D-I-TASSER Q8NDB2-D2

D-I-TASSER results for Q8NDB2-D2

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

Input Sequence in FASTA format

>Q8NDB2 (117 residues)
NIPTDLRAKHSGEISERKEIEELSEASRNTIPLAVVLPTEIPCENPGEIFIILRDEVIGD
TVEVEFTSSNKRIRTRPALWNKKVWCMKALEFPAGSVHVNVYCDGIVKATTKIKYYP

Predicted Secondary Structure

Sequence	20 40 60 80 100 \| \| \| \| \| NIPTDLRAKHSGEISERKEIEELSEASRNTIPLAVVLPTEIPCENPGEIFIILRDEVIGDTVEVEFTSSNKRIRTRPALWNKKVWCMKALEFPAGSVHVNVYCDGIVKATTKIKYYP
Prediction	CCCCCCCCCCCHHHCCCCCCHHHHHHCCCCCCSSSSSCCCCCCCCCCSSSSSSSCCCCCCSSSSSSSCCCCSSSSCCCCCCCCSSSSSSCCCCCCCSSSSSSSCCSSSSSSSSSSCC
Confidence	997011555504421211201221212466744787235555799974999992223671589998335301220344114606888631689973589999532466547877639
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 \| \| \| \| \| NIPTDLRAKHSGEISERKEIEELSEASRNTIPLAVVLPTEIPCENPGEIFIILRDEVIGDTVEVEFTSSNKRIRTRPALWNKKVWCMKALEFPAGSVHVNVYCDGIVKATTKIKYYP
Prediction	834764636356525755536524733453122011133504174333000002441445314342345543242423224530210332613424030302031114234515538
	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

CCCCCCCCCCCHHHCCCCCCHHHHHHCCCCCCSSSSSCCCCCCCCCCSSSSSSSCCCCCCSSSSSSSCCCCSSSSCCCCCCCCSSSSSSCCCCCCCSSSSSSSCCSSSSSSSSSSCC
NIPTDLRAKHSGEISERKEIEELSEASRNTIPLAVVLPTEIPCENPGEIFIILRDEVIGDTVEVEFTSSNKRIRTRPALWNKKVWCMKALEFPAGSVHVNVYCDGIVKATTKIKYYP

2dijA

0.10

0.09

3.45

1.17

DEthreader

TDFSTT-NGK-WFLVNDRSY-QVDRGAYGSFGTIHVGPMMAKP--GVTITIDG-RGFGSSKGTVYFG----TTAVSITSWEDTQIKVKIPAVAGGNYNIKVANAGTASNVYDFEVLG

6swsA

0.25

0.19

5.82

1.87

SPARKS-K

------------------------------SNAMVVQPDRIRCGAETTVYVIVRCKLDDRVTEAEFSPESPSVRMEAKVENEYTISVKAPNLSSGNVSLKIYSGDLVVCETVISYYT

6swsA

0.25

0.19

5.82

1.45

MUSTER

------------------------------SNAMVVQPDRIRCGAETTVYVIVRCKLDDRATEAEFSPEDPSVRMEAKVENEYTISVKAPNLSSGNVSLKIYSGDLVVCETVISYYT

6swsA

0.25

0.19

5.82

4.54

HHsearch

------------------------------SNAMVVQPDRIRCGAETTVYVIVRCKLDDRATEAEFSPEDPSVRMEAKVENEYTISVKAPNLSSGNVSLKIYSGDLVVCETVISYYT

6swsA

0.26

0.19

5.80

1.39

FFAS-3D

-------------------------------NAMVVQPDRIRCGAETTVYVIVRCKLDDRVTEAEFSPEDSSVRMEAKVENEYTISVKAPNLSSGNVSLKIYSGDLVVCETVISYY-

6swsA

0.25

0.19

5.82

1.71

CNFpred

------------------------------SNAMVVQPDRIRCGAETTVYVIVRCKLDDVATEAEFSPESPSVRMEAKVENEYTISVKAPNLSSGNVSLKIYSGDLVVCETVISYYT

1ej6A

0.07

0.06

2.53

1.17

DEthreader

----A-KS-MTFDAAFQQILKICRAWPNCIHGLPMEKRGNFIVGQ-NCSLVIP--GF-NAQDVFNCYFNSALFSTEAQFDTKGEWTLDMVFSDAGIYTMQALVGANPVSLGSFVVDS

1qhoA

0.12

0.11

3.92

1.17

DEthreader

ISNWDD--YGDHKFDLNMTLTSRGTAIQYGFFQISVAPNMG-IP-GNVVTIDG-KGFGTTQGTVTFG----GVTATVKSWTSNRIEVYVPNMAAGLTDVKVTAGGVSSNLYSYNILT

3hrpA1

0.16

0.13

4.24

0.83

SPARKS-K

-----------------------ATYDPNQPVTVESFPVEGK--LREKVIVKGSNFGDKSKVKVYFVDEAAERLSTVIGIDNNTLYCLAPRQLPGGNRIKVIVDGK-EVTTTFKYEQ

6swsA

0.27

0.20

6.04

0.50

MapAlign

-------------------------------SNAVVQPDRIRCGAETTVYVIVRCKLDRVATEAEFSPESPSVRMEAKVENEYTISVKAPNLSSGNVSLKIYSGDLVVCETVISYYT

(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	0.703

(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	6swsA	0.70	1.12	0.264	0.744	model1_6swsA.pdb.gz
2	1qhoA	0.67	3.56	0.101	0.906	model1_1qhoA.pdb.gz
3	4jclA	0.67	3.35	0.138	0.906	model1_4jclA.pdb.gz
4	2dijA	0.67	3.42	0.109	0.914	model1_2dijA.pdb.gz
5	1cygA	0.67	3.45	0.092	0.906	model1_1cygA.pdb.gz
6	4jcmA	0.66	3.38	0.109	0.914	model1_4jcmA.pdb.gz
7	3cu7A	0.65	3.66	0.053	0.957	model1_3cu7A.pdb.gz
8	6vxkB2	0.64	2.08	0.067	0.744	model1_6vxkB2.pdb.gz
9	2b39A	0.64	3.88	0.094	0.992	model1_2b39A.pdb.gz
10	4fxgA	0.64	3.75	0.070	0.966	model1_4fxgA.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:0036312	0.41	phosphatidylinositol 3-kinase regulatory subunit binding
GO:0003824	0.39	catalytic activity
GO:0046872	0.36	metal ion binding
GO:0016740	0.32	transferase activity
GO:0042802	0.30	identical protein binding
GO:0016758	0.30	transferase activity, transferring hexosyl groups

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:1902533	1.00	positive regulation of intracellular signal transduction
GO:0002682	1.00	regulation of immune system process
GO:0031323	0.94	regulation of cellular metabolic process
GO:0042325	0.93	regulation of phosphorylation
GO:0048523	0.87	negative regulation of cellular process
GO:0001932	0.87	regulation of protein phosphorylation
GO:0043408	0.86	regulation of MAPK cascade
GO:0009968	0.86	negative regulation of signal transduction
GO:0002683	0.86	negative regulation of immune system process
GO:0051239	0.62	regulation of multicellular organismal process
GO:0051249	0.61	regulation of lymphocyte activation
GO:0051171	0.61	regulation of nitrogen compound metabolic process
GO:0045937	0.61	positive regulation of phosphate metabolic process
GO:0031326	0.61	regulation of cellular biosynthetic process
GO:0001817	0.61	regulation of cytokine production
GO:2000112	0.60	regulation of cellular macromolecule biosynthetic process
GO:1903531	0.60	negative regulation of secretion by cell
GO:0070201	0.60	regulation of establishment of protein localization
GO:0051250	0.60	negative regulation of lymphocyte activation
GO:0051241	0.60	negative regulation of multicellular organismal process
GO:0032675	0.60	regulation of interleukin-6 production
GO:0010468	0.60	regulation of gene expression
GO:0001934	0.60	positive regulation of protein phosphorylation
GO:1900165	0.59	negative regulation of interleukin-6 secretion
GO:0051898	0.59	negative regulation of protein kinase B signaling
GO:0050869	0.59	negative regulation of B cell activation
GO:0045947	0.59	negative regulation of translational initiation
GO:0043410	0.59	positive regulation of MAPK cascade

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:0016020	1.00	membrane
GO:0005829	1.00	cytosol
GO:0005886	0.83	plasma membrane
GO:0043227	0.74	membrane-bounded organelle
GO:0043231	0.71	intracellular membrane-bounded organelle
GO:0005634	0.66	nucleus
GO:0005737	0.59	cytoplasm
GO:0005576	0.54	extracellular region

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	2dleA	0.521	2.47	0.045	0.675	3.1.3.48	90,100
2	0.066	1k85A	0.485	2.92	0.072	0.675	3.2.1.14	NA
3	0.066	2rq8A	0.501	2.98	0.110	0.692	2.7.11.1	NA
4	0.066	2djmA	0.546	2.79	0.056	0.744	3.2.1.3	NA
5	0.066	2bk8A	0.488	3.30	0.060	0.709	2.7.11.1	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:

No Binding sites was predicted

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

	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.