D-I-TASSER Q6L8Q7-D3

D-I-TASSER results for Q6L8Q7-D3

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

Input Sequence in FASTA format

>Q6L8Q7 (159 residues)
CTFDHRHLYTKKVTEDALIRTVSYNILADTYAQTEFSRTVLYPYCAPYALELDYRQNLIQ
KELTGYNADVICLQEVDRAVFSDSLVPALEAFGLEGVFRIKQHEGLATFYRKSKFDLNAL
EVEQVIPLPSHEEVTTHQALPSVSHPSDHIALVCDLKWK

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 \| \| \| \| \| \| \| CTFDHRHLYTKKVTEDALIRTVSYNILADTYAQTEFSRTVLYPYCAPYALELDYRQNLIQKELTGYNADVICLQEVDRAVFSDSLVPALEAFGLEGVFRIKQHEGLATFYRKSKFDLNALEVEQVIPLPSHEEVTTHQALPSVSHPSDHIALVCDLKWK
Prediction	CCCCCCCCCCCCCCCCCCSSSSSSCCCCHHHCCCCCCCCCCCCCCCHHHCCHHHHHHHHHHHHHHCCCCSSSSSCCCHHHHHHHHHHHHHHCCCSSSSSCCCCCSSSSSSSCCSSSSSSSSSSSSCCCCCCCCCCCCHHHHCCCCCCCCSSSSSSSSSC
Confidence	997532245688899995999985016464467653544566889845458178999999999970986222101458999999999998819837872468960799996460799777899820467740012221332112578858999998659
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 \| \| \| \| \| \| \| CTFDHRHLYTKKVTEDALIRTVSYNILADTYAQTEFSRTVLYPYCAPYALELDYRQNLIQKELTGYNADVICLQEVDRAVFSDSLVPALEAFGLEGVFRIKQHEGLATFYRKSKFDLNALEVEQVIPLPSHEEVTTHQALPSVSHPSDHIALVCDLKWK
Prediction	453542533367437743020002000012014464446411430354123063025201500462513100012034520452036205724040223445420000013442041244331402622457535444213223343200000020438
	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 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.

Top 10 threading templates used by D-I-TASSER

Rank

PDB
hit

ID1

ID2

Cov

Norm.
Zscore

Download
alignment

                  20                  40                  60                  80                 100                 120                 140

                   |                   |                   |                   |                   |                   |                   |

SS
Seq

CCCCCCCCCCCCCCCCCCSSSSSSCCCCHHHCCCCCCCCCCCCCCCHHHCCHHHHHHHHHHHHHHCCCCSSSSSCCCHHHHHHHHHHHHHHCCCSSSSSCCCCCSSSSSSSCCSSSSSSSSSSSSCCCCCCCCCCCCHHHHCCCCCCCCSSSSSSSSSC
CTFDHRHLYTKKVTEDALIRTVSYNILADTYAQTEFSRTVLYPYCAPYALELDYRQNLIQKELTGYNADVICLQEVDRAVFSDSLVPALEAFGLEGVFRIKQHEGLATFYRKSKFDLNALEVEQVIPLPSHEEVTTHQALPSVSHPSDHIALVCDLKWK

4z0vA

0.83

0.72

20.40

1.17

DEthreader

TCFDHRHLYTK-VTEDALIRTVSYNILADTYAQTEFSRTVLYPYCAPYALELDYRQNLIQKELTGYNADVICLQEVDRAVFSDSLVPALEAFGLEGVFRIKQHEGLATFYRKSKFSLLSQHDISFY-------------------QRSSVLQVSVLQST

4z0vA2

0.75

21.21

1.77

SPARKS-K

CTFDHRHLYTKKVTEDALIRTVSYNILADTYAQTEFSRTVLYPYCAPYALELDYRQNLIQKELTGYNADVICLQEVDRAVFSDSLVPALEAFGLEGVFRIKQHEGLATFYRKSKFSLLSQHDISFYEALESDPKELLEKLVLYPLQRSSVLQVSVLQST

4z0vA2

0.75

21.21

1.24

MapAlign

CTFDHRHLYTKKVTEDALIRTVSYNILADTYAQTEFSRTVLYPYCAPYALELDYRQNLIQKELTGYNADVICLQEVDRAVFSDSLVPALEAFGLEGVFRIKQHEGLATFYRKSKFSLLSQHDISFYHKELLEKLVLYPSAQEKVLQRSSVLQVSVLQST

4z0vA2

0.74

21.04

1.28

CEthreader

CTFDHRHLYTKKVTEDALIRTVSYNILADTYAQTEFSRTVLYPYCAPYALELDYRQNLIQKELTGYNADVICLQEVDRAVFSDSLVPALEAFGLEGVFRIKQHEGLATFYRKSKFSLLSQHDISFYEALESDPLVLYPSAQEKVLQRSSVLQVSVLQST

4z0vA2

0.74

21.04

1.66

MUSTER

CTFDHRHLYTKKVTEDALIRTVSYNILADTYAQTEFSRTVLYPYCAPYALELDYRQNLIQKELTGYNADVICLQEVDRAVFSDSLVPALEAFGLEGVFRIKQHEGLATFYRKSKFSLLSQHDISFYEALESDKLVLYPSAQEKVLQRSSVLQVSVLQST

4z0vA

0.74

21.04

2.61

HHsearch

CTFDHRHLYTKKVTEDALIRTVSYNILADTYAQTEFSRTVLYPYCAPYALELDYRQNLIQKELTGYNADVICLQEVDRAVFSDSLVPALEAFGLEGVFRIKQHEGLATFYRKSKFSLLSQHDISFYEALESDKELLEKSAQEKVLQRSSVLQVSVLQST

4z0vA2

0.74

21.04

1.81

FFAS-3D

CTFDHRHLYTKKVTEDALIRTVSYNILADTYAQTEFSRTVLYPYCAPYALELDYRQNLIQKELTGYNADVICLQEVDRAVFSDSLVPALEAFGLEGVFRIKQHEGLATFYRKSKFSLLSQHDISFYEALESDPLVLYPSAQEKVLQRSSVLQVSVLQST

4z0vA2

0.74

21.04

1.32

EigenThreader

CTFDHRHLYTKKVTEDALIRTVSYNILADTYAQTEFSRTVLYPYCAPYALELDYRQNLIQKELTGYNADVICLQEVDRAVFSDSLVPALEAFGLEGVFRIKQHEGLATFYRKSKFSLLSQHDISFYEALESDKLVLYPSAQEKVLQRSSVLQVSVLQST

4z0vA

0.75

21.21

1.77

CNFpred

CTFDHRHLYTKKVTEDALIRTVSYNILADTYAQTEFSRTVLYPYCAPYALELDYRQNLIQKELTGYNADVICLQEVDRAVFSDSLVPALEAFGLEGVFRIKQHEGLATFYRKSKFSLLSQHDISFYEALLLEKLVLYPSAQEKVLQRSSVLQVSVLQST

4z0vA2

0.83

0.72

20.40

1.17

DEthreader

TCFDHRHLYTK-VTEDALIRTVSYNILADTYAQTEFSRTVLYPYCAPYALELDYRQNLIQKELTGYNADVICLQEVDRAVFSDSLVPALEAFGLEGVFRIKQHEGLATFYRKSKFSLLSQHDISFY-------------------QRSSVLQVSVLQST

(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	0.8578

(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	4z0vA	0.96	1.12	0.748	1.000	model1_4z0vA.pdb.gz
2	3ngnA	0.82	2.19	0.287	0.918	model1_3ngnA.pdb.gz
3	6rvzA	0.75	2.23	0.279	0.843	model1_6rvzA.pdb.gz
4	6bt1A	0.74	1.95	0.276	0.824	model1_6bt1A.pdb.gz
5	3g6sA	0.64	2.08	0.212	0.717	model1_3g6sA.pdb.gz
6	3mprA	0.63	2.34	0.195	0.723	model1_3mprA.pdb.gz
7	3l1wA	0.62	1.98	0.174	0.692	model1_3l1wA.pdb.gz
8	3wcxA	0.57	3.27	0.140	0.717	model1_3wcxA.pdb.gz
9	4b8cD	0.42	2.29	0.223	0.465	model1_4b8cD.pdb.gz
10	4pw2A	0.40	5.10	0.038	0.673	model1_4pw2A.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:0016787	0.73	hydrolase activity
GO:0004518	0.72	nuclease activity
GO:0004540	0.71	ribonuclease activity
GO:0004532	0.70	exoribonuclease activity
GO:0000175	0.69	3'-5'-exoribonuclease activity
GO:0004535	0.67	poly(A)-specific ribonuclease activity
GO:0046872	0.52	metal ion binding
GO:0019904	0.51	protein domain specific binding
GO:0008190	0.51	eukaryotic initiation factor 4E 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:0071704	0.96	organic substance metabolic process
GO:0016070	0.94	RNA metabolic process
GO:0016071	0.90	mRNA metabolic process
GO:1901575	0.86	organic substance catabolic process
GO:0006401	0.84	RNA catabolic process
GO:0000956	0.82	nuclear-transcribed mRNA catabolic process
GO:0065007	0.76	biological regulation
GO:0050789	0.74	regulation of biological process
GO:0050794	0.72	regulation of cellular process
GO:0060255	0.69	regulation of macromolecule metabolic process
GO:0048523	0.64	negative regulation of cellular process
GO:0010468	0.62	regulation of gene expression
GO:0044699	0.59	single-organism process
GO:0010608	0.59	posttranscriptional regulation of gene expression
GO:0000289	0.58	nuclear-transcribed mRNA poly(A) tail shortening
GO:0080090	0.57	regulation of primary metabolic process
GO:0051171	0.57	regulation of nitrogen compound metabolic process
GO:0050896	0.57	response to stimulus
GO:0031326	0.57	regulation of cellular biosynthetic process
GO:0010605	0.57	negative regulation of macromolecule metabolic process
GO:0010556	0.57	regulation of macromolecule biosynthetic process
GO:0010629	0.54	negative regulation of gene expression
GO:0006396	0.54	RNA processing
GO:0048518	0.52	positive regulation of biological process
GO:0006397	0.52	mRNA processing
GO:2000113	0.50	negative regulation of cellular macromolecule biosynthetic process
GO:0090503	0.50	RNA phosphodiester bond hydrolysis, exonucleolytic
GO:0051172	0.50	negative regulation of nitrogen compound metabolic process
GO:0044763	0.50	single-organism cellular process

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:0044464	1.00	cell part
GO:0044424	0.99	intracellular part
GO:0043229	0.75	intracellular organelle
GO:0044444	0.72	cytoplasmic part
GO:0043231	0.63	intracellular membrane-bounded organelle
GO:0005829	0.56	cytosol
GO:0005634	0.55	nucleus

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	1iv8A	0.507	4.73	0.041	0.849	5.4.99.15	NA
2	0.060	1booA	0.507	4.09	0.063	0.767	2.1.1.113	NA
3	0.060	2qrvA	0.521	4.28	0.075	0.811	2.1.1.37	NA
4	0.060	1q45B	0.490	4.88	0.083	0.786	1.3.1.42	NA
5	0.060	1cjyA	0.529	5.09	0.052	0.887	3.1.1.4 3.1.1.5	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	0.08	3ngqA	0.821	1.97	0.287	0.912	0.23	1PS	complex1.pdb.gz	23,67,93
2	0.01	3pt6B	0.590	4.30	0.069	0.874	0.20	QNA	complex2.pdb.gz	105,106,107
3	0.01	2z6qA	0.594	4.02	0.051	0.849	0.16	DCZ	complex3.pdb.gz	94,95,96
4	0.01	8mhtA	0.590	4.18	0.051	0.855	0.15	SAH	complex4.pdb.gz	63,65,96
5	0.01	1svuA	0.535	3.70	0.060	0.736	0.12	SAH	complex5.pdb.gz	63,64,97,98
6	0.01	4mhtA	0.595	3.95	0.044	0.843	0.19	SAH	complex6.pdb.gz	70,94,95,96,115,117
7	0.01	2c7oA	0.597	3.93	0.051	0.843	0.10	QNA	complex7.pdb.gz	73,90,93,95,111,112
8	0.01	1hmyA	0.556	3.98	0.051	0.786	0.36	SAM	complex8.pdb.gz	67,69,70,89,90,91,95
9	0.01	2c7qA	0.597	3.92	0.051	0.843	0.10	QNA	complex9.pdb.gz	73,90,93,95
10	0.01	2z6qA	0.594	4.02	0.051	0.849	0.18	QNA	complex10.pdb.gz	95,107,109

	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.