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. 2011 Jun 2;7(6):e1002106. doi: 10.1371/journal.pgen.1002106

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Gómez-Santos et al.

This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited.

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(A) Multiple sequence alignment of the CRD of the 21 ECF σ factors found in prokaryotes. The four invariant Cys are marked on a red background with letters in white. Residues conserved in at least 11 proteins are shown on a green background. The functionally similar amino acids are highlighted in yellow. The number of each gene in the corresponding genome is shown in parenthesis. The codes for the strains, gene identifiers in the genomes (in parentheses), and accession numbers for the proteins are as follows: M. xanthus (MXAN_3426): Myxococcus xanthus DK 1622, YP_631623.1; S. aurantiaca (STIAU_8272): Stigmatella aurantiaca DW4/3-1, ZP_01463028.1; R. palustris (Rpa1_1094): Rhodopseudomonas palustris TIE-1, YP_001990117.1; A. capsulatum (ACP_1212): Acidobacterium capsulatum ATCC 51196, YP_002754310.1; V. spinosum (010100010715): Verrucomicrobium spinosum DSM 4136, ZP_02927111.1; Anaeromyxobacter (Anae109_4009): Anaeromyxobacter sp. Fw109-5, YP_001381261.1; O. terrae (Oter_1731): Opitutus terrae PB90-1, YP_001818615.1; M. xanthus (MXAN_5263): Myxococcus xanthus DK 1622, YP_633415.1; Roseovarius sp. 217 (ROS217_03265): Roseovarius sp. 217, ZP_01038131.1; Roseovarius sp.TM1035 (RTM1035_00365): Roseovarius sp. TM1035, ZP_01881487.1; R. litoralis (RLO149_0305): Roseobacter litoralis Och 149, ZP_02143093.1; Roseovarius sp.217 (ROS217_03325): Roseovarius sp. 217 ZP_01038143.1; C. Nitrospira defluvii (NIDE1902): Candidatus Nitrospira defluvii, YP_003797553.1; Roseovarius sp.TM1035 (RTM1035_00375): Roseovarius sp. TM1035, ZP_01881489.1; Roseovarius sp. 217 (ROS217_03275): Roseovarius sp. 217, ZP_01038133.1; Mesorhizobium (Meso_3863): Mesorhizobium sp. BNC1, YP_676395.1; P. zucineum (PHZ_p0174): Phenylobacterium zucineum HLK1, YP_002128692.1; S. cellulosum (sce8251): Sorangium cellulosum So ce 56,YP_001618901.1; Acidobacterium sp. SP1PR4 (AciPR4DRAFT_0832): Acidobacterium sp. SP1PR4, ZP_07648663.1; Acidobacterium sp.MP5ACTX8 (A9ciX8DRAFT_2097): Acidobacterium sp. MP5ACTX8, ZP_07030792.1; Acidobacterium sp.MP5ACTZ9 (AciX9DRAFT_0224): Acidobacterium sp. MP5ACTX9, ZP_07062224.1. (B) Synteny in the genomic regions where some of the EFC σ factors with CRD are encoded. Genes shown in the same color (except black genes) in the different strains encode proteins with high homology.