D-I-TASSER Q6Q788-D2

D-I-TASSER results for Q6Q788-D2

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

Input Sequence in FASTA format

>Q6Q788 (92 residues)
DKGRVEQIHQQKMAREPATLKDSLEQDLNNMNKFLEKLRPLSGSEAPRLPQDPVGMRRQL
QEELEEVKARLQPYMAEAHELVGWNLEGLRQQ

Predicted Secondary Structure

Sequence	20 40 60 80 \| \| \| \| DKGRVEQIHQQKMAREPATLKDSLEQDLNNMNKFLEKLRPLSGSEAPRLPQDPVGMRRQLQEELEEVKARLQPYMAEAHELVGWNLEGLRQQ
Prediction	CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC
Confidence	81489999986899888999999999788999999997031244533345566999999999999999996258999999999999999829
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 \| \| \| \| DKGRVEQIHQQKMAREPATLKDSLEQDLNNMNKFLEKLRPLSGSEAPRLPQDPVGMRRQLQEELEEVKARLQPYMAEAHELVGWNLEGLRQQ
Prediction	86743551454614552550454146425414402541241356247424743751364146315514442442154136314641552478
	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 DeepPotential. 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

CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC
DKGRVEQIHQQKMAREPATLKDSLEQDLNNMNKFLEKLRPLSGSEAPRLPQDPVGMRRQLQEELEEVKARLQPYMAEAHELVGWNLEGLRQQ

4xa3A

0.11

3.93

1.50

DEthreader

QSRTEALQQLRVNYGSFVSEYNDLTKSLSKANSEVAQWRTKYETDAIQRTEELEEAKKKLAQRLQEAEEAVEAVNAKCSSLEKTKHRLQNEI

6cfeA

0.20

6.28

2.15

HHsearch

SEQVQEELLSSQVETKLNKMQRTMEELKAYKSELEEQLTPVAEETRARLSKELQAAQARLGADMEDVCGRLVQYRGEVQAMLGQSTEELRVR

6f1tX

0.11

3.93

1.50

DEthreader

QMHKELTDKLEHLEQEKHELRRRFENREGEWEGRVSELETDVKQLQDELERQQLHLREADREKTRAVQELSEQNQRLLDQLSRASEVERQLQ

6cfeA

0.16

5.40

0.95

SPARKS-K

SEQVQEELLSSQVETKNKLMQRTMEELKAYKSELEEQLTPVAEETRARLSKELQAAQARLGADMEDVCGRLVQYRGEVQQRLLEDADDLQKR

4wheA

0.12

4.23

0.68

MapAlign

DTLVEVRSTSARALAEKKQLTRRIEQASAREVEWQEKAELALLKEREDLARAALIEKQKLTDLIKSLEHEVTLVDDTLARMKKEIGELENKL

4wheA

0.12

4.23

0.39

CEthreader

DTLVEVRSTSARALAEKKQLTRRIEQASAREVEWQEKAELALLKEREDLARAALIEKQKLTDLIKSLEHEVTLVDDTLARMKKEIGELENKL

2a01A

0.25

7.75

0.79

MUSTER

GRDYVSQFEGSALGKQLNLLLDNWDSVTSTFSKLREQLGPVTQEFWDNLEKETEGLRQEMSKDLEEVKAKVQPYLDDFQKKWQEEMELYRQK

2kc3A

0.20

6.28

2.15

HHsearch

SEQVQEELLSSQVTQELRAMDETMKELKAYKSELEEQLTPVAEETRARLSKELQAAQARLGADMEDVCGRLVQYRGEVQAMLGQSTEELRVR

6cfeA

0.14

4.80

0.96

FFAS-3D

-EQVQEELLSSQVETKLNKMQRTMEELKAYKSELEEQLTPVAEETRARLSKELQAAQARLGADMEELRVRLATHLNKLRQRLLEDADDLQKR

2d4yA

0.05

2.47

0.47

EigenThreader

DAFITNQLRGAQNQSSGLTTRYEQMSKIDNLLADARQALIGKAEGLVNQFKTTDQYLRDQDKQVNIAIGSSVAQINNYAKQIANLNDQISRM

(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	0.6147

(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 DeepPotential, 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	6ykmA	0.85	1.62	0.076	1.000	model1_6ykmA.pdb.gz
2	6ysfE	0.84	1.56	0.065	1.000	model1_6ysfE.pdb.gz
3	4uosA	0.84	1.66	0.122	0.978	model1_4uosA.pdb.gz
4	6yslG	0.82	1.74	0.076	1.000	model1_6yslG.pdb.gz
5	4ke2A	0.80	1.78	0.100	0.978	model1_4ke2A.pdb.gz
6	5j0lA	0.80	1.57	0.082	0.924	model1_5j0lA.pdb.gz
7	4tqlA	0.79	1.96	0.098	1.000	model1_4tqlA.pdb.gz
8	3jacA	0.79	1.85	0.055	0.989	model1_3jacA.pdb.gz
9	6u1sA	0.79	2.07	0.054	1.000	model1_6u1sA.pdb.gz
10	6irdB	0.79	2.15	0.076	1.000	model1_6irdB.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:0060228	1.00	phosphatidylcholine-sterol O-acyltransferase activator activity
GO:0031210	1.00	phosphatidylcholine binding
GO:0017127	1.00	cholesterol transporter activity
GO:0015485	1.00	cholesterol 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:0044763	1.00	single-organism cellular process
GO:0044710	1.00	single-organism metabolic process
GO:0044238	1.00	primary metabolic process
GO:0044237	1.00	cellular metabolic process
GO:0043170	1.00	macromolecule metabolic process
GO:0065007	0.97	biological regulation
GO:0044281	0.97	small molecule metabolic process
GO:1901576	0.96	organic substance biosynthetic process
GO:1901360	0.96	organic cyclic compound metabolic process
GO:0080090	0.96	regulation of primary metabolic process
GO:0048522	0.96	positive regulation of cellular process
GO:0044765	0.96	single-organism transport
GO:0031323	0.96	regulation of cellular metabolic process
GO:0006807	0.96	nitrogen compound metabolic process
GO:0006629	0.96	lipid metabolic process
GO:0070328	0.95	triglyceride homeostasis
GO:0051006	0.95	positive regulation of lipoprotein lipase activity
GO:0046470	0.95	phosphatidylcholine metabolic process
GO:0045723	0.95	positive regulation of fatty acid biosynthetic process
GO:0043691	0.95	reverse cholesterol transport
GO:0042632	0.95	cholesterol homeostasis
GO:0042157	0.95	lipoprotein metabolic process
GO:0034380	0.95	high-density lipoprotein particle assembly
GO:0033700	0.95	phospholipid efflux
GO:0033344	0.95	cholesterol efflux
GO:0031102	0.95	neuron projection regeneration
GO:0030300	0.95	regulation of intestinal cholesterol absorption
GO:0019433	0.95	triglyceride catabolic process
GO:0010898	0.95	positive regulation of triglyceride catabolic process
GO:0010873	0.95	positive regulation of cholesterol esterification
GO:0006695	0.95	cholesterol biosynthetic process
GO:0034369	0.87	plasma lipoprotein particle remodeling
GO:0034372	0.85	very-low-density lipoprotein particle remodeling

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:0072562	1.00	blood microparticle
GO:0042627	1.00	chylomicron
GO:0034364	1.00	high-density lipoprotein particle
GO:0044464	0.65	cell part
GO:0044424	0.55	intracellular 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	0.127	2wieA	0.614	2.43	0.038	0.859	3.6.3.14	NA
2	0.067	1wt6B	0.504	1.69	0.158	0.565	2.7.11.1	NA
3	0.067	1joyA	0.528	2.37	0.078	0.696	2.7.13.3	NA
4	0.067	3e7kH	0.506	1.47	0.075	0.565	2.7.11.1	NA
5	0.066	1cxzB	0.526	2.92	0.151	0.750	2.7.11.13	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.