YRC Public Data Repository - Protein Structure Prediction

Protein:	gi\|229840799, gi...
Organism:	Yersinia pestis biovar Orientalis str. PEXU2
Length:	577 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|229840799, gi....

Description	E-value	Query Range	Subject Range
gi\|238724581, gi... - gi\|77974512\|ref\|ZP_00830052.1\| COG0608: Single-stranded DNA-specific exonuclease [Yersinia frederiks...	0.0	[1..577]	[1..577]
gi\|238792837, gi... - gi\|77978910\|ref\|ZP_00834333.1\| COG0608: Single-stranded DNA-specific exonuclease [Yersinia intermedi...	0.0	[1..577]	[1..577]
gi\|77958935, gi\|... - gi\|77958935\|ref\|ZP_00822961.1\| COG0608: Single-stranded DNA-specific exonuclease [Yersinia bercovier...	0.0	[1..577]	[1..577]
gi\|77963234, gi\|... - gi\|77963234\|ref\|ZP_00827046.1\| COG0608: Single-stranded DNA-specific exonuclease [Yersinia mollareti...	0.0	[1..577]	[1..577]
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...	0.0	[1..576]	[1..576]
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...	0.0	[1..576]	[1..576]
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...	0.0	[1..576]	[1..576]
gi\|187732306, gi... - gi\|75178785\|ref\|ZP_00698821.1\| COG0608: Single-stranded DNA-specific exonuclease [Shigella boydii BS...	0.0	[1..576]	[1..576]
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...	0.0	[1..576]	[1..576]
gi\|81246896, gi\|... - gi\|82545485\|ref\|YP_409432.1\| ssDNA exonuclease RecJ [Shigella boydii Sb227], gi\|81246896\|gb\|ABB67604...	0.0	[1..576]	[1..576]

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Predicted Domain #1

Region A:
Residues: [1-491]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MTLKTQLRRR EAADDSHLPA QLPPLLRRLY ASRGVKDAQE LERGVKGLLA WQKLDGIDAG  60
   61 VTLLQQALAD RRRIVIVGDF DADGATSTAL AVLALRSMGG SNLDYLVPNR FEDGYGLSPE 120
  121 VVEQVAARGA ELIVTVDNGI SSHAGVDLAH AKGIQVLVTD HHLPGETLPA ADAIINPNLA 180
  181 GCDFLSKSLA GVGVTFYLML ALRARLRECG WFEQRTLAVP NLAELLDLVA LGTVADVVPL 240
  241 DANNRILVHQ GLSRIRAGKC RPGIRALLEV ANRDARQLVA NDLGFSLGPR LNAAGRLDDM 300
  301 SIGVALLLSD DIAQARALAI DLDTLNQTRR EIEQGMQVEA LQLCDQLERT SSELPYGIAM 360
  361 YHPEWHQGVV GILASRIKER FHRPVIAFAP AGEGLLKGSG RSVAGLHMRD ALERLDTLNP 420
  421 GLILKFGGHA MAAGLSLEEG KFDEFRQRFA DLVGEWMDAS QLEGVIWSDG ELNGAELSLE 480
  481 TAELLRDGGP W

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	94.522879
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: [492-577]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 GQSFPEPTFD GKFRILQQRL VGERHLKLMV EPLNGGPLLD GIAFNVDTTL WPDSSVREVK  60
   61 LAYKLDINEY RGNRSVQLLV QHLWPY

[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: