Pantoea dispersa strain Lsch plasmid pLsch, complete sequence.
Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales; Erwiniaceae; Pantoea.
Complete genome of Pantoea dispersa Lsch, isolated from a drinking water container in Laos
Submitted (30-AUG-2021) Shuyuan Molecular Biology Laboratory, The Independent Schools Foundation Academy, 1 Kong Sin Wan Road, Pokfulam, Hong Kong HK SAR, Hong Kong
REFSEQ INFORMATION: The reference sequence is identical to\nCP082348.1.\nBacteria and source DNA available from Dr. Simon D. J. Griffin,\nShuyuan Molecular Biology Laboratory, ISF Academy, 1 Kong Sin Road,\nPokfulam, Hong Kong.\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 :: 23-NOV-2020\nAssembly Method :: Unicycler v. v0.4.8-beta\nAssembly Name :: SG_Pantoea_dispersa_Lsch\nGenome Representation :: Full\nExpected Final Version :: Yes\nGenome Coverage :: 102.0x\nSequencing Technology :: Illumina MiSeq; Oxford Nanopore MinION\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 03/25/2023 06:09:46\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) :: 4,603\nCDSs (total) :: 4,494\nGenes (coding) :: 4,441\nCDSs (with protein) :: 4,441\nGenes (RNA) :: 109\nrRNAs :: 8, 7, 7 (5S, 16S, 23S)\ncomplete rRNAs :: 8, 7, 7 (5S, 16S, 23S)\ntRNAs :: 79\nncRNAs :: 8\nPseudo Genes (total) :: 53\nCDSs (without protein) :: 53\nPseudo Genes (ambiguous residues) :: 0 of 53\nPseudo Genes (frameshifted) :: 28 of 53\nPseudo Genes (incomplete) :: 27 of 53\nPseudo Genes (internal stop) :: 15 of 53\nPseudo Genes (multiple problems) :: 16 of 53\nPseudo Genes (short protein) :: 1 of 53\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_013036384.1
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_001159044.1
COORDINATES: similar to AA sequence:RefSeq:WP_013036380.1
COORDINATES: protein motif:HMM:NF018792.2
COORDINATES: similar to AA sequence:RefSeq:WP_019105022.1
COORDINATES: similar to AA sequence:RefSeq:WP_013036371.1
COORDINATES: similar to AA sequence:RefSeq:WP_006322813.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0008170 - N-methyltransferase activity [Evidence IEA]
GO:0006306 - DNA methylation [Evidence IEA]
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_013360165.1
GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]; GO:0043565 - sequence-specific DNA binding [Evidence IEA]
GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
helix-turn-helix domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_013512546.1
phenylacetaldoxime dehydratase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_007373328.1
COORDINATES: similar to AA sequence:RefSeq:WP_013512544.1
COORDINATES: similar to AA sequence:RefSeq:WP_013360170.1
GO:0018822 - nitrile hydratase activity [Evidence IEA]
GO:0050898 - nitrile metabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_007373331.1
COORDINATES: similar to AA sequence:RefSeq:WP_013360172.1
GO:0003674 - molecular_function [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_013360173.1
COORDINATES: similar to AA sequence:RefSeq:WP_013360174.1
COORDINATES: similar to AA sequence:RefSeq:WP_013360175.1
COORDINATES: similar to AA sequence:RefSeq:WP_013512004.1
COORDINATES: similar to AA sequence:RefSeq:WP_013512005.1
GO:0071468 - cellular response to acidic pH [Evidence IEA]
biofilm development regulator YmgB/AriR family protein
COORDINATES: protein motif:HMM:NF022255.2
COORDINATES: similar to AA sequence:RefSeq:WP_017345774.1
COORDINATES: similar to AA sequence:RefSeq:WP_014333035.1
COORDINATES: similar to AA sequence:RefSeq:WP_014598161.1
COORDINATES: similar to AA sequence:RefSeq:WP_010615637.1
COORDINATES: similar to AA sequence:RefSeq:WP_017345770.1
COORDINATES: similar to AA sequence:RefSeq:WP_013512013.1
COORDINATES: similar to AA sequence:RefSeq:WP_013512829.1
COORDINATES: similar to AA sequence:RefSeq:WP_013512015.1
COORDINATES: similar to AA sequence:RefSeq:WP_007854457.1
COORDINATES: similar to AA sequence:RefSeq:WP_008926219.1
COORDINATES: similar to AA sequence:RefSeq:WP_017345744.1
COORDINATES: similar to AA sequence:RefSeq:WP_017345743.1
COORDINATES: similar to AA sequence:RefSeq:WP_013512020.1
COORDINATES: similar to AA sequence:RefSeq:WP_014606784.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0003887 - DNA-directed DNA polymerase activity [Evidence IEA]
GO:0006260 - DNA replication [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.
COORDINATES: similar to AA sequence:RefSeq:WP_001718434.1
GO:0003697 - single-stranded DNA binding [Evidence IEA]
GO:0006974 - cellular response to DNA damage stimulus [Evidence IEA]; GO:0018142 - protein-DNA covalent cross-linking [Evidence IEA]
frameshifted; Derived by automated computational analysis using gene prediction method: Protein Homology.
SOS response-associated peptidase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_013512048.1
COORDINATES: similar to AA sequence:RefSeq:WP_010260788.1
translesion error-prone DNA polymerase V autoproteolytic subunit
COORDINATES: similar to AA sequence:RefSeq:WP_004152351.1
binds processed UmuD protein to form functional DNA pol V (UmuD'2UmuC); involved in translesion polymerization; 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_010260799.1
GO:0015074 - DNA integration [Evidence IEA]; GO:0006310 - DNA recombination [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_013199813.1
COORDINATES: similar to AA sequence:RefSeq:WP_014606795.1
COORDINATES: similar to AA sequence:RefSeq:WP_010260804.1
COORDINATES: similar to AA sequence:RefSeq:WP_013199814.1
GO:0004619 - phosphoglycerate mutase activity [Evidence IEA]
GO:0006096 - glycolytic process [Evidence IEA]
2,3-bisphosphoglycerate-dependent phosphoglycerate mutase
COORDINATES: similar to AA sequence:RefSeq:WP_010260810.1
GO:0004634 - phosphopyruvate hydratase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_010260813.1
COORDINATES: similar to AA sequence:RefSeq:WP_010260815.1
COORDINATES: nucleotide motif:Rfam:14.4:RF01734
Fluoride riboswitches increase expression of downstream genes that help mitigate the toxic effects of very high levels of fluoride; They are found in a wide variety of bacteria and archaea; Derived by automated computational analysis using gene prediction method: cmsearch.
COORDINATES: similar to AA sequence:RefSeq:WP_010260381.1
GO:0003684 - damaged DNA binding [Evidence IEA]
frameshifted; incomplete; partial in the middle of a contig; missing N-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
translesion error-prone DNA polymerase V subunit UmuC
COORDINATES: similar to AA sequence:RefSeq:WP_017802653.1
COORDINATES: similar to AA sequence:RefSeq:WP_000051067.1
COORDINATES: similar to AA sequence:RefSeq:WP_076612015.1
GO:0004803 - transposase activity [Evidence IEA]
programmed frameshift; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_013512848.1
COORDINATES: similar to AA sequence:RefSeq:WP_007762557.1
COORDINATES: similar to AA sequence:RefSeq:WP_007891814.1
type II toxin-antitoxin system RelE/ParE family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_015698567.1
COORDINATES: similar to AA sequence:RefSeq:WP_009092789.1
GO:0006865 - amino acid transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_009092790.1
COORDINATES: similar to AA sequence:RefSeq:WP_019105436.1
COORDINATES: similar to AA sequence:RefSeq:WP_007885492.1
GO:0007059 - chromosome segregation [Evidence IEA]; GO:0000910 - cytokinesis [Evidence IEA]
ParB/RepB/Spo0J family partition protein
COORDINATES: similar to AA sequence:RefSeq:WP_014344450.1
GO:0003887 - DNA-directed DNA polymerase activity [Evidence IEA]
GO:0006270 - DNA replication initiation [Evidence IEA]
RepB family plasmid replication initiator protein
COORDINATES: similar to AA sequence:RefSeq:WP_013023994.1
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_013319785.1
COORDINATES: similar to AA sequence:RefSeq:WP_014701731.1
COORDINATES: similar to AA sequence:RefSeq:WP_014606677.1
dihydrodipicolinate synthase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_012886433.1
COORDINATES: similar to AA sequence:RefSeq:WP_008924631.1
GO:0055085 - transmembrane transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_010671414.1
COORDINATES: protein motif:HMM:NF020387.2
COORDINATES: similar to AA sequence:RefSeq:WP_012850222.1
COORDINATES: similar to AA sequence:RefSeq:WP_001548787.1
GO:0110001 - toxin-antitoxin complex [Evidence IEA]
GO:0004540 - ribonuclease activity [Evidence IEA]
type II toxin-antitoxin system YhaV family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_010260980.1
COORDINATES: similar to AA sequence:RefSeq:WP_014611412.1
COORDINATES: similar to AA sequence:RefSeq:WP_004869856.1
COORDINATES: similar to AA sequence:RefSeq:WP_020317119.1
COORDINATES: similar to AA sequence:RefSeq:WP_001595120.1
type II toxin-antitoxin system Phd/YefM family antitoxin
COORDINATES: protein motif:HMM:NF018516.2
type VI secretion system ImpA family N-terminal domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_012745713.1
GO:0033103 - protein secretion by the type VI secretion system [Evidence IEA]
type VI secretion system contractile sheath small subunit
COORDINATES: similar to AA sequence:RefSeq:WP_017799570.1
GO:0033104 - type VI protein secretion system complex [Evidence IEA]
type VI secretion system contractile sheath large subunit
COORDINATES: similar to AA sequence:RefSeq:WP_002210479.1
type VI secretion system tube protein Hcp
COORDINATES: similar to AA sequence:RefSeq:WP_015378391.1
COORDINATES: protein motif:HMM:NF017733.2
type VI secretion system baseplate subunit TssF
COORDINATES: protein motif:HMM:TIGR03347.1
type VI secretion system baseplate subunit TssG
COORDINATES: similar to AA sequence:RefSeq:WP_019456181.1
GO:0005524 - ATP binding [Evidence IEA]; GO:0016887 - ATP hydrolysis activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_012105682.1
type VI secretion system tip protein VgrG
COORDINATES: protein motif:HMM:NF021456.2
COORDINATES: protein motif:HMM:NF024986.2
COORDINATES: protein motif:HMM:NF023482.2
COORDINATES: similar to AA sequence:RefSeq:WP_002214737.1
COORDINATES: similar to AA sequence:RefSeq:WP_002210470.1
type VI secretion system baseplate subunit TssK
COORDINATES: protein motif:HMM:TIGR03349.1
DotU/TssL family secretion system protein
COORDINATES: protein motif:HMM:TIGR03348.1
type VI secretion system membrane subunit TssM
COORDINATES: protein motif:HMM:NF039398.1
COORDINATES: similar to AA sequence:RefSeq:WP_004966400.1
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.; internal stop; 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_000099160.1
frameshifted; internal stop; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: protein motif:HMM:NF013884.2
GO:0016747 - acyltransferase activity, transferring groups other than amino-acyl groups [Evidence IEA]
COORDINATES: protein motif:HMM:NF025063.2
GO:0015074 - DNA integration [Evidence IEA]
integrase core domain-containing protein
COORDINATES: protein motif:HMM:NF013677.2
GO:0003677 - DNA binding [Evidence IEA]; GO:0004803 - transposase activity [Evidence IEA]
GO:0006313 - transposition, DNA-mediated [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_010657278.1
GO:0004553 - hydrolase activity, hydrolyzing O-glycosyl compounds [Evidence IEA]
GO:0071704 - organic substance metabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_076611473.1
COORDINATES: protein motif:HMM:NF012707.2
COORDINATES: similar to AA sequence:RefSeq:WP_008114634.1
COORDINATES: similar to AA sequence:RefSeq:WP_076611646.1
COORDINATES: similar to AA sequence:RefSeq:WP_076611293.1
COORDINATES: protein motif:HMM:NF012565.2
COORDINATES: protein motif:HMM:NF012635.2
COORDINATES: protein motif:HMM:NF012478.2
GO:0003755 - peptidyl-prolyl cis-trans isomerase activity [Evidence IEA]
FKBP-type peptidyl-prolyl cis-trans isomerase
COORDINATES: protein motif:HMM:NF012422.2
LuxR C-terminal-related transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_076611475.1
COORDINATES: similar to AA sequence:RefSeq:WP_076611683.1
COORDINATES: similar to AA sequence:RefSeq:WP_011898542.1
COORDINATES: similar to AA sequence:RefSeq:WP_016942376.1
COORDINATES: similar to AA sequence:RefSeq:WP_001556711.1
COORDINATES: similar to AA sequence:RefSeq:WP_032495017.1
COORDINATES: similar to AA sequence:RefSeq:WP_039272517.1
GO:0007155 - cell adhesion [Evidence IEA]
COORDINATES: protein motif:HMM:NF012786.2
fimbria/pilus outer membrane usher protein
COORDINATES: similar to AA sequence:RefSeq:WP_000627495.1
COORDINATES: similar to AA sequence:RefSeq:WP_001531258.1
COORDINATES: similar to AA sequence:RefSeq:WP_012606398.1
COORDINATES: similar to AA sequence:RefSeq:WP_010260340.1
COORDINATES: similar to AA sequence:RefSeq:WP_019104920.1
GO:0015035 - protein-disulfide reductase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_019106273.1
COORDINATES: similar to AA sequence:RefSeq:WP_013511887.1
type IV conjugative transfer system coupling protein TraD
COORDINATES: similar to AA sequence:RefSeq:WP_019105782.1
COORDINATES: similar to AA sequence:RefSeq:WP_013512224.1
GO:0019867 - outer membrane [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_007853387.1
conjugal transfer mating-pair stabilization protein TraG
COORDINATES: similar to AA sequence:RefSeq:WP_013512893.1
conjugal transfer pilus assembly protein TraH
COORDINATES: similar to AA sequence:RefSeq:WP_013200029.1
COORDINATES: similar to AA sequence:RefSeq:WP_019105776.1
COORDINATES: similar to AA sequence:RefSeq:WP_019105775.1
COORDINATES: similar to AA sequence:RefSeq:WP_019105773.1
type-F conjugative transfer system pilin assembly protein TraF
COORDINATES: similar to AA sequence:RefSeq:WP_008325102.1
type-F conjugative transfer system mating-pair stabilization protein TraN
COORDINATES: similar to AA sequence:RefSeq:WP_019104691.1
type-F conjugative transfer system pilin assembly protein TrbC
COORDINATES: similar to AA sequence:RefSeq:WP_019104690.1
conjugal transfer pilus assembly protein TraU
COORDINATES: similar to AA sequence:RefSeq:WP_011906568.1
COORDINATES: similar to AA sequence:RefSeq:WP_013512882.1
COORDINATES: similar to AA sequence:RefSeq:WP_019843226.1
type-F conjugative transfer system protein TraW
COORDINATES: similar to AA sequence:RefSeq:WP_014695881.1
type-F conjugative transfer system protein TrbI
COORDINATES: similar to AA sequence:RefSeq:WP_014695880.1
COORDINATES: similar to AA sequence:RefSeq:WP_019105083.1
type IV conjugative transfer system lipoprotein TraV
COORDINATES: similar to AA sequence:RefSeq:WP_013512203.1
COORDINATES: similar to AA sequence:RefSeq:WP_013512873.1
transcription/translation regulatory transformer protein RfaH
COORDINATES: similar to AA sequence:RefSeq:WP_013512872.1
F-type conjugal transfer pilus assembly protein TraB
COORDINATES: similar to AA sequence:RefSeq:WP_019106287.1
COORDINATES: similar to AA sequence:RefSeq:WP_019105070.1
TraE/TraK family type IV conjugative transfer system protein
COORDINATES: similar to AA sequence:RefSeq:WP_013512869.1
type IV conjugative transfer system protein TraL
COORDINATES: similar to AA sequence:RefSeq:WP_013512868.1
COORDINATES: similar to AA sequence:RefSeq:WP_019105067.1
COORDINATES: similar to AA sequence:RefSeq:WP_019106277.1
COORDINATES: similar to AA sequence:RefSeq:WP_013512865.1
lytic transglycosylase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_013087187.1
COORDINATES: similar to AA sequence:RefSeq:WP_013512190.1