Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   103392
Name   oriT_pSZ11R-tetX4 in_silico
Organism   Escherichia sp. strain SZ11R
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_MW940629 (40436..41051 [-], 616 nt)
oriT length   616 nt
IRs (inverted repeats)      599..604, 609..614  (ATGCCC..GGGCAT)
 526..532, 538..544  (CCTCCCG..CGGGAGG)
 462..467, 471..476  (GTTCGC..GCGAAC)
 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: 616 nt

>oriT_pSZ11R-tetX4
TCTTACTTCTTTGCGTAGCTGTTAAATACAGCGTTGTTTTGATAAAATCATCATTATCATCGATAATGCTTTCTTCAATTTTTTTATCCTTACTCTTTAATAAAGCACTTGCTAATAACTTCATACCTTTTGCAACTGTCAAATTTGGTTCATCAGGGTAAATGCTTTTAAGGCATACTAACAAATAATCATGGTCTTCATCTTCAACTCTAAACTGAATTTTTTTCATCATAACTCCCAACAAGAACCGACTGTAGGTCACCGGGCAAACGCTGAAAAATAACGTCGAATGACGTCATTTTGCGGCGTTTGCCCTATCCTGCATCGCAGTGAATCTGGCGCCGCTCATAAATTGTGCTTGAGCATCAACAAAAATGCAAAAAGGCTGATGTTGTCATGGCTGAACATACGTACGTCTGCGACCGGAAACCCGATCAATGCGGTAAGGACAGTGCCGTCAGGTTCGCTCCGCGAACGGTCTGGCAGGAAGCGCAAGCGCAGTCCCGCGCAATATATCAGAAAGCACCTCCCGAAATACGGGAGGGCTTCGGCTATTCAGCTAAGGTTGCTCTGTTCAGGTTGCTGAGTGTAGCCTTCCATGCCCTGACGGGCATCA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


T4CP

ID   2308 GenBank   WP_000108725
Name   t4cp2_KSF44_RS00275_pSZ11R-tetX4 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   2309 GenBank   WP_025755766
Name   t4cp2_KSF44_RS00315_pSZ11R-tetX4 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: 69235.06 Da        Isoelectric Point: 8.0208

>WP_025755766.1 MULTISPECIES: type IV secretory system conjugative DNA transfer family protein [Enterobacteriaceae]
MSLKLPDKGQWAFIILVMCLIAYYTGSVAIYFFNHKTTLYIWKHYDSLLLWRVIIDSSIKSEVRFTALPS
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: 43605..53495

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
KSF44_RS00225 (PHFBNNME_00043) 38903..39148 + 246 WP_000356546 hypothetical protein -
KSF44_RS00230 (PHFBNNME_00044) 39138..39353 + 216 WP_001180116 hypothetical protein -
KSF44_RS00235 (PHFBNNME_00045) 39446..39775 + 330 WP_000866648 hypothetical protein -
KSF44_RS00240 (PHFBNNME_00046) 40014..40211 + 198 WP_001675595 hypothetical protein -
KSF44_RS00245 (PHFBNNME_00047) 40224..40496 + 273 WP_000160399 hypothetical protein -
KSF44_RS00250 (PHFBNNME_00049) 40823..41368 + 546 WP_038976855 DNA distortion polypeptide 1 -
KSF44_RS00255 (PHFBNNME_00050) 41371..42528 + 1158 WP_000538023 DNA distortion polypeptide 2 -
KSF44_RS00260 (PHFBNNME_00051) 42889..43380 + 492 WP_000872475 transcription termination/antitermination NusG family protein -
KSF44_RS00265 (PHFBNNME_00053) 43605..44249 + 645 WP_000953539 lytic transglycosylase domain-containing protein virB1
KSF44_RS00270 (PHFBNNME_00054) 44233..44523 + 291 WP_000921916 TrbC/VirB2 family protein virB2
KSF44_RS00275 (PHFBNNME_00055) 44547..47306 + 2760 WP_000108725 VirB3 family type IV secretion system protein virb4
KSF44_RS00280 (PHFBNNME_00056) 47308..48045 + 738 WP_000737859 type IV secretion system protein -
KSF44_RS00285 (PHFBNNME_00057) 48055..48315 + 261 WP_001228869 EexN family lipoprotein -
KSF44_RS00290 (PHFBNNME_00058) 48327..49382 + 1056 WP_000235774 type IV secretion system protein virB6
KSF44_RS00295 (PHFBNNME_00059) 49572..50294 + 723 WP_000394570 type IV secretion system protein virB8
KSF44_RS00300 (PHFBNNME_00060) 50300..51229 + 930 WP_025755764 TrbG/VirB9 family P-type conjugative transfer protein virB9
KSF44_RS00305 (PHFBNNME_00061) 51226..52440 + 1215 WP_025755765 VirB10/TraB/TrbI family type IV secretion system protein virB10
KSF44_RS00310 (PHFBNNME_00062) 52458..53495 + 1038 WP_000217791 P-type DNA transfer ATPase VirB11 virB11
KSF44_RS00315 (PHFBNNME_00063) 53500..55335 + 1836 WP_025755766 type IV secretory system conjugative DNA transfer family protein -
KSF44_RS00320 (PHFBNNME_00064) 55332..55727 + 396 WP_000733627 cag pathogenicity island Cag12 family protein -
KSF44_RS00340 (PHFBNNME_00065) 55730..56062 + 333 WP_000699980 hypothetical protein -
KSF44_RS00330 (PHFBNNME_00066) 56145..56615 + 471 WP_025755767 thermonuclease family protein -

Host bacterium

ID   3835 GenBank   NZ_MW940629
Plasmid name   pSZ11R-tetX4 Incompatibility group   IncX1
Plasmid size   56939 bp Coordinate of oriT [Strand]   40436..41051 [-]
Host baterium   Escherichia sp. strain SZ11R

Cargo genes

Drug resistance gene   blaSHV-12, tet(A), floR, tet(X4), lnu(F), aadA2
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -