Thioclava nitratireducens strain 25B10_4 plasmid unnamed2, complete sequence.
Bacteria; Pseudomonadota; Alphaproteobacteria; Rhodobacterales; Paracoccaceae; Thioclava.
The complete genome sequence of a sulfur-oxidizing marine bacterium Thioclava sp. 25B10_4T
Submitted (18-JAN-2017) State of Oceanic Administration, The Third Institute of Oceanography, Room 116, Daxue Road 178#, Xiamen, Fujian 361005, P.R.China
Submitted (03-NOV-2016) State of Oceanic Administration, The Third Institute of Oceanography, Room 116, Daxue Road 178#, Xiamen, Fujian 361005, P.R.China
REFSEQ INFORMATION: The reference sequence is identical to\nCP019439.1.\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. 1.2.09\nGenome Coverage :: 250x\nSequencing Technology :: PacBio\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 04/23/2023 02:40:18\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) :: 4,159\nCDSs (total) :: 4,096\nGenes (coding) :: 4,019\nCDSs (with protein) :: 4,019\nGenes (RNA) :: 63\nrRNAs :: 3, 3, 3 (5S, 16S, 23S)\ncomplete rRNAs :: 3, 3, 3 (5S, 16S, 23S)\ntRNAs :: 51\nncRNAs :: 3\nPseudo Genes (total) :: 77\nCDSs (without protein) :: 77\nPseudo Genes (ambiguous residues) :: 0 of 77\nPseudo Genes (frameshifted) :: 51 of 77\nPseudo Genes (incomplete) :: 40 of 77\nPseudo Genes (internal stop) :: 13 of 77\nPseudo Genes (multiple problems) :: 22 of 77\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.
type strain of Thioclava nitratireducens
COORDINATES: ab initio prediction:GeneMarkS-2+
GO:0016491 - oxidoreductase activity [Evidence IEA]
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: similar to AA sequence:RefSeq:WP_013575656.1
GO:0016757 - glycosyltransferase activity [Evidence IEA]
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_007793816.1
frameshifted; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: protein motif:HMM:NF025080.2
internal stop; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_019195760.1
COORDINATES: protein motif:HMM:NF013862.2
GO:0006629 - lipid metabolic process [Evidence IEA]
patatin-like phospholipase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_018426863.1
COORDINATES: similar to AA sequence:RefSeq:WP_006202401.1
COORDINATES: similar to AA sequence:RefSeq:WP_008888192.1
COORDINATES: similar to AA sequence:RefSeq:WP_005855837.1
GO:0022857 - transmembrane transporter activity [Evidence IEA]
GO:0055085 - transmembrane transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_005855835.1
GO:0005886 - plasma membrane [Evidence IEA]
GO:0009410 - response to xenobiotic stimulus [Evidence IEA]; GO:0006855 - xenobiotic transmembrane transport [Evidence IEA]
DHA2 family efflux MFS transporter permease subunit
COORDINATES: similar to AA sequence:RefSeq:WP_013165988.1
COORDINATES: protein motif:HMM:NF014567.2
COORDINATES: protein motif:HMM:NF025063.2
GO:0015074 - DNA integration [Evidence IEA]
integrase core domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_015500866.1
GO:0004803 - transposase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_076611592.1
frameshifted; internal stop; incomplete; partial in the middle of a contig; missing C-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: protein motif:HMM:NF020893.2
COORDINATES: protein motif:HMM:NF016270.2
COORDINATES: protein motif:HMM:NF014687.2
COORDINATES: similar to AA sequence:RefSeq:WP_009826674.1
GO:0008381 - mechanosensitive monoatomic ion channel activity [Evidence IEA]
mechanosensitive ion channel family protein
COORDINATES: protein motif:HMM:TIGR00383.1
GO:0015087 - cobalt ion transmembrane transporter activity [Evidence IEA]; GO:0015095 - magnesium ion transmembrane transporter activity [Evidence IEA]
GO:0006824 - cobalt ion transport [Evidence IEA]; GO:0015693 - magnesium ion transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_008208285.1
trypsin-like peptidase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_009826671.1
bifunctional lysylphosphatidylglycerol flippase/synthetase MprF
COORDINATES: protein motif:HMM:NF019352.2
GO:0005507 - copper ion binding [Evidence IEA]
multicopper oxidase domain-containing protein
COORDINATES: protein motif:HMM:NF019351.2
GO:0005507 - copper ion binding [Evidence IEA]; GO:0016491 - oxidoreductase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_018001747.1
COORDINATES: similar to AA sequence:RefSeq:WP_011992993.1
COORDINATES: similar to AA sequence:RefSeq:WP_011992994.1
rhodanese-like domain-containing protein
COORDINATES: protein motif:HMM:NF019301.2
COORDINATES: similar to AA sequence:RefSeq:WP_005966802.1
COORDINATES: protein motif:HMM:NF019032.2
COORDINATES: similar to AA sequence:RefSeq:WP_076611843.1
programmed frameshift; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_019021901.1
internal stop; 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_009570512.1
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_007676901.1
COORDINATES: protein motif:HMM:NF013577.2
GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]
GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
MurR/RpiR family transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_009574211.1
helix-turn-helix domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_012187368.1
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_011331447.1
COORDINATES: similar to AA sequence:RefSeq:WP_009503866.1
AbrB/MazE/SpoVT family DNA-binding domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_012187365.1
COORDINATES: similar to AA sequence:RefSeq:WP_009815512.1
COORDINATES: similar to AA sequence:RefSeq:WP_012187363.1
COORDINATES: similar to AA sequence:RefSeq:WP_008840017.1
COORDINATES: similar to AA sequence:RefSeq:WP_008327455.1
COORDINATES: similar to AA sequence:RefSeq:WP_009807542.1
zincin-like metallopeptidase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_007120641.1
COORDINATES: similar to AA sequence:RefSeq:WP_012187358.1
COORDINATES: similar to AA sequence:RefSeq:WP_009807539.1
ParB/RepB/Spo0J family partition protein
COORDINATES: similar to AA sequence:RefSeq:WP_009820261.1
COORDINATES: similar to AA sequence:RefSeq:WP_009807954.1
COORDINATES: similar to AA sequence:RefSeq:WP_012187077.1
type II toxin-antitoxin system PrlF family antitoxin
COORDINATES: similar to AA sequence:RefSeq:WP_007120648.1
type II toxin-antitoxin system YhaV family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_009819682.1
COORDINATES: similar to AA sequence:RefSeq:WP_009503768.1
COORDINATES: similar to AA sequence:RefSeq:WP_008327427.1
COORDINATES: similar to AA sequence:RefSeq:WP_012187348.1
COORDINATES: similar to AA sequence:RefSeq:WP_009807532.1
COORDINATES: similar to AA sequence:RefSeq:WP_012187346.1
COORDINATES: similar to AA sequence:RefSeq:WP_009815530.1
COORDINATES: similar to AA sequence:RefSeq:WP_009807529.1
GO:0004252 - serine-type endopeptidase activity [Evidence IEA]
rhomboid family intramembrane serine protease
COORDINATES: similar to AA sequence:RefSeq:WP_013039475.1
COORDINATES: protein motif:HMM:NF019371.2
COORDINATES: similar to AA sequence:RefSeq:WP_009820257.1
COORDINATES: similar to AA sequence:RefSeq:WP_011536569.1
COORDINATES: similar to AA sequence:RefSeq:WP_009503787.1
COORDINATES: similar to AA sequence:RefSeq:WP_009807938.1
relaxase/mobilization nuclease domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_009807937.1
type IV secretory system conjugative DNA transfer family protein
COORDINATES: protein motif:HMM:NF016362.2
GO:0003677 - DNA binding [Evidence IEA]; GO:0004519 - endonuclease activity [Evidence IEA]
GO:0009307 - DNA restriction-modification system [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_005624953.1
COORDINATES: similar to AA sequence:RefSeq:WP_008328988.1
COORDINATES: similar to AA sequence:RefSeq:WP_013960000.1
GO:0003862 - 3-isopropylmalate dehydrogenase activity [Evidence IEA]; GO:0046872 - metal ion binding [Evidence IEA]; GO:0051287 - NAD binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_016354286.1
COORDINATES: similar to AA sequence:RefSeq:WP_018245905.1
COORDINATES: protein motif:HMM:TIGR01730.1
GO:0005215 - transporter activity [Evidence IEA]
efflux RND transporter periplasmic adaptor subunit
COORDINATES: similar to AA sequence:RefSeq:WP_006473457.1
IS1380-like element IS1247 family transposase
COORDINATES: protein motif:HMM:NF024565.2
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_012187154.1
COORDINATES: similar to AA sequence:RefSeq:WP_009807515.1
COORDINATES: similar to AA sequence:RefSeq:WP_008327387.1
COORDINATES: similar to AA sequence:RefSeq:WP_011536592.1
TrbG/VirB9 family P-type conjugative transfer protein
COORDINATES: similar to AA sequence:RefSeq:WP_009808064.1
COORDINATES: similar to AA sequence:RefSeq:WP_009820232.1
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_009503800.1
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_008282965.1
COORDINATES: similar to AA sequence:RefSeq:WP_007120685.1
COORDINATES: similar to AA sequence:RefSeq:WP_007120686.1
COORDINATES: similar to AA sequence:RefSeq:WP_007120687.1
COORDINATES: similar to AA sequence:RefSeq:WP_013069363.1
GO:0008168 - methyltransferase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_009808043.1
COORDINATES: similar to AA sequence:RefSeq:WP_011516023.1
COORDINATES: protein motif:HMM:NF012235.2
ATP-binding cassette domain-containing protein
COORDINATES: protein motif:HMM:NF033587.1
COORDINATES: similar to AA sequence:RefSeq:WP_013124462.1
COORDINATES: similar to AA sequence:RefSeq:WP_008616446.1
COORDINATES: similar to AA sequence:RefSeq:WP_004868411.1
COORDINATES: similar to AA sequence:RefSeq:WP_010665736.1
GO:0016682 - oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor [Evidence IEA]
cytochrome d ubiquinol oxidase subunit II
COORDINATES: similar to AA sequence:RefSeq:WP_019092290.1
GO:0070069 - cytochrome complex [Evidence IEA]
GO:0009055 - electron transfer activity [Evidence IEA]
GO:0019646 - aerobic electron transport chain [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011809173.1
COORDINATES: similar to AA sequence:RefSeq:WP_011339404.1
COORDINATES: similar to AA sequence:RefSeq:WP_011997539.1
IS1380-like element ISPme1 family transposase