Referring to the issue, https://github.com/GuangchuangYu/clusterProfiler/issues/16, it seems that the annotation package, org.EcSakai.eg.db, has no GO annotation.

The GO annotations are based on the gene2go file from NCBI, and if you look at the species for which there are mappings between Entrez Gene ID and GO ID, there is only one E. coli strain, the K12, which has a taxon ID of 511145:

511145    |    Escherichia coli MG1655    |        |    synonym    |
511145    |    Escherichia coli str. K-12 substr. MG1655    |        |    scientific name    |
511145    |    Escherichia coli str. K12 substr. MG1655    |        |    equivalent name    |
511145    |    Escherichia coli str. MG1655    |        |    equivalent name    |
511145    |    Escherichia coli strain MG1655    |        |    equivalent name    |

There may be GO terms for the Sakai strain, but they are not in the gene2go table, and hence are not in the org.EcSakai.eg.db package.