D-I-TASSER Q9Y5B0-D3

D-I-TASSER results for Q9Y5B0-D3

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

Input Sequence in FASTA format

>Q9Y5B0 (151 residues)
NHSRGTEVSEPSPPVRDPEGVTQAPGVEPSNGLEKPARELNGSEAATPRDSPRPGKPDER
DIWPPAQAPTSSQELAGAPEPQGSCAQGGRVAPGQRPAQGATGTDLDFDLSSDSESSSES
EGTKSSSSASDGESEGKRGRQKPKAAPEGAG

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 \| \| \| \| \| \| \| NHSRGTEVSEPSPPVRDPEGVTQAPGVEPSNGLEKPARELNGSEAATPRDSPRPGKPDERDIWPPAQAPTSSQELAGAPEPQGSCAQGGRVAPGQRPAQGATGTDLDFDLSSDSESSSESEGTKSSSSASDGESEGKRGRQKPKAAPEGAG
Prediction	CCCCCCCCCCCCCCCCCHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Confidence	9887767666777778823376567522368888873014798777766777888522368877666766778877789998640137877866678888877766765678877766667765788766676655334446888744589
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 \| \| \| \| \| \| \| NHSRGTEVSEPSPPVRDPEGVTQAPGVEPSNGLEKPARELNGSEAATPRDSPRPGKPDERDIWPPAQAPTSSQELAGAPEPQGSCAQGGRVAPGQRPAQGATGTDLDFDLSSDSESSSESEGTKSSSSASDGESEGKRGRQKPKAAPEGAG
Prediction	8456557346642535437514724424434435433551445542557545344565665444435444446534737545433646654447444565543441414144546556556655445445546576545464464466678
	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

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SS
Seq

CCCCCCCCCCCCCCCCCHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
NHSRGTEVSEPSPPVRDPEGVTQAPGVEPSNGLEKPARELNGSEAATPRDSPRPGKPDERDIWPPAQAPTSSQELAGAPEPQGSCAQGGRVAPGQRPAQGATGTDLDFDLSSDSESSSESEGTKSSSSASDGESEGKRGRQKPKAAPEGAG

4hizA2

0.09

3.32

0.61

CEthreader

TNADLCVTETHSFTVIDDDNYTFAVGYHNGDISPRRLGILYFNNAYSDPSSFTRRTISQEYADNAAEPCIKYYDGILYLTTRGTSTSAAGSTVHHTNLPFAKVGDYLYIFGTERSFGEWEGQELDNRYKGTYPRTFMCKINVSSWPVSLSN

3rjvA

0.04

0.03

1.81

0.47

EigenThreader

EPGSQYQQQAEAGD---------RRAQYYLADWAQKAAAQGDGDALALLAQLKAEKAVEAGSKSGEIVLARVLVNRQLQDAARDSESDAAVDAQLFKGSSSLSRTGYAEYWAGFQQGE---KGFIEPNKQKALHWLNVSCLEGFDTGCEEF

7kwzA

0.12

0.10

3.48

0.38

FFAS-3D

--------------------GGNPGGFGNQGGFGNS----RGGGAGLGNNQGSNMGGGMN-----FGAFSINPAMMAAAQAALQSSWGMMGMLASQQNQSGPSGN--NQNQGNMQREPNQAFGSGNNSYSGSNSGAAIGWGSASNAGSGSG

7jjvA

0.13

0.11

3.67

1.38

SPARKS-K

DGLDGADGTSNGQAGASGLAGGPNC-----NG-GKGGKGAPGVGTAGGAGGVGGAGGTGNTNGGAGGSGGNSDVAAGGAGAAGGAAGGAGTG-------GTGGNGGAG----------------KPGGAPGAGGAGTPAGSAGSPGQTTVL

5h7uA

0.32

0.08

2.40

0.31

CNFpred

-----------------------------------------------------------------------------------------------------------------SESELDQESDDSFFNESESESEADVDSDDSDAKPYGPD

2aw3A

0.05

0.04

1.91

0.67

DEthreader

SPFAKPVANQRHV-N--------YISFLGGLGRLAACFLSMAATGY--NYQYGLVLYQQYFQCACSVAILHHRKLHELADYEV--AIPELLT--TF-------GITPRWICNKLAEVKV-T-GIEINPQAIFEKLIPAKLFSSDRRDYQAQ

2pffB

0.12

0.11

3.97

0.87

MapAlign

GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG-----GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG----GGGGGGGGGGGGGGGGGG-

4k0mC

0.11

4.03

0.91

MUSTER

SLPHGLGKQVRVLAIAKGEKIKEA-EEAGADYVGGEEIIQAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA

5h7uA

0.24

0.13

3.92

0.65

HHsearch

------------------------------------------SESELDDDSFF----NESESESEAD--VDSDD-SDAKGPDWF---------KKSEFRKQGGGSNKFLKSSSDEESD--------------EEDGKKVVKSAKEKLLDEM

1j0nA2

0.12

0.11

3.99

0.49

CEthreader

PIASGTGTSSWTGGVSLAGQYGASGMDLSYGAYNLSARKSISSTAGIPIETVVDNRKLNGAGDNASTGLGVAQTLTGVNWVHLAGNTADGSDIGYYFPGGATLQTKREARTGTW--------KQINNRPATPSTAVTRNYETMWIDHGTNP

(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	0.4218

(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	2jbvB	0.42	4.86	0.053	0.735	model1_2jbvB.pdb.gz
2	6ebnA	0.42	5.52	0.057	0.795	model1_6ebnA.pdb.gz
3	1x31B	0.42	4.78	0.055	0.702	model1_1x31B.pdb.gz
4	7duwA	0.41	5.68	0.046	0.801	model1_7duwA.pdb.gz
5	3qm3A	0.41	4.94	0.030	0.729	model1_3qm3A.pdb.gz
6	1js4A	0.41	5.53	0.048	0.762	model1_1js4A.pdb.gz
7	1kc7A	0.41	5.52	0.060	0.768	model1_1kc7A.pdb.gz
8	7bfqB1	0.40	5.34	0.058	0.735	model1_7bfqB1.pdb.gz
9	6tepA	0.40	5.40	0.087	0.748	model1_6tepA.pdb.gz
10	3h7fB	0.40	5.37	0.096	0.742	model1_3h7fB.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:0008420	1.00	CTD phosphatase 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:0009987	0.97	cellular process
GO:0044260	0.95	cellular macromolecule metabolic process
GO:0044238	0.95	primary metabolic process
GO:0031326	0.94	regulation of cellular biosynthetic process
GO:0019219	0.94	regulation of nucleobase-containing compound metabolic process
GO:0010556	0.94	regulation of macromolecule biosynthetic process
GO:0010468	0.94	regulation of gene expression
GO:0070940	0.93	dephosphorylation of RNA polymerase II C-terminal domain

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:0044428	1.00	nuclear part
GO:0032991	0.91	macromolecular complex
GO:0043234	0.90	protein complex
GO:0044451	0.89	nucleoplasm part
GO:0061695	0.88	transferase complex, transferring phosphorus-containing groups
GO:0055029	0.87	nuclear DNA-directed RNA polymerase complex
GO:0016591	0.86	DNA-directed RNA polymerase II, holoenzyme

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	1gynA	0.415	5.09	0.041	0.755	4.1.2.13	NA
2	0.060	3kaoA	0.401	4.78	0.047	0.689	4.1.2.40	NA
3	0.060	3c46B	0.314	5.23	0.053	0.556	2.7.7.6	39
4	0.060	2gmjA	0.396	4.75	0.057	0.656	1.5.5.1	NA
5	0.060	2c44C	0.388	5.55	0.053	0.748	4.1.99.1	107

	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	1vrpB	0.288	5.97	0.036	0.609	0.13	IOM	complex1.pdb.gz	26,27,77
2	0.01	2h94A	0.405	5.28	0.043	0.742	0.11	FAD	complex2.pdb.gz	27,55,56,66,67,68,69,70
3	0.01	1vrqB	0.307	5.55	0.071	0.603	0.18	DMG	complex3.pdb.gz	26,28,30
4	0.01	1u6rA	0.298	5.85	0.029	0.616	0.15	ADP	complex4.pdb.gz	4,13,14
5	0.01	1qh40	0.399	5.39	0.050	0.735	0.12	III	complex5.pdb.gz	33,34,35,36,37,89,91,94,98
6	0.01	2dw4A	0.398	5.55	0.049	0.788	0.11	FAD	complex6.pdb.gz	27,44,45,47,63,65,110
7	0.01	1vrpA	0.385	5.13	0.040	0.702	0.15	ADP	complex7.pdb.gz	22,24,25
8	0.01	2gmhA	0.403	4.66	0.064	0.662	0.31	SF4	complex8.pdb.gz	36,37,41,42,94,95
9	0.01	1u6rB	0.334	5.73	0.046	0.675	0.17	ADP	complex9.pdb.gz	11,13,16,92,94,99
10	0.01	1vrqB	0.307	5.55	0.071	0.603	0.27	FMN	complex10.pdb.gz	29,30,33,132

	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, Qiqige Wuyun, Yang Li, Quancheng Liu, Xiaogen Zhou, Yiheng Zhu, P. Lydia Freddolino, Yang Zhang. Integrating deep learning potentials with I-TASSER for single- and multi-domain protein structure prediction. Submitted. 2023.