Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   107838
Name   oriT_pJD053-NDM-99K in_silico
Organism   Escherichia fergusonii strain EF21JD053
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP095791 (42068..42159 [-], 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_pJD053-NDM-99K
CGGGGTGTCGGGGCTAAGCCCTGACCAGGTGGTAATCGTATAACCGTGCGTGCGCGGTTATACGATTACACATCCTGTCCCGTTTTTCAGGC

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   5262 GenBank   WP_087526033
Name   Relaxase_MYB88_RS24820_pJD053-NDM-99K 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: 104975.65 Da        Isoelectric Point: 8.4169

>WP_087526033.1 MULTISPECIES: relaxase/mobilization nuclease domain-containing protein [Enterobacteriaceae]
MNAIIPKKRRDGKSSFEDLIAYTSVRDDVPEDELRPDTEMKAEIPHRNRFRRLVDYATRLRNEKFVSLID
VMKDGSQWVNFYGVTCFHNCLSLESAAEEMQKAAELAHFSKDDTDPVFHYILSWPAHESPRSEQLFDCVR
HTLKSLELSKHQYVAAVHTDTDNLHVHVAVNRVHPETGYINCLPWSQEKLSRACRELELKHGFAPDNGCF
VHAPGNRIVRKTALVRERRNAWRRGKKQTFREYIAQMSIAGLREEPAQDWLSLHKRLASDGLYITMQEGE
LVVKDGWDRAREGVALSSFGPSWTAEKLGRKLGEYQPVPTDIFSQVGTPGRYDPEAINVDIRPEKVAETE
SLKQYACRHFAERLPKMARNGELKSCLAVHRTLAEAGLWMGIQHGHLVLHDGFDKQQTPVRADSVWPLMT
LDYMQDLDGGWHSVPKDIFTQVIPGERFRGHSIGTQAVSDYEWYRMRMGTGPQGAIKRELFSDKESLWGY
ALIQCRSQIEEMIAGGDFSWQACHEMFARKGLMLQKQHHGLVIVDAFNHELTPVKASSIHPDLTLSRAEP
QAGPFEIAAADIFERVKPECRYNPELAASDEVEPGFRRDPELRRERREARAAAREDLRARYLAWKEHWRK
PDLRYGERLREIHAACRRRKAHIRVQFRDPQLRKLHYHIAEVQRMQALIRLKENVREERLALMAEGKWYP
LSYRQWVEQQAAQGDRAAVSQLRGWDYRDRRSRNKDKRRTTNADRCVVLCEPGGTPLFNNVAKLEARLQK
NGSVHFRDTRTGKNVCTDYGDRVVFYHHTDRNELAEKLDLIAPVLFSRNGKLGFEPEGSYQQFNDVFAEM
VAWHNAAGITGNGHFTITRPDVDLHRQRSEQYYREYIRQQTRLSESHDDNYTLRQEKTWEPPSPGM

  Protein domains


Predicted by InterproScan.

Relaxase/Mobilisation nuclease domain (Relaxase)

(62-315)


  Protein structure



No available structure.




Auxiliary protein

ID   2412 GenBank   WP_045147294
Name   WP_045147294_pJD053-NDM-99K 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: 12623.76 Da        Isoelectric Point: 10.6096

>WP_045147294.1 MULTISPECIES: plasmid mobilization protein MobA [Enterobacteriaceae]
MIEKKTRSGSEKRQKNVLIAVRFSPEEAEIVKEKAEKNGLTVSTLIRKTVLGKQINARIDEDFLKELMRL
GRLQKHLFVEGKRTGDKEYAEVLVAITELANTLRRDLMGR

  Protein domains


Predicted by InterproScan.

Family of unknown function (DUF6290) (DUF6290)

(19-66)


  Protein structure



No available structure.




T4CP

ID   5506 GenBank   WP_087526032
Name   trbC_MYB88_RS24825_pJD053-NDM-99K 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: 87133.06 Da        Isoelectric Point: 6.6674

>WP_087526032.1 MULTISPECIES: F-type conjugative transfer protein TrbC [Enterobacteriaceae]
MSQHHVNPDLIHRTAWGNPLWNALHNLNIIGLCLAGSIITAMIWPLALPVCLLFTLVTSVIFTLQRWRCP
LRMPMTLSLDDPSQDRKVRRSLFSFWPTLFQYEADETSPARGIFYVGYRRINDIGRELWLSMDDLTRHVM
FFATTGGGKTETTFAWLLNPLCWGRGFTFVDGKAQNDTTRTIWYLSRRFGREDDIEVINFMNGGKSRSEI
IQSGEKSRPQSNTWNPFAFSTEAFTAETMQSMLPQNVQGGEWQSRAIAMNKALVFGTKFWCVREGKTMSL
QMLREHMTLEGMAKLYCRGLDDQWPEEAIAPLRNYLQDVPGFDMSLVRTPSAWTEEPRKQHAYLSGQFSE
TFTTFAETFGDVFAADAGDIDIRDSIHSDRILIVMIPALDTSAHTTSALGRMFITQQSMILARDLGYRLE
GTDAQTLEVKKYKGRFPYICILDEVGAYYTDRIAVEATQVRSLEFSLIMTAQDQERIEGQTSATNTATLM
QNAGTKFAGRIVSDDKTARTVKNAAGEEARARMGSLQRHDGVMGESWVDGNQITIQMESKINVQDLIRLN
AGEFFTVFQGDVVPSASVYIPDSEKSCDSDPVVINRYIAIEAPRLERLRRLVPRTVQRRLPTPEHVSSII
GVLTEKTSRKRRKKHTEPYRIIDTFQDQLKRTQTSLDLLPQYDTDIESRANELWKKAVHTINNTTREERR
VCYITLNRPEEEHSGPEDIPSMKAILNTLLPLEILLPVAENNKSQTINNDHPQKSCGAQPTTDEKY

  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: 47740..89656

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
MYB88_RS24825 (MYB88_24820) 45459..47759 - 2301 WP_087526032 F-type conjugative transfer protein TrbC -
MYB88_RS24830 (MYB88_24825) 47740..48858 - 1119 WP_087526031 DsbC family protein trbB
MYB88_RS24835 (MYB88_24830) 48855..50126 - 1272 WP_087526030 IncI1-type conjugal transfer protein TrbA trbA
MYB88_RS25580 50429..50512 + 84 WP_271298668 DinQ-like type I toxin DqlB -
MYB88_RS24840 (MYB88_24835) 50575..50751 - 177 WP_032172741 hypothetical protein -
MYB88_RS24845 (MYB88_24840) 50902..51369 - 468 WP_000598962 thermonuclease family protein -
MYB88_RS24850 (MYB88_24845) 51528..52151 + 624 WP_001155252 helix-turn-helix domain-containing protein -
MYB88_RS24855 (MYB88_24850) 52349..52564 - 216 WP_000266543 hypothetical protein -
MYB88_RS24860 (MYB88_24855) 52568..52936 - 369 WP_001302696 hypothetical protein -
MYB88_RS24865 (MYB88_24860) 52948..53139 - 192 WP_000751583 hypothetical protein -
MYB88_RS24870 (MYB88_24865) 53236..53478 - 243 WP_000650933 hypothetical protein -
MYB88_RS24875 (MYB88_24870) 53807..53959 + 153 WP_021532728 Hok/Gef family protein -
MYB88_RS24880 (MYB88_24875) 54528..54680 + 153 WP_001536636 Hok/Gef family protein -
MYB88_RS24885 (MYB88_24880) 54994..55125 - 132 Protein_71 ethanolamine utilization protein EutE -
MYB88_RS24890 (MYB88_24885) 55220..55429 + 210 WP_000062946 HEAT repeat domain-containing protein -
MYB88_RS24895 (MYB88_24890) 55494..56147 - 654 WP_087526029 plasmid IncI1-type surface exclusion protein ExcA -
MYB88_RS24900 (MYB88_24895) 56236..58401 - 2166 WP_130565199 DotA/TraY family protein traY
MYB88_RS24905 (MYB88_24900) 58474..59043 - 570 WP_001204060 conjugal transfer protein TraX -
MYB88_RS24910 (MYB88_24905) 59040..60245 - 1206 WP_072643639 conjugal transfer protein TraW traW
MYB88_RS24915 (MYB88_24910) 60203..60823 - 621 WP_072643640 conjugal transfer protein TraV traV
MYB88_RS24920 (MYB88_24915) 60823..63867 - 3045 WP_087526027 conjugal transfer protein traU
MYB88_RS24925 (MYB88_24920) 64353..64778 - 426 WP_165410384 hypothetical protein -
MYB88_RS24930 (MYB88_24925) 64846..65664 - 819 WP_072645885 conjugal transfer protein TraT traT
MYB88_RS24935 (MYB88_24930) 65657..65830 - 174 WP_087526026 TraS protein -
MYB88_RS24940 (MYB88_24935) 65887..66285 - 399 WP_029391936 DUF6750 family protein traR
MYB88_RS24945 (MYB88_24940) 66332..66862 - 531 WP_000987022 conjugal transfer protein TraQ traQ
MYB88_RS24950 (MYB88_24945) 66859..67572 - 714 WP_000787009 conjugal transfer protein TraP traP
MYB88_RS24955 (MYB88_24950) 67569..68900 - 1332 WP_045145399 conjugal transfer protein TraO traO
MYB88_RS24960 (MYB88_24955) 68904..69878 - 975 WP_021532715 DotH/IcmK family type IV secretion protein traN
MYB88_RS24965 (MYB88_24960) 69889..70584 - 696 WP_045145396 DotI/IcmL family type IV secretion protein traM
MYB88_RS24970 (MYB88_24965) 70596..70946 - 351 WP_021532713 hypothetical protein traL
MYB88_RS24975 (MYB88_24970) 70963..75024 - 4062 WP_087526025 LPD7 domain-containing protein -
MYB88_RS24980 (MYB88_24975) 75088..75378 - 291 WP_000817799 hypothetical protein traK
MYB88_RS24985 (MYB88_24980) 75375..76523 - 1149 WP_000625247 plasmid transfer ATPase TraJ virB11
MYB88_RS24990 (MYB88_24985) 76507..77343 - 837 WP_000848138 type IV secretory system conjugative DNA transfer family protein traI
MYB88_RS24995 (MYB88_24990) 77340..77792 - 453 WP_001081199 DotD/TraH family lipoprotein -
MYB88_RS25000 (MYB88_24995) 77841..78011 - 171 WP_001597011 hypothetical protein -
MYB88_RS25005 (MYB88_25000) 78151..79350 - 1200 WP_087526024 conjugal transfer protein TraF -
MYB88_RS25010 (MYB88_25005) 79456..80277 - 822 WP_001681675 hypothetical protein traE
MYB88_RS25015 (MYB88_25010) 80551..80871 + 321 WP_000695052 hypothetical protein -
MYB88_RS25020 (MYB88_25015) 80963..81253 - 291 WP_021532709 hypothetical protein -
MYB88_RS25025 (MYB88_25020) 81295..82464 - 1170 WP_021532708 site-specific integrase -
MYB88_RS25030 (MYB88_25025) 82970..83329 + 360 WP_247859143 hypothetical protein -
MYB88_RS25035 (MYB88_25030) 83924..85261 - 1338 WP_096984667 shufflon system plasmid conjugative transfer pilus tip adhesin PilV -
MYB88_RS25040 (MYB88_25035) 85258..85965 - 708 WP_153789788 A24 family peptidase -
MYB88_RS25045 (MYB88_25040) 85925..86401 - 477 WP_021532704 lytic transglycosylase domain-containing protein virB1
MYB88_RS25050 (MYB88_25045) 86460..86996 - 537 WP_021532703 type 4 pilus major pilin -
MYB88_RS25055 (MYB88_25050) 87046..88146 - 1101 WP_072667218 type II secretion system F family protein -
MYB88_RS25060 (MYB88_25055) 88148..89656 - 1509 WP_021532701 ATPase, T2SS/T4P/T4SS family virB11
MYB88_RS25065 (MYB88_25060) 89753..90349 - 597 WP_029391917 hypothetical protein -
MYB88_RS25070 (MYB88_25065) 90445..90999 - 555 WP_021532699 hypothetical protein -
MYB88_RS25075 (MYB88_25070) 91048..91500 - 453 WP_021532698 type IV pilus biogenesis protein PilP -
MYB88_RS25080 (MYB88_25075) 91490..92785 - 1296 WP_077250483 type 4b pilus protein PilO2 -
MYB88_RS25085 (MYB88_25080) 92806..94425 - 1620 WP_021532696 PilN family type IVB pilus formation outer membrane protein -

Host bacterium

ID   8273 GenBank   NZ_CP095791
Plasmid name   pJD053-NDM-99K Incompatibility group   IncB/O/K/Z
Plasmid size   99658 bp Coordinate of oriT [Strand]   42068..42159 [-]
Host baterium   Escherichia fergusonii strain EF21JD053

Cargo genes

Drug resistance gene   aph(3')-IIa, mph(A), blaNDM-5
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -