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COFACTOR result for job id 76402

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>76402 (872 residues)
MKKQLNPKYDHLQVEKDKYQYWLDKNLFKADINSNKPKFSIILPPPNVTGKLHIGHAWDT
SLQDAIIRFKKLTGYDTLFLPGMDHSGISTQVKVEAKLKQQGIDKNKLGREKFLLEAWKW
KEEYANIIRKQWAKLGLSLDYSTEKFTLDEDINQIVKEIFVKFYNDQIIYKDKQIVNWDP
EQKTAISNVEVIYKETQSKMYYFKYMLEDSNEYLTVATTRPETMFVDQCLVVNPNDSRYQ
KYINKKVINPVNKQVIPIISDEYVDIEFGTGVMKCTPAHDLNDYHLAIKHNLKMPICLNI
DGSVNQLGGKYQGLDRFVARKEIIKNAINEDLFVKEEDIINQVGFSERSNAIVEPYLSDQ
WFVKMDKFKNMVIDLQNSDNKINFYPNRFSDVLNRWMTNAHDWCISRQLWWGHQIPCWYH
KKTNEMYVGINPPSDIENWTQDQDVLDTWFSSGLWAFSTLLNNKGLESEYFKNYFPTSVL
VTGYDIIFFWVARMIFQTLEYTKQIPFKDVLIHGLVRDELNRKMSKSLGNGIDPMDVINN
NGCDSLRLFLLTNSTPGQDIRYSNEKILASSNFINKLWNASRYVFLNLDKDFKFDQNFYK
TDLEITNQWILTELSKTQAYVYEKMNKYEFSLAGNHLWDFVWNKYCSWYIEFSKVNLNND
KFNHQTKQTLFYVLKEILIMIHPLIPFVSEEIYLNMMLKESILLEQWTNLNSNYDTSFID
DVIKMITSIREFKNTKNIKNDVCLSVNVSNTNQNHTKLFKKHFDQIYSFLINFCNTKLVD
YVIKNKTSLSIDEYFIEIANDSFINKNELIKELEQKQNHLNNEITRSQKILNNQEFIKKA
KPEKIQSEKIKYQNYLDQLQAIKDKLKELKND

Download query sequence and structure

Proteins with similar structure

Top 10 structural analogs in PDB (as identified by TM-align)

Rank	PDB Hit	TM-score	RMSD^a	IDEN^a	Cov.	Download Alignment
1	1ivsA	0.97	0.62	0.347	0.973	Download
2	1ffyA	0.77	4.52	0.179	0.876	Download
3	1jzsA	0.77	3.43	0.228	0.837	Download
4	1wz2A	0.66	5.22	0.141	0.784	Download
5	2v0gA	0.60	3.74	0.194	0.652	Download
6	4aq7A	0.59	3.82	0.188	0.644	Download
7	5ah5A	0.58	3.62	0.207	0.635	Download
8	6q89A	0.57	3.66	0.190	0.622	Download
9	3ziuB	0.56	2.54	0.217	0.593	Download
10	5gl7A	0.53	4.16	0.139	0.594	Download

(a)	Query structure is shown in cartoon, while the structural analog is displayed using backbone trace.
(b)	Ranking of proteins is based on TM-score of the structural alignment between the query structure and known structures in the PDB library.
(c)	RMSD^a is the RMSD between residues that are structurally aligned by TM-align.
(d)	IDEN^a is the percentage sequence identity in the structurally aligned region.
(e)	Cov. represents the coverage of the alignment by TM-align and is equal to the number of structurally aligned residues divided by length of the query protein.

Predicted Gene Ontology (GO) Terms

Molecular Function (MF)

GO term	Cscore^GO	Name
GO:0004812	1.00	aminoacyl-tRNA ligase activity
GO:0004832	0.60	valine-tRNA ligase activity
GO:1901363	0.52	heterocyclic compound binding
GO:0097159	0.52	organic cyclic compound binding
GO:0016787	0.51	hydrolase activity

Download full result of the above consensus prediction.

Click the graph to show a high resolution version.

(a)

Cscore^GO is the confidence score of predicted GO terms. Cscore^GO values range in between [0-1]; where a higher value indicates a better confidence in predicting the function using the template.

(b)

The graph shows the predicted terms within the Gene Ontology hierachy for Molecular Function. Confidently predicted terms are color coded by Cscore^GO:

[0.4,0.5)

[0.5,0.6)

[0.6,0.7)

[0.7,0.8)

[0.8,0.9)

[0.9,1.0]

Biological Process (BP)

GO term	Cscore^GO	Name
GO:1901564	1.00	organonitrogen compound metabolic process
GO:0044763	1.00	single-organism cellular process
GO:0043170	1.00	macromolecule metabolic process
GO:0006139	1.00	nucleobase-containing compound metabolic process
GO:0006418	0.99	tRNA aminoacylation for protein translation
GO:0006438	0.60	valyl-tRNA aminoacylation

Download full result of the above consensus prediction.

Click the graph to show a high resolution version.

(a)

Cscore^GO is the confidence score of predicted GO terms. Cscore^GO values range in between [0-1]; where a higher value indicates a better confidence in predicting the function using the template.

(b)

The graph shows the predicted terms within the Gene Ontology hierachy for Biological Process. Confidently predicted terms are color coded by Cscore^GO:

[0.4,0.5)

[0.5,0.6)

[0.6,0.7)

[0.7,0.8)

[0.8,0.9)

[0.9,1.0]

Cellular Component (CC)

GO term	Cscore^GO	Name
GO:0044444	1.00	cytoplasmic part
GO:0005737	1.00	cytoplasm
GO:0005829	0.99	cytosol

Download full result of the above consensus prediction.

Click the graph to show a high resolution version.

(a)

Cscore^GO is the confidence score of predicted GO terms. Cscore^GO values range in between [0-1]; where a higher value indicates a better confidence in predicting the function using the template.

(b)

The graph shows the predicted terms within the Gene Ontology hierachy for Cellular Component. Confidently predicted terms are color coded by Cscore^GO:

[0.4,0.5)

[0.5,0.6)

[0.6,0.7)

[0.7,0.8)

[0.8,0.9)

[0.9,1.0]

Predicted Enzyme Commission (EC) Numbers

Top 5 enzyme homologs in PDB

Rank	Cscore^EC	PDB Hit	TM-score	RMSD^a	IDEN^a	Cov.	EC Number	Predicted Active Site Residues
1	0.241	1gaxA	0.968	0.73	0.347	0.973	6.1.1.9	NA
2	0.131	1ffyA	0.768	4.52	0.179	0.876	6.1.1.5	NA
3	0.083	1a8hA	0.505	2.97	0.187	0.544	6.1.1.10	NA
4	0.078	2ct8A	0.468	2.89	0.213	0.502	6.1.1.10	NA
5	0.067	1pg0A	0.470	3.08	0.158	0.507	6.1.1.10	NA

	Click on the radio buttons to visualize predicted active site residues.
(a)	Cscore^EC is the confidence score for the Enzyme Commission (EC) number prediction. Cscore^EC values range in between [0-1]; where a higher score indicates a more reliable EC number prediction.
(b)	TM-score is a measure of global structural similarity between query and template protein.
(c)	RMSD^a is the RMSD between residues that are structurally aligned by TM-align.
(d)	IDEN^a is the percentage sequence identity in the structurally aligned region.
(e)	Cov. represents the coverage of global structural alignment and is equal to the number of structurally aligned residues divided by length of the query protein.

Predicted Ligand Binding Sites

Template proteins with similar binding site:

Click to view	Rank	Cscore^LB	PDB Hit	TM-score	RMSD^a	IDEN^a	Cov.	BS-score	Lig. Name	Download Complex	Predicted binding site residues
	1	0.01	3c8zA	0.374	3.23	0.119	0.405	0.10	5CA	Download	53,56,57

	Click on the radio buttons to visualize predicted binding site and residues.
(a)	Cscore^LB is the confidence score of predicted binding site. Cscore^LB values range in between [0-1]; where a higher score indicates a more reliable ligand-binding site prediction.
(b)	BS-score is a measure of local similarity (sequence & structure) between template binding site and predicted binding site in the query structure. Based on large scale benchmarking analysis, we have observed that a BS-score >1 reflects a significant local match between the predicted and template binding site.
(c)	TM-score is a measure of global structural similarity between query and template protein.
(d)	RMSD^a the RMSD between residues that are structurally aligned by TM-align.
(e)	IDEN^a is the percentage sequence identity in the structurally aligned region.
(f)	Cov. represents the coverage of global structural alignment and is equal to the number of structurally aligned residues divided by length of the query protein.

[Download result.tar.bz2 for all prediction results]

Reference:

Chengxin Zhang, Peter L Freddolino, and Yang Zhang. COFACTOR: Improved protein function prediction by combining structure, sequence, and protein-protein interaction information. Nucleic Acids Research, 45: W291-299 (2017)
Ambrish Roy, Jianyi Yang, and Yang Zhang. COFACTOR: An accurate comparative algorithm for structure-based protein function annotation. Nucleic Acids Research, 40:W471-W477 (2012).

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