YRC Public Data Repository - Protein Structure Prediction

Protein:	YAFD_ECOLI
Organism:	Escherichia coli
Length:	266 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 YAFD_ECOLI.

Description	E-value	Query Range	Subject Range
YAFD_SHIDS - UPF0294 protein YafD OS=Shigella dysenteriae serotype 1 (strain Sd197) GN=yafD PE=3 SV=1	206.0	[0..1]	[266..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...	204.0	[0..1]	[266..9]
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...	202.0	[0..1]	[266..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	202.0	[0..1]	[266..1]
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...	200.0	[0..1]	[266..1]
gi\|84779085, gi\|... - gi\|85058565\|ref\|YP_454267.1\| hypothetical protein SG0587 [Sodalis glossinidius str. 'morsitans'], gi...	199.0	[0..1]	[266..1]
gi\|194432690, gi... - gi\|83570290\|ref\|ZP_00921736.1\| COG3021: Uncharacterized protein conserved in bacteria [Shigella dyse...	193.0	[0..8]	[266..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...	192.0	[0..8]	[266..1]
gi\|49612792, gi\|... - gi\|50122266\|ref\|YP_051433.1\| hypothetical protein ECA3344 [Pectobacterium atrosepticum SCRI1043], gi...	191.0	[0..1]	[261..1]
gi\|75229811 - gi\|75229811\|ref\|ZP_00716338.1\| COG3021: Uncharacterized protein conserved in bacteria [Escherichia c...	190.0	[0..8]	[266..1]

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Predicted Domain #1

Region A:
Residues: [1-266]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MRKNTYAMRY VAGQPAERIL PPGSFASIGQ ALPPGEPLST EERIRILVWN IYKQQRAEWL  60
   61 SVLKNYGKDA HLVLLQEAQT TPELVQFATA NYLAADQVPA FVLPQHPSGV MTLSAAHPVY 120
  121 CCPLREREPI LRLAKSALVT VYPLPDTRLL MVVNIHAVNF SLGVDVYSKQ LLPIGDQIAH 180
  181 HSGPVIMAGD FNAWSRRRMN ALYRFAREMS LRQVRFTDDQ RRRAFGRPLD FVFYRGLNVS 240
  241 EASVLVTRAS DHNPLLVEFS PGKPDK

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	41.0
Match:	1akoA
Description:	EXONUCLEASE III FROM ESCHERICHIA COLI
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: