Moraxella osloensis strain CCUG 350 plasmid unnamed1, al1l pseudoknot.
Bacteria; Pseudomonadota; Gammaproteobacteria; Moraxellales; Moraxellaceae; Moraxella.
Submitted (02-FEB-2016) Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
REFSEQ INFORMATION: The reference sequence is identical to\nCP014238.1.\nSource DNA and bacterial cultures: T. A. Joyce and F. E. Dewhirst\nDirect requests to the Human Oral Microbiome Project, The Forsyth\nInstitute, 245 First Street, Cambridge, MA, 02142, USA.\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 :: SMRT Analysis RS_HGAP_Assembly.2 v.\n 2.3.0.140936.p4.150482\nAssembly Name :: CCUG350_Moaxella_osloensis\nGenome Coverage :: 238x\nSequencing Technology :: PacBio\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 02/05/2023 20:41:35\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) :: 2,378\nCDSs (total) :: 2,315\nGenes (coding) :: 2,256\nCDSs (with protein) :: 2,256\nGenes (RNA) :: 63\nrRNAs :: 4, 4, 4 (5S, 16S, 23S)\ncomplete rRNAs :: 4, 4, 4 (5S, 16S, 23S)\ntRNAs :: 47\nncRNAs :: 4\nPseudo Genes (total) :: 59\nCDSs (without protein) :: 59\nPseudo Genes (ambiguous residues) :: 0 of 59\nPseudo Genes (frameshifted) :: 16 of 59\nPseudo Genes (incomplete) :: 44 of 59\nPseudo Genes (internal stop) :: 5 of 59\nPseudo Genes (multiple problems) :: 6 of 59\nCRISPR Arrays :: 2\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.
COORDINATES: similar to AA sequence:RefSeq:WP_002710460.1
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_005155726.1
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: protein motif:HMM:NF019474.2
COORDINATES: similar to AA sequence:RefSeq:WP_007115240.1
COORDINATES: similar to AA sequence:RefSeq:WP_007115125.1
GO:0016491 - oxidoreductase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_076612080.1
GO:0004803 - transposase activity [Evidence IEA]
frameshifted; internal stop; Derived by automated computational analysis using gene prediction method: Protein Homology.
programmed frameshift; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_008253046.1
COORDINATES: similar to AA sequence:RefSeq:WP_001138014.1
COORDINATES: protein motif:HMM:TIGR01443.1
COORDINATES: protein motif:HMM:NF016382.2
GO:0004519 - endonuclease activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_076612015.1
GO:0015074 - DNA integration [Evidence IEA]
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_076611465.1
COORDINATES: nucleotide motif:Rfam:14.4:RF01497
AL1L pseudoknot; Derived by automated computational analysis using gene prediction method: cmsearch.
COORDINATES: similar to AA sequence:RefSeq:WP_004738045.1
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_011960365.1
frameshifted; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_002243574.1
COORDINATES: similar to AA sequence:RefSeq:WP_002233960.1
COORDINATES: protein motif:HMM:NF019310.2
GO:0022857 - transmembrane transporter activity [Evidence IEA]
GO:0055085 - transmembrane transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_002237990.1
COORDINATES: protein motif:HMM:NF016099.2
GO:0019290 - siderophore biosynthetic process [Evidence IEA]
COORDINATES: protein motif:HMM:NF024826.2
COORDINATES: similar to AA sequence:RefSeq:WP_004282345.1
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_013319965.1
helix-turn-helix transcriptional regulator
COORDINATES: protein motif:HMM:NF015397.2
relaxase/mobilization nuclease domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_007115229.1
plasmid mobilization relaxosome protein MobC
COORDINATES: similar to AA sequence:RefSeq:WP_007115666.1
COORDINATES: similar to AA sequence:RefSeq:WP_007116192.1
COORDINATES: protein motif:HMM:TIGR00573.1
COORDINATES: similar to AA sequence:RefSeq:WP_000332609.1
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: protein motif:HMM:NF013235.2
COORDINATES: similar to AA sequence:RefSeq:WP_004763413.1
COORDINATES: similar to AA sequence:RefSeq:WP_004778793.1