Alignments

Reliably structurally-aligned portions are in blue; portions not structurally alignable due to gaps in the structures are in red. Files with a ".#.htm" ending are split up into seperate pages for printing. Groups of lines seperated by lines of "=" are 65%+ identical to a sequence with known structure - in our terminology, these are clusters. Areas not in blue (reliably structurally-aligned) are only aligned within clusters.

Sequences with known structure have names which are in all-uppercase or (for less-important cases) have a name beginning with a PDB file and chain id (starting with a number from 1-9, then four letters or numbers). Names of sequences from archaea are in purple; names of sequences from fungi or metazoa are in red; names of sequences from plants are in green; names of sequences from bacteria are in blue.

The postscript files are plots (via the EMBOSS plotcon program) of the degree of residue conservation vs the position along the alignment, with a window of 20 residues. These were done with an all-positive matrix (namely ESIMILARITY+1), so gaps - including at the ends - are considered the same as amino acids not matching at all.

• Alcohol Dehydrogenase Class I (Note that primates have up to three different isozymes for ADH1 (Alpha, Beta, and Gamma). Horses have two isozymes; the sequence shown is for the ethanol-active, not the steroid-active, isozyme.)
• ADH1.plotcon.ESIMILARITY_P.w20.ps
  1. ADH1.showalign.1.htm
  2. ADH1.showalign.2.htm
  3. ADH1.showalign.3.htm
  4. ADH1.showalign.4.htm
  5. ADH1.showalign.5.htm
  6. ADH1.showalign.6.htm
• Catalase
• Catalase.plotcon.ESIMILARITY_P.w20.ps
  1. Catalase.showalign.1.htm
  2. Catalase.showalign.2.htm
  3. Catalase.showalign.3.htm
  4. Catalase.showalign.4.htm
  5. Catalase.showalign.5.htm
  6. Catalase.showalign.6.htm
  7. Catalase.showalign.7.htm
  8. Catalase.showalign.8.htm
  9. Catalase.showalign.9.htm
• Cellulase A (glycosyl hydrolase 5; exo-1,3-beta-glucanase)
• Cellulase_A.plotcon.ESIMILARITY_P.w20.ps
  1. Cellulase_A.showalign.1.htm
  2. Cellulase_A.showalign.2.htm
  3. Cellulase_A.showalign.3.htm
  4. Cellulase_A.showalign.4.htm
  5. Cellulase_A.showalign.5.htm
  6. Cellulase_A.showalign.6.htm
  7. Cellulase_A.showalign.7.htm
• Cellulase B (glycosyl hydrolase 6; 1,4-beta-cellobiohydrolase)
• Cellulase_B.plotcon.ESIMILARITY_P.w20.ps
  1. Cellulase_B.showalign.1.htm
  2. Cellulase_B.showalign.2.htm
  3. Cellulase_B.showalign.3.htm
  4. Cellulase_B.showalign.4.htm
  5. Cellulase_B.showalign.5.htm
  6. Cellulase_B.showalign.6.htm
  7. Cellulase_B.showalign.7.htm
• Cellulase C (glycosyl hydrolase 7; 1,4-beta-cellobiosidase or endo-1,4-beta-glucanase)
• Cellulase_C.plotcon.ESIMILARITY_P.w20.ps
  1. Cellulase_C.showalign.1.htm
  2. Cellulase_C.showalign.2.htm
  3. Cellulase_C.showalign.3.htm
  4. Cellulase_C.showalign.4.htm
  5. Cellulase_C.showalign.5.htm
  6. Cellulase_C.showalign.6.htm
  7. Cellulase_C.showalign.7.htm
  8. Cellulase_C.showalign.8.htm
  9. Cellulase_C.showalign.9.htm
• Cellulase F (glycosyl hydrolase 10; endo-1,4-beta-xylanase)
• Cellulase_F_xylanase.plotcon.ESIMILARITY_P.w20.ps
  1. Cellulase_F_xylanase.showalign.1.htm
  2. Cellulase_F_xylanase.showalign.2.htm
  3. Cellulase_F_xylanase.showalign.3.htm
  4. Cellulase_F_xylanase.showalign.4.htm
  5. Cellulase_F_xylanase.showalign.5.htm
  6. Cellulase_F_xylanase.showalign.6.htm
  7. Cellulase_F_xylanase.showalign.7.htm
• Cellulase G (glycosyl hydrolase 11; endo-1,4-beta-xylanase; 3.2.1.8)
• Cellulase_G_xylanase.plotcon.ESIMILARITY_P.w20.ps
  1. Cellulase_G_xylanase.showalign.1.htm
  2. Cellulase_G_xylanase.showalign.2.htm
  3. Cellulase_G_xylanase.showalign.3.htm
  4. Cellulase_G_xylanase.showalign.4.htm
  5. Cellulase_G_xylanase.showalign.5.htm
  6. Cellulase_G_xylanase.showalign.6.htm
  7. Cellulase_G_xylanase.showalign.7.htm
  8. Cellulase_G_xylanase.showalign.8.htm
  9. Cellulase_G_xylanase.showalign.9.htm
  10. Cellulase_G_xylanase.showalign.10.htm
  11. Cellulase_G_xylanase.showalign.11.htm
  12. Cellulase_G_xylanase.showalign.12.htm
  13. Cellulase_G_xylanase.showalign.13.htm
• Cellulase H (glycosyl hydrolase 12; endo-beta-1,4-glucanase)
• Cellulase_H.plotcon.ESIMILARITY_P.w20.ps
  1. Cellulase_H.showalign.1.htm
  2. Cellulase_H.showalign.2.htm
  3. Cellulase_H.showalign.3.htm
  4. Cellulase_H.showalign.4.htm
  5. Cellulase_H.showalign.5.htm
  6. Cellulase_H.showalign.6.htm
  7. Cellulase_H.showalign.7.htm
• Cinnamyl Alcohol Dehydrogenase
• Cinnamyl_ADH.plotcon.ESIMILARITY_P.w20.ps
  1. Cinnamyl_ADH.showalign.1.htm
  2. Cinnamyl_ADH.showalign.2.htm
  3. Cinnamyl_ADH.showalign.3.htm
  4. Cinnamyl_ADH.showalign.4.htm
  5. Cinnamyl_ADH.showalign.5.htm
• Copper/Zinc Superoxide Dismutase
• CuZnSOD.plotcon.ESIMILARITY_P.w20.ps
  1. CuZnSOD.showalign.1.htm
  2. CuZnSOD.showalign.2.htm
  3. CuZnSOD.showalign.3.htm
  4. CuZnSOD.showalign.4.htm
• Glutathione-S-Transferase Class Pi
• GST_Pi.plotcon.ESIMILARITY_P.w20.ps
  1. GST_Pi.showalign.1.htm
  2. GST_Pi.showalign.2.htm
  3. GST_Pi.showalign.3.htm
  4. GST_Pi.showalign.4.htm
  5. GST_Pi.showalign.5.htm
• Glutathione-S-Transferase Class Sigma or Glutathione-dependent Prostaglandin D Synthase
• GST_Sigma_prostaglandin_D_synthase.plotcon.ESIMILARITY_P.w20.ps
  1. GST_Sigma_prostaglandin_D_synthase.showalign.1.htm
  2. GST_Sigma_prostaglandin_D_synthase.showalign.2.htm
  3. GST_Sigma_prostaglandin_D_synthase.showalign.3.htm
  4. GST_Sigma_prostaglandin_D_synthase.showalign.4.htm
  5. GST_Sigma_prostaglandin_D_synthase.showalign.5.htm
• Glutathione-S-Transferase Class Zeta
• GST_Zeta.plotcon.ESIMILARITY_P.w20.ps
  1. GST_Zeta.showalign.1.htm
  2. GST_Zeta.showalign.2.htm
  3. GST_Zeta.showalign.3.htm
  4. GST_Zeta.showalign.4.htm
• Hemoglobin Alpha or Hemoglobin V (Hemoglobin V is for sea lamprey, from before the alpha/beta split, which has a total of 6 globins, the 5th being the major one)
• Hemoglobin_Alpha.plotcon.ESIMILARITY_P.w20.ps
  1. Hemoglobin_Alpha.showalign.1.htm
  2. Hemoglobin_Alpha.showalign.2.htm
  3. Hemoglobin_Alpha.showalign.3.htm
• Myoglobin
• Myoglobin.plotcon.ESIMILARITY_P.w20.ps
  1. Myoglobin.showalign.1.htm
  2. Myoglobin.showalign.2.htm
  3. Myoglobin.showalign.3.htm
  4. Myoglobin.showalign.4.htm
• Orotidine-5'-phosphate decarboxylase
• ORO.plotcon.ESIMILARITY_P.w20.ps
  1. ORO.showalign.1.htm
  2. ORO.showalign.2.htm
  3. ORO.showalign.3.htm
  4. ORO.showalign.4.htm
• Poly(A) Polymerase
• Poly_A_polymerase.plotcon.ESIMILARITY_P.w20.ps
  1. Poly_A_polymerase.showalign.1.htm
  2. Poly_A_polymerase.showalign.2.htm
  3. Poly_A_polymerase.showalign.3.htm
  4. Poly_A_polymerase.showalign.4.htm
  5. Poly_A_polymerase.showalign.5.htm
  6. Poly_A_polymerase.showalign.6.htm
  7. Poly_A_polymerase.showalign.7.htm
  8. Poly_A_polymerase.showalign.8.htm
  9. Poly_A_polymerase.showalign.9.htm
  10. Poly_A_polymerase.showalign.10.htm
  11. Poly_A_polymerase.showalign.11.htm
  12. Poly_A_polymerase.showalign.12.htm
  13. Poly_A_polymerase.showalign.13.htm
  14. Poly_A_polymerase.showalign.14.htm
• Rad51/RadA/RecA
• RecA.plotcon.ESIMILARITY_P.w20.ps
  1. RecA.showalign.1.htm
  2. RecA.showalign.2.htm
  3. RecA.showalign.3.htm
  4. RecA.showalign.4.htm
  5. RecA.showalign.5.htm
  6. RecA.showalign.6.htm
  7. RecA.showalign.7.htm
  8. RecA.showalign.8.htm
  9. RecA.showalign.9.htm
  10. RecA.showalign.10.htm
  11. RecA.showalign.11.htm
  12. RecA.showalign.12.htm
  13. RecA.showalign.13.htm
  14. RecA.showalign.14.htm
  15. RecA.showalign.15.htm
  16. RecA.showalign.16.htm
  17. RecA.showalign.17.htm
  18. RecA.showalign.18.htm
• Sorbitol Dehydrogenase
• Sorbitol_DH.plotcon.ESIMILARITY_P.w20.ps
  1. Sorbitol_DH.showalign.1.htm
  2. Sorbitol_DH.showalign.2.htm
  3. Sorbitol_DH.showalign.3.htm
  4. Sorbitol_DH.showalign.4.htm
  5. Sorbitol_DH.showalign.5.htm
  6. Sorbitol_DH.showalign.6.htm
  7. Sorbitol_DH.showalign.7.htm
• TATA-Binding Protein (TF2D)
• TBP.plotcon.ESIMILARITY_P.w20.ps
  1. TBP.showalign.1.htm
  2. TBP.showalign.2.htm
  3. TBP.showalign.3.htm
  4. TBP.showalign.4.htm
  5. TBP.showalign.5.htm
  6. TBP.showalign.6.htm
  7. TBP.showalign.7.htm
  8. TBP.showalign.8.htm
  9. TBP.showalign.9.htm
• Triosephosphate Isomerase
• Triosephosphate_isomerase.plotcon.ESIMILARITY_P.w20.ps
  1. Triosephosphate_isomerase.showalign.1.htm
  2. Triosephosphate_isomerase.showalign.2.htm
  3. Triosephosphate_isomerase.showalign.3.htm
  4. Triosephosphate_isomerase.showalign.4.htm
  5. Triosephosphate_isomerase.showalign.5.htm
  6. Triosephosphate_isomerase.showalign.6.htm
  7. Triosephosphate_isomerase.showalign.7.htm
  8. Triosephosphate_isomerase.showalign.8.htm
  9. Triosephosphate_isomerase.showalign.9.htm
• Ubiquitin Conjugating Enzyme (E2-L3; E2-24)
• UBC.plotcon.ESIMILARITY_P.w20.ps
  1. UBC.showalign.1.htm
  2. UBC.showalign.2.htm
  3. UBC.showalign.3.htm
  4. UBC.showalign.4.htm
• Eukaryotic Initiation Factor 2a
• eIF2a.plotcon.ESIMILARITY_P.w20.ps
  1. eIF2a.showalign.1.htm
  2. eIF2a.showalign.2.htm
  3. eIF2a.showalign.3.htm
  4. eIF2a.showalign.4.htm
  5. eIF2a.showalign.5.htm
  6. eIF2a.showalign.6.htm
  7. eIF2a.showalign.7.htm
  8. eIF2a.showalign.8.htm
  9. eIF2a.showalign.9.htm
• Eukaryotic Initiation Factor 4e
• eIF4e.plotcon.ESIMILARITY_P.w20.ps
  1. eIF4e.showalign.1.htm
  2. eIF4e.showalign.2.htm
  3. eIF4e.showalign.3.htm
  4. eIF4e.showalign.4.htm
• Eukaryotic Initiation Factor 6
• eIF6.plotcon.ESIMILARITY_P.w20.ps
  1. eIF6.showalign.1.htm
  2. eIF6.showalign.2.htm
  3. eIF6.showalign.3.htm
  4. eIF6.showalign.4.htm
  5. eIF6.showalign.5.htm
• Eukaryotic Termination Factor 2a
• eTF2a.plotcon.ESIMILARITY_P.w20.ps
  1. eTF2a.showalign.1.htm
  2. eTF2a.showalign.2.htm
  3. eTF2a.showalign.3.htm
  4. eTF2a.showalign.4.htm
  5. eTF2a.showalign.5.htm
  6. eTF2a.showalign.6.htm
  7. eTF2a.showalign.7.htm

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