Detailed information of oriT

oriT

The information of the oriT region

• oriTDB ID: 104188
• Name: oriT_pCB00028_2
• Organism: Citrobacter freundii strain CB00028
• Sequence Completeness: -
• NCBI accession of oriT (coordinates [strand]): NZ_OP378604 (290150..290404 [-], 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_pCB00028_2
GGATTTAGGTTTTTTTTTAATCGCTTCACATTTCGTTAGCATGCGCAGGAATTTTTGATAAAATTCTGGTTAGTTTGGTTAAAAAGTGTTACAAGTAAGCGGTGTGGTTGAAGGGATAGATTTAAGGCTTATTCAAGCCTTAAGAAAATACTAAAAGTTACTTTTCACCCTACCGAACACCTAACAAAAAATCCATGTTGAAGATTTGAACAATTGTAATGGCGCAAGGACAATCAGCACATGTCAGAATCTGAT

oriT secondary structure

Predicted by RNAfold.

Relaxase

mobH_PWC65_RS01530_pCB00028_2

• ID: 3078
• GenBank: WP_012477394
• Name: mobH_PWC65_RS01530_pCB00028_2
• 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_PWC65_RS01535_pCB00028_2

• ID: 2976
• GenBank: WP_001284073
• Name: traD_PWC65_RS01535_pCB00028_2
• 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: 2429..11636

Locus tag	Coordinates	Strand	Size (bp)	Protein ID	Product	Description
PWC65_RS00005	1..876	+	876	WP_000594611	RepB family plasmid replication initiator protein	-
PWC65_RS00010	2025..2378	+	354	WP_000423602	hypothetical protein	-
PWC65_RS00015	2396..2746	+	351	WP_001447770	type IV conjugative transfer system protein TraL	-
PWC65_RS00020	2758..3546	+	789	WP_000783153	TraE/TraK family type IV conjugative transfer system protein	traE
PWC65_RS00025	3546..4817	+	1272	WP_000592092	type-F conjugative transfer system secretin TraK	traK
PWC65_RS00030	4819..5280	+	462	WP_000521242	plasmid transfer protein HtdO	-
PWC65_RS00035	5270..6625	+	1356	WP_000351841	IncHI-type conjugal transfer protein TrhB	traB
PWC65_RS00040	6633..7115	+	483	WP_000377632	hypothetical protein	-
PWC65_RS00045	7234..7986	+	753	WP_182911723	protein-disulfide isomerase HtdT	-
PWC65_RS00050	7996..8946	+	951	WP_001022588	IncHI-type conjugal transfer lipoprotein TrhV	traV
PWC65_RS00055	8955..11636	+	2682	WP_000387412	TraC family protein	virb4
PWC65_RS00060	14185..14346	+	162	WP_001371949	hypothetical protein	-

Host bacterium

• ID: 4627
• GenBank: NZ_OP378604
• Plasmid name: pCB00028_2
• Incompatibility group: IncHI2A
• Plasmid size: 383119 bp
• Coordinate of oriT [Strand]: 290150..290404 [-]
• Host baterium: Citrobacter freundii strain CB00028

Cargo genes

• Drug resistance gene: tet(A), dfrA14, aac(6')-Ib-cr, blaOXA-1, aac(3)-IIa, blaCTX-M-15, blaTEM-1B, aph(6)-Id, aph(3'')-Ib, sul2, ant(3'')-Ia, catA1
• Virulence gene: -
• Metal resistance gene: terW, terZ, terA, terB, terC, terD, terE, merR2, merB, merD, merE, arsR, arsD, arsA, arsB, arsC, pcoE, ncrC, rcnR/yohL, arsH
• Degradation gene: -
• Symbiosis gene: -
• Anti-CRISPR: -