Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   101416
Name   oriT_pB-9428-1 in_silico
Organism   Escherichia coli strain SCPM-O-B-9428
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_JAJIZO010000007 (28051..28136 [-], 86 nt)
oriT length   86 nt
IRs (inverted repeats)     _
Location of nic site      _
Conserved sequence flanking the
  nic site    		  _
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 86 nt

>oriT_pB-9428-1
CGGGGTGTCGGGGCTAAGCCCTGACCAGGTGGTAATCGTATAGCCGTGCGTGCGCGGTTATACGATTACACATCCTGTCCCGTTTT

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   1289 GenBank   WP_083574966
Name   Relaxase_LMH83_RS25640_pB-9428-1 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: 104942.63 Da        Isoelectric Point: 8.2349

>WP_083574966.1 MULTISPECIES: relaxase/mobilization nuclease domain-containing protein [Enterobacteriaceae]
MNAIIPKKRRDGKSSFEDLIAYTSVRDDVPEDELRPDTEMKAEIPHRNRFRRLVDYATRLRNEKFVSLID
VMKDGSQWVNFYGVTCFHNCLSLESAAEEMQKAAELAHFSKDDTDPVFHYILSWPAHESPRSEQLFDCVR
HTLKSLELSKHQYVAAVHTDTDNLHVHVAVNRVHPETGYINCLPWSQEKLSRACRELELKHGFAPDNGCF
VHAPGNRIVRKTALVRERRNAWRRGKKQTFREYIDQMSIAGLREEPAQDWLSLHKRLASDGLYITMQEGE
LVVKDGWDKAREGIALSSFGPSWAAEKLGRKLGEYQPVPTDIFSQVGTPGRYDPEAINVDIRPEKVAETE
SLKQYACRHFAERLPAMARNGELKSCLAVHRTLAEAGLWMGIQHGHLVLHDGFDKQQTPVRADSVWPLMT
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   456 GenBank   WP_001291056
Name   WP_001291056_pB-9428-1 insolico UniProt ID   A0A4P8CE48
Length   110 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  Auxiliary protein sequence


Download         Length: 110 a.a.        Molecular weight: 12597.68 Da        Isoelectric Point: 10.6096

>WP_001291056.1 MULTISPECIES: plasmid mobilization protein MobA [Enterobacteriaceae]
MSEKKTRSGSEKRQKNVLIAVRFSPEEAEIVKEKAEKNGLTVSTLIRKTVLGKQINARIDEDFLKELMRL
GRLQKHLFVEGKRTGDKEYAEVLVAITELANTLRRDLMGR

  Protein domains


Predicted by InterproScan.

Family of unknown function (DUF6290) (DUF6290)

(19-66)


  Protein structure


Source ID Structure
AlphaFold DB A0A4P8CE48


T4CP

ID   902 GenBank   WP_033816586
Name   trbC_LMH83_RS25645_pB-9428-1 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: 86890.73 Da        Isoelectric Point: 6.5117

>WP_033816586.1 MULTISPECIES: F-type conjugative transfer protein TrbC [Enterobacteriaceae]
MSQHHVNPDLIHRTAWGNPLWNALHNLNITGLCLAGSIITALIWPLALPVCLLFTLVTSVIFMLQRWRCP
LRMPMTLSLDDPSQDRKVRRSLFSFWPTLFQYEADETSPARGIFYVGYRRINDIGRELWLSMDDLTRHVM
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: 33717..72553

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
LMH83_RS25645 (LMH83_25630) 31436..33736 - 2301 WP_033816586 F-type conjugative transfer protein TrbC -
LMH83_RS25650 (LMH83_25635) 33717..34841 - 1125 WP_083574964 DsbC family protein trbB
LMH83_RS25655 (LMH83_25640) 34838..36136 - 1299 WP_001402878 IncI1-type conjugal transfer protein TrbA trbA
LMH83_RS27260 36933..37028 + 96 WP_001363141 DinQ-like type I toxin DqlB -
LMH83_RS25665 (LMH83_25650) 37091..37267 - 177 WP_001054907 hypothetical protein -
LMH83_RS25670 (LMH83_25655) 37417..37884 - 468 WP_000598962 thermonuclease family protein -
LMH83_RS25675 (LMH83_25660) 38043..38666 + 624 WP_001155252 helix-turn-helix domain-containing protein -
LMH83_RS25680 (LMH83_25665) 38864..39079 - 216 WP_000266544 hypothetical protein -
LMH83_RS25685 (LMH83_25670) 39083..39451 - 369 WP_143410569 hypothetical protein -
LMH83_RS25690 (LMH83_25675) 39751..39993 - 243 WP_001401586 hypothetical protein -
LMH83_RS25695 (LMH83_25680) 40323..40475 + 153 WP_001302699 Hok/Gef family protein -
LMH83_RS25700 (LMH83_25685) 40613..42199 - 1587 WP_000004560 TnsA endonuclease N-terminal domain-containing protein -
LMH83_RS25705 (LMH83_25690) 42473..43123 - 651 WP_001044247 plasmid IncI1-type surface exclusion protein ExcA -
LMH83_RS25710 (LMH83_25695) 43212..45377 - 2166 WP_000691810 DotA/TraY family protein traY
LMH83_RS25715 (LMH83_25700) 45452..46021 - 570 WP_000650752 conjugal transfer protein TraX -
LMH83_RS25720 (LMH83_25705) 46018..47223 - 1206 WP_001189549 conjugal transfer protein TraW traW
LMH83_RS25725 (LMH83_25710) 47181..47801 - 621 WP_000286854 hypothetical protein traV
LMH83_RS25730 (LMH83_25715) 47801..50845 - 3045 WP_001024767 hypothetical protein traU
LMH83_RS25735 (LMH83_25720) 51140..51958 - 819 WP_072107751 conjugal transfer protein TraT traT
LMH83_RS27265 51873..52124 - 252 WP_001277573 hypothetical protein -
LMH83_RS25745 (LMH83_25730) 52181..52579 - 399 WP_000088813 DUF6750 family protein traR
LMH83_RS25750 (LMH83_25735) 52626..53156 - 531 WP_000987021 conjugal transfer protein TraQ traQ
LMH83_RS25755 (LMH83_25740) 53153..53866 - 714 WP_000787003 conjugal transfer protein TraP traP
LMH83_RS25760 (LMH83_25745) 53863..55200 - 1338 WP_001272017 conjugal transfer protein TraO traO
LMH83_RS25765 (LMH83_25750) 55204..56178 - 975 WP_000547385 DotH/IcmK family type IV secretion protein traN
LMH83_RS25770 (LMH83_25755) 56189..56884 - 696 WP_001287545 DotI/IcmL family type IV secretion protein traM
LMH83_RS25775 (LMH83_25760) 56896..57246 - 351 WP_001056367 hypothetical protein traL
LMH83_RS25780 (LMH83_25765) 57263..61324 - 4062 WP_000842453 LPD7 domain-containing protein -
LMH83_RS25785 (LMH83_25770) 61388..61678 - 291 WP_000817801 IcmT/TraK family protein traK
LMH83_RS25790 (LMH83_25775) 61675..62823 - 1149 WP_000775210 plasmid transfer ATPase TraJ virB11
LMH83_RS25795 (LMH83_25780) 62807..63643 - 837 WP_000745049 type IV secretory system conjugative DNA transfer family protein traI
LMH83_RS25800 (LMH83_25785) 63640..64098 - 459 WP_001170111 DotD/TraH family lipoprotein -
LMH83_RS25805 (LMH83_25790) 64202..65404 - 1203 WP_000979993 conjugal transfer protein TraF -
LMH83_RS25810 (LMH83_25795) 65506..66327 - 822 WP_000845373 hypothetical protein traE
LMH83_RS25815 (LMH83_25800) 66492..66686 - 195 Protein_75 integrase -
LMH83_RS25820 (LMH83_25805) 66800..68161 - 1362 WP_001168171 shufflon system plasmid conjugative transfer pilus tip adhesin PilV -
LMH83_RS25825 (LMH83_25810) 68179..68805 - 627 WP_000939245 prepilin peptidase -
LMH83_RS25830 (LMH83_25815) 68821..69306 - 486 WP_001080767 lytic transglycosylase domain-containing protein virB1
LMH83_RS25835 (LMH83_25820) 69351..69887 - 537 WP_000111521 type 4 pilus major pilin -
LMH83_RS25840 (LMH83_25825) 69949..71043 - 1095 WP_000697154 type II secretion system F family protein -
LMH83_RS25845 (LMH83_25830) 71045..72553 - 1509 WP_000880806 ATPase, T2SS/T4P/T4SS family virB11
LMH83_RS25850 (LMH83_25835) 72657..73115 - 459 WP_000095886 type IV pilus biogenesis protein PilP -
LMH83_RS25855 (LMH83_25840) 73105..74400 - 1296 WP_000129883 type 4b pilus protein PilO2 -
LMH83_RS25860 (LMH83_25845) 74421..76040 - 1620 WP_001035565 PilN family type IVB pilus formation outer membrane protein -
LMH83_RS25865 (LMH83_25850) 76072..76509 - 438 WP_000539951 type IV pilus biogenesis protein PilM -

Host bacterium

ID   1860 GenBank   NZ_JAJIZO010000007
Plasmid name   pB-9428-1 Incompatibility group   IncB/O/K/Z
Plasmid size   83336 bp Coordinate of oriT [Strand]   28051..28136 [-]
Host baterium   Escherichia coli strain SCPM-O-B-9428

Cargo genes

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