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COFACTOR result for job id 76668

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

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>76668 (413 residues)
MNTKINPLIKESLNKELKRQQSHIELIASENYVSQAVLELNGSVLTNKYAEGYPGKRYYG
GCEFIDEIESLGIKTAKELFNAEHANIQPHSGSQANDAAYKALLEPKDRVVAMSLDAGGH
LTHGYHINFSGNTYDFRFYGVNKDTEQLDYQEIEKIILEHKPKLIVAGASAYSRIIDFKK
FREIADKVGAYLMVDMAHIAGLVAAGVHPNPMEYADIVTTTTHKTLRGSRGGLILCKQEF
AKKVDSAVFPGSQGGPLENLIAGKTQALLEASTDEFKEYGKQIVKNTKALANVLQENGLR
LVAGGSDNHLINVDVKSTLQITGKKAEKILESIGIICNKNMIPFDTEKPFYTSGIRLGTP
AMTTRGFKEEEFKQVGLIIVNALKDPSEENLEKLAKQVASLCEKFPIYQSIKY

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	3h7fB	0.98	1.10	0.494	0.995	Download
2	4j5uA	0.97	0.77	0.555	0.986	Download
3	1eqbB	0.97	0.83	0.541	0.986	Download
4	2vmnA	0.97	0.62	0.587	0.973	Download
5	1bj4A	0.96	1.22	0.475	0.988	Download
6	4wxbA	0.96	1.18	0.557	0.978	Download
7	6cczA	0.96	1.01	0.467	0.976	Download
8	2dkjA	0.96	0.94	0.584	0.971	Download
9	4o6zA	0.96	1.21	0.432	0.981	Download
10	3pgyC	0.94	0.74	0.627	0.954	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:0030170	1.00	pyridoxal phosphate binding
GO:0004372	1.00	glycine hydroxymethyltransferase activity
GO:0042802	0.71	identical protein binding
GO:0042803	0.67	protein homodimerization activity
GO:0036094	0.67	small molecule binding
GO:0070905	0.64	serine binding
GO:1901363	0.52	heterocyclic compound binding
GO:0097159	0.52	organic cyclic compound 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:0035999	1.00	tetrahydrofolate interconversion
GO:0019264	1.00	glycine biosynthetic process from serine
GO:0034641	0.85	cellular nitrogen compound metabolic process
GO:0050896	0.78	response to stimulus
GO:0042221	0.75	response to chemical
GO:0043603	0.71	cellular amide metabolic process
GO:0010033	0.71	response to organic substance
GO:1901575	0.68	organic substance catabolic process
GO:0051716	0.68	cellular response to stimulus
GO:0044248	0.68	cellular catabolic process
GO:0044282	0.67	small molecule catabolic process
GO:0016043	0.67	cellular component organization
GO:0006767	0.66	water-soluble vitamin metabolic process
GO:0006565	0.66	L-serine catabolic process
GO:0006139	0.66	nucleobase-containing compound metabolic process
GO:1901700	0.65	response to oxygen-containing compound
GO:0070887	0.65	cellular response to chemical stimulus
GO:0046655	0.65	folic acid metabolic process
GO:1904482	0.64	cellular response to tetrahydrofolate
GO:0043933	0.64	macromolecular complex subunit organization
GO:0065003	0.63	macromolecular complex assembly
GO:0051259	0.62	protein oligomerization
GO:0051262	0.61	protein tetramerization
GO:0044271	0.60	cellular nitrogen compound biosynthetic process
GO:1901362	0.52	organic cyclic compound biosynthetic process
GO:0043170	0.52	macromolecule metabolic process
GO:0019438	0.52	aromatic compound biosynthetic process
GO:0018130	0.52	heterocycle biosynthetic process
GO:0055086	0.51	nucleobase-containing small molecule metabolic process
GO:0051289	0.51	protein homotetramerization
GO:0034654	0.50	nucleobase-containing compound biosynthetic process
GO:0019637	0.50	organophosphate metabolic process
GO:0006796	0.50	phosphate-containing compound 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:0005737	1.00	cytoplasm
GO:0044444	0.97	cytoplasmic part
GO:0043229	0.80	intracellular organelle
GO:0043227	0.80	membrane-bounded organelle
GO:0043231	0.79	intracellular membrane-bounded organelle
GO:0005739	0.62	mitochondrion
GO:0005829	0.60	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	0.600	2vmzA	0.967	0.62	0.587	0.973	2.1.2.1	29,91,121,129,169,197,199,224,230,356
2	0.595	1rv3B	0.970	1.27	0.472	0.995	2.1.2.1	57
3	0.585	1dfoB	0.973	0.86	0.543	0.986	2.1.2.1	195,198,221,224,63
4	0.549	1eqbB	0.974	0.83	0.541	0.986	2.1.2.1	91,93,121,129,170,195,197,224,228,230,253
5	0.239	2dkjA	0.957	0.94	0.584	0.971	2.1.2.1	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	0.74	1kkpA	0.966	0.64	0.590	0.973	1.61	UUU	Download	29,91,92,93,120,169,170,195,197,198,221,223,224,356

	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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