D-I-TASSER Q5VZE5-D3

D-I-TASSER results for Q5VZE5-D3

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

Input Sequence in FASTA format

>Q5VZE5 (215 residues)
ELYSMHEYYYIYWYLSEFLYAWLMSTLSRADGSQMAEERIMEEQQKGRSSKKTKKKKKVR
PLSREITMSQAYQNMCAGMFKTMVAFDMDGKVRKPKFELDSEQVRYEHRFAPFNSVMTPP
PVHYLQFKEMSDLNKYSPPPQSPELYVAASKHFQQAKMILENIPNPDHEVNRILKVAKPN
FVVMKLLAGGHKKESKVPPEFDFSAHKYFPVVKLV

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 200 \| \| \| \| \| \| \| \| \| \| ELYSMHEYYYIYWYLSEFLYAWLMSTLSRADGSQMAEERIMEEQQKGRSSKKTKKKKKVRPLSREITMSQAYQNMCAGMFKTMVAFDMDGKVRKPKFELDSEQVRYEHRFAPFNSVMTPPPVHYLQFKEMSDLNKYSPPPQSPELYVAASKHFQQAKMILENIPNPDHEVNRILKVAKPNFVVMKLLAGGHKKESKVPPEFDFSAHKYFPVVKLV
Prediction	CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHCHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCSSSCCCCCCCCSSSSC
Confidence	99874776287999999999999999999999999887753211023332113331123456789999999999999999999999990998999999997999999997624138999999999999873133125653289999999999999999999668838999999999999899999998306788877735415555424335539
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 200 \| \| \| \| \| \| \| \| \| \| ELYSMHEYYYIYWYLSEFLYAWLMSTLSRADGSQMAEERIMEEQQKGRSSKKTKKKKKVRPLSREITMSQAYQNMCAGMFKTMVAFDMDGKVRKPKFELDSEQVRYEHRFAPFNSVMTPPPVHYLQFKEMSDLNKYSPPPQSPELYVAASKHFQQAKMILENIPNPDHEVNRILKVAKPNFVVMKLLAGGHKKESKVPPEFDFSAHKYFPVVKLV
Prediction	83243411110000001000421340053044124445544564565555555645544442322111130130003001200110333431551646152542104300420451430531316304532535534655423400430151053036105615534520430141033010001002443566553414141531420020416
	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

                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |

SS
Seq

CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHCHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCSSSCCCCCCCCSSSSC
ELYSMHEYYYIYWYLSEFLYAWLMSTLSRADGSQMAEERIMEEQQKGRSSKKTKKKKKVRPLSREITMSQAYQNMCAGMFKTMVAFDMDGKVRKPKFELDSEQVRYEHRFAPFNSVMTPPPVHYLQFKEMSDLNKYSPPPQSPELYVAASKHFQQAKMILENIPNPDHEVNRILKVAKPNFVVMKLLAGGHKKESKVPPEFDFSAHKYFPVVKLV

6ygaB3

0.15

0.14

4.88

1.33

DEthreader

DIYKPFEAYS-FWYVYY-LSHHLETFLKDSQNDIESNINAIHSLRLYRADNEEQLQATKQFLNYLLKEINITKSLCLIEVFQFAILKSFG-LIDNSTPSSNERLIHNLRFKPFNSIGVPELPEYEVFQQTLKDFVIEEKFDLERATNFIETEVRNVVSSIDEIQGISLYYCKLKHTSKALSVNSKVIVNTLKNHEYKVELVHTTGWNYFPIQTLR

6ygaB3

0.15

5.01

1.55

SPARKS-K

DIYKPFEAYS-FW-YVYYLSHHLETFLKDSQNDIESNINAIHKLKKLKAGEKKDQLRLKQFLNYLLKEINITKSLCLIEVFQFAILKSFGLIDNKNSTFSNERLIHNLRFKPFNSIGVPELPEYEVFQQTLKDFVIEEDIKLERATNFIETEVRNVVSSIDEIQLSLEYYCKLKHTSKALSVNSKVIVNTNKDSHEYKVELVHEGWNYFPIQTLR

6ygaB

0.15

0.14

4.88

1.50

MapAlign

DIYKPFEAYS-FWY-VYYLSHHLETFLKDSQNDIESNINAILRLKYRFADNEEQLQATKQFLNYLLKEINITKSLCLIEVFQFAILKSFGLIDNKNSKFSNERLIHNLRFKPFNSIGVPELPEYEVFQQTLVIEEKGAAFKLERATNFIETEVRNVVSSIDEIELSLEYYCKLKHTSKALSVNSKVIVNTLKDSHEYKVELVHTGWNYFPIQTLR

6ygaB3

0.15

5.13

1.59

CEthreader

DIYKPFEAYS--FWYVYYLSHHLETFLKDSQNDIESNINAIHSNKKLKKLKEEQLQATKQFLNYLLKEINITKSLCLIEVFQFAILKSFGLIDNKNSKFSNERLIHNLRFKPFNSIGVPELPEYEVFQQTLKDFVIEFDIKLERATNFIETEVRNVVSSIDEIQGSLEYYCKLKHTSKALSVNSKVIVNTLKHEYKVELVHTTEGWNYFPIQTLR

1wp9A

0.08

3.26

0.52

MUSTER

RAVGNYAYVFIAREYKRQAKNPLVSTPEKIMEVINNLGIEHIEYRSENSPDVRPYVKGIRRVDLPEIYKEVRKLLREMLRDALKPLAETGLLESSSPDIPKEVLRAGQIINEEMAKGNHDLRGLLLYHAMALKLHHAIELLETQGLSALRAYIKKLYEEAKAGSTKASKEIFSDKRMKKAISLLVQAKEIGLDHPKMDIREQLQRKQNSKIIVFT

6ygaB3

0.16

5.26

5.47

HHsearch

DIYKPFEAYS-FWYV-YYLSHHLETFLKDSQNDIESNINAIHSNKKLKKLAGEKKDATKQFLNYLLKEINITKSLCLIEVFQFAILKSFGLIDNKPSKFSNERLIHNLRFKPFNSIGVPELPEYEVFQQTLKDFVIEEKIKLERATNFIETEVRNVVSSIDEIQGSLEYYCKLKHTSKALSVNSKVIVNTIKDSHEYKVELVTEGWNYFPIQTLR

6ygaB3

0.17

5.51

2.28

FFAS-3D

DIYKPFEA-YSFWYVYYLS-HHLETFLKDSQNDIESNINAIHSNKKLKKLKAGEKKDQLRFLNYLLKEINITKSLCLIEVFQFAILKSFGLIDSTPSKFSNERLIHNLRFKPFNSIGVPELPEYEVFQQTLKDFVIEEKGKLERATNFIETEVRNVVSSIDEIQGIKEYYCKLKHTSKALSVNSKVIKNKDSHEYKVELVHTTEGWNYFPIQTLR

6ygaB3

0.14

4.89

1.62

EigenThreader

YKPFEAYSFWYVYYLSHHLETFLKDSQNDIESNINAIHSDQLRLKYRFADNEEQLQATKQFLNYLLKEINITKSLCLIEVFQFAILKSFGLIDNKNSTPSNERLIHNLRFKPFNSIGVPELPEYEVFQQTLKDFVIEEKIKLERATNFIETEVRNVVSSIDEIQLSLEYYCKLKHTSKALSVNSKVIVNTLKKNIKNSHEVHTEGWNYFPIQTLR

4a1sA

0.07

0.05

2.08

0.63

CNFpred

----LRTLSAIYSQLGNAYFYDYNKAMQYHKHDLTLAKSMNDRLGE---------------AKSSGNLGNTLKRFDEAAICCERHLTLARQL-------GDRLSEGRALYNLGNV-------YHAKGKHLGQRNPGKFGDDVKEALTRAVEFYQENLKLMRDL----GDRGAQGRACGNLGNTYYLLG---------------------------

6ygaB

0.15

0.14

4.88

1.33

DEthreader

DIYKPFEAYS-FWYVYY-LSHHLETFLKDSQNDIESNINAIHSLRLYRADNEEQLQATKQFLNYLLKEINITKSLCLIEVFQFAILKSFG-LIDNSTPSSNERLIHNLRFKPFNSIGVPELPEYEVFQQTLKDFVIEEKFDLERATNFIETEVRNVVSSIDEIQGISLYYCKLKHTSKALSVNSKVIVNTLKNHEYKVELVHTTGWNYFPIQTLR

(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	0.8217

(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	6ygaB3	0.92	1.64	0.146	0.991	model1_6ygaB3.pdb.gz
2	5xa5A	0.52	3.57	0.065	0.670	model1_5xa5A.pdb.gz
3	6u4oC	0.51	5.21	0.078	0.837	model1_6u4oC.pdb.gz
4	5j1iA	0.51	3.43	0.042	0.651	model1_5j1iA.pdb.gz
5	2j0oA	0.51	4.32	0.060	0.716	model1_2j0oA.pdb.gz
6	3kbuB	0.50	2.83	0.049	0.600	model1_3kbuB.pdb.gz
7	6a70B	0.50	4.60	0.046	0.721	model1_6a70B.pdb.gz
8	2izpA	0.50	4.52	0.051	0.730	model1_2izpA.pdb.gz
9	1cunA	0.50	3.02	0.065	0.609	model1_1cunA.pdb.gz
10	5j1fA	0.50	3.15	0.058	0.600	model1_5j1fA.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	0.37	heterocyclic compound binding
GO:0097159	0.37	organic cyclic compound binding
GO:0003824	0.37	catalytic 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	1.00	single-organism process
GO:0048523	0.97	negative regulation of cellular process
GO:0048659	0.96	smooth muscle cell proliferation
GO:0043066	0.96	negative regulation of apoptotic process
GO:0009987	0.58	cellular 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:0005737	1.00	cytoplasm
GO:0044444	0.96	cytoplasmic part
GO:0032991	0.96	macromolecular complex
GO:0043234	0.95	protein complex
GO:0031417	0.94	NatC complex
GO:0005844	0.91	polysome

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	2p4qA	0.433	5.55	0.086	0.735	1.1.1.44	NA
2	0.060	1k62B	0.461	5.08	0.061	0.740	4.3.2.1	NA
3	0.060	3gtdA	0.457	5.15	0.077	0.753	4.2.1.2	NA
4	0.060	1h2rL	0.432	4.97	0.058	0.651	1.12.2.1	NA
5	0.060	1yfeA	0.459	5.28	0.049	0.763	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:

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	1ar1A	0.427	5.11	0.042	0.670	0.16	HEA	complex1.pdb.gz	10,13,14,76,80,83,84,87,88,91
2	0.01	1bf5A	0.403	4.11	0.022	0.507	0.24	QNA	complex2.pdb.gz	87,94,131
3	0.01	3omaA	0.453	3.57	0.027	0.567	0.21	HEA	complex3.pdb.gz	11,15,16,80,83,84,86
4	0.01	1rw60	0.452	3.73	0.060	0.600	0.29	III	complex4.pdb.gz	81,85,89
5	0.01	3omaC	0.453	3.55	0.027	0.567	0.22	DMU	complex5.pdb.gz	78,82,86
6	0.01	1m57A	0.449	5.16	0.044	0.688	0.16	HEA	complex6.pdb.gz	78,79,89,142,143,146,149
7	0.01	1k620	0.460	5.09	0.061	0.740	0.25	III	complex7.pdb.gz	3,5,6,79,83,85,86,143,150
8	0.01	2j0n0	0.352	4.14	0.056	0.493	0.34	III	complex8.pdb.gz	53,54,57,61,63,64,65,67,68,70,71,72,75,78,79,82,85,86,90,91
9	0.01	1qleA	0.412	4.73	0.043	0.642	0.18	HEA	complex9.pdb.gz	71,74,75,82,85,89,138,142,145,149,150,152,153,156,185
10	0.01	3om3A	0.421	4.01	0.048	0.572	0.17	HEA	complex10.pdb.gz	78,86,89,146,149,153,156

	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.