Candidatus Nasuia deltocephalinicola strain HICO chromosome.
Bacteria; Pseudomonadota; Betaproteobacteria; Candidatus Nasuia.
A complex interplay of evolutionary forces continues to shape ancient co-occurring symbiont genomes
Erratum:[iScience. 2022 Dec 24;26(1):105810. PMID: 36590156] Publication Status: Online-Only
Submitted (16-MAR-2022) Life and Environmental Sciences, University of California Merced, 5200 Lake Rd, Merced, CA 95340, USA
REFSEQ INFORMATION: The reference sequence is identical to\nCP094197.1.\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 :: SPAdes v. v3.14\nGenome Representation :: Full\nExpected Final Version :: Yes\nGenome Coverage :: 10x\nSequencing Technology :: Illumina MiSeq\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 03/20/2023 12:28:10\nAnnotation Pipeline :: NCBI Prokaryotic Genome Annotation\n Pipeline (PGAP)\nAnnotation Method :: Best-placed reference protein set;\n GeneMarkS-2+\nAnnotation Software revision :: 6.4\nFeatures Annotated :: Gene; CDS; rRNA; tRNA; ncRNA\nGenes (total) :: 160\nCDSs (total) :: 133\nGenes (coding) :: 133\nCDSs (with protein) :: 133\nGenes (RNA) :: 27\nrRNAs :: 1, 1 (16S, 23S)\ncomplete rRNAs :: 1, 1 (16S, 23S)\ntRNAs :: 24\nncRNAs :: 1\nPseudo Genes (total) :: 0\nCDSs (without protein) :: 0\n##Genome-Annotation-Data-END##
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: protein motif:HMM:TIGR00168.2
GO:0003743 - translation initiation factor activity [Evidence IEA]
GO:0006413 - translational initiation [Evidence IEA]
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:TIGR01032.1
GO:0022625 - cytosolic large ribosomal subunit [Evidence IEA]; GO:0000315 - organellar large ribosomal subunit [Evidence IEA]
GO:0003735 - structural constituent of ribosome [Evidence IEA]
COORDINATES: protein motif:HMM:NF013237.2
GO:0030170 - pyridoxal phosphate binding [Evidence IEA]
GO:0019346 - transsulfuration [Evidence IEA]
COORDINATES: protein motif:HMM:NF013212.2
GO:0000774 - adenyl-nucleotide exchange factor activity [Evidence IEA]; GO:0051087 - chaperone binding [Evidence IEA]; GO:0042803 - protein homodimerization activity [Evidence IEA]
GO:0006457 - protein folding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_015001665.1
GO:0005524 - ATP binding [Evidence IEA]; GO:0016887 - ATP hydrolysis activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF013705.2
COORDINATES: protein motif:HMM:NF013348.2
GO:0009055 - electron transfer activity [Evidence IEA]; GO:0020037 - heme binding [Evidence IEA]
COORDINATES: protein motif:HMM:NF015427.2
GO:0006415 - translational termination [Evidence IEA]
COORDINATES: protein motif:HMM:NF015559.2
COORDINATES: protein motif:HMM:NF012382.2
GO:0009058 - biosynthetic process [Evidence IEA]
aminotransferase class I/II-fold pyridoxal phosphate-dependent enzyme
COORDINATES: protein motif:HMM:NF013545.2
COORDINATES: protein motif:HMM:NF012379.2
GO:0003676 - nucleic acid binding [Evidence IEA]
COORDINATES: protein motif:HMM:NF012488.2
aminotransferase class V-fold PLP-dependent enzyme
COORDINATES: protein motif:HMM:NF012339.2
GO:0009055 - electron transfer activity [Evidence IEA]; GO:0051536 - iron-sulfur cluster binding [Evidence IEA]
2Fe-2S iron-sulfur cluster-binding protein
S1 RNA-binding domain-containing protein
COORDINATES: protein motif:HMM:NF012951.2
GO:0004812 - aminoacyl-tRNA ligase activity [Evidence IEA]; GO:0005524 - ATP binding [Evidence IEA]
GO:0043039 - tRNA aminoacylation [Evidence IEA]
COORDINATES: protein motif:HMM:NF013259.2
COORDINATES: protein motif:HMM:NF013658.2
GO:0003824 - catalytic activity [Evidence IEA]
phosphoadenosine phosphosulfate reductase family protein
COORDINATES: protein motif:HMM:NF015983.2
GO:0003824 - catalytic activity [Evidence IEA]; GO:0051536 - iron-sulfur cluster binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_013315494.1
COORDINATES: protein motif:HMM:NF012361.2
GO:0004812 - aminoacyl-tRNA ligase activity [Evidence IEA]; GO:0005524 - ATP binding [Evidence IEA]; GO:0000166 - nucleotide binding [Evidence IEA]
GO:0006418 - tRNA aminoacylation for protein translation [Evidence IEA]
COORDINATES: protein motif:HMM:NF013117.2
GO:0055085 - transmembrane transport [Evidence IEA]
COORDINATES: protein motif:HMM:NF013026.2
COORDINATES: protein motif:HMM:NF013804.2
COORDINATES: similar to AA sequence:RefSeq:WP_003448628.1
GO:0004252 - serine-type endopeptidase activity [Evidence IEA]
ATP-dependent Clp protease proteolytic subunit
COORDINATES: protein motif:HMM:NF019344.2
COORDINATES: protein motif:HMM:NF014296.2
GO:0004489 - methylenetetrahydrofolate reductase (NAD(P)H) activity [Evidence IEA]
GO:0006555 - methionine metabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_006478030.1
COORDINATES: nucleotide motif:Rfam:14.4:RF00023
COORDINATES: protein motif:HMM:NF003556.0
GO:0003871 - 5-methyltetrahydropteroyltriglutamate-homocysteine S-methyltransferase activity [Evidence IEA]; GO:0008270 - zinc ion binding [Evidence IEA]
GO:0008652 - amino acid biosynthetic process [Evidence IEA]; GO:0009086 - methionine biosynthetic process [Evidence IEA]
5-methyltetrahydropteroyltriglutamate-- homocysteine S-methyltransferase
COORDINATES: protein motif:HMM:TIGR00594.1
GO:0009360 - DNA polymerase III complex [Evidence IEA]
GO:0003887 - DNA-directed DNA polymerase activity [Evidence IEA]
GO:0006260 - DNA replication [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_013315413.1
GO:0022627 - cytosolic small ribosomal subunit [Evidence IEA]; GO:0000314 - organellar small ribosomal subunit [Evidence IEA]
COORDINATES: protein motif:HMM:NF013414.2
COORDINATES: protein motif:HMM:TIGR02937.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]; GO:0016987 - sigma factor activity [Evidence IEA]
GO:0006352 - DNA-templated transcription initiation [Evidence IEA]; GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
sigma-70 family RNA polymerase sigma factor
COORDINATES: protein motif:HMM:NF014681.2
GO:0003933 - GTP cyclohydrolase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_015238149.1
COORDINATES: protein motif:HMM:NF013205.2
COORDINATES: similar to AA sequence:RefSeq:WP_018149453.1
COORDINATES: protein motif:HMM:TIGR00061.1
GO:0022625 - cytosolic large ribosomal subunit [Evidence IEA]; GO:0000311 - plastid large ribosomal subunit [Evidence IEA]
GO:0020037 - heme binding [Evidence IEA]
GO:0017004 - cytochrome complex assembly [Evidence IEA]
COORDINATES: protein motif:HMM:TIGR01011.1
COORDINATES: protein motif:HMM:NF013891.2
COORDINATES: protein motif:HMM:NF012343.2
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:NF012344.2
COORDINATES: protein motif:HMM:TIGR01258.1
GO:0004619 - phosphoglycerate mutase activity [Evidence IEA]
GO:0006096 - glycolytic process [Evidence IEA]
2,3-bisphosphoglycerate-dependent phosphoglycerate mutase
COORDINATES: similar to AA sequence:RefSeq:WP_015237826.1
GO:0016887 - ATP hydrolysis activity [Evidence IEA]; GO:0005515 - protein binding [Evidence IEA]
60 kDa chaperone family; promotes refolding of misfolded polypeptides especially under stressful conditions; forms two stacked rings of heptamers to form a barrel-shaped 14mer; ends can be capped by GroES; misfolded proteins enter the barrel where they are refolded when GroES binds; 60 kDa chaperone family; promotes refolding of misfolded polypeptides especially under stressful conditions; forms two stacked rings of heptamers to form a barrel-shaped 14mer; ends can be capped by GroES; misfolded proteins enter the barrel where they are refolded when GroES binds; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: protein motif:HMM:NF014036.2
COORDINATES: protein motif:HMM:TIGR00621.2
GO:0003697 - single-stranded DNA binding [Evidence IEA]
GO:0006310 - DNA recombination [Evidence IEA]; GO:0006281 - DNA repair [Evidence IEA]; GO:0006260 - DNA replication [Evidence IEA]; GO:0006351 - DNA-templated transcription [Evidence IEA]
COORDINATES: protein motif:HMM:TIGR00952.1
COORDINATES: protein motif:HMM:NF012314.2
COORDINATES: protein motif:HMM:TIGR00665.1
GO:0003678 - DNA helicase activity [Evidence IEA]
GO:0019843 - rRNA binding [Evidence IEA]; GO:0003735 - structural constituent of ribosome [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_015482514.1
GO:0022625 - cytosolic large ribosomal subunit [Evidence IEA]; GO:0005762 - mitochondrial large ribosomal subunit [Evidence IEA]
COORDINATES: protein motif:HMM:NF013189.2
COORDINATES: protein motif:HMM:NF003717.0
GO:0015935 - small ribosomal subunit [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_004074888.1
COORDINATES: similar to AA sequence:RefSeq:WP_014353970.1
GO:0003723 - RNA binding [Evidence IEA]; GO:0003735 - structural constituent of ribosome [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_006232360.1
COORDINATES: protein motif:HMM:NF013352.2
COORDINATES: protein motif:HMM:TIGR01071.1
COORDINATES: protein motif:HMM:NF015664.2
COORDINATES: protein motif:HMM:NF012567.2
COORDINATES: protein motif:HMM:NF012627.2
COORDINATES: similar to AA sequence:RefSeq:WP_013315389.1
COORDINATES: protein motif:HMM:NF012877.2
COORDINATES: similar to AA sequence:RefSeq:WP_013315392.1
COORDINATES: similar to AA sequence:RefSeq:WP_007475801.1
COORDINATES: protein motif:HMM:TIGR01009.1
GO:0022627 - cytosolic small ribosomal subunit [Evidence IEA]; GO:0000312 - plastid small ribosomal subunit [Evidence IEA]
COORDINATES: protein motif:HMM:NF012462.2
COORDINATES: similar to AA sequence:RefSeq:WP_007069899.1
COORDINATES: protein motif:HMM:TIGR01171.1
COORDINATES: protein motif:HMM:NF012782.2
COORDINATES: similar to AA sequence:RefSeq:WP_013315400.1
COORDINATES: protein motif:HMM:TIGR01049.1
COORDINATES: similar to AA sequence:RefSeq:WP_013315403.1
GO:0003746 - translation elongation factor activity [Evidence IEA]
GO:0006414 - translational elongation [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_013315404.1
COORDINATES: similar to AA sequence:RefSeq:WP_011091579.1
COORDINATES: protein motif:HMM:TIGR02386.1
GO:0000345 - cytosolic DNA-directed RNA polymerase complex [Evidence IEA]
GO:0003899 - DNA-directed 5'-3' RNA polymerase activity [Evidence IEA]
GO:0006351 - DNA-templated transcription [Evidence IEA]
DNA-directed RNA polymerase subunit beta'
COORDINATES: protein motif:HMM:NF012771.2
COORDINATES: protein motif:HMM:NF012752.2
COORDINATES: protein motif:HMM:NF015879.2
binds directly to 23S ribosomal RNA; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_011793521.1
COORDINATES: protein motif:HMM:NF013653.2
GO:0004635 - phosphoribosyl-AMP cyclohydrolase activity [Evidence IEA]
GO:0000105 - histidine biosynthetic process [Evidence IEA]
COORDINATES: protein motif:HMM:NF013168.2
COORDINATES: protein motif:HMM:TIGR01855.1
GO:0016884 - carbon-nitrogen ligase activity, with glutamine as amido-N-donor [Evidence IEA]; GO:0000107 - imidazoleglycerol-phosphate synthase activity [Evidence IEA]
imidazole glycerol phosphate synthase subunit HisH
COORDINATES: similar to AA sequence:RefSeq:WP_013315365.1
catalyzes the dehydration of D-erythro-1-(imidazol-4-yl)glycerol 3-phosphate to 3-(imidazol-4-yl)-2-oxopropyl phosphate in histidine biosynthesis; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: protein motif:HMM:NF013013.2
GO:0004399 - histidinol dehydrogenase activity [Evidence IEA]
COORDINATES: protein motif:HMM:TIGR00070.1
GO:0003879 - ATP phosphoribosyltransferase activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF021882.2
COORDINATES: protein motif:HMM:NF012796.2
GO:0016491 - oxidoreductase activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF012881.2
COORDINATES: protein motif:HMM:NF001099.0
COORDINATES: protein motif:HMM:NF012781.2
COORDINATES: protein motif:HMM:NF015414.2
GO:0032784 - regulation of DNA-templated transcription elongation [Evidence IEA]
COORDINATES: protein motif:HMM:TIGR00573.1
GO:0004527 - exonuclease activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF013314.2
COORDINATES: protein motif:HMM:NF013584.2
COORDINATES: protein motif:HMM:NF014930.2