D-I-TASSER P30273-D1

D-I-TASSER results for P30273-D1

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

Input Sequence in FASTA format

>P30273 (86 residues)
MIPAVVLLLLLLVEQAAALGEPQLCYILDAILFLYGIVLTLLYCRLKIQVRKAAITSYEK
SDGVYTGLSTRNQETYETLKHEKPPQ

Predicted Secondary Structure

Sequence	20 40 60 80 \| \| \| \| MIPAVVLLLLLLVEQAAALGEPQLCYILDAILFLYGIVLTLLYCRLKIQVRKAAITSYEKSDGVYTGLSTRNQETYETLKHEKPPQ
Prediction	CHHHHHHHHHCCHHHHHCCCCCCSSSHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHCCCCCCC
Confidence	92579999976645664468984432058899999999999999998740445544456888621367899975421106799999
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 \| \| \| \| MIPAVVLLLLLLVEQAAALGEPQLCYILDAILFLYGIVLTLLYCRLKIQVRKAAITSYEKSDGVYTGLSTRNQETYETLKHEKPPQ
Prediction	53320333232334443425423102301333333133312121223145546545647665330541456655415416575688
	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

CHHHHHHHHHCCHHHHHCCCCCCSSSHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHCCCCCCC
MIPAVVLLLLLLVEQAAALGEPQLCYILDAILFLYGIVLTLLYCRLKIQVRKAAITSYEKSDGVYTGLSTRNQETYETLKHEKPPQ

6tmiB

0.09

0.08

3.13

1.17

DEthreader

KYATDTK-CLDYLSTFRTEVE-DQIANYKVALVSQMRRQLTERLVEKLNGIQQAEKLIQGSL-QDVMIRE--VSSFKDLYKSR-EL

6jxra

0.50

0.21

6.07

1.26

MUSTER

--------------QSFGLLDPKLCYLLDGILFIYGVILTALFLRVKFSR------------------------------------

6jxra

0.50

0.21

6.07

3.38

HHsearch

--------------QSFGLLDPKLCYLLDGILFIYGVILTALFLRVKFSR------------------------------------

5xpdA

0.07

2.88

0.46

CEthreader

LSLFLTINAVTWLFYGLAIKDFYVALPNVLGAFLGAVQMILYIIFKTPVAQMKKYTCTVCGYIYNPEDGDPDNGVNPGTDFKDIPD

6m97A

0.07

2.88

0.47

EigenThreader

DFRHGFDILVGQIDDALKLAVKEAQAAAEQLKTTRNAYIQRMLSMAHLLQTVLHVIQVVVSYFLMLVFMTYNAYLCMAVAAGAGLG

6jxra

0.52

0.20

5.72

0.69

FFAS-3D

-----------------GLLDPKLCYLLDGILFIYGVILTALFLRVKFSR------------------------------------

5xj5A2

0.11

0.09

3.35

0.94

SPARKS-K

SPSVALFSFLVWLGIFLWKRYVSLASITATISAFLFLFVAIVIGALIIYRHRENINRLLTGREHRFGTLEVL--------------

6z16D

0.14

0.08

2.79

0.65

CNFpred

IIAAVGVMIFGISIMTPESVEGTIFYLLQDMVMKAMLFLFVGIIFSITRSN-----------------------------------

5mqfK

0.07

0.06

2.42

1.17

DEthreader

NSMAQLEHQAVRIENLELMSHG--CNAWKVYNENLVHMIEHAQKELQKLRKHIQDLNWQRKN-MQLTAGKLRMES-N---------

4c1oA

0.09

3.51

0.71

MapAlign

AGKCWAAYVALEKIFRDTGKEALAALAGEQAEKCAATIVEYIRALRKHLQYVLTEGICLFPDGGWKISSTSNNSWLSKIYLCQFIA

(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	0.4413

(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	2lemA	0.57	3.77	0.098	0.954	model1_2lemA.pdb.gz
2	5owvC	0.56	3.54	0.146	0.954	model1_5owvC.pdb.gz
3	3pltA	0.56	3.66	0.063	0.884	model1_3pltA.pdb.gz
4	6lr0U	0.56	3.32	0.024	0.919	model1_6lr0U.pdb.gz
5	2efkA	0.56	3.69	0.100	0.919	model1_2efkA.pdb.gz
6	5nenA	0.56	3.46	0.078	0.895	model1_5nenA.pdb.gz
7	4uxvA	0.56	3.62	0.060	0.895	model1_4uxvA.pdb.gz
8	2eflA	0.56	3.99	0.095	0.942	model1_2eflA.pdb.gz
9	5m87A	0.56	3.49	0.087	0.895	model1_5m87A.pdb.gz
10	3s84A	0.55	3.56	0.025	0.907	model1_3s84A.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:0032403	0.88	protein complex binding
GO:0004872	0.87	receptor activity
GO:0004871	0.87	signal transducer activity
GO:0004888	0.86	transmembrane signaling receptor activity
GO:0019864	0.85	IgG binding
GO:0019863	0.85	IgE binding
GO:0019767	0.85	IgE receptor 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:0065007	0.93	biological regulation
GO:0050789	0.93	regulation of biological process
GO:0050794	0.92	regulation of cellular process
GO:0007165	0.86	signal transduction
GO:0048518	0.84	positive regulation of biological process
GO:0044699	0.84	single-organism process
GO:0009987	0.84	cellular process
GO:0007166	0.84	cell surface receptor signaling pathway
GO:0050896	0.82	response to stimulus
GO:0044763	0.82	single-organism cellular process
GO:0002376	0.81	immune system process
GO:0048583	0.79	regulation of response to stimulus
GO:0002682	0.79	regulation of immune system process
GO:0050778	0.78	positive regulation of immune response
GO:0002768	0.78	immune response-regulating cell surface receptor signaling pathway
GO:0002429	0.77	immune response-activating cell surface receptor signaling pathway
GO:0048522	0.75	positive regulation of cellular process
GO:0051049	0.70	regulation of transport
GO:0050865	0.69	regulation of cell activation
GO:0050766	0.69	positive regulation of phagocytosis
GO:0038093	0.69	Fc receptor signaling pathway
GO:0006955	0.69	immune response
GO:0002252	0.69	immune effector process
GO:0080134	0.68	regulation of response to stress
GO:0038094	0.68	Fc-gamma receptor signaling pathway
GO:0032101	0.68	regulation of response to external stimulus
GO:0002431	0.68	Fc receptor mediated stimulatory signaling pathway
GO:0051239	0.67	regulation of multicellular organismal process
GO:0006952	0.67	defense response
GO:0001775	0.67	cell activation
GO:0065008	0.66	regulation of biological quality
GO:0046649	0.66	lymphocyte activation
GO:0045087	0.66	innate immune response
GO:0030154	0.66	cell differentiation
GO:0016337	0.66	single organismal cell-cell adhesion
GO:0042742	0.65	defense response to bacterium
GO:0042590	0.65	antigen processing and presentation of exogenous peptide antigen via MHC class I
GO:0030593	0.65	neutrophil chemotaxis
GO:0019886	0.65	antigen processing and presentation of exogenous peptide antigen via MHC class II
GO:0016064	0.65	immunoglobulin mediated immune response
GO:0010543	0.65	regulation of platelet activation
GO:0002292	0.65	T cell differentiation involved in immune response
GO:0002283	0.65	neutrophil activation involved in immune response
GO:0008152	0.60	metabolic process
GO:0071704	0.57	organic substance metabolic process
GO:0044710	0.57	single-organism metabolic process
GO:0044237	0.57	cellular metabolic process
GO:0044260	0.54	cellular macromolecule metabolic process
GO:0051716	0.53	cellular response to stimulus
GO:0010033	0.53	response to organic substance
GO:0071404	0.52	cellular response to low-density lipoprotein particle stimulus
GO:0031623	0.52	receptor internalization

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	1.00	cell part
GO:0044425	0.95	membrane part
GO:0044459	0.94	plasma membrane part
GO:0043234	0.94	protein complex
GO:0098797	0.93	plasma membrane protein complex
GO:0032998	0.74	Fc-epsilon receptor I complex
GO:0009897	0.74	external side of plasma membrane
GO:0044424	0.59	intracellular part
GO:0016020	0.51	membrane

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	1b8fA	0.508	4.12	0.037	0.907	4.3.1.3	NA
2	0.060	1fohC	0.542	3.84	0.026	0.907	1.14.13.7	NA
3	0.060	1mo7A	0.280	4.65	0.025	0.558	3.6.3.9	NA
4	0.060	2e9fB	0.500	4.01	0.105	0.872	4.3.2.1	NA
5	0.060	1vdkA	0.532	3.95	0.103	0.895	4.2.1.2	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:

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	1wdz0	0.523	4.25	0.096	0.965	0.22	III	complex1.pdb.gz	1,7,10,11,14,15,18,19,24,31,35
	2	0.01	3dqbA	0.521	3.54	0.065	0.814	0.21	UUU	complex2.pdb.gz	31,33,38

	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.