PAL2NAL output - - - - - - - - - - - - - - - - - - - - P27302|TKT1_ECOLI --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- M Q Q Q G G F A T I A A T D F P H P F I A2PAD5|A2PAD5_VIBCH atg cag cag cag ggg ggc ttt gcg aca ata gcc gcc act gat ttt ccg cat cca ttc att - - - - - - - - - M S S R K E L A N A I P27302|TKT1_ECOLI --- --- --- --- --- --- --- --- --- atg tcc tca cgt aaa gag ctt gcc aat gct att S L T S H L G V D M S S R K Q L A N A I A2PAD5|A2PAD5_VIBCH tcg ctt act tcc cat tta gga gtc gac atg tct tct cgc aaa caa ctt gcc aat gct att R A L S M D A V Q K A K S G H P G A P M P27302|TKT1_ECOLI cgt gcg ctg agc atg gac gca gta cag aaa gcc aaa tcc ggt cac ccg ggg gcc cct atg R A L S M D G V Q K A N S G H P G A P M A2PAD5|A2PAD5_VIBCH cgt gcc ctg agc atg gac ggc gtt caa aaa gct aac tct ggc cac ccg gga gcc ccg atg G M A D I A E V L W R D F L K H N P Q N P27302|TKT1_ECOLI ggt atg gct gac att gcc gaa gtc ctg tgg cgt gat ttc ctg aaa cac aac ccg cag aat G M A D I A E V L W R S H L N H N P Q N A2PAD5|A2PAD5_VIBCH ggc atg gcg gat atc gcc gaa gtg ctg tgg cgt tca cac tta aac cac aac cca caa aac P S W A D R D R F V L S N G H G S M L I P27302|TKT1_ECOLI ccg tcc tgg gct gac cgt gac cgc ttc gtg ctg tcc aac ggc cac ggc tcc atg ctg atc P N W A D R D R F V L S N G H G S M L I A2PAD5|A2PAD5_VIBCH cca aat tgg gct gac cgc gac cgt ttc gta ctg tct aac ggc cac ggc tct atg ctg att Y S L L H L T G Y D L P M E E L K N F R P27302|TKT1_ECOLI tac agc ctg ctg cac ctc acc ggt tac gat ctg ccg atg gaa gaa ctg aaa aac ttc cgt Y S L L H L S G Y E L S I D D L K N F R A2PAD5|A2PAD5_VIBCH tac tcg ctg ctg cac ctg agc ggc tat gag ctg tcg att gac gat ttg aaa aac ttc cgt Q L H S K T P G H P E S G V T P L G V E P27302|TKT1_ECOLI cag ctg cac tct aaa act ccg ggt cac ccg gaa agt ggg gtt aca ccg ctg ggt gtg gaa Q L H S K T P G H P E Y G Y A P - G I E A2PAD5|A2PAD5_VIBCH caa ctg cac tca aaa aca ccg ggt cac cca gaa tac ggt tac gca ccg --- ggc atc gaa T T T G P L G Q G I A N A V G M A I A E P27302|TKT1_ECOLI acc acc acc ggt ccg ctg ggt cag ggt att gcc aac gca gtc ggt atg gcg att gca gaa T T T G P L G Q G I T N A V G M A I A E A2PAD5|A2PAD5_VIBCH act act acg ggc cca ctc ggc caa ggc atc acc aat gcc gta ggt atg gcg att gct gag K T L A A Q F N R P G H D I V D H Y T Y P27302|TKT1_ECOLI aaa acg ctg gcg gcg cag ttt aac cgt ccg ggc cac gac att gtc gac cac tac acc tac K A L A A Q F N K P G H D I V D H F T Y A2PAD5|A2PAD5_VIBCH aaa gca ctg gcg gcg cag ttc aac aaa ccg ggt cac gac atc gtt gac cac ttc act tat A F M G D G C M M E G I S H E V C S L A P27302|TKT1_ECOLI gcc ttc atg ggc gac ggc tgc atg atg gaa ggc atc tcc cac gaa gtt tgc tct ctg gcg V F M G D G C L M E G I S H E A C S L A A2PAD5|A2PAD5_VIBCH gtg ttc atg ggg gac ggc tgt ttg atg gaa ggt atc tcg cac gaa gcg tgt tca ctg gcg G T L K L G K L I A F Y D D N G I S I D P27302|TKT1_ECOLI ggt acg ctg aag ctg ggt aaa ctg att gca ttc tac gat gac aac ggt att tct atc gat G T L G L G K L I A F W D D N G I S I D A2PAD5|A2PAD5_VIBCH ggt acg ctg ggt ctg ggc aaa ctg att gca ttc tgg gat gac aac ggt att tct atc gac G H V E G W F T D D T A M R F E A Y G W P27302|TKT1_ECOLI ggt cac gtt gaa ggc tgg ttc acc gac gac acc gca atg cgt ttc gaa gct tac ggc tgg G H V E G W F S D D T P K R F E A Y G W A2PAD5|A2PAD5_VIBCH ggt cac gtg gaa ggc tgg ttc tca gac gac aca cca aaa cgt ttt gaa gcg tac ggc tgg H V I R D I D G H D A A S I K R A V E E P27302|TKT1_ECOLI cac gtt att cgc gac atc gac ggt cat gac gcg gca tct atc aaa cgc gca gta gaa gaa H V I P A V D G H D A D A I N A A I E A A2PAD5|A2PAD5_VIBCH cat gtc atc cct gcg gtt gat ggt cac gat gca gat gca att aac gct gcg att gaa gcg A R A V T D K P S L L M C K T I I G F G P27302|TKT1_ECOLI gcg cgc gca gtg act gac aaa cct tcc ctg ctg atg tgc aaa acc atc atc ggt ttc ggt A K A E T S R P T L I C T K T I I G F G A2PAD5|A2PAD5_VIBCH gcg aaa gca gaa acg tct cgc cca acg ctg att tgt acc aaa acc atc atc ggt ttc ggc S P N K A G T H D S H G A P L G D A E I P27302|TKT1_ECOLI tcc ccg aac aaa gcc ggt acc cac gac tcc cac ggt gcg ccg ctg ggc gac gct gaa att S P N K A G S H D C H G A P L G N D E I A2PAD5|A2PAD5_VIBCH tct cca aac aaa gcg ggt tca cac gac tgt cac ggc gca cca ctg ggc aac gat gaa atc A L T R E Q L G W K Y A P F E I P S E I P27302|TKT1_ECOLI gcc ctg acc cgc gaa caa ctg ggc tgg aaa tat gcg ccg ttc gaa atc ccg tct gaa atc K A A R E F L G W E Y A P F E I P A D I A2PAD5|A2PAD5_VIBCH aaa gcc gcg cgt gaa ttc ttg ggt tgg gaa tac gct ccg ttt gaa atc cct gcg gac att Y A Q W D A K E A G Q A K E S A W N E K P27302|TKT1_ECOLI tat gct cag tgg gat gcg aaa gaa gca ggc cag gcg aaa gaa tcc gca tgg aac gag aaa Y A A W D A K Q A G A S K E A A W N E K A2PAD5|A2PAD5_VIBCH tat gct gcg tgg gat gca aaa caa gca ggc gca agc aaa gaa gcc gct tgg aat gag aaa F A A Y A K A Y P Q E A A E F T R R M K P27302|TKT1_ECOLI ttc gct gct tac gcg aaa gct tat ccg cag gaa gcc gct gaa ttt acc cgc cgt atg aaa F A A Y A K A Y P A E A A E Y K R R V A A2PAD5|A2PAD5_VIBCH ttc gcc gct tac gcg aaa gct tac cca gct gaa gct gct gaa tac aaa cgc cgc gta gcg G E M P S D F D A K A K E F I A K L Q A P27302|TKT1_ECOLI ggc gaa atg ccg tct gac ttc gac gct aaa gcg aaa gag ttc atc gct aaa ctg cag gct G E L P A N W E A A T S E I I A N L Q A A2PAD5|A2PAD5_VIBCH ggc gag ctg cca gcg aat tgg gaa gcc gca acc agc gag att atc gct aac ctg caa gct N P A K I A S R K A S Q N A I E A F G P P27302|TKT1_ECOLI aat ccg gcg aaa atc gcc agc cgt aaa gcg tct cag aat gct atc gaa gcg ttc ggt ccg N P A N I A S R K A S Q N A L E A F G K A2PAD5|A2PAD5_VIBCH aac cct gcc aac atc gca tcg cgt aaa gca tca caa aat gcg ctg gaa gcg ttc ggc aaa L L P E F L G G S A D L A P S N L T L W P27302|TKT1_ECOLI ctg ttg ccg gaa ttc ctc ggc ggt tct gct gac ctg gcg ccg tct aac ctg acc ctg tgg L L P E F M G G S A D L A P S N L T M W A2PAD5|A2PAD5_VIBCH ctg ctg cca gaa ttt atg ggt ggt tct gct gac ttg gcg cct tct aac ctc acc atg tgg S G S K A I N - E D A A G N Y I H Y G V P27302|TKT1_ECOLI tct ggt tct aaa gca atc aac --- gaa gat gct gcg ggt aac tac atc cac tac ggt gtt S G S K S L T A E D A S G N Y I H Y G V A2PAD5|A2PAD5_VIBCH tct ggc tct aag tca ctg aca gca gaa gat gcg tca ggc aac tac atc cac tac ggt gtg R E F G M T A I A N G I S L H G G F L P P27302|TKT1_ECOLI cgc gag ttc ggt atg acc gcg att gct aac ggt atc tcc ctg cac ggt ggc ttc ctg ccg R E F G M T A I I N G I A L H G G F V P A2PAD5|A2PAD5_VIBCH cgt gag ttt ggt atg acg gcc atc atc aac ggt atc gcg ctg cac ggc ggt ttt gtc cct Y T S T F L M F V E Y A R N A V R M A A P27302|TKT1_ECOLI tac acc tcc acc ttc ctg atg ttc gtg gaa tac gca cgt aac gcc gta cgt atg gct gcg Y G A T F L M F M E Y A R N A M R M A A A2PAD5|A2PAD5_VIBCH tac ggt gca acc ttc ctg atg ttt atg gaa tac gcg cgt aac gcg atg cgt atg gca gca L M K Q R Q V M V Y T H D S I G L G E D P27302|TKT1_ECOLI ctg atg aaa cag cgt cag gtg atg gtt tac acc cac gac tcc atc ggt ctg ggc gaa gac L M K V Q N I Q V Y T H D S I G L G E D A2PAD5|A2PAD5_VIBCH ctg atg aaa gtg caa aac atc caa gtg tac acg cat gac tcg att ggt ctg ggt gaa gat G P T H Q P V E Q V A S L R V T P N M S P27302|TKT1_ECOLI ggg ccg act cac cag ccg gtt gag cag gtc gct tct ctg cgc gta acc ccg aac atg tct G P T H Q P V E Q I A S L R M T P N M S A2PAD5|A2PAD5_VIBCH ggc cca act cac caa ccc gtt gag caa atc gct tct ctg cgt atg aca cca aac atg agc T W R P C D Q V E S A V A W K Y G V E R P27302|TKT1_ECOLI aca tgg cgt ccg tgt gac cag gtt gaa tcc gcg gtc gcg tgg aaa tac ggt gtt gag cgt T W R P C D Q V E S A V A W K L A I E R A2PAD5|A2PAD5_VIBCH aca tgg cgc cca tgt gac caa gtg gaa tcg gca gtg gct tgg aaa ctg gcc atc gag cgt Q D G P T A L I L S R Q N L A Q Q E R T P27302|TKT1_ECOLI cag gac ggc ccg acc gca ctg atc ctc tcc cgt cag aac ctg gcg cag cag gaa cga act K D A P S A L I F S R Q N L A Q Q P R S A2PAD5|A2PAD5_VIBCH aaa gat gcg cca tct gcg ctg att ttc tcg cgt caa aac cta gcg cag caa cca cgc agc E E Q L A N I A R G G Y V L K D C A G Q P27302|TKT1_ECOLI gaa gag caa ctg gca aac atc gcg cgc ggt ggt tat gtg ctg aaa gac tgc gcc ggt cag A E Q V A N I A K G G Y I L K D C A G Q A2PAD5|A2PAD5_VIBCH gca gag caa gtg gcg aac atc gct aag ggt ggt tac atc ctg aaa gat tgt gca ggc caa P E L I F I A T G S E V E L A V A A Y E P27302|TKT1_ECOLI ccg gaa ctg att ttc atc gct acc ggt tca gaa gtt gaa ctg gct gtt gct gcc tac gaa P E L I L I A T G S E V E L A V A A Y E A2PAD5|A2PAD5_VIBCH cct gaa ctg atc ctg att gcg act ggc tct gaa gtg gaa ctc gcg gtt gcc gct tac gag K L T A E G V K A R V V S M S S T D A F P27302|TKT1_ECOLI aaa ctg act gcc gaa ggc gtg aaa gcg cgc gtg gtg tcc atg tcg tct acc gac gca ttt Q L S A E G K A V R V V S M P S T D A F A2PAD5|A2PAD5_VIBCH caa ctg agc gcc gaa ggc aaa gcg gtt cgc gtg gtg tct atg cca tca acg gat gcg ttt D K Q D A A Y R E S V L P K A V T A R V P27302|TKT1_ECOLI gac aag cag gat gct gct tac cgt gaa tcc gta ctg ccg aaa gcg gtt act gca cgc gtt D K Q D A A Y R E A V L P A A V T K R I A2PAD5|A2PAD5_VIBCH gat aag caa gat gcc gct tac cgt gaa gcc gtt ctg cca gcc gct gtg act aag cgt atc A V E A G I A D Y W Y K Y V G L N G A I P27302|TKT1_ECOLI gct gta gaa gcg ggt att gct gac tac tgg tac aag tat gtt ggc ctg aac ggt gct atc A I E A G I A D F W Y K Y V G F G G R I A2PAD5|A2PAD5_VIBCH gcg att gaa gcg ggt att gca gac ttc tgg tac aag tac gtc ggc ttt ggc ggt cgc atc V G M T T F G E S A P A E L L F E E F G P27302|TKT1_ECOLI gtc ggt atg acc acc ttc ggt gaa tct gct ccg gca gag ctg ctg ttt gaa gag ttc ggc I G M T S F G E S A P A G E L F K L F G A2PAD5|A2PAD5_VIBCH atc ggt atg acc agc ttc ggc gaa tca gca cca gcc ggt gag ctg ttc aaa ctg ttt ggt F T V D N V V A K A K E L L - P27302|TKT1_ECOLI ttc act gtt gat aac gtt gtt gcg aaa gca aaa gaa ctg ctg --- F T T E N V V K Q A K E L L A A2PAD5|A2PAD5_VIBCH ttc acg act gaa aac gta gtg aaa caa gcc aaa gaa ctg ctg gcg Synonymous (KS) and non-synonymous (KA) substitution rates calcualted by codeml in the PAML package: KS = 1.3507 KA = 0.1470 KA/KS = 0.1088 You can see the parameters used in codeml to calculate these values. If you use these values, please cite the following peper: * Goldman, N. and Yang, Z. 1994. A codon-based model of nucleotide substitution for protein-coding DNA sequences. Molecular Biology and Evolution 11:725-736.