D-I-TASSER P20393-D2

D-I-TASSER results for P20393-D2

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

Input Sequence in FASTA format

>P20393 (136 residues)
EPTVEDVISQVARAHREIFTYAHDKLGSSPGNFNANHASGSPPATTPHRWENQGCPPAPN
DNNTLAAQRHNEALNGLRQAPSSYPPTWPPGPAHHSCHQSNSNGHRLCPTHVYAAPEGKA
PANSPRQGNSKNVLLA

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| EPTVEDVISQVARAHREIFTYAHDKLGSSPGNFNANHASGSPPATTPHRWENQGCPPAPNDNNTLAAQRHNEALNGLRQAPSSYPPTWPPGPAHHSCHQSNSNGHRLCPTHVYAAPEGKAPANSPRQGNSKNVLLA
Prediction	CCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCSSCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Confidence	9518999999999998875443333058888887445789998766311115788887530358988862544344634778889778888766765557888716502456678888899998776875100149
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| EPTVEDVISQVARAHREIFTYAHDKLGSSPGNFNANHASGSPPATTPHRWENQGCPPAPNDNNTLAAQRHNEALNGLRQAPSSYPPTWPPGPAHHSCHQSNSNGHRLCPTHVYAAPEGKAPANSPRQGNSKNVLLA
Prediction	8562551143014224421332344244564545354464542444352147452443443442242344163255245466634453464465441545654133001232344456644664345753440237
	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

CCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCSSCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
EPTVEDVISQVARAHREIFTYAHDKLGSSPGNFNANHASGSPPATTPHRWENQGCPPAPNDNNTLAAQRHNEALNGLRQAPSSYPPTWPPGPAHHSCHQSNSNGHRLCPTHVYAAPEGKAPANSPRQGNSKNVLLA

4m0hA

0.10

0.08

3.02

0.57

CEthreader

----------------------SDHLLTEISVNHGEHKQVTLPDGTVVHLNAGTVRYPTEFTSDIRLVEEGEAFFNVRDEGKPFRQADVKVLGGSFNVKAYQEDLAVSVRTGKVEVDVRLLPNEQIIVNNTNGEIL

2vq2A

0.04

1.99

0.50

EigenThreader

LAMEYMRGATASIEDALKSDPKNELAWLVRAEIYQYLKVNDKAQESFRQALSIKPDSAEINNNYGWFLCGRPAESMAYFDKALADTPYIANLNKGICSAKQGQFGLAEAYLKRSLAAQPQFLARTKMLAGQLGDAD

4bmlA

0.08

0.07

2.92

0.39

FFAS-3D

---SKQIGEALATHYDERIARVLAKASAEASPVTGEPGGFHVNIGDERSAPQEGRVAVLSPRQYYSL------ISSVDTNILNREIGNSQGDMNSGKGLYSIAGIRILKSNNLAGLYGQDLSSAAVTGENNDYQVD

7jjvA

0.14

0.12

4.00

1.10

SPARKS-K

----------------------MQCDGLDGADGTSNGQAGASGLAGGPNCNGGKGGKGVGTAGGAGGVGGNGGAGGSGNSDVAAGGAGAAGGAAAGTGGTGGNGGAGKPGGAPGAGGAGTPAGSAGSPGQTTVL--

6j1lA

0.18

0.04

1.20

0.46

CNFpred

LTEIEHLVQSVCKSYRETCQLRLEDLLR------------------------------------------------------------------------------------------------------------

6lr0U

0.07

0.06

2.41

0.83

DEthreader

DDKGTMSDSVILRSIKKFGEEN-DG-F-ES-DKSLIFMFAYYAGVAVLITGYQIFWMALFIQRMTSTIGFLGTIISVCYLAFGSVLYTLVQILSIVLNGNASPC--------------------QCIMFIANVTGR

1rm6B

0.05

2.37

0.71

MapAlign

---PALAQAAESVPTHRAAATLGGNLCQDTRCTFYNQSEWWRSGNGYCLKYKGDKCHVIVKSVAPALMVLDAAWSAAYSKVRIRDAVDFPLAGVAAALQRDGDRIAGLRVAITGSNSAPLMVPVDALLGGNWDDAA

2w0cT

0.11

0.10

3.69

0.67

MUSTER

ANFLTKNFVWILAAGVGVWFYQK--------ADNAAKTATKPIADFLAELQFLVNGSNYVKFPNAGFVLTRDALQDDFIAYDDRIKAWLGTHDRHKDFLAEILDHER-RVKPVYRKGNIIDASTIRAASGVEL---

2nydB1

0.07

0.01

0.60

0.38

HHsearch

AYQKSRAEQLIKQYHPETPVFDFIEIKQ------------------------------------------------------------------------------------------------------------

2cr9A

0.07

0.05

2.14

0.52

CEthreader

--------------------------------GSSGSSGKSEKRMKLTLKGGAAVDPDSGLEHSAHVLEKGGKVFSATL--GLVDIVKGTNSYYKLQLLEDDKENRYWIFRSWGRVGTVIGSNKLEQMPSKEDAIE

(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	0.479

(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	6uebA	0.46	4.93	0.052	0.831	model1_6uebA.pdb.gz
2	7vcfA	0.44	5.18	0.051	0.801	model1_7vcfA.pdb.gz
3	7t3uA	0.42	4.77	0.067	0.699	model1_7t3uA.pdb.gz
4	5a22A	0.41	5.39	0.022	0.772	model1_5a22A.pdb.gz
5	1t3tA2	0.41	5.09	0.037	0.750	model1_1t3tA2.pdb.gz
6	4bedA	0.41	5.09	0.037	0.757	model1_4bedA.pdb.gz
7	8c6iA	0.41	4.92	0.055	0.735	model1_8c6iA.pdb.gz
8	5gm6G	0.40	4.79	0.053	0.721	model1_5gm6G.pdb.gz
9	8c4aA	0.40	4.86	0.059	0.728	model1_8c4aA.pdb.gz
10	6h02A	0.40	4.59	0.030	0.669	model1_6h02A.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	1.00	sequence-specific DNA binding
GO:0000976	0.91	transcription regulatory region sequence-specific DNA binding
GO:0001222	0.90	transcription corepressor binding
GO:0001046	0.90	core promoter sequence-specific DNA binding
GO:0003700	0.53	transcription factor activity, sequence-specific DNA binding
GO:0000981	0.52	RNA polymerase II transcription factor activity, 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:2000188	1.00	regulation of cholesterol homeostasis
GO:0070859	1.00	positive regulation of bile acid biosynthetic process
GO:0061469	1.00	regulation of type B pancreatic cell proliferation
GO:0061178	1.00	regulation of insulin secretion involved in cellular response to glucose stimulus
GO:0060086	1.00	circadian temperature homeostasis
GO:0045893	1.00	positive regulation of transcription, DNA-templated
GO:0045892	1.00	negative regulation of transcription, DNA-templated
GO:0045598	1.00	regulation of fat cell differentiation
GO:0044321	1.00	response to leptin
GO:0042752	1.00	regulation of circadian rhythm
GO:0035947	1.00	regulation of gluconeogenesis by regulation of transcription from RNA polymerase II promoter
GO:0032922	1.00	circadian regulation of gene expression
GO:0010498	1.00	proteasomal protein catabolic process
GO:0005978	1.00	glycogen biosynthetic process

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:0043197	1.00	dendritic spine
GO:0030425	1.00	dendrite
GO:0005737	1.00	cytoplasm
GO:0005634	1.00	nucleus
GO:0044422	0.65	organelle part
GO:0044446	0.64	intracellular organelle part
GO:0044428	0.59	nuclear part
GO:0005654	0.55	nucleoplasm
GO:0032991	0.53	macromolecular complex

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	2zkmX	0.341	5.28	0.023	0.618	3.1.4.11	NA
2	0.060	3fvyA	0.330	4.33	0.015	0.515	3.4.14.4	NA
3	0.060	2h1nA	0.277	3.40	0.036	0.397	3.4.24.-	NA
4	0.060	3bkkA	0.332	3.59	0.000	0.485	3.4.15.1	NA
5	0.060	2vumB	0.279	5.62	0.051	0.574	2.7.7.6	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	1c3oA	0.367	4.76	0.008	0.625	0.21	GLN	complex1.pdb.gz	27,28,34
2	0.01	1ce8C	0.363	4.96	0.046	0.632	0.12	ADP	complex2.pdb.gz	26,27,28,29,30
3	0.01	1a9x2	0.404	5.18	0.037	0.757	0.34	III	complex3.pdb.gz	23,26,27
4	0.01	1a9x0	0.365	4.80	0.015	0.632	0.20	III	complex4.pdb.gz	20,23,24
5	0.01	1a9x1	0.365	4.80	0.015	0.632	0.34	III	complex5.pdb.gz	20,21,23,24
6	0.01	2cg2A	0.359	5.13	0.045	0.647	0.18	SO4	complex6.pdb.gz	31,32,34,36

	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.