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COFACTOR result for job id 76382

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

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>76382 (478 residues)
MTKETLQKRMKRTKVITTIGPSTHSAEAIKELFNNGMTTIRLNFSHGSYEEHGYRIKAAK
KISKALNKPISIILDTKGPEIRLGKFKDNKQEVVKGQSITIYTDTYSYLNKECVQGEMTV
AYDMSVDLKPGDMILIDDGKLELTVDSVEPQIIKATAFNHHIVKTNKRVNLPGIDFSLPF
LSEKDEKDILFGCEQGVDYIAASFVNTAENVRQIKEILNKANANHIQIISKIESQVGLDN
IDEIIEESDGIMIARGDLGLEIPYYDVPYWEKIIIRKCREKGKIVIVATQMLETMTENPS
PTRAEVTDVYFATELGADATMLSGESAAGDYPFLTVHTMSTINKRAEVEFYNKIYYQVQL
DNARNSTSGPRAEIADLLATKTKDGEYKYAIVLSKTGELLKTISKFRPNVTILGVSPDKK
LWTSFGVWHSIFMNKVDTLDNLDNNIEKLSEIAKSWGAKLGEKVLVVRSTAIKEIEVI

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	3hqqX	0.97	1.07	0.376	0.992	Download
2	6du6A	0.97	1.20	0.357	0.990	Download
3	3ma8A	0.96	1.15	0.328	0.983	Download
4	3khdB	0.96	1.33	0.357	0.985	Download
5	3gg8C	0.96	1.39	0.356	0.981	Download
6	2e28A	0.95	1.18	0.366	0.967	Download
7	3t05A	0.94	1.16	0.387	0.962	Download
8	1a3wA	0.94	1.95	0.364	0.983	Download
9	1pkyA	0.93	1.06	0.379	0.950	Download
10	5wrpA	0.92	1.74	0.308	0.958	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:0004743	0.99	pyruvate kinase activity
GO:0030955	0.95	potassium ion binding
GO:0016301	0.95	kinase activity
GO:0000287	0.95	magnesium ion binding
GO:1901363	0.92	heterocyclic compound binding
GO:0097159	0.92	organic cyclic compound binding
GO:0032559	0.90	adenyl ribonucleotide binding
GO:0005524	0.89	ATP binding
GO:0042802	0.83	identical protein binding
GO:0003676	0.53	nucleic acid binding
GO:0003723	0.51	RNA 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	0.99	cellular process
GO:0008152	0.94	metabolic process
GO:0071704	0.93	organic substance metabolic process
GO:0044237	0.93	cellular metabolic process
GO:0044238	0.92	primary metabolic process
GO:0006807	0.90	nitrogen compound metabolic process
GO:0034641	0.88	cellular nitrogen compound metabolic process
GO:0044699	0.87	single-organism process
GO:1901564	0.85	organonitrogen compound metabolic process
GO:0006139	0.85	nucleobase-containing compound metabolic process
GO:0044281	0.84	small molecule metabolic process
GO:0016043	0.84	cellular component organization
GO:0051289	0.83	protein homotetramerization
GO:0019752	0.82	carboxylic acid metabolic process
GO:0050896	0.81	response to stimulus
GO:1901135	0.79	carbohydrate derivative metabolic process
GO:0055086	0.79	nucleobase-containing small molecule metabolic process
GO:0032787	0.79	monocarboxylic acid metabolic process
GO:0019637	0.79	organophosphate metabolic process
GO:0006796	0.79	phosphate-containing compound metabolic process
GO:0009117	0.78	nucleotide metabolic process
GO:0006090	0.78	pyruvate metabolic process
GO:1901575	0.77	organic substance catabolic process
GO:0009150	0.77	purine ribonucleotide metabolic process
GO:0006732	0.77	coenzyme metabolic process
GO:0005975	0.77	carbohydrate metabolic process
GO:0046496	0.76	nicotinamide nucleotide metabolic process
GO:0046034	0.76	ATP metabolic process
GO:0046031	0.76	ADP metabolic process
GO:0042221	0.76	response to chemical
GO:0016052	0.76	carbohydrate catabolic process
GO:0006165	0.76	nucleoside diphosphate phosphorylation
GO:0006091	0.76	generation of precursor metabolites and energy
GO:0006096	0.75	glycolytic process
GO:0006950	0.74	response to stress
GO:0051716	0.73	cellular response to stimulus
GO:1901700	0.71	response to oxygen-containing compound
GO:0010033	0.71	response to organic substance
GO:0070887	0.70	cellular response to chemical stimulus
GO:0032868	0.70	response to insulin
GO:0009628	0.70	response to abiotic stimulus
GO:0032869	0.69	cellular response to insulin stimulus
GO:0009408	0.69	response to heat
GO:0032502	0.58	developmental process
GO:0065007	0.57	biological regulation
GO:0050789	0.56	regulation of biological process
GO:0044767	0.56	single-organism developmental process
GO:0048856	0.55	anatomical structure development
GO:0006810	0.54	transport
GO:0019318	0.53	hexose metabolic process
GO:0009605	0.52	response to external stimulus
GO:0006006	0.52	glucose metabolic process
GO:0044282	0.51	small molecule catabolic process
GO:0055114	0.50	ox.dat.gzion-reduction process
GO:0040007	0.50	growth
GO:0009991	0.50	response to extracellular stimulus

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:0005737	1.00	cytoplasm
GO:0044444	0.93	cytoplasmic part
GO:0005829	0.78	cytosol
GO:0043226	0.71	organelle
GO:0043227	0.69	membrane-bounded organelle
GO:0043229	0.59	intracellular organelle
GO:0043231	0.56	intracellular membrane-bounded organelle
GO:0016020	0.55	membrane

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	0.601	1pklG	0.965	1.32	0.376	0.992	2.7.1.40	41,82,231,289,323,325
2	0.588	2e28A	0.946	1.18	0.366	0.967	2.7.1.40	41,82,231,289,323,325
3	0.476	3ma8A	0.964	1.15	0.328	0.983	2.7.1.40	19,21,43,46,77,184
4	0.234	1pkyA	0.933	1.06	0.379	0.950	2.7.1.40	323,325
5	0.226	1a3wA	0.936	1.95	0.364	0.983	2.7.1.40	323,325

	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	0.69	3qv9A	0.974	1.08	0.373	0.992	1.35	PO4	Download	18,41,323,324,327
2	0.68	3hqpL	0.884	3.25	0.358	0.985	1.36	UUU	Download	18,21,41,43,46,51,52,231,233,254,255,256,257,289,323,324,327
3	0.67	3hqnD	0.969	1.28	0.376	0.992	1.75	K	Download	41,43,44,45,75,76,77,203,231
4	0.49	1t5aB	0.917	2.37	0.346	0.992	1.00	OXL	Download	18,20,43,45,46,76
5	0.49	3gr4A	0.905	2.64	0.338	0.992	0.92	ADP	Download	20,21,41,43,46,323,327
6	0.47	1a5uB	0.967	1.31	0.335	0.992	1.13	NA	Download	41,43,45,75,76,77,203
7	0.42	3pp7B	0.971	1.20	0.376	0.992	1.66	SVR	Download	18,21,41,43,46,47,51,324,327,328
8	0.26	3qv7D	0.971	1.21	0.376	0.992	1.45	QV7	Download	46,47,48,51,328
9	0.07	3n25A	0.926	2.22	0.331	0.992	0.81	PRO	Download	11,12,38,68,426,428,431,432

	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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