Nitrosophilus labii strain HRV44 plasmid pHRV44, complete sequence.
Bacteria; Campylobacterota; Epsilonproteobacteria; Nautiliales; Nitratiruptoraceae; Nitrosophilus.
Biogeochemical Implications of N2O-Reducing Thermophilic Campylobacteria in Deep-Sea Vent Fields, and the Description of Nitratiruptor labii sp. nov
DOI:10.1016/j.isci.2020.101462 Publication Status: Available-Online prior to print
Submitted (26-FEB-2020) Contact:Sayaka Mino Hokkaido University, Faculty of Fisheries Science; 3-1-1 Minato-cho, Hakodate, Hokkaido 041-8611, Japan
REFSEQ INFORMATION: The reference sequence is identical to\nAP022827.1.\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 :: Canu v. 1.6\nGenome Coverage :: 917x\nSequencing Technology :: Illumina MiSeq; PacBio Sequel\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 05/14/2023 09:56:46\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) :: 2,168\nCDSs (total) :: 2,115\nGenes (coding) :: 2,081\nCDSs (with protein) :: 2,081\nGenes (RNA) :: 53\nrRNAs :: 3, 3, 3 (5S, 16S, 23S)\ncomplete rRNAs :: 3, 3, 3 (5S, 16S, 23S)\ntRNAs :: 41\nncRNAs :: 3\nPseudo Genes (total) :: 34\nCDSs (without protein) :: 34\nPseudo Genes (ambiguous residues) :: 0 of 34\nPseudo Genes (frameshifted) :: 20 of 34\nPseudo Genes (incomplete) :: 15 of 34\nPseudo Genes (internal stop) :: 14 of 34\nPseudo Genes (multiple problems) :: 12 of 34\nCRISPR Arrays :: 1\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.
deep-sea hydrothermal vent flange structure
COORDINATES: similar to AA sequence:RefSeq:WP_002795019.1
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: similar to AA sequence:RefSeq:WP_002897649.1
GO:0006259 - DNA metabolic process [Evidence IEA]
COORDINATES: protein motif:HMM:NF037521.2
zincin-like metallopeptidase domain-containing protein
COORDINATES: protein motif:HMM:NF040299.1
COORDINATES: protein motif:HMM:NF024755.2
COORDINATES: protein motif:HMM:NF025085.2
COORDINATES: similar to AA sequence:RefSeq:WP_015967787.1
COORDINATES: similar to AA sequence:RefSeq:WP_015453719.1
COORDINATES: similar to AA sequence:RefSeq:WP_002799350.1
COORDINATES: similar to AA sequence:RefSeq:WP_002938923.1
GO:0015074 - DNA integration [Evidence IEA]; GO:0006310 - DNA recombination [Evidence IEA]
COORDINATES: protein motif:HMM:NF024949.2
helix-turn-helix transcriptional regulator
COORDINATES: protein motif:HMM:NF020305.2
TnsA endonuclease N-terminal domain-containing protein
COORDINATES: protein motif:HMM:NF012870.2
GO:0015074 - DNA integration [Evidence IEA]
DDE-type integrase/transposase/recombinase
Mu transposase C-terminal domain-containing protein
COORDINATES: protein motif:HMM:NF017437.2
COORDINATES: protein motif:HMM:NF018259.2
COORDINATES: protein motif:HMM:NF024139.2
helix-turn-helix domain-containing protein
COORDINATES: protein motif:HMM:NF024635.2
COORDINATES: protein motif:HMM:NF025054.2
GO:0008080 - N-acetyltransferase activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF014442.2
GO:0003677 - DNA binding [Evidence IEA]; GO:0008170 - N-methyltransferase activity [Evidence IEA]
GO:0006306 - DNA methylation [Evidence IEA]
COORDINATES: protein motif:HMM:NF036332.2
COORDINATES: similar to AA sequence:RefSeq:WP_012748925.1
GO:0004803 - transposase activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF013235.2
GO:0003887 - DNA-directed DNA polymerase activity [Evidence IEA]
GO:0006270 - DNA replication initiation [Evidence IEA]
COORDINATES: protein motif:HMM:NF013793.2
COORDINATES: protein motif:HMM:NF013395.2
COORDINATES: similar to AA sequence:RefSeq:WP_006927293.1
COORDINATES: protein motif:HMM:NF014581.2
type IV secretion system DNA-binding domain-containing protein
COORDINATES: protein motif:HMM:NF018666.2
COORDINATES: protein motif:HMM:NF017892.2
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: similar to AA sequence:RefSeq:WP_002839368.1
COORDINATES: similar to AA sequence:RefSeq:WP_005022135.1
GO:0070064 - proline-rich region binding [Evidence IEA]; GO:0005515 - protein binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_005022130.1
COORDINATES: similar to AA sequence:RefSeq:WP_004276270.1
COORDINATES: similar to AA sequence:RefSeq:WP_011990139.1
type-F conjugative transfer system secretin TraK
COORDINATES: similar to AA sequence:RefSeq:WP_002800805.1
TraE/TraK family type IV conjugative transfer system protein
COORDINATES: similar to AA sequence:RefSeq:WP_005022124.1
type IV conjugative transfer system protein TraL
COORDINATES: similar to AA sequence:RefSeq:WP_002793349.1
COORDINATES: similar to AA sequence:RefSeq:WP_002794880.1
COORDINATES: similar to AA sequence:RefSeq:WP_076611481.1
programmed frameshift; internal stop; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: protein motif:HMM:NF012442.2
GO:0030261 - chromosome condensation [Evidence IEA]
COORDINATES: protein motif:HMM:NF037161.2
GO:0000166 - nucleotide binding [Evidence IEA]
GO:0030541 - plasmid partitioning [Evidence IEA]
COORDINATES: protein motif:HMM:NF024064.2
ribbon-helix-helix domain-containing protein
COORDINATES: protein motif:HMM:NF019530.2
conjugal transfer protein TraG N-terminal domain-containing protein
COORDINATES: protein motif:HMM:NF025105.2
COORDINATES: similar to AA sequence:RefSeq:WP_005023041.1
COORDINATES: similar to AA sequence:RefSeq:WP_005022097.1
COORDINATES: protein motif:HMM:NF012772.2
COORDINATES: protein motif:HMM:NF021209.2
TrbC family F-type conjugative pilus assembly protein
COORDINATES: protein motif:HMM:NF024872.2
GO:0005524 - ATP binding [Evidence IEA]; GO:0003678 - DNA helicase activity [Evidence IEA]
GO:0006260 - DNA replication [Evidence IEA]
DnaB-like helicase N-terminal domain-containing protein
COORDINATES: protein motif:HMM:NF012774.2
COORDINATES: protein motif:HMM:NF024252.2
COORDINATES: protein motif:HMM:NF024878.2
COORDINATES: similar to AA sequence:RefSeq:WP_002800912.1
COORDINATES: protein motif:HMM:TIGR00254.1
GO:0009975 - cyclase activity [Evidence IEA]
GO:0009966 - regulation of signal transduction [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_012081636.1
integrase core domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_012012107.1
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]