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COFACTOR result for job id 76575

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>76575 (987 residues)
MNYISLLTIKNQYDFLESLITIDQYIEFIKKNKLNYAFYSETHTMYGVAEFFKKATDNNI
KPIIGLTIEFEDSTKLIIYAKNKKGYQILNFVSSFLNDGFNHYDYEIKEYILELVNNNVV
VVGLINDLDFKSYLINKLNNDFYDVKELNLYFNQISYLDINDQKTYNILNAIKTNKTINQ
IQNINNYFYPDIDYLIKNYSLENIKKVISEINSKVDFNLFDSNQKHLVKYKNINNLSSYE
YLRQVCLLSLKKYQQKIKPNLDLKLYINRLNYELEIIKQMGFSDYFLIVSDYVNFAKKND
ILVGPGRGSAAGSLISYLLRITDIDPLEYDLLFERFLNPDRSNLPDIDLDFQDNRREEVL
EYLFEKYGKYHVGMITTYQTIGYKMAWRDVCRVFNIDLLIVNKISKVLDQYTNSDFLEFI
KENKLLNDYFQNDLFKEIFITMHKIIGLPRQTSTHAAGIVLTDCDLRELVPIKIGFNGIN
QTQFDMNYLDALGLIKMDILGLRNLTTIQEIKHLIYLNQNLKISLNKIDLNDKKAFELLK
NKQTSGIFQLESKGMSDLISKMQVDSIEQISIASALYRPGPQEMIPIYLENKKTNKFKII
DKSVYEILKPTYGIIVYQEQVMQMLNKVANFSYAKADIIRRAMSKKNNKVMQSMKLEFIN
SAIKNNFSYNKANLIWNWIEKFSNYGFNKSHSISYSYISYWLAYFKAHFTTEFYTSLLDQ
NIGNEIKTQQYIKELYDYKIKVNKPSVINSNFNYQIINKQIYMPLTCIKSIGYEVVKKIN
LAKSENENMYLDIHNFILAMIKQKINVNVLQTLIKAGALDIFNYNKKTMIENLDLLISQA
NAYKQVNNILDDEKINLIIYDEYEDEILASFEKELYGFFIDQNPILKLKTNNFNLNLIDI
SKLEYNKVQVILGYILKIKEIKDKNNNKMAFVTVFDNTSELELTIFSSDYKDISDQLIEN
KAYVFKVLKTKTNNKTSIKFISLIKAI

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	3e0dA	0.95	1.42	0.290	0.964	Download
2	5lewA	0.81	1.95	0.286	0.840	Download
3	2hqaA	0.72	4.46	0.273	0.823	Download
4	3f2bA	0.69	3.52	0.190	0.753	Download
5	1ny5B	0.15	7.42	0.024	0.220	Download
6	2b9xA	0.15	7.53	0.049	0.217	Download
7	1pb0A	0.15	4.81	0.076	0.172	Download
8	2w9mB2	0.15	4.54	0.104	0.167	Download
9	3d2rB	0.14	6.49	0.052	0.185	Download
10	4e4fA	0.14	7.22	0.049	0.195	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	0.99	catalytic activity
GO:0003887	0.98	DNA-directed DNA polymerase activity
GO:0016787	0.67	hydrolase activity
GO:1901363	0.56	heterocyclic compound binding
GO:0097159	0.56	organic cyclic compound binding
GO:0016788	0.55	hydrolase activity, acting on ester bonds
GO:0004518	0.54	nuclease activity
GO:0004527	0.53	exonuclease activity
GO:0008408	0.52	3'-5' exonuclease 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	0.98	cellular process
GO:0008152	0.98	metabolic process
GO:0071704	0.97	organic substance metabolic process
GO:0044238	0.97	primary metabolic process
GO:0034641	0.97	cellular nitrogen compound metabolic process
GO:0043170	0.96	macromolecule metabolic process
GO:0006139	0.96	nucleobase-containing compound metabolic process
GO:1901576	0.95	organic substance biosynthetic process
GO:0090304	0.95	nucleic acid metabolic process
GO:0044260	0.95	cellular macromolecule metabolic process
GO:0044249	0.95	cellular biosynthetic process
GO:0034645	0.94	cellular macromolecule biosynthetic process
GO:0006259	0.94	DNA metabolic process
GO:0006260	0.88	DNA replication
GO:0044271	0.55	cellular nitrogen compound biosynthetic 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:0032991	0.88	macromolecular complex
GO:0005737	0.84	cytoplasm
GO:0043234	0.83	protein complex
GO:0044444	0.73	cytoplasmic part
GO:1902494	0.69	catalytic complex
GO:0009360	0.67	DNA polymerase III complex
GO:0043229	0.57	intracellular organelle
GO:0043227	0.56	membrane-bounded organelle
GO:0043231	0.55	intracellular 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	0.140	2hnhA	0.748	4.23	0.276	0.849	2.7.7.7	NA
2	0.090	3f2bA	0.692	3.52	0.190	0.753	2.7.7.7	NA
3	0.060	2pffD	0.302	8.87	0.016	0.470	2.3.1.86	NA
4	0.060	3btaA	0.293	9.05	0.065	0.462	3.4.24.69	NA
5	0.060	1ug9A	0.289	9.09	0.028	0.463	3.2.1.70	358

	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	0.01	1xmsA	0.135	6.28	0.061	0.173	0.16	ANP	Download	5,6,7,8
2	0.01	2qkiD	0.183	7.64	0.026	0.258	0.13	III	Download	80,81,83,86
3	0.01	3cmvD	0.329	8.77	0.042	0.507	0.19	ANP	Download	5,6,8

	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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