Lichenicola cladoniae strain PAMC 26569 plasmid unnamed5, complete sequence.
Bacteria; Pseudomonadota; Alphaproteobacteria; Rhodospirillales; Acetobacteraceae; Lichenicola.
Biodiversity and physiological characteristics of Antarctic and Arctic lichens-associated bacteria
Submitted (19-MAY-2020) Division of Polar Life Sciences, Korea Polar Research institute, 26 Songdomirae-ro, Incheon 21990, South Korea
REFSEQ INFORMATION: The reference sequence is identical to\nCP053712.1.\nBacteria and source DNA available from PAMC, Korea Polar Research\nInstitute.\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 assembler v. v0.4.8\nAssembly Name :: KOPRI_Lcla_1.1\nGenome Representation :: Full\nExpected Final Version :: Yes\nGenome Coverage :: 516.0x\nSequencing Technology :: Illumina MiSeq; Oxford Nanopore\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 03/12/2023 06:14:38\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) :: 5,687\nCDSs (total) :: 5,624\nGenes (coding) :: 5,398\nCDSs (with protein) :: 5,398\nGenes (RNA) :: 63\nrRNAs :: 3, 3, 3 (5S, 16S, 23S)\ncomplete rRNAs :: 3, 3, 3 (5S, 16S, 23S)\ntRNAs :: 50\nncRNAs :: 4\nPseudo Genes (total) :: 226\nCDSs (without protein) :: 226\nPseudo Genes (ambiguous residues) :: 0 of 226\nPseudo Genes (frameshifted) :: 81 of 226\nPseudo Genes (incomplete) :: 148 of 226\nPseudo Genes (internal stop) :: 71 of 226\nPseudo Genes (multiple problems) :: 63 of 226\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.
type strain of Lichenicola cladoniae Noh et al. 2020
COORDINATES: similar to AA sequence:RefSeq:WP_007397622.1
frameshifted; internal stop; 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_006559211.1
GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]
GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: protein motif:HMM:NF020431.2
COORDINATES: similar to AA sequence:RefSeq:WP_011578756.1
GO:0004803 - transposase activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF024997.2
DDE-type integrase/transposase/recombinase
COORDINATES: similar to AA sequence:RefSeq:WP_012090769.1
GO:1904680 - peptide transmembrane transporter activity [Evidence IEA]
GO:0015833 - peptide transport [Evidence IEA]
internal stop; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: protein motif:HMM:NF012570.2
COORDINATES: nucleotide motif:Rfam:14.4:RF01734
Fluoride riboswitches increase expression of downstream genes that help mitigate the toxic effects of very high levels of fluoride; They are found in a wide variety of bacteria and archaea; Derived by automated computational analysis using gene prediction method: cmsearch.
COORDINATES: similar to AA sequence:RefSeq:WP_008616897.1
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:NF012791.2
COORDINATES: similar to AA sequence:RefSeq:WP_012494831.1
COORDINATES: similar to AA sequence:RefSeq:WP_015765791.1
frameshifted; 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_076612038.1
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: similar to AA sequence:RefSeq:WP_013183171.1
programmed frameshift; internal stop; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_012813138.1
COORDINATES: similar to AA sequence:RefSeq:WP_013121859.1
COORDINATES: similar to AA sequence:RefSeq:WP_076611370.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0004803 - transposase activity [Evidence IEA]
GO:0006313 - transposition, DNA-mediated [Evidence IEA]
frameshifted; 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:NF013677.2
COORDINATES: similar to AA sequence:RefSeq:WP_011749831.1
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_008604015.1
COORDINATES: protein motif:HMM:NF024954.2
winged helix-turn-helix domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_013653982.1
PLP-dependent aminotransferase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_012250240.1
GO:0004420 - hydroxymethylglutaryl-CoA reductase (NADPH) activity [Evidence IEA]
GO:0016054 - organic acid catabolic process [Evidence IEA]
hydroxymethylglutaryl-CoA reductase, degradative
COORDINATES: similar to AA sequence:RefSeq:WP_013538552.1
COORDINATES: similar to AA sequence:RefSeq:WP_006384250.1
tripartite tricarboxylate transporter permease
COORDINATES: similar to AA sequence:RefSeq:WP_014241698.1
COORDINATES: similar to AA sequence:RefSeq:WP_020479339.1
frameshifted; internal stop; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_009764868.1
COORDINATES: similar to AA sequence:RefSeq:WP_011853792.1
GO:0015562 - efflux transmembrane transporter activity [Evidence IEA]; GO:0008324 - monoatomic cation transmembrane transporter activity [Evidence IEA]
GO:0006812 - monoatomic cation transport [Evidence IEA]
incomplete; partial in the middle of a contig; missing N-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
cation diffusion facilitator family transporter
COORDINATES: protein motif:HMM:NF019604.2
COORDINATES: similar to AA sequence:RefSeq:WP_006578978.1
Lrp/AsnC family transcriptional regulator
COORDINATES: protein motif:HMM:NF040386.1
COORDINATES: similar to AA sequence:RefSeq:WP_011979499.1
COORDINATES: similar to AA sequence:RefSeq:WP_004624790.1
GO:0015079 - potassium ion transmembrane transporter activity [Evidence IEA]
incomplete; partial in the middle of a contig; missing N-terminus and C-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_076612008.1
COORDINATES: protein motif:HMM:NF012772.2
COORDINATES: similar to AA sequence:RefSeq:WP_012606398.1
internal stop; 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_032489531.1
COORDINATES: similar to AA sequence:RefSeq:WP_076612082.1
COORDINATES: protein motif:HMM:TIGR04416.1
GO:0003964 - RNA-directed DNA polymerase activity [Evidence IEA]
GO:0000373 - Group II intron splicing [Evidence IEA]
group II intron reverse transcriptase/maturase
COORDINATES: protein motif:HMM:NF024950.2
COORDINATES: protein motif:HMM:NF019268.2
COORDINATES: protein motif:HMM:NF011342.0
COORDINATES: similar to AA sequence:RefSeq:WP_011930762.1
GO:0031004 - potassium ion-transporting ATPase complex [Evidence IEA]
GO:0008556 - P-type potassium transmembrane transporter activity [Evidence IEA]
GO:0006813 - potassium ion transport [Evidence IEA]
potassium-transporting ATPase subunit KdpA
COORDINATES: similar to AA sequence:RefSeq:WP_011941713.1
potassium-transporting ATPase subunit KdpB
COORDINATES: similar to AA sequence:RefSeq:WP_011511411.1
potassium-transporting ATPase subunit KdpC
COORDINATES: similar to AA sequence:RefSeq:WP_013639826.1
COORDINATES: similar to AA sequence:RefSeq:WP_007667949.1
COORDINATES: similar to AA sequence:RefSeq:WP_076611774.1
programmed frameshift; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: protein motif:HMM:NF041492.1
COORDINATES: protein motif:HMM:NF039803.1
COORDINATES: similar to AA sequence:RefSeq:WP_014246666.1
helix-turn-helix domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_014242659.1
COORDINATES: similar to AA sequence:RefSeq:WP_015026468.1
COORDINATES: similar to AA sequence:RefSeq:WP_076611116.1
COORDINATES: similar to AA sequence:RefSeq:WP_010512535.1
COORDINATES: similar to AA sequence:RefSeq:WP_076612341.1
COORDINATES: similar to AA sequence:RefSeq:WP_032490240.1
COORDINATES: similar to AA sequence:RefSeq:WP_008604018.1
COORDINATES: protein motif:HMM:TIGR00180.1
GO:0007059 - chromosome segregation [Evidence IEA]; GO:0000910 - cytokinesis [Evidence IEA]
ParB/RepB/Spo0J family partition protein
COORDINATES: protein motif:HMM:NF025001.2
COORDINATES: similar to AA sequence:RefSeq:WP_076611187.1
COORDINATES: protein motif:HMM:NF013793.2
COORDINATES: similar to AA sequence:RefSeq:WP_012753711.1
frameshifted; internal stop; 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_011941969.1
GO:0016491 - oxidoreductase activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF016670.2
COORDINATES: similar to AA sequence:RefSeq:WP_011788482.1
COORDINATES: similar to AA sequence:RefSeq:WP_018067884.1
COORDINATES: similar to AA sequence:RefSeq:WP_011930841.1
COORDINATES: similar to AA sequence:RefSeq:WP_007424906.1
GO:0015074 - DNA integration [Evidence IEA]
COORDINATES: protein motif:HMM:NF015736.2
GO:0005524 - ATP binding [Evidence IEA]; GO:0003678 - DNA helicase activity [Evidence IEA]
GO:0006260 - DNA replication [Evidence IEA]
DnaB-like helicase C-terminal domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_014006133.1
carboxymuconolactone decarboxylase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_011492338.1
helix-turn-helix transcriptional regulator
COORDINATES: protein motif:HMM:NF013584.2
COORDINATES: similar to AA sequence:RefSeq:WP_076611275.1
COORDINATES: similar to AA sequence:RefSeq:WP_015004571.1
COORDINATES: similar to AA sequence:RefSeq:WP_009570229.1
COORDINATES: similar to AA sequence:RefSeq:WP_011389115.1
COORDINATES: similar to AA sequence:RefSeq:WP_008075056.1
GO:0004371 - glycerone kinase activity [Evidence IEA]
GO:0006071 - glycerol metabolic process [Evidence IEA]
COORDINATES: protein motif:HMM:NF016114.2
GO:0030246 - carbohydrate binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_032489185.1
GO:0018786 - haloalkane dehalogenase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_020812778.1
COORDINATES: similar to AA sequence:RefSeq:WP_018328875.1
COORDINATES: similar to AA sequence:RefSeq:WP_003187175.1
NAD-dependent succinate-semialdehyde dehydrogenase
COORDINATES: similar to AA sequence:RefSeq:WP_076611653.1
COORDINATES: similar to AA sequence:RefSeq:WP_015932790.1
COORDINATES: similar to AA sequence:RefSeq:WP_008041916.1
GO:0051920 - peroxiredoxin activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF013228.2
COORDINATES: similar to AA sequence:RefSeq:WP_004273022.1
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_011504024.1
COORDINATES: similar to AA sequence:RefSeq:WP_014106103.1
COORDINATES: similar to AA sequence:RefSeq:WP_076611908.1
COORDINATES: protein motif:HMM:NF024729.2
COORDINATES: similar to AA sequence:RefSeq:WP_076611227.1
COORDINATES: protein motif:HMM:TIGR00254.1
GO:0009975 - cyclase activity [Evidence IEA]
GO:0009966 - regulation of signal transduction [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_019461632.1
GO:0005524 - ATP binding [Evidence IEA]; GO:0003677 - DNA binding [Evidence IEA]; GO:0016787 - hydrolase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_007918191.1
COORDINATES: similar to AA sequence:RefSeq:WP_004522987.1
COORDINATES: similar to AA sequence:RefSeq:WP_013211161.1
frameshifted; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: protein motif:HMM:NF015431.2
COORDINATES: similar to AA sequence:RefSeq:WP_014439060.1
COORDINATES: protein motif:HMM:NF012334.2
SDR family NAD(P)-dependent oxidoreductase
COORDINATES: similar to AA sequence:RefSeq:WP_007407087.1
COORDINATES: similar to AA sequence:RefSeq:WP_008068760.1
COORDINATES: protein motif:HMM:TIGR00229.1
COORDINATES: protein motif:HMM:NF033579.1
COORDINATES: protein motif:HMM:NF012792.2
COORDINATES: protein motif:HMM:NF019205.2
COORDINATES: similar to AA sequence:RefSeq:WP_076611563.1
COORDINATES: similar to AA sequence:RefSeq:WP_020289714.1
COORDINATES: similar to AA sequence:RefSeq:WP_011983039.1
COORDINATES: similar to AA sequence:RefSeq:WP_076611756.1
frameshifted; incomplete; partial in the middle of a contig; missing N-terminus and C-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_009565148.1
COORDINATES: similar to AA sequence:RefSeq:WP_007819645.1
COORDINATES: similar to AA sequence:RefSeq:WP_016555716.1
ATP-binding cassette domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_016555717.1
sugar ABC transporter substrate-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_008911565.1
substrate-binding domain-containing protein
COORDINATES: protein motif:HMM:NF024298.2
COORDINATES: similar to AA sequence:RefSeq:WP_017506642.1