Detailed information of oriT

oriT

The information of the oriT region

• oriTDB ID: 105019
• Name: oriT_pC2601-6
• Organism: Klebsiella pneumoniae strain C2601
• Sequence Completeness: -
• NCBI accession of oriT (coordinates [strand]): NZ_CP039818 (9367..11073 [+], 1707 nt)
• oriT length: 1707 nt
• IRs (inverted repeats): _
• Location of nic site: _
• Conserved sequence flanking the nic site: _
• Note: Predicted by oriTfinder 2.0

oriT sequence

• Length: 1707 nt

>oriT_pC2601-6
GCCGTATGAATGACATTTATTTCCGTCCAATCCATCGCAATCAATATTTTGAGGAAATGAAAGCATGATAAAGAAACTTAAAGTAATCATGTTGGCGGCAATAGTTACCGGATGTTCATCGCCACCGCCTCCCGTTCCTGTAGAGTGGGATAAAGCCGCTGAGCCATTAAATACCAGTTTACCGCAATGGAGTGACAATAACGTTATAGTCCCTTCCCCGACAGTTAACGGTAAATGGACATCATCAATCAGCGCACAAAGTTTCCACGATACAATATGGACTCCAGCAGTATTTTACGCAGCCGCCCATTCAACACGAATTGTCGTCACTGCACAATCCGGTACTGATTTCTTTAATGCTAAAAACTGGCTTCGCCAGAATGGCGCAAAAGGCGTTATTGAATACCAGCCTGTCTTTAATTGCCTGACGTGCAGAGAAACCACTATTTATTTCTCTCGCTAATCCATTTAAGCAACACAATCTAATAAGGATTTATCATGAAAAAAACCGTTATCGCGGCGGCTGTATTATGCCTGACCGCAGGAACGCCGATTTATTCCTTTGCCGCTGACCCGTGCGAAGTTGTTCTTTGCATGTACGGAAAAGCTACAGGTAATAGTGGTGGGAGTGAATGCAGTTCAGCAGAACGCGCATTTTTTAAAATAAACGCATTTAAAAAACACCATCGTTTCAATCCGGGTAAAACATTCGATATGCGAAAAGAATTTTTAGGGGAGTGCAAAGCCGCAGACCCTGAATCAATAAGCAAAATCCTTTCAAAATTTGGTAGAGTGAAAGGATAACTGACATATCCATTTTTATATGAGATGTTCGGAATGATAAATGAAAATTTATTCATTAAGAATATACACTCAAAAAATCAGGACAGAATATCTGTAGCCCTGGTATATGACACGTTATCAAAAGAAGCCCACAGAGGTTGTGGGCTGTATTACGAAATATACGAAAGTTGTTTTATCGGTCTTTTGCGCGATCATCTTTCAGAACTTAATGAGGTTGACGCAAACAAATTAATACGCTATGCCGAAAGCAAAGGCACAAAAATTGATGATGCGTCCTACAGTGAAGCACTGGAAGCTGAAAGGGAGTGCCGGGCTGAAATATACCGCGAGCAAATGTAATCACACAAAACAAAAGTGTATTGTACAATACACAGACTAACAGGCTACGGGATTTTAAGGCTTCATTATTTTTGGCTTCAATTTCAAAGAAATTGTTAAGACGAAAAATAATGAAGTGGTACGCGGAAAGAAAATTCAATTTCGGAGAAATTGCTAATTTTCAGGAACCGCGCCCACCTGCGAACATTCGCCCACAGCGAATTGAGCAGGCCGGGGGGAGCCGCAAAAATTTTGCCGCCCCAGCGAGCAAAAAGGCACGCCCACGTGCCGTTTTTTGTGGGGGGCTTGCCCCGCACACCGTCGCAGCCAGGTAATATAACCCGCCCCAGCGGGGGATATTACCGATTAGGCGCGACCAACCCCTTTAAAGCAGCGTTCCGATTTTTTCGAGCTTGCGAGGAAAAATAGGCTAAACGCAGCGTCTTAAAGGGGTTGGTCGCGCGTAGCGCAAGACGGTGTGCCGCCTTTGACCTTGGGGGGTTTTGGCTCGGCGTCCAGCCGGGACATTACCCCCATGTGTCATGCAGTGAGGGCGTCCAGCCCGAACGTAATGGCACACGCCGT

oriT secondary structure

Predicted by RNAfold.

T4CP

t4cp2_FBF56_RS28560_pC2601-6

• ID: 3467
• GenBank: WP_012457110
• Name: t4cp2_FBF56_RS28560_pC2601-6
• UniProt ID: _
• Length: 912 a.a.
• PDB ID: _
• Note: Predicted by oriTfinder 2.0

T4CP protein sequence

• Length: 912 a.a.
• Molecular weight: 103056.99 Da
• Isoelectric Point: 7.4625

>WP_012457110.1 MULTISPECIES: VirB3 family type IV secretion system protein [Enterobacterales]
MAKLLKAMKRPAALWGVPMVPLLAVTGVTIIVAIWTSVALLFLLPVQFLVMKSLTRNEPMRFNLIAVWLR
AKGKPVANRLFGATTFMPVEHDDVDIKEFLDAMKLNQCATIKKYIPYSSHIHQHVVRSPKSDLYCTWELM
GTPFDCESDESLQFGTNQLHGLIRSFEGMPVTFYIHNDRNTFTDNLHKDSGNPYADEVSRLYYASVGLFR
RNRLFLTVCYRPFVSLEKAERKRMKDSQKLKELDGALLEMLEIKSTLDTALSRYGARPLGTFTEGSAVFS
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_FBF56_RS28620_pC2601-6

• ID: 3468
• GenBank: WP_094309419
• Name: t4cp2_FBF56_RS28620_pC2601-6
• UniProt ID: _
• Length: 578 a.a.
• PDB ID: _
• Note: Predicted by oriTfinder 2.0

T4CP protein sequence

• Length: 578 a.a.
• Molecular weight: 65670.93 Da
• Isoelectric Point: 7.4566

>WP_094309419.1 MULTISPECIES: type IV secretion system DNA-binding domain-containing protein [Enterobacterales]
MGSHLMQRLNAFADAFSFFLLWLQNSPVILSLLAGLTLPFIFHLPREERKNAPFWLKSVACVSIFFFIFG
TISPLTIQGLSYFFKSLDNNILFRVPLWIMTIIFTAAGLIFHIAVRRLLAGEIDNLKHRMIKKSKLERNT
RTDVRKVKELLPDSIEYNPLDYIDLKKGVFIGLNKDDQPQYITIKEFKTQHAAIIGTTGSGKGVTATVLL
YQAILLGEAVFVEDPKDDEWAPHVLREACKKAGKKFTLINLNKLNFQLDLLADISHEQLEELFNAGFSLA
KKGEASDFYRISDRRAARNTSAIYEKGMTLRDLFNTDFVQSLREDVPAFCGELEEIALVNSINATKGFSL
KEVFDEGGCCYIIGSTRNQKIISAQRMILTRLIQIAETRDRINSTPRTVAIFLDELKYHLSRPALEGLGT
ARDKGVHIFMAFQAIDDLRDCPSDLNGDSVIGAIIENAKFKLIYKIQNPETAEWAAKMTGSILVDDEMRK
VRTDLSLTEKVDTDRMIRQAESYYVDSNMFLNLPEKVGFVFTSTELPRATKMFQVQVKKENIELLSFEYK
QATPEKNESQEHKPSINL

Protein domains

Predicted by InterproScan.

• Helicase HerA, central domain (DUF87) (174-280)

• 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: 184..13026

Locus tag	Coordinates	Strand	Size (bp)	Protein ID	Product	Description
FBF56_RS28555 (FBF56_28690)	184..489	+	306	WP_012457109	TrbC/VirB2 family protein	virB2
FBF56_RS28560 (FBF56_28695)	502..3240	+	2739	WP_012457110	VirB3 family type IV secretion system protein	virb4
FBF56_RS28565 (FBF56_28700)	3259..3969	+	711	WP_012457111	type IV secretion system protein	-
FBF56_RS28570 (FBF56_28705)	3979..4206	+	228	WP_004178109	EexN family lipoprotein	-
FBF56_RS28575 (FBF56_28710)	4218..5294	+	1077	WP_012457112	type IV secretion system protein	virB6
FBF56_RS28850	5386..5523	+	138	WP_039109361	hypothetical protein	-
FBF56_RS28585 (FBF56_28715)	5516..6199	+	684	WP_004178111	type IV secretion system protein	virB8
FBF56_RS28590 (FBF56_28720)	6196..7104	+	909	WP_012457114	P-type conjugative transfer protein VirB9	virB9
FBF56_RS28595 (FBF56_28725)	7151..8419	+	1269	WP_139968916	VirB10/TraB/TrbI family type IV secretion system protein	virB10
FBF56_RS28600 (FBF56_28730)	8409..9434	+	1026	WP_032442691	P-type DNA transfer ATPase VirB11	virB11
FBF56_RS28605 (FBF56_28735)	9431..9829	+	399	WP_162262155	cag pathogenicity island Cag12 family protein	-
FBF56_RS28610 (FBF56_28740)	9865..10170	+	306	WP_012457118	hypothetical protein	-
FBF56_RS28615 (FBF56_28745)	10204..10509	+	306	WP_094309429	dpoa decarboxylase	-
FBF56_RS28620 (FBF56_28760)	11290..13026	+	1737	WP_094309419	type IV secretion system DNA-binding domain-containing protein	virb4
FBF56_RS28625 (FBF56_28765)	13035..13790	+	756	WP_023316386	MobC family replication-relaxation protein	-
FBF56_RS28630 (FBF56_28770)	14138..14317	+	180	Protein_16	helix-turn-helix domain-containing protein	-
FBF56_RS28635 (FBF56_28775)	14382..15086	+	705	WP_001067855	IS6-like element IS26 family transposase	-
FBF56_RS28640 (FBF56_28785)	15591..16247	+	657	WP_001516695	quinolone resistance pentapeptide repeat protein QnrS1	-
FBF56_RS28645 (FBF56_28790)	16566..17180	-	615	WP_014839983	recombinase family protein	-

Host bacterium

• ID: 5457
• GenBank: NZ_CP039818
• Plasmid name: pC2601-6
• Incompatibility group: IncFII
• Plasmid size: 35466 bp
• Coordinate of oriT [Strand]: 9367..11073 [+]
• Host baterium: Klebsiella pneumoniae strain C2601

Cargo genes

• Drug resistance gene: qnrS1
• Virulence gene: -
• Metal resistance gene: -
• Degradation gene: -
• Symbiosis gene: -
• Anti-CRISPR: -