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COFACTOR result for job id 76643

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

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>76643 (531 residues)
MKVKRPVLLAILDGWGISEPDKGNAVDNANMVFVEYLKKTYPWLKAHASGKWVGLPDNQM
GNSEVGHIHLGAGRINLESLAKLNHETKTNNIAKNEEIVKSFEYVKNNNSALHLMGLFSN
GGVHSHFDHMIAIYKAAIDYGITNIKFDLITDGRDTKPKLAYDFVKDLLELIKQNNNIGV
ISSISGRYYAMDRDKRFDRSRIAYNAITNRNNVRSFTNILDYIQQEYMINHDDEMIIPAF
NQDDLNGNLKANDAIIMTNFRPDRAIQISSILTNKNYIAWQSEAFSDAEFIGDKIRFVSM
MKYSDSITSPHIAYPPKPLTNTLGQYLSKLGLKQLRIAETEKIAHVTFFFDGGNDYFKNG
LAKNDEITLANAYIDLIPSAKVATYDLKPQMSAVEITDKLLEEIKKDEFDFIVLNFANCD
MVGHTGNNKATEIACKTLDEQLKRIHEEFVLRHNGIMIITADHGNAEIMIDKDGQVNKKH
TTSLVPIIITDLNIKLKQNDPAIAKVAPTILDLMNIEIPKEMELESMIDHN

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	1o98A	0.95	0.44	0.425	0.953	Download
2	5vpuA	0.94	1.22	0.409	0.957	Download
3	3igyB	0.93	1.75	0.295	0.962	Download
4	4my4A	0.71	4.69	0.292	0.898	Download
5	5kglA	0.58	4.79	0.272	0.699	Download
6	3m8wA	0.51	4.33	0.155	0.606	Download
7	3q3qA	0.48	4.72	0.142	0.591	Download
8	2zktB	0.46	4.65	0.130	0.563	Download
9	2vqrA	0.44	3.82	0.161	0.505	Download
10	2i09B2	0.41	2.85	0.197	0.446	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:0016853	0.97	isomerase activity
GO:0016868	0.96	intramolecular transferase activity, phosphotransferases
GO:0004619	0.94	phosphoglycerate mutase activity
GO:0046537	0.89	2,3-bisphosphoglycerate-independent phosphoglycerate mutase activity
GO:0043167	0.87	ion binding
GO:0046914	0.86	transition metal ion binding
GO:0030145	0.85	manganese ion binding

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	0.99	cellular process
GO:0071704	0.98	organic substance metabolic process
GO:0044237	0.98	cellular metabolic process
GO:0044238	0.96	primary metabolic process
GO:0034641	0.94	cellular nitrogen compound metabolic process
GO:1901360	0.93	organic cyclic compound metabolic process
GO:0044699	0.93	single-organism process
GO:0044763	0.92	single-organism cellular process
GO:0006139	0.92	nucleobase-containing compound metabolic process
GO:1901564	0.91	organonitrogen compound metabolic process
GO:1901135	0.91	carbohydrate derivative metabolic process
GO:0044281	0.91	small molecule metabolic process
GO:0005975	0.90	carbohydrate metabolic process
GO:1901575	0.89	organic substance catabolic process
GO:0019752	0.89	carboxylic acid metabolic process
GO:0019637	0.89	organophosphate metabolic process
GO:0006796	0.89	phosphate-containing compound metabolic process
GO:0016052	0.88	carbohydrate catabolic process
GO:0009117	0.88	nucleotide metabolic process
GO:0006096	0.87	glycolytic process
GO:0005996	0.85	monosaccharide metabolic process
GO:0006006	0.84	glucose metabolic process
GO:0044282	0.80	small molecule catabolic process
GO:0006007	0.79	glucose catabolic process
GO:0065007	0.73	biological regulation
GO:0050789	0.73	regulation of biological process
GO:0050793	0.68	regulation of developmental process
GO:1901576	0.67	organic substance biosynthetic process
GO:0032502	0.63	developmental process
GO:0044767	0.62	single-organism developmental process
GO:0043937	0.62	regulation of sporulation
GO:0044262	0.59	cellular carbohydrate metabolic process
GO:0048869	0.56	cellular developmental process
GO:0044283	0.54	small molecule biosynthetic process
GO:0043170	0.53	macromolecule metabolic process
GO:0030154	0.51	cell differentiation
GO:0048646	0.50	anatomical structure formation involved in morphogenesis
GO:0006094	0.50	gluconeogenesis

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:0005829	0.82	cytosol
GO:0043226	0.52	organelle
GO:0043229	0.51	intracellular organelle
GO:0043227	0.50	membrane-bounded organelle

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	0.067	2ifyA	0.593	5.18	0.315	0.753	5.4.2.1	NA
2	0.066	2zktB	0.464	4.65	0.130	0.563	5.4.2.1	53,55
3	0.060	3b8eC	0.392	6.58	0.066	0.586	3.6.3.9	460
4	0.060	1mo7A	0.163	6.44	0.024	0.243	3.6.3.9	NA
5	0.060	1fsuA	0.441	4.21	0.111	0.516	3.1.6.12	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	0.58	1eqjA	0.948	0.44	0.426	0.951	1.65	MN	Download	13,62,63,342,462,463

	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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