Electronic
(ESI) for neighborhood
Metallomics.
SpeciesSupplementary
Mbn operonMaterial
and genomic
This journal is © The Royal Society of Chemistry 2016
Scaffold
8kb
Methylocystis
parvus OBBP (I)
tonB
ECF σ
N- & C-term factor
Methylosinus
sp. LW4
2kb
Methylosinus
sp. R-45379 (I)
Methylosinus
trichosporium
OB3b
Bioreactor
metagenome
PBDCA2†*
Methylocystis
hirsuta CSC1*
fecI
-like
ATP/Zn
protease
9kb
ECF σ
factor
JGI: N/A
NCBI: LUUM01000265.1
TBDT
1kb
JGI: 2507278056
NCBI: ADVE02000001.1
type I
rest./mod. enz.
JGI: N/A
NCBI: AGTN01410593.1†*
ECF σ
factor
moaA 3-HIBADH
11kb
ECF σ
factor
moaA 3-HIBADH
JGI: 2517575364
NCBI: AYNA01000143.1
21kb
ECF σ
factor
moaA
aoxB
arsA arsD arsC
kdpC
kdpB
14kb
carb.
porin
moaA 3-HIBADH
Methylosinus
sp. R-45379 (II)
ECF σ
factor
2-compon.
sig. trans.
tetR-like
4kb
cydB
JGI: 2517287733
NCBI: ARCT01000001.1
lysyl tRNA
synth.
2-compon.
sig. trans.
2-compon. sig. trans.
JGI: 2517093496
NCBI: AZUO01000002.1
2-compon. sig. trans.
JGI: 2563366531
NCBI: JMKQ01000005.1
2-compon. sig. trans.
JGI: N/A
NCBI: LUUM01000262.1
JGI: 2551427318
NCBI: BADK01001132.1
cydA
duf1636 copC/copD sco1 duf461
duf2946
cydB
12kb
cbiM
cydA
JGI: 646312031
NCBI: AP010946.1
tonB copC/copD sco1 duf461
Chromatiales
bacterium
methyl
transfer.
NADbinding
cysP
esterase
ssuE ssuA
ABC ABC
permease ATPase
ssuD
Comamonas
composti
DSM 21721
TBDT
copC
ABC
permease
serine
tRNA
peptidase
Gly
copC/copD duf461
Cupriavidus
basilensis B-8
clpX
III
Pseudomonas
fluorescens NZ17†
Pseudomonas
fluorescens
AU11706
Pseudomonas
otitidis LMG 23769
Pseudomonas
sp. FeS53a
Pseudomonas
sp. ST29
Tistrella mobilis
MCCC-1A021
?
duf2946
copC
NAD-dep.
TBDT duf2946 lyase ald. dehyd.
copC
NAD-dep.
TBDT duf2946 lyase ald. dehyd.
?
duf2946
copC
copC
duf2946
epimerase
copC
JGI: 2663777515
NCBI: N/A
epimerase
fabG
GATase
pnbA
pelA
aroP
HTH/
mocR
hisB
lysR
fam.
memb. flavidoxin
dgoA dgoK reductase hisEhisI hisF hisA hisH
araC
-like
fpr duf4255
TBDT
DUF955
lysR
fam.
copC copD lysRlike
trbI
copC copD lysRlike
10kb
trbG trbF
trbI
trbL
JGI: 2547259455
NCBI: CADT01000094.1
CADT01000100.1†
trbG
trbI
copC copD lysRlike
fatty acid
hydroxylase
trbG trbF
trbL
txn. reg.
phoE hydrolase
mqo
pro. dehyd.
endoI protease yckC
GGCX-like
cof-like hydrolase
luxR-like
luciferase
deoD
deoB
deoC
deoD
acetyl
cystathione
xferase ß-synth. γ-lyase
cutA1 2-oxoglutarate
-like
dehydrogenase E1
deoB
deoC
acetyl
xferase
4kb
cystathione
ß-synth. γ-lyase
65kb
deaminase
reductase
cutA1 2-oxoglutarate
-like
dehydrogenase E1
lyase
Vibrio cholerae
2012 Env-32*
2-compon.
sig. trans.
ß-lactamase 39kb
regulator
terC
+GGDEF
domain
cys. Mexfer.
yscW
-like
Vibrio splendidus
MARa NODE 3*
NADPH quin.
oxidored.
+GGDEF
domain
MATE
adh
eamA
glyox.
lysRlike
Partner of MbnH
(MbnP)
FAD-dependent
oxidoreductase (MbnF)
Di-heme cytochrome c
peroxidase (MbnH)
Sulfotransferase
(MbnS)
Dioxygenase
(MbnD)
Extended MbnB-like
protein (MbnX)
Mobile genetic
element
MbnA (Mbn precursor)
Annotated copperrelated protein
Annotated protein of
unknown relevance
Putative/hypothetical
protein
Annotated region
End of contig
JGI: N/A
NCBI: LT575493.1
JGI: 2690320674
NCBI: LUKE01000006.1
JGI: 637000243
NCBI: BX571860.1
JGI: 650000220
NCBI: AEIU01000072.1
fecE
lysRlike
JGI: N/A
NCBI: CP014035.1
araC
-like
FMN
yoaK
reductase eamA
doxX
chrR
marR
araC
cspA
-like
DMT fam.
NADPH quin.
FMN
oxidored.
reductase perm.
marRaraC
like
-like
Vibrio fluvialis
NBRC-103150
Periplasmic binding
protein
JGI: N/A
NCBI: JSTF01000051.1*
FMN DMT fam.
red. perm.
marRlike
cys. Mexfer.
Aminotransferase
(MbnN)
JGI: N/A
NCBI: JYJI01000251.1
mucB
yscW
-like
MATE efflux
pump (MbnM)
JGI: N/A
NCBI: JZWV01000689.1
luxR-like
phytanoyl
CoA synth.
TonB-dependent
transporter (MbnT)
JGI: N/A
NCBI: JNXV01000254.1,
JNXV01000288.1†
luxR-like
NB-ARC domain
MbnC (unknown Mbn
biosynthesis protein 2)
JGI: 2626599119
NCBI: LJPB01000284.1
luxR-like
NB-ARC domain
FecR-like anti-σ
factor (MbnR)
JGI: N/A
NCBI: LWGQ01000091.1
acetyl
xferase
duf2247
MbnB (unknown Mbn
biosynthesis protein 1)
JGI: N/A, NCBI: N/A
(personal communication
from William Metcalf)
ABC ATPase
YD repeat
ECF σ70 factor,
FecI-like (MbnI)
JGI: N/A
NCBI: BCTP01000066.1*
copC copD lysRlike
hsp33
JGI: 2636415590
NCBI: JUFX02000190.1
JGI: 2617321862
NCBI: JDTI01000169.1
dnaC
Streptomyces sp.
NRRL F-4428
fecD
gntR
JGI: 2681834452
NCBI: BCZR01000001.1
JGI: 2545867061
NCBI: ASXS01000009.1
fecC fecB
Xenorhabdus
sp. NBAII
Planktothrix
agardhii CYA126/8
8kb
copC copD
Vibrio
caribbenthicus
BAA-2122
?
JGI: 651334275
NCBI: AFCH01000034.1
copC copD lysRlike
Streptomyces katrae NRRL ISP-5550
Anabaena cylindrica
PCC 7122
JGI: N/A
NCBI: LPZR01000022.1
20kb
trbG trbF
trbI
JGI: 2597548057
NCBI: N/A
JGI: 2519117617
NCBI: CP003236.1
HTH/
mocR
hisB
DUF955
JGI: 2631006939
NCBI: JYFT01000015.1
JGI: 2687453566
NCBI: AP014628.1
pelB
memb. flavidoxin
dgoA dgoK reductase hisEhisI hisF hisA hisH
araC
-like
mgtC
tetR-like
duf2946
MFS
perm.
MFS
perm.
19kb
TBDT
duf2946
Streptomyces flavotricini NRRL B-5419†
Vibrio
fluvialis PG41
?
cyt. c5
?
cyt. c5
catalase duf2946
Photorhabdus
luminescens
DSPV002N
Photorhabdus
luminescens subsp.
laumondii HP88
Photorhabdus
luminescens subsp.
laumondii TTO1
Vibrio fluvialis
ATCC 33809
pelB
TBDT
yciE
GGDEF lysR-like cbiM
Kitasatospora viridis NRRL B-24578
V
pelA
catalase duf2946
?
duf2946, duf2946
JGI: 2506226229
NCBI: AJXF01000057.1,
AJXF01000183.1†
JGI: 2648527812
NCBI: LCZB01000043.1
GGDEF lysR-like cbiM
Komagataeibacter
xylinus NBRC-15237*
Bdellovibrio
bacteriovorus R0
17kb
TBDT
Komagataeibacter
rhaeticus AF1
Komagataeibacter
rhaeticus iGEM
duf1302
epimerase
?
duf2946
duf1329
JGI: 2667530436
NCBI: N/A
lysR-like
TBDT
duf2946
duf2946
duf1329
duf1302
Zn-dep.
alc. dehyd.
Zn-dep.
alc. dehyd.
duf2946
?
Komagataeibacter
oboediens 174bp2†
IV
JGI: 2524698337
NCBI: AUCQ01000013.1
JGI: 2548975727
NCBI: AHIP01000040.1
lysR-like
duf2946
Gluconacetobacter
sp. SXCC-1
Komagataeibacter
intermedius AF2
clpP
JGI: 2551429696
NCBI: BADE01000957.1†
Rugamonas
rubra ATCC 43154
Tistrella mobilis
KA081020-065
JGI: 2502206949
NCBI: N/A
JGI: 2551344392
NCBI: AKXR01001597.1
fur-like
Methylobacterium
sp. B34†
Pseudomonas
extremaustralis
14-3, substr. 14-3b
Pseudomonas
extremaustralis
DSM17835
JGI: 2540348159
NCBI: HE956757.1
JGI: 2548977259
NCBI: AJTV01000003.1
2-compon. sig. trans.
ECF σ
factor
25kb
JGI: not yet public*
NCBI: N/A
2kb
kdpA
ECF σ
factor
Methylosinus
sp. LW5 (II)
aoxA
3-HIBADH
Methylosinus
sp. LW3 (II)
Azospirillum
sp. B510
fecR
-like
JGI: 2582690639
NCBI: JQNK01000009.1
carb. porin
11kb
Methylocystis
rosea SV97T
Azospirillum
sp. B506
JGI: 2563366531
NCBI: JMKQ01000005.1
(multiple variants on fragmentary contigs)
Methylocystis
parvus OBBP (II)
II
JGI: 2516493502
NCBI: ARAB01000012.1
2-compon.
sig. trans.
tonB
ECF σ fecR- POTRA dom. exbB
N- & C-term factor like
1kb
yidB
ihfA
duf188 mutL
duf yebC
4265
Methylosinus
sp. PW1
Methylocystis
sp. SC2
JGI: 2517093496
NCBI: AZUO01000002.1
fecR- POTRA dom.
like
100kb
Zn, DNA-binding
ECF σ
factor
Methylosinus
sp. LW5 (I)
Methylocystis
sp. SB2
JGI: N/A
NCBI: LXWX01000069.1
DNA met. xfer.
Methylosinus
sp. LW3 (I)
I
JGI: 2548977297
NCBI: AJTV01000041.1
acrB
Methylosinus
sp. 3S-1
Key
JGI: N/A
NCBI: LNRO01000003.1*
JGI: 2634545697
NCBI: JTHK01000121.1
7kb
hsr1
-like
ATP-ase
hsr1-like
ATP-ase
ECF σ
factor
parB
-like
chase2 sensor
CHAT domain
tetratricopeptide
repeat
20kb
WD40 repeat
JGI: 2503985482
NCBI: CP003663.1
JGI: 2503242000
NCBI: ASAK01000013.1
Figure S1. Mbn operons currently found in the JGI and NCBI databases. Operons are grouped according to Mbn operon
type. Operons marked with an asterisk (*) are hand-annotated; MbnA sequences are additionally hand-annotated in most
operons. Operons marked with a cross (†) are incomplete due to contig endpoints, and the fragmentary operons from
the PBDCA2 bioreactor genome and Methylobacterium sp. B34 are not counted as “full operons” since the identity of
other genes in the operon is unknown. Not shown and also not counted as full Mbn operons: defunct Group V operons
from Photorhabdus temperata J3 (NCBI: AXDT01000177.1), Photorhabdus temperata subsp. temperata M1021 (NCBI:
AUXQ01000040.1), and Photorhabdus temperata subsp. temperata Meg1 (NCBI: JGVH01000024.1), wherein MbnB,
MbnC, and MbnX are fragmentary pseudogenes. Additionally not shown are genes found in a microbial mat metagenome
(NCBI: AGSF01004500.1) and a marine metagenome (NCBI: EM170757.1) where contig endpoints make it impossible to
ascertain whether an MbnA is present. The relationship of MbnB homologues in the Anabaena and Planktothrix genomes
to confirmed Mbn operons is unclear; while sequence similarity suggests a relationship to Group V MbnB genes, no
identifiable precursor peptide is adjacent to the gene, and accurate detection of small genes encoding MbnAs in the
absence of neighboring Mbn-related genes remains a challenge.