D-I-TASSER Q9UL01-D3

D-I-TASSER results for Q9UL01-D3

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

Input Sequence in FASTA format

>Q9UL01 (290 residues)
SVPPPDFGTPTLHYFEDWGVVTYGSALPAEINRSFLSFKSGKLGGRAIYDIVHRNKYKDW
IKGWRNFNAGHEHPDQNSFTFAPNGVPFITEALYGPKYTFFNNVLMFSPAVSKSCFSPWV
GQVTEDCSSKWSKYKHDLAASCQGRVVAAEEKNGVVFIRGEGVGAYNPQLNLKNVQRNLI
LLHPQLLLLVDQIHLGEESPLETAASFFHNVDVPFEETVVDGVHGAFIRQRDGLYKMYWM
DDTGYSEKATFASVTYPRGYPYNGTNYVNVTMHLRSPITRAAYLFIGPSI

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 200 220 240 260 280 \| \| \| \| \| \| \| \| \| \| \| \| \| \| SVPPPDFGTPTLHYFEDWGVVTYGSALPAEINRSFLSFKSGKLGGRAIYDIVHRNKYKDWIKGWRNFNAGHEHPDQNSFTFAPNGVPFITEALYGPKYTFFNNVLMFSPAVSKSCFSPWVGQVTEDCSSKWSKYKHDLAASCQGRVVAAEEKNGVVFIRGEGVGAYNPQLNLKNVQRNLILLHPQLLLLVDQIHLGEESPLETAASFFHNVDVPFEETVVDGVHGAFIRQRDGLYKMYWMDDTGYSEKATFASVTYPRGYPYNGTNYVNVTMHLRSPITRAAYLFIGPSI
Prediction	CCCCCCCCCCCCSSSCCCCSSSSCCCCCCCCCCSSSSSSCCCCCCCCHHHHCCCCCCHHHHCCCCCCCCCCCCCCCCSSSSSCCCSSSSSCCCCCCCCCCCCCSSSSCCCCCCCCCCCCCCSSSSCCCCCCCCCCCCCCCCCCCSSSSSSSCCCSSSSSSSHHHCCCCCCCCSSSSSSSSSSCCCSSSSSSSSSSCCCCCHHHHHHHHCCCCCCCSSSSCCCSSSSSSSCCCCSSSSSSSCCCCCCCCCHSHHHHCCCCCCCCCCSSSSSSSSCCCCCSSSSSSSSCCCC
Confidence	98999889986225378317998278988999769999537876543011013333112210212489987678898489942994888506877532345754776487653234543334401675401014556654444359999714998999995134068645944999999998698899999998089981577776540368763232115532477642786278999838999751000000122235777632788987458973168999857889
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 200 220 240 260 280 \| \| \| \| \| \| \| \| \| \| \| \| \| \| SVPPPDFGTPTLHYFEDWGVVTYGSALPAEINRSFLSFKSGKLGGRAIYDIVHRNKYKDWIKGWRNFNAGHEHPDQNSFTFAPNGVPFITEALYGPKYTFFNNVLMFSPAVSKSCFSPWVGQVTEDCSSKWSKYKHDLAASCQGRVVAAEEKNGVVFIRGEGVGAYNPQLNLKNVQRNLILLHPQLLLLVDQIHLGEESPLETAASFFHNVDVPFEETVVDGVHGAFIRQRDGLYKMYWMDDTGYSEKATFASVTYPRGYPYNGTNYVNVTMHLRSPITRAAYLFIGPSI
Prediction	84444745333122054000000114144564110000100321132224224444244225315423441412120000013412200020012431032311021242344433441422023433131242546333513120211245431010102025214672415402000000453000000203355734142012203234241443434412102053463301000013433344230343524461544212101012314440010000031255
	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

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

SS
Seq

CCCCCCCCCCCCSSSCCCCSSSSCCCCCCCCCCSSSSSSCCCCCCCCHHHHCCCCCCHHHHCCCCCCCCCCCCCCCCSSSSSCCCSSSSSCCCCCCCCCCCCCSSSSCCCCCCCCCCCCCCSSSSCCCCCCCCCCCCCCCCCCCSSSSSSSCCCSSSSSSSHHHCCCCCCCCSSSSSSSSSSCCCSSSSSSSSSSCCCCCHHHHHHHHCCCCCCCSSSSCCCSSSSSSSCCCCSSSSSSSCCCCCCCCCHSHHHHCCCCCCCCCCSSSSSSSSCCCCCSSSSSSSSCCCC
SVPPPDFGTPTLHYFEDWGVVTYGSALPAEINRSFLSFKSGKLGGRAIYDIVHRNKYKDWIKGWRNFNAGHEHPDQNSFTFAPNGVPFITEALYGPKYTFFNNVLMFSPAVSKSCFSPWVGQVTEDCSSKWSKYKHDLAASCQGRVVAAEEKNGVVFIRGEGVGAYNPQLNLKNVQRNLILLHPQLLLLVDQIHLGEESPLETAASFFHNVDVPFEETVVDGVHGAFIRQRDGLYKMYWMDDTGYSEKATFASVTYPRGYPYNGTNYVNVTMHLRSPITRAAYLFIGPSI

6hznA

0.93

0.89

25.08

1.33

DEthreader

-----DFGTPTLHYFEDWGVVTYGSALPAEINRSFLSFKSGKLGGRAIYIVHNYDWIK-GW--R-NFNAGHEHPDQNSFTFAPNGVPFITEALYGPKYTFFNNVLMFSPAVSKSCFSPWVGQVEDCSSKWSKYK-HDLAASCQGRVVAAEEKNGVVFIRGEGVGAYNPQLNLKNVQRNLILLHPQLLLLVDQIHLGEESPLETAASFFHNVDVPFEETVVDGVHGAFIRQRDGLYKMYWMDDTGYSEKATFASVTYPRGYPYNGTNYVNVTMHLRSPITRAAYLFIGPSI

6hznA

1.00

28.00

2.73

SPARKS-K

SVPPPDFGTPTLHYFEDWGVVTYGSALPAEINRSFLSFKSGKLGGRAIYDIVHRNKYKDWIKGWRNFNAGHEHPDQNSFTFAPNGVPFITEALYGPKYTFFNNVLMFSPAVSKSCFSPWVGQVTEDCSSKWSKYKHDLAASCQGRVVAAEEKNGVVFIRGEGVGAYNPQLNLKNVQRNLILLHPQLLLLVDQIHLGEESPLETAASFFHNVDVPFEETVVDGVHGAFIRQRDGLYKMYWMDDTGYSEKATFASVTYPRGYPYNGTNYVNVTMHLRSPITRAAYLFIGPSI

6hznA

0.96

0.93

26.11

1.50

MapAlign

-------GTPTLHYFEDWGVVTYGSALPAEINRSFLSFKSGKLGGRAIYDIVHRNKYKDWIKGWRNFNAGHEHPDQNSFTFAPNGVPFITEALYGPKYTFFNNVLMFSPAVSKSCFSPWVGQVTEDCSSKWSKYKHDLAASCQGRVVAAEEKNGVVFIRGEGVGAYNPQLNLKNVQRNLILLHPQLLLLVDQIHLGESPLETAASFFHNVD-VPFEETVVDGVHGAFIRQRDGLYKMYWMDDTGYSEKATFASVTYPRGYPYNGTNYVNVTMHLRSPITRAAYLFIGPSI

6hznA

1.00

28.00

1.30

CEthreader

SVPPPDFGTPTLHYFEDWGVVTYGSALPAEINRSFLSFKSGKLGGRAIYDIVHRNKYKDWIKGWRNFNAGHEHPDQNSFTFAPNGVPFITEALYGPKYTFFNNVLMFSPAVSKSCFSPWVGQVTEDCSSKWSKYKHDLAASCQGRVVAAEEKNGVVFIRGEGVGAYNPQLNLKNVQRNLILLHPQLLLLVDQIHLGEESPLETAASFFHNVDVPFEETVVDGVHGAFIRQRDGLYKMYWMDDTGYSEKATFASVTYPRGYPYNGTNYVNVTMHLRSPITRAAYLFIGPSI

6hznA

1.00

28.00

1.80

MUSTER

SVPPPDFGTPTLHYFEDWGVVTYGSALPAEINRSFLSFKSGKLGGRAIYDIVHRNKYKDWIKGWRNFNAGHEHPDQNSFTFAPNGVPFITEALYGPKYTFFNNVLMFSPAVSKSCFSPWVGQVTEDCSSKWSKYKHDLAASCQGRVVAAEEKNGVVFIRGEGVGAYNPQLNLKNVQRNLILLHPQLLLLVDQIHLGEESPLETAASFFHNVDVPFEETVVDGVHGAFIRQRDGLYKMYWMDDTGYSEKATFASVTYPRGYPYNGTNYVNVTMHLRSPITRAAYLFIGPSI

6hznA

0.99

0.98

27.53

3.96

HHsearch

SVPPPDFGTPTLHYFEDWGVVTYGSALPAEINRSFLSFKSGKLGGRAIYDIVHRNKYKDWIKGWRNFNAGHEHPDQNSFTFAPNGVPFITEALYGPKYTFFNNVLMFSPAVSKSCFSPWVGQVTEDCSSKWSKYKHDLAASCQGRVVAAEEKNGVVFIRGEGVGAYNPQLNLKNVQRNLILLHPQLLLLVDQIHLGEESPLETA-ASFFHVDVPFEETVVDGVHGAFIRQRDGLYKMYWMDDTGYSEKATFASVTYPRGYPYNGTNYVNVTMHLRSPITRAAYLFIGPSI

6hznA3

1.00

0.90

25.10

2.12

FFAS-3D

-----------------------------EINRSFLSFKSGKLGGRAIYDIVHRNKYKDWIKGWRNFNAGHEHPDQNSFTFAPNGVPFITEALYGPKYTFFNNVLMFSPAVSKSCFSPWVGQVTEDCSSKWSKYKHDLAASCQGRVVAAEEKNGVVFIRGEGVGAYNPQLNLKNVQRNLILLHPQLLLLVDQIHLGEESPLETAASFFHNVDVPFEETVVDGVHGAFIRQRDGLYKMYWMDDTGYSEKATFASVTYPRGYPYNGTNYVNVTMHLRSPITRAAYLFIGPS-

6hznA3

0.76

0.67

18.94

1.42

EigenThreader

-----------------------------EINRSFLSFKSGKLGGRAIYDIVHRNKYKDWIKGWRNFNAGHEHPDQNSFTFAPNGVPFITEALYGPKYTFFNNVLMFSPAVSKSCFSPWVGQVTEDCSSKWSKYKHDLAASCQGRVVAAEEKNGVVFIRGEGVGA--YNPQLNLVQRNLILLHPQLLLLDQIHLGEESPLETAASFFHNVDV-PFEETVVDGVHGAFIRQRDGLYKMYWMDGYSEKATFASVTY---PRGYPYNGTNYVNVTMRSPIT-RAAYLFIGPSI

3aflA

0.19

0.16

5.10

3.08

CNFpred

VEAVSPADLPALAVFDDIGWATIQKDMEDPDRHLQFVFKSSPYG-----------------------SLSASHGDQNAFVLYAHGEDLAIQSGYYV-QTRSKNAVLIGG----------KGQYAEK--------DKALARRAAGRIVSVEEQPGHVRIVGDATAAYQVANLVQKVLRETHFVNDSYFVIVDEVECS----EPQELQWLCHTLGAPQTG----RSSFRYNGRKAGFYGQFVYSS--GGTPQISAVEGFPDID-DIHHHVCATVPA-ATRHRLVTLLVPYSL

6hznA3

0.89

0.78

21.92

1.17

DEthreader

-----------------------------EINRSFLSFKSGKLGGRAIYIVHNYKDWIKGW--R-NFNAGHEHPDQNSFTFAPNGVPFITEALYGPKYTFFNNVLMFSPAVSKSCFSPWVGQVEDCSSKW-KYK-HDLAASCQGRVVAAEEKNGVVFIRGEGVGAYNPQLNLKNVQRNLILLHPQLLLLVDQIHLGESPLETAAS-FFHNVDVPFEETVVDGVHGAFIRQRDGLYKMYWMDDTGYSEKATFASVTYPRGYPYNGTNYVNVTMHLRSPITRAAYLFIGPSI

(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	0.8453

(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	6hznA	0.99	0.53	1.000	1.000	model1_6hznA.pdb.gz
2	3a0oA	0.73	2.70	0.196	0.828	model1_3a0oA.pdb.gz
3	6ljaA	0.71	2.67	0.148	0.814	model1_6ljaA.pdb.gz
4	2futA	0.70	3.56	0.135	0.852	model1_2futA.pdb.gz
5	4neiA	0.69	3.24	0.114	0.814	model1_4neiA.pdb.gz
6	4fnvA	0.68	3.07	0.133	0.797	model1_4fnvA.pdb.gz
7	5jmdA	0.67	2.76	0.112	0.769	model1_5jmdA.pdb.gz
8	3etpA	0.30	4.44	0.068	0.403	model1_3etpA.pdb.gz
9	2w39A	0.29	6.30	0.047	0.493	model1_2w39A.pdb.gz
10	3h9uC2	0.29	6.27	0.068	0.493	model1_3h9uC2.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:0047757	1.00	chondroitin-glucuronate 5-epimerase 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:0030205	1.00	dermatan sulfate metabolic process
GO:0044249	0.85	cellular biosynthetic process
GO:0009059	0.85	macromolecule biosynthetic process
GO:0030208	0.84	dermatan sulfate biosynthetic 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:0044444	1.00	cytoplasmic part
GO:0043226	0.90	organelle
GO:0043231	0.89	intracellular membrane-bounded organelle
GO:0005794	0.86	Golgi apparatus
GO:0005783	0.86	endoplasmic reticulum
GO:0044422	0.56	organelle part
GO:0044446	0.55	intracellular organelle part
GO:0016020	0.55	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	0.067	3mwxA	0.615	3.44	0.097	0.745	5.1.3.3	NA
2	0.067	2htaA	0.597	3.68	0.093	0.745	5.1.3.-	NA
3	0.066	3imhA	0.625	3.61	0.054	0.769	5.1.3.3	NA
4	0.066	1l7kB	0.613	3.69	0.059	0.762	5.1.3.3	NA
5	0.066	1lurA	0.585	3.92	0.065	0.738	5.1.3.3	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	0.03	3e80A	0.706	3.48	0.147	0.855	0.19	HS2	complex1.pdb.gz	41,42,45,122,162,164
2	0.03	2fuqA	0.707	3.49	0.142	0.859	0.23	UUU	complex2.pdb.gz	38,39,45,71
3	0.03	2futA	0.707	3.53	0.146	0.859	0.15	H1S	complex3.pdb.gz	17,144,145,178
4	0.01	1z45A	0.622	3.49	0.074	0.762	0.16	NAD	complex4.pdb.gz	23,24,25,26,27,81,82,83,85,211,212
5	0.01	1z45A	0.622	3.49	0.074	0.762	0.16	GUD	complex5.pdb.gz	39,45,74,76
6	0.01	1nsx0	0.613	3.75	0.054	0.765	0.38	III	complex6.pdb.gz	143,144,145,146,147
7	0.01	1so0C	0.599	3.52	0.064	0.741	0.32	GAL	complex7.pdb.gz	159,160,179
8	0.01	1nssA	0.613	3.75	0.054	0.765	0.24	BGC	complex8.pdb.gz	85,151,185
9	0.01	1ns0B	0.613	3.75	0.054	0.765	0.25	GLA	complex9.pdb.gz	144,162,177
10	0.01	1so0A	0.600	3.61	0.059	0.745	0.25	GAL	complex10.pdb.gz	121,144,145,162,163

	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.