D-I-TASSER Q2V2M9-D7

D-I-TASSER results for Q2V2M9-D7

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

Input Sequence in FASTA format

>Q2V2M9 (54 residues)
IVKSATQVPSQRVVPRERKRSRANRKSLRRTLKSGLTPEEARALGLVGTSELQL

Predicted Secondary Structure

Sequence	20 40 \| \| IVKSATQVPSQRVVPRERKRSRANRKSLRRTLKSGLTPEEARALGLVGTSELQL
Prediction	CCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHCCCCCCCCCC
Confidence	963234699978881687676663799999998169999999855778998889
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 \| \| IVKSATQVPSQRVVPRERKRSRANRKSLRRTLKSGLTPEEARALGLVGTSELQL
Prediction	734423634664444564545555353034216552467334223236467367
	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

                   |                   |

SS
Seq

CCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHCCCCCCCCCC
IVKSATQVPSQRVVPRERKRSRANRKSLRRTLKSGLTPEEARALGLVGTSELQL

5owvC

0.08

0.07

2.93

1.00

DEthreader

MH-KNELACNASEFLFKLFKSILELDLFFEKLNLKANVYEFETLLIPIL-TI--

2pf4E

0.12

0.11

3.94

1.05

MapAlign

---AIYCKQWPECVKKMSTNCICLLCLLRMKHEDCYCFDCFRMWFGLDLCEGTL

5zc3B

0.11

3.98

0.46

CEthreader

VTLSSLEAAKHVPSTKRIA-SYLQGQQNQHWLADGKSTDDIFKLLKLNTPSPEN

6hxpA

0.06

2.50

0.43

EigenThreader

PPSAIAARSVASGGNSLNVGVAAGVLAMDIARVLFYGEHCKFAEDVAEEIGRQK

5y81C

0.18

0.15

4.81

0.29

FFAS-3D

-ISPLGVNTESIQRGHRRLRWASMFEAIRKCMKKRETPAEMSLLK---------

4ewcA1

0.15

5.00

0.94

SPARKS-K

VVRRSTATSGIKISREDRQKAVYVDKKIRKFLEEEVAAAIERSVEFDNFSKEAA

3h20A

0.15

0.09

3.13

0.41

CNFpred

--------------------SKCDFIAAQKLASRGRSAEEIGKAMAEASPALAE

3ibjA

0.09

3.48

1.00

DEthreader

RRK-ILCYTTVLTLAQEKKCECQALLQVAKNLFTHVLLQEIITEARNLFELATA

6gykA3

0.04

2.00

0.76

MapAlign

VLDVTKEAQANLLTAKHGMTLRESFEDNVVRFLNEARDKAGRLAIAQMSACVGQ

4l9uA

0.19

0.17

5.37

0.74

MUSTER

-------LPTYQELEQEINTLKADNDALKIQLKYAQKKIESLQLEKSNHVLAQM

(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	0.4834

(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	1ksdA	0.66	2.46	0.056	1.000	model1_1ksdA.pdb.gz
2	7ay1A	0.65	2.51	0.132	0.982	model1_7ay1A.pdb.gz
3	4e6hA4	0.65	2.74	0.115	0.926	model1_4e6hA4.pdb.gz
4	2ooeA	0.61	2.82	0.132	0.907	model1_2ooeA.pdb.gz
5	2g0dA1	0.58	2.66	0.111	1.000	model1_2g0dA1.pdb.gz
6	2fji1	0.56	2.48	0.056	0.778	model1_2fji1.pdb.gz
7	2uy1A2	0.56	2.12	0.140	0.796	model1_2uy1A2.pdb.gz
8	2vk9A1	0.52	2.99	0.058	0.852	model1_2vk9A1.pdb.gz
9	1ga2B1	0.52	3.10	0.056	0.963	model1_1ga2B1.pdb.gz
10	2yikA	0.50	3.69	0.038	0.963	model1_2yikA.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:0008092	0.73	cytoskeletal protein binding
GO:0003779	0.72	actin 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	0.90	single-organism process
GO:0009987	0.90	cellular process
GO:0065007	0.89	biological regulation
GO:0044763	0.89	single-organism cellular process
GO:0050789	0.88	regulation of biological process
GO:0050794	0.87	regulation of cellular process
GO:0051128	0.79	regulation of cellular component organization
GO:0044087	0.78	regulation of cellular component biogenesis
GO:0032956	0.78	regulation of actin cytoskeleton organization
GO:0032502	0.74	developmental process
GO:0065008	0.73	regulation of biological quality
GO:0044767	0.73	single-organism developmental process
GO:0048518	0.69	positive regulation of biological process
GO:0048522	0.68	positive regulation of cellular process
GO:0051130	0.64	positive regulation of cellular component organization
GO:0044089	0.64	positive regulation of cellular component biogenesis
GO:0051496	0.63	positive regulation of stress fiber assembly
GO:0048869	0.59	cellular developmental process
GO:0032879	0.58	regulation of localization
GO:0009653	0.58	anatomical structure morphogenesis
GO:0050793	0.57	regulation of developmental process
GO:0045785	0.57	positive regulation of cell adhesion
GO:0032501	0.57	multicellular organismal process
GO:1900026	0.56	positive regulation of substrate adhesion-dependent cell spreading
GO:0060439	0.56	trachea morphogenesis
GO:0046716	0.56	muscle cell cellular homeostasis
GO:0044319	0.56	wound healing, spreading of cells
GO:0035070	0.56	salivary gland histolysis
GO:0030335	0.56	positive regulation of cell migration
GO:0019233	0.56	sensory perception of pain
GO:0010623	0.56	programmed cell death involved in cell development
GO:0007476	0.56	imaginal disc-derived wing morphogenesis
GO:0003012	0.56	muscle system 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	0.97	cell part
GO:0044424	0.94	intracellular part
GO:0044444	0.86	cytoplasmic part
GO:0043226	0.66	organelle
GO:0043229	0.65	intracellular organelle
GO:0043227	0.63	membrane-bounded organelle
GO:0043231	0.62	intracellular membrane-bounded organelle
GO:0005737	0.61	cytoplasm
GO:0005634	0.60	nucleus
GO:0048471	0.52	perinuclear region of cytoplasm

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	1zl9A	0.581	2.74	0.113	0.982	2.5.1.18	NA
2	0.060	1ho8A	0.578	2.49	0.019	0.963	3.6.3.14	NA
3	0.060	3g4dA	0.567	2.45	0.075	0.889	4.2.3.13	NA
4	0.060	2dqmA	0.569	2.55	0.077	0.963	3.4.11.2	NA
5	0.060	2ashD	0.571	2.63	0.109	0.833	2.4.2.29	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:

No Binding sites was predicted

Click to view	Rank	Cscore^LB	PDB Hit	TM-score	RMSD^a	IDEN^a	Cov.	BS-score	Lig. Name	Download Complex	Predicted binding site residues

	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.