D-I-TASSER P38567-D2

D-I-TASSER results for P38567-D2

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

Input Sequence in FASTA format

>P38567 (136 residues)
INATGQGVTIFYVDRLGYYPYIDSITGVTVNGGIPQKISLQDHLDKAKKDITFYMPVDNL
GMAVIDWEEWRPTWARNWKPKDVYKNRSIELVQQQNVQLSLTEATEKAKQEFEKAGKDFL
VETIKLGKLLRPNHLW

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| INATGQGVTIFYVDRLGYYPYIDSITGVTVNGGIPQKISLQDHLDKAKKDITFYMPVDNLGMAVIDWEEWRPTWARNWKPKDVYKNRSIELVQQQNVQLSLTEATEKAKQEFEKAGKDFLVETIKLGKLLRPNHLW
Prediction	CCCCCCSSSSSSCCCCCCCCSSSCCCCCSSCCCCCCCCCHHHHHHHHHHHHHHHCCCCCCCSSSSSSCCCCCCHHHCCCCHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCC
Confidence	9221895899957889887614568995313883884779999999999999859998883699982022411343588618999999999999889999999999999999999999999999999996867899
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| INATGQGVTIFYVDRLGYYPYIDSITGVTVNGGIPQKISLQDHLDKAKKDITFYMPVDNLGMAVIDWEEWRPTWARNWKPKDVYKNRSIELVQQQNVQLSLTEATEKAKQEFEKAGKDFLVETIKLGKLLRPNHLW
Prediction	6526464000004741130010356764421001114241640152047204620457420000021340312044436435303620251047424714572045224640352035004400520362247348
	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

CCCCCCSSSSSSCCCCCCCCSSSCCCCCSSCCCCCCCCCHHHHHHHHHHHHHHHCCCCCCCSSSSSSCCCCCCHHHCCCCHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCC
INATGQGVTIFYVDRLGYYPYIDSITGVTVNGGIPQKISLQDHLDKAKKDITFYMPVDNLGMAVIDWEEWRPTWARNWKPKDVYKNRSIELVQQQNVQLSLTEATEKAKQEFEKAGKDFLVETIKLGKLLRPNHLW

1fcvA

0.28

0.27

8.33

1.33

DEthreader

KFRGE-EIAILYD-PGMFPALLKDPGNVVARNGGVQLGNLTKHLQVFRDHLINQIDKSFPGVGVIDFESWRPIFRQNWASLQPYKKLSVEVVRREHPFWDDQRVEQEAKRRFEKYGQLFMEETLKAAKRMRPAANW

2pe4A1

0.44

0.43

12.71

3.56

SPARKS-K

QTFRGPDMTIFYSSQLGTYPYYT-PTGEPVFGGLPQNASLIAHLARTFQDILAAIPADFSGLAVIDWEAWRPRWAFNWDTKDIYRQRSRALVQAQHPDWPAPQVEAVAQDQFQGAARAWMAGTLQLGRALRPRGLW

1fcvA

0.33

0.32

9.51

1.74

MapAlign

--FRGEEIAILYD--PGMFPALLNGNVVARNGGVPQLGNLTKHLQVFRDHLINQIDKSFPGVGVIDFESWRPIFRQNWASLQPYKKLSVEVVRREHPFWDDQRVEQEAKRRFEKYGQLFMEETLKAAKRMRPAANW

1fcvA

0.33

0.32

9.72

1.69

CEthreader

DKFRGEEIAILYD--PGMFPALLKDNVVARNGGVPQLGNLTKHLQVFRDHLINQIPKSFPGVGVIDFESWRPIFRQNWASLQPYKKLSVEVVRREHPFWDDQRVEQEAKRRFEKYGQLFMEETLKAAKRMRPAANW

2pe4A1

0.44

0.43

12.71

3.40

MUSTER

QTFRGPDMTIFYSSQLGTYPYYT-PTGEPVFGGLPQNASLIAHLARTFQDILAAIPADFSGLAVIDWEAWRPRWAFNWDTKDIYRQRSRALVQAQHPDWPAPQVEAVAQDQFQGAARAWMAGTLQLGRALRPRGLW

2pe4A

0.44

0.43

12.71

5.20

HHsearch

QTFRGPDMTIFYSSQLGTYPYYT-PTGEPVFGGLPQNASLIAHLARTFQDILAAIPADFSGLAVIDWEAWRPRWAFNWDTKDIYRQRSRALVQAQHPDWPAPQVEAVAQDQFQGAARAWMAGTLQLGRALRPRGLW

2pe4A1

0.44

0.43

12.70

2.41

FFAS-3D

-TFRGPDMTIFYSSQLGTYPYY-TPTGEPVFGGLPQNASLIAHLARTFQDILAAIPADFSGLAVIDWEAWRPRWAFNWDTKDIYRQRSRALVQAQHPDWPAPQVEAVAQDQFQGAARAWMAGTLQLGRALRPRGLW

2pe4A1

0.44

0.43

12.71

1.60

EigenThreader

QTFRGPDMTIFYSSQLGTYPYYT-PTGEPVFGGLPQNASLIAHLARTFQDILAAIPADFSGLAVIDWEAWRPRWAFNWDTKDIYRQRSRALVQAQHPDWPAPQVEAVAQDQFQGAARAWMAGTLQLGRALRPRGLW

2pe4A

0.44

0.43

12.71

1.68

CNFpred

QTFRGPDMTIFYSSQLGTYPYYTP-TGEPVFGGLPQNASLIAHLARTFQDILAAIPADFSGLAVIDWEAWRPRWAFNWDTKDIYRQRSRALVQAQHPDWPAPQVEAVAQDQFQGAARAWMAGTLQLGRALRPRGLW

2atmA

0.28

0.27

8.32

1.33

DEthreader

DFQGD-KIAIFYD-PGEFPALLSKDGKYKKRNGGVQEGNITIHLQKFIENLDKYPNRNFSGIGVIDFERWRPIFRQNWGNMKIHKNFSIDLVRNEHPTWNKK-IELEASKRFEKYARFFMEETLKLAKKTRKQADW

(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	0.8511

(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	2pe4A1	0.95	0.96	0.437	0.993	model1_2pe4A1.pdb.gz
2	1fcvA	0.92	1.58	0.321	0.985	model1_1fcvA.pdb.gz
3	2atmA	0.88	1.78	0.323	0.978	model1_2atmA.pdb.gz
4	4bq2A	0.63	3.62	0.082	0.897	model1_4bq2A.pdb.gz
5	3vocA	0.61	3.72	0.056	0.919	model1_3vocA.pdb.gz
6	1venA3	0.60	3.94	0.054	0.926	model1_1venA3.pdb.gz
7	1fa2A	0.59	4.05	0.055	0.934	model1_1fa2A.pdb.gz
8	1b1yA	0.59	3.99	0.099	0.926	model1_1b1yA.pdb.gz
9	1wdpA	0.59	3.94	0.053	0.926	model1_1wdpA.pdb.gz
10	4uzsA	0.57	4.04	0.083	0.860	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:0004553	0.99	hydrolase activity, hydrolyzing O-glycosyl compounds
GO:0015929	0.98	hexosaminidase activity
GO:0004415	0.97	hyalurononglucosaminidase activity
GO:0004872	0.81	receptor activity
GO:0001618	0.75	virus receptor activity
GO:0016740	0.50	transferase 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	0.87	macromolecule metabolic process
GO:0009987	0.87	cellular process
GO:0006807	0.86	nitrogen compound metabolic process
GO:1901564	0.85	organonitrogen compound metabolic process
GO:0030203	0.84	glycosaminoglycan metabolic process
GO:0009057	0.84	macromolecule catabolic process
GO:0006027	0.82	glycosaminoglycan catabolic process
GO:0051704	0.78	multi-organism process
GO:1903510	0.77	mucopolysaccharide metabolic process
GO:0065007	0.74	biological regulation
GO:0050896	0.74	response to stimulus
GO:0050789	0.73	regulation of biological process
GO:0030212	0.73	hyaluronan metabolic process
GO:0050794	0.72	regulation of cellular process
GO:0006950	0.72	response to stress
GO:0051707	0.71	response to other organism
GO:0044699	0.71	single-organism process
GO:0032502	0.71	developmental process
GO:0030214	0.71	hyaluronan catabolic process
GO:0010033	0.71	response to organic substance
GO:0009628	0.71	response to abiotic stimulus
GO:0071493	0.70	cellular response to UV-B
GO:0071347	0.70	cellular response to interleukin-1
GO:0048856	0.70	anatomical structure development
GO:0048522	0.70	positive regulation of cellular process
GO:0009615	0.70	response to virus
GO:0051216	0.68	cartilage development
GO:0051128	0.68	regulation of cellular component organization
GO:0009719	0.68	response to endogenous stimulus
GO:0071495	0.67	cellular response to endogenous stimulus
GO:0071363	0.67	cellular response to growth factor stimulus
GO:0051240	0.67	positive regulation of multicellular organismal process
GO:0030334	0.67	regulation of cell migration
GO:0030308	0.67	negative regulation of cell growth
GO:0000302	0.67	response to reactive oxygen species
GO:0044763	0.55	single-organism cellular 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	0.99	cell part
GO:0044424	0.94	intracellular part
GO:0044444	0.92	cytoplasmic part
GO:0043231	0.92	intracellular membrane-bounded organelle
GO:0031410	0.89	cytoplasmic vesicle
GO:0005764	0.81	lysosome
GO:0016020	0.65	membrane
GO:0031988	0.56	membrane-bounded vesicle
GO:0044425	0.55	membrane part
GO:0044459	0.51	plasma membrane part
GO:0016023	0.50	cytoplasmic, 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	1kwgA	0.592	4.29	0.040	0.904	3.2.1.23	NA
2	0.060	1bwkA	0.466	4.14	0.070	0.684	1.6.99.1	NA
3	0.060	1wdpA	0.588	3.94	0.053	0.926	3.2.1.2	66
4	0.060	2fhcA	0.524	3.71	0.093	0.779	3.2.1.41	72
5	0.060	1bwlA	0.468	4.15	0.079	0.684	1.6.99.1	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	0.01	1b9zA	0.599	3.97	0.061	0.926	0.56	CA	complex1.pdb.gz	36,113,115

	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.