Amphritea japonica strain JCM 14782 plasmid pJCM14782, 16s ribosomal rna rrna prediction is too short.
Bacteria; Pseudomonadota; Gammaproteobacteria; Oceanospirillales; Oceanospirillaceae; Amphritea.
Taxonomic revision of the genus Amphritea supported by genomic and in silico chemotaxonomic analyses, and the proposal of Aliamphritea gen. nov
Submitted (24-MAY-2022) Contact:Tomoo Sawabe Hokkaido University, Faculty of Fisheries Sciences; 3-1-1 Minato-cho, Hakodate, Hokkaido 041-8611, Japan
REFSEQ INFORMATION: The reference sequence is identical to\nAP025762.1.\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 Method :: Unicycler v. 0.4.7\nGenome Coverage :: 296x\nSequencing Technology :: Illumina MiSeq; Nanopore\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 09/29/2022 10:48:09\nAnnotation Pipeline :: NCBI Prokaryotic Genome\n Annotation Pipeline (PGAP)\nAnnotation Method :: Best-placed reference protein\n set; GeneMarkS-2+\nAnnotation Software revision :: 6.3\nFeatures Annotated :: Gene; CDS; rRNA; tRNA; ncRNA;\n repeat_region\nGenes (total) :: 3,573\nCDSs (total) :: 3,477\nGenes (coding) :: 3,463\nCDSs (with protein) :: 3,463\nGenes (RNA) :: 96\nrRNAs :: 5, 5, 5 (5S, 16S, 23S)\ncomplete rRNAs :: 5, 5, 5 (5S, 16S, 23S)\ntRNAs :: 74\nncRNAs :: 7\nPseudo Genes (total) :: 14\nCDSs (without protein) :: 14\nPseudo Genes (ambiguous residues) :: 0 of 14\nPseudo Genes (frameshifted) :: 2 of 14\nPseudo Genes (incomplete) :: 13 of 14\nPseudo Genes (internal stop) :: 2 of 14\nPseudo Genes (multiple problems) :: 2 of 14\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.
COORDINATES: nucleotide motif:Rfam:14.4:RF00177
Derived by automated computational analysis using gene prediction method: cmsearch.
Derived by automated computational analysis using gene prediction method: tRNAscan-SE.
COORDINATES: nucleotide motif:Rfam:14.4:RF02541
COORDINATES: nucleotide motif:Rfam:14.4:RF00001
COORDINATES: similar to AA sequence:RefSeq:WP_013662757.1
GO:0005951 - carbamoyl-phosphate synthase complex [Evidence IEA]
GO:0004088 - carbamoyl-phosphate synthase (glutamine-hydrolyzing) activity [Evidence IEA]
GO:0009220 - pyrimidine ribonucleotide biosynthetic process [Evidence IEA]
Derived by automated computational analysis using gene prediction method: Protein Homology.
glutamine-hydrolyzing carbamoyl-phosphate synthase small subunit
COORDINATES: similar to AA sequence:RefSeq:WP_020287427.1
GO:0005524 - ATP binding [Evidence IEA]; GO:0046872 - metal ion binding [Evidence IEA]
GO:0006807 - nitrogen compound metabolic process [Evidence IEA]
carbamoyl-phosphate synthase large subunit
COORDINATES: similar to AA sequence:RefSeq:WP_019019088.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0070063 - RNA polymerase binding [Evidence IEA]
GO:0032784 - regulation of DNA-templated transcription elongation [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_012068736.1
COORDINATES: similar to AA sequence:RefSeq:WP_007021189.1
GO:0016436 - rRNA (uridine) methyltransferase activity [Evidence IEA]
GO:0001510 - RNA methylation [Evidence IEA]; GO:0006364 - rRNA processing [Evidence IEA]
23S rRNA (uridine(2552)-2'-O)-methyltransferase RlmE
COORDINATES: similar to AA sequence:RefSeq:WP_010325165.1
GO:0016887 - ATP hydrolysis activity [Evidence IEA]; GO:0004222 - metalloendopeptidase activity [Evidence IEA]
GO:0051301 - cell division [Evidence IEA]; GO:0006508 - proteolysis [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_007021187.1
GO:0004156 - dihydropteroate synthase activity [Evidence IEA]
GO:0009396 - folic acid-containing compound biosynthetic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_013819889.1
GO:0016868 - intramolecular transferase activity, phosphotransferases [Evidence IEA]; GO:0000287 - magnesium ion binding [Evidence IEA]; GO:0008966 - phosphoglucosamine mutase activity [Evidence IEA]
GO:0005975 - carbohydrate metabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_008931993.1
GO:0004807 - triose-phosphate isomerase activity [Evidence IEA]
GO:0006096 - glycolytic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_020683560.1
GO:0005887 - integral component of plasma membrane [Evidence IEA]
GO:0015450 - protein-transporting ATPase activity [Evidence IEA]
GO:0043952 - protein transport by the Sec complex [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_013797347.1
GO:0042274 - ribosomal small subunit biogenesis [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_010325159.1
GO:0006353 - DNA-templated transcription termination [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_010325158.1
GO:0003743 - translation initiation factor activity [Evidence IEA]
GO:0006413 - translational initiation [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011508363.1
GO:0019843 - rRNA binding [Evidence IEA]
GO:0006396 - RNA processing [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_017084245.1
GO:0004730 - pseudouridylate synthase activity [Evidence IEA]
GO:0006400 - tRNA modification [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_012068748.1
GO:0022627 - cytosolic small ribosomal subunit [Evidence IEA]; GO:0000314 - organellar small ribosomal subunit [Evidence IEA]
GO:0003735 - structural constituent of ribosome [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_007021177.1
GO:0004654 - polyribonucleotide nucleotidyltransferase activity [Evidence IEA]
GO:0006402 - mRNA catabolic process [Evidence IEA]
polyribonucleotide nucleotidyltransferase
COORDINATES: similar to AA sequence:RefSeq:WP_008988824.1
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: protein motif:HMM:NF020123.2
GO:0016209 - antioxidant activity [Evidence IEA]; GO:0016491 - oxidoreductase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_013345599.1
COORDINATES: protein motif:HMM:NF018496.2
COORDINATES: similar to AA sequence:RefSeq:WP_020683569.1
GO:0008168 - methyltransferase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011866772.1
16S rRNA pseudouridine(516) synthase RsuA
COORDINATES: similar to AA sequence:RefSeq:WP_020683571.1
COORDINATES: similar to AA sequence:RefSeq:WP_019814919.1
COORDINATES: similar to AA sequence:RefSeq:WP_007021170.1
GO:0004592 - pantoate-beta-alanine ligase activity [Evidence IEA]
GO:0015940 - pantothenate biosynthetic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_010325147.1
GO:0003864 - 3-methyl-2-oxobutanoate hydroxymethyltransferase activity [Evidence IEA]
3-methyl-2-oxobutanoate hydroxymethyltransferase
COORDINATES: similar to AA sequence:RefSeq:WP_008217900.1
GO:0003848 - 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine diphosphokinase activity [Evidence IEA]
2-amino-4-hydroxy-6- hydroxymethyldihydropteridine diphosphokinase
COORDINATES: similar to AA sequence:RefSeq:WP_010325145.1
GO:0004652 - polynucleotide adenylyltransferase activity [Evidence IEA]; GO:0003723 - RNA binding [Evidence IEA]
GO:0006378 - mRNA polyadenylation [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_007021166.1
sigma-54 dependent transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_019623140.1
COORDINATES: similar to AA sequence:RefSeq:WP_007111811.1
COORDINATES: similar to AA sequence:RefSeq:WP_007021164.1
GO:0004812 - aminoacyl-tRNA ligase activity [Evidence IEA]
GO:0043039 - tRNA aminoacylation [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_007021163.1
GO:0019899 - enzyme binding [Evidence IEA]
GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_006451311.1
pyridoxal phosphate-dependent aminotransferase
COORDINATES: similar to AA sequence:RefSeq:WP_007021161.1
GO:0000023 - maltose metabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_020683585.1
GO:0051537 - 2 iron, 2 sulfur cluster binding [Evidence IEA]
COORDINATES: protein motif:HMM:NF015506.2
COORDINATES: similar to AA sequence:RefSeq:WP_020683587.1
COORDINATES: protein motif:HMM:NF010068.0
heme ABC transporter ATP-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_007021158.1
COORDINATES: similar to AA sequence:RefSeq:WP_007021157.1
GO:0009274 - peptidoglycan-based cell wall [Evidence IEA]
GO:0008658 - penicillin binding [Evidence IEA]; GO:0008233 - peptidase activity [Evidence IEA]; GO:0008955 - peptidoglycan glycosyltransferase activity [Evidence IEA]
GO:0009252 - peptidoglycan biosynthetic process [Evidence IEA]; GO:0046677 - response to antibiotic [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_003113238.1
COORDINATES: similar to AA sequence:RefSeq:WP_002927169.1
GO:0016021 - integral component of membrane [Evidence IEA]
GO:0004129 - cytochrome-c oxidase activity [Evidence IEA]; GO:0020037 - heme binding [Evidence IEA]
GO:0009060 - aerobic respiration [Evidence IEA]
cbb3-type cytochrome c oxidase subunit I
COORDINATES: protein motif:HMM:NF024211.2
COORDINATES: similar to AA sequence:RefSeq:WP_006475581.1
COORDINATES: protein motif:HMM:NF015582.2
cytochrome C oxidase subunit IV family protein
COORDINATES: similar to AA sequence:RefSeq:WP_014238130.1
COORDINATES: similar to AA sequence:RefSeq:WP_011311067.1
COORDINATES: protein motif:HMM:NF012257.2
Crp/Fnr family transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_012326585.1
COORDINATES: similar to AA sequence:RefSeq:WP_007018806.1
GO:0042286 - glutamate-1-semialdehyde 2,1-aminomutase activity [Evidence IEA]
GO:0006779 - porphyrin-containing compound biosynthetic process [Evidence IEA]
glutamate-1-semialdehyde 2,1-aminomutase
COORDINATES: similar to AA sequence:RefSeq:WP_020580890.1
GO:0004789 - thiamine-phosphate diphosphorylase activity [Evidence IEA]
GO:0009228 - thiamine biosynthetic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_007021152.1
COORDINATES: similar to AA sequence:RefSeq:WP_017902853.1
GO:0003942 - N-acetyl-gamma-glutamyl-phosphate reductase activity [Evidence IEA]
GO:0006592 - ornithine biosynthetic process [Evidence IEA]
N-acetyl-gamma-glutamyl-phosphate reductase
COORDINATES: similar to AA sequence:RefSeq:WP_020683598.1
GO:0051536 - iron-sulfur cluster binding [Evidence IEA]
GO:0016226 - iron-sulfur cluster assembly [Evidence IEA]
iron-sulfur cluster insertion protein ErpA
COORDINATES: similar to AA sequence:RefSeq:WP_008251316.1
GO:0005524 - ATP binding [Evidence IEA]; GO:0016773 - phosphotransferase activity, alcohol group as acceptor [Evidence IEA]
GO:0006040 - amino sugar metabolic process [Evidence IEA]; GO:0009254 - peptidoglycan turnover [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_020683600.1
peptidoglycan DD-metalloendopeptidase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_020287241.1
GO:0004831 - tyrosine-tRNA ligase activity [Evidence IEA]
GO:0006437 - tyrosyl-tRNA aminoacylation [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_007021254.1
COORDINATES: similar to AA sequence:RefSeq:WP_007021255.1
GO:0003984 - acetolactate synthase activity [Evidence IEA]; GO:0050660 - flavin adenine dinucleotide binding [Evidence IEA]; GO:0000287 - magnesium ion binding [Evidence IEA]; GO:0030976 - thiamine pyrophosphate binding [Evidence IEA]
GO:0009082 - branched-chain amino acid biosynthetic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_008940823.1
GO:1990610 - acetolactate synthase regulator activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_007019999.1
GO:0003674 - molecular_function [Evidence IEA]
GO:0019634 - organic phosphonate metabolic process [Evidence IEA]
phosphonate metabolism protein/1,5-bisphosphokinase (PRPP-forming) PhnN
COORDINATES: similar to AA sequence:RefSeq:WP_005492551.1
COORDINATES: similar to AA sequence:RefSeq:WP_006965219.1
COORDINATES: similar to AA sequence:RefSeq:WP_011505811.1
GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_010504360.1
GO:0071949 - FAD binding [Evidence IEA]; 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:0006744 - ubiquinone biosynthetic process [Evidence IEA]
5-demethoxyubiquinol-8 5-hydroxylase UbiM
COORDINATES: similar to AA sequence:RefSeq:WP_007021335.1
COORDINATES: similar to AA sequence:RefSeq:WP_015047075.1
GO:0003882 - CDP-diacylglycerol-serine O-phosphatidyltransferase activity [Evidence IEA]
GO:0008654 - phospholipid biosynthetic process [Evidence IEA]
CDP-diacylglycerol--serine O-phosphatidyltransferase
COORDINATES: similar to AA sequence:RefSeq:WP_007641868.1
GO:0043546 - molybdopterin cofactor binding [Evidence IEA]; GO:0016667 - oxidoreductase activity, acting on a sulfur group of donors [Evidence IEA]
GO:0030091 - protein repair [Evidence IEA]
protein-methionine-sulfoxide reductase catalytic subunit MsrP
COORDINATES: similar to AA sequence:RefSeq:WP_020682591.1
protein-methionine-sulfoxide reductase heme-binding subunit MsrQ
COORDINATES: similar to AA sequence:RefSeq:WP_007021338.1
GO:0004129 - cytochrome-c oxidase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_010321597.1
COORDINATES: similar to AA sequence:RefSeq:WP_007021340.1
COORDINATES: similar to AA sequence:RefSeq:WP_010321595.1
COORDINATES: protein motif:HMM:NF022587.2
COORDINATES: protein motif:HMM:NF014193.2
COORDINATES: protein motif:HMM:NF014665.2
COORDINATES: similar to AA sequence:RefSeq:WP_007021346.1
GO:0008495 - protoheme IX farnesyltransferase activity [Evidence IEA]
GO:0006783 - heme biosynthetic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_007021347.1
16S ribosomal RNA rRNA prediction is too short