Sphaerotilus sulfidivorans strain D-507 plasmid pSna507_unt12, complete sequence.
Bacteria; Pseudomonadota; Betaproteobacteria; Burkholderiales; Sphaerotilaceae; Sphaerotilus.
Complete Genome Sequence and Methylome Analysis of Sphaerotilus natans subsp. sulfidivorans D-507
Submitted (05-FEB-2019) Genome Biology, NEB, 240 County Rd, Ipswich, MA 01938, USA
REFSEQ INFORMATION: The reference sequence is identical to\nCP035709.1.\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/\nThis genome has a base modification file available.\n\n##Genome-Assembly-Data-START##\nAssembly Date :: 30-MAY-2018\nAssembly Method :: HGAP v. 2.3.0\nAssembly Name :: Sphaerotilus D-507_BP9_50_HGAP3_2\nGenome Representation :: Full\nExpected Final Version :: Yes\nGenome Coverage :: 179.73x\nSequencing Technology :: PacBio RS\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 03/26/2023 03:04:22\nAnnotation Pipeline :: NCBI Prokaryotic Genome\n Annotation Pipeline (PGAP)\nAnnotation Method :: Best-placed reference protein\n set; GeneMarkS-2+\nAnnotation Software revision :: 6.4\nFeatures Annotated :: Gene; CDS; rRNA; tRNA; ncRNA\nGenes (total) :: 4,023\nCDSs (total) :: 3,942\nGenes (coding) :: 3,883\nCDSs (with protein) :: 3,883\nGenes (RNA) :: 81\nrRNAs :: 4, 4, 3 (5S, 16S, 23S)\ncomplete rRNAs :: 4, 4, 3 (5S, 16S, 23S)\ntRNAs :: 67\nncRNAs :: 3\nPseudo Genes (total) :: 59\nCDSs (without protein) :: 59\nPseudo Genes (ambiguous residues) :: 0 of 59\nPseudo Genes (frameshifted) :: 22 of 59\nPseudo Genes (incomplete) :: 39 of 59\nPseudo Genes (internal stop) :: 5 of 59\nPseudo Genes (multiple problems) :: 7 of 59\nCRISPR Arrays :: 3\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.
COORDINATES: similar to AA sequence:RefSeq:WP_019726374.1
GO:0016787 - hydrolase activity [Evidence IEA]
frameshifted; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_015866131.1
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: protein motif:HMM:NF013793.2
COORDINATES: similar to AA sequence:RefSeq:WP_019657404.1
GO:0007059 - chromosome segregation [Evidence IEA]; GO:0000910 - cytokinesis [Evidence IEA]
ParB/RepB/Spo0J family partition protein
COORDINATES: similar to AA sequence:RefSeq:WP_008079151.1
frameshifted; internal stop; Derived by automated computational analysis using gene prediction method: Protein Homology.
PDDEXK nuclease domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_007804361.1
SprT family zinc-dependent metalloprotease
COORDINATES: similar to AA sequence:RefSeq:WP_019936382.1
GO:0019812 - type I site-specific deoxyribonuclease complex [Evidence IEA]
GO:0009035 - type I site-specific deoxyribonuclease activity [Evidence IEA]
GO:0009307 - DNA restriction-modification system [Evidence IEA]
HsdR family type I site-specific deoxyribonuclease
COORDINATES: similar to AA sequence:RefSeq:WP_018606340.1
COORDINATES: protein motif:HMM:NF013579.2
GO:0006304 - DNA modification [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_019868160.1
GO:0015666 - restriction endodeoxyribonuclease activity [Evidence IEA]; GO:0009007 - site-specific DNA-methyltransferase (adenine-specific) activity [Evidence IEA]
GO:0006306 - DNA methylation [Evidence IEA]; GO:0009307 - DNA restriction-modification system [Evidence IEA]
type I restriction-modification system subunit M
COORDINATES: similar to AA sequence:RefSeq:WP_019936378.1
COORDINATES: similar to AA sequence:RefSeq:WP_018990859.1
COORDINATES: similar to AA sequence:RefSeq:WP_011798012.1
COORDINATES: similar to AA sequence:RefSeq:WP_017905903.1
GO:0006629 - lipid metabolic process [Evidence IEA]
patatin-like phospholipase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_011798239.1
GO:0004803 - transposase activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF017528.2
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_011798488.1
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_020201168.1
helix-turn-helix domain-containing protein
COORDINATES: protein motif:HMM:NF023898.2
COORDINATES: similar to AA sequence:RefSeq:WP_013262765.1
COORDINATES: similar to AA sequence:RefSeq:WP_013516299.1
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_076611576.1
programmed frameshift; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_003117273.1
COORDINATES: similar to AA sequence:RefSeq:WP_017279408.1
GO:0015074 - DNA integration [Evidence IEA]; GO:0006310 - DNA recombination [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_005793717.1
COORDINATES: similar to AA sequence:RefSeq:WP_008159538.1
COORDINATES: similar to AA sequence:RefSeq:WP_017507086.1
COORDINATES: similar to AA sequence:RefSeq:WP_011805880.1
GO:0005507 - copper ion binding [Evidence IEA]
multicopper oxidase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_011805882.1
COORDINATES: similar to AA sequence:RefSeq:WP_019562297.1
GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
heavy metal response regulator transcription factor
COORDINATES: similar to AA sequence:RefSeq:WP_013722089.1
GO:0000155 - phosphorelay sensor kinase activity [Evidence IEA]; GO:0004673 - protein histidine kinase activity [Evidence IEA]; GO:0016772 - transferase activity, transferring phosphorus-containing groups [Evidence IEA]
GO:0000160 - phosphorelay signal transduction system [Evidence IEA]; GO:0016310 - phosphorylation [Evidence IEA]
COORDINATES: protein motif:HMM:NF016836.2
COORDINATES: similar to AA sequence:RefSeq:WP_009516048.1
GO:0046872 - metal ion binding [Evidence IEA]
CopK family periplasmic copper-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_011953095.1
COORDINATES: similar to AA sequence:RefSeq:WP_003071679.1
COORDINATES: similar to AA sequence:RefSeq:WP_011798152.1
isoprenylcysteine carboxylmethyltransferase family protein
COORDINATES: protein motif:HMM:NF019351.2
GO:0005507 - copper ion binding [Evidence IEA]; GO:0016491 - oxidoreductase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_012487447.1
COORDINATES: similar to AA sequence:RefSeq:WP_008448009.1
COORDINATES: similar to AA sequence:RefSeq:WP_009552874.1
GO:0005215 - transporter activity [Evidence IEA]
efflux RND transporter periplasmic adaptor subunit
COORDINATES: similar to AA sequence:RefSeq:WP_012202407.1
GO:0015562 - efflux transmembrane transporter activity [Evidence IEA]
GO:0055085 - transmembrane transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_015913621.1
COORDINATES: similar to AA sequence:RefSeq:WP_003279621.1
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]
COORDINATES: protein motif:HMM:NF022853.2
protein-disulfide reductase DsbD N-terminal domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_012347022.1
COORDINATES: protein motif:HMM:NF024853.2
thiol:disulfide interchange protein DsbA/DsbL
COORDINATES: similar to AA sequence:RefSeq:WP_012347375.1
GO:0004197 - cysteine-type endopeptidase activity [Evidence IEA]
GO:0043687 - post-translational protein modification [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_012347374.1
GO:0005575 - cellular_component [Evidence IEA]
GO:0003674 - molecular_function [Evidence IEA]
GO:0008150 - biological_process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_004944027.1
COORDINATES: similar to AA sequence:RefSeq:WP_006754014.1
COORDINATES: protein motif:HMM:NF024803.2
GO:0003677 - DNA binding [Evidence IEA]; GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]; GO:0046872 - metal ion binding [Evidence IEA]
GO:0045893 - positive regulation of DNA-templated transcription [Evidence IEA]
Cd(II)/Pb(II)-responsive transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_009516063.1
COORDINATES: similar to AA sequence:RefSeq:WP_006296625.1
GO:0015035 - protein-disulfide reductase activity [Evidence IEA]
GO:0006457 - protein folding [Evidence IEA]
COORDINATES: protein motif:HMM:NF023903.2
COORDINATES: similar to AA sequence:RefSeq:WP_004195850.1
COORDINATES: similar to AA sequence:RefSeq:WP_005000121.1
type I restriction endonuclease subunit R
COORDINATES: similar to AA sequence:RefSeq:WP_020289069.1
COORDINATES: similar to AA sequence:RefSeq:WP_012470253.1
COORDINATES: similar to AA sequence:RefSeq:WP_001138014.1
COORDINATES: similar to AA sequence:RefSeq:WP_000904911.1
COORDINATES: similar to AA sequence:RefSeq:WP_019577807.1
translesion error-prone DNA polymerase V autoproteolytic subunit
COORDINATES: similar to AA sequence:RefSeq:WP_011485838.1
COORDINATES: similar to AA sequence:RefSeq:WP_009855520.1
COORDINATES: similar to AA sequence:RefSeq:WP_010376679.1
helix-turn-helix transcriptional regulator
COORDINATES: protein motif:HMM:NF012234.2
GO:0005524 - ATP binding [Evidence IEA]; GO:0016887 - ATP hydrolysis activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_015865945.1