D-I-TASSER O75319-D1

D-I-TASSER results for O75319-D1

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

Input Sequence in FASTA format

>O75319 (77 residues)
MRNSETLERGVGGCRVFSCLGSYPGIEGAGLALLADLALGGRLLGTHMSQWHHPRSGWGR
RRDFSGRSSAKKKGGNH

Predicted Secondary Structure

Sequence	20 40 60 \| \| \| MRNSETLERGVGGCRVFSCLGSYPGIEGAGLALLADLALGGRLLGTHMSQWHHPRSGWGRRRDFSGRSSAKKKGGNH
Prediction	CCCCCCHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHHCCHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCC
Confidence	97664212244444213678865675312678888876345167877765204778865563135777533357899
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 \| \| \| MRNSETLERGVGGCRVFSCLGSYPGIEGAGLALLADLALGGRLLGTHMSQWHHPRSGWGRRRDFSGRSSAKKKGGNH
Prediction	75527436401320442434342434433222122323343431343144144454534544425446545655678
	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

CCCCCCHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHHCCHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCC
MRNSETLERGVGGCRVFSCLGSYPGIEGAGLALLADLALGGRLLGTHMSQWHHPRSGWGRRRDFSGRSSAKKKGGNH

3bogA

0.18

0.16

5.06

1.03

SPARKS-K

PGTAGAAGSVGGGCDGGHGGNGGNGNPGCA---------GGV--GGAGGASGGTGVGGRGGKGGSGTPKGADAPGAP

4xriA2

0.03

1.66

1.00

DEthreader

AEAYMFALYLGCMAIGLVSDVTSQ--P-YCDNFMNYLLGNLKPILQCFGDIASAIGGHFTYLTIVAQVLQQAATITV

6nu9A

0.03

1.70

0.66

CEthreader

IVARAGRLTATVKVSQVDGRIDCETLLGNKTFRTSFVDGAVLLSFDASQSTMAAGPFSLTYAASAAGLEVRYVAAGL

2jz1A

0.04

2.00

0.50

EigenThreader

GSPLGQDVFLDYCQKLLEKFRYPWELMPLMYVILKDADANIEEASRRIEEGQY----VVNEYSRQHNLNIYDGGELR

1ohuB

0.12

0.08

2.78

0.28

FFAS-3D

-------------------------SYGRLIGLISFVAAKSLFIKTRINNWKEHNRSWDDFTLGKQKEDYERAEAEK

7jjvA

0.17

0.16

5.13

0.94

SPARKS-K

GAGGTGNTNGGAGGSGGNSDVAAGGAGAAGGAA------GGAGTGGTGGNGGAGKPGGAPGAGGAGTPAGSASPGQT

4xeuA

0.26

0.08

2.40

0.50

CNFpred

---------------------------GQGIANAVGMALAEKVLAAQFNR---------------------------

5u1sA2

0.05

2.35

1.00

DEthreader

--YLIRILLNLSKITKLYINWLIEMD--FVKMLLCYLNFNNFKSIELSLCIKKEYSSIVYADNYLLEAYLSLYMTLF

1to6A1

0.04

1.95

0.76

MapAlign

ILADVVSPLCGHQGATYTFGKQKGLDSTMFEVVDQAIQDFYEPATLKLKGAGAGGGIAGGLCAFAQASI--------

3bogA

0.17

5.55

0.71

MUSTER

CKGADGAH-GVGCPGTAGAAGSVGGPGCDGGHGGNGGNGNPGCAGGVGGAGGASGGTGVGGRGGKGGSGTPKADGAP

(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	0.6153

(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	1ivhA	0.55	3.99	0.014	0.896	model1_1ivhA.pdb.gz
2	4l1fA	0.54	3.73	0.066	0.857	model1_4l1fA.pdb.gz
3	6w2vA	0.54	3.29	0.041	0.883	model1_6w2vA.pdb.gz
4	5z8tA	0.53	4.23	0.105	0.909	model1_5z8tA.pdb.gz
5	6gczA	0.53	3.68	0.069	0.922	model1_6gczA.pdb.gz
6	3da4A	0.53	3.04	0.030	0.831	model1_3da4A.pdb.gz
7	3mxlA	0.53	4.01	0.065	0.896	model1_3mxlA.pdb.gz
8	7byyA	0.53	3.66	0.027	0.870	model1_7byyA.pdb.gz
9	2jifA	0.53	4.08	0.079	0.883	model1_2jifA.pdb.gz
10	1rx0A	0.53	3.85	0.066	0.883	model1_1rx0A.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:0098519	1.00	nucleotide phosphatase activity, acting on free nucleotides
GO:0004651	1.00	polynucleotide 5'-phosphatase activity
GO:1901363	0.81	heterocyclic compound binding
GO:0097159	0.81	organic cyclic compound binding
GO:0003676	0.61	nucleic acid binding
GO:0003723	0.60	RNA binding
GO:0004721	0.59	phosphoprotein phosphatase activity
GO:0004725	0.57	protein tyrosine phosphatase activity
GO:0044822	0.55	poly(A) RNA 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:0098507	1.00	polynucleotide 5' dephosphorylation
GO:0016070	1.00	RNA metabolic process
GO:0019538	0.60	protein metabolic process
GO:0044267	0.58	cellular protein metabolic process
GO:0006464	0.57	cellular protein modification process
GO:0006396	0.56	RNA processing
GO:0006470	0.55	protein dephosphorylation

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:0016607	1.00	nuclear speck
GO:0005739	1.00	mitochondrion
GO:0005634	0.61	nucleus
GO:0044429	0.59	mitochondrial part
GO:0005759	0.58	mitochondrial 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	0.060	2r0nA	0.534	3.97	0.145	0.883	1.3.99.7	NA
2	0.060	2wb8A	0.494	3.74	0.080	0.818	2.7.11.1	33
3	0.060	2ebaA	0.499	4.06	0.123	0.896	1.3.99.7	NA
4	0.060	2wm4A	0.499	4.29	0.054	0.883	1.14.-.-	NA
5	0.060	1rx0A	0.526	3.85	0.066	0.883	1.3.99.-	30

	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	1jqiB	0.517	3.78	0.097	0.883	0.44	FAD	complex1.pdb.gz	30,34,48,74
2	0.02	1t9gB	0.513	3.72	0.079	0.844	0.51	FAD	complex2.pdb.gz	28,31,72,74
3	0.02	1egeA	0.515	3.90	0.079	0.857	0.46	FAD	complex3.pdb.gz	30,71,75
4	0.01	3mdeA	0.512	3.75	0.079	0.844	0.42	FAD	complex4.pdb.gz	29,34,49,72,75
5	0.01	1egcD	0.509	3.74	0.079	0.844	0.54	FAD	complex5.pdb.gz	27,30,50,59
6	0.01	1egdD	0.513	3.80	0.079	0.857	0.44	FAD	complex6.pdb.gz	31,72,73
7	0.01	1ivhC	0.540	3.85	0.014	0.883	0.50	FAD	complex7.pdb.gz	29,30,50
8	0.01	1udyB	0.509	3.76	0.066	0.844	0.42	UUU	complex8.pdb.gz	30,34,71,73,74
9	0.01	1rx0A	0.526	3.85	0.066	0.883	0.42	FAD	complex9.pdb.gz	30,47,48,61,63
10	0.01	3r7kD	0.482	4.06	0.053	0.857	0.40	FDA	complex10.pdb.gz	30,50,51

	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.