D-I-TASSER Q9UHK6-D2

D-I-TASSER results for Q9UHK6-D2

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

Input Sequence in FASTA format

>Q9UHK6 (88 residues)
NMLDGGAPFYTTYRTADGEFMAVGAIEPQFYELLIKGLGLKSDELPNQMSMDDWPEMKKK
FADVFAEKTKAEWCQIFDGTDACVTPVL

Predicted Secondary Structure

Sequence	20 40 60 80 \| \| \| \| NMLDGGAPFYTTYRTADGEFMAVGAIEPQFYELLIKGLGLKSDELPNQMSMDDWPEMKKKFADVFAEKTKAEWCQIFDGTDACVTPVL
Prediction	CCCCCCCCCCCSSSCCCCCSSSSSCCCHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHCCHHHHHHHHCCCCCCSSCCC
Confidence	9888998532427769998899854888999999999299811222357943289999999999995899999999817999533539
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 \| \| \| \| NMLDGGAPFYTTYRTADGEFMAVGAIEPQFYELLIKGLGLKSDELPNQMSMDDWPEMKKKFADVFAEKTKAEWCQIFDGTDACVTPVL
Prediction	8434233131320404433200001334400430163062555425433447416402520361046232621262067370101237
	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

CCCCCCCCCCCSSSCCCCCSSSSSCCCHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHCCHHHHHHHHCCCCCCSSCCC
NMLDGGAPFYTTYRTADGEFMAVGAIEPQFYELLIKGLGLKSDELPNQMSMDDWPEMKKKFADVFAEKTKAEWCQIFDGTDACVTPVL

4hl6A

0.12

0.11

4.05

1.33

DEthreader

HA-HPYMAPFDVFNTQD-KPITICCGNDKLFSALCQALELTVNDPRSSNLVQNQAILKQYIERTLKTQAAEVWLARIHEVGVPVAPLL

2g04A2

0.55

0.51

14.74

2.05

SPARKS-K

------APFYRCYETSDGKYMAVGAIEPQFFAALLSGLGLSAADVPTQLDVAGYPQMYDIFAERFASRTRDEWTRVFAGTDACVTPVL

4hl6A

0.11

0.10

3.72

1.50

MapAlign

-NRHPYMAPFDVFNTQD-KPITICCGNDKLFSALCQALELTE-LVFSSNRVQNQAILKQYIERTLKTQAAEVWLARIHEVGVPVAPL-

2g04A

0.56

16.03

1.25

CEthreader

FLLDGGAPFYRCYETSDGKYMAVGAIEPQFFAALLSGLGLSAADVPTQLDVAGYPQMYDIFAERFASRTRDEWTRVFAGTDACVTPVL

2gd2A

0.53

15.42

1.73

MUSTER

NMLDGGAPYYDTYECADGRYVAVGAIEPQFYAAMLAGLGLDAAELPPQNDRARWPELRALLTEAFASHDRDHWGAVFANSDACVTPVL

2gd2A

0.53

15.42

2.10

HHsearch

NMLDGGAPYYDTYECADGRYVAVGAIEPQFYAAMLAGLGLDAAELPPQNDRARWPELRALLTEAFASHDRDHWGAVFANSDACVTPVL

2g04A2

0.55

0.51

14.74

1.76

FFAS-3D

------APFYRCYETSDGKYMAVGAIEPQFFAALLSGLGLSAADVPTQLDVAGYPQMYDIFAERFASRTRDEWTRVFAGTDACVTPVL

4ed9A1

0.09

3.43

1.17

EigenThreader

-NAHPNIAPYQTLSVSD-GYFIIACGNDGQFGKLSTLLGIGELAKDNSARVANRAALTALLEERTKQWKRDDLLAELAKIGVPAGPIN

1x74A

0.53

15.42

1.19

CNFpred

NMLDGGAPYYDTYECADGRYVAVGAIEPQFYAAMLAGLGLDAAELPPQNDRARWPELRALLTEAFASHDRDHWGAVFANSDACVTPVL

2gd2A

0.45

13.27

1.33

DEthreader

MMWTANMAYYDTYECADGRYVAVGAIEPQFYAAMLAGLGLDAAELPPQNDRARWPELRALLTEAFASHDRDHWGAVFANSDACVTPVL

(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	0.8057

(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	2gd2A	0.96	0.65	0.506	0.989	model1_2gd2A.pdb.gz
2	2g04A	0.95	0.75	0.552	0.989	model1_2g04A.pdb.gz
3	4hl6A	0.79	2.33	0.115	0.977	model1_4hl6A.pdb.gz
4	1pqyA1	0.71	2.51	0.119	0.943	model1_1pqyA1.pdb.gz
5	1xk7A2	0.69	2.55	0.188	0.943	model1_1xk7A2.pdb.gz
6	2vjnA	0.69	2.73	0.116	0.955	model1_2vjnA.pdb.gz
7	2wdrA2	0.42	4.26	0.058	0.773	model1_2wdrA2.pdb.gz
8	3d3yA	0.39	4.87	0.063	0.795	model1_3d3yA.pdb.gz
9	4cw4A	0.36	4.17	0.113	0.659	model1_4cw4A.pdb.gz
10	3ubmA2	0.34	4.14	0.014	0.602	model1_3ubmA2.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	1.00	catalytic activity
GO:0016854	0.95	racemase and epimerase activity
GO:0008111	0.83	alpha-methylacyl-CoA racemase 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:0071704	1.00	organic substance metabolic process
GO:0044237	1.00	cellular metabolic process
GO:0044699	0.94	single-organism process
GO:0044763	0.92	single-organism cellular process
GO:0044710	0.92	single-organism metabolic process
GO:0044281	0.91	small molecule metabolic process
GO:0006082	0.90	organic acid metabolic process
GO:0044238	0.83	primary metabolic process
GO:0006629	0.80	lipid metabolic process
GO:0032787	0.79	monocarboxylic acid metabolic process
GO:1901360	0.72	organic cyclic compound metabolic process
GO:0044255	0.63	cellular lipid metabolic process
GO:0009056	0.61	catabolic process
GO:1901575	0.60	organic substance catabolic process
GO:0044712	0.60	single-organism catabolic process
GO:0044248	0.60	cellular catabolic process
GO:0044242	0.59	cellular lipid catabolic process
GO:0008206	0.58	bile acid metabolic process
GO:1901576	0.56	organic substance biosynthetic process
GO:0044249	0.56	cellular biosynthetic process
GO:1901362	0.54	organic cyclic compound biosynthetic process
GO:0044711	0.53	single-organism biosynthetic process
GO:0044283	0.52	small molecule biosynthetic process
GO:0016053	0.51	organic acid biosynthetic 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:0044464	1.00	cell part
GO:0044424	0.96	intracellular part
GO:0044444	0.93	cytoplasmic part
GO:0043226	0.92	organelle
GO:0043231	0.91	intracellular membrane-bounded organelle
GO:0005777	0.83	peroxisome
GO:0005739	0.70	mitochondrion

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	2fbdA	0.479	3.39	0.013	0.761	3.2.1.17	NA
2	0.060	2z9xB	0.482	3.82	0.143	0.852	2.6.1.30	NA
3	0.060	1lz6A	0.490	3.85	0.065	0.852	3.2.1.17	NA
4	0.060	1ylaA	0.501	3.62	0.064	0.818	6.3.2.19	78
5	0.060	2z9uA	0.485	3.86	0.115	0.864	2.6.1.30	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	0.14	2gd0C	0.960	0.63	0.506	0.989	0.12	MRS	complex1.pdb.gz	17,40,70,71,72
2	0.14	2gciA	0.957	0.66	0.506	0.989	0.11	MRR	complex2.pdb.gz	13,17,25,26,31
3	0.10	2gceB	0.960	0.64	0.506	0.989	0.11	SFC	complex3.pdb.gz	7,13,17,25,26,31
4	0.10	2gceC	0.958	0.66	0.506	0.989	0.11	SFC	complex4.pdb.gz	8,31,32,61,62,65
5	0.08	2gd0D	0.959	0.65	0.506	0.989	0.11	MRS	complex5.pdb.gz	13,17,25,26,31
6	0.08	2gd2B	0.957	0.66	0.506	0.989	0.10	CAA	complex6.pdb.gz	31,34,37,38
7	0.03	1xa4B	0.714	2.66	0.186	0.966	0.19	COA	complex7.pdb.gz	24,25,26
8	0.03	2vjkA	0.691	2.71	0.116	0.955	0.12	COA	complex8.pdb.gz	15,17,18,40,73,76
9	0.03	1q7eA	0.703	2.88	0.128	0.966	0.32	MET	complex9.pdb.gz	37,38,39,62
10	0.02	1t3zA	0.689	2.72	0.116	0.955	0.11	CAO	complex10.pdb.gz	25,38,83,84,85

	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.