Secundilactobacillus paracollinoides strain TMW 1.1979 plasmid pL11979-2, complete sequence.
Bacteria; Bacillota; Bacilli; Lactobacillales; Lactobacillaceae; Secundilactobacillus.
Pediococcus and Lactobacillus from brewery environment - whole genome sequencing and assembly
Submitted (18-MAR-2016) Technische Mikrobiologie, Technische Universitaet Muenchen, Gregor-Mendel-Strasse 4, Freising, Bavaria 85354, Germany
REFSEQ INFORMATION: The reference sequence is identical to\nCP014914.1.\nSource DNA or bacteria available from the culture collection of the\nTechnische Mikrobiologie Weihenstephan upon request and only if\npermitted by a potential cooperation partner. Individual decisions.\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 :: Celera Assembler v. 1\nAssembly Name :: Lparacoll11979-1\nLong Assembly Name :: Lactobacillus paracollinoides TMW 1.1979 1\nGenome Coverage :: 107\nSequencing Technology :: PacBio\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 10/22/2022 03:23:05\nAnnotation Pipeline :: NCBI Prokaryotic Genome\n Annotation Pipeline (PGAP)\nAnnotation Method :: Best-placed reference protein\n set; GeneMarkS-2+\nAnnotation Software revision :: 6.3\nFeatures Annotated :: Gene; CDS; rRNA; tRNA; ncRNA;\n repeat_region\nGenes (total) :: 3,009\nCDSs (total) :: 2,917\nGenes (coding) :: 2,822\nCDSs (with protein) :: 2,822\nGenes (RNA) :: 92\nrRNAs :: 7, 6, 6 (5S, 16S, 23S)\ncomplete rRNAs :: 7, 6, 6 (5S, 16S, 23S)\ntRNAs :: 70\nncRNAs :: 3\nPseudo Genes (total) :: 95\nCDSs (without protein) :: 95\nPseudo Genes (ambiguous residues) :: 0 of 95\nPseudo Genes (frameshifted) :: 51 of 95\nPseudo Genes (incomplete) :: 28 of 95\nPseudo Genes (internal stop) :: 22 of 95\nPseudo Genes (multiple problems) :: 5 of 95\nCRISPR Arrays :: 3\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.
COORDINATES: similar to AA sequence:RefSeq:WP_011672911.1
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_014216117.1
GO:0047632 - agmatine deiminase activity [Evidence IEA]
GO:0009446 - putrescine biosynthetic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_003634647.1
GO:0008804 - carbamate kinase activity [Evidence IEA]
GO:0006520 - amino acid metabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_013727908.1
GO:0004803 - transposase activity [Evidence IEA]
programmed frameshift; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_008841686.1
COORDINATES: similar to AA sequence:RefSeq:WP_008841685.1
MurR/RpiR family transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_076611098.1
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: similar to AA sequence:RefSeq:WP_016527412.1
COORDINATES: similar to AA sequence:RefSeq:WP_016370331.1
COORDINATES: similar to AA sequence:RefSeq:WP_010492166.1
COORDINATES: similar to AA sequence:RefSeq:WP_005728424.1
COORDINATES: similar to AA sequence:RefSeq:WP_005693113.1
GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
type II toxin-antitoxin system RelB/DinJ family antitoxin
COORDINATES: similar to AA sequence:RefSeq:WP_010620892.1
COORDINATES: similar to AA sequence:RefSeq:WP_007124583.1
GO:0005524 - ATP binding [Evidence IEA]; GO:0016301 - kinase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_003603789.1
COORDINATES: similar to AA sequence:RefSeq:WP_012552807.1
COORDINATES: similar to AA sequence:RefSeq:WP_016511122.1
COORDINATES: similar to AA sequence:RefSeq:WP_014940859.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0003916 - DNA topoisomerase activity [Evidence IEA]
GO:0006265 - DNA topological change [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_015474742.1
COORDINATES: similar to AA sequence:RefSeq:WP_002346505.1
COORDINATES: protein motif:HMM:NF028245.2
COORDINATES: similar to AA sequence:RefSeq:WP_010386975.1
GO:0006304 - DNA modification [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_003553103.1
GO:0015666 - restriction endodeoxyribonuclease activity [Evidence IEA]; GO:0009007 - site-specific DNA-methyltransferase (adenine-specific) activity [Evidence IEA]
GO:0006306 - DNA methylation [Evidence IEA]; GO:0009307 - DNA restriction-modification system [Evidence IEA]
type I restriction-modification system subunit M
COORDINATES: similar to AA sequence:RefSeq:WP_015639662.1
GO:0019812 - type I site-specific deoxyribonuclease complex [Evidence IEA]
GO:0009035 - type I site-specific deoxyribonuclease activity [Evidence IEA]
GO:0009307 - DNA restriction-modification system [Evidence IEA]
HsdR family type I site-specific deoxyribonuclease
COORDINATES: protein motif:HMM:NF012789.2
COORDINATES: protein motif:HMM:NF014516.2
COORDINATES: similar to AA sequence:RefSeq:WP_003625677.1
COORDINATES: similar to AA sequence:RefSeq:WP_003645617.1
COORDINATES: similar to AA sequence:RefSeq:WP_003587146.1
COORDINATES: protein motif:HMM:NF040152.1
COORDINATES: similar to AA sequence:RefSeq:WP_013356299.1
adenylate/guanylate cyclase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_014567995.1
COORDINATES: similar to AA sequence:RefSeq:WP_002286155.1
COORDINATES: similar to AA sequence:RefSeq:WP_053338758.1
internal stop; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_002295311.1
GO:0050231 - putrescine carbamoyltransferase activity [Evidence IEA]
GO:0009445 - putrescine metabolic process [Evidence IEA]