Help to interpret the results
Four outputs have been generated:
General: this tab contains the description, occurence in the database and other information related to the selected GI cluster GIC28
GIs list: lists the 1 occurences of the GI cluster within the database. The table reports information on each occurence.
Orthogroup list: lists the 68 orthogroups associated with the GI cluster
Profile: phylogenetic tree annotated with
- the presence of the GI cluster of interest within all the genomes of the database (first column)
- the size of the orthogroup(s) associated with the GI cluster in each genome.
Orthogroups are shown in red if they are found withinin the that particular GI cluster in a given genome , in green otherwise, i.e. if the orthogroup is present in the genome but not in that GI cluster.
Green homologs (same orthogroup) are not found inside the considered GI cluster.
Variations within orthogroups may be due to the clustering of multi domain proteins or because of erroneous homolog clustering or GI cluster prediction.
Description
| Cluster ID | GIC28 |
|---|---|
| Length | 79600 |
Occurence in the database
| GIC28 is associated with 1 different genomic islands |
×
This plot shows the genomic regions of the selected GIs.
Genes in magenta are AMR genes, while purple correspond to VF genes.
Links are coloured wiht a scale of gray reflecting the sequence identity: dark gray for highly conserved, light grey for features with less identity. Click on the link to visualise the percentage of identity. Beginning and end of the regions are shown as dashed line if the region shows a complete circular contig, a double line if the start or end of the region matches the start or end of a linear contig and a single line otherwise.
Genes in magenta are AMR genes, while purple correspond to VF genes.
Links are coloured wiht a scale of gray reflecting the sequence identity: dark gray for highly conserved, light grey for features with less identity. Click on the link to visualise the percentage of identity. Beginning and end of the regions are shown as dashed line if the region shows a complete circular contig, a double line if the start or end of the region matches the start or end of a linear contig and a single line otherwise.
Genomic regions
| ID | Organism | Bioentry | Start | End | Length | |
|---|---|---|---|---|---|---|
| 59 | GI59 | Proteus mirabilis HI4320 | NC_010554 | 2652110 | 2731710 | 79600 |
| Orthogroup | Products | Genes | |
|---|---|---|---|
| 257 | group_257 | rapA (7) | RNA polymerase-associated protein RapA (7) DEAD/DEAH box helicase (1) |
| 4613 | group_4613 | - | hypothetical protein (1) |
| 4869 | group_4869 | - | type IV toxin-antitoxin system AbiEi family antitoxin (1) |
| 264 | group_264 | ybjD (5) | putative ATP-dependent endonuclease of the OLD family, contains P-loop ATPase and TOPRIM domains (5) ATP-dependent endonuclease (2) AAA family ATPase (1) |
| 4877 | group_4877 | - | DEAD/DEAH box helicase (1) |
| 4623 | group_4623 | eexS (1) | entry exclusion protein EexS (1) |
| 4239 | group_4239 | traA (1) | TraA family conjugative transfer protein (1) |
| 4755 | group_4755 | - | hypothetical protein (1) |
| 4372 | group_4372 | - | ParM/StbA family protein (1) |
| 3991 | group_3991 | - | TraE/TraK family type IV conjugative transfer system protein (1) |
| 4887 | group_4887 | - | class I SAM-dependent DNA methyltransferase (1) |
| 4382 | group_4382 | - | DNA-binding protein (1) |
| 3873 | group_3873 | - | AAA family ATPase (1) CbbQ/NirQ/NorQ C-terminal domain-containing protein (1) |
| 3874 | group_3874 | - | porphyrin biosynthesis protein (1) VWA domain-containing protein (1) |
| 1827 | group_1827 | - | DNA primase (5) toprim domain-containing protein (1) primase-helicase zinc-binding domain-containing protein (1) |
| 4260 | group_4260 | traL (1) | type IV conjugative transfer system protein TraL (1) |
| 4257 | group_4257 | - | hypothetical protein (1) |
| 1828 | group_1828 | - | Integrase-like protein (5) site-specific integrase (1) integrase family protein (1) |
| 1703 | group_1703 | bet (5) | phage recombination protein Bet (5) hypothetical protein (1) Phage recombination protein Bet (1) |
| 4264 | group_4264 | - | FlhC family transcriptional regulator (1) |
| 3753 | group_3753 | - | Helix-turn-helix domain-containing protein (1) helix-turn-helix domain-containing protein (1) |
| 4265 | group_4265 | - | hypothetical protein (1) |
| 4391 | group_4391 | - | peptide chain release factor 3 (1) |
| 173 | group_173 | rep (7) | DNA helicase Rep (7) ATP-dependent helicase (1) UvrD-helicase domain-containing protein (1) |
| 4014 | group_4014 | - | dynamin family protein (1) |
| 4655 | group_4655 | - | hypothetical protein (1) |
| 4021 | group_4021 | - | DUF3150 domain-containing protein (1) |
| 442 | group_442 | ssb (2) | Single-stranded DNA-binding protein (5) single-stranded DNA-binding protein (2) |
| 4154 | group_4154 | - | hypothetical protein (1) |
| 4924 | group_4924 | - | S26 family signal peptidase (1) |
| 2490 | group_2490 | traD (6) | type IV conjugative transfer system coupling protein TraD (5) conjugative transfer system coupling protein TraD (1) |
| 3003 | group_3003 | lexA (5) umuD (1) |
SOS-response transcriptional repressor LexA (RecA-mediated autopeptidase) (5) translesion error-prone DNA polymerase V autoproteolytic subunit (1) |
| 2235 | group_2235 | - | Transcriptional regulator, AbiEi antitoxin, Type IV TA system (5) hypothetical protein (1) DUF6088 family protein (1) |
| 2236 | group_2236 | - | Nucleotidyl transferase AbiEii/AbiGii toxin family protein (5) nucleotidyl transferase AbiEii/AbiGii toxin family protein (2) |
| 4161 | group_4161 | - | nucleotidyl transferase AbiEii/AbiGii toxin family protein (1) |
| 4806 | group_4806 | - | DUF6475 domain-containing protein (1) |
| 4038 | group_4038 | - | hypothetical protein (1) |
| 4551 | group_4551 | - | 3'-5' exonuclease (1) |
| 4681 | group_4681 | - | WYL domain-containing protein (1) |
| 3914 | group_3914 | - | lytic transglycosylase domain-containing protein (2) |
| 4939 | group_4939 | - | hypothetical protein (1) |
| 4301 | group_4301 | - | hypothetical protein (1) |
| 4045 | group_4045 | - | YqaJ viral recombinase family protein (1) |
| 4175 | group_4175 | - | hypothetical protein (1) |
| 4305 | group_4305 | traN (1) | conjugal transfer protein TraN (1) |
| 4308 | group_4308 | - | type-F conjugative transfer system secretin TraK (1) |
| 4436 | group_4436 | - | hypothetical protein (1) |
| 218 | group_218 | flhD (7) | flagellar transcriptional regulator FlhD (8) |
| 4826 | group_4826 | mobI (1) | conjugative transfer protein MobI(A/C) (1) |
| 4060 | group_4060 | - | DUF4400 domain-containing protein (1) |
| 4190 | group_4190 | - | TraB/VirB10 family protein (1) |
| 226 | group_226 | endA (5) | Endonuclease I (5) endonuclease (3) |
| 4323 | group_4323 | traV (1) | type IV conjugative transfer system lipoprotein TraV (1) |
| 4836 | group_4836 | - | TraU family protein (1) |
| 4068 | group_4068 | - | hypothetical protein (1) |
| 4073 | group_4073 | - | conjugal transfer protein TraG N-terminal domain-containing protein (1) |
| 3947 | group_3947 | - | conjugal transfer protein TraH (1) |
| 363 | group_363 | radC (8) | DNA repair protein RadC (8) |
| 4077 | group_4077 | - | hypothetical protein (1) |
| 127 | group_127 | dinP (5) umuC (1) |
Nucleotidyltransferase/DNA polymerase DinP involved in DNA repair (5) DUF4113 domain-containing protein (5) translesion error-prone DNA polymerase V subunit UmuC (1) |
| 4336 | group_4336 | - | hypothetical protein (1) |
| 240 | group_240 | dsbC (7) | bifunctional protein-disulfide isomerase/oxidoreductase DsbC (7) DsbC family protein (1) |
| 3954 | group_3954 | traC (1) | type IV secretion system protein TraC (1) |
| 4084 | group_4084 | mobH (1) | MobH family relaxase (1) |
| 4858 | group_4858 | - | TrbC family F-type conjugative pilus assembly protein (1) |
| 4092 | group_4092 | - | thioredoxin family protein (1) |
| 3069 | group_3069 | dnaT (5) | DnaT DNA-binding domain-containing protein (5) hypothetical protein (1) |
| 4479 | group_4479 | - | hypothetical protein (1) |
