Roseomonas mucosa strain FDAARGOS_658 chromosome 1, complete sequence.
Bacteria; Pseudomonadota; Alphaproteobacteria; Rhodospirillales; Acetobacteraceae; Roseomonas.
FDA dAtabase for Regulatory Grade micrObial Sequences (FDA-ARGOS): Supporting development and validation of Infectious Disease Dx tests
Submitted (17-SEP-2019) Center for Devices and Radiological Health, US Food and Drug Administration, 10903 New Hampshire Avenue, Silver Spring, MD 20993-0002, USA
REFSEQ INFORMATION: The reference sequence is identical to\nCP044114.1.\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 :: canu v. 1.4\nGenome Coverage :: 688.09x\nSequencing Technology :: Pacbio; Illumina\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 03/25/2023 01:47:51\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) :: 4,609\nCDSs (total) :: 4,529\nGenes (coding) :: 4,452\nCDSs (with protein) :: 4,452\nGenes (RNA) :: 80\nrRNAs :: 5, 5, 5 (5S, 16S, 23S)\ncomplete rRNAs :: 5, 5, 5 (5S, 16S, 23S)\ntRNAs :: 61\nncRNAs :: 4\nPseudo Genes (total) :: 77\nCDSs (without protein) :: 77\nPseudo Genes (ambiguous residues) :: 0 of 77\nPseudo Genes (frameshifted) :: 20 of 77\nPseudo Genes (incomplete) :: 59 of 77\nPseudo Genes (internal stop) :: 12 of 77\nPseudo Genes (multiple problems) :: 14 of 77\nCRISPR Arrays :: 2\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: similar to AA sequence:RefSeq:WP_019463361.1
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_019462437.1
GO:0008168 - methyltransferase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_043766075.1
GO:0004803 - transposase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_043766072.1
COORDINATES: similar to AA sequence:RefSeq:WP_019462445.1
GO:0003824 - catalytic activity [Evidence IEA]
phosphoadenosine phosphosulfate reductase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_019462446.1
zincin-like metallopeptidase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_011930427.1
COORDINATES: protein motif:HMM:NF021637.2
COORDINATES: similar to AA sequence:RefSeq:WP_007424964.1
COORDINATES: similar to AA sequence:RefSeq:WP_003620405.1
COORDINATES: similar to AA sequence:RefSeq:WP_012224748.1
GO:0016301 - kinase activity [Evidence IEA]
type II toxin-antitoxin system death-on-curing family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_019463073.1
COORDINATES: similar to AA sequence:RefSeq:WP_008944190.1
helix-turn-helix transcriptional regulator
COORDINATES: protein motif:HMM:NF024139.2
helix-turn-helix domain-containing protein
COORDINATES: protein motif:HMM:NF012798.2
COORDINATES: protein motif:HMM:NF025314.2
COORDINATES: protein motif:HMM:NF024949.2
COORDINATES: similar to AA sequence:RefSeq:WP_004274505.1
GO:0030976 - thiamine pyrophosphate binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_076611297.1
programmed frameshift; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: protein motif:HMM:NF019174.2
GO:0004673 - protein histidine kinase activity [Evidence IEA]
incomplete; partial in the middle of a contig; missing N-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
HWE histidine kinase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_019462969.1
HlyD family efflux transporter periplasmic adaptor subunit
COORDINATES: similar to AA sequence:RefSeq:WP_019462970.1
GO:0043190 - ATP-binding cassette (ABC) transporter complex [Evidence IEA]; GO:0016020 - membrane [Evidence IEA]
GO:0005524 - ATP binding [Evidence IEA]; GO:0042626 - ATPase-coupled transmembrane transporter activity [Evidence IEA]
GO:0055085 - transmembrane transport [Evidence IEA]
ribosome-associated ATPase/putative transporter RbbA
COORDINATES: similar to AA sequence:RefSeq:WP_019462971.1
COORDINATES: similar to AA sequence:RefSeq:WP_086558278.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0004803 - transposase activity [Evidence IEA]
GO:0006313 - transposition, DNA-mediated [Evidence IEA]
frameshifted; incomplete; partial in the middle of a contig; missing C-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_076612070.1
incomplete; partial in the middle of a contig; missing N-terminus and C-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: protein motif:HMM:NF024935.2
COORDINATES: protein motif:HMM:NF013677.2
COORDINATES: protein motif:HMM:NF033516.0
COORDINATES: similar to AA sequence:RefSeq:WP_012976042.1
TnpB, as the term is used for proteins encoded by IS66 family insertion elements, is considered an accessory protein, since TnpC, encoded by a neighboring gene, is a DDE family transposase; Derived by automated computational analysis using gene prediction method: Protein Homology.
IS66 family insertion sequence element accessory protein TnpB
COORDINATES: similar to AA sequence:RefSeq:WP_014189972.1
incomplete; partial in the middle of a contig; missing C-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_076611116.1
COORDINATES: similar to AA sequence:RefSeq:WP_012973759.1
COORDINATES: similar to AA sequence:RefSeq:WP_011907535.1
COORDINATES: protein motif:HMM:NF019313.2
COORDINATES: protein motif:HMM:NF018242.2
Qat anti-phage system QueC-like protein QatC
COORDINATES: protein motif:HMM:NF013213.2
GO:0016788 - hydrolase activity, acting on ester bonds [Evidence IEA]
Qat anti-phage system TatD family nuclease QatD
COORDINATES: similar to AA sequence:RefSeq:WP_020084962.1
rhomboid family intramembrane serine protease
COORDINATES: protein motif:HMM:NF016674.2
GO:0016651 - oxidoreductase activity, acting on NAD(P)H [Evidence IEA]
GO:0022900 - electron transport chain [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_000993372.1
COORDINATES: protein motif:HMM:TIGR02937.1
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_016451636.1
GO:0005524 - ATP binding [Evidence IEA]; GO:0016887 - ATP hydrolysis activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011942236.1
GO:0016887 - ATP hydrolysis activity [Evidence IEA]; GO:0004222 - metalloendopeptidase activity [Evidence IEA]
GO:0051301 - cell division [Evidence IEA]; GO:0006508 - proteolysis [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_020084957.1
COORDINATES: similar to AA sequence:RefSeq:WP_007002277.1
COORDINATES: similar to AA sequence:RefSeq:WP_003603273.1
COORDINATES: similar to AA sequence:RefSeq:WP_003603272.1
COORDINATES: similar to AA sequence:RefSeq:WP_011982932.1
phosphate-starvation-inducible PsiE family protein
COORDINATES: similar to AA sequence:RefSeq:WP_003603269.1
COORDINATES: similar to AA sequence:RefSeq:WP_076611992.1
frameshifted; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_006412084.1
GO:0015035 - protein-disulfide reductase activity [Evidence IEA]
GO:0006662 - glycerol ether metabolic process [Evidence IEA]
COORDINATES: protein motif:HMM:NF014074.2
COORDINATES: similar to AA sequence:RefSeq:WP_086558308.1
COORDINATES: similar to AA sequence:RefSeq:WP_076611302.1
COORDINATES: similar to AA sequence:RefSeq:WP_001721696.1
COORDINATES: similar to AA sequence:RefSeq:WP_001022486.1
COORDINATES: protein motif:HMM:NF014654.2
COORDINATES: protein motif:HMM:NF013970.2
type II toxin-antitoxin system VapC family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_076611376.1
COORDINATES: protein motif:HMM:NF016670.2
COORDINATES: similar to AA sequence:RefSeq:WP_076611246.1
COORDINATES: similar to AA sequence:RefSeq:WP_007673474.1
COORDINATES: similar to AA sequence:RefSeq:WP_032685482.1
COORDINATES: protein motif:HMM:NF013828.2
COORDINATES: protein motif:HMM:NF014758.2
GO:0016491 - oxidoreductase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_076611158.1
internal stop; incomplete; partial in the middle of a contig; missing C-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: protein motif:HMM:NF012464.2
COORDINATES: protein motif:HMM:NF024800.2
COORDINATES: protein motif:HMM:NF013793.2
COORDINATES: similar to AA sequence:RefSeq:WP_009797950.1
COORDINATES: similar to AA sequence:RefSeq:WP_012115001.1
COORDINATES: similar to AA sequence:RefSeq:WP_007407174.1
GO:0071949 - FAD binding [Evidence IEA]; GO:0050151 - oleate hydratase activity [Evidence IEA]
GO:0006631 - fatty acid metabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_017503238.1
GO:0016616 - oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_017503239.1
COORDINATES: similar to AA sequence:RefSeq:WP_017503240.1
TetR/AcrR family transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_007407175.1
COORDINATES: protein motif:HMM:TIGR01413.1
GO:0020037 - heme binding [Evidence IEA]; GO:0004601 - peroxidase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_014104248.1
COORDINATES: similar to AA sequence:RefSeq:WP_013634951.1
COORDINATES: similar to AA sequence:RefSeq:WP_052642687.1
COORDINATES: similar to AA sequence:RefSeq:WP_012779116.1
COORDINATES: similar to AA sequence:RefSeq:WP_076612330.1
COORDINATES: protein motif:HMM:NF012744.2
COORDINATES: protein motif:HMM:NF015013.2
O-antigen ligase domain-containing protein
COORDINATES: protein motif:HMM:TIGR01007.1
polysaccharide biosynthesis tyrosine autokinase
COORDINATES: protein motif:HMM:NF024831.2
COORDINATES: protein motif:HMM:NF028151.2
carbohydrate-binding domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_019460317.1
COORDINATES: protein motif:HMM:NF016377.2
COORDINATES: protein motif:HMM:NF021640.2
adenylate/guanylate cyclase domain-containing protein
COORDINATES: protein motif:HMM:NF012437.2
GO:0009190 - cyclic nucleotide biosynthetic process [Evidence IEA]; GO:0035556 - intracellular signal transduction [Evidence IEA]
COORDINATES: protein motif:HMM:NF017885.2
COORDINATES: protein motif:HMM:NF024861.2
COORDINATES: protein motif:HMM:NF012234.2
COORDINATES: protein motif:HMM:NF018691.2
COORDINATES: similar to AA sequence:RefSeq:WP_019016515.1
COORDINATES: protein motif:HMM:TIGR02293.1
COORDINATES: similar to AA sequence:RefSeq:WP_016738583.1
COORDINATES: protein motif:HMM:NF016255.2
COORDINATES: protein motif:HMM:NF021631.2
nucleotidyltransferase domain-containing protein
COORDINATES: protein motif:HMM:NF027267.2
GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]; GO:0097351 - toxin sequestering activity [Evidence IEA]
GO:0001558 - regulation of cell growth [Evidence IEA]
type II toxin-antitoxin system PrlF family antitoxin
COORDINATES: similar to AA sequence:RefSeq:WP_003454727.1
type II toxin-antitoxin system YhaV family toxin
COORDINATES: protein motif:HMM:NF013753.2
COORDINATES: similar to AA sequence:RefSeq:WP_076611858.1
COORDINATES: protein motif:HMM:NF040974.1
COORDINATES: protein motif:HMM:NF013015.2
COORDINATES: protein motif:HMM:NF004225.0
GO:0008408 - 3'-5' exonuclease activity [Evidence IEA]; GO:0003887 - DNA-directed DNA polymerase activity [Evidence IEA]
GO:0006260 - DNA replication [Evidence IEA]
COORDINATES: protein motif:HMM:NF020704.2
COORDINATES: similar to AA sequence:RefSeq:WP_019462458.1
DUF3991 and TOPRIM domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_019462456.1
COORDINATES: protein motif:HMM:NF020084.2
FIST N-terminal domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_008620908.1
type II toxin-antitoxin system prevent-host-death family antitoxin
COORDINATES: similar to AA sequence:RefSeq:WP_012092614.1
COORDINATES: similar to AA sequence:RefSeq:WP_019460407.1
COORDINATES: protein motif:HMM:TIGR04346.1
COORDINATES: similar to AA sequence:RefSeq:WP_019460412.1
COORDINATES: similar to AA sequence:RefSeq:WP_019460417.1
COORDINATES: similar to AA sequence:RefSeq:WP_019460418.1
DotH/IcmK family type IV secretion protein
COORDINATES: protein motif:HMM:NF015688.2
COORDINATES: similar to AA sequence:RefSeq:WP_019460421.1
COORDINATES: similar to AA sequence:RefSeq:WP_019460422.1
COORDINATES: similar to AA sequence:RefSeq:WP_019460424.1
COORDINATES: protein motif:HMM:NF028126.2
Members of this family include DotD of type IVB secretion systems and TraH of plasmid conjugative plasmid systems, both lipoproteins; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_019460426.1
type IV secretory system conjugative DNA transfer family protein
COORDINATES: similar to AA sequence:RefSeq:WP_019460427.1
COORDINATES: similar to AA sequence:RefSeq:WP_010517045.1
COORDINATES: similar to AA sequence:RefSeq:WP_019460430.1
lytic transglycosylase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_019460434.1
type IV secretion system DNA-binding domain-containing protein
COORDINATES: protein motif:HMM:NF013209.2
COORDINATES: similar to AA sequence:RefSeq:WP_076611638.1
frameshifted; incomplete; partial in the middle of a contig; missing N-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_076612078.1
COORDINATES: nucleotide motif:Rfam:14.4:RF01497
AL1L pseudoknot; Derived by automated computational analysis using gene prediction method: cmsearch.
COORDINATES: similar to AA sequence:RefSeq:WP_012778788.1
COORDINATES: similar to AA sequence:RefSeq:WP_013635080.1
COORDINATES: similar to AA sequence:RefSeq:WP_019200205.1
type II toxin-antitoxin system RelE/ParE family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_017502930.1
COORDINATES: protein motif:HMM:NF013704.2
GO:0003677 - DNA binding [Evidence IEA]; GO:0008170 - N-methyltransferase activity [Evidence IEA]
GO:0006306 - DNA methylation [Evidence IEA]
COORDINATES: protein motif:HMM:NF015210.2
COORDINATES: protein motif:HMM:NF037890.2
MAE_28990/MAE_18760 family HEPN-like nuclease
GO:0015074 - DNA integration [Evidence IEA]; GO:0006310 - DNA recombination [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_076612037.1
COORDINATES: similar to AA sequence:RefSeq:WP_076611960.1
COORDINATES: protein motif:HMM:NF015658.2
COORDINATES: protein motif:HMM:NF013188.2
COORDINATES: similar to AA sequence:RefSeq:WP_019462010.1
COORDINATES: similar to AA sequence:RefSeq:WP_007434473.1
GO:0015385 - sodium:proton antiporter activity [Evidence IEA]
GO:1902600 - proton transmembrane transport [Evidence IEA]; GO:0006814 - sodium ion transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_006116885.1
class I SAM-dependent DNA methyltransferase
COORDINATES: similar to AA sequence:RefSeq:WP_008620064.1
COORDINATES: protein motif:HMM:NF013579.2
GO:0006304 - DNA modification [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_010504370.1
GO:0005524 - ATP binding [Evidence IEA]; GO:0003677 - DNA binding [Evidence IEA]; GO:0016787 - hydrolase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_019460438.1
COORDINATES: similar to AA sequence:RefSeq:WP_003626743.1
COORDINATES: protein motif:HMM:NF017496.2
COORDINATES: similar to AA sequence:RefSeq:WP_019463268.1
COORDINATES: similar to AA sequence:RefSeq:WP_019463270.1
COORDINATES: similar to AA sequence:RefSeq:WP_019463271.1
COORDINATES: similar to AA sequence:RefSeq:WP_019463272.1
COORDINATES: protein motif:HMM:TIGR00621.2
GO:0003697 - single-stranded DNA binding [Evidence IEA]
GO:0006310 - DNA recombination [Evidence IEA]; GO:0006281 - DNA repair [Evidence IEA]; GO:0006260 - DNA replication [Evidence IEA]; GO:0006351 - DNA-templated transcription [Evidence IEA]
COORDINATES: protein motif:HMM:NF024109.2
COORDINATES: similar to AA sequence:RefSeq:WP_014239847.1
carboxymuconolactone decarboxylase family protein
COORDINATES: protein motif:HMM:NF015431.2
COORDINATES: similar to AA sequence:RefSeq:WP_015074897.1
COORDINATES: similar to AA sequence:RefSeq:WP_012976048.1
COORDINATES: protein motif:HMM:NF039792.1