Clavibacter californiensis strain CFBP 8216 plasmid pCCa, complete sequence.
Bacteria; Actinomycetota; Actinomycetes; Micrococcales; Microbacteriaceae; Clavibacter.
Comparative genomics of all nine subspecies of the complex genus Clavibacter
Submitted (31-MAY-2019) Plant and Environmental Protection Sciences, University of Hawaii, 3091 Maile Way St. John 312, Honolulu, HI 96822, USA
REFSEQ INFORMATION: The reference sequence is identical to\nCP040793.1.\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 :: 04-APR-2019\nAssembly Method :: HGAP v. 4\nGenome Representation :: Full\nExpected Final Version :: Yes\nGenome Coverage :: 712.0x\nSequencing Technology :: PacBio RSII\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 10/07/2022 04:49:49\nAnnotation Pipeline :: NCBI Prokaryotic Genome\n Annotation Pipeline (PGAP)\nAnnotation Method :: Best-placed reference protein\n set; GeneMarkS-2+\nAnnotation Software revision :: 6.3\nFeatures Annotated :: Gene; CDS; rRNA; tRNA; ncRNA;\n repeat_region\nGenes (total) :: 3,099\nCDSs (total) :: 3,045\nGenes (coding) :: 3,015\nCDSs (with protein) :: 3,015\nGenes (RNA) :: 54\nrRNAs :: 2, 2, 2 (5S, 16S, 23S)\ncomplete rRNAs :: 2, 2, 2 (5S, 16S, 23S)\ntRNAs :: 45\nncRNAs :: 3\nPseudo Genes (total) :: 30\nCDSs (without protein) :: 30\nPseudo Genes (ambiguous residues) :: 0 of 30\nPseudo Genes (frameshifted) :: 6 of 30\nPseudo Genes (incomplete) :: 23 of 30\nPseudo Genes (internal stop) :: 3 of 30\nPseudo Genes (multiple problems) :: 2 of 30\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.
type strain of Clavibacter michiganensis subsp. californiensis
COORDINATES: similar to AA sequence:RefSeq:WP_011931168.1
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_011931167.1
TraM recognition domain-containing protein
COORDINATES: protein motif:HMM:NF027584.2
COORDINATES: similar to AA sequence:RefSeq:WP_018684942.1
GO:0003824 - catalytic activity [Evidence IEA]
NAD-dependent epimerase/dehydratase family protein
COORDINATES: protein motif:HMM:NF012472.2
COORDINATES: similar to AA sequence:RefSeq:WP_012889179.1
COORDINATES: protein motif:HMM:NF013775.2
aminoglycoside phosphotransferase family protein
COORDINATES: protein motif:HMM:NF014893.2
COORDINATES: protein motif:HMM:TIGR02937.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]; GO:0016987 - sigma factor activity [Evidence IEA]
GO:0006352 - DNA-templated transcription initiation [Evidence IEA]; GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
sigma-70 family RNA polymerase sigma factor
COORDINATES: similar to AA sequence:RefSeq:WP_011931165.1
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: similar to AA sequence:RefSeq:WP_011931161.1
COORDINATES: protein motif:HMM:NF024977.2
COORDINATES: similar to AA sequence:RefSeq:WP_013603067.1
frameshifted; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_003946277.1
COORDINATES: similar to AA sequence:RefSeq:WP_011931208.1
COORDINATES: similar to AA sequence:RefSeq:WP_011931257.1
COORDINATES: similar to AA sequence:RefSeq:WP_011931274.1
type IV toxin-antitoxin system AbiEi family antitoxin domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_011931205.1
nucleotidyl transferase AbiEii/AbiGii toxin family protein
COORDINATES: protein motif:HMM:NF017885.2
multiubiquitin domain-containing protein
COORDINATES: protein motif:HMM:NF013094.2
GO:0008641 - ubiquitin-like modifier activating enzyme activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_014922790.1
COORDINATES: similar to AA sequence:RefSeq:WP_011931188.1
COORDINATES: similar to AA sequence:RefSeq:WP_011931187.1
COORDINATES: similar to AA sequence:RefSeq:WP_003419513.1
COORDINATES: protein motif:HMM:NF025390.2
COORDINATES: protein motif:HMM:NF019311.2
COORDINATES: similar to AA sequence:RefSeq:WP_013350282.1
internal stop; Derived by automated computational analysis using gene prediction method: Protein Homology.
PDDEXK nuclease domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_011931183.1
COORDINATES: similar to AA sequence:RefSeq:WP_011931154.1
COORDINATES: protein motif:HMM:NF014273.2
ParB N-terminal domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_011931182.1
helix-turn-helix domain-containing protein
COORDINATES: protein motif:HMM:NF024248.2
winged helix-turn-helix domain-containing protein
COORDINATES: protein motif:HMM:NF017595.2
COORDINATES: similar to AA sequence:RefSeq:WP_011931176.1
COORDINATES: similar to AA sequence:RefSeq:WP_011931175.1
COORDINATES: similar to AA sequence:RefSeq:WP_011931174.1
COORDINATES: similar to AA sequence:RefSeq:WP_011931173.1
COORDINATES: similar to AA sequence:RefSeq:WP_011931172.1
COORDINATES: similar to AA sequence:RefSeq:WP_011931171.1
COORDINATES: similar to AA sequence:RefSeq:WP_011931170.1