>gnl|CDD|162831 TIGR02388, rpoC2_cyan, DNA-directed RNA polymerase, beta'' subunit. The family consists of the product of the rpoC2 gene, a subunit of DNA-directed RNA polymerase of cyanobacteria and chloroplasts. RpoC2 corresponds largely to the C-terminal region of the RpoC (the beta' subunit) of other bacteria. Members of this family are designated beta'' in chloroplasts/plastids, and beta' (confusingly) in Cyanobacteria, where RpoC1 is called beta' in chloroplasts/plastids and gamma in Cyanobacteria. We prefer to name this family beta'', after its organellar members, to emphasize that this RpoC1 and RpoC2 together replace RpoC in other bacteria. Length = 1227

Score = 351 bits (903), Expect = 6e-97 Identities = 211/621 (33%), Positives = 312/621 (50%), Gaps = 81/621 (13%) Query: 593 NQEMIKKNISAMVDTIYRHCGQKSTVAFCDDLMRLGFRYACSSGISFGKDDIIVPESKEK 652 N+ + KK + ++ Y+ G T A D L LGFRYA +G+S DD+ VP +K+ Sbjct: 4 NRVVDKKALKNLISWAYKTYGTARTAAMADKLKDLGFRYATRAGVSISVDDLKVPPAKQD 63 Query: 653 IIAEADKMVKEYENQYNDGLITRGEKYNKVVDLWGKTTDKVTEEMMARIKRVEFDPETGR 712 ++ A+K ++ E +Y G IT E++ KV+D W T +++ +E++ ++ DP Sbjct: 64 LLEAAEKEIRATEERYRRGEITEVERFQKVIDTWNGTNEELKDEVVNNFRQT--DP---- 117 Query: 713 QKKMNSIFMMSHSGARGSIHQMRQLGGMRGLIAKPSGEIIESPIRSHFKGGLCGFEFFQS 772 +NS++MM+ SGARG++ Q+RQL GMRGL+A P GEII+ PI+++F+ GL E+ S Sbjct: 118 ---LNSVYMMAFSGARGNMSQVRQLVGMRGLMANPQGEIIDLPIKTNFREGLTVTEYVIS 174 Query: 773 CVGGRKGLLDVVMRTASSGYLSRRLVDVAQNCVVNQVDCNTKKGLTITHIVDSGQVVYSL 832 G RKGL+D +RTA SGYL+RRLVDV+Q+ +V + DC T++ + + + + + + SL Sbjct: 175 SYGARKGLVDTALRTADSGYLTRRLVDVSQDVIVREEDCGTERSIVVRAMTEGDKKI-SL 233 Query: 833 GSRVLGRTALDDIINPLTNECIVKAGQLILESHVNEIEKCGIRSVRIRSALTCESSRGVC 892 G R+LGR +D+++P E IV I IE GI V +RS LTCE++R VC Sbjct: 234 GDRLLGRLVAEDVLHP-EGEVIVPKNTAIDPDLAKTIETAGISEVVVRSPLTCEAARSVC 292 Query: 893 VLCYGRDLARGSLVNVGEAVGVIAAQSIGEPGTQLTMRTFHLGGAVTVMDRSFIESPCDG 952 CYG LA LV++GEAVG+IAAQSIGEPGTQLTMRTFH GG T + S DG Sbjct: 293 RKCYGWSLAHAHLVDLGEAVGIIAAQSIGEPGTQLTMRTFHTGGVFTGEVARQVRSKIDG 352 Query: 953 IV----KIKNRNVCRNSTNDLISMGRNTTLQILDMSGQEQYSHRI--MYGAKLFVDDGGV 1006 V K++ R D + L I + I G+ LFV+DG Sbjct: 353 TVEFGKKLRTRGYRTRHGEDAKQVEVAGLLIIKPTGSITNKAQEIEVTQGSLLFVEDGQT 412 Query: 1007 IECGQRISE---------WDPHTFPIITEVSGTVGFEDLVDGISVIESIGESTGIAKRKV 1057 ++ GQ ++E + T + ++++G V F D V + G +T IA+R Sbjct: 413 VDAGQLLAEIALGAVRKSTEKATKDVASDLAGEVKF-DKVVPEEKTDRQGNTTRIAQRGG 471 Query: 1058 IDWRFASRSQNLKP--------------------AIVVTDENGVVLKSARGTDARWFLPV 1097 + W + NL P + T+ GVV D+R + Sbjct: 472 LIWVLSGEVYNLPPGAEPVVKNGDRVEQGTVLAETKLSTEHGGVVRLPESVGDSREVEII 531 Query: 1098 DA------------------------------LLSVSPGQKVSTGDVLARLPISSAKTKD 1127 A L +PG KV G V+A L +T Sbjct: 532 TASVLLDQAKVIEESSQGRELYHIETADGQRFRLKAAPGTKVQNGQVVAELIDDRYRTT- 590 Query: 1128 ITSGLPRVA--ELFEARRPKN 1146 T GL + A E+ + + K Sbjct: 591 -TGGLLKYAGVEVAKKGKAKQ 610

RPSBLAST alignment for GI: 254780142 and conserved domain: TIGR02388