Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   104517
Name   oriT_STEFF_10|unnamed1 in_silico
Organism   Shigella flexneri strain STEFF_10
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP055195 (96995..97346 [-], 352 nt)
oriT length   352 nt
IRs (inverted repeats)      255..262, 271..278  (ACCGCTAG..CTAGCGGT)
 192..198, 206..212  (TATAAAA..TTTTATA)
 135..140, 153..158  (CGGCGC..GCGCCG)
 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_10|unnamed1
AGGTTGGTGGTTCTCACCACCAAAAGCACCACACCCCACGCAAAAACAAGTTTTTGCTGATTTTTCTTTATAAATAGAGAGTTATGAAAAATTAGTTTCTCTTACTCTCTTTGCGATATTTAAAAAAGCGGTGCCGGCGCAGCTACAACACCGCGCCGACACCGCTTTGTAGGGGTGGTACTGACTATTTTTATAAAAAACATTATTTTATATTAGGGGTGCTGCTAGCGGCGCGGTGTGTTTTTTTATAGGATACCGCTAGGGGCGCTGCTAGCGGTGCGTCCCTGTTTGCATTATGAATTTTAGTGTTTCGAAATTAACTTTATTTTATGTTCAAAAAAGGTAATCTCTA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   3267 GenBank   WP_000986962
Name   traI_HUZ40_RS23890_STEFF_10|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   1455 GenBank   WP_001369361
Name   WP_001369361_STEFF_10|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   1456 GenBank   WP_001151524
Name   WP_001151524_STEFF_10|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   3197 GenBank   WP_000009324
Name   traD_HUZ40_RS23905_STEFF_10|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   3198 GenBank   WP_001064245
Name   traC_HUZ40_RS23995_STEFF_10|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: 71544..97917

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HUZ40_RS23895 (HUZ40_23740) 70910..71137 + 228 WP_000450520 toxin-antitoxin system antitoxin VapB -
HUZ40_RS23900 (HUZ40_23745) 71137..71535 + 399 WP_000911313 type II toxin-antitoxin system VapC family toxin -
HUZ40_RS23905 (HUZ40_23750) 71544..73697 - 2154 WP_000009324 type IV conjugative transfer system coupling protein TraD virb4
HUZ40_RS23910 (HUZ40_23755) 73950..74681 - 732 WP_023565183 conjugal transfer complement resistance protein TraT -
HUZ40_RS23915 (HUZ40_23760) 74713..75210 - 498 WP_000605857 entry exclusion protein -
HUZ40_RS23920 (HUZ40_23765) 75226..78048 - 2823 WP_001007018 conjugal transfer mating-pair stabilization protein TraG traG
HUZ40_RS23925 (HUZ40_23770) 78045..79418 - 1374 WP_001517790 conjugal transfer pilus assembly protein TraH traH
HUZ40_RS23930 (HUZ40_23775) 79418..79798 - 381 WP_001389370 F-type conjugal transfer protein TrbF -
HUZ40_RS23935 (HUZ40_23780) 79785..80126 - 342 WP_001443031 P-type conjugative transfer protein TrbJ -
HUZ40_RS23940 (HUZ40_23785) 80056..80601 - 546 WP_000059851 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
HUZ40_RS23945 (HUZ40_23790) 80588..80872 - 285 WP_000624109 type-F conjugative transfer system pilin chaperone TraQ -
HUZ40_RS23950 (HUZ40_23795) 80953..81267 + 315 WP_001324103 hypothetical protein -
HUZ40_RS23955 (HUZ40_23800) 81269..81616 - 348 WP_001287910 conjugal transfer protein TrbA -
HUZ40_RS23960 (HUZ40_23805) 81632..82375 - 744 WP_001030393 type-F conjugative transfer system pilin assembly protein TraF traF
HUZ40_RS23965 (HUZ40_23810) 82368..82625 - 258 WP_000864318 conjugal transfer protein TrbE -
HUZ40_RS23970 (HUZ40_23815) 82652..84460 - 1809 WP_000821841 type-F conjugative transfer system mating-pair stabilization protein TraN traN
HUZ40_RS23975 (HUZ40_23820) 84457..85095 - 639 WP_000777700 type-F conjugative transfer system pilin assembly protein TrbC trbC
HUZ40_RS23980 (HUZ40_23825) 85104..86096 - 993 WP_000830183 conjugal transfer pilus assembly protein TraU traU
HUZ40_RS23985 (HUZ40_23830) 86093..86725 - 633 WP_001203720 type-F conjugative transfer system protein TraW traW
HUZ40_RS23990 (HUZ40_23835) 86722..87108 - 387 WP_000099686 type-F conjugative transfer system protein TrbI -
HUZ40_RS23995 (HUZ40_23840) 87105..89732 - 2628 WP_001064245 type IV secretion system protein TraC virb4
HUZ40_RS24000 (HUZ40_23845) 89892..90113 - 222 WP_001278689 conjugal transfer protein TraR -
HUZ40_RS24005 (HUZ40_23850) 90248..90763 - 516 WP_000809838 type IV conjugative transfer system lipoprotein TraV traV
HUZ40_RS24010 (HUZ40_23855) 90760..91011 - 252 WP_001038342 conjugal transfer protein TrbG -
HUZ40_RS24015 (HUZ40_23860) 91023..91220 - 198 WP_001324648 conjugal transfer protein TrbD -
HUZ40_RS24020 (HUZ40_23865) 91207..91797 - 591 WP_001376242 conjugal transfer pilus-stabilizing protein TraP -
HUZ40_RS24025 (HUZ40_23870) 91787..93214 - 1428 WP_000146685 F-type conjugal transfer pilus assembly protein TraB traB
HUZ40_RS24030 (HUZ40_23875) 93214..93942 - 729 WP_001230787 type-F conjugative transfer system secretin TraK traK
HUZ40_RS24035 (HUZ40_23880) 93929..94495 - 567 WP_000399792 type IV conjugative transfer system protein TraE traE
HUZ40_RS24040 (HUZ40_23885) 94517..94828 - 312 WP_000012106 type IV conjugative transfer system protein TraL traL
HUZ40_RS24045 (HUZ40_23890) 94843..95208 - 366 WP_000994779 type IV conjugative transfer system pilin TraA -
HUZ40_RS24050 (HUZ40_23895) 95241..95636 - 396 WP_001309237 conjugal transfer relaxosome DNA-bindin protein TraY -
HUZ40_RS24055 (HUZ40_23900) 95735..96424 - 690 WP_000283385 conjugal transfer transcriptional regulator TraJ -
HUZ40_RS24060 (HUZ40_23905) 96611..96994 - 384 WP_001151524 conjugal transfer relaxosome DNA-binding protein TraM -
HUZ40_RS24065 (HUZ40_23910) 97327..97917 + 591 WP_001376243 transglycosylase SLT domain-containing protein -
HUZ40_RS24070 (HUZ40_23915) 98214..99035 - 822 WP_001234426 DUF932 domain-containing protein -
HUZ40_RS24075 (HUZ40_23920) 99153..99440 - 288 WP_000107535 hypothetical protein -
HUZ40_RS24080 99465..99671 - 207 WP_000547968 hypothetical protein -
HUZ40_RS24085 99741..99913 + 173 Protein_112 hypothetical protein -
HUZ40_RS24090 99911..100141 - 231 WP_071586998 hypothetical protein -
HUZ40_RS24095 (HUZ40_23925) 100361..100486 - 126 WP_001372321 type I toxin-antitoxin system Hok family toxin -
HUZ40_RS24100 100428..100577 - 150 Protein_115 plasmid maintenance protein Mok -
HUZ40_RS24105 (HUZ40_23930) 100599..100787 + 189 WP_001299721 hypothetical protein -
HUZ40_RS24110 (HUZ40_23935) 100756..101518 - 763 Protein_117 plasmid SOS inhibition protein A -
HUZ40_RS24115 (HUZ40_23940) 101515..101949 - 435 WP_000845936 conjugation system SOS inhibitor PsiB -
HUZ40_RS24120 (HUZ40_23945) 102004..102201 - 198 Protein_119 hypothetical protein -
HUZ40_RS24125 (HUZ40_23950) 102229..102462 - 234 WP_000005987 DUF905 family protein -

Host bacterium

ID   4956 GenBank   NZ_CP055195
Plasmid name   STEFF_10|unnamed1 Incompatibility group   IncFIB
Plasmid size   125749 bp Coordinate of oriT [Strand]   96995..97346 [-]
Host baterium   Shigella flexneri strain STEFF_10

Cargo genes

Drug resistance gene   aph(3')-Ia, catA2, sitABCD
Virulence gene   iroB, iroC, iroD, iroE, iroN, iutA, iucC, iucB, iucA
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -