Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   107978
Name   oriT_pEmeITTGR7b in_silico
Organism   Sinorhizobium mexicanum strain ITTG R7
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP041240 (431082..431139 [-], 58 nt)
oriT length   58 nt
IRs (inverted repeats)      25..31, 36..42  (ACGTCGC..GCGACGT)
Location of nic site      _
Conserved sequence flanking the
  nic site    		  _
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 58 nt

>oriT_pEmeITTGR7b
CCCCGCCAGGCGCTCTCAAGAAGAACGTCGCGCCAGCGACGTATAATTGCGCCCTTGG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   5352 GenBank   WP_180942110
Name   traA_FKV68_RS24070_pEmeITTGR7b insolico UniProt ID   _
Length   1103 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1103 a.a.        Molecular weight: 122367.88 Da        Isoelectric Point: 9.7693

>WP_180942110.1 Ti-type conjugative transfer relaxase TraA [Sinorhizobium mexicanum]
MAVPHFSVSIVARGSGRSAVLSAAYRHCAKMEYEREARTIDYRAKRGLLHEEFVIPGDAPQWLGAMIADH
SVSGASEAFWNKVEVFEKRSDAQLAKDITIALPVELSTEQSIALMRDFVERHITSNGMVADWVYHDAPDN
PHVHLMTTLRPLTENGFGAKKLPVVGPDGNPIRNDAGKIVYELWAGSADDFNAFRDGWFACQNKHLALAG
LDISVDGRSFEKQGIELTPTIHLGVGAKAIERKSAEADRDISLERLELQEERRAENARRIQRRPEIVLDL
ITREKSVFDERDVAKVLHRYIGDARLFQILMARILQSPETLRLERERIEFSSGTRAPAKYTTRELIRLEA
QIANRALWLSQRSSHDVRDAVLDATFARHFRLSEEQTSAIAHVAGGERIAAVIGRAGAGKTTMMKAAREA
WEAAGYRVVGGALAGKAAEGLEKEAGILSRTLSSWELRWKEGRNQLDDRTVFVLDEAGMVSSRQMALFVE
AAVNAGAKLVLIGDPEQLQPIEAGAAFRGIADRVGYAELETIYRQRQQWMRDASVDLARGNVRNAVEAYR
AQGHVNGSELKADAVRALIADWNRDYDPAKSSLILAHLRRDVRILNEMARAKLVERGIVADGFVFRTEDG
NRKFAAGDQIVFLKNEGSLGVKNGMLAKVVNAAPGRIVAEVGEGEHRRQVTVEQRFYSHVDHGYATTIHK
SQGATVDRVKVLASLSLDRHLSYVVMTRHRDDFGLYYGRRSFAKAGGLIPILSRKNAKETTLDYVHGSFY
WQALRFAEARGLHLVNVARTVVRDRLDWTIRQKSKLIELGARLATIAGKLGLSAPAVRTSQSHTIKESKP
MVPGITTFPNSLEQSVEDRLAADPGLKKQWEEVSSRFHLVYAEPQAAFKAVNVDAILKDEAAAISTIARI
GSEPESFGALKGRTGILASRTDKQSRETAVTSAPALSRNLERYLRQRTEAERKYEAEERTVRLKVSLDIP
ALSSAAKQTLERVRDAIDRNDLPAGLEYALSDKMVKAELEGFARAVSERFGERTFLSLAAKDTNGQPFQS
VTSGMSAGQKAEVQSAWNSMRTVQQLSAHERTTEALKQAETLRQTKSQGLSLK

  Protein domains


Predicted by InterproScan.

MobA/MobL family (MobA_MobL)

(17-243)

AAA domain (AAA_30)

(382-567)

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

(859-955)


  Protein structure



No available structure.




T4CP

ID   5641 GenBank   WP_180942107
Name   traG_FKV68_RS24055_pEmeITTGR7b insolico UniProt ID   _
Length   640 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 640 a.a.        Molecular weight: 69498.71 Da        Isoelectric Point: 9.1805

>WP_180942107.1 Ti-type conjugative transfer system protein TraG [Sinorhizobium mexicanum]
MTRVMLFLAPCALMLLVIIGMAGTENWLPAFGKSEAAQQTLGRAGIALPYLVAALLGIVFLFASAGSARI
RTAGWGVLAGATATILIAAMREFVRLSAFAAQVPRGKSIFSYVDPATTIGAGAALMSALFGLRVVIAGNA
AFAKAEPKRIYGKRALYGEAEWMKLPEAEKVFPESGGIVIGERYCVDKDSVAAQSFRADSAETWGAGGKA
PLLCFDGSFGPSHGIVFAGSGGFKTTSVTIPTALKWGGALVLLDPSNEVAPMVSKHRGGANRDVFVLDPK
NSEIGFNAIDWIGRFGGTKEEDIASVASWIMSDSGGARGVRDDFFRASALQLLTALIADVCLSGHTREPE
QTLRQVRKNLSEPEPKLRERLQSIYHNSNSDFVKENVAAFVNMTPETFSGVYANAVKETHWLSYPNYAAL
VSGTTFTTSDIAEGNTDVFINVDLKTLETHAGLARVIIGSFLNAIYNRNGEMEGRALFLLDEVARLGYMR
ILETARDAGRKYGIMLTMIYQSIGQMRETYGGRDAASKWFESASWISFAAINDPETADYISRRCGMTTVE
IDQVSRSFQSKGSSRTRSKQLAARPLIQPHEVLRMRADEQIVFTAGNAPLRCGRAIWFRREDMKACVKPN
VFFRASAEKR

  Protein domains


Predicted by InterproScan.

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

(162-635)

  Protein structure



No available structure.



ID   5642 GenBank   WP_180942126
Name   t4cp2_FKV68_RS24155_pEmeITTGR7b insolico UniProt ID   _
Length   818 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 818 a.a.        Molecular weight: 91657.50 Da        Isoelectric Point: 6.2755

>WP_180942126.1 conjugal transfer protein TrbE [Sinorhizobium mexicanum]
MVALRRFRATGASFADLVPYAGLVGNGLLLLKDGSLMAGWYFAGPDSESATALERNELSRQINAILSRLG
SGWMIQVEAIRIPTIDYPSEDRCHFPDPVTRAIDAERRAHFEREQGHFESKHALILTYRPLESKRTALSK
YIYSDEESRKKSYADTVLFMFKNAVREIEQYLANSLSIRRMETHEVSEREGTRVARYDELLQFVRFCITG
HSHPIRLPDVPMYLDWIATAEFEHGLTPKIENRFLGVVAIDGLPAESWPGILNSLDLMPLTYRWSSRFIF
LDAEEARHKLERTRKKWLQKVRPFFDQLFQTQSRSIDQDAMTMVTETEDAIAQASSQLVAYGYYTPVIVL
FDNDREALQEKAEAIRRLIQAEGFGARIETLNATDAFLGSLPGNWYSNIREPLINTSNLADLIPLNAVWS
GRPAAPCPFYPPNSPPLMQVASGSTPYRLNLHVDDVGHTLVFGPTGSGKSTLLALIAAQFRRYENAQIFA
FDKGNSLLPLTLAGGGDHYEIGGDNEGEGRALAFCPLSALGNDADRAWATEWIEMLVALQGVIITPDHRN
AISRQVGLMANAPGRSLSDFVSGVQMREIKDALHHYTVDGPMGQLLDAEQDGLSLGALQTFEIEHLMNMG
ERNLVPVLAYLFRRIERRLDGSPSLIVLDEAWLMLGHPVFRAKIREWLKVLRKANCALVLATQSISDAER
SGIIDVLKESCPTKICLPNGAAREPGTREFYERIGLNERQIDLVARATPKREYYAATPEGRRLFDMALGP
VALSFVGASGKDDLKRIRALKSEHGCDWPIHWLNTRGVHDAASLLNFE

  Protein domains


Predicted by InterproScan.

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

(186-400)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 428507..451006

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
FKV68_RS24015 (FKV68_24525) 423557..424483 + 927 WP_180942101 zincin-like metallopeptidase domain-containing protein -
FKV68_RS24020 (FKV68_24530) 424456..424665 - 210 WP_180942102 hypothetical protein -
FKV68_RS24025 (FKV68_24535) 425121..425432 + 312 WP_180942103 DUF736 domain-containing protein -
FKV68_RS24030 425748..425912 + 165 WP_180942104 hypothetical protein -
FKV68_RS24035 (FKV68_24540) 426394..426687 - 294 WP_245181588 WGR domain-containing protein -
FKV68_RS24040 (FKV68_24545) 426809..427498 - 690 WP_180942105 HAD family phosphatase -
FKV68_RS24045 (FKV68_24550) 427725..428003 - 279 WP_180942323 HU family DNA-binding protein -
FKV68_RS24050 (FKV68_24555) 428275..428502 + 228 WP_180942106 hypothetical protein -
FKV68_RS24055 (FKV68_24560) 428507..430429 - 1923 WP_180942107 Ti-type conjugative transfer system protein TraG virb4
FKV68_RS24060 (FKV68_24565) 430422..430637 - 216 WP_180942108 type IV conjugative transfer system coupling protein TraD -
FKV68_RS24065 (FKV68_24570) 430642..430938 - 297 WP_180942109 conjugal transfer protein TraC -
FKV68_RS24070 (FKV68_24575) 431191..434502 + 3312 WP_180942110 Ti-type conjugative transfer relaxase TraA -
FKV68_RS24075 (FKV68_24580) 434499..435065 + 567 WP_180942111 conjugative transfer signal peptidase TraF -
FKV68_RS24080 (FKV68_24585) 435055..436218 + 1164 WP_180942112 conjugal transfer protein TraB -
FKV68_RS24085 (FKV68_24590) 436234..436836 + 603 WP_180942113 TraH family protein virB1
FKV68_RS24090 436959..437159 - 201 WP_180942114 hypothetical protein -
FKV68_RS24100 (FKV68_24600) 437241..437945 - 705 WP_180942115 autoinducer binding domain-containing protein -
FKV68_RS24105 (FKV68_24605) 438320..439573 + 1254 WP_180942116 ATP-binding protein -
FKV68_RS24110 (FKV68_24615) 439895..440143 - 249 WP_180942117 helix-turn-helix transcriptional regulator -
FKV68_RS24115 (FKV68_24620) 440305..440625 + 321 WP_180942118 transcriptional repressor TraM -
FKV68_RS24120 (FKV68_24625) 440629..441333 - 705 WP_180942119 autoinducer binding domain-containing protein -
FKV68_RS24125 (FKV68_24630) 441667..442968 - 1302 WP_180942120 IncP-type conjugal transfer protein TrbI virB10
FKV68_RS24130 (FKV68_24635) 442980..443417 - 438 WP_180942121 conjugal transfer protein TrbH -
FKV68_RS24135 (FKV68_24640) 443420..444232 - 813 WP_180942122 P-type conjugative transfer protein TrbG virB9
FKV68_RS24140 (FKV68_24645) 444248..444910 - 663 WP_180942123 conjugal transfer protein TrbF virB8
FKV68_RS24145 (FKV68_24650) 444935..446083 - 1149 WP_180942124 P-type conjugative transfer protein TrbL virB6
FKV68_RS24150 (FKV68_24655) 446119..446922 - 804 WP_180942125 P-type conjugative transfer protein TrbJ virB5
FKV68_RS24155 (FKV68_24660) 446894..449350 - 2457 WP_180942126 conjugal transfer protein TrbE virb4
FKV68_RS24160 (FKV68_24665) 449361..449660 - 300 WP_180942127 conjugal transfer protein TrbD virB3
FKV68_RS24165 (FKV68_24670) 449653..450039 - 387 WP_180942128 TrbC/VirB2 family protein virB2
FKV68_RS24170 (FKV68_24675) 450029..451006 - 978 WP_180942129 P-type conjugative transfer ATPase TrbB virB11
FKV68_RS24175 (FKV68_24680) 451017..451640 - 624 WP_180942130 acyl-homoserine-lactone synthase -
FKV68_RS24180 (FKV68_24685) 452017..453240 + 1224 WP_180942131 plasmid partitioning protein RepA -
FKV68_RS24185 (FKV68_24690) 453237..454262 + 1026 WP_180942132 plasmid partitioning protein RepB -
FKV68_RS24190 (FKV68_24695) 454462..455676 + 1215 WP_180942133 plasmid replication protein RepC -

Host bacterium

ID   8413 GenBank   NZ_CP041240
Plasmid name   pEmeITTGR7b Incompatibility group   -
Plasmid size   455676 bp Coordinate of oriT [Strand]   431082..431139 [-]
Host baterium   Sinorhizobium mexicanum strain ITTG R7

Cargo genes

Drug resistance gene   -
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   nodD, nodM, nifX, nifN, mLTONO_5203, nifE, nifD, nifH, nifQ, nifS, nifW, fixA, fixB, fixC, fixX, nifA, nifB, nifZ, nifT, nodH, nodJ, nodI, nodU, nodS, nodC, nodB, nodA
Anti-CRISPR   -