D-I-TASSER P29474-D2

D-I-TASSER results for P29474-D2

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

Input Sequence in FASTA format

>P29474 (84 residues)
RPSPGPPAPEQLLSQARDFINQYYSSIKRSGSQAHEQRLQEVEAEVAATGTYQLRESELV
FGAKQAWRNAPRCVGRIQWGKLQV

Predicted Secondary Structure

Sequence	20 40 60 80 \| \| \| \| RPSPGPPAPEQLLSQARDFINQYYSSIKRSGSQAHEQRLQEVEAEVAATGTYQLRESELVFGAKQAWRNAPRCVGRIQWGKLQV
Prediction	CCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHCCCCCCCCCCCCCCCC
Confidence	999999999999999999999999983646868999999999999993298548989999999999851765755223002669
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 \| \| \| \| RPSPGPPAPEQLLSQARDFINQYYSSIKRSGSQAHEQRLQEVEAEVAATGTYQLRESELVFGAKQAWRNAPRCVGRIQWGKLQV
Prediction	856864544640262045005201523746746414521540362067433252345003200330034143020223166278
	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

CCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHCCCCCCCCCCCCCCCC
RPSPGPPAPEQLLSQARDFINQYYSSIKRSGSQAHEQRLQEVEAEVAATGTYQLRESELVFGAKQAWRNAPRCVGRIQWGKLQV

1vagA

0.49

14.18

1.33

DEthreader

HTRKDVRTKDQLFPLAKEFLDQYYSSIKRFGSKAHMDRLEEVNKEIESTSTYQLKDTELIYGAKHAWRNASRCVGRQWSLAITI

1dm6A

0.94

26.39

2.08

SPARKS-K

RPSPGPPPAEQLLSQARDFINQYYSSIKRSGSQAHEERLQEVEAEVASTGTYHLRESELVFGAKQAWRNAPRCVGRIQWGKLQV

1dm6A

0.94

0.88

24.73

0.97

MapAlign

-----PPPAEQLLSQARDFINQYYSSIKRSGSQAHEERLQEVEAEVASTGTYHLRESELVFGAKQAWRNAPRCVGRIQWGKLQV

1dm6A

0.94

26.39

1.03

CEthreader

RPSPGPPPAEQLLSQARDFINQYYSSIKRSGSQAHEERLQEVEAEVASTGTYHLRESELVFGAKQAWRNAPRCVGRIQWGKLQV

1dm6A

0.94

26.39

2.00

MUSTER

RPSPGPPPAEQLLSQARDFINQYYSSIKRSGSQAHEERLQEVEAEVASTGTYHLRESELVFGAKQAWRNAPRCVGRIQWGKLQV

1dm6A

0.94

26.39

3.31

HHsearch

RPSPGPPPAEQLLSQARDFINQYYSSIKRSGSQAHEERLQEVEAEVASTGTYHLRESELVFGAKQAWRNAPRCVGRIQWGKLQV

1dm6A

0.94

26.39

1.53

FFAS-3D

RPSPGPPPAEQLLSQARDFINQYYSSIKRSGSQAHEERLQEVEAEVASTGTYHLRESELVFGAKQAWRNAPRCVGRIQWGKLQV

1vagA

0.58

16.75

1.07

EigenThreader

RKPEDVRTKDQLFPLAKEFLDQYYSSIKRFGSKAHMDRLEEVNKEIESTSTYQLKDTELIYGAKHAWRNASRCVGRIQWSKLQV

1d0cA

0.94

26.39

1.05

CNFpred

RPSPGPPPAEQLLSQARDFINQYYSSIKRSGSQAHEERLQEVEAEVASTGTYHLRESELVFGAKQAWRNAPRCVGRIQWGKLQV

1dm6A

0.79

22.21

1.33

DEthreader

LQTRPSPPAEQLLSQARDFINQYYSSIKRSGSQAHEERLQEVEAEVASTGTYHLRESELVFGAKQAWRNAPRCVGRQWKLAITV

(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	0.6892

(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	1dm6A	0.95	0.88	0.881	1.000	model1_1dm6A.pdb.gz
2	1vagA	0.94	1.10	0.583	1.000	model1_1vagA.pdb.gz
3	3e7gC	0.92	1.20	0.530	0.988	model1_3e7gC.pdb.gz
4	2flqA	0.84	1.28	0.410	0.917	model1_2flqA.pdb.gz
5	2an0A	0.84	1.20	0.351	0.905	model1_2an0A.pdb.gz
6	1mjtB	0.84	0.89	0.419	0.881	model1_1mjtB.pdb.gz
7	3o8jA	0.42	4.02	0.082	0.798	model1_3o8jA.pdb.gz
8	1vw47	0.40	3.39	0.055	0.631	model1_1vw47.pdb.gz
9	3re2A2	0.36	4.22	0.043	0.571	model1_3re2A2.pdb.gz
10	1vcoA2	0.33	4.51	0.041	0.595	model1_1vcoA2.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:0003824	0.97	catalytic activity
GO:0016491	0.96	oxidoreductase activity
GO:0004517	0.95	nitric-oxide synthase 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:0065007	0.92	biological regulation
GO:0050789	0.91	regulation of biological process
GO:0050794	0.89	regulation of cellular process
GO:0007165	0.84	signal transduction
GO:0007263	0.83	nitric oxide mediated signal transduction
GO:0048518	0.80	positive regulation of biological process
GO:0019222	0.78	regulation of metabolic process
GO:0080090	0.77	regulation of primary metabolic process
GO:0048522	0.77	positive regulation of cellular process
GO:0031323	0.77	regulation of cellular metabolic process
GO:0065008	0.76	regulation of biological quality
GO:0031326	0.76	regulation of cellular biosynthetic process
GO:0031325	0.76	positive regulation of cellular metabolic process
GO:0019220	0.76	regulation of phosphate metabolic process
GO:0019219	0.76	regulation of nucleobase-containing compound metabolic process
GO:1900373	0.75	positive regulation of purine nucleotide biosynthetic process
GO:0051349	0.75	positive regulation of lyase activity
GO:0031281	0.75	positive regulation of cyclase activity
GO:0030804	0.75	positive regulation of cyclic nucleotide biosynthetic process
GO:0031284	0.74	positive regulation of guanylate cyclase activity
GO:0051239	0.73	regulation of multicellular organismal process
GO:0045776	0.73	negative regulation of blood pressure
GO:1903522	0.70	regulation of blood circulation
GO:0032501	0.70	multicellular organismal process
GO:0051240	0.69	positive regulation of multicellular organismal process
GO:0003008	0.69	system process
GO:0045909	0.68	positive regulation of vasodilation
GO:0009987	0.57	cellular process
GO:0044699	0.54	single-organism process
GO:0050896	0.53	response to stimulus

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	0.95	cell part
GO:0044424	0.89	intracellular part
GO:0043226	0.80	organelle
GO:0043229	0.79	intracellular organelle
GO:0043227	0.79	membrane-bounded organelle
GO:0043231	0.78	intracellular membrane-bounded organelle
GO:0044444	0.77	cytoplasmic part
GO:0016020	0.60	membrane
GO:0005737	0.55	cytoplasm
GO:0005829	0.53	cytosol
GO:0044422	0.52	organelle part

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	1tj7A	0.539	3.31	0.049	0.833	4.3.2.1	NA
2	0.060	1rp5A	0.526	3.50	0.041	0.809	3.4.-.-	NA
3	0.060	1tffA	0.539	3.89	0.061	0.905	3.4.19.12	NA
4	0.060	2amoA	0.839	1.17	0.355	0.905	1.14.13.39	NA
5	0.060	2z8yD	0.532	3.57	0.050	0.845	1.2.7.4 1.2.99.2	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	0.40	3nseB	0.938	0.99	0.893	1.000	0.49	ITU	complex1.pdb.gz	45,50,51,52
	2	0.14	9nseA	0.959	0.75	0.929	1.000	0.40	HEM	complex2.pdb.gz	67,70,72,73,74,75,82

	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.