Detailed information of oriT

oriT

The information of the oriT region

• oriTDB ID: 101242
• Name: oriT_pTR3
• Organism: Klebsiella pneumoniae JT4
• Sequence Completeness: -
• NCBI accession of oriT (coordinates [strand]): NZ_JAPZ01000355 (4180..4262 [-], 83 nt)
• oriT length: 83 nt
• IRs (inverted repeats): 27..34, 37..44 (AGTGCGAT..ATCGCACT) 13..18, 32..37 (TAAATC..GATTTA)
• Location of nic site: 55..56
• Conserved sequence flanking the nic site: GGTGTATAGC
• Note: Predicted by oriTfinder 2.0

oriT sequence

• Length: 83 nt

>oriT_pTR3
TTTTTTGTTTTTTAAATCAGTTAGTTAGTGCGATTTATCGCACTGCGTTAGGTGTATAGCAGGTTAAGGGCTAAAAAATAATC

oriT secondary structure

Predicted by RNAfold.

Relaxase

mobF_AH61_RS30290_pTR3

• ID: 1214
• GenBank: WP_014014966
• Name: mobF_AH61_RS30290_pTR3
• UniProt ID: I7CZU5
• Length: 1068 a.a.
• Note: Predicted by oriTfinder 2.0

Relaxase protein sequence

• Length: 1068 a.a.
• Molecular weight: 118452.14 Da
• Isoelectric Point: 6.4309

>WP_014014966.1 MULTISPECIES: MobF family relaxase [Enterobacterales]
MLDITTITRIDIASVVGYYADAKDDYYSKDSSFTAWHGQGAEALGLSGEVSSQRFKELLVGEIDPFTQMK
RSSGDATKERLGYDLTFSAPKGVSMQALIHGDKAIIAAHEKAVAAAVQEAEKLAQARTTHAGKTITQNTG
NLVVASFRHETSRALDPELHTHAFVMNMTQRGDGQWRALKNDELMRAKMHLGDVYKQELALELTKAGYEL
RYNNKNNTFDMAHFTDEQIRGFSRRSAQIEEGLAAMGLTRETADAQTKSRVSMATRDKKTDDYSREDIHK
EWVNRANELGIDFNDLSWAGKGKDGPQTSMNTVPNFTSPEVKADRAIQFALKSLSERDASFDQSRLLAVA
NKKAIGQASKQDIEAAYYRAVAKGAIIEGEARYTTTTDQRSKDAPPLPAMTKAEWQAQLTDKKGMNNDQA
KALVAEGIKSGRLKKTSHRVTTVEGIRVEKAVLNIEARGRGKVIAALTSEQVTAQLVGKTLKAEQQKSVV
DICTTTDRFVAAHGFAGTGKSYMTMSAKAVLESQGFNVTALAPYGTQKKSLEDEGMPARTVAAFVKAKDK
KIDEKSVVFIDEAGVIPARQMKVLMETIEKAGARAVFLGDTSQTKAVEAGKPFEQLISAGMQTSYMKDIQ
RQKNDVLLEAVKLAAEGHISGSLARLSNISAEKDQDKRLEAVANRWLSFSPEQREGTLIISGTNESRVIL
NSQIREALQLQGKGVEVNFLERVDSTQAERRDSKYYQVGQIIIPEKDYKNGLQRGESYRVLDTGPGNLLT
VAGSDGQKISFSPRTHKNLSVYTSVAAELAVGDKVMVTRNDKTLDVANGDRFTVTGTTEKGTFTLTNAKG
REIELDQKQAAYLSYAYATTVHKAQGLTCDRVLFNIDTRSLTTSKDVFYVGISRARHEVEIFTDDKKRLL
SSASRNSPKTTASEIDRFLGMEERYKDVNRSDGQQEKSYGHDAGHQTEEKENTMKNATEAAHDGPDTSGT
ENTSQDLRQREQEEVNAAIRYEQRQEATPEMEANPYHDYERYADEGPDYGDMQDYSTYEEYERARDVELP
QHEHENHQHDHDKEGYGL

Protein domains

Predicted by InterproScan.

• TrwC relaxase (TrwC) (16-288)

• AAA domain (AAA_30) (480-656)

• UvrD-like helicase C-terminal domain (UvrD_C_2) (855-899)

Protein structure

• AlphaFold DB: I7CZU5

T4CP

t4cp2_AH61_RS30285_pTR3

• ID: 825
• GenBank: WP_014014965
• Name: t4cp2_AH61_RS30285_pTR3
• UniProt ID: _
• Length: 510 a.a.
• PDB ID: _
• Note: Predicted by oriTfinder 2.0

T4CP protein sequence

• Length: 510 a.a.
• Molecular weight: 58174.11 Da
• Isoelectric Point: 9.7081

>WP_014014965.1 MULTISPECIES: type IV secretion system DNA-binding domain-containing protein [Enterobacterales]
MTEQERGLIFLCSLLGPIPFVWFITAKFVYGINSETAHYLVPYLLKNTFNLWPLWVAIIAGAVIGLCGFI
GFIIYDKGRVYKGPRFKRVLRGTKLVRASSLAERTKERGHKQLTVAGVPVPTEYETLHFSIGGATGTGKS
TIIKEAIYSSLKRGRDKRVILDPNGEYVETFYRENDIILNPYDKRSPGWSMFNEIRDEFDYDLYAVSIIQ
ESKERSAEEWYRYGRLLYREVSKKLLTHKRNPSMEEVLYWCNVAEYDKVKDFVKGTPAESLFIKGAERAT
GSARFVLGDKLASHLKMPEGNFSLRDWLEDDKPGTLFITWQEQMKKSLNPLISCWLDIMFSSLLGMGKRD
QRTLFFIDELESLEYLPNLQDLLTKGRKSGASVWAGYQTFSQLVERYGINIAETLLGSMRSGIVMGSSRL
GKATLEHMSRALGEIEGEIERRQGGILQSGPNNRPRIETRTVRAVTPTEISELRNLTGYIYFPGDLPVGK
FKTKHVQYTRKNPVPGIIMR

Protein domains

Predicted by InterproScan.

• Type IV secretion-system coupling protein DNA-binding domain (TrwB_AAD_bind) (113-492)

Protein structure

No available structure.

T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 20477..30759

Locus tag	Coordinates	Strand	Size (bp)	Protein ID	Product	Description
AH61_RS30340	15830..16642	-	813	WP_004201164	subclass B1 metallo-beta-lactamase NDM-1	-
AH61_RS30350	16938..17969	+	1032	WP_001395480	IS630-like element ISEc33 family transposase	-
AH61_RS32445	17988..18734	-	747	Protein_18	IS30-like element ISAba125 family transposase	-
AH61_RS30360	19953..20465	-	513	WP_029697418	phospholipase D family protein	-
AH61_RS30365	20477..21478	-	1002	WP_001076634	ATPase, T2SS/T4P/T4SS family	virB11
AH61_RS30370	21529..22668	-	1140	WP_014014945	type IV secretion system protein VirB10	virB10
AH61_RS30375	22668..23555	-	888	WP_014014946	TrbG/VirB9 family P-type conjugative transfer protein	virB9
AH61_RS30380	23566..24261	-	696	WP_014014947	type IV secretion system protein	virB8
AH61_RS30385	24480..25517	-	1038	WP_014014948	type IV secretion system protein	virB6
AH61_RS30390	25534..25776	-	243	WP_000858958	EexN family lipoprotein	-
AH61_RS30395	25786..26487	-	702	WP_014014949	type IV secretion system protein	virB5
AH61_RS30400	26503..29076	-	2574	WP_014014950	VirB4 family type IV secretion/conjugal transfer ATPase	virb4
AH61_RS30405	29077..29394	-	318	WP_000462629	VirB3 family type IV secretion system protein	virB3
AH61_RS30410	29434..29775	-	342	WP_001121032	TrbC/VirB2 family protein	virB2
AH61_RS30415	29977..30759	-	783	WP_014014952	lytic transglycosylase domain-containing protein	virB1
AH61_RS30420	30859..31176	+	318	WP_000960955	H-NS family nucleoid-associated regulatory protein	-
AH61_RS30425	31180..31530	+	351	WP_014014953	hypothetical protein	-
AH61_RS30430	31527..31865	+	339	WP_000040982	hypothetical protein	-
AH61_RS30435	31869..32177	+	309	WP_000733764	hypothetical protein	-
AH61_RS30440	32462..32647	+	186	WP_014014955	ribbon-helix-helix domain-containing protein	-
AH61_RS30445	32644..33252	-	609	WP_042939603	recombinase family protein	-

Host bacterium

• ID: 1686
• GenBank: NZ_JAPZ01000355
• Plasmid name: pTR3
• Incompatibility group: -
• Plasmid size: 33313 bp
• Coordinate of oriT [Strand]: 4180..4262 [-]
• Host baterium: Klebsiella pneumoniae JT4

Cargo genes

• Drug resistance gene: blaNDM-1
• Virulence gene: -
• Metal resistance gene: -
• Degradation gene: -
• Symbiosis gene: -
• Anti-CRISPR: -