D-I-TASSER Q9NV64-D3

D-I-TASSER results for Q9NV64-D3

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

Input Sequence in FASTA format

>Q9NV64 (61 residues)
VPLCCFHQDSRAHLLLTDYNYVVQHEAVEESASTVGGLAKSKDFLSLLLESLKEQFNNAT
P

Predicted Secondary Structure

Sequence	20 40 60 \| \| \| VPLCCFHQDSRAHLLLTDYNYVVQHEAVEESASTVGGLAKSKDFLSLLLESLKEQFNNATP
Prediction	CCSSSSCCCCCCCCCCCCCCCCCCCHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCC
Confidence	9733232588877786667973550555422667666557356999999999999732799
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 \| \| \| VPLCCFHQDSRAHLLLTDYNYVVQHEAVEESASTVGGLAKSKDFLSLLLESLKEQFNNATP
Prediction	6321012454554433442523354633644554434234343103102530474257658
	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

                   |                   |                   |

SS
Seq

CCSSSSCCCCCCCCCCCCCCCCCCCHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCC
VPLCCFHQDSRAHLLLTDYNYVVQHEAVEESASTVGGLAKSKDFLSLLLESLKEQFNNATP

3hm8A

0.05

2.33

1.17

DEthreader

AVLLSTFDASVYLGFKFLSEIESLAQVRALTSDALMVLEVCQAVSQRAAQLCGAGVAAVVK

3jacA

0.03

1.89

1.08

MapAlign

GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG

3jacA

0.03

1.89

0.74

CEthreader

GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG

6wp7A2

0.10

3.66

0.48

EigenThreader

TEHTQSLFEEARAKLAKLFVGAFTGVQVLSRITGRADLAERVADLYRHLRLDRGSRVYEAA

6zywM

0.10

0.08

3.05

0.31

FFAS-3D

--------NHEPEVKATDMEEDMIKRVKEIAINAVKEYKQEKQIAHYIKYEFDKIDGYG--

5h5yA2

0.14

0.10

3.34

0.69

SPARKS-K

------------------RKLSDIYHDIICEQRLRTEDKRDEYLLNLLEKELRE-ISKAQD

1tf2A

0.04

0.03

1.69

0.36

CNFpred

-----------LELIMDRIITKYNEKEEQFGKEQMRE-FEKVIVLRAVDSKWMDHIDAMDQ

5b1qA

0.02

1.41

1.17

DEthreader

NYKNKHMITMK-LHENGLPK-FIKRLIQTTVYNLLFLTSTWNMIYNCKKEIRRLNTWIKYN

4qjyA

0.03

1.89

0.79

MapAlign

YIGTVFGRGEGQIPGYDGHQEIELALLKLYEVTGNENYLVRALYMYTAMAGLAAKMGDESL

5yfpD

0.07

2.77

0.54

MUSTER

SNKTNFTRVTNNDIFKIISISHNGFTSLENYLYNIVNIDIMEKTINKNLEQFIHDQSLNKQ

(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	0.5978

(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	7bp3A	0.68	2.54	0.016	0.918	model1_7bp3A.pdb.gz
2	5cwmA	0.68	2.40	0.066	0.869	model1_5cwmA.pdb.gz
3	2lqgA	0.68	2.73	0.131	1.000	model1_2lqgA.pdb.gz
4	2fzfA	0.67	3.00	0.049	0.984	model1_2fzfA.pdb.gz
5	2yfaA	0.67	2.94	0.033	1.000	model1_2yfaA.pdb.gz
6	6n63A	0.66	2.73	0.115	1.000	model1_6n63A.pdb.gz
7	4yk1A	0.66	2.67	0.000	0.934	model1_4yk1A.pdb.gz
8	5cwnA2	0.61	2.26	0.050	0.853	model1_5cwnA2.pdb.gz
9	5cwoA2	0.60	2.00	0.098	0.754	model1_5cwoA2.pdb.gz
10	5cwqA1	0.60	3.01	0.033	0.918	model1_5cwqA1.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:1901363	0.57	heterocyclic compound binding
GO:0097159	0.57	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:0098792	1.00	xenophagy
GO:0098779	1.00	mitophagy in response to mitochondrial depolarization
GO:0002230	1.00	positive regulation of defense response to virus by host

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:0005737	1.00	cytoplasm
GO:0043229	0.88	intracellular organelle
GO:0016020	0.65	membrane
GO:0043227	0.61	membrane-bounded organelle
GO:0044444	0.59	cytoplasmic part
GO:0005886	0.57	plasma membrane
GO:0044425	0.55	membrane part
GO:0043232	0.53	intracellular non-membrane-bounded organelle
GO:0030054	0.52	cell junction
GO:0005829	0.52	cytosol
GO:0098590	0.51	plasma membrane region
GO:0005856	0.51	cytoskeleton
GO:0042995	0.50	cell projection
GO:0032587	0.50	ruffle 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	1itwB	0.581	2.62	0.033	0.770	1.1.1.42	NA
2	0.060	2ckpB	0.484	3.22	0.057	0.869	2.7.1.32	NA
3	0.060	1k04A	0.600	2.08	0.049	0.770	2.7.10.2	NA
4	0.060	1sk6C	0.573	3.10	0.034	0.934	4.6.1.1	NA
5	0.060	2hwgA	0.612	2.63	0.036	0.885	2.7.3.9	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	1yuz0	0.662	3.12	0.066	1.000	0.11	III	complex1.pdb.gz	20,24,25,27,28,31,32,34
2	0.01	3l3mA	0.574	3.12	0.082	1.000	0.11	A92	complex2.pdb.gz	20,37,38
3	0.01	2paxA	0.413	2.70	0.052	0.623	0.39	4AN	complex3.pdb.gz	34,35,36,40,41
4	0.01	3l3lA	0.420	2.49	0.052	0.607	0.15	L3L	complex4.pdb.gz	38,45,46
5	0.01	2rd6A	0.577	3.10	0.067	0.984	0.20	78P	complex5.pdb.gz	34,35,36,40,41

	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.