D-I-TASSER P14138-D3

D-I-TASSER results for P14138-D3

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

Input Sequence in FASTA format

>P14138 (46 residues)
EEGKVEVKDQQSKQALDLHHPKLMPGSGLALAPSTCPRCLFQEGAP

Predicted Secondary Structure

Sequence	20 40 \| \| EEGKVEVKDQQSKQALDLHHPKLMPGSGLALAPSTCPRCLFQEGAP
Prediction	CCCCSSSCCHHHHHHHHHCCCCCCCCCCCSSCCCCCCHHHHHCCCC
Confidence	9873343102446655204876578976241588895366533899
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 \| \| EEGKVEVKDQQSKQALDLHHPKLMPGSGLALAPSTCPRCLFQEGAP
Prediction	8746353555645432524334334443232335303311256658
	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

                   |                   |

SS
Seq

CCCCSSSCCHHHHHHHHHCCCCCCCCCCCSSCCCCCCHHHHHCCCC
EEGKVEVKDQQSKQALDLHHPKLMPGSGLALAPSTCPRCLFQEGAP

4v0mB2

0.15

5.11

0.59

CEthreader

MNDVVHAYTPTGHKSWSLYLPAMQRTKALIVALSNGEVRVYNEKLL

4qi3A

0.15

5.11

0.47

EigenThreader

QGGFFGVALPASEFIGYLKCARLGGSLLITAWPHEDTVYTSLRFAT

1pnuZ

0.22

6.85

0.23

FFAS-3D

KTSKSKRDMRRSHHALTAPNLTECPQCHKKLSHHICPNCGYYDGR-

4by2A2

0.11

3.89

0.87

SPARKS-K

KDGTVEIHFP--NNSIKIVDPSDTEKLEEWRYADGTHLVQLRNGDK

2qn4A

0.50

0.17

5.04

0.74

CNFpred

---------------------------GLTMAPLPCPLLVAQE---

4xa9a

0.09

3.28

0.83

DEthreader

TYDVAVIGSLHNIT-LLVPKSRLPQPQQLTAFPIGTLI-FAT-VNY

5b2cA

0.05

0.04

2.11

0.61

MapAlign

--SCSIATVPDGCAMYCPGVGSGIYNKLIFPARRVQSAFLVCAWN-

3k85A1

0.16

0.15

5.07

0.55

MUSTER

NSGRIEINDAQCCKSYL--SSQLEIDGEASLIKGVYNRIIRDYRLE

6xr4A3

0.36

0.33

9.72

0.34

HHsearch

EGEEVAVKIQELVVLCHLHHPSLISLLAAGIRP----RMLVMELAS

5lljA

0.04

2.17

0.52

CEthreader

KIRFCYYRTRKRGEWQGPTQVLWGGDGAIVVKDRGTDRYLVIANKD

(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	0.616

(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	5m4sA	0.54	2.32	0.049	0.870	model1_5m4sA.pdb.gz
2	5mqfa	0.52	2.57	0.071	0.913	model1_5mqfa.pdb.gz
3	2rm4A	0.52	2.42	0.024	0.891	model1_2rm4A.pdb.gz
4	5ganm	0.51	2.79	0.047	0.935	model1_5ganm.pdb.gz
5	5mkl14	0.51	2.66	0.119	0.891	model1_5mkl14.pdb.gz
6	5uz5K	0.51	2.65	0.119	0.891	model1_5uz5K.pdb.gz
7	3jb9G	0.51	2.56	0.122	0.891	model1_3jb9G.pdb.gz
8	4c8qF	0.51	2.63	0.140	0.913	model1_4c8qF.pdb.gz
9	3jcr3	0.51	2.57	0.095	0.891	model1_3jcr3.pdb.gz
10	1d3bL	0.51	2.65	0.095	0.891	model1_1d3bL.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:0031708	1.00	endothelin B receptor binding
GO:0005179	1.00	hormone 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:0048016	1.00	inositol phosphate-mediated signaling
GO:0046887	1.00	positive regulation of hormone secretion
GO:0045840	1.00	positive regulation of mitotic nuclear division
GO:0045597	1.00	positive regulation of cell differentiation
GO:0043406	1.00	positive regulation of MAP kinase activity
GO:0030593	1.00	neutrophil chemotaxis
GO:0030072	1.00	peptide hormone secretion
GO:0014826	1.00	vein smooth muscle contraction
GO:0014824	1.00	artery smooth muscle contraction
GO:0010468	1.00	regulation of gene expression
GO:0010460	1.00	positive regulation of heart rate
GO:0008284	1.00	positive regulation of cell proliferation
GO:0008015	1.00	blood circulation
GO:0007275	1.00	multicellular organism development
GO:0007267	1.00	cell-cell signaling
GO:0007166	1.00	cell surface receptor signaling pathway
GO:0003100	1.00	regulation of systemic arterial blood pressure by endothelin
GO:0002690	1.00	positive regulation of leukocyte chemotaxis

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:0005615	1.00	extracellular space
GO:0005576	1.00	extracellular region
GO:0044464	0.69	cell 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	1lqyA	0.459	2.97	0.045	0.957	3.5.1.88	NA
2	0.060	1aksA	0.364	3.55	0.023	0.652	3.4.21.4	NA
3	0.060	1aksB	0.299	3.65	0.024	0.652	3.4.21.4	NA
4	0.060	3e3uA	0.471	2.83	0.023	0.935	3.5.1.88	40,43
5	0.060	3rp2A	0.454	3.29	0.098	0.870	3.4.21.-	26

	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	0.05	1lnxB	0.502	2.57	0.143	0.891	0.55	URI	complex1.pdb.gz	26,29,40,41
2	0.03	3resF	0.499	2.50	0.095	0.913	0.56	ADP	complex2.pdb.gz	24,27,29
3	0.02	3ahuC	0.485	2.62	0.143	0.913	0.64	QNA	complex3.pdb.gz	23,24,28,30,32
4	0.02	3resL	0.496	2.51	0.095	0.913	0.53	ADP	complex4.pdb.gz	24,26,28
5	0.02	1lnxD	0.503	2.57	0.143	0.891	0.51	URI	complex5.pdb.gz	26,29,41
6	0.02	3hsbF	0.485	2.53	0.119	0.913	0.54	QNA	complex6.pdb.gz	24,26,28,31
7	0.01	3hsbB	0.481	2.54	0.119	0.913	0.51	QNA	complex7.pdb.gz	28,29,39,42,44

	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.