Sodalis glossinidius str. 'morsitans' plasmid pSG1, complete sequence.
Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales; Bruguierivoracaceae; Sodalis.
Massive genome erosion and functional adaptations provide insights into the symbiotic lifestyle of Sodalis glossinidius in the tsetse host
Submitted (14-DEC-2004) Contact:Masahira Hattori Graduate School of Frontier Sciences, University of Tokyo; 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8561, Japan
REFSEQ INFORMATION: The reference sequence is identical to\nAP008233.1.\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-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 04/17/2023 01:23:04\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) :: 5,017\nCDSs (total) :: 4,918\nGenes (coding) :: 3,718\nCDSs (with protein) :: 3,718\nGenes (RNA) :: 99\nrRNAs :: 8, 7, 7 (5S, 16S, 23S)\ncomplete rRNAs :: 8, 7, 7 (5S, 16S, 23S)\ntRNAs :: 71\nncRNAs :: 6\nPseudo Genes (total) :: 1,200\nCDSs (without protein) :: 1,200\nPseudo Genes (ambiguous residues) :: 0 of 1,200\nPseudo Genes (frameshifted) :: 890 of 1,200\nPseudo Genes (incomplete) :: 445 of 1,200\nPseudo Genes (internal stop) :: 423 of 1,200\nPseudo Genes (multiple problems) :: 498 of 1,200\nPseudo Genes (short protein) :: 1 of 1,200\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.
isolated from secondary symbiont of Glossina morsitans morsitans
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: similar to AA sequence:RefSeq:WP_016247728.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0003916 - DNA topoisomerase activity [Evidence IEA]
GO:0006265 - DNA topological change [Evidence IEA]
frameshifted; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_000453335.1
Derived by automated computational analysis using gene prediction method: Protein Homology.
Hha/YmoA family nucleoid-associated regulatory protein
COORDINATES: similar to AA sequence:RefSeq:WP_001293125.1
GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
H-NS family nucleoid-associated regulatory protein
putative stable plasmid inheritance protein
COORDINATES: similar to AA sequence:RefSeq:WP_015873781.1
COORDINATES: similar to AA sequence:RefSeq:WP_011279206.1
prevention of the induction of SOS-responses
COORDINATES: similar to AA sequence:RefSeq:WP_020323173.1
COORDINATES: similar to AA sequence:RefSeq:WP_001180119.1
COORDINATES: similar to AA sequence:RefSeq:WP_001025391.1
frameshifted; internal stop; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_006708696.1
internal stop; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_014888259.1
COORDINATES: similar to AA sequence:RefSeq:WP_015981317.1
Rpn family recombination-promoting nuclease/putative transposase
putative DNA-3-methyladenine glycosylase
COORDINATES: similar to AA sequence:RefSeq:WP_016857296.1
COORDINATES: similar to AA sequence:RefSeq:WP_016857298.1
LuxR C-terminal-related transcriptional regulator
COORDINATES: protein motif:HMM:NF012422.2
helix-turn-helix transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_006708968.1
COORDINATES: similar to AA sequence:RefSeq:WP_000953539.1
lytic transglycosylase domain-containing protein
COORDINATES: protein motif:HMM:NF016820.2
COORDINATES: protein motif:HMM:NF016957.2
VirB3 family type IV secretion system protein
COORDINATES: protein motif:HMM:NF015118.2
COORDINATES: similar to AA sequence:RefSeq:WP_011191403.1
COORDINATES: protein motif:HMM:NF033894.1
COORDINATES: protein motif:HMM:NF016491.2
COORDINATES: protein motif:HMM:NF015487.2
TrbG/VirB9 family P-type conjugative transfer protein
COORDINATES: similar to AA sequence:RefSeq:WP_015873770.1
incomplete; partial in the middle of a contig; missing N-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
VirB10/TraB/TrbI family type IV secretion system protein
COORDINATES: similar to AA sequence:RefSeq:WP_003036362.1
GO:0043684 - type IV secretion system complex [Evidence IEA]
GO:0044097 - secretion by the type IV secretion system [Evidence IEA]
COORDINATES: protein motif:HMM:NF021021.2
COORDINATES: protein motif:HMM:NF024517.2
cag pathogenicity island Cag12 family protein
COORDINATES: similar to AA sequence:RefSeq:WP_003854066.1
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_011412274.1
COORDINATES: protein motif:HMM:NF022337.2
COORDINATES: protein motif:HMM:NF018726.2
GO:0005524 - ATP binding [Evidence IEA]; GO:0003677 - DNA binding [Evidence IEA]; GO:0003678 - DNA helicase activity [Evidence IEA]; GO:0016818 - hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides [Evidence IEA]
conjugative transfer relaxase/helicase TraI
COORDINATES: protein motif:HMM:NF024991.2
COORDINATES: protein motif:HMM:NF037215.2
COORDINATES: protein motif:HMM:NF037306.2
COORDINATES: protein motif:HMM:NF025105.2
COORDINATES: similar to AA sequence:RefSeq:WP_001756807.1
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_001473203.1
type-F conjugative transfer system pilin assembly protein TrbC
COORDINATES: similar to AA sequence:RefSeq:NP_490576.1
conjugal transfer pilus assembly protein TraU
COORDINATES: similar to AA sequence:RefSeq:WP_004966201.1
type-F conjugative transfer system protein TraW
COORDINATES: protein motif:HMM:NF021213.2
COORDINATES: similar to AA sequence:RefSeq:WP_005320903.1
COORDINATES: similar to AA sequence:RefSeq:WP_001553749.1
frameshifted; internal stop; 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_008324157.1
type-F conjugative transfer system secretin TraK
COORDINATES: protein motif:HMM:NF017152.2
TraE/TraK family type IV conjugative transfer system protein
COORDINATES: similar to AA sequence:RefSeq:WP_020325114.1
type IV conjugative transfer system protein TraL
COORDINATES: protein motif:HMM:NF017337.2
GO:0005576 - extracellular region [Evidence IEA]
type IV conjugative transfer system pilin TraA
COORDINATES: protein motif:HMM:NF017333.2
COORDINATES: similar to AA sequence:RefSeq:WP_011145283.1
PAS and helix-turn-helix domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_001913678.1
GO:0004803 - transposase activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF018792.2
COORDINATES: similar to AA sequence:RefSeq:WP_006322811.1
COORDINATES: protein motif:HMM:NF020037.2
COORDINATES: protein motif:HMM:NF012993.2
GO:0006807 - nitrogen compound metabolic process [Evidence IEA]
nitrilase-related carbon-nitrogen hydrolase
COORDINATES: similar to AA sequence:RefSeq:WP_011411299.1
COORDINATES: similar to AA sequence:RefSeq:WP_011147726.1
COORDINATES: protein motif:HMM:NF016255.2
COORDINATES: similar to AA sequence:RefSeq:WP_001743492.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0004803 - transposase activity [Evidence IEA]
GO:0006313 - transposition, DNA-mediated [Evidence IEA]
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_076611450.1
COORDINATES: protein motif:HMM:NF033819.0
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; Derived by automated computational analysis using gene prediction method: Protein Homology.
IS66 family insertion sequence element accessory protein TnpB
putative demethylmenaquinone methyltransferase
COORDINATES: similar to AA sequence:RefSeq:WP_017131171.1
COORDINATES: similar to AA sequence:RefSeq:WP_019361519.1
IucA/IucC family C-terminal-domain containing protein
putative ABC-type cobalamin/Fe3+-siderophores transport systems, ATPase component
COORDINATES: similar to AA sequence:RefSeq:WP_013317301.1
GO:0140359 - ABC-type transporter activity [Evidence IEA]; GO:0005524 - ATP binding [Evidence IEA]; GO:0016887 - ATP hydrolysis activity [Evidence IEA]; GO:0042626 - ATPase-coupled transmembrane transporter activity [Evidence IEA]
putative ABC-type Fe3+-siderophore transport system, permease component
COORDINATES: similar to AA sequence:RefSeq:WP_007925441.1
GO:0140359 - ABC-type transporter activity [Evidence IEA]; GO:0042626 - ATPase-coupled transmembrane transporter activity [Evidence IEA]
GO:0006826 - iron ion transport [Evidence IEA]
putative Achromobactin transport system permease protein
COORDINATES: similar to AA sequence:RefSeq:WP_008047304.1
putative Achromobactin-binding periplasmic protein precursor
COORDINATES: similar to AA sequence:RefSeq:WP_017802376.1
GO:0015891 - siderophore transport [Evidence IEA]
iron-siderophore ABC transporter substrate-binding protein
putative siderophore synthetase component
COORDINATES: similar to AA sequence:RefSeq:WP_017683653.1
GO:0019290 - siderophore biosynthetic process [Evidence IEA]
putative 2,4-dihydroxyhept-2-ene-1,7-dioic acid aldolase
COORDINATES: similar to AA sequence:RefSeq:WP_009049138.1
GO:0003824 - catalytic activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_007249607.1
putative permeases of the major facilitator superfamily
COORDINATES: similar to AA sequence:RefSeq:WP_008145613.1
GO:0005886 - plasma membrane [Evidence IEA]
GO:0009410 - response to xenobiotic stimulus [Evidence IEA]; GO:0006855 - xenobiotic transmembrane transport [Evidence IEA]
DHA2 family efflux MFS transporter permease subunit
COORDINATES: similar to AA sequence:RefSeq:WP_003372851.1
COORDINATES: similar to AA sequence:RefSeq:WP_017131160.1
COORDINATES: similar to AA sequence:RefSeq:WP_012885243.1
GO:0015267 - channel activity [Evidence IEA]
GO:0015891 - siderophore transport [Evidence IEA]; GO:0055085 - transmembrane transport [Evidence IEA]
putative 4-aminobutyrate aminotransferase
COORDINATES: protein motif:HMM:NF005386.0
GO:0030170 - pyridoxal phosphate binding [Evidence IEA]; GO:0008483 - transaminase activity [Evidence IEA]
GO:0009058 - biosynthetic process [Evidence IEA]
diaminobutyrate--2-oxoglutarate transaminase
COORDINATES: similar to AA sequence:RefSeq:WP_011410900.1
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_076611812.1
programmed frameshift; internal stop; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: nucleotide motif:Rfam:14.4:RF01497
AL1L pseudoknot; Derived by automated computational analysis using gene prediction method: cmsearch.
COORDINATES: protein motif:HMM:NF022590.2
COORDINATES: similar to AA sequence:RefSeq:WP_032491235.1
COORDINATES: similar to AA sequence:RefSeq:WP_015873678.1
COORDINATES: similar to AA sequence:RefSeq:WP_016857956.1
type II secretion system F family protein
shufflon system plasmid conjugative transfer pilus tip adhesin PilV
COORDINATES: similar to AA sequence:RefSeq:WP_002353191.1