D-I-TASSER Q9BPW9-D1

D-I-TASSER results for Q9BPW9-D1

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

Input Sequence in FASTA format

>Q9BPW9 (106 residues)
MLFWVLGLLILCGFLWTRKGKLKIEDITDKYIFITGCDSGFGNLAARTFDKKGFHVIAAC
LTESGSTALKAETSERLRTVLLDVTDPENVKRTAQWVKNQVGEKGL

Predicted Secondary Structure

Sequence	20 40 60 80 100 \| \| \| \| \| MLFWVLGLLILCGFLWTRKGKLKIEDITDKYIFITGCDSGFGNLAARTFDKKGFHVIAACLTESGSTALKAETSERLRTVLLDVTDPENVKRTAQWVKNQVGEKGL
Prediction	CSSHHHHHHHHHHHHHHHHCCCCCCCCCCCSSSSSCCCCHHHHHHHHHHHHCCCSSSSSSCCHHHHHHHHHHCCCCCSSSSCCCCCHHHHHHHHHHHHHHHCCCCC
Confidence	6115999999999999972455456888958999679974999999999981998999867988999999853899099981599999999999999999399999
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 \| \| \| \| \| MLFWVLGLLILCGFLWTRKGKLKIEDITDKYIFITGCDSGFGNLAARTFDKKGFHVIAACLTESGSTALKAETSERLRTVLLDVTDPENVKRTAQWVKNQVGEKGL
Prediction	3323233333333321323454515625520000011333203100420174302000002447315404744574030130452356105401530274157657
	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

                   |                   |                   |                   |                   |

SS
Seq

CSSHHHHHHHHHHHHHHHHCCCCCCCCCCCSSSSSCCCCHHHHHHHHHHHHCCCSSSSSSCCHHHHHHHHHHCCCCCSSSSCCCCCHHHHHHHHHHHHHHHCCCCC
MLFWVLGLLILCGFLWTRKGKLKIEDITDKYIFITGCDSGFGNLAARTFDKKGFHVIAACLTESGSTALKAETSERLRTVLLDVTDPENVKRTAQWVKNQVGEKGL

4fn4A1

0.20

0.16

5.11

1.17

DEthreader

----------------------SYQSLKNKVVIVTGAGSGIGRAIAKKFALNDSIVVAVELLEDRLNQIVQELRKEVLGVKADVSKKKDVEEFVRRTFETYS-RID

4npcA1

0.22

0.18

5.66

1.38

SPARKS-K

-------------------QIDLNFPLSEKVAIVTGGASGIGAAISKAFIAKGAKVAVLDISADIAKAKAEELGENAKPFVCDVSSQQSVNDAITAVISQFGKIDI

4i08A1

0.22

0.18

5.64

1.40

MUSTER

---------------------SQFMNLEGKVALVTGASRGIGKAIAELLAERGAKVIGTATSESGAQAISDYLGDNGKGMALNVTNPESIEAVLKAITDEFGGVDI

4i5dH1

0.28

0.21

6.34

1.14

FFAS-3D

-------------------------RLLNKTAVITGGNSGIGLATAKRFVAEGAYVFIVGRRRKELEQAAAEIGRNVTAVKADVTKLEDLDRLYAIVREQRGS---

4fn4A

0.20

0.16

5.11

1.17

DEthreader

----------------------SYQSLKNKVVIVTGAGSGIGRAIAKKFALNDSIVVAVELLEDRLNQIVQELRKEVLGVKADVSKKKDVEEFVRRTFETYS-RID

1k2wA1

0.24

0.19

5.87

1.33

SPARKS-K

------------------------MRLDGKTALITGSARGIGRAFAEAYVREGARVAIADINLEAARATAAEIGPAACAIALDVTDQASIDRCVAELLDRWGSIDI

2et6A

0.20

0.19

6.05

0.53

MapAlign

-KSALLGFAETLAKEGAKYNIKATVSLKDKVVLITGAGAGLGKEYAKWFAKYGAKVVVNDFK--DATKTVDEIGGEAWPDQHDV--AKDSEAIIKNVIDKYGTIDI

1fmcA

0.18

0.15

4.91

0.28

CEthreader

------------------MFNSDNLRLDGKCAIITGAGAGIGKEIAITFATAGASVVVSDINADAANHVVDEIQGQAFACRCDITSEQELSALADFAISKLGKVDI

1bdbA1

0.20

0.15

4.85

1.38

MUSTER

------------------------MKLKGEAVLITGGASGLGRALVDRFVAEGAKVAVLDKSAERLAELETDHGDNVLGIVGDVRSLEDQKQAASRCVARFGKIDT

6k8vA

0.22

0.17

5.37

0.59

HHsearch

-----------------------PGRLAGKIAVVTGAAGNLGGHIVTHYLAEGATVVMTGRTPDRTKAAADALGSRLATVALDGGDIASVRAAIAEVVQKFGRIDI

(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	0.7308

(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	1yxmA1	0.74	1.71	0.146	0.811	model1_1yxmA1.pdb.gz
2	1fmcA	0.74	1.33	0.182	0.792	model1_1fmcA.pdb.gz
3	6d9yA	0.74	1.64	0.174	0.811	model1_6d9yA.pdb.gz
4	6zzoA	0.74	1.42	0.253	0.802	model1_6zzoA.pdb.gz
5	5g4kA	0.74	1.51	0.181	0.792	model1_5g4kA.pdb.gz
6	3gvcB	0.74	1.33	0.188	0.802	model1_3gvcB.pdb.gz
7	4npcA1	0.74	1.62	0.218	0.802	model1_4npcA1.pdb.gz
8	5itvA	0.74	1.46	0.274	0.792	model1_5itvA.pdb.gz
9	4o5oA	0.74	1.91	0.172	0.821	model1_4o5oA.pdb.gz
10	6llnA	0.74	2.04	0.180	0.821	model1_6llnA.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	0.99	catalytic activity
GO:0016491	0.98	oxidoreductase activity
GO:0016616	0.86	oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
GO:0004745	0.55	retinol dehydrogenase 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:0044699	0.96	single-organism process
GO:0008152	0.94	metabolic process
GO:0044710	0.89	single-organism metabolic process
GO:0009987	0.88	cellular process
GO:0071704	0.85	organic substance metabolic process
GO:0044238	0.83	primary metabolic process
GO:0044237	0.82	cellular metabolic process
GO:0006629	0.81	lipid metabolic process
GO:0044763	0.80	single-organism cellular process
GO:0044281	0.72	small molecule metabolic process
GO:0044255	0.69	cellular lipid metabolic process
GO:0006721	0.62	terpenoid metabolic process
GO:0001523	0.61	retinoid metabolic process
GO:0065007	0.59	biological regulation
GO:0009058	0.59	biosynthetic process
GO:0044249	0.56	cellular biosynthetic process
GO:1901576	0.54	organic substance biosynthetic process
GO:0044711	0.52	single-organism biosynthetic process
GO:0008610	0.51	lipid biosynthetic process
GO:0044283	0.50	small molecule 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:0044464	1.00	cell part
GO:0044424	0.96	intracellular part
GO:0044444	0.85	cytoplasmic part
GO:0044446	0.82	intracellular organelle part
GO:0044425	0.68	membrane part
GO:0044432	0.57	endoplasmic reticulum part
GO:0016020	0.48	membrane
GO:0043226	0.46	organelle
GO:0043229	0.43	intracellular organelle
GO:0031224	0.42	intrinsic component of membrane
GO:0016021	0.41	integral component of membrane
GO:0043227	0.36	membrane-bounded organelle
GO:0043231	0.33	intracellular membrane-bounded organelle
GO:0030176	0.32	integral component of endoplasmic reticulum 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	0.066	2r25B	0.572	3.67	0.063	0.887	2.7.13.3	44
2	0.060	3ch6B	0.723	1.78	0.119	0.811	1.1.1.146	43,70
3	0.060	1g6kA	0.723	1.38	0.217	0.783	1.1.1.47	49
4	0.060	1ipeB	0.724	1.38	0.106	0.783	1.1.1.236	34,91
5	0.060	1g0oC	0.719	1.53	0.144	0.792	1.1.1.252	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	0.55	2hsdC	0.732	0.97	0.268	0.774	0.49	NAD	complex1.pdb.gz	36,39,41,60,62,82,83,84
2	0.19	1yxmB	0.747	1.72	0.148	0.811	0.47	ADE	complex2.pdb.gz	35,42,43,60
3	0.15	3lz6B	0.725	1.52	0.165	0.802	0.45	A0D	complex3.pdb.gz	10,42,46
4	0.05	2wsbA	0.735	1.86	0.184	0.802	0.45	POL	complex4.pdb.gz	36,41,44
5	0.04	2wsbD	0.738	1.83	0.184	0.802	0.49	POL	complex5.pdb.gz	62,65,68,69
6	0.04	2wsbC	0.735	1.84	0.184	0.802	0.41	POL	complex6.pdb.gz	9,45,49

	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.