D-I-TASSER P25116-D1

D-I-TASSER results for P25116-D1

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

Input Sequence in FASTA format

>P25116 (81 residues)
MGPRRLLLVAACFSLCGPLLSARTRARRPESKATNATLDPRSFLLRNPNDKYEPFWEDEE
KNESGLTEYRLVSINKSSPLQ

Predicted Secondary Structure

Sequence	20 40 60 80 \| \| \| \| MGPRRLLLVAACFSLCGPLLSARTRARRPESKATNATLDPRSFLLRNPNDKYEPFWEDEEKNESGLTEYRLVSINKSSPLQ
Prediction	CCCHHHHHHHHHHHHCCHHHHCCCCCCCCCCCCCCCCCCCCSSSSSCCCCCCCCCCCHHHHCCCCCCHHHHHHCCCCCCCC
Confidence	981223699876510211220145567887656678778614687658998542885255145667113331024689999
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 \| \| \| \| MGPRRLLLVAACFSLCGPLLSARTRARRPESKATNATLDPRSFLLRNPNDKYEPFWEDEEKNESGLTEYRLVSINKSSPLQ
Prediction	854320101123342134324352545546464564335231010234675245145555656743454334434454448
	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

                   |                   |                   |                   |

SS
Seq

CCCHHHHHHHHHHHHCCHHHHCCCCCCCCCCCCCCCCCCCCSSSSSCCCCCCCCCCCHHHHCCCCCCHHHHHHCCCCCCCC
MGPRRLLLVAACFSLCGPLLSARTRARRPESKATNATLDPRSFLLRNPNDKYEPFWEDEEKNESGLTEYRLVSINKSSPLQ

4hg6B

0.12

4.33

0.61

CEthreader

WSDRAQTFVQATLQPVIQTVRRMLRPGDGNLAEWLATRKGTAMLLAPEPGKLWVILLAMAPRSPGGPRGQVAVLGSDGRWS

3bboF

0.06

2.65

0.67

EigenThreader

KLTKPEMGHLEKSGIIPLRHLRLQSIDGFEVTELFKEGDLVDVSGTTIGGTKRKIRKLKIKGALPGKPGNLLRIAPAKIV-

6nbqG

0.24

0.15

4.60

0.32

FFAS-3D

--PFELASVLLLMALIGAVVLARRELVLEPEPILGEEVVPP---LELPERPREP---------------------------

4gl6A1

0.13

0.10

3.43

0.78

SPARKS-K

------EISIKIETYLQEVLSWNQPKLLPSD---NGAIYATCISKNDPKHPFEGSYFNPEEPNSEIEIIYD----------

3auxA

0.12

0.05

1.73

0.55

CNFpred

GGEQIAVALSLRLAIANALIGN----------------RVECIILDEP---------------------------------

3rfuA

0.06

0.05

2.22

0.83

DEthreader

VYFEAAAVITTLVLLGQVLELKAREQTAIALLKLSMVTGE-----R-PIEARMLVVDKVMLKV--VLGLIVAMAPL-ATGT

3kk5M

0.05

2.28

0.74

MapAlign

LDTQERTANIPGSGAGTAAATVTTPDYGNTGTYNEQLAVLDSAKIQLNGQDRFTRKGSYFNKVQPIDNATLSLTYKT----

6c0bA4

0.09

3.26

0.60

MUSTER

GELKILMLNSNHIQQKIDYIGFNSELQKNPYSFVDSEGKENGFINGSTKEGL--FVSELPDVVLIS----KVYMDDSKPSF

1vt4I

0.17

0.15

4.85

0.61

HHsearch

TNPRRLSIIA--ESIRDGLAT-------WD---NWKHVNCDKLIIESSLNVLEPAEYRKSFPPSAHIPTILLSLIWFDVIK

5fki1B

0.12

4.33

0.54

CEthreader

LVQRLKLILSGGNLRCSDACDPERPPTRCVRSWAHVPCDPYVRVQNTGVSVLFQGFFFAEHNNVILASTHSTGMSLSALDD

(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

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Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.4962

(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

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Top 10 structural analogs in PDB (as identified by TM-align)

Rank	PDB Hit	TM-score	RMSD^a	IDEN^a	Cov.	Download Alignment
1	5khnB2	0.48	3.60	0.075	0.827	model1_5khnB2.pdb.gz
2	4iggA	0.47	4.01	0.038	0.852	model1_4iggA.pdb.gz
3	3errA	0.47	4.68	0.090	0.926	model1_3errA.pdb.gz
4	4z3wA1	0.47	3.87	0.056	0.815	model1_4z3wA1.pdb.gz
5	3ayfA	0.47	3.59	0.062	0.802	model1_3ayfA.pdb.gz
6	1wiwB	0.46	4.11	0.096	0.876	model1_1wiwB.pdb.gz
7	3mk7A	0.46	3.73	0.015	0.802	model1_3mk7A.pdb.gz
8	2zr3A	0.45	4.45	0.093	0.914	model1_2zr3A.pdb.gz
9	1nj1A1	0.41	4.54	0.078	0.852	model1_1nj1A1.pdb.gz
10	2yevA1	0.39	3.51	0.074	0.630	model1_2yevA1.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:0031681	1.00	G-protein beta-subunit binding
GO:0004930	1.00	G-protein coupled receptor activity
GO:0001965	1.00	G-protein alpha-subunit binding
GO:0008528	0.55	G-protein coupled peptide receptor activity
GO:0015057	0.51	thrombin receptor activity

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:0098801	1.00	regulation of renal system process
GO:0051241	1.00	negative regulation of multicellular organismal process
GO:0051240	1.00	positive regulation of multicellular organismal process
GO:0051049	1.00	regulation of transport
GO:0048523	1.00	negative regulation of cellular process
GO:0043410	1.00	positive regulation of MAPK cascade
GO:0007204	1.00	positive regulation of cytosolic calcium ion concentration
GO:0007186	1.00	G-protein coupled receptor signaling pathway
GO:0003008	1.00	system process
GO:0050896	0.96	response to stimulus
GO:1900134	0.95	negative regulation of renin secretion into blood stream
GO:0070374	0.95	positive regulation of ERK1 and ERK2 cascade
GO:0048873	0.95	homeostasis of number of cells within a tissue
GO:0045907	0.95	positive regulation of vasoconstriction
GO:0035025	0.95	positive regulation of Rho protein signal transduction
GO:0032651	0.95	regulation of interleukin-1 beta production
GO:0032496	0.95	response to lipopolysaccharide
GO:0030335	0.95	positive regulation of cell migration
GO:0030194	0.95	positive regulation of blood coagulation
GO:0014068	0.95	positive regulation of phosphatidylinositol 3-kinase signaling
GO:0006954	0.95	inflammatory response
GO:0051930	0.87	regulation of sensory perception of pain
GO:0051928	0.87	positive regulation of calcium ion transport
GO:0051482	0.87	positive regulation of cytosolic calcium ion concentration involved in phospholipase C-activating G-protein coupled signaling pathway
GO:0051209	0.87	release of sequestered calcium ion into cytosol
GO:0045987	0.87	positive regulation of smooth muscle contraction
GO:0043524	0.87	negative regulation of neuron apoptotic process
GO:0008284	0.87	positive regulation of cell proliferation
GO:0007529	0.87	establishment of synaptic specificity at neuromuscular junction
GO:0007205	0.87	protein kinase C-activating G-protein coupled receptor signaling pathway
GO:0003105	0.87	negative regulation of glomerular filtration
GO:0000186	0.87	activation of MAPKK activity
GO:0070493	0.86	thrombin receptor signaling pathway
GO:0008152	0.55	metabolic process
GO:0071704	0.53	organic substance metabolic process
GO:0044238	0.53	primary metabolic process
GO:0044237	0.53	cellular metabolic process
GO:0043170	0.52	macromolecule metabolic process
GO:0044707	0.51	single-multicellular organism process
GO:0044260	0.51	cellular macromolecule metabolic process
GO:0031326	0.51	regulation of cellular biosynthetic process
GO:2000112	0.50	regulation of cellular macromolecule biosynthetic process
GO:0043412	0.50	macromolecule modification
GO:0031328	0.50	positive regulation of cellular biosynthetic process
GO:0030168	0.50	platelet activation
GO:0019538	0.50	protein metabolic process
GO:0019219	0.50	regulation of nucleobase-containing compound metabolic process
GO:0015031	0.50	protein transport
GO:0010557	0.50	positive regulation of macromolecule biosynthetic process
GO:0010468	0.50	regulation of gene expression

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:0045211	1.00	postsynaptic membrane
GO:0031594	1.00	neuromuscular junction
GO:0005886	1.00	plasma membrane
GO:0044424	0.71	intracellular part
GO:0043226	0.63	organelle
GO:0043227	0.62	membrane-bounded organelle
GO:0043231	0.61	intracellular membrane-bounded organelle
GO:0045121	0.57	membrane raft
GO:0031094	0.56	platelet dense tubular network
GO:0005901	0.56	caveola

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

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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	2i4nB	0.452	4.53	0.051	0.914	6.1.1.15	NA
2	0.060	1ii2A	0.445	4.19	0.025	0.852	4.1.1.49	NA
3	0.060	1adyD	0.446	4.31	0.083	0.876	6.1.1.21	NA
4	0.060	1ro5A	0.429	3.53	0.063	0.741	2.3.1.184	NA
5	0.060	1z1lA	0.423	3.58	0.090	0.765	3.1.4.17	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

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Template proteins with similar binding site:

No Binding sites was predicted

Click to view	Rank	Cscore^LB	PDB Hit	TM-score	RMSD^a	IDEN^a	Cov.	BS-score	Lig. Name	Download Complex	Predicted binding site residues

	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.