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COFACTOR result for job id 76492

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>76492 (754 residues)
MHNKYNYISFDYREIKDFKDLLNELKKYIKNKSELERIEQAYKYAFKCHFNQTRKNGDPY
IYHPLSAAYYLAQWRMGPNTIIAGLLHDILEDTPIQKEELVELFNEEVANLVESVTKVSF
FAKENRQQIKSKYLRKLYLSMSKDIRVIIIKIADRLHNIYTIKNLRPEKQKIIAQETLEI
YSAIAHRIGMKSAKSLLEDRSFEILNPQEFKKITDLFNSDMQNRQQIINEIIINLEQYLK
KEKNIKIISIFGRPKTIYSIYRKMNVIGKNFEEISDLLAIRIIAKSIDDCYKILGFIHQK
YIPLAGKFKDYIATPKNNVYQSLHTTLSDANGNIFEVQIRTEEMNQVAETGAAAHWRYKE
GEIIDIAKKQKEIDEKIDIFSRILDLDKSEDQQSSIEQSIKDDLFTASIYVLTPNGAVIT
LPYGSTVLDFAYRIHTEIGEKTIGARVDGVFLPINTVLKSGEVVEVKTSPKQEPTHEWLK
IVVTSNARNRIKKYLQKKINEETLDKKDQQKELIRKTEANINAYINQKDWKWKKKTADEI
LETVKTMDYNSLNDFLLDVAKGEFTINEAAEKVFIKQNYSKDDEAYASIKSKIIYDTTIK
NDILVDGIKNIKTTLASCCMPIPYEEVVGFVTKNNGIKVHLKECINIDWTNMKSRLVVVQ
WNEAVAEKNTYTTKLKYFGIDRNKLLYDISKIISGLKVSIINANIFTDEKSLLSSGVITI
KIKNSNQLTQTISALRSIPGINGVERGISNQKIK

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	5kpv33	0.87	0.98	0.286	0.882	Download
2	5iqr8	0.75	2.55	0.294	0.800	Download
3	1vj7A	0.43	1.08	0.423	0.432	Download
4	5xnxA	0.41	2.43	0.393	0.427	Download
5	4o9xA	0.36	8.47	0.030	0.576	Download
6	6eqoA	0.36	8.29	0.025	0.561	Download
7	5cskA	0.34	7.97	0.044	0.524	Download
8	2pffB	0.34	8.51	0.034	0.540	Download
9	3k1qA	0.33	8.30	0.051	0.530	Download
10	2uvcG	0.29	8.33	0.024	0.468	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:0016740	0.99	transferase activity
GO:0016772	0.98	transferase activity, transferring phosphorus-containing groups
GO:0016788	0.97	hydrolase activity, acting on ester bonds
GO:0008728	0.97	GTP diphosphokinase activity
GO:0008893	0.96	guanosine-3',5'-bis(diphosphate) 3'-diphosphatase 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:0071704	1.00	organic substance metabolic process
GO:0044763	1.00	single-organism cellular process
GO:0044238	1.00	primary metabolic process
GO:0044237	1.00	cellular metabolic process
GO:0006807	1.00	nitrogen compound metabolic process
GO:0044281	0.99	small molecule metabolic process
GO:0006139	0.99	nucleobase-containing compound metabolic process
GO:1901564	0.98	organonitrogen compound metabolic process
GO:0055086	0.97	nucleobase-containing small molecule metabolic process
GO:0042594	0.97	response to starvation
GO:1901068	0.96	guanosine-containing compound metabolic process
GO:0034035	0.96	purine ribonucleoside bisphosphate metabolic process
GO:0009259	0.96	ribonucleotide metabolic process
GO:0006163	0.96	purine nucleotide metabolic process
GO:0015969	0.94	guanosine tetraphosphate metabolic process
GO:0043170	0.57	macromolecule 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	0.96	intracellular part
GO:0016020	0.84	membrane
GO:0044444	0.83	cytoplasmic part
GO:0005886	0.74	plasma membrane
GO:0043229	0.73	intracellular organelle
GO:0043231	0.70	intracellular membrane-bounded organelle
GO:0005618	0.64	cell wall

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	2ckjA	0.247	8.37	0.027	0.397	1.17.1.4 1.17.3.2	NA
2	0.060	2vkzG	0.299	8.90	0.034	0.500	2.3.1.38 3.1.2.14	NA
3	0.060	3b8cB	0.273	8.75	0.042	0.450	3.6.3.6	71
4	0.060	3ixzA	0.284	8.70	0.034	0.468	3.6.3.10	NA
5	0.060	2qtcB	0.286	8.05	0.052	0.444	1.2.4.1	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:

Rank	Cscore^LB	PDB Hit	TM-score	RMSD^a	IDEN^a	Cov.	BS-score	Lig. Name	Download Complex	Predicted binding site residues
1	0.05	1vj7A	0.428	1.08	0.423	0.432	0.14	GDP	Download	77,79,87
2	0.01	3lq4B	0.288	7.81	0.023	0.439	0.14	TDP	Download	21,81,83
3	0.01	1l8aA	0.279	7.96	0.040	0.428	0.16	TDP	Download	21,38,39,81,86
4	0.01	2vz9A	0.288	8.98	0.032	0.488	0.10	NAP	Download	49,50,53,85,86,87,152
5	0.01	2qtcB	0.286	8.05	0.052	0.444	0.14	TDK	Download	49,51,61,84,85
6	0.01	2g25B	0.282	7.86	0.036	0.431	0.11	TDK	Download	37,87,110
7	0.01	3lplB	0.287	7.98	0.039	0.446	0.20	TDP	Download	33,79,80,81,82
8	0.01	2g25B	0.282	7.86	0.036	0.431	0.21	TDK	Download	78,81,85

	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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