D-I-TASSER Q7LBE3

D-I-TASSER results for Q7LBE3

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

Summary of the Protein

Uniprot ID: Q7LBE3
Protein Name: Solute carrier family 26 member 9
Gene Name: SLC26A9

Input Sequence in FASTA format

>Q7LBE3 (791 residues)
MSQPRPRYVVDRAAYSLTLFDDEFEKKDRTYPVGEKLRNAFRCSSAKIKAVVFGLLPVLS
WLPKYKIKDYIIPDLLGGLSGGSIQVPQGMAFALLANLPAVNGLYSSFFPLLTYFFLGGV
HQMVPGTFAVISILVGNICLQLAPESKFQVFNNATNESYVDTAAMEAERLHVSATLACLT
AIIQMGLGFMQFGFVAIYLSESFIRGFMTAAGLQILISVLKYIFGLTIPSYTGPGSIVFT
FIDICKNLPHTNIASLIFALISGAFLVLVKELNARYMHKIRFPIPTEMIVVVVATAISGG
CKMPKKYHMQIVGEIQRGFPTPVSPVVSQWKDMIGTAFSLAIVSYVINLAMGRTLANKHG
YDVDSNQEMIALGCSNFFGSFFKIHVICCALSVTLAVDGAGGKSQVASLCVSLVVMITML
VLGIYLYPLPKSVLGALIAVNLKNSLKQLTDPYYLWRKSKLDCCIWVVSFLSSFFLSLPY
GVAVGVAFSVLVVVFQTQFRNGYALAQVMDTDIYVNPKTYNRAQDIQGIKIITYCSPLYF
ANSEIFRQKVIAKTGMDPQKVLLAKQKYLKKQEKRRMRPTQQRRSLFMKTKTVSLQELQQ
DFENAPPTDPNNNQTPANGTSVSYITFSPDSSSPAQSEPPASAEAPGEPSDMLASVPPFV
TFHTLILDMSGVSFVDLMGIKALAKLSSTYGKIGVKVFLVNIHAQVYNDISHGGVFEDGS
LECKHVFPSIHDAVLFAQANARDVTPGHNFQGAPGDAELSLYDSEEDIRSYWDLEQEMFG
SMFHAETLTAL

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	Q7LBE3-D1	1-43,497-791	338		MSQPRPRYVVDRAAYSLTLFDDEFEKKDRTYPVGEKLRNAFRCTQFRNGYALAQVMDTDIYVNPKTYNRAQDIQGIKIITYCSPLYFANSEIFRQKVIAKTGMDPQKVLLAKQKYLKKQEKRRMRPTQQRRSLFMKTKTVSLQELQQDFENAPPTDPNNNQTPANGTSVSYITFSPDSSSPAQSEPPASAEAPGEPSDMLASVPPFVTFHTLILDMSGVSFVDLMGIKALAKLSSTYGKIGVKVFLVNIHAQVYNDISHGGVFEDGSLECKHVFPSIHDAVLFAQANARDVTPGHNFQGAPGDAELSLYDSEEDIRSYWDLEQEMFGSMFHAETLTAL
2	Q7LBE3-D2	44-199,313-421	265		SSAKIKAVVFGLLPVLSWLPKYKIKDYIIPDLLGGLSGGSIQVPQGMAFALLANLPAVNGLYSSFFPLLTYFFLGGVHQMVPGTFAVISILVGNICLQLAPESKFQVFNNATNESYVDTAAMEAERLHVSATLACLTAIIQMGLGFMQFGFVAIYLGEIQRGFPTPVSPVVSQWKDMIGTAFSLAIVSYVINLAMGRTLANKHGYDVDSNQEMIALGCSNFFGSFFKIHVICCALSVTLAVDGAGGKSQVASLCVSLVVMITMLV
3	Q7LBE3-D3	200-312,422-496	188		SESFIRGFMTAAGLQILISVLKYIFGLTIPSYTGPGSIVFTFIDICKNLPHTNIASLIFALISGAFLVLVKELNARYMHKIRFPIPTEMIVVVVATAISGGCKMPKKYHMQIVLGIYLYPLPKSVLGALIAVNLKNSLKQLTDPYYLWRKSKLDCCIWVVSFLSSFFLSLPYGVAVGVAFSVLVVVFQ

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.654

(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	7wk1A	0.80	2.19	0.371	0.834	model1_7wk1A.pdb.gz
2	7xujA	0.79	2.51	0.345	0.834	model1_7xujA.pdb.gz
3	8opqA	0.78	2.11	0.386	0.817	model1_8opqA.pdb.gz
4	7ch1A	0.77	1.73	0.980	0.794	model1_7ch1A.pdb.gz
5	6rtcA	0.76	1.85	0.919	0.785	model1_6rtcA.pdb.gz
6	7s8xA	0.74	3.76	0.356	0.838	model1_7s8xA.pdb.gz
7	7v73A	0.72	2.10	0.464	0.755	model1_7v73A.pdb.gz
8	7xlmA	0.69	3.10	0.328	0.751	model1_7xlmA.pdb.gz
9	7lhvA	0.68	2.63	0.245	0.722	model1_7lhvA.pdb.gz
10	8gv9A	0.47	4.42	0.103	0.541	model1_8gv9A.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:0015103	1.00	inorganic anion transmembrane transporter activity
GO:0015116	0.99	sulfate transmembrane transporter activity
GO:0015291	0.78	secondary active transmembrane transporter activity
GO:0015108	0.73	chloride transmembrane transporter activity
GO:0008514	0.72	organic anion transmembrane transporter activity
GO:0005216	0.72	ion channel activity
GO:0099516	0.71	ion antiporter activity
GO:0015106	0.71	bicarbonate transmembrane transporter activity
GO:0005254	0.71	chloride channel activity
GO:0019531	0.70	oxalate transmembrane transporter activity
GO:0015301	0.70	anion:anion antiporter 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	0.99	transport
GO:0006820	0.98	anion transport
GO:0065007	0.97	biological regulation
GO:0015698	0.97	inorganic anion transport
GO:0050801	0.96	ion homeostasis
GO:0009987	0.96	cellular process
GO:0044763	0.95	single-organism cellular process
GO:0006821	0.95	chloride transport
GO:0051453	0.93	regulation of intracellular pH
GO:0042391	0.93	regulation of membrane potential
GO:0015711	0.93	organic anion transport
GO:0015701	0.92	bicarbonate transport
GO:0055085	0.91	transmembrane transport
GO:0098656	0.89	anion transmembrane transport
GO:1902476	0.88	chloride 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:0044459	1.00	plasma membrane part
GO:0016021	1.00	integral component of membrane
GO:0005887	0.99	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	3h0gA	0.267	8.58	0.026	0.429	2.7.7.6	NA
2	0.060	2cseW	0.278	8.80	0.035	0.455	3.6.4.13	NA
3	0.060	2hpiA	0.268	8.42	0.033	0.429	2.7.7.7	NA
4	0.060	3hmjA	0.288	8.83	0.034	0.478	2.3.1.86	NA
5	0.060	3b8eC	0.280	8.83	0.043	0.468	3.6.3.9	73

	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	3ar9A	0.263	8.35	0.041	0.418	0.20	TM1	complex1.pdb.gz	356,395,403,405,407
2	0.01	3nalA	0.252	8.41	0.037	0.393	0.12	DBK	complex2.pdb.gz	404,406,407
3	0.01	3ar6A	0.287	8.91	0.039	0.479	0.12	12D	complex3.pdb.gz	57,193,341
4	0.01	3ba6A	0.309	8.17	0.054	0.475	0.11	AN2	complex4.pdb.gz	56,189,193
5	0.01	3g61B	0.310	8.39	0.049	0.492	0.13	0JZ	complex5.pdb.gz	406,409,410
6	0.01	3g60A	0.308	8.40	0.042	0.487	0.11	0JZ	complex6.pdb.gz	352,355,356,359
7	0.01	2easA	0.258	8.33	0.041	0.403	0.15	CZA	complex7.pdb.gz	51,189,192,193
8	0.01	3nanA	0.253	8.61	0.026	0.408	0.13	HZ1	complex8.pdb.gz	60,78,80,352,355,356
9	0.01	2by4A	0.255	8.44	0.036	0.401	0.12	AD4	complex9.pdb.gz	68,70,71,74,75,78,82
10	0.01	2yfyA	0.287	8.84	0.032	0.478	0.16	9TN	complex10.pdb.gz	74,77,81

	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.