Yersinia hibernica strain CFS1934 plasmid pCFS1934, complete sequence.
Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales; Yersiniaceae; Yersinia.
Yersinia hibernica sp. nov., isolated from pig-production environments
Submitted (21-SEP-2018) Centre for Food Safety, University College Dublin, UCD O'Brien Science Centre South, Dublin D04 V1W8, Ireland
REFSEQ INFORMATION: The reference sequence is identical to\nCP032488.1.\nBacteria and source DNA available from UCD Centre for Food Safety.\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. 0.4.6\nGenome Representation :: Full\nExpected Final Version :: Yes\nGenome Coverage :: 114.0x\nSequencing Technology :: Illumina HiSeq; Oxford Nanopore MiniION\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 05/05/2023 02:34:44\nAnnotation Pipeline :: NCBI Prokaryotic Genome\n Annotation Pipeline (PGAP)\nAnnotation Method :: Best-placed reference protein\n set; GeneMarkS-2+\nAnnotation Software revision :: 6.5\nFeatures Annotated :: Gene; CDS; rRNA; tRNA; ncRNA\nGenes (total) :: 4,423\nCDSs (total) :: 4,313\nGenes (coding) :: 4,231\nCDSs (with protein) :: 4,231\nGenes (RNA) :: 110\nrRNAs :: 8, 7, 7 (5S, 16S, 23S)\ncomplete rRNAs :: 8, 7, 7 (5S, 16S, 23S)\ntRNAs :: 81\nncRNAs :: 7\nPseudo Genes (total) :: 82\nCDSs (without protein) :: 82\nPseudo Genes (ambiguous residues) :: 0 of 82\nPseudo Genes (frameshifted) :: 22 of 82\nPseudo Genes (incomplete) :: 61 of 82\nPseudo Genes (internal stop) :: 14 of 82\nPseudo Genes (multiple problems) :: 12 of 82\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.
COORDINATES: similar to AA sequence:RefSeq:WP_015060658.1
GO:0004803 - transposase activity [Evidence IEA]
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_000904941.1
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:WP_076611146.1
programmed frameshift; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_004706872.1
inverse autotransporter beta domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_004716216.1
SinI family autotransporter-associated protein
COORDINATES: similar to AA sequence:RefSeq:WP_011193019.1
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: protein motif:HMM:NF012307.2
COORDINATES: similar to AA sequence:RefSeq:WP_016248280.1
COORDINATES: similar to AA sequence:RefSeq:WP_000282312.1
COORDINATES: similar to AA sequence:RefSeq:WP_019281277.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0008170 - N-methyltransferase activity [Evidence IEA]
GO:0006306 - DNA methylation [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_004929864.1
COORDINATES: similar to AA sequence:RefSeq:WP_004929863.1
COORDINATES: similar to AA sequence:RefSeq:WP_019843205.1
COORDINATES: protein motif:HMM:NF018636.2
COORDINATES: protein motif:HMM:NF018044.2
conjugation system SOS inhibitor PsiB family protein
COORDINATES: similar to AA sequence:RefSeq:WP_004966258.1
ParB/RepB/Spo0J family partition protein
COORDINATES: similar to AA sequence:RefSeq:WP_010323162.1
translesion error-prone DNA polymerase V autoproteolytic subunit
COORDINATES: similar to AA sequence:RefSeq:WP_006322746.1
GO:0003684 - damaged DNA binding [Evidence IEA]
translesion error-prone DNA polymerase V subunit UmuC
COORDINATES: similar to AA sequence:RefSeq:WP_004197637.1
COORDINATES: similar to AA sequence:RefSeq:WP_001555635.1
plasmid partitioning/stability family protein
COORDINATES: similar to AA sequence:RefSeq:WP_011977821.1
COORDINATES: similar to AA sequence:RefSeq:WP_017901448.1
COORDINATES: similar to AA sequence:RefSeq:WP_005176595.1
COORDINATES: similar to AA sequence:RefSeq:WP_006322731.1
COORDINATES: similar to AA sequence:RefSeq:WP_019822084.1
COORDINATES: similar to AA sequence:RefSeq:WP_002353252.1
Rpn family recombination-promoting nuclease/putative transposase
COORDINATES: similar to AA sequence:RefSeq:WP_004966268.1
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_000528103.1
COORDINATES: similar to AA sequence:RefSeq:WP_019082178.1
COORDINATES: similar to AA sequence:RefSeq:WP_012606398.1
COORDINATES: similar to AA sequence:RefSeq:WP_002209080.1
COORDINATES: similar to AA sequence:RefSeq:WP_005166219.1
GO:0061077 - chaperone-mediated protein folding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_004391214.1
GO:0015473 - fimbrial usher porin activity [Evidence IEA]
GO:0009297 - pilus assembly [Evidence IEA]
fimbria/pilus outer membrane usher protein
COORDINATES: similar to AA sequence:RefSeq:WP_013649686.1
COORDINATES: similar to AA sequence:RefSeq:WP_007509012.1
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:0005524 - ATP binding [Evidence IEA]; GO:0016887 - ATP hydrolysis activity [Evidence IEA]; GO:0019829 - ATPase-coupled monoatomic cation transmembrane transporter activity [Evidence IEA]; GO:0046872 - metal ion binding [Evidence IEA]; GO:0015662 - P-type ion transporter activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:YP_005220837.1
COORDINATES: similar to AA sequence:RefSeq:WP_001527814.1
COORDINATES: similar to AA sequence:RefSeq:WP_016151351.1
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:NP_417960.1
GO:0008794 - arsenate reductase (glutaredoxin) activity [Evidence IEA]
glutaredoxin-dependent arsenate reductase
COORDINATES: similar to AA sequence:RefSeq:WP_012540054.1
arsenite efflux transporter membrane subunit ArsB
COORDINATES: similar to AA sequence:RefSeq:WP_131199602.1
arsenite efflux transporter ATPase subunit ArsA
COORDINATES: similar to AA sequence:RefSeq:WP_000855179.1
arsenite efflux transporter metallochaperone ArsD
COORDINATES: similar to AA sequence:RefSeq:WP_001114073.1
COORDINATES: protein motif:HMM:NF016255.2
COORDINATES: similar to AA sequence:RefSeq:WP_004720780.1
COORDINATES: similar to AA sequence:RefSeq:WP_000083819.1
COORDINATES: similar to AA sequence:RefSeq:WP_013512907.1
COORDINATES: protein motif:HMM:NF018726.2
GO:0005524 - ATP binding [Evidence IEA]; GO:0003677 - DNA binding [Evidence IEA]; GO:0003678 - DNA helicase activity [Evidence IEA]; GO:0016818 - hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides [Evidence IEA]
conjugative transfer relaxase/helicase TraI