YRC Public Data Repository - Protein Structure Prediction

Protein:	gi\|229839803, gi...
Organism:	Yersinia pestis biovar Orientalis str. PEXU2
Length:	366 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|229839803, gi....

Description	E-value	Query Range	Subject Range
gi\|209161837, gi... - gi\|209400437\|ref\|YP_002273227.1\| DNA polymerase III, beta subunit [Escherichia coli O157:H7 str. EC4... gi\|209921178, gi... - gi\|209921178\|ref\|YP_002295262.1\| DNA polymerase III subunit beta [Escherichia coli SE11], gi\|2099144... gi\|217320369, gi... - gi\|217324148\|ref\|ZP_03440232.1\| DNA polymerase III, beta subunit [Escherichia coli O157:H7 str. TW14... gi\|218358773, gi... - gi\|218551231\|ref\|YP_002385023.1\| DNA polymerase III subunit beta [Escherichia fergusonii ATCC 35469]... gi\|218363035, gi... - gi\|218556266\|ref\|YP_002389180.1\| DNA polymerase III subunit beta [Escherichia coli IAI1], gi\|2183630... gi\|218367545, gi... - gi\|218560776\|ref\|YP_002393689.1\| DNA polymerase III subunit beta [Escherichia coli S88], gi\|21836754... gi\|218429553, gi... - gi\|218691989\|ref\|YP_002400201.1\| DNA polymerase III subunit beta [Escherichia coli ED1a], gi\|2184295... gi\|218697423, gi... - gi\|218697423\|ref\|YP_002405090.1\| DNA polymerase III subunit beta [Escherichia coli 55989], gi\|218354... gi\|81247446, gi\|... - gi\|82546035\|ref\|YP_409982.1\| DNA polymerase III subunit beta [Shigella boydii Sb227], gi\|81247446\|gb... gi\|189378717, gi... - gi\|189378717\|gb\|EDU97133.1\| DNA polymerase III, beta subunit [Escherichia coli O157:H7 str. EC508], ... gi\|89110312, gi\|... - gi\|89110312\|ref\|AP_004092.1\| DNA polymerase III, beta subunit [Escherichia coli str. K-12 substr. W3... gi\|170018063, gi... - gi\|170018063\|ref\|YP_001723017.1\| DNA polymerase III subunit beta [Escherichia coli ATCC 8739], gi\|16... gi\|73857492, gi\|... - gi\|74314015\|ref\|YP_312434.1\| DNA polymerase III subunit beta [Shigella sonnei Ss046], gi\|73857492\|gb... gi\|169891038, gi... - gi\|170083203\|ref\|YP_001732523.1\| DNA polymerase III, beta subunit [Escherichia coli str. K-12 substr... gi\|82779230, gi\|... - gi\|82779230\|ref\|YP_405579.1\| DNA polymerase III subunit beta [Shigella dysenteriae Sd197], gi\|812433... gi\|170520206, gi... - gi\|170682488\|ref\|YP_001746029.1\| DNA polymerase III, beta subunit [Escherichia coli SMS-3-5], gi\|170... gi\|195936322 - gi\|195936322\|ref\|ZP_03081704.1\| DNA polymerase III subunit beta [Escherichia coli O157:H7 str. EC402... gi\|208807282, gi... - gi\|208807282\|ref\|ZP_03249619.1\| DNA polymerase III, beta subunit [Escherichia coli O157:H7 str. EC42... gi\|208813217, gi... - gi\|208813217\|ref\|ZP_03254546.1\| DNA polymerase III, beta subunit [Escherichia coli O157:H7 str. EC40... gi\|208740619, gi... - gi\|208820496\|ref\|ZP_03260816.1\| DNA polymerase III, beta subunit [Escherichia coli O157:H7 str. EC40... gi\|75197599, gi\|... - gi\|75197599\|ref\|ZP_00707669.1\| COG0592: DNA polymerase sliding clamp subunit (PCNA homolog) [Escheri... gi\|75210687, gi\|... - gi\|75210687\|ref\|ZP_00710828.1\| COG0592: DNA polymerase sliding clamp subunit (PCNA homolog) [Escheri... gi\|187730327, gi... - gi\|75177730\|ref\|ZP_00697795.1\| COG0592: DNA polymerase sliding clamp subunit (PCNA homolog) [Shigell... gi\|157156673, gi... - gi\|75188458\|ref\|ZP_00701725.1\| COG0592: DNA polymerase sliding clamp subunit (PCNA homolog) [Escheri... gi\|193063787, gi... - gi\|75258241\|ref\|ZP_00729689.1\| COG0592: DNA polymerase sliding clamp subunit (PCNA homolog) [Escheri... gi\|188487741, gi... - gi\|75514236\|ref\|ZP_00736544.1\| COG0592: DNA polymerase sliding clamp subunit (PCNA homolog) [Escheri... gi\|190904132, gi... - gi\|75231028\|ref\|ZP_00717463.1\| COG0592: DNA polymerase sliding clamp subunit (PCNA homolog) [Escheri... gi\|191170441, gi... - gi\|75242509\|ref\|ZP_00726253.1\| COG0592: DNA polymerase sliding clamp subunit (PCNA homolog) [Escheri... gi\|218702550, gi... - gi\|218702550\|ref\|YP_002410179.1\| DNA polymerase III subunit beta [Escherichia coli IAI39], gi\|218372... gi\|218707347, gi... - gi\|218707347\|ref\|YP_002414866.1\| DNA polymerase III subunit beta [Escherichia coli UMN026], gi\|21843... gi\|194420778, gi... - gi\|83571500\|ref\|ZP_00922940.1\| COG0592: DNA polymerase sliding clamp subunit (PCNA homolog) [Shigell... gi\|194425455, gi... - gi\|83588433\|ref\|ZP_00927057.1\| COG0592: DNA polymerase sliding clamp subunit (PCNA homolog) [Escheri... gi\|188016968, gi... - gi\|188016968\|gb\|EDU55090.1\| DNA polymerase III, beta subunit [Escherichia coli O157:H7 str. EC4113],... gi\|189359039, gi... - gi\|189359039\|gb\|EDU77458.1\| DNA polymerase III, beta subunit [Escherichia coli O157:H7 str. EC4401],... gi\|189369478, gi... - gi\|189369478\|gb\|EDU87894.1\| DNA polymerase III, beta subunit [Escherichia coli O157:H7 str. EC4501],... gi\|189364639, gi... - gi\|189364639\|gb\|EDU83058.1\| DNA polymerase III, beta subunit [Escherichia coli O157:H7 str. EC4486],... gi\|187771361, gi... - gi\|187771361\|gb\|EDU35205.1\| DNA polymerase III, beta subunit [Escherichia coli O157:H7 str. EC4196],... gi\|189002623, gi... - gi\|189002623\|gb\|EDU71609.1\| DNA polymerase III, beta subunit [Escherichia coli O157:H7 str. EC4076],... EG10242 - DNA polymerase III, beta subunit / DNA polymerase III sliding clamp beta subunit; required for high ... gi\|226902765, gi... - gi\|237703501\|ref\|ZP_04533982.1\| DNA polymerase III subunit beta [Escherichia sp. 3_2_53FAA], gi\|2269... gi\|238902791, gi... - gi\|238902791\|ref\|YP_002928587.1\| DNA polymerase III, beta subunit [Escherichia coli BW2952], gi\|2388... gi\|251786967, gi... - gi\|251786967\|ref\|YP_003001271.1\| hypothetical protein B21_03528 [Escherichia coli BL21], gi\|24237924... DPO3B_ECOL6 - DNA polymerase III subunit beta OS=Escherichia coli O6 GN=dnaN PE=3 SV=1 gi\|254290402, gi... - gi\|254290402\|ref\|YP_003056150.1\| DNA polymerase III subunit beta [Escherichia coli BL21(DE3)], gi\|25... gi\|226838883, gi... - gi\|254038918\|ref\|ZP_04872970.1\| DNA polymerase III [Escherichia sp. 1_1_43], gi\|226838883\|gb\|EEH7091... gi\|254163652, gi... - gi\|254163652\|ref\|YP_003046760.1\| DNA polymerase III subunit beta [Escherichia coli B str. REL606], g... gi\|254595104, gi... - gi\|254795704\|ref\|YP_003080541.1\| DNA polymerase III, beta subunit [Escherichia coli O157:H7 str. TW1... gi\|91213223, gi\|... - gi\|91213223\|ref\|YP_543209.1\| DNA polymerase III subunit beta [Escherichia coli UTI89], gi\|91074797\|g... DPO3B_ECOL6 - DNA polymerase III subunit beta OS=Escherichia coli O6:H1 (strain CFT073 / ATCC 700928 / UPEC) GN=dn... gi\|13364111, gi\|... - gi\|15833890\|ref\|NP_312663.1\| DNA polymerase III subunit beta [Escherichia coli O157:H7 str. Sakai], ... DPO3B_ECOLI, DP3... - DNA polymerase III subunit beta (EC 2.7.7.7) - Escherichia coli, (P00583) DNA polymerase III, beta c... DPO3B_ECO57 - DNA polymerase III subunit beta OS=Escherichia coli O157:H7 GN=dnaN PE=3 SV=1 EG10242 - DNA polymerase III, beta subunit / DNA polymerase III sliding clamp beta subunit; required for high ... gi\|12518540, gi\|... - gi\|15804295\|ref\|NP_290334.1\| DNA polymerase III subunit beta [Escherichia coli O157:H7 EDL933], gi\|1... gi\|110644044, gi... - gi\|110644044\|ref\|YP_671774.1\| DNA polymerase III subunit beta [Escherichia coli 536], gi\|110345636\|g... gi\|115515101, gi... - gi\|117625977\|ref\|YP_859300.1\| DNA polymerase III subunit beta [Escherichia coli APEC O1], gi\|1155151... gi\|124500187, gi... - gi\|124529048\|ref\|ZP_01700194.1\| DNA polymerase III, beta subunit [Escherichia coli B], gi\|124500187\|... gi\|227839200, gi... - gi\|227883922\|ref\|ZP_04001727.1\| DNA-directed DNA polymerase [Escherichia coli 83972], gi\|227839200\|g...	0.0	[1..366]	[1..366]
gi\|192957464, gi... - gi\|75236425\|ref\|ZP_00720521.1\| COG0592: DNA polymerase sliding clamp subunit (PCNA homolog) [Escheri...	0.0	[1..366]	[1..366]
gi\|30065009, gi\|... - gi\|30065009\|ref\|NP_839180.1\| DNA polymerase III subunit beta [Shigella flexneri 2a str. 2457T], gi\|3... gi\|56480410, gi\|... - gi\|56480410\|ref\|NP_709499.2\| DNA polymerase III subunit beta [Shigella flexneri 2a str. 301], gi\|563... gi\|110807609, gi... - gi\|110807609\|ref\|YP_691129.1\| DNA polymerase III subunit beta [Shigella flexneri 5 str. 8401], gi\|11...	0.0	[1..366]	[1..366]
gi\|168464832, gi... - gi\|195632425\|gb\|EDX50909.1\| DNA polymerase III, beta subunit [Salmonella enterica subsp. enterica se... gi\|238913090 - gi\|238913090\|ref\|ZP_04656927.1\| DNA polymerase III subunit beta [Salmonella enterica subsp. enterica... gi\|205344390, gi... - gi\|205344390\|gb\|EDZ31154.1\| DNA polymerase III, beta subunit [Salmonella enterica subsp. enterica se... gi\|194457777, gi... - gi\|194471413\|ref\|ZP_03077397.1\| DNA polymerase III, beta subunit [Salmonella enterica subsp. enteric... gi\|197251713, gi... - gi\|197251713\|ref\|YP_002148775.1\| DNA polymerase III, beta subunit [Salmonella enterica subsp. enteri... gi\|161616955, gi... - gi\|161616955\|ref\|YP_001590920.1\| DNA polymerase III subunit beta [Salmonella enterica subsp. enteric... gi\|167548873, gi... - gi\|205325570\|gb\|EDZ13409.1\| DNA polymerase III, beta subunit [Salmonella enterica subsp. enterica se... gi\|205332539, gi... - gi\|205332539\|gb\|EDZ19303.1\| DNA polymerase III, beta subunit [Salmonella enterica subsp. enterica se... gi\|168260378, gi... - gi\|205350419\|gb\|EDZ37050.1\| DNA polymerase III, beta subunit [Salmonella enterica subsp. enterica se... gi\|160866979, gi... - gi\|161505632\|ref\|YP_001572744.1\| DNA polymerase III subunit beta [Salmonella enterica subsp. arizona... gi\|224470164, gi... - gi\|224585636\|ref\|YP_002639435.1\| DNA polymerase III subunit beta [Salmonella enterica subsp. enteric... gi\|16504793, gi\|... - gi\|25288590\|pir\|\|AB0958 DNA polymerase III beta-chain [imported] - Salmonella enterica subsp. enteri... gi\|206710866, gi... - gi\|207859063\|ref\|YP_002245714.1\| DNA polymerase III subunit beta [Salmonella enterica subsp. enteric... gi\|29143976, gi\|... - gi\|29143976\|ref\|NP_807318.1\| DNA polymerase III subunit beta [Salmonella enterica subsp. enterica se... gi\|213648785 - gi\|213648785\|ref\|ZP_03378838.1\| DNA polymerase III subunit beta [Salmonella enterica subsp. enterica... gi\|213865135 - gi\|213865135\|ref\|ZP_03387254.1\| DNA polymerase III subunit beta [Salmonella enterica subsp. enterica... gi\|214001465 - gi\|214001465\|ref\|ZP_03412200.1\| DNA polymerase III subunit beta [Salmonella enterica subsp. enterica... gi\|62129958, gi\|... - gi\|62182325\|ref\|YP_218742.1\| DNA polymerase III subunit beta [Salmonella enterica subsp. enterica se... gi\|197364638, gi... - gi\|197364638\|ref\|YP_002144275.1\| DNA polymerase III subunit beta [Salmonella enterica subsp. enteric... gi\|56415710, gi\|... - gi\|56415710\|ref\|YP_152785.1\| DNA polymerase III subunit beta [Salmonella enterica subsp. enterica se... gi\|198245644, gi... - gi\|198245644\|ref\|YP_002217787.1\| DNA polymerase III, beta subunit [Salmonella enterica subsp. enteri... gi\|16762488 - gi\|16762488\|ref\|NP_458105.1\| DNA polymerase III subunit beta [Salmonella enterica subsp. enterica se... gi\|204928586, gi... - gi\|204928586\|ref\|ZP_03219785.1\| DNA polymerase III, beta subunit [Salmonella enterica subsp. enteric... gi\|205274357, gi... - gi\|205354576\|ref\|YP_002228377.1\| DNA polymerase III subunit beta [Salmonella enterica subsp. enteric...	0.0	[1..366]	[1..366]
gi\|200387477, gi... - gi\|200387477\|ref\|ZP_03214089.1\| DNA polymerase III, beta subunit [Salmonella enterica subsp. enteric... gi\|194449346, gi... - gi\|194449346\|ref\|YP_002047870.1\| DNA polymerase III subunit beta [Salmonella enterica subsp. enteric... DPO3B_SALTY - DNA polymerase III subunit beta OS=Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) GN=d... gi\|194444384, gi... - gi\|194444384\|ref\|YP_002043087.1\| DNA polymerase III, beta subunit [Salmonella enterica subsp. enteri... gi\|205338833, gi... - gi\|205338833\|gb\|EDZ25597.1\| DNA polymerase III, beta subunit [Salmonella enterica subsp. enterica se... lcl\|NC_016856.1_... - [gene=dnaN] [protein=DNA polymerase III subunit beta] [protein_id=YP_005240104.1] [location=compleme... DPO3B_SALTY, DP3... - DNA polymerase III subunit beta OS=Salmonella typhimurium GN=dnaN PE=3 SV=3, (P26464) DNA polymerase... DPO3B_SALTY - DNA polymerase III subunit beta OS=Salmonella typhimurium GN=dnaN PE=3 SV=3 gi\|167992431, gi... - gi\|205329442\|gb\|EDZ16206.1\| DNA polymerase III, beta subunit [Salmonella enterica subsp. enterica se...	0.0	[1..366]	[1..366]
gi\|77958160, gi\|... - gi\|77958160\|ref\|ZP_00822198.1\| COG0592: DNA polymerase sliding clamp subunit (PCNA homolog) [Yersini...	0.0	[1..366]	[1..366]
gi\|238797844, gi... - gi\|77961788\|ref\|ZP_00825618.1\| COG0592: DNA polymerase sliding clamp subunit (PCNA homolog) [Yersini...	0.0	[1..366]	[1..366]
gi\|238793144, gi... - gi\|77976617\|ref\|ZP_00832096.1\| COG0592: DNA polymerase sliding clamp subunit (PCNA homolog) [Yersini...	0.0	[1..366]	[1..366]
gi\|77973771, gi\|... - gi\|77973771\|ref\|ZP_00829316.1\| COG0592: DNA polymerase sliding clamp subunit (PCNA homolog) [Yersini...	0.0	[1..366]	[1..366]
gi\|16974834, gi\|... - gi\|16974834\|pdb\|1JQJ\|B Chain B, Mechanism Of Processivity Clamp Opening By The Delta Subunit Wrench ...	0.0	[1..366]	[1..366]

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Predicted Domain #1

Region A:
Residues: [1-366]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MKFIIEREHL LKPLQQVSSP LGGRPTLPIL GNLLLQVTEG SLRLTGTDLE MEMVACVALS  60
   61 QSHEPGATTV PARKFFDIWR GLPEGAEITV ALDGDRLLVR SGRSRFSLST LPAIDFPNLD 120
  121 DWQSEVEFTL PQATLKRLIE STQFSMAHQD VRYYLNGMLF ETEGEELRTV ATDGHRLAVC 180
  181 SMPIGQTLPS HSVIVPRKGV MELVRLLDGG DTPLRLQIGS NNIRAHVGDF IFTSKLVDGR 240
  241 FPDYRRVLPK NPDKMLEAGC DLLKQAFSRA AILSNEKFRG VRLYVSHNQL KITANNPEQE 300
  301 EAEEILDVSY EGTEMEIGFN VSYVLDVLNA LKCEDVRLLL TDSVSSVQIE DSASQAAAYV 360
  361 VMPMRL

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	132.0
Match:	1mmiA
Description:	E. COLI DNA POLYMERASE BETA SUBUNIT
Matching Structure (courtesy of the PDB):

Predicted functions:

Term	Confidence	Notes
DNA-directed DNA polymerase activity	10.1355867012964	bayes_pls_golite062009
DNA polymerase activity	10.0862166288891	bayes_pls_golite062009
nucleotidyltransferase activity	7.50006430161592	bayes_pls_golite062009
transferase activity, transferring phosphorus-containing groups	3.53479307306028	bayes_pls_golite062009
transferase activity	2.88122926655527	bayes_pls_golite062009
binding	0.65029295764999	bayes_pls_golite062009
DNA polymerase processivity factor activity	0.616404933041	bayes_pls_golite062009
catalytic activity	0.48077242755678	bayes_pls_golite062009
nucleic acid binding	0.4343174930339	bayes_pls_golite062009
DNA binding	0.129085697705275	bayes_pls_golite062009

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: