D-I-TASSER Q6DHY5-D2

D-I-TASSER results for Q6DHY5-D2

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

Input Sequence in FASTA format

>Q6DHY5 (138 residues)
GTVQGLQDQQEHVVATSQPKTMGHQDKKDLCGQCSPLGCLIRILIDGISLGLTLRLWDVY
LVEGEQALMPITRIAFKVQQKRLTKTSRCGPWARFCNRFVDTWARDEDTVLKHLRASMKK
LTRKQGDLPPPAKPEQGS

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| GTVQGLQDQQEHVVATSQPKTMGHQDKKDLCGQCSPLGCLIRILIDGISLGLTLRLWDVYLVEGEQALMPITRIAFKVQQKRLTKTSRCGPWARFCNRFVDTWARDEDTVLKHLRASMKKLTRKQGDLPPPAKPEQGS
Prediction	CCCCHHHHHHHHHHHHHCHHHHHHHHHHCCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCC
Confidence	962235899999999977899999999299857779999999997029889999999999981718999999999999654320278199999999997675056707999999999999999752379888611279
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| GTVQGLQDQQEHVVATSQPKTMGHQDKKDLCGQCSPLGCLIRILIDGISLGLTLRLWDVYLVEGEQALMPITRIAFKVQQKRLTKTSRCGPWARFCNRFVDTWARDEDTVLKHLRASMKKLTRKQGDLPPPAKPEQGS
Prediction	843542452145105622440152157370413211130001001431313002202101333433101200000022234434525244004302630374144444400530451154035454744645467658
	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

                   |                   |                   |                   |                   |                   |

SS
Seq

CCCCHHHHHHHHHHHHHCHHHHHHHHHHCCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCC
GTVQGLQDQQEHVVATSQPKTMGHQDKKDLCGQCSPLGCLIRILIDGISLGLTLRLWDVYLVEGEQALMPITRIAFKVQQKRLTKTSRCGPWARFCNRFVDTWARDEDTVLKHLRASMKKLTRKQGDLPPPAKPEQGS

6jl7A

0.07

2.70

1.33

DEthreader

RDCGRPFHLFRLLIQYHEPELCSYLDTKKITPDSYALNWLGSLFACYCVTQAIWDGYLQQ-ADP-FFIYFL-LIILVNAKEVILTQDSEEVIKFLENTPSS-LNIDIEDLFSLAQYYCSKT---PASRDNHHFGSTL-

3qyeA2

0.07

2.70

1.64

SPARKS-K

IILQIQMYQLSRLLHDYHRDLYNHLEEHEIGPSLYAAPWFLTMFASQFPLGFVARVFDMIFLQGTEVIFKVALSLLGSHKPLILQHNLETIVDFIKSTLPNLGLVQMEKTINQVFEQLQAYEVEYHVLQE--------

3qyeA2

0.06

2.51

1.26

MapAlign

IILQIQMYQLSRLLHDYHRDLYNHLEEHEIGPSLYAAPWFLTMFASQFPLGFVARVFDMIFLQGTEVIFKVALSLLGSHKPLILQHENLTIVDFIKSTLPNLGLVQMEKTINQVFEM--DIAKQLQAYEVEY------

3qyeA

0.07

2.74

0.98

CEthreader

IILQIQMYQLSRLLHDYHRDLYNHLEEHEIGPSLYAAPWFLTMFASQFPLGFVARVFDMIFLQGTEVIFKVALSLLGSHKPLILQHNLETIVDFIKSTLPNLGLVQMEKTINQVFEM--DIAKQLQAYEVEYHVLQE-

3qyeA2

0.08

0.07

2.91

1.61

MUSTER

IILQIQMYQLSRLLHDYHRDLYNHLEEHEIGPSLYAAPWFLTMFASQFPLGFVARVFDMIFLQGTEVIFKVALSLLGSHKPLILQHNLETIVDFIKSTLPNLGLVQMEKTINQVFEIAKQLQAYEVE----HVLQE--

2g77A

0.13

0.12

4.04

2.16

HHsearch

PGILRQVKNLSQLVKRIDADLYNHFQNEHVEFIQFAFRWMNCLLMREFQMGTVIRMWDTYLSETSQFHVFVCAAFLIKWSDQLMEMDFQETITFLQNPPTKDWTETD---IEMLLSEAFIWQSLYKDAT---------

3qyeA2

0.07

0.06

2.46

1.84

FFAS-3D

-ILQIQMYQLSRLLHDYHRDLYNHLEEHEIGPSLYAAPWFLTMFASQFPLGFVARVFDMIFLQGTEVIFKVALSLLGSHKPLILQHNLETIVDFIKSTLPNLGLVQMEKTINQVAKQLQAYEVE--------------

3qyeA2

0.07

2.73

1.67

EigenThreader

IILQIQMYQLSRLLHDYHRDLYNHLEEHEIGPSLYAAPWFLTMFASQFPLGFVARVFDMIFLQGTEVIFKVALSLLGSHKPLILQHNLETIVDFIKSTLPNLGLVQMEKTINQVFEMIAKQLQAYEVEYHVLQE----

3hzjA

0.13

4.51

1.05

CNFpred

EDLHCKFYQLERLMQEQLPDLHSHFSDLNLEAHMYASQWFLTLFTAKFPLCMVFHIIDLLLCEGLNIIFHVALALLKTSKEDLLQADFEGALKFFRVQLPKRY--RAEENARRLMEQACNIKVPTKKLKKYEKEYQTM

6jl7A1

0.07

2.70

1.33

DEthreader

RDCGRPFHLFRLLIQYHEPELCSYLDTKKITPDSYALNWLGSLFACYCVTQAIWDGYLQQ-ADP-FFIYFL-LIILVNAKEVILTQDSEEVIKFLENTPSS-LNIDIEDLFSLAQYYCSKT---PASRDNHHFGSTL-

(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	0.805

(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	5hjnA	0.66	3.06	0.077	0.870	model1_5hjnA.pdb.gz
2	3qyeA	0.65	3.38	0.059	0.899	model1_3qyeA.pdb.gz
3	2g77A	0.64	3.20	0.128	0.891	model1_2g77A.pdb.gz
4	3hzjC	0.63	3.29	0.116	0.862	model1_3hzjC.pdb.gz
5	2qfzA	0.63	3.19	0.158	0.870	model1_2qfzA.pdb.gz
6	3qwlA	0.61	3.28	0.082	0.862	model1_3qwlA.pdb.gz
7	4p17A2	0.60	3.17	0.120	0.804	model1_4p17A2.pdb.gz
8	2qq8A	0.59	3.68	0.153	0.877	model1_2qq8A.pdb.gz
9	1hg4A	0.37	4.88	0.066	0.667	model1_1hg4A.pdb.gz
10	3o1lA	0.36	4.42	0.032	0.609	model1_3o1lA.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:0005096	0.96	GTPase activator activity
GO:0019899	0.93	enzyme binding
GO:0017137	0.92	Rab GTPase binding
GO:0097159	0.56	organic cyclic compound binding
GO:1901363	0.55	heterocyclic compound 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	1.00	biological regulation
GO:0050794	0.98	regulation of cellular process
GO:0033043	0.93	regulation of organelle organization
GO:0060627	0.92	regulation of vesicle-mediated transport
GO:0043087	0.92	regulation of GTPase activity
GO:0006810	0.90	transport
GO:0046907	0.89	intracellular transport
GO:0043085	0.89	positive regulation of catalytic activity
GO:0015031	0.89	protein transport
GO:0090630	0.88	activation of GTPase activity
GO:0031338	0.88	regulation of vesicle fusion
GO:0006886	0.88	intracellular protein transport

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	0.99	cell part
GO:0012505	0.92	endomembrane system
GO:0005622	0.87	intracellular
GO:0044424	0.68	intracellular 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	1ofdA	0.459	4.25	0.058	0.703	1.4.7.1	NA
2	0.060	2vg8A	0.475	4.91	0.085	0.855	2.4.1.218	NA
3	0.060	1y2mB	0.376	4.66	0.049	0.638	4.3.1.24	NA
4	0.060	3czoB	0.344	5.32	0.029	0.601	4.3.1.3	NA
5	0.060	3etdA	0.479	4.50	0.082	0.768	1.4.1.3	2

	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	2vasA	0.491	4.04	0.132	0.739	0.19	UUU	complex1.pdb.gz	38,66,67,68,69,70,71,72,76
2	0.01	1z2bC	0.465	4.93	0.031	0.841	0.31	VLB	complex2.pdb.gz	7,33,35,41
3	0.01	1jffA	0.494	4.87	0.039	0.855	0.11	GTP	complex3.pdb.gz	67,71,72
4	0.01	1z2bC	0.465	4.93	0.031	0.841	0.13	GTP	complex4.pdb.gz	4,5,6,10,65
5	0.01	3ryiA	0.460	5.13	0.031	0.848	0.12	GTP	complex5.pdb.gz	32,76,80,83
6	0.01	1okcA	0.481	4.94	0.049	0.855	0.27	CDL	complex6.pdb.gz	34,35,38,39,40,43
7	0.01	1n20B	0.380	5.24	0.042	0.732	0.16	3AG	complex7.pdb.gz	32,38,39,42,46
8	0.01	2c3eA	0.488	4.87	0.049	0.855	0.29	CDL	complex8.pdb.gz	40,65,66,67,69,72,76,77,118,120
9	0.01	2qveB	0.482	4.17	0.080	0.739	0.14	247	complex9.pdb.gz	28,31,32,39
10	0.01	1okcA	0.481	4.94	0.049	0.855	0.12	LDM	complex10.pdb.gz	34,40,41,68

	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.