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COFACTOR result for job id 76426

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>76426 (1482 residues)
MQTKILSIFKKIGIELDQTDYIYFKDAILVETPRISQIKNKGYLHIEIKDFLPIDVLKKI
EDKLKNNQYFNFKLIIDVKNQEFNKDLLIQYLEFIKMHKSLFNNRSSWKLLDIYNFELIN
NQLVFLVNSQTIKNEISLELDYCLAKLNQFGFKDLSYLINVNEISLDTLDTKQQINKTYD
KPEYEQQIIKPIEKKPSTNNSYKNKRPSLDKPSYNSLLDVEDDAQNIVIQGMVINKEFKL
SKTGRKIFYIDITDFQSSIRCMYFAKSDALCEFDDLTEDELKSKEIQQIKENKIQINDWI
SVKGKTSLSIYDQEQIFYIDDFKKIKKQVDLRIDDAKIKRVELHAHTKMSVMDGVSDPID
YLELISSWNHKAIAFTDHTNVQAFPDIYKALNSINKKRSDQDKIKAIYGLEMNMLNNDLW
YVKNPKNQNLKDARMVFFDLETTGLSPELDEIIEFGAIEYNLKTGERKKIDILIKPKAKL
KAFTQKLTNITEKMLEDKPSIEQAFKQINEIIKDAILVAHNANFDFTFLSYWSEKLGYGK
LENTIIDTLTISRIIYPDLKSHRLGSLAKRVNISYDPSIAHRGDYDADILADIYERMLDE
TRKKIKIITDSDWNKIDPINYADNLNYYKNKGFHTNILVKNQAGLKELYKLVTKSHTTNF
YAFPKIFKDDLIQIKQNNNLLFGASCVNSEIFELARTSTLENLKQAISFYDYIEIQPISV
YKNLLQNDSLDLEQLKQIITNIINIAKQENKLIVASSDCHYTNPELKQIREVYINAKGLG
GIRHPLFDFNNRVKDYPDQHLRTTKEMLNEFEWLNDDDLINEIVITNSNKIADMIDSNVI
PIKDGLFTPKIANVNEKLKDKCYQTAKQMYGEMLPEIVEKRLEKELGSITKHGFAIVYWI
SHLLVKQSLDDGYLVGSRGSVGSSFVATMAQITEVNPLKAHYRCLNCKYSDFNTDPTYKC
GYDLPEKNCPDCNQKLIGDGHDIPFETFLGFDGDKVPDIDLNFSGEYQNQAHNFTKKMFG
ENNVFRAGTISTVAEKTAFGYVKTYFEETKKDVSLPRKTEINRLAKLAQGVKRTTGQHPG
GIIILPNEYEIEDFTPVNYPADDLNSTWKTTHFDFHSIHDNLLKMDILGHDDPTALKMLR
DLTNIDPITIPTDDKNVYSLFSSLQALNLTSDKINDEITGAIGIPEFGTGFVRNMLKETQ
PKTFADLVQISGLSHGTDVWLGNARDLIKDKKADISTVIGCRDDIMVYLINMGLESSLAF
MIMESVRKGKGLKKEWIDVMKQYNVPDWYIDSCLKIKYMFPKAHATAYVLMAYRIAWYKI
YYPTEYYATYLTTRADVFDLKTALGGYDAVLLKLKSQQQRVKNGEKLSKKEEDLEVVYEV
LLEMFARGIKFSNIDFEKSEATKFKVDILQDNSKIIIPPFNVIDSLGEAVALSIINARNT
KPITSVNDLKNRTQTTQTQIKIFEEFNILDSLSVDEQLAFDF

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	3f2bA	0.66	1.54	0.507	0.665	Download
2	3e0dA	0.50	3.71	0.212	0.541	Download
3	5lewA	0.50	3.61	0.205	0.537	Download
4	2hqaA	0.48	3.98	0.206	0.520	Download
5	5kf6A	0.26	9.28	0.035	0.377	Download
6	3cu7A	0.25	10.49	0.044	0.395	Download
7	6eqoA	0.25	9.85	0.029	0.373	Download
8	4e4fA	0.13	6.92	0.055	0.167	Download
9	3e0fA	0.13	3.69	0.149	0.142	Download
10	1zmcD	0.13	6.92	0.040	0.161	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	0.92	catalytic activity
GO:0016740	0.74	transferase activity
GO:0016772	0.72	transferase activity, transferring phosphorus-containing groups
GO:0016779	0.70	nucleotidyltransferase activity
GO:0016787	0.69	hydrolase activity
GO:0097159	0.57	organic cyclic compound binding
GO:0016788	0.56	hydrolase activity, acting on ester bonds
GO:0004518	0.55	nuclease 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:0009987	0.96	cellular process
GO:0071704	0.92	organic substance metabolic process
GO:0044237	0.88	cellular metabolic process
GO:0043170	0.87	macromolecule metabolic process
GO:0044238	0.82	primary metabolic process
GO:1901360	0.81	organic cyclic compound metabolic process
GO:0046483	0.80	heterocycle metabolic process
GO:0006725	0.80	cellular aromatic compound metabolic process
GO:0006807	0.79	nitrogen compound metabolic process
GO:1901576	0.78	organic substance biosynthetic process
GO:0034641	0.76	cellular nitrogen compound metabolic process
GO:0044249	0.74	cellular biosynthetic process
GO:0009059	0.73	macromolecule biosynthetic process
GO:0006139	0.69	nucleobase-containing compound metabolic process
GO:0044260	0.64	cellular macromolecule metabolic process
GO:0090304	0.62	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:0044424	1.00	intracellular part
GO:0005737	0.87	cytoplasm
GO:0044444	0.75	cytoplasmic part
GO:0032991	0.63	macromolecular complex
GO:0043229	0.57	intracellular organelle
GO:0043227	0.55	membrane-bounded organelle
GO:0043231	0.54	intracellular membrane-bounded organelle
GO:0005829	0.52	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	0.163	3f2bA	0.656	1.54	0.507	0.665	2.7.7.7	NA
2	0.067	2hnhA	0.491	4.03	0.219	0.537	2.7.7.7	NA
3	0.060	1ug9A	0.169	9.40	0.023	0.250	3.2.1.70	NA
4	0.060	2ckjA	0.213	10.03	0.036	0.329	1.17.1.4 1.17.3.2	NA
5	0.060	2jfdA	0.114	7.51	0.028	0.150	2.3.1.85	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:

No Binding sites was predicted

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

	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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