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COFACTOR result for job id 76717

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>76717 (447 residues)
MKIVIIGGAASGMTVASRLKKADKKAQIIVIQKEKYVSLGACGLPYFVANPSLKPTDLLA
RTVEQFIEQDILVYSESVVKKIDAENQKVWYEKNNQLLELDYDKLVISTGAKPIVPPIKG
IDLPNIFTLTRLEDATELKEKLKDKNIKKVAVIGSGFIGLECCEMLEHFNKEIVLIEKTS
RLNQRVFDQEITDLLEQNLIKNNVEIIKENGLKSITQTKDKRLSLTLDQNEELEVDLIIL
AIGFRPATEFLKDTKLEMLGNGAIVVDKHGRTNLKNIWSCGDCATVYHKITNQITYTPLA
TVARKFAKVVADDILNVNSEFVGTLQTAILKVFESELVATGVNETLAKELGYDIKTIFIK
DSDHPSYYPNPTPLALKLILNKKTNTLIGAQMYGSNLSVLRINFLISLIWNQIEINQELT
QVDLPYSPPFSRVVDIIHIALEKLIKN

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	2cduA	0.97	0.95	0.270	0.987	Download
2	5er0A	0.97	1.00	0.277	0.987	Download
3	3cgcA	0.97	1.18	0.313	0.987	Download
4	2bc0A	0.96	1.35	0.277	0.987	Download
5	1nhqA	0.96	1.54	0.257	0.991	Download
6	3nt6A	0.95	1.08	0.318	0.964	Download
7	3ictA	0.94	1.24	0.316	0.964	Download
8	1yqzA	0.94	1.40	0.289	0.969	Download
9	3kd9A	0.91	1.29	0.313	0.931	Download
10	3oc4A	0.86	2.21	0.276	0.924	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:0003824	1.00	catalytic activity
GO:0016491	0.99	oxidoreductase activity
GO:0000166	0.96	nucleotide binding
GO:0050660	0.95	flavin adenine dinucleotide binding
GO:0016651	0.85	oxidoreductase activity, acting on NAD(P)H
GO:0016667	0.82	oxidoreductase activity, acting on a sulfur group of donors
GO:0016668	0.81	oxidoreductase activity, acting on a sulfur group of donors, NAD(P) as acceptor
GO:0016853	0.72	isomerase activity
GO:0050661	0.71	NADP binding
GO:0050451	0.70	CoA-disulfide reductase activity
GO:0003756	0.70	protein disulfide isomerase activity

Download full result of the above consensus prediction.

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(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:0009987	1.00	cellular process
GO:0044699	0.99	single-organism process
GO:0008152	0.99	metabolic process
GO:0044763	0.98	single-organism cellular process
GO:0044710	0.98	single-organism metabolic process
GO:0065007	0.97	biological regulation
GO:0055114	0.97	ox.dat.gzion-reduction process
GO:0045454	0.96	cell redox homeostasis
GO:0044237	0.79	cellular metabolic process
GO:0071704	0.75	organic substance metabolic process
GO:0006807	0.64	nitrogen compound metabolic process
GO:0044238	0.63	primary metabolic process

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:0044464	1.00	cell part
GO:0044424	0.98	intracellular part
GO:0044444	0.89	cytoplasmic part
GO:0043226	0.73	organelle
GO:0043229	0.72	intracellular organelle
GO:0043227	0.71	membrane-bounded organelle
GO:0043231	0.70	intracellular membrane-bounded organelle
GO:0005737	0.60	cytoplasm
GO:0005739	0.56	mitochondrion
GO:0044446	0.50	intracellular organelle part

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	0.443	3ladA	0.799	3.41	0.175	0.928	1.8.1.4	186
2	0.411	3kd9A	0.906	1.29	0.313	0.931	1.8.1.14	111,113,115,128,153,240,298
3	0.405	1zdlA	0.812	3.20	0.157	0.926	1.8.1.9	164
4	0.371	3fg2P	0.821	2.76	0.213	0.897	1.18.1.3	34,44,111,157,159,282,303
5	0.363	2v3aA	0.783	2.51	0.214	0.846	1.18.1.1	110,114,115,156,158,241,282,299

	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:

Rank	Cscore^LB	PDB Hit	TM-score	RMSD^a	IDEN^a	Cov.	BS-score	Lig. Name	Download Complex	Predicted binding site residues
1	0.74	3ntaA	0.976	1.09	0.310	0.996	1.42	FAD	Download	6,7,9,10,11,32,33,41,42,45,77,78,79,108,109,110,129,130,157,158,281,282,298,299,300,303
2	0.24	3ntdB	0.978	1.01	0.310	0.996	1.33	COA	Download	9,10,13,14,17,18,21,38,39,41,42,60,61,300,304,308
3	0.07	3cgdA	0.971	0.99	0.313	0.987	0.94	NAD	Download	153,154,156,157,158,161,176,177,178,241,242,243,244,298,299,329
4	0.06	3iwa0	0.824	2.02	0.249	0.870	1.03	III	Download	14,18,304,305,308,319,320,321,324,325,326,327,328,329,338,402,403,404,407,408,434,438

	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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