Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   114331
Name   oriT_IncFIB-IncFIC fusion in_silico
Organism   Salmonella enterica subsp. enterica serovar Schwarzengrund strain SEMD-3
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP130071 (67181..67304 [-], 124 nt)
oriT length   124 nt
IRs (inverted repeats)      101..106, 119..124  (TTTAAT..ATTAAA)
 91..99, 113..121  (AATAATGTA..TACATTATT)
 90..95, 107..112  (AAATAA..TTATTT)
 39..46, 49..56  (GCAAAAAC..GTTTTTGC)
Location of nic site      _
Conserved sequence flanking the
  nic site    		  _
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 124 nt

>oriT_IncFIB-IncFIC fusion
GGTTGGTGGTTCTCACCACTAAAAGCACCACACCCCACGCAAAAACAAGTTTTTGCTGATTTGCTTTTTGAATCATTAGCTTATGTTTTAAATAATGTATTTTAATTTATTTTACATTATTAAA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   9181 GenBank   WP_052940419
Name   traI_QPJ61_RS24270_IncFIB-IncFIC fusion insolico UniProt ID   A0A620RZB1
Length   1756 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1756 a.a.        Molecular weight: 192150.03 Da        Isoelectric Point: 5.9726

>WP_052940419.1 conjugative transfer relaxase/helicase TraI [Salmonella enterica]
MMSIAQVRSAGSAGNYYTDKDNYYVLGSMGERWAGRGAEQLGLQGSVDKDVFTRLLEGRLPDGADLSRMQ
DGSNKHRPGYDLTFSAPKSVSMMAMLGGDKRLIDAHNQAVDFAVRQVEALASTRVMTDGQSETVLTGNLV
MALFNHDTSRDQEPQLHTHAVVANVTQHNGEWKTLSSDKVGKTGFIENVYANQIAFGRLYREKLKEQVEA
LGYETEVVGKHGMWEMPGVPVEAFSGRSQAIREAVGEDASLKSRDVAALDTRKSKQHVDPEVRMAEWMQT
LKETGFDIRAYRDAADQRAETRTQTPGPASQDGPDVQQAVTQAIAGLSERKVQFTYTDVLARTVGILPPE
NGVIERARAGIDEAISREQLIPLDREKGLFTSGIHVLDELSVRALSRDIMKQNRVTVHPEKSVPRTAGYS
DAVSVLAQDRPSLAIVSGQGGAAGQRERVAELVMMAREQGREVQIIAADRRSQMNLKQDERLSGELITGR
RQLQEGMAFTPGNTVIVDQGEKLSLKETLTLLDGAARHNVQVLITDSGQRTGTGSALMAMKDAGVNTYRW
QGGEQRPATIISEPDRNVRYARLAGDFAASVKAGEESVAQVSGVREQAILTQAIRSELKTQGVLGRPEVT
MTALSPVWLDSRSRYLRDMYRPGMVMEQWNPETRSHDRYVIDRVTAQSNSLTLRDAQGETQVVRISSLDS
SWSLFRPEKMPVADGERLRVTGKIPGLRVSGGDRLQVASVSEDAMTVVVPGRAEPASLPVSDSPFMALKL
ENGWVETPGHSVSDSAKVFASVTQMAMDNATLNGLARSGRDVRLYSSLDETRTAEKLARHPSFTVVSEQI
KARAGETLLETAISLQKTGLHTPAQQAIHLALPVVESKNLAFSMVDLLTEAKSFAAEGTSFTELGGEINA
QIKRGDLLYVDVAKGYGTGLLVSRASYEAEKSILRHILEGKEAVTPLMERVPGELMEKLTSGQRAATRMI
LETSDRFTVVQGYAGVGKTTQFRAVMSAVNMLPESERPRVVGLGPTHRAVGEMRSAGVDAQTLASFLHDT
QLLQRSGETPNFSNTLFLLDESSMVGNTDMARAYALIAAGGGRAVASGDTDQLQAIAPGQPFRLQQTRSA
ADVAIMKEIVRQTPELREAVYSLINRDVERALSGLESVKPSQVPRQEGAWVPEHSVTEFSHSQEAKLAEA
QQKAMLKGEAFPDIPMTLYEAIVRDYTGRTPEAREQTLIVTHLNEDRRVLNSMIHDAREKAGELGKEQVM
VPVLNTANIRDGELRRLSTWETHRDALALVDNVYHRIAGISKDDGLITLQDAEGNTRLISPREAVAEGVT
LYTPDTIRVGTGDRMRFTKSDRERGYVANSVWTVTAVSGDSVTLSDGQQTREIRPGQEQAEQHIDLAYAI
TAHGAQGASETFAIALEGTEGNRKLMAGFESAYVALSRMKQHVQVYTDNRQGWTDAINNAVQKGTAHDVF
EPKPDREVMNAERLFSTARELRDVVAGRAVLRQAGLAGGDSPARFIAPGRKYPQPYVALPAFDRNGKSAG
IWLNPLTTDDGNGLRGFSGEGRVKGSGDAQFVALQGSRNGESLLADNMQDGVRIARDNPDSGVVVRIAGE
GRPWNPRTITGGRVWGDIPDNSVQPGAGNGEPVTAEVLAQRQAEEAIRRETERRADEIVRKMAENKPDLP
DGKTEQAVRDIAGLERDRSAISEREAALPESVLREPQRVREAVREVARENLLQERLQQMERDMVRDLQKE
KTLGGD

  Protein domains


Predicted by InterproScan.

AAA domain (AAA_30)

(969-1156)

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

(575-626)

DNA helicase TraI (TraI_C)

(1434-1557)

TrwC relaxase (TrwC)

(10-283)

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

(633-712)


  Protein structure



No available structure.




Auxiliary protein

ID   5358 GenBank   WP_001254386
Name   WP_001254386_IncFIB-IncFIC fusion insolico UniProt ID   A0A3Z6KJB5
Length   75 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  Auxiliary protein sequence


Download         Length: 75 a.a.        Molecular weight: 9005.11 Da        Isoelectric Point: 10.1422

>WP_001254386.1 MULTISPECIES: conjugal transfer relaxosome protein TraY [Gammaproteobacteria]
MRRRNARGGISRTVSVYLDEDTNNRLIKAKDRSGRSKTIEVQIRLRDHLKRFPDFYNEEIFREVTEESES
TFKEL

  Protein domains


Predicted by InterproScan.

TraY domain (TraY)

(14-61)


  Protein structure


Source ID Structure
AlphaFold DB A0A3Z6KJB5

ID   5359 GenBank   WP_000124981
Name   WP_000124981_IncFIB-IncFIC fusion insolico UniProt ID   A0A630FTW9
Length   127 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  Auxiliary protein sequence


Download         Length: 127 a.a.        Molecular weight: 14542.59 Da        Isoelectric Point: 5.0278

>WP_000124981.1 MULTISPECIES: conjugal transfer relaxosome DNA-binding protein TraM [Gammaproteobacteria]
MARVNLYISNEVHEKINMIVEKRRQEGARDKDISLSGTASMLLELGLRVYDAQMERKESAFNQTEFNKLL
LECVVKTQSTVAKILGIESLSPHVSGNPKFEYASMVDDIREKVSVEMDRFFPKNDDE

  Protein domains


Predicted by InterproScan.

TraM protein, DNA-binding (Tra_M)

(1-126)


  Protein structure


Source ID Structure
AlphaFold DB A0A630FTW9


T4CP

ID   10636 GenBank   WP_052940420
Name   traD_QPJ61_RS24275_IncFIB-IncFIC fusion insolico UniProt ID   _
Length   717 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 717 a.a.        Molecular weight: 81432.92 Da        Isoelectric Point: 5.0504

>WP_052940420.1 MULTISPECIES: type IV conjugative transfer system coupling protein TraD [Enterobacteriaceae]
MSFNAKDMTQGGQIASMRIRMFSQIANIMLYCLFIFFWILVGLVLWVKISWQTFVNGCIYWWCTTLEGMR
DLIKSQPVYEIQYYGKTFRMNAAQVLHDKYMIWCGEQLWSAFVLATVVALVICLITFFVVSWILGRQGKQ
QSENEVTGGRQLTDNPKDVARMLKKDGKDSDIRIGDLPIIRDSEIQNFCLHGTVGAGKSEVIRRLANYAR
QRGDMVVIYDRSGEFVKSYYDPSIDKILNPLDARCAAWDLWKECLTQPDFDNTANTLIPMGTKEDPFWQG
SGRTIFAEAAYLMRNDPNRSYSKLVDTLLSIKIEKLRTFLRNSPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEHNGESFTIRDWMRGVREDQKNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WFFCDELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGEKAAATLFDVMNTRAFFRSPSHKIA
EFAAGEIGEKEHLKASEQYSYGADPVRDGVSTGKDMERQTLVSYSDIQSLPDLTCYVTLPGPYPAVKLSL
KYQARPKVAPEFIPRDINPEMENRLSAVLAAREAEGRQMASLFEPDVPEVVSGEDVTQAEQPQQPVSPAI
NDKKSDSGVNVPAGGIEQELKMKPEEEMEQQLPPGISESGEVVDMAAYEAWQQENHPDIQQQMQRREEVN
INVHRERGEDVEPGDDF

  Protein domains


Predicted by InterproScan.

F sex factor protein N terminal (TraD_N)

(32-128)

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

(173-560)

  Protein structure



No available structure.



ID   10637 GenBank   WP_000069764
Name   traC_QPJ61_RS24360_IncFIB-IncFIC fusion insolico UniProt ID   _
Length   876 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 876 a.a.        Molecular weight: 99302.93 Da        Isoelectric Point: 5.8486

>WP_000069764.1 MULTISPECIES: type IV secretion system protein TraC [Enterobacteriaceae]
MSNNPLEAVTQAVNSLVTALKLPDESAKANEVLGEMSFPQFSRLLPYRDYNQESGLFMNDTTMGFMLEAI
PINGANESIVEALDHMLRTKLPRGVPFCIHLMSSQLVGDRIEYGLREFSWSGEQAERFNAITRAYYMNAA
ATQFPLPEGMNLPLTLRHYRVFFSYCSPSKKKSRADILEMENLVKIIRASLQGASITTQAVDAQAFIDIV
GEMINHNPDSLYPKRRQLDPYSDLNYQCVEDSFDLKVRADYLTLGLREKGRNSTARILNFHLARNPEIAF
LWNMADNYSNLLNPELSISCPFILTLTLVVEDQVKTHSEANLKYMDLEKKSKTSYAKWFPSVEKEAKEWG
ELRQRLGSGQSSVVSYFLNITAFCKDNNETALEVEQDILNSFRKNGFELISPRFNHMRNFLTCLPFMAGK
GLFKQLKEAGVVQRAESFNVANLMPLVADNPLTPAGLLAPTYRNQLAFIDIFFRGMNNTNYNMAVCGTSG
AGKTGLIQPLIRSVLDSGGFAVVFDMGDGYKSLCENMGGVYLDGETLRFNPFANITDIDQSAERVRDQLS
VMASPNGNLDEVHEGLLLQAVRASWLAKENRARIDDVVDFLKNASDSEQYAESPTIRSRLDEMIVLLDQY
TANGTYGQYFNSDEPSLRDDAKMVVLELGGLEDRPSLLVAVMFSLIIYIENRMYRTPRNLKKLNVIDEGW
RLLDFKNHKVGEFIEKGYRTARRHTGAYITITQNIVDFDSDKASSAARAAWGNSSYKIILKQSAKEFAKY
NQLYPDQFLPLQRDMIGKFGAAKDQWFSSFLLQVENHSSWHRLFVDPLSRAMYSSDGPDFEFVQQKRKEG
LSIHEAVWQLAWKKSGPEMASLEAWLEEHEKYRSVA

  Protein domains


Predicted by InterproScan.

TraC protein (TraC_F_IV)

(39-277)

TraG P-loop domain (P-loop_TraG)

(468-772)

Family of unknown function (DUF5934) (DUF5934)

(290-447)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 39789..67876

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
QPJ61_RS24275 (QPJ61_24275) 39789..41942 - 2154 WP_052940420 type IV conjugative transfer system coupling protein TraD virb4
QPJ61_RS24280 (QPJ61_24280) 42194..42925 - 732 WP_000850424 conjugal transfer complement resistance protein TraT -
QPJ61_RS24285 (QPJ61_24285) 42939..43448 - 510 WP_000628099 conjugal transfer entry exclusion protein TraS -
QPJ61_RS24290 (QPJ61_24290) 43445..46270 - 2826 WP_001007030 conjugal transfer mating-pair stabilization protein TraG traG
QPJ61_RS24295 (QPJ61_24295) 46267..47643 - 1377 WP_000982833 conjugal transfer pilus assembly protein TraH traH
QPJ61_RS24300 (QPJ61_24300) 47640..48002 - 363 WP_010379880 P-type conjugative transfer protein TrbJ -
QPJ61_RS24305 (QPJ61_24305) 47932..48477 - 546 WP_000052618 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
QPJ61_RS24310 (QPJ61_24310) 48464..48748 - 285 WP_000624110 type-F conjugative transfer system pilin chaperone TraQ -
QPJ61_RS24315 (QPJ61_24315) 48829..49104 + 276 WP_001513501 hypothetical protein -
QPJ61_RS24320 (QPJ61_24320) 49106..49453 - 348 WP_001287907 conjugal transfer protein TrbA -
QPJ61_RS24325 (QPJ61_24325) 49469..50212 - 744 WP_001030378 type-F conjugative transfer system pilin assembly protein TraF traF
QPJ61_RS24330 (QPJ61_24330) 50205..50462 - 258 WP_000864318 conjugal transfer protein TrbE -
QPJ61_RS24335 (QPJ61_24335) 50489..52297 - 1809 WP_052940421 type-F conjugative transfer system mating-pair stabilization protein TraN traN
QPJ61_RS24340 (QPJ61_24340) 52294..52932 - 639 WP_000777692 type-F conjugative transfer system pilin assembly protein TrbC trbC
QPJ61_RS24345 (QPJ61_24345) 52941..53933 - 993 WP_000830854 conjugal transfer pilus assembly protein TraU traU
QPJ61_RS24350 (QPJ61_24350) 53930..54562 - 633 WP_001203720 type-F conjugative transfer system protein TraW traW
QPJ61_RS24355 (QPJ61_24355) 54559..54945 - 387 WP_000214097 type-F conjugative transfer system protein TrbI -
QPJ61_RS24360 (QPJ61_24360) 54942..57572 - 2631 WP_000069764 type IV secretion system protein TraC virb4
QPJ61_RS24365 (QPJ61_24365) 57699..58046 - 348 WP_000802783 hypothetical protein -
QPJ61_RS24370 (QPJ61_24370) 58074..58291 - 218 Protein_64 hypothetical protein -
QPJ61_RS24375 (QPJ61_24375) 58371..58847 - 477 WP_000549579 hypothetical protein -
QPJ61_RS24380 (QPJ61_24380) 58840..59061 - 222 WP_001278695 conjugal transfer protein TraR -
QPJ61_RS24385 (QPJ61_24385) 59196..59711 - 516 WP_000809874 type IV conjugative transfer system lipoprotein TraV traV
QPJ61_RS24390 (QPJ61_24390) 59708..60028 - 321 WP_001057307 conjugal transfer protein TrbD -
QPJ61_RS24395 (QPJ61_24395) 60015..60605 - 591 WP_000002784 conjugal transfer pilus-stabilizing protein TraP -
QPJ61_RS24400 (QPJ61_24400) 60595..62022 - 1428 WP_000146657 F-type conjugal transfer pilus assembly protein TraB traB
QPJ61_RS24405 (QPJ61_24405) 62022..62750 - 729 WP_001230798 type-F conjugative transfer system secretin TraK traK
QPJ61_RS24410 (QPJ61_24410) 62737..63303 - 567 WP_000399792 type IV conjugative transfer system protein TraE traE
QPJ61_RS24415 (QPJ61_24415) 63325..63636 - 312 WP_000012103 type IV conjugative transfer system protein TraL traL
QPJ61_RS24420 (QPJ61_24420) 63651..64010 - 360 WP_000340272 type IV conjugative transfer system pilin TraA -
QPJ61_RS24425 (QPJ61_24425) 64044..64271 - 228 WP_001254386 conjugal transfer relaxosome protein TraY -
QPJ61_RS24430 (QPJ61_24430) 64365..64994 - 630 WP_264105478 PAS domain-containing protein -
QPJ61_RS24435 (QPJ61_24435) 65037..66245 - 1209 WP_006250222 IS4-like element ISVsa5 family transposase -
QPJ61_RS24440 (QPJ61_24440) 66580..66963 - 384 WP_000124981 conjugal transfer relaxosome DNA-binding protein TraM -
QPJ61_RS24445 (QPJ61_24445) 67229..67876 + 648 WP_072101530 transglycosylase SLT domain-containing protein virB1
QPJ61_RS24450 (QPJ61_24450) 68171..68992 - 822 WP_052940441 DUF932 domain-containing protein -
QPJ61_RS24455 (QPJ61_24455) 69111..69397 - 287 Protein_81 hypothetical protein -
QPJ61_RS24460 (QPJ61_24460) 69399..69720 + 322 Protein_82 hypothetical protein -
QPJ61_RS24465 (QPJ61_24465) 70021..70143 - 123 WP_223195199 Hok/Gef family protein -
QPJ61_RS24470 (QPJ61_24470) 70088..70240 - 153 Protein_84 DUF5431 family protein -
QPJ61_RS24475 (QPJ61_24475) 70457..71176 - 720 WP_001276275 plasmid SOS inhibition protein A -
QPJ61_RS24480 (QPJ61_24480) 71173..71607 - 435 WP_000845935 conjugation system SOS inhibitor PsiB -

Host bacterium

ID   14766 GenBank   NZ_CP130071
Plasmid name   IncFIB-IncFIC fusion Incompatibility group   IncFIB
Plasmid size   117139 bp Coordinate of oriT [Strand]   67181..67304 [-]
Host baterium   Salmonella enterica subsp. enterica serovar Schwarzengrund strain SEMD-3

Cargo genes

Drug resistance gene   aph(3'')-Ib, aph(6)-Id, sitABCD
Virulence gene   iucA, iucB, iucC, iutA
Metal resistance gene   yfeC
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -