D-I-TASSER Q6ZVW7-D1

D-I-TASSER results for Q6ZVW7-D1

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

Input Sequence in FASTA format

>Q6ZVW7 (112 residues)
MSRSVLEALTSSTAMQCVPSDGCAMLLRVRASITLHERLRGLEACAMSLDTQETQCQSVW
VARASHRQQGGQQLQVHFGCFAVSVAQHLYVTLRTIPHFCGVQLDQRHLVEA

Predicted Secondary Structure

Sequence	20 40 60 80 100 \| \| \| \| \| MSRSVLEALTSSTAMQCVPSDGCAMLLRVRASITLHERLRGLEACAMSLDTQETQCQSVWVARASHRQQGGQQLQVHFGCFAVSVAQHLYVTLRTIPHFCGVQLDQRHLVEA
Prediction	CCHHHHHHHHHHHHHHCCCCCCCCSSSSSSSSSSCCCCCSSSSSSSSSSCCCCCCSSSSSSSCCCCCCCCCCSSSSSSCSSSSCCCSSSSSSSSSCCCCSSSSSSSSSSSCC
Confidence	9888987532334664389999606899887776168700279998861453123189998122453458817999980698247519999997257600355302543049
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 \| \| \| \| \| MSRSVLEALTSSTAMQCVPSDGCAMLLRVRASITLHERLRGLEACAMSLDTQETQCQSVWVARASHRQQGGQQLQVHFGCFAVSVAQHLYVTLRTIPHFCGVQLDQRHLVEA
Prediction	6454226414233024035764030203042314245414213112331435444144131444544445544040304114243243020203213431213145524268
	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

                   |                   |                   |                   |                   |

SS
Seq

CCHHHHHHHHHHHHHHCCCCCCCCSSSSSSSSSSCCCCCSSSSSSSSSSCCCCCCSSSSSSSCCCCCCCCCCSSSSSSCSSSSCCCSSSSSSSSSCCCCSSSSSSSSSSSCC
MSRSVLEALTSSTAMQCVPSDGCAMLLRVRASITLHERLRGLEACAMSLDTQETQCQSVWVARASHRQQGGQQLQVHFGCFAVSVAQHLYVTLRTIPHFCGVQLDQRHLVEA

2ygtA

0.06

0.05

2.41

1.17

DEthreader

-KSN-S-KITVDASFVDDKFSEMTTIISLKGFIPSGRWPIKYMVDLKNNSLDSIASWNTEFAETRFTDIT-GGFSPNFGVVLTATKSQIEISLKREIPDSKIEETVKFELDH

6hg4B1

0.16

5.32

1.56

SPARKS-K

GPVLAPTHLQTELVLRCQKETDCDLCLRVAVHLAVHGHLQAQVVLSFQAYPT-ARCVLLEVQVPALVQFGQSVGSVVYDCFEAALGSEVRIWSYTQPRYEK-ELQHTQQLPD

6hg4B

0.16

0.15

5.04

0.63

MapAlign

---LAPTHLQTELVLRCQKETDCDLCLRVAVHLAVHSLQAQVVLSFQAY--PTARCVLLEVQVPAALVQFGQSVSVVYDCFEAALGSEVRIWSYTQ-PRYEKELQHTQQLPD

3jvfC1

0.15

5.08

0.64

CEthreader

NLTPSSPDLQIQLHFAHTQQGDLFPVAHIEWTLQTDASLEGAELSVLQLNTNERLCVRFEFLS--KLRHHHRRWRFTFSHFVVDPDQEYEVTVHHLPKPDPNHQSKNFLVPD

3jvfC1

0.17

0.16

5.31

1.01

MUSTER

LTPSSP-DLQIQLHFAHTQQGDLFPVAHIEWTLQTDASLEGAELSVLQLNTNERLCVRFEFLS--KLRHHHRRWRFTFSHFVVDPDQEYEVTVHHLPKPDPNHQSKNFLVPD

6hg4B1

0.20

6.27

4.97

HHsearch

APGPAPTHLQTELVLRCQKETDCDLCLRVAVHLAVHGHWRNASLQALSAYPT-ARCVLLEVPAALV--QFGQSVSVVYDCFEAALGSEVRIWSYTQPRYEK-ELQHTQQLPD

6hg4B1

0.17

0.16

5.30

1.46

FFAS-3D

-PVLAPTHLQTELVLRCQKETDCDLCLRVAVHLAVNASLQAQVVLSFQA-YPTARCVLLEVQVPAALVQFGQSVSVVYDCFEAALGSEVRIWSYTQPRYE-KELQHTQQLP-

6hg4B1

0.19

0.18

5.79

0.60

EigenThreader

APGPVPTHLQTELVLRCQKETDCDLCLRVAVHLAVWESLQAQVVLSFQAPTARCVLLEVQVP--AALVQFGQSVSVVYDCFEAALGSEVRIWSYTQ--PRYEKELQHTQQLP

5nanB

0.16

5.32

1.79

CNFpred

LTPSSPKDLQIQLHFAHTQQGDLFPVAHIEWTLQTILYLEGAELSVLQLNTNERLCVRFEFLSKLRH--HHRRWRFTFSHFVVDPDQEYEVTVHHLPKPDPNHQSKNFLVPD

2lkfA

0.08

3.15

1.17

DEthreader

SDKFKI-SQILTFNFIKDKSYDDTLVLKATGNINSGFWGAKYNVSISSQSDYKNVGWGVEAHKIQMPLSR-SNFNPEFLSVLSHKKSKITVTYQREMNFKTRTFKSTYEIDH

(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	0.7691

(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	6hg4B1	0.84	2.07	0.147	0.973	model1_6hg4B1.pdb.gz
2	3jvfC	0.82	2.12	0.176	0.964	model1_3jvfC.pdb.gz
3	4ypjA	0.74	2.76	0.067	0.938	model1_4ypjA.pdb.gz
4	5t9aA	0.74	2.67	0.029	0.920	model1_5t9aA.pdb.gz
5	5uj6A	0.74	2.67	0.117	0.920	model1_5uj6A.pdb.gz
6	3fn9C	0.72	2.80	0.097	0.920	model1_3fn9C.pdb.gz
7	6hpdA1	0.72	2.74	0.098	0.911	model1_6hpdA1.pdb.gz
8	3cmgA	0.72	2.77	0.078	0.911	model1_3cmgA.pdb.gz
9	5ze3A	0.71	2.87	0.089	1.000	model1_5ze3A.pdb.gz
10	6ed1A	0.71	2.75	0.039	0.911	model1_6ed1A.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:0030368	1.00	interleukin-17 receptor 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:0065007	0.74	biological regulation
GO:0050789	0.73	regulation of biological process
GO:0050794	0.69	regulation of cellular process
GO:0009987	0.68	cellular process
GO:0044699	0.65	single-organism process
GO:0050896	0.62	response to stimulus
GO:0048518	0.61	positive regulation of biological process
GO:0044763	0.60	single-organism cellular process
GO:0048522	0.59	positive regulation of cellular process
GO:0002376	0.59	immune system process
GO:0007165	0.58	signal transduction
GO:0051239	0.57	regulation of multicellular organismal process
GO:0051240	0.56	positive regulation of multicellular organismal process
GO:0010033	0.56	response to organic substance
GO:0006952	0.56	defense response
GO:0001817	0.56	regulation of cytokine production
GO:0098542	0.55	defense response to other organism
GO:0051716	0.55	cellular response to stimulus
GO:0048583	0.55	regulation of response to stimulus
GO:0007166	0.55	cell surface receptor signaling pathway
GO:0001819	0.55	positive regulation of cytokine production
GO:0001775	0.55	cell activation
GO:0080134	0.54	regulation of response to stress
GO:0071310	0.54	cellular response to organic substance
GO:0070201	0.54	regulation of establishment of protein localization
GO:0048584	0.54	positive regulation of response to stimulus
GO:0009620	0.54	response to fungus
GO:2000665	0.53	regulation of interleukin-13 secretion
GO:2000662	0.53	regulation of interleukin-5 secretion
GO:1900015	0.53	regulation of cytokine production involved in inflammatory response
GO:0097530	0.53	granulocyte migration
GO:0071345	0.53	cellular response to cytokine stimulus
GO:0050729	0.53	positive regulation of inflammatory response
GO:0050715	0.53	positive regulation of cytokine secretion
GO:0032754	0.53	positive regulation of interleukin-5 production
GO:0032736	0.53	positive regulation of interleukin-13 production
GO:0032667	0.53	regulation of interleukin-23 production
GO:0030595	0.53	leukocyte chemotaxis

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:0005887	1.00	integral component of plasma 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	0.067	1k85A	0.550	2.81	0.071	0.750	3.2.1.14	92
2	0.067	2rq8A	0.529	3.08	0.049	0.732	2.7.11.1	NA
3	0.066	2amuA	0.636	2.94	0.060	0.839	1.15.1.2	NA
4	0.066	1exgA	0.556	3.11	0.077	0.768	3.2.1.8 3.2.1.91	34,64
5	0.066	2b3rB	0.596	2.98	0.074	0.830	2.7.1.154	65

	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	0.02	2x40A	0.656	2.48	0.124	0.848	0.20	GOL	complex1.pdb.gz	40,41,100
2	0.02	3ijeA	0.612	3.42	0.085	0.893	0.38	UUU	complex2.pdb.gz	41,94,101,102
3	0.01	3ijeA	0.612	3.42	0.085	0.893	0.26	UUU	complex3.pdb.gz	59,60,101,103
4	0.01	1edy0	0.652	3.02	0.061	0.857	0.32	III	complex4.pdb.gz	38,39,40,41,42,102,104,105
5	0.01	3gwjF	0.663	3.25	0.037	0.964	0.14	UUU	complex5.pdb.gz	40,77,79
6	0.01	3gwjA	0.664	3.24	0.037	0.964	0.16	UUU	complex6.pdb.gz	41,61,63,67
7	0.01	2vdqA	0.381	5.12	0.058	0.688	0.27	III	complex7.pdb.gz	41,98,100
8	0.01	3gwjE	0.663	3.24	0.037	0.964	0.12	UUU	complex8.pdb.gz	37,39,40,102

	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.