D-I-TASSER Q9NQX3

D-I-TASSER results for Q9NQX3

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

Summary of the Protein

Uniprot ID: Q9NQX3
Protein Name: Gephyrin
Gene Name: GPHN

Input Sequence in FASTA format

>Q9NQX3 (736 residues)
MATEGMILTNHDHQIRVGVLTVSDSCFRNLAEDRSGINLKDLVQDPSLLGGTISAYKIVP
DEIEEIKETLIDWCDEKELNLILTTGGTGFAPRDVTPEATKEVIEREAPGMALAMLMGSL
NVTPLGMLSRPVCGIRGKTLIINLPGSKKGSQECFQFILPALPHAIDLLRDAIVKVKEVH
DELEDLPSPPPPLSPPPTTSPHKQTEDKGVQCEEEEEEKKDSGVASTEDSSSSHITAAAI
AAKIPDSIISRGVQVLPRDTASLSTTPSESPRAQATSRLSTASCPTPKVQSRCSSKENIL
RASHSAVDITKVARRHRMSPFPLTSMDKAFITVLEMTPVLGTEIINYRDGMGRVLAQDVY
AKDNLPPFPASVKDGYAVRAADGPGDRFIIGESQAGEQPTQTVMPGQVMRVTTGAPIPCG
ADAVVQVEDTELIRESDDGTEELEVRILVQARPGQDIRPIGHDIKRGECVLAKGTHMGPS
EIGLLATVGVTEVEVNKFPVVAVMSTGNELLNPEDDLLPGKIRDSNRSTLLATIQEHGYP
TINLGIVGDNPDDLLNALNEGISRADVIITSGGVSMGEKDYLKQVLDIDLHAQIHFGRVF
MKPGLPTTFATLDIDGVRKIIFALPGNPVSAVVTCNLFVVPALRKMQGILDPRPTIIKAR
LSCDVKLDPRPEYHRCILTWHHQEPLPWAQSTGNQMSSRLMSMRSANGLLMLPPKTEQYV
ELHKGEVVDVMVIGRL

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	Q9NQX3-D1	1-187	187		MATEGMILTNHDHQIRVGVLTVSDSCFRNLAEDRSGINLKDLVQDPSLLGGTISAYKIVPDEIEEIKETLIDWCDEKELNLILTTGGTGFAPRDVTPEATKEVIEREAPGMALAMLMGSLNVTPLGMLSRPVCGIRGKTLIINLPGSKKGSQECFQFILPALPHAIDLLRDAIVKVKEVHDELEDLP
2	Q9NQX3-D2	188-311	124		SPPPPLSPPPTTSPHKQTEDKGVQCEEEEEEKKDSGVASTEDSSSSHITAAAIAAKIPDSIISRGVQVLPRDTASLSTTPSESPRAQATSRLSTASCPTPKVQSRCSSKENILRASHSAVDITK
3	Q9NQX3-D3	312-356,473-653	226		VARRHRMSPFPLTSMDKAFITVLEMTPVLGTEIINYRDGMGRVLAKGTHMGPSEIGLLATVGVTEVEVNKFPVVAVMSTGNELLNPEDDLLPGKIRDSNRSTLLATIQEHGYPTINLGIVGDNPDDLLNALNEGISRADVIITSGGVSMGEKDYLKQVLDIDLHAQIHFGRVFMKPGLPTTFATLDIDGVRKIIFALPGNPVSAVVTCNLFVVPALRKMQGILDPR
4	Q9NQX3-D4	357-472	116		QDVYAKDNLPPFPASVKDGYAVRAADGPGDRFIIGESQAGEQPTQTVMPGQVMRVTTGAPIPCGADAVVQVEDTELIRESDDGTEELEVRILVQARPGQDIRPIGHDIKRGECVLA
5	Q9NQX3-D5	654-736	83		PTIIKARLSCDVKLDPRPEYHRCILTWHHQEPLPWAQSTGNQMSSRLMSMRSANGLLMLPPKTEQYVELHKGEVVDVMVIGRL

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.51

(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	2fu3B	0.54	2.36	0.988	0.568	model1_2fu3B.pdb.gz
2	5g2rA	0.54	1.53	0.473	0.552	model1_5g2rA.pdb.gz
3	2nrpB	0.48	3.28	0.332	0.533	model1_2nrpB.pdb.gz
4	1uz5A	0.46	3.34	0.279	0.516	model1_1uz5A.pdb.gz
5	1wu2A	0.42	3.99	0.232	0.480	model1_1wu2A.pdb.gz
6	7cpxA	0.41	7.22	0.079	0.582	model1_7cpxA.pdb.gz
7	2vz8B	0.37	7.38	0.072	0.534	model1_2vz8B.pdb.gz
8	1mkzB	0.21	1.84	0.286	0.216	model1_1mkzB.pdb.gz
9	2g4rA	0.20	1.34	0.320	0.208	model1_2g4rA.pdb.gz
10	1ez4B	0.18	5.49	0.072	0.226	model1_1ez4B.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:0003824	1.00	catalytic activity
GO:0061599	0.97	molybdopterin molybdotransferase activity
GO:0061598	0.97	molybdopterin adenylyltransferase 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:0009987	1.00	cellular process
GO:0008152	0.90	metabolic process
GO:0071704	0.89	organic substance metabolic process
GO:0044238	0.88	primary metabolic process
GO:0044237	0.88	cellular metabolic process
GO:1901360	0.86	organic cyclic compound metabolic process
GO:0046483	0.86	heterocycle metabolic process
GO:0006807	0.86	nitrogen compound metabolic process
GO:1901576	0.85	organic substance biosynthetic process
GO:1901564	0.85	organonitrogen compound metabolic process
GO:0044249	0.85	cellular biosynthetic process
GO:1901566	0.84	organonitrogen compound biosynthetic process
GO:1901362	0.84	organic cyclic compound biosynthetic process
GO:0090407	0.84	organophosphate biosynthetic process
GO:0051188	0.84	cofactor biosynthetic process
GO:0043545	0.84	molybdopterin cofactor metabolic process
GO:0018130	0.84	heterocycle biosynthetic process
GO:0044699	0.83	single-organism process
GO:0044763	0.79	single-organism cellular process
GO:0043170	0.75	macromolecule metabolic process
GO:0044260	0.73	cellular macromolecule metabolic process
GO:0019538	0.73	protein metabolic process
GO:0044267	0.71	cellular protein metabolic process
GO:0043412	0.71	macromolecule modification
GO:0006777	0.71	Mo-molybdopterin cofactor biosynthetic process
GO:0018315	0.70	molybdenum incorporation into molybdenum-molybdopterin complex
GO:0051179	0.62	localization
GO:1902578	0.60	single-organism localization
GO:0016043	0.57	cellular component organization
GO:0072657	0.56	protein localization to membrane
GO:0072579	0.55	glycine receptor clustering

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:0044424	1.00	intracellular part
GO:0005737	0.98	cytoplasm

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	0.257	2fu3B	0.541	2.36	0.988	0.568	2.7.7.-	354,466,468
2	0.060	2fr0A	0.336	6.17	0.068	0.448	2.3.1.94	636
3	0.060	3ecqB	0.269	8.86	0.033	0.448	3.2.1.97	NA
4	0.060	3l4uA	0.286	8.43	0.044	0.462	3.2.1.20 3.2.1.3	645
5	0.060	2et6A	0.330	6.47	0.058	0.451	1.1.1.-	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	0.04	2nro0	0.450	4.26	0.325	0.527	0.74	III	complex1.pdb.gz	478,479,480,481,482,483,484,486,489,491,513,519,520,523,525,528,529,531,532,533,536,656,657,658,699,700,703,704,729,735
2	0.03	1xi80	0.339	2.52	0.279	0.360	0.84	III	complex2.pdb.gz	347,478,479,480,481,483,524,525,528,529,532,535,656,657,703,704,706,732,733
3	0.01	2fmm9	0.094	4.78	0.072	0.114	0.53	III	complex3.pdb.gz	351,352,353,354,372,373,375,376,377,378

	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.