D-I-TASSER Q8N7X1-D2

D-I-TASSER results for Q8N7X1-D2

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

Input Sequence in FASTA format

>Q8N7X1 (127 residues)
VPPTPGSGSRSRFSHRTRGGGSSPQRPPSQGRPDDGRGYAGYFDLWPYRAPMPRKRGPPP
RHHSSVPDYRPLRGDGNQNGYRGRDHEYTDHPSKGSYREPLKSYGGPCGAAPGRSTDAHS
RGRSDDA

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| VPPTPGSGSRSRFSHRTRGGGSSPQRPPSQGRPDDGRGYAGYFDLWPYRAPMPRKRGPPPRHHSSVPDYRPLRGDGNQNGYRGRDHEYTDHPSKGSYREPLKSYGGPCGAAPGRSTDAHSRGRSDDA
Prediction	CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHCCCCCCCCCCCCCCCCCCCCCCCCC
Confidence	9989888887778878888998998898888888888888766778787889888889988777887668888877778878887776778989866571221688788898889987778766779
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| VPPTPGSGSRSRFSHRTRGGGSSPQRPPSQGRPDDGRGYAGYFDLWPYRAPMPRKRGPPPRHHSSVPDYRPLRGDGNQNGYRGRDHEYTDHPSKGSYREPLKSYGGPCGAAPGRSTDAHSRGRSDDA
Prediction	8555645544552444466364444455444454544445534546527344457344454524234553455234544324145552463466542443165344445244453453346455478
	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

                   |                   |                   |                   |                   |                   |

SS
Seq

CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHCCCCCCCCCCCCCCCCCCCCCCCCC
VPPTPGSGSRSRFSHRTRGGGSSPQRPPSQGRPDDGRGYAGYFDLWPYRAPMPRKRGPPPRHHSSVPDYRPLRGDGNQNGYRGRDHEYTDHPSKGSYREPLKSYGGPCGAAPGRSTDAHSRGRSDDA

6ffyA3

0.05

2.24

0.56

CEthreader

SDFVLMKLPKYALPKDLQIISTDEQQVFVAVQEWNQVDTYNLYQSDLRGVRYSLVLENVRSSRQAEENVVI-----DILEVRGVKGVFLANQKVDGKVTTVITYNKGRDWDYLRPPSTDMNGKPTNC

5c3lB

0.04

2.02

0.45

EigenThreader

LCQDVENFQKFVKEQKQVQEEISRMSSKAMLKVQEDIKALKQLLSV---ASSGLQRNALAIDKLKIETAEELKNAEIALRTQKTPPGLQHENT--APADYFHTLVQQFEVQLQQYRQQIEELENHLA

2rdoL

0.17

5.44

0.44

FFAS-3D

-TLSPAEGSKKAGKRLGRGIGSGLGKTGGRGHKGQKSRSGGGVRRGFEGGQMPLYRRLPKFGFTSRKAAITDLNTLKAANIIGIQIEFAKVILAGEVTTPV-TVRGLRVTKGARAAIEAAGGKIEE-

7jjvA

0.14

0.13

4.31

1.94

SPARKS-K

CDGLDGADGTSNGQAGASGLAGGPNCNGGKGGKGTAGGAGGVGGAGGTGNTNGGAGGSGGNSDVAAGGAGAAGGAAGGAGTGGTGGNGGAKP------------GGAPGAGGAGTPAGSAGSPGQTT

4ujnH

0.28

0.07

2.17

0.08

CNFpred

VPPPSADPSKARKNRPRPSGNEAAIRDKTAGR-----------------------------------------------------------------------------------------------

6m5aA

0.11

0.09

3.41

0.83

DEthreader

--------ADVAYPSFGKGYGSDNYLFTRGIMVAAKIQAYSVYNWKVYRWLSNIENNIPSYMADAFTNNFSIWVAFHYNNYP-DQNEFSI---QL-GTTNWTMVDV----IPGWNYWDKDDKLSSA-

5ce8A

0.05

2.25

0.71

MapAlign

---LVDEEEAKVTVLSPSLNYGFGVFEGIRAYWNGENLYTSMMPVMAKATGIYLNSIMAAVEARARGYDEAIMLNAEGKVVEGSGENIFIVRRGVLMADEAFFVGTAAEITPIIEIDGRVLQRGPIT

1r5sA

0.12

4.14

0.82

MUSTER

LGSPSKDCGSP--KYAYFNGCSSPTAPLSPMSPPGYKLVTGDRNNSSCRNYNKQASE---WANYSAEQNRMGQAGSTISNSHAQPFDFPDDNQNAKKVAAGHELQPLAIVDQRPSSRAS-SRASSRP

3nr6A

0.11

0.09

3.12

0.41

HHsearch

----------TLGDQGGQG-Q-EPPPEPRITFLVDTGAQHSVLTQ----NPGPLSDKSAWKRYWTTDRKVHATGKVTHSFLHV-----PDCPYPLLGRDLLTKLKAQIHFEGPMGQPLQV-------

3i4iA

0.04

2.06

0.44

CEthreader

DGWGNGGVFNCIWRAYNIELKDGILNLSITDDMPSSSKPYAGAEYRTRDKFGYGLYQVRMKPAKNPGIVSSFFTYTGPVHGTPWDEIDIEFLGKDTTKVQFNYYTNSAGNHEYIYDLRFDASEDFHI

(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	0.4629

(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	3q3eA	0.45	4.90	0.064	0.827	model1_3q3eA.pdb.gz
2	3izyP1	0.45	4.81	0.036	0.795	model1_3izyP1.pdb.gz
3	4csu9	0.45	5.03	0.035	0.843	model1_4csu9.pdb.gz
4	2e7zA	0.44	5.05	0.085	0.858	model1_2e7zA.pdb.gz
5	6mq9A	0.44	4.65	0.026	0.787	model1_6mq9A.pdb.gz
6	1krcC2	0.44	5.03	0.086	0.827	model1_1krcC2.pdb.gz
7	3pe3A	0.44	4.94	0.028	0.811	model1_3pe3A.pdb.gz
8	1e9zB2	0.43	4.89	0.017	0.779	model1_1e9zB2.pdb.gz
9	2jlbA	0.43	5.11	0.037	0.827	model1_2jlbA.pdb.gz
10	3la4A3	0.43	4.85	0.026	0.764	model1_3la4A3.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	0.86	heterocyclic compound binding
GO:0097159	0.86	organic cyclic compound binding
GO:0003723	0.82	RNA binding
GO:0044822	0.66	poly(A) RNA binding
GO:0003729	0.65	mRNA binding
GO:0044877	0.56	macromolecular complex binding
GO:0003682	0.54	chromatin binding
GO:0001047	0.54	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	0.89	cellular process
GO:0065007	0.85	biological regulation
GO:0050789	0.79	regulation of biological process
GO:0050794	0.77	regulation of cellular process
GO:0060255	0.75	regulation of macromolecule metabolic process
GO:0080090	0.74	regulation of primary metabolic process
GO:0031323	0.74	regulation of cellular metabolic process
GO:0010468	0.74	regulation of gene expression
GO:0051252	0.73	regulation of RNA metabolic process
GO:0044260	0.73	cellular macromolecule metabolic process
GO:0044238	0.73	primary metabolic process
GO:0034641	0.73	cellular nitrogen compound metabolic process
GO:0048522	0.72	positive regulation of cellular process
GO:0006355	0.71	regulation of transcription, DNA-templated
GO:0051173	0.70	positive regulation of nitrogen compound metabolic process
GO:0044271	0.70	cellular nitrogen compound biosynthetic process
GO:0034645	0.70	cellular macromolecule biosynthetic process
GO:0031328	0.70	positive regulation of cellular biosynthetic process
GO:0019538	0.70	protein metabolic process
GO:0010628	0.70	positive regulation of gene expression
GO:0010557	0.70	positive regulation of macromolecule biosynthetic process
GO:0045893	0.67	positive regulation of transcription, DNA-templated
GO:0016070	0.65	RNA metabolic process
GO:0048024	0.63	regulation of mRNA splicing, via spliceosome
GO:0065003	0.62	macromolecular complex assembly
GO:0000381	0.62	regulation of alternative mRNA splicing, via spliceosome
GO:0006357	0.61	regulation of transcription from RNA polymerase II promoter
GO:0071347	0.60	cellular response to interleukin-1
GO:0045944	0.60	positive regulation of transcription from RNA polymerase II promoter
GO:0006509	0.60	membrane protein ectodomain proteolysis
GO:0006366	0.60	transcription from RNA polymerase II promoter
GO:0031324	0.57	negative regulation of cellular metabolic process
GO:0010605	0.57	negative regulation of macromolecule metabolic process
GO:0051253	0.55	negative regulation of RNA metabolic process
GO:0010629	0.55	negative regulation of gene expression
GO:0051260	0.53	protein homooligomerization
GO:0048026	0.53	positive regulation of mRNA splicing, via spliceosome
GO:0048025	0.53	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:0044464	1.00	cell part
GO:0044424	0.97	intracellular part
GO:0043229	0.88	intracellular organelle
GO:0043227	0.85	membrane-bounded organelle
GO:0043231	0.84	intracellular membrane-bounded organelle
GO:0005634	0.83	nucleus
GO:0044446	0.77	intracellular organelle part
GO:0032991	0.75	macromolecular complex
GO:0044428	0.73	nuclear part
GO:0030529	0.68	intracellular ribonucleoprotein complex
GO:0005681	0.66	spliceosomal complex
GO:0031988	0.65	membrane-bounded vesicle
GO:0070062	0.63	extracellular exosome
GO:0000791	0.63	euchromatin
GO:0071013	0.62	catalytic step 2 spliceosome
GO:0044530	0.62	supraspliceosomal complex
GO:0005719	0.62	nuclear euchromatin

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	3dnyT	0.408	4.82	0.069	0.724	3.6.5.3	68
2	0.060	2guwB	0.340	5.68	0.054	0.732	3.2.2.4	90
3	0.060	2nyfA	0.395	5.35	0.055	0.795	4.3.1.5	NA
4	0.060	1wsvA	0.423	4.85	0.019	0.764	2.1.2.10	98
5	0.060	3e1hB	0.397	4.93	0.028	0.732	2.3.1.74	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	2vpwA	0.425	5.24	0.060	0.827	0.56	SF4	complex1.pdb.gz	81,83,84,86,87,88

	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.