Paroceanicella profunda strain D4M1 plasmid pD4M1D, complete sequence.
Bacteria; Pseudomonadota; Alphaproteobacteria; Rhodobacterales; Paracoccaceae; Paroceanicella.
Genome sequence of Rhodobacteraceae bacterium D4M1
Submitted (02-JUN-2019) Shanghai Engineering Research Center of Hadal Scicence and Technology, College of Marine Sciences, Shanghai Ocean University, 999 Huchenghuan Road, Shanghai 201306, China
Submitted (15-MAY-2019) Shanghai Engineering Research Center of Hadal Scicence and Technology, College of Marine Sciences, Shanghai Ocean University, 999 Huchenghuan Road, Shanghai 201306, China
REFSEQ INFORMATION: The reference sequence is identical to\nCP040822.1.\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 Date :: MAY-2019\nAssembly Method :: Velvet v. 1.2.09\nGenome Representation :: Full\nExpected Final Version :: Yes\nGenome Coverage :: 431.0x\nSequencing Technology :: PacBio RS; Illumina HiSeq\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 05/22/2023 16:18:37\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) :: 4,850\nCDSs (total) :: 4,781\nGenes (coding) :: 4,721\nCDSs (with protein) :: 4,721\nGenes (RNA) :: 69\nrRNAs :: 4, 4, 4 (5S, 16S, 23S)\ncomplete rRNAs :: 4, 4, 4 (5S, 16S, 23S)\ntRNAs :: 54\nncRNAs :: 3\nPseudo Genes (total) :: 60\nCDSs (without protein) :: 60\nPseudo Genes (ambiguous residues) :: 0 of 60\nPseudo Genes (frameshifted) :: 24 of 60\nPseudo Genes (incomplete) :: 38 of 60\nPseudo Genes (internal stop) :: 5 of 60\nPseudo Genes (multiple problems) :: 5 of 60\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: protein motif:HMM:NF016145.2
Derived by automated computational analysis using gene prediction method: Protein Homology.
polysaccharide pyruvyl transferase family protein
COORDINATES: protein motif:HMM:NF025025.2
GO:0016757 - glycosyltransferase activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF012745.2
COORDINATES: similar to AA sequence:RefSeq:WP_007715378.1
GO:0008767 - UDP-galactopyranose mutase activity [Evidence IEA]
GO:0009273 - peptidoglycan-based cell wall biogenesis [Evidence IEA]
COORDINATES: protein motif:HMM:NF015527.2
GO:0008146 - sulfotransferase activity [Evidence IEA]
sulfotransferase family 2 domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_020713600.1
COORDINATES: similar to AA sequence:RefSeq:WP_018308366.1
COORDINATES: protein motif:HMM:NF017062.2
COORDINATES: similar to AA sequence:RefSeq:WP_015225934.1
GO:0008168 - methyltransferase activity [Evidence IEA]; GO:1904047 - S-adenosyl-L-methionine binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_012041351.1
COORDINATES: similar to AA sequence:RefSeq:WP_009029928.1
GO:0008830 - dTDP-4-dehydrorhamnose 3,5-epimerase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_009555136.1
GO:0047343 - glucose-1-phosphate cytidylyltransferase activity [Evidence IEA]
GO:0009103 - lipopolysaccharide biosynthetic process [Evidence IEA]
glucose-1-phosphate cytidylyltransferase
COORDINATES: similar to AA sequence:RefSeq:WP_014876620.1
GO:0004476 - mannose-6-phosphate isomerase activity [Evidence IEA]
mannose-1-phosphate guanylyltransferase/mannose-6-phosphate isomerase
COORDINATES: protein motif:HMM:NF012376.2
GO:0016787 - hydrolase activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF016763.2
COORDINATES: protein motif:HMM:NF014453.2
COORDINATES: protein motif:HMM:NF024968.2
COORDINATES: protein motif:HMM:NF019552.2
COORDINATES: protein motif:HMM:NF012360.2
COORDINATES: similar to AA sequence:RefSeq:WP_018329659.1
COORDINATES: similar to AA sequence:RefSeq:WP_011446857.1
GO:0051287 - NAD binding [Evidence IEA]; GO:0016616 - oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor [Evidence IEA]; GO:0003979 - UDP-glucose 6-dehydrogenase activity [Evidence IEA]
GO:0000271 - polysaccharide biosynthetic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_012187247.1
ParB/RepB/Spo0J family partition protein
COORDINATES: similar to AA sequence:RefSeq:WP_011536552.1
COORDINATES: similar to AA sequence:RefSeq:WP_014889379.1
COORDINATES: protein motif:HMM:NF024831.2
COORDINATES: protein motif:HMM:NF024842.2
COORDINATES: protein motif:HMM:NF019365.2
GO:0015926 - glucosidase activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF016800.2
COORDINATES: protein motif:HMM:NF025001.2
polysaccharide biosynthesis tyrosine autokinase
COORDINATES: protein motif:HMM:NF014606.2
GO:0016020 - membrane [Evidence IEA]; GO:0042597 - periplasmic space [Evidence IEA]
GO:0015159 - polysaccharide transmembrane transporter activity [Evidence IEA]
polysaccharide biosynthesis/export family protein
COORDINATES: similar to AA sequence:RefSeq:WP_012041339.1
COORDINATES: similar to AA sequence:RefSeq:WP_007820764.1
COORDINATES: similar to AA sequence:RefSeq:WP_007012188.1
COORDINATES: similar to AA sequence:RefSeq:WP_007820748.1
COORDINATES: similar to AA sequence:RefSeq:WP_003590459.1
COORDINATES: similar to AA sequence:RefSeq:WP_008562581.1
GO:0009428 - bacterial-type flagellum basal body, distal rod, P ring [Evidence IEA]; GO:0030288 - outer membrane-bounded periplasmic space [Evidence IEA]
GO:0005198 - structural molecule activity [Evidence IEA]
GO:0071973 - bacterial-type flagellum-dependent cell motility [Evidence IEA]
flagellar basal body P-ring protein FlgI
COORDINATES: protein motif:HMM:NF012903.2
COORDINATES: protein motif:HMM:TIGR02492.1
GO:0009424 - bacterial-type flagellum hook [Evidence IEA]
GO:0001539 - cilium or flagellum-dependent cell motility [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_013065754.1
flagellar hook-basal body complex protein
COORDINATES: similar to AA sequence:RefSeq:WP_008281446.1
COORDINATES: protein motif:HMM:NF014235.2
FliM/FliN family flagellar motor switch protein
COORDINATES: similar to AA sequence:RefSeq:WP_008439020.1
GO:0000160 - phosphorelay signal transduction system [Evidence IEA]
COORDINATES: protein motif:HMM:NF014567.2
GO:0005524 - ATP binding [Evidence IEA]; GO:0000155 - phosphorelay sensor kinase activity [Evidence IEA]
GO:0006935 - chemotaxis [Evidence IEA]; GO:0007165 - signal transduction [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_006275181.1
COORDINATES: protein motif:HMM:NF012245.2
GO:0007165 - signal transduction [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_017219455.1
GO:0008168 - methyltransferase activity [Evidence IEA]; GO:0008983 - protein-glutamate O-methyltransferase activity [Evidence IEA]; GO:0016740 - transferase activity [Evidence IEA]
protein-glutamate O-methyltransferase CheR
COORDINATES: similar to AA sequence:RefSeq:WP_020650248.1
catalyzes the conversion of glutamine residues to glutamate on methyl-accepting chemotaxis receptors; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_012249020.1
GO:0000156 - phosphorelay response regulator activity [Evidence IEA]; GO:0008984 - protein-glutamate methylesterase activity [Evidence IEA]; GO:0050568 - protein-glutamine glutaminase activity [Evidence IEA]
GO:0006935 - chemotaxis [Evidence IEA]; GO:0018277 - protein deamination [Evidence IEA]; GO:0006482 - protein demethylation [Evidence IEA]
chemotaxis response regulator protein-glutamate methylesterase
COORDINATES: protein motif:HMM:NF012301.2
COORDINATES: protein motif:HMM:NF013838.2
FliG C-terminal domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_012978237.1
The bacterial flagellar biogenesis protein FliP forms a type III secretion system (T3SS)-type pore required for flagellar assembly; Derived by automated computational analysis using gene prediction method: Protein Homology.
flagellar type III secretion system pore protein FliP
COORDINATES: similar to AA sequence:RefSeq:WP_011540258.1
COORDINATES: similar to AA sequence:RefSeq:WP_010141301.1
GO:0009431 - bacterial-type flagellum basal body, MS ring [Evidence IEA]
flagellar basal-body MS-ring/collar protein FliF
COORDINATES: similar to AA sequence:RefSeq:WP_007796001.1
GO:0009425 - bacterial-type flagellum basal body [Evidence IEA]
GO:0071973 - bacterial-type flagellum-dependent cell motility [Evidence IEA]; GO:0006935 - chemotaxis [Evidence IEA]
flagellar basal body-associated FliL family protein
COORDINATES: protein motif:HMM:NF015413.2
COORDINATES: similar to AA sequence:RefSeq:WP_005980143.1
COORDINATES: similar to AA sequence:RefSeq:WP_011457307.1
COORDINATES: similar to AA sequence:RefSeq:WP_019295219.1
GO:0009426 - bacterial-type flagellum basal body, distal rod [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_005607927.1
GO:0009428 - bacterial-type flagellum basal body, distal rod, P ring [Evidence IEA]
flagellar basal body P-ring formation chaperone FlgA
COORDINATES: similar to AA sequence:RefSeq:WP_019295221.1
GO:0009427 - bacterial-type flagellum basal body, distal rod, L ring [Evidence IEA]
GO:0003774 - cytoskeletal motor activity [Evidence IEA]
flagellar basal body L-ring protein FlgH
COORDINATES: similar to AA sequence:RefSeq:WP_010141290.1
COORDINATES: protein motif:HMM:NF015896.2
flagellar hook capping FlgD N-terminal domain-containing protein
COORDINATES: protein motif:HMM:NF014207.2
flagellar hook-length control protein FliK
COORDINATES: similar to AA sequence:RefSeq:WP_010440740.1
COORDINATES: protein motif:HMM:NF012888.2
COORDINATES: similar to AA sequence:RefSeq:WP_009503995.1
COORDINATES: similar to AA sequence:RefSeq:WP_013069220.1
GO:0044781 - bacterial-type flagellum organization [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_008027525.1
GO:0048027 - mRNA 5'-UTR binding [Evidence IEA]
GO:0006402 - mRNA catabolic process [Evidence IEA]; GO:1902209 - negative regulation of bacterial-type flagellum assembly [Evidence IEA]
COORDINATES: protein motif:HMM:NF018458.2
COORDINATES: similar to AA sequence:RefSeq:WP_009817179.1
GO:0030257 - type III protein secretion system complex [Evidence IEA]
GO:0005524 - ATP binding [Evidence IEA]; GO:0016887 - ATP hydrolysis activity [Evidence IEA]
GO:0046034 - ATP metabolic process [Evidence IEA]
COORDINATES: protein motif:HMM:NF012674.2
COORDINATES: similar to AA sequence:RefSeq:WP_008561350.1
COORDINATES: similar to AA sequence:RefSeq:WP_012179909.1
GO:0009288 - bacterial-type flagellum [Evidence IEA]
GO:0003774 - cytoskeletal motor activity [Evidence IEA]; GO:0005198 - structural molecule activity [Evidence IEA]
flagellar hook-basal body complex protein FliE
COORDINATES: similar to AA sequence:RefSeq:WP_010399363.1
COORDINATES: similar to AA sequence:RefSeq:WP_014876453.1
lytic transglycosylase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_010141294.1
COORDINATES: similar to AA sequence:RefSeq:WP_007255522.1
GO:0006605 - protein targeting [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_008554428.1
GO:0009306 - protein secretion [Evidence IEA]
EscU/YscU/HrcU family type III secretion system export apparatus switch protein
COORDINATES: similar to AA sequence:RefSeq:WP_005850512.1
GO:0016616 - oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor [Evidence IEA]
UDP-glucose/GDP-mannose dehydrogenase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_007254330.1
COORDINATES: similar to AA sequence:RefSeq:WP_017877159.1
COORDINATES: similar to AA sequence:RefSeq:WP_009763888.1
COORDINATES: protein motif:HMM:NF012744.2
COORDINATES: protein motif:HMM:NF020604.2