D-I-TASSER Q9Y2T3-D2

D-I-TASSER results for Q9Y2T3-D2

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

Input Sequence in FASTA format

>Q9Y2T3 (311 residues)
GLVDTHIHASQYSFAGSSIDLPLLEWLTKYTFPAEHRFQNIDFAEEVYTRVVRRTLKNGT
TTACYFATIHTDSSLLLADITDKFGQRAFVGKVCMDLNDTFPEYKETTEESIKETERFVS
EMLQKNYSRVKPIVTPRFSLSCSETLMGELGNIAKTRDLHIQSHISENRDEVEAVKNLYP
SYKNYTSVYDKNNLLTNKTVMAHGCYLSAEELNVFHERGASIAHCPNSNLSLSSGFLNVL
EVLKHEVKIGLGTDVAGGYSYSMLDAIRRAVMVSNILLINKVNEKSLTLKEVFRLATLGG
SQALGLDGEIG

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 200 220 240 260 280 300 \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| GLVDTHIHASQYSFAGSSIDLPLLEWLTKYTFPAEHRFQNIDFAEEVYTRVVRRTLKNGTTTACYFATIHTDSSLLLADITDKFGQRAFVGKVCMDLNDTFPEYKETTEESIKETERFVSEMLQKNYSRVKPIVTPRFSLSCSETLMGELGNIAKTRDLHIQSHISENRDEVEAVKNLYPSYKNYTSVYDKNNLLTNKTVMAHGCYLSAEELNVFHERGASIAHCPNSNLSLSSGFLNVLEVLKHEVKIGLGTDVAGGYSYSMLDAIRRAVMVSNILLINKVNEKSLTLKEVFRLATLGGSQALGLDGEIG
Prediction	CCSSSCCCHHHHHHHHHCCCCCHHHHHHHCHHHHHHCCCCHHHHHHHHHHHHHHHHHCCCCSSSSCCCCCCHHHHHHHHHHHHHCCSSSSSCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCSSSSSSCCCCCCCCHHHHHHHHHHHHHCCCCSSSSSCCCHHHHHHHHHHCCCCCCHHHHHHHHCCCCCCSSSSSSCCCCHHHHHHHHHHCCSSSSCHHHHHHHCCCCCCHHHHHHCCCCSSSSCCCCCCCCCCHHHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCC
Confidence	97430217677878753389987999975453888715999999999999999999619216675203585179999999999299499970102799999511169999999999999998467999848998348999899999999999999709918986289878999999984999998999998099999928998306999999999981997997846755415788889999980996898447899999249999999999985775136899879999999999888889839998889
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 200 220 240 260 280 300 \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| GLVDTHIHASQYSFAGSSIDLPLLEWLTKYTFPAEHRFQNIDFAEEVYTRVVRRTLKNGTTTACYFATIHTDSSLLLADITDKFGQRAFVGKVCMDLNDTFPEYKETTEESIKETERFVSEMLQKNYSRVKPIVTPRFSLSCSETLMGELGNIAKTRDLHIQSHISENRDEVEAVKNLYPSYKNYTSVYDKNNLLTNKTVMAHGCYLSAEELNVFHERGASIAHCPNSNLSLSSGFLNVLEVLKHEVKIGLGTDVAGGYSYSMLDAIRRAVMVSNILLINKVNEKSLTLKEVFRLATLGGSQALGLDGEIG
Prediction	86240100100120102026240142045200210341333400210021002203614020000001012400310030037031000000000023232452353044005202400440374632001000000100101340043005005727020000000045005202631543320010023120033300000000024500510373601000002000300101020430173403000000000121100020021001002023346443420304200200021002003256738
	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                 260                 280                 300

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

SS
Seq

CCSSSCCCHHHHHHHHHCCCCCHHHHHHHCHHHHHHCCCCHHHHHHHHHHHHHHHHHCCCCSSSSCCCCCCHHHHHHHHHHHHHCCSSSSSCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCSSSSSSCCCCCCCCHHHHHHHHHHHHHCCCCSSSSSCCCHHHHHHHHHHCCCCCCHHHHHHHHCCCCCCSSSSSSCCCCHHHHHHHHHHCCSSSSCHHHHHHHCCCCCCHHHHHHCCCCSSSSCCCCCCCCCCHHHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCC
GLVDTHIHASQYSFAGSSIDLPLLEWLTKYTFPAEHRFQNIDFAEEVYTRVVRRTLKNGTTTACYFATIHTDSSLLLADITDKFGQRAFVGKVCMDLNDTFPEYKETTEESIKETERFVSEMLQKNYSRVKPIVTPRFSLSCSETLMGELGNIAKTRDLHIQSHISENRDEVEAVKNLYPSYKNYTSVYDKNNLLTNKTVMAHGCYLSAEELNVFHERGASIAHCPNSNLSLSSGFLNVLEVLKHEVKIGLGTDVAGGYSYSMLDAIRRAVMVSNILLINKVNEKSLTLKEVFRLATLGGSQALGLDGEIG

6oh9A

0.45

0.44

12.98

1.50

DEthreader

GFVDTHNHVSQYPNVGVFGNSTLLDWLEKYTFPIEAALANENIAREVYNKVISKTLSHGTTTVAYYNTIDLKSTKLLAQLSSLLGQRVLVGKVCMDTNG-PEYYIEDTKTSFESTVKVVKYIRETCDPLVNPIVTPRFAPSCSRELMQQLSKLVKDENIHVQTHLSENKEEIQWVQDLFPECESYTDVYDKYGLLTEKTVLAHCIHLTDAEARVIKQRRCGISHCPISNSSLTSGECRVRWLLDQGIKVGLGTDVSAGHSCSILTTGRQAFAVSRHLAMRETDHAKLSVSECLFLATMGGAQVLRMDETLG

6oh9A

0.45

0.44

12.98

1.67

SPARKS-K

GFVDTHNHVSQYPNVGVFGNSTLLDWLEKYTFPIEAALANENIAREVYNKVISKTLSHGTTTVAYYNTIDLKSTKLLAQLSSLLGQRVLVGKVCMDTNGP-EYYIEDTKTSFESTVKVVKYIRETCDPLVNPIVTPRFAPSCSRELMQQLSKLVKDENIHVQTHLSENKEEIQWVQDLFPECESYTDVYDKYGLLTEKTVLAHCIHLTDAEARVIKQRRCGISHCPISNSSLTSGECRVRWLLDQGIKVGLGTDVSAGHSCSILTTGRQAFAVSRHLAMRETDHAKLSVSECLFLATMGGAQVLRMDETLG

6oh9A

0.45

0.44

12.98

0.92

MapAlign

GFVDTHNHVSQYPNVGVFGNSTLLDWLEKYTFPIEAALANENIAREVYNKVISKTLSHGTTTVAYYNTIDLKSTKLLAQLSSLLGQRVLVGKVCMDTNG-PEYYIEDTKTSFESTVKVVKYIREICDPLVNPIVTPRFAPSCSRELMQQLSKLVKDENIHVQTHLSENKEEIQWVQDLFPECESYTDVYDKYGLLTEKTVLAHCIHLTDAEARVIKQRRCGISHCPISNSSLTSGECRVRWLLDQGIKVGLGTDVSAGHSCSILTTGRQAFAVSRHLAMRETDHAKLSVSECLFLATMGGAQVLRMDETLG

6oh9A

0.45

0.44

12.98

0.70

CEthreader

GFVDTHNHVSQYPNVGVFGNSTLLDWLEKYTFPIEAALANENIAREVYNKVISKTLSHGTTTVAYYNTIDLKSTKLLAQLSSLLGQRVLVGKVCMDTNGPE-YYIEDTKTSFESTVKVVKYIREICDPLVNPIVTPRFAPSCSRELMQQLSKLVKDENIHVQTHLSENKEEIQWVQDLFPECESYTDVYDKYGLLTEKTVLAHCIHLTDAEARVIKQRRCGISHCPISNSSLTSGECRVRWLLDQGIKVGLGTDVSAGHSCSILTTGRQAFAVSRHLAMRETDHAKLSVSECLFLATMGGAQVLRMDETLG

3e0lA

0.99

0.98

27.47

1.54

MUSTER

GLVDTHIHASQYSFAGSSIDLPLLEWLTKYTFPAEHRFQNIDFAEEVYTRVVRRTLKNGTTTACYFATIHTDSSLLLADITDKFGQRAFVGKVCMDLNDTFPEYKETTEESIKETERFVSEMLQKNYSRVKPIVTPGNGV--SETLMGELGNIAKTRDLHIQSHISENRDEVEAVKNLYPSYKNYTSVYDKNNLLTNKTVMAHGCYLSAEELNVFHERGASIAHCPNSNLSLSSGFLNVLEVLKHEVKIGLGTDVAGGYSYSMLDAIRRAVMVSNILLINKVNEKSLTLKEVFRLATLGGSQALGLDGEIG

6sj0A2

0.15

0.14

4.79

1.68

HHsearch

-FVNAHWHEMFFTMRGALRPPSDISATFDRFDGLIEAM-TEDEARAIAEYSMWIQLRGGVTTLGDMGSLN--RPLAMVEAARRLGMRFSASTWASDAVLAPFLRTRDADTVLASFEALLGAVAADPTGRIRCRPNVSYVTNMTDELARGMAELVERHDLPFATHVGALRNEADAMRAYHG--ETGVRRLAEAGLVDERLMAGHSAFLDDQEQKLMLAGRAHISHSPGKYGPSGE-SAVVPALRRAGLDVSLSTDAAALPGAGIAETMRAAWQMYNEMSA---DQTEVLPTDALAMATRIAAKGLRWDDAVG

4dzhA2

0.26

0.24

7.55

3.09

FFAS-3D

GLVNAHTHNPMTLLRGVADDLPLMVWLQQHIWPVEAAVIGPEFVADGTTLAIAEMLRGGTTCVNENYFF----ADVQAAVYKQHGFRALVGAVIIDFPTAW---ASSDDEYFARAGELHDQW--RDDPLISTAFAPHAPYTVNDANFERVRMLADQLDMPVHLHTHETAQEVADSVAQY--GQRPLARLDRLGLVNDRLIAVHMTQLTEAEIHLCAERGVSVVHCPESNLKLASGFCPACALQRASVNLAIGTDGASNNDLDMFSENRTAAILAKAVA---NDATALDAATTLRAATLGGARALGFGDRIG

6oh9A

0.43

12.63

1.02

EigenThreader

GFVDTHNHVSQYPNVGVFGNSTLLDWLEKYTFPIEAALANENIAREVYNKVISKTLSHGTTTVAYYNTIDLKSTKLLAQLSSLLGQRVLVGKVCDTNGPEYY--IEDTKTSFESTVKVVKYIRETIDPLVNPIVTPRFAPSCSRELMQQLSKLVKDENIHVQTHLSENKEEIQWVQDLFPECESYTDVYDKYGLLTEKTVLAHCIHLTDAEARVIKQRRCGISHCPISNSSLTSGECRVRWLLDQGIKVGLGTDVSAGHSCSILTTGRQAFAVSRHLAMRETDHAKLSVSECLFLATMGGAQVLRMDETLG

2uz9A

1.00

28.00

2.47

CNFpred

GLVDTHIHASQYSFAGSSIDLPLLEWLTKYTFPAEHRFQNIDFAEEVYTRVVRRTLKNGTTTACYFATIHTDSSLLLADITDKFGQRAFVGKVCMDLNDTFPEYKETTEESIKETERFVSEMLQKNYSRVKPIVTPRFSLSCSETLMGELGNIAKTRDLHIQSHISENRDEVEAVKNLYPSYKNYTSVYDKNNLLTNKTVMAHGCYLSAEELNVFHERGASIAHCPNSNLSLSSGFLNVLEVLKHEVKIGLGTDVAGGYSYSMLDAIRRAVMVSNILLINKVNEKSLTLKEVFRLATLGGSQALGLDGEIG

3e0lA

0.98

0.97

27.12

1.50

DEthreader

GLVDTHIHASQYSFAGSSIDLPLLEWLTKYTFPAEHRFQNIDFAEEVYTRVVRRTLKNGTTTACYFATIHTDSSLLLADITDKFGQRAFVGKVCMDLNDTFPEYKETTEESIKETERFVSEMLQKNYSRVKPIVTPGN--GVSETLMGELGNIAKTRDLHIQSHISENRDEVEAVKNLYPSYKNYTSVYDKNNLLTNKTVMAHGCYLSAEELNVFHERGASIAHCPNSNLSLSSGFLNVLEVLKHEVKIGLGTDVAGGYSYSMLDAIRRAVMVSNILLINKNEK-SLTLKEVFRLATLGGSQALGLDGEIG

(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	0.9004

(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	6oh9A	0.99	0.53	0.445	0.997	model1_6oh9A.pdb.gz
2	3e0lA	0.97	1.10	0.987	0.994	model1_3e0lA.pdb.gz
3	2i9uA	0.96	1.05	0.384	0.987	model1_2i9uA.pdb.gz
4	2oodA	0.95	1.11	0.301	0.971	model1_2oodA.pdb.gz
5	6ohbA	0.94	1.09	0.359	0.968	model1_6ohbA.pdb.gz
6	3ls9A	0.92	2.02	0.192	0.987	model1_3ls9A.pdb.gz
7	4v1xA	0.90	2.03	0.189	0.968	model1_4v1xA.pdb.gz
8	4dzhA2	0.89	1.96	0.256	0.955	model1_4dzhA2.pdb.gz
9	4dykA	0.89	1.95	0.260	0.952	model1_4dykA.pdb.gz
10	3lnpA	0.86	1.99	0.248	0.932	model1_3lnpA.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	1.00	catalytic activity
GO:0019239	0.99	deaminase activity
GO:0016810	0.96	hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds
GO:0016814	0.94	hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amidines
GO:0043167	0.74	ion binding
GO:0046872	0.72	metal ion binding
GO:0046914	0.71	transition metal ion binding
GO:0008892	0.71	guanine deaminase activity
GO:0008270	0.70	zinc ion 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:0009987	1.00	cellular process
GO:0071704	0.99	organic substance metabolic process
GO:0044237	0.99	cellular metabolic process
GO:0044699	0.91	single-organism process
GO:0044281	0.86	small molecule metabolic process
GO:0044763	0.85	single-organism cellular process
GO:0044238	0.83	primary metabolic process
GO:0006807	0.82	nitrogen compound metabolic process
GO:1901360	0.81	organic cyclic compound metabolic process
GO:0046483	0.81	heterocycle metabolic process
GO:0034641	0.81	cellular nitrogen compound metabolic process
GO:0006725	0.81	cellular aromatic compound metabolic process
GO:1901564	0.80	organonitrogen compound metabolic process
GO:0055086	0.80	nucleobase-containing small molecule metabolic process
GO:0072521	0.77	purine-containing compound metabolic process
GO:0006144	0.76	purine nucleobase metabolic process
GO:0046098	0.75	guanine 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:0044464	0.89	cell part
GO:0044424	0.83	intracellular part
GO:0044444	0.78	cytoplasmic part
GO:0043227	0.78	membrane-bounded organelle
GO:0005829	0.70	cytosol
GO:0070062	0.65	extracellular exosome

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	0.380	1zzmA	0.635	3.19	0.122	0.762	3.1.21.-	253
2	0.267	3e0lA	0.970	1.10	0.987	0.994	3.5.4.3	104,167
3	0.193	2uz9A	0.983	0.94	1.000	1.000	3.5.4.3	12,14,16,19,54,231,259,261,265,269
4	0.158	1p1mA	0.838	2.10	0.234	0.907	3.5.4.28	NA
5	0.105	3iarA	0.753	2.65	0.146	0.862	3.5.4.4	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	0.54	2uz9A	0.983	0.94	1.000	1.000	0.96	XAN	complex1.pdb.gz	8,11,23,26,27,31,254
2	0.23	2oodA	0.961	1.11	0.300	0.987	0.84	GUN	complex2.pdb.gz	8,164,167,203,254
3	0.17	3lsbA	0.924	2.01	0.189	0.987	0.87	RYN	complex3.pdb.gz	8,10,11,137,140,164,167,203,228,235,257
4	0.08	2i9u0	0.965	1.05	0.384	0.987	1.14	III	complex4.pdb.gz	12,13,15,16,17,19,20,22,50,169,230,231,233,235,236,259,269,272,275,276,278,279,286
5	0.04	3o7uA	0.777	2.64	0.153	0.881	0.83	PXN	complex5.pdb.gz	50,53,54,57

	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.