Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   121843
Name   oriT_pB in_silico
Organism   Sinorhizobium chiapasense strain S24
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP144207 (10398..10432 [+], 35 nt)
oriT length   35 nt
IRs (inverted repeats)      19..24, 29..34  (CGTCGC..GCGACG)
Location of nic site      _
Conserved sequence flanking the
  nic site    		  _
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 35 nt

>oriT_pB
TCCAAGGGCGCAATTATACGTCGCTGATGCGACGC

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   13786 GenBank   WP_334142256
Name   traA_QM996_RS00080_pB insolico UniProt ID   _
Length   1102 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1102 a.a.        Molecular weight: 122936.89 Da        Isoelectric Point: 9.8349

>WP_334142256.1 Ti-type conjugative transfer relaxase TraA [Sinorhizobium chiapasense]
MAVPHFSVSVVARGSGRSAVLSAAYRHCAKMEYEREARTIDYTRKQGLLHEEFVIPADSPEWLRSMIADR
SVASASEAFWNKVEDFEKRSDAQLAKDVTIALPIELTAEQNIALVRDFVERHVIAKGMVADWVYHDAPGN
PHVHLMTTLRPLTEDGFGAKKIAVLGPDGNPLRNDAGKIVYELWAGSLDDFNAFRDGWFACQNRHLALAG
LDIRIDGRSFEKQGIELTPTIHLGVGTKAIERKVTTEDQSVSLERLELQEEKRAENARRIQRRPEIVLDL
ITRENSVFDERDVAKILHRYIDDPGVFQSLMARILQSPETLRLERERIAFATGIRVPAKHTTRELIRLEA
EMGSRAIWLSRRSSHGVRSEVLEAAFSRHSRLSDEQKTAIEHVAGAERIAAVIGRAGAGKTTMMKAAREA
WEAAGYRVVGGALAGKAAEGLEKEAGIASRTLSSWELRWNEGRNRLDDKTIFVLDEAGMVSSRQMALFVE
TATKAGAKLVLVGDPEQLQPIEAGAAFRAIADRIGYAELETIYRQREQWMRDASLDLARGNVGRAIDAYR
ANGRMMGSELKAEAVQNLVADWDRDYDPTTTTLILAHLRRDVRMLNEMARAKLVERGIVDAGFSFKTEDG
NRRFAPGDQIVFLKNEGALGVKNGMLGKVVEAAQNRIVAEIGEAGDRRQVTVESRFYNNLDHGYATTIHK
SQGATVDRVKVLASLSLDRHLTYVAMTRHREDLGVYYGARSFTKSGGLIEILSRKDSKETTLDYEKATFY
RQALRFAEARGMHLVNVARTIARDRLQWTVRQKQKLNRLAYRLVAIGDKLGLAIGAKPINAQNLKETRPM
VAGIATFPKSIEQAVADKLEADPGLKKQWEDVSTRFHFVYAQPEAAFKAVNVDAILKDETVAKSTVAKIA
SRPDTYGALKGKTGLLASRADKRDRERAERNVPTLAQSLSDYMRQRSRAEQRYQAEELAVRRKVAIDIPA
LSPGARQTLERVRDAIDRNDLPAALEFALADKMVKAELEGFAKAVTERFGERTFLPLAAKDTNGEAFRTI
TAGMSPGQKAEVQTAWNTMRTVQQLNAHERTTEALRQAETLRQTKSQGLSLK

  Protein domains


Predicted by InterproScan.

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

(858-954)

AAA domain (AAA_30)

(382-565)

MobA/MobL family (MobA_MobL)

(17-243)

Viral (Superfamily 1) RNA helicase (Viral_helicase1)

(692-735)


  Protein structure



No available structure.




T4CP

ID   16120 GenBank   WP_334141906
Name   traG_QM996_RS00065_pB insolico UniProt ID   _
Length   638 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 638 a.a.        Molecular weight: 68814.60 Da        Isoelectric Point: 8.6480

>WP_334141906.1 Ti-type conjugative transfer system protein TraG [Sinorhizobium chiapasense]
MTANRITIAVAPLVLMVLAVIGMTGIEQWLSTFGKTEAARLILGRTGIAAPYITAASIGVIFLFASAGST
SIKFAGWGAAAGSIATILIAVMREATRLAAFAAQVPDGKSITSYLDHATMVGATAALMAGCFALRVALVG
NAAFARAEPKRIRGKRALHGEADWMKMQEAAKLFADTGGIVIGERYRVDKDSTAALLFRAGDPETWGAGG
KSSLLCFDGSFGSSHGIVFAGSGGFKTTSVTIPTALKWGGGLVVLDPSNEVAPMVLEQRKGAARFIRILD
PKEPETGFNALDWIGRFGGTKEEDIASVASWIMSDSGGARGVRDDFFRASALQLLTALIADVCLSGHTEQ
EHQTLRQVRSNLAEPEPKLRERLQEIYDNSNSDFVKENVAAFVNMTPETFSGVYANAVKETHWLSYTNYA
ALVSGSTFSTDALADGKTDVFINIDLKTLETHSGLARVIIGSFLNAIYNRDGEVKGRALFLLDEVARLGY
MRILETARDAGRKYGITLTMIYQSIGQMRETYGGRDAASKWFESASWISFAAINDPETADYISKRCGMTT
VETDQVSRSFQAKGSSRTRSKQLAARPLIQPHEVLRMRADEQIVFTAGNAPLRCGRAIWFRREDMAACVG
TNRFHPGG

  Protein domains


Predicted by InterproScan.

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

(163-635)

  Protein structure



No available structure.



ID   16121 GenBank   WP_334141933
Name   t4cp2_QM996_RS00155_pB insolico UniProt ID   _
Length   817 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 817 a.a.        Molecular weight: 91573.47 Da        Isoelectric Point: 6.4279

>WP_334141933.1 conjugal transfer protein TrbE [Sinorhizobium chiapasense]
MVALKRFRATGPSFADLVPYAGLVDNGVLLLKDGSLMAGWYFAGPDSESATDLERNELSRQINAILSRLG
SGWMIQVEAVRIPTFDYPSEDRCHFPDPVTRAIDAERRAHFARERGHFESKHALILTHRPLESKKTALSK
YIYSDEESRKKTYADTVLFIFRNAIREIEQYLANTLSIRRMETREVVERGGERVTRYDELLQFVRFCITG
ENHPIRLPDAPMYLDWIATAELEHGLTPKVENRFLGVVAIDGLPAESWPGILNSLDLMPLTYRWSSRFIF
LDAEAARQKLERTRKKWQQKVRPFFDQLFQTQSRSVDQDAMTMVAETEDAIAQASSQLVTYGYYTPVIVL
FDGDREALQEKAEAIRRLIQAEGFGARIETLNATDAYLGSLPGNWYCNIREPLINTSNLADLVPLNSVWS
GNPIAPCPFYPANSPPLIQVASGSTAFRLNLHVDDVGHTLIFGPTGSGKSTLLALIAAQFRRYGQAQIFA
FDKGSSLLPLTLAARGDHYEIGGDAREAGAALAFCPLSDLENDADRAWATEWIEMLVALQGVTITPDHRN
AISRQVGLMASAPGRSLSDFVSGVQMREIKDALHHYTVDGPMGQLLDAEQDGLTLGAFQTFEIEHLMNMG
ERNLVPVLTYLFRRVEKRLDGSPSLILLDEAWLMLGHPVFRSKIREWLKVLRKANCAVVLATQSISDAER
SGIIDVLKESCPTKICLPNGAARELGTREFYERIGFNERQIEIVSTATPKREYYVATPEGRRLFDMSLGP
VALSFVGASGKEDLKRIRALKSEHGRDWPIHWLQTRGVHDAATLLKA

  Protein domains


Predicted by InterproScan.

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

(191-400)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 15550..28996

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
QM996_RS00085 (QM996_31170) 13814..14380 + 567 WP_334141911 conjugative transfer signal peptidase TraF -
QM996_RS00090 (QM996_31175) 14370..15533 + 1164 WP_334141913 conjugal transfer protein TraB -
QM996_RS00095 (QM996_31180) 15550..16164 + 615 WP_334141915 TraH family protein virB1
QM996_RS00100 (QM996_31185) 16250..17473 - 1224 WP_334141917 ATP-binding protein -
QM996_RS00105 (QM996_31190) 17667..17888 - 222 WP_334141919 helix-turn-helix transcriptional regulator -
QM996_RS00110 (QM996_31195) 18133..18453 + 321 WP_334142258 transcriptional repressor TraM -
QM996_RS00115 (QM996_31200) 18457..19167 - 711 WP_334141921 autoinducer binding domain-containing protein -
QM996_RS00120 (QM996_31205) 19490..20788 - 1299 WP_334141923 IncP-type conjugal transfer protein TrbI virB10
QM996_RS00125 (QM996_31210) 20802..21239 - 438 WP_334141924 conjugal transfer protein TrbH -
QM996_RS00130 (QM996_31215) 21243..22055 - 813 WP_334141926 P-type conjugative transfer protein TrbG virB9
QM996_RS00135 (QM996_31220) 22073..22735 - 663 WP_334141928 conjugal transfer protein TrbF virB8
QM996_RS00140 (QM996_31225) 22759..23901 - 1143 WP_334142260 P-type conjugative transfer protein TrbL virB6
QM996_RS00145 (QM996_31230) 23942..24118 - 177 WP_334141929 entry exclusion protein TrbK -
QM996_RS00150 (QM996_31235) 24112..24912 - 801 WP_334141931 P-type conjugative transfer protein TrbJ virB5
QM996_RS00155 (QM996_31240) 24887..27340 - 2454 WP_334141933 conjugal transfer protein TrbE virb4
QM996_RS00160 (QM996_31245) 27351..27650 - 300 WP_334141934 conjugal transfer protein TrbD virB3
QM996_RS00165 (QM996_31250) 27643..28029 - 387 WP_334141936 TrbC/VirB2 family protein virB2
QM996_RS00170 (QM996_31255) 28019..28996 - 978 WP_334141938 P-type conjugative transfer ATPase TrbB virB11
QM996_RS00175 (QM996_31260) 29007..29633 - 627 WP_334141940 acyl-homoserine-lactone synthase -
QM996_RS00180 (QM996_31265) 29987..31210 + 1224 WP_334142262 plasmid partitioning protein RepA -
QM996_RS00185 (QM996_31270) 31207..32235 + 1029 WP_334141942 plasmid partitioning protein RepB -
QM996_RS00190 (QM996_31275) 32436..33647 + 1212 WP_334141944 plasmid replication protein RepC -

Host bacterium

ID   22270 GenBank   NZ_CP144207
Plasmid name   pB Incompatibility group   -
Plasmid size   444306 bp Coordinate of oriT [Strand]   10398..10432 [+]
Host baterium   Sinorhizobium chiapasense strain S24

Cargo genes

Drug resistance gene   -
Virulence gene   -
Metal resistance gene   -
Degradation gene   bhpD, linJ, dxnH
Symbiosis gene   fixA, fixB
Anti-CRISPR   -