YRC Public Data Repository - Protein Structure Prediction

Protein:	gi\|24113023, gi\|...
Organism:	Shigella flexneri 2a str. 301
Length:	211 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|24113023, gi|....

Description	E-value	Query Range	Subject Range
gi\|113461208, gi... - gi\|23467008\|ref\|ZP_00122593.1\| COG0177: Predicted EndoIII-related endonuclease [Haemophilus somnus 1... gi\|168825935, gi... - gi\|170717806\|ref\|YP_001784869.1\| endonuclease III [Haemophilus somnus 2336], gi\|168825935\|gb\|ACA3130...	255.0	[0..1]	[211..1]
gi\|15602246, gi\|... - gi\|15602246\|ref\|NP_245318.1\| hypothetical protein PM0381 [Pasteurella multocida subsp. multocida str...	254.0	[0..1]	[210..1]
gi\|194431988, gi... - gi\|83571019\|ref\|ZP_00922461.1\| COG0177: Predicted EndoIII-related endonuclease [Shigella dysenteriae...	254.0	[0..1]	[211..1]
gi\|192956462, gi... - gi\|75234946\|ref\|ZP_00719225.1\| COG0177: Predicted EndoIII-related endonuclease [Escherichia coli E11...	254.0	[0..1]	[211..1]
EG10662 - DNA glycosylase and apyrimidinic (AP) lyase (endonuclease III) / Endonuclease III: DNA N-glycosylase... gi\|74312040, gi\|... - gi\|74312040\|ref\|YP_310459.1\| endonuclease III [Shigella sonnei Ss046], gi\|73855517\|gb\|AAZ88224.1\| en... gi\|82543999, gi\|... - gi\|82543999\|ref\|YP_407946.1\| endonuclease III [Shigella boydii Sb227], gi\|81245410\|gb\|ABB66118.1\| en... gi\|193064975, gi... - gi\|75257052\|ref\|ZP_00728612.1\| COG0177: Predicted EndoIII-related endonuclease [Escherichia coli E22... gi\|75512934, gi\|... - gi\|75512934\|ref\|ZP_00735415.1\| COG0177: Predicted EndoIII-related endonuclease [Escherichia coli 536... END3_ECOLI - Endonuclease III (EC 4.2.99.18) (DNA-(apurinic or apyrimidinic site) lyase) - Escherichia coli gi\|170020015, gi... - gi\|170020015\|ref\|YP_001724969.1\| endonuclease III [Escherichia coli ATCC 8739], gi\|169754943\|gb\|ACA7... gi\|170081297, gi... - gi\|170081297\|ref\|YP_001730617.1\| DNA glycosylase and apyrimidinic (AP) lyase (endonuclease III) [Esc... gi\|117623819, gi... - gi\|117623819\|ref\|YP_852732.1\| endonuclease III [Escherichia coli APEC O1], gi\|115512943\|gb\|ABJ01018.... gi\|124499984, gi... - gi\|124529210\|ref\|ZP_01700285.1\| endonuclease III [Escherichia coli B], gi\|124499984\|gb\|EAY47463.1\| e... gi\|170681381, gi... - gi\|170681381\|ref\|YP_001743621.1\| endonuclease III [Escherichia coli SMS-3-5], gi\|170519099\|gb\|ACB172... gi\|187429446, gi... - gi\|75178471\|ref\|ZP_00698517.1\| COG0177: Predicted EndoIII-related endonuclease [Shigella boydii BS51... gi\|157079658, gi... - gi\|75190673\|ref\|ZP_00703940.1\| COG0177: Predicted EndoIII-related endonuclease [Escherichia coli E24... gi\|75230918, gi\|... - gi\|75230918\|ref\|ZP_00717367.1\| COG0177: Predicted EndoIII-related endonuclease [Escherichia coli B7A... gi\|75238806, gi\|... - gi\|75238806\|ref\|ZP_00722790.1\| COG0177: Predicted EndoIII-related endonuclease [Escherichia coli F11... gi\|75195713, gi\|... - gi\|75195713\|ref\|ZP_00705783.1\| COG0177: Predicted EndoIII-related endonuclease [Escherichia coli HS]... gi\|194415944, gi... - gi\|75212970\|ref\|ZP_00712968.1\| COG0177: Predicted EndoIII-related endonuclease [Escherichia coli B17... gi\|83587968, gi\|... - gi\|83587968\|ref\|ZP_00926594.1\| COG0177: Predicted EndoIII-related endonuclease [Escherichia coli 101... gi\|89108475, gi\|... - gi\|89108475\|ref\|AP_002255.1\| DNA glycosylase and apyrimidinic (AP) lyase [Escherichia coli str. K-12... gi\|110343348, gi... - gi\|110641756\|ref\|YP_669486.1\| endonuclease III [Escherichia coli 536], gi\|110343348\|gb\|ABG69585.1\| e... gi\|209918946, gi... - gi\|209918946\|ref\|YP_002293030.1\| endonuclease III [Escherichia coli SE11], gi\|209912205\|dbj\|BAG77279... gi\|215264882, gi... - gi\|215486810\|ref\|YP_002329241.1\| endonuclease III [Escherichia coli O127:H6 str. E2348/69], gi\|21526... gi\|218360969, gi... - gi\|218554201\|ref\|YP_002387114.1\| endonuclease III [Escherichia coli IAI1], gi\|218360969\|emb\|CAQ98542... gi\|218558504, gi... - gi\|218558504\|ref\|YP_002391417.1\| endonuclease III [Escherichia coli S88], gi\|218365273\|emb\|CAR02994.... gi\|218427144, gi... - gi\|218689580\|ref\|YP_002397792.1\| endonuclease III [Escherichia coli ED1a], gi\|218427144\|emb\|CAR08027... gi\|253973596, gi... - gi\|254161695\|ref\|YP_003044803.1\| DNA glycosylase and apyrimidinic (AP) lyase (endonuclease III) [Esc... gi\|218695196, gi... - gi\|218695196\|ref\|YP_002402863.1\| endonuclease III [Escherichia coli 55989], gi\|218351928\|emb\|CAU9765... END3_ECOL6 - Endonuclease III OS=Escherichia coli O6 GN=nth PE=3 SV=1 gi\|253324453, gi... - gi\|254288484\|ref\|YP_003054232.1\| DNA glycosylase and apyrimidinic (AP) lyase (endonuclease III) [Esc... gi\|218699799, gi... - gi\|218699799\|ref\|YP_002407428.1\| endonuclease III [Escherichia coli IAI39], gi\|218369785\|emb\|CAR1755... END3_ECOL6 - Endonuclease III OS=Escherichia coli O6:H1 (strain CFT073 / ATCC 700928 / UPEC) GN=nth PE=3 SV=1 gi\|251785091, gi... - gi\|251785091\|ref\|YP_002999395.1\| hypothetical protein B21_01593 [Escherichia coli BL21], gi\|24237736... gi\|238860816, gi... - gi\|238900849\|ref\|YP_002926645.1\| DNA glycosylase and apyrimidinic (AP) lyase (endonuclease III) [Esc... gi\|237705576, gi... - gi\|237705576\|ref\|ZP_04536057.1\| endonuclease III [Escherichia sp. 3_2_53FAA], gi\|226900333\|gb\|EEH865... gi\|227885951, gi... - gi\|227885951\|ref\|ZP_04003756.1\| DNA-(apurinic or apyrimidinic site) lyase [Escherichia coli 83972], ... EG10662 - DNA glycosylase and apyrimidinic (AP) lyase (endonuclease III) / Endonuclease III: DNA N-glycosylase...	254.0	[0..1]	[211..1]
gi\|126097154, gi... - gi\|126208362\|ref\|YP_001053587.1\| endonuclease III [Actinobacillus pleuropneumoniae L20], gi\|12609715... gi\|190150214, gi... - gi\|190150214\|ref\|YP_001968739.1\| endonuclease III [Actinobacillus pleuropneumoniae serovar 7 str. AP... gi\|32033526 - gi\|32033526\|ref\|ZP_00133853.1\| COG0177: Predicted EndoIII-related endonuclease [Actinobacillus pleur...	252.0	[0..1]	[210..1]
gi\|77868355, gi\|... - gi\|77952798\|ref\|ZP_00817211.1\| Endonuclease III/Nth [Marinobacter aquaeolei VT8], gi\|77868355\|gb\|EAO...	252.0	[0..1]	[210..1]
gi\|91210846, gi\|... - gi\|91210846\|ref\|YP_540832.1\| endonuclease III [Escherichia coli UTI89], gi\|91072420\|gb\|ABE07301.1\| e...	252.0	[0..1]	[211..1]
gi\|168789470, gi... - gi\|189370952\|gb\|EDU89368.1\| endonuclease III [Escherichia coli O157:H7 str. EC869], gi\|168789470\|ref... gi\|188999218, gi... - gi\|188999218\|gb\|EDU68204.1\| endonuclease III [Escherichia coli O157:H7 str. EC4076], gi\|168783456\|re... gi\|195939022 - gi\|195939022\|ref\|ZP_03084404.1\| endonuclease III [Escherichia coli O157:H7 str. EC4024] gi\|168800893, gi... - gi\|189376924\|gb\|EDU95340.1\| endonuclease III [Escherichia coli O157:H7 str. EC508], gi\|168800893\|ref... gi\|15831596, gi\|... - gi\|15831596\|ref\|NP_310369.1\| endonuclease III [Escherichia coli O157:H7], gi\|13361809\|dbj\|BAB35765.1... gi\|168763663, gi... - gi\|189366197\|gb\|EDU84613.1\| endonuclease III [Escherichia coli O157:H7 str. EC4501], gi\|168763663\|re... gi\|189355540, gi... - gi\|189355540\|gb\|EDU73959.1\| endonuclease III [Escherichia coli O157:H7 str. EC4401], gi\|168757451\|re... gi\|168775863, gi... - gi\|187768694\|gb\|EDU32538.1\| endonuclease III [Escherichia coli O157:H7 str. EC4196], gi\|168775863\|re... gi\|209769626, gi... - pir\|\|F90921 endonuclease III [imported] - Escherichia coli (strain O157:H7, substrain RIMD 0509952),... gi\|189359993, gi... - gi\|189359993\|gb\|EDU78412.1\| endonuclease III [Escherichia coli O157:H7 str. EC4486], gi\|168771175\|re... gi\|15831596, gi\|... - gi\|15831596\|ref\|NP_310369.1\| endonuclease III [Escherichia coli O157:H7 str. Sakai], gi\|13361809\|dbj... gi\|188015244, gi... - gi\|188015244\|gb\|EDU53366.1\| endonuclease III [Escherichia coli O157:H7 str. EC4113], gi\|168750553\|re... gi\|254793250, gi... - gi\|254793250\|ref\|YP_003078087.1\| DNA glycosylase and apyrimidinic (AP) lyase (endonuclease III) [Esc... gi\|217328950, gi... - gi\|217328950\|ref\|ZP_03445031.1\| endonuclease III [Escherichia coli O157:H7 str. TW14588], gi\|2173182... gi\|208816785, gi... - gi\|208816785\|ref\|ZP_03257905.1\| endonuclease III [Escherichia coli O157:H7 str. EC4045], gi\|20873112... gi\|208810702, gi... - gi\|208810702\|ref\|ZP_03252578.1\| endonuclease III [Escherichia coli O157:H7 str. EC4206], gi\|20872521... gi\|209396011, gi... - gi\|209396011\|ref\|YP_002270703.1\| endonuclease III [Escherichia coli O157:H7 str. EC4115], gi\|2091574... gi\|208740629, gi... - gi\|208820506\|ref\|ZP_03260826.1\| endonuclease III [Escherichia coli O157:H7 str. EC4042], gi\|20874062...	252.0	[0..1]	[211..1]
gi\|33152238, gi\|... - gi\|33152238\|ref\|NP_873591.1\| endonuclease III, DNA (apurinic or apyrimidinic site) lyase [Haemophilu...	252.0	[0..1]	[211..1]

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Predicted Domain #1

Region A:
Residues: [1-211]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MNKAKRLEIL TRLRENNPHP TTELNFSSPF ELLIAVLLSA QATDISVNKA TAKLYPVANT  60
   61 PAAMLELGVE GVKTYIKTIG LYNSKAENII KTCRILLEQH NGEVPEDRAA LEALPGVGRK 120
  121 TANVVLNTAF GWPTIAVDTH IFRVCNRTQF APGKNVEQVE EKLLKVVPAE FKVDCHHWLI 180
  181 LHGRYTCIAR KPRCGSCIIE DLCEYKEKVD I

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	67.69897
Match:	2abkA
Description:	REFINEMENT OF THE NATIVE STRUCTURE OF ENDONUCLEASE III TO A RESOLUTION OF 1.85 ANGSTROM
Matching Structure (courtesy of the PDB):

Predicted functions:

Term	Confidence	Notes
DNA N-glycosylase activity	4.08559331236111	bayes_pls_golite062009
hydrolase activity, hydrolyzing N-glycosyl compounds	3.73234184319832	bayes_pls_golite062009
DNA-(apurinic or apyrimidinic site) lyase activity	3.12421941323765	bayes_pls_golite062009
hydrolase activity, acting on glycosyl bonds	2.54759386266723	bayes_pls_golite062009
catalytic activity	2.50389926428623	bayes_pls_golite062009
oxidized base lesion DNA N-glycosylase activity	1.80199518353554	bayes_pls_golite062009
alkylbase DNA N-glycosylase activity	1.75218522602775	bayes_pls_golite062009
hydrolase activity	1.39000450534744	bayes_pls_golite062009
DNA-3-methyladenine glycosylase I activity	1.14337995879633	bayes_pls_golite062009
oxidized purine base lesion DNA N-glycosylase activity	0.473206156100251	bayes_pls_golite062009
uracil DNA N-glycosylase activity	0.29478804124408	bayes_pls_golite062009
oxidized pyrimidine base lesion DNA N-glycosylase activity	0.253198605718519	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: