Citrobacter freundii strain FDAARGOS_549 plasmid unnamed, complete sequence.
Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales; Enterobacteriaceae; Citrobacter; Citrobacter freundii complex.
FDA dAtabase for Regulatory Grade micrObial Sequences (FDA-ARGOS): Supporting development and validation of Infectious Disease Dx tests
Submitted (13-NOV-2018) Center for Devices and Radiological Health, US Food and Drug Administration, 10903 New Hampshire Avenue, Silver Spring, MD 20993-0002, USA
REFSEQ INFORMATION: The reference sequence is identical to\nCP033743.1.\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 Method :: SMRT v. 2.3.0, HGAP v. 3.0\nGenome Coverage :: 734.228081176471x\nSequencing Technology :: PacBio; Illumina\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 03/24/2023 23:39:56\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) :: 4,877\nCDSs (total) :: 4,758\nGenes (coding) :: 4,679\nCDSs (with protein) :: 4,679\nGenes (RNA) :: 119\nrRNAs :: 9, 8, 8 (5S, 16S, 23S)\ncomplete rRNAs :: 9, 8, 8 (5S, 16S, 23S)\ntRNAs :: 84\nncRNAs :: 10\nPseudo Genes (total) :: 79\nCDSs (without protein) :: 79\nPseudo Genes (ambiguous residues) :: 0 of 79\nPseudo Genes (frameshifted) :: 25 of 79\nPseudo Genes (incomplete) :: 45 of 79\nPseudo Genes (internal stop) :: 26 of 79\nPseudo Genes (multiple problems) :: 16 of 79\nPseudo Genes (short protein) :: 1 of 79\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.
COORDINATES: similar to AA sequence:RefSeq:WP_000842441.1
incomplete; partial in the middle of a contig; missing C-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: similar to AA sequence:RefSeq:WP_001542523.1
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_001597012.1
COORDINATES: similar to AA sequence:RefSeq:WP_000646094.1
type IV secretory system conjugative DNA transfer family protein
COORDINATES: similar to AA sequence:RefSeq:WP_001755100.1
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_003557916.1
COORDINATES: similar to AA sequence:RefSeq:WP_000488652.1
COORDINATES: similar to AA sequence:RefSeq:WP_001496527.1
shufflon system plasmid conjugative transfer pilus tip adhesin PilV
COORDINATES: protein motif:HMM:NF013632.2
GO:0004190 - aspartic-type endopeptidase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_000012998.1
lytic transglycosylase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_000908226.1
COORDINATES: similar to AA sequence:RefSeq:WP_001699973.1
type II secretion system F family protein
COORDINATES: similar to AA sequence:RefSeq:WP_000362204.1
COORDINATES: similar to AA sequence:RefSeq:WP_003552541.1
GO:0009297 - pilus assembly [Evidence IEA]
COORDINATES: protein motif:HMM:NF018562.2
COORDINATES: similar to AA sequence:RefSeq:WP_001744074.1
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: similar to AA sequence:RefSeq:WP_001744073.1
COORDINATES: protein motif:HMM:NF022136.2
toxin co-regulated pilus biosynthesis Q family protein
COORDINATES: similar to AA sequence:RefSeq:NP_459496.1
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: similar to AA sequence:RefSeq:WP_001303319.1
GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
transcription termination/antitermination NusG family protein
type II toxin-antitoxin system Phd/YefM family antitoxin
COORDINATES: similar to AA sequence:RefSeq:NP_490498.3
GO:0006276 - plasmid maintenance [Evidence IEA]
incFII family plasmid replication initiator RepA
COORDINATES: similar to AA sequence:RefSeq:WP_016487646.1
COORDINATES: protein motif:HMM:NF013080.2
COORDINATES: similar to AA sequence:RefSeq:WP_008322250.1
COORDINATES: similar to AA sequence:RefSeq:WP_004206893.1
COORDINATES: similar to AA sequence:RefSeq:WP_004200905.1
COORDINATES: similar to AA sequence:RefSeq:WP_000375816.1
COORDINATES: protein motif:HMM:NF024573.2
COORDINATES: similar to AA sequence:RefSeq:WP_001697689.1
frameshifted; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_000007431.1
frameshifted; 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_001495930.1
COORDINATES: similar to AA sequence:RefSeq:WP_001307279.1
GO:0051983 - regulation of chromosome segregation [Evidence IEA]
type II toxin-antitoxin system ParD family antitoxin
COORDINATES: similar to AA sequence:RefSeq:WP_015572038.1
type II toxin-antitoxin system RelE/ParE family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_000723069.1
copper resistance system metallochaperone PcoE
COORDINATES: similar to AA sequence:RefSeq:WP_001211179.1
copper resistance membrane spanning protein PcoS
transcriptional regulator responding to pcoS and pcoS*
COORDINATES: similar to AA sequence:RefSeq:WP_020239536.1
copper response regulator transcription factor PcoR
COORDINATES: similar to AA sequence:RefSeq:WP_004098940.1
copper resistance inner membrane protein PcoD
COORDINATES: similar to AA sequence:RefSeq:WP_004098941.1
copper resistance system metallochaperone PcoC
COORDINATES: similar to AA sequence:RefSeq:WP_001378118.1
copper resistance outer membrane transporter PcoB
COORDINATES: similar to AA sequence:RefSeq:WP_001480786.1
COORDINATES: similar to AA sequence:RefSeq:WP_004388333.1
COORDINATES: similar to AA sequence:RefSeq:WP_002436617.1
peptidoglycan DD-metalloendopeptidase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_000843499.1
COORDINATES: similar to AA sequence:RefSeq:WP_008322814.1
COORDINATES: similar to AA sequence:RefSeq:WP_002436620.1
COORDINATES: similar to AA sequence:RefSeq:WP_011711636.1
Cu(+)/Ag(+) efflux RND transporter permease subunit SilA
COORDINATES: similar to AA sequence:RefSeq:WP_017146627.1
Cu(+)/Ag(+) efflux RND transporter periplasmic adaptor subunit SilB
COORDINATES: similar to AA sequence:RefSeq:WP_009654303.1
COORDINATES: similar to AA sequence:RefSeq:WP_001572989.1
Cu(+)/Ag(+) efflux RND transporter outer membrane channel SilC
COORDINATES: similar to AA sequence:RefSeq:WP_001572351.1
copper/silver response regulator transcription factor SilR
COORDINATES: similar to AA sequence:RefSeq:WP_003032875.1
copper/silver sensor histidine kinase SilS
COORDINATES: similar to AA sequence:RefSeq:WP_000790485.1
COORDINATES: similar to AA sequence:RefSeq:WP_000647571.1
COORDINATES: similar to AA sequence:RefSeq:WP_001568530.1
GO:0004519 - endonuclease activity [Evidence IEA]; GO:0003676 - nucleic acid binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:YP_005229632.1
COORDINATES: similar to AA sequence:RefSeq:YP_005229631.1
COORDINATES: similar to AA sequence:RefSeq:YP_005229630.1
COORDINATES: similar to AA sequence:RefSeq:YP_005229629.1
type II toxin-antitoxin system VapB family antitoxin
COORDINATES: similar to AA sequence:RefSeq:WP_001486568.1
COORDINATES: similar to AA sequence:RefSeq:WP_001486567.1
COORDINATES: similar to AA sequence:RefSeq:WP_001123824.1
COORDINATES: similar to AA sequence:RefSeq:WP_016495516.1
COORDINATES: similar to AA sequence:RefSeq:WP_004144461.1
COORDINATES: similar to AA sequence:RefSeq:WP_001505082.1
COORDINATES: similar to AA sequence:RefSeq:WP_001555635.1
plasmid partitioning/stability family protein
COORDINATES: similar to AA sequence:RefSeq:WP_000457545.1
COORDINATES: similar to AA sequence:RefSeq:WP_008455414.1
translesion error-prone DNA polymerase V autoproteolytic subunit
COORDINATES: similar to AA sequence:RefSeq:NP_490546.1
COORDINATES: similar to AA sequence:RefSeq:WP_020314633.1
COORDINATES: similar to AA sequence:RefSeq:WP_013578318.1
COORDINATES: similar to AA sequence:RefSeq:WP_001750289.1
COORDINATES: similar to AA sequence:RefSeq:WP_001485380.1
ParB/RepB/Spo0J family partition protein
COORDINATES: protein motif:HMM:NF010255.1
COORDINATES: similar to AA sequence:RefSeq:WP_000613062.1
COORDINATES: similar to AA sequence:RefSeq:WP_016589766.1
COORDINATES: similar to AA sequence:RefSeq:WP_001481272.1
GO:0004803 - transposase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_003036291.1
COORDINATES: similar to AA sequence:RefSeq:WP_014619352.1
COORDINATES: similar to AA sequence:RefSeq:NP_416083.1
COORDINATES: similar to AA sequence:RefSeq:NP_416082.1
type II toxin-antitoxin system antitoxin RelB
COORDINATES: similar to AA sequence:RefSeq:NP_416081.1
COORDINATES: similar to AA sequence:RefSeq:NP_052660.1
type I toxin-antitoxin system Hok family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_004152749.1
COORDINATES: similar to AA sequence:RefSeq:WP_000080850.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0008170 - N-methyltransferase activity [Evidence IEA]
GO:0006306 - DNA methylation [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_004131746.1
COORDINATES: similar to AA sequence:RefSeq:WP_017900696.1
COORDINATES: similar to AA sequence:RefSeq:WP_000148350.1
helix-turn-helix transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_001403164.1
COORDINATES: protein motif:HMM:NF039307.1
COORDINATES: similar to AA sequence:RefSeq:WP_007869723.1
COORDINATES: similar to AA sequence:RefSeq:WP_001372351.1
molybdopterin-guanine dinucleotide biosynthesis protein MobC
COORDINATES: similar to AA sequence:RefSeq:WP_001281049.1
COORDINATES: similar to AA sequence:RefSeq:WP_001611995.1
relaxase/mobilization nuclease domain-containing protein
COORDINATES: protein motif:HMM:NF025323.2
type II toxin-antitoxin system YafO family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_001289278.1
F-type conjugative transfer protein TrbC
COORDINATES: similar to AA sequence:RefSeq:WP_001303305.1
COORDINATES: protein motif:HMM:NF033891.1
plasmid IncI1-type surface exclusion protein ExcA
COORDINATES: similar to AA sequence:RefSeq:WP_019842539.1
COORDINATES: protein motif:HMM:NF033887.1
COORDINATES: similar to AA sequence:RefSeq:WP_001542514.1
COORDINATES: similar to AA sequence:RefSeq:WP_000286860.1
COORDINATES: similar to AA sequence:RefSeq:WP_001024755.1
COORDINATES: similar to AA sequence:RefSeq:WP_001542519.1
COORDINATES: similar to AA sequence:RefSeq:WP_001090608.1
COORDINATES: protein motif:HMM:NF033885.1
COORDINATES: similar to AA sequence:RefSeq:WP_001272006.1
COORDINATES: similar to AA sequence:RefSeq:WP_001611718.1
DotH/IcmK family type IV secretion protein
COORDINATES: similar to AA sequence:RefSeq:WP_000138553.1
COORDINATES: similar to AA sequence:RefSeq:WP_001623695.1
COORDINATES: protein motif:HMM:NF037421.2