Neotabrizicola shimadae strain N10 plasmid unnamed1, complete sequence.
Bacteria; Proteobacteria; Alphaproteobacteria; Rhodobacterales; Rhodobacteraceae; Neotabrizicola.
Rhodobacter shimadae sp. nov., an aerobic anoxygenic phototrophic bacterium isolated from a hot spring
Submitted (03-FEB-2021) Biological Sciences, Tokyo Metropolitan University, 1-1 Minami-osawa, Hachioji, Tokyo 192-0397, Japan
REFSEQ INFORMATION: The reference sequence is identical to\nCP069371.1.\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 :: 15-MAY-2020\nAssembly Method :: Unicycler v. 0.4.7\nGenome Representation :: Full\nExpected Final Version :: Yes\nGenome Coverage :: 325.0x\nSequencing Technology :: Oxford Nanopore GridION\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 09/07/2022 01:45:18\nAnnotation Pipeline :: NCBI Prokaryotic Genome\n Annotation Pipeline (PGAP)\nAnnotation Method :: Best-placed reference protein\n set; GeneMarkS-2+\nAnnotation Software revision :: 6.2\nFeatures Annotated :: Gene; CDS; rRNA; tRNA; ncRNA;\n repeat_region\nGenes (total) :: 4,272\nCDSs (total) :: 4,215\nGenes (coding) :: 4,155\nCDSs (with protein) :: 4,155\nGenes (RNA) :: 57\nrRNAs :: 2, 2, 2 (5S, 16S, 23S)\ncomplete rRNAs :: 2, 2, 2 (5S, 16S, 23S)\ntRNAs :: 48\nncRNAs :: 3\nPseudo Genes (total) :: 60\nCDSs (without protein) :: 60\nPseudo Genes (ambiguous residues) :: 0 of 60\nPseudo Genes (frameshifted) :: 9 of 60\nPseudo Genes (incomplete) :: 52 of 60\nPseudo Genes (internal stop) :: 6 of 60\nPseudo Genes (multiple problems) :: 7 of 60\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.
COORDINATES: similar to AA sequence:RefSeq:WP_006202555.1
Derived by automated computational analysis using gene prediction method: Protein Homology.
substrate-binding domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_007700380.1
COORDINATES: similar to AA sequence:RefSeq:WP_007795717.1
ATP-binding cassette domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_007537306.1
COORDINATES: similar to AA sequence:RefSeq:WP_006202551.1
COORDINATES: similar to AA sequence:RefSeq:WP_018010114.1
GO:0016491 - oxidoreductase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_006202550.1
GO:0003864 - 3-methyl-2-oxobutanoate hydroxymethyltransferase activity [Evidence IEA]
GO:0015940 - pantothenate biosynthetic process [Evidence IEA]
3-methyl-2-oxobutanoate hydroxymethyltransferase
COORDINATES: similar to AA sequence:RefSeq:WP_012116054.1
GO:0004488 - methylenetetrahydrofolate dehydrogenase (NADP+) activity [Evidence IEA]
bifunctional methylenetetrahydrofolate dehydrogenase/methenyltetrahydrofolate cyclohydrolase FolD
COORDINATES: similar to AA sequence:RefSeq:WP_011976224.1
GO:0008864 - formyltetrahydrofolate deformylase activity [Evidence IEA]
GO:0009152 - purine ribonucleotide biosynthetic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_012040825.1
GO:0050112 - inositol 2-dehydrogenase activity [Evidence IEA]
GO:0019310 - inositol catabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_009819917.1
COORDINATES: protein motif:HMM:NF015688.2
COORDINATES: protein motif:HMM:NF015487.2
TrbG/VirB9 family P-type conjugative transfer protein
COORDINATES: protein motif:HMM:NF016238.2
COORDINATES: protein motif:HMM:NF016491.2
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: protein motif:HMM:NF019608.2
COORDINATES: protein motif:HMM:NF013618.2
lytic transglycosylase domain-containing protein
COORDINATES: protein motif:HMM:NF015118.2
COORDINATES: protein motif:HMM:NF016957.2
VirB3 family type IV secretion system protein
COORDINATES: protein motif:HMM:NF016820.2
COORDINATES: similar to AA sequence:RefSeq:WP_014880577.1
COORDINATES: similar to AA sequence:RefSeq:WP_018065889.1
COORDINATES: similar to AA sequence:RefSeq:WP_008336115.1
COORDINATES: similar to AA sequence:RefSeq:WP_011578666.1
GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]
GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
metalloregulator ArsR/SmtB family transcription factor
COORDINATES: similar to AA sequence:RefSeq:WP_018458505.1
NAD(P)-binding domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_019956276.1
GO:0022857 - transmembrane transporter activity [Evidence IEA]
GO:0055085 - transmembrane transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011908444.1
organoarsenical effux MFS transporter ArsJ
COORDINATES: similar to AA sequence:RefSeq:WP_013067794.1
GO:0051287 - NAD binding [Evidence IEA]; GO:0050661 - NADP binding [Evidence IEA]; GO:0016620 - oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor [Evidence IEA]
GO:0006006 - glucose metabolic process [Evidence IEA]
ArsJ-associated glyceraldehyde-3-phosphate dehydrogenase
COORDINATES: similar to AA sequence:RefSeq:WP_011331465.1
COORDINATES: similar to AA sequence:RefSeq:WP_011908439.1
COORDINATES: similar to AA sequence:RefSeq:WP_003291092.1
COORDINATES: similar to AA sequence:RefSeq:WP_011908441.1
COORDINATES: similar to AA sequence:RefSeq:WP_006724583.1
COORDINATES: protein motif:HMM:TIGR01297.1
cation diffusion facilitator family transporter
COORDINATES: similar to AA sequence:RefSeq:WP_076612068.1
GO:0004803 - transposase activity [Evidence IEA]
frameshifted; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: protein motif:HMM:NF012257.2
Crp/Fnr family transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_008334818.1
COORDINATES: similar to AA sequence:RefSeq:WP_007091423.1
GO:0003674 - molecular_function [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_017932647.1
GO:0008490 - arsenite secondary active transmembrane transporter activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_013069306.1
COORDINATES: similar to AA sequence:RefSeq:WP_019197306.1
PhnD/SsuA/transferrin family substrate-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_009817400.1
HAMP domain-containing sensor histidine kinase
COORDINATES: similar to AA sequence:RefSeq:WP_008027029.1
GO:0000160 - phosphorelay signal transduction system [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_008027031.1
GO:0050611 - arsenate reductase (azurin) activity [Evidence IEA]
arsenate reductase (azurin) small subunit
COORDINATES: similar to AA sequence:RefSeq:WP_008027033.1
arsenate reductase (azurin) large subunit
COORDINATES: similar to AA sequence:RefSeq:WP_008554318.1
COORDINATES: similar to AA sequence:RefSeq:WP_007120629.1
frameshifted; incomplete; partial in the middle of a contig; missing N-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
helix-turn-helix domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_017670926.1
COORDINATES: similar to AA sequence:RefSeq:WP_003093053.1
GO:0016682 - oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor [Evidence IEA]
cytochrome d ubiquinol oxidase subunit II
COORDINATES: similar to AA sequence:RefSeq:WP_014880322.1
COORDINATES: similar to AA sequence:RefSeq:WP_018138855.1
GO:0051920 - peroxiredoxin activity [Evidence IEA]; GO:0008379 - thioredoxin peroxidase activity [Evidence IEA]
GO:0098869 - cellular oxidant detoxification [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_009824137.1
COORDINATES: similar to AA sequence:RefSeq:WP_007602193.1
COORDINATES: similar to AA sequence:RefSeq:WP_008891888.1
COORDINATES: similar to AA sequence:RefSeq:WP_012763799.1
COORDINATES: similar to AA sequence:RefSeq:WP_006726598.1
YeeE/YedE thiosulfate transporter family protein
COORDINATES: similar to AA sequence:RefSeq:WP_007199982.1
COORDINATES: similar to AA sequence:RefSeq:WP_006610476.1
COORDINATES: protein motif:HMM:TIGR01244.1
GO:0016787 - hydrolase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_014284766.1
bifunctional protein tyrosine phosphatase family protein/NAD(P)/FAD-dependent oxidoreductase
COORDINATES: similar to AA sequence:RefSeq:WP_019964229.1
GO:0015116 - sulfate transmembrane transporter activity [Evidence IEA]
GO:0008272 - sulfate transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_009146521.1
COORDINATES: similar to AA sequence:RefSeq:WP_016899617.1
rhodanese-like domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_009807967.1
COORDINATES: similar to AA sequence:RefSeq:WP_009820208.1
COORDINATES: similar to AA sequence:RefSeq:WP_011331447.1
COORDINATES: similar to AA sequence:RefSeq:WP_009503866.1
AbrB/MazE/SpoVT family DNA-binding domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_009827042.1
COORDINATES: similar to AA sequence:RefSeq:WP_010400281.1
COORDINATES: similar to AA sequence:RefSeq:WP_018001792.1
COORDINATES: similar to AA sequence:RefSeq:WP_018001791.1
ParB/RepB/Spo0J family partition protein
COORDINATES: similar to AA sequence:RefSeq:WP_009827215.1
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_011090936.1
COORDINATES: similar to AA sequence:RefSeq:WP_006956108.1
COORDINATES: similar to AA sequence:RefSeq:WP_010398665.1
COORDINATES: similar to AA sequence:RefSeq:WP_019088725.1
COORDINATES: similar to AA sequence:RefSeq:WP_017998436.1
COORDINATES: similar to AA sequence:RefSeq:WP_005859736.1
COORDINATES: similar to AA sequence:RefSeq:WP_019012660.1
COORDINATES: similar to AA sequence:RefSeq:WP_008282093.1
COORDINATES: similar to AA sequence:RefSeq:WP_007594664.1
COORDINATES: similar to AA sequence:RefSeq:WP_007803576.1
COORDINATES: similar to AA sequence:RefSeq:WP_018182507.1
sulfite exporter TauE/SafE family protein
COORDINATES: similar to AA sequence:RefSeq:WP_019860665.1
GO:0015087 - cobalt ion transmembrane transporter activity [Evidence IEA]; GO:0015095 - magnesium ion transmembrane transporter activity [Evidence IEA]
GO:0006824 - cobalt ion transport [Evidence IEA]; GO:0015693 - magnesium ion transport [Evidence IEA]
COORDINATES: protein motif:HMM:NF015424.2
COORDINATES: similar to AA sequence:RefSeq:WP_009818317.1
COORDINATES: similar to AA sequence:RefSeq:WP_009818316.1
COORDINATES: nucleotide motif:Rfam:14.4:RF03058
sul1 is cis-regulatory element that is thought to sense ions involved in sulfur or methionine metabolism; They are found in Alphaproteobacteria; Derived by automated computational analysis using gene prediction method: cmsearch.
COORDINATES: similar to AA sequence:RefSeq:WP_009827208.1
COORDINATES: similar to AA sequence:RefSeq:WP_018065906.1
COORDINATES: similar to AA sequence:RefSeq:WP_009827206.1
COORDINATES: similar to AA sequence:RefSeq:WP_007803272.1
COORDINATES: similar to AA sequence:RefSeq:WP_011646949.1
COORDINATES: similar to AA sequence:RefSeq:WP_009574197.1
COORDINATES: similar to AA sequence:RefSeq:WP_009827203.1
COORDINATES: similar to AA sequence:RefSeq:WP_009820093.1
COORDINATES: similar to AA sequence:RefSeq:WP_007803278.1
antitoxin of toxin-antitoxin stability system
COORDINATES: similar to AA sequence:RefSeq:WP_019404595.1
COORDINATES: similar to AA sequence:RefSeq:WP_007803284.1
nucleotidyl transferase AbiEii/AbiGii toxin family protein
COORDINATES: similar to AA sequence:RefSeq:WP_018065917.1
type IV toxin-antitoxin system AbiEi family antitoxin
COORDINATES: similar to AA sequence:RefSeq:WP_009820102.1
COORDINATES: similar to AA sequence:RefSeq:WP_018065919.1
COORDINATES: similar to AA sequence:RefSeq:WP_009820104.1
COORDINATES: similar to AA sequence:RefSeq:WP_007803302.1
COORDINATES: similar to AA sequence:RefSeq:WP_018065922.1
COORDINATES: similar to AA sequence:RefSeq:WP_009179413.1
SprT family zinc-dependent metalloprotease
COORDINATES: similar to AA sequence:RefSeq:WP_013167445.1
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_012111264.1
COORDINATES: similar to AA sequence:RefSeq:WP_011316276.1
COORDINATES: similar to AA sequence:RefSeq:WP_007681430.1
COORDINATES: similar to AA sequence:RefSeq:WP_012111266.1
COORDINATES: similar to AA sequence:RefSeq:WP_007681434.1
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_013167451.1
COORDINATES: similar to AA sequence:RefSeq:WP_018912701.1
COORDINATES: similar to AA sequence:RefSeq:WP_009565819.1
COORDINATES: similar to AA sequence:RefSeq:WP_015918459.1
COORDINATES: protein motif:HMM:NF018691.2
COORDINATES: protein motif:HMM:NF015397.2
relaxase/mobilization nuclease domain-containing protein
COORDINATES: protein motif:HMM:NF014581.2
type IV secretory system conjugative DNA transfer family protein
COORDINATES: similar to AA sequence:RefSeq:WP_012558112.1
LacI family DNA-binding transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_007537312.1
COORDINATES: similar to AA sequence:RefSeq:WP_007537310.1