D-I-TASSER A0AV02

D-I-TASSER results for A0AV02

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

Summary of the Protein

Uniprot ID: A0AV02
Protein Name: Solute carrier family 12 member 8
Gene Name: SLC12A8

Input Sequence in FASTA format

>A0AV02 (714 residues)
MTQMSQVQELFHEAAQQDALAQPQPWWKTQLFMWEPVLFGTWDGVFTSCMINIFGVVLFL
RTGWLVGNTGVLLGMFLVSFVILVALVTVLSGIGVGERSSIGSGGVYSMISSVLGGQTGG
TIGLLYVFGQCVAGAMYITGFAESISDLLGLGNIWAVRGISVAVLLALLGINLAGVKWII
RLQLLLLFLLAVSTLDFVVGSFTHLDPEHGFIGYSPELLQNNTLPDYSPGESFFTVFGVF
FPAATGVMAGFNMGGDLREPAASIPLGSLAAVGISWFLYIIFVFLLGAICTREALRYDFL
IAEKVSLMGFLFLLGLYISSLASCMGGLYGAPRILQCIAQEKVIPALACLGQGKGPNKTP
VAAICLTSLVTMAFVFVGQVNVLAPIVTINFMLTYVAVDYSYFSLSMCSCSLTPVPEPVL
REGAEGLHCSEHLLLEKAPSYGSEGPAQRVLEGTLLEFTKDMDQLLQLTRKLESSQPRQG
EGNRTPESQKRKSKKATKQTLQDSFLLDLKSPPSFPVEISDRLPAASWEGQESCWNKQTS
KSEGTQPEGTYGEQLVPELCNQSESSGEDFFLKSRLQEQDVWRRSTSFYTHMCNPWVSLL
GAVGSLLIMFVIQWVYTLVNMGVAAIVYFYIGRASPGLHLGSASNFSFFRWMRSLLLPSC
RSLRSPQEQIILAPSLAKVDMEMTQLTQENADFATRDRYHHSSLVNREQLMPHY

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 DeepPotential. 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	A0AV02-D1	1-40	40		MTQMSQVQELFHEAAQQDALAQPQPWWKTQLFMWEPVLFG
2	A0AV02-D2	41-418,589-714	504		TWDGVFTSCMINIFGVVLFLRTGWLVGNTGVLLGMFLVSFVILVALVTVLSGIGVGERSSIGSGGVYSMISSVLGGQTGGTIGLLYVFGQCVAGAMYITGFAESISDLLGLGNIWAVRGISVAVLLALLGINLAGVKWIIRLQLLLLFLLAVSTLDFVVGSFTHLDPEHGFIGYSPELLQNNTLPDYSPGESFFTVFGVFFPAATGVMAGFNMGGDLREPAASIPLGSLAAVGISWFLYIIFVFLLGAICTREALRYDFLIAEKVSLMGFLFLLGLYISSLASCMGGLYGAPRILQCIAQEKVIPALACLGQGKGPNKTPVAAICLTSLVTMAFVFVGQVNVLAPIVTINFMLTYVAVDYSYFSLSMCSCSLTPVPEPYTHMCNPWVSLLGAVGSLLIMFVIQWVYTLVNMGVAAIVYFYIGRASPGLHLGSASNFSFFRWMRSLLLPSCRSLRSPQEQIILAPSLAKVDMEMTQLTQENADFATRDRYHHSSLVNREQLMPHY
3	A0AV02-D3	419-588	170		VLREGAEGLHCSEHLLLEKAPSYGSEGPAQRVLEGTLLEFTKDMDQLLQLTRKLESSQPRQGEGNRTPESQKRKSKKATKQTLQDSFLLDLKSPPSFPVEISDRLPAASWEGQESCWNKQTSKSEGTQPEGTYGEQLVPELCNQSESSGEDFFLKSRLQEQDVWRRSTSF

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.47

(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 DeepPotential, 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	6nplA	0.65	3.21	0.306	0.705	model1_6nplA.pdb.gz
2	7ainB	0.63	3.59	0.256	0.696	model1_7ainB.pdb.gz
3	7d8zB	0.63	3.63	0.249	0.686	model1_7d8zB.pdb.gz
4	6kkrA	0.56	2.13	0.314	0.590	model1_6kkrA.pdb.gz
5	5oqtA	0.54	3.21	0.151	0.598	model1_5oqtA.pdb.gz
6	6f2gA	0.53	3.16	0.153	0.580	model1_6f2gA.pdb.gz
7	7cmhB	0.53	3.27	0.147	0.583	model1_7cmhB.pdb.gz
8	6li9B	0.53	3.09	0.133	0.577	model1_6li9B.pdb.gz
9	6irsB	0.52	3.39	0.122	0.580	model1_6irsB.pdb.gz
10	3l1lA	0.52	3.17	0.132	0.573	model1_3l1lA.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:0022892	1.00	substrate-specific transporter activity
GO:0022857	1.00	transmembrane transporter activity
GO:0022891	0.99	substrate-specific transmembrane transporter activity
GO:0022804	0.95	active transmembrane transporter activity
GO:0015291	0.94	secondary active transmembrane transporter activity
GO:0046943	0.71	carboxylic acid transmembrane transporter activity
GO:0015075	0.60	ion transmembrane transporter activity
GO:0008324	0.56	cation transmembrane transporter activity
GO:0015171	0.55	amino acid transmembrane transporter activity
GO:0008509	0.51	anion transmembrane transporter activity
GO:0015293	0.50	symporter 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	0.95	single-organism process
GO:0006810	0.84	transport
GO:0009987	0.80	cellular process
GO:0044763	0.73	single-organism cellular process
GO:0044765	0.72	single-organism transport
GO:0071702	0.67	organic substance transport
GO:0055085	0.66	transmembrane transport
GO:0071705	0.63	nitrogen compound transport
GO:0015849	0.57	organic acid transport
GO:0006811	0.57	ion transport
GO:1905039	0.53	carboxylic acid transmembrane transport
GO:0006820	0.51	anion 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:0044425	0.99	membrane part
GO:0044459	0.97	plasma membrane part
GO:0016021	0.93	integral component of membrane
GO:0016020	0.89	membrane
GO:0005887	0.79	integral component of plasma membrane
GO:0044424	0.68	intracellular part
GO:0005886	0.62	plasma membrane
GO:0044444	0.54	cytoplasmic part

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	3btaA	0.299	8.09	0.035	0.471	3.4.24.69	NA
2	0.060	1t3tA	0.293	8.38	0.048	0.478	6.3.5.3	48,53
3	0.060	3dy5A	0.285	8.00	0.033	0.454	1.13.11.40 4.2.1.92	NA
4	0.060	1llwA	0.333	8.21	0.038	0.535	1.4.7.1	NA
5	0.060	3fedA	0.289	8.49	0.031	0.475	3.4.17.21	473

	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	0.04	3ob6A	0.522	3.47	0.133	0.584	0.41	ARG	complex1.pdb.gz	46,88,92,96
2	0.03	2qeiA	0.487	5.12	0.105	0.604	0.51	ALA	complex2.pdb.gz	27,40,41,253,254,256
3	0.02	2qeiA	0.487	5.12	0.105	0.604	0.43	CXX	complex3.pdb.gz	92,95,96,99,260
4	0.01	3qs4A	0.481	5.12	0.097	0.598	0.42	TRP	complex4.pdb.gz	44,48,176,180,183
5	0.01	2wsxB	0.417	4.57	0.067	0.499	0.54	NM2	complex5.pdb.gz	40,41,44,180,184

	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.