Query gi|254780282|ref|YP_003064695.1| putative transcription regulator protein [Candidatus Liberibacter asiaticus str. psy62] Match_columns 299 No_of_seqs 183 out of 20759 Neff 10.3 Searched_HMMs 39220 Date Sun May 29 15:56:28 2011 Command /home/congqian_1/programs/hhpred/hhsearch -i 254780282.hhm -d /home/congqian_1/database/cdd/Cdd.hhm No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM 1 PRK10632 putative DNA-binding 100.0 0 0 399.6 13.8 290 3-296 1-294 (309) 2 TIGR03418 chol_sulf_TF putativ 100.0 0 0 396.5 15.0 287 3-293 1-291 (291) 3 PRK09801 transcriptional activ 100.0 0 0 394.4 14.1 288 5-296 8-298 (310) 4 PRK12684 transcriptional regul 100.0 0 0 392.1 14.0 288 3-294 1-295 (313) 5 PRK11242 DNA-binding transcrip 100.0 0 0 391.0 14.5 286 3-293 1-290 (292) 6 PRK11139 DNA-binding transcrip 100.0 0 0 387.8 15.0 286 3-296 5-294 (295) 7 PRK11013 DNA-binding transcrip 100.0 0 0 386.8 15.0 289 1-296 1-296 (309) 8 CHL00180 rbcR LysR transcripti 100.0 0 0 385.3 15.5 293 1-294 3-303 (307) 9 PRK12682 transcriptional regul 100.0 0 0 385.6 14.1 289 3-295 1-296 (309) 10 PRK10086 DNA-binding transcrip 100.0 0 0 383.1 16.3 294 1-298 11-311 (311) 11 PRK12683 transcriptional regul 100.0 0 0 384.8 14.1 290 3-296 1-297 (308) 12 PRK10837 putative DNA-binding 100.0 0 0 384.1 13.9 283 1-293 1-289 (291) 13 PRK11151 DNA-binding transcrip 100.0 0 0 381.0 15.9 288 3-295 1-294 (305) 14 PRK09791 putative DNA-binding 100.0 0 0 378.5 15.4 290 1-296 3-299 (302) 15 PRK11233 nitrogen assimilation 100.0 0 0 374.4 15.7 288 3-298 1-302 (305) 16 PRK12679 cbl transcriptional r 100.0 0 0 373.9 13.9 286 3-292 1-293 (316) 17 PRK09906 DNA-binding transcrip 100.0 0 0 371.6 15.3 289 3-296 1-293 (296) 18 TIGR03339 phn_lysR aminoethylp 100.0 0 0 369.8 15.1 275 7-289 1-278 (279) 19 PRK12681 cysB transcriptional 100.0 0 0 368.9 13.9 286 3-292 1-293 (324) 20 PRK11074 putative DNA-binding 100.0 0 0 367.9 13.3 286 3-297 2-295 (300) 21 PRK10341 DNA-binding transcrip 100.0 0 0 365.7 15.0 286 4-295 8-299 (312) 22 TIGR03298 argP transcriptional 100.0 0 0 358.9 12.1 284 3-297 1-291 (292) 23 PRK12680 transcriptional regul 100.0 0 0 354.1 13.4 284 3-290 1-291 (327) 24 PRK10094 DNA-binding transcrip 100.0 0 0 350.7 13.1 282 3-293 2-292 (308) 25 PRK13348 chromosome replicatio 100.0 0 0 344.3 13.5 284 3-297 2-292 (294) 26 PRK03635 chromosome replicatio 100.0 0 0 344.7 12.8 283 3-297 2-291 (295) 27 PRK03601 transcriptional regul 100.0 0 0 342.6 14.3 269 3-292 1-272 (275) 28 PRK09986 DNA-binding transcrip 100.0 0 0 345.8 11.3 273 13-291 1-277 (278) 29 PRK10082 putative DNA-binding 100.0 0 0 341.2 14.2 285 2-293 10-298 (303) 30 PRK09508 leuO leucine transcri 100.0 0 0 323.7 14.1 287 2-295 21-313 (314) 31 COG0583 LysR Transcriptional r 100.0 0 0 311.9 14.4 288 3-297 1-294 (297) 32 PRK11716 DNA-binding transcrip 100.0 0 0 311.6 11.7 261 27-292 1-268 (269) 33 PRK11062 nhaR transcriptional 100.0 0 0 306.9 14.5 280 1-290 1-289 (296) 34 TIGR02424 TF_pcaQ pca operon t 100.0 0 0 297.1 12.9 292 2-296 2-300 (300) 35 TIGR02036 dsdC D-serine deamin 100.0 0 0 292.5 10.1 288 3-295 8-302 (302) 36 PRK11482 putative DNA-binding 100.0 6.3E-39 1.6E-43 244.9 9.4 260 26-293 1-265 (266) 37 PRK10216 DNA-binding transcrip 100.0 8.5E-33 2.2E-37 209.4 10.7 264 27-296 1-286 (288) 38 pfam03466 LysR_substrate LysR 100.0 3.7E-31 9.3E-36 199.9 9.1 201 89-294 2-208 (209) 39 pfam00126 HTH_1 Bacterial regu 99.8 4.3E-19 1.1E-23 130.0 7.8 60 5-64 1-60 (60) 40 PRK10676 DNA-binding transcrip 98.4 2.9E-07 7.3E-12 61.5 4.5 74 5-78 19-97 (262) 41 COG2005 ModE N-terminal domain 98.3 7.7E-07 2E-11 59.0 4.4 83 3-85 17-104 (130) 42 PRK11050 manganese transport r 97.5 0.0001 2.6E-09 46.7 3.2 73 6-81 40-116 (155) 43 smart00347 HTH_MARR helix_turn 97.3 0.00033 8.5E-09 43.7 4.6 75 2-79 7-90 (101) 44 PRK10677 modA molybdate transp 97.3 0.00075 1.9E-08 41.7 5.9 202 88-293 22-243 (257) 45 PRK03902 manganese transport t 97.2 0.00058 1.5E-08 42.3 4.6 73 6-81 8-84 (142) 46 COG0725 ModA ABC-type molybdat 96.9 0.0061 1.5E-07 36.4 7.8 200 89-294 26-244 (258) 47 smart00529 HTH_DTXR Helix-turn 96.9 0.00059 1.5E-08 42.3 2.4 61 20-83 2-63 (96) 48 COG1846 MarR Transcriptional r 96.8 0.0017 4.4E-08 39.6 4.5 69 3-74 20-97 (126) 49 COG1321 TroR Mn-dependent tran 96.8 0.0031 7.9E-08 38.1 5.4 78 5-84 9-89 (154) 50 PRK03573 transcriptional regul 96.8 0.0023 5.9E-08 38.9 4.7 76 2-80 28-113 (144) 51 TIGR00637 ModE_repress ModE mo 96.7 0.002 5.1E-08 39.2 3.9 79 3-81 2-86 (101) 52 PRK11512 DNA-binding transcrip 96.4 0.0042 1.1E-07 37.4 4.0 70 2-74 37-115 (144) 53 pfam09048 Cro Cro. Members of 96.3 0.0062 1.6E-07 36.4 4.4 45 14-72 9-55 (58) 54 PRK11169 leucine-responsive tr 96.1 0.0098 2.5E-07 35.2 4.5 44 1-44 10-55 (164) 55 TIGR01884 cas_HTH CRISPR locus 95.9 0.033 8.5E-07 32.1 6.5 61 3-63 167-231 (231) 56 PRK10141 DNA-binding transcrip 95.9 0.025 6.3E-07 32.9 5.8 70 4-77 13-86 (106) 57 cd00090 HTH_ARSR Arsenical Res 95.9 0.023 5.8E-07 33.1 5.6 57 4-61 6-65 (78) 58 PRK11886 biotin--protein ligas 95.8 0.051 1.3E-06 31.1 7.1 57 7-64 6-64 (319) 59 TIGR01256 modA molybdate ABC t 95.7 0.025 6.5E-07 32.8 5.3 185 108-293 8-215 (225) 60 COG2998 TupB ABC-type tungstat 95.6 0.09 2.3E-06 29.6 7.9 202 89-294 26-253 (280) 61 pfam00497 SBP_bac_3 Bacterial 95.6 0.13 3.4E-06 28.6 8.6 175 107-295 24-209 (224) 62 pfam01022 HTH_5 Bacterial regu 95.5 0.038 9.6E-07 31.8 5.5 38 7-44 4-42 (47) 63 PRK11179 DNA-binding transcrip 95.5 0.051 1.3E-06 31.0 6.1 44 1-44 5-50 (153) 64 COG4742 Predicted transcriptio 95.3 0.024 6.2E-07 32.9 4.1 76 7-85 15-91 (260) 65 smart00062 PBPb Bacterial peri 95.2 0.22 5.7E-06 27.3 9.5 170 107-295 25-206 (219) 66 COG1522 Lrp Transcriptional re 95.1 0.078 2E-06 30.0 6.1 40 4-44 10-49 (154) 67 TIGR03261 phnS2 putative 2-ami 94.9 0.066 1.7E-06 30.4 5.2 203 88-293 17-273 (334) 68 pfam01047 MarR MarR family. Th 94.8 0.087 2.2E-06 29.7 5.8 42 3-44 1-44 (59) 69 COG1654 BirA Biotin operon rep 94.8 0.098 2.5E-06 29.4 5.9 49 17-66 19-67 (79) 70 smart00344 HTH_ASNC helix_turn 94.5 0.12 3.1E-06 28.9 5.8 42 3-44 1-44 (108) 71 pfam01325 Fe_dep_repress Iron 94.4 0.092 2.3E-06 29.6 5.0 39 6-44 6-47 (58) 72 PRK11260 cystine transporter s 94.2 0.4 1E-05 25.9 8.4 185 91-293 37-243 (264) 73 smart00418 HTH_ARSR helix_turn 94.0 0.059 1.5E-06 30.7 3.4 41 15-56 8-48 (66) 74 COG2522 Predicted transcriptio 93.8 0.11 2.8E-06 29.1 4.5 33 8-40 13-45 (119) 75 TIGR02702 SufR_cyano iron-sulf 93.3 0.11 2.7E-06 29.2 3.7 89 11-115 7-107 (215) 76 cd06170 LuxR_C_like C-terminal 93.3 0.34 8.6E-06 26.3 6.2 45 4-48 2-46 (57) 77 pfam08279 HTH_11 HTH domain. T 93.0 0.31 8E-06 26.5 5.8 49 8-57 3-54 (55) 78 pfam04967 HTH_10 HTH DNA bindi 92.9 0.43 1.1E-05 25.7 6.3 42 4-45 2-51 (53) 79 PRK10870 transcriptional repre 92.7 0.28 7.1E-06 26.8 5.1 70 4-76 54-134 (176) 80 pfam02954 HTH_8 Bacterial regu 92.6 0.12 3.2E-06 28.8 3.2 25 16-40 17-41 (42) 81 COG1910 Periplasmic molybdate- 92.6 0.34 8.6E-06 26.3 5.4 152 130-292 29-199 (223) 82 pfam00196 GerE Bacterial regul 92.5 0.52 1.3E-05 25.2 6.3 46 3-48 4-49 (58) 83 smart00421 HTH_LUXR helix_turn 92.4 0.56 1.4E-05 25.0 6.3 46 3-48 4-49 (58) 84 PRK10859 putative transglycosy 92.2 0.49 1.2E-05 25.4 5.9 156 91-257 41-219 (507) 85 pfam01638 HxlR HxlR-like helix 92.0 0.23 6E-06 27.2 4.0 66 5-73 6-79 (90) 86 TIGR02607 antidote_HigA addict 91.9 0.2 5.1E-06 27.6 3.6 29 19-47 22-61 (81) 87 PRK10651 transcriptional regul 91.9 0.64 1.6E-05 24.7 6.2 38 107-144 17-57 (216) 88 COG4189 Predicted transcriptio 91.8 0.38 9.6E-06 26.0 4.9 37 8-44 26-64 (308) 89 PRK04168 hypothetical protein; 91.7 0.41 1E-05 25.8 5.0 84 88-172 28-122 (336) 90 PRK10797 glutamate and asparta 91.4 1 2.6E-05 23.5 8.6 190 91-295 38-257 (302) 91 PRK09495 glnH glutamine ABC tr 91.3 1 2.7E-05 23.4 6.7 170 92-278 24-216 (247) 92 PRK04217 hypothetical protein; 91.2 0.57 1.4E-05 25.0 5.3 62 3-66 43-105 (110) 93 PRK09775 hypothetical protein; 91.0 0.11 2.7E-06 29.2 1.4 36 13-52 6-43 (443) 94 PRK09744 DNA-binding transcrip 90.6 0.28 7.1E-06 26.8 3.2 37 13-49 6-50 (75) 95 COG0226 PstS ABC-type phosphat 90.2 1.3 3.4E-05 22.9 6.7 202 90-293 40-299 (318) 96 PRK10403 transcriptional regul 90.2 1.1 2.9E-05 23.3 6.1 17 108-124 18-34 (215) 97 COG1339 Transcriptional regula 89.6 0.18 4.6E-06 27.8 1.6 93 18-118 20-116 (214) 98 PRK09958 DNA-binding transcrip 89.6 1.4 3.7E-05 22.7 6.2 15 110-124 62-76 (204) 99 COG1497 Predicted transcriptio 89.5 1 2.7E-05 23.4 5.5 46 18-66 26-72 (260) 100 PRK09834 DNA-binding transcrip 89.1 0.82 2.1E-05 24.0 4.7 54 6-62 12-70 (264) 101 COG4190 Predicted transcriptio 89.1 1.6 4.1E-05 22.4 6.3 41 19-60 80-120 (144) 102 PRK10163 DNA-binding transcrip 89.0 0.51 1.3E-05 25.3 3.6 56 5-61 28-83 (271) 103 COG2345 Predicted transcriptio 89.0 0.63 1.6E-05 24.7 4.0 55 14-69 20-83 (218) 104 COG1733 Predicted transcriptio 88.8 0.71 1.8E-05 24.4 4.2 66 5-73 24-97 (120) 105 pfam01710 Transposase_14 Trans 88.7 0.85 2.2E-05 24.0 4.6 44 1-47 1-46 (120) 106 PRK09483 response regulator; P 88.1 1.9 4.8E-05 22.0 6.2 16 109-124 14-29 (216) 107 PRK09935 transcriptional regul 88.0 1.9 4.8E-05 22.0 6.1 18 109-126 16-33 (210) 108 PRK10360 DNA-binding transcrip 88.0 1.9 4.9E-05 21.9 6.0 37 108-144 13-52 (196) 109 PRK10840 transcriptional regul 87.5 2.1 5.2E-05 21.7 6.0 15 111-125 70-84 (216) 110 PRK04172 pheS phenylalanyl-tRN 87.4 1.7 4.3E-05 22.3 5.4 71 1-71 2-74 (501) 111 cd00134 PBPb Bacterial peripla 86.9 2.2 5.6E-05 21.6 9.7 168 107-293 24-203 (218) 112 pfam02001 DUF134 Protein of un 86.6 1.5 3.9E-05 22.5 4.8 49 3-51 37-86 (100) 113 PRK11477 carbohydrate diacid t 86.5 2.3 5.7E-05 21.5 5.6 20 38-57 15-34 (385) 114 pfam05043 Mga Mga helix-turn-h 86.0 1.4 3.7E-05 22.7 4.4 44 5-49 19-65 (87) 115 PRK09392 ftrB transcriptional 85.5 1.2 3E-05 23.1 3.8 16 111-126 111-126 (236) 116 PRK09390 fixJ response regulat 85.4 2.6 6.7E-05 21.1 6.2 21 109-129 63-83 (202) 117 PRK10014 DNA-binding transcrip 85.1 0.46 1.2E-05 25.5 1.5 82 19-119 8-90 (342) 118 TIGR02337 HpaR homoprotocatech 85.0 0.63 1.6E-05 24.7 2.2 78 2-82 25-112 (130) 119 pfam04545 Sigma70_r4 Sigma-70, 84.1 1.1 2.7E-05 23.4 3.1 27 16-42 19-45 (50) 120 PTZ00326 phenylalanyl-tRNA syn 84.1 1.8 4.6E-05 22.1 4.2 71 1-71 2-74 (505) 121 smart00419 HTH_CRP helix_turn_ 83.7 1.8 4.6E-05 22.1 4.1 37 20-59 11-47 (48) 122 COG1342 Predicted DNA-binding 83.2 3 7.6E-05 20.8 5.0 50 2-51 33-83 (99) 123 COG4197 Uncharacterized protei 82.9 1.7 4.3E-05 22.2 3.7 34 7-40 2-35 (96) 124 COG1568 Predicted methyltransf 82.7 2.1 5.5E-05 21.7 4.1 58 9-69 26-83 (354) 125 PRK11917 bifunctional adhesin/ 82.7 3.5 8.9E-05 20.4 7.1 187 91-293 36-245 (259) 126 PRK11569 transcriptional repre 80.9 1.5 3.9E-05 22.5 2.9 54 5-61 31-86 (274) 127 COG2197 CitB Response regulato 80.6 4.2 0.00011 20.0 5.6 12 111-122 15-26 (211) 128 TIGR03541 reg_near_HchA LuxR f 80.4 4.2 0.00011 19.9 6.1 23 30-52 16-38 (232) 129 COG1414 IclR Transcriptional r 80.1 2.4 6.2E-05 21.3 3.7 53 6-62 8-63 (246) 130 PRK09863 putative frv operon r 79.4 3.3 8.4E-05 20.6 4.2 52 15-66 90-141 (585) 131 PRK06424 transcription factor; 79.1 4.2 0.00011 20.0 4.6 18 225-242 82-99 (144) 132 smart00497 IENR1 Intron encode 78.9 1.1 2.8E-05 23.3 1.6 25 16-40 16-40 (53) 133 pfam09339 HTH_IclR IclR helix- 78.8 2.8 7.2E-05 20.9 3.7 39 6-44 7-45 (52) 134 COG1349 GlpR Transcriptional r 78.8 4.8 0.00012 19.6 5.8 61 1-64 1-63 (253) 135 PRK10188 DNA-binding transcrip 78.2 5 0.00013 19.5 6.3 14 278-291 179-192 (240) 136 smart00346 HTH_ICLR helix_turn 77.8 3.2 8.2E-05 20.6 3.7 60 7-67 7-69 (91) 137 PRK10434 srlR DNA-bindng trans 76.4 5.6 0.00014 19.2 5.6 56 4-62 4-61 (256) 138 COG1609 PurR Transcriptional r 76.0 1.7 4.2E-05 22.3 1.8 111 19-147 2-122 (333) 139 PRK00430 fis DNA-binding prote 75.9 3.3 8.5E-05 20.5 3.4 27 15-41 69-95 (98) 140 COG3888 Predicted transcriptio 75.2 3.9 9.8E-05 20.2 3.5 103 20-144 23-127 (321) 141 TIGR02395 rpoN_sigma RNA polym 74.7 0.72 1.8E-05 24.4 -0.3 10 289-298 319-328 (477) 142 cd06171 Sigma70_r4 Sigma70, re 74.5 6.3 0.00016 18.9 4.7 30 15-44 24-53 (55) 143 PRK00118 putative DNA-binding 73.7 5.4 0.00014 19.3 4.0 32 15-46 31-62 (105) 144 PRK09861 cytoplasmic membrane 73.3 6.7 0.00017 18.8 5.3 195 92-296 31-258 (272) 145 TIGR01529 argR_whole arginine 73.3 1.3 3.3E-05 22.9 0.7 15 27-41 31-46 (155) 146 PRK11553 alkanesulfonate trans 73.3 2.4 6.1E-05 21.4 2.1 196 91-297 25-239 (314) 147 PRK00215 LexA repressor; Valid 73.0 6.1 0.00016 19.0 4.1 45 18-65 24-72 (204) 148 pfam04297 UPF0122 Putative hel 72.6 5.9 0.00015 19.1 3.9 40 6-45 21-61 (101) 149 COG4623 Predicted soluble lyti 72.1 7.2 0.00018 18.6 5.1 150 91-249 21-187 (473) 150 pfam01726 LexA_DNA_bind LexA D 71.3 5.7 0.00015 19.2 3.6 42 3-44 4-53 (65) 151 pfam05225 HTH_psq helix-turn-h 70.9 7.7 0.0002 18.4 4.5 34 7-40 4-39 (45) 152 pfam09862 DUF2089 Protein of u 69.6 8.2 0.00021 18.3 6.1 46 3-48 34-80 (113) 153 pfam04552 Sigma54_DBD Sigma-54 69.2 4.1 0.0001 20.0 2.5 24 17-40 49-72 (160) 154 PRK11475 DNA-binding transcrip 69.0 8.4 0.00021 18.2 5.9 36 109-144 56-96 (205) 155 COG2771 CsgD DNA-binding HTH d 69.0 8.4 0.00021 18.2 6.1 47 2-48 4-50 (65) 156 pfam03180 Lipoprotein_9 NLPA l 68.8 8.5 0.00022 18.2 6.0 191 95-297 1-223 (236) 157 pfam01978 TrmB Sugar-specific 68.3 8.7 0.00022 18.1 5.7 44 2-45 5-50 (68) 158 PRK05932 RNA polymerase factor 67.8 4.8 0.00012 19.6 2.6 22 19-40 18-39 (461) 159 PRK09391 fixK transcriptional 67.6 4.8 0.00012 19.6 2.6 15 111-125 111-125 (224) 160 pfam07453 NUMOD1 NUMOD1 domain 67.4 2 5E-05 21.9 0.6 23 16-38 15-37 (37) 161 cd00092 HTH_CRP helix_turn_hel 67.2 4.7 0.00012 19.7 2.5 34 20-56 28-61 (67) 162 pfam00392 GntR Bacterial regul 66.7 6.5 0.00017 18.8 3.2 26 19-44 26-51 (64) 163 COG1510 Predicted transcriptio 66.2 6 0.00015 19.0 2.9 33 16-48 40-72 (177) 164 cd07377 WHTH_GntR Winged helix 66.0 7.6 0.00019 18.5 3.4 26 19-44 27-52 (66) 165 COG2739 Uncharacterized protei 65.4 9.9 0.00025 17.8 3.9 33 14-46 30-62 (105) 166 PRK11564 stationary phase indu 65.0 10 0.00026 17.7 5.9 47 16-62 29-79 (426) 167 PRK10906 DNA-binding transcrip 65.0 10 0.00026 17.7 6.0 60 1-63 1-62 (252) 168 COG1725 Predicted transcriptio 64.6 10 0.00026 17.7 4.4 51 17-69 35-85 (125) 169 smart00345 HTH_GNTR helix_turn 64.5 8.1 0.00021 18.3 3.3 26 19-44 22-47 (60) 170 PRK01905 DNA-binding protein F 63.9 11 0.00027 17.6 5.0 26 16-41 49-74 (77) 171 pfam07900 DUF1670 Protein of u 63.7 11 0.00028 17.6 5.2 26 24-49 112-137 (220) 172 COG0640 ArsR Predicted transcr 63.5 11 0.00028 17.6 5.4 50 6-56 26-77 (110) 173 TIGR01764 excise DNA binding d 63.1 6.5 0.00016 18.9 2.6 37 18-59 2-38 (49) 174 PRK10411 DNA-binding transcrip 62.8 11 0.00029 17.5 4.0 52 6-60 5-58 (240) 175 cd01392 HTH_LacI Helix-turn-he 62.7 5.4 0.00014 19.3 2.1 19 22-40 2-20 (52) 176 PRK12423 LexA repressor; Provi 61.9 12 0.0003 17.4 5.9 56 3-61 4-70 (202) 177 COG1508 RpoN DNA-directed RNA 61.7 7.1 0.00018 18.6 2.6 21 42-62 39-59 (444) 178 cd00283 GIY-YIG_Cterm GIYX(10- 60.6 6.1 0.00016 19.0 2.1 21 18-38 81-101 (113) 179 pfam00356 LacI Bacterial regul 60.1 9.2 0.00023 18.0 2.9 22 19-40 1-22 (46) 180 smart00354 HTH_LACI helix_turn 59.7 9.2 0.00024 18.0 2.9 22 19-40 2-23 (70) 181 PRK00082 hrcA heat-inducible t 59.6 13 0.00033 17.2 4.1 67 1-68 1-77 (339) 182 COG1458 Predicted DNA-binding 59.6 1.9 4.8E-05 22.0 -0.7 115 27-144 49-178 (221) 183 COG1737 RpiR Transcriptional r 59.5 11 0.00028 17.5 3.3 27 14-40 33-59 (281) 184 PRK11161 fumarate/nitrate redu 58.8 8.6 0.00022 18.1 2.6 17 110-126 117-133 (235) 185 COG3093 VapI Plasmid maintenan 58.8 13 0.00034 17.1 3.8 23 18-40 24-46 (104) 186 PRK12469 RNA polymerase factor 58.8 7.1 0.00018 18.6 2.2 36 15-52 14-49 (475) 187 pfam01418 HTH_6 Helix-turn-hel 58.7 13 0.00034 17.1 3.7 28 14-41 31-58 (106) 188 COG3355 Predicted transcriptio 56.5 14 0.00037 16.8 4.3 58 6-69 28-88 (126) 189 pfam04069 OpuAC Substrate bind 55.7 15 0.00038 16.8 5.5 188 94-289 2-224 (256) 190 PRK11063 metQ DL-methionine tr 55.3 15 0.00039 16.7 5.7 195 93-296 31-257 (271) 191 COG3835 CdaR Sugar diacid util 55.0 15 0.00039 16.7 4.2 16 71-86 55-70 (376) 192 PRK09726 DNA-binding transcrip 54.6 16 0.0004 16.7 4.8 47 17-63 25-82 (88) 193 PRK10727 DNA-binding transcrip 54.4 13 0.00033 17.2 2.9 22 19-40 3-24 (342) 194 PRK09526 lacI lac repressor; R 54.0 13 0.00033 17.1 2.9 22 19-40 7-28 (342) 195 PRK08898 coproporphyrinogen II 53.1 15 0.00037 16.8 3.0 10 118-127 169-178 (393) 196 PRK13870 transcriptional regul 52.3 17 0.00043 16.4 6.1 19 33-51 20-38 (234) 197 PRK11041 DNA-binding transcrip 52.3 15 0.00037 16.8 2.9 110 19-147 11-131 (341) 198 cd00569 HTH_Hin_like Helix-tur 52.1 17 0.00044 16.4 4.6 36 3-38 6-42 (42) 199 PRK05066 arginine repressor; P 51.9 7.7 0.0002 18.4 1.4 36 6-41 9-53 (156) 200 PRK10703 DNA-binding transcrip 51.8 15 0.00038 16.8 2.9 111 19-148 3-124 (335) 201 cd01104 HTH_MlrA-CarA Helix-Tu 51.5 17 0.00045 16.4 3.4 36 19-58 2-37 (68) 202 PRK10401 DNA-binding transcrip 51.2 15 0.00039 16.7 2.9 22 19-40 3-24 (346) 203 COG1777 Predicted transcriptio 51.0 18 0.00045 16.3 5.4 38 10-47 20-58 (217) 204 PRK10339 DNA-binding transcrip 50.6 16 0.0004 16.6 2.8 22 19-40 3-24 (327) 205 pfam02042 RWP-RK RWP-RK domain 50.5 18 0.00046 16.3 4.4 34 3-40 5-38 (52) 206 PRK09464 pdhR transcriptional 50.2 18 0.00047 16.2 4.4 42 19-62 36-77 (254) 207 pfam08222 HTH_CodY CodY helix- 50.2 16 0.0004 16.6 2.8 24 21-44 7-30 (60) 208 PRK11303 DNA-binding transcrip 49.1 16 0.00042 16.5 2.7 22 19-40 2-23 (330) 209 COG3415 Transposase and inacti 49.0 19 0.00049 16.1 3.7 59 3-61 7-66 (138) 210 COG2390 DeoR Transcriptional r 48.3 17 0.00042 16.5 2.7 39 6-44 13-53 (321) 211 PRK10423 transcriptional repre 47.9 13 0.00034 17.1 2.1 108 21-147 2-120 (327) 212 cd04762 HTH_MerR-trunc Helix-T 47.9 18 0.00046 16.3 2.8 22 19-40 2-23 (49) 213 PRK09492 treR trehalose repres 47.8 19 0.00048 16.2 2.9 22 19-40 6-27 (315) 214 smart00420 HTH_DEOR helix_turn 47.7 20 0.00051 16.0 4.0 39 15-56 12-50 (53) 215 PRK09333 30S ribosomal protein 47.3 14 0.00036 16.9 2.1 23 274-296 115-137 (150) 216 PRK09137 DNA topoisomerase I; 47.0 9.6 0.00025 17.9 1.3 22 50-71 506-527 (761) 217 PRK09802 DNA-binding transcrip 46.4 21 0.00054 15.9 6.4 55 6-63 18-74 (269) 218 COG2901 Fis Factor for inversi 46.3 21 0.00054 15.9 3.1 24 17-40 71-94 (98) 219 KOG1168 consensus 44.6 23 0.00057 15.7 3.7 34 45-81 38-74 (385) 220 TIGR03001 Sig-70_gmx1 RNA poly 43.9 23 0.00059 15.7 3.4 11 108-118 40-50 (249) 221 pfam01527 Transposase_8 Transp 43.9 23 0.00059 15.7 4.6 29 14-42 19-48 (75) 222 pfam07022 Phage_CI_repr Bacter 43.8 23 0.00059 15.6 3.9 32 9-40 4-35 (65) 223 PRK04280 arginine repressor; P 43.5 12 0.00032 17.2 1.4 34 8-41 7-48 (149) 224 PRK09729 hypothetical protein; 43.4 14 0.00035 16.9 1.6 40 232-272 1-41 (68) 225 pfam00325 Crp Bacterial regula 43.1 21 0.00052 16.0 2.5 23 22-44 7-29 (32) 226 PRK09954 hypothetical protein; 42.9 22 0.00057 15.7 2.6 55 4-63 2-58 (362) 227 pfam05344 DUF746 Domain of Unk 42.3 25 0.00063 15.5 4.0 33 13-45 9-41 (65) 228 pfam01316 Arg_repressor Argini 41.6 12 0.0003 17.4 1.0 16 26-41 33-48 (70) 229 COG1438 ArgR Arginine represso 41.4 20 0.00052 16.0 2.2 37 5-41 5-49 (150) 230 COG5606 Uncharacterized conser 41.3 18 0.00047 16.2 2.0 19 21-39 45-63 (91) 231 pfam05339 DUF739 Protein of un 40.6 26 0.00066 15.4 4.1 37 1-38 1-37 (69) 232 pfam01381 HTH_3 Helix-turn-hel 40.4 25 0.00064 15.4 2.6 23 17-39 9-31 (55) 233 PRK09764 DNA-binding transcrip 40.4 26 0.00065 15.4 2.6 41 19-61 31-71 (239) 234 TIGR02201 heptsyl_trn_III lipo 40.3 8.5 0.00022 18.2 0.1 38 107-144 15-52 (347) 235 COG3388 Predicted transcriptio 39.4 10 0.00026 17.7 0.5 65 5-72 14-80 (101) 236 cd00186 TOP1Ac DNA Topoisomera 39.4 12 0.0003 17.4 0.7 23 21-43 94-116 (381) 237 pfam08220 HTH_DeoR DeoR-like h 39.3 27 0.0007 15.2 4.1 47 11-60 8-54 (57) 238 TIGR03337 phnR transcriptional 39.2 27 0.0007 15.2 2.7 41 19-61 27-67 (231) 239 PRK03341 arginine repressor; P 39.0 14 0.00037 16.8 1.2 13 28-40 45-57 (168) 240 smart00530 HTH_XRE Helix-turn- 38.8 27 0.0007 15.2 2.6 23 17-39 10-32 (56) 241 cd04763 HTH_MlrA-like Helix-Tu 38.8 28 0.00071 15.2 2.7 35 19-57 2-36 (68) 242 PRK11402 DNA-binding transcrip 38.2 28 0.00073 15.1 2.6 40 19-60 37-76 (243) 243 PRK04158 transcriptional repre 37.6 25 0.00064 15.5 2.2 11 42-52 33-43 (256) 244 PRK03837 transcriptional regul 37.5 29 0.00075 15.1 2.6 38 19-59 40-78 (243) 245 cd06571 Bac_DnaA_C C-terminal 37.3 29 0.00075 15.0 5.8 42 6-47 32-75 (90) 246 TIGR02719 repress_PhaQ poly-be 37.1 7.8 0.0002 18.4 -0.4 55 29-83 55-115 (138) 247 PRK00441 argR arginine repress 36.4 16 0.00042 16.5 1.1 36 6-41 4-47 (149) 248 COG2238 RPS19A Ribosomal prote 35.9 31 0.00079 14.9 2.5 51 244-296 86-137 (147) 249 pfam08281 Sigma70_r4_2 Sigma-7 35.8 31 0.00079 14.9 4.6 31 13-43 22-52 (54) 250 PRK13182 racA polar chromosome 35.4 32 0.00081 14.9 3.0 57 20-80 3-60 (178) 251 pfam04492 Phage_rep_O Bacterio 35.3 32 0.00081 14.9 5.5 52 3-57 30-91 (100) 252 PRK11337 DNA-binding transcrip 35.2 32 0.00081 14.8 3.3 28 14-41 44-71 (293) 253 KOG2947 consensus 35.1 32 0.00081 14.8 3.9 117 134-251 76-198 (308) 254 pfam00376 MerR MerR family reg 35.1 29 0.00075 15.1 2.2 22 19-44 1-22 (38) 255 PHA01976 helix-turn-helix prot 35.0 25 0.00063 15.5 1.8 34 16-49 12-58 (67) 256 PRK11302 DNA-binding transcrip 34.8 32 0.00082 14.8 3.7 28 14-41 31-58 (284) 257 PRK13509 transcriptional repre 34.7 33 0.00083 14.8 6.2 61 1-64 1-63 (251) 258 COG2842 Uncharacterized ATPase 34.2 33 0.00084 14.8 5.2 47 1-47 1-60 (297) 259 pfam00342 PGI Phosphoglucose i 34.1 25 0.00063 15.5 1.7 111 2-127 6-131 (483) 260 PRK10225 DNA-binding transcrip 33.6 34 0.00086 14.7 3.9 40 21-62 37-76 (257) 261 smart00351 PAX Paired Box doma 33.3 32 0.00083 14.8 2.2 32 11-42 26-58 (125) 262 PHA02519 plasmid partition pro 31.6 37 0.00093 14.5 3.0 64 16-93 38-103 (387) 263 TIGR01928 menC_lowGC/arch o-su 31.4 19 0.00049 16.1 0.8 91 74-169 132-229 (326) 264 TIGR03338 phnR_burk phosphonat 31.2 37 0.00095 14.5 2.7 42 19-62 36-77 (212) 265 pfam01090 Ribosomal_S19e Ribos 31.2 34 0.00088 14.7 2.1 22 274-295 115-136 (140) 266 TIGR02195 heptsyl_trn_II lipop 31.1 21 0.00054 15.9 1.0 30 100-129 7-37 (361) 267 PRK11557 putative DNA-binding 30.9 38 0.00096 14.4 3.7 28 14-41 31-58 (282) 268 TIGR03431 PhnD phosphonate ABC 28.9 41 0.001 14.2 6.6 191 93-292 27-248 (288) 269 COG2188 PhnF Transcriptional r 28.8 41 0.001 14.2 2.6 42 19-62 33-74 (236) 270 PRK10079 putative transcriptio 27.8 43 0.0011 14.1 2.7 40 19-60 37-76 (241) 271 COG0761 lytB 4-Hydroxy-3-methy 27.7 12 0.0003 17.4 -0.9 21 34-54 16-39 (294) 272 PRK10421 DNA-binding transcrip 27.4 43 0.0011 14.1 2.6 39 21-61 30-68 (253) 273 pfam06322 Phage_NinH Phage Nin 27.4 43 0.0011 14.1 2.1 32 14-45 13-44 (64) 274 COG2826 Tra8 Transposase and i 26.6 42 0.0011 14.2 1.8 26 15-40 21-46 (318) 275 PRK11014 transcriptional repre 26.6 45 0.0011 14.0 6.0 69 7-78 10-84 (141) 276 PRK09706 transcriptional repre 26.4 45 0.0012 14.0 2.6 19 19-37 20-38 (135) 277 cd00093 HTH_XRE Helix-turn-hel 26.3 46 0.0012 13.9 2.3 23 17-39 12-34 (58) 278 cd00131 PAX Paired Box domain 25.9 46 0.0012 13.9 2.3 32 11-42 26-58 (128) 279 TIGR03453 partition_RepA plasm 25.7 47 0.0012 13.9 2.8 23 16-38 32-54 (387) 280 PRK11523 DNA-binding transcrip 25.6 47 0.0012 13.9 2.6 41 19-61 34-74 (258) 281 PRK09990 DNA-binding transcrip 25.1 48 0.0012 13.8 2.6 43 19-63 33-75 (251) 282 COG3432 Predicted transcriptio 25.1 22 0.00056 15.8 0.2 53 19-74 33-89 (95) 283 cd04765 HTH_MlrA-like_sg2 Heli 25.0 48 0.0012 13.8 3.2 35 19-57 2-36 (99) 284 COG4465 CodY Pleiotropic trans 24.8 49 0.0012 13.8 2.6 17 40-56 34-50 (261) 285 pfam08535 KorB KorB domain. Th 24.4 50 0.0013 13.7 2.4 20 21-40 7-26 (93) 286 PRK01066 porphobilinogen deami 24.3 30 0.00076 15.0 0.7 54 92-145 18-95 (234) 287 cd04764 HTH_MlrA-like_sg1 Heli 23.9 51 0.0013 13.7 3.0 34 19-57 2-35 (67) 288 PRK13507 formate--tetrahydrofo 23.7 51 0.0013 13.7 4.4 63 1-65 1-79 (587) 289 PRK03537 hypothetical protein; 23.4 52 0.0013 13.6 6.5 53 239-294 116-172 (188) 290 pfam08280 HTH_Mga M protein tr 23.4 52 0.0013 13.6 5.3 52 5-56 5-58 (59) 291 PTZ00095 40S ribosomal protein 23.3 52 0.0013 13.6 2.2 22 275-296 142-163 (169) 292 PRK13982 bifunctional SbtC-lik 23.1 4.2 0.00011 19.9 -3.8 30 94-123 73-102 (476) 293 PRK07379 coproporphyrinogen II 23.1 52 0.0013 13.6 3.3 18 274-291 378-396 (399) 294 PRK12520 RNA polymerase sigma 23.1 53 0.0013 13.6 5.2 22 64-85 13-34 (191) 295 pfam12492 DUF3705 Protein of u 22.9 40 0.001 14.3 1.1 16 49-64 2-17 (31) 296 TIGR02995 ectoine_ehuB ectoine 22.7 53 0.0014 13.5 3.3 151 90-249 31-198 (285) 297 pfam12116 SpoIIID Stage III sp 22.6 54 0.0014 13.5 2.8 28 13-40 14-42 (82) 298 pfam00292 PAX 'Paired box' dom 22.3 55 0.0014 13.5 2.3 32 11-42 26-58 (125) 299 PRK08413 consensus 21.9 45 0.0011 14.0 1.3 22 50-71 487-508 (733) 300 PRK09959 hybrid sensory histid 21.6 56 0.0014 13.4 8.3 178 94-292 303-504 (1197) 301 COG1167 ARO8 Transcriptional r 21.5 57 0.0014 13.4 3.3 29 16-44 27-55 (459) 302 PRK13777 transcriptional regul 21.4 37 0.00095 14.4 0.8 49 19-67 62-114 (190) 303 smart00437 TOP1Ac Bacterial DN 21.1 58 0.0015 13.4 2.6 40 21-61 20-59 (259) 304 PRK09057 coproporphyrinogen II 20.9 50 0.0013 13.7 1.3 18 277-294 362-379 (381) 305 TIGR02944 suf_reg_Xantho FeS a 20.7 59 0.0015 13.3 1.8 30 13-42 19-50 (130) 306 smart00422 HTH_MERR helix_turn 20.6 59 0.0015 13.3 2.2 34 19-57 2-36 (70) 307 PRK10803 hypothetical protein; 20.2 61 0.0015 13.2 2.7 73 1-91 1-77 (262) No 1 >PRK10632 putative DNA-binding transcriptional regulator; Provisional Probab=100.00 E-value=0 Score=399.59 Aligned_cols=290 Identities=28% Similarity=0.364 Sum_probs=258.0 Q ss_pred CC-HHHHHHHHHHHHHCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEECCCCEEEEECCCCCCCCCCCCCCCCCHHH Q ss_conf 88-89999999999827689999882899789999999999995882179769946850013433222222222210122 Q gi|254780282|r 3 FD-WDKLRVFYVVARSGSFTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHARGLTLTEQGSKLHRVTSEVYHKLETTQ 81 (299) Q Consensus 3 md-~~~L~~f~~v~~~gs~s~AA~~L~itq~avS~~i~~LE~~lg~~Lf~R~~~~~~lT~~G~~l~~~a~~~l~~~~~~~ 81 (299) || +++|++|++|+++||||+||++|++||||||++|++||++||++||+|++|++.||++|+.++++++.++++++++. T Consensus 1 Md~L~~L~~F~~Vae~gSfs~AA~~L~~s~saVSr~I~~LE~~LG~~Lf~RttR~l~LT~~G~~~~~~~~~il~~~~~~~ 80 (309) T PRK10632 1 MERLKRMSVFAKVVEFGSFTAAARQLQMSVSSISQTVSKLEDELQVKLLNRSTRSIGLTEAGRIYYQGCRRMLHEVQDVH 80 (309) T ss_pred CCCHHHHHHHHHHHHCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCEEECCCCCEECHHHHHHHHHHHHHHHHHHHHH T ss_conf 97678999999999809999999997959889999999999997995689789971289899999999887767888999 Q ss_pred HHCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC Q ss_conf 10012232222223332111000000000135667542000122222222222222222222345654321111223455 Q gi|254780282|r 82 IELQESSVKPSGKLRIATTIDLGQNLLQGNLKEFLLLYPDIQIQLILDNKDIDISMDYADCAIRLRKPIQSSSLIQRKLV 161 (299) Q Consensus 82 ~~~~~~~~~~~g~i~I~~~~~~~~~~l~~~l~~f~~~~P~i~i~i~~~~~~~~l~~~~~Di~i~~~~~~~~~~l~~~~l~ 161 (299) ..+.+......|+|||+++.+++..++++.|.+|.++||+|+|++..++...|+..+++|++|+++. ..++++..++|+ T Consensus 81 ~~~~~~~~~~~G~LrI~~~~~~~~~~l~~~l~~f~~~yP~i~l~l~~~~~~~dl~~~~~Diair~g~-~~~~~l~ar~L~ 159 (309) T PRK10632 81 EQLYAFNNTPIGTLRIGCSSTMAQNVLAGLTAKMLKEYPGLSVNLVTGIPAPDLIADGLDVVIRVGA-LQDSSLFSRRLG 159 (309) T ss_pred HHHHHCCCCCCEEEEECCCHHHHHHHHCCHHHHHHHHCCCCCEEEECCCCCCCHHHCCCCCCEEECC-CCCCCEEEEEEE T ss_conf 9998601787405884157177662306156788876898425776168746355505531034078-899883899914 Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCCCCCCCEEEECCCCHHHHHHHHHCCE Q ss_conf 54332112344321112222221100011235664332110002356652022343212114532420013567873842 Q gi|254780282|r 162 TIHMHAYAAPHYLKNCREPLSIQELDKHNLITFGDLIPKCMEDFNWLATVDRPIGEPRISCLQVNSYLSIMQYCVLGSGI 241 (299) Q Consensus 162 ~~~~~~v~~~~~~~~~~~~~~~~dL~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~v~~g~Gi 241 (299) ..++++|++|+|+..++.|.+++||.+++|+.+....... +.+....+..........+.+|+.+++++++.+|.|| T Consensus 160 ~~~~~l~Asp~yl~~~g~p~~p~dL~~~~~l~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~~n~~~~~~~~~~~G~GI 236 (309) T PRK10632 160 AMPMVVCAAKSYLAQYGTPEKPADLSSHSWLEYSVRPDNE---FELIAPEGISTRLIPQGRFVTNDPMTLVRWLTAGAGI 236 (309) T ss_pred ECCCEEEECHHHHHHCCCCCCHHHHHCCCCEEECCCCCCC---EEEECCCCCEEEECCCCEEEECCHHHHHHHHHHCCCC T ss_conf 0450587278999846999999998389847633789984---3678589977998267709999899999999919991 Q ss_pred EEEEHHHHCC---CCCEEEECCCCCCCCCEEEEEECCCCCCCHHHHHHHHHHHHHHHC Q ss_conf 3311777601---998466177666766008999348778888999999999999850 Q gi|254780282|r 242 ALLPDYIVKD---NPNLVRIMEDVITPSFTVYFCYPEALKNTGKLKAFRNFIFLKARD 296 (299) Q Consensus 242 a~lp~~~~~~---~~~lv~i~~~~~~~~~~~~lv~~~~~~~~~~~~~f~d~l~~~~r~ 296 (299) +++|.+++++ +|+|++++|++...+.++|++|++++..++++++|+|||.+...+ T Consensus 237 a~lP~~~v~~~l~~G~Lv~llp~~~~~~~~~~~vy~~~~~~~~rvr~fidfl~e~f~~ 294 (309) T PRK10632 237 AYVPLMWVIDEINRGELEILLPRYQSDPRPVYALYTEKDKLPLKVQVVINYLTDYFVR 294 (309) T ss_pred HHCCHHHHHHHHHCCCCEEECCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHH T ss_conf 0186999999986899689599986999719999859986489999999999999988 No 2 >TIGR03418 chol_sulf_TF putative choline sulfate-utilization transcription factor. Members of this protein family are transcription factors of the LysR family. Their genes typically are divergently transcribed from choline-sulfatase genes. That enzyme makes choline, a precursor to the osmoprotectant glycine-betaine, available by hydrolysis of choline sulfate. Probab=100.00 E-value=0 Score=396.52 Aligned_cols=287 Identities=25% Similarity=0.391 Sum_probs=251.3 Q ss_pred CCHHHHHHHHHHHHHCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEECCCCEEEEECCCCCCCCCCCCCCCCCHHHH Q ss_conf 88899999999998276899998828997899999999999958821797699468500134332222222222101221 Q gi|254780282|r 3 FDWDKLRVFYVVARSGSFTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHARGLTLTEQGSKLHRVTSEVYHKLETTQI 82 (299) Q Consensus 3 md~~~L~~f~~v~~~gs~s~AA~~L~itq~avS~~i~~LE~~lg~~Lf~R~~~~~~lT~~G~~l~~~a~~~l~~~~~~~~ 82 (299) |||++|++|++|+++||||+||++|++||||||++|++||++||++||+|++|++.||++|+.|+++++.+++.++++.+ T Consensus 1 m~l~~L~~F~~Va~~gS~t~AA~~L~~sqsavS~~I~~LE~~lG~~Lf~R~~r~~~lT~aG~~l~~~a~~~l~~~~~~~~ 80 (291) T TIGR03418 1 LSLQALRVFESAARLASFTAAARELGSTQPAVSQQVKRLEEELGTPLFERGHRGIELTEDGQRLFEAVRAGLDTIDLATA 80 (291) T ss_pred CCHHHHHHHHHHHHHCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCEEECCCCEEECHHHHHHHHHHHHHHHHHHHHHH T ss_conf 97799999999998199999999988788899999999999969965897799546868899999999999999999999 Q ss_pred HCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC Q ss_conf 00122322222233321110000000001356675420001222222222222222222223456543211112234555 Q gi|254780282|r 83 ELQESSVKPSGKLRIATTIDLGQNLLQGNLKEFLLLYPDIQIQLILDNKDIDISMDYADCAIRLRKPIQSSSLIQRKLVT 162 (299) Q Consensus 83 ~~~~~~~~~~g~i~I~~~~~~~~~~l~~~l~~f~~~~P~i~i~i~~~~~~~~l~~~~~Di~i~~~~~~~~~~l~~~~l~~ 162 (299) .+... ..+|.++|+++++++..++++.+.+|++.||++++++.+++...++..+++|++|..+.+ ..++....++++ T Consensus 81 ~l~~~--~~~g~l~i~~~~~~~~~~l~~~l~~f~~~~P~i~v~l~~~~~~~~~~~~~~Dlai~~~~~-~~~~~~~~~l~~ 157 (291) T TIGR03418 81 QLRAR--REHETLTLATDFAFATYWLMPRLHRFKRAMPDVDVSLVTSQDSLDPQRDDIDVAILFGDG-RWPGGEAHRLFS 157 (291) T ss_pred HHHCC--CCCCCEEEECCHHHHHHHHHHHHHHHHHHCCCEEEEEEECCCHHHHHCCCCCEEEEECCC-CCCCCEEEECCC T ss_conf 98554--667824885143887777568767899868980799995474045432787389996478-898863899105 Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHH-HHHHHCCCCCCCCCCEEEECCCCHHHHHHHHHCCE Q ss_conf 43321123443211122222211000112356643321100023-56652022343212114532420013567873842 Q gi|254780282|r 163 IHMHAYAAPHYLKNCREPLSIQELDKHNLITFGDLIPKCMEDFN-WLATVDRPIGEPRISCLQVNSYLSIMQYCVLGSGI 241 (299) Q Consensus 163 ~~~~~v~~~~~~~~~~~~~~~~dL~~~~~i~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~s~~~~~~~v~~g~Gi 241 (299) ++.+++|+|+|+..++.+.+++||.+++++.+....+..+..+. ++...+. ...+....+++|+..+++++|.+|.|| T Consensus 158 ~~~~~v~sp~~~~~~~~~~~~~dL~~~~~i~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~v~~G~Gi 236 (291) T TIGR03418 158 EEVTPVCSPALLAARATPLSAADLLRLPLLHLEPTQPARWFDWAGWFDAHGL-ERPPAPGGLTFNNYTLVIQAAIGGQGV 236 (291) T ss_pred CEEEEEECHHHHHHCCCCCCHHHHHCCCEEEECCCCCCCCHHHHHHHHHCCC-CCCCCCCEEEECCHHHHHHHHHHCCCE T ss_conf 6199998859998669999999993898799538988630123556651583-015778628999899999999978987 Q ss_pred EEEEHHHHCC---CCCEEEECCCCCCCCCEEEEEECCCCCCCHHHHHHHHHHHHH Q ss_conf 3311777601---998466177666766008999348778888999999999999 Q gi|254780282|r 242 ALLPDYIVKD---NPNLVRIMEDVITPSFTVYFCYPEALKNTGKLKAFRNFIFLK 293 (299) Q Consensus 242 a~lp~~~~~~---~~~lv~i~~~~~~~~~~~~lv~~~~~~~~~~~~~f~d~l~~~ 293 (299) |++|.+++++ +|.|+++++++..+.+++|++|++++.++|++++|+|||++| T Consensus 237 a~lp~~~v~~~l~~G~Lv~ll~~~~~~~~~~~lv~~~~~~~~~~~r~Fid~l~~e 291 (291) T TIGR03418 237 ALGWAPLVDELLEAGQLVRLIDEPVVTERGYYLVRPPRKRRGPAVRRFRDWLLDE 291 (291) T ss_pred EEEEHHHHHHHHHCCCEEEECCCCCCCCCEEEEEECCCCCCCHHHHHHHHHHHCC T ss_conf 9611999999987899799798556888639999839987899999999997339 No 3 >PRK09801 transcriptional activator TtdR; Provisional Probab=100.00 E-value=0 Score=394.44 Aligned_cols=288 Identities=24% Similarity=0.370 Sum_probs=253.6 Q ss_pred HHHHHHHHHHHHHCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEECCCCEEEEECCCCCCCCCCCCCCCCCHHHHHC Q ss_conf 89999999999827689999882899789999999999995882179769946850013433222222222210122100 Q gi|254780282|r 5 WDKLRVFYVVARSGSFTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHARGLTLTEQGSKLHRVTSEVYHKLETTQIEL 84 (299) Q Consensus 5 ~~~L~~f~~v~~~gs~s~AA~~L~itq~avS~~i~~LE~~lg~~Lf~R~~~~~~lT~~G~~l~~~a~~~l~~~~~~~~~~ 84 (299) +++|++|++|+++||||+||++|++||||||++|++||++||++||+|++|++.||++|+.|+++++.++.+++++.+.+ T Consensus 8 l~dL~~F~~Va~~gSfs~AA~~L~vs~saVSr~I~~LE~~LG~~Lf~R~tR~l~LTeaG~~l~~~~~~il~~~~~~~~~~ 87 (310) T PRK09801 8 AKDLQVLVEIVHSGSFSAAAATLGQTPAFVTKRIQILENTLATTLLNRSARGVALTESGQRCYEHALEILTQYQRLVDDV 87 (310) T ss_pred HHHHHHHHHHHHHCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCEEECCCCEECCHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 99999999999809999999997959889999999999986993761489984015999999999999999999999987 Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC Q ss_conf 12232222223332111000000000135667542000122222222222222222222345654321111223455543 Q gi|254780282|r 85 QESSVKPSGKLRIATTIDLGQNLLQGNLKEFLLLYPDIQIQLILDNKDIDISMDYADCAIRLRKPIQSSSLIQRKLVTIH 164 (299) Q Consensus 85 ~~~~~~~~g~i~I~~~~~~~~~~l~~~l~~f~~~~P~i~i~i~~~~~~~~l~~~~~Di~i~~~~~~~~~~l~~~~l~~~~ 164 (299) .+....++|.|||+++++++..|++|.|.+|.++||+|++++..++...|+.++++|++|+++.+. ++.+..++++..+ T Consensus 88 ~~~~~~~~G~lrI~~~~~~~~~~L~p~L~~F~~~yP~I~l~l~~~~~~~dl~~~~~Dlair~~~~~-~~~~v~~~l~~~~ 166 (310) T PRK09801 88 TQIKTRPEGMIRIGCSFGFGRSHIAPAITELMRNYPELQVHFELFDRQIDLVQDNIDLDIRINDEI-PDYYIAHLLTKNK 166 (310) T ss_pred HHHHCCCCCCEEEEECCHHHHHHHHHHHHHHHHHCCCEEEEEEECCCCCCCCCCCCCEEEEECCCC-CCCCEEEECCCCC T ss_conf 753237777459994322778889999999998789739999863765542023665568967889-9871789853563 Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCCCCCCCEEEECCCCHHHHHHHHHCCEEEE Q ss_conf 32112344321112222221100011235664332110002356652022343212114532420013567873842331 Q gi|254780282|r 165 MHAYAAPHYLKNCREPLSIQELDKHNLITFGDLIPKCMEDFNWLATVDRPIGEPRISCLQVNSYLSIMQYCVLGSGIALL 244 (299) Q Consensus 165 ~~~v~~~~~~~~~~~~~~~~dL~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~v~~g~Gia~l 244 (299) .++||||+|+.+++.|.+++||.+++++......... ..|.+. .............+.+|+.+++++++.+|.||+++ T Consensus 167 ~~l~ASP~yl~~~~~P~~~~dL~~h~~l~~~~~~~~~-~~w~~~-~~~~~~~v~~~~~~~~n~~~~~~~aa~~G~GIa~l 244 (310) T PRK09801 167 RILCAAPEYLQKYPQPQSLQELSRHDCLVTKERDMTH-GIWELG-NGQEKKSVKVSGHLSSNSGEIVLQWALEGKGIMLR 244 (310) T ss_pred EEEEECHHHHHHCCCCCCHHHHHCCCEEEECCCCCCC-CCEEEC-CCCCEEEEECCCEEEECCHHHHHHHHHHCCEEEEC T ss_conf 6898689999857999998998469889844887776-633622-59823799616638998499999999969928999 Q ss_pred EHHHHCC---CCCEEEECCCCCCCCCEEEEEECCCCCCCHHHHHHHHHHHHHHHC Q ss_conf 1777601---998466177666766008999348778888999999999999850 Q gi|254780282|r 245 PDYIVKD---NPNLVRIMEDVITPSFTVYFCYPEALKNTGKLKAFRNFIFLKARD 296 (299) Q Consensus 245 p~~~~~~---~~~lv~i~~~~~~~~~~~~lv~~~~~~~~~~~~~f~d~l~~~~r~ 296 (299) |.+++.+ +|+||+++|++. ++.++|++|++++..++++|+|+|||.+..++ T Consensus 245 p~~~v~~~l~~G~Lv~vlpd~~-~~~~~~~vy~~~~~~~~rvr~fidfl~~~~~~ 298 (310) T PRK09801 245 SEWDVLPFLESGKLVQVLPEYA-QSANIWAVYREPLYRSMKLRVCVEFLAAWCQQ 298 (310) T ss_pred CHHHHHHHHHCCCEEEECCCCC-CCCCEEEEEECCCCCCHHHHHHHHHHHHHHHH T ss_conf 7999999987899089698888-99868999968987787999999999999999 No 4 >PRK12684 transcriptional regulator CysB-like protein; Reviewed Probab=100.00 E-value=0 Score=392.13 Aligned_cols=288 Identities=22% Similarity=0.275 Sum_probs=252.6 Q ss_pred CCHHHHHHHHHHHHHC-CHHHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEECCCCEE-EEECCCCCCCCCCCCCCCCCHH Q ss_conf 8889999999999827-6899998828997899999999999958821797699468-5001343322222222221012 Q gi|254780282|r 3 FDWDKLRVFYVVARSG-SFTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHARGLT-LTEQGSKLHRVTSEVYHKLETT 80 (299) Q Consensus 3 md~~~L~~f~~v~~~g-s~s~AA~~L~itq~avS~~i~~LE~~lg~~Lf~R~~~~~~-lT~~G~~l~~~a~~~l~~~~~~ 80 (299) ||++||+||++|+++| |||+||++||+||||||++|++||++||++||+|+++++. ||++|+.|+++++.++..++++ T Consensus 1 MdL~qLryf~~va~~~~sft~AA~~L~iSQpavS~~I~~LE~~LG~~Lf~R~~~r~~~LT~aG~~l~~~a~~il~~~~~~ 80 (313) T PRK12684 1 MNLHQLRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEDELGVEIFTRHGKRVRSLTEPGRIILASVERILQEVENL 80 (313) T ss_pred CCHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEECCCCCCCCCHHHHHHHHHHHHHHHHHHHH T ss_conf 94799999999998699999999997897789999999999985998899999998665988999999999999999999 Q ss_pred HHHCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCCCCCCC--CCC-CCCCCCCCCCCCCCCCCCCCCCCC Q ss_conf 21001223222222333211100000000013566754200012222222--222-222222222234565432111122 Q gi|254780282|r 81 QIELQESSVKPSGKLRIATTIDLGQNLLQGNLKEFLLLYPDIQIQLILDN--KDI-DISMDYADCAIRLRKPIQSSSLIQ 157 (299) Q Consensus 81 ~~~~~~~~~~~~g~i~I~~~~~~~~~~l~~~l~~f~~~~P~i~i~i~~~~--~~~-~l~~~~~Di~i~~~~~~~~~~l~~ 157 (299) ...+.+.....+|+|+||++++++.+++|+.+..|+++||++++++...+ ... .+..|++|+||.......++++.. T Consensus 81 ~~~~~~~~~~~~G~l~ig~~~s~~~~~lp~~l~~f~~~~P~v~l~l~~~~~~~~~~~l~~g~~Dl~i~~~~~~~~~~l~~ 160 (313) T PRK12684 81 KRVGKDFAAQDQGNLTIATTHTQARYALPAAIAEFKKRYPKVRLSILQGSPTQIAEMVIHDQADLAIATEAIADYKELVS 160 (313) T ss_pred HHHHHHHCCCCCCEEECCHHHHHHHHCCCHHHHHHHHHCCCEEEEEEECCHHHHHHHHHCCCCCEEECCCCCCCCCCEEE T ss_conf 99999740677751411024555751594999999844898089997178899999997799665504357777787389 Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCCCCCCCEEEECCCCHHHHHHHH Q ss_conf 34555433211234432111222222110001123566433211000235665202234321211453242001356787 Q gi|254780282|r 158 RKLVTIHMHAYAAPHYLKNCREPLSIQELDKHNLITFGDLIPKCMEDFNWLATVDRPIGEPRISCLQVNSYLSIMQYCVL 237 (299) Q Consensus 158 ~~l~~~~~~~v~~~~~~~~~~~~~~~~dL~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~v~~ 237 (299) .++++++++++++++|+...+.+++++||.++|||.+...+..... ........+..+...+++++.+++++||.+ T Consensus 161 ~~l~~~~~~~v~~~~hpla~~~~v~l~dL~~~p~I~~~~~~~~r~~----i~~~~~~~g~~p~~~~e~~~~~~i~~~V~~ 236 (313) T PRK12684 161 LPCYQWNHAVVVPPDHPLLERKPLTLEDLAQYPLITYDDAFAGRSK----INKAFALRGLKPDIVLEAIDADVIKTYVEL 236 (313) T ss_pred EEEEECCEEEEECCCCCCCCCCCCCHHHHCCCCEEECCCCCCHHHH----HHHHHHHCCCCCCEEEEECCHHHHHHHHHH T ss_conf 9803221689953898544699999999859998962899858999----999999779987479999979999999995 Q ss_pred HCCEEEEEHHHHCC--CCCEEEECCCCCCCCCEEEEEECCCCCCCHHHHHHHHHHHHHH Q ss_conf 38423311777601--9984661776667660089993487788889999999999998 Q gi|254780282|r 238 GSGIALLPDYIVKD--NPNLVRIMEDVITPSFTVYFCYPEALKNTGKLKAFRNFIFLKA 294 (299) Q Consensus 238 g~Gia~lp~~~~~~--~~~lv~i~~~~~~~~~~~~lv~~~~~~~~~~~~~f~d~l~~~~ 294 (299) |+||+++|...++. ++.++.++.....+++.+|++|++++++|+++++|+|++.++. T Consensus 237 GlGi~ilP~~a~~~~~~~~L~~lp~~~~~~~~~~~v~~~k~~~ls~~~r~FIe~l~e~l 295 (313) T PRK12684 237 GLGVGIVADMAFDPERDRNLRAIPAGHLFGSNVTRVALKQGAYLRGYVYTFIELFSPTL 295 (313) T ss_pred CCCHHHHHHHHHCHHHCCCEEEEECCCCCCCEEEEEEEECCCCCCHHHHHHHHHHHHHC T ss_conf 98572559998467638987999784677660599999798866899999999987465 No 5 >PRK11242 DNA-binding transcriptional regulator CynR; Provisional Probab=100.00 E-value=0 Score=391.00 Aligned_cols=286 Identities=23% Similarity=0.335 Sum_probs=252.1 Q ss_pred CCHHHHHHHHHHHHHCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEECCCCEEEEECCCCCCCCCCCCCCCCCHHHH Q ss_conf 88899999999998276899998828997899999999999958821797699468500134332222222222101221 Q gi|254780282|r 3 FDWDKLRVFYVVARSGSFTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHARGLTLTEQGSKLHRVTSEVYHKLETTQI 82 (299) Q Consensus 3 md~~~L~~f~~v~~~gs~s~AA~~L~itq~avS~~i~~LE~~lg~~Lf~R~~~~~~lT~~G~~l~~~a~~~l~~~~~~~~ 82 (299) ||+++|+||++|+++||||+||++||+||||||++|++||+++|++||+|++||+.||++|+.|+++++.++.+++++.+ T Consensus 1 M~L~~L~~F~~v~~~gs~t~AA~~L~isQ~avS~~i~~LE~~lg~~Lf~R~~r~~~lT~~G~~l~~~a~~il~~~~~~~~ 80 (292) T PRK11242 1 MLLRHIRYFLAVAEHGNFTRAAEALHVSQPTLSQQIRQLEESLGVQLFDRSGRTVRLTDAGEVYLRYARRALQDLEAGRR 80 (292) T ss_pred CCHHHHHHHHHHHHHCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEECCCCCEECHHHHHHHHHHHHHHHHHHHHHH T ss_conf 93489999999998099999999988798999999999999969873898899854773699999999999999999999 Q ss_pred HCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCCCCCCC--C-CCCCCCCCCCCCCCCCCCCCCCCCCCCC Q ss_conf 001223222222333211100000000013566754200012222222--2-2222222222223456543211112234 Q gi|254780282|r 83 ELQESSVKPSGKLRIATTIDLGQNLLQGNLKEFLLLYPDIQIQLILDN--K-DIDISMDYADCAIRLRKPIQSSSLIQRK 159 (299) Q Consensus 83 ~~~~~~~~~~g~i~I~~~~~~~~~~l~~~l~~f~~~~P~i~i~i~~~~--~-~~~l~~~~~Di~i~~~~~~~~~~l~~~~ 159 (299) .+.+..+..+|.|+||++++++.+++++.+.+|++.||+++|++...+ . ...+..|++|+||.... ..++++...+ T Consensus 81 ~l~~~~~~~~G~l~ig~~~~~~~~~l~~~l~~f~~~~P~i~i~l~~~~~~~~~~~l~~~~~D~~i~~~~-~~~~~l~~~~ 159 (292) T PRK11242 81 AIHDVADLSRGSLRLAMTPTFTAYLIGPLIDAFHARYPGITLTIREMPQERIEALLADDELDVGIAFAP-VHSPEIEAQP 159 (292) T ss_pred HHHHHHCCCCCEEEEECHHHHHHHHHHHHHHHHHHHCCCCCEEEEECCHHHHHHHHHCCCCCEEEEECC-CCCCCCEEEE T ss_conf 998753577765863024577888738998888864889734899768899999986798557998368-8887725654 Q ss_pred CCCCCCCCCCCCCCCCCC-CCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCCCCCCCEEEECCCCHHHHHHHHH Q ss_conf 555433211234432111-2222221100011235664332110002356652022343212114532420013567873 Q gi|254780282|r 160 LVTIHMHAYAAPHYLKNC-REPLSIQELDKHNLITFGDLIPKCMEDFNWLATVDRPIGEPRISCLQVNSYLSIMQYCVLG 238 (299) Q Consensus 160 l~~~~~~~v~~~~~~~~~-~~~~~~~dL~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~v~~g 238 (299) +++++++++++++|+... +.+++++||.++|||.+............++ ...+..+...++++++.+++++|.+| T Consensus 160 l~~~~~~~v~~~~h~la~~~~~is~~~L~~~~~i~~~~~~~~~~~~~~~~----~~~~i~~~~~~~~~~~~~~~~~V~~g 235 (292) T PRK11242 160 LFTETLALVVGRTHPLAARRKPLTLDELADEPLVLLSAEFATREQIDRYF----RRHGITPRVAIEANSISAVLEIVRRG 235 (292) T ss_pred ECCCEEEEEEECCCHHHHCCCCCCHHHHCCCCEEEECCCCCHHHHHHHHH----HHCCCCCCEEEEECCHHHHHHHHHHC T ss_conf 20450799990898042279999999981899899679985799999999----97699985367538899999999979 Q ss_pred CCEEEEEHHHHCCCCCEEEECCCCCCCCCEEEEEECCCCCCCHHHHHHHHHHHHH Q ss_conf 8423311777601998466177666766008999348778888999999999999 Q gi|254780282|r 239 SGIALLPDYIVKDNPNLVRIMEDVITPSFTVYFCYPEALKNTGKLKAFRNFIFLK 293 (299) Q Consensus 239 ~Gia~lp~~~~~~~~~lv~i~~~~~~~~~~~~lv~~~~~~~~~~~~~f~d~l~~~ 293 (299) .|++++|.+++.++++++.+..+.+.+.+++|++|++++..++++++|+|++.++ T Consensus 236 ~Gi~ilP~~~~~~~~~l~~i~l~~~~~~r~i~lv~~k~~~~s~~~~~Fid~l~e~ 290 (292) T PRK11242 236 RLATLLPAAIAREHDDLCAVALDPPLPQRTAALLRRKGAYRSAAARAFIELALER 290 (292) T ss_pred CEEEEEHHHHHHHCCCEEEEECCCCCCEEEEEEEEECCCCCCHHHHHHHHHHHHC T ss_conf 9699702898600899899989899870399999989398899999999999863 No 6 >PRK11139 DNA-binding transcriptional activator GcvA; Provisional Probab=100.00 E-value=0 Score=387.80 Aligned_cols=286 Identities=25% Similarity=0.325 Sum_probs=251.4 Q ss_pred C-CHHHHHHHHHHHHHCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEECCCCEEEEECCCCCCCCCCCCCCCCCHHH Q ss_conf 8-889999999999827689999882899789999999999995882179769946850013433222222222210122 Q gi|254780282|r 3 F-DWDKLRVFYVVARSGSFTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHARGLTLTEQGSKLHRVTSEVYHKLETTQ 81 (299) Q Consensus 3 m-d~~~L~~f~~v~~~gs~s~AA~~L~itq~avS~~i~~LE~~lg~~Lf~R~~~~~~lT~~G~~l~~~a~~~l~~~~~~~ 81 (299) | +|++|++|++|+++||||+||++||+||||||++|++||+++|++||+|++|+++||++|+.|++++++++++++++. T Consensus 5 ~~~L~~L~~F~aVa~~gS~s~AA~~L~~sqsaVS~~I~~LE~~lG~~Lf~R~~r~~~lT~~G~~l~~~a~~il~~~~~~~ 84 (295) T PRK11139 5 LPPLNALRAFEAAARHLSFTRAAEELFVTQAAVSHQIKALEDFLGLKLFRRRNRSLLLTEEGQRYFLDIREAFDQLAEAT 84 (295) T ss_pred CCCHHHHHHHHHHHHHCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCEEECCCCEEECHHHHHHHHHHHHHHHHHHHHH T ss_conf 94979999999999839999999998869889999999999985984489889953680999999999999999999999 Q ss_pred HHCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC Q ss_conf 10012232222223332111000000000135667542000122222222222222222222345654321111223455 Q gi|254780282|r 82 IELQESSVKPSGKLRIATTIDLGQNLLQGNLKEFLLLYPDIQIQLILDNKDIDISMDYADCAIRLRKPIQSSSLIQRKLV 161 (299) Q Consensus 82 ~~~~~~~~~~~g~i~I~~~~~~~~~~l~~~l~~f~~~~P~i~i~i~~~~~~~~l~~~~~Di~i~~~~~~~~~~l~~~~l~ 161 (299) +.+.. ....|+++|+++++++..|+++.|..|+++||++++++..++...++..+++|++|..+. ..++++...+++ T Consensus 85 ~~~~~--~~~~g~l~I~~~~~~~~~~l~p~l~~f~~~~P~i~v~l~~~~~~~~l~~~~~Diai~~~~-~~~~~l~~~~l~ 161 (295) T PRK11139 85 RKLRA--RSAKGALTVSLLPSFAIKWLVPRLSSFNEAHPDIDVRLQAVDRLEDFLRDDVDVAIRYGR-GNWPGLRVEKLL 161 (295) T ss_pred HHHHH--HCCCCEEEEEEECCHHHHHHHHHHHHHHHCCCCEEEEEEECCCHHHHHCCCCEEEEEEEC-CCCCCEEEEEEE T ss_conf 99753--077873999996322777633466666610885899999624166663347438999723-776762799940 Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCCCCCCCEEEECCCCHHHHHHHHHCCE Q ss_conf 54332112344321112222221100011235664332110002356652022343212114532420013567873842 Q gi|254780282|r 162 TIHMHAYAAPHYLKNCREPLSIQELDKHNLITFGDLIPKCMEDFNWLATVDRPIGEPRISCLQVNSYLSIMQYCVLGSGI 241 (299) Q Consensus 162 ~~~~~~v~~~~~~~~~~~~~~~~dL~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~v~~g~Gi 241 (299) .+++++||+|+|+.+.+.+.+++||.+++++..... ..+..|+...+ .........+.+++...++++|.+|.|| T Consensus 162 ~~~~~~vasp~~~~~~~~~~~~~dL~~~~li~~~~~----~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~v~~G~Gi 236 (295) T PRK11139 162 DEYLFPVCSPALLNGGKPLKTPEDLARHTLLHDDSR----EDWRAWFRAAG-LNDINVQQGPIFSHSSMALQAAIHGQGV 236 (295) T ss_pred CCEEEEEECHHHHHHCCCCCCHHHHHCCCEEEECCC----CHHHHHHHHCC-CCCCCCCCCEEECCHHHHHHHHHHCCEE T ss_conf 446999988799964799999999818987963696----21588998569-8654678752887899999999959929 Q ss_pred EEEEHHHHCC---CCCEEEECCCCCCCCCEEEEEECCCCCCCHHHHHHHHHHHHHHHC Q ss_conf 3311777601---998466177666766008999348778888999999999999850 Q gi|254780282|r 242 ALLPDYIVKD---NPNLVRIMEDVITPSFTVYFCYPEALKNTGKLKAFRNFIFLKARD 296 (299) Q Consensus 242 a~lp~~~~~~---~~~lv~i~~~~~~~~~~~~lv~~~~~~~~~~~~~f~d~l~~~~r~ 296 (299) |++|.+++.+ +|+||.++++...+++++|++|++++..+|++++|+|||.+++.+ T Consensus 237 a~lp~~~v~~~l~~G~Lv~~l~~~~~~~~~~~lv~~~~~~~~p~v~~F~~~L~~~~~~ 294 (295) T PRK11139 237 ALGRRVLAQPEIEAGRLVCPFDIVLPSKNAFYLVCPPSQAELPKVAAFRQWLLAEAAQ 294 (295) T ss_pred EECCHHHHHHHHHCCCEEEECCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHCC T ss_conf 9777999999987899799898666788759999808987898999999999998536 No 7 >PRK11013 DNA-binding transcriptional regulator LysR; Provisional Probab=100.00 E-value=0 Score=386.80 Aligned_cols=289 Identities=22% Similarity=0.279 Sum_probs=248.6 Q ss_pred CC-CCHHHHHHHHHHHHHCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEECCCCEEEEECCCCCCCCCCCCCCCCCH Q ss_conf 98-88899999999998276899998828997899999999999958821797699468500134332222222222101 Q gi|254780282|r 1 MS-FDWDKLRVFYVVARSGSFTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHARGLTLTEQGSKLHRVTSEVYHKLET 79 (299) Q Consensus 1 m~-md~~~L~~f~~v~~~gs~s~AA~~L~itq~avS~~i~~LE~~lg~~Lf~R~~~~~~lT~~G~~l~~~a~~~l~~~~~ 79 (299) |+ ||+++|+||++|+++||||+||++||+||||||++|++||++||++||+|++|++.||++|+.|++++++++..+++ T Consensus 1 m~~m~LrqL~~F~aVa~~gsft~AA~~L~isQpavS~~I~~LE~~LG~~Lf~R~~r~v~lT~~G~~l~~~a~~~l~~l~~ 80 (309) T PRK11013 1 MAAVSLRHIEIFHAVMTAGSLTEAARLLHTSQPTVSRELARFEQVIGLTLFERVRGRLHPTVQGLRLFEEVQRSYYGLDR 80 (309) T ss_pred CCCCCHHHHHHHHHHHHCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEECCCCCCCCHHHHHHHHHHHHHHHHHHH T ss_conf 99888899999999998099999999988888899999999999979991898899611768899999999999999999 Q ss_pred HHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCCCCCCCC--C-CCCCCCCCCCCCCCCCCCCCCCCC Q ss_conf 2210012232222223332111000000000135667542000122222222--2-222222222223456543211112 Q gi|254780282|r 80 TQIELQESSVKPSGKLRIATTIDLGQNLLQGNLKEFLLLYPDIQIQLILDNK--D-IDISMDYADCAIRLRKPIQSSSLI 156 (299) Q Consensus 80 ~~~~~~~~~~~~~g~i~I~~~~~~~~~~l~~~l~~f~~~~P~i~i~i~~~~~--~-~~l~~~~~Di~i~~~~~~~~~~l~ 156 (299) +...+...++..+|+++||++++++.+++|+.+.+|+++||++++++...+. . ..+..+++|+||.... ..++++. T Consensus 81 ~~~~~~~~~~~~~G~lri~~~~~~~~~~lp~~l~~f~~~~P~v~v~i~~~~~~~~~~~l~~~~~Dl~l~~~~-~~~~~~~ 159 (309) T PRK11013 81 IVSAAESLREFRQGQLSIACLPVFSQSLLPGLCQPFLARYPDVSLNIVPQESPLLEEWLSAQRHDLGLTETL-HTPAGTE 159 (309) T ss_pred HHHHHHHHHHCCCCCCCCCCCHHHHHHHCCHHHHHHHHHCCCCEEEEEECCHHHHHHHHHCCCCCEEEEECC-CCCCCCE T ss_conf 999999866123676565300678988665231567843898079999898599999997599778996078-8998757 Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCCCCCCCEEEECCCCHHHHHHH Q ss_conf 23455543321123443211122222211000112356643321100023566520223432121145324200135678 Q gi|254780282|r 157 QRKLVTIHMHAYAAPHYLKNCREPLSIQELDKHNLITFGDLIPKCMEDFNWLATVDRPIGEPRISCLQVNSYLSIMQYCV 236 (299) Q Consensus 157 ~~~l~~~~~~~v~~~~~~~~~~~~~~~~dL~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~v~ 236 (299) ..+++.++.+++++++|+...+..++++||.++|||.+....+... ++.......+..+...+++++..+++.+|. T Consensus 160 ~~~l~~~~~~~v~~~~hpla~~~~i~~~dL~~~~~i~~~~~~~~r~----~~~~~~~~~g~~~~~~~e~~~~~~~~~lV~ 235 (309) T PRK11013 160 RTELLTLDEVCVLPDGHPLAAKKVLTPDDFQGENFISLSRTDSYRQ----LLDQLFAEHGVKRRMVVETHSAASVCAMVR 235 (309) T ss_pred EEEEEEEEEEEECCCCCCCCCCCCCCHHHHCCCCEEECCCCCCHHH----HHHHHHHHCCCCCCEEEEECCHHHHHHHHH T ss_conf 8886420146754789800049999999973898696389994999----999999976999776999896999999999 Q ss_pred HHCCEEEEEHHHHCC---CCCEEEECCCCCCCCCEEEEEECCCCCCCHHHHHHHHHHHHHHHC Q ss_conf 738423311777601---998466177666766008999348778888999999999999850 Q gi|254780282|r 237 LGSGIALLPDYIVKD---NPNLVRIMEDVITPSFTVYFCYPEALKNTGKLKAFRNFIFLKARD 296 (299) Q Consensus 237 ~g~Gia~lp~~~~~~---~~~lv~i~~~~~~~~~~~~lv~~~~~~~~~~~~~f~d~l~~~~r~ 296 (299) +|.|++++|.+.+.+ .|-.+..+ .+..++.++++|+++++.||++++|+|||.++++. T Consensus 236 ~G~Gvail~~~~~~~~~~~g~~~~pl--~~~~~~~~~lv~~~~r~~s~~~~aF~~~Lr~~a~a 296 (309) T PRK11013 236 AGLGVSIVNPLTALDYAGSGLVVRPF--SISVPFTVSLIRPLHRPSSALVDAFSEHLQAQAKA 296 (309) T ss_pred HCCEEEEECHHHHHHHHHCCEEEEEC--CCCCCEEEEEEEECCCCCCHHHHHHHHHHHHHHHH T ss_conf 79969994699998662199099988--88996189999989997799999999999999999 No 8 >CHL00180 rbcR LysR transcriptional regulator; Provisional Probab=100.00 E-value=0 Score=385.31 Aligned_cols=293 Identities=22% Similarity=0.184 Sum_probs=253.5 Q ss_pred CCCCHHHHHHHHHHHHHCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEECCCCEEEEECCCCCCCCCCCCCCCCCHH Q ss_conf 98888999999999982768999988289978999999999999588217976994685001343322222222221012 Q gi|254780282|r 1 MSFDWDKLRVFYVVARSGSFTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHARGLTLTEQGSKLHRVTSEVYHKLETT 80 (299) Q Consensus 1 m~md~~~L~~f~~v~~~gs~s~AA~~L~itq~avS~~i~~LE~~lg~~Lf~R~~~~~~lT~~G~~l~~~a~~~l~~~~~~ 80 (299) |.++++||++|++|+++|||++||++||+||||||++|++||+++|++||+|++|++.||++|+.|+++++.++.+++++ T Consensus 3 ~~~tL~qL~~F~~va~~gsft~AA~~L~isQpavS~~I~~LE~~lg~~Lf~R~~r~v~LT~aG~~l~~~a~~il~~~~~~ 82 (307) T CHL00180 3 LPFTLDQLRILKAIASEGSFKKAAESLYVSQPAVSLQIQNLEKQLNIPLFDRGGRKALLTEAGHLLLRYGERILALCEET 82 (307) T ss_pred CCCCHHHHHHHHHHHHCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEECCCCEEECHHHHHHHHHHHHHHHHHHHH T ss_conf 98489999999999980999999999888878999999999998699928998991010987999999899999999999 Q ss_pred HHHCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCCCCCCCC---CCCCCCCCCCCCCCCCC--CCCCCCC Q ss_conf 210012232222223332111000000000135667542000122222222---22222222222234565--4321111 Q gi|254780282|r 81 QIELQESSVKPSGKLRIATTIDLGQNLLQGNLKEFLLLYPDIQIQLILDNK---DIDISMDYADCAIRLRK--PIQSSSL 155 (299) Q Consensus 81 ~~~~~~~~~~~~g~i~I~~~~~~~~~~l~~~l~~f~~~~P~i~i~i~~~~~---~~~l~~~~~Di~i~~~~--~~~~~~l 155 (299) .+.+.+.+...+|+|+||++++++.+++|+.+..|.++||++++++...+. ...+.+|++|++|.... +...+++ T Consensus 83 ~~~~~~~~~~~~g~lrI~~~~s~~~~~lp~~l~~f~~~~P~v~i~l~~~~~~~~~~~l~~~~~D~~i~~~~~~~~~~~~l 162 (307) T CHL00180 83 CRALEDLKNLQGGTLIIGASQTTGTYLMPRLIGLFRQKYPQIAVQLQVHSTRRIAWSVANGQIDLAIIGGEVPTELKDNL 162 (307) T ss_pred HHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHCCCCCEEEEECCHHHHHHHHHCCCEEEEEECCCCCCCCCCCE T ss_conf 97799875112586010104066666435889999998889972789779999999998798009997577886667854 Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCCCCCCCEEEECCCCHHHHHH Q ss_conf 22345554332112344321112222221100011235664332110002356652022343212114532420013567 Q gi|254780282|r 156 IQRKLVTIHMHAYAAPHYLKNCREPLSIQELDKHNLITFGDLIPKCMEDFNWLATVDRPIGEPRISCLQVNSYLSIMQYC 235 (299) Q Consensus 156 ~~~~l~~~~~~~v~~~~~~~~~~~~~~~~dL~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~v 235 (299) ...++++++++++|+++|+...+..++++||.+++||.+............++...+... ......+++++.++++++| T Consensus 163 ~~~~l~~~~~~lv~~~~hpla~~~~v~~~dL~~~~~i~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~l~~~v 241 (307) T CHL00180 163 QVTPYAEDELALILPKSHPFAKLKKIQKEDLYRLRFIALDSQSTIRKVIDNILIQNGIDS-SRFKIEMELNSIEAIKNAV 241 (307) T ss_pred EEEEEECCCEEEEECCCCHHHCCCCCCHHHHHCCCEEEECCCCCHHHHHHHHHHHCCCCC-CCCEEEEEECCHHHHHHHH T ss_conf 999943242799973898022399999999817984871799968999999999769984-5542799978099999999 Q ss_pred HHHCCEEEEEHHHHCC---CCCEEEECCCCCCCCCEEEEEECCCCCCCHHHHHHHHHHHHHH Q ss_conf 8738423311777601---9984661776667660089993487788889999999999998 Q gi|254780282|r 236 VLGSGIALLPDYIVKD---NPNLVRIMEDVITPSFTVYFCYPEALKNTGKLKAFRNFIFLKA 294 (299) Q Consensus 236 ~~g~Gia~lp~~~~~~---~~~lv~i~~~~~~~~~~~~lv~~~~~~~~~~~~~f~d~l~~~~ 294 (299) .+|+||+++|...+.+ .|.++.+..+.+...++++++|++++..||++++|+|||.+.. T Consensus 242 ~~g~Gia~lP~~~v~~~~~~g~l~~~~~~~~~~~r~i~lv~~~~r~~s~a~~~F~~~l~~~f 303 (307) T CHL00180 242 QSGLGAAFVSVSAIEKELELGTLHWAKIENITIKRTLSIITNPNRYRSKAAETFSKEILTLF 303 (307) T ss_pred HHCCEEEECCHHHHHHHHHCCCEEEEECCCCCCEEEEEEEEECCCCCCHHHHHHHHHHHHHC T ss_conf 93994998259999989877988999789998504999999795977999999999999854 No 9 >PRK12682 transcriptional regulator CysB-like protein; Reviewed Probab=100.00 E-value=0 Score=385.58 Aligned_cols=289 Identities=21% Similarity=0.233 Sum_probs=253.0 Q ss_pred CCHHHHHHHHHHHHHC-CHHHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEECCCCE-EEEECCCCCCCCCCCCCCCCCHH Q ss_conf 8889999999999827-689999882899789999999999995882179769946-85001343322222222221012 Q gi|254780282|r 3 FDWDKLRVFYVVARSG-SFTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHARGL-TLTEQGSKLHRVTSEVYHKLETT 80 (299) Q Consensus 3 md~~~L~~f~~v~~~g-s~s~AA~~L~itq~avS~~i~~LE~~lg~~Lf~R~~~~~-~lT~~G~~l~~~a~~~l~~~~~~ 80 (299) ||+++|+||++|+++| |||+||++|++||||||++|++||++||++||+|+++++ .||++|+.|+++++++++.++++ T Consensus 1 M~l~~L~~f~~vv~~~~Sft~AA~~L~isQ~avS~~I~~LE~~Lg~~Lf~R~~~r~~~LT~~G~~l~~~a~~il~~~~~~ 80 (309) T PRK12682 1 MNLQQLRFVREAVRRNLNLTEAAKALHTSQPGVSKAIIELEEELGIEIFERHGKRLKGLTEPGKAVLDVIERILREVGNI 80 (309) T ss_pred CCHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEECCCCCCCCCHHHHHHHHHHHHHHHHHHHH T ss_conf 94799999999998699999999997898789999999999985998899889998570188999999999999999999 Q ss_pred HHHCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCCCCCCCC--C-CCCCCCCCCCCCCCCCCCCCCCCCC Q ss_conf 210012232222223332111000000000135667542000122222222--2-2222222222234565432111122 Q gi|254780282|r 81 QIELQESSVKPSGKLRIATTIDLGQNLLQGNLKEFLLLYPDIQIQLILDNK--D-IDISMDYADCAIRLRKPIQSSSLIQ 157 (299) Q Consensus 81 ~~~~~~~~~~~~g~i~I~~~~~~~~~~l~~~l~~f~~~~P~i~i~i~~~~~--~-~~l~~~~~Di~i~~~~~~~~~~l~~ 157 (299) ...+........|+|+||++++++.+++|+.+..|+++||++++++..++. . ..+..|.+|++|.......++++.. T Consensus 81 ~~~~~~~~~~~~G~lrIg~~~~~~~~~lp~~l~~f~~~~P~v~l~l~~~~~~~~~~~l~~g~~Dl~i~~~~~~~~~~l~~ 160 (309) T PRK12682 81 KRIGDEFSNQDSGTLTIATTHTQARYVLPRVVAKFRKRYPKVNLSLHQGSPDEIAQMVISGEADIGIATESLDDDPDLVT 160 (309) T ss_pred HHHHHHHHCCCCCCCCCCCCHHHHHHCCCHHHHHHHHHCCCCEEEEEECCHHHHHHHHHCCCCCHHHHHCCCCCCCCEEE T ss_conf 99998752567774121243133320386253999987898379998378299999997699764565077778988089 Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCCCCCCCEEEECCCCHHHHHHHH Q ss_conf 34555433211234432111222222110001123566433211000235665202234321211453242001356787 Q gi|254780282|r 158 RKLVTIHMHAYAAPHYLKNCREPLSIQELDKHNLITFGDLIPKCMEDFNWLATVDRPIGEPRISCLQVNSYLSIMQYCVL 237 (299) Q Consensus 158 ~~l~~~~~~~v~~~~~~~~~~~~~~~~dL~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~v~~ 237 (299) .++++++++++++++|+.....+++++||.++|||.+............++ ...+..+...++++|.++++++|.+ T Consensus 161 ~~l~~~~~~~v~~~~h~la~~~~i~~~dL~~~p~I~~~~~~~~r~~~~~~~----~~~g~~p~~~~~~~~~~~~~~~v~~ 236 (309) T PRK12682 161 LPCYDWTHAVIVPSDHPLAQKERITLEDLAEYPLITYHPGFTGRSAIDKAF----AAAGLQPDIVLEAIDSDVIKTYVRL 236 (309) T ss_pred EEEECCCEEEEECCCCHHHCCCCCCHHHHCCCCEEEECCCCCHHHHHHHHH----HHCCCCCCEEEEECCHHHHHHHHHH T ss_conf 993315236761699721149999999982899797279986799999999----9779996269999989999999995 Q ss_pred HCCEEEEEHHHHCC--CCCEEEECCCCCCCCCEEEEEECCCCCCCHHHHHHHHHHHHHHH Q ss_conf 38423311777601--99846617766676600899934877888899999999999985 Q gi|254780282|r 238 GSGIALLPDYIVKD--NPNLVRIMEDVITPSFTVYFCYPEALKNTGKLKAFRNFIFLKAR 295 (299) Q Consensus 238 g~Gia~lp~~~~~~--~~~lv~i~~~~~~~~~~~~lv~~~~~~~~~~~~~f~d~l~~~~r 295 (299) |+||+++|.+.+++ ++++|.++.+...+.+++|++|++++.+++++++|+||+.++.. T Consensus 237 G~Gi~~lp~~~~~~~~~~~Lv~v~~~~~~~~~~~~l~~rk~~~l~~~~~~FId~l~e~l~ 296 (309) T PRK12682 237 GLGVGIIAEMAYRPDRDGDLVALPAGHLFGPNTAWVAVKRGAYLRNYVYDFIELLAPHLS 296 (309) T ss_pred CCEEEHHHHHHHHHHHCCCEEEEECCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHCC T ss_conf 994242289983376479989997988777617999996966118999999999998729 No 10 >PRK10086 DNA-binding transcriptional regulator DsdC; Provisional Probab=100.00 E-value=0 Score=383.07 Aligned_cols=294 Identities=22% Similarity=0.306 Sum_probs=244.2 Q ss_pred CC-CCHHHHHHHHHHHHHCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEECCCCEEEEECCCCCCCCCCCCCCCCCH Q ss_conf 98-88899999999998276899998828997899999999999958821797699468500134332222222222101 Q gi|254780282|r 1 MS-FDWDKLRVFYVVARSGSFTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHARGLTLTEQGSKLHRVTSEVYHKLET 79 (299) Q Consensus 1 m~-md~~~L~~f~~v~~~gs~s~AA~~L~itq~avS~~i~~LE~~lg~~Lf~R~~~~~~lT~~G~~l~~~a~~~l~~~~~ 79 (299) || ++|++|++|++|+++||||+||++|++||||||++|++||++||++||+|++|++.||++|+.|+++++.+++.+++ T Consensus 11 ~~~~~L~~L~~F~aVa~~gSft~AA~~L~vsqsaVS~~I~~LE~~LG~~Lf~R~~R~l~LT~aG~~l~~~~~~~l~~l~~ 90 (311) T PRK10086 11 LNGWQLSKLHTFEVAARHQSFALAADELSLTPSAVSHRINQLEEELGIKLFVRSHRKVELTEEGKRVFWALKSSLDTLNQ 90 (311) T ss_pred CCCCCHHHHHHHHHHHHHCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCEEECCCCEEEHHHHHHHHHHHHHHHHHHHH T ss_conf 68587788999999998299999999978698999999999999859843897599168909999999999999999999 Q ss_pred HHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC Q ss_conf 22100122322222233321110000000001356675420001222222222222222222223456543211112234 Q gi|254780282|r 80 TQIELQESSVKPSGKLRIATTIDLGQNLLQGNLKEFLLLYPDIQIQLILDNKDIDISMDYADCAIRLRKPIQSSSLIQRK 159 (299) Q Consensus 80 ~~~~~~~~~~~~~g~i~I~~~~~~~~~~l~~~l~~f~~~~P~i~i~i~~~~~~~~l~~~~~Di~i~~~~~~~~~~l~~~~ 159 (299) ....+.. ...+|.|+|+++++++..|++|.+.+|.++||+|+|++..++...++..+++|++|+++.. .++++..++ T Consensus 91 ~~~~~~~--~~~~G~LrI~~~~~~~~~~L~p~L~~F~~~~P~i~l~l~~~~~~~dl~~~~~Dlai~~g~~-~~~~l~~~~ 167 (311) T PRK10086 91 EILDIKN--QELSGTLTVYSRPSIAQCWLVPRLADFTRRYPSISLTILTGNENINFQRAGIDLAIYFDDA-PSAQLTHHF 167 (311) T ss_pred HHHHHHC--CCCCCCCCCCCCCHHHHHHHHHHHHHHHHHCCCEEEEEEECCCCCCHHCCCCEEEEEECCC-CCCCCEEEE T ss_conf 9999735--7867851036772799875169999999618976999996477464102675058994788-999848999 Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC---CCCCCCHHHHHHHHCCCCCCCCCCEEEECCCCHHHHHHH Q ss_conf 55543321123443211122222211000112356643---321100023566520223432121145324200135678 Q gi|254780282|r 160 LVTIHMHAYAAPHYLKNCREPLSIQELDKHNLITFGDL---IPKCMEDFNWLATVDRPIGEPRISCLQVNSYLSIMQYCV 236 (299) Q Consensus 160 l~~~~~~~v~~~~~~~~~~~~~~~~dL~~~~~i~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~v~ 236 (299) |+++++++||||+|+.+++.+.++++|.+++++..... ......+..|....+ ....+....+++++.+.++.++. T Consensus 168 L~~~~~~~vasP~y~~~~~~~~~p~~L~~~~ll~~~~~~~~~~~~~~w~~~~~~~~-~~~~~~~~~~~~~~~~~~~~aa~ 246 (311) T PRK10086 168 LMDESILPVCSPEYAERHALTNNPNNLRHCTLLHDRQAWSNDSGTDEWHSWAQHFG-VNLLPDSSGIGFDRSDLAVIAAM 246 (311) T ss_pred CCCCEEEEEECHHHHHHCCCCCCHHHHHHCHHHCCCCCCCCCCCCHHHHHHHHHCC-CCCCCCCCCEEECCHHHHHHHHH T ss_conf 74662999998899975799999899861633134432246788226664775178-52036788259867899999999 Q ss_pred HHCCEEEEEHHHHCC---CCCEEEECCCCCCCCCEEEEEECCCCCCCHHHHHHHHHHHHHHHCCC Q ss_conf 738423311777601---99846617766676600899934877888899999999999985066 Q gi|254780282|r 237 LGSGIALLPDYIVKD---NPNLVRIMEDVITPSFTVYFCYPEALKNTGKLKAFRNFIFLKARDWK 298 (299) Q Consensus 237 ~g~Gia~lp~~~~~~---~~~lv~i~~~~~~~~~~~~lv~~~~~~~~~~~~~f~d~l~~~~r~~~ 298 (299) +|.||+++|.+++.+ +|+||.+++++..+....|.++++++..+|++++|+|||.+++.+-| T Consensus 247 ~G~Gia~~p~~~v~~~l~~G~LV~~l~~~~~~~~~~~~l~~~~~~~~p~vr~Fid~L~e~~~q~e 311 (311) T PRK10086 247 NHIGVAMGRKRLVQKRLASGELVAPFGDMEVKCHQHYYVVTLPGRQWPKIEAFIDWLKEQVAQVE 311 (311) T ss_pred HCCCEEECCHHHHHHHHHCCCCEEECCCCCCCCCCEEEEEECCCCCCHHHHHHHHHHHHHHCCCC T ss_conf 78998963599999999789988889887788886699997899989899999999999857349 No 11 >PRK12683 transcriptional regulator CysB-like protein; Reviewed Probab=100.00 E-value=0 Score=384.83 Aligned_cols=290 Identities=20% Similarity=0.248 Sum_probs=251.4 Q ss_pred CCHHHHHHHHHHHHHC-CHHHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEECCCCEE-EEECCCCCCCCCCCCCCCCCHH Q ss_conf 8889999999999827-6899998828997899999999999958821797699468-5001343322222222221012 Q gi|254780282|r 3 FDWDKLRVFYVVARSG-SFTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHARGLT-LTEQGSKLHRVTSEVYHKLETT 80 (299) Q Consensus 3 md~~~L~~f~~v~~~g-s~s~AA~~L~itq~avS~~i~~LE~~lg~~Lf~R~~~~~~-lT~~G~~l~~~a~~~l~~~~~~ 80 (299) ||++||+||++++++| |||+||++||+||||||++|++||+++|++||+|+++++. ||++|+.|++++++++...+++ T Consensus 1 M~lrqL~~F~~~v~~~~s~t~AA~~L~iSQpavS~~Ik~LE~eLG~~LF~R~~~r~~~LT~~G~~l~~~a~~il~~~~~~ 80 (308) T PRK12683 1 MNFQQLRIIREAVRQNFNLTEVANALYTSQSGVSKQIKDLEDELGVEIFIRRGKRLTGLTEPGKELLQIVERMLLDAENL 80 (308) T ss_pred CCHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEECCCCCCCCCHHHHHHHHHHHHHHHHHHHH T ss_conf 96799999999998689999999997897779999999999996997389869987557876999999999999999999 Q ss_pred HHHCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCCCCCCCC---CCCCCCCCCCCCCCCCCCCCCCCCCC Q ss_conf 210012232222223332111000000000135667542000122222222---22222222222234565432111122 Q gi|254780282|r 81 QIELQESSVKPSGKLRIATTIDLGQNLLQGNLKEFLLLYPDIQIQLILDNK---DIDISMDYADCAIRLRKPIQSSSLIQ 157 (299) Q Consensus 81 ~~~~~~~~~~~~g~i~I~~~~~~~~~~l~~~l~~f~~~~P~i~i~i~~~~~---~~~l~~~~~Di~i~~~~~~~~~~l~~ 157 (299) .+.+++......|+|+||++++++.+++|+.+..|+++||+++|++...+. ...|.+|++|+||........+++.. T Consensus 81 ~~~~~~~~~~~~G~l~Ig~~~~~~~~~lp~~l~~f~~~~P~v~i~l~~~~~~~~~~~L~~g~~Dl~i~~~~~~~~~~l~~ 160 (308) T PRK12683 81 RRLARQFADRDSGRLTVATTHTQARYALPKVVRQFTEVFPKVHLALRQGSPQEIAEMLLNGEADIGIATEALDREPDLVS 160 (308) T ss_pred HHHHHHHHCCCCCEEEECCCCHHHHHCCCHHHHHHHHHCCCCEEEEEECCHHHHHHHHHCCCCCEEECCCCCCCCCCCEE T ss_conf 99998752677762420013201120168466899987899669996078699999997799778806667788877168 Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCCCCCCCEEEECCCCHHHHHHHH Q ss_conf 34555433211234432111222222110001123566433211000235665202234321211453242001356787 Q gi|254780282|r 158 RKLVTIHMHAYAAPHYLKNCREPLSIQELDKHNLITFGDLIPKCMEDFNWLATVDRPIGEPRISCLQVNSYLSIMQYCVL 237 (299) Q Consensus 158 ~~l~~~~~~~v~~~~~~~~~~~~~~~~dL~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~v~~ 237 (299) .++++++++++++++|+.....+++++||.++|||.+...+........++ ...+..+...+++++.++++.+|.+ T Consensus 161 ~~l~~~~~~lv~~~~hpla~~~~v~l~dl~~~p~I~~~~~~~~r~~i~~~~----~~~g~~p~~~~e~~~~~~i~~~V~~ 236 (308) T PRK12683 161 FPYYSWHHVVVVPKGHPLTGRENLTLEALAEYPIITYDQGFTGRSHIDQAF----AEAGAVPDIVLTALDADVIKTYVEL 236 (308) T ss_pred EEECCCCEEEEECCCCCCCCCCCCCHHHHCCCCEEECCCCCCHHHHHHHHH----HHCCCCCCEEEEECCHHHHHHHHHH T ss_conf 761245158984699953369999999985999896189982999999999----9779998579999989999999997 Q ss_pred HCCEEEEEHHHHCC--CCCEEEECCCCCCCCCEEEEEECCCCCCCHHHHHHHHHHHHHHHC Q ss_conf 38423311777601--998466177666766008999348778888999999999999850 Q gi|254780282|r 238 GSGIALLPDYIVKD--NPNLVRIMEDVITPSFTVYFCYPEALKNTGKLKAFRNFIFLKARD 296 (299) Q Consensus 238 g~Gia~lp~~~~~~--~~~lv~i~~~~~~~~~~~~lv~~~~~~~~~~~~~f~d~l~~~~r~ 296 (299) |+|++++|...++. +++++.+..+.....+.+|++|+|++++|+++++|+|++.++..+ T Consensus 237 g~Gi~ilp~~~~~~~~~~~lv~l~~~~~~~~~~~~i~~rk~~~Ls~~a~~Fie~l~~~l~~ 297 (308) T PRK12683 237 GMGVGIVAAMAYDPQRDTGLVALDTQHLFEANTTRVALRRGAYLRGYAYRFIEMFAPHLSE 297 (308) T ss_pred CCCHHHHHHHHHHHHHCCCEEEEECCCCCCCCEEEEEECCCCCCCHHHHHHHHHHHHHHCH T ss_conf 9847078999987886099799989788766179999909685799999999998886298 No 12 >PRK10837 putative DNA-binding transcriptional regulator; Provisional Probab=100.00 E-value=0 Score=384.06 Aligned_cols=283 Identities=20% Similarity=0.222 Sum_probs=243.4 Q ss_pred CCCCHHHHHHHHHHHHHCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEECCCCEEEEECCCCCCCCCCCCCCCCCHH Q ss_conf 98888999999999982768999988289978999999999999588217976994685001343322222222221012 Q gi|254780282|r 1 MSFDWDKLRVFYVVARSGSFTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHARGLTLTEQGSKLHRVTSEVYHKLETT 80 (299) Q Consensus 1 m~md~~~L~~f~~v~~~gs~s~AA~~L~itq~avS~~i~~LE~~lg~~Lf~R~~~~~~lT~~G~~l~~~a~~~l~~~~~~ 80 (299) |+||+++|++|++|+++||||+||++||+||||||++|++||++||++||+|++||+.||++|+.|+++++.++++..++ T Consensus 1 M~m~L~~L~~F~~va~~gsft~AA~~L~isQpavS~~I~~LE~~Lg~~Lf~R~~r~v~lT~~G~~l~~~a~~~l~~~~~~ 80 (291) T PRK10837 1 MHITLRQLEVFAEVLKSGSTTQASVMLALSQSAVSAALTDLEGQLGVQLFDRVGKRLVVNEHGRLLYPRALALLEQAVEI 80 (291) T ss_pred CCCCHHHHHHHHHHHHCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCEEECCCCCCCCHHHHHHHHHHHHHHHHHHHH T ss_conf 98869999999999980999999999888878999999999999699228985996524685999999999999999999 Q ss_pred HHHCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCCCCCCCC---CCCCCCCCCCCCCCCCCCCCCCCCCC Q ss_conf 210012232222223332111000000000135667542000122222222---22222222222234565432111122 Q gi|254780282|r 81 QIELQESSVKPSGKLRIATTIDLGQNLLQGNLKEFLLLYPDIQIQLILDNK---DIDISMDYADCAIRLRKPIQSSSLIQ 157 (299) Q Consensus 81 ~~~~~~~~~~~~g~i~I~~~~~~~~~~l~~~l~~f~~~~P~i~i~i~~~~~---~~~l~~~~~Di~i~~~~~~~~~~l~~ 157 (299) .+. ..+..|.++||++++++.+++|+.+..|+++||+++|++..++. ...+.++++|++|.. .+...+++.. T Consensus 81 ~~~----~~~~~g~l~i~~~~~~~~~~l~~~l~~f~~~~P~v~l~l~~~~~~~~~~~l~~~~~D~~i~~-~~~~~~~l~~ 155 (291) T PRK10837 81 EQL----FREDNGAIRIYASSTIGNYILPAMIARYRHDYPQLPLELSVGNSQDVIQAVLDFRVDIGLIE-GPCHSTEIIS 155 (291) T ss_pred HHH----HCCCCCEEEEEEEHHHHHHHHHHHHHHHHHHCCCCEEEEEECCHHHHHHHHHHCCCCEEEEC-CCCCCCCEEE T ss_conf 997----34788629999617999999999999999648993599998888999999980884166741-7889987189 Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCCCCCCCEEEECCCCHHHHHHHH Q ss_conf 34555433211234432111222222110001123566433211000235665202234321211453242001356787 Q gi|254780282|r 158 RKLVTIHMHAYAAPHYLKNCREPLSIQELDKHNLITFGDLIPKCMEDFNWLATVDRPIGEPRISCLQVNSYLSIMQYCVL 237 (299) Q Consensus 158 ~~l~~~~~~~v~~~~~~~~~~~~~~~~dL~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~v~~ 237 (299) .+++++++++||+|+|+...+ +++++||.++|||.+............++. ..+......+++++.++++++|.+ T Consensus 156 ~~l~~~~~~~v~~p~~~l~~~-~i~~~~l~~~~~i~~~~~~~~r~~~~~~~~----~~~~~~~~~~~~~~~~~i~~~v~~ 230 (291) T PRK10837 156 EPWLEDELVVFAAPDSPLARG-PVTLEQLAAAPWILRERGSGTREIVDYLLL----SHLPRFEMAMELGNSEAIKHAVRH 230 (291) T ss_pred EEEECCCEEEEECCCCHHHCC-CCCHHHHHCCCEEEECCCCCHHHHHHHHHH----HCCCCCCEEEECCCHHHHHHHHHH T ss_conf 994414189998788665379-999899807987994499868999999998----548865301312979999999995 Q ss_pred HCCEEEEEHHHHCC---CCCEEEECCCCCCCCCEEEEEECCCCCCCHHHHHHHHHHHHH Q ss_conf 38423311777601---998466177666766008999348778888999999999999 Q gi|254780282|r 238 GSGIALLPDYIVKD---NPNLVRIMEDVITPSFTVYFCYPEALKNTGKLKAFRNFIFLK 293 (299) Q Consensus 238 g~Gia~lp~~~~~~---~~~lv~i~~~~~~~~~~~~lv~~~~~~~~~~~~~f~d~l~~~ 293 (299) |+||+++|.+++++ .|.|+.+..+.+...+++|++|++++..++++++|+||+.++ T Consensus 231 G~Gia~lp~~~v~~~l~~g~L~~l~~~~~~~~~~~~lv~~k~~~ls~~~~~Fidfl~~a 289 (291) T PRK10837 231 GLGISCLSRRVIADQLQAGTLVEVAVPLPRLMRTLWRIHHRQKHLSNALQRFLSYCQPA 289 (291) T ss_pred CCCEEECCHHHHHHHHHCCCEEEEECCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHC T ss_conf 99189724999999987899799707888861279999989786599999999998620 No 13 >PRK11151 DNA-binding transcriptional regulator OxyR; Provisional Probab=100.00 E-value=0 Score=380.99 Aligned_cols=288 Identities=20% Similarity=0.236 Sum_probs=248.6 Q ss_pred CCHHHHHHHHHHHHHCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEECCCCEEEEECCCCCCCCCCCCCCCCCHHHH Q ss_conf 88899999999998276899998828997899999999999958821797699468500134332222222222101221 Q gi|254780282|r 3 FDWDKLRVFYVVARSGSFTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHARGLTLTEQGSKLHRVTSEVYHKLETTQI 82 (299) Q Consensus 3 md~~~L~~f~~v~~~gs~s~AA~~L~itq~avS~~i~~LE~~lg~~Lf~R~~~~~~lT~~G~~l~~~a~~~l~~~~~~~~ 82 (299) ||+++|+||++|+++||||+||++||+||||||++|++||++||++||+|++||+.||++|+.|+++++.++.+++++.+ T Consensus 1 M~lrqL~~F~aVae~gSfs~AA~~L~isQpavS~~I~~LE~~LG~~LF~R~~r~v~LT~aG~~l~~~a~~il~~~~~~~~ 80 (305) T PRK11151 1 MNIRDLEYLVALAEHKHFRRAADSCHVSQPTLSGQIRKLEDELGVMLLERTSRKVLFTQAGLLLVDQAKTVLREVKVLKE 80 (305) T ss_pred CCHHHHHHHHHHHHCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCEEECCCEEEECHHHHHHHHHHHHHHHHHHHHHH T ss_conf 96799999999997299999999978987899999999999979865898599046888699999999999999999999 Q ss_pred HCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCCCCCCC--C-CCCCCCCCCCCCCCCCCCCCCCCCCCCC Q ss_conf 001223222222333211100000000013566754200012222222--2-2222222222223456543211112234 Q gi|254780282|r 83 ELQESSVKPSGKLRIATTIDLGQNLLQGNLKEFLLLYPDIQIQLILDN--K-DIDISMDYADCAIRLRKPIQSSSLIQRK 159 (299) Q Consensus 83 ~~~~~~~~~~g~i~I~~~~~~~~~~l~~~l~~f~~~~P~i~i~i~~~~--~-~~~l~~~~~Di~i~~~~~~~~~~l~~~~ 159 (299) .+........|.++||++++++.+++|+++.+|+++||+++|++...+ . ...+..|++|++|.. .+...+++...+ T Consensus 81 ~~~~~~~~~~G~lrig~~~~~~~~llp~~l~~f~~~~P~v~i~l~~~~~~~l~~~l~~g~~D~~i~~-~~~~~~~~~~~~ 159 (305) T PRK11151 81 MASQQGETMSGPLHIGLIPTVGPYLLPHIIPMLHQTFPKLEMYLHEAQTHQLLAQLDSGKLDCAILA-LVKESEAFIEVP 159 (305) T ss_pred HHHHHCCCCCCEEEEEEHHHHHHHCCCHHHHHHHHCCCCCEEEEEECCCHHHHHHHHCCCCCEEEEE-CCCCCCCCEEEE T ss_conf 9886317876414311022233323827799986238983799998875777878657885379984-588998726876 Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCCCCCCCEEEECCCCHHHHHHHHHC Q ss_conf 55543321123443211122222211000112356643321100023566520223432121145324200135678738 Q gi|254780282|r 160 LVTIHMHAYAAPHYLKNCREPLSIQELDKHNLITFGDLIPKCMEDFNWLATVDRPIGEPRISCLQVNSYLSIMQYCVLGS 239 (299) Q Consensus 160 l~~~~~~~v~~~~~~~~~~~~~~~~dL~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~v~~g~ 239 (299) +++++++++++++|+...+..++++||.+++||.+..+.........+.. ..+......+++++.+++.+||.+|. T Consensus 160 l~~e~l~lv~~~~hpla~~~~i~l~~L~~~~~i~~~~~~~~r~~~~~~~~----~~g~~~~~~~~~~~~~~i~~lV~~G~ 235 (305) T PRK11151 160 LFDEPMLLAVYEDHPWANRDRVPMSDLAGEKLLMLEDGHCLRDQAMGFCF----EAGADEDTHFRATSLETLRNMVAAGS 235 (305) T ss_pred ECCCCEEEEEECCCCCCCCCCCCHHHHCCCCEEEECCCCCHHHHHHHHHH----HCCCCCCEEEEEECHHHHHHHHHHCC T ss_conf 20462799995898433699989999769988996899859999999999----77999873899944799999999299 Q ss_pred CEEEEEHHHHCC---CCCEEEECCCCCCCCCEEEEEECCCCCCCHHHHHHHHHHHHHHH Q ss_conf 423311777601---99846617766676600899934877888899999999999985 Q gi|254780282|r 240 GIALLPDYIVKD---NPNLVRIMEDVITPSFTVYFCYPEALKNTGKLKAFRNFIFLKAR 295 (299) Q Consensus 240 Gia~lp~~~~~~---~~~lv~i~~~~~~~~~~~~lv~~~~~~~~~~~~~f~d~l~~~~r 295 (299) |++++|.+.+.+ .+.++.++...+.+.++++++|++++++++++++|+|+|.+... T Consensus 236 Gv~ilp~~~v~~~~~~~~l~~~pl~~~~~~r~i~lv~r~~~~ls~~~~~~~e~ir~~l~ 294 (305) T PRK11151 236 GITLLPALAVPNERKRDGVCYLPCIKPEPRRTIGLVYRPGSPLRSRYEQLAEAIRARMD 294 (305) T ss_pred CEEECCHHHHHHHCCCCCEEEEECCCCCCEEEEEEEEECCCCCCHHHHHHHHHHHHHHH T ss_conf 68983599986221269889998889997369999998909878999999999999888 No 14 >PRK09791 putative DNA-binding transcriptional regulator; Provisional Probab=100.00 E-value=0 Score=378.52 Aligned_cols=290 Identities=17% Similarity=0.234 Sum_probs=250.0 Q ss_pred CCCCHHHHHHHHHHHHHCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEECCCCEEEEECCCCCCCCCCCCCCCCCHH Q ss_conf 98888999999999982768999988289978999999999999588217976994685001343322222222221012 Q gi|254780282|r 1 MSFDWDKLRVFYVVARSGSFTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHARGLTLTEQGSKLHRVTSEVYHKLETT 80 (299) Q Consensus 1 m~md~~~L~~f~~v~~~gs~s~AA~~L~itq~avS~~i~~LE~~lg~~Lf~R~~~~~~lT~~G~~l~~~a~~~l~~~~~~ 80 (299) |+||++||+||++|+++||||+||++||+||||||++|++||+++|++||+|++||++||++|+.|+++++.++++++.+ T Consensus 3 ~~m~l~qLr~F~av~~~gs~s~AA~~L~isQpavS~~I~~LE~~lg~~LF~R~~r~~~LT~~G~~l~~~a~~il~~~~~~ 82 (302) T PRK09791 3 FQVKIHQIRAFVEVARQGSIRGASRMLNMSQPALSKSIQELEEGLAAQLFFRRSKGVTLTDAGESFYQHASLILEELRAA 82 (302) T ss_pred CCCCHHHHHHHHHHHHCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEECCCCCCCCHHHHHHHHHHHHHHHHHHHH T ss_conf 88739999999999980999999999789879999999999999599689999998354779999999999999999999 Q ss_pred HHHCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCCCCCCCC---CCCCCCCCCCCCCCCC-CCCCCCCCC Q ss_conf 210012232222223332111000000000135667542000122222222---2222222222223456-543211112 Q gi|254780282|r 81 QIELQESSVKPSGKLRIATTIDLGQNLLQGNLKEFLLLYPDIQIQLILDNK---DIDISMDYADCAIRLR-KPIQSSSLI 156 (299) Q Consensus 81 ~~~~~~~~~~~~g~i~I~~~~~~~~~~l~~~l~~f~~~~P~i~i~i~~~~~---~~~l~~~~~Di~i~~~-~~~~~~~l~ 156 (299) .+.+.+..+...|+++||++++++..++|+++..|+++||+|+|++...+. ..++..|++|++|... ....++++. T Consensus 83 ~~~~~~~~~~~~G~l~Ig~~~~~~~~~lp~~l~~f~~~~P~v~i~i~~~~~~~~~~~l~~g~~D~~i~~~~~~~~~~~l~ 162 (302) T PRK09791 83 QEDIRQRQGQLAGQINIGMGASISRSLMPAVISRFHQQHPQVKVRIMEGQLVSMINELRQGELDFTINTYYQGPYDHEFT 162 (302) T ss_pred HHHHHHHHCCCCCEEEEEECHHHHHHHHHHHHHHHHHHCCCCEEEEEECCHHHHHHHHHCCCCCEEEECCCCCCCCCCEE T ss_conf 99999850676633999862688987119999999998879779999899999999998799778996567887887647 Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCCCCCCCEEEECCCCHHHHHHH Q ss_conf 23455543321123443211122222211000112356643321100023566520223432121145324200135678 Q gi|254780282|r 157 QRKLVTIHMHAYAAPHYLKNCREPLSIQELDKHNLITFGDLIPKCMEDFNWLATVDRPIGEPRISCLQVNSYLSIMQYCV 236 (299) Q Consensus 157 ~~~l~~~~~~~v~~~~~~~~~~~~~~~~dL~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~v~ 236 (299) ..++++++++++++++|+.... .+++|+.+++|+......... .++.......+..+...++++++.+++++|. T Consensus 163 ~~~l~~~~~~~v~~~~hpl~~~--~~l~~l~~~~~~~~~~~~~~~----~~~~~~~~~~g~~p~~~~~~~~~~~~~~lv~ 236 (302) T PRK09791 163 FEKLLEKQFAIFCRPGHPAIGA--RSIKQLLDYSWTMPTPHGSYY----KQLSELLDDQAQTPQVGVVCETFSACISLVA 236 (302) T ss_pred EEEEEEEEEEEEECCCCCCCCC--CCHHHHHCCCEEEECCCCCHH----HHHHHHHHHCCCCCCEEEEECCHHHHHHHHH T ss_conf 9997740159998389843579--899998479938757999799----9999999967999856999992999999999 Q ss_pred HHCCEEEEEHHHHCC---CCCEEEECCCCCCCCCEEEEEECCCCCCCHHHHHHHHHHHHHHHC Q ss_conf 738423311777601---998466177666766008999348778888999999999999850 Q gi|254780282|r 237 LGSGIALLPDYIVKD---NPNLVRIMEDVITPSFTVYFCYPEALKNTGKLKAFRNFIFLKARD 296 (299) Q Consensus 237 ~g~Gia~lp~~~~~~---~~~lv~i~~~~~~~~~~~~lv~~~~~~~~~~~~~f~d~l~~~~r~ 296 (299) .|.||+++|..++.+ .++++.++.+.+.+.+.+|++|++++.++|++++|++++.+++.. T Consensus 237 ~g~gv~ilp~~~~~~~~~~~~lv~lpl~~~~~~~~~~lv~r~~~~~spa~~~fi~~lr~~~~~ 299 (302) T PRK09791 237 KSDFLSILPEEMGCDPLHGQGLVMLPVSEILPKAAYYLIQRRDSRQTPLTASLITQFRRECGY 299 (302) T ss_pred HCCEEEEECHHHHHHHHHCCCEEEEECCCCCCCEEEEEEEECCCCCCHHHHHHHHHHHHHHHH T ss_conf 789679631999987874899999979998860089999989098899999999999999887 No 15 >PRK11233 nitrogen assimilation transcriptional regulator; Provisional Probab=100.00 E-value=0 Score=374.35 Aligned_cols=288 Identities=18% Similarity=0.238 Sum_probs=242.3 Q ss_pred CCHHHHHHHHHHHHHCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEECCCCEEEEECCCCCCCCCCCCCCCCCHHHH Q ss_conf 88899999999998276899998828997899999999999958821797699468500134332222222222101221 Q gi|254780282|r 3 FDWDKLRVFYVVARSGSFTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHARGLTLTEQGSKLHRVTSEVYHKLETTQI 82 (299) Q Consensus 3 md~~~L~~f~~v~~~gs~s~AA~~L~itq~avS~~i~~LE~~lg~~Lf~R~~~~~~lT~~G~~l~~~a~~~l~~~~~~~~ 82 (299) ||+++|+||++|+++||||+||++||+||||||++|++||+++|++||+|++||+.||++|+.|+++++.++..++++.. T Consensus 1 M~lrqLr~F~aVae~gs~s~AA~~L~isQpavS~~I~~LE~~LG~~Lf~R~~r~v~lT~~G~~l~~~a~~il~~~~~~~~ 80 (305) T PRK11233 1 MNFRRLKYFVKIVDIGSLTQAAEVLHIAQPALSQQVATLEGELNQQLLIRTKRGVTPTEAGKILYTHARAILRQCEQAQL 80 (305) T ss_pred CCHHHHHHHHHHHHCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEECCCCEEECHHHHHHHHHHHHHHHHHHHHHH T ss_conf 95799999999998099999999988987899999999999969977998499177988389999999999999999999 Q ss_pred HCCCCCCCCCCCCCCCCCC-CCCCCCCCCHHHHHHHHHHCCCCCCCCCCC---CCCCCCCCCCCCCCCCCCCCCCCCCCC Q ss_conf 0012232222223332111-000000000135667542000122222222---222222222222345654321111223 Q gi|254780282|r 83 ELQESSVKPSGKLRIATTI-DLGQNLLQGNLKEFLLLYPDIQIQLILDNK---DIDISMDYADCAIRLRKPIQSSSLIQR 158 (299) Q Consensus 83 ~~~~~~~~~~g~i~I~~~~-~~~~~~l~~~l~~f~~~~P~i~i~i~~~~~---~~~l~~~~~Di~i~~~~~~~~~~l~~~ 158 (299) .+.+.....+|+++||+.+ +.+..++++.+.+|+++||++++++...+. ...+.+|++|+||.... ...+++... T Consensus 81 ~~~~~~~~~~G~l~ig~~p~~~~~~l~~p~l~~f~~~~P~v~v~l~~~~~~~l~~~l~~g~~Dlai~~~~-~~~~~l~~~ 159 (305) T PRK11233 81 AVHNVGQALSGQVSIGLAPGTAASSITMPLLQAVRAEFPEIVIYLHENSGAVLNEKLINGQLDMAVIYEH-SPVAGVSSQ 159 (305) T ss_pred HHHHHCCCCCCEEEEEEECCHHHHHHHHHHHHHHHHHCCCEEEEEECCCHHHHHHHHHCCCEEEEEEECC-CCCCCCEEE T ss_conf 9997507874049999962155665369999999997894299972388799999987698479998279-898882899 Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCCCCCCCEEEECCCCHHHHHHHHH Q ss_conf 45554332112344321112222221100011235664332110002356652022343212114532420013567873 Q gi|254780282|r 159 KLVTIHMHAYAAPHYLKNCREPLSIQELDKHNLITFGDLIPKCMEDFNWLATVDRPIGEPRISCLQVNSYLSIMQYCVLG 238 (299) Q Consensus 159 ~l~~~~~~~v~~~~~~~~~~~~~~~~dL~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~v~~g 238 (299) ++++++++++++++|+ +..+++.|+.+++++......... ..........+......+++++.+++..+|.+| T Consensus 160 ~l~~~~l~lv~~~~~p---~~~i~l~~l~~~~~i~~~~~~~~r----~~~~~~~~~~~~~~~~~~e~~~~~~i~~~V~~G 232 (305) T PRK11233 160 ALLKEDLFLVGTQDCP---GQSVDLNAIAQMNLFLPRDYSAVR----LRVDEAFSLRRLTAKVIGEIESIATLTAAIASG 232 (305) T ss_pred EEEECCEEEEECCCCC---CCCCCHHHHCCCCEEECCCCCHHH----HHHHHHHHHCCCCCCEEEEECCHHHHHHHHHHC T ss_conf 9985358999847788---787899998089989879998499----999999997799984799999699999999979 Q ss_pred CCEEEEEHHHHCC---CCCEEEECCCCCCCCCEEEEEECCCCCCCHHHHHHHHHHHHHH-------HCCC Q ss_conf 8423311777601---9984661776667660089993487788889999999999998-------5066 Q gi|254780282|r 239 SGIALLPDYIVKD---NPNLVRIMEDVITPSFTVYFCYPEALKNTGKLKAFRNFIFLKA-------RDWK 298 (299) Q Consensus 239 ~Gia~lp~~~~~~---~~~lv~i~~~~~~~~~~~~lv~~~~~~~~~~~~~f~d~l~~~~-------r~~~ 298 (299) .|++++|.+.+++ .+.++.+.+..+...++++++|++++++||++++|+|+|.+.+ |||- T Consensus 233 ~GiailP~~~~~~~~~~~~~~~~~~~~p~~~~~~~l~~~~~r~lspaa~af~d~L~~~~~~p~~e~r~~~ 302 (305) T PRK11233 233 MGVTVLPESAARSLCGAVNGWMSRITTPSMSLSLSLNLSARANLSPQAQAVKEILLSLISSPVMEKRQWQ 302 (305) T ss_pred CEEEEEHHHHHHHHHHCCCEEEEECCCCCCEEEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCCCCCCE T ss_conf 9789871999998753497699925999866599999989098899999999999997747162788661 No 16 >PRK12679 cbl transcriptional regulator Cbl; Reviewed Probab=100.00 E-value=0 Score=373.88 Aligned_cols=286 Identities=23% Similarity=0.281 Sum_probs=250.1 Q ss_pred CCHHHHHHHHHHHHHC-CHHHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEECCCC-EEEEECCCCCCCCCCCCCCCCCHH Q ss_conf 8889999999999827-68999988289978999999999999588217976994-685001343322222222221012 Q gi|254780282|r 3 FDWDKLRVFYVVARSG-SFTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHARG-LTLTEQGSKLHRVTSEVYHKLETT 80 (299) Q Consensus 3 md~~~L~~f~~v~~~g-s~s~AA~~L~itq~avS~~i~~LE~~lg~~Lf~R~~~~-~~lT~~G~~l~~~a~~~l~~~~~~ 80 (299) ||++||+||++|++++ |||+||++||+||||||++|++||++||++||+|.|++ +.||++|+.|++++++++...+++ T Consensus 1 M~l~QLr~f~~va~~~~s~t~AAe~L~iSQPavS~qIk~LE~eLGv~LF~R~gkr~v~LT~~G~~l~~~a~~il~~~~~~ 80 (316) T PRK12679 1 MNFQQLKIIREAARQDYNLTEVANMLFTSQSGVSRHIRELEDELGIEIFVRRGKRLLGMTEPGKALLVIAERILNEASNV 80 (316) T ss_pred CCHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCCEEEEECCCCCCCCHHHHHHHHHHHHHHHHHHHH T ss_conf 96799999999998689999999997897789999999999995991289808998775888999999999999999999 Q ss_pred HHHCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCCCCCCCC--CC-CCCCCCCCCCCCCCCCCCCCCCCC Q ss_conf 210012232222223332111000000000135667542000122222222--22-222222222234565432111122 Q gi|254780282|r 81 QIELQESSVKPSGKLRIATTIDLGQNLLQGNLKEFLLLYPDIQIQLILDNK--DI-DISMDYADCAIRLRKPIQSSSLIQ 157 (299) Q Consensus 81 ~~~~~~~~~~~~g~i~I~~~~~~~~~~l~~~l~~f~~~~P~i~i~i~~~~~--~~-~l~~~~~Di~i~~~~~~~~~~l~~ 157 (299) ...++...+..+|+++||++++++.+++|+.+.+|+++||++++++...+. .. .+..|++|+||.......++++.. T Consensus 81 ~~~~~~~~~~~~G~l~Ig~~~t~a~~~LP~~l~~F~~~~P~v~l~l~~~~~~~i~~~l~~g~~Dl~i~~~~~~~~p~l~~ 160 (316) T PRK12679 81 RRLADLFTNDTSGVLTIATTHTQARYSLPEVIKAFRELFPEVRLELIQGTPQEIATLLQNGEADIGIASERLSNDPQLVA 160 (316) T ss_pred HHHHHHHCCCCCCEEEEEEEECCHHCCCCHHHHHHHHHCCCCEEEEEECCHHHHHHHHHCCCCCEEECCCCCCCCCCCEE T ss_conf 99999853887764999985032010381999999986899538998478799999998799885222467789976079 Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCCCCCCCEEEECCCCHHHHHHHH Q ss_conf 34555433211234432111222222110001123566433211000235665202234321211453242001356787 Q gi|254780282|r 158 RKLVTIHMHAYAAPHYLKNCREPLSIQELDKHNLITFGDLIPKCMEDFNWLATVDRPIGEPRISCLQVNSYLSIMQYCVL 237 (299) Q Consensus 158 ~~l~~~~~~~v~~~~~~~~~~~~~~~~dL~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~v~~ 237 (299) .++++++++++++++|+...+.+++++||.++|||.+..++..... +.......+..+..++++++.++++.+|.+ T Consensus 161 ~p~~~~~~~lvvp~~HpLa~~~~vsl~~L~~~plI~~~~g~~~R~~----id~~f~~~G~~p~i~~e~~~~~~i~~~V~~ 236 (316) T PRK12679 161 FPWFRWHHSLLVPLDHPLTQITPLTLESIAKWPLITYRQGITGRSR----IDDAFARKGLLADIVLSAQDSDVIKTYVAL 236 (316) T ss_pred EEEEECCEEEEECCCCCCCCCCCCCHHHHCCCCEEEECCCCHHHHH----HHHHHHHCCCCCCEEEEECCHHHHHHHHHH T ss_conf 9805534135601899512489989999879998950899849999----999999779999779999989999999998 Q ss_pred HCCEEEEEHHHHC--CCCCEEEECCCCCCCCCEEEEEECCCCCCCHHHHHHHHHHHH Q ss_conf 3842331177760--199846617766676600899934877888899999999999 Q gi|254780282|r 238 GSGIALLPDYIVK--DNPNLVRIMEDVITPSFTVYFCYPEALKNTGKLKAFRNFIFL 292 (299) Q Consensus 238 g~Gia~lp~~~~~--~~~~lv~i~~~~~~~~~~~~lv~~~~~~~~~~~~~f~d~l~~ 292 (299) |+|||++|+..+. ++++++.+.......+..+|+++++++.+++.+..|+++... T Consensus 237 GlGvailp~~a~~~~~~~~l~~~~~~~~~~~~~~~~~~~r~~~l~~~~~~Fi~~~~~ 293 (316) T PRK12679 237 GLGIGLVAEQSSGEQEEKNLIRLDTRHLFDANTVWLGLKRGQLQRNYVWRFLELCNA 293 (316) T ss_pred CCCEEECHHHHCCCCCCCCEEEECCCCCCCCCEEEEEEECCCCCHHHHHHHHHHHHC T ss_conf 990997014450754689889932634676653899996787556999999997520 No 17 >PRK09906 DNA-binding transcriptional regulator HcaR; Provisional Probab=100.00 E-value=0 Score=371.65 Aligned_cols=289 Identities=20% Similarity=0.216 Sum_probs=243.8 Q ss_pred CCHHHHHHHHHHHHHCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEECCCCEEEEECCCCCCCCCCCCCCCCCHHHH Q ss_conf 88899999999998276899998828997899999999999958821797699468500134332222222222101221 Q gi|254780282|r 3 FDWDKLRVFYVVARSGSFTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHARGLTLTEQGSKLHRVTSEVYHKLETTQI 82 (299) Q Consensus 3 md~~~L~~f~~v~~~gs~s~AA~~L~itq~avS~~i~~LE~~lg~~Lf~R~~~~~~lT~~G~~l~~~a~~~l~~~~~~~~ 82 (299) |||++|+||++|+++||||+||++|||||||||++|++||++||++||+|++||++||++|+.|+++++.++..++++.. T Consensus 1 M~l~~L~~F~~va~~gs~s~AA~~L~iSQpalS~~I~~LE~~lG~~Lf~R~~r~v~LT~aG~~l~~~a~~il~~~~~~~~ 80 (296) T PRK09906 1 MELRHLRYFVAVAEELNFTKAAEKLHTAQPSLSQQIKDLENCVGVPLLVRDKRKVALTAAGEVFLQDARLILEQAEKAKL 80 (296) T ss_pred CCHHHHHHHHHHHHHCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEECCCCCEECHHHHHHHHHHHHHHHHHHHHHH T ss_conf 95799999999998099999999988887899999999999859887998899512787089999999999999999999 Q ss_pred HCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCCCCCCCC---CCCCCCCCCCCCCCCCCCCCCCCCCCCC Q ss_conf 0012232222223332111000000000135667542000122222222---2222222222223456543211112234 Q gi|254780282|r 83 ELQESSVKPSGKLRIATTIDLGQNLLQGNLKEFLLLYPDIQIQLILDNK---DIDISMDYADCAIRLRKPIQSSSLIQRK 159 (299) Q Consensus 83 ~~~~~~~~~~g~i~I~~~~~~~~~~l~~~l~~f~~~~P~i~i~i~~~~~---~~~l~~~~~Di~i~~~~~~~~~~l~~~~ 159 (299) ....... ..|.++||++++++..++|+++.+|.+.||++++++...+. ...+..|++|++|.. .+..++++...+ T Consensus 81 ~~~~~~~-~~~~l~ig~~~~~~~~~lp~~l~~f~~~~P~v~v~l~~~~~~~~~~~l~~g~~D~~i~~-~~~~~~~l~~~~ 158 (296) T PRK09906 81 MARKIVQ-EDRQLTIGFVPSAEVNLLPKVLPMFRLRHPDTLIELVSLINTQQEEKLRRGELDVGFMR-HPVYSDEIDYLE 158 (296) T ss_pred HHHHHCC-CCCEEEEEECHHHHHHHHHHHHHHHHHHCCCCCEEEEECCCHHHHHHHHCCCCCEEEEE-CCCCCCCEEEEE T ss_conf 9986506-77138832122569999999999987408986348997580899999986997679873-688998818998 Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCCCCCCCEEEECCCCHHHHHHHHHC Q ss_conf 55543321123443211122222211000112356643321100023566520223432121145324200135678738 Q gi|254780282|r 160 LVTIHMHAYAAPHYLKNCREPLSIQELDKHNLITFGDLIPKCMEDFNWLATVDRPIGEPRISCLQVNSYLSIMQYCVLGS 239 (299) Q Consensus 160 l~~~~~~~v~~~~~~~~~~~~~~~~dL~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~v~~g~ 239 (299) +++++++++++++|+......++++||.+++||.+....... ............+..+...+++++..+++++|..|. T Consensus 159 l~~~~~~~~~~~~hpla~~~~i~~~dl~~~~~i~~~~~~~~~--~~~~~~~~~~~~g~~p~~~~~~~~~~~~~~~v~~G~ 236 (296) T PRK09906 159 LLDEPLVVVLPVDHPLAHEKEITAAQLDGVNFISPDPAQSGS--LAPIIKAWFAQHNSQPNIVQVATNILVTMNLVGMGL 236 (296) T ss_pred EECCEEEEEEECCCCCCCCCCCCHHHHCCCCEEEECCCCCCC--HHHHHHHHHHHCCCCCCEEEEECCHHHHHHHHHHCC T ss_conf 504607999828981005999899997599879636654760--999999999977999746999898999999999498 Q ss_pred CEEEEEHHHHCC-CCCEEEECCCCCCCCCEEEEEECCCCCCCHHHHHHHHHHHHHHHC Q ss_conf 423311777601-998466177666766008999348778888999999999999850 Q gi|254780282|r 240 GIALLPDYIVKD-NPNLVRIMEDVITPSFTVYFCYPEALKNTGKLKAFRNFIFLKARD 296 (299) Q Consensus 240 Gia~lp~~~~~~-~~~lv~i~~~~~~~~~~~~lv~~~~~~~~~~~~~f~d~l~~~~r~ 296 (299) ||+++|.+++.. .++++.++...+.+.+.++++|+++. .+|++++|++|+.++..+ T Consensus 237 Gi~~lP~~~~~~~~~~l~~~pl~~~~~~~~~~l~~r~~~-~spa~~~Fi~~l~e~~a~ 293 (296) T PRK09906 237 GCTIIPGYMNNFNTGQVVFRPLAGNVPSIALLMAWKKGE-MKPALRDFIAIVQERLAS 293 (296) T ss_pred EEEECHHHHHHHCCCCEEEEECCCCCCEEEEEEEECCCC-CCHHHHHHHHHHHHHHCC T ss_conf 999845877310689999998899987028999987999-999999999999998544 No 18 >TIGR03339 phn_lysR aminoethylphosphonate catabolism associated LysR family transcriptional regulator. This group of sequences represents a number of related clades with numerous examples of members adjacent to operons for the degradation of 2-aminoethylphosphonate (AEP) in Pseudomonas, Ralstonia, Bordetella and Burkholderia species. These are transcriptional regulators of the LysR family which contain a helix-turn-helix (HTH) domain (pfam00126) and a periplasmic substrate-binding protein-like domain (pfam03466). Probab=100.00 E-value=0 Score=369.77 Aligned_cols=275 Identities=24% Similarity=0.317 Sum_probs=241.7 Q ss_pred HHHHHHHHHHHCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEECCCCEEEEECCCCCCCCCCCCCCCCCHHHHHCCC Q ss_conf 99999999982768999988289978999999999999588217976994685001343322222222221012210012 Q gi|254780282|r 7 KLRVFYVVARSGSFTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHARGLTLTEQGSKLHRVTSEVYHKLETTQIELQE 86 (299) Q Consensus 7 ~L~~f~~v~~~gs~s~AA~~L~itq~avS~~i~~LE~~lg~~Lf~R~~~~~~lT~~G~~l~~~a~~~l~~~~~~~~~~~~ 86 (299) ||+||++|+++||||+||++|||||||||++|++||++||++||+|++|++.||++|+.|++++++++...+++...+++ T Consensus 1 qL~~F~~va~~gs~s~AA~~L~isQpavS~~I~~LE~~lg~~Lf~R~~r~v~lT~~G~~l~~~a~~il~~~~~~~~~~~~ 80 (279) T TIGR03339 1 QLKAFHAVARCGSFTRAAERLGLSQPTVTDQVRKLEERYGVELFHRNGRRLELTDAGHRLLPIVERLFQQEAEAEFLLRE 80 (279) T ss_pred CHHHHHHHHHHCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEECCCCEEECCCHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 97899999980999999999888889999999999998598859998982589948889999999999999999999985 Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCCCCCCCC---CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC Q ss_conf 232222223332111000000000135667542000122222222---22222222222234565432111122345554 Q gi|254780282|r 87 SSVKPSGKLRIATTIDLGQNLLQGNLKEFLLLYPDIQIQLILDNK---DIDISMDYADCAIRLRKPIQSSSLIQRKLVTI 163 (299) Q Consensus 87 ~~~~~~g~i~I~~~~~~~~~~l~~~l~~f~~~~P~i~i~i~~~~~---~~~l~~~~~Di~i~~~~~~~~~~l~~~~l~~~ 163 (299) ..+...|+++||++ +..++++.+.+|+++||++++++...+. ...|..|++|++|.. .+..++++...+++++ T Consensus 81 ~~~~~~g~l~ig~~---~~~~l~~~l~~f~~~~P~v~i~i~~~~~~~~~~~L~~~~~Di~i~~-~~~~~~~~~~~~l~~~ 156 (279) T TIGR03339 81 SGALREGSLRIAAT---APYYVLDLVARFRQRYPGIEVSVRIGNSQEVLQALQSYRVDVAVSS-EVVDDPRLDRVVLGND 156 (279) T ss_pred CCCCCCCEEEECCC---HHHHHHHHHHHHHHHCCCCCEEEEECCHHHHHHHHHCCCEEEEEEC-CCCCCCCEEEEEEECC T ss_conf 02787451686175---1778999999999858986057895580877754025965899972-7889998399994044 Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCCCCCCCEEEECCCCHHHHHHHHHCCEEE Q ss_conf 33211234432111222222110001123566433211000235665202234321211453242001356787384233 Q gi|254780282|r 164 HMHAYAAPHYLKNCREPLSIQELDKHNLITFGDLIPKCMEDFNWLATVDRPIGEPRISCLQVNSYLSIMQYCVLGSGIAL 243 (299) Q Consensus 164 ~~~~v~~~~~~~~~~~~~~~~dL~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~v~~g~Gia~ 243 (299) +++++++++|+......++++|+.++|||.++...... ..+.......+..+...+++++..+++++|.+|.|+|+ T Consensus 157 ~~~~~~~~~~~la~~~~i~~~~l~~~~~i~~~~~~~~~----~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~G~Giai 232 (279) T TIGR03339 157 PLVAVVHRQHPLAERESVTLEELAGQPLLMREPGSVTR----QTTEEALAAAGVAPRPALEIGSREAIREAVLAGLGVSV 232 (279) T ss_pred CEEEEEECCCHHHCCCCCCHHHHCCCCEEEECCCCCHH----HHHHHHHHHCCCCCCEEEEECCHHHHHHHHHHCCEEEE T ss_conf 48999918863323999999997699989828998399----99999999779987536778969999999997993897 Q ss_pred EEHHHHCCCCCEEEECCCCCCCCCEEEEEECCCCCCCHHHHHHHHH Q ss_conf 1177760199846617766676600899934877888899999999 Q gi|254780282|r 244 LPDYIVKDNPNLVRIMEDVITPSFTVYFCYPEALKNTGKLKAFRNF 289 (299) Q Consensus 244 lp~~~~~~~~~lv~i~~~~~~~~~~~~lv~~~~~~~~~~~~~f~d~ 289 (299) +|...+.++++++.++...+.+.+++|++|++++..+|++++|+|+ T Consensus 233 lP~~~v~~~~~l~~~pl~~~~~~~~~~l~~~~~r~~sp~~~aFie~ 278 (279) T TIGR03339 233 VSAAEVGRDPRLRVLPIVGAEPTMDEYLYCLKERRGARLIAAFLEL 278 (279) T ss_pred EEHHHHHHCCCEEEEECCCCCCCCEEEEEEECCCCCCHHHHHHHHH T ss_conf 1489961098989998988898627999998998689999999965 No 19 >PRK12681 cysB transcriptional regulator CysB; Reviewed Probab=100.00 E-value=0 Score=368.87 Aligned_cols=286 Identities=23% Similarity=0.250 Sum_probs=250.6 Q ss_pred CCHHHHHHHHHHHHHC-CHHHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEECCCCE-EEEECCCCCCCCCCCCCCCCCHH Q ss_conf 8889999999999827-689999882899789999999999995882179769946-85001343322222222221012 Q gi|254780282|r 3 FDWDKLRVFYVVARSG-SFTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHARGL-TLTEQGSKLHRVTSEVYHKLETT 80 (299) Q Consensus 3 md~~~L~~f~~v~~~g-s~s~AA~~L~itq~avS~~i~~LE~~lg~~Lf~R~~~~~-~lT~~G~~l~~~a~~~l~~~~~~ 80 (299) ||++||+||++|+++| |||+||++|++||||||++|++||++||++||+|+||++ .+|++|+.|++++++++..++++ T Consensus 1 M~l~QLryf~~va~~~~n~t~AA~~L~iSQPavS~qIk~LE~eLGv~LF~R~gr~l~~LT~aG~~l~~~a~~iL~~~~~i 80 (324) T PRK12681 1 MKLQQLRYIVEVVNHNLNVSATAESLYTSQPGISKQVRMLEDELGIQIFARSGKHLTQVTPAGEEIIRIAREILSKVESI 80 (324) T ss_pred CCHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEECCCCCCCCCHHHHHHHHHHHHHHHHHHHH T ss_conf 94699999999997699999999997897779999999999984996189889988860988999999999999999999 Q ss_pred HHHCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCCCCCCC--CC-CCCCCCCCCCCCCCCCCCCCCCCCC Q ss_conf 21001223222222333211100000000013566754200012222222--22-2222222222234565432111122 Q gi|254780282|r 81 QIELQESSVKPSGKLRIATTIDLGQNLLQGNLKEFLLLYPDIQIQLILDN--KD-IDISMDYADCAIRLRKPIQSSSLIQ 157 (299) Q Consensus 81 ~~~~~~~~~~~~g~i~I~~~~~~~~~~l~~~l~~f~~~~P~i~i~i~~~~--~~-~~l~~~~~Di~i~~~~~~~~~~l~~ 157 (299) ...+++......|+|+||++++++.+++|+.+.+|+++||+|++++...+ .. ..+..|++|+||........+++.. T Consensus 81 ~~~~~~~~~~~~G~L~Ia~~~t~a~~~LP~~i~~F~~~~P~v~l~l~~~~~~~i~~~l~~g~~DlaI~~e~~~~~~dl~~ 160 (324) T PRK12681 81 KSVAGEHTWPDKGSLYIATTHTQARYALPPVIKGFIKRYPRVSLHMHQGSPTQIAEAAAKGEADFAIATEALHLYDDLIM 160 (324) T ss_pred HHHHHHHCCCCCCEEEEEECHHHHHHHHHHHHHHHHHHCCCCCEEEEECCHHHHHHHHHCCCCCCCCCCCCCCCCCCCEE T ss_conf 99999752887634999853588887725999999987899844653178799999998799872312466666887468 Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCCCCCCCEEEECCCCHHHHHHHH Q ss_conf 34555433211234432111222222110001123566433211000235665202234321211453242001356787 Q gi|254780282|r 158 RKLVTIHMHAYAAPHYLKNCREPLSIQELDKHNLITFGDLIPKCMEDFNWLATVDRPIGEPRISCLQVNSYLSIMQYCVL 237 (299) Q Consensus 158 ~~l~~~~~~~v~~~~~~~~~~~~~~~~dL~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~v~~ 237 (299) .++++++.+++++++|+......++++||.++|+|.+..+.... ..........+..+..++++++.++++.+|.. T Consensus 161 ~P~~~~~~~vvvp~~HPLa~~~~itl~dL~~~plI~~~~g~~~R----~~id~~f~~~g~~P~iv~e~~~~~~I~~~V~~ 236 (324) T PRK12681 161 LPCYHWNRSVVVPPDHPLAKKKKLTIEELAQYPLVTYVFGFTGR----SELDTAFNRAGLTPRIVFTATDADVIKTYVRL 236 (324) T ss_pred EEEEECCCCCCCCCCCCCCCCCCCCHHHHCCCCEEEECCCCCHH----HHHHHHHHHCCCCCEEEEEECCHHHHHHHHHH T ss_conf 64000322245799996557999999998699859614998299----99999999889976079998989999999995 Q ss_pred HCCEEEEEHHHHCC--CCCEEEECCCCCCCCCEEEEEECCCCCCCHHHHHHHHHHHH Q ss_conf 38423311777601--99846617766676600899934877888899999999999 Q gi|254780282|r 238 GSGIALLPDYIVKD--NPNLVRIMEDVITPSFTVYFCYPEALKNTGKLKAFRNFIFL 292 (299) Q Consensus 238 g~Gia~lp~~~~~~--~~~lv~i~~~~~~~~~~~~lv~~~~~~~~~~~~~f~d~l~~ 292 (299) |+||+++|...+.. +.+|+.+.....-.....|++|+++..+++.+..|++.+.. T Consensus 237 GlGV~ilp~mA~~~~~d~~l~~~~~~~~f~~~~t~i~~r~g~~l~~~~~~Fi~~~~p 293 (324) T PRK12681 237 GLGVGVIASMAVDPVADPDLVAIDASHLFAHSTTKIGFRRGTFLRSYMYDFIERFAP 293 (324) T ss_pred CCEEEECHHHHCCCCCCCCEEEEECCCCCCCCEEEEEEECCCCHHHHHHHHHHHHHC T ss_conf 991397035551965578817843655677764799997997157999999998612 No 20 >PRK11074 putative DNA-binding transcriptional regulator; Provisional Probab=100.00 E-value=0 Score=367.89 Aligned_cols=286 Identities=21% Similarity=0.236 Sum_probs=241.4 Q ss_pred CCHHHHHHHHHHHHHCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEECCCCEEEEECCCCCCCCCCCCCCCCCHHHH Q ss_conf 88899999999998276899998828997899999999999958821797699468500134332222222222101221 Q gi|254780282|r 3 FDWDKLRVFYVVARSGSFTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHARGLTLTEQGSKLHRVTSEVYHKLETTQI 82 (299) Q Consensus 3 md~~~L~~f~~v~~~gs~s~AA~~L~itq~avS~~i~~LE~~lg~~Lf~R~~~~~~lT~~G~~l~~~a~~~l~~~~~~~~ 82 (299) .+|++|++|++|+++||||+||++||+||||||++|++||++||++||+|++|+++||++|+.|+++++.++.+++++.. T Consensus 2 ~~~~~L~~F~aVa~~gSft~AA~~L~isqsaVS~~I~~LE~~LG~~Lf~R~~r~v~LT~aG~~ll~~a~~il~~~~~~~~ 81 (300) T PRK11074 2 WSEYSLEVVDAVARNGSFSAAAQELHKVPSAVSYTVRQLEEWLAVPLFERRHRDVELTPAGEWFLKEARSVLKKMEETRR 81 (300) T ss_pred CCHHHHHHHHHHHHCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEECCCCEEECHHHHHHHHHHHHHHHHHHHHHH T ss_conf 98899999999997099999999978887899999999999959963998799669996289999999999999999999 Q ss_pred HCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCCCCCC--CC-CCCCCCCCCCCCCCCCCCC-CCCCCCCC Q ss_conf 00122322222233321110000000001356675420001222222--22-2222222222223456543-21111223 Q gi|254780282|r 83 ELQESSVKPSGKLRIATTIDLGQNLLQGNLKEFLLLYPDIQIQLILD--NK-DIDISMDYADCAIRLRKPI-QSSSLIQR 158 (299) Q Consensus 83 ~~~~~~~~~~g~i~I~~~~~~~~~~l~~~l~~f~~~~P~i~i~i~~~--~~-~~~l~~~~~Di~i~~~~~~-~~~~l~~~ 158 (299) .+.....+.+|+++|+++.+++..++++.+.+|.++||+|++++... +. ...+.+|++|++|...... ..+++..+ T Consensus 82 ~~~~~~~~~~G~lri~~~~~~~~~~l~~~l~~f~~~~P~v~l~l~~~~~~~~~~~l~~g~~Dlai~~~~~~p~~~~~~~~ 161 (300) T PRK11074 82 QTQRVANGWRGQLSIALDNIVRPDRTRQLIADFYRHFDDVELIIRQEVFNGVWDALADGRADIAIGATRAIPVGGRFAFR 161 (300) T ss_pred HHHHHHCCCCCEEEEEECCHHHHHHHHHHHHHHHHHCCCCEEEEEECCCHHHHHHHHCCCCCEEEECCCCCCCCCCEEEE T ss_conf 99976269842599986533578999999999999886957999976636799999769977899437677888865788 Q ss_pred CCCCCCCCCCCCCCCCCC-CCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCCCCCCCEEEECCCCHHHHHHHH Q ss_conf 455543321123443211-1222222110001123566433211000235665202234321211453242001356787 Q gi|254780282|r 159 KLVTIHMHAYAAPHYLKN-CREPLSIQELDKHNLITFGDLIPKCMEDFNWLATVDRPIGEPRISCLQVNSYLSIMQYCVL 237 (299) Q Consensus 159 ~l~~~~~~~v~~~~~~~~-~~~~~~~~dL~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~v~~ 237 (299) +++..++++|++++|+.. .+.+.+.++|.++|+|.+.+..........|... ....+.+++.++++++|.+ T Consensus 162 ~l~~~~~~~v~~~~hpLa~~~~~l~~~~l~~~p~i~~~~~~~~~~~~~~~~~~--------~~~~~~~~~~~~~~~~v~~ 233 (300) T PRK11074 162 DMGMLSWAFVVSSDHPLALMDGPLSDDELRPYPSICLEDTSRTLPKRITWLLD--------NQRRLVVPDWESAINCLSA 233 (300) T ss_pred ECCCCEEEEEECCCCHHHCCCCCCCHHHHHHCCEEEECCCCCCCCCCCEEEEC--------CCCEEEECCHHHHHHHHHH T ss_conf 81442056674589755408998999999619778862662223210003545--------7647998989999999996 Q ss_pred HCCEEEEEHHHHC---CCCCEEEECCCCCCCCCEEEEEECCCCCCCHHHHHHHHHHHHHHHCC Q ss_conf 3842331177760---19984661776667660089993487788889999999999998506 Q gi|254780282|r 238 GSGIALLPDYIVK---DNPNLVRIMEDVITPSFTVYFCYPEALKNTGKLKAFRNFIFLKARDW 297 (299) Q Consensus 238 g~Gia~lp~~~~~---~~~~lv~i~~~~~~~~~~~~lv~~~~~~~~~~~~~f~d~l~~~~r~~ 297 (299) |+||+++|.++++ ++|+|+.+..+.+.+..+++++|+++. .+|++++|+|||.+..+.| T Consensus 234 GlGia~lP~~~~~~~l~~G~Lv~l~~~~~~~~~~~~lv~~~~~-~sPa~r~fld~L~d~~~~~ 295 (300) T PRK11074 234 GLGVGMVPTHFAKPLIESGKLVEKTLENPKPDSPCCLTWNQND-MSPALAWLLDYLGDSETLN 295 (300) T ss_pred CCEEEHHHHHHHHHHHHCCCEEEECCCCCCCCEEEEEEECCCC-CCHHHHHHHHHHHCCHHHH T ss_conf 9968940699999996089999982788888538999988999-9989999999983710022 No 21 >PRK10341 DNA-binding transcriptional activator TdcA; Provisional Probab=100.00 E-value=0 Score=365.67 Aligned_cols=286 Identities=16% Similarity=0.186 Sum_probs=246.4 Q ss_pred CHHHHHHHHHHHHHCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEECCCCEEEEECCCCCCCCCCCCCCCCCHHHHH Q ss_conf 88999999999982768999988289978999999999999588217976994685001343322222222221012210 Q gi|254780282|r 4 DWDKLRVFYVVARSGSFTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHARGLTLTEQGSKLHRVTSEVYHKLETTQIE 83 (299) Q Consensus 4 d~~~L~~f~~v~~~gs~s~AA~~L~itq~avS~~i~~LE~~lg~~Lf~R~~~~~~lT~~G~~l~~~a~~~l~~~~~~~~~ 83 (299) +++||+||++|+++||||+||++||+||||||++|++||++||++||+|++||+.||++|+.|+++++.++++++++.+. T Consensus 8 ~~rqL~~F~aVa~~gS~t~AA~~L~iSQpavS~~I~~LE~eLG~~LF~R~~r~v~LT~~G~~l~~~a~~il~~~~~~~~~ 87 (312) T PRK10341 8 KTQHLVVFQEVIRSGSIGSAAKELGLTQPAVSKIINDIEDYFGVELIVRKNTGVTLTPAGQVLLSRSESITREMKNMVNE 87 (312) T ss_pred CHHHHHHHHHHHHCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEECCCCCEECHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 67799999999981999999999888878999999999998498528988998616788999999999999999999999 Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCCCCCCC--C-CCCCCCCCCCCCCCC-CCCCCCCCCCCCC Q ss_conf 01223222222333211100000000013566754200012222222--2-222222222222345-6543211112234 Q gi|254780282|r 84 LQESSVKPSGKLRIATTIDLGQNLLQGNLKEFLLLYPDIQIQLILDN--K-DIDISMDYADCAIRL-RKPIQSSSLIQRK 159 (299) Q Consensus 84 ~~~~~~~~~g~i~I~~~~~~~~~~l~~~l~~f~~~~P~i~i~i~~~~--~-~~~l~~~~~Di~i~~-~~~~~~~~l~~~~ 159 (299) +........|+++||++++++..++|+.+.+|.+.||++++++...+ . ...+.+|++|++|.. ..+...+++...+ T Consensus 88 ~~~~~~~~~~~l~ig~~~~~~~~~lp~~l~~f~~~~P~v~i~l~~~~~~~~~~~l~~g~~D~~i~~~~~~~~~~~~~~~~ 167 (312) T PRK10341 88 INGMSSEAVVDVSFGFPSLIGFTFMSDMINKFKEVFPKAQVSMYEAQLSSFLPAIRDGRLDFAIGTLSNEMKLQDLHVEP 167 (312) T ss_pred HHHHCCCCCEEEECCCCHHHHHHHHHHHHHHHHHHCCCCEEEEEECCHHHHHHHHHCCCCEEEEEECCCCCCCCCEEEEE T ss_conf 98722687325743540688999999999999998889779999899999999996698619997436877778749999 Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCCCCCCCEEEECCCCHHHHHHHHHC Q ss_conf 55543321123443211122222211000112356643321100023566520223432121145324200135678738 Q gi|254780282|r 160 LVTIHMHAYAAPHYLKNCREPLSIQELDKHNLITFGDLIPKCMEDFNWLATVDRPIGEPRISCLQVNSYLSIMQYCVLGS 239 (299) Q Consensus 160 l~~~~~~~v~~~~~~~~~~~~~~~~dL~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~v~~g~ 239 (299) +++++++++++++|+... +.+++||.+++||.+............++ ...+......+++++..+++++|.+|. T Consensus 168 l~~~~~~lv~~~~~p~~~--~~~l~~L~~~~~il~~~~~~~~~~~~~~~----~~~g~~~~~~~~~~s~~~i~~lv~~g~ 241 (312) T PRK10341 168 LFESEFVLVASKSRTCTG--TTTLESLKNEQWVLPQTNMGYYSELLTTL----QRNGISIENIVKTDSVVTIYNLVLNAD 241 (312) T ss_pred EECCCEEEEECCCCCCCC--CCCHHHHCCCCEEEECCCCCHHHHHHHHH----HHCCCCCCCEEEECHHHHHHHHHHHCC T ss_conf 512428999767542348--97989980798686069985899999999----976999881699890999999999799 Q ss_pred CEEEEEHHHHCC--CCCEEEECCCCCCCCCEEEEEECCCCCCCHHHHHHHHHHHHHHH Q ss_conf 423311777601--99846617766676600899934877888899999999999985 Q gi|254780282|r 240 GIALLPDYIVKD--NPNLVRIMEDVITPSFTVYFCYPEALKNTGKLKAFRNFIFLKAR 295 (299) Q Consensus 240 Gia~lp~~~~~~--~~~lv~i~~~~~~~~~~~~lv~~~~~~~~~~~~~f~d~l~~~~r 295 (299) |++++|.+++.+ +++++.++...+.+.+.++++|++++.++|++++|+|++.+.+. T Consensus 242 gi~~lP~~~~~~~~~~~L~~lpl~~~~~~~~~~lv~~k~~~ls~a~~~fie~~ke~~s 299 (312) T PRK10341 242 FLTVIPCDMTSPFGSNQFITIPIKETLPVARYAAVWSKNYRIKKAASVLVELAKEYSS 299 (312) T ss_pred EEEEEHHHHHHHHCCCCEEEEECCCCCCEEEEEEEEECCCCCCHHHHHHHHHHHHHCC T ss_conf 5897269999663189899998999885118999998939889999999999998706 No 22 >TIGR03298 argP transcriptional regulator, ArgP family. ArgP used to be known as IciA. ArgP is a positive regulator of argK. It is a negative autoregulator in presence of arginine. It competes with DnaA for oriC iteron (13-mer) binding. It activates dnaA and nrd transcription. It has been demonstrated to be part of the pho regulon (PMID:10589831). ArgP mutants convey canavanine (an L-arginine structural homolog) sensitivity (PMID: 15150242). Probab=100.00 E-value=0 Score=358.93 Aligned_cols=284 Identities=19% Similarity=0.206 Sum_probs=237.1 Q ss_pred CCHHHHHHHHHHHHHCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEECCCCEEEEECCCCCCCCCCCCCCCCCHHHH Q ss_conf 88899999999998276899998828997899999999999958821797699468500134332222222222101221 Q gi|254780282|r 3 FDWDKLRVFYVVARSGSFTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHARGLTLTEQGSKLHRVTSEVYHKLETTQI 82 (299) Q Consensus 3 md~~~L~~f~~v~~~gs~s~AA~~L~itq~avS~~i~~LE~~lg~~Lf~R~~~~~~lT~~G~~l~~~a~~~l~~~~~~~~ 82 (299) |||++|++|++|+++||||+||++||+||||||++|++||++||++||+| +|++.||++|+.|++++++++...+++.. T Consensus 1 mdl~~L~~F~aVa~~gSfs~AA~~L~~sqsaVS~~I~~LE~~LG~~Lf~R-tr~v~LT~aG~~l~~~a~~i~~~~~~~~~ 79 (292) T TIGR03298 1 LDYKQLAALAAVVEEGSFERAAAALSVTPSAVSQRIKALEERLGQPLLVR-TQPCRATEAGQRLLRHARQVRLLEAELLA 79 (292) T ss_pred CCHHHHHHHHHHHHHCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCHHEEC-CCCCEECHHHHHHHHHHHHHHHHHHHHHH T ss_conf 98899999999998199999999978887899999999999829623188-99980488999999999999999999999 Q ss_pred HCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCCCCCCC--CCCC-CCCCCCCCCCCCCCCCCCCCCCCCC Q ss_conf 001223222222333211100000000013566754200012222222--2222-2222222223456543211112234 Q gi|254780282|r 83 ELQESSVKPSGKLRIATTIDLGQNLLQGNLKEFLLLYPDIQIQLILDN--KDID-ISMDYADCAIRLRKPIQSSSLIQRK 159 (299) Q Consensus 83 ~~~~~~~~~~g~i~I~~~~~~~~~~l~~~l~~f~~~~P~i~i~i~~~~--~~~~-l~~~~~Di~i~~~~~~~~~~l~~~~ 159 (299) .+........|+++|++++.....|+.|.+..|.+.+ ++.+++..++ ...+ +..|.+|++|.... .+.+++..++ T Consensus 80 ~~~~~~~~~~g~l~i~~~~~~~~~~l~p~l~~f~~~~-~v~l~l~~~~~~~~~d~l~~g~~~~ai~~~~-~~~~~~~~~~ 157 (292) T TIGR03298 80 ELPGLAPGAPVTLSIAVNADSLATWFLPALAPVLAQE-GVLLDLVVEDQDHTAELLRSGEVLGAVTTQA-KPVQGCRVVP 157 (292) T ss_pred HHHCCCCCCCEEEEEEECHHHHHHHHHHHHHHHHHCC-CCEEEEEECCCHHHHHHHHCCCEEEEEECCC-CCCCCCEEEE T ss_conf 8752477774258887635778887899999999808-9879998545245899985697589997578-8898867999 Q ss_pred CCCCCCCCCCCCCCCCCC-CCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCCCCCCCEEEECCCCHHHHHHHHH Q ss_conf 555433211234432111-2222221100011235664332110002356652022343212114532420013567873 Q gi|254780282|r 160 LVTIHMHAYAAPHYLKNC-REPLSIQELDKHNLITFGDLIPKCMEDFNWLATVDRPIGEPRISCLQVNSYLSIMQYCVLG 238 (299) Q Consensus 160 l~~~~~~~v~~~~~~~~~-~~~~~~~dL~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~v~~g 238 (299) |+++++++|++|+|+.++ +.+.++++|.++|++.+....... ..+........... +...++|.++++++|.+| T Consensus 158 L~~~~~~~vasP~~~~~~~~~~~~~~~L~~~p~l~~~~~~~~~---~~~~~~~~~~~~~~--~~~~v~s~~~~~~~v~aG 232 (292) T TIGR03298 158 LGAMRYLAVASPAFAARYFPDGVTAEALARAPVIVFNRKDDLQ---DRFLRRLFGLPVSP--PRHYVPSSEGFVEAARAG 232 (292) T ss_pred CCCEEEEEEECHHHHHHCCCCCCCHHHHHCCCEEEECCCCCHH---HHHHHHCCCCCCCC--CEEEECCHHHHHHHHHHC T ss_conf 1140189998889998628999999999369879965996478---99998505777665--168988899999999949 Q ss_pred CCEEEEEHHHHCC---CCCEEEECCCCCCCCCEEEEEECCCCCCCHHHHHHHHHHHHHHHCC Q ss_conf 8423311777601---9984661776667660089993487788889999999999998506 Q gi|254780282|r 239 SGIALLPDYIVKD---NPNLVRIMEDVITPSFTVYFCYPEALKNTGKLKAFRNFIFLKARDW 297 (299) Q Consensus 239 ~Gia~lp~~~~~~---~~~lv~i~~~~~~~~~~~~lv~~~~~~~~~~~~~f~d~l~~~~r~~ 297 (299) +||+++|.+++++ +|+||+++|+++ .++.++|++++..||++++|+||+.+.+|.| T Consensus 233 lGia~lP~~~v~~~l~~G~LV~llp~~~---~~~~l~~~~~r~~s~~~r~f~d~l~~~ar~~ 291 (292) T TIGR03298 233 LGWGMVPELQAEPHLAAGRLVDLAPGRA---LDVPLYWHHWRLESRVLERLTDAVVAAARRA 291 (292) T ss_pred CEEEECCHHHHHHHHHCCCEEEECCCCC---CCCCEECCCCCCCCHHHHHHHHHHHHHHHHH T ss_conf 9889696999999985898588499987---9821648066867889999999999999864 No 23 >PRK12680 transcriptional regulator CysB-like protein; Reviewed Probab=100.00 E-value=0 Score=354.08 Aligned_cols=284 Identities=18% Similarity=0.205 Sum_probs=244.4 Q ss_pred CCHHHHHHHHHHHHHC-CHHHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEECCCCEE-EEECCCCCCCCCCCCCCCCCHH Q ss_conf 8889999999999827-6899998828997899999999999958821797699468-5001343322222222221012 Q gi|254780282|r 3 FDWDKLRVFYVVARSG-SFTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHARGLT-LTEQGSKLHRVTSEVYHKLETT 80 (299) Q Consensus 3 md~~~L~~f~~v~~~g-s~s~AA~~L~itq~avS~~i~~LE~~lg~~Lf~R~~~~~~-lT~~G~~l~~~a~~~l~~~~~~ 80 (299) ||++||+||++|++++ |||+||++||+|||+||++|++||++||++||+|+||++. ||++|+.++++++.++..++++ T Consensus 1 M~L~QLr~f~aVa~~~~n~s~AA~~L~iSQPaVSkqIk~LE~eLGv~LF~R~gr~l~~LT~aG~~ll~~a~~iL~~~~~i 80 (327) T PRK12680 1 MTLTQLRYLVAIADAELNITLAAARVHATQPGLSKQLKQLEDELGFLLFVRKGRSLDSVTPAGVEVIERARAVLSEVNNI 80 (327) T ss_pred CCHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEECCCCCCCCCHHHHHHHHHHHHHHHHHHHH T ss_conf 92899999999996589999999997897679999999999985996699879987767786999999999999999999 Q ss_pred HHHCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCCCCCCC--CC-CCCCCCCCCCCCCCCCCCCCCCCCC Q ss_conf 21001223222222333211100000000013566754200012222222--22-2222222222234565432111122 Q gi|254780282|r 81 QIELQESSVKPSGKLRIATTIDLGQNLLQGNLKEFLLLYPDIQIQLILDN--KD-IDISMDYADCAIRLRKPIQSSSLIQ 157 (299) Q Consensus 81 ~~~~~~~~~~~~g~i~I~~~~~~~~~~l~~~l~~f~~~~P~i~i~i~~~~--~~-~~l~~~~~Di~i~~~~~~~~~~l~~ 157 (299) .....+.....+|+++||++++.+.+++|+++.+|+++||+|++++...+ .. ..+.+|++|+||.......++++.. T Consensus 81 ~~~~~~~~~~~~G~L~Ig~~~t~a~~~LP~vi~~f~~~yP~V~l~l~~~~~~~l~e~l~~g~~Diai~~~~~~~~~~~~~ 160 (327) T PRK12680 81 RTYAANQRRESQGQLTLTTTHTQARFVLPPAVAQIKQAYPQVSVHLQQAAESAALDLLGQGDADIAVVSTAGGEPSAGIA 160 (327) T ss_pred HHHHHHHCCCCCEEEEEEEECHHHHHHHHHHHHHHHHHCCCCEEEEEECCCHHHHHHHHCCCCCEEEECCCCCCCCCCEE T ss_conf 99998625887337999984227777568999999986899679999898288999997899409994477779976547 Q ss_pred CCCCCCCCCCCCCCCCCC-CCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCCCCCCCEEEECCCCHHHHHHH Q ss_conf 345554332112344321-1122222211000112356643321100023566520223432121145324200135678 Q gi|254780282|r 158 RKLVTIHMHAYAAPHYLK-NCREPLSIQELDKHNLITFGDLIPKCMEDFNWLATVDRPIGEPRISCLQVNSYLSIMQYCV 236 (299) Q Consensus 158 ~~l~~~~~~~v~~~~~~~-~~~~~~~~~dL~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~v~ 236 (299) .+++.++.+++++++|+. ..+.+++++||.++|||.+..+..... .+.......+..+..++++++.++++.+|+ T Consensus 161 ~pl~~~~~~vvvP~~HpL~~~~~~i~L~~La~~plI~~~~g~~~r~----~id~af~~~Gl~P~iv~ea~~~d~Ik~~V~ 236 (327) T PRK12680 161 VPLYRWRRLVVVPRGHALDTPRTAPDMAALAEHPLISYDSSTRPGS----SLQRAFAQVGLEPSIALTALDADLIKTYVR 236 (327) T ss_pred EEEEECCEEEEEECCCCCCCCCCCCCHHHHHCCCEEECCCCCCHHH----HHHHHHHHCCCCCCEEEEECCHHHHHHHHH T ss_conf 6752235799997898100589999999980898896389986799----999999977997647999995999999999 Q ss_pred HHCCEEEEEHHHHCC-CCCEEEECCCCCCCCCEEEEEECCCCCCCHHHHHHHHHH Q ss_conf 738423311777601-998466177666766008999348778888999999999 Q gi|254780282|r 237 LGSGIALLPDYIVKD-NPNLVRIMEDVITPSFTVYFCYPEALKNTGKLKAFRNFI 290 (299) Q Consensus 237 ~g~Gia~lp~~~~~~-~~~lv~i~~~~~~~~~~~~lv~~~~~~~~~~~~~f~d~l 290 (299) .|+|||++|+..++. +.+|+.+.....-.....|++++++..+..-+=.|++.. T Consensus 237 ~GlGV~Ivp~mA~~~~d~~l~~~~~~~l~~~~~~~~~~~~~~~lr~~~~~fi~~~ 291 (327) T PRK12680 237 AGLGVGLVAEMAVNAFDEDLRAWPAPAPIAECIAWAVLPRDRVLRDYALDLVHVL 291 (327) T ss_pred HCCEEEECHHHHHCCCCCCEEEEECCCCCCCCEEEEEEECCCHHHHHHHHHHHHH T ss_conf 4986188164762876898389406457775605999978846899999999986 No 24 >PRK10094 DNA-binding transcriptional activator AllS; Provisional Probab=100.00 E-value=0 Score=350.68 Aligned_cols=282 Identities=22% Similarity=0.276 Sum_probs=232.5 Q ss_pred CCHHHHHHHHHHHHHCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEECCCCEEEEECCCCCCCCCCCCCCCCCHHHH Q ss_conf 88899999999998276899998828997899999999999958821797699468500134332222222222101221 Q gi|254780282|r 3 FDWDKLRVFYVVARSGSFTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHARGLTLTEQGSKLHRVTSEVYHKLETTQI 82 (299) Q Consensus 3 md~~~L~~f~~v~~~gs~s~AA~~L~itq~avS~~i~~LE~~lg~~Lf~R~~~~~~lT~~G~~l~~~a~~~l~~~~~~~~ 82 (299) ||+++|++|++|+++||||+||++||+||||||++|++||++||++||+|++|++.||++|+.|+++|+.++..++++.. T Consensus 2 mDl~~Lr~F~aVae~gSfs~AA~~L~isqsavS~~I~~LE~~LGv~Lf~Rt~R~v~LT~aG~~l~~~a~~il~~~~~~~~ 81 (308) T PRK10094 2 FDPETLRTFIAVAETGSFSKAAERLCKTTATISYRIKLLEENTGVALFFRTTRSVTLTAAGEHLLSQARDWLSWLESMPS 81 (308) T ss_pred CCHHHHHHHHHHHHCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEECCCCCCCCHHHHHHHHHHHHHHHHHHHHHH T ss_conf 89899999999998199999999978987899999999999969963997799743988999999999999999999999 Q ss_pred HCCCCCCCCCCCCCCCCCCCC-CCCCCCCHHHHHHHHHHCCCCCCCCCC---CCCCCCCCCCCCCCCCC-CCCCCCCCCC Q ss_conf 001223222222333211100-000000013566754200012222222---22222222222223456-5432111122 Q gi|254780282|r 83 ELQESSVKPSGKLRIATTIDL-GQNLLQGNLKEFLLLYPDIQIQLILDN---KDIDISMDYADCAIRLR-KPIQSSSLIQ 157 (299) Q Consensus 83 ~~~~~~~~~~g~i~I~~~~~~-~~~~l~~~l~~f~~~~P~i~i~i~~~~---~~~~l~~~~~Di~i~~~-~~~~~~~l~~ 157 (299) .+++...+..|+++|++++.+ ...++++++..|+++||++++++.... ...++..+++|++|.+. .+...+++.. T Consensus 82 ~l~~~~~~~~g~l~i~~~~~~~~~~~l~~ll~~~~~~~P~v~i~i~~~~~~~~~~~l~~~~~dl~i~~~~~~~~~~~~~~ 161 (308) T PRK10094 82 ELQQVNDGVERQVNIVINNLLYNPQAVASLLAWLNERYPFTQFHISRQIYMGVWDSLLYEGFSLAIGVTGTEALANTFSL 161 (308) T ss_pred HHHHHHCCCCCEEEEEECCHHHHHHHHHHHHHHHHHHCCCCEEEEEECCCCCHHHHHHCCCCCEEEEECCCCCCCCCEEE T ss_conf 99864158754499995220111667999999999978998899996023347999974997299993688778887699 Q ss_pred CCCCCCCCCCCCCCCCCCC-CCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCCCCCCCEEEECCCCHHHHHHH Q ss_conf 3455543321123443211-122222211000112356643321100023566520223432121145324200135678 Q gi|254780282|r 158 RKLVTIHMHAYAAPHYLKN-CREPLSIQELDKHNLITFGDLIPKCMEDFNWLATVDRPIGEPRISCLQVNSYLSIMQYCV 236 (299) Q Consensus 158 ~~l~~~~~~~v~~~~~~~~-~~~~~~~~dL~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~v~ 236 (299) .+++++++++||+++|+.. .+.+.+.+++..++++.+............| .. .....+.+++.++++.+|. T Consensus 162 ~~l~~~~~~~v~~~~hpla~~~~~~~~~~l~~~~~i~~~~~~~~~~~~~~~-----~~---~~~~~~~~~~~~~~~~~v~ 233 (308) T PRK10094 162 DPLGSVQWRFVMAADHPLANVEEPLTEAQLRRFPAVNIEDSARTLTKRVAW-----RL---PGQKEIIVPDMETKIAAHL 233 (308) T ss_pred EECCCCHHHHHHCCCCHHHCCCCCCCHHHHHHCCEEEECCCCCCHHHHHEE-----EE---CCCCEEEECCHHHHHHHHH T ss_conf 993130233210789844528999999999619656730651100020125-----50---7875499898999999999 Q ss_pred HHCCEEEEEHHHHCC---CCCEEEECCCCCCCCCEEEEEECCCCCCCHHHHHHHHHHHHH Q ss_conf 738423311777601---998466177666766008999348778888999999999999 Q gi|254780282|r 237 LGSGIALLPDYIVKD---NPNLVRIMEDVITPSFTVYFCYPEALKNTGKLKAFRNFIFLK 293 (299) Q Consensus 237 ~g~Gia~lp~~~~~~---~~~lv~i~~~~~~~~~~~~lv~~~~~~~~~~~~~f~d~l~~~ 293 (299) +|+|||++|.+++++ +|+||.+..+...++++++++|+++. .+|+++.|+|++.+. T Consensus 234 aGlGia~lP~~~v~~~l~~G~LV~~~l~~~~~~~~l~l~wr~~~-~~~~v~~~i~l~~~~ 292 (308) T PRK10094 234 AGVGIGFLPKSLCQSMIDNQQLVSRVIPTMRPPSPLSLAWRKFG-SGKAVEDIVTLFTQR 292 (308) T ss_pred HCCEEECCHHHHHHHHHHCCCEEEEECCCCCCCEEEEEEEECCC-CCHHHHHHHHHHHHC T ss_conf 79988923499999998789889996899999808999997799-987999999999871 No 25 >PRK13348 chromosome replication initiation inhibitor protein; Provisional Probab=100.00 E-value=0 Score=344.27 Aligned_cols=284 Identities=19% Similarity=0.213 Sum_probs=228.5 Q ss_pred CCHHHHHHHHHHHHHCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEECCCCEEEEECCCCCCCCCCCCCCCCCHHHH Q ss_conf 88899999999998276899998828997899999999999958821797699468500134332222222222101221 Q gi|254780282|r 3 FDWDKLRVFYVVARSGSFTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHARGLTLTEQGSKLHRVTSEVYHKLETTQI 82 (299) Q Consensus 3 md~~~L~~f~~v~~~gs~s~AA~~L~itq~avS~~i~~LE~~lg~~Lf~R~~~~~~lT~~G~~l~~~a~~~l~~~~~~~~ 82 (299) |||++|++|++|+++||||+||++||+||||||++|++||+++|++||+| +|++.||++|+.|+++++.+....+++.+ T Consensus 2 md~~~L~~F~aVa~~Gsfs~AA~~L~~sqsavS~~I~~LE~~LG~~Lf~R-tR~~~LT~aG~~l~~~a~~i~~~~~~~~~ 80 (294) T PRK13348 2 LDYKQLEALAAVVETGSFERAARRLHVTRSAVSQRIKALEESLGQPLLVR-TRPCRPTPAGQRLLRHLRQVALLEADLLS 80 (294) T ss_pred CCHHHHHHHHHHHHCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEC-CCCCEECHHHHHHHHHHHHHHHHHHHHHH T ss_conf 89899999999998099999999978887899999999999839843888-99973558999999999999999999998 Q ss_pred HCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCCCCCCCC--C-CCCCCCCCCCCCCCCCCCCCCCCCCCC Q ss_conf 0012232222223332111000000000135667542000122222222--2-222222222223456543211112234 Q gi|254780282|r 83 ELQESSVKPSGKLRIATTIDLGQNLLQGNLKEFLLLYPDIQIQLILDNK--D-IDISMDYADCAIRLRKPIQSSSLIQRK 159 (299) Q Consensus 83 ~~~~~~~~~~g~i~I~~~~~~~~~~l~~~l~~f~~~~P~i~i~i~~~~~--~-~~l~~~~~Di~i~~~~~~~~~~l~~~~ 159 (299) .+... ....+.++++++......++.+.+..|.++ |++.+++..++. . ..+.+|.+|++|... +...+++..++ T Consensus 81 ~~~~~-~~~~~~l~i~~~~~~~~~~l~p~l~~~~~~-p~~~l~l~~~~~~~~~~~l~~g~~d~ai~~~-~~~~~~~~~~~ 157 (294) T PRK13348 81 TLPAE-RGSPITLAIAVNADSLATWFLPALASVLAG-ERILLELIVDDQDHTFALLERGEVVGCVSTQ-SKPMRGCLAEP 157 (294) T ss_pred HHHHC-CCCCCEEEEEECHHHHHHHHHHHHHHHHHC-CCCEEEEEECCCHHHHHHHHCCCCEEEEECC-CCCCCCCEEEE T ss_conf 76533-678603899975678898779999999856-7977888734513689999749412445337-88888856898 Q ss_pred CCCCCCCCCCCCCCCCCC-CCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCCCCCCCEEEECCCCHHHHHHHHH Q ss_conf 555433211234432111-2222221100011235664332110002356652022343212114532420013567873 Q gi|254780282|r 160 LVTIHMHAYAAPHYLKNC-REPLSIQELDKHNLITFGDLIPKCMEDFNWLATVDRPIGEPRISCLQVNSYLSIMQYCVLG 238 (299) Q Consensus 160 l~~~~~~~v~~~~~~~~~-~~~~~~~dL~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~v~~g 238 (299) ++..++++|++|+|...+ ..+.+++++...|++.+........ .+.... ........+...++|.++++++|.+| T Consensus 158 l~~~~~~~vasp~~~~~~~~~~~~~~~l~~~p~~~~~~~~~~~~---~~~~~~-~~~~~~~~~~~~~~s~~~~~~~v~~G 233 (294) T PRK13348 158 LGTMRYRCVAAPAFAARYFPQGLTRHSALKAPAVAFNRKDTLQS---SFLQRL-FGLPVGAYPRHYVPSTHAHLAAIRHG 233 (294) T ss_pred CCCEEEEEEECHHHHHHCCCCCCCHHHHHCCCEEEECCCCCHHH---HHHHHC-CCCCCCCCCEEEECCHHHHHHHHHHC T ss_conf 22515999987789986078999988982598899659971668---999864-68876766468989799999999979 Q ss_pred CCEEEEEHHHHCC---CCCEEEECCCCCCCCCEEEEEECCCCCCCHHHHHHHHHHHHHHHCC Q ss_conf 8423311777601---9984661776667660089993487788889999999999998506 Q gi|254780282|r 239 SGIALLPDYIVKD---NPNLVRIMEDVITPSFTVYFCYPEALKNTGKLKAFRNFIFLKARDW 297 (299) Q Consensus 239 ~Gia~lp~~~~~~---~~~lv~i~~~~~~~~~~~~lv~~~~~~~~~~~~~f~d~l~~~~r~~ 297 (299) +||+++|.+++++ +|+||+++|++ +.+++++|++++..||++++|+|||.+.+|+| T Consensus 234 ~Gi~~lP~~~v~~~l~~G~Lv~vlp~~---~~~v~l~~~~~~~~~p~~~af~d~l~~~a~~~ 292 (294) T PRK13348 234 LGYGMVPELLIGPLLAAGRLVDLAPAH---PVDVALYWHHWEVEPPTMEALSQRVVEAARRL 292 (294) T ss_pred CEEEECCHHHHHHHHHCCCEEECCCCC---CCCEEEEEECCCCCCHHHHHHHHHHHHHHHHH T ss_conf 928966499999998489878917999---77147980068868979999999999999996 No 26 >PRK03635 chromosome replication initiation inhibitor protein; Validated Probab=100.00 E-value=0 Score=344.73 Aligned_cols=283 Identities=20% Similarity=0.253 Sum_probs=224.0 Q ss_pred CCHHHHHHHHHHHHHCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEECCCCEEEEECCCCCCCCCCCCCCCCCHHHH Q ss_conf 88899999999998276899998828997899999999999958821797699468500134332222222222101221 Q gi|254780282|r 3 FDWDKLRVFYVVARSGSFTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHARGLTLTEQGSKLHRVTSEVYHKLETTQI 82 (299) Q Consensus 3 md~~~L~~f~~v~~~gs~s~AA~~L~itq~avS~~i~~LE~~lg~~Lf~R~~~~~~lT~~G~~l~~~a~~~l~~~~~~~~ 82 (299) |||++|++|++|+++|||++||++||+||||||++|++||++||++||+| +|+++||++|+.|+++++++....+++.. T Consensus 2 mdl~~Lr~F~aVa~~GSfs~AA~~L~~tqsaVS~~I~~LE~~LG~~Lf~R-tr~~~LT~aG~~ll~~a~~v~~le~~~~~ 80 (295) T PRK03635 2 LDYKQLEALAAVIREGSFERAAQALHITQSAVSQRIKALEERVGQPLLVR-TQPCRATEAGQRLLRHARQVRLLEAELLG 80 (295) T ss_pred CCHHHHHHHHHHHHHCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCEEC-CCCCEECHHHHHHHHHHHHHHHHHHHHHH T ss_conf 89899999999998099999999978886699999999999949723178-99874488899999999999999999998 Q ss_pred HCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCCCCCCC--CCCC-CCCCCCCCCCCCCCCCCCCCCCCCC Q ss_conf 001223222222333211100000000013566754200012222222--2222-2222222223456543211112234 Q gi|254780282|r 83 ELQESSVKPSGKLRIATTIDLGQNLLQGNLKEFLLLYPDIQIQLILDN--KDID-ISMDYADCAIRLRKPIQSSSLIQRK 159 (299) Q Consensus 83 ~~~~~~~~~~g~i~I~~~~~~~~~~l~~~l~~f~~~~P~i~i~i~~~~--~~~~-l~~~~~Di~i~~~~~~~~~~l~~~~ 159 (299) .+..... .++++|+++......|++|.+.+|.+.|| +.+++..++ ...+ +.+|.+|++|... +.+.+++..++ T Consensus 81 ~~~~~~~--~~~l~l~~~~~~l~~~l~p~l~~f~~~~p-v~l~l~~~~~~~~~~~l~~g~~~~ai~~~-~~~~~g~~~~~ 156 (295) T PRK03635 81 ELPALDP--PLRLSIAVNADSLATWFLPALAPVLAQHG-VLLDLVVDDQDHTLELLRRGEVLGAVTTE-AQPVAGCRVDP 156 (295) T ss_pred HHHCCCC--CCEEEECCCHHHHHHHHHHHHHHHHHHCC-EEEEEEECCHHHHHHHHHCCCEEEEEECC-CCCCCCCEEEE T ss_conf 7207688--82675034603788988999999998174-25777744407799999569627999658-87788867887 Q ss_pred CCCCCCCCCCCCCCCCCC-CCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCCCCCCCEEEECCCCHHHHHHHHH Q ss_conf 555433211234432111-2222221100011235664332110002356652022343212114532420013567873 Q gi|254780282|r 160 LVTIHMHAYAAPHYLKNC-REPLSIQELDKHNLITFGDLIPKCMEDFNWLATVDRPIGEPRISCLQVNSYLSIMQYCVLG 238 (299) Q Consensus 160 l~~~~~~~v~~~~~~~~~-~~~~~~~dL~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~v~~g 238 (299) |+..++++||+|+|..++ +.+.+++||.++|+|.++..... .+.+..... .......+.+.++|.++++++|.+| T Consensus 157 L~~~~~~~vAsP~~~~~~~~~~~~~~~L~~~p~l~~~~~~~~---~~~~~~~~~-~~~~~~~~~~~~~s~~a~~~av~aG 232 (295) T PRK03635 157 LGAMRYLAVASPAFAARYFPDGVTAAALAKAPAVVFNRKDDL---QDRFLRRLF-GLPPGSVPCHYVPSSEGFVRAALAG 232 (295) T ss_pred CCCCEEEEEECHHHHHHHCCCCCCHHHHHCCCEEEECCCCCH---HHHHHHHCC-CCCCCCCCEEEECCHHHHHHHHHHC T ss_conf 256369999878999972799999999943987883698737---899998646-8776767658989899999999969 Q ss_pred CCEEEEEHHHHCC---CCCEEEECCCCCCCCCEEEEEECCCCCCCHHHHHHHHHHHHHHHCC Q ss_conf 8423311777601---9984661776667660089993487788889999999999998506 Q gi|254780282|r 239 SGIALLPDYIVKD---NPNLVRIMEDVITPSFTVYFCYPEALKNTGKLKAFRNFIFLKARDW 297 (299) Q Consensus 239 ~Gia~lp~~~~~~---~~~lv~i~~~~~~~~~~~~lv~~~~~~~~~~~~~f~d~l~~~~r~~ 297 (299) +||+++|.+++++ +|+||+++|+++ .++.++|++.+..||++++|+|||.+.++|| T Consensus 233 lGia~lP~~~v~~~L~~G~LV~llp~~~---~~~~l~~~~~r~~s~~l~~~~~~l~~~~~~~ 291 (295) T PRK03635 233 LGWGMIPELQAEPELASGELVDLTPGRP---LDVPLYWHHWRLESRLLDRLTDALLAAAAQV 291 (295) T ss_pred CEEEECHHHHHHHHHHCCCEEEECCCCC---CCCCEECCCCCCCCHHHHHHHHHHHHHHHHH T ss_conf 9089881999999984898188798997---9800516244547889999999999999987 No 27 >PRK03601 transcriptional regulator HdfR; Provisional Probab=100.00 E-value=0 Score=342.63 Aligned_cols=269 Identities=21% Similarity=0.246 Sum_probs=222.1 Q ss_pred CCHHHHHHHHHHHHHCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEECCCCEEEEECCCCCCCCCCCCCCCCCHHHH Q ss_conf 88899999999998276899998828997899999999999958821797699468500134332222222222101221 Q gi|254780282|r 3 FDWDKLRVFYVVARSGSFTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHARGLTLTEQGSKLHRVTSEVYHKLETTQI 82 (299) Q Consensus 3 md~~~L~~f~~v~~~gs~s~AA~~L~itq~avS~~i~~LE~~lg~~Lf~R~~~~~~lT~~G~~l~~~a~~~l~~~~~~~~ 82 (299) |||++|++|++|+++|||++||++||+||||||++|++||++||++||+|++||+.||++|+.|+++|+.+++..+++.. T Consensus 1 Md~~~L~~F~~va~~gsft~AA~~L~isQsavS~~Ik~LE~~LG~~Lf~R~~~~~~LT~~G~~l~~~A~~il~~~~~~~~ 80 (275) T PRK03601 1 MDTELLKTFLEVSRTRHFGRAAESLYLTQSAVSFRIRQLENQLGVNLFTRHRNNIRLTAAGEKLLPYAETLMNTWQAARK 80 (275) T ss_pred CCHHHHHHHHHHHHHCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEECCCCEEECHHHHHHHHHHHHHHHHHHHHHH T ss_conf 98799999999998099999999978987899999999999969832998799432998899999999999999999999 Q ss_pred HCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCCCCCCCC---CCCCCCCCCCCCCCCCCCCCCCCCCCCC Q ss_conf 0012232222223332111000000000135667542000122222222---2222222222223456543211112234 Q gi|254780282|r 83 ELQESSVKPSGKLRIATTIDLGQNLLQGNLKEFLLLYPDIQIQLILDNK---DIDISMDYADCAIRLRKPIQSSSLIQRK 159 (299) Q Consensus 83 ~~~~~~~~~~g~i~I~~~~~~~~~~l~~~l~~f~~~~P~i~i~i~~~~~---~~~l~~~~~Di~i~~~~~~~~~~l~~~~ 159 (299) ++... ...|.++||++++++..++++.+.+|++.||+++|++..++. ..+|.+|++|++|....| ..+++..++ T Consensus 81 ~~~~~--~~~~~l~ig~~~~~~~~~l~~~l~~~~~~~P~v~l~l~~~~~~~~~~~L~~~~~Dl~i~~~~p-~~~~l~~~~ 157 (275) T PRK03601 81 EVAHT--SRHNEFSIGASASLWECMLNQWLGRLYQNQEELQFEARIAQRQSLVKQLHERQLDLLITTEAP-KMDEFSSQL 157 (275) T ss_pred HHHHC--CCCCCEEEEEEHHHHHHHHHHHHHHHHHHCCCCEEEEEECCHHHHHHHHHCCCCCEEEECCCC-CCCCEEEEE T ss_conf 99725--677609999775778999999999999978896799998898999999977993589977799-888847999 Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCCCCCCCEEEECCCCHHHHHHHHHC Q ss_conf 55543321123443211122222211000112356643321100023566520223432121145324200135678738 Q gi|254780282|r 160 LVTIHMHAYAAPHYLKNCREPLSIQELDKHNLITFGDLIPKCMEDFNWLATVDRPIGEPRISCLQVNSYLSIMQYCVLGS 239 (299) Q Consensus 160 l~~~~~~~v~~~~~~~~~~~~~~~~dL~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~v~~g~ 239 (299) ++++++++++++.+..... .+++........ ..+... .......+.+++++.++++++|.+|. T Consensus 158 l~~~~l~l~~s~~~~~~~~----------~~~i~l~~~~~~----~~~~~~---~~~~~~~p~~~~~s~~~~~~~v~~g~ 220 (275) T PRK03601 158 LGHFTLALYTSAPSKNKSE----------LNYLRLEWGPDF----QQHEAG---LIGADEVPILTTSSAELARQQLATLN 220 (275) T ss_pred ECCEEEEEEECCCCCCCCC----------CCEEEEECCCCH----HHHHHH---HCCCCCCCEEEECHHHHHHHHHHHCC T ss_conf 5235689997786433468----------875882067206----799975---23567798588578999999999789 Q ss_pred CEEEEEHHHHCCCCCEEEECCCCCCCCCEEEEEECCCCCCCHHHHHHHHHHHH Q ss_conf 42331177760199846617766676600899934877888899999999999 Q gi|254780282|r 240 GIALLPDYIVKDNPNLVRIMEDVITPSFTVYFCYPEALKNTGKLKAFRNFIFL 292 (299) Q Consensus 240 Gia~lp~~~~~~~~~lv~i~~~~~~~~~~~~lv~~~~~~~~~~~~~f~d~l~~ 292 (299) |++++|.+++++.|+++.+ ++.+..++++|++|+|++..++.++.|+++... T Consensus 221 Gia~LP~~~~~~~g~L~~v-~~~~~~~rp~y~v~~k~~~~~~~ir~~l~~~~~ 272 (275) T PRK03601 221 GCAWLPVHWAKEKGGLHTV-VDSTTLSRPLYAIWLQNSDKQALIRDLLKIPVL 272 (275) T ss_pred CEEECCHHHHHHCCCEEEC-CCCCCCCEEEEEEEECCCCCHHHHHHHHHHHHC T ss_conf 0999937887118998999-999977147999996889737999999822411 No 28 >PRK09986 DNA-binding transcriptional activator XapR; Provisional Probab=100.00 E-value=0 Score=345.79 Aligned_cols=273 Identities=18% Similarity=0.235 Sum_probs=232.3 Q ss_pred HHHHHCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEECCCCEEEEECCCCCCCCCCCCCCCCCHHHHHCCCCCCCCC Q ss_conf 99982768999988289978999999999999588217976994685001343322222222221012210012232222 Q gi|254780282|r 13 VVARSGSFTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHARGLTLTEQGSKLHRVTSEVYHKLETTQIELQESSVKPS 92 (299) Q Consensus 13 ~v~~~gs~s~AA~~L~itq~avS~~i~~LE~~lg~~Lf~R~~~~~~lT~~G~~l~~~a~~~l~~~~~~~~~~~~~~~~~~ 92 (299) ||||+||||+||++|++||||||++|++||++||++||+|++|++.||++|+.|++++++++..++++...+........ T Consensus 1 AVae~~sft~AAe~L~isQpavS~~I~~LE~~lg~~Lf~R~~r~v~LT~~G~~l~~~a~~il~~~~~~~~~~~~~~~~~~ 80 (278) T PRK09986 1 AVAEELHFGRAAARLNMSQPPLSIHIKELEDQLGTLLFIRHSRSVALTHAGKILMEESRRLLDNANNALARVEQIGRGEA 80 (278) T ss_pred CCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEECCCCEEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCC T ss_conf 92255989999999888888999999999998599869999997708988999999999999999999999998635777 Q ss_pred CCCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCCCCCCC---CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC Q ss_conf 22333211100000000013566754200012222222---222222222222234565432111122345554332112 Q gi|254780282|r 93 GKLRIATTIDLGQNLLQGNLKEFLLLYPDIQIQLILDN---KDIDISMDYADCAIRLRKPIQSSSLIQRKLVTIHMHAYA 169 (299) Q Consensus 93 g~i~I~~~~~~~~~~l~~~l~~f~~~~P~i~i~i~~~~---~~~~l~~~~~Di~i~~~~~~~~~~l~~~~l~~~~~~~v~ 169 (299) |+|+||+.+++...++++.+.+|+++||++++++.... ....|.++++|+||........+++...+++.+++++++ T Consensus 81 g~l~Ig~~~~~~~~~l~~~l~~f~~~~P~i~v~i~~~~~~~~~~~l~~~~~D~a~~~~~~~~~~~~~~~~l~~~~~~~~~ 160 (278) T PRK09986 81 GRIELGVVGTALWGRMRPAMRHFLKENPNVEVLFREKSPSMQMALLERRELDAGIWRMALEPNPGFTSLRLHESAFAVAV 160 (278) T ss_pred CCEEEEECHHHHHHHHHHHHHHHHHHCCCEEEEEEECCHHHHHHHHHCCCCCEEEECCCCCCCCCCEEEEEEECCCEEEE T ss_conf 73368742168887642899999987898399999788699999997799758996377778877426887741637996 Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCCCCCCCEEEECCCCHHHHHHHHHCCEEEEEHHHH Q ss_conf 34432111222222110001123566433211000235665202234321211453242001356787384233117776 Q gi|254780282|r 170 APHYLKNCREPLSIQELDKHNLITFGDLIPKCMEDFNWLATVDRPIGEPRISCLQVNSYLSIMQYCVLGSGIALLPDYIV 249 (299) Q Consensus 170 ~~~~~~~~~~~~~~~dL~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~v~~g~Gia~lp~~~~ 249 (299) +++|+......++++||.+++||.+....... .+........+..+...+++++..+++++|.+|+|++++|++++ T Consensus 161 ~~~hpla~~~~i~~~~l~~~~~i~~~~~~~~~----~~~~~~~~~~g~~~~~~~~~~~~~~~~~~V~~G~Giailp~~~~ 236 (278) T PRK09986 161 PEEHLLASKSSVPLKALRNEYFVTLPSVHSDW----GFLQRVCQQAGFSPQIIREVNEPQTVLAMVSMGIGITLVADSYA 236 (278) T ss_pred CCCCCCCCCCCCCHHHHCCCCEEEECCCCCHH----HHHHHHHHHCCCCCCEEEEECCHHHHHHHHHHCCEEEEEHHHHH T ss_conf 59873336999999998599979867998669----99999999779985179999989999999997998998417774 Q ss_pred CCC-CCEEEECCCCCCCCCEEEEEECCCCCCCHHHHHHHHHHH Q ss_conf 019-984661776667660089993487788889999999999 Q gi|254780282|r 250 KDN-PNLVRIMEDVITPSFTVYFCYPEALKNTGKLKAFRNFIF 291 (299) Q Consensus 250 ~~~-~~lv~i~~~~~~~~~~~~lv~~~~~~~~~~~~~f~d~l~ 291 (299) +.. ++++.+ |-.+.+++.++++|+++. .+|++++|+++|. T Consensus 237 ~~~~~~v~~~-Pl~~~~~~~~~lv~~~~~-~~p~~~~fi~~l~ 277 (278) T PRK09986 237 QMPWPGVVFR-PLKERIPADLYIVYHQQQ-ATPALEKLLAALT 277 (278) T ss_pred CCCCCCEEEE-ECCCCCCEEEEEEECCCC-CCHHHHHHHHHHC T ss_conf 2378999999-889998038999984999-9999999999865 No 29 >PRK10082 putative DNA-binding transcriptional regulator; Provisional Probab=100.00 E-value=0 Score=341.20 Aligned_cols=285 Identities=20% Similarity=0.245 Sum_probs=222.5 Q ss_pred CCCHHHHHHHHHHHHHCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEECCCCEEEEECCCCCCCCCCCCCCCCCHHH Q ss_conf 88889999999999827689999882899789999999999995882179769946850013433222222222210122 Q gi|254780282|r 2 SFDWDKLRVFYVVARSGSFTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHARGLTLTEQGSKLHRVTSEVYHKLETTQ 81 (299) Q Consensus 2 ~md~~~L~~f~~v~~~gs~s~AA~~L~itq~avS~~i~~LE~~lg~~Lf~R~~~~~~lT~~G~~l~~~a~~~l~~~~~~~ 81 (299) |||+++|++|++|+++||||+||++||+||||||++|++||++||++||+|++|++.||++|+.|+++++.+++++++.. T Consensus 10 nmelr~L~~F~~Vae~gSFs~AA~~L~itQpavS~~I~~LE~~LGv~Lf~R~tr~v~LT~aG~~~~~~a~~il~~le~~~ 89 (303) T PRK10082 10 NIETKWLYDFLTLEKCRNFSQAAVSRNVSQPAFSRRIRALEQAIGVELFNRQVTPLQLSEQGKIFHSQIRHLLQQLESNL 89 (303) T ss_pred CCCHHHHHHHHHHHHCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEECCCCEEECHHHHHHHHHHHHHHHHHHHHH T ss_conf 66299999999999809999999997898159999999999996995086799983036889999999999999999999 Q ss_pred HHCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCC-CCCCCCCCCCCC Q ss_conf 1001223222222333211100000000013566754200012222222222222222222234565-432111122345 Q gi|254780282|r 82 IELQESSVKPSGKLRIATTIDLGQNLLQGNLKEFLLLYPDIQIQLILDNKDIDISMDYADCAIRLRK-PIQSSSLIQRKL 160 (299) Q Consensus 82 ~~~~~~~~~~~g~i~I~~~~~~~~~~l~~~l~~f~~~~P~i~i~i~~~~~~~~l~~~~~Di~i~~~~-~~~~~~l~~~~l 160 (299) ..++.......|+++|+++++++.+++|+.++.|...+|..-..+..++....+.+|.+|+++.+.+ +.....+...++ T Consensus 90 ~~l~~~~~~~~g~l~i~a~~~~~~~~Lp~~l~~~~~~~~~~~~~~~~~~~~~~l~~g~~D~~~~~~~~~l~~~~~~~~~l 169 (303) T PRK10082 90 AELRGGSDYAQRKIKIAAAHSLSLGLLPSIISQMPPLFTWAIEAIDVDEAVDKLREGQSDCIFSFHDEDLLEAPFDHIRL 169 (303) T ss_pred HHHHCCCCCCCCEEEEEECHHHHHHHHHHHHHHHHHHCCEEEEEECHHHHHHHHHCCCCCEEEECCCCCCCCCCCCEEEE T ss_conf 99860545675469998317769999999999744127767885048999999987997199983564334477632466 Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCCCCCCCEEEECCCCHHHHHHHHHCC Q ss_conf 55433211234432111222222110001123566433211000235665202234321211453242001356787384 Q gi|254780282|r 161 VTIHMHAYAAPHYLKNCREPLSIQELDKHNLITFGDLIPKCMEDFNWLATVDRPIGEPRISCLQVNSYLSIMQYCVLGSG 240 (299) Q Consensus 161 ~~~~~~~v~~~~~~~~~~~~~~~~dL~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~v~~g~G 240 (299) +.++++++|++++ ++.+....+..++|++.+.............+ .+.........+++++.++++++|.+|+| T Consensus 170 ~~~~~~~v~~~~~---~~~~~~~~~~~~~pll~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~l~~~v~~G~G 243 (303) T PRK10082 170 FESQLFPVCASDE---HGEALFNLAQPHFPLLNYSRNSYMGRLINRTL---TRHSELSFSTFFVSSMSELLKQVALDGCG 243 (303) T ss_pred ECCCEEEEECCCC---CCCCCCCCCCCCCCEEECCCCCCHHHHHHHHH---HHCCCCCCCEEEEECHHHHHHHHHHHCCE T ss_conf 3262699986886---68878664367986796589970879998877---53566667627997589999999996999 Q ss_pred EEEEEHHHHCC---CCCEEEECCCCCCCCCEEEEEECCCCCCCHHHHHHHHHHHHH Q ss_conf 23311777601---998466177666766008999348778888999999999999 Q gi|254780282|r 241 IALLPDYIVKD---NPNLVRIMEDVITPSFTVYFCYPEALKNTGKLKAFRNFIFLK 293 (299) Q Consensus 241 ia~lp~~~~~~---~~~lv~i~~~~~~~~~~~~lv~~~~~~~~~~~~~f~d~l~~~ 293 (299) |+++|.+++++ +|+|+.+.+++...++.+| +|+++++++|++++|+++|.|. T Consensus 244 Ia~lP~~~V~~el~~G~Lv~l~~d~~~~~~~~y-~~~~~~~lsP~a~~F~~~Lre~ 298 (303) T PRK10082 244 IAWLPEYAIQQEIRSGRLVVLNRDELVIPIQAY-AYRMNTRMNPVAERFWRELREL 298 (303) T ss_pred EEECCHHHHHHHHHCCCCEEECCCCCCCCEEEE-EEECCCCCCHHHHHHHHHHHHH T ss_conf 998829999999878981895664565731799-9989898898999999999987 No 30 >PRK09508 leuO leucine transcriptional activator; Reviewed Probab=100.00 E-value=0 Score=323.71 Aligned_cols=287 Identities=13% Similarity=0.141 Sum_probs=235.5 Q ss_pred CCCHHHHHHHHHHHHHCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEECCCCEEEEECCCCCCCCCCCCCCCCCHHH Q ss_conf 88889999999999827689999882899789999999999995882179769946850013433222222222210122 Q gi|254780282|r 2 SFDWDKLRVFYVVARSGSFTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHARGLTLTEQGSKLHRVTSEVYHKLETTQ 81 (299) Q Consensus 2 ~md~~~L~~f~~v~~~gs~s~AA~~L~itq~avS~~i~~LE~~lg~~Lf~R~~~~~~lT~~G~~l~~~a~~~l~~~~~~~ 81 (299) +||+|+|++|.+|+++||||+||++||+||||||++|++||+.||++||+|+|+|++||+.|+.++++++++++.+++.. T Consensus 21 ~~DLNLL~~F~al~e~~svtrAA~~L~vSQpAvS~aL~rLr~~~gd~LFvR~grg~~pT~~a~~L~~~~~~~L~~i~~~~ 100 (314) T PRK09508 21 MVDLNLLTVFDAVMQEQNITRAAHNLGMSQPAVSNAVARLKVMFNDELFVRYGRGIQPTARARQLFGPVRQALQLVQNEL 100 (314) T ss_pred HCCHHHHHHHHHHHHCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEECCCCEEHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 15877899999999829999999997898669999999999981995488349935429989999999999999999762 Q ss_pred HHCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCCCCCCC--CC-CCCCCCCCCCCCCCCCCCCCCCCCCC Q ss_conf 1001223222222333211100000000013566754200012222222--22-22222222222345654321111223 Q gi|254780282|r 82 IELQESSVKPSGKLRIATTIDLGQNLLQGNLKEFLLLYPDIQIQLILDN--KD-IDISMDYADCAIRLRKPIQSSSLIQR 158 (299) Q Consensus 82 ~~~~~~~~~~~g~i~I~~~~~~~~~~l~~~l~~f~~~~P~i~i~i~~~~--~~-~~l~~~~~Di~i~~~~~~~~~~l~~~ 158 (299) ...........+.++|+++.++...++|+++..|.+.+|+++|++.... .. ..|..|++|++|.... ..++++... T Consensus 101 ~~~~f~p~~~~~~~~i~~~~~~~~~llp~ll~~~~~~~P~v~l~~~~~~~~~~~~~L~~g~iDl~I~~~~-~~~~~~~~~ 179 (314) T PRK09508 101 PGSGFEPESSERVFNLCICSPLDNRLASQIYNRIEQIAPNIHLVFKSSLNQNIEHQLRYQETEFVISYEE-FDRPEFTSV 179 (314) T ss_pred HHCCCCCCCCCCEEEEEECCHHHHHHHHHHHHHHHHHCCCCEEEEEECCCHHHHHHHHCCCCCEEEECCC-CCCCCCEEE T ss_conf 1213681004736999963078999999999999986899779998577064999997699529996787-799873489 Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCCCCCCCEEEECCCCHHHHHHHHH Q ss_conf 45554332112344321112222221100011235664332110002356652022343212114532420013567873 Q gi|254780282|r 159 KLVTIHMHAYAAPHYLKNCREPLSIQELDKHNLITFGDLIPKCMEDFNWLATVDRPIGEPRISCLQVNSYLSIMQYCVLG 238 (299) Q Consensus 159 ~l~~~~~~~v~~~~~~~~~~~~~~~~dL~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~v~~g 238 (299) +|++++++++|+++||... .+++.+++..++++..... ... ..........+..+...++++++.++..+|..| T Consensus 180 ~L~~d~~v~v~~~~HP~~~-~~lt~~~~~~~~hv~~s~~-~~~----~~~~~~l~~~~~~r~i~~~~~s~~~~~~lv~~t 253 (314) T PRK09508 180 PLFKDELVLVASKNHPRIK-GPILEEQLYNEQHAVVSLD-RFA----SFSQPWYDTVDKQASIAYQGMALSSVLNVVSQT 253 (314) T ss_pred EEEECCEEEEECCCCCCCC-CCCCHHHHHHCCCEEEECC-CCC----CHHHHHHHHCCCCCEEEEEECCHHHHHHHHHHC T ss_conf 9972464999829997678-9999999961998899639-988----589999995798631899958899999999839 Q ss_pred CCEEEEEHHHHCC---CCCEEEECCCCCCCCCEEEEEECCCCCCCHHHHHHHHHHHHHHH Q ss_conf 8423311777601---99846617766676600899934877888899999999999985 Q gi|254780282|r 239 SGIALLPDYIVKD---NPNLVRIMEDVITPSFTVYFCYPEALKNTGKLKAFRNFIFLKAR 295 (299) Q Consensus 239 ~Gia~lp~~~~~~---~~~lv~i~~~~~~~~~~~~lv~~~~~~~~~~~~~f~d~l~~~~r 295 (299) .|++++|.++++. .+.+..+.++.+.+.++++++||++...+|+.++|.+-|.+-+| T Consensus 254 d~ia~lP~~~a~~~~~~~~l~~~~lP~~~~~~~~~l~WH~r~~~dp~~~WlR~~i~~v~~ 313 (314) T PRK09508 254 HLVAIAPRWLAEEFAESLELQILPLPLKNNSRTCYLSWHESAGRDKGHQWMEDLLVSICK 313 (314) T ss_pred CEEEHHHHHHHHHHHHCCCCEEECCCCCCCCEEEEEEECCCCCCCHHHHHHHHHHHHHHC T ss_conf 977589999999864429957978998988736999978998899899999999999975 No 31 >COG0583 LysR Transcriptional regulator [Transcription] Probab=100.00 E-value=0 Score=311.87 Aligned_cols=288 Identities=30% Similarity=0.356 Sum_probs=235.2 Q ss_pred CCHHHHHHHHHHHHHCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEECCCCEEEEECCCCCCCCCCCCCCCCCHHHH Q ss_conf 88899999999998276899998828997899999999999958821797699468500134332222222222101221 Q gi|254780282|r 3 FDWDKLRVFYVVARSGSFTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHARGLTLTEQGSKLHRVTSEVYHKLETTQI 82 (299) Q Consensus 3 md~~~L~~f~~v~~~gs~s~AA~~L~itq~avS~~i~~LE~~lg~~Lf~R~~~~~~lT~~G~~l~~~a~~~l~~~~~~~~ 82 (299) ||+++|++|++|+++|||++||++|++||||||++|++||++||++||+|+++++.||++|+.++++++.++..++++.. T Consensus 1 ~~l~~L~~F~~v~~~gs~t~AA~~L~isq~avS~~I~~LE~~lg~~Lf~R~~~~~~lT~~G~~l~~~a~~~l~~~~~~~~ 80 (297) T COG0583 1 MDLRQLRAFVAVAEEGSFTRAAERLGLSQSAVSRQIKRLEEELGVPLFERTTRRVRLTEAGERLLERARRILAELEEALA 80 (297) T ss_pred CCHHHHHHHHHHHHCCCHHHHHHHHCCCCHHHHHHHHHHHHHHCCEEEEECCCCCCCCHHHHHHHHHHHHHHHHHHHHHH T ss_conf 98789999999984599899998839990589999999999849864886799845588899999999999999999999 Q ss_pred HCCCCCCCCC-CCCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCCCCCCCC-CCCCCCCCCCCCCCCCCCCCCC-CCCCCC Q ss_conf 0012232222-223332111000000000135667542000122222222-2222222222223456543211-112234 Q gi|254780282|r 83 ELQESSVKPS-GKLRIATTIDLGQNLLQGNLKEFLLLYPDIQIQLILDNK-DIDISMDYADCAIRLRKPIQSS-SLIQRK 159 (299) Q Consensus 83 ~~~~~~~~~~-g~i~I~~~~~~~~~~l~~~l~~f~~~~P~i~i~i~~~~~-~~~l~~~~~Di~i~~~~~~~~~-~l~~~~ 159 (299) .+........ +.++|+++++++..++++.+.+|.+.||++.+++...+. ..++..+++|++|....+ ..+ ++...+ T Consensus 81 ~~~~~~~~~~~~~~~i~~~~~~~~~~l~~~l~~f~~~~P~~~~~~~~~~~~~~~l~~~~~D~~i~~~~~-~~~~~~~~~~ 159 (297) T COG0583 81 EAARLARGEPGGLLRIAAPSTAASSLLPPLLARFRARYPEIELELGTSDRLLEDLVEGELDLAIRAGPP-PPPDGLVARP 159 (297) T ss_pred HHHHHCCCCCCCEEEEEECCHHHHHHHHHHHHHHHHHCCCEEEEEECCHHHHHHHHCCCCEEEEEECCC-CCCCCEEEEE T ss_conf 997512567775599996707679999999999999789839998256649999877993499995886-6888746889 Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCCCCCCCEEEECCCCHHHHHHHHHC Q ss_conf 55543321123443211122222211000112356643321100023566520223432121145324200135678738 Q gi|254780282|r 160 LVTIHMHAYAAPHYLKNCREPLSIQELDKHNLITFGDLIPKCMEDFNWLATVDRPIGEPRISCLQVNSYLSIMQYCVLGS 239 (299) Q Consensus 160 l~~~~~~~v~~~~~~~~~~~~~~~~dL~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~v~~g~ 239 (299) ++.++++++++++|+...+.. ++++..++++.+.................... ....+++++..+++++|.+|. T Consensus 160 l~~~~~~~v~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~~~~~~~~~~~v~~g~ 233 (297) T COG0583 160 LFSEELVLVVPASHPLAARHG--LPDLPGEPLILLEHGCILRRLLDQALALAGWR----PRIRLEVNSAEALLQAVAAGL 233 (297) T ss_pred EECCCEEEEEECCCHHHHCCC--CCCCCCCHHHCCCCCCHHHHHHHHHHHHCCCC----CCCEEEECCHHHHHHHHHHCC T ss_conf 603647999957846651478--64477241230676531577667788862466----686599990999999999699 Q ss_pred CEEEEEHHHHCCC--CCEEEECCCCC-CCCCEEEEEECCCCCCCHHHHHHHHHHHHHHHCC Q ss_conf 4233117776019--98466177666-7660089993487788889999999999998506 Q gi|254780282|r 240 GIALLPDYIVKDN--PNLVRIMEDVI-TPSFTVYFCYPEALKNTGKLKAFRNFIFLKARDW 297 (299) Q Consensus 240 Gia~lp~~~~~~~--~~lv~i~~~~~-~~~~~~~lv~~~~~~~~~~~~~f~d~l~~~~r~~ 297 (299) |++++|..++... +..+.+.+... .....+|++|++++..+++++.|++++.+..++. T Consensus 234 gi~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~ 294 (297) T COG0583 234 GIALLPESLARPDLAGRLVRVLPLPPPPLPRPLYLVWRKSRLLSPAVRAFIDFLREALARL 294 (297) T ss_pred CEEEECHHHHHHHHCCCCEEEECCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHHH T ss_conf 8386419999887548918995477788776399999588668989999999999997653 No 32 >PRK11716 DNA-binding transcriptional regulator IlvY; Provisional Probab=100.00 E-value=0 Score=311.63 Aligned_cols=261 Identities=21% Similarity=0.239 Sum_probs=213.6 Q ss_pred HCCCHHHHHHHHHHHHHHHCCEEEEECCCCEEEEECCCCCCCCCCCCCCCCCHHHHHCCCCCCCCCCCCCCCCCCCCCCC Q ss_conf 28997899999999999958821797699468500134332222222222101221001223222222333211100000 Q gi|254780282|r 27 LHLSQSSISRQISGLETEVGIKLFYRHARGLTLTEQGSKLHRVTSEVYHKLETTQIELQESSVKPSGKLRIATTIDLGQN 106 (299) Q Consensus 27 L~itq~avS~~i~~LE~~lg~~Lf~R~~~~~~lT~~G~~l~~~a~~~l~~~~~~~~~~~~~~~~~~g~i~I~~~~~~~~~ 106 (299) |||||||||++|++||+++|++||+|++|++.||++|+.|+++|++++.+++++...+.......+|+|+||++.+.+.+ T Consensus 1 LhvSQpavS~~I~~LE~~lG~~Lf~R~~r~v~LT~~G~~l~~~a~~il~~~~~~~~~~~~~~~~~~G~lri~~~~t~~~~ 80 (269) T PRK11716 1 MHVSPSTLSRQIQRLEEELGQPLFVRDNRSVTLTEAGEELRPFAQQTLLQWQQLKHTLDQQQPSLSGELSLFCSVTAAYS 80 (269) T ss_pred CCCCHHHHHHHHHHHHHHHCCEEEEECCCCEEECHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCEEEEECHHHHHH T ss_conf 90855899999999999969965998899875878999999999999999999999998405687662699851488777 Q ss_pred CCCCHHHHHHHHHHCCCCCCCCCCC---CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC-CCCCCC Q ss_conf 0000135667542000122222222---222222222222345654321111223455543321123443211-122222 Q gi|254780282|r 107 LLQGNLKEFLLLYPDIQIQLILDNK---DIDISMDYADCAIRLRKPIQSSSLIQRKLVTIHMHAYAAPHYLKN-CREPLS 182 (299) Q Consensus 107 ~l~~~l~~f~~~~P~i~i~i~~~~~---~~~l~~~~~Di~i~~~~~~~~~~l~~~~l~~~~~~~v~~~~~~~~-~~~~~~ 182 (299) ++|+.+.+|+++||+|++++...+. ...+.+|++|+||.......++++...++++++++++++.++... .....+ T Consensus 81 ~lp~~l~~f~~~~P~v~~~l~~~~~~~~~~~l~~g~~D~ai~~~p~~~~~~l~~~~l~~~~l~~v~p~~~~~~~~~~~~~ 160 (269) T PRK11716 81 HLPPILDRFRAEHPLVEIKLTTGDAADAVEKVQSGEADLAIAAKPETLPSSLAFSPIDEIPLVLIAPALPCPVRQQVSQE 160 (269) T ss_pred HCCHHHHHHHHHCCCCEEEEECCCHHHHHHHHHCCCCCEEEEECCCCCCCCEEEEEEEEEEEEEEEECCCCHHHCCCCCC T ss_conf 54678999999888944898428999999999869955899937878999769999656418999978841543635688 Q ss_pred CCCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCCCCCCCEEEECCCCHHHHHHHHHCCEEEEEHHHHCCC---CCEEEEC Q ss_conf 2110001123566433211000235665202234321211453242001356787384233117776019---9846617 Q gi|254780282|r 183 IQELDKHNLITFGDLIPKCMEDFNWLATVDRPIGEPRISCLQVNSYLSIMQYCVLGSGIALLPDYIVKDN---PNLVRIM 259 (299) Q Consensus 183 ~~dL~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~v~~g~Gia~lp~~~~~~~---~~lv~i~ 259 (299) ..|+.++|+|....... ......|+.. .+..+...+++++.+++++||.+|+|++++|+++++++ ++++.+. T Consensus 161 ~~dl~~~p~il~~~~~~-r~~~~~~~~~----~~~~p~i~~e~~~~~~i~~~V~~G~GiailP~~~~~~~~~~~~l~~l~ 235 (269) T PRK11716 161 KPDWSRIPFILPEHGPA-RRRIDLWFRR----HKIKPNIYAQVSGHEAIVSMVALGCGVGILPEVVLDNSPVRDRVQRLE 235 (269) T ss_pred HHHHHCCCEEECCCCCH-HHHHHHHHHH----CCCCCCEEEEECCHHHHHHHHHHCCEEEEHHHHHHHCCCCCCCEEEEE T ss_conf 44683386781589827-9999999997----699971799989799999999979941720599983275579889974 Q ss_pred CCCCCCCCEEEEEECCCCCCCHHHHHHHHHHHH Q ss_conf 766676600899934877888899999999999 Q gi|254780282|r 260 EDVITPSFTVYFCYPEALKNTGKLKAFRNFIFL 292 (299) Q Consensus 260 ~~~~~~~~~~~lv~~~~~~~~~~~~~f~d~l~~ 292 (299) ...+.++++++++|++++..+|++++|+|++.+ T Consensus 236 ~~~~~~~~~i~l~~~~~r~~sPa~~aF~~~l~~ 268 (269) T PRK11716 236 VPPELTPFELGVCCQKKRLHEPLIDAFWQLLEN 268 (269) T ss_pred CCCCCCCEEEEEEEECCCCCCHHHHHHHHHHHH T ss_conf 899887369999997998679999999999965 No 33 >PRK11062 nhaR transcriptional activator NhaR; Provisional Probab=100.00 E-value=0 Score=306.88 Aligned_cols=280 Identities=19% Similarity=0.196 Sum_probs=231.0 Q ss_pred CC-CCHHHHHHHHHHHHHCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEECCCCEEEEECCCCCCCCCCCCCCCCCH Q ss_conf 98-88899999999998276899998828997899999999999958821797699468500134332222222222101 Q gi|254780282|r 1 MS-FDWDKLRVFYVVARSGSFTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHARGLTLTEQGSKLHRVTSEVYHKLET 79 (299) Q Consensus 1 m~-md~~~L~~f~~v~~~gs~s~AA~~L~itq~avS~~i~~LE~~lg~~Lf~R~~~~~~lT~~G~~l~~~a~~~l~~~~~ 79 (299) |+ ||++||+||++|+++|||++||++|++||||||++|++||+++|++||+|++|++.||++|+.+++||++++...++ T Consensus 1 m~~ln~~~L~~F~~va~~gs~~~Aa~~L~~tq~~vS~qi~~LE~~lg~~Lf~R~~r~~~lT~~G~~~~~~a~~i~~l~~e 80 (296) T PRK11062 1 MSHLNYNHLYYFWMVYKEGSVVGAAEALFLTPQTITGQIKALEERLQGKLFKRKGRGLEPTELGELVFRYADKMFTLSYE 80 (296) T ss_pred CCCCCHHHHHHHHHHHHCCCHHHHHHHHCCCCHHHHHHHHHHHHHHCCCCEEECCCCEEECHHHHHHHHHHHHHHHHHHH T ss_conf 99888899999999998099999999968981799999999999959910998899828858999999999999999999 Q ss_pred HHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCCCCCCCC---CCCCCCCCCCCCCCCCC--CCCCCC Q ss_conf 2210012232222223332111000000000135667542000122222222---22222222222234565--432111 Q gi|254780282|r 80 TQIELQESSVKPSGKLRIATTIDLGQNLLQGNLKEFLLLYPDIQIQLILDNK---DIDISMDYADCAIRLRK--PIQSSS 154 (299) Q Consensus 80 ~~~~~~~~~~~~~g~i~I~~~~~~~~~~l~~~l~~f~~~~P~i~i~i~~~~~---~~~l~~~~~Di~i~~~~--~~~~~~ 154 (299) +.+.++. .....+.++||+..+++..++++++..+.+.+|++++.+..++. ..+|..+++|+++.-.+ +...++ T Consensus 81 l~~~~~~-~~~~~~~lrvGi~~tl~k~~~~~lL~~~~~~~~~v~l~~~eg~~~~LL~~L~~~~LDlvLsd~p~~~~~~~~ 159 (296) T PRK11062 81 MLDIVNY-RKESNLLFDVGVADALSKRLVSRVLLAAVPEDESIHLRCFESTHEMLLEQLSQHKLDMILSDCPVDSTQQEG 159 (296) T ss_pred HHHHHHH-CCCCCCEEEEEEHHHHHHHHHHHHHHHHHHCCCCEEEEEECCCHHHHHHHHHCCCCCEEEECCCCCCCCCCC T ss_conf 9999850-457770599985246469899999999972289779999349879999999838987576068887556886 Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCCCCCCCEEEECCCCHHHHH Q ss_conf 12234555433211234432111222222110001123566433211000235665202234321211453242001356 Q gi|254780282|r 155 LIQRKLVTIHMHAYAAPHYLKNCREPLSIQELDKHNLITFGDLIPKCMEDFNWLATVDRPIGEPRISCLQVNSYLSIMQY 234 (299) Q Consensus 155 l~~~~l~~~~~~~v~~~~~~~~~~~~~~~~dL~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~ 234 (299) +.+.+|++.++.+++++.+... ..+++|.+.|++.++..++.......|+... +..+..+.++||..++..+ T Consensus 160 ~~s~~L~~~~v~~~~~~~l~~~----~fP~~L~~~plllp~~~S~lR~~ld~wf~~~----gI~P~Iv~E~dD~allk~~ 231 (296) T PRK11062 160 LFSKKLGECGVSFFCTNPLPEK----PFPACLEERRLLIPGRRTMLGRKLLNWFNSQ----GLNVEILGEFDDAALMKAF 231 (296) T ss_pred EEEEECCCCCEEEEECCCCCCC----CCHHHHCCCCCCCCCCCCHHHHHHHHHHHHC----CCCCEEEEEECCHHHHHHH T ss_conf 3898746684689845744458----7957755798402799875899999999968----9984499985989999999 Q ss_pred HHHHCCEEEEEHHHHCC---CCCEEEECCCCCCCCCEEEEEECCCCCCCHHHHHHHHHH Q ss_conf 78738423311777601---998466177666766008999348778888999999999 Q gi|254780282|r 235 CVLGSGIALLPDYIVKD---NPNLVRIMEDVITPSFTVYFCYPEALKNTGKLKAFRNFI 290 (299) Q Consensus 235 v~~g~Gia~lp~~~~~~---~~~lv~i~~~~~~~~~~~~lv~~~~~~~~~~~~~f~d~l 290 (299) +..|.|++++|..++++ .++++.+ ...+...-.+|+++.+++...|++++..|.- T Consensus 232 a~~G~Gva~~P~~v~~d~~~~~~l~~~-g~~~~v~e~fyAIt~~R~~~hP~v~~i~~~~ 289 (296) T PRK11062 232 GAYHDAIFVAPSIYAQDIYADHSVVEI-GRVENVKEEYHVIFAERMIQHPAVQRICNTD 289 (296) T ss_pred HHHCCCEEECCHHHHHHHHHCCCCEEE-CCCCCCEEEEEEEECCCCCCCHHHHHHHHHH T ss_conf 981998898789999999857991894-4578842679998504468986999999999 No 34 >TIGR02424 TF_pcaQ pca operon transcription factor PcaQ; InterPro: IPR012787 Members of this family are LysR-family transcription factors associated with operons for catabolism of protocatechuate . Members occur only in proteobacteria.; GO: 0003677 DNA binding, 0016563 transcription activator activity, 0019619 protocatechuate catabolic process, 0045941 positive regulation of transcription. Probab=100.00 E-value=0 Score=297.14 Aligned_cols=292 Identities=18% Similarity=0.194 Sum_probs=254.2 Q ss_pred CCCHHHHHHHHHHHHHCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEECCCCEEEEECCCCCCCCCCCCCCCCCHHH Q ss_conf 88889999999999827689999882899789999999999995882179769946850013433222222222210122 Q gi|254780282|r 2 SFDWDKLRVFYVVARSGSFTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHARGLTLTEQGSKLHRVTSEVYHKLETTQ 81 (299) Q Consensus 2 ~md~~~L~~f~~v~~~gs~s~AA~~L~itq~avS~~i~~LE~~lg~~Lf~R~~~~~~lT~~G~~l~~~a~~~l~~~~~~~ 81 (299) ++.+|||+.|++|++.||+++||+.|+||||||||.||+||+-+|.+||+|+++|++||++|+.|+++|..-+..+.+.. T Consensus 2 r~KfRHL~~FvEVAR~~Sv~rAae~L~~tQPAvsKTlrELE~~LG~~L~eR~~~GiRlT~~G~~Fl~hAg~Sl~ALR~Gv 81 (300) T TIGR02424 2 RIKFRHLECFVEVARQGSVKRAAEALHITQPAVSKTLRELEEILGTPLLERDRRGIRLTRYGEVFLRHAGASLAALRQGV 81 (300) T ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHCCCCCEEECCCCCCCCCCCHHHHHHHHHHHHHHHHHH T ss_conf 63188899999999988999999862488107889999999872974511478635637221154666658999998658 Q ss_pred HHCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCCCCCCCC---CCCCCCCCCCCCC-CCCCCCCCCCCCC Q ss_conf 10012232222223332111000000000135667542000122222222---2222222222223-4565432111122 Q gi|254780282|r 82 IELQESSVKPSGKLRIATTIDLGQNLLQGNLKEFLLLYPDIQIQLILDNK---DIDISMDYADCAI-RLRKPIQSSSLIQ 157 (299) Q Consensus 82 ~~~~~~~~~~~g~i~I~~~~~~~~~~l~~~l~~f~~~~P~i~i~i~~~~~---~~~l~~~~~Di~i-~~~~~~~~~~l~~ 157 (299) +.+++......-+++||+-||.+..++|..+++|.+++|+..+.|.++.. ...|..|++|++| +.+.|..-.++.+ T Consensus 82 ~~l~~lg~~~~~~~~~GaLPTVaA~L~P~~~~~f~~~~p~~~~~i~tG~n~~Lld~LR~G~LDlVvGRL~ape~MqGl~F 161 (300) T TIGR02424 82 ASLSQLGEGEGPTVRVGALPTVAARLMPEVVKRFLAEAPRLRLRIVTGENAYLLDQLRVGELDLVVGRLGAPETMQGLSF 161 (300) T ss_pred HHHHHHHHCCCCEEEECCCHHHHHHHHHHHHHHHHHHCCCCEEEEEECCCHHHHHHHCCCCCEEEEECCCCCHHHCCCCC T ss_conf 99998421489648972646689999999999999616895589987785787987228980277606888321158642 Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCCCCCCCEEEECCCCHHHHHHHH Q ss_conf 34555433211234432111222222110001123566433211000235665202234321211453242001356787 Q gi|254780282|r 158 RKLVTIHMHAYAAPHYLKNCREPLSIQELDKHNLITFGDLIPKCMEDFNWLATVDRPIGEPRISCLQVNSYLSIMQYCVL 237 (299) Q Consensus 158 ~~l~~~~~~~v~~~~~~~~~~~~~~~~dL~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~v~~ 237 (299) ++||.|++.+|+.++||+.....+..+.|.+||.+.+..+..-..-..+++..++..... ..+++=|...-.+++.+ T Consensus 162 e~LY~E~v~~VVragHPL~~~p~~~~~~L~~yPvl~P~~g~~IR~~~erll~a~G~~~l~---~r~EtvS~~fgR~y~~~ 238 (300) T TIGR02424 162 EHLYNERVVFVVRAGHPLLAAPSLSVASLADYPVLLPPEGSIIRPLVERLLIACGIPALP---QRIETVSDSFGRRYVRE 238 (300) T ss_pred CCCCCCCEEEEECCCCCCCCCCCCCHHHHHCCCCCCCCCHHHHHHHHHHHHHHCCCCCCC---CHHHHHHHHHHHHHHHH T ss_conf 514477337887085785578877778873388104862226799999999874765566---01344315788777645 Q ss_pred HCCEEEEEHHHHCC---CCCEEEECCCCCCCCCEEEEEECCCCCCCHHHHHHHHHHHHHHHC Q ss_conf 38423311777601---998466177666766008999348778888999999999999850 Q gi|254780282|r 238 GSGIALLPDYIVKD---NPNLVRIMEDVITPSFTVYFCYPEALKNTGKLKAFRNFIFLKARD 296 (299) Q Consensus 238 g~Gia~lp~~~~~~---~~~lv~i~~~~~~~~~~~~lv~~~~~~~~~~~~~f~d~l~~~~r~ 296 (299) ...|=|+|...+.. +|+|+++.-+.....-+++|+.|.+...|++.+.|++.|.+.+.+ T Consensus 239 sdA~WiiS~gvv~~dl~~G~L~~Lp~~~~~t~GPVGL~~R~d~~~s~aaq~f~~alr~~~~~ 300 (300) T TIGR02424 239 SDAVWIISEGVVAKDLADGTLVELPVDTRETAGPVGLCTRPDEQLSRAAQLFVDALRSAAEA 300 (300) T ss_pred CCCEEECCHHHHHHHHCCCCEEECCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHCC T ss_conf 47257726678988752892776465757788770215488877898999999999998519 No 35 >TIGR02036 dsdC D-serine deaminase transcriptional activator; InterPro: IPR011781 This family, part of the LysR family of transcriptional regulators, activates transcription of the gene for D-serine deaminase, dsdA. Trusted members of this family so far are found adjacent to dsdA and only in Gammaproteobacteria, including Escherichia coli, Vibrio cholerae, and Colwellia psychrerythraea.. Probab=100.00 E-value=0 Score=292.53 Aligned_cols=288 Identities=23% Similarity=0.327 Sum_probs=244.0 Q ss_pred CCHHHHHHHHHHHHHCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEECCCCEEEEECCCCCCCCCCCCCCCCCHHHH Q ss_conf 88899999999998276899998828997899999999999958821797699468500134332222222222101221 Q gi|254780282|r 3 FDWDKLRVFYVVARSGSFTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHARGLTLTEQGSKLHRVTSEVYHKLETTQI 82 (299) Q Consensus 3 md~~~L~~f~~v~~~gs~s~AA~~L~itq~avS~~i~~LE~~lg~~Lf~R~~~~~~lT~~G~~l~~~a~~~l~~~~~~~~ 82 (299) ..|-.|.+|.+.|||.||+-||++|.+||||||.||.+||+|||.+||+|+.|+++||.+|+++|-..+.-++.++|=.- T Consensus 8 fQLSKmHTFEVAARH~SFsLAAeELSltPSAiSHRIN~LEeElGI~LF~RsHRKveLT~EG~RiY~alkssl~~LNQEIl 87 (302) T TIGR02036 8 FQLSKMHTFEVAARHQSFSLAAEELSLTPSAISHRINKLEEELGIKLFKRSHRKVELTKEGKRIYIALKSSLDSLNQEIL 87 (302) T ss_pred HHHHHHHHHHHHHHHCCHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHCCCCCCEEEECCCCCCHHHHHHHHHHHHCCEEE T ss_conf 32335667888875133778887531673457775443356521442033565256446774046677876543141210 Q ss_pred HCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC Q ss_conf 00122322222233321110000000001356675420001222222222222222222223456543211112234555 Q gi|254780282|r 83 ELQESSVKPSGKLRIATTIDLGQNLLQGNLKEFLLLYPDIQIQLILDNKDIDISMDYADCAIRLRKPIQSSSLIQRKLVT 162 (299) Q Consensus 83 ~~~~~~~~~~g~i~I~~~~~~~~~~l~~~l~~f~~~~P~i~i~i~~~~~~~~l~~~~~Di~i~~~~~~~~~~l~~~~l~~ 162 (299) +++ .+..+|.|+|..=|+|++-||.|.|.+|.++||.|.+++.+++..+.+...++|+||.+ +...++.|.++.|.+ T Consensus 88 diK--n~E~SG~LT~YSRPSfAQCWLVPri~~F~~~YPsIsL~~LTGNeNinfqg~GIDvAIYF-Dd~~p~kL~c~~im~ 164 (302) T TIGR02036 88 DIK--NQELSGELTVYSRPSFAQCWLVPRIADFKKRYPSISLKVLTGNENINFQGAGIDVAIYF-DDKQPAKLSCKEIMD 164 (302) T ss_pred HHC--CCCCCCCEEECCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCCCCEECCCCCCEEEEEE-CCCCCCCCCHHHHCC T ss_conf 002--67512102002255333443323232120038712211001535320135750378870-788874212012124 Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC---CCCCCCHHHHHHHHCCCCCCCCCCEEEECCCCHHHHHHHHHC Q ss_conf 43321123443211122222211000112356643---321100023566520223432121145324200135678738 Q gi|254780282|r 163 IHMHAYAAPHYLKNCREPLSIQELDKHNLITFGDL---IPKCMEDFNWLATVDRPIGEPRISCLQVNSYLSIMQYCVLGS 239 (299) Q Consensus 163 ~~~~~v~~~~~~~~~~~~~~~~dL~~~~~i~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~v~~g~ 239 (299) |.+++||+|.|..+..-.-++..|.+..++.=... .+....|..|......+ ..+....+.+|-.+.++=++..+. T Consensus 165 E~I~PVCsPEYAq~~~L~~~~~NL~~cTLLHDnQAW~ydS~tDEW~~WAn~~~~n-~L~~ss~IgFDRSDLAVIAA~Nna 243 (302) T TIGR02036 165 ETIVPVCSPEYAQKYALTSKVDNLSQCTLLHDNQAWSYDSDTDEWKSWANAYAVN-NLESSSSIGFDRSDLAVIAAMNNA 243 (302) T ss_pred CCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHH-HHHHHCCCCCCHHHHHHHHHHHHC T ss_conf 3313434813555553654456765211100012037888854789888632132-113222367654479999998504 Q ss_pred CEEEEEHHHHCC---CCCEEEECCCC-CCCCCEEEEEECCCCCCCHHHHHHHHHHHHHHH Q ss_conf 423311777601---99846617766-676600899934877888899999999999985 Q gi|254780282|r 240 GIALLPDYIVKD---NPNLVRIMEDV-ITPSFTVYFCYPEALKNTGKLKAFRNFIFLKAR 295 (299) Q Consensus 240 Gia~lp~~~~~~---~~~lv~i~~~~-~~~~~~~~lv~~~~~~~~~~~~~f~d~l~~~~r 295 (299) |||.--..+++. .|+|++++++. ....-.||+.+.++++.+ +++.|++||.++++ T Consensus 244 GvAMGR~slv~~rl~sGEL~~Pf~d~~v~C~QrYYvaTLPn~~n~-KielFI~WL~~qVk 302 (302) T TIGR02036 244 GVAMGRKSLVKKRLASGELVKPFIDKKVLCKQRYYVATLPNKKNT-KIELFIEWLKEQVK 302 (302) T ss_pred CHHCCHHHHHHHHHCCCCCCCCCCCCEEEECCCEEEECCCCCCCC-HHHHHHHHHHHHCC T ss_conf 411023789886521675326778865562563067408888770-57888799996349 No 36 >PRK11482 putative DNA-binding transcriptional regulator; Provisional Probab=100.00 E-value=6.3e-39 Score=244.90 Aligned_cols=260 Identities=17% Similarity=0.092 Sum_probs=207.0 Q ss_pred HHCCCHHHHHHHHHHHHHHHCCEEEEECCCCEEEEECCCCCCCCCCCCCCCCCHHHHHCCCCCCCCCCCCCCCCCCCCCC Q ss_conf 82899789999999999995882179769946850013433222222222210122100122322222233321110000 Q gi|254780282|r 26 QLHLSQSSISRQISGLETEVGIKLFYRHARGLTLTEQGSKLHRVTSEVYHKLETTQIELQESSVKPSGKLRIATTIDLGQ 105 (299) Q Consensus 26 ~L~itq~avS~~i~~LE~~lg~~Lf~R~~~~~~lT~~G~~l~~~a~~~l~~~~~~~~~~~~~~~~~~g~i~I~~~~~~~~ 105 (299) .||+||||||++|++||+.||++||+|+|+|++||+.|+.|++.+++.++.+.+..+...... .+++++|++++.+.. T Consensus 1 ~L~lSQsAvS~aL~rLR~~~~DpLFvR~g~g~~PT~~A~~L~~~i~~~l~~i~~~l~~~~~~~--~~~~~~i~~~~~~~~ 78 (266) T PRK11482 1 ILNLTPSAISQSIQKLRVIFPDPLFIRKGQGVTPTAYATHLHEYISQGLESILGALDITGSYD--KQRTITIATTPSVGA 78 (266) T ss_pred CCCCCHHHHHHHHHHHHHHHCCCEEEECCCCCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCCC--CCEEEEEEECHHHHH T ss_conf 987687999999999999869950786499726648999999999999999998741568888--652599997588999 Q ss_pred CCCCCHHHHHHHHHHCCCCCCCC-CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC Q ss_conf 00000135667542000122222-22222222222222234565432111122345554332112344321112222221 Q gi|254780282|r 106 NLLQGNLKEFLLLYPDIQIQLIL-DNKDIDISMDYADCAIRLRKPIQSSSLIQRKLVTIHMHAYAAPHYLKNCREPLSIQ 184 (299) Q Consensus 106 ~~l~~~l~~f~~~~P~i~i~i~~-~~~~~~l~~~~~Di~i~~~~~~~~~~l~~~~l~~~~~~~v~~~~~~~~~~~~~~~~ 184 (299) .++|.++..+.+.+|++.++... ++....|..|++|++|.... ..++++..+.|++++++++|+++||... .+++++ T Consensus 79 ~~lp~l~~~l~~~aP~i~l~~~~~~~~~~~L~~~~~Dl~i~~~~-~~~~~~~~~~L~~d~~v~v~~~~HP~~~-~~~t~e 156 (266) T PRK11482 79 LVLPVIYQAIKPHYPQLLLRNIPISDAENQLSQFQTDLIIDTHS-CTNRTIQHHVLFTDNMVLVCRQGHPCLS-LEDDEE 156 (266) T ss_pred HHHHHHHHHHHHHCCCEEEEECCCCCHHHHHHCCCCCEEEECCC-CCCCCEEEEEEEECCEEEEEECCCCCCC-CCCCHH T ss_conf 99999999999779986999568657889985699888985688-8987638999994288999989685569-999999 Q ss_pred CCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCCCCCCCEEEECCCCHHHHHHHHHCCEEEEEHHHHCC---CCCEEEEC-C Q ss_conf 1000112356643321100023566520223432121145324200135678738423311777601---99846617-7 Q gi|254780282|r 185 ELDKHNLITFGDLIPKCMEDFNWLATVDRPIGEPRISCLQVNSYLSIMQYCVLGSGIALLPDYIVKD---NPNLVRIM-E 260 (299) Q Consensus 185 dL~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~v~~g~Gia~lp~~~~~~---~~~lv~i~-~ 260 (299) ++..++++.+........ .........+..+...++++++.++..++.....|+++|..+++. ...++.+. | T Consensus 157 ~~~~~~Hv~~~~~~~~~~----~~~~~l~~~~~~R~i~~~~~~~~~~~~lv~~tdli~~~P~~la~~~~~~~~L~~lp~p 232 (266) T PRK11482 157 TLDNAAHTLLLPEGQNFS----GLRQRLQEMFPDRQISFSSYNILTIAALIASSDMLGLMPSRFYNLFSRCWPLEKLPFP 232 (266) T ss_pred HHHCCCCEEEECCCCCCC----HHHHHHHHCCCCCEEEEEECCHHHHHHHHHHCCEEEEHHHHHHHHHHHHCCCEEECCC T ss_conf 996299999976999877----9999999749998599997999999999984999985899999998876798794689 Q ss_pred CCCCCCCEEEEEECCCCCCCHHHHHHHHHHHHH Q ss_conf 666766008999348778888999999999999 Q gi|254780282|r 261 DVITPSFTVYFCYPEALKNTGKLKAFRNFIFLK 293 (299) Q Consensus 261 ~~~~~~~~~~lv~~~~~~~~~~~~~f~d~l~~~ 293 (299) +...+..+++++||++...+|+.++|+|.+.+. T Consensus 233 p~~~~~~~~~l~Wh~r~~~DP~~~wlr~~i~e~ 265 (266) T PRK11482 233 SLNEEQIDFSLHYNKLSLRDPVLENVIDVIREA 265 (266) T ss_pred CCCCCCEEEEEEECCCCCCCCHHHHHHHHHHHH T ss_conf 988996469999885542676899999999986 No 37 >PRK10216 DNA-binding transcriptional regulator YidZ; Provisional Probab=100.00 E-value=8.5e-33 Score=209.39 Aligned_cols=264 Identities=13% Similarity=0.052 Sum_probs=194.6 Q ss_pred HCCCHHHHHHHHHHHHHHHCCEEEEECCCCEEEEECCCCCCCCCCCCCCCCCHHHHHCCCCCCCCCCCCCCCCCCCCCCC Q ss_conf 28997899999999999958821797699468500134332222222222101221001223222222333211100000 Q gi|254780282|r 27 LHLSQSSISRQISGLETEVGIKLFYRHARGLTLTEQGSKLHRVTSEVYHKLETTQIELQESSVKPSGKLRIATTIDLGQN 106 (299) Q Consensus 27 L~itq~avS~~i~~LE~~lg~~Lf~R~~~~~~lT~~G~~l~~~a~~~l~~~~~~~~~~~~~~~~~~g~i~I~~~~~~~~~ 106 (299) ||+||||||+.+++|++.||++||+|+|+|++||+.++.|.+.++++++.++++......... ...+++|+++..+... T Consensus 1 L~lSQpAvS~aL~RLR~~f~DpLFvR~g~gm~PT~~A~~L~~~l~~~L~~~~~~~~~~~~~~p-~~~~F~ia~~d~~~~~ 79 (288) T PRK10216 1 MNVTPSAVSKSLAKLRAWFDDPLFVNTPLGLSPTPLMVSMEQNLADWMQMGNQLLDKPHHQTP-RGLKFELAAESPLMMI 79 (288) T ss_pred CCCCHHHHHHHHHHHHHHHCCCEEEECCCCCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCC-CCCEEEEEECCHHHHH T ss_conf 998778999999999998799448960992315668999999999999999997378878985-5707999963678999 Q ss_pred CCCCHHHHHHHHHHCCCCCCCCC--CCCCCCCCCCCCCCCCCCCCCC---------CCCCCCCCCCCCCCCCCCCCCCCC Q ss_conf 00001356675420001222222--2222222222222234565432---------111122345554332112344321 Q gi|254780282|r 107 LLQGNLKEFLLLYPDIQIQLILD--NKDIDISMDYADCAIRLRKPIQ---------SSSLIQRKLVTIHMHAYAAPHYLK 175 (299) Q Consensus 107 ~l~~~l~~f~~~~P~i~i~i~~~--~~~~~l~~~~~Di~i~~~~~~~---------~~~l~~~~l~~~~~~~v~~~~~~~ 175 (299) ++|+++..+.++.|++.+++... +....|..|++|++|......+ +..+..+.++++.++++++++||. T Consensus 80 llp~l~~~i~~~AP~v~l~~~~~~~~~~~~L~~g~iDl~i~~~~~~p~~~~~~~~~p~~~~~~~l~~d~~~v~~r~~HP~ 159 (288) T PRK10216 80 MLNALSQQIYQRYPQATIKLRNWDYDSLDAITRGEVDIGFTGRESHPRSRELLSLLPLAIDFEVLFSDLPCVWLRKDHPA 159 (288) T ss_pred HHHHHHHHHHHHCCCCEEEEECCCCCHHHHHHCCCCCEEEECCCCCCCCHHHHHCCCCCCCEEEEEEEEEEEEECCCCCC T ss_conf 99999999997699977996248935599997599768983565686304555127643431799960069998089943 Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCCCCCCCEEEECCCCHHHHHHHHHC--CEEEEEHHHHC--- Q ss_conf 1122222211000112356643321100023566520223432121145324200135678738--42331177760--- Q gi|254780282|r 176 NCREPLSIQELDKHNLITFGDLIPKCMEDFNWLATVDRPIGEPRISCLQVNSYLSIMQYCVLGS--GIALLPDYIVK--- 250 (299) Q Consensus 176 ~~~~~~~~~dL~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~v~~g~--Gia~lp~~~~~--- 250 (299) .. ..++++++..++.+........... ........+..+...++++++.+...++.... .++.+|.+..+ T Consensus 160 ~~-~~ltle~y~~~~Hv~v~~~~~~~~~----~d~~L~~~g~~R~i~~~~~~f~~~~~~~~~~~~~li~t~p~~a~~~~~ 234 (288) T PRK10216 160 LH-EEWNLDTFLRYPHISICWEQSDTWA----LDDVLQELGRERTIALSLPGFEQSLFMAAQPDHLLLATAPRYCQHYNQ 234 (288) T ss_pred CC-CCCCHHHHHHCCCEEEECCCCCCCH----HHHHHHHCCCCCCEEEEECCHHHHHHHHHCCCCCEEEECHHHHHHHHH T ss_conf 46-8989999975898698448888762----799999739865179994988988999956898499810999999987 Q ss_pred C-CCCEEEECCCCCC-----CCCEEEEEECCCCCCCHHHHHHHHHHHHHHHC Q ss_conf 1-9984661776667-----66008999348778888999999999999850 Q gi|254780282|r 251 D-NPNLVRIMEDVIT-----PSFTVYFCYPEALKNTGKLKAFRNFIFLKARD 296 (299) Q Consensus 251 ~-~~~lv~i~~~~~~-----~~~~~~lv~~~~~~~~~~~~~f~d~l~~~~r~ 296 (299) . ...++....+... ...+++++||++...+|+.+++.+-|.+-..+ T Consensus 235 ~~~~~l~~~plP~~~~~~~~~~~~~~l~WH~r~~~dp~h~WLRe~I~~l~a~ 286 (288) T PRK10216 235 LHQLPLVARPLPFDESQQEKLEVPFTLLWHKRNSHNPKIVWLRETIKNLYAS 286 (288) T ss_pred HCCCCEEECCCCCCCCCCCCCCCEEEEECCCCCCCCHHHHHHHHHHHHHHHH T ss_conf 6489957608998874444566338997699887998999999999999985 No 38 >pfam03466 LysR_substrate LysR substrate binding domain. The structure of this domain is known and is similar to the periplasmic binding proteins. Probab=99.97 E-value=3.7e-31 Score=199.92 Aligned_cols=201 Identities=24% Similarity=0.258 Sum_probs=168.0 Q ss_pred CCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCCCCCCCC--CC-CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC Q ss_conf 2222223332111000000000135667542000122222222--22-22222222223456543211112234555433 Q gi|254780282|r 89 VKPSGKLRIATTIDLGQNLLQGNLKEFLLLYPDIQIQLILDNK--DI-DISMDYADCAIRLRKPIQSSSLIQRKLVTIHM 165 (299) Q Consensus 89 ~~~~g~i~I~~~~~~~~~~l~~~l~~f~~~~P~i~i~i~~~~~--~~-~l~~~~~Di~i~~~~~~~~~~l~~~~l~~~~~ 165 (299) .+.+|+||||++++++..++|+.|.+|+++||+|+|++...+. .. .+..|++|+||.... ...+++...+|+++++ T Consensus 2 ~~~~G~i~I~~~~~~~~~~lp~~l~~f~~~~P~i~i~i~~~~~~~i~~~l~~g~~Di~i~~~~-~~~~~~~~~~l~~~~~ 80 (209) T pfam03466 2 GGPRGRLRIGAPPTFAAYLLPPLLARFRERYPDVELELREGDSEELLDLLAEGELDLAIRRGP-PDDPGLEARPLFEEPL 80 (209) T ss_pred CCCCEEEEEEEEHHHHHHHHHHHHHHHHHHCCCCEEEEEECCCHHHHHHHHCCCCEEEEECCC-CCCCCEEEEEEEEEEE T ss_conf 998789999938899999999999999998889289999898488999998698148873178-9999808999762413 Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCCCCCCCEEEECCCCHHHHHHHHHCCEEEEE Q ss_conf 21123443211122222211000112356643321100023566520223432121145324200135678738423311 Q gi|254780282|r 166 HAYAAPHYLKNCREPLSIQELDKHNLITFGDLIPKCMEDFNWLATVDRPIGEPRISCLQVNSYLSIMQYCVLGSGIALLP 245 (299) Q Consensus 166 ~~v~~~~~~~~~~~~~~~~dL~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~v~~g~Gia~lp 245 (299) +++|+++|+...+.+++++||.++++|.+............++ ...+......+++++..++.++|..|.|++++| T Consensus 81 ~~~~s~~~~l~~~~~i~~~~l~~~~~i~~~~~~~~~~~~~~~~----~~~~~~~~~~~~~~~~~~~~~lv~~g~Gi~~lp 156 (209) T pfam03466 81 VLVAPPDHPLAAGEPVSLEDLADEPLILLEPGSGLRDLVDRAL----ERAGLRPRVALEVNSLEALLAAVAAGLGIALLP 156 (209) T ss_pred EEEECCCCHHHCCCCCCHHHHCCCCEEEECCCCCCHHHHHHHH----HHCCCCCCEEEEECCHHHHHHHHHHCCEEEECC T ss_conf 6553367055428975435514665798569987137998778----764876302467478799999999499999913 Q ss_pred HHHHCC---CCCEEEECCCCCCCCCEEEEEECCCCCCCHHHHHHHHHHHHHH Q ss_conf 777601---9984661776667660089993487788889999999999998 Q gi|254780282|r 246 DYIVKD---NPNLVRIMEDVITPSFTVYFCYPEALKNTGKLKAFRNFIFLKA 294 (299) Q Consensus 246 ~~~~~~---~~~lv~i~~~~~~~~~~~~lv~~~~~~~~~~~~~f~d~l~~~~ 294 (299) .+++++ +++++.+......+.+.+|++|++++.++++++.|++|+.++. T Consensus 157 ~~~~~~~~~~~~L~~i~~~~~~~~~~~~li~~~~~~~s~~~~~f~~~l~e~~ 208 (209) T pfam03466 157 RSAVARELADGRLVVLPLPDPPLPRPIYLVYRKGRRLSPAVRAFIDFLREAL 208 (209) T ss_pred HHHHHHHHHCCCEEEEECCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHC T ss_conf 9999988758998999588888744799999894978999999999999963 No 39 >pfam00126 HTH_1 Bacterial regulatory helix-turn-helix protein, lysR family. Probab=99.78 E-value=4.3e-19 Score=129.98 Aligned_cols=60 Identities=57% Similarity=0.801 Sum_probs=58.6 Q ss_pred HHHHHHHHHHHHHCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEECCCCEEEEECCC Q ss_conf 899999999998276899998828997899999999999958821797699468500134 Q gi|254780282|r 5 WDKLRVFYVVARSGSFTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHARGLTLTEQGS 64 (299) Q Consensus 5 ~~~L~~f~~v~~~gs~s~AA~~L~itq~avS~~i~~LE~~lg~~Lf~R~~~~~~lT~~G~ 64 (299) +++|++|++++++|||++||+.|++|||+||++|++||+++|++||+|+++++.||++|+ T Consensus 1 l~~l~~f~~v~~~gs~~~AA~~l~isqs~vs~~i~~LE~~lg~~Lf~R~~~~~~lT~~G~ 60 (60) T pfam00126 1 LRQLRVFVAVAEEGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGLRLTPAGE 60 (60) T ss_pred CHHHHHHHHHHHCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEECCCCEEECCCCC T ss_conf 977999999998099999999979898899999999999959970788899742893749 No 40 >PRK10676 DNA-binding transcriptional regulator ModE; Provisional Probab=98.42 E-value=2.9e-07 Score=61.47 Aligned_cols=74 Identities=20% Similarity=0.205 Sum_probs=63.0 Q ss_pred HHHHHHHHHHHHHCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEEC-----CCCEEEEECCCCCCCCCCCCCCCCC Q ss_conf 8999999999982768999988289978999999999999588217976-----9946850013433222222222210 Q gi|254780282|r 5 WDKLRVFYVVARSGSFTHAAEQLHLSQSSISRQISGLETEVGIKLFYRH-----ARGLTLTEQGSKLHRVTSEVYHKLE 78 (299) Q Consensus 5 ~~~L~~f~~v~~~gs~s~AA~~L~itq~avS~~i~~LE~~lg~~Lf~R~-----~~~~~lT~~G~~l~~~a~~~l~~~~ 78 (299) -+.++.+.++.++||+++||+.+++|=-+-...|..+++.++.||+.|. |+|-.||++|+.+++.-+.+-...+ T Consensus 19 ~~ri~LL~~I~~~gSIs~Aak~~g~SYk~AW~~i~~~n~~~~~plv~~~~GG~~Ggg~~lT~~G~~li~~y~~l~~~~~ 97 (262) T PRK10676 19 PRRISLLKQIALSGSISQGAKDAGISYKSAWDAINEMNQLSEHILVERATGGKGGGGAVLTRYGQRLIQLYDLLAQIQQ 97 (262) T ss_pred CCHHHHHHHHHHHCCHHHHHHHCCCCHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCCEECHHHHHHHHHHHHHHHHHH T ss_conf 6789999999874999999998199699999999999754679779974599999886875789999999999999999 No 41 >COG2005 ModE N-terminal domain of molybdenum-binding protein [General function prediction only] Probab=98.30 E-value=7.7e-07 Score=59.00 Aligned_cols=83 Identities=23% Similarity=0.266 Sum_probs=69.1 Q ss_pred CCHHHHHHHHHHHHHCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEECC-----CCEEEEECCCCCCCCCCCCCCCC Q ss_conf 8889999999999827689999882899789999999999995882179769-----94685001343322222222221 Q gi|254780282|r 3 FDWDKLRVFYVVARSGSFTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHA-----RGLTLTEQGSKLHRVTSEVYHKL 77 (299) Q Consensus 3 md~~~L~~f~~v~~~gs~s~AA~~L~itq~avS~~i~~LE~~lg~~Lf~R~~-----~~~~lT~~G~~l~~~a~~~l~~~ 77 (299) ++-.-.+.+.++.++||+|+||+.+++|=-..-..|+.+|+-+|.+|+++.. .|-.||+.|+.+++.-+.+-..+ T Consensus 17 ~g~g~~~LL~~I~etGSIs~AAk~~GiSYk~AW~~i~~~n~~~~~plVe~~rGGk~gGga~LT~~g~~ll~~y~~l~~~~ 96 (130) T COG2005 17 AGPGRIELLKAIAETGSISAAAKAAGISYKSAWDYIKALNRLLGEPLVERRRGGKGGGGAVLTDFGERLLEEYRLLEKEI 96 (130) T ss_pred CCCHHHHHHHHHHHHCCHHHHHHHCCCCHHHHHHHHHHHHHHHCCCEEEECCCCCCCCCCHHHHHHHHHHHHHHHHHHHH T ss_conf 48369999999999688999999849977999999999999838870663357788885113799999999999999999 Q ss_pred CHHHHHCC Q ss_conf 01221001 Q gi|254780282|r 78 ETTQIELQ 85 (299) Q Consensus 78 ~~~~~~~~ 85 (299) +....... T Consensus 97 ~~~~~~~~ 104 (130) T COG2005 97 EEALRKLE 104 (130) T ss_pred HHHHHHHH T ss_conf 99998874 No 42 >PRK11050 manganese transport regulator MntR; Provisional Probab=97.45 E-value=0.0001 Score=46.69 Aligned_cols=73 Identities=22% Similarity=0.273 Sum_probs=55.3 Q ss_pred HHHHHHHHHHHHCCHHHH---HHHHCCCHHHHHHHHHHHHHHHCCEEEEECC-CCEEEEECCCCCCCCCCCCCCCCCHHH Q ss_conf 999999999982768999---9882899789999999999995882179769-946850013433222222222210122 Q gi|254780282|r 6 DKLRVFYVVARSGSFTHA---AEQLHLSQSSISRQISGLETEVGIKLFYRHA-RGLTLTEQGSKLHRVTSEVYHKLETTQ 81 (299) Q Consensus 6 ~~L~~f~~v~~~gs~s~A---A~~L~itq~avS~~i~~LE~~lg~~Lf~R~~-~~~~lT~~G~~l~~~a~~~l~~~~~~~ 81 (299) +-|+.++.+.+.+...+. |++||||+|+||+.|++|++. -|+...+ +++.||+.|+.+...+..=-..++.+. T Consensus 40 DYlE~I~~L~~~~G~aR~~DIA~~LgVs~pSVt~mlkrL~~~---GlV~~~~Y~~I~LT~~G~~~A~~i~~RHrile~FL 116 (155) T PRK11050 40 DYVELIADLIAEVGEARQVDIAARLGVSQPTVAKMLKRLARD---GLVEMRPYRGVFLTPEGEKLAQESRERHQIVENFL 116 (155) T ss_pred HHHHHHHHHHHCCCCEEHHHHHHHHCCCCHHHHHHHHHHHHC---CCEEECCCCCEEECHHHHHHHHHHHHHHHHHHHHH T ss_conf 999999999982695649999989099933199999999878---99887189884689779999999999999999999 No 43 >smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein. Probab=97.32 E-value=0.00033 Score=43.70 Aligned_cols=75 Identities=25% Similarity=0.328 Sum_probs=60.7 Q ss_pred CCCHHHHHHHHHHHHHC--CHHHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEECC-------CCEEEEECCCCCCCCCCC Q ss_conf 88889999999999827--689999882899789999999999995882179769-------946850013433222222 Q gi|254780282|r 2 SFDWDKLRVFYVVARSG--SFTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHA-------RGLTLTEQGSKLHRVTSE 72 (299) Q Consensus 2 ~md~~~L~~f~~v~~~g--s~s~AA~~L~itq~avS~~i~~LE~~lg~~Lf~R~~-------~~~~lT~~G~~l~~~a~~ 72 (299) +++..++.++..+++.+ +.+.=|+.+++++|+||+.|++||+. -|+.|.. ..+.||+.|+.+++.+.. T Consensus 7 glt~~q~~vL~~l~~~~~~t~~~la~~l~~~~~~vs~~v~~L~~~---glv~r~~~~~D~R~~~i~LT~~G~~~~~~~~~ 83 (101) T smart00347 7 GLTPTQFLVLRILYEEGPLSVSELAKRLGVSPSTVTRVLDRLEKK---GLIRRLPSPEDRRSVLVSLTEEGRELIEELLE 83 (101) T ss_pred CCCHHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHHCC---CCEEEEECCCCCCEEEEEECHHHHHHHHHHHH T ss_conf 949999999999997699799999999896887999999999458---93898218999885898999899999999999 Q ss_pred CCCCCCH Q ss_conf 2222101 Q gi|254780282|r 73 VYHKLET 79 (299) Q Consensus 73 ~l~~~~~ 79 (299) ......+ T Consensus 84 ~~~~~~~ 90 (101) T smart00347 84 ARHETLA 90 (101) T ss_pred HHHHHHH T ss_conf 9999999 No 44 >PRK10677 modA molybdate transporter periplasmic protein; Provisional Probab=97.27 E-value=0.00075 Score=41.67 Aligned_cols=202 Identities=10% Similarity=0.050 Sum_probs=100.8 Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCCCCCCC--CC-CCCCCC-CCCCCCCCCCCCC----CCCCC--- Q ss_conf 3222222333211100000000013566754200012222222--22-222222-2222234565432----11112--- Q gi|254780282|r 88 SVKPSGKLRIATTIDLGQNLLQGNLKEFLLLYPDIQIQLILDN--KD-IDISMD-YADCAIRLRKPIQ----SSSLI--- 156 (299) Q Consensus 88 ~~~~~g~i~I~~~~~~~~~~l~~~l~~f~~~~P~i~i~i~~~~--~~-~~l~~~-~~Di~i~~~~~~~----~~~l~--- 156 (299) .....++|+|.+..++. .-+.++...|.+++ ++++++..+. .+ ..+..| .+|+-+....... ..++. T Consensus 22 ~~a~~~~l~V~aAAsL~-~~~~ei~~~Fek~~-g~~v~~~fgsSg~L~~QI~~GAp~DvF~sAd~~~~~~l~~~~~i~~~ 99 (257) T PRK10677 22 ALADEGKITVFAAASLT-NAMQDIATQYKKEK-GVDVVSSFASSSTLARQIEAGAPADLFISADQKWMDYAVDKKAIDTA 99 (257) T ss_pred CCCCCCEEEEEEECCCH-HHHHHHHHHHHHHH-CCEEEEEECCHHHHHHHHHCCCCCCEEEECCHHHHHHHHHCCCCCCC T ss_conf 32568859999925768-99999999998841-98499996648999999982899658997875778999867785677 Q ss_pred -CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC----CCCCCCC-CCCCCCCCHHHHHHHHCCCCCCCCCCEEEECCCCH Q ss_conf -23455543321123443211122222211000----1123566-43321100023566520223432121145324200 Q gi|254780282|r 157 -QRKLVTIHMHAYAAPHYLKNCREPLSIQELDK----HNLITFG-DLIPKCMEDFNWLATVDRPIGEPRISCLQVNSYLS 230 (299) Q Consensus 157 -~~~l~~~~~~~v~~~~~~~~~~~~~~~~dL~~----~~~i~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~ 230 (299) ...+....++++++++............|+.. ..+..-+ ...|.+..-...+...+.-..... .....++... T Consensus 100 ~~~~~a~n~lvli~pk~~~~~~~~i~~~~d~~~ll~~~riaia~P~~aP~G~ya~~~L~~~gl~~~l~~-klv~~~nV~~ 178 (257) T PRK10677 100 TRQTLLGNSLVVVAPKASEQKDFTIDKKTDWTSLLNGGRLAVGDPDHVPAGIYAKEALQKLGAWDTLSP-KLAPAEDVRG 178 (257) T ss_pred CEEEEECCEEEEEEECCCCCCCCCCCCCCCHHHHCCCCCEEEECCCCCCCHHHHHHHHHHCCCHHHHCC-CEEECCCHHH T ss_conf 645621474999984687778644343323777425880898588888657999999997676655065-4132576999 Q ss_pred HHHHHHHHC-CEEEEEHH--HHCCCCCEEEECCCCCCCCCEEEEEECCCCCCCHHHHHHHHHHHHH Q ss_conf 135678738-42331177--7601998466177666766008999348778888999999999999 Q gi|254780282|r 231 IMQYCVLGS-GIALLPDY--IVKDNPNLVRIMEDVITPSFTVYFCYPEALKNTGKLKAFRNFIFLK 293 (299) Q Consensus 231 ~~~~v~~g~-Gia~lp~~--~~~~~~~lv~i~~~~~~~~~~~~lv~~~~~~~~~~~~~f~d~l~~~ 293 (299) .+..|..|. -+|++-.+ ...+..+.+.+.|.....+..+.++-.++ ...+.++.|++||.+. T Consensus 179 ~l~~v~~G~adaG~Vy~Sda~~~~~~~~~~~~p~~~~~pi~y~~ai~~~-~~~~~a~~F~~fl~S~ 243 (257) T PRK10677 179 ALALVERNEAPLGIVYGSDAVASKGVKVVATFPEDSHKKVEYPMAIVEG-HNNATVSAFYDYLKGP 243 (257) T ss_pred HHHHHHCCCCCEEEEECCHHHCCCCCEEEEECCHHHCCCCEEEEEEECC-CCCHHHHHHHHHHCCH T ss_conf 9999982998789997000222688649998774538961455899759-9999999999997799 No 45 >PRK03902 manganese transport transcriptional regulator; Provisional Probab=97.19 E-value=0.00058 Score=42.31 Aligned_cols=73 Identities=23% Similarity=0.358 Sum_probs=53.2 Q ss_pred HHHHHHHHHHHHC---CHHHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEECC-CCEEEEECCCCCCCCCCCCCCCCCHHH Q ss_conf 9999999999827---689999882899789999999999995882179769-946850013433222222222210122 Q gi|254780282|r 6 DKLRVFYVVARSG---SFTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHA-RGLTLTEQGSKLHRVTSEVYHKLETTQ 81 (299) Q Consensus 6 ~~L~~f~~v~~~g---s~s~AA~~L~itq~avS~~i~~LE~~lg~~Lf~R~~-~~~~lT~~G~~l~~~a~~~l~~~~~~~ 81 (299) +-|+..+.+.+.+ +.+.=|+.|+||+|+||..|++|++. -|+...+ +++.||+.|+.+...+..=-..++.+. T Consensus 8 dYLe~Iy~L~~~~~~vr~~dIA~~L~Vs~~SVs~mikkL~~~---Glv~~~~y~~i~LT~~G~~~A~~i~~rHrlle~FL 84 (142) T PRK03902 8 DYIEQIYLLIEEKGYARVSDIAEALSVHPSSVTKMVQKLDKD---EYLIYEKYRGLVLTPKGKKIGKRLVYRHELLEQFL 84 (142) T ss_pred HHHHHHHHHHHCCCCCCHHHHHHHHCCCCHHHHHHHHHHHHC---CCCEECCCCCEEECHHHHHHHHHHHHHHHHHHHHH T ss_conf 999999999825897129999999789953399999999987---99245589875689879999999999999999999 No 46 >COG0725 ModA ABC-type molybdate transport system, periplasmic component [Inorganic ion transport and metabolism] Probab=96.92 E-value=0.0061 Score=36.41 Aligned_cols=200 Identities=12% Similarity=0.123 Sum_probs=112.3 Q ss_pred CCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCCCCCCC--CC-CCCCCC-CCCCCCCCCCCC----CCCCC----C Q ss_conf 222222333211100000000013566754200012222222--22-222222-222223456543----21111----2 Q gi|254780282|r 89 VKPSGKLRIATTIDLGQNLLQGNLKEFLLLYPDIQIQLILDN--KD-IDISMD-YADCAIRLRKPI----QSSSL----I 156 (299) Q Consensus 89 ~~~~g~i~I~~~~~~~~~~l~~~l~~f~~~~P~i~i~i~~~~--~~-~~l~~~-~~Di~i~~~~~~----~~~~l----~ 156 (299) ......++|.+..++.. -+..+...|.+++ ++++.+..+. .. ..+..| ..|+.|...... ...++ . T Consensus 26 ~~~~~~i~VfAAaSL~~-~l~~i~~~F~~~~-~~~V~~~f~gS~~l~~qIe~Ga~~D~fiSa~~~~~~~l~~~g~~~~~~ 103 (258) T COG0725 26 AQEAATITVFAAASLTD-ALEEIAKQFEKET-GVKVEVEFGGSGALARQIEQGAPADLFISADDAYMDKLEDKGLIYADS 103 (258) T ss_pred CCCCCEEEEEEEHHHHH-HHHHHHHHHHHHH-CCEEEEEECCHHHHHHHHHCCCCCCEEEECCHHHHHHHHHCCCCCCCC T ss_conf 45674099998156689-9999999999987-987999961389999999759986879988888899998668856671 Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC--CCC--CCCCCCCCCHHHHHHHHCCCCCCCCCCEEEECCCCHHH Q ss_conf 23455543321123443211122222211000112--356--64332110002356652022343212114532420013 Q gi|254780282|r 157 QRKLVTIHMHAYAAPHYLKNCREPLSIQELDKHNL--ITF--GDLIPKCMEDFNWLATVDRPIGEPRISCLQVNSYLSIM 232 (299) Q Consensus 157 ~~~l~~~~~~~v~~~~~~~~~~~~~~~~dL~~~~~--i~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~ 232 (299) ...+....++++.+++-.... ..++++...+- +.. ....|.+..-...+...+....... ......+..... T Consensus 104 ~~~fa~n~lvl~~~~~~~~~~---~~~~~l~~~~~~~lai~~p~~~P~G~ya~~~l~~~g~~~~~~~-k~v~~~~v~~~l 179 (258) T COG0725 104 RIVFAGNRLVLAVPKGSKKKI---ESLEDLLERPDVRLAIGDPKTVPAGKYAKEALELLGLWYTLKD-KLVLATNVRQAL 179 (258) T ss_pred EEEEECCEEEEEEECCCCCCC---CHHHHHHCCCCCEEEECCCCCCCCHHHHHHHHHHHCHHHHCCC-CEEECCCHHHHH T ss_conf 577425748999868874565---1298873087857996488769714999999997051453367-546536579899 Q ss_pred HHHHHHC---CEEEEEHHHHCCCCCEEEECCCCCCCCCEEEEEECCCCCCCHHHHHHHHHHHHHH Q ss_conf 5678738---4233117776019984661776667660089993487788889999999999998 Q gi|254780282|r 233 QYCVLGS---GIALLPDYIVKDNPNLVRIMEDVITPSFTVYFCYPEALKNTGKLKAFRNFIFLKA 294 (299) Q Consensus 233 ~~v~~g~---Gia~lp~~~~~~~~~lv~i~~~~~~~~~~~~lv~~~~~~~~~~~~~f~d~l~~~~ 294 (299) ..|..|. |+...++.........+..++.....+..+.+.-.++..+++.++.|++||.+.. T Consensus 180 ~~V~~G~ad~g~vy~sd~~~~~~~~~~~~~~~~~~~Pi~y~iav~~~~~~~~~A~~f~~fl~s~~ 244 (258) T COG0725 180 AYVETGEADAGFVYVSDALLSKKVKIVGVFPEDLHSPIVYPIAVLKNAKNPELAKEFVDFLLSPE 244 (258) T ss_pred HHHHCCCCCEEEEEEEHHHHCCCCEEEEECCCCCCCCEEEEEEEECCCCCHHHHHHHHHHHHCHH T ss_conf 99863787779999763340677608997356668971678999738898599999999971877 No 47 >smart00529 HTH_DTXR Helix-turn-helix diphteria tox regulatory element. iron dependent repressor Probab=96.90 E-value=0.00059 Score=42.29 Aligned_cols=61 Identities=30% Similarity=0.427 Sum_probs=47.1 Q ss_pred HHHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEECC-CCEEEEECCCCCCCCCCCCCCCCCHHHHH Q ss_conf 89999882899789999999999995882179769-94685001343322222222221012210 Q gi|254780282|r 20 FTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHA-RGLTLTEQGSKLHRVTSEVYHKLETTQIE 83 (299) Q Consensus 20 ~s~AA~~L~itq~avS~~i~~LE~~lg~~Lf~R~~-~~~~lT~~G~~l~~~a~~~l~~~~~~~~~ 83 (299) .+.=|+.|+||+|+||+.|++|++. -|+...+ +++.||+.|+.....+..--..++.+..+ T Consensus 2 ~~diA~~L~vs~~sVs~~l~~L~~~---Gli~~~~y~~i~LT~~G~~~A~~i~~rHr~le~fL~~ 63 (96) T smart00529 2 TSEIAERLNVSPPTVTQMLKKLEKD---GLVEYEPYRGITLTEKGRRLARRLLRKHRLLERFLVD 63 (96) T ss_pred HHHHHHHHCCCCHHHHHHHHHHHHC---CCEEECCCCCEEECHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 7889988499916799999999988---8988749989788987999999999999999999999 No 48 >COG1846 MarR Transcriptional regulators [Transcription] Probab=96.84 E-value=0.0017 Score=39.58 Aligned_cols=69 Identities=25% Similarity=0.312 Sum_probs=58.5 Q ss_pred CCHHHHHHHHHHHHHCCH--HHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEECC-------CCEEEEECCCCCCCCCCCC Q ss_conf 888999999999982768--9999882899789999999999995882179769-------9468500134332222222 Q gi|254780282|r 3 FDWDKLRVFYVVARSGSF--THAAEQLHLSQSSISRQISGLETEVGIKLFYRHA-------RGLTLTEQGSKLHRVTSEV 73 (299) Q Consensus 3 md~~~L~~f~~v~~~gs~--s~AA~~L~itq~avS~~i~~LE~~lg~~Lf~R~~-------~~~~lT~~G~~l~~~a~~~ 73 (299) ++..++.++..+.+.+.. +.-|+.+++++|+||+.|++||+. -|+.|.. .-+.+|+.|+.+++..... T Consensus 20 l~~~q~~~L~~l~~~~~~~~~~la~~l~~~~~~vt~~l~~Le~~---glv~r~~~~~DrR~~~l~lT~~G~~~~~~~~~~ 96 (126) T COG1846 20 LTPPQYQVLLALYEAGGITVKELAERLGLDRSTVTRLLKRLEDK---GLIERLRDPEDRRAVLVRLTEKGRELLEQLLPA 96 (126) T ss_pred CCHHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHHHC---CCEEEECCCCCCCEEEEEECHHHHHHHHHHHHH T ss_conf 99899999999998489999999999787888899999999988---993674388886312435562159999997888 Q ss_pred C Q ss_conf 2 Q gi|254780282|r 74 Y 74 (299) Q Consensus 74 l 74 (299) . T Consensus 97 ~ 97 (126) T COG1846 97 A 97 (126) T ss_pred H T ss_conf 9 No 49 >COG1321 TroR Mn-dependent transcriptional regulator [Transcription] Probab=96.78 E-value=0.0031 Score=38.09 Aligned_cols=78 Identities=24% Similarity=0.323 Sum_probs=55.5 Q ss_pred HHHHHHHHHHHHHCC---HHHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEECCCCEEEEECCCCCCCCCCCCCCCCCHHH Q ss_conf 899999999998276---89999882899789999999999995882179769946850013433222222222210122 Q gi|254780282|r 5 WDKLRVFYVVARSGS---FTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHARGLTLTEQGSKLHRVTSEVYHKLETTQ 81 (299) Q Consensus 5 ~~~L~~f~~v~~~gs---~s~AA~~L~itq~avS~~i~~LE~~lg~~Lf~R~~~~~~lT~~G~~l~~~a~~~l~~~~~~~ 81 (299) .+-|++.+.+-+.+. .+.=|+.|+|++|+||+.+++|++ .|.--+++ .+|+.||+.|+............++.+. T Consensus 9 edYL~~Iy~l~~~~~~~~~~diA~~L~Vsp~sVt~ml~rL~~-~GlV~~~~-y~gi~LT~~G~~~a~~~~r~hrlle~fL 86 (154) T COG1321 9 EDYLETIYELLEEKGFARTKDIAERLKVSPPSVTEMLKRLER-LGLVEYEP-YGGVTLTEKGREKAKELLRKHRLLERFL 86 (154) T ss_pred HHHHHHHHHHHHCCCCCCHHHHHHHHCCCCHHHHHHHHHHHH-CCCEEEEC-CCCEEECCCHHHHHHHHHHHHHHHHHHH T ss_conf 999999999984368751999999858992789999999987-89978845-8886788354899999999999999999 Q ss_pred HHC Q ss_conf 100 Q gi|254780282|r 82 IEL 84 (299) Q Consensus 82 ~~~ 84 (299) ... T Consensus 87 ~~~ 89 (154) T COG1321 87 VDV 89 (154) T ss_pred HHH T ss_conf 998 No 50 >PRK03573 transcriptional regulator SlyA; Provisional Probab=96.78 E-value=0.0023 Score=38.85 Aligned_cols=76 Identities=20% Similarity=0.245 Sum_probs=59.7 Q ss_pred CCCHHHHHHHHHHHHHC---CHHHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEECC-------CCEEEEECCCCCCCCCC Q ss_conf 88889999999999827---689999882899789999999999995882179769-------94685001343322222 Q gi|254780282|r 2 SFDWDKLRVFYVVARSG---SFTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHA-------RGLTLTEQGSKLHRVTS 71 (299) Q Consensus 2 ~md~~~L~~f~~v~~~g---s~s~AA~~L~itq~avS~~i~~LE~~lg~~Lf~R~~-------~~~~lT~~G~~l~~~a~ 71 (299) .++.-|..++..+.+.+ +-+.=|+.++|++|+|++.|++||+. -|+.|.. +.+.||+.|+.+++.+. T Consensus 28 gLt~~q~~~L~~L~~~~~g~tq~eLa~~l~v~~~t~tr~ld~LE~~---GlI~R~~~~~DrR~~~i~LT~~G~~l~~~~~ 104 (144) T PRK03573 28 ELTQTHWVTLHNIHQLPPDQSQIQLAKAIGIEQPSLVRTLDQLEEK---GLISRQTCASDRRAKRIKLTEKAEPLISEME 104 (144) T ss_pred CCCHHHHHHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHC---CCEEEECCCCCCCEEEEEECHHHHHHHHHHH T ss_conf 9982599999999973989899999999798783699999999988---8978622867675467678887999999999 Q ss_pred CCCCCCCHH Q ss_conf 222221012 Q gi|254780282|r 72 EVYHKLETT 80 (299) Q Consensus 72 ~~l~~~~~~ 80 (299) .+....++- T Consensus 105 ~~~~~~~~~ 113 (144) T PRK03573 105 AVINKTRAE 113 (144) T ss_pred HHHHHHHHH T ss_conf 999999999 No 51 >TIGR00637 ModE_repress ModE molybdate transport repressor domain; InterPro: IPR003725 Molybdenum-dependent repression of transcription of the Escherichia coli modABCD operon, which encodes the high-affinity molybdate transporter, is mediated by the ModE protein. When molybdate or tungstate bind to ModE there is little change in its alpha-helical content, but a major change in the environment of tryptophan and tyrosine residues occurs . This is the N-terminal domain of molybdenum-binding proteins ModE, ModA, MopA and MopB. These proteins are involved in molybdenum transport. ModE acts both as a repressor and activator of the mod and moa operons, respectively, depending on the properties of the binding site .; GO: 0015098 molybdate ion transmembrane transporter activity, 0015689 molybdate ion transport. Probab=96.70 E-value=0.002 Score=39.22 Aligned_cols=79 Identities=25% Similarity=0.283 Sum_probs=65.2 Q ss_pred CCHHHHHHHHHHHHHCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEEC-----CCC-EEEEECCCCCCCCCCCCCCC Q ss_conf 888999999999982768999988289978999999999999588217976-----994-68500134332222222222 Q gi|254780282|r 3 FDWDKLRVFYVVARSGSFTHAAEQLHLSQSSISRQISGLETEVGIKLFYRH-----ARG-LTLTEQGSKLHRVTSEVYHK 76 (299) Q Consensus 3 md~~~L~~f~~v~~~gs~s~AA~~L~itq~avS~~i~~LE~~lg~~Lf~R~-----~~~-~~lT~~G~~l~~~a~~~l~~ 76 (299) ++-+.++.+..+.++||++.||+..+++--+..-.|+.+++-++.+++++. +.+ ..+|+.|+.++..-..+-.. T Consensus 2 ~~~~~~~ll~~i~~~G~i~~~~~~~g~~y~~~w~~~~~~~~~~~~~~~e~~~GG~~GGgg~~lt~~g~~~~~~y~~~~~~ 81 (101) T TIGR00637 2 VGPRRVALLKAIAREGSISAAAKDAGLSYKSAWDYIKAMNNLLGEPLVEAAPGGKGGGGGAVLTEAGERLIALYGLLERA 81 (101) T ss_pred CCHHHHHHHHHHHHHCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHH T ss_conf 75477899999876120445556405616789899988887642110002578777776421217899999999999999 Q ss_pred CCHHH Q ss_conf 10122 Q gi|254780282|r 77 LETTQ 81 (299) Q Consensus 77 ~~~~~ 81 (299) .+... T Consensus 82 ~~~~~ 86 (101) T TIGR00637 82 LEKAL 86 (101) T ss_pred HHHHH T ss_conf 99875 No 52 >PRK11512 DNA-binding transcriptional repressor MarR; Provisional Probab=96.40 E-value=0.0042 Score=37.35 Aligned_cols=70 Identities=11% Similarity=0.196 Sum_probs=56.9 Q ss_pred CCCHHHHHHHHHHHHHCCH--HHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEECCC-------CEEEEECCCCCCCCCCC Q ss_conf 8888999999999982768--99998828997899999999999958821797699-------46850013433222222 Q gi|254780282|r 2 SFDWDKLRVFYVVARSGSF--THAAEQLHLSQSSISRQISGLETEVGIKLFYRHAR-------GLTLTEQGSKLHRVTSE 72 (299) Q Consensus 2 ~md~~~L~~f~~v~~~gs~--s~AA~~L~itq~avS~~i~~LE~~lg~~Lf~R~~~-------~~~lT~~G~~l~~~a~~ 72 (299) +++.-|..++.++.+.|.+ +.=|+.+++++++||+.|.+||+. -++.|.+. -+.+|+.|+.+++.+.+ T Consensus 37 gLt~~Q~~vL~~L~~~~~~t~~eLa~~l~id~~tvt~~ldrLe~~---GlI~R~~~p~DrR~~~v~LT~~G~~l~~~~~~ 113 (144) T PRK11512 37 DITAAQFKVLCSIRCAACITPVELKKVLSVDLGALTRMLDRLVCK---GWVERLPNPNDKRGVLVKLTTSGAAICEQCHQ 113 (144) T ss_pred CCCHHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHHHC---CCEEECCCCCCCCEEEEEECHHHHHHHHHHHH T ss_conf 999999999999998699799999999788887899999999978---79663579877624787889779999999999 Q ss_pred CC Q ss_conf 22 Q gi|254780282|r 73 VY 74 (299) Q Consensus 73 ~l 74 (299) .. T Consensus 114 ~~ 115 (144) T PRK11512 114 LV 115 (144) T ss_pred HH T ss_conf 99 No 53 >pfam09048 Cro Cro. Members of this family are involved in the repression of transcription by binding as a homodimer to palindromic DNA operator sites in phage lambda: they repress genes expressed in early phage development and are necessary for the late stage of lytic growth. These proteins have a secondary structure consisting of three alpha-helices and three beta-sheets, and dimerize through interactions between the two antiparallel beta-strands. Probab=96.31 E-value=0.0062 Score=36.35 Aligned_cols=45 Identities=31% Similarity=0.425 Sum_probs=35.3 Q ss_pred HHHHCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEECCCCEEEE--ECCCCCCCCCCC Q ss_conf 99827689999882899789999999999995882179769946850--013433222222 Q gi|254780282|r 14 VARSGSFTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHARGLTLT--EQGSKLHRVTSE 72 (299) Q Consensus 14 v~~~gs~s~AA~~L~itq~avS~~i~~LE~~lg~~Lf~R~~~~~~lT--~~G~~l~~~a~~ 72 (299) |.++| -.+||+.|||+|+|+|+.|+. +|.+..| +.|..-.+.++. T Consensus 9 v~~~G-Q~kaA~~lGV~Q~AISKAlra-------------gR~I~v~~~~DG~v~AeEvrp 55 (58) T pfam09048 9 VEEHG-QAKAAKDLGVNQSAISKALRA-------------GRNIEVTVYEDGSVEAEEVRP 55 (58) T ss_pred HHHHC-HHHHHHHCCCCHHHHHHHHHC-------------CCEEEEEECCCCCEEEEEEEC T ss_conf 99976-598999829758999999964-------------881799986899688888615 No 54 >PRK11169 leucine-responsive transcriptional regulator; Provisional Probab=96.08 E-value=0.0098 Score=35.21 Aligned_cols=44 Identities=14% Similarity=0.286 Sum_probs=38.2 Q ss_pred CCCCHHHHHHHHHHHHHCCHHHH--HHHHCCCHHHHHHHHHHHHHH Q ss_conf 98888999999999982768999--988289978999999999999 Q gi|254780282|r 1 MSFDWDKLRVFYVVARSGSFTHA--AEQLHLSQSSISRQISGLETE 44 (299) Q Consensus 1 m~md~~~L~~f~~v~~~gs~s~A--A~~L~itq~avS~~i~~LE~~ 44 (299) ++||--+.+.+..+-+-|..|-+ |+++|+|++||.++|++||+. T Consensus 10 ~~LD~~D~~IL~~Lq~daR~s~~eLA~~vglS~stv~~RikrLe~~ 55 (164) T PRK11169 10 KDLDRIDRNILNELQKDGRISNVELSKRVGLSPTPCLERVRRLERQ 55 (164) T ss_pred CCHHHHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHHHC T ss_conf 4551999999999998489999999999892999999999999978 No 55 >TIGR01884 cas_HTH CRISPR locus-related DNA-binding protein; InterPro: IPR010163 Most but not all examples of this family are associated with CRISPR loci, a combination of DNA repeats and characteristic proteins encoded near the repeat cluster. The C-terminal region of this protein is homologous to DNA-binding helix-turn-helix domains with predicted transcriptional regulatory activity.. Probab=95.90 E-value=0.033 Score=32.13 Aligned_cols=61 Identities=26% Similarity=0.359 Sum_probs=48.2 Q ss_pred CCHHHHHHHHHHHHH-C--CHHHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEE-CCCCEEEEECC Q ss_conf 888999999999982-7--6899998828997899999999999958821797-69946850013 Q gi|254780282|r 3 FDWDKLRVFYVVARS-G--SFTHAAEQLHLSQSSISRQISGLETEVGIKLFYR-HARGLTLTEQG 63 (299) Q Consensus 3 md~~~L~~f~~v~~~-g--s~s~AA~~L~itq~avS~~i~~LE~~lg~~Lf~R-~~~~~~lT~~G 63 (299) ++-+.++.+.+|... | +++.=|+.|++|.++++++|++||+.==+.=-.| .++++.+|+.| T Consensus 167 ~s~~~~~vL~~L~~~~Ge~~v~~iA~~lg~s~~T~~~~~~~Lek~gLv~~~~~~k~~~~~~t~Lg 231 (231) T TIGR01884 167 LSREELKVLEALKAEKGEKSVKNIAKKLGKSLSTISRHLAELEKKGLVESKGRGKGKRYSVTKLG 231 (231) T ss_pred CCHHHHHHHHHHHCCCCEECHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEEECCCCCCCEECCCC T ss_conf 88999999999850788052877998857888799999998874475456304678720001369 No 56 >PRK10141 DNA-binding transcriptional repressor ArsR; Provisional Probab=95.88 E-value=0.025 Score=32.89 Aligned_cols=70 Identities=19% Similarity=0.243 Sum_probs=50.4 Q ss_pred CHHHHHHHHHHHHH--CCHHHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEECCCC--EEEEECCCCCCCCCCCCCCCC Q ss_conf 88999999999982--768999988289978999999999999588217976994--685001343322222222221 Q gi|254780282|r 4 DWDKLRVFYVVARS--GSFTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHARG--LTLTEQGSKLHRVTSEVYHKL 77 (299) Q Consensus 4 d~~~L~~f~~v~~~--gs~s~AA~~L~itq~avS~~i~~LE~~lg~~Lf~R~~~~--~~lT~~G~~l~~~a~~~l~~~ 77 (299) |-..++.+..+.+. -+++.=++.+++|||+||+|++.|++ -|.---.|.|+. +.+.| ....+++++++.. T Consensus 13 D~tRl~Il~lL~~~gelcV~eL~~~l~~sQs~vS~HL~~L~~-aGlV~~rr~G~~vyY~Ln~---~~~~~~~~~l~~~ 86 (106) T PRK10141 13 DETRLGIVLLLRESGELCVCDLCTALDQSQPKISRHLALLRE-SGLLLDRKQGKWVHYRLSP---HIPAWAAKIIEQA 86 (106) T ss_pred CHHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHHH-CCCCEEEECCEEEEEEECC---CCHHHHHHHHHHH T ss_conf 899999999998749956999998869988899999999998-8973037414179987799---8859999999999 No 57 >cd00090 HTH_ARSR Arsenical Resistance Operon Repressor and similar prokaryotic, metal regulated homodimeric repressors. ARSR subfamily of helix-turn-helix bacterial transcription regulatory proteins (winged helix topology). Includes several proteins that appear to dissociate from DNA in the presence of metal ions. Probab=95.87 E-value=0.023 Score=33.09 Aligned_cols=57 Identities=32% Similarity=0.406 Sum_probs=41.1 Q ss_pred CHHHHHHHHHHHHH-CCHHHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEECC--CCEEEEE Q ss_conf 88999999999982-7689999882899789999999999995882179769--9468500 Q gi|254780282|r 4 DWDKLRVFYVVARS-GSFTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHA--RGLTLTE 61 (299) Q Consensus 4 d~~~L~~f~~v~~~-gs~s~AA~~L~itq~avS~~i~~LE~~lg~~Lf~R~~--~~~~lT~ 61 (299) |-..++.+..+.+. .+++.-|+.+++|+|+||+|++.|++. |.---.+.+ +.+.+|+ T Consensus 6 ~~~r~~Il~~L~~~~~~~~eia~~l~is~~~vs~hL~~L~~~-Gli~~~~~~~~~~y~l~~ 65 (78) T cd00090 6 DPTRLRILRLLLEGPLTVSELAERLGLSQSTVSRHLKKLEEA-GLVESRREGRRVYYSLTD 65 (78) T ss_pred CHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHC-CCEEEEEECCEEEEEECC T ss_conf 999999999998489069999877784878999999999988-986899988999999799 No 58 >PRK11886 biotin--protein ligase; Provisional Probab=95.79 E-value=0.051 Score=31.06 Aligned_cols=57 Identities=28% Similarity=0.376 Sum_probs=44.9 Q ss_pred HHHHHHHHHH--HCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEECCCCEEEEECCC Q ss_conf 9999999998--276899998828997899999999999958821797699468500134 Q gi|254780282|r 7 KLRVFYVVAR--SGSFTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHARGLTLTEQGS 64 (299) Q Consensus 7 ~L~~f~~v~~--~gs~s~AA~~L~itq~avS~~i~~LE~~lg~~Lf~R~~~~~~lT~~G~ 64 (299) -|+.+..+++ .-|=..=|++|+||..||.|+|++|++ .|.++--..++|++|...-. T Consensus 6 ~~~lL~~L~~g~~~SGe~la~~LgvSR~aVwK~i~~L~~-~G~~I~s~~~~GYrL~~~~~ 64 (319) T PRK11886 6 MLQLLSLLADGDFHSGEQLAEELGISRAAIWKHIQTLEE-WGLDIFSVKGKGYRLATPLS 64 (319) T ss_pred HHHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHHHHHHH-CCCEEEEECCCCEEECCCCC T ss_conf 999999973799296999999879889999999999997-79739997898738787756 No 59 >TIGR01256 modA molybdate ABC transporter, periplasmic molybdate-binding protein; InterPro: IPR005950 ABC transporters belong to the ATP-Binding Cassette (ABC) superfamily, which uses the hydrolysis of ATP to energize diverse biological systems. ABC transporters are minimally constituted of two conserved regions: a highly conserved ATP binding cassette (ABC) and a less conserved transmembrane domain (TMD). These regions can be found on the same protein or on two different ones. Most ABC transporters function as a dimer and therefore are constituted of four domains, two ABC modules and two TMDs. ABC transporters are involved in the export or import of a wide variety of substrates ranging from small ions to macromolecules. The major function of ABC import systems is to provide essential nutrients to bacteria. They are found only in prokaryotes and their four constitutive domains are usually encoded by independent polypeptides (two ABC proteins and two TMD proteins). Prokaryotic importers require additional extracytoplasmic binding proteins (one or more per systems) for function. In contrast, export systems are involved in the extrusion of noxious substances, the export of extracellular toxins and the targeting of membrane components. They are found in all living organisms and in general the TMD is fused to the ABC module in a variety of combinations. Some eukaryotic exporters encode the four domains on the same polypeptide chain . The ABC module (approximately two hundred amino acid residues) is known to bind and hydrolyze ATP, thereby coupling transport to ATP hydrolysis in a large number of biological processes. The cassette is duplicated in several subfamilies. Its primary sequence is highly conserved, displaying a typical phosphate-binding loop: Walker A, and a magnesium binding site: Walker B. Besides these two regions, three other conserved motifs are present in the ABC cassette: the switch region which contains a histidine loop, postulated to polarize the attaching water molecule for hydrolysis, the signature conserved motif (LSGGQ) specific to the ABC transporter, and the Q-motif (between Walker A and the signature), which interacts with the gamma phosphate through a water bond. The Walker A, Walker B, Q-loop and switch region form the nucleotide binding site , , . The 3D structure of a monomeric ABC module adopts a stubby L-shape with two distinct arms. ArmI (mainly beta-strand) contains Walker A and Walker B. The important residues for ATP hydrolysis and/or binding are located in the P-loop. The ATP-binding pocket is located at the extremity of armI. The perpendicular armII contains mostly the alpha helical subdomain with the signature motif. It only seems to be required for structural integrity of the ABC module. ArmII is in direct contact with the TMD. The hinge between armI and armII contains both the histidine loop and the Q-loop, making contact with the gamma phosphate of the ATP molecule. ATP hydrolysis leads to a conformational change that could facilitate ADP release. In the dimer the two ABC cassettes contact each other through hydrophobic interactions at the antiparallel beta-sheet of armI by a two-fold axis , , , , , . Proteins known to belong to this family are classified in several functional subfamilies depending on the substrate used (for further information see http://www.tcdb.org/tcdb/index.php?tc=3.A.1). This entry describes the molybdate ABC transporter periplasmic binding protein in bacteria and archae. Several of the periplasmic receptors constitute a diverse class of binding proteins that differ widely in size, sequence and ligand specificity. It has been shown experimentally by radioactive labeling that ModA represents a hydrophylioc periplasmic-binding protein in Gram-negative organisms and its counterpart in Gram-positive organisms is a lipoprotein. The other components of the system include ModB, an integral membrane protein and ModC, the ATP-binding subunit. Almost all of them display a common beta/alpha folding motif and have similar tertiary structures consisting of two globular domains.; GO: 0015412 molybdate transmembrane-transporting ATPase activity, 0015689 molybdate ion transport, 0030288 outer membrane-bounded periplasmic space. Probab=95.70 E-value=0.025 Score=32.80 Aligned_cols=185 Identities=12% Similarity=0.037 Sum_probs=104.0 Q ss_pred CCCHHHHHHHHHHCCCCCCC--CCCCC-CCCCCC-CCCCCCCCCCCCC----CCCCC----CCCCCCCCCCCCCCCC-CC Q ss_conf 00013566754200012222--22222-222222-2222234565432----11112----2345554332112344-32 Q gi|254780282|r 108 LQGNLKEFLLLYPDIQIQLI--LDNKD-IDISMD-YADCAIRLRKPIQ----SSSLI----QRKLVTIHMHAYAAPH-YL 174 (299) Q Consensus 108 l~~~l~~f~~~~P~i~i~i~--~~~~~-~~l~~~-~~Di~i~~~~~~~----~~~l~----~~~l~~~~~~~v~~~~-~~ 174 (299) |-++...|.+++|+.++-+. .|..+ ..+..| .+|+-|....... +.++. ...+....++++.+.. +. T Consensus 8 l~~i~~~F~k~~g~~~Vv~sFgsSg~L~~QI~~GAP~D~F~SA~~~~~~~L~~~g~~v~~~~~~~~~n~LVL~~~~~~~~ 87 (225) T TIGR01256 8 LKEIAKQFEKRTGKNKVVFSFGSSGTLYTQIENGAPADVFISADEKRPKKLVDKGLVVKGSEFVYAGNKLVLISPKNSRV 87 (225) T ss_pred HHHHHHHHHCCCCCCEEEEEECCCHHHHHHHHCCCCEEEEECCCCCCCHHHHHCCCEECCCCEEEEEEEEEEEECCCCCC T ss_conf 99999886200899569998768178999997179788766146345404663787302544589862189985355420 Q ss_pred CCCCCCCCCC---CCCCCCCCCC--CCCCCCCCCHHHHHHHHCCCCCCCCCCEEEEC-CCCHHHHHHHHHC-CEEEEEHH Q ss_conf 1112222221---1000112356--64332110002356652022343212114532-4200135678738-42331177 Q gi|254780282|r 175 KNCREPLSIQ---ELDKHNLITF--GDLIPKCMEDFNWLATVDRPIGEPRISCLQVN-SYLSIMQYCVLGS-GIALLPDY 247 (299) Q Consensus 175 ~~~~~~~~~~---dL~~~~~i~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-s~~~~~~~v~~g~-Gia~lp~~ 247 (299) .......+-. .+.+...|.. +..-|.+..-..++...+.-...... ...-. |......+|..|. =+||+=.+ T Consensus 88 ~~~~~~l~~p~~~~~l~~~~vaigdP~~~P~G~~A~E~L~~lgl~~~l~~k-LV~g~P~vrQA~~~V~~~nA~~GiVa~S 166 (225) T TIGR01256 88 VDSLDILKKPGWVIVLKDKTVAIGDPKHAPYGAAAKEVLQKLGLWEKLKKK-LVYGEPDVRQALQFVETGNAPIGIVALS 166 (225) T ss_pred CCCHHHHCCCCEEEEEECCCCCCCCCCCCHHHHHHHHHHHHCCCCHHHHCC-EEECCCCHHHHHHHHHHCCCCEEEEEHH T ss_conf 130221138974899863702346824443579999999707976256448-6524888999988877258866687311 Q ss_pred HH--CC-CCCEEEECCCCCCCCCEEEEEECCCCCCCHHHHHHHHHHHHH Q ss_conf 76--01-998466177666766008999348778888999999999999 Q gi|254780282|r 248 IV--KD-NPNLVRIMEDVITPSFTVYFCYPEALKNTGKLKAFRNFIFLK 293 (299) Q Consensus 248 ~~--~~-~~~lv~i~~~~~~~~~~~~lv~~~~~~~~~~~~~f~d~l~~~ 293 (299) .+ .. ....+.++|.....+..+-++--++..+.+.+++|+|||... T Consensus 167 dv~~~~K~~~~v~~~p~~ly~Pi~yp~~i~~~g~n~~~a~~f~dyL~sp 215 (225) T TIGR01256 167 DVIPSGKKVGSVAVIPEDLYKPIKYPAVIVKGGKNNAAAKAFIDYLKSP 215 (225) T ss_pred EEEECCCCCCEEEEECHHHCCCEEEEEEEEECCCCHHHHHHHHHHHCCH T ss_conf 0220003662799963312796021178871687608999999870796 No 60 >COG2998 TupB ABC-type tungstate transport system, permease component [Coenzyme metabolism] Probab=95.64 E-value=0.09 Score=29.62 Aligned_cols=202 Identities=13% Similarity=0.131 Sum_probs=103.8 Q ss_pred CCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCCCCCCCCCCCC---CCCCCCCCCCCCCCCCCCCC-------CCC Q ss_conf 22222233321110000000001356675420001222222222222---22222222345654321111-------223 Q gi|254780282|r 89 VKPSGKLRIATTIDLGQNLLQGNLKEFLLLYPDIQIQLILDNKDIDI---SMDYADCAIRLRKPIQSSSL-------IQR 158 (299) Q Consensus 89 ~~~~g~i~I~~~~~~~~~~l~~~l~~f~~~~P~i~i~i~~~~~~~~l---~~~~~Di~i~~~~~~~~~~l-------~~~ 158 (299) ....+.+|++.+.+.-..=|.+.+-.--+.+++.++++.....-..| .+|++|+.|... |.....+ .-+ T Consensus 26 sa~~~~LrmATTTSt~dtGLLd~l~p~fE~~~g~~v~~vAvGTG~ALkmge~gdvDvv~vHa-pk~E~~fv~~G~gv~r~ 104 (280) T COG2998 26 SADAAELRMATTTSTEDTGLLDVLLPKFEKYTGYDVQVVAVGTGKALKMGERGDVDVVIVHA-PKAEKEFVKDGFGVDRR 104 (280) T ss_pred CCCCCEEEEEEECCCCCCCCHHHHHHHHHHCCCCEEEEEEECCHHHHHHHCCCCCCEEEEEC-CHHHHHHHHCCCCCCCC T ss_conf 75420378854302455631888777664336965899981235877511268867899837-07789998727886676 Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCC----CCC--CCCCCCCCCCCCCCCCCHHHHHHHHCCCCCCCCCCEEEE---CCCC Q ss_conf 4555433211234432111222222----110--001123566433211000235665202234321211453---2420 Q gi|254780282|r 159 KLVTIHMHAYAAPHYLKNCREPLSI----QEL--DKHNLITFGDLIPKCMEDFNWLATVDRPIGEPRISCLQV---NSYL 229 (299) Q Consensus 159 ~l~~~~~~~v~~~~~~~~~~~~~~~----~dL--~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~s~~ 229 (299) ++.-..+++|.+.+.|...+...+. +-+ .+.+||+-.+.+............. ...|....+-. ..+. T Consensus 105 ~vmYNdFiiVgp~~dpA~~k~~kn~~e~fe~Ia~~ka~FvSRGD~SGT~~~E~~lWk~~---g~~p~~~~wY~s~G~GMg 181 (280) T COG2998 105 PVMYNDFIIVGPADDPAGIKDAKNGKEAFEKIAEEKAKFVSRGDNSGTDSKELSLWKVT---GIEPTVKGWYISAGQGMG 181 (280) T ss_pred CEEEEEEEEECCCCCCHHCCCCHHHHHHHHHHHHCCCEEEECCCCCCCCHHHHHHHHHC---CCCCCCCCCEEECCCCHH T ss_conf 10131179987766611112200089999999972890574278778427788899870---878898860365274457 Q ss_pred HHHHHHHHHCCEEEEEH--HHHC-CCCCEEEECCCCCCCCCEEEE--EECCC--CCCCHHHHHHHHHHHHHH Q ss_conf 01356787384233117--7760-199846617766676600899--93487--788889999999999998 Q gi|254780282|r 230 SIMQYCVLGSGIALLPD--YIVK-DNPNLVRIMEDVITPSFTVYF--CYPEA--LKNTGKLKAFRNFIFLKA 294 (299) Q Consensus 230 ~~~~~v~~g~Gia~lp~--~~~~-~~~~lv~i~~~~~~~~~~~~l--v~~~~--~~~~~~~~~f~d~l~~~~ 294 (299) ..+.|+.+-.+.++-.+ |++- .-+.|+.++...+..-..|.+ +-+++ ..+-.++..|++|+.+.. T Consensus 182 ~tL~~A~Ek~aytLtDrgTylaYr~r~~L~iv~~gd~~L~N~Ysvi~vNP~r~~~vny~~A~kfi~w~~s~~ 253 (280) T COG2998 182 DTLNMANEKKAYTLTDRGTYLAYRNRPTLVIVLEGDPSLFNPYSVIAVNPKRVKGVNYTAATKFIEWLMSEK 253 (280) T ss_pred HHHHHHHHHCEEEEECCCEEEEECCCCCEEEEECCCCCCCCCEEEEEECHHCCCCCCCHHHHHHHHHHHHHH T ss_conf 787776551216861363056762766528996178111671258987610078857118999999996477 No 61 >pfam00497 SBP_bac_3 Bacterial extracellular solute-binding proteins, family 3. Probab=95.59 E-value=0.13 Score=28.65 Aligned_cols=175 Identities=9% Similarity=0.017 Sum_probs=85.8 Q ss_pred CCCCHHHHHHHHHHCCCCCCCCCC---CCCCCCCCCCCCCCC-CC-CCCCCCCC-CCCCCCCCCCCCCCCCCCCCCCCCC Q ss_conf 000013566754200012222222---222222222222234-56-54321111-2234555433211234432111222 Q gi|254780282|r 107 LLQGNLKEFLLLYPDIQIQLILDN---KDIDISMDYADCAIR-LR-KPIQSSSL-IQRKLVTIHMHAYAAPHYLKNCREP 180 (299) Q Consensus 107 ~l~~~l~~f~~~~P~i~i~i~~~~---~~~~l~~~~~Di~i~-~~-~~~~~~~l-~~~~l~~~~~~~v~~~~~~~~~~~~ 180 (299) +..+++..+.+.- ++++++...+ ....+.+|++|+.+. +. .+.....+ ...+++..+.+++++++........ T Consensus 24 ~~~dil~~i~~~l-g~~~~~~~~p~~~~~~~l~~g~~D~~~~~~~~t~~R~~~~~~s~p~~~~~~~~~~~~~~~~~~~~~ 102 (224) T pfam00497 24 FDVDLAKAIAKRL-GVKVEFVPVSWDGLIPALQSGKIDVIIAGMTITPERKKKVDFSDPYYYSGQVLVVRKDSPPKIKSI 102 (224) T ss_pred EHHHHHHHHHHHH-CCCEEEEECCHHHHHHHHHCCCCCEEECCCCCCHHHHHHHCCCCCEEECCEEEEEECCCCCCCCCC T ss_conf 2999999999997-996799985889999999769987661367788555102125753440471799998987654565 Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCCCCCCCEEEECCCCHHHHHHHHHCCEEE-EEHH----HHCCCCCE Q ss_conf 222110001123566433211000235665202234321211453242001356787384233-1177----76019984 Q gi|254780282|r 181 LSIQELDKHNLITFGDLIPKCMEDFNWLATVDRPIGEPRISCLQVNSYLSIMQYCVLGSGIAL-LPDY----IVKDNPNL 255 (299) Q Consensus 181 ~~~~dL~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~v~~g~Gia~-lp~~----~~~~~~~l 255 (299) .+++||.+....... +.. ....+.... .......++++....+.++..|.-=++ .+.. .+++.+.. T Consensus 103 ~~~~dL~~~~I~v~~-g~~----~~~~l~~~~----~~~~~i~~~~~~~~~l~~L~~gr~D~~i~~~~~~~~~~~~~~~~ 173 (224) T pfam00497 103 KDLADLKGKKVGVQK-GTT----QEDLLKELA----PKGAEIVLYDDQAEALQALAAGRVDAVVADSPVAAYLIKKNPGL 173 (224) T ss_pred CCHHHHCCCEEEEEC-CCH----HHHHHHHHC----CCCCEEEEECCHHHHHHHHHCCCEEEEEECHHHHHHHHHHCCCC T ss_conf 898997797799968-977----999998606----24451699542788888987497689995799999999868997 Q ss_pred EEECCCCCCCCCEEEEEECCCCCCCHHHHHHHHHHHHHHH Q ss_conf 6617766676600899934877888899999999999985 Q gi|254780282|r 256 VRIMEDVITPSFTVYFCYPEALKNTGKLKAFRNFIFLKAR 295 (299) Q Consensus 256 v~i~~~~~~~~~~~~lv~~~~~~~~~~~~~f~d~l~~~~r 295 (299) ..+... +....+++++.+++ ++.....++--+++.+ T Consensus 174 ~~~~~~-~~~~~~~~~~~~k~---~~~l~~~~n~~l~~l~ 209 (224) T pfam00497 174 NLVVGE-PLSGEPYGIAVRKG---DPELLAAVNKALAELK 209 (224) T ss_pred EEEECC-CCCCCEEEEEEECC---CHHHHHHHHHHHHHHH T ss_conf 299436-77761499999799---9999999999999999 No 62 >pfam01022 HTH_5 Bacterial regulatory protein, arsR family. Members of this family contains a DNA binding 'helix-turn-helix' motif. This family includes other proteins which are not included in the Prosite definition. Probab=95.50 E-value=0.038 Score=31.81 Aligned_cols=38 Identities=29% Similarity=0.468 Sum_probs=29.9 Q ss_pred HHHHHHHHH-HHCCHHHHHHHHCCCHHHHHHHHHHHHHH Q ss_conf 999999999-82768999988289978999999999999 Q gi|254780282|r 7 KLRVFYVVA-RSGSFTHAAEQLHLSQSSISRQISGLETE 44 (299) Q Consensus 7 ~L~~f~~v~-~~gs~s~AA~~L~itq~avS~~i~~LE~~ 44 (299) .++.+..++ +..+++.=|+.+++|||+||+|++.|++. T Consensus 4 Rl~Il~~L~~~~~~v~el~~~l~~sq~~vS~HL~~L~~~ 42 (47) T pfam01022 4 RLKILYLLSEGELCVCELAEILGLSQSTVSHHLKKLREA 42 (47) T ss_pred HHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHHHC T ss_conf 999999998089969999999895886999999999898 No 63 >PRK11179 DNA-binding transcriptional regulator AsnC; Provisional Probab=95.47 E-value=0.051 Score=31.04 Aligned_cols=44 Identities=11% Similarity=0.215 Sum_probs=37.4 Q ss_pred CCCCHHHHHHHHHHHHHC--CHHHHHHHHCCCHHHHHHHHHHHHHH Q ss_conf 988889999999999827--68999988289978999999999999 Q gi|254780282|r 1 MSFDWDKLRVFYVVARSG--SFTHAAEQLHLSQSSISRQISGLETE 44 (299) Q Consensus 1 m~md~~~L~~f~~v~~~g--s~s~AA~~L~itq~avS~~i~~LE~~ 44 (299) |.||=-+.+.+..+.+-| |++.=|+++|+|.|||.++|++||+. T Consensus 5 ~klD~~D~~IL~~Lq~d~R~s~~eiA~~lglS~stv~~Ri~rLe~~ 50 (153) T PRK11179 5 YQIDNLDRGILEALMENARTPYAELAKQFGVSPGTIHVRVEKMKQA 50 (153) T ss_pred CCCCHHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHHHC T ss_conf 7678999999999998489999999999892999999999999979 No 64 >COG4742 Predicted transcriptional regulator [Transcription] Probab=95.32 E-value=0.024 Score=32.93 Aligned_cols=76 Identities=16% Similarity=0.239 Sum_probs=64.0 Q ss_pred HHHHHHHHHH-HCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEECCCCEEEEECCCCCCCCCCCCCCCCCHHHHHCC Q ss_conf 9999999998-276899998828997899999999999958821797699468500134332222222222101221001 Q gi|254780282|r 7 KLRVFYVVAR-SGSFTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHARGLTLTEQGSKLHRVTSEVYHKLETTQIELQ 85 (299) Q Consensus 7 ~L~~f~~v~~-~gs~s~AA~~L~itq~avS~~i~~LE~~lg~~Lf~R~~~~~~lT~~G~~l~~~a~~~l~~~~~~~~~~~ 85 (299) ..+.+..+.+ -+|+..=-..|++|.+++..|||+|++ ..|+++.++...||+.|+.+.+..+.+++.++-...... T Consensus 15 Rk~lLllL~egPkti~EI~~~l~vs~~ai~pqiKkL~~---~~LV~~~~~~Y~LS~~G~iiv~km~~ll~tl~v~e~n~d 91 (260) T COG4742 15 RKDLLLLLKEGPKTIEEIKNELNVSSSAILPQIKKLKD---KGLVVQEGDRYSLSSLGKIIVEKMEPLLDTLEVFEENYD 91 (260) T ss_pred HHHHHHHHHHCCCCHHHHHHHHCCCCHHHHHHHHHHHH---CCCEEECCCEEEECCHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 99999999858988999998858993888999998713---898785199987340089999999999999999973146 No 65 >smart00062 PBPb Bacterial periplasmic substrate-binding proteins. bacterial proteins, eukaryotic ones are in PBPe Probab=95.18 E-value=0.22 Score=27.33 Aligned_cols=170 Identities=9% Similarity=0.011 Sum_probs=86.0 Q ss_pred CCCCHHHHHHHHHHCCCCCCCCCC---CCCCCCCCCCCCCCCC-CC-CCCCCCC-CCCCCCCCCCCCCCCCCCCCCCCCC Q ss_conf 000013566754200012222222---2222222222222345-65-4321111-2234555433211234432111222 Q gi|254780282|r 107 LLQGNLKEFLLLYPDIQIQLILDN---KDIDISMDYADCAIRL-RK-PIQSSSL-IQRKLVTIHMHAYAAPHYLKNCREP 180 (299) Q Consensus 107 ~l~~~l~~f~~~~P~i~i~i~~~~---~~~~l~~~~~Di~i~~-~~-~~~~~~l-~~~~l~~~~~~~v~~~~~~~~~~~~ 180 (299) +..+++..+.+.- ++++++..-+ ....+..|++|+.+.. .. +.....+ ...++.....++++.++. .+ T Consensus 25 ~~~Dil~~~~~~l-g~~i~~~~~~~~r~~~~l~~g~~D~~~~~~~~~~~r~~~~~~s~p~~~~~~~~~~~~~~-----~~ 98 (219) T smart00062 25 FDVDLAKAIAKEL-GLKVEFVEVSFDNLLTALKSGKIDVVAAGMTITPERAKQVDFSDPYYKSGQVILVRKDS-----PI 98 (219) T ss_pred EHHHHHHHHHHHH-CCCEEEEECCHHHHHHHHHCCCCCEEEEECCCCHHHHHCCCCCCCEECCCEEEEEECCC-----CC T ss_conf 2999999999997-99679998478999999975897705311357867750022245500244479996589-----97 Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCCCCCCCEEEECCCCHHHHHHHHHCC-EEEEEHHHH----CCCCC- Q ss_conf 222110001123566433211000235665202234321211453242001356787384-233117776----01998- Q gi|254780282|r 181 LSIQELDKHNLITFGDLIPKCMEDFNWLATVDRPIGEPRISCLQVNSYLSIMQYCVLGSG-IALLPDYIV----KDNPN- 254 (299) Q Consensus 181 ~~~~dL~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~v~~g~G-ia~lp~~~~----~~~~~- 254 (299) .+++||.+....... +.. ....+..... .....++++...++.++..|.- +.+.+...+ ++.+. T Consensus 99 ~~~~dL~g~~i~~~~-g~~----~~~~l~~~~~-----~~~~~~~~~~~~~~~~l~~g~vD~~i~~~~~~~~~~~~~~~~ 168 (219) T smart00062 99 KSLEDLKGKKVAVVA-GTT----GEELLKKLYP-----EAKIVSYDSQAEALAALKAGRADAAVADAPALAALVKQHGLP 168 (219) T ss_pred CCHHHHCCCEEEEEC-CCH----HHHHHHHHCC-----CCEEEEECCHHHHHHHHHCCCEEEEEECHHHHHHHHHHCCCC T ss_conf 997996797799957-987----9999997287-----852898599999999998398799997799999999848999 Q ss_pred EEEECCCCCCCCCEEEEEECCCCCCCHHHHHHHHHHHHHHH Q ss_conf 46617766676600899934877888899999999999985 Q gi|254780282|r 255 LVRIMEDVITPSFTVYFCYPEALKNTGKLKAFRNFIFLKAR 295 (299) Q Consensus 255 lv~i~~~~~~~~~~~~lv~~~~~~~~~~~~~f~d~l~~~~r 295 (299) -..+.........++++..+++ ++.....++--+++.+ T Consensus 169 ~~~~~~~~~~~~~~~~~~~~~~---~~~l~~~~n~~l~~l~ 206 (219) T smart00062 169 ELKIVGDPLDTPEGYAFAVRKG---DPELLDKINKALKELK 206 (219) T ss_pred CEEEECCCCCCCCEEEEEEECC---CHHHHHHHHHHHHHHH T ss_conf 8378346777764199999599---9999999999999999 No 66 >COG1522 Lrp Transcriptional regulators [Transcription] Probab=95.09 E-value=0.078 Score=29.99 Aligned_cols=40 Identities=40% Similarity=0.395 Sum_probs=33.2 Q ss_pred CHHHHHHHHHHHHHCCHHHHHHHHCCCHHHHHHHHHHHHHH Q ss_conf 88999999999982768999988289978999999999999 Q gi|254780282|r 4 DWDKLRVFYVVARSGSFTHAAEQLHLSQSSISRQISGLETE 44 (299) Q Consensus 4 d~~~L~~f~~v~~~gs~s~AA~~L~itq~avS~~i~~LE~~ 44 (299) |.+-|+.+..=++ .|++.-|+++|+|+|+|+++|++||+. T Consensus 10 D~~IL~~L~~d~r-~~~~eia~~lglS~~~v~~Ri~~L~~~ 49 (154) T COG1522 10 DRRILRLLQEDAR-ISNAELAERVGLSPSTVLRRIKRLEEE 49 (154) T ss_pred HHHHHHHHHHCCC-CCHHHHHHHHCCCHHHHHHHHHHHHHC T ss_conf 9999999997276-579999999797989999999999988 No 67 >TIGR03261 phnS2 putative 2-aminoethylphosphonate ABC transport system, 1-aminoethylphosphonate-binding protein component. This ABC transporter extracellular solute-binding protein is found in a number of genomes in operon-like contexts strongly suggesting a substrate specificity for 2-aminoethylphosphonate (2-AEP). The characterized PhnSTUV system is absent in the genomes in which this system is found. These genomes encode systems for the catabolism of 2-AEP, making the need for a 2-AEP-specific transporter likely. Probab=94.86 E-value=0.066 Score=30.40 Aligned_cols=203 Identities=16% Similarity=0.135 Sum_probs=92.6 Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCCCCCCCC---CCCCCC----CCCCCCCCCCC------------ Q ss_conf 32222223332111000000000135667542000122222222---222222----22222234565------------ Q gi|254780282|r 88 SVKPSGKLRIATTIDLGQNLLQGNLKEFLLLYPDIQIQLILDNK---DIDISM----DYADCAIRLRK------------ 148 (299) Q Consensus 88 ~~~~~g~i~I~~~~~~~~~~l~~~l~~f~~~~P~i~i~i~~~~~---~~~l~~----~~~Di~i~~~~------------ 148 (299) .....++|.|-++ ....++-+++..|.++||+|++++...+. ...|.. ..+|+.+.... T Consensus 17 aa~~~~~l~VYss--~~~~~~~~i~~~Fek~~tgIkV~~v~~~tgel~~rl~aEk~~p~aDV~~g~~~~~~~~~~~~gll 94 (334) T TIGR03261 17 NSKANTELTVYTA--IEDELIAKYKDAFEKVNPDIKINWVRDSTGIITAKLLAEKNNPQADVVWGLAASSLALLDKEGML 94 (334) T ss_pred HHCCCCEEEEEEC--CCHHHHHHHHHHHHHHCCCCEEEEEECCHHHHHHHHHHCCCCCCCEEEEECCHHHHHHHHHCCCC T ss_conf 0302995999969--98889999999999777994899998972999999996457998659984565789998860431 Q ss_pred -CCCCCCCCCC-CCCCC-------------CCCCCCCCCCCCCC--CCCCCCCCCCCCCC---CCCCC-CCCCCC-C-HH Q ss_conf -4321111223-45554-------------33211234432111--22222211000112---35664-332110-0-02 Q gi|254780282|r 149 -PIQSSSLIQR-KLVTI-------------HMHAYAAPHYLKNC--REPLSIQELDKHNL---ITFGD-LIPKCM-E-DF 205 (299) Q Consensus 149 -~~~~~~l~~~-~l~~~-------------~~~~v~~~~~~~~~--~~~~~~~dL~~~~~---i~~~~-~~~~~~-~-~~ 205 (299) +..++.+... +-+.+ ..+++-.++.+... ..|.+.+||.+-.| |.+.. ..+... . .. T Consensus 95 ~~y~~~~~~~l~~~~~d~~~~~~~~g~~~~~~~i~yN~~~~~~~~~p~P~sw~DL~dp~ykg~i~~~~p~~sg~~~~~l~ 174 (334) T TIGR03261 95 KPYKPKGLDALNPKFRDAKNPPHWVGMDAWMAAICFNTVEAKKKGLPKPTSWEDLTKPEYKGHIVMPNPASSGTGFLDVS 174 (334) T ss_pred CCCCCCCHHHCCHHHCCCCCCCEEEEEEEEEEEEEEEHHHCCCCCCCCCCCHHHHCCHHHCCEEECCCCCCCHHHHHHHH T ss_conf 57775305447886529788851688752467899744440425899999999970947489587348886338999999 Q ss_pred HHHHHHCCCCC-------CCCCCEEEECCCCHHHHHHHHHC-CEEEEEHHHH---CCCCCEEE-ECCCCCCCCCEEEEEE Q ss_conf 35665202234-------32121145324200135678738-4233117776---01998466-1776667660089993 Q gi|254780282|r 206 NWLATVDRPIG-------EPRISCLQVNSYLSIMQYCVLGS-GIALLPDYIV---KDNPNLVR-IMEDVITPSFTVYFCY 273 (299) Q Consensus 206 ~~~~~~~~~~~-------~~~~~~~~~~s~~~~~~~v~~g~-Gia~lp~~~~---~~~~~lv~-i~~~~~~~~~~~~lv~ 273 (299) .+....+...+ .... ...+.+......++..|. .+++...+.+ ..+|.-+. +.|........-.+.- T Consensus 175 ~~~~~~G~d~g~~~l~~l~~N~-~~~~~~~~~~~~~v~~Ge~~ig~~~~~~~~~~~~~g~pv~~v~P~eG~~~~~~~~~I 253 (334) T TIGR03261 175 AWLQMMGEDKGWDYMDKLHKNI-AVYTHSGSKPCKLAGMGEFPIGISMAYRALKEKKKGAPIDVVFPKEGLGWDIEATAI 253 (334) T ss_pred HHHHHHCHHHHHHHHHHHHHHH-CCCCCCCCHHHHHHHCCCEEEEEEECCHHHHHHHCCCCEEEEECCCCCEEEEEEEEE T ss_conf 9999735288999999998632-416777638889986598579997354578876438973389458984787735888 Q ss_pred CCCCCCCHHHHHHHHHHHHH Q ss_conf 48778888999999999999 Q gi|254780282|r 274 PEALKNTGKLKAFRNFIFLK 293 (299) Q Consensus 274 ~~~~~~~~~~~~f~d~l~~~ 293 (299) .++..+...++.|+||+++. T Consensus 254 vk~a~n~~~Ak~FidfllS~ 273 (334) T TIGR03261 254 IKGSKNNDAAKKLVDWSISD 273 (334) T ss_pred ECCCCCHHHHHHHHHHHCCH T ss_conf 87998989999999997699 No 68 >pfam01047 MarR MarR family. The Mar proteins are involved in the multiple antibiotic resistance, a non-specific resistance system. The expression of the mar operon is controlled by a repressor, MarR. A large number of compounds induce transcription of the mar operon. This is thought to be due to the compound binding to MarR, and the resulting complex stops MarR binding to the DNA. With the MarR repression lost, transcription of the operon proceeds. The structure of MarR is known and shows MarR as a dimer with each subunit containing a winged-helix DNA binding motif. Probab=94.83 E-value=0.087 Score=29.71 Aligned_cols=42 Identities=19% Similarity=0.445 Sum_probs=36.0 Q ss_pred CCHHHHHHHHHHHHHCC--HHHHHHHHCCCHHHHHHHHHHHHHH Q ss_conf 88899999999998276--8999988289978999999999999 Q gi|254780282|r 3 FDWDKLRVFYVVARSGS--FTHAAEQLHLSQSSISRQISGLETE 44 (299) Q Consensus 3 md~~~L~~f~~v~~~gs--~s~AA~~L~itq~avS~~i~~LE~~ 44 (299) +++.|+.++..+.+.+. .+.-|+.++++++++|+.|++||+. T Consensus 1 lT~~Q~~vL~~l~~~~~~s~~~la~~~~~~~~~vs~~i~~Le~~ 44 (59) T pfam01047 1 LTLTQFHILRILYEHGPLTVSELAEKLGVDRSTVTRVLDRLEKK 44 (59) T ss_pred CCHHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHHHC T ss_conf 98999999999994699299999999885865499999999889 No 69 >COG1654 BirA Biotin operon repressor [Transcription] Probab=94.78 E-value=0.098 Score=29.42 Aligned_cols=49 Identities=24% Similarity=0.287 Sum_probs=41.3 Q ss_pred HCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEECCCCEEEEECCCCC Q ss_conf 27689999882899789999999999995882179769946850013433 Q gi|254780282|r 17 SGSFTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHARGLTLTEQGSKL 66 (299) Q Consensus 17 ~gs~s~AA~~L~itq~avS~~i~~LE~~lg~~Lf~R~~~~~~lT~~G~~l 66 (299) .-|=-+=|++|++|..||.++|++|+ +.|.+.+.+.++|..+...=..+ T Consensus 19 ~~SGe~La~~LgiSRtaVwK~Iq~Lr-~~G~~I~s~~~kGY~L~~~~~ll 67 (79) T COG1654 19 FVSGEKLAEELGISRTAVWKHIQQLR-EEGVDIESVRGKGYLLPQLPDLL 67 (79) T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHH-HHCCCEEECCCCCEECCCCCCCC T ss_conf 66689999997865999999999999-80971686078863656750107 No 70 >smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli Probab=94.47 E-value=0.12 Score=28.86 Aligned_cols=42 Identities=21% Similarity=0.300 Sum_probs=32.4 Q ss_pred CCHHHHHHHHHHHHH--CCHHHHHHHHCCCHHHHHHHHHHHHHH Q ss_conf 888999999999982--768999988289978999999999999 Q gi|254780282|r 3 FDWDKLRVFYVVARS--GSFTHAAEQLHLSQSSISRQISGLETE 44 (299) Q Consensus 3 md~~~L~~f~~v~~~--gs~s~AA~~L~itq~avS~~i~~LE~~ 44 (299) ||=-+.+.+..+-+- -|++.=|+++|+|+++|.++|++||+. T Consensus 1 lD~~D~~Il~~L~~n~R~s~~~iA~~lg~S~~tv~~Ri~~L~~~ 44 (108) T smart00344 1 LDEIDRKILEELQKDARISLAELAKKVGLSPSTVHNRVKRLEEE 44 (108) T ss_pred CCHHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHHHC T ss_conf 98899999999998289999999999893999999999999608 No 71 >pfam01325 Fe_dep_repress Iron dependent repressor, N-terminal DNA binding domain. This family includes the Diphtheria toxin repressor. DNA binding is through a helix-turn-helix motif. Probab=94.39 E-value=0.092 Score=29.57 Aligned_cols=39 Identities=28% Similarity=0.452 Sum_probs=32.0 Q ss_pred HHHHHHHHHHHHCC---HHHHHHHHCCCHHHHHHHHHHHHHH Q ss_conf 99999999998276---8999988289978999999999999 Q gi|254780282|r 6 DKLRVFYVVARSGS---FTHAAEQLHLSQSSISRQISGLETE 44 (299) Q Consensus 6 ~~L~~f~~v~~~gs---~s~AA~~L~itq~avS~~i~~LE~~ 44 (299) +-|+.++.+.+.+. .+.=|++|+||+|+||..|++|++. T Consensus 6 dYLk~Iy~l~~~~~~v~~~~iA~~L~Vs~~SVt~mlkkL~~~ 47 (58) T pfam01325 6 DYLETIYTLSEEKGVVKTKDLAERLNVSPSTVSEMLKKLEKD 47 (58) T ss_pred HHHHHHHHHHCCCCCEEHHHHHHHHCCCCHHHHHHHHHHHHC T ss_conf 999999998826996129999999599925299999999988 No 72 >PRK11260 cystine transporter subunit; Provisional Probab=94.19 E-value=0.4 Score=25.87 Aligned_cols=185 Identities=10% Similarity=0.005 Sum_probs=86.8 Q ss_pred CCCCCCCCCCCCCCCC-----------CCCCHHHHHHHHHHCCCCCCCCC---CCCCCCCCCCCCCCCCCCC--CCCCCC Q ss_conf 2222333211100000-----------00001356675420001222222---2222222222222234565--432111 Q gi|254780282|r 91 PSGKLRIATTIDLGQN-----------LLQGNLKEFLLLYPDIQIQLILD---NKDIDISMDYADCAIRLRK--PIQSSS 154 (299) Q Consensus 91 ~~g~i~I~~~~~~~~~-----------~l~~~l~~f~~~~P~i~i~i~~~---~~~~~l~~~~~Di~i~~~~--~~~~~~ 154 (299) .+|+|+||+.+.+.++ +=.+++..+.++- ++++++... +....|..|++|+++..-. +..... T Consensus 37 ~~G~L~Vg~~~~~pPf~~~d~~G~~~GfdvDl~~~ia~~l-g~~~e~~~~~~~~~i~~L~~g~~Di~~~~~t~T~eR~~~ 115 (264) T PRK11260 37 ERGTLLVGLEGTYPPFSFQGEDGKLTGFEVEFAEALAKHL-GVKASLKPTKWDGMLASLDSKRIDVVINQVTISDERKKK 115 (264) T ss_pred HCCEEEEEECCCCCCCEEECCCCCEEEEEHHHHHHHHHHH-CCCEEEEECCHHHHHHHHHCCCCCEEECCCCCCHHHHHH T ss_conf 6998999977898893689999998887199999999984-995699978889999998669946672575358888851 Q ss_pred CC-CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCCCCCCCEEEECCCCHHHH Q ss_conf 12-23455543321123443211122222211000112356643321100023566520223432121145324200135 Q gi|254780282|r 155 LI-QRKLVTIHMHAYAAPHYLKNCREPLSIQELDKHNLITFGDLIPKCMEDFNWLATVDRPIGEPRISCLQVNSYLSIMQ 233 (299) Q Consensus 155 l~-~~~l~~~~~~~v~~~~~~~~~~~~~~~~dL~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~ 233 (299) +. ..+.+.....+++.++.. ....+++||.+... ....+. ....++... .+......+++....+. T Consensus 116 ~~Fs~PY~~~~~~~~v~~~~~---~~i~~~~dL~Gk~V-~v~~gs----~~~~~l~~~-----~~~~~i~~~~~~~~~~~ 182 (264) T PRK11260 116 YDFSTPYTVSGIQALVKKGNE---GTIKTAADLKGKKV-GVGLGT----NYEEWLRQN-----VQGVDVRTYDDDPTKYQ 182 (264) T ss_pred CCCCCCEEEEEEEEEEECCCC---CCCCCHHHHCCCEE-EEECCC----HHHHHHHHH-----CCCCCEEEECCHHHHHH T ss_conf 776774377445999987897---66689789668716-885697----899999860-----88981686366189999 Q ss_pred HHHHHCCEEEEEHH-----HHCCCCCEEEECCCCCCCCCEEEEEECCCCCCCHHHHHHHHHHHHH Q ss_conf 67873842331177-----7601998466177666766008999348778888999999999999 Q gi|254780282|r 234 YCVLGSGIALLPDY-----IVKDNPNLVRIMEDVITPSFTVYFCYPEALKNTGKLKAFRNFIFLK 293 (299) Q Consensus 234 ~v~~g~Gia~lp~~-----~~~~~~~lv~i~~~~~~~~~~~~lv~~~~~~~~~~~~~f~d~l~~~ 293 (299) .+.+|..=+++-+. .+++.+....+... +....++++..+++ ++.....++.-+.+ T Consensus 183 ~l~~G~vDa~i~d~~~~~~~~~~~~~~~~~~~~-~~~~~~~~iav~k~---~~~L~~~in~~L~~ 243 (264) T PRK11260 183 DLRVGRIDAILVDRLAALDLVKKTNDTLAVTGE-AFSRQESGVALRKG---NPDLLKAVNNAIAE 243 (264) T ss_pred HHHCCCCCEEEECHHHHHHHHHHCCCCEEECCC-CCCCCEEEEEEECC---CHHHHHHHHHHHHH T ss_conf 987598679994599999999868997898068-76665089999899---99999999999999 No 73 >smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor. Probab=94.00 E-value=0.059 Score=30.70 Aligned_cols=41 Identities=27% Similarity=0.276 Sum_probs=32.5 Q ss_pred HHHCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEECCCC Q ss_conf 982768999988289978999999999999588217976994 Q gi|254780282|r 15 ARSGSFTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHARG 56 (299) Q Consensus 15 ~~~gs~s~AA~~L~itq~avS~~i~~LE~~lg~~Lf~R~~~~ 56 (299) -...|++.=|+.+++|||+||+|++.|++. |.-=..|.|+. T Consensus 8 ~~~~~~~ela~~l~is~~tvs~HL~~L~~~-Glv~~~~~G~~ 48 (66) T smart00418 8 EGELCVCELAEILGLSQSTVSHHLKKLREA-GLVESRREGKR 48 (66) T ss_pred CCCCCHHHHHHHHCCCHHHHHHHHHHHHHC-CCEEEEEECCE T ss_conf 399669999999882988887999999988-92689998689 No 74 >COG2522 Predicted transcriptional regulator [General function prediction only] Probab=93.80 E-value=0.11 Score=29.11 Aligned_cols=33 Identities=27% Similarity=0.268 Sum_probs=25.5 Q ss_pred HHHHHHHHHHCCHHHHHHHHCCCHHHHHHHHHH Q ss_conf 999999998276899998828997899999999 Q gi|254780282|r 8 LRVFYVVARSGSFTHAAEQLHLSQSSISRQISG 40 (299) Q Consensus 8 L~~f~~v~~~gs~s~AA~~L~itq~avS~~i~~ 40 (299) +-.-.-+-+--|-.+.|+-||+||||||+-|+. T Consensus 13 ~lA~~L~eeG~Sq~~iA~LLGltqaAVS~Yls~ 45 (119) T COG2522 13 LLAKELIEEGLSQYRIAKLLGLTQAAVSQYLSG 45 (119) T ss_pred HHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCC T ss_conf 999999995886999999968889999999736 No 75 >TIGR02702 SufR_cyano iron-sulfur cluster biosynthesis transcriptional regulator SufR; InterPro: IPR014075 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 members of the SufR cyanobacterial protein family of transcriptional regulators that control the SUF system. In all cases, the sufR gene is encoded near SUF system genes but in the opposite direction. This DNA-binding protein belongs to the DeoR family of helix-loop-helix proteins. All members also have a probable metal-binding motif C-X(12)-C-X(13)-C-X(14)-C near the C-terminus.. Probab=93.29 E-value=0.11 Score=29.19 Aligned_cols=89 Identities=20% Similarity=0.287 Sum_probs=51.1 Q ss_pred HHHHHHHCCHHHH--HHHHCCCHHHHHHHHHHHHHHHCCEEEEEC-------CC---CEEEEECCCCCCCCCCCCCCCCC Q ss_conf 9999982768999--988289978999999999999588217976-------99---46850013433222222222210 Q gi|254780282|r 11 FYVVARSGSFTHA--AEQLHLSQSSISRQISGLETEVGIKLFYRH-------AR---GLTLTEQGSKLHRVTSEVYHKLE 78 (299) Q Consensus 11 f~~v~~~gs~s~A--A~~L~itq~avS~~i~~LE~~lg~~Lf~R~-------~~---~~~lT~~G~~l~~~a~~~l~~~~ 78 (299) +..+-+.|.-|++ |+.|.||+.||-||+|.||.+ .|++-. || .++|...|+.=++. T Consensus 7 L~~LL~~Gq~sA~~lA~~L~iSpQAvRrHLKDLe~e---~Lv~~~~~~~g~~GRPQy~Y~LS~qGRe~l~~--------- 74 (215) T TIGR02702 7 LEYLLKEGQASALALAEELAISPQAVRRHLKDLETE---GLVEYKAVLQGTMGRPQYLYQLSRQGREQLPQ--------- 74 (215) T ss_pred HHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHCC---CHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHH--------- T ss_conf 999886004889999997278867887654332101---03567777650478822542121776776366--------- Q ss_pred HHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHH Q ss_conf 1221001223222222333211100000000013566 Q gi|254780282|r 79 TTQIELQESSVKPSGKLRIATTIDLGQNLLQGNLKEF 115 (299) Q Consensus 79 ~~~~~~~~~~~~~~g~i~I~~~~~~~~~~l~~~l~~f 115 (299) ... + ......|.+-|....|++..+-++-+.+. T Consensus 75 -~~~--r-qqa~~~~~FAl~LLdSl~etlG~~q~~~v 107 (215) T TIGR02702 75 -LVL--R-QQADRHGEFALSLLDSLAETLGPEQFEAV 107 (215) T ss_pred -HHH--H-HHCCCCCHHHHHHHHHHHHHCCHHHHHHH T ss_conf -554--5-41037531678899988963787789999 No 76 >cd06170 LuxR_C_like C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many are active as homodimers. Many are two domain proteins in which the DNA binding property of the C-terminal DNA binding domain is modulated by modifications of the N-terminal domain. For example in the case of Lux R which participates in the regulation of gene expression in response to fluctuations in cell-population density (quorum-sensing), a signaling molecule, the pheromone Acyl HSL (N-acyl derivatives of homoserine lactone), binds to the N-terminal domain and leads to LuxR dimerization. For others phophorylation of the N-terminal domain leads to multimerization, for example Escherichia coli NarL and Sinorhizobium melilot FixJ. NarL controls gene expression of many respiratory-related operons when environmental Probab=93.28 E-value=0.34 Score=26.29 Aligned_cols=45 Identities=16% Similarity=0.293 Sum_probs=41.6 Q ss_pred CHHHHHHHHHHHHHCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCE Q ss_conf 889999999999827689999882899789999999999995882 Q gi|254780282|r 4 DWDKLRVFYVVARSGSFTHAAEQLHLSQSSISRQISGLETEVGIK 48 (299) Q Consensus 4 d~~~L~~f~~v~~~gs~s~AA~~L~itq~avS~~i~~LE~~lg~~ 48 (299) +-++.+.+..+++-.|...-|+.|++|..+|+.+++++-+.||+. T Consensus 2 T~rE~~il~~~~~G~s~~eIA~~L~is~~TV~~~~~~i~~Kl~~~ 46 (57) T cd06170 2 TPREREVLRLLAEGKTNKEIADILGISEKTVKTHLRNIMRKLGVK 46 (57) T ss_pred CHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCC T ss_conf 889999999998079999999998978999999999999986899 No 77 >pfam08279 HTH_11 HTH domain. This family includes helix-turn-helix domains in a wide variety of proteins. Probab=93.02 E-value=0.31 Score=26.48 Aligned_cols=49 Identities=29% Similarity=0.447 Sum_probs=37.1 Q ss_pred HHHHHHHHHHC---CHHHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEECCCCE Q ss_conf 99999999827---689999882899789999999999995882179769946 Q gi|254780282|r 8 LRVFYVVARSG---SFTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHARGL 57 (299) Q Consensus 8 L~~f~~v~~~g---s~s~AA~~L~itq~avS~~i~~LE~~lg~~Lf~R~~~~~ 57 (299) ++.+..+.+.. |-..=|++|+||..||.+.|+.|+ +.|.++....|+|+ T Consensus 3 ~~il~~L~~~~~~vt~~~La~~l~VSr~TV~rdi~~L~-~~G~~I~s~~g~GY 54 (55) T pfam08279 3 LQILELLLQAREPISGQELAEKLGVSRRTIRRDIKALE-ALGVPIESEPGRGY 54 (55) T ss_pred HHHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHHHHHH-HCCCCEEECCCCCC T ss_conf 99999999769991899999996988999999999999-88997884689999 No 78 >pfam04967 HTH_10 HTH DNA binding domain. Probab=92.88 E-value=0.43 Score=25.71 Aligned_cols=42 Identities=17% Similarity=0.328 Sum_probs=35.1 Q ss_pred CHHHHHHHHHHHHHC--------CHHHHHHHHCCCHHHHHHHHHHHHHHH Q ss_conf 889999999999827--------689999882899789999999999995 Q gi|254780282|r 4 DWDKLRVFYVVARSG--------SFTHAAEQLHLSQSSISRQISGLETEV 45 (299) Q Consensus 4 d~~~L~~f~~v~~~g--------s~s~AA~~L~itq~avS~~i~~LE~~l 45 (299) +-+|.+++....+.| |++.=|+.|+||+||+|.++++-|..+ T Consensus 2 T~rQ~evl~~A~~~GYfd~PR~~~l~elA~~lgis~sT~~~hLr~ae~ki 51 (53) T pfam04967 2 TDRQREILRLAYKMGYFDYPRRVTLKDLAKELGISKSTLSEHLRRAESKL 51 (53) T ss_pred CHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHH T ss_conf 88999999999986897788768899999996989999999999999987 No 79 >PRK10870 transcriptional repressor MprA; Provisional Probab=92.66 E-value=0.28 Score=26.80 Aligned_cols=70 Identities=19% Similarity=0.154 Sum_probs=50.9 Q ss_pred CHHHHHHHHHHHHH----CCHHHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEECC-------CCEEEEECCCCCCCCCCC Q ss_conf 88999999999982----7689999882899789999999999995882179769-------946850013433222222 Q gi|254780282|r 4 DWDKLRVFYVVARS----GSFTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHA-------RGLTLTEQGSKLHRVTSE 72 (299) Q Consensus 4 d~~~L~~f~~v~~~----gs~s~AA~~L~itq~avS~~i~~LE~~lg~~Lf~R~~-------~~~~lT~~G~~l~~~a~~ 72 (299) +-.++.++..+... -+-|.=|+.+++|.+++++.+.+||+. -|+.|.. ..+.+|++|+.+++.+.+ T Consensus 54 s~~~f~vL~~L~~~~~~~l~PseLa~~l~~s~a~iTr~vD~LEkk---GlV~R~~s~~DRR~~~V~LT~~G~~ll~~~lP 130 (176) T PRK10870 54 NETLFMALITLESQENHSIQPSELSCALGSSRTNATRIADELEKR---GWIERRESDNDRRCLHLQLTEKGHEFLREVLP 130 (176) T ss_pred CHHHHHHHHHHHCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHC---CCEEEECCCCCCCEEEEEECHHHHHHHHHHHH T ss_conf 888999999997189998598999999778710199999999988---99787237123534788989889999999849 Q ss_pred CCCC Q ss_conf 2222 Q gi|254780282|r 73 VYHK 76 (299) Q Consensus 73 ~l~~ 76 (299) ...+ T Consensus 131 ~~~~ 134 (176) T PRK10870 131 PQHN 134 (176) T ss_pred HHHH T ss_conf 9999 No 80 >pfam02954 HTH_8 Bacterial regulatory protein, Fis family. Probab=92.58 E-value=0.12 Score=28.81 Aligned_cols=25 Identities=24% Similarity=0.393 Sum_probs=22.7 Q ss_pred HHCCHHHHHHHHCCCHHHHHHHHHH Q ss_conf 8276899998828997899999999 Q gi|254780282|r 16 RSGSFTHAAEQLHLSQSSISRQISG 40 (299) Q Consensus 16 ~~gs~s~AA~~L~itq~avS~~i~~ 40 (299) -.||.++||+.||||.+++.+.|++ T Consensus 17 ~~gn~~~aA~~LGisr~tL~~kmkk 41 (42) T pfam02954 17 TGGNKSKAARLLGISRRTLYRKLKK 41 (42) T ss_pred HCCCHHHHHHHHCCCHHHHHHHHHH T ss_conf 4997999999979699999999973 No 81 >COG1910 Periplasmic molybdate-binding protein/domain [Inorganic ion transport and metabolism] Probab=92.55 E-value=0.34 Score=26.29 Aligned_cols=152 Identities=11% Similarity=-0.005 Sum_probs=83.0 Q ss_pred CCCCCCCCCCCCCC-CCCCCCC------------CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC--CCCCC Q ss_conf 22222222222222-3456543------------211112234555433211234432111222222110001--12356 Q gi|254780282|r 130 NKDIDISMDYADCA-IRLRKPI------------QSSSLIQRKLVTIHMHAYAAPHYLKNCREPLSIQELDKH--NLITF 194 (299) Q Consensus 130 ~~~~~l~~~~~Di~-i~~~~~~------------~~~~l~~~~l~~~~~~~v~~~~~~~~~~~~~~~~dL~~~--~~i~~ 194 (299) .....+.+|++|++ +.+.+.. -.+.......+.-+..+++++..|.. ..+++||.+. .+|.- T Consensus 29 gG~~~i~~G~adiag~hlld~~~g~ynip~v~~~~~~~~~LI~g~~Re~Gl~v~~gnpk~---i~~~edl~~~d~~fVNR 105 (223) T COG1910 29 GGLLAIKRGEADIAGIHLLDNESGTYNIPYVKKYLPGEAVLIRGYLREQGLMVQKGNPKN---ISSLEDLLRKDLRFVNR 105 (223) T ss_pred CCHHHHHHCCCCEEEEEECCCCCCCEEHHHHHHCCCCCEEEEEEEEEEEEEEEECCCCCC---CCCHHHHHHCCCEEEEC T ss_conf 554766625451444213257787442300423078846998536651036886489776---62499885267578715 Q ss_pred CCCCCCCCCHHHHHHHHCCCCCCCCCCEEEECCCCHHHHHHHHHC---CEEEEEHHHHCCC-CCEEEECCCCCCCCCEEE Q ss_conf 643321100023566520223432121145324200135678738---4233117776019-984661776667660089 Q gi|254780282|r 195 GDLIPKCMEDFNWLATVDRPIGEPRISCLQVNSYLSIMQYCVLGS---GIALLPDYIVKDN-PNLVRIMEDVITPSFTVY 270 (299) Q Consensus 195 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~v~~g~---Gia~lp~~~~~~~-~~lv~i~~~~~~~~~~~~ 270 (299) ...+.........+...+......+-...++.+.....+.|.+|- |++ -++.++.. ..-+++ ..-+|. T Consensus 106 ~rGSGTR~LlD~~L~~~~~~~~~I~GY~~e~~th~avA~aVa~G~AD~GvG--lr~~A~~~gL~Fipl------~~E~YD 177 (223) T COG1910 106 NRGSGTRILLDELLGELNILPDSIKGYSDEATTHDAVASAVASGRADAGVG--LRHAAEKYGLDFIPL------GDEEYD 177 (223) T ss_pred CCCCCHHHHHHHHHHHCCCCCHHCCCCCCCCCCCHHHHHHHHCCCCCCCCC--HHHHHHHCCCCEEEC------CCCEEE T ss_conf 899658999999998737670105784323212089999997589872501--799999849851774------562578 Q ss_pred EEECCCCCCCHHHHHHHHHHHH Q ss_conf 9934877888899999999999 Q gi|254780282|r 271 FCYPEALKNTGKLKAFRNFIFL 292 (299) Q Consensus 271 lv~~~~~~~~~~~~~f~d~l~~ 292 (299) ++.+|+....|.++.|++.|.+ T Consensus 178 ~virke~~~~~~vr~fi~~L~s 199 (223) T COG1910 178 FVIRKERLDKPVVRAFIKALKS 199 (223) T ss_pred EEEEHHHCCCHHHHHHHHHHCC T ss_conf 9984567058889999998612 No 82 >pfam00196 GerE Bacterial regulatory proteins, luxR family. Probab=92.54 E-value=0.52 Score=25.22 Aligned_cols=46 Identities=15% Similarity=0.205 Sum_probs=42.5 Q ss_pred CCHHHHHHHHHHHHHCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCE Q ss_conf 8889999999999827689999882899789999999999995882 Q gi|254780282|r 3 FDWDKLRVFYVVARSGSFTHAAEQLHLSQSSISRQISGLETEVGIK 48 (299) Q Consensus 3 md~~~L~~f~~v~~~gs~s~AA~~L~itq~avS~~i~~LE~~lg~~ 48 (299) ++-++.+++.-+++-.+-..-|+.|++|..+|+.+++++-+.||+. T Consensus 4 LT~RE~~il~~l~~G~s~~eIA~~L~is~~TV~~h~~~i~~Kl~v~ 49 (58) T pfam00196 4 LSPREREVLRLLAAGKSNKEIADILGISEKTVKVHRSNIMRKLNVH 49 (58) T ss_pred CCHHHHHHHHHHHHCCCHHHHHHHHCCCHHHHHHHHHHHHHHCCCC T ss_conf 7999999999998079999999997888999999999999980999 No 83 >smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon Probab=92.36 E-value=0.56 Score=25.03 Aligned_cols=46 Identities=17% Similarity=0.322 Sum_probs=42.5 Q ss_pred CCHHHHHHHHHHHHHCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCE Q ss_conf 8889999999999827689999882899789999999999995882 Q gi|254780282|r 3 FDWDKLRVFYVVARSGSFTHAAEQLHLSQSSISRQISGLETEVGIK 48 (299) Q Consensus 3 md~~~L~~f~~v~~~gs~s~AA~~L~itq~avS~~i~~LE~~lg~~ 48 (299) ++=++.+++..+++-.|...-|+.|++|..+|..+++++=+.||+. T Consensus 4 LT~rE~~il~~l~~G~s~~eIA~~L~is~~TV~~~~~~i~~Kl~v~ 49 (58) T smart00421 4 LTPREREVLRLLAEGLTNKEIAERLGISEKTVKTHLSNIMRKLGVR 49 (58) T ss_pred CCHHHHHHHHHHHHCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCC T ss_conf 1899999999998179999999898978989999999999984899 No 84 >PRK10859 putative transglycosylase; Provisional Probab=92.19 E-value=0.49 Score=25.36 Aligned_cols=156 Identities=13% Similarity=0.102 Sum_probs=77.8 Q ss_pred CCCCCCCCCCCCCCCCCCC---------CHHHHHHHHHHCCCCCCCCCCC----CCCCCCCCCCCCCC-CC-CCCCCCCC Q ss_conf 2222333211100000000---------0135667542000122222222----22222222222234-56-54321111 Q gi|254780282|r 91 PSGKLRIATTIDLGQNLLQ---------GNLKEFLLLYPDIQIQLILDNK----DIDISMDYADCAIR-LR-KPIQSSSL 155 (299) Q Consensus 91 ~~g~i~I~~~~~~~~~~l~---------~~l~~f~~~~P~i~i~i~~~~~----~~~l~~~~~Di~i~-~~-~~~~~~~l 155 (299) .+|.|+|++..+-..++.. +++.+|.+.. +|++++...+. ...|..|.+|++-. .. .+.....+ T Consensus 41 ~rG~LrV~T~~spttYy~~~~~~~GFEYELak~FA~~L-GV~L~i~~~~~~~el~~~L~~G~~DiaAAgLt~t~~R~~~~ 119 (507) T PRK10859 41 ARGELRVSTIHSPLTYSTINGKPFGLDYELAKQFADYL-GVKLKVTVRQNISQLFDDLDNGNADLLAAGLVYNSERVKNY 119 (507) T ss_pred HCCEEEEEEECCCCEEEECCCCCCCHHHHHHHHHHHHC-CCEEEEEECCCHHHHHHHHHCCCCCEEECCCCCCHHHHHCC T ss_conf 78968999975896599419964779999999999980-99179997499999999986799888955787785367404 Q ss_pred CCC-CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCCCCCCCEEE--ECCCCHHH Q ss_conf 223-455543321123443211122222211000112356643321100023566520223432121145--32420013 Q gi|254780282|r 156 IQR-KLVTIHMHAYAAPHYLKNCREPLSIQELDKHNLITFGDLIPKCMEDFNWLATVDRPIGEPRISCLQ--VNSYLSIM 232 (299) Q Consensus 156 ~~~-~l~~~~~~~v~~~~~~~~~~~~~~~~dL~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~s~~~~~ 232 (299) ... +.....-.+|+.++ ...|.+++||.+..+.... +++ ....+...... ..|.....+ .-+.+.++ T Consensus 120 ~~~p~Y~~v~q~LVyr~g----~~rP~~l~DL~G~~I~V~~-gSs----y~e~L~~Lk~~-~~P~L~w~~~~~~~teeLL 189 (507) T PRK10859 120 QPGPTYYSVSQQLVYRVG----QYRPRTLGDLTGEQLTVAP-GHV----VVNDLQTLKET-KFPELSWKVDDKKGSAELL 189 (507) T ss_pred CCCCCCCCEEEEEEEECC----CCCCCCHHHCCCCEEEECC-CCH----HHHHHHHHHHC-CCCCEEEEECCCCCHHHHH T ss_conf 356865030039999589----9898897783798699817-975----99999998853-4897159955899999999 Q ss_pred HHHHHHC-CEEEEEHHHHCC----CCCEEE Q ss_conf 5678738-423311777601----998466 Q gi|254780282|r 233 QYCVLGS-GIALLPDYIVKD----NPNLVR 257 (299) Q Consensus 233 ~~v~~g~-Gia~lp~~~~~~----~~~lv~ 257 (299) ++|..|. -.+++....+.- .+++.. T Consensus 190 ~~V~~g~IdyTVaDS~~~~l~qr~~P~L~v 219 (507) T PRK10859 190 EQVIEGKLDYTIADSVAISLFQRVHPELAV 219 (507) T ss_pred HHHHCCCCCEEEECCHHHHHHHHHCCCHHC T ss_conf 999759877688554889987764844012 No 85 >pfam01638 HxlR HxlR-like helix-turn-helix. HxlR, a member of this family, is a DNA-binding protein that acts as a positive regulator of the formaldehyde-inducible hxlAB operon in Bacillus subtilis. Probab=92.01 E-value=0.23 Score=27.21 Aligned_cols=66 Identities=21% Similarity=0.394 Sum_probs=45.9 Q ss_pred HHHHHHHHHHHHHCCHHHHHHHH-CCCHHHHHHHHHHHHHHHCCEEEEECC-------CCEEEEECCCCCCCCCCCC Q ss_conf 89999999999827689999882-899789999999999995882179769-------9468500134332222222 Q gi|254780282|r 5 WDKLRVFYVVARSGSFTHAAEQL-HLSQSSISRQISGLETEVGIKLFYRHA-------RGLTLTEQGSKLHRVTSEV 73 (299) Q Consensus 5 ~~~L~~f~~v~~~gs~s~AA~~L-~itq~avS~~i~~LE~~lg~~Lf~R~~-------~~~~lT~~G~~l~~~a~~~ 73 (299) |..+-..........|+.=.+.+ ++|+..+|+++++||+. -|+.|.. -.+.||+.|+.|.+-...+ T Consensus 6 Wt~~Il~~L~~g~~rF~el~~~l~gis~~vLs~rLk~L~~~---gli~r~~~~~~p~~~eY~LT~~G~~l~pvl~~l 79 (90) T pfam01638 6 WKLLILRELLDGPKRFSELKRALPGISQKMLTQRLRELEQD---GIINREVYPEVPPKVEYSLTEKGRSLEPILQAM 79 (90) T ss_pred CHHHHHHHHHCCCCCHHHHHHHCCCCCHHHHHHHHHHHHHC---CCEEEEECCCCCCCEEEEECCCHHHHHHHHHHH T ss_conf 79999999974998899999776576989999999999988---993764569999936874390787899999999 No 86 >TIGR02607 antidote_HigA addiction module antidote protein, HigA family; InterPro: IPR013430 Proteins in this entry form a distinct group of helix-turn-helix proteins, which are strictly bacterial and nearly always shorter than 110 amino acids. They include the characterised member HigA, without which the killer protein HigB cannot be cloned. The hig (host inhibition of growth) system is noted to be unusual in that killer protein is encoded by the upstream member of the gene pair.; GO: 0003677 DNA binding. Probab=91.95 E-value=0.2 Score=27.60 Aligned_cols=29 Identities=31% Similarity=0.438 Sum_probs=25.1 Q ss_pred CHHHHHHHHCCCHHHHHHHHH-----------HHHHHHCC Q ss_conf 689999882899789999999-----------99999588 Q gi|254780282|r 19 SFTHAAEQLHLSQSSISRQIS-----------GLETEVGI 47 (299) Q Consensus 19 s~s~AA~~L~itq~avS~~i~-----------~LE~~lg~ 47 (299) |+++.|+.|+||+++||+-+. +|++.||. T Consensus 22 s~~~LA~~LgVsr~~~sriv~~~~~iT~dmALRL~~~lG~ 61 (81) T TIGR02607 22 SVRALAKALGVSRSTLSRIVNGRRGITADMALRLAKALGT 61 (81) T ss_pred HHHHHHHHCCCCHHHHHHHHHCCCCCCHHHHHHHHHHHCC T ss_conf 6899998709997888888744899888899999997389 No 87 >PRK10651 transcriptional regulator NarL; Provisional Probab=91.93 E-value=0.64 Score=24.70 Aligned_cols=38 Identities=21% Similarity=0.299 Sum_probs=19.1 Q ss_pred CCCCHHHHHHHHHHCCCCCCCCCCC--CCC-CCCCCCCCCC Q ss_conf 0000135667542000122222222--222-2222222223 Q gi|254780282|r 107 LLQGNLKEFLLLYPDIQIQLILDNK--DID-ISMDYADCAI 144 (299) Q Consensus 107 ~l~~~l~~f~~~~P~i~i~i~~~~~--~~~-l~~~~~Di~i 144 (299) .+-..+..+.+..|++++--..++. ..+ +.....|+.| T Consensus 17 l~r~gl~~~L~~~~~~~vv~~a~~~~ea~~~~~~~~pDlvl 57 (216) T PRK10651 17 MLRTGVKQLISMAPDITVVGEASNGEQGIELAESLDPDLIL 57 (216) T ss_pred HHHHHHHHHHHHCCCEEEEEEECCHHHHHHHHHHCCCCEEE T ss_conf 99999999997589938999989999999998707999999 No 88 >COG4189 Predicted transcriptional regulator [Transcription] Probab=91.81 E-value=0.38 Score=26.02 Aligned_cols=37 Identities=32% Similarity=0.473 Sum_probs=29.3 Q ss_pred HHHHHHHHHHC--CHHHHHHHHCCCHHHHHHHHHHHHHH Q ss_conf 99999999827--68999988289978999999999999 Q gi|254780282|r 8 LRVFYVVARSG--SFTHAAEQLHLSQSSISRQISGLETE 44 (299) Q Consensus 8 L~~f~~v~~~g--s~s~AA~~L~itq~avS~~i~~LE~~ 44 (299) ++.+..+-+.| |+..-|++|+++||++|..|+.||+. T Consensus 26 v~Il~lL~~k~plNvneiAe~lgLpqst~s~~ik~Le~a 64 (308) T COG4189 26 VAILQLLHRKGPLNVNEIAEALGLPQSTMSANIKVLEKA 64 (308) T ss_pred HHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHC T ss_conf 999999987179878999988588656666557888864 No 89 >PRK04168 hypothetical protein; Provisional Probab=91.73 E-value=0.41 Score=25.83 Aligned_cols=84 Identities=19% Similarity=0.198 Sum_probs=48.3 Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCCCCCCCC--CCC-CCC-C-CCCCCCCCCCCCCC----CCC--C Q ss_conf 32222223332111000000000135667542000122222222--222-222-2-22222345654321----111--2 Q gi|254780282|r 88 SVKPSGKLRIATTIDLGQNLLQGNLKEFLLLYPDIQIQLILDNK--DID-ISM-D-YADCAIRLRKPIQS----SSL--I 156 (299) Q Consensus 88 ~~~~~g~i~I~~~~~~~~~~l~~~l~~f~~~~P~i~i~i~~~~~--~~~-l~~-~-~~Di~i~~~~~~~~----~~l--~ 156 (299) ...+.|+|.|....|+... +-.+-..|.++||++++....+.+ ... +.+ | .+|+.+......-+ +++ . T Consensus 28 ~~~~~~~l~Vf~AGSL~~p-f~ei~~~Fe~~~p~v~v~~e~~GS~~~ar~Ite~g~~aDVfaSAD~~~i~~ll~p~~adw 106 (336) T PRK04168 28 EAEPPGKLKIFHAGSLSVP-FEEYEKEFEAYYPNVDVQREAGGSVACVRKITELGKPADILASADYTLIPKMMIPEYADW 106 (336) T ss_pred CCCCCEEEEEEECCCCHHH-HHHHHHHHHHHCCCCEEEEEECCHHHHHHHHHHCCCCCCEEEECCHHHHHHHHCCCCCCC T ss_conf 7788615999975525899-999999999878996599984738999999995799988899898578788746443341 Q ss_pred CCCCCCCCCCCCCCCC Q ss_conf 2345554332112344 Q gi|254780282|r 157 QRKLVTIHMHAYAAPH 172 (299) Q Consensus 157 ~~~l~~~~~~~v~~~~ 172 (299) ...+.+.+++++-+++ T Consensus 107 ~v~FA~N~lViayt~~ 122 (336) T PRK04168 107 YVMFATNEIVLAYTDK 122 (336) T ss_pred EEEECCCEEEEEECCC T ss_conf 0121155389997688 No 90 >PRK10797 glutamate and aspartate transporter subunit; Provisional Probab=91.36 E-value=1 Score=23.50 Aligned_cols=190 Identities=10% Similarity=0.059 Sum_probs=92.7 Q ss_pred CCCCCCCCCCCCCCCCCC-----------CCH---HH-HHHH--HHHCCCCCCCC---CCCCCCCCCCCCCCCCCCCCCC Q ss_conf 222233321110000000-----------001---35-6675--42000122222---2222222222222223456543 Q gi|254780282|r 91 PSGKLRIATTIDLGQNLL-----------QGN---LK-EFLL--LYPDIQIQLIL---DNKDIDISMDYADCAIRLRKPI 150 (299) Q Consensus 91 ~~g~i~I~~~~~~~~~~l-----------~~~---l~-~f~~--~~P~i~i~i~~---~~~~~~l~~~~~Di~i~~~~~~ 150 (299) .+|+|+||+..++.+.-. .++ +. .+.+ ..|++++++.. .++...|..|.+|+.+.--... T Consensus 38 ~~G~l~vG~~~~~pPf~~~d~~g~~vGfdvDla~~ia~~l~~~l~~~~~~v~~v~~~~~~rip~L~~gk~Di~~~~~t~T 117 (302) T PRK10797 38 KNGVIVVGHRESSVPFSYYDNQQKVVGYSQDYSNAIVEAVKKKLNKPDLQVKLIPITSQNRIPLLQNGTFDFECGSTTNN 117 (302) T ss_pred HCCEEEEEECCCCCCCEEECCCCCCCCCHHHHHHHHHHHHHHHHCCCCCEEEEEECCHHHHHHHHHCCCCCEEEECCCCC T ss_conf 69989999899989971689999851541799999999998774467734999975788877999789808897357569 Q ss_pred C--CCCC-CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCCCCCCCEEEECC Q ss_conf 2--1111-223455543321123443211122222211000112356643321100023566520223432121145324 Q gi|254780282|r 151 Q--SSSL-IQRKLVTIHMHAYAAPHYLKNCREPLSIQELDKHNLITFGDLIPKCMEDFNWLATVDRPIGEPRISCLQVNS 227 (299) Q Consensus 151 ~--~~~l-~~~~l~~~~~~~v~~~~~~~~~~~~~~~~dL~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s 227 (299) + ...+ ...+.+.....+++.++ ....+++||.+-....- .+.. ...++...... .........+++ T Consensus 118 ~eR~k~vdFS~pY~~~~~~llv~k~-----s~Iks~~DL~GK~V~V~-~GTt----~e~~~~~~~~~-~~~~~~iv~~~~ 186 (302) T PRK10797 118 LERQKQAAFSDTIFVVGTRLLTKKG-----GDIKDFADLKGKAVVVT-SGTT----SEVLLNKLNEE-QKMNMRIISAKD 186 (302) T ss_pred HHHHCCEEECCCCEECCEEEEEECC-----CCCCCHHHHCCCEEEEE-CCCH----HHHHHHHHHHH-HCCCCEEEECCC T ss_conf 7774124214662771468999778-----86667566089979996-7873----99999986675-067723785088 Q ss_pred CCHHHHHHHHHCCEEEEEHH-H-----HC-CCCCEEEECCCCCCCCCEEEEEECCCCCCCHHHHHHHHHHHHHHH Q ss_conf 20013567873842331177-7-----60-199846617766676600899934877888899999999999985 Q gi|254780282|r 228 YLSIMQYCVLGSGIALLPDY-I-----VK-DNPNLVRIMEDVITPSFTVYFCYPEALKNTGKLKAFRNFIFLKAR 295 (299) Q Consensus 228 ~~~~~~~v~~g~Gia~lp~~-~-----~~-~~~~lv~i~~~~~~~~~~~~lv~~~~~~~~~~~~~f~d~l~~~~r 295 (299) ...+...+.+|..-+++-+. . +. ..+....+... +....++++..+|+ .+..+.+++--+++.+ T Consensus 187 ~~~a~~~L~~GrvDA~~~D~~~l~~~~~~~~~~~~~~iv~~-~~~~e~ygia~rKg---d~~L~~~Vn~aL~~l~ 257 (302) T PRK10797 187 HGDSFRTLESGRAVAFMMDDALLAGERAKAKKPDNWEIVGK-PQSQEAYGCMLRKD---DPQFKKLMDDTIAQAQ 257 (302) T ss_pred HHHHHHHHHCCCCCEEEECHHHHHHHHHHCCCCCCEEEECC-CCCCCCEEEEEECC---CHHHHHHHHHHHHHHH T ss_conf 89999999859950998122988899986369975499378-67776079999689---9999999999999999 No 91 >PRK09495 glnH glutamine ABC transporter periplasmic protein; Reviewed Probab=91.28 E-value=1 Score=23.45 Aligned_cols=170 Identities=10% Similarity=0.028 Sum_probs=82.9 Q ss_pred CCCCCCCCCCCCCCCC----------CCCHHHHHHHHHHCCCCCCCCCC---CCCCCCCCCCCCCCC-CCC-CCCCCCC- Q ss_conf 2223332111000000----------00013566754200012222222---222222222222234-565-4321111- Q gi|254780282|r 92 SGKLRIATTIDLGQNL----------LQGNLKEFLLLYPDIQIQLILDN---KDIDISMDYADCAIR-LRK-PIQSSSL- 155 (299) Q Consensus 92 ~g~i~I~~~~~~~~~~----------l~~~l~~f~~~~P~i~i~i~~~~---~~~~l~~~~~Di~i~-~~~-~~~~~~l- 155 (299) .++|+||+.+.+.++- -.+++..+.++- ++++++...+ ....|..|++|+++. +.. +.....+ T Consensus 24 ~~~l~Vg~~~~~pPf~f~~~g~~~GfdvDl~~~ia~~l-g~~~e~~~~~~~~~i~~l~~g~~D~~~~~~~~T~eR~~~~~ 102 (247) T PRK09495 24 DKELVVATDTAFVPFEFKQGDKYVGFDVDLWAAIAKEL-KLDYTLKPMDFSGIIPALQTKNIDLALAGITITDERKKAID 102 (247) T ss_pred CCEEEEEECCCCCCEEECCCCEEEEEHHHHHHHHHHHH-CCCEEEEECCHHHHHHHHHCCCCCEEECCCCCCHHHHHHCC T ss_conf 99499998998798057679927882999999999996-99469997788999999976995636466014789984333 Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCCCCCCCEEEECCCCHHHHHH Q ss_conf 22345554332112344321112222221100011235664332110002356652022343212114532420013567 Q gi|254780282|r 156 IQRKLVTIHMHAYAAPHYLKNCREPLSIQELDKHNLITFGDLIPKCMEDFNWLATVDRPIGEPRISCLQVNSYLSIMQYC 235 (299) Q Consensus 156 ~~~~l~~~~~~~v~~~~~~~~~~~~~~~~dL~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~v 235 (299) ...+.+.....+++..+. ....+++||.+... ....++. ...++... .+......+++...+..++ T Consensus 103 FS~py~~~~~~i~v~~~~----~~i~~~~dL~Gk~v-~v~~Gs~----~~~~~~~~-----~~~~~i~~~~~~~~~~~aL 168 (247) T PRK09495 103 FSDGYYKSGLLVMVKANN----NDIKSVKDLDGKVV-AVKSGTG----SVDYAKAN-----IKTKDLRQFPNIDNAYLEL 168 (247) T ss_pred CCCCCEEEEEEEEEECCC----CCCCCHHHCCCCEE-EEECCCH----HHHHHHHH-----CCCCCEEECCCHHHHHHHH T ss_conf 477707724699998999----77798245489889-9846958----99999963-----8898669659889999987 Q ss_pred HHHCCEEEEEHH-----HHCCC--CCEEEECCCCCCCCCEEEEEECCCCC Q ss_conf 873842331177-----76019--98466177666766008999348778 Q gi|254780282|r 236 VLGSGIALLPDY-----IVKDN--PNLVRIMEDVITPSFTVYFCYPEALK 278 (299) Q Consensus 236 ~~g~Gia~lp~~-----~~~~~--~~lv~i~~~~~~~~~~~~lv~~~~~~ 278 (299) .+|..=+++-+. .++.. +.+ ++... +.....+++..+++.. T Consensus 169 ~~GrvDa~v~d~~~~~~~~~~~~~~~~-~~~~~-~~~~~~~~ia~~k~~~ 216 (247) T PRK09495 169 GTGRADAVLHDTPNILYFIKTAGNGQF-KAVGD-SLEAQQYGIAFPKGSD 216 (247) T ss_pred HCCCEEEEEECHHHHHHHHHHCCCCCE-EEECC-CCCCCEEEEEEECCHH T ss_conf 658734999568999999984899978-99467-7776459999928829 No 92 >PRK04217 hypothetical protein; Provisional Probab=91.21 E-value=0.57 Score=24.98 Aligned_cols=62 Identities=16% Similarity=0.318 Sum_probs=45.1 Q ss_pred CCHHHHHHHHHH-HHHCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEECCCCEEEEECCCCC Q ss_conf 888999999999-9827689999882899789999999999995882179769946850013433 Q gi|254780282|r 3 FDWDKLRVFYVV-ARSGSFTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHARGLTLTEQGSKL 66 (299) Q Consensus 3 md~~~L~~f~~v-~~~gs~s~AA~~L~itq~avS~~i~~LE~~lg~~Lf~R~~~~~~lT~~G~~l 66 (299) |+++.|+.+.-+ .+--+-..||++++||++|+.+-+.+-...+...|+. |+.+..-+.|..+ T Consensus 43 LtvdE~EaiRL~D~egl~qeeaA~~M~VSR~Tf~ril~~AR~KvA~aLv~--Gkal~I~~~g~~~ 105 (110) T PRK04217 43 MTYEEFEALRLVDYEGLTQEEAGKRMGVSRGTVWRALTSARKKVAQMLVE--GRELIILPQGNEV 105 (110) T ss_pred ECHHHHHHHHHHHHCCCCHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHC--CCEEEEECCCCCE T ss_conf 11999999998736079899999884976999999999999999999867--9748997489960 No 93 >PRK09775 hypothetical protein; Provisional Probab=91.01 E-value=0.11 Score=29.22 Aligned_cols=36 Identities=25% Similarity=0.428 Sum_probs=25.3 Q ss_pred HHHHHCCHHHH--HHHHCCCHHHHHHHHHHHHHHHCCEEEEE Q ss_conf 99982768999--98828997899999999999958821797 Q gi|254780282|r 13 VVARSGSFTHA--AEQLHLSQSSISRQISGLETEVGIKLFYR 52 (299) Q Consensus 13 ~v~~~gs~s~A--A~~L~itq~avS~~i~~LE~~lg~~Lf~R 52 (299) ++-+-|-.+.+ |++|+|||||||++|+. +|.+.... T Consensus 6 ~Ll~~Gp~~a~eLa~~lgvSqpTlSR~l~~----l~~~Vv~~ 43 (443) T PRK09775 6 TLLLQGPLSAAELAQRLGISQATLSRLLAA----AGPQVLRF 43 (443) T ss_pred HHHHCCCCCHHHHHHHHCCCHHHHHHHHHH----CCCCEEEE T ss_conf 999739935999999868888889999986----25727885 No 94 >PRK09744 DNA-binding transcriptional regulator DicC; Provisional Probab=90.55 E-value=0.28 Score=26.79 Aligned_cols=37 Identities=24% Similarity=0.153 Sum_probs=26.9 Q ss_pred HHHHHCCHHHHHHHHCCCHHHHHHHH--------HHHHHHHCCEE Q ss_conf 99982768999988289978999999--------99999958821 Q gi|254780282|r 13 VVARSGSFTHAAEQLHLSQSSISRQI--------SGLETEVGIKL 49 (299) Q Consensus 13 ~v~~~gs~s~AA~~L~itq~avS~~i--------~~LE~~lg~~L 49 (299) ++.-.||.++.|+.||||+|+||+-= -+||+.-|-.| T Consensus 6 vi~~FGsk~klA~aLgIs~~aVsqWge~IPE~rAy~le~iT~G~L 50 (75) T PRK09744 6 AIAFFGSKTKLANAAGVRLASVAAWGELVPEGRAMRLQEASGGEL 50 (75) T ss_pred HHHHHCCHHHHHHHHCCCHHHHHHHHHHCCHHHHHHHHHHHCCCE T ss_conf 999961299999994998799988740160688999999858851 No 95 >COG0226 PstS ABC-type phosphate transport system, periplasmic component [Inorganic ion transport and metabolism] Probab=90.18 E-value=1.3 Score=22.86 Aligned_cols=202 Identities=12% Similarity=0.102 Sum_probs=99.6 Q ss_pred CCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCCCCCCC---CCCCCCCCCCCCCCCCCCCCC---CC-------CCC Q ss_conf 22222333211100000000013566754200012222222---222222222222234565432---11-------112 Q gi|254780282|r 90 KPSGKLRIATTIDLGQNLLQGNLKEFLLLYPDIQIQLILDN---KDIDISMDYADCAIRLRKPIQ---SS-------SLI 156 (299) Q Consensus 90 ~~~g~i~I~~~~~~~~~~l~~~l~~f~~~~P~i~i~i~~~~---~~~~l~~~~~Di~i~~~~~~~---~~-------~l~ 156 (299) ...+.|+++-+.+. ..+.-.....|.+.||++.+++.... .......+++|++- ...|.. .. .+. T Consensus 40 ~~~~~l~~~GSttv-~p~~~~~a~~~~~~~~~~~v~~q~~GSg~G~~~~~~~~vDig~-ss~p~~~~e~~~~~~~~~~l~ 117 (318) T COG0226 40 GASGSLTIAGSTTV-APLMEAWAEEFQKAYPNVKVNVQAGGSGAGIKQALAGGVDIGA-SSRPLKDSEKEADAKAGKKLV 117 (318) T ss_pred CCCCEEEEECCCCH-HHHHHHHHHHHHHHCCCEEEEEECCCCHHHHHHHHCCCCCCCC-CCCCCCCCHHHHHHHCCCCCE T ss_conf 55435998365738-9999999999998789947876368661889987526770313-576666326799874079866 Q ss_pred CCCCCCCCCCCCCCCCCCC-CC-----------CCCCCCCCCC----CCCC--CCCCCCCCCCCCHHHHHHHHCC--CCC Q ss_conf 2345554332112344321-11-----------2222221100----0112--3566433211000235665202--234 Q gi|254780282|r 157 QRKLVTIHMHAYAAPHYLK-NC-----------REPLSIQELD----KHNL--ITFGDLIPKCMEDFNWLATVDR--PIG 216 (299) Q Consensus 157 ~~~l~~~~~~~v~~~~~~~-~~-----------~~~~~~~dL~----~~~~--i~~~~~~~~~~~~~~~~~~~~~--~~~ 216 (299) ..++.-+.++++..+.-+. .. +....+.|+. +.+. +.-.+.......+..++..... ..+ T Consensus 118 ~~pva~d~i~vi~N~~~~~~~~Lt~~~l~~If~G~it~W~d~~~~~~n~~I~vv~R~~~SGT~~~F~~~l~~~~~~~~~g 197 (318) T COG0226 118 EFPVAIDAIVVIVNLPNPDVLNLTKDQLADIFSGKITNWNDVGGQLLNPGITVVGRSDGSGTTETFTEYLLGWKKKVGAG 197 (318) T ss_pred EEEEEEEEEEEEECCCCCCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCEEEECCCCCCHHHHHHHHHHHHHHCCCCC T ss_conf 97788777999975898541347999999997088875556686558998568847877776999999987653203456 Q ss_pred --CCCCCEEEECCCCHHHHHHHHH-CCEEEEEHHHHCCC-----------CC---EEE-----ECCCCC-CCCCEEEEEE Q ss_conf --3212114532420013567873-84233117776019-----------98---466-----177666-7660089993 Q gi|254780282|r 217 --EPRISCLQVNSYLSIMQYCVLG-SGIALLPDYIVKDN-----------PN---LVR-----IMEDVI-TPSFTVYFCY 273 (299) Q Consensus 217 --~~~~~~~~~~s~~~~~~~v~~g-~Gia~lp~~~~~~~-----------~~---lv~-----i~~~~~-~~~~~~~lv~ 273 (299) ..........+...+...|... .+|+++--..+.++ +. -+. +..... +..+..|+++ T Consensus 198 ~~~~~~~~~~~~~n~~v~~~v~~tp~aIGYv~~~y~~~n~~~~~~~~~~~~~~~~~v~p~~~~i~~~~y~Pi~~~~~~~v 277 (318) T COG0226 198 KTVDWPAAVGGKGNEGVVAAVSQTPGAIGYVGYAYAVQNNLKLAALANKAGGVGPTVEPTAENIANGKYSPIVRPLFIYV 277 (318) T ss_pred CCCCCCCEECCCCCHHHHHHHHCCCCCEEEEEEHHHHHCCCHHHHHHHCCCCCCCCCCCHHHHHHCCCCCCCEEEEEEEE T ss_conf 65445640036885788988853998459998679652430566642015776666564577753377355125789998 Q ss_pred CCCCC--CCHHHHHHHHHHHHH Q ss_conf 48778--888999999999999 Q gi|254780282|r 274 PEALK--NTGKLKAFRNFIFLK 293 (299) Q Consensus 274 ~~~~~--~~~~~~~f~d~l~~~ 293 (299) .+... ..+.++.|++|.+.. T Consensus 278 ~~~~~~~~~~~~~~Fi~~~~~~ 299 (318) T COG0226 278 NKNPKDTKAPAVKAFLDWALSP 299 (318) T ss_pred ECCCCCCCCHHHHHHHHHHHCC T ss_conf 2776666588999999999678 No 96 >PRK10403 transcriptional regulator NarP; Provisional Probab=90.17 E-value=1.1 Score=23.26 Aligned_cols=17 Identities=18% Similarity=0.546 Sum_probs=8.2 Q ss_pred CCCHHHHHHHHHHCCCC Q ss_conf 00013566754200012 Q gi|254780282|r 108 LQGNLKEFLLLYPDIQI 124 (299) Q Consensus 108 l~~~l~~f~~~~P~i~i 124 (299) +-..+..+.+..|++++ T Consensus 18 ~r~gl~~~L~~~~~~~v 34 (215) T PRK10403 18 MRRGVRQLLELDPGFEV 34 (215) T ss_pred HHHHHHHHHHHCCCEEE T ss_conf 99999999975899289 No 97 >COG1339 Transcriptional regulator of a riboflavin/FAD biosynthetic operon [Transcription / Coenzyme metabolism] Probab=89.59 E-value=0.18 Score=27.85 Aligned_cols=93 Identities=18% Similarity=0.214 Sum_probs=55.7 Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHH-CCEEEEECCCCEEEEECCCCCCCCCCCCCCCCCHHHHHCCCCC-CCCCCCC Q ss_conf 7689999882899789999999999995-8821797699468500134332222222222101221001223-2222223 Q gi|254780282|r 18 GSFTHAAEQLHLSQSSISRQISGLETEV-GIKLFYRHARGLTLTEQGSKLHRVTSEVYHKLETTQIELQESS-VKPSGKL 95 (299) Q Consensus 18 gs~s~AA~~L~itq~avS~~i~~LE~~l-g~~Lf~R~~~~~~lT~~G~~l~~~a~~~l~~~~~~~~~~~~~~-~~~~g~i 95 (299) -+.+..|++|++|+++.|+.|++||+.= =.+-..+.|.-+..|+.|..++... +++....+.... -...|.+ T Consensus 20 ~t~~ela~~l~~S~qta~R~l~~le~~~~I~R~~~~~Gq~i~iTekG~~~L~~~------~~d~~r~~~~~~~i~i~G~V 93 (214) T COG1339 20 VTSSELAKRLGVSSQTAARKLKELEDEGYITRTISKRGQLITITEKGIDLLYKE------YEDLSRIFDSGGNIVIEGEV 93 (214) T ss_pred CCHHHHHHHHCCCCHHHHHHHHHHCCCCCEEEEECCCCCEEEEHHHHHHHHHHH------HHHHHHHHCCCCCEEEEEEE T ss_conf 208999988574707788998864117847888337984898167689999999------99999996688736999889 Q ss_pred CCCCCCCCCCCCC--CCHHHHHHHH Q ss_conf 3321110000000--0013566754 Q gi|254780282|r 96 RIATTIDLGQNLL--QGNLKEFLLL 118 (299) Q Consensus 96 ~I~~~~~~~~~~l--~~~l~~f~~~ 118 (299) .=|+.. +.+++ +..-..|++. T Consensus 94 ~SGlGE--G~yyvS~~~Y~~qf~ek 116 (214) T COG1339 94 VSGLGE--GRYYVSLPGYRRQFREK 116 (214) T ss_pred ECCCCC--CEEEEECHHHHHHHHHH T ss_conf 525556--43797268889999998 No 98 >PRK09958 DNA-binding transcriptional activator EvgA; Provisional Probab=89.56 E-value=1.4 Score=22.66 Aligned_cols=15 Identities=13% Similarity=-0.204 Sum_probs=5.9 Q ss_pred CHHHHHHHHHHCCCC Q ss_conf 013566754200012 Q gi|254780282|r 110 GNLKEFLLLYPDIQI 124 (299) Q Consensus 110 ~~l~~f~~~~P~i~i 124 (299) ..+..+++.+|+..+ T Consensus 62 ~~~~~ir~~~~~~~v 76 (204) T PRK09958 62 QVLETLRKRQYSGII 76 (204) T ss_pred HHHHHHHHHCCCEEE T ss_conf 678889872798059 No 99 >COG1497 Predicted transcriptional regulator [Transcription] Probab=89.51 E-value=1 Score=23.45 Aligned_cols=46 Identities=22% Similarity=0.338 Sum_probs=37.4 Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEECCC-CEEEEECCCCC Q ss_conf 76899998828997899999999999958821797699-46850013433 Q gi|254780282|r 18 GSFTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHAR-GLTLTEQGSKL 66 (299) Q Consensus 18 gs~s~AA~~L~itq~avS~~i~~LE~~lg~~Lf~R~~~-~~~lT~~G~~l 66 (299) -+-+.=|+.|+||..|||.+||+|-++ -|++..|| ....|..|... T Consensus 26 v~q~eIA~~lgiT~QaVsehiK~Lv~e---G~i~~~gR~~Y~iTkkG~e~ 72 (260) T COG1497 26 VKQKEIAKKLGITLQAVSEHIKELVKE---GLIEKEGRGEYEITKKGAEW 72 (260) T ss_pred CCHHHHHHHCCCCHHHHHHHHHHHHHC---CCEEECCCEEEEEEHHHHHH T ss_conf 788899987098799999999999866---46661487258972668999 No 100 >PRK09834 DNA-binding transcriptional activator MhpR; Provisional Probab=89.13 E-value=0.82 Score=24.05 Aligned_cols=54 Identities=24% Similarity=0.325 Sum_probs=38.6 Q ss_pred HHHHHHHHHHH---HCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEE--CCCCEEEEEC Q ss_conf 99999999998---276899998828997899999999999958821797--6994685001 Q gi|254780282|r 6 DKLRVFYVVAR---SGSFTHAAEQLHLSQSSISRQISGLETEVGIKLFYR--HARGLTLTEQ 62 (299) Q Consensus 6 ~~L~~f~~v~~---~gs~s~AA~~L~itq~avS~~i~~LE~~lg~~Lf~R--~~~~~~lT~~ 62 (299) |-|..+.++++ --|++.-|++++++.|++.+.++.|++. | ++.| ..+++.|++. T Consensus 12 Ral~ILe~l~~~~~~lslsela~~lglpksTv~RlL~tL~~~-G--~l~~~~~~~~Y~LG~~ 70 (264) T PRK09834 12 RGLMVLRALNRLDGGATVGLLAELTGLHRTTVRRLLETLQEE-G--YVRRSASDDSFRLTLK 70 (264) T ss_pred HHHHHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHC-C--CEEEECCCCCEECCHH T ss_conf 999999987417999799999999790999999999999978-9--9899679997651607 No 101 >COG4190 Predicted transcriptional regulator [Transcription] Probab=89.08 E-value=1.6 Score=22.36 Aligned_cols=41 Identities=20% Similarity=0.276 Sum_probs=17.3 Q ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEECCCCEEEE Q ss_conf 689999882899789999999999995882179769946850 Q gi|254780282|r 19 SFTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHARGLTLT 60 (299) Q Consensus 19 s~s~AA~~L~itq~avS~~i~~LE~~lg~~Lf~R~~~~~~lT 60 (299) |++.+|+.-+--.+.||+.++.||. +|.--|+++|+..+|+ T Consensus 80 Si~ElAe~vgRdv~nvhr~Ls~l~~-~GlI~fe~~gq~k~P~ 120 (144) T COG4190 80 SINELAELVGRDVKNVHRTLSTLAD-LGLIFFEEDGQRKQPV 120 (144) T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHH-CCEEEEECCCCCCCCE T ss_conf 3899999867546889899999986-4827874177313752 No 102 >PRK10163 DNA-binding transcriptional repressor AllR; Provisional Probab=89.01 E-value=0.51 Score=25.25 Aligned_cols=56 Identities=14% Similarity=0.029 Sum_probs=40.9 Q ss_pred HHHHHHHHHHHHHCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEECCCCEEEEE Q ss_conf 899999999998276899998828997899999999999958821797699468500 Q gi|254780282|r 5 WDKLRVFYVVARSGSFTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHARGLTLTE 61 (299) Q Consensus 5 ~~~L~~f~~v~~~gs~s~AA~~L~itq~avS~~i~~LE~~lg~~Lf~R~~~~~~lT~ 61 (299) ++-|++|-.--..-+++.-|+.++++.|++.+-++.|+++ |.--.+..++.+.|.. T Consensus 28 l~IL~~la~~~~~ltl~eia~~lglpksT~~RlL~tL~~~-G~v~~d~~~~~Y~lG~ 83 (271) T PRK10163 28 IAILQYLEKSGGSSSVSDISLNLDLPLSTTFRLLKVLQAA-DFVYQDSQLGWWHIGL 83 (271) T ss_pred HHHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHC-CCEEEECCCCCEECCH T ss_conf 9999999747999799999999791999999999999968-9889848999176478 No 103 >COG2345 Predicted transcriptional regulator [Transcription] Probab=88.97 E-value=0.63 Score=24.73 Aligned_cols=55 Identities=29% Similarity=0.375 Sum_probs=39.1 Q ss_pred HHHHC--CHHHHHHHHCCCHHHHHHHHHHHHHHH--CCEEEEECCC-----CEEEEECCCCCCCC Q ss_conf 99827--689999882899789999999999995--8821797699-----46850013433222 Q gi|254780282|r 14 VARSG--SFTHAAEQLHLSQSSISRQISGLETEV--GIKLFYRHAR-----GLTLTEQGSKLHRV 69 (299) Q Consensus 14 v~~~g--s~s~AA~~L~itq~avS~~i~~LE~~l--g~~Lf~R~~~-----~~~lT~~G~~l~~~ 69 (299) +-+.| |....|++|+||..||-+|+..||++= ... +.+.++ .+++|+.|..-+++ T Consensus 20 L~~~g~~sa~elA~~Lgis~~avR~HL~~Le~~Glv~~~-~~~~g~GRP~~~y~Lt~~g~~~f~~ 83 (218) T COG2345 20 LKKSGPVSADELAEELGISPMAVRRHLDDLEAEGLVEVE-RQQGGRGRPAKLYRLTEKGREQFPK 83 (218) T ss_pred HHCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEE-ECCCCCCCCCEEEEECCCCHHHCCH T ss_conf 831698249999988599989999999999868666876-4257899973332200262654453 No 104 >COG1733 Predicted transcriptional regulators [Transcription] Probab=88.84 E-value=0.71 Score=24.42 Aligned_cols=66 Identities=24% Similarity=0.335 Sum_probs=44.8 Q ss_pred HHHHHHHHHHHHHCCHHHHHHHHC-CCHHHHHHHHHHHHHHHCCEEEEECCC-------CEEEEECCCCCCCCCCCC Q ss_conf 899999999998276899998828-997899999999999958821797699-------468500134332222222 Q gi|254780282|r 5 WDKLRVFYVVARSGSFTHAAEQLH-LSQSSISRQISGLETEVGIKLFYRHAR-------GLTLTEQGSKLHRVTSEV 73 (299) Q Consensus 5 ~~~L~~f~~v~~~gs~s~AA~~L~-itq~avS~~i~~LE~~lg~~Lf~R~~~-------~~~lT~~G~~l~~~a~~~ 73 (299) |.-+-..........|+.=-+.+. |||-.+|++++.||+. -|+.|.-. ...||+.|+.|.+....+ T Consensus 24 W~~lIl~~L~~g~~RF~eL~r~i~~Is~k~Ls~~Lk~Le~~---Glv~R~~~~~~PprveY~LT~~G~~L~~vl~~l 97 (120) T COG1733 24 WTLLILRDLFDGPKRFNELRRSIGGISPKMLSRRLKELEED---GLVERVVYPEEPPRVEYRLTEKGRDLLPVLLAL 97 (120) T ss_pred CHHHHHHHHHCCCCCHHHHHHHCCCCCHHHHHHHHHHHHHC---CCEEEEECCCCCCEEEEEEHHHHHHHHHHHHHH T ss_conf 49999999954987399998677454899999999999988---998987417899534777634327699999999 No 105 >pfam01710 Transposase_14 Transposase. Transposase proteins are necessary for efficient DNA transposition. This family includes insertion sequences from Synechocystis PCC 6803 three of which are characterized as homologous to bacterial IS5- and IS4- and to several members of the IS630-Tc1-mariner superfamily. Probab=88.74 E-value=0.85 Score=23.98 Aligned_cols=44 Identities=25% Similarity=0.493 Sum_probs=32.1 Q ss_pred CCC--CHHHHHHHHHHHHHCCHHHHHHHHCCCHHHHHHHHHHHHHHHCC Q ss_conf 988--88999999999982768999988289978999999999999588 Q gi|254780282|r 1 MSF--DWDKLRVFYVVARSGSFTHAAEQLHLSQSSISRQISGLETEVGI 47 (299) Q Consensus 1 m~m--d~~~L~~f~~v~~~gs~s~AA~~L~itq~avS~~i~~LE~~lg~ 47 (299) |.. ||++ +++-.+-+.+|.+.||+..+||.++|-+=+++ .+.|. T Consensus 1 MaYS~DlR~-rVl~~ve~G~S~~eaA~~F~Is~~Tv~rWlkr--~~~~~ 46 (120) T pfam01710 1 MAYSLDLRK-KVIDYIESGGSITEASKVFQIGRATIYRWLKR--EKLGA 46 (120) T ss_pred CCCCHHHHH-HHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHC--HHCCC T ss_conf 987689999-99999986999999999937029999999855--00147 No 106 >PRK09483 response regulator; Provisional Probab=88.11 E-value=1.9 Score=21.98 Aligned_cols=16 Identities=13% Similarity=0.291 Sum_probs=7.1 Q ss_pred CCHHHHHHHHHHCCCC Q ss_conf 0013566754200012 Q gi|254780282|r 109 QGNLKEFLLLYPDIQI 124 (299) Q Consensus 109 ~~~l~~f~~~~P~i~i 124 (299) -.-+..+.+..|++++ T Consensus 14 r~gl~~~L~~~~~~~v 29 (216) T PRK09483 14 RAGIRRILEDIKGIKV 29 (216) T ss_pred HHHHHHHHHHCCCCEE T ss_conf 9999999974899589 No 107 >PRK09935 transcriptional regulator FimZ; Provisional Probab=88.04 E-value=1.9 Score=21.95 Aligned_cols=18 Identities=22% Similarity=0.313 Sum_probs=8.4 Q ss_pred CCHHHHHHHHHHCCCCCC Q ss_conf 001356675420001222 Q gi|254780282|r 109 QGNLKEFLLLYPDIQIQL 126 (299) Q Consensus 109 ~~~l~~f~~~~P~i~i~i 126 (299) -.-+..+.+..|++++-. T Consensus 16 r~gl~~~l~~~~~~~vv~ 33 (210) T PRK09935 16 RMSIEVLLQKNSNIQVVL 33 (210) T ss_pred HHHHHHHHHCCCCEEEEE T ss_conf 999999996298928999 No 108 >PRK10360 DNA-binding transcriptional activator UhpA; Provisional Probab=87.96 E-value=1.9 Score=21.92 Aligned_cols=37 Identities=16% Similarity=0.250 Sum_probs=16.3 Q ss_pred CCCHHHHHHHHHHCCCCCCCCCCCC---CCCCCCCCCCCC Q ss_conf 0001356675420001222222222---222222222223 Q gi|254780282|r 108 LQGNLKEFLLLYPDIQIQLILDNKD---IDISMDYADCAI 144 (299) Q Consensus 108 l~~~l~~f~~~~P~i~i~i~~~~~~---~~l~~~~~Di~i 144 (299) +-.-+..+.+.+|++++--..++.. ..+.....|+.| T Consensus 13 ~r~gl~~~l~~~~~~~vv~~~~~~~~~l~~~~~~~~dvvl 52 (196) T PRK10360 13 VRSGFAQLLGLEPDLQVVAEFGSGREALAGLPGRGVQVCI 52 (196) T ss_pred HHHHHHHHHHCCCCEEEEEEECCHHHHHHHHHHCCCCEEE T ss_conf 9999999981299959999989999999988744999999 No 109 >PRK10840 transcriptional regulator RcsB; Provisional Probab=87.46 E-value=2.1 Score=21.75 Aligned_cols=15 Identities=20% Similarity=0.299 Sum_probs=6.7 Q ss_pred HHHHHHHHHHCCCCC Q ss_conf 135667542000122 Q gi|254780282|r 111 NLKEFLLLYPDIQIQ 125 (299) Q Consensus 111 ~l~~f~~~~P~i~i~ 125 (299) .+..+++.+|++.|- T Consensus 70 ~~~~i~~~~p~~~vi 84 (216) T PRK10840 70 LIKYIKRHFPSLSII 84 (216) T ss_pred HHHHHHHHCCCCEEE T ss_conf 999999858998089 No 110 >PRK04172 pheS phenylalanyl-tRNA synthetase subunit alpha; Provisional Probab=87.39 E-value=1.7 Score=22.27 Aligned_cols=71 Identities=21% Similarity=0.198 Sum_probs=54.5 Q ss_pred CCCCHHHHHHHHHHHHH--CCHHHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEECCCCEEEEECCCCCCCCCC Q ss_conf 98888999999999982--768999988289978999999999999588217976994685001343322222 Q gi|254780282|r 1 MSFDWDKLRVFYVVARS--GSFTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHARGLTLTEQGSKLHRVTS 71 (299) Q Consensus 1 m~md~~~L~~f~~v~~~--gs~s~AA~~L~itq~avS~~i~~LE~~lg~~Lf~R~~~~~~lT~~G~~l~~~a~ 71 (299) |.+..++.+.+.++.+. .+....|+.+++.+..|-+.++.|++.==+..-.+....+.||++|+..++.-- T Consensus 2 ~~L~~~E~kIL~~L~~~~~~~~eeLa~~~g~d~~~V~~ai~~L~~kglI~vee~~~~~~~LTeEG~~yle~Gl 74 (501) T PRK04172 2 MELHPNEKKVLKALAELKKATAEELAEKLGLDEEAVMRAAEWLEEKGLVEVEEKVTEFYELTEEGKKYLEEGL 74 (501) T ss_pred CCCCHHHHHHHHHHHHCCCCCHHHHHHHCCCCHHHHHHHHHHHHHCCCEEEEEEEEEEEEECHHHHHHHHCCC T ss_conf 7478789999999974799999999988299999999999988758997999888889998888999997699 No 111 >cd00134 PBPb Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and inorganic ions. PBPs have two cell-membrane translocation functions: bind substrate, and interact with the membrane bound complex. A diverse group of periplasmic transport receptors for lysine/arginine/ornithine (LAO), glutamine, histidine, sulfate, phosphate, molybdate, and methanol are included in the PBPb CD. Probab=86.92 E-value=2.2 Score=21.57 Aligned_cols=168 Identities=8% Similarity=0.037 Sum_probs=79.4 Q ss_pred CCCCHHHHHHHHHHCCCCCCCCCC---CCCCCCCCCCCCCCC-CC-CCCCCCCC-CCCCCCCCCCCCCCCCCCCCCCCCC Q ss_conf 000013566754200012222222---222222222222234-56-54321111-2234555433211234432111222 Q gi|254780282|r 107 LLQGNLKEFLLLYPDIQIQLILDN---KDIDISMDYADCAIR-LR-KPIQSSSL-IQRKLVTIHMHAYAAPHYLKNCREP 180 (299) Q Consensus 107 ~l~~~l~~f~~~~P~i~i~i~~~~---~~~~l~~~~~Di~i~-~~-~~~~~~~l-~~~~l~~~~~~~v~~~~~~~~~~~~ 180 (299) +..+++..+.+.- ++++++...+ ....+..|++|+++. +. .+.....+ ...++.....++++.++. .. T Consensus 24 ~~~dl~~~i~~~l-g~~~~~~~~~~~~~~~~l~~g~~D~~~~~~~~t~~R~~~~~fs~p~~~~~~~~~~~~~~-----~~ 97 (218) T cd00134 24 FDVDLAKAIAKEL-GVKVKFVEVDWDGLITALKSGKVDLIAAGMTITPERAKQVDFSDPYYKSGQVILVKKGS-----PI 97 (218) T ss_pred EHHHHHHHHHHHH-CCCEEEEECCHHHHHHHHHCCCCCEEEEEECCCHHHHCCCCCCCCEECCCEEEEEECCC-----CC T ss_conf 3999999999996-99669997588999999857997768885025856614145576444157079998689-----99 Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCCCCCCCEEEECCCCHHHHHHHHHCCEEEE-EHHH----HCCCC-C Q ss_conf 2221100011235664332110002356652022343212114532420013567873842331-1777----60199-8 Q gi|254780282|r 181 LSIQELDKHNLITFGDLIPKCMEDFNWLATVDRPIGEPRISCLQVNSYLSIMQYCVLGSGIALL-PDYI----VKDNP-N 254 (299) Q Consensus 181 ~~~~dL~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~v~~g~Gia~l-p~~~----~~~~~-~ 254 (299) .+++||.+...... .+.. ....+.... +......+++...++.++..|..=+++ +... .++.+ . T Consensus 98 ~~~~dl~g~~i~v~-~g~~----~~~~l~~~~-----~~~~~~~~~~~~~~~~~l~~G~vD~~v~~~~~~~~~~~~~~~~ 167 (218) T cd00134 98 KSVKDLKGKKVAVQ-KGST----AEKYLKKAL-----PEAKVVSYDDNAEALAALENGRADAVIVDEIALAALLKKHPPE 167 (218) T ss_pred CCHHHHCCCEEEEE-CCCH----HHHHHHHHH-----CCCEEEEECCHHHHHHHHHCCCCEEEEECHHHHHHHHHHCCCC T ss_conf 99899779626795-8988----999999731-----5754999699999999998599469997699999999867998 Q ss_pred EEEECCCCCCCCCEEEEEECCCCCCCHHHHHHHHHHHHH Q ss_conf 466177666766008999348778888999999999999 Q gi|254780282|r 255 LVRIMEDVITPSFTVYFCYPEALKNTGKLKAFRNFIFLK 293 (299) Q Consensus 255 lv~i~~~~~~~~~~~~lv~~~~~~~~~~~~~f~d~l~~~ 293 (299) +..+.+.....+..+++..+++ ++.....++-.+++ T Consensus 168 ~~~~~~~~~~~~~~~~~~~~~~---~~~l~~~~n~~l~~ 203 (218) T cd00134 168 LKIVGPSIDLEPLGFGVAVGKD---NKELLDAVNKALKE 203 (218) T ss_pred CEEECCCCCCCCEEEEEEECCC---CHHHHHHHHHHHHH T ss_conf 1996356676734899997499---99999999999999 No 112 >pfam02001 DUF134 Protein of unknown function DUF134. This family of archaeal proteins has no known function. Probab=86.62 E-value=1.5 Score=22.51 Aligned_cols=49 Identities=14% Similarity=0.215 Sum_probs=36.0 Q ss_pred CCHHHHHHHHHHH-HHCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCEEEE Q ss_conf 8889999999999-827689999882899789999999999995882179 Q gi|254780282|r 3 FDWDKLRVFYVVA-RSGSFTHAAEQLHLSQSSISRQISGLETEVGIKLFY 51 (299) Q Consensus 3 md~~~L~~f~~v~-~~gs~s~AA~~L~itq~avS~~i~~LE~~lg~~Lf~ 51 (299) |..+.|+.+.-+. +--+-..||++++||++|+++-+.+-...+...|+. T Consensus 37 L~~dE~EAiRL~D~egl~QeeaA~~MgVSR~Tf~ril~~ARkKvA~aLv~ 86 (100) T pfam02001 37 ITLDEFEAIRLVDYEDYTQEEAAKLMGISRRTVWRLLTSARKKIADALVE 86 (100) T ss_pred ECHHHHHHHHHHHHCCCCHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHC T ss_conf 34999999998736079899999884976999999999999999999867 No 113 >PRK11477 carbohydrate diacid transcriptional activator CdaR; Provisional Probab=86.47 E-value=2.3 Score=21.52 Aligned_cols=20 Identities=15% Similarity=0.155 Sum_probs=7.7 Q ss_pred HHHHHHHHCCEEEEECCCCE Q ss_conf 99999995882179769946 Q gi|254780282|r 38 ISGLETEVGIKLFYRHARGL 57 (299) Q Consensus 38 i~~LE~~lg~~Lf~R~~~~~ 57 (299) +.++-+.+|...-+=+.+|+ T Consensus 15 V~~~~~ii~~nINimD~~G~ 34 (385) T PRK11477 15 VARTMRIIDTNINVMDARGR 34 (385) T ss_pred HHHHHHHCCCCEEEECCCCE T ss_conf 99999756998699999947 No 114 >pfam05043 Mga Mga helix-turn-helix domain. M regulator protein trans-acting positive regulator (Mga) is a DNA-binding protein that activates the expression of several important virulence genes in group A streptococcus in response to changing environmental conditions. This domain is found in the centre of the Mga proteins. This family also contains a number of bacterial RofA transcriptional regulators that seem to be largely restricted to streptococci. These proteins have been shown to regulate the expression of important bacterial adhesins. This is presumably a DNA-binding domain. Probab=86.02 E-value=1.4 Score=22.65 Aligned_cols=44 Identities=23% Similarity=0.380 Sum_probs=34.0 Q ss_pred HHHHHHHHHHHHHCCHHHHHHHHCCCHHHHHHHHHHHHHHH---CCEE Q ss_conf 89999999999827689999882899789999999999995---8821 Q gi|254780282|r 5 WDKLRVFYVVARSGSFTHAAEQLHLSQSSISRQISGLETEV---GIKL 49 (299) Q Consensus 5 ~~~L~~f~~v~~~gs~s~AA~~L~itq~avS~~i~~LE~~l---g~~L 49 (299) ++-|+.+. -.+.-|+..-|++++||.|++.+.|+++...| |..+ T Consensus 19 f~il~~lf-~~~~~s~~~~a~~l~iS~sTl~R~ik~l~~~L~~~~l~i 65 (87) T pfam05043 19 FQLLKFLF-FHEFFSLTSLAQKLFISESTLYRLIKKLNKLLKEFDLSI 65 (87) T ss_pred HHHHHHHH-CCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHCCEEE T ss_conf 99999998-189998999999978899999999999999999859688 No 115 >PRK09392 ftrB transcriptional activator FtrB; Provisional Probab=85.52 E-value=1.2 Score=23.12 Aligned_cols=16 Identities=13% Similarity=0.110 Sum_probs=7.6 Q ss_pred HHHHHHHHHHCCCCCC Q ss_conf 1356675420001222 Q gi|254780282|r 111 NLKEFLLLYPDIQIQL 126 (299) Q Consensus 111 ~l~~f~~~~P~i~i~i 126 (299) .+..+.+++|++...+ T Consensus 111 ~f~~ll~~~p~l~~~l 126 (236) T PRK09392 111 LVREAMSEDPAFARAV 126 (236) T ss_pred HHHHHHHHCHHHHHHH T ss_conf 9999998799999999 No 116 >PRK09390 fixJ response regulator FixJ; Provisional Probab=85.43 E-value=2.6 Score=21.12 Aligned_cols=21 Identities=5% Similarity=0.010 Sum_probs=14.0 Q ss_pred CCHHHHHHHHHHCCCCCCCCC Q ss_conf 001356675420001222222 Q gi|254780282|r 109 QGNLKEFLLLYPDIQIQLILD 129 (299) Q Consensus 109 ~~~l~~f~~~~P~i~i~i~~~ 129 (299) ...+.++++.+|++.|=+.+. T Consensus 63 ~e~l~~l~~~~p~~~vivlT~ 83 (202) T PRK09390 63 IELLRRLKARGSPLPVIVMTG 83 (202) T ss_pred HHHHHHHHHCCCCCCEEEEEE T ss_conf 079999872289986799974 No 117 >PRK10014 DNA-binding transcriptional repressor MalI; Provisional Probab=85.10 E-value=0.46 Score=25.53 Aligned_cols=82 Identities=13% Similarity=0.086 Sum_probs=41.1 Q ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEECCCCEEEEECCCCCCCCCCCCCCCCCHHHHH-CCCCCCCCCCCCCC Q ss_conf 68999988289978999999999999588217976994685001343322222222221012210-01223222222333 Q gi|254780282|r 19 SFTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHARGLTLTEQGSKLHRVTSEVYHKLETTQIE-LQESSVKPSGKLRI 97 (299) Q Consensus 19 s~s~AA~~L~itq~avS~~i~~LE~~lg~~Lf~R~~~~~~lT~~G~~l~~~a~~~l~~~~~~~~~-~~~~~~~~~g~i~I 97 (299) +++--|+..|||++|||+.|.. ..++. + .--+++.++..++.-.-+. .+..+.+.++.|-+ T Consensus 8 Ti~dIA~~aGVS~aTVSrvLn~-------------~~~Vs--~---eTr~rV~~aa~elgY~pn~~A~~l~~~~t~~Ig~ 69 (342) T PRK10014 8 TIHDVALAAGVSVSTVSLVLSG-------------KGRIS--T---ATGERVNQAIEELGFVRNRQASALRGGQSGVIGL 69 (342) T ss_pred CHHHHHHHHCCCHHHHHHHHCC-------------CCCCC--H---HHHHHHHHHHHHHCCCCCHHHHHHCCCCCCEEEE T ss_conf 7999999989699999999779-------------89999--9---9999999999994899786788641387736886 Q ss_pred CCCCCCCCCCCCCHHHHHHHHH Q ss_conf 2111000000000135667542 Q gi|254780282|r 98 ATTIDLGQNLLQGNLKEFLLLY 119 (299) Q Consensus 98 ~~~~~~~~~~l~~~l~~f~~~~ 119 (299) -+ +.+...+...++..+.+.. T Consensus 70 v~-~~~~~~f~~~~i~gi~~~~ 90 (342) T PRK10014 70 IV-RDLSAPFYAELTAGLTEAL 90 (342) T ss_pred EC-CCCCCHHHHHHHHHHHHHH T ss_conf 05-4457767799999999999 No 118 >TIGR02337 HpaR homoprotocatechuate degradation operon regulator, HpaR; InterPro: IPR012712 This Helix-Turn-Helix transcriptional regulator is a member of the MarR family and is found in association with operons for the degradation of 4-hydroxyphenylacetic acid via homoprotocatechuate.; GO: 0003677 DNA binding, 0016564 transcription repressor activity, 0010124 phenylacetate catabolic process, 0016481 negative regulation of transcription. Probab=85.00 E-value=0.63 Score=24.73 Aligned_cols=78 Identities=23% Similarity=0.323 Sum_probs=61.3 Q ss_pred CCCHHHHHHHHHHHHHCCH--HHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEECC-----CC--EEEEECCCCCCCCCCC Q ss_conf 8888999999999982768--9999882899789999999999995882179769-----94--6850013433222222 Q gi|254780282|r 2 SFDWDKLRVFYVVARSGSF--THAAEQLHLSQSSISRQISGLETEVGIKLFYRHA-----RG--LTLTEQGSKLHRVTSE 72 (299) Q Consensus 2 ~md~~~L~~f~~v~~~gs~--s~AA~~L~itq~avS~~i~~LE~~lg~~Lf~R~~-----~~--~~lT~~G~~l~~~a~~ 72 (299) |++=.|.|++..+++.|++ +.=|...+|=.|++|+-|++||+ ..|+.|.. |+ +.+|++|..|++.+.+ T Consensus 25 ~lTEQQWRilR~L~~~G~~e~~~LA~~A~iL~PSLTgiL~rLE~---~glv~R~k~~~DQRR~~~~lT~~G~~L~~~~~p 101 (130) T TIGR02337 25 GLTEQQWRILRVLAEKGSMEFTELADRACILRPSLTGILARLEK---RGLVVRLKASNDQRRVYISLTKKGQALYESVSP 101 (130) T ss_pred CCCHHHHHHHHHHHCCCCCCHHHHHHHHCCCCCCHHHHHHHHHH---CCCEECCCCCCCCCHHHHHHHHHHHHHHHHHHH T ss_conf 79647899999883389948687886641479965789999974---587022588877441242223789999998515 Q ss_pred CCCC-CCHHHH Q ss_conf 2222-101221 Q gi|254780282|r 73 VYHK-LETTQI 82 (299) Q Consensus 73 ~l~~-~~~~~~ 82 (299) -.+. +++++. T Consensus 102 ~~e~~Y~~I~~ 112 (130) T TIGR02337 102 QVEEIYAAIEE 112 (130) T ss_pred HHHHHHHHHHH T ss_conf 69999999998 No 119 >pfam04545 Sigma70_r4 Sigma-70, region 4. Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 promoter element via a helix-turn-helix motif. Due to the way Pfam works, the threshold has been set artificially high to prevent overlaps with other helix-turn-helix families. Therefore there are many false negatives. Probab=84.14 E-value=1.1 Score=23.40 Aligned_cols=27 Identities=11% Similarity=0.113 Sum_probs=23.7 Q ss_pred HHCCHHHHHHHHCCCHHHHHHHHHHHH Q ss_conf 827689999882899789999999999 Q gi|254780282|r 16 RSGSFTHAAEQLHLSQSSISRQISGLE 42 (299) Q Consensus 16 ~~gs~s~AA~~L~itq~avS~~i~~LE 42 (299) +..++...|+.||+|+++||+.+++-= T Consensus 19 ~~~t~~EIA~~lgis~~~V~~~~~ral 45 (50) T pfam04545 19 EGLTLEEIGERLGISRERVRQIEKRAL 45 (50) T ss_pred CCCHHHHHHHHHCCCHHHHHHHHHHHH T ss_conf 882499999998979999999999999 No 120 >PTZ00326 phenylalanyl-tRNA synthetase; Provisional Probab=84.06 E-value=1.8 Score=22.06 Aligned_cols=71 Identities=21% Similarity=0.180 Sum_probs=50.0 Q ss_pred CCCCHHHHHHHHHHHHHCC--HHHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEECCCCEEEEECCCCCCCCCC Q ss_conf 9888899999999998276--8999988289978999999999999588217976994685001343322222 Q gi|254780282|r 1 MSFDWDKLRVFYVVARSGS--FTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHARGLTLTEQGSKLHRVTS 71 (299) Q Consensus 1 m~md~~~L~~f~~v~~~gs--~s~AA~~L~itq~avS~~i~~LE~~lg~~Lf~R~~~~~~lT~~G~~l~~~a~ 71 (299) |++.-..-..+.++...++ --..|+.+++.+..|-+.++.||+.==+..=.+....+.||++|+..++.-- T Consensus 2 ~~~~~~~~~iL~~L~~~~~~~s~ela~~~g~~~~~Vvgai~sLeskglV~vee~~~~~~~LTeEG~~yle~Gl 74 (505) T PTZ00326 2 MQKEEELNTLLEALESAESVTSLAVAEDLSIDHQDVVGAIKSLEALNYIKTEEIKSNTLKLTKEGKDILESGS 74 (505) T ss_pred CCHHHHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEEEEEEEEEEECHHHHHHHHCCC T ss_conf 6416899999999986699999999998596999999999999868997999998889998988999998599 No 121 >smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein. Probab=83.65 E-value=1.8 Score=22.07 Aligned_cols=37 Identities=30% Similarity=0.420 Sum_probs=28.6 Q ss_pred HHHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEECCCCEEE Q ss_conf 8999988289978999999999999588217976994685 Q gi|254780282|r 20 FTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHARGLTL 59 (299) Q Consensus 20 ~s~AA~~L~itq~avS~~i~~LE~~lg~~Lf~R~~~~~~l 59 (299) -..=|+.+|+|..+||+.+++|+++ -++.+.++.+.+ T Consensus 11 ~~~iA~~lG~tretvsR~l~~l~~~---GlI~~~~~~i~i 47 (48) T smart00419 11 RQEIAELLGLTRETVSRTLKRLEKE---GLISREGGRIVI 47 (48) T ss_pred HHHHHHHHCCCHHHHHHHHHHHHHC---CCEEECCCEEEE T ss_conf 9999999799799999999999988---979978978997 No 122 >COG1342 Predicted DNA-binding proteins [General function prediction only] Probab=83.16 E-value=3 Score=20.80 Aligned_cols=50 Identities=16% Similarity=0.174 Sum_probs=39.7 Q ss_pred CCCHHHHHHHHHH-HHHCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCEEEE Q ss_conf 8888999999999-9827689999882899789999999999995882179 Q gi|254780282|r 2 SFDWDKLRVFYVV-ARSGSFTHAAEQLHLSQSSISRQISGLETEVGIKLFY 51 (299) Q Consensus 2 ~md~~~L~~f~~v-~~~gs~s~AA~~L~itq~avS~~i~~LE~~lg~~Lf~ 51 (299) .|+++.|+.+.-+ ++.-+...||.+++||++|+.+.+++-....-..|+. T Consensus 33 ~lt~eElEAlRLvD~~~l~QeeAA~rMgISr~Tfwr~l~sAR~KvA~aLve 83 (99) T COG1342 33 ILTIEELEALRLVDYEGLTQEEAALRMGISRQTFWRLLTSARKKVADALVE 83 (99) T ss_pred EECHHHHHHHHHHHHHHCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHC T ss_conf 522999889998868610578999984642999999999999999999855 No 123 >COG4197 Uncharacterized protein conserved in bacteria, prophage-related [Function unknown] Probab=82.92 E-value=1.7 Score=22.23 Aligned_cols=34 Identities=29% Similarity=0.387 Sum_probs=30.9 Q ss_pred HHHHHHHHHHHCCHHHHHHHHCCCHHHHHHHHHH Q ss_conf 9999999998276899998828997899999999 Q gi|254780282|r 7 KLRVFYVVARSGSFTHAAEQLHLSQSSISRQISG 40 (299) Q Consensus 7 ~L~~f~~v~~~gs~s~AA~~L~itq~avS~~i~~ 40 (299) .|..|++...-|.=+++|..|+|++|.|+|-++- T Consensus 2 ~ls~~va~~vvg~q~a~a~LLgvsp~~vnQw~~g 35 (96) T COG4197 2 NLSIFVACAVVGGQKALARLLGVSPPSVNQWIKG 35 (96) T ss_pred CHHHHHHHHHHCCHHHHHHHHCCCCHHHHHHHHH T ss_conf 6018899999703899999972681478877652 No 124 >COG1568 Predicted methyltransferases [General function prediction only] Probab=82.68 E-value=2.1 Score=21.65 Aligned_cols=58 Identities=21% Similarity=0.286 Sum_probs=51.0 Q ss_pred HHHHHHHHHCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEECCCCEEEEECCCCCCCC Q ss_conf 9999999827689999882899789999999999995882179769946850013433222 Q gi|254780282|r 9 RVFYVVARSGSFTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHARGLTLTEQGSKLHRV 69 (299) Q Consensus 9 ~~f~~v~~~gs~s~AA~~L~itq~avS~~i~~LE~~lg~~Lf~R~~~~~~lT~~G~~l~~~ 69 (299) +.+.++..+++|-+-+..-..+-|.|+.-++.||++ .++.+..+++.+|+.|+.|.+. T Consensus 26 ~vl~ail~~~d~wkIvd~s~~plp~v~~i~~~l~~e---giv~~~~g~v~~TekG~E~~e~ 83 (354) T COG1568 26 NVLSAILATNDFWKIVDYSDLPLPLVASILEILEDE---GIVKIEEGGVELTEKGEELAEE 83 (354) T ss_pred HHHHHHHCCCCHHHHHHHCCCCCHHHHHHHHHHHHC---CCEEEECCCEEEHHHHHHHHHH T ss_conf 999999747527757653158726899999999866---8189854847642626999998 No 125 >PRK11917 bifunctional adhesin/ABC transporter aspartate/glutamate-binding protein; Reviewed Probab=82.67 E-value=3.5 Score=20.42 Aligned_cols=187 Identities=11% Similarity=0.061 Sum_probs=84.8 Q ss_pred CCCCCCCCCCCCCCCCCC------------CCHHHHHHHHH--HCCCCCCCC---CCCCCCCCCCCCCCCCCCCCCCC-- Q ss_conf 222233321110000000------------00135667542--000122222---22222222222222234565432-- Q gi|254780282|r 91 PSGKLRIATTIDLGQNLL------------QGNLKEFLLLY--PDIQIQLIL---DNKDIDISMDYADCAIRLRKPIQ-- 151 (299) Q Consensus 91 ~~g~i~I~~~~~~~~~~l------------~~~l~~f~~~~--P~i~i~i~~---~~~~~~l~~~~~Di~i~~~~~~~-- 151 (299) .+|+|+||+...+.+.-+ .++...+.+.. .++.+++.. .+....|..|.+|+.+.--...+ T Consensus 36 ~~G~L~vg~~~~~pPf~~~d~~~g~~~GfDvDla~~iAk~llg~~~~v~~v~~~~~~~~p~L~~gkvD~i~~~~tiT~eR 115 (259) T PRK11917 36 SKGQLIVGVKNDVPHYALLDQATGEIKGFEIDVAKLLAKSILGDDKKIKLVAVNAKTRGPLLDNGSVDAVIATFTITPER 115 (259) T ss_pred HCCEEEEEECCCCCCCCEEECCCCCEEEEEHHHHHHHHHHHCCCCCEEEEEEECHHHHHHHHHCCCEEEEEECCCCCCCH T ss_conf 59989999878978862056799967888799999999996599856999970678776898779855998664767654 Q ss_pred CCCC-CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCCCCCCCEEEECCCCH Q ss_conf 1111-223455543321123443211122222211000112356643321100023566520223432121145324200 Q gi|254780282|r 152 SSSL-IQRKLVTIHMHAYAAPHYLKNCREPLSIQELDKHNLITFGDLIPKCMEDFNWLATVDRPIGEPRISCLQVNSYLS 230 (299) Q Consensus 152 ~~~l-~~~~l~~~~~~~v~~~~~~~~~~~~~~~~dL~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~ 230 (299) ...+ ...+.+.....+++.++ ....+++||.+-.. +...... ...+........+.. ....++++... T Consensus 116 ~k~vdFS~PY~~~~~~ilv~k~-----~~i~~~~DL~gk~V-gv~~gst----~~~~~~~~~~~~~~~-~~~~~~~~~~~ 184 (259) T PRK11917 116 KRIYNFSEPYYQDAIGLLVLKE-----KNYKSLADMKGANI-GVAQAAT----TKKAIGEAAKKIGID-VKFSEFPDYPS 184 (259) T ss_pred HCCEEECCCEEEEEEEEEEECC-----CCCCCHHHHCCCCE-EEEECCC----HHHHHHHHHHHCCCC-EEEEECCCHHH T ss_conf 3057622476996559999899-----99999899589817-9992784----699999988860885-16996499999 Q ss_pred HHHHHHHHCCEEEE-EHHHHCC--CCCEEEECCCCCCCCCEEEEEECCCCCCCHHHHHHHHHHHHH Q ss_conf 13567873842331-1777601--998466177666766008999348778888999999999999 Q gi|254780282|r 231 IMQYCVLGSGIALL-PDYIVKD--NPNLVRIMEDVITPSFTVYFCYPEALKNTGKLKAFRNFIFLK 293 (299) Q Consensus 231 ~~~~v~~g~Gia~l-p~~~~~~--~~~lv~i~~~~~~~~~~~~lv~~~~~~~~~~~~~f~d~l~~~ 293 (299) +...+.+|..-+++ ....+.. +... .+.++ +-.+.++++..+++ ++..+.+++-.+.+ T Consensus 185 ~~~~l~~grvDa~~~d~~~~~~~~~~~~-~~~~~-~~~~~~~giavrKg---d~~l~~~vn~~i~~ 245 (259) T PRK11917 185 IKAALDAKRVDAFSVDKSILLGYVDDKS-EILPD-SFEPQSYGIVTKKD---DPAFAKYVDDFVKE 245 (259) T ss_pred HHHHHHCCCEEEEECCHHHHHHHHHCCC-CCCCC-CCCCCEEEEEEECC---CHHHHHHHHHHHHH T ss_conf 9999984980299826999999986198-01688-88752589999489---98999999999999 No 126 >PRK11569 transcriptional repressor IclR; Provisional Probab=80.92 E-value=1.5 Score=22.50 Aligned_cols=54 Identities=17% Similarity=0.179 Sum_probs=37.0 Q ss_pred HHHHHHHHHHHHHCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEECC--CCEEEEE Q ss_conf 89999999999827689999882899789999999999995882179769--9468500 Q gi|254780282|r 5 WDKLRVFYVVARSGSFTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHA--RGLTLTE 61 (299) Q Consensus 5 ~~~L~~f~~v~~~gs~s~AA~~L~itq~avS~~i~~LE~~lg~~Lf~R~~--~~~~lT~ 61 (299) ++-|++|-.--..-+++.-|++++++.|++.+-++.||+. | ++.|.+ +.+.|.+ T Consensus 31 l~IL~~la~~~~~lsl~eia~~lglpksT~~RlL~tL~~~-G--~v~~~~~~~~Y~LG~ 86 (274) T PRK11569 31 LKLLEWIAESNGSVALTELAQQAGLPNSTTHRLLTTMQQQ-G--FVRQVGELGHWAIGA 86 (274) T ss_pred HHHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHC-C--CEEECCCCCEECCCH T ss_conf 9999999638999899999998791999999999999976-9--877869988022457 No 127 >COG2197 CitB Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription] Probab=80.55 E-value=4.2 Score=19.97 Aligned_cols=12 Identities=42% Similarity=0.789 Sum_probs=4.6 Q ss_pred HHHHHHHHHHCC Q ss_conf 135667542000 Q gi|254780282|r 111 NLKEFLLLYPDI 122 (299) Q Consensus 111 ~l~~f~~~~P~i 122 (299) -+..+...++++ T Consensus 15 gl~~~L~~~~~~ 26 (211) T COG2197 15 GLRQLLELEPDL 26 (211) T ss_pred HHHHHHHHCCCC T ss_conf 999999868996 No 128 >TIGR03541 reg_near_HchA LuxR family transcriptional regulatory, chaperone HchA-associated. Members of this protein family belong to the LuxR transcriptional regulator family, and contain both autoinducer binding (pfam03472) and transcriptional regulator (pfam00196) domains. Members, however, occur only in a few members of the Gammaproteobacteria that have the chaperone/aminopeptidase HchA, and are always encoded by the adjacent gene. Probab=80.36 E-value=4.2 Score=19.93 Aligned_cols=23 Identities=13% Similarity=0.286 Sum_probs=15.6 Q ss_pred CHHHHHHHHHHHHHHHCCEEEEE Q ss_conf 97899999999999958821797 Q gi|254780282|r 30 SQSSISRQISGLETEVGIKLFYR 52 (299) Q Consensus 30 tq~avS~~i~~LE~~lg~~Lf~R 52 (299) |...|-..+.++-..+|..-|.= T Consensus 16 t~~~l~~~l~~~~~~~Gfd~~~y 38 (232) T TIGR03541 16 TLEAIQDAVREFAQNLGYDRFVL 38 (232) T ss_pred CHHHHHHHHHHHHHHCCCCEEEE T ss_conf 99999999999999849988999 No 129 >COG1414 IclR Transcriptional regulator [Transcription] Probab=80.07 E-value=2.4 Score=21.32 Aligned_cols=53 Identities=21% Similarity=0.244 Sum_probs=37.0 Q ss_pred HHHHHHHHHHHHC-CHHHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEECC--CCEEEEEC Q ss_conf 9999999999827-689999882899789999999999995882179769--94685001 Q gi|254780282|r 6 DKLRVFYVVARSG-SFTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHA--RGLTLTEQ 62 (299) Q Consensus 6 ~~L~~f~~v~~~g-s~s~AA~~L~itq~avS~~i~~LE~~lg~~Lf~R~~--~~~~lT~~ 62 (299) +-|.+|-. ...+ +++.-|++++++.|++++.+..|++. -+..+.+ +.+.|++. T Consensus 8 ~iL~~l~~-~~~~l~l~ela~~~glpksT~~RlL~tL~~~---G~v~~d~~~grY~Lg~~ 63 (246) T COG1414 8 AILDLLAE-GPGGLSLAELAERLGLPKSTVHRLLQTLVEL---GYVEQDPEDGRYRLGPR 63 (246) T ss_pred HHHHHHHH-CCCCCCHHHHHHHHCCCHHHHHHHHHHHHHC---CCEEECCCCCEEEECHH T ss_conf 99999971-8888879999998791988999999999978---98889799996985789 No 130 >PRK09863 putative frv operon regulatory protein; Provisional Probab=79.42 E-value=3.3 Score=20.56 Aligned_cols=52 Identities=13% Similarity=0.102 Sum_probs=39.4 Q ss_pred HHHCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEECCCCEEEEECCCCC Q ss_conf 9827689999882899789999999999995882179769946850013433 Q gi|254780282|r 15 ARSGSFTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHARGLTLTEQGSKL 66 (299) Q Consensus 15 ~~~gs~s~AA~~L~itq~avS~~i~~LE~~lg~~Lf~R~~~~~~lT~~G~~l 66 (299) .+.=++..=|+.++||.+++.+-++++++++...|-.+...|....-.|... T Consensus 90 ~~~i~l~dLAd~lfVSrsTi~~dl~~vre~l~~~l~i~~k~~~gi~i~g~E~ 141 (585) T PRK09863 90 NTFTPMGQLASALFLSRTWVAERLPRLNQRYERTCCIASRPGLGHFIDETEE 141 (585) T ss_pred CCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHCCCEEEECCCCCEEEECCHH T ss_conf 6898899999985839999999999999987314589104898579835179 No 131 >PRK06424 transcription factor; Provisional Probab=79.14 E-value=4.2 Score=19.97 Aligned_cols=18 Identities=11% Similarity=0.237 Sum_probs=9.9 Q ss_pred ECCCCHHHHHHHHHCCEE Q ss_conf 324200135678738423 Q gi|254780282|r 225 VNSYLSIMQYCVLGSGIA 242 (299) Q Consensus 225 ~~s~~~~~~~v~~g~Gia 242 (299) ++||...+.=++...|++ T Consensus 82 veDy~~~Ir~ARE~~Gls 99 (144) T PRK06424 82 VEDYAELVKNARERLSMS 99 (144) T ss_pred HHHHHHHHHHHHHHCCCC T ss_conf 877999999999984999 No 132 >smart00497 IENR1 Intron encoded nuclease repeat motif. Repeat of unknown function, but possibly DNA-binding via helix-turn-helix motif (Ponting, unpublished). Probab=78.89 E-value=1.1 Score=23.30 Aligned_cols=25 Identities=36% Similarity=0.384 Sum_probs=23.1 Q ss_pred HHCCHHHHHHHHCCCHHHHHHHHHH Q ss_conf 8276899998828997899999999 Q gi|254780282|r 16 RSGSFTHAAEQLHLSQSSISRQISG 40 (299) Q Consensus 16 ~~gs~s~AA~~L~itq~avS~~i~~ 40 (299) ...|++.||+.|++++++||+.++. T Consensus 16 ~f~Si~~aak~l~~~~~~I~~~l~~ 40 (53) T smart00497 16 EFSSIREAAKYLGISHSSISKYLNT 40 (53) T ss_pred HHHHHHHHHHHHCCCCCCHHHHHCC T ss_conf 7787999999858883238887067 No 133 >pfam09339 HTH_IclR IclR helix-turn-helix domain. Probab=78.84 E-value=2.8 Score=20.94 Aligned_cols=39 Identities=21% Similarity=0.140 Sum_probs=29.7 Q ss_pred HHHHHHHHHHHHCCHHHHHHHHCCCHHHHHHHHHHHHHH Q ss_conf 999999999982768999988289978999999999999 Q gi|254780282|r 6 DKLRVFYVVARSGSFTHAAEQLHLSQSSISRQISGLETE 44 (299) Q Consensus 6 ~~L~~f~~v~~~gs~s~AA~~L~itq~avS~~i~~LE~~ 44 (299) +-|++|-.--+.-+++.-|+.++++.|++.+.+..||++ T Consensus 7 ~iL~~~~~~~~~~~l~eia~~~gl~kstv~RlL~tL~~~ 45 (52) T pfam09339 7 AILEALAEAPGGLSLTEIARRTGLPKSTAHRLLQTLVEL 45 (52) T ss_pred HHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHC T ss_conf 999998628999899999999891999999999999988 No 134 >COG1349 GlpR Transcriptional regulators of sugar metabolism [Transcription / Carbohydrate transport and metabolism] Probab=78.75 E-value=4.8 Score=19.63 Aligned_cols=61 Identities=25% Similarity=0.355 Sum_probs=49.6 Q ss_pred CCCCHHHHHHHHHHHHHC--CHHHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEECCCCEEEEECCC Q ss_conf 988889999999999827--6899998828997899999999999958821797699468500134 Q gi|254780282|r 1 MSFDWDKLRVFYVVARSG--SFTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHARGLTLTEQGS 64 (299) Q Consensus 1 m~md~~~L~~f~~v~~~g--s~s~AA~~L~itq~avS~~i~~LE~~lg~~Lf~R~~~~~~lT~~G~ 64 (299) |...-|+-+.+-.|.+.| ++...|+.++||..||-|=|.+||+. -++.|..+|..++..-. T Consensus 1 m~~~eR~~~Il~~l~~~g~v~v~eLa~~~~VS~~TIRRDL~~Le~~---g~l~R~hGGa~~~~~~~ 63 (253) T COG1349 1 MLKEERHQKILELLKEKGKVSVEELAELFGVSEMTIRRDLNELEEQ---GLLLRVHGGAVLPDSES 63 (253) T ss_pred CCHHHHHHHHHHHHHHCCCEEHHHHHHHHCCCHHHHHHHHHHHHHC---CEEEEEECEEECCCCCC T ss_conf 9777899999999998596979999988597899998619999778---92899606188377665 No 135 >PRK10188 DNA-binding transcriptional activator SdiA; Provisional Probab=78.21 E-value=5 Score=19.54 Aligned_cols=14 Identities=7% Similarity=0.038 Sum_probs=6.0 Q ss_pred CCCHHHHHHHHHHH Q ss_conf 88889999999999 Q gi|254780282|r 278 KNTGKLKAFRNFIF 291 (299) Q Consensus 278 ~~~~~~~~f~d~l~ 291 (299) .++++.+-.+.|.. T Consensus 179 ~LT~RE~E~L~W~A 192 (240) T PRK10188 179 NFSKREKEILKWTA 192 (240) T ss_pred CCCHHHHHHHHHHH T ss_conf 89989999999997 No 136 >smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation. Probab=77.79 E-value=3.2 Score=20.64 Aligned_cols=60 Identities=23% Similarity=0.195 Sum_probs=41.1 Q ss_pred HHHHHHHHHHH---CCHHHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEECCCCEEEEECCCCCC Q ss_conf 99999999982---76899998828997899999999999958821797699468500134332 Q gi|254780282|r 7 KLRVFYVVARS---GSFTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHARGLTLTEQGSKLH 67 (299) Q Consensus 7 ~L~~f~~v~~~---gs~s~AA~~L~itq~avS~~i~~LE~~lg~~Lf~R~~~~~~lT~~G~~l~ 67 (299) -+..+..+++. -+++.-|+.++++.|++.+-++.||+. |.--.+..++++.|++.--.+- T Consensus 7 al~IL~~l~~~~~~~sl~eia~~~~l~ksT~~RlL~tL~~~-G~l~~~~~~~~Y~lG~~~~~lg 69 (91) T smart00346 7 GLAVLRALAEEPGGLTLAELAERLGLSKSTAHRLLNTLQEL-GYVEQDGQNGRYRLGPKVLELG 69 (91) T ss_pred HHHHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHC-CCEEEECCCCEEEECHHHHHHH T ss_conf 99999999728999899999999890999999999999988-9968849999775309999999 No 137 >PRK10434 srlR DNA-bindng transcriptional repressor SrlR; Provisional Probab=76.39 E-value=5.6 Score=19.23 Aligned_cols=56 Identities=16% Similarity=0.259 Sum_probs=43.1 Q ss_pred CHHHHHHHHHHHHHC--CHHHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEECCCCEEEEEC Q ss_conf 889999999999827--68999988289978999999999999588217976994685001 Q gi|254780282|r 4 DWDKLRVFYVVARSG--SFTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHARGLTLTEQ 62 (299) Q Consensus 4 d~~~L~~f~~v~~~g--s~s~AA~~L~itq~avS~~i~~LE~~lg~~Lf~R~~~~~~lT~~ 62 (299) .-|+-+..-.+-+.| ++..-|+.++||..||-|=++.||++ .++.|..+|..++.. T Consensus 4 ~eR~~~Il~~L~~~g~v~v~eLa~~l~VS~~TIRRDL~~Le~~---G~l~R~hGGa~~~~~ 61 (256) T PRK10434 4 RQRQAAILEYLQKQGKCSVEELAQYFDTTGTTIRKDLVILEHA---GTVIRTYGGVVLNKE 61 (256) T ss_pred HHHHHHHHHHHHHCCCEEHHHHHHHHCCCHHHHHHHHHHHHHC---CCEEEEECEEECCCC T ss_conf 9999999999998697999999998796998999849999878---988999473864777 No 138 >COG1609 PurR Transcriptional regulators [Transcription] Probab=76.04 E-value=1.7 Score=22.28 Aligned_cols=111 Identities=14% Similarity=0.138 Sum_probs=54.2 Q ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEECCCCEEEEECCCCCCCCCCCCCCCCCHHHHHCCCCCCCCCCCCCCC Q ss_conf 68999988289978999999999999588217976994685001343322222222221012210012232222223332 Q gi|254780282|r 19 SFTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHARGLTLTEQGSKLHRVTSEVYHKLETTQIELQESSVKPSGKLRIA 98 (299) Q Consensus 19 s~s~AA~~L~itq~avS~~i~~LE~~lg~~Lf~R~~~~~~lT~~G~~l~~~a~~~l~~~~~~~~~~~~~~~~~~g~i~I~ 98 (299) ++.--|+..|||.+|||+.+.. +..+. -+--+++.+.++++=-.-+.. .+.++.+..+.|-+- T Consensus 2 TikDVA~~AGVS~sTVSrvln~-------------~~~Vs-~eTr~rV~~a~~elgY~pn~~---Ar~L~~~~s~~Ig~i 64 (333) T COG1609 2 TIKDVAKLAGVSKATVSRVLNG-------------SPYVS-EETREKVLAAIKELGYRPNAV---ARSLRTGRTKTIGLV 64 (333) T ss_pred CHHHHHHHHCCCHHHHHHHHCC-------------CCCCC-HHHHHHHHHHHHHHCCCCCHH---HHHHHHCCCCEEEEE T ss_conf 6899999968999898898779-------------99879-999999999999978998989---999874778889999 Q ss_pred CCCCCCCCCCCCHHHHHHHHHHCCCCCCC--CCCC--------CCCCCCCCCCCCCCCC Q ss_conf 11100000000013566754200012222--2222--------2222222222223456 Q gi|254780282|r 99 TTIDLGQNLLQGNLKEFLLLYPDIQIQLI--LDNK--------DIDISMDYADCAIRLR 147 (299) Q Consensus 99 ~~~~~~~~~l~~~l~~f~~~~P~i~i~i~--~~~~--------~~~l~~~~~Di~i~~~ 147 (299) .+ .+...+...++..+.+..-+-..++. .++. ...+...++|-.|..+ T Consensus 65 ~p-~~~~~~~~~i~~gi~~~~~~~gy~~~l~~~~~~~~~e~~~~~~l~~~~vdGiIi~~ 122 (333) T COG1609 65 VP-DITNPFFAEILKGIEEAAREAGYSLLLANTDDDPEKEREYLETLLQKRVDGLILLG 122 (333) T ss_pred EC-CCCCHHHHHHHHHHHHHHHHCCCEEEEEECCCCHHHHHHHHHHHHHCCCCEEEEEC T ss_conf 46-87775899999999999998399899983789869999999999876989899935 No 139 >PRK00430 fis DNA-binding protein Fis; Provisional Probab=75.88 E-value=3.3 Score=20.53 Aligned_cols=27 Identities=19% Similarity=0.306 Sum_probs=22.6 Q ss_pred HHHCCHHHHHHHHCCCHHHHHHHHHHH Q ss_conf 982768999988289978999999999 Q gi|254780282|r 15 ARSGSFTHAAEQLHLSQSSISRQISGL 41 (299) Q Consensus 15 ~~~gs~s~AA~~L~itq~avS~~i~~L 41 (299) .-.||-++||+.|||+..++-+.|++. T Consensus 69 ~t~gNqskAA~~LGInR~TLRkKlk~y 95 (98) T PRK00430 69 YTRGNQTRAALMLGINRGTLRKKLKKY 95 (98) T ss_pred HHCCCHHHHHHHHCCCHHHHHHHHHHH T ss_conf 966959999999787788999999984 No 140 >COG3888 Predicted transcriptional regulator [Transcription] Probab=75.17 E-value=3.9 Score=20.17 Aligned_cols=103 Identities=20% Similarity=0.135 Sum_probs=57.8 Q ss_pred HHHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEECCCCEEEEECCCCCCCCCCCCCCCCCHHHHHCCCCCCCCCCCCCCCC Q ss_conf 89999882899789999999999995882179769946850013433222222222210122100122322222233321 Q gi|254780282|r 20 FTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHARGLTLTEQGSKLHRVTSEVYHKLETTQIELQESSVKPSGKLRIAT 99 (299) Q Consensus 20 ~s~AA~~L~itq~avS~~i~~LE~~lg~~Lf~R~~~~~~lT~~G~~l~~~a~~~l~~~~~~~~~~~~~~~~~~g~i~I~~ 99 (299) =+.-.+..|.|.|+||..++.||++= .+.|.. -.|+.. +-.|. +..+-...+-+|||+ T Consensus 23 Q~eIeel~GlSKStvSEaLs~LE~~g---iv~Rrk------vsGKs~----rVwLa---------ey~Py~d~~~lRiGi 80 (321) T COG3888 23 QTEIEELMGLSKSTVSEALSELEKQG---IVKRRK------VSGKSK----RVWLA---------EYSPYPDSRFLRIGI 80 (321) T ss_pred HHHHHHHHCCCHHHHHHHHHHHHHCC---EEEEEE------ECCCCE----EEEEC---------CCCCCCCCCCEEEEE T ss_conf 87889885745647999999988568---056655------057533----88620---------037877756078856 Q ss_pred CCCCCCCCCCCHHHHHHHHHHCCCCCCCCC--CCCCCCCCCCCCCCC Q ss_conf 110000000001356675420001222222--222222222222223 Q gi|254780282|r 100 TIDLGQNLLQGNLKEFLLLYPDIQIQLILD--NKDIDISMDYADCAI 144 (299) Q Consensus 100 ~~~~~~~~l~~~l~~f~~~~P~i~i~i~~~--~~~~~l~~~~~Di~i 144 (299) .-+.-...+.+....+.+.-=++.|++.-+ +-.-||..|.+|+|+ T Consensus 81 LRatEYp~~i~aaKnl~e~ki~a~iR~Yddaisit~DLv~g~ld~~l 127 (321) T COG3888 81 LRATEYPFFISAAKNLEERKISATIRFYDDAISITRDLVEGKLDFGL 127 (321) T ss_pred EECCCCHHHHHHHHHHHHCCCEEEEEEECCHHHHHHHHHHHHHHHCC T ss_conf 41233125758987664436408999963577899988764446201 No 141 >TIGR02395 rpoN_sigma RNA polymerase sigma-54 factor; InterPro: IPR000394 Sigma factors are bacterial transcription initiation factors that promote the attachment of the core RNA polymerase to specific initiation sites and are then released. They alter the specificity of promoter recognition. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma- 70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes: the sigma-54 and sigma-70 families. The sigma-70 family has many different sigma factors (see the relevant entry IPR000943 from INTERPRO). The sigma-54 family consists exclusively of sigma-54 factor , required for the transcription of promoters that have a characteristic -24 and -12 consensus recognition element but which are devoid of the typical -10, -35 sequences recognized by the major sigma factors. The sigma-54 factor is also characterised by its interaction with ATP-dependent positive regulatory proteins that bind to upstream activating sequences. Structurally sigma-54 factors consist of three distinct regions: A relatively well conserved N-terminal glutamine-rich region of about 50 residues that contains a potential leucine zipper motif. A region of variable length which is not well conserved. A well conserved C-terminal region of about 350 residues that contains a second potential leucine zipper, a potential DNA-binding 'helix-turn-helix' motif and a perfectly conserved octapeptide whose function is not known. ; GO: 0003677 DNA binding, 0003700 transcription factor activity, 0003899 DNA-directed RNA polymerase activity, 0016987 sigma factor activity, 0006352 transcription initiation, 0006355 regulation of transcription DNA-dependent. Probab=74.65 E-value=0.72 Score=24.40 Aligned_cols=10 Identities=10% Similarity=0.238 Sum_probs=4.6 Q ss_pred HHHHHHHCCC Q ss_conf 9999985066 Q gi|254780282|r 289 FIFLKARDWK 298 (299) Q Consensus 289 ~l~~~~r~~~ 298 (299) ||.++.+||+ T Consensus 319 yl~~k~~eA~ 328 (477) T TIGR02395 319 YLKEKLQEAR 328 (477) T ss_pred HHHHHHHHHH T ss_conf 9999999999 No 142 >cd06171 Sigma70_r4 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or plastid core RNA polymerase to specific promoter elements located upstream of transcription initiation points. The SR4 of Ec sigma70 and other essential primary SFs contact promoter sequences located 35 base-pairs upstream of the initiation point, recognizing a 6-base-pair -35 consensus TTGACA. Sigma70 related SFs also include SFs which are dispensable for bacterial cell growth for example Ec sigmaS, SFs which activate regulons in response to a specific signal for example heat-shock Ec sigmaH, and a group of SFs which includes the extracytoplasmic function (ECF) SFs and is typified by Ec sigmaE which contains SR2 and -4 only. ECF SFs direct the transcription of genes that regulate various responses including periplas Probab=74.46 E-value=6.3 Score=18.93 Aligned_cols=30 Identities=20% Similarity=0.284 Sum_probs=25.8 Q ss_pred HHHCCHHHHHHHHCCCHHHHHHHHHHHHHH Q ss_conf 982768999988289978999999999999 Q gi|254780282|r 15 ARSGSFTHAAEQLHLSQSSISRQISGLETE 44 (299) Q Consensus 15 ~~~gs~s~AA~~L~itq~avS~~i~~LE~~ 44 (299) .+.-|+...|+.||+|.++|+.++.+--+. T Consensus 24 ~~~~s~~EIa~~lgis~~tVk~~l~rA~~~ 53 (55) T cd06171 24 GEGLSYEEIAEILGISRSTVRQRLHRALKK 53 (55) T ss_pred HCCCCHHHHHHHHCCCHHHHHHHHHHHHHH T ss_conf 809999999999895999999999999987 No 143 >PRK00118 putative DNA-binding protein; Validated Probab=73.67 E-value=5.4 Score=19.31 Aligned_cols=32 Identities=19% Similarity=0.217 Sum_probs=26.6 Q ss_pred HHHCCHHHHHHHHCCCHHHHHHHHHHHHHHHC Q ss_conf 98276899998828997899999999999958 Q gi|254780282|r 15 ARSGSFTHAAEQLHLSQSSISRQISGLETEVG 46 (299) Q Consensus 15 ~~~gs~s~AA~~L~itq~avS~~i~~LE~~lg 46 (299) .+--|++.-|+.++||.+||+-.|++-|..|. T Consensus 31 ~~DlSl~EIAe~~~iSRQaV~D~ikr~~~~L~ 62 (105) T PRK00118 31 LDDYSLGEIAEEFNVSRQAVYDNIKRTEKLLE 62 (105) T ss_pred HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH T ss_conf 85499999989969859999999999999999 No 144 >PRK09861 cytoplasmic membrane lipoprotein-28; Provisional Probab=73.32 E-value=6.7 Score=18.77 Aligned_cols=195 Identities=9% Similarity=0.079 Sum_probs=86.0 Q ss_pred CCCCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCCCC-CCCC---CCCCCCCCCCCCCCCCCCC-----CCCCCCCCC--- Q ss_conf 222333211100000000013566754200012222-2222---2222222222223456543-----211112234--- Q gi|254780282|r 92 SGKLRIATTIDLGQNLLQGNLKEFLLLYPDIQIQLI-LDNK---DIDISMDYADCAIRLRKPI-----QSSSLIQRK--- 159 (299) Q Consensus 92 ~g~i~I~~~~~~~~~~l~~~l~~f~~~~P~i~i~i~-~~~~---~~~l~~~~~Di~i~~~~~~-----~~~~l~~~~--- 159 (299) .-+|+||++++....++ .......++.-++++++. .++- ...|..|++|.-+.-..|. ...+..-.. T Consensus 31 ~k~ikVG~~~~p~~~i~-e~~~~~~~ek~G~~leiv~FsDy~~PN~AL~~G~iDaN~fQH~pyL~~~n~~~g~~L~~v~~ 109 (272) T PRK09861 31 AKHIKVGVINGAEQDVA-EVAKKVAKEKYGLDVELVGFSGSLLPNDATNHGELDANVFQHRPFLEQDNQAHGYKLVAVGN 109 (272) T ss_pred CCEEEEEECCCCHHHHH-HHHHHHHHHHCCCEEEEEEECCCCCHHHHHHCCCCCCHHHHHHHHHHHHHHHCCCCEEEEEE T ss_conf 97389996789869999-99998887617976899994686226289767983602455799999999986995799731 Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCCC---------------CCC-CEE Q ss_conf 5554332112344321112222221100011235664332110002356652022343---------------212-114 Q gi|254780282|r 160 LVTIHMHAYAAPHYLKNCREPLSIQELDKHNLITFGDLIPKCMEDFNWLATVDRPIGE---------------PRI-SCL 223 (299) Q Consensus 160 l~~~~~~~v~~~~~~~~~~~~~~~~dL~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~---------------~~~-~~~ 223 (299) ...+++.++.. ...+++||.+-.-|..+.......+-...++..+.-... |.. ... T Consensus 110 ~~~~P~glYS~--------K~ksl~dlp~Ga~IaIPnDpsN~~RAL~lL~~aGLI~Lk~~~~~~~t~~DI~~NPk~lk~~ 181 (272) T PRK09861 110 TFVFPMAGYSK--------KIKTVAQIKEGATVAIPNDPTNLGRALLLLQKEKLITLKEGKGLLPTALDITDNPRHLQIM 181 (272) T ss_pred EEEEEEEECCC--------CCCCHHHCCCCCEEEECCCHHHHHHHHHHHHHCCCEEECCCCCCCCCHHHHHCCCCCCEEE T ss_conf 67830140344--------6598758479998980478126999999999889789779999777744576088776799 Q ss_pred EECCCCHHHHHHHH-HCCEEEEEHHHHCCCC-CE--EEECCCCCCCCCEEEEEECCCCCCCHHHHHHHHHHHHH-HHC Q ss_conf 53242001356787-3842331177760199-84--66177666766008999348778888999999999999-850 Q gi|254780282|r 224 QVNSYLSIMQYCVL-GSGIALLPDYIVKDNP-NL--VRIMEDVITPSFTVYFCYPEALKNTGKLKAFRNFIFLK-ARD 296 (299) Q Consensus 224 ~~~s~~~~~~~v~~-g~Gia~lp~~~~~~~~-~l--v~i~~~~~~~~~~~~lv~~~~~~~~~~~~~f~d~l~~~-~r~ 296 (299) +++.... -+.... ..-.++++...+.+.| .- -.++.+....++-..++.+++...+|.++.|++.+.+. +++ T Consensus 182 e~~aaql-~rsl~Dp~vD~avin~n~a~~agl~p~~dal~~E~~~~py~niiavr~~~~d~~~ik~lv~a~~S~evk~ 258 (272) T PRK09861 182 ELEGAQL-PRVLDDPKVDVAIISTTYIQQTGLSPVHDSVFIEDKNSPYVNILVAREDNKNAENVKEFLQSYQSPEVAK 258 (272) T ss_pred ECCHHHH-HHHHCCCCCCEEEECHHHHHHCCCCCCCCCEEECCCCCCEEEEEEECCCCCCCHHHHHHHHHHCCHHHHH T ss_conf 8267774-6750577616899760579887779440020366899983799998276769989999999977999999 No 145 >TIGR01529 argR_whole arginine repressor; InterPro: IPR001669 The arginine dihydrolase (AD) pathway is found in many prokaryotes and some primitive eukaryotes, an example of the latter being Giardia lamblia . The three-enzyme anaerobic pathway breaks down L-arginine to form 1 mol of ATP, carbon dioxide and ammonia. In simpler bacteria, the first enzyme, arginine deiminase, can account for up to 100f total cell protein . Most prokaryotic arginine deiminase pathways are under the control of a repressor gene, termed ArgR . This is a negative regulator, and will only release the arginine deiminase operon for expression in the presence of arginine . The crystal structure of apo-ArgR from Bacillus stearothermophilus has been determined to 2.5A by means of X-ray crystallography . The protein exists as a hexamer of identical subunits, and is shown to have six DNA-binding domains, clustered around a central oligomeric core when bound to arginine. It predominantly interacts with A.T residues in ARG boxes. This hexameric protein binds DNA at its N terminus to repress arginine biosyntheis or activate arginine catabolism. Some species have several ArgR paralogs. In a neighbour-joining tree, some of these paralogous sequences show long branches and differ significantly from the well-conserved C-terminal region. ; GO: 0003700 transcription factor activity, 0006355 regulation of transcription DNA-dependent. Probab=73.29 E-value=1.3 Score=22.91 Aligned_cols=15 Identities=27% Similarity=0.616 Sum_probs=10.3 Q ss_pred HC-CCHHHHHHHHHHH Q ss_conf 28-9978999999999 Q gi|254780282|r 27 LH-LSQSSISRQISGL 41 (299) Q Consensus 27 L~-itq~avS~~i~~L 41 (299) -. ||||+|||=|++| T Consensus 31 ~~nvTQaTvSRDL~el 46 (155) T TIGR01529 31 VKNVTQATVSRDLREL 46 (155) T ss_pred CCEECCCCHHHHHHHH T ss_conf 7511234067878752 No 146 >PRK11553 alkanesulfonate transporter substrate-binding subunit; Provisional Probab=73.28 E-value=2.4 Score=21.35 Aligned_cols=196 Identities=11% Similarity=0.012 Sum_probs=85.2 Q ss_pred CCCCCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCCCCC---CC-CCCCCCCCCCCCCCCCCCCCCC---CCCCCCCCC-- Q ss_conf 22223332111000000000135667542000122222---22-2222222222222345654321---111223455-- Q gi|254780282|r 91 PSGKLRIATTIDLGQNLLQGNLKEFLLLYPDIQIQLIL---DN-KDIDISMDYADCAIRLRKPIQS---SSLIQRKLV-- 161 (299) Q Consensus 91 ~~g~i~I~~~~~~~~~~l~~~l~~f~~~~P~i~i~i~~---~~-~~~~l~~~~~Di~i~~~~~~~~---~~l~~~~l~-- 161 (299) ...+||||-..+-....+...-.-|.+.+|+++|+... +. ....|..|.+|++..-..|.-- .+.....+. T Consensus 25 ~~~~lrIgyq~~~~~~~~~~~~~~~ek~~~~~kV~w~~F~~G~~~~eAl~aG~iD~~~~g~~p~i~a~a~G~~~~~va~~ 104 (314) T PRK11553 25 SPEALRIGYQKGSIGLVLAKSHQLLEKRFPQTKISWVEFPAGPQMLEALNVGSIDLGSTGDIPPIFAQAAGADLVYVGVE 104 (314) T ss_pred CCCEEEEEECCCCHHHHHHHHCCHHHHHCCCCCEEEEECCCCHHHHHHHHCCCCCEEEECCHHHHHHHHCCCCEEEEEEE T ss_conf 89759999617741589998528676617898358997897489999997699754511585899998669986999986 Q ss_pred ---CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCCCCCCCEEEECCCCHHHHHHHHH Q ss_conf ---54332112344321112222221100011235664332110002356652022343212114532420013567873 Q gi|254780282|r 162 ---TIHMHAYAAPHYLKNCREPLSIQELDKHNLITFGDLIPKCMEDFNWLATVDRPIGEPRISCLQVNSYLSIMQYCVLG 238 (299) Q Consensus 162 ---~~~~~~v~~~~~~~~~~~~~~~~dL~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~v~~g 238 (299) .....++++++ ....+++||.+-.. .+..+...+......+...+..... ...+..+ ......+...| T Consensus 105 ~~~~~~~~i~V~~~-----S~I~s~aDLkGKkV-a~~~Gs~~~~~l~~aL~~aGL~~~D--V~~v~l~-p~d~~aAl~~G 175 (314) T PRK11553 105 PPKPKAEVILVAEN-----SPIKTVADLKGHKV-AFQKGSSSHNLLLRALRQAGLKFTD--IQPTYLT-PADARAAFQQG 175 (314) T ss_pred CCCCCCEEEEEECC-----CCCCCHHHHCCCEE-EEECCCHHHHHHHHHHHHCCCCHHH--EEEEECC-CHHHHHHHHCC T ss_conf 37886418998489-----87788889389989-7417973799999999986998899--1898459-38899999669 Q ss_pred --CCEEEEEHHHH--CCCCCEEEECCCC--CCCCCEEEEEECCCCCC-CHHHHHHHHHHHHHHHCC Q ss_conf --84233117776--0199846617766--67660089993487788-889999999999998506 Q gi|254780282|r 239 --SGIALLPDYIV--KDNPNLVRIMEDV--ITPSFTVYFCYPEALKN-TGKLKAFRNFIFLKARDW 297 (299) Q Consensus 239 --~Gia~lp~~~~--~~~~~lv~i~~~~--~~~~~~~~lv~~~~~~~-~~~~~~f~d~l~~~~r~~ 297 (299) .+++.-..+.. ...+.. +++.+. ......++++.++-... +..++.|++.+.+ +.+| T Consensus 176 ~VDA~~~w~P~~~~a~~~~ga-Rvl~dg~~~~~~~~~~~~~~~fa~~~p~~v~~~l~~l~~-a~~w 239 (314) T PRK11553 176 NVDAWAIWDPYYSAALLQGGV-RVLKDGTDLNQTGSFYLAARPYAEKNGAFIQQVLATLSE-ADAL 239 (314) T ss_pred CCCEEEECCHHHHHHHHCCCC-EEEECCCCCCCCCCEEEECHHHHHHCHHHHHHHHHHHHH-HHHH T ss_conf 978899756789999862895-898537666777616886189888799999999999999-9999 No 147 >PRK00215 LexA repressor; Validated Probab=72.99 E-value=6.1 Score=19.00 Aligned_cols=45 Identities=22% Similarity=0.329 Sum_probs=34.2 Q ss_pred CCHHHHHHHHCC-CHHHHHHHHHHHHHHHCCEEEEE---CCCCEEEEECCCC Q ss_conf 768999988289-97899999999999958821797---6994685001343 Q gi|254780282|r 18 GSFTHAAEQLHL-SQSSISRQISGLETEVGIKLFYR---HARGLTLTEQGSK 65 (299) Q Consensus 18 gs~s~AA~~L~i-tq~avS~~i~~LE~~lg~~Lf~R---~~~~~~lT~~G~~ 65 (299) =|+..=|+.+++ |.++|.++|++||+. -.+.| ..|++++|+.+.. T Consensus 24 Ps~rEI~~~~g~~S~~tV~~~l~~Le~k---G~i~r~~~~~R~i~i~~~~~~ 72 (204) T PRK00215 24 PSRREIADALGLRSPSAVHEHLKALERK---GFIRRDPGRSRAIEVLPAEAA 72 (204) T ss_pred CCHHHHHHHHCCCCCHHHHHHHHHHHHC---CCEECCCCCCCEEEEECCCCC T ss_conf 9899999980999818999999999879---788706999733897157665 No 148 >pfam04297 UPF0122 Putative helix-turn-helix protein, YlxM / p13 like. Members of this family are predicted to contain a helix-turn-helix motif, for example residues 37-55 in Mycoplasma mycoides p13. Genes encoding family members are often part of operons that encode components of the SRP pathway, and this protein may regulate the expression of an operon related to the SRP pathway. Probab=72.56 E-value=5.9 Score=19.10 Aligned_cols=40 Identities=18% Similarity=0.240 Sum_probs=29.2 Q ss_pred HHHHHHHH-HHHHCCHHHHHHHHCCCHHHHHHHHHHHHHHH Q ss_conf 99999999-99827689999882899789999999999995 Q gi|254780282|r 6 DKLRVFYV-VARSGSFTHAAEQLHLSQSSISRQISGLETEV 45 (299) Q Consensus 6 ~~L~~f~~-v~~~gs~s~AA~~L~itq~avS~~i~~LE~~l 45 (299) +|-.+|-. ..+--|++.-|+.++||.+||+-.|++-|..| T Consensus 21 KQ~~~~~lyy~eDlSL~EIAe~~~iSRQaV~D~ikR~~~~L 61 (101) T pfam04297 21 KQKNYFELYYLDDLSLSEIAEEFNVSRQAVYDNIKRTEKML 61 (101) T ss_pred HHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHH T ss_conf 99999999987639899999881985999999999999999 No 149 >COG4623 Predicted soluble lytic transglycosylase fused to an ABC-type amino acid-binding protein [Cell envelope biogenesis, outer membrane] Probab=72.06 E-value=7.2 Score=18.59 Aligned_cols=150 Identities=14% Similarity=0.067 Sum_probs=69.8 Q ss_pred CCCCCCCCCCCCCCCCCCC---------CHHHHHHHHHHCCCCCCCCCCC----CCCCCCCCCCCCCCCCCCCCCCCCCC Q ss_conf 2222333211100000000---------0135667542000122222222----22222222222234565432111122 Q gi|254780282|r 91 PSGKLRIATTIDLGQNLLQ---------GNLKEFLLLYPDIQIQLILDNK----DIDISMDYADCAIRLRKPIQSSSLIQ 157 (299) Q Consensus 91 ~~g~i~I~~~~~~~~~~l~---------~~l~~f~~~~P~i~i~i~~~~~----~~~l~~~~~Di~i~~~~~~~~~~l~~ 157 (299) .+|.+++++..+-..++.. .+.++|. +|=+|++++...+. ..+|..|+.|++- .+--....++.. T Consensus 21 ~rGvLrV~tinsp~sy~~~~~~p~G~eYelak~Fa-~yLgV~Lki~~~~n~dqLf~aL~ng~~DL~A-agl~~~~~~l~~ 98 (473) T COG4623 21 ARGVLRVSTINSPLSYFEDKGGPTGLEYELAKAFA-DYLGVKLKIIPADNIDQLFDALDNGNADLAA-AGLLYNSERLKN 98 (473) T ss_pred HCCEEEEEEECCCCCEECCCCCCCCHHHHHHHHHH-HHHCCEEEEEECCCHHHHHHHHHCCCCCEEC-CCCCCCHHHHCC T ss_conf 66807998405865000037986535599999999-9859768998667788899998579933242-656679667404 Q ss_pred CCCCCCCCCCCCCCC--CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHCC-CCCCCCCCEEEECCCCHHHHH Q ss_conf 345554332112344--32111222222110001123566433211000235665202-234321211453242001356 Q gi|254780282|r 158 RKLVTIHMHAYAAPH--YLKNCREPLSIQELDKHNLITFGDLIPKCMEDFNWLATVDR-PIGEPRISCLQVNSYLSIMQY 234 (299) Q Consensus 158 ~~l~~~~~~~v~~~~--~~~~~~~~~~~~dL~~~~~i~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~s~~~~~~~ 234 (299) -+ ..+...-+|.. |.....+|.++++|.+.... ...+.+ ....+....+ ..+...-..-..-+.+-++++ T Consensus 99 ~~--~gP~y~svs~qlVyRkG~~Rp~~l~~L~g~~i~-v~~gs~----~~~~l~~lk~~kyP~l~~k~d~~~~~~dLle~ 171 (473) T COG4623 99 FQ--PGPTYYSVSQQLVYRKGQYRPRSLGQLKGRQIT-VAKGSA----HVEDLKLLKETKYPELIWKVDDKLGVEDLLEM 171 (473) T ss_pred CC--CCCCEECCCHHHHHHCCCCCCCCHHHCCCCEEE-CCCCCH----HHHHHHHHHHHHCCHHHHHHCCCCCHHHHHHH T ss_conf 67--887200225888765288787888873675564-069968----88999999873163443020221269999999 Q ss_pred HHHH-CCEEEEEHHHH Q ss_conf 7873-84233117776 Q gi|254780282|r 235 CVLG-SGIALLPDYIV 249 (299) Q Consensus 235 v~~g-~Gia~lp~~~~ 249 (299) |..| ++.++.....+ T Consensus 172 v~~Gkldytiads~~i 187 (473) T COG4623 172 VAEGKLDYTIADSVEI 187 (473) T ss_pred HHCCCCCEEEECCHHH T ss_conf 9647766155161888 No 150 >pfam01726 LexA_DNA_bind LexA DNA binding domain. This is the DNA binding domain of the LexA SOS regulon repressor which prevents expression of DNA repair proteins. The aligned region contains a variant form of the helix-turn-helix DNA binding motif. This domain is found associated with pfam00717 the auto-proteolytic domain of LexA EC:3.4.21.88. Probab=71.27 E-value=5.7 Score=19.19 Aligned_cols=42 Identities=21% Similarity=0.227 Sum_probs=30.7 Q ss_pred CCHHHHHHHHHHHHH-------CCHHHHHHHHCC-CHHHHHHHHHHHHHH Q ss_conf 888999999999982-------768999988289-978999999999999 Q gi|254780282|r 3 FDWDKLRVFYVVARS-------GSFTHAAEQLHL-SQSSISRQISGLETE 44 (299) Q Consensus 3 md~~~L~~f~~v~~~-------gs~s~AA~~L~i-tq~avS~~i~~LE~~ 44 (299) |+-+|-++|..+.++ =|+..-|+.+++ |.++|.++|+.||+. T Consensus 4 LT~rQ~~il~~I~~~~~~~G~~Pt~rEI~~~~g~~S~s~v~~~l~~Le~k 53 (65) T pfam01726 4 LTERQREVLDFIKASIEETGYPPSRREIAQALGLRSPNAAEEHLKALERK 53 (65) T ss_pred CCHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHCCCCHHHHHHHHHHHHHC T ss_conf 37999999999999999828898799999993899809999999999998 No 151 >pfam05225 HTH_psq helix-turn-helix, Psq domain. This DNA-binding motif is found in four copies in the pipsqueak protein of Drosophila melanogaster. In pipsqueak this domain binds to GAGA sequence. Probab=70.88 E-value=7.7 Score=18.44 Aligned_cols=34 Identities=26% Similarity=0.426 Sum_probs=25.2 Q ss_pred HHHHHHHHHHHC--CHHHHHHHHCCCHHHHHHHHHH Q ss_conf 999999999827--6899998828997899999999 Q gi|254780282|r 7 KLRVFYVVARSG--SFTHAAEQLHLSQSSISRQISG 40 (299) Q Consensus 7 ~L~~f~~v~~~g--s~s~AA~~L~itq~avS~~i~~ 40 (299) +|.--+.-++.| |+.+||...+|..|++.++++. T Consensus 4 ~l~~Al~av~~g~~S~~kAa~~ygIP~sTL~~r~~g 39 (45) T pfam05225 4 DLAEALEAVRNGKMSLRKAARKYGIPRSTLWRRLRG 39 (45) T ss_pred HHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHCC T ss_conf 999999999919967999999978985899999756 No 152 >pfam09862 DUF2089 Protein of unknown function(DUF2089). This domain, found in various hypothetical prokaryotic proteins, has no known function. Probab=69.58 E-value=8.2 Score=18.27 Aligned_cols=46 Identities=11% Similarity=0.283 Sum_probs=36.7 Q ss_pred CCHHHHHHHHHH-HHHCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCE Q ss_conf 888999999999-9827689999882899789999999999995882 Q gi|254780282|r 3 FDWDKLRVFYVV-ARSGSFTHAAEQLHLSQSSISRQISGLETEVGIK 48 (299) Q Consensus 3 md~~~L~~f~~v-~~~gs~s~AA~~L~itq~avS~~i~~LE~~lg~~ 48 (299) ++-+++...... --.||+..-|+.|+||=|||-.++.++=+.+|-. T Consensus 34 L~~E~l~Fi~~fi~~~Gnlke~~~~lgiSYpTvR~rLd~ii~~lGy~ 80 (113) T pfam09862 34 LTPEQLEFVELFIKCRGNIKEVEKELGISYPTVRNRLDEIIAALGYE 80 (113) T ss_pred CCHHHHHHHHHHHHHCCCHHHHHHHHCCCCHHHHHHHHHHHHHCCCC T ss_conf 89999999999999168899999997888188999999999980898 No 153 >pfam04552 Sigma54_DBD Sigma-54, DNA binding domain. This DNA binding domain is based on peptide fragmentation data. This domain is proximal to DNA in the promoter/holoenzyme complex. Furthermore this region contains a putative helix-turn-helix motif. At the C-terminus, there is a highly conserved region known as the RpoN box and is the signature of the sigma-54 proteins. Probab=69.21 E-value=4.1 Score=20.04 Aligned_cols=24 Identities=25% Similarity=0.380 Sum_probs=18.8 Q ss_pred HCCHHHHHHHHCCCHHHHHHHHHH Q ss_conf 276899998828997899999999 Q gi|254780282|r 17 SGSFTHAAEQLHLSQSSISRQISG 40 (299) Q Consensus 17 ~gs~s~AA~~L~itq~avS~~i~~ 40 (299) --++...|+.|+++.||||+.++. T Consensus 49 PLtlk~iA~~l~lh~STVSRav~~ 72 (160) T pfam04552 49 PLTLREVAEALGMHESTVSRATTN 72 (160) T ss_pred CCCHHHHHHHCCCCCCHHHHHHHH T ss_conf 761999998809981069999961 No 154 >PRK11475 DNA-binding transcriptional activator BglJ; Provisional Probab=69.04 E-value=8.4 Score=18.20 Aligned_cols=36 Identities=19% Similarity=0.298 Sum_probs=20.6 Q ss_pred CCHHHHHHHHHHCCCCCCC-CCCCCC----CCCCCCCCCCC Q ss_conf 0013566754200012222-222222----22222222223 Q gi|254780282|r 109 QGNLKEFLLLYPDIQIQLI-LDNKDI----DISMDYADCAI 144 (299) Q Consensus 109 ~~~l~~f~~~~P~i~i~i~-~~~~~~----~l~~~~~Di~i 144 (299) ...+..+.+.||++++=+. +.+... .|..++++..+ T Consensus 56 L~~~~~L~r~~P~vriLVLTm~d~e~~v~~aL~~aga~Gyl 96 (205) T PRK11475 56 LSCLTELAIKFPRMRRLVIADDDIEARLIGSLSPSPLDGVL 96 (205) T ss_pred HHHHHHHHHHCCCCEEEEEECCCCHHHHHHHHHHHHCCEEE T ss_conf 99999999978997189997476879999999984166888 No 155 >COG2771 CsgD DNA-binding HTH domain-containing proteins [Transcription] Probab=69.02 E-value=8.4 Score=18.20 Aligned_cols=47 Identities=17% Similarity=0.299 Sum_probs=42.2 Q ss_pred CCCHHHHHHHHHHHHHCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCE Q ss_conf 88889999999999827689999882899789999999999995882 Q gi|254780282|r 2 SFDWDKLRVFYVVARSGSFTHAAEQLHLSQSSISRQISGLETEVGIK 48 (299) Q Consensus 2 ~md~~~L~~f~~v~~~gs~s~AA~~L~itq~avS~~i~~LE~~lg~~ 48 (299) .++-++.+....+++-.+...-|..|++|..+|..+++++...+|+. T Consensus 4 ~Lt~rE~~~~~l~~~G~s~~eia~~l~is~~tV~~h~~~i~~Kl~~~ 50 (65) T COG2771 4 DLTPREREILRLVAQGKSNKEIARILGISEETVKTHLRNIYRKLGVK 50 (65) T ss_pred CCCHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCC T ss_conf 13888999999998699899999998779999999999999997758 No 156 >pfam03180 Lipoprotein_9 NLPA lipoprotein. This family of bacterial lipoproteins contains several antigenic members, that may be involved in bacterial virulence. Their precise function is unknown. However they are probably distantly related to pfam00497 which are solute binding proteins. Probab=68.78 E-value=8.5 Score=18.17 Aligned_cols=191 Identities=10% Similarity=0.047 Sum_probs=85.5 Q ss_pred CCCCCCCCCCCCCCCCHHHHHHHHHHCCCCCCCC-CCC---CCCCCCCCCCCCCCCCCCCC-----CCCCCC---CCCCC Q ss_conf 3332111000000000135667542000122222-222---22222222222234565432-----111122---34555 Q gi|254780282|r 95 LRIATTIDLGQNLLQGNLKEFLLLYPDIQIQLIL-DNK---DIDISMDYADCAIRLRKPIQ-----SSSLIQ---RKLVT 162 (299) Q Consensus 95 i~I~~~~~~~~~~l~~~l~~f~~~~P~i~i~i~~-~~~---~~~l~~~~~Di~i~~~~~~~-----~~~l~~---~~l~~ 162 (299) |+||++++-...++ ..+....++. ++++++.. ++- ...|..|++|+-+.-..+.- ..+..- -+.+. T Consensus 1 lkvG~~~~p~~~i~-~~v~~~~~~~-Gi~veiv~F~Dy~~pN~AL~~GeIDaN~fQH~~yl~~~n~~~g~~L~~v~~~~~ 78 (236) T pfam03180 1 LKVGATPGPHAEVL-EVAKPLAKKK-GLDLEIVEFTDYVQPNTALADGEIDANAFQHLPYLDQFNKEGGLDLVAVGNTHV 78 (236) T ss_pred CEEEECCCCHHHHH-HHHHHHHHHC-CCEEEEEEECCCCCHHHHHHCCCCCHHHHCCHHHHHHHHHHCCCCEEEEEEEEE T ss_conf 98964389769999-9999999964-987999981686455079778995524443899999999977996799630467 Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCCC---------------CC-CCEEEEC Q ss_conf 4332112344321112222221100011235664332110002356652022343---------------21-2114532 Q gi|254780282|r 163 IHMHAYAAPHYLKNCREPLSIQELDKHNLITFGDLIPKCMEDFNWLATVDRPIGE---------------PR-ISCLQVN 226 (299) Q Consensus 163 ~~~~~v~~~~~~~~~~~~~~~~dL~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~---------------~~-~~~~~~~ 226 (299) .++.++.. ...+++||.+-.-|..+.......+-...++..+.-... |. ....+++ T Consensus 79 ~p~glYS~--------k~ksl~~lp~Ga~IaIpnD~sN~~RAL~lL~~aGLI~Lk~~~~~~~t~~DI~~Npk~l~~~ev~ 150 (236) T pfam03180 79 EPIGLYSK--------KYKSLSELPDGATIAVPNDPSNEGRALLLLEKAGLIKLKDGAGLLATVKDITENPKNLKIKELE 150 (236) T ss_pred CCEEEEEC--------CCCCHHHCCCCCEEEECCCCCHHHHHHHHHHHCCCEEECCCCCCCCCHHHHHHCCCCCEEEEEC T ss_conf 23795433--------7688758579998981588442999999999889889768999878988897286776699916 Q ss_pred CCCHHHHHHHHHCCEEEEEHHHHCCCC-CEE--EECCCCCCCCCEEEEEECCCCCCCHHHHHHHHHHHHH-HHCC Q ss_conf 420013567873842331177760199-846--6177666766008999348778888999999999999-8506 Q gi|254780282|r 227 SYLSIMQYCVLGSGIALLPDYIVKDNP-NLV--RIMEDVITPSFTVYFCYPEALKNTGKLKAFRNFIFLK-ARDW 297 (299) Q Consensus 227 s~~~~~~~v~~g~Gia~lp~~~~~~~~-~lv--~i~~~~~~~~~~~~lv~~~~~~~~~~~~~f~d~l~~~-~r~~ 297 (299) ...... . ....-.++++...+.+.| ... .+..+....+....++.+++...++.++.|++.+.+. +|+| T Consensus 151 a~ql~~-~-l~dvD~avin~n~a~~agl~p~~~~l~~e~~~~~y~n~ivvr~~~~d~~~ik~l~e~~~s~~vk~~ 223 (236) T pfam03180 151 AAQLPR-A-LDDVDAAVINTNYALQAGLDPKKDALFEEDKDSPYVNIIVVREDDKDDPAVKKLVKAYQSEEVKAF 223 (236) T ss_pred HHHHHH-H-CCCCCEEEECHHHHHHCCCCHHHHHHHCCCCCCCEEEEEEEECCCCCCHHHHHHHHHHCCHHHHHH T ss_conf 777554-2-166578998656798879492121331478899837999981777699999999999879999999 No 157 >pfam01978 TrmB Sugar-specific transcriptional regulator TrmB. One member of this family, TrmB, has been shown to be a sugar-specific transcriptional regulator of the trehalose/maltose ABC transporter in Thermococcus litoralis. Probab=68.33 E-value=8.7 Score=18.12 Aligned_cols=44 Identities=16% Similarity=0.240 Sum_probs=36.4 Q ss_pred CCCHHHHHHHHHHHHHCCH--HHHHHHHCCCHHHHHHHHHHHHHHH Q ss_conf 8888999999999982768--9999882899789999999999995 Q gi|254780282|r 2 SFDWDKLRVFYVVARSGSF--THAAEQLHLSQSSISRQISGLETEV 45 (299) Q Consensus 2 ~md~~~L~~f~~v~~~gs~--s~AA~~L~itq~avS~~i~~LE~~l 45 (299) .++=++-+.+.++.+.|.. +.-|+.++++.|.|-..+++|++.= T Consensus 5 Gls~~E~~vY~~Ll~~g~~t~~eia~~~~i~r~~vY~~L~~L~~kG 50 (68) T pfam01978 5 GLSEYEAKVYLALLKLGPATADEIAEESGVPRSKVYEVLRSLEKKG 50 (68) T ss_pred CCCHHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCC T ss_conf 9899999999999981998899999995988989999999999889 No 158 >PRK05932 RNA polymerase factor sigma-54; Reviewed Probab=67.82 E-value=4.8 Score=19.64 Aligned_cols=22 Identities=23% Similarity=0.345 Sum_probs=10.9 Q ss_pred CHHHHHHHHCCCHHHHHHHHHH Q ss_conf 6899998828997899999999 Q gi|254780282|r 19 SFTHAAEQLHLSQSSISRQISG 40 (299) Q Consensus 19 s~s~AA~~L~itq~avS~~i~~ 40 (299) .+-.|=+-|.++.--+...|++ T Consensus 18 ql~QsikLLql~~~EL~~~I~~ 39 (461) T PRK05932 18 QLQQAIRLLQLSTLELQQEIEQ 39 (461) T ss_pred HHHHHHHHHCCCHHHHHHHHHH T ss_conf 9999999988699999999999 No 159 >PRK09391 fixK transcriptional regulator FixK; Provisional Probab=67.59 E-value=4.8 Score=19.62 Aligned_cols=15 Identities=13% Similarity=0.051 Sum_probs=6.3 Q ss_pred HHHHHHHHHHCCCCC Q ss_conf 135667542000122 Q gi|254780282|r 111 NLKEFLLLYPDIQIQ 125 (299) Q Consensus 111 ~l~~f~~~~P~i~i~ 125 (299) .+..+..++|++... T Consensus 111 ~~~~ll~~~p~la~~ 125 (224) T PRK09391 111 SLEQAAATDVDVARA 125 (224) T ss_pred HHHHHHHHCHHHHHH T ss_conf 999998769899999 No 160 >pfam07453 NUMOD1 NUMOD1 domain. This domain probably represents a DNA-binding helix-turn-helix based on its similarity to other families (Bateman A pers obs). Probab=67.44 E-value=2 Score=21.86 Aligned_cols=23 Identities=30% Similarity=0.434 Sum_probs=19.9 Q ss_pred HHCCHHHHHHHHCCCHHHHHHHH Q ss_conf 82768999988289978999999 Q gi|254780282|r 16 RSGSFTHAAEQLHLSQSSISRQI 38 (299) Q Consensus 16 ~~gs~s~AA~~L~itq~avS~~i 38 (299) ...|++.||+.|+++.+++++.+ T Consensus 15 ~f~Si~~aa~~L~i~~~tI~~~~ 37 (37) T pfam07453 15 KFSSIREAARALGISHSTINKYL 37 (37) T ss_pred HHHHHHHHHHHHCCCHHHHHCCC T ss_conf 24679999998476465665029 No 161 >cd00092 HTH_CRP helix_turn_helix, cAMP Regulatory protein C-terminus; DNA binding domain of prokaryotic regulatory proteins belonging to the catabolite activator protein family. Probab=67.22 E-value=4.7 Score=19.68 Aligned_cols=34 Identities=35% Similarity=0.524 Sum_probs=25.9 Q ss_pred HHHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEECCCC Q ss_conf 8999988289978999999999999588217976994 Q gi|254780282|r 20 FTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHARG 56 (299) Q Consensus 20 ~s~AA~~L~itq~avS~~i~~LE~~lg~~Lf~R~~~~ 56 (299) -..=|+.+|+|.-+||+.+++|+++ -++.+.+++ T Consensus 28 r~eiA~~lG~t~eTVsR~l~~l~~~---G~I~~~gr~ 61 (67) T cd00092 28 RQEIADYLGLTRETVSRTLKELEEE---GLISRRGRG 61 (67) T ss_pred HHHHHHHHCCCHHHHHHHHHHHHHC---CCEEECCCE T ss_conf 9999999789099999999999989---948966986 No 162 >pfam00392 GntR Bacterial regulatory proteins, gntR family. This family of regulatory proteins consists of the N-terminal HTH region of GntR-like bacterial transcription factors. At the C-terminus there is usually an effector-binding/oligomerisation domain. The GntR-like proteins include the following sub-families: MocR, YtrR, FadR, AraR, HutC and PlmA, DevA, DasR. Many of these proteins have been shown experimentally to be autoregulatory, enabling the prediction of operator sites and the discovery of cis/trans relationships. The DasR regulator has been shown to be a global regulator of primary metabolism and development in Streptomyces coelicolor. Probab=66.74 E-value=6.5 Score=18.84 Aligned_cols=26 Identities=23% Similarity=0.347 Sum_probs=22.9 Q ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHH Q ss_conf 68999988289978999999999999 Q gi|254780282|r 19 SFTHAAEQLHLSQSSISRQISGLETE 44 (299) Q Consensus 19 s~s~AA~~L~itq~avS~~i~~LE~~ 44 (299) |...=|+.+++|.++|.+.++.|+++ T Consensus 26 s~~~La~~~~vSr~tvr~Al~~L~~~ 51 (64) T pfam00392 26 SERELAAEFGVSRTTVREALRRLEAE 51 (64) T ss_pred HHHHHHHHHCCCHHHHHHHHHHHHHC T ss_conf 79999999796999999999999988 No 163 >COG1510 Predicted transcriptional regulators [Transcription] Probab=66.23 E-value=6 Score=19.03 Aligned_cols=33 Identities=24% Similarity=0.257 Sum_probs=25.7 Q ss_pred HHCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCE Q ss_conf 827689999882899789999999999995882 Q gi|254780282|r 16 RSGSFTHAAEQLHLSQSSISRQISGLETEVGIK 48 (299) Q Consensus 16 ~~gs~s~AA~~L~itq~avS~~i~~LE~~lg~~ 48 (299) +--+.+.=++.|++|-|.||..+++|++.-=+. T Consensus 40 ~Pmtl~Ei~E~lg~Sks~vS~~lkkL~~~~lV~ 72 (177) T COG1510 40 KPLTLDEIAEALGMSKSNVSMGLKKLQDWNLVK 72 (177) T ss_pred CCCCHHHHHHHHCCCCCHHHHHHHHHHHCCHHH T ss_conf 996699999997778012889999998545688 No 164 >cd07377 WHTH_GntR Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators. This CD represents the winged HTH DNA-binding domain of the GntR (named after the gluconate operon repressor in Bacillus subtilis) family of bacterial transcriptional regulators and their putative homologs found in eukaryota and archaea. The GntR family has over 6000 members distributed among almost all bacterial species, which is comprised of FadR, HutC, MocR, YtrA, AraR, PlmA, and other subfamilies for the regulation of the most varied biological process. The monomeric proteins of the GntR family are characterized by two function domains: a small highly conserved winged helix-turn-helix prokaryotic DNA binding domain in the N-terminus, and a very diverse regulatory ligand-binding domain in the C-terminus for effector-binding/oligomerization, which provides the basis for the subfamily classifications. Binding of the effector to GntR-like transcriptional regulators is Probab=65.97 E-value=7.6 Score=18.47 Aligned_cols=26 Identities=31% Similarity=0.422 Sum_probs=23.3 Q ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHH Q ss_conf 68999988289978999999999999 Q gi|254780282|r 19 SFTHAAEQLHLSQSSISRQISGLETE 44 (299) Q Consensus 19 s~s~AA~~L~itq~avS~~i~~LE~~ 44 (299) |...-|+.+++|.++|.+.++.|+++ T Consensus 27 s~~~La~~~~vSr~tvr~Al~~L~~~ 52 (66) T cd07377 27 SERELAEELGVSRTTVREALRELEAE 52 (66) T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHC T ss_conf 79999999798889999999999988 No 165 >COG2739 Uncharacterized protein conserved in bacteria [Function unknown] Probab=65.42 E-value=9.9 Score=17.80 Aligned_cols=33 Identities=21% Similarity=0.232 Sum_probs=27.6 Q ss_pred HHHHCCHHHHHHHHCCCHHHHHHHHHHHHHHHC Q ss_conf 998276899998828997899999999999958 Q gi|254780282|r 14 VARSGSFTHAAEQLHLSQSSISRQISGLETEVG 46 (299) Q Consensus 14 v~~~gs~s~AA~~L~itq~avS~~i~~LE~~lg 46 (299) ..+--|++.-|+..+||.+||...|++-|..|. T Consensus 30 y~dDlSl~EIAee~~VSRqAIyDnIKr~~~~L~ 62 (105) T COG2739 30 YLDDLSLSEIAEEFNVSRQAIYDNIKRTEKILE 62 (105) T ss_pred HHHHCCHHHHHHHHCCCHHHHHHHHHHHHHHHH T ss_conf 981166999999957509999999999999999 No 166 >PRK11564 stationary phase inducible protein CsiE; Provisional Probab=65.04 E-value=10 Score=17.73 Aligned_cols=47 Identities=6% Similarity=0.075 Sum_probs=36.4 Q ss_pred HHCCHHHHHHHHCCCHHHHHHHHHHHHHHH----CCEEEEECCCCEEEEEC Q ss_conf 827689999882899789999999999995----88217976994685001 Q gi|254780282|r 16 RSGSFTHAAEQLHLSQSSISRQISGLETEV----GIKLFYRHARGLTLTEQ 62 (299) Q Consensus 16 ~~gs~s~AA~~L~itq~avS~~i~~LE~~l----g~~Lf~R~~~~~~lT~~ 62 (299) +.=++-.=|+.++||.+||++=|+++++++ +..|..+.++|+.+.-. T Consensus 29 e~vtl~~L~~~l~VSr~Ti~~DLk~l~~~L~~y~~L~L~~~r~~Gy~I~G~ 79 (426) T PRK11564 29 LTVTLETISQLNGVDDDIARQDIAETAREIQRYHHLTLTTGQDGSYRIEGT 79 (426) T ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHCCEEEEEECCCEEEEECC T ss_conf 973499999996998889999999999998300886999817973899736 No 167 >PRK10906 DNA-binding transcriptional repressor GlpR; Provisional Probab=65.03 E-value=10 Score=17.73 Aligned_cols=60 Identities=23% Similarity=0.357 Sum_probs=44.0 Q ss_pred CCCCHHHHHHHHHHHHHC--CHHHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEECCCCEEEEECC Q ss_conf 988889999999999827--689999882899789999999999995882179769946850013 Q gi|254780282|r 1 MSFDWDKLRVFYVVARSG--SFTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHARGLTLTEQG 63 (299) Q Consensus 1 m~md~~~L~~f~~v~~~g--s~s~AA~~L~itq~avS~~i~~LE~~lg~~Lf~R~~~~~~lT~~G 63 (299) |.=+=|+-+..-.+-+.| ++..-|+.++||..||-|=+..||++ -++.|..+|..+.... T Consensus 1 M~~~eR~~~Il~~l~~~g~v~v~eLa~~~~VS~~TIRRDL~~Le~~---G~l~R~hGGA~~~~~~ 62 (252) T PRK10906 1 MKQTQRHDAIIELVKQQGYVSTEELVEHFSVSPQTIRRDLNELAEQ---NLILRHHGGAALPSSS 62 (252) T ss_pred CCHHHHHHHHHHHHHHCCCEEHHHHHHHHCCCHHHHHHHHHHHHHC---CCEEEEECEEEECCCC T ss_conf 9879999999999998698999999998796998998829999878---9889995849806877 No 168 >COG1725 Predicted transcriptional regulators [Transcription] Probab=64.60 E-value=10 Score=17.68 Aligned_cols=51 Identities=20% Similarity=0.236 Sum_probs=41.0 Q ss_pred HCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEECCCCEEEEECCCCCCCC Q ss_conf 27689999882899789999999999995882179769946850013433222 Q gi|254780282|r 17 SGSFTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHARGLTLTEQGSKLHRV 69 (299) Q Consensus 17 ~gs~s~AA~~L~itq~avS~~i~~LE~~lg~~Lf~R~~~~~~lT~~G~~l~~~ 69 (299) .=|+..=|..++|++-||+|.-+.||++ -=++.+.|.|.-.|+.|....+. T Consensus 35 LPSvRelA~~~~VNpnTv~raY~eLE~e--G~i~t~rg~G~fV~~~~~~~~~~ 85 (125) T COG1725 35 LPSVRELAKDLGVNPNTVQRAYQELERE--GIVETKRGKGTFVTEDAKEILDQ 85 (125) T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHHC--CCEEEECCEEEEECCCCHHHHHH T ss_conf 9759999998198988999999999978--87798667057974771455788 No 169 >smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor. Probab=64.54 E-value=8.1 Score=18.31 Aligned_cols=26 Identities=35% Similarity=0.417 Sum_probs=23.3 Q ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHH Q ss_conf 68999988289978999999999999 Q gi|254780282|r 19 SFTHAAEQLHLSQSSISRQISGLETE 44 (299) Q Consensus 19 s~s~AA~~L~itq~avS~~i~~LE~~ 44 (299) |...-|+.++||.++|.+.++.|+++ T Consensus 22 s~~~la~~~~vSr~tvr~A~~~L~~~ 47 (60) T smart00345 22 SERELAAQLGVSRTTVREALSRLEAE 47 (60) T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHC T ss_conf 09999999894999999999999988 No 170 >PRK01905 DNA-binding protein Fis; Provisional Probab=63.89 E-value=11 Score=17.60 Aligned_cols=26 Identities=19% Similarity=0.362 Sum_probs=23.2 Q ss_pred HHCCHHHHHHHHCCCHHHHHHHHHHH Q ss_conf 82768999988289978999999999 Q gi|254780282|r 16 RSGSFTHAAEQLHLSQSSISRQISGL 41 (299) Q Consensus 16 ~~gs~s~AA~~L~itq~avS~~i~~L 41 (299) -.||-++||+.|||+..|+.+.|++. T Consensus 49 ~~gNQ~kAA~~LGinR~TLRkKlk~y 74 (77) T PRK01905 49 AGGNQSLAAEYLGINRNTLRKKLQQH 74 (77) T ss_pred HCCCHHHHHHHHCCCHHHHHHHHHHH T ss_conf 45949999999786588899999980 No 171 >pfam07900 DUF1670 Protein of unknown function (DUF1670). The hypothetical eukaryotic proteins found in this family are of unknown function. Probab=63.66 E-value=11 Score=17.58 Aligned_cols=26 Identities=31% Similarity=0.387 Sum_probs=10.5 Q ss_pred HHHHCCCHHHHHHHHHHHHHHHCCEE Q ss_conf 98828997899999999999958821 Q gi|254780282|r 24 AEQLHLSQSSISRQISGLETEVGIKL 49 (299) Q Consensus 24 A~~L~itq~avS~~i~~LE~~lg~~L 49 (299) |--|++|.++||+.|+.+|++.|.-| T Consensus 112 a~LL~~S~~TI~~~ik~ye~~~g~vv 137 (220) T pfam07900 112 AILLGVSTTTISRHVKEYEERTGEVV 137 (220) T ss_pred HHHHCCCHHHHHHHHHHHHHHCCCCC T ss_conf 99988988899999999999709663 No 172 >COG0640 ArsR Predicted transcriptional regulators [Transcription] Probab=63.46 E-value=11 Score=17.56 Aligned_cols=50 Identities=28% Similarity=0.327 Sum_probs=37.9 Q ss_pred HHHHHHHHHHH--HCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEECCCC Q ss_conf 99999999998--2768999988289978999999999999588217976994 Q gi|254780282|r 6 DKLRVFYVVAR--SGSFTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHARG 56 (299) Q Consensus 6 ~~L~~f~~v~~--~gs~s~AA~~L~itq~avS~~i~~LE~~lg~~Lf~R~~~~ 56 (299) ..++.+..+.+ .-++..-++.+++++++||++++.|++.--+.. .+.++. T Consensus 26 ~r~~il~~l~~~~~~~~~~l~~~~~~~~~~v~~hL~~L~~~glv~~-~~~~~~ 77 (110) T COG0640 26 TRLEILSLLAEGGELTVGELAEALGLSQSTVSHHLKVLREAGLVEL-RREGRL 77 (110) T ss_pred HHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEE-EEECCE T ss_conf 8999999998735137999998857678899999999987899578-864645 No 173 >TIGR01764 excise DNA binding domain, excisionase family; InterPro: IPR010093 An excisionase, or Xis protein, is a small protein that binds and promotes excisive recombination; it is not enzymatically active. This entry represents a number of putative excisionases and related proteins from temperate phage, plasmids, and transposons, as well as DNA binding domains of other proteins, such as a DNA modification methylase. This entry identifies mostly small proteins and N-terminal regions of large proteins, but some proteins appear to have two copies. This domain appears similar, in both sequence and predicted secondary structure (PSIPRED) to the MerR family of transcriptional regulators (IPR000551 from INTERPRO).; GO: 0003677 DNA binding. Probab=63.09 E-value=6.5 Score=18.87 Aligned_cols=37 Identities=32% Similarity=0.342 Sum_probs=26.8 Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEECCCCEEE Q ss_conf 768999988289978999999999999588217976994685 Q gi|254780282|r 18 GSFTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHARGLTL 59 (299) Q Consensus 18 gs~s~AA~~L~itq~avS~~i~~LE~~lg~~Lf~R~~~~~~l 59 (299) -|+..||+.||||-++|-+-|++ |.==|.|.|+.+.. T Consensus 2 lTv~EaA~yLgv~~~t~~~l~~~-----g~l~~~~~G~~~ri 38 (49) T TIGR01764 2 LTVEEAAEYLGVSKSTVYRLIEE-----GELPAYRVGRHYRI 38 (49) T ss_pred CCHHHHHHHCCCCHHHHHHHHHC-----CCCCEEECCCCEEC T ss_conf 87788997719990578999971-----89850006860202 No 174 >PRK10411 DNA-binding transcriptional activator FucR; Provisional Probab=62.83 E-value=11 Score=17.49 Aligned_cols=52 Identities=19% Similarity=0.261 Sum_probs=38.7 Q ss_pred HHHHHHHHHHHHC--CHHHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEECCCCEEEE Q ss_conf 9999999999827--689999882899789999999999995882179769946850 Q gi|254780282|r 6 DKLRVFYVVARSG--SFTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHARGLTLT 60 (299) Q Consensus 6 ~~L~~f~~v~~~g--s~s~AA~~L~itq~avS~~i~~LE~~lg~~Lf~R~~~~~~lT 60 (299) |+-+..-.+-+.| ++..-|+.++||..||-|=+..||++ -++.|..+|..+. T Consensus 5 R~~~Il~~L~~~g~v~v~eLa~~~~VS~~TIRRDL~~Le~~---G~l~R~hGGA~~~ 58 (240) T PRK10411 5 RQQAIVDLLLNHTSLTTEALAEQLNVSKETIRRDLNELQTQ---GKILRNHGRAKYI 58 (240) T ss_pred HHHHHHHHHHHCCCEEHHHHHHHHCCCHHHHHHHHHHHHHC---CCEEEEEEEEEEC T ss_conf 99999999998697999999998895998999829989778---9889994249975 No 175 >cd01392 HTH_LacI Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators. HTH-DNA binding domain of the LacI (lactose operon repressor) family of bacterial transcriptional regulators and their putative homologs found in plants. The LacI family has more than 500 members distributed among almost all bacterial species. The monomeric proteins of the LacI family contain common structural features that include a small DNA-binding domain with a helix-turn-helix motif in the N-terminus, a regulatory ligand-binding domain which exhibits the type I periplasmic binding protein fold in the C-terminus for oligomerization and for effector binding, and an approximately 18-amino acid linker connecting these two functional domains. In LacI-like transcriptional regulators, the ligands are monosaccharides including lactose, ribose, fructose, xylose, arabinose, galactose/glucose, and other sugars, with a few exceptions. When the C-terminal domain of the LacI family repre Probab=62.65 E-value=5.4 Score=19.34 Aligned_cols=19 Identities=26% Similarity=0.413 Sum_probs=16.3 Q ss_pred HHHHHHCCCHHHHHHHHHH Q ss_conf 9998828997899999999 Q gi|254780282|r 22 HAAEQLHLSQSSISRQISG 40 (299) Q Consensus 22 ~AA~~L~itq~avS~~i~~ 40 (299) .-|+++|+|.++||+.+.. T Consensus 2 diA~~~gvS~~TVSr~ln~ 20 (52) T cd01392 2 DIARAAGVSVATVSRVLNG 20 (52) T ss_pred HHHHHHCCCHHHHHHHHCC T ss_conf 2888878599999999879 No 176 >PRK12423 LexA repressor; Provisional Probab=61.94 E-value=12 Score=17.39 Aligned_cols=56 Identities=18% Similarity=0.293 Sum_probs=38.4 Q ss_pred CCHHHHHHHHHHHHH-------CCHHHHHHHHCC-CHHHHHHHHHHHHHHHCCEEEEE---CCCCEEEEE Q ss_conf 888999999999982-------768999988289-97899999999999958821797---699468500 Q gi|254780282|r 3 FDWDKLRVFYVVARS-------GSFTHAAEQLHL-SQSSISRQISGLETEVGIKLFYR---HARGLTLTE 61 (299) Q Consensus 3 md~~~L~~f~~v~~~-------gs~s~AA~~L~i-tq~avS~~i~~LE~~lg~~Lf~R---~~~~~~lT~ 61 (299) |+-+|-+.+-.+.++ =|++.-|+.+++ |.++|.++|++||+. -.+.| ..|+++++. T Consensus 4 LT~kQ~~iL~fI~~~~~~~G~~Pt~rEI~~~~g~~S~~~v~~hl~~L~~k---G~i~r~~~~~R~i~l~~ 70 (202) T PRK12423 4 LTPKRAAILAFIRERIAQAGQPPSLAEIAQAFGFASRSVARKHVQALAEA---GLIEVVPNQARGIRLPG 70 (202) T ss_pred CCHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHCCCCCHHHHHHHHHHHHC---CCEECCCCCCEEEEECC T ss_conf 08999999999999999629898899999982999867899999999988---79970699953799368 No 177 >COG1508 RpoN DNA-directed RNA polymerase specialized sigma subunit, sigma54 homolog [Transcription] Probab=61.73 E-value=7.1 Score=18.62 Aligned_cols=21 Identities=10% Similarity=-0.092 Sum_probs=12.5 Q ss_pred HHHHCCEEEEECCCCEEEEEC Q ss_conf 999588217976994685001 Q gi|254780282|r 42 ETEVGIKLFYRHARGLTLTEQ 62 (299) Q Consensus 42 E~~lg~~Lf~R~~~~~~lT~~ 62 (299) |+-..-||+++...+-..+-+ T Consensus 39 ~~~e~NPlLe~~~~~~~~~s~ 59 (444) T COG1508 39 QELEDNPLLERKDTDDKEFSD 59 (444) T ss_pred HHHHHCCCCCCCCCCCCCCCC T ss_conf 998629771366677643341 No 178 >cd00283 GIY-YIG_Cterm GIYX(10-11)YIG family of class I homing endonucleases C-terminus (GIY-YIG_Cterm). Homing endonucleases promote the mobility of intron or intein by recognizing and cleaving a homologous allele that lacks the sequence. They catalyze a double-strand break in the DNA near the insertion site of that element to facilitate homing at that site. Class I homing endonucleases are sorted into four families based on the presence of these motifs in their respective N-termini: LAGLIDADG, His-Cys box, HNH, and GIY-YIG. This CD contains several but not all members of the GIY-YIG family. The C-terminus of GIY-YIG is a DNA-binding domain which is separated from the N-terminus by a long, flexible linker. The DNA-binding domain consists of a minor-groove binding alpha-helix, and a helix-turn-helix. Some also contain a zinc finger (i.e. I-TevI) which is not required for DNA binding or catalysis, but is a component of the linker and directs the catalytic domain to cleave the homing sit Probab=60.58 E-value=6.1 Score=19.00 Aligned_cols=21 Identities=38% Similarity=0.438 Sum_probs=9.3 Q ss_pred CCHHHHHHHHCCCHHHHHHHH Q ss_conf 768999988289978999999 Q gi|254780282|r 18 GSFTHAAEQLHLSQSSISRQI 38 (299) Q Consensus 18 gs~s~AA~~L~itq~avS~~i 38 (299) +|...||+.|+++.++||+.| T Consensus 81 ~S~~eAAr~l~~s~~tIs~~~ 101 (113) T cd00283 81 DSTTEAARFLKVHSGTISKNI 101 (113) T ss_pred HHHHHHHHHHCCCCHHHHHHH T ss_conf 349999999689840488996 No 179 >pfam00356 LacI Bacterial regulatory proteins, lacI family. Probab=60.09 E-value=9.2 Score=17.99 Aligned_cols=22 Identities=18% Similarity=0.341 Sum_probs=18.2 Q ss_pred CHHHHHHHHCCCHHHHHHHHHH Q ss_conf 6899998828997899999999 Q gi|254780282|r 19 SFTHAAEQLHLSQSSISRQISG 40 (299) Q Consensus 19 s~s~AA~~L~itq~avS~~i~~ 40 (299) ++.--|+..|||.++||+.+.. T Consensus 1 Ti~DIA~~agVS~~TVSr~ln~ 22 (46) T pfam00356 1 TIKDVARLAGVSKATVSRVLNN 22 (46) T ss_pred CHHHHHHHHCCCHHHHHHHHCC T ss_conf 9999999989799999999879 No 180 >smart00354 HTH_LACI helix_turn _helix lactose operon repressor. Probab=59.71 E-value=9.2 Score=17.97 Aligned_cols=22 Identities=23% Similarity=0.434 Sum_probs=19.0 Q ss_pred CHHHHHHHHCCCHHHHHHHHHH Q ss_conf 6899998828997899999999 Q gi|254780282|r 19 SFTHAAEQLHLSQSSISRQISG 40 (299) Q Consensus 19 s~s~AA~~L~itq~avS~~i~~ 40 (299) ++..-|+..|||+++||+.+.. T Consensus 2 Ti~dvA~~aGVS~sTVSr~ln~ 23 (70) T smart00354 2 TIKDVARLAGVSKATVSRVLNG 23 (70) T ss_pred CHHHHHHHHCCCHHHHHHHHCC T ss_conf 8999999989599999999779 No 181 >PRK00082 hrcA heat-inducible transcription repressor; Provisional Probab=59.61 E-value=13 Score=17.15 Aligned_cols=67 Identities=22% Similarity=0.288 Sum_probs=49.4 Q ss_pred CCC-CHHHHHHHHHHHHH--------CCHHHHHH-HHCCCHHHHHHHHHHHHHHHCCEEEEECCCCEEEEECCCCCCC Q ss_conf 988-88999999999982--------76899998-8289978999999999999588217976994685001343322 Q gi|254780282|r 1 MSF-DWDKLRVFYVVARS--------GSFTHAAE-QLHLSQSSISRQISGLETEVGIKLFYRHARGLTLTEQGSKLHR 68 (299) Q Consensus 1 m~m-d~~~L~~f~~v~~~--------gs~s~AA~-~L~itq~avS~~i~~LE~~lg~~Lf~R~~~~~~lT~~G~~l~~ 68 (299) |+| |=|+.+.|.+++++ ||=+-+-+ .|++|++||-.-++.||+. |.=-=-.+.-|=.||+.|-++|- T Consensus 1 m~mLt~R~~~IL~aiVe~Yi~tg~PVGSk~L~~~~~l~~SsATIRNeMa~LE~~-G~L~qpHTSAGRIPT~kGYR~YV 77 (339) T PRK00082 1 MSMLDERQREILRAIVEDYIATGEPVGSKTLSERYGLGVSSATIRNDMADLEEL-GLLEKPHTSSGRIPTDKGYRYFV 77 (339) T ss_pred CCCCCHHHHHHHHHHHHHHHCCCCCCCHHHHHHHCCCCCCCHHHHHHHHHHHHC-CCCCCCCCCCCCCCCHHHHHHHH T ss_conf 986579999999999999851498556799997649997817899999999978-78367989998785678999999 No 182 >COG1458 Predicted DNA-binding protein containing PIN domain [General function prediction only] Probab=59.60 E-value=1.9 Score=21.97 Aligned_cols=115 Identities=9% Similarity=0.157 Sum_probs=70.7 Q ss_pred HCCCHHHHHHHHHHHHHHHCCE----------EEEECCCCEEEEECCCCCCCCCCCCCCCCCHHHHHCCCCCCCCCCC-C Q ss_conf 2899789999999999995882----------1797699468500134332222222222101221001223222222-3 Q gi|254780282|r 27 LHLSQSSISRQISGLETEVGIK----------LFYRHARGLTLTEQGSKLHRVTSEVYHKLETTQIELQESSVKPSGK-L 95 (299) Q Consensus 27 L~itq~avS~~i~~LE~~lg~~----------Lf~R~~~~~~lT~~G~~l~~~a~~~l~~~~~~~~~~~~~~~~~~g~-i 95 (299) ++|. |+|-+-+...=+..|++ +..+.++..+++--++.|++++..+-..++....-....--...+. . T Consensus 49 cyiP-PsVY~El~~fm~r~gc~~e~~~ki~twivkKtPnryevkiPa~ifyeyV~diR~RinkGlRvAE~~i~eA~~~~~ 127 (221) T COG1458 49 CYIP-PSVYRELMGFMERNGCPEEVIAKIETWIVKKTPNRYEVKIPAAIFYEYVEDIRERINKGLRVAEEAIREASIECY 127 (221) T ss_pred EEEC-HHHHHHHHHHHHHCCCCHHHHHHHHEEEEECCCCCEEECCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 9728-189999999997479968888866603675599822321709999999999999987126468999999988888 Q ss_pred CCCCCCCCCCCCCCCHHHHHHHHHHCCCCCCCCCCCC--CC--CCCCCCCCCC Q ss_conf 3321110000000001356675420001222222222--22--2222222223 Q gi|254780282|r 96 RIATTIDLGQNLLQGNLKEFLLLYPDIQIQLILDNKD--ID--ISMDYADCAI 144 (299) Q Consensus 96 ~I~~~~~~~~~~l~~~l~~f~~~~P~i~i~i~~~~~~--~~--l~~~~~Di~i 144 (299) .+- ...+....+...++.|++.|-.. ++--.-|+. .| |++-++|.++ T Consensus 128 ~~~-~~~i~~e~igk~I~~lR~KYR~a-lR~GiLDSapDlDvLLLAkELdaav 178 (221) T COG1458 128 ELE-KEEIIREVVGKIIRKLREKYREA-LRKGILDSAPDLDVLLLAKELDAAV 178 (221) T ss_pred HHH-HHHHHHHHHHHHHHHHHHHHHHH-HHHCCCCCCCHHHHHHHHHHHCCEE T ss_conf 751-44677888999999999999999-9834446654068999999838637 No 183 >COG1737 RpiR Transcriptional regulators [Transcription] Probab=59.52 E-value=11 Score=17.49 Aligned_cols=27 Identities=19% Similarity=0.095 Sum_probs=24.1 Q ss_pred HHHHCCHHHHHHHHCCCHHHHHHHHHH Q ss_conf 998276899998828997899999999 Q gi|254780282|r 14 VARSGSFTHAAEQLHLSQSSISRQISG 40 (299) Q Consensus 14 v~~~gs~s~AA~~L~itq~avS~~i~~ 40 (299) -+-..|+..=|++.|||+|||.|-.++ T Consensus 33 ~~~~~si~elA~~a~VS~aTv~Rf~~k 59 (281) T COG1737 33 EVALLSIAELAERAGVSPATVVRFARK 59 (281) T ss_pred HHHHCCHHHHHHHHCCCHHHHHHHHHH T ss_conf 885614999998819988899999998 No 184 >PRK11161 fumarate/nitrate reduction transcriptional regulator; Provisional Probab=58.82 E-value=8.6 Score=18.14 Aligned_cols=17 Identities=18% Similarity=0.317 Sum_probs=10.6 Q ss_pred CHHHHHHHHHHCCCCCC Q ss_conf 01356675420001222 Q gi|254780282|r 110 GNLKEFLLLYPDIQIQL 126 (299) Q Consensus 110 ~~l~~f~~~~P~i~i~i 126 (299) ..+..+..+||++...+ T Consensus 117 ~~~~~l~~~~p~l~~~l 133 (235) T PRK11161 117 ETLDDLSGKMPKLRQQI 133 (235) T ss_pred HHHHHHHHHCHHHHHHH T ss_conf 99999997798999999 No 185 >COG3093 VapI Plasmid maintenance system antidote protein [General function prediction only] Probab=58.82 E-value=13 Score=17.07 Aligned_cols=23 Identities=35% Similarity=0.411 Sum_probs=17.6 Q ss_pred CCHHHHHHHHCCCHHHHHHHHHH Q ss_conf 76899998828997899999999 Q gi|254780282|r 18 GSFTHAAEQLHLSQSSISRQISG 40 (299) Q Consensus 18 gs~s~AA~~L~itq~avS~~i~~ 40 (299) -|.+..|+.|+|+..+||.-|.. T Consensus 24 lt~~~lA~~lgV~r~~is~ling 46 (104) T COG3093 24 LTQTELAEALGVTRNTISELING 46 (104) T ss_pred CCHHHHHHHHCCCHHHHHHHHCC T ss_conf 98999999939989999999837 No 186 >PRK12469 RNA polymerase factor sigma-54; Provisional Probab=58.79 E-value=7.1 Score=18.61 Aligned_cols=36 Identities=11% Similarity=0.086 Sum_probs=23.4 Q ss_pred HHHCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEE Q ss_conf 98276899998828997899999999999958821797 Q gi|254780282|r 15 ARSGSFTHAAEQLHLSQSSISRQISGLETEVGIKLFYR 52 (299) Q Consensus 15 ~~~gs~s~AA~~L~itq~avS~~i~~LE~~lg~~Lf~R 52 (299) +=+-.+-.|-+-|.++.--+...|++ +-..-|+++. T Consensus 14 ~LTpql~QsikLLQls~~EL~~~I~~--el~eNPlLE~ 49 (475) T PRK12469 14 ALTPRLQQSLRLLQLSSLEFQQELRE--ALDTNPFLED 49 (475) T ss_pred HHCHHHHHHHHHHCCCHHHHHHHHHH--HHHHCCCCCC T ss_conf 41699999999988498999999999--9982876467 No 187 >pfam01418 HTH_6 Helix-turn-helix domain, rpiR family. This domain contains a helix-turn-helix motif. The best characterized member of this family is RpiR, a regulator of the expression of rpiB gene. Probab=58.70 E-value=13 Score=17.06 Aligned_cols=28 Identities=25% Similarity=0.143 Sum_probs=23.0 Q ss_pred HHHHCCHHHHHHHHCCCHHHHHHHHHHH Q ss_conf 9982768999988289978999999999 Q gi|254780282|r 14 VARSGSFTHAAEQLHLSQSSISRQISGL 41 (299) Q Consensus 14 v~~~gs~s~AA~~L~itq~avS~~i~~L 41 (299) -+...|++.-|++.++|+++|.|-.++| T Consensus 31 ~~~~~si~~lA~~~~vS~atv~Rf~kkl 58 (106) T pfam01418 31 NAIHLSIAELAKAAGVSEASVVRFCRKL 58 (106) T ss_pred HHHHCCHHHHHHHHCCCHHHHHHHHHHH T ss_conf 9988339999989699899999999995 No 188 >COG3355 Predicted transcriptional regulator [Transcription] Probab=56.52 E-value=14 Score=16.84 Aligned_cols=58 Identities=21% Similarity=0.202 Sum_probs=42.5 Q ss_pred HHHHHHHHHH-HH--CCHHHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEECCCCEEEEECCCCCCCC Q ss_conf 9999999999-82--7689999882899789999999999995882179769946850013433222 Q gi|254780282|r 6 DKLRVFYVVA-RS--GSFTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHARGLTLTEQGSKLHRV 69 (299) Q Consensus 6 ~~L~~f~~v~-~~--gs~s~AA~~L~itq~avS~~i~~LE~~lg~~Lf~R~~~~~~lT~~G~~l~~~ 69 (299) .+..+|.++. .. .++-.=|+.|+.+-|+|++.+++|.+ .-|+.|..... +.|...|-| T Consensus 28 ~Dv~v~~~LL~~~~~~tvdelae~lnr~rStv~rsl~~L~~---~GlV~Rek~~~---~~Ggy~yiY 88 (126) T COG3355 28 LDVEVYKALLEENGPLTVDELAEILNRSRSTVYRSLQNLLE---AGLVEREKVNL---KGGGYYYLY 88 (126) T ss_pred HHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHHH---CCCEEEEEECC---CCCCEEEEE T ss_conf 89999999986469957999999978319999999999998---58866664226---788614887 No 189 >pfam04069 OpuAC Substrate binding domain of ABC-type glycine betaine transport system. Part of a high affinity multicomponent binding-protein-dependent transport system involved in bacterial osmoregulation. This domain is often fused to the permease component of the transporter complex. Family members are often integral membrane proteins or predicted to be attached to the membrane by a lipid anchor. Glycine betaine is involved in protection from high osmolarity environments for example in Bacillus subtilis. The family member OpuBC is closely related, and involved in choline transport. Choline is necessary for the biosynthesis of glycine betaine. L-carnitine is important for osmoregulation in Listeria monocytogenes. Family also contains proteins binding l-proline (ProX), histidine (HisX) and taurine (TauA). Probab=55.70 E-value=15 Score=16.76 Aligned_cols=188 Identities=15% Similarity=0.061 Sum_probs=89.6 Q ss_pred CCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCCCCC-CCC---CCCCCCCCCCCCCCCCCCCCC--------CCCCC---C Q ss_conf 23332111000000000135667542000122222-222---222222222222345654321--------11122---3 Q gi|254780282|r 94 KLRIATTIDLGQNLLQGNLKEFLLLYPDIQIQLIL-DNK---DIDISMDYADCAIRLRKPIQS--------SSLIQ---R 158 (299) Q Consensus 94 ~i~I~~~~~~~~~~l~~~l~~f~~~~P~i~i~i~~-~~~---~~~l~~~~~Di~i~~~~~~~~--------~~l~~---~ 158 (299) +|+||.........+..+.....++. +.+++... +.. ...|..|++|+......|... .+... . T Consensus 2 tI~ig~~~w~e~~i~a~i~~~~Le~~-G~~V~~~~~~~~~~~~~al~~G~iDi~~~~w~~~~~~~~~~~~~~~~~~~~~~ 80 (256) T pfam04069 2 TIVIGSKNWTEQEILANIAAQLLEAL-GYVVELVGLGSTAVLFAALASGDIDLYPEEWTGTTYEAYKKAVEEKLGLLVLG 80 (256) T ss_pred EEEEECCCCCHHHHHHHHHHHHHHHC-CCCEEEEECCCCHHHHHHHHCCCCCEEEHHCCCCHHHHHHHHHHCCCCEEECC T ss_conf 29992688628999999999999976-98169854787089999997699758633306625799998751468738613 Q ss_pred C-CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC---------CCCCCCCCCCCCHHHHHHHHCCCCCCCCCCEEEECCC Q ss_conf 4-55543321123443211122222211000112---------3566433211000235665202234321211453242 Q gi|254780282|r 159 K-LVTIHMHAYAAPHYLKNCREPLSIQELDKHNL---------ITFGDLIPKCMEDFNWLATVDRPIGEPRISCLQVNSY 228 (299) Q Consensus 159 ~-l~~~~~~~v~~~~~~~~~~~~~~~~dL~~~~~---------i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~ 228 (299) + .......+++ |.+........+++||.+.+- +...++.+........+...+... .. +...|. T Consensus 81 ~~~~~~~~g~~V-p~~~a~~~~i~si~dL~~~~~~~~~~~~~~~~~~~G~~~~~~~~~~~~~yGl~~----~~-~~~~s~ 154 (256) T pfam04069 81 PLGAGNTYGLAV-PKYVAEKPGIKSISDLAKPADDELGFKGEFIGRPDGWGCTRSTEGLLKAYGLDK----YE-LVEGSE 154 (256) T ss_pred CCCCCCEEEEEE-CHHHHHHCCCCCHHHHHCCCCCCCCCCCCEECCCCCCCCCHHHHHHHHHCCCCC----EE-ECCCCH T ss_conf 577787589998-588883569987999727421024888655327888540067899998639764----01-235855 Q ss_pred C----HHHHHHHHHCCEE---EEEHHHHCCCCCEEEECCCC-C-CCCCEEEEEECCC-CCCCHHHHHHHHH Q ss_conf 0----0135678738423---31177760199846617766-6-7660089993487-7888899999999 Q gi|254780282|r 229 L----SIMQYCVLGSGIA---LLPDYIVKDNPNLVRIMEDV-I-TPSFTVYFCYPEA-LKNTGKLKAFRNF 289 (299) Q Consensus 229 ~----~~~~~v~~g~Gia---~lp~~~~~~~~~lv~i~~~~-~-~~~~~~~lv~~~~-~~~~~~~~~f~d~ 289 (299) . .+..++.+|..+. .-|.++.... +++.+-.+. . .+...++.+.+++ ....|.+..|++- T Consensus 155 ~~~~a~~~~A~~~g~~~v~~~w~p~~~~~~~-dl~~L~Dp~~~~~~~~~v~~v~~~~~~~~~P~~~~~l~~ 224 (256) T pfam04069 155 AAMDALLYAAIKRGEPDVVYAWTPDWMIKKY-DLVVLEDPKGLFPPAYNVVPVVRKGFAEKHPEVAAFLNK 224 (256) T ss_pred HHHHHHHHHHHHCCCCEEEEECCCCHHHHHC-CEEECCCCCCCCCCCCEEEEEECHHHHHHCHHHHHHHHH T ss_conf 5459999999984998899963761655427-969936886457976558752104677779899999986 No 190 >PRK11063 metQ DL-methionine transporter substrate-binding subunit; Provisional Probab=55.28 E-value=15 Score=16.72 Aligned_cols=195 Identities=9% Similarity=0.073 Sum_probs=82.9 Q ss_pred CCCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCCCC-CCCC---CCCCCCCCCCCCCCCCCCCC-----CCCCCCCCC--- Q ss_conf 22333211100000000013566754200012222-2222---22222222222234565432-----111122345--- Q gi|254780282|r 93 GKLRIATTIDLGQNLLQGNLKEFLLLYPDIQIQLI-LDNK---DIDISMDYADCAIRLRKPIQ-----SSSLIQRKL--- 160 (299) Q Consensus 93 g~i~I~~~~~~~~~~l~~~l~~f~~~~P~i~i~i~-~~~~---~~~l~~~~~Di~i~~~~~~~-----~~~l~~~~l--- 160 (299) .+|+||++++....++- ......++--++++++. .++- ...|..|++|+-+.-..|.- ..+.....+ T Consensus 31 ~~ikVG~~~gp~~ei~e-~~~~~~~ek~G~~veiv~FsDy~~pN~AL~~G~iDaN~fQH~~yL~~~nk~~g~~L~~v~~~ 109 (271) T PRK11063 31 NHIKVGVIVGAEQQVAE-VAQKVAKEKYGLDVELVTFNDYVLPNEALSKGDIDANAFQHKPYLDQQIKDRGYKLVAVGNT 109 (271) T ss_pred CEEEEEECCCCHHHHHH-HHHHHHHHHCCCEEEEEEECCCHHHHHHHHCCCCCHHHHHCHHHHHHHHHHCCCCEEEEEEE T ss_conf 81899846898799999-98888886079768999936832155898679844234557999999999779957998667 Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCCCC---------------C-CCEEE Q ss_conf 5543321123443211122222211000112356643321100023566520223432---------------1-21145 Q gi|254780282|r 161 VTIHMHAYAAPHYLKNCREPLSIQELDKHNLITFGDLIPKCMEDFNWLATVDRPIGEP---------------R-ISCLQ 224 (299) Q Consensus 161 ~~~~~~~v~~~~~~~~~~~~~~~~dL~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~---------------~-~~~~~ 224 (299) +..++.+|.. ...+++||.+-.-|..+.......+-...++..+.-...+ . ....+ T Consensus 110 ~~~P~glYS~--------K~ksl~elp~Ga~IaIPND~sN~~RAL~lL~~aGLIkLk~~~~~~~T~~DI~~Npk~l~~~e 181 (271) T PRK11063 110 FVYPIAGYSK--------KIKSLDELQDGSQVAVPNDPTNLGRSLLLLQKVGLIKLKDGVGLLPTVLDIVENPKNLKIVE 181 (271) T ss_pred EEEEEEEEEC--------CCCCHHHCCCCCEEEECCCCCHHHHHHHHHHHCCCEEECCCCCCCCCHHHHHCCCCCCEEEE T ss_conf 7841586423--------65886475699999804885609999999998898897799998789668854887748999 Q ss_pred ECCCCHHHHHHHHHCCEEEEEHHHHCCCC-CEE--EECCCCCCCCCEEEEEECCCCCCCHHHHHHHHHHHHH-HHC Q ss_conf 32420013567873842331177760199-846--6177666766008999348778888999999999999-850 Q gi|254780282|r 225 VNSYLSIMQYCVLGSGIALLPDYIVKDNP-NLV--RIMEDVITPSFTVYFCYPEALKNTGKLKAFRNFIFLK-ARD 296 (299) Q Consensus 225 ~~s~~~~~~~v~~g~Gia~lp~~~~~~~~-~lv--~i~~~~~~~~~~~~lv~~~~~~~~~~~~~f~d~l~~~-~r~ 296 (299) ++.......+-......+++....+.+.| ... .++.+....++-..++.+++...+|.++.|++.+.++ +++ T Consensus 182 ~daaql~rsl~D~dv~~aviN~~~a~~agl~p~kdal~~E~~~~py~Nvivvr~~~kd~~~ik~lv~~~~S~evk~ 257 (271) T PRK11063 182 LEAPQLPRSLDDAQIALAVINTTYASQIGLTPAKDGIFVEDKDSPYVNLIVAREDNKDAENVKKFVQAYQSDEVYE 257 (271) T ss_pred CCHHHHHHHCCCCCEEEEEECHHHHHHCCCCCCCCCEEECCCCCCEEEEEEECCCCCCCHHHHHHHHHHCCHHHHH T ss_conf 0377644313576510898147789777989342504777899983899998277779989999999977999999 No 191 >COG3835 CdaR Sugar diacid utilization regulator [Transcription / Signal transduction mechanisms] Probab=54.98 E-value=15 Score=16.69 Aligned_cols=16 Identities=13% Similarity=0.052 Sum_probs=6.0 Q ss_pred CCCCCCCCHHHHHCCC Q ss_conf 2222221012210012 Q gi|254780282|r 71 SEVYHKLETTQIELQE 86 (299) Q Consensus 71 ~~~l~~~~~~~~~~~~ 86 (299) ++++...++....++. T Consensus 55 ~R~V~Id~~~a~~l~g 70 (376) T COG3835 55 RRVVEIDQAVARKLKG 70 (376) T ss_pred CCEEEEEHHHHHHHCC T ss_conf 8679964888887558 No 192 >PRK09726 DNA-binding transcriptional regulator HipB; Provisional Probab=54.56 E-value=16 Score=16.65 Aligned_cols=47 Identities=11% Similarity=0.126 Sum_probs=33.8 Q ss_pred HCCHHHHHHHHCCCHHHHHHH-----------HHHHHHHHCCEEEEECCCCEEEEECC Q ss_conf 276899998828997899999-----------99999995882179769946850013 Q gi|254780282|r 17 SGSFTHAAEQLHLSQSSISRQ-----------ISGLETEVGIKLFYRHARGLTLTEQG 63 (299) Q Consensus 17 ~gs~s~AA~~L~itq~avS~~-----------i~~LE~~lg~~Lf~R~~~~~~lT~~G 63 (299) --|=+.+|++.|+.|++||+- +=++=..||..|-++..+.-.|+..+ T Consensus 25 gLsQ~~lA~~vGi~Q~TiS~~E~~p~~~~leTLFkiL~aL~Lel~i~~~~~~~p~~~~ 82 (88) T PRK09726 25 GWTQSELAKKIGIKQATISNFENNPDNTTLTTFFKILQSLELSMTLCDAKNASPESTE 82 (88) T ss_pred CCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHCCCEEEEECCCCCCCCCCC T ss_conf 9879999998197499999997599878699999999967876887138999988876 No 193 >PRK10727 DNA-binding transcriptional regulator GalR; Provisional Probab=54.37 E-value=13 Score=17.15 Aligned_cols=22 Identities=23% Similarity=0.314 Sum_probs=19.1 Q ss_pred CHHHHHHHHCCCHHHHHHHHHH Q ss_conf 6899998828997899999999 Q gi|254780282|r 19 SFTHAAEQLHLSQSSISRQISG 40 (299) Q Consensus 19 s~s~AA~~L~itq~avS~~i~~ 40 (299) ++.--|+..|||++|||+.+.. T Consensus 3 TIkDIA~~AGVS~sTVSrvLN~ 24 (342) T PRK10727 3 TIKDVARLAGVSVATVSRVINN 24 (342) T ss_pred CHHHHHHHHCCCHHHHHHHHCC T ss_conf 8899999979699999999779 No 194 >PRK09526 lacI lac repressor; Reviewed Probab=54.04 E-value=13 Score=17.10 Aligned_cols=22 Identities=18% Similarity=0.241 Sum_probs=19.3 Q ss_pred CHHHHHHHHCCCHHHHHHHHHH Q ss_conf 6899998828997899999999 Q gi|254780282|r 19 SFTHAAEQLHLSQSSISRQISG 40 (299) Q Consensus 19 s~s~AA~~L~itq~avS~~i~~ 40 (299) ++.--|+.+|||.+|||+.+.. T Consensus 7 TikDIA~~agVS~sTVSrvLn~ 28 (342) T PRK09526 7 TLYDVARYAGVSYQTVSRVLNQ 28 (342) T ss_pred CHHHHHHHHCCCHHHHHHHHCC T ss_conf 6999999989699999999789 No 195 >PRK08898 coproporphyrinogen III oxidase; Provisional Probab=53.14 E-value=15 Score=16.80 Aligned_cols=10 Identities=10% Similarity=0.554 Sum_probs=4.4 Q ss_pred HHHCCCCCCC Q ss_conf 4200012222 Q gi|254780282|r 118 LYPDIQIQLI 127 (299) Q Consensus 118 ~~P~i~i~i~ 127 (299) .+.+|++++. T Consensus 169 ~f~~iniDLi 178 (393) T PRK08898 169 HFDNFNLDLM 178 (393) T ss_pred HCCCCCCHHH T ss_conf 3746672898 No 196 >PRK13870 transcriptional regulator TraR; Provisional Probab=52.34 E-value=17 Score=16.44 Aligned_cols=19 Identities=5% Similarity=0.235 Sum_probs=9.9 Q ss_pred HHHHHHHHHHHHHCCEEEE Q ss_conf 9999999999995882179 Q gi|254780282|r 33 SISRQISGLETEVGIKLFY 51 (299) Q Consensus 33 avS~~i~~LE~~lg~~Lf~ 51 (299) .+=..++++-+.+|...|- T Consensus 20 ~~~~~l~~~a~~~gf~~~a 38 (234) T PRK13870 20 ILKTGLADIAEHFGFTGYA 38 (234) T ss_pred HHHHHHHHHHHHCCCCCEE T ss_conf 9999999999983998579 No 197 >PRK11041 DNA-binding transcriptional regulator CytR; Provisional Probab=52.26 E-value=15 Score=16.81 Aligned_cols=110 Identities=8% Similarity=0.109 Sum_probs=51.8 Q ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEECCCCEEEEECCCCCCCCCCCCCCCCCHHHHH-CCCCCCCCCCCCCC Q ss_conf 68999988289978999999999999588217976994685001343322222222221012210-01223222222333 Q gi|254780282|r 19 SFTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHARGLTLTEQGSKLHRVTSEVYHKLETTQIE-LQESSVKPSGKLRI 97 (299) Q Consensus 19 s~s~AA~~L~itq~avS~~i~~LE~~lg~~Lf~R~~~~~~lT~~G~~l~~~a~~~l~~~~~~~~~-~~~~~~~~~g~i~I 97 (299) ++.--|+..|||.+|||+.|.. +.++. ++ --+++.+..+++.-.-+. .+..+.+.++.|-+ T Consensus 11 TikDIA~~aGVS~sTVSrvLn~-------------~~~Vs--~~---Tr~rV~~aa~eLgY~pn~~Ar~L~~~~s~~Igv 72 (341) T PRK11041 11 TMKDVALKAGVSTATVSRALMN-------------PEKVS--QS---TRNRVEQAVLEVGYSPQSLGRNLKRNESRTILV 72 (341) T ss_pred CHHHHHHHHCCCHHHHHHHHCC-------------CCCCC--HH---HHHHHHHHHHHHCCCCCHHHHHHHHCCCCEEEE T ss_conf 8999999979799999999789-------------89999--99---999999999981998388888775388888999 Q ss_pred CCCCCCCCCCCCCHHHHHHHHHHCCCCCCCC--C-CC------CCC-CCCCCCCCCCCCC Q ss_conf 2111000000000135667542000122222--2-22------222-2222222223456 Q gi|254780282|r 98 ATTIDLGQNLLQGNLKEFLLLYPDIQIQLIL--D-NK------DID-ISMDYADCAIRLR 147 (299) Q Consensus 98 ~~~~~~~~~~l~~~l~~f~~~~P~i~i~i~~--~-~~------~~~-l~~~~~Di~i~~~ 147 (299) -+ +.+...++..++..+.+..-+-...+.. + +. ..+ +....+|-.|.++ T Consensus 73 i~-p~~~~~~~~~~~~gi~~~~~~~gy~~li~~~~~~~~~e~~~~~~l~~~~vdGiIi~~ 131 (341) T PRK11041 73 IV-PDICDPFFSEIIRGIEVTAAEHGYLVLIGDCAHQNQQEKTFVNLIITKQIDGMLLLG 131 (341) T ss_pred EE-CCCCCCHHHHHHHHHHHHHHHCCCEEEEEECCCCHHHHHHHHHHHHHCCCCEEEEEC T ss_conf 96-776541356766339999997699899982688658899999988754877699956 No 198 >cd00569 HTH_Hin_like Helix-turn-helix domain of Hin and related proteins, a family of DNA-binding domains unique to bacteria and represented by the Hin protein of Salmonella. The basic HTH domain is a simple fold comprised of three core helices that form a right-handed helical bundle. The principal DNA-protein interface is formed by the third helix, the recognition helix, inserting itself into the major groove of the DNA. A diverse array of HTH domains participate in a variety of functions that depend on their DNA-binding properties. HTH_Hin represents one of the simplest versions of the HTH domains; the characterization of homologous relationships between various sequence-diverse HTH domain families remains difficult. The Hin recombinase induces the site-specific inversion of a chromosomal DNA segment containing a promoter, which controls the alternate expression of two genes by reversibly switching orientation. The Hin recombinase consists of a single polypeptide chain containing a D Probab=52.09 E-value=17 Score=16.42 Aligned_cols=36 Identities=19% Similarity=0.274 Sum_probs=26.3 Q ss_pred CCHHHHHHHHHHHHHC-CHHHHHHHHCCCHHHHHHHH Q ss_conf 8889999999999827-68999988289978999999 Q gi|254780282|r 3 FDWDKLRVFYVVARSG-SFTHAAEQLHLSQSSISRQI 38 (299) Q Consensus 3 md~~~L~~f~~v~~~g-s~s~AA~~L~itq~avS~~i 38 (299) |+-++++-.....+.| +.+..|+.++||.++|.+.+ T Consensus 6 lt~~q~~~ar~l~~~G~~~~~iA~~~GVsr~Tiyr~l 42 (42) T cd00569 6 LTPEQIEEARRLLAAGESVAEIARRLGVSRSTLYRYL 42 (42) T ss_pred CCHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHC T ss_conf 9999999999999978989999999797999998659 No 199 >PRK05066 arginine repressor; Provisional Probab=51.86 E-value=7.7 Score=18.42 Aligned_cols=36 Identities=19% Similarity=0.410 Sum_probs=22.3 Q ss_pred HHHHHHHHHHHHCCHHHHHH------HHC---CCHHHHHHHHHHH Q ss_conf 99999999998276899998------828---9978999999999 Q gi|254780282|r 6 DKLRVFYVVARSGSFTHAAE------QLH---LSQSSISRQISGL 41 (299) Q Consensus 6 ~~L~~f~~v~~~gs~s~AA~------~L~---itq~avS~~i~~L 41 (299) +.++.+..+.+...++.=.+ ..| |||++|||-|++| T Consensus 9 ~~~~aIk~lI~~~~I~tQeeL~~~L~~~G~~~VTQATvSRDlkeL 53 (156) T PRK05066 9 ELVKAFKALLKEEKFGSQGEIVTALQEQGFDNINQSKVSRMLTKF 53 (156) T ss_pred HHHHHHHHHHHCCCCCCHHHHHHHHHHCCCCCCHHHHHHHHHHHC T ss_conf 999999999851896679999999997398612088888789982 No 200 >PRK10703 DNA-binding transcriptional repressor PurR; Provisional Probab=51.82 E-value=15 Score=16.77 Aligned_cols=111 Identities=9% Similarity=0.029 Sum_probs=51.3 Q ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEECCCCEEEEECCCCCCCCCCCCCCCCCHHHHH-CCCCCCCCCCCCCC Q ss_conf 68999988289978999999999999588217976994685001343322222222221012210-01223222222333 Q gi|254780282|r 19 SFTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHARGLTLTEQGSKLHRVTSEVYHKLETTQIE-LQESSVKPSGKLRI 97 (299) Q Consensus 19 s~s~AA~~L~itq~avS~~i~~LE~~lg~~Lf~R~~~~~~lT~~G~~l~~~a~~~l~~~~~~~~~-~~~~~~~~~g~i~I 97 (299) ++.--|+..|||.+|||+.+.+ .+++.. .--+++.++.+++.-.-+. .+.++.+.++.|-+ T Consensus 3 TikDIA~~AGVS~aTVSrvLn~-------------~~~Vs~-----~Tr~rV~~aa~eLgY~pn~~Ar~L~~~~s~~Igv 64 (335) T PRK10703 3 TIKDVAKRAGVSTTTVSHVINK-------------TRFVAE-----ETRNAVWAAIKELHYSPSAVARSLKVNHTKSIGL 64 (335) T ss_pred CHHHHHHHHCCCHHHHHHHHCC-------------CCCCCH-----HHHHHHHHHHHHHCCCCCHHHHHHCCCCCCEEEE T ss_conf 8899999979899999999689-------------699899-----9999999999982999787787541177745999 Q ss_pred CCCCCCCCCCCCCHHHHHHHHHHCCCCCCC--CCCC--------CCCCCCCCCCCCCCCCC Q ss_conf 211100000000013566754200012222--2222--------22222222222234565 Q gi|254780282|r 98 ATTIDLGQNLLQGNLKEFLLLYPDIQIQLI--LDNK--------DIDISMDYADCAIRLRK 148 (299) Q Consensus 98 ~~~~~~~~~~l~~~l~~f~~~~P~i~i~i~--~~~~--------~~~l~~~~~Di~i~~~~ 148 (299) -+ +.+...++..++..+.+..-+-...+. .++. ...+....+|-.|.+.. T Consensus 65 iv-~~~~~~~~~~~~~~i~~~~~~~gy~~~l~~~~~~~~~~~~~l~~l~~~~vdGiIi~~~ 124 (335) T PRK10703 65 LA-TSSEAPYFAEIIEAVEKNCYQKGYTLILCNAWNNLEKQRAYLSMLAQKRVDGLLVMCS 124 (335) T ss_pred EE-CCCCCCEEHHHHHHHHHHHHHCCCEEEEEECCCCHHHHHHHHHHHHHCCCCEEEEECC T ss_conf 95-4788865065433699999973997999927898699999999999558877999768 No 201 >cd01104 HTH_MlrA-CarA Helix-Turn-Helix DNA binding domain of the transcription regulators MlrA and CarA. Helix-turn-helix (HTH) transcription regulator MlrA (merR-like regulator A), N-terminal domain. The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. Its close homolog, CarA from Myxococcus xanthus, is involved in activation of the carotenoid biosynthesis genes by light. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA- and CarA-like proteins in this group appear to lack the long dimerization helix seen i Probab=51.55 E-value=17 Score=16.36 Aligned_cols=36 Identities=17% Similarity=0.164 Sum_probs=27.8 Q ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEECCCCEE Q ss_conf 6899998828997899999999999958821797699468 Q gi|254780282|r 19 SFTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHARGLT 58 (299) Q Consensus 19 s~s~AA~~L~itq~avS~~i~~LE~~lg~~Lf~R~~~~~~ 58 (299) +++.+|+.+|||+ +.|+--|+++|..--.|+.+|.+ T Consensus 2 tI~eva~~~gv~~----~tLR~wE~~~~l~~p~R~~~g~R 37 (68) T cd01104 2 TIGAVARLTGVSP----DTLRAWERRYGLPAPQRTDGGHR 37 (68) T ss_pred CHHHHHHHHCCCH----HHHHHHHHHCCCCCCCCCCCCCE T ss_conf 7899999988298----99999998579999974999985 No 202 >PRK10401 DNA-binding transcriptional regulator GalS; Provisional Probab=51.23 E-value=15 Score=16.68 Aligned_cols=22 Identities=23% Similarity=0.356 Sum_probs=18.8 Q ss_pred CHHHHHHHHCCCHHHHHHHHHH Q ss_conf 6899998828997899999999 Q gi|254780282|r 19 SFTHAAEQLHLSQSSISRQISG 40 (299) Q Consensus 19 s~s~AA~~L~itq~avS~~i~~ 40 (299) ++.--|+..|||++|||+.+.. T Consensus 3 Ti~DVA~~AGVS~aTVSrvLn~ 24 (346) T PRK10401 3 TIRDVARQAGVSVATVSRVLNN 24 (346) T ss_pred CHHHHHHHHCCCHHHHHHHHCC T ss_conf 7899999989799999999779 No 203 >COG1777 Predicted transcriptional regulators [Transcription] Probab=51.03 E-value=18 Score=16.32 Aligned_cols=38 Identities=16% Similarity=0.307 Sum_probs=26.2 Q ss_pred HHHHHHHHCCHH-HHHHHHCCCHHHHHHHHHHHHHHHCC Q ss_conf 999999827689-99988289978999999999999588 Q gi|254780282|r 10 VFYVVARSGSFT-HAAEQLHLSQSSISRQISGLETEVGI 47 (299) Q Consensus 10 ~f~~v~~~gs~s-~AA~~L~itq~avS~~i~~LE~~lg~ 47 (299) .+.-+++.-+|. .-++.++|+|-||-+|++.||+.==+ T Consensus 20 Il~lLt~~p~yvsEiS~~lgvsqkAVl~HL~~LE~AGlv 58 (217) T COG1777 20 ILQLLTRRPCYVSEISRELGVSQKAVLKHLRILERAGLV 58 (217) T ss_pred HHHHHHCCCHHHHHHHHHCCCCHHHHHHHHHHHHHCCCC T ss_conf 999985471399987766086789999999999985871 No 204 >PRK10339 DNA-binding transcriptional repressor EbgR; Provisional Probab=50.63 E-value=16 Score=16.65 Aligned_cols=22 Identities=18% Similarity=0.294 Sum_probs=19.0 Q ss_pred CHHHHHHHHCCCHHHHHHHHHH Q ss_conf 6899998828997899999999 Q gi|254780282|r 19 SFTHAAEQLHLSQSSISRQISG 40 (299) Q Consensus 19 s~s~AA~~L~itq~avS~~i~~ 40 (299) ++.--|+..|||.+|||+.|.. T Consensus 3 TikDVA~~AGVS~sTVSrvLn~ 24 (327) T PRK10339 3 TLKDIAIEAGVSLATVSRVLND 24 (327) T ss_pred CHHHHHHHHCCCHHHHHHHHCC T ss_conf 6899999978889999999589 No 205 >pfam02042 RWP-RK RWP-RK domain. This domain is named RWP-RK after a conserved motif at the C terminus of the presumed domain. The domain is found in algal minus dominance proteins as well as plant proteins involved in nitrogen-controlled development. Probab=50.49 E-value=18 Score=16.27 Aligned_cols=34 Identities=12% Similarity=0.181 Sum_probs=24.6 Q ss_pred CCHHHHHHHHHHHHHCCHHHHHHHHCCCHHHHHHHHHH Q ss_conf 88899999999998276899998828997899999999 Q gi|254780282|r 3 FDWDKLRVFYVVARSGSFTHAAEQLHLSQSSISRQISG 40 (299) Q Consensus 3 md~~~L~~f~~v~~~gs~s~AA~~L~itq~avS~~i~~ 40 (299) +++++|+-. =+.++..||+.|||+.+++-+.-++ T Consensus 5 lt~~dl~~~----F~lpi~~AA~~Lgv~~T~LKk~CR~ 38 (52) T pfam02042 5 LTLEDLSKY----FHLPIKEAAKELGVCLTVLKKICRQ 38 (52) T ss_pred CCHHHHHHH----HCCCHHHHHHHHCCCHHHHHHHHHH T ss_conf 569999998----1875999999968779999999998 No 206 >PRK09464 pdhR transcriptional regulator PdhR; Reviewed Probab=50.21 E-value=18 Score=16.24 Aligned_cols=42 Identities=26% Similarity=0.386 Sum_probs=31.9 Q ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEECCCCEEEEEC Q ss_conf 68999988289978999999999999588217976994685001 Q gi|254780282|r 19 SFTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHARGLTLTEQ 62 (299) Q Consensus 19 s~s~AA~~L~itq~avS~~i~~LE~~lg~~Lf~R~~~~~~lT~~ 62 (299) |=..=|+.++||.++|-..|+.|| ..|. +-.|.|+|...+.. T Consensus 36 sE~eLA~~lgVSR~~VREAL~~L~-~~Gl-V~~r~g~G~~V~~~ 77 (254) T PRK09464 36 PERELAKQFDVSRPSLREAIQRLE-AKGL-LLRRQGGGTFVQSS 77 (254) T ss_pred CHHHHHHHHCCCCHHHHHHHHHHH-HCCC-EEEECCCCEEECCC T ss_conf 699999986899559999999999-8899-89717871364677 No 207 >pfam08222 HTH_CodY CodY helix-turn-helix domain. This family consists of the C-terminal helix-turn-helix domain found in several bacterial GTP-sensing transcriptional pleiotropic repressor CodY proteins. CodY has been found to repress the dipeptide transport operon (dpp) of Bacillus subtilis in nutrient-rich conditions. The CodY protein also has a repressor effect on many genes in Lactococcus lactis during growth in milk. Probab=50.16 E-value=16 Score=16.61 Aligned_cols=24 Identities=21% Similarity=0.418 Sum_probs=21.6 Q ss_pred HHHHHHHCCCHHHHHHHHHHHHHH Q ss_conf 999988289978999999999999 Q gi|254780282|r 21 THAAEQLHLSQSSISRQISGLETE 44 (299) Q Consensus 21 s~AA~~L~itq~avS~~i~~LE~~ 44 (299) |+-|++.+||.|-+-..+++||.. T Consensus 7 SkiAd~~giTRSVIVNAlRKlESA 30 (60) T pfam08222 7 SKIADRIGITRSVIVNALRKLESA 30 (60) T ss_pred HHHHHHHCCHHHHHHHHHHHHHHC T ss_conf 566676296189999999876434 No 208 >PRK11303 DNA-binding transcriptional regulator FruR; Provisional Probab=49.05 E-value=16 Score=16.51 Aligned_cols=22 Identities=23% Similarity=0.280 Sum_probs=18.4 Q ss_pred CHHHHHHHHCCCHHHHHHHHHH Q ss_conf 6899998828997899999999 Q gi|254780282|r 19 SFTHAAEQLHLSQSSISRQISG 40 (299) Q Consensus 19 s~s~AA~~L~itq~avS~~i~~ 40 (299) ++.--|+..|||.+|||+.|.. T Consensus 2 TikDVA~~AGVS~aTVSrvLNg 23 (330) T PRK11303 2 KLDEIARLAGVSRTTASYVING 23 (330) T ss_pred CHHHHHHHHCCCHHHHHHHHCC T ss_conf 7899999979799899888389 No 209 >COG3415 Transposase and inactivated derivatives [DNA replication, recombination, and repair] Probab=49.01 E-value=19 Score=16.13 Aligned_cols=59 Identities=24% Similarity=0.081 Sum_probs=41.4 Q ss_pred CCHHHHHHHHHHHHHCCHHHHHHHHCCCHHHHHHHHHHHHHHHCC-EEEEECCCCEEEEE Q ss_conf 888999999999982768999988289978999999999999588-21797699468500 Q gi|254780282|r 3 FDWDKLRVFYVVARSGSFTHAAEQLHLSQSSISRQISGLETEVGI-KLFYRHARGLTLTE 61 (299) Q Consensus 3 md~~~L~~f~~v~~~gs~s~AA~~L~itq~avS~~i~~LE~~lg~-~Lf~R~~~~~~lT~ 61 (299) .|++.+..-..+++--|...||++++||-++|-+=+++.++.=.. +--.+.|+.=.+++ T Consensus 7 ~~~R~~~~~~~~~~G~S~re~Ak~~gvs~sTvy~wv~r~~e~G~~l~~~~~~GrP~kl~~ 66 (138) T COG3415 7 NDLRERVVDAVVGEGLSCREAAKRFGVSISTVYRWVRRYRETGLDLPPKPRKGRPRKLSE 66 (138) T ss_pred HHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCH T ss_conf 899999999999768549999999692299999999873335331567668999732588 No 210 >COG2390 DeoR Transcriptional regulator, contains sigma factor-related N-terminal domain [Transcription] Probab=48.33 E-value=17 Score=16.50 Aligned_cols=39 Identities=21% Similarity=0.181 Sum_probs=25.1 Q ss_pred HHHHHHHHHHHHC--CHHHHHHHHCCCHHHHHHHHHHHHHH Q ss_conf 9999999999827--68999988289978999999999999 Q gi|254780282|r 6 DKLRVFYVVARSG--SFTHAAEQLHLSQSSISRQISGLETE 44 (299) Q Consensus 6 ~~L~~f~~v~~~g--s~s~AA~~L~itq~avS~~i~~LE~~ 44 (299) +++.-...++=.. +=+.=|++||||.+.||+-+++..++ T Consensus 13 ~l~~~~A~lYY~~gltQ~eIA~~LgiSR~~v~rlL~~Ar~~ 53 (321) T COG2390 13 RLLARAAWLYYVEGLTQSEIAERLGISRATVSRLLAKAREE 53 (321) T ss_pred HHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHC T ss_conf 99999999998468879999988398899999999999987 No 211 >PRK10423 transcriptional repressor RbsR; Provisional Probab=47.91 E-value=13 Score=17.08 Aligned_cols=108 Identities=10% Similarity=0.028 Sum_probs=48.6 Q ss_pred HHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEECCCCEEEEECCCCCCCCCCCCCCCCCHHHHH-CCCCCCCCCCCCCCCC Q ss_conf 999988289978999999999999588217976994685001343322222222221012210-0122322222233321 Q gi|254780282|r 21 THAAEQLHLSQSSISRQISGLETEVGIKLFYRHARGLTLTEQGSKLHRVTSEVYHKLETTQIE-LQESSVKPSGKLRIAT 99 (299) Q Consensus 21 s~AA~~L~itq~avS~~i~~LE~~lg~~Lf~R~~~~~~lT~~G~~l~~~a~~~l~~~~~~~~~-~~~~~~~~~g~i~I~~ 99 (299) .--|+..|||.+|||+.+.. .+++.+ ..-+++.++.+++.-.-+. .+.++.+.++.|-+-+ T Consensus 2 kDIA~~AGVS~sTVSrvLn~-------------~~~Vs~-----~tr~rV~~aa~elgY~pn~~Ar~L~~~~s~~Igviv 63 (327) T PRK10423 2 KDVARLAGVSTSTVSHVINK-------------DRFVSE-----AITAKVEAAIKELNYAPSALARSLKLNQTRTIGMLI 63 (327) T ss_pred HHHHHHHCCCHHHHHHHHCC-------------CCCCCH-----HHHHHHHHHHHHHCCCCCHHHHHHHHCCCCEEEEEE T ss_conf 68987869899999999789-------------599999-----999999999998299868888877537876799997 Q ss_pred CCCCCCCCCCCHHHHHHHHHH--CCCCCCCCCCC--------CCCCCCCCCCCCCCCC Q ss_conf 110000000001356675420--00122222222--------2222222222223456 Q gi|254780282|r 100 TIDLGQNLLQGNLKEFLLLYP--DIQIQLILDNK--------DIDISMDYADCAIRLR 147 (299) Q Consensus 100 ~~~~~~~~l~~~l~~f~~~~P--~i~i~i~~~~~--------~~~l~~~~~Di~i~~~ 147 (299) + .....+...++..+.+..- +..+-+...+. ...+....+|-.|.+. T Consensus 64 ~-~~~~~f~~~i~~~i~~~~~~~gy~~~l~~~~~~~~~~~~~l~~l~~~~vdGiIi~~ 120 (327) T PRK10423 64 T-ASTNPFYSELVRGVERSCFERGYSLVLCNTEGDEQRMNRNLETLMQKRVDGLLLLC 120 (327) T ss_pred C-CCCCCHHHHHHHHHHHHHHHCCCEEEEEECCCCHHHHHHHHHHHHHCCCCEEEEEC T ss_conf 3-66551267889999999998599899982689879999999999955987699974 No 212 >cd04762 HTH_MerR-trunc Helix-Turn-Helix DNA binding domain of truncated MerR-like proteins. Proteins in this family mostly have a truncated helix-turn-helix (HTH) MerR-like domain. They lack a portion of the C-terminal region, called Wing 2 and the long dimerization helix that is typically present in MerR-like proteins. These truncated domains are found in response regulator receiver (REC) domain proteins (i.e., CheY), cytosine-C5 specific DNA methylases, IS607 transposase-like proteins, and RacA, a bacterial protein that anchors chromosomes to cell poles. Probab=47.85 E-value=18 Score=16.30 Aligned_cols=22 Identities=32% Similarity=0.360 Sum_probs=18.0 Q ss_pred CHHHHHHHHCCCHHHHHHHHHH Q ss_conf 6899998828997899999999 Q gi|254780282|r 19 SFTHAAEQLHLSQSSISRQISG 40 (299) Q Consensus 19 s~s~AA~~L~itq~avS~~i~~ 40 (299) +.+.||+.|+||+++|-+=.++ T Consensus 2 t~~e~A~~lgVs~~TlrrW~~~ 23 (49) T cd04762 2 TTKEAAELLGVSPSTLRRWVKE 23 (49) T ss_pred CHHHHHHHHCCCHHHHHHHHHC T ss_conf 8899999979899999999987 No 213 >PRK09492 treR trehalose repressor; Provisional Probab=47.83 E-value=19 Score=16.17 Aligned_cols=22 Identities=18% Similarity=0.303 Sum_probs=18.8 Q ss_pred CHHHHHHHHCCCHHHHHHHHHH Q ss_conf 6899998828997899999999 Q gi|254780282|r 19 SFTHAAEQLHLSQSSISRQISG 40 (299) Q Consensus 19 s~s~AA~~L~itq~avS~~i~~ 40 (299) ++.--|+..|||.+|||+.+.. T Consensus 6 TikDIA~~aGVS~aTVSrvLn~ 27 (315) T PRK09492 6 TIKDIARLSGVGKSTVSRVLNN 27 (315) T ss_pred CHHHHHHHHCCCHHHHHHHHCC T ss_conf 7999999989799999999789 No 214 >smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor. Probab=47.71 E-value=20 Score=16.01 Aligned_cols=39 Identities=31% Similarity=0.356 Sum_probs=29.8 Q ss_pred HHHCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEECCCC Q ss_conf 982768999988289978999999999999588217976994 Q gi|254780282|r 15 ARSGSFTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHARG 56 (299) Q Consensus 15 ~~~gs~s~AA~~L~itq~avS~~i~~LE~~lg~~Lf~R~~~~ 56 (299) -..-++..-|+.++||..||-+=|..||++ .++.|..+| T Consensus 12 ~~~~~i~~La~~~~VS~~TiRRDl~~L~~~---g~i~r~hGG 50 (53) T smart00420 12 QGKVSVEELAELLGVSEMTIRRDLNKLEEQ---GLLTRVHGG 50 (53) T ss_pred CCCEEHHHHHHHHCCCHHHHHHHHHHHHHC---CCEEEEECC T ss_conf 697979999999897999999969999988---998997798 No 215 >PRK09333 30S ribosomal protein S19e; Provisional Probab=47.30 E-value=14 Score=16.93 Aligned_cols=23 Identities=9% Similarity=0.007 Sum_probs=18.0 Q ss_pred CCCCCCCHHHHHHHHHHHHHHHC Q ss_conf 48778888999999999999850 Q gi|254780282|r 274 PEALKNTGKLKAFRNFIFLKARD 296 (299) Q Consensus 274 ~~~~~~~~~~~~f~d~l~~~~r~ 296 (299) .+++..+|.-+.++|-+..++.+ T Consensus 115 ~~GR~iT~~G~~~LD~iA~~v~~ 137 (150) T PRK09333 115 KKGRVITPKGRSLLDKLATEVKK 137 (150) T ss_pred CCCCEECHHHHHHHHHHHHHHHH T ss_conf 99867798689999999999999 No 216 >PRK09137 DNA topoisomerase I; Validated Probab=46.95 E-value=9.6 Score=17.87 Aligned_cols=22 Identities=9% Similarity=0.167 Sum_probs=8.5 Q ss_pred EEECCCCEEEEECCCCCCCCCC Q ss_conf 7976994685001343322222 Q gi|254780282|r 50 FYRHARGLTLTEQGSKLHRVTS 71 (299) Q Consensus 50 f~R~~~~~~lT~~G~~l~~~a~ 71 (299) +.+.++.+.||+.|..+.+... T Consensus 506 v~~~~k~l~pT~lG~~v~~~L~ 527 (761) T PRK09137 506 VRLDKKRFIPTDVGRIVNKFLT 527 (761) T ss_pred EEEECCEEEECHHHHHHHHHHH T ss_conf 9965998856467999999998 No 217 >PRK09802 DNA-binding transcriptional regulator AgaR; Provisional Probab=46.39 E-value=21 Score=15.89 Aligned_cols=55 Identities=13% Similarity=0.207 Sum_probs=41.7 Q ss_pred HHHHHHHHHHHHC--CHHHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEECCCCEEEEECC Q ss_conf 9999999999827--689999882899789999999999995882179769946850013 Q gi|254780282|r 6 DKLRVFYVVARSG--SFTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHARGLTLTEQG 63 (299) Q Consensus 6 ~~L~~f~~v~~~g--s~s~AA~~L~itq~avS~~i~~LE~~lg~~Lf~R~~~~~~lT~~G 63 (299) |+-+..-.+-+.| ++..-|+.++||..||-|=++.||++ .+..|..+|..+.+.. T Consensus 18 R~~~Il~~L~~~g~v~v~eLae~~~VS~~TIRRDL~~Le~~---g~l~R~hGGA~~~~~~ 74 (269) T PRK09802 18 RREQIIQRLRQQGSVQVNDLSALYGVSTVTIRNDLAFLEKQ---GIAVRAYGGALICDST 74 (269) T ss_pred HHHHHHHHHHHCCCEEHHHHHHHHCCCHHHHHHHHHHHHHC---CCEEEEECCEEECCCC T ss_conf 99999999998698999999998796988999809999878---9869996878976778 No 218 >COG2901 Fis Factor for inversion stimulation Fis, transcriptional activator [Transcription / DNA replication, recombination, and repair] Probab=46.30 E-value=21 Score=15.88 Aligned_cols=24 Identities=21% Similarity=0.378 Sum_probs=14.6 Q ss_pred HCCHHHHHHHHCCCHHHHHHHHHH Q ss_conf 276899998828997899999999 Q gi|254780282|r 17 SGSFTHAAEQLHLSQSSISRQISG 40 (299) Q Consensus 17 ~gs~s~AA~~L~itq~avS~~i~~ 40 (299) .||=|+||..|||...++-+.+++ T Consensus 71 ~gNQtrAa~mLGinR~TLRKKLkq 94 (98) T COG2901 71 RGNQTRAALMLGINRGTLRKKLKK 94 (98) T ss_pred CCCHHHHHHHHCCCHHHHHHHHHH T ss_conf 264889999974328899999998 No 219 >KOG1168 consensus Probab=44.60 E-value=23 Score=15.72 Aligned_cols=34 Identities=12% Similarity=0.109 Sum_probs=14.1 Q ss_pred HCCEEEEECCCCEEEEE---CCCCCCCCCCCCCCCCCHHH Q ss_conf 58821797699468500---13433222222222210122 Q gi|254780282|r 45 VGIKLFYRHARGLTLTE---QGSKLHRVTSEVYHKLETTQ 81 (299) Q Consensus 45 lg~~Lf~R~~~~~~lT~---~G~~l~~~a~~~l~~~~~~~ 81 (299) ++.+||.|. ..||+ -|..+.-.-..++...+.+. T Consensus 38 ~~S~~~~~a---~lp~~~~~~snifa~~deslLaRaeala 74 (385) T KOG1168 38 FPSELFRRA---CLPSPISRGSNIFAGTDESLLARAEALA 74 (385) T ss_pred CCHHHHHHH---HCCCCCCCCCCCCCCCCHHHHHHHHHHH T ss_conf 750766676---4479656677642334488999887666 No 220 >TIGR03001 Sig-70_gmx1 RNA polymerase sigma-70 factor, Myxococcales family 1; InterPro: IPR011745 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme . RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognized by the major sigma factors , . This entry describes sigma-70 factors in Myxococcus xanthus DK 1622 and in other members of the Mycococcales. Each of the six members in M. xanthusis is encoded near a gene for a predicted serine/threonine kinase. Members of this family show sequence similarity to members of Pfam family IPR007630 from INTERPRO (region 4 of sigma-70 like sigma-factors), a helix-turn-helix family in which trusted and noise cutoffs deliberately are set artificially high and which therefore has many false negatives.; GO: 0003677 DNA binding, 0003700 transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, 0006355 regulation of transcription DNA-dependent. Probab=43.93 E-value=23 Score=15.66 Aligned_cols=11 Identities=9% Similarity=-0.121 Sum_probs=4.8 Q ss_pred CCCHHHHHHHH Q ss_conf 00013566754 Q gi|254780282|r 108 LQGNLKEFLLL 118 (299) Q Consensus 108 l~~~l~~f~~~ 118 (299) .|..+..|-++ T Consensus 40 ~p~Al~~lErh 50 (249) T TIGR03001 40 EPAALAALERH 50 (249) T ss_pred CHHHHHHHHHH T ss_conf 28999999999 No 221 >pfam01527 Transposase_8 Transposase. Transposase proteins are necessary for efficient DNA transposition. This family consists of various E. coli insertion elements and other bacterial transposases some of which are members of the IS3 family. Probab=43.93 E-value=23 Score=15.66 Aligned_cols=29 Identities=14% Similarity=0.159 Sum_probs=24.7 Q ss_pred HHHHC-CHHHHHHHHCCCHHHHHHHHHHHH Q ss_conf 99827-689999882899789999999999 Q gi|254780282|r 14 VARSG-SFTHAAEQLHLSQSSISRQISGLE 42 (299) Q Consensus 14 v~~~g-s~s~AA~~L~itq~avS~~i~~LE 42 (299) +.+.| |++..|+.++|+++++.+=+++.. T Consensus 19 ~~~~g~sv~~var~~gi~~~~l~~W~k~~~ 48 (75) T pfam01527 19 SLEPGASVSELAREHGVSPATLYKWRKKYR 48 (75) T ss_pred HHHCCCCHHHHHHHHCCCHHHHHHHHHHHH T ss_conf 980998499999998959999999999984 No 222 >pfam07022 Phage_CI_repr Bacteriophage CI repressor helix-turn-helix domain. This family consists of several phage CI repressor proteins and related bacterial sequences. The CI repressor is known to function as a transcriptional switch, determining whether transcription is lytic or lysogenic. Probab=43.80 E-value=23 Score=15.65 Aligned_cols=32 Identities=19% Similarity=0.104 Sum_probs=25.1 Q ss_pred HHHHHHHHHCCHHHHHHHHCCCHHHHHHHHHH Q ss_conf 99999998276899998828997899999999 Q gi|254780282|r 9 RVFYVVARSGSFTHAAEQLHLSQSSISRQISG 40 (299) Q Consensus 9 ~~f~~v~~~gs~s~AA~~L~itq~avS~~i~~ 40 (299) +=+..+.-..+-+.=|+.|+|++++||...++ T Consensus 4 ~Rl~~a~G~~t~~eLA~~LgI~~stis~w~~R 35 (65) T pfam07022 4 ERLMKAYGFKSRSELADHLGVSKSTLSTWYKR 35 (65) T ss_pred HHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHC T ss_conf 99999968886999999969888889999986 No 223 >PRK04280 arginine repressor; Provisional Probab=43.54 E-value=12 Score=17.22 Aligned_cols=34 Identities=15% Similarity=0.198 Sum_probs=20.7 Q ss_pred HHHHHHHHHHCCHHH--------HHHHHCCCHHHHHHHHHHH Q ss_conf 999999998276899--------9988289978999999999 Q gi|254780282|r 8 LRVFYVVARSGSFTH--------AAEQLHLSQSSISRQISGL 41 (299) Q Consensus 8 L~~f~~v~~~gs~s~--------AA~~L~itq~avS~~i~~L 41 (299) .+....+..++.++. +++-..+||+||||-|++| T Consensus 7 ~~~I~~lI~~~~I~tQeeL~~~L~~~Gi~vTQATlSRDlkeL 48 (149) T PRK04280 7 HIKIREIITNEEIETQDELVDRLREYGFNVTQATVSRDIKEL 48 (149) T ss_pred HHHHHHHHHHCCCCCHHHHHHHHHHCCCCEEHHHHHHHHHHH T ss_conf 999999997489778999999999859755389889879981 No 224 >PRK09729 hypothetical protein; Provisional Probab=43.37 E-value=14 Score=16.94 Aligned_cols=40 Identities=25% Similarity=0.268 Sum_probs=25.2 Q ss_pred HHHHHHHCCEEEEEHHHHCC-CCCEEEECCCCCCCCCEEEEE Q ss_conf 35678738423311777601-998466177666766008999 Q gi|254780282|r 232 MQYCVLGSGIALLPDYIVKD-NPNLVRIMEDVITPSFTVYFC 272 (299) Q Consensus 232 ~~~v~~g~Gia~lp~~~~~~-~~~lv~i~~~~~~~~~~~~lv 272 (299) ++.++.|+||+++|+...+. .|++..+.. .+..-+.+.+. T Consensus 1 ~~firqglgiallpeltlk~~~g~lcsv~l-eptfyrqisll 41 (68) T PRK09729 1 MNFIRQGLGIALQPELTLKSIAGELCSVPL-EPTFYRQISLL 41 (68) T ss_pred CCHHHHCCCEEECCHHHHHHHCCCEECCCC-CHHHHHHHHHH T ss_conf 926760665222204438874174012346-63799999998 No 225 >pfam00325 Crp Bacterial regulatory proteins, crp family. Probab=43.14 E-value=21 Score=15.96 Aligned_cols=23 Identities=26% Similarity=0.437 Sum_probs=20.1 Q ss_pred HHHHHHCCCHHHHHHHHHHHHHH Q ss_conf 99988289978999999999999 Q gi|254780282|r 22 HAAEQLHLSQSSISRQISGLETE 44 (299) Q Consensus 22 ~AA~~L~itq~avS~~i~~LE~~ 44 (299) .-|+-|+.|.-+||+.+++|+++ T Consensus 7 dIadylGlt~ETVsR~l~~L~~~ 29 (32) T pfam00325 7 EIADYLGLTRETVSRLLKRLREK 29 (32) T ss_pred HHHHHHCCHHHHHHHHHHHHHHC T ss_conf 99998472599999999999985 No 226 >PRK09954 hypothetical protein; Provisional Probab=42.93 E-value=22 Score=15.75 Aligned_cols=55 Identities=22% Similarity=0.308 Sum_probs=35.6 Q ss_pred CHHHHHHHHHHHHHCCHH--HHHHHHCCCHHHHHHHHHHHHHHHCCEEEEECCCCEEEEECC Q ss_conf 889999999999827689--999882899789999999999995882179769946850013 Q gi|254780282|r 4 DWDKLRVFYVVARSGSFT--HAAEQLHLSQSSISRQISGLETEVGIKLFYRHARGLTLTEQG 63 (299) Q Consensus 4 d~~~L~~f~~v~~~gs~s--~AA~~L~itq~avS~~i~~LE~~lg~~Lf~R~~~~~~lT~~G 63 (299) +=|.-+.+-.+=+.--++ .=|+.|++|.|+|.-||.+|=+. =+.+ |||+.+++.- T Consensus 2 t~re~~il~~i~~~p~i~q~ela~~lgisrs~va~hi~~l~~k----g~i~-G~gyi~~~~~ 58 (362) T PRK09954 2 NNREKEILAILRRNPLIQQNEIADILQISRSRVAAHIMDLMRK----GRIK-GKGYILTEQE 58 (362) T ss_pred CHHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHHHC----CEEC-CCEEEECCCC T ss_conf 8689999999987899589999999798799999999988754----7652-5468877997 No 227 >pfam05344 DUF746 Domain of Unknown Function (DUF746). This is a short conserved region found in some transposons. Probab=42.28 E-value=25 Score=15.51 Aligned_cols=33 Identities=18% Similarity=0.209 Sum_probs=28.4 Q ss_pred HHHHHCCHHHHHHHHCCCHHHHHHHHHHHHHHH Q ss_conf 999827689999882899789999999999995 Q gi|254780282|r 13 VVARSGSFTHAAEQLHLSQSSISRQISGLETEV 45 (299) Q Consensus 13 ~v~~~gs~s~AA~~L~itq~avS~~i~~LE~~l 45 (299) -+..--|+..||+.+++++-+|.+-++...+++ T Consensus 9 lLs~p~s~~qaa~~lg~~~~~i~~wv~~fr~~l 41 (65) T pfam05344 9 LLSQPISCAQAADQLGTDEGIIRKWVRMFRRWL 41 (65) T ss_pred HHCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHH T ss_conf 826666599999997878889999999999999 No 228 >pfam01316 Arg_repressor Arginine repressor, DNA binding domain. Probab=41.65 E-value=12 Score=17.37 Aligned_cols=16 Identities=25% Similarity=0.596 Sum_probs=11.7 Q ss_pred HHCCCHHHHHHHHHHH Q ss_conf 8289978999999999 Q gi|254780282|r 26 QLHLSQSSISRQISGL 41 (299) Q Consensus 26 ~L~itq~avS~~i~~L 41 (299) -..+||++|||-|++| T Consensus 33 G~~vTQATlSRDl~eL 48 (70) T pfam01316 33 GINVTQATVSRDLKEL 48 (70) T ss_pred CCCEEEHHHHHHHHHH T ss_conf 9856417888779993 No 229 >COG1438 ArgR Arginine repressor [Transcription] Probab=41.41 E-value=20 Score=15.97 Aligned_cols=37 Identities=16% Similarity=0.355 Sum_probs=22.3 Q ss_pred HHHHHHHHHHHHHCCHHH--------HHHHHCCCHHHHHHHHHHH Q ss_conf 899999999998276899--------9988289978999999999 Q gi|254780282|r 5 WDKLRVFYVVARSGSFTH--------AAEQLHLSQSSISRQISGL 41 (299) Q Consensus 5 ~~~L~~f~~v~~~gs~s~--------AA~~L~itq~avS~~i~~L 41 (299) =+.++.+..+.....++. +.+-..+||++|||-|++| T Consensus 5 ~~R~~~Ik~iI~~~~i~TQ~Elv~~L~~~Gi~vTQaTvSRDlkel 49 (150) T COG1438 5 EERLELIKEIITEEKISTQEELVELLQEEGIEVTQATVSRDLKEL 49 (150) T ss_pred HHHHHHHHHHHHHCCCCCHHHHHHHHHHCCCEEEHHHHHHHHHHC T ss_conf 899999999998677778999999999829758639878779985 No 230 >COG5606 Uncharacterized conserved small protein [Function unknown] Probab=41.28 E-value=18 Score=16.24 Aligned_cols=19 Identities=26% Similarity=0.293 Sum_probs=12.8 Q ss_pred HHHHHHHCCCHHHHHHHHH Q ss_conf 9999882899789999999 Q gi|254780282|r 21 THAAEQLHLSQSSISRQIS 39 (299) Q Consensus 21 s~AA~~L~itq~avS~~i~ 39 (299) +++|+.|+||||.||--.+ T Consensus 45 ~qiae~lgV~qprvS~l~~ 63 (91) T COG5606 45 AQIAELLGVTQPRVSDLAR 63 (91) T ss_pred HHHHHHHCCCCCHHHHHHH T ss_conf 9999983888731889983 No 231 >pfam05339 DUF739 Protein of unknown function (DUF739). This family contains several bacteriophage proteins. Some of the proteins in this family have been labeled putative cro repressor proteins. Probab=40.63 E-value=26 Score=15.36 Aligned_cols=37 Identities=27% Similarity=0.428 Sum_probs=32.2 Q ss_pred CCCCHHHHHHHHHHHHHCCHHHHHHHHCCCHHHHHHHH Q ss_conf 98888999999999982768999988289978999999 Q gi|254780282|r 1 MSFDWDKLRVFYVVARSGSFTHAAEQLHLSQSSISRQI 38 (299) Q Consensus 1 m~md~~~L~~f~~v~~~gs~s~AA~~L~itq~avS~~i 38 (299) |..|+..|+-.. +-++|+.-.=|..+++|.-++|-.+ T Consensus 1 m~~dY~kLrgrI-~Ek~gtq~~Fa~~lg~se~tlslkl 37 (69) T pfam05339 1 MKYDYSKLKGRI-LEKYGTQYNFASAIGLSERSLSLKL 37 (69) T ss_pred CCCCHHHHCCHH-HHHHCCHHHHHHHHCCCHHHHHHHH T ss_conf 976678860328-8995679899999581176888987 No 232 >pfam01381 HTH_3 Helix-turn-helix. This large family of DNA binding helix-turn helix proteins includes Cro and CI. Probab=40.38 E-value=25 Score=15.45 Aligned_cols=23 Identities=35% Similarity=0.280 Sum_probs=17.1 Q ss_pred HCCHHHHHHHHCCCHHHHHHHHH Q ss_conf 27689999882899789999999 Q gi|254780282|r 17 SGSFTHAAEQLHLSQSSISRQIS 39 (299) Q Consensus 17 ~gs~s~AA~~L~itq~avS~~i~ 39 (299) --|-...|+.+++|+++||+--+ T Consensus 9 g~tq~~lA~~~gis~~~is~~E~ 31 (55) T pfam01381 9 GLSQEELAEKLGVSRSTISKIEN 31 (55) T ss_pred CCCHHHHHHHHCCCHHHHHHHHC T ss_conf 99899999998969999999987 No 233 >PRK09764 DNA-binding transcriptional repressor MngR; Provisional Probab=40.37 E-value=26 Score=15.40 Aligned_cols=41 Identities=12% Similarity=0.139 Sum_probs=30.5 Q ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEECCCCEEEEE Q ss_conf 6899998828997899999999999958821797699468500 Q gi|254780282|r 19 SFTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHARGLTLTE 61 (299) Q Consensus 19 s~s~AA~~L~itq~avS~~i~~LE~~lg~~Lf~R~~~~~~lT~ 61 (299) |=..=|+..+||..||-++|+.||++ --+..+.|+|.-.++ T Consensus 31 sE~eLa~~~~VSR~TvR~Al~~L~~e--Gli~r~~G~GTfV~~ 71 (239) T PRK09764 31 TESALQTEFGVSRVTVRQALRQLVEQ--QILESIQGSGTYVKE 71 (239) T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHC--CCEEEECCCEEEECC T ss_conf 99999999797999999999999978--999998687789888 No 234 >TIGR02201 heptsyl_trn_III lipopolysaccharide heptosyltransferase III, putative; InterPro: IPR011916 This family consists of examples of the putative ADP-heptose:LPS heptosyltransferase III, an enzyme of LPS inner core region biosynthesis. LPS, composed of lipid A, a core region, and O antigen, is found in the outer membrane of Gram-negative bacteria. This enzyme may be less widely distributed than heptosyltransferases I and II.. Probab=40.29 E-value=8.5 Score=18.18 Aligned_cols=38 Identities=21% Similarity=0.351 Sum_probs=28.2 Q ss_pred CCCCHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCC Q ss_conf 00001356675420001222222222222222222223 Q gi|254780282|r 107 LLQGNLKEFLLLYPDIQIQLILDNKDIDISMDYADCAI 144 (299) Q Consensus 107 ~l~~~l~~f~~~~P~i~i~i~~~~~~~~l~~~~~Di~i 144 (299) +..|++..+.++||+.+|++..-....+++...=|+.= T Consensus 15 L~TPvi~~LK~~yP~a~iDvLlY~eT~p~L~~NPdI~~ 52 (347) T TIGR02201 15 LTTPVIRALKKRYPDAKIDVLLYRETVPLLSENPDIAR 52 (347) T ss_pred HHHHHHHHHHHCCCCCCEEEEEHHHHHHHHHCCCCHHH T ss_conf 88799999851188850430210315888762883355 No 235 >COG3388 Predicted transcriptional regulator [Transcription] Probab=39.40 E-value=10 Score=17.70 Aligned_cols=65 Identities=15% Similarity=0.195 Sum_probs=50.7 Q ss_pred HHHHHHHHHHHHHCCH--HHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEECCCCEEEEECCCCCCCCCCC Q ss_conf 8999999999982768--9999882899789999999999995882179769946850013433222222 Q gi|254780282|r 5 WDKLRVFYVVARSGSF--THAAEQLHLSQSSISRQISGLETEVGIKLFYRHARGLTLTEQGSKLHRVTSE 72 (299) Q Consensus 5 ~~~L~~f~~v~~~gs~--s~AA~~L~itq~avS~~i~~LE~~lg~~Lf~R~~~~~~lT~~G~~l~~~a~~ 72 (299) .++|.++-.|++++-+ -+-++..|+..--|-..++-||++ .++.-+..|-.+|+.+-.+.+.... T Consensus 14 ~RHl~Vl~~v~eeqPiGI~klS~~TGmp~HKVRYSLRVLEq~---~iI~PS~~GAi~td~~~e~ie~i~~ 80 (101) T COG3388 14 KRHLSVLKVVLEEQPIGIIKLSDETGMPEHKVRYSLRVLEQE---NIISPSRQGAILTDDFPEFIEEIIG 80 (101) T ss_pred HHHHHHHHHHHHHCCCEEEEECHHCCCCHHHHHHHHHHHHHC---CCCCCCCCCCCCCCCHHHHHHHHHH T ss_conf 999999999998388316850010188403345666545235---7567353677138507899999997 No 236 >cd00186 TOP1Ac DNA Topoisomerase, subtype IA; DNA-binding, ATP-binding and catalytic domain of bacterial DNA topoisomerases I and III, and eukaryotic DNA topoisomerase III and eubacterial and archael reverse gyrases. Topoisomerases clevage single or double stranded DNA and then rejoin the broken phosphodiester backbone. Proposed catalytic mechanism of single stranded DNA cleavage is by phosphoryl transfer through a tyrosine nucleophile using acid/base catalysis. Tyr is activated by a nearby group (not yet identified) acting as a general base for nucleophilic attack on the 5' phosphate of the scissile bond. Arg and Lys stabilize the pentavalent transition state. Glu then acts as a proton donor for the leaving 3'-oxygen, upon cleavage of the scissile strand. Probab=39.38 E-value=12 Score=17.37 Aligned_cols=23 Identities=17% Similarity=0.140 Sum_probs=14.2 Q ss_pred HHHHHHHCCCHHHHHHHHHHHHH Q ss_conf 99998828997899999999999 Q gi|254780282|r 21 THAAEQLHLSQSSISRQISGLET 43 (299) Q Consensus 21 s~AA~~L~itq~avS~~i~~LE~ 43 (299) ..|++++++|+.-+-+..++|=+ T Consensus 94 ~~a~~~~g~s~~~tl~iaQ~LYE 116 (381) T cd00186 94 QEASSKLGFSAKKTMQIAQKLYE 116 (381) T ss_pred HHHHHCCCCCHHHHHHHHHHHHH T ss_conf 99986069599999999999986 No 237 >pfam08220 HTH_DeoR DeoR-like helix-turn-helix domain. Probab=39.34 E-value=27 Score=15.24 Aligned_cols=47 Identities=26% Similarity=0.284 Sum_probs=35.4 Q ss_pred HHHHHHHCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEECCCCEEEE Q ss_conf 99999827689999882899789999999999995882179769946850 Q gi|254780282|r 11 FYVVARSGSFTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHARGLTLT 60 (299) Q Consensus 11 f~~v~~~gs~s~AA~~L~itq~avS~~i~~LE~~lg~~Lf~R~~~~~~lT 60 (299) ++.-...-++..-|+.++||..||-+-|..||+. .++.|..+|..+. T Consensus 8 ~l~~~~~v~i~~La~~f~VS~~TiRRDl~~L~~~---g~i~R~~GGA~~~ 54 (57) T pfam08220 8 LLKQQGTLSVEELAELLGVSEMTIRRDLNELEEQ---GLLTRTHGGAVSN 54 (57) T ss_pred HHHHCCCEEHHHHHHHHCCCHHHHHHHHHHHHHC---CCEEEEECCEECC T ss_conf 9998697979999999895999999969999988---9989974957758 No 238 >TIGR03337 phnR transcriptional regulator protein. This family of proteins are members of the GntR family (pfam00392) containing an N-terminal helix-turn-helix (HTH) motif. This clade is found adjacent to or inside of operons for the degradation of 2-aminoethylphosphonate (AEP) in Salmonella, Vibrio Aeromonas hydrophila, Hahella chejuensis and Psychromonas ingrahamii. Probab=39.24 E-value=27 Score=15.23 Aligned_cols=41 Identities=20% Similarity=0.302 Sum_probs=29.1 Q ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEECCCCEEEEE Q ss_conf 6899998828997899999999999958821797699468500 Q gi|254780282|r 19 SFTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHARGLTLTE 61 (299) Q Consensus 19 s~s~AA~~L~itq~avS~~i~~LE~~lg~~Lf~R~~~~~~lT~ 61 (299) |-..=|++.+||..||.++|+.|+++ --+..+.|+|.-.++ T Consensus 27 sE~eLa~~~~VSR~TvR~Al~~L~~e--Gli~r~~G~GTfV~~ 67 (231) T TIGR03337 27 SERDLGERFNTTRVTIREALQQLEAE--GLIYREDRRGWFVSP 67 (231) T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHC--CCEEEECCCEEEECC T ss_conf 89999999797999999999999987--996996686679888 No 239 >PRK03341 arginine repressor; Provisional Probab=38.99 E-value=14 Score=16.84 Aligned_cols=13 Identities=23% Similarity=0.560 Sum_probs=6.5 Q ss_pred CCCHHHHHHHHHH Q ss_conf 8997899999999 Q gi|254780282|r 28 HLSQSSISRQISG 40 (299) Q Consensus 28 ~itq~avS~~i~~ 40 (299) .+||+||||-|++ T Consensus 45 ~vTQATiSRDikE 57 (168) T PRK03341 45 DVTQATLSRDLEE 57 (168) T ss_pred CEEHHHHHHHHHH T ss_conf 6542787752998 No 240 >smart00530 HTH_XRE Helix-turn-helix XRE-family like proteins. Probab=38.84 E-value=27 Score=15.23 Aligned_cols=23 Identities=30% Similarity=0.281 Sum_probs=18.0 Q ss_pred HCCHHHHHHHHCCCHHHHHHHHH Q ss_conf 27689999882899789999999 Q gi|254780282|r 17 SGSFTHAAEQLHLSQSSISRQIS 39 (299) Q Consensus 17 ~gs~s~AA~~L~itq~avS~~i~ 39 (299) --|....|+.+|+|+++||+-.+ T Consensus 10 glsq~~lA~~~gis~~~is~~E~ 32 (56) T smart00530 10 GLTQEELAEKLGVSRSTLSRIEN 32 (56) T ss_pred CCCHHHHHHHHCCCHHHHHHHHC T ss_conf 99999999998959999999997 No 241 >cd04763 HTH_MlrA-like Helix-Turn-Helix DNA binding domain of MlrA-like transcription regulators. Helix-turn-helix (HTH) transcription regulator MlrA (merR-like regulator A) and related proteins, N-terminal domain. The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. Its close homolog, CarA from Myxococcus xanthus, is involved in activation of the carotenoid biosynthesis genes by light. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA-like proteins in this group appear to lack the long dimerization helix seen Probab=38.79 E-value=28 Score=15.19 Aligned_cols=35 Identities=17% Similarity=0.155 Sum_probs=25.9 Q ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEECCCCE Q ss_conf 689999882899789999999999995882179769946 Q gi|254780282|r 19 SFTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHARGL 57 (299) Q Consensus 19 s~s~AA~~L~itq~avS~~i~~LE~~lg~~Lf~R~~~~~ 57 (299) +++.+|+.++|++ ..|+--|+++|..=-.|+.+|. T Consensus 2 sI~eva~~~Gv~~----~tLR~wE~~~~l~~p~R~~~g~ 36 (68) T cd04763 2 TIGEVALLTGIKP----HVLRAWEREFGLLKPQRSDGGH 36 (68) T ss_pred CHHHHHHHHCCCH----HHHHHHHHCCCCCCCCCCCCCC T ss_conf 7889999988794----5758988705899986799999 No 242 >PRK11402 DNA-binding transcriptional regulator FrlR; Provisional Probab=38.23 E-value=28 Score=15.14 Aligned_cols=40 Identities=20% Similarity=0.248 Sum_probs=29.9 Q ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEECCCCEEEE Q ss_conf 689999882899789999999999995882179769946850 Q gi|254780282|r 19 SFTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHARGLTLT 60 (299) Q Consensus 19 s~s~AA~~L~itq~avS~~i~~LE~~lg~~Lf~R~~~~~~lT 60 (299) |-..=|++.+||..||-++|+.|+++ --+..+.|+|.-.. T Consensus 37 sE~eLa~~y~VSR~TVR~Al~~L~~e--Gli~r~~G~GtfV~ 76 (243) T PRK11402 37 TENELCTQYNVSRITIRKAISDLVAD--GVLIRWQGKGTFVQ 76 (243) T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHC--CCEEEECCCEEEEC T ss_conf 99999999797999999999999978--99999779668995 No 243 >PRK04158 transcriptional repressor CodY; Validated Probab=37.60 E-value=25 Score=15.45 Aligned_cols=11 Identities=0% Similarity=0.126 Sum_probs=3.7 Q ss_pred HHHHCCEEEEE Q ss_conf 99958821797 Q gi|254780282|r 42 ETEVGIKLFYR 52 (299) Q Consensus 42 E~~lg~~Lf~R 52 (299) -+-+.+..++= T Consensus 33 ~~vl~~NvyIi 43 (256) T PRK04158 33 SDVIECNVYII 43 (256) T ss_pred HHHHCCEEEEE T ss_conf 86540739999 No 244 >PRK03837 transcriptional regulator NanR; Provisional Probab=37.49 E-value=29 Score=15.07 Aligned_cols=38 Identities=16% Similarity=0.263 Sum_probs=26.9 Q ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHCCEEE-EECCCCEEE Q ss_conf 68999988289978999999999999588217-976994685 Q gi|254780282|r 19 SFTHAAEQLHLSQSSISRQISGLETEVGIKLF-YRHARGLTL 59 (299) Q Consensus 19 s~s~AA~~L~itq~avS~~i~~LE~~lg~~Lf-~R~~~~~~l 59 (299) +-..=|+.++||.++|-..++.||.+ | |+ .|.|+|... T Consensus 40 ~E~eLae~lgVSRtpVREAL~~L~~~-G--lV~~~~g~g~~V 78 (243) T PRK03837 40 SERELMAFFGVGRPSVREALQALKRK-G--LVQISHGERARV 78 (243) T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHC-C--CEEEEECCCCEE T ss_conf 59999999796978999999999988-9--989950897068 No 245 >cd06571 Bac_DnaA_C C-terminal domain of bacterial DnaA proteins. The DNA-binding C-terminal domain of DnaA contains a helix-turn-helix motif that specifically interacts with the DnaA box, a 9-mer motif that occurs repetitively in the replication origin oriC. Multiple copies of DnaA, which is an ATPase, bind to 9-mers at the origin and form an initial complex in which the DNA strands are being separated in an ATP-dependent step. Probab=37.28 E-value=29 Score=15.05 Aligned_cols=42 Identities=7% Similarity=0.140 Sum_probs=32.2 Q ss_pred HHHHHHHHHH-HHCCHHHHHHHHC-CCHHHHHHHHHHHHHHHCC Q ss_conf 9999999999-8276899998828-9978999999999999588 Q gi|254780282|r 6 DKLRVFYVVA-RSGSFTHAAEQLH-LSQSSISRQISGLETEVGI 47 (299) Q Consensus 6 ~~L~~f~~v~-~~gs~s~AA~~L~-itq~avS~~i~~LE~~lg~ 47 (299) +++-++++-- -.-|++.=|+.+| ..++||+..+++.|+++.. T Consensus 32 R~ia~yL~r~~~~~s~~~Ig~~fg~rdHsTV~~a~~kv~~~~~~ 75 (90) T cd06571 32 RQIAMYLARELTGLSLPEIGRAFGGRDHSTVLHAVRKIEELLEE 75 (90) T ss_pred HHHHHHHHHHHHCCCHHHHHHHHCCCCHHHHHHHHHHHHHHHHH T ss_conf 99999999999788999999995899714999999999999983 No 246 >TIGR02719 repress_PhaQ poly-beta-hydroxybutyrate-responsive repressor; InterPro: IPR014091 Members of this family are transcriptional regulatory proteins found in the vicinity of poly-beta-hydroxybutyrate (PHB) operons in several species of Bacillus. This protein appears to have repressor activity modulated by PHB itself. This protein belongs to the larger PadR family.. Probab=37.12 E-value=7.8 Score=18.39 Aligned_cols=55 Identities=15% Similarity=0.175 Sum_probs=29.4 Q ss_pred CCHHHHHHHHHHHHHHH-CCEEEEE-----CCCCEEEEECCCCCCCCCCCCCCCCCHHHHH Q ss_conf 99789999999999995-8821797-----6994685001343322222222221012210 Q gi|254780282|r 29 LSQSSISRQISGLETEV-GIKLFYR-----HARGLTLTEQGSKLHRVTSEVYHKLETTQIE 83 (299) Q Consensus 29 itq~avS~~i~~LE~~l-g~~Lf~R-----~~~~~~lT~~G~~l~~~a~~~l~~~~~~~~~ 83 (299) |-|--|=|.+++||++= =..=-+- ..|=..||++|+..+.-+..-+++++++.+. T Consensus 55 VDQGNVYRTLR~LEK~NLI~S~WDTS~~GPA~RIYSLT~~GEQYL~~~A~SlE~YQNML~~ 115 (138) T TIGR02719 55 VDQGNVYRTLRKLEKDNLISSTWDTSDEGPAKRIYSLTDAGEQYLSTCATSLEQYQNMLDS 115 (138) T ss_pred CCCCHHHHHHHHHHHHHCCCCCCCCCCCCCCCCHHHHHHCHHHHHHHHHHHHHHHHHHHHH T ss_conf 2310377898887665135566646887863000001311057899998789999889999 No 247 >PRK00441 argR arginine repressor; Provisional Probab=36.35 E-value=16 Score=16.52 Aligned_cols=36 Identities=17% Similarity=0.263 Sum_probs=21.6 Q ss_pred HHHHHHHHHHHHCCHHHH--------HHHHCCCHHHHHHHHHHH Q ss_conf 999999999982768999--------988289978999999999 Q gi|254780282|r 6 DKLRVFYVVARSGSFTHA--------AEQLHLSQSSISRQISGL 41 (299) Q Consensus 6 ~~L~~f~~v~~~gs~s~A--------A~~L~itq~avS~~i~~L 41 (299) ...+....+.....++.= .+-..+||+||||-|++| T Consensus 4 ~Rq~~I~~lI~~~~I~tQ~eL~~~L~~~Gi~vTQATlSRDl~eL 47 (149) T PRK00441 4 SRHAKILEIINSKEIETQEELAEELKKMGFDVTQATVSRDIKEL 47 (149) T ss_pred HHHHHHHHHHHHCCCCCHHHHHHHHHHCCCCEEHHHHHHHHHHC T ss_conf 99999999997289678999999999869976658988869981 No 248 >COG2238 RPS19A Ribosomal protein S19E (S16A) [Translation, ribosomal structure and biogenesis] Probab=35.91 E-value=31 Score=14.92 Aligned_cols=51 Identities=14% Similarity=0.189 Sum_probs=27.0 Q ss_pred EEHHHHCCCCCEEE-ECCCCCCCCCEEEEEECCCCCCCHHHHHHHHHHHHHHHC Q ss_conf 11777601998466-177666766008999348778888999999999999850 Q gi|254780282|r 244 LPDYIVKDNPNLVR-IMEDVITPSFTVYFCYPEALKNTGKLKAFRNFIFLKARD 296 (299) Q Consensus 244 lp~~~~~~~~~lv~-i~~~~~~~~~~~~lv~~~~~~~~~~~~~f~d~l~~~~r~ 296 (299) -|......+|..++ ++... ....+---.++++..+|.-+.|+|-+..++.+ T Consensus 86 rP~~~~~gsgsI~RkilqqL--E~~G~V~k~~~GR~ltp~GrsllD~~a~ei~e 137 (147) T COG2238 86 RPEKFRKGSGSIIRKVLQQL--EKAGLVEKTPKGRVLTPKGRSLLDRIATEIKE 137 (147) T ss_pred CCHHHHCCCCHHHHHHHHHH--HHCCCEEECCCCCEECCCCHHHHHHHHHHHHH T ss_conf 94344237736999999999--97785652689865081306589999999999 No 249 >pfam08281 Sigma70_r4_2 Sigma-70, region 4. Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 promoter element via a helix-turn-helix motif. Probab=35.79 E-value=31 Score=14.91 Aligned_cols=31 Identities=19% Similarity=0.249 Sum_probs=26.2 Q ss_pred HHHHHCCHHHHHHHHCCCHHHHHHHHHHHHH Q ss_conf 9998276899998828997899999999999 Q gi|254780282|r 13 VVARSGSFTHAAEQLHLSQSSISRQISGLET 43 (299) Q Consensus 13 ~v~~~gs~s~AA~~L~itq~avS~~i~~LE~ 43 (299) ...+.-|+...|+.||+|.++|..++.+-.+ T Consensus 22 ~~~~~~s~~eIA~~lg~s~~tVk~~l~RA~~ 52 (54) T pfam08281 22 RYLEGLSYAEIAELLGISEGTVKSRLSRARK 52 (54) T ss_pred HHHHCCCHHHHHHHHCCCHHHHHHHHHHHHH T ss_conf 9987859999999989499999999999997 No 250 >PRK13182 racA polar chromosome segregation protein; Reviewed Probab=35.39 E-value=32 Score=14.87 Aligned_cols=57 Identities=12% Similarity=0.138 Sum_probs=35.0 Q ss_pred HHHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEECCCCEEEEECCCC-CCCCCCCCCCCCCHH Q ss_conf 8999988289978999999999999588217976994685001343-322222222221012 Q gi|254780282|r 20 FTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHARGLTLTEQGSK-LHRVTSEVYHKLETT 80 (299) Q Consensus 20 ~s~AA~~L~itq~avS~~i~~LE~~lg~~Lf~R~~~~~~lT~~G~~-l~~~a~~~l~~~~~~ 80 (299) -+.+|++||||+.||-|=+++ |+.+.=.-.-+.+..|+.--. ++.+.+.-+.+-..+ T Consensus 3 T~~vAk~LGVspkTVQRWvKq----~ni~~~rNE~GHy~Ft~e~l~~lLk~~~~q~~qg~~~ 60 (178) T PRK13182 3 TPFVAKKLGVSPKTVQRWVKQ----LNLPIERNEYGHYIFTEDDLDQLLKYHRSQIEQGQNM 60 (178) T ss_pred HHHHHHHHCCCHHHHHHHHHH----HCCCCCCCCCCCEEECHHHHHHHHHHHHHHHHCCCCC T ss_conf 178899939992999999999----5899553655443324989999999999986057545 No 251 >pfam04492 Phage_rep_O Bacteriophage replication protein O. Replication protein O is necessary for the initiation of bacteriophage DNA replication. Protein O interacts with the lambda replication origin, and also with replication protein P to form an oligomer. It is speculated that the N-terminal half interacts with the replication origin while the C terminal half mediates protein-protein interaction. Probab=35.27 E-value=32 Score=14.86 Aligned_cols=52 Identities=21% Similarity=0.276 Sum_probs=32.9 Q ss_pred CCHHHHHHHHHHHHH----------CCHHHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEECCCCE Q ss_conf 888999999999982----------7689999882899789999999999995882179769946 Q gi|254780282|r 3 FDWDKLRVFYVVARS----------GSFTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHARGL 57 (299) Q Consensus 3 md~~~L~~f~~v~~~----------gs~s~AA~~L~itq~avS~~i~~LE~~lg~~Lf~R~~~~~ 57 (299) |.-+++++|.+|++. =+-+.=|+.-+++...||+.+++|.++ .++.+.|+.+ T Consensus 30 lt~rq~kv~~aV~RkTyG~nK~~d~I~~sqi~~mtgi~~~~Vs~a~~~Li~~---~vi~~~G~~i 91 (100) T pfam04492 30 LSGRQLKVLLAVIRKTYGWNKPMDRVTNEQIAELTGLSRTHVSEAKKSLVKR---GIIIQDGRQI 91 (100) T ss_pred CCHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHC---CCCHHCCCEE T ss_conf 8788999999999986077850336229999999788854599999999976---8644149685 No 252 >PRK11337 DNA-binding transcriptional repressor RpiR; Provisional Probab=35.16 E-value=32 Score=14.85 Aligned_cols=28 Identities=21% Similarity=0.262 Sum_probs=24.2 Q ss_pred HHHHCCHHHHHHHHCCCHHHHHHHHHHH Q ss_conf 9982768999988289978999999999 Q gi|254780282|r 14 VARSGSFTHAAEQLHLSQSSISRQISGL 41 (299) Q Consensus 14 v~~~gs~s~AA~~L~itq~avS~~i~~L 41 (299) .+-.-|++.-|+..++|+++|.|-.++| T Consensus 44 ~v~~~si~eLA~~~~vS~aTVvRf~kkL 71 (293) T PRK11337 44 LSCATALKDVAEALAVSEAMIVKVAKLL 71 (293) T ss_pred HHHHCCHHHHHHHHCCCHHHHHHHHHHH T ss_conf 9976669999989599888999999995 No 253 >KOG2947 consensus Probab=35.15 E-value=32 Score=14.85 Aligned_cols=117 Identities=13% Similarity=0.095 Sum_probs=56.5 Q ss_pred CCCCCCCCCCCCCC--CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC-CCCCHHHHHHH Q ss_conf 22222222223456--5432111122345554332112344321112222221100011235664332-11000235665 Q gi|254780282|r 134 DISMDYADCAIRLR--KPIQSSSLIQRKLVTIHMHAYAAPHYLKNCREPLSIQELDKHNLITFGDLIP-KCMEDFNWLAT 210 (299) Q Consensus 134 ~l~~~~~Di~i~~~--~~~~~~~l~~~~l~~~~~~~v~~~~~~~~~~~~~~~~dL~~~~~i~~~~~~~-~~~~~~~~~~~ 210 (299) ++...++|+-=+.. ..++.+.+....=-....++.|.++++.-.-.--.--||..+.||.+....+ ........... T Consensus 76 d~~~rgIdishcp~td~~pp~ssiI~~r~~~trTiv~~dks~p~vT~~dF~kvdl~qy~WihfE~Rnp~etlkM~~~I~~ 155 (308) T KOG2947 76 DLRRRGIDISHCPFTDHSPPFSSIIINRNSGTRTILYCDKSLPDVTATDFEKVDLTQYGWIHFEARNPSETLKMLQRIDA 155 (308) T ss_pred HHHHCCCCCCCCCCCCCCCCCCEEEEECCCCCEEEEEECCCCCCCCHHHHHHCCCCEEEEEEEECCCHHHHHHHHHHHHH T ss_conf 79864877555766578998305888416883489993477852348777542600002699964790999999999998 Q ss_pred HCCCCCCCCCCEEEE---CCCCHHHHHHHHHCCEEEEEHHHHCC Q ss_conf 202234321211453---24200135678738423311777601 Q gi|254780282|r 211 VDRPIGEPRISCLQV---NSYLSIMQYCVLGSGIALLPDYIVKD 251 (299) Q Consensus 211 ~~~~~~~~~~~~~~~---~s~~~~~~~v~~g~Gia~lp~~~~~~ 251 (299) ++...+....+.+++ +..+....+..-+. +.++...+++. T Consensus 156 ~N~r~pe~qrI~vSvd~en~req~~~l~am~D-yVfvsK~~a~~ 198 (308) T KOG2947 156 HNTRQPEEQRIRVSVDVENPREQLFQLFAMCD-YVFVSKDVAKH 198 (308) T ss_pred HHCCCCCCCEEEEEEEECCCHHHHHHHHHHCC-EEEEEHHHHHH T ss_conf 62589830207999980681799998761134-89987898765 No 254 >pfam00376 MerR MerR family regulatory protein. Probab=35.11 E-value=29 Score=15.06 Aligned_cols=22 Identities=18% Similarity=0.172 Sum_probs=16.5 Q ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHH Q ss_conf 68999988289978999999999999 Q gi|254780282|r 19 SFTHAAEQLHLSQSSISRQISGLETE 44 (299) Q Consensus 19 s~s~AA~~L~itq~avS~~i~~LE~~ 44 (299) +++.+|+.++||..+| +..|++ T Consensus 1 ti~e~A~~~gvs~~tl----R~ye~~ 22 (38) T pfam00376 1 TIGEVAKLLGVSPRTL----RYYEKI 22 (38) T ss_pred CHHHHHHHHCCCHHHH----HHHHHC T ss_conf 9899999988799999----999986 No 255 >PHA01976 helix-turn-helix protein Probab=35.05 E-value=25 Score=15.50 Aligned_cols=34 Identities=15% Similarity=0.284 Sum_probs=21.8 Q ss_pred HHCCH--HHHHHHHCCCHHHHHH-----------HHHHHHHHHCCEE Q ss_conf 82768--9999882899789999-----------9999999958821 Q gi|254780282|r 16 RSGSF--THAAEQLHLSQSSISR-----------QISGLETEVGIKL 49 (299) Q Consensus 16 ~~gs~--s~AA~~L~itq~avS~-----------~i~~LE~~lg~~L 49 (299) +..++ ..-|+++|||+++||+ .+.+|-+-||+.+ T Consensus 12 ~~~g~sQ~eLA~~lGVs~~~is~wE~g~~~P~~d~L~~la~~~~VS~ 58 (67) T PHA01976 12 NARAWSAPELSRRAGVRHSLIYDFEADKRLPNLKTLLRLADALGVTL 58 (67) T ss_pred HHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCCH T ss_conf 98699999999994998999999987898999899999999979789 No 256 >PRK11302 DNA-binding transcriptional regulator HexR; Provisional Probab=34.84 E-value=32 Score=14.82 Aligned_cols=28 Identities=21% Similarity=0.262 Sum_probs=24.5 Q ss_pred HHHHCCHHHHHHHHCCCHHHHHHHHHHH Q ss_conf 9982768999988289978999999999 Q gi|254780282|r 14 VARSGSFTHAAEQLHLSQSSISRQISGL 41 (299) Q Consensus 14 v~~~gs~s~AA~~L~itq~avS~~i~~L 41 (299) -+-..|++.=|++.++|+|||+|-.++| T Consensus 31 ~v~~~si~eLA~~~~vS~aTV~Rf~kkL 58 (284) T PRK11302 31 TAIHSSIATLAKMANVSEPTVNRFCRSL 58 (284) T ss_pred HHHHCCHHHHHHHHCCCHHHHHHHHHHH T ss_conf 9976669999989699888999999995 No 257 >PRK13509 transcriptional repressor UlaR; Provisional Probab=34.65 E-value=33 Score=14.80 Aligned_cols=61 Identities=18% Similarity=0.226 Sum_probs=42.0 Q ss_pred CCCCHHHHHHHHHHHHHC--CHHHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEECCCCEEEEECCC Q ss_conf 988889999999999827--6899998828997899999999999958821797699468500134 Q gi|254780282|r 1 MSFDWDKLRVFYVVARSG--SFTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHARGLTLTEQGS 64 (299) Q Consensus 1 m~md~~~L~~f~~v~~~g--s~s~AA~~L~itq~avS~~i~~LE~~lg~~Lf~R~~~~~~lT~~G~ 64 (299) |.-+=|+=+.+..+-+.| ++...|+.++||..||-|=++.||++ -++.|..+|..+.+.+. T Consensus 1 M~~~eR~~~Il~~L~~~g~v~v~eLa~~~~VS~~TIRRDL~~Le~~---g~l~r~~GGA~~~~~~~ 63 (251) T PRK13509 1 MNEAQRHQILLDMLAQLGFVTVEKVIERLGISPATARRDINKLDES---GKLKKVRNGAEAITQQR 63 (251) T ss_pred CCHHHHHHHHHHHHHHCCCEEHHHHHHHHCCCHHHHHHHHHHHHHC---CCEEEEECCEEECCCCC T ss_conf 9889999999999998698989999999896998999839999878---97899988979777777 No 258 >COG2842 Uncharacterized ATPase, putative transposase [General function prediction only] Probab=34.24 E-value=33 Score=14.76 Aligned_cols=47 Identities=9% Similarity=0.087 Sum_probs=30.6 Q ss_pred CCCCHHHHHHHHHHHHHC--CHHHHHHHHCCCHHHHHHHHH-----------HHHHHHCC Q ss_conf 988889999999999827--689999882899789999999-----------99999588 Q gi|254780282|r 1 MSFDWDKLRVFYVVARSG--SFTHAAEQLHLSQSSISRQIS-----------GLETEVGI 47 (299) Q Consensus 1 m~md~~~L~~f~~v~~~g--s~s~AA~~L~itq~avS~~i~-----------~LE~~lg~ 47 (299) |+.|+...+-+...++.. +....|...++++|+||+.+. ++|..++. T Consensus 1 ~~~n~~~~k~~k~f~e~~~~~q~~~a~gi~~~~~~vsk~L~g~~g~~~~~~a~ia~~le~ 60 (297) T COG2842 1 KQINFIEIKKLKEFAEFSGMCQKYLARGIGTSAPALSKYLNGYKGDYATNEAKIAAFLEK 60 (297) T ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHCCCCCHHHHHHHHHHHHHCC T ss_conf 940389999999999861666999998736684457878437674177789999999727 No 259 >pfam00342 PGI Phosphoglucose isomerase. Phosphoglucose isomerase catalyses the interconversion of glucose-6-phosphate and fructose-6-phosphate. Probab=34.12 E-value=25 Score=15.51 Aligned_cols=111 Identities=12% Similarity=0.192 Sum_probs=63.0 Q ss_pred CCCHHHHHHHHHHHHHCCHHHHHHHHCC------C--HHHHHHHHHHHHHHHCCEEEEECCCCEEEEECCCCCCCCCCCC Q ss_conf 8888999999999982768999988289------9--7899999999999958821797699468500134332222222 Q gi|254780282|r 2 SFDWDKLRVFYVVARSGSFTHAAEQLHL------S--QSSISRQISGLETEVGIKLFYRHARGLTLTEQGSKLHRVTSEV 73 (299) Q Consensus 2 ~md~~~L~~f~~v~~~gs~s~AA~~L~i------t--q~avS~~i~~LE~~lg~~Lf~R~~~~~~lT~~G~~l~~~a~~~ 73 (299) .+|=+.|..|..++++-.+..+-+.|.- | +|+..-.++ .+.+-.....|+.+.+.+... T Consensus 6 ~i~~~~l~~l~~la~~~~l~~~~~~lf~G~~vN~tE~r~vlH~~lR-------------~~~~~~~~~~~~~~~~~v~~~ 72 (483) T pfam00342 6 HINDETLSALLKLAEEAGLDAKREAMFLGEKINTTENRAVLHVALR-------------NRSNRPIYVDGKDVMPEVDNV 72 (483) T ss_pred CCCHHHHHHHHHHHHHCCCHHHHHHHHCCCCCCCCCCCCCCCHHHH-------------CCCCCCCCCCCHHHHHHHHHH T ss_conf 5899999999999997885999999967998688999422679995-------------999898547850558999999 Q ss_pred CCCCCHHHHHCCCCC------CCCCCCCCCCCCC-CCCCCCCCCHHHHHHHHHHCCCCCCC Q ss_conf 222101221001223------2222223332111-00000000013566754200012222 Q gi|254780282|r 74 YHKLETTQIELQESS------VKPSGKLRIATTI-DLGQNLLQGNLKEFLLLYPDIQIQLI 127 (299) Q Consensus 74 l~~~~~~~~~~~~~~------~~~~g~i~I~~~~-~~~~~~l~~~l~~f~~~~P~i~i~i~ 127 (299) ++.+.++.+.++... ...+-.|.||..- .+++..+...|..+.... +++.+. T Consensus 73 ~~~~~~~~~~i~~g~~~g~~g~~~~~vV~IGIGGS~LGp~~~~~AL~~~~~~~--~~~~Fv 131 (483) T pfam00342 73 LDKMKDFFERIRSGAWKGYTGKAITDVVNIGIGGSDLGPRMVIEALKHYSENA--LIVFFV 131 (483) T ss_pred HHHHHHHHHHHHCCCEECCCCCCCCEEEEECCCCCCHHHHHHHHHHHHHCCCC--CEEEEE T ss_conf 99999999999729710678982343899565650076999999986533698--228995 No 260 >PRK10225 DNA-binding transcriptional repressor UxuR; Provisional Probab=33.60 E-value=34 Score=14.70 Aligned_cols=40 Identities=20% Similarity=0.349 Sum_probs=29.1 Q ss_pred HHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEECCCCEEEEEC Q ss_conf 999988289978999999999999588217976994685001 Q gi|254780282|r 21 THAAEQLHLSQSSISRQISGLETEVGIKLFYRHARGLTLTEQ 62 (299) Q Consensus 21 s~AA~~L~itq~avS~~i~~LE~~lg~~Lf~R~~~~~~lT~~ 62 (299) ..=|+.+|||.++|-..|+.||.+ |.- -.|.|+|...++. T Consensus 37 reLAe~lgVSRt~VREAL~~Le~~-GLV-~~r~G~Gt~V~~~ 76 (257) T PRK10225 37 REIAEMLDVTRTVVREALIMLEIK-GLV-EVRRGAGIYVLDS 76 (257) T ss_pred HHHHHHHCCCHHHHHHHHHHHHHC-CCE-EEEECCEEEEECC T ss_conf 999999798878999999999988-997-9964887788268 No 261 >smart00351 PAX Paired Box domain. Probab=33.31 E-value=32 Score=14.81 Aligned_cols=32 Identities=19% Similarity=0.257 Sum_probs=22.3 Q ss_pred HHHHHHHC-CHHHHHHHHCCCHHHHHHHHHHHH Q ss_conf 99999827-689999882899789999999999 Q gi|254780282|r 11 FYVVARSG-SFTHAAEQLHLSQSSISRQISGLE 42 (299) Q Consensus 11 f~~v~~~g-s~s~AA~~L~itq~avS~~i~~LE 42 (299) ++.++..| .-..=++.|.||+..|||-+.++. T Consensus 26 IveLa~~G~rpcdISr~L~VShGCVSKIL~Ry~ 58 (125) T smart00351 26 IVELAQNGVRPCDISRQLCVSHGCVSKILGRYY 58 (125) T ss_pred HHHHHHCCCCHHHHHHHHCCCCCHHHHHHHHHH T ss_conf 999998599899987564577106999999997 No 262 >PHA02519 plasmid partition protein SopA; Reviewed Probab=31.61 E-value=37 Score=14.50 Aligned_cols=64 Identities=14% Similarity=0.189 Sum_probs=34.1 Q ss_pred HHCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEECCCCEEE--EECCCCCCCCCCCCCCCCCHHHHHCCCCCCCCCC Q ss_conf 82768999988289978999999999999588217976994685--0013433222222222210122100122322222 Q gi|254780282|r 16 RSGSFTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHARGLTL--TEQGSKLHRVTSEVYHKLETTQIELQESSVKPSG 93 (299) Q Consensus 16 ~~gs~s~AA~~L~itq~avS~~i~~LE~~lg~~Lf~R~~~~~~l--T~~G~~l~~~a~~~l~~~~~~~~~~~~~~~~~~g 93 (299) +.=|.+.||+-++||++++-+. +.+ |++..| ++.|+.= .+..-.+++++.+...+......+.| T Consensus 38 R~Fs~~E~A~l~gvs~~~lR~~----~~~---------g~~P~p~~~~~gr~~-~rr~ytl~~i~~lR~~l~~~~~rp~~ 103 (387) T PHA02519 38 RRWGITEVADLIGVTPQAIRDA----EKS---------GRLPPPDFETRGRVE-RRAGYTIDQISHMRDHFGNPNQRPDD 103 (387) T ss_pred CCCCHHHHHHHHCCCHHHHHHH----HHC---------CCCCCCCCCCCCCCC-CCCCCCHHHHHHHHHHHCCCCCCCCC T ss_conf 7788899999959998999878----756---------899999768888755-33435799999999986456679898 No 263 >TIGR01928 menC_lowGC/arch o-succinylbenzoic acid (OSB) synthetase; InterPro: IPR010197 This entry describes the enzyme o-succinylbenzoic acid synthetase (menC) that is involved in one of the steps of the menaquinone biosynthesis pathway. It takes SHCHC and makes it into 2-succinylbenzoate. Also included are enzymes with the common name of N-acylamino acid racemase (or the more general term, racemase / racemase family), which refers to the enzyme's industrial application as racemases, and not to its biological function as o-succinylbenzoic acid synthetase . Members are restricted to the are low GC Gram-positive bacteria and archaea. . Probab=31.42 E-value=19 Score=16.10 Aligned_cols=91 Identities=16% Similarity=0.214 Sum_probs=53.5 Q ss_pred CCCCCHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCCCCCCCCC--CC---CCC-CCCCCCCCCC Q ss_conf 22210122100122322222233321110000000001356675420001222222222--22---222-2222223456 Q gi|254780282|r 74 YHKLETTQIELQESSVKPSGKLRIATTIDLGQNLLQGNLKEFLLLYPDIQIQLILDNKD--ID---ISM-DYADCAIRLR 147 (299) Q Consensus 74 l~~~~~~~~~~~~~~~~~~g~i~I~~~~~~~~~~l~~~l~~f~~~~P~i~i~i~~~~~~--~~---l~~-~~~Di~i~~~ 147 (299) +...+++..++.+.....-.+|.|-..|.. -..++...+.+||++.+.+-.+.+. .| |.. ++.++. ++. T Consensus 132 l~~~e~~lk~ie~~~~~g~~RIKlKi~Pq~----~~~L~~~~~~~FP~i~L~~DAN~sy~~~D~~~Lk~Ld~~~l~-~IE 206 (326) T TIGR01928 132 LAKLEEMLKEIESLKKEGYKRIKLKISPQI----EVDLVKKVRKRFPDIPLVVDANESYELKDIPRLKELDRYDLL-YIE 206 (326) T ss_pred CCCHHHHHHHHHHHHHCCCEEEEEEECCCC----CHHHHHHHHHHCCCCEEEEECCCCCCCCCCHHHHHHHHCCCE-EEE T ss_conf 476578999999998569807887516887----534767767637972389733778885656576554440620-332 Q ss_pred CCCCCCCCCCCC-CCCCCCCCCC Q ss_conf 543211112234-5554332112 Q gi|254780282|r 148 KPIQSSSLIQRK-LVTIHMHAYA 169 (299) Q Consensus 148 ~~~~~~~l~~~~-l~~~~~~~v~ 169 (299) .|.+..++.... |.+.-.-++| T Consensus 207 ~Pf~~dDl~~l~~l~~~~~tpic 229 (326) T TIGR01928 207 EPFKADDLSELKELKKELLTPIC 229 (326) T ss_pred CCCCCCHHHHHHHHHHCCCCCEE T ss_conf 78984226668777521788631 No 264 >TIGR03338 phnR_burk phosphonate utilization associated transcriptional regulator. This family of proteins are members of the GntR family (pfam00392) containing an N-terminal helix-turn-helix (HTH) motif. This clade is found adjacent to or inside of operons for the degradation of 2-aminoethylphosphonate (AEP) in Polaromonas, Burkholderia, Ralstonia and Verminephrobacter. Probab=31.24 E-value=37 Score=14.46 Aligned_cols=42 Identities=21% Similarity=0.325 Sum_probs=30.1 Q ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEECCCCEEEEEC Q ss_conf 68999988289978999999999999588217976994685001 Q gi|254780282|r 19 SFTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHARGLTLTEQ 62 (299) Q Consensus 19 s~s~AA~~L~itq~avS~~i~~LE~~lg~~Lf~R~~~~~~lT~~ 62 (299) +-..=|++++||.+.|-..++.||.+ |.- -.+.++|+..++. T Consensus 36 ~E~~La~~~gVSRtpvREAL~~L~~e-Glv-~~~~~~G~~V~~~ 77 (212) T TIGR03338 36 NESDIAARLGVSRGPVREAFRALEEA-GLV-RNEKNRGVFVREI 77 (212) T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHC-CCH-HEECCCCEEEECC T ss_conf 89999998896949999999999986-963-3116776155117 No 265 >pfam01090 Ribosomal_S19e Ribosomal protein S19e. Probab=31.21 E-value=34 Score=14.66 Aligned_cols=22 Identities=9% Similarity=-0.144 Sum_probs=17.4 Q ss_pred CCCCCCCHHHHHHHHHHHHHHH Q ss_conf 4877888899999999999985 Q gi|254780282|r 274 PEALKNTGKLKAFRNFIFLKAR 295 (299) Q Consensus 274 ~~~~~~~~~~~~f~d~l~~~~r 295 (299) ..++..+|.-+.++|-+..++- T Consensus 115 ~~GR~iT~~G~~~LD~iA~~v~ 136 (140) T pfam01090 115 KGGRRLTPQGRSDLDRIAAEVL 136 (140) T ss_pred CCCCEECHHHHHHHHHHHHHHH T ss_conf 9993789868999999999999 No 266 >TIGR02195 heptsyl_trn_II lipopolysaccharide heptosyltransferase II; InterPro: IPR011910 This family consists of examples of ADP-heptose:LPS heptosyltransferase II, an enzyme of LPS inner core region biosynthesis. LPS, composed of lipid A, a core region, and O antigen, is found in the outer membrane of Gram-negative bacteria.; GO: 0016757 transferase activity transferring glycosyl groups, 0009103 lipopolysaccharide biosynthetic process. Probab=31.15 E-value=21 Score=15.88 Aligned_cols=30 Identities=17% Similarity=0.263 Sum_probs=18.5 Q ss_pred CCCCCCCCCCC-HHHHHHHHHHCCCCCCCCC Q ss_conf 11000000000-1356675420001222222 Q gi|254780282|r 100 TIDLGQNLLQG-NLKEFLLLYPDIQIQLILD 129 (299) Q Consensus 100 ~~~~~~~~l~~-~l~~f~~~~P~i~i~i~~~ 129 (299) |..++..++.. +.+.+.++||++.|++.+. T Consensus 7 PsWVGDmvMaQ~Lf~~Lk~~yP~~~IDV~AP 37 (361) T TIGR02195 7 PSWVGDMVMAQSLFRLLKKRYPDAVIDVLAP 37 (361) T ss_pred CCCHHHHHHHHHHHHHHHHHCCCCEEEEECC T ss_conf 8736555676899999998589838972075 No 267 >PRK11557 putative DNA-binding transcriptional regulator; Provisional Probab=30.90 E-value=38 Score=14.43 Aligned_cols=28 Identities=32% Similarity=0.239 Sum_probs=24.7 Q ss_pred HHHHCCHHHHHHHHCCCHHHHHHHHHHH Q ss_conf 9982768999988289978999999999 Q gi|254780282|r 14 VARSGSFTHAAEQLHLSQSSISRQISGL 41 (299) Q Consensus 14 v~~~gs~s~AA~~L~itq~avS~~i~~L 41 (299) .+...|++.=|++.++|++||+|-.++| T Consensus 31 ~v~~~si~eLA~~~~vS~aTVvRf~kkL 58 (282) T PRK11557 31 TARHLSSQQLANEAGVSQSSVVKFAQKL 58 (282) T ss_pred HHHHCCHHHHHHHHCCCHHHHHHHHHHH T ss_conf 9976569999989699988999999993 No 268 >TIGR03431 PhnD phosphonate ABC transporter, periplasmic phosphonate binding protein. Note that this model does not identify all phnD-subfamily genes with evident phosphonate context, but all sequences above the trusted context may be inferred to bind phosphonate compounds even in the absence of such context. Furthermore, there is ample evidence to suggest that many other members of the TIGR01098 subfamily have a different primary function. Probab=28.90 E-value=41 Score=14.23 Aligned_cols=191 Identities=9% Similarity=-0.037 Sum_probs=86.7 Q ss_pred CCCCCCCCCCCCCCCCCCHH---HHHHHHHHCCCCCCCCCCC----CCCCCCCCCCCCCCCCCCCC--CCCCCCCCCCC- Q ss_conf 22333211100000000013---5667542000122222222----22222222222234565432--11112234555- Q gi|254780282|r 93 GKLRIATTIDLGQNLLQGNL---KEFLLLYPDIQIQLILDNK----DIDISMDYADCAIRLRKPIQ--SSSLIQRKLVT- 162 (299) Q Consensus 93 g~i~I~~~~~~~~~~l~~~l---~~f~~~~P~i~i~i~~~~~----~~~l~~~~~Di~i~~~~~~~--~~~l~~~~l~~- 162 (299) -++++|+.|.....-+-... .++..+.=+..|++..... ...+..|++|+++....... ......+++.. T Consensus 27 ~~l~~gv~P~~~~~~~~~~~~Pl~~yL~~~lg~~Ve~~~~~~y~~~~eal~~g~~Dia~~~p~~yv~a~~~~~~~~la~~ 106 (288) T TIGR03431 27 KELNFGIIPTENASDLKQRWEPLADYLSKKLGVKVKLFFATDYAGVIEGMRFGKVDIAWYGPSSYAEAYQKANAEAFAIE 106 (288) T ss_pred CEEEEEEECCCCHHHHHHHHHHHHHHHHHHHCCCEEEEECCCHHHHHHHHHCCCCEEEEECCHHHHHHHHCCCCEEEEEE T ss_conf 36899980699999999999999999999878978999689999999999859830999884788998652597488998 Q ss_pred --------CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHH--HH-HHHCCCCCCCCCCEEEECCCCHH Q ss_conf --------43321123443211122222211000112356643321100023--56-65202234321211453242001 Q gi|254780282|r 163 --------IHMHAYAAPHYLKNCREPLSIQELDKHNLITFGDLIPKCMEDFN--WL-ATVDRPIGEPRISCLQVNSYLSI 231 (299) Q Consensus 163 --------~~~~~v~~~~~~~~~~~~~~~~dL~~~~~i~~~~~~~~~~~~~~--~~-~~~~~~~~~~~~~~~~~~s~~~~ 231 (299) ..-++++.++ ....+++||.+..+..-+.. +.+..... .+ ...+............+.+.+.. T Consensus 107 ~~~~g~~~y~s~iivr~D-----s~i~sl~DLkGk~iaf~~~~-StSG~l~P~~~L~~~~g~~~~~~f~~v~~~gshd~~ 180 (288) T TIGR03431 107 VNADGSTGYYSVLIVKKD-----SPIKSLEDLKGKTFGFVDPN-STSGFLVPSYYLFKKNGIKPKEYFKKVTFSGSHEAA 180 (288) T ss_pred ECCCCCCCEEEEEEEECC-----CCCCCHHHHCCCEEEECCCC-CCHHHHHHHHHHHHHCCCCHHHHHHHEEECCCHHHH T ss_conf 515888645799999899-----98887789579876602874-111139999999986599725455313315787899 Q ss_pred HHHHHHHCC-EEEEEHHHHC----C-CCC---EEEECCCCCCCCCEEEEEECCCCCCCHH-HHHHHHHHHH Q ss_conf 356787384-2331177760----1-998---4661776667660089993487788889-9999999999 Q gi|254780282|r 232 MQYCVLGSG-IALLPDYIVK----D-NPN---LVRIMEDVITPSFTVYFCYPEALKNTGK-LKAFRNFIFL 292 (299) Q Consensus 232 ~~~v~~g~G-ia~lp~~~~~----~-~~~---lv~i~~~~~~~~~~~~lv~~~~~~~~~~-~~~f~d~l~~ 292 (299) +..|..|.. +|.+.....+ . .++ -+++.-..+..+...+++ +++ .++. .+.+.+.|++ T Consensus 181 ~~aV~~G~~Dag~~~~~~~~~~~~~~~~~~~~~lrvi~~S~~iP~~~~~v-~~~--l~~~~~~~i~~all~ 248 (288) T TIGR03431 181 ILAVANGTVDAATTNDENLDRMIRKGQPDAMEDLRIIWKSPLIPNGPIVY-RKD--LPADLKAKIRKAFLN 248 (288) T ss_pred HHHHHCCCCCEEEECHHHHHHHHHCCCCCHHHCEEEEEECCCCCCCCEEE-ECC--CCHHHHHHHHHHHHH T ss_conf 99998599329983388899999747963031369998678888771899-699--999999999999980 No 269 >COG2188 PhnF Transcriptional regulators [Transcription] Probab=28.83 E-value=41 Score=14.22 Aligned_cols=42 Identities=21% Similarity=0.278 Sum_probs=30.8 Q ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEECCCCEEEEEC Q ss_conf 68999988289978999999999999588217976994685001 Q gi|254780282|r 19 SFTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHARGLTLTEQ 62 (299) Q Consensus 19 s~s~AA~~L~itq~avS~~i~~LE~~lg~~Lf~R~~~~~~lT~~ 62 (299) |=..=|+.++||.-||-++|+.|+++ --|..+.|+|.-..+. T Consensus 33 sE~eLa~~f~VSR~TvRkAL~~L~~e--Gli~r~~G~GtfV~~~ 74 (236) T COG2188 33 SERELAEQFGVSRMTVRKALDELVEE--GLIVRRQGKGTFVASP 74 (236) T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHC--CCEEEEECCEEEECCC T ss_conf 98999999798899999999999989--9889951667898877 No 270 >PRK10079 putative transcriptional regulator; Provisional Probab=27.76 E-value=43 Score=14.11 Aligned_cols=40 Identities=15% Similarity=0.197 Sum_probs=30.5 Q ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEECCCCEEEE Q ss_conf 689999882899789999999999995882179769946850 Q gi|254780282|r 19 SFTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHARGLTLT 60 (299) Q Consensus 19 s~s~AA~~L~itq~avS~~i~~LE~~lg~~Lf~R~~~~~~lT 60 (299) |=..=|+..+||..||-++|+.|+++ --|..+.|+|.-.+ T Consensus 37 sE~eLa~~y~VSR~TVR~Al~~L~~e--Gli~r~~G~GtfV~ 76 (241) T PRK10079 37 AEQQLAARFEVNRHTLRRAIDQLVER--GWVQRRQGVGVLVL 76 (241) T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHC--CCEEEECCCCEEEE T ss_conf 99999999798899999999999977--98799769625993 No 271 >COG0761 lytB 4-Hydroxy-3-methylbut-2-enyl diphosphate reductase IspH [Lipid metabolism] Probab=27.66 E-value=12 Score=17.39 Aligned_cols=21 Identities=29% Similarity=0.515 Sum_probs=11.6 Q ss_pred HHHHHH---HHHHHHCCEEEEECC Q ss_conf 999999---999995882179769 Q gi|254780282|r 34 ISRQIS---GLETEVGIKLFYRHA 54 (299) Q Consensus 34 vS~~i~---~LE~~lg~~Lf~R~~ 54 (299) |-++|+ +.-+++|.+..+|.. T Consensus 16 V~RAI~ive~al~~~g~pIyv~~e 39 (294) T COG0761 16 VDRAIQIVERALEEYGAPIYVRHE 39 (294) T ss_pred HHHHHHHHHHHHHHCCCCEEEEEC T ss_conf 899999999999971998589700 No 272 >PRK10421 DNA-binding transcriptional repressor LldR; Provisional Probab=27.42 E-value=43 Score=14.07 Aligned_cols=39 Identities=28% Similarity=0.402 Sum_probs=28.7 Q ss_pred HHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEECCCCEEEEE Q ss_conf 99998828997899999999999958821797699468500 Q gi|254780282|r 21 THAAEQLHLSQSSISRQISGLETEVGIKLFYRHARGLTLTE 61 (299) Q Consensus 21 s~AA~~L~itq~avS~~i~~LE~~lg~~Lf~R~~~~~~lT~ 61 (299) ..=|+.++||.++|-..|+.||.+ |. +-.|.|+|...+. T Consensus 30 ~eLae~~GVSRt~VREAL~~L~~e-Gl-V~~~~g~G~~V~~ 68 (253) T PRK10421 30 RQLAMQLGVSRNSLREALAKLVSE-GV-LLSRRGGGTFIRW 68 (253) T ss_pred HHHHHHHCCCHHHHHHHHHHHHHC-CC-EEEEECCEEEECC T ss_conf 999999796989999999999988-98-7997578248734 No 273 >pfam06322 Phage_NinH Phage NinH protein. This family consists of several phage NinH proteins. The function of this family is unknown. Probab=27.40 E-value=43 Score=14.07 Aligned_cols=32 Identities=19% Similarity=0.259 Sum_probs=26.3 Q ss_pred HHHHCCHHHHHHHHCCCHHHHHHHHHHHHHHH Q ss_conf 99827689999882899789999999999995 Q gi|254780282|r 14 VARSGSFTHAAEQLHLSQSSISRQISGLETEV 45 (299) Q Consensus 14 v~~~gs~s~AA~~L~itq~avS~~i~~LE~~l 45 (299) +--.||.+..|+.|+.+..+|-+-....|.+. T Consensus 13 i~~~GN~teVaR~L~c~R~TVrkY~~D~~~k~ 44 (64) T pfam06322 13 IETYGNQTEVARRLNCSRNTVRKYAEDKEGKG 44 (64) T ss_pred HHHHCCHHHHHHHHCCHHHHHHHHHCCCCCCE T ss_conf 99707799997885110888998723555623 No 274 >COG2826 Tra8 Transposase and inactivated derivatives, IS30 family [DNA replication, recombination, and repair] Probab=26.64 E-value=42 Score=14.17 Aligned_cols=26 Identities=31% Similarity=0.344 Sum_probs=23.3 Q ss_pred HHHCCHHHHHHHHCCCHHHHHHHHHH Q ss_conf 98276899998828997899999999 Q gi|254780282|r 15 ARSGSFTHAAEQLHLSQSSISRQISG 40 (299) Q Consensus 15 ~~~gs~s~AA~~L~itq~avS~~i~~ 40 (299) .+--|+..=|+.||..+||||+-|++ T Consensus 21 ~~~~S~reIA~~LgRh~sTIsRElkR 46 (318) T COG2826 21 KAKMSIREIAKQLNRHHSTISRELKR 46 (318) T ss_pred HCCCCHHHHHHHHCCCCCHHHHHHHC T ss_conf 85998999999857686204279866 No 275 >PRK11014 transcriptional repressor NsrR; Provisional Probab=26.63 E-value=45 Score=13.99 Aligned_cols=69 Identities=25% Similarity=0.359 Sum_probs=48.3 Q ss_pred HHHHHHHHHHH--C---CHHHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEECC-CCEEEEECCCCCCCCCCCCCCCCC Q ss_conf 99999999982--7---689999882899789999999999995882179769-946850013433222222222210 Q gi|254780282|r 7 KLRVFYVVARS--G---SFTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHA-RGLTLTEQGSKLHRVTSEVYHKLE 78 (299) Q Consensus 7 ~L~~f~~v~~~--g---s~s~AA~~L~itq~avS~~i~~LE~~lg~~Lf~R~~-~~~~lT~~G~~l~~~a~~~l~~~~ 78 (299) -|+.+..+++. | ++..-|++.+|+++.+.|-+++|.+. |.--=.|+. +|+.|+...+.+- ..++++.++ T Consensus 10 AlraL~~LA~~~~~~~~~~~eIae~~~Ip~~~L~KIl~~L~~a-Glv~S~RG~~GGy~Lar~p~~It--l~dVi~aiE 84 (141) T PRK11014 10 GLRALIYMASLPEGRMTSISEVTEVYGVSRNHMVKIINQLSRA-GYVTAVRGKNGGIRLGKPASTIR--IGDVVRELE 84 (141) T ss_pred HHHHHHHHHHCCCCCEECHHHHHHHHCCCHHHHHHHHHHHHHC-CCEEECCCCCCCEECCCCHHHCC--HHHHHHHHC T ss_conf 9999999983999984749999998794999999999999887-95672047998832148988797--999999946 No 276 >PRK09706 transcriptional repressor DicA; Reviewed Probab=26.38 E-value=45 Score=13.96 Aligned_cols=19 Identities=32% Similarity=0.223 Sum_probs=11.0 Q ss_pred CHHHHHHHHCCCHHHHHHH Q ss_conf 6899998828997899999 Q gi|254780282|r 19 SFTHAAEQLHLSQSSISRQ 37 (299) Q Consensus 19 s~s~AA~~L~itq~avS~~ 37 (299) |-+.-|+.+|||+++||+= T Consensus 20 TQ~eLA~~~Gvs~~tVs~w 38 (135) T PRK09706 20 SQRALAKAVGVSHVSISQW 38 (135) T ss_pred CHHHHHHHHCCCHHHHHHH T ss_conf 9999999969889999999 No 277 >cd00093 HTH_XRE Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators. Probab=26.26 E-value=46 Score=13.95 Aligned_cols=23 Identities=35% Similarity=0.299 Sum_probs=18.8 Q ss_pred HCCHHHHHHHHCCCHHHHHHHHH Q ss_conf 27689999882899789999999 Q gi|254780282|r 17 SGSFTHAAEQLHLSQSSISRQIS 39 (299) Q Consensus 17 ~gs~s~AA~~L~itq~avS~~i~ 39 (299) ..|...-|+.+|+|++++|+-.+ T Consensus 12 ~ls~~~lA~~~gis~~~l~~~e~ 34 (58) T cd00093 12 GLTQEELAEKLGVSRSTISRIEN 34 (58) T ss_pred CCCHHHHHHHCCCCHHHHHHHHC T ss_conf 99999995714999999999987 No 278 >cd00131 PAX Paired Box domain Probab=25.88 E-value=46 Score=13.91 Aligned_cols=32 Identities=22% Similarity=0.279 Sum_probs=18.6 Q ss_pred HHHHHHHCC-HHHHHHHHCCCHHHHHHHHHHHH Q ss_conf 999998276-89999882899789999999999 Q gi|254780282|r 11 FYVVARSGS-FTHAAEQLHLSQSSISRQISGLE 42 (299) Q Consensus 11 f~~v~~~gs-~s~AA~~L~itq~avS~~i~~LE 42 (299) ++.++..|. -..=++.|.||+..|||-+.+.. T Consensus 26 IVeLa~~G~RpcdISR~L~VShGCVSKIL~Ry~ 58 (128) T cd00131 26 IVELAQSGIRPCDISRQLRVSHGCVSKILNRYY 58 (128) T ss_pred HHHHHHCCCCHHHHHHHHCCCCHHHHHHHHHHH T ss_conf 999998599788888763777216899999887 No 279 >TIGR03453 partition_RepA plasmid partitioning protein RepA. Members of this family are the RepA (or ParA) protein involved in replicon partitioning. All known examples occur in bacterial species with two or more replicons, on a plasmid or the smaller chromosome. Note that an apparent exception may be seen as a pseudomolecule from assembly of an incompletely sequenced genome. Members of this family belong to a larger family that also includes the enzyme cobyrinic acid a,c-diamide synthase, but assignment of that name to members of this family would be in error. Probab=25.66 E-value=47 Score=13.88 Aligned_cols=23 Identities=22% Similarity=0.140 Sum_probs=17.3 Q ss_pred HHCCHHHHHHHHCCCHHHHHHHH Q ss_conf 82768999988289978999999 Q gi|254780282|r 16 RSGSFTHAAEQLHLSQSSISRQI 38 (299) Q Consensus 16 ~~gs~s~AA~~L~itq~avS~~i 38 (299) +.=|.+.||+-|+|+++++.+.- T Consensus 32 r~f~~~e~a~l~gv~~~~lr~~~ 54 (387) T TIGR03453 32 RRFTSGEAAKLLGVTDSYLRQLS 54 (387) T ss_pred CCCCHHHHHHHHCCCHHHHHHHH T ss_conf 88888999988496999999998 No 280 >PRK11523 DNA-binding transcriptional repressor ExuR; Provisional Probab=25.58 E-value=47 Score=13.87 Aligned_cols=41 Identities=22% Similarity=0.301 Sum_probs=29.8 Q ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEECCCCEEEEE Q ss_conf 6899998828997899999999999958821797699468500 Q gi|254780282|r 19 SFTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHARGLTLTE 61 (299) Q Consensus 19 s~s~AA~~L~itq~avS~~i~~LE~~lg~~Lf~R~~~~~~lT~ 61 (299) |=..=|+.++||.++|-..|+.||.. |.- -.|.|+|...+. T Consensus 34 sEreLAe~fGVSRt~VREAL~~Le~~-GlV-e~r~G~Gt~V~~ 74 (258) T PRK11523 34 AERFIADEKNVSRTVVREAIIMLEVE-GYV-EVRKGSGIHVVS 74 (258) T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHC-CCE-EEEECCEEEECC T ss_conf 69999999798879999999999988-998-996378158745 No 281 >PRK09990 DNA-binding transcriptional regulator GlcC; Provisional Probab=25.13 E-value=48 Score=13.82 Aligned_cols=43 Identities=23% Similarity=0.290 Sum_probs=30.5 Q ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEECCCCEEEEECC Q ss_conf 689999882899789999999999995882179769946850013 Q gi|254780282|r 19 SFTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHARGLTLTEQG 63 (299) Q Consensus 19 s~s~AA~~L~itq~avS~~i~~LE~~lg~~Lf~R~~~~~~lT~~G 63 (299) +-..-|+.+|||.++|-..++.||.+ |. +-.|.|+|...++.. T Consensus 33 ~E~eLae~~gVSR~~VREAL~~L~~~-Gl-V~~~~g~G~~V~~~~ 75 (251) T PRK09990 33 SERRLTEKLGVSRSALREGLKVLRGR-GI-IETAQGRGSFVARLN 75 (251) T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHC-CC-EEEECCCCCEEECCC T ss_conf 39999999897959999999999988-99-798579850671587 No 282 >COG3432 Predicted transcriptional regulator [Transcription] Probab=25.12 E-value=22 Score=15.81 Aligned_cols=53 Identities=25% Similarity=0.334 Sum_probs=31.5 Q ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEECCCC----EEEEECCCCCCCCCCCCC Q ss_conf 68999988289978999999999999588217976994----685001343322222222 Q gi|254780282|r 19 SFTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHARG----LTLTEQGSKLHRVTSEVY 74 (299) Q Consensus 19 s~s~AA~~L~itq~avS~~i~~LE~~lg~~Lf~R~~~~----~~lT~~G~~l~~~a~~~l 74 (299) .+|+=.-..|++-....+-|..|++. | |+.+...| +.+|+.|+.|++....+- T Consensus 33 ~~Tri~y~aNlny~~~~~yi~~L~~~-G--li~~~~~~~~~~y~lT~KG~~fle~y~~i~ 89 (95) T COG3432 33 GITRIIYGANLNYKRAQKYIEMLVEK-G--LIIKQDNGRRKVYELTEKGKRFLEKYSEIR 89 (95) T ss_pred CCEEEEEECCCCHHHHHHHHHHHHHC-C--CEEECCCCCCCEEEECHHHHHHHHHHHHHH T ss_conf 86246643276779999999999867-8--778614886445898856899999999999 No 283 >cd04765 HTH_MlrA-like_sg2 Helix-Turn-Helix DNA binding domain of putative MlrA-like transcription regulators. Putative helix-turn-helix (HTH) MlrA-like transcription regulators (subgroup 2), N-terminal domain. The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Probab=25.04 E-value=48 Score=13.81 Aligned_cols=35 Identities=29% Similarity=0.159 Sum_probs=26.3 Q ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEECCCCE Q ss_conf 689999882899789999999999995882179769946 Q gi|254780282|r 19 SFTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHARGL 57 (299) Q Consensus 19 s~s~AA~~L~itq~avS~~i~~LE~~lg~~Lf~R~~~~~ 57 (299) |++.+|+.+++++++ |+--|+++|..--.|+.+|. T Consensus 2 sIgEva~~~gv~~~t----LRywE~~~~~~~P~r~~~g~ 36 (99) T cd04765 2 SIGEVAEILGLPPHV----LRYWETEFPQLKPVKRAGGR 36 (99) T ss_pred CHHHHHHHHCCCHHH----HHHHHHHCCCCCCCCCCCCC T ss_conf 788999998949999----99999874774887589988 No 284 >COG4465 CodY Pleiotropic transcriptional repressor [Transcription] Probab=24.79 E-value=49 Score=13.79 Aligned_cols=17 Identities=18% Similarity=0.280 Sum_probs=9.2 Q ss_pred HHHHHHCCEEEEECCCC Q ss_conf 99999588217976994 Q gi|254780282|r 40 GLETEVGIKLFYRHARG 56 (299) Q Consensus 40 ~LE~~lg~~Lf~R~~~~ 56 (299) .|-+-+.+..|+=+++| T Consensus 34 ~ladVi~~N~~iis~kG 50 (261) T COG4465 34 TLADVIECNAFIISRKG 50 (261) T ss_pred HHHHHHHCCEEEEECCC T ss_conf 99877603259992797 No 285 >pfam08535 KorB KorB domain. This family consists of several KorB transcriptional repressor proteins. The korB gene is a major regulatory element in the replication and maintenance of broad host-range plasmid RK2. It negatively controls the replication gene trfA, the host-lethal determinants kilA and kilB, and the korA-korB operon. This domain includes the DNA-binding HTH motif. Probab=24.39 E-value=50 Score=13.74 Aligned_cols=20 Identities=25% Similarity=0.275 Sum_probs=13.4 Q ss_pred HHHHHHHCCCHHHHHHHHHH Q ss_conf 99998828997899999999 Q gi|254780282|r 21 THAAEQLHLSQSSISRQISG 40 (299) Q Consensus 21 s~AA~~L~itq~avS~~i~~ 40 (299) +.=|++||.+.+-||++++- T Consensus 7 ~~IAk~LGks~s~VS~hlaL 26 (93) T pfam08535 7 AEIAKKLGKSKSFVSQHLAL 26 (93) T ss_pred HHHHHHHCCCHHHHHHHHHH T ss_conf 99999978898899999998 No 286 >PRK01066 porphobilinogen deaminase; Provisional Probab=24.30 E-value=30 Score=15.02 Aligned_cols=54 Identities=20% Similarity=0.186 Sum_probs=31.5 Q ss_pred CCCCCCCCCCCCCCCCCCC-HHHHHHHHHHCCCCCCC----CCCCC-------------------CCCCCCCCCCCCC Q ss_conf 2223332111000000000-13566754200012222----22222-------------------2222222222234 Q gi|254780282|r 92 SGKLRIATTIDLGQNLLQG-NLKEFLLLYPDIQIQLI----LDNKD-------------------IDISMDYADCAIR 145 (299) Q Consensus 92 ~g~i~I~~~~~~~~~~l~~-~l~~f~~~~P~i~i~i~----~~~~~-------------------~~l~~~~~Di~i~ 145 (299) +..|+||.=.|-.+.+-.. +...+.+.||++++++. .+|.. ..|..|++|+++- T Consensus 18 kk~IrIGTR~S~LAl~Qa~~V~~~L~~~~p~~~~ei~~i~T~GD~~~~~~L~~iggkG~Ftkele~aLl~g~iDiAVH 95 (234) T PRK01066 18 KRPLRIASRKSPLAKAQVHECLRLLRSFFPKLWFQISTTTTQGDLDQKTPLHLVENTGFFTDDVDFLVLSGKCDLAIH 95 (234) T ss_pred CCCEEEEECCCHHHHHHHHHHHHHHHHHCCCCEEEEEEEECCCCCCCCCCHHHCCCCCEEHHHHHHHHHCCCCCEEEE T ss_conf 884699958879999999999999997689973999999633731457768774897454899999997698778987 No 287 >cd04764 HTH_MlrA-like_sg1 Helix-Turn-Helix DNA binding domain of putative MlrA-like transcription regulators. Putative helix-turn-helix (HTH) MlrA-like transcription regulators (subgroup 1). The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA-like proteins in this group appear to lack the long dimerization helix seen in the N-terminal domains of typical MerR-like proteins. Probab=23.90 E-value=51 Score=13.69 Aligned_cols=34 Identities=15% Similarity=0.241 Sum_probs=22.5 Q ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEECCCCE Q ss_conf 689999882899789999999999995882179769946 Q gi|254780282|r 19 SFTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHARGL 57 (299) Q Consensus 19 s~s~AA~~L~itq~avS~~i~~LE~~lg~~Lf~R~~~~~ 57 (299) +++.+|+.+|||..+ |+--|++++.. ..|+.+|. T Consensus 2 tI~eva~~~Gv~~~t----LRyyEk~~~l~-~~R~~~G~ 35 (67) T cd04764 2 TIKEVSEIIGVKPHT----LRYYEKEFNLY-IPRTENGR 35 (67) T ss_pred CHHHHHHHHCCCHHH----HHHHHHCCCCC-CCCCCCCC T ss_conf 789999998868789----99998737999-99699989 No 288 >PRK13507 formate--tetrahydrofolate ligase; Provisional Probab=23.69 E-value=51 Score=13.66 Aligned_cols=63 Identities=22% Similarity=0.211 Sum_probs=39.9 Q ss_pred CCCC---HHHHHHHHHHHH-HCCHHHHHHHHCCCHHHHH------------HHHHHHHHHHCCEEEEECCCCEEEEECCC Q ss_conf 9888---899999999998-2768999988289978999------------99999999958821797699468500134 Q gi|254780282|r 1 MSFD---WDKLRVFYVVAR-SGSFTHAAEQLHLSQSSIS------------RQISGLETEVGIKLFYRHARGLTLTEQGS 64 (299) Q Consensus 1 m~md---~~~L~~f~~v~~-~gs~s~AA~~L~itq~avS------------~~i~~LE~~lg~~Lf~R~~~~~~lT~~G~ 64 (299) |+|+ +.+++.-.+.-. ...++.-|++|++++..+. .-++++++.=.-+|+.=+ ++.|||+|+ T Consensus 1 ~~~~~~~~sDieIaq~a~~~l~pI~~iA~~lgl~~~~le~YG~~kAKi~~~~~~~~~~~~~~gklILVT--aitPTP~GE 78 (587) T PRK13507 1 MALDPVLMKDWEIAEEAEKFMKSPKQLAEELGLTKEEIIPYGRYIAKVDFAKILSRLKDRPDGKYIDVT--AITPTPLGE 78 (587) T ss_pred CCCCCCCCCHHHHHHHCHHCCCCHHHHHHHCCCCHHHHHHCCCCCEEECHHHHHHHHCCCCCCEEEEEE--ECCCCCCCC T ss_conf 997843347999998543137899999988398979976247754660588988874048996399998--468888889 Q ss_pred C Q ss_conf 3 Q gi|254780282|r 65 K 65 (299) Q Consensus 65 ~ 65 (299) = T Consensus 79 G 79 (587) T PRK13507 79 G 79 (587) T ss_pred C T ss_conf 8 No 289 >PRK03537 hypothetical protein; Provisional Probab=23.40 E-value=52 Score=13.63 Aligned_cols=53 Identities=9% Similarity=0.130 Sum_probs=29.8 Q ss_pred CCEEEEEHHHHC-C-CCC--EEEECCCCCCCCCEEEEEECCCCCCCHHHHHHHHHHHHHH Q ss_conf 842331177760-1-998--4661776667660089993487788889999999999998 Q gi|254780282|r 239 SGIALLPDYIVK-D-NPN--LVRIMEDVITPSFTVYFCYPEALKNTGKLKAFRNFIFLKA 294 (299) Q Consensus 239 ~Gia~lp~~~~~-~-~~~--lv~i~~~~~~~~~~~~lv~~~~~~~~~~~~~f~d~l~~~~ 294 (299) .|++...+.... . ..+ .+.+ |+.......|.+...++. ++.+++|++||++.. T Consensus 116 a~ivY~TdA~~a~~~~~~l~~v~i-P~~~~~~~~Y~iav~~~a--~~~A~~f~~flls~~ 172 (188) T PRK03537 116 IFIGYCTSAALALKEVPDLQIVDL-PEPLAVGANYGLAVLKDA--SEAARPLAEFILSPK 172 (188) T ss_pred EEEEEECCHHHHHHCCCCCEEEEC-CCCCCCCCCEEEEECCCC--CHHHHHHHHHHCCHH T ss_conf 799985147878515898549958-800066632357873688--099999999973999 No 290 >pfam08280 HTH_Mga M protein trans-acting positive regulator (MGA) HTH domain. Mga is a DNA-binding protein that activates the expression of several important virulence genes in group A streptococcus in response to changing environmental conditions. Probab=23.35 E-value=52 Score=13.62 Aligned_cols=52 Identities=21% Similarity=0.243 Sum_probs=40.3 Q ss_pred HHHHHHHHHHHHHC--CHHHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEECCCC Q ss_conf 89999999999827--68999988289978999999999999588217976994 Q gi|254780282|r 5 WDKLRVFYVVARSG--SFTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHARG 56 (299) Q Consensus 5 ~~~L~~f~~v~~~g--s~s~AA~~L~itq~avS~~i~~LE~~lg~~Lf~R~~~~ 56 (299) +++++....+.+.+ ++...|+.||.|.-++-.-|.+|-+.|+..++.-..++ T Consensus 5 ~rk~~Ll~lL~~~~~~~l~el~~~l~ls~~tl~~~i~~L~~~f~~~l~i~~~k~ 58 (59) T pfam08280 5 KRKLKLLELLTENKSITLDELAKQLGLSELTLKSYIHELNELFPDELSIVIKKG 58 (59) T ss_pred HHHHHHHHHHHCCCCEEHHHHHHHCCCCHHHHHHHHHHHHHHCCCCEEEEEECC T ss_conf 899999999980883649999988099799999999999987376469984058 No 291 >PTZ00095 40S ribosomal protein S19; Provisional Probab=23.34 E-value=52 Score=13.62 Aligned_cols=22 Identities=18% Similarity=-0.037 Sum_probs=18.1 Q ss_pred CCCCCCHHHHHHHHHHHHHHHC Q ss_conf 8778888999999999999850 Q gi|254780282|r 275 EALKNTGKLKAFRNFIFLKARD 296 (299) Q Consensus 275 ~~~~~~~~~~~f~d~l~~~~r~ 296 (299) +++..++.-+.++|-+..|+.. T Consensus 142 ~GR~iT~~G~~~LD~iA~qI~~ 163 (169) T PTZ00095 142 SGRRLTRKGCNFANAFARQVTI 163 (169) T ss_pred CCCEECHHHHHHHHHHHHHHHH T ss_conf 9888787478999999999998 No 292 >PRK13982 bifunctional SbtC-like/phosphopantothenoylcysteine decarboxylase/phosphopantothenate synthase; Provisional Probab=23.12 E-value=4.2 Score=19.94 Aligned_cols=30 Identities=0% Similarity=-0.003 Sum_probs=14.5 Q ss_pred CCCCCCCCCCCCCCCCCHHHHHHHHHHCCC Q ss_conf 233321110000000001356675420001 Q gi|254780282|r 94 KLRIATTIDLGQNLLQGNLKEFLLLYPDIQ 123 (299) Q Consensus 94 ~i~I~~~~~~~~~~l~~~l~~f~~~~P~i~ 123 (299) +|-+|++-+++.+--+.+++.+++.--+|+ T Consensus 73 kIlLgVtGsIAAYKa~~LvR~L~k~Ga~V~ 102 (476) T PRK13982 73 RITLIIGGGIAAYKALDLIRRLKERGAEVR 102 (476) T ss_pred EEEEEECCHHHHHHHHHHHHHHHHCCCEEE T ss_conf 799996748999999999999997899899 No 293 >PRK07379 coproporphyrinogen III oxidase; Provisional Probab=23.12 E-value=52 Score=13.59 Aligned_cols=18 Identities=11% Similarity=0.174 Sum_probs=9.7 Q ss_pred CCCCCCCHHH-HHHHHHHH Q ss_conf 4877888899-99999999 Q gi|254780282|r 274 PEALKNTGKL-KAFRNFIF 291 (299) Q Consensus 274 ~~~~~~~~~~-~~f~d~l~ 291 (299) +++...+-.+ ..|+|++- T Consensus 378 p~G~l~~n~I~~~l~d~~~ 396 (399) T PRK07379 378 PEGFLFSNTVLASLFEALE 396 (399) T ss_pred CCCEEEHHHHHHHHHHHHH T ss_conf 7835429899999999875 No 294 >PRK12520 RNA polymerase sigma factor; Provisional Probab=23.11 E-value=53 Score=13.59 Aligned_cols=22 Identities=9% Similarity=-0.049 Sum_probs=11.1 Q ss_pred CCCCCCCCCCCCCCCHHHHHCC Q ss_conf 4332222222222101221001 Q gi|254780282|r 64 SKLHRVTSEVYHKLETTQIELQ 85 (299) Q Consensus 64 ~~l~~~a~~~l~~~~~~~~~~~ 85 (299) ..|+.+|..++..-+.++.-++ T Consensus 13 ~~L~r~A~~~v~d~~~AEDvvQ 34 (191) T PRK12520 13 PYLLRFARLQLRDEAWAEDAVS 34 (191) T ss_pred HHHHHHHHHHCCCHHHHHHHHH T ss_conf 9999999999499999999999 No 295 >pfam12492 DUF3705 Protein of unknown function (DUF3705). This domain family is found in bacteria, and is approximately 30 amino acids in length. Probab=22.92 E-value=40 Score=14.31 Aligned_cols=16 Identities=25% Similarity=0.420 Sum_probs=12.3 Q ss_pred EEEECCCCEEEEECCC Q ss_conf 1797699468500134 Q gi|254780282|r 49 LFYRHARGLTLTEQGS 64 (299) Q Consensus 49 Lf~R~~~~~~lT~~G~ 64 (299) -|.|.++++.||+.++ T Consensus 2 fF~r~gd~f~Pt~~A~ 17 (31) T pfam12492 2 FFVRDGDGFVPTRFAR 17 (31) T ss_pred CEEECCCCCCCCEECC T ss_conf 1685388623243021 No 296 >TIGR02995 ectoine_ehuB ectoine/hydroxyectoine ABC transporter solute-binding protein; InterPro: IPR014337 Members of this entry are the extracellular solute-binding proteins of ABC transporters and they closely resemble amino acid transporters. The member from Sinorhizobium meliloti (Rhizobium meliloti) is involved in ectoine uptake, both for osmoprotection and for catabolism. All other members of the seed alignment are found associated with ectoine catabolic genes.. Probab=22.71 E-value=53 Score=13.55 Aligned_cols=151 Identities=14% Similarity=0.069 Sum_probs=82.0 Q ss_pred CCCCCCCCCCCCCCC----------CCCCCCHHHHHHHHH--HCCCCCCCC-CCCCCCCCCCCCCCCCCCCCCCCCCCCC Q ss_conf 222223332111000----------000000135667542--000122222-2222222222222223456543211112 Q gi|254780282|r 90 KPSGKLRIATTIDLG----------QNLLQGNLKEFLLLY--PDIQIQLIL-DNKDIDISMDYADCAIRLRKPIQSSSLI 156 (299) Q Consensus 90 ~~~g~i~I~~~~~~~----------~~~l~~~l~~f~~~~--P~i~i~i~~-~~~~~~l~~~~~Di~i~~~~~~~~~~l~ 156 (299) +.+|-+|||...-.- .-.-|++=..+.++- -+|.-.++. +...--|..|+.|. |..+.-+.+.++. T Consensus 31 KeQG~~Ria~ANE~Pf~y~g~DGkv~G~~PdvA~aifK~lGi~dVn~~~te~G~lIPGL~AgRfDa-iaAg~~i~PeRCk 109 (285) T TIGR02995 31 KEQGFVRIAIANEVPFAYVGADGKVAGAAPDVARAIFKRLGIKDVNASVTEYGALIPGLKAGRFDA-IAAGLFIKPERCK 109 (285) T ss_pred HCCCEEEEEECCCCCCCCCCCCCCCCCCCHHHHHHHHHHCCCEEEEEEECCCCCCCCCCCCCHHHH-HHHCCCCCHHHHH T ss_conf 235304774006786400268853136855789999985481100000356403145410102568-8611578856664 Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCC---CCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCCCCCCCEEEECCCCHHHH Q ss_conf 234555433211234432111222---22211000112356643321100023566520223432121145324200135 Q gi|254780282|r 157 QRKLVTIHMHAYAAPHYLKNCREP---LSIQELDKHNLITFGDLIPKCMEDFNWLATVDRPIGEPRISCLQVNSYLSIMQ 233 (299) Q Consensus 157 ~~~l~~~~~~~v~~~~~~~~~~~~---~~~~dL~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~ 233 (299) . -+|++|.... +...+...|.| .+.+|+++-|=+...-. ..... ..+.+..|++...++.+.+....+. T Consensus 110 q-Vaft~P~~~~-~eallvkKGNPk~L~sY~DiAknP~~K~a~~--~G~~e----~~~ar~~GVk~eqi~~vPd~~~~l~ 181 (285) T TIGR02995 110 Q-VAFTEPILSL-AEALLVKKGNPKELKSYKDIAKNPEVKVAVV--AGAVE----VKYAREAGVKEEQIVVVPDTASALK 181 (285) T ss_pred H-HHHCCCCCCC-CCCCCCCCCCCCCCCCCCCHHCCCCCEEEEC--CCCHH----HHHHHHCCCCCCEEEEECCCHHHHH T ss_conf 6-4406886447-5521125878888775202006823127612--47237----8999865898660788248716788 Q ss_pred HHHHHCC-EEEEEHHHH Q ss_conf 6787384-233117776 Q gi|254780282|r 234 YCVLGSG-IALLPDYIV 249 (299) Q Consensus 234 ~v~~g~G-ia~lp~~~~ 249 (299) +|++|-. +...|...+ T Consensus 182 ~vq~~RaDay~~t~Lt~ 198 (285) T TIGR02995 182 AVQDKRADAYAATELTV 198 (285) T ss_pred HHHHHCCCEECCCCCCH T ss_conf 87740342200332347 No 297 >pfam12116 SpoIIID Stage III sporulation protein D. This stage III sporulation protein is a small DNA-binding family that is essential for gene expression of the mother-cell compartment during sporulation. The domain is found in bacteria and viruses, and is about 40 amino acids in length. It has a conserved RGG sequence motif. Probab=22.59 E-value=54 Score=13.53 Aligned_cols=28 Identities=14% Similarity=0.351 Sum_probs=21.5 Q ss_pred HHHH-HCCHHHHHHHHCCCHHHHHHHHHH Q ss_conf 9998-276899998828997899999999 Q gi|254780282|r 13 VVAR-SGSFTHAAEQLHLSQSSISRQISG 40 (299) Q Consensus 13 ~v~~-~gs~s~AA~~L~itq~avS~~i~~ 40 (299) -+.+ .-.+..||+..|||-|+|.+-+.. T Consensus 14 YIi~~~aTVR~tAk~FGvSKSTVHkDvTe 42 (82) T pfam12116 14 YIIENKATVRQAAKVFGVSKSTVHKDVTE 42 (82) T ss_pred HHHHCCHHHHHHHHHHCCCHHHHHHHHHH T ss_conf 99962628999999969609889887999 No 298 >pfam00292 PAX 'Paired box' domain. Probab=22.29 E-value=55 Score=13.50 Aligned_cols=32 Identities=22% Similarity=0.318 Sum_probs=19.7 Q ss_pred HHHHHHHCC-HHHHHHHHCCCHHHHHHHHHHHH Q ss_conf 999998276-89999882899789999999999 Q gi|254780282|r 11 FYVVARSGS-FTHAAEQLHLSQSSISRQISGLE 42 (299) Q Consensus 11 f~~v~~~gs-~s~AA~~L~itq~avS~~i~~LE 42 (299) .+.+|..|. -..=++.|.||+..|||-+.+.. T Consensus 26 IVeLa~~G~RpCdISR~L~VShGCVSKIL~Ry~ 58 (125) T pfam00292 26 IVELAHSGVRPCDISRQLRVSHGCVSKILGRYQ 58 (125) T ss_pred HHHHHHCCCCHHHHHHHHCCCCHHHHHHHHHHH T ss_conf 999998499788887762676216899999887 No 299 >PRK08413 consensus Probab=21.94 E-value=45 Score=13.99 Aligned_cols=22 Identities=18% Similarity=0.104 Sum_probs=8.6 Q ss_pred EEECCCCEEEEECCCCCCCCCC Q ss_conf 7976994685001343322222 Q gi|254780282|r 50 FYRHARGLTLTEQGSKLHRVTS 71 (299) Q Consensus 50 f~R~~~~~~lT~~G~~l~~~a~ 71 (299) +.+.++.+.||+.|..+.+... T Consensus 487 v~~~~k~l~pT~~G~~v~~~L~ 508 (733) T PRK08413 487 VKIEKKQIIPTESAFKVIEVLE 508 (733) T ss_pred EEECCCEEEECHHHHHHHHHHH T ss_conf 9941977877469999999998 No 300 >PRK09959 hybrid sensory histidine kinase in two-component regulatory system with EvgA; Provisional Probab=21.59 E-value=56 Score=13.41 Aligned_cols=178 Identities=15% Similarity=0.133 Sum_probs=83.9 Q ss_pred CCCCCCCCCCCCC-----------CCCCHHHHHHHHHHCCCCCCCC-CCC---CCCCCCCCCCCCCCCC-CCCC-CCCCC Q ss_conf 2333211100000-----------0000135667542000122222-222---2222222222223456-5432-11112 Q gi|254780282|r 94 KLRIATTIDLGQN-----------LLQGNLKEFLLLYPDIQIQLIL-DNK---DIDISMDYADCAIRLR-KPIQ-SSSLI 156 (299) Q Consensus 94 ~i~I~~~~~~~~~-----------~l~~~l~~f~~~~P~i~i~i~~-~~~---~~~l~~~~~Di~i~~~-~~~~-~~~l~ 156 (299) .|++++.+.+++. +..+.|..+.. .-+++|+... ++. ...+..|++|+.-... .+.. ..-.. T Consensus 303 ~irv~~~~~~aP~sf~D~~G~~~Gi~aD~L~lIs~-rtGL~Fe~v~~~~~~~~~~~l~~g~~D~l~~~~~s~~r~~~l~f 381 (1197) T PRK09959 303 DLKVLENPYSPPYSMTDENGSVRGVMGDILNIITL-QTGLNFSPITVSHNIHAGTQLNPGGWDILPGAIYSEDRENNVLF 381 (1197) T ss_pred CEEEEECCCCCCEEEECCCCCCCCCHHHHHHHHHH-HHCCEEEEEECCCHHHHHHHHHCCCCHHCCCCCCCCCCCCCCEE T ss_conf 75997179989945788899764327999999999-87966899836987999999876981220323578544346554 Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCCCCCCCEEEECCCCHHHHHHH Q ss_conf 23455543321123443211122222211000112356643321100023566520223432121145324200135678 Q gi|254780282|r 157 QRKLVTIHMHAYAAPHYLKNCREPLSIQELDKHNLITFGDLIPKCMEDFNWLATVDRPIGEPRISCLQVNSYLSIMQYCV 236 (299) Q Consensus 157 ~~~l~~~~~~~v~~~~~~~~~~~~~~~~dL~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~v~ 236 (299) .+++...++++|..++.. ....+..-.-|.. +.......++.. ..|......+++....+++|. T Consensus 382 T~py~~~p~ViV~r~~~~-------~~~~l~~gkrvai----~~~~~~~~~l~~-----~yP~i~~v~v~s~~~al~~v~ 445 (1197) T PRK09959 382 AEAFITTPYVFVMQKAPD-------SEQTLKKGMKVAI----PYYYELHSQLKE-----MYPEVEWIKVDNASAAFHKVK 445 (1197) T ss_pred CCCCCCCCEEEEEECCCC-------CCCCHHCCCEEEE----CCCCCHHHHHHH-----HCCCCEEEEECCHHHHHHHHH T ss_conf 132356875999963786-------3011421988999----178506899998-----689834998099999999997 Q ss_pred HHCCEEEEE-----HHHHCC--CCCEEEECCCCCCCCCEEEEEECCCCCCCHHHHHHHHHHHH Q ss_conf 738423311-----777601--99846617766676600899934877888899999999999 Q gi|254780282|r 237 LGSGIALLP-----DYIVKD--NPNLVRIMEDVITPSFTVYFCYPEALKNTGKLKAFRNFIFL 292 (299) Q Consensus 237 ~g~Gia~lp-----~~~~~~--~~~lv~i~~~~~~~~~~~~lv~~~~~~~~~~~~~f~d~l~~ 292 (299) .|..=+.+- .+++++ .++++.+.... .++..+.+..++ ..|..+..+|=.+. T Consensus 446 ~G~aDa~v~~l~~a~y~i~~~~~~~L~~~~~~~-~~~~~lafaV~~---d~peL~sILnKaL~ 504 (1197) T PRK09959 446 EGELDALVATQLNSRYMIDHYYPNELYHFLIPG-VPNASLSFAFPR---GEPELKDIINKALN 504 (1197) T ss_pred CCCCCEEEEHHHHHHHHHHHHCCCCCEEEECCC-CCCCCEEEEECC---CCHHHHHHHHHHHH T ss_conf 788766742447789999874566504874158-776326999879---98899999999998 No 301 >COG1167 ARO8 Transcriptional regulators containing a DNA-binding HTH domain and an aminotransferase domain (MocR family) and their eukaryotic orthologs [Transcription / Amino acid transport and metabolism] Probab=21.54 E-value=57 Score=13.41 Aligned_cols=29 Identities=34% Similarity=0.437 Sum_probs=26.0 Q ss_pred HHCCHHHHHHHHCCCHHHHHHHHHHHHHH Q ss_conf 82768999988289978999999999999 Q gi|254780282|r 16 RSGSFTHAAEQLHLSQSSISRQISGLETE 44 (299) Q Consensus 16 ~~gs~s~AA~~L~itq~avS~~i~~LE~~ 44 (299) +.-|...-|+.+++|.++|++..++||.+ T Consensus 27 rLPs~R~la~~l~vs~~Tv~~ay~~L~~~ 55 (459) T COG1167 27 RLPSIRQLAQDLGVSRSTVSRAYEELEAR 55 (459) T ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHHHHC T ss_conf 18766999999487488999999999976 No 302 >PRK13777 transcriptional regulator Hpr; Provisional Probab=21.44 E-value=37 Score=14.45 Aligned_cols=49 Identities=20% Similarity=0.116 Sum_probs=19.1 Q ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHH----HCCEEEEECCCCEEEEECCCCCC Q ss_conf 68999988289978999999999999----58821797699468500134332 Q gi|254780282|r 19 SFTHAAEQLHLSQSSISRQISGLETE----VGIKLFYRHARGLTLTEQGSKLH 67 (299) Q Consensus 19 s~s~AA~~L~itq~avS~~i~~LE~~----lg~~Lf~R~~~~~~lT~~G~~l~ 67 (299) |+|.-|+-=-+.-|+.=.-=++||++ +-.+..++.+.-++||+.|+.++ T Consensus 62 sISdiAkfGVMHVSTaFNFSKkLEeRG~L~fsKk~~DKRNTYi~LT~~G~e~~ 114 (190) T PRK13777 62 SISEIAKFGVMHVSTAFNFSKKLEERGYLVFSKKEDDKRNTYIELTDKGEELL 114 (190) T ss_pred CHHHHHHHCCEEEEEHHHHHHHHHHCCCEECCCCCCCCCCCEEEECCCHHHHH T ss_conf 39999870724630032055777755345334002465553588650168999 No 303 >smart00437 TOP1Ac Bacterial DNA topoisomerase I DNA-binding domain. Bacterial DNA topoisomerase I and III, Eukaryotic DNA topoisomeraes III, reverse gyrase alpha subunit Probab=21.10 E-value=58 Score=13.35 Aligned_cols=40 Identities=18% Similarity=0.141 Sum_probs=24.9 Q ss_pred HHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEECCCCEEEEE Q ss_conf 99998828997899999999999958821797699468500 Q gi|254780282|r 21 THAAEQLHLSQSSISRQISGLETEVGIKLFYRHARGLTLTE 61 (299) Q Consensus 21 s~AA~~L~itq~avS~~i~~LE~~lg~~Lf~R~~~~~~lT~ 61 (299) ..|+.++++|..-+-...++|=+ =|.-=.-|+-...-+.+ T Consensus 20 ~~as~~~g~sa~~tl~iaQ~LYe-~g~ITYpRTds~~l~~~ 59 (259) T smart00437 20 QEASRKLGFSAKKTMQIAQKLYE-KGLITYPRTDSTRLSEE 59 (259) T ss_pred HHHHHHCCCCHHHHHHHHHHHHH-CCCEEECCCCCCCCCHH T ss_conf 99998669999999999999986-78553347687463999 No 304 >PRK09057 coproporphyrinogen III oxidase; Provisional Probab=20.91 E-value=50 Score=13.71 Aligned_cols=18 Identities=11% Similarity=0.060 Sum_probs=11.5 Q ss_pred CCCCHHHHHHHHHHHHHH Q ss_conf 788889999999999998 Q gi|254780282|r 277 LKNTGKLKAFRNFIFLKA 294 (299) Q Consensus 277 ~~~~~~~~~f~d~l~~~~ 294 (299) -..++.-+.|.|.+..+. T Consensus 362 l~lT~~G~~l~d~v~~eL 379 (381) T PRK09057 362 LRATPAGRLVLDAVVADL 379 (381) T ss_pred EEECHHHHHHHHHHHHHH T ss_conf 999978879999999997 No 305 >TIGR02944 suf_reg_Xantho FeS assembly SUF system regulator; InterPro: IPR014290 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 proteins belonging to the Rtf2 family of transcriptional regulators and are found, typically, as the first gene of the SUF operon. They are found only in a subset of the genomes that encode the SUF system, including the genus Xanthomonas. The conserved location suggests an autoregulatory role.. Probab=20.72 E-value=59 Score=13.31 Aligned_cols=30 Identities=27% Similarity=0.392 Sum_probs=18.0 Q ss_pred HHHHHCCHHHH--HHHHCCCHHHHHHHHHHHH Q ss_conf 99982768999--9882899789999999999 Q gi|254780282|r 13 VVARSGSFTHA--AEQLHLSQSSISRQISGLE 42 (299) Q Consensus 13 ~v~~~gs~s~A--A~~L~itq~avS~~i~~LE 42 (299) +-..+..||+| |+.=+++-|||||-+|.|- T Consensus 19 A~~~~~~ySAA~lA~~tgL~~pTvsK~Lk~L~ 50 (130) T TIGR02944 19 AQADEQTYSAAELAEQTGLEAPTVSKILKALS 50 (130) T ss_pred HCCCCCHHHHHHHHHHCCCCCCHHHHHHHHHH T ss_conf 52899700688878645988604789988764 No 306 >smart00422 HTH_MERR helix_turn_helix, mercury resistance. Probab=20.60 E-value=59 Score=13.29 Aligned_cols=34 Identities=18% Similarity=0.148 Sum_probs=19.7 Q ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHCCEE-EEECCCCE Q ss_conf 6899998828997899999999999958821-79769946 Q gi|254780282|r 19 SFTHAAEQLHLSQSSISRQISGLETEVGIKL-FYRHARGL 57 (299) Q Consensus 19 s~s~AA~~L~itq~avS~~i~~LE~~lg~~L-f~R~~~~~ 57 (299) |++.+|+.++||++++ +--|++ |.-- -.|+.+|. T Consensus 2 tI~e~a~~~gvs~~tl----R~ye~~-Gll~p~~r~~~g~ 36 (70) T smart00422 2 TIGEVAKLAGVSVRTL----RYYERI-GLLPPPIRTEGGY 36 (70) T ss_pred CHHHHHHHHCCCHHHH----HHHHHC-CCCCCCCCCCCCC T ss_conf 7889999989699999----999985-8989984489997 No 307 >PRK10803 hypothetical protein; Provisional Probab=20.16 E-value=61 Score=13.24 Aligned_cols=73 Identities=12% Similarity=0.114 Sum_probs=44.3 Q ss_pred CCCCHHHHHH----HHHHHHHCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEECCCCEEEEECCCCCCCCCCCCCCC Q ss_conf 9888899999----999998276899998828997899999999999958821797699468500134332222222222 Q gi|254780282|r 1 MSFDWDKLRV----FYVVARSGSFTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHARGLTLTEQGSKLHRVTSEVYHK 76 (299) Q Consensus 1 m~md~~~L~~----f~~v~~~gs~s~AA~~L~itq~avS~~i~~LE~~lg~~Lf~R~~~~~~lT~~G~~l~~~a~~~l~~ 76 (299) ||-|++++-. |+.++--.--.+.|=.-++...++..+|.+||..+... +-. ..++-.+ T Consensus 1 ~~~~~~~~~~~~~~~~~~~~~~~a~a~apv~~~~~gs~e~Rl~~LEr~~~~~-------~~~-----------~~qlq~Q 62 (262) T PRK10803 1 MSSNFRHHLLSLSLLVGIAAPWAAFAQAPISSVGSGSVEDRVTQLERISNAH-------SQL-----------LTQLQQQ 62 (262) T ss_pred CCCHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHCCCCHHHHHHHHHHHHHHH-------HHH-----------HHHHHHH T ss_conf 9741999999999999986078770344376603786999999999999974-------279-----------9999999 Q ss_pred CCHHHHHCCCCCCCC Q ss_conf 101221001223222 Q gi|254780282|r 77 LETTQIELQESSVKP 91 (299) Q Consensus 77 ~~~~~~~~~~~~~~~ 91 (299) ++++..+++.+++.. T Consensus 63 l~~LQ~EV~~LRGqi 77 (262) T PRK10803 63 LSDNQSDIDSLRGQI 77 (262) T ss_pred HHHHHHHHHHHHHHH T ss_conf 999999999998799 Done!