D-I-TASSER P0DP72-D3

D-I-TASSER results for P0DP72-D3

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

Input Sequence in FASTA format

>P0DP72 (91 residues)
GPDKPVITMEPLGLTEEGFWASEREEVTLSCLAASNPPSHYVWLRDHTQVHTGPTYVIAR
AGRVHTGLYTCLARNSYLDTRTQTTVQLTIY

Predicted Secondary Structure

Sequence	20 40 60 80 \| \| \| \| GPDKPVITMEPLGLTEEGFWASEREEVTLSCLAASNPPSHYVWLRDHTQVHTGPTYVIARAGRVHTGLYTCLARNSYLDTRTQTTVQLTIY
Prediction	CCCCCSSSSCCCCCCCCCSSSSCCCCSSSSSSSSCCCCCSSSSSSCCSSCCCCCSSSSCCCCHHHCSSSSSSSSSCCCCCSSSSSSSSSSC
Confidence	9989979707864147874993794299999820129988999999999479987998666823168999999968877468999999989
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 \| \| \| \| GPDKPVITMEPLGLTEEGFWASEREEVTLSCLAASNPPSHYVWLRDHTQVHTGPTYVIARAGRVHTGLYTCLARNSYLDTRTQTTVQLTIY
Prediction	8565240334344344763414445514653415443324036336655156544040450457344443330304345554434040304
	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

                   |                   |                   |                   |

SS
Seq

CCCCCSSSSCCCCCCCCCSSSSCCCCSSSSSSSSCCCCCSSSSSSCCSSCCCCCSSSSCCCCHHHCSSSSSSSSSCCCCCSSSSSSSSSSC
GPDKPVITMEPLGLTEEGFWASEREEVTLSCLAASNPPSHYVWLRDHTQVHTGPTYVIARAGRVHTGLYTCLARNSYLDTRTQTTVQLTIY

5lf5A

0.30

0.27

8.34

1.33

DEthreader

VKYPPVIVE-M--NS--SVEAIEGSHVSLLCGADSNPPPLLTWMRDGMVLREALYLDLEEVTPGEDGVYACLAENA-Y-GQDNRTVELSVM

5oyjC1

0.21

6.62

1.18

SPARKS-K

LAEKPFVAFG--SGMESLVEATVGERVRIPAKYLGYPPPEIKWYKNGIPLESGHVLTIMEVSERDTGNYTVILTNPISKEKQSHVVSLVVY

2fboJ

0.20

0.19

5.96

0.53

MapAlign

--SIMTVRT-----THTEVEVHAGGTVELPCSYQLDQPPVISWLKGSTKVFKGPTLRLTHVHPQDGGRYWCQVAQWSF-GLDAKSVVLKVT

1cs6A3

0.24

0.22

6.87

0.30

CEthreader

RQYAPSIKA----KFPADTYALTGQMVTLECFAFGNPVPQIKWRKLDGWLSSEPLLHIQNVDFEDEGTYECEAENIKG--RDTYQGRIIIH

5uv6A2

0.25

0.23

7.14

1.22

MUSTER

--VPPQIMNIS-----SDITVNEGSSVTLLCLAIGRPEPTVTWRHLSGFVSEDEYLEISDIKRDQSGEYECSALNDVAAP-DVRKVKITVN

6iaaA2

0.19

0.18

5.67

0.40

HHsearch

--APPQFVVRPRDQI-----VAQGRTVTFPCETKGNPQPAVFWQKEGSQNLPTGDLTITNIQRSDAGYYICQALTVAGSILAKAQLEVTDV

2v5tA1

0.13

0.12

4.18

1.61

FFAS-3D

--SMLTFREVV-----SPQEFKQGEDAEVVCRVSSSPAPAVSWLYTTFAMLANNNLQILNINKSDEGIYRCEGRVEARGEIDFRDIIVIV-

5oyjC1

0.18

5.70

0.33

EigenThreader

EKPFVAFGSGMES----LVEATVGERVRIPAKYLGYPPPEIKWYKNGIPLESGHVLTIMEVSERDTGNYTVILTNPISKEKQSHVVSLVVY

5oyjC

0.21

6.62

1.36

CNFpred

LAEKPFVAFGS--GMESLVEATVGERVRIPAKYLGYPPPEIKWYKNGIPLEAGHVLTIMEVSERDTGNYTVILTNPISKEKQSHVVSLVVY

6efyA

0.22

0.21

6.59

1.33

DEthreader

AVIPPDFISEDT-SS--DVIVPEGSSVRLTCRARGYPEPIVTWRREGNPSFRGEVLKLSKISRNEMGSYLCIASNG-VPPSVSKRISLSIH

(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	0.8988

(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	6nrrB	0.86	1.25	0.279	0.945	model1_6nrrB.pdb.gz
2	5eo9B	0.86	1.52	0.230	0.956	model1_5eo9B.pdb.gz
3	6efyA	0.86	1.56	0.230	0.956	model1_6efyA.pdb.gz
4	5lf5A	0.86	1.16	0.298	0.923	model1_5lf5A.pdb.gz
5	6eg0B	0.85	1.53	0.264	0.956	model1_6eg0B.pdb.gz
6	1cs6A	0.85	1.27	0.235	0.934	model1_1cs6A.pdb.gz
7	6dldA	0.85	1.46	0.209	0.945	model1_6dldA.pdb.gz
8	5uv6A	0.85	1.35	0.247	0.934	model1_5uv6A.pdb.gz
9	6efzA	0.85	1.55	0.276	0.956	model1_6efzA.pdb.gz
10	2nziA	0.84	1.73	0.195	0.956	model1_2nziA.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:0004872	0.64	receptor activity
GO:0005102	0.62	receptor binding
GO:0004672	0.57	protein kinase activity
GO:0097367	0.54	carbohydrate derivative binding
GO:0004871	0.54	signal transducer activity
GO:0004888	0.53	transmembrane signaling receptor activity
GO:0004674	0.53	protein serine/threonine kinase activity
GO:0046872	0.51	metal ion binding
GO:0005516	0.51	calmodulin binding
GO:0004713	0.51	protein tyrosine kinase activity
GO:0005524	0.50	ATP 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:0044699	0.86	single-organism process
GO:0009987	0.83	cellular process
GO:0044763	0.82	single-organism cellular process
GO:0032502	0.72	developmental process
GO:0065007	0.71	biological regulation
GO:0044767	0.71	single-organism developmental process
GO:0050789	0.70	regulation of biological process
GO:0050794	0.69	regulation of cellular process
GO:0016043	0.65	cellular component organization
GO:0009653	0.62	anatomical structure morphogenesis
GO:0048869	0.61	cellular developmental process
GO:0048856	0.61	anatomical structure development
GO:0032501	0.60	multicellular organismal process
GO:0007155	0.60	cell adhesion
GO:0098609	0.58	cell-cell adhesion
GO:0051239	0.57	regulation of multicellular organismal process
GO:0050793	0.57	regulation of developmental process
GO:0048518	0.57	positive regulation of biological process
GO:0006928	0.57	movement of cell or subcellular component
GO:0048583	0.56	regulation of response to stimulus
GO:2000026	0.55	regulation of multicellular organismal development
GO:0098742	0.55	cell-cell adhesion via plasma-membrane adhesion molecules
GO:0051128	0.55	regulation of cellular component organization
GO:0048522	0.55	positive regulation of cellular process
GO:0045595	0.55	regulation of cell differentiation
GO:0050896	0.54	response to stimulus
GO:0003008	0.54	system process
GO:0050767	0.53	regulation of neurogenesis
GO:0032989	0.53	cellular component morphogenesis
GO:0019222	0.53	regulation of metabolic process
GO:0009966	0.53	regulation of signal transduction
GO:0048584	0.52	positive regulation of response to stimulus
GO:0048468	0.52	cell development
GO:0032879	0.52	regulation of localization
GO:0032268	0.52	regulation of cellular protein metabolic process
GO:0030030	0.52	cell projection organization
GO:0010975	0.52	regulation of neuron projection development
GO:1902531	0.51	regulation of intracellular signal transduction
GO:0001932	0.51	regulation of protein phosphorylation
GO:0065008	0.50	regulation of biological quality
GO:0051247	0.50	positive regulation of protein metabolic process
GO:0051240	0.50	positive regulation of multicellular organismal process
GO:0051094	0.50	positive regulation of developmental process
GO:0044707	0.50	single-multicellular organism process
GO:0031325	0.50	positive regulation of cellular metabolic process
GO:0009967	0.50	positive regulation of signal transduction
GO:0009628	0.50	response to abiotic stimulus

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	0.98	cell part
GO:0044425	0.74	membrane part
GO:0016020	0.71	membrane
GO:0031224	0.70	intrinsic component of membrane
GO:0016021	0.68	integral component of membrane
GO:0044424	0.65	intracellular part
GO:0044459	0.61	plasma membrane part
GO:0043226	0.61	organelle
GO:0005886	0.61	plasma membrane
GO:0044444	0.53	cytoplasmic part
GO:0043227	0.53	membrane-bounded organelle
GO:0005887	0.51	integral component of plasma membrane
GO:0044422	0.50	organelle part

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	0.158	1u2hA	0.823	1.62	0.241	0.912	2.7.11.1	30,44
2	0.142	2bk8A	0.754	1.80	0.136	0.890	2.7.11.1	NA
3	0.131	2edtA	0.704	2.10	0.179	0.857	2.7.11.1	NA
4	0.090	1rv6Y	0.670	2.31	0.159	0.846	2.7.10.1	70
5	0.086	2edrA	0.696	2.18	0.167	0.857	2.7.11.1	28,31

	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	0.06	2iep0	0.836	1.68	0.259	0.934	0.84	III	complex1.pdb.gz	8,9,26,28,30,32,34,55
2	0.05	1tlk0	0.815	1.69	0.214	0.923	0.79	III	complex2.pdb.gz	3,6,34,36,38,40,41,42,50
3	0.04	1evt2	0.826	2.09	0.182	0.967	0.51	III	complex3.pdb.gz	2,33,35,37,38,39,40,54,75
4	0.04	1evt0	0.826	2.09	0.182	0.967	0.48	III	complex4.pdb.gz	28,30,32,55

	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.