Rahnella victoriana strain JZ-GX1 plasmid unnamed2, complete sequence.
Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales; Yersiniaceae; Rahnella.
Submitted (09-APR-2021) College of Forestry, Nanjing Forestry University, LongPan Road, Nanjing, Jiangsu 211307, China
REFSEQ INFORMATION: The reference sequence is identical to\nCP089921.1.\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 Date :: 09-AUG-2019\nAssembly Method :: Fyle v. V2.5; CANU v. V1.7.1\nGenome Representation :: Full\nExpected Final Version :: Yes\nGenome Coverage :: 262.42x\nSequencing Technology :: Nanopore\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 01/01/2023 16:11:34\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) :: 5,013\nCDSs (total) :: 4,902\nGenes (coding) :: 4,840\nCDSs (with protein) :: 4,840\nGenes (RNA) :: 111\nrRNAs :: 8, 7, 7 (5S, 16S, 23S)\ncomplete rRNAs :: 8, 7, 7 (5S, 16S, 23S)\ntRNAs :: 77\nncRNAs :: 12\nPseudo Genes (total) :: 62\nCDSs (without protein) :: 62\nPseudo Genes (ambiguous residues) :: 0 of 62\nPseudo Genes (frameshifted) :: 30 of 62\nPseudo Genes (incomplete) :: 41 of 62\nPseudo Genes (internal stop) :: 6 of 62\nPseudo Genes (multiple problems) :: 14 of 62\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.
COORDINATES: ab initio prediction:GeneMarkS-2+
GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
LuxR C-terminal-related transcriptional regulator
COORDINATES: protein motif:HMM:NF012786.2
Derived by automated computational analysis using gene prediction method: Protein Homology.
fimbria/pilus outer membrane usher protein
COORDINATES: protein motif:HMM:NF012565.2
GO:0030288 - outer membrane-bounded periplasmic space [Evidence IEA]
GO:0071555 - cell wall organization [Evidence IEA]
COORDINATES: protein motif:HMM:NF028280.2
COORDINATES: protein motif:HMM:NF017655.2
COORDINATES: similar to AA sequence:RefSeq:WP_006815438.1
GO:0051983 - regulation of chromosome segregation [Evidence IEA]
type II toxin-antitoxin system ParD family antitoxin
COORDINATES: similar to AA sequence:RefSeq:WP_015387217.1
type II toxin-antitoxin system RelE/ParE family toxin
COORDINATES: protein motif:HMM:NF012635.2
GO:0007155 - cell adhesion [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_005532914.1
COORDINATES: protein motif:HMM:TIGR01414.1
GO:0009279 - cell outer membrane [Evidence IEA]
GO:0015474 - autotransporter activity [Evidence IEA]
GO:0046819 - protein secretion by the type V secretion system [Evidence IEA]
autotransporter outer membrane beta-barrel domain-containing protein
COORDINATES: protein motif:HMM:NF013073.2
COORDINATES: similar to AA sequence:RefSeq:WP_017893740.1
COORDINATES: similar to AA sequence:RefSeq:WP_017893739.1
COORDINATES: similar to AA sequence:RefSeq:WP_001561275.1
COORDINATES: protein motif:HMM:NF012772.2
COORDINATES: protein motif:HMM:NF012301.2
COORDINATES: protein motif:HMM:NF012422.2
COORDINATES: protein motif:HMM:NF027271.2
COORDINATES: protein motif:HMM:NF012698.2
helix-turn-helix domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_000244358.1
GO:0004803 - transposase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_016059169.1
COORDINATES: similar to AA sequence:RefSeq:WP_000983043.1
GO:0015074 - DNA integration [Evidence IEA]; GO:0006310 - DNA recombination [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_019843123.1
COORDINATES: protein motif:HMM:NF019313.2
COORDINATES: similar to AA sequence:RefSeq:WP_003031986.1
COORDINATES: similar to AA sequence:RefSeq:WP_016193191.1
COORDINATES: similar to AA sequence:RefSeq:WP_012548938.1
Rpn family recombination-promoting nuclease/putative transposase
COORDINATES: similar to AA sequence:RefSeq:WP_009639334.1
GO:0003887 - DNA-directed DNA polymerase activity [Evidence IEA]
GO:0006270 - DNA replication initiation [Evidence IEA]
RepB family plasmid replication initiator protein
COORDINATES: protein motif:HMM:NF020442.2
COORDINATES: similar to AA sequence:RefSeq:WP_005933773.1
ribbon-helix-helix domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_009639336.1
COORDINATES: similar to AA sequence:RefSeq:WP_008807729.1
GO:0003684 - damaged DNA binding [Evidence IEA]
translesion error-prone DNA polymerase V subunit UmuC
COORDINATES: similar to AA sequence:RefSeq:WP_000776034.1
translesion error-prone DNA polymerase V autoproteolytic subunit
COORDINATES: similar to AA sequence:RefSeq:WP_002209100.1
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: similar to AA sequence:RefSeq:WP_001278287.1
COORDINATES: protein motif:HMM:NF014273.2
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_019843205.1
COORDINATES: similar to AA sequence:RefSeq:WP_002211749.1
COORDINATES: similar to AA sequence:RefSeq:WP_013578321.1
COORDINATES: similar to AA sequence:RefSeq:WP_020453970.1
COORDINATES: similar to AA sequence:RefSeq:WP_006322793.1
COORDINATES: protein motif:HMM:NF022728.2
COORDINATES: similar to AA sequence:RefSeq:WP_020805661.1
COORDINATES: similar to AA sequence:RefSeq:WP_012776387.1
type II toxin-antitoxin system RelB/DinJ family antitoxin
COORDINATES: similar to AA sequence:RefSeq:NP_416081.1
COORDINATES: similar to AA sequence:RefSeq:WP_013087187.1
COORDINATES: similar to AA sequence:RefSeq:WP_016192024.1
transglycosylase SLT domain-containing protein
COORDINATES: protein motif:HMM:NF010267.0
conjugal transfer relaxosome DNA-binding protein TraM
COORDINATES: protein motif:HMM:NF017105.2
COORDINATES: similar to AA sequence:RefSeq:WP_013511305.1
COORDINATES: protein motif:HMM:NF017337.2
type IV conjugative transfer system pilin TraA
COORDINATES: similar to AA sequence:RefSeq:WP_006705925.1
type IV conjugative transfer system protein TraL
COORDINATES: similar to AA sequence:RefSeq:WP_016235958.1
type IV conjugative transfer system protein TraE
COORDINATES: similar to AA sequence:RefSeq:WP_017412450.1
type-F conjugative transfer system secretin TraK
COORDINATES: similar to AA sequence:RefSeq:WP_017412451.1
F-type conjugal transfer pilus assembly protein TraB
COORDINATES: similar to AA sequence:RefSeq:WP_005320906.1
type IV conjugative transfer system lipoprotein TraV
COORDINATES: similar to AA sequence:RefSeq:WP_017412454.1
COORDINATES: protein motif:HMM:NF021213.2
type-F conjugative transfer system protein TrbI
COORDINATES: similar to AA sequence:RefSeq:WP_005320899.1
type-F conjugative transfer system protein TraW
COORDINATES: similar to AA sequence:RefSeq:WP_017412458.1
conjugal transfer pilus assembly protein TraU
COORDINATES: protein motif:HMM:TIGR02419.1
GO:0008270 - zinc ion binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_017412459.1
type-F conjugative transfer system pilin assembly protein TrbC
COORDINATES: similar to AA sequence:RefSeq:WP_017412461.1
type-F conjugative transfer system mating-pair stabilization protein TraN
COORDINATES: similar to AA sequence:RefSeq:WP_001203360.1
type-F conjugative transfer system pilin assembly protein TraF
COORDINATES: similar to AA sequence:RefSeq:WP_001486781.1
type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB
COORDINATES: similar to AA sequence:RefSeq:WP_006707021.1
conjugal transfer pilus assembly protein TraH
COORDINATES: protein motif:HMM:NF010295.2
conjugal transfer mating-pair stabilization protein TraG
COORDINATES: similar to AA sequence:RefSeq:WP_020315126.1
type IV conjugative transfer system coupling protein TraD
COORDINATES: similar to AA sequence:RefSeq:WP_017412856.1
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_000428994.1
Hha/YmoA family nucleoid-associated regulatory protein
COORDINATES: similar to AA sequence:RefSeq:WP_006122288.1
COORDINATES: similar to AA sequence:RefSeq:WP_004720780.1
COORDINATES: protein motif:HMM:NF016255.2
COORDINATES: similar to AA sequence:RefSeq:WP_016248732.1
COORDINATES: similar to AA sequence:RefSeq:WP_015841348.1
COORDINATES: similar to AA sequence:RefSeq:WP_015696276.1
COORDINATES: protein motif:HMM:NF015431.2