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COFACTOR result for job id 76716

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

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>76716 (525 residues)
MQDKTNVLLDKFLAIGSWQAAIAIIIFIGIQIGLWFTFKKFKIKFIYRVLIGLAIGLVFG
IIIQAIYKFPQNGLVNKNLPTELAKDGTTTIKINPDFRLWVYQLDIWISLAKNIFINGIL
LLTAPVVFIAIFRVTSKKGNKNVGRISLKGVGLLLLNTAFAFVITFWLGYLIKVGAGSGL
SLDHSIVKNTPKETQPLPKIVWEYLPNNFIQPWLGSMVIPLMVIAGLIGNSVKILSKKKP
VEMDAIRKGMDVAWSIVISILMTFMKIMPLAVMSMIASSVISKPIGALATIGKVLGLGYL
GLTISLLFLTFLLFVNKVNVIAWWKLSFKILIQGFATQSSNATLPMSIETLKDEVKIDDS
AVSTVVPLSTTMGLMGCAGVQSGVITSLLWTGAVSADFHNMGLFTFFILAFVITLIASLG
ISGIPGTATVLTSGVLSGLGLGVWFAPVYAIVGSLDGLFDMGRTGVNVTSGAVVTTIVAK
SEGLIGEESTILSKHQLEKQKIIREKKSKPEIKEAQQTNKVEVKN

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	3kbcA	0.76	0.79	0.253	0.768	Download
2	6gctA	0.67	3.33	0.164	0.762	Download
3	5llmA	0.48	3.72	0.188	0.535	Download
4	4czbA	0.38	6.28	0.075	0.549	Download
5	1zcdA	0.38	5.31	0.094	0.499	Download
6	3ir7A	0.37	7.78	0.056	0.625	Download
7	4cz8A	0.37	6.34	0.094	0.543	Download
8	6ajfA	0.35	7.04	0.064	0.552	Download
9	5aa5C	0.35	6.78	0.062	0.535	Download
10	5lq3A	0.35	6.92	0.057	0.533	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:0022891	0.98	substrate-specific transmembrane transporter activity
GO:0015075	0.90	ion transmembrane transporter activity
GO:0015291	0.80	secondary active transmembrane transporter activity
GO:0008324	0.80	cation transmembrane transporter activity
GO:0003824	0.79	catalytic activity
GO:0015294	0.71	solute:cation symporter activity
GO:0046943	0.66	carboxylic acid transmembrane transporter activity
GO:0015171	0.61	amino acid transmembrane transporter activity
GO:0015077	0.58	monovalent inorganic cation transmembrane transporter activity
GO:0046873	0.56	metal ion transmembrane transporter activity
GO:0008509	0.54	anion transmembrane transporter 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:0006810	0.96	transport
GO:0006811	0.94	ion transport
GO:0071702	0.92	organic substance transport
GO:0009987	0.92	cellular process
GO:0046942	0.89	carboxylic acid transport
GO:0071705	0.80	nitrogen compound transport
GO:0006865	0.78	amino acid transport
GO:0006835	0.74	dicarboxylic acid transport
GO:0008152	0.71	metabolic process
GO:0071704	0.67	organic substance metabolic process
GO:0015807	0.67	L-amino acid transport
GO:0015800	0.62	acidic amino acid transport
GO:0044237	0.61	cellular metabolic process
GO:0044763	0.58	single-organism cellular process
GO:0015813	0.58	L-glutamate transport
GO:0044238	0.56	primary metabolic process
GO:0055085	0.54	transmembrane transport
GO:0034220	0.53	ion transmembrane transport
GO:0006807	0.53	nitrogen compound 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:0044464	1.00	cell part
GO:0016020	0.97	membrane
GO:0005886	0.94	plasma membrane
GO:0044424	0.87	intracellular part
GO:0044425	0.71	membrane part
GO:0044444	0.64	cytoplasmic part
GO:0031224	0.59	intrinsic component of membrane
GO:0043227	0.53	membrane-bounded organelle
GO:0016021	0.53	integral component of 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	0.060	2e1qA	0.309	7.75	0.040	0.520	1.17.3.2 1.17.1.4	NA
2	0.060	2iukA	0.292	7.20	0.035	0.455	1.13.11.12	NA
3	0.060	2pffD	0.320	7.84	0.046	0.537	2.3.1.86	NA
4	0.060	1llwA	0.310	7.90	0.033	0.529	1.4.7.1	NA
5	0.060	1h2rL	0.317	7.36	0.041	0.501	1.12.2.1	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	2drdA	0.324	7.19	0.070	0.510	0.20	MIY	Download	126,421,427
2	0.01	2ivfA	0.339	8.01	0.047	0.585	0.15	SF4	Download	125,130,430
3	0.01	1q16A	0.368	7.74	0.051	0.613	0.13	SF4	Download	118,121,122,126

	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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