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Figure 2 | Biology Direct

Figure 2

From: Unraveling the biochemistry and provenance of pupylation: a prokaryotic analog of ubiquitination

Figure 2

Multiple alignment of PafA-like proteins and other members of the GS fold. Proteins are labeled by gene name, organism abbreviation, and gi number, demarcated by underscores. Secondary structure assignments are given at the top of the alignment; E represents residues in β-strands while H represents residues in α-helices. Family names are listed to the right of the alignment, where new CAL is the new carboxylate-amine ligase of similar size as GCS2 mentioned in the text. Beyond the last helix shown in the alignment four additional conserved helices are predicted in PafA and are also found in the structures of other members of this superfamily. However, as these helices do not contribute to the active site and are poorly conserved in sequence we do not show them here. The residue coloring reflects at least 80% consensus conservation. Consensus similarity designations and coloring scheme are shown in the key. Absolutely conserved positions and residues essential for catalysis are shaded red. Organism abbreviations are as follows: Aae, Aquifex aeolicus; Aaur, Arthrobacter aurescens; Bmul, Burkholderia multivorans; Cbot, Clostridium botulinum; Ceff, Corynebacterium efficiens; Cfla, Chthoniobacter flavus; Dhaf, Desulfitobacterium hafniense; Dnod, Dichelobacter nodosus; Ecol, Escherichia coli; Faln, Frankia alni; Hasp, Halobacterium sp.; Hsap, Homo sapiens; Krad, Kineococcus radiotolerans; Lsp., Leptospirillum sp.; Mtub, Mycobacterium tuberculosis; Mxan, Myxococcus xanthus; Nham, Nitrobacter hamburgensis; Nsp., Nocardioides sp.; Ppac, Plesiocystis pacifica; Rbal, Rhodopirellula baltica; Rrub, Rhodospirillum rubrum; Scer, Saccharomyces cerevisiae; Scoe, Streptomyces coelicolor; Sery, Saccharopolyspora erythraea; Stro, Salinispora tropica; Styp, Salmonella typhimurium; Susi, Solibacter usitatus; Syn, Synechococcus sp.; Tfus, Thermobifida fusca; Tkod, Thermococcus kodakarensis.

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