D-I-TASSER Q9BXL7-D3

D-I-TASSER results for Q9BXL7-D3

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

Input Sequence in FASTA format

>Q9BXL7 (116 residues)
RVRIISGSPLGSLARSSLDATKLLTEKQEELDPESELGKNLSLIPYSLVRAFYCERRRPV
LFTPTVLAKTLVQRLLNSGGAMEFTICKSDIVTRDEFLRRQKTETIIYSREKNPNA

Predicted Secondary Structure

Sequence	20 40 60 80 100 \| \| \| \| \| RVRIISGSPLGSLARSSLDATKLLTEKQEELDPESELGKNLSLIPYSLVRAFYCERRRPVLFTPTVLAKTLVQRLLNSGGAMEFTICKSDIVTRDEFLRRQKTETIIYSREKNPNA
Prediction	CSSSSCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCSSSSCCCCCCCCCSSSCHHHHHHHHHHHHHCCCCCCCCCSCCCCCCCHHHHHHHHCCCCCSSSCCCCCCC
Confidence	95896289876544455432124776312368654300155434413310114899886785235556899999845346764120680116988876654245502442569999
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 \| \| \| \| \| RVRIISGSPLGSLARSSLDATKLLTEKQEELDPESELGKNLSLIPYSLVRAFYCERRRPVLFTPTVLAKTLVQRLLNSGGAMEFTICKSDIVTRDEFLRRQKTETIIYSREKNPNA
Prediction	72302444445434544154344445547636455325531302210203334274421000003211430143024464445154145640376524446644521444565688
	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

CSSSSCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCSSSSCCCCCCCCCSSSCHHHHHHHHHHHHHCCCCCCCCCSCCCCCCCHHHHHHHHCCCCCSSSCCCCCCC
RVRIISGSPLGSLARSSLDATKLLTEKQEELDPESELGKNLSLIPYSLVRAFYCERRRPVLFTPTVLAKTLVQRLLNSGGAMEFTICKSDIVTRDEFLRRQKTETIIYSREKNPNA

2fu3B

0.10

0.09

3.53

1.03

MapAlign

DVIITSG-GVSMGEKDYLKQVLDIDLHAQIHFGRVFMKPGLPTTFATLDIDGVR--KIIFALPGVTCNLFVVPALRKMQGILDPRPTIIKARLSCWAQSTGNQMSSRLMSMRSANG

4wsiA

0.19

0.18

5.86

1.10

HHsearch

TLTLIPSQQIPAKVKAHFDYDPSDEDPNWWPLAGLVPGK-EEILTYEEMSLYPANRKRPIILIPQNCGNELRQRLMN-KEKDRFASAVPHTVSRQAFEADAAGKFI-EHGEFEKNL

2d3bA

0.09

3.56

0.57

CEthreader

IAEYIWIGGSGMDLRSKARTLPGPVTDPSKLPKWNYEDSEVILYPQAIFKDPFRRGNNILVMCDCYIPTNKRYSAAKIFSSPEVAAEEPWYGIEQEYTLLQKDTNWPLGWPIGGFP

5t6oA

0.09

3.29

0.50

EigenThreader

RPLLMVPPCINKYYILDLVEQPDASMAGSTWDDYIEHAAIRAIEVARDI----SGQDKINVLGFAVGGTIVSTALAVLAARGEHPVDLDHIVPWTAAYASTALLANLGAVINPPAK

6w2dk

0.14

0.12

4.14

0.33

FFAS-3D

---VLDEVSVDSLILTKIVPGQTYAIKNKYQPFFQWHGTGLSVMP-----PVFGREHATVMVLPTPIAEEVLQKIL---LFNVYSRVVMQAPGNADMLDVHMHLGSVSYLGHH---

5bq9A1

0.14

0.12

4.13

0.76

SPARKS-K

VTKIIWVSNNGKPNLKIEFVSEEEKSNFFKEVKKKASELGLNFPNSLLIEASNYPGKLAINFGKVELSHFILPKVG---------------VKTEHAEIFKDHNTIFFHKHKLPGV

3kfvA

0.19

0.11

3.63

0.78

CNFpred

------------------------------------------YPPYERVVLREASFKRPVVILG-PVADIAMQKLTAEM---QFEIAETVIIKLDTVRVIAEKDKHALLDVTPSAI

4u3eA

0.06

0.04

1.90

0.83

DEthreader

FAYTLKPIV-EKGLPFIKTI-----------K-SEPAKTFQHVI---------SSGAVGLDFFWIEHFQILTYSLNQPIRTQSPYTN-FTYLDRNYIKAIFEG-ERYPD-------

4p6cA

0.06

0.05

2.29

0.92

MapAlign

VCLCLTEAQADRLALP------------PMVVNNNSANQTAFTVSIEKPEDLARPGHVFPLRARGHTEGTVDLMQMAGLQPAGVLCELTNMAKTPEIIEFGKLHNMPVLTIEDMVQ

1y81A

0.12

0.11

3.96

0.54

MUSTER

KIALVGASKNPAKYGNII-LKDLLSKGFEVLPVNPNYDEIEGLKCYRSVRELPKDVDVIVFVVPPKVGLQVAKEAVEAGFKK---WFQPGAESEEIRRFLEKAGVEYSF----GRC

(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	0.5442

(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	5gw8A	0.52	3.75	0.102	0.793	model1_5gw8A.pdb.gz
2	5ntfA	0.51	4.01	0.062	0.828	model1_5ntfA.pdb.gz
3	5lhkA	0.51	4.27	0.097	0.853	model1_5lhkA.pdb.gz
4	3uueA	0.51	3.51	0.084	0.776	model1_3uueA.pdb.gz
5	5gneA	0.51	3.94	0.092	0.802	model1_5gneA.pdb.gz
6	4ksiA	0.50	4.41	0.028	0.845	model1_4ksiA.pdb.gz
7	5mrwA	0.50	4.14	0.020	0.836	model1_5mrwA.pdb.gz
8	3kzwA	0.50	4.01	0.028	0.819	model1_3kzwA.pdb.gz
9	2ewbA	0.50	4.05	0.045	0.819	model1_2ewbA.pdb.gz
10	6omeA	0.50	3.97	0.054	0.810	model1_6omeA.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:0019904	0.62	protein domain specific binding
GO:0050700	0.61	CARD domain 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:0080090	1.00	regulation of primary metabolic process
GO:0060255	1.00	regulation of macromolecule metabolic process
GO:0048584	1.00	positive regulation of response to stimulus
GO:0048522	1.00	positive regulation of cellular process
GO:0044093	1.00	positive regulation of molecular function
GO:0031323	1.00	regulation of cellular metabolic process
GO:0031325	0.71	positive regulation of cellular metabolic process
GO:0010604	0.71	positive regulation of macromolecule metabolic process
GO:0051246	0.70	regulation of protein metabolic process
GO:0051247	0.69	positive regulation of protein metabolic process
GO:0009966	0.69	regulation of signal transduction
GO:0007165	0.69	signal transduction
GO:1902533	0.68	positive regulation of intracellular signal transduction
GO:0002376	0.67	immune system process
GO:0019219	0.66	regulation of nucleobase-containing compound metabolic process
GO:0002682	0.66	regulation of immune system process
GO:0006355	0.65	regulation of transcription, DNA-templated
GO:0002764	0.65	immune response-regulating signaling pathway
GO:0002684	0.65	positive regulation of immune system process
GO:0001817	0.65	regulation of cytokine production
GO:0050865	0.64	regulation of cell activation
GO:0007166	0.64	cell surface receptor signaling pathway
GO:0001819	0.64	positive regulation of cytokine production
GO:0051092	0.63	positive regulation of NF-kappaB transcription factor activity
GO:0038095	0.63	Fc-epsilon receptor signaling pathway
GO:0031295	0.63	T cell costimulation
GO:0043123	0.53	positive regulation of I-kappaB kinase/NF-kappaB signaling
GO:0009987	0.50	cellular 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:0043234	1.00	protein complex
GO:0044424	0.92	intracellular part
GO:0016020	0.92	membrane
GO:0005886	0.91	plasma membrane
GO:0005737	0.78	cytoplasm
GO:0043227	0.73	membrane-bounded organelle
GO:0044425	0.71	membrane part
GO:0044459	0.69	plasma membrane part
GO:0098802	0.68	plasma membrane receptor complex
GO:0045121	0.68	membrane raft
GO:0044421	0.68	extracellular region part
GO:0031982	0.68	vesicle
GO:0070062	0.67	extracellular exosome
GO:0044444	0.67	cytoplasmic part
GO:0042101	0.67	T cell receptor complex
GO:0005829	0.52	cytosol

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	1jqgA	0.382	4.78	0.062	0.716	3.4.17.1	NA
2	0.060	2v77A	0.479	4.25	0.027	0.810	3.4.17.1	NA
3	0.060	1h8lA	0.467	4.36	0.064	0.793	3.4.17.22	NA
4	0.060	1gytJ	0.494	3.87	0.018	0.793	3.4.11.1	NA
5	0.060	2afmA	0.495	4.48	0.061	0.853	2.3.2.5	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:

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	0.01	3kqzL	0.496	4.19	0.072	0.819	0.15	CO3	complex1.pdb.gz	71,72,73

	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.