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COFACTOR result for job id 76459

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>76459 (617 residues)
MSKVKKVYTKIKKKWSFDNKGKFTFKKFSLFIRMNVEIAKQNPLLFFGVVFFTSLDAIFS
AMLPLFSSKVINTLVENNTQWLFNWMELNSTGWLYVIGINLLIIIICEYFTNFTVALYSA
QIEVMQRLKILKALTDQDVDFYFDHVSGNILTRLVGDTQFLALGVQQFLTNLIYALSGSI
TAIIIMYSQNLIMIATLALIYLLVANLFCIGFFIDMRRKLILAFDVKRETDADMTDRINN
ISLIKASGTEEFEIKRLEEKNQNYEDGLTKFTYSSALLNTSLTFVIQLLIPIIFIIIAVQ
YLTNSQSSNNLGAEIALIFPLLSTLIGGIAILLPSLRSATAASNAANRISELTDPKPMIH
SNLKGYKIDKIDSIVFDNISFSYPKKPERIVIPPTYLTFEKGKSYAFVGQTGSGKTTIAK
LLLRFYAPTDGKILINNEYNLNRINLPAYLDHIGYVEQEPQILYGTFLDNIKYSKFDATD
EEVIKACKKAELHDFIMSLPDQYNTVLGQRGFILSGGQKQRLVIARVFLKDPDVVILDEA
TSALDNVVEKEIQDKLDELIKGRMCITIAHRLTTIKNVDHIYVLGANGTGIVQSGTFDEL
KKQPGHFRNLYEAGLMQ

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	5mkkA	0.93	1.03	0.215	0.943	Download
2	5mkkB	0.89	1.89	0.225	0.924	Download
3	3wmeA	0.86	2.66	0.250	0.932	Download
4	3qf4B	0.84	3.30	0.259	0.945	Download
5	2yl4A	0.84	2.65	0.261	0.908	Download
6	4ry2A	0.81	4.07	0.241	0.929	Download
7	3g61A	0.80	3.95	0.231	0.927	Download
8	3b5xA	0.80	3.57	0.216	0.917	Download
9	3qf4A	0.79	3.87	0.208	0.914	Download
10	4mycA	0.79	4.12	0.205	0.911	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:0005215	0.98	transporter activity
GO:0022857	0.97	transmembrane transporter activity
GO:0017111	0.97	nucleoside-triphosphatase activity
GO:0043492	0.96	ATPase activity, coupled to movement of substances
GO:0042626	0.95	ATPase activity, coupled to transmembrane movement of substances
GO:1901363	0.75	heterocyclic compound binding
GO:0097159	0.75	organic cyclic compound binding
GO:0035639	0.72	purine ribonucleoside triphosphate binding
GO:0032555	0.72	purine ribonucleotide binding
GO:0005524	0.71	ATP 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:0051234	0.95	establishment of localization
GO:0006810	0.94	transport
GO:0009987	0.81	cellular process
GO:0055085	0.74	transmembrane transport
GO:0008152	0.67	metabolic process
GO:0071704	0.65	organic substance metabolic process
GO:0044238	0.62	primary metabolic process
GO:0071702	0.56	organic substance transport
GO:0065007	0.56	biological regulation
GO:0044237	0.51	cellular metabolic process
GO:0043170	0.50	macromolecule metabolic 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:0044425	0.98	membrane part
GO:0044464	0.97	cell part
GO:0016021	0.97	integral component of membrane
GO:0044424	0.79	intracellular part
GO:0016020	0.77	membrane
GO:0005886	0.58	plasma membrane
GO:0044444	0.56	cytoplasmic 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	0.060	2pffD	0.287	8.38	0.039	0.489	2.3.1.86	NA
2	0.060	2fhbA	0.297	7.86	0.054	0.483	3.2.1.41	NA
3	0.060	1q2lA	0.290	6.85	0.038	0.425	3.4.24.55	NA
4	0.060	2vkzG	0.303	7.93	0.041	0.498	2.3.1.38 3.1.2.14	NA
5	0.060	2q1fA	0.307	7.76	0.044	0.489	4.2.2.21	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:

Rank	Cscore^LB	PDB Hit	TM-score	RMSD^a	IDEN^a	Cov.	BS-score	Lig. Name	Download Complex	Predicted binding site residues
1	0.08	1mv5C	0.365	2.40	0.367	0.387	0.41	ATP	Download	130,149,150,151,154,155,156,157
2	0.04	3g60A	0.800	3.96	0.233	0.925	0.50	0JZ	Download	60,63,64,67,290,320,323,326
3	0.04	3nhbA	0.414	2.72	0.342	0.443	0.45	ADP	Download	152,153,154,155,156,157,158

	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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