D-I-TASSER Q8TF65-D2

D-I-TASSER results for Q8TF65-D2

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

Input Sequence in FASTA format

>Q8TF65 (94 residues)
RATLRLRSKGPATVEEMPSETKAKAIEKIDDVLELYMGIRDIDLATTMFEAGKDKVNPDE
FAVALDETLGDFAFPDEFVFDVWGVIGDAKRRGL

Predicted Secondary Structure

Sequence	20 40 60 80 \| \| \| \| RATLRLRSKGPATVEEMPSETKAKAIEKIDDVLELYMGIRDIDLATTMFEAGKDKVNPDEFAVALDETLGDFAFPDEFVFDVWGVIGDAKRRGL
Prediction	CCCSSSCCCCCCSSSSCCCHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHCCCCCHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHCCC
Confidence	9716753799954675476789999999999999637976724789999997169999999999996565248982799999999989985479
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 \| \| \| \| RATLRLRSKGPATVEEMPSETKAKAIEKIDDVLELYMGIRDIDLATTMFEAGKDKVNPDEFAVALDETLGDFAFPDEFVFDVWGVIGDAKRRGL
Prediction	8622423572434245335724550153035205423214336203301410573741540152037415427134410220131034257668
	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

CCCSSSCCCCCCSSSSCCCHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHCCCCCHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHCCC
RATLRLRSKGPATVEEMPSETKAKAIEKIDDVLELYMGIRDIDLATTMFEAGKDKVNPDEFAVALDETLGDFAFPDEFVFDVWGVIGDAKRRGL

5v6bA1

0.70

0.60

16.94

1.17

DEthreader

GGRGT--------VEDLPSAFEEKAIEKVDDLLESYMGIRDTELAATMVELGKDKRNPDELAEALDERLGDFAFPDEFVFDVWGAIGD------

5v6bA1

0.76

0.71

20.18

1.24

SPARKS-K

RGTLRLRSRGPATVEDLPSAFEEKAIEKVDDLLESYMGIRDTELAATMVELGKDKRNPDELAEALDERLGDFAFPDEFVFDVWGAIGD------

5v6bA1

0.76

0.70

19.88

1.16

MapAlign

RGTLRLRSRGPATVEDLPSAFEEKAIEKVDDLLESYMGIRDTELAATMVELGKDKRNPDELAEALDERLGDFAFPDEFVFDVWGAIG-------

5v6bA1

0.76

0.71

20.18

1.34

CEthreader

RGTLRLRSRGPATVEDLPSAFEEKAIEKVDDLLESYMGIRDTELAATMVELGKDKRNPDELAEALDERLGDFAFPDEFVFDVWGAIGD------

5v6bA1

0.76

0.71

20.18

0.75

MUSTER

RGTLRLRSRGPATVEDLPSAFEEKAIEKVDDLLESYMGIRDTELAATMVELGKDKRNPDELAEALDERLGDFAFPDEFVFDVWGAIGD------

5v6bA1

0.76

0.71

20.18

2.25

HHsearch

RGTLRLRSRGPATVEDLPSAFEEKAIEKVDDLLESYMGIRDTELAATMVELGKDKRNPDELAEALDERLGDFAFPDEFVFDVWGAIGD------

5v6bA1

0.76

0.71

20.18

1.43

FFAS-3D

RGTLRLRSRGPATVEDLPSAFEEKAIEKVDDLLESYMGIRDTELAATMVELGKDKRNPDELAEALDERLGDFAFPDEFVFDVWGAIGD------

5v6bA

0.61

0.57

16.45

1.08

EigenThreader

GLTITDNGAGYAFIKRIKEGFEEKAIEKVDDLLESYMGIRDTELAATMVELGKDKRNPDELAEALDERLGDFAFPDEFVFDVWGAI------GD

5v6eA

0.74

0.57

16.29

0.94

CNFpred

---------------------EEKAIEKVDDLLESYMGIRDTELAATMVELGKDKRNPDELAEALDERLGDFAFPDEFVFDVWGAIGDAKVGRY

5v6bA

0.70

0.60

16.94

1.17

DEthreader

GGRGT--------VEDLPSAFEEKAIEKVDDLLESYMGIRDTELAATMVELGKDKRNPDELAEALDERLGDFAFPDEFVFDVWGAIGD------

(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	0.7613

(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	5v6bA1	0.92	0.54	0.761	0.936	model1_5v6bA1.pdb.gz
2	5fbyA	0.63	3.48	0.125	0.936	model1_5fbyA.pdb.gz
3	4r8zA	0.62	2.92	0.122	0.851	model1_4r8zA.pdb.gz
4	5u1sA	0.61	3.66	0.085	0.947	model1_5u1sA.pdb.gz
5	2ix8A	0.61	3.21	0.066	0.894	model1_2ix8A.pdb.gz
6	1u84A	0.60	2.45	0.120	0.798	model1_1u84A.pdb.gz
7	2pi4A	0.60	3.28	0.083	0.883	model1_2pi4A.pdb.gz
8	7a8pA1	0.60	3.78	0.043	0.936	model1_7a8pA1.pdb.gz
9	6yxqA	0.59	3.24	0.110	0.872	model1_6yxqA.pdb.gz
10	3hjeA	0.59	3.66	0.077	0.947	model1_3hjeA.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:0005102	0.30	receptor 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	0.96	single-organism process
GO:0065007	0.80	biological regulation
GO:0050789	0.80	regulation of biological process
GO:0050794	0.79	regulation of cellular process
GO:0009987	0.72	cellular process
GO:0007165	0.72	signal transduction
GO:0040011	0.66	locomotion
GO:0048522	0.60	positive regulation of cellular process
GO:0044763	0.60	single-organism cellular process
GO:0031323	0.59	regulation of cellular metabolic process
GO:0080090	0.58	regulation of primary metabolic process
GO:0060255	0.58	regulation of macromolecule metabolic process
GO:0048519	0.56	negative regulation of biological process
GO:0032268	0.56	regulation of cellular protein metabolic process
GO:0009966	0.56	regulation of signal transduction
GO:0048523	0.55	negative regulation of cellular process
GO:0009967	0.55	positive regulation of signal transduction
GO:0007186	0.55	G-protein coupled receptor signaling pathway
GO:0006810	0.55	transport
GO:0090287	0.54	regulation of cellular response to growth factor stimulus
GO:0065008	0.54	regulation of biological quality
GO:0051726	0.54	regulation of cell cycle
GO:0044765	0.54	single-organism transport
GO:0031324	0.54	negative regulation of cellular metabolic process
GO:0030162	0.54	regulation of proteolysis
GO:0016477	0.54	cell migration
GO:0008104	0.54	protein localization
GO:0048167	0.53	regulation of synaptic plasticity
GO:0043542	0.53	endothelial cell migration
GO:0032467	0.53	positive regulation of cytokinesis
GO:0032435	0.53	negative regulation of proteasomal ubiquitin-dependent protein catabolic process
GO:0031647	0.53	regulation of protein stability
GO:0030511	0.53	positive regulation of transforming growth factor beta receptor signaling pathway
GO:0014047	0.53	glutamate secretion
GO:0007268	0.53	chemical synaptic transmission
GO:0006605	0.53	protein targeting

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:0031982	1.00	vesicle
GO:0031988	0.91	membrane-bounded vesicle
GO:0044464	0.85	cell part
GO:0044421	0.77	extracellular region part
GO:0070062	0.75	extracellular exosome
GO:0044424	0.69	intracellular part
GO:0016020	0.68	membrane
GO:0044444	0.60	cytoplasmic part
GO:0043229	0.59	intracellular organelle
GO:0043231	0.58	intracellular membrane-bounded organelle
GO:0005829	0.52	cytosol
GO:0016023	0.51	cytoplasmic, membrane-bounded vesicle

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	3b8cA	0.547	3.81	0.059	0.883	3.6.3.6	NA
2	0.060	2jg6A	0.544	3.03	0.054	0.798	3.2.2.20	NA
3	0.060	1vlbA	0.577	3.77	0.054	0.947	1.2.99.7	NA
4	0.060	1dgjA	0.571	4.06	0.022	0.957	1.2.-.-	NA
5	0.060	1aroP	0.553	3.63	0.043	0.915	2.7.7.6	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	1czaN	0.586	3.02	0.122	0.840	0.30	ADP	complex1.pdb.gz	41,44,48,52
2	0.04	1dgkN	0.587	3.06	0.122	0.840	0.23	ADP	complex2.pdb.gz	47,48,51,69
3	0.03	2nztA	0.558	3.26	0.121	0.872	0.21	UUU	complex3.pdb.gz	50,51,52,62,65
4	0.03	1qhaA	0.546	3.17	0.144	0.862	0.25	ANP	complex4.pdb.gz	44,51,55
5	0.02	1qhaB	0.588	2.92	0.122	0.830	0.19	ANP	complex5.pdb.gz	45,46,49
6	0.01	1s0vA	0.601	3.69	0.076	0.904	0.26	APC	complex6.pdb.gz	43,47,48,51,52
7	0.01	1qlnA	0.597	3.55	0.065	0.894	0.12	QNA	complex7.pdb.gz	38,40,48,49,50
8	0.01	1s76D	0.418	3.90	0.047	0.692	0.21	APC	complex8.pdb.gz	30,48,52

	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.