[back]

COFACTOR result for job id 76705

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

User Input

>76705 (588 residues)
MHIKVENTEMNNFNSNIKKKKRLKMLSSFSILLLIMLVLMLVSWILYWSKTKTDLVKTIS
FNDWKYDPILSPIYNAWTSKYPNISAGNSQTWIDFMNSNSSLGWVYNSHGWIKDSYTIQH
SGDAIFNGLAPIQPIGIIDVIYAPIKGFVLKSNIIIFTISIGAFLYILVSTKALEGLSQA
IIAKLKGKEAFAIIPLMLFFSIFGTVEGFAEETLGFYMIFIPIMLMAGFDVFTGVLILMV
GAGTGVIGSTVNPFTIPIAVSAINSGIDASTAKLTIGDGLVWRIICWLILTSFSTTFTLL
YALKVKKNPSKSVTFSTLEGDKEFFLAHVSKTIKLDWKKKVSLVAFAISFLVMIFYLVGW
DSIFNNTKMADQAIWIKKNIPYLTALIPGWGNGDLDNVAAFFLLASITLAIINSIGEATF
IKKWFEGASDILSVAFIIATAAGVGYILVQTNLQSLFVKGILSSIGGINNQTAKVIVLFI
VFIPLAFLIPSSSGFATTIFPLLAKSLVDSKTNQLQAYASSGSIMAFTFAIGLVNLITPT
SGVVMGACSLSRMSYAKYLKAMLPIISYLFILCFILLLIGGALPDSIS

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	4r1iA	0.79	2.36	0.128	0.838	Download
2	4r0cA	0.77	1.60	0.105	0.792	Download
3	4f35D	0.53	4.46	0.112	0.646	Download
4	5l24A	0.39	5.24	0.069	0.502	Download
5	3tijA	0.38	5.29	0.068	0.491	Download
6	4ff1A	0.33	7.27	0.044	0.503	Download
7	5dotA	0.33	8.14	0.040	0.554	Download
8	2cse1	0.33	8.16	0.040	0.553	Download
9	1llwA	0.33	7.74	0.040	0.531	Download
10	4zhjA	0.33	7.82	0.042	0.532	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:0005215	1.00	transporter activity
GO:0003824	0.81	catalytic activity
GO:0022857	0.64	transmembrane transporter activity
GO:0015075	0.62	ion transmembrane transporter activity
GO:0008514	0.60	organic anion transmembrane transporter activity
GO:0022804	0.56	active transmembrane transporter activity
GO:0072349	0.54	modified amino acid transmembrane transporter activity
GO:0016740	0.53	transferase activity
GO:0015318	0.53	inorganic solute uptake transmembrane transporter activity
GO:0015291	0.53	secondary active transmembrane transporter activity
GO:0005342	0.51	organic acid 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	1.00	transport
GO:0006811	0.99	ion transport
GO:0006820	0.98	anion transport
GO:0055085	0.97	transmembrane transport
GO:0098656	0.94	anion transmembrane transport
GO:0008152	0.75	metabolic process
GO:0071704	0.74	organic substance metabolic process
GO:0044237	0.72	cellular metabolic process
GO:0044238	0.70	primary metabolic process
GO:0006807	0.66	nitrogen compound metabolic process
GO:1901564	0.57	organonitrogen compound metabolic process
GO:0044281	0.52	small molecule 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	0.99	cell part
GO:0044425	0.95	membrane part
GO:0016021	0.94	integral component of membrane
GO:0044424	0.88	intracellular part
GO:0044444	0.69	cytoplasmic part
GO:0016020	0.54	membrane
GO:0005829	0.50	cytosol

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	0.292	7.98	0.041	0.481	1.17.3.2 1.17.1.4	NA
2	0.060	1llwA	0.326	7.74	0.040	0.531	1.4.7.1	NA
3	0.060	2ckjA	0.290	7.85	0.028	0.474	1.17.1.4 1.17.3.2	NA
4	0.060	2ohyB	0.312	7.02	0.045	0.471	5.4.3.6	NA
5	0.060	1i1iP	0.302	8.18	0.040	0.512	3.4.24.16	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	2ckjD	0.280	8.35	0.028	0.486	0.44	FES	Download	162,163,167,168,208
2	0.01	1llwA	0.326	7.74	0.040	0.531	0.41	F3S	Download	162,164,165,166
3	0.01	2ckjA	0.290	7.85	0.028	0.474	0.48	FES	Download	147,151,154,155

	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).

[back]