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COFACTOR result for job id 76493

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

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>76493 (988 residues)
MLFLKQIRASGFKSFADLTVMDFNYDMTGVVGPNGSGKSNITDAIRWTLGEQSTKTLRGS
KMDDIVFSGNNEKKAADVAEVTLVFNNTHENFSSIKSDVVEITRKFDKNTRESEFYINST
KCKLKDVQSIALEAGLTRSSIAIISQGTVANFTESKPETKREIFDDAAGVSKYKKRKKET
LSKLEKATENLTRLEDIAKEISRRLPNLERQSKKALEYQQKVNELKNIELYILTKDLKVL
VNRIEELRVEKIEYETQIKKLTNEINMSQEEVNLIIDKDSEDNQKLGELNSKFNSIVEKI
ANLKVRKQKAEFKEQENLNTKDQDEYKAALIKKQFDEKQISIKSEKDKLTKAENSLLELK
DKYDYYSNKYNEIYREIETIRTTISRISIQIEAIEHNKKAALQSYQDGVSAILNNQKQIG
GVVGVLKSLINVKEEYQIAISVTASGHMNSLVMKTDQDVKKAIEFLKKNNNLGRVTFLPL
NTLTPNLINPVQRQILEKSEGFVGFANELVEYPETISKAVEYALASIIVVQSYDDAINLA
KNTNFRFNIVSLDGQRILPHGAIVGGSTRNANIFTKQNTQNQDNTLEELKNKIELLEQKE
ISKTKEITEYKTANDSLRDQINDLNGTIRNAKNNLFNWTENLKEFSDEHKSLTGRDLFTG
VYSKSDESESIILAKQISELEIQRDEIQIEINSISFKRTQSMEKQKEMNSKNSKKRDELD
ELKTHAGSINTEYNVLLQRRITIIDRLSNGYQITEETALTMEVENIEDEQVARERIIELT
TYIQNIGNVNMDAIEEYKNEKERFDYYDQQIKDIYDAKEKLESIILDIDIAMESQFKQII
EDVNKALPDVFSKMFGGGYAELIYTDPDNILETGIDIKIFPPGKKITNLNLLSGGEKSLV
ALSVLFAILKARPLPLVILDEAEAPLDPVNVERFARYVRQFSHNTQFIIVTHREGTMTQC
DSLFGVTMQTKGITKIINVKLVEAKNLH

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	5xeiA	0.38	4.01	0.267	0.422	Download
2	4ux3A	0.34	4.83	0.202	0.400	Download
3	5da9A	0.33	4.75	0.141	0.381	Download
4	3zgxA	0.33	3.10	0.409	0.346	Download
5	5y81A	0.31	9.08	0.039	0.491	Download
6	4i99A	0.31	1.60	0.339	0.316	Download
7	1w1wB	0.31	3.04	0.294	0.327	Download
8	2vz8B	0.30	8.95	0.040	0.466	Download
9	3qf7A	0.29	4.43	0.170	0.333	Download
10	3eukH	0.29	4.00	0.113	0.326	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	0.94	catalytic activity
GO:0016787	0.75	hydrolase activity
GO:0017111	0.51	nucleoside-triphosphatase 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:0009987	0.99	cellular process
GO:0008152	0.88	metabolic process
GO:0071704	0.87	organic substance metabolic process
GO:0044238	0.86	primary metabolic process
GO:0044237	0.86	cellular metabolic process
GO:0006807	0.83	nitrogen compound metabolic process
GO:0034641	0.78	cellular nitrogen compound metabolic process
GO:0043170	0.77	macromolecule metabolic process
GO:1901360	0.76	organic cyclic compound metabolic process
GO:0046483	0.76	heterocycle metabolic process
GO:0006725	0.76	cellular aromatic compound metabolic process
GO:0006139	0.75	nucleobase-containing compound metabolic process
GO:0071840	0.72	cellular component organization or biogenesis
GO:0044699	0.72	single-organism process
GO:0044260	0.72	cellular macromolecule metabolic process
GO:0016043	0.71	cellular component organization
GO:0090304	0.69	nucleic acid metabolic process
GO:0044763	0.68	single-organism cellular process
GO:0006996	0.63	organelle organization
GO:0006259	0.59	DNA metabolic process
GO:0050896	0.57	response to stimulus
GO:0022402	0.53	cell cycle process
GO:0006950	0.53	response to stress
GO:0051716	0.52	cellular response to stimulus
GO:0033554	0.51	cellular response to stress
GO:0065007	0.50	biological regulation

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:0044424	0.99	intracellular part
GO:0044422	0.86	organelle part
GO:0044446	0.85	intracellular organelle part
GO:0032991	0.83	macromolecular complex
GO:0043234	0.76	protein complex
GO:0043226	0.66	organelle
GO:0044444	0.65	cytoplasmic part
GO:0043229	0.64	intracellular organelle
GO:0016020	0.59	membrane
GO:0044427	0.53	chromosomal part
GO:0043227	0.53	membrane-bounded organelle
GO:0005886	0.53	plasma membrane
GO:0044425	0.52	membrane part
GO:0043231	0.50	intracellular membrane-bounded organelle

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	2pffB	0.188	8.96	0.041	0.299	2.3.1.86	NA
2	0.060	2vuaA	0.133	7.79	0.041	0.192	3.4.24.69	NA
3	0.060	2pffD	0.242	9.01	0.031	0.379	2.3.1.86	NA
4	0.060	3btaA	0.244	9.21	0.038	0.395	3.4.24.69	NA
5	0.060	1llwA	0.274	9.18	0.041	0.438	1.4.7.1	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:

Click to view	Rank	Cscore^LB	PDB Hit	TM-score	RMSD^a	IDEN^a	Cov.	BS-score	Lig. Name	Download Complex	Predicted binding site residues
	1	0.12	1w1wA	0.266	1.84	0.307	0.272	0.87	ATG	Download	13,14,35,36,37,38,39,40,921

	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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