D-I-TASSER Q9UBV2-D5

D-I-TASSER results for Q9UBV2-D5

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

Input Sequence in FASTA format

>Q9UBV2 (140 residues)
NLIAHMVLGYRYWAGIGVLQSCESALTHYRLVANHVASDISLTGGSVVQRIRLPDEVENP
GMNSGMLEEDLIQYYQFLAEKGDVQAQVGLGQLHLHGGRGVEQNHQRAFDYFNLAANAGN
SHAMAFLGKMYSEGSDIVPQ

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 \| \| \| \| \| \| \| NLIAHMVLGYRYWAGIGVLQSCESALTHYRLVANHVASDISLTGGSVVQRIRLPDEVENPGMNSGMLEEDLIQYYQFLAEKGDVQAQVGLGQLHLHGGRGVEQNHQRAFDYFNLAANAGNSHAMAFLGKMYSEGSDIVPQ
Prediction	CHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHCCCHHHHHCCCCCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHCCCCCCCC
Confidence	88999999999990999788999999999999991999999999999997121012330599987799999999999998199999999999999489998879999999999999919799999999999809998999
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 \| \| \| \| \| \| \| NLIAHMVLGYRYWAGIGVLQSCESALTHYRLVANHVASDISLTGGSVVQRIRLPDEVENPGMNSGMLEEDLIQYYQFLAEKGDVQAQVGLGQLHLHGGRGVEQNHQRAFDYFNLAANAGNSHAMAFLGKMYSEGSDIVPQ
Prediction	72442232030134153145426402500430174424600320020023243454445514425523630150043017352350021202012334502442263025003300744245013120202244642358
	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

                   |                   |                   |                   |                   |                   |                   |

SS
Seq

CHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHCCCHHHHHCCCCCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHCCCCCCCC
NLIAHMVLGYRYWAGIGVLQSCESALTHYRLVANHVASDISLTGGSVVQRIRLPDEVENPGMNSGMLEEDLIQYYQFLAEKGDVQAQVGLGQLHLHGGRGVEQNHQRAFDYFNLAANAGNSHAMAFLGKMYSEGSDIVPQ

2xm6A

0.23

0.21

6.70

1.33

DEthreader

DELGQLHLADMYYFGIGVTQDYTQSRVLFSQSAEQGNSIAQFRLGYILE-QGLA--------GAK-EPLKALEWYRKSAEQGNSDGQYYLAHLYDKGAEGVAKNREQAISWYTKSAEQGDATAQANLGAIYFRL--GSEE

5b26A

0.29

0.27

8.26

1.49

SPARKS-K

DVQAQVGLGQLHLHGGGVEQNHQRAFDYFNLAANAGNSHAMAFLGKMYSE---------GSDIVPQSNETALHYFKKAADMGNPVGQSGLGMAYLYG-RGVQVNYDLALKYFQKAAEQGWVDGQLQLGSMYYNGIGVKRD

1ouvA

0.19

0.17

5.53

0.71

MapAlign

YAEGCASLGGIYHDGKVVTRDFKKAVEYFTKACDLNDGDGCTILGSLYD----------AGRGTPKDLKKALASYDKACDLKDSPGCFNAGNMYHHG-EGATKNFKEALARYSKACELENGGGCFNLGAMQYNGEGV---

1ouvA

0.19

0.17

5.55

0.51

CEthreader

YAEGCASLGGIYHDGKVVTRDFKKAVEYFTKACDLNDGDGCTILGSLYDAGRG----------TPKDLKKALASYDKACDLKDSPGCFNAGNMYHHG-EGATKNFKEALARYSKACELENGGGCFNLGAMQYNGEGVTRN

5b26A

0.29

0.27

8.26

1.25

MUSTER

DVQAQVGLGQLHLHGRGVEQNHQRAFDYFNLAANAGNSHAMAFLGKMYSE---------GSDIVPQSNETALHYFKKAADMGNPVGQSGLGMAYLY-GRGVQVNYDLALKYFQKAAEQGWVDGQLQLGSMYYNGIGVKRD

2xm6A

0.26

0.24

7.29

0.70

HHsearch

EAKAQLELGYRYFQGNETTKDLTQAMDWFRRAAEQGYTPAEYVLGLRYMN----------GEGVPQDYAQAVIWYKKAALKGLPQAQQNLGVMYHEG-NGVKVDKAESVKWFRLAAEQGRDSGQQSMGDAYFEGDGVTRD

5b26A

0.29

0.27

8.26

1.76

FFAS-3D

DVQAQVGLGQLHLHGRGVEQNHQRAFDYFNLAANAGNSHAMA---------FLGKMYSEGSDIVPQSNETALHYFKKAADMGNPVGQSGLGMAYL-YGRGVQVNYDLALKYFQKAAEQGWVDGQLQLGSMYYNGIGVKRD

6dehA

0.25

0.23

7.09

0.63

EigenThreader

NASAQYNLGLMYEQGDGVPKDYQKAAEYFEKAANQGHAKSQLELGYLYDSGKL----------GKSDLQKAAFWYQKSADLGNANAQFNLADMYFYG-DGVGKSLEQSVYWMQKAAEQGYGKAQNQLGIYYRDGIGVAAD

2xm6A

0.26

0.24

7.29

1.13

CNFpred

YTPAEYVLGLRYMNGEGVPQDYAQAVIWYKKAALKGLPQAQQNLGVMYHEGN----------GVKVDKAESVKWFRLAAEQGRDSGQQSMGDAYFEGD-GVTRDYVMAREWYSKAAEQGNVWSCNQLGYMYSRGLGVERN

6dehA

0.24

0.22

6.90

1.33

DEthreader

NASAQYNLGLMYEQGDGVPKDYQKAAEYFEKAANQGHAKSQLELGYLYDSGK-L-G-------KS-DLQKAAFWYQKSADLGNANAQFNLADMYFYGD-GVGKSLEQSVYWMQKAAEQGYGKAQNQLGIYYRDGIGVAAD

(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	0.8053

(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	2xm6A	0.87	1.13	0.256	0.921	model1_2xm6A.pdb.gz
2	6dehA	0.87	1.20	0.240	0.921	model1_6dehA.pdb.gz
3	6ur7A	0.84	1.39	0.256	0.921	model1_6ur7A.pdb.gz
4	6ok3A	0.84	1.26	0.246	0.900	model1_6ok3A.pdb.gz
5	1ouvA	0.84	1.43	0.178	0.921	model1_1ouvA.pdb.gz
6	6orkA	0.82	1.41	0.312	0.893	model1_6orkA.pdb.gz
7	6onwA	0.79	1.65	0.238	0.871	model1_6onwA.pdb.gz
8	5b26A	0.78	2.04	0.285	0.929	model1_5b26A.pdb.gz
9	3e4bC	0.74	2.33	0.151	0.879	model1_3e4bC.pdb.gz
10	1klxA	0.69	2.37	0.150	0.807	model1_1klxA.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	0.60	catalytic 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	0.96	cellular process
GO:0044238	0.94	primary metabolic process
GO:0044237	0.94	cellular metabolic process
GO:0043170	0.94	macromolecule metabolic process
GO:0019538	0.91	protein metabolic process
GO:0030163	0.86	protein catabolic process
GO:0044699	0.83	single-organism process
GO:0050896	0.82	response to stimulus
GO:0044763	0.81	single-organism cellular process
GO:0006950	0.81	response to stress
GO:0044710	0.79	single-organism metabolic process
GO:0006810	0.76	transport
GO:1902578	0.75	single-organism localization
GO:0034976	0.75	response to endoplasmic reticulum stress
GO:0015031	0.75	protein transport
GO:0010033	0.75	response to organic substance
GO:0036503	0.74	ERAD pathway
GO:0009306	0.74	protein secretion
GO:0006641	0.74	triglyceride metabolic process
GO:0065007	0.54	biological regulation
GO:0044260	0.51	cellular macromolecule 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	1.00	cell part
GO:0044424	0.98	intracellular part
GO:0044444	0.97	cytoplasmic part
GO:0043226	0.94	organelle
GO:0043231	0.93	intracellular membrane-bounded organelle
GO:0044446	0.92	intracellular organelle part
GO:0044432	0.90	endoplasmic reticulum part
GO:0044425	0.90	membrane part
GO:0043234	0.89	protein complex
GO:0000836	0.88	Hrd1p ubiquitin ligase complex
GO:0005783	0.82	endoplasmic reticulum
GO:0000839	0.79	Hrd1p ubiquitin ligase ERAD-L complex

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	0.323	1klxA	0.691	2.37	0.150	0.807	3.5.2.6	48,71,74,98,111
2	0.151	1ouvA	0.841	1.43	0.178	0.921	3.5.2.6	83
3	0.132	2fbnA	0.580	3.50	0.092	0.807	5.2.1.8	42,84,90
4	0.087	1tjcA	0.462	2.93	0.070	0.586	1.14.11.2	NA
5	0.060	2if4A	0.552	3.88	0.075	0.814	5.2.1.8	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	0.04	3gz1B	0.619	2.71	0.125	0.800	0.71	III	complex1.pdb.gz	6,7,10,13,29,39,43,46,49,75,89,92,125
2	0.02	2j9q0	0.635	3.13	0.101	0.843	0.55	III	complex2.pdb.gz	14,49,50,85,92,93,98,100,102,110
3	0.02	2c0l0	0.619	3.18	0.118	0.814	0.42	III	complex3.pdb.gz	42,43,46,75,85,89,96,122,128,129,134
4	0.02	2j9q1	0.619	3.37	0.092	0.850	0.50	III	complex4.pdb.gz	14,49,50,89,93,98,100,109,110

	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.