D-I-TASSER Q6ZVD7-D2

D-I-TASSER results for Q6ZVD7-D2

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

Input Sequence in FASTA format

>Q6ZVD7 (92 residues)
HTGEGYFIVTPQTYFITNTTTQENKRMLPSDESRLMPASMTYLVSMESCAESAQENAAPI
SHCQSCQCFRDMHTQDVQEAPVAAEVTRKSHR

Predicted Secondary Structure

Sequence	20 40 60 80 \| \| \| \| HTGEGYFIVTPQTYFITNTTTQENKRMLPSDESRLMPASMTYLVSMESCAESAQENAAPISHCQSCQCFRDMHTQDVQEAPVAAEVTRKSHR
Prediction	CCCCCSSSSCCCSSSSCCCCHHHCCCCCCCCCCCCCCCCSSSSSCCCCHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHCCCC
Confidence	99972699757446753874111442011578999999716985353100111357887555877333777775434478842564421369
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 \| \| \| \| HTGEGYFIVTPQTYFITNTTTQENKRMLPSDESRLMPASMTYLVSMESCAESAQENAAPISHCQSCQCFRDMHTQDVQEAPVAAEVTRKSHR
Prediction	84562110022413202443465444124477546434322122336313531675444453053141247444763764444554465668
	Values range from 0 (buried residue) to 8 (highly exposed residue)

Predicted Contact, Hydrogen and Distance Map Used in D-I-TASSER simulation

Contact Map

Distance Map

Hydrogen bond networks

D-I-TASSER simulation is guided by the consensus contact map (left figure), distance map (middle figure) and Hydrogen bond network (right figure) derived based on confidence scores of AttentionPotential. 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.

Top 10 threading templates used by D-I-TASSER

Rank

PDB
hit

ID1

ID2

Cov

Norm.
Zscore

Download
alignment

                  20                  40                  60                  80

                   |                   |                   |                   |

SS
Seq

CCCCCSSSSCCCSSSSCCCCHHHCCCCCCCCCCCCCCCCSSSSSCCCCHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHCCCC
HTGEGYFIVTPQTYFITNTTTQENKRMLPSDESRLMPASMTYLVSMESCAESAQENAAPISHCQSCQCFRDMHTQDVQEAPVAAEVTRKSHR

1uapA

0.11

3.93

0.59

CEthreader

ATVKSMVREPGEGLAVTVSLIGAYKTGGLDLPSPPTGASLKFYVPCKQCPPMGVSYLLMGQVEENRGPVLPPESFVVLHRPNQDQILTNLSK

3kptB

0.02

1.51

0.62

EigenThreader

NEEPTIDKKILEYDIKTLIPEDIKEYKGKPDFTKDGKKEFHLQIKS---QVK----EGKKGAKIVDENGPTKEDGTLKDPIDVKISENNQTV

3m1cA

0.18

0.13

4.23

0.26

FFAS-3D

-HNAEPRILVPASYVVTHTPLPRGIGYKLTGVDVRRPLFITYL--TATCEGHAREPKRLVRDLGLVGA------------------------

6f1tg2

0.03

1.88

0.99

SPARKS-K

QYPELLVASYNNNEDAPHEPDGVALVWNMKYKKTTPEYVFHCQSAVMSATFAKFHPNLVVGTYSGQIVLWDNRSNKRTPVQRTPLSAAAHTH

5vobA

0.20

0.11

3.47

0.60

CNFpred

--GESFSALTVVSYIVTNQYLIKGISYPVSTTVV--SLIITQTDSQTKCELTR---------------------------------------

6hihA

0.05

0.04

2.01

0.83

DEthreader

EGGIHHVYANAAVLVFDLFD------YQ-EDALVEGKRKLIGVMER-D-AKF-SATWGYEGF--GKPDKRLVTDGQFGCHAYV-FSRLR-D-

2pffB

0.03

0.02

1.37

0.79

MapAlign

GGGGGGGGGGGGGGGGGGGGG-----GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG---------------

5jouA

0.11

3.92

0.54

MUSTER

NKN-GILLDSYFCRFNPNDYSQLNRIFKLYDKTGQEGALTGTYVPKKGETLVRREDSIYFENLKTIENLPKKLPLMGAKVTYEGEIEPAQTG

6cv0A

0.17

0.12

3.92

0.42

HHsearch

RTGQGFITLENQFYIKITNGTRRFRRSITENANCPRAITAGDIVTLTSCQNYVSVNK----------TVITTF---------V---------

7c94A2

0.06

0.05

2.32

0.54

CEthreader

AAPTVSIFPPGASVVCFLNNFYPKDSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC--------------

(a)	ID1 is the number of template residues identical to query divided by number of aligned residues.
(b)	ID2 is the number of template residues identical to query divided by query sequence length.
(c)	Cov is equal the number of aligned template residues divided by query sequence length.
(d)	Norm. Zscore is the normalized Z-score of the threading alignments. A Normalized Z-score >1 means a good alignment and is highlighted in bold.
(e)	Download alignment lists the threading program used to identify the template, and provide the 3D structure of aligned regions of threading templates (threading[1-10].pdb.gz).
(f)	Template residues identical to query sequence are highlighted in color.

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.541

(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 AttentionPotential, 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	3rbyA	0.45	4.16	0.099	0.880	model1_3rbyA.pdb.gz
2	1piiA1	0.45	3.38	0.044	0.696	model1_1piiA1.pdb.gz
3	4ge1A	0.45	4.38	0.026	0.815	model1_4ge1A.pdb.gz
4	1kolA1	0.44	4.44	0.068	0.837	model1_1kolA1.pdb.gz
5	3vsrA	0.44	4.47	0.082	0.826	model1_3vsrA.pdb.gz
6	1i4nA	0.43	3.79	0.072	0.707	model1_1i4nA.pdb.gz
7	4xmcA	0.39	4.22	0.027	0.772	model1_4xmcA.pdb.gz
8	1peeA	0.38	4.37	0.101	0.707	model1_1peeA.pdb.gz
9	2yfrA	0.37	4.21	0.060	0.696	model1_2yfrA.pdb.gz
10	1w18B2	0.37	4.16	0.063	0.674	model1_1w18B2.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:0000977	1.00	RNA polymerase II regulatory region sequence-specific DNA 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:0044699	0.81	single-organism process
GO:0065007	0.71	biological regulation
GO:0032502	0.71	developmental process
GO:0044767	0.70	single-organism developmental process
GO:0048856	0.69	anatomical structure development
GO:0050789	0.68	regulation of biological process
GO:0050794	0.66	regulation of cellular process
GO:0009987	0.66	cellular process
GO:0080090	0.60	regulation of primary metabolic process
GO:0060255	0.60	regulation of macromolecule metabolic process
GO:0048518	0.60	positive regulation of biological process
GO:0031323	0.60	regulation of cellular metabolic process
GO:0065008	0.57	regulation of biological quality
GO:0051246	0.57	regulation of protein metabolic process
GO:0051171	0.57	regulation of nitrogen compound metabolic process
GO:0048583	0.57	regulation of response to stimulus
GO:0048522	0.57	positive regulation of cellular process
GO:2000112	0.56	regulation of cellular macromolecule biosynthetic process
GO:0050896	0.56	response to stimulus
GO:0048519	0.56	negative regulation of biological process
GO:0032268	0.56	regulation of cellular protein metabolic process
GO:0031325	0.56	positive regulation of cellular metabolic process
GO:0010604	0.56	positive regulation of macromolecule metabolic process
GO:0010468	0.56	regulation of gene expression
GO:0051247	0.55	positive regulation of protein metabolic process
GO:0010605	0.55	negative regulation of macromolecule metabolic process
GO:0006357	0.55	regulation of transcription from RNA polymerase II promoter
GO:0001932	0.55	regulation of protein phosphorylation
GO:0080134	0.54	regulation of response to stress
GO:0051716	0.54	cellular response to stimulus
GO:0050790	0.54	regulation of catalytic activity
GO:0033043	0.54	regulation of organelle organization
GO:0001934	0.54	positive regulation of protein phosphorylation
GO:1904031	0.53	positive regulation of cyclin-dependent protein kinase activity
GO:1902882	0.53	regulation of response to oxidative stress
GO:1901858	0.53	regulation of mitochondrial DNA metabolic process
GO:0071500	0.53	cellular response to nitrosative stress
GO:0061418	0.53	regulation of transcription from RNA polymerase II promoter in response to hypoxia
GO:0051881	0.53	regulation of mitochondrial membrane potential
GO:0033138	0.53	positive regulation of peptidyl-serine phosphorylation
GO:0010971	0.53	positive regulation of G2/M transition of mitotic cell cycle
GO:0010800	0.53	positive regulation of peptidyl-threonine phosphorylation
GO:0010629	0.53	negative regulation of gene expression
GO:0010628	0.53	positive regulation of gene expression
GO:0008284	0.53	positive regulation of cell proliferation

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:0005813	1.00	centrosome
GO:0005737	1.00	cytoplasm
GO:0005730	1.00	nucleolus
GO:0005654	1.00	nucleoplasm
GO:0005634	1.00	nucleus
GO:0044444	0.57	cytoplasmic 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	1jx1A	0.409	4.36	0.053	0.761	5.5.1.6	NA
2	0.060	1cptA	0.413	4.77	0.012	0.826	1.14.-.-	NA
3	0.060	1qo9A	0.409	4.34	0.086	0.761	3.1.1.7	NA
4	0.060	1tqnA	0.417	4.83	0.033	0.848	1.14.13.67 1.14.13.32 1.14.13.97	NA
5	0.060	1e9xA	0.429	4.52	0.037	0.815	1.14.13.70	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	0.01	1swgA	0.425	3.92	0.082	0.772	0.26	BTN	complex1.pdb.gz	2,4,6,8,15,17
2	0.01	2wdcA	0.408	4.42	0.036	0.783	0.22	GOL	complex2.pdb.gz	5,6,7,15,16
3	0.01	2jkgA	0.415	4.19	0.041	0.761	0.23	III	complex3.pdb.gz	2,3,38

	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, Chengxin Zhang, Yang Li, Robin Pearce, Eric W. Bell, Yang Zhang. Folding non-homology proteins by coupling deep-learning contact maps with I-TASSER assembly simulations. In preparation, 2020.