Detailed information of oriT

oriT

The information of the oriT region

• oriTDB ID: 120463
• Name: oriT_pR47-309
• Organism: Citrobacter freundii strain R47
• Sequence Completeness: -
• NCBI accession of oriT (coordinates [strand]): NZ_CP040696 (129665..129919 [-], 255 nt)
• oriT length: 255 nt
• IRs (inverted repeats): 153..158, 160..165 (AAAAGT..ACTTTT) 122..130, 135..143 (TTAAGGCTT..AAGCCTTAA) 49..55, 60..66 (GAATTTT..AAAATTC)
• Location of nic site: 78..79
• Conserved sequence flanking the nic site: TTTGGTTAAA
• Note: Predicted by oriTfinder 2.0

oriT sequence

• Length: 255 nt

>oriT_pR47-309
GGATTTAGGTTTTTTTTTAATCGCTTCACATTTCGTTAGCATGCGCAGGAATTTTTGATAAAATTCTGGTTAGTTTGGTTAAAAAGTGTTACAAGTAAGCGGTGTGGTTGAAGGGATAGATTTAAGGCTTATTCAAGCCTTAAGAAAATACTAAAAGTTACTTTTCACCCTACCGAACACCTAACAAAAAATCCATGTTGAAGATTTGAACAATTGTAATGGCGCAAGGACAATCAGCACATGTCAGAATCTGAT

oriT secondary structure

Predicted by RNAfold.

Relaxase

mobH_FGF61_RS00805_pR47-309

• ID: 12887
• GenBank: WP_012477394
• Name: mobH_FGF61_RS00805_pR47-309
• UniProt ID: A0A2Z2E7B6
• Length: 1050 a.a.
• Note: Predicted by oriTfinder 2.0

Relaxase protein sequence

• Length: 1050 a.a.
• Molecular weight: 118067.47 Da
• Isoelectric Point: 4.6347

>WP_012477394.1 MULTISPECIES: MobH family relaxase [Enterobacterales]
MMMNFRALYLCIKRILGIFSSQENDATSVMIEDISSLSPFAQILGDQKYTVPDHPNPEVLKFIEYPTRPT
GIQTFNEQSILSLYREKLHSISMMLAISDSDIRDDAYTFTNLVLKPLVEYVRWIHLLPASENHHHNGIGG
LLSHSLEVAILSLKNAHHSELRPIGYQDEEVVRRKVYLYAAFICGLVHDAGKVYDLDIVSLNLASPIIWT
PSSQSLLDWARENDVVEYEIHWRKRIHNQHNIWSSVFLERILNPVCLAFLDRVNKERVYSKMITALNVYT
DGNDFLSKCVRTADFYSTGTDLNVLRDPIMGLRSNDAAARAISTIKHNFTSININNYNAKPMHIIIVNGE
VYLNENAFLDFVLNDFELHKYNFPQGEAGKTVLVESLVQRGYVEPYDDERVVHYFIPGIYSENEISNIFR
NGIGKLEFYNLLKLRWIGLIFDSYKIPDSVPGLFSVNANKDFIYIDEQKTVTEYRRPVPGRDVITKITDT
VETAVLKVNDLGRSSASIDVDIHSKKNEGSSDDFEKKAESDNEIDNDTQIVKSEGEEAADPVIPDIEESE
DESAKDTESHVLVNQLHELLLSAPLSNDYIVCVDAVPYLNIDTTMALLPGLDEKAFSEEPYFQLTFREGS
LDGMWIVRDIDDLRLVQLGDNCAGFQLTYHEPRRPTTLKSLFNTSMYQALVINDESSVENSAPRPKQTLE
LPPPRVNAVEEHSGDVEYHGTDSASATGPLKTEAVEYEHYQHLFEKEDEEHEIIDYTDFSQLSVSRPEVG
SCATSSSVHNEKLLSEPSELPELNREQNADPQGTNERSMDVSVGQENSEPDTEGNCPPPAEVVYSQTEAA
ATSVMASEEPALPPVLEESNGEHAPTDAKGHHLSPALARLFAPTAPVEKQNPKRNRNKSSDKAEVQKPAS
PVSGHNLNSKVFASTESDQNGEFSLISEGDVTELEFVEIALVLHQILSKMEVAFKRKRKNRFMVSTPNTL
YLTQSCVEKFGSQLEAQDLFNKLPQYLVNSGAVINTKCHAFNMPTLLAASDRAKVDIERIINNLKEAGNL

Protein domains

Predicted by InterproScan.

• Putative helicase (TraI_2) (108-304)

Protein structure

• AlphaFold DB: A0A2Z2E7B6

T4CP

traD_FGF61_RS00810_pR47-309

• ID: 15136
• GenBank: WP_001284073
• Name: traD_FGF61_RS00810_pR47-309
• UniProt ID: _
• Length: 694 a.a.
• PDB ID: _
• Note: Predicted by oriTfinder 2.0

T4CP protein sequence

• Length: 694 a.a.
• Molecular weight: 78123.91 Da
• Isoelectric Point: 8.0177

>WP_001284073.1 MULTISPECIES: conjugative transfer system coupling protein TraD [Enterobacterales]
MSDSKRTNLHAQENFYRPILEYRSASILLICSVSMLYMGLSSDGLDIAPIVLFTSILLFLLCLYRCKTAA
PFLMAHWRVFKRHFMFVSLDSLRVINKSNFFSNERKYRQLVQDYQNKNKDIPERKSYFCDGFEWGPEHAD
RAYQIANLSSDKREIELPFVFNPIKRHFDAMARKMGGSNAIFAVERREPIFVTEDNWFGHTLITGNVGTG
KTVLQRLLSISMLHLGHVVVVIDPKNDAEWRESLMEEAKTLGLPFYKFHPGQPASSVCIDVCNTYTNVSD
LTSRLLSLVTVPGEVNPFVQYAKALVSNVISGLSYIEKKPSIYLIHKNMKSHMSIVNLTVKVMESCYARY
YGYDVWTEKVKYVANDTLPVRFKRLAEWFTAHFMNYEGSEQIDWLDTVSQLIDYSMSDPEHMAKMTAGIM
PVFDMLIEKPLNELLSPNPNSVSSREIVTSEGMFSTGGVLYISLDGLSNPDTAAAISQLIMSDLTSCAGS
RYNAQDGDMSANSRISIFVDEAHSAINNPMINLLAQGRAAKIALFICTQTISDFIAAASVETANRITGLC
NNYISLRVNDTPTQTLVVENFGKSAISTNMVTYTTGSETSLPHNNFSGSISERKQTTLEESIPKDLLGQV
PMFHIVARLQDGRKVVGQIPIAVAEKQMKPNTTLSEMLFKKAGKVTLRQNLDIKNLNKFLRKLH

Protein domains

Predicted by InterproScan.

• Type IV secretion-system coupling protein DNA-binding domain (TrwB_AAD_bind) (406-609)

• AAA-like domain (AAA_10) (199-249)

Protein structure

No available structure.

T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 263956..273196

Locus tag	Coordinates	Strand	Size (bp)	Protein ID	Product	Description
FGF61_RS01600 (FGF61_01600)	259099..259815	-	717	WP_000838219	zinc finger-like domain-containing protein	-
FGF61_RS01605 (FGF61_01605)	259812..260012	-	201	WP_000594930	hypothetical protein	-
FGF61_RS01610 (FGF61_01610)	260032..261084	-	1053	WP_001065778	hypothetical protein	-
FGF61_RS01615 (FGF61_01615)	261561..262436	+	876	WP_000594611	RepB family plasmid replication initiator protein	-
FGF61_RS01625 (FGF61_01625)	263585..263938	+	354	WP_000423602	hypothetical protein	-
FGF61_RS01630 (FGF61_01630)	263956..264306	+	351	WP_001447770	type IV conjugative transfer system protein TraL	traL
FGF61_RS01635 (FGF61_01635)	264318..265106	+	789	WP_000783153	TraE/TraK family type IV conjugative transfer system protein	traE
FGF61_RS01640 (FGF61_01640)	265106..266377	+	1272	WP_000592092	type-F conjugative transfer system secretin TraK	traK
FGF61_RS01645 (FGF61_01645)	266379..266840	+	462	WP_000521242	plasmid transfer protein HtdO	-
FGF61_RS01650 (FGF61_01650)	266830..268185	+	1356	WP_000351841	IncHI-type conjugal transfer protein TrhB	traB
FGF61_RS01655 (FGF61_01655)	268193..268675	+	483	WP_000377632	hypothetical protein	-
FGF61_RS01660 (FGF61_01660)	268794..269546	+	753	WP_182911723	protein-disulfide isomerase HtdT	-
FGF61_RS01665 (FGF61_01665)	269556..270506	+	951	WP_001022588	IncHI-type conjugal transfer lipoprotein TrhV	traV
FGF61_RS01670 (FGF61_01670)	270515..273196	+	2682	WP_000387412	TraC family protein	virb4
FGF61_RS26030	275745..275906	+	162	WP_001371949	hypothetical protein	-

Host bacterium

• ID: 20892
• GenBank: NZ_CP040696
• Plasmid name: pR47-309
• Incompatibility group: IncHI2
• Plasmid size: 309536 bp
• Coordinate of oriT [Strand]: 129665..129919 [-]
• Host baterium: Citrobacter freundii strain R47

Cargo genes

• Drug resistance gene: blaTEM-1B, dfrA19, aph(3'')-Ib, aph(6)-Id, mcr-9, blaSHV-12, tet(D), catA2, sul1, blaDHA-1, qnrB4, qacE, ere(A), aac(6')-IIc
• Virulence gene: -
• Metal resistance gene: terW, terZ, terA, terB, terC, terD, terE, pbrA, merE, merD, merA, merC, merP, merT, merR, pcoS, pcoE, ncrC, rcnR/yohL
• Degradation gene: -
• Symbiosis gene: -
• Anti-CRISPR: -