D-I-TASSER P0DOY3-D1

D-I-TASSER results for P0DOY3-D1

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

Input Sequence in FASTA format

>P0DOY3 (106 residues)
GQPKAAPSVTLFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSK
QSNNKYAASSYLSLTPEQWKSHKSYSCQVTHEGSTVEKTVAPTECS

Predicted Secondary Structure

Sequence	20 40 60 80 100 \| \| \| \| \| GQPKAAPSVTLFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASSYLSLTPEQWKSHKSYSCQVTHEGSTVEKTVAPTECS
Prediction	CCCCCCCSSSSSCCCHHHHCCCCSSSSSSSSCCSCCCSSSSSSSCCSSCCCCSSSCCCSSCCCCCSSSSSSSSSCHHHHCCCCSSSSSSSSCCSCSSSSSSHHHCC
Confidence	9898298899839896873589389999984760997199999899992288672675456998099999999588983589829999998895379987133089
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 \| \| \| \| \| GQPKAAPSVTLFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASSYLSLTPEQWKSHKSYSCQVTHEGSTVEKTVAPTECS
Prediction	8746441403033136652776402010104523175040303356553666354352357873312020304044741566541343041674435541546628
	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

                   |                   |                   |                   |                   |

SS
Seq

CCCCCCCSSSSSCCCHHHHCCCCSSSSSSSSCCSCCCSSSSSSSCCSSCCCCSSSCCCSSCCCCCSSSSSSSSSCHHHHCCCCSSSSSSSSCCSCSSSSSSHHHCC
GQPKAAPSVTLFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASSYLSLTPEQWKSHKSYSCQVTHEGSTVEKTVAPTECS

6ce0E

0.97

0.95

26.71

1.50

DEthreader

GQSKANPSVTLFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASSYLSLTPEQWKSHRSYSCQVTHEGSTVEKTVAPTE--

1nc4C2

0.74

20.87

1.29

SPARKS-K

GQPKSSPSVTLFPPSSEELETNKATLVCTITDFYPGVVTVDWKVDGTPVTQGMETTQPSKQSNNKYMASSYLTLTARAWERHSSYSCQVTHEGHTVEKSLSPAECS

6uk2E

0.34

0.32

9.60

0.47

MapAlign

--NVFPPEVAVFEPSEAEISTQKATLVCLATGFYPDHVELSWWVNGKEVHSGVCTDQPLKENDSRYALSSRLRVSATFWQDPNHFRCQVQFGLQIVSAEAWG----

6wl2C2

0.30

0.29

8.89

0.30

CEthreader

LRNVTPPKVSLREPSKAEIANQKATLQCQARGFFPDHVELSWWVNGKEVHSGVSTDPAYKESNYSYSLSSRLRVSATFWHPRNHFRCQVQFHGQNISAEAWGRAD-

1a8jL2

0.95

26.73

1.55

MUSTER

GQPKANPTVTLFPPSSEELQANKATLVCLISDFYPGAVTVAWKADGSPVKAGVETTKPSKQSNNKYAASSYLSLTPEQWKSHRSYSCQVTHEGSTVEKTVAPTECS

1nc4C2

0.74

20.87

0.50

HHsearch

GQPKSSPSVTLFPPSSEELETNKATLVCTITDFYPGVVTVDWKVDGTPVTQGMETTQPSKQSNNKYMASSYLTLTARAWERHSSYSCQVTHEGHTVEKSLSPAECS

1nc4C2

0.74

20.87

2.20

FFAS-3D

GQPKSSPSVTLFPPSSEELETNKATLVCTITDFYPGVVTVDWKVDGTPVTQGMETTQPSKQSNNKYMASSYLTLTARAWERHSSYSCQVTHEGHTVEKSLSPAECS

1a8jL2

0.95

26.73

0.40

EigenThreader

GQPKANPTVTLFPPSSEELQANKATLVCLISDFYPGAVTVAWKADGSPVKAGVETTKPSKQSNNKYAASSYLSLTPEQWKSHRSYSCQVTHEGSTVEKTVAPTECS

4lldB

0.99

0.94

26.42

2.01

CNFpred

-QPKAAPSVTLFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASSYLSLTPEQWKSHRSYSCQVTHEGSTVEKTVAP----

2rcjT

0.95

0.94

26.46

1.50

DEthreader

GQPKANPTVTLFPPSSEELQANKATLVCLISDFYPGAVTVAWKADGSPVKAGVETTKPSKQSNNKYAASSYLSLTPEQWKSHRSYSCQVTHEGSTVEKTVAPTEC-

(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	0.958

(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	7jz1L	0.97	0.54	0.981	0.991	model1_7jz1L.pdb.gz
2	8bs8L	0.97	0.97	0.764	1.000	model1_8bs8L.pdb.gz
3	6qn7L	0.97	0.68	0.762	0.991	model1_6qn7L.pdb.gz
4	2rcjT	0.96	0.82	0.943	0.991	model1_2rcjT.pdb.gz
5	7lfaD2	0.96	0.37	1.000	0.972	model1_7lfaD2.pdb.gz
6	6mtsL	0.96	0.51	0.981	0.972	model1_6mtsL.pdb.gz
7	7jkbA	0.95	0.53	0.981	0.972	model1_7jkbA.pdb.gz
8	7cqcL2	0.95	0.95	0.657	0.991	model1_7cqcL2.pdb.gz
9	1nc4C2	0.95	1.20	0.736	1.000	model1_1nc4C2.pdb.gz
10	8d3aL	0.95	0.66	0.990	0.972	model1_8d3aL.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:0003823	0.90	antigen binding
GO:0005102	0.70	receptor binding
GO:0034987	0.68	immunoglobulin receptor 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:0002376	0.96	immune system process
GO:0065007	0.86	biological regulation
GO:0050896	0.86	response to stimulus
GO:0050789	0.86	regulation of biological process
GO:0006955	0.84	immune response
GO:0050794	0.83	regulation of cellular process
GO:0048518	0.79	positive regulation of biological process
GO:0002682	0.78	regulation of immune system process
GO:0048522	0.77	positive regulation of cellular process
GO:0009987	0.76	cellular process
GO:0051249	0.73	regulation of lymphocyte activation
GO:0016043	0.73	cellular component organization
GO:0048584	0.71	positive regulation of response to stimulus
GO:0002684	0.71	positive regulation of immune system process
GO:0051251	0.69	positive regulation of lymphocyte activation
GO:0050778	0.69	positive regulation of immune response
GO:0002252	0.68	immune effector process
GO:0006959	0.67	humoral immune response
GO:0002253	0.67	activation of immune response
GO:0050851	0.66	antigen receptor-mediated signaling pathway
GO:0043207	0.66	response to external biotic stimulus
GO:0006952	0.66	defense response
GO:0009617	0.65	response to bacterium
GO:0019538	0.64	protein metabolic process
GO:0045087	0.61	innate immune response
GO:0044699	0.61	single-organism process
GO:0006958	0.61	complement activation, classical pathway
GO:0050871	0.60	positive regulation of B cell activation
GO:0042742	0.60	defense response to bacterium
GO:0006911	0.60	phagocytosis, engulfment
GO:0006910	0.60	phagocytosis, recognition
GO:0050853	0.59	B cell receptor signaling pathway

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	0.95	cell part
GO:0044425	0.84	membrane part
GO:0044459	0.81	plasma membrane part
GO:0043234	0.79	protein complex
GO:0044421	0.77	extracellular region part
GO:0009897	0.69	external side of plasma membrane
GO:0042571	0.61	immunoglobulin complex, circulating
GO:0072562	0.60	blood microparticle
GO:0044424	0.58	intracellular part
GO:0043226	0.58	organelle
GO:0043229	0.52	intracellular organelle

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	0.080	2wwmD	0.642	2.63	0.167	0.821	2.7.11.1	NA
2	0.067	2gg1A	0.549	2.64	0.098	0.736	2.7.7.48 3.4.21.91	NA
3	0.067	1tnnA	0.567	3.10	0.172	0.774	2.7.11.1	NA
4	0.067	2rq8A	0.567	2.85	0.060	0.764	2.7.11.1	NA
5	0.067	2edtA	0.581	3.05	0.057	0.802	2.7.11.1	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	0.02	1oaq1	0.592	2.88	0.136	0.783	0.26	III	complex1.pdb.gz	7,9,11,26,28,30,32,33,34,93,95

	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.