Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   104489
Name   oriT_SWHEFF_60|unnamed1 in_silico
Organism   Shigella flexneri strain SWHEFF_60
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP055038 (111325..111373 [+], 49 nt)
oriT length   49 nt
IRs (inverted repeats)      6..13, 16..23  (GCAAAATT..AATTTTGC)
Location of nic site      32..33
Conserved sequence flanking the
  nic site    		  GGTGTGGTGA
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 49 nt

>oriT_SWHEFF_60|unnamed1
AATCTGCAAAATTTTAATTTTGCGTGGGGTGTGGTGATTTTGTGGTGAG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   3252 GenBank   WP_047665818
Name   traI_HUZ72_RS23390_SWHEFF_60|unnamed1 insolico UniProt ID   A0A0S1TL23
Length   1753 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1753 a.a.        Molecular weight: 190754.90 Da        Isoelectric Point: 6.3385

>WP_047665818.1 MULTISPECIES: conjugative transfer relaxase/helicase TraI [Enterobacterales]
MMSIGSVKSAGSAGNYYTDKDNYYVIGSMDERWQGKGAEALGIDGKAVDKALFTELLKGKLPDGSDLTRI
QDGANKHRPGYDLTFSAPKSVSVMAMLGGDKRLIDAHNQAVTEAVRQLETLAATRVMTDGKSETVLTGNL
IVAKFNHDTNRNQEPQIHTHAVVINATQNGDKWQSLGTDKIGKTGFIENVYANQIAFGKLYREAFKPLVE
KLGYETEVVGKHGMWEMKGVPVEPFSTRSQEVREAAGPDASLKSRDVAALDTRKSKDAIDPAEKMVEWMN
TLKETGFDIRGYREAADARAAELARAPAAPVNTDGPDITDVVTKAIAGLSDRKVQFTYADLLARTVGQLE
AKDGVFELARKGIDAAIEREQLIPLDREKGLFTSNIHVLDELAVKALSQEVQRQNHVSVTPDAFVVRQVP
FSDAVSVLAQDRPVMGIVSGQGGATGQRERVAELTLMAREQGRDVHILAADNRSRDFLAGDVRLAGETVT
GKSALQDGTAFIPGGTLIVDQAEKLSLKETISLLDGAMRHNVQVLLSDSGKRSGTGSALTVLKDSGVNTY
RWQGGHQTTADIISEPDKGARYSRLAQEFAVSVREGQESVAQISGTREQSVLNGLIRDSLRQEGVLGEKD
TTITALTPVWLDSKSRGVRDYYREGMVMERWDPETRTHDRFVIDRVTGSSNMLTLKDREGVRLDLKVSAV
DSQWTLFRADTLPVAEGERLAVLGKIPDTRLKGGESITVMKVEDGQLTVQRPGQKTTQTLAMGAGVFDGI
KIGHGWVESPGRSVSETATVFASVTQRELDNATLNQLAQSGSHLRLYSAQDAARTTEKLSRHTAFSVVSE
QLKTRSGETDLDAAIAQQKAGLRTPAEQAIHLAIPLLESEKLTFSRPQLLATALETGGGKVSMADIDTTI
QAQIRSGQLLNVPVAHGYGNDLLISRQTWDAEKSILTHVLEGKDAVAPLMDRVPASLMTDLTAGQRAATR
MILESTDRFTVVQGYAGVGKTTQLRAVMSAISLLPEETRPRVIGLAPTHRAVGEMQSAGVDARTTASFLH
DTQLLQRNGQTPDFSNTLFLLDESSMVGLADMAKAHSLIVAGGGRAVSSGDNDQLQPIAPGQPFRLTQQR
SAADVAIMKEIVRQMPELRPAVYSLIERDVHRALTTIEQVTPEQVPRKEGAWAPGSSVVEFTPKQEKAIE
KALSEGKTLPEGQPATLYEALVKDYTGRTPEAQSQTLVITHLNKDRRALNSLIHDARRENGETGKEEITL
PVLVTSNIRDGELRKLSTWTAHKEAVALVDNVYHRISKVDKANQLITLTDSEGKERYISPREASAEGVTL
YRQEKITVSQGDRMRFSKSDLERGYVANSIWEVQSVSGDSVTLSDGKLTRTLTPKADQAQQHIDLAYAIT
AHGAQGASEPYAIALEGVAGGREQMASFESAYVALSRMKQHVQVYTDNREGWIKAIKHSPEKATAHDILE
PRNDRAVKTADLLFGRARPLDETAAGRAALQQSGLAQGSSPGKFISPGKKYPQPHVALPAFDKNGKAAGI
WLSPLTDRDGRLEAIGGEGRIMGNEDARFVALQNSRNGESLLAGNMGEGVRMARDNPDTGVVVRLAGDDR
PWNPGAMTGGRVWAEPAPVAPVPQAGADIILPPEVLAQRAAEEQQRREMEKQAEQTAREVAGEARKAGEP
ADRVKEVIGDVIRGLERDRPGTEKTTLPDDPQFRRQEEAIQQVASERLQRERLQAVERDMVRDLNREKTL
GGD

  Protein domains


Predicted by InterproScan.

TrwC relaxase (TrwC)

(10-284)

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

(577-629)

AAA domain (AAA_30)

(971-1157)

DNA helicase TraI (TraI_C)

(1433-1555)

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

(635-714)


  Protein structure



No available structure.




T4CP

ID   3175 GenBank   WP_013023832
Name   traD_HUZ72_RS23395_SWHEFF_60|unnamed1 insolico UniProt ID   _
Length   770 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 770 a.a.        Molecular weight: 85974.10 Da        Isoelectric Point: 5.1149

>WP_013023832.1 MULTISPECIES: type IV conjugative transfer system coupling protein TraD [Enterobacterales]
MSFNAKDMTQGGQIANMRFRMFGQIANIIFYVLFILFWVLCGLMLMYRLSWQTFVNGCVYWWCTTLGPMR
DIIRSQPVYTIQYYGQSLEYTSEQILADKYTIWCGEQLWTSFVFAAVVSLVICIVTFFIASWVLGRQGKQ
QSEDENTGGRQLSDKPKEVARQMKRDGMASDIKIGDLPILKNSEIQNFCLHGTVGSGKSEVIRRLLNYVR
ARGDMAIIYDRSCEFVKSYYDPSLDKILNPLDSRCAAWDLWKECLTLPDFDNISNTLIPMGTKEDPFWQG
SGRTIFAEGAYLMREDKDRSYEKLVDTMLSIKIDKLRAYLQNTPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEKNGEPFTIRDWMRGVREDRPNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WIFADELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGVKPAATLFDVMNTRAFFRSPSKEIA
EFAAGEIGEKEILKASEQYSYGADPVRDGVSTGKEKERETLVSYSDIQTLPDLSCYVTLPGPYPAVKLAL
KYKPRPKIAEGFIPRTLDARVDARLSALLEAREAEGSLARALFTPDAPASGPADTNSHAGEQPEPVSQPA
PADMTVSPAPVKAPPTTKMPAEEPSVRATEPSVLRLTTVPLIKPKAAAAAAAAATASSAGTPAAAAGGTE
QELAQQSAEQGQDMLPAGMNEDGVIEDMQAYDAWLADEQTQRDMQRREEVNINHSHRHDEQDYVEIGGNF

  Protein domains


Predicted by InterproScan.

Type IV secretion-system coupling protein DNA-binding domain (TrwB_AAD_bind)

(172-560)

F sex factor protein N terminal (TraD_N)

(32-128)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 83111..111931

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HUZ72_RS23395 (HUZ72_23205) 83111..85423 - 2313 WP_013023832 type IV conjugative transfer system coupling protein TraD virb4
HUZ72_RS23400 (HUZ72_23210) 85550..86239 - 690 WP_013023831 hypothetical protein -
HUZ72_RS23405 (HUZ72_23215) 86432..87163 - 732 WP_013023830 conjugal transfer complement resistance protein TraT -
HUZ72_RS23410 (HUZ72_23220) 87349..87882 - 534 WP_014343486 conjugal transfer protein TraS -
HUZ72_RS23415 (HUZ72_23225) 87885..90734 - 2850 WP_013609534 conjugal transfer mating-pair stabilization protein TraG traG
HUZ72_RS23420 (HUZ72_23230) 90734..92113 - 1380 WP_014343487 conjugal transfer pilus assembly protein TraH traH
HUZ72_RS23425 (HUZ72_23235) 92091..92534 - 444 WP_013023828 F-type conjugal transfer protein TrbF -
HUZ72_RS23430 (HUZ72_23240) 92580..93137 - 558 WP_013214031 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
HUZ72_RS23435 (HUZ72_23245) 93109..93348 - 240 WP_004144400 type-F conjugative transfer system pilin chaperone TraQ -
HUZ72_RS23440 (HUZ72_23250) 93359..94111 - 753 WP_048337413 type-F conjugative transfer system pilin assembly protein TraF traF
HUZ72_RS23445 (HUZ72_23255) 94132..94458 - 327 WP_004152676 hypothetical protein -
HUZ72_RS23450 (HUZ72_23260) 94471..94719 - 249 WP_004152675 hypothetical protein -
HUZ72_RS23455 (HUZ72_23265) 94697..94951 - 255 WP_004152674 conjugal transfer protein TrbE -
HUZ72_RS23460 (HUZ72_23270) 94983..96938 - 1956 WP_013023827 type-F conjugative transfer system mating-pair stabilization protein TraN traN
HUZ72_RS23465 (HUZ72_23275) 96997..97635 - 639 WP_011977786 type-F conjugative transfer system pilin assembly protein TrbC trbC
HUZ72_RS23470 (HUZ72_23280) 97648..98637 - 990 WP_009309872 conjugal transfer pilus assembly protein TraU traU
HUZ72_RS23475 (HUZ72_23285) 98634..99023 - 390 WP_004194992 hypothetical protein -
HUZ72_RS23480 (HUZ72_23290) 99065..99691 - 627 WP_009309871 type-F conjugative transfer system protein TraW traW
HUZ72_RS23485 (HUZ72_23295) 99691..100080 - 390 WP_004197815 type-F conjugative transfer system protein TrbI -
HUZ72_RS23490 (HUZ72_23300) 100080..102719 - 2640 WP_013023824 type IV secretion system protein TraC virb4
HUZ72_RS23495 (HUZ72_23305) 102791..103189 - 399 WP_013609531 hypothetical protein -
HUZ72_RS23500 (HUZ72_23310) 103565..103969 - 405 WP_004197817 hypothetical protein -
HUZ72_RS23505 (HUZ72_23315) 104036..104347 - 312 WP_015344986 hypothetical protein -
HUZ72_RS23510 (HUZ72_23320) 104348..104566 - 219 WP_015344987 hypothetical protein -
HUZ72_RS23515 (HUZ72_23325) 104672..105082 - 411 WP_009309869 hypothetical protein -
HUZ72_RS23520 (HUZ72_23330) 105214..105798 - 585 WP_013023822 type IV conjugative transfer system lipoprotein TraV traV
HUZ72_RS23525 (HUZ72_23335) 105912..107336 - 1425 WP_004194260 F-type conjugal transfer pilus assembly protein TraB traB
HUZ72_RS23530 (HUZ72_23340) 107336..108076 - 741 WP_013023821 type-F conjugative transfer system secretin TraK traK
HUZ72_RS23535 (HUZ72_23345) 108063..108629 - 567 WP_004144423 type IV conjugative transfer system protein TraE traE
HUZ72_RS23540 (HUZ72_23350) 108649..108954 - 306 WP_004144424 type IV conjugative transfer system protein TraL traL
HUZ72_RS23545 (HUZ72_23355) 108968..109336 - 369 WP_004194426 type IV conjugative transfer system pilin TraA -
HUZ72_RS24340 (HUZ72_23360) 109405..109605 - 201 WP_004194116 TraY domain-containing protein -
HUZ72_RS23550 (HUZ72_23365) 109691..110392 - 702 WP_004194113 hypothetical protein -
HUZ72_RS23555 (HUZ72_23370) 110622..111014 - 393 WP_004194114 conjugal transfer relaxosome DNA-binding protein TraM -
HUZ72_RS23560 (HUZ72_23375) 111446..111931 + 486 WP_001568108 transglycosylase SLT domain-containing protein virB1
HUZ72_RS23565 (HUZ72_23380) 111964..112293 - 330 WP_011977736 DUF5983 family protein -
HUZ72_RS23570 (HUZ72_23385) 112326..113147 - 822 WP_004152492 DUF932 domain-containing protein -
HUZ72_RS23575 (HUZ72_23390) 113955..115163 + 1209 WP_015344990 IS256 family transposase -
HUZ72_RS23580 (HUZ72_23395) 115299..115712 - 414 WP_013023817 helix-turn-helix domain-containing protein -
HUZ72_RS23585 (HUZ72_23400) 115713..115991 - 279 WP_004152721 helix-turn-helix transcriptional regulator -
HUZ72_RS23590 (HUZ72_23405) 115981..116301 - 321 WP_004152720 type II toxin-antitoxin system RelE/ParE family toxin -
HUZ72_RS23595 (HUZ72_23410) 116382..116606 - 225 WP_004152719 hypothetical protein -
HUZ72_RS23600 (HUZ72_23415) 116617..116829 - 213 WP_013023815 hypothetical protein -

Host bacterium

ID   4928 GenBank   NZ_CP055038
Plasmid name   SWHEFF_60|unnamed1 Incompatibility group   IncFII
Plasmid size   140589 bp Coordinate of oriT [Strand]   111325..111373 [+]
Host baterium   Shigella flexneri strain SWHEFF_60

Cargo genes

Drug resistance gene   sul2, aph(3'')-Ib, aph(6)-Id, aph(3')-Ia, aac(3)-IId, aac(6')-Ib-cr, ARR-3, dfrA27, aadA16, qacE, sul1, qnrB91, mph(A), tet(A), floR, blaTEM-1B, blaCTX-M-3, qnrS1
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   AcrIE9