Hafnia paralvei strain AVS0177 plasmid pAVS0177-a, complete sequence.
Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales; Hafniaceae; Hafnia.
Complete Genome Sequence of Hafnia paralvei Isolate AVS0177 harboring mcr-9 on a Plasmid
Submitted (09-SEP-2021) Institute for Food Safety and Hygiene, University of Zurich, Winterthurerstrasse 272, Zurich 8057, Switzerland
REFSEQ INFORMATION: The reference sequence is identical to\nCP083738.1.\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 :: Unicycler v. v0.4.8\nGenome Representation :: Full\nExpected Final Version :: Yes\nGenome Coverage :: 100.0x\nSequencing Technology :: Illumina MiniSeq; Oxford Nanopore MinION\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 03/26/2023 07:08:51\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) :: 4,545\nCDSs (total) :: 4,434\nGenes (coding) :: 4,376\nCDSs (with protein) :: 4,376\nGenes (RNA) :: 111\nrRNAs :: 8, 8, 8 (5S, 16S, 23S)\ncomplete rRNAs :: 8, 8, 8 (5S, 16S, 23S)\ntRNAs :: 81\nncRNAs :: 6\nPseudo Genes (total) :: 58\nCDSs (without protein) :: 58\nPseudo Genes (ambiguous residues) :: 0 of 58\nPseudo Genes (frameshifted) :: 23 of 58\nPseudo Genes (incomplete) :: 41 of 58\nPseudo Genes (internal stop) :: 12 of 58\nPseudo Genes (multiple problems) :: 14 of 58\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.
COORDINATES: ab initio prediction:GeneMarkS-2+
GO:0005524 - ATP binding [Evidence IEA]; GO:0003677 - DNA binding [Evidence IEA]; GO:0016787 - hydrolase activity [Evidence IEA]
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: similar to AA sequence:RefSeq:WP_011846847.1
GO:0004803 - transposase activity [Evidence IEA]
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_001567361.1
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_000167917.1
cation diffusion facilitator family transporter
COORDINATES: similar to AA sequence:RefSeq:WP_001515348.1
cytochrome b/b6 domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_012205798.1
COORDINATES: similar to AA sequence:RefSeq:WP_001743396.1
programmed frameshift; Derived by automated computational analysis using gene prediction method: Protein Homology.
IS1-like element IS1A family transposase
COORDINATES: similar to AA sequence:RefSeq:NP_414838.2
reactive chlorine resistance oxidoreductase RclA
COORDINATES: similar to AA sequence:RefSeq:WP_004407640.1
GO:0018822 - nitrile hydratase activity [Evidence IEA]
GO:0050898 - nitrile metabolic process [Evidence IEA]
frameshifted; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_008109374.1
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_016236494.1
COORDINATES: similar to AA sequence:RefSeq:YP_010051215.1
COORDINATES: similar to AA sequence:RefSeq:NP_418713.1
COORDINATES: similar to AA sequence:RefSeq:NP_418712.1
ferric citrate uptake sigma factor regulator FecR
COORDINATES: similar to AA sequence:RefSeq:NP_418711.1
TonB-dependent Fe(3+) dicitrate receptor FecA
COORDINATES: similar to AA sequence:RefSeq:NP_418710.4
Fe(3+) dicitrate ABC transporter substrate-binding protein FecB
COORDINATES: similar to AA sequence:RefSeq:NP_418709.1
iron-dicitrate ABC transporter permease FecC
COORDINATES: similar to AA sequence:RefSeq:NP_418708.1
Fe(3+) dicitrate ABC transporter permease subunit FecD
COORDINATES: similar to AA sequence:RefSeq:NP_418707.1
Fe(3+) dicitrate ABC transporter ATP-binding protein FecE
COORDINATES: similar to AA sequence:RefSeq:NP_858152.1
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.; incomplete; partial in the middle of a contig; missing C-terminus; 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_076612230.1
frameshifted; incomplete; partial in the middle of a contig; missing N-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
IS1-like element IS1B family transposase
COORDINATES: similar to AA sequence:RefSeq:NP_308426.1
frameshifted; internal stop; 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:NP_414879.3
DNA-binding transcriptional repressor LacI
COORDINATES: similar to AA sequence:RefSeq:NP_308424.1
COORDINATES: similar to AA sequence:RefSeq:NP_414877.1
COORDINATES: similar to AA sequence:RefSeq:NP_414876.1
GO:0016407 - acetyltransferase activity [Evidence IEA]
maltose acetyltransferase domain-containing protein
COORDINATES: protein motif:HMM:NF015365.2
GO:0003677 - DNA binding [Evidence IEA]; GO:0004803 - transposase activity [Evidence IEA]
GO:0006313 - transposition, DNA-mediated [Evidence IEA]
COORDINATES: protein motif:HMM:NF024169.2
COORDINATES: similar to AA sequence:RefSeq:WP_008815950.1
COORDINATES: similar to AA sequence:RefSeq:WP_002211756.1
COORDINATES: similar to AA sequence:RefSeq:WP_011147726.1
Rpn family recombination-promoting nuclease/putative transposase
COORDINATES: similar to AA sequence:RefSeq:WP_004152402.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0000150 - DNA strand exchange activity [Evidence IEA]
GO:0006310 - DNA recombination [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:NP_416498.2
COORDINATES: similar to AA sequence:RefSeq:WP_005120221.1
MetQ/NlpA family ABC transporter substrate-binding protein
COORDINATES: similar to AA sequence:RefSeq:NP_460348.1
GO:0043546 - molybdopterin cofactor binding [Evidence IEA]; GO:0016491 - oxidoreductase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:NP_460349.1
COORDINATES: similar to AA sequence:RefSeq:NP_460350.1
COORDINATES: similar to AA sequence:RefSeq:NP_460351.1
tetrathionate respiration histidine kinase TtrS
COORDINATES: similar to AA sequence:RefSeq:WP_005122830.1
tetrathionate respiration response regulator TtrR
COORDINATES: similar to AA sequence:RefSeq:WP_000528119.1
COORDINATES: similar to AA sequence:RefSeq:WP_008063281.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]; GO:0046872 - metal ion binding [Evidence IEA]
GO:0045893 - positive regulation of DNA-templated transcription [Evidence IEA]
Cd(II)/Pb(II)-responsive transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_008434970.1
GO:0042625 - ATPase-coupled ion transmembrane transporter activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_016246651.1
TnsA endonuclease N-terminal domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_000019445.1
IS5-like element ISKpn26 family transposase
COORDINATES: protein motif:HMM:NF013676.2
COORDINATES: similar to AA sequence:RefSeq:WP_001192442.1
HlyD family efflux transporter periplasmic adaptor subunit
COORDINATES: similar to AA sequence:RefSeq:WP_001567980.1
COORDINATES: similar to AA sequence:RefSeq:WP_001548177.1
GO:0005215 - transporter activity [Evidence IEA]
efflux RND transporter periplasmic adaptor subunit
COORDINATES: similar to AA sequence:RefSeq:WP_000989158.1
GO:0015562 - efflux transmembrane transporter activity [Evidence IEA]
GO:0055085 - transmembrane transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_016243447.1
COORDINATES: similar to AA sequence:RefSeq:WP_001699286.1
COORDINATES: similar to AA sequence:RefSeq:WP_086558260.1
COORDINATES: similar to AA sequence:RefSeq:WP_000647571.1
COORDINATES: similar to AA sequence:RefSeq:WP_000790485.1
COORDINATES: similar to AA sequence:RefSeq:WP_005763473.1
copper/silver sensor histidine kinase SilS
COORDINATES: similar to AA sequence:RefSeq:WP_001572351.1
copper/silver response regulator transcription factor SilR
COORDINATES: similar to AA sequence:RefSeq:WP_001572989.1
Cu(+)/Ag(+) efflux RND transporter outer membrane channel SilC
COORDINATES: similar to AA sequence:RefSeq:WP_009654303.1
Cu(+)/Ag(+) efflux RND transporter periplasmic metallochaperone SilF
COORDINATES: similar to AA sequence:RefSeq:WP_017146627.1
Cu(+)/Ag(+) efflux RND transporter periplasmic adaptor subunit SilB
COORDINATES: similar to AA sequence:RefSeq:WP_011711636.1
Cu(+)/Ag(+) efflux RND transporter permease subunit SilA
COORDINATES: similar to AA sequence:RefSeq:WP_002436620.1
COORDINATES: similar to AA sequence:RefSeq:WP_032489447.1
COORDINATES: similar to AA sequence:RefSeq:WP_000843499.1
COORDINATES: similar to AA sequence:RefSeq:WP_019077272.1
helix-turn-helix transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_001647051.1
type II toxin-antitoxin system RelE/ParE family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_076612074.1
COORDINATES: similar to AA sequence:RefSeq:YP_005221000.1
IS6-like element IS26 family transposase
COORDINATES: similar to AA sequence:RefSeq:NP_490534.1
COORDINATES: similar to AA sequence:RefSeq:NP_490533.1
COORDINATES: similar to AA sequence:RefSeq:WP_001572368.1
QseB-like response regulator transcription factor
COORDINATES: similar to AA sequence:RefSeq:WP_001572371.1
COORDINATES: similar to AA sequence:RefSeq:WP_001572372.1
COORDINATES: similar to AA sequence:RefSeq:WP_001572373.1
phosphoethanolamine--lipid A transferase MCR-9.1
COORDINATES: similar to AA sequence:RefSeq:WP_076611102.1
IS5-like element IS903B family transposase
COORDINATES: similar to AA sequence:RefSeq:WP_001211179.1
copper resistance membrane spanning protein PcoS
COORDINATES: similar to AA sequence:RefSeq:WP_000723069.1
COORDINATES: similar to AA sequence:RefSeq:WP_001572377.1
COORDINATES: similar to AA sequence:RefSeq:NP_310938.1
Ni(II)/Co(II)-binding transcriptional repressor RcnR
COORDINATES: similar to AA sequence:RefSeq:WP_000118563.1
GO:0005886 - plasma membrane [Evidence IEA]
GO:0004190 - aspartic-type endopeptidase activity [Evidence IEA]
GO:0009306 - protein secretion [Evidence IEA]; GO:0006508 - proteolysis [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_016236504.1
COORDINATES: similar to AA sequence:RefSeq:WP_021138877.1
COORDINATES: similar to AA sequence:RefSeq:WP_000838015.1
COORDINATES: protein motif:HMM:NF019029.2
COORDINATES: protein motif:HMM:TIGR04346.1
COORDINATES: similar to AA sequence:RefSeq:WP_004666729.1
COORDINATES: protein motif:HMM:NF033883.1
COORDINATES: protein motif:HMM:NF023713.2
DotH/IcmK family type IV secretion protein
COORDINATES: protein motif:HMM:NF022835.2
COORDINATES: similar to AA sequence:RefSeq:WP_016245688.1
COORDINATES: similar to AA sequence:RefSeq:WP_006705984.1
COORDINATES: similar to AA sequence:RefSeq:WP_006705983.1
COORDINATES: similar to AA sequence:RefSeq:WP_013087364.1
GO:0015074 - DNA integration [Evidence IEA]; GO:0006310 - DNA recombination [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_001317531.1
ParB/RepB/Spo0J family partition protein
COORDINATES: protein motif:HMM:NF018044.2
conjugation system SOS inhibitor PsiB family protein
COORDINATES: protein motif:HMM:NF018636.2
COORDINATES: similar to AA sequence:RefSeq:WP_004197772.1
COORDINATES: similar to AA sequence:RefSeq:WP_000190057.1
COORDINATES: protein motif:HMM:NF013618.2
lytic transglycosylase domain-containing protein
COORDINATES: protein motif:HMM:NF017524.2
plasmid mobilization relaxosome protein MobC
COORDINATES: protein motif:HMM:NF037421.2
COORDINATES: protein motif:HMM:NF022136.2
COORDINATES: similar to AA sequence:RefSeq:WP_001034975.1
GO:0019867 - outer membrane [Evidence IEA]
GO:0009297 - pilus assembly [Evidence IEA]; GO:0009306 - protein secretion [Evidence IEA]
PilN family type IVB pilus formation outer membrane protein
COORDINATES: protein motif:HMM:NF018562.2
COORDINATES: similar to AA sequence:RefSeq:WP_001719583.1
GO:0009297 - pilus assembly [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_001719582.1
COORDINATES: similar to AA sequence:RefSeq:WP_001079825.1
type II secretion system F family protein
COORDINATES: similar to AA sequence:RefSeq:WP_001719580.1
COORDINATES: similar to AA sequence:RefSeq:WP_001719579.1
COORDINATES: similar to AA sequence:RefSeq:WP_001719578.1
shufflon system plasmid conjugative transfer pilus tip adhesin PilV
COORDINATES: similar to AA sequence:RefSeq:WP_001563247.1
COORDINATES: similar to AA sequence:RefSeq:WP_001719577.1
COORDINATES: similar to AA sequence:RefSeq:WP_001719513.1
COORDINATES: protein motif:HMM:NF012403.2
GO:0005524 - ATP binding [Evidence IEA]; GO:0140658 - ATP-dependent chromatin remodeler activity [Evidence IEA]
COORDINATES: protein motif:HMM:TIGR00180.1
GO:0007059 - chromosome segregation [Evidence IEA]; GO:0000910 - cytokinesis [Evidence IEA]
COORDINATES: protein motif:HMM:NF013793.2
COORDINATES: protein motif:HMM:NF005829.0
GO:0003677 - DNA binding [Evidence IEA]; GO:0003916 - DNA topoisomerase activity [Evidence IEA]
GO:0006265 - DNA topological change [Evidence IEA]
COORDINATES: protein motif:HMM:NF024498.2
COORDINATES: protein motif:HMM:TIGR01391.1
GO:0003896 - DNA primase activity [Evidence IEA]
GO:0006269 - DNA replication, synthesis of RNA primer [Evidence IEA]
COORDINATES: protein motif:HMM:NF024108.2
TraM recognition domain-containing protein
COORDINATES: protein motif:HMM:NF014044.2
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: protein motif:HMM:TIGR02525.1
COORDINATES: protein motif:HMM:NF028242.2
type IV secretory system conjugative DNA transfer family protein
COORDINATES: similar to AA sequence:RefSeq:WP_001562850.1
internal stop; 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_001567331.1
COORDINATES: similar to AA sequence:RefSeq:WP_001239408.1
COORDINATES: similar to AA sequence:RefSeq:WP_001541955.1
COORDINATES: similar to AA sequence:RefSeq:WP_001572325.1
COORDINATES: similar to AA sequence:RefSeq:WP_001567366.1
COORDINATES: similar to AA sequence:RefSeq:WP_001572339.1
GO:0010181 - FMN binding [Evidence IEA]; GO:0004457 - lactate dehydrogenase activity [Evidence IEA]
GO:0006089 - lactate metabolic process [Evidence IEA]
FMN-dependent L-lactate dehydrogenase LldD
COORDINATES: similar to AA sequence:RefSeq:WP_010671891.1
frameshifted; incomplete; partial in the middle of a contig; missing C-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
IS5-like element IS5B family transposase
COORDINATES: similar to AA sequence:RefSeq:WP_000091962.1
COORDINATES: similar to AA sequence:RefSeq:WP_008786570.1
COORDINATES: similar to AA sequence:RefSeq:WP_001066652.1
COORDINATES: similar to AA sequence:RefSeq:WP_006320258.1
GO:0004519 - endonuclease activity [Evidence IEA]; GO:0003676 - nucleic acid binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_006118557.1
COORDINATES: protein motif:HMM:NF015489.2
GO:0015643 - toxic substance binding [Evidence IEA]
GO:0030153 - bacteriocin immunity [Evidence IEA]
colicin E1 family microcin immunity protein
COORDINATES: similar to AA sequence:RefSeq:WP_004846643.1
GO:0019835 - cytolysis [Evidence IEA]; GO:0050829 - defense response to Gram-negative bacterium [Evidence IEA]
COORDINATES: protein motif:HMM:NF033828.1
COORDINATES: similar to AA sequence:RefSeq:WP_032495017.1
COORDINATES: similar to AA sequence:RefSeq:WP_001235708.1
COORDINATES: similar to AA sequence:RefSeq:WP_008438401.1