Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   104476
Name   oriT_STIN_80|unnamed1 in_silico
Organism   Shigella flexneri strain STIN_80
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP055001 (88136..88487 [-], 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_80|unnamed1
AGGTTGGTGGTTCTCACCACCAAAAGCACCACACCCCACGCAAAAACAAGTTTTTGCTGATTTTTCTTTATAAATAGAGAGTTATGAAAAATTAGTTTCTCTTACTCTCTTTATGATATTTAAAAAAGCGGTGTCGGCGCGGCTACAACAACGCGCCGACACCGCTTTGTAGGGGTGGTACTGACTATTTTTATAAAAAACATTATTTTATATTAGGGGTGCTGCTAGCGGCGCGGTGTGTTTTTTTATAGGATACCGCTAGGGGCGCTGCTAGCGGTGCGTCCCTGTTTGCATTATGAATTTTAGTGTTTCGAAATTAACTTTATTTTATGTTCAAAAAAGGTAATCTCTA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   3244 GenBank   WP_054377139
Name   traI_HUZ55_RS23865_STIN_80|unnamed1 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   1432 GenBank   WP_001369361
Name   WP_001369361_STIN_80|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   1433 GenBank   WP_001151524
Name   WP_001151524_STIN_80|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   3164 GenBank   WP_039002212
Name   traD_HUZ55_RS23870_STIN_80|unnamed1 insolico UniProt ID   _
Length   729 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 729 a.a.        Molecular weight: 82894.44 Da        Isoelectric Point: 5.0504

>WP_039002212.1 MULTISPECIES: type IV conjugative transfer system coupling protein TraD [Enterobacteriaceae]
MSFNAKDMTQGGQIASMRIRMFSQIANIMLYCLFIFFWILVGLVLWVKISWQTFVNGCIYWWCTTLEGMR
DLIRSQPVYEIQYYGKTFRMNAAQVLHDKYMIWCGEQLWSAFVLATVVALVICLITFFVVSWILGRQGKQ
QSENEVTGGRQLTDNPKDVARMLKKDGKDSDIRIGDLPIIRDSEIQNFCLHGTVGAGKSEVIRRLANYAR
QRGDMVVIYDRSGEFVKSYYDPSIDKILNPLDARCAAWDLWKECLTQPDFDNTANTLIPMGTKEDPFWQG
SGRTIFAEAAYLMRNDPNRSYSKLVDTLLSIKIEKLRTFLRNSPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEHNGESFTIRDWMRGVREDQKNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WFFCDELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGEKAAATLFDVMNTRAFFRSPSHKIA
EFAAGEIGEKEHLKASEQYSYGADPVRDGVSTGKDMERQTLVSYSDIQSLPDLTCYVTLPGPYPAVKLSL
KYQTRPKVAPEFIPRDINPEMENRLSAVLAAREAEGRQMASLFEPDVPEVVSGEDVTQAEQPQQPQQPQQ
PQQPQQPVSSAINDKKSDSGVNVPAGGIEQELKMKPEEEMEQQLPPGISESGEVVDMAAYEAWQQENHPD
IQQQMQRREEVNINVHRERGEDVEPGDDF

  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   3165 GenBank   WP_001064265
Name   traC_HUZ55_RS23945_STIN_80|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: 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.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 63790..89058

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HUZ55_RS23870 (HUZ55_23710) 63790..65979 - 2190 WP_039002212 type IV conjugative transfer system coupling protein TraD virb4
HUZ55_RS23875 (HUZ55_23715) 66232..66963 - 732 WP_000850424 conjugal transfer complement resistance protein TraT -
HUZ55_RS23880 (HUZ55_23720) 66995..67498 - 504 WP_000605510 hypothetical protein -
HUZ55_RS23885 (HUZ55_23725) 67513..70335 - 2823 WP_239592431 conjugal transfer mating-pair stabilization protein TraG traG
HUZ55_RS23890 (HUZ55_23730) 70332..71705 - 1374 WP_170926237 conjugal transfer pilus assembly protein TraH traH
HUZ55_RS23895 (HUZ55_23735) 71705..72067 - 363 WP_001443292 P-type conjugative transfer protein TrbJ -
HUZ55_RS23900 (HUZ55_23740) 71997..72542 - 546 WP_000052613 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
HUZ55_RS23905 (HUZ55_23745) 72529..72765 - 237 WP_054377141 type-F conjugative transfer system pilin chaperone TraQ -
HUZ55_RS23910 (HUZ55_23750) 72926..73669 - 744 WP_039002205 type-F conjugative transfer system pilin assembly protein TraF traF
HUZ55_RS23915 (HUZ55_23755) 73662..73922 - 261 WP_000864348 conjugal transfer protein TrbE -
HUZ55_RS23920 (HUZ55_23760) 73949..75757 - 1809 WP_000821844 type-F conjugative transfer system mating-pair stabilization protein TraN traN
HUZ55_RS23925 (HUZ55_23765) 75754..76392 - 639 WP_000777691 type-F conjugative transfer system pilin assembly protein TrbC trbC
HUZ55_RS23930 (HUZ55_23770) 76401..77393 - 993 WP_023148235 conjugal transfer pilus assembly protein TraU traU
HUZ55_RS23935 (HUZ55_23775) 77390..78022 - 633 WP_001749440 type-F conjugative transfer system protein TraW traW
HUZ55_RS23940 (HUZ55_23780) 78019..78405 - 387 WP_039002198 type-F conjugative transfer system protein TrbI -
HUZ55_RS23945 (HUZ55_23785) 78402..81029 - 2628 WP_001064265 type IV secretion system protein TraC virb4
HUZ55_RS23950 (HUZ55_23790) 81189..81410 - 222 WP_001278692 conjugal transfer protein TraR -
HUZ55_RS23955 (HUZ55_23795) 81545..82060 - 516 WP_000724019 type IV conjugative transfer system lipoprotein TraV traV
HUZ55_RS23960 (HUZ55_23800) 82057..82377 - 321 WP_063078087 conjugal transfer protein TrbD -
HUZ55_RS23965 (HUZ55_23805) 82364..82951 - 588 WP_000002772 conjugal transfer pilus-stabilizing protein TraP -
HUZ55_RS23970 (HUZ55_23810) 82941..84368 - 1428 WP_000146690 F-type conjugal transfer pilus assembly protein TraB traB
HUZ55_RS23975 (HUZ55_23815) 84368..85096 - 729 WP_001230787 type-F conjugative transfer system secretin TraK traK
HUZ55_RS23980 (HUZ55_23820) 85083..85649 - 567 WP_000399792 type IV conjugative transfer system protein TraE traE
HUZ55_RS23985 (HUZ55_23825) 85671..85982 - 312 WP_000012106 type IV conjugative transfer system protein TraL traL
HUZ55_RS23990 (HUZ55_23830) 85987..86349 - 363 WP_000994784 type IV conjugative transfer system pilin TraA -
HUZ55_RS23995 (HUZ55_23835) 86382..86777 - 396 WP_001309237 conjugal transfer relaxosome DNA-bindin protein TraY -
HUZ55_RS24000 (HUZ55_23840) 86876..87565 - 690 WP_039002187 conjugal transfer transcriptional regulator TraJ -
HUZ55_RS24005 (HUZ55_23845) 87752..88135 - 384 WP_001151524 conjugal transfer relaxosome DNA-binding protein TraM -
HUZ55_RS24010 (HUZ55_23850) 88456..89058 + 603 WP_000243712 transglycosylase SLT domain-containing protein virB1
HUZ55_RS24015 (HUZ55_23855) 89355..90176 - 822 WP_072795862 DUF932 domain-containing protein -
HUZ55_RS24020 (HUZ55_23860) 90298..90585 - 288 WP_000107535 hypothetical protein -
HUZ55_RS24025 90610..90816 - 207 WP_000547968 hypothetical protein -
HUZ55_RS24030 90886..91059 + 174 Protein_104 hypothetical protein -
HUZ55_RS24035 91057..91287 - 231 WP_001426396 hypothetical protein -
HUZ55_RS24040 (HUZ55_23865) 91507..91632 - 126 WP_001372321 type I toxin-antitoxin system Hok family toxin -
HUZ55_RS24045 91574..91723 - 150 Protein_107 plasmid maintenance protein Mok -
HUZ55_RS24050 (HUZ55_23870) 91745..91933 + 189 WP_001299721 hypothetical protein -
HUZ55_RS24055 (HUZ55_23875) 91945..92664 - 720 WP_001276232 plasmid SOS inhibition protein A -
HUZ55_RS24060 (HUZ55_23880) 92661..93095 - 435 WP_000845953 conjugation system SOS inhibitor PsiB -

Host bacterium

ID   4915 GenBank   NZ_CP055001
Plasmid name   STIN_80|unnamed1 Incompatibility group   IncFIB
Plasmid size   132056 bp Coordinate of oriT [Strand]   88136..88487 [-]
Host baterium   Shigella flexneri strain STIN_80

Cargo genes

Drug resistance gene   tet(M), ant(3'')-Ia, cmlA1, aadA2, dfrA12, floR, sul2, tet(A), aph(3')-Ia, sul3, blaTEM-1B, lnu(F), aac(3)-IId
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -