--- /dev/null
+# 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
+//
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();
}
}
- 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.
}
return null;
}
+
}
--- /dev/null
+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;
+ }
+}
git://source.jalview.org / jalview.git / commitdiff