Sulfuricella denitrificans skB26 plasmid pSCD, complete sequence.
Bacteria; Pseudomonadota; Betaproteobacteria; Nitrosomonadales; Sulfuricellaceae; Sulfuricella.
Complete genomes of freshwater sulfur oxidizers Sulfuricella denitrificans skB26 and Sulfuritalea hydrogenivorans sk43H: genetic insights into the sulfur oxidation pathway of betaproteobacteria
Draft genome sequence of a psychrotolerant sulfur-oxidizing bacterium, Sulfuricella denitrificans skB26, and proteomic insights into cold adaptation
Submitted (31-MAY-2013) Contact:Hisaya Kojima The Institute of Low Temperature Science, Hokkaido University; Kitaku Kita 18 Nishi 8, Sapporo 060-0819, Japan
REFSEQ INFORMATION: The reference sequence is identical to\nAP013067.1.\nThe annotation was added by the NCBI Prokaryotic Genome Annotation\nPipeline (PGAP). Information about PGAP can be found here:\nhttps://www.ncbi.nlm.nih.gov/genome/annotation_prok/\n\n##Genome-Assembly-Data-START##\nAssembly Method :: GS De Novo Assembler v. 2.3\nGenome Coverage :: 24x\nSequencing Technology :: Genome Sequencer FLX System\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 12/30/2022 01:26:32\nAnnotation Pipeline :: NCBI Prokaryotic Genome\n Annotation Pipeline (PGAP)\nAnnotation Method :: Best-placed reference protein\n set; GeneMarkS-2+\nAnnotation Software revision :: 6.4\nFeatures Annotated :: Gene; CDS; rRNA; tRNA; ncRNA\nGenes (total) :: 3,128\nCDSs (total) :: 3,073\nGenes (coding) :: 3,042\nCDSs (with protein) :: 3,042\nGenes (RNA) :: 55\nrRNAs :: 2, 2, 2 (5S, 16S, 23S)\ncomplete rRNAs :: 2, 2, 2 (5S, 16S, 23S)\ntRNAs :: 45\nncRNAs :: 4\nPseudo Genes (total) :: 31\nCDSs (without protein) :: 31\nPseudo Genes (ambiguous residues) :: 0 of 31\nPseudo Genes (frameshifted) :: 19 of 31\nPseudo Genes (incomplete) :: 14 of 31\nPseudo Genes (internal stop) :: 2 of 31\nPseudo Genes (multiple problems) :: 3 of 31\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.
type strain of Sulfuricella denitrificans
COORDINATES: protein motif:HMM:NF013235.2
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_000104831.1
COORDINATES: similar to AA sequence:RefSeq:WP_017842829.1
GO:0007059 - chromosome segregation [Evidence IEA]; GO:0000910 - cytokinesis [Evidence IEA]
ParB/RepB/Spo0J family partition protein
COORDINATES: similar to AA sequence:RefSeq:WP_018076630.1
translesion error-prone DNA polymerase V autoproteolytic subunit
COORDINATES: similar to AA sequence:RefSeq:WP_015421275.1
COORDINATES: similar to AA sequence:RefSeq:WP_002941071.1
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: similar to AA sequence:RefSeq:WP_008119144.1
helix-turn-helix transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_009206159.1
COORDINATES: similar to AA sequence:RefSeq:WP_009893416.1
zinc ribbon domain-containing protein YjdM
COORDINATES: similar to AA sequence:RefSeq:WP_014028651.1
COORDINATES: similar to AA sequence:RefSeq:WP_017845887.1
COORDINATES: similar to AA sequence:RefSeq:WP_008032031.1
GO:0015116 - sulfate transmembrane transporter activity [Evidence IEA]
GO:0008272 - sulfate transport [Evidence IEA]
COORDINATES: protein motif:HMM:NF012792.2
GO:0008080 - N-acetyltransferase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011111080.1
GO:0004853 - uroporphyrinogen decarboxylase activity [Evidence IEA]
GO:0006779 - porphyrin-containing compound biosynthetic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_008328236.1
GO:0003824 - catalytic activity [Evidence IEA]
bifunctional UDP-4-keto-pentose/UDP-xylose synthase
COORDINATES: similar to AA sequence:RefSeq:WP_011288741.1
COORDINATES: similar to AA sequence:RefSeq:WP_017305739.1
COORDINATES: similar to AA sequence:RefSeq:WP_009206533.1
GO:0009279 - cell outer membrane [Evidence IEA]
peptidoglycan-associated lipoprotein Pal
COORDINATES: similar to AA sequence:RefSeq:WP_006705272.1
type II toxin-antitoxin system Phd/YefM family antitoxin
COORDINATES: similar to AA sequence:RefSeq:WP_018444279.1
type II toxin-antitoxin system VapC family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_015830161.1
COORDINATES: similar to AA sequence:RefSeq:WP_017449860.1
GO:0016788 - hydrolase activity, acting on ester bonds [Evidence IEA]
type II toxin-antitoxin system HigB family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_015720643.1
COORDINATES: protein motif:HMM:NF012790.2
rhodanese-like domain-containing protein
COORDINATES: protein motif:HMM:NF013799.2
COORDINATES: protein motif:HMM:NF014693.2
formylmethanofuran dehydrogenase subunit E family protein
COORDINATES: protein motif:HMM:NF012456.2
COORDINATES: similar to AA sequence:RefSeq:WP_018716750.1
GO:0045261 - proton-transporting ATP synthase complex, catalytic core F(1) [Evidence IEA]
GO:0005524 - ATP binding [Evidence IEA]; GO:0046933 - proton-transporting ATP synthase activity, rotational mechanism [Evidence IEA]
GO:0015986 - proton motive force-driven ATP synthesis [Evidence IEA]
COORDINATES: protein motif:HMM:NF012645.2
GO:0046933 - proton-transporting ATP synthase activity, rotational mechanism [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_014234581.1
GO:0000276 - mitochondrial proton-transporting ATP synthase complex, coupling factor F(o) [Evidence IEA]; GO:0045264 - plasma membrane proton-transporting ATP synthase complex, coupling factor F(o) [Evidence IEA]; GO:0045263 - proton-transporting ATP synthase complex, coupling factor F(o) [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_010652841.1
COORDINATES: similar to AA sequence:RefSeq:WP_020335247.1
COORDINATES: similar to AA sequence:RefSeq:WP_018716745.1
COORDINATES: similar to AA sequence:RefSeq:WP_020680134.1
GO:0000275 - mitochondrial proton-transporting ATP synthase complex, catalytic sector F(1) [Evidence IEA]; GO:0045262 - plasma membrane proton-transporting ATP synthase complex, catalytic core F(1) [Evidence IEA]; GO:0045261 - proton-transporting ATP synthase complex, catalytic core F(1) [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_004291311.1
COORDINATES: protein motif:HMM:NF024491.2
COORDINATES: similar to AA sequence:RefSeq:WP_013124456.1
COORDINATES: protein motif:HMM:NF016064.2
YeeE/YedE thiosulfate transporter family protein
COORDINATES: similar to AA sequence:RefSeq:WP_012823446.1
COORDINATES: similar to AA sequence:RefSeq:WP_013519525.1
COORDINATES: similar to AA sequence:RefSeq:WP_008100970.1
COORDINATES: protein motif:HMM:TIGR01730.1
GO:0005215 - transporter activity [Evidence IEA]
efflux RND transporter periplasmic adaptor subunit
COORDINATES: protein motif:HMM:NF014385.2
COORDINATES: similar to AA sequence:RefSeq:WP_014238461.1
cation diffusion facilitator family transporter
COORDINATES: protein motif:HMM:NF013614.2
GO:0016226 - iron-sulfur cluster assembly [Evidence IEA]
SufD family Fe-S cluster assembly protein
COORDINATES: similar to AA sequence:RefSeq:WP_013250302.1
ATP-binding cassette domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_013029136.1
COORDINATES: similar to AA sequence:RefSeq:WP_011465912.1
COORDINATES: similar to AA sequence:RefSeq:WP_014561673.1
sulfite exporter TauE/SafE family protein
COORDINATES: similar to AA sequence:RefSeq:WP_002990998.1
COORDINATES: similar to AA sequence:RefSeq:WP_020676718.1
COORDINATES: similar to AA sequence:RefSeq:WP_012098450.1
COORDINATES: similar to AA sequence:RefSeq:WP_009205801.1
GO:0022857 - transmembrane transporter activity [Evidence IEA]
GO:0055085 - transmembrane transport [Evidence IEA]
COORDINATES: protein motif:HMM:NF024923.2
GO:0015562 - efflux transmembrane transporter activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_020508376.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]; GO:0016987 - sigma factor activity [Evidence IEA]
GO:0006352 - DNA-templated transcription initiation [Evidence IEA]; GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
sigma-70 family RNA polymerase sigma factor
COORDINATES: similar to AA sequence:RefSeq:WP_011311937.1
COORDINATES: similar to AA sequence:RefSeq:WP_018915135.1
COORDINATES: similar to AA sequence:RefSeq:WP_009205156.1
COORDINATES: similar to AA sequence:RefSeq:WP_009205158.1
COORDINATES: similar to AA sequence:RefSeq:WP_009205159.1
COORDINATES: similar to AA sequence:RefSeq:WP_018413472.1
COORDINATES: similar to AA sequence:RefSeq:WP_007601550.1
GDCCVxC domain-containing (seleno)protein
COORDINATES: similar to AA sequence:RefSeq:WP_009205161.1
GO:0008490 - arsenite secondary active transmembrane transporter activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_012643024.1
COORDINATES: similar to AA sequence:RefSeq:WP_015257783.1
COORDINATES: similar to AA sequence:RefSeq:WP_011534447.1
GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]
GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
metalloregulator ArsR/SmtB family transcription factor
COORDINATES: similar to AA sequence:RefSeq:WP_009207636.1
COORDINATES: similar to AA sequence:RefSeq:WP_014779499.1
GO:0015297 - antiporter activity [Evidence IEA]
GO:0006814 - sodium ion transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_008449114.1
GO:0051539 - 4 iron, 4 sulfur cluster binding [Evidence IEA]
GO:0006777 - Mo-molybdopterin cofactor biosynthetic process [Evidence IEA]
COORDINATES: protein motif:HMM:NF014651.2
COORDINATES: protein motif:HMM:NF015851.2
COORDINATES: similar to AA sequence:RefSeq:WP_008932022.1
4Fe-4S dicluster domain-containing protein
COORDINATES: protein motif:HMM:NF012602.2
GO:0016491 - oxidoreductase activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF012267.2
COORDINATES: similar to AA sequence:RefSeq:WP_011465368.1
PhnD/SsuA/transferrin family substrate-binding protein
COORDINATES: protein motif:HMM:NF014567.2
HAMP domain-containing sensor histidine kinase
COORDINATES: similar to AA sequence:RefSeq:WP_018864014.1
sigma-54 dependent transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_017878358.1
GO:0016779 - nucleotidyltransferase activity [Evidence IEA]
nucleotidyltransferase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_014707353.1
COORDINATES: similar to AA sequence:RefSeq:WP_007182806.1
GO:0015074 - DNA integration [Evidence IEA]; GO:0006310 - DNA recombination [Evidence IEA]