From 1c1cbbbba95796cbd8aeea8db28633eb84aa61a4 Mon Sep 17 00:00:00 2001 From: jprocter Date: Wed, 6 Feb 2013 15:43:50 +0000 Subject: [PATCH] JAL-1199 refactored stockholm test code from main class and added a Pfam Stockholm file for testing purposes (with new PDB dbref test) --- examples/PF00111_seed.stk | 523 +++++++++++++++++++++++++++++++ src/jalview/io/AppletFormatAdapter.java | 201 +----------- test/jalview/io/StockholmFileTest.java | 220 +++++++++++++ 3 files changed, 744 insertions(+), 200 deletions(-) create mode 100644 examples/PF00111_seed.stk create mode 100644 test/jalview/io/StockholmFileTest.java diff --git a/examples/PF00111_seed.stk b/examples/PF00111_seed.stk new file mode 100644 index 0000000..d98c09f --- /dev/null +++ b/examples/PF00111_seed.stk @@ -0,0 +1,523 @@ +# STOCKHOLM 1.0 +#=GF ID Fer2 +#=GF AC PF00111.22 +#=GF DE 2Fe-2S iron-sulfur cluster binding domain +#=GF PI fer2; +#=GF AU Sonnhammer ELL +#=GF SE Prosite +#=GF GA 20.70 15.00; +#=GF TC 20.70 15.70; +#=GF NC 20.60 14.90; +#=GF BM hmmbuild HMM.ann SEED.ann +#=GF SM hmmsearch -Z 15929002 -E 1000 --cpu 4 HMM pfamseq +#=GF TP Domain +#=GF WK Ferredoxin +#=GF DR INTERPRO; IPR001041; +#=GF DR PROSITE; PDOC00175; +#=GF DR PROSITE; PDOC00642; +#=GF DR SCOP; 3fxc; fa; +#=GF DR HOMSTRAD; fer2; +#=GF DR HOMSTRAD; Ald_Xan_dh_1; +#=GF SQ 206 +#=GS FER_GLEJA/8-82 AC P00233.1 +#=GS FER2_RAPSA/9-84 AC P14937.1 +#=GS Q39648_CITSI/61-136 AC Q39648.1 +#=GS FER3_MAIZE/63-138 AC P27788.1 +#=GS FER6_MAIZE/66-141 AC P94044.1 +#=GS FER1_SYNP2/9-83 AC P31965.2 +#=GS FER1_EQUAR/7-81 AC P00235.1 +#=GS FER2_EQUAR/7-80 AC P00237.1 +#=GS FER2_EQUAR/7-80 DR PDB; 1WRI A; 7-80; +#=GS FER2_PLEBO/10-85 AC P46035.2 +#=GS P95533_PSEPU/253-328 AC P95533.1 +#=GS KSHB_MYCTU/273-348 AC P96853.1 +#=GS Q44253_ACISP/251-326 AC Q44253.1 +#=GS Q59656_PLEBO/573-647 AC Q59656.1 +#=GS P71846_MYCTU/600-675 AC P71846.3 +#=GS O84985_PSEPU/271-347 AC O84985.2 +#=GS PAAE_ECOLI/266-342 AC P76081.1 +#=GS HCR_ECOLI/241-316 AC P75824.3 +#=GS O87803_PSEST/5-82 AC O87803.2 +#=GS TMOF_PSEME/4-81 AC Q03304.1 +#=GS O32476_PSESP/4-81 AC O32476.1 +#=GS Q51944_BURPI/5-82 AC Q51944.1 +#=GS Q53028_RHOCO/4-80 AC Q53028.1 +#=GS Q45344_BURPI/10-88 AC Q45344.1 +#=GS Q9ZNP1_COMTE/9-88 AC Q9ZNP1.1 +#=GS Q9Z418_PSEPU/11-90 AC Q9Z418.1 +#=GS Q9ZAN6_9BURK/12-91 AC Q9ZAN6.1 +#=GS FERN_PSEPU/7-85 AC P23263.1 +#=GS O24827_ACISP/7-85 AC O24827.1 +#=GS FERX_PSEPU/8-86 AC P23103.1 +#=GS Q52061_PSEPU/8-86 AC Q52061.1 +#=GS Q52167_PSEPU/8-86 AC Q52167.1 +#=GS O84964_9RALS/4-82 AC O84964.1 +#=GS Q9Z3W9_9SPHN/8-85 AC Q9Z3W9.1 +#=GS DMPP_PSEUF/5-82 AC P19734.3 +#=GS O84963_9RALS/4-81 AC O84963.1 +#=GS Q52574_PSESP/5-83 AC Q52574.1 +#=GS Q9ZNP2_COMTE/5-82 AC Q9ZNP2.1 +#=GS Q43983_ACICA/5-82 AC Q43983.1 +#=GS O87617_PSEAE/3-78 AC O87617.1 +#=GS O52378_9RALS/3-78 AC O52378.1 +#=GS Q51492_PSEAE/3-78 AC Q51492.1 +#=GS NDOR_PSEPU/3-78 AC Q52126.1 +#=GS Q52140_PSEPU/3-78 AC Q52140.1 +#=GS Q9Z9X8_9GAMM/242-317 AC Q9Z9X8.1 +#=GS VANB_PSEUH/234-309 AC O05617.1 +#=GS VANB_PSES9/231-306 AC P12580.1 +#=GS VANB_PSEPU/231-307 AC O54037.1 +#=GS VANB_ACIAD/234-309 AC O24840.1 +#=GS O88034_STRCO/230-305 AC O88034.1 +#=GS P94680_COMTE/234-309 AC P94680.1 +#=GS CBAB_COMTE/232-307 AC Q44257.2 +#=GS POBB_PSEPS/236-311 AC Q52186.1 +#=GS YEAX_ECOLI/237-313 AC P76254.1 +#=GS Q47914_SPHCR/241-316 AC Q47914.2 +#=GS PDR_BURCE/241-314 AC P33164.3 +#=GS PDR_BURCE/241-314 DR PDB; 2PIA A; 240-313; +#=GS PHT2_PSEPU/243-316 AC Q05182.1 +#=GS O86347_MYCTU/231-301 AC O86347.3 +#=GS YFAE_ECOLI/4-77 AC P0ABW3.1 +#=GS Y1309_HAEIN/3-75 AC P45154.1 +#=GS O31003_VIBAN/5-73 AC O31003.1 +#=GS RFBI_SALTY/5-76 AC P26395.1 +#=GS P95461_9PSED/17-94 AC P95461.1 +#=GS O85971_SPHAR/13-90 AC O85971.1 +#=GS XYLA_PSEPU/20-97 AC P21394.1 +#=GS YCBX_ECOLI/293-362 AC P75863.1 +#=GS P96096_THIFE/9-86 AC P96096.1 +#=GS MMOC_METTR/7-81 AC Q53563.1 +#=GS O85675_ACIAD/8-85 AC O85675.1 +#=GS BENC_ACIAD/19-98 AC P07771.2 +#=GS BENC_ACIAD/19-98 DR PDB; 1KRH B; 9-88; +#=GS BENC_ACIAD/19-98 DR PDB; 1KRH A; 9-88; +#=GS XYLZ_PSEPU/8-86 AC P23101.1 +#=GS CBDC_BURCE/8-85 AC Q51603.1 +#=GS O66892_AQUAE/7-72 AC O66892.1 +#=GS O85226_PSEFL/27-86 AC O85226.1 +#=GS O29575_ARCFU/14-75 AC O29575.1 +#=GS O27878_METTH/21-82 AC O27878.1 +#=GS Y092_METJA/14-73 AC Q57557.1 +#=GS FER5_RHOCA/10-107 AC P37097.2 +#=GS Q44501_AZOVI/10-107 AC Q44501.1 +#=GS Q46508_DESFR/6-74 AC Q46508.1 +#=GS Q9ZBV9_STRCO/15-78 AC Q9ZBV9.1 +#=GS NUOG_MYCTU/19-82 AC P95175.2 +#=GS O87815_CUPNE/22-85 AC O87815.1 +#=GS NQO3_THET8/4-88 AC Q56223.2 +#=GS NQO3_THET8/4-88 DR PDB; 3M9S C; 4-88; +#=GS NQO3_THET8/4-88 DR PDB; 3M9S 3; 4-88; +#=GS P74022_SYNY3/6-69 AC P74022.1 +#=GS P94157_SYNP6/6-69 AC P94157.1 +#=GS Q44513_ANAVA/6-69 AC Q44513.1 +#=GS P77908_MOOTH/4-67 AC P77908.3 +#=GS Q9ZJW1_HELPJ/4-65 AC Q9ZJW1.1 +#=GS O05397_BACSU/11-72 AC O05397.1 +#=GS YJGC_BACSU/7-68 AC O34720.1 +#=GS NUOG_SALTI/4-72 AC P0A1Y5.2 +#=GS O66748_AQUAE/6-70 AC O66748.1 +#=GS NDUS1_DICDI/5-71 AC Q34312.1 +#=GS NQO3_PARDE/7-71 AC P29915.4 +#=GS NDUS1_NEUCR/38-101 AC P24918.2 +#=GS NUOG_RICPR/4-67 AC Q9ZCF6.1 +#=GS NDUS1_SOLTU/70-133 AC Q43644.1 +#=GS NDUS1_RECAM/4-67 AC O21241.1 +#=GS NDUS1_BOVIN/34-97 AC P15690.1 +#=GS O52683_THEMA/3-65 AC O52683.1 +#=GS Q46606_DESVU/3-71 AC Q46606.1 +#=GS HOXU_CUPNH/5-66 AC P22318.2 +#=GS P72305_RHOOP/5-66 AC P72305.1 +#=GS Q59261_CLOSA/4-67 AC Q59261.1 +#=GS Q9ZNE4_CLOPE/4-67 AC Q9ZNE4.1 +#=GS PHF1_CLOPA/4-67 AC P29166.1 +#=GS Q59262_CLOAB/4-66 AC Q59262.1 +#=GS P74801_SYNY3/5-63 AC P74801.1 +#=GS XDHE_BACSU/18-77 AC O32143.1 +#=GS HCRC_THAAR/7-66 AC O33818.1 +#=GS HCRC_THAAR/7-66 DR PDB; 1SB3 F; 7-66; +#=GS HCRC_THAAR/7-66 DR PDB; 1RM6 C; 7-66; +#=GS HCRC_THAAR/7-66 DR PDB; 1RM6 F; 7-66; +#=GS HCRC_THAAR/7-66 DR PDB; 1SB3 C; 7-66; +#=GS P95635_RHOPA/15-74 AC P95635.1 +#=GS XDHC_ECOLI/11-69 AC Q46801.1 +#=GS YAGT_ECOLI/65-124 AC P77165.1 +#=GS DCMS_HYDPS/8-67 AC P19915.2 +#=GS Q52589_9PSED/8-67 AC Q52589.1 +#=GS O52837_BRAJA/6-65 AC O52837.1 +#=GS O53709_MYCTU/5-64 AC O53709.1 +#=GS O87682_ARTNI/8-67 AC O87682.1 +#=GS Q59128_ARTNI/14-73 AC Q59128.1 +#=GS P72223_PSEPU/14-73 AC P72223.1 +#=GS P72223_PSEPU/14-73 DR PDB; 1T3Q A; 14-73; +#=GS P72223_PSEPU/14-73 DR PDB; 1T3Q D; 14-73; +#=GS Q9ZBN8_STRCO/5-65 AC Q9ZBN8.1 +#=GS O54050_RHOCA/5-68 AC O54050.1 +#=GS O54050_RHOCA/5-68 DR PDB; 1JRP A; 5-68; +#=GS O54050_RHOCA/5-68 DR PDB; 2W3R A; 5-68; +#=GS O54050_RHOCA/5-68 DR PDB; 2W3S A; 5-68; +#=GS O54050_RHOCA/5-68 DR PDB; 1JRP G; 5-68; +#=GS O54050_RHOCA/5-68 DR PDB; 2W54 E; 5-68; +#=GS O54050_RHOCA/5-68 DR PDB; 1JRP E; 5-68; +#=GS O54050_RHOCA/5-68 DR PDB; 2W55 A; 5-68; +#=GS O54050_RHOCA/5-68 DR PDB; 2W3R E; 5-68; +#=GS O54050_RHOCA/5-68 DR PDB; 2W3S E; 5-68; +#=GS O54050_RHOCA/5-68 DR PDB; 2W54 G; 5-68; +#=GS O54050_RHOCA/5-68 DR PDB; 2W3R G; 5-68; +#=GS O54050_RHOCA/5-68 DR PDB; 2W54 A; 5-68; +#=GS O54050_RHOCA/5-68 DR PDB; 1JRO A; 5-68; +#=GS O54050_RHOCA/5-68 DR PDB; 1JRO E; 5-68; +#=GS O54050_RHOCA/5-68 DR PDB; 2W55 E; 5-68; +#=GS O54050_RHOCA/5-68 DR PDB; 2W55 C; 5-68; +#=GS O54050_RHOCA/5-68 DR PDB; 2W3R C; 5-68; +#=GS O54050_RHOCA/5-68 DR PDB; 1JRO C; 5-68; +#=GS O54050_RHOCA/5-68 DR PDB; 2W54 C; 5-68; +#=GS O54050_RHOCA/5-68 DR PDB; 2W3S G; 5-68; +#=GS O54050_RHOCA/5-68 DR PDB; 2W55 G; 5-68; +#=GS O54050_RHOCA/5-68 DR PDB; 2W3S C; 5-68; +#=GS O54050_RHOCA/5-68 DR PDB; 1JRO G; 5-68; +#=GS O54050_RHOCA/5-68 DR PDB; 1JRP C; 5-68; +#=GS O23887_MAIZE/15-85 AC O23887.1 +#=GS ALDO4_ARATH/8-78 AC Q7G191.2 +#=GS ALDO1_ARATH/23-95 AC Q7G193.2 +#=GS O30328_ACEEU/4-63 AC O30328.1 +#=GS IORA_BREDI/4-64 AC Q51697.1 +#=GS XDH_EMENI/39-108 AC Q12553.2 +#=GS O61198_CAEEL/8-78 AC O61198.2 +#=GS O17892_CAEEL/18-86 AC O17892.1 +#=GS XDH_DROSU/13-83 AC P91711.1 +#=GS O17506_BOMMO/19-89 AC O17506.1 +#=GS Q17250_BOMMO/18-88 AC Q17250.2 +#=GS ADO_BOVIN/9-79 AC P48034.2 +#=GS XDH_BOVIN/8-78 AC P80457.4 +#=GS XDH_BOVIN/8-78 DR PDB; 1V97 B; 8-78; +#=GS XDH_BOVIN/8-78 DR PDB; 3NVY A; 8-78; +#=GS XDH_BOVIN/8-78 DR PDB; 3NVY J; 8-78; +#=GS XDH_BOVIN/8-78 DR PDB; 3NRZ J; 8-78; +#=GS XDH_BOVIN/8-78 DR PDB; 3NVV A; 8-78; +#=GS XDH_BOVIN/8-78 DR PDB; 3NRZ A; 8-78; +#=GS XDH_BOVIN/8-78 DR PDB; 1N5X A; 8-78; +#=GS XDH_BOVIN/8-78 DR PDB; 1N5X B; 8-78; +#=GS XDH_BOVIN/8-78 DR PDB; 1V97 A; 8-78; +#=GS XDH_BOVIN/8-78 DR PDB; 1VDV A; 8-78; +#=GS XDH_BOVIN/8-78 DR PDB; 3NVV J; 8-78; +#=GS XDH_BOVIN/8-78 DR PDB; 1VDV B; 8-78; +#=GS XDH_BOVIN/8-78 DR PDB; 3NS1 A; 8-78; +#=GS XDH_BOVIN/8-78 DR PDB; 3NS1 J; 8-78; +#=GS MOP_DESGI/6-65 AC Q46509.1 +#=GS MOP_DESGI/6-65 DR PDB; 1VLB A; 6-65; +#=GS MOP_DESGI/6-65 DR PDB; 1SIJ A; 6-65; +#=GS O53669_MYCTU/13-78 AC O53669.1 +#=GS O29566_ARCFU/5-80 AC O29566.1 +#=GS O30225_ARCFU/5-84 AC O30225.1 +#=GS NQRF_CHLTR/46-122 AC O84745.1 +#=GS NQRF_HAEIN/43-119 AC O05012.1 +#=GS NQRF_VIBAL/39-115 AC Q56584.1 +#=GS O84062_CHLTR/8-83 AC O84062.1 +#=GS Q9Z8H9_CHLPN/8-83 AC Q9Z8H9.1 +#=GS CSMJ_CHLTE/5-82 AC O68983.1 +#=GS CSMI_CHLTE/5-82 AC O68988.1 +#=GS FER_TRIVA/13-90 AC P21149.1 +#=GS FER_TRIVA/13-90 DR PDB; 1L5P A; 5-83; +#=GS FER_TRIVA/13-90 DR PDB; 1L5P C; 5-83; +#=GS FER_TRIVA/13-90 DR PDB; 1L5P B; 5-83; +#=GS P73774_SYNY3/7-88 AC P73774.1 +#=GS FER_BUCAP/10-92 AC O51882.1 +#=GS O69222_AZOVI/11-93 AC O69222.1 +#=GS FER_HAEIN/10-92 AC P44428.2 +#=GS FER_PSEAE/10-92 AC Q51383.2 +#=GS ADRX_YEAST/67-149 AC Q12184.1 +#=GS ADX_PIG/71-155 AC P00258.2 +#=GS FER2_RICPR/11-93 AC Q9ZDW6.1 +#=GS O49551_ARATH/44-127 AC O49551.1 +#=GS ETP1_SCHPO/525-592 AC Q10361.2 +#=GS ETP1_SCHPO/525-592 DR PDB; 2WLB A; 525-607; +#=GS ETP1_SCHPO/525-592 DR PDB; 2WLB B; 525-607; +#=GS O07876_SPHSX/8-91 AC O07876.1 +#=GS Q9ZAM5_SPHSX/8-91 AC Q9ZAM5.1 +#=GS FER2_CAUCR/8-91 AC P37098.1 +#=GS FER6_RHOCA/7-91 AC P80306.1 +#=GS FER6_RHOCA/7-91 DR PDB; 1UWM A; 7-91; +#=GS P74447_SYNY3/31-113 AC P74447.1 +#=GS P73171_SYNY3/7-85 AC P73171.1 +#=GS FER1_AQUAE/3-83 AC O67065.1 +#=GS FER4_RHOCA/7-86 AC P16022.1 +#=GS P74283_SYNY3/5-88 AC P74283.1 +#=GS PUTX_PSEPU/8-92 AC P00259.3 +#=GS PUTX_PSEPU/8-92 DR PDB; 1PDX A; 7-91; +#=GS PUTX_PSEPU/8-92 DR PDB; 1OQR C; 7-91; +#=GS PUTX_PSEPU/8-92 DR PDB; 1OQR B; 7-91; +#=GS PUTX_PSEPU/8-92 DR PDB; 1XLP C; 7-91; +#=GS PUTX_PSEPU/8-92 DR PDB; 1R7S A; 7-91; +#=GS PUTX_PSEPU/8-92 DR PDB; 1OQR A; 7-91; +#=GS PUTX_PSEPU/8-92 DR PDB; 1YJJ A; 7-91; +#=GS PUTX_PSEPU/8-92 DR PDB; 1R7S C; 7-91; +#=GS PUTX_PSEPU/8-92 DR PDB; 1OQQ B; 7-91; +#=GS PUTX_PSEPU/8-92 DR PDB; 1XLP A; 7-91; +#=GS PUTX_PSEPU/8-92 DR PDB; 1XLP B; 7-91; +#=GS PUTX_PSEPU/8-92 DR PDB; 1R7S B; 7-91; +#=GS PUTX_PSEPU/8-92 DR PDB; 1OQQ A; 7-91; +#=GS PUTX_PSEPU/8-92 DR PDB; 1XLN B; 7-91; +#=GS PUTX_PSEPU/8-92 DR PDB; 1YJI A; 7-91; +#=GS PUTX_PSEPU/8-92 DR PDB; 1XLN A; 7-91; +#=GS TERPB_PSESP/8-92 AC P33007.2 +#=GS P95277_MYCTU/9-84 AC P95277.1 +#=GS O05933_PSEPU/11-88 AC O05933.1 +#=GS DESET_MYCTU/303-373 AC O05875.1 +#=GS O23344_ARATH/57-131 AC O23344.1 +#=GS P74159_SYNY3/11-86 AC P74159.1 +#=GS FER2_SYNP6/8-83 AC P08451.2 +#=GS P73388_SYNY3/9-84 AC P73388.1 +#=GS FER1_HALMA/35-108 AC P00217.2 +#=GS P74449_SYNY3/11-88 AC P74449.1 +#=GS FER2_NOSMU/10-85 AC P00249.2 +#=GS FER2_APHSA/10-86 AC P00251.2 +#=GS FER1_CYAPA/10-85 AC P17007.3 +#=GS FER_PORPU/10-85 AC P51320.2 +#=GS FER_ODOSI/10-85 AC P49522.2 +#=GS FER_BUMFI/9-84 AC P13106.1 +#=GS FER3_CYACA/9-84 AC P00241.1 +#=GS FER2_CYACA/8-83 AC P15789.1 +#=GS FER_BRYMA/8-83 AC P07838.1 +#=GS FER_APHSA/9-83 AC P00250.2 +#=GS FER_THEVL/9-84 AC P0A3D1.2 +#=GS FER_PERBI/6-80 AC P10770.1 +#=GS FER3_RAPSA/8-82 AC P14938.1 +#=GS FER1_SPIOL/58-132 AC P00221.2 +#=GS FER_SILPR/57-131 AC P04669.1 +#=GS FER_WHEAT/54-128 AC P00228.2 +#=GS FER_SAMNI/8-82 AC P00226.1 +#=GS FERA_ALOMA/8-82 AC P81372.1 +#=GS FER_ARCLA/8-82 AC P00223.1 +#=GS FER_DATST/8-82 AC P68165.1 +#=GS FER_PALPL/9-83 AC P07484.1 +#=GS FER_EUGVI/8-82 AC P22341.1 +#=GS FER_CHLFU/6-80 AC P56408.1 +#=GS FER_SYNY4/9-83 AC P00243.2 +#=GS FER1_PHYAM/8-82 AC P00229.1 +#=GS FER2_PHYAM/9-83 AC P00231.1 +#=GS FER2_SPIOL/8-82 AC P00224.1 +#=GS FER_PHYPA/57-132 AC O04166.1 +#=GS FER_MARPO/7-81 AC P09735.1 +FER_GLEJA/8-82 LTPDGE...RTIEVPDDKF.ILDAGE...E.A.GLDLPYSCRA.......GA....CSSCTGKLLDGRV.....DQSE...QSFLDDDQMAEGFV.....................LTCVAYPA +FER2_RAPSA/9-84 IGPEGE..ENEFEVQDDQF.ILDAAE...E.A.GVDLPYSCRA.......GA....CSTCAGQIVKGQV.....DQSE...GSFLEDDHFEKGFV.....................LTCVAYPQ +Q39648_CITSI/61-136 IGPMGE..EHEFEAQEDQY.ILDAAE...E.A.GVDLPYSCRA.......GA....CSTCAGKLVSGSV.....DQSD...GSFLDDNQMEAGYL.....................LTCISYPT +FER3_MAIZE/63-138 VGPEGE..EHEFDAPDDAY.ILDAAE...T.A.GVELPYSCRA.......GA....CSTCAGKIESGSV.....DQSD...GSFLDDGQQEEGYV.....................LTCVSYPK +FER6_MAIZE/66-141 VGPDGT..EHEFEAPDDTY.ILEAAE...T.A.GVELPFSCRA.......GS....CSTCAGRMSAGEV.....DQSE...GSFLDDGQMAEGYL.....................LTCISYPK +FER1_SYNP2/9-83 ITPDGE...VSYDAPDDEY.ILDSAG...D.A.GYDLPASCRA.......GA....CSTCAGKIVSGTV.....DQSE...QSFLDDDQIEAGYV.....................LTCIAYPQ +FER1_EQUAR/7-81 KTPSGE...FTLDVPEGTT.ILDAAE...E.A.GYDLPFSCRA.......GA....CSSCLGKVVSGSV.....DESE...GSFLDDGQMEEGFV.....................LTCIAIPE +FER2_EQUAR/7-80 KTPDGD...ITFDVEPGER.LIDIGS...E.K..ADLPLSCQA.......GA....CSTCLGKIVSGTV.....DQSE...GSFLDDEQIEQGYV.....................LTCIAIPE +#=GR FER2_EQUAR/7-80 SS E-----...EEEEE-----.TT----...-.S..S----SS--.......--....-STT---EEE-EE.....E---...-----HHHHH----.....................-TTT-EEE +FER2_PLEBO/10-85 NKKRNL..DITLPVDEDTT.VLEAAE...E.A.ELDLPFSCHS.......GA....CSSCVGKVVEGEI.....NQDD...QTFLDEEQVAKGFV.....................LLCVTYPR +P95533_PSEPU/253-328 VLMKGQ..THAVPVRAGEL.LLSAML...R.A.GLPAPHACRV.......GE....CASCMCRLQAGEVQ....RLDS....SVLDEDDVAAG.W...................L.LACRTRAA +KSHB_MYCTU/273-348 VELDGQ..THTVSWPRTAK.LLDVLL...A.A.GLDAPFSCRE.......GH....CGACACTLRAGKVN....MGVN....DVLEQQDLDEG.L...................I.LACQSRPE +Q44253_ACISP/251-326 FMLNGI..KNSVMCSEDDFILNEIIK......AGINVPSSCCA.......GN....CGSCMCLLVSGDVI....LESN....TVLDASDEEDGWI.....................LACRSKPR +Q59656_PLEBO/573-647 FAQSGK....EITCTQDDL.ILDIAD.....QAEVAIESSCRS.......GT....CGSCKCTLLEGEV.....SYDS..EPDVLDEHDRASGQI.....................LTCIARPV +P71846_MYCTU/600-675 FTLSGQ..RAIFDLVPGDS.ILEGAL...G..LRSDAPYACMG.......GA....CGTCRAKLIEGNVE....MD....HNFALRKAELDAGYI.....................LTCQSHPT +O84985_PSEPU/271-347 VISDGR..ALTFDLPRNTQNVLDAGN...A.I.GAELPYSCKA.......GV....CSTCKCRVIEGEV.....EMDS...NHALEDYEVAAGYV.....................LSCQTYPV +PAAE_ECOLI/266-342 VRQDGR..DREIVLNADDESILDAAL...R.Q.GADLPYACKG.......GV....CATCKCKVLRGKV.....AMET...NYSLEPDELAAGYV.....................LSCQALPL +HCR_ECOLI/241-316 FTKLQP..AREFYAPVGTT.LLEALE.....SNNVPVVAACRA.......GV....CGCCKTKVVSGEY.....TVSS...TMTLTDAEIAEGYV.....................LACSCHPQ +O87803_PSEST/5-82 IKIADT..DVEFTISDRDT.ILRAAL...R.D.GIPISYECNS.......GG....CGSCKIDVVEGQVE...TLWGE...APGLSPRDKRK.SR...................K.LACQCLAS +TMOF_PSEME/4-81 IQSDDL..LHHFEADSNDT.LLSAAL...R.A.ELVFPYECNS.......GG....CGACKIELLEGEVS...NLWPD...APGLAARELRK.NR...................F.LACQCKPL +O32476_PSESP/4-81 LKIEGQ..APGTCG.SGKS.LLVSAL...A.N.GIGFPYECAS.......GG....CGVCKFELLEGNVQ...SMWPD...APGLSSRDREKGNR...................H.LACQCVAL +Q51944_BURPI/5-82 ITIEGG..SAFSVAADEDT.LLRGAL...R.G.GIALPHECSV.......GG....CGACRFDLLSGLVE...SIWPE...APGLSERDRKR.GK...................H.LACQSRPL +Q53028_RHOCO/4-80 INVQPF..SHEYSCEDGES.LLDGAL..RN...SLLLKYGCKH.......GG....CGTCKVRLLDGDV.....EEPG..SSFALTPEDRENDVI.....................LACASVPL +Q45344_BURPI/10-88 YAWNRP..RSTTHARPPKA.SLTGML...R.LGRKGIPVGCVN.......GG....CGVCKVRVLDGST......RLGR.RQPCPRQRRRRSAGL...................T.LACREAPL +Q9ZNP1_COMTE/9-88 VSVEQT..GDTYACGTHES.LLSGML...R.LGRKGIPVGCVN.......GG....CGVCKVQVLEGAV.....RHLGP.VSCAHVSDLERDQGY...................T.LACRVAPL +Q9Z418_PSEPU/11-90 VHVMQT..GETFPCATDES.LLQGML...R.LGRKGIPVGCVN.......GG....CGVCKVHVIEGQC.....RPLGP.VSRAHVSAAEEARGF...................T.LACRVAPV +Q9ZAN6_9BURK/12-91 VHVAQT..DETFPCAGNES.LLTGMV...R.LGRKGIPVGCVN.......GG....CGVCKVRIVEGQI.....KALGP.ISRAHVTLDEENQGY...................T.LACRVAPQ +FERN_PSEPU/7-85 ITVQPG..GERFVCQPQQS.ALHAME...T.QGKRCLPVGCRG.......GG....CGLCKVRVLAGDY......ESGR.VSCKHLPVEAREQGY...................A.LACRLFAR +O24827_ACISP/7-85 ITEQCS..GQRFPCKAGQS.VLKAME...Q.QGLECAPVGCRG.......GG....CGLCKVTVREGDY......ECGK.MSRVHAPPEALAQGE...................V.LACRIYPL +FERX_PSEPU/8-86 VFEVLS..GQSFRCAEGQS.VLRAME...A.QGKRCIPVGCRG.......GG....CGLCRVRVLSGAY......RSGR.MSRGHVPAKAAAEAL...................A.LACQVFPQ +Q52061_PSEPU/8-86 IRETVS..GQTFRCLPDQS.VLSAME...Q.QGKRCVPVGCRG.......GG....CGLCKVRVLSGTY......QCHK.MSCNHVPPEAAKQGL...................A.LACQLFPQ +Q52167_PSEPU/8-86 VHETNS..GQSFTCRPDQS.VLRAME...E.QGKRCVPVGCRG.......GG....CGLCKVRVLSGDY......QCGR.MSCSQVPPEAAQQGL...................A.LACQLYPR +O84964_9RALS/4-82 VEIADS..GQRYPCDPGQN.LLRAME...V.LGQRGIPAGCRG.......GG....CGVCKVRIESGRY......RTGK.MSRACLSEAEQGQGL...................V.LACKAFPD +Q9Z3W9_9SPHN/8-85 IRILGG..GQ.FACPEGER.VLIAME...Q.FGSSDIGVGCRG.......GG....CGFCLVRVVEGEY......RTGK.MSTAKVSVADQAKGY...................A.LACRIYPM +DMPP_PSEUF/5-82 VTIEPT..GEVIEVEDGQT.ILQAAL...R.Q.GVWLPFACGH.......GT....CATCKVQVVEGEVD...IGEAS...PFALMDIERDERKV.....................LACCAIPL +O84963_9RALS/4-81 LTIEPI..GQTIPIAPGQT.VLDACL...R.S.GVWLPHACCH.......GL....CATCKVQVVEGEVD...QGEAS..SFALMDFER.DNGQC.....................LACCATAQ +Q52574_PSESP/5-83 LTIEPL..GRTLDVAEGQT.LLDAAL...R.S.GVYIPHACGH.......GL....CGTCKVQVTSGEVD...HGAAN..PLRRSWISSGEEGKT.....................LACCATAL +Q9ZNP2_COMTE/5-82 LTLEPL..GASIEVEEGQT.LLDAAL...R.Q.GIYIPHACGH.......GL....CGTCKIQVCDGDVD...HGAAN..PFALMDMER.EDGMT.....................LACCATLQ +Q43983_ACICA/5-82 VTIEPA..GTIIQVEEDQT.ILDAAL...R.Q.GVWLPFACGH.......GT....CGTCKVQVTDGFYD...VGEAS..PFALMDIER.EENKV.....................LACCCKPE +O87617_PSEAE/3-78 LHIQPL..GQTLSVDSGAN.LLEALR...A.AE.VPISYSCMA.......GR....CGTCRCKVLKGQV......L..E.SGREATLTNPHADDY...................V.LACMSAIT +O52378_9RALS/3-78 LVVEPL..NLHLNAETGST.LLDVLR...S.NE.VPISYSCMS.......GR....CGTCRCRVIAGHL......R..D.NGPETGRPQAGKGTY...................V.LACQAVLT +Q51492_PSEAE/3-78 LLVLPN..NRRLPFDSGAN.LLEVLR...E.HR.VGISYSCMS.......GR....CGTCRCRVIDGSV......I..S.SAAKSGDSNRIEEHY...................V.LACQSVLT +NDOR_PSEPU/3-78 LLIQPN..NRIIPFSAGAN.LLEVLR...E.NG.VAISYSCLS.......GR....CGTCRCRVIDGSV......I..D.SGAENGQSNLTDKQY...................V.LACQSVLT +Q52140_PSEPU/3-78 LLIQPN..NRLISFSPGAN.LLEVLR...E.NG.VAISYSCMS.......GR....CGTCRCRVTDGSV......I..D.SGTGSGLPHLVDEHY...................V.LACRSVLT +Q9Z9X8_9GAMM/242-317 VRIASS..GATVHVDKHTT.IVAALA...S.I.GIEVDTSCGE.......GV....CGTCMVDVVSGTP.....EHRD....HCLSKAERASGKV...................I.CCCVSRAR +VANB_PSEUH/234-309 VRIHST..GQVLQVPADQT.VSQVLD...A.A.GIIVPVSCEQ.......GI....CGTCITRVVDGEP.....DHRD....FFLTDAEKAKNDQ...................F.TPCCSRAK +VANB_PSES9/231-306 GRLARS..GLTLQVPAERS.VAQVLD...D.A.GVCIPLACEQ.......GI....CGTCLTRVLDGEP.....EHRD....SFLTDAERARNDQ...................F.TPCCSRAR +VANB_PSEPU/231-307 VQLNST..GQVFEVPADQS.VVHVLE...Q.H.GIAIAMSCEQ.......GI....CGTCLTRVLSGTPE....ASRP....VFLTEQEQALNDQ...................F.TPCCSRSK +VANB_ACIAD/234-309 IEVLGS..DRKIEVSAHQT.ATQALL...E.H.GFDVPVSCEQ.......GI....CGTCITRVVSGTP.....DHRD....VFMTDEEHALNDQ...................F.TPCCSRAK +O88034_STRCO/230-305 VVLARS..GRTVAVPPGTS.VLDAVR...E.T.GVEVLYSCTE.......GT....CGTCETEVVEGEP.....DHRD....SVLTEEERAAGET...................M.LICVSRCR +P94680_COMTE/234-309 LVLQRA..GLSTTVDAHES.VLDAME...R.V.GVDFPWSCRE.......GI....CGTCEAPVLEGEV.....QHLD....YVLSPEERAEQRR...................M.MVCVSRCG +CBAB_COMTE/232-307 VNLARS..GAQYVVREGET.ILDVLR...N.A.GHHVTSSCRQ.......GI....CGMCETTLISGVP.....DHRD....RLLTDSEKASGRT...................M.LICCSRAL +POBB_PSEPS/236-311 VHLARS..GRTIPIAAGCT.ILDALQ...A.G.GVAVPSSCQQ.......GV....CGICETAVLAGVP.....DHRD....LVLSDQERAAGRT...................M.MICCSGSK +YEAX_ECOLI/237-313 LVLARS..GKEFVVPEEMT.ILQVIE...N.NKAAKVECLCRE.......GV....CGTCETAILEGEA.....DHRD....QYFSDEERASQQS...................M.LICCSRAK +Q47914_SPHCR/241-316 VLARRS..GQEFTVEPGMT.ILETLL...Q.N.GISRNYSCTQ.......GV....CGTCETKVLEGEP.....DHRD....WVLSDEKKASNST...................M.LICCSLSK +PDR_BURCE/241-314 VRLSRS..GTSFEIPANRS.ILEVLR...D.A.NVRVPSSCES.......GT....CGSCKTALCSGEA.....DHRD....MVLRDD..EKGTQ...................I.MVCVSRAK +#=GR PDR_BURCE/241-314 SS EEES--..--EEEE-TTS-.HHHHHH...H.T.T-----S---.......--....----EEEEEE--E.....E---....SS--TT..T---E...................E.ETTT-EES +PHT2_PSEPU/243-316 VTLGRS..GIDLEIPVDRS.ILEVLR...D.N.GIRAPSSCES.......GT....CGSCRTRLIEGDV.....EHRD....MVLREDEQH..DQ...................I.MICVSRAR +O86347_MYCTU/231-301 LELARS..RRVLRVPANRS.ALDVML.....DWDPTTAYSCQQ.......GF....CGTCKVRVLAGQV.....DRRG....RIIEGDN.....E...................M.LVCVSRAV +YFAE_ECOLI/4-77 VTLRIT..GTQLLCQDEHP.SLLAAL...E.SHNVAVEYQCRE.......GY....CGSCRTRLVAGQV......D......WIAEPLAFIQPGE...................I.LPCCCRAK +Y1309_HAEIN/3-75 IHLIRH..NTTLEFNNET..SLLDHL...E.KNNIHHEYQCRS.......GY....CGSCRVKIKKGKV......S......YKEMPLAFIQPDE...................I.LLCCCHVE +O31003_VIBAN/5-73 VIVKPS..GVEYQSG..RN.ILDDAF...A.S.SISLEHSCKT.......GD....CGVCCAEVISGLV.....ENEN........GELVTQG.H...................I.LTCQSKAK +RFBI_SALTY/5-76 IKIFPS..NIEFSGREDES.ILDAAL...S.A.GIHLEHSCKA.......GD....CGICESDLLAGEVV....DSKG.........NIFGQGDK...................I.LTCCCKPK +P95461_9PSED/17-94 VQILPQ..DVTIVLEPGQT.LLEAAL...A.N.GIAYPHDCTV.......GT....CASCKTRLKQGRVR...EATPF...GYTLSKAELDA.GY...................I.LACQAFPR +O85971_SPHAR/13-90 VTVEGS..PTTLDIPAGKT.LLEAML...D.A.GLAMPHDCKV.......GS....CGTCKFKLVSGKIG...ELSPS...ALALEGDELRS.GF...................R.LACQAIPR +XYLA_PSEPU/20-97 VSVRGQ..GFQFKVPRGQT.ILESAL...H.Q.GIAFPHDCKV.......GS....CGTCKYKLISGRVN...ELTSS...AMGLSGDLYQS.GY...................R.LGCQCIPK +YCBX_ECOLI/293-362 IDWQGQ....AFRGNNQQV.LLEQLE.....NQGIRIPYSCRA.......GI....CGSCRVQLLEGEV......T.P......LKKSAMGDDGT....................ILCCSCVPK +P96096_THIFE/9-86 HTRDKQ..QVSFVCSEAED.LLSAAD...R.G.SILLPSQCRK.......GT....CGACVATVTAGTYH...LGEVS..MEALPEKAQ.ARGDV.....................LLCRTYPR +MMOC_METTR/7-81 ETEDGE..TCRRMR.PSED.WISR.A...E.A.ERNLLASCRA.......G.....CATCKADCTDGDYE...LIDVK..VQAVPPDEE.EDGKV.....................LLCRTFPR +O85675_ACIAD/8-85 NFADGK..TFFIAVQEDEL.LLDAAV...R.Q.GINLPLDCRE.......GV....CGTCQGTCETGIYE...QEYVD..EDALSERDL.AKRKM.....................LACQTRVK +BENC_ACIAD/19-98 QFEDGV..TRFIRIAQGET.LSDAAY...R.Q.QINIPMDCRE.......GA....CGTCRAFCESGNYD...MPEDNY.IEDALTPEEAQQGYV.....................LACQCRPT +#=GR BENC_ACIAD/19-98 SS E-----..EEEEEE-----.HHHHHH...H.T.T---S-S---.......--....----EEEEEE-EEE...--GGGS.-TTT--HHHHH---E.....................ETTT-EEE +XYLZ_PSEPU/8-86 DFEDGV..TRFIDANTGET.VADAAY...R.Q.GINLPLDCRD.......GA....CGACKCFAESGRYS...LGEE.YIEDALSEAEA.EQGYV.....................LTCQMRAE +CBDC_BURCE/8-85 RFEDDV..TYFITSSEHET.VADAAY...Q.H.GIRIPLDCRN.......GV....CGTCKGFCEHGEYD...GGDY.I.EDALSADEA.REGFV.....................LPCQMQAR +O66892_AQUAE/7-72 RYSDGDFRWEEYEVDGEGKTVLEILQNIKEIDPTLSFRAMCRA.......GI....CGTCVVKVN.....................GEHK..........................LACNTRVY +O85226_PSEFL/27-86 VTA.AL..GETVLSVIQATGLRQVAR...N.DHGQLVGAYCGM.......GV....CHCCLVQIDG...................RHKR...........................RACQTLVK +O29575_ARCFU/14-75 AYWQSFEVPAKR.GMTVLEALYYIKE...NLDSSLAFRASCRM.......GI....CGSCAMKIN.....................DKP..........................RLACETQVL +O27878_METTH/21-82 PHLESYEIPSKE.KMKVLDALQLINK...IHGANIAFRSSCRA.......GQ....CGSCAVKMN.....................GEV..........................VLACRAEVE +Y092_METJA/14-73 EYLESYEVP..E.NITVLEALEYINK...HYEANILFRASCRN.......AQ....CGSCAVTIN.....................GEP..........................RLACETKVE +FER5_RHOCA/10-107 IMKKDK..TIYAVAGNTATILALAKE...H.AIPIPF..ECG........DG...DCASCLIEVTHLDN.....KPAMAMMLTEKEKARLKELQMITAEEIEAA..EVSDLPPRFRLACQFIPR +Q44501_AZOVI/10-107 LMPHNK..KVQAVAGKRSTLLGVAQE...N.GVKIPF..ECQ........DG...NCGSCLVKITHLDG.....ERIKGMLLTDKERNVLKSVGKLPKSEEERA..AVRDLPPTYRLACQTIVT +Q46508_DESFR/6-74 ITIDGK..TTSVPE...GSTILDAAK...T.L.DIDIPTLCYLNLEALSINNKAASCRVCVVE.....................VEGRRN....L....................APSCATPVT +Q9ZBV9_STRCO/15-78 FTLDGQ..EARVPE...GSTILDACR...A.A.GKDVPTLCEGDT..LAPKN...ACRVCVVD.....................VEGART....L....................APACSRKAE +NUOG_MYCTU/19-82 LTIDGV..EISVPK...GTLVIRAAE...L.M.GIQIPRFCDHPL..LEPVG...ACRQCLV.....................EVEGQR....KP....................LASCTTVAT +O87815_CUPNE/22-85 LEVDGV..SVTVPA...GTSVMRAAM...E.A.QIAVPKLCATDS..LRNFG...SCRLCLV.....................EIEGRR....GY....................PASCTTPVE +NQO3_THET8/4-88 VKVNDR..IVEVPP...GTSVMDAVF...H.A.GYDVPLFCSEKH..LSPIG...ACRMCLVRIGLPKKGPDGKPLLNEKGEPEIQWQP....KL....................AASCVTAVA +#=GR NQO3_THET8/4-88 SS EE-SS-..EEEE--...--BHHHHHH...H.-.------SS--TT..S----...----SEEB-------------------------S....S-....................EETTT-B-- +P74022_SYNY3/6-69 LTIDDK..AIAIEE...GASILQAAK...E.A.GVPIPTLCHLEG..ISEAA...ACRLCMVE.....................VEGTNK....L....................MPACVTAVS +P94157_SYNP6/6-69 LQIDDQ..ELAANV...GQTVLQVAR...E.A.SIPIPTLCHLQG..VSDVG...ACRLCVVE.....................VAGSPK....L....................QPACLLTVS +Q44513_ANAVA/6-69 LTINDQ..LISAQE...EETLLQAAQ...E.A.GIHIPTLCHLEG..VGDVG...ACRLCLVE.....................VAGSNK....L....................LPACVTKVA +P77908_MOOTH/4-67 LTIDGQ..RVTAPE...GMTILEVAR...E.N.GIHIPTLCHHPK..LRPLG...YCRLCLVD.....................IEGAAK....P....................MTACNTPVA +Q9ZJW1_HELPJ/4-65 MNINGK..TIECQE...GQSVLEAAR...S.A.GIYIPTICYLSG..CSPTV...ACKMCMV........................EMDG...KR....................IYSCNTKAK +O05397_BACSU/11-72 VRVDGT..EIQARA...GATILDILN...E.N.GIEYPQICHVPE..VDPIQ...TCDTCIV........................EANG...KL....................VRSCATVAE +YJGC_BACSU/7-68 ITINGV..EMEASE...EQTVLQLLN...N.S.SIEVPQVCYHPS..LGPIE...TCDTCIV........................SING...EL....................KRSCSAELK +NUOG_SALTI/4-72 IHVDGK....EYEVNGADN.LLQACL...S.L.GLDIPYFCWHPAL.GSVGA....CRQCAVK..................QYQNAEDTR...GR...................LVMSCMTPAT +O66748_AQUAE/6-70 KIYIDD...VEIEAEKGKTVLQVALE..N....GIDIPYFCYHPR..LSIAG...ACRMCVVY.......................WEDINR......................LVISCNLPVQ +NDUS1_DICDI/5-71 FKINEI..ECEVNEEKEDITILQACT...A.N.GIEIPRFCYHEK..LTIAG...NCRMCLV.....................YVTNEE....KL....................LAACGIPLD +NQO3_PARDE/7-71 IKIDDT....IIEVDPNMT.LIQACE...M.A.GIEVPRFCYHER..LSIAG...NCRMCLVEVVGG........PPK........PA............................ASCAMQVK +NDUS1_NEUCR/38-101 LTIDGK..KVSIEA...GSALIQACE...K.A.GVTIPRYCYHEK..LMIAG...NCRMCLV.....................EVEKVP....KP....................VASCAWPVQ +NUOG_RICPR/4-67 LIIDGS..EIEISE...GSTVYQACI...Q.A.GKEIPHFCYHAR..LKIAG...NCRMCLV.....................EIEKSQ....KP....................VASCAMPVS +NDUS1_SOLTU/70-133 VFVDGY..PVKIPK...GMTVLQACE...I.A.GVDIPRFCYHSR..LSIAG...NCRMCLV.....................EVEKSP....KP....................VASCAMPAL +NDUS1_RECAM/4-67 VFVDGL..SVEVKK...GATILQACA...Q.V.GIEIPRFCYHER..LSIAG...NCRMCLV.....................EVEKSP....KP....................VASCAMPVM +NDUS1_BOVIN/34-97 VFVDGQ..SVMVEP...GTTVLQACE...K.V.GMQIPRFCYHER..LSVAG...NCRMCLV.....................EIEKAP....KV....................VAACAMPVM +O52683_THEMA/3-65 IYVDGR..EVIIN..DNERNLLEALK.....NVGIEIPNLCYLS.....EASIYGACRMCLVEIN.......................GQIT........................TSCTLKPY +Q46606_DESVU/3-71 AFINGK..EVRCEP...GRTILEAAR...E.N.GHFIPTLCELADIGHAPGT....CRVCLVE.....................IWRDKEAGPQI....................VTSCTTPVE +HOXU_CUPNH/5-66 ITIDGK..TLTTEE...GRTLVDVAA...E.N.GVYIPTLCYLKDK.PCLGT....CRVCSVKVN.....................GN......V....................AAACTVRVS +P72305_RHOOP/5-66 IEIDGV..TVTTEE...SRTLVDVAA...E.A.GVYIPTLCYLKGK.PSLGT....CRVCSVK.....................LNGTV..........................VAACTIRVA +Q59261_CLOSA/4-67 IVIDEK..TIQVQE...NTTVIQAAL...A.N.GIDIPSLCYLNEC.GNVGK....CGVCAVE.....................IEGKNN....L....................ALACITKVE +Q9ZNE4_CLOPE/4-67 IIINDK..TIEFDG...DKTILDLAR...E.N.GFDIPVLCELKNC.GNKGQ....CGVCLVE.....................QEGNDR....L....................LRSCAIKAK +PHF1_CLOPA/4-67 IIINGV..QFNTDE...DTTILKFAR...D.N.NIDISALCFLNNCNNDINK....CEICTVE.....................VEGTG.....L....................VTACDTLIE +Q59262_CLOAB/4-66 IILNGN..EVHTDK...DITILELAR...E.N.NVDIPTLCFLKDC.GNFGK....CGVCMVE.....................VEGKG.....F....................RAACVAKVE +P74801_SYNY3/5-63 IHFLPD..DVTVAARVGEPILDVAER......AGVFIPTGCLM.......GS....CHACEVELG.......................DGTP.......................ICACISAVP +XDHE_BACSU/18-77 MTVNGQ..AWEV.AAVPTTHLSDLLR...KEFQLTGTKVSCGI.......GR....CGACSILID.....................GK......L....................ANACMTMAY +HCRC_THAAR/7-66 LTLNGR..ARED.LVPDNMLLLDYLR...ETVGLTGTKQGCDG.......GE....CGACTVLVD.....................DR......P....................RLACSTLAH +#=GR HCRC_THAAR/7-66 SS EEE---..EEEE.EEETT-BHHHHHH...HT------------.......--....----EEEET.....................TE......E....................EEGGGSBGG +P95635_RHOPA/15-74 LNVNGR..WRED.AVTDDMLLVDYLR...DIAGLTGVKTGCDG.......GE....CGACTVLID.....................GE......A....................APSCLVLAV +XDHC_ECOLI/11-69 CTINGM..PFQLHAAPGTP.LSELLR...E.QGLLSVKQGCCV.......GE....CGACTVLVD....................G..TAID.........................SCLYLAA +YAGT_ECOLI/65-124 LKVNGK..TEQL.EVDTRTTLLDTLR...ENLHLIGTKKGCDH.......GQ....CGACTVLVN.....................GR......R....................LNACLTLAV +DCMS_HYDPS/8-67 VNVNGK..AQEK.AVEPRTLLIHFLR...EELNLTGAHIGCET.......SH....CGACTVDID.....................GR......S....................VKSCTHLAV +Q52589_9PSED/8-67 MTVNGR..KVEE.AVEARTLLVHFLR...EKLNLTGTHIGCDT.......SH....CGACTVDVD.....................GK......S....................IKSCTHLAV +O52837_BRAJA/6-65 LIVNGN..PVTA.NVDPRTLLVQFLR...ENLRLTGTHVGCDT.......SQ....CGACVVHLD.....................GK......A....................VKSCTTLAV +O53709_MYCTU/5-64 MTVNGE..PVTA.EVEPRMLLVHFLR...DQLRLTGTHWGCDT.......SN....CGTCVVEVD.....................GV......P....................VKSCTMLAV +O87682_ARTNI/8-67 VEVNGV..THAT.DVEPRRLLADFLR...DDLHLRGTRVGCEH.......GV....CGSCTVLLD.....................GQ......P....................VRSCTVLAV +Q59128_ARTNI/14-73 VEVNGR..RRTV.AVDARETLADHLR...NDQKLTGIKLGCEH.......GV....CGACTILMD.....................GA......A....................VRSCLTLAA +P72223_PSEPU/14-73 ATINGK..PRVF.YVEPRMHLADALR...EVVGLTGTKIGCEQ.......GV....CGSCTILID.....................GA......P....................MRSCLTLAV +#=GR P72223_PSEPU/14-73 SS EEE---..EEEE.EE-TTSBHHHHHH...HT------------.......--....----EEEE-.....................--......E....................EEGGGSBGG +Q9ZBN8_STRCO/5-65 LTVNGR..PQEADDVWEGESLLYVLR...ERMGLPGSKNACEQ.......GE....CGSCTVRLD.....................GVP..........................VCSCLVAAG +O54050_RHOCA/5-68 FLLNGE..TRRVRIEDPTQSLLELLR...A.EGLTGTKEGCNE.......GD....CGACTVMIRD.................AAGSR......A....................VNACLMMLP +#=GR O54050_RHOCA/5-68 SS EEE---..EEEEE-S-TT-BHHHHHH...H.------------.......--....----EEEEES.................----E......E....................EETTTSBGG +O23887_MAIZE/15-85 LAVNGK..RYEAAGVAPSTSLLEFLR...TQTPVRGPKLGCGE.......GG....CGACVVLVSK.................YDPATDEVTEFS....................ASSCLTLLH +ALDO4_ARATH/8-78 FAVNGE..KFEVLSVNPSTTLLEFLR...SNTCFKSVKLSCGE.......GG....CGACIVILSK.................YDPVLDQVEEYS....................INSCLTLLC +ALDO1_ARATH/23-95 FAINGQRFELELSSIDPSTTLVDFLR...NKTPFKSVKLGCGE.......GG....CGACVVLLSK.................YDPLLEKVDEFT....................ISSCLTLLC +O30328_ACEEU/4-63 FRLNGR..EVTV.DVPGDTPLLWVIR...DEVGLTGTKFGCGI.......GM....CGACTIHIG.....................GR......A....................TRSCVTPVS +IORA_BREDI/4-64 FILNGQ..PVRVTEVPEDAPLLWVVR...EHLKLSGTKFGCGL.......GL....CGACTVHIN.....................GE......A....................ARSCITPLS +XDH_EMENI/39-108 FYLNGT..KVILDSVDPEITLLEYLR...G.IGLTGTKLGCAE.......GG....CGACTVVVS..........QIN.....PTTKKL....YHA..................SINACIAPLV +O61198_CAEEL/8-78 FNVNGK..DIKEENVDPELTLAYYLR...NKLGLRGTKLGCEE.......GV....CGSCTVVLGT.................WDDSLNKAVYSA....................VNACLVPLF +O17892_CAEEL/18-86 FYVNGK..RVEEKDVDPKMTLATYLR...DKLKLTGTKIGCNE.......GG....CGACTIMISH.................IENGE..IKHFS....................ANSCLMPVC +XDH_DROSU/13-83 FFVNGK..KVTDTNPDPECTLLTYLR...DKLRLCGTKLGCAE.......GG....CGACTVMISR.................MDRGQHKIRHLA....................VNACLTPVC +O17506_BOMMO/19-89 FYVNGK..KVIESSPDPEWTLLWYLR...KKLRLTGTKLGCAE.......GG....CGACTVMVSK.................YNRQENKIIHLA....................VNACLAPVC +Q17250_BOMMO/18-88 FFVNGK..KVLESNPDPEWTLLFYLR...KKLKLTGTKYGCGE.......GG....CGACTVMVSK.................YLKNEDRINHIA....................VNACLISVC +ADO_BOVIN/9-79 FYVNGR..KVTEKNVDPETMLLPYLR...KKLRLTGTKYGCGG.......GG....CGACTVMISR.................YNPITKKIRHYP....................ANACLTPIC +XDH_BOVIN/8-78 FFVNGK..KVVEKNADPETTLLAYLR...RKLGLRGTKLGCGE.......GG....CGACTVM............LSK.....YDRLQDKIIHFS....................ANACLAPIC +#=GR XDH_BOVIN/8-78 SS EEE---..EEEETT--TT-BHHHHHH...HT------------.......--....----EEE............EEE.....EETTTTEEEEEE....................EETTT-BGG +MOP_DESGI/6-65 ITVNGI..EQNL.FVDAEALLSDVLR...QQLGLTGVKVGCEQ.......GQ....CGACSVILD.....................GK......V....................VRACVTKMK +#=GR MOP_DESGI/6-65 SS EEE---..EEEE.EE-TTSBHHHHHH...HT------------.......--....----EEEE-.....................--......E....................EEGGG-BGG +O53669_MYCTU/13-78 DESCGELREFTVEVNEGEVVLDVILRLQQTQTPDLAVRWNCKA.......GK....CGSCSAEIN.....................GKPR..........................LMCMTRMS +O29566_ARCFU/5-80 TFL.PS..GKRAEVDEGKTILSAAQE...I.GEGIRS..LCGG.......KG...SCGKCL..VVVR........KGDVEILSEEAHEKFVRE..K.................GYYLACQTAVK +O30225_ARCFU/5-84 TFE.PV..GKKVE.DEPDTILEIARR...N.GVLIRS..DCGG.......KG...VCGKCK..VVVVDY......RGSLSDITDHERKHLIEEEISK................GYRLACQARVE +NQRF_CHLTR/46-122 NND.DS..LTKTV.DSGKTLLSSLLD...S.GIAIPS..PCGG.......KA...ACKQCK..VRIT.........KNADEPLETDRSTFSKQQLEQ................GWRLSCQTKVQ +NQRF_HAEIN/43-119 NDD.PE..KAITL.PAGGKLLGALAS...K.GIFVSS..ACGG.......GG...SCGQCI..VKVK.........NGGGEILPTELSHINKREAKE................GYRLACQVNVK +NQRF_VIBAL/39-115 NDD.PS..LAIVT.QPGGKLLSALAG...A.GVFVSS..ACGG.......GG...SCGQCR..VKVK.........SGGGDILPTELDHITKGEARE................GERLACQVAMK +O84062_CHLTR/8-83 ADD......ENQEFHLEDGSSIAEV......CEHSGVPLACT........EG...VCGTCVIEVLEGA........DNLSDFSEAEYDFLGDPEDS.................NERLACQCCIK +Q9Z8H9_CHLPN/8-83 SDD......EQQEFELEDNSEIAEP......CESMGIPFACT........EG...VCGTCVIEVLEGR........ENLSEFTEPEYDFLGEPEDS.................NERLACQCRIK +CSMJ_CHLTE/5-82 IND......KPCNAKVGDLLLNTAK......LNKAHIGYICGG.......NG...ICQSCFVYVLEGA........ECLSEPGEDEKAFISDKLFAE................GGRLACRTTIV +CSMI_CHLTE/5-82 IND......KTASSSVGQTIGKAAR......LNHAHVGYVCGG.......HG...LCQACYITVQEGA........DCLAPLTDVEKAFLSPRQIAA................GGRIACQATIA +FER_TRIVA/13-90 AVKGGVKKQLKFEDDQTLFTVLTEAG.......LMSADDTCQG.......NK...ACGKCICKHVSGKV......A.A..E..DDEKEFLEDQPAN..................ARLACAITLS +#=GR FER_TRIVA/13-90 SS EE----EEEE---TTEEHHHHHHT--.......----TTS---.......--...-----EEEEEE---......-.-..-..HHHHHHCTTS-TT..................EEEGGG-EE- +P73774_SYNY3/7-88 LICLPD..NRLLEIDSNETILDALLK..G....DIAHISVCGG.......KA...NCSTCRIMVLDGIK.....NCSPPTSIEQALAKKLDFPFHV..................R.LACQTKLS +FER_BUCAP/10-92 KLLLPK..GGCFECKEGETILNVALK...N.NIKLEHA..CEK.......SC...ACSTCH..CIIRKG......FLSLSGWSEKEEDVLDKAWGLE...............STSRLSCQAIIG +O69222_AZOVI/11-93 EVHCPE..GRVVEAETGESILEAALR...N.DIEIEHA..CEM.......SC...ACTTCH..VIVRDG......FDSLEPSDELEDDMLDKAWGLE...............PESRLSCQARVG +FER_HAEIN/10-92 EDFCPE..GMVVDAATGDN.LLEVAH...N.A.GVEIHHACDG.......SC...ACTTCHVIVREG........FDSLNETSDQEEDMLDKAWGLE...............MDSRLSCQCVVG +FER_PSEAE/10-92 ADHCPE..GAVFEAKPGET.ILDAAL...R.N.GIEIEHACEK.......SC...ACTTCHVIVREG........LDSMEPSDELEDDMLDKAWGLE...............PDSRLSCQAVVA +ADRX_YEAST/67-149 LKD.GS..QKTYEVCEGETILDIAQG...H.NLDMEG..ACGG.......SC...ACSTCH.VIVDPDY......YDALPEPEDDENDMLDLAYGLT...............ETSRLGCQIKMS +ADX_PIG/71-155 NRD.GK..TLTTQGKVGDSLLDVVIE...N.NLDIDGFGACEG.......TL...ACSTCH.LIFEDHI......FEKLEAITDEENDMLDLAYGLT...............DRSRLGCQICLT +FER2_RICPR/11-93 IND.EE..ERTVEAPIGLSILEIAHS...N.DLDLEG..ACEG.......SL...ACATCH.VMLEEEF......YNKLKKPTEAEEDMLDLAFGLT...............DTSRLGCQIILT +O49551_ARATH/44-127 DKD.GE..EIHIKVPVGMNILEAAHE...N.DIELEG..ACEG.......SL...ACSTCHVIVMDTKY......YNKLEEPTDEENDMLDLAFGLT...............ATSRLGCQVIAK +ETP1_SCHPO/525-592 TPE.GR..EIMIE....GN......E...E.G.......ACEG.......SV...ACSTCHVIVDPEHY.....ELLD..PPEEDEEDMLDLAFGLE...............ETSRLGCQVLLR +#=GR ETP1_SCHPO/525-592 SS ---.--..EEEE-....--......-...-.-.......----.......--...--STT-EEE-HHHH.....HHS-..---HHHHHHHCTB----...............TTEE-----B-- +O07876_SPHSX/8-91 AAD.GR..EIETNVDIGTDLMHAGLY...N.SVPGLLG.ECSG.......GL...ACATCR.VHVPAEW......QGVLPAALPAEAELLGFCEESP...............PEARLSCQIKMT +Q9ZAM5_SPHSX/8-91 SED.GS..ELETTVDVGVDLMHAGLY...N.SIPGILG.ECSG.......GL...ACATCR.VRVPVEW......QSILPPAFPSEAELLGFCDEAP...............PEARLSCQIKMT +FER2_CAUCR/8-91 QHD.GA..EQVIDVKPGLTVMEGAVK...N.NVPGIDA.DCGG.......AC...ACATCH.VYVDEAW......LDKTGDKSAMEESMLDFAENVE...............PNSRLSCQIKVS +FER6_RHOCA/7-91 EHN.GT..RHEVEAKPGLTVMEAARD...N.GVPGIDA.DCGG.......AC...ACSTCH.AYVDPAW......VDKLPKALPTETDMIDFAYEPNP..............ATSRLTCQIKVT +#=GR FER6_RHOCA/7-91 SS ---.--..EEEEE-----BHHHHHHT...-.-------.----.......--...SS-TTE.EEE-HHH......HTTS----HHHHHHHTTSSS--T..............TTEEEGGG-B-- +P74447_SYNY3/31-113 IKLDPIDLKVAIETNDNLLSGLLGQD........LRIMKECGG.......RG...MCATCHVYITAGMES...LSPLNRREQRTLEVITTHNRYS...................R.LACQARVL +P73171_SYNY3/7-85 SFPQTKFLPLSLEFNACLAEYLTPDN........SPILFGCRT.......GL....CGTCLVKVVGEIL......SPEAEEREILAILAPDDVQA...................R.LACQIKLT +FER1_AQUAE/3-83 VIINGK....EFDIPKGVRFGELSHE.....IEKAGIEFGCTD.......GQ....CGVCVARVIKGMECL..NEPSEEEEETLWRVGAVDEDQR.....................LTCQLVIE +FER4_RHOCA/7-86 TFTDVS...ITVNVPTGTRIIEMSEK......VGSGITYGCRE.......GE....CGTCMTHILEGSE.....NLSEPTALEMRVLEENLGGKD...................DRLACQCRVL +P74283_SYNY3/5-88 FVKEQK....DIVVAQGANLREKALQNGVDIYTLKGKLMNCGG......YGQ....CGTCIVEITAGME.....NLSPKTDFENRVLRKKPDNFR.....................LACQTLVN +PUTX_PSEPU/8-92 SHD.GT..RRELDVADGVS.LMQAAV...S.NGIYDIVGDCGG.......SA...SCATCHVYVN................EAFTDKVP.....AANEREIGMLECVTAELKPNSRLCCQIIMT +#=GR PUTX_PSEPU/8-92 SS E--.--..EEEEE-----B.HHHHHH...H.---TTG------.......--...SSSTTEEEE-................TTTGTTS-.....---TTT---GGGSSS---TTEEEGGG-B-- +TERPB_PSESP/8-92 DEQSGE...YAVDAQDGQS.LMEVAT...Q.NGVPGIVAECGG.......SC...VCATCRIEIEDAWV......E.......IVGEANPDENDLLQSTGE........PMTAGTRLSCQVFID +P95277_MYCTU/9-84 GYSDGT..HKTMPVRCDQT.VLDAAE.....EHGVAIVNECQS.......GI....CGTCVATCTAGRYQ....MG.R...TEGLSDVERAARKI.....................LTCQTFVT +O05933_PSEPU/11-88 NFSDGV..SRSFDVEAGTS.ILDAAI.....ESEIPLLYQCRS.......GS....CSTCIAQLTEGEAH....TRAG..ASSTLLASEYASGQR.....................LLCLCQAQ +DESET_MYCTU/303-373 FARSGK....SVAADAATS.LMDAGE.....GAGVQLPFGCRM.......GI....CQSCVVDLVEGHV......R.D.....LRTGQRHEPGTR....................VQTCVSAAS +O23344_ARATH/57-131 VEHDGK..TTELEVEPDETILSKALD...S...GLDVPYDCNL.......GV....CMTCPAKLVTGTV.....DQSG....GMLSDDVVERGYT.....................LLCASYPT +P74159_SYNY3/11-86 DRQNEK..DYSVIVSDDRYILHQAED...Q...GFELPFSCRN.......GA....CTACAVRVISGQIH....QP....EAMGLSPDLQRQGYA.....................LLCVSYAQ +FER2_SYNP6/8-83 VIYQGQ..SQTFTADSDQS.VLDSAQ...A.A.GVDLPASCLT.......GV....CTTCAARILSGEV.....DQPD...AMGVGPEPAKQGYT.....................LLCVAYPR +P73388_SYNY3/9-84 IQHQGQ..TYTISVPEDKT.VLQAAD...D.E.GIQLPTSCGA.......GV....CTTCAALITEGTA.....EQAD...GMGVSAELQAEGYA.....................LLCVAYPR +FER1_HALMA/35-108 DEDYGS.....LEVNEGEY.ILEAAE...A.Q.GYDWPFSCRA.......GA....CANCAAIVLEGDI.....DM..D.MQQILSDEEVEDKNV....................RLTCIGSPD +P74449_SYNY3/11-88 NPATGS..DVTIEVAEDEL.ILEAAE...N.Q.GLDLPYSCRA.......AS....CVACAGRLLEGTVE...HTDKG...SDFLKPEELAAGCV.....................LLCAAYAT +FER2_NOSMU/10-85 NAAEGL..DETIEVPDDEY.ILDAAE...E.A.GLDLPFSCRS.......GS....CSSCNGILKKGTV.....DQSD...QNFLDDDQIAAGNV.....................LTCVAYPT +FER2_APHSA/10-86 NEEEGI..NAILEVADDQT.ILDAGE...E.A.GLDLPSSCRA.......GS....CSTCAGKLVSGAA.......PNQDDQAFLDDDQLAAGWV.....................MTCVAYPT +FER1_CYAPA/10-85 CEEQGL..DTTIECPDDEY.ILDAAE...E.Q.GIDLPYSCRA.......GA....CSTCAGKVVEGTV.....DQSD...QSFLDDAQLAAGYV.....................LTCVAYPS +FER_PORPU/10-85 SEDEGI..DVTFDCSEDTY.ILDAAE...E.A.GIELPYSCRA.......GA....CSTCAGKVTEGSV.....DQSD...QSFLDDEQLLKGYV.....................LTCIAYPE +FER_ODOSI/10-85 SEEHDI..DATIDCNDDVF.LLDAAE...E.Q.GIELPYSCRA.......GA....CSTCAGKVTEGDI.....DQSE...QTFLDDDQVGAGFV.....................LTCIAYPK +FER_BUMFI/9-84 NEEKNI..NAVIKCPDDQF.ILDAAE...E.Q.GIELPYSCRA.......GA....CSTCAGKVLSGTI.....DQSE...QSFLDDDQMGAGFL.....................LTCVAYPT +FER3_CYACA/9-84 NKDQGI..DETIECPDDQY.ILDAAE...E.Q.GLDLPYSCRA.......GA....CSTCAGKLLEGEV.....DQSD...QSFLDDDQVKAGFV.....................LTCVAYPT +FER2_CYACA/8-83 NQKEGV..DVTINCPGDQY.ILDAAE...E.Q.GVDLPYSCRA.......GA....CSTCAGKLVKGSV.....DQSD...QSFLDEEQINNGFI.....................LTCVAYPT +FER_BRYMA/8-83 KLDDGS..EAVIDCDEDSF.ILDVAE...E.E.GIDIPFSCRS.......GS....CSTCAGKIEGGTV.....DQSE...QTFLDDDQMEEGYV.....................LTCVAYPT +FER_APHSA/9-83 KTPDGD..NVIT.VPDDEY.ILDVAE...E.E.GLDLPYSCRA.......GA....CSTCAGKLVSG........PAPDEDQSFLDDDQIQAGYI.....................LTCVAYPT +FER_THEVL/9-84 VRPDGS..ETTIDVPEDEY.ILDVAE...E.Q.GLDLPFSCRA.......GA....CSTCAGKLLEGEV.....DQSD...QSFLDDDQIEKGFV.....................LTCVAYPR +FER_PERBI/6-80 DTPDGK...KSFECPGDSY.ILDKAE...E.E.GLELPYSCRA.......GS....CSSCAGKVLTGSI.....DQSD...QAFLDDDQGGDGYC.....................LTCVTYPT +FER3_RAPSA/8-82 ITPEGE...QEVECDDDVY.VLDAAE...E.A.GIDLPYSCRA.......GS....CSSCAGKVVSGSV.....DQSD...QSFLDDDQIAEGFV.....................LTCAAYPT +FER1_SPIOL/58-132 VTPTGN...VEFQCPDDVY.ILDAAE...E.E.GIDLPYSCRA.......GS....CSSCAGKLKTGSL.....NQDD...QSFLDDDQIDEGWV.....................LTCAAYPV +FER_SILPR/57-131 TKESGT...VTFDCPDDVY.VLDQAE...E.E.GIDLPYSCRA.......GS....CSSCAGKVVAGSV.....DQSD...QSFLDDDQIEAGWV.....................LTCAAYPS +FER_WHEAT/54-128 VTPEGE...VELEVPDDVY.ILDQAE...E.E.GIDLPYSCRA.......GS....CSSCAGKLVSGEI.....DQSD...QSFLDDDQMEAGWV.....................LTCHAYPK +FER_SAMNI/8-82 ITPDGP...QEFECPDDVY.ILEHAE...E.L.GIDIPYSCRA.......GS....CSSCAGKLVAGSV.....DQSD...QSFLDDEQIEEGWV.....................LTCVAYPK +FERA_ALOMA/8-82 VTPQGQ...QEFDCPDDVY.ILDQAE...E.E.GIDLPYSCRA.......GS....CSSCAGKVKQGEV.....DQSD...GSFLDDEQMEQGWV.....................LTCVAFPT +FER_ARCLA/8-82 ITPEGK...QEFEVPDDVY.ILDHAA...E.E.VGDLPYSCRA.......GS....CSSCAGKVTAGSV.....DQSD...GSYLDDDQMEAGWV.....................LTCVAYPT +FER_DATST/8-82 VTPDGP...VEFNCPDDVY.ILDQAE...E.E.GHDLPYSCRA.......GS....CSSCAGKVTAGTV.....DQSD...GNYLDDDQMADGFV.....................LTCVAYPQ +FER_PALPL/9-83 STPGGV...EEIEGDETTY.VLDSAE...D.Q.GIDLPYSCRA.......GA....CSTCAGIVELGTV.....DQSD...QSFLDDDQLNDSFV.....................LTCVAYPT +FER_EUGVI/8-82 INPDGE..VTI.ECGEDQY.ILDAAE...D.A.GIDLPYSCRA.......GA....CSSCTGIVKEGTV.....DQSD...QSFLDDDQMAKGFC.....................LTCTTYPT +FER_CHLFU/6-80 KTPSGE...ETIECPEDTY.ILDAAE...E.A.GLDLPYSCRA.......GA....CSSCAGKVESGEV.....DQSD...QSFLDDAQMGKGFV.....................LTCVAYPT +FER_SYNY4/9-83 ITPDGE...NSIECSDDTY.ILDAAE...E.A.GLDLPYSCRA.......GA....CSTCAGKITAGSV.....DQSD...QSFLDDDQIEAGYV.....................LTCVAYPT +FER1_PHYAM/8-82 VTPSGT...QTIDCPDDTY.VLDAAE...E.A.GLDLPYSCRA.......GS....CSSCTGKVTAGTV.....DQED...QSFLDDDQIEAGFV.....................LTCVAFPK +FER2_PHYAM/9-83 VTPSGT...NTITCPADTY.VLDAAE...E.S.GLDLPYSCRA.......GA....CSSCAGKVTAGAV.....NQED...GSFLEEEQMEAGWV.....................LTCVAYPT +FER2_SPIOL/8-82 VTPSGS...QVIECGDDEY.ILDAAE...E.K.GMDLPYSCRA.......GA....CSSCAGKVTSGSV.....DQSD...QSFLEDGQMEEGWV.....................LTCIAYPT +FER_PHYPA/57-132 DGETGA..ENVXECSDEEY.XLDAAE...R.A.GMDLPYSCRA.......GA....CSSCAGIIKAGEV.....DQSD...QSFLDDSQIDDGFV.....................LTCVAYPA +FER_MARPO/7-81 NTPTGQ...SVIDVEDDEY.ILDAAE...E.A.GLSLPYSCRA.......GA....CSSCAGKVTAGEV.....DQSD...ESFLDDDQMDEGYV.....................LTCIAYPT +#=GC SS_cons EEESS-EEEEEEEEEETTCBHHHHHH...HTT-TTTGTTSS--TT..S..--...SSSTTEEEEEEHCEE....EHCCS..TTHHHHHHHTTSSET-TTT---GGGSSS---TTEEECCCSBGG +#=GC seq_cons hphsup..thphpsssspp.lLcshc...p.t.slslshuCps.......Gs....CusCtsplhtu.................hpspphttt.h.....................LuCtshsp +// diff --git a/src/jalview/io/AppletFormatAdapter.java b/src/jalview/io/AppletFormatAdapter.java index f391a54..67d50ee 100755 --- a/src/jalview/io/AppletFormatAdapter.java +++ b/src/jalview/io/AppletFormatAdapter.java @@ -506,13 +506,6 @@ public class AppletFormatAdapter System.out.println("Reading file: " + f); AppletFormatAdapter afa = new AppletFormatAdapter(); String fName = f.getName(); - String extension = fName.substring(fName.lastIndexOf(".") + 1, - fName.length()); - if (extension.equals("stk") || extension.equals("sto")) - { - afa.test(f); - } - else { Runtime r = Runtime.getRuntime(); System.gc(); @@ -563,199 +556,6 @@ public class AppletFormatAdapter } } - private void test(File f) - { - System.out.println("Reading file: " + f); - String ff = f.getPath(); - try - { - Alignment al = readFile(ff, FILE, - new IdentifyFile().Identify(ff, FILE)); - for (int i = 0; i < al.getSequencesArray().length; ++i) - { - al.getSequenceAt(i).setDatasetSequence(al.getSequenceAt(i)); - } - AlignFile stFile = new StockholmFile(al); - stFile.setSeqs(al.getSequencesArray()); - - String stockholmoutput = stFile.print(); - Alignment al_input = readFile(stockholmoutput, - AppletFormatAdapter.PASTE, "STH"); - if (al != null && al_input != null) - { - System.out.println("Alignment contains: " + al.getHeight() - + " and " + al_input.getHeight() + " sequences; " - + al.getWidth() + " and " + al_input.getWidth() - + " columns."); - AlignmentAnnotation[] aa_new = al_input.getAlignmentAnnotation(); - AlignmentAnnotation[] aa_original = al.getAlignmentAnnotation(); - - // check Alignment annotation - if (aa_new != null && aa_original != null) - { - System.out.println("Alignment contains: " + aa_new.length - + " and " + aa_original.length - + " alignment annotation(s)"); - for (int i = 0; i < aa_original.length; i++) - { - if (!equalss(aa_original[i], aa_new[i])) - System.out.println("Different alignment annotation"); - } - } - - // check sequences, annotation and features - SequenceI[] seq_original = new SequenceI[al.getSequencesArray().length]; - seq_original = al.getSequencesArray(); - SequenceI[] seq_new = new SequenceI[al_input.getSequencesArray().length]; - seq_new = al_input.getSequencesArray(); - SequenceFeature[] sequenceFeatures_original, sequenceFeatures_new; - AlignmentAnnotation annot_original, annot_new; - // - for (int i = 0; i < al.getSequencesArray().length; i++) - { - String name = seq_original[i].getName(); - int start = seq_original[i].getStart(); - int end = seq_original[i].getEnd(); - System.out.println("Check sequence: " + name + "/" + start + "-" - + end); - - // search equal sequence - for (int in = 0; in < al_input.getSequencesArray().length; in++) - { - if (name.equals(seq_new[in].getName()) - && start == seq_new[in].getStart() - && end == seq_new[in].getEnd()) - { - String ss_original = seq_original[i].getSequenceAsString(); - String ss_new = seq_new[in].getSequenceAsString(); - if (!ss_original.equals(ss_new)) - { - System.out.println("The sequences " + name + "/" + start - + "-" + end + " are not equal"); - } - - // compare sequence features - if (seq_original[i].getSequenceFeatures() != null - && seq_new[in].getSequenceFeatures() != null) - { - System.out.println("There are feature!!!"); - sequenceFeatures_original = new SequenceFeature[seq_original[i] - .getSequenceFeatures().length]; - sequenceFeatures_original = seq_original[i] - .getSequenceFeatures(); - sequenceFeatures_new = new SequenceFeature[seq_new[in] - .getSequenceFeatures().length]; - sequenceFeatures_new = seq_new[in].getSequenceFeatures(); - - if (seq_original[i].getSequenceFeatures().length == seq_new[in] - .getSequenceFeatures().length) - { - for (int feat = 0; feat < seq_original[i] - .getSequenceFeatures().length; feat++) - { - if (!sequenceFeatures_original[feat] - .equals(sequenceFeatures_new[feat])) - { - System.out.println("Different features"); - break; - } - } - } - else - { - System.out.println("different number of features"); - } - } - else if (seq_original[i].getSequenceFeatures() == null - && seq_new[in].getSequenceFeatures() == null) - { - System.out.println("No sequence features"); - } - else if (seq_original[i].getSequenceFeatures() != null - && seq_new[in].getSequenceFeatures() == null) - { - System.out - .println("Coudn't compare sequence features new one"); - } - // compare alignment annotation - if (al.getSequenceAt(i).getAnnotation() != null - && al_input.getSequenceAt(in).getAnnotation() != null) - { - for (int j = 0; j < al.getSequenceAt(i).getAnnotation().length; j++) - { - if (al.getSequenceAt(i).getAnnotation()[j] != null - && al_input.getSequenceAt(in).getAnnotation()[j] != null) - { - annot_original = al.getSequenceAt(i).getAnnotation()[j]; - annot_new = al_input.getSequenceAt(in).getAnnotation()[j]; - if (!equalss(annot_original, annot_new)) - System.out.println("Different annotation"); - } - } - } - else if (al.getSequenceAt(i).getAnnotation() == null - && al_input.getSequenceAt(in).getAnnotation() == null) - { - System.out.println("No annotations"); - } - else if (al.getSequenceAt(i).getAnnotation() != null - && al_input.getSequenceAt(in).getAnnotation() == null) - { - System.out.println("Coudn't compare annotations new one"); - } - break; - } - } - } - } - else - { - System.out.println("Couldn't read alignment"); - } - } catch (Exception e) - { - System.err.println("Couln't format the alignment for output file."); - e.printStackTrace(System.err); - } - } - - /* - * compare annotations - */ - private boolean equalss(AlignmentAnnotation annot_or, - AlignmentAnnotation annot_new) - { - if (annot_or.annotations.length != annot_new.annotations.length) - { - return false; - } - for (int i = 0; i < annot_or.annotations.length; i++) - { - if (annot_or.annotations[i] != null - && annot_new.annotations[i] != null) - { - if (!annot_or.annotations[i].displayCharacter - .equals(annot_new.annotations[i].displayCharacter) - && annot_or.annotations[i].secondaryStructure != annot_new.annotations[i].secondaryStructure - && !annot_or.annotations[i].description - .equals(annot_new.annotations[i].description)) - { - return false; - } - } - else if (annot_or.annotations[i] == null - && annot_new.annotations[i] == null) - { - continue; - } - else - { - return false; - } - } - return true; - } - /** * try to discover how to access the given file as a valid datasource that * will be identified as the given type. @@ -926,4 +726,5 @@ public class AppletFormatAdapter } return null; } + } diff --git a/test/jalview/io/StockholmFileTest.java b/test/jalview/io/StockholmFileTest.java new file mode 100644 index 0000000..cac1a88 --- /dev/null +++ b/test/jalview/io/StockholmFileTest.java @@ -0,0 +1,220 @@ +package jalview.io; + +import static org.junit.Assert.*; +import jalview.datamodel.Alignment; +import jalview.datamodel.AlignmentAnnotation; +import jalview.datamodel.AlignmentI; +import jalview.datamodel.SequenceFeature; +import jalview.datamodel.SequenceI; + +import java.io.File; +import java.io.IOException; +import java.io.InputStream; + +import org.junit.Test; + +public class StockholmFileTest +{ + + public static void main(String argv[]) + { + try { + new StockholmFileTest().pfamFileIO(); + + } catch (Exception x) + { + x.printStackTrace(); + } + } + static String PfamFile = "examples/PF00111_seed.stk"; + + @Test + public void pfamFileIO() throws Exception + { + test(new File(PfamFile)); + AppletFormatAdapter af = new AppletFormatAdapter(); + AlignmentI al = af.readFile(PfamFile, af.FILE, new IdentifyFile().Identify(PfamFile, af.FILE)); + int numpdb=0; + for (SequenceI sq:al.getSequences()) + { + if (sq.getPDBId()!=null) + { + numpdb+=sq.getPDBId().size(); + } + } + assertTrue("PF00111 seed alignment has at least 1 PDB file, but the reader found none.",numpdb>0); + } + + private void test(File f) + { + System.out.println("Reading file: " + f); + String ff = f.getPath(); + try + { + Alignment al = new AppletFormatAdapter().readFile(ff, AppletFormatAdapter.FILE, + new IdentifyFile().Identify(ff, AppletFormatAdapter.FILE)); + + for (int i = 0; i < al.getSequencesArray().length; ++i) + { + al.getSequenceAt(i).setDatasetSequence(al.getSequenceAt(i)); + } + AlignFile stFile = new StockholmFile(al); + stFile.setSeqs(al.getSequencesArray()); + + String stockholmoutput = stFile.print(); + Alignment al_input = new AppletFormatAdapter().readFile(stockholmoutput, + AppletFormatAdapter.PASTE, "STH"); + if (al != null && al_input != null) + { + System.out.println("Alignment contains: " + al.getHeight() + + " and " + al_input.getHeight() + " sequences; " + + al.getWidth() + " and " + al_input.getWidth() + + " columns."); + AlignmentAnnotation[] aa_new = al_input.getAlignmentAnnotation(); + AlignmentAnnotation[] aa_original = al.getAlignmentAnnotation(); + + // check Alignment annotation + if (aa_new != null && aa_original != null) + { + System.out.println("Alignment contains: " + aa_new.length + + " and " + aa_original.length + + " alignment annotation(s)"); + for (int i = 0; i < aa_original.length; i++) + { + assertTrue("Different alignment annotation",equalss(aa_original[i], aa_new[i])); + + } + } + + // check sequences, annotation and features + SequenceI[] seq_original = new SequenceI[al.getSequencesArray().length]; + seq_original = al.getSequencesArray(); + SequenceI[] seq_new = new SequenceI[al_input.getSequencesArray().length]; + seq_new = al_input.getSequencesArray(); + SequenceFeature[] sequenceFeatures_original, sequenceFeatures_new; + AlignmentAnnotation annot_original, annot_new; + // + for (int i = 0; i < al.getSequencesArray().length; i++) + { + String name = seq_original[i].getName(); + int start = seq_original[i].getStart(); + int end = seq_original[i].getEnd(); + System.out.println("Check sequence: " + name + "/" + start + "-" + + end); + + // search equal sequence + for (int in = 0; in < al_input.getSequencesArray().length; in++) + { + if (name.equals(seq_new[in].getName()) + && start == seq_new[in].getStart() + && end == seq_new[in].getEnd()) + { + String ss_original = seq_original[i].getSequenceAsString(); + String ss_new = seq_new[in].getSequenceAsString(); + assertTrue("The sequences " + name + "/" + start + + "-" + end + " are not equal", ss_original.equals(ss_new)); + + assertTrue("Sequence Features were not equivalent", (seq_original[i].getSequenceFeatures()==null && seq_new[in].getSequenceFeatures()==null) || (seq_original[i].getSequenceFeatures()!=null && seq_new[in].getSequenceFeatures()!=null)); + // compare sequence features + if (seq_original[i].getSequenceFeatures() != null + && seq_new[in].getSequenceFeatures() != null) + { + System.out.println("There are feature!!!"); + sequenceFeatures_original = new SequenceFeature[seq_original[i] + .getSequenceFeatures().length]; + sequenceFeatures_original = seq_original[i] + .getSequenceFeatures(); + sequenceFeatures_new = new SequenceFeature[seq_new[in] + .getSequenceFeatures().length]; + sequenceFeatures_new = seq_new[in].getSequenceFeatures(); + + assertTrue("different number of features", seq_original[i].getSequenceFeatures().length == seq_new[in] + .getSequenceFeatures().length); + + for (int feat = 0; feat < seq_original[i] + .getSequenceFeatures().length; feat++) + { + assertTrue("Different features",sequenceFeatures_original[feat] + .equals(sequenceFeatures_new[feat])); + } + } + + // compare alignment annotation + if (al.getSequenceAt(i).getAnnotation() != null + && al_input.getSequenceAt(in).getAnnotation() != null) + { + for (int j = 0; j < al.getSequenceAt(i).getAnnotation().length; j++) + { + if (al.getSequenceAt(i).getAnnotation()[j] != null + && al_input.getSequenceAt(in).getAnnotation()[j] != null) + { + annot_original = al.getSequenceAt(i).getAnnotation()[j]; + annot_new = al_input.getSequenceAt(in).getAnnotation()[j]; + assertTrue("Different annotation", equalss(annot_original, annot_new)); + } + } + } + else if (al.getSequenceAt(i).getAnnotation() == null + && al_input.getSequenceAt(in).getAnnotation() == null) + { + System.out.println("No annotations"); + } + else if (al.getSequenceAt(i).getAnnotation() != null + && al_input.getSequenceAt(in).getAnnotation() == null) + { + assertTrue("Annotations differed between sequences ("+al.getSequenceAt(i).getName()+") and ("+al_input.getSequenceAt(i).getName()+")", false); + } + break; + } + } + } + } + else + { + assertTrue("Couldn't read alignment", false); + } + } catch (Exception e) + { + e.printStackTrace(); + assertTrue("Couln't format the alignment for output file.", false); + } + } + + /* + * compare annotations + */ + private boolean equalss(AlignmentAnnotation annot_or, + AlignmentAnnotation annot_new) + { + if (annot_or.annotations.length != annot_new.annotations.length) + { + return false; + } + for (int i = 0; i < annot_or.annotations.length; i++) + { + if (annot_or.annotations[i] != null + && annot_new.annotations[i] != null) + { + // Jim's comment - shouldn't the conditional here be using || not && for all these clauses ? + if (!annot_or.annotations[i].displayCharacter + .equals(annot_new.annotations[i].displayCharacter) + && annot_or.annotations[i].secondaryStructure != annot_new.annotations[i].secondaryStructure + && !annot_or.annotations[i].description + .equals(annot_new.annotations[i].description)) + { + return false; + } + } + else if (annot_or.annotations[i] == null + && annot_new.annotations[i] == null) + { + continue; + } + else + { + return false; + } + } + return true; + } +} -- 1.7.10.2