D-I-TASSER Q2VWP7-D2

D-I-TASSER results for Q2VWP7-D2

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

Input Sequence in FASTA format

>Q2VWP7 (100 residues)
TLEDVPLRPPEISLTSRSPTDILISWLPIPAKYRRGQVVLYRLSFRLSTENSIQVLELPG
TTHEYLLEGLKPDSVYLVRITAATRVGLGESSVWTSHRTP

Predicted Secondary Structure

Sequence	20 40 60 80 100 \| \| \| \| \| TLEDVPLRPPEISLTSRSPTDILISWLPIPAKYRRGQVVLYRLSFRLSTENSIQVLELPGTTHEYLLEGLKPDSVYLVRITAATRVGLGESSVWTSHRTP
Prediction	CCCCCCCCCCCSSSSSCCCCSSSSSSSCCCCCCCCCSSSSSSSSSSSCCCCCSSSSSSCCCSSSSSSCCCCCCCSSSSSSSSSCCCCSCCCCCCSSSSCC
Confidence	9898898998249997479989999968898689954737999999889985199998599109998699999299999999928851999886897686
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 \| \| \| \| \| TLEDVPLRPPEISLTSRSPTDILISWLPIPAKYRRGQVVLYRLSFRLSTENSIQVLELPGTTHEYLLEGLKPDSVYLVRITAATRVGLGESSVWTSHRTP
Prediction	8666244644604045334410424754136745414434442443558674443340546434131565544344343323327444434244242448
	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

CCCCCCCCCCCSSSSSCCCCSSSSSSSCCCCCCCCCSSSSSSSSSSSCCCCCSSSSSSCCCSSSSSSCCCCCCCSSSSSSSSSCCCCSCCCCCCSSSSCC
TLEDVPLRPPEISLTSRSPTDILISWLPIPAKYRRGQVVLYRLSFRLSTENSIQVLELPGTTHEYLLEGLKPDSVYLVRITAATRVGLGESSVWTSHRTP

3f7pE

0.18

0.17

5.56

1.50

DEthreader

GHQEVPSEPGRLAFNVVSSTVTQLSWAEPA--ETNGEITAYEVCYGLVNIGPMKKVLVDNKNRMLLIENLRESQPYRYTVKARNGAGWGPER-EAIINLA

2jllA4

0.20

0.19

6.09

1.59

SPARKS-K

---DVPSSPYGVKIIELSQTTAKVSFNKPDS-HGGVPIHHYQVDVKEVASEIWKIVRSHGVQTMVVLNNLEPNTTYEIRVAAVNGKGQGDYSKIEIFQTL

1uenA

0.27

0.26

8.00

0.39

MapAlign

--EDLPVAPGNVRVNVVNSTLAEVHWDPVPLKSIRGHLQGYRIYYWKTRHIEKKILTFQGSKTHGMLPGLEPFSHYTLNVRVVNGKGEGPASPDRVFNTP

1uenA

0.23

7.21

0.26

CEthreader

GEDLPMVAPGNVRVNVVNSTLAEVHWDPVPLKSIRGHLQGYRIYYWKTQSIEKKILTFQGSKTHGMLPGLEPFSHYTLNVRVVNGKGEGPASPDRVFNTP

1x5hA

0.33

9.91

1.16

MUSTER

TLSDVPAAPQNLSLEVRNSKSIMIHWQPPAPATQNGQITGYKIRYRKASRKSDVTELVSGTQLSQLIEGLDRGTEYNFRVAALTINGTGPATDWLSAETF

4bk4A

0.17

5.57

0.89

HHsearch

TNQAAPSSIALVQAKEVTRYSVALAWLEPD--RPNGVILEYEVKYYEKDQNERSYRIVRTAARNTDIKGLNPLTSYVFHVRARTAAGYGDFSEPLEVTTN

6tpwA2

0.29

0.28

8.52

1.82

FFAS-3D

TQQGVPAQPADFQAEVESDTRIQLSWLLPPQERII----MYELVYWAAEDEDQQHKVTFDPTSSYTLEDLKPDTLYRFQLAARSDMGVGVFTPTIEARTA

2ed9A

0.33

9.90

0.43

EigenThreader

TLSDVPSAPPNVSLEVVNSRSIKVSWLPPPSGTQNGFITGYKIRHRKTTRRGEMETLE-PNNLWYLFTGLEKGSQYSFQVSAMTVNGTGPPSNWYTAETP

4n5uA

0.27

0.26

8.00

1.44

CNFpred

--QSTPSPPQKVMCVSMGSTTVRVSWVPPPADSRNGVITQYSVAYEAVDRGRHVVDGISREHSSWDLVGLEKWTEYRVWVRAHTDVGPGPESSPVLVRTD

1x5hA

0.27

8.29

1.50

DEthreader

LSDVPSAAPQNLSLEVRNSKSIMIHWQPPAPATQNGQITGYKIRYRKASRKDVTETLVSGTQLSQLIEGLDRGTEYNFRVAALTINGTGPATDWLSAETF

(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	0.9068

(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	1x5hA	0.91	1.48	0.270	0.990	model1_1x5hA.pdb.gz
2	6tpwA	0.89	1.39	0.278	0.970	model1_6tpwA.pdb.gz
3	2jllA	0.89	1.28	0.194	0.980	model1_2jllA.pdb.gz
4	1uenA	0.89	1.52	0.230	1.000	model1_1uenA.pdb.gz
5	3l5hA	0.88	1.25	0.206	0.970	model1_3l5hA.pdb.gz
6	1va9A	0.88	1.52	0.250	1.000	model1_1va9A.pdb.gz
7	3p4lA	0.88	1.81	0.245	0.980	model1_3p4lA.pdb.gz
8	4yfeA	0.88	1.71	0.237	0.970	model1_4yfeA.pdb.gz
9	5u8qA	0.88	1.54	0.177	0.960	model1_5u8qA.pdb.gz
10	4hljA	0.87	1.45	0.276	0.980	model1_4hljA.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:0004872	0.80	receptor activity
GO:0004888	0.76	transmembrane signaling receptor activity
GO:0003824	0.54	catalytic activity
GO:0005042	0.52	netrin 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:0044699	0.96	single-organism process
GO:0009987	0.96	cellular process
GO:0044763	0.93	single-organism cellular process
GO:0065007	0.91	biological regulation
GO:0050789	0.88	regulation of biological process
GO:0050794	0.87	regulation of cellular process
GO:0032502	0.86	developmental process
GO:0044767	0.84	single-organism developmental process
GO:0006928	0.83	movement of cell or subcellular component
GO:0048869	0.76	cellular developmental process
GO:0009653	0.73	anatomical structure morphogenesis
GO:0051239	0.72	regulation of multicellular organismal process
GO:0016477	0.71	cell migration
GO:0007411	0.71	axon guidance
GO:2000026	0.70	regulation of multicellular organismal development
GO:0051128	0.69	regulation of cellular component organization
GO:0016043	0.69	cellular component organization
GO:0045595	0.68	regulation of cell differentiation
GO:0050767	0.67	regulation of neurogenesis
GO:0001764	0.67	neuron migration
GO:0022603	0.66	regulation of anatomical structure morphogenesis
GO:0010975	0.66	regulation of neuron projection development
GO:0007165	0.65	signal transduction
GO:0010769	0.64	regulation of cell morphogenesis involved in differentiation
GO:0050770	0.63	regulation of axonogenesis
GO:0050773	0.62	regulation of dendrite development
GO:0048523	0.60	negative regulation of cellular process
GO:0032989	0.59	cellular component morphogenesis
GO:0030030	0.59	cell projection organization
GO:0007166	0.57	cell surface receptor signaling pathway
GO:0048812	0.56	neuron projection morphogenesis
GO:0010941	0.55	regulation of cell death
GO:0051241	0.54	negative regulation of multicellular organismal process
GO:0007409	0.54	axonogenesis
GO:0051093	0.53	negative regulation of developmental process
GO:0048856	0.53	anatomical structure development
GO:0008038	0.53	neuron recognition
GO:0061387	0.52	regulation of extent of cell growth
GO:0051179	0.52	localization
GO:0050768	0.52	negative regulation of neurogenesis
GO:0048638	0.52	regulation of developmental growth
GO:0008152	0.52	metabolic process
GO:1901214	0.51	regulation of neuron death
GO:0032501	0.51	multicellular organismal process
GO:0021952	0.51	central nervous system projection neuron axonogenesis
GO:0010977	0.51	negative regulation of neuron projection development
GO:0097190	0.50	apoptotic signaling pathway
GO:0048671	0.50	negative regulation of collateral sprouting
GO:0044238	0.50	primary metabolic process
GO:0043170	0.50	macromolecule metabolic process
GO:0033564	0.50	anterior/posterior axon guidance
GO:0033563	0.50	dorsal/ventral axon guidance

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	0.96	cell part
GO:0044425	0.68	membrane part
GO:0044459	0.66	plasma membrane part
GO:0097458	0.61	neuron part
GO:0031226	0.59	intrinsic component of plasma membrane
GO:0005887	0.58	integral component of plasma membrane
GO:0042995	0.57	cell projection
GO:0043005	0.55	neuron projection
GO:0030424	0.54	axon
GO:0043025	0.52	neuronal cell body
GO:0030425	0.50	dendrite

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	0.228	2dlhA	0.860	1.76	0.237	0.970	3.1.3.48	30,92
2	0.210	2dleA	0.709	2.41	0.118	0.880	3.1.3.48	18,26,70
3	0.161	1k85A	0.734	1.96	0.184	0.870	3.2.1.14	NA
4	0.073	2djmA	0.622	2.49	0.045	0.830	3.2.1.3	NA
5	0.067	2hvbB	0.660	2.80	0.043	0.880	1.15.1.2	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	0.04	2b5i6	0.820	2.09	0.163	0.980	0.74	III	complex1.pdb.gz	40,41,53,55,56,57,58,59,66,67,68,69,70
2	0.04	2ibg0	0.823	2.05	0.152	0.980	0.61	III	complex2.pdb.gz	38,56,79,83,90,91
3	0.04	1tdq0	0.812	1.95	0.170	0.940	0.40	III	complex3.pdb.gz	47,48,74,75,77

	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.