GOS 1512010

From Metagenes
Warning: this metagenomic sequence has been carefully annotated by students during bioinformatics assignments. These quality annotations are therefore the result of a teaching exercise that you are most welcome to amend and extend if necessary!


Sequence
CAMERA AccNum : JCVI_READ_1091138050647
Annotathon code: GOS_1512010
Sample :
  • GPS :20°31'21n; 85°24'49w
  • Caribbean Sea: Yucatan Channel - Mexico
  • Open Ocean (-2m, 27°C, 0.1-0.8 microns)
Authors
Team : Algarve
Username : SASP1
Annotated on : 2010-07-02 22:32:42
  • a32900 SaraPalhãoFarinhaDaSilva
  • a33844 AlexandraReigadinha
  • a37094 SaraBarão

Synopsis

  • Taxonomy: Proteobacteria (NCBI info)
    Rank: phylum - Genetic Code: Bacterial and Plant Plastid - NCBI Identifier: 1224
    Kingdom: Bacteria - Phylum: Proteobacteria - Class: - Order:
    Bacteria; Proteobacteria;

Genomic Sequence

>JCVI_READ_1091138050647 GOS_1512010 Genomic DNA
AAATCATTGTTGGAAGGAATTGCATCATCATTGACAGAAATTTACGCGCCAGCAATACATCAAGAAAGAATAGCTGGGCTCTCTAAATACTATGATTGGG
CAGATGATTACGCTTTGGCTTATTTTAAAAAAAGAATTAATCAAGCAAGAAGGGATGTAGAATTTGGAAGAGAATGGGTTATTAATAATGCGATTACAAG
GAGTGATCAGGAAGCTGTATTAAATGCCGTACAATTTAAGACTGAAGTTCTCTGGGCCCAGTTAGATGCTCTTTATTATGCTTACATTGATCCTGGAAAT
ATTCCTCCAGGTGCATTTATCCCGTAAAATAATCATAATCAAGAAAATGAGTAAACTAGTTAAACTTGAACCTGATAATATCCCTAGATTACCTAGACAC
GCTAAGCTGAGATATGATGAAGCTAGGAAAAAGTGGATTATAAATGCTCCTGAAAGGGTATTTGAATTGGATGATACTGCAGCAGACATTATGAAACAAG
TAGATGGAGTACTTTCTATTAATGTTATTGTAGATAATGTACATAGGAAATTTAATGAAGCCACAAGAGATCAAATCTCAAGTGACGTAATATTAATGCT
ACGATCACTGGCTGATAAACGGATTTATTGTTAATGAGTAAAATAGAACAAAGTTTTACTACTCCTGAAATAAGTATAAAAACTCTGATACCATATGCTA
TGCTTTGCGAATTAACTCACATATGTCTTCTATCTAGTCCATATTGCTCAAACCCTATTCAACTGGAGG

Translation

[347 - 631/769]   direct strand
>GOS_1512010 Translation [347-631   direct strand]
MSKLVKLEPDNIPRLPRHAKLRYDEARKKWIINAPERVFELDDTAADIMKQVDGVLSINVIVDNVHRKFNEATRDQISSDVILMLRSLADKRIYC

Annotator commentaries

We continued the analysis of the metagenomic sequence with the longest ORF available - ORF number 1 in reading frame 2 on the direct strand - and ran a BLAST query to see if it presented true positive homologs. It did, so we concluded this sequence was coding. The multiple alignement was a little strange with many sequences starting at very diferent positions. Despite so, the G-blocks curated alignement showed that there are some very well conserved regions indicating that our sequence integrates its presumed homolog family convincingly. We changed the position of the first nucleotid of the intitiation codon to its 347th base so the initiation methionine would be closer to the ones of the homologs (making the translated ORF 95 aminoacids long). Using the Ancestor Table at NCBI we identified the Biological Process GO:0018189 - pyrroloquinoline quinone biosynthetic process - (found through our homologs domains, but not available at annotathon) to be a coenzyme metabolic process (GO:0006732) which in turn is a metabolic process (GO:0008152). Regarding the Molecular function our metagenomic sequence appears to be coherent with its homologs results, so we suggest that it has a quinone binding (GO:0048038) function; once again using an ancestor chart we reached the GO:0005488 - binding ontology term.

ORF finding

PROTOCOL


a) SMS ORFinder / forward strand / frames 1, 2 & 3 / min 60 AA / 'any codon' initiation / 'standard' genetic code

b) SMS ORFinder / reverse strand / frames 1, 2 3 / min 60 AA / 'any codon' initiation / 'standard' genetic code



RESULTS ANALYSIS


With the SMS ORFinder we obtained five putative ORFs (2 in the direct strand and 3 in the reverse strand) and we chose the longest available ORF (ORF number 1 in reading frame 2 on the direct strand) which extends from base 3 to base 431(142 aminoacids long) for the remainig analysis. To verify if this sequence was coding we ran a BLASTp query which return valid positive homologs (we consider the e-value threshold of 10^-4 for true homology). After ranning a multiple alignement we decided the sequence should probably initiate further downstream (27 aminoacids away) to be closer to its homologs start Methionines. Still, it is complete at both ends, and so we could calculate its molecular weight.

Regarding the other smaller ORFs, they're probably significant in the metagenomic sequence as they presented domains in the InterPro.



RAW RESULTS

a)forward 

>ORF number 1 in reading frame 1 on the direct strand extends from base 1 to base 327.
AAATCATTGTTGGAAGGAATTGCATCATCATTGACAGAAATTTACGCGCCAGCAATACAT
CAAGAAAGAATAGCTGGGCTCTCTAAATACTATGATTGGGCAGATGATTACGCTTTGGCT
TATTTTAAAAAAAGAATTAATCAAGCAAGAAGGGATGTAGAATTTGGAAGAGAATGGGTT
ATTAATAATGCGATTACAAGGAGTGATCAGGAAGCTGTATTAAATGCCGTACAATTTAAG
ACTGAAGTTCTCTGGGCCCAGTTAGATGCTCTTTATTATGCTTACATTGATCCTGGAAAT
ATTCCTCCAGGTGCATTTATCCCGTAA

>Translation of ORF number 1 in reading frame 1 on the direct strand.
KSLLEGIASSLTEIYAPAIHQERIAGLSKYYDWADDYALAYFKKRINQARRDVEFGREWV
INNAITRSDQEAVLNAVQFKTEVLWAQLDALYYAYIDPGNIPPGAFIP*

>ORF number 1 in reading frame 2 on the direct strand extends from base 266 to base 634.
ATGCTCTTTATTATGCTTACATTGATCCTGGAAATATTCCTCCAGGTGCATTTATCCCGT
AAAATAATCATAATCAAGAAAATGAGTAAACTAGTTAAACTTGAACCTGATAATATCCCT
AGATTACCTAGACACGCTAAGCTGAGATATGATGAAGCTAGGAAAAAGTGGATTATAAAT
GCTCCTGAAAGGGTATTTGAATTGGATGATACTGCAGCAGACATTATGAAACAAGTAGAT
GGAGTACTTTCTATTAATGTTATTGTAGATAATGTACATAGGAAATTTAATGAAGCCACA
AGAGATCAAATCTCAAGTGACGTAATATTAATGCTACGATCACTGGCTGATAAACGGATT
TATTGTTAA

>Translation of ORF number 1 in reading frame 2 on the direct strand.
MLFIMLTLILEIFLQVHLSRKIIIIKKMSKLVKLEPDNIPRLPRHAKLRYDEARKKWIIN
APERVFELDDTAADIMKQVDGVLSINVIVDNVHRKFNEATRDQISSDVILMLRSLADKRI
YC*

No ORFs were found in reading frame 3.

-------------------------------------------------------------

b)reverse

>ORF number 1 in reading frame 1 on the reverse strand extends from base 193 to base 381.
GATTTGATCTCTTGTGGCTTCATTAAATTTCCTATGTACATTATCTACAATAACATTAAT
AGAAAGTACTCCATCTACTTGTTTCATAATGTCTGCTGCAGTATCATCCAATTCAAATAC
CCTTTCAGGAGCATTTATAATCCACTTTTTCCTAGCTTCATCATATCTCAGCTTAGCGTG
TCTAGGTAA

>Translation of ORF number 1 in reading frame 1 on the reverse strand.
DLISCGFIKFPMYIIYNNINRKYSIYLFHNVCCSIIQFKYPFRSIYNPLFPSFIISQLSV
SR*

>ORF number 1 in reading frame 2 on the reverse strand extends from base 200 to base 508.
TCTCTTGTGGCTTCATTAAATTTCCTATGTACATTATCTACAATAACATTAATAGAAAGT
ACTCCATCTACTTGTTTCATAATGTCTGCTGCAGTATCATCCAATTCAAATACCCTTTCA
GGAGCATTTATAATCCACTTTTTCCTAGCTTCATCATATCTCAGCTTAGCGTGTCTAGGT
AATCTAGGGATATTATCAGGTTCAAGTTTAACTAGTTTACTCATTTTCTTGATTATGATT
ATTTTACGGGATAAATGCACCTGGAGGAATATTTCCAGGATCAATGTAAGCATAATAAAG
AGCATCTAA

>Translation of ORF number 1 in reading frame 2 on the reverse strand.
SLVASLNFLCTLSTITLIESTPSTCFIMSAAVSSNSNTLSGAFIIHFFLASSYLSLACLG
NLGILSGSSLTSLLIFLIMIILRDKCTWRNISRINVSIIKSI*

>ORF number 2 in reading frame 2 on the reverse strand extends from base 551 to base 742.
TACAGCTTCCTGATCACTCCTTGTAATCGCATTATTAATAACCCATTCTCTTCCAAATTC
TACATCCCTTCTTGCTTGATTAATTCTTTTTTTAAAATAAGCCAAAGCGTAATCATCTGC
CCAATCATAGTATTTAGAGAGCCCAGCTATTCTTTCTTGATGTATTGCTGGCGCGTAAAT
TTCTGTCAATGA

>Translation of ORF number 2 in reading frame 2 on the reverse strand.
YSFLITPCNRIINNPFSSKFYIPSCLINSFFKISQSVIICPIIVFREPSYSFLMYCWRVN
FCQ*

No ORFs were found in reading frame 3.

Multiple Alignement

PROTOCOL


a)phylogeny.fr/alignement MUSCLE/ CLUSTAL format

b)phylogeny.fr/alignement MUSCLE/ alignement GBLOCKS, default parameters



RESULTS ANALYSIS


The sequences used in the multiple alignement all had diferent lengths and diferent position starts. We decided that our chosen ORF should probably initiate further downstream (27 aminoacids away) to be closer to its homologs starting Methionines. The G-blocks curated alignement showed well conserved regions which seemed to be coherent with the INTERPRO conserved domains found.

RAW RESULTS

a)CLUSTAL FORMAT: MUSCLE (3.7) multiple sequence alignment


GOS_151201      ------------------------------------------------------------
G.bethesde      ------------------------------------------------------------
X.campestr      ------------------------------------------------------------
R.sphaeroi      ------------------------------------------------------------
H.denitrif      ------------------------------------------------------------
A.pasteuri      ------------------------------------------------------------
R.palustri      ------------------------------------------------------------
Bradyrhizo      ------------------------------------------------------------
B.japonicu      ------------------------------------------------------------
M.silvestr      ------------------------------------------------------------
A.cryptum       ------------------------------------------------------------
Roseovariu      ------------------------------------------------------------
D.shibae_g      ------------------------------------------------------------
Citreicell      ------------------------------------------------------------
C.salexige      ------------------------------------------------------------
M.nodulans      ------------------------------------------------------------
M.radiotol      MNAIFPTPDTADSQRLLSPEELEAALRDIGARRYHNLHPFHRLLHDGKLSKDQVRAWALN
M.magnetot      MTAQFPPPAPESEQRLLSHEELEAALRDIGARRYHNLHPFHRLLHDGKLSKDQVRAWALN
Methylovor      ------------------------------------------------------------
M.capsulat      ------------------------------------------------------------
Limnobacte      ------------------------------------------------------------
                                                                            

GOS_151201      ------------------------------------------------------------
G.bethesde      ------------------------------------------------------------
X.campestr      ------------------------------------------------------------
R.sphaeroi      ------------------------------------------------------------
H.denitrif      ------------------------------------------------------------
A.pasteuri      ------------------------------------------------------------
R.palustri      ------------------------------------------------------------
Bradyrhizo      ------------------------------------------------------------
B.japonicu      ------------------------------------------------------------
M.silvestr      ------------------------------------------------------------
A.cryptum       ------------------------------------------------------------
Roseovariu      ------------------------------------------------------------
D.shibae_g      ------------------------------------------------------------
Citreicell      ------------------------------------------------------------
C.salexige      ------------------------------------------------------------
M.nodulans      ------------------------------------------------------------
M.radiotol      RYYYQAMIPVKDAAVLARMTDASLRRIWRQRIVDHDGDHEGDGGIERWLKLAEGVGFDRD
M.magnetot      RYYYQAMIPVKDAALLARLPDASLRRIWRQRIVDHDGDHEGDGGIERWLKLAEGVGFARD
Methylovor      ------------------------------------------------------------
M.capsulat      ------------------------------------------------------------
Limnobacte      ------------------------------------------------------------
                                                                            

GOS_151201      --------------------------------------------------------MLFI
G.bethesde      ------------------------------------------------------------
X.campestr      ------------------------------------------------------------
R.sphaeroi      ------------------------------------------------------------
H.denitrif      ------------------------------------------------------------
A.pasteuri      ------------------------------------------------------------
R.palustri      ------------------------------------------------------------
Bradyrhizo      ------------------------------------------------------------
B.japonicu      ------------------------------------------------------------
M.silvestr      ------------------------------------------------------------
A.cryptum       ------------------------------------------------------------
Roseovariu      ------------------------------------------------------------
D.shibae_g      ------------------------------------------------------------
Citreicell      ------------------------------------------------------------
C.salexige      ------------------------------------------------------------
M.nodulans      ------------------------------------------------------------
M.radiotol      YVLSTRGILSATKFSVEAYVHFVSERTLLEAIASSLTEMFSPTIISERVAGMLKNYDFIT
M.magnetot      YVLSTKGILSATRFSVDAYVHFVSERSLLEAIASSLTEMFSPTIISERVAGMLKNYDFVT
Methylovor      ------------------------------------------------------------
M.capsulat      ------------------------------------------------------------
Limnobacte      ------------------------------------------------------------
                                                                            

GOS_151201      MLTLILEIFLQVHLSRKIIIIKKMSKLVKLEPD---------------------------
G.bethesde      -----------------MSAPQDQALPRALNEE---------------------------
X.campestr      --------------------------MSTISRD---------------------------
R.sphaeroi      ------------------------MSRLELSPE---------------------------
H.denitrif      ------------------MNADAPRTRTMVVPA---------------------------
A.pasteuri      ----------------------------MISEN---------------------------
R.palustri      ----------------------MASRNITVSEA---------------------------
Bradyrhizo      ----------------------MAPRHIQVAET---------------------------
B.japonicu      ---------------------MAGPRHISVSEA---------------------------
M.silvestr      ----------------MSETAQAPGQGVGQGSG---------------------------
A.cryptum       ---------------------------MTLTAD---------------------------
Roseovariu      -----------------------------MTPD---------------------------
D.shibae_g      ----------------------------MMEAG---------------------------
Citreicell      ----------------------------MMQPS---------------------------
C.salexige      --------------------------MTAIQES---------------------------
M.nodulans      ---------------------------MTLTPD---------------------------
M.radiotol      KDTLAYFDKRLTQAPRDADFALDYVKQHATTPELQRQAMAALTFKCTVLWTQLDALYFAY
M.magnetot      KETLAYFDKRLTQAPRDADFALDYVKRHATTPELQRAAMDALTFKCTVLWTQLDALYFAY
Methylovor      -------------------------MTTSVNPA---------------------------
M.capsulat      ---------------------------MSLQPD---------------------------
Limnobacte      ----------------------MNTETTQALPE---------------------------
                                                                            

GOS_151201      -------------------------------------NIPRLPRHAKLRYDEARKKWIIN
G.bethesde      -------------------------------------AVPRFGQGMKFRHDKVRDAWVIL
X.campestr      -------------------------------------SCPALRAGVRLQHDRARDQWVLL
R.sphaeroi      -------------------------------------SVPQLARHARLRFDQSRQHWVLL
H.denitrif      -------------------------------------SKPGLPTHIKLRHDAGRGRWHVL
A.pasteuri      -------------------------------------SILRFARGTRLQHDRVRDVWFIQ
R.palustri      -------------------------------------SRPALPRHAKLRFDETRQRWVIL
Bradyrhizo      -------------------------------------SRVVLPRHTKLKFDETRQVWVIL
B.japonicu      -------------------------------------SRPVLPRHAKLKYDETREVWVIL
M.silvestr      -------------------------------------IVPRLPRGVRLKFDETRGQWLLL
A.cryptum       -------------------------------------SVPHLPRHVRFRFDAARNCHVLL
Roseovariu      -------------------------------------AIPRLPRGVRLQYDRVREDWVLL
D.shibae_g      -------------------------------------DIPELPRGVRLHFDKVRETWVLL
Citreicell      -------------------------------------DIPSLPRGVRLHHDRVRGSWVLL
C.salexige      -------------------------------------DIVRLPRGVRLREDKRRGGWVLL
M.nodulans      -------------------------------------DVPRLPRGVRMHFDGVRGAHVLL
M.radiotol      VAPGMVPPDAWQPGEGLVSEASQ-AKPGASGGKMAAGDRPRLPRGVRLRNDETRGKWVLL
M.magnetot      VSPGLVPPDAWQPGEGLVPEASPAAAPTGVPAAFSGSDVPRLPRGVRLRFDEVRNKHILL
Methylovor      -------------------------------------DIFSLARHYRFQWEEAQQCYVLL
M.capsulat      -------------------------------------TLLELSPLLRMQWEEAQQRYVIL
Limnobacte      --------------------------------------HPKLNRLFRLQYEEAQKTYVLL
                                                         :    .:. :  .    : 

GOS_151201      APERVFELDDTAADIMKQVDGVLSINVIVDNVHRKFNEATRDQISSDVILMLRSLADKRI
G.bethesde      GPERLFQPDPVAAEILKLVDGQKTIGAIIDELVSRFA-APREVIAADVVTMFVDMSAKGA
X.campestr      APERVVELDDIALVVAQRYDGTQSLAQIAQTLAAEFD-ADASEIETDVIELTTTLHQKRL
R.sphaeroi      VPERVMTPDEICVEILQACDGQETVAGLTALFERKYV-AEPGVIAREVLALLQDLADRGY
H.denitrif      APERVFEPDPIAVEILKRCDGATSVEEIATALAKEYN-APLQEILADTISMLQELSDKGV
A.pasteuri      APERAFHADPIAVEVLQLIDGTRNVGGILDLLCQKFA-APRDIIAQDVLTLLRDLATKQV
R.palustri      APERVLAPDDIAVEILQLCDGARSVSAIIDQLATKYT-ADRAEIGTDVVAMLQDLADKGF
Bradyrhizo      APERVLAPDEIAVEVLKLCDGVRSVAGIIDELATKYA-APRDVIATDVVAMLQDLADKGF
B.japonicu      APERVLAPDEIAVEVLQLCNGERSVGDVSDQLAAKYA-APREAILTDVIAMLQDLADKGF
M.silvestr      APERLVKVDDIAVAILKRCDGVATIEAIVEDLAATFA-ADRAQIDADVRRLLNELAAKRM
A.cryptum       APEMVIMPDAIAVAILDAVDGIASVGVIADTLAARYE-APREAVLADCIEMLNDLARKGM
Roseovariu      APERAVRLDPIGHAILSRVDGAQSFGALTADLAATFN-APLDDVTRDSAEFLDGLAERRF
D.shibae_g      APERAVTLDAIGHAILSEIDGTRSFGEITQALSDAYN-APRDQIAADSAGFLTALRNRRF
Citreicell      APERAVMLDATAHAILSRVDGQRSFGEITAELAEAYD-APPEAIAGDAAGLLGALRDRRF
C.salexige      APERVFQLDGIAQAVVGQVDGERSVGTIIDRLCETYQ-APRERIAQDVTAMFAGLVEKRV
M.nodulans      APERTFDLDRNAVAVLSLVDGTRSIRAIADALAEQYD-APRTVIEPDVITMLNGLADKRV
M.radiotol      APERTFDLDDNAVAVLKLVDGARSVSDIADELGKTYA-ADPRAIEADILVMLDGLAEKRV
M.magnetot      APERTFDLDDNAVAVLKLVDGQSSVSQIARTLGQTYD-ADPAVIEADILVMLAGLAQRRV
Methylovor      FPEGMIKLNGGAGEVIKRVDGNKTVSDIVAELQQAF--PDAPDIESDILAMLQLALEKAW
M.capsulat      YPEGMIELNETAAAILELCDGQHNLTSIVDKLERKY---DASGIEPDVREMLESALNNGW
Limnobacte      YPEGMVKLNQSASEILLLCDGSRTVNAIVGALETKFN---TSGLEADVRSMLQEAARRNW
                 **  .  :     :    :*  ..  :   .   :       :  :   :      .  

GOS_151201      YC---------
G.bethesde      IRL--------
X.campestr      LRL--------
R.sphaeroi      LIDREAA----
H.denitrif      VKA--------
A.pasteuri      LQAI-------
R.palustri      LTEARESAP--
Bradyrhizo      LTEVRETTS--
B.japonicu      LTEAREKTS--
M.silvestr      VDL--------
A.cryptum       IAS--------
Roseovariu      LEVR-------
D.shibae_g      LDVRP------
Citreicell      LELA-------
C.salexige      LEVA-------
M.nodulans      LETKPAAPSGA
M.radiotol      LER--------
M.magnetot      LER--------
Methylovor      LEKRN------
M.capsulat      IREIIAY----
Limnobacte      LDA--------
                           

-----------------------------------------------------------------------------------

b) Gblocks 0.91b Results
Processed file: input.fasta
Number of sequences: 21
Alignment assumed to be: Protein
New number of positions: 67 (selected positions are underlined in blue) 

                         10        20        30        40        50        60
                 =========+=========+=========+=========+=========+=========+
GOS_1512010_Tra  ------------------------------------------------------------
G.bethesdensis   ------------------------------------------------------------
X.campestris_gi  ------------------------------------------------------------
R.sphaeroides_g  ------------------------------------------------------------
H.denitrificans  ------------------------------------------------------------
A.pasteurianus   ------------------------------------------------------------
R.palustris_gi|  ------------------------------------------------------------
Bradyrhizobium   ------------------------------------------------------------
B.japonicum_gi|  ------------------------------------------------------------
M.silvestris_gi  ------------------------------------------------------------
A.cryptum_gi|14  ------------------------------------------------------------
Roseovarius_gi|  ------------------------------------------------------------
D.shibae_gi|159  ------------------------------------------------------------
Citreicella_gi|  ------------------------------------------------------------
C.salexigens_gi  ------------------------------------------------------------
M.nodulans_gi|2  ------------------------------------------------------------
M.radiotolerans  MNAIFPTPDTADSQRLLSPEELEAALRDIGARRYHNLHPFHRLLHDGKLSKDQVRAWALN
M.magnetotactic  MTAQFPPPAPESEQRLLSHEELEAALRDIGARRYHNLHPFHRLLHDGKLSKDQVRAWALN
Methylovorus_gi  ------------------------------------------------------------
M.capsulatus_gi  ------------------------------------------------------------
Limnobacter_gi|  ------------------------------------------------------------
                                                                             


                         70        80        90       100       110       120
                 =========+=========+=========+=========+=========+=========+
GOS_1512010_Tra  ------------------------------------------------------------
G.bethesdensis   ------------------------------------------------------------
X.campestris_gi  ------------------------------------------------------------
R.sphaeroides_g  ------------------------------------------------------------
H.denitrificans  ------------------------------------------------------------
A.pasteurianus   ------------------------------------------------------------
R.palustris_gi|  ------------------------------------------------------------
Bradyrhizobium   ------------------------------------------------------------
B.japonicum_gi|  ------------------------------------------------------------
M.silvestris_gi  ------------------------------------------------------------
A.cryptum_gi|14  ------------------------------------------------------------
Roseovarius_gi|  ------------------------------------------------------------
D.shibae_gi|159  ------------------------------------------------------------
Citreicella_gi|  ------------------------------------------------------------
C.salexigens_gi  ------------------------------------------------------------
M.nodulans_gi|2  ------------------------------------------------------------
M.radiotolerans  RYYYQAMIPVKDAAVLARMTDASLRRIWRQRIVDHDGDHEGDGGIERWLKLAEGVGFDRD
M.magnetotactic  RYYYQAMIPVKDAALLARLPDASLRRIWRQRIVDHDGDHEGDGGIERWLKLAEGVGFARD
Methylovorus_gi  ------------------------------------------------------------
M.capsulatus_gi  ------------------------------------------------------------
Limnobacter_gi|  ------------------------------------------------------------
                                                                             


                        130       140       150       160       170       180
                 =========+=========+=========+=========+=========+=========+
GOS_1512010_Tra  --------------------------------------------------------MLFI
G.bethesdensis   ------------------------------------------------------------
X.campestris_gi  ------------------------------------------------------------
R.sphaeroides_g  ------------------------------------------------------------
H.denitrificans  ------------------------------------------------------------
A.pasteurianus   ------------------------------------------------------------
R.palustris_gi|  ------------------------------------------------------------
Bradyrhizobium   ------------------------------------------------------------
B.japonicum_gi|  ------------------------------------------------------------
M.silvestris_gi  ------------------------------------------------------------
A.cryptum_gi|14  ------------------------------------------------------------
Roseovarius_gi|  ------------------------------------------------------------
D.shibae_gi|159  ------------------------------------------------------------
Citreicella_gi|  ------------------------------------------------------------
C.salexigens_gi  ------------------------------------------------------------
M.nodulans_gi|2  ------------------------------------------------------------
M.radiotolerans  YVLSTRGILSATKFSVEAYVHFVSERTLLEAIASSLTEMFSPTIISERVAGMLKNYDFIT
M.magnetotactic  YVLSTKGILSATRFSVDAYVHFVSERSLLEAIASSLTEMFSPTIISERVAGMLKNYDFVT
Methylovorus_gi  ------------------------------------------------------------
M.capsulatus_gi  ------------------------------------------------------------
Limnobacter_gi|  ------------------------------------------------------------
                                                                             


                        190       200       210       220       230       240
                 =========+=========+=========+=========+=========+=========+
GOS_1512010_Tra  MLTLILEIFLQVHLSRKIIIIKKMSKLVKLEPD---------------------------
G.bethesdensis   -----------------MSAPQDQALPRALNEE---------------------------
X.campestris_gi  --------------------------MSTISRD---------------------------
R.sphaeroides_g  ------------------------MSRLELSPE---------------------------
H.denitrificans  ------------------MNADAPRTRTMVVPA---------------------------
A.pasteurianus   ----------------------------MISEN---------------------------
R.palustris_gi|  ----------------------MASRNITVSEA---------------------------
Bradyrhizobium   ----------------------MAPRHIQVAET---------------------------
B.japonicum_gi|  ---------------------MAGPRHISVSEA---------------------------
M.silvestris_gi  ----------------MSETAQAPGQGVGQGSG---------------------------
A.cryptum_gi|14  ---------------------------MTLTAD---------------------------
Roseovarius_gi|  -----------------------------MTPD---------------------------
D.shibae_gi|159  ----------------------------MMEAG---------------------------
Citreicella_gi|  ----------------------------MMQPS---------------------------
C.salexigens_gi  --------------------------MTAIQES---------------------------
M.nodulans_gi|2  ---------------------------MTLTPD---------------------------
M.radiotolerans  KDTLAYFDKRLTQAPRDADFALDYVKQHATTPELQRQAMAALTFKCTVLWTQLDALYFAY
M.magnetotactic  KETLAYFDKRLTQAPRDADFALDYVKRHATTPELQRAAMDALTFKCTVLWTQLDALYFAY
Methylovorus_gi  -------------------------MTTSVNPA---------------------------
M.capsulatus_gi  ---------------------------MSLQPD---------------------------
Limnobacter_gi|  ----------------------MNTETTQALPE---------------------------
                                                                             


                        250       260       270       280       290       300
                 =========+=========+=========+=========+=========+=========+
GOS_1512010_Tra  -------------------------------------NIPRLPRHAKLRYDEARKKWIIN
G.bethesdensis   -------------------------------------AVPRFGQGMKFRHDKVRDAWVIL
X.campestris_gi  -------------------------------------SCPALRAGVRLQHDRARDQWVLL
R.sphaeroides_g  -------------------------------------SVPQLARHARLRFDQSRQHWVLL
H.denitrificans  -------------------------------------SKPGLPTHIKLRHDAGRGRWHVL
A.pasteurianus   -------------------------------------SILRFARGTRLQHDRVRDVWFIQ
R.palustris_gi|  -------------------------------------SRPALPRHAKLRFDETRQRWVIL
Bradyrhizobium   -------------------------------------SRVVLPRHTKLKFDETRQVWVIL
B.japonicum_gi|  -------------------------------------SRPVLPRHAKLKYDETREVWVIL
M.silvestris_gi  -------------------------------------IVPRLPRGVRLKFDETRGQWLLL
A.cryptum_gi|14  -------------------------------------SVPHLPRHVRFRFDAARNCHVLL
Roseovarius_gi|  -------------------------------------AIPRLPRGVRLQYDRVREDWVLL
D.shibae_gi|159  -------------------------------------DIPELPRGVRLHFDKVRETWVLL
Citreicella_gi|  -------------------------------------DIPSLPRGVRLHHDRVRGSWVLL
C.salexigens_gi  -------------------------------------DIVRLPRGVRLREDKRRGGWVLL
M.nodulans_gi|2  -------------------------------------DVPRLPRGVRMHFDGVRGAHVLL
M.radiotolerans  VAPGMVPPDAWQPGEGLVSEASQ-AKPGASGGKMAAGDRPRLPRGVRLRNDETRGKWVLL
M.magnetotactic  VSPGLVPPDAWQPGEGLVPEASPAAAPTGVPAAFSGSDVPRLPRGVRLRFDEVRNKHILL
Methylovorus_gi  -------------------------------------DIFSLARHYRFQWEEAQQCYVLL
M.capsulatus_gi  -------------------------------------TLLELSPLLRMQWEEAQQRYVIL
Limnobacter_gi|  --------------------------------------HPKLNRLFRLQYEEAQKTYVLL
                                                          ###################


                        310       320       330       340       350       360
                 =========+=========+=========+=========+=========+=========+
GOS_1512010_Tra  APERVFELDDTAADIMKQVDGVLSINVIVDNVHRKFNEATRDQISSDVILMLRSLADKRI
G.bethesdensis   GPERLFQPDPVAAEILKLVDGQKTIGAIIDELVSRFA-APREVIAADVVTMFVDMSAKGA
X.campestris_gi  APERVVELDDIALVVAQRYDGTQSLAQIAQTLAAEFD-ADASEIETDVIELTTTLHQKRL
R.sphaeroides_g  VPERVMTPDEICVEILQACDGQETVAGLTALFERKYV-AEPGVIAREVLALLQDLADRGY
H.denitrificans  APERVFEPDPIAVEILKRCDGATSVEEIATALAKEYN-APLQEILADTISMLQELSDKGV
A.pasteurianus   APERAFHADPIAVEVLQLIDGTRNVGGILDLLCQKFA-APRDIIAQDVLTLLRDLATKQV
R.palustris_gi|  APERVLAPDDIAVEILQLCDGARSVSAIIDQLATKYT-ADRAEIGTDVVAMLQDLADKGF
Bradyrhizobium   APERVLAPDEIAVEVLKLCDGVRSVAGIIDELATKYA-APRDVIATDVVAMLQDLADKGF
B.japonicum_gi|  APERVLAPDEIAVEVLQLCNGERSVGDVSDQLAAKYA-APREAILTDVIAMLQDLADKGF
M.silvestris_gi  APERLVKVDDIAVAILKRCDGVATIEAIVEDLAATFA-ADRAQIDADVRRLLNELAAKRM
A.cryptum_gi|14  APEMVIMPDAIAVAILDAVDGIASVGVIADTLAARYE-APREAVLADCIEMLNDLARKGM
Roseovarius_gi|  APERAVRLDPIGHAILSRVDGAQSFGALTADLAATFN-APLDDVTRDSAEFLDGLAERRF
D.shibae_gi|159  APERAVTLDAIGHAILSEIDGTRSFGEITQALSDAYN-APRDQIAADSAGFLTALRNRRF
Citreicella_gi|  APERAVMLDATAHAILSRVDGQRSFGEITAELAEAYD-APPEAIAGDAAGLLGALRDRRF
C.salexigens_gi  APERVFQLDGIAQAVVGQVDGERSVGTIIDRLCETYQ-APRERIAQDVTAMFAGLVEKRV
M.nodulans_gi|2  APERTFDLDRNAVAVLSLVDGTRSIRAIADALAEQYD-APRTVIEPDVITMLNGLADKRV
M.radiotolerans  APERTFDLDDNAVAVLKLVDGARSVSDIADELGKTYA-ADPRAIEADILVMLDGLAEKRV
M.magnetotactic  APERTFDLDDNAVAVLKLVDGQSSVSQIARTLGQTYD-ADPAVIEADILVMLAGLAQRRV
Methylovorus_gi  FPEGMIKLNGGAGEVIKRVDGNKTVSDIVAELQQAF--PDAPDIESDILAMLQLALEKAW
M.capsulatus_gi  YPEGMIELNETAAAILELCDGQHNLTSIVDKLERKY---DASGIEPDVREMLESALNNGW
Limnobacter_gi|  YPEGMVKLNQSASEILLLCDGSRTVNAIVGALETKFN---TSGLEADVRSMLQEAARRNW
                 ####################################    ############        


                        370
                 =========+=
GOS_1512010_Tra  YC---------
G.bethesdensis   IRL--------
X.campestris_gi  LRL--------
R.sphaeroides_g  LIDREAA----
H.denitrificans  VKA--------
A.pasteurianus   LQAI-------
R.palustris_gi|  LTEARESAP--
Bradyrhizobium   LTEVRETTS--
B.japonicum_gi|  LTEAREKTS--
M.silvestris_gi  VDL--------
A.cryptum_gi|14  IAS--------
Roseovarius_gi|  LEVR-------
D.shibae_gi|159  LDVRP------
Citreicella_gi|  LELA-------
C.salexigens_gi  LEVA-------
M.nodulans_gi|2  LETKPAAPSGA
M.radiotolerans  LER--------
M.magnetotactic  LER--------
Methylovorus_gi  LEKRN------
M.capsulatus_gi  IREIIAY----
Limnobacter_gi|  LDA--------
                            


Parameters used
Minimum Number Of Sequences For A Conserved Position: 11
Minimum Number Of Sequences For A Flanking Position: 18
Maximum Number Of Contiguous Nonconserved Positions: 8
Minimum Length Of A Block: 10
Allowed Gap Positions: None
Use Similarity Matrices: Yes

Flank positions of the 2 selected block(s)
Flanks: [282  336]  [341  352]  

New number of positions in input.fasta-gb:  67  (18% of the original 371 positions)

Protein Domains

PROTOCOL


a)InterPro, default parameters at EBI / >GOS_1512010 Translation [266-631 direct strand]

b)InterPro, default parameters at EBI / ORF number 1 in reading frame 1 on the direct strand

c)InterPro, default parameters at EBI / ORF number 1 in reading frame 1 on the reverse strand

d)InterPro, default parameters at EBI / ORF number 1 in reading frame 2 on the reverse strand

e)InterPro, default parameters at EBI / ORF number 2 in reading frame 2 on the reverse strand.



RESULTS ANALYSIS


a)These results were classified as unintegrated. PqqD[pfam05402] and PQQ_PqqD[TIGR03859] are 2 groups that belong to the PqqD superfamily domain, involved in coenzyme pyrrolo-quinoline-quinone (PQQ) biosynthesis. They're described with better detail in the BLASTp field as the BLASTp retrieved homologs also belong to this family.


b)The ORF number 1 in reading frame 1 on the direct strand is probably very important in the metagenomic sequence as well as our chosen ORF. It retrieved domains belonging to the superfamily TENA/THI-4/PQQC, which includes bacterial coenzyme PQQ synthesis protein C or PQQC proteins: PQQC has been found to be required in the synthesis of PQQ but its function is unclear. Pyrroloquinoline quinone (PQQ) is the prosthetic group of several bacterial enzymes,including methanol dehydrogenase of methylotrophs and the glucose dehydrogenase of a number of bacteria.


c),d) & e) no hits reported or unimportant results

RAW RESULTS

a)GOS_1512010	78B1A84DE4C58B9C	95	HMMPfam	PF05402	PqqD	14	92	4.3e-22	T	03-May-2010	NULL	NULL	
  GOS_1512010	78B1A84DE4C58B9C	95	HMMTigr	TIGR03859	PQQ_PqqD: coenzyme PQQ biosynthesis protein	13	94	3.8e-07	T	03-May-2010

b)Translation	C0CDFD4D52B3F370	108	Gene3D	G3DSA:1.20.910.10	no description	1	108	3.8e-30	T	03-May-2010	IPR016084	Haem oxygenase-like, multi-helical	
  Translation	C0CDFD4D52B3F370	108	superfamily	SSF48613	Heme oxygenase-like	2	108	5.2e-28	T	03-May-2010	IPR016084	Haem oxygenase-like, multi-helical	
  Translation	C0CDFD4D52B3F370	108	HMMPfam	PF03070	TENA_THI-4	1	89	3.7e-12	T	03-May-2010	IPR004305	TENA/THI-4 protein/Coenzyme PQQ biosynthesis protein C	

c)No hits reported

d)Translation	EB04C9E4A49AC06D	102	SignalPHMM	SignalP	signal-peptide	1	18	NA	?	03-May-2010	NULL	NULL
  Translation	EB04C9E4A49AC06D	102	TMHMM	tmhmm	transmembrane_regions	38	58	NA	?	03-May-2010	NULL	NULL
  Translation	EB04C9E4A49AC06D	102	TMHMM	tmhmm	transmembrane_regions	64	82	NA	?	03-May-2010	NULL	NULL

e)No hits reported

Phylogeny

PROTOCOL


a) Phylogeny.fr / neighbor-joining (NJ) method /

b) Phylogeny.fr / PhyML method / no bootstrap / default substitution model / out-group: Chromohalobacter salexigens



RESULTS ANALYSIS


The tree obtained by the Neighbor-joining (NJ) method is coherent with the reference phylogeny of species presenting a distinct ingroup branch and a distinct out-group branch. The exceptions are Chromohalobacter_salexigens_DSM_3043_gi_92112975 (e-value_) and Xanthomonas_campestris_ATCC_33913_gi_21232370 (e-value_), out-group sequences that appears within the ingroup branch. Those sequences likely suffered horizontal gene transfer (HGT). The query sequence seems to integrate the ingroup (alpha-proteobacteria) convincingly.


However this tree isn't very coherent with the tree obtained with the PhyML method (which herself isn't coherent at all with the reference tree of species). This tree shows the out-group branch within the ingroup branch and the query sequence closer to the outgroups, so it was not a good inferring method.

RAW RESULTS

a) Neighbor-joining (NJ) method
                                                                                                   
 
              +------------Bradyrhizobium_japonicum_USDA_110_gi_27381849                                      (Rhizobiales)
            +-+
            | +--------Bradyrhizobium_sp._BTAi1_gi_148257542                                                  (Rhizobiales)
         +--+
         |  +-------Rhodopseudomonas_palustris_BisB5_gi_91976509                                              (Rhizobiales)
  +------+
  |      +------------------------------------------Rhodobacter_sphaeroides_2.4.1_gi_77464365                 (Rhodobacterales)
  |
  |
 ++ +-------------------------------------GOS_1512010_Translation_266-631_direct_strand
 || |
 || |        +------------------------------Acidiphilium_cryptum_JF-5_gi_148259101                             (Rhodospirilalles)
 || |   +----+
 |+-+   |    +----------------------------------Hyphomicrobium_denitrificans_ATCC_51888_gi_255336062           (Rhizobiales)
 |  |   |
 |  |   |      +--------------------------Methylocella_silvestris_BL2_gi_217977334                             (Rhizobiales)
 |  |   | +----+
 |  +---+ |    +---------------------------------------Xanthomonas_campestris_ATCC_33913_gi_21232370           (g-Proteobacteria)
 |      | |
 |      | |                   +-------------Magnetospirillum_magnetotacticum_MS-1_gi_46203072                  (Rhodospirilalles)
 |      | |           +-------+
 |      +-+           |       +------Methylobacterium_radiotolerans_JCM_2831_gi_170746951                       (Rhizobiales)
 |        |  +--------+
 |        |  |        |
 |        |  |        +-------------------Methylobacterium_nodulans_ORS_2060_gi_220925817                       (Rhizobiales)
 |        |  |
 |        |  |       +----------------------------Chromohalobacter_salexigens_DSM_3043_gi_92112975              (g-Proteobacteria)
 |        +--+       |
 |           |   +---+               +-----------Citricella_sp._SE45_gi_260429787                               (Rhodobacterales)
 |           |   |   |               |
 |           |   |   +---------------+  +--------------Dinoroseobacter_shibae_DFL_12_gi_159043008               (Rhodobacterales)
 |           |   |                   +--+
 |           +---+                      +---------------------Roseovarius_sp._217_gi_85704760                   (Rhodobacterales)
 |               |
 |               |             +-----------------------------Acetobacter_pasteurianus_IFO_3283-01_gi_258543189  (Rhodospirilalles)
 |               +-------------+
 |                             |
 |                             +--------------------------Granulibacter_bethesdensis_CGDNIH1_gi_114328591       (Rhodospirilalles)
 |
 |                                   +----------------------Limnobacter_sp._MED105_gi_149927644                 (b-Proteobacteria)
 |                           +-------+     
 +---------------------------+       +------------------------Methylococcus_capsulatus_str._Bath_gi_53804507    (g-Proteobacteria)
                             |
                             +-------------------------------Methylotenera_sp._SIP3-4_gi_253999235              (b-Proteobacteria)



--------------------------------------------------------------------------------------------------------------

b) PhyML method 

                       +--------------Methylobacterium_nodulans_ORS_2060_gi_220925817                                     (Rhizobiales)
                       |
                  +----+     +---Methylobacterium_radiotolerans_JCM_2831_gi_170746951                                     (Rhizobiales)
                  |    +-----+ 
                  |          +-------Magnetospirillum_magnetotacticum_MS-1_gi_46203072                                    (Rhodospirilalles)
                  |
                  |                                    +-------------Methylococcus_capsulatus_str._Bath_gi_53804507       (g-Proteobacteria)
                  |                                    |
                  |                                +---+
                  |         +----------------------+   +------------Limnobacter_sp._MED105_gi_149927644                   (b-Proteobacteria)
                  |         |                      |
                  |      +--+                      +---------------------Methylotenera_sp._SIP3-4_gi_253999235            (b-Proteobacteria)
          +-------+      |  |
          |       |      |  +---------------------GOS_1512010_Translation_266-631_direct_strand
          |       |      |
          |       |      |           +Rhodopseudomonas_palustris_BisB5_gi_91976509                                        (Rhizobiales)
          |       |  +---+           |
          |       |  |   | +---------+  +---------------------------Rhodobacter_sphaeroides_2.4.1_gi_77464365             (Rhodobacterales)
          |       |  |   | |         |  |
          |       |  |   | |         +--+  +---Bradyrhizobium_sp._BTAi1_gi_148257542                                      (Rhizobiales)
          |       |  |   | |            +--+
          |       |  |   +-+               +--------Bradyrhizobium_japonicum_USDA_110_gi_27381849                         (Rhizobiales)
          |       +--+     |
       +--+          |     |
       |  |          |     |    +----------------Hyphomicrobium_denitrificans_ATCC_51888_gi_255336062                     (Rhizobiales)
       |  |          |     +----+
       |  |          |          +------------------------Acidiphilium_cryptum_JF-5_gi_148259101                           (Rhodospirilalles)
       |  |          |
       |  |          |      +--------------------------Xanthomonas_campestris_pv._campestris_str._ATCC_33913_gi_21232370  (g-Proteobacteria)
       |  |          +------+
       |  |                 +-------------Methylocella_silvestris_BL2_gi_217977334                                        (Rhizobiales)
 +-----+  |
 |     |  |           +--------------Granulibacter_bethesdensis_CGDNIH1_gi_114328591                                      (Rhodospirilalles)
 |     |  +-----------+
 |     |              +-------------------Acetobacter_pasteurianus_IFO_3283-01_gi_258543189                               (Rhodospirilalles)
 |     |
 |     |
 |     |                      +----------------Roseovarius_sp._217_gi_85704760                                            (Rhodobacterales)
 |     |                +-----+
 |     +----------------+     +--------Dinoroseobacter_shibae_DFL_12_gi_159043008                                         (Rhodobacterales)
 |                      |
 |                      +----Citricella_sp._SE45_gi_260429787                                                             (Rhodobacterales)
 |
 +------Chromohalobacter_salexigens_DSM_3043_gi_92112975                                                                  (g-Proteobacteria)

Taxonomy report

PROTOCOL


BLASTp versus NR, NCBI default parameters apart from "Number of descriptions_1000"



RESULTS ANALYSIS


The following sequences were used in the multiple alignement and divided in ingroups and out-groups. The study group was easily defined as the majority of true positive homolog sequences found were alpha-proteobacteria.


ingroups: alpha-proteobacteria


ref|YP_569168.1| coenzyme PQQ synthesis D [Rhodopseudomonas p... 86.3 1e-15

ref|YP_001753211.1| coenzyme PQQ biosynthesis protein C [Meth... 79.7 1e-13

ref|YP_001242127.1| coenzyme PQQ synthesis protein D [Bradyrh... 79.0 1e-13

ref|YP_002501119.1| coenzyme PQQ synthesis D [Methylobacteriu... 75.9 1e-12

ref|YP_002361481.1| coenzyme PQQ synthesis D [Methylocella si... 75.5 2e-12

ref|ZP_05376971.1| coenzyme PQQ synthesis D [Hyphomicrobium d... 73.2 8e-12

ref|NP_773378.1| putative pyrroloquinoline quinone synthesis ... 73.9 5e-12

ref|ZP_00052131.2| COG5424: Pyrroloquinoline quinone (Coenzym... 70.1 7e-11

ref|YP_001233228.1| coenzyme PQQ synthesis D [Acidiphilium cr... 67.4 4e-10

ref|ZP_01035861.1| coenzyme PQQ synthesis protein D [Roseovar... 66.6 8e-10

ref|YP_353869.1| putative pyrroloquinoline quinone synthesis ... 66.2 1e-09

ref|YP_745748.1| coenzyme PQQ synthesis protein D [Granulibac... 64.7 3e-09

ref|YP_001531802.1| coenzyme PQQ synthesis D [Dinoroseobacter... 63.9 5e-09

ref|YP_003188622.1| coenzyme Pyrrolo-quinoline quinone (PQQ) ... 63.9 5e-09

ref|ZP_05783763.1| bifunctional coenzyme PQQ synthesis protei... 62.0 2e-08


out-group: other proteobacteria (beta & gamma)


ref|YP_572903.1| coenzyme PQQ synthesis D [Chromohalobacter s... 75.1 3e-12

ref|NP_638287.1| PqqC/D protein [Xanthomonas campestris pv. c... 58.2 3e-07

ref|YP_113906.1| pyrroloquinoline quinone biosynthesis protei... 52.4 2e-05

ref|ZP_01915897.1| Pyrroloquinoline quinone synthesis D [Limn... 50.4 6e-05

ref|YP_003051298.1| coenzyme PQQ synthesis D [Methylovorus sp... 48.9 2e-04

RAW RESULTS

Lineage Report

cellular organisms
. Bacteria                   [bacteria]
. . Proteobacteria             [proteobacteria]
. . . Alphaproteobacteria        [a-proteobacteria]
. . . . Rhizobiales                [a-proteobacteria]
. . . . . Bradyrhizobiaceae          [a-proteobacteria]
. . . . . . Rhodopseudomonas           [a-proteobacteria]
. . . . . . . Rhodopseudomonas palustris [a-proteobacteria]
. . . . . . . . Rhodopseudomonas palustris BisB5 ---------------   86 3 hits [a-proteobacteria]  coenzyme PQQ synthesis D [Rhodopseudomonas palustris BisB5]
. . . . . . . . Rhodopseudomonas palustris HaA2 ................   85 3 hits [a-proteobacteria]  coenzyme PQQ synthesis D [Rhodopseudomonas palustris HaA2] 
. . . . . . . . Rhodopseudomonas palustris BisB18 ..............   83 2 hits [a-proteobacteria]  coenzyme PQQ synthesis D [Rhodopseudomonas palustris BisB18
. . . . . . . . Rhodopseudomonas palustris DX-1 ................   77 2 hits [a-proteobacteria]  coenzyme PQQ synthesis D [Rhodopseudomonas palustris DX-1] 
. . . . . . . . Rhodopseudomonas palustris CGA009 ..............   75 2 hits [a-proteobacteria]  coenzyme PQQ synthesis D [Rhodopseudomonas palustris CGA009
. . . . . . . . Rhodopseudomonas palustris .....................   75 1 hit  [a-proteobacteria]  coenzyme PQQ synthesis D [Rhodopseudomonas palustris CGA009
. . . . . . . . Rhodopseudomonas palustris TIE-1 ...............   74 3 hits [a-proteobacteria]  coenzyme PQQ synthesis D [Rhodopseudomonas palustris TIE-1]
. . . . . . . . Rhodopseudomonas palustris BisA53 ..............   73 2 hits [a-proteobacteria]  coenzyme PQQ synthesis D [Rhodopseudomonas palustris BisA53
. . . . . . Bradyrhizobium sp. BTAi1 ---------------------------   78 2 hits [a-proteobacteria]  coenzyme PQQ synthesis protein D [Bradyrhizobium sp. BTAi1]
. . . . . . Bradyrhizobium sp. ORS278 ..........................   77 2 hits [a-proteobacteria]  coenzyme PQQ synthesis protein D (pyrroloquinoline quinone 
. . . . . . Bradyrhizobium japonicum USDA 110 ..................   73 2 hits [a-proteobacteria]  putative pyrroloquinoline quinone synthesis protein D [Brad
. . . . . . Bradyrhizobium japonicum ...........................   73 1 hit  [a-proteobacteria]  putative pyrroloquinoline quinone synthesis protein D [Brad
. . . . . . Nitrobacter winogradskyi Nb-255 ....................   54 2 hits [a-proteobacteria]  coenzyme PQQ synthesis D [Nitrobacter winogradskyi Nb-255] 
. . . . . Methylobacterium radiotolerans JCM 2831 --------------   79 2 hits [a-proteobacteria]  coenzyme PQQ biosynthesis protein C [Methylobacterium radio
. . . . . Methylobacterium nodulans ORS 2060 ...................   75 2 hits [a-proteobacteria]  coenzyme PQQ synthesis D [Methylobacterium nodulans ORS 206
. . . . . Methylocella silvestris BL2 ..........................   75 2 hits [a-proteobacteria]  coenzyme PQQ synthesis D [Methylocella silvestris BL2] >gi|
. . . . . Hyphomicrobium denitrificans ATCC 51888 ..............   73 2 hits [a-proteobacteria]  coenzyme PQQ synthesis D [Hyphomicrobium denitrificans ATCC
. . . . . Methylobacterium populi BJ001 ........................   70 2 hits [a-proteobacteria]  coenzyme PQQ biosynthesis protein C [Methylobacterium popul
. . . . . Methylobacterium sp. 4-46 ............................   70 2 hits [a-proteobacteria]  coenzyme PQQ synthesis D [Methylobacterium sp. 4-46] >gi|16
. . . . . Xanthobacter autotrophicus Py2 .......................   69 2 hits [a-proteobacteria]  coenzyme PQQ synthesis D [Xanthobacter autotrophicus Py2] >
. . . . . Methylobacterium chloromethanicum CM4 ................   68 2 hits [a-proteobacteria]  pyrroloquinoline quinone biosynthesis protein PqqC [Methylo
. . . . . Methylobacterium extorquens AM1 ......................   68 4 hits [a-proteobacteria]  bifunctional coenzyme pyrroloquinoline quinone (PQQ) biosyn
. . . . . Methylobacterium extorquens DM4 ......................   66 2 hits [a-proteobacteria]  bifunctional coenzyme pyrroloquinoline quinone (PQQ) biosyn
. . . . . Methylobacterium extorquens PA1 ......................   66 2 hits [a-proteobacteria]  pyrroloquinoline quinone biosynthesis protein PqqC [Methylo
. . . . . Beijerinckia indica subsp. indica ATCC 9039 ..........   62 2 hits [a-proteobacteria]  coenzyme PQQ synthesis D [Beijerinckia indica subsp. indica
. . . . . Fulvimarina pelagi HTCC2506 ..........................   58 2 hits [a-proteobacteria]  Coenzyme PQQ synthesis D [Fulvimarina pelagi HTCC2506] >gi|
. . . . . Agrobacterium radiobacter K84 ........................   56 2 hits [a-proteobacteria]  hypothetical protein Arad_8718 [Agrobacterium radiobacter K
. . . . . Rhodomicrobium vannielii ATCC 17100 ..................   51 2 hits [a-proteobacteria]  coenzyme PQQ synthesis D [Rhodomicrobium vannielii ATCC 171
. . . . . Sinorhizobium medicae WSM419 .........................   42 2 hits [a-proteobacteria]  coenzyme PQQ synthesis D [Sinorhizobium medicae WSM419] >gi
. . . . . Sinorhizobium meliloti 1021 ..........................   40 2 hits [a-proteobacteria]  putative pyrroloquinoline quinone synthesis protein D [Sino
. . . . . Sinorhizobium meliloti ...............................   40 2 hits [a-proteobacteria]  putative pyrroloquinoline quinone synthesis protein D [Sino
. . . . . Rhizobium sp. NGR234 .................................   39 3 hits [a-proteobacteria]  coenzyme PQQ synthesis protein D [Rhizobium sp. NGR234] >gi
. . . . Magnetospirillum magnetotacticum MS-1 ------------------   70 1 hit  [a-proteobacteria]  COG5424: Pyrroloquinoline quinone (Coenzyme PQQ) biosynthes
. . . . Acidiphilium cryptum JF-5 ..............................   67 4 hits [a-proteobacteria]  coenzyme PQQ synthesis D [Acidiphilium cryptum JF-5] >gi|14
. . . . Roseovarius sp. 217 ....................................   66 2 hits [a-proteobacteria]  coenzyme PQQ synthesis protein D [Roseovarius sp. 217] >gi|
. . . . Roseovarius sp. TM1035 .................................   66 2 hits [a-proteobacteria]  coenzyme PQQ synthesis protein D [Roseovarius sp. TM1035] >
. . . . Rhodobacter sphaeroides 2.4.1 ..........................   66 2 hits [a-proteobacteria]  putative pyrroloquinoline quinone synthesis protein D [Rhod
. . . . Rhodobacter sphaeroides ATCC 17029 .....................   65 2 hits [a-proteobacteria]  coenzyme PQQ synthesis D [Rhodobacter sphaeroides ATCC 1702
. . . . Roseovarius sp. HTCC2601 ...............................   65 2 hits [a-proteobacteria]  coenzyme PQQ synthesis protein D [Roseovarius sp. HTCC2601]
. . . . Granulibacter bethesdensis CGDNIH1 .....................   64 2 hits [a-proteobacteria]  coenzyme PQQ synthesis protein D [Granulibacter bethesdensi
. . . . Dinoroseobacter shibae DFL 12 ..........................   63 2 hits [a-proteobacteria]  coenzyme PQQ synthesis D [Dinoroseobacter shibae DFL 12] >g
. . . . Acetobacter pasteurianus IFO 3283-01 ...................   63 2 hits [a-proteobacteria]  coenzyme Pyrrolo-quinoline quinone (PQQ) synthesis protein 
. . . . Acetobacter pasteurianus IFO 3283-03 ...................   63 1 hit  [a-proteobacteria]  coenzyme Pyrrolo-quinoline quinone (PQQ) synthesis protein 
. . . . Acetobacter pasteurianus IFO 3283-07 ...................   63 1 hit  [a-proteobacteria]  coenzyme Pyrrolo-quinoline quinone (PQQ) synthesis protein 
. . . . Acetobacter pasteurianus IFO 3283-22 ...................   63 1 hit  [a-proteobacteria]  coenzyme Pyrrolo-quinoline quinone (PQQ) synthesis protein 
. . . . Acetobacter pasteurianus IFO 3283-26 ...................   63 1 hit  [a-proteobacteria]  coenzyme Pyrrolo-quinoline quinone (PQQ) synthesis protein 
. . . . Acetobacter pasteurianus IFO 3283-32 ...................   63 1 hit  [a-proteobacteria]  coenzyme Pyrrolo-quinoline quinone (PQQ) synthesis protein 
. . . . Acetobacter pasteurianus IFO 3283-01-42C ...............   63 1 hit  [a-proteobacteria]  coenzyme Pyrrolo-quinoline quinone (PQQ) synthesis protein 
. . . . Acetobacter pasteurianus IFO 3283-12 ...................   63 1 hit  [a-proteobacteria]  coenzyme Pyrrolo-quinoline quinone (PQQ) synthesis protein 
. . . . Rhodobacter sphaeroides KD131 ..........................   63 2 hits [a-proteobacteria]  Coenzyme PQQ synthesis D [Rhodobacter sphaeroides KD131] >g
. . . . Citreicella sp. SE45 ...................................   62 2 hits [a-proteobacteria]  bifunctional coenzyme PQQ synthesis protein C/D [Citreicell
. . . . Rhodobacterales bacterium HTCC2654 .....................   61 2 hits [a-proteobacteria]  putative pyrroloquinoline quinone synthesis protein D [Rhod
. . . . Roseobacter sp. GAI101 .................................   61 2 hits [a-proteobacteria]  bifunctional coenzyme PQQ synthesis protein C/D [Roseobacte
. . . . Rhodobacter sphaeroides ATCC 17025 .....................   60 2 hits [a-proteobacteria]  coenzyme PQQ synthesis D [Rhodobacter sphaeroides ATCC 1702
. . . . Gluconacetobacter diazotrophicus PAl 5 .................   58 4 hits [a-proteobacteria]  putative coenzyme PQQ synthesis protein D [Gluconacetobacte
. . . . Sagittula stellata E-37 ................................   54 2 hits [a-proteobacteria]  coenzyme PQQ synthesis protein D [Sagittula stellata E-37] 
. . . . Roseobacter litoralis Och 149 ..........................   54 2 hits [a-proteobacteria]  coenzyme PQQ synthesis protein D [Roseobacter litoralis Och
. . . . Roseobacter denitrificans OCh 114 ......................   53 2 hits [a-proteobacteria]  coenzyme PQQ synthesis protein D [Roseobacter denitrificans
. . . . Gluconobacter sp. H24 ..................................   53 1 hit  [a-proteobacteria]  PqqD protein [Gluconobacter sp. H24]
. . . . Ruegeria pomeroyi DSS-3 ................................   52 2 hits [a-proteobacteria]  coenzyme PQQ synthesis protein D [Ruegeria pomeroyi DSS-3] 
. . . . Ruegeria pomeroyi ......................................   52 1 hit  [a-proteobacteria]  coenzyme PQQ synthesis protein D [Ruegeria pomeroyi DSS-3] 
. . . . Paracoccus denitrificans PD1222 ........................   51 2 hits [a-proteobacteria]  coenzyme PQQ synthesis D [Paracoccus denitrificans PD1222] 
. . . . Gluconobacter oxydans 621H .............................   50 2 hits [a-proteobacteria]  coenzyme PQQ synthesis protein D [Gluconobacter oxydans 621
. . . . Gluconobacter oxydans ..................................   50 2 hits [a-proteobacteria]  coenzyme PQQ synthesis protein D [Gluconobacter oxydans 621
. . . . Rhodobacterales bacterium Y4I ..........................   46 2 hits [a-proteobacteria]  coenzyme PQQ synthesis protein D [Rhodobacterales bacterium
. . . . Roseobacter sp. AzwK-3b ................................   45 2 hits [a-proteobacteria]  pyrroloquinoline quinone biosynthesis protein PqqE [Roseoba
. . . . Azospirillum sp. B510 ..................................   39 2 hits [a-proteobacteria]  coenzyme PQQ synthesis protein D [Azospirillum sp. B510] >g
. . . . Rhodobacterales bacterium HTCC2255 .....................   35 1 hit  [a-proteobacteria]  coenzyme PQQ synthesis protein D [alpha proteobacterium HTC
. . . Chromohalobacter salexigens DSM 3043 ---------------------   75 2 hits [g-proteobacteria]  coenzyme PQQ synthesis D [Chromohalobacter salexigens DSM 3
. . . Xanthomonas campestris pv. campestris str. B100 ..........   58 2 hits [g-proteobacteria]  coenzyme PQQ synthesis protein D [Xanthomonas campestris pv
. . . Xanthomonas campestris pv. campestris ....................   58 3 hits [g-proteobacteria]  coenzyme PQQ synthesis protein D [Xanthomonas campestris pv
. . . Xanthomonas campestris pv. campestris str. ATCC 33913 ....   58 2 hits [g-proteobacteria]  PqqC/D protein [Xanthomonas campestris pv. campestris str. 
. . . Xanthomonas campestris pv. campestris str. 8004 ..........   58 3 hits [g-proteobacteria]  PqqC/D protein [Xanthomonas campestris pv. campestris str. 
. . . Xanthomonas campestris pv. vesicatoria str. 85-10 ........   55 3 hits [g-proteobacteria]  coenzyme PQQ synthesis protein D [Xanthomonas campestris pv
. . . Xanthomonas axonopodis pv. citri str. 306 ................   55 2 hits [g-proteobacteria]  PqqC/D protein [Xanthomonas axonopodis pv. citri str. 306] 
. . . Xanthomonas axonopodis pv. citri .........................   55 1 hit  [g-proteobacteria]  PqqC/D protein [Xanthomonas axonopodis pv. citri str. 306] 
. . . Methylococcus capsulatus str. Bath .......................   52 2 hits [g-proteobacteria]  pyrroloquinoline quinone biosynthesis protein PqqD [Methylo
. . . Methylococcus capsulatus .................................   52 1 hit  [g-proteobacteria]  pyrroloquinoline quinone biosynthesis protein PqqD [Methylo
. . . marine gamma proteobacterium HTCC2080 ....................   50 2 hits [g-proteobacteria]  pyrroloquinoline quinone biosynthesis protein PqqD [marine 
. . . Acinetobacter sp. ADP1 ...................................   50 3 hits [g-proteobacteria]  pyrroloquinoline quinone biosynthesis protein PqqD [Acineto
. . . Limnobacter sp. MED105 ...................................   50 2 hits [b-proteobacteria]  Pyrroloquinoline quinone synthesis D [Limnobacter sp. MED10
. . . Pseudomonas mendocina ymp ................................   50 2 hits [g-proteobacteria]  pyrroloquinoline quinone biosynthesis protein PqqD [Pseudom
. . . Methylovorus sp. SIP3-4 ..................................   48 2 hits [b-proteobacteria]  coenzyme PQQ synthesis D [Methylovorus sp. SIP3-4] >gi|2539
. . . Xanthomonas oryzae pv. oryzae PXO99A .....................   48 3 hits [g-proteobacteria]  bifunctional coenzyme PQQ synthesis protein C/D (Pyrroloqui
. . . Ralstonia eutropha JMP134 ................................   47 2 hits [b-proteobacteria]  coenzyme PQQ synthesis D [Ralstonia eutropha JMP134] >gi|72
. . . Cronobacter sakazakii ATCC BAA-894 .......................   46 2 hits [enterobacteria]    hypothetical protein ESA_02995 [Cronobacter sakazakii ATCC 
. . . Azotobacter vinelandii DJ ................................   46 3 hits [g-proteobacteria]  Coenzyme PQQ biosynthesis protein D [Azotobacter vinelandii
. . . Xanthomonas campestris pv. vasculorum NCPPB702 ...........   45 1 hit  [g-proteobacteria]  PqqC/D protein [Xanthomonas campestris pv. vasculorum NCPPB
. . . Xanthomonas campestris pv. musacearum NCPPB4381 ..........   45 1 hit  [g-proteobacteria]  PqqC/D protein [Xanthomonas campestris pv. vasculorum NCPPB
. . . Cronobacter turicensis z3032 .............................   45 2 hits [enterobacteria]    Coenzyme PQQ synthesis protein D [Cronobacter turicensis z3
. . . Ralstonia eutropha H16 ...................................   45 2 hits [b-proteobacteria]  pyrroloquinoline quinone (coenzyme PQQ) biosynthesis protei
. . . Cupriavidus taiwanensis ..................................   45 4 hits [b-proteobacteria]  Coenzyme PQQ synthesis protein D [Cupriavidus taiwanensis] 
. . . Ralstonia pickettii 12D ..................................   45 2 hits [b-proteobacteria]  coenzyme PQQ synthesis D [Ralstonia pickettii 12D] >gi|2408
. . . Ralstonia pickettii 12J ..................................   45 4 hits [b-proteobacteria]  coenzyme PQQ synthesis D [Ralstonia pickettii 12J] >gi|1877
. . . Xanthomonas oryzae pv. oryzicola BLS256 ..................   44 1 hit  [g-proteobacteria]  PqqC/D protein [Xanthomonas oryzae pv. oryzicola BLS256]
. . . gamma proteobacterium NOR51-B ............................   44 2 hits [g-proteobacteria]  coenzyme PQQ synthesis protein D [gamma proteobacterium NOR
. . . Xanthomonas oryzae pv. oryzae MAFF 311018 ................   44 3 hits [g-proteobacteria]  PqqC/D protein [Xanthomonas oryzae pv. oryzae MAFF 311018] 
. . . Xanthomonas oryzae pv. oryzae ............................   44 1 hit  [g-proteobacteria]  PqqC/D protein [Xanthomonas oryzae pv. oryzae MAFF 311018] 
. . . Xanthomonas oryzae pv. oryzae KACC10331 ..................   44 1 hit  [g-proteobacteria]  PqqC/D protein [Xanthomonas oryzae pv. oryzae MAFF 311018] 
. . . Verminephrobacter eiseniae EF01-2 ........................   43 2 hits [b-proteobacteria]  coenzyme PQQ synthesis D [Verminephrobacter eiseniae EF01-2
. . . Neptuniibacter caesariensis ..............................   43 2 hits [g-proteobacteria]  coenzyme PQQ synthesis protein D [Oceanospirillum sp. MED92
. . . beta proteobacterium KB13 ................................   42 2 hits [b-proteobacteria]  pyrroloquinoline quinone biosynthesis protein PqqD [beta pr
. . . Polaromonas naphthalenivorans CJ2 ........................   42 2 hits [b-proteobacteria]  coenzyme PQQ synthesis D [Polaromonas naphthalenivorans CJ2
. . . Rickettsiella grylli .....................................   42 2 hits [g-proteobacteria]  coenzyme PQQ synthesis protein D [Rickettsiella grylli] >gi
. . . Serratia odorifera 4Rx13 .................................   42 2 hits [enterobacteria]    coenzyme PQQ synthesis D [Serratia odorifera 4Rx13] >gi|270
. . . Leptothrix cholodnii SP-6 ................................   42 2 hits [b-proteobacteria]  coenzyme PQQ synthesis D [Leptothrix cholodnii SP-6] >gi|17
. . . Serratia marcescens ......................................   41 1 hit  [enterobacteria]    PqqD [Serratia marcescens]
. . . Nitrosococcus halophilus Nc4 .............................   41 2 hits [g-proteobacteria]  coenzyme PQQ synthesis D [Nitrosococcus halophilus Nc4] >gi
. . . Colwellia psychrerythraea 34H ............................   41 2 hits [g-proteobacteria]  pyrroloquinoline quinone biosynthesis protein PqqD [Colwell
. . . Dechloromonas aromatica RCB ..............................   41 2 hits [b-proteobacteria]  coenzyme PQQ synthesis D [Dechloromonas aromatica RCB] >gi|
. . . Pseudomonas aeruginosa 2192 ..............................   40 2 hits [g-proteobacteria]  pyrroloquinoline quinone biosynthesis protein D [Pseudomona
. . . Pseudomonas aeruginosa PAO1 ..............................   40 2 hits [g-proteobacteria]  pyrroloquinoline quinone biosynthesis protein PqqD [Pseudom
. . . Pseudomonas aeruginosa PACS2 .............................   40 1 hit  [g-proteobacteria]  pyrroloquinoline quinone biosynthesis protein PqqD [Pseudom
. . . Pseudomonas aeruginosa UCBPP-PA14 ........................   40 3 hits [g-proteobacteria]  pyrroloquinoline quinone biosynthesis protein PqqD [Pseudom
. . . Pseudomonas aeruginosa LESB58 ............................   40 3 hits [g-proteobacteria]  pyrroloquinoline quinone biosynthesis protein PqqD [Pseudom
. . . Pseudomonas aeruginosa C3719 .............................   40 2 hits [g-proteobacteria]  pyrroloquinoline quinone biosynthesis protein PqqD [Pseudom
. . . Pseudomonas aeruginosa ...................................   40 1 hit  [g-proteobacteria]  pyrroloquinoline quinone biosynthesis protein PqqD [Pseudom
. . . Methylibium petroleiphilum PM1 ...........................   40 2 hits [b-proteobacteria]  pyrroloquinoline quinone biosynthesis protein D [Methylibiu
. . . Azoarcus sp. BH72 ........................................   40 2 hits [b-proteobacteria]  PqqD protein [Azoarcus sp. BH72] >gi|119669893|emb|CAL93806
. . . Thauera sp. MZ1T .........................................   40 2 hits [b-proteobacteria]  coenzyme PQQ synthesis D [Thauera sp. MZ1T] >gi|237624743|g
. . . Shewanella woodyi ATCC 51908 .............................   40 2 hits [g-proteobacteria]  coenzyme PQQ synthesis D [Shewanella woodyi ATCC 51908] >gi
. . . Lutiella nitroferrum 2002 ................................   40 4 hits [b-proteobacteria]  coenzyme PQQ synthesis D [Lutiella nitroferrum 2002] >gi|22
. . . Pseudomonas aeruginosa PA7 ...............................   40 3 hits [g-proteobacteria]  pyrroloquinoline quinone biosynthesis protein PqqD [Pseudom
. . . Pseudomonas syringae pv. oryzae str. 1_6 .................   39 1 hit  [g-proteobacteria]  pyrroloquinoline quinone biosynthesis protein PqqD [Pseudom
. . . Pseudomonas syringae pv. syringae B728a ..................   39 3 hits [g-proteobacteria]  pyrroloquinoline quinone biosynthesis protein PqqD [Pseudom
. . . Pseudomonas stutzeri A1501 ...............................   39 2 hits [g-proteobacteria]  pyrroloquinoline quinone biosynthesis protein D [Pseudomona
. . . Pseudomonas syringae pv. syringae FF5 ....................   38 1 hit  [g-proteobacteria]  pyrroloquinoline quinone biosynthesis protein PqqD [Pseudom
. . . Serratia odorifera DSM 4582 ..............................   38 2 hits [enterobacteria]    coenzyme PQQ synthesis protein D [Serratia odorifera DSM 45
. . . Klebsiella pneumoniae NTUH-K2044 .........................   38 2 hits [enterobacteria]    pyrroloquinoline quinone synthesis protein D [Klebsiella pn
. . . Klebsiella pneumoniae subsp. rhinoscleromatis ATCC 13884 .   38 2 hits [enterobacteria]    pyrroloquinoline quinone synthesis protein D [Klebsiella pn
. . . Klebsiella pneumoniae ....................................   38 2 hits [enterobacteria]    pyrroloquinoline quinone synthesis protein D [Klebsiella pn
. . . Variovorax paradoxus S110 ................................   38 2 hits [b-proteobacteria]  coenzyme PQQ synthesis D [Variovorax paradoxus S110] >gi|23
. . . Nitrosococcus oceani ATCC 19707 ..........................   38 2 hits [g-proteobacteria]  pyrroloquinoline quinone biosynthesis protein PqqD [Nitroso
. . . Nitrosococcus oceani AFC27 ...............................   38 2 hits [g-proteobacteria]  pyrroloquinoline quinone biosynthesis protein PqqD [Nitroso
. . . Burkholderia sp. CCGE1001 ................................   38 2 hits [b-proteobacteria]  coenzyme PQQ synthesis D [Burkholderia sp. CCGE1001] >gi|28
. . . Klebsiella pneumoniae 342 ................................   38 3 hits [enterobacteria]    coenzyme PQQ synthesis protein D [Klebsiella pneumoniae 342
. . . Klebsiella variicola At-22 ...............................   38 2 hits [enterobacteria]    coenzyme PQQ synthesis protein D [Klebsiella pneumoniae 342
. . . Klebsiella sp. 1_1_55 ....................................   38 2 hits [enterobacteria]    coenzyme PQQ synthesis protein D [Klebsiella pneumoniae 342
. . . Pseudomonas syringae pv. tomato T1 .......................   37 2 hits [g-proteobacteria]  coenzyme PQQ synthesis protein D [Pseudomonas syringae pv. 
. . . Alteromonas macleodii ATCC 27126 .........................   37 1 hit  [g-proteobacteria]  pyrroloquinoline quinone biosynthesis protein PqqD [Alterom
. . . Acinetobacter sp. SH024 ..................................   36 2 hits [g-proteobacteria]  conserved hypothetical protein [Acinetobacter sp. SH024] >g
. . . Acinetobacter calcoaceticus ..............................   36 2 hits [g-proteobacteria]  conserved hypothetical protein [Acinetobacter sp. SH024] >g
. . . Acinetobacter calcoaceticus RUH2202 ......................   36 2 hits [g-proteobacteria]  coenzyme PQQ synthesis protein D [Acinetobacter calcoacetic
. . . marine gamma proteobacterium HTCC2143 ....................   36 2 hits [g-proteobacteria]  pyrroloquinoline quinone biosynthesis protein PqqD [marine 
. . . Burkholderia ambifaria AMMD ..............................   36 2 hits [b-proteobacteria]  coenzyme PQQ synthesis D [Burkholderia ambifaria AMMD] >gi|
. . . Burkholderia graminis C4D1M ..............................   36 2 hits [b-proteobacteria]  coenzyme PQQ synthesis D [Burkholderia graminis C4D1M] >gi|
. . . Kluyvera intermedia ......................................   36 2 hits [enterobacteria]    RecName: Full=Coenzyme PQQ synthesis protein D; AltName: Fu
. . . Burkholderia sp. CCGE1003 ................................   36 2 hits [b-proteobacteria]  pyrroloquinoline quinone synthesis D [Burkholderia sp. CCGE
. . . Burkholderia ambifaria MC40-6 ............................   36 2 hits [b-proteobacteria]  coenzyme PQQ synthesis D [Burkholderia ambifaria MC40-6] >g
. . . Pseudomonas entomophila L48 ..............................   36 3 hits [g-proteobacteria]  pyrroloquinoline quinone biosynthesis protein PqqD [Pseudom
. . . Burkholderia ambifaria IOP40-10 ..........................   35 2 hits [b-proteobacteria]  coenzyme PQQ synthesis D [Burkholderia ambifaria IOP40-10] 
. . . Pseudomonas syringae pv. phaseolicola 1448A ..............   35 3 hits [g-proteobacteria]  pyrroloquinoline quinone biosynthesis protein PqqD [Pseudom
. . . Erwinia tasmaniensis Et1/99 ..............................   35 2 hits [enterobacteria]    Coenzyme PQQ synthesis protein D (Pyrroloquinoline quinone 
. . . Pseudomonas syringae pv. aesculi str. NCPPB3681 ..........   35 1 hit  [g-proteobacteria]  pyrroloquinoline quinone biosynthesis protein PqqD [Pseudom
. . . Pseudomonas syringae pv. aesculi str. 2250 ...............   35 1 hit  [g-proteobacteria]  pyrroloquinoline quinone biosynthesis protein PqqD [Pseudom
. . . Rahnella aquatilis .......................................   35 3 hits [enterobacteria]    RecName: Full=Coenzyme PQQ synthesis protein D; AltName: Fu
. . . Marinobacter algicola DG893 ..............................   35 2 hits [g-proteobacteria]  pyrroloquinoline quinone biosynthesis protein PqqD [Marinob
. . . Burkholderia xenovorans LB400 ............................   35 2 hits [b-proteobacteria]  pyrroloquinoline quinone synthesis D [Burkholderia xenovora
. . . Glaciecola sp. HTCC2999 ..................................   35 1 hit  [g-proteobacteria]  coenzyme PQQ synthesis protein D [alpha proteobacterium HTC
. . . Burkholderia sp. CCGE1002 ................................   35 4 hits [b-proteobacteria]  pyrroloquinoline quinone synthesis D [Burkholderia sp. CCGE
. . . Burkholderia ambifaria MEX-5 .............................   35 2 hits [b-proteobacteria]  coenzyme PQQ synthesis D [Burkholderia ambifaria MEX-5] >gi
. . . Burkholderia sp. H160 ....................................   34 2 hits [b-proteobacteria]  coenzyme PQQ synthesis D [Burkholderia sp. H160] >gi|209498
. . . Pseudomonas syringae pv. tomato str. DC3000 ..............   34 2 hits [g-proteobacteria]  coenzyme PQQ synthesis protein D [Pseudomonas syringae pv. 
. . . Pseudomonas syringae pv. tomato ..........................   34 1 hit  [g-proteobacteria]  coenzyme PQQ synthesis protein D [Pseudomonas syringae pv. 
. . . Pseudomonas putida W619 ..................................   33 3 hits [g-proteobacteria]  pyrroloquinoline quinone biosynthesis protein PqqD [Pseudom
. . . Erwinia pyrifoliae Ep1/96 ................................   33 2 hits [enterobacteria]    Coenzyme PQQ synthesis protein D (Pyrroloquinoline quinone 
. . . Erwinia pyrifoliae DSM 12163 .............................   33 1 hit  [enterobacteria]    Coenzyme PQQ synthesis protein D (Pyrroloquinoline quinone 
. . . Pseudomonas fluorescens ..................................   33 1 hit  [g-proteobacteria]  coenzyme PQQ biosynthesis protein PqqD [Pseudomonas fluores
. . Saccharopolyspora erythraea NRRL 2338 ----------------------   49 3 hits [high GC Gram+]     hypothetical protein SACE_4424 [Saccharopolyspora erythraea
. . Methylacidiphilum infernorum V4 ............................   45 3 hits [verrucomicrobia]   Coenzyme PQQ synthesis protein D [Methylacidiphilum inferno
. . Streptomyces rochei ........................................   42 2 hits [high GC Gram+]     pyrroloquinoline quinone biosynthesis protein D [Streptomyc
. . Geodermatophilus obscurus DSM 43160 ........................   42 2 hits [high GC Gram+]     coenzyme PQQ synthesis D [Geodermatophilus obscurus DSM 431
. . Mycobacterium smegmatis str. MC2 155 .......................   38 2 hits [high GC Gram+]     bifunctional coenzyme PQQ synthesis protein C/D [Mycobacter
. . Chthoniobacter flavus Ellin428 .............................   38 2 hits [verrucomicrobia]   coenzyme PQQ synthesis D [Chthoniobacter flavus Ellin428] >
. . Oceanobacillus iheyensis HTE831 ............................   36 2 hits [firmicutes]        DNA polymerase III alpha subunit [Oceanobacillus iheyensis 
. . Stackebrandtia nassauensis DSM 44728 .......................   35 2 hits [high GC Gram+]     coenzyme PQQ synthesis D [Stackebrandtia nassauensis DSM 44
. . Anaerocellum thermophilum DSM 6725 .........................   35 2 hits [firmicutes]        hypothetical protein Athe_1967 [Anaerocellum thermophilum D
. . Kosmotoga olearia TBF 19.5.1 ...............................   35 2 hits [thermotogales]     hypothetical protein Kole_1049 [Kosmotoga olearia TBF 19.5.
. . Streptomyces sp. AA4 .......................................   34 1 hit  [high GC Gram+]     pyrroloquinoline quinone biosynthesis protein D [Streptomyc
. . Hydrogenobacter thermophilus TK-6 ..........................   34 2 hits [aquificales]       coenzyme PQQ synthesis protein D [Hydrogenobacter thermophi
. . Spiroplasma citri ..........................................   34 1 hit  [mycoplasmas]       hypothetical protein [Spiroplasma citri]
. . Faecalibacterium prausnitzii L2-6 ..........................   33 1 hit  [firmicutes]        hypothetical protein [Faecalibacterium prausnitzii L2-6]
. . Streptomyces avermitilis MA-4680 ...........................   33 2 hits [high GC Gram+]     sulfate transporter [Streptomyces avermitilis MA-4680] >gi|
. . Streptomyces hygroscopicus ATCC 53653 ......................   33 1 hit  [high GC Gram+]     coenzyme PQQ synthesis D [Streptomyces hygroscopicus ATCC 5
. Verticillium albo-atrum VaMs.102 -----------------------------   36 1 hit  [ascomycetes]       thermostable beta-glucosidase B [Verticillium albo-atrum Va
. Oryza sativa Japonica Group (Japanese rice) ..................   35 3 hits [monocots]          Os05g0545200 [Oryza sativa (japonica cultivar-group)]

BLAST

PROTOCOL:


a)BLASTp versus NR, NCBI default parameters apart from "Number of descriptions_1000"

b)BLASTp versus SWISSPROT, NCBI default parameters apart from "Number of descriptions_1000"



RESULTS ANALYSIS


a)We ran the BLASTp software for our chosen ORF and obtained 372 significant alignement hits for 186 organisms. Within this results 69 true positive homologs were found (considering that the e-value threshold for valid positive homology is E<10^-04) ranging from 9e-04 to 1e-15. The BLASTp software detected putative conserved domains, all subgroups of the PqqD superfamily to which most of our ORF homolog sequences appear to be connected. PqqD[pfam05402] family (bit score_82.20 & e-value_3e-17) contains several bacterial coenzyme PQQ synthesis protein D (PqqD) sequences required for coenzyme pyrrolo-quinoline-quinone (PQQ) biosynthesis. PQQ_PqqD[TIGR03859] family (bit score_60.40 & e-value_9e-11) also identifies PqqD, a protein involved in the final steps of the biosynthesis of coenzyme PQQ and has a molecular function described as quinone binding (GO:0048038 - Interacting selectively and non-covalently with a quinone, any member of a class of diketones derivable from aromatic compounds by conversion of two CH groups into CO groups with any necessary rearrangement of double bonds). Therefore, the superfamily has a biological process stated as pyrroloquinoline quinone biosynthetic process (GO:0018189 - The chemical reactions and pathways resulting in the formation of the cofactor pyrroloquinoline quinone (PQQ); it is synthesized from a small peptide containing tyrosine and glutamic acid; these amino acids in the peptide are multiply cross-linked and the rest of the peptide is removed).


b)This query returned 46 hits with 17 true positive homologs. E-values ranged from 2e^-04 to 5e^-17.

RAW RESULTS

a)BLASTp vs NR, default NCBI parameters + "1000 max target sequences" 

                                                                   Score     E
Sequences producing significant alignments:                       (Bits)  Value

ref|YP_569168.1|  coenzyme PQQ synthesis D [Rhodopseudomonas p...  86.3    1e-15
ref|YP_487027.1|  coenzyme PQQ synthesis D [Rhodopseudomonas p...  85.5    2e-15
ref|YP_530771.1|  coenzyme PQQ synthesis D [Rhodopseudomonas p...  83.2    8e-15
ref|YP_001753211.1|  coenzyme PQQ biosynthesis protein C [Meth...  79.7    1e-13
ref|YP_001242127.1|  coenzyme PQQ synthesis protein D [Bradyrh...  79.0    1e-13
ref|YP_001207679.1|  coenzyme PQQ synthesis protein D (pyrrolo...  77.8    3e-13
ref|ZP_06359584.1|  coenzyme PQQ synthesis D [Rhodopseudomonas...  77.0    6e-13
ref|YP_002501119.1|  coenzyme PQQ synthesis D [Methylobacteriu...  75.9    1e-12
ref|NP_947294.1|  coenzyme PQQ synthesis D [Rhodopseudomonas p...  75.5    2e-12
ref|YP_002361481.1|  coenzyme PQQ synthesis D [Methylocella si...  75.5    2e-12
ref|YP_572903.1|  coenzyme PQQ synthesis D [Chromohalobacter s...  75.1    3e-12
ref|YP_001991156.1|  coenzyme PQQ synthesis D [Rhodopseudomona...  74.3    4e-12
ref|NP_773378.1|  putative pyrroloquinoline quinone synthesis ...  73.9    5e-12
ref|YP_779780.1|  coenzyme PQQ synthesis D [Rhodopseudomonas p...  73.9    6e-12
ref|ZP_05376971.1|  coenzyme PQQ synthesis D [Hyphomicrobium d...  73.2    8e-12
ref|YP_001924468.1|  coenzyme PQQ biosynthesis protein C [Meth...  70.9    5e-11
ref|ZP_00052131.2|  COG5424: Pyrroloquinoline quinone (Coenzym...  70.1    7e-11
ref|YP_001772489.1|  coenzyme PQQ synthesis D [Methylobacteriu...  70.1    8e-11
ref|YP_001416702.1|  coenzyme PQQ synthesis D [Xanthobacter au...  69.3    1e-10
ref|YP_002420929.1|  pyrroloquinoline quinone biosynthesis pro...  68.2    3e-10
ref|YP_002962870.1|  bifunctional coenzyme pyrroloquinoline qu...  68.2    3e-10
ref|YP_001233228.1|  coenzyme PQQ synthesis D [Acidiphilium cr...  67.4    4e-10
gb|AAB58899.1|  PqqC/D [Methylobacterium extorquens AM1]           67.0    6e-10
ref|ZP_01035861.1|  coenzyme PQQ synthesis protein D [Roseovar...  66.6    8e-10
ref|ZP_01880242.1|  coenzyme PQQ synthesis protein D [Roseovar...  66.6    9e-10
ref|YP_353869.1|  putative pyrroloquinoline quinone synthesis ...  66.2    1e-09
ref|YP_003068039.1|  bifunctional coenzyme pyrroloquinoline qu...  66.2    1e-09
ref|YP_001639288.1|  pyrroloquinoline quinone biosynthesis pro...  66.2    1e-09
ref|YP_001044321.1|  coenzyme PQQ synthesis D [Rhodobacter sph...  65.5    2e-09
ref|ZP_01442693.1|  coenzyme PQQ synthesis protein D [Roseovar...  65.1    2e-09
ref|YP_745748.1|  coenzyme PQQ synthesis protein D [Granulibac...  64.7    3e-09
ref|YP_001531802.1|  coenzyme PQQ synthesis D [Dinoroseobacter...  63.9    5e-09
ref|YP_003188622.1|  coenzyme Pyrrolo-quinoline quinone (PQQ) ...  63.9    5e-09
ref|YP_002526514.1|  Coenzyme PQQ synthesis D [Rhodobacter sph...  63.5    6e-09
ref|YP_001834368.1|  coenzyme PQQ synthesis D [Beijerinckia in...  62.4    1e-08
ref|ZP_05783763.1|  bifunctional coenzyme PQQ synthesis protei...  62.0    2e-08
ref|ZP_01015460.1|  putative pyrroloquinoline quinone synthesi...  61.6    2e-08
ref|ZP_05099407.1|  bifunctional coenzyme PQQ synthesis protei...  61.2    3e-08
ref|YP_001166600.1|  coenzyme PQQ synthesis D [Rhodobacter sph...  60.1    8e-08
ref|ZP_01438458.1|  Coenzyme PQQ synthesis D [Fulvimarina pela...  58.9    2e-07
ref|YP_001601524.1|  putative coenzyme PQQ synthesis protein D...  58.5    2e-07
ref|YP_001902619.1|  coenzyme PQQ synthesis protein D [Xanthom...  58.5    3e-07
ref|NP_638287.1|  PqqC/D protein [Xanthomonas campestris pv. c...  58.2    3e-07
pdb|3G2B|A  Chain A, Crystal Structure Of Pqqd From Xanthomona...  58.2    3e-07
ref|YP_002541520.1|  hypothetical protein Arad_8718 [Agrobacte...  56.6    9e-07
ref|YP_364978.1|  coenzyme PQQ synthesis protein D [Xanthomona...  55.5    2e-06
ref|NP_643425.1|  PqqC/D protein [Xanthomonas axonopodis pv. c...  55.1    3e-06
ref|ZP_01745426.1|  coenzyme PQQ synthesis protein D [Sagittul...  54.7    3e-06
ref|YP_317308.1|  coenzyme PQQ synthesis D [Nitrobacter winogr...  54.3    4e-06
ref|ZP_02142954.1|  coenzyme PQQ synthesis protein D [Roseobac...  54.3    5e-06
ref|YP_681488.1|  coenzyme PQQ synthesis protein D [Roseobacte...  53.5    7e-06
gb|ACN66498.1|  PqqD protein [Gluconobacter sp. H24]               53.5    7e-06
ref|YP_113906.1|  pyrroloquinoline quinone biosynthesis protei...  52.4    2e-05
ref|YP_166742.1|  coenzyme PQQ synthesis protein D [Ruegeria p...  52.4    2e-05
ref|ZP_06348174.1|  coenzyme PQQ synthesis D [Rhodomicrobium v...  51.6    3e-05
ref|YP_916146.1|  coenzyme PQQ synthesis D [Paracoccus denitri...  51.2    4e-05
ref|ZP_01626404.1|  pyrroloquinoline quinone biosynthesis prot...  50.8    4e-05
ref|YP_191412.1|  coenzyme PQQ synthesis protein D [Gluconobac...  50.8    4e-05
ref|YP_047096.1|  pyrroloquinoline quinone biosynthesis protei...  50.4    6e-05
ref|ZP_01915897.1|  Pyrroloquinoline quinone synthesis D [Limn...  50.4    6e-05
ref|YP_001187461.1|  pyrroloquinoline quinone biosynthesis pro...  50.1    7e-05
ref|YP_001106618.1|  hypothetical protein SACE_4424 [Saccharop...  49.7    1e-04
ref|YP_003051298.1|  coenzyme PQQ synthesis D [Methylovorus sp...  48.9    2e-04
ref|ZP_06561401.1|  hypothetical protein SeryN2_02782 [Sacchar...  48.1    3e-04
ref|YP_001914333.1|  bifunctional coenzyme PQQ synthesis prote...  48.1    3e-04
emb|CAZ87237.1|  coenzyme PQQ synthesis protein D [Thiomonas sp.]  47.8    4e-04
ref|YP_295990.1|  coenzyme PQQ synthesis D [Ralstonia eutropha...  47.4    6e-04
ref|ZP_05080523.1|  coenzyme PQQ synthesis protein D [Rhodobac...  46.6    8e-04
ref|YP_001439060.1|  hypothetical protein ESA_02995 [Cronobact...  46.6    9e-04
ref|YP_002801270.1|  Coenzyme PQQ biosynthesis protein D [Azot...  46.6    0.001
ref|ZP_06483578.1|  PqqC/D protein [Xanthomonas campestris pv....  45.8    0.001
ref|YP_001939888.1|  Coenzyme PQQ synthesis protein D [Methyla...  45.4    0.002
ref|YP_003209234.1|  Coenzyme PQQ synthesis protein D [Cronoba...  45.4    0.002
ref|ZP_01903226.1|  pyrroloquinoline quinone biosynthesis prot...  45.4    0.002
ref|YP_840571.1|  pyrroloquinoline quinone (coenzyme PQQ) bios...  45.4    0.002
gb|ABX56619.1|  coenzyme PQQ synthesis protein D [Methylacidip...  45.4    0.002
ref|YP_002007347.1|  Coenzyme PQQ synthesis protein D [Cupriav...  45.4    0.002
ref|YP_002982046.1|  coenzyme PQQ synthesis D [Ralstonia picke...  45.1    0.002
ref|YP_001900055.1|  coenzyme PQQ synthesis D [Ralstonia picke...  45.1    0.002
ref|ZP_02244163.1|  PqqC/D protein [Xanthomonas oryzae pv. ory...  44.7    0.004
ref|ZP_04959204.1|  coenzyme PQQ synthesis protein D [gamma pr...  44.3    0.004
ref|YP_450663.1|  PqqC/D protein [Xanthomonas oryzae pv. oryza...  44.3    0.005
ref|YP_998760.1|  coenzyme PQQ synthesis D [Verminephrobacter ...  43.9    0.005
ref|ZP_01165831.1|  coenzyme PQQ synthesis protein D [Oceanosp...  43.5    0.008
ref|YP_001897883.1|  coenzyme PQQ synthesis D [Ralstonia picke...  43.1    0.010
ref|NP_851428.1|  pyrroloquinoline quinone biosynthesis protei...  42.7    0.013
ref|ZP_05081769.1|  pyrroloquinoline quinone biosynthesis prot...  42.7    0.014
ref|YP_980970.1|  coenzyme PQQ synthesis D [Polaromonas naphth...  42.7    0.014
ref|ZP_02062053.1|  coenzyme PQQ synthesis protein D [Ricketts...  42.7    0.014
ref|YP_001796873.1|  coenzyme Pyrroloquinoline quinone (PQQ) s...  42.4    0.015
ref|ZP_06190123.1|  coenzyme PQQ synthesis D [Serratia odorife...  42.4    0.015
ref|YP_001312659.1|  coenzyme PQQ synthesis D [Sinorhizobium m...  42.4    0.016
ref|YP_001789287.1|  coenzyme PQQ synthesis D [Leptothrix chol...  42.4    0.017
ref|YP_003409497.1|  coenzyme PQQ synthesis D [Geodermatophilu...  42.4    0.019
gb|ABI31436.1|  PqqD [Serratia marcescens]                         41.6    0.031
ref|YP_003528923.1|  coenzyme PQQ synthesis D [Nitrosococcus h...  41.6    0.032
ref|YP_267607.1|  pyrroloquinoline quinone biosynthesis protei...  41.6    0.032
ref|YP_284918.1|  coenzyme PQQ synthesis D [Dechloromonas arom...  41.2    0.040
ref|NP_436740.1|  putative pyrroloquinoline quinone synthesis ...  40.8    0.046
ref|ZP_04933747.1|  pyrroloquinoline quinone biosynthesis prot...  40.4    0.060
ref|NP_250678.1|  pyrroloquinoline quinone biosynthesis protei...  40.4    0.063
ref|YP_001021776.1|  pyrroloquinoline quinone biosynthesis pro...  40.4    0.067
ref|YP_932693.1|  PqqD protein [Azoarcus sp. BH72] >emb|CAL938...  40.4    0.071
ref|YP_002889810.1|  coenzyme PQQ synthesis D [Thauera sp. MZ1...  40.0    0.075
ref|YP_001760626.1|  coenzyme PQQ synthesis D [Shewanella wood...  40.0    0.075
ref|ZP_03699881.1|  coenzyme PQQ synthesis D [Lutiella nitrofe...  40.0    0.077
ref|YP_001348666.1|  pyrroloquinoline quinone biosynthesis pro...  40.0    0.090
ref|ZP_03697008.1|  coenzyme PQQ synthesis D [Lutiella nitrofe...  39.7    0.10 
ref|YP_002822546.1|  coenzyme PQQ synthesis protein D [Rhizobi...  39.7    0.11 
ref|ZP_04590889.1|  pyrroloquinoline quinone biosynthesis prot...  39.3    0.13 
ref|YP_237738.1|  pyrroloquinoline quinone biosynthesis protei...  39.3    0.14 
ref|YP_003451074.1|  coenzyme PQQ synthesis protein D [Azospir...  39.3    0.14 
ref|YP_001172579.1|  pyrroloquinoline quinone biosynthesis pro...  39.3    0.14 
ref|YP_001236052.1|  hypothetical protein Acry_2943 [Acidiphil...  38.9    0.19 
ref|ZP_06495228.1|  pyrroloquinoline quinone biosynthesis prot...  38.9    0.20 
ref|YP_888022.1|  bifunctional coenzyme PQQ synthesis protein ...  38.9    0.20 
ref|ZP_06640393.1|  coenzyme PQQ synthesis protein D [Serratia...  38.5    0.23 
ref|YP_002919581.1|  pyrroloquinoline quinone synthesis protei...  38.5    0.24 
ref|YP_002944939.1|  coenzyme PQQ synthesis D [Variovorax para...  38.5    0.27 
ref|YP_344605.1|  pyrroloquinoline quinone biosynthesis protei...  38.1    0.28 
ref|ZP_03128983.1|  coenzyme PQQ synthesis D [Chthoniobacter f...  38.1    0.29 
ref|ZP_06292352.1|  coenzyme PQQ synthesis D [Burkholderia sp....  38.1    0.34 
ref|YP_002238373.1|  coenzyme PQQ synthesis protein D [Klebsie...  38.1    0.36 
ref|ZP_03395870.1|  coenzyme PQQ synthesis protein D [Pseudomo...  37.7    0.41 
ref|ZP_04717389.1|  pyrroloquinoline quinone biosynthesis prot...  37.7    0.44 
ref|ZP_06690394.1|  conserved hypothetical protein [Acinetobac...  37.0    0.65 
ref|ZP_06056871.1|  coenzyme PQQ synthesis protein D [Acinetob...  37.0    0.69 
ref|ZP_01615250.1|  pyrroloquinoline quinone biosynthesis prot...  37.0    0.78 
gb|EEY21449.1|  thermostable beta-glucosidase B [Verticillium ...  36.6    0.81 
ref|YP_778045.1|  coenzyme PQQ synthesis D [Burkholderia ambif...  36.6    0.98 
ref|ZP_02881220.1|  coenzyme PQQ synthesis D [Burkholderia gra...  36.6    0.99 
sp|P59725.1|PQQD_ENTIT  RecName: Full=Coenzyme PQQ synthesis p...  36.6    1.0  
ref|ZP_06464592.1|  pyrroloquinoline quinone synthesis D [Burk...  36.2    1.2  
ref|YP_001815890.1|  coenzyme PQQ synthesis D [Burkholderia am...  36.2    1.3  
ref|NP_693098.1|  DNA polymerase III alpha subunit [Oceanobaci...  36.2    1.3  
ref|YP_606171.1|  pyrroloquinoline quinone biosynthesis protei...  36.2    1.3  
ref|ZP_02890391.1|  coenzyme PQQ synthesis D [Burkholderia amb...  35.8    1.4  
ref|YP_276809.1|  pyrroloquinoline quinone biosynthesis protei...  35.8    1.4  
ref|YP_001908802.1|  Coenzyme PQQ synthesis protein D (Pyrrolo...  35.8    1.4  
ref|YP_003510961.1|  coenzyme PQQ synthesis D [Stackebrandtia ...  35.8    1.5  
ref|ZP_06457725.1|  pyrroloquinoline quinone biosynthesis prot...  35.8    1.5  
sp|O33505.2|PQQD_RAHAQ  RecName: Full=Coenzyme PQQ synthesis p...  35.8    1.6  
ref|YP_002573827.1|  hypothetical protein Athe_1967 [Anaerocel...  35.8    1.7  
ref|ZP_01893577.1|  pyrroloquinoline quinone biosynthesis prot...  35.8    1.8  
ref|NP_001056210.1|  Os05g0545200 [Oryza sativa (japonica cult...  35.4    2.0  
gb|AAT44179.1|  putative regulator of chromosome condensation ...  35.4    2.0  
ref|YP_552872.1|  pyrroloquinoline quinone synthesis D [Burkho...  35.4    2.1  
ref|YP_002940758.1|  hypothetical protein Kole_1049 [Kosmotoga...  35.4    2.3  
ref|ZP_01448100.1|  coenzyme PQQ synthesis protein D [alpha pr...  35.0    2.7  
ref|ZP_06228260.1|  pyrroloquinoline quinone synthesis D [Burk...  35.0    2.7  
ref|ZP_02905126.1|  coenzyme PQQ synthesis D [Burkholderia amb...  35.0    2.8  
ref|ZP_03269833.1|  coenzyme PQQ synthesis D [Burkholderia sp....  34.7    3.2  
ref|NP_790358.1|  coenzyme PQQ synthesis protein D [Pseudomona...  34.7    3.3  
emb|CBK85074.1|  Coenzyme PQQ synthesis protein D (PqqD). [Ent...  34.7    3.7  
ref|ZP_05480662.1|  pyrroloquinoline quinone biosynthesis prot...  34.7    4.0  
ref|YP_003432872.1|  coenzyme PQQ synthesis protein D [Hydroge...  34.3    4.2  
emb|CAK99141.1|  hypothetical protein [Spiroplasma citri]          34.3    4.6  
emb|CBL00417.1|  hypothetical protein [Faecalibacterium prausn...  33.9    5.3  
gb|AAC38152.1|  ORF1 [Rahnella aquatilis]                          33.9    6.5  
ref|NP_823782.1|  sulfate transporter [Streptomyces avermitili...  33.5    7.1  
ref|YP_001751671.1|  pyrroloquinoline quinone biosynthesis pro...  33.5    7.1  
ref|YP_002647606.1|  Coenzyme PQQ synthesis protein D (Pyrrolo...  33.5    7.5  
ref|ZP_05512375.1|  coenzyme PQQ synthesis D [Streptomyces hyg...  33.5    8.6  
gb|ACT32392.1|  coenzyme PQQ biosynthesis protein PqqD [Pseudo...  33.1    9.1  
gb|ACP19313.1|  PqqD [Rahnella aquatilis]                          33.1    9.2  
ref|ZP_06225430.1|  coenzyme PQQ synthesis D [Burkholderia sp....  33.1    9.4  

ALIGNMENTS
>ref|YP_569168.1| coenzyme PQQ synthesis D [Rhodopseudomonas palustris BisB5]
 sp|Q139H2.1|PQQD_RHOPS RecName: Full=Coenzyme PQQ synthesis protein D; AltName: Full=Pyrroloquinoline 
quinone biosynthesis protein D
 gb|ABE39267.1| coenzyme PQQ synthesis D [Rhodopseudomonas palustris BisB5]
Length=102

 Score = 86.3 bits (212),  Expect = 1e-15, Method: Compositional matrix adjust.
 Identities = 40/79 (50%), Positives = 56/79 (70%), Gaps = 1/79 (1%)

Query  40   PRLPRHAKLRYDEARKKWIINAPERVFELDDTAADIMKQVDGVLSINVIVDNVHRKFNEA  99
            P LPRHAKLR+DE R++W+I APERV   DD A +I++  DG  S++ I+D +  K+  A
Sbjct  14   PALPRHAKLRFDETRQRWVILAPERVLAPDDIAVEILQLCDGARSVSAIIDQLATKYT-A  72

Query  100  TRDQISSDVILMLRSLADK  118
             R +I +DV+ ML+ LADK
Sbjct  73   DRAEIGTDVVAMLQDLADK  91


>ref|YP_487027.1| coenzyme PQQ synthesis D [Rhodopseudomonas palustris HaA2]
 sp|Q2IUJ4.1|PQQD_RHOP2 RecName: Full=Coenzyme PQQ synthesis protein D; AltName: Full=Pyrroloquinoline 
quinone biosynthesis protein D
 gb|ABD08116.1| Coenzyme PQQ synthesis D [Rhodopseudomonas palustris HaA2]
Length=102

 Score = 85.5 bits (210),  Expect = 2e-15, Method: Compositional matrix adjust.
 Identities = 42/90 (46%), Positives = 60/90 (66%), Gaps = 1/90 (1%)

Query  29   SKLVKLEPDNIPRLPRHAKLRYDEARKKWIINAPERVFELDDTAADIMKQVDGVLSINVI  88
            S+ + +   + P LPRHAKLR+DE R++W+I APERV   DD A +I++  DG  S+  I
Sbjct  3    SRHISVSEQSRPMLPRHAKLRFDETRQRWVILAPERVLAPDDIAVEILQLCDGARSVAAI  62

Query  89   VDNVHRKFNEATRDQISSDVILMLRSLADK  118
            +D +  K+  A R +I +DVI ML+ LADK
Sbjct  63   IDTLALKYT-ADRAEIGADVIAMLQDLADK  91


>ref|YP_530771.1| coenzyme PQQ synthesis D [Rhodopseudomonas palustris BisB18]
 gb|ABD86452.1| coenzyme PQQ synthesis D [Rhodopseudomonas palustris BisB18]
Length=105

 Score = 83.2 bits (204),  Expect = 8e-15, Method: Compositional matrix adjust.
 Identities = 42/90 (46%), Positives = 63/90 (70%), Gaps = 1/90 (1%)

Query  29   SKLVKLEPDNIPRLPRHAKLRYDEARKKWIINAPERVFELDDTAADIMKQVDGVLSINVI  88
            S+ + +E  + P LPRHAKLR+D  R++W+I APERV   D+ A +I++  DGV S+  +
Sbjct  6    SRNLTVEEASRPVLPRHAKLRFDVTRQRWVILAPERVLAPDEIAVEILQLCDGVRSVAEM  65

Query  89   VDNVHRKFNEATRDQISSDVILMLRSLADK  118
            +D + RK++ A R+ I +DVI ML+ LADK
Sbjct  66   IDELARKYS-AARELIGADVIAMLQDLADK  94


>ref|YP_001753211.1| coenzyme PQQ biosynthesis protein C [Methylobacterium radiotolerans 
JCM 2831]
 gb|ACB22528.1| coenzyme PQQ biosynthesis protein C [Methylobacterium radiotolerans 
JCM 2831]
Length=361

 Score = 79.7 bits (195),  Expect = 1e-13, Method: Compositional matrix adjust.
 Identities = 39/95 (41%), Positives = 59/95 (62%), Gaps = 1/95 (1%)

Query  26   KKMSKLVKLEPDNIPRLPRHAKLRYDEARKKWIINAPERVFELDDTAADIMKQVDGVLSI  85
            K  +   K+   + PRLPR  +LR DE R KW++ APER F+LDD A  ++K VDG  S+
Sbjct  265  KPGASGGKMAAGDRPRLPRGVRLRNDETRGKWVLLAPERTFDLDDNAVAVLKLVDGARSV  324

Query  86   NVIVDNVHRKFNEATRDQISSDVILMLRSLADKRI  120
            + I D + + +    R  I +D+++ML  LA+KR+
Sbjct  325  SDIADELGKTYAADPR-AIEADILVMLDGLAEKRV  358


>ref|YP_001242127.1| coenzyme PQQ synthesis protein D [Bradyrhizobium sp. BTAi1]
 gb|ABQ38221.1| Coenzyme PQQ synthesis protein D [Bradyrhizobium sp. BTAi1]
Length=102

 Score = 79.0 bits (193),  Expect = 1e-13, Method: Compositional matrix adjust.
 Identities = 38/77 (49%), Positives = 54/77 (70%), Gaps = 1/77 (1%)

Query  42   LPRHAKLRYDEARKKWIINAPERVFELDDTAADIMKQVDGVLSINVIVDNVHRKFNEATR  101
            LPRH KL++DE R+ W+I APERV   D+ A +++K  DGV S+  I+D +  K+  A R
Sbjct  16   LPRHTKLKFDETRQVWVILAPERVLAPDEIAVEVLKLCDGVRSVAGIIDELATKYA-APR  74

Query  102  DQISSDVILMLRSLADK  118
            D I++DV+ ML+ LADK
Sbjct  75   DVIATDVVAMLQDLADK  91


>ref|YP_001207679.1| coenzyme PQQ synthesis protein D (pyrroloquinoline quinone biosynthesis 
protein D)(PqqD) [Bradyrhizobium sp. ORS278]
 emb|CAL79462.1| Coenzyme PQQ synthesis protein D (Pyrroloquinoline quinone biosynthesis 
protein D)(PqqD) [Bradyrhizobium sp. ORS278]
Length=102

 Score = 77.8 bits (190),  Expect = 3e-13, Method: Compositional matrix adjust.
 Identities = 37/77 (48%), Positives = 53/77 (68%), Gaps = 1/77 (1%)

Query  42   LPRHAKLRYDEARKKWIINAPERVFELDDTAADIMKQVDGVLSINVIVDNVHRKFNEATR  101
            LPRH KL+YDE R+ W+I APERV   D+ A ++++  DG  S+  I+D +  K+  A R
Sbjct  16   LPRHTKLKYDETRQVWVILAPERVLAPDEIAVEVLQLCDGARSVAGIIDELAAKYA-APR  74

Query  102  DQISSDVILMLRSLADK  118
            D I++DV+ ML+ LADK
Sbjct  75   DVIATDVVAMLQDLADK  91


>ref|ZP_06359584.1| coenzyme PQQ synthesis D [Rhodopseudomonas palustris DX-1]
 gb|EFC24364.1| coenzyme PQQ synthesis D [Rhodopseudomonas palustris DX-1]
Length=102

 Score = 77.0 bits (188),  Expect = 6e-13, Method: Compositional matrix adjust.
 Identities = 37/79 (46%), Positives = 53/79 (67%), Gaps = 1/79 (1%)

Query  40   PRLPRHAKLRYDEARKKWIINAPERVFELDDTAADIMKQVDGVLSINVIVDNVHRKFNEA  99
            P LPRHA+L++DE R++W+I APERV   D+ A +I++  DG   +  I+D +  K+  A
Sbjct  14   PVLPRHARLKFDETRQRWVILAPERVLAPDEIAVEILQLCDGARDVAAIIDALAAKYA-A  72

Query  100  TRDQISSDVILMLRSLADK  118
             R +I  DVI ML+ LADK
Sbjct  73   GRAEIGRDVIAMLQDLADK  91


>ref|YP_002501119.1| coenzyme PQQ synthesis D [Methylobacterium nodulans ORS 2060]
 gb|ACL60816.1| coenzyme PQQ synthesis D [Methylobacterium nodulans ORS 2060]
Length=99

 Score = 75.9 bits (185),  Expect = 1e-12, Method: Compositional matrix adjust.
 Identities = 38/87 (43%), Positives = 53/87 (60%), Gaps = 1/87 (1%)

Query  34   LEPDNIPRLPRHAKLRYDEARKKWIINAPERVFELDDTAADIMKQVDGVLSINVIVDNVH  93
            L PD++PRLPR  ++ +D  R   ++ APER F+LD  A  ++  VDG  SI  I D + 
Sbjct  3    LTPDDVPRLPRGVRMHFDGVRGAHVLLAPERTFDLDRNAVAVLSLVDGTRSIRAIADALA  62

Query  94   RKFNEATRDQISSDVILMLRSLADKRI  120
             ++ +A R  I  DVI ML  LADKR+
Sbjct  63   EQY-DAPRTVIEPDVITMLNGLADKRV  88


>ref|NP_947294.1| coenzyme PQQ synthesis D [Rhodopseudomonas palustris CGA009]
 sp|Q6N8F4.1|PQQD_RHOPA RecName: Full=Coenzyme PQQ synthesis protein D; AltName: Full=Pyrroloquinoline 
quinone biosynthesis protein D
 emb|CAE27390.1| pyrroloquinoline quinone biosynthesis protein D [Rhodopseudomonas 
palustris CGA009]
Length=102

 Score = 75.5 bits (184),  Expect = 2e-12, Method: Compositional matrix adjust.
 Identities = 35/79 (44%), Positives = 53/79 (67%), Gaps = 1/79 (1%)

Query  40   PRLPRHAKLRYDEARKKWIINAPERVFELDDTAADIMKQVDGVLSINVIVDNVHRKFNEA  99
            P LPRHA+L++D+ R++W+I APERV   D+ A +I++  DG   +  I+D +  K+  A
Sbjct  14   PVLPRHARLKFDDTRQRWVILAPERVLAPDEIAVEILQLCDGACDVAAIIDALAAKYT-A  72

Query  100  TRDQISSDVILMLRSLADK  118
             R +I  DV+ ML+ LADK
Sbjct  73   DRAEIGRDVMAMLQDLADK  91


>ref|YP_002361481.1| coenzyme PQQ synthesis D [Methylocella silvestris BL2]
 gb|ACK50119.1| coenzyme PQQ synthesis D [Methylocella silvestris BL2]
Length=102

 Score = 75.5 bits (184),  Expect = 2e-12, Method: Compositional matrix adjust.
 Identities = 37/82 (45%), Positives = 56/82 (68%), Gaps = 1/82 (1%)

Query  39   IPRLPRHAKLRYDEARKKWIINAPERVFELDDTAADIMKQVDGVLSINVIVDNVHRKFNE  98
            +PRLPR  +L++DE R +W++ APER+ ++DD A  I+K+ DGV +I  IV+++   F  
Sbjct  19   VPRLPRGVRLKFDETRGQWLLLAPERLVKVDDIAVAILKRCDGVATIEAIVEDLAATFA-  77

Query  99   ATRDQISSDVILMLRSLADKRI  120
            A R QI +DV  +L  LA KR+
Sbjct  78   ADRAQIDADVRRLLNELAAKRM  99


>ref|YP_572903.1| coenzyme PQQ synthesis D [Chromohalobacter salexigens DSM 3043]
 gb|ABE58204.1| coenzyme PQQ synthesis D [Chromohalobacter salexigens DSM 3043]
Length=93

 Score = 75.1 bits (183),  Expect = 3e-12, Method: Compositional matrix adjust.
 Identities = 35/90 (38%), Positives = 56/90 (62%), Gaps = 1/90 (1%)

Query  31   LVKLEPDNIPRLPRHAKLRYDEARKKWIINAPERVFELDDTAADIMKQVDGVLSINVIVD  90
            +  ++  +I RLPR  +LR D+ R  W++ APERVF+LD  A  ++ QVDG  S+  I+D
Sbjct  1    MTAIQESDIVRLPRGVRLREDKRRGGWVLLAPERVFQLDGIAQAVVGQVDGERSVGTIID  60

Query  91   NVHRKFNEATRDQISSDVILMLRSLADKRI  120
             +   + +A R++I+ DV  M   L +KR+
Sbjct  61   RLCETY-QAPRERIAQDVTAMFAGLVEKRV  89


>ref|YP_001991156.1| coenzyme PQQ synthesis D [Rhodopseudomonas palustris TIE-1]
 sp|B3QBT1.1|PQQD_RHOPT RecName: Full=Coenzyme PQQ synthesis protein D; AltName: Full=Pyrroloquinoline 
quinone biosynthesis protein D
 gb|ACF00681.1| coenzyme PQQ synthesis D [Rhodopseudomonas palustris TIE-1]
Length=102

 Score = 74.3 bits (181),  Expect = 4e-12, Method: Compositional matrix adjust.
 Identities = 35/79 (44%), Positives = 53/79 (67%), Gaps = 1/79 (1%)

Query  40   PRLPRHAKLRYDEARKKWIINAPERVFELDDTAADIMKQVDGVLSINVIVDNVHRKFNEA  99
            P LPRHA+L++DE R++W+I APERV   D+ A +I++  DG   +  I+D +  ++  A
Sbjct  14   PVLPRHARLKFDETRQRWVILAPERVLAPDEIAVEILQLCDGARDVAAIIDALAVRYT-A  72

Query  100  TRDQISSDVILMLRSLADK  118
             R +I  DV+ ML+ LADK
Sbjct  73   DRAEIGRDVVAMLQDLADK  91


>ref|NP_773378.1| putative pyrroloquinoline quinone synthesis protein D [Bradyrhizobium 
japonicum USDA 110]
 sp|Q89FG2.1|PQQD_BRAJA RecName: Full=Coenzyme PQQ synthesis protein D; AltName: Full=Pyrroloquinoline 
quinone biosynthesis protein D
 dbj|BAC52003.1| pqqD [Bradyrhizobium japonicum USDA 110]
Length=103

 Score = 73.9 bits (180),  Expect = 5e-12, Method: Compositional matrix adjust.
 Identities = 37/79 (46%), Positives = 53/79 (67%), Gaps = 1/79 (1%)

Query  40   PRLPRHAKLRYDEARKKWIINAPERVFELDDTAADIMKQVDGVLSINVIVDNVHRKFNEA  99
            P LPRHAKL+YDE R+ W+I APERV   D+ A ++++  +G  S+  + D +  K+  A
Sbjct  15   PVLPRHAKLKYDETREVWVILAPERVLAPDEIAVEVLQLCNGERSVGDVSDQLAAKYA-A  73

Query  100  TRDQISSDVILMLRSLADK  118
             R+ I +DVI ML+ LADK
Sbjct  74   PREAILTDVIAMLQDLADK  92


>ref|YP_779780.1| coenzyme PQQ synthesis D [Rhodopseudomonas palustris BisA53]
 gb|ABJ04800.1| coenzyme PQQ synthesis D [Rhodopseudomonas palustris BisA53]
Length=109

 Score = 73.9 bits (180),  Expect = 6e-12, Method: Compositional matrix adjust.
 Identities = 41/100 (41%), Positives = 60/100 (60%), Gaps = 10/100 (10%)

Query  19   SRKIIIIKKMSKLVKLEPDNIPRLPRHAKLRYDEARKKWIINAPERVFELDDTAADIMKQ  78
            SR+ I + + S+         P LPRHAKL++D  R++W+I APERV   DD A +I++ 
Sbjct  4    SRRNISVSEASR---------PLLPRHAKLKFDATRQRWVILAPERVLAPDDIAVEILQL  54

Query  79   VDGVLSINVIVDNVHRKFNEATRDQISSDVILMLRSLADK  118
             DG   +  ++D + +K+  A R  I  DVI ML+ LADK
Sbjct  55   CDGARDVASMIDQLAQKY-AADRAVIGVDVIAMLQDLADK  93


>ref|ZP_05376971.1| coenzyme PQQ synthesis D [Hyphomicrobium denitrificans ATCC 51888]
 gb|EET66466.1| coenzyme PQQ synthesis D [Hyphomicrobium denitrificans ATCC 51888]
Length=100

 Score = 73.2 bits (178),  Expect = 8e-12, Method: Compositional matrix adjust.
 Identities = 36/85 (42%), Positives = 53/85 (62%), Gaps = 1/85 (1%)

Query  36   PDNIPRLPRHAKLRYDEARKKWIINAPERVFELDDTAADIMKQVDGVLSINVIVDNVHRK  95
            P + P LP H KLR+D  R +W + APERVFE D  A +I+K+ DG  S+  I   + ++
Sbjct  14   PASKPGLPTHIKLRHDAGRGRWHVLAPERVFEPDPIAVEILKRCDGATSVEEIATALAKE  73

Query  96   FNEATRDQISSDVILMLRSLADKRI  120
            +N A   +I +D I ML+ L+DK +
Sbjct  74   YN-APLQEILADTISMLQELSDKGV  97


>ref|YP_001924468.1| coenzyme PQQ biosynthesis protein C [Methylobacterium populi 
BJ001]
 gb|ACB79933.1| coenzyme PQQ biosynthesis protein C [Methylobacterium populi 
BJ001]
Length=362

 Score = 70.9 bits (172),  Expect = 5e-11, Method: Compositional matrix adjust.
 Identities = 36/83 (43%), Positives = 54/83 (65%), Gaps = 1/83 (1%)

Query  38   NIPRLPRHAKLRYDEARKKWIINAPERVFELDDTAADIMKQVDGVLSINVIVDNVHRKFN  97
            ++PRLPR  +LRYDE R K ++ APER F+LDD A  ++K VDG  S++ I   + + ++
Sbjct  278  DVPRLPRGVRLRYDEVRAKHVLLAPERTFDLDDNAVAVLKLVDGQNSVSQIARTLGQTYD  337

Query  98   EATRDQISSDVILMLRSLADKRI  120
             A    I +D++ ML  LA KR+
Sbjct  338  -ADPAVIEADILPMLAGLAQKRV  359


>ref|ZP_00052131.2| COG5424: Pyrroloquinoline quinone (Coenzyme PQQ) biosynthesis 
protein C [Magnetospirillum magnetotacticum MS-1]
Length=362

 Score = 70.1 bits (170),  Expect = 7e-11, Method: Compositional matrix adjust.
 Identities = 35/83 (42%), Positives = 55/83 (66%), Gaps = 1/83 (1%)

Query  38   NIPRLPRHAKLRYDEARKKWIINAPERVFELDDTAADIMKQVDGVLSINVIVDNVHRKFN  97
            ++PRLPR  +LR+DE R K I+ APER F+LDD A  ++K VDG  S++ I   + + ++
Sbjct  278  DVPRLPRGVRLRFDEVRNKHILLAPERTFDLDDNAVAVLKLVDGQSSVSQIARTLGQTYD  337

Query  98   EATRDQISSDVILMLRSLADKRI  120
             A    I +D+++ML  LA +R+
Sbjct  338  -ADPAVIEADILVMLAGLAQRRV  359


>ref|YP_001772489.1| coenzyme PQQ synthesis D [Methylobacterium sp. 4-46]
 gb|ACA20055.1| coenzyme PQQ synthesis D [Methylobacterium sp. 4-46]
Length=95

 Score = 70.1 bits (170),  Expect = 8e-11, Method: Compositional matrix adjust.
 Identities = 35/89 (39%), Positives = 53/89 (59%), Gaps = 1/89 (1%)

Query  32   VKLEPDNIPRLPRHAKLRYDEARKKWIINAPERVFELDDTAADIMKQVDGVLSINVIVDN  91
            + L P ++PRLPR  ++R+D  R   ++ APER F+LD  A  ++  VDG  SI  I + 
Sbjct  1    MSLTPGDVPRLPRGVRMRFDGVRGAHVLLAPERTFDLDQNAVAVLSLVDGERSIRAIAEA  60

Query  92   VHRKFNEATRDQISSDVILMLRSLADKRI  120
            +  +++ A    I  DVI ML  LA+KR+
Sbjct  61   LSAQYD-APVGVIEPDVITMLNGLAEKRV  88


>ref|YP_001416702.1| coenzyme PQQ synthesis D [Xanthobacter autotrophicus Py2]
 gb|ABS67045.1| coenzyme PQQ synthesis D [Xanthobacter autotrophicus Py2]
Length=91

 Score = 69.3 bits (168),  Expect = 1e-10, Method: Compositional matrix adjust.
 Identities = 35/89 (39%), Positives = 60/89 (67%), Gaps = 1/89 (1%)

Query  32   VKLEPDNIPRLPRHAKLRYDEARKKWIINAPERVFELDDTAADIMKQVDGVLSINVIVDN  91
            ++ E  ++PRLPR  KL+YD+ R++ ++ APER F++D+TAA +++ VDG  +   IVD 
Sbjct  1    MRAEETDVPRLPRGVKLKYDQVRERHVLLAPERAFDIDETAAAVLELVDGQRTCGQIVDA  60

Query  92   VHRKFNEATRDQISSDVILMLRSLADKRI  120
            +  +F+E  R+ I+ DV  M+  L  +R+
Sbjct  61   LALRFDE-KREVIADDVRDMIGDLIARRV  88


>ref|YP_002420929.1| pyrroloquinoline quinone biosynthesis protein PqqC [Methylobacterium 
chloromethanicum CM4]
 gb|ACK83001.1| coenzyme PQQ biosynthesis protein C [Methylobacterium chloromethanicum 
CM4]
Length=372

 Score = 68.2 bits (165),  Expect = 3e-10, Method: Composition-based stats.
 Identities = 34/83 (40%), Positives = 54/83 (65%), Gaps = 1/83 (1%)

Query  38   NIPRLPRHAKLRYDEARKKWIINAPERVFELDDTAADIMKQVDGVLSINVIVDNVHRKFN  97
            ++PRLPR  +LR+DE R K ++ APER F+LDD A  ++K VDG  +++ I   + + + 
Sbjct  288  DVPRLPRGVRLRFDEVRNKHVLLAPERTFDLDDNAVAVLKLVDGRNTVSQIAQILGQTY-  346

Query  98   EATRDQISSDVILMLRSLADKRI  120
            +A    I +D++ ML  LA KR+
Sbjct  347  DADPAIIEADILPMLAGLAQKRV  369

-----------------------------------------------------------------------------------

b)BLASTp vs SWISSPROT, default NCBI parameters + "1000 max target sequences"

                                                                   Score     E
Sequences producing significant alignments:                       (Bits)  Value

sp|Q139H2.1|PQQD_RHOPS  RecName: Full=Coenzyme PQQ synthesis p...  86.3    5e-17
sp|Q2IUJ4.1|PQQD_RHOP2  RecName: Full=Coenzyme PQQ synthesis p...  85.5    8e-17
sp|Q6N8F4.1|PQQD_RHOPA  RecName: Full=Coenzyme PQQ synthesis p...  75.5    8e-14
sp|B3QBT1.1|PQQD_RHOPT  RecName: Full=Coenzyme PQQ synthesis p...  74.3    2e-13
sp|Q89FG2.1|PQQD_BRAJA  RecName: Full=Coenzyme PQQ synthesis p...  73.9    2e-13
sp|Q49150.2|PQQCD_METEA  RecName: Full=Bifunctional coenzyme P...  68.2    1e-11
sp|B0RQ26.1|PQQD_XANCB  RecName: Full=Coenzyme PQQ synthesis p...  58.5    1e-08
sp|Q8P6M8.1|PQQD_XANCP  RecName: Full=Coenzyme PQQ synthesis p...  58.2    1e-08
sp|Q3BQI5.1|PQQD_XANC5  RecName: Full=Coenzyme PQQ synthesis p...  55.5    9e-08
sp|Q8PHY2.1|PQQD_XANAC  RecName: Full=Coenzyme PQQ synthesis p...  55.1    1e-07
sp|Q608P1.1|PQQD_METCA  RecName: Full=Coenzyme PQQ synthesis p...  52.4    6e-07
sp|Q5LTB3.1|PQQD_SILPO  RecName: Full=Coenzyme PQQ synthesis p...  52.4    7e-07
sp|Q9L3B1.1|PQQD_GLUOX  RecName: Full=Coenzyme PQQ synthesis p...  50.8    2e-06
sp|Q6F9J0.1|PQQD_ACIAD  RecName: Full=Coenzyme PQQ synthesis p...  50.4    3e-06
sp|B2SSW2.1|PQQD_XANOP  RecName: Full=Coenzyme PQQ synthesis p...  48.1    1e-05
sp|C1DEW6.1|PQQD_AZOVD  RecName: Full=Coenzyme PQQ synthesis p...  46.6    4e-05
sp|Q05I08.1|PQQD_XANOR  RecName: Full=Coenzyme PQQ synthesis p...  44.3    2e-04
sp|Q9EXU9.1|PQQD_RHIME  RecName: Full=Coenzyme PQQ synthesis p...  40.8    0.002
sp|Q9I2C1.1|PQQD_PSEAE  RecName: Full=Coenzyme PQQ synthesis p...  40.4    0.003
sp|A6V6I1.1|PQQD_PSEA7  RecName: Full=Coenzyme PQQ synthesis p...  40.0    0.004
sp|Q4ZMC2.1|PQQD_PSEU2  RecName: Full=Coenzyme PQQ synthesis p...  39.3    0.006
sp|P27506.1|PQQD_KLEPN  RecName: Full=Coenzyme PQQ synthesis p...  38.5    0.010
sp|B5XX59.1|PQQD_KLEP3  RecName: Full=Coenzyme PQQ synthesis p...  38.1    0.015
sp|P07781.1|PQQD_ACICA  RecName: Full=Coenzyme PQQ synthesis p...  37.0    0.028
sp|P59725.1|PQQD_ENTIT  RecName: Full=Coenzyme PQQ synthesis p...  36.6    0.043
sp|Q1IG48.1|PQQD_PSEE4  RecName: Full=Coenzyme PQQ synthesis p...  36.2    0.058
sp|Q48CT4.1|PQQD_PSE14  RecName: Full=Coenzyme PQQ synthesis p...  35.8    0.060
sp|O33505.2|PQQD_RAHAQ  RecName: Full=Coenzyme PQQ synthesis p...  35.8    0.067
sp|Q88A83.1|PQQD_PSESM  RecName: Full=Coenzyme PQQ synthesis p...  34.7    0.14 
sp|B1JDZ9.1|PQQD_PSEPW  RecName: Full=Coenzyme PQQ synthesis p...  33.5    0.31 
sp|C3K350.1|PQQD_PSEFS  RecName: Full=Coenzyme PQQ synthesis p...  32.7    0.65 
sp|Q4K4U9.1|PQQD_PSEF5  RecName: Full=Coenzyme PQQ synthesis p...  32.0    1.1  
sp|Q88QV7.1|PQQD1_PSEPK  RecName: Full=Coenzyme PQQ synthesis ...  31.6    1.1  
sp|B1LY42.1|RPOC_METRJ  RecName: Full=DNA-directed RNA polymer...  31.6    1.4  
sp|A9HS30.1|PLSX_GLUDA  RecName: Full=Phosphate acyltransferas...  30.4    3.1  
sp|O74939.3|YJB1_SCHPO  RecName: Full=Uncharacterized protein ...  30.0    4.0  
sp|B8E465.1|Y269_SHEB2  RecName: Full=UPF0345 protein Sbal223_...  29.6    4.4  
sp|P29691.4|EF2_CAEEL  RecName: Full=Elongation factor 2; Shor...  29.6    5.5  
sp|A5CZ28.1|PROA_PELTS  RecName: Full=Gamma-glutamyl phosphate...  29.3    6.2  
sp|Q5KME7.1|PRP5_CRYNE  RecName: Full=Pre-mRNA-processing ATP-...  28.9    8.2  
sp|A1SF13.1|KATG_NOCSJ  RecName: Full=Catalase-peroxidase; Sho...  28.9    8.6  
sp|A7NGU9.1|Y567_ROSCS  RecName: Full=UPF0753 protein Rcas_0567    28.9    9.2  

ALIGNMENTS
>sp|Q139H2.1|PQQD_RHOPS RecName: Full=Coenzyme PQQ synthesis protein D; AltName: Full=Pyrroloquinoline 
quinone biosynthesis protein D
Length=102

 Score = 86.3 bits (212),  Expect = 5e-17, Method: Compositional matrix adjust.
 Identities = 40/79 (50%), Positives = 56/79 (70%), Gaps = 1/79 (1%)

Query  40   PRLPRHAKLRYDEARKKWIINAPERVFELDDTAADIMKQVDGVLSINVIVDNVHRKFNEA  99
            P LPRHAKLR+DE R++W+I APERV   DD A +I++  DG  S++ I+D +  K+  A
Sbjct  14   PALPRHAKLRFDETRQRWVILAPERVLAPDDIAVEILQLCDGARSVSAIIDQLATKYT-A  72

Query  100  TRDQISSDVILMLRSLADK  118
             R +I +DV+ ML+ LADK
Sbjct  73   DRAEIGTDVVAMLQDLADK  91


>sp|Q2IUJ4.1|PQQD_RHOP2 RecName: Full=Coenzyme PQQ synthesis protein D; AltName: Full=Pyrroloquinoline 
quinone biosynthesis protein D
Length=102

 Score = 85.5 bits (210),  Expect = 8e-17, Method: Compositional matrix adjust.
 Identities = 42/90 (46%), Positives = 60/90 (66%), Gaps = 1/90 (1%)

Query  29   SKLVKLEPDNIPRLPRHAKLRYDEARKKWIINAPERVFELDDTAADIMKQVDGVLSINVI  88
            S+ + +   + P LPRHAKLR+DE R++W+I APERV   DD A +I++  DG  S+  I
Sbjct  3    SRHISVSEQSRPMLPRHAKLRFDETRQRWVILAPERVLAPDDIAVEILQLCDGARSVAAI  62

Query  89   VDNVHRKFNEATRDQISSDVILMLRSLADK  118
            +D +  K+  A R +I +DVI ML+ LADK
Sbjct  63   IDTLALKYT-ADRAEIGADVIAMLQDLADK  91


>sp|Q6N8F4.1|PQQD_RHOPA RecName: Full=Coenzyme PQQ synthesis protein D; AltName: Full=Pyrroloquinoline 
quinone biosynthesis protein D
Length=102

 Score = 75.5 bits (184),  Expect = 8e-14, Method: Compositional matrix adjust.
 Identities = 35/79 (44%), Positives = 53/79 (67%), Gaps = 1/79 (1%)

Query  40   PRLPRHAKLRYDEARKKWIINAPERVFELDDTAADIMKQVDGVLSINVIVDNVHRKFNEA  99
            P LPRHA+L++D+ R++W+I APERV   D+ A +I++  DG   +  I+D +  K+  A
Sbjct  14   PVLPRHARLKFDDTRQRWVILAPERVLAPDEIAVEILQLCDGACDVAAIIDALAAKYT-A  72

Query  100  TRDQISSDVILMLRSLADK  118
             R +I  DV+ ML+ LADK
Sbjct  73   DRAEIGRDVMAMLQDLADK  91


>sp|B3QBT1.1|PQQD_RHOPT RecName: Full=Coenzyme PQQ synthesis protein D; AltName: Full=Pyrroloquinoline 
quinone biosynthesis protein D
Length=102

 Score = 74.3 bits (181),  Expect = 2e-13, Method: Compositional matrix adjust.
 Identities = 35/79 (44%), Positives = 53/79 (67%), Gaps = 1/79 (1%)

Query  40   PRLPRHAKLRYDEARKKWIINAPERVFELDDTAADIMKQVDGVLSINVIVDNVHRKFNEA  99
            P LPRHA+L++DE R++W+I APERV   D+ A +I++  DG   +  I+D +  ++  A
Sbjct  14   PVLPRHARLKFDETRQRWVILAPERVLAPDEIAVEILQLCDGARDVAAIIDALAVRYT-A  72

Query  100  TRDQISSDVILMLRSLADK  118
             R +I  DV+ ML+ LADK
Sbjct  73   DRAEIGRDVVAMLQDLADK  91


>sp|Q89FG2.1|PQQD_BRAJA RecName: Full=Coenzyme PQQ synthesis protein D; AltName: Full=Pyrroloquinoline 
quinone biosynthesis protein D
Length=103

 Score = 73.9 bits (180),  Expect = 2e-13, Method: Compositional matrix adjust.
 Identities = 37/79 (46%), Positives = 53/79 (67%), Gaps = 1/79 (1%)

Query  40   PRLPRHAKLRYDEARKKWIINAPERVFELDDTAADIMKQVDGVLSINVIVDNVHRKFNEA  99
            P LPRHAKL+YDE R+ W+I APERV   D+ A ++++  +G  S+  + D +  K+  A
Sbjct  15   PVLPRHAKLKYDETREVWVILAPERVLAPDEIAVEVLQLCNGERSVGDVSDQLAAKYA-A  73

Query  100  TRDQISSDVILMLRSLADK  118
             R+ I +DVI ML+ LADK
Sbjct  74   PREAILTDVIAMLQDLADK  92


>sp|Q49150.2|PQQCD_METEA RecName: Full=Bifunctional coenzyme PQQ synthesis protein C/D; 
AltName: Full=Pyrroloquinoline quinone biosynthesis protein 
C/D; Includes: RecName: Full=Pyrroloquinoline-quinone synthase; 
AltName: Full=Coenzyme PQQ synthesis protein C; Includes: 
RecName: Full=Coenzyme PQQ synthesis protein D
Length=372

 Score = 68.2 bits (165),  Expect = 1e-11, Method: Composition-based stats.
 Identities = 34/83 (40%), Positives = 54/83 (65%), Gaps = 1/83 (1%)

Query  38   NIPRLPRHAKLRYDEARKKWIINAPERVFELDDTAADIMKQVDGVLSINVIVDNVHRKFN  97
            ++PRLPR  +LR+DE R K ++ APER F+LDD A  ++K VDG  +++ I   + + + 
Sbjct  288  DVPRLPRGVRLRFDEVRNKHVLLAPERTFDLDDNAVAVLKLVDGRNTVSQIAQILGQTY-  346

Query  98   EATRDQISSDVILMLRSLADKRI  120
            +A    I +D++ ML  LA KR+
Sbjct  347  DADPAIIEADILPMLAGLAQKRV  369


>sp|B0RQ26.1|PQQD_XANCB RecName: Full=Coenzyme PQQ synthesis protein D; AltName: Full=Pyrroloquinoline 
quinone biosynthesis protein D
Length=92

 Score = 58.5 bits (140),  Expect = 1e-08, Method: Compositional matrix adjust.
 Identities = 31/84 (36%), Positives = 50/84 (59%), Gaps = 1/84 (1%)

Query  37   DNIPRLPRHAKLRYDEARKKWIINAPERVFELDDTAADIMKQVDGVLSINVIVDNVHRKF  96
            D+ P L    +L++D AR +W++ APERV ELDD A  + ++ DG  S+  I   +  +F
Sbjct  7    DSCPALRAGVRLQHDRARDQWVLLAPERVVELDDIALVVAQRYDGTQSLAEIAQTLATEF  66

Query  97   NEATRDQISSDVILMLRSLADKRI  120
            + A   +I +DVI +  +L  KR+
Sbjct  67   D-ADASEIETDVIELTTTLHQKRL  89


>sp|Q8P6M8.1|PQQD_XANCP RecName: Full=Coenzyme PQQ synthesis protein D; AltName: Full=Pyrroloquinoline 
quinone biosynthesis protein D
 sp|Q4UXI3.1|PQQD_XANC8 RecName: Full=Coenzyme PQQ synthesis protein D; AltName: Full=Pyrroloquinoline 
quinone biosynthesis protein D
Length=92

 Score = 58.2 bits (139),  Expect = 1e-08, Method: Compositional matrix adjust.
 Identities = 31/84 (36%), Positives = 50/84 (59%), Gaps = 1/84 (1%)

Query  37   DNIPRLPRHAKLRYDEARKKWIINAPERVFELDDTAADIMKQVDGVLSINVIVDNVHRKF  96
            D+ P L    +L++D AR +W++ APERV ELDD A  + ++ DG  S+  I   +  +F
Sbjct  7    DSCPALRAGVRLQHDRARDQWVLLAPERVVELDDIALVVAQRYDGTQSLAQIAQTLAAEF  66

Query  97   NEATRDQISSDVILMLRSLADKRI  120
            + A   +I +DVI +  +L  KR+
Sbjct  67   D-ADASEIETDVIELTTTLHQKRL  89


>sp|Q3BQI5.1|PQQD_XANC5 RecName: Full=Coenzyme PQQ synthesis protein D; AltName: Full=Pyrroloquinoline 
quinone biosynthesis protein D
Length=92

 Score = 55.5 bits (132),  Expect = 9e-08, Method: Compositional matrix adjust.
 Identities = 31/81 (38%), Positives = 48/81 (59%), Gaps = 1/81 (1%)

Query  40   PRLPRHAKLRYDEARKKWIINAPERVFELDDTAADIMKQVDGVLSINVIVDNVHRKFNEA  99
            P L    +L++D AR +W++ APERV ELDD A  + ++ DG  S+  I   +  +F+ A
Sbjct  10   PSLRAGVRLQHDRARDQWVLLAPERVVELDDIALVVAQRYDGTRSLAQIAQELAAEFD-A  68

Query  100  TRDQISSDVILMLRSLADKRI  120
               QI +DVI +  +L  KR+
Sbjct  69   DAAQIEADVIELTDTLHQKRL  89


>sp|Q8PHY2.1|PQQD_XANAC RecName: Full=Coenzyme PQQ synthesis protein D; AltName: Full=Pyrroloquinoline 
quinone biosynthesis protein D
Length=92

 Score = 55.1 bits (131),  Expect = 1e-07, Method: Compositional matrix adjust.
 Identities = 32/84 (38%), Positives = 49/84 (58%), Gaps = 1/84 (1%)

Query  37   DNIPRLPRHAKLRYDEARKKWIINAPERVFELDDTAADIMKQVDGVLSINVIVDNVHRKF  96
            D+ P L    +L+ D AR +W++ APERV ELDD A  + ++ DG  S+  I   +  +F
Sbjct  7    DSRPALRAGVRLQQDRARDQWVLLAPERVVELDDIALVVAQRYDGTRSLAQIAQELAAEF  66

Query  97   NEATRDQISSDVILMLRSLADKRI  120
            + A   QI +DVI +  +L  KR+
Sbjct  67   D-ADAAQIEADVIELTDTLHQKRL  89


>sp|Q608P1.1|PQQD_METCA RecName: Full=Coenzyme PQQ synthesis protein D; AltName: Full=Pyrroloquinoline 
quinone biosynthesis protein D
Length=93

 Score = 52.4 bits (124),  Expect = 6e-07, Method: Compositional matrix adjust.
 Identities = 28/83 (33%), Positives = 52/83 (62%), Gaps = 3/83 (3%)

Query  32   VKLEPDNIPRLPRHAKLRYDEARKKWIINAPERVFELDDTAADIMKQVDGVLSINVIVDN  91
            + L+PD +  L    +++++EA+++++I  PE + EL++TAA I++  DG  ++  IVD 
Sbjct  1    MSLQPDTLLELSPLLRMQWEEAQQRYVILYPEGMIELNETAAAILELCDGQHNLTSIVDK  60

Query  92   VHRKFNEATRDQISSDVILMLRS  114
            + RK++ +    I  DV  ML S
Sbjct  61   LERKYDASG---IEPDVREMLES  80


>sp|Q5LTB3.1|PQQD_SILPO RecName: Full=Coenzyme PQQ synthesis protein D; AltName: Full=Pyrroloquinoline 
quinone biosynthesis protein D
Length=95

 Score = 52.4 bits (124),  Expect = 7e-07, Method: Compositional matrix adjust.
 Identities = 29/84 (34%), Positives = 44/84 (52%), Gaps = 1/84 (1%)

Query  32   VKLEPDNIPRLPRHAKLRYDEARKKWIINAPERVFELDDTAADIMKQVDGVLSINVIVDN  91
            + L P + P LPR  +L  D  R   ++ APE+   LD     I+ +VDG  S+  +VD 
Sbjct  3    LALAPTDRPYLPRGVRLVTDRVRGGIVLLAPEKAVALDAVGEAILSRVDGQTSLAALVDQ  62

Query  92   VHRKFNEATRDQISSDVILMLRSL  115
            +   ++ A R+QI  DV   L+ L
Sbjct  63   LVEAYD-APREQIEQDVQAFLQGL  85


>sp|Q9L3B1.1|PQQD_GLUOX RecName: Full=Coenzyme PQQ synthesis protein D; AltName: Full=Pyrroloquinoline 
quinone biosynthesis protein D
Length=96

 Score = 50.8 bits (120),  Expect = 2e-06, Method: Compositional matrix adjust.
 Identities = 25/77 (32%), Positives = 46/77 (59%), Gaps = 1/77 (1%)

Query  44   RHAKLRYDEARKKWIINAPERVFELDDTAADIMKQVDGVLSINVIVDNVHRKFNEATRDQ  103
            R  +L++D  R  WI+ APE+ F ++  A  I++ +DG  S+  I+  +  +F+ A R+ 
Sbjct  18   RGHRLQHDRVRDVWIVQAPEKAFVVEGAAPHILRLLDGKRSVGEIIQQLAIEFS-APREV  76

Query  104  ISSDVILMLRSLADKRI  120
            I+ DV+ +L  L +K +
Sbjct  77   IAKDVLALLSELTEKNV  93


>sp|Q6F9J0.1|PQQD_ACIAD RecName: Full=Coenzyme PQQ synthesis protein D; AltName: Full=Pyrroloquinoline 
quinone biosynthesis protein D
Length=99

 Score = 50.4 bits (119),  Expect = 3e-06, Method: Compositional matrix adjust.
 Identities = 28/104 (26%), Positives = 60/104 (57%), Gaps = 9/104 (8%)

Query  19   SRKIIIIKKMSKLVKLEPDNIPRLPRHAKLRYDEARKKWIINAPERVFELDDTAADIMKQ  78
            S++II   +MS L+       P   R  + ++++A++ ++I  PE +  L+++A  I+KQ
Sbjct  3    SKRII---RMSDLLH----TTPVFNRGYRFQWEQAQQSYVILYPEGLVRLNESATLILKQ  55

Query  79   VDGVLSINVIVDNVHRKFNEATRDQISSDVILMLRSLADKRIYC  122
            +DG L+++ I+ N+  +F +AT   +  D++  L+    ++  C
Sbjct  56   IDGKLTVHDIIQNLSAQFPDATG--LDQDIVEFLKQAESRQWIC  97


>sp|B2SSW2.1|PQQD_XANOP RecName: Full=Coenzyme PQQ synthesis protein D; AltName: Full=Pyrroloquinoline 
quinone biosynthesis protein D
Length=92

 Score = 48.1 bits (113),  Expect = 1e-05, Method: Compositional matrix adjust.
 Identities = 22/56 (39%), Positives = 33/56 (58%), Gaps = 0/56 (0%)

Query  37  DNIPRLPRHAKLRYDEARKKWIINAPERVFELDDTAADIMKQVDGVLSINVIVDNV  92
           D  P L    +L+YD AR +W++ APERV ELD+ A  + ++ DG  S+  I   +
Sbjct  7   DGQPALRAGVRLQYDRARDQWVLLAPERVVELDEIALVVAQRYDGTRSLAQIAQEL  62


>sp|C1DEW6.1|PQQD_AZOVD RecName: Full=Coenzyme PQQ synthesis protein D; AltName: Full=Pyrroloquinoline 
quinone biosynthesis protein D
Length=92

 Score = 46.6 bits (109),  Expect = 4e-05, Method: Compositional matrix adjust.
 Identities = 27/76 (35%), Positives = 46/76 (60%), Gaps = 2/76 (2%)

Query  37   DNIPRLPRHAKLRYDEARKKWIINAPERVFELDDTAADIMKQVDGVLSINVIVDNVHRKF  96
            ++IP+L R  + +++ A+   ++  PE + +L+D+AA I+ QVDG  SI  IV  +  +F
Sbjct  7    NDIPQLRRGFRFQWEPAQNCHVLLYPEGMVKLNDSAAAILGQVDGDRSIAAIVAALRERF  66

Query  97   NEATRDQISSDVILML  112
             E+  D I  DV+  L
Sbjct  67   PES--DGIEEDVLEFL  80


>sp|Q05I08.1|PQQD_XANOR RecName: Full=Coenzyme PQQ synthesis protein D; AltName: Full=Pyrroloquinoline 
quinone biosynthesis protein D
 sp|Q2P4Y8.1|PQQD_XANOM RecName: Full=Coenzyme PQQ synthesis protein D; AltName: Full=Pyrroloquinoline 
quinone biosynthesis protein D
Length=92

 Score = 44.3 bits (103),  Expect = 2e-04, Method: Compositional matrix adjust.
 Identities = 20/56 (35%), Positives = 33/56 (58%), Gaps = 0/56 (0%)

Query  37  DNIPRLPRHAKLRYDEARKKWIINAPERVFELDDTAADIMKQVDGVLSINVIVDNV  92
           D+ P L    +L++D  R +W++ APERV ELD+ A  + ++ DG  S+  I   +
Sbjct  7   DSQPALRAGVRLQHDRTRDQWVLLAPERVVELDEIALVVAQRYDGTRSLAQIAQEL  62


>sp|Q9EXU9.1|PQQD_RHIME RecName: Full=Coenzyme PQQ synthesis protein D; AltName: Full=Pyrroloquinoline 
quinone biosynthesis protein D
Length=98

 Score = 40.8 bits (94),  Expect = 0.002, Method: Compositional matrix adjust.
 Identities = 24/83 (28%), Positives = 48/83 (57%), Gaps = 1/83 (1%)

Query  38   NIPRLPRHAKLRYDEARKKWIINAPERVFELDDTAADIMKQVDGVLSINVIVDNVHRKFN  97
            ++ +L R  +L  D  R + ++ APER   +DD A  I++ +DG  +++ I  +   KF+
Sbjct  12   SVVKLARGVRLHEDPVRGQTVLLAPERAMAVDDIAVAIVQALDGERNLDRIAADFAEKFD  71

Query  98   EATRDQISSDVILMLRSLADKRI  120
             A  ++I+ DV   ++ L+ +R+
Sbjct  72   -APVEEIAEDVRTFVQELSVRRM  93


>sp|Q9I2C1.1|PQQD_PSEAE RecName: Full=Coenzyme PQQ synthesis protein D; AltName: Full=Pyrroloquinoline 
quinone biosynthesis protein D
 sp|Q02LD5.1|PQQD_PSEAB RecName: Full=Coenzyme PQQ synthesis protein D; AltName: Full=Pyrroloquinoline 
quinone biosynthesis protein D
 sp|B7VAB7.1|PQQD_PSEA8 RecName: Full=Coenzyme PQQ synthesis protein D; AltName: Full=Pyrroloquinoline 
quinone biosynthesis protein D
Length=92

 Score = 40.4 bits (93),  Expect = 0.003, Method: Compositional matrix adjust.
 Identities = 22/76 (28%), Positives = 42/76 (55%), Gaps = 2/76 (2%)

Query  37   DNIPRLPRHAKLRYDEARKKWIINAPERVFELDDTAADIMKQVDGVLSINVIVDNVHRKF  96
            D++P L R  + +++ A+   ++  PE + +L+D+A +I+K VDG   +  IV  +  +F
Sbjct  7    DSVPMLRRGFRFQFEPAQDCHVLLYPEGMVKLNDSAGEILKLVDGRRDVAAIVAALRERF  66

Query  97   NEATRDQISSDVILML  112
             E     I  D++  L
Sbjct  67   PEVP--GIDEDILAFL  80


>sp|A6V6I1.1|PQQD_PSEA7 RecName: Full=Coenzyme PQQ synthesis protein D; AltName: Full=Pyrroloquinoline 
quinone biosynthesis protein D
Length=92

 Score = 40.0 bits (92),  Expect = 0.004, Method: Compositional matrix adjust.
 Identities = 22/76 (28%), Positives = 42/76 (55%), Gaps = 2/76 (2%)

Query  37   DNIPRLPRHAKLRYDEARKKWIINAPERVFELDDTAADIMKQVDGVLSINVIVDNVHRKF  96
            D++P L R  + +++ A+   ++  PE + +L+D+A +I+K VDG   +  IV  +  +F
Sbjct  7    DSVPVLRRGFRFQFEPAQDCHVLLYPEGMVKLNDSAGEILKLVDGRRDVAAIVAALRERF  66

Query  97   NEATRDQISSDVILML  112
             E     I  D++  L
Sbjct  67   PEVP--GIDEDILTFL  80