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COFACTOR result for job id 76633

[Download result.tar.bz2 for all prediction results]

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>76633 (722 residues)
MSVDHLLDLLNPQQLAAVINTDKPVRIIAGAGSGKTRVITTKIAYLIEKKHIDPTRILAV
TFTNKAAKEMKERVLQITKNQKKSPFISTFHAWCSKVLRIDGKHVGLKDKFLIIDSDDQK
RIIKNALKESNIELSENDKKTFDKKILYKIKEWKEELVDPDEAILNANSTYDRNSAIIYK
LYQETLLKNNSIDFDDLQIYVYLLFKNHQEILNKWRNAYDYVLVDEFQDTNDIQFSLIKF
LTINTNHLTVVGDPDQTIYSWRGAKLDIILNFNKTYSNAISIVLNQNYRSTKQILDISNS
FIKNNKFREHKEIFTNNKSGKKVVLKECNSKTSEASYVSFKIKELIKQGYHYKDIFILYR
MNAWSQEFEKELINKKIPFQLIGGIKFRERKVIKDAMAFLKMISIKDDLSSQRVLSLIPK
IGNITIEKIINIANLNHISIFDLITNEDKTLLQSITKNLDELIEVFKTAHQLYLDNTNIE
EILKYLLIQSGYENKLKVKNEHDDLDNINALYDQLKRFDENFDANYYSEDNKLIAFLQEE
ALTSDIDEAQQIDKVSLLTVHAAKGLENKIVFITGLNQGIFPTRLSENNQKELEEERRAL
YVALTRAKEELFLTYVKGDYSHIMQSELKPSKFIHELDKDLYEFESQFLNSQIYDKNQHK
TPSFYVSPKQHNLYNVGDYVEHKLFGKGIITKVINDQLQISFTNSSYGIMIIAANNSALT
KL

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	2is6A	0.89	0.59	0.324	0.895	Download
2	4c2tA	0.85	2.08	0.325	0.884	Download
3	3pjrA	0.83	2.36	0.395	0.881	Download
4	1uaaA	0.74	3.97	0.311	0.859	Download
5	3u44A	0.61	5.04	0.207	0.742	Download
6	3u44B	0.61	4.83	0.117	0.715	Download
7	1w36E	0.57	5.31	0.128	0.709	Download
8	3k70C	0.54	6.16	0.077	0.715	Download
9	5n8oA	0.42	5.39	0.122	0.518	Download
10	5mc6h	0.42	5.68	0.077	0.529	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:0016787	0.97	hydrolase activity
GO:0017111	0.95	nucleoside-triphosphatase activity
GO:0003678	0.94	DNA helicase activity
GO:1901363	0.91	heterocyclic compound binding
GO:0097159	0.91	organic cyclic compound binding
GO:0003676	0.90	nucleic acid binding
GO:0097367	0.89	carbohydrate derivative binding
GO:0042623	0.89	ATPase activity, coupled
GO:0030554	0.89	adenyl nucleotide binding
GO:0008094	0.88	DNA-dependent ATPase activity
GO:0005524	0.88	ATP binding
GO:0003677	0.88	DNA binding
GO:0008026	0.87	ATP-dependent helicase activity
GO:0004003	0.86	ATP-dependent DNA helicase activity
GO:0043167	0.76	ion binding
GO:0043138	0.76	3'-5' DNA helicase activity
GO:0046872	0.75	metal ion binding
GO:0043140	0.75	ATP-dependent 3'-5' DNA helicase activity
GO:0000287	0.74	magnesium ion binding
GO:0043142	0.73	single-stranded DNA-dependent ATPase activity
GO:0017116	0.72	single-stranded DNA-dependent ATP-dependent DNA helicase activity
GO:0015616	0.72	DNA translocase 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	1.00	cellular process
GO:0006259	0.99	DNA metabolic process
GO:0050896	0.92	response to stimulus
GO:0006974	0.91	cellular response to DNA damage stimulus
GO:0006281	0.90	DNA repair
GO:0016043	0.89	cellular component organization
GO:0006996	0.88	organelle organization
GO:0071103	0.87	DNA conformation change
GO:0032508	0.86	DNA duplex unwinding
GO:1901576	0.85	organic substance biosynthetic process
GO:0044249	0.85	cellular biosynthetic process
GO:0006268	0.84	DNA unwinding involved in DNA replication
GO:0034645	0.82	cellular macromolecule biosynthetic process
GO:0006260	0.80	DNA replication
GO:0065007	0.79	biological regulation
GO:0050794	0.78	regulation of cellular process
GO:0060255	0.77	regulation of macromolecule metabolic process
GO:0031323	0.77	regulation of cellular metabolic process
GO:0006298	0.77	mismatch repair
GO:0048523	0.76	negative regulation of cellular process
GO:0043933	0.76	macromolecular complex subunit organization
GO:0019219	0.76	regulation of nucleobase-containing compound metabolic process
GO:0009628	0.76	response to abiotic stimulus
GO:0006261	0.76	DNA-dependent DNA replication
GO:0051052	0.75	regulation of DNA metabolic process
GO:0045934	0.75	negative regulation of nucleobase-containing compound metabolic process
GO:0031297	0.75	replication fork processing
GO:0010605	0.75	negative regulation of macromolecule metabolic process
GO:0009411	0.75	response to UV
GO:0065003	0.74	macromolecular complex assembly
GO:0045910	0.74	negative regulation of DNA recombination
GO:0070581	0.73	rolling circle DNA replication
GO:0060543	0.73	negative regulation of strand invasion
GO:0051260	0.73	protein homooligomerization
GO:0009650	0.73	UV protection
GO:0009605	0.73	response to external stimulus
GO:0006289	0.73	nucleotide-excision repair
GO:0009432	0.72	SOS response

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:0044444	0.80	cytoplasmic part
GO:0032991	0.73	macromolecular complex
GO:0043234	0.63	protein complex
GO:1902494	0.61	catalytic complex
GO:0044446	0.59	intracellular organelle part
GO:0043226	0.57	organelle
GO:0005737	0.57	cytoplasm
GO:0043229	0.56	intracellular organelle
GO:0005829	0.56	cytosol
GO:0043227	0.55	membrane-bounded organelle
GO:0043231	0.54	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	0.247	2is6A	0.891	0.59	0.324	0.895	3.6.4.12	NA
2	0.246	2is4B	0.862	0.99	0.328	0.870	3.6.1.-	NA
3	0.199	3pjrA	0.833	2.36	0.395	0.881	3.6.4.12	NA
4	0.147	1uaaA	0.742	3.97	0.311	0.859	3.6.4.12	NA
5	0.060	1hv8A	0.326	5.18	0.113	0.410	3.6.4.13	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	0.49	3pjrA	0.833	2.36	0.395	0.881	1.56	ATP	Download	9,10,14,31,33,34,35,36,37,256,288,289,567,606

	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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