Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   114620
Name   oriT_ERMR1:05|unnamed3 in_silico
Organism   Rahnella sikkimica strain ERMR1:05
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP019065 (18317..18406 [-], 90 nt)
oriT length   90 nt
IRs (inverted repeats)      44..49, 52..57  (GTCTGC..GCAGAC)
Location of nic site      _
Conserved sequence flanking the
  nic site    		  _
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 90 nt

>oriT_ERMR1:05|unnamed3
GGGGTGTCGGGGCGAAGCCCTGACCAGTAGTTTTGTCATGGCTGTCTGCGTGCAGACGGTAATGACAAAACATTTCCTGTCCCTTATTTT

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   9373 GenBank   WP_104925507
Name   traI_BV494_RS25155_ERMR1:05|unnamed3 insolico UniProt ID   _
Length   654 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 654 a.a.        Molecular weight: 74355.52 Da        Isoelectric Point: 7.5026

>WP_104925507.1 TraI/MobA(P) family conjugative relaxase [Rahnella sikkimica]
MNVIIPTKRRDKKTSFNKLVSYVSTRAEKKEGDVVSAEISNTHVPGTEYVTTPGFGRLISYVGRESQESS
TQIISMSPEGIQRVLSGEVLCETNCFSLGSAAAEMNMTAMQNRHCKDAVYHFILSWQGDEDPTADAIFSS
VRYSLESLGMKDHQYVAAIHRDTDNIHCHVSANRVHPETFRAQNMWNDADTLQKCCRVLERELGFKVDNG
SWNMDEYGDLHRARRNMPAVPRGAAKREIFSDRESLHGYAVRETREAISHVDENGRLDWVSLHNLLHTSG
LGLREQNGGLAVYDLIRPEGISVKASDVHPAISLPAMEQRFGGFQAAPPTFNPECPEDGIVTMDTVYMPQ
LHVRDQDIRRERREARAVVREILRARFDAYRAGWEKPDLRVRARFHQISSHCMAMKSHVRQSVRDPLLRK
LLYRVAEFEKMKAMAELRLQLREERKELAETGTARPLTWKHWVEREALQGNVAAVSQMRGWAYRDKRKTR
QQEKTVGQPNAVVHFGPADDAPLFRSNEHETHLLRDGTVCYLRGGQPAVTDFGDRVEVYVSSDAKSDRFN
NDLAAELTVWRSGDHAVVQGEPTAVNRVLYSGVVRNLNNDDGRHFKVSDSKQQASVIATEIHYRQSDVIT
EQHRIERQPRDDENNQPSIALPRP

  Protein domains


Predicted by InterproScan.

Relaxase/Mobilisation nuclease domain (Relaxase)

(57-322)


  Protein structure



No available structure.




T4CP

ID   10879 GenBank   WP_104925551
Name   trbC_BV494_RS25385_ERMR1:05|unnamed3 insolico UniProt ID   _
Length   727 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 727 a.a.        Molecular weight: 81345.28 Da        Isoelectric Point: 8.2222

>WP_104925551.1 F-type conjugative transfer protein TrbC [Rahnella sikkimica]
MTDSNHPIARDRVNRRVGPSWLADTLSQPGTLAWGMGAAVATGVIYPVSLLLSLPVLSFWSLVVAPGGRW
QMPMRMPADMDREDPSTDREVPAKVLGFLPITRIRIHTDRAAGILYAGYLRGKNAGRELWLSMDDLTRHV
LMFGTTGAGKTETLLGWVFNALCWGKGLVFSDHKAQNDVALAVASLARRFGREDDLRMMNFITGGRSRAQ
ELLEDVKGRPQTNSTNAFGIMQETYTINLMDSMLPKTGNGDGGWQEKARSMNQALIFALVYKCRREGTVM
SQRTIQAHLPLRKIAGLYIQAVDEQWHEDICRVLENYLSTLAGFDMDKVATPSEWDPEANRQHGYLMQQF
TRMLSLFNDTYGHVFARDAGDIDLRDVVHNDRILTVLVPALEISANEGSTLGRLYQSQLAMILSQDLGEK
LEGRPRDIMIVRKFKDRFPFLWIIDEVGAGYSEKLGELATQIRSLGYCLLLAGQEVQRLKTAAGDAVWTL
VANMGTRITGKIMDPKDTLEILQLMAGTEFRAEMNAMVRQEGLAGGSWTDDNRVQLREQKKVDVEEVQSL
QEGENITLFKGKVIRGSSLYIKEADKFASEAVRINRFVEVAPPTEARLLATAPLRQRRSYVRTDRVQQIL
RVLSEEPGSRDTSKLVLTDPALAAVCEFDLECRFSWRREPSAEVRAAVLWRMLQESLPARGRGYRARLRE
PRVLGAGLSAIEQAGQYHVSLPQGTAS

  Protein domains



No domain identified.


  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 29159..63458

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
BV494_RS25185 (BV494_25280) 24580..24993 + 414 WP_104925513 hypothetical protein -
BV494_RS25190 (BV494_25285) 24971..25519 - 549 WP_104925514 hypothetical protein -
BV494_RS25195 (BV494_25290) 25655..27370 + 1716 WP_104925515 PilN family type IVB pilus formation outer membrane protein -
BV494_RS25200 (BV494_25295) 27376..28731 + 1356 WP_104925516 type 4b pilus protein PilO2 -
BV494_RS25205 (BV494_25300) 28718..29149 + 432 WP_104925517 type IV pilus biogenesis protein PilP -
BV494_RS25210 (BV494_25305) 29159..30670 + 1512 WP_104925518 GspE/PulE family protein virB11
BV494_RS25215 (BV494_25310) 30667..31734 + 1068 WP_104925519 type II secretion system F family protein -
BV494_RS25220 (BV494_25315) 31851..32354 + 504 WP_104925520 type 4 pilus major pilin -
BV494_RS25225 (BV494_25320) 32413..33354 + 942 WP_104925521 ATPase, T2SS/T4P/T4SS family virB11
BV494_RS25230 (BV494_25325) 33358..34644 + 1287 WP_104925522 shufflon system plasmid conjugative transfer pilus tip adhesin PilV -
BV494_RS25235 (BV494_25330) 34956..35384 + 429 WP_104925523 type IV pilus biogenesis protein PilM -
BV494_RS25240 (BV494_25335) 35387..36001 + 615 WP_104925524 prepilin peptidase -
BV494_RS25245 (BV494_25340) 36016..36468 + 453 WP_226790162 lytic transglycosylase domain-containing protein virB1
BV494_RS25250 (BV494_25345) 36514..37014 + 501 WP_104925525 hypothetical protein -
BV494_RS25255 (BV494_25350) 37209..37613 + 405 WP_104925526 hypothetical protein -
BV494_RS25260 (BV494_25355) 37764..38201 + 438 WP_226790163 lytic transglycosylase domain-containing protein virB1
BV494_RS25265 (BV494_25360) 38264..38734 + 471 WP_104925528 DotD/TraH family lipoprotein -
BV494_RS25270 (BV494_25365) 38731..39555 + 825 WP_104925529 type IV secretory system conjugative DNA transfer family protein traI
BV494_RS25275 (BV494_25370) 39555..40724 + 1170 WP_104925530 plasmid transfer ATPase TraJ -
BV494_RS25280 (BV494_25375) 40721..41008 + 288 WP_104925531 conjugal transfer protein traK
BV494_RS25285 (BV494_25380) 41041..45930 + 4890 WP_104925532 LPD7 domain-containing protein -
BV494_RS25290 (BV494_25385) 45956..46306 + 351 WP_104925533 conjugal transfer protein traL
BV494_RS25295 (BV494_25390) 46316..47008 + 693 WP_104925534 DotI/IcmL/TraM family protein traM
BV494_RS25300 (BV494_25395) 47019..47969 + 951 WP_104925535 DotH/IcmK family type IV secretion protein traN
BV494_RS25305 (BV494_25400) 47972..49282 + 1311 WP_104925536 conjugal transfer protein TraO traO
BV494_RS25310 (BV494_25405) 49275..50015 + 741 WP_104925537 conjugal transfer protein TraP traP
BV494_RS25315 (BV494_25410) 50025..50564 + 540 WP_104925538 conjugal transfer protein TraQ traQ
BV494_RS25320 (BV494_25415) 50639..51028 + 390 WP_104925539 DUF6750 family protein traR
BV494_RS25325 (BV494_25420) 51117..51740 + 624 WP_104925540 conjugal transfer protein traT
BV494_RS25330 (BV494_25425) 51712..54765 + 3054 WP_104925541 conjugal transfer protein traU
BV494_RS25335 (BV494_25430) 54792..56012 + 1221 WP_104925542 conjugal transfer protein TraW traW
BV494_RS25340 (BV494_25435) 56037..56537 + 501 WP_104925543 hypothetical protein -
BV494_RS25350 (BV494_25445) 56779..57357 + 579 WP_104925545 conjugal transfer protein TraX -
BV494_RS25355 (BV494_25450) 57416..57835 + 420 WP_104925546 hypothetical protein -
BV494_RS25360 (BV494_25455) 57849..58052 + 204 WP_104925593 Hha/YmoA family nucleoid-associated regulatory protein -
BV494_RS25365 (BV494_25460) 58142..60277 + 2136 WP_104925547 DotA/TraY family protein traY
BV494_RS25370 (BV494_25465) 60344..61003 + 660 WP_104925548 plasmid IncI1-type surface exclusion protein ExcA -
BV494_RS25375 (BV494_25470) 61114..62331 + 1218 WP_104925549 conjugal transfer protein trbA
BV494_RS25380 (BV494_25475) 62346..63458 + 1113 WP_104925550 thioredoxin fold domain-containing protein trbB
BV494_RS25385 (BV494_25480) 63445..65628 + 2184 WP_104925551 F-type conjugative transfer protein TrbC -
BV494_RS25390 (BV494_25485) 65732..66214 + 483 WP_104925552 macro domain-containing protein -
BV494_RS25395 (BV494_25490) 66202..66705 + 504 WP_104925553 hypothetical protein -
BV494_RS25400 (BV494_25495) 66975..67508 + 534 WP_104925594 phospholipase D family protein -
BV494_RS25405 (BV494_25500) 67677..67934 + 258 WP_104925554 replication regulatory protein RepA -

Host bacterium

ID   15055 GenBank   NZ_CP019065
Plasmid name   ERMR1:05|unnamed3 Incompatibility group   -
Plasmid size   107727 bp Coordinate of oriT [Strand]   18317..18406 [-]
Host baterium   Rahnella sikkimica strain ERMR1:05

Cargo genes

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