Detailed information of oriT
oriT
The information of the oriT region
| oriTDB ID | 200423 |
| Name | oriT_ICEMjSymATCC33669-α  |
| Organism | Mesorhizobium jarvisii strain ATCC 33669 |
| Sequence Completeness | - |
| NCBI accession of oriT (coordinates [strand]) | CP033507 (94281..94341 [+], 61 nt) |
| oriT length | 61 nt |
| IRs (inverted repeats) | 26..33, 37..44 (ACCGCCTC..GAGGCGGT) |
| Location of nic site | _ |
| Conserved sequence flanking the nic site |
_ |
| Note | Predicted by oriTfinder 2.0 |
oriT sequence
Download Length: 61 nt
>oriT_ICEMjSymATCC33669-α
AAAACGATGTGCAGACAAAGACTTGACCGCCTCGTGGAGGCGGTGCCTTTATCTTGCCTTA
AAAACGATGTGCAGACAAAGACTTGACCGCCTCGTGGAGGCGGTGCCTTTATCTTGCCTTA
Visualization of oriT structure
oriT secondary structure
Predicted by RNAfold.
Download structure file
T4CP
| ID | 16995 | GenBank | QKC67350 |
| Name | t4cp2_EB229_31305_ICEMjSymATCC33669-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: 90140.67 Da Isoelectric Point: 5.9573
>QKC67350.1 conjugal transfer protein TrbE [Mesorhizobium jarvisii]
MLNLSEYRGKADRLADHLPWAALVAPGIVLNKDGSVQRTLRFRGPDLESATEAELIGICARANNALRRLG
SGWTLFFEAERIEALGYPSSRFPDAASWLVDEERRAAFEGKVAHFESRYHLTLLSMPPPDAQARAESALV
DSHHSEGERDWRQEIARFRDETDRVLDLLSGFMPEVRLLDDAETLTYLHDTISTRRHPVAVPETPMYLDG
ILVDVPLTGGLEPMLGEQHLRTLTILGFPNLTRPGILDALNHQDFAYRWMTRFIPLGKTEATKTLTRLRR
QWFAKRKSMVAILREVVSNEPVPLVDSDADNKALDADEALQALGGDHIGFGYLTATVTVWDEDRQAAAEK
LRAVERIINGLGFTTIRESVNAVEAWLGSLPGHVYANVRQPLVHTLNLAHLMPLSSVWAGPAANEHLAEI
TGREAPPLLIAETSGSTPFRLSSHVEDVGHMLIVGPTGAGKSVLLALIALQFRRYAGAQVYVFDKGNSAR
AATLAMGGEHHVLGSDGALAFQPLRNIGDQGRRSWAAEWIAGLIAHENVALTPEVKEAIWSALNSLATAP
AQERTLTGLSVLLQSNALKSALMPYTLDGPFGRLLDADDDRLALSDVQCFETEELMHSQSAVLPVLTYLF
HRLEERFDGRPTLLMLDEAWVDLDNPLFAARIREWLKVLRKKNVSVIFATQSLADIAGSAIAPAIIESCP
QRIFLPNDRAVEPQARTAYERFGLNNRQIELIARATPKRHYYLQSRCGNRRFELGLGPIALALCGASGPA
AQSLIDRVLSEHGQDSFVFRFLGACGLDWAAELLQQFPQPTKEQSS
MLNLSEYRGKADRLADHLPWAALVAPGIVLNKDGSVQRTLRFRGPDLESATEAELIGICARANNALRRLG
SGWTLFFEAERIEALGYPSSRFPDAASWLVDEERRAAFEGKVAHFESRYHLTLLSMPPPDAQARAESALV
DSHHSEGERDWRQEIARFRDETDRVLDLLSGFMPEVRLLDDAETLTYLHDTISTRRHPVAVPETPMYLDG
ILVDVPLTGGLEPMLGEQHLRTLTILGFPNLTRPGILDALNHQDFAYRWMTRFIPLGKTEATKTLTRLRR
QWFAKRKSMVAILREVVSNEPVPLVDSDADNKALDADEALQALGGDHIGFGYLTATVTVWDEDRQAAAEK
LRAVERIINGLGFTTIRESVNAVEAWLGSLPGHVYANVRQPLVHTLNLAHLMPLSSVWAGPAANEHLAEI
TGREAPPLLIAETSGSTPFRLSSHVEDVGHMLIVGPTGAGKSVLLALIALQFRRYAGAQVYVFDKGNSAR
AATLAMGGEHHVLGSDGALAFQPLRNIGDQGRRSWAAEWIAGLIAHENVALTPEVKEAIWSALNSLATAP
AQERTLTGLSVLLQSNALKSALMPYTLDGPFGRLLDADDDRLALSDVQCFETEELMHSQSAVLPVLTYLF
HRLEERFDGRPTLLMLDEAWVDLDNPLFAARIREWLKVLRKKNVSVIFATQSLADIAGSAIAPAIIESCP
QRIFLPNDRAVEPQARTAYERFGLNNRQIELIARATPKRHYYLQSRCGNRRFELGLGPIALALCGASGPA
AQSLIDRVLSEHGQDSFVFRFLGACGLDWAAELLQQFPQPTKEQSS
Protein domains
Predicted by InterproScan.
Protein structure
No available structure.
| ID | 16996 | GenBank | QKC66255 |
| Name | t4cp2_EB229_31330_ICEMjSymATCC33669-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: 75073.54 Da Isoelectric Point: 6.6518
>QKC66255.1 conjugal transfer protein TraG [Mesorhizobium jarvisii]
MTPTKLLIGQIAIVFAIVLLGVWAATQWCAHMLAFQEQLGAPWFVAAGWPIYEPWKLLEWWFQFDAYAPE
VFDKAGMLAGASGFMGCAAAIAGSLWRARQRGLVTTYGSSRWAVTREIEKAGLFQPAGVFLGKLKDRYLR
HDGPEHVMAFAPTRSGKGVGLVVPTLLSWSGSAVIHDIKGENWQLSSGWRSRFSHCLLFNPTDPRSARYN
PLLEVRKGSDEIRDVQNIADILVDPEGALERRNHWEKTSHSLLVGAILHVLYAEEEKTLARVATFLSDPQ
RSFAATLRRMMTTNHLGAANKPQVHPVVASAAREVLNKSENERSGVLSTAMSFLGLYRDPTVAAVTSDCD
WRIADLMDAEWPMSLYLVVPPSDISRTKPLVRLILNQIGRRLTERLEGDPKKSRKHQLLMMLDEFPALGR
LDFFETALAFMAGYGIRAYLIAQSLNQISKAYGDNNAILDNCHLRIAFSSNDERTAKRISDALGTATELR
SMRNYAGHRLAPWLSHVMVSRQETARPLLTPGEVMQLPPADELVLVSGLPPIRAKKLRYYEDHNFTERVL
PSPVLRDGPYADCPMSRPDDWTGQVRGVDRRLASDDESAGAALADEGGVQQQRHPGLPEEHTAVTQEPDQ
DDLSRPADDDSEAMADKRVMDRISTVAGAYGVNEGRGDDKDIVPGF
MTPTKLLIGQIAIVFAIVLLGVWAATQWCAHMLAFQEQLGAPWFVAAGWPIYEPWKLLEWWFQFDAYAPE
VFDKAGMLAGASGFMGCAAAIAGSLWRARQRGLVTTYGSSRWAVTREIEKAGLFQPAGVFLGKLKDRYLR
HDGPEHVMAFAPTRSGKGVGLVVPTLLSWSGSAVIHDIKGENWQLSSGWRSRFSHCLLFNPTDPRSARYN
PLLEVRKGSDEIRDVQNIADILVDPEGALERRNHWEKTSHSLLVGAILHVLYAEEEKTLARVATFLSDPQ
RSFAATLRRMMTTNHLGAANKPQVHPVVASAAREVLNKSENERSGVLSTAMSFLGLYRDPTVAAVTSDCD
WRIADLMDAEWPMSLYLVVPPSDISRTKPLVRLILNQIGRRLTERLEGDPKKSRKHQLLMMLDEFPALGR
LDFFETALAFMAGYGIRAYLIAQSLNQISKAYGDNNAILDNCHLRIAFSSNDERTAKRISDALGTATELR
SMRNYAGHRLAPWLSHVMVSRQETARPLLTPGEVMQLPPADELVLVSGLPPIRAKKLRYYEDHNFTERVL
PSPVLRDGPYADCPMSRPDDWTGQVRGVDRRLASDDESAGAALADEGGVQQQRHPGLPEEHTAVTQEPDQ
DDLSRPADDDSEAMADKRVMDRISTVAGAYGVNEGRGDDKDIVPGF
Protein domains
Predicted by InterproScan.
Protein structure
No available structure.
| ID | 16997 | GenBank | QKC66282 |
| Name | t4cp2_EB229_31515_ICEMjSymATCC33669-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
>QKC66282.1 type IV secretion system protein VirD4 [Mesorhizobium jarvisii]
MSSTKTTPPNIALSIACSLALGFCAASLYATFRHGGSGEALMTFDVRAFWFETPFYLGFATPVFYRGIAI
VLATSAVVLLIQQVVLRRKLEHHGTARWARVDEMRCTGYLRRYRSVTGPVFGKTSGPFWPGYYLTNGEQP
HSLIVAPTRAGKGVGIVIPTLLTFKGSVIALDVKGELFELTSRARKATGDNVFKFAPLDSERRTNCYNPL
LDLIALPPQLQFTEARRLAANLITAKGEGAEGFVSGARDIFVAGILACIERGTPTIGAVYDLFAQPGEKF
KLFAQLAMETRNKEAQRIFDDMAGNDTKILTSYTSVLGDGGLNLWADPAVKAATSRSDFSVYDLRRRRTC
IYLCVGPNDLEVIAPLIRLFFQQIVSILQRSLPRQDEKNEVLFLLDEFKHLGKLEAIETAITTIAGYKGR
FMLIIQSLSALTGAYGEAGKQNFLSNTGLQVFMATADDETPTYISKAIGEYTFEAKSISYSQARTFDWNI
QNSHQGAPLLRPEQVRLLDEDYEIVLIKGLPPLQLRKVRYYSDRILKRIFESQTGALPEPAPLMEAHPDD
TDG
MSSTKTTPPNIALSIACSLALGFCAASLYATFRHGGSGEALMTFDVRAFWFETPFYLGFATPVFYRGIAI
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: 6296109..6305166
| Locus tag | Coordinates | Strand | Size (bp) | Protein ID | Product | Description |
|---|---|---|---|---|---|---|
| EB229_31245 | 6291165..6291314 | - | 150 | QKC66241 | CcoQ/FixQ family Cbb3-type cytochrome c oxidase assembly chaperone | - |
| EB229_31250 | 6291325..6292056 | - | 732 | QKC66242 | cytochrome-c oxidase, cbb3-type subunit II | - |
| EB229_31255 | 6292068..6293678 | - | 1611 | QKC66243 | cytochrome-c oxidase, cbb3-type subunit I | - |
| EB229_31260 | 6293808..6294347 | + | 540 | QKC66244 | hemerythrin domain-containing protein | - |
| EB229_31265 | 6294351..6295106 | - | 756 | QKC66245 | Crp/Fnr family transcriptional regulator | - |
| EB229_31270 | 6295251..6295775 | + | 525 | Protein_6192 | radical SAM protein | - |
| EB229_31275 | 6295851..6296096 | - | 246 | QKC66246 | DUF2274 domain-containing protein | - |
| EB229_31280 | 6296109..6297323 | - | 1215 | QKC67349 | TrbI/VirB10 family protein | virB10 |
| EB229_31285 | 6297335..6298363 | - | 1029 | QKC66247 | P-type conjugative transfer protein TrbG | virB9 |
| EB229_31290 | 6298360..6299085 | - | 726 | QKC66248 | conjugal transfer protein TrbF | virB8 |
| EB229_31295 | 6299086..6300408 | - | 1323 | QKC66249 | P-type conjugative transfer protein TrbL | virB6 |
| EB229_31300 | 6300440..6301165 | - | 726 | QKC66250 | P-type conjugative transfer protein TrbJ | virB5 |
| EB229_31305 | 6301162..6303612 | - | 2451 | QKC67350 | conjugal transfer protein TrbE | virb4 |
| EB229_31310 | 6303606..6303878 | - | 273 | QKC66251 | conjugal transfer protein | virB3 |
| EB229_31315 | 6303878..6304186 | - | 309 | QKC66252 | conjugal transfer protein TrbC | virB2 |
| EB229_31320 | 6304198..6305166 | - | 969 | QKC66253 | P-type conjugative transfer ATPase TrbB | virB11 |
| EB229_31325 | 6305163..6305576 | - | 414 | QKC66254 | CopG family transcriptional regulator | - |
| EB229_31330 | 6305695..6307725 | - | 2031 | QKC66255 | conjugal transfer protein TraG | - |
| EB229_31335 | 6307855..6308092 | + | 238 | Protein_6205 | XRE family transcriptional regulator | - |
| EB229_31340 | 6308390..6308779 | - | 390 | QKC66256 | hypothetical protein | - |
| EB229_31345 | 6308770..6309177 | - | 408 | QKC66257 | hypothetical protein | - |
| EB229_31350 | 6309472..6309762 | + | 291 | QKC66258 | hypothetical protein | - |
Region 2: 6325853..6335275
| Locus tag | Coordinates | Strand | Size (bp) | Protein ID | Product | Description |
|---|---|---|---|---|---|---|
| EB229_31400 | 6321484..6321614 | + | 131 | Protein_6218 | IS630 family transposase | - |
| EB229_31405 | 6321614..6322226 | + | 613 | Protein_6219 | ISKra4 family transposase | - |
| EB229_31410 | 6323199..6325739 | + | 2541 | QKC66266 | two-component system VirA-like sensor kinase | - |
| EB229_31415 | 6325853..6326893 | - | 1041 | QKC66267 | P-type DNA transfer ATPase VirB11 | virB11 |
| EB229_31420 | 6326877..6328016 | - | 1140 | QKC66268 | type IV secretion system protein VirB10 | virB10 |
| EB229_31425 | 6328013..6328894 | - | 882 | QKC66269 | type IV secretion system protein VirB9 | virB9 |
| EB229_31430 | 6328891..6329604 | - | 714 | QKC66270 | type IV secretion system protein VirB8 | virB8 |
| EB229_31435 | 6329601..6329759 | - | 159 | QKC66271 | type IV secretion system lipoprotein VirB7 | - |
| EB229_31440 | 6329786..6330670 | - | 885 | QKC66272 | type IV secretion system protein | virB6 |
| EB229_31445 | 6330729..6331409 | - | 681 | QKC66273 | type IV secretion system protein VirB5 | - |
| EB229_31450 | 6331423..6333792 | - | 2370 | QKC66274 | VirB4 family type IV secretion/conjugal transfer ATPase | virb4 |
| EB229_31455 | 6333792..6334118 | - | 327 | QKC66275 | type IV secretion system protein VirB3 | virB3 |
| EB229_31460 | 6334118..6334483 | - | 366 | QKC66276 | pilin major subunit VirB2 | virB2 |
| EB229_31465 | 6334499..6335275 | - | 777 | QKC66277 | type IV secretion system lytic transglycosylase VirB1 | virB1 |
| EB229_31470 | 6335363..6335560 | - | 198 | QKC66278 | hypothetical protein | - |
| EB229_31475 | 6336339..6337058 | + | 720 | QKC66279 | response regulator | - |
| EB229_31480 | 6337027..6337305 | + | 279 | QKC66280 | hypothetical protein | - |
| EB229_31485 | 6337355..6337573 | - | 219 | QKC66281 | hypothetical protein | - |
Host bacterium
| ID | 377 | Element type | ICE (Integrative and conjugative element) |
| Element name | ICEMjSymATCC33669-α | GenBank | CP033507 |
| Element size | 6934624 bp | Coordinate of oriT [Strand] | 94281..94341 [+] |
| Host bacterium | Mesorhizobium jarvisii strain ATCC 33669 | Coordinate of element | 6285350..6807656 |
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, a9174_31165, nodJ, nodI, nodC, nodA, nodS, mlr6097, nifU, nifN, nifE, nifK, nifD, nifH, nifQ, mLTONO_5203, nifS, nifW, fixA, fixB, fixC, fixX, nifA, nifB, nifZ, fixT, nolK, noeL, nodZ, nodE, nodF, nodU |
| Anti-CRISPR | AcrIIC1 |