D-I-TASSER Q7RTZ1

D-I-TASSER results for Q7RTZ1

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

Summary of the Protein

Uniprot ID: Q7RTZ1
Protein Name: Ovochymase-2
Gene Name: OVCH2

Input Sequence in FASTA format

>Q7RTZ1 (564 residues)
MLISRNKLILLLGIVFFERGKSATLSLPKAPSCGQSLVKVQPWNYFNIFSRILGGSQVEK
GSYPWQVSLKQRQKHICGGSIVSPQWVITAAHCIANRNIVSTLNVTAGEYDLSQTDPGEQ
TLTIETVIIHPHFSTKKPMDYDIALLKMAGAFQFGHFVGPICLPELREQFEAGFICTTAG
WGRLTEGGVLSQVLQEVNLPILTWEECVAALLTLKRPISGKTFLCTGFPDGGRDACQGDS
GGSLMCRNKKGAWTLAGVTSWGLGCGRGWRNNVRKSDQGSPGIFTDISKVLPWIHEHIQT
GNRRKSSRAWCSEQDVIVSGAEGKLHFPESLHLYYESKQRCVWTLLVPEEMHVLLSFSHL
DVESCHHSYLSMYSLEDRPIGKFCGESLPSSILIGSNSLRLKFVSDATDNAARFNLTYKA
LKPNYIPDSGCSYLTVLFEEGLIQSLNYPENYSDKANCDWIFQASKHHLIKLSFQSLEIE
ESGDCTSDYVTVHSDVERKKEIARLCGYDVPTPVLSPSSIMLISFHSDENGTCRGFQATV
SFIPKAGKKIELPTLWFPVLILVM

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	Q7RTZ1-D1	1-306	306		MLISRNKLILLLGIVFFERGKSATLSLPKAPSCGQSLVKVQPWNYFNIFSRILGGSQVEKGSYPWQVSLKQRQKHICGGSIVSPQWVITAAHCIANRNIVSTLNVTAGEYDLSQTDPGEQTLTIETVIIHPHFSTKKPMDYDIALLKMAGAFQFGHFVGPICLPELREQFEAGFICTTAGWGRLTEGGVLSQVLQEVNLPILTWEECVAALLTLKRPISGKTFLCTGFPDGGRDACQGDSGGSLMCRNKKGAWTLAGVTSWGLGCGRGWRNNVRKSDQGSPGIFTDISKVLPWIHEHIQTGNRRKS
2	Q7RTZ1-D2	307-423	117		SRAWCSEQDVIVSGAEGKLHFPESLHLYYESKQRCVWTLLVPEEMHVLLSFSHLDVESCHHSYLSMYSLEDRPIGKFCGESLPSSILIGSNSLRLKFVSDATDNAARFNLTYKALKP
3	Q7RTZ1-D3	424-564	141		NYIPDSGCSYLTVLFEEGLIQSLNYPENYSDKANCDWIFQASKHHLIKLSFQSLEIEESGDCTSDYVTVHSDVERKKEIARLCGYDVPTPVLSPSSIMLISFHSDENGTCRGFQATVSFIPKAGKKIELPTLWFPVLILVM

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.79

(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	1z8gA	0.47	2.55	0.316	0.496	model1_1z8gA.pdb.gz
2	7meqA	0.45	3.00	0.304	0.479	model1_7meqA.pdb.gz
3	1jwtA	0.44	1.76	0.305	0.454	model1_1jwtA.pdb.gz
4	4hzhB	0.43	2.81	0.273	0.465	model1_4hzhB.pdb.gz
5	1a5iA	0.43	1.61	0.319	0.440	model1_1a5iA.pdb.gz
6	2xxlA	0.43	3.13	0.259	0.466	model1_2xxlA.pdb.gz
7	2vntC	0.42	1.75	0.320	0.438	model1_2vntC.pdb.gz
8	4igdA	0.42	3.07	0.271	0.456	model1_4igdA.pdb.gz
9	1zjkA	0.42	3.04	0.261	0.452	model1_1zjkA.pdb.gz
10	1bmlA	0.42	1.98	0.345	0.436	model1_1bmlA.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:0043621	0.97	protein self-association
GO:0008233	0.96	peptidase activity
GO:0008236	0.95	serine-type peptidase activity
GO:0004175	0.92	endopeptidase activity
GO:0004252	0.91	serine-type endopeptidase activity
GO:0043169	0.52	cation binding
GO:0097367	0.51	carbohydrate derivative binding
GO:0046872	0.51	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:0065007	0.99	biological regulation
GO:0050789	0.83	regulation of biological process
GO:0071704	0.81	organic substance metabolic process
GO:0050794	0.81	regulation of cellular process
GO:0044238	0.80	primary metabolic process
GO:0043170	0.80	macromolecule metabolic process
GO:0019538	0.79	protein metabolic process
GO:0065008	0.78	regulation of biological quality
GO:0032501	0.77	multicellular organismal process
GO:0003008	0.71	system process
GO:0044699	0.70	single-organism process
GO:0042981	0.70	regulation of apoptotic process
GO:0009987	0.66	cellular process
GO:0048518	0.63	positive regulation of biological process
GO:0050896	0.61	response to stimulus
GO:0048583	0.60	regulation of response to stimulus
GO:0048522	0.60	positive regulation of cellular process
GO:0048584	0.57	positive regulation of response to stimulus
GO:0051239	0.56	regulation of multicellular organismal process
GO:0009966	0.56	regulation of signal transduction
GO:0050878	0.55	regulation of body fluid levels
GO:0044763	0.55	single-organism cellular process
GO:0032879	0.55	regulation of localization
GO:0032101	0.55	regulation of response to external stimulus
GO:0006810	0.55	transport
GO:0006508	0.55	proteolysis
GO:1902531	0.54	regulation of intracellular signal transduction
GO:0080134	0.54	regulation of response to stress
GO:0051240	0.54	positive regulation of multicellular organismal process
GO:0042221	0.54	response to chemical
GO:0040012	0.54	regulation of locomotion
GO:0009967	0.54	positive regulation of signal transduction
GO:0009605	0.54	response to external stimulus
GO:0051272	0.53	positive regulation of cellular component movement
GO:0044237	0.53	cellular metabolic process
GO:0040017	0.53	positive regulation of locomotion
GO:0032103	0.53	positive regulation of response to external stimulus
GO:0016192	0.53	vesicle-mediated transport
GO:0010033	0.53	response to organic substance
GO:0009719	0.53	response to endogenous stimulus
GO:1902533	0.52	positive regulation of intracellular signal transduction
GO:1901564	0.52	organonitrogen compound metabolic process
GO:1900048	0.52	positive regulation of hemostasis
GO:0090303	0.52	positive regulation of wound healing
GO:0050921	0.52	positive regulation of chemotaxis
GO:0050820	0.52	positive regulation of coagulation
GO:0044260	0.52	cellular macromolecule metabolic process
GO:0030335	0.52	positive regulation of cell migration
GO:0009725	0.52	response to hormone
GO:0002684	0.52	positive regulation of immune system process
GO:1901654	0.51	response to ketone
GO:0051896	0.51	regulation of protein kinase B signaling
GO:0050926	0.51	regulation of positive chemotaxis
GO:0048511	0.51	rhythmic process
GO:0048193	0.51	Golgi vesicle transport
GO:0046907	0.51	intracellular transport
GO:0043434	0.51	response to peptide hormone
GO:0033273	0.51	response to vitamin
GO:0018214	0.51	protein carboxylation
GO:0018200	0.51	peptidyl-glutamic acid modification
GO:0010640	0.51	regulation of platelet-derived growth factor receptor signaling pathway
GO:0006518	0.51	peptide metabolic process
GO:0002688	0.51	regulation of leukocyte chemotaxis
GO:0002687	0.51	positive regulation of leukocyte migration
GO:0044767	0.50	single-organism developmental process
GO:0003073	0.50	regulation of systemic arterial blood pressure

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	0.96	extracellular region part
GO:0005615	0.90	extracellular space
GO:0044464	0.88	cell part
GO:0005576	0.85	extracellular region
GO:0043226	0.83	organelle
GO:0043227	0.82	membrane-bounded organelle
GO:0044424	0.77	intracellular part
GO:0044444	0.69	cytoplasmic part
GO:0031982	0.62	vesicle
GO:0043231	0.58	intracellular membrane-bounded organelle
GO:0031988	0.57	membrane-bounded vesicle
GO:0070062	0.56	extracellular exosome
GO:0016020	0.50	membrane

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	0.204	1bbrH	0.240	1.32	0.348	0.245	3.4.21.5	91,131
2	0.195	1riwB	0.238	1.04	0.353	0.241	3.4.21.5	92,142
3	0.192	1kdqA	0.222	1.68	0.403	0.229	3.4.21.1	92,142
4	0.150	1ym0A	0.406	1.17	0.322	0.413	3.4.21.-	92
5	0.140	1bruP	0.403	1.43	0.330	0.413	3.4.21.71	90

	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	0.44	2c8wB	0.410	1.25	0.347	0.418	1.20	C7M	complex1.pdb.gz	92,139,217,234,235,236,237,240,259,260,261,262,263,264,265,282,283,284
2	0.43	1qj6B	0.413	1.28	0.345	0.422	1.12	167	complex2.pdb.gz	92,138,234,235,236,238,240,259,262,264,282
3	0.40	1bmmH	0.412	1.23	0.346	0.420	0.89	BM2	complex3.pdb.gz	92,234,237,240,260,261,262,263,264
4	0.25	2bvrH	0.409	1.19	0.349	0.417	0.96	4CP	complex4.pdb.gz	235,236,237,259,261,262,264,265,282,283
5	0.24	1nroH	0.412	1.37	0.345	0.422	0.86	III	complex5.pdb.gz	92,186,187,240,260,262,264
6	0.21	1umaH	0.413	1.30	0.345	0.422	1.00	IN2	complex6.pdb.gz	92,234,235,236,237,240,264
7	0.16	1mkwH	0.406	1.28	0.355	0.415	1.37	III	complex7.pdb.gz	56,59,60,61,62,64,65,155,156,159,160,161,162,173,174,175,177,198,247,249,251,252,253
8	0.16	1sb1H	0.409	1.16	0.349	0.417	1.52	NA	complex8.pdb.gz	66,78,179,180,239,242
9	0.09	1nrqH	0.394	1.27	0.357	0.403	1.39	III	complex9.pdb.gz	59,60,62,65,156,159,160,162,175,176,198,228,247,252,253
10	0.07	1abiH	0.412	1.27	0.346	0.420	1.27	III	complex10.pdb.gz	73,74,75,76,77,92,104,106,112,113,114,115,119,120,121,123,137,138,139,217,234,235,236,237,238,240,259,260,261,262,264,282

	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.