D-I-TASSER Q8TE04-D4

D-I-TASSER results for Q8TE04-D4

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

Input Sequence in FASTA format

>Q8TE04 (82 residues)
GGTFLGLCCLLTGCETFEEALEMAAKGDSTNVDKLVKDIYGGDYERFGLQGSAVASSFGN
MMSKEKRDSISKEDLARATLVT

Predicted Secondary Structure

Sequence	20 40 60 80 \| \| \| \| GGTFLGLCCLLTGCETFEEALEMAAKGDSTNVDKLVKDIYGGDYERFGLQGSAVASSFGNMMSKEKRDSISKEDLARATLVT
Prediction	CCCHHHHHHHHHCCCCHHHHHHHHHCCCCCCCCSSSSSCCCCCCCCCCCCCCHHSHCCCCHHHCCCCCCCCHHHHHHHHCCC
Confidence	9425479999829999999999997199755771322235898888899911110111113103551128999999987139
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 \| \| \| \| GGTFLGLCCLLTGCETFEEALEMAAKGDSTNVDKLVKDIYGGDYERFGLQGSAVASSFGNMMSKEKRDSISKEDLARATLVT
Prediction	8223310131024273163025106614464021202102435265361544120001131245665762353110302447
	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

CCCHHHHHHHHHCCCCHHHHHHHHHCCCCCCCCSSSSSCCCCCCCCCCCCCCHHSHCCCCHHHCCCCCCCCHHHHHHHHCCC
GGTFLGLCCLLTGCETFEEALEMAAKGDSTNVDKLVKDIYGGDYERFGLQGSAVASSFGNMMSKEKRDSISKEDLARATLVT

2i7pB

0.85

24.05

1.33

DEthreader

GGTFLGLCSLLTGCESFEEALEMASKGDSTQADKLVRDIYGGDYERFGLPGWAVASSFGNMIYKEKRESVSKEDLARATLVT

2i7pB3

0.85

24.05

3.38

SPARKS-K

GGTFLGLCSLLTGCESFEEALEMASKGDSTQADKLVRDIYGGDYERFGLPGWAVASSFGNMIYKEKRESVSKEDLARATLVT

2i7pB3

0.85

24.05

1.63

MapAlign

GGTFLGLCSLLTGCESFEEALEMASKGDSTQADKLVRDIYGGDYERFGLPGWAVASSFGNMIYKEKRESVSKEDLARATLVT

2i7pB

0.85

24.05

1.57

CEthreader

GGTFLGLCSLLTGCESFEEALEMASKGDSTQADKLVRDIYGGDYERFGLPGWAVASSFGNMIYKEKRESVSKEDLARATLVT

2i7pB3

0.85

24.05

3.16

MUSTER

GGTFLGLCSLLTGCESFEEALEMASKGDSTQADKLVRDIYGGDYERFGLPGWAVASSFGNMIYKEKRESVSKEDLARATLVT

2i7pB3

0.85

24.05

2.97

HHsearch

GGTFLGLCSLLTGCESFEEALEMASKGDSTQADKLVRDIYGGDYERFGLPGWAVASSFGNMIYKEKRESVSKEDLARATLVT

2i7pB3

0.85

24.05

1.68

FFAS-3D

GGTFLGLCSLLTGCESFEEALEMASKGDSTQADKLVRDIYGGDYERFGLPGWAVASSFGNMIYKEKRESVSKEDLARATLVT

2i7pB3

0.85

24.05

1.22

EigenThreader

GGTFLGLCSLLTGCESFEEALEMASKGDSTQADKLVRDIYGGDYERFGLPGWAVASSFGNMIYKEKRESVSKEDLARATLVT

3smpA

1.00

28.00

1.45

CNFpred

GGTFLGLCCLLTGCETFEEALEMAAKGDSTNVDKLVKDIYGGDYERFGLQGSAVASSFGNMMSKEKRDSISKEDLARATLVT

2i7pB3

0.85

24.05

1.33

DEthreader

GGTFLGLCSLLTGCESFEEALEMASKGDSTQADKLVRDIYGGDYERFGLPGWAVASSFGNMIYKEKRESVSKEDLARATLVT

(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	0.7917

(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	2i7pB3	0.98	0.42	0.854	1.000	model1_2i7pB3.pdb.gz
2	6uj5A	0.79	1.83	0.413	0.902	model1_6uj5A.pdb.gz
3	2ewsA	0.76	1.45	0.268	0.866	model1_2ewsA.pdb.gz
4	2nlxA2	0.53	2.44	0.188	0.658	model1_2nlxA2.pdb.gz
5	3o0yA2	0.52	3.85	0.062	0.963	model1_3o0yA2.pdb.gz
6	3gbtA2	0.52	2.34	0.211	0.646	model1_3gbtA2.pdb.gz
7	3i8bA2	0.51	2.23	0.130	0.634	model1_3i8bA2.pdb.gz
8	3h3nX2	0.50	2.48	0.236	0.646	model1_3h3nX2.pdb.gz
9	3ifrA2	0.50	2.34	0.162	0.658	model1_3ifrA2.pdb.gz
10	2dpnA2	0.50	2.23	0.181	0.646	model1_2dpnA2.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:0004594	1.00	pantothenate kinase 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:0009987	0.91	cellular process
GO:0008152	0.88	metabolic process
GO:0044237	0.86	cellular metabolic process
GO:0009058	0.84	biosynthetic process
GO:0044249	0.83	cellular biosynthetic process
GO:0044699	0.82	single-organism process
GO:0009108	0.82	coenzyme biosynthetic process
GO:0071704	0.81	organic substance metabolic process
GO:0044763	0.79	single-organism cellular process
GO:0044238	0.79	primary metabolic process
GO:0044710	0.78	single-organism metabolic process
GO:0044281	0.77	small molecule metabolic process
GO:0034641	0.77	cellular nitrogen compound metabolic process
GO:1901576	0.76	organic substance biosynthetic process
GO:0006139	0.76	nucleobase-containing compound metabolic process
GO:1901564	0.75	organonitrogen compound metabolic process
GO:0044271	0.75	cellular nitrogen compound biosynthetic process
GO:0006796	0.75	phosphate-containing compound metabolic process
GO:1901566	0.74	organonitrogen compound biosynthetic process
GO:1901137	0.74	carbohydrate derivative biosynthetic process
GO:0090407	0.74	organophosphate biosynthetic process
GO:0046128	0.74	purine ribonucleoside metabolic process
GO:0044711	0.74	single-organism biosynthetic process
GO:0034654	0.74	nucleobase-containing compound biosynthetic process
GO:0009150	0.74	purine ribonucleotide metabolic process
GO:0015937	0.73	coenzyme A biosynthetic process
GO:0065007	0.66	biological regulation
GO:0050789	0.63	regulation of biological process
GO:0050794	0.62	regulation of cellular process
GO:0016043	0.54	cellular component organization
GO:0065008	0.52	regulation of biological quality
GO:0006996	0.52	organelle organization
GO:0050896	0.50	response to stimulus
GO:0048869	0.50	cellular developmental process
GO:0048856	0.50	anatomical structure development
GO:0044767	0.50	single-organism developmental process
GO:0044702	0.50	single organism reproductive 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:0044424	1.00	intracellular part
GO:0043229	0.86	intracellular organelle
GO:0005737	0.81	cytoplasm
GO:0044444	0.79	cytoplasmic part
GO:0044446	0.61	intracellular organelle part
GO:0043227	0.58	membrane-bounded organelle
GO:0043231	0.57	intracellular membrane-bounded organelle
GO:0005829	0.57	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	2vqjA	0.448	3.72	0.137	0.793	3.5.1.98	52
2	0.060	2nvrA	0.439	4.19	0.118	0.817	3.5.1.98	49
3	0.060	2nlxA	0.532	2.44	0.188	0.658	2.7.1.17	NA
4	0.060	3enoA	0.450	3.11	0.149	0.658	3.4.24.57	NA
5	0.060	2ifcC	0.444	4.28	0.078	0.842	2.3.3.1	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	0.84	3smpB	0.958	0.70	1.000	1.000	1.17	ACO	complex1.pdb.gz	39,40,44,47,53,54,55
	2	0.78	2i7pB	0.984	0.42	0.854	1.000	0.98	ACO	complex2.pdb.gz	39,40,54,55

	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.