D-I-TASSER Q4V328

D-I-TASSER results for Q4V328

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

Summary of the Protein

Uniprot ID: Q4V328
Protein Name: GRIP1-associated protein 1
Gene Name: GRIPAP1

Input Sequence in FASTA format

>Q4V328 (841 residues)
MAQALSEEEFQRMQAQLLELRTNNYQLSDELRKNGVELTSLRQKVAYLDKEFSKAQKALS
KSKKAQEVEVLLSENEMLQAKLHSQEEDFRLQNSTLMAEFSKLCSQMEQLEQENQQLKEG
AAGAGVAQAGPLVDGELLRLQAENTALQKNVAALQERYGKEAGKFSAVSEGQGDPPGGLA
PTVLAPMPLAEVELKWEMEKEEKRLLWEQLQGLESSKQAETSRLQEELAKLSEKLKKKQE
SFCRLQTEKETLFNDSRNKIEELQQRKEADHKAQLARTQKLQQELEAANQSLAELRDQRQ
GERLEHAAALRALQDQVSIQSADAQEQVEGLLAENNALRTSLAALEQIQTAKTQELNMLR
EQTTGLAAELQQQQAEYEDLMGQKDDLNSQLQESLRANSRLLEQLQEIGQEKEQLTQELQ
EARKSAEKRKAMLDELAMETLQEKSQHKEELGAVRLRHEKEVLGVRARYERELRELHEDK
KRQEEELRGQIREEKARTRELETLQQTVEELQAQVHSMDGAKGWFERRLKEAEESLQQQQ
QEQEEALKQCREQHAAELKGKEEELQDVRDQLEQAQEERDCHLKTISSLKQEVKDTVDGQ
RILEKKGSAALKDLKRQLHLERKRADKLQERLQDILTNSKSRSGLEELVLSEMNSPSRTQ
TGDSSSISSFSYREILREKESSAVPARSLSSSPQAQPPRPAELSDEEVAELFQRLAETQQ
EKWMLEEKVKHLEVSSASMAEDLCRKSAIIETYVMDSRIDVSVAAGHTDRSGLGSVLRDL
VKPGDENLREMNKKLQNMLEEQLTKNMHLHKDMEVLSQEIVRLSKECVGPPDPDLEPGET
S

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	Q4V328-D1	1-841	841		MAQALSEEEFQRMQAQLLELRTNNYQLSDELRKNGVELTSLRQKVAYLDKEFSKAQKALSKSKKAQEVEVLLSENEMLQAKLHSQEEDFRLQNSTLMAEFSKLCSQMEQLEQENQQLKEGAAGAGVAQAGPLVDGELLRLQAENTALQKNVAALQERYGKEAGKFSAVSEGQGDPPGGLAPTVLAPMPLAEVELKWEMEKEEKRLLWEQLQGLESSKQAETSRLQEELAKLSEKLKKKQESFCRLQTEKETLFNDSRNKIEELQQRKEADHKAQLARTQKLQQELEAANQSLAELRDQRQGERLEHAAALRALQDQVSIQSADAQEQVEGLLAENNALRTSLAALEQIQTAKTQELNMLREQTTGLAAELQQQQAEYEDLMGQKDDLNSQLQESLRANSRLLEQLQEIGQEKEQLTQELQEARKSAEKRKAMLDELAMETLQEKSQHKEELGAVRLRHEKEVLGVRARYERELRELHEDKKRQEEELRGQIREEKARTRELETLQQTVEELQAQVHSMDGAKGWFERRLKEAEESLQQQQQEQEEALKQCREQHAAELKGKEEELQDVRDQLEQAQEERDCHLKTISSLKQEVKDTVDGQRILEKKGSAALKDLKRQLHLERKRADKLQERLQDILTNSKSRSGLEELVLSEMNSPSRTQTGDSSSISSFSYREILREKESSAVPARSLSSSPQAQPPRPAELSDEEVAELFQRLAETQQEKWMLEEKVKHLEVSSASMAEDLCRKSAIIETYVMDSRIDVSVAAGHTDRSGLGSVLRDLVKPGDENLREMNKKLQNMLEEQLTKNMHLHKDMEVLSQEIVRLSKECVGPPDPDLEPGETS

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.3215

(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	7abhu	0.41	8.09	0.049	0.629	model1_7abhu.pdb.gz
2	3gjxA	0.40	8.01	0.046	0.604	model1_3gjxA.pdb.gz
3	7dxjA	0.40	8.09	0.053	0.604	model1_7dxjA.pdb.gz
4	6z2wE	0.40	8.36	0.051	0.625	model1_6z2wE.pdb.gz
5	6q82A	0.39	7.87	0.046	0.579	model1_6q82A.pdb.gz
6	3m1iC	0.39	7.86	0.049	0.578	model1_3m1iC.pdb.gz
7	3qmzA	0.39	8.81	0.040	0.630	model1_3qmzA.pdb.gz
8	4fgvA	0.38	7.77	0.060	0.571	model1_4fgvA.pdb.gz
9	5gm6G	0.38	8.13	0.041	0.578	model1_5gm6G.pdb.gz
10	5lqwQ	0.38	7.82	0.046	0.568	model1_5lqwQ.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	0.66	heterocyclic compound binding
GO:0097159	0.66	organic cyclic compound binding
GO:0003676	0.59	nucleic acid 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	0.96	cellular process
GO:0065007	0.89	biological regulation
GO:0044699	0.89	single-organism process
GO:0050789	0.88	regulation of biological process
GO:0050794	0.87	regulation of cellular process
GO:0044763	0.86	single-organism cellular process
GO:0016043	0.83	cellular component organization
GO:0019222	0.71	regulation of metabolic process
GO:0006996	0.71	organelle organization
GO:0080090	0.70	regulation of primary metabolic process
GO:0031323	0.70	regulation of cellular metabolic process
GO:0060255	0.69	regulation of macromolecule metabolic process
GO:0051179	0.69	localization
GO:0051234	0.67	establishment of localization
GO:0051246	0.64	regulation of protein metabolic process
GO:0006810	0.64	transport
GO:0051641	0.63	cellular localization
GO:0050896	0.63	response to stimulus
GO:0048523	0.63	negative regulation of cellular process
GO:0022402	0.62	cell cycle process
GO:0071704	0.61	organic substance metabolic process
GO:0051171	0.61	regulation of nitrogen compound metabolic process
GO:0044238	0.61	primary metabolic process
GO:0031326	0.61	regulation of cellular biosynthetic process
GO:2000112	0.60	regulation of cellular macromolecule biosynthetic process
GO:0043170	0.60	macromolecule metabolic process
GO:0019219	0.60	regulation of nucleobase-containing compound metabolic process
GO:0010468	0.60	regulation of gene expression
GO:1902589	0.59	single-organism organelle organization
GO:0051128	0.59	regulation of cellular component organization
GO:0042221	0.59	response to chemical
GO:0008104	0.59	protein localization
GO:0051726	0.58	regulation of cell cycle
GO:0031324	0.58	negative regulation of cellular metabolic process
GO:0006355	0.58	regulation of transcription, DNA-templated
GO:0033043	0.57	regulation of organelle organization
GO:0071702	0.56	organic substance transport
GO:0032879	0.56	regulation of localization
GO:0019538	0.56	protein metabolic process
GO:0010605	0.56	negative regulation of macromolecule metabolic process
GO:0045934	0.55	negative regulation of nucleobase-containing compound metabolic process
GO:0034613	0.55	cellular protein localization
GO:0031327	0.55	negative regulation of cellular biosynthetic process
GO:0031023	0.55	microtubule organizing center organization
GO:0010564	0.55	regulation of cell cycle process
GO:0006357	0.55	regulation of transcription from RNA polymerase II promoter
GO:1903827	0.54	regulation of cellular protein localization
GO:0070201	0.54	regulation of establishment of protein localization
GO:0051649	0.54	establishment of localization in cell
GO:0051493	0.54	regulation of cytoskeleton organization
GO:0051297	0.54	centrosome organization
GO:0051049	0.54	regulation of transport
GO:0033365	0.54	protein localization to organelle
GO:0050658	0.53	RNA transport
GO:0046605	0.53	regulation of centrosome cycle
GO:0045892	0.53	negative regulation of transcription, DNA-templated
GO:0033157	0.53	regulation of intracellular protein transport
GO:0009057	0.53	macromolecule catabolic process
GO:0051298	0.52	centrosome duplication
GO:0046822	0.52	regulation of nucleocytoplasmic transport
GO:0030163	0.52	protein catabolic process
GO:0009894	0.52	regulation of catabolic process
GO:0046907	0.50	intracellular 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:0044421	1.00	extracellular region part
GO:0044464	0.80	cell part
GO:0072562	0.62	blood microparticle
GO:0044424	0.55	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	3h0gA	0.258	9.15	0.036	0.430	2.7.7.6	NA
2	0.060	3c5wA	0.125	6.06	0.041	0.163	3.1.3.16	NA
3	0.060	1ob2A	0.137	7.30	0.048	0.196	3.6.1.48	NA
4	0.060	2x0sA	0.265	8.78	0.057	0.427	2.7.9.1	NA
5	0.060	2pffA	0.311	8.58	0.033	0.491	2.3.1.41 2.3.1.86	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:

No Binding sites was predicted

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

	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.