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# D-I-TASSER results for Q92934

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

Summary of the Protein

Uniprot ID: Q92934
Protein Name: Bcl2-associated agonist of cell death
Gene Name: BAD

Input Sequence in FASTA format

>Q92934 (168 residues) MFQIPEFEPSEQEDSSSAERGLGPSPAGDGPSGSGKHHRQAPGLLWDASHQQEQPTSSSH HGGAGAVEIRSRHSSYPAGTEDDEGMGEEPSPFRGRSRSAPPNLWAAQRYGRELRRMSDE FVDSFKKGLPRPKSAGTATQMRQSSSWTRVFQSWWDRNLGRGSSAPSQ

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 | Q92934-D1 | 1-168 | 168 |  | MFQIPEFEPSEQEDSSSAERGLGPSPAGDGPSGSGKHHRQAPGLLWDASHQQEQPTSSSHHGGAGAVEIRSRHSSYPAGTEDDEGMGEEPSPFRGRSRSAPPNLWAAQRYGRELRRMSDEFVDSFKKGLPRPKSAGTATQMRQSSSWTRVFQSWWDRNLGRGSSAPSQ

Top 1 final models from D-I-TASSER

Click to view | Ranka | Download | Estimated TM-scoreb
| 1 | model1.pdb.gz | 0.4315
(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 | 6fhwA | 0.47 | 5.04 | 0.062 | 0.804 | model1_6fhwA.pdb.gz
| 2 | 1i5pA | 0.47 | 5.41 | 0.062 | 0.851 | model1_1i5pA.pdb.gz
| 3 | 2vn4A | 0.47 | 5.08 | 0.037 | 0.792 | model1_2vn4A.pdb.gz
| 4 | 6fhvA | 0.46 | 4.89 | 0.019 | 0.786 | model1_6fhvA.pdb.gz
| 5 | 1gaiA | 0.46 | 4.92 | 0.043 | 0.786 | model1_1gaiA.pdb.gz
| 6 | 7bzlA | 0.46 | 5.20 | 0.089 | 0.809 | model1_7bzlA.pdb.gz
| 7 | 5na6A | 0.46 | 5.08 | 0.039 | 0.786 | model1_5na6A.pdb.gz
| 8 | 1qz9A | 0.46 | 5.10 | 0.050 | 0.756 | model1_1qz9A.pdb.gz
| 9 | 5wznA | 0.45 | 5.51 | 0.051 | 0.827 | model1_5wznA.pdb.gz
| 10 | 3caiA | 0.45 | 4.89 | 0.086 | 0.714 | model1_3caiA.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:0019901 | 1.00 | protein kinase binding
GO:0008656 | 1.00 | cysteine-type endopeptidase activator activity involved in apoptotic process
GO:0005543 | 1.00 | phospholipid binding
GO:0019903 | 0.60 | protein phosphatase 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:0051716 | 1.00 | cellular response to stimulus
GO:0043065 | 1.00 | positive regulation of apoptotic process
GO:0042221 | 0.86 | response to chemical
GO:0071310 | 0.85 | cellular response to organic substance
GO:0044699 | 0.84 | single-organism process
GO:0008152 | 0.82 | metabolic process
GO:0080090 | 0.81 | regulation of primary metabolic process
GO:0060255 | 0.81 | regulation of macromolecule metabolic process
GO:0044763 | 0.81 | single-organism cellular process
GO:0031323 | 0.81 | regulation of cellular metabolic process
GO:0007165 | 0.81 | signal transduction
GO:0071704 | 0.80 | organic substance metabolic process
GO:0044281 | 0.80 | small molecule metabolic process
GO:0044238 | 0.80 | primary metabolic process
GO:0044237 | 0.80 | cellular metabolic process
GO:0031325 | 0.80 | positive regulation of cellular metabolic process
GO:0023051 | 0.80 | regulation of signaling
GO:0016043 | 0.80 | cellular component organization
GO:0010646 | 0.80 | regulation of cell communication
GO:1902589 | 0.79 | single-organism organelle organization
GO:0065008 | 0.79 | regulation of biological quality
GO:0051336 | 0.79 | regulation of hydrolase activity
GO:0051049 | 0.79 | regulation of transport
GO:0045937 | 0.79 | positive regulation of phosphate metabolic process
GO:0044802 | 0.79 | single-organism membrane organization
GO:0042325 | 0.79 | regulation of phosphorylation
GO:0035556 | 0.79 | intracellular signal transduction
GO:0032268 | 0.79 | regulation of cellular protein metabolic process
GO:0023056 | 0.79 | positive regulation of signaling
GO:0010647 | 0.79 | positive regulation of cell communication
GO:0010604 | 0.79 | positive regulation of macromolecule metabolic process
GO:0007005 | 0.79 | mitochondrion organization
GO:0006807 | 0.79 | nitrogen compound metabolic process
GO:2000026 | 0.78 | regulation of multicellular organismal development
GO:1904951 | 0.78 | positive regulation of establishment of protein localization
GO:1901698 | 0.78 | response to nitrogen compound
GO:1901564 | 0.78 | organonitrogen compound metabolic process
GO:1901135 | 0.78 | carbohydrate derivative metabolic process
GO:0097193 | 0.78 | intrinsic apoptotic signaling pathway
GO:0051050 | 0.78 | positive regulation of transport
GO:0048878 | 0.78 | chemical homeostasis
GO:0046902 | 0.78 | regulation of mitochondrial membrane permeability
GO:0045595 | 0.78 | regulation of cell differentiation
GO:0043549 | 0.78 | regulation of kinase activity
GO:0043281 | 0.78 | regulation of cysteine-type endopeptidase activity involved in apoptotic process
GO:0043085 | 0.78 | positive regulation of catalytic activity
GO:0042327 | 0.78 | positive regulation of phosphorylation
GO:0032270 | 0.78 | positive regulation of cellular protein metabolic process
GO:0022607 | 0.78 | cellular component assembly
GO:0014070 | 0.78 | response to organic cyclic compound
GO:0009719 | 0.78 | response to endogenous stimulus
GO:0006950 | 0.78 | response to stress
GO:0006796 | 0.78 | phosphate-containing compound metabolic process
GO:0006139 | 0.78 | nucleobase-containing compound metabolic process
GO:2000078 | 0.77 | positive regulation of type B pancreatic cell development
GO:0071316 | 0.77 | cellular response to nicotine
GO:0050679 | 0.77 | positive regulation of epithelial cell proliferation
GO:0046931 | 0.77 | pore complex assembly
GO:0046034 | 0.77 | ATP metabolic process
GO:0046031 | 0.77 | ADP metabolic process
GO:0044342 | 0.77 | type B pancreatic cell proliferation
GO:0042593 | 0.77 | glucose homeostasis
GO:0033133 | 0.77 | positive regulation of glucokinase activity
GO:0032024 | 0.77 | positive regulation of insulin secretion
GO:0010918 | 0.77 | positive regulation of mitochondrial membrane potential
GO:0009628 | 0.77 | response to abiotic stimulus
GO:0006919 | 0.77 | activation of cysteine-type endopeptidase activity involved in apoptotic process
GO:0048583 | 0.61 | regulation of response to stimulus
GO:0048519 | 0.59 | negative regulation of biological process
GO:0009966 | 0.59 | regulation of signal transduction
GO:0048584 | 0.58 | positive regulation of response to stimulus
GO:0048523 | 0.58 | negative regulation of cellular process
GO:0043170 | 0.58 | macromolecule metabolic process
GO:2001233 | 0.57 | regulation of apoptotic signaling pathway
GO:0009967 | 0.57 | positive regulation of signal transduction
GO:2001235 | 0.56 | positive regulation of apoptotic signaling pathway
GO:0060341 | 0.56 | regulation of cellular localization
GO:0019538 | 0.56 | protein metabolic process
GO:0010822 | 0.56 | positive regulation of mitochondrion organization
GO:0033554 | 0.55 | cellular response to stress
GO:0007166 | 0.55 | cell surface receptor signaling pathway
GO:0006915 | 0.55 | apoptotic process
GO:0097202 | 0.54 | activation of cysteine-type endopeptidase activity
GO:0097191 | 0.54 | extrinsic apoptotic signaling pathway
GO:0090200 | 0.54 | positive regulation of release of cytochrome c from mitochondria
GO:0071214 | 0.54 | cellular response to abiotic stimulus
GO:0045918 | 0.54 | negative regulation of cytolysis
GO:0009605 | 0.54 | response to external stimulus
GO:0001666 | 0.54 | response to hypoxia

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:0005739 | 1.00 | mitochondrion
GO:0005829 | 0.76 | cytosol
GO:0044446 | 0.68 | intracellular organelle part
GO:0016020 | 0.67 | membrane
GO:0044429 | 0.64 | mitochondrial part
GO:0031966 | 0.63 | mitochondrial membrane
GO:0005741 | 0.62 | mitochondrial outer membrane

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 | 1w0eA | 0.422 | 4.99 | 0.032 | 0.702 | 1.14.13.67 1.14.14.1 | NA
| 2 | 0.060 | 1o7xC | 0.431 | 5.41 | 0.069 | 0.750 | 2.3.3.1 | NA
| 3 | 0.060 | 2w0aA | 0.407 | 5.35 | 0.019 | 0.702 | 1.14.13.70 | NA
| 4 | 0.060 | 2vn7A | 0.462 | 4.97 | 0.043 | 0.792 | 3.2.1.3 | NA
| 5 | 0.060 | 1vgmA | 0.442 | 5.30 | 0.049 | 0.750 | 4.1.3.7 | 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 | 0.01 | 1qd10 | 0.424 | 5.65 | 0.059 | 0.786 | 0.14 | III | complex1.pdb.gz | 129,141,153,154
| 2 | 0.01 | 3tw6A | 0.364 | 5.48 | 0.031 | 0.649 | 0.20 | COA | complex2.pdb.gz | 110,111,112,113
| 3 | 0.01 | 1glmA | 0.462 | 4.94 | 0.043 | 0.792 | 0.28 | UUU | complex3.pdb.gz | 111,112,113,137,150,151
| 4 | 0.01 | 3rboA | 0.440 | 5.12 | 0.058 | 0.726 | 0.21 | ADP | complex4.pdb.gz | 114,115,116,117
| 5 | 0.01 | 6ctsA | 0.444 | 5.17 | 0.046 | 0.756 | 0.13 | CIC | complex5.pdb.gz | 114,134,135
| 6 | 0.01 | 3eqmA | 0.443 | 5.07 | 0.051 | 0.738 | 0.11 | ASD | complex6.pdb.gz | 84,86,87
| 7 | 0.01 | 6cscB | 0.439 | 5.50 | 0.047 | 0.768 | 0.22 | COF | complex7.pdb.gz | 117,134,135,136
| 8 | 0.01 | 3tw6C | 0.359 | 5.38 | 0.033 | 0.631 | 0.20 | PAE | complex8.pdb.gz | 140,141,142
| 9 | 0.01 | 3sinA | 0.438 | 5.06 | 0.052 | 0.720 | 0.11 | ZD9 | complex9.pdb.gz | 136,138,140
| 10 | 0.01 | 3tw6C | 0.359 | 5.38 | 0.033 | 0.631 | 0.23 | COA | complex10.pdb.gz | 86,90,91,94
| 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.