Detailed information of oriT
oriT
The information of the oriT region
| oriTDB ID | 200445 |
| Name | oriT_ICEMsp.SymSEMIA3007  |
| Organism | Mesorhizobium sp. SEMIA 3007 J5_1 |
| Sequence Completeness | - |
| NCBI accession of oriT (coordinates [strand]) | MDLH01000001 (304177..304237 [-], 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_ICEMsp.SymSEMIA3007
AAAAGGATGTGCAGACAAAGGCTTCGCCGCCTCATGGAGGCGGTGCCTTTATCTTGCCTTA
AAAAGGATGTGCAGACAAAGGCTTCGCCGCCTCATGGAGGCGGTGCCTTTATCTTGCCTTA
Visualization of oriT structure
oriT secondary structure
Predicted by RNAfold.
Download structure file
T4CP
| ID | 17044 | GenBank | ODA93338 |
| Name | t4cp2_BFX40_10970_ICEMsp.SymSEMIA3007 |
UniProt ID | _ |
| Length | 563 a.a. | PDB ID | _ |
| Note | Predicted by oriTfinder 2.0 | ||
T4CP protein sequence
Download Length: 563 a.a. Molecular weight: 62333.54 Da Isoelectric Point: 8.7905
>ODA93338.1 type IV secretion system protein VirD4 [Mesorhizobium sp. SEMIA 3007]
MSSTKTTSPNIAISIACSLALGFCAASLYATFRHGGSGEALMAFDVRAFWFETPFYLGFATPVFYQGAAI
VLSTSAVVLLIQQFVLRRKLEHHGTARWARVDEMRRTGYLRRYRGVTGPVFGKTSGPFWPGYYLTNGEQP
HSLIVAPTRAGKGVGIVIPTLLTFKGSVIALDVKGELFELTSRARKAAGHEVFKFAPLDSERRTNCYNPL
LDLIALHPQQQFTEARRLAANLITAKGEGAEGFVSGARDIFVAGILACIERGTPTIGAVYDLFAQPGEKF
KLFAQLAMETRNKEAQRIFDDMAGNDTKILTSYTSVLGDGGLNLWADPAVKAATSRSDFSVYDLRRRRTC
IYLCVGPNDLEVIAPLIRLFFQQTVSILQRSLPRQDEKHEVLFLLDEFKHLGKLEAIETAITTIAGYKGR
FMLIIQSLSALTGAYGEAGKQNFLSNTGLQVFMATADDETPNYISKAIGEYTFEAKSISYSQSRAFDRNI
QNSFQGAPLLRPEQVRLLNDEYEIVLIKGLPPLQLRKVRYFSDRILKRIFESQTGALPEPAPLMEAHPDD
TDG
MSSTKTTSPNIAISIACSLALGFCAASLYATFRHGGSGEALMAFDVRAFWFETPFYLGFATPVFYQGAAI
VLSTSAVVLLIQQFVLRRKLEHHGTARWARVDEMRRTGYLRRYRGVTGPVFGKTSGPFWPGYYLTNGEQP
HSLIVAPTRAGKGVGIVIPTLLTFKGSVIALDVKGELFELTSRARKAAGHEVFKFAPLDSERRTNCYNPL
LDLIALHPQQQFTEARRLAANLITAKGEGAEGFVSGARDIFVAGILACIERGTPTIGAVYDLFAQPGEKF
KLFAQLAMETRNKEAQRIFDDMAGNDTKILTSYTSVLGDGGLNLWADPAVKAATSRSDFSVYDLRRRRTC
IYLCVGPNDLEVIAPLIRLFFQQTVSILQRSLPRQDEKHEVLFLLDEFKHLGKLEAIETAITTIAGYKGR
FMLIIQSLSALTGAYGEAGKQNFLSNTGLQVFMATADDETPNYISKAIGEYTFEAKSISYSQSRAFDRNI
QNSFQGAPLLRPEQVRLLNDEYEIVLIKGLPPLQLRKVRYFSDRILKRIFESQTGALPEPAPLMEAHPDD
TDG
Protein domains
Predicted by InterproScan.
Protein structure
No available structure.
| ID | 17045 | GenBank | ODA93362 |
| Name | t4cp2_BFX40_11120_ICEMsp.SymSEMIA3007 |
UniProt ID | _ |
| Length | 676 a.a. | PDB ID | _ |
| Note | Predicted by oriTfinder 2.0 | ||
T4CP protein sequence
Download Length: 676 a.a. Molecular weight: 75089.54 Da Isoelectric Point: 6.6518
>ODA93362.1 conjugal transfer protein TraG [Mesorhizobium sp. SEMIA 3007]
MTPTKLLIGQIAIVFAIVLLGVWAATQWCAHMLAFQEQLGAPWFVAAGWPIYEPWKLLEWWFQFDAYAPE
VFDKAGMLAGTSGFMGCAAAIAGSLWRARQRGLVTTYGSSRWAATREIEKAGLFQPAGVFLGKLKDRYLR
HDGPEHVMAFAPTRSGKGVGLVVPTLLSWSGSAVIHDIKGENWQLSSGWRSRFSHCLLFNPTDPRSARYN
PLLEVRKGSDEIRDVQNIADILVDPEGALERRNHWEKTSHSLLVGAILHVLYAEEEKTLARVATFLSDPQ
RSFAATLRRMMTTNHLGAANKPQVHPVVASAAREVLNKSENERSGVLSTAMSFLGLYRDPTVAAVTSDCD
WRIADLMDAEWPMSLYLVVPPSDISRTKPLVRLILNQIGRRLTERLEGDPKKSRKHQLLMMLDEFPALGR
LDFFETALAFMAGYGIRAYLIAQSLNQISKAYGDNNAILDNCHLRIAFSSNDERTAKRISDALGTATELR
SMRNYAGHRLAPWLSHVMVSRQETARPLLTPGEVMQLPPADELVLVSGLPPIRAKKLRYYEDHNFTERVL
PSPVLRDGPYADCPMSRPDDWTGQVRGVDRRLASDDESAGAALADEGGVQQQRHPGLPEEHTAVTQEPDQ
DDLSRPADDDSEAMADKRVMDRISTVAGAYGINEGRGDDKDIVPGF
MTPTKLLIGQIAIVFAIVLLGVWAATQWCAHMLAFQEQLGAPWFVAAGWPIYEPWKLLEWWFQFDAYAPE
VFDKAGMLAGTSGFMGCAAAIAGSLWRARQRGLVTTYGSSRWAATREIEKAGLFQPAGVFLGKLKDRYLR
HDGPEHVMAFAPTRSGKGVGLVVPTLLSWSGSAVIHDIKGENWQLSSGWRSRFSHCLLFNPTDPRSARYN
PLLEVRKGSDEIRDVQNIADILVDPEGALERRNHWEKTSHSLLVGAILHVLYAEEEKTLARVATFLSDPQ
RSFAATLRRMMTTNHLGAANKPQVHPVVASAAREVLNKSENERSGVLSTAMSFLGLYRDPTVAAVTSDCD
WRIADLMDAEWPMSLYLVVPPSDISRTKPLVRLILNQIGRRLTERLEGDPKKSRKHQLLMMLDEFPALGR
LDFFETALAFMAGYGIRAYLIAQSLNQISKAYGDNNAILDNCHLRIAFSSNDERTAKRISDALGTATELR
SMRNYAGHRLAPWLSHVMVSRQETARPLLTPGEVMQLPPADELVLVSGLPPIRAKKLRYYEDHNFTERVL
PSPVLRDGPYADCPMSRPDDWTGQVRGVDRRLASDDESAGAALADEGGVQQQRHPGLPEEHTAVTQEPDQ
DDLSRPADDDSEAMADKRVMDRISTVAGAYGINEGRGDDKDIVPGF
Protein domains
Predicted by InterproScan.
Protein structure
No available structure.
| ID | 17046 | GenBank | ODA93367 |
| Name | t4cp2_BFX40_11145_ICEMsp.SymSEMIA3007 |
UniProt ID | _ |
| Length | 816 a.a. | PDB ID | _ |
| Note | Predicted by oriTfinder 2.0 | ||
T4CP protein sequence
Download Length: 816 a.a. Molecular weight: 90201.74 Da Isoelectric Point: 6.1930
>ODA93367.1 conjugal transfer protein TrbE [Mesorhizobium sp. SEMIA 3007]
MLNLSEYRGKADRLADHLPWAALVGPGIVLNKDGSVQRTLRFRGPDLESSTEAELIGICARANNALRRLG
SGWTLFFEAERIEALGYPSSRFPDAASWLVDEERRAAFEGKVAHFESRYHLTLLSMPPPDAQARAESALV
DSHHSEGERDWRQEMARFRDETDRVLDLLSGFMPEVRPLDDAETLTYLHDTISTRRHPVAVPETPMYLDG
ILVDVPLTGGLEPMLGEQHLRTLTILGFPNLTRPGILDALNHQDFAYRWMTRFIPLGKTEATKTLTRLRR
QWFAKRKSIVAILREVVSNEPVPLVDSDADNKALDADEALQALGGDHVGFGYLTATVTVWDEDRQAAAEK
LRAVERIINGLGFTTIRESVNAVEAWLGSLPGHVYANVRQPLVHTLNLAHLMPLSSVWAGPAANEHLAEV
TGREAPPLLIAETSGSSPFRLSSHVEDVGHMLIVGPTGAGKSVLLALIALQFRRYAGAQVYVFDKGNSAR
AATLAMGGEHHVLGSDGALAFQPLRNIGNQGRRSWAAEWIAGLIAHENVTLTPEVKEAIWSALNSLATAP
AQERTLTGLSVLLQSNALKSALMPYTLDGPFGRLLDADDDRLALSDVQCFETEELMHSQSAVLPVLTYLF
HRLEERFDGRPTLLMLDEAWVYLDNPLFAARIREWLKVLRKKNVSVIFATQSLADIAGSAIAPAIIESCP
QRIFLPNDRAVEPQARTAYERFGLNDRQIELIARATPKRHYYLQSRCGNRLFELGLGPIALALCGASGPA
AQSLIDRVLSKHGQDSFVFRFLGARSLDWAAELLQQFPQPTKEQSS
MLNLSEYRGKADRLADHLPWAALVGPGIVLNKDGSVQRTLRFRGPDLESSTEAELIGICARANNALRRLG
SGWTLFFEAERIEALGYPSSRFPDAASWLVDEERRAAFEGKVAHFESRYHLTLLSMPPPDAQARAESALV
DSHHSEGERDWRQEMARFRDETDRVLDLLSGFMPEVRPLDDAETLTYLHDTISTRRHPVAVPETPMYLDG
ILVDVPLTGGLEPMLGEQHLRTLTILGFPNLTRPGILDALNHQDFAYRWMTRFIPLGKTEATKTLTRLRR
QWFAKRKSIVAILREVVSNEPVPLVDSDADNKALDADEALQALGGDHVGFGYLTATVTVWDEDRQAAAEK
LRAVERIINGLGFTTIRESVNAVEAWLGSLPGHVYANVRQPLVHTLNLAHLMPLSSVWAGPAANEHLAEV
TGREAPPLLIAETSGSSPFRLSSHVEDVGHMLIVGPTGAGKSVLLALIALQFRRYAGAQVYVFDKGNSAR
AATLAMGGEHHVLGSDGALAFQPLRNIGNQGRRSWAAEWIAGLIAHENVTLTPEVKEAIWSALNSLATAP
AQERTLTGLSVLLQSNALKSALMPYTLDGPFGRLLDADDDRLALSDVQCFETEELMHSQSAVLPVLTYLF
HRLEERFDGRPTLLMLDEAWVYLDNPLFAARIREWLKVLRKKNVSVIFATQSLADIAGSAIAPAIIESCP
QRIFLPNDRAVEPQARTAYERFGLNDRQIELIARATPKRHYYLQSRCGNRLFELGLGPIALALCGASGPA
AQSLIDRVLSKHGQDSFVFRFLGARSLDWAAELLQQFPQPTKEQSS
Protein domains
Predicted by InterproScan.
Protein structure
No available structure.
T4SS
T4SS were predicted by using oriTfinder2.
Region 1: 2323129..2332552
| Locus tag | Coordinates | Strand | Size (bp) | Protein ID | Product | Description |
|---|---|---|---|---|---|---|
| BFX40_10990 | 2320781..2321041 | + | 261 | Protein_2180 | hypothetical protein | - |
| BFX40_10995 | 2321101..2321790 | - | 690 | ODA93341 | DNA-binding response regulator | - |
| BFX40_11000 | 2323129..2323911 | + | 783 | ODA93342 | lytic transglycosylase | virB1 |
| BFX40_11005 | 2323926..2324291 | + | 366 | ODA93343 | type IV secretion system protein VirB2 | virB2 |
| BFX40_11010 | 2324291..2324617 | + | 327 | ODA93344 | type IV secretion system protein VirB3 | virB3 |
| BFX40_11015 | 2324617..2326986 | + | 2370 | ODA93345 | type IV secretion system protein VirB4 | virb4 |
| BFX40_11020 | 2327000..2327674 | + | 675 | ODA93346 | type IV secretion system protein VirB5 | - |
| BFX40_11025 | 2327732..2328619 | + | 888 | ODA93347 | type IV secretion system protein VirB6 | virB6 |
| BFX40_11030 | 2328801..2329514 | + | 714 | ODA97459 | type IV secretion system protein VirB8 | virB8 |
| BFX40_11035 | 2329511..2330392 | + | 882 | ODA93348 | type IV secretion system protein VirB9 | virB9 |
| BFX40_11040 | 2330389..2331528 | + | 1140 | ODA93349 | type IV secretion system protein VirB10 | virB10 |
| BFX40_11045 | 2331512..2332552 | + | 1041 | ODA93350 | P-type DNA transfer ATPase VirB11 | virB11 |
| BFX40_11050 | 2332675..2335194 | - | 2520 | ODA97460 | two-component sensor histidine kinase | - |
| BFX40_11055 | 2336073..2336321 | + | 249 | ODA93351 | hypothetical protein | - |
| BFX40_11060 | 2336413..2336595 | - | 183 | ODA93352 | hypothetical protein | - |
Region 2: 2353163..2362219
| Locus tag | Coordinates | Strand | Size (bp) | Protein ID | Product | Description |
|---|---|---|---|---|---|---|
| BFX40_11110 | 2348604..2349189 | - | 586 | Protein_2204 | hypothetical protein | - |
| BFX40_11115 | 2349550..2349939 | + | 390 | ODA93361 | hypothetical protein | - |
| BFX40_11120 | 2350604..2352634 | + | 2031 | ODA93362 | conjugal transfer protein TraG | - |
| BFX40_11125 | 2352753..2353166 | + | 414 | ODA93363 | CopG family transcriptional regulator | - |
| BFX40_11130 | 2353163..2354131 | + | 969 | ODA93364 | P-type conjugative transfer ATPase TrbB | virB11 |
| BFX40_11135 | 2354143..2354451 | + | 309 | ODA93365 | conjugal transfer protein TrbC | virB2 |
| BFX40_11140 | 2354451..2354723 | + | 273 | ODA93366 | conjugal transfer protein | virB3 |
| BFX40_11145 | 2354717..2357167 | + | 2451 | ODA93367 | conjugal transfer protein TrbE | virb4 |
| BFX40_11150 | 2357164..2357889 | + | 726 | ODA93368 | P-type conjugative transfer protein TrbJ | virB5 |
| BFX40_11155 | 2357921..2359243 | + | 1323 | ODA93369 | P-type conjugative transfer protein TrbL | virB6 |
| BFX40_11160 | 2359244..2359969 | + | 726 | ODA93370 | conjugal transfer protein TrbF | virB8 |
| BFX40_11165 | 2359966..2360994 | + | 1029 | ODA93371 | P-type conjugative transfer protein TrbG | virB9 |
| BFX40_11170 | 2361005..2362219 | + | 1215 | ODA93372 | conjugal transfer protein TrbI | virB10 |
| BFX40_11175 | 2362232..2362504 | + | 273 | ODA93373 | transposase | - |
| BFX40_11180 | 2362609..2363958 | - | 1350 | ODA93374 | oxygen-independent coproporphyrinogen III oxidase | - |
| BFX40_11185 | 2364116..2364871 | + | 756 | ODA93375 | transcriptional regulator | - |
| BFX40_11190 | 2364875..2365414 | - | 540 | ODA93376 | hypothetical protein | - |
| BFX40_11195 | 2365544..2367154 | + | 1611 | ODA93377 | cytochrome-c oxidase, cbb3-type subunit I | - |
Host bacterium
| ID | 396 | Element type | ICE (Integrative and conjugative element) |
| Element name | ICEMsp.SymSEMIA3007 | GenBank | MDLH01000001 |
| Element size | 6967896 bp | Coordinate of oriT [Strand] | 304177..304237 [-] |
| Host bacterium | Mesorhizobium sp. SEMIA 3007 J5_1 | Coordinate of element | 1905270..2386134 |
Cargo genes
| Drug resistance gene | - |
| Virulence gene | gmd |
| Metal resistance gene | - |
| Degradation gene | linJ, dxnH, LinG |
| Symbiosis gene | nifA, nodZ, noeL, nolK, nifT, nifZ, nifB, fixX, fixC, fixB, fixA, nifW, nifS, mLTONO_5203, nifQ, nifH, nifD, nifK, nifE, nifN, nifX, nodS, nodA, nodC, nodI, nodJ, bFX40_10435, nodB, nodD, nolL, nodM, fixN, fixO, fixQ, fixP, fixG, fixH, fixI, fixS |
| Anti-CRISPR | AcrIIA9 |