Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   117116
Name   oriT_PNUSAE076676|unnamed2 in_silico
Organism   Shigella flexneri strain PNUSAE076676
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP138848 (24304..24376 [-], 73 nt)
oriT length   73 nt
IRs (inverted repeats)     _
Location of nic site      _
Conserved sequence flanking the
  nic site    		  _
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 73 nt

>oriT_PNUSAE076676|unnamed2
GTCGGGGCAAAGCCCTGACCAGGTGGGGAATGTCTGAGTGCGCGTGCGCGGTCCGACATTCCCACATCCTGTC

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   10905 GenBank   WP_032237734
Name   Relaxase_SH220_RS24990_PNUSAE076676|unnamed2 insolico UniProt ID   _
Length   903 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 903 a.a.        Molecular weight: 104498.85 Da        Isoelectric Point: 7.5347

>WP_032237734.1 MULTISPECIES: relaxase/mobilization nuclease domain-containing protein [Enterobacteriaceae]
MNAIIPHKRRDGRSSFEDLIAYTSVRDDVQENELTEDSEIKSDVPHRNRFRRLVDYATRLRNEKFVSLID
VMKDGSQWVNFYGVTCFHNCNSLETAAEEMQYKADKAVFSRNDTDPVFHYILSWPAHESPRPEQLFDCVR
HTLKSLELSKHQYVAAVHTDTDNLHVHVAVNRVHPETGYINWLSWSQEKLSRACRELELKHGFAPDNGCF
VHAPGNRIVRKTALVRERRNAWRRGKKQTFREYIAQMSIAGLREEPAQDWLSLHKRLASDGLYITMQEGE
LVVKDGWDRAREGVALSSFGPSWTAEKLGRKLGEYQPVPTDIFSQVGTPGRYDPEAINVDIRPEKVAETE
SLKQYACRHFAERLPEMARNGELESCLDVHRTLAKAGLWMGIQHGHLVLHDGFDKQQTPVRADSVWPLMT
LDYMQDLDGGWQPVPKDIFTQVIPGERFRGRNLGTQAVSDYEWYRMRMGTGPQGAIKRELFSDKESLWGY
TTVQCESLIEDMIAGGNFSWQACHEMFARKGLMLQKQHHGLVIVDAFNHELTPVKASSIHPDLTLSRAEP
QAGPFEIAGADIFERVKPECRYNPELAASDEVEPGFRRDPVLRRERREARAAAREDLRARYLAWKEHWRK
PDLRYGERLREIHAACRRRKAYIRVQFRDPQLRKLHYHIAEVQRMQALIRLKESVKEERLSLIAEGKWYP
LSYRQWVEQQAVQGDRAALSQLRGWDYRDRRKDKRRTTNADRCVILCEPGGTPLYEDTGVLEARLQKDGS
VRFRDRRNGELVCVDYGDRVVFYHHQDRNELVDKLNLIAPVLFDREPGMGFEPEGSYQQFNDVFAEMVAW
HNAAGITGSGHFVISRPDVDLHRQRSEQYYHEYIRQQKSISGGHGASYAPVQDNEWTPPSPGM

  Protein domains


Predicted by InterproScan.

Relaxase/Mobilisation nuclease domain (Relaxase)

(62-315)


  Protein structure



No available structure.




Auxiliary protein

ID   6413 GenBank   WP_319795752
Name   WP_319795752_PNUSAE076676|unnamed2 insolico UniProt ID   _
Length   110 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  Auxiliary protein sequence


Download         Length: 110 a.a.        Molecular weight: 12778.60 Da        Isoelectric Point: 10.0947

>WP_319795752.1 plasmid mobilization protein MobA [Shigella flexneri]
MSEKKTRTGSENRKRIVKFTARFTEDEAEIVREKAESSGQTVSTFIRSSSLDKVVNCRTDYRMIDEIMRL
GRLQKHLFVEGKRTGDKEYAEVLVAITEYVNALRRDLMGR

  Protein domains



No domain identified.



  Protein structure



No available structure.




T4CP

ID   12735 GenBank   WP_000077663
Name   trbC_SH220_RS25020_PNUSAE076676|unnamed2 insolico UniProt ID   _
Length   767 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 767 a.a.        Molecular weight: 87012.13 Da        Isoelectric Point: 7.3008

>WP_000077663.1 MULTISPECIES: F-type conjugative transfer protein TrbC [Enterobacteriaceae]
MSQHHVNPDLIHRTAWGNPLWNALHNLNITGLCLAGSIITALIWPLALPVCLLFTLVTSVIFMLQRWRCP
LRMPMTLSLDDPSQDRKVRRSLFSFWPTLFQYEADETFPARGIFYVGYRRINDIGRELWLSMDDLTRHVM
FFATTGGGKTETTFAWLLNPLCWGRGFTFVDGKAQNDTTRTIWYLSRRFGREDDIEVINFMNGGKSRSEI
IQSGEKSRPQSNTWNPFAFSTEAFTAETMQSMLPQNVQGGEWQSRAIAMNKALVFGTKFWCVREGKTMSL
QMLREHMTLEGMAKLYCRGLDDQWPEEAIAPLRNYLQDVPGFDMSLVRTPSAWTEEPRKQHAYLSGQFSE
TFTTFAETFGDVFAADAGDIDIRDSIHSDRILIVMIPALDTSAHTTSALGRMFVTQQSMLLARDLGYRLE
GTDAQTLEVKKYKGSFPYICILDEVGAYYTDRIAVEATQVRSLEFSLIMTAQDQERIEGQTSATNTATLM
QNAGTKFAGRIVSDDKTARTVKNAAGEEARARMGSLQRHDGVMGESWVDGNQITIQMESKIDVQDLIRLN
AGEFFTVFQGDVVPSASVYIPDSEKSCDSDPVVINRYISVEAPRLERLRRLVPRTVQRRLPTPEHVSSII
GVLTAKPSRKRRKNRTEPYRIIDTFQRQLATAQTSLDLLPQYDTDIESRANELWKKAVHTINNTTREERR
VCYITLNRPEEEHSGPEDIPSVKAILNTLLPLEMLLPVPDLTASPPHKKNVAQTPSGGKQESRKKRF

  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: 34475..73501

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
SH220_RS25010 (SH220_25010) 29648..30451 - 804 WP_001082319 aminoglycoside O-phosphotransferase APH(3'')-Ib -
SH220_RS25015 (SH220_25015) 30512..31327 - 816 WP_001043260 sulfonamide-resistant dihydropteroate synthase Sul2 -
SH220_RS25020 (SH220_25020) 32191..34494 - 2304 WP_000077663 F-type conjugative transfer protein TrbC -
SH220_RS25025 (SH220_25025) 34475..35599 - 1125 WP_000152378 DsbC family protein trbB
SH220_RS25030 (SH220_25030) 35596..36912 - 1317 WP_000121919 IncI1-type conjugal transfer protein TrbA trbA
SH220_RS25035 (SH220_25035) 37215..37310 + 96 WP_001388983 DinQ-like type I toxin DqlB -
SH220_RS25040 (SH220_25040) 37899..37994 + 96 WP_001388983 DinQ-like type I toxin DqlB -
SH220_RS25045 (SH220_25045) 38057..38233 - 177 WP_001054907 hypothetical protein -
SH220_RS25050 (SH220_25050) 38383..38850 - 468 WP_000598962 thermonuclease family protein -
SH220_RS25055 (SH220_25055) 39010..39633 + 624 WP_001155250 helix-turn-helix domain-containing protein -
SH220_RS25060 (SH220_25060) 39831..40046 - 216 WP_000266543 hypothetical protein -
SH220_RS25065 (SH220_25065) 40050..40418 - 369 WP_001345852 hypothetical protein -
SH220_RS25070 (SH220_25070) 40430..40621 - 192 WP_000751583 hypothetical protein -
SH220_RS25075 (SH220_25075) 40709..40951 - 243 WP_000650923 hypothetical protein -
SH220_RS25080 (SH220_25080) 41281..41433 + 153 WP_001335079 Hok/Gef family protein -
SH220_RS25085 (SH220_25085) 41571..43157 - 1587 WP_000004564 TnsA endonuclease N-terminal domain-containing protein -
SH220_RS25090 (SH220_25090) 43431..44078 - 648 WP_015056434 plasmid IncI1-type surface exclusion protein ExcA -
SH220_RS25095 (SH220_25095) 44166..46325 - 2160 WP_000691811 DotA/TraY family protein traY
SH220_RS25100 (SH220_25100) 46400..46969 - 570 WP_000650752 conjugal transfer protein TraX -
SH220_RS25105 (SH220_25105) 46966..48171 - 1206 WP_319795749 conjugal transfer protein TraW traW
SH220_RS25110 (SH220_25110) 48129..48749 - 621 WP_000286855 hypothetical protein traV
SH220_RS25115 (SH220_25115) 48749..51793 - 3045 WP_016249708 hypothetical protein traU
SH220_RS25120 (SH220_25120) 52088..52714 - 627 WP_000785703 hypothetical protein traT
SH220_RS25125 (SH220_25125) 52821..53072 - 252 WP_001277573 hypothetical protein -
SH220_RS25130 (SH220_25130) 53129..53527 - 399 WP_000088813 DUF6750 family protein traR
SH220_RS25135 (SH220_25135) 53574..54104 - 531 WP_000987021 conjugal transfer protein TraQ traQ
SH220_RS25140 (SH220_25140) 54101..54814 - 714 WP_000787002 conjugal transfer protein TraP traP
SH220_RS25145 (SH220_25145) 54811..56148 - 1338 WP_001557492 conjugal transfer protein TraO traO
SH220_RS25150 (SH220_25150) 56152..57126 - 975 WP_000547386 DotH/IcmK family type IV secretion protein traN
SH220_RS25155 (SH220_25155) 57137..57832 - 696 WP_001287545 DotI/IcmL family type IV secretion protein traM
SH220_RS25160 (SH220_25160) 57844..58194 - 351 WP_001056367 hypothetical protein traL
SH220_RS25165 (SH220_25165) 58211..62272 - 4062 WP_000842456 LPD7 domain-containing protein -
SH220_RS25170 (SH220_25170) 62336..62626 - 291 WP_000817801 IcmT/TraK family protein traK
SH220_RS25175 (SH220_25175) 62623..63771 - 1149 WP_000775210 plasmid transfer ATPase TraJ virB11
SH220_RS25180 (SH220_25180) 63755..64591 - 837 WP_000745049 type IV secretory system conjugative DNA transfer family protein traI
SH220_RS25185 (SH220_25185) 64588..65046 - 459 WP_001170111 DotD/TraH family lipoprotein -
SH220_RS25190 (SH220_25190) 65150..66352 - 1203 WP_000979993 conjugal transfer protein TraF -
SH220_RS25195 (SH220_25195) 66454..67275 - 822 WP_000845373 hypothetical protein traE
SH220_RS25200 (SH220_25200) 67440..67634 - 195 Protein_71 integrase -
SH220_RS25205 (SH220_25205) 67748..69109 - 1362 WP_001168171 shufflon system plasmid conjugative transfer pilus tip adhesin PilV -
SH220_RS25210 (SH220_25210) 69127..69753 - 627 WP_000939245 prepilin peptidase -
SH220_RS25215 (SH220_25215) 69769..70254 - 486 WP_001080767 lytic transglycosylase domain-containing protein virB1
SH220_RS25220 (SH220_25220) 70299..70835 - 537 WP_000111534 type 4 pilus major pilin -
SH220_RS25225 (SH220_25225) 70897..71991 - 1095 WP_000697158 type II secretion system F family protein -
SH220_RS25230 (SH220_25230) 71993..73501 - 1509 WP_319795750 ATPase, T2SS/T4P/T4SS family virB11
SH220_RS25235 (SH220_25235) 73605..74063 - 459 WP_000095885 type IV pilus biogenesis protein PilP -
SH220_RS25240 (SH220_25240) 74053..75348 - 1296 WP_000129882 type 4b pilus protein PilO2 -
SH220_RS25245 (SH220_25245) 75369..76988 - 1620 WP_001035565 PilN family type IVB pilus formation outer membrane protein -
SH220_RS25250 (SH220_25250) 77020..77433 - 414 WP_124983997 type IV pilus biogenesis protein PilM -

Host bacterium

ID   17549 GenBank   NZ_CP138848
Plasmid name   PNUSAE076676|unnamed2 Incompatibility group   IncB/O/K/Z
Plasmid size   84286 bp Coordinate of oriT [Strand]   24304..24376 [-]
Host baterium   Shigella flexneri strain PNUSAE076676

Cargo genes

Drug resistance gene   dfrA5, qacE, tet(A), blaTEM-1B, aph(6)-Id, aph(3'')-Ib, sul2
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -