D-I-TASSER Q13144

D-I-TASSER results for Q13144

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

Summary of the Protein

Uniprot ID: Q13144
Protein Name: Translation initiation factor eIF-2B subunit epsilon
Gene Name: EIF2B5

Input Sequence in FASTA format

>Q13144 (721 residues)
MAAPVVAPPGVVVSRANKRSGAGPGGSGGGGARGAEEEPPPPLQAVLVADSFDRRFFPIS
KDQPRVLLPLANVALIDYTLEFLTATGVQETFVFCCWKAAQIKEHLLKSKWCRPTSLNVV
RIITSELYRSLGDVLRDVDAKALVRSDFLLVYGDVISNINITRALEEHRLRRKLEKNVSV
MTMIFKESSPSHPTRCHEDNVVVAVDSTTNRVLHFQKTQGLRRFAFPLSLFQGSSDGVEV
RYDLLDCHISICSPQVAQLFTDNFDYQTRDDFVRGLLVNEEILGNQIHMHVTAKEYGARV
SNLHMYSAVCADVIRRWVYPLTPEANFTDSTTQSCTHSRHNIYRGPEVSLGHGSILEENV
LLGSGTVIGSNCFITNSVIGPGCHIGDNVVLDQTYLWQGVRVAAGAQIHQSLLCDNAEVK
ERVTLKPRSVLTSQVVVGPNITLPEGSVISLHPPDAEEDEDDGEFSDDSGADQEKDKVKM
KGYNPAEVGAAGKGYLWKAAGMNMEEEEELQQNLWGLKINMEEESESESEQSMDSEEPDS
RGGSPQMDDIKVFQNEVLGTLQRGKEENISCDNLVLEINSLKYAYNISLKEVMQVLSHVV
LEFPLQQMDSPLDSSRYCALLLPLLKAWSPVFRNYIKRAADHLEALAAIEDFFLEHEALG
ISMAKVLMAFYQLEILAEETILSWFSQRDTTDKGQQLRKNQQLQRFIQWLKEAEEESSED
D

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	Q13144-D1	1-300	300		MAAPVVAPPGVVVSRANKRSGAGPGGSGGGGARGAEEEPPPPLQAVLVADSFDRRFFPISKDQPRVLLPLANVALIDYTLEFLTATGVQETFVFCCWKAAQIKEHLLKSKWCRPTSLNVVRIITSELYRSLGDVLRDVDAKALVRSDFLLVYGDVISNINITRALEEHRLRRKLEKNVSVMTMIFKESSPSHPTRCHEDNVVVAVDSTTNRVLHFQKTQGLRRFAFPLSLFQGSSDGVEVRYDLLDCHISICSPQVAQLFTDNFDYQTRDDFVRGLLVNEEILGNQIHMHVTAKEYGARV
2	Q13144-D2	301-519	219		SNLHMYSAVCADVIRRWVYPLTPEANFTDSTTQSCTHSRHNIYRGPEVSLGHGSILEENVLLGSGTVIGSNCFITNSVIGPGCHIGDNVVLDQTYLWQGVRVAAGAQIHQSLLCDNAEVKERVTLKPRSVLTSQVVVGPNITLPEGSVISLHPPDAEEDEDDGEFSDDSGADQEKDKVKMKGYNPAEVGAAGKGYLWKAAGMNMEEEEELQQNLWGLKI
3	Q13144-D3	520-721	202		NMEEESESESEQSMDSEEPDSRGGSPQMDDIKVFQNEVLGTLQRGKEENISCDNLVLEINSLKYAYNISLKEVMQVLSHVVLEFPLQQMDSPLDSSRYCALLLPLLKAWSPVFRNYIKRAADHLEALAAIEDFFLEHEALGISMAKVLMAFYQLEILAEETILSWFSQRDTTDKGQQLRKNQQLQRFIQWLKEAEEESSEDD

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.53

(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	6jlwJ	0.58	4.33	0.758	0.668	model1_6jlwJ.pdb.gz
2	5b04I	0.55	1.88	0.355	0.566	model1_5b04I.pdb.gz
3	6i3mG	0.52	2.15	0.326	0.545	model1_6i3mG.pdb.gz
4	6ezoI	0.52	2.22	0.913	0.539	model1_6ezoI.pdb.gz
5	5b04E	0.48	2.67	0.168	0.513	model1_5b04E.pdb.gz
6	2ggoA	0.48	2.69	0.144	0.510	model1_2ggoA.pdb.gz
7	7d74A	0.46	2.80	0.182	0.502	model1_7d74A.pdb.gz
8	7d72K	0.46	2.62	0.163	0.494	model1_7d72K.pdb.gz
9	1yp3C	0.45	3.98	0.120	0.513	model1_1yp3C.pdb.gz
10	5l6sA	0.45	3.87	0.124	0.508	model1_5l6sA.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	0.81	heterocyclic compound binding
GO:0097159	0.81	organic cyclic compound binding
GO:0003676	0.72	nucleic acid binding
GO:0003723	0.71	RNA binding
GO:0008135	0.68	translation factor activity, RNA binding
GO:0005085	0.67	guanyl-nucleotide exchange factor activity
GO:0003743	0.67	translation initiation factor 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	0.97	cellular process
GO:0008152	0.96	metabolic process
GO:0044237	0.94	cellular metabolic process
GO:0006413	0.87	translational initiation
GO:0044699	0.86	single-organism process
GO:0044763	0.79	single-organism cellular process
GO:0050896	0.74	response to stimulus
GO:0048856	0.74	anatomical structure development
GO:0044767	0.74	single-organism developmental process
GO:0065007	0.71	biological regulation
GO:0048468	0.71	cell development
GO:0050789	0.70	regulation of biological process
GO:0014003	0.70	oligodendrocyte development
GO:0051716	0.69	cellular response to stimulus
GO:0050794	0.69	regulation of cellular process
GO:0042221	0.68	response to chemical
GO:0006950	0.67	response to stress
GO:2000112	0.66	regulation of cellular macromolecule biosynthetic process
GO:0080090	0.66	regulation of primary metabolic process
GO:0051171	0.66	regulation of nitrogen compound metabolic process
GO:0010468	0.66	regulation of gene expression
GO:0033554	0.65	cellular response to stress
GO:0009408	0.65	response to heat
GO:0034976	0.64	response to endoplasmic reticulum stress
GO:0006417	0.64	regulation of translation
GO:0048708	0.63	astrocyte differentiation
GO:0042552	0.63	myelination
GO:0035690	0.63	cellular response to drug
GO:0014002	0.63	astrocyte development
GO:0006446	0.63	regulation of translational initiation
GO:1901700	0.58	response to oxygen-containing compound
GO:0048518	0.58	positive regulation of biological process
GO:0010033	0.58	response to organic substance
GO:0048522	0.56	positive regulation of cellular process
GO:0051173	0.55	positive regulation of nitrogen compound metabolic process
GO:0043434	0.55	response to peptide hormone
GO:0031328	0.55	positive regulation of cellular biosynthetic process
GO:0022414	0.55	reproductive process
GO:0010628	0.55	positive regulation of gene expression
GO:0010557	0.55	positive regulation of macromolecule biosynthetic process
GO:0009749	0.55	response to glucose
GO:0045948	0.54	positive regulation of translational initiation
GO:0001541	0.54	ovarian follicle development

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:0044444	0.84	cytoplasmic part
GO:0005737	0.77	cytoplasm
GO:0032991	0.72	macromolecular complex
GO:0043234	0.69	protein complex
GO:0005851	0.64	eukaryotic translation initiation factor 2B complex

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	0.387	2ggoA	0.477	2.69	0.144	0.510	2.7.7.24	380
2	0.066	1yp3C	0.454	3.98	0.120	0.513	2.7.7.27	55
3	0.060	2i5kB	0.327	4.86	0.062	0.391	2.7.7.9	133
4	0.060	2oefA	0.316	5.40	0.072	0.393	2.7.7.9	NA
5	0.060	2vdcA	0.327	8.09	0.039	0.517	1.4.1.13	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	0.06	1yp3C	0.454	3.98	0.120	0.513	0.65	ATP	complex1.pdb.gz	47,49,50,93,130,132,133,151,153,154,155,248,268,269
2	0.01	2x60A	0.348	3.62	0.091	0.391	0.78	GTP	complex2.pdb.gz	48,49,51,53,54,55,65,125,129,131,132,135,153
3	0.01	3d8vA	0.353	4.30	0.075	0.409	0.73	UD1	complex3.pdb.gz	48,50,51,125,132,133,136,152,246,270,301

	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.