D-I-TASSER A5YM72-D2

D-I-TASSER results for A5YM72-D2

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

Input Sequence in FASTA format

>A5YM72 (105 residues)
VPATLAFTYKPPGLLRGGDASLGLRLVELSGKEGQETLVKEEVEAFLRSEALGDILQVAV
KLSGWRWRGRQAWRLHPRAELGAVVDTVLALLEKLEEEESVLVEA

Predicted Secondary Structure

Sequence	20 40 60 80 100 \| \| \| \| \| VPATLAFTYKPPGLLRGGDASLGLRLVELSGKEGQETLVKEEVEAFLRSEALGDILQVAVKLSGWRWRGRQAWRLHPRAELGAVVDTVLALLEKLEEEESVLVEA
Prediction	CCCSSSSSCCCCCCCCCCCCCCCSSSSSSCCCCCHHHHHHHHHHHHHHHHCCCCCSSSSSSCCCCCCCCCCCSCCCCCCCCCHHHHHHHHHHHHHHHCCSSSSCC
Confidence	985156641795114799999863899825631456789999999998741475115887157876667644012456675059999999999731111365219
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 \| \| \| \| \| VPATLAFTYKPPGLLRGGDASLGLRLVELSGKEGQETLVKEEVEAFLRSEALGDILQVAVKLSGWRWRGRQAWRLHPRAELGAVVDTVLALLEKLEEEESVLVEA
Prediction	645222102423541647753441321415475236421474034114444344034013425424144543251245354420041014005415654223358
	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                 100

                   |                   |                   |                   |                   |

SS
Seq

CCCSSSSSCCCCCCCCCCCCCCCSSSSSSCCCCCHHHHHHHHHHHHHHHHCCCCCSSSSSSCCCCCCCCCCCSCCCCCCCCCHHHHHHHHHHHHHHHCCSSSSCC
VPATLAFTYKPPGLLRGGDASLGLRLVELSGKEGQETLVKEEVEAFLRSEALGDILQVAVKLSGWRWRGRQAWRLHPRAELGAVVDTVLALLEKLEEEESVLVEA

6julF2

0.18

0.15

4.97

0.79

CEthreader

RSRSHVVTFPQD--------------LTERREDSAVRDLALQTLAEIVEQGRI-VTRVAVTVRTSTFYTRTKIRKLPSTDAGQIVDTALAVLDQFRPVRLLGVRL

4ir1F2

0.15

0.12

4.17

0.78

EigenThreader

KSVGVERTM----------------AEDIHHWSECEAIIERLYPELERRLAKVKLLIQGVKLKFDD--FQQTTQEWPRLNKADLIATARKTWDERRRGVRVGLHV

5ezbA

0.07

0.06

2.39

0.46

FFAS-3D

IPDT--DIYCDVEEYEEVKEYPGIKIFQANTSLANSESYTSALKKKTGVDGSTNVHSLILDFAPVNFVD------------SVGAKTLKSVIKEYNEVGVCVC--

6julF2

0.20

0.17

5.49

0.71

SPARKS-K

--------------VPRSRSHVVTFPQDLTERRE-DSAVRDLALQTLAEIVEQGRTRVAVTVRTSTFYTRTKIRKLPSTDAGQIVDTALAVLDQFELDRLLGVRL

4hc8A

0.08

0.07

2.59

0.63

CNFpred

----------------------SIAVISMDDVNALGPAMQQALNAAIDNADRDDVGALVITGNGRVFSGGFDLKILEVQPAIDMLRGGFELAYRLLSPKPVVMAC

5fl7G

0.05

2.18

1.00

DEthreader

KRLWVVVSSDKGEKIKAQGRPMRLSFGGTGEA-PTFEEAAHIADEILAL--DTQYDDIEIVYNKSFEP--IMKESYSAKADFSLANTIYAAMAEGAAEI------

6julF2

0.20

0.17

5.49

0.76

MapAlign

VPRSRSHVVTF--------------PQDLTER-REDSAVRDLALQTLAEIVEQGRIVTRVAVTVRTSYTRTKIRKLPSTDAGQIVDTALAVLDQFVRLLGVRLEL

1ulzA2

0.25

0.17

5.30

0.52

MUSTER

VPGS-------DGVLKS----------------------LEEAKALAREIG----YPVLLKATAGG-GGRGIRICRNEEELVKNYEQASREAEKAFGRGDLLLEK

6o6sA

0.16

0.12

4.10

0.45

HHsearch

LSDTIGKDF--------------------SSVETLREDVRNRVMDFLDRIGAGREVDVIIAPGIGEFTH---GSFRG--SAMDYYYVLHALSEIIPGDLEVHFDS

3jrwA1

0.07

0.06

2.38

0.54

CEthreader

LPWSGSGLTVEWQGKRISVPEDVYDKGCV--------KDVDEGLEAAERIG----FPLMIKASE----GGGGKGIRKAESAEDFPILFRQVQSEI-PGSPIFLMK

(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	0.7229

(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	5fl7G	0.61	3.08	0.050	0.895	model1_5fl7G.pdb.gz
2	1fs0G	0.60	3.34	0.088	0.905	model1_1fs0G.pdb.gz
3	1kc7A	0.60	3.86	0.143	0.924	model1_1kc7A.pdb.gz
4	3fksG	0.59	3.40	0.078	0.914	model1_3fksG.pdb.gz
5	1vbgA1	0.59	4.06	0.183	0.943	model1_1vbgA1.pdb.gz
6	2x0sA	0.58	4.09	0.107	0.924	model1_2x0sA.pdb.gz
7	4xd7G	0.57	3.29	0.080	0.876	model1_4xd7G.pdb.gz
8	2qe7G	0.57	3.63	0.087	0.914	model1_2qe7G.pdb.gz
9	1yq2A3	0.41	3.72	0.096	0.676	model1_1yq2A3.pdb.gz
10	2fy3A	0.41	4.78	0.087	0.771	model1_2fy3A.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:0047730	1.00	carnosine synthase activity
GO:0016787	0.80	hydrolase activity
GO:0016887	0.78	ATPase 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:0035499	1.00	carnosine biosynthetic process
GO:0044699	0.79	single-organism process
GO:0044710	0.74	single-organism metabolic process
GO:0044281	0.68	small molecule metabolic process
GO:0044238	0.68	primary metabolic process
GO:0044763	0.66	single-organism cellular process
GO:0006082	0.56	organic acid metabolic process
GO:0019752	0.55	carboxylic acid metabolic process
GO:1901575	0.52	organic substance catabolic process
GO:0044282	0.51	small molecule catabolic process
GO:0016054	0.50	organic acid catabolic process
GO:0006520	0.50	cellular amino acid 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:0005829	1.00	cytosol

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	2r8jA	0.499	3.58	0.091	0.829	2.7.7.7	NA
2	0.060	2i5kB	0.507	3.85	0.082	0.790	2.7.7.9	38
3	0.060	4rubU	0.514	3.33	0.071	0.714	4.1.1.39	NA
4	0.060	1l7aA	0.501	4.09	0.081	0.790	3.1.1.72 3.1.1.41	NA
5	0.060	1gupA	0.469	4.48	0.059	0.829	2.7.7.12 2.7.7.10	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	0.01	2w6iG	0.579	3.19	0.050	0.876	0.46	III	complex1.pdb.gz	6,7,8,9,10,32,35,38
2	0.01	3k5eB	0.536	3.65	0.067	0.829	0.49	K5E	complex2.pdb.gz	33,35,36,89,92
3	0.01	1ii6A	0.514	3.70	0.058	0.790	0.50	ADP	complex3.pdb.gz	31,32,34,35,36,37
4	0.01	2hldY	0.401	4.05	0.021	0.676	0.63	III	complex4.pdb.gz	25,26,39,41,42,49

	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.