Bermanella marisrubri strain RED65 plasmid pBma45, complete sequence.
Bacteria; Pseudomonadota; Gammaproteobacteria; Oceanospirillales; Oceanospirillaceae; Bermanella.
Genome-Wide Identification of 5-Methylcytosine Sites in Bacterial Genomes By High-Throughput Sequencing of MspJI Restriction Fragments
Submitted (08-APR-2020) Genome Biology, NEB, 240 County Rd, Ipswich, MA 01938, USA
REFSEQ INFORMATION: The reference sequence is identical to\nCP051184.1.\nBacteria and source DNA available from J. Pinhassi J Craig Venter\nInstitute, 9704 Medical Center Drive, Rockville, MD 20850 USA.\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 :: DEC-2013\nAssembly Method :: HGAP v. 2.1.1\nAssembly Name :: Osp65_HGAP3_4\nGenome Representation :: Full\nExpected Final Version :: Yes\nGenome Coverage :: 132.93x\nSequencing Technology :: PacBio RSII\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 04/28/2023 10:59:40\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) :: 3,304\nCDSs (total) :: 3,243\nGenes (coding) :: 3,235\nCDSs (with protein) :: 3,235\nGenes (RNA) :: 61\nrRNAs :: 3, 3, 3 (5S, 16S, 23S)\ncomplete rRNAs :: 3, 3, 3 (5S, 16S, 23S)\ntRNAs :: 48\nncRNAs :: 4\nPseudo Genes (total) :: 8\nCDSs (without protein) :: 8\nPseudo Genes (ambiguous residues) :: 0 of 8\nPseudo Genes (frameshifted) :: 1 of 8\nPseudo Genes (incomplete) :: 7 of 8\nPseudo Genes (internal stop) :: 2 of 8\nPseudo Genes (multiple problems) :: 2 of 8\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.
COORDINATES: protein motif:HMM:NF013311.2
GO:0003677 - DNA binding [Evidence IEA]; GO:0003916 - DNA topoisomerase activity [Evidence IEA]
GO:0006265 - DNA topological change [Evidence IEA]
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
GO:0003887 - DNA-directed DNA polymerase activity [Evidence IEA]
GO:0006270 - DNA replication initiation [Evidence IEA]
COORDINATES: protein motif:HMM:NF015076.2
COORDINATES: protein motif:HMM:NF021897.2
type IV secretion system DNA-binding domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_019281325.1
lytic transglycosylase domain-containing protein
COORDINATES: protein motif:HMM:NF012894.2
GO:0042834 - peptidoglycan binding [Evidence IEA]; GO:0015288 - porin activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_018694127.1
COORDINATES: protein motif:HMM:NF018836.2
type IV conjugative transfer system protein TraL
COORDINATES: protein motif:HMM:NF017152.2
type IV conjugative transfer system protein TraE
COORDINATES: protein motif:HMM:NF018311.2
type-F conjugative transfer system secretin TraK
COORDINATES: protein motif:HMM:NF015688.2
COORDINATES: protein motif:HMM:NF021212.2
COORDINATES: protein motif:HMM:TIGR02746.1
COORDINATES: protein motif:HMM:NF021213.2
COORDINATES: protein motif:HMM:NF021981.2
COORDINATES: similar to AA sequence:RefSeq:WP_000794400.1
conjugal transfer pilus assembly protein TraU
COORDINATES: protein motif:HMM:NF021209.2
TrbC family F-type conjugative pilus assembly protein
COORDINATES: protein motif:HMM:NF018666.2
COORDINATES: protein motif:HMM:NF025105.2
COORDINATES: protein motif:HMM:NF017892.2
COORDINATES: protein motif:HMM:NF019530.2
conjugal transfer protein TraG N-terminal domain-containing protein
COORDINATES: protein motif:HMM:NF013793.2
COORDINATES: protein motif:HMM:TIGR00180.1
ParB/RepB/Spo0J family partition protein
COORDINATES: similar to AA sequence:RefSeq:WP_018694192.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0008170 - N-methyltransferase activity [Evidence IEA]
GO:0006306 - DNA methylation [Evidence IEA]
COORDINATES: protein motif:HMM:NF012372.2
GO:0008168 - methyltransferase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_019281307.1
zincin-like metallopeptidase domain-containing protein
COORDINATES: protein motif:HMM:NF012905.2
COORDINATES: protein motif:HMM:NF014533.2
GO:1990814 - DNA/DNA annealing activity [Evidence IEA]
GO:0009294 - DNA-mediated transformation [Evidence IEA]