Candidatus Carsonella ruddii HC isolate Thao2000, complete sequence.
Candidatus Carsonella ruddii HC isolate Thao2000
Bacteria; Pseudomonadota; Gammaproteobacteria; Oceanospirillales; Halomonadaceae; Zymobacter group; Candidatus Carsonella.
Genome reduction and co-evolution between the primary and secondary bacterial symbionts of psyllids
Submitted (16-MAY-2012) Ecology and Evolutionary Biology, Yale University, 165 Prospect St, New Haven, CT 06520, USA
REFSEQ INFORMATION: The reference sequence is identical to\nCP003543.1.\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-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 04/17/2023 00:30:28\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) :: 219\nCDSs (total) :: 193\nGenes (coding) :: 192\nCDSs (with protein) :: 192\nGenes (RNA) :: 26\nrRNAs :: 1, 1 (16S, 23S)\ncomplete rRNAs :: 1, 1 (16S, 23S)\ntRNAs :: 24\nncRNAs :: 0\nPseudo Genes (total) :: 1\nCDSs (without protein) :: 1\nPseudo Genes (ambiguous residues) :: 0 of 1\nPseudo Genes (frameshifted) :: 0 of 1\nPseudo Genes (incomplete) :: 1 of 1\nPseudo Genes (internal stop) :: 0 of 1\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.
COORDINATES: protein motif:HMM:TIGR00231.1
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: protein motif:HMM:NF013314.2
COORDINATES: protein motif:HMM:NF012347.2
GO:0045263 - proton-transporting ATP synthase complex, coupling factor F(o) [Evidence IEA]
GO:0015078 - proton transmembrane transporter activity [Evidence IEA]
GO:0015986 - proton motive force-driven ATP synthesis [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_015482645.1
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: similar to AA sequence:RefSeq:WP_011672230.1
GO:0000275 - mitochondrial proton-transporting ATP synthase complex, catalytic sector F(1) [Evidence IEA]; GO:0045262 - plasma membrane proton-transporting ATP synthase complex, catalytic core F(1) [Evidence IEA]; GO:0045261 - proton-transporting ATP synthase complex, catalytic core F(1) [Evidence IEA]
GO:0046933 - proton-transporting ATP synthase activity, rotational mechanism [Evidence IEA]
COORDINATES: protein motif:HMM:NF012456.2
GO:0045261 - proton-transporting ATP synthase complex, catalytic core F(1) [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011672232.1
COORDINATES: protein motif:HMM:NF012412.2
COORDINATES: similar to AA sequence:RefSeq:WP_014895105.1
GO:0003855 - 3-dehydroquinate dehydratase activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF012670.2
ribonucleotide-diphosphate reductase subunit alpha
COORDINATES: protein motif:HMM:NF014296.2
GO:0004489 - methylenetetrahydrofolate reductase (NAD(P)H) activity [Evidence IEA]
GO:0006555 - methionine metabolic process [Evidence IEA]
Derived by automated computational analysis using gene prediction method: tRNAscan-SE.
COORDINATES: protein motif:HMM:NF025953.2
COORDINATES: protein motif:HMM:NF012538.2
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: protein motif:HMM:NF013891.2
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: protein motif:HMM:NF013847.2
5-methyltetrahydropteroyltriglutamate-- homocysteine S-methyltransferase
COORDINATES: protein motif:HMM:TIGR00105.1
GO:0022625 - cytosolic large ribosomal subunit [Evidence IEA]; GO:0000315 - organellar large ribosomal subunit [Evidence IEA]
COORDINATES: protein motif:HMM:NF013887.2
COORDINATES: similar to AA sequence:RefSeq:WP_020033699.1
COORDINATES: protein motif:HMM:NF000586.1
GO:0004372 - glycine hydroxymethyltransferase activity [Evidence IEA]
GO:0019264 - glycine biosynthetic process from serine [Evidence IEA]
COORDINATES: protein motif:HMM:NF012912.2
GO:0004019 - adenylosuccinate synthase activity [Evidence IEA]; GO:0005525 - GTP binding [Evidence IEA]
GO:0006164 - purine nucleotide biosynthetic process [Evidence IEA]
COORDINATES: protein motif:HMM:TIGR01980.1
GO:0005198 - structural molecule activity [Evidence IEA]
GO:0016226 - iron-sulfur cluster assembly [Evidence IEA]
COORDINATES: protein motif:HMM:NF012235.2
ATP-binding cassette domain-containing protein
COORDINATES: protein motif:HMM:NF012488.2
aminotransferase class V-fold PLP-dependent enzyme
COORDINATES: protein motif:HMM:NF015042.2
tRNA (5-methylaminomethyl-2-thiouridylate)-methyltransferase
COORDINATES: similar to AA sequence:RefSeq:WP_010893946.1
GO:0003743 - translation initiation factor activity [Evidence IEA]
GO:0006413 - translational initiation [Evidence IEA]
COORDINATES: protein motif:HMM:NF012611.2
GO:0050661 - NADP binding [Evidence IEA]
NAD(P)-binding domain-containing protein
COORDINATES: protein motif:HMM:NF012640.2
COORDINATES: protein motif:HMM:NF012345.2
Anthranilate/para-aminobenzoate synthase component II
COORDINATES: protein motif:HMM:TIGR01251.1
GO:0004749 - ribose phosphate diphosphokinase activity [Evidence IEA]
GO:0009152 - purine ribonucleotide biosynthetic process [Evidence IEA]
COORDINATES: protein motif:HMM:NF012684.2
GO:0003747 - translation release factor activity [Evidence IEA]
GO:0006415 - translational termination [Evidence IEA]
peptide chain release factor-like protein
COORDINATES: protein motif:HMM:NF014930.2
COORDINATES: protein motif:HMM:NF013584.2
COORDINATES: protein motif:HMM:NF013013.2
GO:0004399 - histidinol dehydrogenase activity [Evidence IEA]
GO:0000105 - histidine biosynthetic process [Evidence IEA]
COORDINATES: protein motif:HMM:NF012781.2
COORDINATES: protein motif:HMM:NF012598.2
COORDINATES: protein motif:HMM:NF012998.2
GO:0004664 - prephenate dehydratase activity [Evidence IEA]
GO:0009094 - L-phenylalanine biosynthetic process [Evidence IEA]
prephenate dehydratase domain-containing protein
COORDINATES: protein motif:HMM:NF012497.2
3-phosphoshikimate 1-carboxyvinyltransferase
COORDINATES: protein motif:HMM:NF012784.2
GO:0003676 - nucleic acid binding [Evidence IEA]
S1 RNA-binding domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_009724705.1
GO:0016887 - ATP hydrolysis activity [Evidence IEA]; GO:0005515 - protein binding [Evidence IEA]
GO:0006457 - protein folding [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; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: protein motif:HMM:NF012393.2
COORDINATES: protein motif:HMM:NF012797.2
GO:0003723 - RNA binding [Evidence IEA]; GO:0008173 - RNA methyltransferase activity [Evidence IEA]
GO:0006396 - RNA processing [Evidence IEA]
COORDINATES: protein motif:HMM:NF015736.2
DnaB-like helicase C-terminal domain-containing protein
COORDINATES: protein motif:HMM:NF024554.2
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:NF012382.2
GO:0030170 - pyridoxal phosphate binding [Evidence IEA]
GO:0009058 - biosynthetic process [Evidence IEA]
aminotransferase class I/II-fold pyridoxal phosphate-dependent enzyme
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: protein motif:HMM:NF012687.2
COORDINATES: protein motif:HMM:NF013804.2
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]
COORDINATES: similar to AA sequence:RefSeq:WP_013333913.1
GO:0005524 - ATP binding [Evidence IEA]; GO:0016887 - ATP hydrolysis activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF017024.2
GO:0008839 - 4-hydroxy-tetrahydrodipicolinate reductase [Evidence IEA]
GO:0009089 - lysine biosynthetic process via diaminopimelate [Evidence IEA]
dihydrodipicolinate reductase C-terminal domain-containing protein
COORDINATES: protein motif:HMM:NF013178.2
carbamoyl-phosphate synthase domain-containing protein
carbamoylphosphate synthase small subunit
COORDINATES: protein motif:HMM:NF003671.0
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: protein motif:HMM:NF012239.2
COORDINATES: protein motif:HMM:NF012788.2
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: similar to AA sequence:RefSeq:WP_011672295.1
GO:0004176 - ATP-dependent peptidase activity [Evidence IEA]; GO:0004252 - serine-type endopeptidase activity [Evidence IEA]
ATP-dependent Clp protease proteolytic subunit
COORDINATES: protein motif:HMM:NF003745.1
GO:0005524 - ATP binding [Evidence IEA]; GO:0016887 - ATP hydrolysis activity [Evidence IEA]; GO:0046983 - protein dimerization activity [Evidence IEA]; GO:0008270 - zinc ion binding [Evidence IEA]
ATP-dependent Clp protease ATP-binding subunit ClpX
COORDINATES: protein motif:HMM:NF024491.2
phospholipase D-like domain-containing protein
COORDINATES: protein motif:HMM:NF012379.2
COORDINATES: protein motif:HMM:NF013030.2
COORDINATES: protein motif:HMM:NF008869.0
GO:0003842 - 1-pyrroline-5-carboxylate dehydrogenase activity [Evidence IEA]; GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]; GO:0016620 - oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor [Evidence IEA]; GO:0004657 - proline dehydrogenase activity [Evidence IEA]
GO:0010133 - proline catabolic process to glutamate [Evidence IEA]; GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
bifunctional proline dehydrogenase/L-glutamate gamma-semialdehyde dehydrogenase PutA
COORDINATES: protein motif:HMM:NF012885.2
COORDINATES: similar to AA sequence:RefSeq:WP_015482452.1
GO:0004107 - chorismate synthase activity [Evidence IEA]
GO:0009073 - aromatic amino acid family biosynthetic process [Evidence IEA]
COORDINATES: protein motif:HMM:NF012550.2
COORDINATES: protein motif:HMM:TIGR00171.1
GO:0009316 - 3-isopropylmalate dehydratase complex [Evidence IEA]
GO:0003861 - 3-isopropylmalate dehydratase activity [Evidence IEA]
GO:0009098 - leucine biosynthetic process [Evidence IEA]
3-isopropylmalate dehydratase small subunit
COORDINATES: protein motif:HMM:NF012407.2
GO:0003862 - 3-isopropylmalate dehydrogenase activity [Evidence IEA]; GO:0046872 - metal ion binding [Evidence IEA]; GO:0051287 - NAD binding [Evidence IEA]
COORDINATES: protein motif:HMM:NF005144.0
COORDINATES: protein motif:HMM:NF012796.2
COORDINATES: protein motif:HMM:NF014688.2
COORDINATES: protein motif:HMM:NF013653.2
GO:0004635 - phosphoribosyl-AMP cyclohydrolase activity [Evidence IEA]
COORDINATES: protein motif:HMM:TIGR00573.1
GO:0004527 - exonuclease activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF012667.2
GO:0019843 - rRNA binding [Evidence IEA]; GO:0003735 - structural constituent of ribosome [Evidence IEA]
COORDINATES: protein motif:HMM:NF012910.2
COORDINATES: protein motif:HMM:NF014796.2
GO:0046872 - metal ion binding [Evidence IEA]; GO:0004784 - superoxide dismutase activity [Evidence IEA]
GO:0006801 - superoxide metabolic process [Evidence IEA]
COORDINATES: protein motif:HMM:NF014036.2
GO:0005525 - GTP binding [Evidence IEA]; GO:0003924 - GTPase activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF012991.2
GO:0003849 - 3-deoxy-7-phosphoheptulonate synthase activity [Evidence IEA]
GO:0009423 - chorismate biosynthetic process [Evidence IEA]
COORDINATES: protein motif:HMM:TIGR00089.1
GO:0051539 - 4 iron, 4 sulfur cluster binding [Evidence IEA]; GO:0008172 - S-methyltransferase activity [Evidence IEA]; GO:0016782 - transferase activity, transferring sulphur-containing groups [Evidence IEA]
MiaB/RimO family radical SAM methylthiotransferase
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:NF014666.2
Catalyzes the only substrate-level phosphorylation in the TCA cycle; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: protein motif:HMM:NF020031.2
COORDINATES: protein motif:HMM:NF020892.2
COORDINATES: similar to AA sequence:RefSeq:WP_011588009.1
GO:0004055 - argininosuccinate synthase activity [Evidence IEA]; GO:0005524 - ATP binding [Evidence IEA]
GO:0006526 - arginine biosynthetic process [Evidence IEA]
COORDINATES: protein motif:HMM:NF012904.2
GO:0016829 - lyase activity [Evidence IEA]
dihydrodipicolinate synthase family protein
COORDINATES: protein motif:HMM:NF017817.2
GO:0008924 - malate dehydrogenase (quinone) activity [Evidence IEA]
GO:0006099 - tricarboxylic acid cycle [Evidence IEA]
COORDINATES: protein motif:HMM:NF005155.0
GO:0004072 - aspartate kinase activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF013570.2
GO:0004813 - alanine-tRNA ligase activity [Evidence IEA]; GO:0005524 - ATP binding [Evidence IEA]; GO:0000166 - nucleotide binding [Evidence IEA]
GO:0006419 - alanyl-tRNA aminoacylation [Evidence IEA]
COORDINATES: protein motif:HMM:NF012381.2
COORDINATES: protein motif:HMM:NF012787.2
GO:0016209 - antioxidant activity [Evidence IEA]; GO:0016491 - oxidoreductase activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF013116.2
GO:0005975 - carbohydrate metabolic process [Evidence IEA]
COORDINATES: nucleotide motif:Rfam:14.4:RF02541
Derived by automated computational analysis using gene prediction method: cmsearch.
COORDINATES: nucleotide motif:Rfam:14.4:RF00177
COORDINATES: protein motif:HMM:TIGR01023.1
COORDINATES: protein motif:HMM:NF013026.2
COORDINATES: protein motif:HMM:NF015427.2
COORDINATES: protein motif:HMM:TIGR00260.1
GO:0004795 - threonine synthase activity [Evidence IEA]
GO:0009088 - threonine biosynthetic process [Evidence IEA]
COORDINATES: protein motif:HMM:NF012945.2
COORDINATES: similar to AA sequence:RefSeq:WP_004672686.1
COORDINATES: protein motif:HMM:NF014795.2
GO:0030976 - thiamine pyrophosphate binding [Evidence IEA]
COORDINATES: protein motif:HMM:NF013045.2
GO:0009982 - pseudouridine synthase activity [Evidence IEA]; GO:0003723 - RNA binding [Evidence IEA]
GO:0001522 - pseudouridine synthesis [Evidence IEA]; GO:0009451 - RNA modification [Evidence IEA]
COORDINATES: protein motif:HMM:NF013205.2
COORDINATES: similar to AA sequence:RefSeq:WP_014895017.1
COORDINATES: protein motif:HMM:NF013025.2
COORDINATES: protein motif:HMM:NF013189.2
GO:0003677 - DNA binding [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 alpha C-terminal domain-containing protein
COORDINATES: protein motif:HMM:NF003717.0
GO:0015935 - small ribosomal subunit [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011672360.1
COORDINATES: protein motif:HMM:NF012633.2
GO:0003723 - RNA binding [Evidence IEA]; GO:0003735 - structural constituent of ribosome [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_003720928.1
COORDINATES: similar to AA sequence:RefSeq:WP_014895008.1
COORDINATES: protein motif:HMM:NF015664.2
located at the back of the 30S subunit body where it stabilizes the conformation of the head with respect to the body; contacts S4 and S8; with S4 and S12 plays a role in translational accuracy; mutations in this gene result in spectinomycin resistance; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: protein motif:HMM:NF012627.2
COORDINATES: protein motif:HMM:NF012477.2
COORDINATES: protein motif:HMM:NF012877.2
COORDINATES: similar to AA sequence:RefSeq:WP_015817037.1
COORDINATES: protein motif:HMM:NF012586.2
COORDINATES: similar to AA sequence:RefSeq:WP_011672372.1
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_011137729.1
COORDINATES: similar to AA sequence:RefSeq:WP_011672376.1
COORDINATES: similar to AA sequence:RefSeq:WP_016856419.1
COORDINATES: protein motif:HMM:NF012518.2
incomplete; partial in the middle of a contig; missing C-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: protein motif:HMM:NF012558.2
COORDINATES: similar to AA sequence:RefSeq:WP_007112008.1
GO:0003746 - translation elongation factor activity [Evidence IEA]
GO:0006414 - translational elongation [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011672381.1
COORDINATES: protein motif:HMM:TIGR01029.1
COORDINATES: similar to AA sequence:RefSeq:WP_011672383.1
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]
DNA-directed RNA polymerase subunit beta'
COORDINATES: protein motif:HMM:TIGR02013.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0003899 - DNA-directed 5'-3' RNA polymerase activity [Evidence IEA]; GO:0032549 - ribonucleoside binding [Evidence IEA]
DNA-directed RNA polymerase subunit beta
COORDINATES: protein motif:HMM:NF012752.2
COORDINATES: protein motif:HMM:NF015879.2
cytochrome o ubiquinol oxidase subunit III
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
branched chain amino acid aminotransferase
COORDINATES: protein motif:HMM:TIGR00079.1
GO:0042586 - peptide deformylase activity [Evidence IEA]
GO:0036211 - protein modification process [Evidence IEA]
COORDINATES: protein motif:HMM:NF012432.2
COORDINATES: protein motif:HMM:NF012500.2
COORDINATES: protein motif:HMM:NF014182.2
GO:0005524 - ATP binding [Evidence IEA]; GO:0004820 - glycine-tRNA ligase activity [Evidence IEA]; GO:0000166 - nucleotide binding [Evidence IEA]
GO:0006426 - glycyl-tRNA aminoacylation [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_019019488.1
GO:0003676 - nucleic acid binding [Evidence IEA]; GO:0003723 - RNA binding [Evidence IEA]; GO:0001072 - transcription antitermination factor activity, RNA binding [Evidence IEA]