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# 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 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.

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 | Ranka | Download | Estimated TM-scoreb
| 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 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)
Click to view | Rank | PDB Hit | TM-score | RMSDa | IDENa | 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) | RMSDa is the RMSD between residues that are structurally aligned by TM-align.
(d) | IDENa 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 | CscoreGO | 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) | CscoreGO is the confidence score of predicted GO terms. CscoreGO 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 CscoreGO:
[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 | CscoreGO | 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) | CscoreGO is the confidence score of predicted GO terms. CscoreGO 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 CscoreGO:
[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 | CscoreGO | 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) | CscoreGO is the confidence score of predicted GO terms. CscoreGO 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 CscoreGO:
[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
Click to view | Rank | CscoreEC | PDB Hit | TM-score | RMSDa | IDENa | 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) | CscoreEC is the confidence score for the Enzyme Commission (EC) number prediction. CscoreEC 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) | RMSDa is the RMSD between residues that are structurally aligned by TM-align.
(d) | IDENa 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 | CscoreLB | PDB Hit | TM-score | RMSDa | IDENa | 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) | CscoreLB is the confidence score of predicted binding site. CscoreLB 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) | RMSDa the RMSD between residues that are structurally aligned by TM-align.
(e) | IDENa 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.