Figure 2

Predicted protein sequence features of HMM domains. (A) A protein sequence HMM logo indicates the relative probabilities of amino acid residues (single letter code) at positions within the canonical 25-residue domain. The logo is shown in tandem duplicate (horizontal arrows). Heights of letters correspond to the relative entropy, indicating the prevalence (observed vs. a priori expected frequency) of residues at the respective position. Positions of conserved hydrophobic residues occurring periodically in the domains are indicated by red arrows. (B-I) Helical wheel projections of HMM domains from assorted taxa. Sequences of 36 residues (to encompass or bridge individual HMM motifs) represent adjacent, canonical domains. Amino acids are denoted by residue number in the ORF and by hydrophobicity as described in Methods: hydrophobic (red-shaded diamonds), hydrophilic (circles), negatively-charged (triangles) and positively-charged (pentagons). Asymmetrically-distributed hydrophobic residues correspond to conserved positions in the logo shown in (A). Directions (arrows) and magnitudes of hydrophobic moments are indicated. Sequences begin with the top inner residue shown and extend clockwise, N- to C- terminal, into the page. Examples include the following taxa, ORFs, residues and sequences: (B) Mmm SC PG1; gi|42561534|ref|NP_975985.1| (LppQ); 243..278 WKTANVKTMRSMFSDTKQFNQDISSWNVSNVKNMKN. (C) Mcc Kid; gi|83319816|ref|YP_424254.1| (MCAP_0268); 210..245 WDTSNLETIDQMFVGAKKFNQDISKWDVSNVRIMDS. (D) Mesoplasma florum L1; gi|50365263|ref|YP_053688.1|; 492..527 WDTSKVTDMSNMFSGSSAFNGDISKWNTSSVTNMSG. (E) Helicobacter hepaticus ATCC 51449; gi|32265549|ref|NP_859581.1|; 638..673 KAKKFNQPLESWNVSNVANMRNMFGETDVFNQPLDK. (F) Microscilla marina ATCC 23134; gi|124008438|ref|ZP_01693132.1|; 243..278 NMGAMFSAAVAFNQPLEGWNTSQVTNMGGMFHWAKV. (G) Salinibacter ruber DSM13855 (plasmid pSR35); gi|83816872|ref|YP_446962.1|; 357..392. WDVSGVTDMSEMFEGAASFNQDISGWDVSNVTDMFE. (H) Ostreococcus tauri; gi|116055666|emb|CAL57751.1|; 852..887 NATEFNQDIAAWNTTSVANMAEMFSNAAAFNQNISA. (I) Micromonas sp. RCC299; gi|226517946|gb|ACO63939.1|; 509..544 WDTSSVTTMYRMFNEAAAFNQDIGRWDTSSVTDMKE.