D-I-TASSER O15228-D3

D-I-TASSER results for O15228-D3

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

Input Sequence in FASTA format

>O15228 (84 residues)
VRPSLVAVALQMTPGFRKEDVYSCFRFLRDVFADEFIFLPGNTLKDFEEGCYLLCKSEAI
QVTTKDILVTEKGNTVLEFLVGLF

Predicted Secondary Structure

Sequence	20 40 60 80 \| \| \| \| VRPSLVAVALQMTPGFRKEDVYSCFRFLRDVFADEFIFLPGNTLKDFEEGCYLLCKSEAIQVTTKDILVTEKGNTVLEFLVGLF
Prediction	CCHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHCCSSSCCCCCCCCHHHHHHHHHHHCCSSSCCCSSSSSCCHHHHHHHHHHHC
Confidence	955799999997234208999999999999974132555897300189999999971815624875899266078999999749
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 \| \| \| \| VRPSLVAVALQMTPGFRKEDVYSCFRFLRDVFADEFIFLPGNTLKDFEEGCYLLCKSEAIQVTTKDILVTEKGNTVLEFLVGLF
Prediction	733110210232166345540152132025114630121146535314400310342422433763030265144014203737
	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

CCHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHCCSSSCCCCCCCCHHHHHHHHHHHCCSSSCCCSSSSSCCHHHHHHHHHHHC
VRPSLVAVALQMTPGFRKEDVYSCFRFLRDVFADEFIFLPGNTLKDFEEGCYLLCKSEAIQVTTKDILVTEKGNTVLEFLVGLF

7jgrG

0.09

0.08

3.18

1.17

DEthreader

LQQKLMLCTLVLMLKISMGRLHEVYRRVCAKRN----I-LALDQAEFTGTVDLVETRGILRIMRHKVLLQWDEEE-VHALDKQL

1fnnA2

0.11

3.83

0.87

SPARKS-K

LHEKLFLLAIVRSPYITFGDAEESYKIVCEEYG-----ERPRVHSQLWSYLNDLREKGIVETRQNTTLISEPLDTLEAVITKLI

2v1uA2

0.13

0.12

4.13

0.61

MapAlign

LHAKLVLLSIMMLEPASTGEIYERYKELTST----LGLEHV-TLRRVSGIISELDMLGIVKSKTREVSLD--ARLAVENALSED

1tbxA

0.17

0.14

4.71

0.43

CEthreader

YPEAIVLAYLYDNEGIATYDLYKKVNAEFP------------STATFYDAKKFLIQEGFVKERQERLYLTEKGKLFAISLKTAI

1yg2A1

0.09

0.08

3.15

0.71

MUSTER

-SLPHVILTVLSTRDATGYDITKEFSA---SIGY----FWKASHQQVYRELNKMGEQGLVTCVLEVYSITQAGRSALGEWFDQP

6tntN2

0.08

0.06

2.38

0.45

HHsearch

LFWTYIQAMLTNLESLSLDRIYN---MLRMFVVTGPALAE-IDLQELQGYLQKKVRDQQLVYSAGVYRL---------------

1i1sA

0.11

0.10

3.46

0.62

FFAS-3D

----VTYIIKASNDVLNE----KTATILITIAKKDFITHPDLGNAVVNSNIGVLIKKGLVEKSGDGLIITGEAQDIISNAATL-

3zcoA

0.09

0.08

3.23

0.70

EigenThreader

LLMRTFLYTLAQEHTLALETVLIKMVKMLRDNSKEIKKVICITIEKLKSVVNDLVGEKLVVVLESIVELK--LPLEINYAFSMD

1w5sA

0.05

2.24

0.58

CNFpred

ELIILRLIAEATMEWINAGLLRQRYEDASLTM----YNVKPRGYTQYHIYLKHLTSLGLVDAKPTLFRLAPPADRLIEVVDNII

7jgrG2

0.09

0.08

3.18

1.17

DEthreader

LQQKLMLCTLVLMLKISMGRLHEVYRRVCAKRN----I-LALDQAEFTGTVDLVETRGILRIMRHKVLLQWDEEE-VHALDKQL

(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	0.7927

(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	1w5tB	0.76	2.23	0.013	0.929	model1_1w5tB.pdb.gz
2	7jgrG2	0.75	2.18	0.091	0.917	model1_7jgrG2.pdb.gz
3	2v1uA	0.75	1.94	0.115	0.929	model1_2v1uA.pdb.gz
4	3zcoA	0.74	2.25	0.073	0.976	model1_3zcoA.pdb.gz
5	1fnnA2	0.73	2.15	0.078	0.905	model1_1fnnA2.pdb.gz
6	2qbyA2	0.72	2.16	0.130	0.917	model1_2qbyA2.pdb.gz
7	4xgcE2	0.66	2.45	0.068	0.881	model1_4xgcE2.pdb.gz
8	1r6bX	0.44	3.72	0.071	0.691	model1_1r6bX.pdb.gz
9	3l80A	0.41	4.03	0.053	0.750	model1_3l80A.pdb.gz
10	4rcnA3	0.40	4.49	0.077	0.798	model1_4rcnA3.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:0016287	1.00	glycerone-phosphate O-acyltransferase activity
GO:0016787	0.54	hydrolase activity
GO:0005102	0.54	receptor binding
GO:0016788	0.53	hydrolase activity, acting on ester bonds
GO:0016290	0.51	palmitoyl-CoA hydrolase 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:0044699	0.93	single-organism process
GO:0008152	0.92	metabolic process
GO:0044710	0.90	single-organism metabolic process
GO:0071704	0.89	organic substance metabolic process
GO:0009987	0.89	cellular process
GO:0044238	0.88	primary metabolic process
GO:0044763	0.87	single-organism cellular process
GO:0044237	0.87	cellular metabolic process
GO:0006629	0.85	lipid metabolic process
GO:0044281	0.84	small molecule metabolic process
GO:0044255	0.84	cellular lipid metabolic process
GO:1901576	0.81	organic substance biosynthetic process
GO:0044711	0.81	single-organism biosynthetic process
GO:0044249	0.80	cellular biosynthetic process
GO:0008610	0.80	lipid biosynthetic process
GO:0008611	0.78	ether lipid biosynthetic 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:0005777	1.00	peroxisome
GO:0044446	0.83	intracellular organelle part
GO:0016020	0.83	membrane
GO:0031090	0.77	organelle membrane
GO:0098588	0.76	bounding membrane of organelle
GO:0098805	0.75	whole membrane
GO:0005778	0.74	peroxisomal membrane
GO:0070013	0.53	intracellular organelle lumen
GO:0005782	0.51	peroxisomal matrix

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	1leaA	0.559	2.18	0.100	0.714	3.4.21.88	NA
2	0.060	2rnpC	0.389	4.36	0.075	0.762	2.7.7.6	NA
3	0.060	2zbkA	0.529	3.07	0.086	0.738	5.99.1.3	NA
4	0.060	1tw2B	0.591	2.33	0.106	0.786	2.1.1.-	54
5	0.060	1mj9A	0.562	2.42	0.138	0.774	2.3.1.48	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	0.03	3aafA	0.689	2.41	0.143	0.917	0.22	QNA	complex1.pdb.gz	15,73,74
2	0.02	3bpv0	0.678	1.74	0.132	0.809	0.20	III	complex2.pdb.gz	42,46,47,48,50,51,53,54,55,58,59
3	0.02	1z910	0.661	2.06	0.130	0.821	0.19	III	complex3.pdb.gz	32,40,41,46,47,50,52,53,54,56,57,58
4	0.02	3m9a0	0.658	2.27	0.130	0.821	0.19	III	complex4.pdb.gz	72,75,77,78,79
5	0.02	2zdb0	0.674	1.98	0.119	0.798	0.13	III	complex5.pdb.gz	10,42,44,45,47,48,49,50,51,54,55,56
6	0.02	2fbi0	0.671	2.14	0.101	0.821	0.22	III	complex6.pdb.gz	42,67,72,73,80,81,83,84
7	0.02	1z9cA	0.637	2.05	0.119	0.798	0.15	QNA	complex7.pdb.gz	34,73,74
8	0.02	1okr0	0.648	2.47	0.086	0.821	0.32	III	complex8.pdb.gz	37,38,40,47,49,50,51,53,55
9	0.02	1ub90	0.656	2.19	0.087	0.821	0.17	III	complex9.pdb.gz	25,29,33,40
10	0.02	2gau0	0.662	1.77	0.090	0.798	0.12	III	complex10.pdb.gz	45,46,47,48,51,52,55,56,58

	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.