D-I-TASSER Q9BQI0-D1

D-I-TASSER results for Q9BQI0-D1

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

Input Sequence in FASTA format

>Q9BQI0 (150 residues)
MSGELSNRFQGGKAFGLLKARQERRLAEINREFLCDQKYSDEENLPEKLTAFKEKYMEFD
LNNEGEIDLMSLKRMMEKLGVPKTHLEMKKMISEVTGGVSDTISYRDFVNMMLGKRSAVL
KLVMMFEGKANESSPKPVGPPPERDIASLP

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 \| \| \| \| \| \| \| MSGELSNRFQGGKAFGLLKARQERRLAEINREFLCDQKYSDEENLPEKLTAFKEKYMEFDLNNEGEIDLMSLKRMMEKLGVPKTHLEMKKMISEVTGGVSDTISYRDFVNMMLGKRSAVLKLVMMFEGKANESSPKPVGPPPERDIASLP
Prediction	CCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHCCCCCCCSCHHHHHHHHHHHCCCCCHHHHHHHHHHHCCCCCCCSCHHHHHHHHHHHCCHHHHHHHHHHHHCCCCCCCCCCCCCCHHHHHCC
Confidence	987422331106777688999999999999997505554440008999999999999975899996179999999999099999999999999984789982519999999998211689999999874657888888886310553078
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 \| \| \| \| \| \| \| MSGELSNRFQGGKAFGLLKARQERRLAEINREFLCDQKYSDEENLPEKLTAFKEKYMEFDLNNEGEIDLMSLKRMMEKLGVPKTHLEMKKMISEVTGGVSDTISYRDFVNMMLGKRSAVLKLVMMFEGKANESSPKPVGPPPERDIASLP
Prediction	864625643622442542356246425512641374751554742663164036105300554524033620340265174723462045205400635634431611241144435422402421454566865566345354416728
	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

                   |                   |                   |                   |                   |                   |                   |

SS
Seq

CCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHCCCCCCCSCHHHHHHHHHHHCCCCCHHHHHHHHHHHCCCCCCCSCHHHHHHHHHHHCCHHHHHHHHHHHHCCCCCCCCCCCCCCHHHHHCC
MSGELSNRFQGGKAFGLLKARQERRLAEINREFLCDQKYSDEENLPEKLTAFKEKYMEFDLNNEGEIDLMSLKRMMEKLGVPKTHLEMKKMISEVTGGVSDTISYRDFVNMMLGKRSAVLKLVMMFEGKANESSPKPVGPPPERDIASLP

2jjzC

1.00

0.77

21.47

1.19

SPARKS-K

------------KAFGLLKARQERRLAEINREFLCDQKYSDEENLPEKLTAFKEKYMEFDLNNEGEIDLMSLKRMMEKLGVPKTHLEMKKMISEVTGGVSDTISYRDFVNMMLGKRSAVLKLVMMFE-----------------------

2g2bA

0.60

17.19

1.42

MUSTER

PLESQTRDLQGGKAFGLLKAQQEERLDEINKQFLDDPKYSSDEDLPSKLEGFKEKYMEFDLNGNGDIDIMSLKRMLEKLGVPKTHLELKKLIGEVSSGSGETFSYPDFLRMMLGKRSAILKMILMYEEKAREKEKPTGPPA-KKAISELP

2g2bA

0.64

0.63

17.89

1.82

FFAS-3D

---SQTRDLQGGKAFGLLKAQQEERLDEINKQFLDDPKYSSDEDLPSKLEGFKEKYMEFDLNGNGDIDIMSLKRMLEKLGVPKTHLELKKLIGEVSSGSGETFSYPDFLRMMLGKRSAILKMILMYEEKAREKE-KPTGPPAKKAISELP

1y1xA

0.09

0.07

2.57

1.00

DEthreader

------------------STGYANAALSFSLTEKLLHMYDEFKDLHHFILSMREGFRKRDSSGDGRLDSNEVRAALLSSGYQVSEQTFQALMRKFDRQRRGSLGFDDYVELSI--F-VCRVRNVFAFY-DRE-R-TGQV-----------

2g2bA

0.58

16.65

1.15

SPARKS-K

PLESQTRDLQGGKAFGLLKAQQEERLDEINKQFLDDPKYSSDEDLPSKLEGFKEKYMEFDLNGNGDIDIMSLKRMLEKLGVPKTHLELKKLIGEVSSGSGETFSYPDFLRMMLGKRSAILKMILMYEEKAREKEKPTGPPAKKAISELP-

3siaA

0.07

2.75

0.58

MapAlign

--FPLLNTIPLDQYTRIYQWFMGVQTALRMMRIFGHISFYEFMAMYKFMELAYNLFVMNARARSGTLEPHEILPALQQLGFYINQRTSLLLHRLFAM---AFCDLNCWIAICA--FAAQTRSAYQMIFMNPYYGPMKPFNPMEFGKFLD-

2g2bA

0.58

16.65

0.36

CEthreader

PLESQTRDLQGGKAFGLLKAQQEERLDEINKQFLDDPKYSSDEDLPSKLEGFKEKYMEFDLNGNGDIDIMSLKRMLEKLGVPKTHLELKKLIGEVSSGSGETFSYPDFLRMMLGKRSAILKMILMYEEKAREKEKPTGPPAKKAISELP-

2jjzC

1.00

0.77

21.47

1.31

MUSTER

------------KAFGLLKARQERRLAEINREFLCDQKYSDEENLPEKLTAFKEKYMEFDLNNEGEIDLMSLKRMMEKLGVPKTHLEMKKMISEVTGGVSDTISYRDFVNMMLGKRSAVLKLVMMFE-----------------------

2g2bA

0.64

0.63

17.91

0.88

HHsearch

PLESQTRDLQGGKAFGLLKAQQEERLDEINKQFLDDPKYSSDEDLPSKLEGFKEKYMEFDLNGNGDIDIMSLKRMLEKLGVPKTHLELKKLIGEVS-GSGETFSYPDFLRMMLGKRSAILKMILMYEEKAREKE-KPTGPPAKKAISELP

2jjzC

1.00

0.77

21.47

1.59

FFAS-3D

------------KAFGLLKARQERRLAEINREFLCDQKYSDEENLPEKLTAFKEKYMEFDLNNEGEIDLMSLKRMMEKLGVPKTHLEMKKMISEVTGGVSDTISYRDFVNMMLGKRSAVLKLVMMFE-----------------------

(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	0.629

(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	2jjzC	0.74	1.18	1.000	0.767	model1_2jjzC.pdb.gz
2	2g2bA	0.67	2.45	0.527	0.807	model1_2g2bA.pdb.gz
3	5i2lA	0.52	2.38	0.283	0.627	model1_5i2lA.pdb.gz
4	7bvcB	0.52	5.19	0.068	0.900	model1_7bvcB.pdb.gz
5	2uvcG	0.52	4.76	0.076	0.847	model1_2uvcG.pdb.gz
6	3u0kA	0.52	3.50	0.174	0.660	model1_3u0kA.pdb.gz
7	2pffB	0.52	4.82	0.049	0.853	model1_2pffB.pdb.gz
8	7bc4B	0.51	4.82	0.042	0.867	model1_7bc4B.pdb.gz
9	3evuA	0.51	4.13	0.162	0.693	model1_3evuA.pdb.gz
10	1dtlA	0.51	3.63	0.211	0.653	model1_1dtlA.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:0032403	0.81	protein complex binding
GO:0008092	0.81	cytoskeletal protein binding
GO:0003779	0.79	actin binding
GO:0051015	0.78	actin filament binding

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:0065007	0.91	biological regulation
GO:0009987	0.91	cellular process
GO:0050789	0.90	regulation of biological process
GO:0050794	0.85	regulation of cellular process
GO:0044699	0.79	single-organism process
GO:0044763	0.75	single-organism cellular process
GO:0007165	0.75	signal transduction
GO:0035556	0.72	intracellular signal transduction
GO:0016043	0.70	cellular component organization
GO:0048518	0.68	positive regulation of biological process
GO:0050896	0.67	response to stimulus
GO:0048522	0.67	positive regulation of cellular process
GO:0032879	0.67	regulation of localization
GO:0048583	0.66	regulation of response to stimulus
GO:0051716	0.65	cellular response to stimulus
GO:0042221	0.64	response to chemical
GO:0048584	0.63	positive regulation of response to stimulus
GO:0010033	0.63	response to organic substance
GO:0002682	0.63	regulation of immune system process
GO:0022607	0.61	cellular component assembly
GO:0006950	0.59	response to stress
GO:0051726	0.58	regulation of cell cycle
GO:0070887	0.57	cellular response to chemical stimulus
GO:0065003	0.57	macromolecular complex assembly
GO:0030030	0.57	cell projection organization
GO:0010564	0.57	regulation of cell cycle process
GO:0002684	0.57	positive regulation of immune system process
GO:2000404	0.56	regulation of T cell migration
GO:1901989	0.56	positive regulation of cell cycle phase transition
GO:0061024	0.56	membrane organization
GO:0051017	0.56	actin filament bundle assembly
GO:0034097	0.56	response to cytokine
GO:0030031	0.56	cell projection assembly
GO:0006461	0.56	protein complex assembly
GO:2000406	0.55	positive regulation of T cell migration
GO:1900087	0.55	positive regulation of G1/S transition of mitotic cell cycle
GO:0097178	0.55	ruffle assembly
GO:0090026	0.55	positive regulation of monocyte chemotaxis
GO:0071673	0.55	positive regulation of smooth muscle cell chemotaxis
GO:0071346	0.55	cellular response to interferon-gamma
GO:0048661	0.55	positive regulation of smooth muscle cell proliferation
GO:0042102	0.55	positive regulation of T cell proliferation
GO:0030041	0.55	actin filament polymerization
GO:0016601	0.55	Rac protein signal transduction
GO:0006954	0.55	inflammatory response
GO:0006911	0.55	phagocytosis, engulfment
GO:0044238	0.53	primary metabolic process
GO:0043170	0.53	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	0.99	cell part
GO:0044424	0.94	intracellular part
GO:0044446	0.86	intracellular organelle part
GO:0043226	0.82	organelle
GO:0044430	0.81	cytoskeletal part
GO:0043229	0.81	intracellular organelle
GO:0044444	0.75	cytoplasmic part
GO:0043227	0.74	membrane-bounded organelle
GO:0016020	0.70	membrane
GO:0005884	0.67	actin filament
GO:0043231	0.64	intracellular membrane-bounded organelle
GO:0005634	0.61	nucleus
GO:0044425	0.58	membrane part
GO:0005829	0.57	cytosol
GO:0042995	0.56	cell projection
GO:0005737	0.56	cytoplasm
GO:0044463	0.55	cell projection part
GO:0044459	0.54	plasma membrane part
GO:0030027	0.53	lamellipodium
GO:0001891	0.53	phagocytic cup
GO:0032587	0.52	ruffle 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	0.060	1gz7C	0.410	5.20	0.083	0.753	3.1.1.3	63,72
2	0.060	2h8oA	0.442	4.31	0.052	0.667	2.5.1.10	NA
3	0.060	1cnsA	0.438	4.42	0.023	0.687	3.2.1.14	NA
4	0.060	1l8aA	0.443	4.72	0.066	0.713	1.2.4.1	NA
5	0.060	3c46B	0.408	5.45	0.067	0.760	2.7.7.6	83

	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:

Click to view	Rank	Cscore^LB	PDB Hit	TM-score	RMSD^a	IDEN^a	Cov.	BS-score	Lig. Name	Download Complex	Predicted binding site residues
	1	0.09	1wy9A	0.575	2.88	0.600	0.700	1.07	CA	complex1.pdb.gz	92,96,102,107
	2	0.03	1dtlA	0.510	3.63	0.211	0.653	0.41	BEP	complex2.pdb.gz	59,67,72

	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.