Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   104483
Name   oriT_STEFF_18|unnamed1 in_silico
Organism   Shigella flexneri strain STEFF_18
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP055180 (93210..93561 [-], 352 nt)
oriT length   352 nt
IRs (inverted repeats)      255..262, 271..278  (ACCGCTAG..CTAGCGGT)
 192..198, 206..212  (TATAAAA..TTTTATA)
 40..47, 50..57  (GCAAAAAC..GTTTTTGC)
 4..11, 16..23  (TTGGTGGT..ACCACCAA)
Location of nic site      _
Conserved sequence flanking the
  nic site    		  _
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 352 nt

>oriT_STEFF_18|unnamed1
AGGTTGGTGGTTCTCACCACCAAAAGCACCACACCCCACGCAAAAACAAGTTTTTGCTGATTTTTCTTTATAAATAGAGAGTTATGAAAAATTAGTTTCTCTTACTCTCTTTATGATATTTAAAAAAGCGGTGTCGGCGCGGCTACAACAACGCGCCGACACCGCTTTGTAGGGGTGGTACTGACTATTTTTATAAAAAACATTATTTTATATTAGGGGTGCTGCTAGCGGCGCGGTGTGTTTTTTTATAGGATACCGCTAGGGGCGCTGCTAGCGGTGCGTCCCTGTTTGCATTATGAATTTTAGTGTTTCGAAATTAACTTTATTTTATGTTCAAAAAAGGTAATCTCTA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   3247 GenBank   WP_000986962
Name   traI_HUZ46_RS23895_STEFF_18|unnamed1 insolico UniProt ID   A0A0K2B7B9
Length   1756 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1756 a.a.        Molecular weight: 192018.92 Da        Isoelectric Point: 5.8722

>WP_000986962.1 MULTISPECIES: conjugative transfer relaxase/helicase TraI [Enterobacteriaceae]
MMSIAQVRSAGSAGNYYTDKDNYYVLGSMGERWAGRGAEQLGLQGSVDKDVFTRLLEGKLPDGADLSRMQ
DGSNKHRPGYDLTFSAPKSVSVMAMLGGDKRLIDAHNQAVDFAVRQVEALASTRVMTDGQSETVLTGNLV
MALFNHDTSRDQEPQLHTHAVVANVTQHNGEWKTLSSDKVGKTGFIENVYANQIAFGRLYREKLKEQVEA
LGYETEVVGKHGMWEMPGVPVEAFSGRSQAIREAVGEDASLKSRDVAALDTRKSKQHVDPEVRMAEWMQT
LKETGFDIRAYRDAADQRAETRTQTPGPASQDGPDVQQAVTQAIAGLSERKVQFTYTDVLARTVGILPPE
NGVIERARAGIDEAISREQLIPLDREKGLFTSGIHVLDELSVRALSRDIMKQNRVTVHPEKSVPRTAGYS
DAVSVLAQDRPSLAIVSGQGGAAGQRERVAELVMMAREQGREVQIIAADRRSQMNLKQDERLSGELITGR
RQLQEGMAFTPGNTVIVDQGEKLSLKETLTLLDGAARHNVQVLITDSGQRTGTGSALMAMKDAGVNTYRW
QGGEQRPATIISEPDRNVRYARLAGDFAASVKAGEESVAQVSGVREQAILTQAIRSELKTQGVLGRPEVT
MTALSPVWLDSRSRYLRDMYRPGMVMEQWNPETRSHDRYVIDRVTAQSNSLTLRDAQDETQVVRISSLDS
SWSLFRPEKMPVADGERLRVTGKIPGLRVSGGDRLQVASVSEDAMTVVVPGRAEPASLPVSDSPFMALKL
ENGWVETPGHSVSDSAKVFASVTQMAMDNATLNGLARSGRDVRLYSSLDETRTAEKLARHPSFTVVSEQI
KARAGETLLETAISLQKTGLHTPAQQAIHLALPVVESKNLAFSMVDLLTEAKSFAAEGTSFTELGGEINA
QIKRGDLLYVDVAKGYGTGLLVSRASYEAEKSILRHILEGKEAVTPLMERVPGELMEKLTSGQRAATRMI
LETSDRFTVVQGYAGVGKTTQFRAVMSAVNMLPESERPRVVGLGPTHRAVGEMRSAGVDAQTLASFLHDT
QLLQRSGETPNFSNTLFLLDESSMVGNTDMARAYALIAAGGGRAVASGDTDQLQAIAPGQPFRLQQTRSA
ADVVIMKEIVRQTPELREAVYSLINRDVERALSGLESVKPSQVPRQEGAWAPEHSVTEFSHSQEAKLAEA
QQKAMLKGEAFPDIPMTLYEAIVRDYTGRTPEAREQTLIVTHLNEDRRVLNSMIHDAREKAGELGKEQVM
VPVLNTANIRDGELRRLSTWENNPDALALVDSVYHRIAGISKDDGLITLEDAEGNTRLISPREAVAEGVT
LYTPDTIRVGTGDRMRFTKSDRERGYVANSVWTVTAVSGDSVTLSDGQQIRVIRPGQERAEQHIDLAYAI
TAHGAQGASETFAIALEGTEGNRKLMAGFESAYVALSRMKQHVQVYTDNRQGWTDAINNAVQKGTAHDVL
EPKSDREVMNAERLFSTARELRDVVAGRAVLRQAGLAGGDSPARFIAPGRKYPQPYVALPAFDRNGKSAG
IWLNPLTTDDGNGLRGFSGEGRVKGSGDAQFVALQGSRNGESLLADNMQDGVRIARDNPDSGVVVRIAGE
GRPWNPRTITGGRVWGDIPDNSVQPGAGNGEPVTAEVLAQRQAEEAIRRETERRADEIVRKMAENKPDLP
DGKTEQAVRDIAGLERDRSAISEREAALPESVLREPQRVREAVREVARENLLQERLQQMERDMVRDLQKE
KTLGGD

  Protein domains


Predicted by InterproScan.

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

(575-626)

AAA domain (AAA_30)

(969-1156)

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   1435 GenBank   WP_001369361
Name   WP_001369361_STEFF_18|unnamed1 insolico UniProt ID   B7LI64
Length   133 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  Auxiliary protein sequence


Download         Length: 133 a.a.        Molecular weight: 15409.70 Da        Isoelectric Point: 9.9240

>WP_001369361.1 MULTISPECIES: conjugal transfer relaxosome DNA-bindin protein TraY [Gammaproteobacteria]
MLLKRFGTRSATGKMVKLKLPVDVESLLIEASNRSGRSRSFEAVIRLKDHLHRYPKFNRAGNIYGKSLVK
YLTMRLDDETNQLLIAAKNRSGWCKTDEAADRVIDHLIKFPDFYNSEIFREADKEEDITFNTL

  Protein domains


Predicted by InterproScan.

TraY domain (TraY)

(18-61)

TraY domain (TraY)

(72-119)


  Protein structure


Source ID Structure
AlphaFold DB B7LI64

ID   1436 GenBank   WP_001151524
Name   WP_001151524_STEFF_18|unnamed1 insolico UniProt ID   A0A5W2DT22
Length   127 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  Auxiliary protein sequence


Download         Length: 127 a.a.        Molecular weight: 14517.48 Da        Isoelectric Point: 5.0516

>WP_001151524.1 MULTISPECIES: conjugal transfer relaxosome DNA-binding protein TraM [Gammaproteobacteria]
MAKVNLYISNDAYEKINAIIEKRRQEGAREKDVSFSATASMLLELGLRVHEAQMERKESAFNQTEFNKLL
LECVVKTQSSVAKILGIESLSPHVSGNPKFEYANMVEDIREKVSSEMERFFPKNDDE

  Protein domains


Predicted by InterproScan.

TraM protein, DNA-binding (Tra_M)

(1-126)


  Protein structure


Source ID Structure
AlphaFold DB A0A5W2DT22


T4CP

ID   3168 GenBank   WP_000009324
Name   traD_HUZ46_RS23910_STEFF_18|unnamed1 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: 81528.14 Da        Isoelectric Point: 5.1126

>WP_000009324.1 MULTISPECIES: type IV conjugative transfer system coupling protein TraD [Enterobacteriaceae]
MSFNAKDMTQGGQIASMRIRMFSQIANIILYCLFIFFWILVGLVLWVKISWQTFVNGCIYWWCTTLEGMR
DLIRSQPVYEIQYYGKTFRMNAAQVLHDKYMIWCGEQLWSAFVLASVVALVICLITFFVVSWILGRQGKQ
QSENEITGGRQLTDNPKEVARMLKKDGKDSDIRIGDLPIIRDSEIQNFCLHGTVGAGKSEVIRRLANYAR
QRGDMVVIYDRSGEFVKSYYDPSIDKILNPLDARCAAWDLWKECLTQPDFDNTANTLIPMGTKEDPFWQG
SGRTIFAEAAYLMRNDPNRSYSKLVDTLLSIKIEKLRTFLRNSPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEHNGEPFTIRDWMRGVREDQKNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WFFCDELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGEKAAATLFDVMNTRAFFRSPSHKIA
EFAAGEIGEKEHLKASEQYSYGADPVRDGVSTGKDMERQTLVSYSDIQSLPDLTCYVTLPGPYPAVKLSL
KYQTRPKVAPEFIPRDINPEMENRLSAVLAAREAEGRQMASLFEPDVPEVVSGEDVTQAEQPQQPVSPAI
NDKKSDAGVNVPAGGIEQELKMKPEEEMEQQLPPGISESGEVVDMAVYEAWQREQNPDIQQKMQRREEVN
INVHRERGEDVEPGDDF

  Protein domains


Predicted by InterproScan.

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

(173-560)

F sex factor protein N terminal (TraD_N)

(32-128)

  Protein structure



No available structure.



ID   3169 GenBank   WP_001064245
Name   traC_HUZ46_RS24000_STEFF_18|unnamed1 insolico UniProt ID   _
Length   875 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 875 a.a.        Molecular weight: 99159.81 Da        Isoelectric Point: 5.8486

>WP_001064245.1 MULTISPECIES: type IV secretion system protein TraC [Enterobacteriaceae]
MNNPLEAVTQAVNSLVTALKLPDESAKANEVLGEMSFPQFSRLLPYRDYNQESGLFMNDTTMGFMLEAIP
INGANESIVEALDHMLRTKLPRGIPLCIHLMSSQLVGDRIEYGLREFSWSGEQAERFNAITRAYYMKAAA
TQFPLPEGMNLPLTLRHYRVFISYCSPSKKKSRADILEMENLVKIIRASLQGASITTQTVDAQAFIDIVG
EMINHNPDSLYPKRRQLDPYSDLNYQCVEDSFDLKVRADYLTLGLRENGRNSTARILNFHLARNPEIAFL
WNVADNYSNLLNPELSISCPFILTLTLVVEDQVKTHSEANLKYMDLEKKSKTSYAKWFPSVEKEAKEWGE
LRQRLGSGQSSVVSYFLNITAFCKDNNETALEVEQDILNSFRKNGFELISPRFNHMRNFLTCLPFMAGKG
LFKQLKEAGVVQRAESFNVANLMPLVADNPLTPAGLLAPTYRNQLAFIDIFFRGMNNTNYNMAVCGTSGA
GKTGLIQPLIRSVLDSGGFAVVFDMGDGYKSLCENMGGVYLDGETLRFNPFANITDIDQSAERVRDQLSV
MASPNGNLDEVHEGLLLQAVRASWLAKENRARIDDVVDFLKNASDSEQYAESPTIRSRLDEMIVLLDQYT
ANGTYGQYFNSDEPSLRDDAKMVVLELGGLEDRPSLLVAVMFSLIIYIENRMYRTPRNLKKLNVIDEGWR
LLDFKNHKVGEFIEKGYRTARRHTGAYITITQNIVDFDSDKASSAARAAWGNSSYKIILKQSAKEFAKYN
QLYPDQFLPLQRDMIGKFGAAKDQWFSSFLLQVENHSSWHRLFVDPLSRAMYSSDGPDFEFVQQKRKEGL
SIHEAVWQLAWKKSGPEMASLEAWLEEHEKYRSVA

  Protein domains


Predicted by InterproScan.

Family of unknown function (DUF5934) (DUF5934)

(289-446)

TraC protein (TraC_F_IV)

(38-276)

TraG P-loop domain (P-loop_TraG)

(467-771)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 66423..94132

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HUZ46_RS23900 (HUZ46_23740) 65789..66016 + 228 WP_000450520 toxin-antitoxin system antitoxin VapB -
HUZ46_RS23905 (HUZ46_23745) 66016..66414 + 399 WP_000911313 type II toxin-antitoxin system VapC family toxin -
HUZ46_RS23910 (HUZ46_23750) 66423..68576 - 2154 WP_000009324 type IV conjugative transfer system coupling protein TraD virb4
HUZ46_RS23915 (HUZ46_23755) 68829..69560 - 732 WP_023565183 conjugal transfer complement resistance protein TraT -
HUZ46_RS23920 (HUZ46_23760) 69592..70089 - 498 WP_000605857 entry exclusion protein -
HUZ46_RS23925 (HUZ46_23765) 70105..72927 - 2823 WP_001007018 conjugal transfer mating-pair stabilization protein TraG traG
HUZ46_RS23930 (HUZ46_23770) 72924..74297 - 1374 WP_001517790 conjugal transfer pilus assembly protein TraH traH
HUZ46_RS23935 (HUZ46_23775) 74297..74677 - 381 WP_001389370 F-type conjugal transfer protein TrbF -
HUZ46_RS23940 (HUZ46_23780) 74664..75005 - 342 WP_001443031 P-type conjugative transfer protein TrbJ -
HUZ46_RS23945 (HUZ46_23785) 74935..75480 - 546 WP_000059851 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
HUZ46_RS23950 (HUZ46_23790) 75467..75751 - 285 WP_000624109 type-F conjugative transfer system pilin chaperone TraQ -
HUZ46_RS23955 (HUZ46_23795) 75832..76146 + 315 WP_001324103 hypothetical protein -
HUZ46_RS23960 (HUZ46_23800) 76148..76495 - 348 WP_001287910 conjugal transfer protein TrbA -
HUZ46_RS23965 (HUZ46_23805) 76511..77254 - 744 WP_001030393 type-F conjugative transfer system pilin assembly protein TraF traF
HUZ46_RS23970 (HUZ46_23810) 77247..77504 - 258 WP_000864318 conjugal transfer protein TrbE -
HUZ46_RS23975 (HUZ46_23815) 77531..79339 - 1809 WP_000821841 type-F conjugative transfer system mating-pair stabilization protein TraN traN
HUZ46_RS23980 (HUZ46_23820) 79336..79974 - 639 WP_000777700 type-F conjugative transfer system pilin assembly protein TrbC trbC
HUZ46_RS23985 (HUZ46_23825) 79983..80975 - 993 WP_000830183 conjugal transfer pilus assembly protein TraU traU
HUZ46_RS23990 (HUZ46_23830) 80972..81604 - 633 WP_001203720 type-F conjugative transfer system protein TraW traW
HUZ46_RS23995 (HUZ46_23835) 81601..81987 - 387 WP_000099686 type-F conjugative transfer system protein TrbI -
HUZ46_RS24000 (HUZ46_23840) 81984..84611 - 2628 WP_001064245 type IV secretion system protein TraC virb4
HUZ46_RS24005 (HUZ46_23845) 84771..84992 - 222 WP_001278689 conjugal transfer protein TraR -
HUZ46_RS24010 (HUZ46_23850) 85127..85642 - 516 WP_000809838 type IV conjugative transfer system lipoprotein TraV traV
HUZ46_RS24015 (HUZ46_23855) 85639..85890 - 252 WP_001038342 conjugal transfer protein TrbG -
HUZ46_RS24020 (HUZ46_23860) 85902..86099 - 198 WP_001324648 conjugal transfer protein TrbD -
HUZ46_RS24025 (HUZ46_23865) 86086..86676 - 591 WP_001376242 conjugal transfer pilus-stabilizing protein TraP -
HUZ46_RS24030 (HUZ46_23870) 86666..88093 - 1428 WP_000146685 F-type conjugal transfer pilus assembly protein TraB traB
HUZ46_RS24035 (HUZ46_23875) 88093..88821 - 729 WP_001230787 type-F conjugative transfer system secretin TraK traK
HUZ46_RS24040 (HUZ46_23880) 88808..89197 - 390 Protein_99 type IV conjugative transfer system protein TraE -
HUZ46_RS24045 (HUZ46_23885) 89291..90519 + 1229 WP_089541817 IS3 family transposase -
HUZ46_RS24050 (HUZ46_23890) 90531..90710 - 180 Protein_101 TraE/TraK family type IV conjugative transfer system protein -
HUZ46_RS24055 (HUZ46_23895) 90732..91043 - 312 WP_000012106 type IV conjugative transfer system protein TraL traL
HUZ46_RS24060 (HUZ46_23900) 91058..91423 - 366 WP_000994779 type IV conjugative transfer system pilin TraA -
HUZ46_RS24065 (HUZ46_23905) 91456..91851 - 396 WP_001309237 conjugal transfer relaxosome DNA-bindin protein TraY -
HUZ46_RS24070 (HUZ46_23910) 91950..92639 - 690 WP_000283385 conjugal transfer transcriptional regulator TraJ -
HUZ46_RS24075 (HUZ46_23915) 92826..93209 - 384 WP_001151524 conjugal transfer relaxosome DNA-binding protein TraM -
HUZ46_RS24080 (HUZ46_23920) 93542..94132 + 591 WP_001376243 transglycosylase SLT domain-containing protein -
HUZ46_RS24085 (HUZ46_23925) 94429..95250 - 822 WP_001234426 DUF932 domain-containing protein -
HUZ46_RS24090 (HUZ46_23930) 95368..95655 - 288 WP_000107535 hypothetical protein -
HUZ46_RS24095 95680..95886 - 207 WP_000547968 hypothetical protein -
HUZ46_RS24100 95956..96128 + 173 Protein_111 hypothetical protein -
HUZ46_RS24105 96126..96356 - 231 WP_071586998 hypothetical protein -
HUZ46_RS24110 (HUZ46_23935) 96576..96701 - 126 WP_001372321 type I toxin-antitoxin system Hok family toxin -
HUZ46_RS24115 96643..96792 - 150 Protein_114 plasmid maintenance protein Mok -
HUZ46_RS24120 (HUZ46_23940) 96814..97002 + 189 WP_001299721 hypothetical protein -
HUZ46_RS24125 (HUZ46_23945) 96971..97733 - 763 Protein_116 plasmid SOS inhibition protein A -
HUZ46_RS24130 (HUZ46_23950) 97730..98164 - 435 WP_000845936 conjugation system SOS inhibitor PsiB -
HUZ46_RS24135 (HUZ46_23955) 98219..98416 - 198 Protein_118 hypothetical protein -
HUZ46_RS24140 (HUZ46_23960) 98444..98677 - 234 WP_000005987 DUF905 family protein -

Host bacterium

ID   4922 GenBank   NZ_CP055180
Plasmid name   STEFF_18|unnamed1 Incompatibility group   IncFIB
Plasmid size   122007 bp Coordinate of oriT [Strand]   93210..93561 [-]
Host baterium   Shigella flexneri strain STEFF_18

Cargo genes

Drug resistance gene   aph(3')-Ia, dfrA14, sul2, aph(3'')-Ib, aph(6)-Id, blaTEM-1B, blaCTX-M-55, sitABCD
Virulence gene   iutA, iucC, iucB, iucA
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -