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COFACTOR result for job id 76713

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>76713 (885 residues)
MFKTKKGNLKSLDYKKQDYVIKLSNTNSNNLESILDSKIGLNNQTRQNNISKFGSNQIVV
KKFLIFKKILETLIEPFNLLLLFIGILELIIYFLFQRNWITLISAFIIFFMIFLASIVDF
IQEYKAYKFNLKLTKIIENDVFVVNDQIKDFNNLNYQNIKNNLIKEKQSNLTIGDVVYLS
KGDIIPSDCRIIWSEDLYLDESTLTGESKAIKKQTTNTKTNFLELENILFKETLIVSGNC
LAVVININKDNYSNSLLDLIDDEVITDYEKGINKVTKILIYLISILVFIITFISLLKTGI
SNWTSSLVFGLSIAVSLTPEALPAIISSNLKLASKRLSKNKVVIKKLSVLQNIGSVNILA
TDKTGTLTLDTTNIETYLDINNQKNKLLMQYFFYNAYFQNNLFDTIDKAIIDQFKTNISD
IKLIDHLSFDHNFRISSVLINFNSSNLLITKGSLEEILEITSFINVNNQVINLCDNYKNM
IIDQVNSYTKKGYKVLVLSYKNSDVIDNKNLIYLGMVVFSDQIRENVKQVIDTFKAYDID
IKVLSGDNLYTCKNVCDQVGINSNTSLIGKQINNLTKEELIKISQSVNIFYKLSPLDKAK
IIDSLKSNNVVGFLGDGVNDAVALKKADVGISVNNASSLAKQSADVILLEKDLNALEHAF
IIGRKTFSNAIKYIKITVASNFGILLTLLLATSLFKFEVMSPIQLLIQNLIFDFANLVFV
FDNVDESSIKKPQKWNIKSIIPFAIFNGLTQVIISFINFMILYFGFNIKGLDTYSIELFQ
TCYFIECILTHIMIILVLRTDKLSFFKSIASKQMLISMLFFSVVCFMIVFISSSFNSLGF
KMMIGNFNNINLSWWFLILFGLEILSWIISELIKKIYLIIFKNWI

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	0.84	4.07	0.190	0.954	Download
2	3ixzA	0.84	4.03	0.191	0.948	Download
3	3ba6A	0.69	5.18	0.138	0.825	Download
4	6a69A	0.69	4.98	0.158	0.817	Download
5	3b8cA	0.67	5.57	0.143	0.835	Download
6	1mhsA	0.60	6.41	0.145	0.794	Download
7	3rfuA	0.55	4.81	0.162	0.658	Download
8	3j08A	0.55	4.63	0.140	0.647	Download
9	6hraB	0.52	6.52	0.122	0.695	Download
10	4umvA	0.51	5.05	0.170	0.619	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:0022892	1.00	substrate-specific transporter activity
GO:0016887	1.00	ATPase activity
GO:0043492	0.99	ATPase activity, coupled to movement of substances
GO:0042625	0.97	ATPase coupled ion transmembrane transporter activity
GO:0008324	0.97	cation transmembrane transporter activity
GO:0019829	0.96	cation-transporting ATPase activity
GO:0022890	0.86	inorganic cation transmembrane transporter activity
GO:0015662	0.84	ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism
GO:0046873	0.78	metal ion transmembrane transporter activity
GO:0015077	0.59	monovalent inorganic cation transmembrane transporter activity
GO:0043167	0.55	ion binding
GO:1901363	0.54	heterocyclic compound binding
GO:0097159	0.54	organic cyclic compound binding
GO:0046872	0.52	metal ion binding
GO:0036094	0.51	small molecule binding
GO:0008556	0.51	potassium-transporting ATPase activity
GO:0005391	0.50	sodium:potassium-exchanging ATPase activity
GO:0000166	0.50	nucleotide binding

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	0.94	biological regulation
GO:0044699	0.92	single-organism process
GO:0044763	0.91	single-organism cellular process
GO:0065008	0.90	regulation of biological quality
GO:0042592	0.89	homeostatic process
GO:0098771	0.88	inorganic ion homeostasis
GO:0055080	0.88	cation homeostasis
GO:0019725	0.88	cellular homeostasis
GO:0030003	0.87	cellular cation homeostasis
GO:0006875	0.77	cellular metal ion homeostasis
GO:0006810	0.77	transport
GO:0006811	0.72	ion transport
GO:0055085	0.68	transmembrane transport
GO:0034220	0.67	ion transmembrane transport
GO:0006812	0.66	cation transport
GO:0098662	0.60	inorganic cation transmembrane transport
GO:0050789	0.60	regulation of biological process
GO:0008152	0.60	metabolic process
GO:0015672	0.58	monovalent inorganic cation transport
GO:1902600	0.57	hydrogen ion transmembrane transport
GO:0030004	0.57	cellular monovalent inorganic cation homeostasis
GO:0071704	0.55	organic substance metabolic process
GO:0044237	0.55	cellular metabolic process
GO:0030001	0.54	metal ion transport
GO:0044238	0.51	primary 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:0044424	0.99	intracellular part
GO:0044425	0.97	membrane part
GO:0016021	0.96	integral component of membrane
GO:0044459	0.91	plasma membrane part
GO:0043231	0.88	intracellular membrane-bounded organelle
GO:0005887	0.88	integral component of plasma membrane
GO:0044444	0.71	cytoplasmic part
GO:0016020	0.67	membrane
GO:0005886	0.50	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	0.419	3b8eA	0.844	4.09	0.186	0.954	3.6.3.9	362
2	0.154	3b8eC	0.844	4.06	0.186	0.953	3.6.3.9	NA
3	0.118	3b8cA	0.674	5.57	0.143	0.835	3.6.3.6	362
4	0.083	1mhsA	0.603	6.41	0.145	0.794	3.6.3.6	362
5	0.060	2pffD	0.323	8.74	0.044	0.508	2.3.1.86	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	0.04	3nalA	0.942	1.26	0.203	0.956	0.14	DBK	Download	41,53,54,164,231
	2	0.04	3fgoA	0.863	3.43	0.190	0.950	0.20	CZA	Download	41,46,178

	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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