D-I-TASSER P22459

D-I-TASSER results for P22459

[Click result.zip to download all results on this page]

Summary of the Protein

Uniprot ID: P22459
Protein Name: Potassium voltage-gated channel subfamily A member 4
Gene Name: KCNA4

Input Sequence in FASTA format

>P22459 (653 residues)
MEVAMVSAESSGCNSHMPYGYAAQARARERERLAHSRAAAAAAVAAATAAVEGSGGSGGG
SHHHHQSRGACTSHDPQSSRGSRRRRRQRSEKKKAHYRQSSFPHCSDLMPSGSEEKILRE
LSEEEEDEEEEEEEEEEGRFYYSEDDHGDECSYTDLLPQDEGGGGYSSVRYSDCCERVVI
NVSGLRFETQMKTLAQFPETLLGDPEKRTQYFDPLRNEYFFDRNRPSFDAILYYYQSGGR
LKRPVNVPFDIFTEEVKFYQLGEEALLKFREDEGFVREEEDRALPENEFKKQIWLLFEYP
ESSSPARGIAIVSVLVILISIVIFCLETLPEFRDDRDLVMALSAGGHGGLLNDTSAPHLE
NSGHTIFNDPFFIVETVCIVWFSFEFVVRCFACPSQALFFKNIMNIIDIVSILPYFITLG
TDLAQQQGGGNGQQQQAMSFAILRIIRLVRVFRIFKLSRHSKGLQILGHTLRASMRELGL
LIFFLFIGVILFSSAVYFAEADEPTTHFQSIPDAFWWAVVTMTTVGYGDMKPITVGGKIV
GSLCAIAGVLTIALPVPVIVSNFNYFYHRETENEEQTQLTQNAVSCPYLPSNLLKKFRSS
TSSSLGDKSEYLEMEEGVKESLCAKEEKCQGKGDDSETDKNNCSNAKAVETDV

Predicted Contact and Distance Map Used in D-I-TASSER simulation

Contact Map

Distance Map

D-I-TASSER simulation is guided by the consensus contact map (left figure) and distance map (right figure) derived based on confidence scores of AttentionPotential. In the contact, distance map and hydrogen bond networks, the axes mark the residue index along the sequence. For the contact map, each dot represents a residue pair with predicted contact, while for the distance map and hydrogen bond network, a color scale represents a distance of 1-20+ angstroms or a angle of 0-180 degree.

Information of Domain

No. of Domain	Domain	Domain Boundary	Length of Domain	Models of Domain	Sequence
1	P22459-D1	1-69,143-274	201		MEVAMVSAESSGCNSHMPYGYAAQARARERERLAHSRAAAAAAVAAATAAVEGSGGSGGGSHHHHQSRGSEDDHGDECSYTDLLPQDEGGGGYSSVRYSDCCERVVINVSGLRFETQMKTLAQFPETLLGDPEKRTQYFDPLRNEYFFDRNRPSFDAILYYYQSGGRLKRPVNVPFDIFTEEVKFYQLGEEALLKFREDEG
2	P22459-D2	70-142,573-653	154		ACTSHDPQSSRGSRRRRRQRSEKKKAHYRQSSFPHCSDLMPSGSEEKILRELSEEEEDEEEEEEEEEEGRFYYNEEQTQLTQNAVSCPYLPSNLLKKFRSSTSSSLGDKSEYLEMEEGVKESLCAKEEKCQGKGDDSETDKNNCSNAKAVETDV
3	P22459-D3	275-460	186		FVREEEDRALPENEFKKQIWLLFEYPESSSPARGIAIVSVLVILISIVIFCLETLPEFRDDRDLVMALSAGGHGGLLNDTSAPHLENSGHTIFNDPFFIVETVCIVWFSFEFVVRCFACPSQALFFKNIMNIIDIVSILPYFITLGTDLAQQQGGGNGQQQQAMSFAILRIIRLVRVFRIFKLSRH
4	P22459-D4	461-572	112		SKGLQILGHTLRASMRELGLLIFFLFIGVILFSSAVYFAEADEPTTHFQSIPDAFWWAVVTMTTVGYGDMKPITVGGKIVGSLCAIAGVLTIALPVPVIVSNFNYFYHRETE

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.48

(a)

D-I-TASSER simulations generate a large ensemble of structural conformations, i.e. decoys. These decoys are clustered by SPICKER based on pairwise structure similarity to report up to five final models from the five largest clusters. Models are ranked in descending order of cluster size. If the simulations converge well, it is possible to have less than 5 models generated, which is usually an indication of good model quality.

(b)

The model confidence is quantitatified by estimated TM-score (eTM-score), calculated based on significance of threading template alignments, contact map satisfaction rate, mean absolute error between distance of model and distance of AttentionPotential, and convergence of D-I-TASSER simulations. eTM-score is typically in the range of [0, 1], with higher eTM-score signifies higher model confidence.

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	5a22A	0.35	7.89	0.032	0.557	model1_5a22A.pdb.gz
2	1kekA	0.35	8.26	0.035	0.582	model1_1kekA.pdb.gz
3	6r9tA	0.35	7.49	0.045	0.533	model1_6r9tA.pdb.gz
4	6uebA	0.35	8.05	0.029	0.564	model1_6uebA.pdb.gz
5	6cinA	0.35	8.29	0.027	0.582	model1_6cinA.pdb.gz
6	1llwA	0.34	7.58	0.043	0.524	model1_1llwA.pdb.gz
7	6w98A	0.34	8.09	0.037	0.547	model1_6w98A.pdb.gz
8	2r9rB	0.34	4.26	0.326	0.384	model1_2r9rB.pdb.gz
9	5mz61	0.34	8.45	0.048	0.568	model1_5mz61.pdb.gz
10	7alpU2	0.33	8.03	0.032	0.531	model1_7alpU2.pdb.gz

(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:0022836	1.00	gated channel activity
GO:0005261	1.00	cation channel activity
GO:0046873	0.99	metal ion transmembrane transporter activity
GO:0022843	0.99	voltage-gated cation channel activity
GO:0015077	0.99	monovalent inorganic cation transmembrane transporter activity
GO:0005249	0.98	voltage-gated potassium channel activity
GO:0005251	0.94	delayed rectifier potassium channel 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:0044699	0.89	single-organism process
GO:0006810	0.88	transport
GO:0006811	0.87	ion transport
GO:0030001	0.85	metal ion transport
GO:0015672	0.84	monovalent inorganic cation transport
GO:0009987	0.84	cellular process
GO:0006813	0.82	potassium ion transport
GO:0044763	0.80	single-organism cellular process
GO:0065007	0.70	biological regulation
GO:0055085	0.60	transmembrane transport
GO:0034220	0.58	ion transmembrane transport
GO:0050789	0.57	regulation of biological process
GO:0098662	0.55	inorganic cation transmembrane transport
GO:0071805	0.54	potassium ion transmembrane 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:0044425	0.98	membrane part
GO:0016021	0.92	integral component of membrane
GO:0044464	0.86	cell part
GO:0016020	0.53	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	1qf6A	0.292	7.97	0.033	0.469	6.1.1.3	243
2	0.060	2vdcF	0.344	7.81	0.043	0.544	1.4.1.13	NA
3	0.060	1ofdA	0.272	8.79	0.032	0.475	1.4.7.1	NA
4	0.060	2rnpC	0.301	7.58	0.012	0.469	2.7.7.6	NA
5	0.060	1bxrA	0.321	8.05	0.037	0.521	6.3.5.5	85

	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	1a9x3	0.310	8.09	0.031	0.499	0.16	III	complex1.pdb.gz	182,183,187,238
2	0.01	1ofdA	0.272	8.79	0.032	0.475	0.26	F3S	complex2.pdb.gz	184,185,186,187,188,221
3	0.01	1bxrE	0.326	7.98	0.027	0.527	0.11	ANP	complex3.pdb.gz	184,185,202,240
4	0.01	1b0pA	0.348	8.09	0.043	0.576	0.11	TPP	complex4.pdb.gz	2,3,224,229,232
5	0.01	1jdbB	0.313	7.93	0.029	0.499	0.19	GLN	complex5.pdb.gz	181,182,183,224
6	0.01	1ce8G	0.320	7.92	0.049	0.513	0.16	IMP	complex6.pdb.gz	200,202,203
7	0.01	1t36A	0.320	8.05	0.036	0.519	0.19	U	complex7.pdb.gz	181,182,220

	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.

[Click result.zip to download all results on this page]

References:
1.	Wei Zheng, Chengxin Zhang, Yang Li, Robin Pearce, Eric W. Bell, Yang Zhang. Folding non-homology proteins by coupling deep-learning contact maps with I-TASSER assembly simulations. In preparation, 2020.