D-I-TASSER Q12794-D2

D-I-TASSER results for Q12794-D2

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

Input Sequence in FASTA format

>Q12794 (139 residues)
NPGQTFRGPDMTIFYSSQLGTYPYYTPTGEPVFGGLPQNASLIAHLARTFQDILAAIPAP
DFSGLAVIDWEAWRPRWAFNWDTKDIYRQRSRALVQAQHPDWPAPQVEAVAQDQFQGAAR
AWMAGTLQLGRALRPRGLW

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| NPGQTFRGPDMTIFYSSQLGTYPYYTPTGEPVFGGLPQNASLIAHLARTFQDILAAIPAPDFSGLAVIDWEAWRPRWAFNWDTKDIYRQRSRALVQAQHPDWPAPQVEAVAQDQFQGAARAWMAGTLQLGRALRPRGLW
Prediction	CCCCCSSCCSSSSSSCCCCCCCCSSCCCCCSSCCCCCCCCCHHHHHHHHHHHHHHHCCCCCCCCSSSSSCCCCCCHHHHCCCCHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCC
Confidence	9987514782899957998877515699984128868737699999999999999678999981289971587630676277618999999999999789999999999999999999999999999999996867899
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| NPGQTFRGPDMTIFYSSQLGTYPYYTPTGEPVFGGLPQNASLIAHLARTFQDILAAIPAPDFSGLAVIDWEAWRPRWAFNWDTKDIYRQRSRALVQAQHPDWPAPQVEAVAQDQFQGAARAWMAGTLQLGRALRPRGLW
Prediction	7775615364010003742130011276654310010142416401520472046204466140000020351332044237435303620251047424714573045224640351035104400520362247348
	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

CCCCCSSCCSSSSSSCCCCCCCCSSCCCCCSSCCCCCCCCCHHHHHHHHHHHHHHHCCCCCCCCSSSSSCCCCCCHHHHCCCCHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCC
NPGQTFRGPDMTIFYSSQLGTYPYYTPTGEPVFGGLPQNASLIAHLARTFQDILAAIPAPDFSGLAVIDWEAWRPRWAFNWDTKDIYRQRSRALVQAQHPDWPAPQVEAVAQDQFQGAARAWMAGTLQLGRALRPRGLW

1fcvA

0.28

0.27

8.37

1.33

DEthreader

NMDKFR-GEEIAILYD-PGMFPALLKDGNVVARNGGVQLGNLTKHLQVFRDHLINQIPDKSFPGVGVIDFESWRPIFRQNWASLQPYKKLSVEVVRREHPFWDDQRVEQEAKRRFEKYGQLFMEETLKAAKRMRPAANW

2pe4A1

1.00

0.99

27.60

3.92

SPARKS-K

--GQTFRGPDMTIFYSSQLGTYPYYTPTGEPVFGGLPQNASLIAHLARTFQDILAAIPAPDFSGLAVIDWEAWRPRWAFNWDTKDIYRQRSRALVQAQHPDWPAPQVEAVAQDQFQGAARAWMAGTLQLGRALRPRGLW

1fcvA

0.32

9.53

1.74

MapAlign

NWMDKFRGEEIAILYD--PGMFPALLKNVVARNGGVPQLGNLTKHLQVFRDHLINQIPDKSFPGVGVIDFESWRPIFRQNWASLQPYKKLSVEVVRREHPFWDDQRVEQEAKRRFEKYGQLFMEETLKAAKRMRPAANW

1fcvA

0.32

9.53

1.69

CEthreader

NWMDKFRGEEIAILYD--PGMFPALLKDPVARNGGVPQLGNLTKHLQVFRDHLINQIPDKSFPGVGVIDFESWRPIFRQNWASLQPYKKLSVEVVRREHPFWDDQRVEQEAKRRFEKYGQLFMEETLKAAKRMRPAANW

2pe4A

1.00

28.00

2.98

MUSTER

NPGQTFRGPDMTIFYSSQLGTYPYYTPTGEPVFGGLPQNASLIAHLARTFQDILAAIPAPDFSGLAVIDWEAWRPRWAFNWDTKDIYRQRSRALVQAQHPDWPAPQVEAVAQDQFQGAARAWMAGTLQLGRALRPRGLW

2pe4A

1.00

28.00

5.19

HHsearch

NPGQTFRGPDMTIFYSSQLGTYPYYTPTGEPVFGGLPQNASLIAHLARTFQDILAAIPAPDFSGLAVIDWEAWRPRWAFNWDTKDIYRQRSRALVQAQHPDWPAPQVEAVAQDQFQGAARAWMAGTLQLGRALRPRGLW

2pe4A1

1.00

0.99

27.60

2.54

FFAS-3D

--GQTFRGPDMTIFYSSQLGTYPYYTPTGEPVFGGLPQNASLIAHLARTFQDILAAIPAPDFSGLAVIDWEAWRPRWAFNWDTKDIYRQRSRALVQAQHPDWPAPQVEAVAQDQFQGAARAWMAGTLQLGRALRPRGLW

2pe4A

1.00

28.00

1.62

EigenThreader

NPGQTFRGPDMTIFYSSQLGTYPYYTPTGEPVFGGLPQNASLIAHLARTFQDILAAIPAPDFSGLAVIDWEAWRPRWAFNWDTKDIYRQRSRALVQAQHPDWPAPQVEAVAQDQFQGAARAWMAGTLQLGRALRPRGLW

2pe4A

1.00

28.00

1.86

CNFpred

NPGQTFRGPDMTIFYSSQLGTYPYYTPTGEPVFGGLPQNASLIAHLARTFQDILAAIPAPDFSGLAVIDWEAWRPRWAFNWDTKDIYRQRSRALVQAQHPDWPAPQVEAVAQDQFQGAARAWMAGTLQLGRALRPRGLW

2atmA2

0.29

0.28

8.55

1.33

DEthreader

NKDDFQ-GDKIAIFYD-PGEFPALLSKGKYKKRNGGVPEGNITIHLQKFIENLDKIYPNRNFSGIGVIDFERWRPIFRQNWGNMKIHKNFSIDLVRNEHPTWNKK-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	0.966

(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	1.00	0.21	1.000	1.000	model1_2pe4A.pdb.gz
2	1fcvA	0.90	1.71	0.314	0.986	model1_1fcvA.pdb.gz
3	2atmA	0.85	2.03	0.324	0.978	model1_2atmA.pdb.gz
4	4bq2A	0.64	3.82	0.087	0.914	model1_4bq2A.pdb.gz
5	6xj9A	0.64	3.76	0.063	0.921	model1_6xj9A.pdb.gz
6	1venA3	0.61	4.35	0.067	0.935	model1_1venA3.pdb.gz
7	3vocA	0.59	3.99	0.031	0.906	model1_3vocA.pdb.gz
8	1b1yA	0.58	4.17	0.068	0.921	model1_1b1yA.pdb.gz
9	4uzsA	0.56	4.16	0.074	0.856	model1_4uzsA.pdb.gz
10	4uniA	0.56	4.13	0.057	0.856	model1_4uniA.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:0004872	0.85	receptor activity
GO:0001618	0.84	virus receptor activity
GO:0016740	0.54	transferase activity
GO:0050501	0.51	hyaluronan synthase activity
GO:0008134	0.51	transcription factor binding

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:0043170	0.96	macromolecule metabolic process
GO:0006807	0.94	nitrogen compound metabolic process
GO:0006022	0.93	aminoglycan metabolic process
GO:0030203	0.92	glycosaminoglycan metabolic process
GO:0009057	0.92	macromolecule catabolic process
GO:0009987	0.91	cellular process
GO:0006026	0.90	aminoglycan catabolic process
GO:0006027	0.89	glycosaminoglycan catabolic process
GO:0065007	0.88	biological regulation
GO:0050789	0.88	regulation of biological process
GO:0051704	0.87	multi-organism process
GO:1903510	0.86	mucopolysaccharide metabolic process
GO:0050794	0.86	regulation of cellular process
GO:0048518	0.84	positive regulation of biological process
GO:0010033	0.84	response to organic substance
GO:0048522	0.83	positive regulation of cellular process
GO:0030212	0.83	hyaluronan metabolic process
GO:0071493	0.82	cellular response to UV-B
GO:0071347	0.82	cellular response to interleukin-1
GO:0009615	0.82	response to virus
GO:0006950	0.82	response to stress
GO:0051240	0.81	positive regulation of multicellular organismal process
GO:0051216	0.81	cartilage development
GO:0030214	0.81	hyaluronan catabolic process
GO:0009719	0.81	response to endogenous stimulus
GO:0051128	0.80	regulation of cellular component organization
GO:0048523	0.80	negative regulation of cellular process
GO:0071495	0.79	cellular response to endogenous stimulus
GO:0071363	0.79	cellular response to growth factor stimulus
GO:0030334	0.79	regulation of cell migration
GO:0030308	0.79	negative regulation of cell growth
GO:0000302	0.79	response to reactive oxygen species
GO:0009059	0.54	macromolecule biosynthetic process
GO:0006952	0.54	defense response
GO:0046677	0.53	response to antibiotic
GO:0006954	0.53	inflammatory response
GO:2000026	0.52	regulation of multicellular organismal development
GO:0051130	0.52	positive regulation of cellular component organization
GO:0051094	0.52	positive regulation of developmental process
GO:0045785	0.52	positive regulation of cell adhesion
GO:1900106	0.50	positive regulation of hyaluranon cable assembly
GO:0071467	0.50	cellular response to pH
GO:0050679	0.50	positive regulation of epithelial cell proliferation
GO:0045766	0.50	positive regulation of angiogenesis
GO:0036120	0.50	cellular response to platelet-derived growth factor stimulus
GO:0030307	0.50	positive regulation of cell growth
GO:0030213	0.50	hyaluronan biosynthetic process
GO:0010634	0.50	positive regulation of epithelial cell migration

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	0.97	intracellular part
GO:0044444	0.96	cytoplasmic part
GO:0043231	0.96	intracellular membrane-bounded organelle
GO:0031410	0.94	cytoplasmic vesicle
GO:0005764	0.90	lysosome
GO:0005737	0.57	cytoplasm
GO:0044421	0.56	extracellular region part
GO:0036117	0.54	hyaluranon cable
GO:0005615	0.54	extracellular space

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	1qbaA	0.531	4.27	0.047	0.791	3.2.1.52	NA
2	0.060	2jepA	0.533	3.54	0.069	0.727	3.2.1.151	NA
3	0.060	1c7sA	0.533	4.25	0.047	0.791	3.2.1.52	NA
4	0.060	1jphA	0.530	4.37	0.065	0.835	4.1.1.37	NA
5	0.060	1b1yA	0.580	4.17	0.068	0.921	3.2.1.2	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	0.15	2pe4A	0.998	0.21	1.000	1.000	0.23	UUU	complex1.pdb.gz	9,65,66,68
2	0.01	1b9zA	0.570	4.22	0.075	0.935	0.31	MAL	complex2.pdb.gz	19,33,34,35,37,38,121
3	0.01	1j0zC	0.578	4.18	0.089	0.942	0.13	GLC	complex3.pdb.gz	21,24,41,119,121
4	0.01	1j10C	0.579	4.30	0.089	0.950	0.34	UUU	complex4.pdb.gz	18,20,36,68
5	0.01	1itcA	0.578	4.32	0.082	0.950	0.16	GLC	complex5.pdb.gz	8,128,129
6	0.01	1kwkA	0.586	4.17	0.070	0.892	0.17	GAL	complex6.pdb.gz	4,65,130,134
7	0.01	1b9zA	0.570	4.22	0.075	0.935	0.15	MAL	complex7.pdb.gz	17,20,36
8	0.01	2xgbA	0.578	4.15	0.062	0.906	0.18	EPG	complex8.pdb.gz	20,124,126,131
9	0.01	2zutA	0.564	3.96	0.072	0.849	0.16	A2G	complex9.pdb.gz	134,135,136,137
10	0.01	1wdsA	0.583	4.16	0.038	0.921	0.15	UUU	complex10.pdb.gz	4,6,65,67

	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.