Detailed information of oriT

oriT

The information of the oriT region

• oriTDB ID: 200252
• Name: oriT_ICEKpnKPNIH32-1
• Organism: Klebsiella pneumoniae subsp. pneumoniae strain KPNIH32
• Sequence Completeness: -
• NCBI accession of oriT (coordinates [strand]): CP009775 (80691..80814 [+], 124 nt)
• oriT length: 124 nt
• IRs (inverted repeats): 95..102, 106..113 (GTCGCGCG..CGCGCGAC) 40..47, 59..66 (ATTTTTTC..GAAAAAAT)
• Location of nic site: _
• Conserved sequence flanking the nic site: _
• Note: Predicted by oriTfinder 2.0

oriT sequence

• Length: 124 nt

>oriT_ICEKpnKPNIH32-1
CCGATTAGGCGCGACCAACCCCTTTAAAGCAGCGTTCCCATTTTTTCGAGCTTGCGAAGAAAAAATAGGCTAAACGCGCGTCTTAAAGGGGTTGGTCGCGCGTAGCGCGCGACGGTGTGCCGCC

oriT secondary structure

Predicted by RNAfold.

T4CP

t4cp2_KPNIH32_17685_ICEKpnKPNIH32-1

• ID: 16752
• GenBank: AIW77463
• Name: t4cp2_KPNIH32_17685_ICEKpnKPNIH32-1
• UniProt ID: _
• Length: 912 a.a.
• PDB ID: _
• Note: Predicted by oriTfinder 2.0

T4CP protein sequence

• Length: 912 a.a.
• Molecular weight: 103084.02 Da
• Isoelectric Point: 7.4625

>AIW77463.1 ATPase [Klebsiella pneumoniae subsp. pneumoniae]
MAKLLKAMKRPAALWGVPMVPLLAVTGVTIIVAIWTSVALLFLLPVQFLVMKSLTRNEPMRFNLIAVWLR
AKGKPVANRLFGATTFMPVEHDDVDIKEFLDAMKLNQCATIKKYIPYSSHIHQHVVRSPKSDLYCTWELM
GTPFDCESDESLQFGTNQLHGLIRSFEGMPVTFYIHNDRNTFTDNLHKDSGNPYADEVSRLYYASVGLFR
RNRLFLTVCYRPFVSLEKAERKRMKDSQKLKELDGALLEMLEIKSTLDTALSRYGARPLGTFTEGNAVFS
SQLAFYEYLLTHQWRKVRVTRTPAYDVMGAAALFFSAESGQINHANGTQYFRGLEVKEFSEETATGMMDS
LLYAPCDYVITQSYTCMSREEAKKAIKRTRRLLMSADDDAVSQRLDLDVALDLLTSGKIAYGKHHFSIMV
YSPSLESLVADTNEISNALNNIGITPVPAEISLSAAYMAQLPGNYNLRPRKGELSSQNFVELAALHNFYP
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_KPNIH32_17740_ICEKpnKPNIH32-1

• ID: 16753
• GenBank: AIW77473
• Name: t4cp2_KPNIH32_17740_ICEKpnKPNIH32-1
• UniProt ID: _
• Length: 579 a.a.
• PDB ID: _
• Note: Predicted by oriTfinder 2.0

T4CP protein sequence

• Length: 579 a.a.
• Molecular weight: 65588.83 Da
• Isoelectric Point: 8.0425

>AIW77473.1 molybdopterin-guanine dinucleotide biosynthesis protein MobB [Klebsiella pneumoniae subsp. pneumoniae]
MGSHLMQRLNAFADAFSFFLLWLQNSPVILSLFAGLTLPFIVNLPREERKNAPFWLKSVACVSIFFFIFG
TISPLTIQGLSYFFKLLDNNILFRIPLWIMTVTFTTAGLFFHIAARRLLAGEIDNLKHRMIKKTKLERNT
RTDVRKVKELLPESIEYNPLDYIDLKKGAFIGLNKNDQPQYITIKEFKTQHAAIIGTTGSGKSVTAAILL
YQAILAGEAVFVEDPKDDEWAPHVLREACKKAGKKFTLINLNKPNFQLDLLADISHEQLEELFNAGFSLA
KKGEASDFYRISDRRAARNTSAIYEKGMTLYDLFNTDFVQSLRQAAPAFFGELEEVALVNSINATNGFSL
KEVFDEGGCCYIIGSTRNQKIISAQRMILTRLIQIAETRDRINSTPRTVAIFLDELKYHLSRPALEGLGT
ARDKGVHIFMAFQAIDDLRDCPSDLNGDAVIGAIIENAKFKLIYKIQNPETAEWAAKMTGSILVDDEMRK
VRTDLSLTEKMDTDRMIRQAESYYVDSNMFLNLPEKVGFVFTTKELAKATKMSPILVKKKHIELLSFENP
QSEQPQTEINEQNKPSINL

Protein domains

Predicted by InterproScan.

• Helicase HerA, central domain (DUF87) (174-227)

• TraM recognition site of TraD and TraG (TraG-D_C) (399-490)

Protein structure

No available structure.

T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 3498947..3512794

Locus tag	Coordinates	Strand	Size (bp)	Protein ID	Product	Description
KPNIH32_17645	3495481..3496407	+	927	AIW77455	hypothetical protein	-
KPNIH32_17650	3496547..3496732	+	186	AIW77456	DNA-binding protein	-
KPNIH32_17655	3496921..3497502	+	582	AIW77457	hypothetical protein	-
KPNIH32_17660	3497492..3497701	+	210	AIW77458	conjugal transfer protein TraR	-
KPNIH32_17665	3497944..3498072	+	129	AIW77459	gene expression modulator	-
KPNIH32_17670	3498641..3498874	+	234	AIW77460	ATP-binding protein	-
KPNIH32_17675	3498947..3499657	+	711	AIW77461	type VI secretion protein	virB1
KPNIH32_17680	3499657..3499950	+	294	AIW77462	TriB protein	virB2
KPNIH32_17685	3499963..3502701	+	2739	AIW77463	ATPase	virb4
KPNIH32_17690	3502719..3503426	+	708	AIW77464	Minor pilin of type IV secretion complex (VirB5)	-
KPNIH32_17695	3503680..3504753	+	1074	AIW77465	conjugal transfer protein TrbL	virB6
KPNIH32_17700	3504826..3504945	-	120	AIW77466	hypothetical protein	-
KPNIH32_17705	3504975..3505658	+	684	AIW77467	membrane protein	virB8
KPNIH32_17710	3505658..3506563	+	906	AIW79483	type VI secretion protein	virB9
KPNIH32_17715	3506607..3507851	+	1245	AIW77468	type VI secretion protein	virB10
KPNIH32_17720	3507863..3508183	+	321	AIW77469	hypothetical protein	-
KPNIH32_17725	3508173..3509198	+	1026	AIW77470	ATPase	virB11
KPNIH32_17730	3509627..3509929	+	303	AIW77471	conjugal transfer protein	-
KPNIH32_17735	3509972..3510277	+	306	AIW77472	dopa decarboxylase	-
KPNIH32_17740	3511055..3512794	+	1740	AIW77473	molybdopterin-guanine dinucleotide biosynthesis protein MobB	virb4
KPNIH32_17745	3512803..3513567	+	765	AIW77474	molybdopterin-guanine dinucleotide biosynthesis protein MobC	-
KPNIH32_17750	3514837..3515349	-	513	AIW77475	hypothetical protein	-
KPNIH32_17755	3515384..3515953	-	570	AIW79484	thioesterase	-
KPNIH32_17760	3516099..3517604	-	1506	AIW77476	beta-lactamase	-

Host bacterium

• ID: 231
• Element type: ICE (Integrative and conjugative element)
• Element name: ICEKpnKPNIH32-1
• GenBank: CP009775
• Element size: 5515525 bp
• Coordinate of oriT [Strand]: 80691..80814 [+]
• Host bacterium: Klebsiella pneumoniae subsp. pneumoniae strain KPNIH32
• Coordinate of element: 3429929..3562951

Cargo genes

• Drug resistance gene: -
• Virulence gene: ybtS, ybtX, ybtQ, ybtP, ybtA, irp2, irp1, ybtU, ybtT, ybtE, fyuA, clbS, clbQ, clbP, clbO, clbN, clbM, clbL, clbJ, clbI, clbH, clbG, clbF, clbE, clbD, clbC
• Metal resistance gene: -
• Degradation gene: -
• Symbiosis gene: -
• Anti-CRISPR: -