ORF AZ18060

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 : AACY01160150.1
Annotathon code: ORF_AZ18060
Sample :
  • GPS :31°10'30n; 64°19'27.6w
  • Sargasso Sea: Sargasso Sea, Station 11 - Bermuda (UK)
  • Open Ocean (-5m, 20.5°C, 0.1-0.8 microns)
Authors
Team : BioCell 2006
Username : amcha
Annotated on : 2008-03-19 18:52:37
  • INNOCENTI charlene
  • Maradji amandine

Synopsis

Genomic Sequence

>AACY01160150.1 ORF_AZ18060 genomic DNA
AAAATTAGCTCTTCAATATGATAAAGATGCTTATCAGGGAAGTATAAACGGAAATCCAATGACTCCTTCAAATGCATCAAGAGATTATTTTCTTGAAGCA
AAACTCTCTTTCAGAAATATTATAGTTGGTTACAGGTTTTGGAAAAATGTTGAGGGATGGGGTGGATGGTATAACGATATGGAAAATGCACCATCAAAAA
ATGGAGCTAACTGGGCTCCTCAAAACAAAACTTTATTTTTAAAATATGACAATAAACTTAGCGAAAAAGTTAGTGTGTCTGTTCAATCATCATTTAAAAA
TCATAGCCTAGGAAGAGAGACCGTTCGTGTCTTATTTAAACCATTTGGAAACCCAGGTGGAAACCTGACACTAATAGATTTAATTCAATATGACTCTATT
CAGAATAGATATCCTGTATACCAAATTGGAGACAATATAATTCCTCAGACAATACCCGCATCATTTCTGAGTTCAGCTCCAACAAGTGAAAAATTTCATG
GTTGGTTAAACAGATATTATTTCTATCAAGCAACTCAAGGACGTTTTGAGGGAAGAATATATTATGATACTGATAAATTTAAATTCATGTCGGGAGTTGA
TTACAGACTAACCTCATCACAAGGAGATTATCTGGTTTTTTATGATTCAAACTGGAGAGGTAGTGACTTTCTTGACAATCAAATAGATCAAAGTTATGCT
CAAGAGTATGGCACAGCTGGCGGAAGTATTACCTCTAACGCAATTCATAATCCAGGCAGCAATC

Translation

[2 - 763/764]   direct strand


Phylogeny


Annotator commentaries

Notre séquence semble être non codante car tout d'abord nous avons effectué un blastp qui ne nous a donné aucun resultat d'homologues. Nous avons donc fait un blastx qui ne nous a donné aucun autre resultat. Pour finir, nous avons fait un blastp pour chacun des ORFs,cela ne nous a rien donner de plus. Nous pouvons donc conclure que soit notre sequence est non codante, soit qu'elle est codante mais qu'il n'existe pas d'homologues dans les banques de données.

Multiple Alignement


BLAST

Nous avons faits un blastp puis un blastX par le biais NCBI


BLASTP 2.2.15 [Oct-15-2006] 

Reference:
Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schäffer, 
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman 
(1997), "Gapped BLAST and PSI-BLAST: a new generation of 
protein database search programs", Nucleic Acids Res. 25:3389-3402.

Reference:
Schäffer, Alejandro A., L. Aravind, Thomas L. Madden, Sergei 
Shavirin, John L. Spouge, Yuri I. Wolf, Eugene V. Koonin, and 
Stephen F. Altschul (2001), "Improving the accuracy of PSI-BLAST 
protein database searches with composition-based statistics 
and other refinements", Nucleic Acids Res. 29:2994-3005.

RID: 1165222461-2016-51917457204.BLASTQ4


Database: All non-redundant GenBank CDS
translations+PDB+SwissProt+PIR+PRF excluding environmental samples
           4,201,456 sequences; 1,445,405,603 total letters
 If you have any problems or questions with the results of this search please refer to the BLAST FAQs
Taxonomy reports

Query=  Translation of ORF number 1 in reading frame 2 on the direct strand.
Length=254


Score     E
Sequences producing significant alignments:                       (Bits)  Value

gi|88857022|ref|ZP_01131665.1|  putative exogenous ferric side...  37.7    0.48 

>gi|88857022|ref|ZP_01131665.1|  putative exogenous ferric siderophore receptor; Iha adhesin [Pseudoalteromonas 
tunicata D2]
 gi|88820219|gb|EAR30031.1|  putative exogenous ferric siderophore receptor; Iha adhesin [Pseudoalteromonas 
tunicata D2]
Length=782

 Score = 37.7 bits (86),  Expect = 0.48, Method: Composition-based stats.
 Identities = 29/119 (24%), Positives = 55/119 (46%), Gaps = 4/119 (3%)

Query  24   NASRDYFLEAKLSFRNIIVGYRFWKNVEGWGGWYNDMENAPSKNGANWAPQNKTLFLKYD  83
            ++SR++ L A  S+ N   G   W+   G+G +Y      P   G+ W   +K  +LK+ 
Sbjct  280  DSSRNWGLLADASYNNFTAGLILWQLNNGYGVYYPSDRAQP---GSAWQRNSKQYYLKHY  336

Query  84   NKLSEKVSVSVQSSFKNHSL-GRETVRVLFKPFGNPGGNLTLIDLIQYDSIQNRYPVYQ  141
             +L+ ++     + ++ + L G         P  N    L+ + L +++SI N + V Q
Sbjct  337  GQLTSQLKTKTLALYRENRLWGDWAEAYPVNPDLNTQNVLSAVSLSKWNSISNSWLVQQ  395

on fait un blast X
BLASTX 2.2.15 [Oct-15-2006] 

Reference:
Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schäffer, 
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman 
(1997), "Gapped BLAST and PSI-BLAST: a new generation of 
protein database search programs", Nucleic Acids Res. 25:3389-3402.

RID: 1165222809-21689-53876072738.BLASTQ4


Database: All non-redundant GenBank CDS
translations+PDB+SwissProt+PIR+PRF excluding environmental samples
           4,201,456 sequences; 1,445,405,603 total letters
 If you have any problems or questions with the results of this search please refer to the BLAST FAQs
Taxonomy reports

Query=  ORF number 1 in reading frame 2 on the direct strand extends from base 
2 to base 763.
Length=762

Score     E
Sequences producing significant alignments:                       (Bits)  Value

gi|88857022|ref|ZP_01131665.1|  putative exogenous ferric side...  41.6    0.038
gi|68542545|ref|ZP_00582273.1|  Twin-arginine translocation pa...  34.3    6.1  
gi|66802920|ref|XP_635303.1|  hypothetical protein DDBDRAFT_01...  33.9    8.0 

  >gi|88857022|ref|ZP_01131665.1|  putative exogenous ferric siderophore receptor; Iha adhesin [Pseudoalteromonas 
tunicata D2]
 gi|88820219|gb|EAR30031.1|  putative exogenous ferric siderophore receptor; Iha adhesin [Pseudoalteromonas 
tunicata D2]
Length=782

 Score = 41.6 bits (96),  Expect = 0.038
 Identities = 28/119 (23%), Positives = 55/119 (46%), Gaps = 4/119 (3%)
 Frame = +1

Query  70   NASRDYFLEAKLSFRNIIVGYRFWKNVEGWGGWYNDMENAPSKNGANWAPQNKTLFLKYD  249
            ++SR++ L A  S+ N   G   W+   G+G +Y      P   G+ W   +K  +LK+ 
Sbjct  280  DSSRNWGLLADASYNNFTAGLILWQLNNGYGVYYPSDRAQP---GSAWQRNSKQYYLKHY  336

Query  250  NKLSEKVSVSVQSSFKNHSLGRETVRVL-FKPFGNPGGNLTLIDLIQYDSIQNRYPVYQ  423
             +L+ ++     + ++ + L  +        P  N    L+ + L +++SI N + V Q
Sbjct  337  GQLTSQLKTKTLALYRENRLWGDWAEAYPVNPDLNTQNVLSAVSLSKWNSISNSWLVQQ  395


>gi|68542545|ref|ZP_00582273.1|  Twin-arginine translocation pathway signal:Periplasmic nitrate 
reductase, large subunit [Shewanella baltica OS155]
 gi|68519724|gb|EAN43249.1|  Twin-arginine translocation pathway signal:Periplasmic nitrate 
reductase, large subunit [Shewanella baltica OS155]
Length=829

 Score = 34.3 bits (77),  Expect = 6.1
 Identities = 31/107 (28%), Positives = 54/107 (50%), Gaps = 8/107 (7%)
 Frame = +1

Query  97   AKLSFRNIIVGYRFWKNVEGWGGWYNDMENAPSKN--GANWAPQNKTLFLKY-DNKLSEK  267
            A+    + +VG+     ++   G Y+DME A +    G+N A  +  L+ +  D +LSE 
Sbjct  176  ARHCMASAVVGFMRTFGIDEPMGCYDDMEAADAFVLWGSNMAEMHPILWSRVTDRRLSEP  235

Query  268  -VSVSVQSSFKNHSLGRETVRVLFKPFGNPGGNLTLIDLIQYDSIQN  405
             V V+V S+F+N S     + ++F     P  +L +++ I    IQN
Sbjct  236  HVKVAVLSTFQNRSFDLADIPIVF----TPQTDLAMLNFIANYIIQN  278


>gi|66802920|ref|XP_635303.1|  hypothetical protein DDBDRAFT_0191589 [Dictyostelium discoideum 
AX4]
 gi|60463606|gb|EAL61791.1|  hypothetical protein DDBDRAFT_0191589 [Dictyostelium discoideum 
AX4]
Length=2552

 Score = 33.9 bits (76),  Expect = 8.0
 Identities = 28/88 (31%), Positives = 43/88 (48%), Gaps = 3/88 (3%)
 Frame = +1

Query  259   SEKVSVSVQSSFKNHSLGRETVRVLFKPFGNPGGNLTLIDLIQYDSIQNRYPVYQIGDNI  438
             +E V   +Q S K     +   R+L   FG   G+L+L+ L + +S+  +YP YQI    
Sbjct  1408  NELVGEIIQESIKPILNEKLVFRIL--EFGGGVGSLSLLVLEKINSLLIQYPNYQIDIEY  1465

Query  439   IPQTIPASFLSSAPTS-EKFHGWLNRYY  519
                 I  SF++ A    EKF+  +N  Y
Sbjct  1466  TWSDISPSFITEAKAKFEKFNDRVNIIY  14

Nous avons fait une recherche d'homologues pour chaque ORF dans les deux sens (directs et indirects).
BLASTP 2.2.15 [Oct-15-2006] 

Reference:
Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schäffer, 
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman 
(1997), "Gapped BLAST and PSI-BLAST: a new generation of 
protein database search programs", Nucleic Acids Res. 25:3389-3402.

Reference:
Schäffer, Alejandro A., L. Aravind, Thomas L. Madden, Sergei 
Shavirin, John L. Spouge, Yuri I. Wolf, Eugene V. Koonin, and 
Stephen F. Altschul (2001), "Improving the accuracy of PSI-BLAST 
protein database searches with composition-based statistics 
and other refinements", Nucleic Acids Res. 29:2994-3005.

RID: 1165223068-3076-128825818698.BLASTQ4


Database: All non-redundant GenBank CDS
translations+PDB+SwissProt+PIR+PRF excluding environmental samples
           4,201,456 sequences; 1,445,405,603 total letters
 If you have any problems or questions with the results of this search please refer to the BLAST FAQs

Query=  Translation of ORF number 1 in reading frame 1 on the reverse strand.
Length=60


No significant similarity found. For reasons why, click here.



  Database: All non-redundant GenBank CDS translations+PDB+SwissProt+PIR+PRF excluding 
environmental samples
    Posted date:  Dec 3, 2006  5:52 PM
  Number of letters in database: 1,445,405,603
  Number of sequences in database:  4,201,456
Lambda     K      H
   0.328    0.144    0.432 
Gapped
Lambda     K      H
   0.267   0.0410    0.140 
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 4201456
Number of Hits to DB: 15779668
Number of extensions: 466570
Number of successful extensions: 1584
Number of sequences better than 10: 0
Number of HSP's better than 10 without gapping: 0
Number of HSP's gapped: 1593
Number of HSP's successfully gapped: 0
Length of query: 60
Length of database: 1445405603
Length adjustment: 33
Effective length of query: 27
Effective length of database: 1306757555
Effective search space: 35282453985
Effective search space used: 35282453985
T: 11
A: 40
X1: 15 (7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (20.0 bits)
S2: 71 (32.0 bits)


ORF finding

Nous avons utilisé "any codon".
Nous avons utilisé le logiciel ORF finder.


brin sens direct:
No ORFs were found in reading frame 1.

>ORF number 1 in reading frame 2 on the direct strand extends from base 2 to base 763.
AAATTAGCTCTTCAATATGATAAAGATGCTTATCAGGGAAGTATAAACGGAAATCCAATG
ACTCCTTCAAATGCATCAAGAGATTATTTTCTTGAAGCAAAACTCTCTTTCAGAAATATT
ATAGTTGGTTACAGGTTTTGGAAAAATGTTGAGGGATGGGGTGGATGGTATAACGATATG
GAAAATGCACCATCAAAAAATGGAGCTAACTGGGCTCCTCAAAACAAAACTTTATTTTTA
AAATATGACAATAAACTTAGCGAAAAAGTTAGTGTGTCTGTTCAATCATCATTTAAAAAT
CATAGCCTAGGAAGAGAGACCGTTCGTGTCTTATTTAAACCATTTGGAAACCCAGGTGGA
AACCTGACACTAATAGATTTAATTCAATATGACTCTATTCAGAATAGATATCCTGTATAC
CAAATTGGAGACAATATAATTCCTCAGACAATACCCGCATCATTTCTGAGTTCAGCTCCA
ACAAGTGAAAAATTTCATGGTTGGTTAAACAGATATTATTTCTATCAAGCAACTCAAGGA
CGTTTTGAGGGAAGAATATATTATGATACTGATAAATTTAAATTCATGTCGGGAGTTGAT
TACAGACTAACCTCATCACAAGGAGATTATCTGGTTTTTTATGATTCAAACTGGAGAGGT
AGTGACTTTCTTGACAATCAAATAGATCAAAGTTATGCTCAAGAGTATGGCACAGCTGGC
GGAAGTATTACCTCTAACGCAATTCATAATCCAGGCAGCAAT

>Translation of ORF number 1 in reading frame 2 on the direct strand.
KLALQYDKDAYQGSINGNPMTPSNASRDYFLEAKLSFRNIIVGYRFWKNVEGWGGWYNDM
ENAPSKNGANWAPQNKTLFLKYDNKLSEKVSVSVQSSFKNHSLGRETVRVLFKPFGNPGG
NLTLIDLIQYDSIQNRYPVYQIGDNIIPQTIPASFLSSAPTSEKFHGWLNRYYFYQATQG
RFEGRIYYDTDKFKFMSGVDYRLTSSQGDYLVFYDSNWRGSDFLDNQIDQSYAQEYGTAG
GSITSNAIHNPGSN

No ORFs were found in reading frame 3.

brin sens indirect:
>ORF number 1 in reading frame 1 on the reverse strand extends from base 187 to base 369.
ATTTATCAGTATCATAATATATTCTTCCCTCAAAACGTCCTTGAGTTGCTTGATAGAAAT
AATATCTGTTTAACCAACCATGAAATTTTTCACTTGTTGGAGCTGAACTCAGAAATGATG
CGGGTATTGTCTGAGGAATTATATTGTCTCCAATTTGGTATACAGGATATCTATTCTGAA
TAG

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

No ORFs were found in reading frame 2.

No ORFs were found in reading frame 3.