Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   200443
Name   oriT_ICEMsp.SymNZP2298 in_silico
Organism   Mesorhizobium sp. NZP2298
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   CP033365 (146676..146735 [+], 60 nt)
oriT length   60 nt
IRs (inverted repeats)      26..32, 36..42  (CCGCCTC..GAGGCGG)
Location of nic site      _
Conserved sequence flanking the
  nic site    		  _
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 60 nt

>oriT_ICEMsp.SymNZP2298
AAACGATGTGCAGACAAAGACTTCGCCGCCTCATGGAGGCGGTGCCTTTATCTTGCCTTA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


T4CP

ID   17038 GenBank   QKC98722
Name   t4cp2_EB231_31845_ICEMsp.SymNZP2298 insolico UniProt ID   _
Length   816 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 816 a.a.        Molecular weight: 90285.86 Da        Isoelectric Point: 6.1178

>QKC98722.1 conjugal transfer protein TrbE [Mesorhizobium sp. NZP2298]
MLNLSEYRGKADRLADHLPWAALVAPGIVLNKDGSVQRTIRFRGPDLESSTEAELIGICARANNALRRLG
SGWTLFFEAERIEALGYPSSRFPDAASWLVDEERRAAFEGKVAHFESRYHLTLLSMPPPDAQARAESALV
DSHHSEGERDWRQEMARFRDETDRVLDLLSGFMPEVRLLDDAETLTYLHDTISTRRHPVAVPETPMYLDG
ILVDVPLTGGLEPMLGEQHLRTLTILGFPNLTRPGILDALNHQDFAYRWMTRFIPLGKTEATKTLTRLRR
QWFAKRKSIVAILREVVSNEPVPLVDSDADNKALDADEALQALGGDHVGFGYLTATVTVWDEDRQAAAEK
LRAVERIINGLGFTTIRESVNAVEAWLGSLPGHVYANVRQPLVHTLNLAHLMPLSSVWAGPAANEHLAEV
TGREAPPLLIAETSGSTPFRLSSHVEDVGHMLIVGPTGAGKSVLLALIALQFRRYAGAQVYVFDKGNSAR
AATLAMGGEHHVLGSDGALAFQPLRNIGDQGRRSWAAEWIAGLIAHENVTLTPEVKEAIWSALNSLATAP
AQERTLTGLSVLLQSNALKSALMPYTLDGPFGRLLDADDDRLALSDVQCFETEELMHRQSAVLPVLTYLF
HRLEERFDGRPTLLMLDEAWVYLDNPLFAARIREWLKVLRKKNVSVIFATQSLADIAGSAIAPAIIESCP
QRIFLPNDRAVEPQARTAYERFGLNNRQIELIARATPKRHYYLQSRCGNRLFELGLGPIALALCGASGPA
AQSLIDRVLSEHGQDSFVFRFLGARGLDWAAELLQQFPQPTKEQSS

  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)

TraG P-loop domain (P-loop_TraG)

(578-730)

  Protein structure



No available structure.



ID   17039 GenBank   QKC98727
Name   t4cp2_EB231_31870_ICEMsp.SymNZP2298 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: 75105.54 Da        Isoelectric Point: 6.6518

>QKC98727.1 conjugal transfer protein TraG [Mesorhizobium sp. NZP2298]
MTPTKLLIGQIAIVFAIVLLGVWAATQWCAHMLAFQEQLGAPWFVAAGWPIYEPWKLLEWWFQFDAYAPE
VFDKAGMLAGTSGFMGCAAAIAGSLWRARQRGLVTTYGSSRWAATREIEKAGLFQPAGVFLGKLKDRYLR
HDGPEHVMAFAPTRSGKGVGLVVPTLLSWSGSAVIHDIKGENWQLSSGWRSRFSHCLLFNPTDPRSARYN
PLLEVRKGSDEIRDVQNIADILVDPEGALERRNHWEKTSHSLLVGAILHVLYAEEEKTLARVATFLSDPQ
RSFAATLRRMMTTNHLGSANKPQVHPVVASAAREVLNKSENERSGVLSTAMSFLGLYRDPTVAAVTSDCD
WRIADLMDAEWPMSLYLVVPPSDISRTKPLVRLILNQIGRRLTERLEGDPKKSRKHQLLMMLDEFPALGR
LDFFETALAFMAGYGIRAYLIAQSLNQISKAYGDNNAILDNCHLRIAFSSNDERTAKRISDALGTATELR
SMRNYAGHRLAPWLSHVMVSRQETARPLLTPGEVMQLPPADELVLVSGLPPIRAKKLRYYEDHNFTERVL
PSPVLRDGPYADCPMSRPDDWTGQVRGVDRRLASDDESAGAALADEGGVQQQRHPGLPEEHTAVTQEPDQ
DDLSRPADDDSEAMADKRVMDRISTVAGAYGINEGRGDDKDIVPGF

  Protein domains


Predicted by InterproScan.

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

(112-559)

  Protein structure



No available structure.



ID   17040 GenBank   QKC98751
Name   t4cp2_EB231_32050_ICEMsp.SymNZP2298 insolico UniProt ID   _
Length   563 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 563 a.a.        Molecular weight: 62345.60 Da        Isoelectric Point: 8.7905

>QKC98751.1 type IV secretion system protein VirD4 [Mesorhizobium sp. NZP2298]
MSSTKTTSPNIAISIACSLALGFCAASLYATFRHGGSGEALMAFDVRAFWFETPFYLGFATPVFYQGAAI
VLSTSAVVLLIQQFVLRRKLEHHGTARWARVDEMRRTGYLRRYRGVTGPVFGKTSGPFWPGYYLTNGEQP
HSLIVAPTRAGKGVGIVIPTLLTFKGSVIALDVKGELFELTSRARKAAGHEVFKFAPLDSERRTNCYNPL
LDLIALHPQQQFTEARRLAANLITAKGEGAEGFVSGARDIFVAGILACIERGTPTIGAVYDLFAQPGEKF
KLFAQLAMETRNKEAQRIFDDMAGNDTKILTSYTSVLGDGGLNLWADPAVKAATSRSDFSVYDLRRRRTC
IYLCVGPNDLEVIAPLIRLFFQQIVSILQRSLPRQDEKHEVLFLLDEFKHLGKLEAIETAITTIAGYKGR
FMLIIQSLSALTGAYGEAGKQNFLSNTGLQVFMATADDETPNYISKAIGEYTFEAKSISYSQSRAFDRNI
QNSFQGAPLLRPEQVRLLNDEYEIVLIKGLPPLQLRKVRYFSDRILKRIFESQTGALPEPAPLMEAHPDD
TDG

  Protein domains


Predicted by InterproScan.

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

(97-540)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 6626037..6635094

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
EB231_31800 6622411..6622950 + 540 QKC98714 hemerythrin domain-containing protein -
EB231_31805 6622947..6623711 - 765 QKC98715 Crp/Fnr family transcriptional regulator -
EB231_31810 6623869..6625218 + 1350 QKC98716 oxygen-independent coproporphyrinogen III oxidase -
EB231_31815 6625755..6626024 - 270 QKC98717 DUF2274 domain-containing protein -
EB231_31820 6626037..6627251 - 1215 QKC99971 TrbI/VirB10 family protein virB10
EB231_31825 6627263..6628291 - 1029 QKC98718 P-type conjugative transfer protein TrbG virB9
EB231_31830 6628288..6629013 - 726 QKC98719 conjugal transfer protein TrbF virB8
EB231_31835 6629014..6630336 - 1323 QKC98720 P-type conjugative transfer protein TrbL virB6
EB231_31840 6630368..6631093 - 726 QKC98721 P-type conjugative transfer protein TrbJ virB5
EB231_31845 6631090..6633540 - 2451 QKC98722 conjugal transfer protein TrbE virb4
EB231_31850 6633534..6633806 - 273 QKC98723 conjugal transfer protein virB3
EB231_31855 6633806..6634114 - 309 QKC98724 conjugal transfer protein TrbC virB2
EB231_31860 6634126..6635094 - 969 QKC98725 P-type conjugative transfer ATPase TrbB virB11
EB231_31865 6635091..6635504 - 414 QKC98726 CopG family transcriptional regulator -
EB231_31870 6635623..6637653 - 2031 QKC98727 conjugal transfer protein TraG -
EB231_31875 6637764..6638010 + 247 Protein_6313 XRE family transcriptional regulator -
EB231_31880 6638309..6638740 - 432 QKC98728 hypothetical protein -
EB231_31885 6638909..6639595 + 687 QKC98729 hypothetical protein -

Region 2: 6656071..6665494

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
EB231_31945 6651676..6651803 + 128 Protein_6327 IS630 family transposase -
EB231_31950 6651803..6652426 + 624 Protein_6328 ISKra4 family transposase -
EB231_31955 6653408..6655948 + 2541 QKC98737 two-component system VirA-like sensor kinase -
EB231_31960 6656071..6657111 - 1041 QKC98738 P-type DNA transfer ATPase VirB11 virB11
EB231_31965 6657095..6658234 - 1140 QKC98739 type IV secretion system protein VirB10 virB10
EB231_31970 6658231..6659112 - 882 QKC98740 type IV secretion system protein VirB9 virB9
EB231_31975 6659109..6659822 - 714 QKC98741 type IV secretion system protein VirB8 virB8
EB231_31980 6659819..6659977 - 159 QKC98742 type IV secretion system lipoprotein VirB7 -
EB231_31985 6660004..6660891 - 888 QKC98743 type IV secretion system protein virB6
EB231_31990 6660949..6661623 - 675 QKC98744 type IV secretion system protein VirB5 -
EB231_31995 6661637..6664006 - 2370 QKC98745 VirB4 family type IV secretion/conjugal transfer ATPase virb4
EB231_32000 6664006..6664332 - 327 QKC98746 type IV secretion system protein VirB3 virB3
EB231_32005 6664332..6664697 - 366 QKC98747 pilin major subunit VirB2 virB2
EB231_32010 6664712..6665494 - 783 QKC98748 type IV secretion system lytic transglycosylase VirB1 virB1
EB231_32015 6666790..6667515 + 726 QKC98749 response regulator -
EB231_32020 6667491..6668108 - 618 QKC98750 hypothetical protein -

Host bacterium

ID   394 Element type   ICE (Integrative and conjugative element)
Element name   ICEMsp.SymNZP2298 GenBank   CP033365
Element size   7336816 bp Coordinate of oriT [Strand]   146676..146735 [+]
Host bacterium   Mesorhizobium sp. NZP2298 Coordinate of element   6602423..7069563

Cargo genes

Drug resistance gene   -
Virulence gene   gmd
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   fixS, fixI, fixH, fixG, fixP, fixQ, fixO, fixN, nodM, nodD, nolL, nodB, eB231_32485, nodJ, nodI, nodC, nodA, nodS, nifU, mlr6097, nifX, nifN, nifE, nifK, nifD, nifH, nifQ, mLTONO_5203, nifS, nifW, fixA, fixB, fixC, fixX, nifA, nifB, nifZ, nifT, nolK, noeL, nodZ
Anti-CRISPR   AcrIIA9, AcrIIC1