Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   107961
Name   oriT_2019-04-27799-1-2|4 in_silico
Organism   Providencia alcalifaciens strain 2019-04-27799-1-2 isolate 2019-04-27799-1-2
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_OU659116 (38373..38407 [-], 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_2019-04-27799-1-2|4
AAATTCTTGCAAAATGAAATTTTGCGTAGTGTGTG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   5340 GenBank   WP_224051218
Name   traI_LDO34_RS20530_2019-04-27799-1-2|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   5617 GenBank   WP_282563892
Name   traD_LDO34_RS20525_2019-04-27799-1-2|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   5618 GenBank   WP_224051197
Name   traC_LDO34_RS20755_2019-04-27799-1-2|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: 37790..56051

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
LDO34_RS20635 (NVI2019_KOLGMIGM_04152) 33952..34242 + 291 WP_224051205 hypothetical protein -
LDO34_RS20640 (NVI2019_KOLGMIGM_04153) 34306..36306 + 2001 WP_224051204 ParB/RepB/Spo0J family partition protein -
LDO34_RS20645 (NVI2019_KOLGMIGM_04154) 36348..37031 + 684 WP_224051203 plasmid SOS inhibition protein A -
LDO34_RS20650 (NVI2019_KOLGMIGM_04156) 37232..37684 + 453 WP_224051221 LPD29 domain-containing protein -
LDO34_RS20655 (NVI2019_KOLGMIGM_04157) 37790..38236 - 447 WP_336431892 transglycosylase SLT domain-containing protein -
LDO34_RS20660 (NVI2019_KOLGMIGM_04158) 38717..39091 + 375 WP_036965543 relaxosome protein TraM -
LDO34_RS20665 (NVI2019_KOLGMIGM_04159) 39100..39417 + 318 WP_036965545 hypothetical protein -
LDO34_RS20670 (NVI2019_KOLGMIGM_04160) 39555..40274 + 720 WP_036965547 hypothetical protein -
LDO34_RS20675 (NVI2019_KOLGMIGM_04161) 40315..40506 + 192 WP_036965549 TraY domain-containing protein -
LDO34_RS20680 (NVI2019_KOLGMIGM_04162) 40780..41148 + 369 WP_036965551 type IV conjugative transfer system pilin TraA -
LDO34_RS20685 (NVI2019_KOLGMIGM_04163) 41167..41472 + 306 WP_071548954 type IV conjugative transfer system protein TraL traL
LDO34_RS20690 (NVI2019_KOLGMIGM_04164) 41486..42055 + 570 WP_036965554 type IV conjugative transfer system protein TraE traE
LDO34_RS20695 (NVI2019_KOLGMIGM_04165) 42039..42812 + 774 WP_036965555 type-F conjugative transfer system secretin TraK traK
LDO34_RS20700 (NVI2019_KOLGMIGM_04166) 42799..44160 + 1362 WP_224051200 TrbI/VirB10 family protein traB
LDO34_RS21705 (NVI2019_KOLGMIGM_04167) 44230..44424 + 195 WP_036965558 hypothetical protein -
LDO34_RS20710 (NVI2019_KOLGMIGM_04168) 44431..44922 + 492 WP_036965560 transcription/translation regulatory transformer protein RfaH -
LDO34_RS20715 (NVI2019_KOLGMIGM_04169) 44943..45281 + 339 WP_036965562 hypothetical protein -
LDO34_RS20720 (NVI2019_KOLGMIGM_04170) 45283..45639 + 357 WP_036965564 hypothetical protein -
LDO34_RS20725 (NVI2019_KOLGMIGM_04171) 45648..45923 + 276 WP_036965565 hypothetical protein -
LDO34_RS20730 (NVI2019_KOLGMIGM_04172) 45950..46246 + 297 WP_036965567 hypothetical protein -
LDO34_RS20735 (NVI2019_KOLGMIGM_04173) 46339..46740 + 402 WP_036965569 hypothetical protein -
LDO34_RS21710 (NVI2019_KOLGMIGM_04174) 46825..47142 + 318 WP_224051199 hypothetical protein -
LDO34_RS20745 (NVI2019_KOLGMIGM_04175) 47113..47991 - 879 WP_070929355 hypothetical protein -
LDO34_RS20750 (NVI2019_KOLGMIGM_04176) 48038..48601 + 564 WP_224051198 type IV conjugative transfer system lipoprotein TraV traV
LDO34_RS20755 (NVI2019_KOLGMIGM_04177) 48603..51314 + 2712 WP_224051197 type IV secretion system protein TraC virb4
LDO34_RS20760 (NVI2019_KOLGMIGM_04178) 51290..51715 + 426 WP_224051196 type-F conjugative transfer system protein TrbI -
LDO34_RS20765 (NVI2019_KOLGMIGM_04179) 51725..52357 + 633 WP_224051195 type-F conjugative transfer system protein TraW -
LDO34_RS20770 (NVI2019_KOLGMIGM_04180) 52354..53349 + 996 WP_036965577 conjugal transfer pilus assembly protein TraU traU
LDO34_RS20775 (NVI2019_KOLGMIGM_04181) 53365..53982 + 618 WP_224051194 type-F conjugative transfer system pilin assembly protein TrbC trbC
LDO34_RS20780 (NVI2019_KOLGMIGM_04182) 53982..55826 + 1845 WP_224051193 conjugal transfer protein TraN -
LDO34_RS20785 (NVI2019_KOLGMIGM_04183) 55823..56611 + 789 WP_224051192 type-F conjugative transfer system pilin assembly protein TraF -
LDO34_RS20790 (NVI2019_KOLGMIGM_04184) 56626..57018 + 393 WP_036965583 hypothetical protein -

Host bacterium

ID   8396 GenBank   NZ_OU659116
Plasmid name   2019-04-27799-1-2|4 Incompatibility group   -
Plasmid size   57474 bp Coordinate of oriT [Strand]   38373..38407 [-]
Host baterium   Providencia alcalifaciens strain 2019-04-27799-1-2 isolate 2019-04-27799-1-2

Cargo genes

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