YRC Public Data Repository - Protein Structure Prediction

Protein:	gi\|49612792, gi\|...
Organism:	Pectobacterium atrosepticum SCRI1043
Length:	262 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|49612792, gi|....

Description	E-value	Query Range	Subject Range
YAFD_SALTY - UPF0294 protein yafD OS=Salmonella typhimurium GN=yafD PE=3 SV=2 YAFD_SALTY - UPF0294 protein yafD OS=Salmonella typhimurium GN=yafD PE=3 SV=2 YAFD_SALTY - UPF0294 protein YafD OS=Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) GN=yafD PE=3 SV... YAFD_SALNS - UPF0294 protein YafD OS=Salmonella newport (strain SL254) GN=yafD PE=3 SV=1 gi\|205327162, gi... - gi\|205327162\|gb\|EDZ13926.1\| protein YafD [Salmonella enterica subsp. enterica serovar 4,[5],12:i:- s... gi\|197261791, gi... - gi\|197261791\|ref\|ZP_03161865.1\| protein YafD [Salmonella enterica subsp. enterica serovar Saintpaul ... gi\|195873887, gi... - gi\|195873887\|ref\|ZP_03080137.1\| protein YafD [Salmonella enterica subsp. enterica serovar Newport st...	221.0	[0..1]	[260..1]
YAFD_SHIDS - UPF0294 protein YafD OS=Shigella dysenteriae serotype 1 (strain Sd197) GN=yafD PE=3 SV=1	220.0	[0..1]	[260..1]
gi\|205360396, gi... - gi\|205360396\|ref\|ZP_03224611.1\| endonuclease/exonuclease/phosphatase family protein [Salmonella ente... gi\|204323816, gi... - gi\|204927151\|ref\|ZP_03218353.1\| endonuclease/exonuclease/phosphatase family protein [Salmonella ente... gi\|200390935, gi... - gi\|200390935\|ref\|ZP_03217546.1\| protein YafD [Salmonella enterica subsp. enterica serovar Virchow st... YAFD_SALA4 - UPF0294 protein YafD OS=Salmonella agona (strain SL483) GN=yafD PE=3 SV=1 gi\|238913722 - gi\|238913722\|ref\|ZP_04657559.1\| hypothetical protein SentesTe_21677 [Salmonella enterica subsp. ente... YAFD_SALSV - UPF0294 protein YafD OS=Salmonella schwarzengrund (strain CVM19633) GN=yafD PE=3 SV=1 gi\|194468873, gi... - gi\|194468873\|ref\|ZP_03074857.1\| protein YafD [Salmonella enterica subsp. enterica serovar Kentucky s... YAFD_SALHS - UPF0294 protein YafD OS=Salmonella heidelberg (strain SL476) GN=yafD PE=3 SV=1 gi\|205344041, gi... - gi\|205344041\|gb\|EDZ30805.1\| protein YafD [Salmonella enterica subsp. enterica serovar Weltevreden st... gi\|168239992, gi... - gi\|205340078\|gb\|EDZ26842.1\| protein YafD [Salmonella enterica subsp. enterica serovar Heidelberg str... gi\|197288558, gi... - gi\|197288558\|gb\|EDY27935.1\| protein YafD [Salmonella enterica subsp. enterica serovar Schwarzengrund... gi\|205333425, gi... - gi\|205333425\|gb\|EDZ20189.1\| protein YafD [Salmonella enterica subsp. enterica serovar Kentucky str. ... gi\|205321519, gi... - gi\|205321519\|gb\|EDZ09358.1\| protein YafD [Salmonella enterica subsp. enterica serovar Saintpaul str.... YAFD_SALCH - UPF0294 protein yafD OS=Salmonella choleraesuis GN=yafD PE=3 SV=1 YAFD_SALCH - UPF0294 protein yafD OS=Salmonella choleraesuis GN=yafD PE=3 SV=1 YAFD_SALCH - UPF0294 protein YafD OS=Salmonella choleraesuis (strain SC-B67) GN=yafD PE=3 SV=1	219.0	[0..1]	[260..1]
gi\|89107084, gi\|... - gi\|89107084\|ref\|AP_000864.1\| hypothetical protein [Escherichia coli str. K-12 substr. W3110], gi\|856... YAFD_ECO24 - UPF0294 protein YafD OS=Escherichia coli O139:H28 (strain E24377A / ETEC) GN=yafD PE=3 SV=1 gi\|251783766, gi... - gi\|251783766\|ref\|YP_002998070.1\| hypothetical protein B21_00207 [Escherichia coli BL21], gi\|24237603... gi\|15829459, gi\|... - gi\|15829459\|ref\|NP_308232.1\| hypothetical protein ECs0205 [Escherichia coli O157:H7 str. Sakai], gi\|... gi\|253972224, gi... - gi\|254160323\|ref\|YP_003043431.1\| hypothetical protein ECB_00202 [Escherichia coli B str. REL606], gi... YAFD_SHIF8 - UPF0294 protein YafD OS=Shigella flexneri serotype 5b (strain 8401) GN=yafD PE=3 SV=1 YAFD_ECOBW - UPF0294 protein YafD OS=Escherichia coli (strain K12 / MC4100 / BW2952) GN=yafD PE=3 SV=1 YAFD_SHISS - UPF0294 protein YafD OS=Shigella sonnei (strain Ss046) GN=yafD PE=3 SV=1 YAFD_SHIBS - UPF0294 protein YafD OS=Shigella boydii serotype 4 (strain Sb227) GN=yafD PE=3 SV=1 gi\|254287126, gi... - gi\|254287126\|ref\|YP_003052874.1\| hypothetical protein ECD_00202 [Escherichia coli BL21(DE3)], gi\|253... gi\|254791336, gi... - gi\|254791336\|ref\|YP_003076173.1\| endonuclease-exonuclease-phosphatase family member [Escherichia col... YAFD_ECO7I - UPF0294 protein YafD OS=Escherichia coli O7:K1 (strain IAI39 / ExPEC) GN=yafD PE=3 SV=1 YAFD_ECOLU - UPF0294 protein YafD OS=Escherichia coli O17:K52:H18 (strain UMN026 / ExPEC) GN=yafD PE=3 SV=1 YAFD_ECO8A - UPF0294 protein YafD OS=Escherichia coli O8 (strain IAI1) GN=yafD PE=3 SV=1 YAFD_ECO45 - UPF0294 protein YafD OS=Escherichia coli O45:K1 (strain S88 / ExPEC) GN=yafD PE=3 SV=1 YAFD_ECO81 - UPF0294 protein YafD OS=Escherichia coli O81 (strain ED1a) GN=yafD PE=3 SV=1 YAFD_ECO55 - UPF0294 protein YafD OS=Escherichia coli (strain 55989 / EAEC) GN=yafD PE=3 SV=1 YAFD_ECO5E - UPF0294 protein YafD OS=Escherichia coli O157:H7 (strain EC4115 / EHEC) GN=yafD PE=3 SV=1 YAFD_ECOL6 - UPF0294 protein yafD OS=Escherichia coli O6 GN=yafD PE=3 SV=1 YAFD_ECO27 - UPF0294 protein YafD OS=Escherichia coli O127:H6 (strain E2348/69 / EPEC) GN=yafD PE=3 SV=1 gi\|217324748, gi... - gi\|217324748\|ref\|ZP_03440832.1\| endonuclease/exonuclease/phosphatase family protein [Escherichia col... YAFD_ESCF3 - UPF0294 protein YafD OS=Escherichia fergusonii (strain ATCC 35469 / DSM 13698 / CDC 0568-73) GN=yafD... gi\|195938581 - gi\|195938581\|ref\|ZP_03083963.1\| hypothetical protein EscherichcoliO157_19492 [Escherichia coli O157:... gi\|208728674, gi... - gi\|208808873\|ref\|ZP_03251210.1\| endonuclease/exonuclease/phosphatase family protein [Escherichia col... gi\|208812648, gi... - gi\|208812648\|ref\|ZP_03253977.1\| endonuclease/exonuclease/phosphatase family protein [Escherichia col... gi\|208738612, gi... - gi\|208818489\|ref\|ZP_03258809.1\| endonuclease/exonuclease/phosphatase family protein [Escherichia col... YAFD_ECOLI - UPF0294 protein yafD - Escherichia coli YAFD_ECOL6 - UPF0294 protein YafD OS=Escherichia coli O6:H1 (strain CFT073 / ATCC 700928 / UPEC) GN=yafD PE=3 SV=... EG11650 - endo /exonuclease /phosphatase family protein / Endo /exonuclease /phosphatase family protein; function ... YAFD_ECOLC - UPF0294 protein YafD OS=Escherichia coli (strain ATCC 8739 / DSM 1576 / Crooks) GN=yafD PE=3 SV=1 sp\|B7UJA5\|YAFD_ECO27 - UPF0294 protein yafD OS=Escherichia coli O127:H6 (strain E2348/69 / EPEC) GN=yafD PE=3 SV=1 gi\|192931159, gi... - gi\|193063251\|ref\|ZP_03044342.1\| endonuclease/exonuclease/phosphatase family protein [Escherichia col... gi\|193067538, gi... - gi\|193067538\|ref\|ZP_03048505.1\| endonuclease/exonuclease/phosphatase family protein [Escherichia col... gi\|194414424, gi... - gi\|194427654\|ref\|ZP_03060202.1\| endonuclease/exonuclease/phosphatase family protein [Escherichia col... gi\|194438248, gi... - gi\|194438248\|ref\|ZP_03070340.1\| endonuclease/exonuclease/phosphatase family protein [Escherichia col... YAFD_ECOSM - UPF0294 protein YafD OS=Escherichia coli (strain SMS-3-5 / SECEC) GN=yafD PE=3 SV=1 gi\|189370750, gi... - gi\|189405315\|ref\|ZP_02814659.2\| endonuclease/exonuclease/phosphatase family protein [Escherichia col... gi\|189377347, gi... - gi\|189405938\|ref\|ZP_02825396.2\| endonuclease/exonuclease/phosphatase family protein [Escherichia col... gi\|191171387, gi... - gi\|191171387\|ref\|ZP_03032936.1\| endonuclease/exonuclease/phosphatase family protein [Escherichia col... gi\|189361059, gi... - gi\|189361059\|gb\|EDU79478.1\| endonuclease/exonuclease/phosphatase family protein [Escherichia coli O1... gi\|168776187, gi... - gi\|187768403\|gb\|EDU32247.1\| endonuclease/exonuclease/phosphatase family protein [Escherichia coli O1... gi\|188999640, gi... - gi\|188999640\|gb\|EDU68626.1\| endonuclease/exonuclease/phosphatase family protein [Escherichia coli O1... YAFD_ECODH - UPF0294 protein YafD OS=Escherichia coli (strain K12 / DH10B) GN=yafD PE=3 SV=1 gi\|168750157, gi... - gi\|188015582\|gb\|EDU53704.1\| endonuclease/exonuclease/phosphatase family protein [Escherichia coli O1... gi\|189354342, gi... - gi\|189354342\|gb\|EDU72761.1\| endonuclease/exonuclease/phosphatase family protein [Escherichia coli O1... gi\|189365064, gi... - gi\|189365064\|gb\|EDU83480.1\| endonuclease/exonuclease/phosphatase family protein [Escherichia coli O1... YAFD_SHIFL - UPF0294 protein YafD OS=Shigella flexneri GN=yafD PE=3 SV=1 gi\|124527829, gi... - gi\|124527829\|ref\|ZP_01699218.1\| Endonuclease/exonuclease/phosphatase [Escherichia coli B], gi\|124500... gi\|30040003, gi\|... - gi\|30061761\|ref\|NP_835932.1\| hypothetical protein S0203 [Shigella flexneri 2a str. 2457T], gi\|300400... gi\|24111640, gi\|... - gi\|24111640\|ref\|NP_706150.1\| hypothetical protein SF0195 [Shigella flexneri 2a str. 301], gi\|2405041... EG11650 - endo /exonuclease /phosphatase family protein / Endo /exonuclease /phosphatase family protein; function ... YAFD_ECO57 - UPF0294 protein YafD OS=Escherichia coli O157:H7 GN=yafD PE=3 SV=1 gi\|12512937, gi\|... - gi\|15799885\|ref\|NP_285897.1\| hypothetical protein Z0232 [Escherichia coli O157:H7 EDL933], gi\|125129...	219.0	[0..1]	[260..1]
gi\|91209277, gi\|... - gi\|91209277\|ref\|YP_539263.1\| hypothetical protein UTI89_C0228 [Escherichia coli UTI89], gi\|91070851\|... gi\|115511615, gi... - gi\|117622491\|ref\|YP_851404.1\| hypothetical protein APECO1_1781 [Escherichia coli APEC O1], gi\|115511... gi\|110342016, gi... - gi\|110640424\|ref\|YP_668152.1\| hypothetical protein ECP_0215 [Escherichia coli 536], gi\|110342016\|gb\|... gi\|237707797, gi... - gi\|237707797\|ref\|ZP_04538278.1\| conserved hypothetical protein [Escherichia sp. 3_2_53FAA], gi\|22689... gi\|26246153, gi\|... - gi\|26246153\|ref\|NP_752192.1\| hypothetical protein c0246 [Escherichia coli CFT073], gi\|26106550\|gb\|AA...	218.0	[0..1]	[260..9]
gi\|213162312 - gi\|213162312\|ref\|ZP_03348022.1\| hypothetical protein Salmoneentericaenterica_20883 [Salmonella enter... YAFD_SALTI - UPF0294 protein yafD OS=Salmonella typhi GN=yafD PE=3 SV=2 gi\|213648816 - gi\|213648816\|ref\|ZP_03378869.1\| hypothetical protein SentesTy_16923 [Salmonella enterica subsp. ente... YAFD_SALTI - UPF0294 protein YafD OS=Salmonella typhi GN=yafD PE=3 SV=2 gi\|213616262 - gi\|213616262\|ref\|ZP_03372088.1\| hypothetical protein SentesTyp_18024 [Salmonella enterica subsp. ent... gi\|213855639 - gi\|213855639\|ref\|ZP_03383879.1\| hypothetical protein SentesT_16990 [Salmonella enterica subsp. enter...	218.0	[0..1]	[260..1]
gi\|84779085, gi\|... - gi\|85058565\|ref\|YP_454267.1\| hypothetical protein SG0587 [Sodalis glossinidius str. 'morsitans'], gi...	214.0	[0..1]	[260..1]
lcl\|NC_016856.1_... - [gene=yafD] [protein=hypothetical protein] [protein_id=YP_005235926.1] [location=298940..299719] gi\|16763641, gi\|... - gi\|16763641\|ref\|NP_459256.1\| hypothetical protein STM0258 [Salmonella typhimurium LT2], gi\|16418757\|...	206.0	[0..8]	[260..1]
gi\|194432690, gi... - gi\|83570290\|ref\|ZP_00921736.1\| COG3021: Uncharacterized protein conserved in bacteria [Shigella dyse...	206.0	[0..8]	[260..1]
gi\|83586290 - gi\|83586290\|ref\|ZP_00924925.1\| COG3021: Uncharacterized protein conserved in bacteria [Escherichia c... gi\|187731404, gi... - gi\|75176773\|ref\|ZP_00696889.1\| COG3021: Uncharacterized protein conserved in bacteria [Shigella boyd... gi\|75189301 - gi\|75189301\|ref\|ZP_00702568.1\| COG3021: Uncharacterized protein conserved in bacteria [Escherichia c... gi\|75194415, gi\|... - gi\|75194415\|ref\|ZP_00704485.1\| COG3021: Uncharacterized protein conserved in bacteria [Escherichia c... gi\|253774769, gi... - gi\|253774769\|ref\|YP_003037600.1\| Endonuclease/exonuclease/phosphatase [Escherichia coli BL21(DE3)], ... gi\|216647, gi\|15... - dbj\|BAA77880.1\| Hypothetical 29.1 kd protein in aspU-dniR intergenic region (orf259). [Escherichia c... gi\|75211238 - gi\|75211238\|ref\|ZP_00711345.1\| COG3021: Uncharacterized protein conserved in bacteria [Escherichia c... gi\|227884788, gi... - gi\|227884788\|ref\|ZP_04002593.1\| endonuclease/exonuclease/phosphatase family protein [Escherichia col... gi\|75238908 - gi\|75238908\|ref\|ZP_00722890.1\| COG3021: Uncharacterized protein conserved in bacteria [Escherichia c... gi\|209917396, gi... - gi\|209917396\|ref\|YP_002291480.1\| hypothetical protein ECSE_0205 [Escherichia coli SE11], gi\|20991065... gi\|75241730 - gi\|75241730\|ref\|ZP_00725567.1\| COG3021: Uncharacterized protein conserved in bacteria [Escherichia c... gi\|216647 - gi\|216647\|dbj\|BAA02172.1\| ORF259 [Escherichia coli W3110] gi\|75258803 - gi\|75258803\|ref\|ZP_00730193.1\| COG3021: Uncharacterized protein conserved in bacteria [Escherichia c... gi\|188487648, gi... - gi\|75513660\|ref\|ZP_00736051.1\| COG3021: Uncharacterized protein conserved in bacteria [Escherichia c...	205.0	[0..8]	[260..1]

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Predicted Domain #1

Region A:
Residues: [1-262]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MRKRTYAMRY VAGQPAERIF PPGEMHYPGQ ALPTGSLLLE GDVLRVMVWN IFKQQRLNWL  60
   61 SVLQNFGKGT QLVLLQEAQS TPDLIRFATT NYLSADQVPA IILPQHPSGV MTLSAAQPVY 120
  121 CCPLREREPL LRLAKSSLVT VYALQNGQRL MVINIHAVNF SFGVEIYTKQ LAAIGEQLLH 180
  181 HQGPAIMAGD FNAWSQQRIN ALNRFAARMG LQEVHFVDDQ RRKAFGRPLD FVFYRDMTVN 240
  241 QSSVLVTQAS DHNPLLVEFS LI

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	40.69897
Match:	1e9nA
Description:	DNA repair endonuclease Hap1
Matching Structure (courtesy of the PDB):

Predicted functions:

Term	Confidence	Notes
catalytic activity	1.23505510330573	bayes_pls_golite062009
hydrolase activity	0.79070010643157	bayes_pls_golite062009
hydrolase activity, acting on ester bonds	0.71596812518333	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: