YRC Public Data Repository - Protein Structure Prediction

Protein:	CLPX_YERPN
Organism:	Yersinia pestis Nepal516
Length:	423 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 CLPX_YERPN.

Description	E-value	Query Range	Subject Range
CLPX_SALTI - ATP-dependent Clp protease ATP-binding subunit ClpX OS=Salmonella typhi GN=clpX PE=3 SV=1 gi\|29138431, gi\|... - gi\|29142799\|ref\|NP_806141.1\| ATP-dependent protease ATP-binding subunit [Salmonella enterica subsp. ... gi\|214001924 - gi\|214001924\|ref\|ZP_03412659.1\| ATP-dependent protease ATP-binding subunit [Salmonella enterica subs... gi\|16759429 - gi\|16759429\|ref\|NP_455046.1\| ATP-dependent protease ATP-binding subunit [Salmonella enterica subsp. ... gi\|213160793 - gi\|213160793\|ref\|ZP_03346503.1\| ATP-dependent protease ATP-binding subunit [Salmonella enterica subs... gi\|213646004 - gi\|213646004\|ref\|ZP_03376057.1\| ATP-dependent protease ATP-binding subunit [Salmonella enterica subs... CLPX_SALTI - ATP-dependent Clp protease ATP-binding subunit clpX OS=Salmonella typhi GN=clpX PE=3 SV=1 gi\|213425857 - gi\|213425857\|ref\|ZP_03358607.1\| ATP-dependent protease ATP-binding subunit [Salmonella enterica subs...	2.0E-90	[1..423]	[1..423]
gi\|205333989, gi... - gi\|205333989\|gb\|EDZ20753.1\| ATP-dependent Clp protease, ATP-binding subunit ClpX [Salmonella enteric... gi\|197289504, gi... - gi\|197289504\|gb\|EDY28867.1\| ATP-dependent Clp protease, ATP-binding subunit ClpX [Salmonella enteric... gi\|168261114, gi... - gi\|205349962\|gb\|EDZ36593.1\| ATP-dependent Clp protease, ATP-binding subunit ClpX [Salmonella enteric... gi\|168465543, gi... - gi\|195631578\|gb\|EDX50098.1\| ATP-dependent Clp protease, ATP-binding subunit ClpX [Salmonella enteric... CLPX_SALPB - ATP-dependent Clp protease ATP-binding subunit clpX OS=Salmonella paratyphi B (strain ATCC BAA-1250 ... CLPX_SALPA - ATP-dependent Clp protease ATP-binding subunit ClpX OS=Salmonella paratyphi A GN=clpX PE=3 SV=1 CLPX_SALCH - ATP-dependent Clp protease ATP-binding subunit clpX OS=Salmonella choleraesuis GN=clpX PE=3 SV=1 gi\|205330906, gi... - gi\|205330906\|gb\|EDZ17670.1\| ATP-dependent Clp protease, ATP-binding subunit ClpX [Salmonella enteric... CLPX_SALPB - ATP-dependent Clp protease ATP-binding subunit ClpX OS=Salmonella paratyphi B (strain ATCC BAA-1250 ... CLPX_SALTY - ATP-dependent Clp protease ATP-binding subunit ClpX OS=Salmonella typhimurium (strain LT2 / SGSC1412... CLPX_SALDC - ATP-dependent Clp protease ATP-binding subunit ClpX OS=Salmonella dublin (strain CT_02021853) GN=clp... CLPX_SALCH - ATP-dependent Clp protease ATP-binding subunit ClpX OS=Salmonella choleraesuis GN=clpX PE=3 SV=1 gi\|199602471, gi... - gi\|200390026\|ref\|ZP_03216637.1\| ATP-dependent Clp protease, ATP-binding subunit ClpX [Salmonella ent... CLPX_SALG2 - ATP-dependent Clp protease ATP-binding subunit ClpX OS=Salmonella gallinarum (strain 287/91 / NCTC 1... CLPX_SALPC - ATP-dependent Clp protease ATP-binding subunit ClpX OS=Salmonella paratyphi C (strain RKS4594) GN=cl... CLPX_SALTY - ATP-dependent Clp protease ATP-binding subunit ClpX OS=Salmonella typhimurium GN=clpX PE=3 SV=1 CLPX_SALSV - ATP-dependent Clp protease ATP-binding subunit ClpX OS=Salmonella schwarzengrund (strain CVM19633) G... CLPX_SALA4 - ATP-dependent Clp protease ATP-binding subunit ClpX OS=Salmonella agona (strain SL483) GN=clpX PE=3 ... CLPX_SALPA - ATP-dependent Clp protease ATP-binding subunit ClpX OS=Salmonella paratyphi A (strain ATCC 9150 / SA... gi\|197263118, gi... - gi\|197263118\|ref\|ZP_03163192.1\| ATP-dependent Clp protease, ATP-binding subunit ClpX [Salmonella ent... CLPX_SALCH - ATP-dependent Clp protease ATP-binding subunit ClpX OS=Salmonella choleraesuis (strain SC-B67) GN=cl... CLPX_SALPK - ATP-dependent Clp protease ATP-binding subunit ClpX OS=Salmonella paratyphi A (strain AKU_12601) GN=... gi\|168818939, gi... - gi\|205344101\|gb\|EDZ30865.1\| ATP-dependent Clp protease, ATP-binding subunit ClpX [Salmonella enteric... lcl\|NC_016856.1_... - [gene=clpX] [protein=ATP-dependent protease ATP-binding subunit] [protein_id=YP_005236146.1] [locati... CLPX_SALNS - ATP-dependent Clp protease ATP-binding subunit ClpX OS=Salmonella newport (strain SL254) GN=clpX PE=... CLPX_SALHS - ATP-dependent Clp protease ATP-binding subunit ClpX OS=Salmonella heidelberg (strain SL476) GN=clpX ... gi\|194471272, gi... - gi\|194471272\|ref\|ZP_03077256.1\| ATP-dependent Clp protease, ATP-binding subunit ClpX [Salmonella ent... CLPX_SALTY - ATP-dependent Clp protease ATP-binding subunit clpX OS=Salmonella typhimurium GN=clpX PE=3 SV=1 gi\|238911420 - gi\|238911420\|ref\|ZP_04655257.1\| ATP-dependent protease ATP-binding subunit ClpX [Salmonella enterica...	2.0E-90	[1..423]	[1..423]
CLPX_YERPS - ATP-dependent Clp protease ATP-binding subunit ClpX OS=Yersinia pseudotuberculosis serotype I (strai... CLPX_YERPS - ATP-dependent Clp protease ATP-binding subunit ClpX OS=Yersinia pseudotuberculosis GN=clpX PE=3 SV=1	2.0E-90	[1..423]	[1..423]
gi\|7594817 - gi\|7594817\|dbj\|BAA94669.1\| ATPase subunit [Salmonella enterica subsp. enterica serovar Typhimurium] gi\|7594817\|dbj\|B... - ATPase subunit [Salmonella typhimurium]	3.0E-90	[1..423]	[1..423]
CLPX_ECO27 - ATP-dependent Clp protease ATP-binding subunit ClpX OS=Escherichia coli O127:H6 (strain E2348/69 / E... CLPX_ECOSE - ATP-dependent Clp protease ATP-binding subunit ClpX OS=Escherichia coli (strain SE11) GN=clpX PE=3 S... CLPX_ECO8A - ATP-dependent Clp protease ATP-binding subunit ClpX OS=Escherichia coli O8 (strain IAI1) GN=clpX PE=... gi\|217322070, gi... - gi\|217325849\|ref\|ZP_03441933.1\| ATP-dependent Clp protease, ATP-binding subunit ClpX [Escherichia co... CLPX_ECO81 - ATP-dependent Clp protease ATP-binding subunit ClpX OS=Escherichia coli O81 (strain ED1a) GN=clpX PE... CLPX_ECO45 - ATP-dependent Clp protease ATP-binding subunit ClpX OS=Escherichia coli O45:K1 (strain S88 / ExPEC) ... CLPX_ECO7I - ATP-dependent Clp protease ATP-binding subunit ClpX OS=Escherichia coli O7:K1 (strain IAI39 / ExPEC)... CLPX_ECO55 - ATP-dependent Clp protease ATP-binding subunit ClpX OS=Escherichia coli (strain 55989 / EAEC) GN=clp... CLPX_ECOSM - ATP-dependent Clp protease ATP-binding subunit ClpX OS=Escherichia coli (strain SMS-3-5 / SECEC) GN=... CLPX_ECODH - ATP-dependent Clp protease ATP-binding subunit ClpX OS=Escherichia coli (strain K12 / DH10B) GN=clpX... CLPX_SHIFL - ATP-dependent Clp protease ATP-binding subunit ClpX OS=Shigella flexneri GN=clpX PE=3 SV=2 gi\|188488172, gi... - gi\|188492973\|ref\|ZP_03000243.1\| ATP-dependent Clp protease, ATP-binding subunit ClpX [Escherichia co... CLPX_ECOLI - ATP-dependent Clp protease ATP-binding subunit clpX - Escherichia coli CLPX_SHIB3 - ATP-dependent Clp protease ATP-binding subunit ClpX OS=Shigella boydii serotype 18 (strain CDC 3083-... gi\|24050613, gi\|... - gi\|24111822\|ref\|NP_706332.1\| ATP-dependent protease ATP-binding subunit [Shigella flexneri 2a str. 3... gi\|208814875, gi... - gi\|208814875\|ref\|ZP_03256054.1\| ATP-dependent Clp protease, ATP-binding subunit ClpX [Escherichia co... CLPX_ECOL6 - ATP-dependent Clp protease ATP-binding subunit ClpX OS=Escherichia coli O6:H1 (strain CFT073 / ATCC ... gi\|208807403, gi... - gi\|208807403\|ref\|ZP_03249740.1\| ATP-dependent Clp protease, ATP-binding subunit ClpX [Escherichia co... gi\|30040184, gi\|... - gi\|30061940\|ref\|NP_836111.1\| ATP-dependent protease ATP-binding subunit [Shigella flexneri 2a str. 2... CLPX_ECO5E - ATP-dependent Clp protease ATP-binding subunit ClpX OS=Escherichia coli O157:H7 (strain EC4115 / EHE... CLPX_ECO57 - ATP-dependent Clp protease ATP-binding subunit ClpX OS=Escherichia coli O157:H7 GN=clpX PE=3 SV=2 gi\|208737100, gi... - gi\|208822907\|ref\|ZP_03263225.1\| ATP-dependent Clp protease, ATP-binding subunit ClpX [Escherichia co... CLPX_ECOLU - ATP-dependent Clp protease ATP-binding subunit ClpX OS=Escherichia coli O17:K52:H18 (strain UMN026 /... gi\|251783946, gi... - gi\|251783946\|ref\|YP_002998250.1\| hypothetical protein B21_00393 [Escherichia coli BL21], gi\|24237621... gi\|254287311, gi... - gi\|254287311\|ref\|YP_003053059.1\| ATP-dependent protease ATP-binding subunit [Escherichia coli BL21(D... gi\|253972408, gi... - gi\|254160507\|ref\|YP_003043615.1\| ATP-dependent protease ATP-binding subunit [Escherichia coli B str.... gi\|254791622, gi... - gi\|254791622\|ref\|YP_003076459.1\| ATPase and specificity subunit of ClpX-ClpP ATP-dependent serine pr... gi\|85674578, gi\|... - gi\|89107308\|ref\|AP_001088.1\| ATPase and specificity subunit of ClpX-ClpP ATP-dependent serine protea... CLPX_SHIDS - ATP-dependent Clp protease ATP-binding subunit ClpX OS=Shigella dysenteriae serotype 1 (strain Sd197... CLPX_ECOL6 - ATP-dependent Clp protease ATP-binding subunit ClpX OS=Escherichia coli O6 GN=clpX PE=3 SV=2 CLPX_SHISS - ATP-dependent Clp protease ATP-binding subunit ClpX OS=Shigella sonnei (strain Ss046) GN=clpX PE=3 S... EG10159 - ATPase and specificity subunit of ClpX-ClpP ATP-dependent serine protease / ATPase subunit of ClpXP ... gi\|12513300, gi\|... - gi\|15800168\|ref\|NP_286180.1\| ATP-dependent protease ATP-binding subunit [Escherichia coli O157:H7 ED... gi\|192929193, gi... - gi\|75257916\|ref\|ZP_00729394.1\| COG1219: ATP-dependent protease Clp, ATPase subunit [Escherichia coli... CLPX_ECOLC - ATP-dependent Clp protease ATP-binding subunit ClpX OS=Escherichia coli (strain ATCC 8739 / DSM 1576... gi\|168768393, gi... - gi\|189362383\|gb\|EDU80802.1\| ATP-dependent Clp protease, ATP-binding subunit ClpX [Escherichia coli O... CLPX_ECOHS - ATP-dependent Clp protease ATP-binding subunit ClpX OS=Escherichia coli O9:H4 (strain HS) GN=clpX PE... gi\|189357986, gi... - gi\|189357986\|gb\|EDU76405.1\| ATP-dependent Clp protease, ATP-binding subunit ClpX [Escherichia coli O... CLPX_ECO24 - ATP-dependent Clp protease ATP-binding subunit ClpX OS=Escherichia coli O139:H28 (strain E24377A / E... gi\|189373571, gi... - gi\|189373571\|gb\|EDU91987.1\| ATP-dependent Clp protease, ATP-binding subunit ClpX [Escherichia coli O... gi\|168778931, gi... - gi\|189002703\|gb\|EDU71689.1\| ATP-dependent Clp protease, ATP-binding subunit ClpX [Escherichia coli O... gi\|124498425, gi... - gi\|124531647\|ref\|ZP_01701835.1\| ATP-dependent Clp protease, ATP-binding subunit ClpX [Escherichia co... sp\|B7UJR1\|CLPX_ECO27 - ATP-dependent Clp protease ATP-binding subunit ClpX OS=Escherichia coli O127:H6 (strain E2348/69 / E... gi\|227838637, gi... - gi\|227884551\|ref\|ZP_04002356.1\| ATP-dependent protease ATP-binding subunit [Escherichia coli 83972],... gi\|226898777, gi... - gi\|237707567\|ref\|ZP_04538048.1\| ATP-dependent protease ATP-binding subunit [Escherichia sp. 3_2_53FA... CLPX_ECOBW - ATP-dependent Clp protease ATP-binding subunit ClpX OS=Escherichia coli (strain K12 / MC4100 / BW295... CLPX_ECOUT - ATP-dependent Clp protease ATP-binding subunit ClpX OS=Escherichia coli (strain UTI89 / UPEC) GN=clp... gi\|13359949, gi\|... - gi\|15829746\|ref\|NP_308519.1\| ATP-dependent protease ATP-binding subunit ClpX [Escherichia coli O157:... CLPX_ECOL5 - ATP-dependent Clp protease ATP-binding subunit ClpX OS=Escherichia coli O6:K15:H31 (strain 536 / UPE... CLPX_SHIF8 - ATP-dependent Clp protease ATP-binding subunit ClpX OS=Shigella flexneri serotype 5b (strain 8401) G... EG10159 - ATPase and specificity subunit of ClpX-ClpP ATP-dependent serine protease / ATPase subunit of ClpXP ... CLPX_ECOK1 - ATP-dependent Clp protease ATP-binding subunit ClpX OS=Escherichia coli O1:K1 / APEC GN=clpX PE=3 SV...	9.0E-90	[1..423]	[1..424]
CLPX_SHIBS - ATP-dependent Clp protease ATP-binding subunit ClpX OS=Shigella boydii serotype 4 (strain Sb227) GN=...	2.0E-89	[1..423]	[1..424]
gi\|238791432, gi... - gi\|77979390\|ref\|ZP_00834809.1\| COG1219: ATP-dependent protease Clp, ATPase subunit [Yersinia interme... gi\|238702548, gi... - gi\|238759261\|ref\|ZP_04620428.1\| ATP-dependent Clp protease ATP-binding subunit clpX [Yersinia aldova...	3.0E-89	[1..423]	[1..423]
gi\|238710697, gi... - gi\|238751007\|ref\|ZP_04612503.1\| ATP-dependent Clp protease ATP-binding subunit clpX [Yersinia rohdei... gi\|238715486, gi... - gi\|77956936\|ref\|ZP_00821008.1\| COG1219: ATP-dependent protease Clp, ATPase subunit [Yersinia bercovi... gi\|238720660, gi... - gi\|77962323\|ref\|ZP_00826144.1\| COG1219: ATP-dependent protease Clp, ATPase subunit [Yersinia mollare...	4.0E-89	[1..423]	[1..423]
gi\|238723957, gi... - gi\|77974302\|ref\|ZP_00829843.1\| COG1219: ATP-dependent protease Clp, ATPase subunit [Yersinia frederi...	4.0E-89	[1..423]	[1..423]
CLPX_YEREN - ATP-dependent Clp protease ATP-binding subunit ClpX OS=Yersinia enterocolitica GN=clpX PE=3 SV=1 CLPX_YERE8 - ATP-dependent Clp protease ATP-binding subunit ClpX OS=Yersinia enterocolitica serotype O:8 / biotyp...	7.0E-89	[1..423]	[1..423]

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Predicted Domain #1

Region A:
Residues: [1-63]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MTDKRKDGSG KLLYCSFCGK SQHEVRKLIA GPSVYICDEC VDLCNDIIRE EIKEVSPHRD  60
   61 RSS

[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: [64-423]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 LPTPHEIRHH LDDYVIGQEP AKKVLAVAVY NHYKRLRNGD TSNGIELGKS NILLIGPTGS  60
   61 GKTLLAETLA RLLDVPFTMA DATTLTEAGY VGEDVENIIQ KLLQKCDYDV QKAQRGIVYI 120
  121 DEIDKISRKS DNPSITRDVS GEGVQQALLK LIEGTIAAVP PQGGRKHPQQ EFLQVDTSKI 180
  181 LFICGGAFAG LDKVIGQRIN TGSGIGFGAV VKGQSEKATE GELLSQVEPE DLIKFGLIPE 240
  241 FIGRLPVVAT LSELSEDALI QILKEPKNAL TKQYQALFSL EGVELEFRDE ALTAIAKKAM 300
  301 ARKTGARGLR SIVEGALLDT MYDLPSMDSV EKVVVDESVI AGQSAPMLIY GQPEAQASGE 360
  361

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	53.0
Match:	1um8A
Description:	Crystal structure of helicobacter pylori ClpX
Matching Structure (courtesy of the PDB):

Predicted functions:

Term	Confidence	Notes
hydrolase activity	2.55157966585974	bayes_pls_golite062009
binding	1.41264401383678	bayes_pls_golite062009
catalytic activity	1.00104173493322	bayes_pls_golite062009
purine nucleotide binding	0.569910969126728	bayes_pls_golite062009
purine ribonucleotide binding	0.568840867400671	bayes_pls_golite062009
ribonucleotide binding	0.568779924702229	bayes_pls_golite062009
nucleotide binding	0.564275755355315	bayes_pls_golite062009
hydrolase activity, acting on acid anhydrides	0.546796591575762	bayes_pls_golite062009
hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides	0.543610140926125	bayes_pls_golite062009
pyrophosphatase activity	0.540750418412449	bayes_pls_golite062009
nucleoside-triphosphatase activity	0.517457589081898	bayes_pls_golite062009
ATP binding	0.1860481660648	bayes_pls_golite062009
adenyl ribonucleotide binding	0.152859582615242	bayes_pls_golite062009
adenyl nucleotide binding	0.138615225841109	bayes_pls_golite062009
nucleic acid binding	0.030747546048349	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: