Lichenicola cladoniae strain PAMC 26569 plasmid unnamed4, 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\nCP053711.1.\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: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: similar to AA sequence:RefSeq:WP_013641047.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0000150 - DNA strand exchange activity [Evidence IEA]
GO:0006310 - DNA recombination [Evidence IEA]
frameshifted; internal stop; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: protein motif:HMM:NF025056.2
Derived by automated computational analysis using gene prediction method: Protein Homology.
toll/interleukin-1 receptor domain-containing protein
COORDINATES: protein motif:HMM:NF020509.2
COORDINATES: similar to AA sequence:RefSeq:WP_014747774.1
internal stop; Derived by automated computational analysis using gene prediction method: Protein Homology.
class I SAM-dependent DNA methyltransferase
COORDINATES: protein motif:HMM:NF017524.2
plasmid mobilization relaxosome protein MobC
COORDINATES: similar to AA sequence:RefSeq:WP_008832815.1
putative addiction module antidote protein
COORDINATES: similar to AA sequence:RefSeq:WP_004089252.1
frameshifted; Derived by automated computational analysis using gene prediction method: Protein Homology.
type II toxin-antitoxin system RelE/ParE family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_012319467.1
COORDINATES: protein motif:HMM:NF024554.2
DUF3991 and TOPRIM domain-containing protein
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:NF013793.2
COORDINATES: similar to AA sequence:RefSeq:WP_011251433.1
COORDINATES: protein motif:HMM:NF013828.2
COORDINATES: similar to AA sequence:RefSeq:WP_012814292.1
GO:0004803 - transposase activity [Evidence IEA]
COORDINATES: protein motif:HMM:TIGR00305.1
GO:0004521 - endoribonuclease activity [Evidence IEA]; GO:0005515 - protein binding [Evidence IEA]
putative toxin-antitoxin system toxin component, PIN family
COORDINATES: similar to AA sequence:RefSeq:WP_011446704.1
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_011388434.1
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: protein motif:HMM:NF015431.2
COORDINATES: similar to AA sequence:RefSeq:WP_018273518.1
GO:0005215 - transporter activity [Evidence IEA]
efflux RND transporter periplasmic adaptor subunit
COORDINATES: similar to AA sequence:RefSeq:WP_018641388.1
GO:0022857 - transmembrane transporter activity [Evidence IEA]
GO:0055085 - transmembrane transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_009476145.1
incomplete; partial in the middle of a contig; missing N-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
DDE-type integrase/transposase/recombinase
COORDINATES: similar to AA sequence:RefSeq:WP_006116974.1
COORDINATES: similar to AA sequence:RefSeq:WP_020095831.1
COORDINATES: protein motif:HMM:NF013982.2
COORDINATES: similar to AA sequence:RefSeq:WP_019403429.1
COORDINATES: similar to AA sequence:RefSeq:WP_007396398.1
COORDINATES: similar to AA sequence:RefSeq:WP_012553267.1
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_014327616.1
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_012553437.1
COORDINATES: similar to AA sequence:RefSeq:WP_006496050.1
COORDINATES: similar to AA sequence:RefSeq:WP_007421931.1
COORDINATES: similar to AA sequence:RefSeq:WP_011355963.1
sugar ABC transporter ATP-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_007424716.1
ABC transporter substrate-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_076612038.1
COORDINATES: similar to AA sequence:RefSeq:WP_014787089.1
GO:0004553 - hydrolase activity, hydrolyzing O-glycosyl compounds [Evidence IEA]
GO:0071704 - organic substance metabolic process [Evidence IEA]
COORDINATES: protein motif:HMM:NF013752.2
GO:0003677 - DNA binding [Evidence IEA]; GO:0004803 - transposase activity [Evidence IEA]
GO:0006313 - transposition, DNA-mediated [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011385685.1
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_012329765.1
COORDINATES: protein motif:HMM:NF024997.2
COORDINATES: similar to AA sequence:RefSeq:WP_007733930.1
COORDINATES: similar to AA sequence:RefSeq:WP_011238416.1
helix-turn-helix domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_007817228.1
substrate-binding 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_016555716.1
ATP-binding cassette domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_007819645.1
COORDINATES: similar to AA sequence:RefSeq:WP_009565148.1
COORDINATES: similar to AA sequence:RefSeq:WP_076611653.1
COORDINATES: similar to AA sequence:RefSeq:WP_012336480.1
COORDINATES: similar to AA sequence:RefSeq:WP_004271443.1
COORDINATES: protein motif:HMM:NF033516.0
COORDINATES: similar to AA sequence:RefSeq:WP_014330531.1
COORDINATES: similar to AA sequence:RefSeq:WP_076611638.1
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:NF024260.2
COORDINATES: similar to AA sequence:RefSeq:WP_004271876.1
COORDINATES: similar to AA sequence:RefSeq:WP_012385537.1
GO:0000160 - phosphorelay signal transduction system [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_013693685.1
COORDINATES: protein motif:HMM:NF015735.2
COORDINATES: protein motif:HMM:NF016494.2
GO:0016747 - acyltransferase activity, transferring groups other than amino-acyl groups [Evidence IEA]
GO:0009245 - lipid A biosynthetic process [Evidence IEA]
LpxD N-terminal domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_076611563.1
frameshifted; incomplete; partial in the middle of a contig; missing N-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
integrase core domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_011090936.1
COORDINATES: similar to AA sequence:RefSeq:WP_014528793.1
COORDINATES: protein motif:HMM:NF012772.2
COORDINATES: similar to AA sequence:RefSeq:WP_012881221.1
COORDINATES: similar to AA sequence:RefSeq:WP_008138537.1
TetR/AcrR family transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_008138538.1
COORDINATES: protein motif:HMM:NF018717.2
COORDINATES: similar to AA sequence:RefSeq:WP_008995161.1
COORDINATES: similar to AA sequence:RefSeq:WP_076612204.1
COORDINATES: similar to AA sequence:RefSeq:WP_012553362.1
COORDINATES: similar to AA sequence:RefSeq:WP_012973766.1
COORDINATES: similar to AA sequence:RefSeq:WP_007558530.1
COORDINATES: similar to AA sequence:RefSeq:WP_015686297.1
GO:0003697 - single-stranded DNA binding [Evidence IEA]
GO:0006974 - cellular response to DNA damage stimulus [Evidence IEA]; GO:0018142 - protein-DNA covalent cross-linking [Evidence IEA]
SOS response-associated peptidase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_012046560.1
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_008956838.1
COORDINATES: protein motif:HMM:NF013677.2
COORDINATES: similar to AA sequence:RefSeq:WP_014106103.1
COORDINATES: similar to AA sequence:RefSeq:WP_006966249.1
COORDINATES: similar to AA sequence:RefSeq:WP_010186313.1
COORDINATES: similar to AA sequence:RefSeq:WP_012275061.1
COORDINATES: protein motif:HMM:NF012580.2
histidine kinase dimerization/phosphoacceptor domain -containing protein
COORDINATES: protein motif:HMM:NF014626.2
COORDINATES: similar to AA sequence:RefSeq:WP_076612082.1
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_076611352.1
COORDINATES: similar to AA sequence:RefSeq:WP_012044998.1
GO:0004673 - protein histidine kinase activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF012301.2
COORDINATES: similar to AA sequence:RefSeq:WP_076611416.1
programmed frameshift; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_012330596.1
COORDINATES: similar to AA sequence:RefSeq:WP_012708515.1
COORDINATES: similar to AA sequence:RefSeq:WP_016919754.1
COORDINATES: similar to AA sequence:RefSeq:WP_012468524.1
COORDINATES: similar to AA sequence:RefSeq:WP_003623877.1
COORDINATES: similar to AA sequence:RefSeq:WP_008604015.1
COORDINATES: protein motif:HMM:NF013188.2
GO:0006812 - monoatomic cation transport [Evidence IEA]; GO:0055085 - transmembrane transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_008604018.1
COORDINATES: similar to AA sequence:RefSeq:WP_032490240.1
COORDINATES: similar to AA sequence:RefSeq:WP_003619144.1
COORDINATES: similar to AA sequence:RefSeq:WP_019088885.1
GO:0005886 - plasma membrane [Evidence IEA]
GO:0009410 - response to xenobiotic stimulus [Evidence IEA]; GO:0006855 - xenobiotic transmembrane transport [Evidence IEA]
DHA2 family efflux MFS transporter permease subunit
COORDINATES: similar to AA sequence:RefSeq:WP_011631761.1
COORDINATES: similar to AA sequence:RefSeq:WP_010164932.1
class III extradiol ring-cleavage dioxygenase
COORDINATES: similar to AA sequence:RefSeq:WP_011631763.1
COORDINATES: similar to AA sequence:RefSeq:WP_007590565.1
COORDINATES: similar to AA sequence:RefSeq:WP_019462891.1
helix-turn-helix transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_018059818.1
COORDINATES: protein motif:HMM:NF025167.2
COORDINATES: similar to AA sequence:RefSeq:WP_012115713.1
COORDINATES: similar to AA sequence:RefSeq:WP_008491906.1
COORDINATES: similar to AA sequence:RefSeq:WP_009797884.1
COORDINATES: similar to AA sequence:RefSeq:WP_010219427.1
COORDINATES: protein motif:HMM:NF018455.2
COORDINATES: similar to AA sequence:RefSeq:WP_010164961.1
HAMP domain-containing sensor histidine kinase
COORDINATES: protein motif:HMM:NF024883.2
COORDINATES: similar to AA sequence:RefSeq:WP_009764868.1
COORDINATES: similar to AA sequence:RefSeq:WP_011112544.1
COORDINATES: protein motif:HMM:NF012655.2
COORDINATES: similar to AA sequence:RefSeq:WP_007666847.1
COORDINATES: similar to AA sequence:RefSeq:WP_011252353.1
COORDINATES: similar to AA sequence:RefSeq:WP_018425141.1
GO:0009279 - cell outer membrane [Evidence IEA]
GO:0015288 - porin activity [Evidence IEA]
efflux transporter outer membrane subunit
COORDINATES: protein motif:HMM:NF012334.2
SDR family NAD(P)-dependent oxidoreductase
COORDINATES: protein motif:HMM:NF024701.2
COORDINATES: similar to AA sequence:RefSeq:WP_076611187.1
COORDINATES: similar to AA sequence:RefSeq:WP_009734117.1
COORDINATES: similar to AA sequence:RefSeq:WP_018389185.1
COORDINATES: similar to AA sequence:RefSeq:WP_013581063.1
COORDINATES: protein motif:HMM:NF033517.1
COORDINATES: protein motif:HMM:TIGR02292.1
COORDINATES: similar to AA sequence:RefSeq:WP_013516321.1
COORDINATES: protein motif:HMM:NF013117.2
COORDINATES: similar to AA sequence:RefSeq:WP_009805248.1
COORDINATES: similar to AA sequence:RefSeq:WP_019463126.1
COORDINATES: similar to AA sequence:RefSeq:WP_012520250.1
lytic transglycosylase domain-containing protein
COORDINATES: protein motif:HMM:NF016820.2
COORDINATES: similar to AA sequence:RefSeq:WP_012520252.1
COORDINATES: similar to AA sequence:RefSeq:WP_011578794.1
VirB4 family type IV secretion/conjugal transfer ATPase
COORDINATES: protein motif:HMM:NF019608.2
COORDINATES: protein motif:HMM:NF033894.1
COORDINATES: protein motif:HMM:NF016491.2
COORDINATES: protein motif:HMM:NF016238.2
COORDINATES: protein motif:HMM:NF015487.2
P-type conjugative transfer protein VirB9
COORDINATES: protein motif:HMM:NF038091.1
COORDINATES: similar to AA sequence:RefSeq:WP_003170556.1
GO:0043684 - type IV secretion system complex [Evidence IEA]
GO:0044097 - secretion by the type IV secretion system [Evidence IEA]
COORDINATES: protein motif:HMM:NF014581.2
type IV secretory system conjugative DNA transfer family protein
COORDINATES: protein motif:HMM:NF037421.2
COORDINATES: protein motif:HMM:NF015397.2
relaxase/mobilization nuclease domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_006831738.1
COORDINATES: protein motif:HMM:NF039499.1
COORDINATES: protein motif:HMM:NF014021.2
nucleotidyltransferase domain-containing protein
COORDINATES: protein motif:HMM:NF012546.2
GO:0008236 - serine-type peptidase activity [Evidence IEA]
prolyl oligopeptidase family serine peptidase
COORDINATES: protein motif:HMM:NF014896.2
COORDINATES: similar to AA sequence:RefSeq:WP_011882024.1
GO:0008800 - beta-lactamase activity [Evidence IEA]
GO:0030655 - beta-lactam antibiotic catabolic process [Evidence IEA]; GO:0046677 - response to antibiotic [Evidence IEA]