Rhodoferax antarcticus strain DSMZ24876 plasmid unnamed2.
Bacteria; Pseudomonadota; Betaproteobacteria; Burkholderiales; Comamonadaceae; Rhodoferax.
Submitted (13-JAN-2017) College of Health Science, Korea University, Anamro, Seoul 02841, South Korea
REFSEQ INFORMATION: The reference sequence is identical to\nCP019242.1.\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 :: PacBio SMRT Analysis v. v2.3\nGenome Representation :: Full\nExpected Final Version :: Yes\nGenome Coverage :: 268.0x\nSequencing Technology :: PacBio\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 04/28/2023 01:57:56\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) :: 3,977\nCDSs (total) :: 3,917\nGenes (coding) :: 3,751\nCDSs (with protein) :: 3,751\nGenes (RNA) :: 60\nrRNAs :: 3, 3, 3 (5S, 16S, 23S)\ncomplete rRNAs :: 3, 3, 3 (5S, 16S, 23S)\ntRNAs :: 48\nncRNAs :: 3\nPseudo Genes (total) :: 166\nCDSs (without protein) :: 166\nPseudo Genes (ambiguous residues) :: 0 of 166\nPseudo Genes (frameshifted) :: 53 of 166\nPseudo Genes (incomplete) :: 125 of 166\nPseudo Genes (internal stop) :: 42 of 166\nPseudo Genes (multiple problems) :: 45 of 166\nCRISPR Arrays :: 2\n##Genome-Annotation-Data-END##
COORDINATES: protein motif:HMM:NF012376.2
GO:0016787 - hydrolase activity [Evidence IEA]; GO:0046872 - metal ion binding [Evidence IEA]
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_009910607.1
COORDINATES: protein motif:HMM:NF037735.2
COORDINATES: protein motif:HMM:NF012234.2
GO:0005524 - ATP binding [Evidence IEA]; GO:0016887 - ATP hydrolysis activity [Evidence IEA]
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: similar to AA sequence:RefSeq:WP_004213304.1
COORDINATES: similar to AA sequence:RefSeq:WP_014005992.1
COORDINATES: protein motif:HMM:NF015397.2
relaxase/mobilization nuclease domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_020502863.1
COORDINATES: protein motif:HMM:NF023550.2
COORDINATES: similar to AA sequence:RefSeq:WP_020565917.1
COORDINATES: similar to AA sequence:RefSeq:WP_011798477.1
GO:0015074 - DNA integration [Evidence IEA]; GO:0006310 - DNA recombination [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_006491129.1
GO:0003964 - RNA-directed DNA polymerase activity [Evidence IEA]
GO:0000373 - Group II intron splicing [Evidence IEA]
group II intron reverse transcriptase/maturase
COORDINATES: protein motif:HMM:TIGR00180.1
GO:0007059 - chromosome segregation [Evidence IEA]; GO:0000910 - cytokinesis [Evidence IEA]
ParB/RepB/Spo0J family partition protein
COORDINATES: similar to AA sequence:RefSeq:WP_012406360.1
COORDINATES: protein motif:HMM:NF013235.2
GO:0003887 - DNA-directed DNA polymerase activity [Evidence IEA]
GO:0006270 - DNA replication initiation [Evidence IEA]
RepB family plasmid replication initiator protein
COORDINATES: similar to AA sequence:RefSeq:WP_013741667.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0000150 - DNA strand exchange activity [Evidence IEA]
GO:0006310 - DNA recombination [Evidence IEA]
incomplete; partial in the middle of a contig; missing N-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
helix-turn-helix domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_012733728.1
GO:0004803 - transposase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011798715.1
frameshifted; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_008328818.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0004803 - transposase activity [Evidence IEA]
GO:0006313 - transposition, DNA-mediated [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_076611202.1
GO:0015074 - DNA integration [Evidence IEA]
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.
integrase core domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_011463447.1
COORDINATES: protein motif:HMM:NF024954.2
COORDINATES: similar to AA sequence:RefSeq:WP_011801138.1
COORDINATES: similar to AA sequence:RefSeq:WP_005797090.1
COORDINATES: similar to AA sequence:RefSeq:WP_010465839.1
COORDINATES: similar to AA sequence:RefSeq:WP_007583969.1
GO:0005524 - ATP binding [Evidence IEA]; GO:0008134 - transcription factor binding [Evidence IEA]
GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
sigma 54-interacting transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_020655811.1
COORDINATES: protein motif:HMM:NF025053.2
GO:0004722 - protein serine/threonine phosphatase activity [Evidence IEA]
PP2C family serine/threonine-protein phosphatase
COORDINATES: protein motif:HMM:NF019334.2
GO:0004672 - protein kinase activity [Evidence IEA]
GO:0006468 - protein phosphorylation [Evidence IEA]
COORDINATES: protein motif:HMM:NF024486.2
COORDINATES: protein motif:HMM:NF019348.2
COORDINATES: protein motif:HMM:NF021352.2
COORDINATES: protein motif:HMM:NF013798.2
COORDINATES: protein motif:HMM:NF012320.2
COORDINATES: similar to AA sequence:RefSeq:WP_005663587.1
COORDINATES: similar to AA sequence:RefSeq:WP_015434776.1
COORDINATES: similar to AA sequence:RefSeq:WP_013512270.1
GO:0003676 - nucleic acid binding [Evidence IEA]
COORDINATES: protein motif:HMM:NF024491.2
phospholipase D-like domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_020456383.1
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_047389784.1
COORDINATES: similar to AA sequence:RefSeq:WP_013616059.1
COORDINATES: similar to AA sequence:RefSeq:WP_003089110.1
COORDINATES: similar to AA sequence:RefSeq:WP_004708599.1
COORDINATES: protein motif:HMM:NF013933.2
GO:0006865 - amino acid transport [Evidence IEA]
COORDINATES: protein motif:HMM:NF012544.2
GO:0022857 - transmembrane transporter activity [Evidence IEA]
GO:0055085 - transmembrane transport [Evidence IEA]
COORDINATES: protein motif:HMM:NF020466.2
COORDINATES: protein motif:HMM:TIGR02281.1
GO:0004190 - aspartic-type endopeptidase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_017052357.1
COORDINATES: similar to AA sequence:RefSeq:WP_007946602.1
COORDINATES: similar to AA sequence:RefSeq:WP_013646134.1
COORDINATES: similar to AA sequence:RefSeq:WP_018293885.1
COORDINATES: similar to AA sequence:RefSeq:WP_012078855.1
COORDINATES: similar to AA sequence:RefSeq:WP_011798564.1
COORDINATES: similar to AA sequence:RefSeq:WP_011798565.1
COORDINATES: similar to AA sequence:RefSeq:WP_011798566.1
COORDINATES: protein motif:HMM:NF024949.2
helix-turn-helix transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_010933132.1
GO:0003953 - NAD+ nucleosidase activity [Evidence IEA]; GO:0005515 - protein binding [Evidence IEA]
GO:0007165 - signal transduction [Evidence IEA]
toll/interleukin-1 receptor domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_013641240.1
frameshifted; internal stop; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_011797924.1
COORDINATES: protein motif:HMM:NF013395.2
COORDINATES: similar to AA sequence:RefSeq:WP_019140479.1
COORDINATES: similar to AA sequence:RefSeq:WP_011798591.1