Detailed information of oriT

oriT

The information of the oriT region

• oriTDB ID: 200171
• Name: oriT_ICEKpnAR_0139-1
• Organism: Klebsiella pneumoniae strain AR_0139
• Sequence Completeness: -
• NCBI accession of oriT (coordinates [strand]): CP021960 (46141..46264 [+], 124 nt)
• oriT length: 124 nt
• IRs (inverted repeats): 42..47, 59..64 (TTTTTC..GAAAAA)
• Location of nic site: _
• Conserved sequence flanking the nic site: _
• Note: Predicted by oriTfinder 2.0

oriT sequence

• Length: 124 nt

>oriT_ICEKpnAR_0139-1
CCGATTAGGCGCGACCAACCCCTTTAAAGCAGCGTTCCGATTTTTTCGAGCTTGCGAGGAAAAATAGGCTAAACGCAGCGTCTTAAAGGGGTTGGTCGCGCGTAGCGGGCGACGGTGTGCCGCC

oriT secondary structure

Predicted by RNAfold.

T4CP

t4cp2_AM386_29305_ICEKpnAR_0139-1

• ID: 16623
• GenBank: ASC25596
• Name: t4cp2_AM386_29305_ICEKpnAR_0139-1
• UniProt ID: _
• Length: 912 a.a.
• PDB ID: _
• Note: Predicted by oriTfinder 2.0

T4CP protein sequence

• Length: 912 a.a.
• Molecular weight: 103113.06 Da
• Isoelectric Point: 7.2988

>ASC25596.1 ATPase [Klebsiella pneumoniae]
MAKLLKAMKRPAALWGVPMVPLLAVTGVTIIVAVWTSVALLFLLPVEFLVMKSLTRNEPMRFNLIAVWLR
VKGKPVANRLFGATTFMPVEHDDVDIKEFLDAMKLNQCATIKKYIPYSSHIHQHVVRSPKSDLYCTWELM
GTPFDCESDESLQFGTNQLHGLIRSFEGMPVTFYIHNDRNTFTDNLHKDSGNPYADEVSRLYYASVGLFR
RNRLFLTVCYRPFVSLEKAERKRMKDSQKLKELDGALQEMLEIKSTLDTALSRYGARPLGTFTEGSAVFS
SQLAFYEYLLTHQWRKVRVTRTPAYDVMGAAALFFSAESGQINHANGTQYFRGLEVKEFSEETATGMMDS
LLYAPCDYVITQSYTCMSREEAKKAIKRTRRLLMSADDDAVSQRLDLDVALDLLTSGKIAYGKHHFSIMV
YSPLLESLVADTNEISNALNNIGITPVPAEISLSAAYMAQLPGNYNLRPRKGELSSQNFVELAALHNFYP
GKRDKAPWGDAMALLRTPSGDGYYINLHNTLADKDEFNEKNPASTCILGTNGSGKTMLMTFFEIMQQKYG
REDSFSPDAKTKRLTTVYLDKDRGAEMNIRALGGRYYRVISGESTGWNPFSLPATKRNINFIKQLMKILC
TRNGSTISPRDERRLSDAVNAVMNDEPQYRVYGITRMLENLPEPATKEAQENGLSIRLSQWAQGGEFGWV
FDNESDTFDISNCDNFGIDGTEFLDDASVCAPISFYLLYRITSLLDGRRLVIFMDEFWKWLRDPVFKDFA
YNKLKTIRKLNGMLVVGTQSPAEIIKDDIAPAVIEQCGTQILAANPNADRAHYVDGMKFEPEVFDVVKGL
DPQARQYVVVKNQFKRGDTKRFAARVTLDLSGIGRYTKVMSGDAPNLEIFESIYREGMQPHEWLDTYLAK
AL

Protein domains

Predicted by InterproScan.

• Type IV secretory pathway, VirB3-like protein (VirB3) (3-79)

• CagE, TrbE, VirB family, component of type IV transporter system (CagE_TrbE_VirB) (269-470)

• TraG P-loop domain (P-loop_TraG) (535-813)

Protein structure

No available structure.

t4cp2_AM386_29375_ICEKpnAR_0139-1

• ID: 16624
• GenBank: ASC25609
• Name: t4cp2_AM386_29375_ICEKpnAR_0139-1
• UniProt ID: _
• Length: 619 a.a.
• PDB ID: _
• Note: Predicted by oriTfinder 2.0

T4CP protein sequence

• Length: 619 a.a.
• Molecular weight: 69580.79 Da
• Isoelectric Point: 6.2731

>ASC25609.1 MFS transporter [Klebsiella pneumoniae]
MILNKLAASLSPIVNGMLALLAFVQQQQLILALLAGLTMPFFASMKSDERQKAPLWKKLIIAFSMLCFLS
GTLAPIVIGSFQWLYKIRLTSDNSALAWSVRIAFTVTGIIFHIMLRRVFTPELDKIKKRLVKKTTLEREL
RTDVRTVKSLLPETLHYDPLDYIDLNKGIFTGMDRENEPMYLPLKDWQKQHADIIGTTGAGKGVATGILL
YQSILAGEGVFVMDPKDDEWAPHLYRKACEDAGKPFALIDLRKQQYQLNLIEDITPDELEELFVAGFSLA
EKGQESDFYRIDDRKAARMAAQFVSDNPSATIRDVYNGDYVQGIAEKIKAFFGKIEELALLNAINSPEGF
SLKHIFDEGGCCYVVGSMRNSKIITAQRMLLVRLYQLAEKRDRVTDVPRPIAIYLSELKYHLSRPALEGL
GAARDKGVHIIMDHQSIADLKDCPADLKGDAVVGAVVENAKFKLVYRVMDPDTAEWVARMSGTILVDDEL
RKAKTDNMLTETIDSERTIRQAERFFIDSNMILNLPDFVSFIFTTKTLPSASLISPIKVRKRQLKIFSVS
PDIATAAAPVKIMLDFGEDDKPAMPDVMTTHPALFFDEREVRPATPKSDDEKDLSPLDF

Protein domains

Predicted by InterproScan.

• TraM recognition site of TraD and TraG (TraG-D_C) (417-516)

Protein structure

No available structure.

T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 5263714..5273631

Locus tag	Coordinates	Strand	Size (bp)	Protein ID	Product	Description
AM386_29260	5260248..5261174	+	927	ASC25587	hypothetical protein	-
AM386_29265	5261314..5261499	+	186	ASC25588	transcriptional regulator	-
AM386_29270	5261521..5261703	+	183	ASC25589	hypothetical protein	-
AM386_29275	5261688..5262269	+	582	ASC25590	hypothetical protein	-
AM386_29280	5262259..5262468	+	210	ASC25591	conjugal transfer protein TraR	-
AM386_29285	5262711..5262839	+	129	ASC25592	transcriptional regulator	-
AM386_29290	5263408..5263641	+	234	ASC25593	hypothetical protein	-
AM386_29295	5263714..5264424	+	711	ASC25594	type VI secretion protein	virB1
AM386_29300	5264424..5264717	+	294	ASC25595	TriB protein	virB2
AM386_29305	5264730..5267468	+	2739	ASC25596	ATPase	virb4
AM386_29310	5267486..5268190	+	705	ASC25597	type IV secretion system protein VirB5	-
AM386_29315	5268200..5268427	+	228	ASC25598	hypothetical protein	-
AM386_29320	5268439..5269518	+	1080	ASC25599	conjugal transfer protein TrbL	virB6
AM386_29325	5269585..5269704	-	120	ASC25600	hypothetical protein	-
AM386_29330	5269734..5270417	+	684	ASC25601	hypothetical protein	virB8
AM386_29335	5270414..5271322	+	909	ASC25602	P-type conjugative transfer protein VirB9	virB9
AM386_29340	5271366..5272616	+	1251	ASC25603	type VI secretion protein	virB10
AM386_29345	5272606..5273631	+	1026	ASC25604	P-type DNA transfer ATPase VirB11	virB11
AM386_29350	5273628..5274035	+	408	ASC25605	Cag pathogenicity island protein Cag12	-
AM386_29355	5274062..5274364	+	303	ASC25606	kikA from plasmid origin	-
AM386_29360	5274558..5274713	+	156	ASC25607	hypothetical protein	-
AM386_29365	5274734..5275121	+	388	Protein_5470	hypothetical protein	-
AM386_29370	5275146..5275406	+	261	ASC25608	hypothetical protein	-
AM386_29375	5275424..5277283	+	1860	ASC25609	MFS transporter	-
AM386_29380	5277293..5278039	+	747	ASC25610	molybdopterin-guanine dinucleotide biosynthesis protein MobC	-

Host bacterium

• ID: 165
• Element type: ICE (Integrative and conjugative element)
• Element name: ICEKpnAR_0139-1
• GenBank: CP021960
• Element size: 5606368 bp
• Coordinate of oriT [Strand]: 46141..46264 [+]
• Host bacterium: Klebsiella pneumoniae strain AR_0139
• Coordinate of element: 5228915..5298133

Cargo genes

• Drug resistance gene: -
• Virulence gene: ybtS, ybtX, ybtQ, ybtP, ybtA, irp2, irp1, ybtU, ybtT, ybtE, fyuA
• Metal resistance gene: -
• Degradation gene: -
• Symbiosis gene: -
• Anti-CRISPR: -