D-I-TASSER Q8IUY3

D-I-TASSER results for Q8IUY3

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

Summary of the Protein

Uniprot ID: Q8IUY3
Protein Name: GRAM domain-containing protein 2A
Gene Name: GRAMD2A

Input Sequence in FASTA format

>Q8IUY3 (354 residues)
MTALSRSEATEEGGNQQMHRKTASLNSPVSCKEKPDRVEEPPDYSLHWPEGLKGEEIKKC
GREGITLNKYNQQYHKLFKDVPLEEVVLKVCSCALQRDFLLQGRLYISPNWLCFHASLFG
KDIKVVIPVVSVQMIKKHKMARLLPNGLAITTNTSQKYIFVSLLSRDSVYDLLRRVCTHL
QPSSKKSLSVREFSGEPESLEVLIPEMKWRKVCPSSRSLSLPDNIPCIPPSSVDSTDSFF
PSRKPPMSEKSRAQVASENGGRWAWPMPGWGPACPKKMPNCSPTAKNAVYEEDELEEEPR
STGELRLWDYRLLKVFFVLICFLVMSSSYLAFRISRLEQQLCSLSWDDPVPGHR

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	Q8IUY3-D1	1-354	354		MTALSRSEATEEGGNQQMHRKTASLNSPVSCKEKPDRVEEPPDYSLHWPEGLKGEEIKKCGREGITLNKYNQQYHKLFKDVPLEEVVLKVCSCALQRDFLLQGRLYISPNWLCFHASLFGKDIKVVIPVVSVQMIKKHKMARLLPNGLAITTNTSQKYIFVSLLSRDSVYDLLRRVCTHLQPSSKKSLSVREFSGEPESLEVLIPEMKWRKVCPSSRSLSLPDNIPCIPPSSVDSTDSFFPSRKPPMSEKSRAQVASENGGRWAWPMPGWGPACPKKMPNCSPTAKNAVYEEDELEEEPRSTGELRLWDYRLLKVFFVLICFLVMSSSYLAFRISRLEQQLCSLSWDDPVPGHR

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.5007

(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	5u1sA	0.40	6.61	0.045	0.675	model1_5u1sA.pdb.gz
2	6mu1A	0.37	6.20	0.050	0.593	model1_6mu1A.pdb.gz
3	1o1dA	0.37	6.61	0.065	0.596	model1_1o1dA.pdb.gz
4	6ysgA	0.37	6.62	0.045	0.602	model1_6ysgA.pdb.gz
5	1yiqA	0.36	6.00	0.033	0.556	model1_1yiqA.pdb.gz
6	6rw9A	0.36	6.82	0.029	0.624	model1_6rw9A.pdb.gz
7	6tedQ	0.36	6.21	0.019	0.565	model1_6tedQ.pdb.gz
8	6vr4A	0.36	6.85	0.040	0.605	model1_6vr4A.pdb.gz
9	5y81A	0.36	6.13	0.043	0.559	model1_5y81A.pdb.gz
10	6l42A1	0.36	6.67	0.041	0.599	model1_6l42A1.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	0.74	catalytic activity
GO:0098772	0.73	molecular function regulator
GO:0008047	0.70	enzyme activator activity
GO:0005096	0.69	GTPase activator activity
GO:0017137	0.68	Rab GTPase binding
GO:0097159	0.67	organic cyclic compound binding
GO:1901363	0.66	heterocyclic compound binding
GO:0016787	0.54	hydrolase activity
GO:0032555	0.53	purine ribonucleotide binding
GO:0035639	0.52	purine ribonucleoside triphosphate binding
GO:0032559	0.52	adenyl ribonucleotide binding
GO:0032550	0.52	purine ribonucleoside binding
GO:0017111	0.52	nucleoside-triphosphatase activity
GO:0008092	0.52	cytoskeletal protein 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:0065007	0.79	biological regulation
GO:0006810	0.79	transport
GO:0071702	0.77	organic substance transport
GO:0050794	0.77	regulation of cellular process
GO:0046907	0.77	intracellular transport
GO:0051128	0.73	regulation of cellular component organization
GO:0050790	0.73	regulation of catalytic activity
GO:0043087	0.72	regulation of GTPase activity
GO:0033043	0.72	regulation of organelle organization
GO:0032879	0.72	regulation of localization
GO:0043085	0.71	positive regulation of catalytic activity
GO:0090630	0.70	activation of GTPase activity
GO:0031338	0.70	regulation of vesicle fusion
GO:0006886	0.70	intracellular protein transport
GO:0009987	0.66	cellular process
GO:0044699	0.64	single-organism process
GO:0008152	0.57	metabolic 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:0016459	1.00	myosin complex
GO:0044444	0.95	cytoplasmic part
GO:0043229	0.92	intracellular organelle
GO:0005737	0.74	cytoplasm
GO:0012505	0.61	endomembrane system
GO:0005622	0.61	intracellular
GO:0043231	0.60	intracellular membrane-bounded organelle
GO:0016020	0.53	membrane
GO:0043232	0.51	intracellular non-membrane-bounded organelle

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	1s4fA	0.324	6.37	0.049	0.528	2.7.7.48	98
2	0.060	1ogyA	0.312	7.33	0.037	0.576	1.7.99.4	NA
3	0.060	2j5wA	0.350	6.30	0.044	0.554	1.16.3.1	NA
4	0.060	1ug9A	0.298	7.29	0.059	0.537	3.2.1.70	NA
5	0.060	1qbaA	0.320	7.01	0.036	0.565	3.2.1.52	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	0.01	2v26A	0.290	7.19	0.015	0.514	0.13	UUU	complex1.pdb.gz	115,126,146,147,148,149,167,170
2	0.01	2jhrA	0.291	6.79	0.021	0.503	0.15	PBQ	complex2.pdb.gz	100,120,121,122
3	0.01	2w68B	0.170	4.94	0.035	0.234	0.13	UUU	complex3.pdb.gz	142,172,173
4	0.01	3juxA	0.243	7.18	0.032	0.435	0.15	ADP	complex4.pdb.gz	102,120,121,122
5	0.01	3bz7A	0.294	7.28	0.043	0.531	0.18	BL4	complex5.pdb.gz	100,103,120
6	0.01	1d0zA	0.308	6.68	0.035	0.517	0.27	PNQ	complex6.pdb.gz	103,104,142,145,146,147,148,167,170
7	0.01	1ffuB	0.324	6.56	0.030	0.537	0.15	CDP	complex7.pdb.gz	97,99,116,117,118
8	0.01	1w9kA	0.301	6.61	0.037	0.508	0.17	UUU	complex8.pdb.gz	103,108,145,146,147,148
9	0.01	1w0pA	0.346	6.35	0.022	0.548	0.19	SIA	complex9.pdb.gz	101,103,162
10	0.01	2uvcG	0.340	6.53	0.042	0.562	0.11	FMN	complex10.pdb.gz	165,166,169,170

	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.