Paroceanicella profunda strain D4M1 plasmid pD4M1F, 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\nCP040824.1.\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_020092417.1
frameshifted; 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_007862954.1
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_010397576.1
GO:0051539 - 4 iron, 4 sulfur cluster binding [Evidence IEA]; GO:1904047 - S-adenosyl-L-methionine binding [Evidence IEA]
GO:0006400 - tRNA modification [Evidence IEA]
frameshifted; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_004123758.1
6-pyruvoyl tetrahydropterin synthase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_019295557.1
GO:0008616 - queuosine biosynthetic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_020011942.1
COORDINATES: similar to AA sequence:RefSeq:WP_020040450.1
GO:0009436 - glyoxylate catabolic process [Evidence IEA]; GO:0071704 - organic substance metabolic process [Evidence IEA]
dihydrodipicolinate synthase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_009208054.1
COORDINATES: similar to AA sequence:RefSeq:WP_019403170.1
ABC transporter substrate-binding protein
COORDINATES: protein motif:HMM:NF018979.2
tripartite tricarboxylate transporter TctB family protein
COORDINATES: similar to AA sequence:RefSeq:WP_013333170.1
tripartite tricarboxylate transporter permease
COORDINATES: similar to AA sequence:RefSeq:WP_009208053.1
LacI family DNA-binding transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_008944295.1
hydantoinase/oxoprolinase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_019015804.1
hydantoinase B/oxoprolinase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_008224984.1
TRAP transporter substrate-binding protein
COORDINATES: protein motif:HMM:NF016200.2
GO:0005886 - plasma membrane [Evidence IEA]; GO:0031317 - tripartite ATP-independent periplasmic transporter complex [Evidence IEA]
GO:0022857 - transmembrane transporter activity [Evidence IEA]
GO:0015740 - C4-dicarboxylate transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_003811597.1
GO:0015556 - C4-dicarboxylate transmembrane transporter activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF019322.2
GO:0003677 - DNA binding [Evidence IEA]; GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF024950.2
GO:0016491 - oxidoreductase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_012113317.1
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_020084317.1
GO:0055085 - transmembrane transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_017709846.1
COORDINATES: similar to AA sequence:RefSeq:WP_018329909.1
GO:0003985 - acetyl-CoA C-acetyltransferase activity [Evidence IEA]
GO:0006631 - fatty acid metabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011747756.1
GO:0008478 - pyridoxal kinase activity [Evidence IEA]
GO:0009443 - pyridoxal 5'-phosphate salvage [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_013393138.1
COORDINATES: protein motif:HMM:NF012961.2
GO:0004553 - hydrolase activity, hydrolyzing O-glycosyl compounds [Evidence IEA]
GO:0005975 - carbohydrate metabolic process [Evidence IEA]
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: similar to AA sequence:RefSeq:WP_007826726.1
COORDINATES: similar to AA sequence:RefSeq:WP_018430856.1
COORDINATES: similar to AA sequence:RefSeq:WP_018302394.1
GO:0140359 - ABC-type transporter activity [Evidence IEA]; GO:0042626 - ATPase-coupled transmembrane transporter activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_013761103.1
GO:0008643 - carbohydrate transport [Evidence IEA]; GO:0055085 - transmembrane transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_007826717.1
GO:0004056 - argininosuccinate lyase activity [Evidence IEA]
GO:0042450 - arginine biosynthetic process via ornithine [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_018302397.1
ATP-binding cassette domain-containing protein
COORDINATES: protein motif:HMM:NF012692.2
COORDINATES: similar to AA sequence:RefSeq:WP_010138300.1
GO:0004342 - glucosamine-6-phosphate deaminase activity [Evidence IEA]
GO:0006046 - N-acetylglucosamine catabolic process [Evidence IEA]
COORDINATES: protein motif:HMM:NF025107.2
helix-turn-helix domain-containing protein
COORDINATES: protein motif:HMM:NF025001.2
COORDINATES: protein motif:HMM:NF014273.2
ParB N-terminal domain-containing protein
COORDINATES: protein motif:HMM:NF024589.2
COORDINATES: similar to AA sequence:RefSeq:WP_012976808.1
GO:0000160 - phosphorelay signal transduction system [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_012976809.1
COORDINATES: protein motif:HMM:NF014661.2
COORDINATES: protein motif:HMM:NF015083.2
COORDINATES: similar to AA sequence:RefSeq:WP_011748628.1
GO:0042625 - ATPase-coupled ion transmembrane transporter activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_017927562.1
COORDINATES: protein motif:HMM:NF012257.2
GO:0030552 - cAMP binding [Evidence IEA]; GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]
Crp/Fnr family transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_012356522.1
GO:0001216 - DNA-binding transcription activator activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_007607812.1
GO:0016787 - hydrolase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_004126985.1
MarR family winged helix-turn-helix transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_019564151.1
COORDINATES: similar to AA sequence:RefSeq:WP_010441323.1
COORDINATES: similar to AA sequence:RefSeq:WP_013165368.1
Lrp/AsnC family transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_014528042.1
GO:0008660 - 1-aminocyclopropane-1-carboxylate deaminase activity [Evidence IEA]
GO:0042217 - 1-aminocyclopropane-1-carboxylate catabolic process [Evidence IEA]
1-aminocyclopropane-1-carboxylate deaminase
COORDINATES: similar to AA sequence:RefSeq:WP_008884156.1
COORDINATES: similar to AA sequence:RefSeq:WP_014537473.1
COORDINATES: similar to AA sequence:RefSeq:WP_008168732.1
GO:0008721 - D-serine ammonia-lyase activity [Evidence IEA]; GO:0030170 - pyridoxal phosphate binding [Evidence IEA]
GO:0046416 - D-amino acid metabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011840446.1
sulfite exporter TauE/SafE family protein
COORDINATES: similar to AA sequence:RefSeq:WP_009451145.1
COORDINATES: similar to AA sequence:RefSeq:WP_005858689.1
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_005858691.1
COORDINATES: similar to AA sequence:RefSeq:WP_005858693.1
COORDINATES: similar to AA sequence:RefSeq:WP_005858695.1
COORDINATES: similar to AA sequence:RefSeq:WP_007691270.1
COORDINATES: similar to AA sequence:RefSeq:WP_020041227.1
GO:0003729 - mRNA binding [Evidence IEA]; GO:0003676 - nucleic acid binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_013079256.1
COORDINATES: similar to AA sequence:RefSeq:WP_018997966.1
GO:0008488 - gamma-glutamyl carboxylase activity [Evidence IEA]
GO:0017187 - peptidyl-glutamic acid carboxylation [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_020295606.1
COORDINATES: protein motif:HMM:NF014073.2
COORDINATES: protein motif:HMM:NF012576.2
COORDINATES: protein motif:HMM:NF024770.2
substrate-binding domain-containing protein
COORDINATES: protein motif:HMM:NF017215.2
COORDINATES: protein motif:HMM:NF014071.2
COORDINATES: protein motif:HMM:NF014585.2
GO:0003824 - catalytic activity [Evidence IEA]