D-I-TASSER Q3B8N2

D-I-TASSER results for Q3B8N2

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

Summary of the Protein

Uniprot ID: Q3B8N2
Protein Name: Galectin-9B
Gene Name: LGALS9B

Input Sequence in FASTA format

>Q3B8N2 (356 residues)
MAFSGSQAPYLSPAVPFSGTIQGGLQDGFQITVNGAVLSSSGTRFAVDFQTGFSGNDIAF
HFNPRFEDGGYVVCNTRQKGRWGPEERKMHMPFQKGMPFDLCFLVQSSDFKVMVNGSLFV
QYFHRVPFHRVDTISVNGSVQLSYISFQNPRTVPVQPAFSTVPFSQPVCFPPRPRGRRQK
PPSVRPANPAPITQTVIHTVQSASGQMFSQTPAIPPMMYPHPAYPMPFITTIPGGLYPSK
SIILSGTVLPSAQRFHINLCSGSHIAFHMNPRFDENAVVRNTQINNSWGSEERSLPRKMP
FVRGQSFSVWILCEAHCLKVAVDGQHVFEYYHRLRNLPTINKLEVGGDIQLTHVQT

Predicted Contact and Distance Map Used in D-I-TASSER simulation

Contact Map

Distance Map

D-I-TASSER simulation is guided by the consensus contact map (left figure) and distance map (right figure) derived based on confidence scores of AttentionPotential. 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.

Information of Domain

No. of Domain	Domain	Domain Boundary	Length of Domain	Models of Domain	Sequence
1	Q3B8N2-D1	1-222	222		MAFSGSQAPYLSPAVPFSGTIQGGLQDGFQITVNGAVLSSSGTRFAVDFQTGFSGNDIAFHFNPRFEDGGYVVCNTRQKGRWGPEERKMHMPFQKGMPFDLCFLVQSSDFKVMVNGSLFVQYFHRVPFHRVDTISVNGSVQLSYISFQNPRTVPVQPAFSTVPFSQPVCFPPRPRGRRQKPPSVRPANPAPITQTVIHTVQSASGQMFSQTPAIPPMMYPHP
2	Q3B8N2-D2	223-356	134		AYPMPFITTIPGGLYPSKSIILSGTVLPSAQRFHINLCSGSHIAFHMNPRFDENAVVRNTQINNSWGSEERSLPRKMPFVRGQSFSVWILCEAHCLKVAVDGQHVFEYYHRLRNLPTINKLEVGGDIQLTHVQT

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.84

(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 AttentionPotential, 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	3wv6A	0.49	3.80	0.573	0.562	model1_3wv6A.pdb.gz
2	5n0bA	0.46	6.42	0.052	0.730	model1_5n0bA.pdb.gz
3	1dykA	0.46	5.72	0.064	0.688	model1_1dykA.pdb.gz
4	3ffzA	0.46	6.11	0.056	0.714	model1_3ffzA.pdb.gz
5	4nsxA	0.46	5.92	0.022	0.699	model1_4nsxA.pdb.gz
6	5wlcLT	0.46	6.21	0.031	0.711	model1_5wlcLT.pdb.gz
7	5oqlO	0.46	6.16	0.048	0.719	model1_5oqlO.pdb.gz
8	5wyjBE	0.46	6.06	0.028	0.699	model1_5wyjBE.pdb.gz
9	1h30A	0.46	5.03	0.090	0.629	model1_1h30A.pdb.gz
10	2zhnA	0.40	0.78	0.952	0.407	model1_2zhnA.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:0097367	0.73	carbohydrate derivative binding
GO:0019899	0.71	enzyme binding
GO:0016936	0.71	galactoside binding
GO:0036094	0.55	small molecule binding
GO:0004871	0.55	signal transducer activity
GO:0030246	0.53	carbohydrate binding
GO:0048030	0.52	disaccharide binding
GO:0005534	0.52	galactose 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	0.84	cellular process
GO:0050896	0.77	response to stimulus
GO:0050794	0.77	regulation of cellular process
GO:0048518	0.75	positive regulation of biological process
GO:0060255	0.74	regulation of macromolecule metabolic process
GO:0048522	0.74	positive regulation of cellular process
GO:0051704	0.73	multi-organism process
GO:0010604	0.73	positive regulation of macromolecule metabolic process
GO:0002682	0.73	regulation of immune system process
GO:0051707	0.72	response to other organism
GO:0016032	0.72	viral process
GO:0010468	0.72	regulation of gene expression
GO:0010033	0.72	response to organic substance
GO:2001181	0.71	positive regulation of interleukin-10 secretion
GO:2000778	0.71	positive regulation of interleukin-6 secretion
GO:2000562	0.71	negative regulation of CD4-positive, alpha-beta T cell proliferation
GO:0098586	0.71	cellular response to virus
GO:0032496	0.71	response to lipopolysaccharide
GO:0010629	0.71	negative regulation of gene expression
GO:0010628	0.71	positive regulation of gene expression
GO:0044699	0.63	single-organism process
GO:0044763	0.60	single-organism cellular process
GO:0007155	0.60	cell adhesion
GO:0002376	0.59	immune system process
GO:0098609	0.58	cell-cell adhesion
GO:0098742	0.57	cell-cell adhesion via plasma-membrane adhesion molecules
GO:0080090	0.57	regulation of primary metabolic process
GO:0031323	0.57	regulation of cellular metabolic process
GO:0032268	0.56	regulation of cellular protein metabolic process
GO:0031325	0.56	positive regulation of cellular metabolic process
GO:0007157	0.56	heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules
GO:0048583	0.55	regulation of response to stimulus
GO:0007165	0.55	signal transduction
GO:0001934	0.55	positive regulation of protein phosphorylation
GO:2000112	0.54	regulation of cellular macromolecule biosynthetic process
GO:0051716	0.54	cellular response to stimulus
GO:0051171	0.54	regulation of nitrogen compound metabolic process
GO:0045088	0.54	regulation of innate immune response
GO:0009966	0.54	regulation of signal transduction
GO:0002684	0.54	positive regulation of immune system process
GO:1902531	0.53	regulation of intracellular signal transduction
GO:0051094	0.53	positive regulation of developmental process
GO:0050870	0.53	positive regulation of T cell activation
GO:0048585	0.53	negative regulation of response to stimulus
GO:0045597	0.53	positive regulation of cell differentiation
GO:0043085	0.53	positive regulation of catalytic activity
GO:0034097	0.53	response to cytokine
GO:0019219	0.53	regulation of nucleobase-containing compound metabolic process
GO:0002224	0.53	toll-like receptor signaling pathway
GO:2001269	0.52	positive regulation of cysteine-type endopeptidase activity involved in apoptotic signaling pathway
GO:2001200	0.52	positive regulation of dendritic cell differentiation
GO:2001190	0.52	positive regulation of T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell
GO:2001184	0.52	positive regulation of interleukin-12 secretion
GO:2000670	0.52	positive regulation of dendritic cell apoptotic process
GO:2000667	0.52	positive regulation of interleukin-13 secretion
GO:2000563	0.52	positive regulation of CD4-positive, alpha-beta T cell proliferation
GO:2000510	0.52	positive regulation of dendritic cell chemotaxis
GO:2000484	0.52	positive regulation of interleukin-8 secretion
GO:1904469	0.52	positive regulation of tumor necrosis factor secretion
GO:1902715	0.52	positive regulation of interferon-gamma secretion
GO:1900744	0.52	regulation of p38MAPK cascade
GO:0097029	0.52	mature conventional dendritic cell differentiation
GO:0071639	0.52	positive regulation of monocyte chemotactic protein-1 production
GO:0071636	0.52	positive regulation of transforming growth factor beta production
GO:0071346	0.52	cellular response to interferon-gamma
GO:0070555	0.52	response to interleukin-1
GO:0070374	0.52	positive regulation of ERK1 and ERK2 cascade
GO:0070241	0.52	positive regulation of activated T cell autonomous cell death
GO:0060135	0.52	maternal process involved in female pregnancy
GO:0051092	0.52	positive regulation of NF-kappaB transcription factor activity
GO:0050718	0.52	positive regulation of interleukin-1 beta secretion
GO:0046598	0.52	positive regulation of viral entry into host cell
GO:0046007	0.52	negative regulation of activated T cell proliferation
GO:0043305	0.52	negative regulation of mast cell degranulation
GO:0042346	0.52	positive regulation of NF-kappaB import into nucleus
GO:0034142	0.52	toll-like receptor 4 signaling pathway
GO:0034134	0.52	toll-like receptor 2 signaling pathway
GO:0032834	0.52	positive regulation of CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation involved in immune response
GO:0032753	0.52	positive regulation of interleukin-4 production
GO:0032720	0.52	negative regulation of tumor necrosis factor production
GO:0032682	0.52	negative regulation of chemokine production
GO:0032674	0.52	regulation of interleukin-5 production
GO:0002519	0.52	natural killer cell tolerance induction

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:0044424	0.84	intracellular part
GO:0044421	0.73	extracellular region part
GO:0043226	0.63	organelle
GO:0043227	0.62	membrane-bounded organelle
GO:0016020	0.60	membrane
GO:0044444	0.59	cytoplasmic part
GO:0005615	0.59	extracellular space
GO:0005737	0.55	cytoplasm
GO:0005576	0.52	extracellular region

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	1kitA	0.400	6.45	0.029	0.646	3.2.1.18	NA
2	0.060	1yr2A	0.406	6.44	0.058	0.652	3.4.21.26	NA
3	0.060	1j0mA	0.384	6.68	0.040	0.638	4.2.2.12	NA
4	0.060	2zxqA	0.410	5.89	0.036	0.610	3.2.1.97	19
5	0.060	3ixzA	0.374	7.17	0.059	0.663	3.6.3.10	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	0.88	2zhkA	0.393	0.59	0.950	0.396	1.84	UUU	complex1.pdb.gz	16,48,61,63,65,75,82,85,87,137
	2	0.35	2yxsA	0.403	1.13	0.374	0.413	0.95	LAT	complex2.pdb.gz	44,61,63,65,75

	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, Chengxin Zhang, Yang Li, Robin Pearce, Eric W. Bell, Yang Zhang. Folding non-homology proteins by coupling deep-learning contact maps with I-TASSER assembly simulations. In preparation, 2020.