Hafnia alvei strain A23BA plasmid pA23BA, complete sequence.
Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales; Hafniaceae; Hafnia.
The Complete Genome of Hafnia alvei A23BA
Submitted (12-MAR-2020) School of Pharmacy and Life Sciences, Robert Gordon University, Garthdee Road, Aberdeen AB10 7GJ, United Kingdom
REFSEQ INFORMATION: The reference sequence is identical to\nCP050151.1.\nBacteria and source DNA available from N626 SIWB Robert Gordon\nUniversity University, Aberdeen. Scotland, UK.\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 Date :: 21-FEB-2020\nAssembly Method :: Unicycler v. Galaxy Version 0.4.8.0\nGenome Representation :: Full\nExpected Final Version :: Yes\nGenome Coverage :: 256.0x\nSequencing Technology :: Illumina HiSeq; Oxford Nanopore GridION\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 03/29/2023 03:57:54\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) :: 4,369\nCDSs (total) :: 4,244\nGenes (coding) :: 4,216\nCDSs (with protein) :: 4,216\nGenes (RNA) :: 125\nrRNAs :: 9, 8, 8 (5S, 16S, 23S)\ncomplete rRNAs :: 9, 8, 8 (5S, 16S, 23S)\ntRNAs :: 92\nncRNAs :: 8\nPseudo Genes (total) :: 28\nCDSs (without protein) :: 28\nPseudo Genes (ambiguous residues) :: 0 of 28\nPseudo Genes (frameshifted) :: 14 of 28\nPseudo Genes (incomplete) :: 20 of 28\nPseudo Genes (internal stop) :: 7 of 28\nPseudo Genes (multiple problems) :: 11 of 28\nCRISPR Arrays :: 2\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.
COORDINATES: similar to AA sequence:RefSeq:WP_020805590.1
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_017694156.1
COORDINATES: similar to AA sequence:RefSeq:WP_001049169.1
helix-turn-helix transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_012988280.1
COORDINATES: similar to AA sequence:RefSeq:WP_012565226.1
COORDINATES: similar to AA sequence:RefSeq:WP_001021260.1
COORDINATES: similar to AA sequence:RefSeq:WP_012565225.1
COORDINATES: similar to AA sequence:RefSeq:WP_001144751.1
COORDINATES: similar to AA sequence:RefSeq:WP_000231973.1
COORDINATES: similar to AA sequence:RefSeq:WP_001238523.1
GO:0030288 - outer membrane-bounded periplasmic space [Evidence IEA]
GO:0071555 - cell wall organization [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_000695297.1
fimbria/pilus outer membrane usher protein
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: similar to AA sequence:RefSeq:WP_020127473.1
GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
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.
LuxR C-terminal-related transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_001233873.1
COORDINATES: similar to AA sequence:RefSeq:WP_004152389.1
frameshifted; 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: similar to AA sequence:RefSeq:NP_309413.1
phosphoadenosine phosphosulfate reductase
COORDINATES: similar to AA sequence:RefSeq:NP_309414.1
ParB/RepB/Spo0J family partition protein
COORDINATES: similar to AA sequence:RefSeq:WP_008455304.1
COORDINATES: similar to AA sequence:RefSeq:WP_004144378.1
COORDINATES: similar to AA sequence:RefSeq:WP_008322799.1
COORDINATES: similar to AA sequence:RefSeq:WP_000078032.1
COORDINATES: similar to AA sequence:RefSeq:WP_004098841.1
COORDINATES: similar to AA sequence:RefSeq:WP_004666893.1
COORDINATES: similar to AA sequence:RefSeq:WP_001568073.1
type-F conjugative transfer system pilin acetylase TraX
COORDINATES: similar to AA sequence:RefSeq:WP_001463032.1
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
COORDINATES: similar to AA sequence:RefSeq:WP_020315126.1
type IV conjugative transfer system coupling protein TraD
COORDINATES: similar to AA sequence:RefSeq:WP_013609534.1
conjugal transfer mating-pair stabilization protein TraG
COORDINATES: similar to AA sequence:RefSeq:WP_009309877.1
conjugal transfer pilus assembly protein TraH
COORDINATES: similar to AA sequence:RefSeq:WP_000059812.1
type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB
COORDINATES: similar to AA sequence:RefSeq:WP_020315123.1
type-F conjugative transfer system pilin chaperone TraQ
COORDINATES: similar to AA sequence:RefSeq:WP_016831052.1
type-F conjugative transfer system pilin assembly protein TraF
COORDINATES: similar to AA sequence:RefSeq:WP_001756807.1
type-F conjugative transfer system mating-pair stabilization protein TraN
COORDINATES: similar to AA sequence:RefSeq:WP_001568086.1
type-F conjugative transfer system pilin assembly protein TrbC
COORDINATES: similar to AA sequence:RefSeq:NP_490576.1
conjugal transfer pilus assembly protein TraU
COORDINATES: similar to AA sequence:RefSeq:WP_004163052.1
type-F conjugative transfer system protein TraW
COORDINATES: similar to AA sequence:RefSeq:WP_000102756.1
type-F conjugative transfer system protein TrbI
COORDINATES: similar to AA sequence:RefSeq:WP_000069745.1
COORDINATES: protein motif:HMM:TIGR02419.1
TraR/DksA family transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_016233168.1
type IV conjugative transfer system lipoprotein TraV
COORDINATES: protein motif:HMM:NF018947.2
COORDINATES: similar to AA sequence:RefSeq:WP_004194260.1
F-type conjugal transfer pilus assembly protein TraB
COORDINATES: similar to AA sequence:RefSeq:WP_001568101.1
type-F conjugative transfer system secretin TraK
COORDINATES: similar to AA sequence:RefSeq:WP_008324158.1
type IV conjugative transfer system protein TraE
COORDINATES: similar to AA sequence:RefSeq:YP_005229718.1
type IV conjugative transfer system protein TraL
COORDINATES: similar to AA sequence:RefSeq:WP_020316649.1
type IV conjugative transfer system pilin TraA
COORDINATES: similar to AA sequence:RefSeq:WP_008324165.1
COORDINATES: protein motif:HMM:NF020037.2
COORDINATES: similar to AA sequence:RefSeq:WP_001063020.1
conjugal transfer relaxosome DNA-binding protein TraM
COORDINATES: similar to AA sequence:RefSeq:WP_020246007.1
transglycosylase SLT domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_001234456.1
COORDINATES: similar to AA sequence:RefSeq:WP_006322793.1
COORDINATES: similar to AA sequence:RefSeq:WP_000503164.1
GO:0004803 - transposase activity [Evidence IEA]
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_000117512.1
ParB N-terminal domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_009652474.1
COORDINATES: similar to AA sequence:RefSeq:WP_004097018.1
COORDINATES: similar to AA sequence:RefSeq:WP_000108571.1
COORDINATES: protein motif:HMM:NF018792.2
COORDINATES: similar to AA sequence:RefSeq:WP_001104903.1
COORDINATES: similar to AA sequence:RefSeq:NP_052645.1
COORDINATES: similar to AA sequence:RefSeq:WP_004194745.1
COORDINATES: similar to AA sequence:RefSeq:WP_004194746.1
COORDINATES: similar to AA sequence:RefSeq:WP_013036361.1
translesion error-prone DNA polymerase V autoproteolytic subunit
COORDINATES: similar to AA sequence:RefSeq:WP_004953852.1
GO:0003684 - damaged DNA binding [Evidence IEA]
translesion error-prone DNA polymerase V subunit UmuC
COORDINATES: similar to AA sequence:RefSeq:WP_002213354.1
ParB/RepB/Spo0J family plasmid partition protein
COORDINATES: similar to AA sequence:RefSeq:WP_010891239.1
COORDINATES: similar to AA sequence:RefSeq:WP_001478804.1
COORDINATES: similar to AA sequence:RefSeq:NP_490541.1
Rpn family recombination-promoting nuclease/putative transposase
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_016193191.1
COORDINATES: similar to AA sequence:RefSeq:WP_013036354.1
GO:0015074 - DNA integration [Evidence IEA]; GO:0006310 - DNA recombination [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_004090339.1
COORDINATES: similar to AA sequence:RefSeq:WP_001418814.1
COORDINATES: similar to AA sequence:RefSeq:YP_005229629.1
type II toxin-antitoxin system VapB family antitoxin
COORDINATES: similar to AA sequence:RefSeq:YP_005229630.1
type II toxin-antitoxin system VapC family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_001442743.1
COORDINATES: similar to AA sequence:RefSeq:WP_005131811.1