Forum "Recherche d'homologues: BLAST"

Thread subject: E VALUE de 8e-08

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E VALUE de 8e-08
NAME
23 Oct 2009 14:11
Non evaluated contribution
Est ce que cette Evalue est suffisante pour parler d'homologie étant donné les résultats obtenus suite à un BLAST X:
                                                                   Score     E
Sequences producing significant alignments:                       (Bits)  Value  N

gb|CP001737.1|  Nakamurella multipartita DSM 44233, complete g...  39.1    8e-08  1
emb|FM209186.1|  Pseudomonas aeruginosa LESB58 complete genome...  46.4    8e-08  1
gb|CP001630.1|  Actinosynnema mirum DSM 43827, complete genome     45.5    1e-07  1
gb|CP000769.1|  Anaeromyxobacter sp. Fw109-5, complete genome      40.0    1e-07  1
dbj|AP009152.1|  Kocuria rhizophila DC2201 DNA, complete genome    36.3    2e-06  1
emb|AM279695.1|  Streptomyces ambofaciens DSM 40697 right term...  44.6    3e-06  1
emb|AM279694.1|  Streptomyces ambofaciens DSM 40697 left termi...  44.6    3e-06  1
dbj|AP006618.1|  Nocardia farcinica IFM 10152 DNA, complete ge...  42.8    3e-06  1
dbj|AP009493.1|  Streptomyces griseus subsp. griseus NBRC 1335...  41.4    4e-06  1
gb|CP001349.1|  Methylobacterium nodulans ORS 2060, complete g...  39.6    4e-06  1
gb|AE017221.1|  Thermus thermophilus HB27, complete genome         45.1    4e-06  1
gb|CP001339.1|  Thioalkalivibrio sp. HL-EbGR7, complete genome     51.9    5e-06  1
gb|CP000927.1|  Caulobacter sp. K31, complete genome               40.5    7e-06  1
gb|CP001029.1|  Methylobacterium populi BJ001, complete genome     41.8    8e-06  1
emb|CT573213.2|  Frankia alni str. ACN14A chromosome, complete...  47.8    9e-06  1
gb|CP000613.1|  Rhodospirillum centenum SW, complete genome        38.2    9e-06  1
gb|CP000509.1|  Nocardioides sp. JS614, complete genome            43.2    1e-05  1
gb|CP000884.1|  Delftia acidovorans SPH-1, complete genome         38.6    1e-05  1
gb|CP000850.1|  Salinispora arenicola CNS-205, complete genome     42.3    1e-05  1
gb|CP001628.1|  Micrococcus luteus NCTC 2665, complete genome      40.5    2e-05  1
gb|CP000943.1|  Methylobacterium sp. 4-46, complete genome         40.9    2e-05  1
emb|AL939126.1|  Streptomyces coelicolor A3(2) complete genome...  35.4    2e-05  1
gb|CP001643.1|  Brachybacterium faecium DSM 4810 strain 6-10, ...  37.3    2e-05  1
gb|CP000667.1|  Salinispora tropica CNB-440, complete genome       39.6    2e-05  1
gb|CP001131.1|  Anaeromyxobacter sp. K, complete genome            45.5    2e-05  1
emb|AL939117.1|  Streptomyces coelicolor A3(2) complete genome...  32.7    3e-05  1
gb|CP001281.2|  Thauera sp. MZ1T, complete genome                  39.1    4e-05  1
gb|CP000747.1|  Phenylobacterium zucineum HLK1, complete genome    46.0    4e-05  1
gb|CP001700.1|  Catenulispora acidiphila DSM 44928, complete g...  41.4    5e-05  1
dbj|BA000030.3|  Streptomyces avermitilis MA-4680 DNA, complet...  43.2    6e-05  1
emb|BX640416.1|  Bordetella pertussis strain Tohama I, complet...  46.0    6e-05  1
gb|CP000386.1|  Rubrobacter xylanophilus DSM 9941, complete ge...  37.7    7e-05  1
dbj|AP008226.1|  Thermus thermophilus HB8 genomic DNA, complet...  40.5    7e-05  1
dbj|AP006840.1|  Symbiobacterium thermophilum IAM 14863 DNA, c...  39.6    7e-05  1
emb|CU695238.1|  Ralstonia solanacearum strain MolK2 Genome Draft  35.4    8e-05  1
gb|AE004091.2|  Pseudomonas aeruginosa PAO1, complete genome       38.6    1e-04  1
gb|CP001001.1|  Methylobacterium radiotolerans JCM 2831, compl...  38.2    1e-04  1
gb|AF533768.1|  Cercopithecine herpesvirus 1 strain E2490, com...  33.1    1e-04  1
gb|CP000438.1|  Pseudomonas aeruginosa UCBPP-PA14, complete ge...  48.7    1e-04  1
gb|DQ272520.1|  Streptomyces aculeolatus A gene locus, complet...  31.8    1e-04  1
emb|AL939108.1|  Streptomyces coelicolor A3(2) complete genome...  40.5    1e-04  1
dbj|AP011115.1|  Rhodococcus opacus B4 DNA, complete genome        41.8    2e-04  1
emb|AM238664.1|  Streptomyces ambofaciens ATCC 23877 right chr...  40.9    2e-04  1
emb|AM920689.1|  Xanthomonas campestris pv. campestris complet...  36.3    2e-04  1
emb|BX640447.1|  Bordetella bronchiseptica strain RB50, comple...  47.3    2e-04  1
gb|CP000251.1|  Anaeromyxobacter dehalogenans 2CP-C, complete ...  37.7    2e-04  1
gb|CP000249.1|  Frankia sp. CcI3, complete genome                  42.3    2e-04  1
gb|EU301739.1|  Actinomadura kijaniata fructokinase gene, part...  37.7    3e-04  1
emb|FN554889.1|  Streptomyces scabiei 87.22 complete genome        40.0    3e-04  1
gb|CP001618.1|  Beutenbergia cavernae DSM 12333, complete genome   40.5    3e-04  1
gb|CP001510.1|  Methylobacterium extorquens AM1, complete genome   38.2    4e-04  1
gb|CP001150.1|  Rhodobacter sphaeroides KD131 chromosome 1, co...  40.5    4e-04  1
gb|CP000143.1|  Rhodobacter sphaeroides 2.4.1 chromosome 1, co...  40.0    4e-04  1
dbj|BA000040.2|  Bradyrhizobium japonicum USDA 110 DNA, comple...  40.9    4e-04  1
gb|CP000750.2|  Kineococcus radiotolerans SRS30216, complete g...  40.5    4e-04  1
emb|FP103042.2|  Methylobacterium extorquens DM4 str. DM4 chro...  40.9    5e-04  1
gb|CP000512.1|  Acidovorax citrulli AAC00-1, complete genome       38.6    5e-04  1
gb|EU827593.1|  Actinosynnema pretiosum subsp. pretiosum strai...  35.0    5e-04  1
gb|AF119361.1|AF119361  Frankia sp. EuIK1 NifK (nifK), NifE (n...  40.0    5e-04  1
gb|CP001359.1|  Anaeromyxobacter dehalogenans 2CP-1, complete ...  42.3    5e-04  1
emb|BX640440.1|  Bordetella bronchiseptica strain RB50, comple...  35.0    5e-04  1
gb|CP000820.1|  Frankia sp. EAN1pec, complete genome               37.7    5e-04  1
gb|CP000699.1|  Sphingomonas wittichii RW1, complete genome        46.9    6e-04  1
emb|AJ937741.1|  Streptomyces ambofaciens ATCC 23877 right ter...  40.9    6e-04  1
emb|AJ937740.1|  Streptomyces ambofaciens ATCC 23877 left term...  40.9    8e-04  1
emb|AL939119.1|  Streptomyces coelicolor A3(2) complete genome...  35.0    8e-04  1
gb|CP000159.1|  Salinibacter ruber DSM 13855, complete genome      39.6    9e-04  1
gb|CP000680.1|  Pseudomonas mendocina ymp, complete genome         41.4    9e-04  1
gb|CP000751.1|  Kineococcus radiotolerans SRS30216 plasmid pKR...  34.5    0.001  1
emb|AJ629247.1|  Streptomyces fradiae neomycin biosynthesis ge...  36.3    0.001  1
gb|CP000113.1|  Myxococcus xanthus DK 1622, complete genome        40.0    0.001  1
gb|CP000453.1|  Alkalilimnicola ehrlichii MLHE-1, complete genome  40.5    0.001  1
gb|AE016958.1|  Mycobacterium avium subsp. paratuberculosis st...  38.2    0.001  1
gb|CP000230.1|  Rhodospirillum rubrum ATCC 11170, complete genome  38.2    0.001  1
gb|CP000529.1|  Polaromonas naphthalenivorans CJ2, complete ge...  39.1    0.001  1
gb|DQ403252.1|  Streptomyces fungicidicus DXP synthase 2 gene,...  39.1    0.001  1
gb|CP000928.1|  Caulobacter sp. K31 plasmid pCAUL01, complete ...  36.8    0.001  1
gb|CP000577.1|  Rhodobacter sphaeroides ATCC 17029 chromosome ...  40.5    0.001  1
gb|AF497482.1|  Micromonospora echinospora calicheamicin biosy...  39.1    0.002  1
emb|BX640430.1|  Bordetella parapertussis strain 12822, comple...  40.0    0.002  1
gb|AY498874.1|  Streptomyces lavendulae linear plasmid pSLV45 ...  30.4    0.002  1
gb|DQ013294.1|  Polyangium cellulosum strain So ce12 disorazol...  34.1    0.002  1
gb|CP000050.1|  Xanthomonas campestris pv. campestris str. 800...  37.7    0.002  1
gb|AE017282.2|  Methylococcus capsulatus str. Bath, complete g...  40.5    0.002  1
emb|AJ874112.1|  Polyangium cellulosum disA gene, disB gene, d...  34.1    0.002  1
emb|BX640446.1|  Bordetella bronchiseptica strain RB50, comple...  46.9    0.002  1
gb|AF509565.1|  Streptomyces sp. JP95 griseorhodin biosynthesi...  37.3    0.002  1
emb|AL939121.1|  Streptomyces coelicolor A3(2) complete genome...  33.6    0.002  1
gb|CP000744.1|  Pseudomonas aeruginosa PA7, complete genome        40.9    0.002  1
dbj|AP009384.1|  Azorhizobium caulinodans ORS 571 DNA, complet...  36.8    0.002  1
emb|AM420293.1|  Saccharopolyspora erythraea NRRL2338 complete...  39.1    0.002  1
gb|CP001189.1|  Gluconacetobacter diazotrophicus PAl 5, comple...  39.6    0.002  1
emb|AM406670.1|  Azoarcus sp. BH72, complete genome                40.9    0.003  1
emb|AJ579650.1|  Streptomyces tenebrarius tobramycin biosynthe...  40.0    0.003  1
emb|AL939122.1|  Streptomyces coelicolor A3(2) complete genome...  34.5    0.003  1
gb|CP001683.1|  Saccharomonospora viridis DSM 43017, complete ...  40.5    0.003  1
gb|AF521085.1|  Streptomyces nanchangensis NS3226 polyether io...  37.7    0.003  1
emb|AM238663.1|  Streptomyces ambofaciens ATCC 23877 left chro...  35.4    0.003  1
emb|CU914168.1|  Ralstonia solanacearum strain IPO1609 Genome ...  39.6    0.003  1
emb|AJ875019.1|  Streptoalloteichus hindustanus partial apramy...  35.0    0.003  1

Nous avons admis que non, mais avons nous raison?

De ce fait nous avons effectué des BLAST P environemental mais nous nous demandions s'il était pertinent d'effectuer un BLAST pour des séquences de 200 nucleotides.

LOGIN:NAME
CHerrmann09
23 Oct 2009 15:32
Game master
Bonjour,

dans l'absolu, il est difficile de répondre à cette question sans regarder les alignements: on est en effet dans cette "zone grise" d'Evalue (twilight zone): l'Evalue est trop grand pour qu'on puisse conclure à l'homologie les yeux fermés, mais suffisamment petite pour que cette hypothèse ne puisse pas être exclu. Donc: regardez l'alignement pour décider!
Cela dit, je suis étonné du résultat: en prenant votre séquence d'ADN et en faisant un blastx contre nr, je trouve des résultats différents, qui semblent exclure une quelconque homologie:
Sequences producing significant alignments:                       (Bits)  Value

ref|YP_226227.1|  translation initiation factor IF-2 [Coryneba...  45.4    0.007 Gene info
ref|NP_601191.1|  translation initiation factor IF-2 [Coryneba...  45.4    0.007 Gene info
ref|YP_001138710.1|  translation initiation factor IF-2 [Coryn...  43.1    0.033 Gene info
gb|ABM21737.1|  PdmP3 [Actinomadura hibisca]                       42.7    0.044
ref|NP_827011.1|  hypothetical protein SAV_5834 [Streptomyces ...  42.7    0.044 Gene info
ref|YP_290671.1|  hypothetical protein Tfu_2615 [Thermobifida ...  41.6    0.097 Gene info
ref|ZP_05516893.1|  hypothetical protein ShygA5_26437 [Strepto...  40.8    0.17
ref|YP_001378638.1|  ribonuclease R [Anaeromyxobacter sp. Fw10...  40.0    0.28  Gene info
sp|P10163.3|PRB4_HUMAN  RecName: Full=Basic salivary proline-r...  39.3    0.48  Gene info
gb|AAI30387.1|  PRB4 protein [Homo sapiens]                        39.3    0.48  Gene info
gb|EAW96231.1|  proline-rich protein BstNI subfamily 4 [Homo s...  39.3    0.48  Gene info
ref|YP_716992.1|  hypothetical protein FRAAL6865 [Frankia alni...  39.3    0.48  Gene info
gb|AAB50687.2|  parotid 'o' protein; Po [Homo sapiens]             39.3    0.48  Gene info
ref|NP_420996.1|  hypothetical protein CC_2193 [Caulobacter cr...  39.3    0.48  Gene info
emb|CAA30542.1|  Po protein [Homo sapiens]                         39.3    0.48  Gene info
ref|XP_002536116.1|  conserved hypothetical protein [Ricinus c...  30.0    0.56  Gene info
ref|XP_002093095.1|  GE21134 [Drosophila yakuba] >gb|EDW92807....  38.5    0.82  Gene info
ref|ZP_01465528.1|  fibrillar collagen chain FAp1 alpha [Stigm...  38.5    0.82
ref|XP_854250.1|  PREDICTED: similar to PRKC, apoptosis, WT1, ...  38.5    0.82  UniGene infoGene info
ref|XP_422575.2|  PREDICTED: similar to WDC146 [Gallus gallus]     38.1    1.1   Gene info
gb|AAR13814.1|  major ampullate spidroin-2 [Argiope amoena]        38.1    1.1  
gb|AAR13807.1|  major ampullate spidroin-2 doubling 2 [synthet...  38.1    1.1  
gb|AAR13808.1|  major ampullate spidroin-2 [Argiope amoena]        38.1    1.1  
gb|AAR13806.1|  major ampullate spidroin-2 doubling 1 [synthet...  38.1    1.1  
gb|AAR13810.1|  major ampullate spidroin-2 [Argiope amoena]        38.1    1.1  
ref|XP_002457454.1|  hypothetical protein SORBIDRAFT_03g007560...  37.7    1.4   Gene info
ref|XP_002191591.1|  PREDICTED: SWI/SNF related, matrix associ...  37.7    1.4   UniGene infoGene info
ref|ZP_03312093.1|  hypothetical protein DESPIG_02018 [Desulfo...  37.7    1.4  
gb|EAW96230.1|  proline-rich protein BstNI subfamily 3 [Homo s...  37.7    1.4   Gene info
ref|XP_418841.2|  PREDICTED: similar to DPY-19-like protein 1 ...  37.7    1.4   UniGene infoGene info
ref|NP_006240.4|  proline-rich protein BstNI subfamily 3 precu...  37.7    1.4   UniGene infoGene info
gb|AAH96211.1|  PRB3 protein [Homo sapiens]                        37.7    1.4   Gene info
ref|YP_439859.1|  polyketide synthase, putative [Burkholderia ...  37.7    1.4   Gene info
ref|ZP_05061403.1|  secretion protein HlyD [gamma proteobacter...  37.4    1.8  
ref|YP_001103592.1|  PE-PGRS family protein [Saccharopolyspora...  37.4    1.8  


Je ne comprends pas comment vous avez obtenu le résultat que vous donnez dans le message...
NAME
23 Oct 2009 15:55
Non evaluated contribution
oui en effet nous avons effectué un nouveau BLAST etl es résultats sont bien différents .
il s'agit d'une erreur de notre part et nous avons bien obtenu les mêmes résultats que vous .
nous avons donc exclu toutes homologies .

cepondant nous nous demandions si nous devons effectuer un BLAST P nr contre environnemental pour des séquences de 200 nucleotides, étant donné que les ORFs les plus longs égalemment analysé avec ce même BLAST exclue toutes homologies.
Nous vous remercions pour vos conseils.

LOGIN: NAME