D-I-TASSER Q9BXF3-D4

D-I-TASSER results for Q9BXF3-D4

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

Input Sequence in FASTA format

>Q9BXF3 (185 residues)
RDPEGSSRKQQPMENGGKSLPPTRRAPSSGDDQSSSSTQPPREVGTSNGRGFSHPLHCGG
TPSQAPFLNQMRPAVPGTFGPLRGSDPATLYGSSGVPEPHPGEPVQQRQPFTMQPPVGIN
SLRGPRLGTPEEKQMCGGLTHLSNMGPHPGSLQLGQISGPSQDGSMYAPAQFQPGFIPPR
HGGAP

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 \| \| \| \| \| \| \| \| \| RDPEGSSRKQQPMENGGKSLPPTRRAPSSGDDQSSSSTQPPREVGTSNGRGFSHPLHCGGTPSQAPFLNQMRPAVPGTFGPLRGSDPATLYGSSGVPEPHPGEPVQQRQPFTMQPPVGINSLRGPRLGTPEEKQMCGGLTHLSNMGPHPGSLQLGQISGPSQDGSMYAPAQFQPGFIPPRHGGAP
Prediction	CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Confidence	98777788888522379899988888887778888888899988878888888887778887888888888988998788888899888889999988999998778998887998677899988888988777788888887889899877888889999997878988888888898889999
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 \| \| \| \| \| \| \| \| \| RDPEGSSRKQQPMENGGKSLPPTRRAPSSGDDQSSSSTQPPREVGTSNGRGFSHPLHCGGTPSQAPFLNQMRPAVPGTFGPLRGSDPATLYGSSGVPEPHPGEPVQQRQPFTMQPPVGINSLRGPRLGTPEEKQMCGGLTHLSNMGPHPGSLQLGQISGPSQDGSMYAPAQFQPGFIPPRHGGAP
Prediction	85674574554337634643444553446565455454534674444545344563436444544544554444444424425375354254545347444474464444142534342554515534447565434443425714444442535624434663543444425653133656568
	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                 160                 180

                   |                   |                   |                   |                   |                   |                   |                   |                   |

SS
Seq

CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
RDPEGSSRKQQPMENGGKSLPPTRRAPSSGDDQSSSSTQPPREVGTSNGRGFSHPLHCGGTPSQAPFLNQMRPAVPGTFGPLRGSDPATLYGSSGVPEPHPGEPVQQRQPFTMQPPVGINSLRGPRLGTPEEKQMCGGLTHLSNMGPHPGSLQLGQISGPSQDGSMYAPAQFQPGFIPPRHGGAP

5nrlP3

0.05

2.46

0.57

CEthreader

FPNNPKSILFIDNHSGKKQCRISLQIDGECLKFGSSDHLYKILICAGDKRLLTYKILVNKDKLSFDIELLHQTEIISPIHAMLKFKNFLLTAMGSTILRRSVTQTPVSITKIVSMHQWNYERLAFIWDPAGNVFIPYVDDSVKRHVTVLKFLDEATVIGADRYGNAWTLRSPPECEKIMSNHDPS

3iygE

0.05

2.26

0.58

EigenThreader

QVEDAKGANGGPEIELIAIATGGRAGLVKDKEQCKNSRAVTIFIRGGNKMIIEEAKRSLHDALCVIRNLIRDNRGGGAAEISCALAVSQEAD---KCPTLEQYAMRAFADALEVIPMALAENSGMNPIQTMTEVRARQVKEV--NPALGIDCLHKGTNDMKHQHVIETLIGKK-----QQISLAT

2xd8A3

0.11

3.91

0.49

FFAS-3D

HETIARDLTKRTLKNGGRMTSSFHTPGTPILGNADKAPPVAEKTIVMDDLLISSASATNFVEPGGTQIRVGSGTNESDAFTASALVNAFYDAAAAMDEKGPFLGKYGVKYGGTTGETSPGNLGSHIGPTPENANATGGVNNDYGTNAELGAKSCGLIFQKEAAGVVEPQVQVTNGDVSVIYQG--

7jjvA

0.14

0.09

3.12

1.29

SPARKS-K

DGADGTSNGQAGAS--GLAGGPNCNGGKGGKGPGVGTAGGAGGVGGAGGTGNTNGGAGGSGGNSDVAAGGAGAAGGAAGGAGTG--------------GTGGNGGAGKPGGA-PGAGGAGTPAGSAGSPGQTTVL--------------------------------------------------

4ltbA

0.10

0.02

0.80

0.14

CNFpred

SLSQASADLEATLRHKLTVMYSQINGASRALDDVRNRQQD-------------------------------------------------------------------------------------------------------------------------------------------------

6lpnA

0.09

0.07

2.65

0.67

DEthreader

LVVTDPEALQAVDW----LRT--LRGCS------MVGGSVPIILSTARM--QAGCVLEERYKGSCH-GGN-ATN----AGGL--R---FLRYGSGTVLGTSLVSILCPPLSAFEFMD--AVCMQLGSESPFYVLGTMVKMLWAERIEALYGHNLHL------------------AEHGVGFRLNP

3g0bB

0.07

0.06

2.72

0.76

MapAlign

-----LLEYNYVKQWRHSYTASYDIYDLNKRQLITEERINTQWVTWSPVGHKLAYVWNNDIYVKIEPNLPSYVTNATSIQITAPASMLIGDHYLCDVTWATQERISLQWLRRDICDYDESSGRWNCLVARQHIEMSPHFTLDGNSFYKIISNEEGYRHICYFQIFITKGTWEVIGIEALTSDYLY

2nbiA

0.17

5.66

0.91

MUSTER

SDLNPSSQPSEPIDECFLPYSDASRPPLSFGRPDCDVLPTPQNINCPRCCATERPDNPMFTPSPDGSPPICSPTMLPTNQPTPPEPSSAPSDCGEVIEECPLDTCFLPTSDPARPPTAVGRPDCDVLPFPNN-LGCPACCPFECSPDNPMFTPSPDGSPPNCSPTMLPPQPSTPTVITPAPSSQP

3tljA1

0.15

0.02

0.73

0.44

HHsearch

VDEKGRKRELSISTYLN----ENSRLL-------------------------HRVI---------------------------------------------------------------------------------------------------------------------------------

1deeB

0.09

0.08

3.12

0.52

CEthreader

GFTFSGYGMHWVRQAPGKGLEWVALISYDESNKYYADSVKGRFTISRDNSKNTLYLQYCAKVKFYDPTAPNDYWGQGTLVTVSSGSASAPTLFPLVSCENPSSTVAVGCLAQDFLPDSI------------TFSWKYKNNSDISSTRGFPSVLRGGKYAATSQVLLPSKDVAQGTNEHVVCKVQH

(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	0.472

(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	4kvjA	0.44	5.08	0.031	0.730	model1_4kvjA.pdb.gz
2	6b1bA	0.43	5.43	0.037	0.751	model1_6b1bA.pdb.gz
3	3p4iA	0.43	5.74	0.046	0.784	model1_3p4iA.pdb.gz
4	4hhrA	0.43	5.41	0.036	0.751	model1_4hhrA.pdb.gz
5	1cvuA	0.41	4.87	0.055	0.676	model1_1cvuA.pdb.gz
6	1cqeB2	0.41	4.96	0.041	0.676	model1_1cqeB2.pdb.gz
7	1mhlC	0.41	5.28	0.028	0.708	model1_1mhlC.pdb.gz
8	2zzgA	0.34	5.86	0.039	0.627	model1_2zzgA.pdb.gz
9	1sazA2	0.32	5.50	0.061	0.568	model1_1sazA2.pdb.gz
10	3fqdA1	0.31	5.61	0.027	0.551	model1_3fqdA1.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:1901363	0.71	heterocyclic compound binding
GO:0097159	0.71	organic cyclic compound binding
GO:0043169	0.66	cation binding
GO:0003824	0.53	catalytic activity
GO:0000166	0.52	nucleotide binding
GO:0035639	0.51	purine ribonucleoside triphosphate binding
GO:0032559	0.51	adenyl ribonucleotide binding
GO:0032550	0.51	purine ribonucleoside binding
GO:0016740	0.50	transferase 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:0097194	1.00	execution phase of apoptosis
GO:0043044	1.00	ATP-dependent chromatin remodeling
GO:0008152	0.69	metabolic process
GO:0071704	0.68	organic substance metabolic process
GO:0044238	0.67	primary metabolic process
GO:0044237	0.67	cellular metabolic process
GO:0044767	0.66	single-organism developmental process
GO:0044260	0.66	cellular macromolecule metabolic process
GO:0048856	0.65	anatomical structure development
GO:0090102	0.64	cochlea development
GO:0060122	0.64	inner ear receptor stereocilium organization
GO:0021915	0.64	neural tube development
GO:0007338	0.64	single fertilization
GO:0001843	0.64	neural tube closure
GO:0001842	0.64	neural fold formation
GO:0006139	0.63	nucleobase-containing compound metabolic process
GO:0090304	0.62	nucleic acid 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:0090537	1.00	CERF complex
GO:0005634	1.00	nucleus
GO:0044427	0.66	chromosomal part
GO:0000785	0.65	chromatin
GO:0005719	0.64	nuclear euchromatin

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	3hm8A	0.399	5.47	0.048	0.697	2.7.1.1	NA
2	0.060	1psnA	0.328	5.99	0.072	0.622	3.4.23.1	16
3	0.060	5coxA	0.405	4.81	0.048	0.665	1.14.99.1	137,166,172
4	0.060	3ilwA	0.392	5.66	0.038	0.714	5.99.1.3	50
5	0.060	1rf4B	0.298	6.20	0.013	0.611	2.5.1.19	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	3mqeA	0.402	4.90	0.055	0.670	0.17	416	complex1.pdb.gz	80,81,89,145,146
2	0.04	3pghB	0.406	4.89	0.055	0.670	0.14	FLP	complex2.pdb.gz	112,145,146
3	0.03	6coxA	0.407	4.90	0.062	0.670	0.14	S58	complex3.pdb.gz	83,85,142,145
4	0.03	3pghA	0.407	4.89	0.055	0.670	0.14	FLP	complex4.pdb.gz	85,91,123
5	0.03	1ddxA	0.408	4.89	0.055	0.676	0.24	PGX	complex5.pdb.gz	80,81,84,85,139,143,146,147
6	0.01	3hs6A	0.406	4.90	0.048	0.676	0.18	EPA	complex6.pdb.gz	85,88,137,143,146,150
7	0.01	3hs6B	0.406	4.89	0.047	0.676	0.12	EPA	complex7.pdb.gz	96,116,159
8	0.01	1pxxA	0.406	4.75	0.042	0.659	0.21	DIF	complex8.pdb.gz	82,129,140,143,147
9	0.01	3krkB	0.407	4.88	0.048	0.670	0.13	ACD	complex9.pdb.gz	142,143,146
10	0.01	1cvuB	0.408	4.90	0.062	0.676	0.14	ACD	complex10.pdb.gz	76,80,85,87,162

	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.