Paroceanicella profunda strain D4M1 plasmid pD4M1C, 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\nCP040821.1.\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+
GO:0016491 - oxidoreductase activity [Evidence IEA]
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: similar to AA sequence:RefSeq:WP_012330530.1
GO:0051537 - 2 iron, 2 sulfur cluster binding [Evidence IEA]; GO:0051536 - iron-sulfur cluster binding [Evidence IEA]; GO:0046872 - metal ion binding [Evidence IEA]
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: protein motif:HMM:NF019349.2
GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF015445.2
GO:0055085 - transmembrane transport [Evidence IEA]
TRAP transporter substrate-binding protein DctP
COORDINATES: similar to AA sequence:RefSeq:WP_006903638.1
COORDINATES: protein motif:HMM:NF019604.2
COORDINATES: similar to AA sequence:RefSeq:WP_007732719.1
COORDINATES: similar to AA sequence:RefSeq:WP_018897715.1
GO:0055052 - ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing [Evidence IEA]; GO:0005886 - plasma membrane [Evidence IEA]
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_015934134.1
COORDINATES: similar to AA sequence:RefSeq:WP_007880136.1
COORDINATES: similar to AA sequence:RefSeq:WP_018897712.1
hydantoinase B/oxoprolinase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_018897711.1
hydantoinase/oxoprolinase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_017620198.1
COORDINATES: similar to AA sequence:RefSeq:WP_007880128.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]; GO:0043565 - sequence-specific DNA binding [Evidence IEA]; GO:0000976 - transcription cis-regulatory region binding [Evidence IEA]
GO:0006351 - DNA-templated transcription [Evidence IEA]; GO:0045892 - negative regulation of DNA-templated transcription [Evidence IEA]; GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
LacI family DNA-binding transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_007256058.1
TAXI family TRAP transporter solute-binding subunit
COORDINATES: similar to AA sequence:RefSeq:WP_013069290.1
COORDINATES: similar to AA sequence:RefSeq:WP_011084786.1
helix-turn-helix transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_011084785.1
type II toxin-antitoxin system HipA family toxin
COORDINATES: protein motif:HMM:NF013594.2
COORDINATES: protein motif:HMM:NF017835.2
AcvB/VirJ family lysyl-phosphatidylglycerol hydrolase
COORDINATES: protein motif:HMM:NF033480.1
bifunctional lysylphosphatidylglycerol flippase/synthetase MprF
COORDINATES: protein motif:HMM:NF025050.2
COORDINATES: protein motif:HMM:NF024880.2
GO:0008168 - methyltransferase activity [Evidence IEA]; GO:1904047 - S-adenosyl-L-methionine binding [Evidence IEA]
COORDINATES: protein motif:HMM:TIGR01686.1
COORDINATES: similar to AA sequence:RefSeq:WP_011687710.1
GO:0000036 - acyl carrier activity [Evidence IEA]
GO:0006633 - fatty acid biosynthetic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_007010752.1
TRAP transporter substrate-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_009756213.1
COORDINATES: similar to AA sequence:RefSeq:WP_007010754.1
GO:0005886 - plasma membrane [Evidence IEA]; GO:0031317 - tripartite ATP-independent periplasmic transporter complex [Evidence IEA]
GO:0022857 - transmembrane transporter activity [Evidence IEA]
GO:0008643 - carbohydrate transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_008945078.1
DeoR/GlpR family DNA-binding transcription regulator
COORDINATES: similar to AA sequence:RefSeq:WP_008945077.1
COORDINATES: similar to AA sequence:RefSeq:WP_008945076.1
ABC transporter substrate-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_011569663.1
GO:0140359 - ABC-type transporter activity [Evidence IEA]; GO:0042626 - ATPase-coupled transmembrane transporter activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_007812696.1
GO:0008643 - carbohydrate transport [Evidence IEA]; GO:0055085 - transmembrane transport [Evidence IEA]
COORDINATES: protein motif:HMM:NF005089.0
GO:0008677 - 2-dehydropantoate 2-reductase activity [Evidence IEA]; GO:0050661 - NADP binding [Evidence IEA]
GO:0015940 - pantothenate biosynthetic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_005854660.1
COORDINATES: similar to AA sequence:RefSeq:WP_015923186.1
COORDINATES: similar to AA sequence:RefSeq:WP_014752253.1
mandelate racemase/muconate lactonizing enzyme family protein
COORDINATES: protein motif:HMM:NF016221.2
GO:0016531 - copper chaperone activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_007010765.1
GO:0031966 - mitochondrial membrane [Evidence IEA]
GO:0033617 - mitochondrial cytochrome c oxidase assembly [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_009506051.1
COORDINATES: similar to AA sequence:RefSeq:WP_018301294.1
GO:0003824 - catalytic activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011425548.1
GO:0016491 - oxidoreductase activity [Evidence IEA]; GO:0016651 - oxidoreductase activity, acting on NAD(P)H [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_017927007.1
GO:0003855 - 3-dehydroquinate dehydratase activity [Evidence IEA]
GO:0009423 - chorismate biosynthetic process [Evidence IEA]
COORDINATES: protein motif:HMM:NF012958.2
COORDINATES: similar to AA sequence:RefSeq:WP_020039376.1
GO:0019867 - outer membrane [Evidence IEA]
GO:0015343 - siderophore-iron transmembrane transporter activity [Evidence IEA]
GO:0015891 - siderophore transport [Evidence IEA]
COORDINATES: protein motif:HMM:NF024242.2
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]
COORDINATES: similar to AA sequence:RefSeq:WP_011582357.1
COORDINATES: similar to AA sequence:RefSeq:WP_011582358.1
GO:0010181 - FMN binding [Evidence IEA]; GO:0016491 - oxidoreductase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_003550967.1
COORDINATES: similar to AA sequence:RefSeq:WP_007800593.1
GO:0030976 - thiamine pyrophosphate binding [Evidence IEA]
thiamine pyrophosphate-requiring protein
COORDINATES: protein motif:HMM:NF012707.2
transporter substrate-binding domain-containing protein
COORDINATES: protein motif:HMM:NF013625.2
COORDINATES: protein motif:HMM:NF013862.2
patatin-like phospholipase family protein
COORDINATES: protein motif:HMM:NF012311.2
GO:0008236 - serine-type peptidase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_009566083.1
ParB N-terminal domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_011339645.1
COORDINATES: similar to AA sequence:RefSeq:WP_008208306.1
GO:0003887 - DNA-directed DNA polymerase activity [Evidence IEA]
GO:0006270 - DNA replication initiation [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_009210029.1
GO:0005215 - transporter activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_008574050.1
internal stop; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_004437852.1
GO:0055052 - ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_010973574.1
COORDINATES: similar to AA sequence:RefSeq:WP_002723841.1
COORDINATES: similar to AA sequence:RefSeq:WP_019997845.1
COORDINATES: similar to AA sequence:RefSeq:WP_008872355.1
GO:0015833 - peptide transport [Evidence IEA]
dipeptide ABC transporter ATP-binding protein
COORDINATES: protein motif:HMM:NF024808.2
COORDINATES: similar to AA sequence:RefSeq:WP_019015053.1
GO:0016810 - hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds [Evidence IEA]; GO:0046872 - metal ion binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_012873071.1
COORDINATES: similar to AA sequence:RefSeq:WP_019173663.1
COORDINATES: similar to AA sequence:RefSeq:WP_020659950.1
COORDINATES: similar to AA sequence:RefSeq:WP_013177888.1
GO:0016787 - hydrolase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_008944298.1
COORDINATES: similar to AA sequence:RefSeq:WP_032488543.1
COORDINATES: similar to AA sequence:RefSeq:WP_015497084.1
COORDINATES: similar to AA sequence:RefSeq:WP_018324364.1
GO:0030170 - pyridoxal phosphate binding [Evidence IEA]
PLP-dependent aminotransferase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_006326002.1
nucleoside/nucleotide kinase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_018916185.1
COORDINATES: similar to AA sequence:RefSeq:WP_007068002.1
COORDINATES: similar to AA sequence:RefSeq:WP_009207991.1
COORDINATES: similar to AA sequence:RefSeq:WP_011508504.1
COORDINATES: similar to AA sequence:RefSeq:WP_007068005.1
COORDINATES: similar to AA sequence:RefSeq:WP_019965617.1
GO:0005524 - ATP binding [Evidence IEA]; GO:0016301 - kinase activity [Evidence IEA]
four-carbon acid sugar kinase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_004115498.1
COORDINATES: protein motif:HMM:NF019174.2
GO:0004673 - protein histidine kinase activity [Evidence IEA]
HWE histidine kinase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_010973948.1
IclR family transcriptional regulator C-terminal domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_007691809.1
GO:0008410 - CoA-transferase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_003505518.1
COORDINATES: similar to AA sequence:RefSeq:WP_003548916.1
GO:0016747 - acyltransferase activity, transferring groups other than amino-acyl groups [Evidence IEA]
GO:0019619 - 3,4-dihydroxybenzoate catabolic process [Evidence IEA]
COORDINATES: protein motif:HMM:NF013434.2
COORDINATES: similar to AA sequence:RefSeq:WP_007794079.1
LLM class flavin-dependent oxidoreductase
COORDINATES: protein motif:HMM:NF012706.2
COORDINATES: protein motif:HMM:NF012738.2
COORDINATES: protein motif:HMM:NF008453.0
COORDINATES: similar to AA sequence:RefSeq:WP_014132310.1
GO:0007165 - signal transduction [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_018043198.1
COORDINATES: similar to AA sequence:RefSeq:WP_010301921.1
COORDINATES: similar to AA sequence:RefSeq:WP_013368541.1
GO:0042597 - periplasmic space [Evidence IEA]
tripartite tricarboxylate transporter substrate binding protein
COORDINATES: protein motif:HMM:NF018979.2
tripartite tricarboxylate transporter TctB family protein
COORDINATES: similar to AA sequence:RefSeq:WP_013368539.1
tripartite tricarboxylate transporter permease
COORDINATES: similar to AA sequence:RefSeq:WP_013542345.1
TetR/AcrR family transcriptional regulator
COORDINATES: protein motif:HMM:NF013429.2
sugar phosphate isomerase/epimerase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_007634841.1
COORDINATES: similar to AA sequence:RefSeq:WP_018700833.1
COORDINATES: similar to AA sequence:RefSeq:WP_018700834.1
dihydrodipicolinate synthase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_018700835.1
COORDINATES: protein motif:HMM:NF012772.2
COORDINATES: similar to AA sequence:RefSeq:WP_014248797.1
GO:0009636 - response to toxic substance [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_018992500.1
COORDINATES: protein motif:HMM:NF015431.2
COORDINATES: similar to AA sequence:RefSeq:WP_004198821.1
COORDINATES: similar to AA sequence:RefSeq:WP_007437427.1
GO:0070497 - 6-carboxy-5,6,7,8-tetrahydropterin synthase activity [Evidence IEA]; GO:0046872 - metal ion binding [Evidence IEA]
GO:0008616 - queuosine biosynthetic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_014188226.1
COORDINATES: similar to AA sequence:RefSeq:WP_013395828.1
GO:0016627 - oxidoreductase activity, acting on the CH-CH group of donors [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_007943210.1
COORDINATES: protein motif:HMM:NF040046.1
COORDINATES: similar to AA sequence:RefSeq:WP_013653249.1
GO:0010181 - FMN binding [Evidence IEA]; GO:0016703 - oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of one atom of oxygen (internal monooxygenases or internal mixed function oxidases) [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_007798323.1
COORDINATES: protein motif:HMM:NF018648.2
GO:0015385 - sodium:proton antiporter activity [Evidence IEA]
GO:1902600 - proton transmembrane transport [Evidence IEA]; GO:0006814 - sodium ion transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_010392492.1
GO:0005886 - plasma membrane [Evidence IEA]
MetQ/NlpA family ABC transporter substrate-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_011911188.1
GO:0033232 - ABC-type D-methionine transporter activity [Evidence IEA]; GO:0042626 - ATPase-coupled transmembrane transporter activity [Evidence IEA]
GO:0048473 - D-methionine transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_020009082.1
GO:0033232 - ABC-type D-methionine 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]
methionine ABC transporter ATP-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_018150866.1
COORDINATES: similar to AA sequence:RefSeq:WP_013093067.1
COORDINATES: similar to AA sequence:RefSeq:WP_006931854.1
COORDINATES: similar to AA sequence:RefSeq:WP_011454409.1
COORDINATES: similar to AA sequence:RefSeq:WP_008194663.1
COORDINATES: similar to AA sequence:RefSeq:WP_009506137.1
COORDINATES: protein motif:HMM:NF012742.2
GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]; GO:0043565 - sequence-specific DNA binding [Evidence IEA]; GO:0000976 - transcription cis-regulatory region binding [Evidence IEA]
COORDINATES: protein motif:HMM:NF012356.2
GO:0005975 - carbohydrate metabolic process [Evidence IEA]
COORDINATES: protein motif:HMM:NF037995.1
COORDINATES: protein motif:HMM:NF016200.2
GO:0015740 - C4-dicarboxylate transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_009803920.1
COORDINATES: similar to AA sequence:RefSeq:WP_010687440.1
COORDINATES: similar to AA sequence:RefSeq:WP_007179604.1
COORDINATES: similar to AA sequence:RefSeq:WP_010686996.1
non-heme iron oxygenase ferredoxin subunit
COORDINATES: similar to AA sequence:RefSeq:WP_007584841.1
GO:0004152 - dihydroorotate dehydrogenase activity [Evidence IEA]
GO:0006221 - pyrimidine nucleotide biosynthetic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_007437158.1
dihydroorotate dehydrogenase electron transfer subunit
COORDINATES: protein motif:HMM:NF024966.2
nuclear transport factor 2 family protein
COORDINATES: protein motif:HMM:NF019498.2
COORDINATES: similar to AA sequence:RefSeq:WP_009803912.1
COORDINATES: similar to AA sequence:RefSeq:WP_006461873.1
COORDINATES: similar to AA sequence:RefSeq:WP_006461874.1
aromatic ring-hydroxylating dioxygenase subunit alpha
COORDINATES: similar to AA sequence:RefSeq:WP_006461856.1
xanthine dehydrogenase family protein molybdopterin-binding subunit
COORDINATES: protein motif:HMM:NF026109.2
oxidoreductase C-terminal domain-containing protein
frameshifted; Derived by automated computational analysis using gene prediction method: Protein Homology.