Detailed information of oriT
oriT
The information of the oriT region
| oriTDB ID | 200441 |
| Name | oriT_ICEMlSymNZP2042-α  |
| Organism | Mesorhizobium loti strain NZP2042 |
| Sequence Completeness | - |
| NCBI accession of oriT (coordinates [strand]) | CP033334 (94876..94936 [+], 61 nt) |
| oriT length | 61 nt |
| IRs (inverted repeats) | 27..33, 37..43 (CCGCCTC..GAGGCGG) |
| Location of nic site | _ |
| Conserved sequence flanking the nic site |
_ |
| Note | Predicted by oriTfinder 2.0 |
oriT sequence
Download Length: 61 nt
>oriT_ICEMlSymNZP2042-α
AAAACGATGTGCAGACAAACGCTTCGCCGCCTCATGGAGGCGGTGCCTTTATCTTGCCTTA
AAAACGATGTGCAGACAAACGCTTCGCCGCCTCATGGAGGCGGTGCCTTTATCTTGCCTTA
Visualization of oriT structure
oriT secondary structure
Predicted by RNAfold.
Download structure file
T4CP
| ID | 17032 | GenBank | QKC73069 |
| Name | t4cp2_EB815_30785_ICEMlSymNZP2042-α |
UniProt ID | _ |
| Length | 816 a.a. | PDB ID | _ |
| Note | Predicted by oriTfinder 2.0 | ||
T4CP protein sequence
Download Length: 816 a.a. Molecular weight: 90221.81 Da Isoelectric Point: 5.9769
>QKC73069.1 conjugal transfer protein TrbE [Mesorhizobium loti]
MLNLSEYRGKADRLADHLPWAALVAPGIVLNKDGSVQRTLRFRGPDLESATEAELIGICARANNALRRLG
SGWTLFFEAERIEALGYPSSRFPDAASWLVDEERRAAFEGKVAHFESRYHLTLLSMPPPDAQARAESALV
DSHHSEGERDWRQEMVRFRDETDRVLDLLSGFMPEVRLLDDAETLTYLHDTISTRRHPVAVPETPMYLDG
ILVDVPLTGGLEPMLGEQHLRTLTILGFPNLTRPGILDALNHQDFAYRWMTRFIPLGKTEATKTLTRLRR
QWFAKRKSIVAILREVVSSEPVPLVDSDADNKALDADEALQALGGDHVGFGYLTATVTVWDEDRQAAAEK
LRAVERIINGLGFTTIRESVNAVEAWLGSLPGHVYANVRQPLVHTLNLAHLMPLSSVWAGPAANEHLAEV
TGREAPPLLIAETSGSTPFRLSSHVEDVGHMLIVGPTGAGKSVLLALIALQFRRYAGAQVYVFDKGNSAR
AATLAMGGEHHVLGSDGALAFQPLRNIGDQGRRSWAAEWIAGLIAHENVTLTPEVKEAIWSALNSLATAP
AQERTLTGLSVLLQSNALKSALMPYTLDGPFGRLLDADDDRLALSDVQCFETEELMRSQSAVLPVLTYLF
HRLEERFDGRPTLLMLDEAWVYLDNPLFAARIREWLKVLRKKNVSVIFATQSLADIAGSAIAPAIIESCP
QRIFLPNDRAVEPQARTAYERFGLNDRQIELIARATPKRHYYLQSRCGNRLFELGLGPIALALCGASGPA
AQSLIDRVLSEHGQDSFVFRFLGARGLDWAAELLQQFPQPTKEQSS
MLNLSEYRGKADRLADHLPWAALVAPGIVLNKDGSVQRTLRFRGPDLESATEAELIGICARANNALRRLG
SGWTLFFEAERIEALGYPSSRFPDAASWLVDEERRAAFEGKVAHFESRYHLTLLSMPPPDAQARAESALV
DSHHSEGERDWRQEMVRFRDETDRVLDLLSGFMPEVRLLDDAETLTYLHDTISTRRHPVAVPETPMYLDG
ILVDVPLTGGLEPMLGEQHLRTLTILGFPNLTRPGILDALNHQDFAYRWMTRFIPLGKTEATKTLTRLRR
QWFAKRKSIVAILREVVSSEPVPLVDSDADNKALDADEALQALGGDHVGFGYLTATVTVWDEDRQAAAEK
LRAVERIINGLGFTTIRESVNAVEAWLGSLPGHVYANVRQPLVHTLNLAHLMPLSSVWAGPAANEHLAEV
TGREAPPLLIAETSGSTPFRLSSHVEDVGHMLIVGPTGAGKSVLLALIALQFRRYAGAQVYVFDKGNSAR
AATLAMGGEHHVLGSDGALAFQPLRNIGDQGRRSWAAEWIAGLIAHENVTLTPEVKEAIWSALNSLATAP
AQERTLTGLSVLLQSNALKSALMPYTLDGPFGRLLDADDDRLALSDVQCFETEELMRSQSAVLPVLTYLF
HRLEERFDGRPTLLMLDEAWVYLDNPLFAARIREWLKVLRKKNVSVIFATQSLADIAGSAIAPAIIESCP
QRIFLPNDRAVEPQARTAYERFGLNDRQIELIARATPKRHYYLQSRCGNRLFELGLGPIALALCGASGPA
AQSLIDRVLSEHGQDSFVFRFLGARGLDWAAELLQQFPQPTKEQSS
Protein domains
Predicted by InterproScan.
Protein structure
No available structure.
| ID | 17033 | GenBank | QKC73074 |
| Name | t4cp2_EB815_30810_ICEMlSymNZP2042-α |
UniProt ID | _ |
| Length | 676 a.a. | PDB ID | _ |
| Note | Predicted by oriTfinder 2.0 | ||
T4CP protein sequence
Download Length: 676 a.a. Molecular weight: 75109.62 Da Isoelectric Point: 6.7849
>QKC73074.1 conjugal transfer protein TraG [Mesorhizobium loti]
MTPTKLLIGQIAIVFAIVLLGVWAATQWCAHMLAFQEQLGAPWFVAAGWPIYEPWKLLEWWFQFDAYAPE
VFDKAGMLAGASGFMGCAAAIAGSLWRARQRGLVTTYGSSRWAVTREIEKAGLFQPAGVFLGKLKDRYLR
HDGPEHVMAFAPTRSGKGVGLVVPTLLSWSGSAVIHDIKGENWQLSSGWRSRFSHCLLFNPTDPRSARYN
PLLEVRKGSDEIRDVQNIADILVDPEGALERRNHWEKTSHSLLVGAILHVLYAEEEKTLARVATFLSDPQ
RSFAATLRRMMTTNHLGAANKPQVHPVVASAAREVLNKSENERSGVLSTAMSFLGLYRDPTVAAVTSDCD
WRIADLMDAEWPMSLYLVVPPSDISRTKPLVRLILNQIGRRLTERLEGDPKKSRKHQLLMMLDEFPALGR
LDFFETALAFMAGYGIRAYLIAQSLNQISKAYGDNNAILDNCHLRIAFSSNDERTAKRISDALGTATELR
SMRNYAGHRLAPWLSHVMVSRQETARPLLTPGEVMQLPPADELVLVSGLPPIRAKKLRYYEDHNFTERVL
PSPVLRDGPYADCPMSRPDDWTGQVRGVDRRLASDDESAGAALADEGGVQQQRHPGLPEEHTAVTQEPDQ
DHLSRPADDDSEAMADKRVMDRISTVAGAYGINEGRGDDKDIVPGF
MTPTKLLIGQIAIVFAIVLLGVWAATQWCAHMLAFQEQLGAPWFVAAGWPIYEPWKLLEWWFQFDAYAPE
VFDKAGMLAGASGFMGCAAAIAGSLWRARQRGLVTTYGSSRWAVTREIEKAGLFQPAGVFLGKLKDRYLR
HDGPEHVMAFAPTRSGKGVGLVVPTLLSWSGSAVIHDIKGENWQLSSGWRSRFSHCLLFNPTDPRSARYN
PLLEVRKGSDEIRDVQNIADILVDPEGALERRNHWEKTSHSLLVGAILHVLYAEEEKTLARVATFLSDPQ
RSFAATLRRMMTTNHLGAANKPQVHPVVASAAREVLNKSENERSGVLSTAMSFLGLYRDPTVAAVTSDCD
WRIADLMDAEWPMSLYLVVPPSDISRTKPLVRLILNQIGRRLTERLEGDPKKSRKHQLLMMLDEFPALGR
LDFFETALAFMAGYGIRAYLIAQSLNQISKAYGDNNAILDNCHLRIAFSSNDERTAKRISDALGTATELR
SMRNYAGHRLAPWLSHVMVSRQETARPLLTPGEVMQLPPADELVLVSGLPPIRAKKLRYYEDHNFTERVL
PSPVLRDGPYADCPMSRPDDWTGQVRGVDRRLASDDESAGAALADEGGVQQQRHPGLPEEHTAVTQEPDQ
DHLSRPADDDSEAMADKRVMDRISTVAGAYGINEGRGDDKDIVPGF
Protein domains
Predicted by InterproScan.
Protein structure
No available structure.
| ID | 17034 | GenBank | QKC73101 |
| Name | t4cp2_EB815_30990_ICEMlSymNZP2042-α |
UniProt ID | _ |
| Length | 563 a.a. | PDB ID | _ |
| Note | Predicted by oriTfinder 2.0 | ||
T4CP protein sequence
Download Length: 563 a.a. Molecular weight: 62321.66 Da Isoelectric Point: 8.3286
>QKC73101.1 type IV secretion system protein VirD4 [Mesorhizobium loti]
MSSTKTTPPNIAISIACSLALGFCAASLYATFRHGGSGEALMTFDVRAFWFETPFYLGFATPVFYRGIAI
VLATSAVVLLIQQVVLRRKLEHHGTARWARVDEMRCTGYLRRYRSVTGPVFGKTSGPFWPGYYLTNGEQP
HSLIVAPTRAGKGVGIVIPTLLTFKGSVIALDVKGELFELTSRARKATGDNVFKFAPLDSERRTNCYNPL
LDLIALPPQLQFTEARRLAANLITAKGEGAEGFVSGARDIFVAGILACIERGTPTIGAVYDLFAQPGEKF
KLFAQLAMETRNKEAQRIFDDMAGNDTKILTSYTSVLGDGGLNLWADPAVKAATSRSDFSVYDLRRRRTC
IYLCVGPNDLEVIAPLIRLFFQQIVSILQRSLPRQDEKNEVLFLLDEFKHLGKLEAIETAITTIAGYKGR
FMLIIQSLSALTGAYGEAGKQNFLSNTGLQVFMATADDETPTYISKAIGEYTFEAKSISYSQARTFDWNI
QNSHQGAPLLRPEQVRLLDEDYEIVLIKGLPPLQLRKVRYYSDRILKRIFESQTGALPEPAPLMEAHPDD
TDG
MSSTKTTPPNIAISIACSLALGFCAASLYATFRHGGSGEALMTFDVRAFWFETPFYLGFATPVFYRGIAI
VLATSAVVLLIQQVVLRRKLEHHGTARWARVDEMRCTGYLRRYRSVTGPVFGKTSGPFWPGYYLTNGEQP
HSLIVAPTRAGKGVGIVIPTLLTFKGSVIALDVKGELFELTSRARKATGDNVFKFAPLDSERRTNCYNPL
LDLIALPPQLQFTEARRLAANLITAKGEGAEGFVSGARDIFVAGILACIERGTPTIGAVYDLFAQPGEKF
KLFAQLAMETRNKEAQRIFDDMAGNDTKILTSYTSVLGDGGLNLWADPAVKAATSRSDFSVYDLRRRRTC
IYLCVGPNDLEVIAPLIRLFFQQIVSILQRSLPRQDEKNEVLFLLDEFKHLGKLEAIETAITTIAGYKGR
FMLIIQSLSALTGAYGEAGKQNFLSNTGLQVFMATADDETPTYISKAIGEYTFEAKSISYSQARTFDWNI
QNSHQGAPLLRPEQVRLLDEDYEIVLIKGLPPLQLRKVRYYSDRILKRIFESQTGALPEPAPLMEAHPDD
TDG
Protein domains
Predicted by InterproScan.
Protein structure
No available structure.
T4SS
T4SS were predicted by using oriTfinder2.
Region 1: 6284849..6293906
| Locus tag | Coordinates | Strand | Size (bp) | Protein ID | Product | Description |
|---|---|---|---|---|---|---|
| EB815_30725 | 6279907..6280059 | - | 153 | QKC73059 | cbb3-type cytochrome c oxidase subunit 3 | - |
| EB815_30730 | 6280072..6280803 | - | 732 | QKC73060 | cytochrome-c oxidase, cbb3-type subunit II | - |
| EB815_30735 | 6280815..6282425 | - | 1611 | QKC73061 | cytochrome-c oxidase, cbb3-type subunit I | - |
| EB815_30740 | 6282546..6283064 | + | 519 | Protein_6093 | hemerythrin domain-containing protein | - |
| EB815_30745 | 6283091..6283846 | - | 756 | QKC73062 | Crp/Fnr family transcriptional regulator | - |
| EB815_30750 | 6283991..6284515 | + | 525 | Protein_6095 | radical SAM protein | - |
| EB815_30755 | 6284591..6284836 | - | 246 | QKC73063 | DUF2274 domain-containing protein | - |
| EB815_30760 | 6284849..6286063 | - | 1215 | QKC73064 | TrbI/VirB10 family protein | virB10 |
| EB815_30765 | 6286075..6287103 | - | 1029 | QKC73065 | P-type conjugative transfer protein TrbG | virB9 |
| EB815_30770 | 6287100..6287825 | - | 726 | QKC73066 | conjugal transfer protein TrbF | virB8 |
| EB815_30775 | 6287826..6289148 | - | 1323 | QKC73067 | P-type conjugative transfer protein TrbL | virB6 |
| EB815_30780 | 6289180..6289905 | - | 726 | QKC73068 | P-type conjugative transfer protein TrbJ | virB5 |
| EB815_30785 | 6289902..6292352 | - | 2451 | QKC73069 | conjugal transfer protein TrbE | virb4 |
| EB815_30790 | 6292346..6292618 | - | 273 | QKC73070 | conjugal transfer protein | virB3 |
| EB815_30795 | 6292618..6292926 | - | 309 | QKC73071 | conjugal transfer protein TrbC | virB2 |
| EB815_30800 | 6292938..6293906 | - | 969 | QKC73072 | P-type conjugative transfer ATPase TrbB | virB11 |
| EB815_30805 | 6293903..6294316 | - | 414 | QKC73073 | CopG family transcriptional regulator | - |
| EB815_30810 | 6294435..6296465 | - | 2031 | QKC73074 | conjugal transfer protein TraG | - |
| EB815_30815 | 6296625..6296834 | + | 210 | Protein_6108 | XRE family transcriptional regulator | - |
| EB815_30820 | 6297132..6297563 | - | 432 | QKC73075 | hypothetical protein | - |
| EB815_30825 | 6298214..6298504 | + | 291 | QKC73076 | ZinT family metal-binding protein | - |
Region 2: 6316463..6325885
| Locus tag | Coordinates | Strand | Size (bp) | Protein ID | Product | Description |
|---|---|---|---|---|---|---|
| EB815_30885 | 6312098..6312228 | + | 131 | Protein_6122 | IS630 family transposase | - |
| EB815_30890 | 6312228..6312839 | + | 612 | Protein_6123 | ISKra4 family transposase | - |
| EB815_30895 | 6313809..6316349 | + | 2541 | QKC73086 | two-component system VirA-like sensor kinase | - |
| EB815_30900 | 6316463..6317503 | - | 1041 | QKC73087 | P-type DNA transfer ATPase VirB11 | virB11 |
| EB815_30905 | 6317487..6318626 | - | 1140 | QKC73088 | type IV secretion system protein VirB10 | virB10 |
| EB815_30910 | 6318623..6319504 | - | 882 | QKC73089 | type IV secretion system protein VirB9 | virB9 |
| EB815_30915 | 6319501..6320214 | - | 714 | QKC73090 | type IV secretion system protein VirB8 | virB8 |
| EB815_30920 | 6320211..6320369 | - | 159 | QKC73091 | type IV secretion system lipoprotein VirB7 | - |
| EB815_30925 | 6320396..6321280 | - | 885 | QKC73092 | type IV secretion system protein | virB6 |
| EB815_30930 | 6321339..6322019 | - | 681 | QKC73093 | type IV secretion system protein VirB5 | traI |
| EB815_30935 | 6322033..6324402 | - | 2370 | QKC73094 | VirB4 family type IV secretion/conjugal transfer ATPase | virb4 |
| EB815_30940 | 6324402..6324728 | - | 327 | QKC73095 | type IV secretion system protein VirB3 | virB3 |
| EB815_30945 | 6324728..6325093 | - | 366 | QKC73096 | pilin major subunit VirB2 | virB2 |
| EB815_30950 | 6325109..6325885 | - | 777 | QKC73097 | type IV secretion system lytic transglycosylase VirB1 | virB1 |
| EB815_30955 | 6326948..6327667 | + | 720 | QKC73098 | response regulator | - |
| EB815_30960 | 6327880..6328140 | + | 261 | QKC73099 | hypothetical protein | - |
Host bacterium
| ID | 392 | Element type | ICE (Integrative and conjugative element) |
| Element name | ICEMlSymNZP2042-α | GenBank | CP033334 |
| Element size | 6870350 bp | Coordinate of oriT [Strand] | 94876..94936 [+] |
| Host bacterium | Mesorhizobium loti strain NZP2042 | Coordinate of element | 6274097..6749011 |
Cargo genes
| Drug resistance gene | - |
| Virulence gene | gmd |
| Metal resistance gene | - |
| Degradation gene | - |
| Symbiosis gene | fixS, fixI, nifX, fixG, fixP, fixQ, fixO, fixN, nodM, nodD, nolL, nodB, eB815_31285, nodJ, nodI, nodC, nodA, nodS, nifU, nifN, nifE, nifK, nifD, nifH, nifQ, nifS, nifW, fixA, fixB, fixC, fixX, nifB, nifZ, nifT, nolK, noeL, nodZ, nifA, nodE, nodF, nodU |
| Anti-CRISPR | AcrIIA9, AcrIIC1 |