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COFACTOR result for job id 76304

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>76304 (648 residues)
MNKKKKKSTFWFWIILIVGFIILLSVISITSRGTTQNLTIEQLNSLFDQGKPFNNVVLQR
NNIQGIDIITGWYNNGSGWTKFTVNTNPNAINGFSDAFKNFVWRSNTTRYTESSWFSLLS
SLLPMLILILFYIGLFYFMAKGGAAGAGANGLFGMGKNKARREKSNVKFSDVAGIEEEKS
ELVELVDYLKQPAKYASAGARAPKGVLMEGPPGTGKTLLAKAVAGEANVSFFSIAGSEFE
EMFVGVGASRVREMFNEAKKAAPAIIFIDEIDAVGRKRNSAIGTGTNEQTLNQLLVELDG
FETNSGIIVMAATNRVDVLDPALLRPGRFDRVIQVSLPDIKEREQILKLHARNKKIDPSI
DWHRIAERTPGFSGAQLENVLNEAAILMVREGKTVIGINEIDEAIDRVVGGPAKKSRAMT
MHDKEIVSYHESGHALIGLKLESASKVQKVTIIPRGNAGGYTIMTPKDETLFSSKTDLYA
MIAGYLGGRAAEEIKFGKDNVTTGAHDDFDKATAIARRMVMQFGMSELGITKFLTMADEA
YGKTEGSYSEKTAAKIDAEVERILEESYKLAIKVISENMETLELLAESLRVLETITAEQI
DYINKNKKLPEAVIYEKEKYKQEQEKINSGKIIDLDINDVKEEEDKDK

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	6az0A	0.67	0.61	0.434	0.676	Download
2	6nyyA	0.61	3.12	0.457	0.682	Download
3	3kdsE	0.61	2.56	0.520	0.656	Download
4	5e7pA	0.45	6.13	0.131	0.586	Download
5	6matA	0.45	5.35	0.182	0.551	Download
6	3cf1B	0.45	5.35	0.197	0.552	Download
7	5g4fA	0.45	5.76	0.189	0.568	Download
8	6mdmB	0.42	5.65	0.150	0.523	Download
9	5vy9A	0.42	5.62	0.091	0.531	Download
10	6e101	0.41	5.89	0.116	0.539	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:0016787	1.00	hydrolase activity
GO:0016887	0.99	ATPase activity
GO:0042623	0.91	ATPase activity, coupled
GO:1901363	0.64	heterocyclic compound binding
GO:0097159	0.64	organic cyclic compound binding
GO:0070011	0.61	peptidase activity, acting on L-amino acid peptides
GO:0008237	0.59	metallopeptidase activity
GO:0000166	0.57	nucleotide binding
GO:0017076	0.56	purine nucleotide binding
GO:0035639	0.55	purine ribonucleoside triphosphate binding
GO:0032555	0.55	purine ribonucleotide binding
GO:0030554	0.55	adenyl nucleotide binding
GO:0005524	0.54	ATP binding

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:0009987	0.97	cellular process
GO:0071704	0.92	organic substance metabolic process
GO:0044238	0.91	primary metabolic process
GO:0043170	0.87	macromolecule metabolic process
GO:0044237	0.85	cellular metabolic process
GO:0019538	0.81	protein metabolic process
GO:0044260	0.73	cellular macromolecule metabolic process
GO:0006508	0.73	proteolysis
GO:0006807	0.71	nitrogen compound metabolic process
GO:0016043	0.68	cellular component organization
GO:0065007	0.67	biological regulation
GO:0034641	0.67	cellular nitrogen compound metabolic process
GO:0050789	0.65	regulation of biological process
GO:0044699	0.65	single-organism process
GO:0050794	0.64	regulation of cellular process
GO:0044763	0.63	single-organism cellular process
GO:1901575	0.61	organic substance catabolic process
GO:1901360	0.61	organic cyclic compound metabolic process
GO:0031323	0.61	regulation of cellular metabolic process
GO:0006139	0.60	nucleobase-containing compound metabolic process
GO:0009057	0.59	macromolecule catabolic process
GO:0080090	0.58	regulation of primary metabolic process
GO:0060255	0.58	regulation of macromolecule metabolic process
GO:0030163	0.58	protein catabolic process
GO:1901576	0.57	organic substance biosynthetic process
GO:0051171	0.57	regulation of nitrogen compound metabolic process
GO:0044249	0.56	cellular biosynthetic process
GO:0019219	0.56	regulation of nucleobase-containing compound metabolic process
GO:0048518	0.55	positive regulation of biological process
GO:0031326	0.55	regulation of cellular biosynthetic process
GO:0010556	0.55	regulation of macromolecule biosynthetic process
GO:0010468	0.55	regulation of gene expression
GO:0031325	0.54	positive regulation of cellular metabolic process
GO:0006355	0.54	regulation of transcription, DNA-templated
GO:0051173	0.53	positive regulation of nitrogen compound metabolic process
GO:0010628	0.53	positive regulation of gene expression
GO:0045893	0.52	positive regulation of transcription, DNA-templated
GO:0044271	0.52	cellular nitrogen compound biosynthetic process
GO:0090304	0.51	nucleic acid 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	0.99	intracellular part
GO:0044444	0.89	cytoplasmic part
GO:0043229	0.75	intracellular organelle
GO:0043227	0.74	membrane-bounded organelle
GO:0044446	0.73	intracellular organelle part
GO:0043231	0.73	intracellular membrane-bounded organelle
GO:0016020	0.65	membrane
GO:0032991	0.62	macromolecular complex
GO:0005737	0.52	cytoplasm
GO:0005634	0.50	nucleus

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	0.060	1b0pA	0.322	8.30	0.036	0.529	1.2.7.1	NA
2	0.060	1djnA	0.337	8.24	0.039	0.563	1.5.8.2 1.5.99.7	NA
3	0.060	2e1qA	0.297	8.25	0.038	0.491	1.17.3.2 1.17.1.4	NA
4	0.060	1llwA	0.325	8.04	0.046	0.528	1.4.7.1	NA
5	0.060	2ckjA	0.290	8.04	0.037	0.468	1.17.1.4 1.17.3.2	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	0.40	2ce7A	0.388	3.35	0.403	0.426	1.48	ADP	Download	171,172,173,213,214,215,216,217,218,346,350,374,375,378

	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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