Table 5. Genes unique to G. thermodenitrificans NG80-2 Gene ID Gene name Gene product COG functional category

Size: px
Start display at page:

Download "Table 5. Genes unique to G. thermodenitrificans NG80-2 Gene ID Gene name Gene product COG functional category"

Transcription

1 Table 5. Genes unique to G. thermodenitrificans NG80-2 GT0030 gt30 Methionine--tRNA ligase/methionyl-trna synthetase COG0143, Translation GT0033 gt33 Unknown GT0106 gt106 Ribosomal protein L3 COG0087, Translation GT0146 gt146 Transposase COG3464, Replication, recombination and repair GT0153 gt153 Conserved hypothetical protein COG1853, General function prediction only GT0154 gt154 Putative truncated transposase GT0157 gt157 Oligopeptide transport system permease protein OppC(disrupted) GT0158 gt158 Oligopeptide transport system permease protein OppC(disrupted) GT0164 gt164 Unknown GT0165 gt165 Putative reductase COG0431, General function prediction only GT0176 gt176 Unknown GT0182 gt182 Sensory transduction histidine kinases COG0642, Signal transduction mechanisms GT0183 gt183 Response regulators consisting of a CheY-like receiver domain and a COG0745, Signal transduction mechanisms HTH DNA-binding domain GT0184 gt184 Unknown GT0185 gt185 Unknown GT0186 gt186 Unknown GT0208 gt208 Unknown GT0227 gt227 Putative metal ion transport protein COG1914, Inorganic ion transport and metabolism GT0232 gt232 Transposase (02) COG3464, Replication, recombination and repair GT0233 gt233 Unknown

2 GT0252 gt252 Unknown GT0278 gt278 Unknown GT0279 gt279 Conserved hypothetical protein COG1583, Replication, recombination and repair GT0280 gt280 Conserved hypothetical protein COG4405, Function unknown GT0287 gt287 Unknown GT0291 gt291 Tartrate dehydrogenase COG0473, Energy production and conversion GT0293 gt293 Aldehyde dehydrogenase COG1012, Energy production and conversion GT0303 gt303 Conserved hypothetical protein COG4898, Function unknown GT0304 gt304 Unknown GT0305 gt305 type I restriction-modification system R subunit (endonuclease)(part) GT0310 gt310 Conserved hypothetical protein GT0312 gt312 Unknown GT0313 gt313 Unknown GT0314 gt314 Transposase COG3464, Replication, recombination and repair GT0316 gt316 Unknown GT0317 gt317 Sodium:dicarboxylate symporter family protein COG3633, Amino acid transport and metabolism GT0321 gt321 Putative transposase GT0323 gt323 Conserved hypothetical protein GT0325 gt325 Unknown GT0326 gt326 Unknown COG4185, Function unknown GT0327 gt327 Unknown GT0330 rese Sensor protein ResE COG0642, Signal transduction mechanisms

3 GT0331 gt331 Transcriptional regulatory component of sensory transduction COG0745, Signal transduction mechanisms system GT0332 gt332 ABC transporter ATP-binding protein COG4591, Cell wall/membrane biogenesis GT0358 gt358 Unknown GT0374 gt374 Putative transposase GT0402 gt402 Transcription regulator GT0404 gt404 Sugar transporter sugar binding protein COG1653, Carbohydrate transport and metabolism GT0406 gt406 Putative integral membrane binding-protein-dependent transport COG0395, Carbohydrate transport and metabolism protein GT0409 gt409 Conserved hypothetical protein GT0410 gt410 Unknown GT0411 gt411 Conserved hypothetical protein GT0412 gt412 Unknown GT0415 gt415 Unknown GT0421 gt421 Conserved hypothetical protein GT0423 gt423 Unknown GT0424 gt424 Conserved hypothetical protein GT0427 gt427 Conserved hypothetical protein GT0428 gt428 Unknown GT0431 gt431 Unknown GT0432 gt432 Conserved hypothetical protein GT0435 gt435 Transposase

4 GT0436 gt436 IS426 transposase GT0450 gt450 Conserved hypothetical protein GT0475 gt475 Unknown GT0482 gt482 Glutamate synthase GT0600 gt600 Unknown GT0628 gt628 Transposase (04) COG3328, Replication, recombination and repair GT0629 gt629 Transposase COG3328, Replication, recombination and repair GT0631 gt631 Transposase (04) COG3328, Replication, recombination and repair GT0633 gt633 Unknown GT0646 gt646 Unknown GT0648 gt648 Unknown GT0651 gt651 Similar to acetolactate synthase large subunit COG0028, Amino acid transport and metabolism GT0652 gt652 Unknown GT0653 narg Respiratory nitrate reductase alpha subunit COG5013, Energy production and conversion GT0654 narh Nitrate reductase beta subunit COG1140, Energy production and conversion GT0655 narj Nitrate reductase protein J COG2180, Energy production and conversion GT0656 nari Respiratory nitrate reductase gamma subunit COG2181, Energy production and conversion GT0667 gt667 Putative transposase GT0669 gt669 Unknown GT0679 gt679 Transcriptional regulator, TetR family GT0681 gt681 Unknown GT0687 gt687 Conserved hypothetical protein

5 GT0703 gt703 Unknown GT0719 gt719 Unknown GT0738 gt738 Unknown GT0753 gt753 Unknown GT0754 gt754 Unknown GT0755 gt755 Unknown GT0757 gt757 Unknown GT0758 gt758 Transposase(AGR_pAT_536p) COG2963, Replication, recombination and repair GT0760 gt760 Conserved hypothetical protein COG0419, Replication, recombination and repair GT0764 gt764 Unknown GT0765 gt765 Transposase (04) COG3328, Replication, recombination and repair GT0766 gt766 Unknown GT0767 gt767 Chromosome partitioning ATPase ParA family COG1192, Cell cycle control, mitosis and meiosis GT0768 gt768 IS426 transposase GT0769 gt769 Transposase GT0770 gt770 Unknown GT0771 gt771 Unknown GT0772 gt772 Unknown GT0773 gt773 Unknown GT0774 gt774 Conserved hypothetical protein COG3428, Function unknown GT0775 gt775 Conserved hypothetical protein COG3402, Function unknown GT0777 gt777 IS426 transposase

6 GT0778 gt778 Transposase GT0782 fixa FixA protein COG2086, Energy production and conversion GT0783 fixb FixB protein COG2025, Energy production and conversion GT0784 gt784 FixC (disrupted by IS) COG0644, Energy production and conversion GT0785 gt785 Transposase (02) COG3464, Replication, recombination and repair GT0786 gt786 FixC (disrupted by IS) COG0644, Energy production and conversion GT0787 gt787 Ferredoxin COG2440, Energy production and conversion GT0788 gt788 Unknown GT0789 gt789 Unknown GT0797 gt797 Unknown GT0798 gt798 Unknown GT0799 gt799 Unknown GT0800 gt800 Unknown GT0801 gt801 Unknown GT0827 gt827 Unknown GT0828 gt828 Unknown GT0830 gt830 Unknown GT0859 gt859 Unknown GT0877 gt877 Transcription antiterminator COG3711, Transcription GT0919 gt919 Unknown GT0928 gt928 Unknown GT1014 gt1014 Phosphoglycerate mutase family protein

7 GT1039 gt1039 Unknown GT1092 gt1092 Flagella-associated protein COG1419, Cell motility GT1150 gt1150 Unknown GT1165 gt1165 Methyl-accepting chemotaxis protein(disrupted) GT1193 gt1193 Transposase (02) COG3464, Replication, recombination and repair GT1213 gt1213 Unknown GT1217 gt1217 Unknown GT1218 gt1218 Unknown GT1219 gt1219 Unknown GT1220 gt1220 Unknown GT1234 gt1234 Oxidoreductase COG3384, Function unknown GT1235 gt1235 Unknown GT1237 gt1237 Conserved hypothetical protein GT1240 gt1240 D-alanyl-D-alanine dipeptidase COG2173, Cell wall/membrane biogenesis GT1243 gt1243 Unknown GT1244 gt1244 Unknown GT1245 gt1245 Transposase (02) COG3464, Replication, recombination and repair GT1246 gt1246 Unknown GT1248 gt1248 Conserved cypothetical protein GT1255 gt1255 Unknown GT1256 gt1256 Similar to 3-oxoacyl-(acyl carrier protein) reductase COG1028, Lipid transport and metabolism GT1257 gt1257 Unknown

8 GT1258 gt1258 Unknown GT1261 gt1261 Unknown GT1263 gt1263 Putative RNA polymerase sigma factor COG1595, Transcription GT1277 gt1277 Conserved hypothetical protein GT1278 gt1278 Putative periplasmic protein COG2885, Cell wall/membrane biogenesis GT1279 gt1279 Unknown GT1280 gt1280 Patative DNA/RNA helicase(snf2 family) COG0553, Transcription GT1281 gt1281 Unknown GT1322 gt1322 Unknown GT1323 gt1323 Unknown GT1346 gt1346 ABC transporter (permease) COG2011, Inorganic ion transport and metabolism GT1396 gt1396 Conserved Hypothetical protein GT1401 gt1401 Conserved Hypothetical protein COG1695, Transcription GT1431 gt1431 Conserved hypothetical protein GT1432 gt1432 Conserved hypothetical protein GT1438 gt1438 Unknown GT1444 gt1444 Unknown GT1453 gt1453 Unknown GT1457 gt1457 Unknown GT1460 gt1460 Unknown GT1470 gt1470 Unknown GT1485 gt1485 Conserved Hypothetical protein

9 GT1487 gt ketogluconate transporter COG2271, Carbohydrate transport and metabolism GT1523 gt1523 Unknown GT1532 gt1532 Unknown GT1536 gt1536 Conserved hypothetical protein GT1544 gt1544 Unknown GT1548 gt1548 Unknown COG1586, Amino acid transport and metabolism GT1549 gt1549 Unknown GT1553 gt1553 Unknown GT1557 gt1557 Transposase (04) COG3328, Replication, recombination and repair GT1558 gt1558 Conserved hypothetical protein GT1560 gt1560 Sensory box protein COG2199, Signal transduction mechanisms GT1562 gt1562 Putative NTP pyrophosphohydrolase COG1051, Nucleotide transport and metabolism GT1563 gt1563 Unknown GT1566 gt1566 Unknown GT1570 gt1570 Unknown GT1572 gt1572 Hydrolase, carbon-nitrogen family COG0388, General function prediction only GT1576 gt1576 Unknown GT1578 gt1578 Putative acetyltransferase COG1670, Translation GT1584 gt1584 Transposase COG3464, Replication, recombination and repair GT1585 gt1585 Possible aminoglycoside phosphotransferase(disrupted) GT1586 gt1586 Possible aminoglycoside phosphotransferase(disrupted) GT1589 gt1589 Unknown

10 GT1591 gt1591 Transposase COG2963, Replication, recombination and repair GT1592 gt1592 transposase GT1593 gt1593 Transposase GT1595 gt1595 Unknown GT1596 gt1596 Conserved hypothetical protein COG0789, Transcription GT1605 gt1605 Unknown GT1606 gt1606 Conserved hypothetical protein GT1613 gt1613 Unknown GT1615 gt1615 Copper-transporting ATPase COG2217, Inorganic ion transport and metabolism GT1616 gt1616 Copper-importing ATPase COG2217, Inorganic ion transport and metabolism GT1619 gt1619 Unknown GT1620 gt1620 Permease GT1621 gt1621 Conserved hypothetical protein GT1623 gt1623 IS426 transposase GT1624 gt1624 Transposase GT1625 gt1625 Unknown GT1627 gt1627 Unknown GT1636 gt1636 Unknown GT1649 gt1649 Unknown GT1653 gt1653 Unknown GT1660 gt1660 Unknown GT1716 gt1716 Conserved hypothetical protein COG3945, Function unknown

11 GT1717 pora Pyruvate synthase subunit PorA COG0674, Energy production and conversion GT1718 porg Gamma subunit of pyruvate oxidoreductase COG1014, Energy production and conversion GT1729 gt1729 Unknown GT1730 nosf ABC transporter ATP-binding protein COG1131, Defense mechanisms GT1731 nosy Copper ABC transporter (permease) GT1732 nosd Copper binding periplasmic protein COG3420, Inorganic ion transport and metabolism GT1733 gt1733 Unknown GT1734 nosz Nitrous oxide reductase COG4263, Energy production and conversion GT1735 gt1735 Unknown GT1745 gt1745 Predicted UDP-glucuronosyltransferase COG0707, Cell wall/membrane biogenesis GT1760 gt1760 NGG1-interacting factor 3 GT1767 kdga 2-keto-3-deoxy-6-phospho-gluconate aldolase COG0800, Carbohydrate transport and metabolism GT1774 xyna2 Intra-cellular xylanase COG3693, Carbohydrate transport and metabolism GT1783 gt1783 Oxidoreductase GT1784 gt1784 Transposase GT1786 gt1786 Transposase GT1787 gt1787 Transposase GT1797 gt1797 L-ribulose 5-phosphate 4-epimerase COG0235, Carbohydrate transport and metabolism GT1813 gt1813 D-ribose-binding periplasmic protein COG1879, Carbohydrate transport and metabolism GT1814 gt1814 Ribose ABC transporter (permease) COG1172, Carbohydrate transport and metabolism GT1815 gt1815 ATP-binding transport protein COG1129, Carbohydrate transport and metabolism GT1816 gt1816 Oxidoreductase COG0673, General function prediction only

12 GT1818 gt1818 Unknown COG0773, Cell wall/membrane biogenesis GT1821 gt1821 Putative integral membrane transport protein COG0395, Carbohydrate transport and metabolism GT1822 gt1822 Putative integral membrane transport protein COG1175, Carbohydrate transport and metabolism GT1823 gt1823 Putative extracellular solute-binding lipoprotein COG1653, Carbohydrate transport and metabolism GT1824 gt1824 transcriptional regulator COG1609, Transcription GT1830 gt1830 Guanidinobutyrase COG0010, Amino acid transport and metabolism GT1842 tctb Putative tricarboxylate transport protein TctB GT1848 gt1848 Unknown GT1854 gt1854 Probable galactonate dehydratase protein GT1871 gt1871 Probable ABC transporter integral membrane protein COG1593, Carbohydrate transport and metabolism GT1872 gt1872 Probable ABC transporter integral membrane protein GT1883 gt1883 Unknown GT1898 gt1898 putative Enoyl-CoA hydratase/isomerase COG1024, Lipid transport and metabolism GT1900 gt1900 Unknown GT1903 gt1903 Unknown GT1905 gt1905 Unknown GT1906 gt1906 Unknown GT1908 gt1908 Glycerol-3-phosphate-binding protein(disrupted) GT1909 gt1909 Glycerol-3-phosphate-binding protein(disrupted) GT1935 gt1935 Conserved hypothetical protein GT1936 gt1936 Unknown GT1937 gt1937 Unknown

13 GT1939 gt1939 Transcriptional regulator (LacI-family) COG1609, Transcription GT1940 gt1940 Conserved hypothetical protein COG1804, Energy production and conversion GT1942 gt1942 Transcriptional regulator (IclR family) COG1414, Transcription GT1946 gt1946 Putative ABC transporter periplasmic solute-binding protein COG1638, Carbohydrate transport and metabolism GT1947 gt1947 Unknown GT1949 gt1949 Acetolactate synthase large subunit COG0028, Amino acid transport and metabolism GT1951 gt1951 Aldehyde dehydrogenase COG1012, Energy production and conversion GT1952 gt1952 Citrate synthase I COG0372, Energy production and conversion GT1953 gt1953 Unknown GT1954 gt1954 Unknown GT1956 gt1956 Unknown COG1343, Replication, recombination and repair GT1957 gt1957 Unknown GT1958 gt1958 DNA-binding response regulator COG0745, Signal transduction mechanisms GT1963 gt1963 Putative integrase/recombinase COG4973, Replication, recombination and repair GT1965 gt1965 Unknown GT1966 gt1966 Unknown GT1967 gt1967 Unknown GT1968 gt1968 Unknown GT1969 gt1969 Unknown GT1971 gt1971 Unknown GT1973 gt1973 Unknown COG2510, Function unknown GT1976 gt1976 Unknown

14 GT1985 gt1985 Similar to multidrug resistance protein B GT1991 gt1991 Unknown GT1992 gt1992 Unknown GT1993 gt1993 Transposase, IS605 family GT1995 gt1995 Peptide ABC transporter ATP-binding protein COG4608, Amino acid transport and metabolism GT1997 gt1997 Oligopeptide ABC transporter (permease) COG1173, Amino acid transport and metabolism GT2000 gt2000 Conserved Hypothetical protein COG5476, Function unknown GT2001 gt2001 Conserved Hypothetical protein COG3457, Amino acid transport and metabolism GT2002 gt2002 Methyl-accepting chemotaxis protein COG0840, Cell motility GT2003 gt2003 Unknown GT2004 gt2004 Unknown GT2005 gt2005 Unknown GT2006 gt2006 Unknown GT2007 gt2007 Unknown GT2010 gt2010 Unknown GT2034 gt2034 Unknown GT2035 gt2035 Similar to 3-oxoacyl-(acyl carrier protein) reductase COG1028, Lipid transport and metabolism GT2039 gt2039 Possible acyl protein synthase/acyl-coa reductase-like protein GT2040 gt2040 Possible acyl protein synthase/acyl-coa reductase-like protein GT2041 gt2041 Putative transposase GT2045 gt2045 Unknown GT2046 gt2046 Unknown

15 GT2047 gt2047 Unknown GT2049 gt2049 Unknown GT2050 gt2050 Conserved Hypothetical protein GT2052 gt2052 Unknown GT2053 gt2053 Unknown GT2054 gt2054 Unknown GT2055 gt2055 Unknown GT2056 gt2056 Unknown GT2057 gt2057 Unknown GT2058 gt2058 Unknown GT2059 gt2059 Transcriptional regulator, Cro/CI family GT2066 gt2066 Transposase (02) COG3464, Replication, recombination and repair GT2067 gt2067 Putative integrase/recombinase XerD COG4974, Replication, recombination and repair GT2068 gt2068 Unknown GT2070 gt2070 Unknown GT2071 gt2071 Putative transposase GT2072 tnpa Transposition regulatory protein TnpA COG4974, Replication, recombination and repair GT2073 tnpb Transposition regulatory protein TnpB GT2076 gt2076 Unknown COG1403, Defense mechanisms GT2077 gt2077 Conserved hypothetical protein GT2079 gt2079 Integrase-recombinase protein COG4974, Replication, recombination and repair GT2080 gt2080 Unknown

16 GT2158 gt2158 Similar to spore germination protein GerKB GT2159 gt2159 Similar to spore germination protein GerKA(disrupted) GT2160 gt2160 Similar to spore germination protein GerKA(disrupted) GT2201 gt2201 Conserved hypothetical protein GT2216 gt2216 Unknown GT2226 gt2226 Unknown GT2228 gt2228 Unknown GT2229 gt2229 Conserved hypothetical protein GT2254 gt2254 Conserved Hypothetical protein GT2269 gt2269 Similar to N-acyl-L-amino acid amidohydrolase COG1473, General function prediction only GT2271 gt2271 Ornithine cyclodeaminase COG2423, Amino acid transport and metabolism GT2273 gt2273 Unknown GT2276 gt2276 Similar to threonine dehydratase COG1171, Amino acid transport and metabolism GT2278 gt2278 Unknown GT2279 gt2279 Amino acid ABC transporter ATP-binding protein COG1126, Amino acid transport and metabolism GT2280 gt2280 Amino acid ABC transporter (permease) COG0765, Amino acid transport and metabolism GT2281 gt2281 Amino acid ABC transporter (permease) COG0765, Amino acid transport and metabolism GT2282 gt2282 ABC transporter COG0834, Amino acid transport and metabolism GT2283 gt2283 SoxB-like sarcosine oxidase, beta subunit related COG0665, Amino acid transport and metabolism GT2284 gt2284 Similar to electron transfer flavoprotein beta subunit COG2086, Energy production and conversion GT2285 gt2285 Similar to electron transfer flavoprotein alpha subunit COG2025, Energy production and conversion GT2286 gt2286 Similar to N-acyl-L-amino acid amidohydrolase COG1473, General function prediction only

17 GT2288 gt2288 Xaa-Pro aminopeptidase COG0006, Amino acid transport and metabolism GT2294 gt2294 Unknown GT2301 gt2301 Unknown GT2325 gt2325 Exodeoxyribonuclease VII large subunit(disrupted) COG1570, Replication, recombination and repair GT2350 gt2350 Unknown GT2353 gt2353 Conserved hypothetical protein GT2356 gt2356 Unknown GT2357 gt2357 Ribonucleoside-diphosphate reductase (major subunit)(disrupted) COG0209, Nucleotide transport and metabolism GT2471 gt2471 Unknown GT2490 gt2490 Unknown GT2561 gt2561 Unknown GT2602 gt2602 Unknown GT2605 gt2605 Unknown GT2625 gt2625 Unknown GT2650 gt2650 Unknown GT2673 gt2673 Conserved hypothetical protein COG4994, Function unknown GT2684 gt2684 Unknown GT2685 gt2685 Unknown GT2705 gt2705 Similar to 2-dehydropantoate 2-reductase COG1893, Coenzyme transport and metabolism GT2706 gt2706 Sodium/pantothenate symporter COG0591, Amino acid transport and metabolism GT2707 gt2707 Hypothetical cytosolic protein COG3246, Function unknown GT2708 gt2708 Sigma-54-dependent transcriptional activator COG3829, Transcription

18 GT2736 gt2736 Unknown GT2763 gt2763 Unknown GT2765 gt2765 Periplasmic serine proteinase COG0265, Posttranslational modification, protein turnover, chaperones GT2793 gt2793 Predicted acetyltransferase COG0456, General function prediction only GT2797 gt2797 Unknown GT2801 yolb YolB GT2803 gt2803 Unknown GT2804 gt2804 Conserved hypothetical protein COG4889, General function prediction only GT2806 gt2806 Unknown GT2810 gt2810 Unknown GT2816 gt2816 Unknown GT2817 gt2817 Unknown GT2818 gt2818 Unknown GT2819 gt2819 Unknown GT2820 gt2820 Conserved hypothetical protein GT2821 gt2821 Unknown GT2822 gt2822 Unknown GT2823 gt2823 Unknown GT2824 gt2824 Unknown GT2827 gt2827 Putative phage protein GT2830 gt2830 Putative phage protein

19 GT2831 gt2831 Unknown GT2833 gt2833 Unknown GT2834 gt2834 Unknown GT2835 gt2835 Similar to Bacillus subtilis YqaS COG5484, Function unknown GT2836 gt2836 Conserved hypothetical protein GT2837 gt2837 Unknown GT2839 gt2839 Conserved hypothetical protein GT2840 chey Chemotaxis response regulator CheY COG2201, Cell motility GT2841 gt2841 Gp53 protein GT2842 gt2842 Putative phage protein GT2843 gt2843 Putative phage protein GT2845 gt2845 Unknown GT2846 gt2846 Putative phage protein GT2847 gt2847 Single-strand DNA binding protein COG0629, Replication, recombination and repair GT2848 gt2848 Conserved hypothetical protein GT2849 gt2849 Unknown GT2850 gt2850 Replicative DNA helicase COG0305, Replication, recombination and repair GT2851 gt2851 Putative phage protein GT2853 gt2853 Unknown GT2854 gt2854 Putative phage protein GT2856 gt2856 Unknown GT2857 gt2857 Unknown

20 GT2858 gt2858 Unknown GT2867 gt2867 Unknown GT2871 gt2871 Unknown GT2873 gt2873 Unknown GT2874 gt2874 Unknown GT2895 gt2895 Unknown GT2936 gt2936 Unknown GT2937 gt2937 Unknown GT2938 gt2938 Unknown GT2940 gt2940 Unknown GT2941 gt2941 Unknown GT2948 gt2948 Unknown GT2968 gt2968 Unknown GT2969 gt2969 Unknown GT2970 gt2970 DAPA aminotransferase COG0161, Coenzyme transport and metabolism GT2973 hpac Flavin reductase COG1853, General function prediction only GT2974 gt2974 Unknown GT2978 gt2978 Putative transposase GT2996 gt2996 Glutathione peroxidase COG0386, Posttranslational modification, protein turnover, chaperones GT3019 gt3019 Unknown GT3050 gt3050 Unknown

21 GT3073 gt3073 Unknown GT3083 gt3083 Conserved hypothetical protein GT3084 gt3084 Conserved hypothetical protein GT3087 gt3087 Unknown GT3089 gt3089 Unknown GT3090 gt3090 Unknown GT3092 gt3092 Membrane protein of ExoQ family(involved in exopolysaccharide COG3307, Cell wall/membrane biogenesis production) GT3100 gt3100 Unknown GT3105 gt3105 Unknown GT3110 gt3110 Unknown GT3122 gt3122 Unknown GT3131 gt3131 Putative C4-dicarboxylate transporter COG1275, Inorganic ion transport and metabolism GT3132 gt3132 Conserved hypothetical protein GT3142 gt3142 Conserved hypothetical protein GT3149 gt3149 Unknown GT3158 gt3158 NADH-dependent FMN reductase COG0431, General function prediction only GT3162 gt3162 Conserved hypothetical protein GT3163 gt3163 Conserved hypothetical protein GT3164 gt3164 CRP, cyclic AMP receptor protein regulatory protein GT3177 gt3177 Unknown GT3190 gt3190 Unknown

22 GT3192 gt3192 Unknown GT3195 gt3195 Unknown GT3196 gt3196 Unknown COG2852, Function unknown GT3211 gt3211 Unknown GT3212 gt3212 Unknown GT3213 gt3213 Unknown GT3215 gt3215 Sucrose phosphorylase related protein COG0366, Carbohydrate transport and metabolism GT3217 gt3217 Phosphotransferase system, fructose-specific IIC component COG1299, Carbohydrate transport and metabolism GT3221 gt3221 Unknown GT3228 gt3228 Probable transcriptional regulator COG2188, Transcription GT3233 gt3233 Unknown GT3234 gt3234 Conserved hypothetical protein GT3236 gt3236 Indole-3-acetyl-L-aspartic acid hydrolase COG1473, General function prediction only GT3238 gt3238 Unknown GT3239 gt3239 Putative anhydromuramoyl-peptide exo-beta-nacetylglucosaminidase COG1472, Carbohydrate transport and metabolism GT3240 gt3240 Sugar kinase COG1940, Transcription GT3242 gt3242 Beta-glucosidase(disrupted) COG2723, Carbohydrate transport and metabolism GT3243 gt3243 Sugar ABC transporter (permease) COG1175, Carbohydrate transport and metabolism GT3248 gt3248 Unknown GT3252 gt3252 Transcriptional regulator COG1609, Transcription GT3253 gt3253 UDP-glucose 4-epimerase(disrupted) COG1087, Cell wall/membrane biogenesis

23 GT3254 gt3254 UDP-glucose 4-epimerase(disrupted) COG1087, Cell wall/membrane biogenesis GT3255 gt3255 Glycosyltransferase COG0438, Cell wall/membrane biogenesis GT3257 wzy Polymerase GT3259 gt3259 Unknown GT3270 gt3270 Conserved hypothetical protein GT3281 gt3281 Oligopeptide ABC transporter ATP-binding protein COG4608, Amino acid transport and metabolism GT3284 gt3284 Oligopeptide ABC transporter (permease) COG1173, Amino acid transport and metabolism GT3309 gt3309 ATP synthase c subunit GT3312 gt3312 Unknown GT3341 gt3341 Acetyl-CoA acetyltransferase COG0183, Lipid transport and metabolism GT3365 gt3365 Unknown GT3366 gt3366 Similar to 1,4-dihydroxy-2-naphthodate octaprenyltransferase COG1575, Coenzyme transport and metabolism GT3382 gt3382 Unknown GT3394 gt3394 Transposase GT3395 gt3395 Unknown GT3400 gt3400 Unknown GT3403 gt3403 Unknown GT3404 gt3404 Putative transposase GT3406 gt3406 Putative transposase GT3409 gt3409 Unknown GT3429 gt3429 Conserved hypothetical protein GT3430 gt3430 Conserved hypothetical protein COG0243, Energy production and conversion

24

GO ID GO term Number of members GO: translation 225 GO: nucleosome 50 GO: calcium ion binding 76 GO: structural

GO ID GO term Number of members GO: translation 225 GO: nucleosome 50 GO: calcium ion binding 76 GO: structural GO ID GO term Number of members GO:0006412 translation 225 GO:0000786 nucleosome 50 GO:0005509 calcium ion binding 76 GO:0003735 structural constituent of ribosome 170 GO:0019861 flagellum 23 GO:0005840

More information

Genomic insights into high exopolysaccharide-producing dairy starter. bacterium Streptococcus thermophilus ASCC 1275

Genomic insights into high exopolysaccharide-producing dairy starter. bacterium Streptococcus thermophilus ASCC 1275 Supplementary information of Genomic insights into high exopolysaccharide-producing dairy starter bacterium Streptococcus thermophilus ASCC 1275 Qinglong Wu, Hein Min Tun, Frederick Chi-Ching Leung, Nagendra

More information

Table S1. 10μM_rfp_B1 2,074, ohr 10μM_rfp_C2 2,074, ohr

Table S1. 10μM_rfp_B1 2,074, ohr 10μM_rfp_C2 2,074, ohr Table S1 Selection without RpoD Insert Start Position Insert End Position Potential Tolerance Gene Candidates 0μM_rfp_A1 2,076,184 -- ohr 0μM_rfp_B1 2,082,864 -- ohr 0μM_rfp_C1 2,076,798 -- ohr 1μM_rfp_A1

More information

COG1487 Predicted nucleic acid binding protein, contains PIN domain R General function prediction only

COG1487 Predicted nucleic acid binding protein, contains PIN domain R General function prediction only COG Function Functional Category COG2258 Uncharacterized protein conserved in bacteria S Function unknown COG4251 Bacteriophytochrome (light regulated signal transduction histidine kinase) T Signal transduction

More information

(starvation). Description a. Predicted operon members b. Gene no. a. Relative change in expression (n-fold) mutant vs. wild type.

(starvation). Description a. Predicted operon members b. Gene no. a. Relative change in expression (n-fold) mutant vs. wild type. 1 Table S1. Genes whose expression differ in the phyr mutant 8402 and/or in the ecfg mutant 8404 compared with the wild type when grown to the mid-exponential phase (OD600 0.5-0.7) in rich medium (PSY)

More information

Biological Process Term Enrichment

Biological Process Term Enrichment Biological Process Term Enrichment cellular protein localization cellular macromolecule localization intracellular protein transport intracellular transport generation of precursor metabolites and energy

More information

A genome sequence based discriminator for vancomycin intermediate Staphyolococcus aureus Supplementary Methods

A genome sequence based discriminator for vancomycin intermediate Staphyolococcus aureus Supplementary Methods 1 Journal of Bacteriology Computational Biology Section 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 Supplementary Information for: A genome sequence based discriminator

More information

MOLECULAR ACTIVITIES OF PLANT CELLS

MOLECULAR ACTIVITIES OF PLANT CELLS MOLECULAR ACTIVITIES OF PLANT CELLS An introduction to plant biochemistry JOHN W. ANDERSON BAgrSc, PhD Reader, Botany Department, School of Biological Sciences, La Trobe University, Bundoora, Victoria,

More information

What is an enzyme? Lecture 12: Enzymes & Kinetics I Introduction to Enzymes and Kinetics. Margaret A. Daugherty Fall 2004 KEY FEATURES OF ENZYMES

What is an enzyme? Lecture 12: Enzymes & Kinetics I Introduction to Enzymes and Kinetics. Margaret A. Daugherty Fall 2004 KEY FEATURES OF ENZYMES Lecture 12: Enzymes & Kinetics I Introduction to Enzymes and Kinetics Margaret A. Daugherty Fall 2004 What is an enzyme? General Properties Mostly proteins, but some are actually RNAs Biological catalysts

More information

What is an enzyme? Lecture 12: Enzymes & Kinetics I Introduction to Enzymes and Kinetics. Margaret A. Daugherty Fall General Properties

What is an enzyme? Lecture 12: Enzymes & Kinetics I Introduction to Enzymes and Kinetics. Margaret A. Daugherty Fall General Properties Lecture 12: Enzymes & Kinetics I Introduction to Enzymes and Kinetics Margaret A. Daugherty Fall 2003 ENZYMES: Why, what, when, where, how? All but the who! What: proteins that exert kinetic control over

More information

Parkhill et al. Comparative analysis of the genome sequences of Bordetella pertussis, Bordetella parapertussis and Bordetella bronchiseptica

Parkhill et al. Comparative analysis of the genome sequences of Bordetella pertussis, Bordetella parapertussis and Bordetella bronchiseptica Parkhill et al. Comparative analysis of the genome sequences of Bordetella pertussis, Bordetella parapertussis and Bordetella bronchiseptica Supplementary table 1: Genes unique to each Bordetella species

More information

Table S1: Domain based (meta)genome comparison of selected metagenomes of methanotrophs and genomes of selected methanogens*

Table S1: Domain based (meta)genome comparison of selected metagenomes of methanotrophs and genomes of selected methanogens* ANME-1-s ANME-1-m ANME-2a ANME-2d-h ANME-2d-a AM A M-1 M-2 M-3 H-1 H-2 H-3 H-4 S Table S1: Domain based (meta)genome comparison of selected metagenomes of methanotrophs and genomes of selected methanogens*

More information

Module organization and variance in protein-protein interaction networks

Module organization and variance in protein-protein interaction networks Module organization and variance in protein-protein interaction networks Chun-Yu Lin 1, Tsai-Ling Lee 1, Yi-Yuan Chiu 1, Yi-Wei Lin 1, Yu-Shu Lo 1, Chih-Ta Lin 1, and Jinn-Moon Yang 1,2* 1 Institute of

More information

Energy and Cellular Metabolism

Energy and Cellular Metabolism 1 Chapter 4 About This Chapter Energy and Cellular Metabolism 2 Energy in biological systems Chemical reactions Enzymes Metabolism Figure 4.1 Energy transfer in the environment Table 4.1 Properties of

More information

Characters related to higher starch accumulation in cassava storage roots

Characters related to higher starch accumulation in cassava storage roots Characters related to higher starch accumulation in cassava storage roots You-Zhi Li **1, Jian-Yu Zhao *1, San-Min Wu 1, Xian-Wei Fan 1, Xing-Lu Luo 1 & Bao-Shan Chen **1 1 State Key Laboratory for Conservation

More information

Biologic catalysts 1. Shared properties with chemical catalysts a. Enzymes are neither consumed nor produced during the course of a reaction. b.

Biologic catalysts 1. Shared properties with chemical catalysts a. Enzymes are neither consumed nor produced during the course of a reaction. b. Enzyme definition Enzymes are protein catalysts that increase the velocity of a chemical reaction and are not consumed during the reaction they catalyze. [Note: Some types of RNA can act like enzymes,

More information

Genes for transport and metabolism of spermidine in Ruegeria pomeroyi DSS-3 and other marine bacteria

Genes for transport and metabolism of spermidine in Ruegeria pomeroyi DSS-3 and other marine bacteria The following supplement accompanies the article Genes for transport and metabolism of spermidine in Ruegeria pomeroyi DSS-3 and other marine bacteria Xiaozhen Mou 1,, Shulei Sun 2, Pratibha Rayapati 2,

More information

Comparative RNA-seq analysis of transcriptome dynamics during petal development in Rosa chinensis

Comparative RNA-seq analysis of transcriptome dynamics during petal development in Rosa chinensis Title Comparative RNA-seq analysis of transcriptome dynamics during petal development in Rosa chinensis Author list Yu Han 1, Huihua Wan 1, Tangren Cheng 1, Jia Wang 1, Weiru Yang 1, Huitang Pan 1* & Qixiang

More information

Strain or plasmid Relevant characteristics Reference

Strain or plasmid Relevant characteristics Reference Table S1. Bacterial strains, and plasmids Strain or plasmid Relevant characteristics Reference M. xanthus strains DK1622 Wild-type M. xanthus 1 AG306 pnbc6::nla6, Kan r 2 AG1151 DK 1622 pkg51::mxan2688

More information

The roles of RelA/(p)ppGpp in glucose-starvation induced adaptive

The roles of RelA/(p)ppGpp in glucose-starvation induced adaptive Supplementary Information The roles of RelA/(p)ppGpp in glucose-starvation induced adaptive response in the zoonotic Streptococcus suis Tengfei Zhang, 1, 2, a Jiawen Zhu, 1, a Shun Wei, 1 Qingping Luo,

More information

Transcriptome analysis of leaf tissue from Bermudagrass (Cynodon dactylon) using a normalised cdna library

Transcriptome analysis of leaf tissue from Bermudagrass (Cynodon dactylon) using a normalised cdna library Ó CSIRO 2008 ISSN 1445-4408 10.1071/FP08133_AC Functional Plant Biology, 2008, 35, 585 594 Transcriptome analysis of leaf tissue from Bermudagrass (Cynodon dactylon) using a normalised cdna library Changsoo

More information

Generation of new compounds through unbalanced transcription of landomycin A

Generation of new compounds through unbalanced transcription of landomycin A Applied Microbiology and Biotechnology Generation of new compounds through unbalanced transcription of landomycin A cluster Maksym Myronovskyi #1, Elke Brötz #1, Birgit Rosenkränzer 1, Niko Manderscheid

More information

Supplementary Figure 1. The proportion S. aureus CFU of the total CFU (S. aureus + E. faecalis CFU) per host in worms

Supplementary Figure 1. The proportion S. aureus CFU of the total CFU (S. aureus + E. faecalis CFU) per host in worms Supplementary Figure 1. The proportion S. aureus CFU of the total CFU (S. aureus + E. faecalis CFU) per host in worms alive or dead at 24 hours of exposure. Two sample t-test: t = 1.22, df = 10, P= 0.25.

More information

Translation and Operons

Translation and Operons Translation and Operons You Should Be Able To 1. Describe the three stages translation. including the movement of trna molecules through the ribosome. 2. Compare and contrast the roles of three different

More information

Chapter 16 Lecture. Concepts Of Genetics. Tenth Edition. Regulation of Gene Expression in Prokaryotes

Chapter 16 Lecture. Concepts Of Genetics. Tenth Edition. Regulation of Gene Expression in Prokaryotes Chapter 16 Lecture Concepts Of Genetics Tenth Edition Regulation of Gene Expression in Prokaryotes Chapter Contents 16.1 Prokaryotes Regulate Gene Expression in Response to Environmental Conditions 16.2

More information

BBS2710 Microbial Physiology. Module 5 - Energy and Metabolism

BBS2710 Microbial Physiology. Module 5 - Energy and Metabolism BBS2710 Microbial Physiology Module 5 - Energy and Metabolism Topics Energy production - an overview Fermentation Aerobic respiration Alternative approaches to respiration Photosynthesis Summary Introduction

More information

Photoperiodic effect on protein profiles of potato petiole

Photoperiodic effect on protein profiles of potato petiole Photoperiodic effect on protein profiles of potato petiole Shweta Shah 1, Young Jin-Lee 2, David J. Hannapel 3 and A. Gururaj Rao* 1 1 Department of Biochemistry, Biophysics and Molecular Biology, Iowa

More information

atgaaaacgttatata

atgaaaacgttatata Additional file 4. List of the up-regulated genes involved in carbohydrates metabolism after ccpa inactivation as well as their putative CcpA binding sites (CREs). Gene locus Annotation Gene Expression

More information

From gene to protein. Premedical biology

From gene to protein. Premedical biology From gene to protein Premedical biology Central dogma of Biology, Molecular Biology, Genetics transcription replication reverse transcription translation DNA RNA Protein RNA chemically similar to DNA,

More information

Biology I Fall Semester Exam Review 2014

Biology I Fall Semester Exam Review 2014 Biology I Fall Semester Exam Review 2014 Biomolecules and Enzymes (Chapter 2) 8 questions Macromolecules, Biomolecules, Organic Compunds Elements *From the Periodic Table of Elements Subunits Monomers,

More information

Number of questions TEK (Learning Target) Biomolecules & Enzymes

Number of questions TEK (Learning Target) Biomolecules & Enzymes Unit Biomolecules & Enzymes Number of questions TEK (Learning Target) on Exam 8 questions 9A I can compare and contrast the structure and function of biomolecules. 9C I know the role of enzymes and how

More information

Chapter 12. Genes: Expression and Regulation

Chapter 12. Genes: Expression and Regulation Chapter 12 Genes: Expression and Regulation 1 DNA Transcription or RNA Synthesis produces three types of RNA trna carries amino acids during protein synthesis rrna component of ribosomes mrna directs protein

More information

Molecular Biology, Genetic Engineering & Biotechnology Operons ???

Molecular Biology, Genetic Engineering & Biotechnology Operons ??? 1 Description of Module Subject Name?? Paper Name Module Name/Title XV- 04: 2 OPERONS OBJECTIVES To understand how gene is expressed and regulated in prokaryotic cell To understand the regulation of Lactose

More information

Prokaryotic Regulation

Prokaryotic Regulation Prokaryotic Regulation Control of transcription initiation can be: Positive control increases transcription when activators bind DNA Negative control reduces transcription when repressors bind to DNA regulatory

More information

Introduction. Gene expression is the combined process of :

Introduction. Gene expression is the combined process of : 1 To know and explain: Regulation of Bacterial Gene Expression Constitutive ( house keeping) vs. Controllable genes OPERON structure and its role in gene regulation Regulation of Eukaryotic Gene Expression

More information

RECONSTRUCTING GENE REGULATORY NETWORKS FROM FUNGAL TRANSCRIPTOMIC DATA USING BAYESIAN NETWORK

RECONSTRUCTING GENE REGULATORY NETWORKS FROM FUNGAL TRANSCRIPTOMIC DATA USING BAYESIAN NETWORK RECONSTRUCTING GENE REGULATORY NETWORKS FROM FUNGAL TRANSCRIPTOMIC DATA USING BAYESIAN NETWORK Li Guo Fungal Comparative Genomics Laboratory Department of Biochemistry and Molecular biology University

More information

Enzyme Catalysis & Biotechnology

Enzyme Catalysis & Biotechnology L28-1 Enzyme Catalysis & Biotechnology Bovine Pancreatic RNase A Biochemistry, Life, and all that L28-2 A brief word about biochemistry traditionally, chemical engineers used organic and inorganic chemistry

More information

Supporting Information

Supporting Information Supporting Information Proteomic Analyses of Cysteine Redox in High-fat-fed and Fasted Mouse Livers: Implications for Liver Metabolic Homeostasis Yixing Li 1#, Zupeng Luo 1#, Xilong Wu 2, Jun Zhu 2, Kai

More information

Supplementary Table 3. Membrane/Signaling/Neural Genes of the DmSP. FBgn CG5265 acetyltransferase amino acid metabolism

Supplementary Table 3. Membrane/Signaling/Neural Genes of the DmSP. FBgn CG5265 acetyltransferase amino acid metabolism Supplementary Table 3 Membrane/Signaling/Neural Genes of the DmSP FlyBase ID Gene Name Molecular function summary Membrane Biological process summary FBgn0038486 CG5265 acetyltransferase amino acid metabolism

More information

Chem Lecture 10 Lipid, Amino Acid, and Nucleotide Metabolism Part III: Nucleotide Metabolism

Chem Lecture 10 Lipid, Amino Acid, and Nucleotide Metabolism Part III: Nucleotide Metabolism Chem 352 - Lecture 10 Lipid, Amino Acid, and Nucleotide Metabolism Part III: Nucleotide Metabolism Lipid Metabolism Chem 352, Lecture 10, Part I: Lipid Metabolism 2 Lipid Metabolism Question: Draw a general

More information

Oxidative Phosphorylation versus. Photophosphorylation

Oxidative Phosphorylation versus. Photophosphorylation Photosynthesis Oxidative Phosphorylation versus Photophosphorylation Oxidative Phosphorylation Electrons from the reduced cofactors NADH and FADH 2 are passed to proteins in the respiratory chain. In eukaryotes,

More information

Center for Academic Services & Advising

Center for Academic Services & Advising March 2, 2017 Biology I CSI Worksheet 6 1. List the four components of cellular respiration, where it occurs in the cell, and list major products consumed and produced in each step. i. Hint: Think about

More information

Chapter 1. DNA is made from the building blocks adenine, guanine, cytosine, and. Answer: d

Chapter 1. DNA is made from the building blocks adenine, guanine, cytosine, and. Answer: d Chapter 1 1. Matching Questions DNA is made from the building blocks adenine, guanine, cytosine, and. Answer: d 2. Matching Questions : Unbranched polymer that, when folded into its three-dimensional shape,

More information

CELL BIOLOGY, BIOINFORMATICS AND SYSTEMS BIOLOGY BIO160 (GU); UMF012 (Chalmers) schedule 2010

CELL BIOLOGY, BIOINFORMATICS AND SYSTEMS BIOLOGY BIO160 (GU); UMF012 (Chalmers) schedule 2010 CELL BIOLOGY, BIOINFORMATICS AND SYSTEMS BIOLOGY BIO160 (GU); UMF012 (Chalmers) schedule 2010 Head of course: Markus Tamas (MT) Cell and Molecular Biology-Microbiology Medicinaregatan 9C Lundberg Laboratory

More information

Chapter 10, 11, 14: Gene Expression, Regulation, and Development Exam

Chapter 10, 11, 14: Gene Expression, Regulation, and Development Exam Chapter 10, 11, 14: Gene Expression, Regulation, and Development Exam Multiple Choice Identify the choice that best completes the statement or answers the question. 1. Why did the original one-gene, one-enzyme

More information

Name: SBI 4U. Gene Expression Quiz. Overall Expectation:

Name: SBI 4U. Gene Expression Quiz. Overall Expectation: Gene Expression Quiz Overall Expectation: - Demonstrate an understanding of concepts related to molecular genetics, and how genetic modification is applied in industry and agriculture Specific Expectation(s):

More information

Chapter 2 Chemical Aspects of Life

Chapter 2 Chemical Aspects of Life Chapter 2 Chemical Aspects of Life Multiple Choice Questions 1. Anything that has weight and occupies space can be described as A. an atom. B. matter. C. a compound. D. a molecule. #1 Learning Outcome:

More information

Proteins. Department of Biochemistry Faculty of medicine University of Szeged

Proteins. Department of Biochemistry Faculty of medicine University of Szeged Proteins Classification Function Structure Connecting peptide parts Synthesis Transcription - nucleus Translation - cytoplasma Posttranslation changes (folding) - endoplasmatic reticulum Amino acids Amino

More information

Agrobacterium tumefasciens, the Ti Plasmid, and Crown Gall Tumorigenesis

Agrobacterium tumefasciens, the Ti Plasmid, and Crown Gall Tumorigenesis Agrobacterium tumefasciens, the Ti Plasmid, and Crown Gall Tumorigenesis BOM-11: 10.9 Plasmids: General Principles (review) p. 274 10.11 Conjugation: Essential Features (review) p. 278 19.21 Agrobacterium

More information

Chapter 8 Metabolism: Energy, Enzymes, and Regulation

Chapter 8 Metabolism: Energy, Enzymes, and Regulation Chapter 8 Metabolism: Energy, Enzymes, and Regulation Energy: Capacity to do work or cause a particular change. Thus, all physical and chemical processes are the result of the application or movement of

More information

Chapters 12&13 Notes: DNA, RNA & Protein Synthesis

Chapters 12&13 Notes: DNA, RNA & Protein Synthesis Chapters 12&13 Notes: DNA, RNA & Protein Synthesis Name Period Words to Know: nucleotides, DNA, complementary base pairing, replication, genes, proteins, mrna, rrna, trna, transcription, translation, codon,

More information

2. All of the following are accurate statements regarding the above graph EXCEPT:

2. All of the following are accurate statements regarding the above graph EXCEPT: General Biology 115 Summer 2014: Exam I Form A Name: 1. Which of the following best explains why FADH2 yields less ATP than NADH during cell respiration? a. Energy captured by FADH2 contributes less to

More information

Division Ave. High School AP Biology

Division Ave. High School AP Biology Overview 10 reactions u convert () to pyruvate (3C) u produces: 4 & NADH u consumes: u net: & NADH C-C-C-C-C-C fructose-1,6bp P-C-C-C-C-C-C-P DHAP P-C-C-C G3P C-C-C-P H P i P i pyruvate C-C-C 4 4 NAD +

More information

The Mitochondrion. Renáta Schipp

The Mitochondrion. Renáta Schipp The Mitochondrion Renáta Schipp Origin Endosymbiothic theory the Mitochondria (and Chloroplastids) were originally free-living cells they lived in an endosymbiosis with a hostcell organellfree anaerobe

More information

Topic 4 - #14 The Lactose Operon

Topic 4 - #14 The Lactose Operon Topic 4 - #14 The Lactose Operon The Lactose Operon The lactose operon is an operon which is responsible for the transport and metabolism of the sugar lactose in E. coli. - Lactose is one of many organic

More information

2. Cellular and Molecular Biology

2. Cellular and Molecular Biology 2. Cellular and Molecular Biology 2.1 Cell Structure 2.2 Transport Across Cell Membranes 2.3 Cellular Metabolism 2.4 DNA Replication 2.5 Cell Division 2.6 Biosynthesis 2.1 Cell Structure What is a cell?

More information

Regulation of Gene Expression at the level of Transcription

Regulation of Gene Expression at the level of Transcription Regulation of Gene Expression at the level of Transcription (examples are mostly bacterial) Diarmaid Hughes ICM/Microbiology VT2009 Regulation of Gene Expression at the level of Transcription (examples

More information

Lectures by Kathleen Fitzpatrick

Lectures by Kathleen Fitzpatrick Chapter 10 Chemotrophic Energy Metabolism: Aerobic Respiration Lectures by Kathleen Fitzpatrick Simon Fraser University Figure 10-1 Figure 10-6 Conversion of pyruvate The conversion of pyruvate to acetyl

More information

Bio 119 Solute Transport 7/11/2004 SOLUTE TRANSPORT. READING: BOM-10 Sec. 4.7 Membrane Transport Systems p. 71

Bio 119 Solute Transport 7/11/2004 SOLUTE TRANSPORT. READING: BOM-10 Sec. 4.7 Membrane Transport Systems p. 71 SOLUTE TRANSPORT READG: BOM10 Sec. 4.7 Membrane Transport Systems p. 71 DISCUSSION QUESTIONS BOM10: Chapter 4; #6, #8 1. What are the 4 essential features of carrier mediated transport? 2. What does it

More information

Reading Assignments. A. Genes and the Synthesis of Polypeptides. Lecture Series 7 From DNA to Protein: Genotype to Phenotype

Reading Assignments. A. Genes and the Synthesis of Polypeptides. Lecture Series 7 From DNA to Protein: Genotype to Phenotype Lecture Series 7 From DNA to Protein: Genotype to Phenotype Reading Assignments Read Chapter 7 From DNA to Protein A. Genes and the Synthesis of Polypeptides Genes are made up of DNA and are expressed

More information

Table S1. 45 significantly up-regulated P. mirabilis HI4320 genes as determined by SAM during iron-limiting microarray a

Table S1. 45 significantly up-regulated P. mirabilis HI4320 genes as determined by SAM during iron-limiting microarray a Table S1. 45 significantly up-regulated P. mirabilis HI4320 genes as determined by SAM during iron-limiting microarray a PMI no. Gene Description Log 2 fold-change b PMI0029 exbb biopolymer transport protein

More information

active site Region of an enzyme surface to which a substrate molecule binds in order to undergo a catalyzed reaction.

active site Region of an enzyme surface to which a substrate molecule binds in order to undergo a catalyzed reaction. Glossary acetyl Chemical group derived from acetic acid. Acetyl groups are important in metabolism and are added covalently to some proteins as a posttranslational modification. actin Abundant protein

More information

Laith AL-Mustafa. Protein synthesis. Nabil Bashir 10\28\ First

Laith AL-Mustafa. Protein synthesis. Nabil Bashir 10\28\ First Laith AL-Mustafa Protein synthesis Nabil Bashir 10\28\2015 http://1drv.ms/1gigdnv 01 First 0 Protein synthesis In previous lectures we started talking about DNA Replication (DNA synthesis) and we covered

More information

Biochemistry 3300 Problems (and Solutions) Metabolism I

Biochemistry 3300 Problems (and Solutions) Metabolism I (1) Provide a reasonable systematic name for an enzyme that catalyzes the following reaction: fructose + ATP > fructose-1 phosphate + ADP (2) The IUBMB has a developed a set of rules for classifying enzymes

More information

UNIT 5. Protein Synthesis 11/22/16

UNIT 5. Protein Synthesis 11/22/16 UNIT 5 Protein Synthesis IV. Transcription (8.4) A. RNA carries DNA s instruction 1. Francis Crick defined the central dogma of molecular biology a. Replication copies DNA b. Transcription converts DNA

More information

INTERNAL STRUCTURE Cytoplasmic membrane peripheral integral

INTERNAL STRUCTURE Cytoplasmic membrane peripheral integral INTERNAL STRUCTURE Cytoplasmic membrane Under the cell wall and generally same structure with bacteria It consists of two layers On the surface of periplasmic space and cytoplasm, protein and phospholipid

More information

Cell and Molecular Biology

Cell and Molecular Biology Cell and Molecular Biology (3000719): academic year 2013 Content & Objective :Cell Chemistry and Biosynthesis 3 rd Edition, 1994, pp. 41-88. 4 th Edition, 2002, pp. 47-127. 5 th Edition, 2008, pp. 45-124.

More information

Population transcriptomics uncovers the regulation of gene. expression variation in adaptation to changing environment

Population transcriptomics uncovers the regulation of gene. expression variation in adaptation to changing environment Supplementary information Population transcriptomics uncovers the regulation of gene expression variation in adaptation to changing environment Qin Xu 1, Caiyun Zhu 2,4, Yangyang Fan 1,4, Zhihong Song

More information

S1 Gene ontology (GO) analysis of the network alignment results

S1 Gene ontology (GO) analysis of the network alignment results 1 Supplementary Material for Effective comparative analysis of protein-protein interaction networks by measuring the steady-state network flow using a Markov model Hyundoo Jeong 1, Xiaoning Qian 1 and

More information

Controlling Gene Expression

Controlling Gene Expression Controlling Gene Expression Control Mechanisms Gene regulation involves turning on or off specific genes as required by the cell Determine when to make more proteins and when to stop making more Housekeeping

More information

Transmembrane Domains (TMDs) of ABC transporters

Transmembrane Domains (TMDs) of ABC transporters Transmembrane Domains (TMDs) of ABC transporters Most ABC transporters contain heterodimeric TMDs (e.g. HisMQ, MalFG) TMDs show only limited sequence homology (high diversity) High degree of conservation

More information

Cell division control protein Q02457 P40341 Q06629 P50087 MIC26 Q synthase ATP-dependent. Dicarboxylic amino Q02785 P53388

Cell division control protein Q02457 P40341 Q06629 P50087 MIC26 Q synthase ATP-dependent. Dicarboxylic amino Q02785 P53388 Supplemental Material for IAS: Interaction specific GO term associations for predicting Protein-Protein Interaction Networks Satwica Yerneni, Ishita K. Khan, Qing Wei, and Daisuke Kihara Contact: dkihara@purdue.edu

More information

Mean Hes score. Threshold

Mean Hes score. Threshold Mean Hes score 0.1 0.09 Common 0.08 Family 0.07 0.06 0.05 0.04 0.03 0.02 0.01 0 0 0.01 0.02 0.03 0.04 0.05 0.06 0.07 0.08 Threshold SUPPLEMENTARY FIG. 1. Trend of mean Hes scores calculated based on the

More information

Membrane-associated proteomics of chickpea identifies Sad1/UNC-84 protein (CaSUN1), a novel component of dehydration signaling

Membrane-associated proteomics of chickpea identifies Sad1/UNC-84 protein (CaSUN1), a novel component of dehydration signaling Membrane-associated proteomics of chickpea identifies Sad/UNC-84 (CaSUN), a novel component of dehydration signaling Dinesh Kumar Jaiswal, Poonam Mishra, Pratigya Subba, Divya Rathi, Subhra Chakraborty*

More information

Life of the Cell. Learning Objectives

Life of the Cell. Learning Objectives Life of the Cell Society on a micro-scale 1 Learning Objectives 1. What are the characteristics that distinguish prokaryotic and eukaryotic cells? Which type of cell is believed to be older (more primitive)?

More information

Midterm Review Guide. Unit 1 : Biochemistry: 1. Give the ph values for an acid and a base. 2. What do buffers do? 3. Define monomer and polymer.

Midterm Review Guide. Unit 1 : Biochemistry: 1. Give the ph values for an acid and a base. 2. What do buffers do? 3. Define monomer and polymer. Midterm Review Guide Name: Unit 1 : Biochemistry: 1. Give the ph values for an acid and a base. 2. What do buffers do? 3. Define monomer and polymer. 4. Fill in the Organic Compounds chart : Elements Monomer

More information

SUPPLEMENTAL MATERIAL

SUPPLEMENTAL MATERIAL SUPPLEMENTAL MATERIAL SUPPLEMENTAL RESULTS Microarray analysis of F. tularensis LVS within hepatocytes: As described in Materials and Methods, the global gene expression of LVS organisms grown in FL83B

More information

PROTEIN SYNTHESIS INTRO

PROTEIN SYNTHESIS INTRO MR. POMERANTZ Page 1 of 6 Protein synthesis Intro. Use the text book to help properly answer the following questions 1. RNA differs from DNA in that RNA a. is single-stranded. c. contains the nitrogen

More information

Additional File 9. Gene families amplified in A. adeninivorans.

Additional File 9. Gene families amplified in A. adeninivorans. Additional File. Gene families amplified in A. adeninivorans. Figure SA Duplication rate per gene per branch of the species tree leading to A. adeninivorans. Species tree showing the evolution of the species

More information

Ch 10, 11 &14 Preview

Ch 10, 11 &14 Preview Ch 10, 11 &14 Preview Multiple Choice Identify the choice that best completes the statement or answers the question. 1. Why did the original one-gene, one-enzyme hypothesis have to be modified? a. Some

More information

Unit Two Chemistry of the Human Body

Unit Two Chemistry of the Human Body I. Introduction to atoms Unit Two Chemistry of the Human Body A. Chemistry is the branch of science that concerns itself with the structure of matter, including the interaction between atoms. 1. Atoms-

More information

Giving you the energy you need!

Giving you the energy you need! Giving you the energy you need! Use your dominant hand Open and close the pin (with your thumb and forefinger) as many times as you can for 20 seconds while holding the other fingers straight out! Repeat

More information

SUPPLEMENTARY INFORMATION

SUPPLEMENTARY INFORMATION doi: 10.1038/nature05362 SUPPLEMENTARY INFORMATION SUPPLEMENTARY METHODS Detection of metalloproteins by luminal staining. A rapid procedure to directly stain non-denaturing 2-D gels for metalloproteins

More information

Introduction to Microbiology BIOL 220 Summer Session I, 1996 Exam # 1

Introduction to Microbiology BIOL 220 Summer Session I, 1996 Exam # 1 Name I. Multiple Choice (1 point each) Introduction to Microbiology BIOL 220 Summer Session I, 1996 Exam # 1 B 1. Which is possessed by eukaryotes but not by prokaryotes? A. Cell wall B. Distinct nucleus

More information

WJEC. BY4 Photosynthesis Questions

WJEC. BY4 Photosynthesis Questions NAME: OPTION GROUP WJEC BY4 Photosynthesis Questions Question Book 2 (Legacy Qs from Jan 2000 to June 2014) Question Number(s) Due Date & Pass Mark Homework Mark Resist Question number(s) Resist Due Date

More information

REVIEW 1: BIOCHEMISTRY UNIT. A. Top 10 If you learned anything from this unit, you should have learned:

REVIEW 1: BIOCHEMISTRY UNIT. A. Top 10 If you learned anything from this unit, you should have learned: Period Date REVIEW 1: BIOCHEMISTRY UNIT A. Top 10 If you learned anything from this unit, you should have learned: 1. All living matter made up of CHONPS 2. Bonds a. covalent bonds are strong b. hydrogen

More information

A genomic insight into evolution and virulence of Corynebacterium diphtheriae

A genomic insight into evolution and virulence of Corynebacterium diphtheriae A genomic insight into evolution and virulence of Corynebacterium diphtheriae Vartul Sangal, Ph.D. Northumbria University, Newcastle vartul.sangal@northumbria.ac.uk @VartulSangal Newcastle University 8

More information

CHAPTER : Prokaryotic Genetics

CHAPTER : Prokaryotic Genetics CHAPTER 13.3 13.5: Prokaryotic Genetics 1. Most bacteria are not pathogenic. Identify several important roles they play in the ecosystem and human culture. 2. How do variations arise in bacteria considering

More information

32 Gene regulation, continued Lecture Outline 11/21/05

32 Gene regulation, continued Lecture Outline 11/21/05 32 Gene regulation, continued Lecture Outline 11/21/05 Review the operon concept Repressible operons (e.g. trp) Inducible operons (e.g. lac) Positive regulation of lac () Practice applying the operon concept

More information

Review Quizzes Chapters 6-10

Review Quizzes Chapters 6-10 Review Quizzes Chapters 6-10 1. The product(s) of the light reactions of photosynthesis is/are a. pyruvate b. glucose c. ATP and NADPH d. CO 2 and H 2 O e. ribulose bisphosphate (RuBP) 1. The product(s)

More information

MONTGOMERY COUNTY COMMUNITY COLLEGE BIO 140 CHAPTER 4. Functional Anatomy of Prokaryotic and Eukaryotic Cells

MONTGOMERY COUNTY COMMUNITY COLLEGE BIO 140 CHAPTER 4. Functional Anatomy of Prokaryotic and Eukaryotic Cells MONTGOMERY COUNTY COMMUNITY COLLEGE BIO 140 CHAPTER 4 Functional Anatomy of Prokaryotic and Eukaryotic Cells I. PROKARYOTES A. Structure Of The Cell: Chemical Composition And Function 1. Cell Wall a. composition

More information

2015 FALL FINAL REVIEW

2015 FALL FINAL REVIEW 2015 FALL FINAL REVIEW Biomolecules & Enzymes Illustrate table and fill in parts missing 9A I can compare and contrast the structure and function of biomolecules. 9C I know the role of enzymes and how

More information

Cell Energy: The Big Picture. So, What Exactly is ATP. Adenosine Triphosphate. Your turn to Practice converting ATP to ADP:

Cell Energy: The Big Picture. So, What Exactly is ATP. Adenosine Triphosphate. Your turn to Practice converting ATP to ADP: Understanding How Living Things Obtain and Use Energy. Cell Energy: The Big Picture Most Autotrophs produce food (sugar) using light energy during Photosynthesis. Then, both Autotrophs and Heterotroph

More information

Introduction to molecular biology. Mitesh Shrestha

Introduction to molecular biology. Mitesh Shrestha Introduction to molecular biology Mitesh Shrestha Molecular biology: definition Molecular biology is the study of molecular underpinnings of the process of replication, transcription and translation of

More information

Chapter 03. Lecture and Animation Outline

Chapter 03. Lecture and Animation Outline Chapter 03 Lecture and Animation Outline To run the animations you must be in Slideshow View. Use the buttons on the animation to play, pause, and turn audio/text on or off. Please Note: Once you have

More information

Chapter 8: Energy and Metabolism

Chapter 8: Energy and Metabolism Chapter 8: Energy and Metabolism Why do organisms need energy? How do organisms manage their energy needs? Defining terms and issues: energy and thermodynamics metabolic reactions and energy transfers

More information

The Mitochondrion. Definition Structure, ultrastructure Functions

The Mitochondrion. Definition Structure, ultrastructure Functions The Mitochondrion Definition Structure, ultrastructure Functions Organelle definition Etymology of the name Carl Benda (1903): (mitos) thread; (khondrion) granule. Light microscopy identification First

More information

20. Electron Transport and Oxidative Phosphorylation

20. Electron Transport and Oxidative Phosphorylation 20. Electron Transport and Oxidative Phosphorylation 20.1 What Role Does Electron Transport Play in Metabolism? Electron transport - Role of oxygen in metabolism as final acceptor of electrons - In inner

More information

Enzymes I. Dr. Mamoun Ahram Summer semester,

Enzymes I. Dr. Mamoun Ahram Summer semester, Enzymes I Dr. Mamoun Ahram Summer semester, 2017-2018 Resources Mark's Basic Medical Biochemistry Other resources NCBI Bookshelf: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=books The Medical Biochemistry

More information

Biochemistry Prokaryotic translation

Biochemistry Prokaryotic translation 1 Description of Module Subject Name Paper Name Module Name/Title Dr. Vijaya Khader Dr. MC Varadaraj 2 1. Objectives 2. Understand the concept of genetic code 3. Understand the concept of wobble hypothesis

More information