Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   119628
Name   oriT_RL97|unnamed in_silico
Organism   Escherichia sp. RL97
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP141241 (58836..58908 [-], 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_RL97|unnamed
GTCGGGGCAAAGCCCTGACCAGGTGGGGAATGTCTGAGTGCGCGTGCGCGGTCCGACATTCCCACATCCTGTC

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   12405 GenBank   WP_029391987
Name   Relaxase_VJF87_RS00375_RL97|unnamed insolico UniProt ID   A0A2H5C199
Length   906 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 906 a.a.        Molecular weight: 105112.51 Da        Isoelectric Point: 8.2682

>WP_029391987.1 MULTISPECIES: relaxase/mobilization nuclease domain-containing protein [Enterobacteriaceae]
MNAIIPHKRRDGRSSFEDLIAYTSVRDDVQENELTEDSEIKSDVPHRNRFRRLVDYATRLRNEKFVSLID
VMKDGSQWVNFYGVTCFHNCNSLETAAEEMQYKADKAVFSRNDTDPVFHYILSWPAHESPRPEQLFDCVR
HTLKSLELSKHQYVAAVHTDTDNLHVHVAVNRVHPETGYINWLSWSQEKLSRACRELELKHGFAPDNGCF
VHAPGNRIVRKTALVRERRNAWRRGKKQTFREYIAQMSIAGLREEPAQDWLSLHKRLASDGLYITMQEGE
LVVKDGWDRAREGVALSSFGPSWTAEKLGRKLGEYQPVPTDIFSQVGTPGRYDPEAINVDIRPEKVAETE
SLKQYACRHFAERLPEMARNGELESCLDVHRTLAKAGLWMGIQHGHLVLHDGFDKQQTPVRADSVWPLMT
LDYMQDLDGGWQPVPKDIFTQVIPGERFRGHSIGTQAVSDYEWYRMRMGTGPQGAIKRELFSDKESLWGY
ALIQCRSQIEEMIAGGDFSWQACHEMFARKGLMLQKQHHGLVIVDAFNHELTPVKASSIHPDLTLSRAEP
QAGPFEIAGADIFERVKPECRYNPELAASDEVEPGFRRDPVLRRERREARAAAREDLRARYLAWKEHWRK
PDLRYGERLREIHAACRRRKAYIRVQFRDPQVRKLHYHIAEVQRMQALIRLKESVKEERLSLIAEGKWYP
LSYRQWVEQQAAQGDRAAVSQLRGWDYRDRRSRNKDKRRTTNADRCVVLCEPGGTPLFNNVAKLEARLQK
NGSVHFRDTRTGKNVCTDYGDRVVFYHHTDRNELAEKLDLIAPVLFSRNGKLGFEPEGSYQQFNDVFAEM
VAWHNAAGITGNGHFTITRPDVDLHRQRSEQYYREYIRQQTRLSESHDDNYTLRQEKTWEPPSPGM

  Protein domains


Predicted by InterproScan.

Relaxase/Mobilisation nuclease domain (Relaxase)

(62-315)


  Protein structure


Source ID Structure
AlphaFold DB A0A2H5C199


Auxiliary protein

ID   7061 GenBank   WP_001291058
Name   WP_001291058_RL97|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   14562 GenBank   WP_029392471
Name   trbC_VJF87_RS00380_RL97|unnamed 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: 87239.20 Da        Isoelectric Point: 6.6676

>WP_029392471.1 MULTISPECIES: F-type conjugative transfer protein TrbC [Enterobacteriaceae]
MSQHHVNPDLIHRTAWGNPLWNALHNLNIIGLCLAGSIITALIWPLALPVCLLFTLVTSVIFTLQRWRCP
LRMPMTLSLDDPSQDRKVRRSLFSFWPTLFQYEADETSPARGIFYVGYRRINDIGRELWLSMDDLTRHII
FFSTTGGGKTETTFAWLLNPLCWGRGFTFVDGKAQNDTTRTIWYLSRRFGREDDIEVINFMNGGKSRSEI
IQSGEKSRPQSNTWNPFAFSTEAFTAETMQSMLPQNVQGGEWQSRAIAMNKALVFGTKFWCVRERKTMSL
QMLREHMTLEGMAKLYCRGLDDQWPEEAIAPLRNYLQDVPGFDMSLVRTPSAWTEEPRKQHAYLSGQFSE
TFTTFAETFGDVFAADAGDIDIRDSIHSDRILIVMIPALDTSAHTTSALGRMFITQQSMILARDLGYRLE
GTDAQTLEVKKYKGRFPYICILDEVGAYYTDRIAVEATQVRSLEFSLIMMAQDQERIEGQTSATNTATLM
QNAGTKFAGRIVSDDKTARTVKNAAGEEARARMGSLQRHDGLMGESWVDGNQITIQMESKIDVQDLIRLN
AGEFFTVFQGDVVPSASVYIPDSEKSCDSDPVVINRYIAIEAPRLERLRRLVPRTVQRRLPTPEHVSSII
GVLTEKTSRKRRKKHTEPYRIIDTFQDQLKRTQTSLDLLPQYDTDIESRANELWKKAVHTINNTTREERR
VCYITLNRPEEEHSGPEDIPSVKAILNTLLPLEILLPVAENNKSQTINNDHPQKSCGAQPTTDEKY

  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: 64495..110704

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
VJF87_RS00380 62214..64514 - 2301 WP_029392471 F-type conjugative transfer protein TrbC -
VJF87_RS00385 64495..65613 - 1119 WP_029391999 DsbC family protein trbB
VJF87_RS00390 65610..66962 - 1353 WP_065749868 conjugal transfer protein TrbA trbA
VJF87_RS00395 67273..67356 + 84 WP_271298668 DinQ-like type I toxin DqlB -
VJF87_RS00400 67419..67595 - 177 WP_032172741 hypothetical protein -
VJF87_RS00405 67746..68213 - 468 WP_000598962 thermonuclease family protein -
VJF87_RS00410 68373..68996 + 624 WP_001155252 helix-turn-helix domain-containing protein -
VJF87_RS00415 69194..69409 - 216 WP_000266543 hypothetical protein -
VJF87_RS00420 69413..69781 - 369 WP_029391948 hypothetical protein -
VJF87_RS00425 70080..70322 - 243 WP_029391947 hypothetical protein -
VJF87_RS00430 70651..70803 + 153 WP_021532728 Hok/Gef family protein -
VJF87_RS00435 70800..70961 - 162 WP_021580032 hypothetical protein -
VJF87_RS00440 71117..71248 - 132 Protein_87 ethanolamine utilization protein EutE -
VJF87_RS00445 71343..71552 + 210 WP_000062946 HEAT repeat domain-containing protein -
VJF87_RS00450 71617..72270 - 654 WP_029391946 plasmid IncI1-type surface exclusion protein ExcA -
VJF87_RS00455 72358..74523 - 2166 WP_029391945 DotA/TraY family protein traY
VJF87_RS00460 74596..75165 - 570 WP_000650755 conjugal transfer protein TraX -
VJF87_RS00465 75162..76367 - 1206 WP_029391944 conjugal transfer protein TraW traW
VJF87_RS00470 76328..76945 - 618 WP_029391943 hypothetical protein traV
VJF87_RS00475 76945..79989 - 3045 WP_029391942 conjugal transfer protein traU
VJF87_RS00480 80165..80545 - 381 WP_000690886 hypothetical protein -
VJF87_RS00485 80545..80853 - 309 WP_029391941 hypothetical protein -
VJF87_RS00490 81049..81366 + 318 WP_000118520 quaternary ammonium compound efflux SMR transporter SugE -
VJF87_RS00495 81363..81896 - 534 WP_001221666 lipocalin family protein -
VJF87_RS00500 81990..83135 - 1146 WP_000976514 extended-spectrum class C beta-lactamase CMY-2 -
VJF87_RS00505 83459..84721 - 1263 WP_000608644 IS1380-like element ISEcp1 family transposase -
VJF87_RS00510 85058..85684 - 627 WP_001597015 hypothetical protein traT
VJF87_RS00515 85791..86042 - 252 WP_021532719 hypothetical protein -
VJF87_RS00520 86099..86497 - 399 WP_029391936 DUF6750 family protein traR
VJF87_RS00525 86544..87074 - 531 WP_000987022 conjugal transfer protein TraQ traQ
VJF87_RS00530 87071..87784 - 714 WP_021532717 conjugal transfer protein TraP traP
VJF87_RS00535 87781..89112 - 1332 WP_029391934 conjugal transfer protein TraO traO
VJF87_RS00540 89116..90090 - 975 WP_029391933 DotH/IcmK family type IV secretion protein traN
VJF87_RS00545 90101..90796 - 696 WP_029391932 DotI/IcmL family type IV secretion protein traM
VJF87_RS00550 90808..91158 - 351 WP_021532713 hypothetical protein traL
VJF87_RS00555 91175..95236 - 4062 WP_029391931 LPD7 domain-containing protein -
VJF87_RS00560 95300..95590 - 291 WP_000817799 hypothetical protein traK
VJF87_RS00565 95587..96735 - 1149 WP_000625247 plasmid transfer ATPase TraJ virB11
VJF87_RS00570 96719..97555 - 837 WP_029391930 type IV secretory system conjugative DNA transfer family protein traI
VJF87_RS00575 97552..98004 - 453 WP_001081199 DotD/TraH family lipoprotein -
VJF87_RS00580 98242..98373 + 132 WP_257792844 hypothetical protein -
VJF87_RS00585 98363..99565 - 1203 WP_029391929 conjugal transfer protein TraF -
VJF87_RS00590 99655..100476 - 822 WP_000804089 hypothetical protein traE
VJF87_RS00595 100727..101272 - 546 WP_029391928 hypothetical protein -
VJF87_RS00600 101391..101672 - 282 WP_029391927 hypothetical protein -
VJF87_RS00605 101713..102882 - 1170 WP_029391926 site-specific integrase -
VJF87_RS00610 103345..103704 + 360 WP_225092544 shufflon protein B -
VJF87_RS00615 103714..104097 - 384 WP_236926536 shufflon protein D' -
VJF87_RS00620 104580..104969 + 390 Protein_123 phage tail protein -
VJF87_RS00625 104974..106308 - 1335 WP_059327959 shufflon system plasmid conjugative transfer pilus tip adhesin PilV -
VJF87_RS00630 106305..107012 - 708 WP_202110611 A24 family peptidase -
VJF87_RS00635 106972..107448 - 477 WP_029391914 lytic transglycosylase domain-containing protein virB1
VJF87_RS00640 107507..108043 - 537 WP_029391915 type 4 pilus major pilin -
VJF87_RS00645 108094..109194 - 1101 WP_029391916 type II secretion system F family protein -
VJF87_RS00650 109196..110704 - 1509 WP_021532701 GspE/PulE family protein virB11
VJF87_RS00655 110801..111397 - 597 WP_029391917 hypothetical protein -
VJF87_RS00660 111493..112047 - 555 WP_021532699 hypothetical protein -
VJF87_RS00665 112096..112548 - 453 WP_029391918 type IV pilus biogenesis protein PilP -
VJF87_RS00670 112538..113833 - 1296 WP_021532697 type 4b pilus protein PilO2 -
VJF87_RS00675 113854..115473 - 1620 WP_021532696 PilN family type IVB pilus formation outer membrane protein -

Host bacterium

ID   20058 GenBank   NZ_CP141241
Plasmid name   RL97|unnamed Incompatibility group   IncB/O/K/Z
Plasmid size   120705 bp Coordinate of oriT [Strand]   58836..58908 [-]
Host baterium   Escherichia sp. RL97

Cargo genes

Drug resistance gene   tet(A), sul1, qacE, aac(3)-VIa, ant(3'')-Ia, blaCMY-2
Virulence gene   htpB
Metal resistance gene   merR, merT, merP, merA, merD, merE
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -