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

Esparza, Mario; Cárdenas, Juan Pablo; Bowien, Botho; Jedlicki, Eugenia; Holmes, David S

doi:10.1186/1471-2180-10-229

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 name	^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 [4.1.1.39]	Halothiobacillus neapolitanus	94	882	0	PD417314, PD000044, Pfam00016, Pfam02788, COG1850
ACK77836.1	cbbS1	Ribulose bisphosphate carboxylase small subunit 1 [4.1.1.39]	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 [4.1.2.13]	Bradyrhizobium sp.	61	295	3e-78	PD002376, PD030418, Pfam01116, Pfam07876, COG191
Operon *cbb2*
ACK80366.1	cbbL2	Ribulose bisphosphate carboxylase/oxygenase large subunit 2 [4.1.1.39]	Thiobacillus denitrificans	97	920	0	PD417314, PD000044, Pfam00016, Pfam02788, COG1850
ACK79774.1	cbbS2	Ribulose bisphosphate carboxylase/oxygenase small subunit 2 [4.1.1.39]	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 [3.1.3.25]	Methylococcus capsulatus	66	646	8e-66	PD001491, PD013702, pfam00459, pfam00316, COG0483, COG1218
ACK80404.1	cbbF	Fructose-1,6-bisphosphatase [3.1.3.11]	Mariprofundus ferrooxydans	71	823	3e-86	PD007014, PD863173, pfam03320, COG1494
ACK79091.1	cbbT	Transketolase [2.2.1.1]	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 [2.7.2.3]	Alcanivorax borkumensis	80	1296	6e-141	PD000619, PDA014E1, pfam00162, COG0126
ACK78522.1	pykA	Pyruvate kinase II [2.7.1.40]	Thiobacillus denitrificans	79	1491	2e-163	PD983049, PD745602, pfam00224, pfam02887, COG0469
ACK79923.1	cbbA	Fructose-bisphosphate aldolase [4.1.2.13]	Nitrosococcus oceani	90	1474	1e-161	PD875785, PD002376, pfam01116, COG0191
ACK80630.1	cbbE	Ribulose-5-phosphate 3-epimerase [5.1.3.1]	Herminiimonas arsenicoxydans	80	753	2e-78	PD003683, PD591639, pfam00834, COG0036
ACK80633.1	cbbZ	Phosphoglycolate phosphatase [3.1.3.18]	Thiobacillus denitrificans	64	484	4e-47	PD946755, PDA11895, pfam00702, COG0546, COG0637
ACK78314.1	trpE	Anthranilate synthase component I [4.1.3.27]	Methylococcus capsulatus	77	1569	2e-172	PD005777, PD105823, pfam00425, pfam04715, COG0147, COG1169
ACK78895.1	trpG	Anthranilate synthase component II [4.1.3.27]	Nitrosomonas europaea	86	770	2e-80	PD806135, PD976090, pfam00117, pfam07722, COG0512, COG0518
Operon *cbb4*
ACK79981.1	metK	S-adenosylmethionine synthetase [2.5.1.6]	Ralstonia eutropha	86	591	2e-167	PD499406, PD606972, pfam02773, pfam02772, COG0192
ACK78713.1	sahA	S-adenosyl-L-homocysteine hydrolase [3.3.1.1]	Pseudomonas stutzeri	88	748	0	PD730548, PD551162, pfam05221, pfam00670, COG0499
ACK78001.1	metF	5,10-methylenetetrahydrofolate reductase [1.7.99.5]	Methylococcus capsulatus	69	306	1e-81	PD756524, PD763008, pfam02219, COG0685
ACK78673.1	cbbP	Phosphoribulokinase [2.7.1.19]	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

* 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, http://www.jcvi.org) and in GenBank/EMBL/DDBJ accession number CP001219.
^a Proposed gene name.
^b Proposed enzyme activity with EC number if available
^c Organism with the best BlastP hit to the candidate gene.
^d Percentage of similarity (% Sim) of candidate gene to that found in the organism listed in row (c).
^e Score of BlastP match.
^f E value of BlastP match.
^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

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