TABLE 1.
Summary of iron-related protein families that are represented as pHMMs in FeGenie.
| Category | Function | Protein Families |
| Iron acquisition | Iron(II)/(III) transport | EfeUOB1, FbpABC2, SfuABC3, YfuABC4, FeoAB(C)5, FutA16, FutA26, FutB6, FutC6, YfeABCD7 |
| Heme oxygenase | ChuS8, ChuZ9, HemO10,11, PigA10,11, HemRSTUV12, HmoB13, HmuO14, HugZ15, HupZ16, Isd-LmHde17, IsdG18, IsdI19, MhuD20, PhuS21 (in PhuRSTUVW) | |
| Heme transport | HasRADE(B)F22, HmuRSTUV22, HmuY23, HmuY’23, HutZ24, HxuCBA25, IsdX126, IsdX226, PhuRSTUVW21, Rv020327 | |
| Transferrin/Lactoferrin | TbpAB (LbpAB)28, SstABCD29 | |
| Siderophore synthesis | AcsABCDEF30, AmoA31, AngR32, AsbABCDEF33, DhbACEBF34, entD-fepA-fes-entF-fepECGDB-entCEBA-ybdA35, IroD in IroNBCDE36, IucABCD37,38, IutA37,38, MbtIJABCDEFGH35, LbtA39 (in LbtUABC), PchABCDREFGHI35, PvdQAPMNOFEDJIHLGS40, PvsABCDE41, VenB42, Vab genes in VabR-fur-vabGA-fur-VabCEBSFH-fur-fvtA-vabD43, Vib genes in VibB-vibEC-vibA-vibH-viuPDGC-vibD and viuAB-vibF44–46, RhbABCDEF-rhrA-rhtA47 | |
| Siderophore transport | BesA48, CbrABCD49, TonB-ExbB-ExbD50, FatABCD51, FecIRABCDE52, FeuABC-yusV53, FhuACDB54–56, FhuF54–56, FptABCX57, FpuAB58, FpuC58, FpuD58, FpvIR-FpvA-FpvGHJKCDEF59, FvtA in VabR-fur-vabGA-fur-VabCEBSFH-fur-fvtA-vabD43, HatCDB37, IroNBCDE36, LbtUABC39, PirA60, PiuA60, PvuABCDE41, Viu genes in VibB-vibEC-vibA-vibH-viuPDGC-vibD and viuAB-vibF44–46, YfiZ-yfhA61, YfiY61, YqjH62, ybdA and Fep genes in entD-fepA-fes-entF-fepECGDB-entCEBA-ybdA35 | |
| Iron Gene regulation | Transcriptional regulation | DtxR63, FecR (in FecIRABCDE)52, FeoC in FeoAB(C)5, Fur64, IdeR65, YqjI62, RhrA in RhbABCDEF-rhrA-rhtA47 |
| Iron oxidation and reduction | Iron oxidation | Cyc166,67, Cyc266,67,68, FoxABC69, FoxEYZ70, Sulfocyanin71, PioABC72 |
| Probable iron oxidation and possible iron reduction | MtoAB73, Cyc2 (cluster 3) | |
| Dissimilatory iron reduction | CymA74, MtrCAB75, OmcF76, OmcS76, OmcZ76, FmnA-dmkA-fmnB-pplA-ndh2-eetAB-dmkB77, DFE_0448-0451, DFE_0461-046578 | |
| Probable iron reduction | MtrCB, MtrAB, MtoAB-MtrC | |
| Iron storage | Iron storage | Bfr79, DpsA80, Ftn81 |
| Magnetosome-related | Magnetosome formation | MamABEKLMOPQI82,83 (Note: These genes are found in all known magnetotactic microorganisms, except for mamL which is found in magnetite-producing magnetotactic microorganisms81) |
Bolded and underlined HMMs are derived from Pfam or TIGRFAMs databases. Other HMMs were created by using select sequences. See Supplementary Table S1 for more information, including the corresponding Pfam or TIGRFAMs families and the sequences used to create the HMMs. 1Miethke et al., 2013, 2Adhikari et al., 1996, 3Angerer et al., 1990, 4Gong et al., 2001, 5Lau et al., 2016, 6Katoh et al., 2001, 7Bearden et al., 1998, 8Suits et al., 2006, 9Zhang et al., 2011, 10Friedman et al., 2003, 11Friedman et al., 2004, 12Schneider et al., 2006, 13Park et al., 2012, 14Matsui et al., 2005, 15Hu et al., 2011, 16Sachla et al., 2016, 17Duong et al., 2014, 18Reniere et al., 2010, 19Skaar et al., 2004, 20Graves et al., 2014, 21Ochsner et al., 2000, 22Tong and Guo, 2009, 23Wójtowicz et al., 2009, 24Liu X. et al., 2012, 25Morton et al., 2007, 26Honsa et al., 2014, 27Tullius et al., 2011, 28Gray-Owen et al., 1995, 29Morrissey et al., 2000, 30Carroll and Moore, 2018, 31Barghouthi et al., 1991, 32Wertheimer et al., 1999, 33Oves-Costales et al., 2007, 34May et al., 2001, 35Crosa and Walsh, 2002, 36Hantke et al., 2003, 37Suzuki et al., 2006, 38Martínez et al., 1994, 39Cianciotto, 2015, 40Lamont and Martin, 2003, 41Tanabe et al., 2003, 42Tan et al., 2014, 43Balado et al., 2008, 44Wyckoff et al., 2001, 45Keating et al., 2000, 46Wyckoff et al., 1999, 47Lynch et al., 2001, 48Miethke et al., 2006, 49Mahé et al., 1995, 50Garcia-Herrero et al., 2007, 51Lemos et al., 2010, 52Braun, 2003, 53Peuckert et al., 2011, 54Köster and Braun, 1989, 55Coulton et al., 1987, 56Braun et al., 2002, 57Youard et al., 2011, 58Dixon et al., 2012, 59Brillet et al., 2012, 60Moynie et al., 2017, 61Ollinger et al., 2006, 62Wang et al., 2011, 63Guedon and Helmann, 2003,64Escolar et al., 1998, 65Rodriguez et al., 2002, 66Castelle et al., 2008, 67Barco et al., 2015, 68McAllister et al., 2019, 69Bathe and Norris, 2007, 70Croal et al., 2007, 71Ilbert and Bonnefoy, 2013, 72Liu J. et al., 2012, 73Jiao and Newman, 2007, 74Castelle et al., 2015, 75Pitts et al., 2003, 76Santos et al., 2015, 77Light et al., 2018, 78Deng et al., 2018, 79Grossman et al., 1992, 80Grant et al., 1998, 81Andrews, 1998, 82Uebe and Schuler, 2016, 83Kolinko et al., 2016.