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COFACTOR result for job id 76574

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>76574 (911 residues)
MKTKILVVDGNSLIFRAFYATAYSPNTSLLKTKSGVLTNAVYSFINMLLSVIHQRGPYDH
ILIAFDKGKKTFRHDLLSDYKANRIKTPNELVEQFSVVREFLTKANIQWFEQENIEADDI
VGSICKYAEKQFDNLQAEILSSDKDMYQLITNKVICLNPVQGVNELEEVDTNKLFEKWQI
LPNQVPDYKAIVGDSSDNLKGVNGIGQKGAIKLIQQYQNLENIYNNLEQIKGAIKTKLEQ
DKKMAFLCKDLATIKTDVILENFSFKKLDFNVDNIYEFLNKYEMYSLKKRFTNILNLDFN
PYQNKKQNLDVKIINSWSKDYEDSINYLYVESLEEDYHKDKIIGIGISNNKGNFYLDFKN
KAQQLSFFEDTTLSSTDSLFEEFLNNSNLKKYTYDIKKTTYLLKNHKYNVLASNFDFDFM
VACYSLNANVVSDLSNQIKLVDNLIELETIDQIFGKGVKKNPDIDLDIKSKYISKKAYLL
KKYSDQLIEQLKQTNTYDLYLKIDHPLIEVLYDIEVQGILIDKEQLKLQTQQILKKINHI
EGQMKILVAEEIDNNFNFSSPKQIQELLFDKLKLPNLEKGTTSKEVLEKLITYHPIINLL
LEHRKYTKLYTTYLKGFEKFIFDDSKVHTIFNHTLTNTGRLSSSYPNIQNISIRDNEQKE
VRKIFITNNNKTFLSYDYSQIELRVLAQMSKETNLINAFNQNADIHLQAAKLIFNLSDDQ
ITSEQRRIAKVFNFGILYGLTDFGLASDLNISVNQAKQMIKDYYSAFPSLLEFKEKQVEI
ATSQGYITTLSNRRRYINELNSTNHNIRQFGKRIAVNTPIQGTASDILKVAMISIYKKLK
EQNLDARIVCQIHDEIILEVDDNQLEQTKRIVVSELENALEKLFLDLNIKEQVVVKLKVG
ESVGKTWFDLK

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	1bgxT	0.88	0.71	0.314	0.889	Download
2	2kzzA	0.60	3.04	0.272	0.640	Download
3	2hhtA	0.59	2.81	0.338	0.630	Download
4	4xviA	0.56	4.46	0.219	0.637	Download
5	2ajqA	0.53	3.73	0.166	0.593	Download
6	3ikmD1	0.50	5.53	0.098	0.610	Download
7	1s5jA	0.25	6.75	0.040	0.341	Download
8	1ul1Z	0.24	4.37	0.094	0.274	Download
9	1rxwA	0.23	4.20	0.114	0.266	Download
10	1qhtA3	0.17	3.95	0.091	0.191	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:0016740	1.00	transferase activity
GO:0003887	0.99	DNA-directed DNA polymerase activity
GO:0016787	0.98	hydrolase activity
GO:0004518	0.96	nuclease activity
GO:0004527	0.94	exonuclease activity
GO:0008409	0.92	5'-3' exonuclease activity
GO:1901363	0.54	heterocyclic compound binding
GO:0097159	0.54	organic cyclic compound binding
GO:0003676	0.50	nucleic acid 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:0006259	1.00	DNA metabolic process
GO:0006260	0.97	DNA replication
GO:0006261	0.94	DNA-dependent DNA replication
GO:0050896	0.81	response to stimulus
GO:0006950	0.79	response to stress
GO:0033554	0.78	cellular response to stress
GO:0006974	0.77	cellular response to DNA damage stimulus
GO:0006281	0.76	DNA repair

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:0005634	1.00	nucleus
GO:0005737	0.97	cytoplasm
GO:0044444	0.71	cytoplasmic part
GO:0032991	0.54	macromolecular complex
GO:0044446	0.51	intracellular organelle part

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	0.602	1bgxT	0.885	0.71	0.314	0.889	2.7.7.7	81
2	0.121	1d8yA	0.599	3.14	0.271	0.643	2.7.7.7	NA
3	0.109	1qssA	0.546	2.92	0.276	0.579	2.7.7.7	NA
4	0.060	2iukA	0.276	8.55	0.044	0.430	1.13.11.12	NA
5	0.060	2pffB	0.189	8.76	0.032	0.294	2.3.1.86	92

	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	0.20	2hhxA	0.586	2.83	0.353	0.625	0.40	QNA	Download	731,734,735,738,744,745,748,810,813,814,817,821
	2	0.04	1taqA	0.576	1.46	0.192	0.586	1.29	ZN	Download	9,12,118,121,143

	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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