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. 2014 Dec 5;15(1):946. doi: 10.1186/1471-2164-15-946

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© Allen et al.; licensee BioMed Central. 2014

This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.

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New cyd -related small proteins identified in this study. (A) The CydY small protein found in Epsilon and Deltaproteobacter species downstream of cydAB operons encoding CydA with a long Q-loop. (B) The CydZ small protein found in over 150 cydAB operons encoding CydA with a short Q-loop. Operon organization is shown on top of each figure, with an example alignment shown below followed by a consensus sequence logo shown at the bottom of the figure. Species are as follows: Desulfurispirillum indicum S5 (“Desulfurispirillum”), Campylobacter concisus 13826 (“Campylobacter”), Sulfuricurvum kujiense DSM 16994 (“Sulfuricurvum”), Arcobacter butzleri RM4018 (“Arcobacter”), Campylobacter jejuni subsp. doylei 269.97 (“Campylobacter”), Serratia sp. AS12 (“Serratia”), Vibrio parahaemolyticus RIMD 2210663 (“Vibrio”), Enterobacter aerogenes KCTC 2190 (“Enterobacter”), Pseudomonas aeruginosa LESB58 (“Pseudomonas”), Achromobacter xylosoxidans A8 (“Achromobacter”), Bordetella parapertussis 12822 (“Bordetella”), Zymomonas mobilis subsp. mobilis ZM4 (“Zymomonas”). Sequence logos were generated using the program WebLogo [57]. Alignments were generated using the program MUSCLE [54]. ‘*’ indicates that the residues are identical in all sequences and ‘:’ and ‘.’, respectively, indicated conserved and semi-conserved substitutions as defined by MUSCLE.