D-I-TASSER Q8NER5-D1

D-I-TASSER results for Q8NER5-D1

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

Input Sequence in FASTA format

>Q8NER5 (151 residues)
MTRALCSALRQALLLLAAAAELSPGLKCVCLLCDSSNFTCQTEGACWASVMLTNGKEQVI
KSCVSLPELNAQVFCHSSNNVTKTECCFTDFCNNITLHLPTASPNAPKLGPMELAIIITV
PVCLLSIAAMLTVWACQGRQCSYRKKKRPNV

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 \| \| \| \| \| \| \| MTRALCSALRQALLLLAAAAELSPGLKCVCLLCDSSNFTCQTEGACWASVMLTNGKEQVIKSCVSLPELNAQVFCHSSNNVTKTECCFTDFCNNITLHLPTASPNAPKLGPMELAIIITVPVCLLSIAAMLTVWACQGRQCSYRKKKRPNV
Prediction	CCCHHHHHHHHHHHHHHHCCCCCCCSSSSCCCCCCCCCSSCCCCSSSSSSSSCCCCSSSSSSCCCCCCCCCCSSSCCCCCCCCCSSCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCC
Confidence	9611344567888887622576775399856888999746017888999999099199998734666689855856999985211288877899988888899988887723556778999999999999999999987776413333489
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 \| \| \| \| \| \| \| MTRALCSALRQALLLLAAAAELSPGLKCVCLLCDSSNFTCQTEGACWASVMLTNGKEQVIKSCVSLPELNAQVFCHSSNNVTKTECCFTDFCNNITLHLPTASPNAPKLGPMELAIIITVPVCLLSIAAMLTVWACQGRQCSYRKKKRPNV
Prediction	7555134303200010123363241020205306766230403130000034576444234211546647320203357644313004421024453533445465643231200010233333233333222100122334454555478
	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

                   |                   |                   |                   |                   |                   |                   |

SS
Seq

CCCHHHHHHHHHHHHHHHCCCCCCCSSSSCCCCCCCCCSSCCCCSSSSSSSSCCCCSSSSSSCCCCCCCCCCSSSCCCCCCCCCSSCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCC
MTRALCSALRQALLLLAAAAELSPGLKCVCLLCDSSNFTCQTEGACWASVMLTNGKEQVIKSCVSLPELNAQVFCHSSNNVTKTECCFTDFCNNITLHLPTASPNAPKLGPMELAIIITVPVCLLSIAAMLTVWACQGRQCSYRKKKRPNV

2pjyC

0.42

0.21

6.03

2.01

SPARKS-K

------------------------ALQCFCHLCTKDNFTCVTDGLCFVSVTETTDKVIHNSSCIAEIDLIPPFVCAPSGSVTTTYCCNQDHCNKIEL------------------------------------------------------

2l5sA

0.38

0.20

5.89

1.00

CNFpred

--------------------GSATALQCFCHLCTKDNFTCVTDGLCFVSVTETTDKVIHNSMCIAEIDLDRPFVCAPSSSVTTTYCCNQDHCNKIELPT----------------------------------------------------

2pjyC

0.42

0.21

6.03

1.31

MUSTER

------------------------ALQCFCHLCTKDNFTCVTDGLCFVSVTETTDKVIHNSSCIAEIDLIPPFVCAPSGSVTTTYCCNQDHCNKIEL------------------------------------------------------

2qjbD

0.27

0.15

4.48

2.02

HHsearch

---------------------TLPFLKCYCSHCPEINNTCITNGHCFTMIEEDQGETTLTSGCLGLEG--SDFQCRDTPQRRSIECCRTNLCNQYLQPTLPPVVIG---------------------------------------------

2qjbD

0.26

0.15

4.50

0.69

CEthreader

---------------------TLPFLKCYCSHHDAINNTCITNGHCFTMIEEDDGETTLTSGCLGLEGSDFQCDTPIPHQRRSIECCRTNLCNQYLQPTLPPVVIG---------------------------------------------

4d3sA

0.04

0.03

1.83

0.72

EigenThreader

DSPAEALRAHAVMYRVLESDLKGRTILNLGSDTPAASRAAGARYVTGGVMS------PSFYSGDRAAFEENKALLEVLT---ATDFREDPGLAQVYYQILLDLFWTTMTGYLHALAVARAEMFFEGTSAAVAEGEAVLSLFRRGLDAGFAE

2qjbD

0.25

0.14

4.31

0.88

FFAS-3D

---------------------TLPFLKCYCSHHCPINNTCITNGHCFTMIEEDQGETTLTSGCLGLEGSDFQCRDTPIPHQRSIECCRTNLCNQYLQPTLPPVVI----------------------------------------------

2qjbD

0.26

0.14

4.30

1.76

SPARKS-K

---------------------TLPFLKCYCSHCPEINNTCITNGHCFTMIEEDQGETTLTSGCLGLFQCRDT---PIPHQRRSIECCRTNLCNQYLQPTLPPVVIG---------------------------------------------

2pjyC

0.42

0.21

6.03

0.94

CNFpred

------------------------ALQCFCHLCTKDNFTCVTDGLCFVSVTETTDKVIHNSSCIAEIDLIRPFVCAPSSSVTTTYCCNQDHCNKIEL------------------------------------------------------

5a1uD

0.02

1.42

0.83

DEthreader

IRCMQINCIDASFHPELPIIHSSTQQANLKA----MGSCEIYPQTIQHNPN------GRFVVVCGDQEFAKH-KTGLWVGFLGYYLG----L--N-IVSYSLLVSTIPKRTVSTDPRFQLAVESWKECLHQDYGLLAAKVAFMCLREAAFE

(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	0.5257

(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	3eqxA	0.54	4.54	0.087	0.828	model1_3eqxA.pdb.gz
2	6y5rA	0.49	4.15	0.040	0.715	model1_6y5rA.pdb.gz
3	1l8wD	0.48	5.07	0.094	0.808	model1_1l8wD.pdb.gz
4	5vkuL	0.48	4.92	0.076	0.834	model1_5vkuL.pdb.gz
5	4rglA	0.47	4.92	0.023	0.781	model1_4rglA.pdb.gz
6	5nd1A	0.47	5.53	0.061	0.894	model1_5nd1A.pdb.gz
7	7d7qA	0.47	4.98	0.087	0.795	model1_7d7qA.pdb.gz
8	6oqqA	0.47	4.78	0.063	0.775	model1_6oqqA.pdb.gz
9	5zihA	0.46	4.76	0.031	0.722	model1_5zihA.pdb.gz
10	7akwA	0.46	4.66	0.084	0.722	model1_7akwA.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:0004675	0.96	transmembrane receptor protein serine/threonine kinase activity
GO:0019838	0.89	growth factor binding
GO:0005025	0.83	transforming growth factor beta receptor activity, type I
GO:0005057	0.81	receptor signaling protein activity
GO:0050431	0.77	transforming growth factor beta 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:0044699	0.99	single-organism process
GO:0009987	0.99	cellular process
GO:0050794	0.97	regulation of cellular process
GO:0044763	0.96	single-organism cellular process
GO:0032502	0.95	developmental process
GO:0048856	0.94	anatomical structure development
GO:0048869	0.93	cellular developmental process
GO:0044767	0.93	single-organism developmental process
GO:0031323	0.93	regulation of cellular metabolic process
GO:0007165	0.93	signal transduction
GO:0080090	0.92	regulation of primary metabolic process
GO:0060255	0.92	regulation of macromolecule metabolic process
GO:0007178	0.92	transmembrane receptor protein serine/threonine kinase signaling pathway
GO:0048518	0.91	positive regulation of biological process
GO:0048522	0.90	positive regulation of cellular process
GO:0016043	0.90	cellular component organization
GO:0051239	0.88	regulation of multicellular organismal process
GO:0010604	0.88	positive regulation of macromolecule metabolic process
GO:0050793	0.87	regulation of developmental process
GO:0032924	0.87	activin receptor signaling pathway
GO:0031325	0.87	positive regulation of cellular metabolic process
GO:0030154	0.86	cell differentiation
GO:0006355	0.86	regulation of transcription, DNA-templated
GO:2000026	0.84	regulation of multicellular organismal development
GO:0042127	0.82	regulation of cell proliferation
GO:0010628	0.79	positive regulation of gene expression
GO:0009653	0.79	anatomical structure morphogenesis
GO:0051128	0.78	regulation of cellular component organization
GO:0048513	0.78	animal organ development
GO:0045893	0.78	positive regulation of transcription, DNA-templated
GO:0045595	0.78	regulation of cell differentiation
GO:0032989	0.78	cellular component morphogenesis
GO:0022603	0.76	regulation of anatomical structure morphogenesis
GO:0001936	0.76	regulation of endothelial cell proliferation
GO:0060317	0.75	cardiac epithelial to mesenchymal transition
GO:0042118	0.75	endothelial cell activation
GO:0035556	0.75	intracellular signal transduction
GO:0007179	0.75	transforming growth factor beta receptor signaling pathway
GO:0001938	0.75	positive regulation of endothelial cell proliferation
GO:0048762	0.74	mesenchymal cell differentiation
GO:0010717	0.74	regulation of epithelial to mesenchymal transition
GO:0007507	0.74	heart 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:0016020	0.94	membrane
GO:0005623	0.79	cell
GO:0044464	0.74	cell part
GO:0044424	0.56	intracellular part

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	1z0hB	0.352	5.17	0.073	0.636	3.4.24.69	NA
2	0.060	1h1lA	0.443	5.11	0.054	0.781	1.18.6.1	NA
3	0.060	1kizA	0.434	4.39	0.047	0.695	4.2.3.6	NA
4	0.060	3eueA	0.426	4.94	0.031	0.715	2.4.2.3	NA
5	0.060	1qleA	0.458	5.07	0.094	0.775	1.9.3.1	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:

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	3dinA	0.458	4.97	0.028	0.755	0.11	UUU	complex1.pdb.gz	24,25,39,40,46

	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.