YRC Public Data Repository - Protein Structure Prediction

Protein:	gi\|229838759, gi...
Organism:	Yersinia pestis biovar Orientalis str. PEXU2
Length:	784 amino acids
Reference:	Drew K, et al. (2011) The proteome folding project: Proteome-scale prediction of structure and function. Genome Res. 2011 Sep 16

[What does the above image mean?]

[Show Ginzu Version Information]

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|229838759, gi....

Description	E-value	Query Range	Subject Range
gi\|88920619, gi\|... - gi\|88940588\|ref\|ZP_01146023.1\| ATP-dependent protease La [Acidiphilium cryptum JF-5], gi\|88920619\|gb...	0.0	[4..783]	[16..794]
gi\|77635227, gi\|... - gi\|77635227\|ref\|ZP_00797314.1\| COG0466: ATP-dependent Lon protease, bacterial type [Yersinia pestis ...	0.0	[1..784]	[1..784]
gi\|108808641, gi... - gi\|108808641\|ref\|YP_652557.1\| DNA-binding ATP-dependent protease La [Yersinia pestis Antiqua], gi\|10... gi\|145600050, gi... - gi\|145600050\|ref\|YP_001164126.1\| DNA-binding ATP-dependent protease La [Yersinia pestis Pestoides F]... gi\|22124936, gi\|... - gi\|22124936\|ref\|NP_668359.1\| DNA-binding ATP-dependent protease La [Yersinia pestis KIM], gi\|2195777... gi\|45435482, gi\|... - gi\|45440625\|ref\|NP_992164.1\| DNA-binding ATP-dependent protease La [Yersinia pestis biovar Microtus ... gi\|108774748, gi... - gi\|108811100\|ref\|YP_646867.1\| DNA-binding ATP-dependent protease La [Yersinia pestis Nepal516], gi\|1...	0.0	[1..784]	[19..802]
gi\|238723958, gi... - gi\|77974301\|ref\|ZP_00829842.1\| COG0466: ATP-dependent Lon protease, bacterial type [Yersinia frederi... gi\|122090301, gi... - gi\|123443340\|ref\|YP_001007314.1\| DNA-binding ATP-dependent protease La [Yersinia enterocolitica subs...	0.0	[1..784]	[1..784]
gi\|238720659, gi... - gi\|77962324\|ref\|ZP_00826145.1\| COG0466: ATP-dependent Lon protease, bacterial type [Yersinia mollare...	0.0	[1..784]	[1..784]
gi\|77956935, gi\|... - gi\|77956935\|ref\|ZP_00821007.1\| COG0466: ATP-dependent Lon protease, bacterial type [Yersinia bercovi...	0.0	[1..784]	[1..784]
gi\|238729049, gi... - gi\|77979389\|ref\|ZP_00834808.1\| COG0466: ATP-dependent Lon protease, bacterial type [Yersinia interme...	0.0	[1..784]	[1..784]
gi\|187427314, gi... - gi\|75177623\|ref\|ZP_00697704.1\| COG0466: ATP-dependent Lon protease, bacterial type [Shigella boydii ... gi\|82542927, gi\|... - gi\|82542927\|ref\|YP_406874.1\| DNA-binding ATP-dependent protease La [Shigella boydii Sb227], gi\|81244...	0.0	[1..784]	[1..784]
gi\|146644 - gi\|146644\|gb\|AAA24079.1\| ATP-dependent proteinase (lon) [Escherichia coli]	0.0	[1..777]	[1..777]
gi\|304908 - gi\|304908\|gb\|AAA16837.1\| ATP-dependent protease [Escherichia coli str. K-12 substr. W3110] gi\|304908 - gi\|304908\|gb\|AAA16837.1\| ATP-dependent protease	0.0	[1..784]	[1..784]

Back

Predicted Domain #1

Region A:
Residues: [1-121]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MNPERSERIE IPVLPLRDVV VYPHMVIPLF VGREKSIRCL EAAMDHDKRI MLVAQKEAST  60
   61 DEPGINDLFS VGTVASILQM LKLPDGTVKV LVEGLQRARI TTLSDSGEHF AAQAEYLESP 120
  121 V

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	27.39794
Match:	2aneA
Description:	Crystal structure of N-terminal domain of E.Coli Lon Protease
Matching Structure (courtesy of the PDB):

Predicted functions:

Term	Confidence	Notes
binding	1.06253923016595	bayes_pls_golite062009
nucleic acid binding	0.436354359069435	bayes_pls_golite062009
catalytic activity	0.147263815852997	bayes_pls_golite062009
protein binding	0.124422697243688	bayes_pls_golite062009
DNA binding	0.109973109354783	bayes_pls_golite062009
transcription regulator activity	0.0749443638226208	bayes_pls_golite062009

Predicted Domain #2

Region A:
Residues: [122-199]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MDDREQEVLV RTAINQFEGY IKLNKKIPPE VLASLHSIDD AARLADTIAA HMPLKLNDKQ  60
   61 AVLEMFDITE RLEYLMAM

[Run NCBI BLAST on this sequence.]

Detection Method:	FFAS03
Confidence:	1.88
Match:	1zboA
Description:	Crystal Structure of the Hypothetical Protein BPP1347 from Bordetella parapertussis, Northeast Structural Genomics Target BoR27.
Matching Structure (courtesy of the PDB):

Predicted Domain #3

Region A:
Residues: [200-306]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MESEIDLLQV EKRIRNRVKK QMEKSQREYY LNEQMKAIQK ELGEMDDTPD EHEALKRKIE  60
   61 AAKMPKDARE KTEAELQKLK MMSPMSAEAT VVRGYIDWML QVPWNSR

[Run NCBI BLAST on this sequence.]

Detection Method:	FFAS03
Confidence:	1.91
Match:	1us7B
Description:	Complex of Hsp90 and P50
Matching Structure (courtesy of the PDB):

Predicted Domain #4

Region A:
Residues: [307-396]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 SKVKKDLVKA QEVLDTDHYG LERVKDRILE YLAVQSRVSK IKGPILCLVG PPGVGKTSLG  60
   61 QSIAKATGRQ YVRMALGGVR DEAEIRGHRR

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	3.39794
Match:	2c9oA
Description:	No description for 2c9oA was found.

Predicted Domain #5

Region A:
Residues: [397-493]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 TYIGSMPGKL IQKMAKVGVK NPLFLLDEID KMASDMRGDP ASALLEVLDP EQNVAFNDHY  60
   61 LEVDYDLSDV MFVATSNSMN IPAPLLDRME VIRLSGY

[Run NCBI BLAST on this sequence.]

Detection Method:	FFAS03
Confidence:	2.26
Match:	1ksfX
Description:	N-terminal, ClpS-binding domain of ClpA, an Hsp100 chaperone; ClpA, an Hsp100 chaperone, AAA+ modules
Matching Structure (courtesy of the PDB):

Predicted Domain #6

Region A:
Residues: [494-586]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 TEDEKLNIAK QHLLPKQFER NAIKKGELTI DDSAIMSIIR YYTREAGVRS LEREISKLCR  60
   61 KAVKNLLMDK TVKHIEINGD NLKDFLGVQK VDY

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	7.0
Match:	1qzmA
Description:	alpha-domain of ATPase
Matching Structure (courtesy of the PDB):

Predicted functions:

Term	Confidence	Notes
hydrolase activity	2.18454736627863	bayes_pls_golite062009
binding	1.95152348156631	bayes_pls_golite062009
catalytic activity	1.00104173493322	bayes_pls_golite062009
nucleic acid binding	0.775560967092349	bayes_pls_golite062009
purine nucleotide binding	0.428373955572763	bayes_pls_golite062009
purine ribonucleotide binding	0.424644011903671	bayes_pls_golite062009
ribonucleotide binding	0.424583288440993	bayes_pls_golite062009
nucleotide binding	0.422354428195324	bayes_pls_golite062009
DNA binding	0.226110787229935	bayes_pls_golite062009
hydrolase activity, acting on acid anhydrides	0.22341412535263	bayes_pls_golite062009
hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides	0.222180491809685	bayes_pls_golite062009
pyrophosphatase activity	0.219296317139543	bayes_pls_golite062009
nucleoside-triphosphatase activity	0.194147556947887	bayes_pls_golite062009
ATP binding	0.04834397972685	bayes_pls_golite062009
adenyl ribonucleotide binding	0.0149501427627318	bayes_pls_golite062009
adenyl nucleotide binding	0.00365326483311895	bayes_pls_golite062009

Predicted Domain #7

Region A:
Residues: [587-653]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 GRADTENRVG QVTGLAWTEV GGDLLTIETA CVPGKGKLTY TGSLGEVMQE SIQAALTVVR  60
   61 ARADKLG

[Run NCBI BLAST on this sequence.]

Detection Method:	Pfam
Confidence:	7.886057
Match:	PF05362.4
Description:	No description for PF05362.4 was found.

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 #8

Region A:
Residues: [654-784]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 INPDFYEKRD IHVHVPEGAT PKDGPSAGIA MCTALVSCLT GNPVRADVAM TGEITLRGLV  60
   61 LPIGGLKEKL LAAHRGGIKV VLIPDDNKRD LEEIPDNVIA DLEIHPVKRI DDVLAIALEH 120
  121 PAFGAQPVAP K

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	42.69897
Match:	1rr9A
Description:	Catalytic domain of E.coli Lon protease
Matching Structure (courtesy of the PDB):

Predicted functions:

Term	Confidence	Notes
hydrolase activity	1.18773479836745	bayes_pls_golite062009
structural constituent of ribosome	1.18642233210148	bayes_pls_golite062009
structural molecule activity	0.95398657951177	bayes_pls_golite062009
ribonuclease activity	0.927662190590087	bayes_pls_golite062009
catalytic activity	0.878454819018611	bayes_pls_golite062009
binding	0.806477220933291	bayes_pls_golite062009
peptidase activity	0.46678532223973	bayes_pls_golite062009
nucleic acid binding	0.417420176258912	bayes_pls_golite062009
3'-5'-exoribonuclease activity	0.41034151894281	bayes_pls_golite062009
exoribonuclease activity	0.343836551142441	bayes_pls_golite062009
exoribonuclease activity, producing 5'-phosphomonoesters	0.321834241843501	bayes_pls_golite062009
peptidase activity, acting on L-amino acid peptides	0.161393552073973	bayes_pls_golite062009
transcription regulator activity	0.0234248386796159	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:

Predicted functions: