D-I-TASSER Q9Y4P1

D-I-TASSER results for Q9Y4P1

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

Summary of the Protein

Uniprot ID: Q9Y4P1
Protein Name: Cysteine protease ATG4B
Gene Name: ATG4B

Input Sequence in FASTA format

>Q9Y4P1 (393 residues)
MDAATLTYDTLRFAEFEDFPETSEPVWILGRKYSIFTEKDEILSDVASRLWFTYRKNFPA
IGGTGPTSDTGWGCMLRCGQMIFAQALVCRHLGRDWRWTQRKRQPDSYFSVLNAFIDRKD
SYYSIHQIAQMGVGEGKSIGQWYGPNTVAQVLKKLAVFDTWSSLAVHIAMDNTVVMEEIR
RLCRTSVPCAGATAFPADSDRHCNGFPAGAEVTNRPSPWRPLVLLIPLRLGLTDINEAYV
ETLKHCFMMPQSLGVIGGKPNSAHYFIGYVGEELIYLDPHTTQPAVEPTDGCFIPDESFH
CQHPPCRMSIAELDPSIAVGFFCKTEDDFNDWCQQVKKLSLLGGALPMFELVELQPSHLA
CPDVLNLSLDSSDVERLERFFDSEDEDFEILSL

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	Q9Y4P1-D1	1-393	393		MDAATLTYDTLRFAEFEDFPETSEPVWILGRKYSIFTEKDEILSDVASRLWFTYRKNFPAIGGTGPTSDTGWGCMLRCGQMIFAQALVCRHLGRDWRWTQRKRQPDSYFSVLNAFIDRKDSYYSIHQIAQMGVGEGKSIGQWYGPNTVAQVLKKLAVFDTWSSLAVHIAMDNTVVMEEIRRLCRTSVPCAGATAFPADSDRHCNGFPAGAEVTNRPSPWRPLVLLIPLRLGLTDINEAYVETLKHCFMMPQSLGVIGGKPNSAHYFIGYVGEELIYLDPHTTQPAVEPTDGCFIPDESFHCQHPPCRMSIAELDPSIAVGFFCKTEDDFNDWCQQVKKLSLLGGALPMFELVELQPSHLACPDVLNLSLDSSDVERLERFFDSEDEDFEILSL

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.787

(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	2d1iA	0.84	1.15	0.991	0.858	model1_2d1iA.pdb.gz
2	2p82A	0.77	1.48	0.612	0.794	model1_2p82A.pdb.gz
3	1a6rA	0.42	5.24	0.064	0.575	model1_1a6rA.pdb.gz
4	7ojeA	0.42	4.49	0.123	0.511	model1_7ojeA.pdb.gz
5	1cb5A	0.41	5.25	0.047	0.565	model1_1cb5A.pdb.gz
6	2avwD	0.41	4.17	0.046	0.511	model1_2avwD.pdb.gz
7	3pw3A	0.39	4.74	0.070	0.509	model1_3pw3A.pdb.gz
8	3qj3A	0.38	3.69	0.068	0.453	model1_3qj3A.pdb.gz
9	3oisA	0.37	3.76	0.101	0.440	model1_3oisA.pdb.gz
10	3tnxA2	0.36	3.67	0.053	0.435	model1_3tnxA2.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:0004197	0.99	cysteine-type endopeptidase 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	0.99	cellular process
GO:0044763	0.98	single-organism cellular process
GO:0071704	0.97	organic substance metabolic process
GO:0006914	0.97	autophagy
GO:0006810	0.97	transport
GO:1902582	0.96	single-organism intracellular transport
GO:0044802	0.96	single-organism membrane organization
GO:0006605	0.96	protein targeting
GO:0006508	0.96	proteolysis
GO:0000045	0.96	autophagosome assembly
GO:1902589	0.95	single-organism organelle organization
GO:0043687	0.95	post-translational protein modification
GO:0022411	0.95	cellular component disassembly
GO:0016485	0.95	protein processing
GO:0007005	0.95	mitochondrion organization
GO:0006612	0.95	protein targeting to membrane
GO:0051697	0.94	protein delipidation
GO:0044804	0.94	nucleophagy
GO:0006501	0.94	C-terminal protein lipidation
GO:0000422	0.94	mitophagy

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:0044444	1.00	cytoplasmic part
GO:0005829	0.99	cytosol

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	1csbE	0.267	3.93	0.035	0.326	3.4.22.1	NA
2	0.060	1kfxL	0.353	5.76	0.051	0.501	3.4.22.53	NA
3	0.060	1cb5A	0.414	5.25	0.047	0.565	3.4.22.40	NA
4	0.060	1pbhA	0.378	4.50	0.046	0.478	3.4.22.1	NA
5	0.060	1a6rA	0.417	5.24	0.064	0.575	3.4.22.40 3.4.22.-	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	0.47	2z0d0	0.748	1.05	0.958	0.758	1.95	III	complex1.pdb.gz	54,71,72,73,74,75,137,142,143,144,145,146,150,154,170,171,172,227,228,229,232,233,263,314,316,317,347,350
2	0.01	2dc8A	0.357	4.01	0.074	0.438	0.72	59A	complex2.pdb.gz	54,73,74,75,142,143,261,262,280
3	0.01	2uzjB	0.374	3.81	0.092	0.453	0.66	E64	complex3.pdb.gz	74,75,142,143,257,262
4	0.01	1gmyA	0.360	4.09	0.055	0.443	0.70	UUU	complex4.pdb.gz	55,74,75,138,140,141,142,143,258,261,316

	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.