Serratia entomophila strain A1 plasmid pADAP, complete sequence.
Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales; Yersiniaceae; Serratia.

Complete Serratia entomophila genome annotation, comparison and evolutionary placement in the phylogenetic tree

Submitted (01-SEP-2021) Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Blegdamsvej 3b, Copenhagen N 2200, Denmark

REFSEQ INFORMATION: The reference sequence is identical to\nCP082788.1.\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-Assembly-Data-START##\nAssembly Date :: APR-2021\nAssembly Method :: Flye v. v. 2.8.2\nAssembly Name :: UCPH_Sent_1.0\nGenome Representation :: Full\nExpected Final Version :: Yes\nGenome Coverage :: 200.0x\nSequencing Technology :: Oxford Nanopore MinION; DNBseq; PacBio\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 09/23/2022 13:00:14\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) :: 4,913\nCDSs (total) :: 4,781\nGenes (coding) :: 4,731\nCDSs (with protein) :: 4,731\nGenes (RNA) :: 132\nrRNAs :: 8, 7, 7 (5S, 16S, 23S)\ncomplete rRNAs :: 8, 7, 7 (5S, 16S, 23S)\ntRNAs :: 89\nncRNAs :: 21\nPseudo Genes (total) :: 51\nCDSs (without protein) :: 50\nPseudo Genes (ambiguous residues) :: 0 of 51\nPseudo Genes (frameshifted) :: 14 of 51\nPseudo Genes (incomplete) :: 36 of 51\nPseudo Genes (internal stop) :: 8 of 51\nPseudo Genes (multiple problems) :: 7 of 51\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.

COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.

COORDINATES: similar to AA sequence:RefSeq:WP_017891014.1
Derived by automated computational analysis using gene prediction method: Protein Homology.

COORDINATES: similar to AA sequence:RefSeq:WP_015873475.1

COORDINATES: similar to AA sequence:RefSeq:WP_017891141.1

COORDINATES: protein motif:HMM:NF033884.1

COORDINATES: similar to AA sequence:RefSeq:WP_000348307.1

COORDINATES: similar to AA sequence:RefSeq:WP_017891136.1

COORDINATES: similar to AA sequence:RefSeq:WP_017891135.1

COORDINATES: protein motif:HMM:NF033887.1

COORDINATES: similar to AA sequence:RefSeq:WP_017891133.1

COORDINATES: similar to AA sequence:RefSeq:WP_017891131.1

COORDINATES: similar to AA sequence:RefSeq:WP_000963393.1
type IV secretory system conjugative DNA transfer family protein

COORDINATES: similar to AA sequence:RefSeq:WP_017891127.1

COORDINATES: protein motif:HMM:NF015397.2
relaxase/mobilization nuclease domain-containing protein

COORDINATES: similar to AA sequence:RefSeq:WP_017891124.1

COORDINATES: similar to AA sequence:RefSeq:WP_017891123.1

COORDINATES: protein motif:HMM:NF039307.1

COORDINATES: similar to AA sequence:RefSeq:WP_000113358.1

COORDINATES: similar to AA sequence:RefSeq:WP_019077937.1
helix-turn-helix domain-containing protein

COORDINATES: similar to AA sequence:RefSeq:WP_017465947.1
GO:0016788 - hydrolase activity, acting on ester bonds [Evidence IEA]
type II toxin-antitoxin system HigB family toxin

COORDINATES: similar to AA sequence:RefSeq:WP_017891115.1

COORDINATES: similar to AA sequence:RefSeq:WP_004953890.1

COORDINATES: similar to AA sequence:RefSeq:WP_017891113.1
ParB/RepB/Spo0J family partition protein

COORDINATES: similar to AA sequence:RefSeq:WP_000761758.1

COORDINATES: similar to AA sequence:RefSeq:WP_000108571.1
frameshifted; Derived by automated computational analysis using gene prediction method: Protein Homology.

COORDINATES: protein motif:HMM:NF037233.2

COORDINATES: protein motif:HMM:NF013540.2
helix-turn-helix transcriptional regulator

COORDINATES: similar to AA sequence:RefSeq:WP_017891109.1
plasmid partitioning/stability family protein

COORDINATES: similar to AA sequence:RefSeq:WP_017891108.1

COORDINATES: protein motif:HMM:NF022728.2

COORDINATES: similar to AA sequence:RefSeq:WP_017891104.1

COORDINATES: similar to AA sequence:RefSeq:WP_017891103.1
ParB/RepB/Spo0J family plasmid partition protein

COORDINATES: similar to AA sequence:RefSeq:WP_010891239.1

COORDINATES: similar to AA sequence:RefSeq:WP_017891101.1

COORDINATES: similar to AA sequence:RefSeq:WP_001165419.1
type II toxin-antitoxin system RelE/ParE family toxin

COORDINATES: similar to AA sequence:RefSeq:WP_004114519.1
type II toxin-antitoxin system Phd/YefM family antitoxin

COORDINATES: similar to AA sequence:RefSeq:WP_017891097.1

COORDINATES: similar to AA sequence:RefSeq:WP_019456402.1

COORDINATES: similar to AA sequence:RefSeq:WP_001567368.1
GO:0004803 - transposase activity [Evidence IEA]
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_076611902.1

internal stop; Derived by automated computational analysis using gene prediction method: Protein Homology.

COORDINATES: similar to AA sequence:RefSeq:WP_012218041.1
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_004721407.1

COORDINATES: similar to AA sequence:RefSeq:WP_004721410.1
GO:0005524 - ATP binding [Evidence IEA]; GO:0016887 - ATP hydrolysis activity [Evidence IEA]

COORDINATES: protein motif:HMM:NF039901.1
contractile injection system tape measure protein

COORDINATES: protein motif:HMM:NF039577.1

COORDINATES: similar to AA sequence:RefSeq:WP_015834376.1

COORDINATES: protein motif:HMM:NF016595.2

COORDINATES: similar to AA sequence:RefSeq:WP_015835466.1

COORDINATES: protein motif:HMM:NF039278.1

COORDINATES: similar to AA sequence:RefSeq:WP_011145969.1

COORDINATES: similar to AA sequence:RefSeq:WP_011146622.1
phage tail sheath subtilisin-like domain-containing protein

COORDINATES: similar to AA sequence:RefSeq:WP_011146011.1

COORDINATES: similar to AA sequence:RefSeq:WP_011145991.1

COORDINATES: similar to AA sequence:RefSeq:WP_006120907.1

COORDINATES: protein motif:HMM:NF027409.2

COORDINATES: protein motif:HMM:NF015218.2

COORDINATES: protein motif:HMM:TIGR01594.1

COORDINATES: protein motif:HMM:NF014417.2

COORDINATES: similar to AA sequence:RefSeq:WP_063945310.1

COORDINATES: similar to AA sequence:RefSeq:WP_001536669.1
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.; incomplete; partial in the middle of a contig; missing C-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
IS66 family insertion sequence element accessory protein TnpB

COORDINATES: protein motif:HMM:NF013677.2

COORDINATES: protein motif:HMM:NF025677.2
transposase zinc-binding domain-containing protein

COORDINATES: protein motif:HMM:NF016847.2
GO:0003677 - DNA binding [Evidence IEA]; GO:0004803 - transposase activity [Evidence IEA]
GO:0006313 - transposition, DNA-mediated [Evidence IEA]
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_000098783.1
internal stop; 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_016193176.1

COORDINATES: similar to AA sequence:RefSeq:WP_002210949.1

COORDINATES: protein motif:HMM:NF022181.2

COORDINATES: similar to AA sequence:RefSeq:WP_020197550.1
SpvB/TcaC N-terminal domain-containing protein

COORDINATES: similar to AA sequence:RefSeq:WP_010846094.1
neuraminidase-like domain-containing protein

COORDINATES: similar to AA sequence:RefSeq:WP_010115763.1

COORDINATES: protein motif:HMM:NF028241.2

COORDINATES: protein motif:HMM:NF012772.2

COORDINATES: similar to AA sequence:RefSeq:WP_017145861.1
GO:0007155 - cell adhesion [Evidence IEA]

COORDINATES: similar to AA sequence:RefSeq:WP_013026595.1
GO:0030288 - outer membrane-bounded periplasmic space [Evidence IEA]
GO:0071555 - cell wall organization [Evidence IEA]

COORDINATES: protein motif:HMM:NF012635.2

COORDINATES: similar to AA sequence:RefSeq:WP_017374948.1

COORDINATES: similar to AA sequence:RefSeq:WP_017372048.1
GO:0015473 - fimbrial usher porin activity [Evidence IEA]
GO:0009297 - pilus assembly [Evidence IEA]
fimbria/pilus outer membrane usher protein

COORDINATES: similar to AA sequence:RefSeq:WP_013814940.1

COORDINATES: protein motif:HMM:NF012698.2

COORDINATES: protein motif:HMM:NF019542.2

COORDINATES: similar to AA sequence:RefSeq:WP_001117543.1

COORDINATES: similar to AA sequence:RefSeq:WP_001493761.1

COORDINATES: similar to AA sequence:RefSeq:WP_017189937.1

COORDINATES: similar to AA sequence:RefSeq:WP_006880978.1

COORDINATES: similar to AA sequence:RefSeq:WP_005437669.1

COORDINATES: similar to AA sequence:RefSeq:WP_009315591.1

COORDINATES: similar to AA sequence:RefSeq:WP_009315590.1

COORDINATES: similar to AA sequence:RefSeq:WP_006317361.1

COORDINATES: similar to AA sequence:RefSeq:WP_017891035.1

COORDINATES: similar to AA sequence:RefSeq:WP_017891034.1

COORDINATES: protein motif:HMM:NF022136.2
toxin co-regulated pilus biosynthesis Q family protein

COORDINATES: protein motif:HMM:NF019064.2

COORDINATES: similar to AA sequence:RefSeq:WP_004720794.1
GO:0019867 - outer membrane [Evidence IEA]
GO:0009297 - pilus assembly [Evidence IEA]; GO:0009306 - protein secretion [Evidence IEA]
PilN family type IVB pilus formation outer membrane protein

COORDINATES: protein motif:HMM:NF018562.2

COORDINATES: similar to AA sequence:RefSeq:WP_017891027.1

COORDINATES: similar to AA sequence:RefSeq:WP_017891026.1

COORDINATES: similar to AA sequence:RefSeq:WP_017891025.1
type II secretion system F family protein

COORDINATES: similar to AA sequence:RefSeq:WP_017891024.1

COORDINATES: similar to AA sequence:RefSeq:WP_017891023.1
lytic transglycosylase domain-containing protein

COORDINATES: protein motif:HMM:NF013632.2
GO:0004190 - aspartic-type endopeptidase activity [Evidence IEA]

COORDINATES: similar to AA sequence:RefSeq:WP_017891021.1
shufflon system plasmid conjugative transfer pilus tip adhesin PilV

COORDINATES: similar to AA sequence:RefSeq:WP_004720812.1
Members of this family include DotD of type IVB secretion systems and TraH of plasmid conjugative plasmid systems, both lipoproteins; Derived by automated computational analysis using gene prediction method: Protein Homology.

COORDINATES: similar to AA sequence:RefSeq:WP_017891019.1

COORDINATES: similar to AA sequence:RefSeq:WP_017891018.1

COORDINATES: similar to AA sequence:RefSeq:WP_017891017.1