D-I-TASSER O95897-D2

D-I-TASSER results for O95897-D2

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

Input Sequence in FASTA format

>O95897 (99 residues)
METLMRSLDARLRAADGSLSAKSFQELKDRMTELLPLSSVLEQYKADTRTIVRLREEVRN
LSGSLAAIQEEMGAYGYEDLQQRVMALEARLHACAQKLG

Predicted Secondary Structure

Sequence	20 40 60 80 \| \| \| \| METLMRSLDARLRAADGSLSAKSFQELKDRMTELLPLSSVLEQYKADTRTIVRLREEVRNLSGSLAAIQEEMGAYGYEDLQQRVMALEARLHACAQKLG
Prediction	CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHC
Confidence	933899999999999997525669999999998610199999998889999999999998999999999997244699999999999999999998729
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 \| \| \| \| METLMRSLDARLRAADGSLSAKSFQELKDRMTELLPLSSVLEQYKADTRTIVRLREEVRNLSGSLAAIQEEMGAYGYEDLQQRVMALEARLHACAQKLG
Prediction	755315424541542564244641551453155034034105524431420540353045134314303542444426403430440363045127638
	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

CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHC
METLMRSLDARLRAADGSLSAKSFQELKDRMTELLPLSSVLEQYKADTRTIVRLREEVRNLSGSLAAIQEEMGAYGYEDLQQRVMALEARLHACAQKLG

5zleA

0.05

2.35

1.33

DEthreader

GFLSVIFALVWVLHYR-EGALEFNWHPVLMVTGFFIQGIAIIVYRPVYSGIVIFGTVIATALMGLTEKLIFSLPPEGVFVNTLGLLILVFGALIFWIVT

5vr2A

0.09

0.04

1.55

1.11

HHsearch

AYNNLLRDKSALEE-EKRQLEQENEDLARRLESSSEEVTRLRRGQC-----------------------------------------------------

2l10A

0.10

3.73

0.52

CEthreader

AAAGLNQAATELVQASPQDLARASGRFGQDFSTFLEAGVEMAGQADRAQVVSNLKGISMSSSKLLLAAKALSTPNLKSQLAAAARAVTDSINQLITMCT

6bfiA4

0.16

5.36

0.63

EigenThreader

DLISLVKQMARKMAMMSKYTRGMAKEIALNAQELLKLARQIANACMDKRAKTNLLQLLDTISTQLKILATVKATSMLVGNAENLMRTIRASEAACIRLR

3na7A1

0.16

0.15

5.03

0.79

FFAS-3D

LEPLIREKRKDLDKALNDKEAKAILNLEEEKLALKLQVSKNETLQDTNAKIASIQKKMSEIKSELRSLNIEE-----DIAKERSNQANREIENLQNEI-

4yayA1

0.15

0.14

4.79

0.76

SPARKS-K

LEDNWETLNDNLKVIEKA---DNAAQVKDALTKMRAAALDAQKATPPSPEMKDFRHGFDILVGQIDDALKLANEGKVKEAQAAAEQLKTTRNAYIQKYL

5xg2A

0.12

4.27

0.67

CNFpred

LRIKLSDLEKELELARLEKVLAEERAVREEIEVAKRRINELDTLIEERGELAKLRGRIERLERKRDKLKKALENPEARELTEKIRAVEKEIAALREELS

6r9tA

0.10

3.73

1.33

DEthreader

AKAVASAAAALVLKAKSVAVIAAATQCALSTSQLVACTKVVAPTISSPVCQEQLVEAGRLVAKAVEGCVSASALLGVGAAATAVTQALNELLQHVKAHA

3jacA

0.05

2.36

0.87

MapAlign

GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG

6nr82

0.14

4.80

0.65

MUSTER

-SAEQVIAGFNRLRQEQRGLASKAAELEMELNEHSLVIDTLKEVDETRKCYRMVERTVKEVLPALENNKEQIQK-IIETLTQQLQAKGKELNEFREKHN

(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	0.5724

(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	6kuxA	0.74	2.78	0.092	0.990	model1_6kuxA.pdb.gz
2	6m31A	0.73	2.63	0.053	0.960	model1_6m31A.pdb.gz
3	4l6rA1	0.73	2.84	0.092	0.980	model1_4l6rA1.pdb.gz
4	4jkvA	0.72	2.71	0.092	0.970	model1_4jkvA.pdb.gz
5	6rz4A	0.72	2.66	0.093	0.950	model1_6rz4A.pdb.gz
6	4ea3B	0.72	2.79	0.102	0.980	model1_4ea3B.pdb.gz
7	6me6A	0.72	2.66	0.093	0.950	model1_6me6A.pdb.gz
8	3u8pA	0.71	2.64	0.113	0.950	model1_3u8pA.pdb.gz
9	6ko5A	0.71	2.57	0.093	0.950	model1_6ko5A.pdb.gz
10	4or2A	0.71	2.67	0.082	0.960	model1_4or2A.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:1901363	0.41	heterocyclic compound binding
GO:0097159	0.41	organic cyclic compound binding
GO:0004872	0.41	receptor activity
GO:0099600	0.39	transmembrane receptor activity
GO:0043167	0.39	ion binding
GO:0046872	0.37	metal ion binding
GO:0004871	0.33	signal transducer activity
GO:0046914	0.31	transition metal ion binding
GO:0004888	0.31	transmembrane signaling receptor activity
GO:0020037	0.30	heme binding
GO:0009055	0.30	electron carrier activity
GO:0005506	0.30	iron ion 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:0044699	0.96	single-organism process
GO:0009987	0.96	cellular process
GO:0044763	0.95	single-organism cellular process
GO:0065007	0.87	biological regulation
GO:0050789	0.87	regulation of biological process
GO:0050794	0.85	regulation of cellular process
GO:0048518	0.82	positive regulation of biological process
GO:0044767	0.82	single-organism developmental process
GO:0051094	0.81	positive regulation of developmental process
GO:0048869	0.81	cellular developmental process
GO:0048522	0.79	positive regulation of cellular process
GO:0045597	0.78	positive regulation of cell differentiation
GO:0016043	0.66	cellular component organization
GO:0032989	0.64	cellular component morphogenesis
GO:0051239	0.63	regulation of multicellular organismal process
GO:2000026	0.62	regulation of multicellular organismal development
GO:0051240	0.62	positive regulation of multicellular organismal process
GO:0060255	0.61	regulation of macromolecule metabolic process
GO:0048519	0.60	negative regulation of biological process
GO:0010604	0.60	positive regulation of macromolecule metabolic process
GO:0010468	0.60	regulation of gene expression
GO:0051130	0.59	positive regulation of cellular component organization
GO:0022603	0.59	regulation of anatomical structure morphogenesis
GO:0010720	0.59	positive regulation of cell development
GO:0010628	0.59	positive regulation of gene expression
GO:0060317	0.58	cardiac epithelial to mesenchymal transition
GO:0010718	0.58	positive regulation of epithelial to mesenchymal transition
GO:0010629	0.58	negative regulation of gene expression
GO:0003190	0.58	atrioventricular valve formation

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:0044464	0.83	cell part
GO:0005623	0.67	cell
GO:0044424	0.64	intracellular part
GO:0043226	0.55	organelle
GO:0043229	0.54	intracellular organelle
GO:0043231	0.52	intracellular membrane-bounded organelle

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	0.094	1wu0A	0.483	2.47	0.063	0.606	3.6.3.14	NA
2	0.067	3eziA	0.546	3.98	0.117	0.929	2.7.13.3	NA
3	0.067	2ksfA	0.573	3.53	0.070	0.869	2.7.13.3	NA
4	0.067	3g4xA	0.622	3.24	0.077	0.919	1.15.1.1	NA
5	0.066	1tqgA	0.593	3.39	0.102	0.879	2.7.13.3	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	0.13	3rqfA	0.682	2.93	0.121	0.990	0.59	III	complex1.pdb.gz	62,63,70,73
2	0.11	3b71B	0.662	3.21	0.091	1.000	0.74	III	complex2.pdb.gz	27,30,62,65,66,69,70,72
3	0.09	3rqgC	0.629	3.52	0.103	0.980	0.48	III	complex3.pdb.gz	22,29,32,62,64,65,72

	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.