D-I-TASSER Q96PE1-D7

D-I-TASSER results for Q96PE1-D7

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

Input Sequence in FASTA format

>Q96PE1 (213 residues)
LLWMGVKARVLHKELTWRAPPPQEGDPALPTPSPMLRFYLIAGGIPLIICGITAAVNIHN
YRDHSPYCWLVWRPSLGAFYIPVALILLITWIYFLCAGLRLRGPLAQNPKAGNSRASLEA
GEELRGSTRLRGSGPLLSDSGSLLATGSARVGTPGPPEDGDSLYSPGVQLGALVTTHFLY
LAMWACGALAVSQRWLPRVVCSCLYGVAASALG

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 200 \| \| \| \| \| \| \| \| \| \| LLWMGVKARVLHKELTWRAPPPQEGDPALPTPSPMLRFYLIAGGIPLIICGITAAVNIHNYRDHSPYCWLVWRPSLGAFYIPVALILLITWIYFLCAGLRLRGPLAQNPKAGNSRASLEAGEELRGSTRLRGSGPLLSDSGSLLATGSARVGTPGPPEDGDSLYSPGVQLGALVTTHFLYLAMWACGALAVSQRWLPRVVCSCLYGVAASALG
Prediction	CCSHHHHHHHHHHHHHHHCCCCCCCCCCCCCCHHHHHHHHHHSCCCSSSSSSSSSSSCCCCCCCCCCSSSSCCCCSSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHCCCHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHCC
Confidence	931135599999999951567666766777552465344431142331256778873012789999126762772453158899999999999999999999876533123344555666655430211010256566654433346666667776521111121899999999999999999999999860765123339899999998639
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 200 \| \| \| \| \| \| \| \| \| \| LLWMGVKARVLHKELTWRAPPPQEGDPALPTPSPMLRFYLIAGGIPLIICGITAAVNIHNYRDHSPYCWLVWRPSLGAFYIPVALILLITWIYFLCAGLRLRGPLAQNPKAGNSRASLEAGEELRGSTRLRGSGPLLSDSGSLLATGSARVGTPGPPEDGDSLYSPGVQLGALVTTHFLYLAMWACGALAVSQRWLPRVVCSCLYGVAASALG
Prediction	430010003200220043243465555443143200100020133102000000001264136444000013332000122332212221331231011102233454464464444354455245444244444334454433444344334344353444332331102010101211331120000002463212000000100002018
	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                 100                 120                 140                 160                 180                 200

                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |

SS
Seq

CCSHHHHHHHHHHHHHHHCCCCCCCCCCCCCCHHHHHHHHHHSCCCSSSSSSSSSSSCCCCCCCCCCSSSSCCCCSSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHCCCHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHCC
LLWMGVKARVLHKELTWRAPPPQEGDPALPTPSPMLRFYLIAGGIPLIICGITAAVNIHNYRDHSPYCWLVWRPSLGAFYIPVALILLITWIYFLCAGLRLRGPLAQNPKAGNSRASLEAGEELRGSTRLRGSGPLLSDSGSLLATGSARVGTPGPPEDGDSLYSPGVQLGALVTTHFLYLAMWACGALAVSQRWLPRVVCSCLYGVAASALG

5tgzA

0.10

0.09

3.32

1.17

DEthreader

VGSLFLAAIDRYISIHR-PLAY----KRIVTRPKAVVAFCLMWTIAIVIAVLPLGWNCEKLQVCS-IFPHIDKTYLMFWIGVVSVLLLFIVYAYMYILWKAHSHAV----AK--A---L-IVYTEYAETIA--RELADAGYEVDSRLFVARKEIVQAHRGAPDRMDIELAKTLVLILVVLIICWGPLLAIMDMIKTVFAFCSMLCLLNSTVNP

6bd4A

0.09

0.08

3.23

1.10

SPARKS-K

SIWWVILTLTWFLAAG----------LKWGHEMHSSYFHIAAWAIPAVKTIVILIMRLVDADELTGLCYVGNQNLTGFVVAPLFTYLVIGTLFIAAGLVALFKIRSNMKKYTCTVCGYINPEDGDPDNGVNPGTDFKDIPDDWVCPLCGVGKDQFEEVEEDKLERLMVKIGVFSVLYTVPATIVIACYFYEISNSAMAVEMLKIFMSLLVGIT

4grvA

0.09

0.08

3.26

0.66

MapAlign

ALNVASLSVARYLAICH----PFKAKTLMSRSRTKKFISA-IWLASALLAIPMLFTMGLQNRSADGTHGLVCTPIIQVNTFMSLFPMLVISILNTVIANKLTVMVNIFEMLRIDEGLRLKIYKDTEGYYTIGIGHLLQTPNRAKRVITTFRTGTWDAYGSGSVQALRHGVLVARAVVIAFVVCWLPYHVRRLMFFDFYHYFYMLTNALAYASS

6iiuA

0.08

3.28

0.51

CEthreader

GLSPLLLGAAMASERYLGITRPFSRPAVASQRRAWATVGLVWAAALALGLLPLLGVGRYTVQYPGSWCFLTLVAFGLLFSMLGGLSVGLSFLLNTVSVATLCHVYHGMKKYTCTVCGYIYNPEDGDPDNGVNPG-TDFKDIPDDWVCPLCGVGKDQFEEVEERDSEVEMMAQALGIMVVASVCWLPLLVFIAQTLIYLRVATWNQILDPWVYI

4k5yA2

0.20

0.14

4.49

0.81

MUSTER

FFWMFGEGCYLHTAIVLWDAYDR---------LRAWMFICIGWGVPFPIIVAWAIGKL---YYDNEKCWAGKRPTDYIYQGPMALVLLINFIFLFNIVRILMTKLRASTT--------------------------------------------------SETIQARKAVKATLVLLPLLGITYMLAFV----NEVSRVVFIYFNAFLESFQG

6fj3A

0.12

4.11

2.60

HHsearch

YYWIAVEGLYLHSLIFKAFF---------SEKKYLWGFTVFGWGLPAIFVAVWVSVRATLANT---GCWDLSSNNKWIIQVPILASIVLNFILFINIVRVLATKGIDS-FWNESYLTGSRDERKKKARSLEEKHGNSRREVPIATNETAGDELSRSMSFSDTRQQYRKLAKSTLVLMPLFGVHYIVFMLTPYTEGTLWQVRMHYEMLFNSFQG

5ee7A

0.18

0.12

3.99

1.48

FFAS-3D

TPNRAKRVITTFRTGTWDA---------YPERSFFSLYLGIGWGAPALFVVPWAVVKCLF---ENVQCWTNMG-FWWILRFPVFLAILINFFIFVRIVQLLVAKLRARQMHHTD--------------------------------------------------YAFRLAKSTLTLIPLLGVHFVVFAFVTDEH---RSAKLFFDLALSSFQG

4ib4A

0.07

2.87

0.85

EigenThreader

IWHLCAISVDRYIAIKK-----PIQANQYNSRATAFIKITVVWLISIGIAIPVPIKGIET-NPNNITCVLTKERFGDFMLFGSLAAFFTPLAIMIVTYFLTIHALQKKAADLEDNWETLNDNLKVIEKADNAAQVKDALTKMRAAAIDDALKLANEGKVKEAQAAAEQASKVLGIVFFLFLLMWCPFFITNITLVLCLEIFVWIGYVSSGVNP

6niyR

0.17

0.11

3.71

1.03

CNFpred

YFWMLCEGIYLHTLIVVAVFTE---------KQRLRWYYLLGWGFPLVPTTIHAITRAVY---FNDNCWLSVEHLLYIIHGPVMAALVVNFFFLLNIVRVLVTKMR---------------------------------------------------------HMYLKAVKATMILVPLLGIQFVVFPWRPS-NKMLGKIYDYVMHSLIHFQG

5ztyA

0.12

0.10

3.66

1.00

DEthreader

VGSLLLAAIDRYLCLRY-PPSY-----KALTRGRALVLLGIMWVLSALVSYLPLGWTCCP--CSE-LFPLIPNDYLLSWLLFIAFLFSGIIYTYGHVLWKAHQHVASNEMLRIDVAALN--MLRWEAVN--------KRV-TTFRTGTW-------D-AYARMRLDVELAKTLGLVLAVLLICWFPVLALMSLVKKAFAFCSMLCLINSMVNP

(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	0.6583

(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	5ztyA	0.67	3.77	0.081	0.869	model1_5ztyA.pdb.gz
2	6bqgA	0.67	3.51	0.089	0.845	model1_6bqgA.pdb.gz
3	2rh1A	0.67	4.03	0.095	0.878	model1_2rh1A.pdb.gz
4	6kuxA	0.66	3.90	0.072	0.864	model1_6kuxA.pdb.gz
5	6a93A	0.66	3.39	0.095	0.831	model1_6a93A.pdb.gz
6	4iaqA	0.66	3.75	0.073	0.836	model1_4iaqA.pdb.gz
7	6li0A	0.65	3.77	0.079	0.845	model1_6li0A.pdb.gz
8	5wiuA	0.64	3.60	0.063	0.803	model1_5wiuA.pdb.gz
9	4phuA	0.64	4.07	0.095	0.864	model1_4phuA.pdb.gz
10	4xnvA	0.64	3.79	0.064	0.822	model1_4xnvA.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:0004930	1.00	G-protein coupled receptor 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:0050794	1.00	regulation of cellular process
GO:0044699	0.81	single-organism process
GO:0007165	0.79	signal transduction
GO:0032502	0.77	developmental process
GO:0048856	0.76	anatomical structure development
GO:0044767	0.76	single-organism developmental process
GO:0048731	0.75	system development
GO:0002040	0.75	sprouting angiogenesis
GO:0009987	0.73	cellular process
GO:0044763	0.64	single-organism cellular process
GO:0048583	0.61	regulation of response to stimulus
GO:0051239	0.60	regulation of multicellular organismal process
GO:0050793	0.60	regulation of developmental process
GO:0006928	0.60	movement of cell or subcellular component
GO:0050920	0.59	regulation of chemotaxis
GO:0045765	0.59	regulation of angiogenesis
GO:0043542	0.59	endothelial cell migration
GO:0007417	0.59	central nervous system development
GO:0007186	0.59	G-protein coupled receptor signaling pathway

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:0044464	0.93	cell part
GO:0044425	0.73	membrane part
GO:0044424	0.63	intracellular part
GO:0016021	0.60	integral component of 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	2iukA	0.442	5.00	0.053	0.671	1.13.11.12	NA
2	0.060	3b8eA	0.418	5.32	0.046	0.695	3.6.3.9	NA
3	0.060	2pfmA	0.425	5.05	0.051	0.667	4.3.2.2	NA
4	0.060	1fftA	0.488	3.86	0.067	0.643	1.10.3.-	NA
5	0.060	2fenD	0.435	4.56	0.047	0.653	5.5.1.2	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	0.06	3gujA	0.258	5.10	0.076	0.413	0.49	BNZ	complex1.pdb.gz	5,42,45,46
2	0.01	1c6mA	0.266	4.92	0.023	0.404	0.46	KR	complex2.pdb.gz	53,54,78
3	0.01	1c6aA	0.266	4.89	0.023	0.404	0.41	KR	complex3.pdb.gz	38,41,42,45
4	0.01	3htgA	0.246	5.08	0.049	0.390	0.40	JZ7	complex4.pdb.gz	49,50,54,78,82,85
5	0.01	1ovhA	0.266	4.90	0.023	0.404	0.42	2CM	complex5.pdb.gz	2,46,49,50,82,86
6	0.01	1owyA	0.265	4.92	0.023	0.404	0.47	PRY	complex6.pdb.gz	46,49,50,79,83
7	0.01	3htfA	0.246	5.05	0.049	0.390	0.47	JZ6	complex7.pdb.gz	48,49,53,75,83
8	0.01	2nthA	0.278	4.26	0.052	0.390	0.41	MTN	complex8.pdb.gz	45,48,52,77,83,86
9	0.01	2ou8A	0.271	4.91	0.023	0.413	0.57	MTN	complex9.pdb.gz	42,45,49
10	0.01	148lE	0.249	5.37	0.089	0.408	0.45	III	complex10.pdb.gz	46,47,55,56,57,73,76,77,78,79,82

	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.