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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
  1. 1 Gene annotations and locus tag numbers are colored based on their presence in all three samples (bold), in the 3dN2 and 5dNH4 samples (italic), in the 3dN2 and 3dNH4 samples (underscore), in the 3dNH4 and 5dNH4 samples (italic/underscore), and in one of the three samples (normal font).
  2. 2 RPKM (Reads per Kilobase Million) = (# reads per ORF)/(size of ORF in kilobases × millions of reads in the dataset).