Pantoea deleyi strain LMG24200 plasmid Plas3, complete sequence.
Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales; Erwiniaceae; Pantoea.
Genome sequence of soft rot disease pathogen
Submitted (02-MAR-2021) Institute of Plant and Environment Protection, Beijing Academy of Agriculture and Forestry Sciences, shuguanghuayuan road, beijing 100097, China
REFSEQ INFORMATION: The reference sequence is identical to\nCP071408.1.\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 :: 20-FEB-2021\nAssembly Method :: Unicycler v. v0.4.8\nAssembly Name :: LMG24200\nGenome Representation :: Full\nExpected Final Version :: Yes\nGenome Coverage :: 290x\nSequencing Technology :: Oxford Nanopore PromethION\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 04/07/2023 05:38:31\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) :: 4,362\nCDSs (total) :: 4,252\nGenes (coding) :: 4,205\nCDSs (with protein) :: 4,205\nGenes (RNA) :: 110\nrRNAs :: 8, 7, 7 (5S, 16S, 23S)\ncomplete rRNAs :: 8, 7, 7 (5S, 16S, 23S)\ntRNAs :: 77\nncRNAs :: 11\nPseudo Genes (total) :: 47\nCDSs (without protein) :: 47\nPseudo Genes (ambiguous residues) :: 0 of 47\nPseudo Genes (frameshifted) :: 21 of 47\nPseudo Genes (incomplete) :: 30 of 47\nPseudo Genes (internal stop) :: 14 of 47\nPseudo Genes (multiple problems) :: 15 of 47\nPseudo Genes (short protein) :: 1 of 47\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: protein motif:HMM:NF039218.1
Derived by automated computational analysis using gene prediction method: Protein Homology.
SGNH hydrolase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_010671421.1
GO:0003684 - damaged DNA binding [Evidence IEA]
translesion error-prone DNA polymerase V subunit UmuC
COORDINATES: similar to AA sequence:RefSeq:WP_010671422.1
COORDINATES: similar to AA sequence:RefSeq:WP_001670144.1
COORDINATES: similar to AA sequence:RefSeq:WP_012439780.1
COORDINATES: similar to AA sequence:RefSeq:WP_016266442.1
COORDINATES: similar to AA sequence:RefSeq:WP_013036429.1
thioredoxin fold domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_013036428.1
COORDINATES: similar to AA sequence:RefSeq:WP_013036427.1
plasmid IncI1-type surface exclusion protein ExcA
COORDINATES: similar to AA sequence:RefSeq:WP_013036426.1
COORDINATES: similar to AA sequence:RefSeq:WP_019105438.1
Hha/YmoA family nucleoid-associated regulatory protein
COORDINATES: similar to AA sequence:RefSeq:WP_013036425.1
COORDINATES: similar to AA sequence:RefSeq:WP_013036423.1
COORDINATES: similar to AA sequence:RefSeq:WP_013036422.1
COORDINATES: protein motif:HMM:NF033888.1
COORDINATES: similar to AA sequence:RefSeq:WP_012439769.1
COORDINATES: similar to AA sequence:RefSeq:WP_006122229.1
type II toxin-antitoxin system RelE/ParE family toxin
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_011051388.1
COORDINATES: similar to AA sequence:RefSeq:WP_013036372.1
COORDINATES: similar to AA sequence:RefSeq:WP_016495620.1
COORDINATES: similar to AA sequence:RefSeq:WP_019105022.1
COORDINATES: similar to AA sequence:RefSeq:WP_019104971.1
COORDINATES: similar to AA sequence:RefSeq:WP_006322813.1
COORDINATES: similar to AA sequence:RefSeq:WP_019105477.1
COORDINATES: similar to AA sequence:RefSeq:WP_013512851.1
COORDINATES: similar to AA sequence:RefSeq:WP_010260374.1
frameshifted; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_004171349.1
COORDINATES: similar to AA sequence:RefSeq:WP_004161085.1
GO:0016616 - oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:YP_005228626.1
COORDINATES: similar to AA sequence:RefSeq:WP_004105313.1
COORDINATES: similar to AA sequence:RefSeq:WP_004853905.1
LacI family DNA-binding transcriptional regulator
LuxR C-terminal-related transcriptional regulator
COORDINATES: protein motif:HMM:NF012698.2
GO:0000160 - phosphorelay signal transduction system [Evidence IEA]; GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
winged helix-turn-helix domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_008460566.1
COORDINATES: similar to AA sequence:RefSeq:WP_008107322.1
COORDINATES: similar to AA sequence:RefSeq:WP_015376531.1
TcfC E-set like domain-containing protein
COORDINATES: protein motif:HMM:NF019078.2
COORDINATES: similar to AA sequence:RefSeq:WP_001424685.1
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_000148350.1
helix-turn-helix domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_010260379.1
translesion error-prone DNA polymerase V autoproteolytic subunit
COORDINATES: similar to AA sequence:RefSeq:WP_000457546.1
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_017802650.1
COORDINATES: similar to AA sequence:RefSeq:WP_013511994.1
COORDINATES: similar to AA sequence:RefSeq:WP_013511995.1
COORDINATES: similar to AA sequence:RefSeq:WP_013199858.1
COORDINATES: similar to AA sequence:RefSeq:WP_015701125.1
GO:0007165 - signal transduction [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_009092786.1
GO:0001216 - DNA-binding transcription activator activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_007891167.1
GO:0008080 - N-acetyltransferase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011147074.1
GO:0006865 - amino acid transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_019104957.1
GO:0004803 - transposase activity [Evidence IEA]
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; 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_013512914.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0004803 - transposase activity [Evidence IEA]
GO:0006313 - transposition, DNA-mediated [Evidence IEA]
IS66-like element accessory protein TnpA
COORDINATES: similar to AA sequence:RefSeq:WP_013199721.1
COORDINATES: similar to AA sequence:RefSeq:WP_013360048.1
COORDINATES: similar to AA sequence:RefSeq:WP_013357654.1
COORDINATES: similar to AA sequence:RefSeq:WP_006297806.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_013360055.1
COORDINATES: similar to AA sequence:RefSeq:WP_010245756.1
COORDINATES: similar to AA sequence:RefSeq:WP_017802604.1
GO:0052621 - diguanylate cyclase activity [Evidence IEA]; GO:0046872 - metal ion binding [Evidence IEA]
sensor domain-containing diguanylate cyclase
COORDINATES: similar to AA sequence:RefSeq:WP_006118233.1
sensor domain-containing phosphodiesterase
COORDINATES: similar to AA sequence:RefSeq:WP_014594672.1
COORDINATES: similar to AA sequence:RefSeq:WP_010256895.1
COORDINATES: similar to AA sequence:RefSeq:WP_014594671.1
COORDINATES: similar to AA sequence:RefSeq:WP_010260381.1
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_013317263.1
COORDINATES: similar to AA sequence:RefSeq:WP_019105454.1
COORDINATES: protein motif:HMM:NF025027.2
COORDINATES: similar to AA sequence:RefSeq:WP_000928600.1
COORDINATES: protein motif:HMM:NF028182.2
putative phage abortive infection protein
COORDINATES: similar to AA sequence:RefSeq:WP_017802808.1
COORDINATES: similar to AA sequence:RefSeq:WP_013199719.1
COORDINATES: similar to AA sequence:RefSeq:WP_013199720.1
COORDINATES: similar to AA sequence:RefSeq:WP_020805646.1
COORDINATES: protein motif:HMM:NF014566.2
GO:0004222 - metalloendopeptidase activity [Evidence IEA]
GO:0071586 - CAAX-box protein processing [Evidence IEA]
CPBP family intramembrane metalloprotease
COORDINATES: protein motif:HMM:NF013884.2
GO:0016747 - acyltransferase activity, transferring groups other than amino-acyl groups [Evidence IEA]