Deferribacter desulfuricans SSM1 megaplasmid pDF308, complete sequence.
Bacteria; Deferribacterota; Deferribacteres; Deferribacterales; Deferribacteraceae; Deferribacter.
Bacterial lifestyle in a deep-sea hydrothermal vent chimney revealed by the genome sequence of the thermophilic bacterium Deferribacter desulfuricans SSM1
Deferribacter desulfuricans sp. nov., a novel sulfur-, nitrate- and arsenate-reducing thermophile isolated from a deep-sea hydrothermal vent
Int J Syst Evol Microbiol 53 (Pt 3), 839-846 (2003)
Submitted (09-JUN-2009) Contact:Yoshihiro Takaki Japan Agency for Maine-Earth Science and Technology, Extremobiosphere Research Program; 2-15 Natsushima-cho, Yokosuka, Kanagawa 237-0026, Japan URL :http://www.jamstec.go.jp
REFSEQ INFORMATION: The reference sequence is identical to\nAP011530.1.\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-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 12/24/2022 01:50:23\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) :: 2,527\nCDSs (total) :: 2,474\nGenes (coding) :: 2,472\nCDSs (with protein) :: 2,472\nGenes (RNA) :: 53\nrRNAs :: 2, 2, 2 (5S, 16S, 23S)\ncomplete rRNAs :: 2, 2, 2 (5S, 16S, 23S)\ntRNAs :: 43\nncRNAs :: 4\nPseudo Genes (total) :: 2\nCDSs (without protein) :: 2\nPseudo Genes (ambiguous residues) :: 0 of 2\nPseudo Genes (frameshifted) :: 0 of 2\nPseudo Genes (incomplete) :: 2 of 2\nPseudo Genes (internal stop) :: 0 of 2\nCRISPR Arrays :: 4\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.
type strain of Deferribacter desulfuricans
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: similar to AA sequence:RefSeq:WP_001278583.1
GO:0004803 - transposase activity [Evidence IEA]
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_019896116.1
RNA-guided endonuclease TnpB family protein
COORDINATES: protein motif:HMM:NF022179.2
late competence development ComFB family protein
COORDINATES: protein motif:HMM:NF013311.2
COORDINATES: protein motif:HMM:NF013878.2
COORDINATES: protein motif:HMM:NF012787.2
GO:0016209 - antioxidant activity [Evidence IEA]; GO:0016491 - oxidoreductase activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF019575.2
prepilin-type N-terminal cleavage/methylation domain-containing protein
COORDINATES: protein motif:HMM:NF012485.2
type II and III secretion system protein
COORDINATES: protein motif:HMM:NF012652.2
COORDINATES: protein motif:HMM:NF012694.2
type II secretion system F family protein
COORDINATES: protein motif:HMM:NF021897.2
type IV secretion system DNA-binding domain-containing protein
COORDINATES: protein motif:HMM:NF018894.2
COORDINATES: protein motif:HMM:NF040179.1
COORDINATES: similar to AA sequence:RefSeq:WP_007760557.1
COORDINATES: protein motif:HMM:NF013752.2
GO:0003677 - DNA binding [Evidence IEA]; GO:0004803 - transposase activity [Evidence IEA]
GO:0006313 - transposition, DNA-mediated [Evidence IEA]
COORDINATES: protein motif:HMM:NF012493.2
COORDINATES: protein motif:HMM:NF012376.2
GO:0016787 - hydrolase activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF025710.2
COORDINATES: similar to AA sequence:RefSeq:WP_018123388.1
GO:0004170 - dUTP diphosphatase activity [Evidence IEA]; GO:0000287 - magnesium ion binding [Evidence IEA]
GO:0006226 - dUMP biosynthetic process [Evidence IEA]; GO:0046081 - dUTP catabolic process [Evidence IEA]
COORDINATES: protein motif:HMM:NF024853.2
COORDINATES: protein motif:HMM:NF014605.2
COORDINATES: similar to AA sequence:RefSeq:WP_013008251.1
GO:0046872 - metal ion binding [Evidence IEA]
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_012673588.1
CRISPR-associated helicase/endonuclease Cas3
COORDINATES: similar to AA sequence:RefSeq:WP_012674044.1
GO:0003674 - molecular_function [Evidence IEA]
GO:0043571 - maintenance of CRISPR repeat elements [Evidence IEA]
type I-B CRISPR-associated protein Cas5b
COORDINATES: similar to AA sequence:RefSeq:WP_013007284.1
type I-B CRISPR-associated protein Cas7/Csh2
COORDINATES: protein motif:HMM:NF021033.2
TIGR02556 family CRISPR-associated protein
COORDINATES: similar to AA sequence:RefSeq:WP_012673859.1
GO:0004521 - endoribonuclease activity [Evidence IEA]
nucleotidyl transferase AbiEii/AbiGii toxin family protein
COORDINATES: similar to AA sequence:RefSeq:WP_013007160.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0003899 - DNA-directed 5'-3' RNA polymerase activity [Evidence IEA]; GO:0016987 - sigma factor activity [Evidence IEA]
GO:0006352 - DNA-templated transcription initiation [Evidence IEA]
FliA/WhiG family RNA polymerase sigma factor
COORDINATES: protein motif:HMM:NF012774.2
pneumococcal-type histidine triad protein
COORDINATES: similar to AA sequence:RefSeq:WP_013008995.1
COORDINATES: similar to AA sequence:RefSeq:WP_013009035.1
COORDINATES: similar to AA sequence:RefSeq:WP_013007040.1
COORDINATES: protein motif:HMM:NF013319.2
COORDINATES: protein motif:HMM:NF021631.2
nucleotidyltransferase domain-containing protein
COORDINATES: protein motif:HMM:NF025120.2
helix-turn-helix domain-containing protein
COORDINATES: protein motif:HMM:NF019421.2
type II toxin-antitoxin system HipA family toxin
ankyrin repeat domain-containing protein
COORDINATES: protein motif:HMM:NF037233.2
COORDINATES: protein motif:HMM:NF020933.2
DNA double-strand break repair nuclease NurA
COORDINATES: protein motif:HMM:NF014044.2
COORDINATES: similar to AA sequence:RefSeq:WP_013890615.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0008170 - N-methyltransferase activity [Evidence IEA]
GO:0006306 - DNA methylation [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_013507116.1
COORDINATES: similar to AA sequence:RefSeq:WP_013008960.1
COORDINATES: protein motif:HMM:NF015983.2
GO:0003824 - catalytic activity [Evidence IEA]; GO:0051536 - iron-sulfur cluster binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_013008666.1
COORDINATES: protein motif:HMM:NF025843.2
helix-hairpin-helix domain-containing protein
COORDINATES: protein motif:HMM:NF024991.2
COORDINATES: protein motif:HMM:NF012311.2
GO:0008236 - serine-type peptidase activity [Evidence IEA]
COORDINATES: protein motif:HMM:TIGR00254.1
COORDINATES: similar to AA sequence:RefSeq:WP_013007169.1
COORDINATES: similar to AA sequence:RefSeq:WP_013007369.1
GO:0007165 - signal transduction [Evidence IEA]
COORDINATES: protein motif:HMM:NF024139.2
COORDINATES: protein motif:HMM:TIGR00377.1
COORDINATES: protein motif:HMM:NF013731.2
GO:0000160 - phosphorelay signal transduction system [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_013451058.1
COORDINATES: similar to AA sequence:RefSeq:WP_013007166.1
GO:0006935 - chemotaxis [Evidence IEA]; GO:0007165 - signal transduction [Evidence IEA]
COORDINATES: protein motif:HMM:NF018508.2
COORDINATES: similar to AA sequence:RefSeq:WP_003869986.1
GO:0005524 - ATP binding [Evidence IEA]; GO:0003677 - DNA binding [Evidence IEA]; GO:0003918 - DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) activity [Evidence IEA]
GO:0006265 - DNA topological change [Evidence IEA]
COORDINATES: protein motif:HMM:NF024554.2
GO:0003677 - DNA binding [Evidence IEA]; GO:0003896 - DNA primase activity [Evidence IEA]; GO:0008270 - zinc ion binding [Evidence IEA]
GO:0006260 - DNA replication [Evidence IEA]
CHC2 zinc finger domain-containing protein
COORDINATES: protein motif:HMM:NF004044.1
COORDINATES: similar to AA sequence:RefSeq:WP_013008961.1
COORDINATES: protein motif:HMM:NF012772.2
COORDINATES: protein motif:HMM:NF012529.2
COORDINATES: protein motif:HMM:NF013793.2
COORDINATES: protein motif:HMM:TIGR00180.1
GO:0007059 - chromosome segregation [Evidence IEA]; GO:0000910 - cytokinesis [Evidence IEA]
ParB/RepB/Spo0J family partition protein
COORDINATES: protein motif:HMM:TIGR02504.1
GO:0004748 - ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor [Evidence IEA]
adenosylcobalamin-dependent ribonucleoside-diphosphate reductase
COORDINATES: protein motif:HMM:NF015736.2
DnaB-like helicase C-terminal domain-containing protein
COORDINATES: protein motif:HMM:NF013528.2
GO:0003676 - nucleic acid binding [Evidence IEA]
COORDINATES: protein motif:HMM:NF037081.2
COORDINATES: protein motif:HMM:NF037161.2
COORDINATES: protein motif:HMM:TIGR02532.1
COORDINATES: protein motif:HMM:NF013755.2
COORDINATES: protein motif:HMM:NF040319.1
COORDINATES: protein motif:HMM:NF020419.2
COORDINATES: protein motif:HMM:NF012688.2
GO:0003677 - DNA binding [Evidence IEA]; GO:0003887 - DNA-directed DNA polymerase activity [Evidence IEA]