Paracoccus sanguinis strain OM2164 plasmid pPspOM122, complete sequence.
Bacteria; Pseudomonadota; Alphaproteobacteria; Rhodobacterales; Paracoccaceae; Paracoccus.
Genome-Wide Identification of 5-Methylcytosine Sites in Bacterial Genomes By High-Throughput Sequencing of MspJI Restriction Fragments
Submitted (13-APR-2020) Genome Biology, NEB, 240 County Rd, Ipswich, MA 01938, USA
REFSEQ INFORMATION: The reference sequence is identical to\nCP051543.1.\nBacteria and source DNA available from NEB microbial collection\n1783.\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 :: MAR-2017\nAssembly Method :: HGAP v. 2.3.0\nAssembly Name :: PspOM_new_HGAP3_2\nGenome Representation :: Full\nExpected Final Version :: Yes\nGenome Coverage :: 164.22x\nSequencing Technology :: PacBio RSII\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 04/28/2023 10:59:31\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) :: 3,248\nCDSs (total) :: 3,190\nGenes (coding) :: 3,116\nCDSs (with protein) :: 3,116\nGenes (RNA) :: 58\nrRNAs :: 2, 2, 2 (5S, 16S, 23S)\ncomplete rRNAs :: 2, 2, 2 (5S, 16S, 23S)\ntRNAs :: 48\nncRNAs :: 4\nPseudo Genes (total) :: 74\nCDSs (without protein) :: 74\nPseudo Genes (ambiguous residues) :: 0 of 74\nPseudo Genes (frameshifted) :: 21 of 74\nPseudo Genes (incomplete) :: 60 of 74\nPseudo Genes (internal stop) :: 2 of 74\nPseudo Genes (multiple problems) :: 9 of 74\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.
COORDINATES: similar to AA sequence:RefSeq:WP_010142104.1
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_009157377.1
COORDINATES: similar to AA sequence:RefSeq:WP_007118675.1
COORDINATES: similar to AA sequence:RefSeq:WP_013066849.1
COORDINATES: similar to AA sequence:RefSeq:WP_011747997.1
COORDINATES: similar to AA sequence:RefSeq:WP_008884609.1
GO:0042597 - periplasmic space [Evidence IEA]
GO:0030058 - amine dehydrogenase activity [Evidence IEA]
GO:0009310 - amine catabolic process [Evidence IEA]
quinohemoprotein amine dehydrogenase subunit alpha
COORDINATES: similar to AA sequence:RefSeq:WP_009542142.1
GO:0051539 - 4 iron, 4 sulfur cluster binding [Evidence IEA]; GO:1904047 - S-adenosyl-L-methionine binding [Evidence IEA]
GO:0043687 - post-translational protein modification [Evidence IEA]
quinohemoprotein amine dehydrogenase maturation protein
COORDINATES: similar to AA sequence:RefSeq:WP_020193816.1
quinohemoprotein amine dehydrogenase subunit gamma
COORDINATES: similar to AA sequence:RefSeq:WP_011748001.1
quinohemoprotein amine dehydrogenase subunit beta
COORDINATES: similar to AA sequence:RefSeq:WP_010395465.1
COORDINATES: similar to AA sequence:RefSeq:WP_018001310.1
GO:0005524 - ATP binding [Evidence IEA]; GO:0042626 - ATPase-coupled transmembrane transporter activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF024039.2
AraC family transcriptional regulator ligand-binding domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_010395468.1
GO:0016491 - oxidoreductase activity [Evidence IEA]
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_010914433.1
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: similar to AA sequence:RefSeq:WP_018304285.1
GO:0055052 - ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing [Evidence IEA]; GO:0009898 - cytoplasmic side of plasma membrane [Evidence IEA]
GO:0015412 - ABC-type molybdate transporter activity [Evidence IEA]; GO:0005524 - ATP binding [Evidence IEA]
GO:0015689 - molybdate ion transport [Evidence IEA]
molybdenum ABC transporter ATP-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_011748946.1
GO:0015098 - molybdate ion transmembrane transporter activity [Evidence IEA]
molybdate ABC transporter permease subunit
COORDINATES: similar to AA sequence:RefSeq:WP_010140401.1
GO:0055052 - ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing [Evidence IEA]; GO:0009897 - external side of plasma membrane [Evidence IEA]; GO:0030288 - outer membrane-bounded periplasmic space [Evidence IEA]
GO:0015412 - ABC-type molybdate transporter activity [Evidence IEA]; GO:0030973 - molybdate ion binding [Evidence IEA]
molybdate ABC transporter substrate-binding protein
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: protein motif:HMM:NF012485.2
pilus assembly protein N-terminal domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_006392826.1
GO:0009306 - protein secretion [Evidence IEA]
type III secretion system export apparatus subunit SctV
COORDINATES: protein motif:HMM:NF020557.2
EscE/YscE/SsaE family type III secretion system needle protein co-chaperone
COORDINATES: protein motif:HMM:NF013479.2
EscU/YscU/HrcU family type III secretion system export apparatus switch protein
COORDINATES: protein motif:HMM:NF013478.2
GO:0006605 - protein targeting [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_014331082.1
GO:0030254 - protein secretion by the type III secretion system [Evidence IEA]
type III secretion system export apparatus subunit SctS
COORDINATES: similar to AA sequence:RefSeq:WP_009520936.1
GO:0030257 - type III protein secretion system complex [Evidence IEA]
type III secretion system export apparatus subunit SctR
COORDINATES: protein motif:HMM:NF013236.2
FliM/FliN family flagellar motor switch protein
COORDINATES: similar to AA sequence:RefSeq:WP_019403908.1
GO:0005524 - ATP binding [Evidence IEA]; GO:0016887 - ATP hydrolysis activity [Evidence IEA]
GO:0046034 - ATP metabolic process [Evidence IEA]
COORDINATES: protein motif:HMM:NF018358.2
COORDINATES: similar to AA sequence:RefSeq:WP_018238591.1
type III secretion inner membrane ring lipoprotein SctJ
outer membrane protein assembly factor BamE
COORDINATES: protein motif:HMM:NF013630.2
LysM peptidoglycan-binding domain-containing protein
COORDINATES: protein motif:HMM:NF027340.2
COORDINATES: similar to AA sequence:RefSeq:WP_004119398.1
COORDINATES: protein motif:HMM:NF024854.2
GO:0003677 - DNA binding [Evidence IEA]; GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_015318372.1
GO:0022857 - transmembrane transporter activity [Evidence IEA]
GO:0055085 - transmembrane transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_010915458.1
GO:0005886 - plasma membrane [Evidence IEA]
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_008033221.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0004803 - transposase activity [Evidence IEA]
GO:0006313 - transposition, DNA-mediated [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011749831.1
TnpB, as the term is used for proteins encoded by IS66 family insertion elements, is considered an accessory protein, since TnpC, encoded by a neighboring gene, is a DDE family transposase; Derived by automated computational analysis using gene prediction method: Protein Homology.
IS66 family insertion sequence element accessory protein TnpB
COORDINATES: similar to AA sequence:RefSeq:WP_008554852.1
GO:0004803 - transposase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_076611562.1
programmed frameshift; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: protein motif:HMM:NF025025.2
COORDINATES: similar to AA sequence:RefSeq:WP_008983863.1
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: protein motif:HMM:NF033580.1
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_014876578.1
COORDINATES: similar to AA sequence:RefSeq:WP_008281647.1
COORDINATES: protein motif:HMM:NF021390.2
COORDINATES: similar to AA sequence:RefSeq:WP_013960764.1
COORDINATES: similar to AA sequence:RefSeq:WP_013385077.1
GO:0005215 - transporter activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_013385078.1
GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
TetR/AcrR family transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_017203838.1
LLM class flavin-dependent oxidoreductase
COORDINATES: similar to AA sequence:RefSeq:WP_015915310.1
helix-turn-helix domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_017793716.1
GO:0016705 - oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_018296814.1
NAD(P)-binding domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_014358897.1
COORDINATES: similar to AA sequence:RefSeq:WP_012207438.1
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_009175440.1
COORDINATES: similar to AA sequence:RefSeq:WP_011907450.1
GO:0048472 - threonine-phosphate decarboxylase activity [Evidence IEA]
GO:0009236 - cobalamin biosynthetic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_002720982.1
GO:0003824 - catalytic activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_010393413.1
GO:0008817 - corrinoid adenosyltransferase activity [Evidence IEA]
cob(I)yrinic acid a,c-diamide adenosyltransferase
COORDINATES: nucleotide motif:Rfam:14.4:RF00174
cobalamin riboswitch; Derived by automated computational analysis using gene prediction method: cmsearch.
COORDINATES: similar to AA sequence:RefSeq:WP_007422877.1
COORDINATES: similar to AA sequence:RefSeq:WP_005850078.1
COORDINATES: similar to AA sequence:RefSeq:WP_007422876.1
COORDINATES: similar to AA sequence:RefSeq:WP_007422875.1
GO:0016709 - oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen [Evidence IEA]
GO:0019250 - aerobic cobalamin biosynthetic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_014496544.1
GO:0016993 - precorrin-8X methylmutase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_014428078.1
GO:0030788 - precorrin-2 C20-methyltransferase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_008071954.1
GO:0030789 - precorrin-3B C17-methyltransferase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_013067766.1
GO:0016994 - precorrin-6A reductase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_002719984.1
GO:0046025 - precorrin-6Y C5,15-methyltransferase (decarboxylating) activity [Evidence IEA]
GO:0046140 - corrin biosynthetic process [Evidence IEA]
precorrin-6y C5,15-methyltransferase (decarboxylating) subunit CbiE
COORDINATES: similar to AA sequence:RefSeq:WP_008071957.1
COORDINATES: similar to AA sequence:RefSeq:WP_017998764.1
GO:0046026 - precorrin-4 C11-methyltransferase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_014428084.1
GO:0042242 - cobyrinic acid a,c-diamide synthase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011663655.1
GO:0000041 - transition metal ion transport [Evidence IEA]
energy-coupling factor ABC transporter permease
COORDINATES: similar to AA sequence:RefSeq:WP_008031230.1
GO:0043819 - precorrin-6A synthase (deacetylating) activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_002720973.1
COORDINATES: similar to AA sequence:RefSeq:WP_009504830.1
GO:0016880 - acid-ammonia (or amide) ligase activity [Evidence IEA]
adenosylcobinamide-phosphate synthase CbiB
COORDINATES: protein motif:HMM:NF028132.2
COORDINATES: similar to AA sequence:RefSeq:WP_076611976.1
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_018634181.1
ATP-binding cassette domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_019964718.1
GO:0016787 - hydrolase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_018634179.1
COORDINATES: similar to AA sequence:RefSeq:WP_018430399.1
COORDINATES: similar to AA sequence:RefSeq:WP_018634283.1
GO:0016853 - isomerase activity [Evidence IEA]; GO:0048029 - monosaccharide binding [Evidence IEA]
GO:0005996 - monosaccharide metabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011242084.1
DnaA N-terminal domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_007803648.1
COORDINATES: similar to AA sequence:RefSeq:WP_011749186.1
ParB N-terminal domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_007198137.1
GO:0009055 - electron transfer activity [Evidence IEA]; GO:0020037 - heme binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_007089040.1
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_076611875.1
COORDINATES: similar to AA sequence:RefSeq:WP_013067811.1
COORDINATES: similar to AA sequence:RefSeq:WP_076611554.1
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_009819198.1
COORDINATES: similar to AA sequence:RefSeq:WP_013652210.1
Twin-arginine translocation pathway signal
COORDINATES: similar to AA sequence:RefSeq:WP_007795360.1
COORDINATES: similar to AA sequence:RefSeq:WP_006932702.1
ribbon-helix-helix domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_009562618.1