D-I-TASSER A0A1B0GU33-D1

D-I-TASSER results for A0A1B0GU33-D1

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

Input Sequence in FASTA format

>A0A1B0GU33 (70 residues)
MGSKIFCCCRKTSEGSSTTVGFHNPRMFEQHHPRSFNLNTNSLHSAVPKRHPRLPYDNRM
MLKACILRRP

Predicted Secondary Structure

Sequence	20 40 60 \| \| \| MGSKIFCCCRKTSEGSSTTVGFHNPRMFEQHHPRSFNLNTNSLHSAVPKRHPRLPYDNRMMLKACILRRP
Prediction	CCCSSSSSSSCCCCCCCCSSSCCCCHHHHHCCCCCCCCCCCCHHHCCCCCCCCCCCCHHHHHHHHHHCCC
Confidence	9961889860367887524412583345542986335786312221655589998650678887862389
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 \| \| \| MGSKIFCCCRKTSEGSSTTVGFHNPRMFEQHHPRSFNLNTNSLHSAVPKRHPRLPYDNRMMLKACILRRP
Prediction	8644010003436745433332432431564345525153641353246534524364421032123548
	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

CCCSSSSSSSCCCCCCCCSSSCCCCHHHHHCCCCCCCCCCCCHHHCCCCCCCCCCCCHHHHHHHHHHCCC
MGSKIFCCCRKTSEGSSTTVGFHNPRMFEQHHPRSFNLNTNSLHSAVPKRHPRLPYDNRMMLKACILRRP

1xe8B

0.06

0.04

1.89

0.56

CEthreader

QRGKGQYVLVYPDGQVKSFKVGFDYKNGEVSQ-------------------WVVPGGVFKASFLLPNEEF

6nabA

0.03

1.74

0.53

EigenThreader

PFIWQEGHSAFKEVFTILELYKRVYEELLAVPVITKTENE--KFAGATNGNFSKMFKIYQNSWGLSTRTL

6fbzB

0.21

0.14

4.54

0.23

FFAS-3D

---------------QSLRSARFLPGIVQDIYPPGIKSPNPALNEAVQKKGRIFKYDVQFLLQ-------

2ic4A3

0.07

0.06

2.39

0.77

SPARKS-K

----------RKCYFPYLENGYNQNYGRKFVQGKSIDVACHPGYALPKAQTTVTCMENGWSPTPRCIRV-

4lojA

0.07

0.01

0.21

0.36

CNFpred

--RRLYILFPLDCGVPD-----------------------------------------------------

7d8zB

0.00

0.94

1.00

DEthreader

YLPCLQNFGVIMIFPVTGITIATTSAVSVVISSTAGLQSLTGAPRLLQAISRDGI-VPFLQFALTAC---

5xnrA2

0.06

2.54

0.66

MapAlign

HLVATQIHGDKSAGIDDAMVMRLEGNHLFASFNGGKLRSDLYLIKDGGNDYVMDLNYDQSYFKIGNYTQS

1g47A

0.12

0.11

4.04

0.62

MUSTER

MANALASATCERCKGGFAPAEKIVNSNGELYHEQCFVCAQ---CFQQFPEGLFYEFEGRKYCEHDMLFAP

1vt4I

0.19

6.01

0.44

HHsearch

MDFKIFWLNLKNCNSPETVLNWTSRSDHSSIKLRIHSIQAERLLKSKPYLLVLLNVQNAKAWNAFNLSCK

2j3wA

0.10

3.70

0.56

CEthreader

SGSFYFVIVGHHDNPVFEMEFLPPGKAESKDDHDLVDENMWLSNNMYLKTVSAFVTAGHMRFIMLHDVRQ

(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	0.6154

(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	2xriA	0.46	3.97	0.075	0.943	model1_2xriA.pdb.gz
2	1ri6A	0.46	4.22	0.016	0.914	model1_1ri6A.pdb.gz
3	3iygA	0.45	3.80	0.029	0.886	model1_3iygA.pdb.gz
4	5m1fA	0.45	3.87	0.087	0.929	model1_5m1fA.pdb.gz
5	2h39B	0.45	3.31	0.017	0.757	model1_2h39B.pdb.gz
6	4gfhA4	0.40	4.10	0.069	0.800	model1_4gfhA4.pdb.gz
7	1gmlA	0.37	4.63	0.029	0.843	model1_1gmlA.pdb.gz
8	1asxA	0.37	4.70	0.044	0.843	model1_1asxA.pdb.gz
9	1zbuB2	0.37	4.15	0.046	0.771	model1_1zbuB2.pdb.gz
10	3bwsA2	0.36	4.06	0.050	0.700	model1_3bwsA2.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:0017057	0.13	6-phosphogluconolactonase 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:0071044	0.07	histone mRNA catabolic process
GO:0031047	0.07	gene silencing by RNA
GO:0006457	0.07	protein folding
GO:0006098	0.07	pentose-phosphate shunt
GO:0006006	0.07	glucose metabolic process
GO:0000467	0.07	exonucleolytic trimming to generate mature 3'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)

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:0044424	0.80	intracellular part
GO:0044444	0.60	cytoplasmic part
GO:0005737	0.60	cytoplasm
GO:0032991	0.50	macromolecular complex

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	3a3iA	0.409	4.10	0.015	0.757	3.4.16.4	NA
2	0.060	3bp1D	0.439	4.32	0.014	0.843	1.7.1.13	NA
3	0.060	3e9dA	0.414	3.69	0.085	0.800	3.1.3.46	NA
4	0.060	2gc7A	0.374	4.37	0.048	0.843	1.4.99.3	NA
5	0.060	1x9nA	0.402	4.06	0.063	0.871	6.5.1.1	11

	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	0.04	1gjqA	0.444	4.25	0.045	0.886	0.20	HEC	complex1.pdb.gz	3,4,21,22
2	0.01	3dbaB	0.435	3.81	0.069	0.814	0.19	35G	complex2.pdb.gz	2,19,20,46
3	0.01	2h2n0	0.434	3.86	0.016	0.800	0.11	III	complex3.pdb.gz	15,17,22,57,58,59,60,61
4	0.01	1n15A	0.444	4.26	0.045	0.886	0.17	HEC	complex4.pdb.gz	1,2,20,41,42,43
5	0.01	2rcaA	0.424	3.52	0.029	0.729	0.14	GLY	complex5.pdb.gz	2,3,4
6	0.01	3dbaA	0.428	4.17	0.065	0.829	0.19	35G	complex6.pdb.gz	15,17,27
7	0.01	1ghmA	0.353	3.19	0.016	0.629	0.13	CED	complex7.pdb.gz	18,20,25
8	0.01	2rcbA	0.427	3.50	0.029	0.729	0.16	DSN	complex8.pdb.gz	3,4,5,45
9	0.01	1ghpA	0.420	3.78	0.058	0.800	0.25	PNM	complex9.pdb.gz	16,22,24
10	0.01	1nirB	0.442	4.28	0.045	0.886	0.20	HEC	complex10.pdb.gz	15,17,19,38,66

	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.