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Table 3 Predicted genes of cbb operons

From: Genes and pathways for CO2 fixation in the obligate, chemolithoautotrophic acidophile, Acidithiobacillus ferrooxidans, Carbon fixation in A. ferrooxidans

*Accession aGene
bPredicted function cBest BlastP hit d% Similarity eScore fE-value gDomains and motifs
Operon cbb1        
ACK78724.1 cbbR LysR family transcriptional regulatory protein CbbR Nitrococcus mobilis 76 363 7e-99 PD462572, PD756396, Pfam03466, Pfam00126, COG0583
ACK79627.1 cbbL1 Ribulose bisphosphate carboxylase large subunit 1 [] Halothiobacillus neapolitanus 94 882 0 PD417314, PD000044, Pfam00016, Pfam02788, COG1850
ACK77836.1 cbbS1 Ribulose bisphosphate carboxylase small subunit 1 [] Methylococcus capsulatus 80 161 8e-39 PD000290, Pfam00101, COG4451
ACK78689.1 csoS2 Carboxysome structural peptide Thiobacillus denitrificans 59 325 9e-87 PD579361, tat signal peptide
ACK80925.1 csoS3 Carboxysome structural peptide Thiobacillus denitrificans 65 537 5e-151 PD191834, Pfam08936
ACK80352.1 csoS4A Carboxysome peptide A Thiobacillus denitrificans 93 139 6e-32 PD012510, Pfam03319, COG4576, tat signal peptide
ACK79436.1 csoS4B Carboxysome peptide B Thiobacillus denitrificans 82 119 7e-26 PD012510, Pfam03319, COG4576
ACK78722.1 csoS1C Microcompartments protein Nitrosomonas eutropha 97 142 6e-33 PD003442, Pfam00936, COG4577
ACK79154.1 csoS1A Microcompartments protein Nitrosomonas eutropha 97 144 1e-33 PD003442, Pfam00936, COG4577
ACK79584.1 csoS1B Microcompartments protein Nitrosomonas eutropha 95 146 3e-34 PD003442, Pfam00936, COG4577
ACK79096.1 bfrA Bacterioferritin Thiobacillus denitrificans 70 135 6e-31 PDA00179, Pfam00210, COG1633
ACK77923.1 hyp1 Hypothetical protein Thiobacillus denitrificans 81 68 2e-10 PDA1E0I5
ACK80576.1 parA Partition protein A Thiobacillus denitrificans 72 196 6e-49 PD194671, Pfam01656, COG1192
ACK78664.1 hyp2 Hypothetical protein Acidithiobacillus ferrooxidans 100 156 1e-09  
ACK80060.1 cbbQ1 Rubisco activation protein Nitrosomonas europaea 92 489 5e-137 PD490543, Pfam08406, Pfam07728, COG0714, COG5271
ACK80817.1 cbbO1 Rubisco activation protein Thiobacillus denitrificans 74 940 0 PD140693, PD679436, Pfam00092, COG4867, COG4548
ACK80290.1 cbbA Fructose-bisphosphate aldolase [] Bradyrhizobium sp. 61 295 3e-78 PD002376, PD030418, Pfam01116, Pfam07876, COG191
Operon cbb2        
ACK80366.1 cbbL2 Ribulose bisphosphate carboxylase/oxygenase large subunit 2 [] Thiobacillus denitrificans 97 920 0 PD417314, PD000044, Pfam00016, Pfam02788, COG1850
ACK79774.1 cbbS2 Ribulose bisphosphate carboxylase/oxygenase small subunit 2 [] Thiobacillus denitrificans 88 203 3e-51 PD000290, Pfam00101, COG4451
ACK80953.1 cbbQ2 Rubisco activation protein Nitrosomonas europaea 92 483 6e-135 PD490543, PD372819; Pfam08406, Pfam07728, COG0714
ACK78928.1 cbbO2 Rubisco activation protein Thiobacillus denitrificans 76 965 0 PD140693, PD025507, COG4548
Operon cbb3        
ACK80740.1 hyp3 Hypothetical protein Thiobacillus denitrificans 49 149 8e-9 PD796582
ACK78212.1 suhB Inositol-phosphate phosphatase [] Methylococcus capsulatus 66 646 8e-66 PD001491, PD013702, pfam00459, pfam00316, COG0483, COG1218
ACK80404.1 cbbF Fructose-1,6-bisphosphatase [] Mariprofundus ferrooxydans 71 823 3e-86 PD007014, PD863173, pfam03320, COG1494
ACK79091.1 cbbT Transketolase [] Methylococcus capsulatus 75 2264 0.0 PD308336, pfam00456, pfam02779, COG3959, COG0021
ACK78716.1 cbbG Glyceraldehyde-3-phosphate dehydrogenase type I [1.2.1.-] Burkholderia thailandensis 82 1189 1e-128 PD959395, PD859695, pfam02800, pfam00044, COG0057
ACK79414.1 cbbK Phosphoglycerate kinase [] Alcanivorax borkumensis 80 1296 6e-141 PD000619, PDA014E1, pfam00162, COG0126
ACK78522.1 pykA Pyruvate kinase II [] Thiobacillus denitrificans 79 1491 2e-163 PD983049, PD745602, pfam00224, pfam02887, COG0469
ACK79923.1 cbbA Fructose-bisphosphate aldolase [] Nitrosococcus oceani 90 1474 1e-161 PD875785, PD002376, pfam01116, COG0191
ACK80630.1 cbbE Ribulose-5-phosphate 3-epimerase [] Herminiimonas arsenicoxydans 80 753 2e-78 PD003683, PD591639, pfam00834, COG0036
ACK80633.1 cbbZ Phosphoglycolate phosphatase [] Thiobacillus denitrificans 64 484 4e-47 PD946755, PDA11895, pfam00702, COG0546, COG0637
ACK78314.1 trpE Anthranilate synthase component I [] Methylococcus capsulatus 77 1569 2e-172 PD005777, PD105823, pfam00425, pfam04715, COG0147, COG1169
ACK78895.1 trpG Anthranilate synthase component II [] Nitrosomonas europaea 86 770 2e-80 PD806135, PD976090, pfam00117, pfam07722, COG0512, COG0518
Operon cbb4        
ACK79981.1 metK S-adenosylmethionine synthetase [] Ralstonia eutropha 86 591 2e-167 PD499406, PD606972, pfam02773, pfam02772, COG0192
ACK78713.1 sahA S-adenosyl-L-homocysteine hydrolase [] Pseudomonas stutzeri 88 748 0 PD730548, PD551162, pfam05221, pfam00670, COG0499
ACK78001.1 metF 5,10-methylenetetrahydrofolate reductase [] Methylococcus capsulatus 69 306 1e-81 PD756524, PD763008, pfam02219, COG0685
ACK78673.1 cbbP Phosphoribulokinase [] Nitrosococcus oceani 78 402 2e-110 PD739884, PD015803, pfam00485, COG3954
ACK79243.1 ynbD Phosphosterase, PA-phosphatase Polaromonas naphthalenivorans 81 759 1e-81 PD589889, pfam 01569, COG0474, CD03386, CD00127
  1. * The sequence and annotation of the complete A. ferrooxidans strain ATCC 23270 genome is available at the Comprehensive Microbial Resource (CMR) (J. Craig Venter Institute, and in GenBank/EMBL/DDBJ accession number CP001219.
  2. a Proposed gene name.
  3. b Proposed enzyme activity with EC number if available
  4. c Organism with the best BlastP hit to the candidate gene.
  5. d Percentage of similarity (% Sim) of candidate gene to that found in the organism listed in row (c).
  6. e Score of BlastP match.
  7. f E value of BlastP match.
  8. g Motif and domains identified in the candidate proteins: CD, Conserved Domains; COG, Clusters of Orthologous Groups of Proteins; Pfam, protein families; PD, Prodom (protein domains); PS, Prosite tat signal peptide