Ponticoccus alexandrii strain C31 plasmid p-SCP3.
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\nCP047169.1.\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##
shallow sea, symbosis with harmful algal bloom algae
COORDINATES: similar to AA sequence:RefSeq:WP_018097044.1
GO:0016491 - oxidoreductase activity [Evidence IEA]
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_005863018.1
GO:0005524 - ATP binding [Evidence IEA]; GO:0019200 - carbohydrate kinase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_020048071.1
GO:0140359 - ABC-type transporter activity [Evidence IEA]; GO:0042626 - ATPase-coupled transmembrane transporter activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_020050263.1
GO:0008643 - carbohydrate transport [Evidence IEA]; GO:0055085 - transmembrane transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_005863011.1
COORDINATES: similar to AA sequence:RefSeq:WP_005863010.1
GO:0140359 - ABC-type transporter activity [Evidence IEA]; GO:0005524 - ATP binding [Evidence IEA]
sn-glycerol-3-phosphate ABC transporter ATP-binding protein UgpC
COORDINATES: protein motif:HMM:NF015925.2
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: similar to AA sequence:RefSeq:WP_008887924.1
COORDINATES: similar to AA sequence:RefSeq:WP_011909534.1
GO:0008080 - N-acetyltransferase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_009818602.1
GO:0005215 - transporter activity [Evidence IEA]
GO:0055085 - transmembrane transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_009760112.1
COORDINATES: similar to AA sequence:RefSeq:WP_013960551.1
GO:0004356 - glutamate-ammonia ligase activity [Evidence IEA]
GO:0006542 - glutamine biosynthetic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_008280792.1
GO:0015930 - glutamate synthase activity [Evidence IEA]; GO:0016638 - oxidoreductase activity, acting on the CH-NH2 group of donors [Evidence IEA]
GO:0006537 - glutamate biosynthetic process [Evidence IEA]
FMN-binding glutamate synthase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_009818607.1
COORDINATES: similar to AA sequence:RefSeq:WP_009818608.1
glutamine amidotransferase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_008280802.1
GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]; GO:0043565 - sequence-specific DNA binding [Evidence IEA]
GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
helix-turn-helix domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_011566371.1
COORDINATES: similar to AA sequence:RefSeq:WP_008281098.1
GO:0008115 - sarcosine oxidase activity [Evidence IEA]
sarcosine oxidase subunit alpha family protein
COORDINATES: similar to AA sequence:RefSeq:WP_008281097.1
COORDINATES: similar to AA sequence:RefSeq:WP_008281096.1
GO:0046653 - tetrahydrofolate metabolic process [Evidence IEA]
sarcosine oxidase subunit beta family protein
COORDINATES: similar to AA sequence:RefSeq:WP_008883317.1
TetR/AcrR family transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_009570694.1
efflux RND transporter periplasmic adaptor subunit
COORDINATES: similar to AA sequence:RefSeq:WP_009506272.1
GO:0015562 - efflux transmembrane transporter activity [Evidence IEA]
GO:0042908 - xenobiotic transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_007802936.1
NAD-dependent succinate-semialdehyde dehydrogenase
COORDINATES: similar to AA sequence:RefSeq:WP_076611844.1
GO:0004803 - transposase activity [Evidence IEA]
frameshifted; internal stop; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_018001668.1
GO:0008864 - formyltetrahydrofolate deformylase activity [Evidence IEA]
GO:0009152 - purine ribonucleotide biosynthetic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_009505681.1
GO:0051539 - 4 iron, 4 sulfur cluster binding [Evidence IEA]; GO:0003941 - L-serine ammonia-lyase activity [Evidence IEA]
GO:0009063 - amino acid catabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_009572621.1
GO:0004372 - glycine hydroxymethyltransferase activity [Evidence IEA]; GO:0030170 - pyridoxal phosphate binding [Evidence IEA]; GO:0070905 - serine binding [Evidence IEA]; GO:0008270 - zinc ion binding [Evidence IEA]
GO:0019264 - glycine biosynthetic process from serine [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_008887358.1
GO:0005515 - protein binding [Evidence IEA]; GO:0008115 - sarcosine oxidase activity [Evidence IEA]
GO:1901053 - sarcosine catabolic process [Evidence IEA]
sarcosine oxidase subunit gamma family protein
COORDINATES: similar to AA sequence:RefSeq:WP_020010180.1
COORDINATES: similar to AA sequence:RefSeq:WP_008887495.1
COORDINATES: similar to AA sequence:RefSeq:WP_008507740.1
COORDINATES: similar to AA sequence:RefSeq:WP_009572615.1
GO:0022857 - transmembrane transporter activity [Evidence IEA]
GO:0071705 - nitrogen compound transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_009505674.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_006936816.1
GO:0009055 - electron transfer activity [Evidence IEA]
electron transfer flavoprotein subunit beta/FixA family protein
COORDINATES: similar to AA sequence:RefSeq:WP_002965036.1
COORDINATES: similar to AA sequence:RefSeq:WP_007404995.1
GO:0004488 - methylenetetrahydrofolate dehydrogenase (NADP+) activity [Evidence IEA]
bifunctional methylenetetrahydrofolate dehydrogenase/methenyltetrahydrofolate cyclohydrolase FolD
COORDINATES: similar to AA sequence:RefSeq:WP_018517808.1
COORDINATES: similar to AA sequence:RefSeq:WP_003535578.1
GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_008887337.1
GO:0051537 - 2 iron, 2 sulfur cluster binding [Evidence IEA]; GO:0016491 - oxidoreductase activity [Evidence IEA]
aromatic ring-hydroxylating dioxygenase subunit alpha
COORDINATES: similar to AA sequence:RefSeq:WP_011747513.1
hybrid-cluster NAD(P)-dependent oxidoreductase
COORDINATES: similar to AA sequence:RefSeq:WP_007801589.1
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: protein motif:HMM:NF016200.2
COORDINATES: protein motif:HMM:NF015445.2
TRAP transporter substrate-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_007801599.1
hydantoinase B/oxoprolinase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_007801600.1
hydantoinase/oxoprolinase family protein
COORDINATES: protein motif:HMM:NF019349.2
COORDINATES: similar to AA sequence:RefSeq:WP_007801604.1
COORDINATES: similar to AA sequence:RefSeq:WP_008885348.1
COORDINATES: similar to AA sequence:RefSeq:WP_008885162.1
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_009571983.1
GO:0015803 - branched-chain amino acid transport [Evidence IEA]
branched-chain amino acid ABC transporter permease
COORDINATES: similar to AA sequence:RefSeq:WP_007801612.1
COORDINATES: similar to AA sequence:RefSeq:WP_009571981.1
ABC transporter substrate-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_008883772.1
COORDINATES: similar to AA sequence:RefSeq:WP_013529934.1
COORDINATES: similar to AA sequence:RefSeq:WP_020054835.1
COORDINATES: similar to AA sequence:RefSeq:WP_011569699.1
COORDINATES: similar to AA sequence:RefSeq:WP_013960825.1
GO:0008643 - carbohydrate transport [Evidence IEA]
COORDINATES: protein motif:HMM:NF033681.1
ExeM/NucH family extracellular endonuclease
COORDINATES: protein motif:HMM:NF017394.2
nitrous oxide reductase accessory protein NosL
COORDINATES: similar to AA sequence:RefSeq:WP_006725143.1
COORDINATES: similar to AA sequence:RefSeq:WP_007196341.1
COORDINATES: similar to AA sequence:RefSeq:WP_010443510.1
TRAP transporter substrate-binding protein DctP
COORDINATES: similar to AA sequence:RefSeq:WP_009491742.1
COORDINATES: protein motif:HMM:NF012904.2
GO:0009436 - glyoxylate catabolic process [Evidence IEA]; GO:0071704 - organic substance metabolic process [Evidence IEA]
dihydrodipicolinate synthase family protein
COORDINATES: protein motif:HMM:NF007922.1
GO:0051287 - NAD binding [Evidence IEA]; GO:0043115 - precorrin-2 dehydrogenase activity [Evidence IEA]; GO:0051266 - sirohydrochlorin ferrochelatase activity [Evidence IEA]; GO:0004851 - uroporphyrin-III C-methyltransferase activity [Evidence IEA]
GO:0019354 - siroheme biosynthetic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_009572170.1
COORDINATES: similar to AA sequence:RefSeq:WP_007791925.1
COORDINATES: similar to AA sequence:RefSeq:WP_007791928.1
GO:0051537 - 2 iron, 2 sulfur cluster binding [Evidence IEA]; GO:0008942 - nitrite reductase [NAD(P)H] activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_005979995.1
GO:0050660 - flavin adenine dinucleotide binding [Evidence IEA]; GO:0050661 - NADP binding [Evidence IEA]; GO:0008942 - nitrite reductase [NAD(P)H] activity [Evidence IEA]; GO:0016491 - oxidoreductase activity [Evidence IEA]
GO:0042128 - nitrate assimilation [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_020041966.1
COORDINATES: similar to AA sequence:RefSeq:WP_020041967.1
GO:0005524 - ATP binding [Evidence IEA]; GO:0016887 - ATP hydrolysis activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_019296407.1
GO:0005524 - ATP binding [Evidence IEA]; GO:0022857 - transmembrane transporter activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_007791945.1
GO:0055052 - ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing [Evidence IEA]
CmpA/NrtA family ABC transporter substrate-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_009572164.1
COORDINATES: similar to AA sequence:RefSeq:WP_008885510.1
COORDINATES: similar to AA sequence:RefSeq:WP_015253183.1
GO:0016765 - transferase activity, transferring alkyl or aryl (other than methyl) groups [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_010141558.1
GO:0008966 - phosphoglucosamine mutase activity [Evidence IEA]
GO:0009103 - lipopolysaccharide biosynthetic process [Evidence IEA]; GO:0009252 - peptidoglycan biosynthetic process [Evidence IEA]
COORDINATES: protein motif:HMM:NF012573.2
GO:0005509 - calcium ion binding [Evidence IEA]
COORDINATES: protein motif:HMM:NF012415.2
COORDINATES: protein motif:HMM:NF022436.2
COORDINATES: similar to AA sequence:RefSeq:WP_012187400.1
GO:0008460 - dTDP-glucose 4,6-dehydratase activity [Evidence IEA]
GO:0019305 - dTDP-rhamnose biosynthetic process [Evidence IEA]; GO:0009243 - O antigen biosynthetic process [Evidence IEA]
COORDINATES: protein motif:HMM:NF037016.2
COORDINATES: similar to AA sequence:RefSeq:WP_076611444.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0004803 - transposase activity [Evidence IEA]
GO:0006313 - DNA transposition [Evidence IEA]
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_076611570.1
frameshifted; 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.
COORDINATES: similar to AA sequence:RefSeq:WP_076611470.1
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: protein motif:HMM:NF024854.2
MarR family winged helix-turn-helix transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_009504273.1
COORDINATES: similar to AA sequence:RefSeq:WP_009504271.1
COORDINATES: similar to AA sequence:RefSeq:WP_009504269.1
COORDINATES: similar to AA sequence:RefSeq:WP_007803100.1
GO:0016034 - maleylacetoacetate isomerase activity [Evidence IEA]
GO:0006559 - L-phenylalanine catabolic process [Evidence IEA]; GO:0006572 - tyrosine catabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_007118074.1
COORDINATES: similar to AA sequence:RefSeq:WP_009504265.1
COORDINATES: similar to AA sequence:RefSeq:WP_007757906.1
GO:0016787 - hydrolase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_007803096.1
GO:0004334 - fumarylacetoacetase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_008190383.1
GO:0004411 - homogentisate 1,2-dioxygenase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_010437564.1
COORDINATES: similar to AA sequence:RefSeq:WP_007791754.1
frameshifted; incomplete; partial in the middle of a contig; missing C-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_018431088.1
GO:0004180 - carboxypeptidase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_019170338.1
GO:0008152 - metabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_008944215.1
COORDINATES: similar to AA sequence:RefSeq:WP_018431091.1
COORDINATES: similar to AA sequence:RefSeq:WP_014397662.1
COORDINATES: similar to AA sequence:RefSeq:WP_018431093.1
COORDINATES: similar to AA sequence:RefSeq:WP_019170332.1
COORDINATES: similar to AA sequence:RefSeq:WP_019170331.1
COORDINATES: similar to AA sequence:RefSeq:WP_018431096.1
COORDINATES: similar to AA sequence:RefSeq:WP_018431097.1
rhodanese-like domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_018431098.1
COORDINATES: similar to AA sequence:RefSeq:WP_008888248.1
COORDINATES: similar to AA sequence:RefSeq:WP_009815512.1
COORDINATES: protein motif:HMM:NF040974.1
COORDINATES: similar to AA sequence:RefSeq:WP_009452798.1
LysR substrate-binding domain-containing protein
COORDINATES: protein motif:HMM:NF012706.2
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: protein motif:HMM:NF015431.2
COORDINATES: similar to AA sequence:RefSeq:WP_005859827.1
COORDINATES: similar to AA sequence:RefSeq:WP_005859825.1
COORDINATES: similar to AA sequence:RefSeq:WP_005859823.1
COORDINATES: similar to AA sequence:RefSeq:WP_005859821.1
COORDINATES: similar to AA sequence:RefSeq:WP_005859818.1
COORDINATES: protein motif:HMM:NF024109.2
COORDINATES: similar to AA sequence:RefSeq:WP_020042784.1
COORDINATES: similar to AA sequence:RefSeq:WP_011842467.1
COORDINATES: protein motif:HMM:NF040071.1
COORDINATES: similar to AA sequence:RefSeq:WP_009561198.1
tannase/feruloyl esterase family alpha/beta hydrolase
COORDINATES: similar to AA sequence:RefSeq:WP_005848490.1
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.
frameshifted; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_007427970.1
COORDINATES: similar to AA sequence:RefSeq:WP_018430913.1
GO:0016627 - oxidoreductase activity, acting on the CH-CH group of donors [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_020041658.1
COORDINATES: similar to AA sequence:RefSeq:WP_018430911.1
COORDINATES: similar to AA sequence:RefSeq:WP_018326527.1
COORDINATES: similar to AA sequence:RefSeq:WP_018326528.1
GO:0004139 - deoxyribose-phosphate aldolase activity [Evidence IEA]
GO:0009264 - deoxyribonucleotide catabolic process [Evidence IEA]