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Genomic neighbourhood. GO database.

Last update on the 8th of May, 2018

The task is dedicated to search for clusters of orthologous groups (COGs) of mercuric reductase (MerA) protein.

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Genomic neighbourhood with size of 9 cognat_9.pdf
Genomic neighbourhood with size of 15 cognat_15.pdf

COG for MerA

The COG was found using CDD service. There were found 13 COGs, the best of which is Lpd:

  • Accession: COG1249
  • E-value: 7.27e-170
  • Interval: 6-477 out of 477
  • Name: Pyruvate/2-oxoglutarate dehydrogenase complex, dihydrolipoamide dehydrogenase (E3) component or related enzyme
  • Name, rus: Пируват/2-окоглутарат дегидрогеназный комплекс, дигидролипоамиддегидрогеназа, E3 компонент или соответствующий белок
  • Function: Energy production and covertion
  • Function, rus: Производство и преобразование энергии

Genomic neighbourhood of COG1249

cognat_9.pdf, cognat_15.pdf

The genomic neighbourhood of COG1249 was inferred with COGNAT tool. The size of GN was set to 9, threshold to 20% and corresponding species were sorted by taxonomy (fig. 1, cognat_9.pdf). Besides COG1249, the COG0508 (Pyruvate/2-oxoglutarate dehydrogenase complex, dihydrolipoamide acyltransferase (E2) component) was found to be colocalized with COG1249 across Prokaryota in several taxa. There were found 4 types of that colocalization:

  1. No (Crenarchaeota, Cyanobacteria);
  2. Upstream (Euryarchaeota, Proteobacteria);
  3. Downstream (Actinobacteria);
  4. Up- or downstream in same species (Firmicutes).

Small taxa (in COG database) were not taken under consideration. Apart from colocalization, there were found similar GN organizations in Firmicutes suggesting certain kinship of these species.

Fig. 1. Several types of COG1249 genomic neighbourhood in huge prokaryotic taxa.
Yellow — COG1249, orange — COG0508. Red and green arrows correspond to similar GN organizations in Firmicutes.

No enrichment in COGs or in conservatism was observed when GN was extended to 15. In total, no conservatism in GN of COG1249 was found, only variable colocalization with COG0508 in certain GNs.

MerA from Halocynthiibacter arcticus in GO terms

The MerA protein was quieried with AmiGO BLAST against its database to find the most similar available protein. This one is mercuric reductase GSU_3424 from Geobacter sulfurreducens PCA with p-value of 2.2e-66. Apparently, it is dihydrolipoamide dehydrogenase (similar to COG1249) in Uniprot with AC Q746U4, ID Q746U4_GEOSL. Its GO terms were than associated with MerA protein (table 1).

Table 1. GO terms related to protein Q746U4 (Q746U4_GEOSL).
Onthology GO ID GO term Go term, rus Evidence
Biological process GO:0046689 Response to mercury ion Ответ на присутствие ионов ртути ISS
Molecular function GO:0016152 Mercury (II) reductase activity Восстановление Hg(II) ISS

As the MerA, the protein is related to repsonse to mercury ion and catalyzes the following reaction: Hg2+ + NADPH = H+ + Hg + NADP+. Terms were inferred from sequnce similarity with SwissProt P30341 MerA of Streptomyces lividans. The code ISS stands for sequence or structural similarity, i.e. from manual analysis of genome annotation or from structural similarity with experimentally characterized gene products.