D-I-TASSER Q9UJT1-D1

D-I-TASSER results for Q9UJT1-D1

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

Input Sequence in FASTA format

>Q9UJT1 (315 residues)
MSIVTVQLGQCGNQIGFEVFDALLSDSHSSQGLCSMRENEAYQASCKERFFSEEENGVPI
ARAVLVDMEPKVINQMLSKAAQSGQWKYGQHACFCQKQGSGNNWAYGYSVHGPRHEESIM
NIIRKEVEKCDSFSGFFIIMSMAGGTGSGLGAFVTQNLEDQYSNSLKMNQIIWPYGTGEV
IVQNYNSILTLSHLYRSSDALLLHENDAIHKICAKLMNIKQISFSDINQVLAHQLGSVFQ
PTYSAESSFHYRRNPLGDLMEHLVPHPEFKMLGKAWNMFASKAYIHQYTKFGIEEEDFLD
SFTSLEQVVASYCNL

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 200 220 240 260 280 300 \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| MSIVTVQLGQCGNQIGFEVFDALLSDSHSSQGLCSMRENEAYQASCKERFFSEEENGVPIARAVLVDMEPKVINQMLSKAAQSGQWKYGQHACFCQKQGSGNNWAYGYSVHGPRHEESIMNIIRKEVEKCDSFSGFFIIMSMAGGTGSGLGAFVTQNLEDQYSNSLKMNQIIWPYGTGEVIVQNYNSILTLSHLYRSSDALLLHENDAIHKICAKLMNIKQISFSDINQVLAHQLGSVFQPTYSAESSFHYRRNPLGDLMEHLVPHPEFKMLGKAWNMFASKAYIHQYTKFGIEEEDFLDSFTSLEQVVASYCNL
Prediction	CSSSSSSCCCCHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCSSSSSSSCCCCCCCSCCCCCCCCCCCCCCCCCCSSSCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCHHHCHCCCCCCCCCCCHHHHHHHHHHHHHCHCCCCSSSSCCCCCCCCSSSCCCCHHHHHHHHHHCCSSSSCCCHHHHHHHHHHCCCCCCCCCCCCHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHHHHHCCCCCCCSSSSSCCCCCCCHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHCCCC
Confidence	908999517626899999999999986189987753787533232323421114788632345551699611011233445578767886524642578876654321133036789998898877772798012000123579988865889999999973011231156457767873011022144321466504512311432788998663189999833342244432100124566555689998998999999708998714643135665662555543215673799999985501456650589
	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 \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| MSIVTVQLGQCGNQIGFEVFDALLSDSHSSQGLCSMRENEAYQASCKERFFSEEENGVPIARAVLVDMEPKVINQMLSKAAQSGQWKYGQHACFCQKQGSGNNWAYGYSVHGPRHEESIMNIIRKEVEKCDSFSGFFIIMSMAGGTGSGLGAFVTQNLEDQYSNSLKMNQIIWPYGTGEVIVQNYNSILTLSHLYRSSDALLLHENDAIHKICAKLMNIKQISFSDINQVLAHQLGSVFQPTYSAESSFHYRRNPLGDLMEHLVPHPEFKMLGKAWNMFASKAYIHQYTKFGIEEEDFLDSFTSLEQVVASYCNL
Prediction	411000000000000011003100221001233230443442343232221333343422322022345332223223322232303241212122322021001222212222012201421441143020021020011012232000000002102412232031101011342242002112011012223210410232433201110242141640314321420222133223332213231412212024004200020200000200001134422441344604542024003504413462477
	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                 220                 240                 260                 280                 300

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

SS
Seq

CSSSSSSCCCCHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCSSSSSSSCCCCCCCSCCCCCCCCCCCCCCCCCCSSSCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCHHHCHCCCCCCCCCCCHHHHHHHHHHHHHCHCCCCSSSSCCCCCCCCSSSCCCCHHHHHHHHHHCCSSSSCCCHHHHHHHHHHCCCCCCCCCCCCHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHHHHHCCCCCCCSSSSSCCCCCCCHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHCCCC
MSIVTVQLGQCGNQIGFEVFDALLSDSHSSQGLCSMRENEAYQASCKERFFSEEENGVPIARAVLVDMEPKVINQMLSKAAQSGQWKYGQHACFCQKQGSGNNWAYGYSVHGPRHEESIMNIIRKEVEKCDSFSGFFIIMSMAGGTGSGLGAFVTQNLEDQYSNSLKMNQIIWPYGTGEVIVQNYNSILTLSHLYRSSDALLLHENDAIHKICAKLMNIKQISFSDINQVLAHQLGSVFQPTYSAESSFHYRRNPLGDLMEHLVPHPEFKMLGKAWNMFASKAYIHQYTKFGIEEEDFLDSFTSLEQVVASYCNL

6kppA

0.24

0.23

7.32

1.50

DEthreader

RECISIHVGQAGVQIGNACWELYCLEHGIQ--GQMPSDKT-GGDDSFNTFFSETGAGKHVPRAVFVDLEPTVIDEVRTGTYR---QLFHPEQLITGKEDAANNYARGHYTIGKEIIDLVLDRIRKLADQCTGLQGFLVFHSFGGGTGSGFTSLLMERLSVDYGKKSKLEFSIYPAPQSTAVVEPYNSILTTHTTLEHSDCAFMVDNEAIYDICRRNLDIERPTYTNLNRLISQIVSSITASLRF-DG-ALNVDLEFQNLVHPLNIAAWARLDHKFDLMYAKRAFVHWYVGEGMEEGEFSEAREDMAALEKDYEEV

6kppA1

0.25

0.24

7.57

2.62

SPARKS-K

RECISIHVGQAGVQIGNACWELYCLEHGIQP-DGQMPSTIGGGDDSFNTFFSETGAGKHVPRAVFVDLEPTVIDEVRTGTY---RQLFHPEQLITGKEDAANNYARGHYTIGKEIIDLVLDRIRKLADQCTGLQGFLVFHSFGGGTGSGFTSLLMERLSVDYGKKSKLEFSIYPAPQSTAVVEPYNSILTTHTTLEHSDCAFMVDNEAIYDICRRNLDIERPTYTNLNRLISQIVSSITASLRFDGA----LNVDLTEFQTNLVPYAWARLDHKFDLMYAKRAFVHWYVGEGMEEGEFSEAREDMAALEKDYEEV

6kppB

0.25

0.24

7.48

1.39

MapAlign

REIVHIQAGQCGNQIGAKFWEVISDEHG-IDPTGSYHGDSDLQLERINVYYNEATGNKYVPRAILVDLEPGTMDSVRSGPF---GQIFRPDNFVFGQSGAGNNWAKGHYTEGAELVDSVLDVVRKESESCDCLQGFQLTHSLGGGTGSGMGTLLISKIREEYPDRIMNTFSVMPSKVSDTVVEPYNATLSVHQLVENTDETYCIDNEALYDICFRTLKLTTPTYGDLNHLVSATMSGVTTCLRF----PGQLNADLRKLAVNAIQELFKRISEQFTAMFRRKAFLHWYTGEGMDEMEFTEAESNMNDLVSEYQ--

6kppB

0.24

7.42

0.90

CEthreader

REIVHIQAGQCGNQIGAKFWEVISDEHGIDP-TGSYHGDSDLQLERINVYYNEATGNKYVPRAILVDLEPGTMDSVRSGPFG---QIFRPDNFVFGQSGAGNNWAKGHYTEGAELVDSVLDVVRKESESCDCLQGFQLTHSLGGGTGSGMGTLLISKIREEYPDRIMNTFSVMPSKVSDTVVEPYNATLSVHQLVENTDETYCIDNEALYDICFRTLKLTTPTYGDLNHLVSATMSGVTTCLRFPGQLNRMSMKEVDEQMLNVIQELFKRISEQFTAMFRRKAFLHWYTGEGMDEMEFTEAESNMNDLVSEYQQY

6gj4A1

0.26

0.25

7.75

2.34

MUSTER

RECISIHVGQAGVQIGNACWELYCLEHGI-QPDGQMPSDKTGGDDSFNTFFSETGAGKHVPRAVFVDLEPTVIDEVRTGTY---RQLFHPEQLITGKEDAANNYARGHYTIGKEIIDLVLDRIRKLADQCTGLQGFLVFHSFGGGTGSGFTSLLMERLSVDYGKKSKLEFSIYPAPVSTAVVEPYNSILTTHTTLEHSDCAFMVDNEAIYDICRRNLDIERPTYTNLNRLISQIVSSITASLRFDGA----LNVDLTEFQTNLVPYPRARLDHKFDLMYAKRAFVHWYVGEGMEEGEFSEAREDMAALEKDYEEV

6gj4B

0.25

7.66

2.95

HHsearch

REIVHIQAGQCGNQIGAKFWEVISDEHGIDP-TGSYHGDSDLQLERINVYYNEATGNKYVPRAILVDLEPGTMDSVRSGPF---GQIFRPDNFVFGQSGAGNNWAKGHYTEGAELVDSVLDVVRKESESCDCLQGFQLTHSLGGGTGSGMGTLLISKIREEYPDRIMNTFSVMPSPVSDTVVEPYNATLSVHQLVENTDETYCIDNEALYDICFRTLKLTTPTYGDLNHLVSATMSGVTTCLRFPGQL----NADLRKLAVNMVPELFKRISEQFTAMFRRKAFLHWYTGEGMDEMEFTEAESNMNDLVSEYQQY

6gj4B

0.26

0.25

7.83

2.89

FFAS-3D

MEIVHIQAGQCGNQIGAKFWEVISDEHG-IDPTGSYHGDSDLQLERINVYYNEATGNKYVPRAILVDLEPGTMDSVRSGPF---GQIFRPDNFVFGQSGAGNNWAKGHYTEGAELVDSVLDVVRKESESCDCLQGFQLTHSLGGGTGSGMGTLLISKIREEYPDRIMNTFSVMPSPKSDTVVEPYNATLSVHQLVENTDETYCIDNEALYDICFRTLKLTTPTYGDLNHLVSATMSGVTTCLRFP----GQLNADLRKLAVNMVPFPRKRISEQFTAMFRRKAFLHWYTGEGMDEMEFTEAESNMNDLVSEYQQY

6kppA1

0.23

7.07

1.52

EigenThreader

RECISIHVGQAGVQIGNACWELYCLEHGIQPDGQMPSDKTIGGGDDFNTFFSETGAGKHVPRAVFVDLEPTVIDEVRTGTY---RQLFHPEQLITGKEDAANNYARGHYTIGKEIIDLVLDRIRKLADQCTGLQGFLVFHSFGGGTGSGFTSLLMERLSVDYGKKSKLEFSIPAPQVSTAVVEPYNSILTTHTTLEHSDCAFMVDNEAIYDICRRNLDIERPTYTNLNRLISQIVSSITASLRF---DGALNVDLTEFQTNLVIAEAWARLDHKFDLMYAKRAFVHWYVGEGMEEGEFSEAREDMAALEKDYEEV

3rycB

0.23

0.22

6.76

2.44

CNFpred

REIVHIQAGQCGNQIGAKFWEVISDEHGIDP-TGSYHGDSDLQLERINVYYNEATGNKYVPRAILVDLEPGTMDSVRSGP---FGQIFRPDNFVFGQSGAGNNWAKGHYTEGAELVDSVLDVVRKESESCDCLQGFQLTHSLGGGTGSGMGTLLISKIREEYPDRIMNTFSVMPSPKVDTVVEPYNATLSVHQLVENTDETYSIDNEALYDICFRTLKLTTPTYGDLNHLVSATMSGVTTCLRFPGQL----NADLRKLAVNMVPFPRL--------HFFMPGFAPLTSRGSQQYRAL-----TVPELTQQMFDS

6gj4B

0.24

0.23

7.23

1.50

DEthreader

REIVHIQAGQCGNQIGAKFWEVISDEHGI---GSYHGDSDLQLERIN-VYYNEATGNKYVPRAILVDLEPGTMDSVRSGPFG---QIFRPDNFVFGQSGAGNNWAKGHYTEGAELVDSVLDVVRKESESCDCLQGFQLTHSLGGGTGSGMGTLLISKIREEYPDRIMNTFSVMPSPKSDTVVEPYNATLSVHQLVENTDETYCIDNEALYDICFRTLKLTTPTYGDLNHLVSATMSGVTTCLRFPGQ-LNADLRKLANMFTIGNIQLFKRISEQFTAMFRRKAFLHWYTGEGMDEMEFTEAESNMNDLVSEYQQY

(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	0.8764

(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	6gj4B	0.95	1.14	0.240	0.978	model1_6gj4B.pdb.gz
2	6kppA	0.94	1.41	0.241	0.971	model1_6kppA.pdb.gz
3	3cb2A	0.93	1.78	0.300	0.984	model1_3cb2A.pdb.gz
4	2btoB	0.92	1.77	0.234	0.965	model1_2btoB.pdb.gz
5	5flzC	0.89	2.26	0.247	0.978	model1_5flzC.pdb.gz
6	1tubA1	0.69	2.51	0.233	0.759	model1_1tubA1.pdb.gz
7	3r3sA	0.47	4.27	0.069	0.619	model1_3r3sA.pdb.gz
8	1cruB	0.36	6.69	0.038	0.625	model1_1cruB.pdb.gz
9	3ba6A	0.29	7.14	0.045	0.549	model1_3ba6A.pdb.gz
10	3vhlA	0.29	5.99	0.030	0.460	model1_3vhlA.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:0005198	0.98	structural molecule activity
GO:0000166	0.98	nucleotide binding
GO:0005525	0.97	GTP binding
GO:0005200	0.97	structural constituent of cytoskeleton
GO:0003924	0.94	GTPase 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:0009987	0.99	cellular process
GO:0044699	0.98	single-organism process
GO:0044763	0.97	single-organism cellular process
GO:0016043	0.92	cellular component organization
GO:0007017	0.89	microtubule-based process
GO:0006996	0.88	organelle organization
GO:1902589	0.84	single-organism organelle organization
GO:0000226	0.83	microtubule cytoskeleton organization
GO:0022402	0.78	cell cycle process
GO:0007020	0.74	microtubule nucleation
GO:0031122	0.73	cytoplasmic microtubule organization
GO:1903047	0.68	mitotic cell cycle process
GO:0022414	0.64	reproductive process
GO:0050794	0.62	regulation of cellular process
GO:0050896	0.58	response to stimulus
GO:0044702	0.57	single organism reproductive process
GO:0051179	0.56	localization
GO:1903046	0.55	meiotic cell cycle process
GO:0051641	0.54	cellular localization
GO:0006928	0.54	movement of cell or subcellular component
GO:0000086	0.54	G2/M transition of mitotic cell cycle
GO:0051234	0.53	establishment of localization
GO:0000212	0.53	meiotic spindle organization
GO:0006810	0.52	transport
GO:0051649	0.51	establishment of localization in cell
GO:0051640	0.51	organelle localization

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	1.00	cell part
GO:0044424	0.98	intracellular part
GO:0044446	0.88	intracellular organelle part
GO:0044430	0.84	cytoskeletal part
GO:0043226	0.72	organelle
GO:0005874	0.71	microtubule
GO:0043229	0.65	intracellular organelle
GO:0044444	0.64	cytoplasmic part
GO:0043227	0.57	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	0.060	3kvnX	0.485	5.09	0.071	0.686	3.1.1.1	172
2	0.060	1nasA	0.479	4.40	0.084	0.635	1.1.1.153	NA
3	0.060	2pm8A	0.477	5.24	0.024	0.689	3.1.1.8	NA
4	0.060	1z6zA	0.479	4.48	0.102	0.638	1.1.1.153	NA
5	0.060	2masA	0.496	4.90	0.079	0.695	3.2.2.1	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	0.77	1z5wA	0.899	1.64	0.313	0.943	1.49	GTP	complex1.pdb.gz	9,10,11,14,101,102,141,143,144,145,146,172,174,183,206,224,227,228
2	0.46	3n2gD	0.947	1.60	0.241	0.987	1.38	GDP	complex2.pdb.gz	9,10,11,15,141,143,146,147,179,206,224,227,228
3	0.38	3e22C	0.925	1.31	0.243	0.956	1.68	MG	complex3.pdb.gz	99,102,145,146
4	0.06	3e22B	0.946	1.30	0.240	0.978	1.34	TZT	complex4.pdb.gz	10,14,72,178,179,222,223,224,225
5	0.06	2btq2	0.881	1.75	0.264	0.927	0.97	III	complex5.pdb.gz	98,102,106,179,180,181,278,281,282,283,284,286,287

	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.