D-I-TASSER P36888-D3

D-I-TASSER results for P36888-D3

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

Input Sequence in FASTA format

>P36888 (44 residues)
FTIDLNQTPQTTLPQLFLKVGEPLWIRCKAVHVNHGFGLTWELE

Predicted Secondary Structure

Sequence	20 40 \| \| FTIDLNQTPQTTLPQLFLKVGEPLWIRCKAVHVNHGFGLTWELE
Prediction	CSSCCCCCCCCCCHHHHHHCCCSSSSSSSSSSSSCCCSSSSSSC
Confidence	94416789999747888763961689877788620230789869
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 \| \| FTIDLNQTPQTTLPQLFLKVGEPLWIRCKAVHVNHGFGLTWELE
Prediction	65243564574423402242443020303332453725241538
	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

                   |                   |

SS
Seq

CSSCCCCCCCCCCHHHHHHCCCSSSSSSSSSSSSCCCSSSSSSC
FTIDLNQTPQTTLPQLFLKVGEPLWIRCKAVHVNHGFGLTWELE

2avgA

0.07

2.84

1.16

MapAlign

FSARVAGALKPPVVKWFKGKWVDLLQLHDSYDASKVYLFELHIT

3qs9E

1.00

28.00

1.04

CNFpred

FTIDLNQTPQTTLPQLFLKVGEPLWIRCKAVHVNHGFGLTWELE

7jmrA

0.07

2.82

0.83

DEthreader

SCKGLFTEDAT-VWTTIHITDCDCRFIFFCEKDGAWKAKYVKLF

3qs7E4

1.00

28.00

1.00

SPARKS-K

FTIDLNQTPQTTLPQLFLKVGEPLWIRCKAVHVNHGFGLTWELE

6efyA3

0.05

2.23

0.68

MapAlign

QIECHVEASPKSINYWIKDTGEMIYHVQESSQSMYETKMSMIVR

4iiqC

0.16

5.30

0.54

CEthreader

LNCYVYGFHPPQIEIDLLKNGEKIKSEQSSFSKDWSFYLLSHAE

3qs7E4

1.00

28.00

0.81

MUSTER

FTIDLNQTPQTTLPQLFLKVGEPLWIRCKAVHVNHGFGLTWELE

2e9wB

0.20

6.52

0.39

HHsearch

FILKVRPAFKVSKASYLLREGEEFTVTCTIKDVSSSVYSTWKRE

3qs7E4

1.00

28.00

0.63

FFAS-3D

FTIDLNQTPQTTLPQLFLKVGEPLWIRCKAVHVNHGFGLTWELE

2w2sA

0.07

2.84

0.43

EigenThreader

INGKICSVYSASPMTLIFHGPEELEYSQEITWEFVSLQIRVSAK

(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	0.5548

(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	3a7rA	0.49	2.39	0.048	0.795	model1_3a7rA.pdb.gz
2	7abiA	0.48	2.60	0.077	0.795	model1_7abiA.pdb.gz
3	6kjkA	0.48	3.57	0.047	0.977	model1_6kjkA.pdb.gz
4	5nrlA	0.47	2.66	0.051	0.795	model1_5nrlA.pdb.gz
5	3x29A	0.47	2.62	0.098	0.932	model1_3x29A.pdb.gz
6	4i43B2	0.47	2.56	0.051	0.795	model1_4i43B2.pdb.gz
7	7bvrB	0.47	3.67	0.023	0.977	model1_7bvrB.pdb.gz
8	2p8rA	0.47	2.64	0.105	0.795	model1_2p8rA.pdb.gz
9	3sbgA2	0.46	2.66	0.051	0.795	model1_3sbgA2.pdb.gz
10	1vqzA1	0.45	2.85	0.049	0.795	model1_1vqzA1.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	0.73	catalytic activity
GO:0016740	0.70	transferase activity
GO:0004888	0.69	transmembrane signaling receptor activity
GO:0004672	0.69	protein kinase activity
GO:0004896	0.68	cytokine receptor activity
GO:0004713	0.68	protein tyrosine kinase 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:0071310	1.00	cellular response to organic substance
GO:0048513	1.00	animal organ development
GO:0044767	1.00	single-organism developmental process
GO:0065007	0.79	biological regulation
GO:0050789	0.79	regulation of biological process
GO:0008152	0.78	metabolic process
GO:0071704	0.77	organic substance metabolic process
GO:0050794	0.77	regulation of cellular process
GO:0044238	0.77	primary metabolic process
GO:0044237	0.77	cellular metabolic process
GO:0043170	0.76	macromolecule metabolic process
GO:0044260	0.75	cellular macromolecule metabolic process
GO:0048518	0.72	positive regulation of biological process
GO:0044763	0.72	single-organism cellular process
GO:0019222	0.72	regulation of metabolic process
GO:0080090	0.71	regulation of primary metabolic process
GO:0060255	0.71	regulation of macromolecule metabolic process
GO:0048522	0.71	positive regulation of cellular process
GO:0031323	0.71	regulation of cellular metabolic process
GO:0007165	0.71	signal transduction
GO:0031325	0.70	positive regulation of cellular metabolic process
GO:0019538	0.70	protein metabolic process
GO:0010604	0.70	positive regulation of macromolecule metabolic process
GO:0065008	0.69	regulation of biological quality
GO:0048869	0.69	cellular developmental process
GO:0007166	0.69	cell surface receptor signaling pathway
GO:0006796	0.69	phosphate-containing compound metabolic process
GO:0006464	0.69	cellular protein modification process
GO:0002376	0.69	immune system process
GO:0001934	0.69	positive regulation of protein phosphorylation
GO:0097028	0.68	dendritic cell differentiation
GO:0071345	0.68	cellular response to cytokine stimulus
GO:0046777	0.68	protein autophosphorylation
GO:0046651	0.68	lymphocyte proliferation
GO:0042127	0.68	regulation of cell proliferation
GO:0035726	0.68	common myeloid progenitor cell proliferation
GO:0030183	0.68	B cell differentiation
GO:0030097	0.68	hemopoiesis
GO:0019221	0.68	cytokine-mediated signaling pathway
GO:0002328	0.68	pro-B cell differentiation
GO:0002318	0.68	myeloid progenitor cell differentiation
GO:0001776	0.68	leukocyte homeostasis

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:0044424	0.76	intracellular part
GO:0016020	0.72	membrane
GO:0044425	0.71	membrane part
GO:0005886	0.70	plasma membrane
GO:0044459	0.69	plasma membrane part
GO:0043226	0.56	organelle
GO:0043229	0.55	intracellular organelle
GO:0043227	0.54	membrane-bounded organelle
GO:0043231	0.53	intracellular membrane-bounded 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	0.060	1hdgQ	0.436	3.15	0.023	0.841	1.2.1.12	NA
2	0.060	2ke0A	0.456	3.25	0.083	0.818	5.2.1.8	NA
3	0.060	1tnnA	0.403	2.83	0.167	0.795	2.7.11.1	NA
4	0.060	3bcfA	0.433	3.67	0.068	0.977	3.2.1.98	NA
5	0.060	1xizB	0.432	3.18	0.023	0.818	2.7.1.69	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	3a7aC	0.485	2.41	0.048	0.795	0.13	UUU	complex1.pdb.gz	6,12,34,36

	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.