Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   104485
Name   oriT_SWHIN_97|unnamed1 in_silico
Organism   Shigella flexneri strain SWHIN_97
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP055071 (111173..111524 [+], 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_97|unnamed1
AGGTTGGTGGTTCTCACCACCAAAAGCACCACACCCCACGCAAAAACAAGTTTTTGCTGATTTTTCTTTATAAATAGAGAGTTATGAAAAATTAGTTTCTCTTACTCTCTTTATGATATTTAAAAAAGCGGTGTCGGCGCGGCTACAACAACGCGCCGACACCGCTTTGTAGGGGTGGTACTGACTATTTTTATAAAAAACATTATTTTATATTAGGGGTGCTGCTAGCGGCGCGGTGTGTTTTTTTATAGGATACCGCTAGGGGCGCTGCTAGCGGTGCGTCCCTGTTTGCATTATGAATTTTAGTGTTTCGAAATTAACTTTATTTTATGTTCAAAAAAGGTAATCTCTA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   3249 GenBank   WP_239606305
Name   traI_HUZ91_RS24045_SWHIN_97|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: 191927.78 Da        Isoelectric Point: 6.1576

>WP_239606305.1 conjugative transfer relaxase/helicase TraI [Shigella flexneri]
MMSIAQVRSAGSAGNYYTDKDNYYVLGSMGERWAGRGAEQLGLQGSVDKDVFTRLLEGRLPDGADLSRMQ
DGSNKHRPGYDLTFSAPKSVSMMAMLGGDKRLIDAHNQAVDFAVRQVEALASTRVMTDGQSETVLTGNLV
MALFNHDTSRDQEPQLHTHTVVANVTQHNGEWKTLSSDKVGKTGFIENVYANQIAFGRLYREKLKEQVEA
LGYETEVVGKHGMWEMPGVPVEAFSGRSQAIREAVGEDASLKSRDVAALDTRKSKQHVDPEVRMAEWMQT
LKETGFDIRAYRDAADQRAETRTQAPGAVSQEGPDVQQAVTQAIAGLSERKVQFTYTDVLARTVGILPPE
NGVIERARAGIDEAISREQLIPLDREKGLFTSGIHVLDELSVRALSRDIMKQNRVTVHPEKSVPRTAGYS
DAVSVLAQDRPSLAIVSGQGGAAGQRERVAELVMMAREQGREVQIIAADRRSQMNLKQDERLSGELITGR
RQLLEGMAFTPGSTVIVDQGEKLSLKETLTLLDGAARHNVQVLITDSGQRTGTGSALMAMKDAGVNSYRW
QGGEQRPATIISEPDRNVRYARLAGDFAASVKAGEESVAQVSGVREQAILTQAIRSELKTQGVLGHPEVT
MTALSPVWLDSRSRYLRDMYRPGMVMEQWNPETRSHDRYVIDRVTAQSHSLTLRDAQGETQVVRISSLDS
SWSLFRPEKMPVADGERLRVTGKIPGLRVSGGDRLQVTSVSEDAMTVVVPGRAEPASLPVADSPFTALKL
ENGWVETPGHSVSDSATVFASVTQMAMDNATLNGLARSGRDVRLYSSLDETRTAEKLARHPSFTVVSEQI
KARAGEILLETAISLQKAGLHTPAQQAIHLALPVLESKNLAFSMVDLLTEAKSFAAEGTSFTDLGGEINA
QIKRGDLLYVDVAKGYGTGLLVSRASYEAEKSILRHILEGKEAVTPLMERVPGELMEKLTSGQRAATRMI
LETSDRFTVVQGYAGVGKTTQFRAVMSAVNMRPESGRPRVVGLGPTHRAVGEMRSAGVDAQTLASFLHDT
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)

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)

AAA domain (AAA_30)

(969-1156)


  Protein structure



No available structure.




Auxiliary protein

ID   1437 GenBank   WP_001151524
Name   WP_001151524_SWHIN_97|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

ID   1438 GenBank   WP_001369361
Name   WP_001369361_SWHIN_97|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


T4CP

ID   3170 GenBank   WP_001064265
Name   traC_HUZ91_RS23965_SWHIN_97|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.



ID   3171 GenBank   WP_063078088
Name   traD_HUZ91_RS24040_SWHIN_97|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.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 110602..135861

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HUZ91_RS23850 (HUZ91_23660) 106564..106998 + 435 WP_000845953 conjugation system SOS inhibitor PsiB -
HUZ91_RS23855 (HUZ91_23665) 106995..107714 + 720 WP_001276232 plasmid SOS inhibition protein A -
HUZ91_RS23860 (HUZ91_23670) 107726..107914 - 189 WP_001299721 hypothetical protein -
HUZ91_RS23865 107936..108085 + 150 Protein_123 plasmid maintenance protein Mok -
HUZ91_RS23870 (HUZ91_23675) 108027..108152 + 126 WP_001372321 type I toxin-antitoxin system Hok family toxin -
HUZ91_RS23875 108372..108602 + 231 WP_001426396 hypothetical protein -
HUZ91_RS23880 108600..108773 - 174 Protein_126 hypothetical protein -
HUZ91_RS23885 108843..109049 + 207 WP_000547968 hypothetical protein -
HUZ91_RS23890 (HUZ91_23680) 109074..109361 + 288 WP_000107535 hypothetical protein -
HUZ91_RS23895 (HUZ91_23685) 109484..110305 + 822 WP_239606300 DUF932 domain-containing protein -
HUZ91_RS23900 (HUZ91_23690) 110602..111204 - 603 WP_000243712 transglycosylase SLT domain-containing protein virB1
HUZ91_RS23905 (HUZ91_23695) 111525..111908 + 384 WP_001151524 conjugal transfer relaxosome DNA-binding protein TraM -
HUZ91_RS23910 (HUZ91_23700) 112095..112784 + 690 WP_039002187 conjugal transfer transcriptional regulator TraJ -
HUZ91_RS23915 (HUZ91_23705) 112883..113278 + 396 WP_001309237 conjugal transfer relaxosome DNA-bindin protein TraY -
HUZ91_RS23920 (HUZ91_23710) 113311..113673 + 363 WP_000994784 type IV conjugative transfer system pilin TraA -
HUZ91_RS23925 (HUZ91_23715) 113678..113989 + 312 WP_000012106 type IV conjugative transfer system protein TraL traL
HUZ91_RS23930 (HUZ91_23720) 114011..114577 + 567 WP_000399792 type IV conjugative transfer system protein TraE traE
HUZ91_RS23935 (HUZ91_23725) 114564..115292 + 729 WP_001230787 type-F conjugative transfer system secretin TraK traK
HUZ91_RS23940 (HUZ91_23730) 115292..116719 + 1428 WP_000146690 F-type conjugal transfer pilus assembly protein TraB traB
HUZ91_RS23945 (HUZ91_23735) 116709..117296 + 588 WP_000002772 conjugal transfer pilus-stabilizing protein TraP -
HUZ91_RS23950 (HUZ91_23740) 117283..117603 + 321 WP_239606302 conjugal transfer protein TrbD -
HUZ91_RS23955 (HUZ91_23745) 117600..118115 + 516 WP_000724019 type IV conjugative transfer system lipoprotein TraV traV
HUZ91_RS23960 (HUZ91_23750) 118250..118471 + 222 WP_001278692 conjugal transfer protein TraR -
HUZ91_RS23965 (HUZ91_23755) 118631..121258 + 2628 WP_001064265 type IV secretion system protein TraC virb4
HUZ91_RS23970 (HUZ91_23760) 121255..121641 + 387 WP_039002198 type-F conjugative transfer system protein TrbI -
HUZ91_RS23975 (HUZ91_23765) 121638..122270 + 633 WP_001749440 type-F conjugative transfer system protein TraW traW
HUZ91_RS23980 (HUZ91_23770) 122267..123259 + 993 WP_023148235 conjugal transfer pilus assembly protein TraU traU
HUZ91_RS23985 (HUZ91_23775) 123268..123906 + 639 WP_000777691 type-F conjugative transfer system pilin assembly protein TrbC trbC
HUZ91_RS23990 (HUZ91_23780) 123903..125711 + 1809 WP_000821844 type-F conjugative transfer system mating-pair stabilization protein TraN traN
HUZ91_RS23995 (HUZ91_23785) 125738..125998 + 261 WP_000864348 conjugal transfer protein TrbE -
HUZ91_RS24000 (HUZ91_23790) 125991..126734 + 744 WP_039002205 type-F conjugative transfer system pilin assembly protein TraF traF
HUZ91_RS24005 (HUZ91_23795) 126895..127131 + 237 WP_054377141 type-F conjugative transfer system pilin chaperone TraQ -
HUZ91_RS24010 (HUZ91_23800) 127118..127663 + 546 WP_000052613 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
HUZ91_RS24015 (HUZ91_23805) 127593..127955 + 363 WP_001443292 P-type conjugative transfer protein TrbJ -
HUZ91_RS24020 (HUZ91_23810) 127955..129328 + 1374 WP_170926237 conjugal transfer pilus assembly protein TraH traH
HUZ91_RS24025 (HUZ91_23815) 129325..132147 + 2823 WP_001007048 conjugal transfer mating-pair stabilization protein TraG traG
HUZ91_RS24030 (HUZ91_23820) 132162..132665 + 504 WP_000605510 hypothetical protein -
HUZ91_RS24035 (HUZ91_23825) 132697..133428 + 732 WP_000850424 conjugal transfer complement resistance protein TraT -
HUZ91_RS24040 (HUZ91_23830) 133681..135861 + 2181 WP_063078088 type IV conjugative transfer system coupling protein TraD virb4

Host bacterium

ID   4924 GenBank   NZ_CP055071
Plasmid name   SWHIN_97|unnamed1 Incompatibility group   IncR
Plasmid size   144275 bp Coordinate of oriT [Strand]   111173..111524 [+]
Host baterium   Shigella flexneri strain SWHIN_97

Cargo genes

Drug resistance gene   oqxA, oqxB, qnrS1, sul3
Virulence gene   -
Metal resistance gene   silP, silA, silB, silF, silC, silR, silS, silE
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -