Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   104473
Name   oriT_STEFF_22|unnamed1 in_silico
Organism   Shigella flexneri strain STEFF_22
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP055171 (88127..88478 [-], 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_STEFF_22|unnamed1
AGGTTGGTGGTTCTCACCACCAAAAGCACCACACCCCACGCAAAAACAAGTTTTTGCTGATTTTTCTTTATAAATAGAGAGTTATGAAAAATTAGTTTCTCTTACTCTCTTTATGATATTTAAAAAAGCGGTGTCGGCGCGGCTACAACAACGCGCCGACACCGCTTTGTAGGGGTGGTACTGACTATTTTTATAAAAAACATTATTTTATATTAGGGGTGCTGCTAGCGGCGCGGTGTGTTTTTTTATAGGATACCGCTAGGGGCGCTGCTAGCGGTGCGTCCCTGTTTGCATTATGAATTTTAGTGTTTCGAAATTAACTTTATTTTATGTTCAAAAAAGGTAATCTCTA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   3242 GenBank   WP_239592000
Name   traI_HUZ49_RS23500_STEFF_22|unnamed1 insolico UniProt ID   _
Length   1756 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1756 a.a.        Molecular weight: 191898.78 Da        Isoelectric Point: 6.1058

>WP_239592000.1 conjugative transfer relaxase/helicase TraI [Shigella flexneri]
MMSIAQVRSAGSAGNYYTDKDNYYVLGSMGERWAGRGAEQLGLQGSVDKDVFTRLLEGRLPDGADLSRMQ
DGSNKHRPGYDLTFSAPKSVSMMAMLGGDKRLIDAHNQAVDFAVRQVEALASTRVMTDGQSETVLTGNLV
MALFNHDTSRDQEPQLHTHTVVANVTQHNGEWKTLSSDKVGKTGFIENVYANQIAFGRLYREKLKEQVEA
LGYETEVVGKHGMWEMPGVPVEAFSGRSQAIREAVGEDASLKSRDVAALDTRKSKQHVDPEVRMAEWMQT
LKETGFDIRAYRDAADQRAETRTQAPGAVSQEGPDVQQAVTQAIAGLSERKVQFTYTDVLARTVGILPPE
NGVIERARAGIDEAISREQLIPLDREKGLFTSGIHVLDELSVRALSRDIMKQNRVTVHPEKSVPRTAGYS
DAVSVLAQDRPSLAIVSGQGGAAGQRERVAELVMMAREQGREVQIIAADRRSQMNLKQDERLSGELITGR
RQLLEGMAFTPGSTVIVDQGEKLSLKETLTLLDGAARHNVQVLITDSGQRTGTGSALMAMKDAGVNSYRW
QGGEQRPATIISEPDRNVRYARLAGDFAASVKAGEESVAQVSGVREQAILTQAIRSELKTQGVLGHPEVT
MTALSPVWLDSRSRYLRDMYRPGMVMEQWNPETRSHDRYVIDRVTAQSHSLTLRDAQGETQVVRISSLDS
SWSLFRPEKMPVADGERLRVTGKIPGLRVSGGDRLQVTSVSEDAMTVVVPGRAEPASLPVADSPFTALKL
ENGWVETPGHSVSDSATVFASVTQMAMDNATLNGLARSGRDVRLYSSLDETRTAEKLARHPSFTVVSEQI
KARAGEILLETAISLQKAGLHTPAQQAIHLALPVLESKNLAFSMVDLLTEAKSFAAEGTSFTDLGGEINA
QIKRGDLLYVDVAKGYGTGLLVSRASYEAEKSILRHILEGKEAVTPLMERVPGELMEKLTSGQRAATRMI
LETSDRFTVVQGYAGVGKTTQFRAVMSAVNMLPESGRPRVVGLGPTHRAVGEMRSAGVDAQTLASFLHDT
QLQQRSGETPDFSNTLFLLDESSMVGNTDMARAYALIAAGGGRAVASGDTDQLQAIAPGQPFRLQQTRSA
ADVAIMKEIVRQTPELREAVYSLINRDVERALSGLESVKPSQVPRQEGAWAPEHSVTEFSHSQEAKLAEA
QQKAMLKGEAFPDVPMTLYEAIVRDYTGRTPEAREQTLIVTHLNEDRRVLNSMIHDAREKAGELGKEQVM
VPVLNTANIRDGELRRLSTWETHRDALVLVDNVYHRIAGISKDDGLITLQDAEGNTRLISPREAVAEGVT
LYTPDTIRVGAGDRMRFTKSDRERGYVANSVWTVTAVSGDSVTLSGRQQTRVIRPAQERAEQHIDLAYAI
TAHGAQGASETFAIALEGTEGSRKLMAGFESAYVALSRMKQHVQVYTDNRQGWTDAINNAIQKGTAHDVF
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   1430 GenBank   WP_001369361
Name   WP_001369361_STEFF_22|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   1431 GenBank   WP_001151524
Name   WP_001151524_STEFF_22|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   3162 GenBank   WP_063078088
Name   traD_HUZ49_RS23505_STEFF_22|unnamed1 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.



ID   3163 GenBank   WP_001064265
Name   traC_HUZ49_RS23580_STEFF_22|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..89049

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HUZ49_RS23505 (HUZ49_23395) 63790..65970 - 2181 WP_063078088 type IV conjugative transfer system coupling protein TraD virb4
HUZ49_RS23510 (HUZ49_23400) 66223..66954 - 732 WP_000850424 conjugal transfer complement resistance protein TraT -
HUZ49_RS23515 (HUZ49_23405) 66986..67489 - 504 WP_000605510 hypothetical protein -
HUZ49_RS23520 (HUZ49_23410) 67504..70326 - 2823 WP_001007048 conjugal transfer mating-pair stabilization protein TraG traG
HUZ49_RS23525 (HUZ49_23415) 70323..71696 - 1374 WP_170926237 conjugal transfer pilus assembly protein TraH traH
HUZ49_RS23530 (HUZ49_23420) 71696..72058 - 363 WP_001443292 P-type conjugative transfer protein TrbJ -
HUZ49_RS23535 (HUZ49_23425) 71988..72533 - 546 WP_000052613 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
HUZ49_RS23540 (HUZ49_23430) 72520..72756 - 237 WP_054377141 type-F conjugative transfer system pilin chaperone TraQ -
HUZ49_RS23545 (HUZ49_23435) 72917..73660 - 744 WP_039002205 type-F conjugative transfer system pilin assembly protein TraF traF
HUZ49_RS23550 (HUZ49_23440) 73653..73913 - 261 WP_000864348 conjugal transfer protein TrbE -
HUZ49_RS23555 (HUZ49_23445) 73940..75748 - 1809 WP_000821844 type-F conjugative transfer system mating-pair stabilization protein TraN traN
HUZ49_RS23560 (HUZ49_23450) 75745..76383 - 639 WP_000777691 type-F conjugative transfer system pilin assembly protein TrbC trbC
HUZ49_RS23565 (HUZ49_23455) 76392..77384 - 993 WP_023148235 conjugal transfer pilus assembly protein TraU traU
HUZ49_RS23570 (HUZ49_23460) 77381..78013 - 633 WP_001749440 type-F conjugative transfer system protein TraW traW
HUZ49_RS23575 (HUZ49_23465) 78010..78396 - 387 WP_039002198 type-F conjugative transfer system protein TrbI -
HUZ49_RS23580 (HUZ49_23470) 78393..81020 - 2628 WP_001064265 type IV secretion system protein TraC virb4
HUZ49_RS23585 (HUZ49_23475) 81180..81401 - 222 WP_001278692 conjugal transfer protein TraR -
HUZ49_RS23590 (HUZ49_23480) 81536..82051 - 516 WP_000724019 type IV conjugative transfer system lipoprotein TraV traV
HUZ49_RS23595 (HUZ49_23485) 82048..82368 - 321 WP_063078087 conjugal transfer protein TrbD -
HUZ49_RS23600 (HUZ49_23490) 82355..82942 - 588 WP_000002772 conjugal transfer pilus-stabilizing protein TraP -
HUZ49_RS23605 (HUZ49_23495) 82932..84359 - 1428 WP_000146690 F-type conjugal transfer pilus assembly protein TraB traB
HUZ49_RS23610 (HUZ49_23500) 84359..85087 - 729 WP_001230787 type-F conjugative transfer system secretin TraK traK
HUZ49_RS23615 (HUZ49_23505) 85074..85640 - 567 WP_000399792 type IV conjugative transfer system protein TraE traE
HUZ49_RS23620 (HUZ49_23510) 85662..85973 - 312 WP_000012106 type IV conjugative transfer system protein TraL traL
HUZ49_RS23625 (HUZ49_23515) 85978..86340 - 363 WP_000994784 type IV conjugative transfer system pilin TraA -
HUZ49_RS23630 (HUZ49_23520) 86373..86768 - 396 WP_001309237 conjugal transfer relaxosome DNA-bindin protein TraY -
HUZ49_RS23635 (HUZ49_23525) 86867..87556 - 690 WP_039002187 conjugal transfer transcriptional regulator TraJ -
HUZ49_RS23640 (HUZ49_23530) 87743..88126 - 384 WP_001151524 conjugal transfer relaxosome DNA-binding protein TraM -
HUZ49_RS23645 (HUZ49_23535) 88459..89049 + 591 WP_001376243 transglycosylase SLT domain-containing protein -
HUZ49_RS23650 (HUZ49_23540) 89346..90167 - 822 WP_072795862 DUF932 domain-containing protein -
HUZ49_RS23655 (HUZ49_23545) 90289..90576 - 288 WP_000107535 hypothetical protein -
HUZ49_RS23660 (HUZ49_23550) 90578..90775 + 198 Protein_103 hypothetical protein -
HUZ49_RS23665 90773..91003 - 231 WP_001426396 hypothetical protein -
HUZ49_RS23670 (HUZ49_23555) 91223..91348 - 126 WP_001372321 type I toxin-antitoxin system Hok family toxin -
HUZ49_RS23675 91290..91439 - 150 Protein_106 plasmid maintenance protein Mok -
HUZ49_RS23680 (HUZ49_23560) 91461..91649 + 189 WP_001299721 hypothetical protein -
HUZ49_RS23685 (HUZ49_23565) 91661..92380 - 720 WP_001276232 plasmid SOS inhibition protein A -
HUZ49_RS23690 (HUZ49_23570) 92377..92811 - 435 WP_000845953 conjugation system SOS inhibitor PsiB -

Host bacterium

ID   4912 GenBank   NZ_CP055171
Plasmid name   STEFF_22|unnamed1 Incompatibility group   IncFIB
Plasmid size   131772 bp Coordinate of oriT [Strand]   88127..88478 [-]
Host baterium   Shigella flexneri strain STEFF_22

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   -