D-I-TASSER P11831-D2

D-I-TASSER results for P11831-D2

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

Input Sequence in FASTA format

>P11831 (158 residues)
TAGALYSGSEGDSESGEEEELGAERRGLKRSLSEMEIGMVVGGPEASAAATGGYGPVSGA
VSGAKPGSDSSGETKDTLKPAFTVTNLPGTTSTIQTAPSTSTTMQVSSGPSFPITNYLAP
VSASVSPSAVSSANGTVLKSTGSGPVSSGGLMQLPTSF

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 \| \| \| \| \| \| \| TAGALYSGSEGDSESGEEEELGAERRGLKRSLSEMEIGMVVGGPEASAAATGGYGPVSGAVSGAKPGSDSSGETKDTLKPAFTVTNLPGTTSTIQTAPSTSTTMQVSSGPSFPITNYLAPVSASVSPSAVSSANGTVLKSTGSGPVSSGGLMQLPTSF
Prediction	CCCCCCCCCCCCCCCCCHHHCCCCCCCHHHHHCHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCSSSCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCSCCCCCCCCCCCCCSCCCCCC
Confidence	97653256666665420222242102223211100012113675456778888788788776778886678885777784022157988777876688887566767899987666436533688865567889961035677766767521078889
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 \| \| \| \| \| \| \| TAGALYSGSEGDSESGEEEELGAERRGLKRSLSEMEIGMVVGGPEASAAATGGYGPVSGAVSGAKPGSDSSGETKDTLKPAFTVTNLPGTTSTIQTAPSTSTTMQVSSGPSFPITNYLAPVSASVSPSAVSSANGTVLKSTGSGPVSSGGLMQLPTSF
Prediction	84533242455457545566344645425554564523444446545444434334244424435435644454464242523345144435436535446444425534424134222333343555434565343244444443443213423668
	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

                   |                   |                   |                   |                   |                   |                   |

SS
Seq

CCCCCCCCCCCCCCCCCHHHCCCCCCCHHHHHCHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCSSSCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCSCCCCCCCCCCCCCSCCCCCC
TAGALYSGSEGDSESGEEEELGAERRGLKRSLSEMEIGMVVGGPEASAAATGGYGPVSGAVSGAKPGSDSSGETKDTLKPAFTVTNLPGTTSTIQTAPSTSTTMQVSSGPSFPITNYLAPVSASVSPSAVSSANGTVLKSTGSGPVSSGGLMQLPTSF

4yuuo2

0.10

0.09

3.27

0.64

CEthreader

TKLMTRATYTLANIEGELVNENGTWKFIEKDGMD-------YAATTVQIPGGERVPFLFSIKKLVASLNNAISTSTELGGEFKVPSYRVFQETSGRIELAVNKVDPTSN---EIGGVFVSEQLSDTD----------MGAKEPKKLLLKGVFYARILP

3nvnB3

0.11

0.10

3.62

0.68

EigenThreader

RNLAVAATYVLPEPETASRCNPAASDHD----TAIALKDTEGR----SLATQELGRCEGAGSLHFVDAFNG---SIYFP-YYPYNYT---SGAATGWP--SM-ARIAQEVLFGQASLDCGHGHPDGRRLLLSALDGVFSAAARRSPTTTCLFRMAKRV

2b9mY

0.21

0.18

5.81

0.33

FFAS-3D

-----------ELPAEEREALKPELEEAAKKLDELYHQTLLNFPHAEKPGAGGVDLTPGPEAGIDYGENAYG----LLSPEAGVHRLVRPSPFDASGRRHTSFAGVEVIPEVD-----EEVEVVLKPEELRID---VMRASGPGTDSAVRVVHLPTGI

7jjvA

0.15

0.12

4.03

1.08

SPARKS-K

---MQCDGLDG-ADGTSNGQAGASGLAGGPNCNGGKGGKGAPGVGTAGGAGGGGAGGTGNTNGGAGGSGGNSD---------VAAGGAGAAGGAAGGAGTGGTGNGGAGKPGGA----PGAGGAGTPAGSAGSPGQTTVL------------------

6lveA

0.14

0.03

1.09

0.37

CNFpred

---------------------------------------------------------------------------------------------------------------FSVHLFLWSTTPS--------GRQGIASRWND--RQSGWNLAIEDGR

2et6A

0.06

0.04

1.99

0.83

DEthreader

KDKVVIITG-AGGGLYSLVVIVAVA--DYNNVDGDVETAV-----KNFG-----T-VHVIINN-AG-IL--RDADY-VIHLAFTKAWQQKYGRIVNTSSPAG--------NYSAALLGAETAK-GAKYNIKANAIV--LS-AENELTGQFF-WDQQVI

5hy7A1

0.05

2.32

0.74

MapAlign

------GVRRVIPGQYLAADPKGRACLIASVENKLVYVLNRNAQAELTISSPLEA-HKPGVIVLSLVALDVGYSNPVFAALEYEYSEAKQLEMQLVYYTIVAGVMHSAGAFFFLLQTEDGDLFKVTIDMVEDEKGNPTVKRVKIKYFDTVPIAHSLCI

4k0mC

0.08

3.22

0.78

MUSTER

TVEVAKLGIDPRRSDQNVRGTVSLPHGLGKQVEKIKEAEEAGADYVGGEEIIQAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA

1edyA

0.10

0.03

1.18

0.67

HHsearch

------------------------------------------------------------------------------EAPFTLKVNTLPLNFDKAEHHRKFQIHINV-------SYIGE---------RPNSNMVIV------------DVKMVSGF

2kdyA

0.08

3.05

0.62

CEthreader

LKSLTLEDSISQNGTLTLSAQGAEKTYGNGDSLNTGIRQIEVDGQLITLESGEFQVYKQSHSALTALQEKMVAKRRFRIGDIAGEHTSFDKLPKDVMATYRGTAFGSDDAGGKLTYTIDFAAKQGHVAYIKPDEKHHAVISGSVLYNQDEKGSYSLGI

(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	0.4924

(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	1n63B3	0.44	5.06	0.071	0.772	model1_1n63B3.pdb.gz
2	3fahA	0.44	5.20	0.066	0.791	model1_3fahA.pdb.gz
3	2yeqA	0.44	5.18	0.041	0.817	model1_2yeqA.pdb.gz
4	4zohA1	0.44	5.20	0.070	0.778	model1_4zohA1.pdb.gz
5	1dgjA	0.43	5.29	0.081	0.791	model1_1dgjA.pdb.gz
6	1jroB	0.43	5.46	0.058	0.817	model1_1jroB.pdb.gz
7	1xjjA	0.43	5.31	0.032	0.772	model1_1xjjA.pdb.gz
8	1ffvB3	0.43	5.49	0.065	0.797	model1_1ffvB3.pdb.gz
9	5y6qC	0.43	5.27	0.081	0.791	model1_5y6qC.pdb.gz
10	1t1eA2	0.43	5.00	0.082	0.734	model1_1t1eA2.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:0043565	0.91	sequence-specific DNA binding
GO:0070878	0.61	primary miRNA binding
GO:0042803	0.61	protein homodimerization activity
GO:0010736	0.61	serum response element binding
GO:0008134	0.61	transcription factor binding
GO:0001077	0.61	transcriptional activator activity, RNA polymerase II core promoter proximal region sequence-specific binding
GO:0000983	0.61	transcription factor activity, RNA polymerase II core promoter sequence-specific
GO:0000978	0.61	RNA polymerase II core promoter proximal region sequence-specific DNA 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:0050794	1.00	regulation of cellular process
GO:0044699	0.97	single-organism process
GO:0045893	0.96	positive regulation of transcription, DNA-templated
GO:0044763	0.96	single-organism cellular process
GO:0051716	0.93	cellular response to stimulus
GO:0048523	0.93	negative regulation of cellular process
GO:0019725	0.93	cellular homeostasis
GO:0010033	0.93	response to organic substance
GO:0008152	0.73	metabolic process
GO:0045944	0.66	positive regulation of transcription from RNA polymerase II promoter
GO:0051128	0.65	regulation of cellular component organization
GO:1902895	0.62	positive regulation of pri-miRNA transcription from RNA polymerase II promoter
GO:1902894	0.62	negative regulation of pri-miRNA transcription from RNA polymerase II promoter
GO:1900222	0.62	negative regulation of beta-amyloid clearance
GO:0090398	0.62	cellular senescence
GO:0060261	0.62	positive regulation of transcription initiation from RNA polymerase II promoter
GO:0051091	0.62	positive regulation of sequence-specific DNA binding transcription factor activity
GO:0050793	0.62	regulation of developmental process
GO:0048878	0.62	chemical homeostasis
GO:0048646	0.62	anatomical structure formation involved in morphogenesis
GO:0048468	0.62	cell development
GO:0046716	0.62	muscle cell cellular homeostasis
GO:0045987	0.62	positive regulation of smooth muscle contraction
GO:0045597	0.62	positive regulation of cell differentiation
GO:0042789	0.62	mRNA transcription from RNA polymerase II promoter
GO:0034097	0.62	response to cytokine
GO:0010735	0.62	positive regulation of transcription via serum response element binding
GO:0009725	0.62	response to hormone
GO:0007611	0.62	learning or memory
GO:0007507	0.62	heart development
GO:0003257	0.62	positive regulation of transcription from RNA polymerase II promoter involved in myocardial precursor cell differentiation
GO:0002042	0.62	cell migration involved in sprouting angiogenesis
GO:0001947	0.62	heart looping
GO:0001829	0.62	trophectodermal cell differentiation

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	0.99	intracellular membrane-bounded organelle
GO:0005634	0.96	nucleus
GO:0005737	0.65	cytoplasm
GO:0044444	0.60	cytoplasmic part
GO:0005829	0.59	cytosol

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	1n63B	0.435	5.43	0.058	0.791	1.2.99.2	NA
2	0.060	1dd8A	0.361	5.41	0.066	0.671	2.3.1.41	NA
3	0.060	2e1qA	0.421	5.44	0.067	0.785	1.17.3.2 1.17.1.4	NA
4	0.060	3a2pA	0.424	4.94	0.083	0.728	3.5.2.12	NA
5	0.060	2p8uA	0.406	4.75	0.044	0.690	2.3.3.10	94,154

	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	1dgjA	0.433	5.29	0.081	0.791	0.71	FES	complex1.pdb.gz	37,38,39,40,48,49,50,52,55
2	0.01	3fahA	0.444	5.20	0.066	0.791	0.55	GOL	complex2.pdb.gz	60,61,63
3	0.01	1sn7A	0.365	5.44	0.030	0.690	0.77	CA	complex3.pdb.gz	105,106,109,110,111
4	0.01	1xjmB	0.366	5.30	0.061	0.639	0.53	TTP	complex4.pdb.gz	36,37,63,84,85,154,155,158

	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.