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COFACTOR result for job id 76652

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>76652 (704 residues)
MESKIIEILKKNHHKISLNKLLTYFKALDYSLVKNYLDQLEKNNNIAISLENNIYLLDEI
YKKGTIKLNPKGFGFINDVNDLTTEDHFIAGVDLNNSIHQDEVVYILKQEEDNRLKAIVI
DLIKRNKVYLIGEINRSFDKRFLDFIPNDKSFDSFRFVIVNKNEFKYEEFNIIKAKIISC
KERKIFIRLIKIIGNSKKASDRILAIAEEFDIKTSFDKQTLDNAKQINLSTDKLEKEFLK
RQNNSLVNKTIVTIDGIDSKDLDDAICVEKLENNNYKLFVAIADVSYFVRYKTSLDKEAL
LRGNSTYLANKVIPMLPNILSDDLCSLNPNTKKLVFVCEMEFDNNANMLNKKVYESVIIS
KARLNYDEVNNYFKTKTWTHDDKTKKMLDIAYELYKKLEDLKAKKGTISFDVREPKIILD
KNLNVIDIKTKTADQAEKLIEQFMVSCNEAVAELIYQKDLPFLYRNHNKPDEDELINWYK
SLKTFGINPKLTNKQVLDPIFINHTLSQIKEQIKDETEVELLNISLLRYMDKAKYGLENI
GHFGLASDCYTHFTSPIRRYSDLLVHRYLKQYLITKDLEKTSLENNTNYVNKVSNIINDT
ETKSVECEREVIKACMCEYMLNKVNNTYTATISAVLKFGIFIQLDNLVEGLVHISNMNSD
LVYDETNRILIKPDNTYYRMGQKVKVKLINVDIKKRTIDFVLIE

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	5xguB	0.86	0.51	0.304	0.861	Download
2	6fszJJ	0.82	3.71	0.225	0.922	Download
3	6d6qK	0.81	3.20	0.248	0.891	Download
4	4pmwA	0.81	3.47	0.222	0.903	Download
5	2id0A	0.73	3.81	0.180	0.814	Download
6	2r7dA	0.56	3.32	0.173	0.617	Download
7	1l8nA	0.25	8.83	0.041	0.425	Download
8	4c8hA	0.19	7.08	0.046	0.273	Download
9	4leiA	0.19	7.28	0.036	0.283	Download
10	2enxA	0.18	6.79	0.034	0.261	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:0004540	0.99	ribonuclease activity
GO:0000175	0.98	3'-5'-exoribonuclease activity
GO:0004519	0.54	endonuclease activity
GO:1901363	0.53	heterocyclic compound binding
GO:0097159	0.53	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:0090304	1.00	nucleic acid metabolic process
GO:0044260	1.00	cellular macromolecule metabolic process
GO:0016070	0.99	RNA metabolic process
GO:0034470	0.98	ncRNA processing
GO:0006401	0.98	RNA catabolic process
GO:0006364	0.97	rRNA processing
GO:0006402	0.79	mRNA catabolic process
GO:0016075	0.78	rRNA catabolic 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:0000178	0.99	exosome (RNase complex)
GO:0044444	0.95	cytoplasmic part
GO:0044446	0.87	intracellular organelle part
GO:0044428	0.82	nuclear part
GO:0000177	0.78	cytoplasmic exosome (RNase complex)
GO:0000176	0.78	nuclear exosome (RNase complex)
GO:0043229	0.72	intracellular organelle
GO:0005737	0.68	cytoplasm
GO:0043227	0.58	membrane-bounded organelle
GO:0043231	0.57	intracellular membrane-bounded organelle
GO:0043232	0.52	intracellular non-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	0.150	2id0C	0.735	3.71	0.185	0.815	3.1.13.1	96,102
2	0.060	1llwA	0.380	8.41	0.044	0.621	1.4.7.1	NA
3	0.060	2fhbA	0.308	8.54	0.050	0.511	3.2.1.41	101
4	0.060	2ckjA	0.317	8.64	0.035	0.528	1.17.1.4 1.17.3.2	NA
5	0.060	1h0hA	0.303	8.51	0.042	0.500	1.2.1.2	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	0.05	2vnuD	0.802	3.59	0.237	0.902	0.77	QNA	Download	64,78,255,256,259,261,263,264,307,366,414,441,444,445,464,542,550,552,554,558,559,602,609
	2	0.04	2ix1A	0.751	3.82	0.187	0.841	0.50	QNA	Download	148,149,150,151,255,259,261,263,264,307,366,409,411,433,440,441,444,445,466,506,531,534,542,544,545,550,552,554,555,558,600,604,653,692,695,697

	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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