Sample Evolutionary Traces
The following sample Evolutionary Traces were utilized in:
Yao, H., D. M. Kristensen, I. Mihalek, M. E. Sowa, C. Shaw, M. Kimmel, L. Kavraki, and O. Lichtarge. 2003. "An Accurate, Sensitive, and Scalable Method to Identify Functional Sites in Protein Structures." J Mol Biol. 326:255-261.
For each protein the table shows its Protein Data Bank (PDB) code, Enzyme Classification (EC) number, size, number of sequences in the trace alignment, minimum percent sequence identity of the alignment evolutionary breadth (E=Eukaryota, B=Bacteria, A=Archaea, V=Viruses), and, for each of the 4 statistics, the %fraction of ranks with significant trace clusters that also have a significant overlap with the functional site. TCR=Total Connected Residues, LCO=Largest Cluster Overlap; AO=Average Overlap; HG=Hypergeometric Distribution. Functional sites are then shown in green, and finally Trace clusters are colored individually: red=largest, blue=second largest, etc. Single-residue clusters are black. Ligands are colored yellow/orange or blue if they are peptides. There are no ligands shown in the EC set.
Protein-ligand set:
Name |
PDB
|
EC #
|
Protein
|
No.
|
Minimum
|
Evolutionary
|
TCR |
LCO |
AO |
HG |
SGI set:
Name |
PDB
|
EC #
|
Protein
|
No.
|
Minimum
|
Evolutionary
|
TCR |
LCO |
AO |
HG |
EC set:
Name |
PDB
|
EC #
|
Protein
|
No.
|
Minimum
|
Evolutionary
|
TCR |
LCO |
AO |
HG |
The following sample Evolutionary Traces are displayed following the format presented in:
Madabushi, S., H. Yao, M. Marsh, D.M. Kristensen, A. Philippi, M.E. Sowa, and O. Lichtarge. 2002. "Structural Clusters of Evolutionary Trace Residues are Statistically Significant" J. Mol. Biol. 316:1 (Feb 8), p139-154.
In addition to the full name of the protein, also listed for each are the PDB identifier, class, size (amino acids), known function, number of sequences in the multiple sequence alignment, minimum percent identity between sequences in the alignment and the selected protein structure, the best significance level the protein achieves using the "Number of Clusters" statistical method, the best significance level the protein achieves using the "Size of Largest Cluster" method, and the evolutionary breadth of the protein family tree (E = eukaryotic, P = prokaryotic, V = viral).
Name |
PDB |
Class |
Size |
Function |
No. |
Min % |
Sig. of |
Sig. of |
Evolutionary |
| Regulator of G-protein signaling | 1fqi | all alpha proteins | 133 | regulator of G-protein signaling | 43 | 43 | 0.3 | 0.3 | E |
| Rhodopsin | 1f88 | membrane and cell surface protein | 338 | signaling protein | 59 | 33 | 0.3 | 0.3 | E |
| Annexin III | 1axn | all alpha proteins | 323 | calcium/phospholipid binding protein | 70 | 40 | 0.3 | 5 | E |
| Alpha amylase | 1bag | all beta proteins | 425 | alpha-amylase | 55 | 24 | 0.3 | 0.3 | E+P |
| HIV Reverse Transcriptase | 1c1b | alpha and beta proteins | 536 | reverse transcriptase | 278 | 61 | 1 | 5 | V |
| Phosphoglycerate kinase | 16pk | alpha and beta proteins | 415 | kinase | 95 | 41 | 0.3 | 0.3 | E+P |
| citrate synthase | 1a59 | all alpha proteins | 377 | synthase | 63 | 32 | 0.3 | 0.3 | E+P |
| Dd-Peptidase Penicillin-Target Enzyme | 3pte | ||||||||
| Serine/Threonine phosphatase | 1a6q | alpha and beta proteins | 363 | hydrolase | 58 | 38 | 0.3 | 0.3 | E |
| Peroxidase | 1aru | all alpha proteins | 336 | peroxidase | 29 | 55 | 0.3 | 0.3 | E |
| Protein phospatase-1 | 1fjm | alpha and beta proteins | 294 | hydrolase | 68 | 65 | 0.3 | 0.3 | E |
| Cyclins | 1fin-A | all alpha proteins | 298 | transferase | 37 | 64 | 0.3 | 0.3 | E |
| Signal sequence recognition protein | 1ng1 | all alpha proteins | 294 | 73 | 45 | 0.3 | 0.3 | E+P | |
| Endonuclease IV | 1qum | alpha and beta proteins | 279 | endonuclease | 27 | 39 | 0.3 | 0.3 | E+P |
| 2,5-diketo-D-gluconic acid reductase A | 1a80 | alpha and beta proteins | 277 | Oxidoreductase | 83 | 46 | 0.3 | 0.3 | E+P |
| Deacetoxycephalosporin C | 1rxg | all beta proteins | 275 | Oxidoreductase | 24 | 25 | 0.3 | 1 | E+P |
| Cyclins | 1fin-B | all alpha proteins | 260 | transferase | 23 | 34 | 0.3 | 0.3 | E |
| Triosephosphate isomerase | 1amk | alpha and beta proteins | 250 | gluconeogenesis | 73 | 47 | 0.3 | 0.3 | E+P |
| Indole-3-glyceophosphate synthase | 1a53 | alpha and beta proteins | 247 | Synthase | 19 | 30 | 0.3 | 0.3 | E+P |
| Estrogen receptor | 3ert | all alpha proteins | 247 | Nuclear receptor | 93 | 44 | 0.3 | 0.3 | E |
| Adenylate kinase | 1aky | alpha and beta proteins | 218 | phosphotransferase | 42 | 45 | 0.3 | 0.3 | E+P |
| HSP-90 | 1am1 | alpha and beta proteins | 213 | chaperone | 78 | 55 | 0.3 | 0.3 | E+P |
| Dihydropteroate Synthase | 1aj2 | alpha and beta proteins | 282 | Synthase | 42 | 37 | 0.3 | 0.3 | P |
| Astacin | 1ast | alpha and beta proteins | 200 | Metalloproteinase (hydrolase) | 38 | 44 | 0.3 | 0.3 | E |
| Growth hormone receptor | 1a22-B | all alpha proteins | 192 | Growth hormone receptor | 21 | 30 | 1 | 0.3 | E |
| Growth hormone | 1a22-A | all alpha proteins | 180 | Growth hormone | 67 | 36 | 0.3 | 0.3 | E |
| Tpr1 domain of Hop | 1elr | all alpha proteins | 128 | Chaperone | 41 | 30 | 0.3 | 1 | E+P |
| Pseudoazurin | 1bqk | all beta proteins | 124 | electron transport | 29 | 37 | 1 | 10 | E+P |
| Acyl CoA binding protein | 1aca | all alpha proteins | 86 | Binding protein | 38 | 46 | 5 | 0.3 | E |
| Biotinyl domain | 1bdo | beta proteins | 80 | Carboxylase | 37 | 45 | >30 | 20 | E+P |
| Poly-A binding protein | 1cvj | alpha and beta proteins | 169 | Gene regulation | 73 | 26 | 0.3 | 0.3 | E |
| Myoglobin | 1a6m | all alpha proteins | 151 | Oxygen transport | 171 | 35 | 5 | 0.3 | E |
| Galectin-3 CRD | 1a3k | all beta proteins | 137 | Galectin carbohydrate recognition domain | 70 | 32 | 1 | 1 | E |
| Tpr2a-domain of Hop | 1elw | all alpha proteins | 117 | Chaperone | 42 | 41 | 1 | 1 | E |
| Pyruvate decarboxylase | 1pvd | alpha and beta proteins | 537 | Carbon-Carbon lyase | 43 | 37 | 0.3 | 0.3 | E+P |
| Mannose binding protein | 2msb | alpha and beta proteins | 113 | Binds Mannose | 71 | 34 | 5 | 0.3 | E |
| c-Src tyrosine kinase; SH3 | 1nlo | all beta proteins | 56 | Tyrosine Kinase | 71 | 37 | 5 | 0.3 | E |
| c-Src tyrosine kinase; SH2 | 1a09 | alpha and beta proteins | 106 | Tyrosine Kinase | 137 | 34 | 1 | 0.3 | E |