D-I-TASSER Q8WWV3-D1

D-I-TASSER results for Q8WWV3-D1

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

Input Sequence in FASTA format

>Q8WWV3 (252 residues)
MEFLKTCVLRRNACTAVCFWRSKVVQKPSVRRISTTSPRSTVMPAWVIDKYGKNEVLRFT
QNMMMPIIHYPNEVIVKVHAASVNPIDVNMRSGYGATALNMKRDPLHVKIKGEEFPLTLG
RDVSGVVMECGLDVKYFKPGDEVWAAVPPWKQGTLSEFVVVSGNEVSHKPKSLTHTQAAS
LPYVALTAWSAINKVGGFFMASGPCLDDIAELVDAGKIRPVIEQTFPFSKVPEAFLKVER
GHARGKTVINVV

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 200 220 240 \| \| \| \| \| \| \| \| \| \| \| \| MEFLKTCVLRRNACTAVCFWRSKVVQKPSVRRISTTSPRSTVMPAWVIDKYGKNEVLRFTQNMMMPIIHYPNEVIVKVHAASVNPIDVNMRSGYGATALNMKRDPLHVKIKGEEFPLTLGRDVSGVVMECGLDVKYFKPGDEVWAAVPPWKQGTLSEFVVVSGNEVSHKPKSLTHTQAASLPYVALTAWSAINKVGGFFMASGPCLDDIAELVDAGKIRPVIEQTFPFSKVPEAFLKVERGHARGKTVINVV
Prediction	CCHHHHHHCCCCCCCSSSCCCCCCCCCCCCCCCCCCCCCCCCSSSSSSCCCCCHHHCSSSCCCCCCCCCCCCSSSSSSSSSSSCHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCSCCSSSSSSSSSSCCCCCCCCCCCSSSSSCCCCCCCSCCSSSSSCHHHHSCCCCCCCHHHHHHCHHHHHHHHHHHHHHHHCCCCCCCCCSSSSSSCCCCCSSSSSSSSSSHHHHHHHHHHHHHCCCCCCSSSSSC
Confidence	942454430467641010144422467765666789999763089998677993442663126888889869799999999838899998628875332322333344567678997311257899999779998889981899833899991120248974898331899999899854013466499999999721344444330122200024325516888835677999999997386664898729
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 200 220 240 \| \| \| \| \| \| \| \| \| \| \| \| MEFLKTCVLRRNACTAVCFWRSKVVQKPSVRRISTTSPRSTVMPAWVIDKYGKNEVLRFTQNMMMPIIHYPNEVIVKVHAASVNPIDVNMRSGYGATALNMKRDPLHVKIKGEEFPLTLGRDVSGVVMECGLDVKYFKPGDEVWAAVPPWKQGTLSEFVVVSGNEVSHKPKSLTHTQAASLPYVALTAWSAINKVGGFFMASGPCLDDIAELVDAGKIRPVIEQTFPFSKVPEAFLKVERGHARGKTVINVV
Prediction	451144022434343122224243264343443454454442310000352341410423551641416464100010200000300010123224333424433444544445112000200001013015706654203100000244420010220003052014236604130000000000001200220243343233322302311443403200331041650340142035140311000325
	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                 180                 200                 220                 240

                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |

SS
Seq

CCHHHHHHCCCCCCCSSSCCCCCCCCCCCCCCCCCCCCCCCCSSSSSSCCCCCHHHCSSSCCCCCCCCCCCCSSSSSSSSSSSCHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCSCCSSSSSSSSSSCCCCCCCCCCCSSSSSCCCCCCCSCCSSSSSCHHHHSCCCCCCCHHHHHHCHHHHHHHHHHHHHHHHCCCCCCCCCSSSSSSCCCCCSSSSSSSSSSHHHHHHHHHHHHHCCCCCCSSSSSC
MEFLKTCVLRRNACTAVCFWRSKVVQKPSVRRISTTSPRSTVMPAWVIDKYGKNEVLRFTQNMMMPIIHYPNEVIVKVHAASVNPIDVNMRSGYGATALNMKRDPLHVKIKGEEFPLTLGRDVSGVVMECGLDVKYFKPGDEVWAAVPPWKQGTLSEFVVVSGNEVSHKPKSLTHTQAASLPYVALTAWSAINKVGGFFMASGPCLDDIAELVDAGKIRPVIEQTFPFSKVPEAFLKVERGHARGKTVINVV

2vn8A

0.92

0.77

21.62

1.33

DEthreader

-------------------------------------L-YFQSMAWVIDKYGKNEVLRFTQNMMMPIIHYPNEVIVKVHAASVNPIDVNMRSGYGATALNMKRDVKIKG---EEFPLTLGRDVSGVVMECGLDVKYFKPGDEVWAAVPPWKQGTLSEFVVVSGNEVSHKPKSLTHTQAASLPYVALTAWSAINVGGLAFFMSGPCLDDIAELVDAGKIRPVIEQTFPFSKVPEAFLKVERGHARGKTVINVV

2vn8A1

0.97

0.82

23.03

2.58

SPARKS-K

--------------------------------------LYFQSMAWVIDKYGKNEVLRFTQNMMMPIIHYPNEVIVKVHAASVNPIDVNMRSGYGATALNMKRDPLHVKIKGEEFPLTLGRDVSGVVMECGLDVKYFKPGDEVWAAVPPWKQGTLSEFVVVSGNEVSHKPKSLTHTQAASLPYVALTAWSAINKVGGLFMASGPCLDDIAELVDAGKIRPVIEQTFPFSKVPEAFLKVERGHARGKTVINVV

4a0sA

0.26

0.22

6.73

0.63

MapAlign

--------------------------------------VPDTYLALHLRMFKDVRSLRLGE-VPMPEL-APDEVLVAVMASSINYNTVWSAMFEPIPTLKQNARQGGWATRHDQPYHVLGSDCSGVVVRTGIGVRRWKPGDHVIVHWGFTNFGGLAEYGVVRASQLLPKPAHLTWEEAAVSPLCAGTAYRMLSDRGASHGANHEEQQATNRLFESGAVVPAMSAVYPLAEAAEACRVVQTSRQVGKVAVLCM

2vn8A

0.97

0.82

23.03

0.36

CEthreader

--------------------------------------LYFQSMAWVIDKYGKNEVLRFTQNMMMPIIHYPNEVIVKVHAASVNPIDVNMRSGYGATALNMKRDPLHVKIKGEEFPLTLGRDVSGVVMECGLDVKYFKPGDEVWAAVPPWKQGTLSEFVVVSGNEVSHKPKSLTHTQAASLPYVALTAWSAINKVGAFFMASGPCLDDIAELVDAGKIRPVIEQTFPFSKVPEAFLKVERGHARGKTVINVV

2vn8A1

0.97

0.83

23.13

2.05

MUSTER

--------------------------------------LYFQSMAWVIDKYGKNEVLRFTQNMMMPIIHYPNEVIVKVHAASVNPIDVNMRSGYGATALNMKRDPLHVKIKGEEFPLTLGRDVSGVVMECGLDVKYFKPGDEVWAAVPPWKQGTLSEFVVVSGNEVSHKPKSLTHTQAASLPYVALTAWSAINKVGGFFMASGPCLDDIAELVDAGKIRPVIEQTFPFSKVPEAFLKVERGHARGKTVINVV

2vn8A1

0.97

0.83

23.13

1.08

HHsearch

--------------------------------------LYFQSMAWVIDKYGKNEVLRFTQNMMMPIIHYPNEVIVKVHAASVNPIDVNMRSGYGATALNMKRDPLHVKIKGEEFPLTLGRDVSGVVMECGLDVKYFKPGDEVWAAVPPWKQGTLSEFVVVSGNEVSHKPKSLTHTQAASLPYVALTAWSAINKVGGFFMASGPCLDDIAELVDAGKIRPVIEQTFPFSKVPEAFLKVERGHARGKTVINVV

2vn8A1

0.97

0.82

23.03

2.87

FFAS-3D

--------------------------------------LYFQSMAWVIDKYGKNEVLRFTQNMMMPIIHYPNEVIVKVHAASVNPIDVNMRSGYGATALNMKRDPLHVKIKGEEFPLTLGRDVSGVVMECGLDVKYFKPGDEVWAAVPPWKQGTLSEFVVVSGNEVSHKPKSLTHTQAASLPYVALTAWSAINKVGGLFMASGPCLDDIAELVDAGKIRPVIEQTFPFSKVPEAFLKVERGHARGKTVINVV

2vn8A

0.97

0.83

23.13

0.92

EigenThreader

--------------------------------------LYFQSMAWVIDKYGKNEVLRFTQNMMMPIIHYPNEVIVKVHAASVNPIDVNMRSGYGATALNMKRDPLHVKIKGEEFPLTLGRDVSGVVMECGLDVKYFKPGDEVWAAVPPWKQGTLSEFVVVSGNEVSHKPKSLTHTQAASLPYVALTAWSAINKVGGFFMASGPCLDDIAELVDAGKIRPVIEQTFPFSKVPEAFLKVERGHARGKTVINVV

2vn8A

0.79

0.64

18.06

2.28

CNFpred

---------------------------------------YFQSMAWVIDKYGKNEVLRFTQNMMMPIIHYPNEVIVKVHAASVNPIDVNMRSGYGATALNMKRDPLHVKIKGEEFPLTLGRDVSGVVMECGLDVKYFKPGDEVWAAVPPWKQGTLSEFVVVSGNEVSHKPKSLTHTQAASLPYVALTAWSAINKVGGLNDASGGVGTFAIQVMKAW--DAHVTAVCSQ----DASELVRKL--GADDVIDYK

2vn8A1

0.93

0.78

21.94

1.33

DEthreader

-------------------------------------L-YFQSMAWVIDKYGKNEVLRFTQNMMMPIIHYPNEVIVKVHAASVNPIDVNMRSGYGATALNMKRDVKIKG---EEFPLTLGRDVSGVVMECGLDVKYFKPGDEVWAAVPPWKQGTLSEFVVVSGNEVSHKPKSLTHTQAASLPYVALTAWSAINVGGLFFMASGPCLDDIAELVDAGKIRPVIEQTFPFSKVPEAFLKVERGHARGKTVINVV

(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	0.7629

(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	2vn8A	0.83	0.88	0.963	0.849	model1_2vn8A.pdb.gz
2	4a0sA	0.81	2.69	0.237	0.913	model1_4a0sA.pdb.gz
3	3krtA	0.81	2.89	0.203	0.929	model1_3krtA.pdb.gz
4	4gi2A	0.79	2.15	0.245	0.861	model1_4gi2A.pdb.gz
5	4idaA	0.78	1.84	0.346	0.825	model1_4idaA.pdb.gz
6	4y0kA	0.78	2.71	0.267	0.877	model1_4y0kA.pdb.gz
7	6eqoA	0.77	2.23	0.179	0.857	model1_6eqoA.pdb.gz
8	5a3jA	0.74	1.44	0.330	0.782	model1_5a3jA.pdb.gz
9	5k1sA	0.74	2.00	0.246	0.806	model1_5k1sA.pdb.gz
10	4dvjA	0.73	1.59	0.325	0.770	model1_4dvjA.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:0003824	0.92	catalytic activity
GO:0016491	0.89	oxidoreductase activity
GO:0036094	0.72	small molecule binding
GO:1901363	0.71	heterocyclic compound binding
GO:0097159	0.71	organic cyclic compound binding
GO:1901265	0.70	nucleoside phosphate binding
GO:0008270	0.60	zinc ion binding
GO:0050662	0.58	coenzyme binding
GO:0043880	0.52	crotonyl-CoA reductase activity

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	0.62	single-organism process
GO:0008152	0.53	metabolic process

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:0044424	1.00	intracellular part
GO:0044444	0.88	cytoplasmic part
GO:0016020	0.49	membrane
GO:0044446	0.46	intracellular organelle part
GO:0043226	0.44	organelle
GO:0043227	0.42	membrane-bounded organelle
GO:0005829	0.41	cytosol
GO:0031966	0.40	mitochondrial membrane
GO:0005741	0.36	mitochondrial outer membrane
GO:0043229	0.33	intracellular organelle
GO:0043231	0.32	intracellular membrane-bounded organelle

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	0.119	1yb5A	0.715	1.81	0.284	0.770	1.6.5.5	NA
2	0.095	1pl6A	0.689	2.19	0.224	0.766	1.1.1.14	NA
3	0.067	2obyA	0.710	1.89	0.290	0.766	1.-.-.-	94
4	0.067	1qorB	0.701	1.72	0.237	0.754	1.6.5.5	119,147
5	0.067	1zsyA	0.680	2.50	0.204	0.782	1.3.1.38	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	0.14	2vn8A	0.834	0.88	0.963	0.849	0.82	NDP	complex1.pdb.gz	85,183,187,198,199,243,244
2	0.07	1hldA	0.709	1.99	0.189	0.778	0.50	UUU	complex2.pdb.gz	84,86,121,148
3	0.07	3btoB	0.707	2.01	0.189	0.778	0.42	SSB	complex3.pdb.gz	84,86,120
4	0.04	1mgoB	0.708	2.01	0.189	0.778	0.49	PFB	complex4.pdb.gz	165,166,167

	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.