The organism assigned to me is Methanococcus jannaschii. I tried to follow the methods described in the assignment. The first COG took less than half an hour to find--I guess I was fortunate in picking COG that had proteins that happened to meet the 50-bp criteria. The second one took a little longer, but it was still under a couple of hours. The third one took more than a few hours to find. 1. Highly-related proteins The first set of highly-related proteins I found are from COG0013 (Alanyl-tRNA synthetase). This COG includes a total of 43 proteins from prokaryotes. In addition, there are also 4 proteins from eukaryotes that are similar to the proteins in the set. The protein 15668744 (MJ0564) from Methanococcus jannaschii is in COG0013. There were 8 other genes that had a high match with MJ0564 (E-Value at least as good as e-100). Of these 2 genes (PAB1245 and PH0297) had non-encoding upstream sequences of less than 50 base pairs, leaving me with a total of 7 genes that coded proteins were highly related and had non-encoding upstream sequences of at least 50 base-pairs: Gene ProteinID E-Val Upstrm Protein Description Organism ------------------------------------------------------------------------ ------------------------ MJ0564 15668744 0.0 1156 alanyl-tRNA synthetase Methanococcus jannaschii APE2166 14601887 0.0 229 alanyl-tRNA synthetase Aeropyrum pernix TVN0819 13541650 e-172 143 Alanyl-tRNA synthetase Thermoplasma volcanium Ta0849 16081904 e-170 96 alanyl-tRNA synthetase Thermoplasma acidophilum MTH1683 15679677 0.0 90 alanyl-tRNA synthetase Methanobacterium thermoautotrophicum VNG2283G 15791093 0.0 62 alanyl-tRNA synthetase Halobacterium sp. NRC-1 AF2255 11499836 0.0 54 alanyl-tRNA synthetase Archaeoglobus fulgidus The second set of highly-related proteins I found are from COG0017 (Aspartyl/asparaginyl-tRNA synthetases). This COG includes a total of 40 proteins from prokaryotes. In addition, there are also 5 proteins from eukaryotes that are similar to the proteins in the set. The protein 15669750 (MJ1555) from Methanococcus jannaschii is in COG0017. There were 6 other genes that had a high match with MJ1555(E-Value at least as good as e-100). Of these 1 gene (AF0920) had non-encoding upstream sequences of less than 50 base pairs, leaving me with a total of 7 genes that coded prote6ns were highly related and had non-encoding upstream sequences of at least 50 base-pairs: Gene ProteinID E-Val Upstrm Protein Description Organism ------------------------------------------------------------------------ ------------------------ Ta0946 16081991 e-118 471 aspartyl-tRNA synthetase Thermoplasma acidophilum TVN1090 13541921 e-118 385 Aspartyl-tRNA synthetase Thermoplasma volcanium MJ1555 15669750 0.0 251 aspartyl-tRNA synthetase Methanococcus jannaschii MTH226 15678254 e-165 94 aspartyl-tRNA synthetase Methanothermobacter thermautotrophicus PH1020 14590860 e-145 66 aspartyl-tRNA synthetase Pyrococcus horikoshii PAB0646 14521164 e-144 62 aspartyl-tRNA synthetase Pyrococcus abyssi The third set of highly-related proteins I found are from COG0495 (Leucyl-tRNA synthetase). This COG includes a total of 45 proteins from prokaryotes. In addition, there are also 4 proteins from eukaryotes that are similar to the proteins in the set. The protein 15668814 (MJ0633) from Methanococcus jannaschii is in COG0495. There were 7 other genes that had a high match with MJ0633 (E-Value at least as good as e-100). Of these 3 genes (MTH1508, TVN0761 and Ta0777) had non-encoding upstream sequences of less than 50 base pairs, leaving me with a total of 5 genes that coded proteins were highly related and had non-encoding upstream sequences of at least 50 base-pairs: Gene ProteinID E-Val Upstrm Protein Description Organism ------------------------------------------------------------------------ ------------------------ PAB1782 14521079 0.0 793 leucyl-tRNA synthetase Pyrococcus abyssi PH0965 14590812 0.0 287 leucyl-tRNA synthetase Pyrococcus horikoshii MJ0633 15668814 0.0 138 leucyl-tRNA synthetase Methanococcus jannaschii APE1015 14601141 0.0 126 leucyl-tRNA synthetase Aeropyrum pernix AF2421 11499997 0.0 59 leucyl-tRNA synthetase Archaeoglobus fulgidus