Fuscovulum blasticum strain 28/5 plasmid pRsa, complete sequence.
Bacteria; Pseudomonadota; Alphaproteobacteria; Rhodobacterales; Paracoccaceae; Fuscovulum.
Complete Genome Sequences of Two Rhodobacter Strains
Submitted (24-MAR-2017) New England Biolabs, 240 County Rd, Ipswich, MA 01938, USA
REFSEQ INFORMATION: The reference sequence is identical to\nCP020471.1.\nBacteria and source DNA available from Rhodopseudomonas blasticus/\nNEB collection 28/5.\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 Date :: 14-OCT-2016\nAssembly Method :: HGAP3 v. October-2016\nAssembly Name :: Rsa_HGAP3\nGenome Representation :: Full\nExpected Final Version :: Yes\nGenome Coverage :: 81.0x\nSequencing Technology :: PacBio\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 02/06/2023 08:23:48\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) :: 3,636\nCDSs (total) :: 3,579\nGenes (coding) :: 3,549\nCDSs (with protein) :: 3,549\nGenes (RNA) :: 57\nrRNAs :: 2, 2, 2 (5S, 16S, 23S)\ncomplete rRNAs :: 2, 2, 2 (5S, 16S, 23S)\ntRNAs :: 47\nncRNAs :: 4\nPseudo Genes (total) :: 30\nCDSs (without protein) :: 30\nPseudo Genes (ambiguous residues) :: 0 of 30\nPseudo Genes (frameshifted) :: 10 of 30\nPseudo Genes (incomplete) :: 22 of 30\nPseudo Genes (internal stop) :: 3 of 30\nPseudo Genes (multiple problems) :: 5 of 30\nCRISPR Arrays :: 2\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.
S. Kaplan, University of Wisconsin, obtained this bacterium from G. Drews, University of Freiburg, Freiburg Germany.
originally released as Rhodobacter sphaeroides but identified as blasticus by the submitter
COORDINATES: protein motif:HMM:NF015431.2
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_011456202.1
dehydrogenase E1 component subunit alpha/beta
COORDINATES: similar to AA sequence:RefSeq:WP_012589563.1
dihydrolipoamide acetyltransferase family protein
COORDINATES: protein motif:HMM:NF024950.2
COORDINATES: protein motif:HMM:NF013098.2
COORDINATES: similar to AA sequence:RefSeq:WP_010398755.1
COORDINATES: similar to AA sequence:RefSeq:WP_015498411.1
sulfite exporter TauE/SafE family protein
COORDINATES: protein motif:HMM:NF018294.2
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: protein motif:HMM:NF004396.0
GO:0003677 - DNA binding [Evidence IEA]; GO:0070063 - RNA polymerase binding [Evidence IEA]
GO:0032784 - regulation of DNA-templated transcription elongation [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_008562709.1
COORDINATES: similar to AA sequence:RefSeq:WP_018430443.1
COORDINATES: similar to AA sequence:RefSeq:WP_007811349.1
COORDINATES: similar to AA sequence:RefSeq:WP_011970376.1
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: protein motif:HMM:NF024408.2
COORDINATES: similar to AA sequence:RefSeq:WP_007813144.1
GO:0004803 - transposase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_086558278.1
frameshifted; 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:NF033587.1
COORDINATES: similar to AA sequence:RefSeq:WP_013635061.1
incomplete; partial in the middle of a contig; missing N-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
DDE-type integrase/transposase/recombinase
COORDINATES: protein motif:HMM:NF017243.2
COORDINATES: similar to AA sequence:RefSeq:WP_076612253.1
COORDINATES: similar to AA sequence:RefSeq:WP_018184293.1
COORDINATES: similar to AA sequence:RefSeq:WP_011440488.1
GO:0005524 - ATP binding [Evidence IEA]; GO:0016887 - ATP hydrolysis activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_018098623.1
COORDINATES: protein motif:HMM:NF024800.2
recombinase zinc beta ribbon domain-containing protein
COORDINATES: protein motif:HMM:NF024589.2
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_003551028.1
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: similar to AA sequence:RefSeq:WP_007198577.1
GO:0015074 - DNA integration [Evidence IEA]; GO:0006310 - DNA recombination [Evidence IEA]
COORDINATES: protein motif:HMM:NF024685.2
COORDINATES: similar to AA sequence:RefSeq:WP_010812292.1
type II toxin-antitoxin system Phd/YefM family antitoxin
COORDINATES: similar to AA sequence:RefSeq:WP_017914821.1
type II toxin-antitoxin system VapC family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_010140516.1
GO:0008408 - 3'-5' exonuclease activity [Evidence IEA]; GO:0003887 - DNA-directed DNA polymerase activity [Evidence IEA]
GO:0006260 - DNA replication [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_012187344.1
COORDINATES: similar to AA sequence:RefSeq:WP_012187343.1
COORDINATES: similar to AA sequence:RefSeq:WP_012043539.1
GO:0003697 - single-stranded DNA binding [Evidence IEA]
GO:0006974 - cellular response to DNA damage stimulus [Evidence IEA]; GO:0018142 - protein-DNA covalent cross-linking [Evidence IEA]
SOS response-associated peptidase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_006115554.1
COORDINATES: similar to AA sequence:RefSeq:WP_012813213.1
COORDINATES: protein motif:HMM:NF012573.2
COORDINATES: similar to AA sequence:RefSeq:WP_076612142.1
frameshifted; 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: similar to AA sequence:RefSeq:WP_076612406.1
frameshifted; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_009562933.1
COORDINATES: similar to AA sequence:RefSeq:WP_002719306.1
COORDINATES: protein motif:HMM:NF020893.2
COORDINATES: similar to AA sequence:RefSeq:WP_004754586.1
COORDINATES: protein motif:HMM:NF012234.2
COORDINATES: protein motif:HMM:NF024676.2
COORDINATES: similar to AA sequence:RefSeq:WP_015496866.1
ADP-ribosylglycohydrolase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_015496881.1
COORDINATES: similar to AA sequence:RefSeq:WP_010336180.1
COORDINATES: similar to AA sequence:RefSeq:WP_010336181.1
COORDINATES: protein motif:HMM:NF016724.2
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_018065928.1
COORDINATES: similar to AA sequence:RefSeq:WP_019863965.1
COORDINATES: protein motif:HMM:NF018841.2
COORDINATES: similar to AA sequence:RefSeq:WP_005848984.1
GO:0008657 - DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) inhibitor activity [Evidence IEA]
GO:0006276 - plasmid maintenance [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011910853.1
type II toxin-antitoxin system CcdA family antitoxin
COORDINATES: similar to AA sequence:RefSeq:WP_009573266.1
COORDINATES: protein motif:HMM:NF024795.2
COORDINATES: similar to AA sequence:RefSeq:WP_013069292.1
COORDINATES: similar to AA sequence:RefSeq:WP_013069291.1
COORDINATES: similar to AA sequence:RefSeq:WP_008186599.1
COORDINATES: similar to AA sequence:RefSeq:WP_007803926.1
COORDINATES: similar to AA sequence:RefSeq:WP_012643364.1
COORDINATES: protein motif:HMM:NF021242.2
type I-E CRISPR-associated endoribonuclease Cas2
COORDINATES: similar to AA sequence:RefSeq:WP_019646155.1
COORDINATES: similar to AA sequence:RefSeq:WP_009816030.1
COORDINATES: similar to AA sequence:RefSeq:WP_020009989.1
ABC transporter substrate-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_011950286.1
GO:0055085 - transmembrane transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_002723841.1
COORDINATES: similar to AA sequence:RefSeq:WP_020813549.1
COORDINATES: similar to AA sequence:RefSeq:WP_011910843.1
ATP-binding cassette domain-containing protein
COORDINATES: protein motif:HMM:NF013884.2
COORDINATES: protein motif:HMM:NF024880.2
methyltransferase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_010974007.1
COORDINATES: similar to AA sequence:RefSeq:WP_010974008.1
GO:0003824 - catalytic activity [Evidence IEA]
NAD-dependent epimerase/dehydratase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_007792467.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0004803 - transposase activity [Evidence IEA]
GO:0006313 - transposition, DNA-mediated [Evidence IEA]
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_003571872.1
COORDINATES: similar to AA sequence:RefSeq:WP_018429008.1
COORDINATES: similar to AA sequence:RefSeq:WP_002967209.1
MetQ/NlpA family ABC transporter substrate-binding protein
COORDINATES: protein motif:HMM:NF019474.2
COORDINATES: similar to AA sequence:RefSeq:WP_010684218.1
COORDINATES: similar to AA sequence:RefSeq:WP_017998856.1
COORDINATES: similar to AA sequence:RefSeq:WP_017998855.1
COORDINATES: similar to AA sequence:RefSeq:WP_012093424.1
GO:0008927 - mannonate dehydratase activity [Evidence IEA]
GO:0006064 - glucuronate catabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_012093423.1
COORDINATES: similar to AA sequence:RefSeq:WP_012093422.1
COORDINATES: similar to AA sequence:RefSeq:WP_012093421.1
COORDINATES: similar to AA sequence:RefSeq:WP_012093420.1
TRAP transporter substrate-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_008888088.1
COORDINATES: protein motif:HMM:NF037997.1
COORDINATES: similar to AA sequence:RefSeq:WP_003523976.1
COORDINATES: similar to AA sequence:RefSeq:WP_019611191.1
COORDINATES: similar to AA sequence:RefSeq:WP_014528756.1
COORDINATES: similar to AA sequence:RefSeq:WP_018429779.1
substrate-binding domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_018429778.1
MurR/RpiR family transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_013385087.1
COORDINATES: protein motif:HMM:NF013227.2
DegT/DnrJ/EryC1/StrS family aminotransferase
COORDINATES: protein motif:HMM:NF025072.2
COORDINATES: protein motif:HMM:NF012792.2
COORDINATES: similar to AA sequence:RefSeq:WP_076611656.1
COORDINATES: protein motif:HMM:NF012422.2
GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
LuxR C-terminal-related transcriptional regulator
COORDINATES: protein motif:HMM:NF024949.2
helix-turn-helix transcriptional regulator
COORDINATES: protein motif:HMM:NF012744.2
COORDINATES: protein motif:HMM:NF016296.2
LytTR family DNA-binding domain-containing protein
COORDINATES: protein motif:HMM:NF025189.2
COORDINATES: similar to AA sequence:RefSeq:WP_076611556.1
COORDINATES: protein motif:HMM:NF015722.2
formylglycine-generating enzyme family protein
COORDINATES: similar to AA sequence:RefSeq:WP_076612354.1
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_002711103.1
SDR family NAD(P)-dependent oxidoreductase
COORDINATES: similar to AA sequence:RefSeq:WP_007870395.1
branched-chain amino acid ABC transporter permease
COORDINATES: similar to AA sequence:RefSeq:WP_012416771.1
COORDINATES: similar to AA sequence:RefSeq:WP_007870404.1
COORDINATES: similar to AA sequence:RefSeq:WP_017452736.1
COORDINATES: protein motif:HMM:NF024850.2