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COFACTOR result for job id 76656

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>76656 (745 residues)
MLTQTNKSSFKDKLKAFGANIMPTLSKLSKAFLLPIALLPIAGVFLGVGAAIAANTPEQS
ALWFIGKVMGNMGDVCFGNLPVLFCISVALAYTKDSGVAAITAVVGFLVFNGVQAPLFTQ
GQVQSDKVSEYSLLWYKHVSNSLTGSNMGILSLNTGVLGGIFVGAIAAKCYNKFHQTQLP
TAISFFSGTKLVPIITFVAVIPLSFIFMMAWPVIGLGLNKFGQVSGTLPYGTDSLIFEIV
ERSLVPFGLHHVFYAPLWWTSAGGSIAEGFNNLSKQSEAIQKVFVDSYNSLHGTHHTKLQ
EIIDIVQKNKELWGAVGDQIISQRVIGHLNILNFTDVEKLGINLGRFQSGKFGFMLLGLP
AAALAMWLAAPKENRQQVFGIYFSAAFTCFLTGITEPIEYTFLFVAPWLFYGVHMPLASI
AFWATGALQTHITQTVSGGIIDYIVFGIIPFISGAMKPISAFGVLGVAVVLAPIYFCAFY
FLIKLFNVKTPGRDGNAEAKLYTKADFKASKGLNVDGSKMSSSTDDKEQARLAKAAAIIE
YLGGEENIVDVDSCASRLRLTVVDAKKADIDGIKSLGGTTGALVKGNNIQIVYGGEQEAI
KPRMQKLLEQQRQEKMMGHSEMKSEEMKSENMSMTCESNQACDKKDEACGCEKDCMCEEP
NKDEEQPVSEMKVEEKVVDEMKVEKPKQTRTKSTKAKSTTSKSTKSTSKSSSKSTKSTSS
KAKSTSSKPKTTKAKSTSSKTKTTK

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	5iwsA	0.56	1.16	0.287	0.566	Download
2	3qnqA	0.34	5.91	0.108	0.446	Download
3	2x2hA	0.29	8.36	0.036	0.466	Download
4	1bxrA	0.29	7.30	0.048	0.427	Download
5	1kekA	0.29	8.42	0.044	0.464	Download
6	5nd1B	0.28	8.13	0.054	0.442	Download
7	6ar6A	0.28	8.02	0.033	0.439	Download
8	4r04A	0.28	7.93	0.020	0.434	Download
9	6btmB	0.28	7.88	0.044	0.428	Download
10	5jouA	0.28	7.49	0.025	0.411	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	0.91	catalytic activity
GO:0022891	0.90	substrate-specific transmembrane transporter activity
GO:0022804	0.90	active transmembrane transporter activity
GO:0090563	0.87	protein-phosphocysteine-sugar phosphotransferase 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:

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[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:0044699	1.00	single-organism process
GO:0071702	0.94	organic substance transport
GO:0044765	0.94	single-organism transport
GO:0008643	0.92	carbohydrate transport
GO:0009401	0.88	phosphoenolpyruvate-dependent sugar phosphotransferase system

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:0044464	1.00	cell part
GO:0016020	0.96	membrane
GO:0005886	0.88	plasma membrane
GO:0044424	0.56	intracellular part
GO:0005737	0.51	cytoplasm

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	2fhbA	0.253	8.26	0.041	0.401	3.2.1.41	NA
2	0.060	2jfdA	0.181	6.57	0.036	0.248	2.3.1.85	NA
3	0.060	2nyaF	0.227	8.83	0.036	0.381	1.7.99.4	NA
4	0.060	1h0hA	0.254	8.65	0.019	0.416	1.2.1.2	NA
5	0.060	1vlbA	0.268	8.02	0.050	0.409	1.2.99.7	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:

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	1a9xA	0.272	8.43	0.040	0.434	0.14	ADP	Download	29,159,167
2	0.01	2x2iA	0.291	8.29	0.030	0.462	0.23	QPS	Download	90,91,160,164,165
3	0.01	1ce8E	0.269	8.20	0.045	0.424	0.13	ADP	Download	38,43,76
4	0.01	2x2iD	0.290	8.32	0.029	0.463	0.24	QPS	Download	28,82,159,164
5	0.01	2x2iC	0.293	8.32	0.039	0.463	0.27	QPS	Download	27,28,29,34,164,165
6	0.01	1m6vC	0.269	8.22	0.029	0.424	0.15	ADP	Download	29,30,31,88,89,90,165
7	0.01	1a9xE	0.285	7.61	0.036	0.429	0.27	ORN	Download	27,28,33,87,161,162,165
8	0.01	1ce8C	0.270	8.20	0.029	0.425	0.14	ADP	Download	32,33,34,76
9	0.01	1b0pA	0.282	8.51	0.051	0.462	0.20	SF4	Download	31,35,160,164

	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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