Query gi|254780346|ref|YP_003064759.1| riboflavin synthase subunit beta [Candidatus Liberibacter asiaticus str. psy62] Match_columns 149 No_of_seqs 114 out of 1909 Neff 5.8 Searched_HMMs 39220 Date Sun May 29 15:13:28 2011 Command /home/congqian_1/programs/hhpred/hhsearch -i 254780346.hhm -d /home/congqian_1/database/cdd/Cdd.hhm No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM 1 PRK00061 ribH riboflavin synth 100.0 0 0 344.7 18.2 144 1-148 8-154 (154) 2 PRK12419 riboflavin synthase s 100.0 0 0 340.7 17.6 141 4-148 9-155 (158) 3 pfam00885 DMRL_synthase 6,7-di 100.0 0 0 332.0 17.6 139 5-147 3-144 (144) 4 COG0054 RibH Riboflavin syntha 100.0 0 0 321.0 16.7 139 4-146 11-152 (152) 5 TIGR00114 lumazine-synth 6,7-d 100.0 0 0 317.8 14.3 138 6-143 1-147 (148) 6 KOG3243 consensus 100.0 2.4E-36 6.2E-41 245.9 13.2 136 5-144 17-156 (158) 7 PRK06455 riboflavin synthase; 98.2 7.7E-05 2E-09 51.0 13.0 130 5-147 1-135 (155) 8 COG1731 Archaeal riboflavin sy 97.8 0.00021 5.4E-09 48.3 8.8 129 5-143 1-131 (154) 9 TIGR01506 ribC_arch riboflavin 97.7 0.00015 3.9E-09 49.2 6.9 116 23-145 14-131 (152) 10 cd06284 PBP1_LacI_like_6 Ligan 96.7 0.029 7.3E-07 35.1 10.0 126 5-142 115-247 (267) 11 cd06288 PBP1_sucrose_transcrip 96.6 0.035 9E-07 34.6 9.9 126 5-142 116-249 (269) 12 cd06291 PBP1_Qymf_like Ligand 96.6 0.05 1.3E-06 33.6 10.3 126 5-142 112-244 (265) 13 cd06271 PBP1_AglR_RafR_like Li 96.2 0.062 1.6E-06 33.0 9.3 125 6-142 121-252 (268) 14 cd06270 PBP1_GalS_like Ligand 96.0 0.11 2.9E-06 31.4 9.6 122 6-142 117-248 (268) 15 cd06294 PBP1_ycjW_transcriptio 96.0 0.16 4E-06 30.5 10.2 126 5-142 122-254 (270) 16 cd01537 PBP1_Repressors_Sugar_ 95.9 0.14 3.7E-06 30.8 9.8 126 5-142 118-249 (264) 17 cd06296 PBP1_CatR_like Ligand- 95.8 0.11 2.8E-06 31.5 8.8 126 5-142 117-249 (270) 18 cd06293 PBP1_LacI_like_11 Liga 95.6 0.22 5.7E-06 29.6 9.8 126 5-142 116-248 (269) 19 PRK10703 DNA-binding transcrip 95.6 0.22 5.7E-06 29.6 9.6 123 5-142 178-310 (335) 20 cd06275 PBP1_PurR Ligand-bindi 95.5 0.16 4.1E-06 30.5 8.8 126 5-142 117-249 (269) 21 cd01545 PBP1_SalR Ligand-bindi 95.5 0.25 6.4E-06 29.3 9.9 123 5-142 118-250 (270) 22 cd06267 PBP1_LacI_sugar_bindin 95.4 0.23 5.8E-06 29.5 9.3 126 5-142 116-248 (264) 23 cd06290 PBP1_LacI_like_9 Ligan 95.3 0.15 3.8E-06 30.7 8.1 126 5-142 115-247 (265) 24 cd06281 PBP1_LacI_like_5 Ligan 95.3 0.29 7.3E-06 28.9 10.1 123 5-142 116-247 (269) 25 cd06286 PBP1_CcpB_like Ligand- 95.2 0.29 7.5E-06 28.9 9.7 123 5-142 114-244 (260) 26 PRK10014 DNA-binding transcrip 95.2 0.3 7.8E-06 28.8 10.5 128 5-142 182-323 (342) 27 cd06295 PBP1_CelR Ligand bindi 95.2 0.28 7.1E-06 29.0 9.1 126 5-142 125-257 (275) 28 PRK10423 transcriptional repre 95.1 0.33 8.3E-06 28.6 9.4 102 6-119 175-277 (327) 29 cd06285 PBP1_LacI_like_7 Ligan 94.9 0.23 5.8E-06 29.6 8.1 123 5-142 114-246 (265) 30 PRK11041 DNA-binding transcrip 94.4 0.5 1.3E-05 27.4 10.4 121 6-141 185-315 (341) 31 cd06325 PBP1_ABC_uncharacteriz 94.3 0.34 8.6E-06 28.5 7.8 116 5-142 131-250 (281) 32 cd01575 PBP1_GntR Ligand-bindi 93.9 0.61 1.6E-05 26.9 10.4 126 5-142 116-248 (268) 33 cd06279 PBP1_LacI_like_3 Ligan 93.8 0.64 1.6E-05 26.8 11.0 123 5-142 116-265 (283) 34 PRK10401 DNA-binding transcrip 93.5 0.72 1.8E-05 26.4 9.0 103 6-120 177-280 (346) 35 cd06287 PBP1_LacI_like_8 Ligan 93.4 0.74 1.9E-05 26.4 10.6 125 5-142 118-249 (269) 36 cd01536 PBP1_ABC_sugar_binding 93.4 0.74 1.9E-05 26.4 10.7 123 6-142 122-253 (267) 37 cd06289 PBP1_MalI_like Ligand- 93.4 0.75 1.9E-05 26.3 9.3 125 6-142 118-249 (268) 38 COG1609 PurR Transcriptional r 93.1 0.83 2.1E-05 26.1 10.3 126 5-142 175-308 (333) 39 PRK09526 lacI lac repressor; R 92.5 1 2.6E-05 25.5 9.2 125 5-142 181-311 (342) 40 cd06273 PBP1_GntR_like_1 This 92.5 1 2.6E-05 25.5 9.8 125 6-142 117-249 (268) 41 cd06272 PBP1_hexuronate_repres 92.4 1.1 2.7E-05 25.4 10.0 123 5-142 111-243 (261) 42 cd06310 PBP1_ABC_sugar_binding 92.4 1.1 2.7E-05 25.4 8.2 35 7-41 1-35 (273) 43 pfam00532 Peripla_BP_1 family. 92.2 1.1 2.8E-05 25.3 8.4 33 8-40 124-156 (281) 44 cd01543 PBP1_XylR Ligand-bindi 91.9 1.2 3E-05 25.1 11.1 122 6-142 110-243 (265) 45 cd06274 PBP1_FruR Ligand bindi 91.9 1.2 3E-05 25.1 8.8 124 5-142 116-249 (264) 46 cd06298 PBP1_CcpA_like Ligand- 91.7 1.2 3.2E-05 25.0 9.3 122 5-142 116-248 (268) 47 PRK10727 DNA-binding transcrip 91.7 1.2 3.2E-05 25.0 9.6 123 5-142 176-308 (342) 48 cd06299 PBP1_LacI_like_13 Liga 91.6 1.3 3.3E-05 24.9 9.6 121 5-142 116-246 (265) 49 cd06277 PBP1_LacI_like_1 Ligan 91.3 1.4 3.5E-05 24.7 9.7 124 5-142 118-248 (268) 50 cd06280 PBP1_LacI_like_4 Ligan 91.2 1.4 3.6E-05 24.7 10.0 121 6-142 116-243 (263) 51 cd06292 PBP1_LacI_like_10 Liga 91.0 1.5 3.7E-05 24.5 9.6 120 6-142 123-252 (273) 52 cd06278 PBP1_LacI_like_2 Ligan 90.8 1.5 3.9E-05 24.4 9.8 124 5-142 115-246 (266) 53 PRK10339 DNA-binding transcrip 90.7 1.6 4E-05 24.3 9.9 125 5-142 174-305 (327) 54 PRK13337 putative lipid kinase 90.6 1.6 4E-05 24.3 7.1 92 4-113 1-93 (305) 55 PRK11303 DNA-binding transcrip 90.6 1.6 4.1E-05 24.3 11.1 120 6-142 180-309 (330) 56 PRK10936 periplasmic sensory p 89.8 1.6 4.2E-05 24.2 6.7 64 6-71 46-109 (340) 57 pfam04392 ABC_sub_bind ABC tra 89.1 2.1 5.4E-05 23.5 10.6 116 5-142 130-249 (292) 58 TIGR01481 ccpA catabolite cont 89.0 1.9 4.8E-05 23.9 6.5 97 5-117 177-279 (332) 59 cd01574 PBP1_LacI Ligand-bindi 88.7 2.3 5.7E-05 23.4 9.6 122 5-142 116-245 (264) 60 cd06308 PBP1_sensor_kinase_lik 88.4 2.3 6E-05 23.3 11.4 127 5-142 122-255 (270) 61 COG1454 EutG Alcohol dehydroge 88.2 1.9 4.9E-05 23.8 6.1 62 5-73 29-94 (377) 62 cd06317 PBP1_ABC_sugar_binding 87.8 2.5 6.5E-05 23.1 10.8 124 5-142 125-259 (275) 63 cd06282 PBP1_GntR_like_2 Ligan 87.6 2.6 6.7E-05 23.0 9.8 123 5-142 116-247 (266) 64 cd03132 GATase1_catalase Type 87.2 0.85 2.2E-05 26.0 3.8 107 6-124 2-113 (142) 65 cd01544 PBP1_GalR Ligand-bindi 86.9 2.9 7.3E-05 22.7 10.4 124 6-142 113-250 (270) 66 cd01542 PBP1_TreR_like Ligand- 86.8 2.9 7.4E-05 22.7 10.2 121 5-142 114-244 (259) 67 PRK09423 gldA glycerol dehydro 86.3 3.1 7.9E-05 22.5 7.4 62 6-73 30-92 (366) 68 cd06306 PBP1_TorT-like TorT-li 85.6 3.4 8.6E-05 22.3 7.1 87 7-108 1-87 (268) 69 PRK09140 2-dehydro-3-deoxy-6-p 85.5 1.9 4.8E-05 23.9 4.8 106 5-122 10-124 (206) 70 cd06321 PBP1_ABC_sugar_binding 85.2 3.5 9E-05 22.2 11.2 124 6-142 122-254 (271) 71 cd06316 PBP1_ABC_sugar_binding 84.2 3.9 9.9E-05 21.9 9.1 63 7-72 1-63 (294) 72 cd06297 PBP1_LacI_like_12 Liga 83.2 4.3 0.00011 21.7 10.5 111 17-142 131-249 (269) 73 cd06283 PBP1_RegR_EndR_KdgR_li 82.4 4.6 0.00012 21.5 9.1 122 6-142 117-249 (267) 74 cd06305 PBP1_methylthioribose_ 82.2 4.7 0.00012 21.4 8.9 36 7-42 1-36 (273) 75 PRK13805 bifunctional acetalde 80.5 5.3 0.00014 21.1 5.6 62 5-73 482-547 (862) 76 PRK13055 putative lipid kinase 80.5 5.4 0.00014 21.1 8.9 89 4-113 1-94 (334) 77 cd01541 PBP1_AraR Ligand-bindi 80.4 5.4 0.00014 21.0 9.9 35 7-41 1-35 (273) 78 COG2984 ABC-type uncharacteriz 80.3 5.4 0.00014 21.0 8.4 116 6-142 160-278 (322) 79 PRK09701 D-allose transporter 80.2 5.5 0.00014 21.0 10.4 89 5-107 24-112 (311) 80 PRK05569 flavodoxin; Provision 79.3 5.5 0.00014 21.0 5.2 101 5-123 1-108 (141) 81 cd01539 PBP1_GGBP Periplasmic 79.2 5.9 0.00015 20.8 9.4 33 7-39 1-33 (303) 82 cd06314 PBP1_tmGBP Periplasmic 78.8 6.1 0.00015 20.7 11.1 123 5-142 120-251 (271) 83 PRK05568 flavodoxin; Provision 78.3 5.6 0.00014 20.9 5.1 38 5-44 1-39 (142) 84 cd06320 PBP1_allose_binding Pe 77.9 6.5 0.00016 20.6 11.8 63 7-71 1-63 (275) 85 PRK08104 consensus 77.4 3.5 8.8E-05 22.2 3.8 104 6-122 16-128 (212) 86 PRK07114 keto-hydroxyglutarate 77.3 3.1 7.9E-05 22.5 3.5 93 26-122 32-133 (223) 87 pfam00465 Fe-ADH Iron-containi 76.9 6.9 0.00018 20.4 6.3 61 6-73 23-87 (312) 88 PRK10310 galactitol-specific P 75.9 7.3 0.00019 20.2 6.3 84 4-122 1-88 (94) 89 cd06302 PBP1_LsrB_Quorum_Sensi 75.5 7.5 0.00019 20.2 10.2 123 6-142 124-257 (298) 90 PRK07580 Mg-protoporphyrin IX 73.8 4.3 0.00011 21.6 3.5 74 17-109 91-164 (230) 91 cd06323 PBP1_ribose_binding Pe 73.1 8.6 0.00022 19.8 11.4 28 7-34 123-150 (268) 92 PRK07053 glutamine amidotransf 72.9 8.7 0.00022 19.8 6.7 101 4-126 1-103 (235) 93 PRK13411 molecular chaperone D 72.6 2.8 7.3E-05 22.8 2.3 89 16-113 303-400 (655) 94 PRK06857 consensus 71.4 7.1 0.00018 20.3 4.2 88 27-122 29-125 (209) 95 PRK09492 treR trehalose repres 70.6 9.8 0.00025 19.4 7.3 65 5-73 62-126 (315) 96 PRK07455 keto-hydroxyglutarate 70.6 8.9 0.00023 19.7 4.5 102 7-121 15-125 (210) 97 cd06309 PBP1_YtfQ_like Peripla 70.4 9.9 0.00025 19.4 11.7 125 5-142 124-258 (273) 98 PRK06552 keto-hydroxyglutarate 70.2 9 0.00023 19.7 4.4 92 26-122 29-129 (209) 99 cd06319 PBP1_ABC_sugar_binding 70.1 10 0.00026 19.4 12.1 32 7-38 1-32 (277) 100 COG0655 WrbA Multimeric flavod 70.1 8.4 0.00022 19.8 4.3 40 7-46 2-42 (207) 101 PRK13410 molecular chaperone D 69.0 5.7 0.00014 20.9 3.2 89 16-113 304-400 (719) 102 PRK08904 consensus 68.6 9.9 0.00025 19.4 4.4 88 27-122 27-123 (207) 103 PRK06015 keto-hydroxyglutarate 67.7 10 0.00026 19.4 4.3 89 26-122 31-128 (212) 104 PRK00290 dnaK molecular chaper 65.9 4.4 0.00011 21.6 2.1 89 16-113 304-400 (631) 105 cd06315 PBP1_ABC_sugar_binding 65.6 12 0.00032 18.8 6.2 84 6-106 1-85 (280) 106 PRK10714 undecaprenyl phosphat 65.5 12 0.00032 18.8 5.2 46 4-49 4-55 (324) 107 PRK09860 putative alcohol dehy 65.3 13 0.00032 18.8 6.4 62 5-73 31-96 (383) 108 pfam01081 Aldolase KDPG and KH 63.8 13 0.00034 18.6 5.0 102 8-122 11-121 (196) 109 cd01538 PBP1_ABC_xylose_bindin 63.8 13 0.00034 18.6 9.1 35 7-41 1-35 (288) 110 PRK10624 L-1,2-propanediol oxi 63.8 13 0.00034 18.6 6.3 62 5-73 29-94 (381) 111 TIGR02350 prok_dnaK chaperone 63.0 4.9 0.00012 21.3 1.9 69 16-84 301-377 (598) 112 cd01540 PBP1_arabinose_binding 62.7 14 0.00036 18.5 6.8 34 7-40 1-34 (289) 113 cd06300 PBP1_ABC_sugar_binding 60.6 15 0.00039 18.2 8.9 123 6-142 126-256 (272) 114 cd06301 PBP1_rhizopine_binding 60.1 16 0.0004 18.2 11.4 122 7-142 125-256 (272) 115 PTZ00009 heat shock 70 kDa pro 59.3 8.4 0.00022 19.8 2.6 92 17-113 309-409 (657) 116 PRK05718 keto-hydroxyglutarate 58.9 16 0.00042 18.1 6.2 102 8-122 18-128 (212) 117 PTZ00186 heat shock 70 kDa pre 56.3 2.9 7.4E-05 22.7 -0.2 87 18-113 331-425 (657) 118 pfam10087 DUF2325 Uncharacteri 56.2 18 0.00046 17.8 7.0 85 21-122 9-94 (96) 119 PRK13243 glyoxylate reductase; 54.7 17 0.00044 17.9 3.6 53 4-73 1-53 (333) 120 pfam00012 HSP70 Hsp70 protein. 54.6 13 0.00034 18.6 3.0 93 12-113 294-399 (598) 121 TIGR02021 BchM-ChlM magnesium 54.2 20 0.0005 17.6 5.2 88 17-123 82-171 (224) 122 TIGR01991 HscA Fe-S protein as 53.9 14 0.00036 18.4 3.0 59 20-78 319-385 (628) 123 pfam02514 CobN-Mg_chel CobN/Ma 53.3 20 0.00052 17.5 7.6 106 5-123 68-175 (1064) 124 COG2039 Pcp Pyrrolidone-carbox 53.1 17 0.00043 18.0 3.3 41 83-123 138-179 (207) 125 cd06322 PBP1_ABC_sugar_binding 52.5 21 0.00053 17.4 10.4 117 6-142 122-251 (267) 126 cd06318 PBP1_ABC_sugar_binding 52.3 21 0.00054 17.4 8.6 32 7-38 1-32 (282) 127 PRK10653 D-ribose transporter 51.9 21 0.00054 17.3 11.6 37 5-41 26-62 (295) 128 PRK05183 hscA chaperone protei 51.6 11 0.00027 19.2 2.1 89 17-112 310-406 (621) 129 PRK01433 hscA chaperone protei 51.4 12 0.00031 18.8 2.4 88 17-113 287-380 (595) 130 CHL00094 dnaK heat shock prote 51.2 16 0.00041 18.1 2.9 88 17-113 305-400 (622) 131 pfam00781 DAGK_cat Diacylglyce 50.7 22 0.00057 17.2 6.0 82 25-122 18-99 (127) 132 PRK13059 putative lipid kinase 48.5 24 0.00061 17.0 8.8 87 5-112 1-90 (294) 133 PRK08309 short chain dehydroge 46.7 26 0.00065 16.8 4.4 88 7-96 48-164 (182) 134 COG1597 LCB5 Sphingosine kinas 44.9 27 0.0007 16.7 7.0 100 4-123 1-101 (301) 135 PRK06490 glutamine amidotransf 44.5 28 0.00071 16.6 5.9 100 4-125 10-109 (243) 136 cd06307 PBP1_uncharacterized_s 43.9 28 0.00072 16.6 8.3 30 7-36 1-30 (275) 137 PRK00861 putative lipid kinase 42.8 30 0.00075 16.5 5.8 90 4-114 1-91 (296) 138 COG0400 Predicted esterase [Ge 40.8 32 0.00081 16.3 3.4 49 3-51 144-192 (207) 139 PRK08782 consensus 40.8 32 0.00081 16.3 6.0 87 27-121 34-129 (219) 140 PRK11914 diacylglycerol kinase 39.1 34 0.00086 16.1 7.2 90 3-112 4-94 (304) 141 KOG3857 consensus 39.1 34 0.00086 16.1 4.9 67 6-83 71-141 (465) 142 COG0800 Eda 2-keto-3-deoxy-6-p 38.8 29 0.00074 16.5 2.7 87 27-121 30-125 (211) 143 PRK00286 xseA exodeoxyribonucl 38.6 34 0.00087 16.1 9.4 89 5-110 135-233 (443) 144 COG1879 RbsB ABC-type sugar tr 38.6 34 0.00088 16.1 8.6 65 6-72 34-98 (322) 145 cd06334 PBP1_ABC_ligand_bindin 38.2 35 0.00089 16.0 7.6 65 3-74 138-204 (351) 146 TIGR01182 eda 2-dehydro-3-deox 37.1 36 0.00092 15.9 6.1 86 28-121 26-121 (205) 147 PRK02155 ppnK inorganic polyph 36.3 37 0.00095 15.8 4.5 103 1-122 1-116 (291) 148 PRK13054 lipid kinase; Reviewe 35.9 38 0.00096 15.8 9.3 92 4-114 3-94 (299) 149 PRK03767 TrpR binding protein 35.7 38 0.00097 15.8 4.8 40 5-45 1-41 (200) 150 PRK10161 transcriptional regul 33.7 41 0.001 15.6 7.8 118 4-146 1-122 (229) 151 cd01391 Periplasmic_Binding_Pr 33.6 41 0.0011 15.6 9.4 31 6-37 125-155 (269) 152 PRK09739 hypothetical protein; 33.0 42 0.0011 15.5 4.7 39 4-42 2-41 (201) 153 cd03817 GT1_UGDG_like This fam 31.9 44 0.0011 15.4 3.3 36 7-42 1-38 (374) 154 COG3364 Zn-ribbon containing p 31.1 14 0.00036 18.5 0.1 47 5-51 1-76 (112) 155 PRK10307 predicted glycosyl tr 30.2 47 0.0012 15.2 3.6 37 7-43 2-40 (415) 156 TIGR00504 pyro_pdase pyrrolido 30.0 47 0.0012 15.2 5.0 62 80-141 138-204 (220) 157 PRK00012 gatA aspartyl/glutamy 29.4 49 0.0012 15.1 5.2 44 3-46 255-301 (485) 158 cd00452 KDPG_aldolase KDPG and 28.6 50 0.0013 15.0 6.9 104 6-122 5-117 (190) 159 cd01741 GATase1_1 Subgroup of 28.0 51 0.0013 15.0 6.1 97 7-125 1-100 (188) 160 PRK00453 rpsF 30S ribosomal pr 27.7 52 0.0013 14.9 3.5 48 8-55 7-54 (95) 161 PRK02645 ppnK inorganic polyph 26.5 54 0.0014 14.8 5.2 99 4-122 2-112 (304) 162 PRK13057 putative lipid kinase 26.4 55 0.0014 14.8 8.3 73 22-115 13-85 (287) 163 pfam02601 Exonuc_VII_L Exonucl 26.1 56 0.0014 14.8 9.5 93 4-110 13-115 (295) 164 PRK07235 amidase; Provisional 25.3 57 0.0015 14.7 4.5 43 3-45 273-319 (504) 165 TIGR00707 argD acetylornithine 25.1 51 0.0013 15.0 2.0 21 125-145 97-117 (402) 166 PRK13689 hypothetical protein; 24.7 59 0.0015 14.6 3.1 29 11-39 3-31 (75) 167 PRK11574 hypothetical protein; 23.7 62 0.0016 14.5 2.5 94 4-106 1-103 (196) 168 cd06326 PBP1_STKc_like Type I 23.4 63 0.0016 14.5 7.4 63 4-73 135-199 (336) 169 cd03795 GT1_like_4 This family 23.2 63 0.0016 14.4 3.1 36 7-42 1-38 (357) 170 TIGR02040 PpsR-CrtJ transcript 22.8 25 0.00065 16.9 0.1 62 13-76 39-109 (453) 171 KOG1017 consensus 22.5 65 0.0017 14.3 3.1 34 79-114 88-124 (267) 172 pfam08967 DUF1884 Domain of un 22.4 65 0.0017 14.3 2.9 52 20-71 10-66 (85) 173 cd06311 PBP1_ABC_sugar_binding 22.0 67 0.0017 14.3 10.2 122 5-142 127-258 (274) 174 PRK11036 putative metallothion 21.8 67 0.0017 14.3 3.1 49 18-75 73-122 (256) 175 smart00851 MGS MGS-like domain 21.8 67 0.0017 14.3 3.8 68 26-106 21-89 (90) 176 cd04104 p47_IIGP_like p47 (47- 21.4 68 0.0017 14.2 5.1 77 42-129 58-134 (197) 177 pfam03358 FMN_red NADPH-depend 21.1 70 0.0018 14.2 4.4 37 7-43 2-39 (147) 178 cd06335 PBP1_ABC_ligand_bindin 21.0 70 0.0018 14.2 7.2 62 5-73 138-201 (347) 179 cd06313 PBP1_ABC_sugar_binding 20.5 71 0.0018 14.1 11.2 122 5-142 123-254 (272) 180 KOG3135 consensus 20.2 73 0.0019 14.0 4.4 43 5-48 1-43 (203) 181 TIGR02196 GlrX_YruB Glutaredox 20.1 73 0.0019 14.0 4.7 51 25-78 14-68 (79) No 1 >PRK00061 ribH riboflavin synthase subunit beta; Provisional Probab=100.00 E-value=0 Score=344.69 Aligned_cols=144 Identities=33% Similarity=0.561 Sum_probs=135.9 Q ss_pred CCCCCCEEEEEEECHHHHHHHHHHHHHHHHHHHCCCC---EEEEEHHHHHHHHHHHHHHHHHHHCCCCCCEEEEEEEEEC Q ss_conf 9665871799980312899999999999999987995---5555300144226999999863311378535665412000 Q gi|254780346|r 1 MEVFIPHVLIIEARFYENLSAMLFEGCVNVLHSRAVQ---WSSIVTPGVLEIPAAVSMVMNAKTRSVTYDGIIVLGVVMR 77 (149) Q Consensus 1 m~~~~~kI~IV~s~~~~~i~~~ll~ga~~~l~~~~~~---~~~i~VPGa~EiP~a~~~~~~~~~~~~~~D~vIaLG~VIk 77 (149) ++-...||+||.|+||++|+++|++||.+.|.++|+. +++++||||||||++++++++ +++|||+|||||||| T Consensus 8 ~~~~~~rI~IV~s~~n~~It~~L~~ga~~~L~~~g~~~~~i~~~~VPGa~EiP~a~~~l~~----~~~~DavIalG~VIk 83 (154) T PRK00061 8 LDAKGLRIGIVVARFNDFITDALLEGAIDALKRHGVSEENIDVVRVPGAFEIPLAAKKLAE----SGKYDAVIALGAVIR 83 (154) T ss_pred CCCCCCEEEEEEECCCHHHHHHHHHHHHHHHHHCCCCHHHEEEEECCCHHHHHHHHHHHHH----CCCCCEEEEEEEEEE T ss_conf 2688989999980385899999999999999985999312699987968889999999986----399887999999981 Q ss_pred CCCCHHHHHHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHC Q ss_conf 66524678999999999999974399705654255889999995065657456999999999999998636 Q gi|254780346|r 78 GKTAHCDVIAHAVTRGLVDLSINGSLPIGNGIVVVDSEQQAFDRVSPSHLDRGGCAARSALAMIELKKSLS 148 (149) Q Consensus 78 GeT~H~e~I~~~v~~gl~~lsl~~~~PI~~gILt~~n~~QA~~R~~~~~~nkG~eaa~Aal~mi~l~~~l~ 148 (149) |||+|||+||++|++|||++|+++++||+||||||+|++||++|++++.+|||.|||+||++|++|+|+|. T Consensus 84 GeT~H~d~I~~~v~~gl~~lsl~~~~PI~~GVLT~~n~~QA~~Ra~~~~~nkG~eaA~aal~Mi~l~~~l~ 154 (154) T PRK00061 84 GETPHFEYVANEVAKGLADVSLETGVPVAFGVLTTDTIEQAIERAGTKAGNKGAEAALAALEMANLLKALK 154 (154) T ss_pred CCCCHHHHHHHHHHHHHHHHHHCCCCCEEEEECCCCCHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHC T ss_conf 89746899999999999999835798179985578998999998089877857999999999999999609 No 2 >PRK12419 riboflavin synthase subunit beta; Provisional Probab=100.00 E-value=0 Score=340.74 Aligned_cols=141 Identities=18% Similarity=0.296 Sum_probs=131.7 Q ss_pred CCCEEEEEEECHHHHHHHHHHHHHHHHHHHCCCC---EEEEEHHHHHHHHHHHHHHHHHHHCCCCCCEEEEEEEEECCCC Q ss_conf 5871799980312899999999999999987995---5555300144226999999863311378535665412000665 Q gi|254780346|r 4 FIPHVLIIEARFYENLSAMLFEGCVNVLHSRAVQ---WSSIVTPGVLEIPAAVSMVMNAKTRSVTYDGIIVLGVVMRGKT 80 (149) Q Consensus 4 ~~~kI~IV~s~~~~~i~~~ll~ga~~~l~~~~~~---~~~i~VPGa~EiP~a~~~~~~~~~~~~~~D~vIaLG~VIkGeT 80 (149) .-+||+||.|+||++|++.|++||.+.|.++|+. +++++||||||||++++++++ +.+||++||||||||||| T Consensus 9 ~~~riaIV~s~~n~~It~~Ll~ga~~~L~~~gv~~~~i~v~~VPGAfEiP~aa~~l~~----~~~~daiIalG~VIrGeT 84 (158) T PRK12419 9 TPQRIAFVQARWHADIVDQAREGFVAEIAARGGAASQVDVFEVPGAFEIPLHAKTLAK----TGRYAAIVAAALVVDGGI 84 (158) T ss_pred CCCEEEEEECCCCHHHHHHHHHHHHHHHHHCCCCHHHEEEEECCCHHHHHHHHHHHHH----CCCCCEEEEEEEEECCCC T ss_conf 8986999976775899999999999999985998554589982867899999999985----599988998878982897 Q ss_pred CHHHHHHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHHCC---CCCCCHHHHHHHHHHHHHHHHHHC Q ss_conf 24678999999999999974399705654255889999995065---657456999999999999998636 Q gi|254780346|r 81 AHCDVIAHAVTRGLVDLSINGSLPIGNGIVVVDSEQQAFDRVSP---SHLDRGGCAARSALAMIELKKSLS 148 (149) Q Consensus 81 ~H~e~I~~~v~~gl~~lsl~~~~PI~~gILt~~n~~QA~~R~~~---~~~nkG~eaa~Aal~mi~l~~~l~ 148 (149) +||||||++|++|||++|+++++||+||||||+|.+||++|++. +.+|||.|||+||++|++++|+|. T Consensus 85 ~Hfd~V~~~v~~gl~~lsl~~~iPV~~GVLT~~n~eQA~eR~~~~~~~~~nKG~EaA~aalemi~l~~~Lr 155 (158) T PRK12419 85 YRHEFVAQAVIDGLMQVQLETEVPVFSVVLTPHHFHESEEHQDFFRAHFVVKGAEAAHACADTLLSRERLR 155 (158) T ss_pred CCHHHHHHHHHHHHHHHHHHCCCCEEEEECCCCCHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHC T ss_conf 52478999999999999862498769998368988999998732136777668999999999999999851 No 3 >pfam00885 DMRL_synthase 6,7-dimethyl-8-ribityllumazine synthase. This family includes the beta chain of 6,7-dimethyl-8- ribityllumazine synthase EC:2.5.1.9, an enzyme involved in riboflavin biosynthesis. The family also includes a subfamily of distant archaebacterial proteins that may also have the same function. Probab=100.00 E-value=0 Score=332.00 Aligned_cols=139 Identities=34% Similarity=0.580 Sum_probs=132.8 Q ss_pred CCEEEEEEECHHHHHHHHHHHHHHHHHHHCCCC---EEEEEHHHHHHHHHHHHHHHHHHHCCCCCCEEEEEEEEECCCCC Q ss_conf 871799980312899999999999999987995---55553001442269999998633113785356654120006652 Q gi|254780346|r 5 IPHVLIIEARFYENLSAMLFEGCVNVLHSRAVQ---WSSIVTPGVLEIPAAVSMVMNAKTRSVTYDGIIVLGVVMRGKTA 81 (149) Q Consensus 5 ~~kI~IV~s~~~~~i~~~ll~ga~~~l~~~~~~---~~~i~VPGa~EiP~a~~~~~~~~~~~~~~D~vIaLG~VIkGeT~ 81 (149) ..||+||.|+||++|+++|+++|.+.|.+.|+. ++.++||||||||++++++++ +++|||+|+|||||||||+ T Consensus 3 ~~kI~IV~s~~n~~i~~~l~~~a~~~l~~~g~~~~~i~~~~VPGa~EiP~~~~~l~~----~~~~d~iIalG~VIkGeT~ 78 (144) T pfam00885 3 GLRIAIVVARFNADITDRLLEGALDALKRHGVSEEDIDVVRVPGAFELPLAAKKLAK----SGRYDAVVALGAVIRGGTY 78 (144) T ss_pred CCEEEEEECCCCHHHHHHHHHHHHHHHHHCCCCHHHEEEEECCCHHHHHHHHHHHHH----CCCCCEEEEEEEEEECCCC T ss_conf 988999980375999999999999999986999310589987968899999999986----4898879999999837984 Q ss_pred HHHHHHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHH Q ss_conf 467899999999999997439970565425588999999506565745699999999999999863 Q gi|254780346|r 82 HCDVIAHAVTRGLVDLSINGSLPIGNGIVVVDSEQQAFDRVSPSHLDRGGCAARSALAMIELKKSL 147 (149) Q Consensus 82 H~e~I~~~v~~gl~~lsl~~~~PI~~gILt~~n~~QA~~R~~~~~~nkG~eaa~Aal~mi~l~~~l 147 (149) |||+||++|++|||++++++++||+||||||+|++||++|++++++|||+|||+||++|++++|+| T Consensus 79 H~e~I~~~v~~gl~~l~l~~~~PI~~gILt~~n~eQA~~R~~~~~~nkG~eaA~aal~m~~l~~~l 144 (144) T pfam00885 79 HFDYVAQEVSRGLMQVSLETGVPVGFGVLTTDTFEQALERAGGKAGNKGAEAALAALEMANLLKKL 144 (144) T ss_pred HHHHHHHHHHHHHHHHHHCCCCCEEEEECCCCCHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHCC T ss_conf 899999999999999982679807998627899899999828988786899999999999998509 No 4 >COG0054 RibH Riboflavin synthase beta-chain [Coenzyme metabolism] Probab=100.00 E-value=0 Score=320.98 Aligned_cols=139 Identities=33% Similarity=0.572 Sum_probs=132.1 Q ss_pred CCCEEEEEEECHHHHHHHHHHHHHHHHHHHCCCCEE---EEEHHHHHHHHHHHHHHHHHHHCCCCCCEEEEEEEEECCCC Q ss_conf 587179998031289999999999999998799555---55300144226999999863311378535665412000665 Q gi|254780346|r 4 FIPHVLIIEARFYENLSAMLFEGCVNVLHSRAVQWS---SIVTPGVLEIPAAVSMVMNAKTRSVTYDGIIVLGVVMRGKT 80 (149) Q Consensus 4 ~~~kI~IV~s~~~~~i~~~ll~ga~~~l~~~~~~~~---~i~VPGa~EiP~a~~~~~~~~~~~~~~D~vIaLG~VIkGeT 80 (149) .+.||+||.||||.+|+|.|++||.+.|+++|..++ +++|||+||||++++++++ +.+|||||+|||||||+| T Consensus 11 ~~~riaIV~arfn~~I~d~ll~gA~~~l~~~G~~~~~i~vv~VPGa~EiPl~a~~La~----~~~yDAvv~lG~VIrG~T 86 (152) T COG0054 11 KGLRIAIVVARFNDDITDALLEGAVDALKRHGADVDNIDVVRVPGAFEIPLAAKKLAR----TGKYDAVVALGAVIRGET 86 (152) T ss_pred CCCEEEEEEEEHHHHHHHHHHHHHHHHHHHCCCCCCCCEEEEECCCCHHHHHHHHHHH----CCCCCEEEEEEEEEECCC T ss_conf 7756999975432799999999999999982997445269982872326899999973----189566999646981797 Q ss_pred CHHHHHHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHH Q ss_conf 246789999999999999743997056542558899999950656574569999999999999986 Q gi|254780346|r 81 AHCDVIAHAVTRGLVDLSINGSLPIGNGIVVVDSEQQAFDRVSPSHLDRGGCAARSALAMIELKKS 146 (149) Q Consensus 81 ~H~e~I~~~v~~gl~~lsl~~~~PI~~gILt~~n~~QA~~R~~~~~~nkG~eaa~Aal~mi~l~~~ 146 (149) +||||||+++++||+++|+++++||+|||||++|++||++|++.+.+|||.+||.||++|++++++ T Consensus 87 ~Hfd~Va~~~~~gl~~vsl~~~~PV~~GVLt~~~~eqA~~rag~~~gnkG~~Aa~aAlem~~l~~~ 152 (152) T COG0054 87 YHFDYVANEVARGLMDVSLETGVPVTFGVLTTDNIEQAIERAGTKAGNKGAEAAEAALEMANLLKK 152 (152) T ss_pred CCHHHHHHHHHHHHHHHHHHHCCCEEEEECCCCCHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHCC T ss_conf 408999989999999988740997586623788699999872764444289999999999998619 No 5 >TIGR00114 lumazine-synth 6,7-dimethyl-8-ribityllumazine synthase; InterPro: IPR002180 This family includes the beta chain of 6,7-dimethyl-8-ribityllumazine synthase 2.5.1.9 from EC, an enzyme involved in riboflavin biosynthesis. The family also includes a subfamily of distant archaebacterial proteins that may also have the same function for example O28856 from SWISSPROT.; GO: 0004746 riboflavin synthase activity, 0009231 riboflavin biosynthetic process, 0009349 riboflavin synthase complex. Probab=100.00 E-value=0 Score=317.82 Aligned_cols=138 Identities=31% Similarity=0.511 Sum_probs=130.6 Q ss_pred CEEEEEEECHHHHHHHHHHHHHHHHHHHCCCCEE----EEEHHHHHHHHHHHHHHHHHHH-CCCCCCEEEEEEEEECCCC Q ss_conf 7179998031289999999999999998799555----5530014422699999986331-1378535665412000665 Q gi|254780346|r 6 PHVLIIEARFYENLSAMLFEGCVNVLHSRAVQWS----SIVTPGVLEIPAAVSMVMNAKT-RSVTYDGIIVLGVVMRGKT 80 (149) Q Consensus 6 ~kI~IV~s~~~~~i~~~ll~ga~~~l~~~~~~~~----~i~VPGa~EiP~a~~~~~~~~~-~~~~~D~vIaLG~VIkGeT 80 (149) -||+||.||||.+|+|.|+++|.+.++.+|++.+ .+|||||||+|+++++++..+. ..++||+||+|||||||+| T Consensus 1 ~rvg~v~ARFN~~It~~L~~gA~d~~~~~G~~~~~~i~~~~VPGafElP~~~~kL~~~~~klGkP~DAVi~LG~VIrG~T 80 (148) T TIGR00114 1 VRVGIVIARFNRFITDKLLEGAIDALKRLGAEVDENIDVIRVPGAFELPLAVKKLAESGKKLGKPYDAVIALGAVIRGGT 80 (148) T ss_pred CEEEEEEEHHHHHHHHHHHHHHHHHHHHCCCCCCCCEEEEECCCCCCHHHHHHHHHHHHHHCCCCCCEEEECCEEEECCC T ss_conf 92678771220689998999999999966895278635897068311268999998500201796335885114773796 Q ss_pred CHHHHHHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHHCCCCC----CCHHHHHHHHHHHHHH Q ss_conf 24678999999999999974399705654255889999995065657----4569999999999999 Q gi|254780346|r 81 AHCDVIAHAVTRGLVDLSINGSLPIGNGIVVVDSEQQAFDRVSPSHL----DRGGCAARSALAMIEL 143 (149) Q Consensus 81 ~H~e~I~~~v~~gl~~lsl~~~~PI~~gILt~~n~~QA~~R~~~~~~----nkG~eaa~Aal~mi~l 143 (149) +||||||+++++||+++++++++||+||||||+|+|||.+|++.+.+ |||.|||.++++|+++ T Consensus 81 ~HfeyV~~~A~~gia~~a~~~~~PV~fGilTt~~~eqA~~raG~~ag~sm~nkG~eaa~~a~e~~~~ 147 (148) T TIGR00114 81 PHFEYVADEAAKGIADLALDYDVPVIFGILTTETIEQAIERAGDKAGVSMENKGVEAAVKALEMAKL 147 (148) T ss_pred CCHHHHHHHHHHHHHHHHHHCCCCEEECCCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHC T ss_conf 6557777789999999998659877603328867999999601120121356679999999999850 No 6 >KOG3243 consensus Probab=100.00 E-value=2.4e-36 Score=245.88 Aligned_cols=136 Identities=24% Similarity=0.420 Sum_probs=126.8 Q ss_pred CCEEEEEEECHHHHHHHHHHHHHHHHHHHCCCCE---EEEEHHHHHHHHHHHHHHHHHHHCCCCCCEEEEEEEEECCCCC Q ss_conf 8717999803128999999999999999879955---5553001442269999998633113785356654120006652 Q gi|254780346|r 5 IPHVLIIEARFYENLSAMLFEGCVNVLHSRAVQW---SSIVTPGVLEIPAAVSMVMNAKTRSVTYDGIIVLGVVMRGKTA 81 (149) Q Consensus 5 ~~kI~IV~s~~~~~i~~~ll~ga~~~l~~~~~~~---~~i~VPGa~EiP~a~~~~~~~~~~~~~~D~vIaLG~VIkGeT~ 81 (149) ..|++||++|||.-+++.|++||.++++++++.. ++.||||+||+|..++.+.+ +.+||++|++|++|||+|. T Consensus 17 ~lR~~IvhARwN~vvi~~LvkGAiEtm~~~~V~eenI~ie~VPGS~Elp~g~~~~~~----r~~~daVi~IGvlIkGsTm 92 (158) T KOG3243 17 GLRFAIVHARWNEVVIKLLVKGAIETMKKYSVREENIEIEWVPGSFELPVGAQNLGK----RGKFDAVICIGVLIKGSTM 92 (158) T ss_pred CEEEEEEEEHHHHHHHHHHHHHHHHHHHHHCCCHHCEEEEECCCCEECCHHHHHHHH----CCCCEEEEEEEEEEECCCH T ss_conf 707999864467899999998899999982840226069972883564488886401----3675089887789706711 Q ss_pred HHHHHHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHHCCCCC-CCHHHHHHHHHHHHHHH Q ss_conf 4678999999999999974399705654255889999995065657-45699999999999999 Q gi|254780346|r 82 HCDVIAHAVTRGLVDLSINGSLPIGNGIVVVDSEQQAFDRVSPSHL-DRGGCAARSALAMIELK 144 (149) Q Consensus 82 H~e~I~~~v~~gl~~lsl~~~~PI~~gILt~~n~~QA~~R~~~~~~-nkG~eaa~Aal~mi~l~ 144 (149) ||||||++++.|+|+++++.++|++||+|||.|+|||+.|++++.+ |+|.+++.||++|.... T Consensus 93 Hfeyis~s~~hglm~~~~~sgvPvIfGlLTc~~eeQAL~RaG~~~ghNhG~dwg~aAvEMa~kf 156 (158) T KOG3243 93 HFEYISNSAAHGLMSASINSGVPVIFGLLTCEDEEQALNRAGGKAGHNHGADWGLAAVEMASKF 156 (158) T ss_pred HHHHHHHHHHHHHHHHCCCCCCCEEEEEEEECCHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHH T ss_conf 0788877788777531135799779987554568999986123211246426788999999864 No 7 >PRK06455 riboflavin synthase; Provisional Probab=98.21 E-value=7.7e-05 Score=51.02 Aligned_cols=130 Identities=18% Similarity=0.244 Sum_probs=92.5 Q ss_pred CCEEEEEEECHHHHHHHHHHHHHHHHHHHCC--CCEEEEEHHHHHHHHHHHHHHHHHHHCCCCCCEEEEEEEEECCCCCH Q ss_conf 8717999803128999999999999999879--95555530014422699999986331137853566541200066524 Q gi|254780346|r 5 IPHVLIIEARFYENLSAMLFEGCVNVLHSRA--VQWSSIVTPGVLEIPAAVSMVMNAKTRSVTYDGIIVLGVVMRGKTAH 82 (149) Q Consensus 5 ~~kI~IV~s~~~~~i~~~ll~ga~~~l~~~~--~~~~~i~VPGa~EiP~a~~~~~~~~~~~~~~D~vIaLG~VIkGeT~H 82 (149) |.+|+|+-..|-. -.|-.-|++.|++.. +.+..++|||.=.+|.++++++.. ..+|++++||-+ |.|+- T Consensus 1 m~kiGi~DTTFaR---vdMg~~Aidel~~~~~~~~i~RyTVPGiKDlPvaakkLiee----~gCdiVmalGmp--G~~~~ 71 (155) T PRK06455 1 MKKIGIADTTFAR---VDMGSAAIDELRKLVPGAKIIRYTVPGIKDLPVAAKKLIEE----EGCDIVMALGMP--GPTEK 71 (155) T ss_pred CCEEEEECCCHHH---HHHHHHHHHHHHHHCCCCEEEEEECCCCCCCHHHHHHHHHH----CCCCEEEECCCC--CCCCH T ss_conf 9657873250222---21489999999973999638998179844467999999987----099789985776--87431 Q ss_pred HHHHHHHHHHHHHHHHHHCCCCCEEEEECCC---CHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHH Q ss_conf 6789999999999999743997056542558---8999999506565745699999999999999863 Q gi|254780346|r 83 CDVIAHAVTRGLVDLSINGSLPIGNGIVVVD---SEQQAFDRVSPSHLDRGGCAARSALAMIELKKSL 147 (149) Q Consensus 83 ~e~I~~~v~~gl~~lsl~~~~PI~~gILt~~---n~~QA~~R~~~~~~nkG~eaa~Aal~mi~l~~~l 147 (149) ..+-..+.+.||+.+++.+++-|+---.--+ +++...+-+ .|+-+|-|.-++.|+.--+.| T Consensus 72 DK~~a~~aS~GLi~~Ql~T~kHIieVfVHEDEa~d~keL~~la----~~RareHa~N~v~ll~~p~~L 135 (155) T PRK06455 72 DKYSAHEASIGLIMAQLMTNKHIIEVFVHEDEAKDEKELKELA----EDRAREHAENLVKLLFKPEAL 135 (155) T ss_pred HHHHHHHHHHHHHHHHHHHCCEEEEEEEECCCCCCHHHHHHHH----HHHHHHHHHHHHHHHHCHHHH T ss_conf 4788999978999999982885899987144568989999999----999999999999998696988 No 8 >COG1731 Archaeal riboflavin synthase [Coenzyme metabolism] Probab=97.79 E-value=0.00021 Score=48.28 Aligned_cols=129 Identities=19% Similarity=0.210 Sum_probs=87.7 Q ss_pred CCEEEEEEECHHHHHHHHHHHHHHHHHHHC--CCCEEEEEHHHHHHHHHHHHHHHHHHHCCCCCCEEEEEEEEECCCCCH Q ss_conf 871799980312899999999999999987--995555530014422699999986331137853566541200066524 Q gi|254780346|r 5 IPHVLIIEARFYENLSAMLFEGCVNVLHSR--AVQWSSIVTPGVLEIPAAVSMVMNAKTRSVTYDGIIVLGVVMRGKTAH 82 (149) Q Consensus 5 ~~kI~IV~s~~~~~i~~~ll~ga~~~l~~~--~~~~~~i~VPGa~EiP~a~~~~~~~~~~~~~~D~vIaLG~VIkGeT~H 82 (149) |.+|+|+-..|-. -.|=.-|.+.|++. |+++..++|||.-.+|.++++++.. .-+|++++||-+ |.|.- T Consensus 1 ~~kvGiaDTTFaR---vdMg~vai~~lk~~~~~~~i~R~TVPGIKdlpvaakrLiee----eGCd~Vi~lG~~--G~t~~ 71 (154) T COG1731 1 MTKVGIADTTFAR---VDMGSVAIDELKKLLPGIKIKRYTVPGIKDLPVAAKRLIEE----EGCDIVIALGWV--GPTEK 71 (154) T ss_pred CCEEEEECCCEEE---ECCHHHHHHHHHHHCCCCCEEEEECCCCCCCHHHHHHHHHH----CCCCEEEECCCC--CCCHH T ss_conf 9625541350123---20147799999963899834886279844375899998876----188489983676--85014 Q ss_pred HHHHHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHHCCCCCCCHHHHHHHHHHHHHH Q ss_conf 6789999999999999743997056542558899999950656574569999999999999 Q gi|254780346|r 83 CDVIAHAVTRGLVDLSINGSLPIGNGIVVVDSEQQAFDRVSPSHLDRGGCAARSALAMIEL 143 (149) Q Consensus 83 ~e~I~~~v~~gl~~lsl~~~~PI~~gILt~~n~~QA~~R~~~~~~nkG~eaa~Aal~mi~l 143 (149) ..+-..+.+-||+.+++-+++-|+---.-- ++...++-...=..|+-+|-|+-++.|+.- T Consensus 72 Dk~~~~~aS~GLi~~QlmTn~hiidV~VHE-DEa~dekeL~~la~~RareHa~Nlv~ll~~ 131 (154) T COG1731 72 DKYSYLAASIGLIMAQLMTNKHIIDVTVHE-DEAEDEKELKELAVDRAREHAENLVKLLFK 131 (154) T ss_pred HHHHHHHHHHHHHHHHHHCCCEEEEEEEEC-CCCCCHHHHHHHHHHHHHHHHHHHHHHHHC T ss_conf 579999985689999998087489999604-454798999999999999999999999868 No 9 >TIGR01506 ribC_arch riboflavin synthase; InterPro: IPR006399 These archaeal proteins, bacterial riboflavin biosynthesis alpha chain, catalyze the final step in riboflavin biosynthesis. However, it is more similar in sequence to 6,7-dimethyl-8-ribityllumazine synthase, which catalyzes the previous reaction and which (in bacteria) is called the riboflavin synthase beta chain. ; GO: 0004746 riboflavin synthase activity, 0009231 riboflavin biosynthetic process. Probab=97.70 E-value=0.00015 Score=49.17 Aligned_cols=116 Identities=17% Similarity=0.261 Sum_probs=87.1 Q ss_pred HHHHHHHHHHHC--CCCEEEEEHHHHHHHHHHHHHHHHHHHCCCCCCEEEEEEEEECCCCCHHHHHHHHHHHHHHHHHHH Q ss_conf 999999999987--995555530014422699999986331137853566541200066524678999999999999974 Q gi|254780346|r 23 LFEGCVNVLHSR--AVQWSSIVTPGVLEIPAAVSMVMNAKTRSVTYDGIIVLGVVMRGKTAHCDVIAHAVTRGLVDLSIN 100 (149) Q Consensus 23 ll~ga~~~l~~~--~~~~~~i~VPGa~EiP~a~~~~~~~~~~~~~~D~vIaLG~VIkGeT~H~e~I~~~v~~gl~~lsl~ 100 (149) |=.-|.+.|+++ ++.+...+|||.=++|.|+++++.-. =+|.||+||-+ |.+.-+.+=....+-||..+++= T Consensus 14 MG~~AideLr~~~~gi~i~R~TVPGIKDLP~AaKklleE~----GCe~VitLGwv--G~~ekDklsy~~aS~GLi~vqlm 87 (152) T TIGR01506 14 MGKVAIDELRKKLAGIKIVRRTVPGIKDLPVAAKKLLEEK----GCEIVITLGWV--GREEKDKLSYLAASVGLIIVQLM 87 (152) T ss_pred HHHHHHHHHHHHCCCCCEEEEECCCCCCCHHHHHHHHCCC----CCCEEEECCCC--CCCHHHHHHHHHHHHHHHHHHHH T ss_conf 0067899876425896357510689504467887641216----88558866889--96024788999887888654321 Q ss_pred CCCCCEEEEECCCCHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHH Q ss_conf 399705654255889999995065657456999999999999998 Q gi|254780346|r 101 GSLPIGNGIVVVDSEQQAFDRVSPSHLDRGGCAARSALAMIELKK 145 (149) Q Consensus 101 ~~~PI~~gILt~~n~~QA~~R~~~~~~nkG~eaa~Aal~mi~l~~ 145 (149) +|+-|+-- ---|+++.+.+--..=..|+-+|=|+-++.|+.-=. T Consensus 88 Tnk~vidV-tvHEDEaedpeeL~~~A~nRaReHa~Nl~~ll~~p~ 131 (152) T TIGR01506 88 TNKHVIDV-TVHEDEAEDPEELKVVAENRAREHARNLVALLVEPD 131 (152) T ss_pred CCCEEEEE-EEECCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCC T ss_conf 08788888-753586678678898874556689999999860783 No 10 >cd06284 PBP1_LacI_like_6 Ligand-binding domain of an uncharacterized transcription regulator from Actinobacillus succinogenes and its close homologs from other bacteria. This group includes the ligand-binding domain of an uncharacterized transcription regulator from Actinobacillus succinogenes and its close homologs from other bacteria. This group belongs to the the LacI-GalR family repressors and are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding. Probab=96.74 E-value=0.029 Score=35.13 Aligned_cols=126 Identities=17% Similarity=0.144 Sum_probs=87.7 Q ss_pred CCEEEEEEECHHHHHHHHHHHHHHHHHHHCCCCEEEE-EHHHHHHHHHHHHHHHHHHHCCCCCCEEEEEEEEECCCCCHH Q ss_conf 8717999803128999999999999999879955555-300144226999999863311378535665412000665246 Q gi|254780346|r 5 IPHVLIIEARFYENLSAMLFEGCVNVLHSRAVQWSSI-VTPGVLEIPAAVSMVMNAKTRSVTYDGIIVLGVVMRGKTAHC 83 (149) Q Consensus 5 ~~kI~IV~s~~~~~i~~~ll~ga~~~l~~~~~~~~~i-~VPGa~EiP~a~~~~~~~~~~~~~~D~vIaLG~VIkGeT~H~ 83 (149) ..||+++.+......+..-.+|+.+.+++++..++.. .++|.+..-.+.+.+.+-.....++||++|. . T Consensus 115 ~~~i~~i~~~~~~~~~~~R~~Gf~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~ai~~~----------n 184 (267) T cd06284 115 HRRIALITGPRDNPLARDRLEGYRQALAEAGLPADEELIQEGDFSLESGYAAARRLLALPDRPTAIFCF----------S 184 (267) T ss_pred CCEEEEECCCCCCHHHHHHHHHHHHHHHHCCCCCCCEEEECCCCCHHHHHHHHHHHHHCCCCCCEEEEC----------C T ss_conf 976999628888725999999999999983998551277327876777889999999659999802657----------8 Q ss_pred HHHHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHHC------CCCCCCHHHHHHHHHHHHH Q ss_conf 7899999999999997439970565425588999999506------5657456999999999999 Q gi|254780346|r 84 DVIAHAVTRGLVDLSINGSLPIGNGIVVVDSEQQAFDRVS------PSHLDRGGCAARSALAMIE 142 (149) Q Consensus 84 e~I~~~v~~gl~~lsl~~~~PI~~gILt~~n~~QA~~R~~------~~~~nkG~eaa~Aal~mi~ 142 (149) |.++-.+.+.+.+.. ..+|=-..|++.++.+.+.--.- .....-|.+|++.++++++ T Consensus 185 D~~A~g~~~~l~~~g--~~vP~di~vigfd~~~~~~~~~p~lttv~~~~~~~g~~a~~~ll~~i~ 247 (267) T cd06284 185 DEMAIGAISALKELG--LRVPEDISVVGFDDIDFARMTTPPLTTIRQPRYEIGRTAAELLLDIIE 247 (267) T ss_pred CHHHHHHHHHHHHCC--CCCCCEEEEEEECCHHHHHHCCCCCEEEEECHHHHHHHHHHHHHHHHC T ss_conf 688999999999839--999962799987784899824898339985999999999999999976 No 11 >cd06288 PBP1_sucrose_transcription_regulator Ligand-binding domain of DNA-binding regulatory proteins specific to sucrose that are members of the LacI-GalR family of bacterial transcription repressors. This group includes the ligand-binding domain of DNA-binding regulatory proteins specific to sucrose that are members of the LacI-GalR family of bacterial transcription repressors. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor. Probab=96.63 E-value=0.035 Score=34.55 Aligned_cols=126 Identities=15% Similarity=0.149 Sum_probs=85.6 Q ss_pred CCEEEEEEECHHHHHHHHHHHHHHHHHHHCCCCEEEE-EHHHHHHHHHHHHHHHHHHHCCCCCCEEEEEEEEECCCCCHH Q ss_conf 8717999803128999999999999999879955555-300144226999999863311378535665412000665246 Q gi|254780346|r 5 IPHVLIIEARFYENLSAMLFEGCVNVLHSRAVQWSSI-VTPGVLEIPAAVSMVMNAKTRSVTYDGIIVLGVVMRGKTAHC 83 (149) Q Consensus 5 ~~kI~IV~s~~~~~i~~~ll~ga~~~l~~~~~~~~~i-~VPGa~EiP~a~~~~~~~~~~~~~~D~vIaLG~VIkGeT~H~ 83 (149) -.||+.+.+.-+...+..-..|+.+.+.++|.+++.. ..++.++.-.+.+.+.+-.....++||++|. . T Consensus 116 ~~~i~~i~~~~~~~~~~~R~~gf~~a~~~~~i~~~~~~i~~~~~~~~~~~~~~~~ll~~~~~~dai~~~----------~ 185 (269) T cd06288 116 HRRIAFINGEPWMLAAKDRLKGYRQALAEAGIPFDPDLVVHGDWSADDGYEAAAALLDLDDRPTAIFCG----------N 185 (269) T ss_pred CCCEEEEECCCCCHHHHHHHHHHHHHHHHCCCCCCCCEEECCCCCHHHHHHHHHHHHHCCCCCCEECCC----------C T ss_conf 875578748988757999999999999976998664224126776677777779998558998610147----------7 Q ss_pred HHHHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHHCCC-------CCCCHHHHHHHHHHHHH Q ss_conf 789999999999999743997056542558899999950656-------57456999999999999 Q gi|254780346|r 84 DVIAHAVTRGLVDLSINGSLPIGNGIVVVDSEQQAFDRVSPS-------HLDRGGCAARSALAMIE 142 (149) Q Consensus 84 e~I~~~v~~gl~~lsl~~~~PI~~gILt~~n~~QA~~R~~~~-------~~nkG~eaa~Aal~mi~ 142 (149) |.++-.+.+.+.+. ...+|=-..|++-+|.+.+-+...++ ...-|..|++..+++++ T Consensus 186 d~~A~g~~~~l~~~--gi~vP~di~iigfD~~~~~~~~~~P~lTti~q~~~~~g~~A~~~l~~~i~ 249 (269) T cd06288 186 DRMAMGAYQALLER--GLRIPQDVSVVGFDNQEIIAEHLRPPLTTVALPHYEMGRWAVELLLDGIE 249 (269) T ss_pred HHHHHHHHHHHHHC--CCCCCCCEEEEEECCCHHHHHHCCCCCEEEEECHHHHHHHHHHHHHHHHC T ss_conf 89999999999985--99999988999988868999637899649980999999999999999975 No 12 >cd06291 PBP1_Qymf_like Ligand binding domain of the lacI-like transcription regulator from a novel metal-reducing bacterium Alkaliphilus Metalliredigens (strain Qymf) and its close homologs. This group includes the ligand binding domain of the lacI-like transcription regulator from a novel metal-reducing bacterium Alkaliphilus Metalliredigens (strain Qymf) and its close homologs. Qymf is a strict anaerobe that could be grown in the presence of borax and its cells are straight rods that produce endospores. This group is a member of the LacI-GalR family repressors that are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription Probab=96.57 E-value=0.05 Score=33.61 Aligned_cols=126 Identities=16% Similarity=0.116 Sum_probs=82.5 Q ss_pred CCEEEEEEECHHHHH-HHHHHHHHHHHHHHCCCCEEEEEHHHHHHHHHHHHHHHHHHHCCCCCCEEEEEEEEECCCCCHH Q ss_conf 871799980312899-9999999999999879955555300144226999999863311378535665412000665246 Q gi|254780346|r 5 IPHVLIIEARFYENL-SAMLFEGCVNVLHSRAVQWSSIVTPGVLEIPAAVSMVMNAKTRSVTYDGIIVLGVVMRGKTAHC 83 (149) Q Consensus 5 ~~kI~IV~s~~~~~i-~~~ll~ga~~~l~~~~~~~~~i~VPGa~EiP~a~~~~~~~~~~~~~~D~vIaLG~VIkGeT~H~ 83 (149) -.||+++.+...... ...=+.|+.+.++++|.+.+.+.+++.+......+.+.+-.....++||++|. . T Consensus 112 hr~I~~i~~~~~~~~~~~~R~~Gf~~al~~~g~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~Ai~~~----------n 181 (265) T cd06291 112 CKHIAHIGGPNNTVSPTNLRYEGFLDVLKENGLEVRIIEIQENFDDAEKKEEIKELLEEYPDIDGIFAS----------N 181 (265) T ss_pred CCEEEEEECCCCCCCHHHHHHHHHHHHHHHCCCCCEEEEECCCCCHHHHHHHHHHHHHCCCCCCEEECC----------C T ss_conf 964999966888874899999999999997699960899768898699999999998559998843216----------6 Q ss_pred HHHHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHHC------CCCCCCHHHHHHHHHHHHH Q ss_conf 7899999999999997439970565425588999999506------5657456999999999999 Q gi|254780346|r 84 DVIAHAVTRGLVDLSINGSLPIGNGIVVVDSEQQAFDRVS------PSHLDRGGCAARSALAMIE 142 (149) Q Consensus 84 e~I~~~v~~gl~~lsl~~~~PI~~gILt~~n~~QA~~R~~------~~~~nkG~eaa~Aal~mi~ 142 (149) |.++-.+.+++.+..+ .+|==..|++-+|.+.+.--.- .....-|..|++.++++++ T Consensus 182 D~~A~g~~~al~~~g~--~vP~disvigfDd~~~~~~~~p~LTtv~~~~~~~g~~A~~~Ll~~i~ 244 (265) T cd06291 182 DLTAILVLKEAQQRGI--RVPEDLQIIGYDGTKLTRLYTPELTTIRQPIEEIAKTAVDLLIKQIE 244 (265) T ss_pred HHHHHHHHHHHHHCCC--CCCCCEEEEEECCHHHHHHCCCCCEEEECCHHHHHHHHHHHHHHHHC T ss_conf 8999999999998199--99998699998880999843999559973999999999999999965 No 13 >cd06271 PBP1_AglR_RafR_like Ligand-binding domain of DNA transcription repressors specific for raffinose (RafR) and alpha-glucosides (AglR) which are members of the LacI-GalR family of bacterial transcription regulators. Ligand-binding domain of DNA transcription repressors specific for raffinose (RafR) and alpha-glucosides (AglR) which are members of the LacI-GalR family of bacterial transcription regulators. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the represso Probab=96.25 E-value=0.062 Score=33.04 Aligned_cols=125 Identities=11% Similarity=0.041 Sum_probs=80.1 Q ss_pred CEEEEEEECHHHHHHHHHHHHHHHHHHHCCCCEEEEE-HHHHHHHHHHHHHHHHHHHCCCCCCEEEEEEEEECCCCCHHH Q ss_conf 7179998031289999999999999998799555553-001442269999998633113785356654120006652467 Q gi|254780346|r 6 PHVLIIEARFYENLSAMLFEGCVNVLHSRAVQWSSIV-TPGVLEIPAAVSMVMNAKTRSVTYDGIIVLGVVMRGKTAHCD 84 (149) Q Consensus 6 ~kI~IV~s~~~~~i~~~ll~ga~~~l~~~~~~~~~i~-VPGa~EiP~a~~~~~~~~~~~~~~D~vIaLG~VIkGeT~H~e 84 (149) .||+++.+.-.......-+.|+.+.+.++|.+.+..+ .+|.+......+.+.+-.....++||++|. .| T Consensus 121 ~~I~~i~~~~~~~~~~~R~~Gf~~al~~~gl~~~~~~~~~~~~~~~~~~~~~~~ll~~~~~p~Ai~~~----------nD 190 (268) T cd06271 121 RRIALLNPPEDLTFAQHRRAGYRRALAEAGLPLDPALIVSGDMTEEGGYAAAAELLALPDRPTAIVCS----------SE 190 (268) T ss_pred CEEEECCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCEEEECCCCHHHHHHHHHHHHHCCCCCCEEEEC----------CH T ss_conf 74875488754607999999999999983999771136506875777999999999659998689977----------77 Q ss_pred HHHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHH------CCCCCCCHHHHHHHHHHHHH Q ss_conf 89999999999999743997056542558899999950------65657456999999999999 Q gi|254780346|r 85 VIAHAVTRGLVDLSINGSLPIGNGIVVVDSEQQAFDRV------SPSHLDRGGCAARSALAMIE 142 (149) Q Consensus 85 ~I~~~v~~gl~~lsl~~~~PI~~gILt~~n~~QA~~R~------~~~~~nkG~eaa~Aal~mi~ 142 (149) .++-.+.+.+.+.. ..+|=-..|++-+|.+.+.--. ......-|..|++-.+++++ T Consensus 191 ~~A~g~l~~l~~~g--~~vP~DisvigfD~~~~~~~~~p~LTti~~~~~~~g~~A~~~Ll~~i~ 252 (268) T cd06271 191 LMALGVLAALAEAG--LRPGRDVSVVGFDDSPPLLFFSPPLTTVRSDLRAAGRRLAELLLARIA 252 (268) T ss_pred HHHHHHHHHHHHCC--CCCCCCEEEEEECCCHHHHHCCCCEEEEECCHHHHHHHHHHHHHHHHC T ss_conf 99999999999829--998999799997882899827898089980999999999999999977 No 14 >cd06270 PBP1_GalS_like Ligand binding domain of DNA transcription iso-repressor GalS, which is one of two regulatory proteins involved in galactose transport and metabolism. Ligand binding domain of DNA transcription iso-repressor GalS, which is one of two regulatory proteins involved in galactose transport and metabolism. Transcription of the galactose regulon genes is regulated by Gal iso-repressor (GalS) and Gal repressor (GalR) in different ways, but both repressors recognize the same DNA binding site in the absence of D-galactose. GalS is a dimeric protein like GalR,and its major role is in regulating expression of the high-affinity galactose transporter encoded by the mgl operon, whereas GalR is the exclusive regulator of galactose permease, the low-affinity galactose transporter. GalS and GalR are members of the LacI-GalR family of transcription regulators and both contain the type I periplasmic binding protein-like fold. Hence, they are homologous to the periplasmic sugar bindi Probab=96.00 E-value=0.11 Score=31.42 Aligned_cols=122 Identities=16% Similarity=0.188 Sum_probs=79.9 Q ss_pred CEEEEEEECHHHHHHHHHHHHHHHHHHHCCCCEEEE-EHHHHHHHHH---HHHHHHHHHHCCCCCCEEEEEEEEECCCCC Q ss_conf 717999803128999999999999999879955555-3001442269---999998633113785356654120006652 Q gi|254780346|r 6 PHVLIIEARFYENLSAMLFEGCVNVLHSRAVQWSSI-VTPGVLEIPA---AVSMVMNAKTRSVTYDGIIVLGVVMRGKTA 81 (149) Q Consensus 6 ~kI~IV~s~~~~~i~~~ll~ga~~~l~~~~~~~~~i-~VPGa~EiP~---a~~~~~~~~~~~~~~D~vIaLG~VIkGeT~ 81 (149) .||+++.+.........-+.|+.+.+.++|...+.. .+.|.|..-. +++.++ ....++||++|. T Consensus 117 ~~i~~i~~~~~~~~~~~R~~Gf~~al~~~gl~~~~~~i~~~~~~~~~g~~~~~~ll---~~~~~~~ai~~~--------- 184 (268) T cd06270 117 RKIACITGPLTKEDARLRLQGYRDALAEAGIALDESLIIEGDFTEEGGYAAMQELL---ARGAPFTAVFCA--------- 184 (268) T ss_pred CCEEEECCCCCCCHHHHHHHHHHHHHHHCCCCCCCEEEEECCCCHHHHHHHHHHHH---HCCCCCCEEEEC--------- T ss_conf 83898459888831999999999999985999780047616776788999889999---569998745533--------- Q ss_pred HHHHHHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHH------CCCCCCCHHHHHHHHHHHHH Q ss_conf 46789999999999999743997056542558899999950------65657456999999999999 Q gi|254780346|r 82 HCDVIAHAVTRGLVDLSINGSLPIGNGIVVVDSEQQAFDRV------SPSHLDRGGCAARSALAMIE 142 (149) Q Consensus 82 H~e~I~~~v~~gl~~lsl~~~~PI~~gILt~~n~~QA~~R~------~~~~~nkG~eaa~Aal~mi~ 142 (149) .|.++-.+.+.+.+..+ .+|==..|++-+|.+.+.-=. ......-|.+|++.++++++ T Consensus 185 -nD~~A~g~~~~l~~~g~--~vP~disvigfdd~~~~~~~~P~LTti~~~~~~~g~~A~~~Ll~~i~ 248 (268) T cd06270 185 -NDEMAAGAISALREHGI--SVPQDVSIIGFDDVLLARYLYPKLTTVHYPIEEMAQMAAKLALQLVY 248 (268) T ss_pred -CHHHHHHHHHHHHHCCC--CCCCCEEEEEECCHHHHHHCCCCCEEEECCHHHHHHHHHHHHHHHHC T ss_conf -77999999999998299--99997699998986899714899549964999999999999999974 No 15 >cd06294 PBP1_ycjW_transcription_regulator_like Ligand-binding domain of uncharacterized transcription regulator ycjW which is a member of the LacI-GalR family repressors. This group includes the ligand-binding domain of uncharacterized transcription regulator ycjW which is a member of the LacI-GalR family repressors that are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor. Probab=95.97 E-value=0.16 Score=30.55 Aligned_cols=126 Identities=13% Similarity=0.070 Sum_probs=78.2 Q ss_pred CCEEEEEEECHHHHHHHHHHHHHHHHHHHCCCCEEEEEH-HHHHHHHHHHHHHHHHHHCCCCCCEEEEEEEEECCCCCHH Q ss_conf 871799980312899999999999999987995555530-0144226999999863311378535665412000665246 Q gi|254780346|r 5 IPHVLIIEARFYENLSAMLFEGCVNVLHSRAVQWSSIVT-PGVLEIPAAVSMVMNAKTRSVTYDGIIVLGVVMRGKTAHC 83 (149) Q Consensus 5 ~~kI~IV~s~~~~~i~~~ll~ga~~~l~~~~~~~~~i~V-PGa~EiP~a~~~~~~~~~~~~~~D~vIaLG~VIkGeT~H~ 83 (149) -.||+++.+.-+...+..=++|+.+.+.++|...+..++ .+.|......+.+.+-.....++||++|. . T Consensus 122 hr~I~~i~~~~~~~~~~~R~~Gf~~al~~~g~~~~~~~~~~~~~~~~~~~~~~~~ll~~~~~~tai~~~----------n 191 (270) T cd06294 122 HKKIAFVGGDLDLEVTQDRLQGYKQALEDHGIPDRNEVIISLDFSEEGGYKALKKLLEQHPRPTAIVAT----------D 191 (270) T ss_pred CCEEEEECCCCCCHHHHHHHHHHHHHHHHCCCCCCCCEEECCCCCHHHHHHHHHHHHHCCCCCCEEEEC----------C T ss_conf 956999818998658999999999999986999773333137766788999999998469998489987----------7 Q ss_pred HHHHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHH------CCCCCCCHHHHHHHHHHHHH Q ss_conf 789999999999999743997056542558899999950------65657456999999999999 Q gi|254780346|r 84 DVIAHAVTRGLVDLSINGSLPIGNGIVVVDSEQQAFDRV------SPSHLDRGGCAARSALAMIE 142 (149) Q Consensus 84 e~I~~~v~~gl~~lsl~~~~PI~~gILt~~n~~QA~~R~------~~~~~nkG~eaa~Aal~mi~ 142 (149) |.++-.+.+++.+.. ..+|=-..|++-++...+.--. ......-|+.|++.++++++ T Consensus 192 D~~A~g~~~al~~~g--~~iP~disvvgfDd~~~~~~~~P~LTtv~q~~~~~G~~A~~~Ll~~i~ 254 (270) T cd06294 192 DLLALGVLKVLNELG--LKVPEDLSIIGFNNSILSELAHPPLTSVDINPRELGYEAAELLIDLIE 254 (270) T ss_pred HHHHHHHHHHHHHCC--CCCCCCEEEEEECCHHHHHHCCCCCEEEECCHHHHHHHHHHHHHHHHC T ss_conf 499999999999839--999998499998972899842898179973999999999999999966 No 16 >cd01537 PBP1_Repressors_Sugar_Binding_like Ligand-binding domain of the LacI-GalR family of transcription regulators and the sugar-binding domain of ABC-type transport systems. Ligand-binding domain of the LacI-GalR family of transcription regulators and the sugar-binding domain of ABC-type transport systems, all of which contain the type I periplasmic binding protein-like fold. Their specific ligands include lactose, ribose, fructose, xylose, arabinose, galactose/glucose, and other sugars. The LacI family of proteins consists of transcriptional regulators related to the lac repressor; in general the sugar binding domain in this family binds a sugar, which in turn changes the DNA binding activity of the repressor domain. The core structure of the periplasmic binding proteins is classified into two types and they differ in number and order of beta strands in each domain: type I, which has six beta strands, and type II, which has five beta strands. These two distinct structural arrangem Probab=95.92 E-value=0.14 Score=30.78 Aligned_cols=126 Identities=13% Similarity=0.108 Sum_probs=68.3 Q ss_pred CCEEEEEEECHHHHHHHHHHHHHHHHHHHCCCCEEEEEHHHHHHHHHHHHHHHHHHHCCCCCCEEEEEEEEECCCCCHHH Q ss_conf 87179998031289999999999999998799555553001442269999998633113785356654120006652467 Q gi|254780346|r 5 IPHVLIIEARFYENLSAMLFEGCVNVLHSRAVQWSSIVTPGVLEIPAAVSMVMNAKTRSVTYDGIIVLGVVMRGKTAHCD 84 (149) Q Consensus 5 ~~kI~IV~s~~~~~i~~~ll~ga~~~l~~~~~~~~~i~VPGa~EiP~a~~~~~~~~~~~~~~D~vIaLG~VIkGeT~H~e 84 (149) ..||+++...-.......-.+|+.+.+.+++.......+++.+....+.+.+.+......++||+++. .| T Consensus 118 ~~~i~~i~~~~~~~~~~~R~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~dai~~~----------~d 187 (264) T cd01537 118 HRRIALLAGPLGSSTARERVAGFKDALKEAGPIEIVLVQEGDWDAEKGYQAAEELLTAHPDPTAIFAA----------ND 187 (264) T ss_pred CCCEEECCCCCCCCHHHHHHHHHHHHHHHCCCCCCEEEEECCCCHHHHHHHHHHHHHHCCCCEEEEEC----------CH T ss_conf 86245304887770699999999999997799985379957999899999999998508997699989----------86 Q ss_pred HHHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHHC------CCCCCCHHHHHHHHHHHHH Q ss_conf 899999999999997439970565425588999999506------5657456999999999999 Q gi|254780346|r 85 VIAHAVTRGLVDLSINGSLPIGNGIVVVDSEQQAFDRVS------PSHLDRGGCAARSALAMIE 142 (149) Q Consensus 85 ~I~~~v~~gl~~lsl~~~~PI~~gILt~~n~~QA~~R~~------~~~~nkG~eaa~Aal~mi~ 142 (149) .++..+.+.+.+..+ .+|==..|++.+|...+....- .....-|..|++.++++++ T Consensus 188 ~~A~gv~~al~~~g~--~ip~di~ivg~d~~~~~~~~~p~ltti~~~~~~~g~~a~~~l~~~i~ 249 (264) T cd01537 188 DMALGALRALREAGL--RVPDDISVIGFDGTPEALLAGPPLTTVRQPPDELGRAAVELLLELLN 249 (264) T ss_pred HHHHHHHHHHHHCCC--CCCCCEEEEEECCHHHHHHHCCCEEEEECCHHHHHHHHHHHHHHHHC T ss_conf 999999999997499--99998399999974999971998299983999999999999999965 No 17 >cd06296 PBP1_CatR_like Ligand-binding domain of a LacI-like transcriptional regulator, CatR which is involved in catechol degradation. This group includes the ligand-binding domain of a LacI-like transcriptional regulator, CatR which is involved in catechol degradation. This group belongs to the the LacI-GalR family repressors that are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor. Probab=95.78 E-value=0.11 Score=31.52 Aligned_cols=126 Identities=16% Similarity=0.080 Sum_probs=82.6 Q ss_pred CCEEEEEEECHHHHHHHHHHHHHHHHHHHCCCCEEE-EEHHHHHHHHHHHHHHHHHHHCCCCCCEEEEEEEEECCCCCHH Q ss_conf 871799980312899999999999999987995555-5300144226999999863311378535665412000665246 Q gi|254780346|r 5 IPHVLIIEARFYENLSAMLFEGCVNVLHSRAVQWSS-IVTPGVLEIPAAVSMVMNAKTRSVTYDGIIVLGVVMRGKTAHC 83 (149) Q Consensus 5 ~~kI~IV~s~~~~~i~~~ll~ga~~~l~~~~~~~~~-i~VPGa~EiP~a~~~~~~~~~~~~~~D~vIaLG~VIkGeT~H~ 83 (149) -+||+++...-+......-+.|+.+.+.++|.+.+. ...+|.|....+.+.+.+-.....++||++|. . T Consensus 117 ~~~I~~i~~~~~~~~~~~R~~Gf~~a~~~~~~~~~~~~i~~~~~~~~~~~~~~~~ll~~~~~~~aii~~----------~ 186 (270) T cd06296 117 HRRIGFITGPPDLLCSRARLDGYRAALAEAGIPVDPALVREGDFSTESGFRAAAELLALPERPTAIFAG----------N 186 (270) T ss_pred CCCEEEECCCCCCHHHHHHHHHHHHHHHHCCCCCCHHHEEECCCHHHHHHHHHHHHHHCCCCCCCEEEC----------C T ss_conf 972888459988655999999999999986999885553306501789999999999549988620347----------8 Q ss_pred HHHHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHH------CCCCCCCHHHHHHHHHHHHH Q ss_conf 789999999999999743997056542558899999950------65657456999999999999 Q gi|254780346|r 84 DVIAHAVTRGLVDLSINGSLPIGNGIVVVDSEQQAFDRV------SPSHLDRGGCAARSALAMIE 142 (149) Q Consensus 84 e~I~~~v~~gl~~lsl~~~~PI~~gILt~~n~~QA~~R~------~~~~~nkG~eaa~Aal~mi~ 142 (149) |.++-.+.+.+.+.. ..+|=-..|++-+|...+.--. ......-|..|++.++++++ T Consensus 187 D~~A~g~~~~l~~~g--i~vP~di~iigfd~~~~~~~~~p~lttI~~~~~~~g~~a~~~ll~~i~ 249 (270) T cd06296 187 DLMALGVYEAARERG--LRIPEDLSVVGFDDLPEARWVSPPLTTVRQPLREMGRAAVRLLLRLIE 249 (270) T ss_pred CHHHHHHHHHHHHCC--CCCCCCCEEEEECCHHHHHHCCCCEEEEEECHHHHHHHHHHHHHHHHC T ss_conf 689999999999869--999998879997887899852898389982999999999999999965 No 18 >cd06293 PBP1_LacI_like_11 Ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. This group includes the ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor. Probab=95.61 E-value=0.22 Score=29.60 Aligned_cols=126 Identities=14% Similarity=-0.002 Sum_probs=79.2 Q ss_pred CCEEEEEEECHHHHHHHHHHHHHHHHHHHCCCCEEEEE-HHHHHHHHHHHHHHHHHHHCCCCCCEEEEEEEEECCCCCHH Q ss_conf 87179998031289999999999999998799555553-00144226999999863311378535665412000665246 Q gi|254780346|r 5 IPHVLIIEARFYENLSAMLFEGCVNVLHSRAVQWSSIV-TPGVLEIPAAVSMVMNAKTRSVTYDGIIVLGVVMRGKTAHC 83 (149) Q Consensus 5 ~~kI~IV~s~~~~~i~~~ll~ga~~~l~~~~~~~~~i~-VPGa~EiP~a~~~~~~~~~~~~~~D~vIaLG~VIkGeT~H~ 83 (149) -.||+++.+.-....+..-++|+++.+.+++...+..+ ..|.+..-..-+.+........++||++|. . T Consensus 116 ~~~I~~i~~~~~~~~~~~R~~G~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~av~~~----------n 185 (269) T cd06293 116 HRRIAFVGGPDALISARERYAGYREALAEAHIPEVPEYVCFGDYTREFGRAAAAQLLARGDPPTAIFAA----------S 185 (269) T ss_pred CCEEEEECCCCCCCHHHHHHHHHHHHHHHCCCCCCCEEEEECCCCHHHHHHHHHHHHHCCCCCCEEEEC----------C T ss_conf 983899548877633999999999999976999993489955631135999999998479998589968----------8 Q ss_pred HHHHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHHC------CCCCCCHHHHHHHHHHHHH Q ss_conf 7899999999999997439970565425588999999506------5657456999999999999 Q gi|254780346|r 84 DVIAHAVTRGLVDLSINGSLPIGNGIVVVDSEQQAFDRVS------PSHLDRGGCAARSALAMIE 142 (149) Q Consensus 84 e~I~~~v~~gl~~lsl~~~~PI~~gILt~~n~~QA~~R~~------~~~~nkG~eaa~Aal~mi~ 142 (149) |.++-.+.+.+.+.. ..+|=-.+|++-+|.+.+..-.- .....-|.+|++..+++++ T Consensus 186 D~~A~g~l~~l~~~g--i~vP~disiigfd~~~~~~~~~P~lTti~q~~~~ig~~A~~~Ll~~i~ 248 (269) T cd06293 186 DEIAIGLLEVLRERG--LSIPGDMSLVGFDDVGPAHLFAPPLTTIRQPVRELGRRAVALLLATLW 248 (269) T ss_pred HHHHHHHHHHHHHCC--CCCCCCEEEEEECCHHHHHHCCCCEEEEECCHHHHHHHHHHHHHHHHC T ss_conf 599999999999849--999996599988880999830898489965999999999999999845 No 19 >PRK10703 DNA-binding transcriptional repressor PurR; Provisional Probab=95.55 E-value=0.22 Score=29.61 Aligned_cols=123 Identities=12% Similarity=0.118 Sum_probs=77.8 Q ss_pred CCEEEEEEECHHHHHHHHHHHHHHHHHHHCCCCEEEE-EHHHHHHHHHH---HHHHHHHHHCCCCCCEEEEEEEEECCCC Q ss_conf 8717999803128999999999999999879955555-30014422699---9999863311378535665412000665 Q gi|254780346|r 5 IPHVLIIEARFYENLSAMLFEGCVNVLHSRAVQWSSI-VTPGVLEIPAA---VSMVMNAKTRSVTYDGIIVLGVVMRGKT 80 (149) Q Consensus 5 ~~kI~IV~s~~~~~i~~~ll~ga~~~l~~~~~~~~~i-~VPGa~EiP~a---~~~~~~~~~~~~~~D~vIaLG~VIkGeT 80 (149) -.||+++.+..+......-++|+.+.+.++|...+.- .+.|.|+.... ++.++ .....++|++|. T Consensus 178 hr~Ia~i~~~~~~~~~~~R~~gf~~al~~~gl~~~~~~i~~~~~~~~~g~~~~~~ll---~~~~~ptAi~~~-------- 246 (335) T PRK10703 178 HRDIGVIPGPLERNTGAGRLAGFMKAMEEANIKVPEEWIVQGDFEPESGYEAMQQIL---SQEHRPTAVFCG-------- 246 (335) T ss_pred CCEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCCCHHEEEECCCCHHHHHHHHHHHH---HCCCCCCEEEEC-------- T ss_conf 986999958876521789999999999985999881328965788588999999999---569998668968-------- Q ss_pred CHHHHHHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHHC------CCCCCCHHHHHHHHHHHHH Q ss_conf 2467899999999999997439970565425588999999506------5657456999999999999 Q gi|254780346|r 81 AHCDVIAHAVTRGLVDLSINGSLPIGNGIVVVDSEQQAFDRVS------PSHLDRGGCAARSALAMIE 142 (149) Q Consensus 81 ~H~e~I~~~v~~gl~~lsl~~~~PI~~gILt~~n~~QA~~R~~------~~~~nkG~eaa~Aal~mi~ 142 (149) .|.++-.+.+++.+.. ..+|==..|++-+|...+.--.- ......|..|++..+++++ T Consensus 247 --nD~~A~g~~~~l~~~g--~~VP~DisvigfDd~~~~~~~~P~LTtv~~~~~~~g~~A~~~Ll~~i~ 310 (335) T PRK10703 247 --GDIMAMGAICAADEMG--LRVPQDISVIGYDNVRNARYFTPALTTIHQPKDRLGETAFNMLLDRIV 310 (335) T ss_pred --CHHHHHHHHHHHHHCC--CCCCCCEEEEEECCCHHHHHCCCCCEEEECCHHHHHHHHHHHHHHHHC T ss_conf --7599999999999719--999997499998882899825898279982999999999999999961 No 20 >cd06275 PBP1_PurR Ligand-binding domain of purine repressor, PurR, which functions as the master regulatory protein of de novo purine nucleotide biosynthesis in Escherichia coli. Ligand-binding domain of purine repressor, PurR, which functions as the master regulatory protein of de novo purine nucleotide biosynthesis in Escherichia coli. This dimeric PurR belongs to the LacI-GalR family of transcription regulators and is activated to bind to DNA operator sites by initially binding either of high affinity corepressors, hypoxanthine or guanine. PurR is composed of two functional domains: aan N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the purine transcription repressor undergoes a Probab=95.52 E-value=0.16 Score=30.50 Aligned_cols=126 Identities=11% Similarity=0.039 Sum_probs=76.8 Q ss_pred CCEEEEEEECHHHHHHHHHHHHHHHHHHHCCCCEEEEE-HHHHHHHHHHHHHHHHHHHCCCCCCEEEEEEEEECCCCCHH Q ss_conf 87179998031289999999999999998799555553-00144226999999863311378535665412000665246 Q gi|254780346|r 5 IPHVLIIEARFYENLSAMLFEGCVNVLHSRAVQWSSIV-TPGVLEIPAAVSMVMNAKTRSVTYDGIIVLGVVMRGKTAHC 83 (149) Q Consensus 5 ~~kI~IV~s~~~~~i~~~ll~ga~~~l~~~~~~~~~i~-VPGa~EiP~a~~~~~~~~~~~~~~D~vIaLG~VIkGeT~H~ 83 (149) ..||+++...........-+.|+.+.+.+++.+....+ +.|-++..-+.+.+.+-.....++||++|. . T Consensus 117 ~~~i~~i~~~~~~~~~~~R~~Gf~~al~~~~i~~~~~~i~~~~~~~~~~~~~~~~~l~~~~~~~aii~~----------~ 186 (269) T cd06275 117 HRRIGCITGPLEKAPAQQRLAGFRRAMAEAGLPVNPGWIVEGDFECEGGYEAMQRLLAQPKRPTAVFCG----------N 186 (269) T ss_pred CCEEEECCCCCCCHHHHHHHHHHHHHHHHCCCCCCHHHHCCCCCCHHHHHHHHHHHHHHCCCCCEEECC----------C T ss_conf 971775569977716999999999999985999765550367777688999999999708996612318----------7 Q ss_pred HHHHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHH------CCCCCCCHHHHHHHHHHHHH Q ss_conf 789999999999999743997056542558899999950------65657456999999999999 Q gi|254780346|r 84 DVIAHAVTRGLVDLSINGSLPIGNGIVVVDSEQQAFDRV------SPSHLDRGGCAARSALAMIE 142 (149) Q Consensus 84 e~I~~~v~~gl~~lsl~~~~PI~~gILt~~n~~QA~~R~------~~~~~nkG~eaa~Aal~mi~ 142 (149) |.++..+.+.+.+..+ .+|==..|.+.++...+.--. ......-|..|++-++++++ T Consensus 187 d~~A~g~~~~l~~~gi--~vP~di~vvgfd~~~~~~~~~p~ltti~q~~~~~g~~a~~~L~~~i~ 249 (269) T cd06275 187 DLMAMGALCAAQEAGL--RVPQDLSIIGYDDIELARYFSPPLTTIHQPKDRLGELAVNMLLERIK 249 (269) T ss_pred HHHHHHHHHHHHHCCC--CCCCCCEEEEECCHHHHHHCCCCEEEEECCHHHHHHHHHHHHHHHHC T ss_conf 4999999999998088--78998679987787999833898589961999999999999999966 No 21 >cd01545 PBP1_SalR Ligand-binding domain of DNA transcription repressor SalR, a member of the LacI-GalR family of bacterial transcription regulators. Ligand-binding domain of DNA transcription repressor SalR, a member of the LacI-GalR family of bacterial transcription regulators. The SalR binds to glucose based compound Salicin which is chemically related to aspirin. The ligand-binding of SalR is structurally homologous to the periplasmic sugar-binding domain of ABC-transporters and both domains contain the type I periplasmic binding protein-like fold. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the type I periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand bind Probab=95.45 E-value=0.25 Score=29.27 Aligned_cols=123 Identities=16% Similarity=0.108 Sum_probs=80.0 Q ss_pred CCEEEEEEECHHHHHHHHHHHHHHHHHHHCCCCEEE-EEHHH--HHHHHHH-HHHHHHHHHCCCCCCEEEEEEEEECCCC Q ss_conf 871799980312899999999999999987995555-53001--4422699-9999863311378535665412000665 Q gi|254780346|r 5 IPHVLIIEARFYENLSAMLFEGCVNVLHSRAVQWSS-IVTPG--VLEIPAA-VSMVMNAKTRSVTYDGIIVLGVVMRGKT 80 (149) Q Consensus 5 ~~kI~IV~s~~~~~i~~~ll~ga~~~l~~~~~~~~~-i~VPG--a~EiP~a-~~~~~~~~~~~~~~D~vIaLG~VIkGeT 80 (149) ..||+++...-.......-++|+.+.+.++|...+. ..++| ++|-... ++.++. ...+++|++|. T Consensus 118 ~~~I~~i~g~~~~~~~~~R~~Gf~~a~~~~gi~~~~~~i~~~~~s~~~~~~~~~~ll~---~~~~~tai~~~-------- 186 (270) T cd01545 118 HRRIAFIAGPPDHRASAERLEGYRDALAEAGLPLDPELVAQGDFTFESGLEAAEALLA---LPDRPTAIFAS-------- 186 (270) T ss_pred CCEEEEECCCCCCCHHHHHHHHHHHHHHHCCCCCCCCEEECCCCCCHHHHHHHHHHHH---CCCCCCEEEEC-------- T ss_conf 9659993699777369999999999999839997721220265310269999999985---59998589978-------- Q ss_pred CHHHHHHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHH------CCCCCCCHHHHHHHHHHHHH Q ss_conf 246789999999999999743997056542558899999950------65657456999999999999 Q gi|254780346|r 81 AHCDVIAHAVTRGLVDLSINGSLPIGNGIVVVDSEQQAFDRV------SPSHLDRGGCAARSALAMIE 142 (149) Q Consensus 81 ~H~e~I~~~v~~gl~~lsl~~~~PI~~gILt~~n~~QA~~R~------~~~~~nkG~eaa~Aal~mi~ 142 (149) .|.++-.+.+.+.+..+ .+|==..|++-+|...+.--+ .-....-|..|++..++.++ T Consensus 187 --nD~~A~g~~~~l~~~g~--~iP~dvsiigfD~~~~~~~~~P~LTti~q~~~~~g~~A~~~Ll~~i~ 250 (270) T cd01545 187 --NDDMAAGVLAVAHRRGL--RVPDDLSVVGFDDTPIATTIWPPLTTVRQPIAEMARAAAELLIARLR 250 (270) T ss_pred --CHHHHHHHHHHHHHHCC--CCCCCEEEEEECCHHHHHHCCCCCEEEECCHHHHHHHHHHHHHHHHC T ss_conf --88999999999998189--99998699998885999835898249971999999999999999956 No 22 >cd06267 PBP1_LacI_sugar_binding_like Ligand binding domain of the LacI tanscriptional regulator family belonging to the type I periplasmic-binding fold protein superfamily. Ligand binding domain of the LacI tanscriptional regulator family belonging to the type I periplasmic-binding fold protein superfamily. In most cases, ligands are monosaccharide including lactose, ribose, fructose, xylose, arabinose, galactose/glucose, and other sugars. The LacI family of proteins consists of transcriptional regulators related to the lac repressor. In this case, the domain sugar binding changes the DNA binding activity of the repressor domain. Probab=95.41 E-value=0.23 Score=29.54 Aligned_cols=126 Identities=17% Similarity=0.103 Sum_probs=76.2 Q ss_pred CCEEEEEEECHHHHHHHHHHHHHHHHHHHCCCCEEEE-EHHHHHHHHHHHHHHHHHHHCCCCCCEEEEEEEEECCCCCHH Q ss_conf 8717999803128999999999999999879955555-300144226999999863311378535665412000665246 Q gi|254780346|r 5 IPHVLIIEARFYENLSAMLFEGCVNVLHSRAVQWSSI-VTPGVLEIPAAVSMVMNAKTRSVTYDGIIVLGVVMRGKTAHC 83 (149) Q Consensus 5 ~~kI~IV~s~~~~~i~~~ll~ga~~~l~~~~~~~~~i-~VPGa~EiP~a~~~~~~~~~~~~~~D~vIaLG~VIkGeT~H~ 83 (149) .+||+++...-.......-.+|+.+.+++++...... ..++.+....+.+.+.+-.....++||++|. . T Consensus 116 ~~~i~~i~~~~~~~~~~~R~~gf~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~ai~~~----------~ 185 (264) T cd06267 116 HRRIAFIGGPPDLSTARERLEGYREALEEAGIPLDEELIVEGDFSEESGYEAARELLASGERPTAIFAA----------N 185 (264) T ss_pred CCCEEEECCCCCCCHHHHHHHHHHHHHHHCCCCCCHHEEECCCCCHHHHHHHHHHHHHCCCCCCEEEEC----------C T ss_conf 885689638987706999999999999986999885307527897799999999999659999899878----------8 Q ss_pred HHHHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHH------CCCCCCCHHHHHHHHHHHHH Q ss_conf 789999999999999743997056542558899999950------65657456999999999999 Q gi|254780346|r 84 DVIAHAVTRGLVDLSINGSLPIGNGIVVVDSEQQAFDRV------SPSHLDRGGCAARSALAMIE 142 (149) Q Consensus 84 e~I~~~v~~gl~~lsl~~~~PI~~gILt~~n~~QA~~R~------~~~~~nkG~eaa~Aal~mi~ 142 (149) |.++-.+.+.+.+.. ..+|=-.+|++.+|...+.--. ......-|..|++.++++++ T Consensus 186 D~~A~g~~~~l~~~g--~~iP~di~Iig~d~~~~~~~~~p~lttv~~~~~~ig~~a~~~l~~~i~ 248 (264) T cd06267 186 DLMAIGALRALRELG--LRVPEDVSVVGFDDIPLAELLTPPLTTVRQPIEEMGRAAAELLLERIE 248 (264) T ss_pred HHHHHHHHHHHHHCC--CCCCCCEEEEEECCHHHHHCCCCCCEEEEECHHHHHHHHHHHHHHHHC T ss_conf 799999999999829--999997799999984898534899479990999999999999999965 No 23 >cd06290 PBP1_LacI_like_9 Ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. This group includes the ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor. Probab=95.33 E-value=0.15 Score=30.71 Aligned_cols=126 Identities=16% Similarity=0.124 Sum_probs=76.2 Q ss_pred CCEEEEEEECHHHHHHHHHHHHHHHHHHHCCCCEEE-EEHHHHHHHHHHHHHHHHHHHCCCCCCEEEEEEEEECCCCCHH Q ss_conf 871799980312899999999999999987995555-5300144226999999863311378535665412000665246 Q gi|254780346|r 5 IPHVLIIEARFYENLSAMLFEGCVNVLHSRAVQWSS-IVTPGVLEIPAAVSMVMNAKTRSVTYDGIIVLGVVMRGKTAHC 83 (149) Q Consensus 5 ~~kI~IV~s~~~~~i~~~ll~ga~~~l~~~~~~~~~-i~VPGa~EiP~a~~~~~~~~~~~~~~D~vIaLG~VIkGeT~H~ 83 (149) -.||+++...-....+..-..|+.+.++++|...+. ..++|.+....+.+.+.+......++||++|. . T Consensus 115 ~~~i~~i~~~~~~~~~~~R~~Gf~~a~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~ai~~~----------n 184 (265) T cd06290 115 HRRIAHITGPRGHIDARDRLAGYRKALEEAGLEVQPDLIVQGDFEEESGLEAVEELLQRGPDFTAIFAA----------N 184 (265) T ss_pred CCCEEEECCCCCCHHHHHHHHHHHHHHHHCCCCCCHHHEECCCCCCHHHHHHHHHHHHHCCCCCCCEEC----------C T ss_conf 986556048878701999999999999986999988883416677178999999999719998842105----------7 Q ss_pred HHHHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHH------CCCCCCCHHHHHHHHHHHHH Q ss_conf 789999999999999743997056542558899999950------65657456999999999999 Q gi|254780346|r 84 DVIAHAVTRGLVDLSINGSLPIGNGIVVVDSEQQAFDRV------SPSHLDRGGCAARSALAMIE 142 (149) Q Consensus 84 e~I~~~v~~gl~~lsl~~~~PI~~gILt~~n~~QA~~R~------~~~~~nkG~eaa~Aal~mi~ 142 (149) |.++-.+.+++.+.. ..+|==..|++-+|...+.-=+ .....--|..|++..+++++ T Consensus 185 D~~A~g~~~~~~~~g--~~vP~di~vigfD~~~~~~~~~p~ltti~~~~~~~G~~A~~~L~~~i~ 247 (265) T cd06290 185 DQTAYGARLALYRRG--LRVPEDVSLIGFDDLPLSAYTTPPLTTVRQPIEEMGQIAARALLALIN 247 (265) T ss_pred HHHHHHHHHHHHHHC--CCCCCCEEEEEECCHHHHHHCCCCEEEEEECHHHHHHHHHHHHHHHHC T ss_conf 899999999999809--999998799999987899732898289995999999999999999975 No 24 >cd06281 PBP1_LacI_like_5 Ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. This group includes the ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor. Probab=95.28 E-value=0.29 Score=28.92 Aligned_cols=123 Identities=11% Similarity=0.034 Sum_probs=77.4 Q ss_pred CCEEEEEEECHHHHHHHHHHHHHHHHHHHCCCCEEE--EEHHHHHHHHHH-HHHHHHHHHCCCCCCEEEEEEEEECCCCC Q ss_conf 871799980312899999999999999987995555--530014422699-99998633113785356654120006652 Q gi|254780346|r 5 IPHVLIIEARFYENLSAMLFEGCVNVLHSRAVQWSS--IVTPGVLEIPAA-VSMVMNAKTRSVTYDGIIVLGVVMRGKTA 81 (149) Q Consensus 5 ~~kI~IV~s~~~~~i~~~ll~ga~~~l~~~~~~~~~--i~VPGa~EiP~a-~~~~~~~~~~~~~~D~vIaLG~VIkGeT~ 81 (149) -+||+++....+...+..-++|+.+.+.++|...+. +...+..+-.+. +..++ ....++||++|. T Consensus 116 ~~~I~~i~~~~~~~~~~~R~~G~~~al~~~g~~~~~~~~~~~~~~~~~~~~~~~ll---~~~~~p~ai~~~--------- 183 (269) T cd06281 116 HRRIALVGGGSNTRPGRERLEGYKAAFAAAGLPPDPALVRLSTPAASGFDATRALL---ALPDRPTAIIAG--------- 183 (269) T ss_pred CCCEEEEECCCCCHHHHHHHHHHHHHHHHCCCCCCCEEEECCCCHHHHHHHHHHHH---HCCCCCCEEEEC--------- T ss_conf 98668980788776799999999999997799999439977997489999999998---079999656512--------- Q ss_pred HHHHHHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHH------CCCCCCCHHHHHHHHHHHHH Q ss_conf 46789999999999999743997056542558899999950------65657456999999999999 Q gi|254780346|r 82 HCDVIAHAVTRGLVDLSINGSLPIGNGIVVVDSEQQAFDRV------SPSHLDRGGCAARSALAMIE 142 (149) Q Consensus 82 H~e~I~~~v~~gl~~lsl~~~~PI~~gILt~~n~~QA~~R~------~~~~~nkG~eaa~Aal~mi~ 142 (149) .|.++-.+.+.+.+. ...+|=-..|++.+|...+.-=. ......-|..|++..+++++ T Consensus 184 -~d~~A~g~l~~l~~~--g~~VP~disviGfD~~~~~~~~~P~LTTi~~~~~~~g~~A~~~Ll~~i~ 247 (269) T cd06281 184 -GTQVLVGVLRALREA--GLRIPRDLSVISIGDSDLAELMDPPITALRRDREAVGRTAAELMLDRLE 247 (269) T ss_pred -CHHHHHHHHHHHHHC--CCCCCCCEEEEEECCHHHHHHCCCCCEEEECCHHHHHHHHHHHHHHHHC T ss_conf -338899999999981--9999998699998887999835899679974999999999999999966 No 25 >cd06286 PBP1_CcpB_like Ligand-binding domain of a novel transcription factor implicated in catabolite repression in Bacillus and Clostridium species. This group includes the ligand-binding domain of a novel transcription factor implicated in catabolite repression in Bacillus and Clostridium species. CcpB is 30% identical in sequence to CcpA which functions as the major transcriptional regulator of carbon catabolite repression/regulation (CCR), a process in which enzymes necessary for the metabolism of alternative sugars are inhibited in the presence of glucose. Like CcpA, the DNA-binding protein CcpB exerts its catabolite-repressing effect by a mechanism dependent on the presence of HPr(Ser-P), the small phosphocarrier proteins of the phosphoenolpyruvate-sugar phosphotransferase system, but with a less significant degree. Probab=95.24 E-value=0.29 Score=28.85 Aligned_cols=123 Identities=13% Similarity=0.004 Sum_probs=81.2 Q ss_pred CCEEEEEEECHHHHHHHHHHHHHHHHHHHCCCCEEEEE-HHH--HHHHHHHH-HHHHHHHHCCCCCCEEEEEEEEECCCC Q ss_conf 87179998031289999999999999998799555553-001--44226999-999863311378535665412000665 Q gi|254780346|r 5 IPHVLIIEARFYENLSAMLFEGCVNVLHSRAVQWSSIV-TPG--VLEIPAAV-SMVMNAKTRSVTYDGIIVLGVVMRGKT 80 (149) Q Consensus 5 ~~kI~IV~s~~~~~i~~~ll~ga~~~l~~~~~~~~~i~-VPG--a~EiP~a~-~~~~~~~~~~~~~D~vIaLG~VIkGeT 80 (149) -.||+++.+.-+...+..-.+|+.+.+.++|...+.-+ ..+ .+|-...+ +.++ ....++||++|. T Consensus 114 ~~~i~~i~~~~~~~~~~~R~~Gf~~al~~~g~~~~~~~~~~~~~~~~~g~~~~~~~~---~~~~~p~ai~~~-------- 182 (260) T cd06286 114 YRKIAYCIGRKKSLNSQSRKKAYKDALEEYGLTPDEEWIFEGCFTIEDGERIGHQLL---KMKDRPDAIFTG-------- 182 (260) T ss_pred CCEEEEEECCCCCHHHHHHHHHHHHHHHHCCCCCCCEEEECCCCCHHHHHHHHHHHH---HCCCCCCEEEEC-------- T ss_conf 973999938988704999999999999977999773036446520667999999998---449998736736-------- Q ss_pred CHHHHHHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHH----CCCCCCCHHHHHHHHHHHHH Q ss_conf 246789999999999999743997056542558899999950----65657456999999999999 Q gi|254780346|r 81 AHCDVIAHAVTRGLVDLSINGSLPIGNGIVVVDSEQQAFDRV----SPSHLDRGGCAARSALAMIE 142 (149) Q Consensus 81 ~H~e~I~~~v~~gl~~lsl~~~~PI~~gILt~~n~~QA~~R~----~~~~~nkG~eaa~Aal~mi~ 142 (149) .|.++-.+.+.+.+. ...+|=-..|++.++..-+..-. ......-|++|++..+++++ T Consensus 183 --nd~~A~g~~~al~~~--g~~vP~di~vigfdd~~~~~~p~lTtv~~~~~~~g~~A~~~ll~~i~ 244 (260) T cd06286 183 --SDEVAAGIITEAKKQ--GIRVPEDLAIIGFDNQPISELLGITTIDQPVKELGEKAFELLLNQLE 244 (260) T ss_pred --CHHHHHHHHHHHHHC--CCCCCCCEEEEEECCHHHHCCCCCCEEECCHHHHHHHHHHHHHHHHC T ss_conf --899999999999972--99999976999989849982899758935999999999999999976 No 26 >PRK10014 DNA-binding transcriptional repressor MalI; Provisional Probab=95.20 E-value=0.3 Score=28.76 Aligned_cols=128 Identities=12% Similarity=0.024 Sum_probs=78.2 Q ss_pred CCEEEEEEECHHHHHHHHHHHHHHHHHHHCCCCEEEEE-HHHHHHHHHHHHHHHHHHHCCCCCCEEEEEEEEECCCCCHH Q ss_conf 87179998031289999999999999998799555553-00144226999999863311378535665412000665246 Q gi|254780346|r 5 IPHVLIIEARFYENLSAMLFEGCVNVLHSRAVQWSSIV-TPGVLEIPAAVSMVMNAKTRSVTYDGIIVLGVVMRGKTAHC 83 (149) Q Consensus 5 ~~kI~IV~s~~~~~i~~~ll~ga~~~l~~~~~~~~~i~-VPGa~EiP~a~~~~~~~~~~~~~~D~vIaLG~VIkGeT~H~ 83 (149) -.||+.+.+.-.......-+.|..+.|.++|.+.+.-+ +.+.++-..+.+.+.+-.....+++|++| .. T Consensus 182 hr~Ia~i~~~~~~~~~~~R~~gf~~al~~~~l~~~~~~i~~~~~~~~~~~~~~~~ll~~~~~~tAi~c----------~~ 251 (342) T PRK10014 182 HQRIAWLGGQSSSLTRAERVGGYCATLLKFGLPFHSEWVLECTSSQKQAAEAITALLRHNPTISAVVC----------YN 251 (342) T ss_pred CCEEEEEECCCCCHHHHHHHHHHHHHHHHCCCCCCCCEEEECCCCHHHHHHHHHHHHHCCCCCCEEEE----------EC T ss_conf 98699995788863399999999999997699988334896689789999999999836999718999----------67 Q ss_pred HHHHHHHHHHHHHHHHHCC-------CCCEEEEECCCCHHHHHHHH------CCCCCCCHHHHHHHHHHHHH Q ss_conf 7899999999999997439-------97056542558899999950------65657456999999999999 Q gi|254780346|r 84 DVIAHAVTRGLVDLSINGS-------LPIGNGIVVVDSEQQAFDRV------SPSHLDRGGCAARSALAMIE 142 (149) Q Consensus 84 e~I~~~v~~gl~~lsl~~~-------~PI~~gILt~~n~~QA~~R~------~~~~~nkG~eaa~Aal~mi~ 142 (149) |.++-.+..++.+..++-. +|=-..|++.+|...+..-. ......-|..|++..+++++ T Consensus 252 D~~A~g~~~~l~~~g~~v~~d~~~~~ip~~vsIigfdd~~~~~~~~P~LTtv~~~~~~ig~~a~~~Ll~~i~ 323 (342) T PRK10014 252 ETIAMGAWFGLLRAGRQSGESGVDRYFEQQVALAAFTDVPEAELDDPPLTWASTPAREIGRTLADRMMQRIT 323 (342) T ss_pred HHHHHHHHHHHHHHCHHCCCCCCCCCCCCCEEEEEECCHHHHHCCCCCCEEEECCHHHHHHHHHHHHHHHHC T ss_conf 899999999999958221755333478985899998884888625898569983999999999999999966 No 27 >cd06295 PBP1_CelR Ligand binding domain of a transcription regulator of cellulose genes, CelR, which is highly homologous to the LacI-GalR family of bacterial transcription regulators. This group includes the ligand binding domain of a transcription regulator of cellulose genes, CelR, which is highly homologous to the LacI-GalR family of bacterial transcription regulators. The binding of CelR to the celE promoter is inhibited specifically by cellobiose. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn chang Probab=95.18 E-value=0.28 Score=29.00 Aligned_cols=126 Identities=16% Similarity=0.152 Sum_probs=73.0 Q ss_pred CCEEEEEEECHHHHHHHHHHHHHHHHHHHCCCCEEEE-EHHHHHHHHHHHHHHHHHHHCCCCCCEEEEEEEEECCCCCHH Q ss_conf 8717999803128999999999999999879955555-300144226999999863311378535665412000665246 Q gi|254780346|r 5 IPHVLIIEARFYENLSAMLFEGCVNVLHSRAVQWSSI-VTPGVLEIPAAVSMVMNAKTRSVTYDGIIVLGVVMRGKTAHC 83 (149) Q Consensus 5 ~~kI~IV~s~~~~~i~~~ll~ga~~~l~~~~~~~~~i-~VPGa~EiP~a~~~~~~~~~~~~~~D~vIaLG~VIkGeT~H~ 83 (149) -++|+++.+.-.......-+.|+.+.+.+++...+.. .+++.|..-.+.+.+.+-.....++||++|. . T Consensus 125 ~~~I~~i~~~~~~~~~~~R~~Gf~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~ai~~~----------n 194 (275) T cd06295 125 RRRIAFLGGPQDMPEGEERLEGYREALAEAGLPLDPRLVAPGDFTEESGRAAMRALLERGPDFDAVFAA----------S 194 (275) T ss_pred CCEEEEECCCCCCCHHHHHHHHHHHHHHHCCCCCCCCEEEECCCCHHHHHHHHHHHHHCCCCCCEEEEC----------C T ss_conf 987987058866726999999999999986999994179965776687999988898549998703414----------7 Q ss_pred HHHHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHH------CCCCCCCHHHHHHHHHHHHH Q ss_conf 789999999999999743997056542558899999950------65657456999999999999 Q gi|254780346|r 84 DVIAHAVTRGLVDLSINGSLPIGNGIVVVDSEQQAFDRV------SPSHLDRGGCAARSALAMIE 142 (149) Q Consensus 84 e~I~~~v~~gl~~lsl~~~~PI~~gILt~~n~~QA~~R~------~~~~~nkG~eaa~Aal~mi~ 142 (149) |.++-.+.+.+.+.. ..+|=-..|++.++.+.+.-=. ......-|..|++.++++++ T Consensus 195 D~~A~g~~~~~~~~g--~~iP~disIigfd~~~~~~~~~P~LTtI~~~~~~ig~~A~~~Ll~~i~ 257 (275) T cd06295 195 DLMALGALRALREAG--RRVPEDVAVVGFDDIPLAAYADPPLTTVRQDIEEAGRLLVDLLLALIA 257 (275) T ss_pred CHHHHHHHHHHHHCC--CCCCCCEEEEEECCHHHHHHCCCCEEEEEECHHHHHHHHHHHHHHHHC T ss_conf 587899999999749--998985699996786899834898699980999999999999999967 No 28 >PRK10423 transcriptional repressor RbsR; Provisional Probab=95.09 E-value=0.33 Score=28.57 Aligned_cols=102 Identities=12% Similarity=0.146 Sum_probs=40.6 Q ss_pred CEEEEEEECHHHHHHHHHHHHHHHHHHHCCCCEEE-EEHHHHHHHHHHHHHHHHHHHCCCCCCEEEEEEEEECCCCCHHH Q ss_conf 71799980312899999999999999987995555-53001442269999998633113785356654120006652467 Q gi|254780346|r 6 PHVLIIEARFYENLSAMLFEGCVNVLHSRAVQWSS-IVTPGVLEIPAAVSMVMNAKTRSVTYDGIIVLGVVMRGKTAHCD 84 (149) Q Consensus 6 ~kI~IV~s~~~~~i~~~ll~ga~~~l~~~~~~~~~-i~VPGa~EiP~a~~~~~~~~~~~~~~D~vIaLG~VIkGeT~H~e 84 (149) .||+++.+.........=++|+.+.+.++|..... ..+.|.|+.....+.+.+-.....++||++|. .| T Consensus 175 r~I~~i~~~~~~~~~~~R~~gf~~al~~~gl~~~~~~~~~~~~~~~~g~~~~~~ll~~~~~ptAi~~~----------nD 244 (327) T PRK10423 175 TRIACITGPLDKTPARLRLEGYRAAMKRAGLNIPDGYEVTGDFEFNGGFDAMQQLLAHPLRPQAVFTG----------ND 244 (327) T ss_pred CEEEEECCCCCCCHHHHHHHHHHHHHHHCCCCCCCCEEEECCCCHHHHHHHHHHHHHCCCCCCEEEEC----------CC T ss_conf 74999668876617999999999999985999884369960467378999999998479999845517----------80 Q ss_pred HHHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHH Q ss_conf 89999999999999743997056542558899999 Q gi|254780346|r 85 VIAHAVTRGLVDLSINGSLPIGNGIVVVDSEQQAF 119 (149) Q Consensus 85 ~I~~~v~~gl~~lsl~~~~PI~~gILt~~n~~QA~ 119 (149) .++-.+.+++.+.. ..+|==..|++.+|...+. T Consensus 245 ~~A~g~~~al~~~g--~~iP~DisvigfDd~~~~~ 277 (327) T PRK10423 245 AMAVGVYQALYQAG--LQVPQDIAVIGYDDIELAS 277 (327) T ss_pred HHHHHHHHHHHHCC--CCCCCCEEEEEECCCHHHH T ss_conf 99999999999869--9999975999975828998 No 29 >cd06285 PBP1_LacI_like_7 Ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. This group includes the ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor. Probab=94.91 E-value=0.23 Score=29.56 Aligned_cols=123 Identities=13% Similarity=0.085 Sum_probs=77.5 Q ss_pred CCEEEEEEECHHHHHHHHHHHHHHHHHHHCCCCEEEEE-HHHHHHHHHH---HHHHHHHHHCCCCCCEEEEEEEEECCCC Q ss_conf 87179998031289999999999999998799555553-0014422699---9999863311378535665412000665 Q gi|254780346|r 5 IPHVLIIEARFYENLSAMLFEGCVNVLHSRAVQWSSIV-TPGVLEIPAA---VSMVMNAKTRSVTYDGIIVLGVVMRGKT 80 (149) Q Consensus 5 ~~kI~IV~s~~~~~i~~~ll~ga~~~l~~~~~~~~~i~-VPGa~EiP~a---~~~~~~~~~~~~~~D~vIaLG~VIkGeT 80 (149) ..||+++...-+......-..|+.+.+.++|.+....+ +.+.+..-.. ++.++ ....++||++|. T Consensus 114 ~~~i~~l~~~~~~~~~~~R~~Gf~~a~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~l---~~~~~~~ai~~~-------- 182 (265) T cd06285 114 HRRIAVLAGPDYASTARDRLAGFRAALAEAGIEVPPERIVYSGFDIEGGEAAAEKLL---RSDSPPTAIFAV-------- 182 (265) T ss_pred CCCEEECCCCCCCCHHHHHHHHHHHHHHHCCCCCCHHHEECCCCCHHHHHHHHHHHH---HCCCCCCCEECC-------- T ss_conf 865875478877705999999999999986999875660136621556999999998---569998810037-------- Q ss_pred CHHHHHHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHH------CCCCCCCHHHHHHHHHHHHH Q ss_conf 246789999999999999743997056542558899999950------65657456999999999999 Q gi|254780346|r 81 AHCDVIAHAVTRGLVDLSINGSLPIGNGIVVVDSEQQAFDRV------SPSHLDRGGCAARSALAMIE 142 (149) Q Consensus 81 ~H~e~I~~~v~~gl~~lsl~~~~PI~~gILt~~n~~QA~~R~------~~~~~nkG~eaa~Aal~mi~ 142 (149) .|.++-.+.+.+.+.. ..+|=-..|++-+|...+..=. .-....-|+.|++..+++++ T Consensus 183 --nD~~A~g~~~~l~~~g--~~iP~di~iigfd~~~~~~~~~p~LTti~q~~~~ig~~A~~~ll~~i~ 246 (265) T cd06285 183 --NDFAAIGVMGAARDRG--LRVPDDVALVGYNDIPLVARLPVPLTTVRSPFHQIGRTALRLLLETIA 246 (265) T ss_pred --CHHHHHHHHHHHHHCC--CCCCCCEEEEEECCHHHHHHCCCCCEEEECCHHHHHHHHHHHHHHHHC T ss_conf --8899999999999859--999998799998782899707899579972999999999999999847 No 30 >PRK11041 DNA-binding transcriptional regulator CytR; Provisional Probab=94.36 E-value=0.5 Score=27.45 Aligned_cols=121 Identities=16% Similarity=0.091 Sum_probs=59.1 Q ss_pred CEEEEEEECHHHHHHHHHHHHHHHHHHHCCCCEEEEE-HHHHH--HHHH-HHHHHHHHHHCCCCCCEEEEEEEEECCCCC Q ss_conf 7179998031289999999999999998799555553-00144--2269-999998633113785356654120006652 Q gi|254780346|r 6 PHVLIIEARFYENLSAMLFEGCVNVLHSRAVQWSSIV-TPGVL--EIPA-AVSMVMNAKTRSVTYDGIIVLGVVMRGKTA 81 (149) Q Consensus 6 ~kI~IV~s~~~~~i~~~ll~ga~~~l~~~~~~~~~i~-VPGa~--EiP~-a~~~~~~~~~~~~~~D~vIaLG~VIkGeT~ 81 (149) .||+.+.+..+....+.-++|+.+.+.++|++.+.-+ +.|.| |-.. +++.++ .....+||++|. T Consensus 185 r~I~~i~~~~~~~~~~~R~~G~~~al~~~gl~~~~~~i~~~~~~~~~g~~~~~~ll---~~~~~ptAi~~~--------- 252 (341) T PRK11041 185 KRIACIAGPEEMPLCHYRLQGYVQALRRCGITVDPQYIARGDFTFEAGAKAMQQLL---ELPQPPTAVFCH--------- 252 (341) T ss_pred CEEEEEECCCCCHHHHHHHHHHHHHHHHCCCCCCCCEEEECCCCHHHHHHHHHHHH---HCCCCCCEEEEC--------- T ss_conf 76999968987768999999999999986999991048954676799999999999---559998579876--------- Q ss_pred HHHHHHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHH------CCCCCCCHHHHHHHHHHHH Q ss_conf 46789999999999999743997056542558899999950------6565745699999999999 Q gi|254780346|r 82 HCDVIAHAVTRGLVDLSINGSLPIGNGIVVVDSEQQAFDRV------SPSHLDRGGCAARSALAMI 141 (149) Q Consensus 82 H~e~I~~~v~~gl~~lsl~~~~PI~~gILt~~n~~QA~~R~------~~~~~nkG~eaa~Aal~mi 141 (149) .|.++-.+.+++.+.. ..+|==..|++.+|...+.--. ......-|..|++-.++++ T Consensus 253 -nD~~A~g~l~al~~~G--l~VP~DisViGfdd~~~~~~~~P~LTTV~~~~~~~g~~A~~~L~~~i 315 (341) T PRK11041 253 -SDVMALGALSQAKRQG--LKVPQDLSIIGFDNIDLAQFCDPPLTTIAQPRYEIGREAMLLLLDQL 315 (341) T ss_pred -CHHHHHHHHHHHHHHC--CCCCCCEEEEEECCHHHHHCCCCCEEEEECCHHHHHHHHHHHHHHHH T ss_conf -7799999999999718--98999659999888389852699836998199999999999999996 No 31 >cd06325 PBP1_ABC_uncharacterized_transporter Type I periplasmic ligand-binding domain of uncharacterized ABC-type transport systems that are predicted to be involved in the uptake of amino acids, peptides, or inorganic ions. This group includes the type I periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type transport systems that are predicted to be involved in the uptake of amino acids, peptides, or inorganic ions. This subgroup has high sequence similarity to members of the family of hydrophobic amino acid transporters (HAAT), such as leucine/isoleucine/valine binding protein (LIVBP); its ligand specificity has not been determined experimentally. Probab=94.33 E-value=0.34 Score=28.48 Aligned_cols=116 Identities=10% Similarity=0.088 Sum_probs=77.6 Q ss_pred CCEEEEEEECHHHHHHHHHHHHHHHHHHHCCCCEEEEEHHHHHHHHHHHHHHHHHHHCCCCCCEEEEEEEEECCCCCHHH Q ss_conf 87179998031289999999999999998799555553001442269999998633113785356654120006652467 Q gi|254780346|r 5 IPHVLIIEARFYENLSAMLFEGCVNVLHSRAVQWSSIVTPGVLEIPAAVSMVMNAKTRSVTYDGIIVLGVVMRGKTAHCD 84 (149) Q Consensus 5 ~~kI~IV~s~~~~~i~~~ll~ga~~~l~~~~~~~~~i~VPGa~EiP~a~~~~~~~~~~~~~~D~vIaLG~VIkGeT~H~e 84 (149) .+||++++..=.. -....++..++...+.|+++....|+..-|++.+++.+. .+.|++... |+. T Consensus 131 ~k~igvlyn~~e~-ns~~~~~~~~~~a~~~Gi~v~~~~v~~~~ei~~a~~~l~------~~~Dal~~~-------~d~-- 194 (281) T cd06325 131 AKTVGVLYNPSEA-NSVVQVKELKKAAAKLGIEVVEATVSSSNDVQQAAQSLA------GKVDAIYVP-------TDN-- 194 (281) T ss_pred CCEEEEEECCCCC-CHHHHHHHHHHHHHHCCCEEEEEECCCHHHHHHHHHHHH------HCCCEEEEE-------CCC-- T ss_conf 8589999579986-569999999999997698899994598889999999756------258999991-------881-- Q ss_pred HHHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHH----CCCCCCCHHHHHHHHHHHHH Q ss_conf 89999999999999743997056542558899999950----65657456999999999999 Q gi|254780346|r 85 VIAHAVTRGLVDLSINGSLPIGNGIVVVDSEQQAFDRV----SPSHLDRGGCAARSALAMIE 142 (149) Q Consensus 85 ~I~~~v~~gl~~lsl~~~~PI~~gILt~~n~~QA~~R~----~~~~~nkG~eaa~Aal~mi~ 142 (149) ++. +....+.+++.++.+|+..+ +..+...-+ +.+..+-|+.+|+-+.+.++ T Consensus 195 ~v~-s~~~~i~~~a~~~~iPv~~~-----~~~~v~~G~L~s~g~~~~~~G~~aa~~a~rIL~ 250 (281) T cd06325 195 TVA-SAMEAVVKVANEAKIPVIAS-----DDDMVKRGGLATYGIDYYELGRQTGKMAAKILK 250 (281) T ss_pred HHH-HHHHHHHHHHHHCCCCEEEC-----CHHHHHCCCEEEECCCHHHHHHHHHHHHHHHHC T ss_conf 277-79999999998749988936-----778861672799827899999999999999978 No 32 >cd01575 PBP1_GntR Ligand-binding domain of DNA transcription repressor GntR specific for gluconate, a member of the LacI-GalR family of bacterial transcription regulators. This group represents the ligand-binding domain of DNA transcription repressor GntR specific for gluconate, a member of the LacI-GalR family of bacterial transcription regulators. The ligand-binding domain of GntR is structurally homologous to the periplasmic sugar-binding domain of ABC-type transporters and both domains contain the type I periplasmic binding protein-like fold. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the type I periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding, Probab=93.90 E-value=0.61 Score=26.87 Aligned_cols=126 Identities=17% Similarity=0.102 Sum_probs=78.9 Q ss_pred CCEEEEEEECHHHHHHHHHHHHHHHHHHHCCCCEEEEEH-HHHHHHHHHHHHHHHHHHCCCCCCEEEEEEEEECCCCCHH Q ss_conf 871799980312899999999999999987995555530-0144226999999863311378535665412000665246 Q gi|254780346|r 5 IPHVLIIEARFYENLSAMLFEGCVNVLHSRAVQWSSIVT-PGVLEIPAAVSMVMNAKTRSVTYDGIIVLGVVMRGKTAHC 83 (149) Q Consensus 5 ~~kI~IV~s~~~~~i~~~ll~ga~~~l~~~~~~~~~i~V-PGa~EiP~a~~~~~~~~~~~~~~D~vIaLG~VIkGeT~H~ 83 (149) -.||+++...-....+..-+.|+.+.+.++|......+. .+.+......+.+-+-.....++||++|. . T Consensus 116 ~~~i~~i~~~~~~~~~~~R~~G~~~al~~~g~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~dai~~~----------n 185 (268) T cd01575 116 YRRIGFLGARMDDTRAQQRLEGFRAALRAAGLDPPLVVTTPEPSSFALGRELLAELLARWPDLDAVFCS----------N 185 (268) T ss_pred CCEEEEECCCCCCHHHHHHHHHHHHHHHHCCCCCCEEEEECCCCCHHHHHHHHHHHHHCCCCCCEEEEC----------C T ss_conf 976999848988736999999999999976989880899548998899999999999569998379987----------8 Q ss_pred HHHHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHH------CCCCCCCHHHHHHHHHHHHH Q ss_conf 789999999999999743997056542558899999950------65657456999999999999 Q gi|254780346|r 84 DVIAHAVTRGLVDLSINGSLPIGNGIVVVDSEQQAFDRV------SPSHLDRGGCAARSALAMIE 142 (149) Q Consensus 84 e~I~~~v~~gl~~lsl~~~~PI~~gILt~~n~~QA~~R~------~~~~~nkG~eaa~Aal~mi~ 142 (149) |.++-.+.+.+.+.. ..+|==..|++.+|...+.-=. ......-|..|++.++++++ T Consensus 186 D~~A~g~~~~l~~~g--~~iP~disvigfdd~~~~~~~~p~ltti~~~~~~~g~~a~~~l~~~i~ 248 (268) T cd01575 186 DDLALGALFECQRRG--ISVPEDIAIAGFGDLEIAAALPPALTTVRTPRREIGRRAAELLLARLA 248 (268) T ss_pred HHHHHHHHHHHHHHC--CCCCCCEEEEEECCHHHHHCCCCCCEEEEECHHHHHHHHHHHHHHHHC T ss_conf 899999999999838--999997799998973899616899679996999999999999999976 No 33 >cd06279 PBP1_LacI_like_3 Ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. This group includes the ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor. Probab=93.80 E-value=0.64 Score=26.76 Aligned_cols=123 Identities=19% Similarity=0.178 Sum_probs=76.1 Q ss_pred CCEEEEEEE-----------------CHHHHHHHHHHHHHHHHHHHCCCCEEEEE--HHHHHHHHH---HHHHHHHHHHC Q ss_conf 871799980-----------------31289999999999999998799555553--001442269---99999863311 Q gi|254780346|r 5 IPHVLIIEA-----------------RFYENLSAMLFEGCVNVLHSRAVQWSSIV--TPGVLEIPA---AVSMVMNAKTR 62 (149) Q Consensus 5 ~~kI~IV~s-----------------~~~~~i~~~ll~ga~~~l~~~~~~~~~i~--VPGa~EiP~---a~~~~~~~~~~ 62 (149) -+||+++.. .........=++|+.+.+.++|...+..+ -.|.+.... +++.++. . T Consensus 116 h~~Ia~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~R~~G~~~al~~~gl~~~~~~i~~~~~~~~~~g~~~~~~ll~---~ 192 (283) T cd06279 116 HRRIGILGLRLGRDRNTGRVTDERLASATFSVARERLEGYLEALEEAGIDISDVPIWEIPENDRASGEEAARELLD---A 192 (283) T ss_pred CCEEEEEECCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCCEEEEECCCCCHHHHHHHHHHHHH---C T ss_conf 9869999524556654443221013664247799999999999998599977205784599999999999999995---5 Q ss_pred CCCCCEEEEEEEEECCCCCHHHHHHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHHCC-----CCCCCHHHHHHHH Q ss_conf 37853566541200066524678999999999999974399705654255889999995065-----6574569999999 Q gi|254780346|r 63 SVTYDGIIVLGVVMRGKTAHCDVIAHAVTRGLVDLSINGSLPIGNGIVVVDSEQQAFDRVSP-----SHLDRGGCAARSA 137 (149) Q Consensus 63 ~~~~D~vIaLG~VIkGeT~H~e~I~~~v~~gl~~lsl~~~~PI~~gILt~~n~~QA~~R~~~-----~~~nkG~eaa~Aa 137 (149) ..++||++|. .|.++-.+.+++.+.. ..+|==..|++-+|...|..+-.- ....-|..|++-. T Consensus 193 ~~~ptai~~~----------nD~~A~g~~~~l~~~G--i~VP~DvsviGfDd~~~a~~~P~LTTI~q~~~~~G~~A~~~L 260 (283) T cd06279 193 SPRPTAILCM----------SDVLALGALQVARELG--LRVPEDLSVVGFDGIPEARLRPGLTTVRQPSEEKGRLAARLL 260 (283) T ss_pred CCCCCEEEEC----------CHHHHHHHHHHHHHHC--CCCCCCEEEEEECCCHHHHCCCCCEEEECCHHHHHHHHHHHH T ss_conf 9999669857----------7299999999999818--999996599958988899458997089619999999999999 Q ss_pred HHHHH Q ss_conf 99999 Q gi|254780346|r 138 LAMIE 142 (149) Q Consensus 138 l~mi~ 142 (149) +++++ T Consensus 261 l~~i~ 265 (283) T cd06279 261 LDLLE 265 (283) T ss_pred HHHHC T ss_conf 99964 No 34 >PRK10401 DNA-binding transcriptional regulator GalS; Provisional Probab=93.51 E-value=0.72 Score=26.45 Aligned_cols=103 Identities=14% Similarity=0.121 Sum_probs=59.5 Q ss_pred CEEEEEEECHHHHHHHHHHHHHHHHHHHCCCCEEEEE-HHHHHHHHHHHHHHHHHHHCCCCCCEEEEEEEEECCCCCHHH Q ss_conf 7179998031289999999999999998799555553-001442269999998633113785356654120006652467 Q gi|254780346|r 6 PHVLIIEARFYENLSAMLFEGCVNVLHSRAVQWSSIV-TPGVLEIPAAVSMVMNAKTRSVTYDGIIVLGVVMRGKTAHCD 84 (149) Q Consensus 6 ~kI~IV~s~~~~~i~~~ll~ga~~~l~~~~~~~~~i~-VPGa~EiP~a~~~~~~~~~~~~~~D~vIaLG~VIkGeT~H~e 84 (149) .||+++.+.........-.+|+.+.+.++|...+..+ ..|.+......+.+..-.....++||++|. .| T Consensus 177 rrI~~i~~~~~~~~~~~R~~G~~~al~~~gl~~~~~~v~~~~~~~~~~~~~~~~ll~~~~~~tAi~~~----------nD 246 (346) T PRK10401 177 QRIGYLSSSHGIEDDAMRKAGWLSALKEQGIIPPESWIGTGTPDMQGGEAAMVELLGRNLQLTAVFAY----------ND 246 (346) T ss_pred CCEEEEECCCCCCHHHHHHHHHHHHHHHCCCCCCHHEEEECCCCHHHHHHHHHHHHHCCCCCCCCEEC----------CH T ss_conf 82899947988716899999999999984999870148726875788999999998159998861444----------88 Q ss_pred HHHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHH Q ss_conf 899999999999997439970565425588999999 Q gi|254780346|r 85 VIAHAVTRGLVDLSINGSLPIGNGIVVVDSEQQAFD 120 (149) Q Consensus 85 ~I~~~v~~gl~~lsl~~~~PI~~gILt~~n~~QA~~ 120 (149) .++-.+.+++.+.. ..+|==..|++-+|...+.- T Consensus 247 ~~A~g~l~al~~~G--l~VP~DisViGfDd~~~a~~ 280 (346) T PRK10401 247 NMAAGALTALKDNG--IAIPLHLSIIGFDDIPIARY 280 (346) T ss_pred HHHHHHHHHHHHCC--CCCCCCEEEEEECCHHHHHC T ss_conf 99999999999859--98998728999898089852 No 35 >cd06287 PBP1_LacI_like_8 Ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. This group includes the ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor. Probab=93.45 E-value=0.74 Score=26.39 Aligned_cols=125 Identities=13% Similarity=0.027 Sum_probs=80.8 Q ss_pred CCEEEEEEECHHHHHHHHHHHHHHHHHHHCCCCEEEEEHHHHHHHHHHHHHHHHHHHCCCCCCEEEEEEEEECCCCCHHH Q ss_conf 87179998031289999999999999998799555553001442269999998633113785356654120006652467 Q gi|254780346|r 5 IPHVLIIEARFYENLSAMLFEGCVNVLHSRAVQWSSIVTPGVLEIPAAVSMVMNAKTRSVTYDGIIVLGVVMRGKTAHCD 84 (149) Q Consensus 5 ~~kI~IV~s~~~~~i~~~ll~ga~~~l~~~~~~~~~i~VPGa~EiP~a~~~~~~~~~~~~~~D~vIaLG~VIkGeT~H~e 84 (149) -.||+++.+.-.......-..|..+.+.++|.+...+++++.+.-....+...+-.....++||++|. .| T Consensus 118 hrrIa~i~g~~~~~~~~~R~~gy~~a~~~~gl~~~~~~~~~~~~~~~g~~a~~~ll~~~~~~~AI~~~----------nD 187 (269) T cd06287 118 ARQIALIVGSARRNSYLEAEAAYRAFAAEHGMPPVVLRVDEAGGEEAGYAACAQLLAQHPDLDALCVP----------VD 187 (269) T ss_pred CCEEEEEECCCCCHHHHHHHHHHHHHHHHCCCCCCEEEECCCCCHHHHHHHHHHHHCCCCCCCEEEEE----------CH T ss_conf 98799996898675899999999999987799984799768898599999999997179999779982----------79 Q ss_pred HHHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHHCCC-------CCCCHHHHHHHHHHHHH Q ss_conf 89999999999999743997056542558899999950656-------57456999999999999 Q gi|254780346|r 85 VIAHAVTRGLVDLSINGSLPIGNGIVVVDSEQQAFDRVSPS-------HLDRGGCAARSALAMIE 142 (149) Q Consensus 85 ~I~~~v~~gl~~lsl~~~~PI~~gILt~~n~~QA~~R~~~~-------~~nkG~eaa~Aal~mi~ 142 (149) .++-.+.+++.+..+ .+|==..|++.++...+.- ..+. ...-|++|++-+++.++ T Consensus 188 ~~A~g~l~al~~~Gl--~VP~DvsVvgfdD~~~a~~-~~P~LTtV~qp~~e~G~~A~~lLl~~i~ 249 (269) T cd06287 188 AFAVGAVRAATELGR--AVPDQLRVVTRYDGLRART-SEPPLTAVDLHLDEVAEQAVDLLFAHLE 249 (269) T ss_pred HHHHHHHHHHHHHCC--CCCCCCEEEEECCCHHHHC-CCCCCEEEEECHHHHHHHHHHHHHHHHC T ss_conf 999999999998588--7798766998159289734-5888548971999999999999999966 No 36 >cd01536 PBP1_ABC_sugar_binding_like Periplasmic sugar-binding domain of active transport systems that are members of the type I periplasmic binding protein (PBP1) superfamily. Periplasmic sugar-binding domain of active transport systems that are members of the type I periplasmic binding protein (PBP1) superfamily. The members of this family function as the primary receptors for chemotaxis and transport of many sugar based solutes in bacteria and archaea. The sugar binding domain is also homologous to the ligand-binding domain of eukaryotic receptors such as glutamate receptor (GluR) and DNA-binding transcriptional repressors such as LacI and GalR. Moreover, this periplasmic binding domain, also known as Venus flytrap domain, undergoes transition from an open to a closed conformational state upon the binding of ligands such as lactose, ribose, fructose, xylose, arabinose, galactose/glucose, and other sugars. This family also includes the periplasmic binding domain of autoinducer-2 (AI-2 Probab=93.43 E-value=0.74 Score=26.37 Aligned_cols=123 Identities=18% Similarity=0.131 Sum_probs=51.3 Q ss_pred CEEEEEEECHHHHHHHHHHHHHHHHHHHCCCCEEEEEHHHHHHHHHHHHHHHHHHHCCCCCCEEEEEEEEECCCCCHHHH Q ss_conf 71799980312899999999999999987995555530014422699999986331137853566541200066524678 Q gi|254780346|r 6 PHVLIIEARFYENLSAMLFEGCVNVLHSRAVQWSSIVTPGVLEIPAAVSMVMNAKTRSVTYDGIIVLGVVMRGKTAHCDV 85 (149) Q Consensus 6 ~kI~IV~s~~~~~i~~~ll~ga~~~l~~~~~~~~~i~VPGa~EiP~a~~~~~~~~~~~~~~D~vIaLG~VIkGeT~H~e~ 85 (149) .||+++.+.-....+..=++|+.+.|++++-.......++.+....+.+.+-+-.....++|+++|. .|. T Consensus 122 ~~i~~i~g~~~~~~~~~R~~Gf~~al~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~ai~~~----------nd~ 191 (267) T cd01536 122 GKVAIIEGPPGSSNAQERVKGFRDALKEYPDIEIVAVQDGNWDREKALQAMEDLLQANPDIDAIFAA----------NDS 191 (267) T ss_pred CEEEEECCCCCCHHHHHHHHHHHHHHHHCCCCCCCHHHCCCCCHHHHHHHHHHHHHCCCCCEEEEEC----------CCH T ss_conf 4799954899886899999999999984558662022200110257889999776417986299971----------649 Q ss_pred HHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHHC---------CCCCCCHHHHHHHHHHHHH Q ss_conf 99999999999997439970565425588999999506---------5657456999999999999 Q gi|254780346|r 86 IAHAVTRGLVDLSINGSLPIGNGIVVVDSEQQAFDRVS---------PSHLDRGGCAARSALAMIE 142 (149) Q Consensus 86 I~~~v~~gl~~lsl~~~~PI~~gILt~~n~~QA~~R~~---------~~~~nkG~eaa~Aal~mi~ 142 (149) ++-.+.+++.+ .++|=-..|++.++...+..... .....-|+.|++.++++++ T Consensus 192 ~a~g~~~al~~----~g~~~di~viG~D~~~~~~~~~~~~~~lttv~q~~~~~G~~a~~~l~~~i~ 253 (267) T cd01536 192 MALGAVAALKA----AGRKGDVKIVGVDGSPEALAAIKEGGILATVAQDPYTQGYLAVEAAVKLLK 253 (267) T ss_pred HHHHHHHHHHH----CCCCCCEEEEEECCCHHHHHHHHCCCCEEEEECCHHHHHHHHHHHHHHHHC T ss_conf 99999999997----699999399998983999999855996599927999999999999999976 No 37 >cd06289 PBP1_MalI_like Ligand-binding domain of MalI, a transcription regulator of the maltose system of Escherichia coli and its close homologs from other bacteria. This group includes the ligand-binding domain of MalI, a transcription regulator of the maltose system of Escherichia coli and its close homologs from other bacteria. They are members of the LacI-GalR family of repressor proteins which are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor. Probab=93.39 E-value=0.75 Score=26.33 Aligned_cols=125 Identities=16% Similarity=0.106 Sum_probs=52.1 Q ss_pred CEEEEEEECHHHHHHHHHHHHHHHHHHHCCCCEEEEE-HHHHHHHHHHHHHHHHHHHCCCCCCEEEEEEEEECCCCCHHH Q ss_conf 7179998031289999999999999998799555553-001442269999998633113785356654120006652467 Q gi|254780346|r 6 PHVLIIEARFYENLSAMLFEGCVNVLHSRAVQWSSIV-TPGVLEIPAAVSMVMNAKTRSVTYDGIIVLGVVMRGKTAHCD 84 (149) Q Consensus 6 ~kI~IV~s~~~~~i~~~ll~ga~~~l~~~~~~~~~i~-VPGa~EiP~a~~~~~~~~~~~~~~D~vIaLG~VIkGeT~H~e 84 (149) +||+++...-.......-.+|+.+.+.+++...+..+ .++-+..-...+.+.+-.....++||++|. .| T Consensus 118 ~~i~~i~~~~~~~~~~~R~~Gf~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~aii~~----------~D 187 (268) T cd06289 118 RRIAFIGGLEDSSTRRERLAGYRAALAEAGLPFDSELVVEGPPSRQGGAEAVAQLLDLPPRPTAIVCF----------ND 187 (268) T ss_pred CEEEEECCCCCCCHHHHHHHHHHHHHHHCCCCCCCCEEECCCCCHHHHHHHHHHHHHCCCCCCEECCC----------CH T ss_conf 70999528988706999999999999976998664345316886556999999998469998620357----------68 Q ss_pred HHHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHH------CCCCCCCHHHHHHHHHHHHH Q ss_conf 89999999999999743997056542558899999950------65657456999999999999 Q gi|254780346|r 85 VIAHAVTRGLVDLSINGSLPIGNGIVVVDSEQQAFDRV------SPSHLDRGGCAARSALAMIE 142 (149) Q Consensus 85 ~I~~~v~~gl~~lsl~~~~PI~~gILt~~n~~QA~~R~------~~~~~nkG~eaa~Aal~mi~ 142 (149) .++-.+.+++.+..+ .+|==..|++.++..++.--. .-....-|..|++.++++++ T Consensus 188 ~~A~g~l~~l~~~gi--~vp~disiigfd~~~~~~~~~p~ltti~~~~~~~g~~a~~~l~~~i~ 249 (268) T cd06289 188 LVAFGAMSGLRRAGL--TPGRDIAVVGFDDVAEAALATPALTTVSTDPREIGRRAAELLLRRIA 249 (268) T ss_pred HHHHHHHHHHHHCCC--CCCCCEEEEEECCHHHHHHCCCCEEEEEECHHHHHHHHHHHHHHHHC T ss_conf 999999999998499--99985499995787899722897169984999999999999999976 No 38 >COG1609 PurR Transcriptional regulators [Transcription] Probab=93.10 E-value=0.83 Score=26.05 Aligned_cols=126 Identities=17% Similarity=0.143 Sum_probs=78.4 Q ss_pred CCEEEEEEECHHHHHHHHHHHHHHHHHHHCCCCE-EEEEHHHHHHHHHHHHHHHHHHHCCCC-CCEEEEEEEEECCCCCH Q ss_conf 8717999803128999999999999999879955-555300144226999999863311378-53566541200066524 Q gi|254780346|r 5 IPHVLIIEARFYENLSAMLFEGCVNVLHSRAVQW-SSIVTPGVLEIPAAVSMVMNAKTRSVT-YDGIIVLGVVMRGKTAH 82 (149) Q Consensus 5 ~~kI~IV~s~~~~~i~~~ll~ga~~~l~~~~~~~-~~i~VPGa~EiP~a~~~~~~~~~~~~~-~D~vIaLG~VIkGeT~H 82 (149) -.||+++...-....+..-++|..+.+.++|... +....+|.|..-...+.+.+-.....+ +||++|. T Consensus 175 ~~~i~~i~~~~~~~~~~~R~~Gf~~al~~~~~~~~~~~i~~~~~~~~~g~~~~~~ll~~~~~~ptAif~~---------- 244 (333) T COG1609 175 HRRIAFIGGPLDSSASRERLEGYRAALREAGLPINPEWIVEGDFSEESGYEAAERLLARGEPRPTAIFCA---------- 244 (333) T ss_pred CCEEEEEECCCCCCCHHHHHHHHHHHHHHCCCCCCCCEEEECCCCHHHHHHHHHHHHHCCCCCCCEEEEC---------- T ss_conf 9859999679877218999999999999759997742366167887899999999985489999789987---------- Q ss_pred HHHHHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHHC------CCCCCCHHHHHHHHHHHHH Q ss_conf 67899999999999997439970565425588999999506------5657456999999999999 Q gi|254780346|r 83 CDVIAHAVTRGLVDLSINGSLPIGNGIVVVDSEQQAFDRVS------PSHLDRGGCAARSALAMIE 142 (149) Q Consensus 83 ~e~I~~~v~~gl~~lsl~~~~PI~~gILt~~n~~QA~~R~~------~~~~nkG~eaa~Aal~mi~ 142 (149) .|.++-.+.+.+.+..+. +|==..|++-+|.+.+.--.- ......|++|++..+++++ T Consensus 245 nD~~Alg~l~~~~~~g~~--vP~disviGfDd~~~~~~~~P~LTTv~~~~~~~G~~A~~~Ll~~i~ 308 (333) T COG1609 245 NDLMALGALRALRELGLR--VPEDLSVIGFDDIELARFLTPPLTTVRQPIEELGRRAAELLLERIN 308 (333) T ss_pred CCHHHHHHHHHHHHCCCC--CCCCEEEEEECCHHHHHHCCCCEEEEECCHHHHHHHHHHHHHHHHH T ss_conf 809999999999980899--9987899998884776515898069950999999999999998743 No 39 >PRK09526 lacI lac repressor; Reviewed Probab=92.49 E-value=1 Score=25.53 Aligned_cols=125 Identities=11% Similarity=0.136 Sum_probs=72.9 Q ss_pred CCEEEEEEECHHHHHHHHHHHHHHHHHHHCCCCEEEEEHHHHHHHHHHHHHHHHHHHCCCCCCEEEEEEEEECCCCCHHH Q ss_conf 87179998031289999999999999998799555553001442269999998633113785356654120006652467 Q gi|254780346|r 5 IPHVLIIEARFYENLSAMLFEGCVNVLHSRAVQWSSIVTPGVLEIPAAVSMVMNAKTRSVTYDGIIVLGVVMRGKTAHCD 84 (149) Q Consensus 5 ~~kI~IV~s~~~~~i~~~ll~ga~~~l~~~~~~~~~i~VPGa~EiP~a~~~~~~~~~~~~~~D~vIaLG~VIkGeT~H~e 84 (149) ..||+++.+..+...+..=+.|+.+.+.+++.....+ ..|-|+..-..+.+.+-.....++||++|. .| T Consensus 181 hr~I~~i~~~~~~~~~~~R~~Gf~~~~~~~~l~~~~~-~~~~~~~~~~~~~~~~~l~~~~~ptai~~~----------~D 249 (342) T PRK09526 181 HQQIALLAGPLSSVSARLRLAGWLEYLTRNQLSPIAV-REGDWSAMSGYQQTLQMLNEGPVFTAVLVA----------ND 249 (342) T ss_pred CCEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCCCEE-EECCCCHHHHHHHHHHHHHCCCCCCEEEEC----------CH T ss_conf 9759999589766009999999999999779896169-956898789999999998369999758756----------77 Q ss_pred HHHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHH------CCCCCCCHHHHHHHHHHHHH Q ss_conf 89999999999999743997056542558899999950------65657456999999999999 Q gi|254780346|r 85 VIAHAVTRGLVDLSINGSLPIGNGIVVVDSEQQAFDRV------SPSHLDRGGCAARSALAMIE 142 (149) Q Consensus 85 ~I~~~v~~gl~~lsl~~~~PI~~gILt~~n~~QA~~R~------~~~~~nkG~eaa~Aal~mi~ 142 (149) .++-.+.+.+.+. ...+|==..|++-++..-+.--. ......-|..|++.++++++ T Consensus 250 ~~A~g~i~~l~~~--g~~vP~DisIigfDd~~~~~~~~P~LTtv~~p~~~ig~~A~~~Ll~~i~ 311 (342) T PRK09526 250 QMALGVLRALHES--GLRVPGDISVIGYDDTEDSSYFIPPLTTIKQDFRLLGKEAVDRLLSLSD 311 (342) T ss_pred HHHHHHHHHHHHH--CCCCCCCEEEEEECCCHHHHHCCCCEEEEEECHHHHHHHHHHHHHHHHC T ss_conf 9999999999980--9999997499998980899824898089981999999999999999865 No 40 >cd06273 PBP1_GntR_like_1 This group includes the ligand-binding domain of putative DNA transcription repressors which are highly similar to that of the repressor specific for gluconate (GntR), a member of the LacI-GalR family of bacterial transcription regulators. This group includes the ligand-binding domain of putative DNA transcription repressors which are highly similar to that of the repressor specific for gluconate (GntR), a member of the LacI-GalR family of bacterial transcription regulators. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational Probab=92.48 E-value=1 Score=25.53 Aligned_cols=125 Identities=15% Similarity=0.088 Sum_probs=69.0 Q ss_pred CEEEEEEEC-HHHHHHHHHHHHHHHHHHHCCCCEEEEE-HHHHHHHHHHHHHHHHHHHCCCCCCEEEEEEEEECCCCCHH Q ss_conf 717999803-1289999999999999998799555553-00144226999999863311378535665412000665246 Q gi|254780346|r 6 PHVLIIEAR-FYENLSAMLFEGCVNVLHSRAVQWSSIV-TPGVLEIPAAVSMVMNAKTRSVTYDGIIVLGVVMRGKTAHC 83 (149) Q Consensus 6 ~kI~IV~s~-~~~~i~~~ll~ga~~~l~~~~~~~~~i~-VPGa~EiP~a~~~~~~~~~~~~~~D~vIaLG~VIkGeT~H~ 83 (149) +||+++.+. -....+..-+.|+.+.+.++|......+ ..+.|..-.+.+.+.+......++||++|. . T Consensus 117 ~~i~~i~~~~~~~~~~~~R~~gf~~al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~ai~~~----------n 186 (268) T cd06273 117 RRIAMIFGPTQGNDRARARRAGVRAALAEAGLELPELWQVEAPYSIADGRAALRQLLEQPPRPTAVICG----------N 186 (268) T ss_pred CCEEEEECCCCCCHHHHHHHHHHHHHHHHHCCCCCHHHEEECCCCHHHHHHHHHHHHHCCCCCCEEEEC----------C T ss_conf 747999468777778999999999999980999871420315789899999999998479998489977----------8 Q ss_pred HHHHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHH------CCCCCCCHHHHHHHHHHHHH Q ss_conf 789999999999999743997056542558899999950------65657456999999999999 Q gi|254780346|r 84 DVIAHAVTRGLVDLSINGSLPIGNGIVVVDSEQQAFDRV------SPSHLDRGGCAARSALAMIE 142 (149) Q Consensus 84 e~I~~~v~~gl~~lsl~~~~PI~~gILt~~n~~QA~~R~------~~~~~nkG~eaa~Aal~mi~ 142 (149) |.++-.+.+.+.+.. ..+|=-..|++-+|..-+.--. ......-|.+|++.++++++ T Consensus 187 d~~A~g~i~~l~~~g--~~iP~disvigfd~~~~~~~~~p~lTti~~~~~~~g~~a~~~L~~~i~ 249 (268) T cd06273 187 DVLALGALYEARRLG--LSVPEDLSIVGFDDIDGSAELEPALTTVRVPAREIGRIAAEALLALLG 249 (268) T ss_pred HHHHHHHHHHHHHCC--CCCCCCEEEEEECCHHHHHHHCCCCEEEEECHHHHHHHHHHHHHHHHC T ss_conf 799999999999639--999996799999982889841899479991999999999999999966 No 41 >cd06272 PBP1_hexuronate_repressor_like Ligand-binding domain of DNA transcription repressor for the hexuronate utilization operon from Bacillus species and its close homologs from other bacteria, all of which are a member of the LacI-GalR family of bacterial transcription regulators. Ligand-binding domain of DNA transcription repressor for the hexuronate utilization operon from Bacillus species and its close homologs from other bacteria, all of which are a member of the LacI-GalR family of bacterial transcription regulators. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor Probab=92.35 E-value=1.1 Score=25.43 Aligned_cols=123 Identities=17% Similarity=0.037 Sum_probs=75.1 Q ss_pred CCEEEEEEECHHHHHHHHHHHHHHHHHHHCCCCEEE--EEHH-HHHHHH-HHHHHHHHHHHCCCCCCEEEEEEEEECCCC Q ss_conf 871799980312899999999999999987995555--5300-144226-999999863311378535665412000665 Q gi|254780346|r 5 IPHVLIIEARFYENLSAMLFEGCVNVLHSRAVQWSS--IVTP-GVLEIP-AAVSMVMNAKTRSVTYDGIIVLGVVMRGKT 80 (149) Q Consensus 5 ~~kI~IV~s~~~~~i~~~ll~ga~~~l~~~~~~~~~--i~VP-Ga~EiP-~a~~~~~~~~~~~~~~D~vIaLG~VIkGeT 80 (149) -.||+++...-...-...-..|+.+.+.++|...+. +... -.++-. .+++.+++ ...++||++|. T Consensus 111 ~~~i~~i~~~~~~~~~~~R~~gf~~al~~~g~~~~~~~i~~~~~~~~~~~~~~~~ll~---~~~~p~Ai~~~-------- 179 (261) T cd06272 111 HKKIAYIGDLSLDRRQRKRFKGFLETCDENGISISDSHIDVDGLSAEGGDNAAKKLLK---ESDLPTAIICG-------- 179 (261) T ss_pred CCCEEEECCCCCCHHHHHHHHHHHHHHHHCCCCCCCEEEEECCCHHHHHHHHHHHHHH---CCCCCCCEEEC-------- T ss_conf 9828996698887359999999999999859985513898303103679999999985---27898610127-------- Q ss_pred CHHHHHHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHHC------CCCCCCHHHHHHHHHHHHH Q ss_conf 2467899999999999997439970565425588999999506------5657456999999999999 Q gi|254780346|r 81 AHCDVIAHAVTRGLVDLSINGSLPIGNGIVVVDSEQQAFDRVS------PSHLDRGGCAARSALAMIE 142 (149) Q Consensus 81 ~H~e~I~~~v~~gl~~lsl~~~~PI~~gILt~~n~~QA~~R~~------~~~~nkG~eaa~Aal~mi~ 142 (149) .|.++-.+.+++.+. ...+|==..|++-+|...+.--.- .....-|+.|++..+++++ T Consensus 180 --nD~~A~g~~~~l~~~--g~~vP~dvsviGfDd~~~~~~~~P~LTtv~q~~~~ig~~A~~~L~~~i~ 243 (261) T cd06272 180 --SYDIALGVLSALNKQ--GISIPEDIEIISYDNIPQMAIIDPPLTAVDVPIEEIAKKSLELLLKLIT 243 (261) T ss_pred --CHHHHHHHHHHHHHH--CCCCCCCEEEEEECCCHHHHHHCCCCEEEEECHHHHHHHHHHHHHHHHC T ss_conf --689999999999980--9999995599998881889950998479980999999999999999964 No 42 >cd06310 PBP1_ABC_sugar_binding_like_2 Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems. Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily, which consists of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis. Probab=92.35 E-value=1.1 Score=25.43 Aligned_cols=35 Identities=6% Similarity=0.032 Sum_probs=19.8 Q ss_pred EEEEEEECHHHHHHHHHHHHHHHHHHHCCCCEEEE Q ss_conf 17999803128999999999999999879955555 Q gi|254780346|r 7 HVLIIEARFYENLSAMLFEGCVNVLHSRAVQWSSI 41 (149) Q Consensus 7 kI~IV~s~~~~~i~~~ll~ga~~~l~~~~~~~~~i 41 (149) ||++|...-..+.-..+.+|+.+..++.|+++... T Consensus 1 kIg~i~~~~~npf~~~v~~G~e~aA~~~G~~v~~~ 35 (273) T cd06310 1 KIALVPKGTTSDFWQAVKAGAEAAAKELGVKVTFQ 35 (273) T ss_pred CEEEECCCCCCHHHHHHHHHHHHHHHHCCCEEEEE T ss_conf 98999599998599999999999999809989997 No 43 >pfam00532 Peripla_BP_1 family. This family includes the periplasmic binding proteins, and the LacI family transcriptional regulators. The periplasmic binding proteins are the primary receptors for chemotaxis and transport of many sugar based solutes. The LacI family of proteins consist of transcriptional regulators related to the lac repressor. In this case, generally the sugar binding domain binds a sugar which changes the DNA binding activity of the repressor domain (pfam00356). Probab=92.16 E-value=1.1 Score=25.29 Aligned_cols=33 Identities=6% Similarity=0.038 Sum_probs=16.0 Q ss_pred EEEEEECHHHHHHHHHHHHHHHHHHHCCCCEEE Q ss_conf 799980312899999999999999987995555 Q gi|254780346|r 8 VLIIEARFYENLSAMLFEGCVNVLHSRAVQWSS 40 (149) Q Consensus 8 I~IV~s~~~~~i~~~ll~ga~~~l~~~~~~~~~ 40 (149) |+++.+.-+......-++|+.+.|.++|.+.+. T Consensus 124 i~~~~~~~~~~~~~~R~~Gf~~al~~~g~~~~~ 156 (281) T pfam00532 124 IAVMAGPASALTARERVQGFMAALAAAGREVKI 156 (281) T ss_pred EEEECCCCCCHHHHHHHHHHHHHHHHCCCCCCC T ss_conf 477307876507899999999999975999982 No 44 >cd01543 PBP1_XylR Ligand-binding domain of DNA transcription repressor specific for xylose (XylR). Ligand-binding domain of DNA transcription repressor specific for xylose (XylR), a member of the LacI-GalR family of bacterial transcription regulators. The ligand-binding domain of XylR is structurally homologous to the periplasmic sugar-binding domain of ABC-type transporters and both domains contain the type I periplasmic binding protein-like fold. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the type I periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor. Probab=91.94 E-value=1.2 Score=25.13 Aligned_cols=122 Identities=14% Similarity=0.037 Sum_probs=77.0 Q ss_pred CEEEEEEECHHHHHHHHHHHHHHHHHHHCCCCEEEEE-----HHHHHHHHHHHHHHHHHHHCCCCCCEEEEEEEEECCCC Q ss_conf 7179998031289999999999999998799555553-----00144226999999863311378535665412000665 Q gi|254780346|r 6 PHVLIIEARFYENLSAMLFEGCVNVLHSRAVQWSSIV-----TPGVLEIPAAVSMVMNAKTRSVTYDGIIVLGVVMRGKT 80 (149) Q Consensus 6 ~kI~IV~s~~~~~i~~~ll~ga~~~l~~~~~~~~~i~-----VPGa~EiP~a~~~~~~~~~~~~~~D~vIaLG~VIkGeT 80 (149) .||+.+ +.-....+..-..|+.+.+.++|++...+. .+..++- +.+.+.+......+++|++|. T Consensus 110 r~I~~i-g~~~~~~~~~R~~Gf~~al~~~g~~~~~~~~~~~~~~~~~~~--~~~~l~~~l~~~~~ptAi~~~-------- 178 (265) T cd01543 110 RHFAFY-GLPGARWSDEREEAFRQLVAEAGYECSFFYRGLSTDAQSWEE--EQEELAQWLQSLPKPVGIFAC-------- 178 (265) T ss_pred CEEEEE-CCCCCHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCHHH--HHHHHHHHHHCCCCCEEEEEC-------- T ss_conf 749998-999880699999999999997799976341245446753999--999999998359998399988-------- Q ss_pred CHHHHHHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHHCC-------CCCCCHHHHHHHHHHHHH Q ss_conf 24678999999999999974399705654255889999995065-------657456999999999999 Q gi|254780346|r 81 AHCDVIAHAVTRGLVDLSINGSLPIGNGIVVVDSEQQAFDRVSP-------SHLDRGGCAARSALAMIE 142 (149) Q Consensus 81 ~H~e~I~~~v~~gl~~lsl~~~~PI~~gILt~~n~~QA~~R~~~-------~~~nkG~eaa~Aal~mi~ 142 (149) .|.++-.+.+++.+..+ .+|==.+|++-+|...+-+-+.+ .....|.+||+..+++++ T Consensus 179 --nD~~A~g~l~~l~~~Gi--~VP~disViGfD~~~~~~~~~~P~LTtV~q~~~~mG~~Aa~lL~~~i~ 243 (265) T cd01543 179 --TDARARQLLEACRRAGI--AVPEEVAVLGVDNDELICELSRPPLSSVEQNAERIGYEAAKLLDRLMR 243 (265) T ss_pred --CHHHHHHHHHHHHHHHC--CCCCCEEEEEECCCHHHHHHCCCCCCEEEECHHHHHHHHHHHHHHHHC T ss_conf --36999999999998322--577755999982868889527999733962999999999999999967 No 45 >cd06274 PBP1_FruR Ligand binding domain of DNA transcription repressor specific for fructose (FruR) and its close homologs. Ligand binding domain of DNA transcription repressor specific for fructose (FruR) and its close homologs, all of which are a member of the LacI-GalR family of bacterial transcription regulators. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to members of the type I periplasmic binding protein superfamily. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor Probab=91.92 E-value=1.2 Score=25.11 Aligned_cols=124 Identities=13% Similarity=-0.039 Sum_probs=78.3 Q ss_pred CCEEEEEEECHHHHHHHHHHHHHHHHHHHCCCCEEEEE-HHHHHHHHHHH---HHHHHHHHCCCCCCEEEEEEEEECCCC Q ss_conf 87179998031289999999999999998799555553-00144226999---999863311378535665412000665 Q gi|254780346|r 5 IPHVLIIEARFYENLSAMLFEGCVNVLHSRAVQWSSIV-TPGVLEIPAAV---SMVMNAKTRSVTYDGIIVLGVVMRGKT 80 (149) Q Consensus 5 ~~kI~IV~s~~~~~i~~~ll~ga~~~l~~~~~~~~~i~-VPGa~EiP~a~---~~~~~~~~~~~~~D~vIaLG~VIkGeT 80 (149) -.||+++.+......+..-+.|+.+.+.++|...+..+ ..+.|...... ..++.. ....+||++|. T Consensus 116 hr~I~~i~~~~~~~~~~~R~~Gf~~al~~~g~~~~~~~i~~~~~~~~~g~~~~~~~l~~--~~~~p~ai~~~-------- 185 (264) T cd06274 116 PEEVLFLGGLPELSPSRERLAGFRQALADAGLPVQPDWIYAEGYSPESGYQLMAELLAR--LGRLPRALFTT-------- 185 (264) T ss_pred CCEEEEECCCCCCCCHHHHHHHHHHHHHHCCCCCCCEEEEECCCCHHHHHHHHHHHHHH--CCCCCCCCCCC-------- T ss_conf 96699976898773099999999999997799877407982688878999999999986--56887422017-------- Q ss_pred CHHHHHHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHHC------CCCCCCHHHHHHHHHHHHH Q ss_conf 2467899999999999997439970565425588999999506------5657456999999999999 Q gi|254780346|r 81 AHCDVIAHAVTRGLVDLSINGSLPIGNGIVVVDSEQQAFDRVS------PSHLDRGGCAARSALAMIE 142 (149) Q Consensus 81 ~H~e~I~~~v~~gl~~lsl~~~~PI~~gILt~~n~~QA~~R~~------~~~~nkG~eaa~Aal~mi~ 142 (149) .|.++-.+.+.+.+..+ .+|==..|++-+|...|.--.- -....-|.+|++-.+++++ T Consensus 186 --nd~~a~g~l~~l~~~g~--~vP~disvvgfDd~~~a~~~~p~LTtv~q~~~~~g~~A~~lLl~~i~ 249 (264) T cd06274 186 --SYTLLEGVLRFLRERPG--LAPSDLRIATFDDHPLLDFLPFPVHSVPQDHEALAEAAFELALAALG 249 (264) T ss_pred --CHHHHHHHHHHHHHCCC--CCCCCEEEEEECCHHHHHHCCCCCEEEECCHHHHHHHHHHHHHHHHC T ss_conf --69999999999998599--99998799998986899737999769967999999999999999867 No 46 >cd06298 PBP1_CcpA_like Ligand-binding domain of the catabolite control protein A (CcpA), which functions as the major transcriptional regulator of carbon catabolite repression/regulation. Ligand-binding domain of the catabolite control protein A (CcpA), which functions as the major transcriptional regulator of carbon catabolite repression/regulation (CCR), a process in which enzymes necessary for the metabolism of alternative sugars are inhibited in the presence of glucose. In gram-positive bacteria, CCR is controlled by HPr, a phosphoenolpyruvate:sugar phsophotrasnferase system (PTS) and a transcriptional regulator CcpA. Moreover, CcpA can regulate sporulation and antibiotic resistance as well as play a role in virulence development of certain pathogens such as the group A streptococcus. The ligand binding domain of CcpA is a member of the LacI-GalR family of bacterial transcription regulators. Probab=91.75 E-value=1.2 Score=25.00 Aligned_cols=122 Identities=13% Similarity=0.141 Sum_probs=76.0 Q ss_pred CCEEEEEEECHHHHH-HHHHHHHHHHHHHHCCCCEEE--E-EHHHHHHHHHHH-HHHHHHHHCCCCCCEEEEEEEEECCC Q ss_conf 871799980312899-999999999999987995555--5-300144226999-99986331137853566541200066 Q gi|254780346|r 5 IPHVLIIEARFYENL-SAMLFEGCVNVLHSRAVQWSS--I-VTPGVLEIPAAV-SMVMNAKTRSVTYDGIIVLGVVMRGK 79 (149) Q Consensus 5 ~~kI~IV~s~~~~~i-~~~ll~ga~~~l~~~~~~~~~--i-~VPGa~EiP~a~-~~~~~~~~~~~~~D~vIaLG~VIkGe 79 (149) -.||+++...+.... .+.-++|+.+.+.++|..... + .....++-...+ +.++ ...++||++|. T Consensus 116 ~~~I~~i~~~~~~~~~~~~R~~gf~~a~~~~g~~~~~~~i~~~~~~~~~~~~~~~~l~----~~~~~~ai~~~------- 184 (268) T cd06298 116 HKKIAFISGPLEDSINGDERLAGYKEALSEANIEFDESLIFEGDYTYESGYELAEELL----EDGKPTAAFVT------- 184 (268) T ss_pred CCEEEEEECCCCCCHHHHHHHHHHHHHHHHCCCCCCHHHEECCCHHHHHHHHHHHHHH----HCCCCCEEEEC------- T ss_conf 9669999678777625999999999999984999760120035403778999999998----36999789966------- Q ss_pred CCHHHHHHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHH------CCCCCCCHHHHHHHHHHHHH Q ss_conf 5246789999999999999743997056542558899999950------65657456999999999999 Q gi|254780346|r 80 TAHCDVIAHAVTRGLVDLSINGSLPIGNGIVVVDSEQQAFDRV------SPSHLDRGGCAARSALAMIE 142 (149) Q Consensus 80 T~H~e~I~~~v~~gl~~lsl~~~~PI~~gILt~~n~~QA~~R~------~~~~~nkG~eaa~Aal~mi~ 142 (149) .|.++-.+.+.+.+..+ .+|=-..|++.++.+-|.--. ......-|+.|++..+++++ T Consensus 185 ---nD~~A~g~l~~l~~~g~--~vP~disvigfDd~~~a~~~~P~LTtv~~~~~~~G~~A~~~l~~~i~ 248 (268) T cd06298 185 ---DDELAIGILNAAQDAGL--KVPEDFEIIGFNNTKLASMVRPQLTSVTQPLYDIGAVAMRLLTKLMN 248 (268) T ss_pred ---CHHHHHHHHHHHHHCCC--CCCCCEEEEEECCHHHHHCCCCCCEEEECCHHHHHHHHHHHHHHHHC T ss_conf ---87999999999997499--99987499997881899714899769972999999999999999966 No 47 >PRK10727 DNA-binding transcriptional regulator GalR; Provisional Probab=91.71 E-value=1.2 Score=24.97 Aligned_cols=123 Identities=15% Similarity=0.119 Sum_probs=71.8 Q ss_pred CCEEEEEEECHHHHHHHHHHHHHHHHHHHCCCCEEE-EEHHHHHHHH---HHHHHHHHHHHCCCCCCEEEEEEEEECCCC Q ss_conf 871799980312899999999999999987995555-5300144226---999999863311378535665412000665 Q gi|254780346|r 5 IPHVLIIEARFYENLSAMLFEGCVNVLHSRAVQWSS-IVTPGVLEIP---AAVSMVMNAKTRSVTYDGIIVLGVVMRGKT 80 (149) Q Consensus 5 ~~kI~IV~s~~~~~i~~~ll~ga~~~l~~~~~~~~~-i~VPGa~EiP---~a~~~~~~~~~~~~~~D~vIaLG~VIkGeT 80 (149) -.||+++.+.........-++|+.+.+.++|...+. +...+.+.-- .++..++. ...+++|++|. T Consensus 176 hr~Ia~i~~~~~~~~~~~R~~g~~~al~~~gl~~~~~~i~~~~~~~~~~~~~~~~ll~---~~~~~tAi~~~-------- 244 (342) T PRK10727 176 HTRIGYLCSNHSISDAEDRLQGYYDALAESGIPANDRLVTFGEPDESGGEQAMTELLG---RGRNFTAVACY-------- 244 (342) T ss_pred CCEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCCCCCEEEECCCCHHHHHHHHHHHHH---CCCCCCCCEEC-------- T ss_conf 9759999689888359999999999999769999820588157877889999999985---59997741554-------- Q ss_pred CHHHHHHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHH------CCCCCCCHHHHHHHHHHHHH Q ss_conf 246789999999999999743997056542558899999950------65657456999999999999 Q gi|254780346|r 81 AHCDVIAHAVTRGLVDLSINGSLPIGNGIVVVDSEQQAFDRV------SPSHLDRGGCAARSALAMIE 142 (149) Q Consensus 81 ~H~e~I~~~v~~gl~~lsl~~~~PI~~gILt~~n~~QA~~R~------~~~~~nkG~eaa~Aal~mi~ 142 (149) .|.++-.+.+++.+..+ .+|==..|++-+|...+.--. .......|..|++-++++++ T Consensus 245 --nD~~A~g~l~al~~~Gl--~VP~DisViGfDd~~~~~~~~P~LTTV~~p~~e~g~~A~~lLl~~i~ 308 (342) T PRK10727 245 --NDSMAAGAMGVLNDNGI--DVPGEISLIGFDDVLVSRYVRPRLTTVRYPIVTMATQAAELALALAD 308 (342) T ss_pred --CHHHHHHHHHHHHHCCC--CCCCCEEEEEECCHHHHHCCCCCCEEEECCHHHHHHHHHHHHHHHHC T ss_conf --69999999999998299--99998699988971898648899858977999999999999999855 No 48 >cd06299 PBP1_LacI_like_13 Ligand-binding domain of DNA-binding regulatory protein from Corynebacterium glutamicum which has a unique ability to produce significant amounts of L-glutamate directly from cheap sugar and ammonia. This group includes the ligand-binding domain of DNA-binding regulatory protein from Corynebacterium glutamicum which has a unique ability to produce significant amounts of L-glutamate directly from cheap sugar and ammonia. This regulatory protein is a member of the LacI-GalR family of bacterial transcription repressors. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial trans Probab=91.57 E-value=1.3 Score=24.88 Aligned_cols=121 Identities=12% Similarity=0.010 Sum_probs=74.7 Q ss_pred CCEEEEEEECHHHHHHHHHHHHHHHHHHHCCCCEEEE-EHHHHHHHHHHH---HHHHHHHHCCCCCCEEEEEEEEECCCC Q ss_conf 8717999803128999999999999999879955555-300144226999---999863311378535665412000665 Q gi|254780346|r 5 IPHVLIIEARFYENLSAMLFEGCVNVLHSRAVQWSSI-VTPGVLEIPAAV---SMVMNAKTRSVTYDGIIVLGVVMRGKT 80 (149) Q Consensus 5 ~~kI~IV~s~~~~~i~~~ll~ga~~~l~~~~~~~~~i-~VPGa~EiP~a~---~~~~~~~~~~~~~D~vIaLG~VIkGeT 80 (149) -.||+++.+.-.......-++|+.+.+.+++...+.. ...+.+...... +.++ ...+|+++|. T Consensus 116 ~~~i~~i~~~~~~~~~~~R~~gf~~a~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~l-----~~~p~ai~~~-------- 182 (265) T cd06299 116 HKKIGYISGPQDTSTGRERLEAFRQACASLGLEVNEDLVVLGGYSQESGYAGATKLL-----DQGATAIIAG-------- 182 (265) T ss_pred CCEEEEECCCCCCHHHHHHHHHHHHHHHHCCCCCCCCEEEEECCCHHHHHHHHHHHH-----HCCCCEEECC-------- T ss_conf 983886048988756999999999999976999993059984035578999999999-----6399854506-------- Q ss_pred CHHHHHHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHHC------CCCCCCHHHHHHHHHHHHH Q ss_conf 2467899999999999997439970565425588999999506------5657456999999999999 Q gi|254780346|r 81 AHCDVIAHAVTRGLVDLSINGSLPIGNGIVVVDSEQQAFDRVS------PSHLDRGGCAARSALAMIE 142 (149) Q Consensus 81 ~H~e~I~~~v~~gl~~lsl~~~~PI~~gILt~~n~~QA~~R~~------~~~~nkG~eaa~Aal~mi~ 142 (149) .|.++-.+.+.+.+. ...+|=-..|++.+|.+.+.-..- .....-|.+|++.++++++ T Consensus 183 --nD~~A~g~~~~l~~~--g~~vP~dvsvvgfd~~~~~~~~~p~lTTv~~~~~~~g~~A~~~L~~~i~ 246 (265) T cd06299 183 --DSMMTIGAIRAIHDA--GLVIGEDISLIGFDDLPVFRLQTPPLTVIDQQVEQMGKRAVDMLLSLIA 246 (265) T ss_pred --CCHHHHHHHHHHHHH--CCCCCCCEEEEEECCHHHHHHCCCCEEEEECCHHHHHHHHHHHHHHHHC T ss_conf --858899999999983--8999993499999975889853998399980999999999999999962 No 49 >cd06277 PBP1_LacI_like_1 Ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. This group includes the ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor. Probab=91.27 E-value=1.4 Score=24.69 Aligned_cols=124 Identities=12% Similarity=0.096 Sum_probs=72.8 Q ss_pred CCEEEEEEECHHHHHHHHHHHHHHHHHHHCCCCEEEE-EHHHHHHHHHHHHHHHHHHHCCCCCCEEEEEEEEECCCCCHH Q ss_conf 8717999803128999999999999999879955555-300144226999999863311378535665412000665246 Q gi|254780346|r 5 IPHVLIIEARFYENLSAMLFEGCVNVLHSRAVQWSSI-VTPGVLEIPAAVSMVMNAKTRSVTYDGIIVLGVVMRGKTAHC 83 (149) Q Consensus 5 ~~kI~IV~s~~~~~i~~~ll~ga~~~l~~~~~~~~~i-~VPGa~EiP~a~~~~~~~~~~~~~~D~vIaLG~VIkGeT~H~ 83 (149) -.||+++....+..-...-+.|+.+.+.++|.+.+.. ...+..+.-..+..++.. ....++|++|. . T Consensus 118 hr~I~~i~~~~~~~~~~~R~~Gf~~al~~~gl~~~~~~~~~~~~~~~~~~~~~~~~--~~~~ptAi~~~----------n 185 (268) T cd06277 118 HRKIGFVGDPLYSPSFEERYEGYKKALLDHGIPFNEDYDITEKEEDEEDIGKFIDE--LKPLPTAFFCS----------N 185 (268) T ss_pred CCCEEEEECCCCCCHHHHHHHHHHHHHHHCCCCCCCCEEEECCCCHHHHHHHHHHH--CCCCCCEEEEC----------C T ss_conf 98369972788881299999999999998599998224662587779999999984--78899879968----------8 Q ss_pred HHHHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHH------CCCCCCCHHHHHHHHHHHHH Q ss_conf 789999999999999743997056542558899999950------65657456999999999999 Q gi|254780346|r 84 DVIAHAVTRGLVDLSINGSLPIGNGIVVVDSEQQAFDRV------SPSHLDRGGCAARSALAMIE 142 (149) Q Consensus 84 e~I~~~v~~gl~~lsl~~~~PI~~gILt~~n~~QA~~R~------~~~~~nkG~eaa~Aal~mi~ 142 (149) |.++-.+.+.+.+.. ..+|==..|++.+|.+.+.--. ......-|++|++..+++++ T Consensus 186 D~~A~g~~~~l~~~g--~~vP~Disivgfdd~~~~~~~~P~LTtv~~~~~~~G~~A~~~Ll~~i~ 248 (268) T cd06277 186 DGVAFLLIKVLKEMG--IRVPEDVSVIGFDDIEYATIFTPPLTTVRVDKEEMGKLAVKRLLEKLE 248 (268) T ss_pred HHHHHHHHHHHHHCC--CCCCCCCEEEEECCHHHHHHCCCCEEEEEECHHHHHHHHHHHHHHHHC T ss_conf 599999999999859--999986289997887899844898089992999999999999999966 No 50 >cd06280 PBP1_LacI_like_4 Ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. This group includes the ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor. Probab=91.25 E-value=1.4 Score=24.68 Aligned_cols=121 Identities=8% Similarity=0.004 Sum_probs=77.8 Q ss_pred CEEEEEEECHHHHHHHHHHHHHHHHHHHCCCCEEEEEHHHHHHHHHH-HHHHHHHHHCCCCCCEEEEEEEEECCCCCHHH Q ss_conf 71799980312899999999999999987995555530014422699-99998633113785356654120006652467 Q gi|254780346|r 6 PHVLIIEARFYENLSAMLFEGCVNVLHSRAVQWSSIVTPGVLEIPAA-VSMVMNAKTRSVTYDGIIVLGVVMRGKTAHCD 84 (149) Q Consensus 6 ~kI~IV~s~~~~~i~~~ll~ga~~~l~~~~~~~~~i~VPGa~EiP~a-~~~~~~~~~~~~~~D~vIaLG~VIkGeT~H~e 84 (149) .||+.+.+.-. .....-+.|+.+.+.++|.+.+..+++-..|--.. +..++ ....++||++|. .| T Consensus 116 r~I~~l~g~~~-~~~~~R~~Gf~~al~~~gi~~~~~~~~~~~~~~~~~~~~~l---~~~~~~~ai~~~----------nD 181 (263) T cd06280 116 RRIGGLFGNAS-TTGAERRAGYEDAMRRHGLAPDARFVAPTAEAAEAALAAWL---AAPERPEALVAS----------NG 181 (263) T ss_pred CEEEEEECCCC-CCHHHHHHHHHHHHHHCCCCCCEEEECCCHHHHHHHHHHHH---HCCCCCCEEEEC----------CH T ss_conf 66999938998-43999999999999976999763782487678999999998---279999789967----------88 Q ss_pred HHHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHH------CCCCCCCHHHHHHHHHHHHH Q ss_conf 89999999999999743997056542558899999950------65657456999999999999 Q gi|254780346|r 85 VIAHAVTRGLVDLSINGSLPIGNGIVVVDSEQQAFDRV------SPSHLDRGGCAARSALAMIE 142 (149) Q Consensus 85 ~I~~~v~~gl~~lsl~~~~PI~~gILt~~n~~QA~~R~------~~~~~nkG~eaa~Aal~mi~ 142 (149) .++-.+.+++.+.. ..+|==..|++-+|...+.--. .-....-|.+|++-.+++++ T Consensus 182 ~~A~g~l~~l~~~g--~~vP~disviGfDd~~~a~~~~P~LTTv~~~~~~~g~~A~~~Ll~~i~ 243 (263) T cd06280 182 LLLLGALRAVRAAG--LRIPQDLALAGFDNDPWTELVGPGITVIEQPVEEIGRAAMSLLLERLA 243 (263) T ss_pred HHHHHHHHHHHHHC--CCCCCCCEEEEECCHHHHHCCCCCCEEEEECHHHHHHHHHHHHHHHHC T ss_conf 99999999999848--999998789997785888617999779980999999999999999966 No 51 >cd06292 PBP1_LacI_like_10 Ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. This group includes the ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor. Probab=91.02 E-value=1.5 Score=24.54 Aligned_cols=120 Identities=12% Similarity=-0.005 Sum_probs=72.3 Q ss_pred CEEEEEEECHHHHHHHHHHHHHHHHHHHCCCCEEEE---EHHHHHHHHHHH-HHHHHHHHCCCCCCEEEEEEEEECCCCC Q ss_conf 717999803128999999999999999879955555---300144226999-9998633113785356654120006652 Q gi|254780346|r 6 PHVLIIEARFYENLSAMLFEGCVNVLHSRAVQWSSI---VTPGVLEIPAAV-SMVMNAKTRSVTYDGIIVLGVVMRGKTA 81 (149) Q Consensus 6 ~kI~IV~s~~~~~i~~~ll~ga~~~l~~~~~~~~~i---~VPGa~EiP~a~-~~~~~~~~~~~~~D~vIaLG~VIkGeT~ 81 (149) .||+++...-....+..-+.|+.+.+++++...+.. ..+...|..... ..++ +.++||++|. T Consensus 123 ~~i~~i~~~~~~~~~~~R~~G~~~a~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~l-----~~~~~ai~~~--------- 188 (273) T cd06292 123 RRIGFASGPGRTVPRRRKIAGFRAALEEAGLEPPEALVARGMFSVEGGQAAAVELL-----GSGPTAIVAA--------- 188 (273) T ss_pred CEEEEECCCCCCCHHHHHHHHHHHHHHHCCCCCCCEEEEECCCCHHHHHHHHHHHH-----HCCCCEEEEC--------- T ss_conf 80899517877715999999999999984999771489716777788999999997-----4799657745--------- Q ss_pred HHHHHHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHHC------CCCCCCHHHHHHHHHHHHH Q ss_conf 467899999999999997439970565425588999999506------5657456999999999999 Q gi|254780346|r 82 HCDVIAHAVTRGLVDLSINGSLPIGNGIVVVDSEQQAFDRVS------PSHLDRGGCAARSALAMIE 142 (149) Q Consensus 82 H~e~I~~~v~~gl~~lsl~~~~PI~~gILt~~n~~QA~~R~~------~~~~nkG~eaa~Aal~mi~ 142 (149) .|.++-.+.+.+.+. ...+|==..|++.+|...+.--.- ......|..|++..+++++ T Consensus 189 -nD~~A~g~~~~l~~~--g~~ip~di~VigfD~~~~~~~~~p~LTtI~q~~~~~g~~a~~~ll~~i~ 252 (273) T cd06292 189 -SDLMALGAIRAARRR--GLRVPEDVSVVGYDDSALMAFTDPPLTTVRQPVEEMAAAAVDRLMARID 252 (273) T ss_pred -CCHHHHHHHHHHHHC--CCCCCCCEEEEEECCHHHHHHCCCCCEEEECCHHHHHHHHHHHHHHHHC T ss_conf -859999999999983--9989996599999985899815899679995999999999999999966 No 52 >cd06278 PBP1_LacI_like_2 Ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. This group includes the ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor. Probab=90.84 E-value=1.5 Score=24.43 Aligned_cols=124 Identities=15% Similarity=-0.023 Sum_probs=74.7 Q ss_pred CCEEEEEEECHHHHHHHHHHHHHHHHHHHCCCCEEEEEH-HHHHHHHH-HHHHHHHHHHCCCCCCEEEEEEEEECCCCCH Q ss_conf 871799980312899999999999999987995555530-01442269-9999986331137853566541200066524 Q gi|254780346|r 5 IPHVLIIEARFYENLSAMLFEGCVNVLHSRAVQWSSIVT-PGVLEIPA-AVSMVMNAKTRSVTYDGIIVLGVVMRGKTAH 82 (149) Q Consensus 5 ~~kI~IV~s~~~~~i~~~ll~ga~~~l~~~~~~~~~i~V-PGa~EiP~-a~~~~~~~~~~~~~~D~vIaLG~VIkGeT~H 82 (149) -+||+++.+.-+......=++|+.+.|.++|.+...+.. +..+|-.. +.+.++ ....++||++|. T Consensus 115 h~~I~~i~~~~~~~~~~~R~~G~~~al~~~gl~~~~~~~~~~~~~~g~~~~~~ll---~~~~~ptAi~~~---------- 181 (266) T cd06278 115 CRRIAFIGGPADTSTSRERERGFRDALAAAGVPVVVEEAGDYSYEGGYEAARRLL---ASRPRPDAIFCA---------- 181 (266) T ss_pred CCEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCCEEEECCCCCHHHHHHHHHHHH---HCCCCCCCCEEC---------- T ss_conf 9889999688888149999999999999869994389818999899999999998---459998862507---------- Q ss_pred HHHHHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHHC------CCCCCCHHHHHHHHHHHHH Q ss_conf 67899999999999997439970565425588999999506------5657456999999999999 Q gi|254780346|r 83 CDVIAHAVTRGLVDLSINGSLPIGNGIVVVDSEQQAFDRVS------PSHLDRGGCAARSALAMIE 142 (149) Q Consensus 83 ~e~I~~~v~~gl~~lsl~~~~PI~~gILt~~n~~QA~~R~~------~~~~nkG~eaa~Aal~mi~ 142 (149) -|.++-.+.+.+.+ .+...+|==..|++-+|.+.+.--.- .....-|+.|++..+++++ T Consensus 182 nD~~A~g~l~~l~~-~~g~~vP~disvvgfD~~~~~~~~~p~LTtv~~~~~~~g~~A~~~Ll~~i~ 246 (266) T cd06278 182 NDLLAIGVMDAARQ-EGGLRVPEDVSVIGFDDIPMAAWPSYQLTTVRQPVDRMAEEAVDLLEARIE 246 (266) T ss_pred CHHHHHHHHHHHHH-HCCCCCCCCEEEEEECCHHHHHCCCCCEEEEECCHHHHHHHHHHHHHHHHC T ss_conf 78999999999997-358888886699987880898544998489983999999999999999971 No 53 >PRK10339 DNA-binding transcriptional repressor EbgR; Provisional Probab=90.69 E-value=1.6 Score=24.35 Aligned_cols=125 Identities=12% Similarity=0.028 Sum_probs=72.7 Q ss_pred CCEEEEEEECHHHHHHHHHHHHHHHHHHHCCCC-EEEEEHHHHHHHHHHHHHHHHHHHCCCCCCEEEEEEEEECCCCCHH Q ss_conf 871799980312899999999999999987995-5555300144226999999863311378535665412000665246 Q gi|254780346|r 5 IPHVLIIEARFYENLSAMLFEGCVNVLHSRAVQ-WSSIVTPGVLEIPAAVSMVMNAKTRSVTYDGIIVLGVVMRGKTAHC 83 (149) Q Consensus 5 ~~kI~IV~s~~~~~i~~~ll~ga~~~l~~~~~~-~~~i~VPGa~EiP~a~~~~~~~~~~~~~~D~vIaLG~VIkGeT~H~ 83 (149) -.||+++.+.-+....+.-..|..+.+...+.. .+.++ .|.|......+....-......+||++|. . T Consensus 174 ~r~I~~i~~~~~~~~~~~R~~~~~~~~~~~~~~~~~~i~-~~~~~~~~g~~~~~~ll~~~~~p~ai~~~----------n 242 (327) T PRK10339 174 VNRIGFIGGEDEPGKADIREVAFAEYGRLKQVVREEDIW-RGGFSSSSGYELAKQMLAREDYPKALFVA----------S 242 (327) T ss_pred CCEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCCHHHEE-ECCCCHHHHHHHHHHHHHCCCCCCEEEEC----------C T ss_conf 983999957887644999999999999875999737558-66898699999999998469999748977----------7 Q ss_pred HHHHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHHC------CCCCCCHHHHHHHHHHHHH Q ss_conf 7899999999999997439970565425588999999506------5657456999999999999 Q gi|254780346|r 84 DVIAHAVTRGLVDLSINGSLPIGNGIVVVDSEQQAFDRVS------PSHLDRGGCAARSALAMIE 142 (149) Q Consensus 84 e~I~~~v~~gl~~lsl~~~~PI~~gILt~~n~~QA~~R~~------~~~~nkG~eaa~Aal~mi~ 142 (149) |.++-.+.+.+.+.. ..+|==.+|++.+|...+.--.- .....-|.+|++-.++.++ T Consensus 243 D~~A~g~l~al~~~g--i~VP~DisVigfdd~~~~~~~~P~LTtv~~~~~~~g~~Av~~Ll~~i~ 305 (327) T PRK10339 243 DSIAIGVLRAIHERG--LNIPQDISLISVNDIPTARFTFPPLSTVRIHSEMMGSQGVNLLYEKAR 305 (327) T ss_pred HHHHHHHHHHHHHCC--CCCCCCEEEEEECCHHHHHHCCCCCEEEECCHHHHHHHHHHHHHHHHH T ss_conf 799999999999829--999997599998973889833899569986999999999999999973 No 54 >PRK13337 putative lipid kinase; Reviewed Probab=90.62 E-value=1.6 Score=24.34 Aligned_cols=92 Identities=20% Similarity=0.186 Sum_probs=53.5 Q ss_pred CCCEEEEEEECH-HHHHHHHHHHHHHHHHHHCCCCEEEEEHHHHHHHHHHHHHHHHHHHCCCCCCEEEEEEEEECCCCCH Q ss_conf 587179998031-2899999999999999987995555530014422699999986331137853566541200066524 Q gi|254780346|r 4 FIPHVLIIEARF-YENLSAMLFEGCVNVLHSRAVQWSSIVTPGVLEIPAAVSMVMNAKTRSVTYDGIIVLGVVMRGKTAH 82 (149) Q Consensus 4 ~~~kI~IV~s~~-~~~i~~~ll~ga~~~l~~~~~~~~~i~VPGa~EiP~a~~~~~~~~~~~~~~D~vIaLG~VIkGeT~H 82 (149) ||+|+++|+-.. -+.-..+.++...+.|.+++++++...+.+.-+.--.++.. ....||.+|+.| ||=. T Consensus 1 mmkr~~~I~NP~sG~g~~~~~~~~i~~~l~~~g~~~~~~~T~~~g~a~~~a~~~-----~~~~~d~vv~~G----GDGT- 70 (305) T PRK13337 1 MMKRARIIYNPTSGRELFKKNLPDVLQKLEQAGYETSAHATTGPGDATLAARQA-----AERNFDLVIAAG----GDGT- 70 (305) T ss_pred CCCEEEEEECCCCCCCCHHHHHHHHHHHHHHCCCEEEEEEECCHHHHHHHHHHH-----HHCCCCEEEEEE----CCHH- T ss_conf 984599999975688646778999999999879969999827802899999998-----777999899995----7628- Q ss_pred HHHHHHHHHHHHHHHHHHCCCCCEEEEECCC Q ss_conf 6789999999999999743997056542558 Q gi|254780346|r 83 CDVIAHAVTRGLVDLSINGSLPIGNGIVVVD 113 (149) Q Consensus 83 ~e~I~~~v~~gl~~lsl~~~~PI~~gILt~~ 113 (149) -+++.+|++.. +.....|||-.. T Consensus 71 ----v~evvngl~~~----~~~~~lgiiP~G 93 (305) T PRK13337 71 ----LNEVVNGLAEK----ENRPKLGIIPVG 93 (305) T ss_pred ----HHHHHHHHHCC----CCCCEEEEEECC T ss_conf ----99999998558----998628997078 No 55 >PRK11303 DNA-binding transcriptional regulator FruR; Provisional Probab=90.57 E-value=1.6 Score=24.28 Aligned_cols=120 Identities=14% Similarity=0.060 Sum_probs=63.7 Q ss_pred CEEEEEEECHHHHHHHHHHHHHHHHHHHCCCCEEEEEHHHHHHHHHH---HHHHHHHHHCCCCCCEEEEEEEEECCCCCH Q ss_conf 71799980312899999999999999987995555530014422699---999986331137853566541200066524 Q gi|254780346|r 6 PHVLIIEARFYENLSAMLFEGCVNVLHSRAVQWSSIVTPGVLEIPAA---VSMVMNAKTRSVTYDGIIVLGVVMRGKTAH 82 (149) Q Consensus 6 ~kI~IV~s~~~~~i~~~ll~ga~~~l~~~~~~~~~i~VPGa~EiP~a---~~~~~~~~~~~~~~D~vIaLG~VIkGeT~H 82 (149) .||+++.+.-.......-..|+.+.+.++|.+.+.++. +.|..-.. ++.++ .....+||++|. T Consensus 180 rrI~~i~~~~~~~~~~~R~~Gf~~al~~~g~~~~~~~~-~~~~~~~g~~~~~~ll---~~~~~p~Ai~~~---------- 245 (330) T PRK11303 180 ESILLLGALPELSVSFLREQGFRQALKDDPREVHFLYA-ESFSREAGAQLFEKWL---ETHGMPDALFTT---------- 245 (330) T ss_pred CEEEEEECCCCCHHHHHHHHHHHHHHHHCCCCEEEEEC-CCCCHHHHHHHHHHHH---HCCCCCCEEEEC---------- T ss_conf 97999968975637999999999999967998059964-8899899999999998---379999779974---------- Q ss_pred HHHHHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHHCCC-------CCCCHHHHHHHHHHHHH Q ss_conf 6789999999999999743997056542558899999950656-------57456999999999999 Q gi|254780346|r 83 CDVIAHAVTRGLVDLSINGSLPIGNGIVVVDSEQQAFDRVSPS-------HLDRGGCAARSALAMIE 142 (149) Q Consensus 83 ~e~I~~~v~~gl~~lsl~~~~PI~~gILt~~n~~QA~~R~~~~-------~~nkG~eaa~Aal~mi~ 142 (149) -|.++-.+.+++.+..+ .+|==..|++-+|.+.+.- ..+. ...-|..|++-++++++ T Consensus 246 nD~~A~g~l~al~~~g~--~VP~DvsvigfDd~~~~~~-~~p~LTtv~q~~~~~g~~A~~~Ll~~i~ 309 (330) T PRK11303 246 SYTLLQGVLDVLLERPG--KLPSDLAIATFGDNELLDF-LPCPVNAVAQQHRLIAERALELALAALD 309 (330) T ss_pred CHHHHHHHHHHHHHCCC--CCCCCEEEEEECCHHHHHC-CCCCCEEEECCHHHHHHHHHHHHHHHHC T ss_conf 89999999999998599--9999759999996288971-7999729967999999999999999965 No 56 >PRK10936 periplasmic sensory protein associated with the TorRS two-component regulatory system; Provisional Probab=89.81 E-value=1.6 Score=24.25 Aligned_cols=64 Identities=9% Similarity=0.070 Sum_probs=52.2 Q ss_pred CEEEEEEECHHHHHHHHHHHHHHHHHHHCCCCEEEEEHHHHHHHHHHHHHHHHHHHCCCCCCEEEE Q ss_conf 717999803128999999999999999879955555300144226999999863311378535665 Q gi|254780346|r 6 PHVLIIEARFYENLSAMLFEGCVNVLHSRAVQWSSIVTPGVLEIPAAVSMVMNAKTRSVTYDGIIV 71 (149) Q Consensus 6 ~kI~IV~s~~~~~i~~~ll~ga~~~l~~~~~~~~~i~VPGa~EiP~a~~~~~~~~~~~~~~D~vIa 71 (149) -||+++........=..+-.|+.+..++.|++..++..+|-.++.-=.+.+-+.- ..++||++. T Consensus 46 ~ki~~~~p~lkd~yW~~v~~G~~~~Ak~lGv~l~v~~a~~~~d~~~Q~~qie~~i--~~~vDAIil 109 (340) T PRK10936 46 WKLCALYPHLKDSYWLSVNYGLVQEAKRLGVDLKVLEAGGYYNLATQQQQLEQCV--AWGADAILL 109 (340) T ss_pred CEEEEEECCCCCHHHHHHHHHHHHHHHHHCCEEEEECCCCCCCHHHHHHHHHHHH--HCCCCEEEE T ss_conf 1799980688886999999999999998098699985899889999999999999--759999998 No 57 >pfam04392 ABC_sub_bind ABC transporter substrate binding protein. This family contains many hypothetical proteins and some ABC transporter substrate binding proteins. Probab=89.06 E-value=2.1 Score=23.55 Aligned_cols=116 Identities=15% Similarity=0.149 Sum_probs=76.6 Q ss_pred CCEEEEEEECHHHHHHHHHHHHHHHHHHHCCCCEEEEEHHHHHHHHHHHHHHHHHHHCCCCCCEEEEEEEEECCCCCHHH Q ss_conf 87179998031289999999999999998799555553001442269999998633113785356654120006652467 Q gi|254780346|r 5 IPHVLIIEARFYENLSAMLFEGCVNVLHSRAVQWSSIVTPGVLEIPAAVSMVMNAKTRSVTYDGIIVLGVVMRGKTAHCD 84 (149) Q Consensus 5 ~~kI~IV~s~~~~~i~~~ll~ga~~~l~~~~~~~~~i~VPGa~EiP~a~~~~~~~~~~~~~~D~vIaLG~VIkGeT~H~e 84 (149) .+||+++++.-... ...+++..++.+.+.|++.....|+..=|++.+.+.+. .+.|+++.+ ++++ T Consensus 130 ~k~igviyn~~e~~-s~~~~~~~~~~a~~~gi~l~~~~v~~~~ei~~a~~~l~------~~~Dal~i~-------~d~~- 194 (292) T pfam04392 130 VKSIGVYYSPSEAN-SVSLVEEIKKYAKKSGIKVVEASVPSSNDVPSAMSSMA------GKVDAIFIP-------TDNL- 194 (292) T ss_pred CCEEEEEECCCCCC-HHHHHHHHHHHHHHCCCEEEEEECCCHHHHHHHHHHHH------CCCCEEEEE-------CCCC- T ss_conf 85899995799865-79999999999997699899996688667999999743------289889993-------7810- Q ss_pred HHHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHH----CCCCCCCHHHHHHHHHHHHH Q ss_conf 89999999999999743997056542558899999950----65657456999999999999 Q gi|254780346|r 85 VIAHAVTRGLVDLSINGSLPIGNGIVVVDSEQQAFDRV----SPSHLDRGGCAARSALAMIE 142 (149) Q Consensus 85 ~I~~~v~~gl~~lsl~~~~PI~~gILt~~n~~QA~~R~----~~~~~nkG~eaa~Aal~mi~ 142 (149) +. +....+.+++.++++|+... +..+...-+ +.+..+-|++||+=+.++++ T Consensus 195 -v~-s~~~~i~~~a~~~kiPv~~~-----~~~~V~~Gal~s~g~~~~~~G~~aa~~a~rIL~ 249 (292) T pfam04392 195 -IA-SAFTAVLQEANKAKIPVITS-----DTSSVERGACAAVGVDYKQIGVQAANIVAKILK 249 (292) T ss_pred -HH-HHHHHHHHHHHHCCCCEEEC-----CHHHHHCCCEEEEECCHHHHHHHHHHHHHHHHC T ss_conf -78-89999999999749998957-----788884796799946999999999999999978 No 58 >TIGR01481 ccpA catabolite control protein A; InterPro: IPR006377 Catabolite control protein A is a LacI family global transcriptional regulator found in Gram-positive bacteria. CcpA is involved in repressing carbohydrate utilization genes [ex: alpha-amylase (amyE), acetyl-coenzyme A synthase (acsA)] and in activating genes involved in transporting excess carbon from the cell [e.g. acetate kinase (ackA), alpha-acetolactate synthase (alsS)]. Additionally, disruption of CcpA in Bacillus megaterium, Staphylococcus xylosus, Lactobacillus casei and Lactocacillus pentosus also decreases growth rate, which suggests CcpA is involved in the regulation of other metabolic pathways.; GO: 0030528 transcription regulator activity, 0045449 regulation of transcription. Probab=89.02 E-value=1.9 Score=23.89 Aligned_cols=97 Identities=8% Similarity=0.267 Sum_probs=73.6 Q ss_pred CCEEEEEEECHHHHHH-HHHHHHHHHHHHHCCCCEEE-EEHHH--HHHHHHHHHHHHHHHHCCCCCCEEEEEEEEECCCC Q ss_conf 8717999803128999-99999999999987995555-53001--44226999999863311378535665412000665 Q gi|254780346|r 5 IPHVLIIEARFYENLS-AMLFEGCVNVLHSRAVQWSS-IVTPG--VLEIPAAVSMVMNAKTRSVTYDGIIVLGVVMRGKT 80 (149) Q Consensus 5 ~~kI~IV~s~~~~~i~-~~ll~ga~~~l~~~~~~~~~-i~VPG--a~EiP~a~~~~~~~~~~~~~~D~vIaLG~VIkGeT 80 (149) .++|++|..+..+.|- +--+.|-++.|++.|++++. .-.-| +|.--+.+..-+ ...+.+++|++|. T Consensus 177 hK~iAfv~G~L~~~~N~~~~l~GykE~L~~~gI~~~e~L~~~~~YsY~~G~K~~~~l--~~s~p~~tAv~v~-------- 246 (332) T TIGR01481 177 HKKIAFVSGSLSDSVNGEVRLEGYKEALKKAGIAYEEDLVIEAKYSYDAGVKLAAEL--LESSPKITAVVVA-------- 246 (332) T ss_pred CCEEEEEECCCCCCCCCEECCCHHHHHHHHCCCCCCCCEEEECCCCCHHHHHHHHHH--HHCCCCCCEEEEC-------- T ss_conf 826888736757110452013304678873687414221330455504469999999--8538996589981-------- Q ss_pred CHHHHHHHHHHHHHHHHHHHC--CCCCEEEEECCCCHHH Q ss_conf 246789999999999999743--9970565425588999 Q gi|254780346|r 81 AHCDVIAHAVTRGLVDLSING--SLPIGNGIVVVDSEQQ 117 (149) Q Consensus 81 ~H~e~I~~~v~~gl~~lsl~~--~~PI~~gILt~~n~~Q 117 (149) +++-+=|+++-+++. ++|==+.|+|-+|..- T Consensus 247 ------~DE~A~G~lnaa~D~Gi~VPeDLevitsnnt~l 279 (332) T TIGR01481 247 ------DDELAIGILNAALDAGIKVPEDLEVITSNNTKL 279 (332) T ss_pred ------CHHHHHHHHHHHHHCCCCCCCCCEEECCCCCEE T ss_conf ------828899999999857898876456741066023 No 59 >cd01574 PBP1_LacI Ligand-binding domain of DNA transcription repressor LacI specific for lactose, a member of the LacI-GalR family of bacterial transcription regulators. Ligand-binding domain of DNA transcription repressor LacI specific for lactose, a member of the LacI-GalR family of bacterial transcription regulators. The ligand-binding domain of LacI is structurally homologous to the periplasmic sugar-binding domain of ABC-type transporters and both domains contain the type I periplasmic binding protein-like fold. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the type I periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA b Probab=88.67 E-value=2.3 Score=23.39 Aligned_cols=122 Identities=16% Similarity=0.099 Sum_probs=74.2 Q ss_pred CCEEEEEEECHHHHHHHHHHHHHHHHHHHCCCCEEEEEH-HHHHHHHH-HHHHHHHHHHCCCCCCEEEEEEEEECCCCCH Q ss_conf 871799980312899999999999999987995555530-01442269-9999986331137853566541200066524 Q gi|254780346|r 5 IPHVLIIEARFYENLSAMLFEGCVNVLHSRAVQWSSIVT-PGVLEIPA-AVSMVMNAKTRSVTYDGIIVLGVVMRGKTAH 82 (149) Q Consensus 5 ~~kI~IV~s~~~~~i~~~ll~ga~~~l~~~~~~~~~i~V-PGa~EiP~-a~~~~~~~~~~~~~~D~vIaLG~VIkGeT~H 82 (149) -++|+++.+.-+......-.+|+.+.+.+++.+...+.. ....|--+ +.+.++ ...++||++|- T Consensus 116 ~~~i~~i~~~~~~~~~~~R~~G~~~al~~~~i~~~~~~~~~~~~~~~~~~~~~l~----~~~~~~aii~~---------- 181 (264) T cd01574 116 HRTIAHVAGPEEWLSARARLAGWRAALEAAGIAPPPVLEGDWSAESGYRAGRELL----REGDPTAVFAA---------- 181 (264) T ss_pred CCCEEECCCCCCCHHHHHHHHHHHHHHHHCCCCCCEEEECCCCHHHHHHHHHHHH----HCCCCCEEEEC---------- T ss_conf 9827325899777579999999999999869897448866899799999999998----37999689636---------- Q ss_pred HHHHHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHH------CCCCCCCHHHHHHHHHHHHH Q ss_conf 6789999999999999743997056542558899999950------65657456999999999999 Q gi|254780346|r 83 CDVIAHAVTRGLVDLSINGSLPIGNGIVVVDSEQQAFDRV------SPSHLDRGGCAARSALAMIE 142 (149) Q Consensus 83 ~e~I~~~v~~gl~~lsl~~~~PI~~gILt~~n~~QA~~R~------~~~~~nkG~eaa~Aal~mi~ 142 (149) .|.++-.+.+.+.+..+ .+|==..|++-+|...+.--. .-....-|.+|++.++++++ T Consensus 182 ~D~~A~g~i~~l~~~g~--~iP~di~iigfd~~~~~~~~~p~lTtI~~~~~~~g~~A~~~l~~~i~ 245 (264) T cd01574 182 NDQMALGVLRALHELGL--RVPDDVSVVGFDDIPESAYFIPPLTTVRQDFAALGRRAVELLLALLE 245 (264) T ss_pred CHHHHHHHHHHHHHHCC--CCCCCCEEEEECCCHHHHHCCCCEEEEEECHHHHHHHHHHHHHHHHC T ss_conf 42999999999998299--88988479986881788950898589981999999999999999976 No 60 >cd06308 PBP1_sensor_kinase_like Periplasmic binding domain of two-component sensor kinase signaling systems. Periplasmic binding domain of two-component sensor kinase signaling systems, some of which are fused with a C-terminal histidine kinase A domain (HisK) and/or a signal receiver domain (REC). Members of this group share homology with a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily and are predicted to be involved in sensing of environmental stimuli; their substrate specificities, however, are not known in detail. Probab=88.40 E-value=2.3 Score=23.27 Aligned_cols=127 Identities=12% Similarity=-0.020 Sum_probs=68.8 Q ss_pred CCEEEEEEECHHHHHHHHHHHHHHHHHHHCCCCEEEEEHHHHHHHHHHHHHHHHHHHCCCCCCEEEEEEEEECCCCCHHH Q ss_conf 87179998031289999999999999998799555553001442269999998633113785356654120006652467 Q gi|254780346|r 5 IPHVLIIEARFYENLSAMLFEGCVNVLHSRAVQWSSIVTPGVLEIPAAVSMVMNAKTRSVTYDGIIVLGVVMRGKTAHCD 84 (149) Q Consensus 5 ~~kI~IV~s~~~~~i~~~ll~ga~~~l~~~~~~~~~i~VPGa~EiP~a~~~~~~~~~~~~~~D~vIaLG~VIkGeT~H~e 84 (149) ..||+++...-....+..-.+|+.+.|+++.--..+...+|-|..-.+.+..-+-.....++|++.|. .| T Consensus 122 ~~~i~~i~G~~~~~~~~~R~~Gf~~~l~~~~~~~vv~~~~~~~~~~~a~~~~~~~L~~~pdi~aI~a~----------nD 191 (270) T cd06308 122 KGNILEIWGLEGSSPAIERHDGFKEALSKYPKIKIVAQQDGDWLKEKAEEKMEELLQANPDIDLVYAH----------ND 191 (270) T ss_pred CCEEEEECCCCCCCHHHHHHHHHHHHHHHCCCCEEEEEECCCCCHHHHHHHHHHHHHHCCCCCEEEEC----------CC T ss_conf 85499962799985499999999999986689524668617667999999999998508888889977----------86 Q ss_pred HHHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHHCCCC-------CCCHHHHHHHHHHHHH Q ss_conf 899999999999997439970565425588999999506565-------7456999999999999 Q gi|254780346|r 85 VIAHAVTRGLVDLSINGSLPIGNGIVVVDSEQQAFDRVSPSH-------LDRGGCAARSALAMIE 142 (149) Q Consensus 85 ~I~~~v~~gl~~lsl~~~~PI~~gILt~~n~~QA~~R~~~~~-------~nkG~eaa~Aal~mi~ 142 (149) ..+-.+.+++.+.....+++|. |+=......++++-..... .-.|+.|+++++.+++ T Consensus 192 ~~A~Ga~~Al~~aG~~~~i~vv-g~D~~~~~~~~l~~i~~g~~~~t~~~p~~G~~av~~a~~~l~ 255 (270) T cd06308 192 PMALGAYLAAKRAGREKEIKFI-GIDGLPGPGGGIEAVRDGELDATFLYPTGGKEAIEVAMKILN 255 (270) T ss_pred HHHHHHHHHHHHCCCCCCCEEE-EECCCCCHHHHHHHHHCCCCEEEEECHHHHHHHHHHHHHHHC T ss_conf 5899999999976999995899-888993369999998738616999883789999999999977 No 61 >COG1454 EutG Alcohol dehydrogenase, class IV [Energy production and conversion] Probab=88.16 E-value=1.9 Score=23.80 Aligned_cols=62 Identities=19% Similarity=0.282 Sum_probs=42.5 Q ss_pred CCEEEEEEECHHHHHHHHHHHHHHHHHHHCCCCEEEEE-HHH---HHHHHHHHHHHHHHHHCCCCCCEEEEEE Q ss_conf 87179998031289999999999999998799555553-001---4422699999986331137853566541 Q gi|254780346|r 5 IPHVLIIEARFYENLSAMLFEGCVNVLHSRAVQWSSIV-TPG---VLEIPAAVSMVMNAKTRSVTYDGIIVLG 73 (149) Q Consensus 5 ~~kI~IV~s~~~~~i~~~ll~ga~~~l~~~~~~~~~i~-VPG---a~EiP~a~~~~~~~~~~~~~~D~vIaLG 73 (149) .+|.+||..+. -..-.+++...+.|++.++++.++. |++ .=++-.+++. .+..++|.+|+|| T Consensus 29 ~~r~liVTd~~--~~~~g~~~~v~~~L~~~~i~~~if~~v~p~P~~~~v~~~~~~-----~~~~~~D~iIalG 94 (377) T COG1454 29 AKRALIVTDRG--LAKLGLLDKVLDSLDAAGIEYEVFDEVEPEPTIETVEAGAEV-----AREFGPDTIIALG 94 (377) T ss_pred CCCEEEEECCC--CCCCHHHHHHHHHHHHCCCEEEEECCCCCCCCHHHHHHHHHH-----HHHCCCCEEEEEC T ss_conf 87159997986--311066999999987449828995688999988899999999-----9816999899977 No 62 >cd06317 PBP1_ABC_sugar_binding_like_8 Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems. Pperiplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily, which consists of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis. Probab=87.84 E-value=2.5 Score=23.06 Aligned_cols=124 Identities=14% Similarity=0.200 Sum_probs=75.0 Q ss_pred CCEEEEEEECHHHHHHHHHHHHHHHHHHHCCCCEEEE-EHHHHHHHHHHHHHHHHHHHC-CCCCCEEEEEEEEECCCCCH Q ss_conf 8717999803128999999999999999879955555-300144226999999863311-37853566541200066524 Q gi|254780346|r 5 IPHVLIIEARFYENLSAMLFEGCVNVLHSRAVQWSSI-VTPGVLEIPAAVSMVMNAKTR-SVTYDGIIVLGVVMRGKTAH 82 (149) Q Consensus 5 ~~kI~IV~s~~~~~i~~~ll~ga~~~l~~~~~~~~~i-~VPGa~EiP~a~~~~~~~~~~-~~~~D~vIaLG~VIkGeT~H 82 (149) +.+|+++...-.......-.+|+.+.|.+.+-+++.+ .+++-|....+.+..-+-... ..+.|++++ + T Consensus 125 ~~~v~~i~g~~~~~~~~~R~~Gf~~~l~~~~~~i~iv~~~~~~~~~~~a~~~~~~lL~~~~~~i~~I~~----------~ 194 (275) T cd06317 125 KGQIVVIAGQPGNGTAIERQKGFEDELAEVCPGVEVLDTQPADWDREKAQVAMEALITKFGDDIDGVYA----------G 194 (275) T ss_pred CCEEEEEECCCCCHHHHHHHHHHHHHHHHHCCCCEEEEEEECCCCHHHHHHHHHHHHHHCCCCCCEEEC----------C T ss_conf 961799937999859999999999999985887569888741477899999999998734575334405----------8 Q ss_pred HHHHHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHHCCCC---------CCCHHHHHHHHHHHHH Q ss_conf 67899999999999997439970565425588999999506565---------7456999999999999 Q gi|254780346|r 83 CDVIAHAVTRGLVDLSINGSLPIGNGIVVVDSEQQAFDRVSPSH---------LDRGGCAARSALAMIE 142 (149) Q Consensus 83 ~e~I~~~v~~gl~~lsl~~~~PI~~gILt~~n~~QA~~R~~~~~---------~nkG~eaa~Aal~mi~ 142 (149) .|..+-.+.+++.+..++.+++| .| .+...++++...... ..-|+.+++.++++++ T Consensus 195 nd~~a~Ga~~Al~~~G~~~~v~v-vg---~d~~~~~~~~i~~G~~~~tv~q~p~~~G~~av~~~~~~l~ 259 (275) T cd06317 195 DDNMARGALNAAKEAGLAGGIVI-VG---ANNFAVGYEAIRAGKYYGTIYQSPVDDGEAALQTAMDVLN 259 (275) T ss_pred CCHHHHHHHHHHHHCCCCCCCEE-EE---ECCCHHHHHHHHCCCCEEEEECCHHHHHHHHHHHHHHHHC T ss_conf 95789999999997499899879-98---7980999999985998399925999999999999999977 No 63 >cd06282 PBP1_GntR_like_2 Ligand-binding domain of putative DNA transcription repressors highly similar to that of the repressor specific for gluconate (GntR) which is a member of the LacI-GalR family of bacterial transcription regulators. This group includes the ligand-binding domain of putative DNA transcription repressors highly similar to that of the repressor specific for gluconate (GntR) which is a member of the LacI-GalR family of bacterial transcription regulators. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding Probab=87.57 E-value=2.6 Score=22.96 Aligned_cols=123 Identities=19% Similarity=0.176 Sum_probs=72.0 Q ss_pred CCEEEEEEECHHH-HHHHHHHHHHHHHHHHCCCCEE-EEEHHHHHHH-HHHHHHHHHHHHCCCCCCEEEEEEEEECCCCC Q ss_conf 8717999803128-9999999999999998799555-5530014422-69999998633113785356654120006652 Q gi|254780346|r 5 IPHVLIIEARFYE-NLSAMLFEGCVNVLHSRAVQWS-SIVTPGVLEI-PAAVSMVMNAKTRSVTYDGIIVLGVVMRGKTA 81 (149) Q Consensus 5 ~~kI~IV~s~~~~-~i~~~ll~ga~~~l~~~~~~~~-~i~VPGa~Ei-P~a~~~~~~~~~~~~~~D~vIaLG~VIkGeT~ 81 (149) ..||+++...++. +....-.+|+.+.+.+++.+.. .+..+...+- -..+..++ ....++||++|. T Consensus 116 ~~~i~~i~~~~~~~~~~~~R~~Gf~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~l---~~~~~~~ai~~~--------- 183 (266) T cd06282 116 HRRIAMLAGRLAASDRARQRYAGYRAAMRAAGLAPLPPVEIPFNTAALPSALLALL---TAHPAPTAIFCS--------- 183 (266) T ss_pred CCEEEEEECCCCCCHHHHHHHHHHHHHHHHCCCCCCCEEEECCCHHHHHHHHHHHH---HCCCCCCEEEEC--------- T ss_conf 95699997778888689999999999999869997617993487268999999998---379998479853--------- Q ss_pred HHHHHHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHH------CCCCCCCHHHHHHHHHHHHH Q ss_conf 46789999999999999743997056542558899999950------65657456999999999999 Q gi|254780346|r 82 HCDVIAHAVTRGLVDLSINGSLPIGNGIVVVDSEQQAFDRV------SPSHLDRGGCAARSALAMIE 142 (149) Q Consensus 82 H~e~I~~~v~~gl~~lsl~~~~PI~~gILt~~n~~QA~~R~------~~~~~nkG~eaa~Aal~mi~ 142 (149) .|.++-.+.+++.+.. ..+|=-..|++-+|...+.--. .-....-|..|++.++++++ T Consensus 184 -nD~~A~g~l~al~~~g--~~vP~disIigfd~~~~~~~~~P~lTti~q~~~~~g~~A~~~l~~~i~ 247 (266) T cd06282 184 -NDLLALAVIRALRRLG--LRVPDDLSVVGFDGIAIGRLLTPPLATVAQPNRDIGRQAVQRLLARIA 247 (266) T ss_pred -CCHHHHHHHHHHHHCC--CCCCCCEEEEEECCHHHHHCCCCCCEEEECCHHHHHHHHHHHHHHHHC T ss_conf -8889999999999849--999998499998970899707999679986999999999999999977 No 64 >cd03132 GATase1_catalase Type 1 glutamine amidotransferase (GATase1)-like domain found in at the C-terminal of several large catalases. Type 1 glutamine amidotransferase (GATase1)-like domain found in at the C-terminal of several large catalases. Catalase catalyzes the dismutation of hydrogen peroxide (H2O2) to water and oxygen. This group includes the large catalases: Neurospora crassa Catalase-1 and Catalase-3 and, Escherichia coli HP-II. This GATase1-like domain has an essential role in HP-II catalase activity. However, it lacks enzymatic activity and the catalytic triad typical of GATase1 domains. Catalase-1 and -3 are homotetrameric, HP-II is homohexameric. It has been proposed that this domain may facilitate the folding and oligomerization process. The interface between this GATase1-like domain of HP-II and the core of the subunit forms part of a channel which provides access to the deeply buried catalase active sites of HPII. Catalase-1 is associated with non-growing cells; C Probab=87.25 E-value=0.85 Score=26.00 Aligned_cols=107 Identities=18% Similarity=0.194 Sum_probs=64.2 Q ss_pred CEEEEEEECHHHHHHHHHHHHHHHHHHHCCCCEEEEE-HHH----HHHHHHHHHHHHHHHHCCCCCCEEEEEEEEECCCC Q ss_conf 7179998031289999999999999998799555553-001----44226999999863311378535665412000665 Q gi|254780346|r 6 PHVLIIEARFYENLSAMLFEGCVNVLHSRAVQWSSIV-TPG----VLEIPAAVSMVMNAKTRSVTYDGIIVLGVVMRGKT 80 (149) Q Consensus 6 ~kI~IV~s~~~~~i~~~ll~ga~~~l~~~~~~~~~i~-VPG----a~EiP~a~~~~~~~~~~~~~~D~vIaLG~VIkGeT 80 (149) .||+|..+. ...+.-+...++.|.+.|+.++++- -.| .-.-+..++.-+. ...+..|||++..| |.. T Consensus 2 rkVaiLv~d---g~~~~e~~~~~~al~~aG~~v~via~~~g~v~~~~g~~~~vd~t~~-~~~s~~fDAvvipg----G~~ 73 (142) T cd03132 2 RKVGILVAD---GVDAAELSALKAALKAAGANVKVVAPTLGGVVDSDGKTLEVDQTYA-GAPSVLFDAVVVPG----GAE 73 (142) T ss_pred CEEEEEECC---CCCHHHHHHHHHHHHHCCCEEEEEECCCCCEECCCCCEEECCEEEC-CCCHHHCCEEEECC----CCC T ss_conf 889999669---9888999999999998899899995798707758998880544353-68964713688438----877 Q ss_pred CHHHHHHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHHCC Q ss_conf 24678999999999999974399705654255889999995065 Q gi|254780346|r 81 AHCDVIAHAVTRGLVDLSINGSLPIGNGIVVVDSEQQAFDRVSP 124 (149) Q Consensus 81 ~H~e~I~~~v~~gl~~lsl~~~~PI~~gILt~~n~~QA~~R~~~ 124 (149) .-..+-.+.-+..+.+=+.+|++||+.- ..-.+.++.++. T Consensus 74 ~~~~L~~~~~~~~fv~eay~h~KpI~a~----~~~~~lL~~agi 113 (142) T cd03132 74 AAFALAPSGRALHFVTEAFKHGKPIGAV----GEGSDLLEAAGI 113 (142) T ss_pred CHHHHCCCHHHHHHHHHHHHCCCEEEEE----CCHHHHHHHCCC T ss_conf 9888644867999999999769979993----772999997697 No 65 >cd01544 PBP1_GalR Ligand-binding domain of DNA transcription repressor GalR which is one of two regulatory proteins involved in galactose transport and metabolism. Ligand-binding domain of DNA transcription repressor GalR which is one of two regulatory proteins involved in galactose transport and metabolism. Transcription of the galactose regulon genes is regulated by Gal iso-repressor (GalS) and Gal repressor (GalR) in different ways, but both repressors recognize the same DNA binding site in the absence of D-galactose. GalR is a dimeric protein like GalS and is exclusively involved in the regulation of galactose permease, the low-affinity galactose transporter. GalS is involved in regulating expression of the high-affinity galactose transporter encoded by the mgl operon. GalS and GalR are members of the LacI-GalR family of transcription regulators and both contain the type I periplasmic binding protein-like fold. Hence, they are structurally homologous to the periplasmic sugar bindi Probab=86.95 E-value=2.9 Score=22.74 Aligned_cols=124 Identities=10% Similarity=0.069 Sum_probs=75.7 Q ss_pred CEEEEEEE-----CHHHHHHHHHHHHHHHHHHHCCCCEEEEEHHHHHHHHHH---HHHHHHHHHCCCCCCEEEEEEEEEC Q ss_conf 71799980-----312899999999999999987995555530014422699---9999863311378535665412000 Q gi|254780346|r 6 PHVLIIEA-----RFYENLSAMLFEGCVNVLHSRAVQWSSIVTPGVLEIPAA---VSMVMNAKTRSVTYDGIIVLGVVMR 77 (149) Q Consensus 6 ~kI~IV~s-----~~~~~i~~~ll~ga~~~l~~~~~~~~~i~VPGa~EiP~a---~~~~~~~~~~~~~~D~vIaLG~VIk 77 (149) .||+.+.+ ..+....+.=+.|..+.+.++|.........|.|..... ++.+++.. ....+||++|. T Consensus 113 r~I~~i~g~~~~~~~~~~~~~~R~~Gy~~al~~~g~~~~~~~~~~~~~~~~g~~~~~~~l~~~-~~~~ptAi~~~----- 186 (270) T cd01544 113 TRIGFIGGEEKTTDGHEYIEDPRETAFREYMKEKGLYDPELIYIGDFTVESGYQLMKEALKSL-GDNLPTAFFIA----- 186 (270) T ss_pred CEEEEEECCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEECCCCHHHHHHHHHHHHHCC-CCCCCCEEEEC----- T ss_conf 869999577667751225689999999999998599996449966899799999999999728-87899789982----- Q ss_pred CCCCHHHHHHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHH------CCCCCCCHHHHHHHHHHHHH Q ss_conf 665246789999999999999743997056542558899999950------65657456999999999999 Q gi|254780346|r 78 GKTAHCDVIAHAVTRGLVDLSINGSLPIGNGIVVVDSEQQAFDRV------SPSHLDRGGCAARSALAMIE 142 (149) Q Consensus 78 GeT~H~e~I~~~v~~gl~~lsl~~~~PI~~gILt~~n~~QA~~R~------~~~~~nkG~eaa~Aal~mi~ 142 (149) .|.++-.+.+++.+.. ..+|==..|++.+|..-+.--. .-.....|.+|++.+++.++ T Consensus 187 -----nD~~A~g~l~~l~~~g--l~VP~DisviGfDd~~~~~~~~P~LTTV~q~~~~iG~~A~~~Ll~~i~ 250 (270) T cd01544 187 -----SDPMAIGALRALQEAG--IKVPEDVSVISFNDIEVAKYVSPPLSTVKIDTEEMGETAVDLLLERIN 250 (270) T ss_pred -----CCHHHHHHHHHHHHCC--CCCCCCEEEEEECCHHHHHHCCCCCEEEECCHHHHHHHHHHHHHHHHH T ss_conf -----3188999999999879--988776599997780789826899369982999999999999999961 No 66 >cd01542 PBP1_TreR_like Ligand-binding domain of DNA transcription repressor specific for trehalose (TreR) which is a member of the LacI-GalR family of bacterial transcription regulators. Ligand-binding domain of DNA transcription repressor specific for trehalose (TreR) which is a member of the LacI-GalR family of bacterial transcription regulators. The ligand-binding domain of TreR is structurally homologous to the periplasmic sugar-binding domain of ABC-type transporters and both domains contain the type I periplasmic binding protein-like fold. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the type I periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding wh Probab=86.82 E-value=2.9 Score=22.70 Aligned_cols=121 Identities=16% Similarity=0.142 Sum_probs=73.3 Q ss_pred CCEEEEEEEC-HHHHHHHHHHHHHHHHHHHCCCCEEEEEHHHHHHHHHH---HHHHHHHHHCCCCCCEEEEEEEEECCCC Q ss_conf 8717999803-12899999999999999987995555530014422699---9999863311378535665412000665 Q gi|254780346|r 5 IPHVLIIEAR-FYENLSAMLFEGCVNVLHSRAVQWSSIVTPGVLEIPAA---VSMVMNAKTRSVTYDGIIVLGVVMRGKT 80 (149) Q Consensus 5 ~~kI~IV~s~-~~~~i~~~ll~ga~~~l~~~~~~~~~i~VPGa~EiP~a---~~~~~~~~~~~~~~D~vIaLG~VIkGeT 80 (149) -.||+++... .+......=+.|..+.+.++|.+...+. .+.|....+ ++.+++ ..++||++|. T Consensus 114 hr~I~~i~~~~~~~~~~~~R~~G~~~al~~~g~~~~~~~-~~~~~~~~~~~~~~~ll~----~~~~~Ai~~~-------- 180 (259) T cd01542 114 HKNIAYLGVSESDIAVGILRKQGYLDALKEHGICPPNIV-ETDFSYESAYEAAQELLE----PQPPDAIVCA-------- 180 (259) T ss_pred CCEEEEEECCCCCCHHHHHHHHHHHHHHHHCCCCCCEEE-ECCCCHHHHHHHHHHHHH----CCCCCCEEEC-------- T ss_conf 985999955865606799999999999997699963599-657877789999999974----5799832434-------- Q ss_pred CHHHHHHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHHC------CCCCCCHHHHHHHHHHHHH Q ss_conf 2467899999999999997439970565425588999999506------5657456999999999999 Q gi|254780346|r 81 AHCDVIAHAVTRGLVDLSINGSLPIGNGIVVVDSEQQAFDRVS------PSHLDRGGCAARSALAMIE 142 (149) Q Consensus 81 ~H~e~I~~~v~~gl~~lsl~~~~PI~~gILt~~n~~QA~~R~~------~~~~nkG~eaa~Aal~mi~ 142 (149) .|.++-.+.+++.+.. ..+|==..|++-+|...+.--.- .....-|+.|++.++++++ T Consensus 181 --nD~~A~g~~~~l~~~g--~~vP~Disvigfdd~~~~~~~~P~LTtv~q~~~~~G~~A~~~Ll~~i~ 244 (259) T cd01542 181 --TDTIALGAMKYLQELG--RRIPEDISVAGFGGYELSSVVTPSLTTVDFGYKEAGKKAAELLLQLIE 244 (259) T ss_pred --CHHHHHHHHHHHHHCC--CCCCCCEEEEEECCHHHHHHCCCCCEEEEECHHHHHHHHHHHHHHHHC T ss_conf --5899999999999819--999998699998982999826899789995999999999999999966 No 67 >PRK09423 gldA glycerol dehydrogenase; Provisional Probab=86.31 E-value=3.1 Score=22.53 Aligned_cols=62 Identities=16% Similarity=0.159 Sum_probs=30.4 Q ss_pred CEEEEEEECHHHHHHHHHHHHHHHHHHHCCCCEEEEEHHHHHHHHHH-HHHHHHHHHCCCCCCEEEEEE Q ss_conf 71799980312899999999999999987995555530014422699-999986331137853566541 Q gi|254780346|r 6 PHVLIIEARFYENLSAMLFEGCVNVLHSRAVQWSSIVTPGVLEIPAA-VSMVMNAKTRSVTYDGIIVLG 73 (149) Q Consensus 6 ~kI~IV~s~~~~~i~~~ll~ga~~~l~~~~~~~~~i~VPGa~EiP~a-~~~~~~~~~~~~~~D~vIaLG 73 (149) +|++||... ...+.+.+...+.|++.|+++....++| |.+.. ++...+ ..+..++|.||++| T Consensus 30 ~r~liVtd~---~~~~~~~~~v~~~L~~~gi~~~~~~~~~--~pt~~~v~~~~~-~~~~~~~D~IiavG 92 (366) T PRK09423 30 KRALLIADE---FVLGIVGDTVEASLKDAGLDVVFEVFNG--ECSDNEIDRLVA-IAEENGCDVIIGIG 92 (366) T ss_pred CEEEEEECC---HHHHHHHHHHHHHHHHCCCEEEEEECCC--CCCHHHHHHHHH-HHHHCCCCEEEEEC T ss_conf 958999895---2899899999999986798699973389--999999999999-99864999899937 No 68 >cd06306 PBP1_TorT-like TorT-like proteins, a periplasmic binding protein family that activates induction of the Tor respiratory system upon trimethylamine N-oxide (TMAO) electron-acceptor binding in bacteria. TorT-like proteins, a periplasmic binding protein family that activates induction of the Tor respiratory system upon trimethylamine N-oxide (TMAO) electron-acceptor binding in bacteria. The Tor respiratory system is consists of three proteins (TorC, TorA, and TorD) and is induced in the presence of TMAO. The TMAO control is tightly regulated by three proteins: TorS, TorT, and TorR. Thus, the disruption of any of these proteins can abolish the Tor respiratory induction. TorT shares homology with the sugar-binding domain of the type I periplasmic binding proteins. The members of TorT-like family bind TMAO or related compounds and are predicted to be involved in signal transduction and/or substrate transport. Probab=85.56 E-value=3.4 Score=22.30 Aligned_cols=87 Identities=10% Similarity=0.132 Sum_probs=54.4 Q ss_pred EEEEEEECHHHHHHHHHHHHHHHHHHHCCCCEEEEEHHHHHHHHHHHHHHHHHHHCCCCCCEEEEEEEEECCCCCHHHHH Q ss_conf 17999803128999999999999999879955555300144226999999863311378535665412000665246789 Q gi|254780346|r 7 HVLIIEARFYENLSAMLFEGCVNVLHSRAVQWSSIVTPGVLEIPAAVSMVMNAKTRSVTYDGIIVLGVVMRGKTAHCDVI 86 (149) Q Consensus 7 kI~IV~s~~~~~i~~~ll~ga~~~l~~~~~~~~~i~VPGa~EiP~a~~~~~~~~~~~~~~D~vIaLG~VIkGeT~H~e~I 86 (149) ||+++........=..+.+|+.+..++.|+++..+..+|-..+.-=++.+-+ .....+||+|.- ..-.+-+ T Consensus 1 ki~v~~~~l~npfw~~~~~Ga~~aA~e~G~~v~~~~~~~~~d~~~Qi~~ie~--~i~~gvDaIii~-------p~d~~al 71 (268) T cd06306 1 KLCVLYPHLKDAYWLSVNYGMVEEAKRLGVSLKLLEAGGYPNLAKQIAQLED--CAAWGADAILLG-------AVSPDGL 71 (268) T ss_pred CEEEEECCCCCHHHHHHHHHHHHHHHHHCCEEEEEECCCCCCHHHHHHHHHH--HHHCCCCEEEEC-------CCCHHHH T ss_conf 9899957889879999999999999996997999958999999999999999--998399999986-------7986777 Q ss_pred HHHHHHHHHHHHHHCCCCCEEE Q ss_conf 9999999999997439970565 Q gi|254780346|r 87 AHAVTRGLVDLSINGSLPIGNG 108 (149) Q Consensus 87 ~~~v~~gl~~lsl~~~~PI~~g 108 (149) ..+.+. .+.++||+.- T Consensus 72 -----~~~~~a-~~agIPVV~~ 87 (268) T cd06306 72 -----NEILQQ-VAASIPVIAL 87 (268) T ss_pred -----HHHHHH-HHCCCEEEEE T ss_conf -----899999-9869829999 No 69 >PRK09140 2-dehydro-3-deoxy-6-phosphogalactonate aldolase; Reviewed Probab=85.48 E-value=1.9 Score=23.87 Aligned_cols=106 Identities=10% Similarity=0.180 Sum_probs=72.3 Q ss_pred CCEEEEEEECHHHHHHHHHHHHHHHHHHHCCCCE-EE-EEHHHHHHHHHHHHHHHHHHHCCCCCCEEEEEEEEECCCCCH Q ss_conf 8717999803128999999999999999879955-55-530014422699999986331137853566541200066524 Q gi|254780346|r 5 IPHVLIIEARFYENLSAMLFEGCVNVLHSRAVQW-SS-IVTPGVLEIPAAVSMVMNAKTRSVTYDGIIVLGVVMRGKTAH 82 (149) Q Consensus 5 ~~kI~IV~s~~~~~i~~~ll~ga~~~l~~~~~~~-~~-i~VPGa~EiP~a~~~~~~~~~~~~~~D~vIaLG~VIkGeT~H 82 (149) .+=|+|+.+.-.++. ....+.|.+.|+.. |+ .++|+++|+ ++.+-+ ...-+..|-.|.|...|+-+ T Consensus 10 ~plvaIlR~~~~~~a-----~~~~~al~~~Gi~~iEVTl~tp~a~~~---I~~l~~----~~~~~~~iGAGTVlt~e~~~ 77 (206) T PRK09140 10 LPLIAILRGITPDEA-----LAHVGALIEAGFRAIEIPLNSPDPFDS---IAALVK----ALGDDALIGAGTVLSPEQVD 77 (206) T ss_pred CCEEEEEECCCHHHH-----HHHHHHHHHCCCCEEEEECCCCCHHHH---HHHHHH----HCCCCEEEEEEECCCHHHHH T ss_conf 997999958999999-----999999998699889991799769999---999999----67986599862046799999 Q ss_pred HHH-------HHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHH Q ss_conf 678-------9999999999999743997056542558899999950 Q gi|254780346|r 83 CDV-------IAHAVTRGLVDLSINGSLPIGNGIVVVDSEQQAFDRV 122 (149) Q Consensus 83 ~e~-------I~~~v~~gl~~lsl~~~~PI~~gILt~~n~~QA~~R~ 122 (149) .-. ||-.....+.+.+.++++|.+-|++|+....||+++- T Consensus 78 ~ai~aGA~FiVSP~~~~~vi~~a~~~~i~~iPG~~TPsEi~~A~~~G 124 (206) T PRK09140 78 RLADAGGRLIVTPNIDPEVIRRAVAYGMTVMPGVATPTEAFAALRAG 124 (206) T ss_pred HHHHCCCCEEECCCCCHHHHHHHHHCCCCCCCCCCCHHHHHHHHHCC T ss_conf 99985999999999989999999982996527859999999999859 No 70 >cd06321 PBP1_ABC_sugar_binding_like_11 Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems. This group includes the periplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily, which consist of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis. Probab=85.15 E-value=3.5 Score=22.18 Aligned_cols=124 Identities=12% Similarity=0.045 Sum_probs=65.8 Q ss_pred CEEEEEEECHHHHHHHHHHHHHHHHHHHCC-CCEEEEEHHHHHHHHHHHHHHHHHHHCCCCCCEEEEEEEEECCCCCHHH Q ss_conf 717999803128999999999999999879-9555553001442269999998633113785356654120006652467 Q gi|254780346|r 6 PHVLIIEARFYENLSAMLFEGCVNVLHSRA-VQWSSIVTPGVLEIPAAVSMVMNAKTRSVTYDGIIVLGVVMRGKTAHCD 84 (149) Q Consensus 6 ~kI~IV~s~~~~~i~~~ll~ga~~~l~~~~-~~~~~i~VPGa~EiP~a~~~~~~~~~~~~~~D~vIaLG~VIkGeT~H~e 84 (149) .+|+++...-.....+ -++|+++.|.++. .........|.+....+.+..-+-.....++||++|. .| T Consensus 122 ~~i~~~~g~~~~~~~~-R~~G~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~~p~~~aifa~----------nD 190 (271) T cd06321 122 GNVAILNGPPVSAVLD-RVAGCKAALAKYPGIKLLSDDQNGKGSRDGGLRVMQGLLTRFPKLDGVFAI----------ND 190 (271) T ss_pred EEEEEECCCCCHHHHH-HHHHHHHHHHHCCCCEEEEEEECCCCCHHHHHHHHHHHHHCCCCCCEEEEC----------CC T ss_conf 0799975998535999-999999999877997688767228878999999999998508867789977----------86 Q ss_pred HHHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHHCC--------CCCCCHHHHHHHHHHHHH Q ss_conf 8999999999999974399705654255889999995065--------657456999999999999 Q gi|254780346|r 85 VIAHAVTRGLVDLSINGSLPIGNGIVVVDSEQQAFDRVSP--------SHLDRGGCAARSALAMIE 142 (149) Q Consensus 85 ~I~~~v~~gl~~lsl~~~~PI~~gILt~~n~~QA~~R~~~--------~~~nkG~eaa~Aal~mi~ 142 (149) ..+-.+.+++.+... +.|...|+-..++..+++.+-.+ ....-|+.|++.++++++ T Consensus 191 ~~A~Ga~~a~~~~G~--~~i~ivg~dg~~~~~~~~~~~~~~~~~tv~Q~~~~mG~~av~~l~~~i~ 254 (271) T cd06321 191 PTAIGADLAAKQAGR--NDIKITSVDGAPDAEKAILSGNSLIIATAAQDPRAMARKAVEIGYDILN 254 (271) T ss_pred HHHHHHHHHHHHCCC--CCCEEEEEECCHHHHHHHHCCCCCCEEEEECCHHHHHHHHHHHHHHHHC T ss_conf 899999999997597--9998999969679999986699972799848999999999999999977 No 71 >cd06316 PBP1_ABC_sugar_binding_like_7 Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems. Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily, which consists of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis. Probab=84.22 E-value=3.9 Score=21.92 Aligned_cols=63 Identities=14% Similarity=0.098 Sum_probs=35.7 Q ss_pred EEEEEEECHHHHHHHHHHHHHHHHHHHCCCCEEEEEHHHHHHHHHHHHHHHHHHHCCCCCCEEEEE Q ss_conf 179998031289999999999999998799555553001442269999998633113785356654 Q gi|254780346|r 7 HVLIIEARFYENLSAMLFEGCVNVLHSRAVQWSSIVTPGVLEIPAAVSMVMNAKTRSVTYDGIIVL 72 (149) Q Consensus 7 kI~IV~s~~~~~i~~~ll~ga~~~l~~~~~~~~~i~VPGa~EiP~a~~~~~~~~~~~~~~D~vIaL 72 (149) ||++|...-+.+.-..|.+|+++..++.|++... ..++-+...--++.+-+.. ...+|+++.. T Consensus 1 kia~v~~~~~n~f~~~~~~Ga~~aA~~lG~~v~~-~~da~~d~~~Q~~~i~~~I--~~gvDaIii~ 63 (294) T cd06316 1 KAAIVMHTSGSDWSNAQVRGAKDEFAKLGIEVVA-TTDAQFDPAKQVADIETTI--SQKPDIIISI 63 (294) T ss_pred CEEEEECCCCCHHHHHHHHHHHHHHHHHCCEEEE-ECCCCCCHHHHHHHHHHHH--HCCCCEEEEE T ss_conf 9899957889989999999999999983998999-6699889999999999999--8599999993 No 72 >cd06297 PBP1_LacI_like_12 Ligand-binding domain of uncharacterized transcription regulators from Thermus thermophilus and close homologs. Ligand-binding domain of uncharacterized transcription regulators from Thermus thermophilus and close homologs from other bacteria. This group belongs to the the LacI-GalR family repressors that are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding. Probab=83.20 E-value=4.3 Score=21.66 Aligned_cols=111 Identities=14% Similarity=0.068 Sum_probs=61.5 Q ss_pred HHHHHHHHHHHHHHHHHCCCCEEE-EEHHHHHHHHHH---HHHHHHHHHCCCCCCEEEEEEEEECCCCCHHHHHHHHHHH Q ss_conf 899999999999999987995555-530014422699---9999863311378535665412000665246789999999 Q gi|254780346|r 17 ENLSAMLFEGCVNVLHSRAVQWSS-IVTPGVLEIPAA---VSMVMNAKTRSVTYDGIIVLGVVMRGKTAHCDVIAHAVTR 92 (149) Q Consensus 17 ~~i~~~ll~ga~~~l~~~~~~~~~-i~VPGa~EiP~a---~~~~~~~~~~~~~~D~vIaLG~VIkGeT~H~e~I~~~v~~ 92 (149) ......-++|+.+.|+++|..++. ....|.+..... ++.++ ....++||++|. .|.++-.+.+ T Consensus 131 ~~~~~~R~~Gf~~al~~~g~~~~~~~~~~~~~~~~~g~~~~~~ll---~~~~~p~Ai~~~----------nD~~A~g~l~ 197 (269) T cd06297 131 RTVFAERRAGFQQALKDAGRPFSPDLLAITDHSEEGGRLAMRHLL---EKASPPLAVFAS----------ADQQALGALQ 197 (269) T ss_pred CHHHHHHHHHHHHHHHHCCCCCCCCEEECCCCCHHHHHHHHHHHH---HCCCCCCEEEEC----------CHHHHHHHHH T ss_conf 268999999999999982998662234137863656999999998---369998589989----------7899999999 Q ss_pred HHHHHHHHCCCCCEEEEECCCCHHHHHHHHC----CCCCCCHHHHHHHHHHHHH Q ss_conf 9999997439970565425588999999506----5657456999999999999 Q gi|254780346|r 93 GLVDLSINGSLPIGNGIVVVDSEQQAFDRVS----PSHLDRGGCAARSALAMIE 142 (149) Q Consensus 93 gl~~lsl~~~~PI~~gILt~~n~~QA~~R~~----~~~~nkG~eaa~Aal~mi~ 142 (149) ++.+. ...+|==..|++-+|...+..-+- .....-|+.|++..+++++ T Consensus 198 ~l~~~--Gi~vP~DisviGfDd~~~a~~~~LTTv~q~~~~~G~~A~~~Ll~~i~ 249 (269) T cd06297 198 EAVEL--GLTVGEDVRVVGFDDHPFAREAGLSTLAQPVEAMGARAAQLLLERLE 249 (269) T ss_pred HHHHC--CCCCCCCEEEEEECCHHHHHCCCCCEEECCHHHHHHHHHHHHHHHHC T ss_conf 99983--99889966999989848972489867963999999999999999966 No 73 >cd06283 PBP1_RegR_EndR_KdgR_like Ligand-binding domain of DNA transcription repressor RegR and other putative regulators such as KdgR and EndR. Ligand-binding domain of DNA transcription repressor RegR and other putative regulators such as KdgR and EndR, all of which are members of the LacI-GalR family of bacterial transcription regulators. RegR regulates bacterial competence and the expression of virulence factors, including hyaluronidase. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA b Probab=82.43 E-value=4.6 Score=21.48 Aligned_cols=122 Identities=19% Similarity=0.205 Sum_probs=69.0 Q ss_pred CEEEEEEECHHHHHH-HHHHHHHHHHHHHCCCCEEE--EEHHH--HHHHHHHHHHHHHHHHCCCCCCEEEEEEEEECCCC Q ss_conf 717999803128999-99999999999987995555--53001--44226999999863311378535665412000665 Q gi|254780346|r 6 PHVLIIEARFYENLS-AMLFEGCVNVLHSRAVQWSS--IVTPG--VLEIPAAVSMVMNAKTRSVTYDGIIVLGVVMRGKT 80 (149) Q Consensus 6 ~kI~IV~s~~~~~i~-~~ll~ga~~~l~~~~~~~~~--i~VPG--a~EiP~a~~~~~~~~~~~~~~D~vIaLG~VIkGeT 80 (149) .||+++.......-+ ..-.+|+.+.+.+++..... +..++ .-+...+++.+++ ...++||++|. T Consensus 117 ~~i~~i~~~~~~~~~~~~R~~g~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~---~~~~~~aii~~-------- 185 (267) T cd06283 117 ERILFVTEPLDEISPRMERYEGFKEALAEHGIGVNEELIEIDDEDADELDERLRQLLN---KPKKKTAIFAA-------- 185 (267) T ss_pred CEEEEEECCCCCCCHHHHHHHHHHHHHHHCCCCCCCEEEEECCCCHHHHHHHHHHHHH---CCCCCCEECCC-------- T ss_conf 7299995687788379999999999999759976514898335426779999999984---79998642037-------- Q ss_pred CHHHHHHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHHC------CCCCCCHHHHHHHHHHHHH Q ss_conf 2467899999999999997439970565425588999999506------5657456999999999999 Q gi|254780346|r 81 AHCDVIAHAVTRGLVDLSINGSLPIGNGIVVVDSEQQAFDRVS------PSHLDRGGCAARSALAMIE 142 (149) Q Consensus 81 ~H~e~I~~~v~~gl~~lsl~~~~PI~~gILt~~n~~QA~~R~~------~~~~nkG~eaa~Aal~mi~ 142 (149) .|.++-.+.+.+.+.. ..+|=-..|.+.++.+++.--.- .....-|+.|++.++++++ T Consensus 186 --~D~~A~g~~~~l~~~g--~~vP~disVvg~dd~~~~~~~~p~lTtv~~~~~~~g~~av~~l~~~i~ 249 (267) T cd06283 186 --NGLILLEVLKALKELG--IRIPEDVGLIGFDDTEWAELIGPGITTIAQPTYEMGKTAAELLLERIE 249 (267) T ss_pred --CCHHHHHHHHHHHHCC--CCCCCCCEEEEECCHHHHHHCCCCCEEEECCHHHHHHHHHHHHHHHHC T ss_conf --7099999999999829--988987668853886999842999539983999999999999999977 No 74 >cd06305 PBP1_methylthioribose_binding_like Methylthioribose-binding protein-like of ABC-type transport systems that belong to a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein (PBP1) superfamily. Methylthioribose-binding protein-like of ABC-type transport systems that belong to a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein (PBP1) superfamily, which consists of two alpha/beta globular domains connected by a three-stranded hinge. This Venus flytrap-like domain undergoes transition from an open to a closed conformational state upon ligand binding. The sugar-binding domain of the periplasmic proteins in this group is also homologous to the ligand-binding domain of eukaryotic receptors such as metabotropic glutamate receptor (mGluR), DNA-binding transcriptional repressors such as LacI and GalR. Probab=82.23 E-value=4.7 Score=21.43 Aligned_cols=36 Identities=3% Similarity=-0.028 Sum_probs=24.2 Q ss_pred EEEEEEECHHHHHHHHHHHHHHHHHHHCCCCEEEEE Q ss_conf 179998031289999999999999998799555553 Q gi|254780346|r 7 HVLIIEARFYENLSAMLFEGCVNVLHSRAVQWSSIV 42 (149) Q Consensus 7 kI~IV~s~~~~~i~~~ll~ga~~~l~~~~~~~~~i~ 42 (149) ||++|......+.-..+.+|+++..++.|++..... T Consensus 1 kIa~~~~~~~~~f~~~~~~G~~~~A~~~G~~~~v~d 36 (273) T cd06305 1 RIAVVRYGGSGDFDQAYLAGTKAEAEALGGDLRVYD 36 (273) T ss_pred CEEEEECCCCCHHHHHHHHHHHHHHHHCCCEEEEEC T ss_conf 989997178897999999999999997499899973 No 75 >PRK13805 bifunctional acetaldehyde-CoA/alcohol dehydrogenase; Provisional Probab=80.54 E-value=5.3 Score=21.07 Aligned_cols=62 Identities=21% Similarity=0.290 Sum_probs=41.2 Q ss_pred CCEEEEEEECHHHHHHHHHHHHHHHHHHHCCCCEEEEE-H---HHHHHHHHHHHHHHHHHHCCCCCCEEEEEE Q ss_conf 87179998031289999999999999998799555553-0---014422699999986331137853566541 Q gi|254780346|r 5 IPHVLIIEARFYENLSAMLFEGCVNVLHSRAVQWSSIV-T---PGVLEIPAAVSMVMNAKTRSVTYDGIIVLG 73 (149) Q Consensus 5 ~~kI~IV~s~~~~~i~~~ll~ga~~~l~~~~~~~~~i~-V---PGa~EiP~a~~~~~~~~~~~~~~D~vIaLG 73 (149) .+|.+||.-++-. .-++++...+.|++.|++++++. | |-.-.+--.++.+ +..++|.+|+|| T Consensus 482 ~kralIVTD~~~~--~~G~vd~v~~~L~~~gi~~~vFd~V~pdPt~~~V~~G~~~~-----~~~~~D~IIalG 547 (862) T PRK13805 482 KKRAFIVTDRGMV--ELGYVDKVTDVLRANGVETEVFSEVEPDPTLSTVRKGAELM-----RSFKPDTIIALG 547 (862) T ss_pred CCEEEEECCHHHH--HCCCHHHHHHHHHHCCCEEEEECCCCCCCCHHHHHHHHHHH-----HHCCCCEEEEEC T ss_conf 9779998785187--67889999999998698399966989993979999999999-----864999999947 No 76 >PRK13055 putative lipid kinase; Reviewed Probab=80.50 E-value=5.4 Score=21.06 Aligned_cols=89 Identities=15% Similarity=0.172 Sum_probs=55.5 Q ss_pred CCCEEEEEEECHH-HHHHHHHHHHHHHHHHHCCCCEEEEEH---HH-HHHHHHHHHHHHHHHHCCCCCCEEEEEEEEECC Q ss_conf 5871799980312-899999999999999987995555530---01-442269999998633113785356654120006 Q gi|254780346|r 4 FIPHVLIIEARFY-ENLSAMLFEGCVNVLHSRAVQWSSIVT---PG-VLEIPAAVSMVMNAKTRSVTYDGIIVLGVVMRG 78 (149) Q Consensus 4 ~~~kI~IV~s~~~-~~i~~~ll~ga~~~l~~~~~~~~~i~V---PG-a~EiP~a~~~~~~~~~~~~~~D~vIaLG~VIkG 78 (149) ||+|+++|+=..= ..-..+.+....+.|.+.+++...+.. || +.++ .+ .+....||.+|+.| | T Consensus 1 MmKr~~lIvNP~SG~g~~~~~~~~i~~~L~~~g~e~~~~~tt~~~~~a~~~-------a~-~a~~~g~d~Iva~G----G 68 (334) T PRK13055 1 MQKRARLIYNPTSGQEIMKKNVADILDILEQAGYETSAFQTTPEPNSAKNE-------AR-RAAKAGFDLIIAAG----G 68 (334) T ss_pred CCEEEEEEECCCCCCCCHHHHHHHHHHHHHHCCCEEEEEEEECCCCHHHHH-------HH-HHHHCCCCEEEEEC----C T ss_conf 970699999987789757889999999999869859999944178579999-------99-87657998999987----7 Q ss_pred CCCHHHHHHHHHHHHHHHHHHHCCCCCEEEEECCC Q ss_conf 65246789999999999999743997056542558 Q gi|254780346|r 79 KTAHCDVIAHAVTRGLVDLSINGSLPIGNGIVVVD 113 (149) Q Consensus 79 eT~H~e~I~~~v~~gl~~lsl~~~~PI~~gILt~~ 113 (149) |=. -++|.+|++ ..+.|...|||.+. T Consensus 69 DGT-----inevvngl~----~~~~~~~LgiIP~G 94 (334) T PRK13055 69 DGT-----INEVVNGIA----PLEKRPKMAIIPAG 94 (334) T ss_pred CCH-----HHHHHHHHH----CCCCCCEEEEEECC T ss_conf 608-----999999873----46999718998077 No 77 >cd01541 PBP1_AraR Ligand-binding domain of DNA transcription repressor specific for arabinose (AraR) which is a member of the LacI-GalR family of bacterial transcription regulators. Ligand-binding domain of DNA transcription repressor specific for arabinose (AraR) which is a member of the LacI-GalR family of bacterial transcription regulators. The ligand-binding domain of AraR is structurally homologous to the periplasmic sugar-binding domain of ABC-type transporters and both domains contain the type I periplasmic binding protein-like fold. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the type I periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which i Probab=80.36 E-value=5.4 Score=21.03 Aligned_cols=35 Identities=11% Similarity=0.171 Sum_probs=20.0 Q ss_pred EEEEEEECHHHHHHHHHHHHHHHHHHHCCCCEEEE Q ss_conf 17999803128999999999999999879955555 Q gi|254780346|r 7 HVLIIEARFYENLSAMLFEGCVNVLHSRAVQWSSI 41 (149) Q Consensus 7 kI~IV~s~~~~~i~~~ll~ga~~~l~~~~~~~~~i 41 (149) +|++|..+.....-..+++|..+.+.++|+..-.. T Consensus 1 ~IGvivp~l~n~ff~~~~~gi~~~~~~~gy~~li~ 35 (273) T cd01541 1 NIGVITTYISDYIFPSIIRGIESVLSEKGYSLLLA 35 (273) T ss_pred CEEEEECCCCCHHHHHHHHHHHHHHHHCCCEEEEE T ss_conf 98999588765799999999999999869989999 No 78 >COG2984 ABC-type uncharacterized transport system, periplasmic component [General function prediction only] Probab=80.31 E-value=5.4 Score=21.02 Aligned_cols=116 Identities=16% Similarity=0.198 Sum_probs=68.7 Q ss_pred CEEEEEEECHHHHHHHHHHHHHHHHHHHCCCCEEEEEHHHHHHHHHHHHHHHHHHHCCCCCCEEEEEEEEECCCCCHHHH Q ss_conf 71799980312899999999999999987995555530014422699999986331137853566541200066524678 Q gi|254780346|r 6 PHVLIIEARFYENLSAMLFEGCVNVLHSRAVQWSSIVTPGVLEIPAAVSMVMNAKTRSVTYDGIIVLGVVMRGKTAHCDV 85 (149) Q Consensus 6 ~kI~IV~s~~~~~i~~~ll~ga~~~l~~~~~~~~~i~VPGa~EiP~a~~~~~~~~~~~~~~D~vIaLG~VIkGeT~H~e~ 85 (149) ++|.++++. .++-+..+++..+..+..+|+++-...+|-+-|+|.+.+-+. ++.|++... | |. T Consensus 160 k~Igv~Y~p-~E~ns~~l~eelk~~A~~~Gl~vve~~v~~~ndi~~a~~~l~------g~~d~i~~p-------~---dn 222 (322) T COG2984 160 KSIGVLYNP-GEANSVSLVEELKKEARKAGLEVVEAAVTSVNDIPRAVQALL------GKVDVIYIP-------T---DN 222 (322) T ss_pred EEEEEEECC-CCCCCHHHHHHHHHHHHHCCCEEEEEECCCCCCCHHHHHHHC------CCCCEEEEE-------C---CH T ss_conf 069999579-886608999999999987798899983476320089999734------787679986-------6---06 Q ss_pred HHHHHHHHHHHHHHHCCCCCEEEEECCCC---HHHHHHHHCCCCCCCHHHHHHHHHHHHH Q ss_conf 99999999999997439970565425588---9999995065657456999999999999 Q gi|254780346|r 86 IAHAVTRGLVDLSINGSLPIGNGIVVVDS---EQQAFDRVSPSHLDRGGCAARSALAMIE 142 (149) Q Consensus 86 I~~~v~~gl~~lsl~~~~PI~~gILt~~n---~~QA~~R~~~~~~nkG~eaa~Aal~mi~ 142 (149) -..+....+...+.+.++|++. .++ ++-|..-++.+..+-|.+++.-+.++++ T Consensus 223 ~i~s~~~~l~~~a~~~kiPli~----sd~~~V~~Ga~aA~gvdy~~~G~qtg~~v~~ILk 278 (322) T COG2984 223 LIVSAIESLLQVANKAKIPLIA----SDTSSVKEGALAALGVDYKDLGKQTGEMVVKILK 278 (322) T ss_pred HHHHHHHHHHHHHHHHCCCEEC----CCHHHHHCCCCEEECCCHHHHHHHHHHHHHHHHC T ss_conf 7788899999998870897354----7778876686036606799988999999999976 No 79 >PRK09701 D-allose transporter subunit; Provisional Probab=80.22 E-value=5.5 Score=21.00 Aligned_cols=89 Identities=9% Similarity=0.085 Sum_probs=56.0 Q ss_pred CCEEEEEEECHHHHHHHHHHHHHHHHHHHCCCCEEEEEHHHHHHHHHHHHHHHHHHHCCCCCCEEEEEEEEECCCCCHHH Q ss_conf 87179998031289999999999999998799555553001442269999998633113785356654120006652467 Q gi|254780346|r 5 IPHVLIIEARFYENLSAMLFEGCVNVLHSRAVQWSSIVTPGVLEIPAAVSMVMNAKTRSVTYDGIIVLGVVMRGKTAHCD 84 (149) Q Consensus 5 ~~kI~IV~s~~~~~i~~~ll~ga~~~l~~~~~~~~~i~VPGa~EiP~a~~~~~~~~~~~~~~D~vIaLG~VIkGeT~H~e 84 (149) ..+|++|...+....-..+.+|+.+..++.|++++.+..|.--....=++.+-+. ....+||++.--. T Consensus 24 ~~~iavi~k~~~npf~~~~~~Ga~~aAk~~G~~v~v~~~~~~~D~~~Qi~~Ie~~--I~~gvdaIii~p~---------- 91 (311) T PRK09701 24 AAEYAVVLKTLSNPFWVDMKKGIEDEAKTLGVSVDIFASPSEGDFQSQLQLFEDL--SNKNYKGIAFAPL---------- 91 (311) T ss_pred CCCEEEEECCCCCHHHHHHHHHHHHHHHHHCCEEEEEECCCCCCHHHHHHHHHHH--HHCCCCEEEEECC---------- T ss_conf 6849999688899899999999999999869979999279878999999999999--9759999999189---------- Q ss_pred HHHHHHHHHHHHHHHHCCCCCEE Q ss_conf 89999999999999743997056 Q gi|254780346|r 85 VIAHAVTRGLVDLSINGSLPIGN 107 (149) Q Consensus 85 ~I~~~v~~gl~~lsl~~~~PI~~ 107 (149) .........+-..+.++||+. T Consensus 92 --d~~a~~~~i~~A~~aGIpVV~ 112 (311) T PRK09701 92 --SSVNLVMPVARAWKKGIYLVN 112 (311) T ss_pred --CHHHHHHHHHHHHHCCCCEEE T ss_conf --877889999999977991896 No 80 >PRK05569 flavodoxin; Provisional Probab=79.25 E-value=5.5 Score=21.01 Aligned_cols=101 Identities=14% Similarity=0.017 Sum_probs=58.8 Q ss_pred CCEEEEEEECHHHHHHHHHHHHHHHHHHHCCCCEEEEEHHHHHHHHHHHHHHHHHHHCCCCCCEEEEEEEEECCCCCHHH Q ss_conf 87179998031289999999999999998799555553001442269999998633113785356654120006652467 Q gi|254780346|r 5 IPHVLIIEARFYENLSAMLFEGCVNVLHSRAVQWSSIVTPGVLEIPAAVSMVMNAKTRSVTYDGIIVLGVVMRGKTAHCD 84 (149) Q Consensus 5 ~~kI~IV~s~~~~~i~~~ll~ga~~~l~~~~~~~~~i~VPGa~EiP~a~~~~~~~~~~~~~~D~vIaLG~VIkGeT~H~e 84 (149) |+||+||+.+-| .=|+.|-+...+.+.+.|++++...+. +.+ ...++ ++|+ |++|| -|.+.+ T Consensus 1 M~Kv~IvY~S~~-GnTe~mA~~IaeG~~~~G~ev~v~~~~---~~~--~~di~-------~~d~-i~~Gs----pT~~~~ 62 (141) T PRK05569 1 MKKVSIIYWSCG-GNVEVLANTIADGAKEAGAEVTIKHVA---DAK--VEDVL-------EADA-VAFGS----PSMDNN 62 (141) T ss_pred CCEEEEEEECCC-CHHHHHHHHHHHHHHHCCCEEEEEECC---CCC--HHHHH-------HCCE-EEEEC----CCCCCC T ss_conf 974999998996-089999999999999769819999842---399--88997-------1890-59905----455888 Q ss_pred HHHH-HH---HHHHHHHHHHCCCCCEEEEECCC---CHHHHHHHHC Q ss_conf 8999-99---99999999743997056542558---8999999506 Q gi|254780346|r 85 VIAH-AV---TRGLVDLSINGSLPIGNGIVVVD---SEQQAFDRVS 123 (149) Q Consensus 85 ~I~~-~v---~~gl~~lsl~~~~PI~~gILt~~---n~~QA~~R~~ 123 (149) .+-+ .+ ...+..+.++..+-..||--.-. ...+..+|.. T Consensus 63 ~~~~~~~~~~l~~l~~~~~~~K~~a~FGSyGW~~Ge~~~~~~~~l~ 108 (141) T PRK05569 63 NIEQEEMAPFLDQFKLTPNENKKCILFGSYGWDNGEFMKLWKDRMK 108 (141) T ss_pred CCCHHHHHHHHHHHHCCCCCCCEEEEEECCCCCCCHHHHHHHHHHH T ss_conf 7771769999999853455898899996677886469999999999 No 81 >cd01539 PBP1_GGBP Periplasmic glucose/galactose-binding protein (GGBP) involved in chemotaxis towards, and active transport of, glucose and galactose in various bacterial species. Periplasmic glucose/galactose-binding protein (GGBP) involved in chemotaxis towards, and active transport of, glucose and galactose in various bacterial species. GGBP is a member of the pentose/hexose sugar-binding protein family of the type I periplasmic binding protein superfamily which consists of two alpha/beta globular domains connected by a three-stranded hinge. This Venus flytrap-like domain undergoes transition from an open to a closed conformational state upon ligand binding. Moreover, the periplasmic GGBP is homologous to the ligand-binding domain of eukaryotic receptors such as glutamate receptor (GluR) and DNA-binding transcriptional repressors such as LacI and GalR. Probab=79.25 E-value=5.9 Score=20.81 Aligned_cols=33 Identities=3% Similarity=0.108 Sum_probs=15.0 Q ss_pred EEEEEEECHHHHHHHHHHHHHHHHHHHCCCCEE Q ss_conf 179998031289999999999999998799555 Q gi|254780346|r 7 HVLIIEARFYENLSAMLFEGCVNVLHSRAVQWS 39 (149) Q Consensus 7 kI~IV~s~~~~~i~~~ll~ga~~~l~~~~~~~~ 39 (149) ||+++...+....-..|.+|+.+..++.|.+++ T Consensus 1 kIGv~~~~~~npF~~~~~~g~e~~a~e~g~~v~ 33 (303) T cd01539 1 KIGVFLYKFDDTFISLVRKNLEDIQKENGGKVE 33 (303) T ss_pred CEEEEECCCCCHHHHHHHHHHHHHHHHHCCCEE T ss_conf 989996488998999999999999998599579 No 82 >cd06314 PBP1_tmGBP Periplasmic sugar-binding domain of Thermotoga maritima glucose-binding protein (tmGBP) and its close homologs. Periplasmic sugar-binding domain of Thermotoga maritima glucose-binding protein (tmGBP) and its close homologs from other bacteria. They are a member of the type I periplasmic binding protein superfamily which consists of two domains connected by a three-stranded hinge. TmGBP is specific for glucose and its binding pocket is buried at the interface of the two domains. TmGBP also exhibits high thermostability and the highest structural similarity to E. coli glucose binding protein (ecGBP). Probab=78.78 E-value=6.1 Score=20.72 Aligned_cols=123 Identities=12% Similarity=0.089 Sum_probs=72.3 Q ss_pred CCEEEEEEECHHHHHHHHHHHHHHHHHHHCCCCEEEEEHHHHHHHHHHHHHHHHHHHCCCCCCEEEEEEEEECCCCCHHH Q ss_conf 87179998031289999999999999998799555553001442269999998633113785356654120006652467 Q gi|254780346|r 5 IPHVLIIEARFYENLSAMLFEGCVNVLHSRAVQWSSIVTPGVLEIPAAVSMVMNAKTRSVTYDGIIVLGVVMRGKTAHCD 84 (149) Q Consensus 5 ~~kI~IV~s~~~~~i~~~ll~ga~~~l~~~~~~~~~i~VPGa~EiP~a~~~~~~~~~~~~~~D~vIaLG~VIkGeT~H~e 84 (149) ..+++++.......-...-.+|+.+.|+++++++-.+ ..+.++.+-+.+.+-.......+.|++++.. + T Consensus 120 ~g~v~i~~g~~~~~~~~~R~~Gf~~~l~~~~~~iv~~-~~~~~~~~~a~~~~~~~L~~~pdi~~i~~~~----------~ 188 (271) T cd06314 120 GGKVAIFVGSLGADNAKERIQGIKDAIKDSKIEIVDT-RGDEEDFAKAKSNAEDALNAHPDLKCMFGLY----------A 188 (271) T ss_pred CCEEEEEECCCCCHHHHHHHHHHHHHHHHCCCEEEEE-ECCCCCHHHHHHHHHHHHHHCCCCCEEEEEC----------C T ss_conf 9869999458998789999999999996258579875-1577638899999999997589987899808----------8 Q ss_pred HHHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHHCCCC---------CCCHHHHHHHHHHHHH Q ss_conf 899999999999997439970565425588999999506565---------7456999999999999 Q gi|254780346|r 85 VIAHAVTRGLVDLSINGSLPIGNGIVVVDSEQQAFDRVSPSH---------LDRGGCAARSALAMIE 142 (149) Q Consensus 85 ~I~~~v~~gl~~lsl~~~~PI~~gILt~~n~~QA~~R~~~~~---------~nkG~eaa~Aal~mi~ 142 (149) ..+..+.+++.+......+. |.+.+...++.+...... -.-|+.+.+++.+.++ T Consensus 189 ~~a~ga~~Al~~~g~~~~i~----vvg~D~~~~~~~~i~~G~i~~tv~Q~p~~~G~~av~~~~~~l~ 251 (271) T cd06314 189 YNGPAIAEAVKAAGKLGKVK----IVGFDEDPDTLQGVKEGTIQGTVVQRPYQMGYLSVTVLAALLK 251 (271) T ss_pred CCHHHHHHHHHHHCCCCCCE----EEEECCCHHHHHHHHCCCCEEEEECCHHHHHHHHHHHHHHHHC T ss_conf 51699999999847589967----9987898999999982998599838999999999999999976 No 83 >PRK05568 flavodoxin; Provisional Probab=78.29 E-value=5.6 Score=20.92 Aligned_cols=38 Identities=5% Similarity=-0.032 Sum_probs=30.5 Q ss_pred CCEEEEEE-ECHHHHHHHHHHHHHHHHHHHCCCCEEEEEHH Q ss_conf 87179998-03128999999999999999879955555300 Q gi|254780346|r 5 IPHVLIIE-ARFYENLSAMLFEGCVNVLHSRAVQWSSIVTP 44 (149) Q Consensus 5 ~~kI~IV~-s~~~~~i~~~ll~ga~~~l~~~~~~~~~i~VP 44 (149) |+||+||+ |.|.+ |+.|-+--.+.+.+.|++++...+. T Consensus 1 M~kv~IvY~S~~Gn--Te~mA~~Iaegl~~~Gv~V~~~~~~ 39 (142) T PRK05568 1 MKKLNIIYWSGTGN--TEAMANLIAEGAKENGLEVKLLNVS 39 (142) T ss_pred CCEEEEEEECCCCH--HHHHHHHHHHHHHHCCCEEEEEEEC T ss_conf 97299999899854--9999999999998669839999800 No 84 >cd06320 PBP1_allose_binding Periplasmic allose-binding domain of bacterial transport systems that function as a primary receptor of active transport and chemotaxis. Periplasmic allose-binding domain of bacterial transport systems that function as a primary receptor of active transport and chemotaxis. The members of this group are belonging to a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily. Like other periplasmic receptors of the ABC-type transport systems, the allose-binding protein consists of two alpha/beta domains connected by a three-stranded hinge. This Venus flytrap-like domain undergoes transition from an open to a closed conformational state upon ligand binding. Probab=77.87 E-value=6.5 Score=20.55 Aligned_cols=63 Identities=16% Similarity=0.160 Sum_probs=34.6 Q ss_pred EEEEEEECHHHHHHHHHHHHHHHHHHHCCCCEEEEEHHHHHHHHHHHHHHHHHHHCCCCCCEEEE Q ss_conf 17999803128999999999999999879955555300144226999999863311378535665 Q gi|254780346|r 7 HVLIIEARFYENLSAMLFEGCVNVLHSRAVQWSSIVTPGVLEIPAAVSMVMNAKTRSVTYDGIIV 71 (149) Q Consensus 7 kI~IV~s~~~~~i~~~ll~ga~~~l~~~~~~~~~i~VPGa~EiP~a~~~~~~~~~~~~~~D~vIa 71 (149) ||++|...+....-..+.+|+.+..+++|+.+.....++-.+..--.+.+-. .....+||+|. T Consensus 1 kIGviv~~~~npf~~~~~~g~e~~a~~~G~~v~v~~~~~~~d~~~q~~~i~~--~i~~~vdgii~ 63 (275) T cd06320 1 KYGVVLKTLSNEFWRSLKEGYENEAKKLGVSVDIQAAPSEGDQQGQLSIAEN--MINKGYKGLLF 63 (275) T ss_pred CEEEEECCCCCHHHHHHHHHHHHHHHHCCCEEEEEECCCCCCHHHHHHHHHH--HHHCCCCEEEE T ss_conf 9899948998889999999999999974998999968997589999999999--99749987987 No 85 >PRK08104 consensus Probab=77.43 E-value=3.5 Score=22.24 Aligned_cols=104 Identities=20% Similarity=0.226 Sum_probs=70.3 Q ss_pred CEEEEEEECHHHHHHHHHHHHHHHHHHHCCCCEEEE--EHHHHHHHHHHHHHHHHHHHCCCCCCEEEEEEEEECCCCCHH Q ss_conf 717999803128999999999999999879955555--300144226999999863311378535665412000665246 Q gi|254780346|r 6 PHVLIIEARFYENLSAMLFEGCVNVLHSRAVQWSSI--VTPGVLEIPAAVSMVMNAKTRSVTYDGIIVLGVVMRGKTAHC 83 (149) Q Consensus 6 ~kI~IV~s~~~~~i~~~ll~ga~~~l~~~~~~~~~i--~VPGa~EiP~a~~~~~~~~~~~~~~D~vIaLG~VIkGeT~H~ 83 (149) +=|.|+..+ ..+-.. ...+.|.+.|+..-.| +.|+++|.- +.+.+ .-+|.+|-.|.|+.-|+-+. T Consensus 16 ~iipVir~~-~~~~a~----~la~al~~gGi~~iEiTlrt~~a~~~I---~~l~~-----~~p~~~vGaGTV~~~e~~~~ 82 (212) T PRK08104 16 PVVPVIVIN-KLEHAV----PLAKALVAGGVRVLEVTLRTPCALEAI---RAIAK-----EVPEAIVGAGTVLNPQQLAE 82 (212) T ss_pred CEEEEEECC-CHHHHH----HHHHHHHHCCCCEEEEECCCCHHHHHH---HHHHH-----HCCCCEEEEEECCCHHHHHH T ss_conf 868999779-999999----999999987998899968881499999---99998-----68985685420267999999 Q ss_pred HH-------HHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHH Q ss_conf 78-------9999999999999743997056542558899999950 Q gi|254780346|r 84 DV-------IAHAVTRGLVDLSINGSLPIGNGIVVVDSEQQAFDRV 122 (149) Q Consensus 84 e~-------I~~~v~~gl~~lsl~~~~PI~~gILt~~n~~QA~~R~ 122 (149) -. ||-.....+.+.+.++++|.+=|+.|+....||++.- T Consensus 83 ai~aGA~FiVSP~~~~~v~~~a~~~~i~~iPGv~TpsEi~~A~~~G 128 (212) T PRK08104 83 VTEAGAQFAISPGLTEELLKAATEGTIPLIPGISTVSELMLGMDYG 128 (212) T ss_pred HHHCCCCEEECCCCCHHHHHHHHHCCCCEECCCCCHHHHHHHHHCC T ss_conf 9985999998489999999999982997656769999999999879 No 86 >PRK07114 keto-hydroxyglutarate-aldolase/keto-deoxy-phosphogluconate aldolase; Provisional Probab=77.30 E-value=3.1 Score=22.52 Aligned_cols=93 Identities=13% Similarity=0.037 Sum_probs=66.8 Q ss_pred HHHHHHHHCCCCEEEE--EHHHHHHHHHHHHHHHHHHHCCCCCCEEEEEEEEECCCCCHHH-------HHHHHHHHHHHH Q ss_conf 9999999879955555--3001442269999998633113785356654120006652467-------899999999999 Q gi|254780346|r 26 GCVNVLHSRAVQWSSI--VTPGVLEIPAAVSMVMNAKTRSVTYDGIIVLGVVMRGKTAHCD-------VIAHAVTRGLVD 96 (149) Q Consensus 26 ga~~~l~~~~~~~~~i--~VPGa~EiP~a~~~~~~~~~~~~~~D~vIaLG~VIkGeT~H~e-------~I~~~v~~gl~~ 96 (149) ...+.|.+.|+..-.| +.|+++|.-..+.+... ...+|..|-.|.|+.-++-+-- .||-.....+.+ T Consensus 32 ~~a~aL~~gGi~~iEiTlrt~~a~~~i~~l~~~~~----~~~p~~~iGaGTVl~~~~~~~a~~aGA~FiVSP~~~~~v~~ 107 (223) T PRK07114 32 KVVKACYDGGVRAFEFTNRGDFAHEVFGELVKYAA----KECPEMILGVGSIVDAATAALYIQLGANFVVGPLFNEDIAK 107 (223) T ss_pred HHHHHHHHCCCCEEEEECCCCCHHHHHHHHHHHHH----HHCCCCEEEEECCCCHHHHHHHHHCCCCEEECCCCCHHHHH T ss_conf 99999998899889995889658999999999998----66898089655188999999999859989999999999999 Q ss_pred HHHHCCCCCEEEEECCCCHHHHHHHH Q ss_conf 99743997056542558899999950 Q gi|254780346|r 97 LSINGSLPIGNGIVVVDSEQQAFDRV 122 (149) Q Consensus 97 lsl~~~~PI~~gILt~~n~~QA~~R~ 122 (149) ...++++|.+-|+.|+....+|++.- T Consensus 108 ~~~~~~~~~iPGv~TptEi~~A~~~G 133 (223) T PRK07114 108 VCNRRKIPYSPGCGSVSEIGFAEELG 133 (223) T ss_pred HHHHCCCCCCCCCCCHHHHHHHHHCC T ss_conf 99983997537319999999999879 No 87 >pfam00465 Fe-ADH Iron-containing alcohol dehydrogenase. Probab=76.91 E-value=6.9 Score=20.39 Aligned_cols=61 Identities=20% Similarity=0.279 Sum_probs=39.1 Q ss_pred CEEEEEEECHHHHHHHHHHHHHHHHHHHCCCCEEEEE-H---HHHHHHHHHHHHHHHHHHCCCCCCEEEEEE Q ss_conf 7179998031289999999999999998799555553-0---014422699999986331137853566541 Q gi|254780346|r 6 PHVLIIEARFYENLSAMLFEGCVNVLHSRAVQWSSIV-T---PGVLEIPAAVSMVMNAKTRSVTYDGIIVLG 73 (149) Q Consensus 6 ~kI~IV~s~~~~~i~~~ll~ga~~~l~~~~~~~~~i~-V---PGa~EiP~a~~~~~~~~~~~~~~D~vIaLG 73 (149) +|++||.++.-. ...+++...+.|++.++++..+. + |-.-++--+++. .+..++|.||++| T Consensus 23 ~r~llVt~~~~~--~~g~~~~l~~~L~~~~~~~~~~~~v~~~p~~~~v~~~~~~-----~~~~~~D~IIaiG 87 (312) T pfam00465 23 ARALIVTDPSLK--KLGLLDRVLDSLEEAGIEVVVFDGVEPNPTLEEVDEAAAA-----AREEGADVIIAVG 87 (312) T ss_pred CEEEEEECCCHH--HCCHHHHHHHHHHHCCCEEEEECCCCCCCCHHHHHHHHHH-----HHHCCCCEEEECC T ss_conf 979999895856--6763999999999749949998582799999999999999-----9964998999808 No 88 >PRK10310 galactitol-specific PTS system component IIB; Provisional Probab=75.95 E-value=7.3 Score=20.23 Aligned_cols=84 Identities=13% Similarity=0.078 Sum_probs=53.3 Q ss_pred CCCEEEEEEECHHHHHHHHHHH-HHHHHHHHCCCCEEEEEHHHHHHHHHHHHHHHHHHHCCCCCCEEEEEEEEECCCCCH Q ss_conf 5871799980312899999999-999999987995555530014422699999986331137853566541200066524 Q gi|254780346|r 4 FIPHVLIIEARFYENLSAMLFE-GCVNVLHSRAVQWSSIVTPGVLEIPAAVSMVMNAKTRSVTYDGIIVLGVVMRGKTAH 82 (149) Q Consensus 4 ~~~kI~IV~s~~~~~i~~~ll~-ga~~~l~~~~~~~~~i~VPGa~EiP~a~~~~~~~~~~~~~~D~vIaLG~VIkGeT~H 82 (149) |++||++.+..==. |..+.. -..+.++++|++++...++ .-|+| ...+.+|.+|...-+ T Consensus 1 MkKkIlVACGsGIA--TSTvva~kv~~~~~e~gi~v~i~Q~~-i~ev~----------~~~~~~DlivtTt~~------- 60 (94) T PRK10310 1 MKRKIIVACGGAVA--TSTMAAEEIKELCQSHNIPVELIQCR-VNEIE----------TYMDGVHLICTTARV------- 60 (94) T ss_pred CCCEEEEECCCCHH--HHHHHHHHHHHHHHHCCCEEEEEEEE-HHHHH----------HCCCCCCEEEEECCC------- T ss_conf 99559998588375--99999999999999859806899974-78755----------416897789992253------- Q ss_pred HHHHHHHHHHHHHHHHHHC-CCCCEEEE--ECCCCHHHHHHHH Q ss_conf 6789999999999999743-99705654--2558899999950 Q gi|254780346|r 83 CDVIAHAVTRGLVDLSING-SLPIGNGI--VVVDSEQQAFDRV 122 (149) Q Consensus 83 ~e~I~~~v~~gl~~lsl~~-~~PI~~gI--Lt~~n~~QA~~R~ 122 (149) .-++ ++|+++|+ ||==++++.++.. T Consensus 61 ---------------~~~~g~iPvi~g~~fLTGiG~d~~~~~I 88 (94) T PRK10310 61 ---------------DRSFGDIPLVHGMPFVSGVGIEALQNKI 88 (94) T ss_pred ---------------CCCCCCCCEEECCCCCCCCCHHHHHHHH T ss_conf ---------------7765888779634200037889999999 No 89 >cd06302 PBP1_LsrB_Quorum_Sensing Periplasmic binding domain of autoinducer-2 (AI-2) receptor LsrB from Salmonella typhimurium and its close homologs. Periplasmic binding domain of autoinducer-2 (AI-2) receptor LsrB from Salmonella typhimurium and its close homologs from other bacteria. The members of this group are homologous to a family of periplasmic pentose/hexose sugar-binding proteins that function as the primary receptors for chemotaxis and transporters of many sugar based solutes in bacteria and archaea and that are a member of the type I periplasmic binding protein superfamily. LsrB binds a chemically distinct form of the AI-2 signal that lacks boron, in contrast to the Vibrio harveyi AI-2 signaling molecule that has an unusual furanosyl borate diester. Hence, many bacteria coordinate their gene expression according to the local density of their population by producing species specific AI-2. This process of quorum sensing allows LsrB to function as a periplasmic AI-2 binding p Probab=75.51 E-value=7.5 Score=20.15 Aligned_cols=123 Identities=14% Similarity=0.091 Sum_probs=62.3 Q ss_pred CEEEEEEECHHHHHHHHHHHHHHHHHHHCCCC-EEEE-EHHHHHHHHHHHHHHHHHHHCCCCCCEEEEEEEEECCCCCHH Q ss_conf 71799980312899999999999999987995-5555-300144226999999863311378535665412000665246 Q gi|254780346|r 6 PHVLIIEARFYENLSAMLFEGCVNVLHSRAVQ-WSSI-VTPGVLEIPAAVSMVMNAKTRSVTYDGIIVLGVVMRGKTAHC 83 (149) Q Consensus 6 ~kI~IV~s~~~~~i~~~ll~ga~~~l~~~~~~-~~~i-~VPGa~EiP~a~~~~~~~~~~~~~~D~vIaLG~VIkGeT~H~ 83 (149) .+|+++...-...-...-.+|+.+.+++.+.+ .+++ ..++-+...-+.+..-.-.....+.|++++. . T Consensus 124 g~v~i~~g~~~~~~~~~R~~g~~~~l~~~~~~~~~vv~~~~~~~~~~~a~~~~~~~L~~~Pdi~~I~~~----------n 193 (298) T cd06302 124 GEYAIFVGSLTATNQNAWIDAAKAYQKEKYYPMLELVDRQYGDDDADKSYQTAQELLKAYPDLKGIIGP----------T 193 (298) T ss_pred CCEEEEECCCCCHHHHHHHHHHHHHHHHCCCCCEEEEEEECCCCCHHHHHHHHHHHHHHCCCCCEEEEC----------C T ss_conf 958999858898679999999999986348998799986137874899999999999759991299978----------9 Q ss_pred HHHHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHHCCCC---------CCCHHHHHHHHHHHHH Q ss_conf 7899999999999997439970565425588999999506565---------7456999999999999 Q gi|254780346|r 84 DVIAHAVTRGLVDLSINGSLPIGNGIVVVDSEQQAFDRVSPSH---------LDRGGCAARSALAMIE 142 (149) Q Consensus 84 e~I~~~v~~gl~~lsl~~~~PI~~gILt~~n~~QA~~R~~~~~---------~nkG~eaa~Aal~mi~ 142 (149) +..+..+.++|.+..++..+. +.|. +...++.+...... -.-|+.++++++++++ T Consensus 194 d~~a~Ga~~Al~~aG~~~~V~-vvG~---D~~~~~~~~I~~G~i~atv~Q~P~~~G~~av~~a~~~~~ 257 (298) T cd06302 194 SVGIPGAARAVEEAGLKGKVA-VTGL---GLPNQMAPYVKSGAVKEFALWNPADLGYAAVYVAKALLE 257 (298) T ss_pred CHHHHHHHHHHHHCCCCCCEE-EEEE---CCCHHHHHHHHCCCCEEEEECCHHHHHHHHHHHHHHHHC T ss_conf 816999999999679999859-9996---887999999985982699984999999999999999977 No 90 >PRK07580 Mg-protoporphyrin IX methyl transferase; Validated Probab=73.76 E-value=4.3 Score=21.63 Aligned_cols=74 Identities=16% Similarity=0.147 Sum_probs=51.6 Q ss_pred HHHHHHHHHHHHHHHHHCCCCEEEEEHHHHHHHHHHHHHHHHHHHCCCCCCEEEEEEEEECCCCCHHHHHHHHHHHHHHH Q ss_conf 89999999999999998799555553001442269999998633113785356654120006652467899999999999 Q gi|254780346|r 17 ENLSAMLFEGCVNVLHSRAVQWSSIVTPGVLEIPAAVSMVMNAKTRSVTYDGIIVLGVVMRGKTAHCDVIAHAVTRGLVD 96 (149) Q Consensus 17 ~~i~~~ll~ga~~~l~~~~~~~~~i~VPGa~EiP~a~~~~~~~~~~~~~~D~vIaLG~VIkGeT~H~e~I~~~v~~gl~~ 96 (149) -||+..|++-|.+...+.|....+-+..|-+|-. .+.||.|+|+.++| ||.- ......|.. T Consensus 91 vDiS~~mi~~A~~Ra~~~g~~~~v~F~~gDle~~------------~G~FD~Vv~mdvLi-----HYp~--~d~~~~l~~ 151 (230) T PRK07580 91 SDISPQMVEEARERAPEAGLDGNITFEVGDLESL------------LGSFDTVVCLDVLI-----HYPQ--EDAERMLAH 151 (230) T ss_pred EECCHHHHHHHHHHHHHHCCCCCCEEEECCCCCC------------CCCCCCHHHCCCEE-----ECCH--HHHHHHHHH T ss_conf 8389999999997558627876753896676545------------79866023337155-----4578--899999999 Q ss_pred HHHHCCCCCEEEE Q ss_conf 9974399705654 Q gi|254780346|r 97 LSINGSLPIGNGI 109 (149) Q Consensus 97 lsl~~~~PI~~gI 109 (149) ++-..+-.++|-. T Consensus 152 la~~~~~~~ifTf 164 (230) T PRK07580 152 LASLTRGSLIFTF 164 (230) T ss_pred HHHCCCCEEEEEE T ss_conf 9725588599996 No 91 >cd06323 PBP1_ribose_binding Periplasmic sugar-binding domain of the thermophilic Thermoanaerobacter tengcongensis ribose binding protein (ttRBP) and its mesophilic homologs. Periplasmic sugar-binding domain of the thermophilic Thermoanaerobacter tengcongensis ribose binding protein (ttRBP) and its mesophilic homologs. Members of this group are belonging to the type I periplasmic binding protein superfamily, whose members are involved in chemotaxis, ATP-binding cassette transport, and intercellular communication in central nervous system. The thermophilic and mesophilic ribose-binding proteins are structurally very similar, but differ substantially in thermal stability. Probab=73.08 E-value=8.6 Score=19.78 Aligned_cols=28 Identities=11% Similarity=-0.015 Sum_probs=12.2 Q ss_pred EEEEEEECHHHHHHHHHHHHHHHHHHHC Q ss_conf 1799980312899999999999999987 Q gi|254780346|r 7 HVLIIEARFYENLSAMLFEGCVNVLHSR 34 (149) Q Consensus 7 kI~IV~s~~~~~i~~~ll~ga~~~l~~~ 34 (149) ||+++.+.....-...-.+|+.+.++++ T Consensus 123 ~i~~~~g~~~~~~~~~R~~gf~~a~~~~ 150 (268) T cd06323 123 KVVELQGIPGASAARERGKGFHEVVDKY 150 (268) T ss_pred EEEEECCCCCCHHHHHHHHHHHHHHHHC T ss_conf 6999638999858999999999999877 No 92 >PRK07053 glutamine amidotransferase; Provisional Probab=72.92 E-value=8.7 Score=19.76 Aligned_cols=101 Identities=18% Similarity=0.149 Sum_probs=63.8 Q ss_pred CCCEEEEEEECHHHHHHHHHHHHHHHHHHHCCCCEEEEEHHHHHH-HHHHHHHHHHHHHCCCCCCEEEEEEEEECC-CCC Q ss_conf 587179998031289999999999999998799555553001442-269999998633113785356654120006-652 Q gi|254780346|r 4 FIPHVLIIEARFYENLSAMLFEGCVNVLHSRAVQWSSIVTPGVLE-IPAAVSMVMNAKTRSVTYDGIIVLGVVMRG-KTA 81 (149) Q Consensus 4 ~~~kI~IV~s~~~~~i~~~ll~ga~~~l~~~~~~~~~i~VPGa~E-iP~a~~~~~~~~~~~~~~D~vIaLG~VIkG-eT~ 81 (149) ||+||+|+.-.-.+.- .-..+.|.+.|+.++.+.+. .-+ +| .....||++|.+|-=--- |++ T Consensus 1 mmk~ilvlqH~~~E~p-----G~i~~~l~~~g~~~~~~~~~-~~~~~p----------~~~~~~d~livlGGpms~~d~~ 64 (235) T PRK07053 1 MMKTAVAIRHVAFEDL-----GSFEQVLGERGYRVRYVDVG-VDDLEV----------LDALEPDLLVVLGGPIGVYDDA 64 (235) T ss_pred CCCEEEEEECCCCCCC-----HHHHHHHHHCCCEEEEEECC-CCCCCC----------CCCCCCCEEEEECCCCCCCCCC T ss_conf 9953999968998898-----69999999789959999678-898899----------9966679999938998988776 Q ss_pred HHHHHHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHHCCCC Q ss_conf 467899999999999997439970565425588999999506565 Q gi|254780346|r 82 HCDVIAHAVTRGLVDLSINGSLPIGNGIVVVDSEQQAFDRVSPSH 126 (149) Q Consensus 82 H~e~I~~~v~~gl~~lsl~~~~PI~~gILt~~n~~QA~~R~~~~~ 126 (149) -|-++.+ -..+++-.++.++|+.=-=|. .|.+.++-+.. T Consensus 65 ~~Pwl~~--e~~lIr~a~~~~~PvLGIClG----~QLlA~AlGG~ 103 (235) T PRK07053 65 LYPFLAP--EIALLRQRLAAGLPTLGICLG----AQLIARALGAR 103 (235) T ss_pred CCCCHHH--HHHHHHHHHHCCCCEEEECHH----HHHHHHHHCCE T ss_conf 6855899--999999999869988998473----89999970977 No 93 >PRK13411 molecular chaperone DnaK; Provisional Probab=72.61 E-value=2.8 Score=22.76 Aligned_cols=89 Identities=21% Similarity=0.259 Sum_probs=59.1 Q ss_pred HHHHHHHHHHHHHHHHHHCCCCEE----EEEHHHHHHHHHHHHHHHHHHH-----CCCCCCEEEEEEEEECCCCCHHHHH Q ss_conf 289999999999999998799555----5530014422699999986331-----1378535665412000665246789 Q gi|254780346|r 16 YENLSAMLFEGCVNVLHSRAVQWS----SIVTPGVLEIPAAVSMVMNAKT-----RSVTYDGIIVLGVVMRGKTAHCDVI 86 (149) Q Consensus 16 ~~~i~~~ll~ga~~~l~~~~~~~~----~i~VPGa~EiP~a~~~~~~~~~-----~~~~~D~vIaLG~VIkGeT~H~e~I 86 (149) ..++.++.++-+.+.|++.+...+ ++-|=|+-.+|..-+.+-+... .+-++|-.||+|+-|+|..-- T Consensus 303 ~~~L~~rt~~pv~~aL~dA~l~~~dId~ViLVGGSTRIP~Vq~~v~~~F~gk~~~~~iNPDEaVA~GAAiqa~iL~---- 378 (655) T PRK13411 303 AKDLVEATIEPVQQALKDAGLTPEDIDRIILVGGSTRIPAVQEAIQQFFGGKQPDRSVNPDEAVALGAAIQAGVLG---- 378 (655) T ss_pred HHHHHHHHHHHHHHHHHHHCCCHHHEEEEEEECCCCCCHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHC---- T ss_conf 9999999998899999980998311789999888146579999999982899888897821689886999888753---- Q ss_pred HHHHHHHHHHHHHHCCCCCEEEEECCC Q ss_conf 999999999999743997056542558 Q gi|254780346|r 87 AHAVTRGLVDLSINGSLPIGNGIVVVD 113 (149) Q Consensus 87 ~~~v~~gl~~lsl~~~~PI~~gILt~~ 113 (149) .. ..++.+---+|...||=|.. T Consensus 379 -g~----~~d~~llDV~PlsLGiet~g 400 (655) T PRK13411 379 -GE----VKDLLLLDVTPLSLGIETLG 400 (655) T ss_pred -CC----CCCEEEEEECCCEEEEEECC T ss_conf -77----55438998427236889769 No 94 >PRK06857 consensus Probab=71.41 E-value=7.1 Score=20.29 Aligned_cols=88 Identities=15% Similarity=0.152 Sum_probs=64.9 Q ss_pred HHHHHHHCCCCEEE--EEHHHHHHHHHHHHHHHHHHHCCCCCCEEEEEEEEECCCCCHHHH-------HHHHHHHHHHHH Q ss_conf 99999987995555--530014422699999986331137853566541200066524678-------999999999999 Q gi|254780346|r 27 CVNVLHSRAVQWSS--IVTPGVLEIPAAVSMVMNAKTRSVTYDGIIVLGVVMRGKTAHCDV-------IAHAVTRGLVDL 97 (149) Q Consensus 27 a~~~l~~~~~~~~~--i~VPGa~EiP~a~~~~~~~~~~~~~~D~vIaLG~VIkGeT~H~e~-------I~~~v~~gl~~l 97 (149) ..+.|.+.|+..-. .+.|+++|.- +.+.+ ..+|.+|-.|.|...|+-+.=. ||-.....+.+. T Consensus 29 ~~~al~~gGi~~iEiTlrt~~a~~~I---~~l~~-----~~p~~~vGaGTV~~~e~~~~a~~aGA~FiVSP~~~~~v~~~ 100 (209) T PRK06857 29 LAKVLAENGLPVAEITFRSAAAAEAI---RLLRE-----AYPDMLIGAGTVLTPEQVDAAKEAGADFIVSPGFNPNTVKY 100 (209) T ss_pred HHHHHHHCCCCEEEEECCCCCHHHHH---HHHHH-----HCCCCEEEEEECCCHHHHHHHHHCCCCEEECCCCCHHHHHH T ss_conf 99999987998899958993299999---99997-----58994899993767999999998399999908999999999 Q ss_pred HHHCCCCCEEEEECCCCHHHHHHHH Q ss_conf 9743997056542558899999950 Q gi|254780346|r 98 SINGSLPIGNGIVVVDSEQQAFDRV 122 (149) Q Consensus 98 sl~~~~PI~~gILt~~n~~QA~~R~ 122 (149) +.++++|.+=|+.|+....+|++.- T Consensus 101 a~~~~i~~iPGv~TpsEi~~A~~~G 125 (209) T PRK06857 101 CQQLNIPIVPGVNNPSLVEQALEMG 125 (209) T ss_pred HHHCCCCEECCCCCHHHHHHHHHCC T ss_conf 9974996547879999999999879 No 95 >PRK09492 treR trehalose repressor; Provisional Probab=70.61 E-value=9.8 Score=19.43 Aligned_cols=65 Identities=15% Similarity=0.142 Sum_probs=33.3 Q ss_pred CCEEEEEEECHHHHHHHHHHHHHHHHHHHCCCCEEEEEHHHHHHHHHHHHHHHHHHHCCCCCCEEEEEE Q ss_conf 871799980312899999999999999987995555530014422699999986331137853566541 Q gi|254780346|r 5 IPHVLIIEARFYENLSAMLFEGCVNVLHSRAVQWSSIVTPGVLEIPAAVSMVMNAKTRSVTYDGIIVLG 73 (149) Q Consensus 5 ~~kI~IV~s~~~~~i~~~ll~ga~~~l~~~~~~~~~i~VPGa~EiP~a~~~~~~~~~~~~~~D~vIaLG 73 (149) .+.|++|..++.......++.+..+.+.++|+..-.....+.-+. .+..++. -...++||+|..| T Consensus 62 t~~Ig~i~~~~~~~~~~~~~~~i~~~~~~~gy~~~i~~~~~~~~~---~~~~~~~-l~~~~vdGiIl~~ 126 (315) T PRK09492 62 DKVVGIIVSRLDSPSENLAVQTMLPAFYQQGYDPIIMESQFSPQL---VNEHLGV-LRRRNVDGVILFG 126 (315) T ss_pred CCEEEEECCCCCCHHHHHHHHHHHHHHHHCCCCEEEEECCCCHHH---HHHHHHH-HHHCCCCEEEEEC T ss_conf 864666226778836789999999999974981899946899799---9999999-9967989899968 No 96 >PRK07455 keto-hydroxyglutarate-aldolase/keto-deoxy-phosphogluconate aldolase; Provisional Probab=70.59 E-value=8.9 Score=19.70 Aligned_cols=102 Identities=16% Similarity=0.158 Sum_probs=69.3 Q ss_pred EEEEEEECHHHHHHHHHHHHHHHHHHHCCCCEEEE--EHHHHHHHHHHHHHHHHHHHCCCCCCEEEEEEEEECCCCCHHH Q ss_conf 17999803128999999999999999879955555--3001442269999998633113785356654120006652467 Q gi|254780346|r 7 HVLIIEARFYENLSAMLFEGCVNVLHSRAVQWSSI--VTPGVLEIPAAVSMVMNAKTRSVTYDGIIVLGVVMRGKTAHCD 84 (149) Q Consensus 7 kI~IV~s~~~~~i~~~ll~ga~~~l~~~~~~~~~i--~VPGa~EiP~a~~~~~~~~~~~~~~D~vIaLG~VIkGeT~H~e 84 (149) =|.|+...=.+ -. ....+.|.+.|+..-.| +.|+++|.- +.+.+ .-.|..|-.|.|..-|+-+.- T Consensus 15 vi~Vlr~~~~~-~a----~~~~~al~~gGi~~iEiTl~t~~a~~~I---~~l~~-----~~p~~~iGaGTV~~~e~~~~a 81 (210) T PRK07455 15 AIAVIRAPDLE-LG----LQMAEAVAAGGMRLIEITWNSDQPAELI---SQLRE-----KLPECIIGTGTLLTLEDLEEA 81 (210) T ss_pred EEEEEECCCHH-HH----HHHHHHHHHCCCCEEEEECCCCCHHHHH---HHHHH-----HCCCCEEEEEECCCHHHHHHH T ss_conf 79999759999-99----9999999987998899968998899999---99998-----789968988818789999999 Q ss_pred -------HHHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHH Q ss_conf -------8999999999999974399705654255889999995 Q gi|254780346|r 85 -------VIAHAVTRGLVDLSINGSLPIGNGIVVVDSEQQAFDR 121 (149) Q Consensus 85 -------~I~~~v~~gl~~lsl~~~~PI~~gILt~~n~~QA~~R 121 (149) .||-.....+.+.+.++++|.+-|+.|+....+|++. T Consensus 82 ~~aGA~FiVSP~~~~~vi~~a~~~~i~~iPGv~TpsEi~~A~~~ 125 (210) T PRK07455 82 IAAGAQFCFTPHVDLELIQAAVAADIPIIPGALTPTEIVTAWQA 125 (210) T ss_pred HHCCCCEEECCCCCHHHHHHHHHCCCCEECCCCCHHHHHHHHHC T ss_conf 98699999868888999999998299765886999999999986 No 97 >cd06309 PBP1_YtfQ_like Periplasmic binding domain of ABC-type YtfQ-like transport systems. Periplasmic binding domain of ABC-type YtfQ-like transport systems. The YtfQ protein from Escherichia coli is up-regulated under glucose-limited conditions and shares homology with a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily. Members of this group are predicted to be involved in the transport of sugar-containing molecules across cellular and organellar membranes; however their ligand specificity is not determined experimentally. Probab=70.43 E-value=9.9 Score=19.41 Aligned_cols=125 Identities=10% Similarity=0.077 Sum_probs=73.7 Q ss_pred CCEEEEEEECHHHHHHHHHHHHHHHHHHHCCCCEEEE-EHHHHHHHHHHHHHHHHHHHCC-CCCCEEEEEEEEECCCCCH Q ss_conf 8717999803128999999999999999879955555-3001442269999998633113-7853566541200066524 Q gi|254780346|r 5 IPHVLIIEARFYENLSAMLFEGCVNVLHSRAVQWSSI-VTPGVLEIPAAVSMVMNAKTRS-VTYDGIIVLGVVMRGKTAH 82 (149) Q Consensus 5 ~~kI~IV~s~~~~~i~~~ll~ga~~~l~~~~~~~~~i-~VPGa~EiP~a~~~~~~~~~~~-~~~D~vIaLG~VIkGeT~H 82 (149) ..+|+++........+..-.+|+.+.|.++. ..+.+ ..+|-|.-..+.+.+-...... .++|+++|. T Consensus 124 ~~~i~~i~g~~~~~~~~~R~~Gf~~~l~~~~-~~~iv~~~~~~~~~~~~~~~~~~~L~~~p~~i~ai~~~---------- 192 (273) T cd06309 124 KGNIVELQGTVGSSVAIDRKKGFAEVIKKYP-NMKIVASQTGDFTRAKGKEVMEALLKAHGDDIDAVYAH---------- 192 (273) T ss_pred CCEEEEEECCCCCHHHHHHHHHHHHHHHHCC-CCEEEEEECCCCCHHHHHHHHHHHHHHCCCCCCEEEEC---------- T ss_conf 8079998289898599999999999998789-98676541234688999999999997278888889867---------- Q ss_pred HHHHHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHHCCCC--------CCCHHHHHHHHHHHHH Q ss_conf 67899999999999997439970565425588999999506565--------7456999999999999 Q gi|254780346|r 83 CDVIAHAVTRGLVDLSINGSLPIGNGIVVVDSEQQAFDRVSPSH--------LDRGGCAARSALAMIE 142 (149) Q Consensus 83 ~e~I~~~v~~gl~~lsl~~~~PI~~gILt~~n~~QA~~R~~~~~--------~nkG~eaa~Aal~mi~ 142 (149) .|.++-.+.+++.+..++ +|=-..|.+.++..+++++..... -.-|+.|+++++++++ T Consensus 193 nd~~a~Ga~~al~~~G~~--~~~di~ivg~D~~~~~~~~i~~g~l~~~~~~~p~~G~~Av~~l~~~l~ 258 (273) T cd06309 193 NDEMALGAIQAIKAAGKK--PGKDIKIVSIDGTKDAFQAMADGKLNATVECNPLFGPLAFDTLEKYLA 258 (273) T ss_pred CCHHHHHHHHHHHHCCCC--CCCCEEEEEECCCHHHHHHHHCCCCEEEEECCHHHHHHHHHHHHHHHC T ss_conf 857999999999983999--999869999899999999987699719997839999999999999977 No 98 >PRK06552 keto-hydroxyglutarate-aldolase/keto-deoxy-phosphogluconate aldolase; Provisional Probab=70.18 E-value=9 Score=19.68 Aligned_cols=92 Identities=13% Similarity=0.119 Sum_probs=66.2 Q ss_pred HHHHHHHHCCCCEEEE--EHHHHHHHHHHHHHHHHHHHCCCCCCEEEEEEEEECCCCCHHH-------HHHHHHHHHHHH Q ss_conf 9999999879955555--3001442269999998633113785356654120006652467-------899999999999 Q gi|254780346|r 26 GCVNVLHSRAVQWSSI--VTPGVLEIPAAVSMVMNAKTRSVTYDGIIVLGVVMRGKTAHCD-------VIAHAVTRGLVD 96 (149) Q Consensus 26 ga~~~l~~~~~~~~~i--~VPGa~EiP~a~~~~~~~~~~~~~~D~vIaLG~VIkGeT~H~e-------~I~~~v~~gl~~ 96 (149) ...+.|.+.|+..-.| +.|+++|.- +.+.++ ....+|..|-.|.|+.-|+-+.= .||-.....+.+ T Consensus 29 ~~~~al~~gGi~~iEITl~tp~a~~~i---~~l~~~--~~~~p~~~iGaGTV~~~e~~~~a~~aGA~FiVSP~~~~~v~~ 103 (209) T PRK06552 29 KISLAVIKGGIKAIEVTYTNPFASEVI---KELVER--YKDDPEVLIGAGTVLDAVTARQAILAGAQFIVSPSFNRETAK 103 (209) T ss_pred HHHHHHHHCCCCEEEEECCCCCHHHHH---HHHHHH--HCCCCCEEEEEECCCCHHHHHHHHHCCCCEEECCCCCHHHHH T ss_conf 999999987998899967897599999---999998--177998189887274899999999859988976999899999 Q ss_pred HHHHCCCCCEEEEECCCCHHHHHHHH Q ss_conf 99743997056542558899999950 Q gi|254780346|r 97 LSINGSLPIGNGIVVVDSEQQAFDRV 122 (149) Q Consensus 97 lsl~~~~PI~~gILt~~n~~QA~~R~ 122 (149) .+.++++|.+-|+.|+....+|++.- T Consensus 104 ~a~~~~i~~iPG~~TpsEi~~A~~~G 129 (209) T PRK06552 104 ICNRYQIPYLPGCMTVTEIVTALEAG 129 (209) T ss_pred HHHHCCCCEECCCCCHHHHHHHHHCC T ss_conf 99985996417979999999999869 No 99 >cd06319 PBP1_ABC_sugar_binding_like_10 Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems. Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily, which consists of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis. Probab=70.11 E-value=10 Score=19.37 Aligned_cols=32 Identities=6% Similarity=0.002 Sum_probs=15.8 Q ss_pred EEEEEEECHHHHHHHHHHHHHHHHHHHCCCCE Q ss_conf 17999803128999999999999999879955 Q gi|254780346|r 7 HVLIIEARFYENLSAMLFEGCVNVLHSRAVQW 38 (149) Q Consensus 7 kI~IV~s~~~~~i~~~ll~ga~~~l~~~~~~~ 38 (149) ||++|..+.....-..+.+|+.+.+++.|++. T Consensus 1 kIg~vv~~~~npF~~~~~~G~~~~a~~~G~~~ 32 (277) T cd06319 1 QIAYIVSDLRIPFWQIMGRGVKSKAKALGYDA 32 (277) T ss_pred CEEEEECCCCCHHHHHHHHHHHHHHHHCCCEE T ss_conf 98999189998699999999999999729989 No 100 >COG0655 WrbA Multimeric flavodoxin WrbA [General function prediction only] Probab=70.07 E-value=8.4 Score=19.83 Aligned_cols=40 Identities=18% Similarity=0.098 Sum_probs=33.1 Q ss_pred EEEEEEECHH-HHHHHHHHHHHHHHHHHCCCCEEEEEHHHH Q ss_conf 1799980312-899999999999999987995555530014 Q gi|254780346|r 7 HVLIIEARFY-ENLSAMLFEGCVNVLHSRAVQWSSIVTPGV 46 (149) Q Consensus 7 kI~IV~s~~~-~~i~~~ll~ga~~~l~~~~~~~~~i~VPGa 46 (149) |+..|...+| ..-+..|++.+.+.+++.|++.+.+.+|+- T Consensus 2 ki~~I~gs~r~~G~t~~l~~~~~~g~~~~G~E~~~i~v~~~ 42 (207) T COG0655 2 KILGINGSPRSNGNTAKLAEAVLEGAEEAGAEVEIIRLPEK 42 (207) T ss_pred EEEEEEEECCCCCHHHHHHHHHHHHHHHCCCEEEEEEECCC T ss_conf 07899982699874999999999999864985899984788 No 101 >PRK13410 molecular chaperone DnaK; Provisional Probab=68.96 E-value=5.7 Score=20.91 Aligned_cols=89 Identities=13% Similarity=0.244 Sum_probs=57.2 Q ss_pred HHHHHHHHHHHHHHHHHHCCCCEE----EEEHHHHHHHHHHHHHHHHHHH----CCCCCCEEEEEEEEECCCCCHHHHHH Q ss_conf 289999999999999998799555----5530014422699999986331----13785356654120006652467899 Q gi|254780346|r 16 YENLSAMLFEGCVNVLHSRAVQWS----SIVTPGVLEIPAAVSMVMNAKT----RSVTYDGIIVLGVVMRGKTAHCDVIA 87 (149) Q Consensus 16 ~~~i~~~ll~ga~~~l~~~~~~~~----~i~VPGa~EiP~a~~~~~~~~~----~~~~~D~vIaLG~VIkGeT~H~e~I~ 87 (149) ..++.++.++-+.+.|.++++..+ ++-|=|+--+|..-+.+-+... .+-++|-+||+||-|++....-+ T Consensus 304 ~~~L~~Rt~~pv~~aL~dAgl~~~dId~VILVGGSTRIP~Vq~~V~e~FGkep~~~iNPDEaVA~GAAiQA~iLsg~--- 380 (719) T PRK13410 304 CGDLVSRLRRPVKRALKDAGLSPVQIDEVVLVGGSTRMPMVKQLVRSLIDREPNQNVNPDEVVAVGAAIQAGILAGE--- 380 (719) T ss_pred HHHHHHHHHHHHHHHHHHHCCCHHHEEEEEEECCCCCCHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHCCC--- T ss_conf 99999999999999999838994141399997882554889999999849997888997177503188864310477--- Q ss_pred HHHHHHHHHHHHHCCCCCEEEEECCC Q ss_conf 99999999999743997056542558 Q gi|254780346|r 88 HAVTRGLVDLSINGSLPIGNGIVVVD 113 (149) Q Consensus 88 ~~v~~gl~~lsl~~~~PI~~gILt~~ 113 (149) +.++-|---+|...||=|.. T Consensus 381 ------~~d~lllDVtPlSLGiet~g 400 (719) T PRK13410 381 ------VKDILLLDVTPLSLGLETIG 400 (719) T ss_pred ------CCCEEEEEEECCCEEEEECC T ss_conf ------56538897315635898618 No 102 >PRK08904 consensus Probab=68.56 E-value=9.9 Score=19.41 Aligned_cols=88 Identities=16% Similarity=0.188 Sum_probs=64.8 Q ss_pred HHHHHHHCCCCEEE--EEHHHHHHHHHHHHHHHHHHHCCCCCCEEEEEEEEECCCCCHHH-------HHHHHHHHHHHHH Q ss_conf 99999987995555--53001442269999998633113785356654120006652467-------8999999999999 Q gi|254780346|r 27 CVNVLHSRAVQWSS--IVTPGVLEIPAAVSMVMNAKTRSVTYDGIIVLGVVMRGKTAHCD-------VIAHAVTRGLVDL 97 (149) Q Consensus 27 a~~~l~~~~~~~~~--i~VPGa~EiP~a~~~~~~~~~~~~~~D~vIaLG~VIkGeT~H~e-------~I~~~v~~gl~~l 97 (149) ..+.|.+.|+..-. .+.|+++|.- +.+.+ .-+|.+|-.|.|...++-+.= .||-.....+.+. T Consensus 27 ~a~al~~~Gi~~iEiTlrtp~a~~~i---~~l~~-----~~p~~~vGaGTVl~~e~~~~a~~aGA~FiVSP~~~~~v~~~ 98 (207) T PRK08904 27 LSRALVEGGIPTLEITLRTPVGLDAI---RLIAK-----EVPNAIVGAGTVTNPEQLKAVEDAGAVFAISPGLHESLAKA 98 (207) T ss_pred HHHHHHHCCCCEEEEECCCCHHHHHH---HHHHH-----HCCCCEEEEEECCCHHHHHHHHHCCCCEEECCCCCHHHHHH T ss_conf 99999987998899957991399999---99998-----68987685531368999999998499999848998999999 Q ss_pred HHHCCCCCEEEEECCCCHHHHHHHH Q ss_conf 9743997056542558899999950 Q gi|254780346|r 98 SINGSLPIGNGIVVVDSEQQAFDRV 122 (149) Q Consensus 98 sl~~~~PI~~gILt~~n~~QA~~R~ 122 (149) ..++++|.+=|+.|+....+|++.- T Consensus 99 a~~~~i~~iPGv~TpsEi~~A~~~G 123 (207) T PRK08904 99 GHNSGIPLIPGVATPGEIQLALEHG 123 (207) T ss_pred HHHCCCCEECCCCCHHHHHHHHHCC T ss_conf 9983997657869999999999879 No 103 >PRK06015 keto-hydroxyglutarate-aldolase/keto-deoxy-phosphogluconate aldolase; Provisional Probab=67.75 E-value=10 Score=19.36 Aligned_cols=89 Identities=15% Similarity=0.184 Sum_probs=64.1 Q ss_pred HHHHHHHHCCCCEEEE--EHHHHHHHHHHHHHHHHHHHCCCCCCEEEEEEEEECCCCCHHH-------HHHHHHHHHHHH Q ss_conf 9999999879955555--3001442269999998633113785356654120006652467-------899999999999 Q gi|254780346|r 26 GCVNVLHSRAVQWSSI--VTPGVLEIPAAVSMVMNAKTRSVTYDGIIVLGVVMRGKTAHCD-------VIAHAVTRGLVD 96 (149) Q Consensus 26 ga~~~l~~~~~~~~~i--~VPGa~EiP~a~~~~~~~~~~~~~~D~vIaLG~VIkGeT~H~e-------~I~~~v~~gl~~ 96 (149) ...+.|.+.|+..-.| +.|+++|.- +.+.+ .-+|.+|-.|.|...|+-+.= .||-.....+.+ T Consensus 31 ~~~~al~~gGi~~iEITlrt~~a~~~I---~~l~~-----~~p~~~vGaGTVl~~e~~~~a~~aGA~FiVSP~~~~~v~~ 102 (212) T PRK06015 31 PLARALARGGLPAIEITLRTPAALDAI---RAVAA-----EVEEAIVGAGTILNAKQFEDAAKAGSRFIVSPGTTQELLA 102 (212) T ss_pred HHHHHHHHCCCCEEEEECCCCCHHHHH---HHHHH-----HCCCCEEEEEECCCHHHHHHHHHCCCCEEECCCCCHHHHH T ss_conf 999999987998899968995199999---99998-----6999679542115699999999849989985899999999 Q ss_pred HHHHCCCCCEEEEECCCCHHHHHHHH Q ss_conf 99743997056542558899999950 Q gi|254780346|r 97 LSINGSLPIGNGIVVVDSEQQAFDRV 122 (149) Q Consensus 97 lsl~~~~PI~~gILt~~n~~QA~~R~ 122 (149) .+.+.++|.+=|+.|+....+|++.- T Consensus 103 ~a~~~~i~~iPGv~TpsEi~~A~~~G 128 (212) T PRK06015 103 AANDSDVPLLPGAITPSEVMALREEG 128 (212) T ss_pred HHHHCCCCEECCCCCHHHHHHHHHCC T ss_conf 99983997737869999999999879 No 104 >PRK00290 dnaK molecular chaperone DnaK; Provisional Probab=65.93 E-value=4.4 Score=21.61 Aligned_cols=89 Identities=21% Similarity=0.340 Sum_probs=55.5 Q ss_pred HHHHHHHHHHHHHHHHHHCCCCEE----EEEHHHHHHHHHHHHHHHHHHH----CCCCCCEEEEEEEEECCCCCHHHHHH Q ss_conf 289999999999999998799555----5530014422699999986331----13785356654120006652467899 Q gi|254780346|r 16 YENLSAMLFEGCVNVLHSRAVQWS----SIVTPGVLEIPAAVSMVMNAKT----RSVTYDGIIVLGVVMRGKTAHCDVIA 87 (149) Q Consensus 16 ~~~i~~~ll~ga~~~l~~~~~~~~----~i~VPGa~EiP~a~~~~~~~~~----~~~~~D~vIaLG~VIkGeT~H~e~I~ 87 (149) ..++.++.+.-+.+.|.+.+...+ ++-|=|+--+|..-+.+-+... .+-++|-.||+|+-|+|.---- T Consensus 304 ~~~l~~r~~~~v~~aL~~A~l~~~dId~ViLVGGsTRiP~Vq~~v~~~Fgk~~~~~inPDeaVA~GAAiqa~iLsg---- 379 (631) T PRK00290 304 TEDLVERTIEPCRQALKDAGLSVSDIDEVILVGGSTRMPAVQELVKEFFGKEPNKGVNPDEVVAVGAAIQGGVLAG---- 379 (631) T ss_pred HHHHHHHHHHHHHHHHHHHCCCHHHEEEEEEECCCCCCHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHCC---- T ss_conf 9999999999999999980898222159999178245679999999996889777969126899879999988638---- Q ss_pred HHHHHHHHHHHHHCCCCCEEEEECCC Q ss_conf 99999999999743997056542558 Q gi|254780346|r 88 HAVTRGLVDLSINGSLPIGNGIVVVD 113 (149) Q Consensus 88 ~~v~~gl~~lsl~~~~PI~~gILt~~ 113 (149) . +.++-|---+|...||=|.. T Consensus 380 -~----~~d~~LlDVtPlSLGiet~g 400 (631) T PRK00290 380 -D----VKDVLLLDVTPLSLGIETLG 400 (631) T ss_pred -C----CCCCEEEECCCCCEEEEECC T ss_conf -7----66736896034531378639 No 105 >cd06315 PBP1_ABC_sugar_binding_like_6 Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems. Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily, which consists of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis. Probab=65.57 E-value=12 Score=18.80 Aligned_cols=84 Identities=15% Similarity=0.155 Sum_probs=56.6 Q ss_pred CEEEEEEECHHHHHHHHHHHHHHHHHHHCCCCEEEEEHHHHHHH-HHHHHHHHHHHHCCCCCCEEEEEEEEECCCCCHHH Q ss_conf 71799980312899999999999999987995555530014422-69999998633113785356654120006652467 Q gi|254780346|r 6 PHVLIIEARFYENLSAMLFEGCVNVLHSRAVQWSSIVTPGVLEI-PAAVSMVMNAKTRSVTYDGIIVLGVVMRGKTAHCD 84 (149) Q Consensus 6 ~kI~IV~s~~~~~i~~~ll~ga~~~l~~~~~~~~~i~VPGa~Ei-P~a~~~~~~~~~~~~~~D~vIaLG~VIkGeT~H~e 84 (149) |+|.+|.|..+..-.-.+.+|+++..+..|.+..+++--|.-+- --+++.. ...+.||+|.-|. + T Consensus 1 k~i~~va~~l~n~g~~~v~~G~~eaA~~lGw~v~v~D~~g~~~~~~~~i~~a-----i~~k~D~Iii~~~------D--- 66 (280) T cd06315 1 KNIIFVASDLKNGGILGVGEGVREAAKAIGWNLRILDGRGSEAGQAAALNQA-----IALKPDGIVLGGV------D--- 66 (280) T ss_pred CEEEEEEEECCCCCHHHHHHHHHHHHHHCCCEEEEECCCCCHHHHHHHHHHH-----HHCCCCEEEECCC------C--- T ss_conf 9399998726687415498899999997598799988999999999999999-----9639999999982------9--- Q ss_pred HHHHHHHHHHHHHHHHCCCCCE Q ss_conf 8999999999999974399705 Q gi|254780346|r 85 VIAHAVTRGLVDLSINGSLPIG 106 (149) Q Consensus 85 ~I~~~v~~gl~~lsl~~~~PI~ 106 (149) +.++...|.... +-++|++ T Consensus 67 --~~~~~~~l~~A~-~agIPvv 85 (280) T cd06315 67 --AAELQAELELAQ-KAGIPVV 85 (280) T ss_pred --HHHHHHHHHHHH-HCCCCEE T ss_conf --788789999999-8799789 No 106 >PRK10714 undecaprenyl phosphate 4-deoxy-4-formamido-L-arabinose transferase; Provisional Probab=65.48 E-value=12 Score=18.79 Aligned_cols=46 Identities=13% Similarity=0.132 Sum_probs=36.7 Q ss_pred CCCEEEEEEECHHHHH-HHHHHHHHHHHHHHCCCCEEEEEH-----HHHHHH Q ss_conf 5871799980312899-999999999999987995555530-----014422 Q gi|254780346|r 4 FIPHVLIIEARFYENL-SAMLFEGCVNVLHSRAVQWSSIVT-----PGVLEI 49 (149) Q Consensus 4 ~~~kI~IV~s~~~~~i-~~~ll~ga~~~l~~~~~~~~~i~V-----PGa~Ei 49 (149) -|+||.||..-||++= ...+++...+.+...+.+++.+.| -+++|+ T Consensus 4 pmkkiSIViP~yNEe~~i~~~~~~~~~~l~~~~~~~EiI~VDDgS~D~T~~~ 55 (324) T PRK10714 4 PIKKVSVVIPVYNEQESLPELIRRTTAACESLGKEYEILLIDDGSSDNSAEM 55 (324) T ss_pred CCCEEEEEEECCCCHHHHHHHHHHHHHHHHHCCCCEEEEEEECCCCCCHHHH T ss_conf 9986999980177787799999999999986799989999989998677999 No 107 >PRK09860 putative alcohol dehydrogenase; Provisional Probab=65.29 E-value=13 Score=18.76 Aligned_cols=62 Identities=18% Similarity=0.276 Sum_probs=41.4 Q ss_pred CCEEEEEEECHHHHHHHHHHHHHHHHHHHCCCCEEEEE-H---HHHHHHHHHHHHHHHHHHCCCCCCEEEEEE Q ss_conf 87179998031289999999999999998799555553-0---014422699999986331137853566541 Q gi|254780346|r 5 IPHVLIIEARFYENLSAMLFEGCVNVLHSRAVQWSSIV-T---PGVLEIPAAVSMVMNAKTRSVTYDGIIVLG 73 (149) Q Consensus 5 ~~kI~IV~s~~~~~i~~~ll~ga~~~l~~~~~~~~~i~-V---PGa~EiP~a~~~~~~~~~~~~~~D~vIaLG 73 (149) .+|++||....-. -..+++...+.|.+.|+.+.++. | |-.-.+--+++.. +..++|.+|++| T Consensus 31 ~k~~lvvt~~~~~--~~g~~~~v~~~L~~~gi~~~~f~~V~~nP~~~~v~~~~~~~-----r~~~~D~ivavG 96 (383) T PRK09860 31 FTRTLIVTDNMLT--KLGMAGDVQKALEERNIFSVIYDGTQPNPTTENVAAGLKLL-----KENNCDSVISLG 96 (383) T ss_pred CCEEEEECCCCHH--HCCHHHHHHHHHHHCCCCEEEECCCCCCCCHHHHHHHHHHH-----HHCCCCEEEEEC T ss_conf 9879998284566--57469999999987699589968952796999999999999-----873999999938 No 108 >pfam01081 Aldolase KDPG and KHG aldolase. This family includes the following members: 4-hydroxy-2-oxoglutarate aldolase (KHG-aldolase) Phospho-2-dehydro-3-deoxygluconate aldolase (KDPG-aldolase) Probab=63.79 E-value=13 Score=18.59 Aligned_cols=102 Identities=15% Similarity=0.206 Sum_probs=67.8 Q ss_pred EEEEEECHHHHHHHHHHHHHHHHHHHCCCCEEEE--EHHHHHHHHHHHHHHHHHHHCCCCCCEEEEEEEEECCCCCHHH- Q ss_conf 7999803128999999999999999879955555--3001442269999998633113785356654120006652467- Q gi|254780346|r 8 VLIIEARFYENLSAMLFEGCVNVLHSRAVQWSSI--VTPGVLEIPAAVSMVMNAKTRSVTYDGIIVLGVVMRGKTAHCD- 84 (149) Q Consensus 8 I~IV~s~~~~~i~~~ll~ga~~~l~~~~~~~~~i--~VPGa~EiP~a~~~~~~~~~~~~~~D~vIaLG~VIkGeT~H~e- 84 (149) |.|+... ..+-.. ...+.|.+.|+..-.+ +.|+++|.- +.+.+ ...|..|-.|.|..-|+-+-= T Consensus 11 ipV~r~~-~~~~a~----~~~~al~~~Gi~~iEiTl~t~~a~~~I---~~l~~-----~~p~~~iGaGTV~~~e~~~~a~ 77 (196) T pfam01081 11 VPVIVIK-DKEDAL----PLAEALAAGGIRVLEVTLRTPCALDAI---RLLRK-----NRPDALVGAGTVLNAQQLAEAA 77 (196) T ss_pred EEEEECC-CHHHHH----HHHHHHHHCCCCEEEEECCCHHHHHHH---HHHHH-----HCCCCEEEEEECCCHHHHHHHH T ss_conf 9999779-999999----999999987998899947982799999---99996-----4999679998376899999999 Q ss_pred ------HHHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHH Q ss_conf ------89999999999999743997056542558899999950 Q gi|254780346|r 85 ------VIAHAVTRGLVDLSINGSLPIGNGIVVVDSEQQAFDRV 122 (149) Q Consensus 85 ------~I~~~v~~gl~~lsl~~~~PI~~gILt~~n~~QA~~R~ 122 (149) .||-.....+.+.+.++++|.+=|+.|+....||++.- T Consensus 78 ~aGA~FivSP~~~~~v~~~a~~~~i~~iPGv~TpsEi~~A~~~G 121 (196) T pfam01081 78 EAGAQFVVSPGLTADLLKHAVDVKIPLIPGVSTPSEIMLGLDLG 121 (196) T ss_pred HCCCCEEECCCCHHHHHHHHHHCCCCEECCCCCHHHHHHHHHCC T ss_conf 74999999787639999999973996637859999999999879 No 109 >cd01538 PBP1_ABC_xylose_binding Periplasmic xylose-binding component of the ABC-type transport systems that belong to a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein (PBP1) superfamily. Periplasmic xylose-binding component of the ABC-type transport systems that belong to a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein (PBP1) superfamily, which consists of two alpha/beta globular domains connected by a three-stranded hinge. This Venus flytrap-like domain undergoes a transition from an open to a closed conformational state upon ligand binding. Moreover, the periplasmic xylose-binding protein is homologous to the ligand-binding domain of eukaryotic receptors such as glutamate receptor (GluR) and DNA-binding transcriptional repressors such as LacI and GalR. Probab=63.76 E-value=13 Score=18.59 Aligned_cols=35 Identities=6% Similarity=-0.222 Sum_probs=17.1 Q ss_pred EEEEEEECHHHHHHHHHHHHHHHHHHHCCCCEEEE Q ss_conf 17999803128999999999999999879955555 Q gi|254780346|r 7 HVLIIEARFYENLSAMLFEGCVNVLHSRAVQWSSI 41 (149) Q Consensus 7 kI~IV~s~~~~~i~~~ll~ga~~~l~~~~~~~~~i 41 (149) ||+++..+...+.=..+.+|+.+..++.|++.... T Consensus 1 kIGv~vp~l~n~ff~~~~~g~e~~A~e~G~~v~~~ 35 (288) T cd01538 1 KIGLSLPTKTEERWIRDRPNFEAALKELGAEVIVQ 35 (288) T ss_pred CEEEEECCCCCHHHHHHHHHHHHHHHHCCCEEEEE T ss_conf 98999079889799999999999999769989997 No 110 >PRK10624 L-1,2-propanediol oxidoreductase; Provisional Probab=63.76 E-value=13 Score=18.59 Aligned_cols=62 Identities=11% Similarity=0.221 Sum_probs=41.9 Q ss_pred CCEEEEEEECHHHHHHHHHHHHHHHHHHHCCCCEEEEE-H---HHHHHHHHHHHHHHHHHHCCCCCCEEEEEE Q ss_conf 87179998031289999999999999998799555553-0---014422699999986331137853566541 Q gi|254780346|r 5 IPHVLIIEARFYENLSAMLFEGCVNVLHSRAVQWSSIV-T---PGVLEIPAAVSMVMNAKTRSVTYDGIIVLG 73 (149) Q Consensus 5 ~~kI~IV~s~~~~~i~~~ll~ga~~~l~~~~~~~~~i~-V---PGa~EiP~a~~~~~~~~~~~~~~D~vIaLG 73 (149) .+|++||..+.-.+ ..+++...+.|++.++.+.++. | |-.=.+--+++.+ +....|.||++| T Consensus 29 ~k~~lvvtd~~~~k--~g~~~~v~~~L~~~~i~~~vf~~v~pnP~~~~V~~~~~~~-----r~~~~D~IiavG 94 (381) T PRK10624 29 YHKALIVTDKTLVQ--CGVVAKVTDKLDAAGLAYEIYDGVKPNPTISVVKEGLEVF-----QASGADYLIAIG 94 (381) T ss_pred CCEEEEEECCCHHH--CCHHHHHHHHHHHCCCEEEEECCCCCCCCHHHHHHHHHHH-----HHCCCCEEEEEC T ss_conf 98799996965455--6369999999987698399988925898999999999999-----864999899808 No 111 >TIGR02350 prok_dnaK chaperone protein DnaK; InterPro: IPR012725 Molecular chaperones are a diverse family of proteins that function to protect proteins in the intracellular milieu from irreversible aggregation during synthesis and in times of cellular stress. The bacterial molecular chaperone DnaK is an enzyme that couples cycles of ATP binding, hydrolysis, and ADP release by an N-terminal ATP-hydrolysing domain to cycles of sequestration and release of unfolded proteins by a C-terminal substrate binding domain. In prokaryotes, the grpE protein is a co-chaperone for DnaK, and acts as a nucleotide exchange factor, stimulating the rate of ADP release 5000-fold . DnaK is itself a weak ATPase; ATP hydrolysis by DnaK is stimulated by its interaction with another co-chaperone, DnaJ. Thus the co-chaperones DnaJ and GrpE are capable of tightly regulating the nucleotide-bound and substrate-bound state of DnaK in ways that are necessary for the normal housekeeping functions and stress-related functions of the DnaK molecular chaperone cycle. Members of this family are the chaperone DnaK, of the DnaK-DnaJ-GrpE chaperone system. All members of the seed alignment were taken from completely sequenced bacterial or archaeal genomes and (except for the Mycoplasma sequence) found clustered with other genes of this systems. This entry excludes DnaK homologues that are not DnaK itself, such as the heat shock cognate protein HscA (IPR010236 from INTERPRO). However, it is not designed to distinguish among DnaK paralogs in eukaryotes. Note that a number of DnaK genes have shadow ORFs in the same reverse (relative to dnaK) reading frame, a few of which have been assigned glutamate dehydrogenase activity. The significance of this observation is unclear; the lengths of such shadow ORFs are highly variable as if the presumptive protein product is not conserved.; GO: 0005524 ATP binding, 0051082 unfolded protein binding, 0006457 protein folding. Probab=63.04 E-value=4.9 Score=21.30 Aligned_cols=69 Identities=23% Similarity=0.300 Sum_probs=49.3 Q ss_pred HHHHHHHHHHHHHHHHHHCCCCEE----EEEHHHHHHHHHHHHHHHHHH----HCCCCCCEEEEEEEEECCCCCHHH Q ss_conf 289999999999999998799555----553001442269999998633----113785356654120006652467 Q gi|254780346|r 16 YENLSAMLFEGCVNVLHSRAVQWS----SIVTPGVLEIPAAVSMVMNAK----TRSVTYDGIIVLGVVMRGKTAHCD 84 (149) Q Consensus 16 ~~~i~~~ll~ga~~~l~~~~~~~~----~i~VPGa~EiP~a~~~~~~~~----~~~~~~D~vIaLG~VIkGeT~H~e 84 (149) -.++.++...-+...|.+++...+ ++-|=|+=-+|.+-+.+-... .++-+||-+||+|+-|+|.--.-| T Consensus 301 ~~dLv~~~~~p~~~aL~DA~l~~~~I~~v~LVGG~TRiP~V~~~V~~~~GK~p~~~vNPDEvVAiGAAiQgGVL~Gd 377 (598) T TIGR02350 301 TADLVERTKEPVRQALKDAGLSASDIDEVILVGGSTRIPAVQELVKEFFGKEPNKSVNPDEVVAIGAAIQGGVLKGD 377 (598) T ss_pred HHHHHHHHHHHHHHHHHHCCCCHHHCCEEEEECCCCCHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHCCCC T ss_conf 99999998999999997537884366668985588412489999998729887888880588888788875431787 No 112 >cd01540 PBP1_arabinose_binding Periplasmic L-arabinose-binding protein (ABP), a member of a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily. Periplasmic L-arabinose-binding protein (ABP), a member of a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily. ABP is only involved in transport contrary to other related sugar-binding proteins such as the glucose/galactose-binding protein (GGBP) and the ribose-binding protein (RBP), both of which are involved in chemotaxis as well as transport. The periplasmic ABP consists of two alpha/beta globular domains connected by a three-stranded hinge, a Venus flytrap-like domain, which undergoes a transition from an open to a closed conformational state upon ligand binding. Moreover, ABP is homologous to the ligand-binding domain of eukaryotic receptors such as metabotropic glutamate receptor (mGluR) and DNA-binding transcriptional repressors such a Probab=62.66 E-value=14 Score=18.46 Aligned_cols=34 Identities=6% Similarity=-0.082 Sum_probs=18.0 Q ss_pred EEEEEEECHHHHHHHHHHHHHHHHHHHCCCCEEE Q ss_conf 1799980312899999999999999987995555 Q gi|254780346|r 7 HVLIIEARFYENLSAMLFEGCVNVLHSRAVQWSS 40 (149) Q Consensus 7 kI~IV~s~~~~~i~~~ll~ga~~~l~~~~~~~~~ 40 (149) ||+++....+...=..|.+|+++..++.|++... T Consensus 1 KIg~~~~tl~npff~~~~~g~~~~A~e~G~~l~~ 34 (289) T cd01540 1 KIGFIVKQPEEPWFQTEWKFAKKAAKEKGFTVVK 34 (289) T ss_pred CEEEEECCCCCHHHHHHHHHHHHHHHHHCCEEEE T ss_conf 9899958998839999999999999984987999 No 113 >cd06300 PBP1_ABC_sugar_binding_like_1 Periplasmic sugar-binding component of uncharacterized ABC-type transport systems that are members of the pentose/hexose sugar-binding protein family of the type I periplasmic binding protein superfamily. Periplasmic sugar-binding component of uncharacterized ABC-type transport systems that are members of the pentose/hexose sugar-binding protein family of the type I periplasmic binding protein superfamily, which consists of two alpha/beta globular domains connected by a three-stranded hinge. This Venus flytrap-like domain undergoes transition from an open to a closed conformational state upon ligand binding. Members of this group are predicted to be involved in the transport of sugar-containing molecules across cellular and organellar membranes; however their substrate specificity is not known in detail. Probab=60.63 E-value=15 Score=18.24 Aligned_cols=123 Identities=15% Similarity=0.091 Sum_probs=65.4 Q ss_pred CEEEEEEECHHHHHHHHHHHHHHHHHHHCCCCEEEE-EHHHHHHHHHHHHHHHHHHHCCCCCCEEEEEEEEECCCCCHHH Q ss_conf 717999803128999999999999999879955555-3001442269999998633113785356654120006652467 Q gi|254780346|r 6 PHVLIIEARFYENLSAMLFEGCVNVLHSRAVQWSSI-VTPGVLEIPAAVSMVMNAKTRSVTYDGIIVLGVVMRGKTAHCD 84 (149) Q Consensus 6 ~kI~IV~s~~~~~i~~~ll~ga~~~l~~~~~~~~~i-~VPGa~EiP~a~~~~~~~~~~~~~~D~vIaLG~VIkGeT~H~e 84 (149) .+|+++...-....+..-.+|+.+.|.+++ .++++ ..+|-|....+.+..-.......+.|++++- + + T Consensus 126 g~i~~i~G~~~~~~~~~R~~Gf~~~l~~~p-~i~iv~~~~~~~~~~~a~~~~~~~L~~~pdid~I~~~------d----~ 194 (272) T cd06300 126 GNVLVVRGLAGHPVDEDRYAGAKEVLKEYP-GIKIVGEVYGDWDQAVAQKAVADFLASNPDVDGIWTQ------G----G 194 (272) T ss_pred CCEEEEECCCCCHHHHHHHHHHHHHHHHCC-CEEEEEEECCCCCHHHHHHHHHHHHHHCCCCEEEEEC------C----C T ss_conf 763899448898499999999999986414-2488655448888899999999999868996099977------8----2 Q ss_pred HHHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHHCC-------CCCCCHHHHHHHHHHHHH Q ss_conf 8999999999999974399705654255889999995065-------657456999999999999 Q gi|254780346|r 85 VIAHAVTRGLVDLSINGSLPIGNGIVVVDSEQQAFDRVSP-------SHLDRGGCAARSALAMIE 142 (149) Q Consensus 85 ~I~~~v~~gl~~lsl~~~~PI~~gILt~~n~~QA~~R~~~-------~~~nkG~eaa~Aal~mi~ 142 (149) .+-.+.+++.+... ..|+..|.-..........+-+. +...-|+.|+++++++++ T Consensus 195 -~a~Ga~~Al~~aG~--~~~~~~g~~~~~~~~~~~~~~g~~~a~~~q~p~~~G~~av~~a~~~l~ 256 (272) T cd06300 195 -DAVGAVQAFEQAGR--DIPPVTGEDENGFLRWRLWKDKGLKGIAISNPPGQSAAALRAAVQALE 256 (272) T ss_pred -CHHHHHHHHHHCCC--CCCEEEEECCCHHHHHHHHCCCCEEEEEECCHHHHHHHHHHHHHHHHC T ss_conf -18999999996699--988699975957899998348975999970859999999999999977 No 114 >cd06301 PBP1_rhizopine_binding_like Periplasmic binding proteins specific to rhizopines. Periplasmic binding proteins specific to rhizopines, which are simple sugar-like compounds produced in the nodules induced by the symbiotic root nodule bacteria, such as Rhizobium and Sinorhizobium. Rhizopine-binding-like proteins from other bacteria are also included. Two inositol based rhizopine compounds are known to date: L-3-O-methly-scyllo-inosamine (3-O-MSI) and scyllo-inosamine. Bacterial strains that can metabolize rhizopine have a greater competitive advantage in nodulation and rhizopine synthesis is regulated by NifA/NtrA regulatory transcription activators which are maximally expressed at the onset of nitrogen fixation in bacteroids. The members of this group belong to the pentose/hexose sugar-binding protein family of the type I periplasmic binding protein superfamily. Probab=60.15 E-value=16 Score=18.19 Aligned_cols=122 Identities=15% Similarity=0.127 Sum_probs=50.7 Q ss_pred EEEEEEECHHHHHHHHHHHHHHHHHHHCCCCEEEE-EHHHHHHHHHHHHHHHHHHHCCCCCCEEEEEEEEECCCCCHHHH Q ss_conf 17999803128999999999999999879955555-30014422699999986331137853566541200066524678 Q gi|254780346|r 7 HVLIIEARFYENLSAMLFEGCVNVLHSRAVQWSSI-VTPGVLEIPAAVSMVMNAKTRSVTYDGIIVLGVVMRGKTAHCDV 85 (149) Q Consensus 7 kI~IV~s~~~~~i~~~ll~ga~~~l~~~~~~~~~i-~VPGa~EiP~a~~~~~~~~~~~~~~D~vIaLG~VIkGeT~H~e~ 85 (149) +|+++...-.......-.+|+.+.|.++. ..+.+ ..+|-|....+.+.+-+-.....+.|++++. .|. T Consensus 125 ~v~~i~g~~~~~~~~~R~~Gf~~~l~~~~-~~~iv~~~~~~~~~~~a~~~~~~~L~~~~~~~aI~~~----------nd~ 193 (272) T cd06301 125 NVAILMGPLGQSAQIDRTKGVEEVLAKYP-DIKVVEEQTANWSRAEAMDLMENWLSSGGKIDAVVAN----------NDE 193 (272) T ss_pred EEEEECCCCCCHHHHHHHHHHHHHHHHCC-CCEEEEEECCCHHHHHHHHHHHHHHHHCCCCCEEEEC----------CCH T ss_conf 18973589997689999999999998789-9658876313123578999999999836777879955----------827 Q ss_pred HHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHHCCCC---------CCCHHHHHHHHHHHHH Q ss_conf 99999999999997439970565425588999999506565---------7456999999999999 Q gi|254780346|r 86 IAHAVTRGLVDLSINGSLPIGNGIVVVDSEQQAFDRVSPSH---------LDRGGCAARSALAMIE 142 (149) Q Consensus 86 I~~~v~~gl~~lsl~~~~PI~~gILt~~n~~QA~~R~~~~~---------~nkG~eaa~Aal~mi~ 142 (149) .+-.+.++|.+..+. |=-..|.+.+...++.+...... ..-|+.|++.++++++ T Consensus 194 ~a~Ga~~al~~~g~~---~~~i~v~G~D~~~~~~~~i~~g~~~~tv~q~~~~~G~~av~~~~~~l~ 256 (272) T cd06301 194 MALGAIMALKAAGKS---DKDVPVAGIDGTPDALAAVKKGDLDVTVFQDAKGQGAGALDAALKLAK 256 (272) T ss_pred HHHHHHHHHHHCCCC---CCCEEEEEECCCHHHHHHHHCCCCEEEEECCHHHHHHHHHHHHHHHHC T ss_conf 899999999986989---998799998985999999874997699806999999999999999977 No 115 >PTZ00009 heat shock 70 kDa protein; Provisional Probab=59.34 E-value=8.4 Score=19.83 Aligned_cols=92 Identities=14% Similarity=0.221 Sum_probs=52.8 Q ss_pred HHHHHHHHHHHHHHHHHCCCCEE----EEEHHHHHHHHHHHHHHHHHHH-----CCCCCCEEEEEEEEECCCCCHHHHHH Q ss_conf 89999999999999998799555----5530014422699999986331-----13785356654120006652467899 Q gi|254780346|r 17 ENLSAMLFEGCVNVLHSRAVQWS----SIVTPGVLEIPAAVSMVMNAKT-----RSVTYDGIIVLGVVMRGKTAHCDVIA 87 (149) Q Consensus 17 ~~i~~~ll~ga~~~l~~~~~~~~----~i~VPGa~EiP~a~~~~~~~~~-----~~~~~D~vIaLG~VIkGeT~H~e~I~ 87 (149) .++.++.+.-+.+.|++.++..+ ++-|=|+-.+|..-+.+-+... .+-++|-.||+||-+++...- T Consensus 309 ~~l~~r~~~~i~~aL~~a~l~~~dId~ViLVGGsTRiP~Vq~~l~~~f~gk~~~~~iNpDEaVA~GAAiqaa~Ls----- 383 (657) T PTZ00009 309 GDLFRSTLQPVEKVLQDAKMDKRSVHDVVLVGGSTRIPKVQSLISDFFNGKELNKSINPDEAVAYGAAVQAAILT----- 383 (657) T ss_pred HHHHHHHHHHHHHHHHHHCCCHHHEEEEEECCCCCCCHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHC----- T ss_conf 999998999999999973799525149998088146768999999981898888897831466654899999871----- Q ss_pred HHHHHHHHHHHHHCCCCCEEEEECCC Q ss_conf 99999999999743997056542558 Q gi|254780346|r 88 HAVTRGLVDLSINGSLPIGNGIVVVD 113 (149) Q Consensus 88 ~~v~~gl~~lsl~~~~PI~~gILt~~ 113 (149) ..-.....++.+.--+|+..||=|.. T Consensus 384 g~~~~~v~~~~l~Dv~PlslGie~~g 409 (657) T PTZ00009 384 GGQSKQTQGLLLLDVAPLSLGLETAG 409 (657) T ss_pred CCCCCCCCEEEEEECCCEEEEEEECC T ss_conf 89655412368996164047888659 No 116 >PRK05718 keto-hydroxyglutarate-aldolase/keto-deoxy-phosphogluconate aldolase; Provisional Probab=58.89 E-value=16 Score=18.05 Aligned_cols=102 Identities=17% Similarity=0.199 Sum_probs=68.6 Q ss_pred EEEEEECHHHHHHHHHHHHHHHHHHHCCCCEEEE--EHHHHHHHHHHHHHHHHHHHCCCCCCEEEEEEEEECCCCCHHH- Q ss_conf 7999803128999999999999999879955555--3001442269999998633113785356654120006652467- Q gi|254780346|r 8 VLIIEARFYENLSAMLFEGCVNVLHSRAVQWSSI--VTPGVLEIPAAVSMVMNAKTRSVTYDGIIVLGVVMRGKTAHCD- 84 (149) Q Consensus 8 I~IV~s~~~~~i~~~ll~ga~~~l~~~~~~~~~i--~VPGa~EiP~a~~~~~~~~~~~~~~D~vIaLG~VIkGeT~H~e- 84 (149) |.||.. -..+-...+ .+.|.+.|+..-.| +.|+++|. ++.+.+ .-.|..|-.|.|...|+-+.= T Consensus 18 i~Vlr~-~~~~~a~~i----~~al~~gGi~~iEiTl~tp~a~~~---I~~l~~-----~~p~~~vGaGTV~~~e~~~~a~ 84 (212) T PRK05718 18 VPVIVI-NKLEDAVPL----AKALVAGGLPVLEVTLRTPAALEA---IRAIRK-----EVPEALIGAGTVLNPEQLAQAI 84 (212) T ss_pred EEEEEC-CCHHHHHHH----HHHHHHCCCCEEEEECCCCHHHHH---HHHHHH-----HCCCCEEEEEEECCHHHHHHHH T ss_conf 999974-899999999----999998799789995789619999---999997-----5898179653313488999999 Q ss_pred ------HHHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHH Q ss_conf ------89999999999999743997056542558899999950 Q gi|254780346|r 85 ------VIAHAVTRGLVDLSINGSLPIGNGIVVVDSEQQAFDRV 122 (149) Q Consensus 85 ------~I~~~v~~gl~~lsl~~~~PI~~gILt~~n~~QA~~R~ 122 (149) .||-.....+.+.+.+.++|.+=|+.|+....+|++.- T Consensus 85 ~aGA~FiVSP~~~~~v~~~a~~~~i~~iPGv~TpsEi~~A~~~G 128 (212) T PRK05718 85 EAGAQFIVSPGLTPPLLKACQDGPIPLIPGVNTPSELMLAMELG 128 (212) T ss_pred HCCCCEEECCCCCHHHHHHHHHCCCCEECCCCCHHHHHHHHHCC T ss_conf 84998998489989999999981997657869999999999879 No 117 >PTZ00186 heat shock 70 kDa precursor protein; Provisional Probab=56.34 E-value=2.9 Score=22.72 Aligned_cols=87 Identities=21% Similarity=0.316 Sum_probs=54.4 Q ss_pred HHHHHHHHHHHHHHHHCCCCEE----EEEHHHHHHHHHHHHHHHHHHH----CCCCCCEEEEEEEEECCCCCHHHHHHHH Q ss_conf 9999999999999998799555----5530014422699999986331----1378535665412000665246789999 Q gi|254780346|r 18 NLSAMLFEGCVNVLHSRAVQWS----SIVTPGVLEIPAAVSMVMNAKT----RSVTYDGIIVLGVVMRGKTAHCDVIAHA 89 (149) Q Consensus 18 ~i~~~ll~ga~~~l~~~~~~~~----~i~VPGa~EiP~a~~~~~~~~~----~~~~~D~vIaLG~VIkGeT~H~e~I~~~ 89 (149) ++.++.+.-+.+.|++.++..+ ++-|=|+--+|..-+++-+... .+-++|-.||+|+-|.|.--.-+ T Consensus 331 ~Ll~rt~~~v~~aL~dAgl~~~dId~VILVGGSTRIP~Vq~~l~~~Fgkep~~~iNPDEaVA~GAAiqa~iL~g~----- 405 (657) T PTZ00186 331 RLIERSIAPCKQCMKDAGVELKEINDVVLVGGMTRMPKVVEEVKKFFQKDPFRGVNPDEAVALGAATLGGVLRGD----- 405 (657) T ss_pred HHHHHHHHHHHHHHHHHCCCHHHEEEEEEECCCCCCHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHCCC----- T ss_conf 999999999999999818998780089995784154799999999858997779791189999899988876387----- Q ss_pred HHHHHHHHHHHCCCCCEEEEECCC Q ss_conf 999999999743997056542558 Q gi|254780346|r 90 VTRGLVDLSINGSLPIGNGIVVVD 113 (149) Q Consensus 90 v~~gl~~lsl~~~~PI~~gILt~~ 113 (149) ..++-|---+|...||=|.. T Consensus 406 ----~~~~~LlDVtPlSLGiet~g 425 (657) T PTZ00186 406 ----VKGLVLLDVTPLSLGIETLG 425 (657) T ss_pred ----CCCEEEEEEECCEEEEEECC T ss_conf ----55348998555517999718 No 118 >pfam10087 DUF2325 Uncharacterized protein conserved in bacteria (DUF2325). Members of this family of hypothetical bacterial proteins have no known function. Probab=56.17 E-value=18 Score=17.77 Aligned_cols=85 Identities=13% Similarity=0.105 Sum_probs=56.7 Q ss_pred HHHHHHHHHHHHHCCCCEEEEEHHHHHHHHHHHHHHHHHHHCCCCCCEEEEEEEEECCCCCHHHHHHHHHHHHHHHHHHH Q ss_conf 99999999999987995555530014422699999986331137853566541200066524678999999999999974 Q gi|254780346|r 21 AMLFEGCVNVLHSRAVQWSSIVTPGVLEIPAAVSMVMNAKTRSVTYDGIIVLGVVMRGKTAHCDVIAHAVTRGLVDLSIN 100 (149) Q Consensus 21 ~~ll~ga~~~l~~~~~~~~~i~VPGa~EiP~a~~~~~~~~~~~~~~D~vIaLG~VIkGeT~H~e~I~~~v~~gl~~lsl~ 100 (149) +.++....+.+++.|++....+ |..+=. . +.+ . ..-.+.|.||++ -|+|++..+.-+.+..=+ T Consensus 9 ~~~~~~~~~~~~~~G~~~~~h~--~g~~~~-~-~~l-~--~~i~~aDlVI~~----------td~vsH~~~~~vK~~akk 71 (96) T pfam10087 9 DDRLGHYRKLLEKYGGEFIVHD--GGREKK-K-KKI-P--ALLKKADLVIVF----------TDCVSHDAMWRVKEEAKK 71 (96) T ss_pred HHHHHHHHHHHHHCCCEEEEEC--CCCCCH-H-HHH-H--HCCCCCCEEEEE----------CCCCCHHHHHHHHHHHHH T ss_conf 5678999999998399899965--898733-5-567-7--505898889997----------176687999999999998 Q ss_pred CCCCCEEEE-ECCCCHHHHHHHH Q ss_conf 399705654-2558899999950 Q gi|254780346|r 101 GSLPIGNGI-VVVDSEQQAFDRV 122 (149) Q Consensus 101 ~~~PI~~gI-Lt~~n~~QA~~R~ 122 (149) +++|+.+.= =...+..++++|. T Consensus 72 ~~~p~v~~~s~s~~~l~~~l~~~ 94 (96) T pfam10087 72 RGIPVVFSRSRSLSALERALARL 94 (96) T ss_pred HCCCEEEECCCCHHHHHHHHHHH T ss_conf 49978997687499999999996 No 119 >PRK13243 glyoxylate reductase; Reviewed Probab=54.68 E-value=17 Score=17.92 Aligned_cols=53 Identities=15% Similarity=0.291 Sum_probs=26.0 Q ss_pred CCCEEEEEEECHHHHHHHHHHHHHHHHHHHCCCCEEEEEHHHHHHHHHHHHHHHHHHHCCCCCCEEEEEE Q ss_conf 5871799980312899999999999999987995555530014422699999986331137853566541 Q gi|254780346|r 4 FIPHVLIIEARFYENLSAMLFEGCVNVLHSRAVQWSSIVTPGVLEIPAAVSMVMNAKTRSVTYDGIIVLG 73 (149) Q Consensus 4 ~~~kI~IV~s~~~~~i~~~ll~ga~~~l~~~~~~~~~i~VPGa~EiP~a~~~~~~~~~~~~~~D~vIaLG 73 (149) |+|||+|.. +.+ +.+.+.|+++ ++++...-+.. ++. +.+++ .-.++|++|+.+ T Consensus 1 Mk~Kvlvt~-~i~--------~~~~~~L~~~-~~v~~~~~~~~--~~~--~~l~~---~i~~~d~li~~~ 53 (333) T PRK13243 1 MKPRVFITR-EIP--------ENGIEMLEEH-FEVEVWEDERE--IPR--EVLLE---KVKDVDALVTML 53 (333) T ss_pred CCCEEEEEC-CCC--------HHHHHHHHHC-CCEEEECCCCC--CCH--HHHHH---HHCCCCEEEECC T ss_conf 997899969-889--------9999999717-95999269999--999--99999---867982999858 No 120 >pfam00012 HSP70 Hsp70 protein. Hsp70 chaperones help to fold many proteins. Hsp70 assisted folding involves repeated cycles of substrate binding and release. Hsp70 activity is ATP dependent. Hsp70 proteins are made up of two regions: the amino terminus is the ATPase domain and the carboxyl terminus is the substrate binding region. Probab=54.59 E-value=13 Score=18.63 Aligned_cols=93 Identities=22% Similarity=0.324 Sum_probs=53.3 Q ss_pred EECHHH---HHHHHHHHHHHHHHHHCCCCEE----EEEHHHHHHHHHHHHHHHHHHH----CCCCCCEEEEEEEEECCC- Q ss_conf 803128---9999999999999998799555----5530014422699999986331----137853566541200066- Q gi|254780346|r 12 EARFYE---NLSAMLFEGCVNVLHSRAVQWS----SIVTPGVLEIPAAVSMVMNAKT----RSVTYDGIIVLGVVMRGK- 79 (149) Q Consensus 12 ~s~~~~---~i~~~ll~ga~~~l~~~~~~~~----~i~VPGa~EiP~a~~~~~~~~~----~~~~~D~vIaLG~VIkGe- 79 (149) .++|.+ ++.+++.+-+.+.|.+.++..+ ++-|=|+--+|..-+.+-+... .+-++|-.||.||-+++. T Consensus 294 R~eFE~l~~~l~~r~~~~i~~~L~~a~l~~~dId~ViLvGGssRiP~Vq~~l~~~fg~~~~~~inpdeaVa~GAA~~aa~ 373 (598) T pfam00012 294 RAKFEELCADLFERTLEPVEKALKDAKLSKSEIDEVVLVGGSTRIPAVQELVKEFFGKEPSKTVNPDEAVAIGAAVQAGV 373 (598) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHEEEEEECCCCCCCHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHH T ss_conf 99999999999999999998789872899545125786188656768999999986899666868531423308999987 Q ss_pred -CCHHHHHHHHHHHHHHHHHHHCCCCCEEEEECCC Q ss_conf -5246789999999999999743997056542558 Q gi|254780346|r 80 -TAHCDVIAHAVTRGLVDLSINGSLPIGNGIVVVD 113 (149) Q Consensus 80 -T~H~e~I~~~v~~gl~~lsl~~~~PI~~gILt~~ 113 (149) +..|. ..++.+.--+|...||-+.. T Consensus 374 ls~~~~---------v~~~~~~Dv~p~slgi~~~~ 399 (598) T pfam00012 374 LSGTFD---------VKDVLLLDVTPLSLGIETLG 399 (598) T ss_pred HCCCCC---------CCCEEEEEECCCEEEEEECC T ss_conf 578764---------56528998547358999818 No 121 >TIGR02021 BchM-ChlM magnesium protoporphyrin O-methyltransferase; InterPro: IPR010251 Chlorophyll and bacteriochlorophyll are essential photosynthetic pigments involved in oxygenic and non-oxygenic photosythesis respectively. They are both synthesised from protoporphyrin IX in complex pathways which share many common steps. The second committed step in both pathways is the methylation of magnesium protoporphyrin IX, catalysed by magnesium protoporphyrin O-methyltransferase with S-adenosyl methionine (SAM) as the methyl donor , , .Sequence alignments suggest that the protein contains the characteristic seven-stranded beta-sheet fold found in other SAM-dependent methyltransferases. This entry represents magnesium protoporphyrin O-methyltransferase from cyanobacteria and plants, where it is known as ChlM, and from other photosynthetic bacteria, where it is known as BchM.; GO: 0046406 magnesium protoporphyrin IX methyltransferase activity, 0015979 photosynthesis, 0015995 chlorophyll biosynthetic process. Probab=54.17 E-value=20 Score=17.57 Aligned_cols=88 Identities=10% Similarity=0.073 Sum_probs=63.7 Q ss_pred HHHHHHHHHHHHHHHHHCCCCEEEE-EHHHHHHHHHHHHHHHHHHHCC-CCCCEEEEEEEEECCCCCHHHHHHHHHHHHH Q ss_conf 8999999999999999879955555-3001442269999998633113-7853566541200066524678999999999 Q gi|254780346|r 17 ENLSAMLFEGCVNVLHSRAVQWSSI-VTPGVLEIPAAVSMVMNAKTRS-VTYDGIIVLGVVMRGKTAHCDVIAHAVTRGL 94 (149) Q Consensus 17 ~~i~~~ll~ga~~~l~~~~~~~~~i-~VPGa~EiP~a~~~~~~~~~~~-~~~D~vIaLG~VIkGeT~H~e~I~~~v~~gl 94 (149) -||+++|++-|.+.....+.....+ .+-|.+|= .. ++||.|||+=++|- |=.+.....| T Consensus 82 ~DIS~~mv~~A~~r~~~~~~~~nl~~FeV~Dl~s------------~~~G~fD~VV~mDvlIH-------Yp~~d~~~~l 142 (224) T TIGR02021 82 VDISEQMVELARERAEKEDEAGNLVEFEVNDLES------------LELGKFDAVVAMDVLIH-------YPAEDIAKAL 142 (224) T ss_pred EHHHHHHHHHHHHHCCCCCCCCCCCEEEECCHHH------------HCCCCCCEEEEEHHHHH-------CCHHHHHHHH T ss_conf 2376899999986210021016700354530444------------13898555675212232-------0222279999 Q ss_pred HHHHHHCCCCCEEEEECCCCHHHHHHHHC Q ss_conf 99997439970565425588999999506 Q gi|254780346|r 95 VDLSINGSLPIGNGIVVVDSEQQAFDRVS 123 (149) Q Consensus 95 ~~lsl~~~~PI~~gILt~~n~~QA~~R~~ 123 (149) .+|.-..+-|++|-.=--.+.=.++.+.| T Consensus 143 ~~Laslt~~~~~ftfAP~T~~l~~~~~IG 171 (224) T TIGR02021 143 EHLASLTKERVIFTFAPKTAYLAFLKAIG 171 (224) T ss_pred HHHHHHHCCCEEEEECCCCHHHHHHHHHH T ss_conf 99887435864898678767899999851 No 122 >TIGR01991 HscA Fe-S protein assembly chaperone HscA; InterPro: IPR010236 Iron-sulphur (FeS) clusters are important cofactors for numerous proteins involved in electron transfer, in redox and non-redox catalysis, in gene regulation, and as sensors of oxygen and iron. These functions depend on the various FeS cluster prosthetic groups, the most common being [2Fe-2S] and [4Fe-4S] . FeS cluster assembly is a complex process involving the mobilisation of Fe and S atoms from storage sources, their assembly into [Fe-S] form, their transport to specific cellular locations, and their transfer to recipient apoproteins. So far, three FeS assembly machineries have been identified, which are capable of synthesising all types of [Fe-S] clusters: ISC (iron-sulphur cluster), SUF (sulphur assimilation), and NIF (nitrogen fixation) systems. The ISC system is conserved in eubacteria and eukaryotes (mitochondria), and has broad specificity, targeting general FeS proteins , . It is encoded by the isc operon (iscRSUA-hscBA-fdx-iscX). IscS is a cysteine desulphurase, which obtains S from cysteine (converting it to alanine) and serves as a S donor for FeS cluster assembly. IscU and IscA act as scaffolds to accept S and Fe atoms, assembling clusters and transfering them to recipient apoproteins. HscA is a molecular chaperone and HscB is a co-chaperone. Fdx is a [2Fe-2S]-type ferredoxin. IscR is a transcription factor that regulates expression of the isc operon. IscX (also known as YfhJ) appears to interact with IscS and may function as an Fe donor during cluster assembly . The SUF system is an alternative pathway to the ISC system that operates under iron starvation and oxidative stress. It is found in eubacteria, archaea and eukaryotes (plastids). The SUF system is encoded by the suf operon (sufABCDSE), and the six encoded proteins are arranged into two complexes (SufSE and SufBCD) and one protein (SufA). SufS is a pyridoxal-phosphate (PLP) protein displaying cysteine desulphurase activity. SufE acts as a scaffold protein that accepts S from SufS and donates it to SufA . SufC is an ATPase with an unorthodox ATP-binding cassette (ABC)-like component. No specific functions have been assigned to SufB and SufD. SufA is homologous to IscA , acting as a scaffold protein in which Fe and S atoms are assembled into [FeS] cluster forms, which can then easily be transferred to apoproteins targets. In the NIF system, NifS and NifU are required for the formation of metalloclusters of nitrogenase in Azotobacter vinelandii, and other organisms, as well as in the maturation of other FeS proteins. Nitrogenase catalyses the fixation of nitrogen. It contains a complex cluster, the FeMo cofactor, which contains molybdenum, Fe and S. NifS is a cysteine desulphurase. NifU binds one Fe atom at its N-terminal, assembling an FeS cluster that is transferred to nitrogenase apoproteins . Nif proteins involved in the formation of FeS clusters can also be found in organisms that do not fix nitrogen . This entry represents the HscA chaperone protein from the SUF system. HscA (or Hsc66) is a specialised bacterial Hsp70-class molecular chaperone that participates in the assembly of iron-sulphur cluster proteins. HscA resembles DnaK, but belongs to a separate clade. HscA interacts with IscU, which is believed to serve as a template for Fe-S cluster formation. The HscA-IscU interaction is facilitated by the J-type co-chaperone protein HscB (or Hsc20), which binds to both HscA and IscU, bringing them into contact with each other. HscA recognises a conserved LPPVK sequence motif at positions 99-103 of IscU .; GO: 0005524 ATP binding, 0016887 ATPase activity, 0051082 unfolded protein binding, 0016226 iron-sulfur cluster assembly. Probab=53.91 E-value=14 Score=18.44 Aligned_cols=59 Identities=17% Similarity=0.294 Sum_probs=42.5 Q ss_pred HHHHHHHHHHHHHHCCCCEE----EEEHHHHHHHHHHHHHHHHHHHC----CCCCCEEEEEEEEECC Q ss_conf 99999999999998799555----55300144226999999863311----3785356654120006 Q gi|254780346|r 20 SAMLFEGCVNVLHSRAVQWS----SIVTPGVLEIPAAVSMVMNAKTR----SVTYDGIIVLGVVMRG 78 (149) Q Consensus 20 ~~~ll~ga~~~l~~~~~~~~----~i~VPGa~EiP~a~~~~~~~~~~----~~~~D~vIaLG~VIkG 78 (149) +.+=+..|...|++.|++.+ +|-|=||=-+|-+=+.+..-... +-+||-|||||.-|+- T Consensus 319 V~rtl~~crrAlkDaGV~~~e~~~VvmVGGSTRvp~Vr~~VaelFg~~PL~~ldPD~VVAlGAAiQA 385 (628) T TIGR01991 319 VKRTLLPCRRALKDAGVEKEEVKGVVMVGGSTRVPKVREAVAELFGREPLTDLDPDKVVALGAAIQA 385 (628) T ss_pred HHHHHHHHHHHHHHCCCCHHHCCEEEEECCCCCHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHH T ss_conf 9852167888887527883253265786265461679999988637787888875142465589987 No 123 >pfam02514 CobN-Mg_chel CobN/Magnesium Chelatase. This family contains a domain common to the cobN protein and to magnesium protoporphyrin chelatase. CobN is implicated in the conversion of hydrogenobyrinic acid a,c-diamide to cobyrinic acid. Magnesium protoporphyrin chelatase is involved in chlorophyll biosynthesis. Probab=53.33 E-value=20 Score=17.49 Aligned_cols=106 Identities=20% Similarity=0.221 Sum_probs=60.0 Q ss_pred CCEEEEEEECHHHHHH-HHHHHHHHHHHHHCCCCEEEEEHHHHHHHHHHHHHHHHHHHCCCCCCEEEEEE-EEECCCCCH Q ss_conf 8717999803128999-99999999999987995555530014422699999986331137853566541-200066524 Q gi|254780346|r 5 IPHVLIIEARFYENLS-AMLFEGCVNVLHSRAVQWSSIVTPGVLEIPAAVSMVMNAKTRSVTYDGIIVLG-VVMRGKTAH 82 (149) Q Consensus 5 ~~kI~IV~s~~~~~i~-~~ll~ga~~~l~~~~~~~~~i~VPGa~EiP~a~~~~~~~~~~~~~~D~vIaLG-~VIkGeT~H 82 (149) .|.|+|+.-+-|--=. -..++.-.+.|.+.|+++-.++++ .+..-++...+... .....|++|.+- .-+.|... T Consensus 68 ~p~Vgilfyr~~~~~g~~~~idali~~Le~~G~nvipvf~~--~~~~~~~~~~~~~~-~~~~vd~iI~~~~F~l~~~~~- 143 (1064) T pfam02514 68 APTVGILFYRSYLLAGDTAHIDALIRALEARGLNVIPVFSD--LDSREAVRDFFFRD-GEPKVDAIINLTGFSLVGGPA- 143 (1064) T ss_pred CCEEEEEECHHHHHCCCCHHHHHHHHHHHHCCCEEEEEEEC--CCCCHHHHHHHHHC-CCCCCCEEEECCCCCCCCCCC- T ss_conf 98799996555664398489999999999789969999945--75509999999847-998873899738423668882- Q ss_pred HHHHHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHHC Q ss_conf 67899999999999997439970565425588999999506 Q gi|254780346|r 83 CDVIAHAVTRGLVDLSINGSLPIGNGIVVVDSEQQAFDRVS 123 (149) Q Consensus 83 ~e~I~~~v~~gl~~lsl~~~~PI~~gILt~~n~~QA~~R~~ 123 (149) .++.--+ -+.++|+..+|.........|+.+. T Consensus 144 --------~~~~~~l-~~lnVPvl~~i~~~~~s~~~W~~s~ 175 (1064) T pfam02514 144 --------ENGVELL-KKLDVPVLQAIPLYFQSREEWEASS 175 (1064) T ss_pred --------HHHHHHH-HHCCCCEEEEEECCCCCHHHHHHCC T ss_conf --------1677899-8779988997525899999997388 No 124 >COG2039 Pcp Pyrrolidone-carboxylate peptidase (N-terminal pyroglutamyl peptidase) [Posttranslational modification, protein turnover, chaperones] Probab=53.11 E-value=17 Score=17.96 Aligned_cols=41 Identities=20% Similarity=0.261 Sum_probs=36.6 Q ss_pred HHHHHHHHHHHHHHHHHHCCCCCEEEEECCC-CHHHHHHHHC Q ss_conf 6789999999999999743997056542558-8999999506 Q gi|254780346|r 83 CDVIAHAVTRGLVDLSINGSLPIGNGIVVVD-SEQQAFDRVS 123 (149) Q Consensus 83 ~e~I~~~v~~gl~~lsl~~~~PI~~gILt~~-n~~QA~~R~~ 123 (149) --|+||.++.+++...-+++-|+-.|-+-+. +.+||..+-+ T Consensus 138 GTyvCNhvmY~~l~~~~~~~~~~~~GFiHvPy~peqa~~~~~ 179 (207) T COG2039 138 GTYVCNHVMYGLLHHLAKKGPPVRAGFIHVPYLPEQAARKPN 179 (207) T ss_pred CHHHHHHHHHHHHHHHHHHCCCCCCEEEEECCCHHHHHCCCC T ss_conf 142247899999999997488876515760678899817999 No 125 >cd06322 PBP1_ABC_sugar_binding_like_12 Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems. This group includes the periplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily, which consist of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis. Probab=52.52 E-value=21 Score=17.41 Aligned_cols=117 Identities=15% Similarity=0.160 Sum_probs=53.8 Q ss_pred CEEEEEEECHHHHHHHHHHHHHHHHHHHCCCCEEEEEHHHHHHHHHH---HHHHHHHHHCCCCCCEEEEEEEEECCCCCH Q ss_conf 71799980312899999999999999987995555530014422699---999986331137853566541200066524 Q gi|254780346|r 6 PHVLIIEARFYENLSAMLFEGCVNVLHSRAVQWSSIVTPGVLEIPAA---VSMVMNAKTRSVTYDGIIVLGVVMRGKTAH 82 (149) Q Consensus 6 ~kI~IV~s~~~~~i~~~ll~ga~~~l~~~~~~~~~i~VPGa~EiP~a---~~~~~~~~~~~~~~D~vIaLG~VIkGeT~H 82 (149) .+|+++...-.... ..=++|+.+.|.++. ..+.+.+...+..+-+ .+.++. ...++||++|. T Consensus 122 ~~i~~i~~~~~~~~-~~R~~Gf~~al~~~~-~~~~~~~~~~~~~~~~~~~~~~~L~---~~p~~~aI~~~---------- 186 (267) T cd06322 122 GQVAIIDYPTVQSV-VDRVRGFKEALADYP-NIKIVAVQPGITRAEALTAAQNILQ---ANPDLDGIFAF---------- 186 (267) T ss_pred CEEEEEECCCCHHH-HHHHHHHHHHHHHCC-CCEEEEEECCCCHHHHHHHHHHHHH---HCCCCCEEEEC---------- T ss_conf 45999917997369-999999999999779-9469998357887999999999986---28777489981---------- Q ss_pred HHHHHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHH---CCC-------CCCCHHHHHHHHHHHHH Q ss_conf 6789999999999999743997056542558899999950---656-------57456999999999999 Q gi|254780346|r 83 CDVIAHAVTRGLVDLSINGSLPIGNGIVVVDSEQQAFDRV---SPS-------HLDRGGCAARSALAMIE 142 (149) Q Consensus 83 ~e~I~~~v~~gl~~lsl~~~~PI~~gILt~~n~~QA~~R~---~~~-------~~nkG~eaa~Aal~mi~ 142 (149) .|.++-.+.+++.+..++ ++ .|++.++..+|..-. ++. ...-|+.|++.++++++ T Consensus 187 nD~~A~Ga~~al~~~g~~-di----~vvGfD~~~~a~~~i~~~~p~~ttv~Q~~~~~G~~av~~l~~~i~ 251 (267) T cd06322 187 GDDAALGAVSAIKAAGRD-NV----KVIGFDGMPEARKAVDGEPPFVAVIRQYPDQMGKKAIDAAADVLN 251 (267) T ss_pred CCHHHHHHHHHHHHCCCC-CC----EEEEECCCHHHHHHHHHCCCCEEEEECCHHHHHHHHHHHHHHHHC T ss_conf 879999999999975999-98----899994949999999708987899968999999999999999977 No 126 >cd06318 PBP1_ABC_sugar_binding_like_9 Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems. Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily, which consists of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis. Probab=52.26 E-value=21 Score=17.38 Aligned_cols=32 Identities=9% Similarity=-0.001 Sum_probs=16.2 Q ss_pred EEEEEEECHHHHHHHHHHHHHHHHHHHCCCCE Q ss_conf 17999803128999999999999999879955 Q gi|254780346|r 7 HVLIIEARFYENLSAMLFEGCVNVLHSRAVQW 38 (149) Q Consensus 7 kI~IV~s~~~~~i~~~ll~ga~~~l~~~~~~~ 38 (149) ||+++........-..+.+|+.+..++.|++. T Consensus 1 kIG~~~~~~~npf~~~~~~g~~~~a~~~G~~v 32 (282) T cd06318 1 KIGFSQYTLNSPFFAALTEAAKAHAKALGYEL 32 (282) T ss_pred CEEEEECCCCCHHHHHHHHHHHHHHHHCCCEE T ss_conf 98999489989799999999999999729999 No 127 >PRK10653 D-ribose transporter subunit RbsB; Provisional Probab=51.86 E-value=21 Score=17.34 Aligned_cols=37 Identities=5% Similarity=0.069 Sum_probs=26.3 Q ss_pred CCEEEEEEECHHHHHHHHHHHHHHHHHHHCCCCEEEE Q ss_conf 8717999803128999999999999999879955555 Q gi|254780346|r 5 IPHVLIIEARFYENLSAMLFEGCVNVLHSRAVQWSSI 41 (149) Q Consensus 5 ~~kI~IV~s~~~~~i~~~ll~ga~~~l~~~~~~~~~i 41 (149) .+-|++|........-..+++|+.+.++++|++.-.. T Consensus 26 ~~TIgvivp~i~npff~~v~~gie~~a~~~Gy~l~v~ 62 (295) T PRK10653 26 KDTIALVVSTLNNPFFVSLKDGAQKEADKLGYNLVVL 62 (295) T ss_pred CCEEEEEECCCCCHHHHHHHHHHHHHHHHCCCEEEEE T ss_conf 9979999489879799999999999999769989998 No 128 >PRK05183 hscA chaperone protein HscA; Provisional Probab=51.58 E-value=11 Score=19.24 Aligned_cols=89 Identities=17% Similarity=0.254 Sum_probs=49.3 Q ss_pred HHHHHHHHHHHHHHHHHCCCCEE----EEEHHHHHHHHHHHHHHHHHHH----CCCCCCEEEEEEEEECCCCCHHHHHHH Q ss_conf 89999999999999998799555----5530014422699999986331----137853566541200066524678999 Q gi|254780346|r 17 ENLSAMLFEGCVNVLHSRAVQWS----SIVTPGVLEIPAAVSMVMNAKT----RSVTYDGIIVLGVVMRGKTAHCDVIAH 88 (149) Q Consensus 17 ~~i~~~ll~ga~~~l~~~~~~~~----~i~VPGa~EiP~a~~~~~~~~~----~~~~~D~vIaLG~VIkGeT~H~e~I~~ 88 (149) .++.++.+.-+...|+++++..+ ++-|=|+--+|..-+.+-+... .+-++|-+||+|+-|.+.-- +. T Consensus 310 ~~L~~rt~~~v~~aL~dA~l~~~dId~ViLVGGSTRiP~Vq~~v~~~Fgk~~~~~inPDeaVA~GAAiQa~iL-----~g 384 (621) T PRK05183 310 APLVKRTLLACRRALRDAGVEADEVLEVVMVGGSTRVPLVREAVGEFFGRTPLTSIDPDKVVALGAAIQADIL-----AG 384 (621) T ss_pred HHHHHHHHHHHHHHHHHHCCCHHHCEEEEEECCCCCCHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHH-----CC T ss_conf 9999999999999998713683002099992885456689999999859896668990168887699999986-----28 Q ss_pred HHHHHHHHHHHHCCCCCEEEEECC Q ss_conf 999999999974399705654255 Q gi|254780346|r 89 AVTRGLVDLSINGSLPIGNGIVVV 112 (149) Q Consensus 89 ~v~~gl~~lsl~~~~PI~~gILt~ 112 (149) ... ..++-+---+|...||=|. T Consensus 385 ~~~--~~~~lllDV~PlSLGIEt~ 406 (621) T PRK05183 385 NKP--DSDMLLLDVIPLSLGLETM 406 (621) T ss_pred CCC--CCCEEEEEECCCCEEEEEC T ss_conf 976--6706999612541356862 No 129 >PRK01433 hscA chaperone protein HscA; Provisional Probab=51.43 E-value=12 Score=18.81 Aligned_cols=88 Identities=14% Similarity=0.168 Sum_probs=51.5 Q ss_pred HHHHHHHHHHHHHHHHHCCCC-E-EEEEHHHHHHHHHHHHHHHHHHH----CCCCCCEEEEEEEEECCCCCHHHHHHHHH Q ss_conf 899999999999999987995-5-55530014422699999986331----13785356654120006652467899999 Q gi|254780346|r 17 ENLSAMLFEGCVNVLHSRAVQ-W-SSIVTPGVLEIPAAVSMVMNAKT----RSVTYDGIIVLGVVMRGKTAHCDVIAHAV 90 (149) Q Consensus 17 ~~i~~~ll~ga~~~l~~~~~~-~-~~i~VPGa~EiP~a~~~~~~~~~----~~~~~D~vIaLG~VIkGeT~H~e~I~~~v 90 (149) .++.++.++-+.+.|.+.+.+ + +++-|=|+--+|..-+.+-+... .+-++|-+||+|+-|.+..- +.. T Consensus 287 ~~L~~r~~~~v~~~L~~a~~~dId~ViLVGGsTRiP~Vq~~l~~~Fg~~~~~~inPDEaVA~GAAiqa~~L-----~~~- 360 (595) T PRK01433 287 LPLVERTINIAQECLEQAGNPNIDGVILVGGATRIPLIKDELYKAFKVDILSDIDPDKAVVWGAALQAENL-----IAP- 360 (595) T ss_pred HHHHHHHHHHHHHHHHHCCCCCCCEEEEECCCCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHH-----CCC- T ss_conf 99999999999999997693535548996785545899999999858997789784789999899987764-----377- Q ss_pred HHHHHHHHHHCCCCCEEEEECCC Q ss_conf 99999999743997056542558 Q gi|254780346|r 91 TRGLVDLSINGSLPIGNGIVVVD 113 (149) Q Consensus 91 ~~gl~~lsl~~~~PI~~gILt~~ 113 (149) ..++-+---+|...||=|.. T Consensus 361 ---~~~~~llDV~PlSLGiEt~g 380 (595) T PRK01433 361 ---HTNSLLIDVVPLSLGMELYG 380 (595) T ss_pred ---CCCEEEEEECCCCEEEEECC T ss_conf ---66539999517636899749 No 130 >CHL00094 dnaK heat shock protein 70 Probab=51.21 E-value=16 Score=18.12 Aligned_cols=88 Identities=18% Similarity=0.255 Sum_probs=49.3 Q ss_pred HHHHHHHHHHHHHHHHHCCCCE---E-EEEHHHHHHHHHHHHHHHHHHH----CCCCCCEEEEEEEEECCCCCHHHHHHH Q ss_conf 8999999999999999879955---5-5530014422699999986331----137853566541200066524678999 Q gi|254780346|r 17 ENLSAMLFEGCVNVLHSRAVQW---S-SIVTPGVLEIPAAVSMVMNAKT----RSVTYDGIIVLGVVMRGKTAHCDVIAH 88 (149) Q Consensus 17 ~~i~~~ll~ga~~~l~~~~~~~---~-~i~VPGa~EiP~a~~~~~~~~~----~~~~~D~vIaLG~VIkGeT~H~e~I~~ 88 (149) .++.++..+-+.+.|.+.++.. + ++-|=|+-.+|..-+.+-+... .+-++|-.||+||-|++... +. T Consensus 305 ~~l~~r~~~~v~~~L~~a~l~~~dId~ViLVGGstRiP~V~~~l~~~fgk~~~~~inpDeaVA~GAAiqa~~l-----s~ 379 (622) T CHL00094 305 SDLIDRCRIPVENALKDAKLDKSDIDEVVLVGGSTRIPAIQELVKSLLGKDPNQSVNPDEVVAIGAAIQAGVL-----AG 379 (622) T ss_pred HHHHHHHHHHHHHHHHHCCCCHHHCEEEEEECCCCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHH-----CC T ss_conf 9999999999999999819998894399993881256789999999858996779681589999899986765-----48 Q ss_pred HHHHHHHHHHHHCCCCCEEEEECCC Q ss_conf 9999999999743997056542558 Q gi|254780346|r 89 AVTRGLVDLSINGSLPIGNGIVVVD 113 (149) Q Consensus 89 ~v~~gl~~lsl~~~~PI~~gILt~~ 113 (149) ...++.+.--+|...||=|.. T Consensus 380 ----~~~~~~l~Dv~PlslGie~~g 400 (622) T CHL00094 380 ----EVKDILLLDVTPLSLGVETLG 400 (622) T ss_pred ----CCCCEEEEEEECCCEEEEECC T ss_conf ----655359999844517889729 No 131 >pfam00781 DAGK_cat Diacylglycerol kinase catalytic domain. Diacylglycerol (DAG) is a second messenger that acts as a protein kinase C activator. The catalytic domain is assumed from the finding of bacterial homologues. YegS is the Escherichia coli protein in this family whose crystal structure reveals an active site in the inter-domain cleft formed by four conserved sequence motifs, revealing a novel metal-binding site. The residues of this site are conserved across the family. Probab=50.72 E-value=22 Score=17.23 Aligned_cols=82 Identities=18% Similarity=0.157 Sum_probs=49.0 Q ss_pred HHHHHHHHHCCCCEEEEEHHHHHHHHHHHHHHHHHHHCCCCCCEEEEEEEEECCCCCHHHHHHHHHHHHHHHHHHHCCCC Q ss_conf 99999999879955555300144226999999863311378535665412000665246789999999999999743997 Q gi|254780346|r 25 EGCVNVLHSRAVQWSSIVTPGVLEIPAAVSMVMNAKTRSVTYDGIIVLGVVMRGKTAHCDVIAHAVTRGLVDLSINGSLP 104 (149) Q Consensus 25 ~ga~~~l~~~~~~~~~i~VPGa~EiP~a~~~~~~~~~~~~~~D~vIaLG~VIkGeT~H~e~I~~~v~~gl~~lsl~~~~P 104 (149) +.+.+.|.+.+..++.+.+.+.-... .+.........+|.+++.| ||= --+++.+||+........| T Consensus 18 ~~i~~~l~~~~~~~~~~~t~~~~~~~----~~~~~~~~~~~~d~vv~~G----GDG-----Tv~evvngl~~~~~~~~~p 84 (127) T pfam00781 18 DKVLEKLRKALNEAQVFETEEGGPAV----ALELARALGDFKDLVVVAG----GDG-----TVNEVLNGLAGREDRLKPP 84 (127) T ss_pred HHHHHHHHHCCCCEEEEECCCCCHHH----HHHHHHHHCCCCCEEEEEC----CCC-----HHHHHHHHHHHCCCCCCCC T ss_conf 99999999879975999989888799----9999985235888899988----975-----7999999997468877897 Q ss_pred CEEEEECCCCHHHHHHHH Q ss_conf 056542558899999950 Q gi|254780346|r 105 IGNGIVVVDSEQQAFDRV 122 (149) Q Consensus 105 I~~gILt~~n~~QA~~R~ 122 (149) .|||-.-+-.. +.|+ T Consensus 85 --lgiIP~GTgNd-fa~~ 99 (127) T pfam00781 85 --LGIIPLGTGND-FARA 99 (127) T ss_pred --EEEECCCCHHH-HHHH T ss_conf --89924876758-9998 No 132 >PRK13059 putative lipid kinase; Reviewed Probab=48.50 E-value=24 Score=17.01 Aligned_cols=87 Identities=20% Similarity=0.243 Sum_probs=50.2 Q ss_pred CCEEEEEEECHH-HHHHHHHHHHHHHHHHHCCCCEEEEEHH--HHHHHHHHHHHHHHHHHCCCCCCEEEEEEEEECCCCC Q ss_conf 871799980312-8999999999999999879955555300--1442269999998633113785356654120006652 Q gi|254780346|r 5 IPHVLIIEARFY-ENLSAMLFEGCVNVLHSRAVQWSSIVTP--GVLEIPAAVSMVMNAKTRSVTYDGIIVLGVVMRGKTA 81 (149) Q Consensus 5 ~~kI~IV~s~~~-~~i~~~ll~ga~~~l~~~~~~~~~i~VP--Ga~EiP~a~~~~~~~~~~~~~~D~vIaLG~VIkGeT~ 81 (149) |+|+++|+=.-= ..=..+.++...+.|.++++++..+..+ ++.+. +.+ +....||.+|+.| ||=. T Consensus 1 Mkk~~~I~NP~sG~g~~~~~~~~i~~~l~~~~~~~~~~~t~~~~~~~~--a~~------~~~~~~d~vv~~G----GDGT 68 (294) T PRK13059 1 MKKVKFIYNPYSGENAIISELDKVIEIHQKYGYLVVPYRISLGCDLKE--AFK------DIDESYKYILIAG----GDGT 68 (294) T ss_pred CCEEEEEECCCCCCCCHHHHHHHHHHHHHHCCCEEEEEEEECCCHHHH--HHH------HHHCCCCEEEEEE----CCCH T ss_conf 977999999766886668899999999997798899998535608999--999------8874898899995----6788 Q ss_pred HHHHHHHHHHHHHHHHHHHCCCCCEEEEECC Q ss_conf 4678999999999999974399705654255 Q gi|254780346|r 82 HCDVIAHAVTRGLVDLSINGSLPIGNGIVVV 112 (149) Q Consensus 82 H~e~I~~~v~~gl~~lsl~~~~PI~~gILt~ 112 (149) -++|.+|++.. +.++| .|||-. T Consensus 69 -----inevvngl~~~--~~~~~--lgiiP~ 90 (294) T PRK13059 69 -----VDNVVNAMKKL--NIDIP--IGILPV 90 (294) T ss_pred -----HHHHHHHHHHC--CCCCC--EEEEEC T ss_conf -----99999999856--99985--799826 No 133 >PRK08309 short chain dehydrogenase; Provisional Probab=46.74 E-value=26 Score=16.85 Aligned_cols=88 Identities=6% Similarity=0.112 Sum_probs=42.9 Q ss_pred EEEEEEECHHHHHHHHHHHHHHHHHHHCC-CCEEEEEHH-HHHHHHHH-HHHHHHH----------------------HH Q ss_conf 17999803128999999999999999879-955555300-14422699-9999863----------------------31 Q gi|254780346|r 7 HVLIIEARFYENLSAMLFEGCVNVLHSRA-VQWSSIVTP-GVLEIPAA-VSMVMNA----------------------KT 61 (149) Q Consensus 7 kI~IV~s~~~~~i~~~ll~ga~~~l~~~~-~~~~~i~VP-Ga~EiP~a-~~~~~~~----------------------~~ 61 (149) +|--+..+|+. .+.|-..-.+++++.| ++.-+.|+- .+=+-+.+ ++.+... +. T Consensus 48 ~i~~l~~DY~d--~~~l~~~l~~ai~q~Gp~dl~VaWiHssa~~al~~v~~~l~~~~~~~~l~HVlGS~~~~~~~~~e~~ 125 (182) T PRK08309 48 SITCLPLDYHD--DDAVKLAIKRTIEQNGPITLAVAWIHSSAKDALSVVCRELDLSSETYRLFHVLGSPAKASRIASEKI 125 (182) T ss_pred CEEEEECCCCC--HHHHHHHHHHHHHCCCCCCEEEEEEECCCHHHHHHHHHHHHCCCCCCEEEEEECCCCCCCCCCCCCC T ss_conf 32578746488--6999999999996189856899998357224599999998548998169999468778653510002 Q ss_pred CCCCCCEE-EEEEEEECCCCCH---HHHHHHHHHHHHHH Q ss_conf 13785356-6541200066524---67899999999999 Q gi|254780346|r 62 RSVTYDGI-IVLGVVMRGKTAH---CDVIAHAVTRGLVD 96 (149) Q Consensus 62 ~~~~~D~v-IaLG~VIkGeT~H---~e~I~~~v~~gl~~ 96 (149) .....+-. |.||.++.|+... .|-||+.|..++.. T Consensus 126 ~~~~~~y~~ViLGFv~e~~~sRWLTHeEIS~GVi~Ai~~ 164 (182) T PRK08309 126 GPLRCSYRRVILGFILEDTYSRWLTHEEISDGVIKAIES 164 (182) T ss_pred CCCCCCEEEEEEEEEEECCCCCCCCHHHHHHHHHHHHHC T ss_conf 335786288998889718864146458999999999865 No 134 >COG1597 LCB5 Sphingosine kinase and enzymes related to eukaryotic diacylglycerol kinase [Lipid metabolism / General function prediction only] Probab=44.93 E-value=27 Score=16.67 Aligned_cols=100 Identities=21% Similarity=0.221 Sum_probs=59.9 Q ss_pred CCCEEEEEEECHH-HHHHHHHHHHHHHHHHHCCCCEEEEEHHHHHHHHHHHHHHHHHHHCCCCCCEEEEEEEEECCCCCH Q ss_conf 5871799980312-899999999999999987995555530014422699999986331137853566541200066524 Q gi|254780346|r 4 FIPHVLIIEARFY-ENLSAMLFEGCVNVLHSRAVQWSSIVTPGVLEIPAAVSMVMNAKTRSVTYDGIIVLGVVMRGKTAH 82 (149) Q Consensus 4 ~~~kI~IV~s~~~-~~i~~~ll~ga~~~l~~~~~~~~~i~VPGa~EiP~a~~~~~~~~~~~~~~D~vIaLG~VIkGeT~H 82 (149) +|+|+.++.-... ....+..+..+.+.|.+.+.+.....+-..=+..-.++.+ ....||.+|+.| | T Consensus 1 ~~~~~~~i~Np~sG~~~~~~~~~~~~~~l~~~g~~~~~~~t~~~g~a~~~a~~a-----~~~~~D~via~G----G---- 67 (301) T COG1597 1 RMKKALLIYNPTSGKGKAKKLLREVEELLEEAGHELSVRVTEEAGDAIEIAREA-----AVEGYDTVIAAG----G---- 67 (301) T ss_pred CCCEEEEEECCCCCCCCHHHHHHHHHHHHHHHCCEEEEEEECCCHHHHHHHHHH-----HHCCCCEEEEEC----C---- T ss_conf 995289998887765005777999999999728646999703752299999998-----645898899963----4---- Q ss_pred HHHHHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHHC Q ss_conf 67899999999999997439970565425588999999506 Q gi|254780346|r 83 CDVIAHAVTRGLVDLSINGSLPIGNGIVVVDSEQQAFDRVS 123 (149) Q Consensus 83 ~e~I~~~v~~gl~~lsl~~~~PI~~gILt~~n~~QA~~R~~ 123 (149) |=.-++|++||.. ...|. .|||-+-+.. .+.|+- T Consensus 68 -DGTv~evingl~~----~~~~~-LgilP~GT~N-dfAr~L 101 (301) T COG1597 68 -DGTVNEVANGLAG----TDDPP-LGILPGGTAN-DFARAL 101 (301) T ss_pred -CCHHHHHHHHHHC----CCCCC-EEEECCCCHH-HHHHHC T ss_conf -8879999988733----79981-7993486577-889985 No 135 >PRK06490 glutamine amidotransferase; Provisional Probab=44.47 E-value=28 Score=16.63 Aligned_cols=100 Identities=13% Similarity=0.074 Sum_probs=65.7 Q ss_pred CCCEEEEEEECHHHHHHHHHHHHHHHHHHHCCCCEEEEEHHHHHHHHHHHHHHHHHHHCCCCCCEEEEEEEEECCCCCHH Q ss_conf 58717999803128999999999999999879955555300144226999999863311378535665412000665246 Q gi|254780346|r 4 FIPHVLIIEARFYENLSAMLFEGCVNVLHSRAVQWSSIVTPGVLEIPAAVSMVMNAKTRSVTYDGIIVLGVVMRGKTAHC 83 (149) Q Consensus 4 ~~~kI~IV~s~~~~~i~~~ll~ga~~~l~~~~~~~~~i~VPGa~EiP~a~~~~~~~~~~~~~~D~vIaLG~VIkGeT~H~ 83 (149) .++||+||.-.=.+.- .-..+.|.+.|++.++++..---++|- .-..|||+|.+|-=.- -.+-+ T Consensus 10 ~~k~vLviqH~~~e~p-----G~i~~~L~~~G~~~~i~r~~~gd~lP~----------~l~~~dglvVlGGpms-a~D~~ 73 (243) T PRK06490 10 DKRPILIVLHQERSTP-----GRVGQLLRERGYPLDIRRPRLGDPLPE----------TLEDHAGAVIFGGPMS-ANDPD 73 (243) T ss_pred CCCCEEEEECCCCCCC-----HHHHHHHHHCCCEEEEEECCCCCCCCC----------CCCCCCEEEEECCCCC-CCCCC T ss_conf 8985799966899997-----299999997898589996789998999----------7546058999289999-89987 Q ss_pred HHHHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHHCCC Q ss_conf 789999999999999743997056542558899999950656 Q gi|254780346|r 84 DVIAHAVTRGLVDLSINGSLPIGNGIVVVDSEQQAFDRVSPS 125 (149) Q Consensus 84 e~I~~~v~~gl~~lsl~~~~PI~~gILt~~n~~QA~~R~~~~ 125 (149) .++..+. .+.+-.++.++|+.-==|. .|.+.|+-+. T Consensus 74 p~l~~e~--~~I~~~l~~~~P~LGICLG----aQLlA~alGg 109 (243) T PRK06490 74 DFIRREI--DWISVPLKENKPFLGICLG----AQMLARHLGA 109 (243) T ss_pred CHHHHHH--HHHHHHHHCCCCEEEECHH----HHHHHHHHCC T ss_conf 1799999--9999999869988998884----9999998398 No 136 >cd06307 PBP1_uncharacterized_sugar_binding Periplasmic sugar-binding domain of uncharacterized transport systems. Periplasmic sugar-binding domain of uncharacterized transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein (PBP1) superfamily. The members of this group are predicted to be involved in the transport of sugar-containing molecules across cellular and organellar membranes. Probab=43.90 E-value=28 Score=16.57 Aligned_cols=30 Identities=3% Similarity=-0.165 Sum_probs=16.5 Q ss_pred EEEEEEECHHHHHHHHHHHHHHHHHHHCCC Q ss_conf 179998031289999999999999998799 Q gi|254780346|r 7 HVLIIEARFYENLSAMLFEGCVNVLHSRAV 36 (149) Q Consensus 7 kI~IV~s~~~~~i~~~ll~ga~~~l~~~~~ 36 (149) ||+++..+.+...-..+.+|+.+..++.+. T Consensus 1 kIgvv~~~~~npF~~~i~~Gie~aa~~~~~ 30 (275) T cd06307 1 RLGFLLPKGSNAFYRELAAALEAAAAAFPD 30 (275) T ss_pred CEEEEECCCCCHHHHHHHHHHHHHHHHCCC T ss_conf 989995799996999999999999986568 No 137 >PRK00861 putative lipid kinase; Reviewed Probab=42.76 E-value=30 Score=16.47 Aligned_cols=90 Identities=14% Similarity=0.153 Sum_probs=45.1 Q ss_pred CCCEEEEEEECHH-HHHHHHHHHHHHHHHHHCCCCEEEEEHHHHHHHHHHHHHHHHHHHCCCCCCEEEEEEEEECCCCCH Q ss_conf 5871799980312-899999999999999987995555530014422699999986331137853566541200066524 Q gi|254780346|r 4 FIPHVLIIEARFY-ENLSAMLFEGCVNVLHSRAVQWSSIVTPGVLEIPAAVSMVMNAKTRSVTYDGIIVLGVVMRGKTAH 82 (149) Q Consensus 4 ~~~kI~IV~s~~~-~~i~~~ll~ga~~~l~~~~~~~~~i~VPGa~EiP~a~~~~~~~~~~~~~~D~vIaLG~VIkGeT~H 82 (149) |++|+++|+=..= ..-....+....+.|. .+++++++.+...-+.. .+.+. +....||.+|+.| ||=. T Consensus 1 M~kr~~~IvNP~aG~g~~~~~~~~i~~~l~-~~~~~~v~~T~~~~~a~----~la~~-a~~~~~d~vv~~G----GDGT- 69 (296) T PRK00861 1 MTRSACLIFNPVAGQGNPEVDLALIRAILQ-PEMDLDIYLTTPEIGAD----ALAQE-AVERGAELIIASG----GDGT- 69 (296) T ss_pred CCEEEEEEECCCCCCCCHHHHHHHHHHHHH-CCCCEEEEEECCCCCHH----HHHHH-HHHCCCCEEEEEC----CHHH- T ss_conf 970799999867899864657999999997-29968999957888699----99999-9867998999988----8189- Q ss_pred HHHHHHHHHHHHHHHHHHCCCCCEEEEECCCC Q ss_conf 67899999999999997439970565425588 Q gi|254780346|r 83 CDVIAHAVTRGLVDLSINGSLPIGNGIVVVDS 114 (149) Q Consensus 83 ~e~I~~~v~~gl~~lsl~~~~PI~~gILt~~n 114 (149) -++|.++++ ..++| .||+-..| T Consensus 70 ----v~ev~~gl~----~~~~~--lgiiP~GT 91 (296) T PRK00861 70 ----ISAVAGALI----GTDIP--LGIIPRGT 91 (296) T ss_pred ----HHHHHHHHC----CCCCC--EEEEECCC T ss_conf ----999997533----58961--69980766 No 138 >COG0400 Predicted esterase [General function prediction only] Probab=40.81 E-value=32 Score=16.28 Aligned_cols=49 Identities=16% Similarity=0.082 Sum_probs=23.7 Q ss_pred CCCCEEEEEEECHHHHHHHHHHHHHHHHHHHCCCCEEEEEHHHHHHHHH Q ss_conf 6587179998031289999999999999998799555553001442269 Q gi|254780346|r 3 VFIPHVLIIEARFYENLSAMLFEGCVNVLHSRAVQWSSIVTPGVLEIPA 51 (149) Q Consensus 3 ~~~~kI~IV~s~~~~~i~~~ll~ga~~~l~~~~~~~~~i~VPGa~EiP~ 51 (149) +...+|++.....-+-+--.+-..+.+.|...|.+++..+.++.-|||. T Consensus 144 ~~~~pill~hG~~Dpvvp~~~~~~l~~~l~~~g~~v~~~~~~~GH~i~~ 192 (207) T COG0400 144 LAGTPILLSHGTEDPVVPLALAEALAEYLTASGADVEVRWHEGGHEIPP 192 (207) T ss_pred CCCCEEEEECCCCCCCCCHHHHHHHHHHHHHCCCCEEEEEECCCCCCCH T ss_conf 4797288714676884688899999999998199779998368886899 No 139 >PRK08782 consensus Probab=40.79 E-value=32 Score=16.28 Aligned_cols=87 Identities=14% Similarity=0.148 Sum_probs=63.1 Q ss_pred HHHHHHHCCCCEEEE--EHHHHHHHHHHHHHHHHHHHCCCCCCEEEEEEEEECCCCCHHH-------HHHHHHHHHHHHH Q ss_conf 999999879955555--3001442269999998633113785356654120006652467-------8999999999999 Q gi|254780346|r 27 CVNVLHSRAVQWSSI--VTPGVLEIPAAVSMVMNAKTRSVTYDGIIVLGVVMRGKTAHCD-------VIAHAVTRGLVDL 97 (149) Q Consensus 27 a~~~l~~~~~~~~~i--~VPGa~EiP~a~~~~~~~~~~~~~~D~vIaLG~VIkGeT~H~e-------~I~~~v~~gl~~l 97 (149) ..+.|.+.|+..-.| +.|+++|+- +.+.+ ..+|..+-.|.|+..|+-+.= .||-.....+.+. T Consensus 34 ~~eal~~gGi~~iEiTlrt~~a~~~i---~~l~~-----~~p~~~vGaGTV~~~e~~~~a~~aGA~FiVSP~~~~~v~~~ 105 (219) T PRK08782 34 VADALLEGGLPAIELTLRTPVAIEAL---AMLKR-----ELPNIVIGAGTVLSERQLRQSVDAGADFLVTPGTPAPLARL 105 (219) T ss_pred HHHHHHHCCCCEEEEECCCCHHHHHH---HHHHH-----HCCCCEEEEEEECCHHHHHHHHHCCCCEEECCCCCHHHHHH T ss_conf 99999987998799967993399999---99998-----68994799997058999999998499899878997999999 Q ss_pred HHHCCCCCEEEEECCCCHHHHHHH Q ss_conf 974399705654255889999995 Q gi|254780346|r 98 SINGSLPIGNGIVVVDSEQQAFDR 121 (149) Q Consensus 98 sl~~~~PI~~gILt~~n~~QA~~R 121 (149) +.+.++|.+-|+.|+....+|++. T Consensus 106 a~~~~i~~iPGv~TpSEi~~A~~~ 129 (219) T PRK08782 106 LADAPIPAVPGAATPTELLTLMGL 129 (219) T ss_pred HHHCCCCEECCCCCHHHHHHHHHC T ss_conf 998199764785999999999987 No 140 >PRK11914 diacylglycerol kinase; Reviewed Probab=39.10 E-value=34 Score=16.11 Aligned_cols=90 Identities=20% Similarity=0.262 Sum_probs=50.8 Q ss_pred CCCCEEEEEEECHH-HHHHHHHHHHHHHHHHHCCCCEEEEEHHHHHHHHHHHHHHHHHHHCCCCCCEEEEEEEEECCCCC Q ss_conf 65871799980312-89999999999999998799555553001442269999998633113785356654120006652 Q gi|254780346|r 3 VFIPHVLIIEARFY-ENLSAMLFEGCVNVLHSRAVQWSSIVTPGVLEIPAAVSMVMNAKTRSVTYDGIIVLGVVMRGKTA 81 (149) Q Consensus 3 ~~~~kI~IV~s~~~-~~i~~~ll~ga~~~l~~~~~~~~~i~VPGa~EiP~a~~~~~~~~~~~~~~D~vIaLG~VIkGeT~ 81 (149) ..|+|+++|+=..= ..-..+..+...+.|.+.+++++....-+.-+.- .+.+. +....||.+|+.| ||=. T Consensus 4 ~~m~kv~vIvNP~aG~g~~~~~~~~i~~~l~~~g~~~~~~~t~~~~~a~----~la~~-a~~~g~d~vv~~G----GDGT 74 (304) T PRK11914 4 HEIGKVTVLTNPLSGHGAAPHAAERAIARLHHRGVDVVEIVGTDAHHAR----HLVAA-ALAKGTDALVVVG----GDGV 74 (304) T ss_pred CCCCEEEEEECCCCCCCCHHHHHHHHHHHHHHCCCCEEEEECCCHHHHH----HHHHH-HHHCCCCEEEEEE----CCHH T ss_conf 4586699999977799856889999999999879909999327878999----99998-8864996999995----6259 Q ss_pred HHHHHHHHHHHHHHHHHHHCCCCCEEEEECC Q ss_conf 4678999999999999974399705654255 Q gi|254780346|r 82 HCDVIAHAVTRGLVDLSINGSLPIGNGIVVV 112 (149) Q Consensus 82 H~e~I~~~v~~gl~~lsl~~~~PI~~gILt~ 112 (149) -+++.+++. +.++| .||+-. T Consensus 75 -----v~ev~~~l~----~~~~p--lgiiP~ 94 (304) T PRK11914 75 -----ISNALQVLA----GTDIP--LGIIPA 94 (304) T ss_pred -----HHHHHHHHC----CCCCE--EEEECC T ss_conf -----889876413----57860--899638 No 141 >KOG3857 consensus Probab=39.07 E-value=34 Score=16.11 Aligned_cols=67 Identities=18% Similarity=0.313 Sum_probs=40.1 Q ss_pred CEEEEEEECHHHHHHHHHHHHHHHHHHHCCCCEEEEE---H-HHHHHHHHHHHHHHHHHHCCCCCCEEEEEEEEECCCCC Q ss_conf 7179998031289999999999999998799555553---0-01442269999998633113785356654120006652 Q gi|254780346|r 6 PHVLIIEARFYENLSAMLFEGCVNVLHSRAVQWSSIV---T-PGVLEIPAAVSMVMNAKTRSVTYDGIIVLGVVMRGKTA 81 (149) Q Consensus 6 ~kI~IV~s~~~~~i~~~ll~ga~~~l~~~~~~~~~i~---V-PGa~EiP~a~~~~~~~~~~~~~~D~vIaLG~VIkGeT~ 81 (149) +|.++|.-.=- +--.+.+-+++.|.+.++++++++ + |-.=-.-.+++. +++..||.+|++| |... T Consensus 71 Kk~llvTDkni--~~~~~~~~a~~~L~~~~I~~~vyD~v~~ePtv~s~~~alef-----ak~~~fDs~vaiG----GGSa 139 (465) T KOG3857 71 KKTLLVTDKNI--AKLGLVKVAQDSLEENGINVEVYDKVQPEPTVGSVTAALEF-----AKKKNFDSFVAIG----GGSA 139 (465) T ss_pred CCEEEEECCCH--HHCCCHHHHHHHHHHCCCCEEEECCCCCCCCHHHHHHHHHH-----HHHCCCCEEEEEC----CCCH T ss_conf 42589607774--44141789999999759816972476479862349999999-----8733665589876----8504 Q ss_pred HH Q ss_conf 46 Q gi|254780346|r 82 HC 83 (149) Q Consensus 82 H~ 83 (149) |. T Consensus 140 ~D 141 (465) T KOG3857 140 HD 141 (465) T ss_pred HH T ss_conf 55 No 142 >COG0800 Eda 2-keto-3-deoxy-6-phosphogluconate aldolase [Carbohydrate transport and metabolism] Probab=38.77 E-value=29 Score=16.51 Aligned_cols=87 Identities=15% Similarity=0.178 Sum_probs=60.6 Q ss_pred HHHHHHHCCCCE-EE-EEHHHHHHHHHHHHHHHHHHHCCCCCCEEEEEEEEECCCCCHHH-------HHHHHHHHHHHHH Q ss_conf 999999879955-55-53001442269999998633113785356654120006652467-------8999999999999 Q gi|254780346|r 27 CVNVLHSRAVQW-SS-IVTPGVLEIPAAVSMVMNAKTRSVTYDGIIVLGVVMRGKTAHCD-------VIAHAVTRGLVDL 97 (149) Q Consensus 27 a~~~l~~~~~~~-~~-i~VPGa~EiP~a~~~~~~~~~~~~~~D~vIaLG~VIkGeT~H~e-------~I~~~v~~gl~~l 97 (149) ..+.|-+.|+.. ++ .++|.++|.--.+... ..+++|--|.|..-++-.-- .||-.....+.+. T Consensus 30 ~a~Ali~gGi~~IEITl~sp~a~e~I~~l~~~--------~p~~lIGAGTVL~~~q~~~a~~aGa~fiVsP~~~~ev~~~ 101 (211) T COG0800 30 LAKALIEGGIPAIEITLRTPAALEAIRALAKE--------FPEALIGAGTVLNPEQARQAIAAGAQFIVSPGLNPEVAKA 101 (211) T ss_pred HHHHHHHCCCCEEEEECCCCCHHHHHHHHHHH--------CCCCEECCCCCCCHHHHHHHHHCCCCEEECCCCCHHHHHH T ss_conf 99999976987699964798789999999986--------7465882455669999999998599789899999999999 Q ss_pred HHHCCCCCEEEEECCCCHHHHHHH Q ss_conf 974399705654255889999995 Q gi|254780346|r 98 SINGSLPIGNGIVVVDSEQQAFDR 121 (149) Q Consensus 98 sl~~~~PI~~gILt~~n~~QA~~R 121 (149) ..++++|++=|+.|+--..+|++. T Consensus 102 a~~~~ip~~PG~~TptEi~~Ale~ 125 (211) T COG0800 102 ANRYGIPYIPGVATPTEIMAALEL 125 (211) T ss_pred HHHCCCCCCCCCCCHHHHHHHHHC T ss_conf 986799636887998999999980 No 143 >PRK00286 xseA exodeoxyribonuclease VII large subunit; Reviewed Probab=38.62 E-value=34 Score=16.07 Aligned_cols=89 Identities=20% Similarity=0.238 Sum_probs=54.7 Q ss_pred CCEEEEEEECHHHHHHHHHHHHHHHHHHHCCC--CEEEE--EHHHH---HHHHHHHHHHHHHHHCCCCCCEEEEEEEEEC Q ss_conf 87179998031289999999999999998799--55555--30014---4226999999863311378535665412000 Q gi|254780346|r 5 IPHVLIIEARFYENLSAMLFEGCVNVLHSRAV--QWSSI--VTPGV---LEIPAAVSMVMNAKTRSVTYDGIIVLGVVMR 77 (149) Q Consensus 5 ~~kI~IV~s~~~~~i~~~ll~ga~~~l~~~~~--~~~~i--~VPGa---~EiP~a~~~~~~~~~~~~~~D~vIaLG~VIk 77 (149) -.||+||.|. +-.-+......+.+..- ++..+ .|-|. -||--+++.+ ....+||.+| |+| T Consensus 135 P~~IgvITS~-----tgAa~~Di~~~~~~R~p~~~i~l~p~~VQG~~A~~~I~~ai~~~----~~~~~~DvII----i~R 201 (443) T PRK00286 135 PKRIGVITSP-----TGAAIRDILTVLSRRFPSVEVIIYPTLVQGEGAAASIVEAIERA----NARGEVDVLI----VAR 201 (443) T ss_pred CCEEEEEECC-----CHHHHHHHHHHHHCCCCCEEEEEEECCCCHHHHHHHHHHHHHHH----HHHCCCCEEE----EEC T ss_conf 5579998368-----43899999999850499659999814562654799999999998----5224888899----936 Q ss_pred CCCCHHHHHH---HHHHHHHHHHHHHCCCCCEEEEE Q ss_conf 6652467899---99999999999743997056542 Q gi|254780346|r 78 GKTAHCDVIA---HAVTRGLVDLSINGSLPIGNGIV 110 (149) Q Consensus 78 GeT~H~e~I~---~~v~~gl~~lsl~~~~PI~~gIL 110 (149) |.=+--|+-| ..+++++ .+..+||+.||= T Consensus 202 GGGS~eDL~~FNdE~varaI----~~s~iPVISaIG 233 (443) T PRK00286 202 GGGSLEDLWAFNDEAVARAI----AASKIPVISAVG 233 (443) T ss_pred CCCCHHHHHHCCCHHHHHHH----HHCCCCEEECCC T ss_conf 87888897651879999999----848997895146 No 144 >COG1879 RbsB ABC-type sugar transport system, periplasmic component [Carbohydrate transport and metabolism] Probab=38.61 E-value=34 Score=16.07 Aligned_cols=65 Identities=8% Similarity=0.113 Sum_probs=45.2 Q ss_pred CEEEEEEECHHHHHHHHHHHHHHHHHHHCCCCEEEEEHHHHHHHHHHHHHHHHHHHCCCCCCEEEEE Q ss_conf 7179998031289999999999999998799555553001442269999998633113785356654 Q gi|254780346|r 6 PHVLIIEARFYENLSAMLFEGCVNVLHSRAVQWSSIVTPGVLEIPAAVSMVMNAKTRSVTYDGIIVL 72 (149) Q Consensus 6 ~kI~IV~s~~~~~i~~~ll~ga~~~l~~~~~~~~~i~VPGa~EiP~a~~~~~~~~~~~~~~D~vIaL 72 (149) .+|+++...-.......|.+|+.+..++.|.......+++-+..+.-++.+-+. ...++|+++.- T Consensus 34 ~~i~~~~~~~~~~f~~~~~~g~~~~a~~~g~~~~~~~~~~~~d~~~Q~~~i~~~--ia~~~daIiv~ 98 (322) T COG1879 34 KTIGVVVPTLGNPFFQAVRKGAEAAAKKLGVVVAVVIADAQNDVAKQIAQIEDL--IAQGVDAIIIN 98 (322) T ss_pred CEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCCCCHHHHHHHHHHH--HHCCCCEEEEE T ss_conf 879999477888189999999999998649955897157888819999999999--85599889992 No 145 >cd06334 PBP1_ABC_ligand_binding_like_1 Type I periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type active transport systems that are predicted to be involved in transport of amino acids, peptides, or inorganic ions. This subgroup includes the type I periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type active transport systems that are predicted to be involved in transport of amino acids, peptides, or inorganic ions. Members of this group are sequence-similar to members of the family of ABC-type hydrophobic amino acid transporters, such as leucine-isoleucine-valine-binding protein (LIVBP); however their ligand specificity has not been determined experimentally. Probab=38.25 E-value=35 Score=16.03 Aligned_cols=65 Identities=11% Similarity=0.031 Sum_probs=45.5 Q ss_pred CCCCEEEEEEECHHHHHHHHHHHHHHHHHHHCCCCEEE--EEHHHHHHHHHHHHHHHHHHHCCCCCCEEEEEEE Q ss_conf 65871799980312899999999999999987995555--5300144226999999863311378535665412 Q gi|254780346|r 3 VFIPHVLIIEARFYENLSAMLFEGCVNVLHSRAVQWSS--IVTPGVLEIPAAVSMVMNAKTRSVTYDGIIVLGV 74 (149) Q Consensus 3 ~~~~kI~IV~s~~~~~i~~~ll~ga~~~l~~~~~~~~~--i~VPGa~EiP~a~~~~~~~~~~~~~~D~vIaLG~ 74 (149) +..+||++|...+ +......+.+.+.+++.|+++-. ..-||.-+.-..+.++. ..++|+++..|. T Consensus 138 ~~~kkva~v~~d~--~~G~~~~~~~~~~~~~~G~~vv~~~~~~~~~~Dft~~l~~i~-----~a~pD~V~~~~~ 204 (351) T cd06334 138 LKGKKIALVYHDS--PFGKEPIEALKALAEKLGFEVVLEPVPPPGPNDQKAQWLQIR-----RSGPDYVILWGW 204 (351) T ss_pred CCCCEEEEEECCC--HHHHHHHHHHHHHHHHCCCEEEEEEECCCCCCCHHHHHHHHH-----HCCCCEEEEECC T ss_conf 4887899995686--276899999999999769979888806999835899999999-----769899999377 No 146 >TIGR01182 eda 2-dehydro-3-deoxyphosphogluconate aldolase/4-hydroxy-2-oxoglutarate aldolase; InterPro: IPR000887 4-Hydroxy-2-oxoglutarate aldolase (4.1.3.16 from EC) (KHG-aldolase) catalyzes the interconversion of 4-hydroxy-2-oxoglutarate into pyruvate and glyoxylate. Phospho-2-dehydro-3-deoxygluconate aldolase (4.1.2.14 from EC) (KDPG-aldolase) catalyzes the interconversion of 6-phospho-2-dehydro-3-deoxy-D-gluconate into pyruvate and glyceraldehyde 3-phosphate. These two enzymes are structurally and functionally related . They are both homotrimeric proteins of approximately 220 amino-acid residues. They are class I aldolases whose catalytic mechanism involves the formation of a Schiff-base intermediate between the substrate and the epsilon-amino group of a lysine residue. In both enzymes, an arginine is required for catalytic activity.; GO: 0003824 catalytic activity, 0008152 metabolic process. Probab=37.12 E-value=36 Score=15.92 Aligned_cols=86 Identities=17% Similarity=0.222 Sum_probs=61.3 Q ss_pred HHHHHHCCCCE-EE-EEHHHHHHHHHHHHHHHHHHHCCCCC-CEEEEEEEEECCCCCHHH-------HHHHHHHHHHHHH Q ss_conf 99999879955-55-53001442269999998633113785-356654120006652467-------8999999999999 Q gi|254780346|r 28 VNVLHSRAVQW-SS-IVTPGVLEIPAAVSMVMNAKTRSVTY-DGIIVLGVVMRGKTAHCD-------VIAHAVTRGLVDL 97 (149) Q Consensus 28 ~~~l~~~~~~~-~~-i~VPGa~EiP~a~~~~~~~~~~~~~~-D~vIaLG~VIkGeT~H~e-------~I~~~v~~gl~~l 97 (149) .+.|-+-|+.. |+ +++|.+.|.=- .+ + ...+ |..|--|.|+.=|.-.-= .||=.+..-|.+. T Consensus 26 A~aL~egG~~~~EvTlRT~~A~~aI~---~l-~----~~~P~~~~iGAGTVL~~~Q~~~A~~AGA~F~vSPG~~p~l~~~ 97 (205) T TIGR01182 26 AKALIEGGLRVLEVTLRTPVALEAIR---AL-R----KEVPKDALIGAGTVLNPEQLRQAVAAGAQFIVSPGLTPELAKH 97 (205) T ss_pred HHHHHHCCCEEEEEEECCCCHHHHHH---HH-H----HHCCCCCEECCCCCCCHHHHHHHHHCCCCEEECCCCCHHHHHH T ss_conf 99998679808988514721689999---99-9----7282334871676489899999997089578769788899999 Q ss_pred HHHCCCCCEEEEECCCCHHHHHHH Q ss_conf 974399705654255889999995 Q gi|254780346|r 98 SINGSLPIGNGIVVVDSEQQAFDR 121 (149) Q Consensus 98 sl~~~~PI~~gILt~~n~~QA~~R 121 (149) ..++++|++=||.|+--.+||+++ T Consensus 98 ~~~~~~P~iPGV~tpsEi~~Al~~ 121 (205) T TIGR01182 98 AKDKGIPIIPGVATPSEIMLALEL 121 (205) T ss_pred HHHCCCCEECCCCCHHHHHHHHHC T ss_conf 850888121777687899999875 No 147 >PRK02155 ppnK inorganic polyphosphate/ATP-NAD kinase; Provisional Probab=36.33 E-value=37 Score=15.84 Aligned_cols=103 Identities=18% Similarity=0.155 Sum_probs=59.9 Q ss_pred CCCCCCEEEEEEECHHHHHHHHHHHHHHHHHHHCCCCEEEE-EH---HHHHHHHHHHHHHHHHHHCCCCCCEEEEEEEEE Q ss_conf 96658717999803128999999999999999879955555-30---014422699999986331137853566541200 Q gi|254780346|r 1 MEVFIPHVLIIEARFYENLSAMLFEGCVNVLHSRAVQWSSI-VT---PGVLEIPAAVSMVMNAKTRSVTYDGIIVLGVVM 76 (149) Q Consensus 1 m~~~~~kI~IV~s~~~~~i~~~ll~ga~~~l~~~~~~~~~i-~V---PGa~EiP~a~~~~~~~~~~~~~~D~vIaLG~VI 76 (149) |.-.-+||+||.. .+..-+..++....+.|.++|+++-.- .+ .|.=+.|.. .......+.|-+|++| T Consensus 1 M~~~fk~Vgiv~k-~~~~~~~~~~~~l~~~L~~~g~~v~~e~~~a~~~~~~~~~~~-----~~~~~~~~~Dlvi~lG--- 71 (291) T PRK02155 1 MGSQFRTVALVGR-YQTPGIAEPLEALAACIAKRGFEVVFEADTARNTGLTGYPAL-----TPAEIGARADVAVVLG--- 71 (291) T ss_pred CCCCCCEEEEEEC-CCCHHHHHHHHHHHHHHHHCCCEEEEEHHHHHHCCCCCCCCC-----CHHHHCCCCCEEEEEC--- T ss_conf 9987989999914-898689999999999999788999995557776399887747-----9799463767899976--- Q ss_pred CCCCCHHHHHHHHHHHHHHHHHHHCCCCCE------EEEECCC---CHHHHHHHH Q ss_conf 066524678999999999999974399705------6542558---899999950 Q gi|254780346|r 77 RGKTAHCDVIAHAVTRGLVDLSINGSLPIG------NGIVVVD---SEQQAFDRV 122 (149) Q Consensus 77 kGeT~H~e~I~~~v~~gl~~lsl~~~~PI~------~gILt~~---n~~QA~~R~ 122 (149) || .+.-...+....+++||. .|-||.- +.++++++. T Consensus 72 -GD---------GTlL~~a~~~~~~~~PilGiN~G~lGFLt~~~~~~~~~~l~~i 116 (291) T PRK02155 72 -GD---------GTMLGIGRQLAPYGTPLIGINHGRLGFITDIPLSDMQEALPPM 116 (291) T ss_pred -CC---------HHHHHHHHHHHCCCCCEEEEECCCEEECCCCCHHHHHHHHHHH T ss_conf -78---------8999999987115996899854751340688778899999999 No 148 >PRK13054 lipid kinase; Reviewed Probab=35.93 E-value=38 Score=15.80 Aligned_cols=92 Identities=17% Similarity=0.198 Sum_probs=52.3 Q ss_pred CCCEEEEEEECHHHHHHHHHHHHHHHHHHHCCCCEEEEEHHHHHHHHHHHHHHHHHHHCCCCCCEEEEEEEEECCCCCHH Q ss_conf 58717999803128999999999999999879955555300144226999999863311378535665412000665246 Q gi|254780346|r 4 FIPHVLIIEARFYENLSAMLFEGCVNVLHSRAVQWSSIVTPGVLEIPAAVSMVMNAKTRSVTYDGIIVLGVVMRGKTAHC 83 (149) Q Consensus 4 ~~~kI~IV~s~~~~~i~~~ll~ga~~~l~~~~~~~~~i~VPGa~EiP~a~~~~~~~~~~~~~~D~vIaLG~VIkGeT~H~ 83 (149) |++-.+||...- . ..+-+..+.+.|.+.++++++..+-..-+ +..+.+. +....||.+|+.| ||= T Consensus 3 ~~k~lli~N~~~--~-g~~~~~~~~~~l~~~~~~~~~~~T~~~gd----a~~la~~-a~~~g~d~vv~~G----GDG--- 67 (299) T PRK13054 3 FPKSLLILNGKS--A-GNEELREAVGLLREEGHTLHVRVTWEKGD----AARYVEE-ALALGVATVIAGG----GDG--- 67 (299) T ss_pred CCEEEEEECCCC--C-CHHHHHHHHHHHHHCCCEEEEEECCCCCH----HHHHHHH-HHHCCCCEEEEEC----CCH--- T ss_conf 856999981700--0-50689999999997698799996489745----9999999-9877998999987----722--- Q ss_pred HHHHHHHHHHHHHHHHHCCCCCEEEEECCCC Q ss_conf 7899999999999997439970565425588 Q gi|254780346|r 84 DVIAHAVTRGLVDLSINGSLPIGNGIVVVDS 114 (149) Q Consensus 84 e~I~~~v~~gl~~lsl~~~~PI~~gILt~~n 114 (149) --++|.+||++.. ...+...|||-.-+ T Consensus 68 --Tv~evvngl~~~~--~~~~~~LgiiP~GT 94 (299) T PRK13054 68 --TLNEVATALAQLE--GDDRPSLGILPLGT 94 (299) T ss_pred --HHHHHHHHHHHCC--CCCCCEEEEECCCC T ss_conf --9999999997478--87786399963875 No 149 >PRK03767 TrpR binding protein WrbA; Provisional Probab=35.71 E-value=38 Score=15.78 Aligned_cols=40 Identities=13% Similarity=0.173 Sum_probs=26.1 Q ss_pred CCEEEEEEECHHHHHHHHHHHHHHHHHHH-CCCCEEEEEHHH Q ss_conf 87179998031289999999999999998-799555553001 Q gi|254780346|r 5 IPHVLIIEARFYENLSAMLFEGCVNVLHS-RAVQWSSIVTPG 45 (149) Q Consensus 5 ~~kI~IV~s~~~~~i~~~ll~ga~~~l~~-~~~~~~~i~VPG 45 (149) |+||+||.-+=| .-+..|-+...+-..+ .|++....+||- T Consensus 1 M~kI~IvyyS~~-G~t~~lA~~ia~Ga~~~~G~ev~l~~v~e 41 (200) T PRK03767 1 MAKVLVLYYSMY-GHIETMAEAVAEGAREVAGAEVTIKRVPE 41 (200) T ss_pred CCCEEEEEECCC-CHHHHHHHHHHHHHHHCCCCEEEEEECCC T ss_conf 970899993899-88999999999766551797799985556 No 150 >PRK10161 transcriptional regulator PhoB; Provisional Probab=33.75 E-value=41 Score=15.59 Aligned_cols=118 Identities=13% Similarity=0.101 Sum_probs=60.5 Q ss_pred CCCEEEEEEECHHHHHHHHHHHHHHHHHHHCCCCEEEEEHHHHHHHHHHHHHHHHHHHCCCCCCEEEEEEEEECCCCCHH Q ss_conf 58717999803128999999999999999879955555300144226999999863311378535665412000665246 Q gi|254780346|r 4 FIPHVLIIEARFYENLSAMLFEGCVNVLHSRAVQWSSIVTPGVLEIPAAVSMVMNAKTRSVTYDGIIVLGVVMRGKTAHC 83 (149) Q Consensus 4 ~~~kI~IV~s~~~~~i~~~ll~ga~~~l~~~~~~~~~i~VPGa~EiP~a~~~~~~~~~~~~~~D~vIaLG~VIkGeT~H~ 83 (149) |++||+||.-+- .+.+.-...|...|+++... ....-+.+.+ ....||.+|. -.-.- +.+=+ T Consensus 1 M~~kILiVEDd~------~l~~~l~~~L~~~g~~v~~a-----~~g~~a~~~l-----~~~~~Dliil-Di~lP-~~dG~ 62 (229) T PRK10161 1 MARRILVVEDEA------PIREMVCFVLEQNGFQPVEA-----EDYDSAVNQL-----NEPWPDLILL-DWMLP-GGSGI 62 (229) T ss_pred CCCCEEEEECCH------HHHHHHHHHHHHCCCEEEEE-----CCHHHHHHHH-----HCCCCCEEEE-ECCCC-CCCCH T ss_conf 997199995999------99999999999779999998-----9999999998-----5289989999-78998-87633 Q ss_pred HHHHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHH----CCCCCCCHHHHHHHHHHHHHHHHH Q ss_conf 789999999999999743997056542558899999950----656574569999999999999986 Q gi|254780346|r 84 DVIAHAVTRGLVDLSINGSLPIGNGIVVVDSEQQAFDRV----SPSHLDRGGCAARSALAMIELKKS 146 (149) Q Consensus 84 e~I~~~v~~gl~~lsl~~~~PI~~gILt~~n~~QA~~R~----~~~~~nkG~eaa~Aal~mi~l~~~ 146 (149) + +++.|.+-+...++||++ ||..+.++-.-++ .....-|--+...=..++-.+.|+ T Consensus 63 ~-----~~~~ir~~~~~~~~PII~--lta~~~~~d~v~gl~~GADDYl~KPf~~~EL~aRi~a~lrR 122 (229) T PRK10161 63 Q-----FIKHLKRESMTRDIPVVM--LTARGEEEDRVRGLETGADDYITKPFSPKELVARIKAVMRR 122 (229) T ss_pred H-----HHHHHHHCCCCCCCCEEE--EECCCCHHHHHHHHHCCCCEEEECCCCHHHHHHHHHHHHHH T ss_conf 5-----878877502468975899--95566657799998769876520899989999999999712 No 151 >cd01391 Periplasmic_Binding_Protein_Type_1 Type 1 periplasmic binding fold superfamily. Type 1 periplasmic binding fold superfamily. This model and hierarchy represent the ligand binding domains of the LacI family of transcriptional regulators, periplasmic binding proteins of the ABC-type transport systems, the family C G-protein couples receptors (GPCRs), membrane bound guanylyl cyclases including the family of natriuretic peptide receptors (NPRs), and the N-terminal leucine/isoleucine/valine- binding protein (LIVBP)-like domains of the ionotropic glutamate receptors (iGluRs). In LacI-like transcriptional regulator and the bacterial periplasmic binding proteins the ligands are monosaccharides including lactose, ribose, fructose, xylose, arabinose, galactose/glucose, and other sugars, with a few exceptions. Periplasmic sugar binding proteins are one of the components of ABC transporters and are involved in the active transport of water-soluble ligands. The LacI family of proteins con Probab=33.57 E-value=41 Score=15.57 Aligned_cols=31 Identities=16% Similarity=0.133 Sum_probs=14.3 Q ss_pred CEEEEEEECHHHHHHHHHHHHHHHHHHHCCCC Q ss_conf 71799980312899999999999999987995 Q gi|254780346|r 6 PHVLIIEARFYENLSAMLFEGCVNVLHSRAVQ 37 (149) Q Consensus 6 ~kI~IV~s~~~~~i~~~ll~ga~~~l~~~~~~ 37 (149) .||+++..... .......+|+.+.+++++.+ T Consensus 125 ~~i~~i~~~~~-~~~~~r~~g~~~~~~~~g~~ 155 (269) T cd01391 125 KRVALIYGDDG-AYGRERLEGFKAALKKAGIE 155 (269) T ss_pred CEEEEECCCCC-HHHHHHHHHHHHHHHHCCCC T ss_conf 61699737985-77999999999999986998 No 152 >PRK09739 hypothetical protein; Provisional Probab=32.97 E-value=42 Score=15.51 Aligned_cols=39 Identities=13% Similarity=0.123 Sum_probs=28.0 Q ss_pred CCCEEEEEEECHHH-HHHHHHHHHHHHHHHHCCCCEEEEE Q ss_conf 58717999803128-9999999999999998799555553 Q gi|254780346|r 4 FIPHVLIIEARFYE-NLSAMLFEGCVNVLHSRAVQWSSIV 42 (149) Q Consensus 4 ~~~kI~IV~s~~~~-~i~~~ll~ga~~~l~~~~~~~~~i~ 42 (149) .++||+||.+-=++ -.+..|.+.+.+.|.+.|.++++++ T Consensus 2 ~~kkiLIV~aHP~~~S~~~ala~~~~~~l~~~GheV~v~D 41 (201) T PRK09739 2 QSERIYLVWAHPRHDSLTAKVADAIHQRAQERGIQVTELD 41 (201) T ss_pred CCCEEEEEECCCCCCCHHHHHHHHHHHHHHHCCCEEEEEE T ss_conf 9777999973899865689999999999998799599997 No 153 >cd03817 GT1_UGDG_like This family is most closely related to the GT1 family of glycosyltransferases. UDP-glucose-diacylglycerol glucosyltransferase (UGDG; also known as 1,2-diacylglycerol 3-glucosyltransferase) catalyzes the transfer of glucose from UDP-glucose to 1,2-diacylglycerol forming 3-D-glucosyl-1,2-diacylglycerol. Probab=31.89 E-value=44 Score=15.40 Aligned_cols=36 Identities=11% Similarity=0.137 Sum_probs=25.9 Q ss_pred EEEEEEECHHHHH--HHHHHHHHHHHHHHCCCCEEEEE Q ss_conf 1799980312899--99999999999998799555553 Q gi|254780346|r 7 HVLIIEARFYENL--SAMLFEGCVNVLHSRAVQWSSIV 42 (149) Q Consensus 7 kI~IV~s~~~~~i--~~~ll~ga~~~l~~~~~~~~~i~ 42 (149) ||+||...|++.+ +......-.+.|.+.|.++.++. T Consensus 1 kIaivt~~y~P~~GG~~~~~~~La~~L~~~GheV~Vit 38 (374) T cd03817 1 KIGIFTDTYLPQVNGVATSIRRLAEELEKRGHEVYVVA 38 (374) T ss_pred CEEEECCCCCCCCCCHHHHHHHHHHHHHHCCCEEEEEE T ss_conf 98999589899998099999999999997799899997 No 154 >COG3364 Zn-ribbon containing protein [General function prediction only] Probab=31.15 E-value=14 Score=18.45 Aligned_cols=47 Identities=23% Similarity=0.396 Sum_probs=25.4 Q ss_pred CCEEEEEEECHHHHHHHHHHHHH---------------------------HHHHHHCCCCEEEEE--HHHHHHHHH Q ss_conf 87179998031289999999999---------------------------999998799555553--001442269 Q gi|254780346|r 5 IPHVLIIEARFYENLSAMLFEGC---------------------------VNVLHSRAVQWSSIV--TPGVLEIPA 51 (149) Q Consensus 5 ~~kI~IV~s~~~~~i~~~ll~ga---------------------------~~~l~~~~~~~~~i~--VPGa~EiP~ 51 (149) |++..+=...-|++-...|+.|| .+...+.|-.++.|. -||.|||-+ T Consensus 1 MpH~CtrCG~vf~~g~~~il~GCp~CG~nkF~yv~~e~rpa~~e~~d~~vrde~~a~ge~ietIrI~~pG~YeiNl 76 (112) T COG3364 1 MPHQCTRCGEVFDDGSEEILSGCPKCGCNKFLYVPEEKRPAVAEAADPEVRDEDGAQGEPIETIRILRPGVYEINL 76 (112) T ss_pred CCCEECCCCCCCCCCCHHHHCCCCCCCCHHEEECCCCCCCCHHHHCCCCCCCHHHCCCCCCEEEEEECCCEEEEEH T ss_conf 9752140445636512998815720163114763444563114441876641122036750489994496489744 No 155 >PRK10307 predicted glycosyl transferase; Provisional Probab=30.15 E-value=47 Score=15.22 Aligned_cols=37 Identities=14% Similarity=0.186 Sum_probs=28.3 Q ss_pred EEEEEEECHHHHHH--HHHHHHHHHHHHHCCCCEEEEEH Q ss_conf 17999803128999--99999999999987995555530 Q gi|254780346|r 7 HVLIIEARFYENLS--AMLFEGCVNVLHSRAVQWSSIVT 43 (149) Q Consensus 7 kI~IV~s~~~~~i~--~~ll~ga~~~l~~~~~~~~~i~V 43 (149) ||++|...|++++. ......-.+.|.+.|.+++++.. T Consensus 2 rIl~vs~~y~P~~~G~~~~~~~La~~L~~~GheV~Vit~ 40 (415) T PRK10307 2 KILVYGINYAPELTGIGKYTGEMAEWLAARGHEVRVITA 40 (415) T ss_pred EEEEECCCCCCCCCCHHHHHHHHHHHHHHCCCEEEEEEC T ss_conf 899985848997887999999999999978998999977 No 156 >TIGR00504 pyro_pdase pyrrolidone-carboxylate peptidase; InterPro: IPR000816 Peptidases are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry. Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. Cysteine peptidases have characteristic molecular topologies, which can be seen not only in their three-dimensional structures, but commonly also in the two-dimensional structures. These are peptidases in which the nucleophile is the sulphydryl group of a cysteine residue. Cysteine proteases are divided into clans (proteins which are evolutionary related), and further sub-divided into families, on the basis of the architecture of their catalytic dyad or triad . This group of cysteine peptidases belong to MEROPS peptidase family C15 (pyroglutamyl peptidase I, clan CF). The type example being pyroglutamyl peptidase I of Bacillus amyloliquefaciens. Pyroglutamyl/pyrrolidone carboxyl peptidase (Pcp or PYRase) is an exopeptidase that hydrolytically removes the pGlu from pGlu-peptides or pGlu-proteins , . PYRase has been found in prokaryotes and eukaryotes where at least two different classes have been characterised: the first containing bacterial and animal type I PYRases, and the second containing animal type II and serum PYRases. Type I and bacterial PYRases are soluble enzymes, while type II PYRases are membrane-bound. The primary application of PYRase has been its utilisation for protein or peptide sequencing, and bacterial diagnosis . The conserved residues Cys-144 and His-168 have been identified by inhibition and mutagenesis studies , .; GO: 0004219 pyroglutamyl-peptidase I activity, 0006508 proteolysis. Probab=30.00 E-value=47 Score=15.20 Aligned_cols=62 Identities=18% Similarity=0.213 Sum_probs=43.9 Q ss_pred CCHHHHHHHHHHHHHHHHHHHCCCCCEEEEECCC-CHHHHHHH---HCCCC-CCCHHHHHHHHHHHH Q ss_conf 5246789999999999999743997056542558-89999995---06565-745699999999999 Q gi|254780346|r 80 TAHCDVIAHAVTRGLVDLSINGSLPIGNGIVVVD-SEQQAFDR---VSPSH-LDRGGCAARSALAMI 141 (149) Q Consensus 80 T~H~e~I~~~v~~gl~~lsl~~~~PI~~gILt~~-n~~QA~~R---~~~~~-~nkG~eaa~Aal~mi 141 (149) -.=--||||.++.++++-.-+++.|+.-|=+=+. .-+|+.+. ..++- .+--..+.++|++.+ T Consensus 138 ~tAGTFvCN~~~Yl~lh~~A~~G~p~raGFIHvPy~P~q~~~~~nl~~PSmSld~~v~Gv~~Ai~~A 204 (220) T TIGR00504 138 YTAGTFVCNYLMYLLLHHLAQKGLPVRAGFIHVPYLPEQVAEKKNLNVPSMSLDTAVAGVEIAIETA 204 (220) T ss_pred HHHHHHHHHHHHHHHHHHHHCCCCCCCCCEEECCCCHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHH T ss_conf 3534789999999999987405897112014438871344300358897378999999999999998 No 157 >PRK00012 gatA aspartyl/glutamyl-tRNA amidotransferase subunit A; Reviewed Probab=29.38 E-value=49 Score=15.13 Aligned_cols=44 Identities=14% Similarity=0.094 Sum_probs=30.9 Q ss_pred CCCCEEEEEEECHHHH---HHHHHHHHHHHHHHHCCCCEEEEEHHHH Q ss_conf 6587179998031289---9999999999999987995555530014 Q gi|254780346|r 3 VFIPHVLIIEARFYEN---LSAMLFEGCVNVLHSRAVQWSSIVTPGV 46 (149) Q Consensus 3 ~~~~kI~IV~s~~~~~---i~~~ll~ga~~~l~~~~~~~~~i~VPGa 46 (149) +...||+++...|... -+...++.+.+.|++.|+++..+..|.. T Consensus 255 ~~~lrIgv~~~~~~~~~d~~v~~a~~~a~~~L~~~G~~v~ei~~p~~ 301 (485) T PRK00012 255 LKGLKIGVPKEYFGEGLDPEVKEAVEAAIKVLKDLGAEIVEVSLPHT 301 (485) T ss_pred CCCCEEEEECCCCCCCCCHHHHHHHHHHHHHHHHCCCEEEEECCCCH T ss_conf 66767997110025778999999999999999977988999448666 No 158 >cd00452 KDPG_aldolase KDPG and KHG aldolase. This family belongs to the class I adolases whose reaction mechanism involves Schiff base formation between a substrate carbonyl and lysine residue in the active site. 2-keto-3-deoxy-6-phosphogluconate (KDPG) aldolase, is best known for its role in the Entner-Doudoroff pathway of bacteria, where it catalyzes the reversible cleavage of KDPG to pyruvate and glyceraldehyde-3-phosphate. 2-keto-4-hydroxyglutarate (KHG) aldolase, which has enzymatic specificity toward glyoxylate, forming KHG in the presence of pyruvate, and is capable of regulating glyoxylate levels in the glyoxylate bypass, an alternate pathway when bacteria are grown on acetate carbon sources. Probab=28.55 E-value=50 Score=15.05 Aligned_cols=104 Identities=17% Similarity=0.233 Sum_probs=67.4 Q ss_pred CEEEEEEECHHHHHHHHHHHHHHHHHHHCCCCEEEE--EHHHHHHHHHHHHHHHHHHHCCCCCCEEEEEEEEECCCCCHH Q ss_conf 717999803128999999999999999879955555--300144226999999863311378535665412000665246 Q gi|254780346|r 6 PHVLIIEARFYENLSAMLFEGCVNVLHSRAVQWSSI--VTPGVLEIPAAVSMVMNAKTRSVTYDGIIVLGVVMRGKTAHC 83 (149) Q Consensus 6 ~kI~IV~s~~~~~i~~~ll~ga~~~l~~~~~~~~~i--~VPGa~EiP~a~~~~~~~~~~~~~~D~vIaLG~VIkGeT~H~ 83 (149) +-|.|+...= .+-. ....+.|.+.|+..-.| +.|+++|.- +.+.+ . -.|..|-.|.|...++-+. T Consensus 5 ~iiaVlr~~~-~~~a----~~~~~al~~~Gi~~iEitl~t~~a~~~i---~~l~~----~-~~~~~iGaGTV~~~~~~~~ 71 (190) T cd00452 5 PLVAVLRGDD-AEDA----LALAEALIEGGIRAIEITLRTPGALEAI---RALRK----E-FPEALIGAGTVLTPEQADA 71 (190) T ss_pred CEEEEEECCC-HHHH----HHHHHHHHHCCCCEEEEECCCCHHHHHH---HHHHH----H-CCCCEEEECCCCCHHHHHH T ss_conf 7799997799-9999----9999999986998899967880299999---99998----6-8980896523477999999 Q ss_pred H-------HHHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHH Q ss_conf 7-------89999999999999743997056542558899999950 Q gi|254780346|r 84 D-------VIAHAVTRGLVDLSINGSLPIGNGIVVVDSEQQAFDRV 122 (149) Q Consensus 84 e-------~I~~~v~~gl~~lsl~~~~PI~~gILt~~n~~QA~~R~ 122 (149) = .||-.....+.+.+.++++|.+-|+.|+....||++.- T Consensus 72 a~~aGa~FivsP~~~~~v~~~a~~~~~~~iPGv~TpsEi~~A~~~G 117 (190) T cd00452 72 AIAAGAQFIVSPGLDPEVVKAANRAGIPLLPGVATPTEIMQALELG 117 (190) T ss_pred HHHCCCCEEECCCCCHHHHHHHHHCCCCEECCCCCHHHHHHHHHCC T ss_conf 9985998997377999999999982996657879999999999879 No 159 >cd01741 GATase1_1 Subgroup of proteins having the Type 1 glutamine amidotransferase (GATase1) domain. This group contains a subgroup of proteins having the Type 1 glutamine amidotransferase (GATase1) domain. GATase activity catalyses the transfer of ammonia from the amide side chain of glutamine to an acceptor substrate. Glutamine amidotransferases (GATase) includes the triad family of amidotransferases which have a conserved Cys-His-Glu catalytic triad in the glutaminase active site. In this subgroup this triad is conserved. GATase activity can be found in a range of biosynthetic enzymes, including: glutamine amidotransferase, formylglycinamide ribonucleotide, GMP synthetase , anthranilate synthase component II, glutamine-dependent carbamoyl phosphate synthase, cytidine triphosphate synthetase, gamma-glutamyl hydrolase, imidazole glycerol phosphate synthase and, cobyric acid synthase. Glutamine amidotransferase (GATase) domains can occur either as single polypeptides, as in glutamine Probab=27.99 E-value=51 Score=14.98 Aligned_cols=97 Identities=15% Similarity=0.199 Sum_probs=51.6 Q ss_pred EEEEEEECHHHHHHHHHHHHHHHHHHHCC---CCEEEEEHHHHHHHHHHHHHHHHHHHCCCCCCEEEEEEEEECCCCCHH Q ss_conf 17999803128999999999999999879---955555300144226999999863311378535665412000665246 Q gi|254780346|r 7 HVLIIEARFYENLSAMLFEGCVNVLHSRA---VQWSSIVTPGVLEIPAAVSMVMNAKTRSVTYDGIIVLGVVMRGKTAHC 83 (149) Q Consensus 7 kI~IV~s~~~~~i~~~ll~ga~~~l~~~~---~~~~~i~VPGa~EiP~a~~~~~~~~~~~~~~D~vIaLG~VIkGeT~H~ 83 (149) ||+|+...-.+. .....+.|.+.+ ++++.+.+...-.+| .-.+|||+|..|.=--=+++-+ T Consensus 1 ~i~il~~~~~~~-----~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~-----------~~~~~dgvii~Gg~~~~~~~~~ 64 (188) T cd01741 1 RILILQHDTPEG-----PGLFEDLLREAGAETIEIDVVDVYAGELLP-----------DLDDYDGLVILGGPMSVDEDDY 64 (188) T ss_pred CEEEEECCCCCC-----CHHHHHHHHHCCCCCEEEEEEECCCCCCCC-----------CHHHCCEEEEECCCCCCCCCCC T ss_conf 989997799999-----748999999669984689999666698997-----------8444088999699877786788 Q ss_pred HHHHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHHCCC Q ss_conf 789999999999999743997056542558899999950656 Q gi|254780346|r 84 DVIAHAVTRGLVDLSINGSLPIGNGIVVVDSEQQAFDRVSPS 125 (149) Q Consensus 84 e~I~~~v~~gl~~lsl~~~~PI~~gILt~~n~~QA~~R~~~~ 125 (149) ..+.+ ...+.+-.++.++|+.-==+ -.|.+.++-+. T Consensus 65 pwi~~--~~~~i~~~~~~~~PilGIC~----G~Qlla~alGg 100 (188) T cd01741 65 PWLKK--LKELIRQALAAGKPVLGICL----GHQLLARALGG 100 (188) T ss_pred HHHHH--HHHHHHHHHHCCCCEEEECH----HHHHHHHHCCC T ss_conf 66999--99999999987999999846----89999998399 No 160 >PRK00453 rpsF 30S ribosomal protein S6; Reviewed Probab=27.67 E-value=52 Score=14.95 Aligned_cols=48 Identities=15% Similarity=0.172 Sum_probs=40.7 Q ss_pred EEEEEECHHHHHHHHHHHHHHHHHHHCCCCEEEEEHHHHHHHHHHHHH Q ss_conf 799980312899999999999999987995555530014422699999 Q gi|254780346|r 8 VLIIEARFYENLSAMLFEGCVNVLHSRAVQWSSIVTPGVLEIPAAVSM 55 (149) Q Consensus 8 I~IV~s~~~~~i~~~ll~ga~~~l~~~~~~~~~i~VPGa~EiP~a~~~ 55 (149) +.|+.+...++-.+.+++...+.+.+.|..+..+...|--.+++.++. T Consensus 7 ~~il~p~l~~~~~~~~~~~~~~~i~~~gg~v~~~~~~G~r~LAY~I~k 54 (95) T PRK00453 7 VFILRPDLSEEQVKALVERYKGVITKNGGEIHKVEDWGRRRLAYPINK 54 (95) T ss_pred EEEECCCCCHHHHHHHHHHHHHHHHHCCCEEEEEECCCCCCCCCEECC T ss_conf 999889999899999999999999979988999850212004423066 No 161 >PRK02645 ppnK inorganic polyphosphate/ATP-NAD kinase; Provisional Probab=26.54 E-value=54 Score=14.82 Aligned_cols=99 Identities=19% Similarity=0.209 Sum_probs=60.2 Q ss_pred CCCEEEEEEECHHHHHHHHHHHHHHHHHHHCCCCEEEE-EHHHHHHHHHHHHHHHHHHHCCCCCCEEEEEEEEECCCCCH Q ss_conf 58717999803128999999999999999879955555-30014422699999986331137853566541200066524 Q gi|254780346|r 4 FIPHVLIIEARFYENLSAMLFEGCVNVLHSRAVQWSSI-VTPGVLEIPAAVSMVMNAKTRSVTYDGIIVLGVVMRGKTAH 82 (149) Q Consensus 4 ~~~kI~IV~s~~~~~i~~~ll~ga~~~l~~~~~~~~~i-~VPGa~EiP~a~~~~~~~~~~~~~~D~vIaLG~VIkGeT~H 82 (149) .++||+|| ++..+.....+.....+.|.+.|+++-.. ..++..++|.- .. ....+.|-+|+|| | T Consensus 2 ~lk~VlIV-~k~~~~~A~~~a~~l~~~L~~rGi~v~~~~~~~~~~~~~~~----~~--~~~~~~Dlvi~lG----G---- 66 (304) T PRK02645 2 QLKLVIIA-YKAGSPQAKEAAERCAKQLEARGIKVLMGPSGPKDNPYPVF----LA--SAEELPDLAIVLG----G---- 66 (304) T ss_pred CCCEEEEE-ECCCCHHHHHHHHHHHHHHHHCCCEEEECCCCCCCCCCCCC----CC--CCCCCCCEEEEEC----C---- T ss_conf 74599999-85899999999999999999888999984443444777620----01--4466888999978----6---- Q ss_pred HHHHHHHHHHHHHHHHHHCCCCCE-------EEEECC-C---CHHHHHHHH Q ss_conf 678999999999999974399705-------654255-8---899999950 Q gi|254780346|r 83 CDVIAHAVTRGLVDLSINGSLPIG-------NGIVVV-D---SEQQAFDRV 122 (149) Q Consensus 83 ~e~I~~~v~~gl~~lsl~~~~PI~-------~gILt~-~---n~~QA~~R~ 122 (149) +.+.-...+....+++||. .|-||- . ..++++++. T Consensus 67 -----DGT~L~aar~~~~~~iPilGiN~~G~lGFLte~~~~~~~~~~l~~l 112 (304) T PRK02645 67 -----DGTVLAAARHLAPHDIPILSFNVGGHLGFLTHPRDLLQDESVWDRL 112 (304) T ss_pred -----CHHHHHHHHHHCCCCCCEEEEECCCEEEEECCCCCCCCHHHHHHHH T ss_conf -----8899999998542699889982486469716764221178999999 No 162 >PRK13057 putative lipid kinase; Reviewed Probab=26.35 E-value=55 Score=14.80 Aligned_cols=73 Identities=21% Similarity=0.261 Sum_probs=45.5 Q ss_pred HHHHHHHHHHHHCCCCEEEEEHHHHHHHHHHHHHHHHHHHCCCCCCEEEEEEEEECCCCCHHHHHHHHHHHHHHHHHHHC Q ss_conf 99999999999879955555300144226999999863311378535665412000665246789999999999999743 Q gi|254780346|r 22 MLFEGCVNVLHSRAVQWSSIVTPGVLEIPAAVSMVMNAKTRSVTYDGIIVLGVVMRGKTAHCDVIAHAVTRGLVDLSING 101 (149) Q Consensus 22 ~ll~ga~~~l~~~~~~~~~i~VPGa~EiP~a~~~~~~~~~~~~~~D~vIaLG~VIkGeT~H~e~I~~~v~~gl~~lsl~~ 101 (149) .....+...|.+.|++++.......-+.- .++++. ...||.+|+.| || =--++++++++ ++ T Consensus 13 ~~~~~~~~~l~~~g~~~~~~~T~~~g~a~----~~~~~~--~~~~d~vv~~G----GD-----GTv~ev~~gl~----~~ 73 (287) T PRK13057 13 AALGAARAALEAAGLELVEPHPESPADLS----EVIEAH--ADGVDLVIVGG----GD-----GTLNAAAPALV----ET 73 (287) T ss_pred HHHHHHHHHHHHCCCEEEEEECCCHHHHH----HHHHHH--HCCCCEEEEEC----CH-----HHHHHHHHHHC----CC T ss_conf 31999999999879979999549878999----999998--66999899988----58-----99999999860----57 Q ss_pred CCCCEEEEECCCCH Q ss_conf 99705654255889 Q gi|254780346|r 102 SLPIGNGIVVVDSE 115 (149) Q Consensus 102 ~~PI~~gILt~~n~ 115 (149) ++| .|||-.-|- T Consensus 74 ~~~--lgiiP~GTg 85 (287) T PRK13057 74 GLP--LGILPLGTA 85 (287) T ss_pred CCC--EEEECCCCH T ss_conf 983--699738864 No 163 >pfam02601 Exonuc_VII_L Exonuclease VII, large subunit. This family consist of exonuclease VII, large subunit EC:3.1.11.6 This enzyme catalyses exonucleolytic cleavage in either 5'-3' or 3'-5' direction to yield 5'-phosphomononucleotides. This exonuclease VII enzyme is composed of one large subunit and 4 small ones. Probab=26.06 E-value=56 Score=14.77 Aligned_cols=93 Identities=18% Similarity=0.355 Sum_probs=55.6 Q ss_pred CCCEEEEEEECHHHHHHHHHHHHHHHHHHHCCCC--EEEE--EHHHH---HHHHHHHHHHHHHHHCCCCCCEEEEEEEEE Q ss_conf 5871799980312899999999999999987995--5555--30014---422699999986331137853566541200 Q gi|254780346|r 4 FIPHVLIIEARFYENLSAMLFEGCVNVLHSRAVQ--WSSI--VTPGV---LEIPAAVSMVMNAKTRSVTYDGIIVLGVVM 76 (149) Q Consensus 4 ~~~kI~IV~s~~~~~i~~~ll~ga~~~l~~~~~~--~~~i--~VPGa---~EiP~a~~~~~~~~~~~~~~D~vIaLG~VI 76 (149) +-.||+||.|. +-.-+......+.+.... +..+ .|-|. -||--+++.+-. .....+||.+| |+ T Consensus 13 ~p~~IgvITS~-----~gAa~~Di~~~~~~r~p~~~i~l~p~~VQG~~a~~~I~~ai~~~~~-~~~~~~~Dvii----i~ 82 (295) T pfam02601 13 FPKRIAVITSA-----TGAAYQDFLRTARRRGPLVEIEIYPTLVQGDGAAESIVSALERANE-RETALDYDVIV----II 82 (295) T ss_pred CCCEEEEEECC-----CCHHHHHHHHHHHHHCCCCEEEEECCCCCCCHHHHHHHHHHHHHHH-CCCCCCCCEEE----EE T ss_conf 99989998489-----4089999999999819996799947357650489999999999984-68989983899----95 Q ss_pred CCCCCHHHHHH---HHHHHHHHHHHHHCCCCCEEEEE Q ss_conf 06652467899---99999999999743997056542 Q gi|254780346|r 77 RGKTAHCDVIA---HAVTRGLVDLSINGSLPIGNGIV 110 (149) Q Consensus 77 kGeT~H~e~I~---~~v~~gl~~lsl~~~~PI~~gIL 110 (149) ||.=+--|+-| ..+++.+. +..+||+.||= T Consensus 83 RGGGS~eDL~~FN~e~laraI~----~~~iPvisaIG 115 (295) T pfam02601 83 RGGGSKEDLWVFNDEELARAIA----NSPIPVITGIG 115 (295) T ss_pred CCCCCHHHHHHCCHHHHHHHHH----HCCCCEEECCC T ss_conf 7868889874558899999998----38998780678 No 164 >PRK07235 amidase; Provisional Probab=25.33 E-value=57 Score=14.69 Aligned_cols=43 Identities=14% Similarity=0.039 Sum_probs=32.8 Q ss_pred CCCCEEEEEEECHH----HHHHHHHHHHHHHHHHHCCCCEEEEEHHH Q ss_conf 65871799980312----89999999999999998799555553001 Q gi|254780346|r 3 VFIPHVLIIEARFY----ENLSAMLFEGCVNVLHSRAVQWSSIVTPG 45 (149) Q Consensus 3 ~~~~kI~IV~s~~~----~~i~~~ll~ga~~~l~~~~~~~~~i~VPG 45 (149) +...||+|+...|. +.-++..++.+.+.|.+.|+.++.+.+|- T Consensus 273 ~~~lrIGv~~~~~~~~~~d~~v~~av~~a~~~L~~~Ga~V~ev~~P~ 319 (504) T PRK07235 273 VKGLKIGVLREGFGLPNSEPEVDEAVRAAAERLESLGATVEEVSIPW 319 (504) T ss_pred CCCCEEEEECCCCCCCCCCHHHHHHHHHHHHHHHHCCCEEEEECCCC T ss_conf 44563443033458888889999999999999986698589844850 No 165 >TIGR00707 argD acetylornithine and succinylornithine aminotransferases; InterPro: IPR004636 This family of proteins, for which ornithine aminotransferases form an outgroup, consists mostly of proteins designated acetylornithine aminotransferase. However, the two very closely related members from Escherichia coli are assigned different enzymatic activities. One is acetylornithine aminotransferase (2.6.1.11 from EC), ArgD, an enzyme of arginine biosynthesis, while another is succinylornithine aminotransferase, an enzyme of the arginine succinyltransferase pathway, an ammonia-generating pathway of arginine catabolism . Members of this family may also act on ornithine, like ornithine aminotransferase (2.6.1.13 from EC) and on succinyldiaminopimelate, like N-succinyldiaminopmelate-aminotransferase (2.6.1.17 from EC, DapC, an enzyme of lysine biosynthesis) . ; GO: 0008483 transaminase activity, 0006525 arginine metabolic process. Probab=25.11 E-value=51 Score=15.01 Aligned_cols=21 Identities=19% Similarity=0.154 Sum_probs=14.4 Q ss_pred CCCCCHHHHHHHHHHHHHHHH Q ss_conf 657456999999999999998 Q gi|254780346|r 125 SHLDRGGCAARSALAMIELKK 145 (149) Q Consensus 125 ~~~nkG~eaa~Aal~mi~l~~ 145 (149) -.+|=|.||-.|||++++..- T Consensus 97 FFCNSGaEAnEAAlKlARk~~ 117 (402) T TIGR00707 97 FFCNSGAEANEAALKLARKYT 117 (402) T ss_pred EEECCHHHHHHHHHHHHHHHH T ss_conf 751474789999999989864 No 166 >PRK13689 hypothetical protein; Provisional Probab=24.65 E-value=59 Score=14.61 Aligned_cols=29 Identities=10% Similarity=0.197 Sum_probs=26.2 Q ss_pred EEECHHHHHHHHHHHHHHHHHHHCCCCEE Q ss_conf 98031289999999999999998799555 Q gi|254780346|r 11 IEARFYENLSAMLFEGCVNVLHSRAVQWS 39 (149) Q Consensus 11 V~s~~~~~i~~~ll~ga~~~l~~~~~~~~ 39 (149) +.|+|..+-++.++..-...|+++++..| T Consensus 3 i~SKYs~~qvE~il~el~~vLeKH~Ap~D 31 (75) T PRK13689 3 QQSKYSDEQVEQLLAELLAVLEKHKAPTD 31 (75) T ss_pred CCCCCCHHHHHHHHHHHHHHHHHCCCCCC T ss_conf 53202389999999999999986599941 No 167 >PRK11574 hypothetical protein; Provisional Probab=23.71 E-value=62 Score=14.50 Aligned_cols=94 Identities=10% Similarity=0.042 Sum_probs=55.2 Q ss_pred CCCEEEEEEECHHHHHHHHHHHHHHHHHHHCCCCEEEE--------EHHHHHHHHHHHHHHHHHHHCCCCCCEEEEEEEE Q ss_conf 58717999803128999999999999999879955555--------3001442269999998633113785356654120 Q gi|254780346|r 4 FIPHVLIIEARFYENLSAMLFEGCVNVLHSRAVQWSSI--------VTPGVLEIPAAVSMVMNAKTRSVTYDGIIVLGVV 75 (149) Q Consensus 4 ~~~kI~IV~s~~~~~i~~~ll~ga~~~l~~~~~~~~~i--------~VPGa~EiP~a~~~~~~~~~~~~~~D~vIaLG~V 75 (149) |.+|++|..+.=.+|+- .-...+.|.+.|+++... .|.|+.-+...+...+..- ...+||+++-=| T Consensus 1 M~kk~LV~lA~GfEEiE---a~~~vDvLRRagi~V~~asv~~~~~~~v~gs~gi~i~aD~~l~~v-~~~~yD~ivlPG-- 74 (196) T PRK11574 1 MSASALVCLAPGSEETE---AVTTIDLLVRGGIKVTTASVASDGNLTITCSRGVKLLADAPLVEV-ADGEYDVIVLPG-- 74 (196) T ss_pred CCCEEEEECCCCCCHHH---HHHHHHHHHHCCCEEEEEEECCCCCCEEEECCCCEEECCCCHHHC-CCCCCCEEECCC-- T ss_conf 98569999169850212---518999997779849999853899737994799789578677777-825588899178-- Q ss_pred ECCCCCHHHHHH-HHHHHHHHHHHHHCCCCCE Q ss_conf 006652467899-9999999999974399705 Q gi|254780346|r 76 MRGKTAHCDVIA-HAVTRGLVDLSINGSLPIG 106 (149) Q Consensus 76 IkGeT~H~e~I~-~~v~~gl~~lsl~~~~PI~ 106 (149) ..+-.+... ++....+.+-..+.+++|. T Consensus 75 ---G~~ga~~L~~~~~v~~~lk~~~~~gK~iA 103 (196) T PRK11574 75 ---GIKGAECFRDSPLLVETVKQFHRSGRIVA 103 (196) T ss_pred ---CCHHHHHHHHCHHHHHHHHHHHHCCCEEE T ss_conf ---80379998739899999999998799199 No 168 >cd06326 PBP1_STKc_like Type I periplasmic binding domain of uncharacterized extracellular ligand-binding proteins. The type I periplasmic binding domain of uncharacterized extracellular ligand-binding proteins, some of which contain a conserved catalytic serine/threonine protein kinase (STKc) domain in the N-terminal region. Members of this group are sequence-similar to the branched-chain amino acid ABC transporter leucine-isoleucine-valine-binding protein (LIVBP); their ligand specificity has not been determined experimentally, however. Probab=23.37 E-value=63 Score=14.45 Aligned_cols=63 Identities=13% Similarity=0.222 Sum_probs=43.9 Q ss_pred CCCEEEEEEECHHHHHHHHHHHHHHHHHHHCCCCEE-EEE-HHHHHHHHHHHHHHHHHHHCCCCCCEEEEEE Q ss_conf 587179998031289999999999999998799555-553-0014422699999986331137853566541 Q gi|254780346|r 4 FIPHVLIIEARFYENLSAMLFEGCVNVLHSRAVQWS-SIV-TPGVLEIPAAVSMVMNAKTRSVTYDGIIVLG 73 (149) Q Consensus 4 ~~~kI~IV~s~~~~~i~~~ll~ga~~~l~~~~~~~~-~i~-VPGa~EiP~a~~~~~~~~~~~~~~D~vIaLG 73 (149) ..+|++|+..+ .+....+.+.+.+.+++.|.++- ... -||.-+.-..+.++. ..++|+++..| T Consensus 135 g~kkvavl~~d--~~~g~~~~~~~~~~~~~~G~~vv~~~~~~~~~~Dfs~~l~~i~-----~~~pD~v~~~~ 199 (336) T cd06326 135 GLKRIAVFYQD--DAFGKDGLAGVEKALAARGLKPVATASYERNTADVAAAVAQLA-----AARPQAVIMVG 199 (336) T ss_pred CCCEEEEEECC--CHHHHHHHHHHHHHHHHCCCCEEEEEEECCCCCCHHHHHHHHH-----HCCCCEEEEEC T ss_conf 99759999358--7588999999999999779937999986899877799999998-----47979999927 No 169 >cd03795 GT1_like_4 This family is most closely related to the GT1 family of glycosyltransferases. Glycosyltransferases catalyze the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming glycosidic bonds. The acceptor molecule can be a lipid, a protein, a heterocyclic compound, or another carbohydrate residue. This group of glycosyltransferases is most closely related to the previously defined glycosyltransferase family 1 (GT1). The members of this family may transfer UDP, ADP, GDP, or CMP-linked sugars. The diverse enzymatic activities among members of this family reflect a wide range of biological functions. The protein structure available for this family has the GTB topology, one of the two protein topologies observed for nucleotide-sugar-dependent glycosyltransferases. GTB proteins have distinct N- and C- terminal domains each containing a typical Rossmann fold. The two domains have high structural homology despite minimal sequence homolog Probab=23.19 E-value=63 Score=14.43 Aligned_cols=36 Identities=11% Similarity=0.162 Sum_probs=26.7 Q ss_pred EEEEEEECHHHHH--HHHHHHHHHHHHHHCCCCEEEEE Q ss_conf 1799980312899--99999999999998799555553 Q gi|254780346|r 7 HVLIIEARFYENL--SAMLFEGCVNVLHSRAVQWSSIV 42 (149) Q Consensus 7 kI~IV~s~~~~~i--~~~ll~ga~~~l~~~~~~~~~i~ 42 (149) ||++|...|++++ ++..+..-.+.|.+.|.++.++. T Consensus 1 kIL~i~~~f~P~~GG~e~~~~~L~~~L~~~Gh~V~v~~ 38 (357) T cd03795 1 RVLHVGKFYPPDRGGIEQVIRDLAEGLAARGIEVAVLC 38 (357) T ss_pred CEEEECCCCCCCCCCHHHHHHHHHHHHHHCCCEEEEEE T ss_conf 99999382899898299999999999997799899998 No 170 >TIGR02040 PpsR-CrtJ transcriptional regulator PpsR; InterPro: IPR011785 This entry represents the transcriptional regulator PpsR which is strictly associated with photosynthetic proteobacteria and found in photosynthetic operons. PpsR has been reported to be a repressor . These proteins contain a Helix-Turn-Helix motif of the "fis" type.. Probab=22.76 E-value=25 Score=16.88 Aligned_cols=62 Identities=21% Similarity=0.263 Sum_probs=39.2 Q ss_pred ECHHHHHHHHHHHHHHHHHHHCCCC--------EEEEEHHHHHHHHHHHHHHHHHHH-CCCCCCEEEEEEEEE Q ss_conf 0312899999999999999987995--------555530014422699999986331-137853566541200 Q gi|254780346|r 13 ARFYENLSAMLFEGCVNVLHSRAVQ--------WSSIVTPGVLEIPAAVSMVMNAKT-RSVTYDGIIVLGVVM 76 (149) Q Consensus 13 s~~~~~i~~~ll~ga~~~l~~~~~~--------~~~i~VPGa~EiP~a~~~~~~~~~-~~~~~D~vIaLG~VI 76 (149) -+|++-+++.=.+-+...|.+..-+ ...+-.|+.+|+|.-. .+-... ..++..+++++|==. T Consensus 39 ~~w~ei~~~es~~k~~~~l~~a~~~g~~a~r~~~~~~~~P~~~ElP~~F--~~~~L~~sdGk~~~vLa~GrdL 109 (453) T TIGR02040 39 RRWEEIVTEESKEKVEALLSEAKRTGVGAVRVELNRFVLPSDLELPMEF--VLVRLGASDGKDEGVLALGRDL 109 (453) T ss_pred CCHHHHCCHHHHHHHHHHHHHCCCCCCCHHHHHHHHHCCCCCCCCCEEE--EEECCCCCCCCCCCEEEECCCC T ss_conf 8444413577899999999714688885777766541179997244034--6761678788887358884652 No 171 >KOG1017 consensus Probab=22.46 E-value=65 Score=14.34 Aligned_cols=34 Identities=24% Similarity=0.361 Sum_probs=14.8 Q ss_pred CCCHHHHHHHHHHHHHHHHHHH---CCCCCEEEEECCCC Q ss_conf 6524678999999999999974---39970565425588 Q gi|254780346|r 79 KTAHCDVIAHAVTRGLVDLSIN---GSLPIGNGIVVVDS 114 (149) Q Consensus 79 eT~H~e~I~~~v~~gl~~lsl~---~~~PI~~gILt~~n 114 (149) .|.|-||+-+ ++-|++|-++ +.+|-.-+-.|+.+ T Consensus 88 st~rsDF~F~--ADRLiRLViEE~LNqLPytec~VtTPT 124 (267) T KOG1017 88 STNRSDFVFN--ADRLIRLVIEECLNQLPYTECTVTTPT 124 (267) T ss_pred CCCCCCEEEE--HHHHHHHHHHHHHHCCCCCCEEEECCC T ss_conf 6864343660--888999999988622885320542688 No 172 >pfam08967 DUF1884 Domain of unknown function (DUF1884). This domain is found in a set of hypothetical bacterial proteins. It shows similarity to the N-terminus of ATP-synthase. Probab=22.41 E-value=65 Score=14.34 Aligned_cols=52 Identities=21% Similarity=0.239 Sum_probs=32.2 Q ss_pred HHHHHHHHHHHHHHCCCCEEEEEH-HHHHHH-HHHHHHHHHHHH---CCCCCCEEEE Q ss_conf 999999999999987995555530-014422-699999986331---1378535665 Q gi|254780346|r 20 SAMLFEGCVNVLHSRAVQWSSIVT-PGVLEI-PAAVSMVMNAKT---RSVTYDGIIV 71 (149) Q Consensus 20 ~~~ll~ga~~~l~~~~~~~~~i~V-PGa~Ei-P~a~~~~~~~~~---~~~~~D~vIa 71 (149) +-..++.+.+.|+.-|++.|++-| |+++|- +--+-.+.+-+- .---+||+|+ T Consensus 10 il~~ie~~inELk~eG~ePDiiL~G~e~~efl~e~~l~~~~lkv~~ieELG~DAVv~ 66 (85) T pfam08967 10 ILEIIEEKINELKMEGFEPDIILVGPEFYEFLSEDFLKVSNLKVYIIEELGSDAVIA 66 (85) T ss_pred HHHHHHHHHHHHHHCCCCCCEEEECHHHHHHHHHHHHHHHCCEEEEHHHCCCCEEEE T ss_conf 999999999999865899876998489998813888876186688787618851897 No 173 >cd06311 PBP1_ABC_sugar_binding_like_3 Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems. Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily, which consists of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis. Probab=22.00 E-value=67 Score=14.29 Aligned_cols=122 Identities=8% Similarity=0.020 Sum_probs=72.6 Q ss_pred CCEEEEEEECHHHHHHHHHHHHHHHHHHHCCCCEEEEEHHHHHHHHHHHHHHHHHHHCCCCCCEEEEEEEEECCCCCHHH Q ss_conf 87179998031289999999999999998799555553001442269999998633113785356654120006652467 Q gi|254780346|r 5 IPHVLIIEARFYENLSAMLFEGCVNVLHSRAVQWSSIVTPGVLEIPAAVSMVMNAKTRSVTYDGIIVLGVVMRGKTAHCD 84 (149) Q Consensus 5 ~~kI~IV~s~~~~~i~~~ll~ga~~~l~~~~~~~~~i~VPGa~EiP~a~~~~~~~~~~~~~~D~vIaLG~VIkGeT~H~e 84 (149) ..||+++.+.= ...+..-.+|+.+.++++++++ +-..+|-|+--.+.+.+-+-.....+.|++.+. .| T Consensus 127 ~g~v~il~G~~-~~~~~~R~~Gf~~~l~~~~i~v-v~~~~~~~~~~~a~~~~~~~L~~~pdi~~Ifa~----------nD 194 (274) T cd06311 127 NGNIVVLRGIP-TPIDNERVDAFDAAIAKYPIKI-LDRQYANWNRDDAFSVMQDLLTKFPKIDAVWAH----------DD 194 (274) T ss_pred CCCEEEEECCC-CCHHHHHHHHHHHHHHHCCCEE-EEEECCCCCHHHHHHHHHHHHHCCCCCCEEEEC----------CC T ss_conf 78579996899-8457999999999998779889-985038756899999999998438888889988----------98 Q ss_pred HHHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHH-CCCC---------CCCHHHHHHHHHHHHH Q ss_conf 89999999999999743997056542558899999950-6565---------7456999999999999 Q gi|254780346|r 85 VIAHAVTRGLVDLSINGSLPIGNGIVVVDSEQQAFDRV-SPSH---------LDRGGCAARSALAMIE 142 (149) Q Consensus 85 ~I~~~v~~gl~~lsl~~~~PI~~gILt~~n~~QA~~R~-~~~~---------~nkG~eaa~Aal~mi~ 142 (149) -.+-.+.++|.+.... +.+++.|. +-..++.+.. .++. ..-|+.|++.++++++ T Consensus 195 ~ma~Ga~~Al~~aG~~-~~~~vvG~---Dg~~~~~~~i~~G~~~~~atv~~~p~~~~~Av~~a~~~l~ 258 (274) T cd06311 195 DMAVGVLAAIKQAGRT-DIKFVVGG---AGSKDMIKMIMDGDPLIPADVLYPPSMIASAIDLTVALFQ 258 (274) T ss_pred CHHHHHHHHHHHCCCC-CCCEEEEE---CCCHHHHHHHHCCCCEEEEEEECCHHHHHHHHHHHHHHHC T ss_conf 0589999999976999-99789996---5998999999769974899980899999999999999977 No 174 >PRK11036 putative metallothionein SmtA; Provisional Probab=21.82 E-value=67 Score=14.26 Aligned_cols=49 Identities=16% Similarity=0.150 Sum_probs=30.3 Q ss_pred HHHHHHHHHHHHHHHHCCCCEEEEEHHHHH-HHHHHHHHHHHHHHCCCCCCEEEEEEEE Q ss_conf 999999999999999879955555300144-2269999998633113785356654120 Q gi|254780346|r 18 NLSAMLFEGCVNVLHSRAVQWSSIVTPGVL-EIPAAVSMVMNAKTRSVTYDGIIVLGVV 75 (149) Q Consensus 18 ~i~~~ll~ga~~~l~~~~~~~~~i~VPGa~-EiP~a~~~~~~~~~~~~~~D~vIaLG~V 75 (149) |++..|++.|+..+.+.|+....-++-+.. +++-. ....||.|+|.+++ T Consensus 73 D~S~~mL~~A~~~a~~~gv~~~~~~v~~~~q~l~~~---------~~~~fDlVlcHaVL 122 (256) T PRK11036 73 DLSAEMIQRAKQAAEAKGVSDNMQFIHCAAQDIAQH---------LETPVDLILFHAVL 122 (256) T ss_pred CCCHHHHHHHHHHHHHCCCCCEEEEEECCHHHHHHH---------CCCCCCEEEEEHHH T ss_conf 699999999999988649661279885689988542---------36886678651367 No 175 >smart00851 MGS MGS-like domain. This domain composes the whole protein of methylglyoxal synthetase and the domain is also found in Carbamoyl phosphate synthetase (CPS) where it forms a regulatory domain that binds to the allosteric effector ornithine. This family also includes inosicase. The known structures in this family show a common phosphate binding site PUBMED:10526357. Probab=21.81 E-value=67 Score=14.26 Aligned_cols=68 Identities=18% Similarity=0.182 Sum_probs=37.1 Q ss_pred HHHHHHHHCCCCEEEEEHHHHHH-HHHHHHHHHHHHHCCCCCCEEEEEEEEECCCCCHHHHHHHHHHHHHHHHHHHCCCC Q ss_conf 99999998799555553001442-26999999863311378535665412000665246789999999999999743997 Q gi|254780346|r 26 GCVNVLHSRAVQWSSIVTPGVLE-IPAAVSMVMNAKTRSVTYDGIIVLGVVMRGKTAHCDVIAHAVTRGLVDLSINGSLP 104 (149) Q Consensus 26 ga~~~l~~~~~~~~~i~VPGa~E-iP~a~~~~~~~~~~~~~~D~vIaLG~VIkGeT~H~e~I~~~v~~gl~~lsl~~~~P 104 (149) |..+.|+++|+++..+ +|-..| .|-..+++ ..+++|.||..- +.+.-....-...+.+.++++++| T Consensus 21 GTa~~L~~~Gi~v~~l-~~ki~~g~~~i~~~i-----~~~~IdlVInt~-------~~~~~~~~~d~~~iRr~a~~~~Ip 87 (90) T smart00851 21 GTAKFLREAGLPVKTL-HPKVHGGILAILDLI-----KNGEIDLVINTL-------YPLGAQPHEDGKALRRAAENIDIP 87 (90) T ss_pred HHHHHHHHCCCCCEEE-ECCCCCCCCCHHHHH-----CCCCEEEEEEEC-------CCCCCHHHHCCCCHHHHHHCCCCC T ss_conf 5899999759971043-024435610489981-----978879999846-------876323653588899998808988 Q ss_pred CE Q ss_conf 05 Q gi|254780346|r 105 IG 106 (149) Q Consensus 105 I~ 106 (149) .. T Consensus 88 ~~ 89 (90) T smart00851 88 GA 89 (90) T ss_pred CC T ss_conf 70 No 176 >cd04104 p47_IIGP_like p47 (47-kDa) family. The p47 GTPase family consists of several highly homologous proteins, including IGTP, TGTP/Mg21, IRG-47, GTPI, LRG-47, and IIGP1. They are found in higher eukaryotes where they play a role in immune resistance against intracellular pathogens. p47 proteins exist at low resting levels in mouse cells, but are strongly induced by Type II interferon (IFN-gamma). ITGP is critical for resistance to Toxoplasma gondii infection and in involved in inhibition of Coxsackievirus-B3-induced apoptosis. TGTP was shown to limit vesicular stomatitis virus (VSV) infection of fibroblasts in vitro. IRG-47 is involved in resistance to T. gondii infection. LRG-47 has been implicated in resistance to T. gondii, Listeria monocytogenes, Leishmania, and mycobacterial infections. IIGP1 has been shown to localize to the ER and to the Golgi membranes in IFN-induced cells and inflamed tissues. In macrophages, IIGP1 interacts with hook3, a microtubule binding protei Probab=21.41 E-value=68 Score=14.21 Aligned_cols=77 Identities=14% Similarity=0.090 Sum_probs=43.0 Q ss_pred EHHHHHHHHHHHHHHHHHHHCCCCCCEEEEEEEEECCCCCHHHHHHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHH Q ss_conf 30014422699999986331137853566541200066524678999999999999974399705654255889999995 Q gi|254780346|r 42 VTPGVLEIPAAVSMVMNAKTRSVTYDGIIVLGVVMRGKTAHCDVIAHAVTRGLVDLSINGSLPIGNGIVVVDSEQQAFDR 121 (149) Q Consensus 42 ~VPGa~EiP~a~~~~~~~~~~~~~~D~vIaLG~VIkGeT~H~e~I~~~v~~gl~~lsl~~~~PI~~gILt~~n~~QA~~R 121 (149) +.||+=-.-+..+..++.. .-.+||.||.+ -...|..--- .|...--+.++|.-+-.=-+++.-++..| T Consensus 58 DlPG~Gt~~f~~~~Yl~~~-~~~~yD~fiii------ss~rf~~nd~----~la~~i~~~gK~fyfVRsK~D~dl~n~~~ 126 (197) T cd04104 58 DLPGIGSTAFPPDDYLEEM-KFSEYDFFIII------SSTRFSSNDV----KLAKAIQCMGKKFYFVRTKVDRDLSNEQR 126 (197) T ss_pred CCCCCCCCCCCHHHHHHHC-CCCCCCEEEEE------ECCCCCHHHH----HHHHHHHHCCCCEEEEEECCCCCCCHHHH T ss_conf 2899998765989999865-85545789998------3886414269----99999998099289998612140005663 Q ss_pred HCCCCCCC Q ss_conf 06565745 Q gi|254780346|r 122 VSPSHLDR 129 (149) Q Consensus 122 ~~~~~~nk 129 (149) +.+..-|+ T Consensus 127 ~~p~~f~~ 134 (197) T cd04104 127 SKPRSFNR 134 (197) T ss_pred CCCCCCCH T ss_conf 78766599 No 177 >pfam03358 FMN_red NADPH-dependent FMN reductase. Probab=21.06 E-value=70 Score=14.17 Aligned_cols=37 Identities=16% Similarity=0.133 Sum_probs=28.8 Q ss_pred EEEEEEECHHH-HHHHHHHHHHHHHHHHCCCCEEEEEH Q ss_conf 17999803128-99999999999999987995555530 Q gi|254780346|r 7 HVLIIEARFYE-NLSAMLFEGCVNVLHSRAVQWSSIVT 43 (149) Q Consensus 7 kI~IV~s~~~~-~i~~~ll~ga~~~l~~~~~~~~~i~V 43 (149) ||+++.++-.+ -.+..|.+-+.+.|.+.|.+.+.++. T Consensus 2 kil~i~GS~r~~s~t~~l~~~~~~~l~~~g~e~~~idl 39 (147) T pfam03358 2 KILVISGSPRKGSNTRKLAEWAAELLEEAGAEVELIDL 39 (147) T ss_pred EEEEEECCCCCCCHHHHHHHHHHHHHHHCCCCEEEEEC T ss_conf 79999767998876999999999998776992599632 No 178 >cd06335 PBP1_ABC_ligand_binding_like_2 Type I periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type active transport systems that are predicted to be involved in transport of amino acids, peptides, or inorganic ions. This subgroup includes the type I periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type active transport systems that are predicted to be involved in transport of amino acids, peptides, or inorganic ions. Members of this group are sequence-similar to members of the family of ABC-type hydrophobic amino acid transporters, such as leucine-isoleucine-valine-binding protein (LIVBP); however their ligand specificity has not been determined experimentally. Probab=20.99 E-value=70 Score=14.16 Aligned_cols=62 Identities=15% Similarity=0.145 Sum_probs=43.3 Q ss_pred CCEEEEEEECHHHHHHHHHHHHHHHHHHHCCCCEEE-E-EHHHHHHHHHHHHHHHHHHHCCCCCCEEEEEE Q ss_conf 871799980312899999999999999987995555-5-30014422699999986331137853566541 Q gi|254780346|r 5 IPHVLIIEARFYENLSAMLFEGCVNVLHSRAVQWSS-I-VTPGVLEIPAAVSMVMNAKTRSVTYDGIIVLG 73 (149) Q Consensus 5 ~~kI~IV~s~~~~~i~~~ll~ga~~~l~~~~~~~~~-i-~VPGa~EiP~a~~~~~~~~~~~~~~D~vIaLG 73 (149) .+|++|+... .+....+.+++.+.+++.|.++-. . .-||.-+.-..+.++. ..++|+|+..| T Consensus 138 ~kkvai~~~d--~~~G~~~~~~~~~~~~~~G~~vv~~~~~~~~~~Df~~~l~~i~-----~~~pD~V~~~~ 201 (347) T cd06335 138 FKKVALLLDN--TGWGRSNRKDLTAALAARGLKPVAVEWFNWGDKDMTAQLLRAK-----AAGADAIIIVG 201 (347) T ss_pred CCEEEEEEEC--CHHHHHHHHHHHHHHHHCCCEEEEEEEECCCCCCHHHHHHHHH-----HCCCCEEEEEC T ss_conf 8669999707--6366899999999998659867578840799834899999998-----66999999947 No 179 >cd06313 PBP1_ABC_sugar_binding_like_5 Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems. Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily, which consists of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis. Probab=20.55 E-value=71 Score=14.10 Aligned_cols=122 Identities=16% Similarity=0.160 Sum_probs=67.6 Q ss_pred CCEEEEEEECHHHHHHHHHHHHHHHHHHHCCCCEEEE-EHHHHHHHHHHHHHHHHHHHCCCCCCEEEEEEEEECCCCCHH Q ss_conf 8717999803128999999999999999879955555-300144226999999863311378535665412000665246 Q gi|254780346|r 5 IPHVLIIEARFYENLSAMLFEGCVNVLHSRAVQWSSI-VTPGVLEIPAAVSMVMNAKTRSVTYDGIIVLGVVMRGKTAHC 83 (149) Q Consensus 5 ~~kI~IV~s~~~~~i~~~ll~ga~~~l~~~~~~~~~i-~VPGa~EiP~a~~~~~~~~~~~~~~D~vIaLG~VIkGeT~H~ 83 (149) ..+|+++...-.....+.-.+|+.+.+++. -.++++ ..|+-|..--+.+..-.-.....+.|++++ |. T Consensus 123 ~g~v~ii~g~~~~~~~~~R~~Gf~~~l~~~-~~i~vv~~~~~~~~~~~a~~~~~~~L~~~pdid~I~~----------~n 191 (272) T cd06313 123 KGKIAMLQGALGHTGAQGRAQGFNDVIKKY-PDIEVVDEQPANWDVSKAARIWETWLTKYPQLDGAFC----------HN 191 (272) T ss_pred CCEEEEEECCCCCHHHHHHHHHHHHHHHHC-CCCEEEEEEECCCCHHHHHHHHHHHHHHCCCCCEEEE----------CC T ss_conf 972999847988689999999999999877-9919999862687689999999999964999878998----------88 Q ss_pred HHHHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHHCCCC---------CCCHHHHHHHHHHHHH Q ss_conf 7899999999999997439970565425588999999506565---------7456999999999999 Q gi|254780346|r 84 DVIAHAVTRGLVDLSINGSLPIGNGIVVVDSEQQAFDRVSPSH---------LDRGGCAARSALAMIE 142 (149) Q Consensus 84 e~I~~~v~~gl~~lsl~~~~PI~~gILt~~n~~QA~~R~~~~~---------~nkG~eaa~Aal~mi~ 142 (149) |..+-.+.+++.... ..++. |.+.+...++++...... -.-|+.+++++++.++ T Consensus 192 D~~a~Ga~~Al~~aG-~~~v~----v~g~Dg~~~~l~~I~~G~~~atv~q~~~~~G~~av~~a~~~~~ 254 (272) T cd06313 192 DSMALAAYQIMKAAG-RTKIV----IGGVDGDPPAIQAVSDGRMVATVRNPACRIHGGAIAAGVRIVR 254 (272) T ss_pred CHHHHHHHHHHHHCC-CCCCE----EEEECCCHHHHHHHHCCCCEEEEECCHHHHHHHHHHHHHHHHC T ss_conf 477899999999769-99868----9997899999999985991899806999999999999999976 No 180 >KOG3135 consensus Probab=20.16 E-value=73 Score=14.05 Aligned_cols=43 Identities=23% Similarity=0.241 Sum_probs=29.6 Q ss_pred CCEEEEEEECHHHHHHHHHHHHHHHHHHHCCCCEEEEEHHHHHH Q ss_conf 87179998031289999999999999998799555553001442 Q gi|254780346|r 5 IPHVLIIEARFYENLSAMLFEGCVNVLHSRAVQWSSIVTPGVLE 48 (149) Q Consensus 5 ~~kI~IV~s~~~~~i~~~ll~ga~~~l~~~~~~~~~i~VPGa~E 48 (149) |+||+||.=+.|..| +.|-+.-++-.+..+-+-+...||..+- T Consensus 1 ~~kv~iv~ys~yghv-~~lAe~~kkGie~a~geA~i~qVpEtl~ 43 (203) T KOG3135 1 MPKVAIVIYSTYGHV-AKLAEAEKKGIESAGGEATIYQVPETLS 43 (203) T ss_pred CCEEEEEEEECCCHH-HHHHHHHHHHHHCCCCEEEEEECCCCCC T ss_conf 963899999802289-9999999700330698168997655168 No 181 >TIGR02196 GlrX_YruB Glutaredoxin-like protein, YruB-family; InterPro: IPR011911 Glutaredoxins , , , also known as thioltransferases (disulphide reductases, are small proteins of approximately one hundred amino-acid residues which utilise glutathione and NADPH as cofactors. Oxidized glutathione is regenerated by glutathione reductase. Together these components compose the glutathione system . Glutaredoxin functions as an electron carrier in the glutathione-dependent synthesis of deoxyribonucleotides by the enzyme ribonucleotide reductase. Like thioredoxin, which functions in a similar way, glutaredoxin possesses an active centre disulphide bond . It exists in either a reduced or an oxidized form where the two cysteine residues are linked in an intramolecular disulphide bond. Glutaredoxin has been sequenced in a variety of species. On the basis of extensive sequence similarity, it has been proposed that Vaccinia virus protein O2L is most probably a glutaredoxin. Finally, it must be noted that Bacteriophage T4 thioredoxin seems also to be evolutionary related. In position 5 of the pattern T4 thioredoxin has Val instead of Pro. This glutaredoxin-like protein family contains the conserved CxxC motif and includes the Clostridium pasteurianum protein YruB which has been cloned from a rubredoxin operon . Somewhat related to NrdH, it is unknown whether this protein actually interacts with glutathione/glutathione reducatase, or, like NrdH, some other reductant system.. Probab=20.07 E-value=73 Score=14.04 Aligned_cols=51 Identities=16% Similarity=0.089 Sum_probs=33.6 Q ss_pred HHHHHHHHHCCCCEEEEEHHHHHHHHHHHHHHHHHHH-CCCCCCEE---EEEEEEECC Q ss_conf 9999999987995555530014422699999986331-13785356---654120006 Q gi|254780346|r 25 EGCVNVLHSRAVQWSSIVTPGVLEIPAAVSMVMNAKT-RSVTYDGI---IVLGVVMRG 78 (149) Q Consensus 25 ~ga~~~l~~~~~~~~~i~VPGa~EiP~a~~~~~~~~~-~~~~~D~v---IaLG~VIkG 78 (149) ..|++.|..+|++++.+.|- .=+.|.+.+++... ..+-+-.+ |.=+-||.| T Consensus 14 ~~aK~yL~~~gv~f~~~dV~---~d~~A~~~~~k~~gG~~gVPv~vsGdi~~~~i~~G 68 (79) T TIGR02196 14 KKAKEYLTSKGVAFEEIDVE---KDSAAREELLKKLGGQRGVPVIVSGDIGTHKIIVG 68 (79) T ss_pred HHHHHHHHHCCCCEEEECCC---CCHHHHHHHHHHHCCCCCCCEEEECCCCCCEEEEE T ss_conf 89999999549945763433---69788999999838985455576342379724870 Done!