Ponticoccus alexandrii strain C31 plasmid p-SCP1, 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\nCP047167.1.\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: similar to AA sequence:RefSeq:WP_011427422.1
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.
helix-turn-helix domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_008887729.1
GO:0004399 - histidinol dehydrogenase activity [Evidence IEA]
GO:0000105 - histidine biosynthetic process [Evidence IEA]
frameshifted; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_008331397.1
Derived by automated computational analysis using gene prediction method: Protein Homology.
LacI family DNA-binding transcriptional regulator
COORDINATES: protein motif:HMM:NF019349.2
GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_007803086.1
GO:0050660 - flavin adenine dinucleotide binding [Evidence IEA]; GO:0016614 - oxidoreductase activity, acting on CH-OH group of donors [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_013945847.1
GO:0016491 - oxidoreductase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_006464862.1
sugar ABC transporter substrate-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_017453565.1
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]
sugar ABC transporter ATP-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_017455449.1
GO:0005886 - plasma membrane [Evidence IEA]
GO:0022857 - transmembrane transporter activity [Evidence IEA]
GO:0008643 - carbohydrate transport [Evidence IEA]
COORDINATES: protein motif:HMM:NF020243.2
COORDINATES: protein motif:HMM:NF033550.5
GO:0004803 - transposase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_076611342.1
COORDINATES: similar to AA sequence:RefSeq:WP_006468971.1
catalyzes the thiolytic cleavage of beta-ketoadipyl-CoA to succinate and acetyl-CoA; 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_002721020.1
GO:0004476 - mannose-6-phosphate isomerase activity [Evidence IEA]
GO:0009103 - lipopolysaccharide biosynthetic process [Evidence IEA]
mannose-1-phosphate guanylyltransferase/mannose-6-phosphate isomerase
COORDINATES: similar to AA sequence:RefSeq:WP_008281612.1
GO:0008830 - dTDP-4-dehydrorhamnose 3,5-epimerase activity [Evidence IEA]
GO:0019305 - dTDP-rhamnose biosynthetic process [Evidence IEA]; GO:0009243 - O antigen biosynthetic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_008332710.1
GO:0008767 - UDP-galactopyranose mutase activity [Evidence IEA]
GO:0009273 - peptidoglycan-based cell wall biogenesis [Evidence IEA]
COORDINATES: protein motif:HMM:NF020137.2
GO:0005615 - extracellular space [Evidence IEA]
GO:0005509 - calcium ion binding [Evidence IEA]
M10 family metallopeptidase C-terminal domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_010400754.1
COORDINATES: similar to AA sequence:RefSeq:WP_008886418.1
COORDINATES: similar to AA sequence:RefSeq:WP_017929941.1
COORDINATES: similar to AA sequence:RefSeq:WP_018001157.1
COORDINATES: similar to AA sequence:RefSeq:WP_009504423.1
GO:0008879 - glucose-1-phosphate thymidylyltransferase activity [Evidence IEA]
glucose-1-phosphate thymidylyltransferase RfbA
COORDINATES: similar to AA sequence:RefSeq:WP_009803885.1
ParB N-terminal domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_009803884.1
COORDINATES: similar to AA sequence:RefSeq:WP_008563361.1
DnaA N-terminal domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_018425598.1
GO:0047472 - 3-carboxy-cis,cis-muconate cycloisomerase activity [Evidence IEA]
3-carboxy-cis,cis-muconate cycloisomerase
COORDINATES: similar to AA sequence:RefSeq:WP_007674322.1
UDP-N-acetylglucosamine 4,6-dehydratase (inverting)
COORDINATES: protein motif:HMM:TIGR03590.1
GO:0016758 - hexosyltransferase activity [Evidence IEA]
UDP-2,4-diacetamido-2,4, 6-trideoxy-beta-L-altropyranose hydrolase
COORDINATES: similar to AA sequence:RefSeq:WP_014200326.1
GO:0003824 - catalytic activity [Evidence IEA]
UDP-4-amino-4, 6-dideoxy-N-acetyl-beta-L-altrosamine transaminase
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: protein motif:HMM:NF012573.2
COORDINATES: protein motif:HMM:NF014409.2
COORDINATES: protein motif:HMM:NF017011.2
COORDINATES: protein motif:HMM:NF012745.2
COORDINATES: protein motif:HMM:NF015038.2
internal stop; Derived by automated computational analysis using gene prediction method: Protein Homology.
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_011253661.1
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_008888317.1
GO:0005524 - ATP binding [Evidence IEA]; GO:0000156 - phosphorelay response regulator activity [Evidence IEA]; GO:0004673 - protein histidine kinase activity [Evidence IEA]
GO:0007165 - signal transduction [Evidence IEA]
HAMP domain-containing sensor histidine kinase
COORDINATES: similar to AA sequence:RefSeq:WP_008888264.1
GO:0000160 - phosphorelay signal transduction system [Evidence IEA]; GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_008228312.1
COORDINATES: similar to AA sequence:RefSeq:WP_008755533.1
bifunctional lysylphosphatidylglycerol flippase/synthetase MprF
COORDINATES: similar to AA sequence:RefSeq:WP_008228110.1
COORDINATES: similar to AA sequence:RefSeq:WP_008888105.1
GO:0009410 - response to xenobiotic stimulus [Evidence IEA]; GO:0006855 - xenobiotic transmembrane transport [Evidence IEA]
DHA2 family efflux MFS transporter permease subunit
COORDINATES: similar to AA sequence:RefSeq:WP_005855837.1
GO:0055085 - transmembrane transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_005855839.1
COORDINATES: similar to AA sequence:RefSeq:WP_008888100.1
COORDINATES: similar to AA sequence:RefSeq:WP_005855843.1
COORDINATES: similar to AA sequence:RefSeq:WP_008888203.1
COORDINATES: similar to AA sequence:RefSeq:WP_008226964.1
cytochrome b/b6 domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_005855846.1
COORDINATES: similar to AA sequence:RefSeq:WP_008888231.1
patatin-like phospholipase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_007803278.1
antitoxin of toxin-antitoxin stability system
COORDINATES: similar to AA sequence:RefSeq:WP_008030522.1
COORDINATES: similar to AA sequence:RefSeq:WP_010138207.1
COORDINATES: similar to AA sequence:RefSeq:WP_018270231.1
COORDINATES: similar to AA sequence:RefSeq:WP_008283111.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF017747.2
COORDINATES: similar to AA sequence:RefSeq:WP_011047916.1
GO:0016810 - hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_008208368.1
GO:0050480 - imidazolonepropionase activity [Evidence IEA]
GO:0006548 - histidine catabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_008283109.1
GO:0004397 - histidine ammonia-lyase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_007196324.1
GO:0050129 - N-formylglutamate deformylase activity [Evidence IEA]
GO:0019557 - histidine catabolic process to glutamate and formate [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_010973441.1
GO:0016153 - urocanate hydratase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_014249442.1
transporter substrate-binding domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_010393775.1
GO:0140359 - ABC-type transporter activity [Evidence IEA]; GO:0042626 - ATPase-coupled transmembrane transporter activity [Evidence IEA]
GO:0006865 - amino acid transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011747063.1
COORDINATES: similar to AA sequence:RefSeq:WP_019949796.1
amino acid ABC transporter ATP-binding protein
COORDINATES: protein motif:HMM:TIGR01141.1
GO:0004400 - histidinol-phosphate transaminase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_020094572.1
GO:0050660 - flavin adenine dinucleotide binding [Evidence IEA]; GO:0016491 - oxidoreductase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_010974513.1
ABC transporter substrate-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_007004431.1
COORDINATES: similar to AA sequence:RefSeq:WP_007004432.1
COORDINATES: similar to AA sequence:RefSeq:WP_013722777.1
COORDINATES: similar to AA sequence:RefSeq:WP_008943390.1
COORDINATES: similar to AA sequence:RefSeq:WP_010974518.1
GO:0016787 - hydrolase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_010974519.1
COORDINATES: similar to AA sequence:RefSeq:WP_005861787.1
COORDINATES: similar to AA sequence:RefSeq:WP_011842470.1
GO:0005515 - protein binding [Evidence IEA]
GO:0006749 - glutathione metabolic process [Evidence IEA]
glutathione S-transferase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_005861783.1
COORDINATES: similar to AA sequence:RefSeq:WP_005861781.1
GO:0016829 - lyase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_005861779.1
COORDINATES: similar to AA sequence:RefSeq:WP_009572280.1
COORDINATES: similar to AA sequence:RefSeq:WP_011842475.1
COORDINATES: similar to AA sequence:RefSeq:WP_005861773.1
GO:0055052 - ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing [Evidence IEA]; GO:0005886 - plasma membrane [Evidence IEA]
GO:0015837 - amine transport [Evidence IEA]
The N-terminal region of this protein, as described by TIGR01726, is a three transmembrane segment that identifies a subfamily of ABC transporter permease subunits, which specificities that include histidine, arginine, glutamine, glutamate, L-cystine (sic), the opines (in Agrobacterium) octopine and nopaline, etc.; The N-terminal region of this protein, as described by TIGR01726, is a three transmembrane segment that identifies a subfamily of ABC transporter permease subunits, which specificities that include histidine, arginine, glutamine, glutamate, L-cystine (sic), the opines (in Agrobacterium) octopine and nopaline, etc; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_005861771.1
GO:0055052 - ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing [Evidence IEA]
amino acid ABC transporter substrate-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_005861769.1
GO:0004121 - cystathionine beta-lyase activity [Evidence IEA]
GO:0009086 - methionine biosynthetic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_009175392.1
frameshifted; 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: protein motif:HMM:NF015905.2
COORDINATES: similar to AA sequence:RefSeq:WP_037302177.1
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_014109356.1
GO:0000036 - acyl carrier activity [Evidence IEA]
GO:0006633 - fatty acid biosynthetic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_008642189.1
SDR family NAD(P)-dependent oxidoreductase
COORDINATES: protein motif:HMM:NF012711.2
COORDINATES: similar to AA sequence:RefSeq:WP_008642196.1
COORDINATES: protein motif:HMM:NF017686.2
GO:0003995 - acyl-CoA dehydrogenase activity [Evidence IEA]
GO:0008218 - bioluminescence [Evidence IEA]