Detailed information of oriT
oriT
The information of the oriT region
| oriTDB ID | 200421 |
| Name | oriT_ICEMeSymNZP2014  |
| Organism | Mesorhizobium erdmanii strain NZP2014 |
| Sequence Completeness | - |
| NCBI accession of oriT (coordinates [strand]) | CP033361 (107097..107154 [+], 58 nt) |
| oriT length | 58 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: 58 nt
>oriT_ICEMeSymNZP2014
AAAACGATGTGCAGACAAACGCTTCGCCGCCTCATGGAGGCGGTGCCTTTATCTTGCC
AAAACGATGTGCAGACAAACGCTTCGCCGCCTCATGGAGGCGGTGCCTTTATCTTGCC
Visualization of oriT structure
oriT secondary structure
Predicted by RNAfold.
Download structure file
T4CP
| ID | 16990 | GenBank | QKC79071 |
| Name | t4cp2_EB233_29180_ICEMeSymNZP2014 |
UniProt ID | _ |
| Length | 816 a.a. | PDB ID | _ |
| Note | Predicted by oriTfinder 2.0 | ||
T4CP protein sequence
Download Length: 816 a.a. Molecular weight: 90192.77 Da Isoelectric Point: 6.0387
>QKC79071.1 conjugal transfer protein TrbE [Mesorhizobium erdmanii]
MLNLSEYRGKADRLADHLPWAALVAPGIVLNKDGSVQRTLRFRGPDLESATEAELIGICARANNALRRLG
SGWTLFFEAERIEALGYPSSRFPDAASWLVDEERRAAFEGKVAHFESRYHLTLLSMPPPDAQARAESALV
DSHHSEGERDWRQEMARFRDETDRVLDLLSGFMPEVRLLDDAETLTYLHDTISTRRHPVAVPETPMYLDG
ILVDVPLTGGLEPMLGEQHLRTLTILGFPNLTRPGILDALNHQDFAYRWMTRFIPLGKTEATKTLTRLRR
QWFAKRKSMVAILREVVSNEPVPLVDSDADNKALDADEALQALGGDHIGFGYLTATVTVWDEDRQAAAEK
LRAVERIINGLGFTTIRESVNAVEAWLGSLPGHVYANVRQPLVHTLNLAHLMPLSSVWAGPAANEHLAEV
TGREAPPLLIAETSGSTPFRLSSHVEDVGHMLIVGPTGAGKSVLLALIALQFRRYAGAQVYVFDKGNSAR
AATLAMGGEHHVLGSDGALAFQPLRNIGDQGRRSWAAEWIAGLIAHENVALTPEVKEAIWSALNSLATAP
AQERTLTGLSVLLQSNALKSALMPYTLDGPFGRLLDADDDRLALSDVQCFETEELMHSQSAVLPVLTYLF
HRLEERFDGRPTLLMLDEAWVYLDNPLFAARIREWLKVLRKKNVSVIFATQSLADIAGSAIAPAIIESCP
QRIFLPNDRAVEPQARTAYERFGLNNRQIELIARATPKRHYYLQSRCGNRRFELGLGPIALALCGASGPA
AQSLIDRVLSEHGQDSFVFRFLGACGLDWAAELLQQFPQPTKEQSS
MLNLSEYRGKADRLADHLPWAALVAPGIVLNKDGSVQRTLRFRGPDLESATEAELIGICARANNALRRLG
SGWTLFFEAERIEALGYPSSRFPDAASWLVDEERRAAFEGKVAHFESRYHLTLLSMPPPDAQARAESALV
DSHHSEGERDWRQEMARFRDETDRVLDLLSGFMPEVRLLDDAETLTYLHDTISTRRHPVAVPETPMYLDG
ILVDVPLTGGLEPMLGEQHLRTLTILGFPNLTRPGILDALNHQDFAYRWMTRFIPLGKTEATKTLTRLRR
QWFAKRKSMVAILREVVSNEPVPLVDSDADNKALDADEALQALGGDHIGFGYLTATVTVWDEDRQAAAEK
LRAVERIINGLGFTTIRESVNAVEAWLGSLPGHVYANVRQPLVHTLNLAHLMPLSSVWAGPAANEHLAEV
TGREAPPLLIAETSGSTPFRLSSHVEDVGHMLIVGPTGAGKSVLLALIALQFRRYAGAQVYVFDKGNSAR
AATLAMGGEHHVLGSDGALAFQPLRNIGDQGRRSWAAEWIAGLIAHENVALTPEVKEAIWSALNSLATAP
AQERTLTGLSVLLQSNALKSALMPYTLDGPFGRLLDADDDRLALSDVQCFETEELMHSQSAVLPVLTYLF
HRLEERFDGRPTLLMLDEAWVYLDNPLFAARIREWLKVLRKKNVSVIFATQSLADIAGSAIAPAIIESCP
QRIFLPNDRAVEPQARTAYERFGLNNRQIELIARATPKRHYYLQSRCGNRRFELGLGPIALALCGASGPA
AQSLIDRVLSEHGQDSFVFRFLGACGLDWAAELLQQFPQPTKEQSS
Protein domains
Predicted by InterproScan.
Protein structure
No available structure.
| ID | 16991 | GenBank | QKC79076 |
| Name | t4cp2_EB233_29205_ICEMeSymNZP2014 |
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
>QKC79076.1 conjugal transfer protein TraG [Mesorhizobium erdmanii]
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 | 16992 | GenBank | QKC79101 |
| Name | t4cp2_EB233_29395_ICEMeSymNZP2014 |
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
>QKC79101.1 type IV secretion system protein VirD4 [Mesorhizobium erdmanii]
MSSTKTTPPNIALSIACSLALGFCAASLYATFRHGGSGEALMTFDVRAFWFETPFYLGFATPVFYRGVAI
VLATSAVVLLIQQVVLRRKLEHHGTARWARVDEMRCTGYLRRYRSVTGPVFGKTSGPFWPGYYLTNGEQP
HSLIVAPTRAGKGIGIVIPTLLTFKGSVIALDVKGELFELTSRARKATGDNVFKFAPLDSERRTNCYNPL
LDLIALPPQLQFTEARRLAANLITAKGEGAEGFVSGARDIFVAGILACIERGTPTIGAVYDLFAQPGEKF
KLFAQLAMETRNKEAQRIFDDMAGNDTKILTSYTSVLGDGGLNLWADPAVKAATSRSDFSVYDLRRRRTC
IYLCVGPNDLEVIAPLIRLFFQQIVSILQRSLPRQDEKNEVLFLLDEFKHLGKLEAIETAITTIAGYKGR
FMLIIQSLSALTGAYGEAGKQNFLSNTGLQVFMATADDETPTYISKAIGEYTFEAKSISYSQARTFDWNI
QNSHQGAPLLRPEQVRLLDEDYEIVLIKGLPPLQLRKVRYYSDRILKRIFESQTGALPEPAPLMEAHPDD
TDG
MSSTKTTPPNIALSIACSLALGFCAASLYATFRHGGSGEALMTFDVRAFWFETPFYLGFATPVFYRGVAI
VLATSAVVLLIQQVVLRRKLEHHGTARWARVDEMRCTGYLRRYRSVTGPVFGKTSGPFWPGYYLTNGEQP
HSLIVAPTRAGKGIGIVIPTLLTFKGSVIALDVKGELFELTSRARKATGDNVFKFAPLDSERRTNCYNPL
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: 5973445..5982502
| Locus tag | Coordinates | Strand | Size (bp) | Protein ID | Product | Description |
|---|---|---|---|---|---|---|
| EB233_29135 | 5969817..5970356 | + | 540 | QKC79064 | hemerythrin domain-containing protein | - |
| EB233_29140 | 5970360..5971115 | - | 756 | QKC79065 | Crp/Fnr family transcriptional regulator | - |
| EB233_29145 | 5971273..5972623 | + | 1351 | Protein_5766 | oxygen-independent coproporphyrinogen III oxidase | - |
| EB233_29150 | 5973160..5973432 | - | 273 | QKC79066 | DUF2274 domain-containing protein | - |
| EB233_29155 | 5973445..5974659 | - | 1215 | QKC80182 | TrbI/VirB10 family protein | virB10 |
| EB233_29160 | 5974671..5975699 | - | 1029 | QKC79067 | P-type conjugative transfer protein TrbG | virB9 |
| EB233_29165 | 5975696..5976421 | - | 726 | QKC79068 | conjugal transfer protein TrbF | virB8 |
| EB233_29170 | 5976422..5977744 | - | 1323 | QKC79069 | P-type conjugative transfer protein TrbL | virB6 |
| EB233_29175 | 5977776..5978501 | - | 726 | QKC79070 | P-type conjugative transfer protein TrbJ | virB5 |
| EB233_29180 | 5978498..5980948 | - | 2451 | QKC79071 | conjugal transfer protein TrbE | virb4 |
| EB233_29185 | 5980942..5981214 | - | 273 | QKC79072 | conjugal transfer protein | virB3 |
| EB233_29190 | 5981214..5981522 | - | 309 | QKC79073 | conjugal transfer protein TrbC | virB2 |
| EB233_29195 | 5981534..5982502 | - | 969 | QKC79074 | P-type conjugative transfer ATPase TrbB | virB11 |
| EB233_29200 | 5982499..5982912 | - | 414 | QKC79075 | CopG family transcriptional regulator | - |
| EB233_29205 | 5983031..5985061 | - | 2031 | QKC79076 | conjugal transfer protein TraG | - |
| EB233_29210 | 5985191..5985428 | + | 238 | Protein_5779 | XRE family transcriptional regulator | - |
| EB233_29215 | 5985726..5986115 | - | 390 | QKC79077 | hypothetical protein | - |
| EB233_29220 | 5986106..5986513 | - | 408 | QKC79078 | hypothetical protein | - |
Region 2: 6005979..6015401
| Locus tag | Coordinates | Strand | Size (bp) | Protein ID | Product | Description |
|---|---|---|---|---|---|---|
| EB233_29280 | 6001614..6001744 | + | 131 | Protein_5793 | IS630 family transposase | - |
| EB233_29285 | 6001744..6002355 | + | 612 | Protein_5794 | ISKra4 family transposase | - |
| EB233_29290 | 6003325..6005865 | + | 2541 | QKC79084 | two-component system VirA-like sensor kinase | - |
| EB233_29295 | 6005979..6007019 | - | 1041 | QKC79085 | P-type DNA transfer ATPase VirB11 | virB11 |
| EB233_29300 | 6007003..6008142 | - | 1140 | QKC79086 | type IV secretion system protein VirB10 | virB10 |
| EB233_29305 | 6008139..6009020 | - | 882 | QKC79087 | type IV secretion system protein VirB9 | virB9 |
| EB233_29310 | 6009017..6009730 | - | 714 | QKC79088 | type IV secretion system protein VirB8 | virB8 |
| EB233_29315 | 6009727..6009885 | - | 159 | QKC79089 | type IV secretion system lipoprotein VirB7 | - |
| EB233_29320 | 6009912..6010796 | - | 885 | QKC79090 | type IV secretion system protein | virB6 |
| EB233_29325 | 6010855..6011535 | - | 681 | QKC79091 | type IV secretion system protein VirB5 | traI |
| EB233_29330 | 6011549..6013918 | - | 2370 | QKC79092 | VirB4 family type IV secretion/conjugal transfer ATPase | virb4 |
| EB233_29335 | 6013918..6014244 | - | 327 | QKC79093 | type IV secretion system protein VirB3 | virB3 |
| EB233_29340 | 6014244..6014609 | - | 366 | QKC79094 | pilin major subunit VirB2 | virB2 |
| EB233_29345 | 6014625..6015401 | - | 777 | QKC79095 | type IV secretion system lytic transglycosylase VirB1 | virB1 |
| EB233_29350 | 6015489..6015686 | - | 198 | QKC79096 | hypothetical protein | - |
| EB233_29355 | 6016465..6017184 | + | 720 | QKC79097 | response regulator | - |
| EB233_29360 | 6017397..6017657 | + | 261 | QKC79098 | hypothetical protein | - |
Host bacterium
| ID | 376 | Element type | ICE (Integrative and conjugative element) |
| Element name | ICEMeSymNZP2014 | GenBank | CP033361 |
| Element size | 6602217 bp | Coordinate of oriT [Strand] | 107097..107154 [+] |
| Host bacterium | Mesorhizobium erdmanii strain NZP2014 | Coordinate of element | 5949545..6478456 |
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, eB233_29665, nodJ, nodI, nodC, nodA, nodS, mlr6097, nifU, nifX, nifN, nifE, nifK, nifD, nifH, nifQ, nifS, nifW, fixA, fixB, fixC, fixX, nifA, nifB, nifZ, fixT, nolK, noeL, nodZ, nodE, nodF, nodU, mlr1025 |
| Anti-CRISPR | AcrIIA9, AcrIIC1 |