D-I-TASSER Q12908

D-I-TASSER results for Q12908

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

Summary of the Protein

Uniprot ID: Q12908
Protein Name: Ileal sodium/bile acid cotransporter
Gene Name: SLC10A2

Input Sequence in FASTA format

>Q12908 (348 residues)
MNDPNSCVDNATVCSGASCVVPESNFNNILSVVLSTVLTILLALVMFSMGCNVEIKKFLG
HIKRPWGICVGFLCQFGIMPLTGFILSVAFDILPLQAVVVLIIGCCPGGTASNILAYWVD
GDMDLSVSMTTCSTLLALGMMPLCLLIYTKMWVDSGSIVIPYDNIGTSLVSLVVPVSIGM
FVNHKWPQKAKIILKIGSIAGAILIVLIAVVGGILYQSAWIIAPKLWIIGTIFPVAGYSL
GFLLARIAGLPWYRCRTVAFETGMQNTQLCSTIVQLSFTPEELNVVFTFPLIYSIFQLAF
AAIFLGFYVAYKKCHGKNKAEIPESKENGTEPESSFYKANGGFQPDEK

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	Q12908-D1	1-348	348		MNDPNSCVDNATVCSGASCVVPESNFNNILSVVLSTVLTILLALVMFSMGCNVEIKKFLGHIKRPWGICVGFLCQFGIMPLTGFILSVAFDILPLQAVVVLIIGCCPGGTASNILAYWVDGDMDLSVSMTTCSTLLALGMMPLCLLIYTKMWVDSGSIVIPYDNIGTSLVSLVVPVSIGMFVNHKWPQKAKIILKIGSIAGAILIVLIAVVGGILYQSAWIIAPKLWIIGTIFPVAGYSLGFLLARIAGLPWYRCRTVAFETGMQNTQLCSTIVQLSFTPEELNVVFTFPLIYSIFQLAFAAIFLGFYVAYKKCHGKNKAEIPESKENGTEPESSFYKANGGFQPDEK

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.767

(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	4n7wA	0.86	1.27	0.225	0.879	model1_4n7wA.pdb.gz
2	3zuxA	0.84	1.69	0.242	0.879	model1_3zuxA.pdb.gz
3	4czbA	0.67	4.33	0.090	0.885	model1_4czbA.pdb.gz
4	4bwzA	0.65	4.77	0.108	0.902	model1_4bwzA.pdb.gz
5	4cz8A	0.65	4.38	0.076	0.865	model1_4cz8A.pdb.gz
6	1zcdA	0.64	3.97	0.088	0.816	model1_1zcdA.pdb.gz
7	6z3yB	0.62	4.52	0.073	0.842	model1_6z3yB.pdb.gz
8	6iwwA	0.51	5.05	0.087	0.695	model1_6iwwA.pdb.gz
9	6gctA	0.50	5.27	0.052	0.707	model1_6gctA.pdb.gz
10	3kbcA	0.49	5.50	0.069	0.721	model1_3kbcA.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:0005342	1.00	organic acid transmembrane transporter activity
GO:0015075	0.73	ion transmembrane transporter activity
GO:0022804	0.72	active transmembrane transporter activity
GO:0015291	0.71	secondary active transmembrane transporter activity
GO:0008324	0.71	cation transmembrane transporter activity
GO:0046873	0.70	metal ion transmembrane transporter activity
GO:0015077	0.70	monovalent inorganic cation transmembrane transporter activity
GO:0015370	0.69	solute:sodium symporter activity
GO:0005319	0.69	lipid transporter activity
GO:0008508	0.68	bile acid:sodium 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:0006810	0.95	transport
GO:0044699	0.94	single-organism process
GO:0071702	0.87	organic substance transport
GO:0044765	0.86	single-organism transport
GO:0006811	0.81	ion transport
GO:0015850	0.80	organic hydroxy compound transport
GO:0015711	0.80	organic anion transport
GO:0015718	0.76	monocarboxylic acid transport
GO:0006869	0.74	lipid transport
GO:0015721	0.73	bile acid and bile salt transport
GO:0009987	0.53	cellular 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:0005887	1.00	integral component of 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	0.060	2fknB	0.375	6.44	0.053	0.612	4.2.1.49	78
2	0.060	2b3xA	0.340	7.24	0.035	0.626	4.2.1.3	NA
3	0.060	2i7vA	0.363	6.50	0.065	0.595	3.1.27.-	NA
4	0.060	1reqA	0.380	6.73	0.043	0.644	5.4.99.2	NA
5	0.060	1biqB	0.344	6.24	0.036	0.546	1.17.4.1	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	0.19	3zuxA	0.841	1.69	0.242	0.879	1.49	TCH	complex1.pdb.gz	67,70,248,249,250,251
2	0.18	3zuxA	0.841	1.69	0.242	0.879	1.45	NA	complex2.pdb.gz	75,79,108,261,262,263,264,265
3	0.08	3zuyA	0.842	1.68	0.245	0.879	0.86	PTY	complex3.pdb.gz	242,243,245,246
4	0.08	3zuxA	0.841	1.69	0.242	0.879	0.62	PTY	complex4.pdb.gz	235,238,242,259
5	0.01	1siwA	0.369	7.02	0.033	0.647	0.63	SF4	complex5.pdb.gz	76,83,105,107,263
6	0.01	1kqfA	0.342	7.25	0.039	0.603	0.61	SF4	complex6.pdb.gz	69,71,72,74,130,132,133

	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, Qiqige Wuyun, Yang Li, Quancheng Liu, Xiaogen Zhou, Yiheng Zhu, P. Lydia Freddolino, Yang Zhang. Integrating deep learning potentials with I-TASSER for single- and multi-domain protein structure prediction. Submitted. 2023.