Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   104527
Name   oriT_SWHIN_107|unnamed1 in_silico
Organism   Shigella flexneri strain SWHIN_107
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP055100 (143077..143428 [-], 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_107|unnamed1
AGGTTGGTGGTTCTCACCACCAAAAGCACCACACCCCACGCAAAAACAAGTTTTTGCTGATTTTTCTTTATAAATAGAGAGTTATGAAAAATTAGTTTCTCTTACTCTCTTTATGATATTTAAAAAAGCGGTGTCGGCGCGGCTACAACAACGCGCCGACACCGCTTTGTAGGGGTGGTACTGACTATTTTTATAAAAAACATTATTTTATATTAGGGGTGCTGCTAGCGGCGCGGTGTGTTTTTTTATAGGATACCGCTAGGGGCGCTGCTAGCGGTGCGTCCCTGTTTGCATTATGAATTTTAGTGTTTCGAAATTAACTTTATTTTATGTTCAAAAAAGGTAATCTCTA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   3273 GenBank   WP_000986962
Name   traI_HUZ84_RS23955_SWHIN_107|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   1463 GenBank   WP_001369361
Name   WP_001369361_SWHIN_107|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   1464 GenBank   WP_001151524
Name   WP_001151524_SWHIN_107|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   3203 GenBank   WP_000009324
Name   traD_HUZ84_RS23970_SWHIN_107|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   3204 GenBank   WP_001064245
Name   traC_HUZ84_RS24060_SWHIN_107|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: 117626..143999

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HUZ84_RS23960 (HUZ84_23780) 116992..117219 + 228 WP_000450520 toxin-antitoxin system antitoxin VapB -
HUZ84_RS23965 (HUZ84_23785) 117219..117617 + 399 WP_000911313 type II toxin-antitoxin system VapC family toxin -
HUZ84_RS23970 (HUZ84_23790) 117626..119779 - 2154 WP_000009324 type IV conjugative transfer system coupling protein TraD virb4
HUZ84_RS23975 (HUZ84_23795) 120032..120763 - 732 WP_023565183 conjugal transfer complement resistance protein TraT -
HUZ84_RS23980 (HUZ84_23800) 120795..121292 - 498 WP_000605857 entry exclusion protein -
HUZ84_RS23985 (HUZ84_23805) 121308..124130 - 2823 WP_001007018 conjugal transfer mating-pair stabilization protein TraG traG
HUZ84_RS23990 (HUZ84_23810) 124127..125500 - 1374 WP_001517790 conjugal transfer pilus assembly protein TraH traH
HUZ84_RS23995 (HUZ84_23815) 125500..125880 - 381 WP_001389370 F-type conjugal transfer protein TrbF -
HUZ84_RS24000 (HUZ84_23820) 125867..126208 - 342 WP_001443031 P-type conjugative transfer protein TrbJ -
HUZ84_RS24005 (HUZ84_23825) 126138..126683 - 546 WP_000059851 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
HUZ84_RS24010 (HUZ84_23830) 126670..126954 - 285 WP_000624109 type-F conjugative transfer system pilin chaperone TraQ -
HUZ84_RS24015 (HUZ84_23835) 127035..127349 + 315 WP_001324103 hypothetical protein -
HUZ84_RS24020 (HUZ84_23840) 127351..127698 - 348 WP_001287910 conjugal transfer protein TrbA -
HUZ84_RS24025 (HUZ84_23845) 127714..128457 - 744 WP_001030393 type-F conjugative transfer system pilin assembly protein TraF traF
HUZ84_RS24030 (HUZ84_23850) 128450..128707 - 258 WP_000864318 conjugal transfer protein TrbE -
HUZ84_RS24035 (HUZ84_23855) 128734..130542 - 1809 WP_000821841 type-F conjugative transfer system mating-pair stabilization protein TraN traN
HUZ84_RS24040 (HUZ84_23860) 130539..131177 - 639 WP_000777700 type-F conjugative transfer system pilin assembly protein TrbC trbC
HUZ84_RS24045 (HUZ84_23865) 131186..132178 - 993 WP_000830183 conjugal transfer pilus assembly protein TraU traU
HUZ84_RS24050 (HUZ84_23870) 132175..132807 - 633 WP_001203720 type-F conjugative transfer system protein TraW traW
HUZ84_RS24055 (HUZ84_23875) 132804..133190 - 387 WP_000099686 type-F conjugative transfer system protein TrbI -
HUZ84_RS24060 (HUZ84_23880) 133187..135814 - 2628 WP_001064245 type IV secretion system protein TraC virb4
HUZ84_RS24065 (HUZ84_23885) 135974..136195 - 222 WP_001278689 conjugal transfer protein TraR -
HUZ84_RS24070 (HUZ84_23890) 136330..136845 - 516 WP_000809838 type IV conjugative transfer system lipoprotein TraV traV
HUZ84_RS24075 (HUZ84_23895) 136842..137093 - 252 WP_001038342 conjugal transfer protein TrbG -
HUZ84_RS24080 (HUZ84_23900) 137105..137302 - 198 WP_001324648 conjugal transfer protein TrbD -
HUZ84_RS24085 (HUZ84_23905) 137289..137879 - 591 WP_001376242 conjugal transfer pilus-stabilizing protein TraP -
HUZ84_RS24090 (HUZ84_23910) 137869..139296 - 1428 WP_000146685 F-type conjugal transfer pilus assembly protein TraB traB
HUZ84_RS24095 (HUZ84_23915) 139296..140024 - 729 WP_001230787 type-F conjugative transfer system secretin TraK traK
HUZ84_RS24100 (HUZ84_23920) 140011..140577 - 567 WP_000399792 type IV conjugative transfer system protein TraE traE
HUZ84_RS24105 (HUZ84_23925) 140599..140910 - 312 WP_000012106 type IV conjugative transfer system protein TraL traL
HUZ84_RS24110 (HUZ84_23930) 140925..141290 - 366 WP_000994779 type IV conjugative transfer system pilin TraA -
HUZ84_RS24115 (HUZ84_23935) 141323..141718 - 396 WP_001309237 conjugal transfer relaxosome DNA-bindin protein TraY -
HUZ84_RS24120 (HUZ84_23940) 141817..142506 - 690 WP_000283385 conjugal transfer transcriptional regulator TraJ -
HUZ84_RS24125 (HUZ84_23945) 142693..143076 - 384 WP_001151524 conjugal transfer relaxosome DNA-binding protein TraM -
HUZ84_RS24130 (HUZ84_23950) 143409..143999 + 591 WP_001376243 transglycosylase SLT domain-containing protein -
HUZ84_RS24135 (HUZ84_23955) 144296..145117 - 822 WP_001234426 DUF932 domain-containing protein -
HUZ84_RS24140 (HUZ84_23960) 145235..145522 - 288 WP_000107535 hypothetical protein -
HUZ84_RS24145 145547..145753 - 207 WP_000547968 hypothetical protein -
HUZ84_RS24150 145823..145995 + 173 Protein_164 hypothetical protein -
HUZ84_RS24155 145993..146223 - 231 WP_071586998 hypothetical protein -
HUZ84_RS24160 (HUZ84_23965) 146443..146568 - 126 WP_001372321 type I toxin-antitoxin system Hok family toxin -
HUZ84_RS24165 146510..146659 - 150 Protein_167 plasmid maintenance protein Mok -
HUZ84_RS24170 (HUZ84_23970) 146681..146869 + 189 WP_001299721 hypothetical protein -
HUZ84_RS24175 (HUZ84_23975) 146838..147600 - 763 Protein_169 plasmid SOS inhibition protein A -
HUZ84_RS24180 (HUZ84_23980) 147597..148031 - 435 WP_000845936 conjugation system SOS inhibitor PsiB -
HUZ84_RS24185 (HUZ84_23985) 148086..148283 - 198 Protein_171 hypothetical protein -
HUZ84_RS24190 (HUZ84_23990) 148311..148544 - 234 WP_000005987 DUF905 family protein -

Host bacterium

ID   4966 GenBank   NZ_CP055100
Plasmid name   SWHIN_107|unnamed1 Incompatibility group   IncFIB
Plasmid size   171874 bp Coordinate of oriT [Strand]   143077..143428 [-]
Host baterium   Shigella flexneri strain SWHIN_107

Cargo genes

Drug resistance gene   oqxA, oqxB, sul2, aph(3'')-Ib, aph(6)-Id, tet(A), 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   -