Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   105802
Name   oriT_pMHMC-003 in_silico
Organism   Shigella sonnei strain 506
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP053754 (63393..63479 [+], 87 nt)
oriT length   87 nt
IRs (inverted repeats)     _
Location of nic site      _
Conserved sequence flanking the
  nic site    		  _
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 87 nt

>oriT_pMHMC-003
GGGGTGTCGGGGCGAAGCCCTGACCAGGAGGCAATTGTATAATCGCGCGTGCGCGGTTATACAATTGCACATCCTGTCCCGTTTTTC

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   3919 GenBank   WP_021520371
Name   nikB_COO90_RS26485_pMHMC-003 insolico UniProt ID   A0A446GKR4
Length   899 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 899 a.a.        Molecular weight: 103939.37 Da        Isoelectric Point: 7.3426

>WP_021520371.1 MULTISPECIES: IncI1-type relaxase NikB [Enterobacteriaceae]
MNAVIPKKRRDGKSSFEDLVSYVSVRDDMTDEELDLSSSSQAEQPHRSRFSRLVDYATRLRNESFVALVD
VMKDGCEWVNFYGVTCFHNCTSLETAAADMEYIARQAHYAKDDTDPVFHYILSWQSHESPRPEQIYDSVR
HTLKSLGLADHQYVSAVHTDTDNLHVHVAVNRVHPETGYLNRLSWSQEKLSRACRELELKHGFAPDNGCW
VHAPGNRIVRKTAVERDRQNAWTRGKKQTFREYVAQTAVAGLRSEPVNDWLSLHRRLAEDGLYLSQMDGK
FLVMDGWDRNREGVQLDSFGPSWCAEKLMKKMGDYTPVPKDIFSQVEAPGRYNPDFIAADVRPEKIAETE
SLQQYACRHLGERLPEMAREGRLENCQAIHRTLAEAGLWMRVQHGHLVICDGYDHNQTPVRADSVWSLLT
LDNVNQLDGGWQPVPTDIFLQVTPTERFRGRRMESCPATDKEWHRMRTGTGPQGAIKRELFSDKESLWGY
SISHCSPQIEEMITQGEFTWQRCHELFAQQGLMLQKQHHGLVVVDAFNHEQTPVKASSIHPDLTLGRAEP
QAGPFVSAPADLFDRVQPESRYNPELAVSDRYGVSSKRDPMLRRQRREARAEARADLRARYLAWREQWRK
PDLRYGERCREIHQACRLRKSHIRAQYDDPALRKLHYHIAEVQRMQALIRLKEDIRNERQKLIADGKWYP
PSYRQWVEIQAAQGDRAAVSQLRGWDYRDRRKDKSRTTTTDRCVVLCEPGGTPVYGNTGDLEARLQKNGS
VRFRDRRTGEFVCTDYGDRVVFRNHHDRNALADKLDLIAPVLFGRDPRMGFEPEGNDKQFNQVFAEMVAW
HNVTGRTGHEDYRITRPDVDHHREGSERYYRDYIAANSNDDASLPPPEQDKRWEPPSPG

  Protein domains


Predicted by InterproScan.

Relaxase/Mobilisation nuclease domain (Relaxase)

(62-314)


  Protein structure


Source ID Structure
AlphaFold DB A0A446GKR4


Auxiliary protein

ID   1765 GenBank   WP_001281051
Name   WP_001281051_pMHMC-003 insolico UniProt ID   A0A3U8I0C6
Length   110 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  Auxiliary protein sequence


Download         Length: 110 a.a.        Molecular weight: 12646.44 Da        Isoelectric Point: 10.4030

>WP_001281051.1 MULTISPECIES: plasmid mobilization protein MobA [Enterobacteriaceae]
MSDKRQRSGSERRQKTILRAVRFSPDEDETICKNAEDSGLTVSAYIRNAALNKRINSRTDDAFLKELMRL
GRMQKHLFVQGKRTGDKEYAEVLVAITELTNTLRKQLMEG

  Protein domains



No domain identified.



  Protein structure


Source ID Structure
AlphaFold DB A0A3U8I0C6


T4CP

ID   3932 GenBank   WP_021520372
Name   trbC_COO90_RS26480_pMHMC-003 insolico UniProt ID   _
Length   763 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 763 a.a.        Molecular weight: 86911.08 Da        Isoelectric Point: 6.7713

>WP_021520372.1 MULTISPECIES: F-type conjugative transfer protein TrbC [Enterobacteriaceae]
MSEHRVNPELLHRTAWGNPVWNALQSLNIYGFCLVASLVASFIWPLALPACLLFTLITMLVFSLQRWRCP
LRMPMTLECADPSQDRMIKRSLFSFWPTLFQYEVILESPASGIFYVGYQRVRDIGRELWLSMDDLTRHIM
FFATTGGGKTETIFAWAINPLCWARGFTLVDGKAQNDTARTIWYLARRFGREDDVEVINFMNGGKSRSEI
ILSGEKTRPQSNTWNPFCYSTEAFTAETMQSMLPQNVQGGEWQSRAIAMNKALVFGTKFWCVREGKTMSL
QMLREHMTLEGMAKLYCRGLDDQWPEEAIAPLRNYLQDVPGFDLSLVRTPSAWTEEPRKQHAYLSGQFSE
TFSTFTEAFGDIFAEDSGDIDIRDSIHSDRILMVMIPALDTSAHTTSALGRMFITQKSMILARDLGYRLE
GTDSDALEVKKYKGRFPYLCFLDEVGAYYTDRIAVEATQVRSLDFALILMAQDQERIEGQTTATNTATLM
QNTGTKFAGRIVSEGSTARTLKSAAGEEARARMNNLQRQDGIFGESWIDSPQISILMESKINVQELIELH
PGEFFSIFRGETVPSASFFIPDDEKSCSSDPVVINRYISVDAPRLDRLRRLVPRTAQRRIPSPENVSAII
GVLTAKPSRKRRKIRTEPHTIVDTFQQRIAGRQAAMAMLEEYDTDINARESALWETAVNTLKTTTREERR
IRYITLNRPELPETKEENQISVRAERAGINLLTLPQDNNHPTGRPVNGFHHKKTNRPDWDGMY

  Protein domains



No domain identified.


  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 18767..58014

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
COO90_RS26255 (COO90_26055) 13829..14896 + 1068 WP_012783947 type IV pilus biogenesis lipoprotein PilL -
COO90_RS26260 (COO90_26060) 14896..15333 + 438 WP_000539807 type IV pilus biogenesis protein PilM -
COO90_RS26265 (COO90_26065) 15347..17029 + 1683 WP_000748143 PilN family type IVB pilus formation outer membrane protein -
COO90_RS26270 (COO90_26070) 17022..18317 + 1296 WP_001388364 type 4b pilus protein PilO2 -
COO90_RS26275 (COO90_26075) 18304..18756 + 453 WP_001247870 type IV pilus biogenesis protein PilP -
COO90_RS26280 (COO90_26080) 18767..20320 + 1554 WP_001492932 ATPase, T2SS/T4P/T4SS family virB11
COO90_RS26285 (COO90_26085) 20333..21430 + 1098 WP_001492931 type II secretion system F family protein -
COO90_RS26290 (COO90_26090) 21448..22062 + 615 WP_001542527 type 4 pilus major pilin -
COO90_RS26295 (COO90_26095) 22072..22632 + 561 WP_000014116 lytic transglycosylase domain-containing protein virB1
COO90_RS26300 (COO90_26100) 22617..23273 + 657 WP_001193553 prepilin peptidase -
COO90_RS26305 (COO90_26105) 23273..24563 + 1291 Protein_26 shufflon system plasmid conjugative transfer pilus tip adhesin PilV -
COO90_RS26310 (COO90_26110) 25513..25686 - 174 WP_254103232 hypothetical protein -
COO90_RS26315 (COO90_26115) 25798..26951 + 1154 Protein_28 site-specific integrase -
COO90_RS26320 (COO90_26120) 27102..27926 + 825 WP_001238932 conjugal transfer protein TraE traE
COO90_RS26325 (COO90_26125) 28012..29214 + 1203 WP_000976353 conjugal transfer protein TraF -
COO90_RS26330 (COO90_26130) 29274..29858 + 585 WP_000977522 histidine phosphatase family protein -
COO90_RS26335 (COO90_26135) 30252..30710 + 459 WP_001079808 IncI1-type conjugal transfer lipoprotein TraH -
COO90_RS26340 (COO90_26140) 30707..31525 + 819 WP_000646098 IncI1-type conjugal transfer lipoprotein TraI traI
COO90_RS26345 (COO90_26145) 31522..32670 + 1149 WP_001024972 plasmid transfer ATPase TraJ virB11
COO90_RS26350 (COO90_26150) 32667..32957 + 291 WP_001299214 hypothetical protein traK
COO90_RS26355 (COO90_26155) 32972..33523 + 552 WP_000014583 phospholipase D family protein -
COO90_RS26360 (COO90_26160) 33613..37380 + 3768 WP_001141527 LPD7 domain-containing protein -
COO90_RS26365 (COO90_26165) 37398..37745 + 348 WP_001055900 conjugal transfer protein traL
COO90_RS26370 (COO90_26170) 37742..38434 + 693 WP_000138550 DotI/IcmL family type IV secretion protein traM
COO90_RS26375 (COO90_26175) 38445..39428 + 984 WP_001191877 IncI1-type conjugal transfer protein TraN traN
COO90_RS26380 (COO90_26180) 39431..40720 + 1290 WP_042004726 conjugal transfer protein TraO traO
COO90_RS26385 (COO90_26185) 40720..41424 + 705 WP_000801920 IncI1-type conjugal transfer protein TraP traP
COO90_RS26390 (COO90_26190) 41424..41951 + 528 WP_001055569 conjugal transfer protein TraQ traQ
COO90_RS26395 (COO90_26195) 42002..42406 + 405 WP_000086965 IncI1-type conjugal transfer protein TraR traR
COO90_RS26400 (COO90_26200) 42470..42658 + 189 WP_001277253 putative conjugal transfer protein TraS -
COO90_RS26405 (COO90_26205) 42642..43442 + 801 WP_001164784 IncI1-type conjugal transfer protein TraT traT
COO90_RS26410 (COO90_26210) 43532..46576 + 3045 WP_001024789 IncI1-type conjugal transfer protein TraU traU
COO90_RS26415 (COO90_26215) 46576..47190 + 615 WP_000337399 IncI1-type conjugal transfer protein TraV traV
COO90_RS26420 (COO90_26220) 47157..48359 + 1203 WP_042004725 IncI1-type conjugal transfer protein TraW traW
COO90_RS26425 (COO90_26225) 48388..48972 + 585 WP_001037987 IncI1-type conjugal transfer protein TraX -
COO90_RS26430 (COO90_26230) 49069..51237 + 2169 WP_000698357 DotA/TraY family protein traY
COO90_RS26435 (COO90_26235) 51311..51961 + 651 WP_001178506 plasmid IncI1-type surface exclusion protein ExcA -
COO90_RS26440 (COO90_26240) 52033..52242 - 210 WP_000062603 HEAT repeat domain-containing protein -
COO90_RS26445 (COO90_26245) 52634..52810 + 177 WP_001054898 hypothetical protein -
COO90_RS27490 52875..52970 - 96 WP_001303310 DinQ-like type I toxin DqlB -
COO90_RS26455 (COO90_26250) 53469..53720 + 252 WP_001291964 hypothetical protein -
COO90_RS26460 (COO90_26255) 53792..53944 - 153 WP_001331364 Hok/Gef family protein -
COO90_RS26465 (COO90_26260) 54513..55499 + 987 WP_001257838 hypothetical protein -
COO90_RS26470 (COO90_26265) 55717..56925 + 1209 WP_001383960 IncI1-type conjugal transfer protein TrbA trbA
COO90_RS26475 (COO90_26270) 56944..58014 + 1071 WP_000151583 IncI1-type conjugal transfer protein TrbB trbB
COO90_RS26480 (COO90_26275) 58007..60298 + 2292 WP_021520372 F-type conjugative transfer protein TrbC -

Host bacterium

ID   6239 GenBank   NZ_CP053754
Plasmid name   pMHMC-003 Incompatibility group   IncI1
Plasmid size   88060 bp Coordinate of oriT [Strand]   63393..63479 [+]
Host baterium   Shigella sonnei strain 506

Cargo genes

Drug resistance gene   -
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -