YRC Public Data Repository - Protein Structure Prediction

Protein:	YBAE_ECOLI
Organism:	Escherichia coli
Length:	566 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 YBAE_ECOLI.

Description	E-value	Query Range	Subject Range
gi\|77996922, gi\|... - gi\|78044807\|ref\|YP_359974.1\| oligopeptide/dipeptide ABC transporter, peptide-binding protein [Carbox...	449.0	[0..85]	[559..1]
gi\|51893453, gi\|... - gi\|51893453\|ref\|YP_076144.1\| dipeptide ABC transporter substrate-binding protein [Symbiobacterium th...	437.0	[0..107]	[561..33]
gi\|15602101, gi\|... - gi\|15602101\|ref\|NP_245173.1\| hypothetical protein PM0236 [Pasteurella multocida subsp. multocida str...	436.0	[0..88]	[562..1]
gi\|78218637, gi\|... - gi\|78356232\|ref\|YP_387681.1\| putative oligopeptide ABC transporter binding protein [Desulfovibrio de...	434.0	[0..89]	[562..1]
gi\|52347194, gi\|... - gi\|52784692\|ref\|YP_090521.1\| hypothetical protein BLi00894 [Bacillus licheniformis ATCC 14580], gi\|5...	433.0	[0..88]	[562..1]
gi\|89100171, gi\|... - gi\|89100171\|ref\|ZP_01173039.1\| hypothetical protein B14911_14460 [Bacillus sp. NRRL B-14911], gi\|890...	432.0	[0..113]	[562..34]
gi\|218372296, gi... - gi\|218702310\|ref\|YP_002409939.1\| dipeptide transporter ; periplasmic-binding component of ABC superf... gi\|117625828, gi... - gi\|117625828\|ref\|YP_859151.1\| dipeptide transporter protein DppA [Escherichia coli APEC O1], gi\|1155... gi\|218367391, gi... - gi\|218560622\|ref\|YP_002393535.1\| dipeptide transporter ; periplasmic-binding component of ABC superf... gi\|218429393, gi... - gi\|218691829\|ref\|YP_002400041.1\| dipeptide transporter ; periplasmic-binding component of ABC superf... gi\|170679624, gi... - gi\|170679624\|ref\|YP_001745830.1\| dipeptide ABC transporter, periplasmic dipeptide-binding protein [E... gi\|191170334, gi... - gi\|191170334\|ref\|ZP_03031887.1\| dipeptide ABC transporter, periplasmic dipeptide-binding protein [Es... gi\|237703312, gi... - gi\|237703312\|ref\|ZP_04533793.1\| periplasmic dipeptide transporter [Escherichia sp. 3_2_53FAA], gi\|22... gi\|26250183, gi\|... - gi\|26250183\|ref\|NP_756223.1\| periplasmic dipeptide transport protein precursor [Escherichia coli CFT... gi\|110643793, gi... - gi\|110643793\|ref\|YP_671523.1\| periplasmic dipeptide transport protein precursor [Escherichia coli 53... gi\|91213056, gi\|... - gi\|91213056\|ref\|YP_543042.1\| periplasmic dipeptide transport protein precursor [Escherichia coli UTI... gi\|227839288, gi... - gi\|227883708\|ref\|ZP_04001513.1\| dipeptide/oligopeptide/nickel (Ni2+) ABC superfamily ATP binding cas...	432.0	[0..86]	[562..1]
gi\|16762672 - gi\|16762672\|ref\|NP_458289.1\| periplasmic dipeptide transport protein precursor [Salmonella enterica ... gi\|16504978, gi\|... - gi\|25296405\|pir\|\|AE0983 periplasmic dipeptide transport protein precursor STY4168 [imported] - Salmo... gi\|29139796, gi\|... - gi\|29144159\|ref\|NP_807501.1\| periplasmic dipeptide transport protein precursor [Salmonella enterica ...	430.0	[0..100]	[562..8]
gi\|218556099, gi... - gi\|218556099\|ref\|YP_002389012.1\| dipeptide transporter ; periplasmic-binding component of ABC superf... DPPA_ECOLI - Periplasmic dipeptide transport protein precursor (Dipeptide-binding protein) (DBP) - Escherichia co... gi\|209914267, gi... - gi\|209921008\|ref\|YP_002295092.1\| dipeptide ABC transporter substrate binding component [Escherichia ... gi\|194435630, gi... - gi\|194435630\|ref\|ZP_03067733.1\| dipeptide ABC transporter, periplasmic dipeptide-binding protein [Es... gi\|194428690, gi... - gi\|194428690\|ref\|ZP_03061227.1\| dipeptide ABC transporter, periplasmic dipeptide-binding protein [Es... gi\|218697257, gi... - gi\|218697257\|ref\|YP_002404924.1\| dipeptide transporter ; periplasmic-binding component of ABC superf... gi\|169753154, gi... - gi\|170018226\|ref\|YP_001723180.1\| 4-phytase [Escherichia coli ATCC 8739], gi\|169753154\|gb\|ACA75853.1\|... EG10248 - dipeptide /heme ABC transporter periplasmic binding protein; dipeptide chemotaxis receptor / Dipeptid... gi\|192932707, gi... - gi\|193061917\|ref\|ZP_03043014.1\| dipeptide ABC transporter, periplasmic dipeptide-binding protein [Es... gi\|238902633, gi... - gi\|238902633\|ref\|YP_002928429.1\| dipeptide transporter [Escherichia coli BW2952], gi\|238860779\|gb\|AC... gi\|157163019, gi... - gi\|157163019\|ref\|YP_001460337.1\| dipeptide ABC transporter, periplasmic dipeptide-binding protein [E... gi\|191165311, gi... - gi\|191165311\|ref\|ZP_03027154.1\| dipeptide ABC transporter, periplasmic dipeptide-binding protein [Es... gi\|157159059, gi... - gi\|157159059\|ref\|YP_001465018.1\| dipeptide ABC transporter, periplasmic dipeptide-binding protein [E... gi\|188494631, gi... - gi\|188494631\|ref\|ZP_03001901.1\| dipeptide ABC transporter, periplasmic dipeptide-binding protein [Es... gi\|254290218, gi... - gi\|254290218\|ref\|YP_003055966.1\| dipeptide transporter [Escherichia coli BL21(DE3)], gi\|253979525\|gb... gi\|170083053, gi... - gi\|170083053\|ref\|YP_001732373.1\| peptide ABC transporter periplasmic substrate-binding protein [Esch... gi\|251786789, gi... - gi\|251786789\|ref\|YP_003001093.1\| hypothetical protein B21_03346 [Escherichia coli BL21], gi\|24237906... gi\|253975369, gi... - gi\|254163468\|ref\|YP_003046576.1\| dipeptide transporter [Escherichia coli B str. REL606], gi\|25397536... gi\|226839232, gi... - gi\|254038726\|ref\|ZP_04872782.1\| dipeptide ABC transporter [Escherichia sp. 1_1_43], gi\|226839232\|gb\|... gi\|89110469, gi\|... - gi\|89110469\|ref\|AP_004249.1\| dipeptide transporter [Escherichia coli str. K-12 substr. W3110], gi\|85... EG10248 - dipeptide /heme ABC transporter periplasmic binding protein; dipeptide chemotaxis receptor / Dipeptid... gi\|124499882, gi... - gi\|124529424\|ref\|ZP_01700428.1\| extracellular solute-binding protein, family 5 [Escherichia coli B],...	430.0	[0..86]	[562..1]
gi\|75242664 - gi\|75242664\|ref\|ZP_00726408.1\| COG0747: ABC-type dipeptide transport system, periplasmic component [...	430.0	[0..102]	[562..1]

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Predicted Domain #1

Region A:
Residues: [1-111]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MRLLNRLNQY QRLWQPSAGK PQTVTVSELA ERCFCSERHV RTLLRQAQEA GWLEWQAQSG  60
   61 RGKRGQLRFL VTPESLRNAM MEQALETGKQ QDVLELAQLA PGELRTLLQP F

[Run NCBI BLAST on this sequence.]

Detection Method:	FFAS03
Confidence:	1.21
Match:	1bi0A
Description:	STRUCTURE OF APO-AND HOLO-DIPHTHERIA TOXIN REPRESSOR
Matching Structure (courtesy of the PDB):

Predicted functions:

Term	Confidence	Notes
binding	2.0250202903001	bayes_pls_golite062009
protein binding	0.15188391702134	bayes_pls_golite062009

Predicted Domain #2

Region A:
Residues: [112-566]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MGGQWQNDTP TLRIPYYRPL EPLQPGFLPG RAEQHLAGQI FSGLTRFDNN TQRPIGDLAH  60
   61 HWETSTDGLR WDFYLRSTLH WHNGDAVKAS HLHQRLLMLL QLPALDQLFI SVKRIEVTHP 120
  121 QCLTFFLHRP DYWLAHRLAS YCSHLAHPQF PLIGTGPFRL TQFTAELVRL ESHDYYHLRH 180
  181 PLLKAVEYWI TPPLFEKDLG TSCRHPVQIT IGKPEELQRV SQVSSGISLG FCYLTLRKSP 240
  241 RLSLWQARKV ISIIHQSGLL QTLEVGENLI TASHALLPGW TIPHWQVPDE VKLPKTLTLV 300
  301 YHLPIELHTM AERLQATLAA EGCELTIIFH NAKNWDDTTL QAHADLMMGD RLIGEAPEYT 360
  361 LEQWLRCDPL WPHVFDAPAY AHLQSTLDAV QIMPDEENRF NALKAVFSQL MTDATLTPLF 420
  421 NYHYRISAPP GVNGVRLTPR GWFEFTEAWL PAPSQ

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	119.0
Match:	1dppA
Description:	Dipeptide-binding protein
Matching Structure (courtesy of the PDB):

Predicted functions:

Term	Confidence	Notes
transporter activity	2.40545849033896	bayes_pls_golite062009
transmembrane transporter activity	2.14350700163645	bayes_pls_golite062009
active transmembrane transporter activity	1.78426408099234	bayes_pls_golite062009
P-P-bond-hydrolysis-driven transmembrane transporter activity	1.67192694800915	bayes_pls_golite062009
primary active transmembrane transporter activity	1.67011353320924	bayes_pls_golite062009
hydrolase activity, acting on acid anhydrides, catalyzing transmembrane movement of substances	1.66243055906859	bayes_pls_golite062009
ATPase activity, coupled to movement of substances	1.66243055906859	bayes_pls_golite062009
ATPase activity, coupled to transmembrane movement of substances	1.66071693096018	bayes_pls_golite062009
substrate-specific transporter activity	1.63640317740517	bayes_pls_golite062009
ATPase activity, coupled	1.52675709081397	bayes_pls_golite062009
nucleoside-triphosphatase activity	1.4521463765384	bayes_pls_golite062009
ATPase activity	1.40678917547155	bayes_pls_golite062009
pyrophosphatase activity	1.40509342124518	bayes_pls_golite062009
hydrolase activity, acting on acid anhydrides	1.38450733218732	bayes_pls_golite062009
hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides	1.38349438029763	bayes_pls_golite062009
binding	1.28024527565554	bayes_pls_golite062009
substrate-specific transmembrane transporter activity	1.01146367558475	bayes_pls_golite062009
hydrolase activity	0.458908097342689	bayes_pls_golite062009
ion transmembrane transporter activity	0.0662041278342053	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:

Predicted functions: