Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   200142
Name   oriT_ICEMcSym(1271)-alpha in_silico
Organism   Mesorhizobium ciceri biovar biserrulae WSM1271
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NC_014923 (39081..39140 [+], 60 nt)
oriT length   60 nt
IRs (inverted repeats)     _
Location of nic site      _
Conserved sequence flanking the
  nic site    		  _
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 60 nt

>oriT_ICEMcSym(1271)-alpha
AAAATGATGTGCAGACAAACACTTCGCCGCCTCTTGGAGGGGGTGTCTTTATCTTGCCTT

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


T4CP

ID   16581 GenBank   WP_013533267
Name   trbE_MESCI_RS27635_ICEMcSym(1271)-alpha insolico UniProt ID   _
Length   813 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 813 a.a.        Molecular weight: 89740.25 Da        Isoelectric Point: 6.6374

>WP_013533267.1 MULTISPECIES: conjugal transfer protein TrbE [Mesorhizobium]
MLNLSEYRGKADRLADHLPWAALVAPGIVLNKDGSFQRSFGFRGPDLESATEAELIGICARANNALRRLG
SGWALFFEAERIEALGYPSSRFPDAASWLVDEERRAAFQGKVAHYESRYHLTLTFMPPPDSQARAQSALV
DSHHSGGEREWRQELTRFRDETGRVLDLLSGFMPEIRALDDAETLTYLHGTISTRRHPVAAPETPIYLDG
ILVDAPLTGGLEPMLGNHHLRTLTILGFPNVTRPGILDALNHQDFPYRWMTRFIPLDKTEATRTLTRLRR
QWFAKRKSIVAILREVVTSEPVPLVDTDAENKALDADAALQALGGDHVGFGYLTTTVTVWDEDHQAAAGK
LRAVERVVNGLGFATIREGVNAVEAWLGSLPGHVYANVRQPLVHTLNLAHLMPLSSVWAGPAANEHLAKV
TQAEAPPLLFASTSGSTPFRLSTHVDDVGHMLIVGPTGAGKSVLVALFALQFRRYAGAQVYVFDKGNSAR
AAILAMGGEHHALRAHGALAFQPLRKIDDPAIRSWAAEWIAGLIAHENVTVTPEAKEAIWSALTSLATAP
AQERTLTGLSVLLQSNALKSALMPYTLDGPFGRLLDADDDRLALSDVQCFETEELMHSQGAVLPVLTYLF
HRLEARFDGRPTLLMLDEAWLYLDNPLFAGRIREWLKVLRKKNVSVIFATQSLADVAGSAIAPAIIESCP
QRIFLPNDRAVEPQAREAYERFGLNERQIELVARATPKRQYYLQSRRGNRLFQLGLGPIALALCGASDPA
SQTQIDRILSEHGQDGFAFHFVNARGLYWAAELLRQFPQPDME

  Protein domains


Predicted by InterproScan.

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

(307-389)

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

(179-286)

  Protein structure



No available structure.



ID   16582 GenBank   WP_013533272
Name   t4cp2_MESCI_RS27660_ICEMcSym(1271)-alpha insolico UniProt ID   _
Length   676 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 676 a.a.        Molecular weight: 75022.45 Da        Isoelectric Point: 6.9385

>WP_013533272.1 MULTISPECIES: conjugal transfer protein TraG [Mesorhizobium]
MTPTKLLIGQIVVVFAIVMLGVWTATQWCAHMLGHQPPLGAPWFVAAGWPIYKPWKLFEWWYHFDAYAPE
VFDKAGALAGASGFVGCAAAIGGSLWRARQLGSVTTYGSSRWATTQEIVTAGLFRPAGVFLGKLKDRYLR
HDGPEHVMAFAPTRSGKGVGLVVPTLLSWTGSAVIHDIKGENWQLTSGWRSKFSYCLLFNPTDPRSARYN
PLLEVRKGPQEVRDVQNIADILVDPEGALDRRNHWEKTSHSLLVGAVLHVLYAEEEKTLARVATFLSDPQ
RSFSATLQRMMTTNHLGTPDKPEVHPVVASAARELLNKSENERSGVLSTAMSFLGLYRDPTVAAATSTCD
WRIVDLMDAERPISLYLVVPPSDISRTKPLVRLILNQIGRRLTERLEGDPSRSRKHRLLMMLDEFPALGR
LDFFETALAFMAGYGIRAYLIAQSLNQISKAYGENSAILDNCHVRIAFSSNDERTAKRISDALGTATELR
SMRNYAGHRLAPWLSHVMVSRQETARPLLTPGEVMQLPQTDELVLISGLPPLRAQKLRYYEDWNFTERVL
PSPVLRDSPYADRPASRTDDWTGRVRGVDGRLAAGDEIADAAIGDEGGVQQQRHPALAEDQVVLSPEAEQ
DDLFKSVDDDSEPVADKRVMDRISTAARAYGINEGRGDDKDIVPGF

  Protein domains


Predicted by InterproScan.

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

(110-560)

  Protein structure



No available structure.



ID   16583 GenBank   WP_013533349
Name   virD4_MESCI_RS28080_ICEMcSym(1271)-alpha insolico UniProt ID   _
Length   581 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 581 a.a.        Molecular weight: 64406.99 Da        Isoelectric Point: 8.2007

>WP_013533349.1 MULTISPECIES: type IV secretion system ATPase VirD4 [Mesorhizobium]
MPSTKTTTPNLAVSIACSLAVGFCAASLYATFRHGGGGEALMAFDVRAFWFETPFYLGFATPVFYRGAAI
VLSTSVVVLLIQQVVLRRKLEHHGTARWARVDEMRRTGYLRRYRGVKGPVFGKTSGPFWPGYYLTNGEQP
HSLIVAPTRAGKGVGVVIPTLLTFKGSVIALDVKGELFELTSRARKAAGDDVFKFAPLDSERRTNCYNPL
LDLIALPPQLQFTEARRLAANLITAKGEGAEGFISGARDIFVAGILACIERGTPTIGAVYDLFAQPGEKF
KLFAQLAMETRNKEAQRIFDDMAGNDTKILTSYTSVLGDGGLNLWADPAVKAATSRSDFSVYDLRRRRTC
IYLCVGPNDLEVIAPLIRLFFQQIVSILQRSLPRPEEKHEVLFLLDEFKHLGKLEAIETAITTIAGYKGR
FMLIIQSLSALTGAYGEAGKQNFLSNTGLQVFMATADDETPNYISKAIGEYTFEAKSISYSQARRFDWNI
QNSHQGAPLLRPEQVRLLDDDYEIVLIKGLPPLQLRKVRYFSDRILKRIFEGQTGALPEPAPLTEAEEEL
STDFRLDEPPRGLAQEFNDTV

  Protein domains


Predicted by InterproScan.

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

(97-538)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 5702686..5711747

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
MESCI_RS27590 (Mesci_5510) 5697955..5699583 - 1629 WP_013533258 cytochrome-c oxidase, cbb3-type subunit I -
MESCI_RS27595 (Mesci_5511) 5700027..5700776 - 750 WP_013533259 Crp/Fnr family transcriptional regulator -
MESCI_RS27600 (Mesci_5512) 5700932..5702278 + 1347 WP_013533260 oxygen-independent coproporphyrinogen III oxidase -
MESCI_RS27605 (Mesci_5513) 5702411..5702683 - 273 WP_013533261 DUF2274 domain-containing protein -
MESCI_RS27610 (Mesci_5514) 5702686..5703906 - 1221 WP_013533262 TrbI/VirB10 family protein virB10
MESCI_RS27615 (Mesci_5515) 5703920..5704948 - 1029 WP_013533263 P-type conjugative transfer protein TrbG virB9
MESCI_RS27620 (Mesci_5516) 5704938..5705669 - 732 WP_013533264 conjugal transfer protein TrbF virB8
MESCI_RS27625 (Mesci_5517) 5705670..5706992 - 1323 WP_013533265 P-type conjugative transfer protein TrbL virB6
MESCI_RS27630 (Mesci_5518) 5707021..5707746 - 726 WP_013533266 P-type conjugative transfer protein TrbJ virB5
MESCI_RS27635 (Mesci_5519) 5707752..5710193 - 2442 WP_013533267 conjugal transfer protein TrbE virb4
MESCI_RS27640 (Mesci_5520) 5710187..5710459 - 273 WP_013533268 VirB3 family type IV secretion system protein virB3
MESCI_RS27645 (Mesci_5521) 5710459..5710767 - 309 WP_013533269 TrbC/VirB2 family protein virB2
MESCI_RS27650 (Mesci_5522) 5710779..5711747 - 969 WP_013533270 P-type conjugative transfer ATPase TrbB virB11
MESCI_RS27655 (Mesci_5523) 5711744..5712157 - 414 WP_013533271 CopG family transcriptional regulator -
MESCI_RS27660 (Mesci_5524) 5712273..5714303 - 2031 WP_013533272 conjugal transfer protein TraG -
MESCI_RS27665 (Mesci_5525) 5714504..5716327 - 1824 WP_013533273 glutamine--fructose-6-phosphate transaminase (isomerizing) -

Region 2: 5773468..5782890

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
MESCI_RS27975 (Mesci_5587) 5768665..5768997 - 333 WP_013533331 helix-turn-helix transcriptional regulator -
MESCI_RS27980 (Mesci_5588) 5769981..5770733 + 753 WP_013533332 carbonic anhydrase -
MESCI_RS27985 (Mesci_5589) 5770905..5773349 + 2445 WP_013533333 ATP-binding protein -
MESCI_RS27990 (Mesci_5590) 5773468..5774508 - 1041 WP_013533334 P-type DNA transfer ATPase VirB11 virB11
MESCI_RS27995 (Mesci_5591) 5774492..5775634 - 1143 WP_013533335 type IV secretion system protein VirB10 virB10
MESCI_RS28000 (Mesci_5592) 5775631..5776512 - 882 WP_013533336 TrbG/VirB9 family P-type conjugative transfer protein virB9
MESCI_RS28005 (Mesci_5593) 5776509..5777222 - 714 WP_013533337 type IV secretion system protein VirB8 virB8
MESCI_RS28010 (Mesci_5594) 5777219..5777377 - 159 WP_013533338 type IV secretion system lipoprotein VirB7 -
MESCI_RS28015 (Mesci_5595) 5777400..5778287 - 888 WP_013533339 type IV secretion system protein virB6
MESCI_RS28020 (Mesci_5596) 5778346..5779029 - 684 WP_013533340 type IV secretion system protein VirB5 -
MESCI_RS28025 (Mesci_5597) 5779042..5781411 - 2370 WP_013533341 VirB4 family type IV secretion/conjugal transfer ATPase virb4
MESCI_RS28030 (Mesci_5598) 5781411..5781737 - 327 WP_013533342 type IV secretion system protein VirB3 virB3
MESCI_RS28035 (Mesci_5599) 5781737..5782102 - 366 WP_013533343 pilin major subunit VirB2 virB2
MESCI_RS28040 (Mesci_5600) 5782117..5782890 - 774 WP_013533344 type IV secretion system lytic transglycosylase VirB1 virB1
MESCI_RS28050 (Mesci_5602) 5784124..5784849 + 726 WP_013533346 response regulator -
MESCI_RS33115 5785000..5785134 - 135 Protein_5597 hypothetical protein -
MESCI_RS33120 5785253..5785396 - 144 WP_245306699 transposase domain-containing protein -
MESCI_RS32785 5785434..5785856 - 423 WP_245262912 IS66 family transposase -
MESCI_RS32790 5785904..5785969 - 66 WP_245263014 hypothetical protein -
MESCI_RS32795 5785954..5786563 - 610 Protein_5601 IS66 family transposase zinc-finger binding domain-containing protein -
MESCI_RS28070 5787113..5787487 - 375 WP_174299069 hypothetical protein -

Host bacterium

ID   144 Element type   ICE (Integrative and conjugative element)
Element name   ICEMcSym(1271)-alpha GenBank   NC_014923
Element size   6264489 bp Coordinate of oriT [Strand]   39081..39140 [+]
Host bacterium   Mesorhizobium ciceri biovar biserrulae WSM1271 Coordinate of element   5680050..6125270

Cargo genes

Drug resistance gene   -
Virulence gene   -
Metal resistance gene   -
Degradation gene   bphA
Symbiosis gene   fixS, fixI, fixH, fixG, fixP, fixQ, fixO, fixN, nodM, mlr6097, nifX, nifN, nifE, nifK, nifD, nifH, nifQ, nifS, nifW, fixA, fixB, fixC, fixX, nifB, nifZ, nifT, nifA, nodD, nodA, nodF, nodE, nodB, nodC, nodI, nodJ, nodH, eB233_29665, nodU
Anti-CRISPR   -