D-I-TASSER Q13133-D1

D-I-TASSER results for Q13133-D1

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

Input Sequence in FASTA format

>Q13133 (76 residues)
MSLWLGAPVPDIPPDSAVELWKPGAQDASSQAQGGSSCILREEARMPHSAGGTAGVGLEA
AEPTALLTRAEPPSEP

Predicted Secondary Structure

Sequence	20 40 60 \| \| \| MSLWLGAPVPDIPPDSAVELWKPGAQDASSQAQGGSSCILREEARMPHSAGGTAGVGLEAAEPTALLTRAEPPSEP
Prediction	CCCCCCCCCCCCCCCHHHHHCCCCCCCCHHHHCCCCCSSSCCCCCCCCCCCCCCCSCCCCCCCSSSSSCCCCCCCC
Confidence	9611469999999520333215766450334126875032466679988787320010247970442147789999
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 \| \| \| MSLWLGAPVPDIPPDSAVELWKPGAQDASSQAQGGSSCILREEARMPHSAGGTAGVGLEAAEPTALLTRAEPPSEP
Prediction	6523453534624473224124463553454454444222476453454444434243644534231434644688
	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

CCCCCCCCCCCCCCCHHHHHCCCCCCCCHHHHCCCCCSSSCCCCCCCCCCCCCCCSCCCCCCCSSSSSCCCCCCCC
MSLWLGAPVPDIPPDSAVELWKPGAQDASSQAQGGSSCILREEARMPHSAGGTAGVGLEAAEPTALLTRAEPPSEP

6w1cE2

0.11

0.08

2.87

0.54

CEthreader

----APEALVRSGKREATLSLHPIHPTLLITAQTEVTIPVPVEGVEYQWGNHKPQRFVVA----------------

6mgjA1

0.04

2.07

0.63

EigenThreader

TQGVADTASSQPTGFYITYSNGVGPYDGYGFGGLAVSSLNAWWPDETSTSLDPSPKLGWGDLEIYGTGATIYKVNI

2f40A

0.09

0.08

3.01

0.28

FFAS-3D

-SKWIK-FTTNLTPEEAKIVQRDEFYRVFINPYAKVAEVVIDDSKVNIE------ELKEKLKGEVIEEKEITLQE-

3boiA

0.17

0.16

5.21

0.86

SPARKS-K

ADGAHGVNGCPGTAGAAGSVGGPGCDNGGNGNPGCAGGGGAGGASGGTGVGGRGGKGGSGTPKG----ADGAPGAP

5oarB

0.19

0.07

2.12

0.58

CNFpred

----------------VMQSWNNGLEYISNLTARGYDVIVSS----------------------------------

3d30A

0.15

0.12

3.97

0.67

DEthreader

TSGGGAFLLDPIPSDMEITAI---NPADLALA---GSY-------LEV--TTVYVTDLYPEGALDLSAF--APITG

5lqwX1

0.02

0.01

1.18

0.58

MapAlign

--ATSSKTQLIISLSNYELVYFKIDVSSDLIELTTHPELDTMPSKVAIVHADLLAIADNEGMIKI-----------

2nbiA

0.19

0.18

5.96

0.58

MUSTER

DECFLPYSDASRPPSCL-SFGRPDCDVLTPQNINCPRCCATECRPDNPMFTPSPDGSPPICSPTMLPTNQPTPPEP

3qh6A

0.14

0.08

2.68

0.39

HHsearch

CSVLL--CLSGEKAGWGL-FFSGEYPQDVDWGAGDTAIILRFSSA-------------------------------

4unmA2

0.04

2.07

0.46

CEthreader

TKRYEKLKLDKKDFQGIRDAFEFDPVAEKYIKVDPMHEARWYPTLTTLGDGKILSVSGLDDIGQLVPGKNEVYDPK

(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	0.5383

(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	4ce5A	0.45	3.86	0.056	0.816	model1_4ce5A.pdb.gz
2	1iyeA2	0.45	3.78	0.138	0.803	model1_1iyeA2.pdb.gz
3	6ozdA2	0.43	3.94	0.127	0.829	model1_6ozdA2.pdb.gz
4	1txoB	0.43	4.29	0.015	0.842	model1_1txoB.pdb.gz
5	2j86B	0.42	4.28	0.074	0.842	model1_2j86B.pdb.gz
6	1a0gB2	0.41	4.23	0.015	0.789	model1_1a0gB2.pdb.gz
7	2xpfA	0.39	4.34	0.070	0.776	model1_2xpfA.pdb.gz
8	2va8B4	0.34	4.13	0.078	0.684	model1_2va8B4.pdb.gz
9	2abjA	0.33	4.52	0.028	0.671	model1_2abjA.pdb.gz
10	2v06A	0.31	4.75	0.046	0.697	model1_2v06A.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:0003677	1.00	DNA binding
GO:0043565	0.73	sequence-specific DNA binding
GO:0004871	0.67	signal transducer activity
GO:0005102	0.57	receptor binding
GO:0035257	0.55	nuclear hormone receptor binding
GO:0046965	0.54	retinoid X receptor 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:2000188	1.00	regulation of cholesterol homeostasis
GO:0045893	1.00	positive regulation of transcription, DNA-templated
GO:0044699	0.87	single-organism process
GO:0008152	0.87	metabolic process
GO:0071704	0.85	organic substance metabolic process
GO:0044238	0.84	primary metabolic process
GO:0009987	0.75	cellular process
GO:0044237	0.69	cellular metabolic process
GO:1901576	0.63	organic substance biosynthetic process
GO:0044249	0.62	cellular biosynthetic process
GO:0006810	0.59	transport
GO:0050896	0.58	response to stimulus
GO:0048523	0.58	negative regulation of cellular process
GO:0044765	0.58	single-organism transport
GO:0044710	0.58	single-organism metabolic process
GO:0051247	0.57	positive regulation of protein metabolic process
GO:0051239	0.57	regulation of multicellular organismal process
GO:0042221	0.57	response to chemical
GO:0032268	0.57	regulation of cellular protein metabolic process
GO:0006357	0.57	regulation of transcription from RNA polymerase II promoter
GO:0080134	0.56	regulation of response to stress
GO:0051716	0.56	cellular response to stimulus
GO:0051336	0.56	regulation of hydrolase activity
GO:0051128	0.56	regulation of cellular component organization
GO:0050878	0.56	regulation of body fluid levels
GO:0050709	0.56	negative regulation of protein secretion
GO:0048585	0.56	negative regulation of response to stimulus
GO:0045944	0.56	positive regulation of transcription from RNA polymerase II promoter
GO:0045923	0.56	positive regulation of fatty acid metabolic process
GO:0045892	0.56	negative regulation of transcription, DNA-templated
GO:0044093	0.56	positive regulation of molecular function
GO:0042592	0.56	homeostatic process
GO:0042304	0.56	regulation of fatty acid biosynthetic process
GO:0032570	0.56	response to progesterone
GO:0032270	0.56	positive regulation of cellular protein metabolic process
GO:0032101	0.56	regulation of response to external stimulus
GO:0009967	0.56	positive regulation of signal transduction
GO:0009605	0.56	response to external stimulus
GO:2000189	0.55	positive regulation of cholesterol homeostasis
GO:0090341	0.55	negative regulation of secretion of lysosomal enzymes
GO:0090188	0.55	negative regulation of pancreatic juice secretion
GO:0071222	0.55	cellular response to lipopolysaccharide
GO:0070328	0.55	triglyceride homeostasis
GO:0051006	0.55	positive regulation of lipoprotein lipase activity
GO:0050728	0.55	negative regulation of inflammatory response
GO:0048550	0.55	negative regulation of pinocytosis
GO:0045723	0.55	positive regulation of fatty acid biosynthetic process
GO:0043277	0.55	apoptotic cell clearance
GO:0043031	0.55	negative regulation of macrophage activation
GO:0042632	0.55	cholesterol homeostasis
GO:0034145	0.55	positive regulation of toll-like receptor 4 signaling pathway
GO:0032369	0.55	negative regulation of lipid transport
GO:0010887	0.55	negative regulation of cholesterol storage
GO:0010875	0.55	positive regulation of cholesterol efflux
GO:0010870	0.55	positive regulation of receptor biosynthetic process
GO:0010867	0.55	positive regulation of triglyceride biosynthetic process
GO:0000122	0.55	negative regulation of transcription from RNA polymerase II promoter
GO:0006629	0.50	lipid 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:0005634	1.00	nucleus
GO:0044446	0.67	intracellular organelle part
GO:0032991	0.63	macromolecular complex
GO:0043234	0.61	protein complex
GO:0044428	0.60	nuclear part
GO:0005667	0.57	transcription factor complex
GO:0043235	0.56	receptor complex
GO:0000790	0.56	nuclear chromatin
GO:0090575	0.55	RNA polymerase II transcription factor complex

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	1txoB	0.431	4.29	0.015	0.842	3.1.3.16	6
2	0.060	3b9jC	0.300	4.71	0.036	0.684	1.17.3.2 1.17.1.4	NA
3	0.060	1fo4A	0.391	3.65	0.016	0.697	1.17.1.4	NA
4	0.060	1jqgA	0.313	4.87	0.056	0.750	3.4.17.1	NA
5	0.060	2vvmA	0.397	3.86	0.049	0.724	1.4.3.4	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:

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
	1	0.01	3fhbA	0.384	4.63	0.066	0.855	0.54	GAB	complex1.pdb.gz	51,54,69,74

	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.