Pseudoalteromonas luteoviolacea strain H2 plasmid plas_H2_1, whole genome shotgun sequence.
Bacteria; Pseudomonadota; Gammaproteobacteria; Alteromonadales; Pseudoalteromonadaceae; Pseudoalteromonas.
Larvae of Pocillopora damicornis (Anthozoa) settle and metamorphose in response to surface-biofilm bacteria
Submitted (17-JUN-2019) SCELSE, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
REFSEQ INFORMATION: The reference sequence is identical to\nCM017106.1.\nBacteria and source DNA available from Michael Hadfield, Hawaii.\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 Date :: 2019\nAssembly Method :: SPAdes v. 3.11.1\nGenome Representation :: Full\nExpected Final Version :: Yes\nGenome Coverage :: 0.97x\nSequencing Technology :: Illumina MiSeq; Oxford Nanopore MiniION\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 04/28/2023 03:32:28\nAnnotation Pipeline :: NCBI Prokaryotic Genome\n Annotation Pipeline (PGAP)\nAnnotation Method :: Best-placed reference protein\n set; GeneMarkS-2+\nAnnotation Software revision :: 6.5\nFeatures Annotated :: Gene; CDS; rRNA; tRNA; ncRNA\nGenes (total) :: 5,202\nCDSs (total) :: 5,044\nGenes (coding) :: 5,024\nCDSs (with protein) :: 5,024\nGenes (RNA) :: 158\nrRNAs :: 10, 11, 12 (5S, 16S, 23S)\ncomplete rRNAs :: 10, 10, 10 (5S, 16S, 23S)\npartial rRNAs :: 1, 2 (16S, 23S)\ntRNAs :: 120\nncRNAs :: 5\nPseudo Genes (total) :: 20\nCDSs (without protein) :: 20\nPseudo Genes (ambiguous residues) :: 0 of 20\nPseudo Genes (frameshifted) :: 8 of 20\nPseudo Genes (incomplete) :: 15 of 20\nPseudo Genes (internal stop) :: 5 of 20\nPseudo Genes (multiple problems) :: 7 of 20\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.
Glass slide place on reef flat in natural environment
COORDINATES: similar to AA sequence:RefSeq:WP_019615706.1
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_017790341.1
GO:0009279 - cell outer membrane [Evidence IEA]
GO:0044874 - lipoprotein localization to outer membrane [Evidence IEA]; GO:0042953 - lipoprotein transport [Evidence IEA]
outer membrane lipoprotein-sorting protein
COORDINATES: similar to AA sequence:RefSeq:WP_011497995.1
frameshifted; internal stop; Derived by automated computational analysis using gene prediction method: Protein Homology.
helix-turn-helix domain-containing protein
COORDINATES: protein motif:HMM:TIGR00467.1
GO:0017101 - aminoacyl-tRNA synthetase multienzyme complex [Evidence IEA]
GO:0004824 - lysine-tRNA ligase activity [Evidence IEA]
GO:0006430 - lysyl-tRNA aminoacylation [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_007661167.1
GO:0016616 - oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor [Evidence IEA]
Derived by automated computational analysis using gene prediction method: tRNAscan-SE.
COORDINATES: protein motif:HMM:NF022645.2
STY4526/YPO1902 family pathogenicity island replication protein
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: protein motif:HMM:NF024252.2
helix-turn-helix transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_003487959.1
PDDEXK nuclease domain-containing protein
COORDINATES: protein motif:HMM:NF025063.2
GO:0015074 - DNA integration [Evidence IEA]
integrase core 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: similar to AA sequence:RefSeq:WP_007992394.1
COORDINATES: protein motif:HMM:NF012870.2
DDE-type integrase/transposase/recombinase
COORDINATES: protein motif:HMM:NF017300.2
GO:0006274 - DNA replication termination [Evidence IEA]
DNA replication terminus site-binding protein
COORDINATES: protein motif:HMM:NF012798.2
GO:0015074 - DNA integration [Evidence IEA]; GO:0006310 - DNA recombination [Evidence IEA]
COORDINATES: protein motif:HMM:NF024949.2
COORDINATES: similar to AA sequence:RefSeq:WP_019964963.1
GO:0033743 - peptide-methionine (R)-S-oxide reductase activity [Evidence IEA]
GO:0030091 - protein repair [Evidence IEA]; GO:0006979 - response to oxidative stress [Evidence IEA]
peptide-methionine (R)-S-oxide reductase MsrB
COORDINATES: similar to AA sequence:RefSeq:WP_007616663.1
GO:0033744 - L-methionine:thioredoxin-disulfide S-oxidoreductase activity [Evidence IEA]; GO:0008113 - peptide-methionine (S)-S-oxide reductase activity [Evidence IEA]
peptide-methionine (S)-S-oxide reductase MsrA
COORDINATES: similar to AA sequence:RefSeq:WP_012154176.1
GO:0008080 - N-acetyltransferase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_015464743.1
COORDINATES: nucleotide motif:Rfam:14.4:RF00168
Lysine riboswitch is most abundant in Firmicutes and Gammaproteobacteria where they are found upstream of a number of genes involved in lysine biosynthesis, transport and catabolism; Derived by automated computational analysis using gene prediction method: cmsearch.
COORDINATES: similar to AA sequence:RefSeq:WP_010371897.1
GO:0004072 - aspartate kinase activity [Evidence IEA]
GO:0009089 - lysine biosynthetic process via diaminopimelate [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_008127030.1
GO:0008840 - 4-hydroxy-tetrahydrodipicolinate synthase activity [Evidence IEA]
4-hydroxy-tetrahydrodipicolinate synthase
COORDINATES: protein motif:HMM:NF040977.1
COORDINATES: protein motif:HMM:NF024242.2
GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]; GO:0043565 - sequence-specific DNA binding [Evidence IEA]
GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_076611593.1
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:NF024954.2
COORDINATES: protein motif:HMM:NF012711.2