Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   113602
Name   oriT_S17BD05944|p39 in_silico
Organism   Shigella sonnei strain S17BD05944
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP099774 (34421..34512 [-], 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_S17BD05944|p39
CGGGGTGTCGGGGCTAAGCCCTGACCAGGTGGTAATCGTATAGCCGTGCGTGCGCGGTTATACGATTACACATCCTGTCCCGTTTTTCAGGC

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   8711 GenBank   WP_044810581
Name   Relaxase_NHV82_RS00230_S17BD05944|p39 insolico UniProt ID   _
Length   906 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 906 a.a.        Molecular weight: 104926.61 Da        Isoelectric Point: 8.3624

>WP_044810581.1 MULTISPECIES: relaxase/mobilization nuclease domain-containing protein [Enterobacteriaceae]
MNAIIPKKRRDGKSSFEDLIAYTSVRDDVPEDELRPDTEMKAEIPHRNRFRRLVDYATRLRNEKFVSLID
VMKDGSQWVNFYGVTCFHNCLSLESAAEEMQKAAELAHFSKDDTDPVFHYILSWPAHESPRSEQLFDCVR
HTLKSLELSKHQYVAAVHTDTDNLHVHVAVNRVHPETGYINCLPWSQEKLSRACRELELKHGFAPDNGCF
VHAPGNRIVRKTALVRERRNAWRRGKKQTFREYIDQMSIAGLREEPAQDWLSLHKRLASDGLYITMQEGV
LVVKDGWDKAREGIALSSFGPSWTAEKLGRKLGEYQPVPTDIFSQVGTPGRYDPEAINVDIRPEKVAETE
SLKQYACRHFAERLPAMARNGELKSSLAVHRTLAEAGLWMGIQHGHLVLHDGFDKQQTPVRADSVWPLMT
LDYMQDLDGGWQPVPKDIFTQVVPGERFRGHSIGSQPVSDYEWYRMRMGTGPQGAIKRELFSDKESLWGY
GLIQCRSLIEEMIADGDFSWQACHEMFARKGLMLQKQHHGLVIVDAFNHELTPVKASSIHPDLTLSRAEP
QAGPFEIAAADIFERVKPECRYNPELAASDEVEPGFRRDPEIRRERREARAAAREDLRARYLAWKEHWRK
PDLRYGERLREIHAACRRRKAYIRVQFRDPQLRKLHYHIAEVQRMQALIRLKESVKEERLSLIAEGKWYP
LSYRQWVEQQAAQGDRAAVSQLRGWDYRDRRSRNKDKRRTTNVDRCVVLCEPGGTPLFNNVAKLEARLQK
NGSVHFRDTRTGKNVCTDYGDRVVFYHHTDRNELAEKLNLIAPVLFSRNGKLGFEPEGSYQQFNDVFAEM
VAWHNAAGITGNGHFTITRPDVDLHRQRSEQYYREYIRQQTRLSESHDDNYTLRQEKTWEPPSPGM

  Protein domains


Predicted by InterproScan.

Relaxase/Mobilisation nuclease domain (Relaxase)

(62-315)


  Protein structure



No available structure.




Auxiliary protein

ID   5095 GenBank   WP_001291057
Name   WP_001291057_S17BD05944|p39 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   10086 GenBank   WP_000077662
Name   trbC_NHV82_RS00235_S17BD05944|p39 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: 86964.85 Da        Isoelectric Point: 6.5117

>WP_000077662.1 MULTISPECIES: F-type conjugative transfer protein TrbC [Enterobacteriaceae]
MSQHHVNPDLIHRTAWGNPLWNALHNLNITGLCLAGSIITALIWPLALPVCLLFTLVTSVIFMLQRWRCP
LRMPMTLSLDDPSQDRKVRRSLFSFWPTLFQYEADETFPARGIFYVGYRRINDIGRELWLSMDDLTRHIM
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: 40093..81318

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
NHV82_RS00235 37812..40112 - 2301 WP_000077662 F-type conjugative transfer protein TrbC -
NHV82_RS00240 40093..41217 - 1125 WP_000152380 DsbC family protein trbB
NHV82_RS00245 41214..42539 - 1326 WP_024186660 IncI1-type conjugal transfer protein TrbA trbA
NHV82_RS00510 43336..43431 + 96 WP_001363141 DinQ-like type I toxin DqlB -
NHV82_RS00255 43494..43670 - 177 WP_001054907 hypothetical protein -
NHV82_RS00260 43820..44287 - 468 WP_000598962 thermonuclease family protein -
NHV82_RS00265 44447..45070 + 624 WP_001155250 helix-turn-helix domain-containing protein -
NHV82_RS00270 45268..45483 - 216 WP_000266544 hypothetical protein -
NHV82_RS00275 45487..45855 - 369 WP_001302696 hypothetical protein -
NHV82_RS00280 46154..46396 - 243 WP_001363144 hypothetical protein -
NHV82_RS00285 46726..46878 + 153 WP_001335079 Hok/Gef family protein -
NHV82_RS00290 47016..48602 - 1587 WP_000004561 TnsA endonuclease N-terminal domain-containing protein -
NHV82_RS00295 48876..49526 - 651 WP_001044247 plasmid IncI1-type surface exclusion protein ExcA -
NHV82_RS00300 49615..51780 - 2166 WP_052894952 DotA/TraY family protein traY
NHV82_RS00305 51855..52424 - 570 WP_000650752 conjugal transfer protein TraX -
NHV82_RS00310 52421..53626 - 1206 WP_001189548 conjugal transfer protein TraW traW
NHV82_RS00315 53584..54204 - 621 WP_000286854 hypothetical protein traV
NHV82_RS00320 54204..57248 - 3045 WP_001024766 conjugal transfer protein traU
NHV82_RS00325 57299..57550 + 252 WP_052971984 hypothetical protein -
NHV82_RS00330 57543..58169 - 627 WP_000785703 hypothetical protein traT
NHV82_RS00515 58276..58527 - 252 WP_001277573 hypothetical protein -
NHV82_RS00340 58584..58982 - 399 WP_000088813 DUF6750 family protein traR
NHV82_RS00345 59029..59559 - 531 WP_000987021 conjugal transfer protein TraQ traQ
NHV82_RS00350 59556..60269 - 714 WP_044810583 conjugal transfer protein TraP traP
NHV82_RS00355 60266..61603 - 1338 WP_001272018 conjugal transfer protein TraO traO
NHV82_RS00360 61607..62581 - 975 WP_000547385 DotH/IcmK family type IV secretion protein traN
NHV82_RS00365 62592..63287 - 696 WP_001287545 DotI/IcmL family type IV secretion protein traM
NHV82_RS00370 63299..63649 - 351 WP_001056367 hypothetical protein traL
NHV82_RS00375 63666..67727 - 4062 WP_108433737 LPD7 domain-containing protein -
NHV82_RS00380 67791..68081 - 291 WP_000817801 IcmT/TraK family protein traK
NHV82_RS00385 68078..69226 - 1149 WP_000775210 plasmid transfer ATPase TraJ virB11
NHV82_RS00390 69210..70046 - 837 WP_000745049 type IV secretory system conjugative DNA transfer family protein traI
NHV82_RS00395 70043..70501 - 459 WP_001170111 DotD/TraH family lipoprotein -
NHV82_RS00400 70605..71807 - 1203 WP_021529228 conjugal transfer protein TraF -
NHV82_RS00405 71909..72730 - 822 WP_044810585 hypothetical protein traE
NHV82_RS00410 72943..74067 - 1125 WP_021511763 site-specific integrase -
NHV82_RS00415 74391..74546 - 156 WP_001358489 hypothetical protein -
NHV82_RS00420 74904..75284 - 381 WP_253075073 pilus assembly protein -
NHV82_RS00425 75565..76926 - 1362 WP_052977226 shufflon system plasmid conjugative transfer pilus tip adhesin PilV -
NHV82_RS00430 76944..77570 - 627 WP_044810571 prepilin peptidase -
NHV82_RS00435 77586..78071 - 486 WP_001080767 lytic transglycosylase domain-containing protein virB1
NHV82_RS00440 78116..78652 - 537 WP_000111534 type 4 pilus major pilin -
NHV82_RS00445 78714..79808 - 1095 WP_044810572 type II secretion system F family protein -
NHV82_RS00450 79810..81318 - 1509 WP_044810573 GspE/PulE family protein virB11
NHV82_RS00455 81421..81879 - 459 WP_000095884 type IV pilus biogenesis protein PilP -
NHV82_RS00460 81869..83164 - 1296 WP_044810574 type 4b pilus protein PilO2 -
NHV82_RS00465 83185..84804 - 1620 WP_001035559 PilN family type IVB pilus formation outer membrane protein -
NHV82_RS00470 84836..85249 - 414 WP_124983997 type IV pilus biogenesis protein PilM -

Host bacterium

ID   14037 GenBank   NZ_CP099774
Plasmid name   S17BD05944|p39 Incompatibility group   IncB/O/K/Z
Plasmid size   92062 bp Coordinate of oriT [Strand]   34421..34512 [-]
Host baterium   Shigella sonnei strain S17BD05944

Cargo genes

Drug resistance gene   blaCTX-M-15, blaTEM-1B
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -