Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   100030
Name   oriT_p1658/97 in_silico
Organism   Escherichia coli
Sequence Completeness      intact
NCBI accession of oriT (coordinates [strand])   NC_004998 (2103..2392 [-], 290 nt)
oriT length   290 nt
IRs (inverted repeats)      225..232, 235..242  (GCAAAAAC..GTTTTTGC)
Location of nic site      251..252
Conserved sequence flanking the
  nic site    		  GTGGGGTGT|GG
Note   _

  oriT sequence  


Download         Length: 290 nt

>oriT_p1658/97
CGCACCGCTAGCAGCGCCCCTAGCGGTATCCTATAAAAAAACACACCGCGCCGCTAGCAGCACCCCTAATATAAAATAATGTTTTTTATAAAAATAGTCAGTACCACCCCTACAAAACGGTGTCGGCGCGTTGTTGTAGCCGCGCCGACACCGCTTTTTTAAATATCATAAAGAGAGTAAGAGAAACTAATTTTTCATAACACTCTATTTATAAAGAAAAATCAGCAAAAACTTGTTTTTGCGTGGGGTGTGGTGCTTTTGGTGGTGAGAACCACCAACCTGTTGAGCCT

Visualization of oriT structure



Relaxase

ID   29 GenBank   NP_862951
Name   TraI_p1658/97 insolico UniProt ID   Q84A21
Length   1756 a.a. PDB ID   
Note   conjugal transfer nickase/helicase TraI

  Relaxase protein sequence


Download         Length: 1756 a.a.        Molecular weight: 192202.14 Da        Isoelectric Point: 5.9371

>NP_862951.1 conjugal transfer nickase/helicase TraI (plasmid) [Escherichia coli]
MMSIAQVRSAGSAGNYYTDKDNYYVLGSMGERWAGRGAEQLGLQGSVDKDVFTRLLEGRLPDGADLSRMQ
DGSNRHRPGYDLTFSAPKSVSMMAMLGGDKRLIDAHNQAVDFAVRQVEALASTRVMTDGQSETVLTGNLV
MALFNHDTSRDQEPQLHTHAVVANVTQHNGEWKTLSSDKVGKTGFIENVYANQIAFGRLYREKLKEQVEA
LGYETEVVGKHGMWEMPGVPVEAFSGRSQTIREAVGEDASLKSRDVAALDTRKSKQHVDPEIKMVEWMQT
LKETGFDIRAYRDAADQRADLRTLTPGPASQDGPDVQQAVTQAIAGLSERKVQFTYTDVLARTVGILPPE
NGVIERARAGIDEAISREQLIPLDREKGLFTSGIHVLDELSVRALSRDIMKQNRVTVHPEKSVPRTAGYS
DAVSVLAQDRPSLAIVSGQGGAAGQRERVAELVMMAREQGREVQIIAADRRSQMNMKQDERLSGELITGR
RQLLEGMTFTPGSTVIVDQGEKLSLKETLTLLDGAARHNVQVLIIDSGQRTGTGSALMAMKDAGVNTYRW
QGGEQRPATIISEPDRNVRYARLAGDFAVSVKAGEESVAQVSGVREQAMLTQTIRSELKTQGVLGHPEVT
MTALSPVWLDSRSRYLRDMYRPGMVMEQWNPETRSHDRYVIDRVTAQSHSLTLRDAQGETQVVRISSLDS
SWSLFRPEKMPVADGERLRVTGKIPGLRVSGGDRLQVSSVSEDAMTVVVPGRAEPATLPVSDSPFTALKL
ENGWVETPGHSVSDSATVFASVTQMAMDNATLNGLARSGRDVRLYSSLDETRTAEKLARHPSFTVVSEQI
KTRAGETSLETAISHQKSALHTPAQQAIHLALPVVESKKLAFSMVDLLTEAKSFAAEGTGFTELGGEINA
QIKRGDLLYVDVAKGYGTGLLVSRASYEAEKSILRHILEGKEAVMPLMERVPGELMEKLTSGQRAATRMI
LETSDRFTVVQGYAGVGKTTQFRAVMSAVNMLPESERPRVVGLGPTHRAVGEMRSAGVDAQTLASFLHDT
QLQQRSGETPDFSNTLFLLDESSMVGNTDMARAYALIAAGGGRAVASGDTDQLQAIAPGQPFRLQQTRSA
ADVAIMKEIVRQTPELREAVYSLINRDVERALSGLESVKPSQVPRQEGAWAPEHSVTEFSHSQEAKLAEA
QQKAMLKGEAFPDVPMTLYEAIVRDYTGRTPEAREQTLIVTHLNEDRRVLNSMIHDVREKAGELGKEQVM
VPVLNTANIRDGELRRLSTWETHRDALVLVDNVYHRIAGISKDDGLITLQDAEGNTRLISPREAVAEGVT
LYTPDTIRVGTGDRMRFTKSDRERGYVANSVWTVTAVSGDSVTLSDGQQTREIRPGQEQAEQHIDLAYAI
TAHGAQGASETFAIALEGTEGNRKLMAGFESAYVALSRMKQHVQVYTDNRQGWTDAINNAVQKGTAHDVF
EPKPDREVMNAERLFSTARELRDVAAGRAVLRQAGLAGGDSPARFIAPGRKYPQPYVALPAFDRNGKSAG
IWLNPLTTDDGNGLRGFSGEGRVKGSGDAQFVALQGSRNGESLLADNMQDGVRIARDNPDSGVVVRIAGE
GRPWNPGAITGGRVWGDIPDNSVQPGAGNGEPVTAEVLAQRQAEEAIRRETERRADEIVRKMAENKPDLP
DGKTEQAVREIAGQERDRAAITEREAALPEGVLREPQRVREAVREIARENLLQERLQQMERDMVRDLQKE
KTLGGD

  Protein domains


Predicted by InterproScan.

TrwC relaxase (TrwC)

(10-283)

AAA domain (AAA_30)

(969-1156)

DNA helicase TraI (TraI_C)

(1434-1557)

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

(633-712)

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

(575-626)


  Protein structure



No available structure.



  Reference


[1] Zienkiewicz M et al. (2007) Mosaic structure of p1658/97, a 125-kilobase plasmid harboring an active amplicon with the extended-spectrum beta-lactamase gene blaSHV-5. Antimicrob Agents Chemother . 51(4):1164-71. [PMID:17220406]


Auxiliary protein

ID   44 GenBank   NP_862916
Name   TraM_p1658/97 insolico UniProt ID   Q84A34
Length   127 a.a. PDB ID   _
Note   conjugal transfer protein TraM

  Auxiliary protein sequence


Download         Length: 127 a.a.        Molecular weight: 14517.48 Da        Isoelectric Point: 5.0516

>NP_862916.1 conjugal transfer protein TraM (plasmid) [Escherichia coli]
MAKVNLYISNDAYEKINAIIEKRRQEGAREKDVSFSATASMLLELGLRVHEAQMERKESAFNQTEFNKLL
LECVVKTQSSVAKILGIESLSPHVSGNPKFEYANMVEDIREKVSSEMERFFPKNDDE

  Protein domains


Predicted by InterproScan.

TraM protein, DNA-binding (Tra_M)

(1-126)


  Protein structure


Source ID Structure
AlphaFold DB Q84A34

  Reference


[1] Zienkiewicz M et al. (2007) Mosaic structure of p1658/97, a 125-kilobase plasmid harboring an active amplicon with the extended-spectrum beta-lactamase gene blaSHV-5. Antimicrob Agents Chemother . 51(4):1164-71. [PMID:17220406]

ID   45 GenBank   NP_862918
Name   TraY_p1658/97 insolico UniProt ID   Q7B3W9
Length   131 a.a. PDB ID   _
Note   conjugal transfer protein TraY

  Auxiliary protein sequence


Download         Length: 131 a.a.        Molecular weight: 15183.38 Da        Isoelectric Point: 9.9240

>NP_862918.1 conjugal transfer protein TraY (plasmid) [Escherichia coli]
MKRFGTRSATGKMVKLKLPVDVESLLIEASNRSGRSRSFEAVIRLKDHLHRYPKFNRAGNIYGKSLVKYL
TMRLDDETNQLLIAAKNRSGWCKTDEAADRVIDHLIKFPDFYNSEIFREADKEEDITFNTL

  Protein domains


Predicted by InterproScan.

TraY domain (TraY)

(70-117)

TraY domain (TraY)

(16-59)


  Protein structure


Source ID Structure
AlphaFold DB Q7B3W9

  Reference


[1] Zienkiewicz M et al. (2007) Mosaic structure of p1658/97, a 125-kilobase plasmid harboring an active amplicon with the extended-spectrum beta-lactamase gene blaSHV-5. Antimicrob Agents Chemother . 51(4):1164-71. [PMID:17220406]


T4CP

ID   29 GenBank   NP_862947
Name   TraD_p1658/97 insolico UniProt ID   P09130
Length   717 a.a. PDB ID   3D8A
Note   Type IV Secretion System Coupling Protein

  T4CP protein sequence


Download         Length: 717 a.a.        Molecular weight: 81488.99 Da        Isoelectric Point: 5.0504

>NP_862947.1 conjugal transfer protein TraD (plasmid) [Escherichia coli]
MSFNAKDMTQGGQIASMRIRMFSQIANIMLYCLFIFFWILVGLVLWIKISWQTFVNGCIYWWCTTLEGMR
DLIKSQPVYEIQYYGKTFRMNAAQVLHDKYMIWCSEQLWSAFVLAAVVALVICLITFFVVSWILGRQGKQ
QSENEVTGGRQLTDNPKDVARMLKKDGKDSDIRIGDLPIIRDSEIQNFCLHGTVGAGKSEVIRRLANYAR
QRGDMVVIYDRSGEFVKSYYDPSIDKILNPLDARCAAWDLWKECLTQPDFDNTANTLIPMGTKEDPFWQG
SGRTIFAEAAYLMRNDPNRSYSKLVDTLLSIKIEKLRTYLRNSPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEHNGEPFTIRDWMRGVREDQKNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WFFCDELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGEKAAASLFDVMNTRAFFRSPSHKIA
EFAAGEIGEKEHLKASEQYSYGADPVRDGVSTGKDMERQTLVSYSDIQSLPDLTCYVTLPGPYPAVKLSL
KYQTRPKVAPEFIPRDINPEMENRLSAVLAAREAEGRQMASLFEPDVPEVVSGEDVTQAEQPQQPVSPAI
NDKKSDSGVNVPAGGIEQELKMKPEEEMEQQLPPGISESGEVVDMAAYEAWQQENHPDIQQQMQRREEVN
INVHRERGEDVEPGDDF

  Protein domains


Predicted by InterproScan.

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

(173-560)

F sex factor protein N terminal (TraD_N)

(32-128)

  Protein structure


Source ID Structure
PDB 3D8A
AlphaFold DB P09130

  Reference


[1] Zienkiewicz M et al. (2007) Mosaic structure of p1658/97, a 125-kilobase plasmid harboring an active amplicon with the extended-spectrum beta-lactamase gene blaSHV-5. Antimicrob Agents Chemother . 51(4):1164-71. [PMID:17220406]


T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 1541..27943

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HKK51_RS00005 (p165897_001) 14..301 + 288 WP_000107535 hypothetical protein -
HKK51_RS00010 (p165897_002) 423..1244 + 822 WP_001234469 DUF932 domain-containing protein -
HKK51_RS00015 (p165897_003) 1541..2143 - 603 WP_000243709 transglycosylase SLT domain-containing protein virB1
HKK51_RS00020 (p165897_004) 2464..2847 + 384 WP_001151524 conjugal transfer relaxosome DNA-binding protein TraM -
HKK51_RS00025 (p165897_005) 3034..3723 + 690 WP_000283385 conjugal transfer transcriptional regulator TraJ -
HKK51_RS00030 (p165897_006) 3816..4217 + 402 WP_001369361 conjugal transfer relaxosome DNA-bindin protein TraY -
HKK51_RS00035 (p165897_007) 4250..4615 + 366 WP_000994779 type IV conjugative transfer system pilin TraA -
HKK51_RS00040 (p165897_008) 4630..4941 + 312 WP_000012106 type IV conjugative transfer system protein TraL traL
HKK51_RS00045 (p165897_009) 4963..5529 + 567 WP_000399792 type IV conjugative transfer system protein TraE traE
HKK51_RS00050 (p165897_010) 5516..6244 + 729 WP_001230787 type-F conjugative transfer system secretin TraK traK
HKK51_RS00055 (p165897_011) 6244..7671 + 1428 WP_011117353 F-type conjugal transfer pilus assembly protein TraB traB
HKK51_RS00060 (p165897_012) 7661..8251 + 591 WP_000002792 conjugal transfer pilus-stabilizing protein TraP -
HKK51_RS00065 (p165897_013) 8244..8435 + 192 WP_032072783 conjugal transfer protein TrbD -
HKK51_RS00070 (p165897_014) 8447..8698 + 252 WP_001038342 conjugal transfer protein TrbG -
HKK51_RS00075 (p165897_015) 8695..9210 + 516 WP_000809841 type IV conjugative transfer system lipoprotein TraV traV
HKK51_RS00080 (p165897_016) 9345..9566 + 222 WP_001278689 conjugal transfer protein TraR -
HKK51_RS00085 (p165897_017) 9726..12353 + 2628 WP_001064247 type IV secretion system protein TraC virb4
HKK51_RS00090 (p165897_018) 12350..12736 + 387 WP_000097319 type-F conjugative transfer system protein TrbI -
HKK51_RS00095 (p165897_019) 12733..13365 + 633 WP_001203720 type-F conjugative transfer system protein TraW traW
HKK51_RS00100 (p165897_020) 13362..14354 + 993 WP_000830187 conjugal transfer pilus assembly protein TraU traU
HKK51_RS00105 (p165897_021) 14363..15001 + 639 WP_011117354 type-F conjugative transfer system pilin assembly protein TrbC trbC
HKK51_RS00110 (p165897_022) 14998..16806 + 1809 WP_000821847 type-F conjugative transfer system mating-pair stabilization protein TraN traN
HKK51_RS00115 (p165897_023) 16833..17090 + 258 WP_000864318 conjugal transfer protein TrbE -
HKK51_RS00120 (p165897_024) 17083..17826 + 744 WP_001030367 type-F conjugative transfer system pilin assembly protein TraF traF
HKK51_RS00125 (p165897_025) 17842..18189 + 348 WP_001287913 conjugal transfer protein TrbA -
HKK51_RS00130 (p165897_026) 18191..18505 - 315 WP_000415567 hypothetical protein -
HKK51_RS00135 (p165897_027) 18586..18870 + 285 WP_000624109 type-F conjugative transfer system pilin chaperone TraQ -
HKK51_RS00140 (p165897_028) 18857..19402 + 546 WP_000059850 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
HKK51_RS00145 (p165897_029) 19332..19673 + 342 WP_001443031 P-type conjugative transfer protein TrbJ -
HKK51_RS00150 (p165897_030) 19660..20054 + 395 Protein_29 F-type conjugal transfer protein TrbF -
HKK51_RS00155 (p165897_031) 20041..21414 + 1374 WP_021553026 conjugal transfer pilus assembly protein TraH traH
HKK51_RS00160 (p165897_032) 21411..24227 + 2817 WP_001007054 conjugal transfer mating-pair stabilization protein TraG traG
HKK51_RS00165 (p165897_033) 24260..24781 + 522 WP_000632670 conjugal transfer entry exclusion protein TraS -
HKK51_RS00170 (p165897_034) 24806..25537 + 732 WP_000850422 conjugal transfer complement resistance protein TraT -
HKK51_RS00175 (p165897_035) 25790..27943 + 2154 WP_000009350 type IV conjugative transfer system coupling protein TraD virb4
HKK51_RS00180 (p165897_037) 27952..28350 - 399 WP_000911324 type II toxin-antitoxin system VapC family toxin -
HKK51_RS00185 (p165897_038) 28350..28577 - 228 WP_000450532 toxin-antitoxin system antitoxin VapB -

Host bacterium

ID   29 GenBank   NC_004998
Plasmid name   p1658/97 Incompatibility group   IncFIB
Plasmid size   125491 bp Coordinate of oriT [Strand]   2103..2392 [-]
Host baterium   Escherichia coli

Cargo genes

Drug resistance gene   sul1, qacE, ant(3'')-Ia, aac(3)-Ia, blaSHV-5
Virulence gene   -
Metal resistance gene   merR, arsH
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -