D-I-TASSER P13645-D1

D-I-TASSER results for P13645-D1

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

Input Sequence in FASTA format

>P13645 (136 residues)
MSVRYSSSKHYSSSRSGGGGGGGGCGGGGGVSSLRISSSKGSLGGGFSSGGFSGGSFSRG
SSGGGCFGGSSGGYGGLGGFGGGSFRGSYGSSSFGGSYGGIFGGGSFGGGSFGGGSFGGG
GFGGGGFGGGFGGGFG

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| MSVRYSSSKHYSSSRSGGGGGGGGCGGGGGVSSLRISSSKGSLGGGFSSGGFSGGSFSRGSSGGGCFGGSSGGYGGLGGFGGGSFRGSYGSSSFGGSYGGIFGGGSFGGGSFGGGSFGGGGFGGGGFGGGFGGGFG
Prediction	CCCSCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Confidence	9610156755333456788888777888886565113567766776577887888767788888876788888777778888888877678788876677667887678787888767888888876777678889
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| MSVRYSSSKHYSSSRSGGGGGGGGCGGGGGVSSLRISSSKGSLGGGFSSGGFSGGSFSRGSSGGGCFGGSSGGYGGLGGFGGGSFRGSYGSSSFGGSYGGIFGGGSFGGGSFGGGSFGGGGFGGGGFGGGFGGGFG
Prediction	7534354454244446444342222233333332424444443233234333333323434432312233433331222333333323334432323332333333223243333322333332322233444458
	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

CCCSCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
MSVRYSSSKHYSSSRSGGGGGGGGCGGGGGVSSLRISSSKGSLGGGFSSGGFSGGSFSRGSSGGGCFGGSSGGYGGLGGFGGGSFRGSYGSSSFGGSYGGIFGGGSFGGGSFGGGSFGGGGFGGGGFGGGFGGGFG

7jjvA

0.31

0.28

8.43

2.18

SPARKS-K

---------------MQCDGLDGADGTSNGQAGASGLAGGPNCNGGKGGKGAPGVGTAGGAGGVGGAGGTGNTNGGAGGSGGNSDVAAGGAGAAGGAAGGAGTGGTGGNGGAGGGAPGAGGAGTPAGSAGSPGQTT

2pffA3

0.51

14.70

1.31

MUSTER

GSLTFNSKNIQSKDSYGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG

7luvC

0.50

0.46

13.44

1.80

HHsearch

HIWRDYLDNGG--GGGGGGGGGGGGGGG--GGGGGGGGGGGG-GGGGGGGGGG----GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG

2y0kA

0.09

3.38

0.57

CEthreader

QVFSANRIGGRSDAFDFAGGDYRLTPALTASLHQGRLKDIYRQTFAGLVHTLDLGRSLKSDLRFARASEDGGFRELDNRAFGALFSLRLGAHAVAAGYQRISGDDPYPYIAGSDPYLVNFIQIGDFGNVDERSWQL

5xa5A

0.03

1.79

0.58

EigenThreader

PIANGAVQDTGQVMIQTGRDFVRDSTSTNKRAIATNSGRNLLTAVDKVDEVLLISQIEELDITVRRRAIDLVKPNQRDDLLAARSALRQTAPLLYTSTRTFVRHPEHEEARRNRDYTADEMHSALNALESVLNGQQ

6edoA

0.52

0.49

14.03

0.69

FFAS-3D

----------FETMGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG

3bogA

0.31

0.18

5.55

1.63

SPARKS-K

----------------------------------------------CKGADGAHGVGCPGTAGAAGSVGGPGCDGGHGGNGGNGNPGCAGGV--GGAGGASGGTGV--GGRGGKGGSGTPKGADGAPGAP------

7bwmA

0.06

0.05

2.29

0.83

DEthreader

QTPDRVDHLDAMTYWRPKWGLWKARDLLQTTGFFIIGWPALLFSGMVNKQTDGL--K--LPFNYVPRMVAGALVL----TMNAYQP--NSL--TGFVLDYVRYGN-TFRGGSLAWT-PQDVGLFQLVLTGLDALAP

4fspA

0.10

0.09

3.28

0.71

MapAlign

--------------FDLAGLDYRIAPDWTGSYHYGELEQVYAQHFLGLKGRIGIAADSLESDLRSLTYRLRNGQAFGLGYQRMSGDHGFPYLEGTDPYLVNFGQYNDFAEAGESSWQLRYDCDFAPLGVPGLSLMT

2pffA1

0.49

14.10

1.27

MUSTER

GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG

(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	0.4896

(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	4y23A	0.49	4.50	0.092	0.816	model1_4y23A.pdb.gz
2	3v8hA	0.49	4.23	0.017	0.787	model1_3v8hA.pdb.gz
3	7a23I	0.49	5.04	0.089	0.875	model1_7a23I.pdb.gz
4	4a8jC	0.48	4.68	0.039	0.838	model1_4a8jC.pdb.gz
5	1qzfA	0.47	4.17	0.034	0.765	model1_1qzfA.pdb.gz
6	2h2qA	0.47	4.27	0.034	0.757	model1_2h2qA.pdb.gz
7	3ix6B	0.47	4.57	0.027	0.772	model1_3ix6B.pdb.gz
8	1b02A	0.47	4.45	0.034	0.772	model1_1b02A.pdb.gz
9	1kzjA	0.46	4.10	0.026	0.735	model1_1kzjA.pdb.gz
10	1vzaA2	0.42	4.68	0.046	0.713	model1_1vzaA2.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:0030280	1.00	structural constituent of epidermis

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:0030216	1.00	keratinocyte 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:0070062	1.00	extracellular exosome
GO:0016020	1.00	membrane
GO:0005882	1.00	intermediate filament
GO:0005737	1.00	cytoplasm
GO:0005634	1.00	nucleus
GO:0005615	1.00	extracellular space

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	3k2hA	0.465	4.14	0.026	0.743	2.1.1.45	NA
2	0.060	3maxA	0.455	5.34	0.069	0.868	3.5.1.98	96
3	0.060	1fdjA	0.443	5.20	0.040	0.853	4.1.2.13	NA
4	0.060	1xfbA	0.449	4.99	0.073	0.831	4.1.2.13	NA
5	0.060	1eceB	0.458	5.11	0.078	0.831	3.2.1.4	123

	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	3rkoN	0.477	5.22	0.098	0.882	0.57	LFA	complex1.pdb.gz	81,84,85,90
2	0.01	2c2bA	0.491	5.11	0.076	0.912	0.73	SAM	complex2.pdb.gz	70,71,72,73,75,77
3	0.01	1ofeA	0.427	5.02	0.092	0.787	0.43	ONL	complex3.pdb.gz	25,31,51,79
4	0.01	1ofdA	0.417	5.06	0.089	0.787	0.53	F3S	complex4.pdb.gz	42,43,44,45,46,66,75,77,78

	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.