Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   104534
Name   oriT_STLEFF_38|unnamed2 in_silico
Organism   Shigella flexneri strain STLEFF_38
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP058855 (934..1549 [-], 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_STLEFF_38|unnamed2
TCTTACTTCTTTGCGTAGCTGTTAAATACAGCGTTGTTTTGATAAAATCATCATTATCATCGATAATGCTTTCTTCAATTTTTTTATCCTTACTCTTTAATAAAGCACTTGCTAATAACTTCATACCTTTTGCAACTGTCAAATTTGGTTCATCAGGGTAAATGCTTTTAAGGCATACTAACAAATAATCATGGTCTTCATCTTCAACTCTAAACTGAATTTTTTTCATCATAACTCCCAACAAGAACCGACTGTAGGTCACCGGGCAAACGCTGAAAAATAACGTCGAATGACGTCATTTTGCGGCGTTTGCCCTATCCTGCATCGCAGTGAATCTGGCGCCGCTCATAAATTGTGCTTGAGCATCAACAAAAATGCAAAAAGGCTGATGTTGTCATGGCTGAACATACGTACGTCTGCGACCGGAAACCCGATCAATGCGGTAAGGACAGTGCCGTCAGGTTCGCTCCGCGAACGGTCTGGCAGGAAGCGCAAGCGCAGTCCCGCGCAATATATCAGAAAGCACCTCCCGAAATACGGGAGGGCTTCGGCTATTCAGCTAAGGTTGCTCTGTTCAGGTTGCTGAGTGTAGCCTTCCATGCCCTGACGGGCATCA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


T4CP

ID   3210 GenBank   WP_000108725
Name   t4cp2_HZT29_RS23250_STLEFF_38|unnamed2 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   3211 GenBank   WP_000053826
Name   t4cp2_HZT29_RS23290_STLEFF_38|unnamed2 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: 4103..13993

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HZT29_RS23215 (HZT29_22995) 560..709 + 150 WP_000003880 hypothetical protein -
HZT29_RS23220 (HZT29_23000) 722..994 + 273 WP_000160399 hypothetical protein -
HZT29_RS23225 (HZT29_23005) 1321..1866 + 546 WP_038976855 DNA distortion polypeptide 1 -
HZT29_RS23230 (HZT29_23010) 1869..3026 + 1158 WP_000538023 DNA distortion polypeptide 2 -
HZT29_RS23235 (HZT29_23015) 3387..3878 + 492 WP_000872475 transcription termination/antitermination NusG family protein -
HZT29_RS23240 (HZT29_23020) 4103..4747 + 645 WP_000953539 lytic transglycosylase domain-containing protein virB1
HZT29_RS23245 (HZT29_23025) 4731..5021 + 291 WP_000921916 TrbC/VirB2 family protein virB2
HZT29_RS23250 (HZT29_23030) 5045..7804 + 2760 WP_000108725 VirB3 family type IV secretion system protein virb4
HZT29_RS23255 (HZT29_23035) 7806..8543 + 738 WP_000737859 type IV secretion system protein -
HZT29_RS23260 (HZT29_23040) 8553..8813 + 261 WP_001228869 EexN family lipoprotein -
HZT29_RS23265 (HZT29_23045) 8825..9880 + 1056 WP_000235774 type IV secretion system protein virB6
HZT29_RS23270 (HZT29_23050) 10070..10792 + 723 WP_000394570 type IV secretion system protein virB8
HZT29_RS23275 (HZT29_23055) 10798..11727 + 930 WP_000776689 TrbG/VirB9 family P-type conjugative transfer protein virB9
HZT29_RS23280 (HZT29_23060) 11724..12938 + 1215 WP_001295061 VirB10/TraB/TrbI family type IV secretion system protein virB10
HZT29_RS23285 (HZT29_23065) 12956..13993 + 1038 WP_000217791 P-type DNA transfer ATPase VirB11 virB11
HZT29_RS23290 (HZT29_23070) 13998..15833 + 1836 WP_000053826 type IV secretory system conjugative DNA transfer family protein -
HZT29_RS23295 (HZT29_23075) 15830..16225 + 396 WP_000733627 cag pathogenicity island Cag12 family protein -
HZT29_RS23300 16228..16560 + 333 WP_000699980 hypothetical protein -
HZT29_RS23305 (HZT29_23085) 16803..17618 + 816 WP_000018321 aminoglycoside O-phosphotransferase APH(3')-Ia -
HZT29_RS23310 (HZT29_23090) 17695..18570 + 876 WP_073503518 SDR family oxidoreductase -
HZT29_RS23315 (HZT29_23095) 18662..18991 + 330 WP_073503519 ATP-binding cassette domain-containing protein -

Host bacterium

ID   4973 GenBank   NZ_CP058855
Plasmid name   STLEFF_38|unnamed2 Incompatibility group   IncX1
Plasmid size   39362 bp Coordinate of oriT [Strand]   934..1549 [-]
Host baterium   Shigella flexneri strain STLEFF_38

Cargo genes

Drug resistance gene   aph(3')-Ia, qnrS2, floR
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -