Zophobihabitans entericus strain IPMB12 plasmid pIPMB12, complete sequence.
Bacteria; Proteobacteria; Gammaproteobacteria; Orbales; Orbaceae; Zophobihabitans.
Complete genome sequence of Orbus sp. IPMB12 (BCRC 80908)
Submitted (18-MAR-2020) Institute of Plant and Microbial Biology, Academia Sinica, 128 Sec. 2, Academia Rd, Taipei 11529, Taiwan
REFSEQ INFORMATION: The reference sequence is identical to\nCP050254.1.\nBacteria and source DNA available from BCRC 80908.\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 Method :: Velvet v. v1.2.09\nGenome Representation :: Full\nExpected Final Version :: Yes\nGenome Coverage :: 203.8x\nSequencing Technology :: Illumina HiSeq\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 12/01/2022 02:25:16\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\nGenes (total) :: 2,414\nCDSs (total) :: 2,350\nGenes (coding) :: 2,327\nCDSs (with protein) :: 2,327\nGenes (RNA) :: 64\nrRNAs :: 5, 4, 4 (5S, 16S, 23S)\ncomplete rRNAs :: 5, 4, 4 (5S, 16S, 23S)\ntRNAs :: 46\nncRNAs :: 5\nPseudo Genes (total) :: 23\nCDSs (without protein) :: 23\nPseudo Genes (ambiguous residues) :: 0 of 23\nPseudo Genes (frameshifted) :: 4 of 23\nPseudo Genes (incomplete) :: 21 of 23\nPseudo Genes (internal stop) :: 1 of 23\nPseudo Genes (multiple problems) :: 3 of 23\nCRISPR Arrays :: 1\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.
type strain of Zophobihabitans entericus
COORDINATES: similar to AA sequence:RefSeq:WP_011013261.1
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+.
COORDINATES: protein motif:HMM:TIGR04359.1
GO:0005886 - plasma membrane [Evidence IEA]
GO:0009292 - horizontal gene transfer [Evidence IEA]
COORDINATES: protein motif:HMM:NF017655.2
COORDINATES: protein motif:HMM:TIGR00621.2
GO:0003697 - single-stranded DNA binding [Evidence IEA]
GO:0006310 - DNA recombination [Evidence IEA]; GO:0006281 - DNA repair [Evidence IEA]; GO:0006260 - DNA replication [Evidence IEA]; GO:0006351 - DNA-templated transcription [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_014579503.1
incomplete; partial in the middle of a contig; missing C-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: protein motif:HMM:NF019069.2
TrbM/KikA/MpfK family conjugal transfer protein
COORDINATES: protein motif:HMM:TIGR02783.1
GO:0009291 - unidirectional conjugation [Evidence IEA]
P-type conjugative transfer protein TrbL
COORDINATES: similar to AA sequence:RefSeq:WP_020433685.1
P-type conjugative transfer protein TrbJ
COORDINATES: similar to AA sequence:RefSeq:WP_011114050.1
COORDINATES: protein motif:HMM:NF018934.2
COORDINATES: similar to AA sequence:RefSeq:WP_000753228.1
P-type conjugative transfer protein TrbG
COORDINATES: protein motif:HMM:NF016238.2
COORDINATES: similar to AA sequence:RefSeq:WP_020485800.1
VirB4 family type IV secretion/conjugal transfer ATPase
COORDINATES: similar to AA sequence:RefSeq:WP_010676131.1
COORDINATES: similar to AA sequence:RefSeq:WP_011114046.1
COORDINATES: similar to AA sequence:RefSeq:WP_004091417.1
COORDINATES: similar to AA sequence:RefSeq:WP_003381772.1
type II toxin-antitoxin system RelB/DinJ family antitoxin
COORDINATES: similar to AA sequence:RefSeq:WP_006706130.1
type II toxin-antitoxin system mRNA interferase toxin, RelE/StbE family
COORDINATES: similar to AA sequence:RefSeq:WP_014579490.1
zincin-like metallopeptidase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_003454292.1
COORDINATES: similar to AA sequence:RefSeq:WP_011114056.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0003916 - DNA topoisomerase activity [Evidence IEA]
GO:0006265 - DNA topological change [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_000086826.1
GO:0030288 - outer membrane-bounded periplasmic space [Evidence IEA]
GO:0008233 - peptidase activity [Evidence IEA]
conjugative transfer signal peptidase TraF
COORDINATES: similar to AA sequence:RefSeq:WP_011544437.1
type IV secretory system conjugative DNA transfer family protein
COORDINATES: protein motif:HMM:NF015397.2
relaxase/mobilization nuclease domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_011978708.1
GO:0006402 - mRNA catabolic process [Evidence IEA]; GO:0006109 - regulation of carbohydrate metabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_017166882.1
COORDINATES: similar to AA sequence:RefSeq:WP_010676180.1
COORDINATES: protein motif:HMM:NF023087.2
COORDINATES: protein motif:HMM:TIGR00180.1
GO:0007059 - chromosome segregation [Evidence IEA]; GO:0000910 - cytokinesis [Evidence IEA]
ParB/RepB/Spo0J family partition protein
COORDINATES: protein motif:HMM:NF013793.2
COORDINATES: similar to AA sequence:RefSeq:WP_008929989.1
COORDINATES: similar to AA sequence:RefSeq:WP_019842081.1
COORDINATES: protein motif:HMM:NF010465.0
helix-turn-helix domain-containing protein