Supplementary material

Table S1. SoxB alignment showing indels among selected representatives of the major phylogenetic SOB lineages supporting the inferred relationships including the postulated LGTs of soxB among the investigated SOB species. Amino acid positions according to the enumeration of Paracoccus denitrificans str. GB17 proteins. Identical indel positions in SoxB sequences are indicated by boxes.

SoxB sequences of representatives of major chemo- and phototrophic SOB lineages / Alignment of SoxB sequences (indels characteristic for the phylogenetic lineages highlighted by boxes)
193 SoxB 199 / 208 SoxB 217 / 268 SoxB 273 / 312 SoxB 317 / 408 SoxB 413

Epsilonproteobacteria

Helicobacteraceae

Sulfurimonas denitrificans

/ I G M - - - - F R G / G D D S ------F S D E ------F E E L - - - I F E / K D E H K V D / I V I - - - - D G - T / D E M - - K C D

Aquificae

Aquificaceae

Aquifex aeolicus

/ I K E L E E - A G C / E V D E ------F G F E ------G D L - - - V F K / R E K H K V D / Y K V - - - P G T N T / D Y Y G G D L D

Deinococci

Thermaceae

/

Thermus thermophilus str. HB8

/ L G L - - - - F R G / D D L ------F G D P - - - L F P / R A E - G A N / W R V - - - - - G K T / A I Y - P E V E

Alphaproteobacteria I

Bradyrhizobiaceae

Bradyrhizobium japonicum str. USDA 110

/ I E G - - - - L G F / D T E ------W N E A - - - A F E / R K D - G A Q / V K V - - - - - G K T / Q E R - - D A D

Rhodopseudomonas palustris str. BisB5

/ A E Q - - - - A S F / D N E ------W Q E P - - - V F E / R A E - G A E / V K V - - - - - G D T / K Q R - - D T E

Aurantimonadaceae

Aurantimonas sp. str. SI85-9A1

/ I A A - - - - L P F / D R E ------W D E P - - - A F E / R A A - G A D / V Q V - - - - - G N T / A E R - - D A E

Phyllobacteriaceae

Pseudoaminobacter salicylatoxidans str. KTC001

/ V E S - - - - L P F / D T E ------W D E P - - - A F D / R A E - G A D / L L V - - - - - D K T / E V R - - E A D

Hyphomicrobiaceae

Starkeya novella

/ V E K - - - - A P F / S V E ------W Q E P - - - V F E / R A A - G A G / V M V - - - - - G S T / A E R - - D A E

Xanthobacter autotrophicus str. Py2

/ K E K - - - - A P F / S T E ------W G E P - - - V F D / R A G - G A D / T E V - - - - - G K T / K E R - - D A E

Rhodospirillaceae

Rhodospirillum photometricum

/ A E K - - - - A P F / D N E ------W Q E D - - - V F K / R A E - G A Q / V R V - - - - - G D T / S E R - - D A E

Rhodobacteraceae

Paracoccus denitrificans str. GB17

/ V E T - - - Q L K F / D V E ------W D E P - - - A F E / R A E - G V D / I L I - - - - - G E T / T E R - - D V Q

Rhodobacter sphaeroides str. ATCC 17025

/ V D A - - - - L P F / D K E ------W D E P - - - A F P / R E K - G V D / L L V - - - - - G E T / S E R - - D A E

Roseobacter sp. str. MED193

/ V E G - - - - L P F / D S E ------W D E P A E - L F K / R A A - G A D / V L V - - - - - G K T / S E R - - E A D

Sulfitobacter sp. str. NAS-14.1

/ V E G - - - - L P F / D A E ------W D E P T E - L F P / R A K - G A E / V L V - - - - - G E T / S E R - - E A D

Spirochaetes

Spirochaeta sp. str. M6

/ V E G - - - - L P F / D A E ------W D E P T E - L F P / R A K - G A E / V L V - - - - - G D T / S E R - - E A D

Betaproteobacteria

Comamonadaceae

Methylibium petroleiphilum str. PM1

/ V D E D F R - G R I / T T D ------F G D E - - - V F K / R A A - G A Q / V V V A N P - - G G K / E V Q - - G A E

Rhodocyclaceae

Dechloromonas aromatica

/ E E K D F A - G Q I / T T D ------F G D A - - - V F K / R A A - G A Q / V V V K N A - - G G Q / K V K - - D A E

Hydrogenophilaceae

Thiobacillus denitrificans str. ATCC 25259

/ V N G D F K K A N I / T N D ------F G D Q - - - V F K / R A E - G A K / T K V K N A - - K G V / E V K - - G A D

Thiobacillus aquaesulis

/ V N N D F K K A G I / T A D ------F G D Q - - - V F K / R A N - G A Q / V Q V R N A - - K G I / E V K - - G A D

Burkholderiaceae

Ralstonia solanacearum str. GMI1000

/ V D H D F R - N K V / T T D ------F G D P - - - V F D / R G K - G A R / V R V S N P - - G G T / Q A Q - - G A E

Deltaproteobacteria

Anaeromyxobacter dehalogenans str. 2CP-C

/ V E K D L A - G K V / T A D ------F G D P - - - V F E / R A K - G A R / I P V K N R - - G G Q / A E K - - D A E

Gammaproteobacteria

Thiovirga sulfuroxydans str. A7

/ R S K - G A E / V Q V R N S - - G G V / A V Q - - D A E

Gammaproteobacteria I

Free-living relatives of invertebrate symbionts

OBII2

/ I E N D F A - D N I / D V D ------W Q E P - - - V F Q / R D E - G A Q / V E V A N A - - G G K / E V Q - - D A E

Thiotrichaceae

Thiothrix nivea

/ R S K - G A K / V V V E N A - - G G K / Q E L - - D A P

Leucothrix mucor

/ R G K - G A Q / V I V E N S - - G G K / E E L - - D A P

Halothiobacillaceae

Halothiobacillus kellyii

/ I K D L E S S T L N / D F D ------F E D Y - - - V F K / R S E - G A E / T I V K N K - S G Q T / D E N - - D A Q

Ectothiorhodospiraceae

Ectothiorhodospira shaposhnikovii

/ L Q N D F A - G H I / D V D ------W E E R - - - V F K / R A E - G A E / L E V K T P - D G G T / E Q V - - D A Q

Gammaproteobacteria IV

Ectothiorhodospiraceae

Halorhodospira halophila

/ V A D L D G A G - V / D R D ------W L D P - - - I F D / R D D - G A Q / E Q V E D A - D G E S / E G R - - D A E

Gammaproteobacteria II

Invertebrate symbionts and free-living relatives

Riftia pachyptila symbiont

/ R E N E K P D / T I V K N A - G G K T / T V N - - D A Q

OAII2

/ V R D - - - - F K G / V K D D A A F D Y R F A D F E G ------F D E D S Q R A F K / P A T E K P D / S I V K N K - G G Q T / E V G - - G A E

Chromatiaceae

Allochromatium vinosum

/ I A E - - - - F Q G / V R E E A L F D Y R F E D F A G ------F D E D S G L A F E / R E Q E K P G / I L V E N P - G G K T / R V H - - D A Q

Halochromatium salexigens

/ V E A - - - - F N G / V R E E A L F D Y Q F E D F G G ------F Q E D A G L A F K / R D E E S P D / T I V D N A - K G K T / K V N - - D A Q

Marichromatium gracile

/ I A A - - - - F A G / V R E E A L F D Y R F E D F A G ------F D E D L G L A F D / R E R E R P A / Q V V D N P - G G R T / T V K - - D A E

Thiocapsa roseopersina DSM 217

/ V G E - - - - F K G / V R E E A L F D Y R F A D F P G ------F D E D L G R A F K / R E E E K P D / T I V E N A - S G K T / K V N - - D A Q

Thiocystis violacea DSM 207

/ I G A - - - - F K G / V R E E A L F D Y R F A D F P G ------F D E D A G L A F E / R E D E K P A / T L V E N S - G G K T / K V K - - E A Q

Thiorhodococcus minor

/ V G A - - - - F K G / V R E E A L F D Y R F E D F A G ------F D E D R G L A F E / R G K E S P A / S S V E N P - G G K T / K V H - - D A Q

Oceanospirillaceae

Oceanospirillum sp. str. MED92

/ I K A - - - - F N G / V T E D A L F D G - A D E Y F H ------D E D S G H V F K / R A E E S V D / T V V K N N - A G Q T / E Q N - - D A Q

Piscirickettsiaceae

Thiomicrospira crunogena str. XCL-2

/ L N N - - - - F K G / V K E D S L F G D S Y R D M V D R H N G T G L Y D E D E G R A F K / R E T K K V A / T P V K T P E G G V C / E E H - - D A Q

“Cdt. Ruthia magnifica“ str. CM

/ I S F - - - - F K G / I I E D T L M G D E Y I T M T E K Y G G N G L F D E N E G L P F K / R K N E K P D / V E V K N A - G G V T / E E H - - D A N

Chlorobia

Chlorobiaceae

Chlorobium phaeovibioides DSM 265

/ L A A - - - - F K G / T K E V A M F E G A Q A Y D E N ------T G H T F R / R A K E K P D / F V V K N A - K G R T / E R N - - E A Q

Chlorobium clathratiforme DSM 5477

/ L A A - - - - F K G / V K E D A L F N G A Q A F D E R ------S G H A F R / R S K E K P D / F E V R N K - T G R T / S R N - - E A Q

Chlorobaculum tepidum

/ L A A - - - - F K G / V K E E A L F S G A K A F D E N ------T G H A F R / R A K E K P D / F I V K N A - R G R T / Q R N - - D A Q

Gammaproteobacteria III

Uncertain affiliation

Congregibacter litoralis str. KT 71

/ I E A - - - - F N G / A T E D A L F D G V P V Y D E D ------T G H V F K / R S S E K P D / I E V E N S - G G K T / E E L - - D A Q

Alphaproteobacteria II

Bradyrhizobiaceae

Bradyrhizobium japonicum str. USDA 110

/ L E R - - - - F K G / L T E E A A F N D A R A F D K A ------T G R V F K / R T A D K V D / I P V T N A - G G T T / S E L - - D A E

Nitrobacter hamburgensis str. X14

/ L S R - - - - F N G / L T E E A A F N D T P A F D A A ------S G R V F K / R D V D R V D / I A V S N A - G G T T / G A F - - D A E

Acetobacteraceae

Acidiphilium cryptum str. JF-5

/ I K A - - - - L H G / L S A E S Q M M G A P A F D Q K ------T G R V F Q / R E V K K V D / V P V K N P - G G I T / E A T - - G A Q