Paroceanicella profunda strain D4M1 plasmid pD4M1E, 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\nCP040823.1.\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: similar to AA sequence:RefSeq:WP_009815479.1
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_009573590.1
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_009573591.1
GO:0005886 - plasma membrane [Evidence IEA]
GO:0004190 - aspartic-type endopeptidase activity [Evidence IEA]
GO:0009306 - protein secretion [Evidence IEA]; GO:0006508 - proteolysis [Evidence IEA]
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_007803463.1
GO:0046873 - metal ion transmembrane transporter activity [Evidence IEA]
GO:0030001 - metal ion transport [Evidence IEA]
frameshifted; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_013959872.1
COORDINATES: similar to AA sequence:RefSeq:WP_009807977.1
GO:0046872 - metal ion binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_008889345.1
GO:0031966 - mitochondrial membrane [Evidence IEA]
GO:0033617 - mitochondrial cytochrome c oxidase assembly [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_009503840.1
GO:0016531 - copper chaperone activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_018001721.1
COORDINATES: similar to AA sequence:RefSeq:WP_007803474.1
GO:0015035 - protein-disulfide reductase activity [Evidence IEA]
GO:0006457 - protein folding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_009827282.1
COORDINATES: similar to AA sequence:RefSeq:WP_018303599.1
helix-turn-helix domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_009573601.1
GO:0008324 - monoatomic cation transmembrane transporter activity [Evidence IEA]
GO:0006812 - monoatomic cation transport [Evidence IEA]; GO:0055085 - transmembrane transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_010138164.1
cation diffusion facilitator family transporter
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: similar to AA sequence:RefSeq:WP_009503822.1
COORDINATES: similar to AA sequence:RefSeq:WP_009503821.1
GO:0017004 - cytochrome complex assembly [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_007796189.1
COORDINATES: similar to AA sequence:RefSeq:WP_009820197.1
COORDINATES: similar to AA sequence:RefSeq:WP_013959912.1
GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]
GO:0006878 - intracellular copper ion homeostasis [Evidence IEA]; GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
Cu(I)-responsive transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_007120890.1
GO:0005524 - ATP binding [Evidence IEA]; GO:0019829 - ATPase-coupled monoatomic cation transmembrane transporter activity [Evidence IEA]
GO:0006812 - monoatomic cation transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_009503816.1
heavy-metal-associated domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_008282876.1
COORDINATES: similar to AA sequence:RefSeq:WP_009824197.1
COORDINATES: similar to AA sequence:RefSeq:WP_009820147.1
GO:0015562 - efflux transmembrane transporter activity [Evidence IEA]
GO:0055085 - transmembrane transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_010968681.1
COORDINATES: similar to AA sequence:RefSeq:WP_007120885.1
COORDINATES: similar to AA sequence:RefSeq:WP_009503811.1
GO:0042625 - ATPase-coupled ion transmembrane transporter activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_010141876.1
GO:0004803 - transposase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_009808043.1
COORDINATES: similar to AA sequence:RefSeq:WP_009815553.1
COORDINATES: similar to AA sequence:RefSeq:WP_007120686.1
helix-turn-helix transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_007120685.1
COORDINATES: similar to AA sequence:RefSeq:WP_009808056.1
COORDINATES: similar to AA sequence:RefSeq:WP_008327370.1
GO:0016798 - hydrolase activity, acting on glycosyl bonds [Evidence IEA]
lytic transglycosylase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_009808058.1
COORDINATES: similar to AA sequence:RefSeq:WP_008327373.1
VirB3 family type IV secretion system protein
COORDINATES: similar to AA sequence:RefSeq:WP_009807508.1
type IV secretion system DNA-binding domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_009503800.1
COORDINATES: similar to AA sequence:RefSeq:WP_007120678.1
COORDINATES: similar to AA sequence:RefSeq:WP_009820232.1
COORDINATES: similar to AA sequence:RefSeq:WP_009807512.1
COORDINATES: similar to AA sequence:RefSeq:WP_009808065.1
TrbG/VirB9 family P-type conjugative transfer protein
COORDINATES: similar to AA sequence:RefSeq:WP_008327387.1
COORDINATES: similar to AA sequence:RefSeq:WP_009820228.1
COORDINATES: similar to AA sequence:RefSeq:WP_007120672.1
COORDINATES: similar to AA sequence:RefSeq:WP_007120671.1
COORDINATES: similar to AA sequence:RefSeq:WP_009808070.1
COORDINATES: similar to AA sequence:RefSeq:WP_014131758.1
COORDINATES: similar to AA sequence:RefSeq:WP_014132721.1
GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_009807937.1
type IV secretory system conjugative DNA transfer family protein
COORDINATES: similar to AA sequence:RefSeq:WP_009807938.1
relaxase/mobilization nuclease domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_007120663.1
COORDINATES: similar to AA sequence:RefSeq:WP_011536569.1
COORDINATES: similar to AA sequence:RefSeq:WP_009820257.1
COORDINATES: similar to AA sequence:RefSeq:WP_020312521.1
COORDINATES: similar to AA sequence:RefSeq:WP_015879334.1
GO:0005524 - ATP binding [Evidence IEA]; GO:0016887 - ATP hydrolysis activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_003522058.1
COORDINATES: similar to AA sequence:RefSeq:WP_011539288.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]
TetR/AcrR family transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_009503774.1
GO:0004252 - serine-type endopeptidase activity [Evidence IEA]
rhomboid family intramembrane serine protease
COORDINATES: similar to AA sequence:RefSeq:WP_009815530.1
COORDINATES: similar to AA sequence:RefSeq:WP_012187346.1
COORDINATES: similar to AA sequence:RefSeq:WP_009807948.1
COORDINATES: similar to AA sequence:RefSeq:WP_009819681.1
COORDINATES: similar to AA sequence:RefSeq:WP_009807537.1
COORDINATES: similar to AA sequence:RefSeq:WP_009820261.1
COORDINATES: similar to AA sequence:RefSeq:WP_009807539.1
ParB/RepB/Spo0J family partition protein
COORDINATES: similar to AA sequence:RefSeq:WP_012187358.1
COORDINATES: protein motif:HMM:NF040380.1
COORDINATES: similar to AA sequence:RefSeq:WP_009807542.1
zincin-like metallopeptidase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_008282917.1
COORDINATES: similar to AA sequence:RefSeq:WP_009566891.1
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_009824440.1
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_009570513.1
GO:0005506 - iron ion binding [Evidence IEA]; GO:0016491 - oxidoreductase activity [Evidence IEA]
GO:0008610 - lipid biosynthetic process [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_008837282.1
metalloregulator ArsR/SmtB family transcription factor
COORDINATES: similar to AA sequence:RefSeq:WP_010398608.1
GO:0009055 - electron transfer activity [Evidence IEA]; GO:0020037 - heme binding [Evidence IEA]; GO:0046872 - metal ion binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_010398610.1
COORDINATES: similar to AA sequence:RefSeq:WP_010398612.1
GO:0005507 - copper ion binding [Evidence IEA]; GO:0016491 - oxidoreductase activity [Evidence IEA]
multicopper oxidase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_018001746.1
COORDINATES: similar to AA sequence:RefSeq:WP_007121331.1
COORDINATES: similar to AA sequence:RefSeq:WP_019956940.1
GO:0022857 - transmembrane transporter activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_007203965.1
COORDINATES: similar to AA sequence:RefSeq:WP_007817281.1
COORDINATES: similar to AA sequence:RefSeq:WP_009574206.1
ParB N-terminal domain-containing protein
COORDINATES: protein motif:HMM:NF015393.2
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_009503864.1
COORDINATES: similar to AA sequence:RefSeq:WP_007803223.1
COORDINATES: similar to AA sequence:RefSeq:WP_009815502.1
COORDINATES: similar to AA sequence:RefSeq:WP_009808024.1
Mu transposase C-terminal domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_009573575.1
COORDINATES: similar to AA sequence:RefSeq:WP_009573576.1
COORDINATES: similar to AA sequence:RefSeq:WP_009815501.1
GO:0005507 - copper ion binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_009573580.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]; GO:0046983 - protein dimerization activity [Evidence IEA]; GO:0046914 - transition metal ion binding [Evidence IEA]
manganese-binding transcriptional regulator MntR
COORDINATES: similar to AA sequence:RefSeq:WP_009573581.1
COORDINATES: similar to AA sequence:RefSeq:WP_009503858.1
COORDINATES: similar to AA sequence:RefSeq:WP_009573583.1
COORDINATES: similar to AA sequence:RefSeq:WP_009573584.1
COORDINATES: similar to AA sequence:RefSeq:WP_005613370.1
GO:0009055 - electron transfer activity [Evidence IEA]; GO:0020037 - heme binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_009503854.1
GO:0016746 - acyltransferase activity [Evidence IEA]; GO:0071972 - peptidoglycan L,D-transpeptidase activity [Evidence IEA]
GO:0018104 - peptidoglycan-protein cross-linking [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_010138178.1
COORDINATES: similar to AA sequence:RefSeq:WP_009807971.1
COORDINATES: similar to AA sequence:RefSeq:WP_009503851.1
COORDINATES: similar to AA sequence:RefSeq:WP_008889351.1
GO:0016740 - transferase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_009815494.1
COORDINATES: protein motif:HMM:NF013927.2
GO:0016787 - hydrolase activity [Evidence IEA]
GO:0017000 - antibiotic biosynthetic process [Evidence IEA]
internal stop; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_008282832.1
COORDINATES: similar to AA sequence:RefSeq:WP_009815491.1
GO:0016410 - N-acyltransferase activity [Evidence IEA]
GO:0042158 - lipoprotein biosynthetic process [Evidence IEA]; GO:0006497 - protein lipidation [Evidence IEA]