Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   119056
Name   oriT_pSO87_003 in_silico
Organism   Shigella sonnei strain ST152
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP140621 (27316..27407 [-], 92 nt)
oriT length   92 nt
IRs (inverted repeats)     _
Location of nic site      _
Conserved sequence flanking the
  nic site    		  _
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 92 nt

>oriT_pSO87_003
CGGGGTGTCGGGGCTAAGCCCTGACCAGGTGGTAATCGTATAGCCGTGCGTGCGCGGTTATACGATTACACATCCTGTCCCGTTTTTCAGGC

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   12037 GenBank   WP_000991405
Name   Relaxase_O5Y90_RS25680_pSO87_003 insolico UniProt ID   A0A896Z1V0
Length   906 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 906 a.a.        Molecular weight: 104972.66 Da        Isoelectric Point: 8.2349

>WP_000991405.1 MULTISPECIES: relaxase/mobilization nuclease domain-containing protein [Enterobacteriaceae]
MNAIIPKKRRDGKSSFEDLIAYTSVRDDVPEDELRPDTEMKAEIPHRNRFRRLVDYATRLRNEKFVSLID
VMKDGSQWVNFYGVTCFHNCLSLESAAEEMQKAAELAHFSKDDTDPVFHYILSWPAHESPRSEQLFDCVR
HTLKSLELSKHQYVAAVHTDTDNLHVHVAVNRVHPETGYINCLPWSQEKLSRACRELELKHGFAPDNGCF
VHAPGNRIVRKTALVRERRNAWRRGKKQTFREYIDQMSIAGLREEPAQDWLSLHKRLASDGLYITMQEGE
LVVKDGWDKAREGIALSSFGPSWTAEKLGRKLGEYQPVPTDIFSQVGTPGRYDPEAINVDIRPEKVAETE
SLKQYACRHFAERLPAMARNGELKSCLAVHRTLAEAGLWMGIQHGHLVLHDGFDKQQTPVRADSVWPLMT
LDYMQDLDGGWQPVPKDIFTQVVPGERFRGHSIGSQPVSDYEWYRMRMGTGPQGAIKRELFSDKESLWGY
GLIQCRSLIEEMIADGDFSWQACHEMFARKGLMLQKQHHGLVIVDAFNHELTPVKASSIHPDLTLSRAEP
QAGPFEIAAADIFERVKPECRYNPELAASDEVEPGFRRDPEIRRERREARAAAREDLRARYLAWKEHWRK
PDLRYGERLREIHAACRRRKAYIRVQFRDPQLRKLHYHIAEVQRMQALIRLKESVKEERLSLIAEGKWYP
LSYRQWVEQQAAQGDRAAVSQLRGWDYRDRRSRNKDKRRTTNVDRCVVLCEPGGTPLFNNVAKLEARLQK
NGSVHFRDTRTGKNVCTDYGDRVVFYHHTDRNELAEKLNLIAPVLFSRNGKLGFEPEGSYQQFNDVFAEM
VAWHNAAGITGNGHFTITRPDVDLHRQRSEQYYREYIRQQTRLSESHDDNYTLRQEKTWEPPSPGM

  Protein domains


Predicted by InterproScan.

Relaxase/Mobilisation nuclease domain (Relaxase)

(62-315)


  Protein structure


Source ID Structure
AlphaFold DB A0A896Z1V0


Auxiliary protein

ID   6873 GenBank   WP_001291057
Name   WP_001291057_pSO87_003 insolico UniProt ID   A0A142CND4
Length   110 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  Auxiliary protein sequence


Download         Length: 110 a.a.        Molecular weight: 12596.69 Da        Isoelectric Point: 10.7335

>WP_001291057.1 MULTISPECIES: plasmid mobilization protein MobA [Enterobacteriaceae]
MSEKKTRSGSEKRQKNVLIAVRFSPEEAEIVKEKAEKNGLTVSTLIRKTVLGKQINARIDEDFLKELMRL
GRLQKHLFVEGKRTGDKEYAEVLVAITELANTLRRNLMGR

  Protein domains


Predicted by InterproScan.

Family of unknown function (DUF6290) (DUF6290)

(19-66)


  Protein structure


Source ID Structure
AlphaFold DB A0A142CND4


T4CP

ID   14097 GenBank   WP_013307869
Name   trbC_O5Y90_RS25685_pSO87_003 insolico UniProt ID   _
Length   766 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 766 a.a.        Molecular weight: 86950.82 Da        Isoelectric Point: 6.5117

>WP_013307869.1 MULTISPECIES: F-type conjugative transfer protein TrbC [Enterobacteriaceae]
MSQHHVNPDLIHRTAWGNPLWNALHNLNITGLCLAGSIITALIWPLALPVCLLFTLVTSVIFMLQRWRCP
LRMPMTLSLDDPSQDRKVRRSLFSFWPTLFQYEADETFPARGIFYVGYRRINDIGRELWLSMDDLTRHVM
FFATTGGGKTETTFAWLLNPLCWGRGFTFVDGKAQNDTTRTIWYLSRRFGREDDIEVINFMNGGKSRSEI
IQSGEKSRPQSNTWNPFAFSTEAFTAETMQSMLPQNVQGGEWQSRAIAMNKALVFGTKFWCVREGKTMSL
QMLREHMTLEGMAKLYCRGLDDQWPEEAIAPLRNYLQDVPGFDMSLVRTPSAWTEEPRKQHAYLSGQFSE
TFTTFAETFGDVFAADAGDIDIRDSIHSDRILIVMIPALDTSAHTTSALGRMFVTQQSMLLARDLGYRLE
GTDAQTLEVKKYKGSFPYICILDEVGAYYTDRIAVEATQVRSLEFSLIMTAQDQERIEGQTSATNTATLM
QNAGTKFAGRIVSDDKTARTVKNAAGEEARARMGSLQRHDGVMGESWVDGNQITIQMESKIDVQDLIRLN
AGEFFTVFQGDVVPSASVYIPDSEKSCDSDPVVINRYISVEAPRLERLRRLVPRTVQRRLPTPEHVSSII
GVLTAKPSRKRRKNRTEPYRIIDTFQRQLATAQTSLDLLPQYDTDIESRANELWKKAVHTINNTTREERR
VCYITLNRPEEEHSGPEDIPSVKVILNTLLPLEILLPVAENNKSQTINNDHPQKSCGAQPTTDEKY

  Protein domains


Predicted by InterproScan.

TraM recognition site of TraD and TraG (TraG-D_C)

(439-528)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 32988..76102

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
O5Y90_RS25685 (O5Y90_25680) 30707..33007 - 2301 WP_013307869 F-type conjugative transfer protein TrbC -
O5Y90_RS25690 (O5Y90_25685) 32988..34112 - 1125 WP_000152382 DsbC family protein trbB
O5Y90_RS25695 (O5Y90_25690) 34109..35452 - 1344 WP_032253916 hypothetical protein trbA
O5Y90_RS25700 (O5Y90_25695) 36249..36344 + 96 WP_001363141 DinQ-like type I toxin DqlB -
O5Y90_RS25705 (O5Y90_25700) 36407..36583 - 177 WP_001054907 hypothetical protein -
O5Y90_RS25710 (O5Y90_25705) 36733..37200 - 468 WP_000598962 thermonuclease family protein -
O5Y90_RS25715 (O5Y90_25710) 37359..37982 + 624 WP_001155247 helix-turn-helix domain-containing protein -
O5Y90_RS25720 (O5Y90_25715) 38180..38395 - 216 WP_000266543 hypothetical protein -
O5Y90_RS25725 (O5Y90_25720) 38399..38767 - 369 WP_001345852 hypothetical protein -
O5Y90_RS25730 (O5Y90_25725) 38779..38970 - 192 WP_000751583 hypothetical protein -
O5Y90_RS25735 (O5Y90_25730) 39058..39300 - 243 WP_000650923 hypothetical protein -
O5Y90_RS25740 (O5Y90_25735) 39630..39782 + 153 WP_001302699 Hok/Gef family protein -
O5Y90_RS25745 (O5Y90_25740) 39920..41602 - 1683 WP_323739365 TnsA endonuclease N-terminal domain-containing protein -
O5Y90_RS25750 (O5Y90_25745) 41522..42218 + 697 WP_094110542 IS1 family transposase -
O5Y90_RS25755 (O5Y90_25750) 42556..43209 - 654 WP_001401768 plasmid IncI1-type surface exclusion protein ExcA -
O5Y90_RS25760 (O5Y90_25755) 43297..45462 - 2166 WP_000691808 DotA/TraY family protein traY
O5Y90_RS25765 (O5Y90_25760) 45537..46106 - 570 WP_000650752 conjugal transfer protein TraX -
O5Y90_RS25770 (O5Y90_25765) 46103..47308 - 1206 WP_001189548 conjugal transfer protein TraW traW
O5Y90_RS25775 (O5Y90_25770) 47266..47886 - 621 WP_000286854 hypothetical protein traV
O5Y90_RS25780 (O5Y90_25775) 47886..50930 - 3045 WP_001024766 conjugal transfer protein traU
O5Y90_RS25785 (O5Y90_25780) 51225..51851 - 627 WP_000785703 hypothetical protein traT
O5Y90_RS25790 (O5Y90_25785) 51958..52242 - 285 WP_001353683 hypothetical protein -
O5Y90_RS25795 (O5Y90_25790) 52266..52664 - 399 WP_000088812 DUF6750 family protein traR
O5Y90_RS25800 (O5Y90_25795) 52711..53241 - 531 WP_000987023 conjugal transfer protein TraQ traQ
O5Y90_RS25805 (O5Y90_25800) 53238..53951 - 714 WP_000787003 conjugal transfer protein TraP traP
O5Y90_RS25810 (O5Y90_25805) 53948..55285 - 1338 WP_013307873 conjugal transfer protein TraO traO
O5Y90_RS25815 (O5Y90_25810) 55289..56263 - 975 WP_000547383 DotH/IcmK family type IV secretion protein traN
O5Y90_RS25820 (O5Y90_25815) 56274..56969 - 696 WP_001681668 DotI/IcmL family type IV secretion protein traM
O5Y90_RS25825 (O5Y90_25820) 56981..57331 - 351 WP_001056367 hypothetical protein traL
O5Y90_RS25830 (O5Y90_25825) 57348..61409 - 4062 WP_013307874 LPD7 domain-containing protein -
O5Y90_RS25835 (O5Y90_25830) 61763..62344 - 582 WP_025750394 hypothetical protein -
O5Y90_RS25840 (O5Y90_25835) 62576..62866 - 291 WP_000817801 IcmT/TraK family protein traK
O5Y90_RS25845 (O5Y90_25840) 62863..64011 - 1149 WP_013307876 plasmid transfer ATPase TraJ virB11
O5Y90_RS25850 (O5Y90_25845) 63995..64831 - 837 WP_000745049 type IV secretory system conjugative DNA transfer family protein traI
O5Y90_RS25855 (O5Y90_25850) 64828..65286 - 459 WP_001170111 DotD/TraH family lipoprotein -
O5Y90_RS25860 (O5Y90_25855) 65390..66592 - 1203 WP_013307879 conjugal transfer protein TraF -
O5Y90_RS25865 (O5Y90_25860) 66694..67515 - 822 WP_001681675 hypothetical protein traE
O5Y90_RS25870 (O5Y90_25865) 67728..68852 - 1125 WP_013307880 site-specific integrase -
O5Y90_RS25875 (O5Y90_25870) 68916..69305 + 390 Protein_77 phage tail protein -
O5Y90_RS25880 (O5Y90_25875) 69310..69549 - 240 WP_000271302 hypothetical protein -
O5Y90_RS25885 (O5Y90_25880) 70475..71710 - 1236 WP_085008799 shufflon system plasmid conjugative transfer pilus tip adhesin PilV -
O5Y90_RS25890 (O5Y90_25885) 71728..72354 - 627 WP_013307883 prepilin peptidase -
O5Y90_RS25895 (O5Y90_25890) 72370..72855 - 486 WP_001080767 lytic transglycosylase domain-containing protein virB1
O5Y90_RS25900 (O5Y90_25895) 72900..73436 - 537 WP_000111521 type 4 pilus major pilin -
O5Y90_RS25905 (O5Y90_25900) 73498..74592 - 1095 WP_000697154 type II secretion system F family protein -
O5Y90_RS25910 (O5Y90_25905) 74594..76102 - 1509 WP_000880806 GspE/PulE family protein virB11
O5Y90_RS25915 (O5Y90_25910) 76205..76663 - 459 WP_000095887 type IV pilus biogenesis protein PilP -
O5Y90_RS25920 (O5Y90_25915) 76653..77948 - 1296 WP_000129885 type 4b pilus protein PilO2 -
O5Y90_RS25925 (O5Y90_25920) 77969..79588 - 1620 WP_001035562 PilN family type IVB pilus formation outer membrane protein -
O5Y90_RS25930 (O5Y90_25925) 79620..80033 - 414 WP_124983997 type IV pilus biogenesis protein PilM -

Host bacterium

ID   19488 GenBank   NZ_CP140621
Plasmid name   pSO87_003 Incompatibility group   IncB/O/K/Z
Plasmid size   86884 bp Coordinate of oriT [Strand]   27316..27407 [-]
Host baterium   Shigella sonnei strain ST152

Cargo genes

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