D-I-TASSER Q92738-D1

D-I-TASSER results for Q92738-D1

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

Input Sequence in FASTA format

>Q92738 (97 residues)
MNSDQDVALKLAQERAEIVAKYDRGREGAEIEPWEDADYLVYKVTDRFGFLHEEELPDHN
VAVERQKHLEIERTTKWLKMLKGWEKYKNTEKFHRRI

Predicted Secondary Structure

Sequence	20 40 60 80 \| \| \| \| MNSDQDVALKLAQERAEIVAKYDRGREGAEIEPWEDADYLVYKVTDRFGFLHEEELPDHNVAVERQKHLEIERTTKWLKMLKGWEKYKNTEKFHRRI
Prediction	CCHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCSSCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHCC
Confidence	9525647888998999999999805666878889999854233456431223777999866999999999999999999996178888706666349
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 \| \| \| \| MNSDQDVALKLAQERAEIVAKYDRGREGAEIEPWEDADYLVYKVTDRFGFLHEEELPDHNVAVERQKHLEIERTTKWLKMLKGWEKYKNTEKFHRRI
Prediction	8646642643445425501530453474553554756616224334322133574246664554444532363452124015617645447304727
	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                  60                  80

                   |                   |                   |                   |

SS
Seq

CCHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCSSCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHCC
MNSDQDVALKLAQERAEIVAKYDRGREGAEIEPWEDADYLVYKVTDRFGFLHEEELPDHNVAVERQKHLEIERTTKWLKMLKGWEKYKNTEKFHRRI

7d6aA

0.09

3.51

0.49

CEthreader

GAWLNAEIQSDFGHFADVCFGAFGDRVKYVAVRHGYMLGTYPPSRCSPPFGHCARGGDSHAEPYVAAHNVILSHATAIEIYKRKYQSKQRGMIGMVL

3qweA

0.05

2.35

0.53

EigenThreader

LQYIYTLFLEHDLSLGTLAMETVAQQKRDYYQPLAAKRTEIEKWRK----EFKEQWMKEQKRMNEAVQALRRAQLQYVQRSEDLRAREAQAKAQEAE

4p17A

0.19

0.09

3.00

0.53

FFAS-3D

-------------------------------------------VHDLYGFPIQED------ERRSCDVNAEREVPLWQHYIEKDKLPSNETKLKEMI

5cwiA1

0.11

0.10

3.75

0.79

SPARKS-K

--DIEKLCKKAESEAREARSKAEELRQRHPDSQAARDAQSQAEEAVKLACELAQEHPNAD-IAKLCIKAASEAAEAASKAAELAQRHPDSQAARDAI

5luzA

0.08

0.07

2.85

0.46

CNFpred

KTRTEELIVQTKQVYDAVGMLGIEEVTENCLQALADVEVKYIVERTMLDFPQHVS----DKEVRAASTEADKRLSRFDIEMS------MRGDIFERI

6j72A

0.04

2.03

1.00

DEthreader

PAVKLSEVLSRQNDRIRDQIVDEIRSAAEHLLERRKQEAQDAQTAL--------QQLSDGIADLTADVDHDLRHRFRIIAAHTEKVIDGMLVRNEAA

5t88A

0.08

3.23

0.58

MapAlign

NKRFREFIGELSDKLFPEVWEQFDKDEERVLLRYTSFTIPYRLYEFKDDLRLIEERRAGMRENKQNVFDDFIAVLEKLKKVAAWGRSNGGLLVSATL

4lu2A

0.11

0.10

3.70

0.62

MUSTER

-EFSEDCENIFHDNAYLLKLDCEAG----RVDPVEYDDISDEEI---YEITVDVGVSSEDQEKVAKIIRECIAQTKFSEIYDCYMKKKICNYYPENM

4p17A2

0.19

0.09

3.00

1.79

HHsearch

-------------------------------------------VHDLYGFPIQED------ERRSCDVNAEREVPLWQHYIEKDKLPSNETKLKEMI

5chsA

0.10

3.78

0.48

CEthreader

LILNAVSEVELLNLARTFKGKVRRSSHGTNICRIRVPSLGPTFISEGWAYFKKLDILMDRNFLLMVKDVIIGRMQTVLSMVCRIDNLFSEQDIFSLL

(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	0.3464

(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	6xssA	0.68	2.58	0.163	0.887	model1_6xssA.pdb.gz
2	5cwpA2	0.63	3.13	0.138	0.897	model1_5cwpA2.pdb.gz
3	6jlcA	0.61	3.15	0.071	0.866	model1_6jlcA.pdb.gz
4	7crzA	0.61	2.78	0.012	0.845	model1_7crzA.pdb.gz
5	5h6iA1	0.61	3.00	0.084	0.856	model1_5h6iA1.pdb.gz
6	3nz4A	0.60	3.32	0.071	0.866	model1_3nz4A.pdb.gz
7	3op0A1	0.60	3.47	0.034	0.887	model1_3op0A1.pdb.gz
8	1fbvA1	0.59	3.19	0.092	0.866	model1_1fbvA1.pdb.gz
9	2nyfA2	0.58	3.73	0.082	0.866	model1_2nyfA2.pdb.gz
10	5cwoA1	0.53	3.36	0.118	0.856	model1_5cwoA1.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	0.99	GTPase activator activity
GO:0017137	0.95	Rab GTPase 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:0043087	0.98	regulation of GTPase activity
GO:0060627	0.95	regulation of vesicle-mediated transport
GO:0033043	0.95	regulation of organelle organization
GO:0006810	0.95	transport
GO:0090630	0.94	activation of GTPase activity
GO:0031338	0.94	regulation of vesicle fusion
GO:0006886	0.94	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	0.95	endomembrane system
GO:0005622	0.80	intracellular
GO:0044424	0.70	intracellular part
GO:0044444	0.51	cytoplasmic 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	1dcnB	0.521	3.56	0.047	0.783	4.3.2.1	89
2	0.060	1ivhA	0.537	3.68	0.034	0.804	1.3.99.10	17
3	0.060	1b8fA	0.583	3.54	0.072	0.876	4.3.1.3	NA
4	0.060	2ix6A	0.528	3.22	0.048	0.773	1.3.3.6	NA
5	0.060	2z8yP	0.547	3.18	0.047	0.783	2.3.1.169	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	0.01	1occA	0.561	3.63	0.093	0.876	0.16	HEA	complex1.pdb.gz	15,19,22,23,45
2	0.01	3buwB	0.589	3.45	0.091	0.887	0.12	III	complex2.pdb.gz	45,50,70
3	0.01	3ag4N	0.559	3.57	0.082	0.866	0.25	CDL	complex3.pdb.gz	72,76,79,83
4	0.01	3o0rB	0.584	3.15	0.081	0.887	0.14	HEM	complex4.pdb.gz	11,15,16,18,22
5	0.01	3ob2B	0.551	3.26	0.101	0.814	0.10	III	complex5.pdb.gz	77,80,82
6	0.01	3o0rB	0.584	3.15	0.081	0.887	0.16	HEM	complex6.pdb.gz	12,16,17,19,20
7	0.01	2eijN	0.563	3.56	0.082	0.866	0.14	HEA	complex7.pdb.gz	18,21,22,25,26
8	0.01	3ag1A	0.557	3.32	0.060	0.866	0.26	CDL	complex8.pdb.gz	26,49,77
9	0.01	2zxwA	0.539	3.80	0.052	0.856	0.17	UUU	complex9.pdb.gz	14,21,22,25,91,94,95

	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.