Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   107965
Name   oriT_2019-04-29034-1-3|4 in_silico
Organism   Providencia alcalifaciens strain 2019-04-29034-1-3 isolate 2019-04-29034-1-3
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_OU659128 (47856..47890 [+], 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_2019-04-29034-1-3|4
AAATTCTTGCAAAATGAAATTTTGCGTAGTGTGTG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   5343 GenBank   WP_224051218
Name   traI_LDO30_RS20550_2019-04-29034-1-3|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   5623 GenBank   WP_282563892
Name   traD_LDO30_RS20555_2019-04-29034-1-3|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.



ID   5624 GenBank   WP_224051197
Name   traC_LDO30_RS20645_2019-04-29034-1-3|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.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 17910..48473

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
LDO30_RS20555 (NVI2019_ANGEOOBF_04135) 17916..20138 - 2223 WP_224051219 type IV conjugative transfer system coupling protein TraD -
LDO30_RS20560 (NVI2019_ANGEOOBF_04136) 20350..20739 - 390 WP_155251352 hypothetical protein -
LDO30_RS20565 (NVI2019_ANGEOOBF_04137) 20794..21000 - 207 WP_036965596 TraR/DksA C4-type zinc finger protein -
LDO30_RS20570 (NVI2019_ANGEOOBF_04138) 21121..21849 - 729 WP_036965594 complement resistance protein TraT -
LDO30_RS20575 (NVI2019_ANGEOOBF_04139) 22028..24916 - 2889 WP_051473561 conjugal transfer mating-pair stabilization protein TraG traG
LDO30_RS20580 (NVI2019_ANGEOOBF_04140) 24929..26305 - 1377 WP_036965592 conjugal transfer pilus assembly protein TraH traH
LDO30_RS20585 (NVI2019_ANGEOOBF_04141) 26502..26897 - 396 WP_224051220 hypothetical protein -
LDO30_RS21710 (NVI2019_ANGEOOBF_04142) 26894..27322 - 429 WP_036965590 hypothetical protein -
LDO30_RS20595 (NVI2019_ANGEOOBF_04143) 27334..27858 - 525 WP_071992030 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
LDO30_RS20600 (NVI2019_ANGEOOBF_04144) 27864..28163 - 300 WP_036965586 hypothetical protein -
LDO30_RS20605 (NVI2019_ANGEOOBF_04145) 28322..29257 + 936 WP_036965584 hypothetical protein -
LDO30_RS20610 (NVI2019_ANGEOOBF_04146) 29245..29637 - 393 WP_036965583 hypothetical protein -
LDO30_RS20615 (NVI2019_ANGEOOBF_04147) 29652..30440 - 789 WP_224051192 type-F conjugative transfer system pilin assembly protein TraF -
LDO30_RS20620 (NVI2019_ANGEOOBF_04148) 30437..32281 - 1845 WP_224051193 conjugal transfer protein TraN -
LDO30_RS20625 (NVI2019_ANGEOOBF_04149) 32281..32898 - 618 WP_224051194 type-F conjugative transfer system pilin assembly protein TrbC trbC
LDO30_RS20630 (NVI2019_ANGEOOBF_04150) 32914..33909 - 996 WP_036965577 conjugal transfer pilus assembly protein TraU traU
LDO30_RS20635 (NVI2019_ANGEOOBF_04151) 33906..34538 - 633 WP_224051195 type-F conjugative transfer system protein TraW -
LDO30_RS20640 (NVI2019_ANGEOOBF_04152) 34548..34973 - 426 WP_224051196 type-F conjugative transfer system protein TrbI -
LDO30_RS20645 (NVI2019_ANGEOOBF_04153) 34949..37660 - 2712 WP_224051197 type IV secretion system protein TraC virb4
LDO30_RS20650 (NVI2019_ANGEOOBF_04154) 37662..38225 - 564 WP_224051198 type IV conjugative transfer system lipoprotein TraV traV
LDO30_RS20655 (NVI2019_ANGEOOBF_04155) 38272..39150 + 879 WP_070929355 hypothetical protein -
LDO30_RS21715 (NVI2019_ANGEOOBF_04156) 39121..39438 - 318 WP_224051199 hypothetical protein -
LDO30_RS20665 (NVI2019_ANGEOOBF_04157) 39523..39924 - 402 WP_036965569 hypothetical protein -
LDO30_RS20670 (NVI2019_ANGEOOBF_04158) 40017..40313 - 297 WP_036965567 hypothetical protein -
LDO30_RS20675 (NVI2019_ANGEOOBF_04159) 40340..40615 - 276 WP_036965565 hypothetical protein -
LDO30_RS20680 (NVI2019_ANGEOOBF_04160) 40624..40980 - 357 WP_036965564 hypothetical protein -
LDO30_RS20685 (NVI2019_ANGEOOBF_04161) 40982..41320 - 339 WP_036965562 hypothetical protein -
LDO30_RS20690 (NVI2019_ANGEOOBF_04162) 41341..41832 - 492 WP_036965560 transcription/translation regulatory transformer protein RfaH -
LDO30_RS21720 (NVI2019_ANGEOOBF_04163) 41839..42033 - 195 WP_036965558 hypothetical protein -
LDO30_RS20700 (NVI2019_ANGEOOBF_04164) 42103..43464 - 1362 WP_224051200 TrbI/VirB10 family protein traB
LDO30_RS20705 (NVI2019_ANGEOOBF_04165) 43451..44224 - 774 WP_036965555 type-F conjugative transfer system secretin TraK traK
LDO30_RS20710 (NVI2019_ANGEOOBF_04166) 44208..44777 - 570 WP_036965554 type IV conjugative transfer system protein TraE traE
LDO30_RS20715 (NVI2019_ANGEOOBF_04167) 44791..45099 - 309 WP_224051201 type IV conjugative transfer system protein TraL -
LDO30_RS20720 (NVI2019_ANGEOOBF_04168) 45115..45483 - 369 WP_036965551 type IV conjugative transfer system pilin TraA -
LDO30_RS20725 (NVI2019_ANGEOOBF_04169) 45757..45948 - 192 WP_036965549 TraY domain-containing protein -
LDO30_RS20730 (NVI2019_ANGEOOBF_04170) 45989..46708 - 720 WP_036965547 hypothetical protein -
LDO30_RS20735 (NVI2019_ANGEOOBF_04171) 46846..47163 - 318 WP_036965545 hypothetical protein -
LDO30_RS20740 (NVI2019_ANGEOOBF_04172) 47172..47546 - 375 WP_036965543 relaxosome protein TraM -
LDO30_RS20745 (NVI2019_ANGEOOBF_04173) 48027..48473 + 447 WP_336431892 transglycosylase SLT domain-containing protein -
LDO30_RS20750 (NVI2019_ANGEOOBF_04174) 48579..49031 - 453 WP_224051221 LPD29 domain-containing protein -
LDO30_RS20755 (NVI2019_ANGEOOBF_04176) 49232..49915 - 684 WP_224051203 plasmid SOS inhibition protein A -
LDO30_RS20760 (NVI2019_ANGEOOBF_04177) 49957..51957 - 2001 WP_224051204 ParB/RepB/Spo0J family partition protein -
LDO30_RS20765 (NVI2019_ANGEOOBF_04178) 52021..52311 - 291 WP_224051205 hypothetical protein -

Host bacterium

ID   8400 GenBank   NZ_OU659128
Plasmid name   2019-04-29034-1-3|4 Incompatibility group   -
Plasmid size   57474 bp Coordinate of oriT [Strand]   47856..47890 [+]
Host baterium   Providencia alcalifaciens strain 2019-04-29034-1-3 isolate 2019-04-29034-1-3

Cargo genes

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