YRC Public Data Repository - Protein Structure Prediction

Protein:	YCBB_ECOLI
Organism:	Escherichia coli
Length:	615 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 YCBB_ECOLI.

Description	E-value	Query Range	Subject Range
gi\|218364599, gi... - gi\|218557830\|ref\|YP_002390743.1\| hypothetical protein ECS88_0953 [Escherichia coli S88], gi\|21836459... gi\|91071601, gi\|... - gi\|91210027\|ref\|YP_540013.1\| hypothetical protein UTI89_C0997 [Escherichia coli UTI89], gi\|91071601\|... gi\|226898297, gi... - gi\|237707087\|ref\|ZP_04537568.1\| YcbB [Escherichia sp. 3_2_53FAA], gi\|226898297\|gb\|EEH84556.1\| YcbB [... gi\|117623143, gi... - gi\|117623143\|ref\|YP_852056.1\| hypothetical protein APECO1_37 [Escherichia coli APEC O1], gi\|11551226...	518.0	[0..1]	[615..1]
gi\|192955927, gi... - gi\|193070734\|ref\|ZP_03051669.1\| putative peptidoglycan binding domain [Escherichia coli E110019], gi... gi\|193064628, gi... - gi\|193064628\|ref\|ZP_03045707.1\| putative peptidoglycan binding domain [Escherichia coli E22], gi\|192... gi\|191166981, gi... - gi\|191166981\|ref\|ZP_03028804.1\| putative peptidoglycan binding domain [Escherichia coli B7A], gi\|190... gi\|81246078, gi\|... - gi\|82544667\|ref\|YP_408614.1\| hypothetical protein SBO_2216 [Shigella boydii Sb227], gi\|81246078\|gb\|A... gi\|218351131, gi... - gi\|218694399\|ref\|YP_002402066.1\| hypothetical protein EC55989_0971 [Escherichia coli 55989], gi\|2183... gi\|218553512, gi... - gi\|218553512\|ref\|YP_002386425.1\| hypothetical protein ECIAI1_0966 [Escherichia coli IAI1], gi\|218360... gi\|209918175, gi... - gi\|209918175\|ref\|YP_002292259.1\| hypothetical protein ECSE_0984 [Escherichia coli SE11], gi\|20991143... gi\|194413551, gi... - gi\|194428336\|ref\|ZP_03060877.1\| putative peptidoglycan binding domain protein [Escherichia coli B171...	518.0	[0..1]	[615..1]
gi\|82777551, gi\|... - gi\|82777551\|ref\|YP_403900.1\| hypothetical protein SDY_2332 [Shigella dysenteriae Sd197], gi\|81241699...	517.0	[0..1]	[615..1]
gi\|110641122, gi... - gi\|110641122\|ref\|YP_668852.1\| hypothetical protein ECP_0936 [Escherichia coli 536], gi\|110342714\|gb\|... gi\|191172097, gi... - gi\|191172097\|ref\|ZP_03033641.1\| putative peptidoglycan binding domain [Escherichia coli F11], gi\|190...	517.0	[0..1]	[615..1]
gi\|13360467, gi\|... - gi\|15830262\|ref\|NP_309035.1\| hypothetical protein ECs1008 [Escherichia coli O157:H7 str. Sakai], gi\|... gi\|189361134, gi... - gi\|189361134\|gb\|EDU79553.1\| putative peptidoglycan binding domain [Escherichia coli O157:H7 str. EC4... gi\|189366781, gi... - gi\|189366781\|gb\|EDU85197.1\| putative peptidoglycan binding domain [Escherichia coli O157:H7 str. EC4... gi\|168757018, gi... - gi\|189355931\|gb\|EDU74350.1\| putative peptidoglycan binding domain [Escherichia coli O157:H7 str. EC4... gi\|168751189, gi... - gi\|188014739\|gb\|EDU52861.1\| putative peptidoglycan binding domain [Escherichia coli O157:H7 str. EC4... gi\|209774750, gi... - pir\|\|F85618 probable amidase ycbB [imported] - Escherichia coli (strain O157:H7, substrain EDL933),... gi\|217322452, gi... - gi\|217326231\|ref\|ZP_03442315.1\| putative peptidoglycan binding domain protein [Escherichia coli O157... gi\|208738135, gi... - gi\|208822650\|ref\|ZP_03262969.1\| putative peptidoglycan binding domain protein [Escherichia coli O157... gi\|12514097, gi\|... - gi\|15800786\|ref\|NP_286800.1\| hypothetical protein Z1272 [Escherichia coli O157:H7 EDL933], gi\|125140... gi\|195939660 - gi\|195939660\|ref\|ZP_03085042.1\| hypothetical protein EscherichcoliO157_25185 [Escherichia coli O157:... gi\|254792124, gi... - gi\|254792124\|ref\|YP_003076961.1\| predicted carboxypeptidase [Escherichia coli O157:H7 str. TW14359],... gi\|13360467, gi\|... - gi\|15830262\|ref\|NP_309035.1\| putative amidase [Escherichia coli O157:H7], gi\|13360467\|dbj\|BAB34431.1... gi\|189372669, gi... - gi\|189372669\|gb\|EDU91085.1\| putative peptidoglycan binding domain [Escherichia coli O157:H7 str. EC8...	517.0	[0..1]	[615..1]
gi\|26107352, gi\|... - gi\|26246952\|ref\|NP_752992.1\| hypothetical protein c1067 [Escherichia coli CFT073], gi\|26107352\|gb\|AA... gi\|227838862, gi... - gi\|227884110\|ref\|ZP_04001915.1\| peptidoglycan binding domain protein [Escherichia coli 83972], gi\|22...	517.0	[0..1]	[615..1]
gi\|24112334, gi\|... - gi\|24112334\|ref\|NP_706844.1\| hypothetical protein SF0922 [Shigella flexneri 2a str. 301], gi\|2405119...	515.0	[0..1]	[615..1]
gi\|30062460, gi\|... - gi\|30062460\|ref\|NP_836631.1\| hypothetical protein S0986 [Shigella flexneri 2a str. 2457T], gi\|300407...	515.0	[0..1]	[615..1]
gi\|73854960, gi\|... - gi\|74311483\|ref\|YP_309902.1\| hypothetical protein SSON_0928 [Shigella sonnei Ss046], gi\|73854960\|gb\|...	513.0	[0..1]	[615..1]
gi\|75189980 - gi\|75189980\|ref\|ZP_00703247.1\| COG2989: Uncharacterized protein conserved in bacteria [Escherichia c...	510.0	[0..5]	[615..1]

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Predicted Domain #1

Region A:
Residues: [1-61]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MLLNMMCGRQ LSAISLCLAV TFAPLFNAQA DEPEVIPGDS PVAVSEQGEA LPQAQATAIM  60
   61 A

[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.

Predicted Domain #2

Region A:
Residues: [62-232]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 GIQPLPEGAA EKARTQIESQ LPAGYKPVYL NQLQLLYAAR DMQPMWENRD AVKAFQQQLA  60
   61 EVAIAGFQPQ FNKWVELLTD PGVNGMARDV VLSDAMMGYL HFIANIPVKG TRWLYSSKPY 120
  121 ALATPPLSVI NQWQLALDKG QLPTFVAGLA PQHPQYAAMH ESLLALLCDT K

[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.

Predicted Domain #3

Region A:
Residues: [233-474]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 PWPQLTGKAT LRPGQWSNDV PALREILQRT GMLDGGPKIT LPGDDTPTDA VVSPSAVTVE  60
   61 TAETKPMDKQ TTSRSKPAPA VRAAYDNELV EAVKRFQAWQ GLGADGAIGP ATRDWLNVTP 120
  121 AQRAGVLALN IQRLRLLPTE LSTGIMVNIP AYSLVYYQNG NQVLDSRVIV GRPDRKTPMM 180
  181 SSALNNVVVN PPWNVPPTLA RKDILPKVRN DPGYLESHGY TVMRGWNSRE AIDPWQVDWS 240
  241 TI

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	5.09691
Match:	1zatA
Description:	No description for 1zatA was found.

Predicted Domain #4

Region A:
Residues: [475-615]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 TASNLPFRFQ QAPGPRNSLG RYKFNMPSSE AIYLHDTPNH NLFKRDTRAL SSGCVRVNKA  60
   61 SDLANMLLQD AGWNDKRISD ALKQGDTRYV NIRQSIPVNL YYLTAFVGAD GRTQYRTDIY 120
  121 NYDLPARSSS QIVSKAEQLI R

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	13.69897
Match:	1y7mA
Description:	Crystal Structure of the B. subtilis YkuD protein at 2 A resolution
Matching Structure (courtesy of the PDB):

Predicted functions:

Term	Confidence	Notes
binding	0.877949200621699	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: