YRC Public Data Repository - Protein Structure Prediction

Protein:	gi\|24372539, gi\|...
Organism:	Shewanella oneidensis MR-1
Length:	574 amino acids
Reference:	Drew K, et al. (2011) The proteome folding project: Proteome-scale prediction of structure and function. Genome Res. 2011 Sep 16

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Top Sequence Alignment Hits

Listed below are up to the top 10 sequence alignment matches, by species, for the PSI-BLAST search against the protein sequence for gi|24372539, gi|....

Description	E-value	Query Range	Subject Range
gi\|238792837, gi... - gi\|77978910\|ref\|ZP_00834333.1\| COG0608: Single-stranded DNA-specific exonuclease [Yersinia intermedi...	691.0	[0..1]	[573..3]
gi\|166010309, gi... - gi\|166010309\|ref\|ZP_02231207.1\| single-stranded-DNA-specific exonuclease RecJ [Yersinia pestis biova... gi\|165925149, gi... - gi\|165925149\|ref\|ZP_02220981.1\| single-stranded-DNA-specific exonuclease RecJ [Yersinia pestis biova... gi\|89104788, gi\|... - gi\|89104788\|ref\|ZP_01177321.1\| COG0608: Single-stranded DNA-specific exonuclease [Yersinia pestis bi... gi\|21960211, gi\|... - gi\|22127150\|ref\|NP_670573.1\| ssDNA exonuclease RecJ [Yersinia pestis KIM], gi\|21960211\|gb\|AAM86824.1... gi\|25331604 - pir\|\|AC0109 single-stranded-DNA-specific exonuclease (EC 3.1.-.-) [imported] - Yersinia pestis (stra... gi\|51597476, gi\|... - gi\|51597476\|ref\|YP_071667.1\| ssDNA exonuclease RecJ [Yersinia pseudotuberculosis IP 32953], gi\|51590... gi\|45443321, gi\|... - gi\|45443321\|ref\|NP_994860.1\| ssDNA exonuclease RecJ [Yersinia pestis biovar Microtus str. 91001], gi... Q666T1\|Q666T1_YERPS - Single-stranded-DNA-specific exonuclease - Yersinia pseudotuberculosis gi\|218928063, gi... - gi\|218928063\|ref\|YP_002345938.1\| ssDNA exonuclease RecJ [Yersinia pestis CO92], gi\|16121195\|ref\|NP_4... gi\|149289507, gi... - gi\|150260099\|ref\|ZP_01916827.1\| single-stranded-DNA-specific exonuclease [Yersinia pestis CA88-4125]... gi\|145209628, gi... - gi\|145597932\|ref\|YP_001162008.1\| ssDNA exonuclease RecJ [Yersinia pestis Pestoides F], gi\|145209628\|... gi\|229704264, gi... - gi\|229837576\|ref\|ZP_04457738.1\| ssDNA exonuclease, 5' --> 3'-specific [Yersinia pestis Pestoides A],... gi\|108806376, gi... - gi\|108806376\|ref\|YP_650292.1\| ssDNA exonuclease RecJ [Yersinia pestis Antiqua], gi\|108778289\|gb\|ABG1... gi\|229840799, gi... - gi\|229840799\|ref\|ZP_04460958.1\| ssDNA exonuclease, 5' --> 3'-specific [Yersinia pestis biovar Orient... gi\|229679475, gi... - gi\|229903705\|ref\|ZP_04518818.1\| ssDNA exonuclease, 5' --> 3'-specific [Yersinia pestis Nepal516], gi... gi\|229842642, gi... - gi\|229842642\|ref\|ZP_04462797.1\| ssDNA exonuclease, 5' --> 3'-specific [Yersinia pestis biovar Orient... gi\|167400018, gi... - gi\|167400018\|ref\|ZP_02305536.1\| single-stranded-DNA-specific exonuclease RecJ [Yersinia pestis biova... gi\|166212665, gi... - gi\|166212665\|ref\|ZP_02238700.1\| single-stranded-DNA-specific exonuclease RecJ [Yersinia pestis biova... gi\|167055648, gi... - gi\|167425248\|ref\|ZP_02317001.1\| single-stranded-DNA-specific exonuclease RecJ [Yersinia pestis biova... gi\|167418963, gi... - gi\|167418963\|ref\|ZP_02310716.1\| single-stranded-DNA-specific exonuclease RecJ [Yersinia pestis biova... gi\|167470507 - gi\|167470507\|ref\|ZP_02335211.1\| single-stranded-DNA-specific exonuclease RecJ [Yersinia pestis FV-1] gi\|162354213, gi... - gi\|77635817\|ref\|ZP_00797897.1\| COG0608: Single-stranded DNA-specific exonuclease [Yersinia pestis An... gi\|152959207, gi... - gi\|77630142\|ref\|ZP_00792728.1\| COG0608: Single-stranded DNA-specific exonuclease [Yersinia pseudotub...	690.0	[0..1]	[573..3]
gi\|238724581, gi... - gi\|77974512\|ref\|ZP_00830052.1\| COG0608: Single-stranded DNA-specific exonuclease [Yersinia frederiks...	689.0	[0..1]	[573..3]
gi\|91212270, gi\|... - gi\|91212270\|ref\|YP_542256.1\| ssDNA exonuclease RecJ [Escherichia coli UTI89], gi\|91073844\|gb\|ABE0872... gi\|218706398, gi... - gi\|218706398\|ref\|YP_002413917.1\| ssDNA exonuclease RecJ [Escherichia coli UMN026], gi\|218433495\|emb\|... gi\|110344632, gi... - gi\|110643040\|ref\|YP_670770.1\| ssDNA exonuclease RecJ [Escherichia coli 536], gi\|110344632\|gb\|ABG7086... gi\|218366654, gi... - gi\|218559885\|ref\|YP_002392798.1\| ssDNA exonuclease RecJ [Escherichia coli S88], gi\|218366654\|emb\|CAR... gi\|226899504, gi... - gi\|237706464\|ref\|ZP_04536945.1\| ssDNA exonuclease RecJ [Escherichia sp. 3_2_53FAA], gi\|226899504\|gb\|... gi\|190906496, gi... - gi\|75239236\|ref\|ZP_00723209.1\| COG0608: Single-stranded DNA-specific exonuclease [Escherichia coli F...	688.0	[0..1]	[574..1]
gi\|26249307, gi\|... - gi\|26249307\|ref\|NP_755347.1\| ssDNA exonuclease RecJ [Escherichia coli CFT073], gi\|26109715\|gb\|AAN819... gi\|215488192, gi... - gi\|215488192\|ref\|YP_002330623.1\| ssDNA exonuclease RecJ [Escherichia coli O127:H6 str. E2348/69], gi... gi\|218428581, gi... - gi\|218691017\|ref\|YP_002399229.1\| ssDNA exonuclease RecJ [Escherichia coli ED1a], gi\|218428581\|emb\|CA... gi\|227888441, gi... - gi\|227888441\|ref\|ZP_04006246.1\| ssDNA exonuclease RecJ [Escherichia coli 83972], gi\|227834710\|gb\|EEJ...	688.0	[0..1]	[574..1]
gi\|191165982, gi... - gi\|75230865\|ref\|ZP_00717323.1\| COG0608: Single-stranded DNA-specific exonuclease [Escherichia coli B... gi\|218555440, gi... - gi\|218555440\|ref\|YP_002388353.1\| ssDNA exonuclease RecJ [Escherichia coli IAI1], gi\|218362208\|emb\|CA...	688.0	[0..1]	[574..1]
gi\|253323311, gi... - gi\|254289564\|ref\|YP_003055312.1\| ssDNA exonuclease, 5' -> 3'-specific [Escherichia coli BL21(DE3)], ... gi\|242378423, gi... - gi\|251786150\|ref\|YP_003000454.1\| hypothetical protein B21_02687 [Escherichia coli BL21], gi\|24237842... gi\|254162804, gi... - gi\|254162804\|ref\|YP_003045912.1\| ssDNA exonuclease, 5' -> 3'-specific [Escherichia coli B str. REL60... gi\|188494077, gi... - gi\|75515325\|ref\|ZP_00737509.1\| COG0608: Single-stranded DNA-specific exonuclease [Escherichia coli 5... gi\|192956143, gi... - gi\|75234620\|ref\|ZP_00718951.1\| COG0608: Single-stranded DNA-specific exonuclease [Escherichia coli E...	688.0	[0..1]	[574..1]
gi\|81246896, gi\|... - gi\|82545485\|ref\|YP_409432.1\| ssDNA exonuclease RecJ [Shigella boydii Sb227], gi\|81246896\|gb\|ABB67604...	688.0	[0..1]	[574..1]
gi\|75258491, gi\|... - gi\|75258491\|ref\|ZP_00729913.1\| COG0608: Single-stranded DNA-specific exonuclease [Escherichia coli E... gi\|194426412, gi... - gi\|75212494\|ref\|ZP_00712518.1\| COG0608: Single-stranded DNA-specific exonuclease [Escherichia coli B...	687.0	[0..1]	[574..1]
gi\|75187608, gi\|... - gi\|75187608\|ref\|ZP_00700875.1\| COG0608: Single-stranded DNA-specific exonuclease [Escherichia coli E... gi\|209913605, gi... - gi\|209920346\|ref\|YP_002294430.1\| ssDNA exonuclease RecJ [Escherichia coli SE11], gi\|209913605\|dbj\|BA... gi\|218696487, gi... - gi\|218696487\|ref\|YP_002404154.1\| ssDNA exonuclease RecJ [Escherichia coli 55989], gi\|218353219\|emb\|C...	687.0	[0..1]	[574..1]

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Predicted Domain #1

Region A:
Residues: [1-489]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MIHKIIRRPT VDDSHLPTHL PPLLRQLYAR RGVLPSECEL VLKGLLRPDT MKGLDLAAKL  60
   61 IADAMQLDKS ILIVGDFDAD GATSTSVCIL ALRMMGASKV DYLIPNRFDY GYGLSPEIVA 120
  121 VAASKQAQLL ITVDNGISSI EGVAAAKAFG MQVVITDHHL PGHELPKADA IVNPNQPGCQ 180
  181 FASKSIAGVG VAFYLMTALR AELRARNWYQ ARGIAEPNLG TLLDIVALGT VADVVSLDTN 240
  241 NRILVEAGLQ RVRSGRCRVG ITALLEVAKR NPARIVASDF GFAVGPRLNA AGRLDEMALG 300
  301 VETLLCEDMM YARRMAAELD SLNQERRELE VGMQQEALKS LEYLKLNEEQ LPWGIALFQE 360
  361 DWHQGVIGIL ASRIKDKYHR PVIAFADAGN GEIKGSARSI KGLHMRDLLE LVNSRHPGLI 420
  421 SKFGGHAMAA GLTLKSGGFA TFAKAYDDAV REQLKPEQLT GELWSDGELT PTELTLEIAQ 480
  481 LLRNAGPWG

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	95.0
Match:	1ir6A
Description:	Exonuclease RecJ
Matching Structure (courtesy of the PDB):

Predicted functions:

Term	Confidence	Notes
deoxyribonuclease activity	3.0051764426766	bayes_pls_golite062009
exodeoxyribonuclease activity	2.95229098929295	bayes_pls_golite062009
exodeoxyribonuclease activity, producing 5'-phosphomonoesters	2.9500987818733	bayes_pls_golite062009
single-stranded DNA specific exodeoxyribonuclease activity	2.72110588435439	bayes_pls_golite062009
exonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 5'-phosphomonoesters	2.59454342567539	bayes_pls_golite062009
exonuclease activity	2.57506733103287	bayes_pls_golite062009
catalytic activity	2.15198373249096	bayes_pls_golite062009
hydrolase activity	1.87485052902921	bayes_pls_golite062009
nuclease activity	1.375718110904	bayes_pls_golite062009
hydrolase activity, acting on ester bonds	1.17433205668743	bayes_pls_golite062009

Predicted Domain #2

Region A:
Residues: [490-574]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 QSFEEPLFDG YFKIIQQRIV GDRHLKLVLE TQCGTVMLDA IAFNVALHTW PDATIQHARI  60
   61 VYKLDVNEYR GNFTLQLMVE QIEPM

[Run NCBI BLAST on this sequence.]

Detection Method:

MSA

Shown below is our most confident prediction for this domain.
Click here to view all matches.

Found no confident structure predictions for this domain.

TMHMM	2.0c	PSIPRED	v2.61
SignalP	3.0	COILS	1999
DISOPRED	v0.1	NCBI nr	06/2007
PSI-BLAST	2.2.18	FFAS	ffas03
PDB	06/2007	Pfam	22
HMMER	2.3.2

View Structure Prediction Details

Top Sequence Alignment Hits

Predicted functions: