Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   104523
Name   oriT_SWHIN_101|unnamed1 in_silico
Organism   Shigella flexneri strain SWHIN_101
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP055114 (102915..103266 [-], 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_SWHIN_101|unnamed1
AGGTTGGTGGTTCTCACCACCAAAAGCACCACACCCCACGCAAAAACAAGTTTTTGCTGATTTTTCTTTATAAATAGAGAGTTATGAAAAATTAGTTTCTCTTACTCTCTTTATGATATTTAAAAAAGCGGTGTCGGCGCGGCTACAACAACGCGCCGACACCGCTTTGTAGGGGTGGTACTGACTATTTTTATAAAAAACATTATTTTATATTAGGGGTGCTGCTAGCGGCGCGGTGTGTTTTTTTATAGGATACCGCTAGGGGCGCTGCTAGCGGTGCGTCCCTGTTTGCATTATGAATTTTAGTGTTTCGAAATTAACTTTATTTTATGTTCAAAAAAGGTAATCTCTA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   3271 GenBank   WP_000986962
Name   traI_HUZ81_RS24440_SWHIN_101|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   1460 GenBank   WP_001369361
Name   WP_001369361_SWHIN_101|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   1461 GenBank   WP_001151524
Name   WP_001151524_SWHIN_101|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   3201 GenBank   WP_000009324
Name   traD_HUZ81_RS24455_SWHIN_101|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.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 86609..103837

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HUZ81_RS24445 (HUZ81_24240) 85975..86202 + 228 WP_000450520 toxin-antitoxin system antitoxin VapB -
HUZ81_RS24450 (HUZ81_24245) 86202..86600 + 399 WP_000911313 type II toxin-antitoxin system VapC family toxin -
HUZ81_RS24455 (HUZ81_24250) 86609..88762 - 2154 WP_000009324 type IV conjugative transfer system coupling protein TraD virb4
HUZ81_RS24460 (HUZ81_24255) 89015..89746 - 732 WP_023565183 conjugal transfer complement resistance protein TraT -
HUZ81_RS24465 (HUZ81_24260) 89778..90275 - 498 WP_000605857 entry exclusion protein -
HUZ81_RS24470 (HUZ81_24265) 90291..93113 - 2823 WP_001007018 conjugal transfer mating-pair stabilization protein TraG traG
HUZ81_RS24475 (HUZ81_24270) 93110..94483 - 1374 WP_001517790 conjugal transfer pilus assembly protein TraH traH
HUZ81_RS24480 (HUZ81_24275) 94483..94863 - 381 WP_001389370 F-type conjugal transfer protein TrbF -
HUZ81_RS24485 (HUZ81_24280) 94850..95191 - 342 WP_001443031 P-type conjugative transfer protein TrbJ -
HUZ81_RS24490 (HUZ81_24285) 95121..95666 - 546 WP_000059851 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
HUZ81_RS24495 (HUZ81_24290) 95653..95937 - 285 WP_000624109 type-F conjugative transfer system pilin chaperone TraQ -
HUZ81_RS24500 (HUZ81_24295) 96018..96332 + 315 WP_001324103 hypothetical protein -
HUZ81_RS24505 (HUZ81_24300) 96334..96681 - 348 WP_001287910 conjugal transfer protein TrbA -
HUZ81_RS24510 (HUZ81_24305) 96697..97440 - 744 WP_001030393 type-F conjugative transfer system pilin assembly protein TraF traF
HUZ81_RS24515 (HUZ81_24310) 97433..97690 - 258 WP_000864318 conjugal transfer protein TrbE -
HUZ81_RS24520 (HUZ81_24315) 97717..98538 - 822 Protein_103 conjugal transfer protein TraN -
HUZ81_RS24525 (HUZ81_24320) 98529..99134 - 606 Protein_104 conjugal transfer protein TraB -
HUZ81_RS24530 (HUZ81_24325) 99134..99862 - 729 WP_001230787 type-F conjugative transfer system secretin TraK traK
HUZ81_RS24535 (HUZ81_24330) 99849..100415 - 567 WP_000399792 type IV conjugative transfer system protein TraE traE
HUZ81_RS24540 (HUZ81_24335) 100437..100748 - 312 WP_000012106 type IV conjugative transfer system protein TraL traL
HUZ81_RS24545 (HUZ81_24340) 100763..101128 - 366 WP_000994779 type IV conjugative transfer system pilin TraA -
HUZ81_RS24550 (HUZ81_24345) 101161..101556 - 396 WP_001309237 conjugal transfer relaxosome DNA-bindin protein TraY -
HUZ81_RS24555 (HUZ81_24350) 101655..102344 - 690 WP_000283385 conjugal transfer transcriptional regulator TraJ -
HUZ81_RS24560 (HUZ81_24355) 102531..102914 - 384 WP_001151524 conjugal transfer relaxosome DNA-binding protein TraM -
HUZ81_RS24565 (HUZ81_24360) 103247..103837 + 591 WP_001376243 transglycosylase SLT domain-containing protein -
HUZ81_RS24570 (HUZ81_24365) 104134..104955 - 822 WP_001234426 DUF932 domain-containing protein -
HUZ81_RS24575 (HUZ81_24370) 105073..105360 - 288 WP_000107535 hypothetical protein -
HUZ81_RS24580 105385..105591 - 207 WP_000547968 hypothetical protein -
HUZ81_RS24585 105661..105833 + 173 Protein_116 hypothetical protein -
HUZ81_RS24590 105831..106061 - 231 WP_071586998 hypothetical protein -
HUZ81_RS24595 (HUZ81_24375) 106281..106406 - 126 WP_001372321 type I toxin-antitoxin system Hok family toxin -
HUZ81_RS24600 106348..106497 - 150 Protein_119 plasmid maintenance protein Mok -
HUZ81_RS24605 (HUZ81_24380) 106519..106707 + 189 WP_001299721 hypothetical protein -
HUZ81_RS24610 (HUZ81_24385) 106676..107438 - 763 Protein_121 plasmid SOS inhibition protein A -
HUZ81_RS24615 (HUZ81_24390) 107435..107869 - 435 WP_000845936 conjugation system SOS inhibitor PsiB -
HUZ81_RS24620 (HUZ81_24395) 107924..108121 - 198 Protein_123 hypothetical protein -
HUZ81_RS24625 (HUZ81_24400) 108149..108382 - 234 WP_000005987 DUF905 family protein -

Host bacterium

ID   4962 GenBank   NZ_CP055114
Plasmid name   SWHIN_101|unnamed1 Incompatibility group   IncFIB
Plasmid size   131712 bp Coordinate of oriT [Strand]   102915..103266 [-]
Host baterium   Shigella flexneri strain SWHIN_101

Cargo genes

Drug resistance gene   oqxA, oqxB, sul2, aph(3'')-Ib, aph(6)-Id, aph(3')-Ia, sitABCD
Virulence gene   iroN, iroE, iroD, iroC, iroB, iutA, iucC, iucB, iucA
Metal resistance gene   merE, merD, merA, merP, merT, merR
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -