YRC Public Data Repository - Protein Structure Prediction

Protein:	gi\|16504411, gi\|...
Organism:	Salmonella enterica subsp. enterica serovar Typhi
Length:	455 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|16504411, gi|....

Description	E-value	Query Range	Subject Range
gi\|62129489, gi\|... - gi\|62181856\|ref\|YP_218273.1\| serine endoprotease [Salmonella enterica subsp. enterica serovar Choler...	2.0E-98	[1..455]	[1..455]
gi\|205328083, gi... - gi\|205328083\|gb\|EDZ14847.1\| protease DegQ [Salmonella enterica subsp. enterica serovar 4,[5],12:i:- ... gi\|16421907, gi\|... - gi\|16766643\|ref\|NP_462258.1\| serine endoprotease [Salmonella typhimurium LT2], gi\|16421907\|gb\|AAL222... lcl\|NC_016856.1_... - [gene=degQ] [protein=serine endoprotease] [protein_id=YP_005239532.1] [location=3529313..3530680]	3.0E-98	[1..455]	[1..455]
gi\|226899060, gi... - gi\|237706020\|ref\|ZP_04536501.1\| serine endoprotease DegQ [Escherichia sp. 3_2_53FAA], gi\|226899060\|g... gi\|26110243, gi\|... - gi\|26249815\|ref\|NP_755855.1\| serine endoprotease [Escherichia coli CFT073], gi\|26110243\|gb\|AAN82429.... gi\|91074228, gi\|... - gi\|91212654\|ref\|YP_542640.1\| serine endoprotease [Escherichia coli UTI89], gi\|91074228\|gb\|ABE09109.1...	4.0E-98	[1..455]	[15..469]
gi\|227887949, gi... - gi\|227887949\|ref\|ZP_04005754.1\| serine endoprotease [Escherichia coli 83972], gi\|227835345\|gb\|EEJ458... gi\|75237911, gi\|... - gi\|75237911\|ref\|ZP_00721922.1\| COG0265: Trypsin-like serine proteases, typically periplasmic, contai... gi\|218560296, gi... - gi\|218560296\|ref\|YP_002393209.1\| serine endoprotease [Escherichia coli S88], gi\|218367065\|emb\|CAR048... gi\|117625518, gi... - gi\|117625518\|ref\|YP_858841.1\| serine endoprotease [Escherichia coli APEC O1], gi\|115514642\|gb\|ABJ027...	4.0E-98	[1..455]	[1..455]
gi\|170519768, gi... - gi\|170682050\|ref\|YP_001745506.1\| serine peptidase DegQ [Escherichia coli SMS-3-5], gi\|170519768\|gb\|A... gi\|82778542, gi\|... - gi\|82778542\|ref\|YP_404891.1\| serine endoprotease [Shigella dysenteriae Sd197], gi\|81242690\|gb\|ABB634...	4.0E-98	[1..455]	[1..455]
gi\|238902335, gi... - gi\|238902335\|ref\|YP_002928131.1\| serine endoprotease, periplasmic [Escherichia coli BW2952], gi\|2388... gi\|242378772, gi... - gi\|251786499\|ref\|YP_003000803.1\| hypothetical protein B21_03045 [Escherichia coli BL21], gi\|24237877... gi\|169753450, gi... - gi\|170018522\|ref\|YP_001723476.1\| serine endoprotease [Escherichia coli ATCC 8739], gi\|169753450\|gb\|A... gi\|254289921, gi... - gi\|254289921\|ref\|YP_003055669.1\| serine endoprotease, periplasmic [Escherichia coli BL21(DE3)], gi\|2... gi\|169890601, gi... - gi\|170082766\|ref\|YP_001732086.1\| serine endoprotease, periplasmic [Escherichia coli str. K-12 substr... gi\|254163171, gi... - gi\|254163171\|ref\|YP_003046279.1\| serine endoprotease, periplasmic [Escherichia coli B str. REL606], ... gi\|209920704, gi... - gi\|209920704\|ref\|YP_002294788.1\| serine endoprotease [Escherichia coli SE11], gi\|209913963\|dbj\|BAG79... gi\|218362566, gi... - gi\|218555798\|ref\|YP_002388711.1\| serine endoprotease [Escherichia coli IAI1], gi\|218362566\|emb\|CAR00... gi\|75188034, gi\|... - gi\|75188034\|ref\|ZP_00701301.1\| COG0265: Trypsin-like serine proteases, typically periplasmic, contai... gi\|75176080, gi\|... - gi\|75176080\|ref\|ZP_00696248.1\| COG0265: Trypsin-like serine proteases, typically periplasmic, contai... gi\|194412828, gi... - gi\|75209671\|ref\|ZP_00709883.1\| COG0265: Trypsin-like serine proteases, typically periplasmic, contai... gi\|157068392, gi... - gi\|75197177\|ref\|ZP_00707247.1\| COG0265: Trypsin-like serine proteases, typically periplasmic, contai... gi\|192956395, gi... - gi\|75234858\|ref\|ZP_00719149.1\| COG0265: Trypsin-like serine proteases, typically periplasmic, contai... gi\|75228640, gi\|... - gi\|75228640\|ref\|ZP_00715265.1\| COG0265: Trypsin-like serine proteases, typically periplasmic, contai... gi\|984379, gi\|55... - gi\|984379\|gb\|AAC44005.1\| DegQ, gi\|89109996\|ref\|AP_003776.1\| serine endoprotease, periplasmic [Escher... gi\|75511870, gi\|... - gi\|75511870\|ref\|ZP_00734482.1\| COG0265: Trypsin-like serine proteases, typically periplasmic, contai... DEGQ_ECOLI - Protease degQ precursor (EC 3.4.21.-) - Escherichia coli EG12612 - serine endoprotease, periplasmic / Periplasmic serine endoprotease; multicopy suppressor of prc and ... gi\|194439204, gi... - gi\|83585395\|ref\|ZP_00924041.1\| COG0265: Trypsin-like serine proteases, typically periplasmic, contai... gi\|124528508, gi... - gi\|124528508\|ref\|ZP_01699797.1\| protease Do [Escherichia coli B], gi\|124500531\|gb\|EAY48003.1\| protea... gi\|218353665, gi... - gi\|218696933\|ref\|YP_002404600.1\| serine endoprotease [Escherichia coli 55989], gi\|218353665\|emb\|CAU9... gi\|218433945, gi... - gi\|218706848\|ref\|YP_002414367.1\| serine endoprotease [Escherichia coli UMN026], gi\|218433945\|emb\|CAR... EG12612 - serine endoprotease, periplasmic / Periplasmic serine endoprotease; multicopy suppressor of prc and ...	9.0E-98	[1..455]	[1..455]
gi\|81246948, gi\|... - gi\|82545537\|ref\|YP_409484.1\| serine endoprotease [Shigella boydii Sb227], gi\|81246948\|gb\|ABB67656.1\|...	1.0E-97	[1..455]	[1..455]
gi\|50119263, gi\|... - gi\|50119263\|ref\|YP_048430.1\| exported protease [Pectobacterium atrosepticum SCRI1043], gi\|49609789\|e...	1.0E-97	[1..455]	[1..456]
gi\|208726827, gi... - gi\|208807026\|ref\|ZP_03249363.1\| serine peptidase DegQ [Escherichia coli O157:H7 str. EC4206], gi\|208... gi\|13363580, gi\|... - gi\|15833361\|ref\|NP_312134.1\| serine endoprotease [Escherichia coli O157:H7 str. Sakai], gi\|13363580\|... gi\|195939430 - gi\|195939430\|ref\|ZP_03084812.1\| serine endoprotease [Escherichia coli O157:H7 str. EC4024] gi\|168800945, gi... - gi\|189376842\|gb\|EDU95258.1\| serine peptidase DegQ [Escherichia coli O157:H7 str. EC508], gi\|16880094... gi\|189374104, gi... - gi\|189374104\|gb\|EDU92520.1\| serine peptidase DegQ [Escherichia coli O157:H7 str. EC869], gi\|16878611... gi\|217327093, gi... - gi\|217327093\|ref\|ZP_03443176.1\| serine peptidase DegQ [Escherichia coli O157:H7 str. TW14588], gi\|21... gi\|209399719, gi... - gi\|209399719\|ref\|YP_002272697.1\| serine peptidase DegQ [Escherichia coli O157:H7 str. EC4115], gi\|20... gi\|208741708, gi... - gi\|208821585\|ref\|ZP_03261905.1\| serine peptidase DegQ [Escherichia coli O157:H7 str. EC4042], gi\|208... gi\|208733346, gi... - gi\|208812069\|ref\|ZP_03253398.1\| serine peptidase DegQ [Escherichia coli O157:H7 str. EC4045], gi\|208... gi\|13363580, gi\|... - gi\|15833361\|ref\|NP_312134.1\| serine endoprotease [Escherichia coli O157:H7], gi\|13363580\|dbj\|BAB3753... gi\|168754214, gi... - gi\|189358656\|gb\|EDU77075.1\| serine peptidase DegQ [Escherichia coli O157:H7 str. EC4401], gi\|1687542... gi\|209757780, gi... - pir\|\|C91142 serine endoproteinase [imported] - Escherichia coli (strain O157:H7, substrain RIMD 0509... gi\|189000984, gi... - gi\|189000984\|gb\|EDU69970.1\| serine peptidase DegQ [Escherichia coli O157:H7 str. EC4076], gi\|1687813... gi\|254795177, gi... - gi\|254795177\|ref\|YP_003080014.1\| serine endoprotease, periplasmic [Escherichia coli O157:H7 str. TW1... gi\|187767163, gi... - gi\|187767163\|gb\|EDU31007.1\| serine peptidase DegQ [Escherichia coli O157:H7 str. EC4196], gi\|1687776... gi\|168769088, gi... - gi\|189361824\|gb\|EDU80243.1\| serine peptidase DegQ [Escherichia coli O157:H7 str. EC4486], gi\|1687690... gi\|168763769, gi... - gi\|189366157\|gb\|EDU84573.1\| serine peptidase DegQ [Escherichia coli O157:H7 str. EC4501], gi\|1687637...	1.0E-97	[1..455]	[1..455]
gi\|192926984, gi... - gi\|75256604\|ref\|ZP_00728234.1\| COG0265: Trypsin-like serine proteases, typically periplasmic, contai...	2.0E-97	[1..455]	[1..455]

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Predicted Domain #1

Region A:
Residues: [1-455]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MKKHTQLLSA LALSVGLTLS APFPALASIP GQVPGQATLP SLAPMLEKVL PAVVSVKVEG  60
   61 TATQSQKVPE EFKKFFGEDL PDQPSQPFEG LGSGVIIDAA KGYVLTNNHV INQAQKISIQ 120
  121 LNDGREFDAK LIGGDDQSDI ALLQIQNPSK LTQIAIADSD KLRVGDFAVA VGNPFGLGQT 180
  181 ATSGIISALG RSGLNLEGLE NFIQTDASIN RGNSGGALLN LNGELIGINT AILAPGGGSI 240
  241 GIGFAIPSNM AQTLAQQLIQ FGEIKRGLLG IKGTEMTADI AKAFKLNVQR GAFVSEVLPN 300
  301 SGSAKAGVKS GDVIISLNGK PLNSFAELRS RIATTEPGTK VKLGLLRDGK PLEVEVTLDS 360
  361 NTSSSASAEM IAPALQGATL SDGQLKDGTK GVKVDSVEKS SPAAQAGLQK DDVIIGVNRD 420
  421 RISSIAEMRK VMAAKPSIIA LQVVRGNENI YLLLR

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	84.154902
Match:	1ky9A
Description:	Protease Do (DegP, HtrA), C-terminal domains; Protease Do (DegP, HtrA), catalytic domain
Matching Structure (courtesy of the PDB):

Predicted functions:

Term	Confidence	Notes
peptidase activity	5.28251016030465	bayes_pls_golite062009
peptidase activity, acting on L-amino acid peptides	4.93232564230667	bayes_pls_golite062009
endopeptidase activity	4.76863192965644	bayes_pls_golite062009
hydrolase activity	4.7420645083083	bayes_pls_golite062009
serine hydrolase activity	3.40985043278892	bayes_pls_golite062009
serine-type peptidase activity	3.40724860044542	bayes_pls_golite062009
serine-type endopeptidase activity	3.13486560415684	bayes_pls_golite062009
catalytic activity	1.40927913545237	bayes_pls_golite062009
protein binding	0.0013332686405948	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: