D-I-TASSER Q9GZV3

D-I-TASSER results for Q9GZV3

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

Summary of the Protein

Uniprot ID: Q9GZV3
Protein Name: High affinity choline transporter 1
Gene Name: SLC5A7

Input Sequence in FASTA format

>Q9GZV3 (580 residues)
MAFHVEGLIAIIVFYLLILLVGIWAAWRTKNSGSAEERSEAIIVGGRDIGLLVGGFTMTA
TWVGGGYINGTAEAVYVPGYGLAWAQAPIGYSLSLILGGLFFAKPMRSKGYVTMLDPFQQ
IYGKRMGGLLFIPALMGEMFWAAAIFSALGATISVIIDVDMHISVIISALIATLYTLVGG
LYSVAYTDVVQLFCIFVGLWISVPFALSHPAVADIGFTAVHAKYQKPWLGTVDSSEVYSW
LDSFLLLMLGGIPWQAYFQRVLSSSSATYAQVLSFLAAFGCLVMAIPAILIGAIGASTDW
NQTAYGLPDPKTTEEADMILPIVLQYLCPVYISFFGLGAVSAAVMSSADSSILSASSMFA
RNIYQLSFRQNASDKEIVWVMRITVFVFGASATAMALLTKTVYGLWYLSSDLVYIVIFPQ
LLCVLFVKGTNTYGAVAGYVSGLFLRITGGEPYLYLQPLIFYPGYYPDDNGIYNQKFPFK
TLAMVTSFLTNICISYLAKYLFESGTLPPKLDVFDAVVARHSEENMDKTILVKNENIKLD
ELALVKPRQSMTLSSTFTNKEAFLDVDSSPEGSGTEDNLQ

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	Q9GZV3-D1	1-580	580		MAFHVEGLIAIIVFYLLILLVGIWAAWRTKNSGSAEERSEAIIVGGRDIGLLVGGFTMTATWVGGGYINGTAEAVYVPGYGLAWAQAPIGYSLSLILGGLFFAKPMRSKGYVTMLDPFQQIYGKRMGGLLFIPALMGEMFWAAAIFSALGATISVIIDVDMHISVIISALIATLYTLVGGLYSVAYTDVVQLFCIFVGLWISVPFALSHPAVADIGFTAVHAKYQKPWLGTVDSSEVYSWLDSFLLLMLGGIPWQAYFQRVLSSSSATYAQVLSFLAAFGCLVMAIPAILIGAIGASTDWNQTAYGLPDPKTTEEADMILPIVLQYLCPVYISFFGLGAVSAAVMSSADSSILSASSMFARNIYQLSFRQNASDKEIVWVMRITVFVFGASATAMALLTKTVYGLWYLSSDLVYIVIFPQLLCVLFVKGTNTYGAVAGYVSGLFLRITGGEPYLYLQPLIFYPGYYPDDNGIYNQKFPFKTLAMVTSFLTNICISYLAKYLFESGTLPPKLDVFDAVVARHSEENMDKTILVKNENIKLDELALVKPRQSMTLSSTFTNKEAFLDVDSSPEGSGTEDNLQ

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.6912

(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	3dh4A	0.77	2.86	0.174	0.843	model1_3dh4A.pdb.gz
2	5nv9A	0.74	2.80	0.167	0.795	model1_5nv9A.pdb.gz
3	5i6xA	0.60	4.85	0.078	0.741	model1_5i6xA.pdb.gz
4	6m17A	0.60	4.86	0.073	0.731	model1_6m17A.pdb.gz
5	4m48A	0.59	4.99	0.085	0.736	model1_4m48A.pdb.gz
6	6zbvA	0.59	4.70	0.084	0.714	model1_6zbvA.pdb.gz
7	5m87A	0.58	4.73	0.103	0.710	model1_5m87A.pdb.gz
8	2jlnA	0.57	4.48	0.113	0.695	model1_2jlnA.pdb.gz
9	6nplA	0.57	5.13	0.091	0.716	model1_6nplA.pdb.gz
10	6y5rA	0.57	5.73	0.078	0.743	model1_6y5rA.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:0022857	1.00	transmembrane transporter activity
GO:0015293	0.99	symporter activity
GO:0022891	0.82	substrate-specific transmembrane transporter activity
GO:0015075	0.79	ion transmembrane transporter activity
GO:0008324	0.76	cation transmembrane transporter activity
GO:0046873	0.74	metal ion transmembrane transporter activity
GO:0015294	0.73	solute:cation symporter activity
GO:0015077	0.73	monovalent inorganic cation transmembrane transporter activity
GO:0015370	0.72	solute:sodium symporter activity
GO:0043167	0.51	ion binding
GO:0043169	0.50	cation 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:0044699	0.98	single-organism process
GO:0006810	0.98	transport
GO:0009987	0.86	cellular process
GO:0006811	0.85	ion transport
GO:0008152	0.84	metabolic process
GO:0044763	0.82	single-organism cellular process
GO:0071704	0.81	organic substance metabolic process
GO:0044710	0.79	single-organism metabolic process
GO:0044237	0.79	cellular metabolic process
GO:0006812	0.78	cation transport
GO:0065007	0.75	biological regulation
GO:0006807	0.73	nitrogen compound metabolic process
GO:0065008	0.70	regulation of biological quality
GO:1901576	0.69	organic substance biosynthetic process
GO:0071705	0.69	nitrogen compound transport
GO:0044249	0.69	cellular biosynthetic process
GO:0044711	0.68	single-organism biosynthetic process
GO:0008292	0.67	acetylcholine biosynthetic process
GO:0015871	0.63	choline 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:0016021	1.00	integral component of membrane
GO:0005887	0.98	integral component of plasma membrane
GO:0044424	0.51	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	1ogyA	0.322	7.39	0.040	0.507	1.7.99.4	139
2	0.060	3ffzA	0.307	8.15	0.055	0.528	3.4.24.69	NA
3	0.060	2nyaF	0.321	7.31	0.049	0.502	1.7.99.4	60
4	0.060	1bxrA	0.330	7.10	0.041	0.502	6.3.5.5	381
5	0.060	3dwbA	0.313	7.58	0.043	0.497	3.4.24.71	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	0.02	2q72A	0.564	4.40	0.089	0.679	0.50	IXX	complex1.pdb.gz	42,45,56,256
2	0.01	2q6hA	0.564	4.40	0.088	0.681	0.43	CXX	complex2.pdb.gz	18,21,182,183,342
3	0.01	1kqfA	0.359	7.77	0.056	0.585	0.44	SF4	complex3.pdb.gz	18,19,22,23,179

	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.