D-I-TASSER P37059-D1

D-I-TASSER results for P37059-D1

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

Input Sequence in FASTA format

>P37059 (75 residues)
MSTFFSDTAWICLAVPTVLCGTVFCKYKKSSGQLWSWMVCLAGLCAVCLLILSPFWGLIL
FSVSCFLMYTYLSGQ

Predicted Secondary Structure

Sequence	20 40 60 \| \| \| MSTFFSDTAWICLAVPTVLCGTVFCKYKKSSGQLWSWMVCLAGLCAVCLLILSPFWGLILFSVSCFLMYTYLSGQ
Prediction	CCCCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCC
Confidence	975324224788999999868998650368742110344687568999999859999999999999997532599
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 \| \| \| MSTFFSDTAWICLAVPTVLCGTVFCKYKKSSGQLWSWMVCLAGLCAVCLLILSPFWGLILFSVSCFLMYTYLSGQ
Prediction	744334433112133333311111132454646333300000333131123133331333333313311123368
	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

                   |                   |                   |

SS
Seq

CCCCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCC
MSTFFSDTAWICLAVPTVLCGTVFCKYKKSSGQLWSWMVCLAGLCAVCLLILSPFWGLILFSVSCFLMYTYLSGQ

5f0oA4

0.10

0.09

3.49

1.17

DEthreader

KSSFYAFNRRQDQMSTVLWKFIEFCEETNSQSAASLSDTKLIKTVEWIS-SFLVNTVFRVLIYAAPII-FNISNL

5xj5A

0.07

2.80

0.36

CEthreader

TRALGKKYGVLVFFLDFLKGFIPALIAVKSFGISWVLTFTGLASVLGHMYPVFFGFKGGKGVATALGVVFAVSPS

5ezmA3

0.11

0.09

3.36

0.57

EigenThreader

IPNSFYRAYAVWVAVAFVVMLLGIAVARLLLRRGVLPSVAVYAMG------------MYLGFTVALLGHETVGRP

4xydA1

0.07

2.76

0.56

FFAS-3D

MKYQSQSIAYFAVALGLFAIQVSGGLLLGLPFNIVRMLHTNSLIVWLLLGFMGAAYFVIIMVLGTLGVVVTY---

2vpyC2

0.16

5.32

0.78

SPARKS-K

NRPLWNGLMAGLFPLTALVLALGLAALLKSPWALFPLRVLAGASLLLALLGLFLLLGLGTFPWAGLLAAAGLRAL

5oqtA

0.09

0.08

3.08

0.74

CNFpred

------VLSFILSGLACVFAALCYAEFASTVPVSGSAYTYSYATFGELIAWILGWDLILEYGVASSAVAVGWSGY

6xkwn

0.09

3.51

1.00

DEthreader

DGIRAGVIATTFWGIVGFLVAVIIAFQLAFPANLENNFGRLRPLHTSIEYAVLVGA-LNGMTFLGIMAYNLWATA

6h7dA

0.08

3.15

0.74

MapAlign

FDNQMLQLFTSSLYLAALVASFMASVIT-RKHGRKVSMFIGGLAFLIGALFNMLIIGRLLLGVGVGFANQSTPVY

4rngA

0.12

4.21

0.79

MUSTER

--DLNNLIGIIAGAITTSALIPQALKIYKTKSSLAMFIFMAIGITLWFFYGVLIEIPVILANLISLILIFLIIFM

7ks0B

0.12

0.11

3.73

0.55

HHsearch

LN-PLSPDIWMYVLLAYLGVSVVLFVIARALS--TRGGIWWF----FTLIIISSYTA----NLAAFLTVERMESP

(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	0.5219

(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	2n39A	0.65	2.37	0.087	0.893	model1_2n39A.pdb.gz
2	4rr2D	0.65	2.54	0.099	0.920	model1_4rr2D.pdb.gz
3	5l9wA1	0.65	2.62	0.054	0.880	model1_5l9wA1.pdb.gz
4	5ydpA	0.63	3.45	0.041	0.907	model1_5ydpA.pdb.gz
5	3fr8B2	0.63	2.99	0.055	0.947	model1_3fr8B2.pdb.gz
6	4b6at	0.62	3.60	0.068	0.973	model1_4b6at.pdb.gz
7	3nd0A	0.62	2.64	0.028	0.840	model1_3nd0A.pdb.gz
8	2q8kA	0.60	3.39	0.096	0.960	model1_2q8kA.pdb.gz
9	4ipaA	0.60	3.59	0.096	0.960	model1_4ipaA.pdb.gz
10	3tavA	0.56	3.07	0.085	0.853	model1_3tavA.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:0047035	1.00	testosterone dehydrogenase (NAD+) activity
GO:0004303	1.00	estradiol 17-beta-dehydrogenase activity
GO:0047006	0.56	17-alpha,20-alpha-dihydroxypregn-4-en-3-one dehydrogenase 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:0042221	1.00	response to chemical
GO:0033993	0.83	response to lipid
GO:0032526	0.82	response to retinoic acid
GO:0044699	0.78	single-organism process
GO:0008152	0.76	metabolic process
GO:0044710	0.54	single-organism metabolic process

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:0044424	1.00	intracellular part
GO:0044444	0.90	cytoplasmic part
GO:0044446	0.85	intracellular organelle part
GO:0016020	0.85	membrane
GO:0044425	0.83	membrane part
GO:0044432	0.82	endoplasmic reticulum part
GO:0005789	0.81	endoplasmic reticulum membrane

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	0.066	2w1aD	0.556	2.48	0.046	0.773	5.4.99.5	NA
2	0.060	3fmrB	0.568	3.25	0.042	0.893	3.4.11.18	NA
3	0.060	1cxpC	0.570	3.23	0.045	0.880	1.11.1.7	NA
4	0.060	2zdxA	0.568	3.47	0.028	0.893	2.7.11.2	NA
5	0.060	2pulA	0.599	2.91	0.055	0.880	2.7.1.100	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	0.02	3oawA	0.534	3.04	0.127	0.827	0.23	OAW	complex1.pdb.gz	43,48,62,63,64
2	0.01	3qk0A	0.533	2.97	0.111	0.827	0.11	QK0	complex2.pdb.gz	43,58,59,60
3	0.01	1e8wA	0.565	3.91	0.027	0.933	0.13	QUE	complex3.pdb.gz	42,62,63
4	0.01	3nzuA	0.557	3.96	0.042	0.907	0.11	NZU	complex4.pdb.gz	24,43,45
5	0.01	3r7rA	0.573	3.99	0.027	0.920	0.12	FAZ	complex5.pdb.gz	23,45,61,62,63
6	0.01	2olc0	0.591	3.14	0.041	0.907	0.13	III	complex6.pdb.gz	12,16,20,21,24,25,38,39,41,42,43,46,49
7	0.01	3nzsA	0.560	3.81	0.028	0.893	0.11	NZS	complex7.pdb.gz	47,59,64
8	0.01	1zk80	0.588	3.15	0.014	0.853	0.21	III	complex8.pdb.gz	38,39,42,43,45,46,49,50,51,53
9	0.01	3l17A	0.570	3.81	0.027	0.920	0.10	JZY	complex9.pdb.gz	44,57,58,59,67
10	0.01	3apcA	0.573	3.73	0.028	0.907	0.18	MMD	complex10.pdb.gz	45,47,58,61

	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.