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COFACTOR result for job id 76343

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

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>76343 (353 residues)
MKKANVLNLIRYHIEENDISFRKEARIIAEEFYKMGDDELAEYVLFMLRDANHFVPQIDQ
EYDIQIPFTQKIELERNSEPLPLPQVISEEIKGVINAISKNRKINKFLFQGFPGTGKTET
VKQIARILNRNLFMVDFNNLIDSHLGQSSKNIAELFQKINQTPNPKKIIICFDEIDALAL
DRTNKTDLREMGRVTTAVFQGLDKLDTDIIVFATTNLFKHFDKALIRRFDLVIDFNRYTK
KDMLDIAEIILKHYIKKVDNIKSELRLFRKIISLSEELIYPGDLKNIIKSSIYLSDYEDQ
YDYLKRIYKKITDDKLDIRQLNENNFTVREIEILKGLSKSSVALKVKELNSNE

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	5e7pA	0.71	4.28	0.162	0.881	Download
2	5g4fA	0.70	3.99	0.191	0.836	Download
3	3cf1B	0.69	3.58	0.167	0.807	Download
4	2dhrA	0.66	2.92	0.193	0.739	Download
5	3eihA	0.66	2.51	0.180	0.722	Download
6	6he8H	0.66	3.08	0.202	0.745	Download
7	5l4gH	0.65	3.20	0.145	0.753	Download
8	3d8bA	0.65	2.68	0.163	0.720	Download
9	5kzfA	0.64	3.39	0.143	0.737	Download
10	3b9pA	0.64	2.61	0.169	0.711	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	1.00	catalytic activity
GO:0016887	0.99	ATPase activity
GO:0042623	0.90	ATPase activity, coupled
GO:1901363	0.84	heterocyclic compound binding
GO:0097159	0.84	organic cyclic compound binding
GO:0035639	0.80	purine ribonucleoside triphosphate binding
GO:0032555	0.80	purine ribonucleotide binding
GO:0030554	0.80	adenyl nucleotide binding
GO:0005524	0.79	ATP binding
GO:0043167	0.55	ion binding
GO:0043169	0.53	cation 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:0009987	0.98	cellular process
GO:0071704	0.92	organic substance metabolic process
GO:0044238	0.91	primary metabolic process
GO:0044237	0.88	cellular metabolic process
GO:0043170	0.88	macromolecule metabolic process
GO:0071840	0.81	cellular component organization or biogenesis
GO:0016043	0.80	cellular component organization
GO:0044260	0.79	cellular macromolecule metabolic process
GO:0019538	0.79	protein metabolic process
GO:0006807	0.79	nitrogen compound metabolic process
GO:0006508	0.76	proteolysis
GO:0065007	0.75	biological regulation
GO:0034641	0.75	cellular nitrogen compound metabolic process
GO:0050794	0.74	regulation of cellular process
GO:0044699	0.73	single-organism process
GO:0044763	0.72	single-organism cellular process
GO:0006139	0.72	nucleobase-containing compound metabolic process
GO:0019222	0.71	regulation of metabolic process
GO:0031323	0.70	regulation of cellular metabolic process
GO:1901575	0.69	organic substance catabolic process
GO:0080090	0.69	regulation of primary metabolic process
GO:0060255	0.69	regulation of macromolecule metabolic process
GO:0051171	0.69	regulation of nitrogen compound metabolic process
GO:0019219	0.68	regulation of nucleobase-containing compound metabolic process
GO:0090304	0.67	nucleic acid metabolic process
GO:0051603	0.67	proteolysis involved in cellular protein catabolic process
GO:0044248	0.67	cellular catabolic process
GO:2000112	0.66	regulation of cellular macromolecule biosynthetic process
GO:1903506	0.66	regulation of nucleic acid-templated transcription
GO:0048522	0.66	positive regulation of cellular process
GO:0010468	0.66	regulation of gene expression
GO:0009057	0.66	macromolecule catabolic process
GO:0051254	0.65	positive regulation of RNA metabolic process
GO:0051128	0.65	regulation of cellular component organization
GO:0044265	0.65	cellular macromolecule catabolic process
GO:0030163	0.65	protein catabolic process
GO:0010628	0.65	positive regulation of gene expression
GO:0006357	0.65	regulation of transcription from RNA polymerase II promoter
GO:0045893	0.64	positive regulation of transcription, DNA-templated
GO:1901576	0.63	organic substance biosynthetic process
GO:0051130	0.63	positive regulation of cellular component organization
GO:0044249	0.63	cellular biosynthetic process
GO:0044087	0.63	regulation of cellular component biogenesis
GO:0006511	0.63	ubiquitin-dependent protein catabolic process
GO:0045898	0.62	regulation of RNA polymerase II transcriptional preinitiation complex assembly
GO:0043161	0.62	proteasome-mediated ubiquitin-dependent protein catabolic process
GO:0050896	0.60	response to stimulus
GO:0044271	0.59	cellular nitrogen compound biosynthetic process
GO:0016070	0.58	RNA metabolic process
GO:0009059	0.58	macromolecule biosynthetic process
GO:0006810	0.58	transport
GO:0006259	0.57	DNA metabolic process
GO:0071702	0.56	organic substance transport
GO:0043933	0.56	macromolecular complex subunit organization
GO:0022607	0.56	cellular component assembly
GO:0006950	0.56	response to stress
GO:0065003	0.55	macromolecular complex assembly
GO:0051716	0.55	cellular response to stimulus
GO:0051641	0.55	cellular localization
GO:0045184	0.55	establishment of protein localization
GO:0034654	0.55	nucleobase-containing compound biosynthetic process
GO:0008104	0.55	protein localization
GO:0034613	0.54	cellular protein localization
GO:0033554	0.54	cellular response to stress
GO:0015031	0.54	protein transport
GO:1902578	0.53	single-organism localization
GO:0046907	0.53	intracellular transport
GO:0006996	0.53	organelle organization
GO:0006461	0.53	protein complex assembly
GO:0044765	0.52	single-organism transport
GO:0042221	0.52	response to chemical
GO:0006974	0.52	cellular response to DNA damage stimulus
GO:0034622	0.51	cellular macromolecular complex assembly
GO:0043623	0.50	cellular protein complex assembly
GO:0032774	0.50	RNA biosynthetic process
GO:0016192	0.50	vesicle-mediated transport

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	0.86	cytoplasmic part
GO:0043229	0.78	intracellular organelle
GO:0032991	0.78	macromolecular complex
GO:0044446	0.76	intracellular organelle part
GO:0043231	0.76	intracellular membrane-bounded organelle
GO:0043234	0.69	protein complex
GO:0005634	0.63	nucleus
GO:0005737	0.62	cytoplasm
GO:1902494	0.56	catalytic complex
GO:0000502	0.56	proteasome complex
GO:0044428	0.50	nuclear 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	0.248	1in5A	0.574	3.16	0.142	0.654	3.6.4.12	215
2	0.095	1ixsB	0.563	3.35	0.122	0.654	3.6.4.12	NA
3	0.067	1nsfA	0.535	3.67	0.147	0.646	3.6.4.6	NA
4	0.066	2c9oC	0.559	3.64	0.150	0.680	3.6.1.-	NA
5	0.060	3glfG	0.529	3.46	0.108	0.626	2.7.7.7	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	0.62	2r65B	0.603	2.30	0.204	0.657	1.10	ADP	Download	81,113,114,115,116,117,118,119,173,246,250,281,282
	2	0.09	1ofhB	0.555	3.60	0.122	0.669	1.47	PO4	Download	111,112,113,117,173,174

	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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