D-I-TASSER A4D0T7-D1

D-I-TASSER results for A4D0T7-D1

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

Input Sequence in FASTA format

>A4D0T7 (59 residues)
MTSVSTQLSLVLMSLLLVLPVVEAVEAGDAIALLLGVVLSITGICACLGVYARKRNGQM

Predicted Secondary Structure

Sequence	20 40 \| \| MTSVSTQLSLVLMSLLLVLPVVEAVEAGDAIALLLGVVLSITGICACLGVYARKRNGQM
Prediction	CCHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCC
Confidence	93388999999999999863231102210899998678888878899999999865899
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 \| \| MTSVSTQLSLVLMSLLLVLPVVEAVEAGDAIALLLGVVLSITGICACLGVYARKRNGQM
Prediction	75424331313333333313324325434110233233233333121212234456478
	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

CCHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCC
MTSVSTQLSLVLMSLLLVLPVVEAVEAGDAIALLLGVVLSITGICACLGVYARKRNGQM

7jg5b

0.08

3.29

1.50

DEthreader

QVAAAQADYEKEMAEARAQASALRDEARAAGRSVVDEKRAQASGEVAQTLTQADQQAQG

3dl8C

0.11

0.07

2.42

1.01

SPARKS-K

---KATISVIIFSLAIGVYLWILDLTFTKIISFILSLR---------------------

6gmhQ

0.07

2.83

1.50

DEthreader

VARARKQDEEERELRAKQEQEKELLRQKLLKEQEEKRLREKEEQKKLLEQRAQYVEKTI

1mztA

0.05

0.03

1.58

0.97

SPARKS-K

-------AKAAFDSLQASATEYIGYAWAMVVVIVGATIGIKLFKKF-------------

3v5sA1

0.07

2.83

0.82

MapAlign

GVGYFLLGLILLYYGSDWFVLGSERFSLVLLIIGLIGVLVGAELFVDGAKKIALALDIS

3rkoL1

0.05

2.37

0.43

CEthreader

ADNLLLMYLGWEGVGLCSYLLIGPKNGAAAMKAFVVTRVGDVFLAFALFILYNELGTLN

1h2sB

0.21

0.20

6.47

0.84

MUSTER

-GAVFIFVGALTVLFGAIAEVTAAAATGDAAAVQEAAVSAILGLIILLGINLGLVAATL

6v3fA

0.15

5.12

0.58

HHsearch

LLCSLSEAICFFLGALTPMPAVRTFALTSGLAIILDFLLQMTAFVALLSLDSKRQEASR

6m49B

0.14

4.63

0.52

FFAS-3D

--NMATELGIILIGYFTLVPAIQEFCLFAVVGLVSDFFLQMLFFTTVLSIDIRRMELAR

7lumH

0.07

2.83

0.42

EigenThreader

VRKTDNNRIARACILSEVERNLQDAMQVCRNVLLDPYRAVAQALEVIPRTLIQNCGAST

(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	0.5851

(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	1qu7A	0.78	2.12	0.034	1.000	model1_1qu7A.pdb.gz
2	6ei3A2	0.77	2.12	0.000	0.966	model1_6ei3A2.pdb.gz
3	6l35A1	0.77	2.30	0.034	0.966	model1_6l35A1.pdb.gz
4	5cwmA	0.77	1.98	0.069	0.949	model1_5cwmA.pdb.gz
5	3x29A	0.76	2.22	0.052	0.983	model1_3x29A.pdb.gz
6	3g67A	0.75	2.19	0.051	1.000	model1_3g67A.pdb.gz
7	5cwqA1	0.69	2.32	0.068	0.966	model1_5cwqA1.pdb.gz
8	2ah6B	0.68	2.14	0.088	0.932	model1_2ah6B.pdb.gz
9	4uvkA	0.64	2.73	0.153	1.000	model1_4uvkA.pdb.gz
10	5cwnA2	0.61	2.50	0.017	0.949	model1_5cwnA2.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:0099600	0.49	transmembrane receptor activity
GO:0043169	0.49	cation binding
GO:0038023	0.49	signaling receptor activity
GO:0019901	0.49	protein kinase 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:1901700	0.49	response to oxygen-containing compound
GO:0051674	0.49	localization of cell
GO:0042330	0.49	taxis
GO:0010243	0.49	response to organonitrogen compound
GO:0006928	0.49	movement of cell or subcellular component
GO:0001101	0.49	response to acid chemical
GO:0007165	0.43	signal transduction
GO:0044800	0.35	multi-organism membrane fusion
GO:0044650	0.35	adhesion of symbiont to host cell
GO:0030260	0.35	entry into host cell
GO:0019058	0.35	viral life cycle

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:0016020	0.89	membrane
GO:0044464	0.83	cell part
GO:0043229	0.72	intracellular organelle
GO:0005886	0.72	plasma membrane
GO:0044444	0.67	cytoplasmic part
GO:0044425	0.67	membrane part
GO:0043231	0.67	intracellular membrane-bounded organelle
GO:0044446	0.56	intracellular organelle part
GO:0005773	0.56	vacuole
GO:0031982	0.50	vesicle
GO:0005768	0.50	endosome
GO:0005737	0.50	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	0.182	1fyjA	0.487	2.52	0.093	0.763	6.1.1.15 6.1.1.17	38,46
2	0.168	1urfA	0.645	2.45	0.035	0.966	2.7.11.13	7,12,44
3	0.155	1joyA	0.583	2.03	0.122	0.831	2.7.13.3	11,15,19
4	0.148	2jwaA	0.479	2.46	0.073	0.593	2.7.10.1	44
5	0.133	2k9yA	0.452	1.37	0.122	0.525	2.7.10.1	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	0.08	3p4wD	0.721	2.46	0.119	0.983	0.59	DSF	complex1.pdb.gz	4,44,47,48
2	0.05	2o01B	0.671	2.15	0.070	0.966	0.55	PQN	complex2.pdb.gz	6,7,10,11,44
3	0.04	1nkd0	0.612	2.19	0.184	0.831	1.01	III	complex3.pdb.gz	6,7,10,11,13,14,17,21,24,33,36,37,40,43,44,47,48
4	0.03	2g380	0.663	2.59	0.140	0.966	0.84	III	complex4.pdb.gz	3,7,10,14,18,22,24,25,33,36,39,40,43,44,47,51

	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.