Biology Reference
In-Depth Information
Table 5.
Hydrogenase clusters associated with nitrogen fixation.
VIMSS id
Orthologs
Putative function
Size, aas
581358
HoxK/HyaNHupS
hydrogenase- I small subunit
363
581359
HoxG/HyaB/HupL
hydrogenase- I, nickel-dependent, large subunit
598
581360
HoxZ/HyaC/HupC
Ni/Fe-hydrogenase I b-type cytochrome subunit
234
581361
HoxM/HyaD/HupD
hydrogenase expression/formation protein
204
581362
HoxUHypC/HupF
hydrogenase assembly chaperone
100
581363
HoxO/HyaE!HupG
hydrogenase- I expression
152
581364
HoxQ/HyaF/HupH
nickel incorporation into hydrogenase- I proteins
287
581365
HoxR/Hupl
rubredoxin-type Fe( Cys )4 protein
66
581366
Hupj/(similar to HoxT)
hydrogenase accessory protein
156
581367
HoxV/HupV
membrane-bound hydrogenase accessory protein
308
581368
HypA
hydrogenase nickel insertion protein
113
581369
HypB
hydrogenase accessory factor Ni(2+)-binding GTPase
352
581370
HypF
hydrogenase maturation protein
763
581371
ABC protein
periplasmic component, ABC transporter
260
581372
GGDEF domain
signal transduction, GGDEF
523
581373
HybO
hydrogenase-2 small subunit
394
581374
HybA
Fe-5-cluster-containing hydrogenase component
351
581375
HybB
cytochrome Ni/Fe component of hydrogenase-2
386
581376
HybC/HynA
hydrogenase-2 large subunit
570
581377
HybD/HynC
Ni, Fe-hydrogenase maturation factor
159
581378
HupF/HypC
hydrogenase assembly chaperone
96
581379
HybE/Hupj
hydrogenase accessory protein
183
581380
HypC
hydrogenase maturation protein
81
581381
HypD
hydrogenase maturation protein
374
581382/
3337851
HypE
hydrogenase maturation protein
330
581383
HoxX/HypX
formation of active hydrogenase
558
581384
HoxA
response regulator with CheY domain (signal transduction)
495
581385
HoxB/HupU
regulatory [NiFe] Hydrogenase small subunit (sensor)
333
581386
HoxC/HupV
regulatory [NiFe] Hydrogenase large subunit (sensor)
472
581397
HupT
histidine kinase with PAS domain sensor
448
581398
HoxN/HupN/NixA
nickel transporter
269
Carbon Fixation via the Calvin-Benson-Bassham Cycle
The genes indicative of carbon fixation, using the Calvin cycle, are present in the
D.
aromatica
genome. This includes Ribulose 1,5-bisphosphate carboxylase (RuBisCo,
VIMSS581681), phosphoribulokinase (cbbP/PrkB, VIMSS581690), and a fructose
bisphosphate (fba, VIMSS581693) of the Calvin cycle sub-type. The RuBisCo
cbbM
gene is of the fairly rare type II form.
Dechloromonas
aromatica
cbbM displays a
surprisingly high 77% amino acid identity to cbbM found in the deep-sea tube worm
Riftia pachyptila symbiont [91]. In a recent study of aquatic sediments, Rhodoferax
fermentans, Rhodospirillum fulvum and R. rubrum were also found to possess the
