D-I-TASSER Q5T7V8

D-I-TASSER results for Q5T7V8

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

Summary of the Protein

Uniprot ID: Q5T7V8
Protein Name: RAB6-interacting golgin
Gene Name: GORAB

Input Sequence in FASTA format

>Q5T7V8 (394 residues)
MSWAAVLAVAAARFGHFWGCRWPGPMAQGWAGFSEEELRRLKQTKDPFEPQRRLPAKKSR
QQLQREKALVEQSQKLGLQDGSTSLLPEQLLSAPKQRVNVQKPPFSSPTLPSHFTLTSPV
GDGQPQGIESQPKELGLENSHDGHNNVEILPPKPDCKLEKKKVELQEKSRWEVLQQEQRL
MEEKNKRKKALLAKAIAERSKRTQAETMKLKRIQKELQALDDMVSADIGILRNRIDQASL
DYSYARKRFDRAEAEYIAAKLDIQRKTEIKEQLTEHLCTIIQQNELRKAKKLEELMQQLD
VEADEETLELEVEVERLLHEQEVESRRPVVRLERPFQPAEESVTLEFAKENRKCQEQAVS
PKVDDQCGNSSSIPFLSPNCPNQEGNDISAALAT

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	Q5T7V8-D1	1-394	394		MSWAAVLAVAAARFGHFWGCRWPGPMAQGWAGFSEEELRRLKQTKDPFEPQRRLPAKKSRQQLQREKALVEQSQKLGLQDGSTSLLPEQLLSAPKQRVNVQKPPFSSPTLPSHFTLTSPVGDGQPQGIESQPKELGLENSHDGHNNVEILPPKPDCKLEKKKVELQEKSRWEVLQQEQRLMEEKNKRKKALLAKAIAERSKRTQAETMKLKRIQKELQALDDMVSADIGILRNRIDQASLDYSYARKRFDRAEAEYIAAKLDIQRKTEIKEQLTEHLCTIIQQNELRKAKKLEELMQQLDVEADEETLELEVEVERLLHEQEVESRRPVVRLERPFQPAEESVTLEFAKENRKCQEQAVSPKVDDQCGNSSSIPFLSPNCPNQEGNDISAALAT

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.5298

(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	2o8cB	0.39	7.02	0.054	0.662	model1_2o8cB.pdb.gz
2	6p2kA	0.39	6.67	0.071	0.645	model1_6p2kA.pdb.gz
3	2pffA	0.39	6.01	0.055	0.591	model1_2pffA.pdb.gz
4	3ffzA	0.39	6.69	0.050	0.622	model1_3ffzA.pdb.gz
5	2zxqA	0.39	7.15	0.055	0.673	model1_2zxqA.pdb.gz
6	1tg7A	0.39	7.16	0.038	0.667	model1_1tg7A.pdb.gz
7	6x99A	0.39	6.70	0.051	0.629	model1_6x99A.pdb.gz
8	3btaA	0.38	6.70	0.042	0.627	model1_3btaA.pdb.gz
9	3f93C	0.38	6.99	0.042	0.642	model1_3f93C.pdb.gz
10	6mgjA	0.38	7.30	0.027	0.660	model1_6mgjA.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:1901363	0.56	heterocyclic compound binding
GO:0097159	0.56	organic cyclic compound 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:0009987	0.97	cellular process
GO:0044699	0.92	single-organism process
GO:0044763	0.90	single-organism cellular process
GO:0065007	0.89	biological regulation
GO:0050789	0.88	regulation of biological process
GO:0050794	0.87	regulation of cellular process
GO:0016043	0.85	cellular component organization
GO:0006996	0.80	organelle organization
GO:0048518	0.79	positive regulation of biological process
GO:0048522	0.78	positive regulation of cellular process
GO:0044767	0.77	single-organism developmental process
GO:1902589	0.75	single-organism organelle organization
GO:0048583	0.75	regulation of response to stimulus
GO:0022607	0.75	cellular component assembly
GO:0023051	0.74	regulation of signaling
GO:0010646	0.74	regulation of cell communication
GO:0050793	0.73	regulation of developmental process
GO:0032501	0.73	multicellular organismal process
GO:0009966	0.73	regulation of signal transduction
GO:0009653	0.73	anatomical structure morphogenesis
GO:2000026	0.72	regulation of multicellular organismal development
GO:0070925	0.72	organelle assembly
GO:0048646	0.72	anatomical structure formation involved in morphogenesis
GO:0048584	0.72	positive regulation of response to stimulus
GO:0044707	0.72	single-multicellular organism process
GO:0051962	0.71	positive regulation of nervous system development
GO:0030031	0.71	cell projection assembly
GO:0010927	0.71	cellular component assembly involved in morphogenesis
GO:0009967	0.71	positive regulation of signal transduction
GO:1901622	0.70	positive regulation of smoothened signaling pathway involved in dorsal/ventral neural tube patterning
GO:0035058	0.70	nonmotile primary cilium assembly
GO:0031069	0.70	hair follicle morphogenesis

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:0005794	1.00	Golgi apparatus
GO:0005737	1.00	cytoplasm
GO:0005730	1.00	nucleolus
GO:0005654	1.00	nucleoplasm
GO:0005634	1.00	nucleus

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	1yiqA	0.341	6.84	0.040	0.569	1.1.99.-	NA
2	0.060	2pffA	0.391	6.01	0.055	0.591	2.3.1.41 2.3.1.86	NA
3	0.060	1kv9A	0.345	6.96	0.043	0.574	1.1.99.-	NA
4	0.060	2vdcA	0.370	7.05	0.058	0.604	1.4.1.13	NA
5	0.060	1t7lA	0.347	6.92	0.047	0.586	2.1.1.14	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:

Click to view	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	1ea0B	0.379	7.38	0.047	0.665	0.12	FMN	complex1.pdb.gz	34,61,231,232

	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.