D-I-TASSER Q8NFG4-D3

D-I-TASSER results for Q8NFG4-D3

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

Input Sequence in FASTA format

>Q8NFG4 (84 residues)
SVDVVDQCLVCLKEEWMNKVKVLFKFTKVDSRPKEDTQKLLSILGASEEDNVKLLKFWMT
GLSKTYKSHLMSTVRSPTASESRN

Predicted Secondary Structure

Sequence	20 40 60 80 \| \| \| \| SVDVVDQCLVCLKEEWMNKVKVLFKFTKVDSRPKEDTQKLLSILGASEEDNVKLLKFWMTGLSKTYKSHLMSTVRSPTASESRN
Prediction	CHHHHHHHHHHHHHHHHHHHHHHHHSSSSCCCCHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCC
Confidence	858999999997899999989764113305886267999999978884336168889999988999999999972777675789
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 \| \| \| \| SVDVVDQCLVCLKEEWMNKVKVLFKFTKVDSRPKEDTQKLLSILGASEEDNVKLLKFWMTGLSKTYKSHLMSTVRSPTASESRN
Prediction	855125300421454114303011303534567664243024115134775140132023103541354025225445546568
	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

                   |                   |                   |                   |

SS
Seq

CHHHHHHHHHHHHHHHHHHHHHHHHSSSSCCCCHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCC
SVDVVDQCLVCLKEEWMNKVKVLFKFTKVDSRPKEDTQKLLSILGASEEDNVKLLKFWMTGLSKTYKSHLMSTVRSPTASESRN

6nzdH

0.98

0.70

19.68

1.00

DEthreader

SVDVVDQCLVCLKEEWMNKVKVLFKFTK---RPKEDTQKLLSILGASEEDNVKLLKFWMTGL-S--------------------

6nzdH2

1.00

0.71

20.00

1.06

MUSTER

SVDVVDQCLVCLKEEWMNKVKVLFKFTK---RPKEDTQKLLSILGASEEDNVKLLKFWMTGLS---------------------

6nzdH2

1.00

0.71

20.00

2.85

HHsearch

SVDVVDQCLVCLKEEWMNKVKVLFKFTK---RPKEDTQKLLSILGASEEDNVKLLKFWMTGLS---------------------

6nzdH

1.00

0.71

20.00

1.14

FFAS-3D

SVDVVDQCLVCLKEEWMNKVKVLFKFTK---RPKEDTQKLLSILGASEEDNVKLLKFWMTGLS---------------------

6nzdH2

0.98

0.70

19.68

1.00

DEthreader

SVDVVDQCLVCLKEEWMNKVKVLFKFTK---RPKEDTQKLLSILGASEEDNVKLLKFWMTGL-S--------------------

6nzdH2

1.00

0.71

20.00

0.92

SPARKS-K

SVDVVDQCLVCLKEEWMNKVKVLFKFTK---RPKEDTQKLLSILGASEEDNVKLLKFWMTGLS---------------------

3wb8A

0.07

2.93

0.66

MapAlign

AIQIYQQLVRVLENILQPMIVSGMEHETIQTYTLDSILRQLNSFPELIKQVVKQMFYIVGITKGMQIRYNVSQLEEWLRDKNLM

4j5mA

0.11

3.89

0.59

CEthreader

LSDLSIQIYQQLIKIAEGVLQPMIVSAMLESYCLEAIIRQMNAFHLDPEIILQVFKQLFYMINAVTLNNLLLRKDVCSWSTGMQ

6nzdH

1.00

0.71

20.00

1.06

MUSTER

SVDVVDQCLVCLKEEWMNKVKVLFKFTK---RPKEDTQKLLSILGASEEDNVKLLKFWMTGLS---------------------

3v42A

0.97

0.69

19.36

2.83

HHsearch

SVDVVDQALVALKEEWMNKVKVLFKFTKV---PKEDTQKLLSILGASEEDNVKLLKFWMTGLS---------------------

(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	0.6271

(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	6nzdH2	0.68	0.75	1.000	0.714	model1_6nzdH2.pdb.gz
2	5doqB	0.62	3.65	0.074	0.952	model1_5doqB.pdb.gz
3	6lt0B	0.61	1.82	0.074	0.750	model1_6lt0B.pdb.gz
4	2h09A	0.59	2.88	0.115	0.881	model1_2h09A.pdb.gz
5	7cb0A2	0.59	3.61	0.089	0.881	model1_7cb0A2.pdb.gz
6	2p4qA2	0.59	3.85	0.051	0.905	model1_2p4qA2.pdb.gz
7	6xjbA2	0.59	3.68	0.048	0.976	model1_6xjbA2.pdb.gz
8	6xjaP	0.59	3.60	0.048	0.988	model1_6xjaP.pdb.gz
9	2iz1B2	0.58	3.93	0.060	0.905	model1_2iz1B2.pdb.gz
10	2jkvA3	0.58	3.88	0.048	0.893	model1_2jkvA3.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	1.00	protein complex 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:2001170	1.00	negative regulation of ATP biosynthetic process
GO:2000973	1.00	regulation of pro-B cell differentiation
GO:2000506	1.00	negative regulation of energy homeostasis
GO:1901723	1.00	negative regulation of cell proliferation involved in kidney development
GO:1900181	1.00	negative regulation of protein localization to nucleus
GO:0070373	1.00	negative regulation of ERK1 and ERK2 cascade
GO:0051898	1.00	negative regulation of protein kinase B signaling
GO:0045944	1.00	positive regulation of transcription from RNA polymerase II promoter
GO:0045785	1.00	positive regulation of cell adhesion
GO:0043065	1.00	positive regulation of apoptotic process
GO:0035065	1.00	regulation of histone acetylation
GO:0035024	1.00	negative regulation of Rho protein signal transduction
GO:0032465	1.00	regulation of cytokinesis
GO:0032008	1.00	positive regulation of TOR signaling
GO:0032007	1.00	negative regulation of TOR signaling
GO:0031929	1.00	TOR signaling
GO:0030511	1.00	positive regulation of transforming growth factor beta receptor signaling pathway
GO:0030336	1.00	negative regulation of cell migration
GO:0030308	1.00	negative regulation of cell growth
GO:0030097	1.00	hemopoiesis
GO:0010823	1.00	negative regulation of mitochondrion organization
GO:0007043	1.00	cell-cell junction assembly
GO:0001934	1.00	positive regulation of protein phosphorylation
GO:0000122	1.00	negative regulation of transcription from RNA polymerase II promoter
GO:0007275	0.77	multicellular organism development
GO:0001701	0.76	in utero embryonic development

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:0044291	1.00	cell-cell contact zone
GO:0030496	1.00	midbody
GO:0005886	1.00	plasma membrane
GO:0005737	1.00	cytoplasm
GO:0005634	1.00	nucleus

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	1g8mA	0.386	4.40	0.014	0.774	3.5.4.10 2.1.2.3	NA
2	0.060	3ihyC	0.547	2.90	0.131	0.774	2.7.1.137	NA
3	0.060	2gaiA	0.524	3.87	0.134	0.929	5.99.1.2	NA
4	0.060	2h1nA	0.469	3.80	0.043	0.750	3.4.24.-	NA
5	0.060	2qvrA	0.553	3.19	0.062	0.786	3.1.3.11	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	3kcuA	0.556	2.83	0.036	0.786	0.87	MA5	complex1.pdb.gz	20,52,53,55,56,59

	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.