Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   115342
Name   oriT_pNIHE10-0087_ndm in_silico
Organism   Enterobacter hormaechei strain NIHE10-0087
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_AP025036 (152588..152682 [+], 95 nt)
oriT length   95 nt
IRs (inverted repeats)      73..78, 85..90  (AAAAAA..TTTTTT)
 73..78, 84..89  (AAAAAA..TTTTTT)
 27..34, 37..44  (AGCGTGAT..ATCACGCT)
 13..19, 31..37  (TAAATCA..TGATTTA)
Location of nic site      55..56
Conserved sequence flanking the
  nic site    		  GGTGTATAGC
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 95 nt

>oriT_pNIHE10-0087_ndm
TTTTTTTTCTTTTAAATCAGTGAGATAGCGTGATTTATCACGCTGCGTTAGGTGTATAGCAGGTTAAGGGATAAAAAATCATCTTTTTTTGGTAG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


T4CP

ID   11423 GenBank   WP_058655869
Name   traD_LDO06_RS00640_pNIHE10-0087_ndm insolico UniProt ID   _
Length   729 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 729 a.a.        Molecular weight: 83387.45 Da        Isoelectric Point: 5.0412

>WP_058655869.1 MULTISPECIES: type IV conjugative transfer system coupling protein TraD [Enterobacteriaceae]
MSSTKHITQGGQVFSYMLNMFMQVNRRIAFWLLNLFFVLTPLFFWMRVPWQDMRNGGLYWWLYLSAGGEK
ALFNVPPVYDVPYDGQTLHFTSAAILKDPYMTYAGQLTLQELFIAVFLASCVVLAVAYGVYYLLRRLGEK
QAQDDLVGGRTLTEDVKAVARTLHRNNEASPLHFDQLPLLLDSEVKNLLLHGTPGSGKSNALNKLLQQLR
ARGDMVIVYDKGCSLVKRHFNENIDKLLNPRDKRCENWDLWLECQTTSDFDSIGNTLIPQSTKEDPFWTG
SARTIFTSVSKRFQNDPHRSYNALLRTLLAINLKALREYVQGTEASNLMEEKVEKTAISIRGVLTNYVKA
LRYMQGIERTGKPRFAIREWMKQVNEPGQRNGWLWITSNAREHESQKPLISMWLAQAANCLLEMGENPTR
RVWFIYDELTSLHKLPELPGVLSEARKFGGCFVLGFQNKPQLDFTYGREFADAMMDLLNTRFFFRSPDEG
VANYVMRQLGQRRAKVFNEQYSYGADTVRDGVSFSKQEDDQYLVNYSDIQSLPDLTCYVTLPGNYPVVRM
NMTYEKMDFIAAEFLPRELNDSLDQEIEEEITRRELDEDSIDRLLAVQSNEPAVPATTAPVATVSSVTAA
IETINSSPQPPATVSSSVPDTRSSQITTSPVQNGGRVKEYDGLQVDTQTGEILTEPDRYEDYAAYEQEAL
QAMKEEEKNILVHREHDEPDREYEPGDRW

  Protein domains


Predicted by InterproScan.

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

(173-562)

F sex factor protein N terminal (TraD_N)

(31-126)

  Protein structure



No available structure.



ID   11424 GenBank   WP_032713695
Name   traC_LDO06_RS00720_pNIHE10-0087_ndm insolico UniProt ID   _
Length   871 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 871 a.a.        Molecular weight: 97564.93 Da        Isoelectric Point: 5.7411

>WP_032713695.1 MULTISPECIES: type IV secretion system protein TraC [Enterobacteriaceae]
MALHDELFRRLMTDWQRKDGAAKAGEALDDMDYPSLVSVLPYQHYDKDSGLFVNQNTMGFILECTPLIGA
NDGIVEALDNFLRNKLPREQPLSVLLLGSKCVSHLLDNGLSDMAWQGEQATRFDHITRAFYEHGALYGLP
NNKGYPLSLRNYRLFISYAEPLRRDVDELFASLGQTLSIVQQSLFAANLHSEVLDDRGLVGLVREIVNFR
HDRITPPPDEVDPYEELNAQCVARSINLKVTPDCLHQSQSSAEGGRVKTRIMSYMPEKNPVKFALWQGGN
NLSNLLDPTSTVPCPFAITLTTELDVQAKSQNEAVRKFATNDKRANSPFGKWVPGVKKAAREWDGLRERL
STGQSALARYSLGVTLFCEDDNDKALMCELALQNTFRANGISLCSPTFMQLRNWLSLFPFMMPEGLWSDM
RRSGATLRAESFNVANLLPVVADNRICPKGVPIPSYRNQLSYLDLFDSKSGLGNDNYNLGVCGTSGGGKS
FLMQTIIRHILDSGGRAWVFDMGDSYKALCANVGGVYVDATDLKFNPFAGIVNIVESAESIRDLLLVLSS
PSGKVDDTAKSILLNAVQAVWEGEAPSKRRGNAVLIDDVSDLLNVWTTSEKYRDATTVRNLMEEMVVSLH
KYTTGGIYGEYFNSPEPALDDNVRFCVLEMGRLKNKPDLLAAIMFSMMIYVEQRMFLSPRSERKAAIIDE
AWKLLASENGFIGDFIENGYRTARKYGGAYITITQGIEDFDGDKASIAAKAAWSNSSFKIILRQNREAFR
KYNQKNEGQFSSSEQTIIEGFPSAKDAHFSAFMLRVAGQVSYHRLILDPLSRVMFSSDGDDFEFREQCLK
EGKTVHEALWLLARKKYAKEMEVLEQWQIQS

  Protein domains


Predicted by InterproScan.

TraG P-loop domain (P-loop_TraG)

(463-774)

TraC protein (TraC_F_IV)

(34-245)

Family of unknown function (DUF5934) (DUF5934)

(287-441)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 111087..132704

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
LDO06_RS00640 (NIHE100087_pN1260) 111087..113276 - 2190 WP_058655869 type IV conjugative transfer system coupling protein TraD virb4
LDO06_RS00645 (NIHE100087_pN1270) 113273..113503 - 231 WP_058655870 hypothetical protein -
LDO06_RS00650 (NIHE100087_pN1280) 113699..114310 - 612 WP_058655871 hypothetical protein -
LDO06_RS00655 (NIHE100087_pN1290) 114307..117195 - 2889 WP_058655872 conjugal transfer mating-pair stabilization protein TraG traG
LDO06_RS00660 (NIHE100087_pN1300) 117195..118562 - 1368 WP_058655873 conjugal transfer pilus assembly protein TraH traH
LDO06_RS00665 (NIHE100087_pN1310) 118555..118896 - 342 WP_058655874 hypothetical protein -
LDO06_RS00670 (NIHE100087_pN1320) 118953..119498 - 546 WP_017694234 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
LDO06_RS00675 (NIHE100087_pN1330) 119498..119794 - 297 WP_017694233 hypothetical protein -
LDO06_RS00680 (NIHE100087_pN1340) 119808..120614 - 807 WP_223174891 type-F conjugative transfer system pilin assembly protein TraF traF
LDO06_RS00685 (NIHE100087_pN1350) 120611..122440 - 1830 WP_058655876 type-F conjugative transfer system mating-pair stabilization protein TraN traN
LDO06_RS00690 (NIHE100087_pN1360) 122437..123063 - 627 WP_058655877 type-F conjugative transfer system pilin assembly protein TrbC trbC
LDO06_RS00695 (NIHE100087_pN1370) 123082..124077 - 996 WP_058655878 conjugal transfer pilus assembly protein TraU traU
LDO06_RS00700 (NIHE100087_pN1380) 124074..124472 - 399 WP_058655879 hypothetical protein -
LDO06_RS00705 (NIHE100087_pN1390) 124472..125098 - 627 WP_058655880 type-F conjugative transfer system protein TraW traW
LDO06_RS00710 (NIHE100087_pN1400) 125098..125313 - 216 WP_058655881 TraR/DksA C4-type zinc finger protein -
LDO06_RS00715 (NIHE100087_pN1410) 125306..125788 - 483 WP_072201922 type-F conjugative transfer system protein TrbI -
LDO06_RS00720 (NIHE100087_pN1420) 125770..128385 - 2616 WP_032713695 type IV secretion system protein TraC virb4
LDO06_RS00725 128388..128975 - 588 WP_058655882 type IV conjugative transfer system lipoprotein TraV traV
LDO06_RS00730 129051..129296 - 246 WP_017694222 hypothetical protein virb4
LDO06_RS00735 (NIHE100087_pN1440) 129323..129703 - 381 WP_058655883 hypothetical protein -
LDO06_RS00740 (NIHE100087_pN1450) 129700..131058 - 1359 WP_058655884 TrbI/VirB10 family protein traB
LDO06_RS00745 (NIHE100087_pN1460) 131051..131827 - 777 WP_058655885 type-F conjugative transfer system secretin TraK traK
LDO06_RS00750 (NIHE100087_pN1470) 131811..132380 - 570 WP_017694218 type IV conjugative transfer system protein TraE traE
LDO06_RS00755 (NIHE100087_pN1480) 132399..132704 - 306 WP_017694217 type IV conjugative transfer system protein TraL traL
LDO06_RS00760 (NIHE100087_pN1490) 132803..133507 - 705 WP_001067858 IS6-like element IS26 family transposase -
LDO06_RS00765 (NIHE100087_pN1500) 133571..134827 - 1257 Protein_151 Tn3-like element Tn3 family transposase -
LDO06_RS00770 (NIHE100087_pN1510) 134991..135548 + 558 WP_058672054 recombinase family protein -
LDO06_RS00775 (NIHE100087_pN1520) 135731..136591 + 861 WP_000027057 broad-spectrum class A beta-lactamase TEM-1 -
LDO06_RS00780 136739..136939 + 201 Protein_154 Tn3 family transposase -

Host bacterium

ID   15776 GenBank   NZ_AP025036
Plasmid name   pNIHE10-0087_ndm Incompatibility group   IncR
Plasmid size   154527 bp Coordinate of oriT [Strand]   152588..152682 [+]
Host baterium   Enterobacter hormaechei strain NIHE10-0087

Cargo genes

Drug resistance gene   catA2, blaNDM-1, rmtB, blaTEM-1B, aac(3)-IId, aac(6')-Ib-cr, blaOXA-1, catB3, ARR-3, qacE, sul1
Virulence gene   htpB
Metal resistance gene   merE, merD, merA, merC, merP, merT, merR
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -