Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   104879
Name   oriT_pRSpC104b in_silico
Organism   Rhizobium sp. C104
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP092354 (105299..105354 [+], 56 nt)
oriT length   56 nt
IRs (inverted repeats)      23..29, 34..40  (ACGTCGC..GCGACGT)
Location of nic site      _
Conserved sequence flanking the
  nic site    		  _
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 56 nt

>oriT_pRSpC104b
CCCCGCCAGGGTGGCAAAAGGCACGTCGCGACAGCGACGTATAATTGCGCCCTTGG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   3451 GenBank   WP_239621282
Name   traA_MF410_RS34460_pRSpC104b insolico UniProt ID   _
Length   1100 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1100 a.a.        Molecular weight: 122448.56 Da        Isoelectric Point: 9.9799

>WP_239621282.1 Ti-type conjugative transfer relaxase TraA [Rhizobium sp. C104]
MAIAHFSVSIVGRGEGRSAVLSAAYRHCAKMDYEREARTIDYTRKQGLLHEEFSLPADAPDWARTLIADR
AVSGASEAFWNRVEAFEKRTDAQLAKDLTIALPVELTAEQNIALVRDFVDKHVVSKGMVADWVYHDNPGN
PHIHLMTTLRPLAEDGFGAKKVAVMGEDGQPLKTKAGKIVYELWAGGAAEFNALRDGWFERQNHHLALNG
ISLRVDGRSYEKQGIALEPTIHLGVGAKAIERKAERQGVRPELERLDLNEARRTENTRRILRNPAVVLDL
ITREKSVFNQRDIAKVLHRYVDDPGLFQQLMARILQSPEVLRLQRDTIDFATGERVPARYTTRAMIALEA
EMASRAIWLSRQSSHGVKQVLLQTTFARHAQLSDEQKTAIEHVAGPARIAAIVGRAGAGKTTMMKAAREA
WEAAGYRVVGGALAGKAAEGLEKEAGIQSRTLSAWELRGQRGRDGLDTKTIFVLDEAGMVGSRQMAGFVE
AVVRAGAKLVLVGDPDQLQPIEAGAAFRSIADRIGYAELETIYRQREDWMRTASLDLARGNVGAALVSYQ
SHDRLHGSTLKAEAVEQMIGDWNRDYDPAKTTLMLAHLRRDVRMLNDMARKRLVERGLVSEGHAFRTADG
MRPFAAGDQIVFLKNDTALGVKNGMLGRVVEAAPNRVVVAVGEGEHRRQVTVEQRAYNNLDHGYATTIHK
SQGATVDRVKVLASLSLDRHLTYVAMTRHREDLQVYYGERSFGFNGGLEKVLSRRNAKETTLDYQRGTLY
HQALSFAENRGLHLVQVARTLVRDRLDWTLRQKEKLVDLTKRMRAIGERLGLLQSPTRKQKKELAPMVAG
VKQFAFSVNDTIDQKLGEDPALKGQWDEVSTRFRYVFADPETAFRAMNFDAVLVDGQAAKQALQKLVDEP
ASIGALNGKTGLLAGKSDREARRVAEVNLPALKRDIEHYLAMRETARARIEGEEKTLRHRVSIDIPALSP
EARTVLERVRDAIDRNDLPAALGFAISNREAKLEIDGFNKAISERFGERTLLTNAARNPDGPLFDKMASG
LQPAEKESLKAAWPVMRTAQQLAAHERTTATLKQVEELRLTQRQTPALKQ

  Protein domains


Predicted by InterproScan.

AAA domain (AAA_30)

(381-568)

MobA/MobL family (MobA_MobL)

(17-243)

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

(855-950)

Viral (Superfamily 1) RNA helicase (Viral_helicase1)

(683-736)


  Protein structure



No available structure.




T4CP

ID   3396 GenBank   WP_239621246
Name   t4cp2_MF410_RS34280_pRSpC104b insolico UniProt ID   _
Length   819 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 819 a.a.        Molecular weight: 91646.21 Da        Isoelectric Point: 5.4141

>WP_239621246.1 conjugal transfer protein TrbE [Rhizobium sp. C104]
MVALKPFRYSGPSFADLVPYAGLVDNGILLLKDGSLMAGWYFAGPDSESSTDAERNEVSRQINAILSRLG
SGWIIQVEAARVPTIDYPAETDCHFPDDVTRAIDAERRAHFERESGHFESRHALILTWRPPEPRRSGLTR
YVYADAGSRSATYADSALDSFRTSIREVEQYLANVVTIRRMRTDEAEERGGFRIARYDELFQFIRFCVTG
ENHPVRLPEIPMYLDWLVTAELQHGLTPTIENRFLGVVAIDGLPAASWPGILNALDLMPLTYRWSSRFVF
LDEQEARARLERTRKKWQQKVRPFFDQLFQTQSRSLDQDAMMMVAESEDAIAEAASQLVSYGYYTPVIVL
FDDEQSRLQEKCEAIRRLIQAEGFGARIETLNATDAFLGSLPGVSYANIREPLINTRNLADLVPLNSVWS
GSPVAPCPFYPPASPPLMQVASGSTPFRLNLHVDDVGHTLIFGPTGSGKSTLLALIAAQFRRYRDAQLFA
FDKGRSMLPLTLAVGGDHYEIGGDTGGEGEGNSPRLAFCPLAELSTDGDRAWATEWLETLVSLQGVTVTP
DHRNAISRQIALMAQSRGRSLSDFVSGVQMREIKDALHHYTVDGPMGQLLDAEEDGLTLGAFQCFEVEEL
MNMGERNLVPVLTYLFRRVEKRLTGAPSLIILDEAWLMLGHPLFRDKIREWLKVLRKANCAVVLATQSIS
DAERSGIIDVLKESCPTKICLPNGAAREPGTREFYERIGFNERQIEIVATALPKREYYVASPDGRRLFDM
ALGPVALSFVGASGKGDLKRIRALYAEHRDNWPLLWLQQRGIAHAETYL

  Protein domains


Predicted by InterproScan.

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

(193-400)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 66460..76097

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
MF410_RS34245 (MF410_34230) 61788..63032 - 1245 WP_239621232 plasmid replication protein RepC -
MF410_RS34250 (MF410_34235) 63189..64184 - 996 WP_239621233 plasmid partitioning protein RepB -
MF410_RS34255 (MF410_34240) 64269..65459 - 1191 WP_239621236 plasmid partitioning protein RepA -
MF410_RS34260 (MF410_34245) 65825..66463 + 639 WP_239621238 acyl-homoserine-lactone synthase TraI -
MF410_RS34265 (MF410_34250) 66460..67431 + 972 WP_239621240 P-type conjugative transfer ATPase TrbB virB11
MF410_RS34270 (MF410_34255) 67421..67828 + 408 WP_239621242 conjugal transfer pilin TrbC virB2
MF410_RS34275 (MF410_34260) 67821..68120 + 300 WP_239621244 conjugal transfer protein TrbD virB3
MF410_RS34280 (MF410_34265) 68131..70590 + 2460 WP_239621246 conjugal transfer protein TrbE virb4
MF410_RS34285 (MF410_34270) 70640..71380 + 741 WP_239621311 P-type conjugative transfer protein TrbJ virB5
MF410_RS34290 (MF410_34275) 71377..71598 + 222 WP_239621248 entry exclusion protein TrbK -
MF410_RS34295 (MF410_34280) 71592..72782 + 1191 WP_239621250 P-type conjugative transfer protein TrbL virB6
MF410_RS34300 (MF410_34285) 72801..73463 + 663 WP_239621252 conjugal transfer protein TrbF virB8
MF410_RS34305 (MF410_34290) 73480..74325 + 846 WP_239621254 P-type conjugative transfer protein TrbG virB9
MF410_RS34310 (MF410_34295) 74325..74786 + 462 WP_239621255 conjugal transfer protein TrbH -
MF410_RS34315 (MF410_34300) 74799..76097 + 1299 WP_239621256 IncP-type conjugal transfer protein TrbI virB10
MF410_RS34320 (MF410_34305) 76267..77052 - 786 WP_239621257 ABC transporter permease -
MF410_RS34325 (MF410_34310) 77049..77900 - 852 WP_239621259 ABC transporter permease -
MF410_RS34330 (MF410_34315) 77893..78504 - 612 WP_345774749 ABC transporter ATP-binding protein -
MF410_RS34335 (MF410_34320) 78490..79005 - 516 Protein_65 ATP-binding cassette domain-containing protein -
MF410_RS34340 (MF410_34325) 79002..80117 - 1116 WP_239621260 extracellular solute-binding protein -

Host bacterium

ID   5317 GenBank   NZ_CP092354
Plasmid name   pRSpC104b Incompatibility group   -
Plasmid size   127383 bp Coordinate of oriT [Strand]   105299..105354 [+]
Host baterium   Rhizobium sp. C104

Cargo genes

Drug resistance gene   -
Virulence gene   -
Metal resistance gene   -
Degradation gene   linJ, LinG
Symbiosis gene   -
Anti-CRISPR   -