Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   114328
Name   oriT_IncFIB-IncFIC fusion in_silico
Organism   Salmonella enterica subsp. enterica serovar Schwarzengrund strain SECVM-16
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP130100 (94882..95005 [-], 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   9178 GenBank   WP_052940419
Name   traI_QPJ63_RS24085_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   10632 GenBank   WP_052940420
Name   traD_QPJ63_RS24090_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   10633 GenBank   WP_000069764
Name   traC_QPJ63_RS24175_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: 68828..95577

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
QPJ63_RS24090 (QPJ63_24090) 68828..70981 - 2154 WP_052940420 type IV conjugative transfer system coupling protein TraD virb4
QPJ63_RS24095 (QPJ63_24095) 71233..71964 - 732 WP_000850424 conjugal transfer complement resistance protein TraT -
QPJ63_RS24100 (QPJ63_24100) 71978..72487 - 510 WP_000628099 conjugal transfer entry exclusion protein TraS -
QPJ63_RS24105 (QPJ63_24105) 72484..75309 - 2826 WP_001007030 conjugal transfer mating-pair stabilization protein TraG traG
QPJ63_RS24110 (QPJ63_24110) 75306..76682 - 1377 WP_000982833 conjugal transfer pilus assembly protein TraH traH
QPJ63_RS24115 (QPJ63_24115) 76679..77041 - 363 WP_010379880 P-type conjugative transfer protein TrbJ -
QPJ63_RS24120 (QPJ63_24120) 76971..77516 - 546 WP_000052618 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
QPJ63_RS24125 (QPJ63_24125) 77503..77787 - 285 WP_000624110 type-F conjugative transfer system pilin chaperone TraQ -
QPJ63_RS24130 (QPJ63_24130) 77868..78143 + 276 WP_001513501 hypothetical protein -
QPJ63_RS24135 (QPJ63_24135) 78145..78492 - 348 WP_001287907 conjugal transfer protein TrbA -
QPJ63_RS24140 (QPJ63_24140) 78508..79251 - 744 WP_001030378 type-F conjugative transfer system pilin assembly protein TraF traF
QPJ63_RS24145 (QPJ63_24145) 79244..79501 - 258 WP_000864318 conjugal transfer protein TrbE -
QPJ63_RS24150 (QPJ63_24150) 79528..81336 - 1809 WP_052940421 type-F conjugative transfer system mating-pair stabilization protein TraN traN
QPJ63_RS24155 (QPJ63_24155) 81333..81971 - 639 WP_000777692 type-F conjugative transfer system pilin assembly protein TrbC trbC
QPJ63_RS24160 (QPJ63_24160) 81980..82972 - 993 WP_000830854 conjugal transfer pilus assembly protein TraU traU
QPJ63_RS24165 (QPJ63_24165) 82969..83601 - 633 WP_001203720 type-F conjugative transfer system protein TraW traW
QPJ63_RS24170 (QPJ63_24170) 83598..83984 - 387 WP_000214097 type-F conjugative transfer system protein TrbI -
QPJ63_RS24175 (QPJ63_24175) 83981..86611 - 2631 WP_000069764 type IV secretion system protein TraC virb4
QPJ63_RS24180 (QPJ63_24180) 86738..87085 - 348 WP_000802783 hypothetical protein -
QPJ63_RS24185 (QPJ63_24185) 87113..87330 - 218 Protein_96 hypothetical protein -
QPJ63_RS24190 (QPJ63_24190) 87410..87886 - 477 WP_000549579 hypothetical protein -
QPJ63_RS24195 (QPJ63_24195) 87879..88100 - 222 WP_001278695 conjugal transfer protein TraR -
QPJ63_RS24200 (QPJ63_24200) 88235..88750 - 516 WP_000809874 type IV conjugative transfer system lipoprotein TraV traV
QPJ63_RS24205 (QPJ63_24205) 88747..89067 - 321 WP_001057307 conjugal transfer protein TrbD -
QPJ63_RS24210 (QPJ63_24210) 89054..89644 - 591 WP_000002784 conjugal transfer pilus-stabilizing protein TraP -
QPJ63_RS24215 (QPJ63_24215) 89634..91061 - 1428 WP_000146657 F-type conjugal transfer pilus assembly protein TraB traB
QPJ63_RS24220 (QPJ63_24220) 91061..91789 - 729 WP_001230798 type-F conjugative transfer system secretin TraK traK
QPJ63_RS24225 (QPJ63_24225) 91776..92342 - 567 WP_000399792 type IV conjugative transfer system protein TraE traE
QPJ63_RS24230 (QPJ63_24230) 92364..92675 - 312 WP_000012103 type IV conjugative transfer system protein TraL traL
QPJ63_RS24235 (QPJ63_24235) 92690..93049 - 360 WP_000340272 type IV conjugative transfer system pilin TraA -
QPJ63_RS24240 (QPJ63_24240) 93083..93310 - 228 WP_001254386 conjugal transfer relaxosome protein TraY -
QPJ63_RS24245 (QPJ63_24245) 93404..94090 - 687 WP_000332484 PAS domain-containing protein -
QPJ63_RS24250 (QPJ63_24250) 94281..94664 - 384 WP_000124981 conjugal transfer relaxosome DNA-binding protein TraM -
QPJ63_RS24255 (QPJ63_24255) 94930..95577 + 648 WP_072101530 transglycosylase SLT domain-containing protein virB1
QPJ63_RS24260 (QPJ63_24260) 95872..96693 - 822 WP_052940441 DUF932 domain-containing protein -
QPJ63_RS24265 (QPJ63_24265) 96812..97098 - 287 Protein_112 hypothetical protein -
QPJ63_RS24270 (QPJ63_24270) 97100..97421 + 322 Protein_113 hypothetical protein -
QPJ63_RS24275 (QPJ63_24275) 97722..97844 - 123 WP_223195199 Hok/Gef family protein -
QPJ63_RS24280 (QPJ63_24280) 97789..97941 - 153 Protein_115 DUF5431 family protein -
QPJ63_RS24285 (QPJ63_24285) 98158..98877 - 720 WP_001276275 plasmid SOS inhibition protein A -
QPJ63_RS24290 (QPJ63_24290) 98874..99308 - 435 WP_000845935 conjugation system SOS inhibitor PsiB -

Host bacterium

ID   14763 GenBank   NZ_CP130100
Plasmid name   IncFIB-IncFIC fusion Incompatibility group   IncFIB
Plasmid size   144840 bp Coordinate of oriT [Strand]   94882..95005 [-]
Host baterium   Salmonella enterica subsp. enterica serovar Schwarzengrund strain SECVM-16

Cargo genes

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