Pantoea alhagi strain LTYR-11Z plasmid pPALTYR11Z, complete sequence.
Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales; Erwiniaceae; Pantoea.
Complete genome sequence of the drought resistance-promoting endophyte Pantoea alhagi LTYR-11Z
Submitted (14-FEB-2017) College of Life Sciences, Northwest A&F University, No.3 Taicheng Road, Yangling, Shaanxi 712100, China
REFSEQ INFORMATION: The reference sequence is identical to\nCP019707.1.\nBacteria and source DNA available from Lei Zhang, College of Life\nSciences, Northwest A&F University, Yangling, Shaanxi 712100, PR\nChina.\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 :: JUN-2016\nAssembly Method :: RS_HGAP_Assembly.3 v. 3\nGenome Representation :: Full\nExpected Final Version :: Yes\nGenome Coverage :: 159.0x\nSequencing Technology :: PacBio\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 02/06/2023 05:20:01\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) :: 4,098\nCDSs (total) :: 3,981\nGenes (coding) :: 3,887\nCDSs (with protein) :: 3,887\nGenes (RNA) :: 117\nrRNAs :: 8, 7, 7 (5S, 16S, 23S)\ncomplete rRNAs :: 8, 7, 7 (5S, 16S, 23S)\ntRNAs :: 85\nncRNAs :: 10\nPseudo Genes (total) :: 94\nCDSs (without protein) :: 94\nPseudo Genes (ambiguous residues) :: 0 of 94\nPseudo Genes (frameshifted) :: 32 of 94\nPseudo Genes (incomplete) :: 67 of 94\nPseudo Genes (internal stop) :: 10 of 94\nPseudo Genes (multiple problems) :: 15 of 94\nPseudo Genes (short protein) :: 1 of 94\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_000493378.1
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: protein motif:HMM:NF019313.2
COORDINATES: similar to AA sequence:RefSeq:WP_019104931.1
COORDINATES: similar to AA sequence:RefSeq:WP_009093282.1
COORDINATES: protein motif:HMM:NF024830.2
COORDINATES: similar to AA sequence:RefSeq:WP_009092747.1
COORDINATES: similar to AA sequence:RefSeq:WP_007733236.1
COORDINATES: similar to AA sequence:RefSeq:WP_007706040.1
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:NP_490541.1
Rpn family recombination-promoting nuclease/putative transposase
COORDINATES: similar to AA sequence:RefSeq:WP_001553091.1
GO:0015074 - DNA integration [Evidence IEA]; GO:0006310 - DNA recombination [Evidence IEA]
COORDINATES: protein motif:HMM:NF014895.2
COORDINATES: protein motif:HMM:NF013468.2
GO:0003725 - double-stranded RNA binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_015671526.1
GO:0004803 - transposase activity [Evidence IEA]
programmed frameshift; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: protein motif:HMM:NF024242.2
helix-turn-helix transcriptional regulator
COORDINATES: protein motif:HMM:NF024109.2
COORDINATES: similar to AA sequence:RefSeq:WP_011354192.1
COORDINATES: similar to AA sequence:RefSeq:WP_009894077.1
COORDINATES: similar to AA sequence:RefSeq:WP_015585260.1
COORDINATES: similar to AA sequence:RefSeq:WP_010260340.1
COORDINATES: similar to AA sequence:RefSeq:WP_001495657.1
COORDINATES: similar to AA sequence:RefSeq:WP_020804818.1
COORDINATES: protein motif:HMM:TIGR02759.1
type IV conjugative transfer system coupling protein TraD
COORDINATES: protein motif:HMM:NF040300.1
COORDINATES: similar to AA sequence:RefSeq:WP_076612015.1
COORDINATES: protein motif:HMM:NF018044.2
conjugation system SOS inhibitor PsiB family protein
COORDINATES: similar to AA sequence:RefSeq:WP_000194654.1
COORDINATES: similar to AA sequence:RefSeq:WP_000168322.1
COORDINATES: similar to AA sequence:RefSeq:WP_009093276.1
frameshifted; Derived by automated computational analysis using gene prediction method: Protein Homology.
translesion error-prone DNA polymerase V autoproteolytic subunit
COORDINATES: similar to AA sequence:RefSeq:WP_004150760.1
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_014594566.1
COORDINATES: similar to AA sequence:RefSeq:WP_019454347.1
COORDINATES: similar to AA sequence:RefSeq:WP_014916473.1
COORDINATES: similar to AA sequence:RefSeq:WP_015742253.1
COORDINATES: similar to AA sequence:RefSeq:WP_020239536.1
GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
heavy metal response regulator transcription factor
COORDINATES: similar to AA sequence:RefSeq:WP_007708053.1
GO:0000155 - phosphorelay sensor kinase activity [Evidence IEA]; GO:0004673 - protein histidine kinase activity [Evidence IEA]; GO:0016772 - transferase activity, transferring phosphorus-containing groups [Evidence IEA]
GO:0000160 - phosphorelay signal transduction system [Evidence IEA]; GO:0016310 - phosphorylation [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_086558297.1
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_007885483.1
GO:0003684 - damaged DNA binding [Evidence IEA]
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_002353184.1
COORDINATES: similar to AA sequence:RefSeq:YP_005229620.1
COORDINATES: similar to AA sequence:RefSeq:WP_013199723.1
COORDINATES: similar to AA sequence:RefSeq:WP_019843123.1