D-I-TASSER Q9NTN9-D3

D-I-TASSER results for Q9NTN9-D3

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

Input Sequence in FASTA format

>Q9NTN9 (170 residues)
LAPDVRLLYVLAIAALGGLCLILASSLLYVACLREGRRGRRRKYSLGRASRAGGSAVQLQ
TVSGQCPGEEDEGDDEGAGGLEGSCLQIIPGEGAPAPPPPPPPPPPAELTNGLVALPSRL
RRMNGNSYVLLRQSNNGVPAGPCSFAEELSRILEKRKHTQLVEQLDESSV

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 \| \| \| \| \| \| \| \| LAPDVRLLYVLAIAALGGLCLILASSLLYVACLREGRRGRRRKYSLGRASRAGGSAVQLQTVSGQCPGEEDEGDDEGAGGLEGSCLQIIPGEGAPAPPPPPPPPPPAELTNGLVALPSRLRRMNGNSYVLLRQSNNGVPAGPCSFAEELSRILEKRKHTQLVEQLDESSV
Prediction	CCCCCSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCSSSSSSCCCCCCCCCCCCCCCCCCCCCCSSSSCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHCCCSSSSSSSCCCCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCC
Confidence	99872105689999999999999999999999752035665541003566678861688872256888767776565677788727982699999999999999921014645676899997359817999726889999875479999999998632122126674679
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 \| \| \| \| \| \| \| \| LAPDVRLLYVLAIAALGGLCLILASSLLYVACLREGRRGRRRKYSLGRASRAGGSAVQLQTVSGQCPGEEDEGDDEGAGGLEGSCLQIIPGEGAPAPPPPPPPPPPAELTNGLVALPSRLRRMNGNSYVLLRQSNNGVPAGPCSFAEELSRILEKRKHTQLVEQLDESSV
Prediction	73451310101213331231332132101010134455456442413436545433141421354146665656545444244100200337454444664454453514412430342046254422110233674444432412530450155453352265257668
	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                 140                 160

                   |                   |                   |                   |                   |                   |                   |                   |

SS
Seq

CCCCCSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCSSSSSSCCCCCCCCCCCCCCCCCCCCCCSSSSCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHCCCSSSSSSSCCCCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCC
LAPDVRLLYVLAIAALGGLCLILASSLLYVACLREGRRGRRRKYSLGRASRAGGSAVQLQTVSGQCPGEEDEGDDEGAGGLEGSCLQIIPGEGAPAPPPPPPPPPPAELTNGLVALPSRLRRMNGNSYVLLRQSNNGVPAGPCSFAEELSRILEKRKHTQLVEQLDESSV

4cofA

0.08

0.07

2.78

0.57

CEthreader

---------------------QSVNDPGNMSFVKETVDKLLKGYDIRLRPDFGGPPVCVGMNIDIASIDMVSEVNMDYTLTMYFQQYWRDKRLAYSGIPLNLTLDNSFVHGVTVKNRMIRLHPDGTVLYGLRITTTAACMMDLRRYPLDEQNCTLEIESYGYTTDDIEFY

6lvfB

0.10

3.68

0.55

EigenThreader

VDGLWLRLIAIAILAALAFVVYAGIYAIAVGLGVLSHVPAGFGVFETIIIAWLGSSPLVIAIAAISVAELRSSMRRIGARLMPQLLSAFALLLGMMLVFSSVTPTHNLIVESAHFLSSLLGLAIIVAARGLSQ----RLDGAWWVSTFSALFALFFSLLGWLTAIAVVCI

7cu3A7

0.10

0.08

3.06

0.40

FFAS-3D

LPRTTNILKRSGEQIWSVSIFLLFFLLLYGILGVQMFGTFTYHCVVNDTKPGNVTWNSLAIPDTHCSPELEEGYQCPPGFK---------CMDLEDLGLSRQELGYSGFNEIGTSIFTVYEASSQEGWLVKNV-------FIAVIIETFAEIRVQFQQM-----------

4btgA

0.09

3.33

0.67

SPARKS-K

PMVAIAALRTGASNDLKRSMFNYYAAVMHYAVAHNPE----VVVSEHQGVAAEQGSLYLV-----WNVRTELRIPVGYNAIEGGSIRTPENKPIQPSEVLQAKVLDHEASTEFAYEDAYSVTIRNKRYAEVKERRERVRILKPTDDRTLAAARRTSRDDAEKLAIDGRRM

3gi9C

0.03

0.01

0.36

0.58

CNFpred

IGDNIITGALSILLWMSYVISIALFAKGFAGYFLP---------------------------------------------------------------------------------------------------------------------------------------

6xljD

0.08

0.06

2.57

0.83

DEthreader

-----AAPDIIVRNEKRMLQEAVDALLDSLADMIKGRFRQNLGKRNRTRGVCAAILSPAN-------------------TAGLTRLVAQDL-VVTEDCGTGIMMTPVEPLRDRVLGRVRSVCACYAIGAAIGEPG-TQLYRGVKINDKHI-EVIVRQMLRKAVYSK--R-

5tsjN

0.07

2.86

0.71

MapAlign

ALKLKPPVLAKLVYILNWMVFWTVVWGLIYGEFFGTFLEHLGVFGTPEHPGLIPILGVVMVFAGLILRAYLGLKHRHMAHFWEGVGYLGGLLG-------ILALAASYLGNLQAGWLSALMYLGFGVFLLSVVMSSIWLMIPEIFTQAGHILSHIRIYAVGAAGGILAGL

6h9hB1

0.13

0.10

3.47

0.49

MUSTER

--------------------------------------GQQHRFALPAGKKLWPNDLREALAKHDLPPLFFSRDPQTGHAITRAMRNEKRVRGYIEQHGHEPPPPTEEQRANPLAIPG-IRIVGSSTWVGILATGERYKPLLEAATLPAIQIVTQRCGRGVGVELEQHTL

1hi8A

0.10

0.09

3.25

0.58

HHsearch

RRRTA-GGPFALNAPI---AVAQPVRNKYAYTFHHTVKEW--SLCVATDDHDTFWPGWLRDL--ICDEAPWWVKLKLPVYVGAP----APEQGHTPSNPDLEVGLSSQGATD---L-GTL--LS-ITY-LV-QLDH-TAPHLPSACRFLDSYWQGHEEIRQISKSDDALG

6x3sA

0.08

0.06

2.59

0.57

CEthreader

---------------------------SNMSLVKETVDRLLKGYDIRLRPDFGGPPVAVGMNIDIASIDMVSEVNMDYTLTMYFQQAWRDKRLSYNVIPLNLTLDNSFVHGVTVKNRMIRLHPDGTVLYGLRITTTAACMMDLRRYPLDEQNCTLEIESYGYTTDDIEFY

(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	0.473

(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	1ffvB	0.45	6.05	0.067	0.912	model1_1ffvB.pdb.gz
2	6idfB	0.44	4.93	0.068	0.700	model1_6idfB.pdb.gz
3	6gdtA	0.44	5.11	0.036	0.741	model1_6gdtA.pdb.gz
4	1hxgA	0.44	5.92	0.101	0.853	model1_1hxgA.pdb.gz
5	5dgqA	0.44	5.13	0.042	0.741	model1_5dgqA.pdb.gz
6	3g4dA	0.44	5.93	0.063	0.818	model1_3g4dA.pdb.gz
7	4qs4A1	0.44	5.53	0.020	0.759	model1_4qs4A1.pdb.gz
8	1t3qB	0.39	5.62	0.063	0.747	model1_1t3qB.pdb.gz
9	1ga2B1	0.39	5.18	0.024	0.682	model1_1ga2B1.pdb.gz
10	1sb3D2	0.39	5.81	0.066	0.735	model1_1sb3D2.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:0045499	1.00	chemorepellent activity
GO:0038191	1.00	neuropilin binding
GO:0030215	1.00	semaphorin receptor 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:0071526	1.00	semaphorin-plexin signaling pathway
GO:0050919	1.00	negative chemotaxis
GO:0048843	1.00	negative regulation of axon extension involved in axon guidance
GO:0030335	1.00	positive regulation of cell migration
GO:0001755	1.00	neural crest cell migration

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:0005615	1.00	extracellular space
GO:0044464	0.70	cell 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	3gk0A	0.417	4.91	0.067	0.682	2.6.99.2	141
2	0.060	2xalA	0.409	5.05	0.072	0.676	2.7.1.158	30,57
3	0.060	2e9yA	0.403	5.53	0.083	0.729	2.7.2.2	NA
4	0.060	2fiqC	0.405	5.38	0.052	0.712	2.7.1.144	122,125
5	0.060	2j5tD	0.403	5.79	0.097	0.771	2.7.2.11	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	1hbnA	0.425	5.73	0.073	0.824	0.42	UUU	complex1.pdb.gz	114,117,120
	2	0.01	3m2rD	0.431	5.86	0.072	0.841	0.50	F43	complex2.pdb.gz	20,21,22,110,113

	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.