Thiomicrorhabdus aquaedulcis strain HaS4 plasmid pTmrp1, complete sequence.
Bacteria; Pseudomonadota; Gammaproteobacteria; Thiotrichales; Piscirickettsiaceae; Thiomicrorhabdus.
Thiomicrorhabdus aquaedulcis sp. nov., a sulfur-oxidizing bacterium isolated from lake water
Genomes of Neutrophilic Sulfur-Oxidizing Chemolithoautotrophs Representing 9 Proteobacterial Species From 8 Genera
DOI:10.3389/fmicb.2019.00316 Publication Status: Online-Only
Submitted (19-JUN-2018) Contact:Hisaya Kojima Hokkaido University; Kita-19, Nishi-8, Kita-ku, Sapporo, Hokkaido 060-0819, Japan
REFSEQ INFORMATION: The reference sequence is identical to\nAP018723.1.\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 Method :: RS_HGAP_Assembly v. 3\nGenome Coverage :: 105x\nSequencing Technology :: PacBio RS II\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 03/13/2023 13:23:02\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) :: 2,447\nCDSs (total) :: 2,391\nGenes (coding) :: 2,316\nCDSs (with protein) :: 2,316\nGenes (RNA) :: 56\nrRNAs :: 3, 3, 3 (5S, 16S, 23S)\ncomplete rRNAs :: 3, 3, 3 (5S, 16S, 23S)\ntRNAs :: 44\nncRNAs :: 3\nPseudo Genes (total) :: 75\nCDSs (without protein) :: 75\nPseudo Genes (ambiguous residues) :: 0 of 75\nPseudo Genes (frameshifted) :: 61 of 75\nPseudo Genes (incomplete) :: 17 of 75\nPseudo Genes (internal stop) :: 2 of 75\nPseudo Genes (multiple problems) :: 4 of 75\nCRISPR Arrays :: 2\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.
type strain of Thiomicrorhabdus aquaedulcis
COORDINATES: protein motif:HMM:NF013235.2
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: similar to AA sequence:RefSeq:WP_019894148.1
COORDINATES: similar to AA sequence:RefSeq:WP_009146687.1
COORDINATES: protein motif:HMM:TIGR00616.1
COORDINATES: protein motif:HMM:NF012245.2
GO:0007165 - signal transduction [Evidence IEA]
COORDINATES: protein motif:HMM:TIGR00229.1
COORDINATES: protein motif:HMM:NF013618.2
lytic transglycosylase domain-containing protein
COORDINATES: protein motif:HMM:NF018666.2
COORDINATES: similar to AA sequence:RefSeq:WP_016791698.1
COORDINATES: protein motif:HMM:NF025035.2
incomplete; partial in the middle of a contig; missing N-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
adenine-specific methyltransferase EcoRI family protein
COORDINATES: protein motif:HMM:NF019976.2
nuclease-related domain-containing protein
COORDINATES: protein motif:HMM:NF018691.2
GO:0007059 - chromosome segregation [Evidence IEA]; GO:0000910 - cytokinesis [Evidence IEA]
ParB/RepB/Spo0J family partition protein
COORDINATES: protein motif:HMM:NF012694.2
type II secretion system F family protein
COORDINATES: protein motif:HMM:NF015347.2
BspA family leucine-rich repeat surface protein
COORDINATES: protein motif:HMM:NF012485.2
COORDINATES: protein motif:HMM:NF012652.2
COORDINATES: protein motif:HMM:NF012651.2
GO:0003697 - single-stranded DNA binding [Evidence IEA]
COORDINATES: protein motif:HMM:NF024755.2
COORDINATES: similar to AA sequence:RefSeq:WP_001704145.1
COORDINATES: protein motif:HMM:NF019348.2
GO:0005524 - ATP binding [Evidence IEA]; GO:0016887 - ATP hydrolysis activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF022792.2
COORDINATES: protein motif:HMM:NF016364.2
transglutaminase-like cysteine peptidase
COORDINATES: protein motif:HMM:NF012798.2
GO:0015074 - DNA integration [Evidence IEA]; GO:0006310 - DNA recombination [Evidence IEA]
COORDINATES: protein motif:HMM:NF019530.2
conjugal transfer protein TraG N-terminal domain-containing protein
COORDINATES: protein motif:HMM:NF017892.2
COORDINATES: protein motif:HMM:NF025105.2
COORDINATES: protein motif:HMM:NF024254.2
COORDINATES: protein motif:HMM:NF022580.2
COORDINATES: protein motif:HMM:NF021212.2
COORDINATES: protein motif:HMM:NF024498.2
COORDINATES: protein motif:HMM:NF015688.2
COORDINATES: protein motif:HMM:NF018311.2
type-F conjugative transfer system secretin TraK
COORDINATES: protein motif:HMM:NF017152.2
TraE/TraK family type IV conjugative transfer system protein
COORDINATES: protein motif:HMM:NF018836.2
type IV conjugative transfer system protein TraL
COORDINATES: protein motif:HMM:NF041281.1
TraA family conjugative transfer protein
COORDINATES: protein motif:HMM:NF017124.2
GO:0045893 - positive regulation of DNA-templated transcription [Evidence IEA]; GO:1902208 - regulation of bacterial-type flagellum assembly [Evidence IEA]
COORDINATES: protein motif:HMM:NF041494.1
COORDINATES: protein motif:HMM:NF014044.2
COORDINATES: protein motif:HMM:NF024108.2
TraM recognition domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_012607034.1
COORDINATES: protein motif:HMM:NF012894.2
COORDINATES: protein motif:HMM:TIGR00254.1
COORDINATES: protein motif:HMM:NF012772.2
COORDINATES: protein motif:HMM:TIGR02742.1
type-F conjugative transfer system pilin assembly protein TrbC
COORDINATES: similar to AA sequence:RefSeq:WP_018079002.1
COORDINATES: protein motif:HMM:NF021981.2
GO:0004252 - serine-type endopeptidase activity [Evidence IEA]
GO:0009306 - protein secretion [Evidence IEA]; GO:0006465 - signal peptide processing [Evidence IEA]
COORDINATES: protein motif:HMM:NF039622.1
COORDINATES: protein motif:HMM:NF024642.2
COORDINATES: protein motif:HMM:NF018028.2
COORDINATES: protein motif:HMM:NF013395.2
GO:0016787 - hydrolase activity [Evidence IEA]; GO:0046872 - metal ion binding [Evidence IEA]; GO:0003676 - nucleic acid binding [Evidence IEA]
COORDINATES: protein motif:HMM:NF020252.2
COORDINATES: protein motif:HMM:NF020006.2
COORDINATES: protein motif:HMM:NF016724.2
GO:0005524 - ATP binding [Evidence IEA]; GO:0003677 - DNA binding [Evidence IEA]; GO:0016787 - hydrolase activity [Evidence IEA]