Haematobacter massiliensis strain OT1 plasmid pOT1-5, complete sequence.
Bacteria; Pseudomonadota; Alphaproteobacteria; Rhodobacterales; Paracoccaceae; Haematobacter.
The first complete genome sequence of Haematobacter massiliensis OT1 isolated from human skin
Submitted (28-JAN-2019) Bio Health Science, Changwon National University, Changwondaero, Changwon, Gyeongnam 51140, Korea, Republic of
REFSEQ INFORMATION: The reference sequence is identical to\nCP035515.1.\nBacteria and source DNA available from Prof. Kyoung Lee.\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/\nThis genome has a base modification file available.\n\n##Genome-Assembly-Data-START##\nAssembly Method :: HGAP v. 2.3\nGenome Representation :: Full\nExpected Final Version :: Yes\nGenome Coverage :: 233.0x\nSequencing Technology :: PacBio RSII\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 04/12/2023 03:47:07\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) :: 4,015\nCDSs (total) :: 3,954\nGenes (coding) :: 3,873\nCDSs (with protein) :: 3,873\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) :: 81\nCDSs (without protein) :: 81\nPseudo Genes (ambiguous residues) :: 0 of 81\nPseudo Genes (frameshifted) :: 32 of 81\nPseudo Genes (incomplete) :: 55 of 81\nPseudo Genes (internal stop) :: 7 of 81\nPseudo Genes (multiple problems) :: 13 of 81\nCRISPR Arrays :: 1\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.
COORDINATES: similar to AA sequence:RefSeq:WP_013069338.1
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_013069339.1
COORDINATES: protein motif:HMM:NF040974.1
COORDINATES: similar to AA sequence:RefSeq:WP_018001791.1
ParB/RepB/Spo0J family partition protein
COORDINATES: similar to AA sequence:RefSeq:WP_009827215.1
COORDINATES: similar to AA sequence:RefSeq:WP_018065899.1
COORDINATES: similar to AA sequence:RefSeq:WP_008030608.1
COORDINATES: similar to AA sequence:RefSeq:WP_018634351.1
helix-turn-helix domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_008030612.1
COORDINATES: protein motif:HMM:NF016107.2
COORDINATES: similar to AA sequence:RefSeq:WP_008030617.1
GO:0005886 - plasma membrane [Evidence IEA]
GO:0004190 - aspartic-type endopeptidase activity [Evidence IEA]
GO:0009306 - protein secretion [Evidence IEA]; GO:0006508 - proteolysis [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_008030619.1
GO:0015035 - protein-disulfide reductase activity [Evidence IEA]
GO:0006457 - protein folding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_008030621.1
COORDINATES: similar to AA sequence:RefSeq:WP_008030622.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]; GO:0046983 - protein dimerization activity [Evidence IEA]; GO:0046914 - transition metal ion binding [Evidence IEA]
GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
manganese-binding transcriptional regulator MntR
COORDINATES: similar to AA sequence:RefSeq:WP_008030623.1
GO:0022857 - transmembrane transporter activity [Evidence IEA]
GO:0055085 - transmembrane transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_008030624.1
GO:0031966 - mitochondrial membrane [Evidence IEA]
GO:0033617 - mitochondrial cytochrome c oxidase assembly [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_008030626.1
GO:0016531 - copper chaperone activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_009805273.1
COORDINATES: similar to AA sequence:RefSeq:WP_008030629.1
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: similar to AA sequence:RefSeq:WP_010398667.1
COORDINATES: similar to AA sequence:RefSeq:WP_005859736.1
COORDINATES: similar to AA sequence:RefSeq:WP_011471110.1
COORDINATES: similar to AA sequence:RefSeq:WP_007068977.1
COORDINATES: similar to AA sequence:RefSeq:WP_019012660.1
COORDINATES: protein motif:HMM:NF018294.2
COORDINATES: similar to AA sequence:RefSeq:WP_011237482.1
COORDINATES: similar to AA sequence:RefSeq:WP_006340005.1
sulfite exporter TauE/SafE family protein
COORDINATES: protein motif:HMM:NF024091.2
GO:0140359 - ABC-type transporter activity [Evidence IEA]; GO:0042626 - ATPase-coupled transmembrane transporter activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_013493483.1
COORDINATES: similar to AA sequence:RefSeq:WP_003498073.1
COORDINATES: protein motif:HMM:NF013460.2
cytochrome b/b6 domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_011339150.1
GO:0000160 - phosphorelay signal transduction system [Evidence IEA]; GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
COORDINATES: protein motif:HMM:NF014567.2
GO:0005524 - ATP binding [Evidence IEA]; GO:0000156 - phosphorelay response regulator activity [Evidence IEA]; GO:0004673 - protein histidine kinase activity [Evidence IEA]
GO:0007165 - signal transduction [Evidence IEA]
HAMP domain-containing sensor histidine kinase
COORDINATES: protein motif:HMM:NF021425.2
COORDINATES: similar to AA sequence:RefSeq:WP_009209007.1
COORDINATES: similar to AA sequence:RefSeq:WP_009827208.1
COORDINATES: similar to AA sequence:RefSeq:WP_009503785.1
COORDINATES: similar to AA sequence:RefSeq:WP_009827206.1
COORDINATES: similar to AA sequence:RefSeq:WP_007803272.1
COORDINATES: similar to AA sequence:RefSeq:WP_018065909.1
COORDINATES: similar to AA sequence:RefSeq:WP_005859714.1
COORDINATES: similar to AA sequence:RefSeq:WP_009820093.1
COORDINATES: similar to AA sequence:RefSeq:WP_009450564.1
antitoxin of toxin-antitoxin stability system
COORDINATES: similar to AA sequence:RefSeq:WP_019404595.1
COORDINATES: similar to AA sequence:RefSeq:WP_007803284.1
nucleotidyl transferase AbiEii/AbiGii toxin family protein
COORDINATES: similar to AA sequence:RefSeq:WP_018065917.1
type IV toxin-antitoxin system AbiEi family antitoxin
COORDINATES: similar to AA sequence:RefSeq:WP_009820102.1
COORDINATES: similar to AA sequence:RefSeq:WP_009820103.1
bifunctional class I SAM-dependent methyltransferase/DEAD/DEAH box helicase
COORDINATES: similar to AA sequence:RefSeq:WP_008336055.1
incomplete; partial in the middle of a contig; missing C-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_015597236.1
COORDINATES: similar to AA sequence:RefSeq:WP_008495806.1
GO:0015074 - DNA integration [Evidence IEA]; GO:0006310 - DNA recombination [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_010400741.1
COORDINATES: similar to AA sequence:RefSeq:WP_010400739.1
COORDINATES: similar to AA sequence:RefSeq:WP_017286272.1
GO:0016151 - nickel cation binding [Evidence IEA]; GO:0009039 - urease activity [Evidence IEA]
GO:0019627 - urea metabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_002632669.1
GO:0035550 - urease complex [Evidence IEA]
GO:0009039 - urease activity [Evidence IEA]
GO:0043419 - urea catabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_015343410.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0016151 - nickel cation binding [Evidence IEA]
GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]; GO:0010045 - response to nickel cation [Evidence IEA]
nickel-responsive transcriptional regulator NikR
COORDINATES: protein motif:HMM:NF024755.2
COORDINATES: similar to AA sequence:RefSeq:WP_010400842.1
GO:0004803 - transposase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_007803302.1
COORDINATES: similar to AA sequence:RefSeq:WP_013123186.1
AbrB/MazE/SpoVT family DNA-binding domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_007668085.1
type II toxin-antitoxin system VapC family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_007120663.1
COORDINATES: similar to AA sequence:RefSeq:WP_009807938.1
relaxase/mobilization nuclease domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_008327405.1
type IV secretory system conjugative DNA transfer family protein
COORDINATES: protein motif:HMM:NF025495.2
GO:0004518 - nuclease activity [Evidence IEA]
dsDNA nuclease domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_009808070.1
COORDINATES: similar to AA sequence:RefSeq:WP_007120671.1
COORDINATES: similar to AA sequence:RefSeq:WP_007120672.1
COORDINATES: similar to AA sequence:RefSeq:WP_018065939.1
COORDINATES: similar to AA sequence:RefSeq:WP_008327387.1
COORDINATES: similar to AA sequence:RefSeq:WP_009807513.1
TrbG/VirB9 family P-type conjugative transfer protein
COORDINATES: similar to AA sequence:RefSeq:WP_009807512.1
COORDINATES: similar to AA sequence:RefSeq:WP_009808063.1
COORDINATES: similar to AA sequence:RefSeq:WP_007120678.1
GO:0016798 - hydrolase activity, acting on glycosyl bonds [Evidence IEA]
lytic transglycosylase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_009807508.1
type IV secretion system DNA-binding domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_008327373.1
VirB3 family type IV secretion system protein
COORDINATES: similar to AA sequence:RefSeq:WP_009808058.1
COORDINATES: similar to AA sequence:RefSeq:WP_008327370.1
COORDINATES: similar to AA sequence:RefSeq:WP_009808056.1
COORDINATES: similar to AA sequence:RefSeq:WP_008282966.1
COORDINATES: similar to AA sequence:RefSeq:WP_007120686.1
helix-turn-helix transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_008282968.1
COORDINATES: similar to AA sequence:RefSeq:WP_012187172.1
COORDINATES: similar to AA sequence:RefSeq:WP_007815264.1
COORDINATES: similar to AA sequence:RefSeq:WP_018065923.1
COORDINATES: protein motif:HMM:NF012403.2
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:NF012492.2
GO:0005524 - ATP binding [Evidence IEA]; GO:0003676 - nucleic acid binding [Evidence IEA]
COORDINATES: protein motif:HMM:NF024642.2
COORDINATES: protein motif:HMM:NF024803.2
COORDINATES: protein motif:HMM:NF025141.2
COORDINATES: similar to AA sequence:RefSeq:WP_019087712.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0000150 - DNA strand exchange activity [Evidence IEA]
GO:0006310 - DNA recombination [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_008878338.1
COORDINATES: similar to AA sequence:RefSeq:WP_076612398.1
COORDINATES: similar to AA sequence:RefSeq:WP_003501156.1
COORDINATES: protein motif:HMM:TIGR02325.1
GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]
GO:0015716 - organic phosphonate transport [Evidence IEA]
phosphonate metabolism transcriptional regulator PhnF
COORDINATES: protein motif:HMM:NF011987.0
alpha-D-ribose 1-methylphosphonate 5-triphosphate diphosphatase
COORDINATES: similar to AA sequence:RefSeq:WP_018387882.1
PhnD/SsuA/transferrin family substrate-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_018387883.1
ATP-binding cassette domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_008279572.1
GO:0055052 - ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing [Evidence IEA]; GO:0005886 - plasma membrane [Evidence IEA]
GO:0015416 - ABC-type phosphonate transporter activity [Evidence IEA]
phosphonate ABC transporter, permease protein PhnE
COORDINATES: similar to AA sequence:RefSeq:WP_006725517.1
COORDINATES: similar to AA sequence:RefSeq:WP_006725516.1
COORDINATES: similar to AA sequence:RefSeq:WP_006725515.1
COORDINATES: similar to AA sequence:RefSeq:WP_006725514.1
GO:0043190 - ATP-binding cassette (ABC) transporter complex [Evidence IEA]
internal stop; Derived by automated computational analysis using gene prediction method: Protein Homology.
phosphonate ABC transporter substrate-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_006725513.1
GO:0055052 - ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing [Evidence IEA]; GO:0009898 - cytoplasmic side of plasma membrane [Evidence IEA]
GO:0015416 - ABC-type phosphonate transporter activity [Evidence IEA]; GO:0005524 - ATP binding [Evidence IEA]
phosphonate ABC transporter ATP-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_018000155.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0004803 - transposase activity [Evidence IEA]
GO:0006313 - transposition, DNA-mediated [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011749831.1
TnpB, as the term is used for proteins encoded by IS66 family insertion elements, is considered an accessory protein, since TnpC, encoded by a neighboring gene, is a DDE family transposase; Derived by automated computational analysis using gene prediction method: Protein Homology.
IS66 family insertion sequence element accessory protein TnpB
COORDINATES: similar to AA sequence:RefSeq:WP_008554852.1
COORDINATES: similar to AA sequence:RefSeq:WP_006725512.1
COORDINATES: similar to AA sequence:RefSeq:WP_006725511.1
COORDINATES: similar to AA sequence:RefSeq:WP_006725510.1
COORDINATES: similar to AA sequence:RefSeq:WP_006725509.1
GO:0051539 - 4 iron, 4 sulfur cluster binding [Evidence IEA]; GO:0016829 - lyase activity [Evidence IEA]
GO:0019700 - organic phosphonate catabolic process [Evidence IEA]
alpha-D-ribose 1-methylphosphonate 5-phosphate C-P-lyase PhnJ
COORDINATES: similar to AA sequence:RefSeq:WP_006562615.1
GO:0019634 - organic phosphonate metabolic process [Evidence IEA]
carbon-phosphorus lyase complex subunit PhnI
COORDINATES: similar to AA sequence:RefSeq:WP_009574060.1
phosphonate C-P lyase system protein PhnH
COORDINATES: similar to AA sequence:RefSeq:WP_006725506.1
GO:0019634 - organic phosphonate metabolic process [Evidence IEA]; GO:0015716 - organic phosphonate transport [Evidence IEA]
phosphonate C-P lyase system protein PhnG
COORDINATES: similar to AA sequence:RefSeq:WP_006725505.1
COORDINATES: similar to AA sequence:RefSeq:WP_006724019.1
COORDINATES: similar to AA sequence:RefSeq:WP_011971025.1
COORDINATES: similar to AA sequence:RefSeq:WP_017963751.1
type II toxin-antitoxin system prevent-host-death family antitoxin
COORDINATES: similar to AA sequence:RefSeq:WP_011579009.1
COORDINATES: similar to AA sequence:RefSeq:WP_007801540.1
COORDINATES: similar to AA sequence:RefSeq:WP_012755578.1
GO:0110001 - toxin-antitoxin complex [Evidence IEA]
type II toxin-antitoxin system Phd/YefM family antitoxin
COORDINATES: similar to AA sequence:RefSeq:WP_015341782.1
COORDINATES: similar to AA sequence:RefSeq:WP_007538502.1
COORDINATES: similar to AA sequence:RefSeq:WP_011983018.1
COORDINATES: similar to AA sequence:RefSeq:WP_012454981.1
COORDINATES: similar to AA sequence:RefSeq:WP_011383609.1
COORDINATES: similar to AA sequence:RefSeq:WP_076611638.1
COORDINATES: similar to AA sequence:RefSeq:WP_014330531.1
COORDINATES: similar to AA sequence:RefSeq:WP_076611865.1
GO:0015074 - DNA integration [Evidence IEA]
incomplete; partial in the middle of a contig; missing N-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
integrase core domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_006466776.1
COORDINATES: similar to AA sequence:RefSeq:WP_007875100.1
COORDINATES: similar to AA sequence:RefSeq:WP_006470433.1
COORDINATES: similar to AA sequence:RefSeq:WP_007875098.1
COORDINATES: similar to AA sequence:RefSeq:WP_012092082.1
COORDINATES: similar to AA sequence:RefSeq:WP_008123404.1
GO:0018835 - carbon phosphorus lyase activity [Evidence IEA]
phosphonate C-P lyase system protein PhnK
COORDINATES: similar to AA sequence:RefSeq:WP_012092081.1
phosphonate C-P lyase system protein PhnL
COORDINATES: similar to AA sequence:RefSeq:WP_006470440.1
COORDINATES: similar to AA sequence:RefSeq:WP_006466784.1
GO:0016787 - hydrolase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_004685664.1
GO:0003674 - molecular_function [Evidence IEA]
phosphonate metabolism protein/1,5-bisphosphokinase (PRPP-forming) PhnN
COORDINATES: similar to AA sequence:RefSeq:WP_076611806.1
COORDINATES: similar to AA sequence:RefSeq:WP_003501082.1
COORDINATES: similar to AA sequence:RefSeq:WP_003603269.1
COORDINATES: similar to AA sequence:RefSeq:WP_020456375.1
COORDINATES: similar to AA sequence:RefSeq:WP_017140222.1
GO:0003824 - catalytic activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_018184844.1
GO:0140359 - ABC-type transporter activity [Evidence IEA]; GO:0005524 - ATP binding [Evidence IEA]; GO:0016887 - ATP hydrolysis activity [Evidence IEA]; GO:0042626 - ATPase-coupled transmembrane transporter activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_008536751.1
COORDINATES: similar to AA sequence:RefSeq:WP_012653949.1
COORDINATES: similar to AA sequence:RefSeq:WP_003595628.1
COORDINATES: similar to AA sequence:RefSeq:WP_018900863.1
TM0106 family RecB-like putative nuclease
COORDINATES: similar to AA sequence:RefSeq:WP_003574508.1
COORDINATES: similar to AA sequence:RefSeq:WP_013761204.1
GO:0003676 - nucleic acid binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_009811278.1
COORDINATES: similar to AA sequence:RefSeq:WP_009503774.1
GO:0004252 - serine-type endopeptidase activity [Evidence IEA]
rhomboid family intramembrane serine protease
COORDINATES: similar to AA sequence:RefSeq:WP_013046145.1
bifunctional (p)ppGpp synthetase/guanosine-3',5'-bis(diphosphate) 3'-pyrophosphohydrolase
COORDINATES: similar to AA sequence:RefSeq:WP_008327468.1
COORDINATES: similar to AA sequence:RefSeq:WP_006951057.1
COORDINATES: similar to AA sequence:RefSeq:WP_011331391.1
COORDINATES: similar to AA sequence:RefSeq:WP_011331447.1
COORDINATES: similar to AA sequence:RefSeq:WP_009503866.1