Detailed information of oriT

oriT

The information of the oriT region

• oriTDB ID: 107422
• Name: oriT_pPOta2VIM-11
• Organism: Pseudomonas aeruginosa strain Ota2
• Sequence Completeness: -
• NCBI accession of oriT (coordinates [strand]): NZ_MW300276 (32349..32447 [-], 99 nt)
• oriT length: 99 nt
• IRs (inverted repeats): 24..31, 34..41 (TAACCGGC..GCCGGTTA)
• Location of nic site: 60..61
• Conserved sequence flanking the nic site: TCCTGCCCGC
• Note: Predicted by oriTfinder 2.0

oriT sequence

• Length: 99 nt

>oriT_pPOta2VIM-11
GAATAAGGGACAGTGAAGATAGATAACCGGCTCGCCGGTTAGCTAACTTCACACATCCTGCCCGCCTTACGGCGTTAATAACACCAAGGAAAGTCTACA

oriT secondary structure

Predicted by RNAfold.

Relaxase

Relaxase_JYH21_RS00190_pPOta2VIM-11

• ID: 4958
• GenBank: WP_011342947
• Name: Relaxase_JYH21_RS00190_pPOta2VIM-11
• UniProt ID: A0A077KSK4
• Length: 746 a.a.
• Note: Predicted by oriTfinder 2.0

Relaxase protein sequence

• Length: 746 a.a.
• Molecular weight: 82038.71 Da
• Isoelectric Point: 10.7900

>WP_011342947.1 MULTISPECIES: TraI/MobA(P) family conjugative relaxase [Pseudomonadota]
MIAKHVPMRSLGKSDFAGLANYITDAQSKDHRLGHVQATNCEAGSIQDAITEVLATQHTNTRAKGDKTYH
LIVSFRAGEQPSADTLRAIEERICVGLGYGEHQRISAVHNDTDNLHIHIAINKIHPTRHTMHEPYYPHRA
LAELCTALERDYGLERDNHEPRKRGAEGRAADMERHAGVESLVGWIKRECLDEIKGAQSWQELHQVMRDN
GMELRVRANGLVFEAGDGTMVKASTVARDLSKPSLEARLGPFEASPERQAQTTAKRQYRKDPIRLRVNTV
ELYAKYKAEQQSLTTARAQALERARHRKDRLIEAAKRSNRLRRATIKVVGEGRANKKLLYAQASKALRSE
IQAINKQFQQERTALYAEHSRRTWADWLKKEAQHGGADALAALRAREAAQGLKGNTIRGEGQAKPGHAPA
VDNITKKGTIIFRAGMSAVRDDGDRLQVSREATREGLQEALRLAMQRYGNRITVNGTVEFKAQMIRAAVD
SQLPITFTDPALESRRQALLNKENTHERTERPEHRGRTGRGAGGPGQRPAADQHATGAAAVARAGDGRPA
AGRGDRADAGLHAATVHRKPDVGRLGRKPPPQSQHRLRALSELGVVRIAGGSEVLLPRDVPRHVEQQGTQ
PDHALRRGISRPGTGVGQTPPGVAAADKYIAEREAKRLKGFDIPKHSRYTAGDGALTFQGTRTIEGQALA
LLKRGDEVMVMPIDQATARRLTRIAVGDAVSITAKGSIKTSKGRSR

Protein domains

Predicted by InterproScan.

• Large polyvalent protein-associated domain 7 (LPD7) (422-508)

• Relaxase/Mobilisation nuclease domain (Relaxase) (12-251)

Protein structure

• AlphaFold DB: A0A077KSK4

T4CP

t4cp2_JYH21_RS00070_pPOta2VIM-11

• ID: 5157
• GenBank: WP_011114047
• Name: t4cp2_JYH21_RS00070_pPOta2VIM-11
• UniProt ID: _
• Length: 852 a.a.
• PDB ID: _
• Note: Predicted by oriTfinder 2.0

T4CP protein sequence

• Length: 852 a.a.
• Molecular weight: 93980.15 Da
• Isoelectric Point: 6.3901

>WP_011114047.1 MULTISPECIES: VirB4 family type IV secretion/conjugal transfer ATPase [Bacteria]
MIEAIAIAIAVLGAVLLLILFARIRAVDAELKLKKHRAKDAGLADLLNYAAVVDDGVIVGKNGSFMAAWL
YKGDDNASSTEEQREMVSFRINQALAGLGNGWMVHVDAVRRPAPNYSERGVSSFPDSVSFAIDEERRRLF
EGLGAMFEGYFVLTVTWFPPVLAQRKFVELMFDDDAVAPDHTARTTGLIAQFKREITSLESRLSSAVKMT
RLRGQKVVSEEGREVTHDDFLSWLQFCVTGLHHPVMLPSNPMYLDAVIGGQELWGGVVPKIGRKFIQVVA
IEGFPLESTPGVLSALAELPSEYRWSSRFIFMDQHESLKHLDKFRKKWKQKIRGFFDQVFNTNTGSINQD
AAAMVGDAEAAIAEVNSGLVAAGYYTSVVVLMDEDRERLAASALLVEKAVNRLAFAARIETINTLDAYLG
SLPGHGVENVRRPLINTMNLADLLPTSSIWTGSATAPCPMYPPLSPALMHCVTVGATPFRLNLHVRDLGH
TFMFGPTGAGKSTHLGIIAAQLRRYAGMSIYAFDKGMSMYPLAAGIRAATKGKSGLHFTVAADDDRLAFC
PLQFLETKGDRAWAMEWIDTILALNGVNTTPAQRNEIGNAIMSMHASGARTLSEFSVTIQDEAIREAIKQ
YTVDGSMGHLLDAEEDGLSLSDFTVFEIEELMNLGEKFALPVLLYLFRRIERALKGQPSVIILDEAWLML
GHPAFRAKIREWLKVLRKANCLVLMATQSLSDAANSGILDVIVESTATKIFLPNVYARDEDTSALYRRMG
LNARQIEILATAIPKRQYYYVSENGRRLYDLALGPMALAFVGASDKESVATIKSLEAKFGHEWVHEWLAG
RGLNLNDYLEAA

Protein domains

Predicted by InterproScan.

• TraG P-loop domain (P-loop_TraG) (626-754)

• CagE, TrbE, VirB family, component of type IV transporter system (CagE_TrbE_VirB) (218-431)

Protein structure

No available structure.

t4cp2_JYH21_RS00195_pPOta2VIM-11

• ID: 5158
• GenBank: WP_019373230
• Name: t4cp2_JYH21_RS00195_pPOta2VIM-11
• UniProt ID: _
• Length: 637 a.a.
• PDB ID: _
• Note: Predicted by oriTfinder 2.0

T4CP protein sequence

• Length: 637 a.a.
• Molecular weight: 69925.10 Da
• Isoelectric Point: 8.2999

>WP_019373230.1 MULTISPECIES: type IV secretory system conjugative DNA transfer family protein [Pseudomonadota]
MKIKMNNAVGPQVRTAKPKPSKLLPVLGAASMVGGLQAATQFFAHTFAYHATLGPNVGHVYAPWSILHWT
YKWYSQYPDEIMKAGSMGMLVSTVGLLGVAVARVVTSNSSKANEYLHGSARWAEKKDIQAAGLLPRERNV
LEIVTGKAAPTATGVYVGGWQDKDGNFFYLRHSGPEHVLTYAPTRSGKGVGLVVPTLLSWGASSVITDLK
GELWALTAGWRQKHAKNKVLRFEPASTSGGVCWNPLDEIRLGTEYEVGDVQNLATLIVDPDGKGLDSHWQ
KTAFALLVGVILHALYKAKDDGGTATLPSVDAMLADPNRDIGELWMEMATYGHVDGQNHHAIGSAARDMM
DRPEEEAGSVLSTAKSYLALYRDPVVARNVSRSDFRIKQLMHEDDPVSLYIVTQPNDKARLRPLVRVMVN
MIVRLLADKMDFEGGRPVAHYKHRLLMMLDEFPSLGKLEIMQESLAFVAGYGIKCYLICQDINQLKSRET
GYGHDESITSNCHVQNAYPPNRVETAEHLSRLTGQTTVVKEQITTSGRRTAAMLGQVSRTYQEVQRPLLT
PDECLRMPGPKKNAQGEIEEAGDMVIYVAGYPAIYGKQPLYFKDPVFSARAAIPAPKVSDRLRAVAQAET
EGEGITI

Protein domains

Predicted by InterproScan.

• Type IV secretory system Conjugative DNA transfer (T4SS-DNA_transf) (121-620)

Protein structure

No available structure.

T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 7413..18090

Locus tag	Coordinates	Strand	Size (bp)	Protein ID	Product	Description
JYH21_RS00010	3290..4303	-	1014	WP_204884877	class 1 integron integrase IntI1	-
JYH21_RS00015	4428..5228	+	801	WP_034080264	subclass B1 metallo-beta-lactamase VIM-11	-
JYH21_RS00020	5289..5636	+	348	WP_000679427	quaternary ammonium compound efflux SMR transporter QacE delta 1	-
JYH21_RS00025	5630..6469	+	840	WP_000259031	sulfonamide-resistant dihydropteroate synthase Sul1	-
JYH21_RS00030	6808..7395	-	588	WP_010890138	TrbM/KikA/MpfK family conjugal transfer protein	-
JYH21_RS00035	7413..9131	-	1719	WP_027814021	P-type conjugative transfer protein TrbL	virB6
JYH21_RS00040	9142..9369	-	228	WP_000644148	entry exclusion lipoprotein TrbK	-
JYH21_RS00045	9379..10143	-	765	WP_010890135	P-type conjugative transfer protein TrbJ	virB5
JYH21_RS00050	10164..11585	-	1422	WP_172693339	TrbI/VirB10 family protein	virB10
JYH21_RS00055	11590..12078	-	489	WP_006122479	conjugal transfer protein TrbH	-
JYH21_RS00060	12081..12980	-	900	WP_006122480	P-type conjugative transfer protein TrbG	virB9
JYH21_RS00065	12998..13780	-	783	WP_006122481	conjugal transfer protein TrbF	virB8
JYH21_RS00070	13777..16335	-	2559	WP_011114047	VirB4 family type IV secretion/conjugal transfer ATPase	virb4
JYH21_RS00075	16332..16643	-	312	WP_001207961	conjugal transfer protein TrbD	virB3
JYH21_RS00080	16647..17111	-	465	WP_011114046	conjugal transfer system pilin TrbC	virB2
JYH21_RS00085	17128..18090	-	963	WP_000132020	P-type conjugative transfer ATPase TrbB	virB11
JYH21_RS00090	18400..18762	-	363	WP_010890126	transcriptional regulator	-
JYH21_RS00095	18874..20036	+	1163	WP_085947771	IS3-like element IS3 family transposase	-
JYH21_RS00100	20161..21021	+	861	WP_000027057	broad-spectrum class A beta-lactamase TEM-1	-
JYH21_RS00105	21177..21881	+	705	WP_001067855	IS6-like element IS26 family transposase	-

Host bacterium

• ID: 7857
• GenBank: NZ_MW300276
• Plasmid name: pPOta2VIM-11
• Incompatibility group: IncP1
• Plasmid size: 44597 bp
• Coordinate of oriT [Strand]: 32349..32447 [-]
• Host baterium: Pseudomonas aeruginosa strain Ota2

Cargo genes

• Drug resistance gene: blaVIM-11, sul1, blaTEM-1B
• Virulence gene: -
• Metal resistance gene: -
• Degradation gene: -
• Symbiosis gene: -
• Anti-CRISPR: -