Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   100296
Name   oriT_pSmeSM11b in_silico
Organism   Sinorhizobium meliloti SM11
Sequence Completeness      core
NCBI accession of oriT (coordinates [strand])   NC_010865 (157465..157499 [+], 35 nt)
oriT length   35 nt
IRs (inverted repeats)      16..23, 28..35  (TACGTCGC..GCGACGTG)
Location of nic site      7..8
Conserved sequence flanking the
  nic site    		  AGGG|CGCA
Note   predicted by the oriTfinder

  oriT sequence  


Download         Length: 35 nt

>oriT_pSmeSM11b
CCAAGGGCGCAATTATACGTCGCTGGCGCGACGTG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   367 GenBank   YP_001965642
Name   TraA_pSmeSM11b insolico UniProt ID   A4KVP8
Length   1210 a.a. PDB ID   
Note   putative relaxase

  Relaxase protein sequence


Download         Length: 1210 a.a.        Molecular weight: 134098.77 Da        Isoelectric Point: 7.6395

>YP_001965642.1 TraA (plasmid) [Sinorhizobium meliloti SM11]
MAVPHFSVSIVARGSGRSAVLSAAYRHCAKMDFEREARTIDYTRKQGLLHEEFVIPEDAPEWLRAMISDR
SVSGASEAFWNSVEAFEKRSDAQLAKDVTIALPIELSAEQNIDLVQDFVARHITAQGMVADWVYHDAPGN
PHIHMMTTLRPLTDDGFGSKKVAVLGPDGRPQRNDAGKIVYELWAGGADDFNAFRDGWFACQNRHLALAG
LDIRVDGRSFEKQGIALEPTIHVGVGATAIERKADTAVETASAAAVKLERIELQEERREENARRIQRDPG
LVLDLITREKSVFDERDIARVLHRYIDDPALFQDLMARVLQHPDALRLDSERISFSTGARSPAKYTTYDL
IRIEAEMAQRALWLGRQHSYHVPTRVLGQVFKRHDRLADEQKSAIQHISRDVGIAAVVGRAGAGKTTMMK
AAREAWEAAGYRVVGAALAGKAAEGLEKEAGTASRTLSAWELRWDQDRDNLDDKTVMVLDEAGMVSSRQM
ARFVEAATISGAKLVLVGDPDQLQPIEAGAAFRAISERIGYAGLETIYRQREQWMRDASLDLARGNVSAA
LAAYEQRDMVRTGWTRDDAITTLIADWDRDYDPAKSSLILAHRRRDVRMLNEMARDKLVERGLIEKGHAF
KTEEGSRQFAVGDQIVFLKNEGSIGVKNGMLARVVEAQPGRLVAEIGSGDDCRQVVVEQRFYANVDHGYA
TTVHKSQGATVDRVKVLASSTLDRHLAYVAMTRHREAAELYVGLEEFAQRRGGVLIAHGEAPFEHKPGNR
SSYYVTLGFANGQEHTLWGVDLARAMDVADARIGDRIGIEHAGSERVRLPDGTEANRNSWKVVPVEDLAM
ARMHERLSRDASKETTLDYQNASSYRAALRFADRRGLHLMSVGRTLLRDRLQWTIRQKEKLTDLMSRLAA
VGERLGLRPSVGGERQVRGASEIRNQTNSIIQEDRKPMVAGITTFAKSIEKSVEDKVSADPALKSQWQEV
SARFHLVYADPQAAFNAVNVDAMVGSSETAKATLATISRQPVTFGPLKGKTGLFAGKADSQARETALVNV
PALARDLDEYLQKRAEAERRYEAEERAVRLKVSIDIPALSGAAKQTLERVRDAIDRNDLPSGLEYALADK
MVKAELEGFAKAVSERFGERTFLPLAAKEADGKVFEKLSAGMAPAQKAELHSAWNTMRTVQRLSAHERTA
TALKQAEIMRQAKTTGLSLK

  Protein domains


Predicted by InterproScan.

AAA domain (AAA_30)

(387-573)

BID domain of Bartonella effector protein (Bep) (Bep_C_terminal)

(966-1062)

Viral (Superfamily 1) RNA helicase (Viral_helicase1)

(697-740)

MobA/MobL family (MobA_MobL)

(17-243)


  Protein structure


Source ID Structure
AlphaFold DB A4KVP8


T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 154897..180871

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HS558_RS00625 (pSmeSM11b_p131) 150415..151227 + 813 WP_012477325 IS21-like element ISRm9 family helper ATPase IstB -
HS558_RS00630 (pSmeSM11b_p132) 151558..151770 + 213 Protein_128 zincin-like metallopeptidase domain-containing protein -
HS558_RS00635 151774..151947 - 174 WP_017273099 hypothetical protein -
HS558_RS00640 (pSmeSM11b_p133) 152405..152713 + 309 WP_012477327 DUF736 domain-containing protein -
HS558_RS00645 153034..153204 + 171 WP_017273098 hypothetical protein -
HS558_RS00650 (pSmeSM11b_p135) 153467..153640 + 174 WP_012477329 hypothetical protein -
HS558_RS00655 (pSmeSM11b_p136) 153678..154166 - 489 WP_017273097 thermonuclease family protein -
HS558_RS00660 (pSmeSM11b_p137) 154202..154468 - 267 WP_012477331 WGR domain-containing protein -
HS558_RS00665 (pSmeSM11b_p139) 154683..154916 - 234 WP_012477333 hypothetical protein -
HS558_RS00670 (pSmeSM11b_p140) 154897..156855 - 1959 WP_012477334 Ti-type conjugative transfer system protein TraG virb4
HS558_RS00675 (pSmeSM11b_p141) 156842..157057 - 216 WP_017273095 type IV conjugative transfer system coupling protein TraD -
HS558_RS00680 (pSmeSM11b_p142) 157062..157325 - 264 WP_012477336 TraC family protein -
HS558_RS00685 (pSmeSM11b_p143) 157577..161209 + 3633 WP_012477337 Ti-type conjugative transfer relaxase TraA -
HS558_RS00690 (pSmeSM11b_p144) 161266..161772 + 507 WP_012477338 conjugative transfer signal peptidase TraF -
HS558_RS00695 (pSmeSM11b_p145) 161762..162928 + 1167 WP_012477339 conjugal transfer protein TraB -
HS558_RS00700 (pSmeSM11b_p146) 162943..163560 + 618 WP_012477340 TraH family protein virB1
HS558_RS00705 (pSmeSM11b_p147) 163620..164426 + 807 WP_012477341 DUF3800 domain-containing protein -
HS558_RS00710 (pSmeSM11b_p148) 164732..166261 + 1530 WP_012477342 IS21 family transposase -
HS558_RS00715 (pSmeSM11b_p149) 166274..167011 + 738 WP_012477343 IS21-like element helper ATPase IstB -
HS558_RS00720 (pSmeSM11b_p150) 167198..168193 - 996 WP_017273092 alpha/beta hydrolase -
HS558_RS00725 (pSmeSM11b_p151) 168183..169793 - 1611 WP_026030850 hypothetical protein -
HS558_RS00730 (pSmeSM11b_p153) 170098..170811 + 714 WP_012477347 autoinducer binding domain-containing protein -
HS558_RS00735 (pSmeSM11b_p154) 170812..171111 - 300 WP_012477348 transcriptional repressor TraM -
HS558_RS00740 (pSmeSM11b_p155) 171319..172617 - 1299 WP_012477349 IncP-type conjugal transfer protein TrbI virB10
HS558_RS00745 (pSmeSM11b_p156) 172633..173079 - 447 WP_012477350 conjugal transfer protein TrbH -
HS558_RS00750 (pSmeSM11b_p157) 173083..173913 - 831 WP_012477351 P-type conjugative transfer protein TrbG virB9
HS558_RS00755 (pSmeSM11b_p158) 173929..174591 - 663 WP_012477352 conjugal transfer protein TrbF virB8
HS558_RS00760 (pSmeSM11b_p159) 174613..175794 - 1182 WP_012477353 P-type conjugative transfer protein TrbL virB6
HS558_RS00765 (pSmeSM11b_p160) 175788..175943 - 156 WP_234705592 entry exclusion protein TrbK -
HS558_RS00770 (pSmeSM11b_p161) 175988..176794 - 807 WP_012477355 P-type conjugative transfer protein TrbJ virB5
HS558_RS00775 (pSmeSM11b_p163) 176787..179221 - 2435 Protein_157 conjugal transfer protein TrbE -
HS558_RS00780 (pSmeSM11b_p164) 179232..179531 - 300 WP_012477358 conjugal transfer protein TrbD virB3
HS558_RS00785 (pSmeSM11b_p165) 179524..179916 - 393 WP_017273081 TrbC/VirB2 family protein virB2
HS558_RS00790 (pSmeSM11b_p166) 179906..180871 - 966 WP_012477360 P-type conjugative transfer ATPase TrbB virB11

Host bacterium

ID   758 GenBank   NC_010865
Plasmid name   pSmeSM11b Incompatibility group   _
Plasmid size   181251 bp Coordinate of oriT [Strand]   157465..157499 [+]
Host baterium   Sinorhizobium meliloti SM11

Cargo genes

Drug resistance gene   -
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -