Thermus parvatiensis strain RL plasmid pTP143, complete sequence.
Bacteria; Deinococcota; Deinococci; Thermales; Thermaceae; Thermus.
Genome sequence of Thermus parvatiensis, a thermophile isolated from a hot water spring
Submitted (22-JAN-2016) Department of Zoology, University of Delhi, Chhatra Marg, Delhi 110007, India
REFSEQ INFORMATION: The reference sequence is identical to\nCP014142.1.\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/\nThis genome has a base modification file available.\n\n##Genome-Assembly-Data-START##\nAssembly Method :: HGAP v. October-2015\nGenome Representation :: Full\nExpected Final Version :: Yes\nGenome Coverage :: 428.0x\nSequencing Technology :: PacBio\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 03/24/2023 13:46:40\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) :: 2,302\nCDSs (total) :: 2,246\nGenes (coding) :: 1,785\nCDSs (with protein) :: 1,785\nGenes (RNA) :: 56\nrRNAs :: 2, 2, 2 (5S, 16S, 23S)\ncomplete rRNAs :: 2, 2, 2 (5S, 16S, 23S)\ntRNAs :: 47\nncRNAs :: 3\nPseudo Genes (total) :: 461\nCDSs (without protein) :: 461\nPseudo Genes (ambiguous residues) :: 0 of 461\nPseudo Genes (frameshifted) :: 417 of 461\nPseudo Genes (incomplete) :: 58 of 461\nPseudo Genes (internal stop) :: 3 of 461\nPseudo Genes (multiple problems) :: 16 of 461\nCRISPR Arrays :: 1\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.
COORDINATES: similar to AA sequence:RefSeq:WP_019550639.1
GO:0009325 - nitrate reductase complex [Evidence IEA]
GO:0008940 - nitrate reductase activity [Evidence IEA]
GO:0009061 - anaerobic respiration [Evidence IEA]
frameshifted; 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_014511193.1
frameshifted; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: protein motif:HMM:NF014695.2
GO:0019645 - anaerobic electron transport chain [Evidence IEA]
respiratory nitrate reductase subunit gamma
COORDINATES: similar to AA sequence:RefSeq:WP_014511191.1
GO:0022857 - transmembrane transporter activity [Evidence IEA]
GO:0055085 - transmembrane transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_014511190.1
COORDINATES: protein motif:HMM:NF021520.2
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_015717622.1
COORDINATES: protein motif:HMM:NF022995.2
COORDINATES: similar to AA sequence:RefSeq:WP_016329270.1
COORDINATES: similar to AA sequence:RefSeq:WP_014630621.1
COORDINATES: protein motif:HMM:NF012742.2
substrate-binding domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_018465738.1
incomplete; partial in the middle of a contig; missing N-terminus and C-terminus; 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:NF014719.2
COORDINATES: similar to AA sequence:RefSeq:WP_011229158.1
COORDINATES: similar to AA sequence:RefSeq:WP_014511174.1
GO:0004370 - glycerol kinase activity [Evidence IEA]
GO:0006071 - glycerol metabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_014511173.1
GO:0016491 - oxidoreductase activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF014750.2
GO:0051536 - iron-sulfur cluster binding [Evidence IEA]; GO:0016491 - oxidoreductase activity [Evidence IEA]; GO:0016625 - oxidoreductase activity, acting on the aldehyde or oxo group of donors, iron-sulfur protein as acceptor [Evidence IEA]
aldehyde ferredoxin oxidoreductase N-terminal domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_014511172.1
incomplete; partial in the middle of a contig; missing C-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
CPBP family intramembrane metalloprotease
COORDINATES: protein motif:HMM:TIGR01054.1
GO:0003678 - DNA helicase activity [Evidence IEA]; GO:0003916 - DNA topoisomerase activity [Evidence IEA]; GO:0003917 - DNA topoisomerase type I (single strand cut, ATP-independent) activity [Evidence IEA]
GO:0006265 - DNA topological change [Evidence IEA]
COORDINATES: protein motif:HMM:NF012492.2
COORDINATES: similar to AA sequence:RefSeq:WP_014630417.1
COORDINATES: similar to AA sequence:RefSeq:WP_014511169.1
COORDINATES: similar to AA sequence:RefSeq:WP_014630419.1
COORDINATES: protein motif:HMM:TIGR00614.1
GO:0004386 - helicase activity [Evidence IEA]
GO:0006310 - DNA recombination [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_019551365.1
COORDINATES: similar to AA sequence:RefSeq:WP_008630830.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0004803 - transposase activity [Evidence IEA]
GO:0006313 - transposition, DNA-mediated [Evidence IEA]
COORDINATES: protein motif:HMM:NF016056.2
DCC1-like thiol-disulfide oxidoreductase family protein
COORDINATES: protein motif:HMM:NF013970.2
COORDINATES: similar to AA sequence:RefSeq:WP_013616019.1
GO:0004803 - transposase activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF024980.2
winged helix-turn-helix domain-containing protein
COORDINATES: protein motif:HMM:NF024940.2
helix-turn-helix domain-containing protein
COORDINATES: protein motif:HMM:NF017541.2
COORDINATES: similar to AA sequence:RefSeq:WP_019551678.1
COORDINATES: similar to AA sequence:RefSeq:WP_008633617.1
COORDINATES: similar to AA sequence:RefSeq:WP_008633616.1
COORDINATES: protein motif:HMM:NF014516.2
COORDINATES: similar to AA sequence:RefSeq:WP_015983999.1
COORDINATES: protein motif:HMM:NF040570.1
COORDINATES: protein motif:HMM:NF013752.2
COORDINATES: similar to AA sequence:RefSeq:WP_013157072.1
COORDINATES: protein motif:HMM:NF024571.2
COORDINATES: protein motif:HMM:NF025019.2
COORDINATES: similar to AA sequence:RefSeq:WP_012975283.1
frameshifted; internal stop; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_014630458.1
COORDINATES: similar to AA sequence:RefSeq:WP_008633607.1
COORDINATES: similar to AA sequence:RefSeq:WP_008630619.1
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_008633605.1
COORDINATES: similar to AA sequence:RefSeq:WP_008633604.1
type II toxin-antitoxin system VapC family toxin
COORDINATES: protein motif:HMM:NF012798.2
GO:0015074 - DNA integration [Evidence IEA]; GO:0006310 - DNA recombination [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_014630468.1
COORDINATES: similar to AA sequence:RefSeq:WP_014511107.1
COORDINATES: similar to AA sequence:RefSeq:WP_008633599.1
AbrB/MazE/SpoVT family DNA-binding domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_011228558.1
COORDINATES: similar to AA sequence:RefSeq:WP_011228296.1
IS256-like element ISTth4 family transposase
COORDINATES: similar to AA sequence:RefSeq:WP_011174362.1
COORDINATES: similar to AA sequence:RefSeq:WP_013012854.1
GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_008633013.1
COORDINATES: similar to AA sequence:RefSeq:WP_013704078.1
COORDINATES: similar to AA sequence:RefSeq:WP_014630479.1
type IV toxin-antitoxin system AbiEi family antitoxin domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_014630480.1
nucleotidyl transferase AbiEii/AbiGii toxin family protein
COORDINATES: protein motif:HMM:NF024117.2
GO:0005524 - ATP binding [Evidence IEA]; GO:0016787 - hydrolase activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF012789.2
COORDINATES: similar to AA sequence:RefSeq:WP_008631376.1
GO:0042242 - cobyrinic acid a,c-diamide synthase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_008631380.1
GO:0008817 - corrinoid adenosyltransferase activity [Evidence IEA]
GO:0009236 - cobalamin biosynthetic process [Evidence IEA]
cob(I)yrinic acid a,c-diamide adenosyltransferase
COORDINATES: similar to AA sequence:RefSeq:WP_011174549.1
COORDINATES: protein motif:HMM:NF014685.2
GO:0051073 - adenosylcobinamide-GDP ribazoletransferase activity [Evidence IEA]; GO:0008818 - cobalamin 5'-phosphate synthase activity [Evidence IEA]
adenosylcobinamide-GDP ribazoletransferase
COORDINATES: similar to AA sequence:RefSeq:WP_014630525.1
COORDINATES: similar to AA sequence:RefSeq:WP_014511292.1
GO:0008939 - nicotinate-nucleotide-dimethylbenzimidazole phosphoribosyltransferase activity [Evidence IEA]
nicotinate-nucleotide--dimethylbenzimidazole phosphoribosyltransferase
COORDINATES: similar to AA sequence:RefSeq:WP_008631398.1
COORDINATES: nucleotide motif:Rfam:14.4:RF00174
cobalamin riboswitch; Derived by automated computational analysis using gene prediction method: cmsearch.
COORDINATES: similar to AA sequence:RefSeq:WP_014630526.1
COORDINATES: similar to AA sequence:RefSeq:WP_008631402.1
GO:0008168 - methyltransferase activity [Evidence IEA]
cobalt-precorrin-5B (C(1))-methyltransferase
COORDINATES: similar to AA sequence:RefSeq:WP_014630527.1
COORDINATES: similar to AA sequence:RefSeq:WP_008631406.1
bifunctional cobalt-precorrin-7 (C(5))-methyltransferase/cobalt-precorrin-6B (C(15))-methyltransferase
COORDINATES: similar to AA sequence:RefSeq:WP_014511288.1
COORDINATES: protein motif:HMM:NF012799.2
COORDINATES: similar to AA sequence:RefSeq:WP_014630531.1
GO:0030789 - precorrin-3B C17-methyltransferase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_003045512.1
COORDINATES: similar to AA sequence:RefSeq:WP_003045510.1
GO:0016829 - lyase activity [Evidence IEA]
CbiX/SirB N-terminal domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_008631423.1
COORDINATES: similar to AA sequence:RefSeq:WP_008631424.1
GO:0004851 - uroporphyrin-III C-methyltransferase activity [Evidence IEA]
GO:0019354 - siroheme biosynthetic process [Evidence IEA]
uroporphyrinogen-III C-methyltransferase
COORDINATES: similar to AA sequence:RefSeq:WP_014511285.1
GO:0016722 - oxidoreductase activity, acting on metal ions [Evidence IEA]
GO:0009236 - cobalamin biosynthetic process [Evidence IEA]; GO:0032363 - FMN catabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_008631428.1
GO:0016880 - acid-ammonia (or amide) ligase activity [Evidence IEA]
adenosylcobinamide-phosphate synthase CbiB
COORDINATES: similar to AA sequence:RefSeq:WP_014511283.1
COORDINATES: similar to AA sequence:RefSeq:WP_003048753.1
nucleotidyltransferase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_008631435.1
COORDINATES: similar to AA sequence:RefSeq:WP_015065315.1
COORDINATES: similar to AA sequence:RefSeq:WP_014630539.1
GO:0003824 - catalytic activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011229222.1
COORDINATES: similar to AA sequence:RefSeq:WP_011174534.1
GO:0008448 - N-acetylglucosamine-6-phosphate deacetylase activity [Evidence IEA]
GO:0006040 - amino sugar metabolic process [Evidence IEA]
N-acetylglucosamine-6-phosphate deacetylase
COORDINATES: protein motif:HMM:NF024950.2
COORDINATES: similar to AA sequence:RefSeq:WP_014511275.1
COORDINATES: similar to AA sequence:RefSeq:WP_014630543.1
COORDINATES: similar to AA sequence:RefSeq:WP_014511274.1
COORDINATES: similar to AA sequence:RefSeq:WP_014511080.1
COORDINATES: similar to AA sequence:RefSeq:WP_011229192.1
COORDINATES: similar to AA sequence:RefSeq:WP_014630564.1
phytoene/squalene synthase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_011229194.1
COORDINATES: similar to AA sequence:RefSeq:WP_011174504.1
COORDINATES: similar to AA sequence:RefSeq:WP_011229196.1
COORDINATES: similar to AA sequence:RefSeq:WP_003044894.1
COORDINATES: similar to AA sequence:RefSeq:WP_014630560.1
COORDINATES: similar to AA sequence:RefSeq:WP_014630559.1
COORDINATES: similar to AA sequence:RefSeq:WP_011229206.1
GO:0008422 - beta-glucosidase activity [Evidence IEA]
GO:0030245 - cellulose catabolic process [Evidence IEA]
COORDINATES: protein motif:HMM:NF012738.2
COORDINATES: similar to AA sequence:RefSeq:WP_014695689.1
LacI family DNA-binding transcriptional regulator
COORDINATES: protein motif:HMM:NF013757.2
COORDINATES: protein motif:HMM:NF012296.2
GO:0020037 - heme binding [Evidence IEA]; GO:0005506 - iron ion binding [Evidence IEA]; GO:0016705 - oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_014630567.1
lycopene cyclase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_011174497.1
COORDINATES: similar to AA sequence:RefSeq:WP_014630570.1
type II toxin-antitoxin system Phd/YefM family antitoxin
COORDINATES: similar to AA sequence:RefSeq:WP_003048855.1
COORDINATES: similar to AA sequence:RefSeq:WP_008631494.1
GO:0016166 - phytoene dehydrogenase activity [Evidence IEA]
GO:0016117 - carotenoid biosynthetic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011229187.1
GO:0004452 - isopentenyl-diphosphate delta-isomerase activity [Evidence IEA]
GO:0008299 - isoprenoid biosynthetic process [Evidence IEA]
type 2 isopentenyl-diphosphate Delta-isomerase
COORDINATES: similar to AA sequence:RefSeq:WP_008631496.1
COORDINATES: similar to AA sequence:RefSeq:WP_011174358.1
COORDINATES: similar to AA sequence:RefSeq:WP_011174478.1
GO:0007059 - chromosome segregation [Evidence IEA]; GO:0000910 - cytokinesis [Evidence IEA]
ParB/RepB/Spo0J family partition protein
COORDINATES: similar to AA sequence:RefSeq:WP_008631501.1
COORDINATES: similar to AA sequence:RefSeq:WP_011174476.1
COORDINATES: similar to AA sequence:RefSeq:WP_014511223.1
GO:0043546 - molybdopterin cofactor binding [Evidence IEA]; GO:0016491 - oxidoreductase activity [Evidence IEA]
molybdopterin dinucleotide binding domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_014511219.1
COORDINATES: similar to AA sequence:RefSeq:WP_008631509.1
COORDINATES: similar to AA sequence:RefSeq:WP_015717647.1
COORDINATES: similar to AA sequence:RefSeq:WP_015717646.1
COORDINATES: similar to AA sequence:RefSeq:WP_015717645.1
COORDINATES: similar to AA sequence:RefSeq:WP_015065483.1
COORDINATES: similar to AA sequence:RefSeq:WP_015716433.1
COORDINATES: protein motif:HMM:NF014312.2
COORDINATES: similar to AA sequence:RefSeq:WP_014630592.1
TIGR04053 family radical SAM/SPASM domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_014511209.1
COORDINATES: similar to AA sequence:RefSeq:WP_008633693.1
GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011229167.1
frameshifted; incomplete; partial in the middle of a contig; missing N-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
peptide-methionine (S)-S-oxide reductase
COORDINATES: similar to AA sequence:RefSeq:WP_014630599.1
COORDINATES: similar to AA sequence:RefSeq:WP_011229165.1
COORDINATES: similar to AA sequence:RefSeq:WP_019551189.1
COORDINATES: similar to AA sequence:RefSeq:WP_019550627.1
COORDINATES: similar to AA sequence:RefSeq:WP_014630607.1
COORDINATES: similar to AA sequence:RefSeq:WP_014630608.1
COORDINATES: protein motif:HMM:NF019292.2
nucleoside recognition domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_008633679.1
Crp/Fnr family transcriptional regulator
COORDINATES: protein motif:HMM:NF015649.2
BTAD domain-containing putative transcriptional regulator
COORDINATES: protein motif:HMM:NF013736.2
COORDINATES: similar to AA sequence:RefSeq:WP_014630612.1
COORDINATES: similar to AA sequence:RefSeq:WP_016329282.1