D-I-TASSER Q7L8A9

D-I-TASSER results for Q7L8A9

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

Summary of the Protein

Uniprot ID: Q7L8A9
Protein Name: Tubulinyl-Tyr carboxypeptidase 1
Gene Name: VASH1

Input Sequence in FASTA format

>Q7L8A9 (365 residues)
MPGGKKVAGGGSSGATPTSAAATAPSGVRRLETSEGTSAQRDEEPEEEGEEDLRDGGVPF
FVNRGGLPVDEATWERMWKHVAKIHPDGEKVAQRIRGATDLPKIPIPSVPTFQPSTPVPE
RLEAVQRYIRELQYNHTGTQFFEIKKSRPLTGLMDLAKEMTKEALPIKCLEAVILGIYLT
NSMPTLERFPISFKTYFSGNYFRHIVLGVNFAGRYGALGMSRREDLMYKPPAFRTLSELV
LDFEAAYGRCWHVLKKVKLGQSVSHDPHSVEQIEWKHSVLDVERLGRDDFRKELERHARD
MRLKIGKGTGPPSPTKDRKKDVSSPQRAQSSPHRRNSRSERRPSGDKKTSEPKAMPDLNG
YQIRV

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	Q7L8A9-D1	1-365	365		MPGGKKVAGGGSSGATPTSAAATAPSGVRRLETSEGTSAQRDEEPEEEGEEDLRDGGVPFFVNRGGLPVDEATWERMWKHVAKIHPDGEKVAQRIRGATDLPKIPIPSVPTFQPSTPVPERLEAVQRYIRELQYNHTGTQFFEIKKSRPLTGLMDLAKEMTKEALPIKCLEAVILGIYLTNSMPTLERFPISFKTYFSGNYFRHIVLGVNFAGRYGALGMSRREDLMYKPPAFRTLSELVLDFEAAYGRCWHVLKKVKLGQSVSHDPHSVEQIEWKHSVLDVERLGRDDFRKELERHARDMRLKIGKGTGPPSPTKDRKKDVSSPQRAQSSPHRRNSRSERRPSGDKKTSEPKAMPDLNGYQIRV

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.6268

(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	6j4uA	0.67	0.70	0.988	0.677	model1_6j4uA.pdb.gz
2	6qbyA	0.66	0.77	0.620	0.671	model1_6qbyA.pdb.gz
3	3vthA	0.42	6.88	0.038	0.710	model1_3vthA.pdb.gz
4	5m59A	0.41	6.78	0.052	0.690	model1_5m59A.pdb.gz
5	4g9iA	0.41	6.94	0.077	0.707	model1_4g9iA.pdb.gz
6	6uebA	0.41	7.00	0.056	0.699	model1_6uebA.pdb.gz
7	5gm6B	0.41	6.77	0.041	0.688	model1_5gm6B.pdb.gz
8	7bzlA	0.40	6.51	0.049	0.657	model1_7bzlA.pdb.gz
9	6qkgA	0.40	6.73	0.067	0.660	model1_6qkgA.pdb.gz
10	5h3zA	0.40	6.47	0.059	0.647	model1_5h3zA.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:0046872	0.54	metal ion 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:0045765	1.00	regulation of angiogenesis
GO:0001936	1.00	regulation of endothelial cell proliferation
GO:0044699	0.88	single-organism process
GO:0044767	0.86	single-organism developmental process
GO:0048646	0.84	anatomical structure formation involved in morphogenesis
GO:0048518	0.71	positive regulation of biological process
GO:0050896	0.69	response to stimulus
GO:0048519	0.69	negative regulation of biological process
GO:0048523	0.68	negative regulation of cellular process
GO:0032879	0.68	regulation of localization
GO:0048583	0.67	regulation of response to stimulus
GO:0010596	0.67	negative regulation of endothelial cell migration
GO:0006950	0.67	response to stress
GO:0001525	0.67	angiogenesis
GO:2000772	0.66	regulation of cellular senescence
GO:1901491	0.66	negative regulation of lymphangiogenesis
GO:0043537	0.66	negative regulation of blood vessel endothelial cell migration
GO:0016525	0.66	negative regulation of angiogenesis
GO:0009611	0.66	response to wounding
GO:0001937	0.66	negative regulation of endothelial cell proliferation
GO:0048856	0.52	anatomical structure development
GO:0048513	0.50	animal organ 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:0005737	1.00	cytoplasm
GO:0043226	0.77	organelle
GO:0043229	0.75	intracellular organelle
GO:0044444	0.74	cytoplasmic part
GO:0043227	0.73	membrane-bounded organelle
GO:0043231	0.72	intracellular membrane-bounded organelle
GO:0044421	0.70	extracellular region part
GO:0045177	0.67	apical part of cell
GO:0005783	0.67	endoplasmic reticulum
GO:0005615	0.66	extracellular space

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	1fo4A	0.370	6.93	0.038	0.636	1.17.1.4	NA
2	0.060	1gw0A	0.395	6.68	0.057	0.649	1.10.3.2	NA
3	0.060	3fu7B	0.396	6.62	0.054	0.647	1.10.3.2	NA
4	0.060	1yiqA	0.381	7.09	0.061	0.663	1.1.99.-	NA
5	0.060	3ffzA	0.366	6.87	0.037	0.627	3.4.24.69	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	0.07	1bxrA	0.391	7.20	0.061	0.696	0.19	ANP	complex1.pdb.gz	130,188,207,218,219
2	0.01	1ce8C	0.371	7.02	0.038	0.657	0.27	ADP	complex2.pdb.gz	177,178,179,206,219,220
3	0.01	2ih8A	0.396	6.64	0.050	0.649	0.33	UUU	complex3.pdb.gz	134,206,208,220,244
4	0.01	1ce8A	0.371	7.01	0.044	0.657	0.20	IMP	complex4.pdb.gz	173,175,176,205
5	0.01	3fu7B	0.396	6.62	0.054	0.647	0.31	UUU	complex5.pdb.gz	206,208,219,226
6	0.01	1jdbE	0.367	7.06	0.040	0.647	0.28	GLN	complex6.pdb.gz	180,209,218
7	0.01	2q9oB	0.395	6.64	0.057	0.649	0.11	UUU	complex7.pdb.gz	122,217,219
8	0.01	1ce8E	0.371	6.84	0.044	0.638	0.21	IMP	complex8.pdb.gz	133,175,226,227
9	0.01	1a9xA	0.361	7.25	0.049	0.638	0.22	PO4	complex9.pdb.gz	208,217,219,221
10	0.01	1gw0B	0.394	6.69	0.057	0.649	0.27	UUU	complex10.pdb.gz	207,216,218

	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.