Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   100110
Name   oriT_QKH54 in_silico
Organism   Uncultured bacterium IncP-1gamma
Sequence Completeness      core
NCBI accession of oriT (coordinates [strand])   AM157767 (68225..68314 [+], 90 nt)
oriT length   90 nt
IRs (inverted repeats)      1..19, 22..40  (GTGAAGATAGTTAACCGGC..GCCGGTTAGCTAACTTCAC)
Location of nic site      48..49
Conserved sequence flanking the
  nic site    		  TATCTTG|C
Note   _

  oriT sequence  


Download         Length: 90 nt

>oriT_QKH54
GTGAAGATAGTTAACCGGCTTGCCGGTTAGCTAACTTCACCTATCTTGCCCGGCTCTTCGAGCCGTTTAACGCCAGGTGAGTATCGCATA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file

  Reference


[1] Pachulec E et al. (2010) Conjugative Plasmids of Neisseria gonorrhoeae. PLoS One. 5(4):e9962. [PMID:20376355]
[2] Haines AS et al. (2006) Plasmids from freshwater environments capable of IncQ retrotransfer are diverse and include pQKH54, a new IncP-1 subgroup archetype. Microbiology. 152(Pt 9):2689-701. [PMID:16946264]


Relaxase

ID   105 GenBank   CAJ43356
Name   TraI_QKH54 insolico UniProt ID   Q1H9W9
Length   802 a.a. PDB ID   
Note   TraI DNA relaxase

  Relaxase protein sequence


Download         Length: 802 a.a.        Molecular weight: 87521.06 Da        Isoelectric Point: 10.7582

>CAJ43356.1 TraI DNA relaxase (plasmid) [uncultured bacterium]
MIAKRIPMNSAKKSSFAGLVKYITSSQGINERVGQVRVTNCQTEELSWAVHEVLHTQKINTRAEGDKTYH
LLISLAPGEQPSSEVLRDIEDRVCSAIGYQDHQRVSAVHNDTDCLHIHIAINKIHPERHTLHEPYRDFKT
LGDICARLELEHGLQQVNHARKKSVSEGRANDMEQHAGIESLITWVRRECLEQVQGAKNWTELHQVLHEN
GLELRERGNGLVITDQAGTMVKASTVARDLSKGKLEERLGAFENQQQQARASHNQGKPLPRKPGIGRVGR
RPPPASKNRLRGLSTLQAIQIDSGKRYEKSPVKHKSDTTELYARFRDEQNAVRHTKAKELAAARERRDRA
IEQAKNVAKLKRSSIKLMATPGLTKKLLYASTHKSLQEQITSLRAEHIKAIENINTLNKARQWADWLQAK
ALDGDQDALKALRARQGVKGLQGDAVAAKGQQHSAKAVPIEQDHITKEGTVIYRAGTSAIRDDGSKLQLS
RGANFDGIETALRMAAARYGEKITITGSDQFKELVAQTAAIRSLPIKFDDPALEQRRQSLQQAIEKERNN
VGRTDRGRAAGSGAGVDGLHAARGGRGIGAGGTTGAGRGTGVRGSTAGTQLSGRAGTAASGRITVRAPGG
TPKPGVARVGRKPPPESQNRLRALSKLGVVQLTQGSEVLLPRDVPGVVEHQGAKPDNGLRRDVSRSGGIA
AEGKTISSAQAARQYVAEREDKRAKGFDIPKHRLYNQADDGPATFEGLRQVEGQSMALLKRGDELLVLPV
NEATARRMKRMKLGDPVTANATGAIKSKGRSR

  Protein domains


Predicted by InterproScan.

Relaxase/Mobilisation nuclease domain (Relaxase)

(12-250)

Large polyvalent protein-associated domain 7 (LPD7)

(462-550)


  Protein structure


Source ID Structure
AlphaFold DB Q1H9W9

  Reference


[1] Pachulec E et al. (2010) Conjugative Plasmids of Neisseria gonorrhoeae. PLoS One. 5(4):e9962. [PMID:20376355]
[2] Haines AS et al. (2006) Plasmids from freshwater environments capable of IncQ retrotransfer are diverse and include pQKH54, a new IncP-1 subgroup archetype. Microbiology. 152(Pt 9):2689-701. [PMID:16946264]


Auxiliary protein

ID   157 GenBank   CAJ43359
Name   TraJ_QKH54 insolico UniProt ID   Q1H9W6
Length   118 a.a. PDB ID   _
Note   TraJ oriT-binding protein

  Auxiliary protein sequence


Download         Length: 118 a.a.        Molecular weight: 13116.33 Da        Isoelectric Point: 9.8934

>CAJ43359.1 TraJ oriT-binding protein (plasmid) [uncultured bacterium]
MDEKKITRKDTHLRVPVLPEEKAKIEESARAAGKSVAAYMRAVGLGYELQSVIDSRLVLELAKVNADQGR
LGGLLKMWLVSDKRLAGIEEEQLHRTIRVVLDRIGETQAALLELAKKA

  Protein domains



No domain identified.



  Protein structure


Source ID Structure
AlphaFold DB Q1H9W6

  Reference


[1] Pachulec E et al. (2010) Conjugative Plasmids of Neisseria gonorrhoeae. PLoS One. 5(4):e9962. [PMID:20376355]
[2] Haines AS et al. (2006) Plasmids from freshwater environments capable of IncQ retrotransfer are diverse and include pQKH54, a new IncP-1 subgroup archetype. Microbiology. 152(Pt 9):2689-701. [PMID:16946264]

ID   158 GenBank   CAJ43360
Name   TraK_QKH54 insolico UniProt ID   Q1H9W5
Length   142 a.a. PDB ID   _
Note   TraK oriT-binding protein

  Auxiliary protein sequence


Download         Length: 142 a.a.        Molecular weight: 15552.88 Da        Isoelectric Point: 10.7786

>CAJ43360.1 TraK oriT-binding protein (plasmid) [uncultured bacterium]
MAKNGKSLSERIAERAQKKKQPGRAGKNRAAFLAVRDEVRQALDDGWPVKDVWETLYAEGAIAFRYDAFI
GYVKKLIRQPPTVATSIPVVQEAPARPATPAKTPTAKPKPTPKPATRDPVVTKPSTPGSFSFDSTPRKED
LL

  Protein domains


Predicted by InterproScan.

Family of unknown function (DUF5338) (DUF5338)

(6-75)


  Protein structure


Source ID Structure
AlphaFold DB Q1H9W5

  Reference


[1] Pachulec E et al. (2010) Conjugative Plasmids of Neisseria gonorrhoeae. PLoS One. 5(4):e9962. [PMID:20376355]
[2] Haines AS et al. (2006) Plasmids from freshwater environments capable of IncQ retrotransfer are diverse and include pQKH54, a new IncP-1 subgroup archetype. Microbiology. 152(Pt 9):2689-701. [PMID:16946264]

ID   159 GenBank   CAJ43357
Name   TraH_QKH54 insolico UniProt ID   Q1H9W8
Length   139 a.a. PDB ID   _
Note   TraH relaxosome stabilising protein

  Auxiliary protein sequence


Download         Length: 139 a.a.        Molecular weight: 15447.10 Da        Isoelectric Point: 3.6758

>CAJ43357.1 TraH relaxosome stabilising protein (plasmid) [uncultured bacterium]
MSEELTEDELLAQALASMDSTPPGGDEESGPEEPPEPGEVLEFGEAPPEPSFLDELEQPPVDESPFAPLE
EPQSLVLQELDESRRPKARTVCERCPNSVWFSSPKEVKCYCRVMFLVSWSTKEPNQITGCDGMFLGQEE

  Protein domains



No domain identified.



  Protein structure


Source ID Structure
AlphaFold DB Q1H9W8

  Reference


[1] Pachulec E et al. (2010) Conjugative Plasmids of Neisseria gonorrhoeae. PLoS One. 5(4):e9962. [PMID:20376355]
[2] Haines AS et al. (2006) Plasmids from freshwater environments capable of IncQ retrotransfer are diverse and include pQKH54, a new IncP-1 subgroup archetype. Microbiology. 152(Pt 9):2689-701. [PMID:16946264]


T4CP

ID   105 GenBank   CAJ43355
Name   TraG_QKH54 insolico UniProt ID   Q1H9X0
Length   638 a.a. PDB ID   _
Note   TraG coupling protein

  T4CP protein sequence


Download         Length: 638 a.a.        Molecular weight: 70160.41 Da        Isoelectric Point: 8.9574

>CAJ43355.1 TraG coupling protein (plasmid) [uncultured bacterium]
MISKDKFNNAVGPQVRAKKPGVGKVIPALSLLSIGVGLAAATQYFAYDFKYQDVLGPHVNHIYAPWSILT
WASKWYGTYPEAVMRAGSIGVLASGVGLLALAITKMIQANSSKANEYLHGSARWANKKDIQAAGLLQRGR
TALEVVTSKSPPTHTGVYVGAWLDENGVQHYLRHNGPEHILTYAPTRSGKGVGLVIPTLLSWPASTVVTD
LKGELWALTSGWRQKHANNKVLRFEPATSNGGVRWNPLDEIRIGTENEVGDVQNLATLIVDPDGKGLESH
WQKTSQALLVGLIMHVLYKSKIEGTLATLPEVDRILADPDRDLGELWMEMTTYGHVNGKNHPVVGSSARD
MMDRPEEEAGSVLSTAKSYLSLYRDPIVARNVSASEFKVKDLMNHDNPVSLYIVTQPNDKARLRPLVRVL
INMIIRLLADKMDFENGRPVAHYNHRLLAMLDEFPSLGKLEILQESLAFVAGYGIKCYLICQDINQLKSR
ETGYGPDETITSNCHVQNAYPPNRVETAEHLSKLTGQTTVVKEQITTSGRRTSALLGQVSRTMQEVQRPL
LTPDECLRMPGPVKSAAGDITQAGDMVVYMAGYPAIYGKQPLYFKDPVFQARASIPAPKASDKLRFVQDH
SQAEAITI

  Protein domains


Predicted by InterproScan.

Type IV secretory system Conjugative DNA transfer (T4SS-DNA_transf)

(123-620)

  Protein structure


Source ID Structure
AlphaFold DB Q1H9X0

  Reference


[1] Haines AS et al. (2006) Plasmids from freshwater environments capable of IncQ retrotransfer are diverse and include pQKH54, a new IncP-1 subgroup archetype. Microbiology. 152(Pt 9):2689-701. [PMID:16946264]


T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 25373..35954

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
Locus_24 20439..21335 - 897 CAJ43305 putative alpha-ketoglutarate-dependent taurine dioxygenase -
Locus_25 21459..22487 + 1029 CAJ43306 putative regulator -
Locus_26 23120..24241 - 1122 CAJ43307 trans-acting replication factor A -
Locus_27 24282..24641 - 360 CAJ43308 single-stranded DNA binding protein -
Locus_28 24803..25120 + 318 CAJ43309 TrbA repressor protein -
Locus_29 25373..26344 + 972 CAJ43310 TrbB mating pair formation protein virB11
Locus_30 26364..26771 + 408 CAJ43311 TrbC prepillin virB2
Locus_31 26774..27085 + 312 CAJ43312 TrbD mating pair formation protein virB3
Locus_32 27082..29640 + 2559 CAJ43313 TrbE mating pair formation protein virb4
Locus_33 29637..30356 + 720 CAJ43314 TrbF mating pair formation protein virB8
Locus_34 30368..31258 + 891 CAJ43315 TrbG mating pair formation protein virB9
Locus_35 31262..31729 + 468 CAJ43316 TrbH mating pair formation protein -
Locus_36 31736..33154 + 1419 CAJ43317 TrbI mating pair formation protein virB10
Locus_37 33177..33962 + 786 CAJ43318 TrbJ mating pair formation protein virB5
Locus_38 33974..34210 + 237 CAJ43319 TrbK -
Locus_39 34218..35954 + 1737 CAJ43320 putative topoisomerase virB6
Locus_40 35967..36287 + 321 CAJ43321 hypothetical protein -
Locus_41 36297..36929 + 633 CAJ43322 putative muramidase -
Locus_42 36929..37399 + 471 CAJ43323 hypothetical protein -
Locus_43 37403..38140 + 738 CAJ43324 TrbP mating pair formation protein -
Locus_44 38150..38395 + 246 CAJ43325 hypothetical protein -
Locus_45 38413..39075 + 663 CAJ43326 hypothetical protein -
Locus_46 39086..39412 + 327 CAJ43327 hypothetical protein -
Locus_47 39435..39704 + 270 CAJ43328 hypothetical protein -
Locus_48 39804..40832 + 1029 CAJ43329 transposase -

Host bacterium

ID   105 GenBank   AM157767
Plasmid name   QKH54 Incompatibility group   IncP1
Plasmid size   69966 bp Coordinate of oriT [Strand]   68225..68314 [+]
Host baterium   Uncultured bacterium IncP-1gamma

Cargo genes

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