[back]

COFACTOR result for job id 76657

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

User Input

>76657 (942 residues)
MFLFKKRKFSPKKITRHKKKTHFANERFIKQVSNLEQNEVLEIMQLQHFGLTNEQYESRL
KKYGTNELKKKRFNLIAEFLHAFFGPFNIVLLLISLYNFISYATNGFYQDTNSSDSKFEL
VGALIILVMVLASGLASFIQSLRSHLVTKKISSIVKSTTNIIRHKNDEDVEDYLKITKRN
QLDLIRLGEEIDVKQLVPGDLIYLSSGDMLPADVRIIQSTDLFINQSSLTGESIPVEKHA
NNKKNTNNILDLENICYTGTSVVSGSALAVVLATANDTYFSTISKAILEKRPDSSFTKGI
KQVTRMLLIFMLVMVPTVYLAKSIIGTISSGGSFDSIKDNPWFQAIFFAVAVAVGLTPEM
LPMIVTTNLANGASKMSKQKVVVKQLEAIQSLGAIDVLCTDKTGTLTNDKIELVDYLRVD
KKADPTLLKYLYINSYYQTGLKNPMDKAIVDYVNKHNHNFSIQDITKIDEIPFDFNRRKL
TIIFDDENEKRFMVTKGSVEEILNSCTRVIQDDKVVNLTDTFKRQIIAYYETINQQGKRL
LGVAYKKIRDNQAKFSPKDEESLIFMGFASFLDTPKPSTKQTIKLLKKYGVDLKILTGDS
EPITRAICKMVNLDIKGLVTGEEIDAASEYELKKIVEDNNIFVKLNPLQKVKIIQVLKQN
NHVVGYMGDGINDAPVLRQSDVAISVNNATEIAKDASDIILLEKSLLVLEKGIIQGRTIF
GNILKYIKITTASNFGNALSVLIGTVWLPFSPMAPAQILLQNLIYDFSQFGVALDRVDST
FLTSPQRWQSKDLLPFTTINGSISTIFDLITFAIAGYYFGFITSYNSAIAQNNSLLAAQS
LAQFHACWFIIGLLSQTFVFQILRTEQLPVIQSRSTWPVYVIGALATIMAFSIVYISQIG
SLVQLQSPGLIYIPISIAIIFSYCLIAQLTKVGYKKVFKKWL

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	3kdpA	0.82	4.28	0.184	0.927	Download
2	3ixzA	0.81	4.06	0.183	0.914	Download
3	3ba6A	0.68	5.62	0.160	0.824	Download
4	6a69A	0.67	5.25	0.157	0.807	Download
5	3b8cA	0.65	5.62	0.139	0.797	Download
6	1mhsA	0.58	6.32	0.143	0.756	Download
7	3rfuA	0.53	4.82	0.173	0.631	Download
8	3j08A	0.53	4.79	0.156	0.619	Download
9	6hraB	0.51	6.54	0.126	0.666	Download
10	4umvA	0.49	5.03	0.173	0.587	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:0043492	1.00	ATPase activity, coupled to movement of substances
GO:0022892	1.00	substrate-specific transporter activity
GO:0022857	0.95	transmembrane transporter activity
GO:0022804	0.94	active transmembrane transporter activity
GO:0015075	0.94	ion transmembrane transporter activity
GO:0019829	0.93	cation-transporting ATPase activity
GO:0022890	0.80	inorganic cation transmembrane transporter activity
GO:0015662	0.78	ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism
GO:0046873	0.71	metal ion 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:0009987	0.98	cellular process
GO:0065007	0.91	biological regulation
GO:0044699	0.90	single-organism process
GO:0044763	0.88	single-organism cellular process
GO:0065008	0.87	regulation of biological quality
GO:0019725	0.85	cellular homeostasis
GO:0098771	0.84	inorganic ion homeostasis
GO:0030003	0.84	cellular cation homeostasis
GO:0006875	0.73	cellular metal ion homeostasis
GO:0006810	0.72	transport
GO:0006811	0.65	ion transport
GO:0008152	0.63	metabolic process
GO:0055085	0.60	transmembrane transport
GO:0034220	0.59	ion transmembrane transport
GO:0006812	0.59	cation transport
GO:0071704	0.57	organic substance metabolic process
GO:0044237	0.57	cellular metabolic process
GO:0044238	0.53	primary metabolic process
GO:0098662	0.52	inorganic cation transmembrane transport
GO:0015672	0.50	monovalent inorganic cation transport

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:0016021	0.96	integral component of membrane
GO:0044459	0.87	plasma membrane part
GO:0043231	0.87	intracellular membrane-bounded organelle
GO:0005887	0.85	integral component of plasma membrane
GO:0044444	0.72	cytoplasmic part
GO:0016020	0.71	membrane
GO:0005886	0.52	plasma 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	0.454	3b8eA	0.816	4.29	0.190	0.926	3.6.3.9	401
2	0.176	3b8cA	0.647	5.62	0.139	0.797	3.6.3.6	401
3	0.155	3b8eC	0.816	4.27	0.186	0.924	3.6.3.9	NA
4	0.125	1mhsA	0.584	6.32	0.143	0.756	3.6.3.6	401
5	0.073	3ixzA	0.811	4.06	0.183	0.914	3.6.3.10	401

	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:

No Binding sites was predicted

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

	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]