Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   107973
Name   oriT_2019-04-29292-1-3|4 in_silico
Organism   Providencia alcalifaciens strain 2019-04-29292-1-3 isolate 2019-04-29292-1-3
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_OU659165 (17632..17666 [-], 35 nt)
oriT length   35 nt
IRs (inverted repeats)      9..15, 19..25  (GCAAAAT..ATTTTGC)
Location of nic site      _
Conserved sequence flanking the
  nic site    		  _
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 35 nt

>oriT_2019-04-29292-1-3|4
AAATTCTTGCAAAATGAAATTTTGCGTAGTGTGTG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   5348 GenBank   WP_224051218
Name   traI_LDO74_RS20790_2019-04-29292-1-3|4 insolico UniProt ID   _
Length   1708 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1708 a.a.        Molecular weight: 187773.80 Da        Isoelectric Point: 5.7090

>WP_224051218.1 conjugative transfer relaxase/helicase TraI [Providencia alcalifaciens]
MLTVAPIANNAANYYTHEDNYYFLGNLEARWMGEGAKSLGLEGEVTKDQLGEILEGRLPNDQSLERMENG
KNVHREGHDLTFSAPKSVSVLGIVLGDKRMIEAHNRAVEVALHEVEGLASTRMMVEGKTSLEMTKNLVVA
AFNHDTSREHDPQLHTHALVMNMTEHNGEWRTLSSDTRSKMGFSEALYDLRIALGEIYQNTLRKEIEGMG
FKTHNAGRNSLWEIDGVPVTPFSQRRQQILDAVGHEASLKSRDVAALDTRQAKTTPEKSELLTDWFDRLE
KNSFGADARKSFYAEAEQRLAKGQMGDASRDIQPDITRAVTDAIALLSDKQLSMTYSQVLAKTLGGLEAR
AGMIAQVREAIDVAIEQRQLIPLDEKKGLFTSSIHLMDELKLQQIATDMKQHNRTVSFQARTEALSPVME
KVADTLPSIAIVASQGLGKAQRDGVLDGITMAQSQGRDVAVMTLDTTSRQAFANDKRFAYVPKMTLGDGQ
PLKPNSTLVVANAEKLSLKSALSLLESAQSANVQVLMMDSGGRKGTGNVLATLQDAGVPRFQGESSAVLT
VKTAHIPDKNHRYAALAAEYAQLHSDMKSVVAQVSGVREQKIVTDTIRQTLTERGMLSEKTVTVTQLKPV
WLDSHSRKQIDSYREGMVMERWNADKKEVERYTIDRVTPETRSVTLLDSQGQKQVMKPQQFDGQWSAYQR
QTMDIAQGEQLTILAKQNKLSARDAVTVTGFMPNAIMVNFNGKTHRIDVRDGVKADYGYVTVPGQQANDT
GTVLLAASARDTQPTLLNTVARSGEHITVYTPLDKMETERRLSRSPVYQQARQLAGVEGLDSKAIEQAAD
KATEALLSKPEKALQQGMALAQESQVFFSRIDAIAKALPLHNSLDSQSLGKAFDRLVAQKAIIPVTSGKG
AAQQHYVTASTWAMEKQILTTILAGKDTQAPLMASVPEAQLNGLTSGQKAATELILGSRDQFVGIQGYAG
VGKTTQFTAVLKALDTLPATQRPEVIGLAPTHRAVGEMAAVGVKAQTLQAFLMDANQRQQLGETLDFKNT
LFLVDESSMIGNRNLSEVLQIIAQGGGRGVLSGDTAQLLSVDSGTPFALAQDRSALDTAIMKEIVRQNPE
LRPAIEAIIAGQVQMAMDTMNSVTPDVVPRRAGAELPEQSVIDAGDRVIARILDDYRGRTPEAQKETLIV
VQTNVDKDVINSGIHDILIEQGQLQGGKFVPILVRENTRTEALLSTAGMAEHAGKIALIQEQYYRIEVTQ
EGVSDGVVTLVDEQGKGHLLSAFESSLRDIGIYRQEARHIAAGEKINFTRTDKERGRVMNSDWTVSEVNE
HGQITLTNGEESRVLDPNSELTDQHLDYGYAGTAYKAQGASSPYVIVLGGVELGRRMLATLRDAYVALSR
TKAHVQTYSDDLDKWTSKITNPGNRKTAHDVLLAEQDYAAKVGNQLFDHAKPLNDTAIGRALSRQMGLGE
SHEGKFVYPSTKHPEPHVAWPAYDVHGKAQGTVLQAIELEGDKLQGLRTEGRLLGSEQAQFIVVKPSQNG
HTVIVNSLESAFETMAQQPEQGVVVQLNPDERLHTTMIEKITQGEVDNAYANPNTAQTDKADSDPKNLQT
PEEQAIDNALKEAEAALRQQANGEPKVPELSEDELRQVMAQERDSLLKGEHDLMEAKERVIEKAVQFERE
HQQQQRDVLRQQEREMVMEKTRDREFGD

  Protein domains


Predicted by InterproScan.

DNA relaxase TraI 2B/2B-like domain (TraI_2B)

(627-705)

single-stranded DNA binding TraI N-terminal subdomain (ssDNA_TraI_N)

(568-619)

TrwC relaxase (TrwC)

(8-280)

AAA domain (AAA_30)

(954-1141)

DNA helicase TraI (TraI_C)

(1396-1508)


  Protein structure



No available structure.




T4CP

ID   5633 GenBank   WP_224051197
Name   traC_LDO74_RS20695_2019-04-29292-1-3|4 insolico UniProt ID   _
Length   903 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 903 a.a.        Molecular weight: 101474.94 Da        Isoelectric Point: 6.5159

>WP_224051197.1 type IV secretion system protein TraC [Providencia alcalifaciens]
MNEKPSLIDKLLAPFLPKSKDIVFDDEPEPVSLQEALFKNLFTAWREPDGNKRAAEALENMDYPSFCSLL
PYRNYDAKSGLFINKTTIGFALECTPLVGANEKIVDALDYFLRNKLPRKIPLTFMLLGSKCISEQLGYGL
KDFGWQGEEAEKFNHITRAFYERGALVGLDNKLNLPLSLRNYRLFVCYAEEHKKADALTLQKVNQILSIV
MKSLAGASLHCEQMNDKGLLQLVREISNFRHDQIALPSSQVDPYESLNDQCADRSLTLEIRPDAIHQSLS
MGKGQKSQTRIMNYMLEKNPTQFALWQTGDNLSNLLDPASSVSCPFAITMTVYVEDLVKTQNEAKKKFIT
NNSRANSKYINWVPGVKRKAEEWGALREGLDTNQMALARYSYGITLFCEDDDDKALEAEMALMNTYTTNH
LKLCPPTFMQLRNYLALFPFVMQEGLWGDMVRSGGTLRAKAFNVANLLPVVADNRICQKGLPIPSYRHQL
SFLDIFERGSGLGNDNFNAAVCGTSGSGKSFLMQALIRQVLDAGGWAYVLDMGDSYKELCHSLGGVYVDA
RDLKFNPFAGVVDIKETAESIRDLLIVLANPSGDMDDVSKSILLNAVQEVWEGKGPNGRKGNKVLIDDVH
DYLEAEVKAAYFDPQSTVQNKMQEIIVALKKYTTKGLYGEYFNSDKPALNEQVRFTVLEMGGLQNKPDLL
AAVMFSMMIFIQQRMYLTARSIKKLAAIDEGWKLLDNKSRFVADFIESGYRTARKYGGSYITISQGIDDF
DGDGASTAAKAAWSNSSFKIILRQNMEAFRKYNQKNPDQFNPVERAIIEGFPAAGDAHFSAFMLRIAGRS
SFHRLVTDPISRALYSTDGDDFQFRENLMAEGLSQQAALLALAKRKFPQEMETLSQWQSQTRH

  Protein domains


Predicted by InterproScan.

Family of unknown function (DUF5934) (DUF5934)

(319-471)

TraG P-loop domain (P-loop_TraG)

(505-795)

TraC protein (TraC_F_IV)

(64-276)

  Protein structure



No available structure.



ID   5634 GenBank   WP_282563892
Name   traD_LDO74_RS20785_2019-04-29292-1-3|4 insolico UniProt ID   _
Length   742 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 742 a.a.        Molecular weight: 84918.85 Da        Isoelectric Point: 5.1648

>WP_282563892.1 type IV conjugative transfer system coupling protein TraD [Providencia alcalifaciens]
MSSTKHITQGGQVFSYMLGMFMQVNKRISFWLILLFLMIFPIIFYFKVPLQEIKNGGLYWWLYLTAGGEK
ALYRVAPIYEVDFDGQLYRFTSDAILKDDYMIYAGNIVLQELGLSLLWACIIVIVLFFVIYRVFHGLGKR
QANDDVIGGRTLTEDIKHVRNMLHARREASPITFDGLPLKLNSEVQNMLMHGTPGSGKSNTINKLLIQLR
KRGDMVIVFDKGCSLVKRHYNENIDKLLNPLDERCENWDLWGECLTTPDFDSVANTLIPQSTSEDPFWTG
SARTIFTTVAAKLGSDDQRSYNKLLRTLLAIDLKSLRAYVEKTEASNLMEEKVEKTAISIRGVLTNYVKA
LRYLQGIERNGKAPFAIREWMKSVNEPKQRQGWLWITSNARQHESLKPLISMWLAQAANCLLEMGENPER
RVWFIYDELASLHKLPELPQVLSEARKFGGCFILGFQNKPQLDYTYGHDYANAMMDLLNTRFFFRSPDES
VAKWVRDQLGQTRKKVASEQYSFGPETVRDGVSFSKQQEDVDLVNYSDVQSLPDLDCYITLPGQYPVVKI
SMRYEKIKPIAAEFTPRPINDSLDQEIEAEIKSRMQDDALPAVMNQIIDNLISGKPIETPVDTAQNNTAL
EVTQTQPQSTVELTSQSVTQNSTPITTETAASDNPPENQGGQEVIIDNVKVNTETGEILGRVIDEEQNPQ
DLYDSYTRMRQDEKEIFNRPKPSQEKPKHINDDHDEPEMWWC

  Protein domains


Predicted by InterproScan.

F sex factor protein N terminal (TraD_N)

(32-128)

Type IV secretion-system coupling protein DNA-binding domain (TrwB_AAD_bind)

(172-562)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 17049..47612

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
LDO74_RS20575 (NVI2019_OGMBKCAO_04136) 13211..13501 + 291 WP_224051205 hypothetical protein -
LDO74_RS20580 (NVI2019_OGMBKCAO_04137) 13565..15565 + 2001 WP_224051204 ParB/RepB/Spo0J family partition protein -
LDO74_RS20585 (NVI2019_OGMBKCAO_04138) 15607..16290 + 684 WP_224051203 plasmid SOS inhibition protein A -
LDO74_RS20590 (NVI2019_OGMBKCAO_04140) 16512..16943 + 432 WP_263422653 LPD29 domain-containing protein -
LDO74_RS20595 (NVI2019_OGMBKCAO_04141) 17049..17501 - 453 WP_224051202 transglycosylase SLT domain-containing protein virB1
LDO74_RS20600 (NVI2019_OGMBKCAO_04142) 17976..18350 + 375 WP_036965543 relaxosome protein TraM -
LDO74_RS20605 (NVI2019_OGMBKCAO_04143) 18359..18676 + 318 WP_036965545 hypothetical protein -
LDO74_RS20610 (NVI2019_OGMBKCAO_04144) 18814..19533 + 720 WP_036965547 hypothetical protein -
LDO74_RS20615 (NVI2019_OGMBKCAO_04145) 19574..19765 + 192 WP_036965549 TraY domain-containing protein -
LDO74_RS20620 (NVI2019_OGMBKCAO_04146) 20039..20407 + 369 WP_036965551 type IV conjugative transfer system pilin TraA -
LDO74_RS20625 (NVI2019_OGMBKCAO_04147) 20426..20731 + 306 WP_071548954 type IV conjugative transfer system protein TraL traL
LDO74_RS20630 (NVI2019_OGMBKCAO_04148) 20745..21314 + 570 WP_036965554 type IV conjugative transfer system protein TraE traE
LDO74_RS20635 (NVI2019_OGMBKCAO_04149) 21298..22071 + 774 WP_036965555 type-F conjugative transfer system secretin TraK traK
LDO74_RS20640 (NVI2019_OGMBKCAO_04150) 22058..23419 + 1362 WP_224051200 TrbI/VirB10 family protein traB
LDO74_RS21770 (NVI2019_OGMBKCAO_04151) 23489..23683 + 195 WP_036965558 hypothetical protein -
LDO74_RS20650 (NVI2019_OGMBKCAO_04152) 23690..24181 + 492 WP_036965560 transcription/translation regulatory transformer protein RfaH -
LDO74_RS20655 (NVI2019_OGMBKCAO_04153) 24202..24540 + 339 WP_036965562 hypothetical protein -
LDO74_RS20660 (NVI2019_OGMBKCAO_04154) 24542..24898 + 357 WP_036965564 hypothetical protein -
LDO74_RS20665 (NVI2019_OGMBKCAO_04155) 24907..25182 + 276 WP_036965565 hypothetical protein -
LDO74_RS20670 (NVI2019_OGMBKCAO_04156) 25209..25505 + 297 WP_036965567 hypothetical protein -
LDO74_RS20675 (NVI2019_OGMBKCAO_04157) 25598..25999 + 402 WP_036965569 hypothetical protein -
LDO74_RS21775 (NVI2019_OGMBKCAO_04158) 26084..26401 + 318 WP_224051199 hypothetical protein -
LDO74_RS20685 (NVI2019_OGMBKCAO_04159) 26372..27250 - 879 WP_070929355 hypothetical protein -
LDO74_RS20690 (NVI2019_OGMBKCAO_04160) 27297..27860 + 564 WP_224051198 type IV conjugative transfer system lipoprotein TraV traV
LDO74_RS20695 (NVI2019_OGMBKCAO_04161) 27862..30573 + 2712 WP_224051197 type IV secretion system protein TraC virb4
LDO74_RS20700 (NVI2019_OGMBKCAO_04162) 30549..30974 + 426 WP_224051196 type-F conjugative transfer system protein TrbI -
LDO74_RS20705 (NVI2019_OGMBKCAO_04163) 30984..31616 + 633 WP_224051195 type-F conjugative transfer system protein TraW -
LDO74_RS20710 (NVI2019_OGMBKCAO_04164) 31613..32608 + 996 WP_036965577 conjugal transfer pilus assembly protein TraU traU
LDO74_RS20715 (NVI2019_OGMBKCAO_04165) 32624..33241 + 618 WP_224051194 type-F conjugative transfer system pilin assembly protein TrbC trbC
LDO74_RS20720 (NVI2019_OGMBKCAO_04166) 33241..35085 + 1845 WP_224051193 conjugal transfer protein TraN -
LDO74_RS20725 (NVI2019_OGMBKCAO_04167) 35082..35870 + 789 WP_224051192 type-F conjugative transfer system pilin assembly protein TraF -
LDO74_RS20730 (NVI2019_OGMBKCAO_04168) 35885..36277 + 393 WP_036965583 hypothetical protein -
LDO74_RS20735 (NVI2019_OGMBKCAO_04169) 36265..37200 - 936 WP_036965584 hypothetical protein -
LDO74_RS20740 (NVI2019_OGMBKCAO_04170) 37359..37658 + 300 WP_036965586 hypothetical protein -
LDO74_RS20745 (NVI2019_OGMBKCAO_04171) 37664..38188 + 525 WP_071992030 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
LDO74_RS21780 (NVI2019_OGMBKCAO_04172) 38200..38628 + 429 WP_036965590 hypothetical protein -
LDO74_RS20755 (NVI2019_OGMBKCAO_04173) 38625..39020 + 396 WP_224051220 hypothetical protein -
LDO74_RS20760 (NVI2019_OGMBKCAO_04174) 39217..40593 + 1377 WP_036965592 conjugal transfer pilus assembly protein TraH traH
LDO74_RS20765 (NVI2019_OGMBKCAO_04175) 40606..43494 + 2889 WP_051473561 conjugal transfer mating-pair stabilization protein TraG traG
LDO74_RS20770 (NVI2019_OGMBKCAO_04176) 43673..44401 + 729 WP_036965594 complement resistance protein TraT -
LDO74_RS20775 (NVI2019_OGMBKCAO_04177) 44522..44728 + 207 WP_036965596 TraR/DksA C4-type zinc finger protein -
LDO74_RS20780 (NVI2019_OGMBKCAO_04178) 44783..45172 + 390 WP_155251352 hypothetical protein -
LDO74_RS20785 (NVI2019_OGMBKCAO_04179) 45384..47606 + 2223 WP_224051219 type IV conjugative transfer system coupling protein TraD -

Host bacterium

ID   8408 GenBank   NZ_OU659165
Plasmid name   2019-04-29292-1-3|4 Incompatibility group   -
Plasmid size   57474 bp Coordinate of oriT [Strand]   17632..17666 [-]
Host baterium   Providencia alcalifaciens strain 2019-04-29292-1-3 isolate 2019-04-29292-1-3

Cargo genes

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