Table 2 The top 100 highly expressed coding ORFs predicted by RPKM values
From: Transcriptomes of Frankia sp. strain CcI3 in growth transitions
3dNH41 | Locus tag | RPKM2 | 3dN2 | Locus tag | RPKM | 5dNH4 | Locus tag | RPKM |
|---|---|---|---|---|---|---|---|---|
heat shock protein Hsp20 | Francci3_1179 | 10755 | heat shock protein Hsp20 | Francci3_1179 | 3553 | hypothetical protein | Francci3_1017 | 4967 |
aldehyde dehydrogenase | Francci3_2944 | 7165 | aldehyde dehydrogenase | Francci3_2944 | 3152 | heat shock protein Hsp20 | Francci3_1179 | 2077 |
chaperonin GroEL | Francci3_4398 | 5923 | hypothetical protein | Francci3_1545 | 2327 | hypothetical protein | Francci3_3999 | 1926 |
cold-shock DNA-binding | Francci3_0260 | 5495 | transposase IS66 | Francci3_1864 | 2261 | transposase IS66 | Francci3_1864 | 1801 |
OsmC-like protein | Francci3_4465 | 5490 | hypothetical protein | Francci3_2178 | 1993 | polysaccharide deacetylase | Francci3_0165 | 1616 |
co-chaperonin GroES | Francci3_0632 | 5362 | response regulator receiver | Francci3_0120 | 1823 | hypothetical protein | Francci3_2101 | 1596 |
Hemerythrin HHE cation | Francci3_1066 | 4392 | Hemerythrin HHE cation | Francci3_1066 | 1807 | phage integrase | Francci3_4274 | 1451 |
hypothetical protein | Francci3_1545 | 4225 | hypothetical protein | Francci3_1936 | 1789 | Radical SAM | Francci3_1753 | 1392 |
NAD/NADP transhydrogenase | Francci3_2947 | 3226 | OsmC-like protein | Francci3_4465 | 1777 | hypothetical protein | Francci3_2241 | 1333 |
UspA | Francci3_2760 | 3221 | hypothetical protein | Francci3_3999 | 1614 | hypothetical protein | Francci3_2890 | 1265 |
hypothetical protein | Francci3_3494 | 3190 | cold-shock DNA-binding | Francci3_0260 | 1592 | phosphoribosyl-ATPphosphatase | Francci3_4317 | 1245 |
hypothetical protein | Francci3_2178 | 3071 | sigma 54 modulation | Francci3_0764 | 1574 | hypothetical protein | Francci3_0159 | 1184 |
sigma 54 modulation protein | Francci3_0764 | 3004 | cold-shock DNA-binding | Francci3_4469 | 1458 | ribonucleaseHII | Francci3_3588 | 1161 |
cold-shock DNA-binding | Francci3_4469 | 2949 | putative DNA-binding | Francci3_1949 | 1392 | GDP-mannose 4,6-dehydratase | Francci3_1307 | 1134 |
Alcohol dehydrogenase | Francci3_2945 | 2916 | LuxR family regulator | Francci3_0765 | 1361 | hypothetical protein | Francci3_4023 | 1122 |
putative Lsr2-like protein | Francci3_3498 | 2659 | chaperoninGroEL | Francci3_4398 | 1199 | major facilitator superfamily | Francci3_2289 | 1122 |
hypothetical protein | Francci3_1936 | 2577 | hypothetical protein | Francci3_4123 | 1176 | RNA-directed DNA polymerase | Francci3_2318 | 1088 |
hypothetical protein | Francci3_2270 | 2529 | hypothetical protein | Francci3_3494 | 1175 | methionine-S-oxide reductase | Francci3_2268 | 1071 |
thioredoxin-related | Francci3_0447 | 2355 | hypothetical protein | Francci3_2269 | 1174 | HypA | Francci3_1937 | 1047 |
SsgA | Francci3_3418 | 2154 | transcriptional regulator | Francci3_4255 | 1167 | acyltransferase 3 | Francci3_2337 | 987 |
luciferase-like | Francci3_2761 | 2117 | co-chaperoninGroES | Francci3_0632 | 1150 | hypothetical protein | Francci3_3302 | 982 |
molecular chaperone DnaK | Francci3_4352 | 2036 | hypothetical protein | Francci3_2442 | 1117 | Serine acetyltransferase-like | Francci3_3842 | 970 |
globin | Francci3_2581 | 1935 | SsgA | Francci3_3418 | 1043 | hypothetical protein | Francci3_0227 | 970 |
LuxR family regulator | Francci3_0765 | 1934 | SecE subunit | Francci3_0567 | 1037 | hypothetical protein | Francci3_1719 | 965 |
thioredoxin reductase | Francci3_4536 | 1913 | putative Lsr2-like protein | Francci3_3498 | 1022 | hypothetical protein | Francci3_0238 | 957 |
Rhodanese-like | Francci3_0449 | 1881 | PEP phosphomutase | Francci3_1533 | 1005 | hypothetical protein | Francci3_2200 | 947 |
carbonic anhydrase | Francci3_0708 | 1859 | hypothetical protein | Francci3_2270 | 973 | hypothetical protein | Francci3_1831 | 945 |
superfamily MFS_1 | Francci3_2752 | 1811 | chaperone hypC/hupF | Francci3_1946 | 954 | serine/threonine kinase | Francci3_4051 | 938 |
hypothetical protein | Francci3_3250 | 1807 | transposase, IS4 | Francci3_3990 | 953 | signal transduction kinase | Francci3_0085 | 938 |
exodeoxyribonuclease III | Francci3_1180 | 1754 | thioredoxin-related | Francci3_0447 | 951 | hypothetical protein | Francci3_4019 | 922 |
PEP phosphomutase | Francci3_1533 | 1742 | ATP synthase F0 | Francci3_3713 | 928 | hypothetical protein | Francci3_0396 | 914 |
STAS (anti-σ factor antagonist) | Francci3_0441 | 1728 | mannose 4,6-dehydratase | Francci3_1053 | 921 | CRISPR-associated protein | Francci3_0021 | 899 |
hypothetical protein | Francci3_1935 | 1687 | phage integrase | Francci3_4338 | 919 | hypothetical protein | Francci3_0038 | 899 |
sigma 38 | Francci3_3505 | 1673 | protein of unknown function | Francci3_3347 | 892 | Recombinase | Francci3_3989 | 898 |
hypothetical protein | Francci3_0227 | 1665 | transposase, IS4 | Francci3_0391 | 878 | aldo/keto reductase | Francci3_3416 | 890 |
hypothetical protein | Francci3_1615 | 1634 | major facilitator MFS_1 | Francci3_2752 | 865 | transposase, IS4 | Francci3_1873 | 875 |
hypothetical protein | Francci3_2943 | 1629 | NAD/NADP transhydrogenase | Francci3_2947 | 863 | Excisionase/Xis, DNA-binding | Francci3_0405 | 875 |
hypothetical protein | Francci3_0054 | 1629 | hypothetical protein | Francci3_4084 | 855 | transposase, IS4 | Francci3_0151 | 874 |
transposase IS66 | Francci3_1864 | 1625 | hypothetical protein | Francci3_2380 | 839 | CRISPR-associated protein | Francci3_0020 | 869 |
transcriptional regulator, CarD | Francci3_4255 | 1596 | hypothetical protein | Francci3_4114 | 821 | CRISPR-associated protein | Francci3_3345 | 863 |
alanine dehydrogenase/PNT-like | Francci3_2946 | 1532 | Alcohol dehydrogenase | Francci3_2945 | 796 | glycosyl transferase | Francci3_3318 | 859 |
serine phosphatase | Francci3_3249 | 1453 | hypothetical protein | Francci3_3791 | 782 | metallophosphoesterase | Francci3_1990 | 839 |
chaperonin GroEL | Francci3_0633 | 1439 | acyl-CoA dehydrogenase | Francci3_1000 | 781 | hypothetical protein | Francci3_3339 | 837 |
hypothetical protein | Francci3_0949 | 1437 | transcriptional regulator | Francci3_3081 | 780 | transcriptional regulator | Francci3_3081 | 834 |
transcription factor WhiB | Francci3_3759 | 1430 | hypothetical protein | Francci3_0037 | 779 | hypothetical protein | Francci3_3317 | 826 |
fatty acid desaturase, type 2 | Francci3_0307 | 1430 | Amino acid adenylation | Francci3_2461 | 777 | hypothetical protein | Francci3_4072 | 824 |
STAS | Francci3_4302 | 1405 | hypothetical protein | Francci3_1615 | 775 | transcriptional regulator | Francci3_0908 | 816 |
Heavy metal transportprotein | Francci3_0489 | 1368 | hypothetical protein | Francci3_2179 | 775 | hypothetical protein | Francci3_4129 | 809 |
sigma-24 | Francci3_3768 | 1353 | hypothetical protein | Francci3_1534 | 773 | transposase, IS4 | Francci3_4227 | 803 |
transcriptional regulator, TetR | Francci3_2758 | 1349 | hypothetical protein | Francci3_2329 | 767 | Antibiotic biosynthesis | Francci3_0875 | 800 |
hypothetical protein | Francci3_3417 | 1343 | carbonic anhydrase | Francci3_0708 | 764 | hypothetical protein | Francci3_3336 | 796 |
SecE subunit | Francci3_0567 | 1339 | transcription factor WhiB | Francci3_3759 | 751 | hypothetical protein | Francci3_2440 | 781 |
Excisionase/Xis, DNA-binding | Francci3_0099 | 1327 | UspA | Francci3_2760 | 747 | hypothetical protein | Francci3_4509 | 778 |
hypothetical protein | Francci3_3791 | 1315 | exodeoxyribonuclease III | Francci3_1180 | 747 | putative copper resistance | Francci3_2497 | 771 |
ATP synthase F0, A subunit | Francci3_3713 | 1263 | hypothetical protein | Francci3_1832 | 737 | transcriptional regulator | Francci3_0210 | 765 |
30S ribosomal proteinS1 | Francci3_1057 | 1256 | protein of unknown function | Francci3_2628 | 714 | hypothetical protein | Francci3_1090 | 764 |
heat shock protein Hsp20 | Francci3_2174 | 1241 | hypothetical protein | Francci3_4509 | 714 | hypothetical protein | Francci3_4156 | 760 |
NAD(P) transhydrogenase, beta | Francci3_2948 | 1231 | hypothetical protein | Francci3_1650 | 709 | RNA-binding S4 | Francci3_3479 | 747 |
putative transcriptional regulator | Francci3_1674 | 1218 | STAS | Francci3_0441 | 701 | hypothetical protein | Francci3_1545 | 746 |
protein of unknown function | Francci3_0450 | 1215 | molecularchaperoneDnaK | Francci3_4352 | 694 | hypothetical protein | Francci3_3238 | 746 |
Alcohol dehydrogenase | Francci3_1544 | 1206 | hypothetical protein | Francci3_0159 | 693 | hypothetical protein | Francci3_3301 | 737 |
putative DNA-binding protein | Francci3_1949 | 1203 | acyl transferase region | Francci3_0991 | 691 | hypothetical protein | Francci3_1985 | 724 |
glutaredoxin 2 | Francci3_0483 | 1202 | regulatory protein GntR | Francci3_3218 | 690 | Rhodanese-like | Francci3_2753 | 721 |
translation elongation factor Tu | Francci3_0580 | 1179 | CRISPR-associated protein | Francci3_3346 | 680 | Thiolase | Francci3_2502 | 718 |
thioredoxin | Francci3_4537 | 1165 | hypothetical protein | Francci3_1874 | 678 | response regulator receiver | Francci3_0120 | 715 |
cytochrome P450 | Francci3_4464 | 1164 | hypothetical protein | Francci3_1935 | 672 | hypothetical protein | Francci3_0498 | 705 |
hypothetical protein | Francci3_2582 | 1156 | IS630 family transposase | Francci3_1872 | 670 | DNApolymeraseIIIsubunitalpha | Francci3_4168 | 703 |
hypothetical protein | Francci3_1534 | 1106 | globin | Francci3_2581 | 663 | hypothetical protein | Francci3_0037 | 693 |
protein of unknown function | Francci3_1406 | 1054 | hypothetical protein | Francci3_4127 | 657 | hypothetical protein | Francci3_3241 | 684 |
Vesicle-fusing ATPase | Francci3_2630 | 1041 | thioredoxin | Francci3_4537 | 653 | 30SribosomalproteinS6 | Francci3_4522 | 683 |
HesB/YadR/YfhF | Francci3_3121 | 1032 | hypothetical protein | Francci3_0066 | 644 | putative hydrolase | Francci3_2567 | 682 |
hypothetical protein | Francci3_0532 | 1022 | Alcohol dehydrogenase | Francci3_1544 | 644 | transposase IS116/IS110 | Francci3_2124 | 681 |
acyl transferase region | Francci3_0991 | 1015 | hypothetical protein | Francci3_2440 | 642 | hypothetical protein | Francci3_1807 | 675 |
Superoxide dismutase | Francci3_2817 | 1013 | Tetratricopeptide TPR_4 | Francci3_1951 | 639 | hypothetical protein | Francci3_1805 | 675 |
hypothetical protein | Francci3_2185 | 1007 | hypothetical protein | Francci3_0227 | 635 | hypothetical protein | Francci3_2364 | 675 |
hypothetical protein | Francci3_4343 | 1006 | hypothetical protein | Francci3_2315 | 634 | hypothetical protein | Francci3_2380 | 671 |
serine/threonine kinase | Francci3_4051 | 989 | hypothetical protein | Francci3_4019 | 633 | response regulator receiver | Francci3_4048 | 670 |
acyl-CoA dehydrogenase | Francci3_1000 | 989 | hypothetical protein | Francci3_0949 | 633 | putative O-methyltransferase | Francci3_0204 | 670 |
conserved hypothetical protein | Francci3_0096 | 986 | serine phosphatase | Francci3_3249 | 632 | channel protein | Francci3_3898 | 669 |
hypothetical protein | Francci3_3886 | 983 | Amino acid adenylation | Francci3_2459 | 632 | hypothetical protein | Francci3_2032 | 667 |
Rhodanese-like | Francci3_2753 | 982 | transposase IS116/IS110 | Francci3_2124 | 630 | hypothetical protein | Francci3_1459 | 664 |
hypothetical protein | Francci3_4042 | 973 | hypothetical protein | Francci3_3417 | 628 | flavoprotein | Francci3_1816 | 662 |
hypothetical protein | Francci3_3999 | 971 | Antibiotic biosynthesis | Francci3_0875 | 626 | hypothetical protein | Francci3_0160 | 660 |
protein of unknown function | Francci3_2628 | 958 | protein of unknown function | Francci3_1406 | 621 | AMP-dependent synthetase | Francci3_1806 | 659 |
LuxR family regulator | Francci3_3253 | 958 | hypothetical protein | Francci3_3247 | 621 | serine/threonine protein kinase | Francci3_3395 | 659 |
50SribosomalproteinL24 | Francci3_0593 | 944 | hypothetical protein | Francci3_2943 | 620 | hypothetical protein | Francci3_4161 | 655 |
ribosomal protein S2 | Francci3_3581 | 936 | transcription factor WhiB | Francci3_3790 | 618 | hypC/hupF | Francci3_1946 | 655 |
hypothetical protein | Francci3_2736 | 934 | hypothetical protein | Francci3_3997 | 618 | hypothetical protein | Francci3_0494 | 655 |
hypothetical protein | Francci3_2269 | 932 | transcriptional regulator | Francci3_4158 | 614 | transcriptional regulator | Francci3_0985 | 654 |
hypothetical protein | Francci3_2809 | 929 | hypothetical protein | Francci3_2184 | 610 | Excisionase/Xis, DNA-binding | Francci3_1856 | 653 |
acyl-CoA dehydrogenase-like | Francci3_0053 | 915 | hypothetical protein | Francci3_0054 | 608 | phosphohydrolase | Francci3_1134 | 648 |
Antibiotic biosynthesis | Francci3_0875 | 911 | CRISPR-associated protein | Francci3_0023 | 608 | SsgA | Francci3_3418 | 646 |
2-oxoacid oxidoreductase | Francci3_3248 | 906 | Recombinase | Francci3_2373 | 607 | major facilitator MFS_1 | Francci3_2752 | 643 |
translationinitiationfactorIF-1 | Francci3_0605 | 904 | CRISPR-associated protein | Francci3_3345 | 606 | Inorganic diphosphatase | Francci3_4310 | 636 |
electron transfer flavoprotein | Francci3_3659 | 889 | hypothetical protein | Francci3_2219 | 606 | hypothetical protein | Francci3_1032 | 636 |
hypothetical protein | Francci3_4326 | 884 | hypothetical protein | Francci3_3299 | 605 | DNA-directed RNA polymerase | Francci3_3194 | 635 |
50SribosomalproteinL33 | Francci3_0563 | 880 | LuxR family regulator | Francci3_3253 | 604 | chaperoninGroEL | Francci3_4398 | 635 |
hypothetical protein | Francci3_3625 | 856 | hypothetical protein | Francci3_2101 | 604 | UspA | Francci3_2760 | 633 |
Cytochrome-c oxidase | Francci3_2009 | 855 | transcriptional regulator | Francci3_1674 | 600 | Aldehyde dehydrogenase | Francci3_2944 | 632 |
GrpE protein | Francci3_4353 | 846 | transcriptional regulator | Francci3_0908 | 596 | hypothetical protein | Francci3_1014 | 631 |