Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   100762
Name   oriT_pRM10607 in_silico
Organism   Salmonella enterica subsp. enterica serovar Typhimurium strain RM10607
Sequence Completeness      intact
NCBI accession of oriT (coordinates [strand])   NZ_CP013721 (60661..60919 [-], 259 nt)
oriT length   259 nt
IRs (inverted repeats)      115..128, 134..147  (ATAGCGGTGCCGGC..GCCTGCACCGCTAT)
Location of nic site      241..242
Conserved sequence flanking the
  nic site    		  GTGGGGTGT|GG
Note   predicted by the oriTfinder

  oriT sequence  


Download         Length: 259 nt

>oriT_pRM10607
GCAGCGCCCCCAGGGGTGTTACTTAAAAACAGGCACAGCGACGCTAGCAGCGCCCCTGATATAATGCAATGTTTTTTATAAAAATAGTCAGTACTACCCCTGTATAGCGTCGTCATAGCGGTGCCGGCGACGTGCCTGCACCGCTATTTAATACATTAAAATAAATTAAATTACATTATTATGAACATAACTCACTGTTACTAAAAACAAATCAGAAAAATTTTAATTTTGCGTGGGGTGTGGTGCTTTTGGTGGTGAG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   834 GenBank   WP_000986921
Name   TraI_pRM10607 insolico UniProt ID   _
Length   1752 a.a. PDB ID   
Note   putative relaxase

  Relaxase protein sequence


Download         Length: 1752 a.a.        Molecular weight: 191683.72 Da        Isoelectric Point: 5.9311

>WP_000986921.1 MULTISPECIES: conjugative transfer relaxase/helicase TraI [Salmonella]
MMSIAQVRSAGSAAGYYSDRDNYYVLGSMEERWAGKGAEQLGLQGTVDKEVFTRVLEGRLPDGADLSRQQ
DGGNKHRPGYDLTFSAPKSVSLMAMLAGDKRLTEAHNQAVDIAVRQVEALASTRVMTDGQSETVLTGNLV
MALFNHDTSRDQEPQLHTHAVVVNVTQHDGEWKTLSSDKVGKTGFIENVYANQIAFGKIYRAVLKEKVEA
LGYETEVVGKHGMWEMPGVPVEAFSSRSQAIREAVGEDASLKSRDVAALDTRKSKQHVDPEVKMAEWMQT
LKDTGFDISAYRESADRRAEIQAAQPVPSQEQPDIQQAVTQAIAGLSDRKVQFTYTDVLARTVGMLPPEA
GVIEKARAGIDEAISREQLIPLDREKGLFTSGIHVLDELSVRALSSDIMKQNRVTVHPEKSVPRTGSYSD
AVSVLAQDRPSLAIISGQGGAAGQRERVAELTMMAREQGREVQIIVADRRSQTNLKQDERLSGELITGRR
QLQEGMLFSPGSTVIVDQGEKLSLKETLTLLDGAARHNVQVLITDSGQRTGTGSALMAMKEAGVNSYRWQ
GRQQTPATVISEPDRNVRYARLAGDFVAAVKAGEESVAQVSGMREQAILAGMIRSELKTQGILGQQDTMM
TALSPVWLDSRNRYLRDMYREGMVMEQWNPEKRSHDRYVIDRVTAQSHSLTLRDAQGETQMVRISALDSS
WSLFRPEKMPVADGERLMVTGKIPGLRVSVGDRLQVSAVNDGVMTVTVPGRAEPASLPVGDSPFTALKLE
NGWVETPGHSVSDSAKVFASVTQMAMDNATLNSLARSGRDVRLYSSLDETRTAEKLSRHPSFTVVSEQIK
ARAGEVSLETAISRQKAGLHTPAQQAIHLALPVVESKNLAFSQVDLLTEAKSFAAEGTGFADLGREIDAQ
IKRGDLLYVDVAKGYGTDLLISRASYDAEKSILHHILEGKEAVTPLMERVPGELMETLTSGQRAATRMIL
ETKDRFTVVQGYAGVGKTTQFRAVMSAVNLLPESERPRVVGLGPTHRAVGEMRSAGVEAQTLASFLHDTQ
LQQRSGETPDFSNTLFLLDESSMVGNTDMARAYALIAAGGGRAVASGDTDQLQAIAPGQPFRLQQTRSAA
DVAIMKEIVRQTPELRDAVYSLINRDVNKALSGLENVKPVQVPRLKGAWAPENSVTEFSRLQERELAKAA
QEAEKKGEAFPDVPVTLYEAIVRDYTGRTPEAREQTLIVTHLNEDRRVLNSMIQDALAKPGEQQVTVPVL
TTANIRDGELRRLSTWEAHPGALALVDNVYHRIAGISKEDGLITLEDKAGNTRLISPREAAAEGVTLYNP
ETIRVGAGDRMRFTKSDRERGYVANSVWTVTAVSGDSVTLSDGKQTRVVRPGQDRAEQHIDLAYAITAHS
AQGASETFAIALEGTEGGRKQMAGFESAYVALSRMKQHVQVYTDDRQGWVKAINSAEQKGTAHDVLEPKS
EREMMNAERLFSTARELRDVAAGRAVLRNAGLAQGDSRARFIAPGRKYPQPYVALPAFDRNGKSAGIWLN
PLTTDDGAGLRGFTGEGRVKGSEEAQFVALQGSRNGESLLAGSMQDGVRIARENPDSGVVVRIVGDGRPW
NPVAITGGRVWGDIPDSNVQPGAGNGEPVTAEILAQRQAEEAVRRETERRADEIVRKMAEDKSDLPEEKT
AQAVREIAGQEQDRMTPPEREPPLPESVLREPQRERETIREVARENRGRERLQQMEQEMVRDLQKEKTPG
GD

  Protein domains


Predicted by InterproScan.

AAA domain (AAA_30)

(967-1158)

TrwC relaxase (TrwC)

(11-282)

DNA relaxase TraI 2B/2B-like domain (TraI_2B)

(632-711)

single-stranded DNA binding TraI N-terminal subdomain (ssDNA_TraI_N)

(574-626)

DNA helicase TraI (TraI_C)

(1430-1553)


  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 60117..86552

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
SEETMRM10607_RS25460 (SEETMRM10607_25400) 55273..57270 + 1998 WP_000117513 ParB/RepB/Spo0J family partition protein -
SEETMRM10607_RS25465 (SEETMRM10607_25405) 57310..57744 + 435 WP_010999943 conjugation system SOS inhibitor PsiB -
SEETMRM10607_RS25470 (SEETMRM10607_25410) 57741..58478 + 738 WP_000581933 plasmid SOS inhibition protein A -
SEETMRM10607_RS25475 58988..59257 + 270 WP_001677523 DUF932 domain-containing protein -
SEETMRM10607_RS25480 59261..59389 + 129 WP_077679772 DUF932 domain-containing protein -
SEETMRM10607_RS25485 59304..59594 + 291 WP_001677522 DUF932 domain-containing protein -
SEETMRM10607_RS25490 (SEETMRM10607_25415) 60117..60587 - 471 WP_001526856 transglycosylase SLT domain-containing protein virB1
SEETMRM10607_RS25495 60804..61009 + 206 Protein_87 hypothetical protein -
SEETMRM10607_RS25500 (SEETMRM10607_25420) 61002..61382 + 381 WP_001151546 conjugal transfer relaxosome DNA-binding protein TraM -
SEETMRM10607_RS25505 (SEETMRM10607_25425) 61575..62261 + 687 WP_000336297 PAS domain-containing protein -
SEETMRM10607_RS25510 (SEETMRM10607_25430) 62262..62582 + 321 WP_001697172 conjugal transfer relaxosome protein TraY -
SEETMRM10607_RS25515 (SEETMRM10607_25435) 62624..62986 + 363 WP_001274201 type IV conjugative transfer system pilin TraA -
SEETMRM10607_RS25520 (SEETMRM10607_25440) 63001..63312 + 312 WP_000012129 type IV conjugative transfer system protein TraL traL
SEETMRM10607_RS25525 (SEETMRM10607_25445) 63334..63900 + 567 WP_000399768 type IV conjugative transfer system protein TraE traE
SEETMRM10607_RS25530 (SEETMRM10607_25450) 63887..64627 + 741 WP_001230719 type-F conjugative transfer system secretin TraK traK
SEETMRM10607_RS25535 (SEETMRM10607_25455) 64627..66048 + 1422 WP_000146700 F-type conjugal transfer pilus assembly protein TraB traB
SEETMRM10607_RS25540 66038..66632 + 595 Protein_96 conjugal transfer protein TraP -
SEETMRM10607_RS25545 (SEETMRM10607_25460) 66610..66855 + 246 WP_010999944 DUF2689 domain-containing protein virb4
SEETMRM10607_RS25550 (SEETMRM10607_25465) 66852..67367 + 516 WP_001079995 type IV conjugative transfer system lipoprotein TraV traV
SEETMRM10607_RS25555 (SEETMRM10607_25470) 67502..67723 + 222 WP_001278699 conjugal transfer protein TraR -
SEETMRM10607_RS25560 (SEETMRM10607_25475) 67716..68183 + 468 WP_000549562 hypothetical protein -
SEETMRM10607_RS25565 68300..68563 + 264 WP_001239256 hypothetical protein -
SEETMRM10607_RS25570 (SEETMRM10607_25480) 68579..71227 + 2649 WP_078086284 type IV secretion system protein TraC virb4
SEETMRM10607_RS25575 (SEETMRM10607_25485) 71202..71588 + 387 WP_000105164 type-F conjugative transfer system protein TrbI -
SEETMRM10607_RS25580 (SEETMRM10607_25490) 71585..72217 + 633 WP_000871995 type-F conjugative transfer system protein TraW traW
SEETMRM10607_RS25585 (SEETMRM10607_25495) 72214..73206 + 993 WP_000833320 conjugal transfer pilus assembly protein TraU traU
SEETMRM10607_RS25590 (SEETMRM10607_25500) 73225..73533 + 309 WP_010999945 hypothetical protein -
SEETMRM10607_RS25595 (SEETMRM10607_25505) 73518..74156 + 639 WP_000554823 type-F conjugative transfer system pilin assembly protein TrbC trbC
SEETMRM10607_RS25600 (SEETMRM10607_25510) 74193..74612 + 420 WP_001229397 HNH endonuclease signature motif containing protein -
SEETMRM10607_RS25605 (SEETMRM10607_25515) 74609..76435 + 1827 WP_000827528 type-F conjugative transfer system mating-pair stabilization protein TraN traN
SEETMRM10607_RS25610 (SEETMRM10607_25520) 76446..76661 + 216 WP_000700023 conjugal transfer protein TrbE -
SEETMRM10607_RS25615 (SEETMRM10607_25525) 76673..77422 + 750 WP_001226854 type-F conjugative transfer system pilin assembly protein TraF traF
SEETMRM10607_RS25620 77636..77929 + 294 WP_001233881 type-F conjugative transfer system pilin chaperone TraQ -
SEETMRM10607_RS25625 (SEETMRM10607_25535) 77916..78464 + 549 WP_000055840 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
SEETMRM10607_RS25630 (SEETMRM10607_25540) 78454..79836 + 1383 WP_001161719 conjugal transfer pilus assembly protein TraH traH
SEETMRM10607_RS25635 (SEETMRM10607_25545) 79833..82655 + 2823 WP_001007086 conjugal transfer mating-pair stabilization protein TraG traG
SEETMRM10607_RS25640 (SEETMRM10607_25550) 82671..83165 + 495 WP_010999946 entry exclusion protein -
SEETMRM10607_RS25645 (SEETMRM10607_25555) 83201..83932 + 732 WP_000782438 conjugal transfer complement resistance protein TraT -
SEETMRM10607_RS25650 (SEETMRM10607_25560) 84309..86552 + 2244 WP_000009320 type IV conjugative transfer system coupling protein TraD prgC
SEETMRM10607_RS25655 86561..86959 - 399 WP_000911322 type II toxin-antitoxin system VapC family toxin -
SEETMRM10607_RS25660 86959..87189 - 231 WP_001526804 toxin-antitoxin system antitoxin VapB -

Host bacterium

ID   1222 GenBank   NZ_CP013721
Plasmid name   pRM10607 Incompatibility group   IncFII
Plasmid size   93925 bp Coordinate of oriT [Strand]   60661..60919 [-]
Host baterium   Salmonella enterica subsp. enterica serovar Typhimurium strain RM10607

Cargo genes

Drug resistance gene   -
Virulence gene   Salmonella plasmid virulence
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -