D-I-TASSER P43007

D-I-TASSER results for P43007

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

Summary of the Protein

Uniprot ID: P43007
Protein Name: Neutral amino acid transporter A
Gene Name: SLC1A4

Input Sequence in FASTA format

>P43007 (532 residues)
MEKSNETNGYLDSAQAGPAAGPGAPGTAAGRARRCAGFLRRQALVLLTVSGVLAGAGLGA
ALRGLSLSRTQVTYLAFPGEMLLRMLRMIILPLVVCSLVSGAASLDASCLGRLGGIAVAY
FGLTTLSASALAVALAFIIKPGSGAQTLQSSDLGLEDSGPPPVPKETVDSFLDLARNLFP
SNLVVAAFRTYATDYKVVTQNSSSGNVTHEKIPIGTEIEGMNILGLVLFALVLGVALKKL
GSEGEDLIRFFNSLNEATMVLVSWIMWYVPVGIMFLVGSKIVEMKDIIVLVTSLGKYIFA
SILGHVIHGGIVLPLIYFVFTRKNPFRFLLGLLAPFATAFATCSSSATLPSMMKCIEENN
GVDKRISRFILPIGATVNMDGAAIFQCVAAVFIAQLNNVELNAGQIFTILVTATASSVGA
AGVPAGGVLTIAIILEAIGLPTHDLPLILAVDWIVDRTTTVVNVEGDALGAGILHHLNQK
ATKKGEQELAEVKVEAIPNCKSEEETSPLVTHQNPAGPVASAPELESKESVL

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	P43007-D1	1-532	532		MEKSNETNGYLDSAQAGPAAGPGAPGTAAGRARRCAGFLRRQALVLLTVSGVLAGAGLGAALRGLSLSRTQVTYLAFPGEMLLRMLRMIILPLVVCSLVSGAASLDASCLGRLGGIAVAYFGLTTLSASALAVALAFIIKPGSGAQTLQSSDLGLEDSGPPPVPKETVDSFLDLARNLFPSNLVVAAFRTYATDYKVVTQNSSSGNVTHEKIPIGTEIEGMNILGLVLFALVLGVALKKLGSEGEDLIRFFNSLNEATMVLVSWIMWYVPVGIMFLVGSKIVEMKDIIVLVTSLGKYIFASILGHVIHGGIVLPLIYFVFTRKNPFRFLLGLLAPFATAFATCSSSATLPSMMKCIEENNGVDKRISRFILPIGATVNMDGAAIFQCVAAVFIAQLNNVELNAGQIFTILVTATASSVGAAGVPAGGVLTIAIILEAIGLPTHDLPLILAVDWIVDRTTTVVNVEGDALGAGILHHLNQKATKKGEQELAEVKVEAIPNCKSEEETSPLVTHQNPAGPVASAPELESKESVL

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.6787

(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	6gctA	0.77	1.83	0.664	0.804	model1_6gctA.pdb.gz
2	6s3qA	0.76	2.15	0.476	0.806	model1_6s3qA.pdb.gz
3	3kbcA	0.69	2.35	0.317	0.746	model1_3kbcA.pdb.gz
4	5llmA	0.50	4.98	0.311	0.635	model1_5llmA.pdb.gz
5	4czbA	0.41	5.42	0.080	0.541	model1_4czbA.pdb.gz
6	6uebA	0.39	8.02	0.038	0.682	model1_6uebA.pdb.gz
7	4cz8A	0.38	5.66	0.091	0.528	model1_4cz8A.pdb.gz
8	1zcdA	0.38	5.43	0.066	0.502	model1_1zcdA.pdb.gz
9	6z3yB	0.38	5.39	0.090	0.500	model1_6z3yB.pdb.gz
10	3ir7A	0.38	7.55	0.050	0.613	model1_3ir7A.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:0022891	0.99	substrate-specific transmembrane transporter activity
GO:0046943	0.87	carboxylic acid transmembrane transporter activity
GO:0015171	0.85	amino acid transmembrane transporter activity
GO:0015075	0.82	ion transmembrane transporter activity
GO:0008509	0.67	anion transmembrane transporter activity
GO:0022804	0.60	active transmembrane transporter activity
GO:0015291	0.59	secondary active transmembrane transporter activity
GO:0015293	0.58	symporter activity
GO:0008324	0.58	cation transmembrane transporter activity
GO:0015294	0.57	solute:cation symporter activity
GO:0015172	0.52	acidic amino acid transmembrane transporter activity
GO:0008514	0.52	organic anion transmembrane transporter activity
GO:0005313	0.51	L-glutamate 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:0006810	0.94	transport
GO:0071702	0.92	organic substance transport
GO:0006820	0.86	anion transport
GO:0071705	0.85	nitrogen compound transport
GO:0046942	0.85	carboxylic acid transport
GO:0006865	0.79	amino acid transport
GO:0015807	0.68	L-amino acid transport
GO:0009987	0.65	cellular process
GO:0006835	0.58	dicarboxylic acid transport
GO:0044763	0.51	single-organism cellular process
GO:0015800	0.51	acidic amino acid 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:0016020	0.95	membrane
GO:0005886	0.87	plasma membrane
GO:0044424	0.65	intracellular 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	3b9jI	0.145	5.84	0.091	0.201	1.17.1.4 1.17.3.2	282
2	0.060	1h2aL	0.327	7.15	0.066	0.513	1.12.2.1	NA
3	0.060	2z8yD	0.302	7.75	0.049	0.500	1.2.7.4 1.2.99.2	433
4	0.060	1frvB	0.325	7.21	0.061	0.515	1.12.2.1	NA
5	0.060	2e1qA	0.314	7.19	0.043	0.489	1.17.3.2 1.17.1.4	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:

Rank	Cscore^LB	PDB Hit	TM-score	RMSD^a	IDEN^a	Cov.	BS-score	Lig. Name	Download Complex	Predicted binding site residues
1	0.06	2nwxB	0.448	3.73	0.257	0.504	0.22	ASP	complex1.pdb.gz	54,55,56,75
2	0.05	3kbcA	0.695	2.35	0.317	0.746	0.10	ASP	complex2.pdb.gz	96,102,103
3	0.01	2nwwA	0.449	5.54	0.109	0.607	0.34	TB1	complex3.pdb.gz	55,75,78,79,82
4	0.01	3ir6A	0.373	7.56	0.051	0.607	0.14	GDP	complex4.pdb.gz	58,80,82,278
5	0.01	1n38A	0.332	7.64	0.043	0.543	0.24	QNA	complex5.pdb.gz	49,50,55,82,83
6	0.01	1n38A	0.332	7.64	0.043	0.543	0.39	CH1	complex6.pdb.gz	82,83,446
7	0.01	3ir5A	0.375	7.48	0.051	0.607	0.24	SF4	complex7.pdb.gz	57,59,60,277
8	0.01	1n35A	0.344	7.99	0.031	0.583	0.11	QNA	complex8.pdb.gz	55,56,57,61,280,296
9	0.01	2iw3A	0.339	7.08	0.048	0.524	0.17	ADP	complex9.pdb.gz	90,97,259
10	0.01	1yqwQ	0.329	7.14	0.052	0.521	0.18	UUU	complex10.pdb.gz	54,59,60

	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.