D-I-TASSER P15382-D1

D-I-TASSER results for P15382-D1

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

Input Sequence in FASTA format

>P15382 (129 residues)
MILSNTTAVTPFLTKLWQETVQQGGNMSGLARRSPRSSDGKLEALYVLMVLGFFGFFTLG
IMLSYIRSKKLEHSNDPFNVYIESDAWQEKDKAYVQARVLESYRSCYVVENHLAIEQPNT
HLPETKPSP

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| MILSNTTAVTPFLTKLWQETVQQGGNMSGLARRSPRSSDGKLEALYVLMVLGFFGFFTLGIMLSYIRSKKLEHSNDPFNVYIESDAWQEKDKAYVQARVLESYRSCYVVENHLAIEQPNTHLPETKPSP
Prediction	CCCCCHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCSHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCCSSSSCHHHHCCCCCCCCCCCCCC
Confidence	987640245899988620257766666543567866788861212479999999999999999976665313578935676666556776578888887504676278744112027665577889999
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| MILSNTTAVTPFLTKLWQETVQQGGNMSGLARRSPRSSDGKLEALYVLMVLGFFGFFTLGIMLSYIRSKKLEHSNDPFNVYIESDAWQEKDKAYVQARVLESYRSCYVVENHLAIEQPNTHLPETKPSP
Prediction	753554431441024225534545554545454545646432111101333333333331211230444436577532331145531465345413443166251121133531254344414746688
	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

CCCCCHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCSHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCCSSSSCHHHHCCCCCCCCCCCCCC
MILSNTTAVTPFLTKLWQETVQQGGNMSGLARRSPRSSDGKLEALYVLMVLGFFGFFTLGIMLSYIRSKKLEHSNDPFNVYIESDAWQEKDKAYVQARVLESYRSCYVVENHLAIEQPNTHLPETKPSP

2k21A

0.98

27.58

1.90

SPARKS-K

MILSNTTAVTPFLTKLWQETVQQGGNMSGLARRSPRSGDGKLEALYVLMVLGFFGFFTLGIMLSYIRSKKLEHSNDPFNVYIESDAWQEKDKAYVQARVLESYKSCYVVENHLAIEQPNTHLPETKPSP

2k21A

0.98

27.58

2.54

MUSTER

MILSNTTAVTPFLTKLWQETVQQGGNMSGLARRSPRSGDGKLEALYVLMVLGFFGFFTLGIMLSYIRSKKLEHSNDPFNVYIESDAWQEKDKAYVQARVLESYKSCYVVENHLAIEQPNTHLPETKPSP

2k21A

0.98

27.58

6.27

HHsearch

MILSNTTAVTPFLTKLWQETVQQGGNMSGLARRSPRSGDGKLEALYVLMVLGFFGFFTLGIMLSYIRSKKLEHSNDPFNVYIESDAWQEKDKAYVQARVLESYKSCYVVENHLAIEQPNTHLPETKPSP

2k21A

0.98

27.58

2.57

FFAS-3D

MILSNTTAVTPFLTKLWQETVQQGGNMSGLARRSPRSGDGKLEALYVLMVLGFFGFFTLGIMLSYIRSKKLEHSNDPFNVYIESDAWQEKDKAYVQARVLESYKSCYVVENHLAIEQPNTHLPETKPSP

7apxD

0.11

0.09

3.06

1.00

DEthreader

------------------------SNDDKLTEISLKESAHLRFLDLQSSIDTKKVADENWETCQQETLAKLEN-LK-DKLPDIKSIHSKLLLRIGKLQGLYDSVQVINREVEGLSEG--SKGPKES---

2m0qA

0.20

0.18

5.72

0.67

SPARKS-K

TLSNFTQTLEDVFRRIFITYMDNWTAEQEALQAKVDAENFYYVILYLMVMIGMFSFIIVAILVSTVKSKRREHSNDPYHQY-IVEDWQEKYKSQILNLEESKATIHENIGAAGFKMSP-----------

7cu3A

0.02

1.42

0.61

MapAlign

GKKLGSLVVFTASLLIVMSAISLQMFCFVEELDRFTTFPRAFMSMFQILHLFATLILLSLFVAVILDNLVMITVTICSCISMFRRVMHAPTLQIAEYVFVIFMSIELNLKIMADGLFFTPTAVIRDFGG

6exsA1

0.08

3.09

0.36

CEthreader

FFGHPRGLGVLFFVEFWERFSYYGMRAMLIFYMYFAIHQNGLGIDKTTAMSIMSVYGALIYMSSIPGAWIADRITGTRGATLLGAVLIIIGGSGLMKPNISNIVGRLYPENDTRIDAGFVIFYMSVNLG

2m0qA

0.28

0.26

7.81

1.52

MUSTER

MSLSNFTTLEDVFRRIFITYMDNWTAEQEALQAKVDAENFYYVILYLMVMIGMFSFIIVAILVSTVKSKRREHSNDPYHQYIVED-WQE--KYKSQILNLEESK-ATIHENIGAAGFKMSP--------

2m0qA

0.28

0.26

7.81

4.76

HHsearch

STLSNFTTLEDVFRRIFITYMDNWNTTAEQLQAKVDAENFYYVILYLMVMIGMFSFIIVAILVSTVKSKRREHSNDPYHQYIVED-WQEKYKS--QILNLEESK-ATIHENIGAAGFKMSP--------

(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	0.4477

(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	6a69A1	0.51	4.86	0.060	0.837	model1_6a69A1.pdb.gz
2	7cyqA	0.50	4.54	0.052	0.830	model1_7cyqA.pdb.gz
3	7ky5A1	0.50	4.71	0.008	0.822	model1_7ky5A1.pdb.gz
4	7b3bA	0.50	4.52	0.052	0.837	model1_7b3bA.pdb.gz
5	4z3nA	0.49	4.51	0.051	0.822	model1_4z3nA.pdb.gz
6	2yvkA	0.49	4.51	0.070	0.806	model1_2yvkA.pdb.gz
7	6lcpA4	0.49	4.65	0.026	0.814	model1_6lcpA4.pdb.gz
8	6hraA	0.49	4.59	0.067	0.798	model1_6hraA.pdb.gz
9	5yf0A	0.49	4.25	0.059	0.752	model1_5yf0A.pdb.gz
10	3mktA	0.48	4.59	0.088	0.814	model1_3mktA.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:0016247	0.88	channel regulator activity
GO:0015459	0.87	potassium channel regulator activity
GO:0015267	0.83	channel activity
GO:0008324	0.83	cation transmembrane transporter activity
GO:0005267	0.82	potassium channel activity
GO:0005244	0.80	voltage-gated ion channel activity
GO:0005249	0.79	voltage-gated potassium channel activity
GO:0005251	0.69	delayed rectifier potassium channel 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:0065007	0.94	biological regulation
GO:0050794	0.93	regulation of cellular process
GO:1904062	0.91	regulation of cation transmembrane transport
GO:0010959	0.91	regulation of metal ion transport
GO:1901379	0.90	regulation of potassium ion transmembrane transport
GO:0044699	0.88	single-organism process
GO:0009987	0.88	cellular process
GO:0044763	0.85	single-organism cellular process
GO:0048519	0.78	negative regulation of biological process
GO:0065009	0.77	regulation of molecular function
GO:0048523	0.77	negative regulation of cellular process
GO:1902260	0.76	negative regulation of delayed rectifier potassium channel activity
GO:0008152	0.72	metabolic process
GO:0071704	0.71	organic substance metabolic process
GO:0044238	0.70	primary metabolic process
GO:0044237	0.69	cellular metabolic process
GO:0044710	0.68	single-organism metabolic process
GO:0044260	0.68	cellular macromolecule metabolic process
GO:0019538	0.66	protein metabolic process
GO:0005975	0.66	carbohydrate metabolic process
GO:0006487	0.65	protein N-linked glycosylation
GO:0006493	0.64	protein O-linked glycosylation

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:0044459	1.00	plasma membrane part
GO:0008076	0.99	voltage-gated potassium channel complex
GO:0016020	0.82	membrane
GO:0005886	0.72	plasma membrane
GO:0044424	0.62	intracellular 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	2q9fA	0.466	4.87	0.103	0.783	1.14.13.98	NA
2	0.060	2wm4A	0.466	4.13	0.055	0.698	1.14.-.-	10,54
3	0.060	2wuzA	0.450	4.84	0.066	0.791	1.14.13.70	NA
4	0.060	1n40A	0.468	4.34	0.087	0.721	1.14.-.-	NA
5	0.060	1og2A	0.476	4.81	0.064	0.775	1.14.14.1	10,54

	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	2vufA	0.514	4.66	0.066	0.876	0.52	FUA	complex1.pdb.gz	8,9,56,57,60,61,65
2	0.01	2vdbA	0.443	4.94	0.063	0.798	0.53	NPS	complex2.pdb.gz	13,17,50,57,114
3	0.01	1e7cA	0.429	4.93	0.055	0.783	0.64	HLT	complex3.pdb.gz	59,62,66
4	0.01	2bxmA	0.474	4.27	0.051	0.767	0.51	IMN	complex4.pdb.gz	9,12,13,52,53,56,57,60

	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.