Candidatus Protochlamydia naegleriophila strain KNic plasmid pPNK, complete sequence.
Candidatus Protochlamydia naegleriophila
Bacteria; Chlamydiota; Chlamydiia; Parachlamydiales; Parachlamydiaceae; Candidatus Protochlamydia.
Submitted (14-SEP-2015) CHUV-UNIL, Bugnon 48, 1011 Lausanne, Switzerland
REFSEQ INFORMATION: The reference sequence is identical to\nLN879503.1.\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 :: 12/24/2022 02:48:42\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) :: 2,592\nCDSs (total) :: 2,535\nGenes (coding) :: 2,511\nCDSs (with protein) :: 2,511\nGenes (RNA) :: 57\nrRNAs :: 4, 4, 4 (5S, 16S, 23S)\ncomplete rRNAs :: 4, 4, 4 (5S, 16S, 23S)\ntRNAs :: 42\nncRNAs :: 3\nPseudo Genes (total) :: 24\nCDSs (without protein) :: 24\nPseudo Genes (ambiguous residues) :: 0 of 24\nPseudo Genes (frameshifted) :: 9 of 24\nPseudo Genes (incomplete) :: 16 of 24\nPseudo Genes (internal stop) :: 11 of 24\nPseudo Genes (multiple problems) :: 10 of 24\nCRISPR Arrays :: 1\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.
reference material of Candidatus Protochlamydia naegleriophila
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: protein motif:HMM:NF013540.2
Derived by automated computational analysis using gene prediction method: Protein Homology.
helix-turn-helix domain-containing protein
COORDINATES: protein motif:HMM:NF017843.2
COORDINATES: similar to AA sequence:RefSeq:WP_011174924.1
COORDINATES: similar to AA sequence:RefSeq:WP_011175572.1
COORDINATES: similar to AA sequence:RefSeq:WP_011175571.1
GO:0016301 - kinase activity [Evidence IEA]
type II toxin-antitoxin system death-on-curing family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_013182396.1
COORDINATES: similar to AA sequence:RefSeq:WP_010883059.1
COORDINATES: protein motif:HMM:NF014639.2
COORDINATES: protein motif:HMM:NF015354.2
COORDINATES: similar to AA sequence:RefSeq:WP_013925500.1
COORDINATES: similar to AA sequence:RefSeq:WP_002217728.1
COORDINATES: protein motif:HMM:TIGR03696.1
RHS repeat-associated core domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_019272554.1
COORDINATES: protein motif:HMM:NF013776.2
COORDINATES: similar to AA sequence:RefSeq:WP_006341956.1
COORDINATES: similar to AA sequence:RefSeq:WP_012646310.1
COORDINATES: similar to AA sequence:RefSeq:WP_015117834.1
helix-turn-helix transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_011382085.1
type II toxin-antitoxin system RelE/ParE family toxin
COORDINATES: protein motif:HMM:NF012235.2
COORDINATES: similar to AA sequence:RefSeq:WP_013944208.1
winged helix-turn-helix domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_013924817.1
COORDINATES: protein motif:HMM:NF019843.2
COORDINATES: protein motif:HMM:NF020419.2
nucleotidyl transferase AbiEii/AbiGii toxin family protein
COORDINATES: similar to AA sequence:RefSeq:WP_017259804.1
COORDINATES: similar to AA sequence:RefSeq:WP_012975084.1
COORDINATES: similar to AA sequence:RefSeq:WP_003117273.1
GO:0004803 - transposase activity [Evidence IEA]
GO:0006313 - transposition, DNA-mediated [Evidence IEA]
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_006869880.1
COORDINATES: protein motif:HMM:NF025079.2
COORDINATES: similar to AA sequence:RefSeq:WP_014834018.1
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: protein motif:HMM:NF017355.2
incomplete; partial in the middle of a contig; missing N-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
toxin-antitoxin system HicB family antitoxin
COORDINATES: similar to AA sequence:RefSeq:WP_009708607.1
COORDINATES: protein motif:HMM:NF025113.2
COORDINATES: similar to AA sequence:RefSeq:WP_076611815.1
programmed frameshift; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: protein motif:HMM:NF033579.1
COORDINATES: similar to AA sequence:RefSeq:WP_011175287.1
COORDINATES: similar to AA sequence:RefSeq:WP_076611555.1
frameshifted; internal stop; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: protein motif:HMM:NF024734.2
type IV toxin-antitoxin system AbiEi family antitoxin domain-containing protein
COORDINATES: protein motif:HMM:NF024854.2
GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]
GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
COORDINATES: protein motif:HMM:NF013989.2
COORDINATES: protein motif:HMM:NF024736.2
incomplete; partial in the middle of a contig; missing C-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
GO:0003677 - DNA binding [Evidence IEA]; GO:0004803 - transposase activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF024339.2
COORDINATES: similar to AA sequence:RefSeq:WP_006510351.1
frameshifted; incomplete; partial in the middle of a contig; missing N-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: protein motif:HMM:NF025224.2
GO:0005515 - protein binding [Evidence IEA]
COORDINATES: protein motif:HMM:NF013395.2
GO:0016787 - hydrolase activity [Evidence IEA]; GO:0046872 - metal ion binding [Evidence IEA]; GO:0003676 - nucleic acid binding [Evidence IEA]
Derived by automated computational analysis using gene prediction method: tRNAscan-SE.
COORDINATES: protein motif:HMM:NF013068.2
COORDINATES: similar to AA sequence:RefSeq:WP_013181580.1
COORDINATES: protein motif:HMM:NF025797.2
nucleic acid/nucleotide deaminase domain-containing protein
COORDINATES: protein motif:HMM:NF015627.2
COORDINATES: protein motif:HMM:NF013793.2
COORDINATES: protein motif:HMM:TIGR02759.1
type IV conjugative transfer system coupling protein TraD
COORDINATES: protein motif:HMM:NF019530.2
conjugal transfer protein TraG N-terminal domain-containing protein
COORDINATES: protein motif:HMM:NF017892.2
COORDINATES: protein motif:HMM:TIGR02739.1
type-F conjugative transfer system pilin assembly protein TraF
COORDINATES: protein motif:HMM:NF018666.2
COORDINATES: protein motif:HMM:NF018536.2
COORDINATES: protein motif:HMM:TIGR02742.1
type-F conjugative transfer system pilin assembly protein TrbC
COORDINATES: protein motif:HMM:TIGR02743.1
type-F conjugative transfer system protein TraW
COORDINATES: protein motif:HMM:NF021981.2
COORDINATES: protein motif:HMM:TIGR02746.1
COORDINATES: protein motif:HMM:NF024853.2
COORDINATES: protein motif:HMM:NF015688.2
COORDINATES: protein motif:HMM:NF018311.2
type-F conjugative transfer system secretin TraK
COORDINATES: protein motif:HMM:TIGR02761.1
type IV conjugative transfer system protein TraE
COORDINATES: protein motif:HMM:TIGR02762.1
type IV conjugative transfer system protein TraL