Hydrogenophilus thermoluteolus strain TH-1 plasmid pTH1, complete sequence.
Bacteria; Pseudomonadota; Hydrogenophilia; Hydrogenophilales; Hydrogenophilaceae; Hydrogenophilus.
Complete Genome Sequence of a Moderately Thermophilic Facultative Chemolithoautotrophic Hydrogen-Oxidizing Bacterium, Hydrogenophilus thermoluteolus TH-1
Microbiol Resour Announc 7, e00857-18 (2018)
Submitted (18-APR-2018) Contact:Hiroyuki Arai The University of Tokyo, Department of Biotechnology; Yayoi 1-1-1, Bunkyo-ku, Tokyo 113-8657, Japan
REFSEQ INFORMATION: The reference sequence is identical to\nAP018559.1.\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 :: Velvet v. 1.2.08\nGenome Coverage :: 42x\nSequencing Technology :: 454 GS FLX Titanium; ABI 3730\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 12/25/2022 03:38:58\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) :: 2,232\nCDSs (total) :: 2,170\nGenes (coding) :: 2,150\nCDSs (with protein) :: 2,150\nGenes (RNA) :: 62\nrRNAs :: 3, 3, 3 (5S, 16S, 23S)\ncomplete rRNAs :: 3, 3, 3 (5S, 16S, 23S)\ntRNAs :: 49\nncRNAs :: 4\nPseudo Genes (total) :: 20\nCDSs (without protein) :: 20\nPseudo Genes (ambiguous residues) :: 0 of 20\nPseudo Genes (frameshifted) :: 7 of 20\nPseudo Genes (incomplete) :: 16 of 20\nPseudo Genes (internal stop) :: 0 of 20\nPseudo Genes (multiple problems) :: 3 of 20\nCRISPR Arrays :: 2\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.
type strain of Hydrogenophilus thermoluteolus
COORDINATES: similar to AA sequence:RefSeq:WP_017173693.1
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_014293677.1
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: similar to AA sequence:RefSeq:WP_012212527.1
GO:0004803 - transposase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_010108018.1
type II toxin-antitoxin system PemK/MazF family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_004668272.1
COORDINATES: protein motif:HMM:NF015397.2
relaxase/mobilization nuclease domain-containing protein
COORDINATES: protein motif:HMM:NF017524.2
plasmid mobilization relaxosome protein MobC
COORDINATES: similar to AA sequence:RefSeq:WP_004115504.1
incomplete; partial in the middle of a contig; missing N-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_018002649.1
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_019303585.1
COORDINATES: similar to AA sequence:RefSeq:WP_015497693.1
COORDINATES: similar to AA sequence:RefSeq:WP_004086683.1
RNA-guided endonuclease TnpB family protein
COORDINATES: similar to AA sequence:RefSeq:WP_016857444.1
COORDINATES: similar to AA sequence:RefSeq:WP_009906856.1
type II toxin-antitoxin system RelE/ParE family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_006749194.1
frameshifted; incomplete; partial in the middle of a contig; missing N-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_019592953.1
GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_008869929.1
GO:0004521 - endoribonuclease activity [Evidence IEA]; GO:0005515 - protein binding [Evidence IEA]
putative toxin-antitoxin system toxin component, PIN family
COORDINATES: protein motif:HMM:NF024861.2
COORDINATES: similar to AA sequence:RefSeq:WP_017325232.1
GO:0015074 - DNA integration [Evidence IEA]; GO:0006310 - DNA recombination [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_076611243.1
COORDINATES: similar to AA sequence:RefSeq:WP_019364073.1
GO:0003676 - nucleic acid binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_008871360.1
type II toxin-antitoxin system prevent-host-death family antitoxin
COORDINATES: similar to AA sequence:RefSeq:WP_014239393.1
COORDINATES: similar to AA sequence:RefSeq:WP_005933773.1
COORDINATES: similar to AA sequence:RefSeq:WP_010505780.1
COORDINATES: similar to AA sequence:RefSeq:WP_002941086.1
COORDINATES: similar to AA sequence:RefSeq:WP_011804026.1
COORDINATES: similar to AA sequence:RefSeq:WP_003690227.1
COORDINATES: similar to AA sequence:RefSeq:WP_018422563.1
COORDINATES: similar to AA sequence:RefSeq:WP_004261291.1
COORDINATES: similar to AA sequence:RefSeq:WP_006521470.1
COORDINATES: similar to AA sequence:RefSeq:WP_013012870.1
GO:0005524 - ATP binding [Evidence IEA]; GO:0003677 - DNA binding [Evidence IEA]; GO:0016787 - hydrolase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011228558.1
COORDINATES: similar to AA sequence:RefSeq:WP_086557969.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0000150 - DNA strand exchange activity [Evidence IEA]
GO:0006310 - DNA recombination [Evidence IEA]
helix-turn-helix domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_006412423.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0004803 - transposase activity [Evidence IEA]
GO:0006313 - transposition, DNA-mediated [Evidence IEA]
COORDINATES: protein motif:HMM:NF016819.2
COORDINATES: similar to AA sequence:RefSeq:WP_009613390.1
GO:0046872 - metal ion binding [Evidence IEA]; GO:0016530 - metallochaperone activity [Evidence IEA]
GO:0019627 - urea metabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_018412785.1
COORDINATES: similar to AA sequence:RefSeq:WP_011767225.1
GO:0016151 - nickel cation binding [Evidence IEA]
GO:0006457 - protein folding [Evidence IEA]; GO:0065003 - protein-containing complex assembly [Evidence IEA]; GO:0019627 - urea metabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_019881620.1
GO:0016151 - nickel cation binding [Evidence IEA]; GO:0009039 - urease activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_020167139.1
GO:0035550 - urease complex [Evidence IEA]
GO:0043419 - urea catabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_002939924.1
GO:0009039 - urease activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_015438161.1
COORDINATES: similar to AA sequence:RefSeq:WP_019574793.1
GO:0055052 - ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing [Evidence IEA]; GO:0009898 - cytoplasmic side of plasma membrane [Evidence IEA]
GO:0005524 - ATP binding [Evidence IEA]; GO:0033221 - ATPase-coupled urea transmembrane transporter activity [Evidence IEA]
GO:0015840 - urea transport [Evidence IEA]
urea ABC transporter ATP-binding subunit UrtE
COORDINATES: similar to AA sequence:RefSeq:WP_015765758.1
urea ABC transporter ATP-binding protein UrtD
COORDINATES: similar to AA sequence:RefSeq:WP_011764411.1
GO:0055052 - ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing [Evidence IEA]; GO:0005886 - plasma membrane [Evidence IEA]
GO:0033221 - ATPase-coupled urea transmembrane transporter activity [Evidence IEA]
urea ABC transporter permease subunit UrtC
COORDINATES: similar to AA sequence:RefSeq:WP_008167605.1
urea ABC transporter permease subunit UrtB
COORDINATES: similar to AA sequence:RefSeq:WP_003612717.1
GO:0055052 - ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing [Evidence IEA]; GO:0030288 - outer membrane-bounded periplasmic space [Evidence IEA]
GO:0033221 - ATPase-coupled urea transmembrane transporter activity [Evidence IEA]; GO:0033219 - urea binding [Evidence IEA]
urea ABC transporter substrate-binding protein
COORDINATES: protein motif:HMM:NF012798.2
COORDINATES: protein motif:HMM:NF028103.2
DNA-primase RepB domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_012347357.1
COORDINATES: similar to AA sequence:RefSeq:WP_015278668.1
COORDINATES: protein motif:HMM:NF014250.2
COORDINATES: protein motif:HMM:NF012789.2
COORDINATES: similar to AA sequence:RefSeq:WP_011112623.1
COORDINATES: similar to AA sequence:RefSeq:WP_007293093.1
Rpn family recombination-promoting nuclease/putative transposase
COORDINATES: protein motif:HMM:TIGR00287.1
GO:0004520 - endodeoxyribonuclease activity [Evidence IEA]; GO:0046872 - metal ion binding [Evidence IEA]
GO:0043571 - maintenance of CRISPR repeat elements [Evidence IEA]