Ponticoccus alexandrii strain C31 plasmid p-SCP2, complete sequence.
Bacteria; Pseudomonadota; Alphaproteobacteria; Rhodobacterales; Roseobacteraceae; Ponticoccus.
Complete Genome Sequence of a Quorum-Sensing Bacterium,Rhodobacteraceae bacterium C31, Isolated from a marine microalgae symbiotic bacteria
Submitted (12-DEC-2019) Ecological center, First Institute of Oceanography, MNR, 6 Xianxialing Road, Laoshan District, QingDao 266061, China
REFSEQ INFORMATION: The reference sequence is identical to\nCP047168.1.\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 :: HGAP v. 2.3\nGenome Representation :: Full\nExpected Final Version :: No\nGenome Coverage :: 150.0x\nSequencing Technology :: PacBio\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 06/17/2023 04:59:53\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) :: 4,836\nCDSs (total) :: 4,782\nGenes (coding) :: 4,651\nCDSs (with protein) :: 4,651\nGenes (RNA) :: 54\nrRNAs :: 2, 2, 2 (5S, 16S, 23S)\ncomplete rRNAs :: 2, 2, 2 (5S, 16S, 23S)\ntRNAs :: 45\nncRNAs :: 3\nPseudo Genes (total) :: 131\nCDSs (without protein) :: 131\nPseudo Genes (ambiguous residues) :: 0 of 131\nPseudo Genes (frameshifted) :: 66 of 131\nPseudo Genes (incomplete) :: 94 of 131\nPseudo Genes (internal stop) :: 29 of 131\nPseudo Genes (multiple problems) :: 50 of 131\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.
shallow sea, symbosis with harmful algal bloom algae
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
tripartite tricarboxylate transporter permease
COORDINATES: similar to AA sequence:RefSeq:WP_013653264.1
frameshifted; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: protein motif:HMM:NF027681.2
GO:0016491 - oxidoreductase activity [Evidence IEA]
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_008971022.1
GO:0003855 - 3-dehydroquinate dehydratase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_009450401.1
COORDINATES: protein motif:HMM:NF016228.2
COORDINATES: similar to AA sequence:RefSeq:WP_015934187.1
COORDINATES: similar to AA sequence:RefSeq:WP_006391584.1
COORDINATES: protein motif:HMM:NF013757.2
GO:0003677 - DNA binding [Evidence IEA]; GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]
GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_019015396.1
GO:0016491 - oxidoreductase activity [Evidence IEA]; GO:0016651 - oxidoreductase activity, acting on NAD(P)H [Evidence IEA]
COORDINATES: protein motif:HMM:NF024852.2
COORDINATES: protein motif:HMM:NF013429.2
GO:0003824 - catalytic activity [Evidence IEA]
sugar phosphate isomerase/epimerase family protein
COORDINATES: protein motif:HMM:NF013530.2
COORDINATES: protein motif:HMM:NF015925.2
GO:0004497 - monooxygenase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_009450403.1
COORDINATES: protein motif:HMM:NF012235.2
ATP-binding cassette domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_009098781.1
COORDINATES: similar to AA sequence:RefSeq:WP_010141884.1
type IV secretory system conjugative DNA transfer family protein
COORDINATES: similar to AA sequence:RefSeq:WP_007803321.1
relaxase/mobilization nuclease domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_008336066.1
plasmid mobilization relaxosome protein MobC
COORDINATES: similar to AA sequence:RefSeq:WP_007803318.1
COORDINATES: similar to AA sequence:RefSeq:WP_009574175.1
COORDINATES: similar to AA sequence:RefSeq:WP_009574176.1
COORDINATES: similar to AA sequence:RefSeq:WP_008335773.1
COORDINATES: similar to AA sequence:RefSeq:WP_002725006.1
GO:0004803 - transposase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_008759231.1
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_076611355.1
programmed frameshift; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_008555709.1
COORDINATES: similar to AA sequence:RefSeq:WP_009208497.1
COORDINATES: similar to AA sequence:RefSeq:WP_020187883.1
COORDINATES: similar to AA sequence:RefSeq:WP_011049304.1
GO:0003676 - nucleic acid binding [Evidence IEA]; GO:0003723 - RNA binding [Evidence IEA]; GO:0001072 - transcription antitermination factor activity, RNA binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_020039693.1
COORDINATES: similar to AA sequence:RefSeq:WP_005861918.1
COORDINATES: protein motif:HMM:NF017934.2
COORDINATES: similar to AA sequence:RefSeq:WP_010141867.1
COORDINATES: similar to AA sequence:RefSeq:WP_007803302.1
COORDINATES: similar to AA sequence:RefSeq:WP_008336055.1
COORDINATES: similar to AA sequence:RefSeq:WP_009574191.1
COORDINATES: similar to AA sequence:RefSeq:WP_009820102.1
COORDINATES: similar to AA sequence:RefSeq:WP_012561404.1
nucleotidyl transferase AbiEii/AbiGii toxin family protein
COORDINATES: similar to AA sequence:RefSeq:WP_019404595.1
COORDINATES: similar to AA sequence:RefSeq:WP_009450564.1
COORDINATES: similar to AA sequence:RefSeq:WP_009820093.1
COORDINATES: similar to AA sequence:RefSeq:WP_005859714.1
COORDINATES: similar to AA sequence:RefSeq:WP_018065909.1
COORDINATES: similar to AA sequence:RefSeq:WP_007803272.1
COORDINATES: similar to AA sequence:RefSeq:WP_009827206.1
COORDINATES: similar to AA sequence:RefSeq:WP_018065906.1
COORDINATES: similar to AA sequence:RefSeq:WP_009827208.1
COORDINATES: similar to AA sequence:RefSeq:WP_005859736.1
COORDINATES: similar to AA sequence:RefSeq:WP_009820079.1
COORDINATES: protein motif:HMM:TIGR01695.1
GO:0034204 - lipid translocation [Evidence IEA]; GO:0009252 - peptidoglycan biosynthetic process [Evidence IEA]
murein biosynthesis integral membrane protein MurJ
COORDINATES: similar to AA sequence:RefSeq:WP_008280856.1
COORDINATES: similar to AA sequence:RefSeq:WP_011910653.1
GO:0055052 - ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing [Evidence IEA]; GO:0009898 - cytoplasmic side of plasma membrane [Evidence IEA]
GO:0015419 - ABC-type sulfate transporter activity [Evidence IEA]; GO:0005524 - ATP binding [Evidence IEA]
GO:0008272 - sulfate transport [Evidence IEA]
sulfate ABC transporter ATP-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_013383359.1
GO:0055052 - ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing [Evidence IEA]; GO:0005886 - plasma membrane [Evidence IEA]
GO:0015419 - ABC-type sulfate transporter activity [Evidence IEA]
sulfate ABC transporter permease subunit CysW
COORDINATES: similar to AA sequence:RefSeq:WP_002724659.1
sulfate ABC transporter permease subunit CysT
COORDINATES: similar to AA sequence:RefSeq:WP_013383361.1
sulfate ABC transporter substrate-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_008280857.1
COORDINATES: similar to AA sequence:RefSeq:WP_019966450.1
Lrp/AsnC family transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_007803257.1
COORDINATES: similar to AA sequence:RefSeq:WP_009505363.1
GO:0042625 - ATPase-coupled ion transmembrane transporter activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_007803253.1
GO:0005886 - plasma membrane [Evidence IEA]
GO:0046872 - metal ion binding [Evidence IEA]; GO:0016740 - transferase activity [Evidence IEA]
GO:0017013 - protein flavinylation [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_006643175.1
internal stop; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_013654751.1
COORDINATES: similar to AA sequence:RefSeq:WP_007803249.1
COORDINATES: similar to AA sequence:RefSeq:WP_007803247.1
COORDINATES: similar to AA sequence:RefSeq:WP_009505369.1
COORDINATES: similar to AA sequence:RefSeq:WP_007817689.1
GO:0000160 - phosphorelay signal transduction system [Evidence IEA]; GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_007803242.1
COORDINATES: similar to AA sequence:RefSeq:WP_018065899.1
COORDINATES: similar to AA sequence:RefSeq:WP_009827215.1
COORDINATES: similar to AA sequence:RefSeq:WP_018001791.1
ParB/RepB/Spo0J family partition protein
COORDINATES: protein motif:HMM:NF015393.2
helix-turn-helix domain-containing protein
COORDINATES: protein motif:HMM:TIGR00180.1
GO:0007059 - chromosome segregation [Evidence IEA]; GO:0000910 - cytokinesis [Evidence IEA]
COORDINATES: protein motif:HMM:TIGR03453.1
COORDINATES: similar to AA sequence:RefSeq:WP_011331448.1
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_012187059.1
GO:0051983 - regulation of chromosome segregation [Evidence IEA]
type II toxin-antitoxin system ParD family antitoxin
COORDINATES: similar to AA sequence:RefSeq:WP_009819734.1
GO:0008657 - DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) inhibitor activity [Evidence IEA]; GO:0042803 - protein homodimerization activity [Evidence IEA]
GO:0030541 - plasmid partitioning [Evidence IEA]; GO:0051290 - protein heterotetramerization [Evidence IEA]
type II toxin-antitoxin system RelE/ParE family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_005859468.1
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_017140420.1
FadR/GntR family transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_011842338.1
GO:0022857 - transmembrane transporter activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_002723068.1
GO:0005886 - plasma membrane [Evidence IEA]; GO:0031317 - tripartite ATP-independent periplasmic transporter complex [Evidence IEA]
GO:0015556 - C4-dicarboxylate transmembrane transporter activity [Evidence IEA]
GO:0015740 - C4-dicarboxylate transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_009561204.1
GO:0030288 - outer membrane-bounded periplasmic space [Evidence IEA]; GO:0031317 - tripartite ATP-independent periplasmic transporter complex [Evidence IEA]
GO:0005488 - binding [Evidence IEA]; GO:0005215 - transporter activity [Evidence IEA]
DctP family TRAP transporter solute-binding subunit
COORDINATES: similar to AA sequence:RefSeq:WP_002723062.1
carbon-nitrogen hydrolase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_011842334.1
COORDINATES: similar to AA sequence:RefSeq:WP_009561201.1
4-hydroxy-4-methyl-2-oxoglutarate aldolase
COORDINATES: similar to AA sequence:RefSeq:WP_002723057.1
COORDINATES: similar to AA sequence:RefSeq:WP_011842331.1
GO:0047448 - 5-dehydro-4-deoxyglucarate dehydratase activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF019349.2
GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF012706.2
ABC transporter substrate-binding protein
COORDINATES: protein motif:HMM:NF024771.2
mandelate racemase/muconate lactonizing enzyme family protein
COORDINATES: similar to AA sequence:RefSeq:WP_014753255.1
GO:0140359 - ABC-type transporter activity [Evidence IEA]; GO:0005524 - ATP binding [Evidence IEA]; GO:0016887 - ATP hydrolysis activity [Evidence IEA]; GO:0042626 - ATPase-coupled transmembrane transporter activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_018270427.1
COORDINATES: similar to AA sequence:RefSeq:WP_014753252.1
GO:0055085 - transmembrane transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_014753251.1
GO:0140359 - ABC-type transporter activity [Evidence IEA]; GO:0042626 - ATPase-coupled transmembrane transporter activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_019400555.1
GO:0051287 - NAD binding [Evidence IEA]; GO:0050661 - NADP binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_020187605.1
COORDINATES: similar to AA sequence:RefSeq:WP_007635327.1
COORDINATES: similar to AA sequence:RefSeq:WP_076611960.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0004803 - transposase activity [Evidence IEA]
GO:0006313 - DNA transposition [Evidence IEA]
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_076611905.1
COORDINATES: similar to AA sequence:RefSeq:WP_012187345.1
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_012187342.1
GO:0008233 - peptidase activity [Evidence IEA]; GO:0003697 - single-stranded DNA binding [Evidence IEA]
GO:0018142 - protein-DNA covalent cross-linking [Evidence IEA]; GO:0009432 - SOS response [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_076612405.1
COORDINATES: protein motif:HMM:NF025189.2
COORDINATES: similar to AA sequence:RefSeq:WP_052096176.1
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_008336115.1
COORDINATES: similar to AA sequence:RefSeq:WP_010398642.1
COORDINATES: similar to AA sequence:RefSeq:WP_018001728.1
COORDINATES: similar to AA sequence:RefSeq:WP_008336095.1
COORDINATES: similar to AA sequence:RefSeq:WP_005859613.1
COORDINATES: similar to AA sequence:RefSeq:WP_010138156.1
COORDINATES: similar to AA sequence:RefSeq:WP_005859617.1
GO:0016798 - hydrolase activity, acting on glycosyl bonds [Evidence IEA]
lytic transglycosylase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_010138154.1
COORDINATES: similar to AA sequence:RefSeq:WP_008327373.1
VirB3 family type IV secretion system protein
COORDINATES: similar to AA sequence:RefSeq:WP_005859622.1
COORDINATES: similar to AA sequence:RefSeq:WP_009574154.1
COORDINATES: similar to AA sequence:RefSeq:WP_005859624.1
COORDINATES: similar to AA sequence:RefSeq:WP_010139195.1
COORDINATES: similar to AA sequence:RefSeq:WP_010139194.1
COORDINATES: similar to AA sequence:RefSeq:WP_009574160.1
TrbG/VirB9 family P-type conjugative transfer protein
COORDINATES: similar to AA sequence:RefSeq:WP_008336084.1
COORDINATES: similar to AA sequence:RefSeq:WP_009574167.1
COORDINATES: similar to AA sequence:RefSeq:WP_009574168.1
COORDINATES: similar to AA sequence:RefSeq:WP_018001741.1
GO:0015074 - DNA integration [Evidence IEA]
integrase core domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_060835708.1
COORDINATES: similar to AA sequence:RefSeq:WP_076611275.1
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: similar to AA sequence:RefSeq:WP_007803406.1
GO:0005507 - copper ion binding [Evidence IEA]
internal stop; 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.
multicopper oxidase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_012330183.1
COORDINATES: protein motif:HMM:NF024950.2
COORDINATES: similar to AA sequence:RefSeq:WP_008966924.1
COORDINATES: similar to AA sequence:RefSeq:WP_015934194.1
LysR substrate-binding domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_019426067.1
COORDINATES: protein motif:HMM:NF015366.2
GO:0042597 - periplasmic space [Evidence IEA]
tripartite tricarboxylate transporter substrate binding protein
COORDINATES: protein motif:HMM:NF018979.2
tripartite tricarboxylate transporter TctB family protein