Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   104502
Name   oriT_STIN_92|unnamed3 in_silico
Organism   Shigella flexneri strain STIN_92
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP054980 (91693..92044 [+], 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_STIN_92|unnamed3
AGGTTGGTGGTTCTCACCACCAAAAGCACCACACCCCACGCAAAAACAAGTTTTTGCTGATTTTTCTTTATAAATAGAGAGTTATGAAAAATTAGTTTCTCTTACTCTCTTTATGATATTTAAAAAAGCGGTGTCGGCGCGGCTACAACAACGCGCCGACACCGCTTTGTAGGGGTGGTACTGACTATTTTTATAAAAAACATTATTTTATATTAGGGGTGCTGCTAGCGGCGCGGTGTGTTTTTTTATAGGATACCGCTAGGGGCGCTGCTAGCGGTGCGTCCCTGTTTGCATTATGAATTTTAGTGTTTCGAAATTAACTTTATTTTATGTTCAAAAAAGGTAATCTCTA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   3260 GenBank   WP_054377139
Name   traI_HUZ60_RS26030_STIN_92|unnamed3 insolico UniProt ID   A0A5W1N632
Length   1756 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1756 a.a.        Molecular weight: 191884.75 Da        Isoelectric Point: 6.1058

>WP_054377139.1 MULTISPECIES: conjugative transfer relaxase/helicase TraI [Enterobacteriaceae]
MMSIAQVRSAGSAGNYYTDKDNYYVLGSMGERWAGRGAEQLGLQGSVDKDVFTRLLEGRLPDGADLSRMQ
DGSNKHRPGYDLTFSAPKSVSMMAMLGGDKRLIDAHNQAVDFAVRQVEALASTRVMTDGQSETVLTGNLV
MALFNHDTSRDQEPQLHTHTVVANVTQHNGEWKTLSSDKVGKTGFIENVYANQIAFGRLYREKLKEQVEA
LGYETEVVGKHGMWEMPGVPVEAFSGRSQAIREAVGEDASLKSRDVAALDTRKSKQHVDPEVRMAEWMQT
LKETGFDIRAYRDAADQRAETRTQAPGAVSQEGPDVQQAVTQAIAGLSERKVQFTYTDVLARTVGILPPE
NGVIERARAGIDEAISREQLIPLDREKGLFTSGIHVLDELSVRALSRDIMKQNRVTVHPEKSVPRTAGYS
DAVSVLAQDRPSLAIVSGQGGAAGQRERVAELVMMAREQGREVQIIAADRRSQMNLKQDERLSGELITGR
RQLLEGMAFTPGSTVIVDQGEKLSLKETLTLLDGAARHNVQVLITDSGQRTGTGSALMAMKDAGVNSYRW
QGGEQRPATIISEPDRNVRYARLAGDFAASVKAGEESVAQVSGVREQAILTQAIRSELKTQGVLGHPEVT
MTALSPVWLDSRSRYLRDMYRPGMVMEQWNPETRSHDRYVIDRVTAQSHSLTLRDAQGETQVVRISSLDS
SWSLFRPEKMPVADGERLRVTGKIPGLRVSGGDRLQVTSVSEDAMTVVVPGRAEPASLPVADSPFTALKL
ENGWVETPGHSVSDSATVFASVTQMAMDNATLNGLARSGRDVRLYSSLDETRTAEKLARHPSFTVVSEQI
KARAGEILLETAISLQKAGLHTPAQQAIHLALPVLESKNLAFSMVDLLTEAKSFAAEGTSFTDLGGEINA
QIKRGDLLYVDVAKGYGTGLLVSRASYEAEKSILRHILEGKEAVTPLMERVPGELMEKLTSGQRAATRMI
LETSDRFTVVQGYAGVGKTTQFRAVMSAVNMLPESGRPRVVGLGPTHRAVGEMRSAGVDAQTLASFLHDT
QLQQRSGETPDFSNTLFLLDESSMVGNTDMARAYALIAAGGGRAVASGDTDQLQAIAPGQPFRLQQTRSA
ADVAIMKEIVRQTPELREAVYSLINRDVERALSGLESVKPSQVPRQEGAWAPEHSVTEFSHSQEAKLAEA
QQKAMLKGEAFPDVPMTLYEAIVRDYTGRTPEAREQTLIVTHLNEDRRVLNSMIHDAREKAGELGKEQVM
VPVLNTANIRDGELRRLSTWETHRDALVLVDNVYHRIAGISKDDGLITLQDAEGNTRLISPREAVAEGVT
LYTPDTIRVGAGDRMRFTKSDRERGYVANSVWTVTAVSGDSVTLSGRQQTRVIRPAQERAEQHIDLAYAI
TAHGAQGASETFAIALEGTEGSRKLMAGFESAYVALSRMKQHVQVYTDNRQGWTDAINNAVQKGTAHDVF
EPKPDREVMNAERLFSTARELRDVAAGRAVLRQAGLAGGDSPARFIAPGRKYPQPYVALPAFDRNGKSAG
IWLNPLTTDDGNGLRGFSGEGRVKGSGDAQFVALQGSRNGESLLADNMQDGVRIARDNPDSGVVVRIAGE
GRPWNPGAITGGRVWGDIPDNSVQPGAGNGEPVTAEVLAQRQAEEAIRRETVRRADEIVRKMAENKPDLP
DSKTEQAVREIAGQERDRSAISEREAALPESVLRESQREREAVREIARENLLQERLQQMERDMVRDLQKE
KTLGGD

  Protein domains


Predicted by InterproScan.

DNA relaxase TraI 2B/2B-like domain (TraI_2B)

(633-712)

AAA domain (AAA_30)

(969-1156)

DNA helicase TraI (TraI_C)

(1434-1557)

TrwC relaxase (TrwC)

(10-283)

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

(575-626)


  Protein structure



No available structure.




Auxiliary protein

ID   1445 GenBank   WP_001151524
Name   WP_001151524_STIN_92|unnamed3 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

ID   1446 GenBank   WP_001369361
Name   WP_001369361_STIN_92|unnamed3 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


T4CP

ID   3186 GenBank   WP_001064265
Name   traC_HUZ60_RS25950_STIN_92|unnamed3 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: 99296.07 Da        Isoelectric Point: 6.3032

>WP_001064265.1 MULTISPECIES: type IV secretion system protein TraC [Enterobacteriaceae]
MNNPLEAVTQAVNSLVTALKLPDESAKANEVLGEMSFPQFSRLLPYRDYNQESGLFMNDTTMGFMLEAIP
INGANESIVEALDHMLRTKLPRGVPFCIHLMSSQLVGDRIEYGLREFSWSGEQAERFNAITRAYYMNAAA
TQFPLPEGMNLPLTLRHYRVFFSYCSPSKKKSRADILEMENLVKIIRASLQGASITTQAVDAQAFIDIVG
EMINHNPDSLYPKRRQLDPYSDLNYQCVEDSFDLKVRADYLTLGLREKGRNSTARILNFHLARNPEIAFL
WNMADNYSNLLNPELSISCPFILTLTLVVEDQVKTHSEANLKYMDLEKKSKTSYAKWFPSVEKEAKEWGE
LRQRLGSGQSSVVSYFLNITAFCKDNNETALEVEQDILNSFRKNGFELISPRFNHMRNFLTCLPFMAGKG
LFKQLKEAGVVQRAESFNVANLMPLVADNPLTPAGLLAPTYRNQLAFIDIFFRGMNNTNYNMAVCGTSGA
GKTGLIQPLIRSVLDSGGFAVVFDMGDGYKSLCENMGGVYLDGETLRFNPFANITDIDQSAERVRDQLSV
MASPNGNLDEVHEGLLLQAVRASWLAKKNRARIDDVVDFLKNARDNDQYVESPTIRSRLDEMIVLLDQYT
AGGTYGRYFNSDEPSLRDDAKMVVLELGGLEDRPSLLVAVMFSLIIYIENRMYRTPRNLKKLNVIDEGWR
LLDFKNHKVGEFIEKGYRTARRHTGAYITITQNIVDFDSDKASSAARAAWGNSSYKIILKQSAKEFAKYN
QLYPDQFLPLQRDMIGKFGAAKDQWFSSFLLQVENHSSWHRLFVDPLSRAMYSSDGPDFEFVQQKRKEGL
SIHEAVWQLAWKKSGPEMASLEAWLEEHEKYRSVA

  Protein domains


Predicted by InterproScan.

TraC protein (TraC_F_IV)

(38-276)

TraG P-loop domain (P-loop_TraG)

(467-771)

Family of unknown function (DUF5934) (DUF5934)

(289-446)

  Protein structure



No available structure.



ID   3187 GenBank   WP_063078088
Name   traD_HUZ60_RS26025_STIN_92|unnamed3 insolico UniProt ID   _
Length   726 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 726 a.a.        Molecular weight: 82541.06 Da        Isoelectric Point: 5.0504

>WP_063078088.1 MULTISPECIES: type IV conjugative transfer system coupling protein TraD [Enterobacteriaceae]
MSFNAKDMTQGGQIASMRIRMFSQIANIMLYCLFIFFWILVGLVLWVKISWQTFVNGCIYWWCTTLEGMR
DLIRSQPVYEIQYYGKTFRMNAAQVLHDKYMIWCGEQLWSAFVLATVVALVICLITFFVVSWILGRQGKQ
QSENEVTGGRQLTDNPKDVARMLKKDGKDSDIRIGDLPIIRDSEIQNFCLHGTVGAGKSEVIRRLANYAR
QRGDMVVIYDRSGEFVKSYYDPSIDKILNPLDARCAAWDLWKECLTQPDFDNTANTLIPMGTKEDPFWQG
SGRTIFAEAAYLMRNDPNRSYSKLVDTLLSIKIEKLRTFLRNSPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEHNGESFTIRDWMRGVREDQKNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WFFCDELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGEKAAATLFDVMNTRAFFRSPSHKIA
EFAAGEIGEKEHLKASEQYSYGADPVRDGVSTGKDMERQTLVSYSDIQSLPDLTCYVTLPGPYPAVKLSL
KYQTRPKVAPEFIPRDINPEMENRLSAVLAAREAEGRQMASLFEPDVPEVVSGEDVTQAEQPQQPQQPQQ
PQQPVSSAINDKKSDSGVNVPAGGIEQELKMKPEEEMEQQLPPGISESGEVVDMAAYEAWQQENHPDIQQ
QMQRREEVNINVHRERGEDVEPGDDF

  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: 91122..116381

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HUZ60_RS25835 (HUZ60_25505) 87084..87518 + 435 WP_000845953 conjugation system SOS inhibitor PsiB -
HUZ60_RS25840 (HUZ60_25510) 87515..88234 + 720 WP_001276232 plasmid SOS inhibition protein A -
HUZ60_RS25845 (HUZ60_25515) 88246..88434 - 189 WP_001299721 hypothetical protein -
HUZ60_RS25850 88456..88605 + 150 Protein_107 plasmid maintenance protein Mok -
HUZ60_RS25855 (HUZ60_25520) 88547..88672 + 126 WP_001372321 type I toxin-antitoxin system Hok family toxin -
HUZ60_RS25860 88892..89122 + 231 WP_001426396 hypothetical protein -
HUZ60_RS25865 89120..89293 - 174 Protein_110 hypothetical protein -
HUZ60_RS25870 89363..89569 + 207 WP_000547968 hypothetical protein -
HUZ60_RS25875 (HUZ60_25525) 89594..89881 + 288 WP_000107535 hypothetical protein -
HUZ60_RS25880 (HUZ60_25530) 90004..90825 + 822 WP_001234469 DUF932 domain-containing protein -
HUZ60_RS25885 (HUZ60_25535) 91122..91712 - 591 WP_001376243 transglycosylase SLT domain-containing protein -
HUZ60_RS25890 (HUZ60_25540) 92045..92428 + 384 WP_001151524 conjugal transfer relaxosome DNA-binding protein TraM -
HUZ60_RS25895 (HUZ60_25545) 92615..93304 + 690 WP_039002187 conjugal transfer transcriptional regulator TraJ -
HUZ60_RS25900 (HUZ60_25550) 93403..93798 + 396 WP_001309237 conjugal transfer relaxosome DNA-bindin protein TraY -
HUZ60_RS25905 (HUZ60_25555) 93831..94193 + 363 WP_000994784 type IV conjugative transfer system pilin TraA -
HUZ60_RS25910 (HUZ60_25560) 94198..94509 + 312 WP_000012106 type IV conjugative transfer system protein TraL traL
HUZ60_RS25915 (HUZ60_25565) 94531..95097 + 567 WP_000399792 type IV conjugative transfer system protein TraE traE
HUZ60_RS25920 (HUZ60_25570) 95084..95812 + 729 WP_001230787 type-F conjugative transfer system secretin TraK traK
HUZ60_RS25925 (HUZ60_25575) 95812..97239 + 1428 WP_000146690 F-type conjugal transfer pilus assembly protein TraB traB
HUZ60_RS25930 (HUZ60_25580) 97229..97816 + 588 WP_000002772 conjugal transfer pilus-stabilizing protein TraP -
HUZ60_RS25935 (HUZ60_25585) 97803..98123 + 321 WP_239606302 conjugal transfer protein TrbD -
HUZ60_RS25940 (HUZ60_25590) 98120..98635 + 516 WP_000724019 type IV conjugative transfer system lipoprotein TraV traV
HUZ60_RS25945 (HUZ60_25595) 98770..98991 + 222 WP_001278692 conjugal transfer protein TraR -
HUZ60_RS25950 (HUZ60_25600) 99151..101778 + 2628 WP_001064265 type IV secretion system protein TraC virb4
HUZ60_RS25955 (HUZ60_25605) 101775..102161 + 387 WP_039002198 type-F conjugative transfer system protein TrbI -
HUZ60_RS25960 (HUZ60_25610) 102158..102790 + 633 WP_001749440 type-F conjugative transfer system protein TraW traW
HUZ60_RS25965 (HUZ60_25615) 102787..103779 + 993 WP_023148235 conjugal transfer pilus assembly protein TraU traU
HUZ60_RS25970 (HUZ60_25620) 103788..104426 + 639 WP_000777691 type-F conjugative transfer system pilin assembly protein TrbC trbC
HUZ60_RS25975 (HUZ60_25625) 104423..106231 + 1809 WP_000821844 type-F conjugative transfer system mating-pair stabilization protein TraN traN
HUZ60_RS25980 (HUZ60_25630) 106258..106518 + 261 WP_000864348 conjugal transfer protein TrbE -
HUZ60_RS25985 (HUZ60_25635) 106511..107254 + 744 WP_039002205 type-F conjugative transfer system pilin assembly protein TraF traF
HUZ60_RS25990 (HUZ60_25640) 107415..107651 + 237 WP_054377141 type-F conjugative transfer system pilin chaperone TraQ -
HUZ60_RS25995 (HUZ60_25645) 107638..108183 + 546 WP_000052613 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
HUZ60_RS26000 (HUZ60_25650) 108113..108475 + 363 WP_001443292 P-type conjugative transfer protein TrbJ -
HUZ60_RS26005 (HUZ60_25655) 108475..109848 + 1374 WP_170926237 conjugal transfer pilus assembly protein TraH traH
HUZ60_RS26010 (HUZ60_25660) 109845..112667 + 2823 WP_001007048 conjugal transfer mating-pair stabilization protein TraG traG
HUZ60_RS26015 (HUZ60_25665) 112682..113185 + 504 WP_000605510 hypothetical protein -
HUZ60_RS26020 (HUZ60_25670) 113217..113948 + 732 WP_000850424 conjugal transfer complement resistance protein TraT -
HUZ60_RS26025 (HUZ60_25675) 114201..116381 + 2181 WP_063078088 type IV conjugative transfer system coupling protein TraD virb4

Host bacterium

ID   4941 GenBank   NZ_CP054980
Plasmid name   STIN_92|unnamed3 Incompatibility group   IncR
Plasmid size   124795 bp Coordinate of oriT [Strand]   91693..92044 [+]
Host baterium   Shigella flexneri strain STIN_92

Cargo genes

Drug resistance gene   blaTEM-1B, dfrA12, aadA2, cmlA1, ant(3'')-Ia, tet(M), sul3
Virulence gene   -
Metal resistance gene   silP, silA, silB, silF, silC, silR, silS, silE
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -