D-I-TASSER Q9P2X3-D2

D-I-TASSER results for Q9P2X3-D2

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

Input Sequence in FASTA format

>Q9P2X3 (193 residues)
KKTEEEDVECEDDLILACQPESSLKALDFDISETRTEVEVEELPPIDHGIPITDRRSTFQ
AHLAPVVCPKQVKMVLSKLYENKKIASATHNIYAYRIYCEDKQTFLQDCEDDGETAAGGR
LLHLMEILNVKNVMVVVSRWYGGILLGPDRFKHINNCARNILVEKNYTNSPEESSKALGK
NKKVRKDKKRNEH

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 \| \| \| \| \| \| \| \| \| KKTEEEDVECEDDLILACQPESSLKALDFDISETRTEVEVEELPPIDHGIPITDRRSTFQAHLAPVVCPKQVKMVLSKLYENKKIASATHNIYAYRIYCEDKQTFLQDCEDDGETAAGGRLLHLMEILNVKNVMVVVSRWYGGILLGPDRFKHINNCARNILVEKNYTNSPEESSKALGKNKKVRKDKKRNEH
Prediction	CCCCCCCCCCCCCCSSCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCSSSSSCCSSSSSSSSCCCHHHHHHHHHHHHHHCCCCCCCCSSSSSSSSCCCCCCSSSCCCCCCCCCCCHHHHHHHHHCCCCCSSSSSSSSSCCSSCCCHHHHHHHHHHHHHHHHHCCCHHHHHHHHHCCCCSSCCCCCCCCCC
Confidence	9531012222234321489865556556776444666666789975433259991846899999679999999999999984677777421689999559986157436899998522899999996297529999999848723271277899999999999948520355554312430001101001469
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 \| \| \| \| \| \| \| \| \| KKTEEEDVECEDDLILACQPESSLKALDFDISETRTEVEVEELPPIDHGIPITDRRSTFQAHLAPVVCPKQVKMVLSKLYENKKIASATHNIYAYRIYCEDKQTFLQDCEDDGETAAGGRLLHLMEILNVKNVMVVVSRWYGGILLGPDRFKHINNCARNILVEKNYTNSPEESSKALGKNKKVRKDKKRNEH
Prediction	8656575254455223436564645446453555455364552341534440404402010102306337204500540374452450311010011236744333452644324310430141046340310000001223434122320320240034004535226435534644444543457554678
	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                 180

                   |                   |                   |                   |                   |                   |                   |                   |                   |

SS
Seq

CCCCCCCCCCCCCCSSCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCSSSSSCCSSSSSSSSCCCHHHHHHHHHHHHHHCCCCCCCCSSSSSSSSCCCCCCSSSCCCCCCCCCCCHHHHHHHHHCCCCCSSSSSSSSSCCSSCCCHHHHHHHHHHHHHHHHHCCCHHHHHHHHHCCCCSSCCCCCCCCCC
KKTEEEDVECEDDLILACQPESSLKALDFDISETRTEVEVEELPPIDHGIPITDRRSTFQAHLAPVVCPKQVKMVLSKLYENKKIASATHNIYAYRIYCEDKQTFLQDCEDDGETAAGGRLLHLMEILNVKNVMVVVSRWYGGILLGPDRFKHINNCARNILVEKNYTNSPEESSKALGKNKKVRKDKKRNEH

1vi7A

0.22

0.16

4.91

1.00

DEthreader

-------------------------------------------PAAPVTVVEEIKKSRFITMLAHTDGVEAAKAFVESVRAE--HPDARHHCVAWVAGAP-DDSQQLGFSDDGEATAGKPMLAQLMGSGVGEITAVVVRYYGGILLGTGLVKAYGGGVNQALRQLT-T-QR-K-TPL-TEY-ALAIEEE----

6u1lA2

0.41

0.30

8.69

3.06

SPARKS-K

------------------------------EPVQQSDIPTDPFEGWTASDPITDRGSTFMAFAAHVTSEEQAFAMLDLLKTDSKMRKANHVMSAWRIKQDGSAATYQDSDDDGETAAGSRMLHLITIMDVWNVIVVVARWFGGAHIGPDRFKHINSTAREAVVRAGFDS------------------------

1vi7A1

0.22

0.15

4.56

1.66

MapAlign

------------------------------------------IPAAPVTVVEEIKKSRFITMLAHTDGVEAAKAFVESVR--AEHPDARHHCVAWVAGA-PDDSQQLGFSDDGEPTAGKPMLAQLMGSGVGEITAVVVRYYGGILLTGGLVKAYGGGVNQALRQLTTQRK-----------------------

1vi7A

0.20

0.16

5.13

1.41

CEthreader

------------------------------------LMESWLIPAAPVTVVEEIKKSRFITMLAHTDGVEAAKAFVESVR--AEHPDARHHCVAWVAGAPD-DSQQLGFSDDGEPTAGKPMLAQLMGSGVGEITAVVVRYYGGILLTGGLVKAYGGGVNQALRQLTTQRKTPLTEYTLQCEYHQLTGIEALLG

6bqiA2

0.37

0.31

9.08

2.36

MUSTER

-HRGSV-LTELDGVLYVEPEEETE-------PVQQSDIPTDPFEGWTASDPITDRGSTFMAFAAHVTSEEQAFAMLDLLKTDSKMRKANHVMSAWRIKQDGSAATYQDSDDDGETAAGSRMLHLITIMDVWNVIVVVARWFGGAHIGPDRFKHINSTAREAVVRAGFDS------------------------

6u1lA

0.35

0.31

9.12

4.40

HHsearch

LYDMDSVF--HRGSVCLFDFLTELDGVLYVEPEQQSDIPTDPFEGWTASDPITDRGSTFMAFAAHVTSEEQAFAMLDLLKTDSKMRKANHVMSAWRIKQDGSAATYQDSDDDGETAAGSRMLHLITIMDVWNVIVVVARWFGGAHIGPDRFKHINSTAREAVVRAGFDS------------------------

6u1lA2

0.41

0.30

8.69

2.06

FFAS-3D

-------------------------------PVQQSDIPTDPFEGWTASDPITDRGSTFMAFAAHVTSEEQAFAMLDLLKTDSKMRKANHVMSAWRIKQDGSAATYQDSDDDGETAAGSRMLHLITIMDVWNVIVVVARWFGGAHIGPDRFKHINSTAREAVVRAGFDS------------------------

6bqiA2

0.36

0.30

8.95

1.15

EigenThreader

-------HRGSVCLFDFLTELDGVLYVEPEEETEPVQQSDDPFEGWTASDPITDRGSTFMAFAAHVTSEEQAFAMLDLLKTDSKMRKANHVMSAWRIKQDGSAATYQDSDDDGETAAGSRMLHLITIMDVWNVIVVVARWFGGAHIGPDRFKHINSTAREAVVRAGFDS------------------------

2cveA

0.30

0.19

5.65

1.54

CNFpred

------------------------------------------------VYEEEIQKSRFIAKAAPVASEEEALAFLAENR----EPEATHNGHAYKIGL------LYRFSDDGEPTAGRPILHAIEAQGLDRVAVLVVRYFGGVKLGAGLVRAYGGVAAEALRRAPKVPLVERVGLA----------------

1vi7A1

0.23

0.15

4.70

1.00

DEthreader

--------------------------------------------AAPVTVVEEIKKSRFITMLAHTDGVEAAKAFVESVRAE--HPDARHHCVAWVAGAP-DDSQQLGFSDDGEATAGKPMLAQLMGSGVGEITAVVVRYYGGILLGTGLVKAYGGGVNQALRQLT-T-QR-K--TP----------------

(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	0.7757

(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	1vi7A	0.62	2.90	0.190	0.700	model1_1vi7A.pdb.gz
2	2cveA	0.61	2.36	0.273	0.668	model1_2cveA.pdb.gz
3	6bqiA	0.53	3.40	0.299	0.653	model1_6bqiA.pdb.gz
4	5anbK	0.47	3.93	0.073	0.632	model1_5anbK.pdb.gz
5	5mqfB	0.47	3.55	0.025	0.622	model1_5mqfB.pdb.gz
6	2e1rA	0.47	4.08	0.042	0.637	model1_2e1rA.pdb.gz
7	3jb9B	0.47	4.19	0.047	0.648	model1_3jb9B.pdb.gz
8	6u43A2	0.47	3.93	0.070	0.642	model1_6u43A2.pdb.gz
9	5h7jA	0.47	3.99	0.078	0.648	model1_5h7jA.pdb.gz
10	3j38z	0.47	4.03	0.054	0.637	model1_3j38z.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:0044877	0.88	macromolecular complex binding
GO:0043022	0.87	ribosome binding
GO:0003779	0.87	actin 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	1.00	single-organism process
GO:0050794	0.96	regulation of cellular process
GO:0009987	0.96	cellular process
GO:0044763	0.95	single-organism cellular process
GO:0048523	0.94	negative regulation of cellular process
GO:0034198	0.94	cellular response to amino acid starvation
GO:0072755	0.90	cellular response to benomyl
GO:0071468	0.90	cellular response to acidic pH
GO:0070301	0.90	cellular response to hydrogen peroxide
GO:0060548	0.90	negative regulation of cell death
GO:2000112	0.87	regulation of cellular macromolecule biosynthetic process
GO:0051171	0.87	regulation of nitrogen compound metabolic process
GO:0032268	0.87	regulation of cellular protein metabolic process
GO:0010468	0.87	regulation of gene expression
GO:0006417	0.86	regulation of translation
GO:0044767	0.85	single-organism developmental process
GO:0051128	0.83	regulation of cellular component organization
GO:0048583	0.83	regulation of response to stimulus
GO:0060733	0.82	regulation of eIF2 alpha phosphorylation by amino acid starvation
GO:0043555	0.82	regulation of translation in response to stress
GO:0031333	0.82	negative regulation of protein complex assembly
GO:0001933	0.82	negative regulation of protein phosphorylation
GO:0048522	0.80	positive regulation of cellular process
GO:0051239	0.79	regulation of multicellular organismal process
GO:0051173	0.79	positive regulation of nitrogen compound metabolic process
GO:0050793	0.79	regulation of developmental process
GO:0031328	0.79	positive regulation of cellular biosynthetic process
GO:0010628	0.79	positive regulation of gene expression
GO:0010557	0.79	positive regulation of macromolecule biosynthetic process
GO:0006355	0.79	regulation of transcription, DNA-templated
GO:1990253	0.78	cellular response to leucine starvation
GO:1990138	0.78	neuron projection extension
GO:0097201	0.78	negative regulation of transcription from RNA polymerase II promoter in response to stress
GO:0071494	0.78	cellular response to UV-C
GO:0071264	0.78	positive regulation of translational initiation in response to starvation
GO:0045666	0.78	positive regulation of neuron differentiation
GO:0042149	0.78	cellular response to glucose starvation
GO:0031953	0.78	negative regulation of protein autophosphorylation

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:0005844	0.97	polysome

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	2j5cB	0.421	4.81	0.041	0.663	4.2.3.-	NA
2	0.060	2wbaA	0.418	5.91	0.035	0.782	1.8.1.12	NA
3	0.060	2v4iG	0.326	5.21	0.059	0.534	2.3.1.35	61
4	0.060	1b65A	0.427	5.12	0.079	0.689	3.4.11.9	NA
5	0.060	1s95B	0.414	5.44	0.086	0.725	3.1.3.16	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:

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	3a4kD	0.441	5.36	0.097	0.746	0.58	QNA	complex1.pdb.gz	112,147,154
2	0.01	2y2qB	0.445	5.38	0.051	0.736	0.44	Z06	complex2.pdb.gz	56,57,138,141
3	0.01	2y2iA	0.439	5.47	0.047	0.736	0.45	NA	complex3.pdb.gz	57,89,140,142

	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.