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. 2004 Feb 27;32(4):1439–1447. doi: 10.1093/nar/gkh283

Figure 2.

Figure 2

Figure 2

Multiple alignment of the HerA protein family with selected proteins of the FtsK, TrwB/VirB4 and VirD4 ATPase families. Highly conserved residues are shown with bold type. The positions of the first and last residues of the aligned segments in the respective proteins are indicated by numbers. Poorly conserved regions not included in the alignment are denoted by the number of amino acid residues in parentheses. The secondary structure assignments are from the crystal structure of TrwB (PDB code 1E9R): H indicates α-helix and E indicates extended conformation (β-strand). The sequences are arranged in the following groups (designated to the right of the alignment): I, HerA proteins encoded within conserved archaeal operons; II, the remaining archaeal HerA proteins; III, bacterial HerA proteins; IV, bacteriophage ATPase; V, FtsK family ATPases; VI, TrwB/VirB4 family ATPases; VII, VirD4 family ATPases. The HerA family is represented in its entirety; for the other families, only selected sequences are shown. The sequences are denoted with the gene name followed by abbreviated species name, and the GI numbers. The S.acidocaldarius sequence has been submitted to the DDBJ/EMBL/GenBank databases under accession no. CAE51870. Species abbreviations are as follows: Archaea: Af, Archaeoglobus fulgidus; Ape, Aeropyrum pernix; Hsp, Halobacterium sp.; Mac, Methanosarcina acetivorans; Mj, Methanocaldococcus jannaschii; Mka, Methanopyrus kandleri; Mma, Methanosarcina mazei; Mta, Methanothermobacter thermoautotrophicus; Pab, Pyrococcus abyssi; Paer, Pyrobaculum aerophilum; Sac, Sulfolobus acidocaldarius; Sso, Sulfolobus solfataricus; Tac, Thermoplasma acidophilum; Tvo, Thermoplasma volcanium. Bacteria: Aae, Aquifex aeolicus; Atu, Agrobacterium tumefaciens; Bjap, Bradirhizobium japonicum; Bme, Brucella melitensis; Bper, Bordetella pertussis; Cau, Chloroflexus aurantiacus; Cje, Campylobacter jejuni; Ct, Chlamydia trachomatis; Ec, Escherichia coli; Fnu, Fusobacterium nucleatum; Hp, Helicobacter pylori; Lpne, Legionella pneumophila; Mtu, Mycobacterium tuberculosis; Npu, Nostoc punctiforme; Pae, Pseudomonas aeruginosa; Pput, Pseudomonas putida; Rme, Ralstonia metallidurans; Rsph, Rhodobacter sphaeroides; Rp, Rickettsia prowazekii; Sau, Staphylococcus aureus; Sme, Sinorhizobium meliloti; Ssp, Synechocystis sp.; Sty, Salmonella typhi; Tel, Thermosynechococcus elongatus BP-1; Tp, Treponema pallidum; Wol, Wolinella succinogenes.