D-I-TASSER P55273-D1

D-I-TASSER results for P55273-D1

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

Input Sequence in FASTA format

>P55273 (65 residues)
MLLEEVRAGDRLSGAAARGDVQEVRRLLHRELVHPDALNRFGKTALQVMMFGSTAIALEL
LKQGA

Predicted Secondary Structure

Sequence	20 40 60 \| \| \| MLLEEVRAGDRLSGAAARGDVQEVRRLLHRELVHPDALNRFGKTALQVMMFGSTAIALELLKQGA
Prediction	CCCCCCCCCCHHHHHHHHCCHHHHHHHHHHCCCCCCCCCCCCCCHHHHHHHCCHHHHHHHHHHCC
Confidence	98777777427999998199999999999379999876888998999999489699999998079
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 \| \| \| MLLEEVRAGDRLSGAAARGDVQEVRRLLHRELVHPDALNRFGKTALQVMMFGSTAIALELLKQGA
Prediction	64345464354014114544264035007646143524354432001003343350042027458
	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

                   |                   |                   |

SS
Seq

CCCCCCCCCCHHHHHHHHCCHHHHHHHHHHCCCCCCCCCCCCCCHHHHHHHCCHHHHHHHHHHCC
MLLEEVRAGDRLSGAAARGDVQEVRRLLHRELVHPDALNRFGKTALQVMMFGSTAIALELLKQGA

3v30A

0.25

7.62

1.33

DEthreader

-ERGLAKRESALSLASTGGYTDIVGLLLERD-VDINIYDWNGGTPLLYVRGNHVKCVEALLARGA

4gmrA2

0.25

7.63

2.38

SPARKS-K

PNAKDSDGKTPLHLAAENGHKEVVKLLLSQ-GADPNTSDSDGRTPLDLAREGNEEVVKLLEKQGG

1bu9A

0.22

0.20

6.31

0.45

MapAlign

------EGNLPLHLAAKEGHLRVVEFLVKHTASNVGHRNHKGDTACLARLYGRNEVVSLMQANGA

1bu9A

0.22

6.82

0.25

CEthreader

VNIEDNEGNLPLHLAAKEGHLRVVEFLVKHTASNVGHRNHKGDTACDLARLGRNEVVSLMQANGA

4rlvA

0.20

6.38

1.31

MUSTER

VDSATKKGNTALHIASLAGQAEVVKVLVKEG-ANINAQSQNGFTPLYAAQENHIDVVKYLLENGA

6mwqA

0.30

0.29

8.88

0.80

HHsearch

VNALDRFGLTPLHLAAQRGHLEIVEVLLK-CGADVNAADLWGQTPLHAATAGHLEIVEVLLKYGA

3b95A3

0.18

5.98

1.27

FFAS-3D

VDPKDAEGSTCLHLAAKKGHYEVVQYLLSNGQMDVNCQDDGGWTPMIWATYKHVDLVKLLLSKGS

1wg0A3

0.17

5.57

0.63

EigenThreader

VNLDYPSGWTPFHIACSVGNLEVVKSLYDPLKPDLNKITNQGVTCLHAVGKKWFEVSQFLIENGA

1bi8B

1.00

0.92

25.85

1.08

CNFpred

-----VRAGDRLSGAAARGDVQEVRRLLHRELVHPDALNRFGKTALQVMMFGSTAIALELLKQGA

3twqA

0.27

0.26

8.05

1.33

DEthreader

SLGNRDIQSTPLHFAAGYNRVSVVEYLLQHG-ADVHAKDKGGLVPLHNCSYGHYEVAELLVKHGA

(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	0.8187

(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	7tbnA	0.81	1.70	0.328	0.985	model1_7tbnA.pdb.gz
2	1ap7A	0.80	1.47	0.905	0.969	model1_1ap7A.pdb.gz
3	6c9kA	0.79	1.65	0.333	0.969	model1_6c9kA.pdb.gz
4	5d68A1	0.78	1.99	0.203	0.939	model1_5d68A1.pdb.gz
5	5g4xA	0.78	2.21	0.188	0.985	model1_5g4xA.pdb.gz
6	4o1oA1	0.78	2.18	0.308	0.954	model1_4o1oA1.pdb.gz
7	6fesA	0.77	1.42	0.322	0.908	model1_6fesA.pdb.gz
8	4oauC6	0.77	1.98	0.277	0.939	model1_4oauC6.pdb.gz
9	7dsya	0.77	2.19	0.323	0.954	model1_7dsya.pdb.gz
10	1wdyA	0.77	1.98	0.277	0.939	model1_1wdyA.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:0004861	0.92	cyclin-dependent protein serine/threonine kinase inhibitor activity
GO:0019901	0.87	protein kinase 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:0009987	1.00	cellular process
GO:0050794	0.97	regulation of cellular process
GO:0048519	0.96	negative regulation of biological process
GO:0048523	0.95	negative regulation of cellular process
GO:0008285	0.92	negative regulation of cell proliferation
GO:0044699	0.90	single-organism process
GO:0045786	0.88	negative regulation of cell cycle
GO:0080090	0.87	regulation of primary metabolic process
GO:0060255	0.87	regulation of macromolecule metabolic process
GO:0050896	0.87	response to stimulus
GO:0031323	0.87	regulation of cellular metabolic process
GO:0050790	0.86	regulation of catalytic activity
GO:0032268	0.86	regulation of cellular protein metabolic process
GO:0044763	0.84	single-organism cellular process
GO:0022402	0.83	cell cycle process
GO:0009892	0.83	negative regulation of metabolic process
GO:0001932	0.83	regulation of protein phosphorylation
GO:0044772	0.82	mitotic cell cycle phase transition
GO:0042326	0.82	negative regulation of phosphorylation
GO:0007050	0.82	cell cycle arrest
GO:0000079	0.82	regulation of cyclin-dependent protein serine/threonine kinase activity
GO:0048583	0.77	regulation of response to stimulus
GO:0042221	0.77	response to chemical
GO:0031667	0.67	response to nutrient levels
GO:0009966	0.67	regulation of signal transduction
GO:0048518	0.66	positive regulation of biological process
GO:0048522	0.65	positive regulation of cellular process
GO:0051716	0.62	cellular response to stimulus
GO:0007584	0.62	response to nutrient
GO:0048869	0.53	cellular developmental process
GO:0070887	0.52	cellular response to chemical 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:0044424	1.00	intracellular part
GO:0005737	0.91	cytoplasm
GO:0043229	0.89	intracellular organelle
GO:0043231	0.88	intracellular membrane-bounded organelle
GO:0005634	0.87	nucleus
GO:0044446	0.67	intracellular organelle part
GO:0044428	0.58	nuclear part
GO:0005654	0.53	nucleoplasm

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	1t64A	0.526	2.86	0.137	0.785	3.5.1.98	NA
2	0.060	1c7gA	0.555	2.92	0.094	0.815	4.1.99.2	NA
3	0.060	1ukwA	0.554	2.75	0.085	0.862	1.3.99.3	NA
4	0.060	1g0cA	0.527	2.73	0.127	0.831	3.2.1.4	NA
5	0.060	2dqmA	0.545	3.34	0.103	0.892	3.4.11.2	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:

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	0.71	1bi81	0.908	0.36	1.000	0.923	1.04	III	complex1.pdb.gz	14,18,20,22,39,40,41,43,48,49,50,51,52
	2	0.06	3q9nD	0.777	1.68	0.339	0.954	0.95	COA	complex2.pdb.gz	14,17,53

	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.