Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   102634
Name   oriT_pUMNturkey4_IncX in_silico
Organism   Escherichia coli strain UMNturkey4
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_JRPZ01000033 (5236..5876 [-], 641 nt)
oriT length   641 nt
IRs (inverted repeats)      597..602, 607..612  (ATGCCC..GGGCAT)
 526..532, 537..543  (CCTCCCG..CGGGAGG)
 460..465, 469..474  (GTTCGC..GCGAAC)
 345..350, 358..363  (ACTGAA..TTCAGT)
 52..58, 62..68  (CATTATC..GATAATG)
 40..45, 54..59  (TGATAA..TTATCA)
Location of nic site      322..323
Conserved sequence flanking the
  nic site    		  TCCTGCATCG
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 641 nt

>oriT_pUMNturkey4_IncX
TCTTACTTCTTTGCGTAGCTGTTAAATACAGCGTTGTTTTGATAAAATCATCATTATCATCGATAATGCTTTCTTCAATTTTTTTATCCTTACTCTTTAATAAAGCACTTGCTAATAACTTCATACCTTTTGCAACTGTCAAATTTGGTTCATCAGGGTAAATGCTTTTAAGGCATACTAACAAATAATCATGGTCTTCATCTTCAACTCTAAACTGAATTTTTTTCATCATAACTCCCAACAAGAACCGACTGTAGGTCACCGGGCAAACGCTGAAAAATAACGTCGAATGACGTCATTTTGCGGCGTTTGCCCTATCCTGCATCGCAGTAGAAAATGCCACAACTGAAATTGTGCTTCAGTATGTACAGAAATGCAAAATCTGAGGGATTTCGTAGCTGAAAGATCGCCAGTCTTCGACCGTAAGGATAGGAGTTGCTGTAAGACCTGTGCGGGGCTGTTCGCTTCGCGAACGGGTCTGGCAGGGGGCGCAAGCGCTGTGCTGTGATATATGCAAAAGAAGCACCTCCCGCAAACGGGAGGGCTTCGGCGAATCGACTATAGTGATCTATTTACCCGGCTGATTGTCGCCTTCTATGCCCTCGCGGGCATCATGCAACCAGTGCCTGAATTTAGTTATA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


T4CP

ID   1585 GenBank   WP_000108725
Name   t4cp2_LS40_RS15190_pUMNturkey4_IncX insolico UniProt ID   _
Length   919 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 919 a.a.        Molecular weight: 104758.78 Da        Isoelectric Point: 6.1962

>WP_000108725.1 MULTISPECIES: VirB3 family type IV secretion system protein [Enterobacteriaceae]
MSTVFKGLTRPALIRGLGVPLYPFLAMCVLVVLLGVWIDDLMYFLILPGWFAIKRVTKIDERFFDLLYLR
AVVKGHPLANKRFSAVHYAGSQYDEVDISKVDNFMKLKDQASIEALIPYSSHITDDLVVTKNRDLLATWQ
VDGAYFECVDDEDLTLLTDQLNTLIRSFEGRAITFYTHRVRVRKEVKVGFNSKIPFVNRVMNDYYSSLSE
PEYFENRLYLTICYKPFNIEDKVSHFISKNKKENNIFDEPINDMNEICGRLDTYLSRFHAHRLGLVEENG
RVFSDQLSLFQYLLSGKWQKVRVTNSPFYTYLGGKDLFFGNDAGQITASQNARYFRSIEIKDYFQETDAG
IFDALMYLPVEYVFTSSFTSMDKQAAVKALDDQIDKLELTDDAAKSLLADLRVGLDMVSSGYNSFGKCHQ
TLIVFADTPERLVKDTNIVTTTLEDLGLIVTYSTLSLGAAFFSQLPGNYNLRPRLSMLSSLNFAEMESFH
NFFHGKATGNTWGNSLMALRGSGNDVYHLNYHMTTENINFFGKNPTLGHCEILGTSNVGKTVLMMIMSYA
AQQFGTPESFPENRKVRKLTTVFFDKDRAGEVGIRAMGGAYFRVKGGEPTGWNPAALPPTKRNIAFVKDI
IRLICKLNGNTVDDYQHSLISSAVDRLMQREDRSFPISKLIPLIMEPDDTETKRHGLKARLRAWKQGGEY
GWLLDNASDSFDVAHLDVFGIDGTEFLDDKVVAPVASFYLIYRVTMLADGRRLLIYMDEFWQWINNDAFK
DFVYNKLKTGRKLDMVLVPATQSPDELIKSPIAAAVREQCATHIYLANPKAKRNEYVDELQVRDLYFDKI
KAIDPLSRQFLVVKNPQRQGERDDFAAFAKLDLGKAAYYLPILSASAEQLELFDEIWSEGMAPEEWIDTY
LERANRGVK

  Protein domains


Predicted by InterproScan.

TraG P-loop domain (P-loop_TraG)

(689-817)

CagE, TrbE, VirB family, component of type IV transporter system (CagE_TrbE_VirB)

(272-474)

Type IV secretory pathway, VirB3-like protein (VirB3)

(2-83)

  Protein structure



No available structure.



ID   1586 GenBank   WP_000053826
Name   t4cp2_LS40_RS15230_pUMNturkey4_IncX insolico UniProt ID   _
Length   611 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 611 a.a.        Molecular weight: 69231.07 Da        Isoelectric Point: 8.0208

>WP_000053826.1 MULTISPECIES: type IV secretory system conjugative DNA transfer family protein [Enterobacteriaceae]
MSLKLPDKGQWAFIILVMCLIAYYTGSVAIYFFNHKTPLYIWKHYDSLLLWRVIIDSSIKSEVRFTALPS
LLSGALASLAAPAFIIWKLNQKDAPLFGDAKFASDSDLKKSKLLKWEKENDTDILVGRYKGKYLWYTAPD
FVSLGAGTRAGKGAAIGIPNMLVKKHSIIALDPKQELWKITSKVREQILGNKVYLLDPFNTKTHKCNPLF
YVDLKSESGAKDLLKLVEILFPSFGLTGAEAHFNNLAGQYWTGLAKLLHFFINFAPEWIEELRVKPVFSI
GTVVDLYSNIDREQVLSNRETFEELAQGNETALFHLKDALTKIREYHETEDEQRSSIDGSFRKKMSLFYL
PTVRKCTDGNDFDLRQMRREDITVYVGVNAEDMILAYDFLNLFFNLVVEVTLRENPDFDPTLKHDCLLFL
DEFPSIGYMPIIKKGSGYIAGYKLKLLTIYQNISQLNEIYGTEGAKTLLSAHPCRVIYAVSEEDDAKKIS
EKLGYITARSKGSSKTSGKATSRSNSENEAQRALVLPQELGTLDFSEEMIILKGEHPVKAEKALYYLDNY
FMERLMLVSPKLTALTASINRSNKIFGVKGIKYPSKEKMLSVGELESEVLL

  Protein domains


Predicted by InterproScan.

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

(102-581)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 8430..18320

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
LS40_RS15145 (LS40_15145) 3895..4158 + 264 WP_052158570 hypothetical protein -
LS40_RS15150 (LS40_15150) 4151..4369 + 219 WP_015058250 hypothetical protein -
LS40_RS29785 4465..4809 + 345 WP_015058251 hypothetical protein -
LS40_RS29790 4886..5035 + 150 WP_165839134 hypothetical protein -
LS40_RS15160 (LS40_15160) 5051..5308 + 258 WP_015058252 hypothetical protein -
LS40_RS15165 (LS40_15165) 5648..6193 + 546 WP_038976855 DNA distortion polypeptide 1 -
LS40_RS15170 (LS40_15170) 6196..7353 + 1158 WP_000538023 DNA distortion polypeptide 2 -
LS40_RS15175 (LS40_15175) 7714..8205 + 492 WP_000872475 transcription termination/antitermination NusG family protein -
LS40_RS15180 (LS40_15180) 8430..9074 + 645 WP_000953539 lytic transglycosylase domain-containing protein virB1
LS40_RS15185 (LS40_15185) 9058..9348 + 291 WP_000921916 TrbC/VirB2 family protein virB2
LS40_RS15190 (LS40_15190) 9372..12131 + 2760 WP_000108725 VirB3 family type IV secretion system protein virb4
LS40_RS15195 (LS40_15195) 12133..12870 + 738 WP_000737859 type IV secretion system protein -
LS40_RS15200 (LS40_15200) 12880..13140 + 261 WP_001228869 EexN family lipoprotein -
LS40_RS15205 (LS40_15205) 13152..14207 + 1056 WP_000235774 type IV secretion system protein virB6
LS40_RS15210 (LS40_15210) 14397..15119 + 723 WP_000394570 type IV secretion system protein virB8
LS40_RS15215 (LS40_15215) 15125..16054 + 930 WP_000776689 TrbG/VirB9 family P-type conjugative transfer protein virB9
LS40_RS15220 (LS40_15220) 16051..17265 + 1215 WP_001295061 VirB10/TraB/TrbI family type IV secretion system protein virB10
LS40_RS15225 (LS40_15225) 17283..18320 + 1038 WP_000217791 P-type DNA transfer ATPase VirB11 virB11
LS40_RS15230 (LS40_15230) 18325..20160 + 1836 WP_000053826 type IV secretory system conjugative DNA transfer family protein -
LS40_RS15235 (LS40_15235) 20157..20552 + 396 WP_000733627 cag pathogenicity island Cag12 family protein -
LS40_RS30255 20555..20887 + 333 WP_000699980 hypothetical protein -
LS40_RS15245 (LS40_15245) 21130..21945 + 816 WP_000018321 aminoglycoside O-phosphotransferase APH(3')-Ia -
LS40_RS29020 (LS40_15250) 22099..22395 - 297 WP_226156972 carcinine hydrolase/isopenicillin-N N-acyltransferase family protein -
LS40_RS29025 (LS40_15255) 22453..22572 - 120 Protein_27 IS6 family transposase -

Host bacterium

ID   3078 GenBank   NZ_JRPZ01000033
Plasmid name   pUMNturkey4_IncX Incompatibility group   IncX2
Plasmid size   22572 bp Coordinate of oriT [Strand]   5236..5876 [-]
Host baterium   Escherichia coli strain UMNturkey4

Cargo genes

Drug resistance gene   aph(3')-Ia
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -