Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   200427
Name   oriT_ICEMsp.SymM1D-1 in_silico
Organism   Mesorhizobium sp. M1D.F.Ca.ET.043.01.1.1
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   CP034444 (122615..122675 [-], 61 nt)
oriT length   61 nt
IRs (inverted repeats)     _
Location of nic site      _
Conserved sequence flanking the
  nic site    		  _
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 61 nt

>oriT_ICEMsp.SymM1D-1
AAAACGATGTGCAGACAAAGACTTCACCACCTCAAAGAGGCGGTGCCTTTATCTTGCCTTA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


T4CP

ID   17005 GenBank   AZO75806
Name   t4cp2_EJ067_10100_ICEMsp.SymM1D-1 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: 90306.56 Da        Isoelectric Point: 6.1682

>AZO75806.1 conjugal transfer protein TrbE [Mesorhizobium sp. M1D.F.Ca.ET.043.01.1.1]
MLNLSEYRGKADRLADHLPWVALVAPGIVLNKDGSFQRTLRFRGPDLESATEAELVGICARANNALRRLG
SGWALFFEAERVEALGYPQSRFPDPASWLVDEERRAAFEGKVAHFESRYHLTLLFMPSPDSQARAESALV
DSHHSEGERDWRQEMTRFRDETARVLDLLSGFMPEVRGLEDAETLTYLHGTIATRRHPVTVPETPMYLDG
FLVDVPLTGGLEPMLGDQHLRTLTILGFPNLTRPGILDALNNQDFAYRWVTRFIPLDKTAATKTLTRLRR
QWFAKRKSISAILREVVTNEPVPLVDSDADNKAHDADEALQALGGDHVGFGYLTTTVTVWDEDRQAAAEK
LRAVERVINGLGFTTIRESVNAVEAWLGSLPGHVYANIRQPLVHTLNLAHLMPLSSVWAGPATNEHVAKV
TQTDAPPLLFAETSGSTPFRLSTHVDDVGHMLIVGPTGAGKSVLLALVALQFRRYAGAQVYVFDKGNSAR
AATLAMGGEHHALGADGSLAFQPLRNIGDHATRSWAAEWIAGLIAHENVTLTPEVKEAVWSALSSLATAP
AQERTLTGLSVLLQSNALKSALMPYTLDGPFGRLLDADDDLLALSDVQCFETEQLMHSQGAVTTPVLTYL
FHRLEERFDGRPTLLMLDEAWVYLDNPFFAARIREWLKVLRKKNVSVIFATQSLADIAGSSIAPAIIESC
PQRIFLPNDRAVEPQARAAYERFGLNERQIELVARATPKRHYYLQSRRGNRLFELGLGPITLALCGASDP
ATQTLIDSVLSKHGQDSFASRFLGARGLDWAAELLRQFPQSDMEQSS

  Protein domains


Predicted by InterproScan.

TraG P-loop domain (P-loop_TraG)

(578-732)

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

(307-389)

  Protein structure



No available structure.



ID   17006 GenBank   AZO71488
Name   t4cp2_EJ067_10125_ICEMsp.SymM1D-1 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: 75143.54 Da        Isoelectric Point: 6.7153

>AZO71488.1 conjugal transfer protein TraG [Mesorhizobium sp. M1D.F.Ca.ET.043.01.1.1]
MTPTKLLIGQIAIVFAIVLIGVWAATQWCAQMLAFQEQLGAPWFVAAGWPIYEPWKLLEWWFQFDAYAPE
VFDKAGMLAGTSGLMGFAAAIAGSLWRARQRGLVTTYGSSRWAATREIDKAGLFQPAGVFLGKLQDRYLR
HDGPEHVMAFAPTRSGKGVGLVVPTLLSWSGSAVIHDIKGENWQLTSGWRSKFSYCLLFNPTDPRSARYN
PLLEVRKGPNEVRDVQNIADILVDPEGALERRNHWEKTSHSLLVGAILHVLYAEEEKTLARVATFLSDPQ
RSFVATLQRMMTTNHLGAAERPQVHPVVASAAREVLNKSENERSGVLSTAMSFLGLYHDPTVAAATSSCD
WRIADLMDAARPTSLYLVVPPSDISRTKPLVRLILNQIGRRLTERLEGDPKKGRKHQLLMMLDEFPALGR
LDFFETALAFMAGYGIRAYLIAQSLNQISKAYGENNAILDNCHVRIAFSSNDERTAKRISDALGTATELR
SMRNYAGHRLAPWLSHVMVSRQETARQLLTPGEVMQLPPSDELVLVSGLPPIRAKKLRYYEDQNFTERML
PAPVLHDTLYADSPAPRQDDWTGQVRRVDRRLASDDENAGAALADEGGVQQQRHPGLPEEHTAVTREPDQ
DDLSPPADDDSEAMADKRVMDRISTVGRAYGINEGRGDDKDIVPGF

  Protein domains


Predicted by InterproScan.

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

(123-560)

  Protein structure



No available structure.



ID   17007 GenBank   AZO75828
Name   t4cp2_EJ067_11195_ICEMsp.SymM1D-1 insolico UniProt ID   _
Length   576 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 576 a.a.        Molecular weight: 63918.59 Da        Isoelectric Point: 8.9642

>AZO75828.1 type IV secretion system protein VirD4 [Mesorhizobium sp. M1D.F.Ca.ET.043.01.1.1]
MASTKTTPNIALSIACSLALGFCAASLYATFRHWRSGAALMTFDVRAFWFETPFYLGFATPVFYRGVAIV
LSTSAVVLLIQQIVTRRNLEHHGTARWARVDEMRRPGFLRRYRGVTGPVFGKTSGPFWPGYYLTNGEQPH
SLIVAPTRAGKGVGIVIPTLLTFKGSVIALDVKGELFELTSRARQAAGAEVFKFAPLDSERRTNCFNPLL
DLIALPPQQQFTEARRLAANLITAKGEGAEGFVNGARDLFVAGILACIERGTPTIGAVYDLFAQPGEKFK
LFARLAMETRNKEAQRIFDDMAGNDTKILTSYTSVLGDGGLNLWADPAVKAATSRSDFSVYDLRRRRTCI
YLCVSPNDLEVVAPLVRLFFQQVVSILQRSMPRQDEKYEVLFLLDEFKHLGKLEAIETAITTIAGYKGRF
MLIIQSLSALTGAYGEAGKQNFLSNTGLQVFMATADDETPNYISKAIGEYTFEAKSISYSQARTFDWNIQ
KSNQGAPLLRPEQVRLLDDDYEIVLIKGLPPLKLRKVRYFSDRILKRIFESQAGVLPEPAPLTIADEGLS
AESQLDDPLPELTQRL

  Protein domains


Predicted by InterproScan.

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

(96-537)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 2027285..2036348

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
EJ067_10045 2022680..2022835 - 156 AZO71474 cbb3-type cytochrome c oxidase subunit 3 -
EJ067_10050 2022846..2023577 - 732 AZO71475 cytochrome-c oxidase, cbb3-type subunit II -
EJ067_10055 2023589..2025196 - 1608 AZO71476 cytochrome-c oxidase, cbb3-type subunit I -
EJ067_10060 2025282..2025857 + 576 Protein_2000 hemerythrin domain-containing protein -
EJ067_10065 2025854..2026612 - 759 AZO71477 Crp/Fnr family transcriptional regulator -
EJ067_10070 2026999..2027271 - 273 AZO71478 DUF2274 domain-containing protein -
EJ067_10075 2027285..2028502 - 1218 AZO71479 TrbI/VirB10 family protein virB10
EJ067_10080 2028514..2029542 - 1029 AZO71480 P-type conjugative transfer protein TrbG virB9
EJ067_10085 2029532..2030263 - 732 AZO71481 conjugal transfer protein TrbF virB8
EJ067_10090 2030264..2031586 - 1323 AZO71482 P-type conjugative transfer protein TrbL virB6
EJ067_10095 2031613..2032344 - 732 AZO71483 P-type conjugative transfer protein TrbJ virB5
EJ067_10100 2032341..2034794 - 2454 AZO75806 conjugal transfer protein TrbE virb4
EJ067_10105 2034788..2035060 - 273 AZO71484 conjugal transfer protein virB3
EJ067_10110 2035060..2035368 - 309 AZO71485 conjugal transfer protein TrbC virB2
EJ067_10115 2035380..2036348 - 969 AZO71486 P-type conjugative transfer ATPase TrbB virB11
EJ067_10120 2036345..2036758 - 414 AZO71487 CopG family transcriptional regulator -
EJ067_10125 2036875..2038905 - 2031 AZO71488 conjugal transfer protein TraG -
EJ067_10130 2039049..2039279 + 231 Protein_2014 XRE family transcriptional regulator -
EJ067_10135 2039470..2039859 - 390 AZO71489 hypothetical protein -

Region 2: 4157960..4167013

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
EJ067_20125 4155409..4157433 + 2025 AZO73166 conjugal transfer protein TraG -
EJ067_20130 4157550..4157963 + 414 AZO73167 CopG family transcriptional regulator -
EJ067_20135 4157960..4158928 + 969 AZO73168 P-type conjugative transfer ATPase TrbB virB11
EJ067_20140 4158941..4159249 + 309 AZO73169 conjugal transfer protein TrbC virB2
EJ067_20145 4159249..4159521 + 273 AZO73170 conjugal transfer protein virB3
EJ067_20150 4159515..4161965 + 2451 AZO73171 conjugal transfer protein TrbE virb4
EJ067_20155 4161962..4162687 + 726 AZO73172 P-type conjugative transfer protein TrbJ virB5
EJ067_20160 4162721..4164043 + 1323 AZO73173 P-type conjugative transfer protein TrbL virB6
EJ067_20165 4164044..4164775 + 732 AZO73174 conjugal transfer protein TrbF virB8
EJ067_20170 4164765..4165802 + 1038 AZO73175 P-type conjugative transfer protein TrbG virB9
EJ067_20175 4165799..4167013 + 1215 AZO73176 TrbI/VirB10 family protein virB10
EJ067_20180 4167026..4167268 + 243 AZO73177 DUF2274 domain-containing protein -
EJ067_20185 4167504..4168853 - 1350 AZO75956 oxygen-independent coproporphyrinogen III oxidase -
EJ067_20190 4169006..4169749 + 744 AZO73178 Crp/Fnr family transcriptional regulator -
EJ067_20195 4170246..4171865 + 1620 AZO73179 cytochrome-c oxidase, cbb3-type subunit I -

Host bacterium

ID   381 Element type   ICE (Integrative and conjugative element)
Element name   ICEMsp.SymM1D-1 GenBank   CP034444
Element size   7127907 bp Coordinate of oriT [Strand]   122615..122675 [-]
Host bacterium   Mesorhizobium sp. M1D.F.Ca.ET.043.01.1.1 Coordinate of element   1983612..2315722

Cargo genes

Drug resistance gene   -
Virulence gene   btpB
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   fixS, fixI, nifX, fixG, fixP, fixQ, fixO, fixN, nodM, nodD, nolL, nodU, nodB, eJ067_10535, nodJ, nodI, nodA, nifU, nifN, nifE, nifK, nifD, nifH, nifQ, mLTONO_5203, nifS, fixA, fixB, fixC, fixX, nifA, nifB, nifZ, nifT, nodF, nodE, nodC, nodH, fixU, nifW, mlr6097, nopC, nolV, nolU, nolT, nolB, nolW, nolX, fixH
Anti-CRISPR   AcrIIC1, AcrVA1