D-I-TASSER Q6IAA8-D1

D-I-TASSER results for Q6IAA8-D1

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

Input Sequence in FASTA format

>Q6IAA8 (161 residues)
MGCCYSSENEDSDQDREERKLLLDPSSPPTKALNGAEPNYHSLPSARTDEQALLSSILAK
TASNIIDVSAADSQGMEQHEYMDRARQYSTRLAVLSSSLTHWKKLPPLPSLTSQPHQVLA
SEPIPFSDLQQVSRIAAYAYSALSQIRVDAKEELVVQFGIP

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 \| \| \| \| \| \| \| \| MGCCYSSENEDSDQDREERKLLLDPSSPPTKALNGAEPNYHSLPSARTDEQALLSSILAKTASNIIDVSAADSQGMEQHEYMDRARQYSTRLAVLSSSLTHWKKLPPLPSLTSQPHQVLASEPIPFSDLQQVSRIAAYAYSALSQIRVDAKEELVVQFGIP
Prediction	CCCSCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCSSSCCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCSSSSCCCC
Confidence	98501578887889840113478998887666678899888889985128999999999999740110114788776066889999999999986257887544565567899811332289989999999999999999999857644455557731699
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 \| \| \| \| \| \| \| \| MGCCYSSENEDSDQDREERKLLLDPSSPPTKALNGAEPNYHSLPSARTDEQALLSSILAKTASNIIDVSAADSQGMEQHEYMDRARQYSTRLAVLSSSLTHWKKLPPLPSLTSQPHQVLASEPIPFSDLQQVSRIAAYAYSALSQIRVDAKEELVVQFGIP
Prediction	70001115666675567334413547545454464455644543556644452045105412431020112345615444035215413530442446154255244135546414421345213472252045005403510550415445402231538
	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                 100                 120                 140                 160

                   |                   |                   |                   |                   |                   |                   |                   |

SS
Seq

CCCSCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCSSSCCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCSSSSCCCC
MGCCYSSENEDSDQDREERKLLLDPSSPPTKALNGAEPNYHSLPSARTDEQALLSSILAKTASNIIDVSAADSQGMEQHEYMDRARQYSTRLAVLSSSLTHWKKLPPLPSLTSQPHQVLASEPIPFSDLQQVSRIAAYAYSALSQIRVDAKEELVVQFGIP

6ehrE

1.00

0.71

19.83

1.65

FFAS-3D

----------------------------------------------RTDEQALLSSILAKTASNIIDVSAADSQGMEQHEYMDRARQYSTRLAVLSSSLTHWKKLPPLPSLTSQPHQVLASEPIPFSDLQQVSRIAAYAYSALSQIRVDAKEELVVQFGI-

6ehrE

1.00

0.71

20.00

1.52

MUSTER

---------------------------------------------ARTDEQALLSSILAKTASNIIDVSAADSQGMEQHEYMDRARQYSTRLAVLSSSLTHWKKLPPLPSLTSQPHQVLASEPIPFSDLQQVSRIAAYAYSALSQIRVDAKEELVVQFGI-

6ehrE

1.00

0.71

20.00

4.49

HHsearch

---------------------------------------------ARTDEQALLSSILAKTASNIIDVSAADSQGMEQHEYMDRARQYSTRLAVLSSSLTHWKKLPPLPSLTSQPHQVLASEPIPFSDLQQVSRIAAYAYSALSQIRVDAKEELVVQFGI-

1vt4I

0.02

1.67

0.51

CEthreader

GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG

5aj3d

0.07

0.06

2.56

0.62

EigenThreader

YRQYRQTVRALRLEFMSEVRKKLHEARAGVQAERKAQEDAAEHRELMAWNQAENQRLHELRLARLRQEALEQERRQAEEAVLQAREAQAWAQLKEQEVLQLQEEAKTFITRENLEARVEEALDSPK-------------------SYNWAITREGLVVRPQ

6jwpC

0.19

0.11

3.42

0.64

FFAS-3D

--------------------------------------------QKLLAREQELRDIVANTNDKLIDISMINNSGIVIQGTDLQEAL------------------DKRNTFTLLTSPDSAKI-----SKEQLKKLHSNILNEISQSQVNKPGPLTVPF---

6ehrE

1.00

0.71

20.00

0.77

SPARKS-K

---------------------------------------------ARTDEQALLSSILAKTASNIIDVSAADSQGMEQHEYMDRARQYSTRLAVLSSSLTHWKKLPPLPSLTSQPHQVLASEPIPFSDLQQVSRIAAYAYSALSQIRVDAKEELVVQFGI-

4p9tA

0.12

0.06

1.99

0.49

CNFpred

----------------------------------------------------VLAASVEQATQNFLEKGEQIASQDLKEELVAAVEDVRKQGETMR-----------------IASSEFADDPCSSVKRGTMVRAARALLSAVTRLL--------------

6yvuA

0.10

0.08

2.99

0.83

DEthreader

QKAELNSLIKKSITKQMS------------E-QESEERKYLFQNLELETEQLSSELDSNKTLLHLKISLKLENSDLEGKIRGVEDDLVTVQTELNEEKKRLMDIDELNETLIKKKQDEKKS-EL---KLVHDLNKYKSNTNNMEI---DTY----------

5mu1A

0.07

3.01

0.79

MapAlign

DIFISEKHEKQIHLSKHWVERLRAGGDVPTVFFDGFPIPREDNWLRVMNHRLMQDLQALQQAGYFGMLLTVVADLDDIEGQELVYYALRFRKSNFLASSNMKAGDNFVILNGRVLGPITSADDFKKEDFEVFLQAEVAVLKVLSVQLVLETENNPHFADTI

(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	0.4188

(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	2pfmA	0.60	3.85	0.056	0.851	model1_2pfmA.pdb.gz
2	1c3cA	0.59	3.91	0.070	0.851	model1_1c3cA.pdb.gz
3	3c8tA1	0.59	3.98	0.070	0.857	model1_3c8tA1.pdb.gz
4	4eeiA	0.59	3.93	0.084	0.857	model1_4eeiA.pdb.gz
5	4a01A	0.58	4.21	0.079	0.857	model1_4a01A.pdb.gz
6	1yfmA	0.56	4.66	0.086	0.857	model1_1yfmA.pdb.gz
7	1yfeA	0.56	4.42	0.053	0.832	model1_1yfeA.pdb.gz
8	1vdkA	0.56	4.58	0.077	0.857	model1_1vdkA.pdb.gz
9	2j91B	0.55	4.64	0.045	0.876	model1_2j91B.pdb.gz
10	2e9fB	0.53	4.10	0.067	0.776	model1_2e9fB.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:0032947	1.00	protein complex scaffold
GO:0005085	1.00	guanyl-nucleotide exchange factor activity
GO:1901363	0.53	heterocyclic compound binding
GO:0097159	0.53	organic cyclic compound 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:0009987	0.98	cellular process
GO:0071230	0.97	cellular response to amino acid stimulus
GO:0065007	0.96	biological regulation
GO:0051179	0.96	localization
GO:0050794	0.95	regulation of cellular process
GO:0060255	0.93	regulation of macromolecule metabolic process
GO:0048518	0.93	positive regulation of biological process
GO:0044763	0.93	single-organism cellular process
GO:0060620	0.92	regulation of cholesterol import
GO:0043410	0.92	positive regulation of MAPK cascade
GO:0042632	0.92	cholesterol homeostasis
GO:0034613	0.92	cellular protein localization
GO:0032439	0.92	endosome localization
GO:0032418	0.92	lysosome localization
GO:0032008	0.92	positive regulation of TOR signaling
GO:0016049	0.92	cell growth
GO:0010874	0.92	regulation of cholesterol efflux
GO:0010872	0.92	regulation of cholesterol esterification
GO:0007040	0.92	lysosome organization
GO:0007032	0.92	endosome organization
GO:0001919	0.92	regulation of receptor recycling

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:0044444	1.00	cytoplasmic part
GO:0043231	1.00	intracellular membrane-bounded organelle
GO:0016020	1.00	membrane
GO:0044446	0.85	intracellular organelle part
GO:0098588	0.82	bounding membrane of organelle
GO:0044437	0.82	vacuolar part
GO:0044425	0.82	membrane part
GO:0032991	0.82	macromolecular complex
GO:0005773	0.82	vacuole
GO:0098796	0.81	membrane protein complex
GO:0044440	0.81	endosomal part
GO:0005774	0.81	vacuolar membrane
GO:0005764	0.81	lysosome
GO:0071986	0.80	Ragulator complex
GO:0045121	0.80	membrane raft
GO:0031902	0.80	late endosome membrane
GO:0005886	0.51	plasma membrane

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	1t9gC	0.514	4.76	0.069	0.826	1.3.99.3	61
2	0.060	2pfmA	0.599	3.85	0.056	0.851	4.3.2.2	NA
3	0.060	1vdkA	0.557	4.58	0.077	0.857	4.2.1.2	NA
4	0.060	3no9A	0.550	4.71	0.066	0.845	4.2.1.2	NA
5	0.060	1yfmA	0.563	4.66	0.086	0.857	4.2.1.2	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:

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.