D-I-TASSER O43820-D2

D-I-TASSER results for O43820-D2

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

Input Sequence in FASTA format

>O43820 (137 residues)
FHGQNMTIFYKNQLGLYPYFGPRGTAHNGGIPQALPLDRHLALAAYQIHHSLRPGFAGPA
VLDWEEWCPLWAGNWGRRRAYQAASWAWAQQVFPDLDPQEQLYKAYTGFEQAARALMEDT
LRVAQALRPHGLWGFYH

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| FHGQNMTIFYKNQLGLYPYFGPRGTAHNGGIPQALPLDRHLALAAYQIHHSLRPGFAGPAVLDWEEWCPLWAGNWGRRRAYQAASWAWAQQVFPDLDPQEQLYKAYTGFEQAARALMEDTLRVAQALRPHGLWGFYH
Prediction	CCCCSSSSSSCCCCCCCCSSCCCCCSSCCCCCCCCCHHHHHHHHHHHHHHHCCCCCCCSSSSSCCCCCCCHHHCCCCCHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCC
Confidence	99983999856889977625699974238969857599999999999998299988825999715876415661675179999999999998899999999999999999999999999999999949888375579
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| FHGQNMTIFYKNQLGLYPYFGPRGTAHNGGIPQALPLDRHLALAAYQIHHSLRPGFAGPAVLDWEEWCPLWAGNWGRRRAYQAASWAWAQQVFPDLDPQEQLYKAYTGFEQAARALMEDTLRVAQALRPHGLWGFYH
Prediction	86464000003742130011377644310011142416401520472046213761300000203513320441264353036202510474257145720452145403520351044005203622352303328
	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

CCCCSSSSSSCCCCCCCCSSCCCCCSSCCCCCCCCCHHHHHHHHHHHHHHHCCCCCCCSSSSSCCCCCCCHHHCCCCCHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCC
FHGQNMTIFYKNQLGLYPYFGPRGTAHNGGIPQALPLDRHLALAAYQIHHSLRPGFAGPAVLDWEEWCPLWAGNWGRRRAYQAASWAWAQQVFPDLDPQEQLYKAYTGFEQAARALMEDTLRVAQALRPHGLWGFYH

1fcvA

0.27

8.28

1.33

DEthreader

FRGEEIAILYD-PGMFPALLKDGNVVARNGVPQLGNLTKHLQVFRDHLINQIPDSFPGVGVIDFESWRPIFRQNWASLQPYKKLSVEVVRREHPFWDDQRVEQEAKRRFEKYGQLFMEETLKAAKRMRPAANWGYYY

2pe4A1

0.46

0.45

13.20

3.37

SPARKS-K

FRGPDMTIFYSSQLGTYPYYTPTGEPVFGGLPQNASLIAHLARTFQDILAAIAPDFSGLAVIDWEAWRPRWAFNWDTKDIYRQRSRALVQAQHPDWPAPQVEAVAQDQFQGAARAWMAGTLQLGRALRPRGLWGF--

1fcvA

0.31

9.26

1.74

MapAlign

FRGEEIAILYD--PGMFPALLKNVVARNGGVPQLGNLTKHLQVFRDHLINQIDKSFPGVGVIDFESWRPIFRQNWASLQPYKKLSVEVVRREHPFWDDQRVEQEAKRRFEKYGQLFMEETLKAAKRMRPAANWGYYA

1fcvA

0.31

9.26

1.75

CEthreader

FRGEEIAILY--DPGMFPALLKDVVARNGGVPQLGNLTKHLQVFRDHLINQIDKSFPGVGVIDFESWRPIFRQNWASLQPYKKLSVEVVRREHPFWDDQRVEQEAKRRFEKYGQLFMEETLKAAKRMRPAANWGYYA

2pe4A1

0.46

0.45

13.20

3.28

MUSTER

FRGPDMTIFYSSQLGTYPYYTPTGEPVFGGLPQNASLIAHLARTFQDILAAIAPDFSGLAVIDWEAWRPRWAFNWDTKDIYRQRSRALVQAQHPDWPAPQVEAVAQDQFQGAARAWMAGTLQLGRALRPRGLWGF--

2pe4A

0.46

13.42

5.07

HHsearch

FRGPDMTIFYSSQLGTYPYYTPTGEPVFGGLPQNASLIAHLARTFQDILAAIAPDFSGLAVIDWEAWRPRWAFNWDTKDIYRQRSRALVQAQHPDWPAPQVEAVAQDQFQGAARAWMAGTLQLGRALRPRGLWGFYG

2pe4A1

0.45

13.01

2.52

FFAS-3D

FRGPDMTIFYSSQLGTYPYYTPTGEPVFGGLPQNASLIAHLARTFQDILAAIPADFSGLAVIDWEAWRPRWAFNWDTKDIYRQRSRALVQAQHPDWPAPQVEAVAQDQFQGAARAWMAGTLQLGRALRPRGLWGF--

2atmA2

0.31

0.30

9.06

1.50

EigenThreader

FQGDKIAIFYD--PGEFPALLKDGKYRNGGVPQEGNITIHLQKFIENLDKIYNRNFSGIGVIDFERWRPIFRQNWGNMKIHKNFSIDLVRNEHPTWNK-KIELEASKRFEKYARFFMEETLKLAKKTRKQADWGYYG

2pe4A

0.46

13.42

1.67

CNFpred

FRGPDMTIFYSSQLGTYPYYTPTGEPVFGGLPQNASLIAHLARTFQDILAAIPPDFSGLAVIDWEAWRPRWAFNWDTKDIYRQRSRALVQAQHPDWPAPQVEAVAQDQFQGAARAWMAGTLQLGRALRPRGLWGFYG

2pe4A

0.45

13.02

1.33

DEthreader

QRGPDMTIFYSSQLGTYPYYTPTGEPVFGGLPQNASLIAHLARTFQDILAAIPADFSGLAVIDWEAWRPRWAFNWDTKDIYRQRSRALVQAQHPDWPAPQVEAVAQDQFQGAARAWMAGTLQLGRALRPRGLWGFYF

(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	0.8767

(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	2pe4A	0.96	0.91	0.453	1.000	model1_2pe4A.pdb.gz
2	1fcvA	0.94	1.06	0.311	0.985	model1_1fcvA.pdb.gz
3	2atmA	0.90	1.41	0.284	0.978	model1_2atmA.pdb.gz
4	4bq2A	0.64	3.62	0.071	0.912	model1_4bq2A.pdb.gz
5	6xj9A	0.64	3.60	0.071	0.920	model1_6xj9A.pdb.gz
6	1venA3	0.64	4.26	0.090	0.949	model1_1venA3.pdb.gz
7	3vocA	0.63	4.28	0.084	0.934	model1_3vocA.pdb.gz
8	1b1yA	0.63	4.12	0.068	0.942	model1_1b1yA.pdb.gz
9	4uniA	0.58	4.13	0.089	0.883	model1_4uniA.pdb.gz
10	4uzsA	0.58	4.14	0.096	0.876	model1_4uzsA.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:0015929	0.98	hexosaminidase activity
GO:0004415	0.96	hyalurononglucosaminidase activity
GO:0001618	0.82	virus receptor 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	0.92	organic substance metabolic process
GO:0043170	0.91	macromolecule metabolic process
GO:0030203	0.89	glycosaminoglycan metabolic process
GO:0009057	0.89	macromolecule catabolic process
GO:0006027	0.87	glycosaminoglycan catabolic process
GO:0009987	0.86	cellular process
GO:1903510	0.84	mucopolysaccharide metabolic process
GO:0051704	0.84	multi-organism process
GO:0030212	0.81	hyaluronan metabolic process
GO:0071493	0.79	cellular response to UV-B
GO:0071347	0.79	cellular response to interleukin-1
GO:0030214	0.79	hyaluronan catabolic process
GO:0009615	0.79	response to virus
GO:0006950	0.79	response to stress
GO:0051216	0.75	cartilage development
GO:0071495	0.71	cellular response to endogenous stimulus
GO:0071363	0.71	cellular response to growth factor stimulus
GO:0051240	0.71	positive regulation of multicellular organismal process
GO:0048522	0.71	positive regulation of cellular process
GO:0030334	0.71	regulation of cell migration
GO:0030308	0.71	negative regulation of cell growth
GO:0000302	0.71	response to reactive oxygen species

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	0.97	cell part
GO:0043231	0.93	intracellular membrane-bounded organelle
GO:0031410	0.93	cytoplasmic vesicle
GO:0005764	0.86	lysosome
GO:0031988	0.50	membrane-bounded vesicle

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	1icpA	0.535	3.80	0.056	0.766	1.3.1.42	NA
2	0.060	2jf6B	0.537	3.92	0.053	0.810	3.2.1.105	25
3	0.060	2e9lA	0.527	3.97	0.065	0.781	3.2.1.21	NA
4	0.060	3cyvA	0.546	4.15	0.050	0.847	4.1.1.37	NA
5	0.060	1dwaM	0.546	4.14	0.053	0.832	3.2.1.147	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	0.08	2pe4A	0.962	0.91	0.453	1.000	0.20	UUU	complex1.pdb.gz	15,16,18,35
2	0.06	1fcvA	0.938	1.06	0.311	0.985	0.12	UUU	complex2.pdb.gz	59,61,62
3	0.02	1b9zA	0.601	3.99	0.092	0.927	0.29	MAL	complex3.pdb.gz	16,18,29,112
4	0.02	1j12D	0.607	3.98	0.106	0.942	0.11	EBG	complex4.pdb.gz	2,60,124
5	0.02	1j0yA	0.607	3.88	0.099	0.927	0.13	BGC	complex5.pdb.gz	15,31,113
6	0.02	1j0zC	0.608	3.87	0.099	0.927	0.12	GLC	complex6.pdb.gz	9,57,124
7	0.02	1j0yB	0.606	3.90	0.092	0.920	0.15	BGC	complex7.pdb.gz	14,48,59,124,133
8	0.02	1j0zA	0.605	3.96	0.106	0.934	0.27	UUU	complex8.pdb.gz	67,68,112
9	0.02	1b9zA	0.601	3.99	0.092	0.927	0.12	MAL	complex9.pdb.gz	11,13,31
10	0.02	1j10A	0.606	3.95	0.106	0.934	0.21	UUU	complex10.pdb.gz	16,17,18,34

	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.