D-I-TASSER P28482-D1

D-I-TASSER results for P28482-D1

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

Input Sequence in FASTA format

>P28482 (140 residues)
MAAAAAAGAGPEMVRGQVFDVGPRYTNLSYIGEGAYGMVCSAYDNVNKVRVAIKKISPFE
HQTYCQRTLREIKILLRFRHENIIGINDIIRAPTIEQMKDVYIVQDAPFKFDMELDDLPK
EKLKELIFEETARFQPGYRS

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 \| \| \| \| \| \| \| MAAAAAAGAGPEMVRGQVFDVGPRYTNLSYIGEGAYGMVCSAYDNVNKVRVAIKKISPFEHQTYCQRTLREIKILLRFRHENIIGINDIIRAPTIEQMKDVYIVQDAPFKFDMELDDLPKEKLKELIFEETARFQPGYRS
Prediction	CCCCCCCCCCSSSSCCSSSSCCCCSSSSSSSCCCCCSSSSSSSSCCCCCSSSSSSSCCCCCCHHHHHHHHHHHHHHHCCCCCSCCSSSSSCCCCCCCCCSSSSSSCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHCC
Confidence	99988998605998897876167748867611245669999998899979999961476773047999999999987699876325677648985458579999606211010436999899899999999998576439
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 \| \| \| \| \| \| \| MAAAAAAGAGPEMVRGQVFDVGPRYTNLSYIGEGAYGMVCSAYDNVNKVRVAIKKISPFEHQTYCQRTLREIKILLRFRHENIIGINDIIRAPTIEQMKDVYIVQDAPFKFDMELDDLPKEKLKELIFEETARFQPGYRS
Prediction	84555676433240453414047316414412510101001031474643000110454665420320020020045061610030330031753741420000000323212545704662011001020232234168
	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                 140

                   |                   |                   |                   |                   |                   |                   |

SS
Seq

CCCCCCCCCCSSSSCCSSSSCCCCSSSSSSSCCCCCSSSSSSSSCCCCCSSSSSSSCCCCCCHHHHHHHHHHHHHHHCCCCCSCCSSSSSCCCCCCCCCSSSSSSCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHCC
MAAAAAAGAGPEMVRGQVFDVGPRYTNLSYIGEGAYGMVCSAYDNVNKVRVAIKKISPFEHQTYCQRTLREIKILLRFRHENIIGINDIIRAPTIEQMKDVYIVQDAPFKFDMELDDLPKEKLKELIFEETARFQPGYRS

5z33A

0.31

0.28

8.41

1.17

DEthreader

-----GR--KIFKVFNQDFIVDERYTVTKELGQGAYGIVCAAVNNQTSEGVAIKKVTVFSKKILAKRALREIKLLQHFGHRNITCLYDMDIPRPDN-FNETYLYEELMECDLAAIIR----KGN-CDFG-LAR-GFSCTT

3i5zA2

0.95

0.87

24.44

1.87

SPARKS-K

-------GAGPEMVRGQVFDVGPRYTNLSYIGEGAYGMVCSAYDNVNKVRVAIKKISPFEHQTYCQRTLREIKILLRFRHENIIGINDIIRAPTIEQMKDVYIVQDLKFDMEL--DDLPKEKLKELIFEETARFQPG---

1q99B

0.21

0.18

5.68

0.47

MapAlign

-----------YHPAFKGEPYKARYILVRKLGWGHFSTVWLAKDMVNNTHVAMKIVRGDK--VYTEAAEDEIKLLQRVNANHILKLLDHFNHKG-PNGVHVVMVFEVLLFEPDEGHSYTKDDDHIAQIIELLGE------

2pziA1

0.15

5.04

0.28

CEthreader

WCPYCGSPYSFLPQLNPGDIVAGQYEVKGCIAHGGLGWIYLALDRNNGRPVVLKGLVHSGDAEAQAMAMAERQFLAEVVHPSIVQIFNFVEHTDRHGDPVGYIVMEYVGGQSLK-QKLPVAEAIAYLLEILPALSYLHSI

3i5zA2

0.95

0.87

24.44

1.87

MUSTER

-------GAGPEMVRGQVFDVGPRYTNLSYIGEGAYGMVCSAYDNVNKVRVAIKKISPFEHQTYCQRTLREIKILLRFRHENIIGINDIIRAPTIEQMKDVYIVQDLKFDMEL--DDLPKEKLKELIFEETARFQPG---

6ygnA

0.15

0.14

4.54

0.69

HHsearch

SKPSEPSPTITSMTKASHSSTYEKYMIAEDLGRGEFGIVHRCVETSSKKTYMAKFVKVKG--TDQVLVKKEISILNIARHRNILHLHESFESM-----EELVMIFEF----------ISGLDIFERINTSAFELNEREIV

3i5zA2

0.95

0.86

24.25

2.04

FFAS-3D

-------GAGPEMVRGQVFDVGPRYTNLSYIGEGAYGMVCSAYDNVNKVRVAIKKISPFEHQTYCQRTLREIKILLRFRHENIIGINDIIRAPTIEQMKDVYIVQDLKFDMELD--DLPKEKLKELIFEETARFQPG---

3itzA1

0.30

9.10

0.65

EigenThreader

MLEMSQERPTFQELNKTIWEVPERYQNLSPVGSGAYGSVCAAFDTKTGLRVAVKKLRPFQSIIHAKRTYRELRLLKHMKHENVIGLLDVFTPASLEEFNDVYLVTHLMGADLNNIVKCQKYIHSAAQALAHAYFAQYHDP

3teiA

0.81

0.70

19.76

1.69

CNFpred

---------GPEMVRGQVFDVGPRYTNLSYIGEGAYGMVCSAYDNVNKVRVAIKKISPFEHQTYCQRTLREIKILLAFRHENIIGINDIIRAPTIEQMKDVYIVQDLMETDLYKLQHLSNDHICYFLYQI----------

3i5zA

0.81

0.72

20.36

1.17

DEthreader

-------GAGPEMVRGQVFDVGPRYTNLSYIGEGAYGMVCSAYDNVNKVRVAIKKISPFEHQTYCQRTLREIKILLRFRHENIIGINDIIRAPTIEQMKDVYIVQDLMETDLYKLLK----KSN-DFGL-AR--VK-AAP

(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	0.7078

(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	3i5zA	0.75	2.75	0.777	0.900	model1_3i5zA.pdb.gz
2	5z33A	0.74	3.10	0.277	0.907	model1_5z33A.pdb.gz
3	2h96A	0.73	3.15	0.313	0.914	model1_2h96A.pdb.gz
4	3coiA	0.72	3.23	0.263	0.893	model1_3coiA.pdb.gz
5	4o2zA	0.72	3.31	0.250	0.907	model1_4o2zA.pdb.gz
6	4qnyA	0.72	3.11	0.276	0.886	model1_4qnyA.pdb.gz
7	5ci6A1	0.71	3.42	0.305	0.900	model1_5ci6A1.pdb.gz
8	3n9xA	0.71	3.41	0.264	0.893	model1_3n9xA.pdb.gz
9	2b9iA	0.70	3.25	0.352	0.879	model1_2b9iA.pdb.gz
10	1cm8A	0.69	3.15	0.254	0.871	model1_1cm8A.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:0016740	0.98	transferase activity
GO:0004672	0.97	protein kinase activity
GO:0004674	0.95	protein serine/threonine kinase activity
GO:0004702	0.75	receptor signaling protein serine/threonine kinase activity
GO:0004707	0.69	MAP kinase activity
GO:0005524	0.60	ATP 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:0009987	0.89	cellular process
GO:0065007	0.86	biological regulation
GO:0050789	0.85	regulation of biological process
GO:0050794	0.84	regulation of cellular process
GO:0044260	0.82	cellular macromolecule metabolic process
GO:0044238	0.82	primary metabolic process
GO:0006468	0.81	protein phosphorylation
GO:0044699	0.73	single-organism process
GO:0007165	0.69	signal transduction
GO:0044763	0.67	single-organism cellular process
GO:0050896	0.61	response to stimulus
GO:0048518	0.61	positive regulation of biological process
GO:0048522	0.59	positive regulation of cellular process
GO:0018193	0.59	peptidyl-amino acid modification
GO:0019222	0.58	regulation of metabolic process
GO:0018105	0.58	peptidyl-serine phosphorylation
GO:0080090	0.57	regulation of primary metabolic process
GO:0060255	0.57	regulation of macromolecule metabolic process
GO:0035556	0.57	intracellular signal transduction
GO:0031323	0.57	regulation of cellular metabolic process
GO:0048583	0.55	regulation of response to stimulus
GO:0044767	0.55	single-organism developmental process
GO:0010646	0.54	regulation of cell communication
GO:0023051	0.53	regulation of signaling
GO:0010604	0.53	positive regulation of macromolecule metabolic process
GO:0051246	0.52	regulation of protein metabolic process
GO:0051128	0.52	regulation of cellular component organization
GO:0031325	0.52	positive regulation of cellular metabolic process
GO:0009966	0.52	regulation of signal transduction
GO:2000112	0.51	regulation of cellular macromolecule biosynthetic process
GO:0065009	0.51	regulation of molecular function
GO:0048856	0.51	anatomical structure development
GO:0042221	0.51	response to chemical
GO:0032268	0.51	regulation of cellular protein metabolic process
GO:0019220	0.51	regulation of phosphate metabolic process
GO:0019219	0.51	regulation of nucleobase-containing compound metabolic process
GO:0010468	0.51	regulation of gene expression
GO:0065008	0.50	regulation of biological quality
GO:0051247	0.50	positive regulation of protein metabolic process
GO:0007049	0.50	cell cycle
GO:0001932	0.50	regulation of protein phosphorylation

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:0044464	1.00	cell part
GO:0044424	0.92	intracellular part
GO:0043226	0.72	organelle
GO:0043229	0.71	intracellular organelle
GO:0005737	0.70	cytoplasm
GO:0043227	0.69	membrane-bounded organelle
GO:0043231	0.68	intracellular membrane-bounded organelle
GO:0005634	0.64	nucleus
GO:0044444	0.50	cytoplasmic 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	3itzA	0.686	3.46	0.287	0.886	2.7.11.24	89
2	0.060	2hakB	0.638	2.89	0.207	0.764	2.7.11.1	NA
3	0.060	1yqjA	0.681	3.10	0.304	0.857	2.7.11.24 2.7.1.37	NA
4	0.060	2h96A	0.731	3.15	0.313	0.914	2.7.11.24	NA
5	0.060	2qnjB	0.647	3.22	0.208	0.800	2.7.11.1	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	0.89	3erkA	0.740	2.77	0.775	0.893	1.29	SB4	complex1.pdb.gz	39,52,54,84,103,105,106,108
2	0.89	3i5zA	0.755	2.75	0.777	0.900	1.24	Z48	complex2.pdb.gz	33,34,37,39,52,54,56,105,106,108,109
3	0.74	2z7lA	0.655	3.41	0.746	0.829	0.92	S91	complex3.pdb.gz	31,32,39,54,105,106
4	0.44	1jnkA	0.726	3.00	0.303	0.886	1.13	ANP	complex4.pdb.gz	31,32,33,34,35,36,39,52,54,106,108,122,123
5	0.43	2h96A	0.731	3.15	0.313	0.914	0.93	893	complex5.pdb.gz	31,32,39,41,54,105,107,108,109,110
6	0.41	1pmqA	0.715	3.22	0.303	0.900	0.85	880	complex6.pdb.gz	31,34,39,52,53,54,84,86,103,105,107,108,110

	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.