Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   104506
Name   oriT_SWHIN_104|unnamed1 in_silico
Organism   Shigella flexneri strain SWHIN_104
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP055110 (148541..148892 [-], 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_104|unnamed1
AGGTTGGTGGTTCTCACCACCAAAAGCACCACACCCCACGCAAAAACAAGTTTTTGCTGATTTTTCTTTATAAATAGAGAGTTATGAAAAATTAGTTTCTCTTACTCTCTTTATGATATTTAAAAAAGCGGTGTCGGCGCGGCTACAACAACGCGCCGACACCGCTTTGTAGGGGTGGTACTGACTATTTTTATAAAAAACATTATTTTATATTAGGGGTGCTGCTAGCGGCGCGGTGTGTTTTTTTATAGGATACCGCTAGGGGCGCTGCTAGCGGTGCGTCCCTGTTTGCATTATGAATTTTAGTGTTTCGAAATTAACTTTATTTTATGTTCAAAAAAGGTAATCTCTA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   3261 GenBank   WP_000986962
Name   traI_HUZ82_RS23790_SWHIN_104|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   1447 GenBank   WP_001369361
Name   WP_001369361_SWHIN_104|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   1448 GenBank   WP_001151524
Name   WP_001151524_SWHIN_104|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   3188 GenBank   WP_000009324
Name   traD_HUZ82_RS23805_SWHIN_104|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   3189 GenBank   WP_001064245
Name   traC_HUZ82_RS23895_SWHIN_104|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: 123090..149463

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HUZ82_RS23795 (HUZ82_23610) 122456..122683 + 228 WP_000450520 toxin-antitoxin system antitoxin VapB -
HUZ82_RS23800 (HUZ82_23615) 122683..123081 + 399 WP_000911313 type II toxin-antitoxin system VapC family toxin -
HUZ82_RS23805 (HUZ82_23620) 123090..125243 - 2154 WP_000009324 type IV conjugative transfer system coupling protein TraD virb4
HUZ82_RS23810 (HUZ82_23625) 125496..126227 - 732 WP_023565183 conjugal transfer complement resistance protein TraT -
HUZ82_RS23815 (HUZ82_23630) 126259..126756 - 498 WP_000605857 entry exclusion protein -
HUZ82_RS23820 (HUZ82_23635) 126772..129594 - 2823 WP_001007018 conjugal transfer mating-pair stabilization protein TraG traG
HUZ82_RS23825 (HUZ82_23640) 129591..130964 - 1374 WP_001517790 conjugal transfer pilus assembly protein TraH traH
HUZ82_RS23830 (HUZ82_23645) 130964..131344 - 381 WP_001389370 F-type conjugal transfer protein TrbF -
HUZ82_RS23835 (HUZ82_23650) 131331..131672 - 342 WP_001443031 P-type conjugative transfer protein TrbJ -
HUZ82_RS23840 (HUZ82_23655) 131602..132147 - 546 WP_000059851 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
HUZ82_RS23845 (HUZ82_23660) 132134..132418 - 285 WP_000624109 type-F conjugative transfer system pilin chaperone TraQ -
HUZ82_RS23850 (HUZ82_23665) 132499..132813 + 315 WP_001324103 hypothetical protein -
HUZ82_RS23855 (HUZ82_23670) 132815..133162 - 348 WP_001287910 conjugal transfer protein TrbA -
HUZ82_RS23860 (HUZ82_23675) 133178..133921 - 744 WP_001030393 type-F conjugative transfer system pilin assembly protein TraF traF
HUZ82_RS23865 (HUZ82_23680) 133914..134171 - 258 WP_000864318 conjugal transfer protein TrbE -
HUZ82_RS23870 (HUZ82_23685) 134198..136006 - 1809 WP_000821841 type-F conjugative transfer system mating-pair stabilization protein TraN traN
HUZ82_RS23875 (HUZ82_23690) 136003..136641 - 639 WP_000777700 type-F conjugative transfer system pilin assembly protein TrbC trbC
HUZ82_RS23880 (HUZ82_23695) 136650..137642 - 993 WP_000830183 conjugal transfer pilus assembly protein TraU traU
HUZ82_RS23885 (HUZ82_23700) 137639..138271 - 633 WP_001203720 type-F conjugative transfer system protein TraW traW
HUZ82_RS23890 (HUZ82_23705) 138268..138654 - 387 WP_000099686 type-F conjugative transfer system protein TrbI -
HUZ82_RS23895 (HUZ82_23710) 138651..141278 - 2628 WP_001064245 type IV secretion system protein TraC virb4
HUZ82_RS23900 (HUZ82_23715) 141438..141659 - 222 WP_001278689 conjugal transfer protein TraR -
HUZ82_RS23905 (HUZ82_23720) 141794..142309 - 516 WP_000809838 type IV conjugative transfer system lipoprotein TraV traV
HUZ82_RS23910 (HUZ82_23725) 142306..142557 - 252 WP_001038342 conjugal transfer protein TrbG -
HUZ82_RS23915 (HUZ82_23730) 142569..142766 - 198 WP_001324648 conjugal transfer protein TrbD -
HUZ82_RS23920 (HUZ82_23735) 142753..143343 - 591 WP_001376242 conjugal transfer pilus-stabilizing protein TraP -
HUZ82_RS23925 (HUZ82_23740) 143333..144760 - 1428 WP_000146685 F-type conjugal transfer pilus assembly protein TraB traB
HUZ82_RS23930 (HUZ82_23745) 144760..145488 - 729 WP_001230787 type-F conjugative transfer system secretin TraK traK
HUZ82_RS23935 (HUZ82_23750) 145475..146041 - 567 WP_000399792 type IV conjugative transfer system protein TraE traE
HUZ82_RS23940 (HUZ82_23755) 146063..146374 - 312 WP_000012106 type IV conjugative transfer system protein TraL traL
HUZ82_RS23945 (HUZ82_23760) 146389..146754 - 366 WP_000994779 type IV conjugative transfer system pilin TraA -
HUZ82_RS23950 (HUZ82_23765) 146787..147182 - 396 WP_001309237 conjugal transfer relaxosome DNA-bindin protein TraY -
HUZ82_RS23955 (HUZ82_23770) 147281..147970 - 690 WP_000283385 conjugal transfer transcriptional regulator TraJ -
HUZ82_RS23960 (HUZ82_23775) 148157..148540 - 384 WP_001151524 conjugal transfer relaxosome DNA-binding protein TraM -
HUZ82_RS23965 (HUZ82_23780) 148873..149463 + 591 WP_001376243 transglycosylase SLT domain-containing protein -
HUZ82_RS23970 (HUZ82_23785) 149760..150581 - 822 WP_001234426 DUF932 domain-containing protein -
HUZ82_RS23975 (HUZ82_23790) 150699..150986 - 288 WP_000107535 hypothetical protein -
HUZ82_RS23980 151011..151217 - 207 WP_000547968 hypothetical protein -
HUZ82_RS23985 151287..151459 + 173 Protein_169 hypothetical protein -
HUZ82_RS23990 151457..151687 - 231 WP_071586998 hypothetical protein -
HUZ82_RS23995 (HUZ82_23795) 151907..152032 - 126 WP_001372321 type I toxin-antitoxin system Hok family toxin -
HUZ82_RS24000 151974..152123 - 150 Protein_172 plasmid maintenance protein Mok -
HUZ82_RS24005 (HUZ82_23800) 152145..152333 + 189 WP_001299721 hypothetical protein -
HUZ82_RS24010 (HUZ82_23805) 152302..153064 - 763 Protein_174 plasmid SOS inhibition protein A -
HUZ82_RS24015 (HUZ82_23810) 153061..153495 - 435 WP_000845936 conjugation system SOS inhibitor PsiB -
HUZ82_RS24020 (HUZ82_23815) 153550..153747 - 198 Protein_176 hypothetical protein -
HUZ82_RS24025 (HUZ82_23820) 153775..154008 - 234 WP_000005987 DUF905 family protein -

Host bacterium

ID   4945 GenBank   NZ_CP055110
Plasmid name   SWHIN_104|unnamed1 Incompatibility group   IncFIB
Plasmid size   177080 bp Coordinate of oriT [Strand]   148541..148892 [-]
Host baterium   Shigella flexneri strain SWHIN_104

Cargo genes

Drug resistance gene   tet(A), oqxA, oqxB, sul2, aph(3'')-Ib, aph(6)-Id, floR, blaCTX-M-55, blaTEM-1B, fosA3, dfrA14, dfrA12, aadA2, mph(A), aph(3')-Ia, aac(3)-IId, sitABCD
Virulence gene   iroB, iroC, iroD, iroE, iroN, iutA, iucC, iucB, iucA
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -