YRC Public Data Repository - Protein Structure Prediction

Protein:	gi\|16501479, gi\|...
Organism:	Salmonella enterica subsp. enterica serovar Typhi
Length:	840 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|16501479, gi|....

Description	E-value	Query Range	Subject Range
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...	0.0	[1..840]	[1..840]
gi\|62126393, gi\|... - gi\|62178760\|ref\|YP_215177.1\| penicillin-binding protein 1b [Salmonella enterica subsp. enterica sero...	0.0	[1..840]	[1..840]
gi\|56126723, gi\|... - gi\|56412466\|ref\|YP_149541.1\| penicillin-binding protein 1b [Salmonella enterica subsp. enterica sero... gi\|197092877, gi... - gi\|197361402\|ref\|YP_002141037.1\| penicillin-binding protein 1b [Salmonella enterica subsp. enterica ...	0.0	[1..840]	[1..840]
gi\|1360957, gi\|8... - gi\|887415\|emb\|CAA90232.1\| penicillin-binding protein 1B (PBP1B) [Citrobacter freundii], pir\|\|S57580 ...	0.0	[1..840]	[1..846]
gi\|81239688, gi\|... - gi\|82775540\|ref\|YP_401887.1\| penicillin-binding protein 1b [Shigella dysenteriae Sd197], gi\|81239688...	0.0	[1..840]	[1..844]
gi\|253774823, gi... - gi\|254287072\|ref\|YP_003052820.1\| penicillin-binding protein 1b [Escherichia coli BL21(DE3)], gi\|2539... gi\|242375982, gi... - gi\|251783709\|ref\|YP_002998013.1\| hypothetical protein B21_00147 [Escherichia coli BL21], gi\|24237598... gi\|254160269, gi... - gi\|254160269\|ref\|YP_003043377.1\| penicillin-binding protein 1b [Escherichia coli B str. REL606], gi\|... gi\|83585466, gi\|... - gi\|83585466\|ref\|ZP_00924111.1\| COG0744: Membrane carboxypeptidase (penicillin-binding protein) [Esch...	0.0	[1..840]	[1..841]
gi\|74310770, gi\|... - gi\|74310770\|ref\|YP_309189.1\| penicillin-binding protein 1b [Shigella sonnei Ss046], gi\|73854247\|gb\|A...	0.0	[1..840]	[1..844]
gi\|187427652, gi... - gi\|75176505\|ref\|ZP_00696642.1\| COG0744: Membrane carboxypeptidase (penicillin-binding protein) [Shig...	0.0	[1..840]	[1..840]
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...	0.0	[1..840]	[1..844]
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...	0.0	[1..840]	[1..844]

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Predicted Domain #1

Region A:
Residues: [1-97]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MAGNDREPIG RKGKPSRPVK QKVSRRRQHD DDYDDDYEDE EPMPRKGKGK GRKPRGKRGW  60
   61 LWLLLKLFIV FVVLFAIYGV YLDQKIRSRI DGKVWQL

[Run NCBI BLAST on this sequence.]

Detection Method:

deduced

Shown below are all of our de novo (Rosetta) predictions for this domain.
Click here to view only most confident match.

		MCM Score	SCOP Match	SCOP Description
View	Download	0.239	a.8.1	Bacterial immunoglobulin/albumin-binding domains
View	Download	0.211	g.16.1	Trefoil

Predicted Domain #2

Region A:
Residues: [98-171]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 PAAVYGRMVN LEPDMPVSKN EMVKLLEATQ YRLVTKMTRP GEFTVQANSI EMIRRPFDFP  60
   61 DSKEGQVRAR LTFS

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	43.0
Match:	1t5lA
Description:	Crystal structure of the DNA repair protein UvrB point mutant Y96A revealing a novel fold for domain 2
Matching Structure (courtesy of the PDB):

Predicted Domain #3

Region A:
Residues: [172-840]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 DGRLETIVNL DNNRQFGFFR LDPRLITMLS SPNGEQRLFV PRSGFPDLLV DTLLATEDRR  60
   61 FYEHDGISLY SIGRAVLANL TAGRTVQGAS TLTQQLVKNL FLSSERSYWR KANEAYMALI 120
  121 MDARYSKDRI LELYMNEVYL GQSGDNEIRG FPLASLYYFG RPVEELSLDQ QALLVGMVKG 180
  181 ASIYNPWRNP KLALERRNLV LRLLQQQKII DQELYDMLSA RPLGVQPRGG VISPQPAFMQ 240
  241 MVRQELQAKL GDKIKDLSGV KIFTTFDSVA QDAAEKAVVE GIPALKKQRK LSDLETAMVV 300
  301 VDRFSGEVRA MVGGAEPQYA GYNRAMQARR SIGSLAKPAT YLTALSQPNL YRLNTWIADA 360
  361 PISLRQPNGQ VWSPENDDRR YSESGKVMLV DALTRSMNVP TVNLGMALGL PAVTDTWTKL 420
  421 GVPKDQLNPV PAMLLGALNL TPIEVAQAFQ TIASGGNRAP LSALRSVIAE DGKVLYQSYP 480
  481 QAERAVPAQA AYLTLWTMQQ VVQRGTGRQL GAKYPGLHLV GKTGTTNNNV DTWFAGIDGS 540
  541 QVTITWVGRD NNQPTKLYGA SGAMAIYQRY LANQTPTPLV LTPPEDVVDM GVDYDGNFVC 600
  601 NGGMRTLPVW TDDPNTLCQQ GEMMQQQQQP SGNPFDQSSQ PQQPAQQQPP KEEKSDGVAG 660
  661 WIKEMFGGN

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	95.0
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: