D-I-TASSER Q3SY69-D1

D-I-TASSER results for Q3SY69-D1

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

Input Sequence in FASTA format

>Q3SY69 (126 residues)
MLRRGSQALRRFSTGRVYFKNKLKLALIGQSLFGQEVYSHLRKEGHRVVGVFTVPDKDGK
ADPLALAAEKDGTPVFKLPKWRVKGKTIKEVAEAYRSVGAELNVLPFCTQFIPMDIIDSP
KHGSII

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| MLRRGSQALRRFSTGRVYFKNKLKLALIGQSLFGQEVYSHLRKEGHRVVGVFTVPDKDGKADPLALAAEKDGTPVFKLPKWRVKGKTIKEVAEAYRSVGAELNVLPFCTQFIPMDIIDSPKHGSII
Prediction	CCCCCCCCHHHCCCCHHHHHCCCSSSSSCCCHHHHHHHHHHHHCCCCSSSSSSCCCCCCCCCHHHHHHHHHCCCSSCCCCCCCCCCCCHHHHHHHHHHCCCSSSSSCCCCCCCHHHHHCCCCCCCC
Confidence	976555430004533223305865999589689999999999809928999927999999997899999919963273110455779999999999709999999512221899999458988369
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| MLRRGSQALRRFSTGRVYFKNKLKLALIGQSLFGQEVYSHLRKEGHRVVGVFTVPDKDGKADPLALAAEKDGTPVFKLPKWRVKGKTIKEVAEAYRSVGAELNVLPFCTQFIPMDIIDSPKHGSII
Prediction	643534532452444443045401000001141014004302746240000002235744452024104737041230641457655244015204715020000020232125302720532025
	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                  60                  80                 100                 120

                   |                   |                   |                   |                   |                   |

SS
Seq

CCCCCCCCHHHCCCCHHHHHCCCSSSSSCCCHHHHHHHHHHHHCCCCSSSSSSCCCCCCCCCHHHHHHHHHCCCSSCCCCCCCCCCCCHHHHHHHHHHCCCSSSSSCCCCCCCHHHHHCCCCCCCC
MLRRGSQALRRFSTGRVYFKNKLKLALIGQSLFGQEVYSHLRKEGHRVVGVFTVPDKDGKADPLALAAEKDGTPVFKLPKWRVKGKTIKEVAEAYRSVGAELNVLPFCTQFIPMDIIDSPKHGSII

2cfiA

0.70

0.59

16.70

1.17

DEthreader

----------------FQ---SMKIAVIGQSLFGQEVYCHLRKEGHEVVGVFTVPDKDGKADPLGLEAEKDGVPVFKYSRWRAGQAL-PDVVAKYQALGAELNVLPFCSQFIPMEIISAPRHGSII

2cfiA1

0.71

0.60

16.91

1.74

SPARKS-K

-------------------FQSMKIAVIGQSLFGQEVYCHLRKEGHEVVGVFTVPDKDGKADPLGLEAEKDGVPVFKYSRWRAKGQALPDVVAKYQALGAELNVLPFCSQFIPMEIISAPRHGSI-

2cfiA

0.72

0.60

17.12

0.89

MapAlign

---------------------SMKIAVIGQSLFGQEVYCHLRKEGHEVVGVFTVPDKDGKADPLGLEAEKDGVPVFKYSRWRAKGQALPDVVAKYQALGAELNVLPFCSQFIPMEIISAPRHGSII

2cfiA

0.71

0.60

17.13

0.62

CEthreader

-------------------FQSMKIAVIGQSLFGQEVYCHLRKEGHEVVGVFTVPDKDGKADPLGLEAEKDGVPVFKYSRWRAKGQALPDVVAKYQALGAELNVLPFCSQFIPMEIISAPRHGSII

2cfiA

0.71

0.60

17.13

1.36

MUSTER

-------------------FQSMKIAVIGQSLFGQEVYCHLRKEGHEVVGVFTVPDKDGKADPLGLEAEKDGVPVFKYSRWRAKGQALPDVVAKYQALGAELNVLPFCSQFIPMEIISAPRHGSII

2fmtA

0.29

0.24

7.24

0.99

HHsearch

-------------------SESLRIIFAGTPDFAARHLDALLSSGHNVVGVFTQPDRPGMPSPVKVLAEEKGLPVFQPVSLRP-----QENQQLVAELQADVMVVVAYGLILPKAVLEMPRLGCIN

2cfiA1

0.71

0.60

16.90

1.72

FFAS-3D

--------------------QSMKIAVIGQSLFGQEVYCHLRKEGHEVVGVFTVPDKDGKADPLGLEAEKDGVPVFKYSRWRAKGQALPDVVAKYQALGAELNVLPFCSQFIPMEIISAPRHGSI-

3w7bA

0.13

4.37

0.65

EigenThreader

PGIVAAVSGFLYAHDPEGGSERKRTAILVPAHALLELLWRYRVGELPMELVISN------HPDHREEVERFGIPYHHVPVEGRKEEAEERILALLEAEGVELVVLARYMQILSPGFVERFPMRI-I

2bw0A

0.72

0.60

17.12

1.46

CNFpred

---------------------SMKIAVIGQSLFGQEVYCHLRKEGHEVVGVFTVPDKDGKADPLGLEAEKDGVPVFKYSRWRAKGQALPDVVAKYQALGAELNVLPFCSQFIPMEIISAPRHGSII

2cfiA1

0.70

0.58

16.48

1.17

DEthreader

----------------FQ---SMKIAVIGQSLFGQEVYCHLRKEGHEVVGVFTVPDKDGKADPLGLEAEKDGVPVFKYSRWRAGQAL-PDVVAKYQALGAELNVLPFCSQFIPMEIISAPRHGSI-

(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	0.7652

(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	2cfiA	0.82	0.88	0.710	0.849	model1_2cfiA.pdb.gz
2	2fmtA	0.75	1.33	0.275	0.809	model1_2fmtA.pdb.gz
3	3rfoA	0.74	1.33	0.307	0.802	model1_3rfoA.pdb.gz
4	3q0iA	0.70	1.32	0.240	0.762	model1_3q0iA.pdb.gz
5	1z7eD1	0.68	1.50	0.161	0.738	model1_1z7eD1.pdb.gz
6	1mejB	0.64	2.46	0.089	0.802	model1_1mejB.pdb.gz
7	3h2sA	0.53	2.68	0.128	0.682	model1_3h2sA.pdb.gz
8	3qy9A	0.49	2.22	0.189	0.587	model1_3qy9A.pdb.gz
9	2qytA1	0.48	3.88	0.089	0.698	model1_2qytA1.pdb.gz
10	2rjoA2	0.46	3.81	0.084	0.722	model1_2rjoA2.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:0016491	0.97	oxidoreductase activity
GO:0016155	0.94	formyltetrahydrofolate dehydrogenase activity
GO:0047105	0.92	4-trimethylammoniobutyraldehyde dehydrogenase activity
GO:0019145	0.92	aminobutyraldehyde dehydrogenase 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	1.00	cellular process
GO:0044699	0.94	single-organism process
GO:0044763	0.89	single-organism cellular process
GO:0008152	0.87	metabolic process
GO:0071704	0.80	organic substance metabolic process
GO:0044237	0.78	cellular metabolic process
GO:0044710	0.73	single-organism metabolic process
GO:0006807	0.73	nitrogen compound metabolic process
GO:1901564	0.71	organonitrogen compound metabolic process
GO:1901360	0.70	organic cyclic compound metabolic process
GO:0046483	0.70	heterocycle metabolic process
GO:0034641	0.70	cellular nitrogen compound metabolic process
GO:0006725	0.70	cellular aromatic compound metabolic process
GO:0044281	0.69	small molecule metabolic process
GO:0006732	0.67	coenzyme metabolic process
GO:0006575	0.66	cellular modified amino acid metabolic process
GO:0006760	0.65	folic acid-containing compound metabolic process
GO:0006082	0.56	organic 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:0044444	1.00	cytoplasmic part
GO:0043226	0.89	organelle
GO:0043227	0.88	membrane-bounded organelle
GO:0070062	0.85	extracellular exosome
GO:0043229	0.76	intracellular organelle
GO:0043231	0.75	intracellular membrane-bounded organelle
GO:0005739	0.71	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	0.066	2iftA	0.590	3.37	0.037	0.833	2.1.1.52	NA
2	0.060	3cmmC	0.635	3.54	0.116	0.897	6.3.2.19	29,68
3	0.060	3igyB	0.670	3.42	0.138	0.968	5.4.2.1	NA
4	0.060	1pq3A	0.631	3.64	0.085	0.913	3.5.3.1	NA
5	0.060	1hqfA	0.629	3.59	0.110	0.913	3.5.3.1	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:

Rank	Cscore^LB	PDB Hit	TM-score	RMSD^a	IDEN^a	Cov.	BS-score	Lig. Name	Download Complex	Predicted binding site residues
1	0.20	3r8xA	0.756	1.43	0.250	0.818	0.46	MET	complex1.pdb.gz	27,29,34,50,52
2	0.11	2cfiA	0.818	0.88	0.710	0.849	0.73	ZZZ	complex2.pdb.gz	108,109,110,111,112,117,126
3	0.08	3dcjB	0.650	2.67	0.120	0.825	0.64	THH	complex3.pdb.gz	35,36,38,52
4	0.05	3dcjA	0.650	2.69	0.119	0.825	0.46	THH	complex4.pdb.gz	34,35,36,52,55
5	0.04	4cevB	0.639	3.61	0.076	0.913	0.46	ORN	complex5.pdb.gz	42,48,50,65,71,72
6	0.04	1e3jA	0.648	2.72	0.092	0.841	0.76	PO4	complex6.pdb.gz	34,54,63
7	0.04	3cevA	0.640	3.60	0.068	0.913	0.47	ARG	complex7.pdb.gz	30,64,66
8	0.04	3tozD	0.643	2.99	0.119	0.857	0.44	NAD	complex8.pdb.gz	29,30,31,32,33,53,54,107,108,109,111

	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, Qiqige Wuyun, Yang Li, Quancheng Liu, Xiaogen Zhou, Yiheng Zhu, P. Lydia Freddolino, Yang Zhang. Integrating deep learning potentials with I-TASSER for single- and multi-domain protein structure prediction. Submitted. 2023.