YRC Public Data Repository - Protein Structure Prediction

Protein:	PBPB_ECOLI
Organism:	Escherichia coli
Length:	844 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 PBPB_ECOLI.

Description	E-value	Query Range	Subject Range
gi\|81239688, gi\|... - gi\|82775540\|ref\|YP_401887.1\| penicillin-binding protein 1b [Shigella dysenteriae Sd197], gi\|81239688...	732.0	[0..1]	[844..1]
gi\|205334956, gi... - gi\|205334956\|gb\|EDZ21720.1\| penicillin-binding protein 1B [Salmonella enterica subsp. enterica serov... gi\|195632997, gi... - gi\|195632997\|gb\|EDX51451.1\| penicillin-binding protein 1B [Salmonella enterica subsp. enterica serov... gi\|238911257 - gi\|238911257\|ref\|ZP_04655094.1\| penicillin-binding protein 1b [Salmonella enterica subsp. enterica s... gi\|205331528, gi... - gi\|205331528\|gb\|EDZ18292.1\| penicillin-binding protein 1B [Salmonella enterica subsp. enterica serov... gi\|16763580, gi\|... - gi\|16763580\|ref\|NP_459195.1\| penicillin-binding protein 1b [Salmonella typhimurium LT2], gi\|16418693... gi\|199605075, gi... - gi\|200387977\|ref\|ZP_03214589.1\| penicillin-binding protein 1B [Salmonella enterica subsp. enterica s... gi\|206707509, gi... - gi\|207855706\|ref\|YP_002242357.1\| penicillin-binding protein 1b [Salmonella enterica subsp. enterica ... gi\|197251303, gi... - gi\|197251303\|ref\|YP_002145192.1\| penicillin-binding protein 1B [Salmonella enterica subsp. enterica ... gi\|197262144, gi... - gi\|197262144\|ref\|ZP_03162218.1\| penicillin-binding protein 1B [Salmonella enterica subsp. enterica s... lcl\|NC_016856.1_... - [gene=mrcB] [protein=penicillin-binding protein 1b] [protein_id=YP_005235857.1] [location=221628..22... gi\|194401003, gi... - gi\|194442340\|ref\|YP_002039426.1\| penicillin-binding protein 1B [Salmonella enterica subsp. enterica ... gi\|194455010, gi... - gi\|194468646\|ref\|ZP_03074630.1\| penicillin-binding protein 1B [Salmonella enterica subsp. enterica s...	725.0	[0..1]	[844..1]
gi\|1360957, gi\|8... - gi\|887415\|emb\|CAA90232.1\| penicillin-binding protein 1B (PBP1B) [Citrobacter freundii], pir\|\|S57580 ...	725.0	[0..1]	[844..1]
gi\|74310770, gi\|... - gi\|74310770\|ref\|YP_309189.1\| penicillin-binding protein 1b [Shigella sonnei Ss046], gi\|73854247\|gb\|A...	725.0	[0..1]	[844..1]
gi\|124529626, gi... - gi\|124529626\|ref\|ZP_01700570.1\| penicillin-binding protein 1B [Escherichia coli B], gi\|124499782\|gb\|... gi\|188493396, gi... - gi\|75512025\|ref\|ZP_00734620.1\| COG0744: Membrane carboxypeptidase (penicillin-binding protein) [Esch... gi\|170021497, gi... - gi\|170021497\|ref\|YP_001726451.1\| penicillin-binding protein 1b [Escherichia coli ATCC 8739], gi\|1697...	724.0	[0..1]	[844..1]
gi\|56383164, gi\|... - gi\|56479613\|ref\|NP_706097.2\| penicillin-binding protein 1b [Shigella flexneri 2a str. 301], gi\|56383... gi\|193063219, gi... - gi\|75258860\|ref\|ZP_00730250.1\| COG0744: Membrane carboxypeptidase (penicillin-binding protein) [Esch... gi\|194413689, gi... - gi\|75210474\|ref\|ZP_00710625.1\| COG0744: Membrane carboxypeptidase (penicillin-binding protein) [Esch... gi\|110804204, gi... - gi\|110804204\|ref\|YP_687724.1\| penicillin-binding protein 1b [Shigella flexneri 5 str. 8401], gi\|1106... gi\|157159615, gi... - gi\|75194361\|ref\|ZP_00704431.1\| COG0744: Membrane carboxypeptidase (penicillin-binding protein) [Esch... gi\|157080249, gi... - gi\|75189246\|ref\|ZP_00702513.1\| COG0744: Membrane carboxypeptidase (penicillin-binding protein) [Esch... gi\|218350347, gi... - gi\|218693615\|ref\|YP_002401282.1\| penicillin-binding protein 1b [Escherichia coli 55989], gi\|21835034... gi\|218703405, gi... - gi\|218703405\|ref\|YP_002410924.1\| penicillin-binding protein 1b [Escherichia coli UMN026], gi\|2184305... gi\|30061709, gi\|... - gi\|30061709\|ref\|NP_835880.1\| penicillin-binding protein 1b [Shigella flexneri 2a str. 2457T], gi\|300... gi\|209917340, gi... - gi\|209917340\|ref\|YP_002291424.1\| penicillin-binding protein 1b [Escherichia coli SE11], gi\|209910599...	723.0	[0..1]	[844..1]
gi\|13359609, gi\|... - gi\|15829407\|ref\|NP_308180.1\| penicillin-binding protein 1b [Escherichia coli O157:H7 str. Sakai], gi... gi\|168782041, gi... - gi\|189000447\|gb\|EDU69433.1\| penicillin-binding protein 1B [Escherichia coli O157:H7 str. EC4076], gi... gi\|189371080, gi... - gi\|189371080\|gb\|EDU89496.1\| penicillin-binding protein 1B [Escherichia coli O157:H7 str. EC869], gi\|... gi\|189375666, gi... - gi\|189375666\|gb\|EDU94082.1\| penicillin-binding protein 1B [Escherichia coli O157:H7 str. EC508], gi\|... gi\|195938168 - gi\|195938168\|ref\|ZP_03083550.1\| penicillin-binding protein 1b [Escherichia coli O157:H7 str. EC4024] gi\|208808031, gi... - gi\|208808031\|ref\|ZP_03250368.1\| penicillin-binding protein 1B [Escherichia coli O157:H7 str. EC4206]... gi\|208735425, gi... - gi\|208814148\|ref\|ZP_03255477.1\| penicillin-binding protein 1B [Escherichia coli O157:H7 str. EC4045]... gi\|208739175, gi... - gi\|208819052\|ref\|ZP_03259372.1\| penicillin-binding protein 1B [Escherichia coli O157:H7 str. EC4042]... gi\|209400125, gi... - gi\|209400125\|ref\|YP_002268758.1\| penicillin-binding protein 1B [Escherichia coli O157:H7 str. EC4115... gi\|209746042, gi... - pir\|\|A99648 peptidoglycan synthetase MrcB [imported] - Escherichia coli (strain O157:H7, substrain ... gi\|12512870, gi\|... - gi\|15799833\|ref\|NP_285845.1\| penicillin-binding protein 1b [Escherichia coli O157:H7 EDL933], gi\|125... gi\|13359609, gi\|... - gi\|15829407\|ref\|NP_308180.1\| penicillin-binding protein 1b [Escherichia coli O157:H7], gi\|13359609\|d... gi\|168751369, gi... - gi\|188014588\|gb\|EDU52710.1\| penicillin-binding protein 1B [Escherichia coli O157:H7 str. EC4113], gi... gi\|254791284, gi... - gi\|254791284\|ref\|YP_003076121.1\| bifunctional glycosyl transferase/transpeptidase [Escherichia coli ... gi\|189357010, gi... - gi\|189357010\|gb\|EDU75429.1\| penicillin-binding protein 1B [Escherichia coli O157:H7 str. EC4401], gi... gi\|168764345, gi... - gi\|189365657\|gb\|EDU84073.1\| penicillin-binding protein 1B [Escherichia coli O157:H7 str. EC4501], gi... gi\|168770379, gi... - gi\|189360722\|gb\|EDU79141.1\| penicillin-binding protein 1B [Escherichia coli O157:H7 str. EC4486], gi... gi\|168776986, gi... - gi\|187767688\|gb\|EDU31532.1\| penicillin-binding protein 1B [Escherichia coli O157:H7 str. EC4196], gi... gi\|75230488, gi\|... - gi\|75230488\|ref\|ZP_00716969.1\| COG0744: Membrane carboxypeptidase (penicillin-binding protein) [Esch... gi\|217326047, gi... - gi\|217326047\|ref\|ZP_03442131.1\| penicillin-binding protein 1B [Escherichia coli O157:H7 str. TW14588... gi\|218552730, gi... - gi\|218552730\|ref\|YP_002385643.1\| penicillin-binding protein 1b [Escherichia coli IAI1], gi\|218359498...	723.0	[0..1]	[844..1]
gi\|214000856 - gi\|214000856\|ref\|ZP_03411591.1\| penicillin-binding protein 1b [Salmonella enterica subsp. enterica s... gi\|16501479, gi\|... - gi\|25297725\|pir\|\|AG0526 penicillin-binding protein 1b, peptidoglycan synthetase [imported] - Salmone... gi\|29136363, gi\|... - gi\|29140739\|ref\|NP_804081.1\| penicillin-binding protein 1b [Salmonella enterica subsp. enterica sero... gi\|16759189 - gi\|16759189\|ref\|NP_454806.1\| penicillin-binding protein 1b [Salmonella enterica subsp. enterica sero... gi\|213425925 - gi\|213425925\|ref\|ZP_03358675.1\| penicillin-binding protein 1b [Salmonella enterica subsp. enterica s...	722.0	[0..1]	[844..1]
gi\|218425590, gi... - gi\|218688026\|ref\|YP_002396238.1\| penicillin-binding protein 1b [Escherichia coli ED1a], gi\|218425590... gi\|226902220, gi... - gi\|237704308\|ref\|ZP_04534789.1\| penicillin-binding protein 1b [Escherichia sp. 3_2_53FAA], gi\|226902... gi\|115511560, gi... - gi\|117622436\|ref\|YP_851349.1\| penicillin-binding protein 1b [Escherichia coli APEC O1], gi\|115511560... gi\|227884937, gi... - gi\|227884937\|ref\|ZP_04002742.1\| penicillin-binding protein 1b [Escherichia coli 83972], gi\|227838075... gi\|191172780, gi... - gi\|75240260\|ref\|ZP_00724207.1\| COG0744: Membrane carboxypeptidase (penicillin-binding protein) [Esch... gi\|91070793, gi\|... - gi\|91209219\|ref\|YP_539205.1\| penicillin-binding protein 1b [Escherichia coli UTI89], gi\|91070793\|gb\|... gi\|26246094, gi\|... - gi\|26246094\|ref\|NP_752133.1\| penicillin-binding protein 1b [Escherichia coli CFT073], gi\|26106491\|gb... gi\|110640370, gi... - gi\|110640370\|ref\|YP_668098.1\| penicillin-binding protein 1b [Escherichia coli 536], gi\|110341962\|gb\|... gi\|218557092, gi... - gi\|218557092\|ref\|YP_002390005.1\| penicillin-binding protein 1b [Escherichia coli S88], gi\|218363861\|...	722.0	[0..1]	[844..1]
gi\|75238854, gi\|... - gi\|75238854\|ref\|ZP_00722836.1\| COG0744: Membrane carboxypeptidase (penicillin-binding protein) [Esch...	722.0	[0..1]	[844..1]

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Predicted Domain #1

Region A:
Residues: [1-174]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MAGNDREPIG RKGKPTRPVK QKVSRRRYED DDDYDDYDDY EDEEPMPRKG KGKGKGRKPR  60
   61 GKRGWLWLLL KLAIVFAVLI AIYGVYLDQK IRSRIDGKVW QLPAAVYGRM VNLEPDMTIS 120
  121 KNEMVKLLEA TQYRQVSKMT RPGEFTVQAN SIEMIRRPFD FPDSKEGQVR ARLT

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	40.0
Match:	2fdcA
Description:	No description for 2fdcA was found.

Predicted functions:

Term	Confidence	Notes
binding	1.8576045268999	bayes_pls_golite062009
nucleoside-triphosphatase activity	0.899518010026156	bayes_pls_golite062009
pyrophosphatase activity	0.85586999556549	bayes_pls_golite062009
hydrolase activity, acting on acid anhydrides	0.834450827636679	bayes_pls_golite062009
hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides	0.83347444578978	bayes_pls_golite062009
catalytic activity	0.458437698837681	bayes_pls_golite062009
protein binding	0.378225828131122	bayes_pls_golite062009
hydrolase activity	0.0674634697044169	bayes_pls_golite062009
nucleotide binding	0.0601614967638421	bayes_pls_golite062009
purine nucleotide binding	0.0518926528648858	bayes_pls_golite062009
purine ribonucleotide binding	0.0231586743339878	bayes_pls_golite062009
ribonucleotide binding	0.0231035204040646	bayes_pls_golite062009

Predicted Domain #2

Region A:
Residues: [175-844]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 FDGDHLATIV NMENNRQFGF FRLDPRLITM ISSPNGEQRL FVPRSGFPDL LVDTLLATED  60
   61 RHFYEHDGIS LYSIGRAVLA NLTAGRTVQG ASTLTQQLVK NLFLSSERSY WRKANEAYMA 120
  121 LIMDARYSKD RILELYMNEV YLGQSGDNEI RGFPLASLYY FGRPVEELSL DQQALLVGMV 180
  181 KGASIYNPWR NPKLALERRN LVLRLLQQQQ IIDQELYDML SARPLGVQPR GGVISPQPAF 240
  241 MQLVRQELQA KLGDKVKDLS GVKIFTTFDS VAQDAAEKAA VEGIPALKKQ RKLSDLETAI 300
  301 VVVDRFSGEV RAMVGGSEPQ FAGYNRAMQA RRSIGSLAKP ATYLTALSQP KIYRLNTWIA 360
  361 DAPIALRQPN GQVWSPQNDD RRYSESGRVM LVDALTRSMN VPTVNLGMAL GLPAVTETWI 420
  421 KLGVPKDQLH PVPAMLLGAL NLTPIEVAQA FQTIASGGNR APLSALRSVI AEDGKVLYQS 480
  481 FPQAERAVPA QAAYLTLWTM QQVVQRGTGR QLGAKYPNLH LAGKTGTTNN NVDTWFAGID 540
  541 GSTVTITWVG RDNNQPTKLY GASGAMSIYQ RYLANQTPTP LNLVPPEDIA DMGVDYDGNF 600
  601 VCSGGMRILP VWTSDPQSLC QQSEMQQQPS GNPFDQSSQP QQQPQQQPAQ QEQKDSDGVA 660
  661 GWIKDMFGSN

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	108.0
Match:	2oluA
Description:	No description for 2oluA was found.

Predicted functions:

Term	Confidence	Notes
drug binding	3.68379051298286	bayes_pls_golite062009
serine-type D-Ala-D-Ala carboxypeptidase activity	3.12650314537616	bayes_pls_golite062009
penicillin binding	2.89507018520983	bayes_pls_golite062009
serine-type carboxypeptidase activity	2.70174066798582	bayes_pls_golite062009
serine-type exopeptidase activity	2.69091897402517	bayes_pls_golite062009
carboxypeptidase activity	1.96547160092829	bayes_pls_golite062009
catalytic activity	1.85492008367309	bayes_pls_golite062009
hydrolase activity, hydrolyzing O-glycosyl compounds	1.71682392634357	bayes_pls_golite062009
hydrolase activity, acting on glycosyl bonds	1.62647051069622	bayes_pls_golite062009
exopeptidase activity	1.44522375970439	bayes_pls_golite062009
binding	0.967786931456022	bayes_pls_golite062009
protein binding	0.274057433888583	bayes_pls_golite062009
peptidase activity	0.231714711049091	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: