Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   119620
Name   oriT_HBI04|unnamed in_silico
Organism   Escherichia sp. HBI04
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP141226 (40579..40651 [-], 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_HBI04|unnamed
GTCGGGGCAAAGCCCTGACCAGGTGGGGAATGTCTGAGTGCGCGTGCGCGGTCCGACATTCCCACATCCTGTC

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   12397 GenBank   WP_000991387
Name   Relaxase_VJF80_RS00285_HBI04|unnamed insolico UniProt ID   A0A7I0L2J7
Length   903 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 903 a.a.        Molecular weight: 104567.95 Da        Isoelectric Point: 7.5259

>WP_000991387.1 MULTISPECIES: relaxase/mobilization nuclease domain-containing protein [Enterobacteriaceae]
MNAIIPHKRRDGRSSFEDLIAYTSVRDDVQENELTEDSEIKSDVPHRNRFRRLVDYATRLRNEKFVSLID
VMKDGSQWVNFYGVTCFHNCNSLETAAEEMQYKADKAVFSRNDTDPVFHYILSWPAHESPRPEQLFDCVR
HTLKSLELSKHQYVAAVHTDTDNLHVHVAVNRVHPETGYINWLSWSQEKLSRACRELELKHGFAPDNGCF
VHAPGNRIVRKTALVRERRNAWRRGKKQTFREYIAQMSIAGLREEPAQDWLSLHKRLASDGLYITMQEGE
LVVKDGWDRAREGVALSSFGPSWTAEKLGRKLGEYQPVPTDIFSQVGTPGRYDPEAINVDIRPEKVAETE
SLKQYACRYFAERLPEMARNGELESCLDVHRTLAKAGLWMGIQHGHLVLHDGFDKQQTPVRADSVWPLMT
LDYMQDLDGGWQPVPKDIFTQVIPGERFRGRNLGTQAVSDYEWYRMRMGTGPQGAIKRELFSDKESLWGY
TTVQCESLIEDMIAGGNFSWQACHEMFARKGLMLQKQHHGLVIVDAFNHELTPVKASSIHPDLTLSRAEL
QAGPFEIAGADIFERVKPECRYNPELAASDEVEPGFRRDPVLRRERREARAAAREDLRARYLAWKEHWRK
PDLRYGERLREIHAACRRRKAYIRVQFRDPQLRKLHYHIAEVQRMQALIRLKESVKEERLSLIAEGKWYP
LSYRQWVEQQAVQGDRAALSQLRGWDYRDRRKDKRRTTNADRCVILCEPGGTPLYEDTGVLEARLQKDGS
VRFRDRRNGELVCVDYGDRVVFYHHQDRNELVDKLNLIAPVLFDREPGMGFEPEGSYQQFNDVFAEMVAW
HNAAGITGNGHFVISRPDVDLHRQRSEQYYHEYIRQQKSISGGHGASYAPVQDNEWTPPSPGM

  Protein domains


Predicted by InterproScan.

Relaxase/Mobilisation nuclease domain (Relaxase)

(62-315)


  Protein structure


Source ID Structure
AlphaFold DB A0A7I0L2J7


Auxiliary protein

ID   7053 GenBank   WP_001291058
Name   WP_001291058_HBI04|unnamed insolico UniProt ID   A0A7I0L241
Length   110 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  Auxiliary protein sequence


Download         Length: 110 a.a.        Molecular weight: 12730.52 Da        Isoelectric Point: 9.9656

>WP_001291058.1 MULTISPECIES: plasmid mobilization protein MobA [Enterobacteriaceae]
MSEKKTRTGSENRKRIVKFTARFTEDEAEIVREKAESSGQTVSTFIRSSSLDKVVNCRTDDRMIDEIMRL
GRLQKHLFVEGKRTGDKEYAEVLVAITEYVNALRRDLMGR

  Protein domains



No domain identified.



  Protein structure


Source ID Structure
AlphaFold DB A0A7I0L241


T4CP

ID   14555 GenBank   WP_000077664
Name   trbC_VJF80_RS00305_HBI04|unnamed 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: 87040.19 Da        Isoelectric Point: 7.4857

>WP_000077664.1 MULTISPECIES: F-type conjugative transfer protein TrbC [Enterobacteriaceae]
MSQHHVNPDLIHRTAWGNPLWNALHNLNITGLCLAGSIITALIWPLALPVCLLFTLVTSVIFMLQRWRCP
LRMPMTLSLDDPSQDRKVRRSLFSFWPTLFQYEADETFPARGIFYVGYRRINDIGRELWLSMDDLTRHVM
FFATTGGGKTETTFAWLLNPLCWGRGFTFVDGKAQNDTTRTIWYLSRRFGREDDIEVINFMNGGKSRSEI
IQSGEKSRPQSNTWNPFAFSTEAFTAETMQSMLPQNVQGGEWQSRAIAMNKALVFGTKFWCVREGKTMSL
QMLREHMTLEGMAKLYCRGLDDQWPEEAIAPLRNYLQDVPGFDMSLVRTPSAWTEEPRKQHAYLSGQFSE
TFTTFAETFGDVFAADAGDIDIRDSIHSDRILIVMIPALDTSAHTTSALGRMFVTQQSMLLARDLGYRLE
GTDAQTLEVKKYKGSFPYICILDEVGAYYTDRIAVEATQVRSLEFSLIMTAQDQERIEGQTSATNTATLM
QNAGTKFAGRIVSDDKTARTVKNAAGEEARARMGSLQRHDGVMGESWVDGNQITIQMESKIDVQDLIRLN
AGEFFTVFQGDVVPSASVYIPDSEKSCDSDPVVINRYISVEAPRLERLRRLVPRTVQRRLPTPEHVSSII
GVLTAKPSRKRRKNRTEPYRIIDTFQRRLATAQTSLDLLPQYDTDIESRANELWKKAVHTINNTTREERR
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: 47305..87376

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
VJF80_RS00290 43795..44226 + 432 WP_001335086 cell envelope integrity TolA C-terminal domain-containing protein -
VJF80_RS00295 44324..44554 - 231 WP_065406859 hypothetical protein -
VJF80_RS00300 44614..44907 - 294 WP_001401584 hypothetical protein -
VJF80_RS00305 45021..47324 - 2304 WP_000077664 F-type conjugative transfer protein TrbC -
VJF80_RS00310 47305..48429 - 1125 WP_000152382 DsbC family protein trbB
VJF80_RS00315 48426..49742 - 1317 WP_001401585 IncI1-type conjugal transfer protein TrbA trbA
VJF80_RS00320 50539..50634 + 96 WP_001363141 DinQ-like type I toxin DqlB -
VJF80_RS00325 50697..50873 - 177 WP_001054907 hypothetical protein -
VJF80_RS00330 51023..51490 - 468 WP_000598962 thermonuclease family protein -
VJF80_RS00335 51649..52272 + 624 WP_001155252 helix-turn-helix domain-containing protein -
VJF80_RS00340 52470..52685 - 216 WP_000266543 hypothetical protein -
VJF80_RS00345 52689..53057 - 369 WP_001302696 hypothetical protein -
VJF80_RS00350 53348..53590 - 243 WP_001401586 hypothetical protein -
VJF80_RS00355 53920..54072 + 153 WP_001302699 Hok/Gef family protein -
VJF80_RS00360 54210..55796 - 1587 WP_000004564 TnsA endonuclease N-terminal domain-containing protein -
VJF80_RS00365 56070..56717 - 648 WP_015056434 plasmid IncI1-type surface exclusion protein ExcA -
VJF80_RS00370 56805..58964 - 2160 WP_021515450 DotA/TraY family protein traY
VJF80_RS00375 59039..59608 - 570 WP_000650752 conjugal transfer protein TraX -
VJF80_RS00380 59605..60810 - 1206 WP_001189548 conjugal transfer protein TraW traW
VJF80_RS00385 60768..61388 - 621 WP_000286854 hypothetical protein traV
VJF80_RS00390 61388..64432 - 3045 WP_001024766 conjugal transfer protein traU
VJF80_RS00395 64657..65202 + 546 WP_001390888 hypothetical protein -
VJF80_RS00400 65175..65555 - 381 WP_000690881 hypothetical protein -
VJF80_RS00405 65555..65959 - 405 WP_236918857 hypothetical protein -
VJF80_RS00410 65969..66595 - 627 WP_000785708 hypothetical protein traT
VJF80_RS00415 66702..66953 - 252 WP_001277573 hypothetical protein -
VJF80_RS00420 67010..67408 - 399 WP_000088813 DUF6750 family protein traR
VJF80_RS00425 67455..67985 - 531 WP_000987023 conjugal transfer protein TraQ traQ
VJF80_RS00430 67982..68695 - 714 WP_000787003 conjugal transfer protein TraP traP
VJF80_RS00435 68692..70023 - 1332 WP_001288252 conjugal transfer protein TraO traO
VJF80_RS00440 70027..71001 - 975 WP_000547383 DotH/IcmK family type IV secretion protein traN
VJF80_RS00445 71012..71707 - 696 WP_001287545 DotI/IcmL family type IV secretion protein traM
VJF80_RS00450 71719..72069 - 351 WP_001056367 hypothetical protein traL
VJF80_RS00455 72086..76147 - 4062 WP_000842453 LPD7 domain-containing protein -
VJF80_RS00460 76211..76501 - 291 WP_000817801 IcmT/TraK family protein traK
VJF80_RS00465 76498..77646 - 1149 WP_000775210 plasmid transfer ATPase TraJ virB11
VJF80_RS00470 77630..78466 - 837 WP_000745049 type IV secretory system conjugative DNA transfer family protein traI
VJF80_RS00475 78463..78921 - 459 WP_001170111 DotD/TraH family lipoprotein -
VJF80_RS00480 79025..80227 - 1203 WP_000979993 conjugal transfer protein TraF -
VJF80_RS00485 80329..81150 - 822 WP_000845373 hypothetical protein traE
VJF80_RS00490 81315..81509 - 195 Protein_97 integrase -
VJF80_RS00495 81623..82984 - 1362 WP_001168171 shufflon system plasmid conjugative transfer pilus tip adhesin PilV -
VJF80_RS00500 83002..83538 - 537 WP_023649457 prepilin peptidase -
VJF80_RS00505 83644..84129 - 486 WP_001080767 lytic transglycosylase domain-containing protein virB1
VJF80_RS00510 84174..84710 - 537 WP_000111534 type 4 pilus major pilin -
VJF80_RS00515 84772..85866 - 1095 WP_000697158 type II secretion system F family protein -
VJF80_RS00520 85868..87376 - 1509 WP_000880807 GspE/PulE family protein virB11
VJF80_RS00525 87479..87937 - 459 WP_000095885 type IV pilus biogenesis protein PilP -
VJF80_RS00530 87927..89222 - 1296 WP_000129883 type 4b pilus protein PilO2 -
VJF80_RS00535 89243..90862 - 1620 WP_001035562 PilN family type IVB pilus formation outer membrane protein -
VJF80_RS00540 90894..91307 - 414 WP_124983997 type IV pilus biogenesis protein PilM -

Host bacterium

ID   20050 GenBank   NZ_CP141226
Plasmid name   HBI04|unnamed Incompatibility group   IncB/O/K/Z
Plasmid size   98160 bp Coordinate of oriT [Strand]   40579..40651 [-]
Host baterium   Escherichia sp. HBI04

Cargo genes

Drug resistance gene   blaCMY-2
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -