D-I-TASSER Q6S8J7-D1

D-I-TASSER results for Q6S8J7-D1

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

Input Sequence in FASTA format

>Q6S8J7 (57 residues)
MVAEVSPKLAASPMKKPFGFRGKMGKWCCCCFPCCRGSGKNNMGAWRDHDDSAFTEP

Predicted Secondary Structure

Sequence	20 40 \| \| MVAEVSPKLAASPMKKPFGFRGKMGKWCCCCFPCCRGSGKNNMGAWRDHDDSAFTEP
Prediction	CCCCCCCCCCCCCCCCCCCCCCCCCCSSSSCCCCCCCCCCCCCCCCCCCCCCCCCCC
Confidence	964225776631115875520001230100275458878788765544577544489
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 \| \| MVAEVSPKLAASPMKKPFGFRGKMGKWCCCCFPCCRGSGKNNMGAWRDHDDSAFTEP
Prediction	744634744436425543414542141012012114434664234435454433468
	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 DeepPotential. 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

                   |                   |

SS
Seq

CCCCCCCCCCCCCCCCCCCCCCCCCCSSSSCCCCCCCCCCCCCCCCCCCCCCCCCCC
MVAEVSPKLAASPMKKPFGFRGKMGKWCCCCFPCCRGSGKNNMGAWRDHDDSAFTEP

1ntlA4

0.05

2.39

1.15

SPARKS-K

--RKQCKTPSDPELVHVHTGIEFGSRINYTCNQGYRLIGSSSAVCVITDQSVDWDTE

4hr3A

0.04

1.93

1.00

DEthreader

HKFIQG-RLGPGVHHARLIGINQTRLLVLHAWLLDVGMALSAVSEIKVAAPNMAQQV

5zvqA

0.05

2.39

1.39

MapAlign

--ACRECGNLAEGELCPICQDEDRDRSLLAVVESGLYHVLGGALNPLEGIGPKELNL

2r6fA2

0.18

5.74

0.72

CEthreader

DVFASTNEAKVRGYKKGRFSFNVKGGRCEACHGVCHGKRYNRETLEVTYKGKNIAEV

4mt4A

0.04

1.89

0.52

EigenThreader

GKYRDTYRASK---SGFKASEYDYEAARLSVISNTVQTYFNLVNAYENENALKEAYE

6em3J

0.09

0.07

2.67

0.22

FFAS-3D

-----NNTKAMKHALERVQLPWKKHSFQEHQ--SVTSETNTDEHIKDIYDD------

1ntjA4

0.07

2.88

1.13

SPARKS-K

CIRKQCETPLDPQNGIVHVNTDIRFG-SSITYTCNEGIGSSSAMCIISDQSVAWDAE

6mvjA

0.33

0.07

2.11

0.91

CNFpred

-----------------------ESSWCCACYALT----------------------

6cxtB

0.04

1.91

1.00

DEthreader

YGFSMD-WERCLAI-FVAMQMGVLESARLMLYYAAQKNAVMSKLAISEAFVQSGIDR

6xj0A

0.07

2.86

1.18

MapAlign

--EAGETQLLPGAKTKTWGYNTSLLGQTIVYRRMVIVKDDHEASLPLPRNYGVDDIP

(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	0.5456

(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 DeepPotential, 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	3ctdB	0.49	2.85	0.089	0.789	model1_3ctdB.pdb.gz
2	2pfmA3	0.49	3.55	0.074	0.860	model1_2pfmA3.pdb.gz
3	2r9gL	0.49	2.81	0.065	0.807	model1_2r9gL.pdb.gz
4	6zu9q	0.48	2.87	0.038	0.825	model1_6zu9q.pdb.gz
5	5t1aA1	0.48	3.23	0.038	0.860	model1_5t1aA1.pdb.gz
6	5opzA	0.48	3.39	0.042	0.842	model1_5opzA.pdb.gz
7	3pvsA2	0.48	3.27	0.061	0.842	model1_3pvsA2.pdb.gz
8	5lqxU	0.48	3.31	0.061	0.825	model1_5lqxU.pdb.gz
9	1c3cA3	0.47	3.32	0.074	0.842	model1_1c3cA3.pdb.gz
10	2a7uB	0.47	3.22	0.061	0.842	model1_2a7uB.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:0003677	0.50	DNA binding
GO:0046872	0.19	metal ion binding
GO:0038023	0.14	signaling receptor activity
GO:0070626	0.13	(S)-2-(5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxamido)succinate AMP-lyase (fumarate-forming) activity
GO:0004018	0.13	N6-(1,2-dicarboxyethyl)AMP AMP-lyase (fumarate-forming) activity
GO:0043565	0.11	sequence-specific DNA 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:0001895	1.00	retina homeostasis
GO:0009987	0.59	cellular process
GO:0090304	0.53	nucleic acid metabolic process
GO:0034654	0.53	nucleobase-containing compound biosynthetic process
GO:0034645	0.53	cellular macromolecule biosynthetic process
GO:0006351	0.51	transcription, DNA-templated

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:0070062	1.00	extracellular exosome
GO:0044424	1.00	intracellular part
GO:0005615	1.00	extracellular space
GO:0005634	0.77	nucleus
GO:0044444	0.57	cytoplasmic part
GO:0072562	0.51	blood microparticle

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	1cc1L	0.440	2.61	0.049	0.702	1.12.99.6	4,31
2	0.060	1u8xX	0.436	3.66	0.059	0.842	3.2.1.122	NA
3	0.060	2uv8G	0.451	3.25	0.019	0.789	2.3.1.86	NA
4	0.060	3c6tA	0.417	3.25	0.037	0.737	2.7.7.49 2.7.7.7	NA
5	0.060	1g59A	0.428	3.28	0.060	0.754	6.1.1.17	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	2kgaA	0.419	3.40	0.082	0.807	0.89	SXH	complex1.pdb.gz	21,24,25,46
2	0.01	2kgdA	0.451	3.19	0.063	0.807	0.92	SXV	complex2.pdb.gz	21,22,25,48,50,53
3	0.01	2aw44	0.292	3.80	0.000	0.632	0.43	III	complex3.pdb.gz	25,26,27,46
4	0.01	2kg9A	0.436	3.33	0.061	0.825	0.74	PSR	complex4.pdb.gz	24,27,28,43

	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.