D-I-TASSER Q8N7X1-D8

D-I-TASSER results for Q8N7X1-D8

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

Input Sequence in FASTA format

>Q8N7X1 (123 residues)
GGGRYEEYRGPSPDAHSGGRDSSIKSYGLSDRYGGGGHYEEYQGSLPDAYSGDHDRSSNS
YGRSDRYSRGRDRVGRPDRGLPLPMETGSPPLHDSYSRSGCRVPRGGGRQGGRFERGEGR
SRY

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| GGGRYEEYRGPSPDAHSGGRDSSIKSYGLSDRYGGGGHYEEYQGSLPDAYSGDHDRSSNSYGRSDRYSRGRDRVGRPDRGLPLPMETGSPPLHDSYSRSGCRVPRGGGRQGGRFERGEGRSRY
Prediction	CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Confidence	987521135899877678877788889999877998777766688865568887777877677543356777656777789986456999985433556654788888767622236886679
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| GGGRYEEYRGPSPDAHSGGRDSSIKSYGLSDRYGGGGHYEEYQGSLPDAYSGDHDRSSNSYGRSDRYSRGRDRVGRPDRGLPLPMETGSPPLHDSYSRSGCRVPRGGGRQGGRFERGEGRSRY
Prediction	865446636455463354446444554334543334442573444446425444544444324443344245413467543434275533344632454434345533543543666654668
	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                 120

                   |                   |                   |                   |                   |                   |

SS
Seq

CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
GGGRYEEYRGPSPDAHSGGRDSSIKSYGLSDRYGGGGHYEEYQGSLPDAYSGDHDRSSNSYGRSDRYSRGRDRVGRPDRGLPLPMETGSPPLHDSYSRSGCRVPRGGGRQGGRFERGEGRSRY

6t4dA

0.12

4.29

0.75

CEthreader

GELYEGYWKNDKVHGKGTLTYSKGDKYIGEWKYAKKCGEGELIYASGDKFKGQWKNDKANGYGILLYNNGNKYEGRHGMGTFTCKEDGTIYSGHFQFNRKHGKGTLTFVNGHILQGIWNSGLL

1p4kA

0.06

2.54

0.48

EigenThreader

NKPIVLSANVEAWKVLSKGGKALDAVEKGVRLVEDDPTERSVGYGGRPDRDGRVTGMAYKMHGRVGDSPIIGAGLEIGEEVIRTVGTHLVVELMNQGRTPQQACKEAVERIVKIVNRRGKNLK

2k7mA

0.16

0.13

4.34

0.48

FFAS-3D

---------GPLGST------SLVQGLTPPPDFNQCL-----KNSPDEKFFSDFSNNMGSRKNPDPLATEEVPNQEQPEEGFIHTQYGQKPEQPSGASAGHRFPQGYHSDKRRLSKASSKAR-

7jjvA

0.16

0.15

5.13

1.76

SPARKS-K

----MQCDGLDGADGTSNGQAGASGLAGGPNCNGGGGKGAPGVGTAGGAGGGGAGGTGNTNGGAGGSGGNSDVAAGGAGAAGGAAGGAGTGGTGGNGGAGKPGG-APGAGGAGTPAGSAGSPG

3s3zA

0.16

0.04

1.35

0.37

CNFpred

--------------------------------------------------------------------------------------------LGKFSQTCYNSAIQGSVLTSTCERTNGGYNT

1wkvB

0.03

0.02

1.54

0.83

DEthreader

LVFDISVPEMVF-PS-------PLFERKPT-PLVRWLKLEWNFDRAVISRL-SRRVEKGALYYRAVHVNQNDANFAHLTSMLVQPAAEVTEMEAEV---RSDG--LVIGPSGGAAVKALAKKA

6ar6A

0.10

3.57

0.97

MapAlign

-------VTVGDDKYYFNPINGGAASIGETIIDDKNYYFNTEDGFKYFAPANTLDENLEGEAIDDNYRGAVEWKELDGEMHYFSPETGKAFKGLNQIGDYKYYFNSDGVMQKGFVSINDNKH-

1r5sA

0.15

0.14

4.67

0.73

MUSTER

GPGSPSKDCGSPKYAYFNGCSSPTAPLSPMSP-------PGYKLVTGDRNNSSCRNYNKQASEWANYSAEQNRMGSNSHAQPFDFPDDNQNAKKVAGHELQPLAIVDQRPSSRASSRASRPRP

1mqsA3

0.19

0.11

3.66

0.61

HHsearch

NSSTTDSYLYIDPKIT-RGSHTRKPKRQSYNKVGG-GNYLEYQN-LQE-WAHSKKVY----GSTAITTPEISRLGASN---SS----------------------------------------

4yy8A2

0.06

2.54

0.56

CEthreader

IIPNVEAYDHRMKAWVEVAPLNTPRSSAMCVAFDNKIYVIGGTNGERLNSIEVYEEKMNKWEQFPYALLEARSSGAAQIYVVGGIDNEHNILDSVEFLNGVPEKKMNFGAAITGGENGEVLNS

(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	0.4921

(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	4mifA	0.47	4.41	0.040	0.797	model1_4mifA.pdb.gz
2	3salA	0.47	4.86	0.045	0.837	model1_3salA.pdb.gz
3	3vtaA	0.46	4.45	0.051	0.805	model1_3vtaA.pdb.gz
4	6qp7A	0.46	4.78	0.063	0.829	model1_6qp7A.pdb.gz
5	3ol2B	0.46	4.76	0.062	0.846	model1_3ol2B.pdb.gz
6	3bg7A	0.46	4.42	0.059	0.797	model1_3bg7A.pdb.gz
7	2uzyB1	0.44	5.01	0.044	0.829	model1_2uzyB1.pdb.gz
8	1wmfA	0.44	4.69	0.054	0.821	model1_1wmfA.pdb.gz
9	2zwoA	0.43	5.13	0.080	0.837	model1_2zwoA.pdb.gz
10	1b9tA	0.42	4.62	0.031	0.780	model1_1b9tA.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	1.00	heterocyclic compound binding
GO:0097159	1.00	organic cyclic compound binding
GO:0003723	0.99	RNA binding
GO:0044822	0.81	poly(A) RNA binding
GO:0003729	0.66	mRNA binding
GO:0044877	0.58	macromolecular complex binding
GO:0044212	0.58	transcription regulatory region DNA binding
GO:0003682	0.56	chromatin binding
GO:0001047	0.56	core promoter 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:0009987	0.99	cellular process
GO:0008152	0.96	metabolic process
GO:0071704	0.95	organic substance metabolic process
GO:0044238	0.95	primary metabolic process
GO:0044260	0.93	cellular macromolecule metabolic process
GO:0016070	0.92	RNA metabolic process
GO:0010468	0.77	regulation of gene expression
GO:2000112	0.76	regulation of cellular macromolecule biosynthetic process
GO:0080090	0.76	regulation of primary metabolic process
GO:0051171	0.76	regulation of nitrogen compound metabolic process
GO:0051173	0.73	positive regulation of nitrogen compound metabolic process
GO:0031328	0.73	positive regulation of cellular biosynthetic process
GO:0010628	0.73	positive regulation of gene expression
GO:0010557	0.73	positive regulation of macromolecule biosynthetic process
GO:0045893	0.72	positive regulation of transcription, DNA-templated
GO:0044249	0.72	cellular biosynthetic process
GO:0009059	0.72	macromolecule biosynthetic process
GO:0032774	0.71	RNA biosynthetic process
GO:0016043	0.68	cellular component organization
GO:0065003	0.67	macromolecular complex assembly
GO:0034645	0.66	cellular macromolecule biosynthetic process
GO:0050896	0.65	response to stimulus
GO:0006351	0.65	transcription, DNA-templated
GO:0071347	0.63	cellular response to interleukin-1
GO:0045944	0.63	positive regulation of transcription from RNA polymerase II promoter
GO:0006509	0.63	membrane protein ectodomain proteolysis
GO:0006366	0.63	transcription from RNA polymerase II promoter
GO:0000381	0.63	regulation of alternative mRNA splicing, via spliceosome
GO:0010629	0.59	negative regulation of gene expression
GO:0051260	0.56	protein homooligomerization
GO:0048026	0.56	positive regulation of mRNA splicing, via spliceosome
GO:0048025	0.56	negative regulation of mRNA splicing, via spliceosome

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:0044424	1.00	intracellular part
GO:0043231	0.88	intracellular membrane-bounded organelle
GO:0032991	0.87	macromolecular complex
GO:0005634	0.87	nucleus
GO:0044446	0.85	intracellular organelle part
GO:0044428	0.84	nuclear part
GO:0030529	0.81	intracellular ribonucleoprotein complex
GO:0005681	0.78	spliceosomal complex
GO:0044421	0.64	extracellular region part
GO:0016020	0.63	membrane
GO:0071013	0.62	catalytic step 2 spliceosome
GO:0070062	0.62	extracellular exosome
GO:0044530	0.61	supraspliceosomal complex
GO:0005719	0.61	nuclear euchromatin
GO:0016021	0.53	integral component of membrane

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	1r9mB	0.437	4.61	0.045	0.797	3.4.14.5	NA
2	0.060	2vskC	0.436	4.90	0.049	0.813	3.2.1.18	NA
3	0.060	2ebsB	0.439	4.71	0.035	0.780	3.2.1.150	29
4	0.060	1tt0A	0.472	4.31	0.078	0.805	1.1.3.10	NA
5	0.060	2vsmA	0.450	5.01	0.036	0.846	3.2.1.18	68

	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	0.01	2cmlC	0.461	4.98	0.081	0.846	0.66	ZMR	complex1.pdb.gz	25,27,43,44,82,83
2	0.01	1e8vA	0.456	4.87	0.046	0.837	0.53	CA	complex2.pdb.gz	11,21,22,24
3	0.01	1v3bB	0.432	5.07	0.038	0.821	0.47	CA	complex3.pdb.gz	31,33,34,35,36
4	0.01	1v2iB	0.448	5.13	0.044	0.870	0.44	CA	complex4.pdb.gz	31,34,36

	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.