TABLE 2.

Response regulators with unusual domain organizations

Family name, domain organizationTotal no.Example Output domain
Organism nameGene name (accession no.)Pfam entryCOG no.Reference(s)
DNA-binding, REC-HTH
    Spo0A-like15 Bacillus subtilis BSU24220 (CAB14353 )PB00515478
    YcbB (GlnL)-like14 Bacillus subtilis BSU02450 (CAB12039 )PF08664113
    REC-SARP (REC-HTH-BTAD)5 Deinococcus radiodurans DR2556 (AAF12095 )PF00486 PF037043947152, 154
    REC-CRP2 Gloeobacter violaceus glr1768 (BAC89709 )PF00325066449
DNA-binding, HTH-REC
    RpoE-REC15 Caulobacter crescentus CC3477 (AAK25439 )PF04542 PF04545159526
    MerR-REC6 Treponema denticola TDE0855 (AAS11346 )PF00376245225
    BetR-REC5 Chromobacterium violaceum CV0537 (AAQ58214 )PF08667This work
    AlpA-REC2 Dehalococcoides ethenogenes DET1294 (AAW39407 )PF059303311139
    HlxR-REC1 Haloarcula marismortui rrnB0301 (AAV48466 )PF016381733155
    LysR-REC1 Silicibacter pomeroyi SPO3037 (AAV96273 )PF00126058393
RNA-binding, CsrA-REC1 Rhodopirellula baltica RB8820 (CAD75938 )PF0259950
Enzymatic
    Ser/Thr protein kinase REC-RsbW or REC-RsbU-RsbW14 Leptospira interrogans LA2951 (AAN50149 )2172153
    Phosphoaspartate phosphatase REC-CheC13 Vibrio cholerae VCA0189 (AAF96102 )PF04509177698, 129
    Adenylate cyclase REC-ACyc6 Bradyrhizobium japonicum Blr2288 (BAC47553 )PF002112114156
    ParA family ATPase REC-Soj5 Ralstonia solanacearum RSc0653 (CAD14183 )PF00991045577
    NAD(P)H:disulfide oxidoreductase REC-TrxB3 Nocardia farcinica Nfa52850 (BAD60137 )PF00070234572
    Poly-N-acetylglucos amine deacetylase REC-LmbE1 Leifsonia xyli Lxx09320 (AAT88820 )PF025852120132
    Glycosyltransferase REC-WcaA1 Methanobacterium thermoauto-trophicum MTH548 (AAB85054 )PF005351215133
    PilB-like ATPase REC-PulE2 Dechloromonas aromatica Daro_0966 (AAZ45722 )PF004372804102
    Predicted phosphatase REC-PglZ1 Porphyromonas gingivalis PG0928 (AAQ66063 )PF08665This work
    Predicted phosphodiesterase REC-HDOD4 Vibrio cholerae VC1081 (AAF94240 )PF086681639This work
    Ser/Thr protein kinase REC-STYK1 Rhodopirellula baltica RB10329 (CAD78826 )PF000690515117
Protein-protein interaction
    REC-TPR (VieB-like)20 Desulfovibrio vulgaris DVU2937 (AAS97409 )PF00515045721
    Hnr-like18 Escherichia coli RssB (AAC74317 )15
    REC-HPt9 Xylella fastidiosa XF2359 (AAF85158 )PF01627219863
    REC-PAS4 Haloarcula marismortui RrnAC0674 (AAV45676 )PF016272202136
    REC-GAF4 Geobacter sulfurreducens GSU1316 (AAR34692 )PF01590220354
Ligand-binding
    REC-PilZ2 Geobacter sulfurreducens GSU0877 (AAR34207 )PF0723832154
    REC-cNMPbinding2 Bdellovibrio bacteriovorus Bd3065 (CAE80821 )PF00027066433
Uncharacterized
    PatA-type21 Nostoc sp. PCC7120all0521 (BAB72479 )80, 83
    Ycf55-type7 Nostoc sp. PCC7120alr0960 (BAB72917 )This work
    REC-HalX9 Halobacterium sp. NRC-1VNG2036G (AAG20197 )PF08663This work
    OsaB-type2 Streptomyces coelicolor SCO5749 (CAA19850 )20