Query psy3760
Match_columns 306
No_of_seqs 189 out of 1511
Neff 11.2
Searched_HMMs 46136
Date Fri Aug 16 16:35:15 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy3760.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/3760hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PRK12681 cysB transcriptional 100.0 1.7E-58 3.6E-63 381.3 36.2 302 1-303 1-303 (324)
2 PRK12682 transcriptional regul 100.0 1.5E-58 3.2E-63 380.8 35.2 303 1-303 1-303 (309)
3 PRK12683 transcriptional regul 100.0 3.2E-58 7E-63 378.0 37.1 304 1-304 1-304 (309)
4 PRK12684 transcriptional regul 100.0 5.8E-58 1.3E-62 377.4 36.1 304 1-304 1-304 (313)
5 PRK11151 DNA-binding transcrip 100.0 5.7E-58 1.2E-62 377.1 33.9 296 1-299 1-297 (305)
6 PRK12679 cbl transcriptional r 100.0 1.8E-57 3.9E-62 374.9 35.2 299 1-301 1-301 (316)
7 PRK11242 DNA-binding transcrip 100.0 1.6E-57 3.4E-62 373.4 34.7 292 1-297 1-293 (296)
8 PRK12680 transcriptional regul 100.0 2.2E-57 4.7E-62 374.9 35.0 302 1-305 1-305 (327)
9 PRK10341 DNA-binding transcrip 100.0 1.5E-57 3.3E-62 375.2 33.7 298 1-302 7-305 (312)
10 CHL00180 rbcR LysR transcripti 100.0 3.4E-57 7.3E-62 372.1 34.4 294 1-296 5-304 (305)
11 TIGR02424 TF_pcaQ pca operon t 100.0 2.1E-57 4.4E-62 373.2 33.0 294 1-296 3-299 (300)
12 PRK11013 DNA-binding transcrip 100.0 1.1E-56 2.4E-61 369.5 35.1 296 1-300 4-299 (309)
13 PRK09791 putative DNA-binding 100.0 1.1E-56 2.4E-61 368.9 33.3 293 1-297 5-299 (302)
14 PRK11233 nitrogen assimilation 100.0 5.2E-56 1.1E-60 364.8 34.5 296 1-302 1-298 (305)
15 PRK09906 DNA-binding transcrip 100.0 7E-56 1.5E-60 363.4 34.2 291 1-297 1-293 (296)
16 PRK10837 putative DNA-binding 100.0 3.8E-56 8.2E-61 364.2 32.5 285 1-293 3-288 (290)
17 PRK15421 DNA-binding transcrip 100.0 1.3E-55 2.7E-60 363.4 33.2 290 1-298 2-292 (317)
18 PRK09986 DNA-binding transcrip 100.0 1.5E-55 3.2E-60 361.4 32.8 286 1-291 7-294 (294)
19 TIGR03339 phn_lysR aminoethylp 100.0 1.3E-54 2.8E-59 353.5 32.3 279 5-291 1-279 (279)
20 PRK09508 leuO leucine transcri 100.0 3.4E-55 7.4E-60 361.5 27.2 291 1-296 22-313 (314)
21 PRK11074 putative DNA-binding 100.0 8.7E-55 1.9E-59 357.0 28.8 287 1-294 2-291 (300)
22 PRK15243 transcriptional regul 100.0 2.9E-54 6.4E-59 348.3 30.0 280 4-298 7-295 (297)
23 PRK10094 DNA-binding transcrip 100.0 2.8E-53 6.1E-58 348.5 30.5 288 1-295 2-293 (308)
24 PRK11062 nhaR transcriptional 100.0 1.4E-53 3E-58 349.1 28.6 282 1-290 4-288 (296)
25 PRK09801 transcriptional activ 100.0 6.4E-54 1.4E-58 352.4 22.6 291 1-298 6-299 (310)
26 PRK11139 DNA-binding transcrip 100.0 6.7E-53 1.4E-57 345.7 27.7 285 1-298 6-295 (297)
27 PRK11482 putative DNA-binding 100.0 3.5E-52 7.6E-57 343.0 28.2 287 1-295 29-317 (317)
28 PRK10632 transcriptional regul 100.0 3.8E-53 8.2E-58 348.3 22.3 286 1-296 1-293 (309)
29 PRK13348 chromosome replicatio 100.0 8.2E-52 1.8E-56 338.9 29.7 288 1-297 2-291 (294)
30 TIGR03298 argP transcriptional 100.0 1.1E-51 2.3E-56 337.9 30.2 287 1-297 1-290 (292)
31 PRK03601 transcriptional regul 100.0 1.2E-51 2.6E-56 333.9 29.2 269 1-290 1-269 (275)
32 PRK03635 chromosome replicatio 100.0 1.5E-51 3.2E-56 336.9 29.4 287 1-297 2-291 (294)
33 PRK10216 DNA-binding transcrip 100.0 1.5E-51 3.3E-56 340.5 29.5 290 1-296 8-316 (319)
34 PRK14997 LysR family transcrip 100.0 1.8E-52 3.9E-57 343.9 22.8 289 1-297 2-297 (301)
35 TIGR03418 chol_sulf_TF putativ 100.0 6.8E-53 1.5E-57 344.9 19.9 284 1-293 1-290 (291)
36 PRK10086 DNA-binding transcrip 100.0 7.6E-52 1.6E-56 340.9 26.1 286 1-297 14-309 (311)
37 PRK10082 cell density-dependen 100.0 1.5E-50 3.2E-55 332.4 30.4 285 1-294 11-298 (303)
38 PRK15092 DNA-binding transcrip 100.0 4.7E-50 1E-54 328.8 31.4 277 1-296 11-289 (310)
39 TIGR02036 dsdC D-serine deamin 100.0 1.1E-50 2.4E-55 332.7 26.7 284 1-295 8-301 (302)
40 COG0583 LysR Transcriptional r 100.0 1.3E-47 2.9E-52 315.1 32.2 290 1-297 1-293 (297)
41 PRK11716 DNA-binding transcrip 100.0 2.9E-47 6.2E-52 308.7 28.9 266 26-293 1-268 (269)
42 PF03466 LysR_substrate: LysR 100.0 6E-33 1.3E-37 216.2 20.9 207 89-296 2-209 (209)
43 cd08444 PBP2_Cbl The C-termina 100.0 1.7E-29 3.7E-34 195.2 21.4 198 94-291 1-198 (198)
44 cd08413 PBP2_CysB_like The C-t 100.0 1.9E-29 4E-34 195.0 21.2 198 94-291 1-198 (198)
45 cd08421 PBP2_LTTR_like_1 The C 100.0 4.2E-29 9E-34 192.8 22.4 197 94-291 1-198 (198)
46 cd08411 PBP2_OxyR The C-termin 100.0 4.8E-29 1E-33 192.8 21.7 198 93-291 1-200 (200)
47 cd08459 PBP2_DntR_NahR_LinR_li 100.0 1.6E-29 3.4E-34 195.7 18.9 200 94-295 1-201 (201)
48 cd08433 PBP2_Nac The C-teminal 100.0 5.5E-29 1.2E-33 192.1 21.5 197 94-291 1-198 (198)
49 cd08437 PBP2_MleR The substrat 100.0 7.8E-29 1.7E-33 191.3 22.1 196 94-291 1-198 (198)
50 cd08435 PBP2_GbpR The C-termin 100.0 6.9E-29 1.5E-33 191.9 21.4 198 94-291 1-201 (201)
51 cd08438 PBP2_CidR The C-termin 100.0 6.9E-29 1.5E-33 191.2 21.2 197 94-291 1-197 (197)
52 cd08443 PBP2_CysB The C-termin 100.0 8.6E-29 1.9E-33 191.3 21.3 197 94-290 1-197 (198)
53 cd08417 PBP2_Nitroaromatics_li 100.0 4.3E-29 9.2E-34 193.0 19.0 198 94-293 1-199 (200)
54 cd08440 PBP2_LTTR_like_4 TThe 100.0 1.5E-28 3.2E-33 189.2 21.6 197 94-291 1-197 (197)
55 cd08426 PBP2_LTTR_like_5 The C 100.0 1.9E-28 4E-33 189.3 21.1 197 94-291 1-199 (199)
56 cd08412 PBP2_PAO1_like The C-t 100.0 2.9E-28 6.3E-33 188.0 21.9 196 94-291 1-198 (198)
57 cd08425 PBP2_CynR The C-termin 100.0 2.4E-28 5.2E-33 188.4 21.4 195 93-290 1-196 (197)
58 cd08434 PBP2_GltC_like The sub 100.0 3.2E-28 7E-33 187.1 22.0 195 94-291 1-195 (195)
59 cd08436 PBP2_LTTR_like_3 The C 100.0 3.7E-28 7.9E-33 186.7 22.0 194 94-291 1-194 (194)
60 cd08415 PBP2_LysR_opines_like 100.0 2.9E-28 6.4E-33 187.6 21.1 196 94-291 1-196 (196)
61 cd08464 PBP2_DntR_like_2 The C 100.0 9E-29 1.9E-33 191.2 18.1 198 94-293 1-199 (200)
62 cd08463 PBP2_DntR_like_4 The C 100.0 2E-28 4.4E-33 189.9 20.0 199 94-293 1-202 (203)
63 cd08420 PBP2_CysL_like C-termi 100.0 4.3E-28 9.3E-33 187.3 21.8 197 94-291 1-201 (201)
64 cd08418 PBP2_TdcA The C-termin 100.0 3.5E-28 7.5E-33 188.0 21.1 199 94-294 1-201 (201)
65 cd08458 PBP2_NocR The C-termin 100.0 4.7E-28 1E-32 186.8 21.7 196 94-291 1-196 (196)
66 cd08456 PBP2_LysR The C-termin 100.0 4.4E-28 9.5E-33 186.7 21.5 196 94-291 1-196 (196)
67 cd08423 PBP2_LTTR_like_6 The C 100.0 2.5E-28 5.3E-33 188.6 20.0 196 94-291 1-200 (200)
68 cd08460 PBP2_DntR_like_1 The C 100.0 1.1E-28 2.4E-33 190.9 17.9 198 94-294 1-199 (200)
69 cd08419 PBP2_CbbR_RubisCO_like 100.0 4.1E-28 8.8E-33 186.9 20.9 196 94-291 1-197 (197)
70 cd08462 PBP2_NodD The C-termin 100.0 2.1E-28 4.4E-33 189.4 18.7 197 94-293 1-199 (200)
71 cd08466 PBP2_LeuO The C-termin 100.0 1.8E-28 3.9E-33 189.6 18.2 197 94-293 1-199 (200)
72 cd08467 PBP2_SyrM The C-termin 100.0 3.9E-28 8.4E-33 187.9 19.0 197 95-293 2-199 (200)
73 cd08414 PBP2_LTTR_aromatics_li 100.0 8.7E-28 1.9E-32 185.1 20.8 194 94-290 1-196 (197)
74 cd08441 PBP2_MetR The C-termin 100.0 7E-28 1.5E-32 186.0 20.3 196 94-290 1-197 (198)
75 cd08453 PBP2_IlvR The C-termin 100.0 8.8E-28 1.9E-32 185.8 20.8 195 94-290 1-199 (200)
76 cd08442 PBP2_YofA_SoxR_like Th 100.0 1.1E-27 2.5E-32 183.9 20.8 192 94-291 1-193 (193)
77 cd08449 PBP2_XapR The C-termin 100.0 1.2E-27 2.7E-32 184.3 21.0 195 94-291 1-197 (197)
78 cd08486 PBP2_CbnR The C-termin 100.0 2E-27 4.3E-32 183.7 22.1 195 93-290 1-197 (198)
79 cd08461 PBP2_DntR_like_3 The C 100.0 4.6E-28 1E-32 187.0 17.6 196 94-293 1-197 (198)
80 cd08468 PBP2_Pa0477 The C-term 100.0 1.4E-27 2.9E-32 185.1 19.6 198 94-293 1-201 (202)
81 cd08446 PBP2_Chlorocatechol Th 100.0 2.5E-27 5.4E-32 182.9 20.8 195 93-290 1-197 (198)
82 cd08450 PBP2_HcaR The C-termin 100.0 3.5E-27 7.5E-32 181.7 21.5 194 94-290 1-195 (196)
83 cd08457 PBP2_OccR The C-termin 100.0 3.3E-27 7.1E-32 182.0 20.9 196 94-291 1-196 (196)
84 cd08427 PBP2_LTTR_like_2 The C 100.0 2.9E-27 6.4E-32 181.9 20.5 194 94-291 1-195 (195)
85 cd08445 PBP2_BenM_CatM_CatR Th 100.0 4.9E-27 1.1E-31 182.1 21.5 198 94-294 2-202 (203)
86 cd08430 PBP2_IlvY The C-termin 100.0 2E-27 4.2E-32 183.5 19.1 196 94-290 1-198 (199)
87 cd08485 PBP2_ClcR The C-termin 100.0 6.6E-27 1.4E-31 180.7 21.9 196 93-291 1-198 (198)
88 cd08416 PBP2_MdcR The C-termin 100.0 7.2E-27 1.6E-31 180.4 21.8 197 94-291 1-199 (199)
89 cd08448 PBP2_LTTR_aromatics_li 100.0 7.3E-27 1.6E-31 179.9 21.5 195 94-291 1-197 (197)
90 cd08469 PBP2_PnbR The C-termin 100.0 2.1E-27 4.5E-32 186.7 18.5 198 94-293 1-220 (221)
91 cd08429 PBP2_NhaR The C-termin 100.0 3.5E-27 7.6E-32 183.1 19.2 198 95-294 2-202 (204)
92 cd08451 PBP2_BudR The C-termin 100.0 1.2E-26 2.7E-31 179.0 20.7 196 94-291 1-199 (199)
93 cd05466 PBP2_LTTR_substrate Th 100.0 1.7E-26 3.7E-31 177.2 21.2 196 94-291 1-197 (197)
94 cd08465 PBP2_ToxR The C-termin 100.0 6.6E-27 1.4E-31 181.0 18.5 198 94-293 1-199 (200)
95 cd08452 PBP2_AlsR The C-termin 100.0 2.1E-26 4.5E-31 177.7 20.6 193 95-290 2-196 (197)
96 cd08447 PBP2_LTTR_aromatics_li 100.0 2.9E-26 6.3E-31 176.8 20.9 195 94-291 1-198 (198)
97 cd08431 PBP2_HupR The C-termin 99.9 1.3E-25 2.8E-30 172.9 16.5 192 94-291 1-195 (195)
98 cd08432 PBP2_GcdR_TrpI_HvrB_Am 99.9 1.3E-25 2.9E-30 172.5 13.6 192 94-291 1-194 (194)
99 cd08475 PBP2_CrgA_like_6 The C 99.9 1.7E-25 3.6E-30 172.7 11.3 196 93-291 1-199 (199)
100 cd08471 PBP2_CrgA_like_2 The C 99.9 2.1E-25 4.6E-30 172.4 11.7 198 93-294 1-200 (201)
101 cd08478 PBP2_CrgA The C-termin 99.9 7.7E-26 1.7E-30 174.7 8.7 196 92-291 2-199 (199)
102 cd08422 PBP2_CrgA_like The C-t 99.9 3E-25 6.6E-30 170.8 11.6 195 93-291 1-197 (197)
103 cd08481 PBP2_GcdR_like The C-t 99.9 9.1E-25 2E-29 167.9 13.5 190 94-291 1-194 (194)
104 cd08474 PBP2_CrgA_like_5 The C 99.9 3.4E-25 7.5E-30 171.4 10.6 195 92-291 2-202 (202)
105 cd08472 PBP2_CrgA_like_3 The C 99.9 9.7E-25 2.1E-29 168.8 12.1 196 93-293 1-201 (202)
106 cd08477 PBP2_CrgA_like_8 The C 99.9 1.2E-24 2.6E-29 167.7 10.1 195 93-291 1-197 (197)
107 cd08479 PBP2_CrgA_like_9 The C 99.9 1.2E-24 2.6E-29 167.9 9.8 195 93-291 1-198 (198)
108 cd08439 PBP2_LrhA_like The C-t 99.9 1.1E-22 2.5E-27 155.2 20.5 182 94-291 1-185 (185)
109 cd08428 PBP2_IciA_ArgP The C-t 99.9 4.2E-23 9.1E-28 158.9 18.2 191 94-290 1-194 (195)
110 cd08470 PBP2_CrgA_like_1 The C 99.9 1.6E-24 3.5E-29 167.0 9.8 195 93-294 1-196 (197)
111 cd08473 PBP2_CrgA_like_4 The C 99.9 2.3E-24 4.9E-29 166.7 10.6 197 92-291 2-202 (202)
112 cd08476 PBP2_CrgA_like_7 The C 99.9 4.8E-24 1E-28 164.1 9.9 193 93-291 1-197 (197)
113 TIGR00637 ModE_repress ModE mo 99.9 1.6E-23 3.5E-28 139.2 10.6 83 1-85 2-89 (99)
114 cd08483 PBP2_HvrB The C-termin 99.9 2.3E-23 5E-28 159.6 12.7 187 94-291 1-190 (190)
115 PF00126 HTH_1: Bacterial regu 99.9 7.2E-24 1.6E-28 128.5 6.5 60 3-64 1-60 (60)
116 TIGR02136 ptsS_2 phosphate bin 99.9 1.7E-22 3.7E-27 163.8 16.1 211 91-303 34-282 (287)
117 cd08480 PBP2_CrgA_like_10 The 99.9 2.1E-23 4.6E-28 161.0 8.5 191 93-291 1-198 (198)
118 cd08482 PBP2_TrpI The C-termin 99.9 2.6E-22 5.7E-27 154.5 14.2 190 94-291 1-195 (195)
119 cd08488 PBP2_AmpR The C-termin 99.9 2.5E-22 5.5E-27 154.1 12.8 186 94-291 1-191 (191)
120 cd08487 PBP2_BlaA The C-termin 99.9 3.9E-22 8.4E-27 152.7 13.5 186 94-291 1-189 (189)
121 cd08484 PBP2_LTTR_beta_lactama 99.9 5.3E-22 1.1E-26 152.0 13.3 186 94-291 1-189 (189)
122 PRK14498 putative molybdopteri 99.8 9.5E-20 2.1E-24 163.1 15.4 186 92-294 416-624 (633)
123 PRK10676 DNA-binding transcrip 99.8 2.4E-19 5.2E-24 141.8 11.8 98 2-115 18-120 (263)
124 PF12727 PBP_like: PBP superfa 99.4 1E-11 2.2E-16 94.1 15.7 171 113-292 2-193 (193)
125 PRK11553 alkanesulfonate trans 99.3 7.7E-11 1.7E-15 97.5 15.8 201 89-295 23-237 (314)
126 PRK00489 hisG ATP phosphoribos 99.2 1.8E-10 3.9E-15 93.5 10.9 166 114-296 36-207 (287)
127 COG2005 ModE N-terminal domain 99.2 3.7E-10 8E-15 77.4 10.3 83 2-86 18-105 (130)
128 cd00134 PBPb Bacterial peripla 99.0 1.9E-08 4.2E-13 78.1 14.9 185 106-304 23-214 (218)
129 TIGR02122 TRAP_TAXI TRAP trans 99.0 1.9E-08 4.2E-13 83.6 15.5 167 90-261 27-219 (320)
130 TIGR01728 SsuA_fam ABC transpo 98.9 1.2E-07 2.6E-12 77.5 16.0 195 95-295 1-211 (288)
131 PRK09729 hypothetical protein; 98.9 1E-08 2.3E-13 62.8 6.4 62 232-295 2-63 (68)
132 smart00062 PBPb Bacterial peri 98.8 4.9E-07 1.1E-11 70.1 16.2 184 106-304 24-215 (219)
133 PF13531 SBP_bac_11: Bacterial 98.8 1.8E-06 3.8E-11 68.2 18.7 200 95-299 1-223 (230)
134 PF12849 PBP_like_2: PBP super 98.6 6.1E-07 1.3E-11 73.1 11.5 202 91-293 8-279 (281)
135 COG2998 TupB ABC-type tungstat 98.6 3.1E-05 6.8E-10 58.2 19.0 212 88-300 25-258 (280)
136 COG0725 ModA ABC-type molybdat 98.5 0.00012 2.5E-09 58.3 20.7 204 90-301 27-250 (258)
137 PRK11050 manganese transport r 98.5 6.9E-07 1.5E-11 65.1 7.4 61 18-82 53-114 (152)
138 TIGR01256 modA molybdenum ABC 98.5 6.8E-05 1.5E-09 58.5 19.2 186 105-298 5-210 (216)
139 COG1910 Periplasmic molybdate- 98.5 6.4E-06 1.4E-10 61.6 12.3 153 131-293 27-199 (223)
140 PF00497 SBP_bac_3: Bacterial 98.4 1.2E-05 2.6E-10 62.9 14.0 193 104-304 21-219 (225)
141 PRK10677 modA molybdate transp 98.4 0.00026 5.7E-09 56.7 21.4 199 90-294 24-243 (257)
142 TIGR02337 HpaR homoprotocatech 98.4 2.6E-06 5.6E-11 59.5 8.5 76 1-81 26-110 (118)
143 smart00529 HTH_DTXR Helix-turn 98.4 2.3E-06 5E-11 57.4 7.8 60 19-82 2-62 (96)
144 TIGR00975 3a0107s03 phosphate 98.4 4.4E-05 9.6E-10 63.0 16.4 152 96-248 2-199 (314)
145 PRK11917 bifunctional adhesin/ 98.3 0.00025 5.5E-09 57.0 18.8 179 91-278 36-232 (259)
146 PRK03902 manganese transport t 98.3 8.8E-06 1.9E-10 58.8 8.8 74 5-81 9-84 (142)
147 smart00347 HTH_MARR helix_turn 98.2 1.8E-05 3.9E-10 53.5 9.2 76 1-80 8-91 (101)
148 TIGR03730 tungstate_WtpA tungs 98.2 0.00081 1.8E-08 54.1 19.5 194 94-291 2-273 (273)
149 PRK04168 molybdate ABC transpo 98.0 0.001 2.2E-08 55.3 17.7 203 91-297 30-306 (334)
150 PRK11260 cystine transporter s 97.9 0.0013 2.8E-08 53.2 16.2 175 91-277 39-231 (266)
151 PF13556 HTH_30: PucR C-termin 97.8 3.3E-05 7.3E-10 46.2 4.3 43 6-48 2-44 (59)
152 PRK09495 glnH glutamine ABC tr 97.8 0.0031 6.7E-08 50.3 16.7 199 90-304 22-238 (247)
153 TIGR00363 lipoprotein, YaeC fa 97.8 0.01 2.2E-07 47.5 18.9 200 93-301 18-247 (258)
154 PRK13777 transcriptional regul 97.8 0.0002 4.3E-09 53.7 8.6 78 1-80 43-126 (185)
155 TIGR01096 3A0103s03R lysine-ar 97.8 0.0035 7.5E-08 50.1 16.3 140 93-242 24-177 (250)
156 COG0226 PstS ABC-type phosphat 97.8 0.0033 7E-08 52.1 16.3 204 91-296 41-301 (318)
157 TIGR02995 ectoine_ehuB ectoine 97.8 0.003 6.4E-08 51.4 15.8 204 91-305 31-257 (275)
158 PRK14165 winged helix-turn-hel 97.8 0.00014 3.1E-09 55.7 7.5 101 18-127 23-133 (217)
159 TIGR03871 ABC_peri_MoxJ_2 quin 97.7 0.01 2.3E-07 46.7 18.4 185 105-304 19-224 (232)
160 PRK11512 DNA-binding transcrip 97.7 0.00032 7E-09 50.8 8.7 70 1-74 38-115 (144)
161 PRK10797 glutamate and asparta 97.7 0.0089 1.9E-07 49.3 17.8 147 92-245 39-205 (302)
162 TIGR01098 3A0109s03R phosphate 97.7 0.011 2.4E-07 47.3 18.1 180 91-278 30-239 (254)
163 PRK03573 transcriptional regul 97.7 0.00037 8E-09 50.5 8.5 75 1-79 29-112 (144)
164 PRK10859 membrane-bound lytic 97.6 0.0035 7.6E-08 55.2 15.6 177 92-277 42-235 (482)
165 PF13379 NMT1_2: NMT1-like fam 97.6 0.006 1.3E-07 48.9 15.2 202 91-295 4-233 (252)
166 PRK10918 phosphate ABC transpo 97.6 0.017 3.7E-07 48.3 17.8 151 93-246 27-222 (346)
167 PRK11063 metQ DL-methionine tr 97.6 0.027 5.9E-07 45.5 19.0 201 93-302 31-261 (271)
168 TIGR01889 Staph_reg_Sar staphy 97.6 0.00064 1.4E-08 46.6 8.0 72 2-76 24-106 (109)
169 COG1321 TroR Mn-dependent tran 97.5 0.00064 1.4E-08 49.4 8.0 62 19-83 27-88 (154)
170 COG1846 MarR Transcriptional r 97.5 0.00032 7E-09 49.4 6.5 73 1-78 20-101 (126)
171 PRK09861 cytoplasmic membrane 97.5 0.014 3.1E-07 47.0 16.3 205 93-303 32-263 (272)
172 PRK10870 transcriptional repre 97.5 0.00076 1.6E-08 50.6 7.9 73 2-79 54-137 (176)
173 PF02954 HTH_8: Bacterial regu 97.5 0.00032 7E-09 38.6 4.4 32 8-39 10-41 (42)
174 PF13601 HTH_34: Winged helix 97.4 0.0017 3.6E-08 41.5 7.7 65 12-77 11-79 (80)
175 TIGR02285 conserved hypothetic 97.4 0.029 6.4E-07 45.3 16.7 212 92-305 17-257 (268)
176 PRK15010 ABC transporter lysin 97.4 0.012 2.5E-07 47.4 14.1 203 91-304 24-249 (260)
177 TIGR00122 birA_repr_reg BirA b 97.3 0.00064 1.4E-08 42.2 5.1 56 1-62 1-56 (69)
178 PF13412 HTH_24: Winged helix- 97.3 0.00076 1.7E-08 38.4 5.0 43 1-43 1-44 (48)
179 TIGR01729 taurine_ABC_bnd taur 97.3 0.02 4.2E-07 47.2 15.1 192 95-294 1-209 (300)
180 TIGR01884 cas_HTH CRISPR locus 97.3 0.00058 1.3E-08 52.6 5.7 58 2-63 142-203 (203)
181 PF01022 HTH_5: Bacterial regu 97.3 0.00041 8.8E-09 39.3 3.6 40 4-43 3-42 (47)
182 PF12802 MarR_2: MarR family; 97.3 0.00069 1.5E-08 41.1 4.9 43 1-43 3-48 (62)
183 PF13463 HTH_27: Winged helix 97.3 0.00057 1.2E-08 42.3 4.5 60 2-63 2-68 (68)
184 PF12974 Phosphonate-bd: ABC t 97.3 0.0087 1.9E-07 47.6 12.3 177 109-295 17-218 (243)
185 PF12840 HTH_20: Helix-turn-he 97.2 0.0014 3E-08 39.5 5.7 49 4-53 11-60 (61)
186 TIGR03414 ABC_choline_bnd chol 97.2 0.075 1.6E-06 43.5 17.3 197 92-295 7-235 (290)
187 COG1654 BirA Biotin operon rep 97.2 0.00087 1.9E-08 42.3 4.4 43 18-62 21-63 (79)
188 TIGR01276 thiB thiamine ABC tr 97.1 0.1 2.2E-06 43.2 17.1 199 93-294 2-251 (309)
189 PRK15437 histidine ABC transpo 97.1 0.074 1.6E-06 42.7 15.9 205 90-305 23-250 (259)
190 PRK10141 DNA-binding transcrip 97.1 0.015 3.2E-07 40.1 9.9 64 4-68 17-82 (117)
191 PRK15007 putative ABC transpor 97.0 0.089 1.9E-06 41.7 16.0 199 90-303 18-236 (243)
192 PF09048 Cro: Cro; InterPro: 97.0 0.00056 1.2E-08 39.6 2.3 28 19-51 15-42 (59)
193 COG4742 Predicted transcriptio 97.0 0.0084 1.8E-07 47.2 9.5 80 5-88 15-94 (260)
194 TIGR03261 phnS2 putative 2-ami 97.0 0.12 2.6E-06 43.4 17.2 203 90-294 19-273 (334)
195 cd00090 HTH_ARSR Arsenical Res 97.0 0.0045 9.7E-08 39.1 6.6 68 4-73 8-76 (78)
196 PF03180 Lipoprotein_9: NLPA l 97.0 0.13 2.7E-06 40.6 15.6 197 95-302 1-227 (237)
197 PF14947 HTH_45: Winged helix- 96.9 0.0055 1.2E-07 38.9 6.5 64 9-76 12-75 (77)
198 PF13404 HTH_AsnC-type: AsnC-t 96.9 0.0039 8.5E-08 34.2 4.9 24 18-41 19-42 (42)
199 PF09084 NMT1: NMT1/THI5 like; 96.9 0.056 1.2E-06 42.0 13.5 183 105-295 6-206 (216)
200 PHA00738 putative HTH transcri 96.9 0.0028 6.2E-08 42.1 5.0 58 4-62 13-72 (108)
201 smart00421 HTH_LUXR helix_turn 96.9 0.0042 9E-08 36.8 5.3 45 2-47 5-49 (58)
202 PF04967 HTH_10: HTH DNA bindi 96.8 0.0058 1.3E-07 35.3 5.5 43 2-44 2-51 (53)
203 TIGR03870 ABC_MoxJ methanol ox 96.8 0.19 4.1E-06 40.1 16.5 130 107-243 21-168 (246)
204 PF04069 OpuAC: Substrate bind 96.8 0.018 3.9E-07 46.3 10.1 192 94-292 2-227 (257)
205 smart00346 HTH_ICLR helix_turn 96.7 0.02 4.3E-07 37.7 8.4 63 5-71 7-73 (91)
206 PF13936 HTH_38: Helix-turn-he 96.7 0.0026 5.6E-08 35.4 3.3 34 6-39 10-43 (44)
207 PRK11480 tauA taurine transpor 96.7 0.12 2.7E-06 43.0 14.8 192 91-295 21-232 (320)
208 PF01047 MarR: MarR family; I 96.7 0.0053 1.1E-07 36.7 4.9 43 1-43 1-44 (59)
209 smart00418 HTH_ARSR helix_turn 96.6 0.0071 1.5E-07 36.7 5.4 55 13-69 8-64 (66)
210 TIGR00971 3a0106s03 sulfate/th 96.6 0.075 1.6E-06 44.1 12.8 196 94-294 12-257 (315)
211 COG2358 Imp TRAP-type uncharac 96.6 0.028 6E-07 45.9 9.4 168 91-263 24-217 (321)
212 PF00196 GerE: Bacterial regul 96.5 0.0061 1.3E-07 36.3 4.4 45 2-47 5-49 (58)
213 PRK11119 proX glycine betaine 96.5 0.09 2E-06 43.8 12.7 202 89-292 25-281 (331)
214 PRK04172 pheS phenylalanyl-tRN 96.5 0.012 2.6E-07 51.8 8.0 77 1-81 4-84 (489)
215 smart00419 HTH_CRP helix_turn_ 96.5 0.0059 1.3E-07 34.6 3.9 39 18-60 10-48 (48)
216 PRK10852 thiosulfate transport 96.5 0.26 5.7E-06 41.2 15.0 196 94-294 28-274 (338)
217 cd00092 HTH_CRP helix_turn_hel 96.4 0.0055 1.2E-07 37.7 3.7 40 18-61 27-67 (67)
218 cd06170 LuxR_C_like C-terminal 96.4 0.014 3.1E-07 34.3 5.4 45 2-47 2-46 (57)
219 PF08279 HTH_11: HTH domain; 96.4 0.019 4.1E-07 33.7 5.8 38 18-56 17-54 (55)
220 PF13011 LZ_Tnp_IS481: leucine 96.3 0.033 7.1E-07 35.6 6.8 62 6-67 15-76 (85)
221 COG4623 Predicted soluble lyti 96.3 0.16 3.4E-06 42.2 12.0 190 92-294 22-232 (473)
222 COG1339 Transcriptional regula 96.2 0.0097 2.1E-07 44.0 4.8 93 18-118 21-116 (214)
223 PF13518 HTH_28: Helix-turn-he 96.2 0.013 2.8E-07 33.9 4.6 38 6-45 3-40 (52)
224 PRK10434 srlR DNA-bindng trans 96.2 0.066 1.4E-06 42.9 10.0 40 18-61 21-60 (256)
225 PRK11205 tbpA thiamine transpo 96.2 0.6 1.3E-05 39.1 20.5 199 91-294 21-272 (330)
226 PF01638 HxlR: HxlR-like helix 96.2 0.029 6.2E-07 36.9 6.6 68 8-80 10-86 (90)
227 PF05225 HTH_psq: helix-turn-h 96.2 0.017 3.6E-07 32.2 4.5 31 10-40 9-40 (45)
228 TIGR03431 PhnD phosphonate ABC 96.2 0.56 1.2E-05 38.4 16.7 150 93-248 27-199 (288)
229 smart00345 HTH_GNTR helix_turn 96.2 0.012 2.6E-07 35.1 4.4 36 18-55 22-57 (60)
230 smart00344 HTH_ASNC helix_turn 96.1 0.015 3.3E-07 39.7 5.2 43 1-43 1-44 (108)
231 TIGR02702 SufR_cyano iron-sulf 96.1 0.018 3.9E-07 44.4 5.9 49 18-69 17-73 (203)
232 PRK09959 hybrid sensory histid 96.1 0.27 5.8E-06 49.0 15.3 143 92-246 55-213 (1197)
233 PF09862 DUF2089: Protein of u 96.0 0.032 7E-07 37.8 5.9 44 3-46 36-79 (113)
234 PF13384 HTH_23: Homeodomain-l 95.9 0.011 2.4E-07 33.8 3.2 36 6-42 8-43 (50)
235 PRK01905 DNA-binding protein F 95.9 0.019 4E-07 36.4 4.3 30 11-40 45-74 (77)
236 COG0715 TauA ABC-type nitrate/ 95.9 0.23 5.1E-06 41.6 12.2 197 92-295 30-247 (335)
237 PF01325 Fe_dep_repress: Iron 95.8 0.011 2.4E-07 35.3 3.0 26 18-43 24-49 (60)
238 PRK09959 hybrid sensory histid 95.8 0.72 1.6E-05 46.0 16.9 193 92-302 301-513 (1197)
239 PF07453 NUMOD1: NUMOD1 domain 95.8 0.0075 1.6E-07 32.1 1.9 23 14-37 15-37 (37)
240 COG1342 Predicted DNA-binding 95.8 0.014 3E-07 37.6 3.3 50 1-50 34-83 (99)
241 PF02796 HTH_7: Helix-turn-hel 95.7 0.013 2.9E-07 32.7 2.7 36 3-38 8-43 (45)
242 PRK11179 DNA-binding transcrip 95.7 0.028 6.2E-07 41.1 5.2 42 2-43 8-50 (153)
243 PRK04217 hypothetical protein; 95.6 0.04 8.7E-07 37.4 5.4 51 1-51 43-93 (110)
244 PF09114 MotA_activ: Transcrip 95.5 0.14 3E-06 32.6 6.9 73 3-79 16-91 (96)
245 PF14549 P22_Cro: DNA-binding 95.5 0.02 4.2E-07 34.1 3.0 25 11-36 5-29 (60)
246 PRK09834 DNA-binding transcrip 95.4 0.18 4E-06 40.6 9.6 62 5-68 13-76 (263)
247 PRK13509 transcriptional repre 95.4 0.35 7.6E-06 38.7 10.8 48 6-56 8-56 (251)
248 PRK11886 bifunctional biotin-- 95.4 0.043 9.3E-07 45.6 5.8 44 18-63 20-63 (319)
249 TIGR01481 ccpA catabolite cont 95.3 0.48 1E-05 39.5 12.2 109 18-149 3-122 (329)
250 COG1733 Predicted transcriptio 95.3 0.11 2.4E-06 36.1 6.9 62 14-79 35-103 (120)
251 COG1609 PurR Transcriptional r 95.3 0.23 4.9E-06 41.7 10.1 137 18-174 2-146 (333)
252 cd06171 Sigma70_r4 Sigma70, re 95.3 0.074 1.6E-06 30.6 5.3 43 2-44 12-54 (55)
253 cd07377 WHTH_GntR Winged helix 95.3 0.046 9.9E-07 33.3 4.4 40 18-60 27-66 (66)
254 COG3888 Predicted transcriptio 95.3 0.11 2.4E-06 40.5 7.2 177 19-242 23-212 (321)
255 PF02001 DUF134: Protein of un 95.2 0.026 5.6E-07 37.8 3.3 48 1-48 42-89 (106)
256 PHA02591 hypothetical protein; 95.2 0.034 7.4E-07 34.3 3.4 31 8-38 51-81 (83)
257 PRK00430 fis global DNA-bindin 95.2 0.046 9.9E-07 36.2 4.3 26 15-40 67-92 (95)
258 cd06571 Bac_DnaA_C C-terminal 95.1 0.072 1.6E-06 35.0 5.2 43 4-46 32-75 (90)
259 COG1522 Lrp Transcriptional re 95.1 0.052 1.1E-06 39.7 5.1 36 6-43 14-49 (154)
260 COG2522 Predicted transcriptio 95.1 0.03 6.4E-07 38.4 3.3 28 11-38 17-44 (119)
261 PRK11169 leucine-responsive tr 95.0 0.039 8.4E-07 40.9 4.0 42 2-43 13-55 (164)
262 PF02621 VitK2_biosynth: Menaq 95.0 0.74 1.6E-05 36.8 11.6 183 95-296 1-199 (251)
263 TIGR03427 ABC_peri_uca ABC tra 95.0 1.9 4E-05 36.1 16.7 189 93-293 2-213 (328)
264 smart00497 IENR1 Intron encode 94.9 0.029 6.3E-07 32.5 2.7 25 14-39 16-40 (53)
265 COG2508 Regulator of polyketid 94.9 0.056 1.2E-06 46.9 5.3 44 5-48 355-398 (421)
266 COG0834 HisJ ABC-type amino ac 94.9 1.7 3.6E-05 35.0 16.3 189 107-304 61-259 (275)
267 PF00325 Crp: Bacterial regula 94.8 0.035 7.6E-07 28.2 2.4 24 20-43 6-29 (32)
268 PRK09413 IS2 repressor TnpA; R 94.8 0.55 1.2E-05 32.8 9.3 38 6-43 19-56 (121)
269 PRK10906 DNA-binding transcrip 94.8 0.35 7.6E-06 38.7 9.3 36 18-56 21-56 (252)
270 TIGR01610 phage_O_Nterm phage 94.8 0.087 1.9E-06 35.0 5.0 42 2-43 24-74 (95)
271 PF09339 HTH_IclR: IclR helix- 94.7 0.07 1.5E-06 30.8 3.9 40 4-43 4-45 (52)
272 smart00420 HTH_DEOR helix_turn 94.6 0.067 1.5E-06 30.8 3.8 37 17-56 15-51 (53)
273 TIGR01254 sfuA ABC transporter 94.5 2.3 5E-05 35.1 16.9 197 93-294 2-252 (304)
274 PRK00118 putative DNA-binding 94.4 0.15 3.3E-06 34.2 5.4 42 4-45 21-62 (104)
275 COG1732 OpuBC Periplasmic glyc 94.2 1.9 4.1E-05 35.0 12.0 210 90-302 30-277 (300)
276 PF04545 Sigma70_r4: Sigma-70, 94.2 0.2 4.3E-06 28.6 5.1 37 6-42 10-46 (50)
277 PRK01686 hisG ATP phosphoribos 94.2 1.7 3.8E-05 33.6 11.4 159 124-297 47-213 (215)
278 PRK15201 fimbriae regulatory p 94.2 0.16 3.4E-06 37.4 5.3 45 1-46 134-178 (198)
279 TIGR00721 tfx DNA-binding prot 94.1 0.31 6.7E-06 34.6 6.7 77 2-79 8-89 (137)
280 PF13730 HTH_36: Helix-turn-he 94.1 0.08 1.7E-06 31.0 3.3 26 18-43 27-52 (55)
281 COG4190 Predicted transcriptio 94.1 0.29 6.3E-06 33.9 6.2 56 4-61 65-121 (144)
282 PF08281 Sigma70_r4_2: Sigma-7 94.1 0.17 3.7E-06 29.4 4.6 40 4-43 14-53 (54)
283 smart00351 PAX Paired Box doma 94.1 0.17 3.7E-06 35.5 5.4 35 9-43 26-60 (125)
284 PRK05638 threonine synthase; V 94.0 0.13 2.9E-06 44.9 5.8 63 5-70 373-441 (442)
285 TIGR03227 PhnS 2-aminoethylpho 94.0 3.4 7.4E-05 35.2 16.6 200 92-294 35-292 (367)
286 PF01379 Porphobil_deam: Porph 94.0 2.2 4.8E-05 33.0 12.8 175 94-278 1-207 (215)
287 PRK09744 DNA-binding transcrip 94.0 0.08 1.7E-06 32.5 3.0 21 15-36 10-30 (75)
288 PF08280 HTH_Mga: M protein tr 94.0 0.12 2.6E-06 30.8 3.8 50 4-55 9-58 (59)
289 PF01634 HisG: ATP phosphoribo 93.8 1.8 4E-05 31.9 10.4 149 131-294 3-162 (163)
290 PRK10411 DNA-binding transcrip 93.8 1.2 2.7E-05 35.3 10.4 36 18-56 20-55 (240)
291 COG0040 HisG ATP phosphoribosy 93.8 2.7 5.9E-05 34.0 12.1 162 124-300 45-218 (290)
292 PRK11477 carbohydrate diacid t 93.6 0.15 3.2E-06 43.7 5.3 42 7-48 325-366 (385)
293 PF13613 HTH_Tnp_4: Helix-turn 93.6 0.12 2.5E-06 30.0 3.2 39 8-47 12-50 (53)
294 cd00131 PAX Paired Box domain 93.5 0.79 1.7E-05 32.3 7.9 38 10-47 27-64 (128)
295 PRK14987 gluconate operon tran 93.5 1.1 2.3E-05 37.4 10.3 112 18-149 7-126 (331)
296 COG1349 GlpR Transcriptional r 93.5 1.1 2.3E-05 36.0 9.6 58 4-64 6-64 (253)
297 PF13551 HTH_29: Winged helix- 93.4 0.24 5.1E-06 33.9 5.2 44 7-52 3-48 (112)
298 TIGR02719 repress_PhaQ poly-be 93.4 0.36 7.7E-06 34.4 6.0 57 26-82 53-114 (138)
299 PF08220 HTH_DeoR: DeoR-like h 93.3 0.23 5E-06 29.3 4.2 43 10-56 9-51 (57)
300 PRK03975 tfx putative transcri 93.2 0.87 1.9E-05 32.6 7.7 77 2-79 8-89 (141)
301 PF04297 UPF0122: Putative hel 93.2 0.17 3.6E-06 33.7 3.9 41 4-44 21-61 (101)
302 PF01710 HTH_Tnp_IS630: Transp 93.2 0.13 2.8E-06 35.8 3.6 43 1-44 57-99 (119)
303 PRK10423 transcriptional repre 93.2 0.8 1.7E-05 38.1 9.0 110 20-149 2-119 (327)
304 COG3221 PhnD ABC-type phosphat 93.2 4.2 9E-05 33.5 15.1 194 93-295 35-259 (299)
305 TIGR03433 padR_acidobact trans 93.1 0.44 9.5E-06 32.0 5.9 55 25-82 34-96 (100)
306 PF05344 DUF746: Domain of Unk 93.1 0.29 6.3E-06 29.4 4.3 40 5-44 2-41 (65)
307 cd00569 HTH_Hin_like Helix-tur 93.0 0.25 5.4E-06 25.8 4.0 33 5-37 10-42 (42)
308 COG4189 Predicted transcriptio 92.9 0.22 4.8E-06 38.2 4.6 27 17-43 38-64 (308)
309 COG2771 CsgD DNA-binding HTH d 92.9 0.43 9.2E-06 28.8 5.3 45 2-47 6-50 (65)
310 PRK10163 DNA-binding transcrip 92.8 0.62 1.3E-05 37.8 7.5 57 5-63 27-85 (271)
311 PHA00542 putative Cro-like pro 92.8 0.25 5.5E-06 31.7 4.2 32 6-37 21-52 (82)
312 COG0181 HemC Porphobilinogen d 92.6 4.8 0.0001 32.8 11.9 141 93-243 2-166 (307)
313 PF00356 LacI: Bacterial regul 92.6 0.15 3.2E-06 28.6 2.6 21 18-38 1-21 (46)
314 PRK10752 sulfate transporter s 92.6 3.6 7.7E-05 34.5 11.8 101 94-199 24-146 (329)
315 PF05043 Mga: Mga helix-turn-h 92.6 0.17 3.8E-06 32.9 3.3 44 12-60 27-73 (87)
316 PRK09802 DNA-binding transcrip 92.6 1.9 4E-05 35.0 9.9 36 18-56 33-68 (269)
317 PRK15320 transcriptional activ 92.3 0.42 9.1E-06 35.9 5.3 45 2-47 166-210 (251)
318 PF08222 HTH_CodY: CodY helix- 92.3 0.21 4.5E-06 28.9 2.8 25 19-43 7-31 (61)
319 TIGR00498 lexA SOS regulatory 92.2 0.37 7.9E-06 37.0 5.3 41 2-43 5-53 (199)
320 COG1497 Predicted transcriptio 92.2 1.4 3E-05 34.3 8.0 60 5-67 14-73 (260)
321 TIGR02431 pcaR_pcaU beta-ketoa 92.1 0.72 1.6E-05 36.8 7.0 54 6-63 12-67 (248)
322 PRK10727 DNA-binding transcrip 92.1 1.6 3.5E-05 36.7 9.4 109 18-149 3-122 (343)
323 PRK00082 hrcA heat-inducible t 91.9 0.31 6.7E-06 40.8 4.8 50 18-69 27-78 (339)
324 PF14424 Toxin-deaminase: The 91.8 1.1 2.4E-05 31.8 6.8 36 93-129 97-132 (133)
325 PRK10840 transcriptional regul 91.6 0.48 1E-05 36.8 5.4 45 2-47 152-196 (216)
326 TIGR03879 near_KaiC_dom probab 91.6 0.29 6.3E-06 30.4 3.2 28 15-42 31-58 (73)
327 smart00550 Zalpha Z-DNA-bindin 91.6 0.57 1.2E-05 28.8 4.6 36 8-43 11-49 (68)
328 COG4197 Uncharacterized protei 91.5 0.38 8.1E-06 31.0 3.7 33 6-39 3-35 (96)
329 TIGR02531 yecD_yerC TrpR-relat 91.4 0.41 8.9E-06 31.1 3.9 32 6-38 41-72 (88)
330 PRK10703 DNA-binding transcrip 91.3 1.8 3.9E-05 36.3 9.0 112 18-149 3-122 (341)
331 PRK10401 DNA-binding transcrip 91.3 2.1 4.6E-05 36.0 9.4 109 18-149 3-122 (346)
332 TIGR03541 reg_near_HchA LuxR f 91.2 0.53 1.2E-05 37.1 5.3 44 2-46 173-216 (232)
333 PF13542 HTH_Tnp_ISL3: Helix-t 91.2 0.53 1.2E-05 27.0 4.0 31 8-39 20-50 (52)
334 PF03444 HrcA_DNA-bdg: Winged 91.2 1.9 4.1E-05 27.1 6.5 61 2-68 3-74 (78)
335 PRK10188 DNA-binding transcrip 91.1 0.58 1.2E-05 37.2 5.4 45 2-47 181-225 (240)
336 PF01978 TrmB: Sugar-specific 91.1 0.3 6.4E-06 30.0 3.0 39 5-43 10-49 (68)
337 PF04218 CENP-B_N: CENP-B N-te 91.1 0.74 1.6E-05 26.7 4.5 36 6-42 13-48 (53)
338 TIGR00070 hisG ATP phosphoribo 91.0 2 4.4E-05 32.3 7.8 95 124-228 42-141 (182)
339 cd04763 HTH_MlrA-like Helix-Tu 91.0 1.2 2.7E-05 27.2 5.8 53 17-73 1-53 (68)
340 PRK11569 transcriptional repre 90.8 1.9 4.1E-05 35.1 8.2 55 6-62 31-87 (274)
341 PLN02245 ATP phosphoribosyl tr 90.7 7.1 0.00015 33.3 11.5 171 124-300 113-303 (403)
342 COG1464 NlpA ABC-type metal io 90.7 7.5 0.00016 31.1 13.9 204 93-303 29-259 (268)
343 PRK11303 DNA-binding transcrip 90.6 3.2 7E-05 34.5 9.8 111 18-149 2-124 (328)
344 PRK11475 DNA-binding transcrip 90.6 0.73 1.6E-05 35.6 5.4 44 2-46 136-179 (207)
345 PRK15411 rcsA colanic acid cap 90.6 0.7 1.5E-05 35.8 5.3 44 2-46 139-182 (207)
346 PRK13719 conjugal transfer tra 90.5 0.79 1.7E-05 35.3 5.3 44 2-46 145-188 (217)
347 COG3355 Predicted transcriptio 90.5 0.84 1.8E-05 31.8 5.0 46 4-52 28-75 (126)
348 TIGR02417 fruct_sucro_rep D-fr 90.1 3 6.6E-05 34.7 9.2 110 18-149 1-123 (327)
349 COG1414 IclR Transcriptional r 90.1 3.6 7.9E-05 32.8 9.1 57 5-65 6-66 (246)
350 COG2739 Uncharacterized protei 90.0 0.47 1E-05 31.2 3.2 40 5-44 22-61 (105)
351 PF01527 HTH_Tnp_1: Transposas 89.9 0.6 1.3E-05 29.3 3.8 36 6-41 13-48 (76)
352 PRK06474 hypothetical protein; 89.9 0.97 2.1E-05 34.0 5.4 41 3-43 11-54 (178)
353 cd04762 HTH_MerR-trunc Helix-T 89.8 0.38 8.2E-06 26.9 2.6 22 18-39 2-23 (49)
354 PRK09483 response regulator; P 89.7 0.87 1.9E-05 35.1 5.4 44 2-46 150-193 (217)
355 PRK01066 porphobilinogen deami 89.7 8.4 0.00018 30.1 17.3 183 92-290 15-225 (231)
356 PRK09775 putative DNA-binding 89.6 0.44 9.6E-06 41.4 3.8 26 14-40 12-37 (442)
357 PRK13870 transcriptional regul 89.5 0.93 2E-05 35.8 5.3 45 2-47 175-219 (234)
358 cd04764 HTH_MlrA-like_sg1 Heli 89.5 1.8 4E-05 26.3 5.6 53 17-74 1-53 (67)
359 PRK10014 DNA-binding transcrip 89.5 5.7 0.00012 33.2 10.5 112 18-149 8-127 (342)
360 PF01726 LexA_DNA_bind: LexA D 89.4 0.6 1.3E-05 28.4 3.3 25 18-42 27-52 (65)
361 PRK00072 hemC porphobilinogen 89.3 11 0.00023 30.9 17.1 183 93-291 3-218 (295)
362 TIGR01764 excise DNA binding d 89.3 0.44 9.5E-06 26.7 2.5 22 18-39 3-24 (49)
363 COG2512 Predicted membrane-ass 89.3 0.91 2E-05 36.3 5.0 58 3-60 195-254 (258)
364 PRK09954 putative kinase; Prov 89.2 0.8 1.7E-05 38.9 5.1 54 1-60 1-55 (362)
365 PF12728 HTH_17: Helix-turn-he 89.2 0.43 9.4E-06 27.3 2.5 22 18-39 3-24 (51)
366 cd00494 HMBS Hydroxymethylbila 89.1 11 0.00024 30.8 16.6 181 95-291 1-214 (292)
367 TIGR01321 TrpR trp operon repr 89.0 0.7 1.5E-05 30.3 3.5 33 6-38 45-77 (94)
368 PF08461 HTH_12: Ribonuclease 88.9 0.44 9.5E-06 29.1 2.4 37 27-66 29-65 (66)
369 PRK15046 2-aminoethylphosphona 88.9 13 0.00029 31.4 16.5 98 90-191 32-157 (349)
370 PF13744 HTH_37: Helix-turn-he 88.6 0.41 9E-06 30.5 2.3 24 15-38 30-53 (80)
371 COG1568 Predicted methyltransf 88.4 1.7 3.8E-05 34.7 5.9 57 7-68 26-82 (354)
372 TIGR02405 trehalos_R_Ecol treh 88.4 13 0.00028 30.7 12.5 21 18-38 3-23 (311)
373 PRK00215 LexA repressor; Valid 88.4 1.2 2.7E-05 34.3 5.3 42 2-43 3-51 (205)
374 COG1910 Periplasmic molybdate- 88.1 0.27 5.7E-06 37.5 1.3 48 130-177 138-185 (223)
375 PF03401 TctC: Tripartite tric 88.0 8.7 0.00019 31.2 10.1 137 162-305 74-240 (274)
376 PRK09526 lacI lac repressor; R 88.0 15 0.00032 30.8 12.5 112 18-149 7-127 (342)
377 PRK15090 DNA-binding transcrip 88.0 4.5 9.7E-05 32.5 8.4 45 17-65 29-75 (257)
378 PF07022 Phage_CI_repr: Bacter 87.6 0.35 7.5E-06 29.6 1.4 32 6-38 3-35 (66)
379 PRK10100 DNA-binding transcrip 87.4 1.6 3.4E-05 34.1 5.3 44 2-46 157-200 (216)
380 PF05732 RepL: Firmicute plasm 87.4 0.68 1.5E-05 34.2 3.1 42 18-62 77-118 (165)
381 PF12727 PBP_like: PBP superfa 87.1 0.57 1.2E-05 35.8 2.7 50 127-176 129-179 (193)
382 TIGR02684 dnstrm_HI1420 probab 87.1 1.2 2.5E-05 29.1 3.7 30 7-37 35-64 (89)
383 PRK10651 transcriptional regul 87.0 1.6 3.6E-05 33.4 5.3 43 3-46 158-200 (216)
384 PF13309 HTH_22: HTH domain 86.9 0.37 8.1E-06 29.2 1.3 20 18-37 44-63 (64)
385 cd01104 HTH_MlrA-CarA Helix-Tu 86.9 3.5 7.6E-05 25.1 5.7 53 17-73 1-53 (68)
386 COG1458 Predicted DNA-binding 86.8 1 2.2E-05 33.6 3.6 93 26-121 49-152 (221)
387 PF01418 HTH_6: Helix-turn-hel 86.5 0.56 1.2E-05 29.7 2.0 25 15-40 34-58 (77)
388 PRK13325 bifunctional biotin-- 86.4 2 4.4E-05 39.0 6.1 50 5-56 8-58 (592)
389 COG1725 Predicted transcriptio 86.4 6.6 0.00014 27.4 7.2 67 15-85 35-103 (125)
390 PHA02943 hypothetical protein; 86.3 10 0.00022 27.3 9.2 52 10-61 17-69 (165)
391 PRK13583 hisG ATP phosphoribos 86.3 14 0.00031 28.9 10.0 148 124-279 47-212 (228)
392 PF02042 RWP-RK: RWP-RK domain 86.2 1 2.2E-05 25.9 2.7 22 18-39 17-38 (52)
393 PF02376 CUT: CUT domain; Int 86.2 1.2 2.6E-05 28.9 3.4 49 22-83 33-81 (87)
394 TIGR02277 PaaX_trns_reg phenyl 86.0 1.9 4.2E-05 35.1 5.2 78 15-102 20-97 (280)
395 cd04761 HTH_MerR-SF Helix-Turn 85.8 0.88 1.9E-05 25.6 2.4 21 17-37 1-21 (49)
396 PRK09492 treR trehalose repres 85.7 8.4 0.00018 31.8 9.2 21 18-38 6-26 (315)
397 PRK12423 LexA repressor; Provi 85.5 2.4 5.2E-05 32.6 5.4 41 2-43 5-53 (202)
398 TIGR02944 suf_reg_Xantho FeS a 85.1 2.2 4.8E-05 30.1 4.7 37 6-42 12-51 (130)
399 COG3877 Uncharacterized protei 85.1 5 0.00011 26.6 5.7 46 2-47 43-88 (122)
400 PRK15369 two component system 85.0 2.4 5.2E-05 32.2 5.3 43 3-46 152-194 (211)
401 PRK10681 DNA-binding transcrip 84.7 12 0.00027 29.9 9.3 38 5-42 9-47 (252)
402 PF13545 HTH_Crp_2: Crp-like h 84.7 1.5 3.3E-05 27.4 3.4 41 18-62 30-70 (76)
403 PF01316 Arg_repressor: Argini 84.7 1.6 3.4E-05 27.0 3.2 17 26-42 34-50 (70)
404 PRK09333 30S ribosomal protein 84.6 2.4 5.2E-05 30.5 4.5 40 29-72 94-133 (150)
405 COG3388 Predicted transcriptio 84.5 7.5 0.00016 25.3 6.2 68 4-76 15-84 (101)
406 PRK10403 transcriptional regul 84.5 2.6 5.6E-05 32.2 5.3 44 2-46 155-198 (215)
407 smart00094 TR_FER Transferrin. 84.4 21 0.00045 30.0 10.7 75 121-200 26-115 (332)
408 PF14502 HTH_41: Helix-turn-he 84.3 3.5 7.7E-05 23.1 4.1 38 18-55 8-45 (48)
409 COG2197 CitB Response regulato 84.2 3 6.4E-05 32.4 5.4 45 2-47 150-194 (211)
410 COG1510 Predicted transcriptio 84.1 1.3 2.9E-05 32.4 3.2 35 18-52 43-78 (177)
411 PF09012 FeoC: FeoC like trans 83.8 1.7 3.7E-05 26.7 3.2 39 3-42 2-40 (69)
412 PRK13182 racA polar chromosome 83.7 3.4 7.4E-05 30.9 5.2 54 18-76 2-55 (175)
413 COG4588 AcfC Accessory coloniz 83.6 18 0.00038 27.7 15.2 198 90-298 18-243 (252)
414 COG3415 Transposase and inacti 83.5 6 0.00013 28.3 6.1 54 7-62 12-67 (138)
415 COG2345 Predicted transcriptio 83.5 9.6 0.00021 29.6 7.7 49 18-67 27-81 (218)
416 PF13343 SBP_bac_6: Bacterial 83.4 10 0.00023 29.9 8.5 136 160-298 49-204 (242)
417 PRK09958 DNA-binding transcrip 83.2 3.3 7.2E-05 31.4 5.4 43 3-46 146-188 (204)
418 PF11972 HTH_13: HTH DNA bindi 83.1 1.9 4.2E-05 24.9 2.9 25 18-42 15-39 (54)
419 PF01710 HTH_Tnp_IS630: Transp 83.1 1.8 3.9E-05 30.1 3.4 34 10-46 13-46 (119)
420 PRK09416 lstR lineage-specific 82.3 3.2 7E-05 29.3 4.4 54 26-80 73-128 (135)
421 PF00392 GntR: Bacterial regul 82.1 2.1 4.5E-05 25.8 3.1 26 18-43 26-51 (64)
422 cd01392 HTH_LacI Helix-turn-he 82.1 0.9 1.9E-05 26.0 1.4 17 21-37 2-18 (52)
423 PF12116 SpoIIID: Stage III sp 81.7 4 8.6E-05 25.7 4.1 33 6-38 9-41 (82)
424 TIGR00331 hrcA heat shock gene 81.5 3.1 6.7E-05 34.9 4.8 48 18-69 23-74 (337)
425 cd04765 HTH_MlrA-like_sg2 Heli 81.3 7.5 0.00016 26.0 5.8 55 17-75 1-55 (99)
426 PF01381 HTH_3: Helix-turn-hel 81.3 1.7 3.6E-05 25.2 2.4 25 14-38 7-31 (55)
427 COG3432 Predicted transcriptio 81.2 6.4 0.00014 25.9 5.1 56 18-76 33-91 (95)
428 PF04703 FaeA: FaeA-like prote 81.2 2.1 4.6E-05 25.7 2.8 38 6-44 6-43 (62)
429 PRK09863 putative frv operon r 81.1 2.4 5.2E-05 38.7 4.4 42 18-60 94-137 (584)
430 PF01371 Trp_repressor: Trp re 81.0 7.4 0.00016 25.3 5.3 38 5-42 38-75 (87)
431 PF01090 Ribosomal_S19e: Ribos 80.6 2.1 4.5E-05 30.4 3.0 36 31-70 95-131 (139)
432 TIGR00635 ruvB Holliday juncti 80.6 3.9 8.5E-05 33.7 5.2 62 4-68 239-304 (305)
433 PRK12527 RNA polymerase sigma 79.9 5.7 0.00012 29.0 5.4 45 3-47 108-152 (159)
434 PF00165 HTH_AraC: Bacterial r 79.8 2.6 5.6E-05 22.8 2.7 22 18-39 10-31 (42)
435 PF00376 MerR: MerR family reg 79.6 1.2 2.7E-05 23.6 1.3 22 18-43 1-22 (38)
436 smart00354 HTH_LACI helix_turn 79.6 1.8 3.8E-05 26.8 2.2 20 18-37 2-21 (70)
437 COG2963 Transposase and inacti 79.3 18 0.00038 24.9 9.0 45 6-50 14-59 (116)
438 PRK09047 RNA polymerase factor 79.3 6.1 0.00013 28.9 5.4 44 5-48 111-154 (161)
439 PF03551 PadR: Transcriptional 79.2 3.4 7.3E-05 25.8 3.4 43 26-68 27-74 (75)
440 TIGR00212 hemC porphobilinogen 79.0 34 0.00075 28.0 16.5 181 95-291 1-214 (292)
441 PF06322 Phage_NinH: Phage Nin 78.9 4.5 9.9E-05 23.9 3.5 32 12-44 13-44 (64)
442 PRK12546 RNA polymerase sigma 78.9 3.7 8.1E-05 31.2 4.2 49 4-52 117-165 (188)
443 COG3835 CdaR Sugar diacid util 78.6 3.2 6.9E-05 34.3 3.8 36 12-48 322-357 (376)
444 PRK09935 transcriptional regul 78.5 5.8 0.00013 30.1 5.4 43 4-47 153-195 (210)
445 PF13443 HTH_26: Cro/C1-type H 77.7 4 8.6E-05 24.3 3.3 27 12-38 6-32 (63)
446 cd00283 GIY-YIG_Cterm GIYX(10- 77.6 2.3 5.1E-05 29.2 2.5 26 13-39 78-103 (113)
447 PRK11564 stationary phase indu 77.3 3.8 8.3E-05 35.7 4.3 42 18-60 32-77 (426)
448 PF06056 Terminase_5: Putative 77.2 6.3 0.00014 23.3 3.9 31 11-41 8-38 (58)
449 PF07750 GcrA: GcrA cell cycle 77.0 4.1 8.9E-05 30.1 3.8 37 4-40 6-43 (162)
450 PRK09590 celB cellobiose phosp 77.0 18 0.0004 24.4 6.6 55 94-149 3-57 (104)
451 PRK10344 DNA-binding transcrip 76.9 5.5 0.00012 25.7 3.8 36 2-37 7-42 (92)
452 PHA01976 helix-turn-helix prot 76.9 5.7 0.00012 24.0 3.9 22 15-36 14-35 (67)
453 PLN02691 porphobilinogen deami 76.8 45 0.00096 28.2 17.0 184 92-291 41-261 (351)
454 COG0640 ArsR Predicted transcr 76.8 18 0.00039 23.6 8.5 50 5-55 27-77 (110)
455 TIGR02960 SigX5 RNA polymerase 76.6 31 0.00068 28.7 9.5 68 7-75 149-218 (324)
456 TIGR03697 NtcA_cyano global ni 76.6 2.1 4.5E-05 32.5 2.3 40 18-61 145-184 (193)
457 PRK09642 RNA polymerase sigma 76.5 8.2 0.00018 28.2 5.4 43 6-48 112-154 (160)
458 PLN02853 Probable phenylalanyl 76.4 9.5 0.00021 33.6 6.3 62 6-69 6-70 (492)
459 PRK08359 transcription factor; 76.2 4.3 9.2E-05 30.3 3.7 39 14-52 96-145 (176)
460 PTZ00326 phenylalanyl-tRNA syn 76.2 10 0.00022 33.6 6.4 62 5-69 8-73 (494)
461 COG2113 ProX ABC-type proline/ 75.8 44 0.00096 27.6 12.5 197 89-291 27-254 (302)
462 PRK12511 RNA polymerase sigma 75.7 8.4 0.00018 29.0 5.3 40 5-44 116-155 (182)
463 KOG2892|consensus 75.7 41 0.00088 27.2 10.5 58 92-149 5-83 (320)
464 TIGR02959 SigZ RNA polymerase 75.2 9.4 0.0002 28.3 5.4 43 4-46 104-146 (170)
465 PTZ00095 40S ribosomal protein 74.9 7.1 0.00015 28.7 4.4 39 29-71 118-158 (169)
466 PRK00441 argR arginine repress 74.8 4.6 0.0001 29.3 3.5 29 13-42 16-49 (149)
467 PRK06704 RNA polymerase factor 74.8 9 0.0002 30.2 5.4 43 5-47 121-163 (228)
468 PRK03341 arginine repressor; P 74.8 4.6 9.9E-05 30.0 3.5 25 18-42 31-60 (168)
469 PRK12516 RNA polymerase sigma 74.7 9.1 0.0002 29.0 5.3 42 4-45 120-161 (187)
470 TIGR00738 rrf2_super rrf2 fami 74.7 15 0.00032 25.9 6.1 47 18-66 27-74 (132)
471 TIGR02787 codY_Gpos GTP-sensin 74.7 4.1 8.9E-05 31.9 3.3 48 18-67 200-248 (251)
472 PF02082 Rrf2: Transcriptional 74.5 7.6 0.00017 24.8 4.2 55 6-62 11-70 (83)
473 TIGR03070 couple_hipB transcri 74.4 3.1 6.7E-05 24.1 2.2 24 14-37 13-36 (58)
474 PF13560 HTH_31: Helix-turn-he 74.4 2.9 6.3E-05 25.2 2.1 22 15-36 13-34 (64)
475 PRK12524 RNA polymerase sigma 74.3 9.3 0.0002 29.1 5.3 43 5-47 141-183 (196)
476 PRK10622 pheA bifunctional cho 74.2 57 0.0012 28.1 13.1 147 94-250 103-260 (386)
477 PRK12520 RNA polymerase sigma 74.1 9.6 0.00021 28.9 5.4 44 5-48 136-179 (191)
478 PRK15431 ferrous iron transpor 74.1 12 0.00025 23.7 4.6 41 2-43 3-43 (78)
479 TIGR02844 spore_III_D sporulat 73.9 6.9 0.00015 24.9 3.7 34 4-37 7-40 (80)
480 PF04552 Sigma54_DBD: Sigma-54 73.9 1 2.3E-05 33.0 0.0 22 18-39 51-72 (160)
481 PRK07377 hypothetical protein; 73.8 28 0.0006 26.1 7.2 57 91-149 73-136 (184)
482 PRK12533 RNA polymerase sigma 73.8 8.5 0.00018 30.0 5.0 45 4-48 138-182 (216)
483 TIGR02607 antidote_HigA addict 73.4 4.6 9.9E-05 25.3 2.9 24 13-36 15-38 (78)
484 PF00292 PAX: 'Paired box' dom 73.4 8.5 0.00018 26.9 4.3 61 9-71 26-88 (125)
485 COG1427 Predicted periplasmic 73.3 45 0.00098 26.6 9.1 113 124-250 25-144 (252)
486 PRK09647 RNA polymerase sigma 73.2 11 0.00023 29.1 5.4 44 5-48 143-186 (203)
487 PRK12540 RNA polymerase sigma 72.8 11 0.00023 28.5 5.3 41 4-44 115-155 (182)
488 PRK12542 RNA polymerase sigma 72.8 11 0.00023 28.5 5.3 45 4-48 126-170 (185)
489 PRK12545 RNA polymerase sigma 72.6 11 0.00023 29.0 5.3 44 5-48 144-187 (201)
490 PRK09391 fixK transcriptional 72.1 4.3 9.3E-05 32.0 3.1 40 18-61 181-221 (230)
491 smart00422 HTH_MERR helix_turn 72.1 19 0.00042 21.8 5.6 51 17-73 1-53 (70)
492 TIGR02647 DNA conserved hypoth 71.9 9.9 0.00021 23.7 3.8 59 17-77 17-75 (77)
493 cd02395 SF1_like-KH Splicing f 71.8 6.7 0.00014 27.3 3.6 20 35-54 26-45 (120)
494 PRK09644 RNA polymerase sigma 71.7 12 0.00026 27.6 5.2 44 4-48 112-156 (165)
495 PF07900 DUF1670: Protein of u 71.2 7.4 0.00016 30.0 3.9 48 5-52 92-141 (220)
496 COG1570 XseA Exonuclease VII, 71.1 19 0.00041 31.3 6.7 95 91-189 132-243 (440)
497 COG2238 RPS19A Ribosomal prote 71.1 8.8 0.00019 27.1 3.9 46 29-78 94-140 (147)
498 COG5625 Predicted transcriptio 71.0 20 0.00044 23.7 5.3 83 5-87 23-110 (113)
499 PRK13918 CRP/FNR family transc 71.0 5 0.00011 30.7 3.2 41 18-62 151-191 (202)
500 PF06970 RepA_N: Replication i 70.6 3.5 7.6E-05 26.0 1.8 24 17-40 53-76 (76)
No 1
>PRK12681 cysB transcriptional regulator CysB; Reviewed
Probab=100.00 E-value=1.7e-58 Score=381.34 Aligned_cols=302 Identities=45% Similarity=0.789 Sum_probs=277.9
Q ss_pred CchhhHHHHHHHHHh-cCCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCCccccCHhHHHHHHHHHHHHHHHHH
Q psy3760 1 MNLHQFRFVREAVRQ-NFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKPGQAILRSIEIIMQEIEG 79 (306)
Q Consensus 1 m~~~~l~~f~~v~~~-~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~~~lT~~G~~l~~~a~~il~~~~~ 79 (306)
|++++|+||++|+++ | ||++||++||+||||||++|++||++||++||+|+++++.+||++|+.|+++++++++.+++
T Consensus 1 M~~~~L~~f~avae~g~-S~s~AA~~L~iSQpavS~~I~~LE~~lG~~LF~R~~r~~~~LT~~G~~l~~~a~~il~~~~~ 79 (324)
T PRK12681 1 MKLQQLRYIVEVVNHNL-NVSATAEGLYTSQPGISKQVRMLEDELGIQIFARSGKHLTQVTPAGEEIIRIAREILSKVES 79 (324)
T ss_pred CCHHHHHHHHHHHHccC-CHHHHHHHhcCCcHHHHHHHHHHHHHhCCEeEEECCCCCCccCHHHHHHHHHHHHHHHHHHH
Confidence 899999999999999 7 99999999999999999999999999999999999999723999999999999999999999
Q ss_pred HHHHHHhhccCCCCcEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccCCCCCce
Q psy3760 80 LKKIGKEFSAYDTGNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLI 159 (306)
Q Consensus 80 ~~~~~~~~~~~~~~~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~~~~~~ 159 (306)
+...+.+......|+|+||++++++..++++++..|.+.||++++++....++++.+.|.+|++|++|+..+....+++.
T Consensus 80 ~~~~~~~~~~~~~g~l~Ig~~~~~~~~~l~~~l~~f~~~~P~i~i~i~~~~~~~~~~~L~~g~iDl~i~~~~~~~~~~l~ 159 (324)
T PRK12681 80 IKSVAGEHTWPDKGSLYIATTHTQARYALPPVIKGFIERYPRVSLHMHQGSPTQIAEAAAKGNADFAIATEALHLYDDLI 159 (324)
T ss_pred HHHHHHHhhCCCCCeEEEEechhHHHHhhHHHHHHHHHHCCCcEEEEEeCCHHHHHHHHHcCCCCEEEecCcccCCCCeE
Confidence 99999888777889999999999999999999999999999999999999999999999999999999865423356789
Q ss_pred eeccccceEEEEecCCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCceeEEEEecCHHHHHHHHHhccc
Q psy3760 160 SIPCYQWEYVIIVPLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMG 239 (306)
Q Consensus 160 ~~~l~~~~~~~v~~~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~g 239 (306)
+.+++.++++++++++||++....++++||.++||+.+..+...+..++.++...|+.|++.+++++..++..++.+|.|
T Consensus 160 ~~~l~~~~~~~v~~~~hpl~~~~~~~~~~L~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~v~~g~G 239 (324)
T PRK12681 160 MLPCYHWNRSVVVPPDHPLAKKKKLTIEELAQYPLVTYVFGFTGRSELDTAFNRAGLTPRIVFTATDADVIKTYVRLGLG 239 (324)
T ss_pred EEEeccceeEEEeCCCChhhcCCCcCHHHHhCCCeEeccCCCchHHHHHHHHHHcCCCCceEEEeCCHHHHHHHHHhCCC
Confidence 99999999999999999999888899999999999999887777778888898899999999999999999999999999
Q ss_pred eeeeecceecccccCCceeeecCCCCccceEEEEEeCCccccHHHHHHHHHHhHHhhHHHHHhh
Q psy3760 240 IGIIASIAFDSNRDKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLLSPKLNRKFINKI 303 (306)
Q Consensus 240 i~~~p~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~ 303 (306)
++++|.+.......++++.+++++......++++|+++...++.++.|++++++.+.+..++.+
T Consensus 240 i~~lp~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~fi~~~~~~~~~~~~~~~ 303 (324)
T PRK12681 240 VGVIASMAVDPVADPDLVAIDASHLFSHSTTKIGFRRGTFLRSYMYDFIERFAPHLTRDVVEKA 303 (324)
T ss_pred EEEeehhhcccccCCceEEeecCCCCCceEEEEEEECCchhhHHHHHHHHHHHHHHHHHHHHHH
Confidence 9999998776554578999998775667799999999999999999999999999888877653
No 2
>PRK12682 transcriptional regulator CysB-like protein; Reviewed
Probab=100.00 E-value=1.5e-58 Score=380.84 Aligned_cols=303 Identities=56% Similarity=0.963 Sum_probs=279.1
Q ss_pred CchhhHHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCCccccCHhHHHHHHHHHHHHHHHHHH
Q psy3760 1 MNLHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKPGQAILRSIEIIMQEIEGL 80 (306)
Q Consensus 1 m~~~~l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~~~lT~~G~~l~~~a~~il~~~~~~ 80 (306)
|++++|+||++++++|+||++||++||+||||||++|++||++||++||+|++++++.||++|+.|++++++++++++++
T Consensus 1 m~l~~L~~F~~v~~~~~s~s~AA~~L~isq~avSr~I~~LE~~lg~~LF~R~~~~~~~lT~~G~~l~~~~~~~l~~~~~~ 80 (309)
T PRK12682 1 MNLQQLRFVREAVRRNLNLTEAAKALHTSQPGVSKAIIELEEELGIEIFIRHGKRLKGLTEPGKAVLDVIERILREVGNI 80 (309)
T ss_pred CCHHHHHHHHHHHHccCCHHHHHHHhcCccHHHHHHHHHHHHHhCCeeEEECCCCcCccCHhHHHHHHHHHHHHHHHHHH
Confidence 89999999999999844999999999999999999999999999999999999996259999999999999999999999
Q ss_pred HHHHHhhccCCCCcEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccCCCCCcee
Q psy3760 81 KKIGKEFSAYDTGNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLIS 160 (306)
Q Consensus 81 ~~~~~~~~~~~~~~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~~~~~~~ 160 (306)
...+........|.|+||++++++..++++++..|.+.||++++++...+.+++.+.|.+|++|++|+..+....+++.+
T Consensus 81 ~~~~~~~~~~~~g~l~Ig~~~~~~~~~l~~~l~~~~~~~P~i~i~i~~~~~~~~~~~l~~g~~D~~i~~~~~~~~~~l~~ 160 (309)
T PRK12682 81 KRIGDDFSNQDSGTLTIATTHTQARYVLPRVVAAFRKRYPKVNLSLHQGSPDEIARMVISGEADIGIATESLADDPDLAT 160 (309)
T ss_pred HHHHHHhcCCCCCeEEEeeCchHHHHHHHHHHHHHHHhCCCeEEEEecCCHHHHHHHHHcCCccEEEecCcccCCCcceE
Confidence 99998888888899999999999999999999999999999999999999999999999999999998644334678999
Q ss_pred eccccceEEEEecCCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCceeEEEEecCHHHHHHHHHhccce
Q psy3760 161 IPCYQWEYVIIVPLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMGI 240 (306)
Q Consensus 161 ~~l~~~~~~~v~~~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi 240 (306)
.++++++++++++++||++.+..++++||.++|++.+..+...+..++.++...|+.+++.+++++..++++++..|.|+
T Consensus 161 ~~l~~~~~~~~~~~~~pl~~~~~~~~~~L~~~~~i~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~v~~g~Gi 240 (309)
T PRK12682 161 LPCYDWQHAVIVPPDHPLAQEERITLEDLAEYPLITYHPGFTGRSRIDRAFAAAGLQPDIVLEAIDSDVIKTYVRLGLGV 240 (309)
T ss_pred EEeeeeeEEEEecCCCccccCCCcCHHHHhcCCceeeCCCccHHHHHHHHHHHcCCCCcEEEEeCCHHHHHHHHHhCCce
Confidence 99999999999999999998778999999999999998876677788899999999999999999999999999999999
Q ss_pred eeeecceecccccCCceeeecCCCCccceEEEEEeCCccccHHHHHHHHHHhHHhhHHHHHhh
Q psy3760 241 GIIASIAFDSNRDKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLLSPKLNRKFINKI 303 (306)
Q Consensus 241 ~~~p~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~ 303 (306)
+++|.+.+.....++++.+|+.+......+|++|+++...++.++.|++++++.+..+.+.++
T Consensus 241 ~~lp~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~f~~~l~~~~~~~~~~~~ 303 (309)
T PRK12682 241 GIVAEMAYRPDRDGDLVALPAGHLFGPNTAWVALKRGAYLRNYVYKFIELCAPHLSRELIKRA 303 (309)
T ss_pred EEehhhhhhhccCCcEEEeeCCCCCcceeEEEeeecCCcCCHHHHHHHHHHHHHcCcHHHHHH
Confidence 999998776545788999999875556789999999999999999999999999999888775
No 3
>PRK12683 transcriptional regulator CysB-like protein; Reviewed
Probab=100.00 E-value=3.2e-58 Score=377.98 Aligned_cols=304 Identities=50% Similarity=0.891 Sum_probs=279.0
Q ss_pred CchhhHHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCCccccCHhHHHHHHHHHHHHHHHHHH
Q psy3760 1 MNLHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKPGQAILRSIEIIMQEIEGL 80 (306)
Q Consensus 1 m~~~~l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~~~lT~~G~~l~~~a~~il~~~~~~ 80 (306)
||+++|++|++++++|+||++||++||+||||+|++|++||++||++||+|++++++.||++|+.|++++++++..++++
T Consensus 1 m~~~~L~~F~~v~~~~~S~s~AA~~L~isQpavS~~I~~LE~~lg~~Lf~R~~r~~~~lT~~G~~l~~~a~~il~~~~~~ 80 (309)
T PRK12683 1 MNFQQLRIIREAVRQNFNLTEVANALYTSQSGVSKQIKDLEDELGVEIFIRRGKRLTGLTEPGKELLQIVERMLLDAENL 80 (309)
T ss_pred CCHHHHHHHHHHHHccCCHHHHHHHhcCCcHHHHHHHHHHHHHhCCeeEeeCCCCcCCcCHHHHHHHHHHHHHHHHHHHH
Confidence 89999999999999833999999999999999999999999999999999999996149999999999999999999999
Q ss_pred HHHHHhhccCCCCcEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccCCCCCcee
Q psy3760 81 KKIGKEFSAYDTGNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLIS 160 (306)
Q Consensus 81 ~~~~~~~~~~~~~~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~~~~~~~ 160 (306)
...++.......|.|+||+++++...++++++..|.+.||++++++....++++.+.|.+|++|++|+..+....+++..
T Consensus 81 ~~~~~~~~~~~~g~l~Ig~~~~~~~~~l~~~i~~f~~~~P~i~l~~~~~~~~~~~~~L~~~~~D~~i~~~~~~~~~~l~~ 160 (309)
T PRK12683 81 RRLAEQFADRDSGHLTVATTHTQARYALPKVVRQFKEVFPKVHLALRQGSPQEIAEMLLNGEADIGIATEALDREPDLVS 160 (309)
T ss_pred HHHHHHhcCCCCceEEEEeccchHHHHHHHHHHHHHHHCCCceEEEEeCCHHHHHHHHHcCCccEEEecCCCCCCCCceE
Confidence 99999888888899999999999999999999999999999999999999999999999999999998644334678999
Q ss_pred eccccceEEEEecCCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCceeEEEEecCHHHHHHHHHhccce
Q psy3760 161 IPCYQWEYVIIVPLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMGI 240 (306)
Q Consensus 161 ~~l~~~~~~~v~~~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi 240 (306)
.+++.++++++++++||++.+..++++||.++|+|.++.+...+..++.++...++.++..+++++..++..++..|.|+
T Consensus 161 ~~l~~~~~~~v~~~~hpl~~~~~~~~~~L~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~Gi 240 (309)
T PRK12683 161 FPYYSWHHVVVVPKGHPLTGRENLTLEAIAEYPIITYDQGFTGRSRIDQAFAEAGLVPDIVLTALDADVIKTYVELGMGV 240 (309)
T ss_pred EEcccCeEEEEecCCCCcccCCccCHHHHhcCCeEeccCCCcHHHHHHHHHHHCCCCceeEEEeccHHHHHHHHHhCCCe
Confidence 99999999999999999998888999999999999998888888889999999999999999999999999999999999
Q ss_pred eeeecceecccccCCceeeecCCCCccceEEEEEeCCccccHHHHHHHHHHhHHhhHHHHHhhh
Q psy3760 241 GIIASIAFDSNRDKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLLSPKLNRKFINKIL 304 (306)
Q Consensus 241 ~~~p~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~ 304 (306)
+++|.+.+.....++++.+++++.....+++++|++++..++.++.|++++++...+..+--++
T Consensus 241 ~~lp~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~fi~~l~~~~~~~~~~~~~ 304 (309)
T PRK12683 241 GIVAAMAYDPQRDTGLVALDTDHLFEANTTRVGLRRGAYLRGYAYRFIELFAPHLSEAEIAAAL 304 (309)
T ss_pred EEeehhhccccCCCceEEEeCCCCcccceEEEEEECCCcCCHHHHHHHHHHHhhhhHHHHHHHH
Confidence 9999988765445679999987755567999999999999999999999999988777665443
No 4
>PRK12684 transcriptional regulator CysB-like protein; Reviewed
Probab=100.00 E-value=5.8e-58 Score=377.38 Aligned_cols=304 Identities=63% Similarity=1.069 Sum_probs=280.3
Q ss_pred CchhhHHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCCccccCHhHHHHHHHHHHHHHHHHHH
Q psy3760 1 MNLHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKPGQAILRSIEIIMQEIEGL 80 (306)
Q Consensus 1 m~~~~l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~~~lT~~G~~l~~~a~~il~~~~~~ 80 (306)
|++++|++|.+++++|+||++||++||+||||+|++|++||++||++||+|++++++.||++|+.|+++++++++.++++
T Consensus 1 m~l~~L~~f~~v~~~g~S~s~AA~~L~isQpavS~~ik~LE~~lg~~Lf~R~~r~~~~lT~~G~~l~~~a~~il~~~~~~ 80 (313)
T PRK12684 1 MNLHQLRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEDELGVEIFTRHGKRLRGLTEPGRIILASVERILQEVENL 80 (313)
T ss_pred CCHHHHHHHHHHHHcCCCHHHHHHHhcCCChHHHHHHHHHHHHhCCeeEEEcCCcccccChhHHHHHHHHHHHHHHHHHH
Confidence 89999999999999955999999999999999999999999999999999999995259999999999999999999999
Q ss_pred HHHHHhhccCCCCcEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccCCCCCcee
Q psy3760 81 KKIGKEFSAYDTGNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLIS 160 (306)
Q Consensus 81 ~~~~~~~~~~~~~~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~~~~~~~ 160 (306)
...+........|.|+||++++++..++++++..|.+.||++++++...++.++.+.|.+|++|++|+.......+++.+
T Consensus 81 ~~~~~~~~~~~~g~l~Ig~~~~~~~~~l~~~l~~~~~~~p~i~l~~~~~~~~~~~~~L~~g~~D~~i~~~~~~~~~~l~~ 160 (313)
T PRK12684 81 KRVGKEFAAQDQGNLTIATTHTQARYALPAAIKEFKKRYPKVRLSILQGSPTQIAEMVLHGQADLAIATEAIADYKELVS 160 (313)
T ss_pred HHHHHHHhccCCCeEEEEechHHHHHHhHHHHHHHHHHCCCceEEEEeCChHHHHHHHHCCCcCEEEeecCCCCCCCceE
Confidence 99998888888899999999999999999999999999999999999999999999999999999998644334578999
Q ss_pred eccccceEEEEecCCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCceeEEEEecCHHHHHHHHHhccce
Q psy3760 161 IPCYQWEYVIIVPLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMGI 240 (306)
Q Consensus 161 ~~l~~~~~~~v~~~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi 240 (306)
.++++++++++++++||+..+.+++++||.++|+|.++.+...+..++.++...++.|++.+++++...+.++|.+|.|+
T Consensus 161 ~~l~~~~~~~v~~~~~pl~~~~~i~~~dL~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~Gv 240 (313)
T PRK12684 161 LPCYQWNHCVVVPPDHPLLERKPLTLEDLAQYPLITYDFAFAGRSKINKAFALRGLKPDIVLEAIDADVIKTYVELGLGV 240 (313)
T ss_pred EEeccceEEEEeCCCCccccCCCcCHHHHhcCCcEecCCCCcHHHHHHHHHHHcCCCCCeEEEeCCHHHHHHHHHhCCce
Confidence 99999999999999999998888999999999999998877777888999999999999999999999999999999999
Q ss_pred eeeecceecccccCCceeeecCCCCccceEEEEEeCCccccHHHHHHHHHHhHHhhHHHHHhhh
Q psy3760 241 GIIASIAFDSNRDKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLLSPKLNRKFINKIL 304 (306)
Q Consensus 241 ~~~p~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~ 304 (306)
+++|.........++++.+++.++.....++++|+++...+|.++.|++++++.+.+...+.++
T Consensus 241 ~~lp~~~~~~~~~~~l~~~~i~~~~~~~~~~l~~~~~~~~~~~~~~f~~~l~~~~~~~~~~~~~ 304 (313)
T PRK12684 241 GIVADMAFDPERDRNLRAIDAGHLFGSSTTRLGLRRGAYLRGYVYTFIELFAPTLNRKLVEQAL 304 (313)
T ss_pred EEeehhhccccccCCeEEEECCCCCcceeEEEEEECCCcCCHHHHHHHHHHHHHhCHHHHHHHh
Confidence 9999987665445689999998755667899999999999999999999999999888777654
No 5
>PRK11151 DNA-binding transcriptional regulator OxyR; Provisional
Probab=100.00 E-value=5.7e-58 Score=377.06 Aligned_cols=296 Identities=18% Similarity=0.308 Sum_probs=273.9
Q ss_pred CchhhHHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCCccccCHhHHHHHHHHHHHHHHHHHH
Q psy3760 1 MNLHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKPGQAILRSIEIIMQEIEGL 80 (306)
Q Consensus 1 m~~~~l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~~~lT~~G~~l~~~a~~il~~~~~~ 80 (306)
||+++|++|++|+|+| ||++||++||+||||+|++|++||++||++||+|+++|+ .||++|+.|++++++++++++++
T Consensus 1 m~l~~L~~f~~v~~~g-S~s~AA~~L~itQpavS~~i~~LE~~lg~~LF~R~~r~~-~lT~~G~~l~~~a~~~l~~~~~~ 78 (305)
T PRK11151 1 MNIRDLEYLVALAEHR-HFRRAADSCHVSQPTLSGQIRKLEDELGVMLLERTSRKV-LFTQAGLLLVDQARTVLREVKVL 78 (305)
T ss_pred CCHHHHHHHHHHHHhC-CHHHHHHHhCCCchHHHHHHHHHHHHhCchheeeCCCce-eECccHHHHHHHHHHHHHHHHHH
Confidence 8999999999999999 999999999999999999999999999999999999999 79999999999999999999999
Q ss_pred HHHHHhhccCCCCcEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccCCCCCcee
Q psy3760 81 KKIGKEFSAYDTGNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLIS 160 (306)
Q Consensus 81 ~~~~~~~~~~~~~~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~~~~~~~ 160 (306)
............|.++||++++++..++++++..|.+.||++++++...+.+++.+.|.+|++|++|+... ...+++.+
T Consensus 79 ~~~~~~~~~~~~g~l~i~~~~~~~~~~~~~~l~~~~~~~P~v~i~~~~~~~~~~~~~l~~g~~Dl~i~~~~-~~~~~l~~ 157 (305)
T PRK11151 79 KEMASQQGETMSGPLHIGLIPTVGPYLLPHIIPMLHQTFPKLEMYLHEAQTHQLLAQLDSGKLDCAILALV-KESEAFIE 157 (305)
T ss_pred HHHHHHhcccCCceEEEEecchhHHHHHHHHHHHHHHHCCCcEEEEEeCCHHHHHHHHHcCCccEEEEecC-CCCCCeEE
Confidence 98887777778899999999999999999999999999999999999999999999999999999998654 45578999
Q ss_pred eccccceEEEEecCCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCceeEEEEecCHHHHHHHHHhccce
Q psy3760 161 IPCYQWEYVIIVPLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMGI 240 (306)
Q Consensus 161 ~~l~~~~~~~v~~~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi 240 (306)
.+++.++++++++++||++.++.++++||.++|+|.+..+...+..+..++...+..+++.+++++...+.+++..|.|+
T Consensus 158 ~~l~~~~~~~~~~~~hpl~~~~~i~~~~L~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi 237 (305)
T PRK11151 158 VPLFDEPMLLAVYEDHPWANRDRVPMSDLAGEKLLMLEDGHCLRDQAMGFCFEAGADEDTHFRATSLETLRNMVAAGSGI 237 (305)
T ss_pred EEeccCcEEEEecCCCCcccCCccCHHHhcCCCeEeecCCccHHHHHHHHHHHCCCCCCceEEeccHHHHHHHHHcCCCE
Confidence 99999999999999999998888999999999999998876676677788888898899999999999999999999999
Q ss_pred eeeecceeccc-ccCCceeeecCCCCccceEEEEEeCCccccHHHHHHHHHHhHHhhHHH
Q psy3760 241 GIIASIAFDSN-RDKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLLSPKLNRKF 299 (306)
Q Consensus 241 ~~~p~~~~~~~-~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~ 299 (306)
+++|.+.+... ..++++.+|++...+..++|++|+++...+|.++.|++++++.+...+
T Consensus 238 ~ilp~~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~ 297 (305)
T PRK11151 238 TLLPALAVPNERKRDGVCYLPCIKPEPRRTIGLVYRPGSPLRSRYEQLAEAIRARMDGHF 297 (305)
T ss_pred EEeeHHhhhhhcccCCEEEEECcCCccceEEEEEEcCCCcchHHHHHHHHHHHHHhcccH
Confidence 99999888554 457799999977666789999999999999999999999998887544
No 6
>PRK12679 cbl transcriptional regulator Cbl; Reviewed
Probab=100.00 E-value=1.8e-57 Score=374.92 Aligned_cols=299 Identities=43% Similarity=0.756 Sum_probs=275.7
Q ss_pred CchhhHHHHHHHHHh-cCCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCC-ccccCHhHHHHHHHHHHHHHHHH
Q psy3760 1 MNLHQFRFVREAVRQ-NFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKR-IRGLTKPGQAILRSIEIIMQEIE 78 (306)
Q Consensus 1 m~~~~l~~f~~v~~~-~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~-~~~lT~~G~~l~~~a~~il~~~~ 78 (306)
|++++|+||++++++ | ||++||++||+||||+|++|++||++||++||+|++++ + +||++|+.|+++++++++.++
T Consensus 1 m~~~~l~~f~~v~~~~~-s~s~AA~~L~iSQ~avSr~I~~LE~~lg~~LF~R~~~~~~-~lT~~G~~l~~~a~~il~~~~ 78 (316)
T PRK12679 1 MNFQQLKIIREAARQDY-NLTEVANMLFTSQSGVSRHIRELEDELGIEIFIRRGKRLL-GMTEPGKALLVIAERILNEAS 78 (316)
T ss_pred CChHHHHHHHHHHHcCC-CHHHHHHHhcCCchHHHHHHHHHHHHhCCEEEEECCCccc-ccCHhHHHHHHHHHHHHHHHH
Confidence 899999999999999 7 99999999999999999999999999999999999888 5 699999999999999999999
Q ss_pred HHHHHHHhhccCCCCcEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccCCCCCc
Q psy3760 79 GLKKIGKEFSAYDTGNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKL 158 (306)
Q Consensus 79 ~~~~~~~~~~~~~~~~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~~~~~ 158 (306)
++............|.++||++++++..++++++..|.+.||++.+++...+++++.+.|.+|++|++|+..+...++++
T Consensus 79 ~~~~~~~~~~~~~~g~lrIg~~~~~~~~~l~~~l~~f~~~~P~i~l~l~~~~~~~~~~~L~~g~~Dl~i~~~~~~~~~~l 158 (316)
T PRK12679 79 NVRRLADLFTNDTSGVLTIATTHTQARYSLPEVIKAFRELFPEVRLELIQGTPQEIATLLQNGEADIGIASERLSNDPQL 158 (316)
T ss_pred HHHHHHHHhccccCceEEEEechHhhhcchHHHHHHHHHHCCCeEEEEecCCHHHHHHHHHcCCCCEEEecccCCCCCCc
Confidence 99888877777778999999999999999999999999999999999999999999999999999999986543346789
Q ss_pred eeeccccceEEEEecCCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCceeEEEEecCHHHHHHHHHhcc
Q psy3760 159 ISIPCYQWEYVIIVPLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRM 238 (306)
Q Consensus 159 ~~~~l~~~~~~~v~~~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~ 238 (306)
...++++++++++++++||++.+.+++++||.++|||.+..+...+..++.++...|..|++.+++++...+++++..|.
T Consensus 159 ~~~~l~~~~~~~v~~~~hpl~~~~~i~~~~L~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~v~~g~ 238 (316)
T PRK12679 159 VAFPWFRWHHSLLVPHDHPLTQITPLTLESIAKWPLITYRQGITGRSRIDDAFARKGLLADIVLSAQDSDVIKTYVALGL 238 (316)
T ss_pred eEEEccCCcEEEEecCCCccccCCCCCHHHHhCCCeEEecCCCcHHHHHHHHHHHcCCCceEEEEeccHHHHHHHHHcCC
Confidence 99999999999999999999888889999999999999988877777889999999999999999999999999999999
Q ss_pred ceeeeecceecccccCCceeeecCCCCccceEEEEEeCCccccHHHHHHHHHHhHHhhHHHHH
Q psy3760 239 GIGIIASIAFDSNRDKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLLSPKLNRKFIN 301 (306)
Q Consensus 239 gi~~~p~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~~ 301 (306)
|++++|...+.....+.++.+++..+....++|++|+++...+|.+++|++++++.+.-..+.
T Consensus 239 Gi~~lp~~~~~~~~~~~L~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~f~~~~~~~~~~~~~~ 301 (316)
T PRK12679 239 GIGLVAEQSSGEQEESNLIRLDTRHLFDANTVWLGLKRGQLQRNYVWRFLELCNAGLSVEDIK 301 (316)
T ss_pred cEEEecccccccccCCcEEEEECcccCCCceEEEEEeCCchhhHHHHHHHHHHhcccCHHHHH
Confidence 999999988765467889999887655667999999999999999999999999988766663
No 7
>PRK11242 DNA-binding transcriptional regulator CynR; Provisional
Probab=100.00 E-value=1.6e-57 Score=373.42 Aligned_cols=292 Identities=23% Similarity=0.394 Sum_probs=271.0
Q ss_pred CchhhHHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCCccccCHhHHHHHHHHHHHHHHHHHH
Q psy3760 1 MNLHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKPGQAILRSIEIIMQEIEGL 80 (306)
Q Consensus 1 m~~~~l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~~~lT~~G~~l~~~a~~il~~~~~~ 80 (306)
|++++|++|.+|+++| ||++||++||+||||+|++|++||++||++||+|+++|+ +||++|+.|+++++++++.++++
T Consensus 1 m~l~~L~~f~~v~~~g-s~s~AA~~L~isqsavS~~i~~LE~~lg~~Lf~R~~~~~-~lT~~G~~l~~~~~~il~~~~~~ 78 (296)
T PRK11242 1 MLLRHIRYFLAVAEHG-NFTRAAEALHVSQPTLSQQIRQLEESLGVQLFDRSGRTV-RLTDAGEVYLRYARRALQDLEAG 78 (296)
T ss_pred CChHHHHHHHHHHHhC-CHHHHHHHcCCCchHHHHHHHHHHHHhCCeeEeEcCCce-eechhHHHHHHHHHHHHHHHHHH
Confidence 8999999999999999 999999999999999999999999999999999999999 79999999999999999999999
Q ss_pred HHHHHhhccCCCCcEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccCCCCCcee
Q psy3760 81 KKIGKEFSAYDTGNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLIS 160 (306)
Q Consensus 81 ~~~~~~~~~~~~~~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~~~~~~~ 160 (306)
...++.......|.|+||++++++..++++++..|.++||++++++....+.++.+.|.+|++|++|...+ ...+++.+
T Consensus 79 ~~~~~~~~~~~~~~i~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~g~~Dl~i~~~~-~~~~~l~~ 157 (296)
T PRK11242 79 RRAIHDVADLSRGSLRLAMTPTFTAYLIGPLIDAFHARYPGITLTIREMSQERIEALLADDELDVGIAFAP-VHSPEIEA 157 (296)
T ss_pred HHHHHHhcCCCeeEEEEEeccchhhhhhHHHHHHHHHHCCCCEEEEEeCCHHHHHHHHHCCCCcEEEEecC-CCCcceeE
Confidence 99888776667789999999999999999999999999999999999999999999999999999998655 56678999
Q ss_pred eccccceEEEEecCCCCCCCCCC-cChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCceeEEEEecCHHHHHHHHHhccc
Q psy3760 161 IPCYQWEYVIIVPLDHPLLLLNS-ISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMG 239 (306)
Q Consensus 161 ~~l~~~~~~~v~~~~~~l~~~~~-i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~g 239 (306)
.++++++++++++++||+++... ++++||.++||+.+..+...+..++.++...++.++..+.+++..++.+++..|.|
T Consensus 158 ~~l~~~~~~~~~~~~~pl~~~~~~i~~~~L~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~g 237 (296)
T PRK11242 158 QPLFTETLALVVGRHHPLAARRKALTLDELADEPLVLLSAEFATREQIDRYFRRHGVTPRVAIEANSISAVLEIVRRGRL 237 (296)
T ss_pred EEeeeccEEEEEcCCCcccccCCCcCHHHHhCCCcEeeCCCccHHHHHHHHHHHcCCCccEEEEeccHHHHHHHHHhCCe
Confidence 99999999999999999987654 99999999999999887667778889999999999999999999999999999999
Q ss_pred eeeeecceecccccCCceeeecCCCCccceEEEEEeCCccccHHHHHHHHHHhHHhhH
Q psy3760 240 IGIIASIAFDSNRDKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLLSPKLNR 297 (306)
Q Consensus 240 i~~~p~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~ 297 (306)
++++|.+++.. .++++.+|+.+.....+++++|+++...++.+++|++++++.+.+
T Consensus 238 i~~~p~~~~~~--~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~ 293 (296)
T PRK11242 238 ATLLPAAIARE--HDGLCAIPLDPPLPQRTAALLRRKGAYRSAAARAFIELALERRAE 293 (296)
T ss_pred EEEeehhhccc--CCCeEEEECCCCCccceEEEEEeCCCCCCHHHHHHHHHHHHhhhh
Confidence 99999988765 577899898875566799999999999999999999999887654
No 8
>PRK12680 transcriptional regulator CysB-like protein; Reviewed
Probab=100.00 E-value=2.2e-57 Score=374.92 Aligned_cols=302 Identities=28% Similarity=0.549 Sum_probs=274.8
Q ss_pred CchhhHHHHHHHHHh-cCCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCCccc-cCHhHHHHHHHHHHHHHHHH
Q psy3760 1 MNLHQFRFVREAVRQ-NFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRG-LTKPGQAILRSIEIIMQEIE 78 (306)
Q Consensus 1 m~~~~l~~f~~v~~~-~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~~~-lT~~G~~l~~~a~~il~~~~ 78 (306)
||+++|++|++|+++ | ||++||++||+||||||++|++||++||++||+|+++++ + ||++|+.|+++++.+++.++
T Consensus 1 m~l~~L~~F~~vae~~g-S~s~AA~~L~isQpavS~~I~~LE~~lG~~LF~R~~r~v-~~LT~~G~~l~~~a~~il~~~~ 78 (327)
T PRK12680 1 MTLTQLRYLVAIADAEL-NITLAAARVHATQPGLSKQLKQLEDELGFLLFVRKGRSL-ESVTPAGVEVIERARAVLSEAN 78 (327)
T ss_pred CCHHHHHHHHHHHHccC-CHHHHHHHhcCCchHHHHHHHHHHHHhCCeEEEECCCcC-CccCccHHHHHHHHHHHHHHHH
Confidence 899999999999997 9 999999999999999999999999999999999999998 7 99999999999999999999
Q ss_pred HHHHHHHhhccCCCCcEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccCCCCCc
Q psy3760 79 GLKKIGKEFSAYDTGNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKL 158 (306)
Q Consensus 79 ~~~~~~~~~~~~~~~~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~~~~~ 158 (306)
++...++.......|.|+||++++++..++++++..|.+.||++++++...+++++.+.|.+|++|++|...+.......
T Consensus 79 ~~~~~~~~~~~~~~g~lrIg~~~~~~~~~l~~~l~~f~~~~P~v~i~l~~~~~~~~~~~l~~g~~Dl~i~~~~~~~~~~~ 158 (327)
T PRK12680 79 NIRTYAANQRRESQGQLTLTTTHTQARFVLPPAVAQIKQAYPQVSVHLQQAAESAALDLLGQGDADIAIVSTAGGEPSAG 158 (327)
T ss_pred HHHHHHHHhccCCceEEEEEecchhHHHhhHHHHHHHHHHCCCcEEEEEeCChHHHHHHHHCCCCcEEEEecCCCCCCcc
Confidence 99998887777788999999999999999999999999999999999999999999999999999999986543333445
Q ss_pred eeeccccceEEEEecCCCCCCCC-CCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCceeEEEEecCHHHHHHHHHhc
Q psy3760 159 ISIPCYQWEYVIIVPLDHPLLLL-NSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELR 237 (306)
Q Consensus 159 ~~~~l~~~~~~~v~~~~~~l~~~-~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g 237 (306)
...++++++++++++++||++.+ .+++++||.++|+|.+..+...+..+++++...|..+++.+++++..++.++|.+|
T Consensus 159 ~~~~l~~~~~~l~~~~~hpl~~~~~~~~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~G 238 (327)
T PRK12680 159 IAVPLYRWRRLVVVPRGHALDTPRRAPDMAALAEHPLISYESSTRPGSSLQRAFAQLGLEPSIALTALDADLIKTYVRAG 238 (327)
T ss_pred eEEEeeccceEEEEeCCChhhccCCCCCHHHHhcCCEEEecCCCchHHHHHHHHHHCCCCCcEEEEECCHHHHHHHHHcC
Confidence 58999999999999999999864 57999999999999999888778889999999999999999999999999999999
Q ss_pred cceeeeecceecccccCCceeeecCCCCccceEEEEEeCCccccHHHHHHHHHHhHHhhHHHHHhhhc
Q psy3760 238 MGIGIIASIAFDSNRDKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLLSPKLNRKFINKILN 305 (306)
Q Consensus 238 ~gi~~~p~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~ 305 (306)
.|++++|..++.. ..+.++.+|++.+.....+|++|++++..++.++.|++++...++....+++++
T Consensus 239 ~Gia~lp~~~~~~-~~~~l~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~ 305 (327)
T PRK12680 239 LGVGLLAEMAVNA-NDEDLRAWPAPAPIAECIAWAVLPRDRVLRDYALELVHVLAPQIDKRDLRRVLD 305 (327)
T ss_pred CCEEEeechhccC-CCCCeEEEECCCCCCCceEEEEEeCCchhHHHHHHHHHHhcCCCCHHHHHHHhc
Confidence 9999999988875 356799999876545567889999999999999999999988887766655543
No 9
>PRK10341 DNA-binding transcriptional activator TdcA; Provisional
Probab=100.00 E-value=1.5e-57 Score=375.17 Aligned_cols=298 Identities=16% Similarity=0.193 Sum_probs=274.5
Q ss_pred CchhhHHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCCccccCHhHHHHHHHHHHHHHHHHHH
Q psy3760 1 MNLHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKPGQAILRSIEIIMQEIEGL 80 (306)
Q Consensus 1 m~~~~l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~~~lT~~G~~l~~~a~~il~~~~~~ 80 (306)
|++++|++|++++++| ||++||++||+||||+|++|++||++||++||+|+++++ +||++|+.|+++++++++.++++
T Consensus 7 ~~~~~L~~F~av~e~g-s~s~AA~~L~iSQpavS~~I~~LE~~lg~~LF~R~~r~~-~lT~~G~~l~~~a~~il~~~~~~ 84 (312)
T PRK10341 7 PKTQHLVVFQEVIRSG-SIGSAAKELGLTQPAVSKIINDIEDYFGVELIVRKNTGV-TLTPAGQVLLSRSESITREMKNM 84 (312)
T ss_pred ccHHHHHHHHHHHHcC-CHHHHHHHhCCChHHHHHHHHHHHHHhCCeEEEEcCCCc-eEChhHHHHHHHHHHHHHHHHHH
Confidence 5899999999999999 999999999999999999999999999999999999999 79999999999999999999999
Q ss_pred HHHHHhhccCCCCcEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEcccc-CCCCCce
Q psy3760 81 KKIGKEFSAYDTGNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEIL-SPSDKLI 159 (306)
Q Consensus 81 ~~~~~~~~~~~~~~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~-~~~~~~~ 159 (306)
.+.+........|.|+||++++++..++++++..|.+.||++++++....+.++.+.|.+|++|++|...+. ...+++.
T Consensus 85 ~~~~~~~~~~~~~~l~ig~~~~~~~~~l~~~l~~~~~~~p~v~i~~~~~~~~~~~~~l~~g~~Dl~i~~~~~~~~~~~l~ 164 (312)
T PRK10341 85 VNEINGMSSEAVVDVSFGFPSLIGFTFMSDMINKFKEVFPKAQVSMYEAQLSSFLPAIRDGRLDFAIGTLSNEMKLQDLH 164 (312)
T ss_pred HHHHHHHcCCCceEEEEEechHHhHhhHHHHHHHHHHhCCCCEEEEEeCCHHHHHHHHHcCCCcEEEecCCcccccCCee
Confidence 999998877788999999999999999999999999999999999999999999999999999999986432 2357899
Q ss_pred eeccccceEEEEecCCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCceeEEEEecCHHHHHHHHHhccc
Q psy3760 160 SIPCYQWEYVIIVPLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMG 239 (306)
Q Consensus 160 ~~~l~~~~~~~v~~~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~g 239 (306)
..++++++++++++++||+. ..++++||.++||+....+...+..+.+++...++.+++.+++++..++.+++.+|.|
T Consensus 165 ~~~l~~~~~~lv~~~~~pl~--~~i~~~dL~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~g 242 (312)
T PRK10341 165 VEPLFESEFVLVASKSRTCT--GTTTLESLKNEQWVLPQTNMGYYSELLTTLQRNGISIENIVKTDSVVTIYNLVLNADF 242 (312)
T ss_pred EEEEecccEEEEEcCCCchh--ccCCHHHHhCCCeEccCCCCcHHHHHHHHHHHcCcCCCceEEecCHHHHHHHHHhCCc
Confidence 99999999999999999985 3689999999999998877777777788888889999999999999999999999999
Q ss_pred eeeeecceecccccCCceeeecCCCCccceEEEEEeCCccccHHHHHHHHHHhHHhhHHHHHh
Q psy3760 240 IGIIASIAFDSNRDKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLLSPKLNRKFINK 302 (306)
Q Consensus 240 i~~~p~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~ 302 (306)
++++|..+......++++.+++++......++++|+++...+|+++.|++++++.+..+++++
T Consensus 243 i~~~p~~~~~~~~~~~l~~i~l~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~ 305 (312)
T PRK10341 243 LTVIPCDMTSPFGSNQFITIPIEETLPVAQYAAVWSKNYRIKKAASVLVELAKEYSSYNGCRR 305 (312)
T ss_pred EEEeeHHhcCccccCcEEEEecCCCCCCCcEEEEEecCCCCCHHHHHHHHHHHHHhhhcchhh
Confidence 999999887654456799999987555678999999999999999999999999998888765
No 10
>CHL00180 rbcR LysR transcriptional regulator; Provisional
Probab=100.00 E-value=3.4e-57 Score=372.12 Aligned_cols=294 Identities=24% Similarity=0.358 Sum_probs=271.0
Q ss_pred CchhhHHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCCccccCHhHHHHHHHHHHHHHHHHHH
Q psy3760 1 MNLHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKPGQAILRSIEIIMQEIEGL 80 (306)
Q Consensus 1 m~~~~l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~~~lT~~G~~l~~~a~~il~~~~~~ 80 (306)
||+++|++|++++|+| ||++||++||+|||++|++|++||++||++||+|+++++ +||++|+.|+++++++++.++++
T Consensus 5 ~~l~~L~~f~~v~e~g-s~s~AA~~L~isqpavS~~i~~LE~~lg~~Lf~R~~r~~-~lT~~G~~l~~~a~~ll~~~~~~ 82 (305)
T CHL00180 5 FTLDQLRILKAIATEG-SFKKAAESLYISQPAVSLQIKNLEKQLNIPLFDRSKNKA-SLTEAGELLLRYGNRILALCEET 82 (305)
T ss_pred ccHHHHHHHHHHHHcC-CHHHHHHHhcCCChHHHHHHHHHHHHhCCEEEEecCCCc-eECHhHHHHHHHHHHHHHHHHHH
Confidence 7899999999999999 999999999999999999999999999999999999999 89999999999999999999999
Q ss_pred HHHHHhhccCCCCcEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccCC--CCCc
Q psy3760 81 KKIGKEFSAYDTGNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSP--SDKL 158 (306)
Q Consensus 81 ~~~~~~~~~~~~~~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~--~~~~ 158 (306)
.+.+++......|.++||+.++++..++++++..|.+.||++++++....+..+.+.|.+|++|++|+...... .+++
T Consensus 83 ~~~~~~~~~~~~g~l~ig~~~~~~~~~~~~~l~~~~~~~P~v~i~~~~~~~~~~~~~l~~g~~Dl~i~~~~~~~~~~~~~ 162 (305)
T CHL00180 83 CRALEDLKNLQRGTLIIGASQTTGTYLMPRLIGLFRQRYPQINVQLQVHSTRRIAWNVANGQIDIAIVGGEVPTELKKIL 162 (305)
T ss_pred HHHHHHhhcccCceEEEEEcCcchHhHHHHHHHHHHHHCCCceEEEEeCCHHHHHHHHHcCCccEEEEcCccCcccccce
Confidence 99999888888999999999999999999999999999999999999988999999999999999998643222 2568
Q ss_pred eeeccccceEEEEecCCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCce---eEEEEecCHHHHHHHHH
Q psy3760 159 ISIPCYQWEYVIIVPLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTP---YIVLETINSDIIKTYVE 235 (306)
Q Consensus 159 ~~~~l~~~~~~~v~~~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~v~ 235 (306)
...+++.++++++++++||++.+..++++||.++|+|.+..+...+..+.+++...+..+ ++.+.+++..++.+++.
T Consensus 163 ~~~~l~~~~~~~v~~~~~pl~~~~~i~~~dL~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~ 242 (305)
T CHL00180 163 EITPYVEDELALIIPKSHPFAKLKKIQKEDLYRLNFITLDSNSTIRKVIDNILIQNGIDSKRFKIEMELNSIEAIKNAVQ 242 (305)
T ss_pred eEEEeccCcEEEEECCCCccccCCccCHHHHccCCceEecCCCcHHHHHHHHHHHcCCCcccceEEEEeCCHHHHHHHHH
Confidence 999999999999999999999988999999999999999988777778889999888765 57899999999999999
Q ss_pred hccceeeeecceeccc-ccCCceeeecCCCCccceEEEEEeCCccccHHHHHHHHHHhHHhh
Q psy3760 236 LRMGIGIIASIAFDSN-RDKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLLSPKLN 296 (306)
Q Consensus 236 ~g~gi~~~p~~~~~~~-~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~ 296 (306)
+|.|++++|.+.+... ..+.++.+|+++....+.+|++|++++..++.++.|++++++.++
T Consensus 243 ~g~g~~~lp~~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~f~~~~~~~~~ 304 (305)
T CHL00180 243 SGLGAAFVSVSAIEKELELGLLHWIKIENITIKRMLSIITNPNRYKSKASETFYNEILTLFN 304 (305)
T ss_pred cCCcEEEeEhHHHHHHhhcCcEEEEEcCCCCceEEEEEEEeCCCccCHHHHHHHHHHHHHhc
Confidence 9999999999877655 677899999887656789999999999999999999999997654
No 11
>TIGR02424 TF_pcaQ pca operon transcription factor PcaQ. Members of this family are LysR-family transcription factors associated with operons for catabolism of protocatechuate. Members occur only in Proteobacteria.
Probab=100.00 E-value=2.1e-57 Score=373.19 Aligned_cols=294 Identities=21% Similarity=0.270 Sum_probs=272.5
Q ss_pred CchhhHHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCCccccCHhHHHHHHHHHHHHHHHHHH
Q psy3760 1 MNLHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKPGQAILRSIEIIMQEIEGL 80 (306)
Q Consensus 1 m~~~~l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~~~lT~~G~~l~~~a~~il~~~~~~ 80 (306)
|++++|++|++|+++| ||++||++||+|||+||++|++||++||++||+|+++|+ +||++|+.|+++++++++.++++
T Consensus 3 m~l~~l~~f~~v~~~g-S~s~AA~~L~isq~avS~~I~~LE~~lg~~LF~R~~~~~-~lT~~G~~l~~~a~~~l~~~~~~ 80 (300)
T TIGR02424 3 IKFRHLQCFVEVARQG-SVKRAAEALHITQPAVSKTLRELEEILGTPLFERDRRGI-RLTRYGELFLRHAGASLAALRQG 80 (300)
T ss_pred ccHHHHHHHHHHHHhC-CHHHHHHHhCCChHHHHHHHHHHHHHhCCeEEEEcCCCc-cccHhHHHHHHHHHHHHHHHHHH
Confidence 8999999999999999 999999999999999999999999999999999999999 89999999999999999999999
Q ss_pred HHHHHhhccCCCCcEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEcccc-CCCCCce
Q psy3760 81 KKIGKEFSAYDTGNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEIL-SPSDKLI 159 (306)
Q Consensus 81 ~~~~~~~~~~~~~~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~-~~~~~~~ 159 (306)
...++.......|.++||+++++...++++++..|.++||++++++...+..++.+.+.+|++|++|+.... ...+++.
T Consensus 81 ~~~~~~~~~~~~~~l~I~~~~~~~~~~~~~~l~~~~~~~P~~~i~~~~~~~~~~~~~l~~g~~D~~i~~~~~~~~~~~~~ 160 (300)
T TIGR02424 81 VASLSQLGEGEGPTVRIGALPTVAARLMPEVVKRFLARAPRLRVRIMTGPNAYLLDQLRVGALDLVVGRLGAPETMQGLS 160 (300)
T ss_pred HHHHHHhcCCCCceEEEecccHHHHhhhHHHHHHHHHhCCCcEEEEEeCchHHHHHHHHCCCCCEEEEecCCccccccee
Confidence 999988878889999999999999999999999999999999999999999999999999999999975332 2347899
Q ss_pred eeccccceEEEEecCCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCce-eEEEEecCHHHHHHHHHhcc
Q psy3760 160 SIPCYQWEYVIIVPLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTP-YIVLETINSDIIKTYVELRM 238 (306)
Q Consensus 160 ~~~l~~~~~~~v~~~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~v~~g~ 238 (306)
..++++++++++++++||++.+..++++||.++|++.+..+...+..++.++...+..+ ++.+++++...+..++..|.
T Consensus 161 ~~~l~~~~~~~~~~~~hpl~~~~~i~~~dL~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~ 240 (300)
T TIGR02424 161 FEHLYNEPVVFVVRAGHPLLAAPSLPVASLADYPVLLPPEGSAIRPLAERLFIACGIPPPPQRIETVSGSFGRRYVQESD 240 (300)
T ss_pred eeeecCCceEEEEcCCCccccCCCCCHHHHhCCCEEecCCCCchHHHHHHHHHHCCCCCCCceEEeccHHHHHHHHHhCC
Confidence 99999999999999999999988899999999999999887777788899999999875 56789999999999999999
Q ss_pred ceeeeecceeccc-ccCCceeeecCCCCccceEEEEEeCCccccHHHHHHHHHHhHHhh
Q psy3760 239 GIGIIASIAFDSN-RDKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLLSPKLN 296 (306)
Q Consensus 239 gi~~~p~~~~~~~-~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~ 296 (306)
|++++|.+.+... ..++++.++++......+++++|+++...+|.+++|++++++.++
T Consensus 241 gi~~lp~~~~~~~~~~~~l~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~ 299 (300)
T TIGR02424 241 AIWIISRGVVALDLADGTLVELPFDTRETGGPVGLCTRPDTQLSRAAQLFVDALRSAAA 299 (300)
T ss_pred ceEeCcHHHHhhhhcCCcEEEccCCCCCCCCceEEEEeCCCCCCHHHHHHHHHHHHHhc
Confidence 9999999888765 678899999887666679999999999999999999999988764
No 12
>PRK11013 DNA-binding transcriptional regulator LysR; Provisional
Probab=100.00 E-value=1.1e-56 Score=369.53 Aligned_cols=296 Identities=18% Similarity=0.266 Sum_probs=273.1
Q ss_pred CchhhHHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCCccccCHhHHHHHHHHHHHHHHHHHH
Q psy3760 1 MNLHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKPGQAILRSIEIIMQEIEGL 80 (306)
Q Consensus 1 m~~~~l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~~~lT~~G~~l~~~a~~il~~~~~~ 80 (306)
||+++|++|++|+++| ||++||+.||+||||||++|++||++||++||+|+++++ .||++|+.|+++++++++.++.+
T Consensus 4 ~~l~~L~~f~av~~~g-S~s~AAe~L~isqsavS~~Ik~LE~~lg~~Lf~R~~~~v-~LT~~G~~l~~~a~~~l~~~~~~ 81 (309)
T PRK11013 4 VSLRHIEIFHAVMTAG-SLTEAARLLHTSQPTVSRELARFEKVIGLKLFERVRGRL-HPTVQGLRLFEEVQRSYYGLDRI 81 (309)
T ss_pred ccHHHHHHHHHHHHhC-cHHHHHHHHCCCcHHHHHHHHHHHHHhCceeeeecCCCc-ccCHHHHHHHHHHHHHHHHHHHH
Confidence 7999999999999999 999999999999999999999999999999999999998 79999999999999999999999
Q ss_pred HHHHHhhccCCCCcEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccCCCCCcee
Q psy3760 81 KKIGKEFSAYDTGNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLIS 160 (306)
Q Consensus 81 ~~~~~~~~~~~~~~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~~~~~~~ 160 (306)
...++.......|.++||++++++..++++++..|.+.||++++++...+..++.+.|.+|++|++|.... ...+++..
T Consensus 82 ~~~~~~~~~~~~g~l~I~~~~~~~~~~l~~~l~~~~~~~P~v~i~i~~~~~~~~~~~l~~~~~Dl~i~~~~-~~~~~~~~ 160 (309)
T PRK11013 82 VSAAESLREFRQGQLSIACLPVFSQSLLPGLCQPFLARYPDVSLNIVPQESPLLEEWLSAQRHDLGLTETL-HTPAGTER 160 (309)
T ss_pred HHHHHHHHcCCCCcEEEEEcHHHHHhhHHHHHHHHHHHCCCCeEEEEeCCHHHHHHHHHcCCCCEEEEcCC-CCCCCcee
Confidence 99888888778899999999999999999999999999999999999999999999999999999998644 45678999
Q ss_pred eccccceEEEEecCCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCceeEEEEecCHHHHHHHHHhccce
Q psy3760 161 IPCYQWEYVIIVPLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMGI 240 (306)
Q Consensus 161 ~~l~~~~~~~v~~~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi 240 (306)
.++++++++++++++||++..++++++||.++|+|.++.+...+..++.++...|+.+++..++++...+..++.+|.|+
T Consensus 161 ~~l~~~~~~~~~~~~~pl~~~~~i~~~dL~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~Gv 240 (309)
T PRK11013 161 TELLTLDEVCVLPAGHPLAAKKVLTPDDFAGENFISLSRTDSYRQLLDQLFAEHGVKRRMVVETHSAASVCAMVRAGVGV 240 (309)
T ss_pred eeecceeEEEEEcCCCccccCCccCHHHHCCCcEEeecCCCcHHHHHHHHHHHcCCCcceEEEeccHHHHHHHHHcCCeE
Confidence 99999999999999999998888999999999999999887778888999999999999999999999999999999999
Q ss_pred eeeecceecccccCCceeeecCCCCccceEEEEEeCCccccHHHHHHHHHHhHHhhHHHH
Q psy3760 241 GIIASIAFDSNRDKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLLSPKLNRKFI 300 (306)
Q Consensus 241 ~~~p~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~ 300 (306)
+++|...+......++..+|++.. ....++++|++++..++.++.|++++++.+.+...
T Consensus 241 ~~~p~~~~~~~~~~~l~~~~~~~~-~~~~~~l~~~~~~~~~~~~~~f~~~i~~~~~~~~~ 299 (309)
T PRK11013 241 SIVNPLTALDYAGSGLVVRRFSIS-VPFTVSLIRPLHRPASALVDAFSEHLQQQAPALVT 299 (309)
T ss_pred EEeChhhhccccCCCEEEEeCCCC-CceeEEEEecCCCCCCHHHHHHHHHHHHHHHHhhh
Confidence 999987766553455888888764 44699999999999999999999999998765543
No 13
>PRK09791 putative DNA-binding transcriptional regulator; Provisional
Probab=100.00 E-value=1.1e-56 Score=368.85 Aligned_cols=293 Identities=21% Similarity=0.272 Sum_probs=270.8
Q ss_pred CchhhHHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCCccccCHhHHHHHHHHHHHHHHHHHH
Q psy3760 1 MNLHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKPGQAILRSIEIIMQEIEGL 80 (306)
Q Consensus 1 m~~~~l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~~~lT~~G~~l~~~a~~il~~~~~~ 80 (306)
||+++|++|++|+++| ||++||++||+||||||++|++||+++|++||+|+++++ +||++|+.|+++++++++.++++
T Consensus 5 ~~l~~L~~f~~v~~~g-s~s~AA~~L~isQ~avS~~i~~LE~~lG~~LF~R~~r~~-~lT~~G~~l~~~a~~~l~~~~~~ 82 (302)
T PRK09791 5 VKIHQIRAFVEVARQG-SIRGASRMLNMSQPALTKSIQELEEGLAAQLFFRRSKGV-TLTDAGESFYQHASLILEELRAA 82 (302)
T ss_pred ccHHHHHHHHHHHHcC-CHHHHHHHhCCChHHHHHHHHHHHHHhCCeEEEEcCCCc-eECccHHHHHHHHHHHHHHHHHH
Confidence 7999999999999999 999999999999999999999999999999999999999 79999999999999999999999
Q ss_pred HHHHHhhccCCCCcEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEcc-ccCCCCCce
Q psy3760 81 KKIGKEFSAYDTGNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTE-ILSPSDKLI 159 (306)
Q Consensus 81 ~~~~~~~~~~~~~~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~-~~~~~~~~~ 159 (306)
...++.......|.|+||++++++..++++++..|.+.||++++++....+.++.+.|.+|++|++|+.. .....+++.
T Consensus 83 ~~~~~~~~~~~~g~l~I~~~~~~~~~~l~~~l~~~~~~~p~i~~~~~~~~~~~~~~~l~~g~~Di~i~~~~~~~~~~~~~ 162 (302)
T PRK09791 83 QEDIRQRQGQLAGQINIGMGASIARSLMPAVISRFHQQHPQVKVRIMEGQLVSMINELRQGELDFTINTYYQGPYDHEFT 162 (302)
T ss_pred HHHHHHhhcccceEEEEEechHHHHhhhHHHHHHHHHHCCCeEEEEEeCChHHHHHHHHCCCccEEEEecCCccccccee
Confidence 9999988888899999999999999999999999999999999999999999999999999999999843 222356799
Q ss_pred eeccccceEEEEecCCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCceeEEEEecCHHHHHHHHHhccc
Q psy3760 160 SIPCYQWEYVIIVPLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMG 239 (306)
Q Consensus 160 ~~~l~~~~~~~v~~~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~g 239 (306)
+.++++++++++++++||+... .+++||.++|++.+..+...+..+.+++...+..+++.+++++..++.+++..|.|
T Consensus 163 ~~~l~~~~~~l~~~~~~~~~~~--~~~~~l~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~g 240 (302)
T PRK09791 163 FEKLLEKQFAVFCRPGHPAIGA--RSLKQLLDYSWTMPTPHGSYYKQLSELLDDQAQTPQVGVVCETFSACISLVAKSDF 240 (302)
T ss_pred EEEeccceEEEEEcCCCCcCCC--CCHHHHhcCCeecCCCCCcHHHHHHHHHHhcCCCCCcceEEccHHHHHHHHHcCCe
Confidence 9999999999999999998753 47999999999998877677788889999999999999999999999999999999
Q ss_pred eeeeecceeccc-ccCCceeeecCCCCccceEEEEEeCCccccHHHHHHHHHHhHHhhH
Q psy3760 240 IGIIASIAFDSN-RDKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLLSPKLNR 297 (306)
Q Consensus 240 i~~~p~~~~~~~-~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~ 297 (306)
++++|..++... ..++++.++++...+...+|++|+++...++.++.|++++++.++.
T Consensus 241 i~~lp~~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~ 299 (302)
T PRK09791 241 LSILPEEMGCDPLHGQGLVMLPVSEILPKATYYLIQRRDTRQTPLTASLITLFRRECGY 299 (302)
T ss_pred EEEeeHhhhcccccCCceEEEecCCCCCCcceEEEEecCCCCCHHHHHHHHHHHHHHHH
Confidence 999999888665 6788999999876667899999999999999999999999987654
No 14
>PRK11233 nitrogen assimilation transcriptional regulator; Provisional
Probab=100.00 E-value=5.2e-56 Score=364.85 Aligned_cols=296 Identities=20% Similarity=0.268 Sum_probs=268.8
Q ss_pred CchhhHHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCCccccCHhHHHHHHHHHHHHHHHHHH
Q psy3760 1 MNLHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKPGQAILRSIEIIMQEIEGL 80 (306)
Q Consensus 1 m~~~~l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~~~lT~~G~~l~~~a~~il~~~~~~ 80 (306)
||+++|+||++|+++| ||++||++||+||||||++|++||++||++||+|+++++ .||++|+.|+++++++++.++++
T Consensus 1 m~l~~L~~F~~v~~~~-S~s~AA~~L~isQ~avS~~I~~LE~~lg~~LF~R~~r~v-~lT~~G~~l~~~a~~~l~~~~~~ 78 (305)
T PRK11233 1 MNFRRLKYFVKIVDIG-SLTQAAEVLHIAQPALSQQVATLEGELNQQLLIRTKRGV-TPTEAGKILYTHARAILRQCEQA 78 (305)
T ss_pred CCHHHHHHHHHHHHcC-CHHHHHHHhCCCchHHHHHHHHHHHHhCCceEEeCCCCc-eECHhHHHHHHHHHHHHHHHHHH
Confidence 8999999999999999 999999999999999999999999999999999999999 79999999999999999999999
Q ss_pred HHHHHhhccCCCCcEEEEecccch-hhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccCCCCCce
Q psy3760 81 KKIGKEFSAYDTGNLTIATTHTQA-RYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLI 159 (306)
Q Consensus 81 ~~~~~~~~~~~~~~l~I~~~~~~~-~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~~~~~~ 159 (306)
...+........|.++||+++++. ..++++++..|.+.||++.+.+......++.+.|.+|++|++|+..+ ...+++.
T Consensus 79 ~~~~~~~~~~~~g~l~I~~~~~~~~~~~~~~~l~~~~~~~p~i~l~~~~~~~~~~~~~l~~g~~Di~i~~~~-~~~~~~~ 157 (305)
T PRK11233 79 QLAVHNVGQALSGQVSIGLAPGTAASSLTMPLLQAVRAEFPGIVLYLHENSGATLNEKLMNGQLDMAVIYEH-SPVAGLS 157 (305)
T ss_pred HHHHHhhccccCceEEEEcccchhhHHHHHHHHHHHHHHCCCcEEEEEECCcHHHHHHHHCCCCCEEEEcCC-cCCCCcE
Confidence 999888877788999999987654 57889999999999999999999988889999999999999998654 5567899
Q ss_pred eeccccceEEEEecCCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCceeEEEEecCHHHHHHHHHhccc
Q psy3760 160 SIPCYQWEYVIIVPLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMG 239 (306)
Q Consensus 160 ~~~l~~~~~~~v~~~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~g 239 (306)
..++++++++++++++|| +..++++||.++|++....+...+..++.++...|..|++..++++..++..++.+|.|
T Consensus 158 ~~~l~~~~~~lv~~~~~~---~~~~~~~~l~~~~~i~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~v~~g~g 234 (305)
T PRK11233 158 SQPLLKEDLFLVGTQDCP---GQSVDLAAVAQMNLFLPRDYSAVRLRVDEAFSLRRLTAKVIGEIESIATLTAAIASGMG 234 (305)
T ss_pred EEEEeeeeEEEEEcCccC---CCCcCHHHHhCCCeecCCCCccHHHHHHHHHHHcCCCCceEEEEcCHHHHHHHHHcCCe
Confidence 999999999999999987 46799999999999988766666777888999999999988999999999999999999
Q ss_pred eeeeecceeccc-ccCCceeeecCCCCccceEEEEEeCCccccHHHHHHHHHHhHHhhHHHHHh
Q psy3760 240 IGIIASIAFDSN-RDKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLLSPKLNRKFINK 302 (306)
Q Consensus 240 i~~~p~~~~~~~-~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~ 302 (306)
++++|.+.+... ..+.++.+++..+.....++++|++++..++.++.|++++++.+.+...++
T Consensus 235 i~~lp~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~~~l~~~~~~~~~~~ 298 (305)
T PRK11233 235 VTVLPESAARSLCGAVNGWMARITTPSMSLSLSLNLSARLPLSPQAQAVKEILLSLVSSPVMEK 298 (305)
T ss_pred eEecchhHhhcccccCceeEEeecCCccceEEEEEecCCCCCCHHHHHHHHHHHHHHHHHhhhh
Confidence 999999887654 455677777766556689999999999999999999999999988777654
No 15
>PRK09906 DNA-binding transcriptional regulator HcaR; Provisional
Probab=100.00 E-value=7e-56 Score=363.42 Aligned_cols=291 Identities=21% Similarity=0.328 Sum_probs=265.4
Q ss_pred CchhhHHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCCccccCHhHHHHHHHHHHHHHHHHHH
Q psy3760 1 MNLHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKPGQAILRSIEIIMQEIEGL 80 (306)
Q Consensus 1 m~~~~l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~~~lT~~G~~l~~~a~~il~~~~~~ 80 (306)
||+++|++|++|+++| ||++||++||+|||||||+|++||++||++||+|+++|+ +||++|+.|+++++++++.++++
T Consensus 1 m~l~~L~~f~~v~~~g-s~s~AA~~L~isQ~avSr~i~~LE~~lg~~Lf~R~~~~~-~lT~~G~~l~~~a~~~l~~~~~~ 78 (296)
T PRK09906 1 MELRHLRYFVAVAEEL-NFTKAAEKLHTAQPSLSQQIKDLENCVGVPLLVRDKRKV-ALTAAGEVFLQDARAILEQAEKA 78 (296)
T ss_pred CcHHHHHHHHHHHhhC-CHHHHHHHhCCCCcHHHHHHHHHHHHhCCeeeeeCCCcc-eEcHhHHHHHHHHHHHHHHHHHH
Confidence 8999999999999999 999999999999999999999999999999999999999 79999999999999999999999
Q ss_pred HHHHHhhccCCCCcEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccCCCCCcee
Q psy3760 81 KKIGKEFSAYDTGNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLIS 160 (306)
Q Consensus 81 ~~~~~~~~~~~~~~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~~~~~~~ 160 (306)
...+...... .+.++||+++++...++++++..|.+.||++.+++...+++++.+.|.+|++|++|+..+ ...+++.+
T Consensus 79 ~~~~~~~~~~-~~~l~Ig~~~~~~~~~l~~~~~~~~~~~p~v~i~~~~~~~~~~~~~l~~~~~D~~i~~~~-~~~~~l~~ 156 (296)
T PRK09906 79 KLRARKIVQE-DRQLTIGFVPSAEVNLLPKVLPMFRLRHPDTLIELVSLITTQQEEKLRRGELDVGFMRHP-VYSDEIDY 156 (296)
T ss_pred HHHHHhhhcc-CCcEEEEEecchhhhHHHHHHHHHHHHCCCeEEEEEeCCcHHHHHHHHcCCeeEEEecCC-CCCCCceE
Confidence 9988876554 455999999999999999999999999999999999999999999999999999999765 46678999
Q ss_pred eccccceEEEEecCCCCCCCCCCcChhhhcCCCeEeecCCC--CcHHHHHHHHHhCCCceeEEEEecCHHHHHHHHHhcc
Q psy3760 161 IPCYQWEYVIIVPLDHPLLLLNSISLKEISNYPLITYDLSF--SGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRM 238 (306)
Q Consensus 161 ~~l~~~~~~~v~~~~~~l~~~~~i~~~dl~~~~~i~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~ 238 (306)
.+++.++++++++++||++.+..++++||.++|++.+..+. ..+..+..++...++.++..+++++..++++++.+|.
T Consensus 157 ~~l~~~~~~~v~~~~~pl~~~~~i~~~~L~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~ 236 (296)
T PRK09906 157 LELLDEPLVVVLPVDHPLAHEKEITAAQLDGVNFISTDPAYSGSLAPIIKAWFAQHNSQPNIVQVATNILVTMNLVGMGL 236 (296)
T ss_pred EEEecccEEEEecCCCccccCCCcCHHHHcCCCEEeccCCCCchHHHHHHHHHHHcCCCcceEEEeccHHHHHHHHHcCC
Confidence 99999999999999999998888999999999999987653 3467778899999999999999999999999999999
Q ss_pred ceeeeecceecccccCCceeeecCCCCccceEEEEEeCCccccHHHHHHHHHHhHHhhH
Q psy3760 239 GIGIIASIAFDSNRDKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLLSPKLNR 297 (306)
Q Consensus 239 gi~~~p~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~ 297 (306)
|++++|.+.+.. ...+++.+++++......+|++|+++. .++.++.|++++++.++.
T Consensus 237 g~~~~p~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~l~~~~~~ 293 (296)
T PRK09906 237 GCTIIPGYMNNF-NTGQVVFRPLAGNVPSIALLMAWKKGE-MKPALRDFIAIVQERLAS 293 (296)
T ss_pred cEEEeeHHHhhc-CCCCEEEeeCCCCcceeEEEEEECCCC-CCHHHHHHHHHHHhhhhc
Confidence 999999987654 345678888877555678999998875 699999999999988754
No 16
>PRK10837 putative DNA-binding transcriptional regulator; Provisional
Probab=100.00 E-value=3.8e-56 Score=364.18 Aligned_cols=285 Identities=22% Similarity=0.319 Sum_probs=262.2
Q ss_pred CchhhHHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCCccccCHhHHHHHHHHHHHHHHHHHH
Q psy3760 1 MNLHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKPGQAILRSIEIIMQEIEGL 80 (306)
Q Consensus 1 m~~~~l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~~~lT~~G~~l~~~a~~il~~~~~~ 80 (306)
||+++|++|.+|+|+| ||++||++||+||||||++|++||+++|++||+|+++|+ +||++|+.|+++++++++.++++
T Consensus 3 m~l~~L~~f~~v~e~~-s~t~AA~~L~isqpavS~~I~~LE~~lg~~Lf~R~~r~~-~lT~~G~~l~~~a~~~l~~~~~~ 80 (290)
T PRK10837 3 ITLRQLEVFAEVLKSG-STTQASVMLALSQSAVSAALTDLEGQLGVQLFDRVGKRL-VVNEHGRLLYPRALALLEQAVEI 80 (290)
T ss_pred CcHHHHHHHHHHHHcC-CHHHHHHHhCCCccHHHHHHHHHHHHhCCccEeecCCeE-EECHhHHHHHHHHHHHHHHHHHH
Confidence 7999999999999999 999999999999999999999999999999999999999 89999999999999999999988
Q ss_pred HHHHHhhccCCCCcEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccCCCCCcee
Q psy3760 81 KKIGKEFSAYDTGNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLIS 160 (306)
Q Consensus 81 ~~~~~~~~~~~~~~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~~~~~~~ 160 (306)
.+... +..|.++||++++++..++++++..|.+.||++.+++...++.++.+.+.+|++|++|...+ ...+++..
T Consensus 81 ~~~~~----~~~g~l~i~~~~~~~~~~~~~~l~~~~~~~P~i~i~v~~~~~~~~~~~l~~g~~Di~i~~~~-~~~~~~~~ 155 (290)
T PRK10837 81 EQLFR----EDNGALRIYASSTIGNYILPAMIARYRRDYPQLPLELSVGNSQDVINAVLDFRVDIGLIEGP-CHSPELIS 155 (290)
T ss_pred HHHHH----hhCCeEEEEecchhHhhhhHHHHHHHHHHCCCceEEEEECCHHHHHHHHHhCCceEEEecCC-CCCCceeE
Confidence 75443 35689999999999999999999999999999999999999999999999999999998644 45678999
Q ss_pred eccccceEEEEecCCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCceeEEEEecCHHHHHHHHHhccce
Q psy3760 161 IPCYQWEYVIIVPLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMGI 240 (306)
Q Consensus 161 ~~l~~~~~~~v~~~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi 240 (306)
.++++++++++++++||++ ...++++||.++||+.++.+...+..+..++...+..+++.+++++...+..++.+|.|+
T Consensus 156 ~~l~~~~~~lv~~~~hpl~-~~~i~~~~L~~~~~i~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi 234 (290)
T PRK10837 156 EPWLEDELVVFAAPDSPLA-RGPVTLEQLAAAPWILRERGSGTREIVDYLLLSHLPRFELAMELGNSEAIKHAVRHGLGI 234 (290)
T ss_pred EEeecceEEEEEcCCChhh-cCCCCHHHHhcCCeEEecCCCcHHHHHHHHHHHcCCCCceEEEeCCHHHHHHHHHhCCcE
Confidence 9999999999999999998 467999999999999998877777788888888888899999999999999999999999
Q ss_pred eeeecceeccc-ccCCceeeecCCCCccceEEEEEeCCccccHHHHHHHHHHhH
Q psy3760 241 GIIASIAFDSN-RDKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLLSP 293 (306)
Q Consensus 241 ~~~p~~~~~~~-~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~ 293 (306)
+++|.+.+... ..+.++.++++.+....++|++|+++...++.+++|++++++
T Consensus 235 ~~~p~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~~~~~~ 288 (290)
T PRK10837 235 SCLSRRVIADQLQAGTLVEVAVPLPRLMRTLYRIHHRQKHLSNALQRFLSYCQE 288 (290)
T ss_pred EEeeHHHHHHHHhCCcEEEEEcCCccceEEEEEEEeCCCCCCHHHHHHHHHHHh
Confidence 99999987665 677899999877666789999999999999999999999865
No 17
>PRK15421 DNA-binding transcriptional regulator MetR; Provisional
Probab=100.00 E-value=1.3e-55 Score=363.42 Aligned_cols=290 Identities=17% Similarity=0.267 Sum_probs=260.7
Q ss_pred CchhhHHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCCccccCHhHHHHHHHHHHHHHHHHHH
Q psy3760 1 MNLHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKPGQAILRSIEIIMQEIEGL 80 (306)
Q Consensus 1 m~~~~l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~~~lT~~G~~l~~~a~~il~~~~~~ 80 (306)
||+++|++|++|+++| ||++||++||+||||||++|++||++||++||+|+++++ +||++|+.|+++++++++.++++
T Consensus 2 m~l~~L~~f~av~~~g-s~s~AA~~L~iSqpaVS~~Ik~LE~~lg~~LF~R~~r~v-~lT~~G~~l~~~a~~il~~~~~~ 79 (317)
T PRK15421 2 IEVKHLKTLQALRNCG-SLAAAAATLHQTQSALSHQFSDLEQRLGFRLFVRKSQPL-RFTPQGEILLQLANQVLPQISQA 79 (317)
T ss_pred ccHHHHHHHHHHHHcC-CHHHHHHHhCCCHHHHHHHHHHHHHHhCCEEEEecCCCc-eECHhHHHHHHHHHHHHHHHHHH
Confidence 8999999999999999 999999999999999999999999999999999999999 89999999999999999999998
Q ss_pred HHHHHhhccCCCCcEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccCCCCCcee
Q psy3760 81 KKIGKEFSAYDTGNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLIS 160 (306)
Q Consensus 81 ~~~~~~~~~~~~~~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~~~~~~~ 160 (306)
....+ ....|.|+||++.++...++++++..|.+.||++.+++....+.++.+.|.+|++|++|+..+ ...+++.+
T Consensus 80 ~~~~~---~~~~g~l~Ig~~~~~~~~~l~~~l~~~~~~~P~i~l~~~~~~~~~~~~~L~~g~~Dl~i~~~~-~~~~~~~~ 155 (317)
T PRK15421 80 LQACN---EPQQTRLRIAIECHSCIQWLTPALENFHKNWPQVEMDFKSGVTFDPQPALQQGELDLVMTSDI-LPRSGLHY 155 (317)
T ss_pred HHHhc---ccCceeEEEEecccchHHHHHHHHHHHHHHCCCceEEEEeCccHHHHHHHHCCCcCEEEecCc-ccCCCceE
Confidence 76543 345689999999988889999999999999999999999998889999999999999998654 55678999
Q ss_pred eccccceEEEEecCCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCceeEEEEecCHHHHHHHHHhccce
Q psy3760 161 IPCYQWEYVIIVPLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMGI 240 (306)
Q Consensus 161 ~~l~~~~~~~v~~~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi 240 (306)
.++++++++++++++||++.+..++++||.++|++....+...+..+..++...|+.+++. .+++...+.+++.+|.|+
T Consensus 156 ~~l~~~~~~lv~~~~hpl~~~~~i~~~~L~~~p~i~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~v~~g~Gi 234 (317)
T PRK15421 156 SPMFDYEVRLVLAPDHPLAAKTRITPEDLASETLLIYPVQRSRLDVWRHFLQPAGVSPSLK-SVDNTLLLIQMVAARMGI 234 (317)
T ss_pred EEeccceEEEEEcCCCCccccCcCCHHHhCCCcEEecCCchhhHHHHHHHHHHhCCCCcee-ecCCHHHHHHHHHhCCcE
Confidence 9999999999999999999888999999999999998776555667778888889888765 789999999999999999
Q ss_pred eeeecceeccc-ccCCceeeecCCCCccceEEEEEeCCccccHHHHHHHHHHhHHhhHH
Q psy3760 241 GIIASIAFDSN-RDKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLLSPKLNRK 298 (306)
Q Consensus 241 ~~~p~~~~~~~-~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~ 298 (306)
+++|.+++... ..+.++.+++++ .....++++|+++...++.++.|++++++.+...
T Consensus 235 ~i~p~~~~~~~~~~~~l~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~fi~~l~~~~~~~ 292 (317)
T PRK15421 235 AALPHWVVESFERQGLVVTKTLGE-GLWSRLYAAVRDGEQRQPVTEAFIRSARNHACDH 292 (317)
T ss_pred EEecchhcchhhcCCcEEEeecCC-cceeEEEEEEEcCCCCChHHHHHHHHHHHhhhhh
Confidence 99999988765 556666666655 3456899999999999999999999999877654
No 18
>PRK09986 DNA-binding transcriptional activator XapR; Provisional
Probab=100.00 E-value=1.5e-55 Score=361.38 Aligned_cols=286 Identities=20% Similarity=0.255 Sum_probs=260.6
Q ss_pred CchhhHHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCCccccCHhHHHHHHHHHHHHHHHHHH
Q psy3760 1 MNLHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKPGQAILRSIEIIMQEIEGL 80 (306)
Q Consensus 1 m~~~~l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~~~lT~~G~~l~~~a~~il~~~~~~ 80 (306)
||+++|++|++|+++| ||++||++|+|||||||++|++||++||++||+|+++++ +||++|+.|++++++++++++++
T Consensus 7 ~~l~~l~~f~~v~~~g-s~t~AA~~L~itq~avS~~i~~LE~~lg~~Lf~R~~r~~-~lT~~G~~l~~~a~~~l~~~~~~ 84 (294)
T PRK09986 7 IDLKLLRYFLAVAEEL-HFGRAAARLNISQPPLSIHIKELEDQLGTPLFIRHSRSV-VLTHAGKILMEESRRLLDNAEQS 84 (294)
T ss_pred hhHHHHHHHHHHHHhc-CHHHHHHHhCCCCCHHHHHHHHHHHHhCCeeEeeCCCce-eECHhHHHHHHHHHHHHHHHHHH
Confidence 7999999999999999 999999999999999999999999999999999999999 79999999999999999999999
Q ss_pred HHHHHhhccCCCCcEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccc-cCCCCCce
Q psy3760 81 KKIGKEFSAYDTGNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEI-LSPSDKLI 159 (306)
Q Consensus 81 ~~~~~~~~~~~~~~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~-~~~~~~~~ 159 (306)
...++.......|.++||+++++...++++++..|.++||++++++...+++++.+.|.+|++|++|+... .....++.
T Consensus 85 ~~~~~~~~~~~~~~l~I~~~~~~~~~~l~~~l~~f~~~~p~i~l~i~~~~~~~~~~~l~~g~~D~~i~~~~~~~~~~~l~ 164 (294)
T PRK09986 85 LARVEQIGRGEAGRIEIGIVGTALWGRLRPAMRHFLKENPNVEWLLRELSPSMQMAALERRELDAGIWRMADLEPNPGFT 164 (294)
T ss_pred HHHHHHHhccCcceEEEEEehHHhHHHHHHHHHHHHHhCCCeEEEEEeCCHHHHHHHHHcCCCCEEEecCCccCCCCCeE
Confidence 99988877777899999999999999999999999999999999999998889999999999999998543 24567899
Q ss_pred eeccccceEEEEecCCCCCCCCCCcChhhhcCCCeEeecCCCCc-HHHHHHHHHhCCCceeEEEEecCHHHHHHHHHhcc
Q psy3760 160 SIPCYQWEYVIIVPLDHPLLLLNSISLKEISNYPLITYDLSFSG-RIKLDREFSLQKLTPYIVLETINSDIIKTYVELRM 238 (306)
Q Consensus 160 ~~~l~~~~~~~v~~~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~ 238 (306)
+.++++++++++++++||+..+..++++||.++|+|.+..+... ...+.+++...++.+++.+++++..++..+|.+|.
T Consensus 165 ~~~l~~~~~~~v~~~~~~l~~~~~~~~~dL~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~ 244 (294)
T PRK09986 165 SRRLHESAFAVAVPEEHPLASRSSVPLKALRNEYFITLPFVHSDWGKFLQRVCQQAGFSPQIIRQVNEPQTVLAMVSMGI 244 (294)
T ss_pred EEEeecccEEEEEcCCCCcccCCccCHHHHcCCCEEecCCCchhHHHHHHHHHHHCCCCCceeeecCCHHHHHHHHHcCC
Confidence 99999999999999999999888899999999999998775443 34778888889999999999999999999999999
Q ss_pred ceeeeecceecccccCCceeeecCCCCccceEEEEEeCCccccHHHHHHHHHH
Q psy3760 239 GIGIIASIAFDSNRDKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLL 291 (306)
Q Consensus 239 gi~~~p~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l 291 (306)
|++++|.+.+.. ..+++..+|++.. ...+++++|+++. .++.++.|++++
T Consensus 245 gi~~l~~~~~~~-~~~~l~~~~~~~~-~~~~~~l~~~~~~-~~~~~~~f~~~~ 294 (294)
T PRK09986 245 GITLLPDSYAQI-PWPGVVFRPLKER-IPADLYAVYHPDQ-VTPALNKLLAAL 294 (294)
T ss_pred eEEEccHHHhhc-CCCCeEEEECCCC-CceeEEEEEeCCC-CChHHHHHHhhC
Confidence 999999987653 3457888898764 4579999999886 699999999874
No 19
>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=1.3e-54 Score=353.49 Aligned_cols=279 Identities=23% Similarity=0.353 Sum_probs=257.2
Q ss_pred hHHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCCccccCHhHHHHHHHHHHHHHHHHHHHHHH
Q psy3760 5 QFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKPGQAILRSIEIIMQEIEGLKKIG 84 (306)
Q Consensus 5 ~l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~~~lT~~G~~l~~~a~~il~~~~~~~~~~ 84 (306)
+|++|++|+++| ||++||++||+||||||++|++||++||++||+|+++++ +||++|+.|+++++++++.++++...+
T Consensus 1 ~l~~f~~v~~~g-s~~~AA~~L~isqsavS~~i~~LE~~lg~~Lf~R~~~~~-~lT~~G~~l~~~a~~~l~~~~~~~~~~ 78 (279)
T TIGR03339 1 QLKAFHAVARCG-SFTRAAERLGLSQPTVTDQVRKLEERYGVELFHRNGRRL-ELTDAGHRLLPIVERLFQQEAEAEFLL 78 (279)
T ss_pred CchhhHHHHhcC-CHHHHHHHhcCCchHHHHHHHHHHHHhCCccEEEcCCeE-EEChhHHHHHHHHHHHHHHHHHHHHHH
Confidence 589999999999 999999999999999999999999999999999999999 899999999999999999999999999
Q ss_pred HhhccCCCCcEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccCCCCCceeeccc
Q psy3760 85 KEFSAYDTGNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLISIPCY 164 (306)
Q Consensus 85 ~~~~~~~~~~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~~~~~~~~~l~ 164 (306)
........|.++||++. ..++++++..|.+.||++++++...++.++.+.|.+|++|++|+... ...+++...+++
T Consensus 79 ~~~~~~~~~~l~ig~~~---~~~~~~~l~~~~~~~p~v~l~i~~~~~~~~~~~l~~g~~Dl~i~~~~-~~~~~~~~~~l~ 154 (279)
T TIGR03339 79 RESGALREGSLRIAATA---PYYVLDLVARFRQRYPGIEVSVRIGNSQEVLQALQSYRVDVAVSSEV-VDDPRLDRVVLG 154 (279)
T ss_pred HHhccCcceEEEEeCch---HHHHHHHHHHHHHHCCCcEEEEEECCHHHHHHHHHcCCCcEEEEecc-cCCCceEEEEcC
Confidence 98877778999999984 45899999999999999999999999999999999999999998644 556789999999
Q ss_pred cceEEEEecCCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCceeEEEEecCHHHHHHHHHhccceeeee
Q psy3760 165 QWEYVIIVPLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMGIGIIA 244 (306)
Q Consensus 165 ~~~~~~v~~~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~~~p 244 (306)
++++++|++++||++...+++++||.++|++.+..+...+..++.++...++.++..+++++..++.+++.+|.|++++|
T Consensus 155 ~~~~~lv~s~~~pl~~~~~i~~~~L~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~~lp 234 (279)
T TIGR03339 155 NDPLVAVVHRQHPLAERESVTLEELAGQPLLMREPGSVTRQTTEEALAAAGVAPRPALEIGSREAIREAVLAGLGVSVVS 234 (279)
T ss_pred CceEEEEECCCCccccCCCcCHHHHhCCCeEEecCCCChHHHHHHHHHHcCCCccEEEEeCCHHHHHHHHHcCCCEEEcc
Confidence 99999999999999988889999999999999988777778889999999999999999999999999999999999999
Q ss_pred cceecccccCCceeeecCCCCccceEEEEEeCCccccHHHHHHHHHH
Q psy3760 245 SIAFDSNRDKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLL 291 (306)
Q Consensus 245 ~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l 291 (306)
.+.... .++++.+++++......++++|+++...+|.++.|++.+
T Consensus 235 ~~~~~~--~~~l~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~ 279 (279)
T TIGR03339 235 AAEVGR--DPRLRVLPIVGAEPTMDEYLYCLKERRGARLIAAFLELA 279 (279)
T ss_pred hhhhcc--CCceEEEECCCCcccceEEEEEECCCCCCHHHHHHHhhC
Confidence 976543 577999998775556799999999999999999999753
No 20
>PRK09508 leuO leucine transcriptional activator; Reviewed
Probab=100.00 E-value=3.4e-55 Score=361.49 Aligned_cols=291 Identities=14% Similarity=0.133 Sum_probs=258.3
Q ss_pred CchhhHHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCCccccCHhHHHHHHHHHHHHHHHHHH
Q psy3760 1 MNLHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKPGQAILRSIEIIMQEIEGL 80 (306)
Q Consensus 1 m~~~~l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~~~lT~~G~~l~~~a~~il~~~~~~ 80 (306)
||+++|++|++|+|+| ||++||++||+||||||++|++||++||++||+|+++|+ +||++|+.|+++++++++.++..
T Consensus 22 ~~l~~L~~f~avae~g-s~s~AA~~L~isQpavS~~I~~LE~~lg~~LF~R~~r~~-~lT~~G~~l~~~~~~~l~~~~~~ 99 (314)
T PRK09508 22 VDLNLLTVFDAVMQEQ-NITRAAHNLGMSQPAVSNAVARLKVMFNDELFVRYGRGI-QPTARARQLFGPVRQALQLVQNE 99 (314)
T ss_pred cChHHHHHHHHHHhcC-CHHHHHHHhCCCHHHHHHHHHHHHHhhCCCcEEEcCCCC-cCcHHHHHHHHHHHHHHHHHHHh
Confidence 7999999999999999 999999999999999999999999999999999999999 79999999999999999998875
Q ss_pred HHHHHhhccCCCCcEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccCCCCCcee
Q psy3760 81 KKIGKEFSAYDTGNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLIS 160 (306)
Q Consensus 81 ~~~~~~~~~~~~~~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~~~~~~~ 160 (306)
............+.++||+..++...++++++..|.++||++.+++...+..++.+.|.+|++|++|+..+ ...+++..
T Consensus 100 ~~~~~~~~~~~~~~i~i~~~~~~~~~~l~~~l~~f~~~~P~i~l~i~~~~~~~~~~~l~~g~~Di~i~~~~-~~~~~l~~ 178 (314)
T PRK09508 100 LPGSGFEPESSERVFNLCICSPLDIRLTSQIYNRIEQIAPNIHVVFKSSLNQNIEHQLRYQETEFVISYEE-FDRPEFTS 178 (314)
T ss_pred cCCCCCCccccccEEEEEechhHHHHHHHHHHHHHHHhCCCcEEEEEeCcchhHHHHHhcCCccEEEecCC-CCccccce
Confidence 43222112234678999999888788999999999999999999999998889999999999999999754 45678999
Q ss_pred eccccceEEEEecCCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCceeEEEEecCHHHHHHHHHhccce
Q psy3760 161 IPCYQWEYVIIVPLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMGI 240 (306)
Q Consensus 161 ~~l~~~~~~~v~~~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi 240 (306)
.++++++++++++++||+. +..++++||.+++++..... .....++.++...|..+++.+++++...+.+++.+|.|+
T Consensus 179 ~~l~~~~~~lv~~~~hpl~-~~~~~~~~L~~~~~~~~~~~-~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~v~~g~gi 256 (314)
T PRK09508 179 VPLFKDELVLVASKNHPRI-KGPITEEQLYNEQHAVVSLD-RFASFSQPWYDTVDKQASIAYQGTALSSVLNVVSQTHLV 256 (314)
T ss_pred eeeecCceEEEEcCCCCcc-CCCCCHHHHhhCCCEEecCC-CCccHHHHHHHhcCcCceEEEEcCcHHHHHHHHHhCChH
Confidence 9999999999999999987 45799999999998766532 234456778888899999999999999999999999999
Q ss_pred eeeecceeccc-ccCCceeeecCCCCccceEEEEEeCCccccHHHHHHHHHHhHHhh
Q psy3760 241 GIIASIAFDSN-RDKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLLSPKLN 296 (306)
Q Consensus 241 ~~~p~~~~~~~-~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~ 296 (306)
+++|.+.+... ..++++.++++.....+.++++|+++...+|+.++|.+.+++.++
T Consensus 257 ~~~p~~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~p~~~~l~~~i~~~~~ 313 (314)
T PRK09508 257 AIAPRWLAEEFAESLELQILPLPLKNNSRTCYLSWHESAGRDKGHQWMEELLVSICK 313 (314)
T ss_pred HHHHHHHHHHhhhccCceEeCCCCCCCCceEEEEeccccCCChHHHHHHHHHHHHhc
Confidence 99999888665 577899999987666789999999999999999999999998765
No 21
>PRK11074 putative DNA-binding transcriptional regulator; Provisional
Probab=100.00 E-value=8.7e-55 Score=356.98 Aligned_cols=287 Identities=16% Similarity=0.208 Sum_probs=255.0
Q ss_pred CchhhHHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCCccccCHhHHHHHHHHHHHHHHHHHH
Q psy3760 1 MNLHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKPGQAILRSIEIIMQEIEGL 80 (306)
Q Consensus 1 m~~~~l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~~~lT~~G~~l~~~a~~il~~~~~~ 80 (306)
||+++|++|.+|+++| ||++||++||+||||||++|++||++||++||+|+++++ +||++|+.|+++++++++.++++
T Consensus 2 ~~~~~L~~f~~v~e~~-s~s~AA~~L~isQpavS~~I~~LE~~lg~~LF~R~~r~~-~lT~~G~~l~~~~~~~l~~~~~~ 79 (300)
T PRK11074 2 WSEYSLEVVDAVARTG-SFSAAAQELHRVPSAVSYTVRQLEEWLAVPLFERRHRDV-ELTPAGEWFVKEARSVIKKMQET 79 (300)
T ss_pred CCHHHHHHHHHHHHhC-CHHHHHHHhCCCHHHHHHHHHHHHHHhCCeeEEeCCCCc-eECccHHHHHHHHHHHHHHHHHH
Confidence 7999999999999999 999999999999999999999999999999999999999 89999999999999999999999
Q ss_pred HHHHHhhccCCCCcEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEcccc-CCCCCce
Q psy3760 81 KKIGKEFSAYDTGNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEIL-SPSDKLI 159 (306)
Q Consensus 81 ~~~~~~~~~~~~~~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~-~~~~~~~ 159 (306)
.+.+++......|.++||++++++..++++++..|.+.||++++++......++.+.|.+|++|++|+..+. ...+++.
T Consensus 80 ~~~~~~~~~~~~g~l~Ig~~~~~~~~~l~~~l~~~~~~~p~i~i~i~~~~~~~~~~~l~~g~~Dl~i~~~~~~~~~~~l~ 159 (300)
T PRK11074 80 RRQCQQVANGWRGQLSIAVDNIVRPDRTRQLIVDFYRHFDDVELIIRQEVFNGVWDALADGRVDIAIGATRAIPVGGRFA 159 (300)
T ss_pred HHHHHHHhcCCCceEEEEEcCccchhHHHHHHHHHHHhCCCceEEEEehhhhHHHHHHHCCCCCEEEecCccCCcccccc
Confidence 999998888889999999999999999999999999999999999999988999999999999999986432 2346799
Q ss_pred eeccccceEEEEecCCCCCCCCC-CcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCceeEEEEecCHHHHHHHHHhcc
Q psy3760 160 SIPCYQWEYVIIVPLDHPLLLLN-SISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRM 238 (306)
Q Consensus 160 ~~~l~~~~~~~v~~~~~~l~~~~-~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~ 238 (306)
+.++++++++++++++||++.+. .++++||.++|++....+.........++ ..++..+.+++...++++|.+|.
T Consensus 160 ~~~l~~~~~~~v~~~~hpl~~~~~~~~~~dl~~~p~i~~~~~~~~~~~~~~~~----~~~~~~~~~~~~~~~~~~v~~g~ 235 (300)
T PRK11074 160 FRDMGMLSWACVVSSDHPLASMDGPLSDDELRPYPSLCLEDTSRTLPKRITWL----LDNQRRLVVPDWESAINCLSAGL 235 (300)
T ss_pred eeecccceEEEEEcCCCcccccCCCCCHHHHhhCCEEEecCCCcccccCccce----ecCCceEEECCHHHHHHHHHcCC
Confidence 99999999999999999998764 69999999999999876543211112222 12345788999999999999999
Q ss_pred ceeeeecceeccc-ccCCceeeecCCCCccceEEEEEeCCccccHHHHHHHHHHhHH
Q psy3760 239 GIGIIASIAFDSN-RDKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLLSPK 294 (306)
Q Consensus 239 gi~~~p~~~~~~~-~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~ 294 (306)
|++++|.+.+... ..+.++.+++++....++++++|+++. .+|.+++|++++++.
T Consensus 236 gi~~lp~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~i~~~ 291 (300)
T PRK11074 236 CVGMVPTHFAKPLINSGKLVELTLENPFPDSPCCLTWQQND-MSPALAWLLDYLGDS 291 (300)
T ss_pred eEEeCCHHHhHHHHhCCceEEEecCCCCCCceEEEEEecCC-CChHHHHHHHHHhhc
Confidence 9999999988765 677899999987667789999999875 699999999999663
No 22
>PRK15243 transcriptional regulator SpvR; Provisional
Probab=100.00 E-value=2.9e-54 Score=348.33 Aligned_cols=280 Identities=15% Similarity=0.152 Sum_probs=246.9
Q ss_pred hhHHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCCccccCHhHHHHHHHHHHHHHHHHHHHHH
Q psy3760 4 HQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKPGQAILRSIEIIMQEIEGLKKI 83 (306)
Q Consensus 4 ~~l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~~~lT~~G~~l~~~a~~il~~~~~~~~~ 83 (306)
++|+||++|+++| ||++||++||+||||+|++|++||++||++||+|+++++ +||++|+.||++|+++++.++++...
T Consensus 7 rqL~~F~aVae~g-Sfs~AA~~L~isQpavS~~Ik~LE~eLG~~LF~R~~r~~-~LT~aG~~ll~~a~~il~~~~~~~~~ 84 (297)
T PRK15243 7 KKLKIFITLMETG-SFSIATSVLYITRTPLSRVISDLERELKQRLFIRKNGTL-IPTEFAQTIYRKVKSHYIFLHALEQE 84 (297)
T ss_pred HHHHHHHHHHHcC-CHHHHHHHHCcCHHHHHHHHHHHHHHhCCccEEeCCCCe-eECHHHHHHHHHHHHHHHHHHHHHHH
Confidence 7999999999999 999999999999999999999999999999999999999 79999999999999999999999998
Q ss_pred HHhhccCCCCcEEEEecccchhhhhHHHHHHH-----HHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccCCCCCc
Q psy3760 84 GKEFSAYDTGNLTIATTHTQARYALPKIIKEF-----TIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKL 158 (306)
Q Consensus 84 ~~~~~~~~~~~l~I~~~~~~~~~~l~~~l~~~-----~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~~~~~ 158 (306)
+.... ..|.|+||+.. ++|+++..| ...||++++.+...++..+.+.+.+|. |++++.......+++
T Consensus 85 ~~~~~--~~G~L~Ig~~~-----~lP~~~~~~~~~~~~~~~P~v~i~~~~~~~~~~~~~l~~~~-~i~i~~~~~~~~~~l 156 (297)
T PRK15243 85 IGPTG--KTKQLEIIFDE-----IYPESLKNLIISALTISGQKTNIMGRAVNSQIIEELCQTNN-CIVISARNYFHRESL 156 (297)
T ss_pred HHhcC--CCceEEEEEec-----cchHHHHHHHHHHHHhhCCceEEEEecCCHHHHHHHHcCCC-cEEEecCCCCCCCCe
Confidence 87643 36999999653 666677665 447999999999888777777776665 688864332356889
Q ss_pred eeeccccceEEEEecCCCCCCCCCCcChhhhcCCCeEeecCCCCc-HHHHHHHHHh-CCCceeEEEEecCHHHHHHH--H
Q psy3760 159 ISIPCYQWEYVIIVPLDHPLLLLNSISLKEISNYPLITYDLSFSG-RIKLDREFSL-QKLTPYIVLETINSDIIKTY--V 234 (306)
Q Consensus 159 ~~~~l~~~~~~~v~~~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~-~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~--v 234 (306)
.+.++++++++++++++||++.++ ++.||.++|||....+.+. +..++++|.. .|+ |++.+++++.++++++ |
T Consensus 157 ~~~~l~~e~lvlv~~~~hpla~~~--~l~~l~~~p~il~~~~~~~~r~~~~~~~~~~~gi-~~~~~e~~s~e~i~~lv~v 233 (297)
T PRK15243 157 VCRTSVEGGVMLFIPKKFFLCGKP--DINRLAGTPVLFHEGAKNFNLDTIYHFFEQTLGI-TNPAFSFDNVDLFSSLYRL 233 (297)
T ss_pred eEEEeccCCEEEEEcCCCccccCC--CHHHHhcCCeEEecCCCccHHHHHHHHHHHhcCC-ChhheecccHHHHHHHHHH
Confidence 999999999999999999998765 8999999999999999886 7799999996 999 7899999999999999 4
Q ss_pred HhccceeeeecceecccccCCceeeecCCCCccceEEEEEeCCccccHHHHHHHHHHhHHhhHH
Q psy3760 235 ELRMGIGIIASIAFDSNRDKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLLSPKLNRK 298 (306)
Q Consensus 235 ~~g~gi~~~p~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~ 298 (306)
.+|.|++++|...+.....+.++.+|+++.. ...+++|+++++.+|+++.|++.+++.+++.
T Consensus 234 ~~glGia~lp~~~~~~~~~~~L~~~~i~~~~--~~~~lv~~k~~~ls~~~~~f~~~~~~~~~~~ 295 (297)
T PRK15243 234 QQGLAMLLIPVRVCRALGLSTDHALHIKGVA--LCTSLYYPTKKRETPDYRKAIKLIQQELKQS 295 (297)
T ss_pred hcCCeeecccHHHHHHHhhCceEEeccCcCc--eeEEEEecCCCCCChhHHHHHHHHHHHHhhc
Confidence 9999999999888775588899999998733 3459999999999999999999998777654
No 23
>PRK10094 DNA-binding transcriptional activator AllS; Provisional
Probab=100.00 E-value=2.8e-53 Score=348.54 Aligned_cols=288 Identities=13% Similarity=0.153 Sum_probs=252.3
Q ss_pred CchhhHHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCCccccCHhHHHHHHHHHHHHHHHHHH
Q psy3760 1 MNLHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKPGQAILRSIEIIMQEIEGL 80 (306)
Q Consensus 1 m~~~~l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~~~lT~~G~~l~~~a~~il~~~~~~ 80 (306)
||+++|++|++++|+| ||++||++||+||||||++|++||++||++||+|+++++ +||++|+.|+++++++++.++++
T Consensus 2 ~~~~~L~~f~~v~e~g-s~s~AA~~L~iSQpavS~~I~~LE~~lg~~Lf~R~~r~~-~lT~~G~~l~~~a~~il~~~~~~ 79 (308)
T PRK10094 2 FDPETLRTFIAVAETG-SFSKAAERLCKTTATISYRIKLLEENTGVALFFRTTRSV-TLTAAGEHLLSQARDWLSWLESM 79 (308)
T ss_pred CCHHHHHHHHHHHHhC-CHHHHHHHhcCCHHHHHHHHHHHHHHhCCEEEeeCCCce-eECHhHHHHHHHHHHHHHHHHHH
Confidence 7999999999999999 999999999999999999999999999999999999999 79999999999999999999999
Q ss_pred HHHHHhhccCCCCcEEEEecccc-hhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccc-cCCCCCc
Q psy3760 81 KKIGKEFSAYDTGNLTIATTHTQ-ARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEI-LSPSDKL 158 (306)
Q Consensus 81 ~~~~~~~~~~~~~~l~I~~~~~~-~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~-~~~~~~~ 158 (306)
.+.+.....+..|.++||+.+.. ...++++++..|+++||++++++....+.++.+.|.+|++|++|+... ....+++
T Consensus 80 ~~~~~~~~~~~~g~l~Ig~~~~~~~~~~l~~~l~~~~~~~P~i~l~l~~~~~~~~~~~l~~g~~D~~i~~~~~~~~~~~l 159 (308)
T PRK10094 80 PSELQQVNDGVERQVNIVINNLLYNPQAVAQLLAWLNERYPFTQFHISRQIYMGVWDSLLYEGFSLAIGVTGTEALANTF 159 (308)
T ss_pred HHHHHHhcCCCCccEEEEecccccCHHHHHHHHHHHHHhCCCcEEEEEeehhhhHHHHHhCCCccEEEecccCccccCCe
Confidence 99998887788999999998763 467899999999999999999999999999999999999999997432 2346789
Q ss_pred eeeccccceEEEEecCCCCCCCC-CCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCceeEEEEecCHHHHHHHHHhc
Q psy3760 159 ISIPCYQWEYVIIVPLDHPLLLL-NSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELR 237 (306)
Q Consensus 159 ~~~~l~~~~~~~v~~~~~~l~~~-~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g 237 (306)
...++++++++++++++||++++ ..++++||.++|+|.+..+... ...... ....+...+.+++..+++.+|..|
T Consensus 160 ~~~~l~~~~~~~v~~~~hpl~~~~~~~~~~~L~~~~~i~~~~~~~~--~~~~~~--~~~~~~~~~~~~~~~~~~~~v~~g 235 (308)
T PRK10094 160 SLDPLGSVQWRFVMAADHPLANVEEPLTEAQLRRFPAVNIEDSART--LTKRVA--WRLPGQKEIIVPDMETKIAAHLAG 235 (308)
T ss_pred eEEEecceeEEEEECCCCCCcCCCCCCCHHHHHhCCeeEeeccccc--cchhhc--cccCCCcEEEECCHHHHHHHHHcC
Confidence 99999999999999999999874 4799999999999998765421 111111 112234567899999999999999
Q ss_pred cceeeeecceeccc-ccCCceeeecCCCCccceEEEEEeCCccccHHHHHHHHHHhHHh
Q psy3760 238 MGIGIIASIAFDSN-RDKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLLSPKL 295 (306)
Q Consensus 238 ~gi~~~p~~~~~~~-~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~ 295 (306)
.|++++|...+... ..+.++.++++......+++++|+++.. +|+++.|++.+++..
T Consensus 236 ~gi~~lp~~~~~~~~~~~~l~~~~l~~~~~~~~~~l~~~~~~~-~~~~~~~~~~~~~~~ 293 (308)
T PRK10094 236 VGIGFLPKSLCQSMIDNQQLVSRVIPTMRPPSPLSLAWRKFGS-GKAVEDIVTLFTQRR 293 (308)
T ss_pred CcEEeCChHhhhHHhhcCceEEEeCCCCCCCcceEEEEecCCC-CcHHHHHHHHHhCCC
Confidence 99999999888765 6678999998876667899999999874 999999999998654
No 24
>PRK11062 nhaR transcriptional activator NhaR; Provisional
Probab=100.00 E-value=1.4e-53 Score=349.06 Aligned_cols=282 Identities=14% Similarity=0.138 Sum_probs=256.1
Q ss_pred CchhhHHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCCccccCHhHHHHHHHHHHHHHHHHHH
Q psy3760 1 MNLHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKPGQAILRSIEIIMQEIEGL 80 (306)
Q Consensus 1 m~~~~l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~~~lT~~G~~l~~~a~~il~~~~~~ 80 (306)
||+++|++|++|+|+| ||++||++||+||||+|++|++||++||++||+|+++|+ +||++|+.|+++++++++.++++
T Consensus 4 m~l~~L~~F~~v~e~g-s~s~AA~~L~isqpavS~~I~~LE~~lg~~Lf~R~~r~~-~lT~~G~~l~~~a~~il~~~~~~ 81 (296)
T PRK11062 4 INYNHLYYFWMVCKEG-SVVGAAEALFLTPQTITGQIKALEERLQGKLFKRKGRGL-EPTELGELVFRYADKMFTLSQEM 81 (296)
T ss_pred cCHHHHHHHHHHHhcC-CHHHHHHHhCCChHHHHHHHHHHHHHcCccceeecCCce-eECHhHHHHHHHHHHHHHHHHHH
Confidence 8999999999999999 999999999999999999999999999999999999999 89999999999999999999999
Q ss_pred HHHHHhhccCCCCcEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccC--CCCCc
Q psy3760 81 KKIGKEFSAYDTGNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILS--PSDKL 158 (306)
Q Consensus 81 ~~~~~~~~~~~~~~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~--~~~~~ 158 (306)
.+..+ ......|.|+||++++++..++++++..|...||++++++....+.++...|.+|++|++|+..+.. ..+++
T Consensus 82 ~~~~~-~~~~~~g~l~i~~~~~~~~~~l~~~l~~f~~~~P~i~l~~~~~~~~~~~~~l~~g~~D~~i~~~~~~~~~~~~l 160 (296)
T PRK11062 82 LDIVN-YRKESNLLFDVGVADALSKRLVSRVLLTAVPEDESIHLRCFESTHEMLLEQLSQHKLDMILSDCPVDSTQQEGL 160 (296)
T ss_pred HHHhc-ccccCceEEEEEecchhhHhhHHHHHHHHHhcCCceEEEEEeCCHHHHHHHHHcCCCCEEEecCCCccccccch
Confidence 98764 4566788999999999999999999999999999999999988888999999999999999853322 34679
Q ss_pred eeeccccceEEEEecCCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCceeEEEEecCHHHHHHHHHhcc
Q psy3760 159 ISIPCYQWEYVIIVPLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRM 238 (306)
Q Consensus 159 ~~~~l~~~~~~~v~~~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~ 238 (306)
...++++++++++++++||+. .++++|.++|++.+..+...+..+..++...+..+++.+++++..++.+++.+|.
T Consensus 161 ~~~~l~~~~~~~~~~~~~~~~----~~~~~l~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~ 236 (296)
T PRK11062 161 FSKKLGECGVSFFCTNPLPEK----PFPACLEERRLLIPGRRTMLGRKLLNWFNSQGLNVEILGEFDDAALMKAFGAYHD 236 (296)
T ss_pred hhhhhhccCcceEecCCCccc----cChHHHhcCCeeecCCCchHHHHHHHHHHHcCCCceeeeeeCcHHHHHHHHHcCC
Confidence 999999999999999999853 3689999999999887766677788999999999999999999999999999999
Q ss_pred ceeeeecceeccc-ccCCceeeecCCCCccceEEEEEeCCccccHHHHHHHHH
Q psy3760 239 GIGIIASIAFDSN-RDKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKL 290 (306)
Q Consensus 239 gi~~~p~~~~~~~-~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~ 290 (306)
|++++|.+.+... ..++++.++... ....++|++|+++...+|.++.|++.
T Consensus 237 Gi~~lp~~~~~~~~~~~~l~~l~~~~-~~~~~~~lv~~~~~~~~~~~~~f~~~ 288 (296)
T PRK11062 237 AIFVAPSLYAQDFYADHSVVEIGRVD-NVKEEYHVIFAERMIQHPAVQRICNT 288 (296)
T ss_pred ceEECCHHHHHHHHHcCCeEEcCCcc-ccceEEEEEEecCCCCcHHHHHHHhh
Confidence 9999999998766 678899887643 45679999999999999999999986
No 25
>PRK09801 transcriptional activator TtdR; Provisional
Probab=100.00 E-value=6.4e-54 Score=352.42 Aligned_cols=291 Identities=14% Similarity=0.117 Sum_probs=247.3
Q ss_pred CchhhHHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCCccccCHhHHHHHHHHHHHHHHHHHH
Q psy3760 1 MNLHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKPGQAILRSIEIIMQEIEGL 80 (306)
Q Consensus 1 m~~~~l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~~~lT~~G~~l~~~a~~il~~~~~~ 80 (306)
|++++|+||++|+++| ||++||++||+||||||++|++||++||++||+|+++|+ +||++|+.|+++++++++.++++
T Consensus 6 ~~~~~L~~F~~v~~~g-s~t~AA~~L~iSQpavS~~I~~LE~~LG~~Lf~R~~r~~-~lT~~G~~l~~~a~~il~~~~~l 83 (310)
T PRK09801 6 PLAKDLQVLVEIVHSG-SFSAAAATLGQTPAFVTKRIQILENTLATTLLNRSARGV-ALTESGQRCYEHALEILTQYQRL 83 (310)
T ss_pred HHHHHHHHHHHHHHcC-CHHHHHHHhCcCHHHHHHHHHHHHHHhCCEeeeecCCCC-cccHhHHHHHHHHHHHHHHHHHH
Confidence 5789999999999999 999999999999999999999999999999999999999 89999999999999999999999
Q ss_pred HHHHHhhccCCCCcEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccCCCCCcee
Q psy3760 81 KKIGKEFSAYDTGNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLIS 160 (306)
Q Consensus 81 ~~~~~~~~~~~~~~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~~~~~~~ 160 (306)
.+.+++......|.|+||++++++..++++++..|.++||++++++...+. ..+ +..|++|++|...+ ..++.+..
T Consensus 84 ~~~~~~~~~~~~g~lrIg~~~~~~~~~l~~~l~~f~~~~P~i~l~i~~~~~--~~~-~l~~~~Dl~i~~~~-~~~~~~~~ 159 (310)
T PRK09801 84 VDDVTQIKTRPEGMIRIGCSFGFGRSHIAPAITELMRNYPELQVHFELFDR--QID-LVQDNIDLDIRIND-EIPDYYIA 159 (310)
T ss_pred HHHHHhccCCCceEEEEeCcHHHHHHHHHHHHHHHHHHCCCeEEEEEecCC--ccC-cccCCceEEEEeCC-CCCCCeEE
Confidence 999999888788999999999999999999999999999999999986442 344 44688999998544 44567888
Q ss_pred eccccceEEEEecCCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHH--HHhCCCceeEEEEecCHHHHHHHHHhcc
Q psy3760 161 IPCYQWEYVIIVPLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDRE--FSLQKLTPYIVLETINSDIIKTYVELRM 238 (306)
Q Consensus 161 ~~l~~~~~~~v~~~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~v~~g~ 238 (306)
..+.+++++++++++|+......++++||.++|++....+...+..+... ....+..+++.+++++..++.++|.+|.
T Consensus 160 ~~l~~~~~~~~~~~~~~~~~~~~~~~~~L~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~v~~g~ 239 (310)
T PRK09801 160 HLLTKNKRILCAAPEYLQKYPQPQSLQELSRHDCLVTKERDMTHGIWELGNGQEKKSVKVSGHLSSNSGEIVLQWALEGK 239 (310)
T ss_pred EEeeccceEEEECHHHHHhcCCCCCHHHHhhCCEEEecCCCCCCCceEEecCCCEEEEecCCcEEECCHHHHHHHHHcCC
Confidence 88999999999999996443467999999999999877654443222211 1122445666889999999999999999
Q ss_pred ceeeeecceeccc-ccCCceeeecCCCCccceEEEEEeCCccccHHHHHHHHHHhHHhhHH
Q psy3760 239 GIGIIASIAFDSN-RDKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLLSPKLNRK 298 (306)
Q Consensus 239 gi~~~p~~~~~~~-~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~ 298 (306)
|++++|.+.+... ..+.++.+ +++....++++++|++++..+++++.|++++++.++++
T Consensus 240 Gia~lp~~~~~~~~~~~~l~~~-~~~~~~~~~~~lv~~~~~~~~~~~~~~i~~l~~~~~~~ 299 (310)
T PRK09801 240 GIMLRSEWDVLPFLESGKLVQV-LPEYAQSANIWAVYREPLYRSMKLRVCVEFLAAWCQQR 299 (310)
T ss_pred CEEecchhhHHHHHhCCCeEEe-CCCCCCCCcEEEEEcCCCcCCHHHHHHHHHHHHHHHHh
Confidence 9999999887654 56778865 44434567999999999999999999999998876543
No 26
>PRK11139 DNA-binding transcriptional activator GcvA; Provisional
Probab=100.00 E-value=6.7e-53 Score=345.67 Aligned_cols=285 Identities=16% Similarity=0.119 Sum_probs=249.6
Q ss_pred CchhhHHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCCccccCHhHHHHHHHHHHHHHHHHHH
Q psy3760 1 MNLHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKPGQAILRSIEIIMQEIEGL 80 (306)
Q Consensus 1 m~~~~l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~~~lT~~G~~l~~~a~~il~~~~~~ 80 (306)
+++++|++|++|+++| ||++||++||+||||||++|++||++||++||+|+++|+ +||++|+.||++++++++.++++
T Consensus 6 ~~l~~l~~f~~v~~~g-s~s~AA~~L~isq~avS~~i~~LE~~lg~~Lf~R~~r~l-~lT~~G~~l~~~~~~~l~~~~~~ 83 (297)
T PRK11139 6 PPLNALRAFEAAARHL-SFTRAAEELFVTQAAVSHQIKALEDFLGLKLFRRRNRSL-LLTEEGQRYFLDIREIFDQLAEA 83 (297)
T ss_pred CchHHHHHHHHHHHhC-CHHHHHHHhCCChHHHHHHHHHHHHHhCchheEecCCce-eECHhHHHHHHHHHHHHHHHHHH
Confidence 5899999999999999 999999999999999999999999999999999999999 79999999999999999999999
Q ss_pred HHHHHhhccCCCCcEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccCCCCCcee
Q psy3760 81 KKIGKEFSAYDTGNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLIS 160 (306)
Q Consensus 81 ~~~~~~~~~~~~~~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~~~~~~~ 160 (306)
...+.. ....|.++||++++++..++++++..|.+.||++++++...+. .+.+.+|++|++|+..+ ...+++..
T Consensus 84 ~~~~~~--~~~~g~l~I~~~~~~~~~~l~~~l~~f~~~~p~i~i~l~~~~~---~~~l~~g~~Dl~i~~~~-~~~~~l~~ 157 (297)
T PRK11139 84 TRKLRA--RSAKGALTVSLLPSFAIQWLVPRLSSFNEAHPDIDVRLKAVDR---LEDFLRDDVDVAIRYGR-GNWPGLRV 157 (297)
T ss_pred HHHHhc--CCCCceEEEecChHHHHHHHHHHHHHHHHHCCCceEEEEeCCC---hhhhccCCCCEEEEeCC-CCCCCceE
Confidence 987764 3457899999999999999999999999999999999986433 57888999999999654 55678999
Q ss_pred eccccceEEEEecCCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCC---ceeEEEEecCHHHHHHHHHhc
Q psy3760 161 IPCYQWEYVIIVPLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKL---TPYIVLETINSDIIKTYVELR 237 (306)
Q Consensus 161 ~~l~~~~~~~v~~~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~v~~g 237 (306)
.++++++++++++++||++.+.+++++||.++|+|..... ..+..++...+. .++..+++++.+.+.+++.+|
T Consensus 158 ~~l~~~~~~~~~~~~~~~~~~~~i~~~dL~~~p~i~~~~~----~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g 233 (297)
T PRK11139 158 EKLLDEYLLPVCSPALLNGGKPLKTPEDLARHTLLHDDSR----EDWRAWFRAAGLDDLNVQQGPIFSHSSMALQAAIHG 233 (297)
T ss_pred EEeccceeEEEeCHHHhcccCCCCCHHHhhcCceEeecCc----ccHHHHHHHhCCCCcCcccceeeCCHHHHHHHHHhC
Confidence 9999999999999999988888899999999999987653 244567766665 456678899999999999999
Q ss_pred cceeeeecceeccc-ccCCceeeecCCCC-ccceEEEEEeCCccccHHHHHHHHHHhHHhhHH
Q psy3760 238 MGIGIIASIAFDSN-RDKNLRSISASHLF-GTTISRVIIKQGTYLRSYVYSFIKLLSPKLNRK 298 (306)
Q Consensus 238 ~gi~~~p~~~~~~~-~~~~l~~~~~~~~~-~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~ 298 (306)
.|++++|.+.+... ..+.++ .++++.. ..+.++++|++++..+++++.|++++.+.++++
T Consensus 234 ~gi~~lp~~~~~~~~~~~~l~-~~~~~~~~~~~~~~l~~~~~~~~~~~~~~f~~~l~~~~~~~ 295 (297)
T PRK11139 234 QGVALGNRVLAQPEIEAGRLV-CPFDTVLPSPNAFYLVCPDSQAELPKVAAFRQWLLAEAAQE 295 (297)
T ss_pred CCeEecchhhhHHHHHCCcee-cccccCcCCCccEEEEeccccccChhHHHHHHHHHHHhhcc
Confidence 99999999887665 445554 5555532 357899999999999999999999999887654
No 27
>PRK11482 putative DNA-binding transcriptional regulator; Provisional
Probab=100.00 E-value=3.5e-52 Score=342.97 Aligned_cols=287 Identities=17% Similarity=0.162 Sum_probs=244.6
Q ss_pred CchhhHHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCCccccCHhHHHHHHHHHHHHHHHHHH
Q psy3760 1 MNLHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKPGQAILRSIEIIMQEIEGL 80 (306)
Q Consensus 1 m~~~~l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~~~lT~~G~~l~~~a~~il~~~~~~ 80 (306)
||+++|++|++|+++| ||++||++||+||||||++|++||++||++||+|+++|+ +||++|+.|++++++++++++++
T Consensus 29 m~l~~L~~f~av~e~g-s~s~AA~~L~isQpavS~~I~~LE~~lG~~LF~R~~r~v-~lT~~G~~l~~~~~~~l~~l~~~ 106 (317)
T PRK11482 29 IDLNLLTIFEAVYVHK-GIVNAAKILNLTPSAISQSIQKLRVIFPDPLFIRKGQGV-TPTAYATHLHEYISQGLESILGA 106 (317)
T ss_pred cchhHHHHHHHHHHcC-CHHHHHHHhCCChHHHHHHHHHHHHHhCCcceEecCCCc-cCCHHHHHHHHHHHHHHHHHHHH
Confidence 7999999999999999 999999999999999999999999999999999999999 79999999999999999999887
Q ss_pred HHHHHhhccCCCCcEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccCCCCCcee
Q psy3760 81 KKIGKEFSAYDTGNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLIS 160 (306)
Q Consensus 81 ~~~~~~~~~~~~~~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~~~~~~~ 160 (306)
.+.... ....|.|+||++++++..++++++..|.+.||++.++.. .+.++.+.|.+|++|++|...+ ...+++.+
T Consensus 107 ~~~~~~--~~~~~~l~Ig~~~~~~~~~l~~~l~~f~~~~P~i~i~~~--~~~~~~~~l~~g~~Dl~i~~~~-~~~~~~~~ 181 (317)
T PRK11482 107 LDITGS--YDKQRTITIATTPSVGALVMPVIYQAIKTHYPQLLLRNI--PISDAENQLSQFQTDLIIDTHS-CSNRTIQH 181 (317)
T ss_pred hCCCcC--CCCCceEEEEecHHHHHHHHHHHHHHHHHHCCCCEEEEe--cchhHHHHHHCCCcCEEEeccC-CCCCceEE
Confidence 654332 234689999999999999999999999999999988754 4457899999999999998655 56688999
Q ss_pred eccccceEEEEecCCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCceeEEEEecCHHHHHHHHHhccce
Q psy3760 161 IPCYQWEYVIIVPLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMGI 240 (306)
Q Consensus 161 ~~l~~~~~~~v~~~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi 240 (306)
.++++++++++++++||++.. .++++||.++|++...........+.+++......+++.+.+++..++..++.+|.|+
T Consensus 182 ~~l~~~~~~lv~~~~hpl~~~-~~~~~dL~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gv 260 (317)
T PRK11482 182 HVLFTDNVVLVCRQGHPLLSL-EDDEETLDNAEHTLLLPEGQNFSGLRQRLQEMFPDRQISFSSYNILTIAALIASSDML 260 (317)
T ss_pred EEEecCcEEEEEeCCCCccCC-CCCHHHHhhCCCEEEecCCCCcchHHHHHHHhCCCceEEEEcCcHHHHHHHHHcCCee
Confidence 999999999999999999864 6899999998754433222211233455555555677889999999999999999999
Q ss_pred eeeecceeccc-ccCCceeeecCCCC-ccceEEEEEeCCccccHHHHHHHHHHhHHh
Q psy3760 241 GIIASIAFDSN-RDKNLRSISASHLF-GTTISRVIIKQGTYLRSYVYSFIKLLSPKL 295 (306)
Q Consensus 241 ~~~p~~~~~~~-~~~~l~~~~~~~~~-~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~ 295 (306)
+++|...+... ..+.+..+++.+.. ..++++++|++++..+|.+++|++++++++
T Consensus 261 ~ilp~~~~~~~~~~~~l~~~~l~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~i~~~~ 317 (317)
T PRK11482 261 GIMPSRFYNLFSRCWPLEKLPFPSLNEEQIDFSLHYNKLSLRDPVLENVIDVIRNAF 317 (317)
T ss_pred EEeHHHHHHHHHhhCCceEecCCCCCCCCeEEEEEecccccCCcHHHHHHHHHHHhC
Confidence 99999887654 45678888886532 457999999999999999999999998753
No 28
>PRK10632 transcriptional regulator; Provisional
Probab=100.00 E-value=3.8e-53 Score=348.34 Aligned_cols=286 Identities=17% Similarity=0.229 Sum_probs=246.4
Q ss_pred Cc-hhhHHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCCccccCHhHHHHHHHHHHHHHHHHH
Q psy3760 1 MN-LHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKPGQAILRSIEIIMQEIEG 79 (306)
Q Consensus 1 m~-~~~l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~~~lT~~G~~l~~~a~~il~~~~~ 79 (306)
|+ +++|++|++|+|+| ||++||++||+||||||++|++||++||++||+|+++++ +||++|+.|+++++++++.+++
T Consensus 1 ~~~l~~L~~F~~v~e~g-S~t~AA~~L~isQpavS~~I~~LE~~lg~~Lf~R~~r~i-~lT~~G~~l~~~a~~il~~~~~ 78 (309)
T PRK10632 1 MERLKRMSVFAKVVEFG-SFTAAARQLQMSVSSISQTVSKLEDELQVKLLNRSTRSI-GLTEAGRIYYQGCRRMLHEVQD 78 (309)
T ss_pred CcchHHHHHHHHHHhcC-CHHHHHHHhCCCHHHHHHHHHHHHHHhCCeeecccCCCc-eechhHHHHHHHHHHHHHHHHH
Confidence 66 99999999999999 999999999999999999999999999999999999999 8999999999999999999999
Q ss_pred HHHHHHhhccCCCCcEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccCCCCCce
Q psy3760 80 LKKIGKEFSAYDTGNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLI 159 (306)
Q Consensus 80 ~~~~~~~~~~~~~~~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~~~~~~ 159 (306)
+.+.++.......|.++||++++++..++++++..|.+.||++.+++...+.. ..+.+|++|++|+..+ ...+++.
T Consensus 79 ~~~~~~~~~~~~~g~l~I~~~~~~~~~~l~~~l~~~~~~~P~i~i~l~~~~~~---~~l~~~~~Dl~i~~~~-~~~~~l~ 154 (309)
T PRK10632 79 VHEQLYAFNNTPIGTLRIGCSSTMAQNVLAGLTAKMLKEYPGLSVNLVTGIPA---PDLIADGLDVVIRVGA-LQDSSLF 154 (309)
T ss_pred HHHHHHhccCCCceEEEEeccHHHHHHHHHHHHHHHHHHCCCeEEEEEecCcc---cCcccCCeeEEEEecC-CCCCCeE
Confidence 99999988777789999999999999999999999999999999999886542 4678899999998654 5567899
Q ss_pred eeccccceEEEEecCCCCCCCC-CCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCC----CceeEEEEecCHHHHHHHH
Q psy3760 160 SIPCYQWEYVIIVPLDHPLLLL-NSISLKEISNYPLITYDLSFSGRIKLDREFSLQK----LTPYIVLETINSDIIKTYV 234 (306)
Q Consensus 160 ~~~l~~~~~~~v~~~~~~l~~~-~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~----~~~~~~~~~~~~~~~~~~v 234 (306)
..+++++++++|++++| ++.. .+++++||.++|++.+....... ...+...+ ..++..+++++...++++|
T Consensus 155 ~~~l~~~~~~~v~~~~~-l~~~~~~~~~~~L~~~~~i~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~V 230 (309)
T PRK10632 155 SRRLGAMPMVVCAAKSY-LAQYGTPEKPADLSSHSWLEYSVRPDNE---FELIAPEGISTRLIPQGRFVTNDPQTLVRWL 230 (309)
T ss_pred EEEEeccceEEEECHHH-HHhCCCCCCHHHHhhCCeEEecCCCCCc---ceEecCCCeEEEEecCCeEEECCHHHHHHHH
Confidence 99999999998887654 6543 47899999999999986532111 12233333 2456688999999999999
Q ss_pred Hhccceeeeecceeccc-ccCCceeeecCCCCccceEEEEEeCCccccHHHHHHHHHHhHHhh
Q psy3760 235 ELRMGIGIIASIAFDSN-RDKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLLSPKLN 296 (306)
Q Consensus 235 ~~g~gi~~~p~~~~~~~-~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~ 296 (306)
.+|.|++++|...+... ..+.++.++.+.....+.+|++|+++...++.++.|++++++.++
T Consensus 231 ~~g~Gv~~lp~~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~f~~~l~~~~~ 293 (309)
T PRK10632 231 TAGAGIAYVPLMWVIDEINRGELEILFPRYQSDPRPVYALYTEKDKLPLKVQVCINYLTDYFV 293 (309)
T ss_pred HcCCcEEEcCHHHHHHHHhcCCeEEeCCCccCCCCcEEEEecCCCCCcHHHHHHHHHHHHHHH
Confidence 99999999999877655 567787776655455789999999999999999999999988874
No 29
>PRK13348 chromosome replication initiation inhibitor protein; Provisional
Probab=100.00 E-value=8.2e-52 Score=338.89 Aligned_cols=288 Identities=12% Similarity=0.114 Sum_probs=246.4
Q ss_pred CchhhHHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCCccccCHhHHHHHHHHHHHHHHHHHH
Q psy3760 1 MNLHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKPGQAILRSIEIIMQEIEGL 80 (306)
Q Consensus 1 m~~~~l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~~~lT~~G~~l~~~a~~il~~~~~~ 80 (306)
||+++|+||.+|+++| ||++||++||+||||||++|++||++||++||+|+ +++ +||++|+.|++++++++...+++
T Consensus 2 m~l~~L~~f~~v~~~g-s~t~AA~~L~iSQ~avS~~i~~LE~~lg~~Lf~R~-r~i-~lT~~G~~l~~~a~~~~~~~~~~ 78 (294)
T PRK13348 2 LDYKQLEALAAVVETG-SFERAARRLHVTPSAVSQRIKALEESLGQPLLVRG-RPC-RPTPAGQRLLRHLRQVALLEADL 78 (294)
T ss_pred CCHHHHHHHHHHHHcC-CHHHHHHHhCCCchHHHHHHHHHHHHhCceeeecC-CCC-ccChhHHHHHHHHHHHHHHHHHH
Confidence 8999999999999999 99999999999999999999999999999999997 688 89999999999999998888888
Q ss_pred HHHHHhhccCCCCcEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccCCCCCcee
Q psy3760 81 KKIGKEFSAYDTGNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLIS 160 (306)
Q Consensus 81 ~~~~~~~~~~~~~~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~~~~~~~ 160 (306)
...... .....|+++||++++....++++.+..|... |++++++...++.++.+.|.+|++|++|...+ ...+++.+
T Consensus 79 ~~~~~~-~~~~~g~l~I~~~~~~~~~~~~~~l~~~~~~-~~i~i~~~~~~~~~~~~~L~~~~~d~~i~~~~-~~~~~~~~ 155 (294)
T PRK13348 79 LSTLPA-ERGSPPTLAIAVNADSLATWFLPALAAVLAG-ERILLELIVDDQDHTFALLERGEVVGCVSTQP-KPMRGCLA 155 (294)
T ss_pred HHHHHh-hcCCceEEEEEecchhHHHHHHHHHHHHHhC-CCeEEEEEEcchHHHHHHHhcCCeEEEEecCC-cccCCccc
Confidence 776654 4567799999998766777888999999876 89999999999999999999999999998543 44578999
Q ss_pred eccccceEEEEecCCCCCCC-CCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCceeEEEEecCHHHHHHHHHhccc
Q psy3760 161 IPCYQWEYVIIVPLDHPLLL-LNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMG 239 (306)
Q Consensus 161 ~~l~~~~~~~v~~~~~~l~~-~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~g 239 (306)
.++++++++++++++|+... ...++++||.++|+|.++.+....+.+...+...+..+.+..++++...+.++|.+|.|
T Consensus 156 ~~l~~~~~~~v~~~~~~~~~~~~~v~~~~l~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~g 235 (294)
T PRK13348 156 EPLGTMRYRCVASPAFAARYFAQGLTRHSALKAPAVAFNRKDTLQDSFLEQLFGLPVGAYPRHYVPSTHAHLAAIRHGLG 235 (294)
T ss_pred ccccccceEEEEccchhhhhccCCCCHHHHcCCCEEEecCCchHHHHHHHHHHhccccccceEEeCcHHHHHHHHHcCCe
Confidence 99999999999999997543 46799999999999998876655444444443334445667789999999999999999
Q ss_pred eeeeecceeccc-ccCCceeeecCCCCccceEEEEEeCCccccHHHHHHHHHHhHHhhH
Q psy3760 240 IGIIASIAFDSN-RDKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLLSPKLNR 297 (306)
Q Consensus 240 i~~~p~~~~~~~-~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~ 297 (306)
++++|.+++... ..+.++.++. ...++++++|++++..+|.+++|++++++...+
T Consensus 236 i~~lp~~~~~~~~~~~~l~~l~~---~~~~~~~l~~~~~~~~~~~~~~~~~~i~~~~~~ 291 (294)
T PRK13348 236 YGMVPELLIGPLLAAGRLVDLAP---GHPVDVALYWHHWEVESPTMEALSQRVVEAARR 291 (294)
T ss_pred eEeCCHHHHHHHHhcCeeeecCC---CCCCCceeEEeeccccChHHHHHHHHHHHHHHH
Confidence 999999988755 5556665542 246789999999999999999999999987654
No 30
>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 (PubMed:10589831). ArgP mutants convey canavanine (an L-arginine structural homolog) sensitivity (PubMed: 15150242).
Probab=100.00 E-value=1.1e-51 Score=337.90 Aligned_cols=287 Identities=16% Similarity=0.177 Sum_probs=250.0
Q ss_pred CchhhHHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCCccccCHhHHHHHHHHHHHHHHHHHH
Q psy3760 1 MNLHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKPGQAILRSIEIIMQEIEGL 80 (306)
Q Consensus 1 m~~~~l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~~~lT~~G~~l~~~a~~il~~~~~~ 80 (306)
||+++|++|++++++| ||++||++||+||||||++|++||++||++||+|+ +++ +||++|+.|++++++++...+.+
T Consensus 1 m~l~~l~~f~~v~~~~-s~t~AA~~L~isQpavS~~I~~LE~~lg~~Lf~R~-r~~-~lT~~G~~l~~~~~~il~~~~~~ 77 (292)
T TIGR03298 1 LDYRQLAALAAVVEEG-SFERAAAALSVTPSAVSQRIKALEERLGQPLLVRT-QPC-RATEAGQRLLRHARQVRLLEAEL 77 (292)
T ss_pred CCHHHHHHHHHHHHcC-CHHHHHHHhCCCHHHHHHHHHHHHHHhCchheecC-CCC-cCCHhHHHHHHHHHHHHHHHHHH
Confidence 8999999999999999 99999999999999999999999999999999996 798 79999999999999999999999
Q ss_pred HHHHHhhccCCCCcEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccCCCCCcee
Q psy3760 81 KKIGKEFSAYDTGNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLIS 160 (306)
Q Consensus 81 ~~~~~~~~~~~~~~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~~~~~~~ 160 (306)
...+........|.|+||+++.....++++++..|.+++ ++.+++...++.++.+.|.+|++|++|...+ ...+++.+
T Consensus 78 ~~~~~~~~~~~~g~l~i~~~~~~~~~~l~~~l~~~~~~~-~i~i~l~~~~~~~~~~~l~~g~~d~~i~~~~-~~~~~l~~ 155 (292)
T TIGR03298 78 LAELPGLAPGAPVTLSIAVNADSLATWFLPALAPVLAQE-GVLLDLVVEDQDHTAELLRSGEVLGAVTTQA-KPVQGCRV 155 (292)
T ss_pred HHHHHhhhccCCceEEEecccchhhhhhHHHHHHHHhCC-CceEEEEeCcchhHHHHHhCCCceEEEecCC-CCCCCceE
Confidence 988888777778999999987777788999999999986 8999999999889999999999999998654 55678999
Q ss_pred eccccceEEEEecCCCCCCC-CCCcChhhhcCCCeEeecCCCCcHH-HHHHHHHhCCCceeEEEEecCHHHHHHHHHhcc
Q psy3760 161 IPCYQWEYVIIVPLDHPLLL-LNSISLKEISNYPLITYDLSFSGRI-KLDREFSLQKLTPYIVLETINSDIIKTYVELRM 238 (306)
Q Consensus 161 ~~l~~~~~~~v~~~~~~l~~-~~~i~~~dl~~~~~i~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~ 238 (306)
.++++++++++++++|+... ...++++||.++|+|.+..+...+. .+...+...+ .+ +.+++++.+.+.++|..|.
T Consensus 156 ~~l~~~~~~~v~~~~~~~~~~~~~i~~~dL~~~~~i~~~~~~~~~~~~~~~~~~~~~-~~-~~~~~~~~~~~~~~v~~g~ 233 (292)
T TIGR03298 156 VPLGAMRYLAVASPAFAARYFPDGVTAEALARAPVIVFNRKDDLQDRFLRRLFGLPV-SP-PRHYVPSSEGFVEAARAGL 233 (292)
T ss_pred EecCCceEEEEECchhhhhccCCCCCHHHhcCCCEEEeCCCCccHHHHHHHHhcCCC-CC-CeEecCCHHHHHHHHHhCC
Confidence 99999999999999987542 3579999999999999987765543 4444554433 34 3589999999999999999
Q ss_pred ceeeeecceeccc-ccCCceeeecCCCCccceEEEEEeCCccccHHHHHHHHHHhHHhhH
Q psy3760 239 GIGIIASIAFDSN-RDKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLLSPKLNR 297 (306)
Q Consensus 239 gi~~~p~~~~~~~-~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~ 297 (306)
|++++|...+... ..+.++.++.+ ...+++++|++++..+|.+++|++++++..++
T Consensus 234 Gi~~~p~~~~~~~~~~~~l~~~~~~---~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~ 290 (292)
T TIGR03298 234 GWGMVPELQAEPHLAAGRLVDLAPG---RALDVPLYWHHWRLESRVLERLTDALVAAARR 290 (292)
T ss_pred CeEeCcHHHHHHHHhcCCeEEecCC---CCCCceEEEeccCCCChHHHHHHHHHHHHHhh
Confidence 9999999888765 55666666532 35688999999999999999999999887654
No 31
>PRK03601 transcriptional regulator HdfR; Provisional
Probab=100.00 E-value=1.2e-51 Score=333.94 Aligned_cols=269 Identities=17% Similarity=0.191 Sum_probs=238.5
Q ss_pred CchhhHHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCCccccCHhHHHHHHHHHHHHHHHHHH
Q psy3760 1 MNLHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKPGQAILRSIEIIMQEIEGL 80 (306)
Q Consensus 1 m~~~~l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~~~lT~~G~~l~~~a~~il~~~~~~ 80 (306)
||+++|++|.+|+++| ||++||++||+||||||++|++||++||++||+|+++++ +||++|+.|+++++++++.++++
T Consensus 1 m~~~~l~~f~~v~~~g-s~s~AA~~L~isqpavS~~I~~LE~~lG~~LF~R~~r~~-~lT~~G~~l~~~a~~~l~~~~~~ 78 (275)
T PRK03601 1 MDTELLKTFLEVSRTR-HFGRAAESLYLTQSAVSFRIRQLENQLGVNLFTRHRNNI-RLTAAGERLLPYAETLMNTWQAA 78 (275)
T ss_pred CCHHHHHHHHHHHHcC-CHHHHHHHhCCChHHHHHHHHHHHHHhCCceEEECCCce-EECHhHHHHHHHHHHHHHHHHHH
Confidence 8999999999999999 999999999999999999999999999999999999999 89999999999999999999999
Q ss_pred HHHHHhhccCCCCcEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccCCCCCcee
Q psy3760 81 KKIGKEFSAYDTGNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLIS 160 (306)
Q Consensus 81 ~~~~~~~~~~~~~~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~~~~~~~ 160 (306)
.+.+... ...|.++||++.++...++++++..|.+.||++++++....+.++.+.|.+|++|++|+... ...+++.+
T Consensus 79 ~~~~~~~--~~~~~l~Ig~~~~~~~~~l~~~l~~f~~~~P~v~v~~~~~~~~~~~~~l~~g~~Dl~i~~~~-~~~~~l~~ 155 (275)
T PRK03601 79 KKEVAHT--SQHNELSIGASASLWECMLTPWLGRLYQNQEALQFEARIAQRQSLVKQLHERQLDLLITTEA-PKMDEFSS 155 (275)
T ss_pred HHHHhhc--ccCceEEEeccHHHHHHHHHHHHHHHHHhCCCcEEEEEECChHHHHHHHHcCCCCEEEEcCC-CccCCccE
Confidence 9888753 34689999999999999999999999999999999999999999999999999999998644 55678999
Q ss_pred eccccceEEEEecCCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCceeEEEEecCHHHHHHHHHhccce
Q psy3760 161 IPCYQWEYVIIVPLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMGI 240 (306)
Q Consensus 161 ~~l~~~~~~~v~~~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi 240 (306)
.++++++++++++++||+. .++|++....+...+......+ ..+ +.+.+++++...+.+++.+|.|+
T Consensus 156 ~~l~~~~~~~v~~~~~~~~----------~~~~~i~~~~~~~~~~~~~~~~-~~~--~~~~~~~~~~~~~~~~v~~g~gv 222 (275)
T PRK03601 156 QLLGHFTLALYTSAPSKKK----------SELNYIRLEWGADFQQHEAGLI-GAD--EVPILTTSSAELARQLLATLNGC 222 (275)
T ss_pred EEecceeEEEEecCchhhc----------ccCCeEEccCCccHhHHHHHhc-ccC--CcceEEeCcHHHHHHHHHhCCCE
Confidence 9999999999999999853 3678998887766654433333 333 34578999999999999999999
Q ss_pred eeeecceecccccCCceeeecCCCCccceEEEEEeCCccccHHHHHHHHH
Q psy3760 241 GIIASIAFDSNRDKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKL 290 (306)
Q Consensus 241 ~~~p~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~ 290 (306)
+++|...+.. .++++.++... ....++|++|+++...+|.++.|.+.
T Consensus 223 ~~~p~~~~~~--~~~l~~~~~~~-~~~~~~~l~~~~~~~~~~~~~~~~~~ 269 (275)
T PRK03601 223 AFLPVHWAKE--KGGLHTVPDST-TLSRPLYAIWLQNSDKQALIRDLLKT 269 (275)
T ss_pred EEEcHHHHhh--cCCeEEcCCCc-cceeeeEEEeecCCccchHHHHHHhh
Confidence 9999988764 46788887643 45789999999999999999999875
No 32
>PRK03635 chromosome replication initiation inhibitor protein; Validated
Probab=100.00 E-value=1.5e-51 Score=336.93 Aligned_cols=287 Identities=15% Similarity=0.161 Sum_probs=248.9
Q ss_pred CchhhHHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCCccccCHhHHHHHHHHHHHHHHHHHH
Q psy3760 1 MNLHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKPGQAILRSIEIIMQEIEGL 80 (306)
Q Consensus 1 m~~~~l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~~~lT~~G~~l~~~a~~il~~~~~~ 80 (306)
||+++|++|++++|+| ||++||++||+||||+|++|++||++||++||+|+ +|+ +||++|+.|+++++++++..+.+
T Consensus 2 m~~~~L~~f~~v~e~g-s~s~AA~~L~isq~avS~~I~~LE~~lg~~LF~R~-~~~-~lT~~G~~l~~~a~~~~~~~~~~ 78 (294)
T PRK03635 2 LDYKQLEALAAVVREG-SFERAAQKLHITQSAVSQRIKALEERVGQVLLVRT-QPC-RPTEAGQRLLRHARQVRLLEAEL 78 (294)
T ss_pred CCHHHHHHHHHHHHcC-CHHHHHHHhCCChHHHHHHHHHHHHHhCceeeecC-CCC-ccCHHHHHHHHHHHHHHHHHHHH
Confidence 8999999999999999 99999999999999999999999999999999997 798 79999999999999999999888
Q ss_pred HHHHHhhccCCCCcEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccCCCCCcee
Q psy3760 81 KKIGKEFSAYDTGNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLIS 160 (306)
Q Consensus 81 ~~~~~~~~~~~~~~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~~~~~~~ 160 (306)
...++.... ..|.|+||+++++...++++.+..|.++ |++++++......++.+.+.+|++|++|+..+ ...+++.+
T Consensus 79 ~~~~~~~~~-~~g~l~I~~~~~~~~~~l~~~l~~f~~~-~~i~i~l~~~~~~~~~~~l~~~~~d~~i~~~~-~~~~~l~~ 155 (294)
T PRK03635 79 LGELPALDG-TPLTLSIAVNADSLATWFLPALAPVLAR-SGVLLDLVVEDQDHTAELLRRGEVVGAVTTEP-QPVQGCRV 155 (294)
T ss_pred HHHHhcccc-cceEEEEeecchhHHHHHHHHHHHHHhC-CCcEEEEEecCcHHHHHHHhCCCceEEEeccC-CCCCCcee
Confidence 887777666 7899999999877888999999999986 79999999998889999999999999998644 45578999
Q ss_pred eccccceEEEEecCCCCCCC-CCCcChhhhcCCCeEeecCCCCcHHHH-HHHHHhCCCceeEEEEecCHHHHHHHHHhcc
Q psy3760 161 IPCYQWEYVIIVPLDHPLLL-LNSISLKEISNYPLITYDLSFSGRIKL-DREFSLQKLTPYIVLETINSDIIKTYVELRM 238 (306)
Q Consensus 161 ~~l~~~~~~~v~~~~~~l~~-~~~i~~~dl~~~~~i~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~ 238 (306)
.++++++++++++++||... ..+++++||.++|||.+..+...+..+ .+++... ..+++.+++++..+++++|..|.
T Consensus 156 ~~l~~~~~~lv~~~~~~~~~~~~~~~~~~l~~~~~I~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~v~~g~ 234 (294)
T PRK03635 156 DPLGAMRYLAVASPAFAARYFPDGVTAEALAKAPAVVFNRKDDLQDRFLRQAFGLP-PGSVPCHYVPSSEAFVRAALAGL 234 (294)
T ss_pred eecccceEEEEEcchHHHhhccCCCCHHHHhhCCeEeecCCCchHHHHHHHhhccC-cccCceeecCCHHHHHHHHHhCC
Confidence 99999999999999998543 256899999999999998776655433 3455443 23567899999999999999999
Q ss_pred ceeeeecceeccc-ccCCceeeecCCCCccceEEEEEeCCccccHHHHHHHHHHhHHhhH
Q psy3760 239 GIGIIASIAFDSN-RDKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLLSPKLNR 297 (306)
Q Consensus 239 gi~~~p~~~~~~~-~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~ 297 (306)
|++++|.+.+... ..+.++.++ . .....++++|+++...++.+++|++++++..++
T Consensus 235 gi~~lp~~~~~~~~~~~~l~~l~--~-~~~~~~~l~~~~~~~~~~~~~~~~~~i~~~~~~ 291 (294)
T PRK03635 235 GWGMIPELQIEPELASGELVDLT--P-GRPLDVPLYWQHWRLESRLLDRLTDALLAAAAQ 291 (294)
T ss_pred CeEeCcHHHHhhhhccCceeecC--C-CCCCCceeeeeeeccCCHHHHHHHHHHHHHHHh
Confidence 9999999988765 455555443 2 235688999999999999999999999987654
No 33
>PRK10216 DNA-binding transcriptional regulator YidZ; Provisional
Probab=100.00 E-value=1.5e-51 Score=340.47 Aligned_cols=290 Identities=13% Similarity=0.089 Sum_probs=251.0
Q ss_pred CchhhHHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCCccccCHhHHHHHHHHHHHHHHHHHH
Q psy3760 1 MNLHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKPGQAILRSIEIIMQEIEGL 80 (306)
Q Consensus 1 m~~~~l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~~~lT~~G~~l~~~a~~il~~~~~~ 80 (306)
||+++|++|++|+|+| ||++||++||+||||+|++|++||++||++||+|+++|+ .||++|+.+++.++.+++..+++
T Consensus 8 mdl~~L~~f~av~e~g-s~t~AA~~L~iSQpavS~~I~~LE~~lg~~LF~R~~r~~-~lT~~G~~l~~~~~~~~~~~~~~ 85 (319)
T PRK10216 8 LDLNLLLCLQLLMQER-SVTKAAKRMNVTPSAVSKSLAKLRAWFDDPLFVNTPLGL-SPTPLMVSMEQNLAEWMQMGNQL 85 (319)
T ss_pred cCHHHHHHHHHHHHhC-CHHHHHHHhCCCHHHHHHHHHHHHHHhCCceEEecCCCc-ccCHHHHHHHHHHHHHHHHHHHH
Confidence 8999999999999999 999999999999999999999999999999999999999 79999999999999999988888
Q ss_pred HHHHHhhccCCCC-cEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccCC-----
Q psy3760 81 KKIGKEFSAYDTG-NLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSP----- 154 (306)
Q Consensus 81 ~~~~~~~~~~~~~-~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~----- 154 (306)
.+.... ....+ .++||++++++..++++++..|.+.||++++++...+. ...+.|.+|++|++|+..+...
T Consensus 86 ~~~~~~--~~~~~~~l~I~~~~~~~~~~~~~~l~~f~~~~P~v~v~i~~~~~-~~~~~l~~g~~D~~i~~~~~~~~~~~~ 162 (319)
T PRK10216 86 LDKPHH--QTPRGLKFELAAESPLMMIMLNALSKRIYQRYPQATIKLRNWDY-DSLDAITRGEVDIGFTGRESHPRSREL 162 (319)
T ss_pred hccccC--CCccCCEEEEEecchhHHHHHHHHHHHHHHHCCCCEEEEEeCCc-chHHHHhcCCccEEEecCCCCcccccc
Confidence 753221 23456 79999999999999999999999999999999998755 4789999999999998543211
Q ss_pred ----CCCceeeccccceEEEEecCCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCceeEEEEecCHHHH
Q psy3760 155 ----SDKLISIPCYQWEYVIIVPLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDII 230 (306)
Q Consensus 155 ----~~~~~~~~l~~~~~~~v~~~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 230 (306)
+..+...+++.++++++++++||+.. .+++++||.++|||.+..+......++.++...|..|++.+++++..++
T Consensus 163 ~~~~~~~~~~~~l~~~~~~~v~~~~hp~~~-~~~~~~dL~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 241 (319)
T PRK10216 163 LSLLPLAIDFEVLFSDLPCVWLRKDHPALH-EEWNLDTFLRYPHISICWEQSDTWALDDVLQELGRERTIALSLPEFEQS 241 (319)
T ss_pred ccccccccceeeeeecceEEEEeCCCCccC-CCCCHHHHhhCCCeEecCCCCCcchHHHHHHHhCCccceEEECCcHHHH
Confidence 23578899999999999999999765 4799999999999999776555667889999999999999999999999
Q ss_pred HHHHHhc--cceeeeecceecc-c-ccCCceeeecCCCC-----ccceEEEEEeCCccccHHHHHHHHHHhHHhh
Q psy3760 231 KTYVELR--MGIGIIASIAFDS-N-RDKNLRSISASHLF-----GTTISRVIIKQGTYLRSYVYSFIKLLSPKLN 296 (306)
Q Consensus 231 ~~~v~~g--~gi~~~p~~~~~~-~-~~~~l~~~~~~~~~-----~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~ 296 (306)
..++..| .|++++|.+.... . ..++++.+|++.+. ..++++++|++++..+|.+++|++.+++.+.
T Consensus 242 ~~~v~~~~~~gi~ilp~~~~~~~~~~~~~l~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~i~~~~~ 316 (319)
T PRK10216 242 LFMAAQPDHLLLATAPRYCQYYNQLHQLPLVALPLPFDESQQKKLEVPFTLLWHKRNSHNPKIVWLRETIKNLYA 316 (319)
T ss_pred HHHHHcCCcceEeccHHHHHHHHhhcCCceEecCCCCCcccccccceeEEEEeCCccCCCHHHHHHHHHHHHHHH
Confidence 9999985 5899999975431 1 33468888776432 3568999999999999999999999988764
No 34
>PRK14997 LysR family transcriptional regulator; Provisional
Probab=100.00 E-value=1.8e-52 Score=343.88 Aligned_cols=289 Identities=14% Similarity=0.192 Sum_probs=243.4
Q ss_pred CchhhHHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCCccccCHhHHHHHHHHHHHHHHHHHH
Q psy3760 1 MNLHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKPGQAILRSIEIIMQEIEGL 80 (306)
Q Consensus 1 m~~~~l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~~~lT~~G~~l~~~a~~il~~~~~~ 80 (306)
||+++|+||++|+++| ||++||++||+||||||++|++||++||++||+|+++++ +||++|+.|++++++++..++++
T Consensus 2 ~~l~~L~~f~~va~~g-s~s~AA~~L~isQpavS~~I~~LE~~lG~~LF~R~~r~~-~lT~~G~~l~~~a~~il~~~~~~ 79 (301)
T PRK14997 2 TDLNDFAWFVHVVEEG-GFAAAGRALDEPKSKLSRRIAQLEERLGVRLIQRTTRQF-NVTEVGQTFYEHCKAMLVEAQAA 79 (301)
T ss_pred ccHHHHHHHHHHHHcC-CHHHHHHHhCCCHHHHHHHHHHHHHHhCCEeeeeccCcc-eEcHhHHHHHHHHHHHHHHHHHH
Confidence 8999999999999999 999999999999999999999999999999999999999 89999999999999999999999
Q ss_pred HHHHHhhccCCCCcEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEcccc-CCCCCce
Q psy3760 81 KKIGKEFSAYDTGNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEIL-SPSDKLI 159 (306)
Q Consensus 81 ~~~~~~~~~~~~~~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~-~~~~~~~ 159 (306)
...+++......|.|+||++++++..++++++..|.++||++++++...+.. . .+.+|++|++|+..+. ...+++.
T Consensus 80 ~~~~~~~~~~~~g~lrIg~~~~~~~~~l~~~l~~~~~~~P~i~i~~~~~~~~--~-~~~~~~~Dl~i~~~~~~~~~~~~~ 156 (301)
T PRK14997 80 QDAIAALQVEPRGIVKLTCPVTLLHVHIGPMLAKFMARYPDVSLQLEATNRR--V-DVVGEGVDVAIRVRPRPFEDSDLV 156 (301)
T ss_pred HHHHHhccCCCceeEEEECcHHHHHHHHHHHHHHHHHHCCCeEEEEEecCCc--c-ccccccccEEEEecCCcCCCCCce
Confidence 9999888777889999999999999999999999999999999999876543 3 3557889999986432 2457799
Q ss_pred eeccccceEEEEecCCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCC----CceeEEEEecCHHHHHHHHH
Q psy3760 160 SIPCYQWEYVIIVPLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQK----LTPYIVLETINSDIIKTYVE 235 (306)
Q Consensus 160 ~~~l~~~~~~~v~~~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~----~~~~~~~~~~~~~~~~~~v~ 235 (306)
..++++++++++++++|+...+.+++++||.++|++....+.... .+ ..+...+ ..+.+.+.+++..++.++|.
T Consensus 157 ~~~l~~~~~~l~~~~~~~~~~~~~~~~~~L~~~~~i~~~~~~~~~-~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~ 234 (301)
T PRK14997 157 MRVLADRGHRLFASPDLIARMGIPSAPAELSHWPGLSLASGKHIH-RW-ELYGPQGARAEVHFTPRMITTDMLALREAAM 234 (301)
T ss_pred EEEccccceEEEECHHHHHhCCCCCCHHHHhcCCceeecCCCCCC-ce-eEecCCCceEEEeCCCcEEECCHHHHHHHHH
Confidence 999999999999999997554567899999999999986654321 11 1111112 12344568899999999999
Q ss_pred hccceeeeecceeccc-ccCCceeeecCCCC-ccceEEEEEeCCccccHHHHHHHHHHhHHhhH
Q psy3760 236 LRMGIGIIASIAFDSN-RDKNLRSISASHLF-GTTISRVIIKQGTYLRSYVYSFIKLLSPKLNR 297 (306)
Q Consensus 236 ~g~gi~~~p~~~~~~~-~~~~l~~~~~~~~~-~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~ 297 (306)
+|.|++++|.+.+... ..+.++.+ +++.. ....+|++|+++...+|.++.|++++++.+.+
T Consensus 235 ~G~Gi~~~p~~~~~~~~~~~~l~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~f~~~l~~~~~~ 297 (301)
T PRK14997 235 AGVGLVQLPVLMVKEQLAAGELVAV-LEEWEPRREVIHAVFPSRRGLLPSVRALVDFLTEEYAR 297 (301)
T ss_pred hCCCEEECcHHHHHHHHHcCCeEEe-CCCccCCCCcEEEEECCCCccCHHHHHHHHHHHHHHHH
Confidence 9999999999988765 56677754 44322 23468999999999999999999999887644
No 35
>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=6.8e-53 Score=344.89 Aligned_cols=284 Identities=20% Similarity=0.167 Sum_probs=245.6
Q ss_pred CchhhHHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCCccccCHhHHHHHHHHHHHHHHHHHH
Q psy3760 1 MNLHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKPGQAILRSIEIIMQEIEGL 80 (306)
Q Consensus 1 m~~~~l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~~~lT~~G~~l~~~a~~il~~~~~~ 80 (306)
.|+++|+||++|+++| ||++||++||+||||||++|++||++||++||+|+++++ +||++|+.|+++++++++.++++
T Consensus 1 ~~l~~L~~f~~v~~~g-s~s~AA~~L~itqpavS~~Ik~LE~~lg~~LF~R~~r~~-~lT~~G~~l~~~a~~il~~~~~~ 78 (291)
T TIGR03418 1 LSLQALRVFESAARLA-SFTAAARELGSTQPAVSQQVKRLEEELGTPLFERGHRGI-ELTEDGQRLFEAVRAGLDTIDLA 78 (291)
T ss_pred CCHHHHHHHHHHHHhC-CHHHHHHHhCCCHHHHHHHHHHHHHHhCcHHhhcCCCce-eEcHhHHHHHHHHHHHHHHHHHH
Confidence 3799999999999999 999999999999999999999999999999999999999 89999999999999999999999
Q ss_pred HHHHHhhccCCCCcEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccCCCCCcee
Q psy3760 81 KKIGKEFSAYDTGNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLIS 160 (306)
Q Consensus 81 ~~~~~~~~~~~~~~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~~~~~~~ 160 (306)
.+.++.. ...|.++||++++++..++++++..|.+.||++.+++...+. .. .+.+|++|++|...+ ...+++..
T Consensus 79 ~~~~~~~--~~~g~l~ig~~~~~~~~~l~~~l~~~~~~~p~i~i~~~~~~~--~~-~~~~~~~D~~i~~~~-~~~~~~~~ 152 (291)
T TIGR03418 79 TAQLRAR--REHETLTLATDFAFATYWLMPRLHRFKRAMPDVDVSLVTSQD--SL-DPQRDDIDVAILFGD-GRWPGGEA 152 (291)
T ss_pred HHHHhcC--CCCceEEEeccHHHHHHHHhhhhHHHHHhCCCceEEEEecCC--cc-cccCCCCcEEEEeCC-CCCCCchH
Confidence 9988753 357899999999999999999999999999999999987543 23 457899999998654 45678999
Q ss_pred eccccceEEEEecCCCCCCCCCCcChhhhcCCCeEeecCCCCcHH-HHHHHHHhCCCce---eEEEEecCHHHHHHHHHh
Q psy3760 161 IPCYQWEYVIIVPLDHPLLLLNSISLKEISNYPLITYDLSFSGRI-KLDREFSLQKLTP---YIVLETINSDIIKTYVEL 236 (306)
Q Consensus 161 ~~l~~~~~~~v~~~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~-~~~~~~~~~~~~~---~~~~~~~~~~~~~~~v~~ 236 (306)
.++++++++++++++||++....++++||.++|+|.+..+..... .++.++...+..+ ...+++++...+..++..
T Consensus 153 ~~l~~~~~~~~~~~~~~~~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~ 232 (291)
T TIGR03418 153 HRLFSEEVTPVCSPALLAARATPLSAADLLRLPLLHLEPTQPARWFDWAGWFDAHGLERPPAPGGLTFNNYTLVIQAAIG 232 (291)
T ss_pred hHhhcchhhhcCCHHHHhhcCCCCChhHHhhCCEEeeccccCCCCccHHHHHHHcCCCcccCCCCeeeccHHHHHHHHHh
Confidence 999999999999999998877789999999999999876544332 3678888888754 347889999999999999
Q ss_pred ccceeeeecceeccc-ccCCceeeecCCCC-ccceEEEEEeCCccccHHHHHHHHHHhH
Q psy3760 237 RMGIGIIASIAFDSN-RDKNLRSISASHLF-GTTISRVIIKQGTYLRSYVYSFIKLLSP 293 (306)
Q Consensus 237 g~gi~~~p~~~~~~~-~~~~l~~~~~~~~~-~~~~~~l~~~~~~~~~~~~~~~~~~l~~ 293 (306)
|.|++++|...+... ..+.++ .++++.. ....+|++|++++..+|+++.|++++++
T Consensus 233 g~gi~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~l~~~~~~~~~~~~~~f~~~~~~ 290 (291)
T TIGR03418 233 GQGVALGWAPLVDELLEAGQLV-RLIDEPVVTERGYYLVRPPRKRRGPAVRRFRDWLLD 290 (291)
T ss_pred CCceEEechHhhHHHHhCCccc-ccCCcccCCCCcEEEEeCchhhcChHHHHHHHHHhc
Confidence 999999999776554 444444 5555433 3579999999999999999999999865
No 36
>PRK10086 DNA-binding transcriptional regulator DsdC; Provisional
Probab=100.00 E-value=7.6e-52 Score=340.93 Aligned_cols=286 Identities=18% Similarity=0.187 Sum_probs=242.5
Q ss_pred CchhhHHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCCccccCHhHHHHHHHHHHHHHHHHHH
Q psy3760 1 MNLHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKPGQAILRSIEIIMQEIEGL 80 (306)
Q Consensus 1 m~~~~l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~~~lT~~G~~l~~~a~~il~~~~~~ 80 (306)
|++++|+||++|+++| ||++||+.||+||||||++|++||++||++||+|+++++ +||++|+.|+++|+++++.++++
T Consensus 14 ~~l~~L~~f~~va~~g-s~s~AA~~L~iSQpavS~~I~~LE~~lG~~LF~R~~r~~-~LT~~G~~l~~~a~~~l~~~~~~ 91 (311)
T PRK10086 14 WQLSKLHTFEVAARHQ-SFALAADELSLTPSAVSHRINQLEEELGIKLFVRSHRKV-ELTEEGKRVFWALKSSLDTLNQE 91 (311)
T ss_pred CcHHHHHHHHHHHHcC-CHHHHHHHHCCCHHHHHHHHHHHHHHhCCeeEEEcCCCc-ccCHhHHHHHHHHHHHHHHHHHH
Confidence 7899999999999999 999999999999999999999999999999999999999 89999999999999999999988
Q ss_pred HHHHHhhccCCCCcEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccCCCCCcee
Q psy3760 81 KKIGKEFSAYDTGNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLIS 160 (306)
Q Consensus 81 ~~~~~~~~~~~~~~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~~~~~~~ 160 (306)
...+.. ....|.++||++.+++..++++++..|.+.||++.+++...+... .+.+|++|++|+..+ ...+++.+
T Consensus 92 ~~~~~~--~~~~g~lrIg~~~~~~~~~l~~~l~~f~~~~P~i~i~~~~~~~~~---~l~~~~~Di~i~~~~-~~~~~l~~ 165 (311)
T PRK10086 92 ILDIKN--QELSGTLTVYSRPSIAQCWLVPRLADFTRRYPSISLTILTGNENV---NFQRAGIDLAIYFDD-APSAQLTH 165 (311)
T ss_pred HHHHHh--cCCCceEEEEecchHHHHHHHHHHHHHHHHCCCeEEEEEeCCccc---CCccCCccEEEEeCC-CCCCCceE
Confidence 776653 345789999999999999999999999999999999998876542 688999999998654 45678999
Q ss_pred eccccceEEEEecCCCCCCCCCCcChhhhcCCCeEeecC----CCCcHHHHHHHHHhCCCc---eeEEEEecCHHHHHHH
Q psy3760 161 IPCYQWEYVIIVPLDHPLLLLNSISLKEISNYPLITYDL----SFSGRIKLDREFSLQKLT---PYIVLETINSDIIKTY 233 (306)
Q Consensus 161 ~~l~~~~~~~v~~~~~~l~~~~~i~~~dl~~~~~i~~~~----~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~ 233 (306)
.++++++++++++++|+.......++.||.++|++.... +... ..+..++...++. ++..+.+++...+..+
T Consensus 166 ~~l~~~~~~lv~~~~~~~~~~l~~~~~~l~~~~li~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 244 (311)
T PRK10086 166 HFLMDEEILPVCSPEYAERHALTGNPDNLRHCTLLHDRQAWSNDSGT-DEWHSWAQHFGVNLLPPSSGIGFDRSDLAVIA 244 (311)
T ss_pred EEeecccEEEecCHHHHhhcCCCCCHHHHHhchhhcccccccccccc-cchHHHHHhcCCCcccCCCCceeccHHHHHHH
Confidence 999999999999998653222234689999999987541 1122 3455666777765 4668899999999999
Q ss_pred HHhccceeeeecceeccc-ccCCceeeecCCC--CccceEEEEEeCCccccHHHHHHHHHHhHHhhH
Q psy3760 234 VELRMGIGIIASIAFDSN-RDKNLRSISASHL--FGTTISRVIIKQGTYLRSYVYSFIKLLSPKLNR 297 (306)
Q Consensus 234 v~~g~gi~~~p~~~~~~~-~~~~l~~~~~~~~--~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~ 297 (306)
+.+|.|++++|...+... ..+.++ +++++. .....+|++|+++ ..+|.++.|++++++.++.
T Consensus 245 v~~G~Gi~~lp~~~~~~~~~~g~l~-~~~~~~~~~~~~~~~l~~~~~-~~~~~~~~fi~~l~~~~~~ 309 (311)
T PRK10086 245 AMNHIGVAMGRKRLVQKRLASGELV-APFGDMEVKCHQHYYVTTLPG-RQWPKIEAFIDWLKEQVKT 309 (311)
T ss_pred HHhCCceEeecHHhHHHHHhCCcee-cccCCCccCCCCcEEEEeCCc-cCCHHHHHHHHHHHHHhhc
Confidence 999999999999887765 555565 577653 2467899999999 8999999999999887653
No 37
>PRK10082 cell density-dependent motility repressor; Provisional
Probab=100.00 E-value=1.5e-50 Score=332.40 Aligned_cols=285 Identities=17% Similarity=0.196 Sum_probs=244.3
Q ss_pred CchhhHHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCCccccCHhHHHHHHHHHHHHHHHHHH
Q psy3760 1 MNLHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKPGQAILRSIEIIMQEIEGL 80 (306)
Q Consensus 1 m~~~~l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~~~lT~~G~~l~~~a~~il~~~~~~ 80 (306)
||+++|++|++|+|+| ||++||++||+||||||++|++||++||++||+|+++++ +||++|+.|+++++.++++++++
T Consensus 11 m~~~~l~~F~av~e~g-S~t~AA~~L~iSQpavS~~I~~LE~~lG~~Lf~R~~r~~-~lT~~G~~l~~~a~~~l~~~e~~ 88 (303)
T PRK10082 11 IETKWLYDFLTLEKCR-NFSQAAVSRNVSQPAFSRRIRALEQAIGVELFNRQVTPL-QLSEQGKIFHSQIRHLLQQLESN 88 (303)
T ss_pred cchHHHHHHHHHHhcC-CHHHHHHHhCCChHHHHHHHHHHHHHcCCEEEEecCCCC-ccCHHHHHHHHHHHHHHHHHHHH
Confidence 8999999999999999 999999999999999999999999999999999999999 79999999999999999999999
Q ss_pred HHHHHhhccCCCCcEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccC-CCCCce
Q psy3760 81 KKIGKEFSAYDTGNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILS-PSDKLI 159 (306)
Q Consensus 81 ~~~~~~~~~~~~~~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~-~~~~~~ 159 (306)
.+.+.+......|.|+||+..+++..++++++..|.. .+.+.+....+.++.+.+.+|++|++|+..+.. ..+++.
T Consensus 89 ~~~~~~~~~~~~g~lrIg~~~~~~~~~l~~~l~~f~~---~~~~~~~~~~~~~~~~~l~~g~~Dlai~~~~~~~~~~~~~ 165 (303)
T PRK10082 89 LAELRGGSDYAQRKIKIAAAHSLSLGLLPSIISQMPP---LFTWAIEAIDVDEAVDKLREGQSDCIFSFHDEDLLEAPFD 165 (303)
T ss_pred HHHHHhhccccCceEEEEecchhHHHHhHHHHHhhhh---hceEEEecCCHHHHHHHHHCCCCCEEEEecCccccccCee
Confidence 9988887777789999999999999999999998874 456777777888999999999999999864422 246799
Q ss_pred eeccccceEEEEecCCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCC-CceeEEEEecCHHHHHHHHHhcc
Q psy3760 160 SIPCYQWEYVIIVPLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQK-LTPYIVLETINSDIIKTYVELRM 238 (306)
Q Consensus 160 ~~~l~~~~~~~v~~~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~v~~g~ 238 (306)
+.+++.++++++++++||. .+.... ++.++|++.+..+...+..+..+++..+ +.++..+.+++...+..++.+|.
T Consensus 166 ~~~l~~~~~~~v~~~~~~~--~~~~~~-~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~ 242 (303)
T PRK10082 166 HIRLFESQLFPVCASDEHG--EALFNL-AQPHFPLLNYSRNSYMGRLINRTLTRHSELSFSTFFVSSMSELLKQVALDGC 242 (303)
T ss_pred EEEecceeEEEEecCCccC--Cccccc-ccCCCceEEeCCCccHHHHHHHHHhhhcccceeeEEEechHHHHHHHHHcCC
Confidence 9999999999999998863 222233 3588999998877666666777777765 67777788888889999999999
Q ss_pred ceeeeecceeccc-ccCCceeeecCCCCccceEEEEEeCCccccHHHHHHHHHHhHH
Q psy3760 239 GIGIIASIAFDSN-RDKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLLSPK 294 (306)
Q Consensus 239 gi~~~p~~~~~~~-~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~ 294 (306)
|++++|.+.+... ..++++.++++.......++ +|++++..++++++|++++++.
T Consensus 243 Gi~~lp~~~~~~~~~~~~l~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~f~~~~~~~ 298 (303)
T PRK10082 243 GIAWLPEYAIQQEIRSGQLVVLNRDELVIPIQAY-AYRMNTRMNPVAERFWRELREL 298 (303)
T ss_pred CEEEcChHHHHHHHHcCCEEEecCCccceeEEEE-EEecccccCHHHHHHHHHHhhc
Confidence 9999999887655 56789988876533334454 6999988999999999999874
No 38
>PRK15092 DNA-binding transcriptional repressor LrhA; Provisional
Probab=100.00 E-value=4.7e-50 Score=328.84 Aligned_cols=277 Identities=17% Similarity=0.178 Sum_probs=243.6
Q ss_pred CchhhHHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCCccccCHhHHHHHHHHHHHHHHHHHH
Q psy3760 1 MNLHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKPGQAILRSIEIIMQEIEGL 80 (306)
Q Consensus 1 m~~~~l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~~~lT~~G~~l~~~a~~il~~~~~~ 80 (306)
|++++|++|++|+++| ||++||++|++||||||++|++||++||++||+|+++++ .||++|+.|+++++++++.++++
T Consensus 11 m~l~~L~~F~~v~e~g-s~s~AA~~L~iSQpavS~~I~~LE~~lG~~LF~R~~~~~-~LT~~G~~l~~~a~~il~~~~~~ 88 (310)
T PRK15092 11 LDLDLLRTFVAVADLN-TFAAAAAAVCRTQSAVSQQMQRLEQLVGKELFARHGRNK-LLTEHGIQLLGYARKILRFNDEA 88 (310)
T ss_pred CCHHHHHHHHHHHHcC-CHHHHHHHhCCChHHHHHHHHHHHHHhCcceEEECCCCc-eECHhHHHHHHHHHHHHHHHHHH
Confidence 8999999999999999 999999999999999999999999999999999999999 79999999999999999999998
Q ss_pred HHHHHhhccCCCCcEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccCCCCCcee
Q psy3760 81 KKIGKEFSAYDTGNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLIS 160 (306)
Q Consensus 81 ~~~~~~~~~~~~~~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~~~~~~~ 160 (306)
...+. .....|.|+||++++++..++++++..|.++||++++++....+.++.+.|.+|++|++|+..+ .+++..
T Consensus 89 ~~~~~--~~~~~g~l~Ig~~~~~~~~~l~~~l~~f~~~~P~i~i~l~~~~~~~~~~~l~~g~~Di~i~~~~---~~~~~~ 163 (310)
T PRK15092 89 CSSLM--YSNLQGVLTIGASDDTADTILPFLLNRVSSVYPKLALDVRVKRNAFMMEMLESQEVDLAVTTHR---PSSFPA 163 (310)
T ss_pred HHHhc--CCCceeEEEEeCChHHHHHHHHHHHHHHHHHCCCcEEEEEECCcHHHHHHHhCCCeeEEEEecC---CCCCCc
Confidence 87764 3457889999999999999999999999999999999999998889999999999999998643 234566
Q ss_pred eccccceEEEEecCCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCceeEEEEecCHHHHHHHHHhccce
Q psy3760 161 IPCYQWEYVIIVPLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMGI 240 (306)
Q Consensus 161 ~~l~~~~~~~v~~~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi 240 (306)
.++..++++++++++||+.... ..|++....+...+..+..++...+..+++.+++++..++.++|.+|.|+
T Consensus 164 ~~l~~~~~~~~~~~~~~l~~~~--------~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~Gi 235 (310)
T PRK15092 164 LNLRTSPTLWYCAAEYVLQKGE--------PIPLVLLDEPSPFRDMALATLNAAGIPWRIAYVASTLSAVRAAVKAGLGV 235 (310)
T ss_pred eEeeecCcEEEecCCCCCCCCC--------ceeEEecCCCChHHHHHHHHHHHcCCCeeEEEEcCCHHHHHHHHHcCceE
Confidence 6788889999999999876432 34889888777777788889998898999999999999999999999999
Q ss_pred eeeecceecccccCCceeeecCC--CCccceEEEEEeCCccccHHHHHHHHHHhHHhh
Q psy3760 241 GIIASIAFDSNRDKNLRSISASH--LFGTTISRVIIKQGTYLRSYVYSFIKLLSPKLN 296 (306)
Q Consensus 241 ~~~p~~~~~~~~~~~l~~~~~~~--~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~ 296 (306)
+++|...+. ++++.+++.. +.....++++|+++...++.++.|++++++...
T Consensus 236 ~~lp~~~~~----~~l~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~~~l~~~~~ 289 (310)
T PRK15092 236 TARPVEMMS----PDLRVLGESEGLPPLPDTEYLLCRDPNSNNELAQVIFQAMESYHN 289 (310)
T ss_pred EEcchhhcC----ccceecccccCCCCCCCeEEEEEECCCcCCHHHHHHHHHHHHHhc
Confidence 999987653 3566665532 223457899999999999999999999988753
No 39
>TIGR02036 dsdC D-serine deaminase transcriptional activator. 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 E. coli, Vibrio cholerae, and Colwellia psychrerythraea.
Probab=100.00 E-value=1.1e-50 Score=332.67 Aligned_cols=284 Identities=18% Similarity=0.185 Sum_probs=236.7
Q ss_pred CchhhHHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCCccccCHhHHHHHHHHHHHHHHHHHH
Q psy3760 1 MNLHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKPGQAILRSIEIIMQEIEGL 80 (306)
Q Consensus 1 m~~~~l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~~~lT~~G~~l~~~a~~il~~~~~~ 80 (306)
||+++|++|++|+++| ||++||+.||+||||||++|++||++||++||+|+++++ .||++|+.|+++++++++.++++
T Consensus 8 ~~l~~L~~F~~va~~g-s~s~AA~~L~isQpavS~~I~~LE~~lg~~Lf~R~~r~~-~lT~~G~~l~~~a~~~l~~~~~~ 85 (302)
T TIGR02036 8 FQLSKMHTFEVAARHQ-SFSLAAEELSLTPSAISHRINQLEEELGIQLFVRSHRKV-ELTHEGKRIYWALKSSLDTLNQE 85 (302)
T ss_pred cCHHHHHHHHHHHHhC-CHHHHHHHHCCCHHHHHHHHHHHHHHhCCceEEECCCce-eECHhHHHHHHHHHHHHHHHHHH
Confidence 7999999999999999 999999999999999999999999999999999999999 79999999999999999999998
Q ss_pred HHHHHhhccCCCCcEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccCCCCCcee
Q psy3760 81 KKIGKEFSAYDTGNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLIS 160 (306)
Q Consensus 81 ~~~~~~~~~~~~~~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~~~~~~~ 160 (306)
...+. .....|.|+||++.+++..++++++..|.++||++.+++...+.. ..+.++++|++|+..+ ...+++.+
T Consensus 86 ~~~~~--~~~~~g~l~i~~~~~~~~~~l~~~l~~f~~~~P~i~l~l~~~~~~---~~l~~~~~Dl~i~~~~-~~~~~l~~ 159 (302)
T TIGR02036 86 ILDIK--NQELSGTLTLYSRPSFAQCWLVPRIGDFTRRYPSISLTVLTGNEN---INFQGAGIDVAIYFDD-APPAKLTC 159 (302)
T ss_pred HHHHH--hCCCCCeEEEEechHHHHHHHHHHHHHHHHHCCCceEEEEeCCcc---cccccCCccEEEEcCC-CCCCCcee
Confidence 87665 244578999999999999999999999999999999999876642 2467789999998654 45678999
Q ss_pred eccccceEEEEecCCCCCCCCCCcChhhhcCCCeEeec----CCCCcHHHHHHHHHhC---CCceeEEEEecCHHHHHHH
Q psy3760 161 IPCYQWEYVIIVPLDHPLLLLNSISLKEISNYPLITYD----LSFSGRIKLDREFSLQ---KLTPYIVLETINSDIIKTY 233 (306)
Q Consensus 161 ~~l~~~~~~~v~~~~~~l~~~~~i~~~dl~~~~~i~~~----~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~ 233 (306)
.++++++++++++++|+.....+.+++||.++|||... .+.... .+..|.... +..++..+.+++...+..+
T Consensus 160 ~~l~~~~~~~v~~~~~~~~~~~~~~~~~L~~~~~i~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 238 (302)
T TIGR02036 160 HFIMDETILPVCSPEYAQRHALTNTVINLCHCTLLHDNQAWSYDSGTD-EWHSWANHYAVNNLPTSSGIGFDRSDLAVIA 238 (302)
T ss_pred EEeecCcEEEEECHHHHhhccCCCCHHHHhCCCceeeccccccCCCCC-chHHHHHHcCCCccCcCCCceecChHHHHHH
Confidence 99999999999999986333345799999999999764 222222 233344432 2334556788999999999
Q ss_pred HHhccceeeeecceeccc-ccCCceeeecCCC--CccceEEEEEeCCccccHHHHHHHHHHhHHh
Q psy3760 234 VELRMGIGIIASIAFDSN-RDKNLRSISASHL--FGTTISRVIIKQGTYLRSYVYSFIKLLSPKL 295 (306)
Q Consensus 234 v~~g~gi~~~p~~~~~~~-~~~~l~~~~~~~~--~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~ 295 (306)
+.+|.|++++|.+++... ..+.++. ++++. ....++|++|+++. .+|.++.|++++++.+
T Consensus 239 v~~g~Gi~~lp~~~~~~~~~~g~l~~-~l~~~~~~~~~~~~lv~~~~~-~~~~~~~fi~~l~~~~ 301 (302)
T TIGR02036 239 AMNNAGVAMGRKSLVQKRLASGELVA-PFGDMTVKCHQRYYVATLPNR-QNPKIELFIIWLREQV 301 (302)
T ss_pred HHhCCcEEEechHhHHHHHHCCCEEc-ccCCcCCCCCCcEEEEeCCCc-CChHHHHHHHHHHHhh
Confidence 999999999999887655 6777775 45442 24568999999986 4899999999997653
No 40
>COG0583 LysR Transcriptional regulator [Transcription]
Probab=100.00 E-value=1.3e-47 Score=315.11 Aligned_cols=290 Identities=27% Similarity=0.394 Sum_probs=253.8
Q ss_pred CchhhHHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCCccccCHhHHHHHHHHHHHHHHHHHH
Q psy3760 1 MNLHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKPGQAILRSIEIIMQEIEGL 80 (306)
Q Consensus 1 m~~~~l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~~~lT~~G~~l~~~a~~il~~~~~~ 80 (306)
||+++|++|++|+++| ||++||++|++||||+|++|++||++||++||+|+++++ .||++|+.|+++++++++.++++
T Consensus 1 ~~l~~L~~F~~v~~~~-s~t~AA~~L~isqsavS~~I~~LE~~lg~~Lf~R~~~~~-~lT~~G~~l~~~a~~~l~~~~~~ 78 (297)
T COG0583 1 MDLRQLRAFVAVAEEG-SFTRAAERLGLSQSAVSRQIKRLEEELGVPLFERTTRRV-RLTEAGERLLERARRILAELEEA 78 (297)
T ss_pred CcHHHHHHHHHHHHcC-cHHHHHHHhCCCChHHHHHHHHHHHHhCchheeecCCce-eeCHhHHHHHHHHHHHHHHHHHH
Confidence 8999999999999999 999999999999999999999999999999999999998 79999999999999999999999
Q ss_pred HHHHHhhccCCC-CcEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccCCCC-Cc
Q psy3760 81 KKIGKEFSAYDT-GNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSD-KL 158 (306)
Q Consensus 81 ~~~~~~~~~~~~-~~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~~~-~~ 158 (306)
............ +.++||+++++...++++++..|.+.||++.+.+...+ .+.+.+.+|++|++|...+. ..+ ++
T Consensus 79 ~~~~~~~~~~~~~~~~~i~~~~~~~~~~l~~~l~~~~~~~P~~~~~~~~~~--~~~~~l~~~~~D~~i~~~~~-~~~~~~ 155 (297)
T COG0583 79 LAEAARLARGEPGGLLRIAAPSTAASSLLPPLLARFRARYPEIELELGTSD--RLLEDLVEGELDLAIRAGPP-PPPDGL 155 (297)
T ss_pred HHHHHHHhccCCCceEEEEecchhhhhhhHHHHHHHHHhCCCeEEEeCchH--HHHHHHHcCCCCEEEecCCC-CCCCce
Confidence 987776554444 59999999999988999999999999996666665543 47889999999999997653 333 89
Q ss_pred eeeccccceEEEEecCCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCceeEEEEecCHHHHHHHHHhcc
Q psy3760 159 ISIPCYQWEYVIIVPLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRM 238 (306)
Q Consensus 159 ~~~~l~~~~~~~v~~~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~ 238 (306)
...+++.++++++++++||+..+.. ++++...+++........+......+...+..+...+.+++..++++++.+|.
T Consensus 156 ~~~~l~~~~~~~v~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~ 233 (297)
T COG0583 156 VARPLFSEELVLVVPASHPLAARHG--LPDLPGEPLILLEHGCILRRLLDQALALAGWRPRIRLEVNSAEALLQAVAAGL 233 (297)
T ss_pred EEEEcccceEEEEecCCCCCccccc--HHHHhcCCEEecCCCccHHHHHHHHHHHcCCCccceeeecCHHHHHHHHHcCC
Confidence 9999999999999999999988765 89999999999998888888888888888777778889999999999999999
Q ss_pred ceeeeecceeccc-ccCCceeeecCCCCccceEEEEEeCCccccHHHHHHHHHHhHHhhH
Q psy3760 239 GIGIIASIAFDSN-RDKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLLSPKLNR 297 (306)
Q Consensus 239 gi~~~p~~~~~~~-~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~ 297 (306)
|++++|..++... ....+..++...+.....+|++|+++...++.+++|++++++.+..
T Consensus 234 gi~~lp~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~ 293 (297)
T COG0583 234 GIALLPESLARPDLAGRLVRVLPLPPPPLPRPLYLVWRKSRLLSPAVRAFIDFLREALAR 293 (297)
T ss_pred CcEECcHHHhhccCCcCceEEeeccCCCCceeEEEEEeCCccCCHHHHHHHHHHHHhhhc
Confidence 9999999988776 3245667777663444459999998656799999999999987654
No 41
>PRK11716 DNA-binding transcriptional regulator IlvY; Provisional
Probab=100.00 E-value=2.9e-47 Score=308.67 Aligned_cols=266 Identities=20% Similarity=0.299 Sum_probs=238.7
Q ss_pred hCCCchHHHHHHHHHHHHcCceeEEecCCCccccCHhHHHHHHHHHHHHHHHHHHHHHHHhhccCCCCcEEEEecccchh
Q psy3760 26 LYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKPGQAILRSIEIIMQEIEGLKKIGKEFSAYDTGNLTIATTHTQAR 105 (306)
Q Consensus 26 l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~~~lT~~G~~l~~~a~~il~~~~~~~~~~~~~~~~~~~~l~I~~~~~~~~ 105 (306)
||+||||||++|++||++||++||+|+++++ +||++|+.|+++++++++.++++.+.++.......|.++||+++.++.
T Consensus 1 L~isQpavS~~I~~LE~~lg~~Lf~R~~r~~-~lT~~G~~l~~~a~~~l~~~~~~~~~~~~~~~~~~~~l~I~~~~~~~~ 79 (269)
T PRK11716 1 MHVSPSTLSRQIQRLEEELGQPLFVRDNRSV-TLTEAGEELRPFAQQTLLQWQQLRHTLDQQGPSLSGELSLFCSVTAAY 79 (269)
T ss_pred CCcChHHHHHHHHHHHHHhCCeeEEecCCce-eECHhHHHHHHHHHHHHHHHHHHHHHHHhhccccCceEEEEecchHHH
Confidence 7999999999999999999999999999999 899999999999999999999999999887778899999999999999
Q ss_pred hhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccCCCCCceeeccccceEEEEecCCCCCCC-CCCc
Q psy3760 106 YALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLISIPCYQWEYVIIVPLDHPLLL-LNSI 184 (306)
Q Consensus 106 ~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~~~~~~~~~l~~~~~~~v~~~~~~l~~-~~~i 184 (306)
.++++++..|.+.||++++++....+.++.+.|.+|++|++|+..+....+++...+++.++++++++++||+.. ....
T Consensus 80 ~~~~~~l~~~~~~~p~i~l~i~~~~~~~~~~~l~~~~~D~~i~~~~~~~~~~~~~~~l~~~~~~~v~~~~~~~~~~~~~~ 159 (269)
T PRK11716 80 SHLPPILDRFRAEHPLVEIKLTTGDAADAVEKVQSGEADLAIAAKPETLPASVAFSPIDEIPLVLIAPALPCPVRQQLSQ 159 (269)
T ss_pred HHHHHHHHHHHHHCCCeEEEEEECCHHHHHHHHHCCCccEEEEecCCCCCcceEEEEcccceEEEEEcCCcchhhhcccc
Confidence 999999999999999999999999999999999999999999865433356689999999999999999997543 3456
Q ss_pred ChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCceeEEEEecCHHHHHHHHHhccceeeeecceeccc-ccCCceeeecCC
Q psy3760 185 SLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMGIGIIASIAFDSN-RDKNLRSISASH 263 (306)
Q Consensus 185 ~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~~~p~~~~~~~-~~~~l~~~~~~~ 263 (306)
+..++.++|++....+ ..+..+..+++..++.+++.+++++...+++++.+|.|++++|.+++... ..+.++.++++.
T Consensus 160 ~~~~l~~~~~i~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~~~p~~~~~~~~~~~~l~~~~~~~ 238 (269)
T PRK11716 160 EKPDWSRIPFILPEHG-PARRRIDLWFRRHKIKPNIYATVSGHEAIVSMVALGCGVGLLPEVVLENSPVRNRVQILERVP 238 (269)
T ss_pred chhhHhhCCeeecCCC-chHHHHHHHHHHcCCCCCeEEEechHHHHHHHHHcCCCeEeccHHHhhcCcccCCeeeccCCC
Confidence 8889999999987554 34567788999999999999999999999999999999999999988665 556788888876
Q ss_pred CCccceEEEEEeCCccccHHHHHHHHHHhH
Q psy3760 264 LFGTTISRVIIKQGTYLRSYVYSFIKLLSP 293 (306)
Q Consensus 264 ~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~ 293 (306)
.....+++++|++++..+|.+++|+++++.
T Consensus 239 ~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~ 268 (269)
T PRK11716 239 PITPFELGVCVQKKRLEEPLIDAFWQLLEN 268 (269)
T ss_pred CCCcceEEEEEccccCcCHHHHHHHHHHhc
Confidence 556679999999999999999999999875
No 42
>PF03466 LysR_substrate: LysR substrate binding domain; InterPro: IPR005119 The structure of this domain is known and is similar to the periplasmic binding proteins []. This domain is found in members of the LysR family of prokaryotic transcriptional regulatory proteins IPR000847 from INTERPRO which share sequence similarities over approximately 280 residues including a putative helix-turn-helix DNA-binding motif at their N terminus.; PDB: 3ONM_B 3FZJ_J 3FXR_B 3N6T_A 3FXQ_A 3FXU_A 3N6U_A 2QSX_B 3HO7_B 1IZ1_B ....
Probab=100.00 E-value=6e-33 Score=216.19 Aligned_cols=207 Identities=24% Similarity=0.352 Sum_probs=194.3
Q ss_pred cCCCCcEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccCCCCCceeeccccceE
Q psy3760 89 AYDTGNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLISIPCYQWEY 168 (306)
Q Consensus 89 ~~~~~~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~~~~~~~~~l~~~~~ 168 (306)
++.+|+|+||+++++...++++++..|.+.||++++++...++.++.+.|.+|++|++|+..+ ...+++.+.+++++++
T Consensus 2 ~~~~~~l~Ig~~~~~~~~~l~~~l~~~~~~~P~i~i~~~~~~~~~~~~~l~~g~~Dl~i~~~~-~~~~~~~~~~l~~~~~ 80 (209)
T PF03466_consen 2 QGERGTLRIGASPSFASSLLPPLLAEFRERHPNIRIEIREGDSDELIEALRSGELDLAITFGP-PPPPGLESEPLGEEPL 80 (209)
T ss_dssp CTSEEEEEEEEEHHHHHHTHHHHHHHHHHHSTTEEEEEEEESHHHHHHHHHTTSSSEEEESSS-SSSTTEEEEEEEEEEE
T ss_pred CccceEEEEEEEhHHHHHHHHHHHHHHHHHCCCcEEEEEeccchhhhHHHhcccccEEEEEee-ccccccccccccceee
Confidence 356789999999999999999999999999999999999999999999999999999999765 5889999999999999
Q ss_pred EEEecCCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCceeEEEEecCHHHHHHHHHhccceeeeeccee
Q psy3760 169 VIIVPLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMGIGIIASIAF 248 (306)
Q Consensus 169 ~~v~~~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~~~p~~~~ 248 (306)
+++++++||++.+++++++||.++|++.+..+...+..+.+++...++.++..+++++..++..++.+|.|++++|.+++
T Consensus 81 ~~~~~~~~pl~~~~~i~~~dL~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~~~p~~~~ 160 (209)
T PF03466_consen 81 VLVVSPDHPLAQKKPITLEDLADYPLILLSPGSPYRDQLDRWLREHGFSPNIVIEVDSFESILSLVASGDGIAILPDSLA 160 (209)
T ss_dssp EEEEETTSGGGTTSSSSGGGGTTSEEEEESTTTSHHHHHHHHHHHTTEEEEEEEEESSHHHHHHHHHTTSEBEEEEHHHH
T ss_pred eeeeeccccccccccchhhhhhhccccccccccccccccccccccccccccccccccchhhhccccccccceeecCcccc
Confidence 99999999999999999999999999999988889999999999999999999999999999999999999999999998
Q ss_pred ccc-ccCCceeeecCCCCccceEEEEEeCCccccHHHHHHHHHHhHHhh
Q psy3760 249 DSN-RDKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLLSPKLN 296 (306)
Q Consensus 249 ~~~-~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~ 296 (306)
... ..++++.+++++.....+++++|++++..+|.+++|++++++.++
T Consensus 161 ~~~~~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~ 209 (209)
T PF03466_consen 161 QDELESGELVFLPLPDPPLPRPIYLVWRKDRPLSPAIQWFIDLLREHFA 209 (209)
T ss_dssp HHHHHCTTEEEEEESSSTEEEEEEEEEETTGTTHHHHHHHHHHHHHHH-
T ss_pred cccccCCCEEEEECCCCCCceEEEEEEECCCCCCHHHHHHHHHHHHHhC
Confidence 665 789999999998555689999999999999999999999998763
No 43
>cd08444 PBP2_Cbl The C-terminal substrate binding domain of LysR-type transcriptional regulator Cbl, which is required for expression of sulfate starvation-inducible (ssi) genes, contains the type 2 periplasmic binding fold. Cbl is a member of the LysR transcriptional regulators that comprise the largest family of prokaryotic transcription factor. Cbl shows high sequence similarity to CysB, the LysR-type transcriptional activator of genes involved in sulfate and thiosulfate transport, sulfate reduction, and cysteine synthesis. In Escherichia coli, the function of Cbl is required for expression of sulfate starvation-inducible (ssi) genes, coupled with the biosynthesis of cysteine from the organic sulfur sources (sulfonates). The ssi genes include the ssuEADCB and tauABCD operons encoding uptake systems for organosulfur compounds, aliphatic sulfonates, and taurine. The genes in these operons encode an ABC-type transport system required for uptake of aliphatic sulfonates and a desulfonati
Probab=99.97 E-value=1.7e-29 Score=195.20 Aligned_cols=198 Identities=49% Similarity=0.866 Sum_probs=177.2
Q ss_pred cEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccCCCCCceeeccccceEEEEec
Q psy3760 94 NLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLISIPCYQWEYVIIVP 173 (306)
Q Consensus 94 ~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~~~~~~~~~l~~~~~~~v~~ 173 (306)
+|+||++++++..++++++..|+++||++++++....++++.+.|.+|++|++|+.......+++...++++++++++++
T Consensus 1 ~l~ig~~~~~~~~~l~~~l~~~~~~~P~v~l~i~~~~~~~~~~~l~~g~~Dl~i~~~~~~~~~~~~~~~l~~~~~~~~~~ 80 (198)
T cd08444 1 ELTIATTHTQARYALPWVVQAFKEQFPNVHLVLHQGSPEEIASMLANGQADIGIATEALENHPELVSFPYYDWHHHIIVP 80 (198)
T ss_pred CeEEeecchhhhhhhhHHHHHHHHHCCCeEEEEEeCCHHHHHHHHHCCCccEEEeccccCCCcCcEEeeccccceeEEec
Confidence 48999999999999999999999999999999999999999999999999999986442345789999999999999999
Q ss_pred CCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCceeEEEEecCHHHHHHHHHhccceeeeecceeccccc
Q psy3760 174 LDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMGIGIIASIAFDSNRD 253 (306)
Q Consensus 174 ~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~~~p~~~~~~~~~ 253 (306)
++||++.+.+++++||.++|++.+..+...+..+..++...++.++..+++++..++++++.+|.|++++|.+.+.....
T Consensus 81 ~~hpl~~~~~~~~~~l~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~Gi~~lp~~~~~~~~~ 160 (198)
T cd08444 81 VGHPLESITPLTIETIAKWPIITYHGGFTGRSRIDRAFSRAELTPNIVLSALDADVIKTYVGLGMGIGIVAEMAFEGQRD 160 (198)
T ss_pred CCCccccCCCcCHHHHhCCCEEEecCCCchHHHHHHHHHHcCCCCceEEEeCCHHHHHHHHHcCCcEEeccHHHHhhhhc
Confidence 99999887889999999999999887766777788899999999999999999999999999999999999988765444
Q ss_pred CCceeeecCCCCccceEEEEEeCCccccHHHHHHHHHH
Q psy3760 254 KNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLL 291 (306)
Q Consensus 254 ~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l 291 (306)
++++.+++.+......+|++|++++..++.++.|++++
T Consensus 161 ~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~~~~ 198 (198)
T cd08444 161 TNLIKLDTSHLFGKNTTWIALRRGGDLRNFAYRFIELC 198 (198)
T ss_pred CceEEeecCCCccceeEEEEEcCCCccCHHHHHHHhhC
Confidence 67888888665556799999999999999999999864
No 44
>cd08413 PBP2_CysB_like The C-terminal substrate domain of LysR-type transcriptional regulators CysB-like contains type 2 periplasmic binding fold. CysB is a transcriptional activator of genes involved in sulfate and thiosulfate transport, sulfate reduction, and cysteine synthesis. In Escherichia coli, the regulation of transcription in response to sulfur source is attributed to two transcriptional regulators, CysB and Cbl. CysB, in association with Cbl, downregulates the expression of ssuEADCB operon which is required for the utilization of sulfur from aliphatic sulfonates, in the presence of cysteine. Also, Cbl and CysB together directly function as transcriptional activators of tauABCD genes, which are required for utilization of taurine as sulfur source for growth. Like many other members of the LTTR family, CysB is composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-bi
Probab=99.97 E-value=1.9e-29 Score=194.97 Aligned_cols=198 Identities=52% Similarity=0.955 Sum_probs=178.5
Q ss_pred cEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccCCCCCceeeccccceEEEEec
Q psy3760 94 NLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLISIPCYQWEYVIIVP 173 (306)
Q Consensus 94 ~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~~~~~~~~~l~~~~~~~v~~ 173 (306)
+++||++++++..++++++..|.++||++++++....+.++.+.|.+|++|++|........+++.+.++++++++++++
T Consensus 1 ~l~ig~~~~~~~~~l~~~l~~~~~~~P~i~v~~~~~~~~~~~~~l~~g~~D~~i~~~~~~~~~~~~~~~l~~~~~~~v~~ 80 (198)
T cd08413 1 QLTIATTHTQARYVLPPVIAAFRKRYPKVKLSLHQGTPSQIAEMVLKGEADIAIATEALDDHPDLVTLPCYRWNHCVIVP 80 (198)
T ss_pred CeEEeecchhhhhhccHHHHHHHHhCCceEEEEEeCCHHHHHHHHHcCCCCEEEEccCCCCCCCcEEEEeeeeeEEEEec
Confidence 48999999999999999999999999999999999998899999999999999986443346789999999999999999
Q ss_pred CCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCceeEEEEecCHHHHHHHHHhccceeeeecceeccccc
Q psy3760 174 LDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMGIGIIASIAFDSNRD 253 (306)
Q Consensus 174 ~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~~~p~~~~~~~~~ 253 (306)
++||++.++.++++||.++|++.+..+...+..+..++...++.++..+++++..++++++.+|.|++++|.+.+.....
T Consensus 81 ~~hpl~~~~~i~~~~l~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~Gi~~lp~~~~~~~~~ 160 (198)
T cd08413 81 PGHPLADLGPLTLEDLAQYPLITYDFGFTGRSSIDRAFARAGLEPNIVLTALDADVIKTYVRLGLGVGIIAEMAYDPQRD 160 (198)
T ss_pred CCCcccccCCCCHHHHhcCCEEECCCCccHHHHHHHHHHHcCCCcceEEEeCCHHHHHHHHHhCCCEEEccccccCcccc
Confidence 99999988889999999999999887766677788899999999999999999999999999999999999987765456
Q ss_pred CCceeeecCCCCccceEEEEEeCCccccHHHHHHHHHH
Q psy3760 254 KNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLL 291 (306)
Q Consensus 254 ~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l 291 (306)
++++.+++.+......++++|+++...++.++.|++++
T Consensus 161 ~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~f~~~~ 198 (198)
T cd08413 161 ADLVALDAGHLFGPNTTRIALRRGTYLRSYAYDFIELF 198 (198)
T ss_pred CcEEEeecCCcCcceeEEEEEeehhhhhHHHHHHHhhC
Confidence 78999999875566789999999999999999999863
No 45
>cd08421 PBP2_LTTR_like_1 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator, contains the type 2 periplasmic binding fold. LysR-transcriptional regulators comprise the largest family of prokaryotic transcription factor. Homologs of some of LTTRs with similar domain organizations are also found in the archaea and eukaryotic organisms. The LTTRs are composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcriptional repressor undergoes a conformational change upon substrate binding which in turn changes the DNA binding affinity of the repressor. The genes controlled by the LTTRs have diverse functi
Probab=99.97 E-value=4.2e-29 Score=192.77 Aligned_cols=197 Identities=17% Similarity=0.215 Sum_probs=178.7
Q ss_pred cEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccCCCCCceeeccccceEEEEec
Q psy3760 94 NLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLISIPCYQWEYVIIVP 173 (306)
Q Consensus 94 ~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~~~~~~~~~l~~~~~~~v~~ 173 (306)
+|+||++++++..++++++..|.+.||++++++....+.++.+.|.+|++|++|+..+ ...+++.+.++++++++++++
T Consensus 1 ~l~I~~~~~~~~~~l~~~l~~~~~~~P~i~i~~~~~~~~~~~~~l~~~~~D~~i~~~~-~~~~~~~~~~l~~~~~~~v~~ 79 (198)
T cd08421 1 HVRLLANTSAIVEFLPEDLASFLAAHPDVRIDLEERLSADIVRAVAEGRADLGIVAGN-VDAAGLETRPYRTDRLVVVVP 79 (198)
T ss_pred CEEEEeccchhhhhhHHHHHHHHHHCCCceEEEEecCcHHHHHHHhcCCceEEEEecC-CCCCCcEEEEeecCcEEEEeC
Confidence 4899999999999999999999999999999999988889999999999999999654 556789999999999999999
Q ss_pred CCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCceeEEEEecCHHHHHHHHHhccceeeeecceeccc-c
Q psy3760 174 LDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMGIGIIASIAFDSN-R 252 (306)
Q Consensus 174 ~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~~~p~~~~~~~-~ 252 (306)
++||++.+..++++||.++|++.+..+...+..+.++++..+..+++.+++++...+..++.+|.|++++|...+... .
T Consensus 80 ~~~pl~~~~~~~~~~l~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gia~~p~~~~~~~~~ 159 (198)
T cd08421 80 RDHPLAGRASVAFADTLDHDFVGLPAGSALHTFLREAAARLGRRLRLRVQVSSFDAVCRMVAAGLGIGIVPESAARRYAR 159 (198)
T ss_pred CCCCccccCCCCHHHhcCCceEeecCCcchHHHHHHHHHHcCCCceEEEEECCHHHHHHHHHcCCCeEEccchhhhhhcc
Confidence 999998888899999999999999877777777888888899999999999999999999999999999999888754 6
Q ss_pred cCCceeeecCCCCccceEEEEEeCCccccHHHHHHHHHH
Q psy3760 253 DKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLL 291 (306)
Q Consensus 253 ~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l 291 (306)
.++++.+++.+.....+++++|++++..++.++.|++++
T Consensus 160 ~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 198 (198)
T cd08421 160 ALGLRVVPLDDAWARRRLLLCVRSFDALPPAARALVDHL 198 (198)
T ss_pred cCCeEEEeccCCcccceEEEEEeCCCcCCHHHHHHHhhC
Confidence 788999988765456789999999999999999999864
No 46
>cd08411 PBP2_OxyR The C-terminal substrate-binding domain of the LysR-type transcriptional regulator OxyR, a member of the type 2 periplasmic binding fold protein superfamily. OxyR senses hydrogen peroxide and is activated through the formation of an intramolecular disulfide bond. The OxyR activation induces the transcription of genes necessary for the bacterial defense against oxidative stress. The OxyR of LysR-type transcriptional regulator family is composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcriptional repressor undergoes a conformational change upon substrate binding which in turn changes the DNA binding affinity of the repre
Probab=99.97 E-value=4.8e-29 Score=192.81 Aligned_cols=198 Identities=18% Similarity=0.287 Sum_probs=179.3
Q ss_pred CcEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccCCCCCceeeccccceEEEEe
Q psy3760 93 GNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLISIPCYQWEYVIIV 172 (306)
Q Consensus 93 ~~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~~~~~~~~~l~~~~~~~v~ 172 (306)
|+++||++++++..++++++..|.++||++++++...++.++.+.|.+|++|++|+..+ ...+++....++++++++++
T Consensus 1 g~l~I~~~~~~~~~~l~~~l~~~~~~~P~i~i~i~~~~~~~~~~~l~~~~~Dl~i~~~~-~~~~~~~~~~l~~~~~~~v~ 79 (200)
T cd08411 1 GPLRLGVIPTIAPYLLPRLLPALRQAYPKLRLYLREDQTERLLEKLRSGELDAALLALP-VDEPGLEEEPLFDEPFLLAV 79 (200)
T ss_pred CeEEEEecHHHHhhhhHHHHHHHHHHCCCcEEEEEeCcHHHHHHHHHcCCccEEEEecc-CCCCCceEEEeeccceEEEe
Confidence 57999999999999999999999999999999999998999999999999999998654 44578999999999999999
Q ss_pred cCCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCceeEEEEecCHHHHHHHHHhccceeeeecceecc-c
Q psy3760 173 PLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMGIGIIASIAFDS-N 251 (306)
Q Consensus 173 ~~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~~~p~~~~~~-~ 251 (306)
+++||++.+..++++||.++|++.+..+...++.+..++...+..++..+++++...+.+++..|.|++++|...+.. .
T Consensus 80 ~~~~pl~~~~~~~~~~l~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~~~p~~~~~~~~ 159 (200)
T cd08411 80 PKDHPLAKRKSVTPEDLAGERLLLLEEGHCLRDQALELCRLAGAREQTDFEATSLETLRQMVAAGLGITLLPELAVPSEE 159 (200)
T ss_pred cCCCCccccCccCHHHHcCCceEecCCCCcHHHHHHHHHHHcCCCcceEEEeccHHHHHHHHHcCCCEEEeCHHHhcccc
Confidence 999999888889999999999999887766777888899999998999999999999999999999999999998876 3
Q ss_pred -ccCCceeeecCCCCccceEEEEEeCCccccHHHHHHHHHH
Q psy3760 252 -RDKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLL 291 (306)
Q Consensus 252 -~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l 291 (306)
..+.+..+++++.....+++++|+++...++.++.|++++
T Consensus 160 ~~~~~l~~~~l~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~ 200 (200)
T cd08411 160 LRGDRLVVRPFAEPAPSRTIGLVWRRSSPRAAAFEALAELI 200 (200)
T ss_pred cCCCceEEEECCCCCcceEEEEEEcCCccCCHHHHHHHhhC
Confidence 5667888888765556799999999999999999999874
No 47
>cd08459 PBP2_DntR_NahR_LinR_like The C-terminal substrate binding domain of LysR-type transcriptional regulators that are involved in the catabolism of dinitrotoluene, naphthalene and gamma-hexachlorohexane; contains the type 2 periplasmic binding fold. This CD includes LysR-like bacterial transcriptional regulators, DntR, NahR, and LinR, which are involved in the degradation of aromatic compounds. The transcription of the genes encoding enzymes involved in such degradation is regulated and expression of these enzymes is enhanced by inducers, which are either an intermediate in the metabolic pathway or compounds to be degraded. DntR from Burkholderia species controls genes encoding enzymes for oxidative degradation of the nitro-aromatic compound 2,4-dinitrotoluene. The active form of DntR is homotetrameric, consisting of a dimer of dimers. NahR is a salicylate-dependent transcription activator of the nah and sal operons for naphthalene degradation. Salicylic acid is an intermediate o
Probab=99.97 E-value=1.6e-29 Score=195.69 Aligned_cols=200 Identities=14% Similarity=0.127 Sum_probs=179.9
Q ss_pred cEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccCCCCCceeeccccceEEEEec
Q psy3760 94 NLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLISIPCYQWEYVIIVP 173 (306)
Q Consensus 94 ~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~~~~~~~~~l~~~~~~~v~~ 173 (306)
+++||++.+++..++++++..|.+.||++.+++....+.++.+.|.+|++|++|...+ ..++++...++++++++++++
T Consensus 1 ~l~I~~~~~~~~~~l~~~l~~~~~~~P~v~v~i~~~~~~~~~~~l~~g~~D~~i~~~~-~~~~~l~~~~l~~~~~~~v~~ 79 (201)
T cd08459 1 TFRIAMSDIGEMYFLPRLLAALREVAPGVRIETVRLPVDELEEALESGEIDLAIGYLP-DLGAGFFQQRLFRERYVCLVR 79 (201)
T ss_pred CeEEEeChHHHHHHHHHHHHHHHHHCCCCeEEEEecCccCHHHHhhCCCceEEEEcCC-CCcccceEEEeecCceEEEEc
Confidence 4899999999999999999999999999999999998889999999999999998654 446789999999999999999
Q ss_pred CCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCceeEEEEecCHHHHHHHHHhccceeeeecceeccc-c
Q psy3760 174 LDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMGIGIIASIAFDSN-R 252 (306)
Q Consensus 174 ~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~~~p~~~~~~~-~ 252 (306)
++||++.+. ++++||.++|++.+..+...+..+.+++...++.++..+++++..++.+++.+|.|++++|.+.+... .
T Consensus 80 ~~~~l~~~~-i~~~~L~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~~lp~~~~~~~~~ 158 (201)
T cd08459 80 KDHPRIGST-LTLEQFLAARHVVVSASGTGHGLVEQALREAGIRRRIALRVPHFLALPLIVAQTDLVATVPERLARLFAR 158 (201)
T ss_pred CCCccccCC-cCHHHHhhCCcEEEccCCCCcchHHHHHHHhCccccEEEEcCcHHHHHHHHhcCCEEEecHHHHHHHHhh
Confidence 999988665 99999999999998876556667888999999999999999999999999999999999999887655 5
Q ss_pred cCCceeeecCCCCccceEEEEEeCCccccHHHHHHHHHHhHHh
Q psy3760 253 DKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLLSPKL 295 (306)
Q Consensus 253 ~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~ 295 (306)
.++++.++++......+++++|+++...+|.+++|++.+++.|
T Consensus 159 ~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 201 (201)
T cd08459 159 AGGLRIVPLPFPLPPFEVKLYWHRRFHRDPGNRWLRQLVAELF 201 (201)
T ss_pred cCCeeEecCCCCCCCceEEEEEccccCCChHHHHHHHHHHhhC
Confidence 6789999887755678999999999999999999999998764
No 48
>cd08433 PBP2_Nac The C-teminal substrate binding domain of LysR-like nitrogen assimilation control (NAC) protein, contains the type 2 periplasmic binding fold. The NAC is a LysR-type transcription regulator that activates expression of operons such as hut (histidine utilization) and ure (urea utilization), allowing use of non-preferred (poor) nitrogen sources, and represses expression of operons, such as glutamate dehydrogenase (gdh), allowing assimilation of the preferred nitrogen source. The expression of the nac gene is fully dependent on the nitrogen regulatory system (NTR) and the sigma54-containing RNA polymerase (sigma54-RNAP). In response to nitrogen starvation, NTR system activates the expression of nac, and NAC activates the expression of hut, ure, and put (proline utilization). NAC is not involved in the transcription of Sigma70-RNAP operons such as glnA, which directly respond by the NTR system, but activates the transcription of sigma70-RNAP dependent operons such as hut.
Probab=99.97 E-value=5.5e-29 Score=192.14 Aligned_cols=197 Identities=18% Similarity=0.243 Sum_probs=179.2
Q ss_pred cEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccCCCCCceeeccccceEEEEec
Q psy3760 94 NLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLISIPCYQWEYVIIVP 173 (306)
Q Consensus 94 ~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~~~~~~~~~l~~~~~~~v~~ 173 (306)
+++||++++++..++++++..|.+.||++++++....+.++.+.|.+|++|++|+..+ ...+++...++++++++++++
T Consensus 1 ~l~Ig~~~~~~~~~l~~~l~~~~~~~P~i~i~~~~~~~~~~~~~l~~~~~D~~i~~~~-~~~~~~~~~~l~~~~~~~~~~ 79 (198)
T cd08433 1 RVSVGLPPSAASVLAVPLLRAVRRRYPGIRLRIVEGLSGHLLEWLLNGRLDLALLYGP-PPIPGLSTEPLLEEDLFLVGP 79 (198)
T ss_pred CeEEEechhhhhhcchHHHHHHHHHCCCcEEEEEecCcHHHHHHHhCCCCcEEEEeCC-CCCCCeeEEEeccccEEEEec
Confidence 4899999999999999999999999999999999988889999999999999999654 456789999999999999999
Q ss_pred CCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCceeEEEEecCHHHHHHHHHhccceeeeecceeccc-c
Q psy3760 174 LDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMGIGIIASIAFDSN-R 252 (306)
Q Consensus 174 ~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~~~p~~~~~~~-~ 252 (306)
++||++.+..++++||.++|++....+...+..+.++++..+..++..+++++...+.+++..|.|++++|...+... .
T Consensus 80 ~~~~~~~~~~~~~~~l~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gia~~p~~~~~~~~~ 159 (198)
T cd08433 80 ADAPLPRGAPVPLAELARLPLILPSRGHGLRRLVDEAAARAGLTLNVVVEIDSVATLKALVAAGLGYTILPASAVAAEVA 159 (198)
T ss_pred CCCccccCCCCCHHHhCCCceEEcCCCCcHHHHHHHHHHHcCCCceeEEEeCcHHHHHHHHHcCCcEEEcchhhhhhhhh
Confidence 999998777899999999999998877667778889999999999999999999999999999999999999888765 6
Q ss_pred cCCceeeecCCCCccceEEEEEeCCccccHHHHHHHHHH
Q psy3760 253 DKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLL 291 (306)
Q Consensus 253 ~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l 291 (306)
.++++.++++......+++++|+++...+|.++.|++++
T Consensus 160 ~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~ 198 (198)
T cd08433 160 AGRLVAAPIVDPALTRTLSLATPRDRPLSPAALAVRDLL 198 (198)
T ss_pred cCceEEEECCCCCcceEEEEEEcCCCCCCHHHHHHHHhC
Confidence 788999998765567899999999999999999999864
No 49
>cd08437 PBP2_MleR The substrate binding domain of LysR-type transcriptional regulator MleR which required for malolactic fermentation, contains type 2 periplasmic binidning fold. MleR, a transcription activator of malolactic fermentation system, is found in gram-positive bacteria and belongs to the lysR family of bacterial transcriptional regulators. The mleR gene is required for the expression and induction of malolactic fermentation. This substrate binding domain has significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase dom
Probab=99.97 E-value=7.8e-29 Score=191.35 Aligned_cols=196 Identities=21% Similarity=0.302 Sum_probs=176.0
Q ss_pred cEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEcccc-CCCCCceeeccccceEEEEe
Q psy3760 94 NLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEIL-SPSDKLISIPCYQWEYVIIV 172 (306)
Q Consensus 94 ~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~-~~~~~~~~~~l~~~~~~~v~ 172 (306)
+++||++++++..++++++..|.++||++++++....+.++.+.|.+|++|++|+.... ...+++...+++++++++++
T Consensus 1 ~l~Ig~~~~~~~~~l~~~l~~~~~~~P~v~i~~~~~~~~~~~~~l~~g~~Dl~i~~~~~~~~~~~l~~~~l~~~~~~~~~ 80 (198)
T cd08437 1 KLRFGLPPIIGNYYFPKLAKDLIKTGLMIQIDTYEGGSAELLEQLLQGDLDIALLGSLTPLENSALHSKIIKTQHFMIIV 80 (198)
T ss_pred CeEEeeChHHHHHHhHHHHHHHHHhCCceEEEEEEcCHHHHHHHHHcCCCCEEEecCCCCCCcccceEEEeecceEEEEe
Confidence 48999999999999999999999999999999999999999999999999999986431 24578999999999999999
Q ss_pred cCCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCceeEEEEecCHHHHHHHHHhccceeeeecceecccc
Q psy3760 173 PLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMGIGIIASIAFDSNR 252 (306)
Q Consensus 173 ~~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~~~p~~~~~~~~ 252 (306)
+++||++.+..++++||.++|++....+...+..++.++...|..+++.+++++..++.+++.+|.|++++|...+..
T Consensus 81 ~~~hpl~~~~~i~~~dL~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~~~p~~~~~~-- 158 (198)
T cd08437 81 SKDHPLAKAKKVNFADLKKENFILLNEHFVHPKAFDSLCQQANFQPNIVYRTNDIHILKSMVRENVGIGFLTDIAVKP-- 158 (198)
T ss_pred cCCCcccccCcccHHHHcCCCeEEecccchHHHHHHHHHHHcCCCccEEEEeCcHHHHHHHHHcCCcEEEEEhhhccC--
Confidence 999999988889999999999999887766677788889999999999999999999999999999999999987743
Q ss_pred cCCceeeecCC-CCccceEEEEEeCCccccHHHHHHHHHH
Q psy3760 253 DKNLRSISASH-LFGTTISRVIIKQGTYLRSYVYSFIKLL 291 (306)
Q Consensus 253 ~~~l~~~~~~~-~~~~~~~~l~~~~~~~~~~~~~~~~~~l 291 (306)
.++++.+++++ ....++++++|+++...++.++.|++++
T Consensus 159 ~~~l~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 198 (198)
T cd08437 159 DDHLVAIPLLDNEQPTFYISLAHRKDQLLTPAQKKLLDLL 198 (198)
T ss_pred CCCeEEEEccCCcccCeEEEEEEcCccCCCHHHHHHHhhC
Confidence 67788888876 4557899999999999999999998864
No 50
>cd08435 PBP2_GbpR The C-terminal substrate binding domain of galactose-binding protein regulator contains the type 2 periplasmic binding fold. Galactose-binding protein regulator (GbpR), a member of the LysR family of bacterial transcriptional regulators, regulates the expression of chromosomal virulence gene chvE. The chvE gene is involved in the uptake of specific sugars, in chemotaxis to these sugars, and in the VirA-VirG two-component signal transduction system. In the presence of an inducing sugar such as L-arabinose, D-fucose, or D-galactose, GbpR activates chvE expression, while in the absence of an inducing sugar, GbpR represses expression. The topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a ma
Probab=99.97 E-value=6.9e-29 Score=191.86 Aligned_cols=198 Identities=17% Similarity=0.256 Sum_probs=177.8
Q ss_pred cEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccC-CCCCceeeccccceEEEEe
Q psy3760 94 NLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILS-PSDKLISIPCYQWEYVIIV 172 (306)
Q Consensus 94 ~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~-~~~~~~~~~l~~~~~~~v~ 172 (306)
+|+||++++++..++++++..|.++||++++++...++.++.+.+.+|++|++|+..+.. ..+++...+++++++++++
T Consensus 1 ~l~Ig~~~~~~~~~l~~~l~~~~~~~P~v~i~i~~~~~~~~~~~l~~~~~Dl~i~~~~~~~~~~~~~~~~l~~~~~~~~~ 80 (201)
T cd08435 1 TVRVGAVPAAAPVLLPPAIARLLARHPRLTVRVVEGTSDELLEGLRAGELDLAIGRLADDEQPPDLASEELADEPLVVVA 80 (201)
T ss_pred CeEEEechHHHHHHHHHHHHHHHHHCCCeEEEEEeCCHHHHHHHHHcCCccEEEEecCcccCCCCcEEEEcccCcEEEEE
Confidence 489999999999999999999999999999999999899999999999999999864422 2578999999999999999
Q ss_pred cCCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCc-eeEEEEecCHHHHHHHHHhccceeeeecceeccc
Q psy3760 173 PLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLT-PYIVLETINSDIIKTYVELRMGIGIIASIAFDSN 251 (306)
Q Consensus 173 ~~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~v~~g~gi~~~p~~~~~~~ 251 (306)
+++||++.+..++++||.++|++.+..+...+..+.++++..+.. +++.+++++..++.+++.+|.|++++|.+++...
T Consensus 81 ~~~~~l~~~~~~~~~dL~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~~~p~~~~~~~ 160 (201)
T cd08435 81 RPGHPLARRARLTLADLADYPWVLPPPGTPLRQRLEQLFAAAGLPLPRNVVETASISALLALLARSDMLAVLPRSVAEDE 160 (201)
T ss_pred eCCCcCcccCCcCHHHHhcCCEEecCCCCcHHHHHHHHHHHcCCCCCCceEEEccHHHHHHHHhcCCeEEEeEHHHhhhh
Confidence 999999988889999999999999988777777888999999986 6788999999999999999999999999988765
Q ss_pred -ccCCceeeecCCCCccceEEEEEeCCccccHHHHHHHHHH
Q psy3760 252 -RDKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLL 291 (306)
Q Consensus 252 -~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l 291 (306)
..++++.+++++......++++|++++..++.+++|++++
T Consensus 161 ~~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l 201 (201)
T cd08435 161 LRAGVLRELPLPLPTSRRPIGITTRRGGPLSPAARALLDAL 201 (201)
T ss_pred hccCceEEecccCCCCcccEEEEEcCCCCCCHHHHHHHHhC
Confidence 6778998888765567799999999998999999999874
No 51
>cd08438 PBP2_CidR The C-terminal substrate binding domain of LysR-like transcriptional regulator CidR, contains the type 2 periplasmic binding fold. This CD includes the substrate binding domain of CidR which positively up-regulates the expression of cidABC operon in the presence of acetic acid produced by the metabolism of excess glucose. The CidR affects the control of murein hydrolase activity by enhancing cidABC expression in the presence of acetic acid. Thus, up-regulation of cidABC expression results in increased murein hydrolase activity. This substrate binding domain has significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate
Probab=99.97 E-value=6.9e-29 Score=191.23 Aligned_cols=197 Identities=18% Similarity=0.307 Sum_probs=178.1
Q ss_pred cEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccCCCCCceeeccccceEEEEec
Q psy3760 94 NLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLISIPCYQWEYVIIVP 173 (306)
Q Consensus 94 ~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~~~~~~~~~l~~~~~~~v~~ 173 (306)
+++||++.+++..++++++..|.++||++++++...++.++.+.|.+|++|++|+..+ ...+++.+.++++++++++++
T Consensus 1 ~l~Ig~~~~~~~~~l~~~l~~~~~~~p~v~i~i~~~~~~~~~~~L~~~~~Dl~i~~~~-~~~~~~~~~~l~~~~~~~v~~ 79 (197)
T cd08438 1 HLRLGLPPLGGSLLFAPLLAAFRQRYPNIELELVEYGGKKVEQAVLNGELDVGITVLP-VDEEEFDSQPLCNEPLVAVLP 79 (197)
T ss_pred CeEEEecchhhhhhcHHHHHHHHHHCcCeEEEEEEcCcHHHHHHHHcCCCCEEEEecc-cccCCceeEEeccccEEEEec
Confidence 4899999999999999999999999999999999999999999999999999999654 456789999999999999999
Q ss_pred CCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCceeEEEEecCHHHHHHHHHhccceeeeecceeccccc
Q psy3760 174 LDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMGIGIIASIAFDSNRD 253 (306)
Q Consensus 174 ~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~~~p~~~~~~~~~ 253 (306)
++||++.+..++++||.++|++.+..+...+..+.+++...+..++..+++++...+++++.+|.|++++|.+.+.....
T Consensus 80 ~~~~l~~~~~~~~~~l~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gia~~p~~~~~~~~~ 159 (197)
T cd08438 80 RGHPLAGRKTVSLADLADEPFILFNEDFALHDRIIDACQQAGFTPNIAARSSQWDFIAELVAAGLGVALLPRSIAQRLDN 159 (197)
T ss_pred CCCChhhccccCHHHHcCCCeEEECCCccHHHHHHHHHHHcCCCCCEEEeeCCHHHHHHHHHcCCceEEechhhHhhhcc
Confidence 99999988889999999999999987776677788889999999999999999999999999999999999988764456
Q ss_pred CCceeeecCCCCccceEEEEEeCCccccHHHHHHHHHH
Q psy3760 254 KNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLL 291 (306)
Q Consensus 254 ~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l 291 (306)
++++.+++.+......++++|+++...++.++.|++++
T Consensus 160 ~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~ 197 (197)
T cd08438 160 AGVKVIPLTDPDLRWQLALIWRKGRYLSHAARAWLALL 197 (197)
T ss_pred CCeEEEEcCCCCceEEEEEEEeCCCcCCHHHHHHHhhC
Confidence 67999998765566799999999988899999998864
No 52
>cd08443 PBP2_CysB The C-terminal substrate domain of LysR-type transcriptional regulator CysB contains type 2 periplasmic binding fold. CysB is a transcriptional activator of genes involved in sulfate and thiosulfate transport, sulfate reduction, and cysteine synthesis. In Escherichia coli, the regulation of transcription in response to sulfur source is attributed to two transcriptional regulators, CysB and Cbl. CysB, in association with Cbl, downregulates the expression of ssuEADCB operon which is required for the utilization of sulfur from aliphatic sulfonates, in the presence of cysteine. Also, Cbl and CysB together directly function as transcriptional activators of tauABCD genes, which are required for utilization of taurine as sulfur source for growth. Like many other members of the LTTR family, CysB is composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding speci
Probab=99.97 E-value=8.6e-29 Score=191.27 Aligned_cols=197 Identities=46% Similarity=0.840 Sum_probs=178.0
Q ss_pred cEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccCCCCCceeeccccceEEEEec
Q psy3760 94 NLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLISIPCYQWEYVIIVP 173 (306)
Q Consensus 94 ~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~~~~~~~~~l~~~~~~~v~~ 173 (306)
.|+||++++++..++++++..|.+.||++++++...++.++.+.+.+|++|++|........+++...++++++++++++
T Consensus 1 ~l~Ig~~~~~~~~~l~~~l~~f~~~~P~~~i~i~~~~~~~~~~~l~~g~~Dl~i~~~~~~~~~~~~~~~l~~~~~~~v~~ 80 (198)
T cd08443 1 SLYVATTHTQARYVLPPVIKGFIERYPRVSLQMHQGSPTQIAEMVSKGLVDFAIATEALHDYDDLITLPCYHWNRCVVVK 80 (198)
T ss_pred CEEEeeccceeeeECcHHHHHHHHHCCCeEEEEEeCCHHHHHHHHHCCCccEEEEeccccccCCceEeeeeeceEEEEEc
Confidence 48999999999999999999999999999999999999999999999999999986442345789999999999999999
Q ss_pred CCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCceeEEEEecCHHHHHHHHHhccceeeeecceeccccc
Q psy3760 174 LDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMGIGIIASIAFDSNRD 253 (306)
Q Consensus 174 ~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~~~p~~~~~~~~~ 253 (306)
++||++.+.+++++||.++|++.++.+...+..++.++...++.++..+++++..++.+++.+|.|++++|.+.......
T Consensus 81 ~~hpl~~~~~i~~~~l~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~Gia~~p~~~~~~~~~ 160 (198)
T cd08443 81 RDHPLADKQSISIEELATYPIVTYTFGFTGRSELDTAFNRAGLTPNIVLTATDADVIKTYVRLGLGVGVIASMAYDPVDD 160 (198)
T ss_pred CCCccccCCCCCHHHHhcCCEEEecCCccHHHHHHHHHHHcCCCceEEEEECCHHHHHHHHHcCCcEEEeecccccccCC
Confidence 99999988889999999999999987766677788899999999999999999999999999999999999987755456
Q ss_pred CCceeeecCCCCccceEEEEEeCCccccHHHHHHHHH
Q psy3760 254 KNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKL 290 (306)
Q Consensus 254 ~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~ 290 (306)
++++.+++.+......++++|+++...++.+++|++.
T Consensus 161 ~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 197 (198)
T cd08443 161 PDLVIRDARDLFPWSVTKIAFRRGTFLRSYMYDFIQR 197 (198)
T ss_pred CCEEEEEcccccCceeeeeEEEcCCcCCHHHHHHHhh
Confidence 6899999987666778999999999999999999874
No 53
>cd08417 PBP2_Nitroaromatics_like The C-terminal substrate binding domain of LysR-type transcriptional regulators that involved in the catabolism of nitroaromatic/naphthalene compounds and that of related regulators; contains the type 2 periplasmic binding fold. This CD includes the C-terminal substrate binding domain of LysR-type transcriptional regulators involved in the catabolism of dinitrotoluene and similar compounds, such as DntR, NahR, and LinR. The transcription of the genes encoding enzymes involved in such degradation is regulated and expression of these enzymes is enhanced by inducers, which are either an intermediate in the metabolic pathway or compounds to be degraded. Also included are related LysR-type regulators clustered together in phylogenetic trees, including NodD, ToxR, LeuO, SyrM, TdcA, and PnbR. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrate
Probab=99.97 E-value=4.3e-29 Score=193.02 Aligned_cols=198 Identities=15% Similarity=0.145 Sum_probs=179.6
Q ss_pred cEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccCCCCCceeeccccceEEEEec
Q psy3760 94 NLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLISIPCYQWEYVIIVP 173 (306)
Q Consensus 94 ~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~~~~~~~~~l~~~~~~~v~~ 173 (306)
+|+||++++++..++++++..|.++||++++++....+.++.+.|.+|++|++|+..+ ...+++...++++++++++++
T Consensus 1 ~l~Ig~~~~~~~~~~~~~i~~~~~~~P~i~l~~~~~~~~~~~~~l~~g~~D~~i~~~~-~~~~~~~~~~l~~~~~~~v~~ 79 (200)
T cd08417 1 TFRIAASDYLEALLLPPLLARLRQEAPGVRLRFVPLDRDDLEEALESGEIDLAIGVFP-ELPPGLRSQPLFEDRFVCVAR 79 (200)
T ss_pred CeEEeccHHHHHHHHHHHHHHHHhhCCCeEEEeccCCHHHHHHHHHcCCCCEEEeecc-cCCCccchhhhhcCceEEEec
Confidence 4899999999999999999999999999999999999999999999999999999755 456789999999999999999
Q ss_pred CCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCceeEEEEecCHHHHHHHHHhccceeeeecceeccc-c
Q psy3760 174 LDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMGIGIIASIAFDSN-R 252 (306)
Q Consensus 174 ~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~~~p~~~~~~~-~ 252 (306)
++||++. ..++++||.++|++.+..+...++.+..++...++.+++.+++++..++++++..|.|++++|...+... .
T Consensus 80 ~~~~~~~-~~~~~~~L~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~~lp~~~~~~~~~ 158 (200)
T cd08417 80 KDHPLAG-GPLTLEDYLAAPHVLVSPRGRGHGLVDDALAELGLSRRVALTVPHFLAAPALVAGTDLIATVPRRLAEALAE 158 (200)
T ss_pred CCCcccc-cccCHHHHhCCCeEEeccccchHHHHHHHHHHcCcccceEEeeCcHHHHHHHHhcCCeeeeccHHHHHhhcc
Confidence 9999987 7799999999999998877667788899999999999999999999999999999999999999887665 4
Q ss_pred cCCceeeecCCCCccceEEEEEeCCccccHHHHHHHHHHhH
Q psy3760 253 DKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLLSP 293 (306)
Q Consensus 253 ~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~ 293 (306)
.++++.++++...+...++++|++++..++.+++|++.+++
T Consensus 159 ~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 199 (200)
T cd08417 159 RLGLRVLPLPFELPPFTVSLYWHPRRDRDPAHRWLRELIAE 199 (200)
T ss_pred cCCcEEecCCCCCCcceeEEEeccccccChHHHHHHHHHhh
Confidence 67888888876555689999999999899999999998875
No 54
>cd08440 PBP2_LTTR_like_4 TThe C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator, contains the type 2 periplasmic binding fold. LysR-transcriptional regulators comprise the largest family of prokaryotic transcription factor. Homologs of some of LTTRs with similar domain organizations are also found in the archaea and eukaryotic organisms. The LTTRs are composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcriptional repressor undergoes a conformational change upon substrate binding which in turn changes the DNA binding affinity of the repressor. The genes controlled by the LTTRs have diverse funct
Probab=99.97 E-value=1.5e-28 Score=189.20 Aligned_cols=197 Identities=22% Similarity=0.342 Sum_probs=177.0
Q ss_pred cEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccCCCCCceeeccccceEEEEec
Q psy3760 94 NLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLISIPCYQWEYVIIVP 173 (306)
Q Consensus 94 ~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~~~~~~~~~l~~~~~~~v~~ 173 (306)
+|+||+++++...++++++..|.++||++++++....+.++.+.|.+|++|++|+..+ ...+++...++++++++++++
T Consensus 1 ~l~Ig~~~~~~~~~l~~~l~~~~~~~p~v~i~i~~~~~~~~~~~l~~g~~D~~i~~~~-~~~~~~~~~~l~~~~~~~~~~ 79 (197)
T cd08440 1 RVRVAALPSLAATLLPPVLAAFRRRHPGIRVRLRDVSAEQVIEAVRSGEVDFGIGSEP-EADPDLEFEPLLRDPFVLVCP 79 (197)
T ss_pred CeEEEeccchhhhHHHHHHHHHHHhCCCcEEEEEeCChHHHHHHHHcCCccEEEEeCC-CCCCCeeEEEeecccEEEEec
Confidence 4899999999999999999999999999999999988889999999999999999654 456789999999999999999
Q ss_pred CCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCceeEEEEecCHHHHHHHHHhccceeeeecceeccccc
Q psy3760 174 LDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMGIGIIASIAFDSNRD 253 (306)
Q Consensus 174 ~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~~~p~~~~~~~~~ 253 (306)
++||++.++.++++||.++|++.+..+...+..+.+++...++.++..+.+++..++.+++.+|.|++++|.+.+.....
T Consensus 80 ~~~pl~~~~~~~~~~l~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~~~p~~~~~~~~~ 159 (197)
T cd08440 80 KDHPLARRRSVTWAELAGYPLIALGRGSGVRALIDRALAAAGLTLRPAYEVSHMSTALGMVAAGLGVAVLPALALPLADH 159 (197)
T ss_pred CCCCcccCCccCHHHHccCCEEecCCCccHHHHHHHHHHHcCCCcceEEEeccHHHHHHHHHcCCeEEEcchhHHHHhhc
Confidence 99999887789999999999999887766777788899999999999999999999999999999999999987653356
Q ss_pred CCceeeecCCCCccceEEEEEeCCccccHHHHHHHHHH
Q psy3760 254 KNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLL 291 (306)
Q Consensus 254 ~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l 291 (306)
++++.++++.......++++|+++...++.+++|++++
T Consensus 160 ~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l 197 (197)
T cd08440 160 PGLVARPLTEPVVTRTVGLIRRRGRSLSPAAQAFLDLL 197 (197)
T ss_pred CceEEEEcCCCccceEEEEEEcCCCcCCHHHHHHHHhC
Confidence 77898988765567799999999998999999999864
No 55
>cd08426 PBP2_LTTR_like_5 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator, contains the type 2 periplasmic binding fold. LysR-transcriptional regulators comprise the largest family of prokaryotic transcription factor. Homologs of some of LTTRs with similar domain organizations are also found in the archaea and eukaryotic organisms. The LTTRs are composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcriptional repressor undergoes a conformational change upon substrate binding which in turn changes the DNA binding affinity of the repressor. The genes controlled by the LTTRs have diverse functi
Probab=99.97 E-value=1.9e-28 Score=189.27 Aligned_cols=197 Identities=23% Similarity=0.308 Sum_probs=177.5
Q ss_pred cEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccCCCCCceeeccccceEEEEec
Q psy3760 94 NLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLISIPCYQWEYVIIVP 173 (306)
Q Consensus 94 ~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~~~~~~~~~l~~~~~~~v~~ 173 (306)
+++||++++++..++++++..|.++||++++++...++.++.+.+.+|++|++|+..+ ...+++...++++++++++++
T Consensus 1 ~l~I~~~~~~~~~~l~~~l~~~~~~~P~i~l~i~~~~~~~~~~~l~~~~~D~~i~~~~-~~~~~~~~~~l~~~~~~~v~~ 79 (199)
T cd08426 1 RVRVATGEGLAAELLPSLIARFRQRYPGVFFTVDVASTADVLEAVLSGEADIGLAFSP-PPEPGIRVHSRQPAPIGAVVP 79 (199)
T ss_pred CeEEEecHHHHHHHHHHHHHHHHHhCCCeEEEEEeCCcHHHHHHHHCCCccEEEecCC-CCCCCeEEEeeccCcEEEEec
Confidence 4899999999999999999999999999999999998899999999999999998644 455789999999999999999
Q ss_pred CCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCceeEEEEecCHHHHHHHHHhccceeeeecceeccc-c
Q psy3760 174 LDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMGIGIIASIAFDSN-R 252 (306)
Q Consensus 174 ~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~~~p~~~~~~~-~ 252 (306)
++||++..+.++++||.++|++.+..+...+..+..++...+..+++.+++++...+.+++.+|.|++++|.+.+... .
T Consensus 80 ~~hpl~~~~~~~~~~l~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~~~p~~~~~~~~~ 159 (199)
T cd08426 80 PGHPLARQPSVTLAQLAGYPLALPPPSFSLRQILDAAFARAGVQLEPVLISNSIETLKQLVAAGGGISLLTELAVRREIR 159 (199)
T ss_pred CCCCcccCCccCHHHHhCCCeEecCCcchHHHHHHHHHHHcCCCcceEEecCCHHHHHHHHHcCCCEEEEchHhhhHhhh
Confidence 999998888899999999999998877667777888999999999999999999999999999999999999887655 6
Q ss_pred cCCceeeecCCCC-ccceEEEEEeCCccccHHHHHHHHHH
Q psy3760 253 DKNLRSISASHLF-GTTISRVIIKQGTYLRSYVYSFIKLL 291 (306)
Q Consensus 253 ~~~l~~~~~~~~~-~~~~~~l~~~~~~~~~~~~~~~~~~l 291 (306)
.++++.+++++.. ...+++++|+++...++.++.|++++
T Consensus 160 ~~~l~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l 199 (199)
T cd08426 160 RGQLVAVPLADPHMNHRQLELQTRAGRQLPAAASAFLQLL 199 (199)
T ss_pred cCcEEEEEcCCcccCceEEEEEEcCCCCCCHHHHHHHHhC
Confidence 7789999888643 34689999999999999999999864
No 56
>cd08412 PBP2_PAO1_like The C-terminal substrate-binding domain of putative LysR-type transcriptional regulator PAO1-like, a member of the type 2 periplasmic binding fold protein superfamily. This family includes the C-terminal substrate domain of a putative LysR-type transcriptional regulator from the plant pathogen Pseudomonas aeruginosa PAO1and its closely related homologs. The LysR-type transcriptional regulators (LTTRs) are composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcriptional repressor undergoes a conformational change upon substrate binding which in turn changes the DNA binding affinity of the repressor. The genes controll
Probab=99.97 E-value=2.9e-28 Score=187.98 Aligned_cols=196 Identities=22% Similarity=0.375 Sum_probs=175.6
Q ss_pred cEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccCCCCCceeeccccceEEEEec
Q psy3760 94 NLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLISIPCYQWEYVIIVP 173 (306)
Q Consensus 94 ~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~~~~~~~~~l~~~~~~~v~~ 173 (306)
+++||++++++..++++++..|.++||++++++...++.++.+.|.+|++|++|+..+ ...+++...++++++++++++
T Consensus 1 ~l~I~~~~~~~~~~l~~~l~~~~~~~P~i~l~i~~~~~~~~~~~l~~~~~D~~i~~~~-~~~~~~~~~~l~~~~~~~~~~ 79 (198)
T cd08412 1 TLRIGCFSTLAPYYLPGLLRRFREAYPGVEVRVVEGNQEELEEGLRSGELDLALTYDL-DLPEDIAFEPLARLPPYVWLP 79 (198)
T ss_pred CEEEecccccchhhhHHHHHHHHHHCCCcEEEEEECCHHHHHHHHHcCCCcEEEEcCC-CCCcccceeeeeccceEEEec
Confidence 4899999999999999999999999999999999999999999999999999999654 456889999999999999999
Q ss_pred CCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCceeEEEEecCHHHHHHHHHhccceeeeecceecc-c-
Q psy3760 174 LDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMGIGIIASIAFDS-N- 251 (306)
Q Consensus 174 ~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~~~p~~~~~~-~- 251 (306)
++||++.++.++++||.++|++....+. .+..+.+++...++.+++.+++++..++.+++.+|.|++++|.+.+.. .
T Consensus 80 ~~~~l~~~~~~~~~~l~~~~~i~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~~~p~~~~~~~~~ 158 (198)
T cd08412 80 ADHPLAGKDEVSLADLAAEPLILLDLPH-SREYFLSLFAAAGLTPRIAYRTSSFEAVRSLVANGLGYSLLNDRPYRPWSY 158 (198)
T ss_pred CCCCCCCCCcCCHHHHcCCcEEecCchh-HHHHHHHHHHHcCCCccEEEEeCcHHHHHHHHHcCCCEEEeeccccccccc
Confidence 9999988778999999999999986643 455677889999999999999999999999999999999999988875 3
Q ss_pred ccCCceeeecCCCCccceEEEEEeCCccccHHHHHHHHHH
Q psy3760 252 RDKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLL 291 (306)
Q Consensus 252 ~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l 291 (306)
..+.++.+|++.......++++|++++..+|.+++|++++
T Consensus 159 ~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 198 (198)
T cd08412 159 DGKRLVRRPLADPVPPLRLGLAWRRGARLTRAARAFVDFA 198 (198)
T ss_pred CCCceEEeecCCccccEEEEEEEecCCCCCHHHHHHHhhC
Confidence 5678999998765566799999999999999999999864
No 57
>cd08425 PBP2_CynR The C-terminal substrate-binding domain of the LysR-type transcriptional regulator CynR, contains the type 2 periplasmic binding fold. CynR is a LysR-like transcriptional regulator of the cyn operon, which encodes genes that allow cyanate to be used as a sole source of nitrogen. The operon includes three genes in the following order: cynT (cyanate permease), cynS (cyanase), and cynX (a protein of unknown function). CynR negatively regulates its own expression independently of cyanate. CynR binds to DNA and induces bending of DNA in the presence or absence of cyanate, but the amount of bending is decreased by cyanate. The CynR of LysR-type transcriptional regulator family is composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding
Probab=99.97 E-value=2.4e-28 Score=188.43 Aligned_cols=195 Identities=21% Similarity=0.338 Sum_probs=175.7
Q ss_pred CcEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccCCCCCceeeccccceEEEEe
Q psy3760 93 GNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLISIPCYQWEYVIIV 172 (306)
Q Consensus 93 ~~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~~~~~~~~~l~~~~~~~v~ 172 (306)
|.++||+++++...++++++..|.++||++++++......++.+.|.+|++|++|+..+ ...+++...+++++++++++
T Consensus 1 g~l~Ig~~~~~~~~~l~~~l~~~~~~~P~v~i~i~~~~~~~~~~~l~~g~~Dl~i~~~~-~~~~~~~~~~l~~~~~~~v~ 79 (197)
T cd08425 1 GSLRLAMTPTFTAYLIGPLIDRFHARYPGIALSLREMPQERIEAALADDRLDLGIAFAP-VRSPDIDAQPLFDERLALVV 79 (197)
T ss_pred CeEEEEechhhhhhhhHHHHHHHHHHCCCcEEEEEECcHHHHHHHHHcCCccEEEEecC-CCCCCcEEEEeccccEEEEe
Confidence 57999999999999999999999999999999999988889999999999999998654 55678999999999999999
Q ss_pred cCCCCCCCCC-CcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCceeEEEEecCHHHHHHHHHhccceeeeecceeccc
Q psy3760 173 PLDHPLLLLN-SISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMGIGIIASIAFDSN 251 (306)
Q Consensus 173 ~~~~~l~~~~-~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~~~p~~~~~~~ 251 (306)
+++||++... .++++||.++|++.+......+..+..++...+..+++.+++++..++.+++.+|.|++++|...+..
T Consensus 80 ~~~~pl~~~~~~~~~~dL~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~~~p~~~~~~- 158 (197)
T cd08425 80 GATHPLAQRRTALTLDDLAAEPLALLSPDFATRQHIDRYFQKQGIKPRIAIEANSISAVLEVVRRGRLATILPDAIARE- 158 (197)
T ss_pred cCCCchhHhcccCCHHHHhcCCcEecCCCccHHHHHHHHHHHcCCCeeeEEeeCcHHHHHHHHhcCCcEEeechhhhcc-
Confidence 9999998765 49999999999999887766777788999999999999999999999999999999999999988754
Q ss_pred ccCCceeeecCCCCccceEEEEEeCCccccHHHHHHHHH
Q psy3760 252 RDKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKL 290 (306)
Q Consensus 252 ~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~ 290 (306)
.++++.+++........++++|++++..++.++.|+++
T Consensus 159 -~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 196 (197)
T cd08425 159 -QPGLCAVALEPPLPGRTAALLRRKGAYRSAAARAFAAL 196 (197)
T ss_pred -cCCeEEEECCCCCcCceEEEEEcCCcccCHHHHHHHhh
Confidence 46788888876555678999999999899999999875
No 58
>cd08434 PBP2_GltC_like The substrate binding domain of LysR-type transcriptional regulator GltC, which activates gltA expression of glutamate synthase operon, contains type 2 periplasmic binding fold. GltC, a member of the LysR family of bacterial transcriptional factors, activates the expression of gltA gene of glutamate synthase operon and is essential for cell growth in the absence of glutamate. Glutamate synthase is a heterodimeric protein that encoded by gltA and gltB, whose expression is subject to nutritional regulation. GltC also negatively auto-regulates its own expression. This substrate-binding domain has strong homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity,
Probab=99.97 E-value=3.2e-28 Score=187.12 Aligned_cols=195 Identities=21% Similarity=0.387 Sum_probs=175.6
Q ss_pred cEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccCCCCCceeeccccceEEEEec
Q psy3760 94 NLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLISIPCYQWEYVIIVP 173 (306)
Q Consensus 94 ~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~~~~~~~~~l~~~~~~~v~~ 173 (306)
+++||++++++..++++++..|.++||++++++....+.++.+.+.+|++|++|+..+ ...+++...++++++++++++
T Consensus 1 ~l~Ig~~~~~~~~~l~~~l~~~~~~~P~i~i~i~~~~~~~~~~~l~~~~~Dl~i~~~~-~~~~~l~~~~l~~~~~~~v~~ 79 (195)
T cd08434 1 TVRLGFLHSLGTSLVPDLIRAFRKEYPNVTFELHQGSTDELLDDLKNGELDLALCSPV-PDEPDIEWIPLFTEELVLVVP 79 (195)
T ss_pred CeEEEecchhhhhhhHHHHHHHHHhCCCeEEEEecCcHHHHHHHHHcCCccEEEEccC-CCCCCeeEEEeecceEEEEec
Confidence 4899999999999999999999999999999999999999999999999999999654 456789999999999999999
Q ss_pred CCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCceeEEEEecCHHHHHHHHHhccceeeeecceeccccc
Q psy3760 174 LDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMGIGIIASIAFDSNRD 253 (306)
Q Consensus 174 ~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~~~p~~~~~~~~~ 253 (306)
++||++.+.+++++||.++|++....+...+..+.+++...+..++..+++++..++.+++.+|.|++++|.+.+. ..
T Consensus 80 ~~~~l~~~~~~~~~~l~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~~~p~~~~~--~~ 157 (195)
T cd08434 80 KDHPLAGRDSVDLAELADEPFVLLSPGFGLRPIVDELCAAAGFTPKIAFEGEEDSTIAGLVAAGLGVAILPEMTLL--NP 157 (195)
T ss_pred CCCccccCCccCHHHhcCCceEEecCCccHHHHHHHHHHHcCCccceEEEEccHHHHHHHHHcCCceEEecchhhh--CC
Confidence 9999988888999999999999987766666677888888898888889999999999999999999999998872 35
Q ss_pred CCceeeecCCCCccceEEEEEeCCccccHHHHHHHHHH
Q psy3760 254 KNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLL 291 (306)
Q Consensus 254 ~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l 291 (306)
++++.++++.......++++|+++...++.+++|++++
T Consensus 158 ~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l 195 (195)
T cd08434 158 PGVKKIPIKDPDAERTIGLAWLKDRYLSPAARRFKDFV 195 (195)
T ss_pred CceEEEECCCCCccEEEEEEEcCCcccCHHHHHHHHhC
Confidence 67888998865566789999999999999999999874
No 59
>cd08436 PBP2_LTTR_like_3 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator, contains the type 2 periplasmic binding fold. LysR-transcriptional regulators comprise the largest family of prokaryotic transcription factor. Homologs of some of LTTRs with similar domain organizations are also found in the archaea and eukaryotic organisms. The LTTRs are composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcriptional repressor undergoes a conformational change upon substrate binding which in turn changes the DNA binding affinity of the repressor. The genes controlled by the LTTRs have diverse functi
Probab=99.97 E-value=3.7e-28 Score=186.73 Aligned_cols=194 Identities=20% Similarity=0.294 Sum_probs=175.7
Q ss_pred cEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccCCCCCceeeccccceEEEEec
Q psy3760 94 NLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLISIPCYQWEYVIIVP 173 (306)
Q Consensus 94 ~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~~~~~~~~~l~~~~~~~v~~ 173 (306)
+++||++++++..++++++..|.++||++++++....+.++.+.+.+|++|++|+..+....+++...++++++++++++
T Consensus 1 ~l~Ig~~~~~~~~~l~~~l~~~~~~~P~v~i~i~~~~~~~~~~~l~~~~~Dl~i~~~~~~~~~~~~~~~l~~~~~~~~~~ 80 (194)
T cd08436 1 RLAIGTITSLAAVDLPELLARFHRRHPGVDIRLRQAGSDDLLAAVREGRLDLAFVGLPERRPPGLASRELAREPLVAVVA 80 (194)
T ss_pred CEEEEeehHHHHHHHHHHHHHHHHHCCCcEEEEecCCHHHHHHHHHcCCccEEEEecCCCCCCCcEEEEeecceEEEEec
Confidence 48999999999999999999999999999999999988899999999999999986553256889999999999999999
Q ss_pred CCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCceeEEEEecCHHHHHHHHHhccceeeeecceeccccc
Q psy3760 174 LDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMGIGIIASIAFDSNRD 253 (306)
Q Consensus 174 ~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~~~p~~~~~~~~~ 253 (306)
++||++.+..++++||.++|++.+..+...+..+..++...+..++..+++++...+.+++.+|.|++++|.+.+. ..
T Consensus 81 ~~~~l~~~~~~~~~~L~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~~~p~~~~~--~~ 158 (194)
T cd08436 81 PDHPLAGRRRVALADLADEPFVDFPPGTGARRQVDRAFAAAGVRRRVAFEVSDVDLLLDLVARGLGVALLPASVAA--RL 158 (194)
T ss_pred CCCcccCCCccCHHHHhCCCeEEecCcccHHHHHHHHHHHcCCCCceEEEeccHHHHHHHHHcCCceEEecchhhc--CC
Confidence 9999988878999999999999988776667788889998998888999999999999999999999999998874 36
Q ss_pred CCceeeecCCCCccceEEEEEeCCccccHHHHHHHHHH
Q psy3760 254 KNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLL 291 (306)
Q Consensus 254 ~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l 291 (306)
++++.++++ .....+++++|+++.. ++.++.|++++
T Consensus 159 ~~l~~~~~~-~~~~~~~~l~~~~~~~-~~~~~~~~~~~ 194 (194)
T cd08436 159 PGLAALPLE-PAPRRRLYLAWSAPPP-SPAARAFLELL 194 (194)
T ss_pred CCeEEEecC-CcceEEEEEEEeCCCC-CHHHHHHHhhC
Confidence 789988887 4667899999999999 99999999864
No 60
>cd08415 PBP2_LysR_opines_like The C-terminal substrate-domain of LysR-type transcriptional regulators involved in the catabolism of opines and that of related regulators, contains the type 2 periplasmic binding fold. This CD includes the C-terminal substrate-domain of LysR-type transcriptional regulators, OccR and NocR, involved in the catabolism of opines and that of LysR for lysine biosynthesis which clustered together in phylogenetic trees. Opines, such as octopine and nopaline, are low molecular weight compounds found in plant crown gall tumors that are produced by the parasitic bacterium Agrobacterium. There are at least 30 different opines identified so far. Opines are utilized by tumor-colonizing bacteria as a source of carbon, nitrogen, and energy. NocR and OccR belong to the family of LysR-type transcriptional regulators that positively regulates the catabolism of nopaline and octopine, respectively. Both nopaline and octopalin are arginine derivatives. In Agrobacterium tumefa
Probab=99.97 E-value=2.9e-28 Score=187.63 Aligned_cols=196 Identities=23% Similarity=0.279 Sum_probs=176.6
Q ss_pred cEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccCCCCCceeeccccceEEEEec
Q psy3760 94 NLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLISIPCYQWEYVIIVP 173 (306)
Q Consensus 94 ~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~~~~~~~~~l~~~~~~~v~~ 173 (306)
+|+||++++++..++++++..|.+.||++++++....+.++.+.|.+|++|++|+..+ ...+++.+.++++++++++++
T Consensus 1 ~l~Ig~~~~~~~~~l~~~l~~~~~~~P~i~l~i~~~~~~~~~~~l~~~~~Dl~i~~~~-~~~~~~~~~~l~~~~~~~v~~ 79 (196)
T cd08415 1 TLRIAALPALALSLLPRAIARFRARHPDVRISLHTLSSSTVVEAVLSGQADLGLASLP-LDHPGLESEPLASGRAVCVLP 79 (196)
T ss_pred CeEEEecccccccccHHHHHHHHHHCCCcEEEEEecchHHHHHHHHcCCccEEEEeCC-CCCCcceeeeecccceEEEEc
Confidence 4899999999999999999999999999999999999999999999999999999654 446789999999999999999
Q ss_pred CCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCceeEEEEecCHHHHHHHHHhccceeeeecceeccccc
Q psy3760 174 LDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMGIGIIASIAFDSNRD 253 (306)
Q Consensus 174 ~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~~~p~~~~~~~~~ 253 (306)
++||++..+.++++||.++|++....+...+..+.+++...+..++..+++++...+.+++.+|.|++++|.+++.....
T Consensus 80 ~~~~l~~~~~~~~~~l~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~~lp~~~~~~~~~ 159 (196)
T cd08415 80 PGHPLARKDVVTPADLAGEPLISLGRGDPLRQRVDAAFERAGVEPRIVIETQLSHTACALVAAGLGVAIVDPLTAAGYAG 159 (196)
T ss_pred CCCChHhcCccCHHHhcCCcEEEeCCCccHHHHHHHHHHHcCCCceEEEEEeHHHHHHHHHHcCCCeEEechhhhhcccC
Confidence 99999888889999999999999987766677888899999999999999999999999999999999999988765445
Q ss_pred CCceeeecCCCCccceEEEEEeCCccccHHHHHHHHHH
Q psy3760 254 KNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLL 291 (306)
Q Consensus 254 ~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l 291 (306)
++++.+|+.. ....+++++|+++...+|.+++|+++|
T Consensus 160 ~~l~~~~~~~-~~~~~~~l~~~~~~~~~~~~~~~~~~l 196 (196)
T cd08415 160 AGLVVRPFRP-AIPFEFALVRPAGRPLSRLAQAFIDLL 196 (196)
T ss_pred CCeEEeecCC-CcceEEEEEEecCccCCHHHHHHHHhC
Confidence 5788888876 346789999999998999999999864
No 61
>cd08464 PBP2_DntR_like_2 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator similar to DntR, which is involved in the catabolism of dinitrotoluene; contains the type 2 periplasmic binding fold. This CD includes an uncharacterized LysR-type transcriptional regulator similar to DntR, NahR, and LinR, which are involved in the degradation of aromatic compounds. The transcription of the genes encoding enzymes involved in such degradation is regulated and expression of these enzymes is enhanced by inducers, which are either an intermediate in the metabolic pathway or compounds to be degraded. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytra
Probab=99.97 E-value=9e-29 Score=191.21 Aligned_cols=198 Identities=13% Similarity=0.077 Sum_probs=178.0
Q ss_pred cEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccCCCCCceeeccccceEEEEec
Q psy3760 94 NLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLISIPCYQWEYVIIVP 173 (306)
Q Consensus 94 ~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~~~~~~~~~l~~~~~~~v~~ 173 (306)
+++||++++++..++++++..|.++||++++++....+.++.+.|.+|++|++|+..+ ...+++...++++++++++++
T Consensus 1 ~l~Ig~~~~~~~~~l~~~l~~~~~~~P~v~l~i~~~~~~~~~~~l~~g~~D~~i~~~~-~~~~~~~~~~l~~~~~~~v~~ 79 (200)
T cd08464 1 TFRIGLSDDVESWLAPPLLAALRAEAPGVRLVFRQVDPFNVGDMLDRGEIDLAIGVFG-ELPAWLKREVLYTEGYACLFD 79 (200)
T ss_pred CEEEEechHHHHHHHHHHHHHHHHHCCCcEEEEecCCcccHHHHHhcCcccEEEecCC-CCcccceeeeecccceEEEEe
Confidence 4899999999999999999999999999999999998889999999999999999654 456889999999999999999
Q ss_pred CCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCceeEEEEecCHHHHHHHHHhccceeeeecceeccc-c
Q psy3760 174 LDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMGIGIIASIAFDSN-R 252 (306)
Q Consensus 174 ~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~~~p~~~~~~~-~ 252 (306)
++||+.. .+++++||.++|++....+...+..+.+++...|+.++..+++++..++..++.+|.|++++|.+.+... .
T Consensus 80 ~~~~~~~-~~~~~~~l~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~~~p~~~~~~~~~ 158 (200)
T cd08464 80 PQQLSLS-APLTLEDYVARPHVLVSYRGGLRGFVDDALAELGRSRRVVASTPHFAALPALLRGTPLIATVPARLARAWAA 158 (200)
T ss_pred CCCcccc-CCCCHHHHhcCCcEEecCCCCCcchHHHHHHHcCCCcceEEEcCchhhHHHHHcCCCceeecHHHHHHHhhh
Confidence 9998764 6799999999999998776666667889999999999999999999999999999999999999988765 5
Q ss_pred cCCceeeecCCCCccceEEEEEeCCccccHHHHHHHHHHhH
Q psy3760 253 DKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLLSP 293 (306)
Q Consensus 253 ~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~ 293 (306)
.++++.++++.......++++|+++...++.+++|++.+++
T Consensus 159 ~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~l~~~~~~ 199 (200)
T cd08464 159 ALGLRASPPPLDLPEFPISLLWHARTDNDPALVWLREQIVQ 199 (200)
T ss_pred cCCceeecCCCCCCCceEEEEEcccccCCchHHHHHHHHhh
Confidence 67899888876555679999999999999999999998875
No 62
>cd08463 PBP2_DntR_like_4 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator similar to DntR, which is involved in the catabolism of dinitrotoluene; contains the type 2 periplasmic binding fold. This CD includes an uncharacterized LysR-type transcriptional regulator similar to DntR, NahR, and LinR, which are involved in the degradation of aromatic compounds. The transcription of the genes encoding enzymes involved in such degradation is regulated and expression of these enzymes is enhanced by inducers, which are either an intermediate in the metabolic pathway or compounds to be degraded. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytra
Probab=99.97 E-value=2e-28 Score=189.95 Aligned_cols=199 Identities=15% Similarity=0.115 Sum_probs=178.1
Q ss_pred cEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeC-ChhHHHHHHHcCCeeEEEEccccCCCCCceeeccccceEEEEe
Q psy3760 94 NLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQG-NPKQITEMIRNDQADIAIVTEILSPSDKLISIPCYQWEYVIIV 172 (306)
Q Consensus 94 ~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~-~~~~~~~~l~~~~~Di~i~~~~~~~~~~~~~~~l~~~~~~~v~ 172 (306)
.++||+++++...++++++..|.++||++.+++... .++++.+.|.+|++|++|...+ ...+++...+++++++++++
T Consensus 1 ~~~Ig~~~~~~~~~~~~~l~~~~~~~P~~~v~~~~~~~~~~l~~~L~~g~lDl~i~~~~-~~~~~l~~~~l~~~~~~lv~ 79 (203)
T cd08463 1 TFRIAAPDYLNALFLPELVARFRREAPGARLEIHPLGPDFDYERALASGELDLVIGNWP-EPPEHLHLSPLFSDEIVCLM 79 (203)
T ss_pred CEEEEechhhHHHHhHHHHHHHHHHCCCCEEEEEeCCcchhHHHHHhcCCeeEEEeccc-cCCCCcEEeEeecCceEEEE
Confidence 489999999999999999999999999999999985 4578999999999999998544 45577999999999999999
Q ss_pred cCCCCCCCCCCcChhhhcCCCeEeecCCC-CcHHHHHHHHHhCCCceeEEEEecCHHHHHHHHHhccceeeeecceeccc
Q psy3760 173 PLDHPLLLLNSISLKEISNYPLITYDLSF-SGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMGIGIIASIAFDSN 251 (306)
Q Consensus 173 ~~~~~l~~~~~i~~~dl~~~~~i~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~~~p~~~~~~~ 251 (306)
+++||++.+..++++||.++|++.+..+. ..+..+.++++..++.+++.+++++..++.+++.+|+|++++|...+...
T Consensus 80 ~~~h~l~~~~~i~~~~l~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~v~~~~~i~~~p~~~~~~~ 159 (203)
T cd08463 80 RADHPLARRGLMTLDDYLEAPHLAPTPYSVGQRGVIDSHLARLGLKRNIVVTVPYFGLAPYMLAQSDLVFTTGRHFAEHY 159 (203)
T ss_pred eCCCCcccCCCCCHHHHhhCCcEEEEcCCCCCCchHHHHHHHcCCCceEEEEeChHHHHHHHHhCCCeeEecHHHHHHHh
Confidence 99999988888999999999999986543 45677888999999999999999999999999999999999999887665
Q ss_pred -ccCCceeeecCCCCccceEEEEEeCCccccHHHHHHHHHHhH
Q psy3760 252 -RDKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLLSP 293 (306)
Q Consensus 252 -~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~ 293 (306)
..++++.++++......+++++|++++..+|++++|++.+++
T Consensus 160 ~~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~l~~~~~~ 202 (203)
T cd08463 160 AKLLPLAVVDAPIEFPRMRYYQLWHERSHRSPEHRWLRRLVAS 202 (203)
T ss_pred hhhcCceEeCCCCCCCCeeEEEeecccccCChHHHHHHHHHhh
Confidence 567899999887666789999999999999999999999875
No 63
>cd08420 PBP2_CysL_like C-terminal substrate binding domain of LysR-type transcriptional regulator CysL, which activates the transcription of the cysJI operon encoding sulfite reductase, contains the type 2 periplasmic binding fold. CysL, also known as YwfK, is a regular of sulfur metabolism in Bacillus subtilis. Sulfur is required for the synthesis of proteins and essential cofactors in all living organism. Sulfur can be assimilated either from inorganic sources (sulfate and thiosulfate), or from organic sources (sulfate esters, sulfamates, and sulfonates). CysL activates the transcription of the cysJI operon encoding sulfite reductase, which reduces sulfite to sulfide. Both cysL mutant and cysJI mutant are unable to grow using sulfate or sulfite as the sulfur source. Like other LysR-type regulators, CysL also negatively regulates its own transcription. In Escherichia coli, three LysR-type activators are involved in the regulation of sulfur metabolism: CysB, Cbl and MetR. The topology
Probab=99.96 E-value=4.3e-28 Score=187.25 Aligned_cols=197 Identities=27% Similarity=0.414 Sum_probs=176.9
Q ss_pred cEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccCCCCCceeeccccceEEEEec
Q psy3760 94 NLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLISIPCYQWEYVIIVP 173 (306)
Q Consensus 94 ~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~~~~~~~~~l~~~~~~~v~~ 173 (306)
+|+||+++++...++++++..|.+.||++++++...++.++.+.|.+|++|++|+..+ ...+++...++++++++++++
T Consensus 1 ~l~i~~~~~~~~~~l~~~l~~~~~~~P~~~l~~~~~~~~~~~~~l~~g~~D~~i~~~~-~~~~~~~~~~l~~~~~~~v~~ 79 (201)
T cd08420 1 TLRIGASTTIGEYLLPRLLARFRKRYPEVRVSLTIGNTEEIAERVLDGEIDLGLVEGP-VDHPDLIVEPFAEDELVLVVP 79 (201)
T ss_pred CeEEeeccchhhhhhHHHHHHHHHHCCCceEEEEeCCcHHHHHHHHCCCccEEEecCC-CCCcceEEEeecCccEEEEec
Confidence 4899999999999999999999999999999999999999999999999999999654 456789999999999999999
Q ss_pred CCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCC---CceeEEEEecCHHHHHHHHHhccceeeeecceecc
Q psy3760 174 LDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQK---LTPYIVLETINSDIIKTYVELRMGIGIIASIAFDS 250 (306)
Q Consensus 174 ~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~~v~~g~gi~~~p~~~~~~ 250 (306)
++||++.+..++++||.++|++.+..+...+..+..++...+ ..+++.+++++..++.+++.+|.|++++|.+.+..
T Consensus 80 ~~~~~~~~~~i~~~~l~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~~~p~~~~~~ 159 (201)
T cd08420 80 PDHPLAGRKEVTAEELAAEPWILREPGSGTREVFERALAEAGLDGLDLNIVMELGSTEAIKEAVEAGLGISILSRLAVRK 159 (201)
T ss_pred CCCCccccCccCHHHHhcCCEEEecCCCCHHHHHHHHHHHcCcccccCceEEEECCHHHHHHHHHcCCCEEEeeHHHHHh
Confidence 999999888899999999999999887777777888888554 45678899999999999999999999999988765
Q ss_pred c-ccCCceeeecCCCCccceEEEEEeCCccccHHHHHHHHHH
Q psy3760 251 N-RDKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLL 291 (306)
Q Consensus 251 ~-~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l 291 (306)
. ..++++.+++++......++++|+++...++.+++|++++
T Consensus 160 ~~~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l 201 (201)
T cd08420 160 ELELGRLVALPVEGLRLTRPFSLIYHKDKYLSPAAEAFLEFL 201 (201)
T ss_pred hhcCCceEEEECCCCcceEEEEEEEecCCcCCHHHHHHHHhC
Confidence 5 6788999999865667799999999998999999999864
No 64
>cd08418 PBP2_TdcA The C-terminal substrate binding domain of LysR-type transcriptional regulator TdcA, which is involved in the degradation of L-serine and L-threonine, contains the type 2 periplasmic binding fold. TdcA, a member of the LysR family, activates the expression of the anaerobically-regulated tdcABCDEFG operon which is involved in the degradation of L-serine and L-threonine to acetate and propionate, respectively. The tdc operon is comprised of one regulatory gene tdcA and six structural genes, tdcB to tdcG. The expression of the tdc operon is affected by several transcription factors including the cAMP receptor protein (CRP), integration host factor (IHF), histone-like protein (HU), and the operon specific regulators TdcA and TcdR. TcdR is divergently transcribed from the operon and encodes a small protein that is required for efficient expression of the Escherichia coli tdc operon. This substrate-binding domain shows significant homology to the type 2 periplasmic binding
Probab=99.96 E-value=3.5e-28 Score=188.01 Aligned_cols=199 Identities=20% Similarity=0.237 Sum_probs=177.6
Q ss_pred cEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccC-CCCCceeeccccceEEEEe
Q psy3760 94 NLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILS-PSDKLISIPCYQWEYVIIV 172 (306)
Q Consensus 94 ~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~-~~~~~~~~~l~~~~~~~v~ 172 (306)
+++||++++++..++++++..|.++||++++++....+.++.+.|.+|++|++|+..+.. ..+++.+.+++++++++++
T Consensus 1 ~l~Ig~~~~~~~~~l~~~l~~~~~~~P~i~l~i~~~~~~~~~~~l~~g~~Dl~i~~~~~~~~~~~~~~~~l~~~~~~~v~ 80 (201)
T cd08418 1 KVSIGVSSLIAHTLMPAVINRFKEQFPDVQISIYEGQLSSLLPELRDGRLDFAIGTLPDEMYLKELISEPLFESDFVVVA 80 (201)
T ss_pred CEEEEechHHHHhhhHHHHHHHHHHCCCceEEEEeCcHHHHHHHHHcCCCcEEEEecCCCCCCcceeEEeecCCceEEEe
Confidence 489999999999999999999999999999999999999999999999999999864422 2468999999999999999
Q ss_pred cCCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCceeEEEEecCHHHHHHHHHhccceeeeecceeccc-
Q psy3760 173 PLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMGIGIIASIAFDSN- 251 (306)
Q Consensus 173 ~~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~~~p~~~~~~~- 251 (306)
+++||+.. ..+++||.++|++....+...+..+.+++...+..+++.+++++...+.+++.+|.|++++|..++...
T Consensus 81 ~~~~~~~~--~~~~~~l~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~~~p~~~~~~~~ 158 (201)
T cd08418 81 RKDHPLQG--ARSLEELLDASWVLPGTRMGYYNNLLEALRRLGYNPRVAVRTDSIVSIINLVEKADFLTILSRDMGRGPL 158 (201)
T ss_pred CCCCcccc--CCCHHHHcCCCCEecCCCCCHHHHHHHHHHHcCCCCCceEEecCHHHHHHHHHhCCEEEEeEHHHhhhhh
Confidence 99999875 359999999999998776666777888999999999999999999999999999999999999888765
Q ss_pred ccCCceeeecCCCCccceEEEEEeCCccccHHHHHHHHHHhHH
Q psy3760 252 RDKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLLSPK 294 (306)
Q Consensus 252 ~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~ 294 (306)
..++++.++++.......++++|+++...+|.+++|++.++++
T Consensus 159 ~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~ 201 (201)
T cd08418 159 DSFRLITIPVEEPLPSADYYLIYRKKSRLTPLAEQLVELFRRY 201 (201)
T ss_pred hcCCEEEecCCCCCCCCceEEEEecCCCCCHHHHHHHHHHHhC
Confidence 5788999988775566799999999988999999999998763
No 65
>cd08458 PBP2_NocR The C-terminal substrate-domain of LysR-type transcriptional regulator, NocR, involved in the catabolism of nopaline, contains the type 2 periplasmic binding fold. This CD includes the C-terminal substrate-domain of LysR-type transcriptional regulator NocR, which is involved in the catabolism of nopaline. Opines are low molecular weight compounds found in plant crown gall tumors produced by the parasitic bacterium Agrobacterium. There are at least 30 different opines identified so far. Opines are utilized by tumor-colonizing bacteria as a source of carbon, nitrogen, and energy. In Agrobacterium tumefaciens, NocR regulates expression of the divergently transcribed nocB and nocR genes of the nopaline catabolism (noc) region. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, an
Probab=99.96 E-value=4.7e-28 Score=186.78 Aligned_cols=196 Identities=16% Similarity=0.150 Sum_probs=175.5
Q ss_pred cEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccCCCCCceeeccccceEEEEec
Q psy3760 94 NLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLISIPCYQWEYVIIVP 173 (306)
Q Consensus 94 ~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~~~~~~~~~l~~~~~~~v~~ 173 (306)
+++||++++++..++++++..|+++||++++++...+..++.+.+.+|++|++|...+ ...+++...++++++++++++
T Consensus 1 ~l~ig~~~~~~~~~l~~~l~~f~~~~P~v~i~~~~~~~~~~~~~l~~g~~Dl~i~~~~-~~~~~~~~~~l~~~~~~~v~~ 79 (196)
T cd08458 1 SLRVACYTAPALSFMSGVIQTFIADRPDVSVYLDTVPSQTVLELVSLQHYDLGISILA-GDYPGLTTEPVPSFRAVCLLP 79 (196)
T ss_pred CeEEEEcchhhhhhhHHHHHHHHHHCCCcEEEEeccChHHHHHHHHcCCCCEEEEecc-CCCCCceEEEeccCceEEEec
Confidence 4899999999999999999999999999999999999989999999999999999654 455789999999999999999
Q ss_pred CCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCceeEEEEecCHHHHHHHHHhccceeeeecceeccccc
Q psy3760 174 LDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMGIGIIASIAFDSNRD 253 (306)
Q Consensus 174 ~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~~~p~~~~~~~~~ 253 (306)
++||++.++.++++||.++|++....+...+..+..+++..+..+++.+++++..++++++.+|.|++++|...+.....
T Consensus 80 ~~hpl~~~~~i~~~dL~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~Gia~l~~~~~~~~~~ 159 (196)
T cd08458 80 PGHRLEDKETVHATDLEGESLICLSPVSLLRMQTDAALDSCGVHCNRRIESSLALNLCDLVSRGMGVGIVDPFTADYYSA 159 (196)
T ss_pred CCCccccCCccCHHHhCCCccEEecCCCcHHHHHHHHHHHcCCCcceEEEeccHHHHHHHHHcCCcEEEECchhhhhccC
Confidence 99999988889999999999999887777778888999999998899999999999999999999999999987755444
Q ss_pred CCceeeecCCCCccceEEEEEeCCccccHHHHHHHHHH
Q psy3760 254 KNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLL 291 (306)
Q Consensus 254 ~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l 291 (306)
+++..+++.. .....++++|+++...++.++.|++.+
T Consensus 160 ~~~~~~~~~~-~~~~~~~l~~~~~~~~~~~~~~f~~~~ 196 (196)
T cd08458 160 NPVIQRSFDP-VVPYHFAIVLPTDSPPPRLVSEFRAAL 196 (196)
T ss_pred CCeEEeeCCC-CceEEEEEEeeCCCCCCHHHHHHHhhC
Confidence 6788888864 345789999999988899999999864
No 66
>cd08456 PBP2_LysR The C-terminal substrate binding domain of LysR, transcriptional regulator for lysine biosynthesis, contains the type 2 periplasmic binding fold. LysR, the transcriptional activator of lysA encoding diaminopimelate decarboxylase, catalyses the decarboxylation of diaminopimelate to produce lysine. The LysR-transcriptional regulators comprise the largest family of prokaryotic transcription factor. Homologs of some of LTTRs with similar domain organizations are also found in the archaea and eukaryotic organisms. The LTTRs are composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcriptional repressor undergoes a conformational
Probab=99.96 E-value=4.4e-28 Score=186.73 Aligned_cols=196 Identities=18% Similarity=0.238 Sum_probs=175.2
Q ss_pred cEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccCCCCCceeeccccceEEEEec
Q psy3760 94 NLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLISIPCYQWEYVIIVP 173 (306)
Q Consensus 94 ~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~~~~~~~~~l~~~~~~~v~~ 173 (306)
.++||++++++..++++++..|.++||++++++....+.++.+.+.+|++|++|+..+ ...+++...++++++++++++
T Consensus 1 ~l~Ig~~~~~~~~~l~~~l~~~~~~~P~i~~~i~~~~~~~~~~~l~~g~~Dl~i~~~~-~~~~~~~~~~l~~~~~~~~~~ 79 (196)
T cd08456 1 ELRIAVLPALSQSFLPRAIKAFLQRHPDVTISIHTRDSPTVEQWLSAQQCDLGLVSTL-HEPPGIERERLLRIDGVCVLP 79 (196)
T ss_pred CeEEEecHHHHHhhHHHHHHHHHHHCCCcEEEEEeCCHHHHHHHHHcCCccEEEEecC-CCCCCeeEEEeeccCeEEEec
Confidence 4899999999999999999999999999999999999889999999999999998644 456789999999999999999
Q ss_pred CCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCceeEEEEecCHHHHHHHHHhccceeeeecceeccccc
Q psy3760 174 LDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMGIGIIASIAFDSNRD 253 (306)
Q Consensus 174 ~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~~~p~~~~~~~~~ 253 (306)
++||++.+..++++||.++|++.+..+...+..++.++...++.+++.+++++..++++++..|.|++++|...+.....
T Consensus 80 ~~~~l~~~~~~~~~~l~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~~~p~~~~~~~~~ 159 (196)
T cd08456 80 PGHRLAVKKVLTPSDLEGEPFISLARTDGTRQRVDALFEQAGVKRRIVVETSYAATICALVAAGVGVSVVNPLTALDYAA 159 (196)
T ss_pred CCCchhccCccCHHHcCCCcEEEecCCcchHHHHHHHHHHCCCCcceEEEEccHHHHHHHHHcCCeEEEeChhhhccccc
Confidence 99999888889999999999999887766677788899999999999999999999999999999999999987766534
Q ss_pred CCceeeecCCCCccceEEEEEeCCccccHHHHHHHHHH
Q psy3760 254 KNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLL 291 (306)
Q Consensus 254 ~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l 291 (306)
+++..++++. .....++++|+++...++.++.|++++
T Consensus 160 ~~l~~~~~~~-~~~~~~~l~~~~~~~~~~~~~~~~~~l 196 (196)
T cd08456 160 AGLVVRRFSP-AVPFEVSLIRPKHRPSSALVAAFSACL 196 (196)
T ss_pred CCEEEeeCCC-CCcceEEEEecCCCCCCHHHHHHHhhC
Confidence 5688888875 346789999999988999999999864
No 67
>cd08423 PBP2_LTTR_like_6 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator, contains the type 2 periplasmic binding fold. LysR-transcriptional regulators comprise the largest family of prokaryotic transcription factor. Homologs of some of LTTRs with similar domain organizations are also found in the archaea and eukaryotic organisms. The LTTRs are composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcriptional repressor undergoes a conformational change upon substrate binding which in turn changes the DNA binding affinity of the repressor. The genes controlled by the LTTRs have diverse functi
Probab=99.96 E-value=2.5e-28 Score=188.61 Aligned_cols=196 Identities=19% Similarity=0.271 Sum_probs=176.7
Q ss_pred cEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEcccc----CCCCCceeeccccceEE
Q psy3760 94 NLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEIL----SPSDKLISIPCYQWEYV 169 (306)
Q Consensus 94 ~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~----~~~~~~~~~~l~~~~~~ 169 (306)
+++||++++++..++++++..|.+.||++++++...++.++.+.+.+|++|++|+.... ...+++...++++++++
T Consensus 1 ~l~I~~~~~~~~~~l~~~l~~~~~~~P~i~i~~~~~~~~~~~~~l~~~~~Dl~i~~~~~~~~~~~~~~~~~~~l~~~~~~ 80 (200)
T cd08423 1 TLRVGAFPTAAAALLPPALAALRARHPGLEVRLREAEPPESLDALRAGELDLAVVFDYPVTPPPDDPGLTRVPLLDDPLD 80 (200)
T ss_pred CEEEEehhHHHHHhhhHHHHHHHHhCCCCeEEEEeCCHHHHHHHHhcCCccEEEEeccccccCCCCCCcEEEEeccCcEE
Confidence 48999999999999999999999999999999999988899999999999999986431 34678999999999999
Q ss_pred EEecCCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCceeEEEEecCHHHHHHHHHhccceeeeecceec
Q psy3760 170 IIVPLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMGIGIIASIAFD 249 (306)
Q Consensus 170 ~v~~~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~~~p~~~~~ 249 (306)
++++++||++.++.++++||.++|++....+...+..+.+++...+..++..+++++..++.+++.+|.|++++|.+.+.
T Consensus 81 ~~~~~~~p~~~~~~~~~~~l~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~~~p~~~~~ 160 (200)
T cd08423 81 LVLPADHPLAGREEVALADLADEPWIAGCPGSPCHRWLVRACRAAGFTPRIAHEADDYATVLALVAAGLGVALVPRLALG 160 (200)
T ss_pred EEecCCCCccccCCCCHHHhcCCceEEecCCchHHHHHHHHHHHcCCCCCeeeeeccHHHHHHHHHcCCCHhhhhhHHHH
Confidence 99999999998888999999999999988777677777888999999999999999999999999999999999998876
Q ss_pred ccccCCceeeecCCCCccceEEEEEeCCccccHHHHHHHHHH
Q psy3760 250 SNRDKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLL 291 (306)
Q Consensus 250 ~~~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l 291 (306)
. ..+++..++++.. ....++++|++++..++.++.|++++
T Consensus 161 ~-~~~~l~~~~~~~~-~~~~~~l~~~~~~~~~~~~~~~~~~~ 200 (200)
T cd08423 161 A-RPPGVVVRPLRPP-PTRRIYAAVRAGAARRPAVAAALEAL 200 (200)
T ss_pred h-hcCCeEEEeCCCC-CceEEEEEEcCCcccChHHHHHHhhC
Confidence 5 5677888888765 66799999999998999999999864
No 68
>cd08460 PBP2_DntR_like_1 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator similar to DntR, which is involved in the catabolism of dinitrotoluene; contains the type 2 periplasmic binding fold. This CD includes an uncharacterized LysR-type transcriptional regulator similar to DntR, NahR, and LinR, which are involved in the degradation of aromatic compounds. The transcription of the genes encoding enzymes involved in such degradation is regulated and expression of these enzymes is enhanced by inducers, which are either an intermediate in the metabolic pathway or compounds to be degraded. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytra
Probab=99.96 E-value=1.1e-28 Score=190.88 Aligned_cols=198 Identities=12% Similarity=0.055 Sum_probs=177.2
Q ss_pred cEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccCCCCCceeeccccceEEEEec
Q psy3760 94 NLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLISIPCYQWEYVIIVP 173 (306)
Q Consensus 94 ~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~~~~~~~~~l~~~~~~~v~~ 173 (306)
+++||++++++..++++++..|.++||++++++....+ ++.+.|.+|++|++|+... ...+++...++++++++++++
T Consensus 1 ~~~i~~~~~~~~~~l~~~l~~~~~~~P~v~v~l~~~~~-~~~~~l~~g~~D~~i~~~~-~~~~~~~~~~l~~~~~~~v~~ 78 (200)
T cd08460 1 TFTIRANDGFVAAFGPALLAAVAAEAPGVRLRFVPESD-KDVDALREGRIDLEIGVLG-PTGPEIRVQTLFRDRFVGVVR 78 (200)
T ss_pred CEEEEechhHHHHHHHHHHHHHHHHCCCCEEEEecCch-hHHHHHHCCCccEEEecCC-CCCcchheeeeeccceEEEEe
Confidence 48999999999999999999999999999999998877 8899999999999998644 345679999999999999999
Q ss_pred CCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCceeEEEEecCHHHHHHHHHhccceeeeecceeccc-c
Q psy3760 174 LDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMGIGIIASIAFDSN-R 252 (306)
Q Consensus 174 ~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~~~p~~~~~~~-~ 252 (306)
++||++.+ .++++||.++|++.+..+...+..+..++...+..+++.+++++..++.+++.+|.|++++|..++... .
T Consensus 79 ~~hpl~~~-~~~l~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~~lp~~~~~~~~~ 157 (200)
T cd08460 79 AGHPLARG-PITPERYAAAPHVSVSRRGRLHGPIDDALAALGLTRRVVAVVPTFAAALFLARGSDLIALVPERVTAAARA 157 (200)
T ss_pred CCCCCCCC-CCCHHHHhcCCCEEEecCCCCcchHHHHHHhcCCceeEEEEcCcHHHHHHHHhcCCHHHHHHHHHHHHHhh
Confidence 99999875 589999999999999877777778899999999999999999999999999999999999999887654 4
Q ss_pred cCCceeeecCCCCccceEEEEEeCCccccHHHHHHHHHHhHH
Q psy3760 253 DKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLLSPK 294 (306)
Q Consensus 253 ~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~ 294 (306)
.++++.++++.+....+++++|+++...++++++|.+.+++.
T Consensus 158 ~~~l~~~~~~~~~~~~~i~l~~~~~~~~~~~~~~l~~~~~~~ 199 (200)
T cd08460 158 GLGLRTFPLPLELPAVTVSQAWHPRFDADPAHRWLRECVREV 199 (200)
T ss_pred cCCceEECCCCCCCCeeeEEeEcCccccChHHHHHHHHHHHh
Confidence 577888888865567899999999999999999999988765
No 69
>cd08419 PBP2_CbbR_RubisCO_like The C-terminal substrate binding of LysR-type transcriptional regulator (CbbR) of RubisCO operon, which is involved in the carbon dioxide fixation, contains the type 2 periplasmic binding fold. CbbR, a LysR-type transcriptional regulator, is required to activate expression of RubisCO, one of two unique enzymes in the Calvin-Benson-Bassham (CBB) cycle pathway. All plants, cyanobacteria, and many autotrophic bacteria use the CBB cycle to fix carbon dioxide. Thus, this cycle plays an essential role in assimilating CO2 into organic carbon on earth. The key CBB cycle enzyme is ribulose 1,5-bisphosphate carboxylase/oxygenase (RubisCO), which catalyzes the actual CO2 fixation reaction. The CO2 concentration affects the expression of RubisCO genes. It has also shown that NADPH enhances the DNA-binding ability of the CbbR. RubisCO is composed of eight large (CbbL) and eight small subunits (CbbS). The topology of this substrate-binding domain is most similar to t
Probab=99.96 E-value=4.1e-28 Score=186.94 Aligned_cols=196 Identities=22% Similarity=0.366 Sum_probs=175.5
Q ss_pred cEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccCCCCCceeeccccceEEEEec
Q psy3760 94 NLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLISIPCYQWEYVIIVP 173 (306)
Q Consensus 94 ~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~~~~~~~~~l~~~~~~~v~~ 173 (306)
+|+||++ +....++++++..|.++||++++++....+.++.+.|.+|++|++|...+ ...+++...++++++++++++
T Consensus 1 ~l~Ig~~-~~~~~~l~~~l~~~~~~~P~i~l~i~~~~~~~~~~~l~~g~~Dl~i~~~~-~~~~~~~~~~l~~~~~~~~~~ 78 (197)
T cd08419 1 RLRLAVV-STAKYFAPRLLGAFCRRHPGVEVSLRVGNREQVLERLADNEDDLAIMGRP-PEDLDLVAEPFLDNPLVVIAP 78 (197)
T ss_pred CEEEEEe-chhHhHhhHHHHHHHHHCCCceEEEEECCHHHHHHHHhcCCccEEEecCC-CCCCCeEEEEeccCCEEEEec
Confidence 4899999 77888999999999999999999999999999999999999999998644 445689999999999999999
Q ss_pred CCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCceeEEEEecCHHHHHHHHHhccceeeeecceeccc-c
Q psy3760 174 LDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMGIGIIASIAFDSN-R 252 (306)
Q Consensus 174 ~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~~~p~~~~~~~-~ 252 (306)
++||++....++++||.++|++....+...+..+..++...+..+++.+++++..++.+++.+|.|++++|.+.+... .
T Consensus 79 ~~~~l~~~~~~~~~~l~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~~~p~~~~~~~~~ 158 (197)
T cd08419 79 PDHPLAGQKRIPLERLAREPFLLREPGSGTRLAMERFFAEHGVTLRVRMELGSNEAIKQAVMAGLGLSVLSLHTLALELA 158 (197)
T ss_pred CCCCCcCCCCcCHHHHhCCCcEEecCCCcHHHHHHHHHHHCCCCcceEEEECCHHHHHHHHHhCCceEeecHHHHHHHHh
Confidence 999998877899999999999998877666777888999999999999999999999999999999999999887655 6
Q ss_pred cCCceeeecCCCCccceEEEEEeCCccccHHHHHHHHHH
Q psy3760 253 DKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLL 291 (306)
Q Consensus 253 ~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l 291 (306)
.+.++.++++.......++++|+++...++.+++|++++
T Consensus 159 ~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l 197 (197)
T cd08419 159 TGRLAVLDVEGFPIRRQWYVVHRKGKRLSPAAQAFLDFL 197 (197)
T ss_pred hCCeEEEEcCCcceEEEEEEEEcCCCcCCHHHHHHHhhC
Confidence 778999888765556789999999988999999998864
No 70
>cd08462 PBP2_NodD The C-terminal substsrate binding domain of NodD family of LysR-type transcriptional regulators that regulates the expression of nodulation (nod) genes; contains the type 2 periplasmic binding fold. The nodulation (nod) genes in soil bacteria play important roles in the development of nodules. nod genes are involved in synthesis of Nod factors that are required for bacterial entry into root hairs. Thirteen nod genes have been identified and are classified into five transcription units: nodD, nodABCIJ, nodFEL, nodMNT, and nodO. NodD is negatively auto-regulates its own expression of nodD gene, while other nod genes are inducible and positively regulated by NodD in the presence of flavonoids released by plant roots. This substrate-binding domain has significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. T
Probab=99.96 E-value=2.1e-28 Score=189.42 Aligned_cols=197 Identities=17% Similarity=0.148 Sum_probs=174.2
Q ss_pred cEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccCCCCCceeeccccceEEEEec
Q psy3760 94 NLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLISIPCYQWEYVIIVP 173 (306)
Q Consensus 94 ~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~~~~~~~~~l~~~~~~~v~~ 173 (306)
.++||++++++..++++++..|.+.||++.+++..... ++.+.|.+|++|++|+... ...+++...++++++++++++
T Consensus 1 ~l~I~~~~~~~~~~l~~~i~~~~~~~P~i~l~i~~~~~-~~~~~l~~g~~D~~i~~~~-~~~~~~~~~~l~~~~~~~v~~ 78 (200)
T cd08462 1 HFRIIASDYVITVLLPPVIERVAREAPGVRFELLPPDD-QPHELLERGEVDLLIAPER-FMSDGHPSEPLFEEEFVCVVW 78 (200)
T ss_pred CEEEEecHHhHHHHHHHHHHHHHHHCCCCEEEEecCCh-hHHHHHhcCCeeEEEecCC-CCCCCceeeeeeccceEEEEc
Confidence 48999999999999999999999999999999998766 9999999999999999654 455789999999999999999
Q ss_pred CCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHH-HHHHHhCCCceeEEEEecCHHHHHHHHHhccceeeeecceeccc-
Q psy3760 174 LDHPLLLLNSISLKEISNYPLITYDLSFSGRIKL-DREFSLQKLTPYIVLETINSDIIKTYVELRMGIGIIASIAFDSN- 251 (306)
Q Consensus 174 ~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~~~p~~~~~~~- 251 (306)
++||++. ..++++||.++|++.+..+...+..+ +.++...++.+++.+++++..++.+++.+|.|++++|.+.+...
T Consensus 79 ~~hpl~~-~~~~~~~l~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~giailp~~~~~~~~ 157 (200)
T cd08462 79 ADNPLVG-GELTAEQYFSAGHVVVRFGRNRRPSFEDWFLNEYGLKRRVEVVTPSFSSIPPLLVGTNRIATLHRRLAEQFA 157 (200)
T ss_pred CCCCccC-CCCCHHHHhhCCCEEEecCCCCCccHHHHHHHHcCCcceEEEEeChHHHHHHHHHcCchhhhhHHHHHHhhh
Confidence 9999985 67999999999999987765544444 34568889999999999999999999999999999999888665
Q ss_pred ccCCceeeecCCCCccceEEEEEeCCccccHHHHHHHHHHhH
Q psy3760 252 RDKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLLSP 293 (306)
Q Consensus 252 ~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~ 293 (306)
..+.++.++++......+++++|++++..++.+++|++.+++
T Consensus 158 ~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~i~~ 199 (200)
T cd08462 158 RRLPLRILPLPFPLPPMREALQWHRYRNNDPGLIWLRELIIE 199 (200)
T ss_pred hcCCceEeCCCcCCCCeeEEEEEcccccCChHHHHHHHHHhc
Confidence 667799999886566789999999999999999999998875
No 71
>cd08466 PBP2_LeuO The C-terminal substrate binding domain of LysR-type transcriptional regulator LeuO, an activator of leucine synthesis operon, contains the type 2 periplasmic binding fold. LeuO, a LysR-type transcriptional regulator, was originally identified as an activator of the leucine synthesis operon (leuABCD). Subsequently, LeuO was found to be not a specific regulator of the leu gene but a global regulator of unrelated various genes. LeuO activates bglGFB (utilization of beta-D-glucoside) and represses cadCBA (lysine decarboxylation) and dsrA (encoding a regulatory small RNA for translational control of rpoS and hns). LeuO also regulates the yjjQ-bglJ operon which coding for a LuxR-type transcription factor. In Salmonella enterica serovar Typhi, LeuO is a positive regulator of ompS1 (encoding an outer membrane), ompS2 (encoding a pathogenicity determinant), and assT, while LeuO represses the expression of OmpX and Tpx. Both osmS1 and osmS2 influence virulence in the mouse mo
Probab=99.96 E-value=1.8e-28 Score=189.56 Aligned_cols=197 Identities=16% Similarity=0.123 Sum_probs=175.1
Q ss_pred cEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccCCCCCceeeccccceEEEEec
Q psy3760 94 NLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLISIPCYQWEYVIIVP 173 (306)
Q Consensus 94 ~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~~~~~~~~~l~~~~~~~v~~ 173 (306)
+++||++++++..++++++..|.++||++++++...++.++.+.|.+|++|++|+..+ ...+++.+.++++++++++++
T Consensus 1 ~~~Ig~~~~~~~~~l~~~l~~f~~~~P~v~l~~~~~~~~~~~~~l~~g~~Dl~i~~~~-~~~~~~~~~~l~~~~~~lv~~ 79 (200)
T cd08466 1 TFNIAANETLDLLLLPRLLARLKQLAPNISLRESPSSEEDLFEDLRLQEVDLVIDYVP-FRDPSFKSELLFEDELVCVAR 79 (200)
T ss_pred CEEEEechHHHHHHHHHHHHHHHHHCCCCEEEEecCchHhHHHHHHcCCccEEEeccc-CCCCCceeeeecccceEEEEe
Confidence 4899999999999999999999999999999999999989999999999999998654 446789999999999999999
Q ss_pred CCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCC-ceeEEEEecCHHHHHHHHHhccceeeeecceeccc-
Q psy3760 174 LDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKL-TPYIVLETINSDIIKTYVELRMGIGIIASIAFDSN- 251 (306)
Q Consensus 174 ~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~v~~g~gi~~~p~~~~~~~- 251 (306)
++||++. ..++++||.+++++.++.. .....+..++...+. .+++.+++++..++.+++.+|.|++++|..++...
T Consensus 80 ~~~~~~~-~~~~~~~L~~~~~i~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~~lp~~~~~~~~ 157 (200)
T cd08466 80 KDHPRIQ-GSLSLEQYLAEKHVVLSLR-RGNLSALDLLTEEVLPQRNIAYEVSSLLSMLAVVSQTDLIAIAPRWLADQYA 157 (200)
T ss_pred CCCCCCC-CCcCHHHHhhCCcEEecCC-CCcchHHHHHHHhcCCcccEEEEcCchhhHHHHHcCCCeehhhHHHHHHHhh
Confidence 9999875 4689999999999998743 344567888888888 78889999999999999999999999999888765
Q ss_pred ccCCceeeecCCCCccceEEEEEeCCccccHHHHHHHHHHhH
Q psy3760 252 RDKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLLSP 293 (306)
Q Consensus 252 ~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~ 293 (306)
..++++.++++......+++++|++++..+|.+++|++.+++
T Consensus 158 ~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 199 (200)
T cd08466 158 EQLNLQILPLPFKTKPIPLYMVWHKSRERDPAHQWLREQIKQ 199 (200)
T ss_pred hcCCeeEecCCCCCCCccEEEEEcCCCCCChHHHHHHHHHhh
Confidence 567899888876555679999999999999999999998875
No 72
>cd08467 PBP2_SyrM The C-terminal substrate binding of LysR-type symbiotic regulator SyrM, which activates expression of nodulation gene NodD3, contains the type 2 periplasmic binding fold. Rhizobium is a nitrogen fixing bacteria present in the roots of leguminous plants, which fixes atmospheric nitrogen to the soil. Most Rhizobium species possess multiple nodulation (nod) genes for the development of nodules. For example, Rhizobium meliloti possesses three copies of nodD genes. NodD1 and NodD2 activate nod operons when Rhizobium is exposed to inducers synthesized by the host plant, while NodD3 acts independent of plant inducers and requires the symbiotic regulator SyrM for nod gene expression. SyrM activates the expression of the regulatory nodulation gene nodD3. In turn, NodD3 activates expression of syrM. In addition, SyrM is involved in exopolysaccharide synthesis. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are
Probab=99.96 E-value=3.9e-28 Score=187.89 Aligned_cols=197 Identities=14% Similarity=0.088 Sum_probs=175.2
Q ss_pred EEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccCCCCCceeeccccceEEEEecC
Q psy3760 95 LTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLISIPCYQWEYVIIVPL 174 (306)
Q Consensus 95 l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~~~~~~~~~l~~~~~~~v~~~ 174 (306)
++||++++++..++++++..|.++||++++++....+.++.+.|.+|++|++|+..+ ...+++...+++++++++++++
T Consensus 2 ~~I~~~~~~~~~~l~~~l~~~~~~~P~i~l~~~~~~~~~~~~~l~~g~~D~~i~~~~-~~~~~~~~~~l~~~~~~~v~~~ 80 (200)
T cd08467 2 FTLAMPDYAEVALLPRLAPRLRERAPGLDLRLCPIGDDLAERGLEQGTIDLAVGRFA-VPPDGLVVRRLYDDGFACLVRH 80 (200)
T ss_pred eEEEechhhHHHHHHHHHHHHHhhCCCCEEEEecCCcccHHHHhhCCCcCEEEecCC-CCCccceeEEeeeccEEEEEcC
Confidence 799999999999999999999999999999999998889999999999999998643 3456799999999999999999
Q ss_pred CCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCceeEEEEecCHHHHHHHHHhccceeeeecceeccc-cc
Q psy3760 175 DHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMGIGIIASIAFDSN-RD 253 (306)
Q Consensus 175 ~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~~~p~~~~~~~-~~ 253 (306)
+||++.+ .++++||.++|++.+..+...+..+..+++..|+.+++.+++++..++.+++.+|.|++++|...+... ..
T Consensus 81 ~h~l~~~-~~~~~dL~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~~lp~~~~~~~~~~ 159 (200)
T cd08467 81 GHPALAQ-EWTLDDFATLRHVAIAPPGRLFGGIYKRLENLGLKRNVAIAVSSFLTAAATVAATDLIATVPRRVATQVAAM 159 (200)
T ss_pred CCccccC-CCCHHHHhCCCCEEEcCCCCCCchHHHHHHhcCCcccEEEEecchHHHHHHHhcCCeEEeeHHHHHHHHhhc
Confidence 9999865 589999999999999877666677888999999999999999999999999999999999999887654 44
Q ss_pred CCceeeecCCCCccceEEEEEeCCccccHHHHHHHHHHhH
Q psy3760 254 KNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLLSP 293 (306)
Q Consensus 254 ~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~ 293 (306)
+.++.++++.....++++++|+++...++..++|.+.|++
T Consensus 160 ~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~l~~~i~~ 199 (200)
T cd08467 160 LPLRVVPPPVDLGTFPVMLIWHERYQHDPAHRWLRKLIAA 199 (200)
T ss_pred CCeeEecCCCCCCCeeEEEEecccccCChHHHHHHHHHhh
Confidence 6788787765445679999999999999999999998875
No 73
>cd08414 PBP2_LTTR_aromatics_like The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in the catabolism of aromatic compounds and that of other related regulators, contains type 2 periplasmic binding fold. This CD includes the C-terminal substrate binding domain of LTTRs involved in degradation of aromatic compounds, such as CbnR, BenM, CatM, ClcR and TfdR, as well as that of other transcriptional regulators clustered together in phylogenetic trees, including XapR, HcaR, MprR, IlvR, BudR, AlsR, LysR, and OccR. The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they ca
Probab=99.96 E-value=8.7e-28 Score=185.07 Aligned_cols=194 Identities=18% Similarity=0.263 Sum_probs=174.5
Q ss_pred cEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccCCCCCceeeccccceEEEEec
Q psy3760 94 NLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLISIPCYQWEYVIIVP 173 (306)
Q Consensus 94 ~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~~~~~~~~~l~~~~~~~v~~ 173 (306)
+++||++++++..++++++..|+++||++++++....+.++.+.|.+|++|++|+..+ ...+++...++++++++++++
T Consensus 1 ~l~Ig~~~~~~~~~l~~~l~~~~~~~p~i~i~i~~~~~~~~~~~l~~~~~Dl~i~~~~-~~~~~~~~~~l~~~~~~~v~~ 79 (197)
T cd08414 1 RLRIGFVGSALYGLLPRLLRRFRARYPDVELELREMTTAEQLEALRAGRLDVGFVRPP-PDPPGLASRPLLREPLVVALP 79 (197)
T ss_pred CEEEEeeHHHHHHHHHHHHHHHHHHCCCcEEEEecCChHHHHHHHHcCCccEEEEcCC-CCCCCeeEEEEeeccEEEEec
Confidence 4899999999999999999999999999999999998899999999999999999654 456789999999999999999
Q ss_pred CCCCCCCCCCcChhhhcCCCeEeecCCC--CcHHHHHHHHHhCCCceeEEEEecCHHHHHHHHHhccceeeeecceeccc
Q psy3760 174 LDHPLLLLNSISLKEISNYPLITYDLSF--SGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMGIGIIASIAFDSN 251 (306)
Q Consensus 174 ~~~~l~~~~~i~~~dl~~~~~i~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~~~p~~~~~~~ 251 (306)
++||+.....++++||.++|++.+..+. ..+..+..++...+..++..+++++..++.+++.+|.|++++|...+..
T Consensus 80 ~~~~l~~~~~~~~~~L~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~~~p~~~~~~- 158 (197)
T cd08414 80 ADHPLAARESVSLADLADEPFVLFPREPGPGLYDQILALCRRAGFTPRIVQEASDLQTLLALVAAGLGVALVPASVARL- 158 (197)
T ss_pred CCCccccCCccCHHHhccCCEEEecCCcchhHHHHHHHHHHHcCCCcccceecccHHHHHHHHHcCCcEEEccChhhhc-
Confidence 9999988888999999999999987763 4667888999999998888899999999999999999999999988765
Q ss_pred ccCCceeeecCCCCccceEEEEEeCCccccHHHHHHHHH
Q psy3760 252 RDKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKL 290 (306)
Q Consensus 252 ~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~ 290 (306)
..+++..+++++.....+++++|+++.. ++.++.|+++
T Consensus 159 ~~~~l~~~~~~~~~~~~~~~l~~~~~~~-~~~~~~f~~~ 196 (197)
T cd08414 159 QRPGVVYRPLADPPPRSELALAWRRDNA-SPALRAFLEL 196 (197)
T ss_pred cCCCeEEEECCCCCcceEEEEEEecCCC-CHHHHHHHhh
Confidence 4567888888775567899999999988 9999999875
No 74
>cd08441 PBP2_MetR The C-terminal substrate binding domain of LysR-type transcriptional regulator metR, which regulates the expression of methionine biosynthetic genes, contains type 2 periplasmic binding fold. MetR, a member of the LysR family, is a positive regulator for the metA, metE, metF, and metH genes. The sulfur-containing amino acid methionine is the universal initiator of protein synthesis in all known organisms and its derivative S-adenosylmethionine (SAM) and autoinducer-2 (AI-2) are involved in various cellular processes. SAM plays a central role as methyl donor in methylation reactions, which are essential for the biosynthesis of phospholipids, proteins, DNA and RNA. The interspecies signaling molecule AI-2 is involved in cell-cell communication process (quorum sensing) and gene regulation in bacteria. Although methionine biosynthetic enzymes and metabolic pathways are well conserved in bacteria, the regulation of methionine biosynthesis involves various regulatory mecha
Probab=99.96 E-value=7e-28 Score=186.02 Aligned_cols=196 Identities=17% Similarity=0.195 Sum_probs=175.6
Q ss_pred cEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccCCCCCceeeccccceEEEEec
Q psy3760 94 NLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLISIPCYQWEYVIIVP 173 (306)
Q Consensus 94 ~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~~~~~~~~~l~~~~~~~v~~ 173 (306)
.|+||++.+++..++++++..|.++||++++++....+.++.+.|.+|++|++|...+ ...+++...++++++++++++
T Consensus 1 ~l~Ig~~~~~~~~~~~~~l~~~~~~~P~i~i~i~~~~~~~~~~~l~~g~~Dl~i~~~~-~~~~~~~~~~l~~~~~~~~~~ 79 (198)
T cd08441 1 RLRIAVECHSCFDWLMPVLDQFRERWPDVELDLSSGFHFDPLPALLRGELDLVITSDP-LPLPGIAYEPLFDYEVVLVVA 79 (198)
T ss_pred CEEEEeeccchhhhhHHHHHHHHHhCCCeEEEEEeCCchhHHHHHHcCCceEEEecCC-cCCCCcEEEEccCCcEEEEEc
Confidence 4899999999999999999999999999999999998889999999999999998654 456789999999999999999
Q ss_pred CCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCceeEEEEecCHHHHHHHHHhccceeeeecceeccc-c
Q psy3760 174 LDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMGIGIIASIAFDSN-R 252 (306)
Q Consensus 174 ~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~~~p~~~~~~~-~ 252 (306)
++||++....++++||.++|++.+..+...+..+..++...++.++..+++++..++.+++.+|.|++++|...+... .
T Consensus 80 ~~~~l~~~~~~~~~~l~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~~lp~~~~~~~~~ 159 (198)
T cd08441 80 PDHPLAAKEFITPEDLADETLITYPVERERLDVFRHFLQPAGIEPKRRRTVELTLMILQLVASGRGVAALPNWAVREYLD 159 (198)
T ss_pred CCCChHHcccCCHHHhcCCceEEecCCccHHHHHHHHHHhcCCCCCccEEeCCHHHHHHHHHhCCcEEEeeHHHHHHHHh
Confidence 999998777899999999999998776666677888999999988888999999999999999999999999887665 6
Q ss_pred cCCceeeecCCCCccceEEEEEeCCccccHHHHHHHHH
Q psy3760 253 DKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKL 290 (306)
Q Consensus 253 ~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~ 290 (306)
.+.++.+++.++.....++++|+++...++.++.|++.
T Consensus 160 ~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~f~~~ 197 (198)
T cd08441 160 QGLVVARPLGEEGLWRTLYAAVRTEDADQPYLQDFLEL 197 (198)
T ss_pred cCceEEEeccCCceEEEEEEEEEcCCcCChHHHHHHhh
Confidence 67899898865455679999999998889999999874
No 75
>cd08453 PBP2_IlvR The C-terminal substrate binding domain of LysR-type transcriptional regulator, IlvR, involved in the biosynthesis of isoleucine, leucine and valine; contains type 2 periplasmic binding fold. The IlvR is an activator of the upstream and divergently transcribed ilvD gene, which encodes dihydroxy acid dehydratase that participates in isoleucine, leucine, and valine biosynthesis. As in the case of other members of the LysR family, the expression of ilvR gene is repressed in the presence of its own gene product. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport
Probab=99.96 E-value=8.8e-28 Score=185.75 Aligned_cols=195 Identities=17% Similarity=0.217 Sum_probs=172.7
Q ss_pred cEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccC--CCCCceeeccccceEEEE
Q psy3760 94 NLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILS--PSDKLISIPCYQWEYVII 171 (306)
Q Consensus 94 ~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~--~~~~~~~~~l~~~~~~~v 171 (306)
.|+||+.++++..++++++..|.++||++++++....+.++.+.|.+|++|++|...+.. .++++...++++++++++
T Consensus 1 ~l~ig~~~~~~~~~l~~~l~~~~~~~P~i~l~i~~~~~~~~~~~l~~g~~D~~i~~~~~~~~~~~~~~~~~l~~~~~~~v 80 (200)
T cd08453 1 RLSLAFVSTADYSVLPELVRRFREAYPDVELQLREATSDVQLEALLAGEIDAGIVIPPPGASAPPALAYRPLLSEPLVLA 80 (200)
T ss_pred CEEEEEechHHhHHHHHHHHHHHHhCCCceEEEEeCCHHHHHHHHHcCCCCEEEEecCcccCCCcceeEEEeeeCceEEE
Confidence 489999999999999999999999999999999999888999999999999999864422 257899999999999999
Q ss_pred ecCCCCCCCCCCcChhhhcCCCeEeecCCC--CcHHHHHHHHHhCCCceeEEEEecCHHHHHHHHHhccceeeeecceec
Q psy3760 172 VPLDHPLLLLNSISLKEISNYPLITYDLSF--SGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMGIGIIASIAFD 249 (306)
Q Consensus 172 ~~~~~~l~~~~~i~~~dl~~~~~i~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~~~p~~~~~ 249 (306)
++++||++.++.++++||.++|++.++.+. ..++.+..++...+..++..+++++..++++++.+|.|++++|.++..
T Consensus 81 ~~~~hp~~~~~~i~~~~L~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~~~p~~~~~ 160 (200)
T cd08453 81 VPAAWAAEGGAPLALAAVAAEPLVIFPRRIAPAFHDAVTGYYRAAGQTPRIAQEAIQMQTIISLVSAGMGVALVPASLRN 160 (200)
T ss_pred EECCCccccCCCCCHHHhccCCEEeccCCcCCcHHHHHHHHHHHcCCCCceeeccccHHHHHHHHHcCCcEEEeEhHHhh
Confidence 999999998888999999999999987654 356778899999999999999999999999999999999999997753
Q ss_pred ccccCCceeeecCCCCccceEEEEEeCCccccHHHHHHHHH
Q psy3760 250 SNRDKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKL 290 (306)
Q Consensus 250 ~~~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~ 290 (306)
...++++.+++++......++++|+++.. ++.+++|+++
T Consensus 161 -~~~~~l~~~~~~~~~~~~~~~l~~~~~~~-~~~~~~~~~~ 199 (200)
T cd08453 161 -LARPGVVYRELADPAPVLETGLVWRRDDA-SPVLARFLDL 199 (200)
T ss_pred -cCCCceEEEECCCCCcceeEEEEEccccc-ChHHHHHHhh
Confidence 34577999998875556799999998875 9999999875
No 76
>cd08442 PBP2_YofA_SoxR_like The C-terminal substrate binding domain of LysR-type transcriptional regulators, YofA and SoxR, contains the type 2 periplasmic binding fold. YofA is a LysR-like transcriptional regulator of cell growth in Bacillus subtillis. YofA controls cell viability and the formation of constrictions during cell division. YofaA positively regulates expression of the cell division gene ftsW, and thus is essential for cell viability during stationary-phase growth of Bacillus substilis. YofA shows significant homology to SoxR from Arthrobacter sp. TE1826. SoxR is a negative regulator for the sarcosine oxidase gene soxA. Sarcosine oxidase catalyzes the oxidative demethylation of sarcosine, which is involved in the metabolism of creatine and choline. The topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides
Probab=99.96 E-value=1.1e-27 Score=183.91 Aligned_cols=192 Identities=21% Similarity=0.351 Sum_probs=173.1
Q ss_pred cEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccCCCCCceeeccccceEEEEec
Q psy3760 94 NLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLISIPCYQWEYVIIVP 173 (306)
Q Consensus 94 ~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~~~~~~~~~l~~~~~~~v~~ 173 (306)
.++||++++++..++++++..|.++||++++++....+.++.+.+.+|++|++|+..+ ...+++...++++++++++++
T Consensus 1 ~l~Ig~~~~~~~~~l~~~l~~~~~~~P~i~l~i~~~~~~~~~~~l~~g~~Dl~i~~~~-~~~~~~~~~~l~~~~~~~v~~ 79 (193)
T cd08442 1 PLRLGSMETTAAVRLPPLLAAYHARYPKVDLSLSTGTTGALIQAVLEGRLDGAFVAGP-VEHPRLEQEPVFQEELVLVSP 79 (193)
T ss_pred CeEEeccccchhhhhHHHHHHHHHHCCCceEEEEeCCcHHHHHHHHCCCccEEEEeCC-CCCCCcEEEEeecCcEEEEec
Confidence 4899999999999999999999999999999999999989999999999999998644 456789999999999999999
Q ss_pred CCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCceeEEEEecCHHHHHHHHHhccceeeeecceeccc-c
Q psy3760 174 LDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMGIGIIASIAFDSN-R 252 (306)
Q Consensus 174 ~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~~~p~~~~~~~-~ 252 (306)
++||++. +++||.++|++.+..+...+..+..++...++.++..+++++..++++++.+|.|++++|.+++... .
T Consensus 80 ~~~~~~~----~~~~l~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~~~p~~~~~~~~~ 155 (193)
T cd08442 80 KGHPPVS----RAEDLAGSTLLAFRAGCSYRRRLEDWLAEEGVSPGKIMEFGSYHAILGCVAAGMGIALLPRSVLDSLQG 155 (193)
T ss_pred CCCcccc----cHHHhCCCceEEecCCCcHHHHHHHHHHHcCCCcceEEecCCHHHHHHHHHhCCcEEEcCHHHHhhhhh
Confidence 9999763 6999999999999877777778889999999999999999999999999999999999999988765 5
Q ss_pred cCCceeeecCCCCccceEEEEEeCCccccHHHHHHHHHH
Q psy3760 253 DKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLL 291 (306)
Q Consensus 253 ~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l 291 (306)
.+.++.++++.......++++|++++. ++.+++|++++
T Consensus 156 ~~~l~~~~~~~~~~~~~~~l~~~~~~~-~~~~~~~~~~~ 193 (193)
T cd08442 156 RGSVSIHPLPEPFADVTTWLVWRKDSF-TAALQAFLDLL 193 (193)
T ss_pred cCceEEEecCCCCCceEEEEEEeCCCC-CHHHHHHHHhC
Confidence 678888888765556789999999998 99999999864
No 77
>cd08449 PBP2_XapR The C-terminal substrate binding domain of LysR-type transcriptional regulator XapR involved in xanthosine catabolism, contains the type 2 periplasmic binding fold. In Escherichia coli, XapR is a positive regulator for the expression of xapA gene, encoding xanthosine phosphorylase, and xapB gene, encoding a polypeptide similar to the nucleotide transport protein NupG. As an operon, the expression of both xapA and xapB is fully dependent on the presence of both XapR and the inducer xanthosine. Expression of the xapR is constitutive but not auto-regulated, unlike many other LysR family proteins. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their
Probab=99.96 E-value=1.2e-27 Score=184.32 Aligned_cols=195 Identities=17% Similarity=0.210 Sum_probs=172.6
Q ss_pred cEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccC-CCCCceeeccccceEEEEe
Q psy3760 94 NLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILS-PSDKLISIPCYQWEYVIIV 172 (306)
Q Consensus 94 ~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~-~~~~~~~~~l~~~~~~~v~ 172 (306)
+++||++++++..++++++..|.++||++++++....+.+..+.|.+|++|++|+..... ..+++...+++++++++++
T Consensus 1 ~l~ig~~~~~~~~~l~~~l~~~~~~~P~i~i~~~~~~~~~~~~~l~~~~~Dl~i~~~~~~~~~~~~~~~~l~~~~~~~v~ 80 (197)
T cd08449 1 HLNIGMVGSVLWGGLGPALRRFKRQYPNVTVRFHELSPEAQKAALLSKRIDLGFVRFADTLNDPPLASELLWREPMVVAL 80 (197)
T ss_pred CeEEEEechHhhhhHHHHHHHHHHHCCCeEEEEEECCHHHHHHHHhCCCccEEEecccccCCCCCceEEEEEEeeEEEEe
Confidence 489999999999999999999999999999999999899999999999999999854422 2678999999999999999
Q ss_pred cCCCCCCCCCCcChhhhcCCCeEeecC-CCCcHHHHHHHHHhCCCceeEEEEecCHHHHHHHHHhccceeeeecceeccc
Q psy3760 173 PLDHPLLLLNSISLKEISNYPLITYDL-SFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMGIGIIASIAFDSN 251 (306)
Q Consensus 173 ~~~~~l~~~~~i~~~dl~~~~~i~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~~~p~~~~~~~ 251 (306)
+++||++.+..++++||.++|++.+.. +...+..+.+++...+..++..+++++..++.+++.+|.|++++|..++..
T Consensus 81 ~~~~~~~~~~~~~~~~L~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~~~p~~~~~~- 159 (197)
T cd08449 81 PEEHPLAGRKSLTLADLRDEPFVFLRLANSRFADFLINCCLQAGFTPQITQEVVEPQTLMALVAAGFGVALVPESYARL- 159 (197)
T ss_pred cCCCCCCCCCCCCHHHHCCCCEEEecCCCchHHHHHHHHHHhCCCCCceeccCCchHhHHHHhhcCCcEEEchhhhhcc-
Confidence 999999888789999999999999876 344566778888889998888999999999999999999999999987754
Q ss_pred ccCCceeeecCCCCccceEEEEEeCCccccHHHHHHHHHH
Q psy3760 252 RDKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLL 291 (306)
Q Consensus 252 ~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l 291 (306)
..++++.+++++. ...+++++|+++.. ++.++.|++++
T Consensus 160 ~~~~l~~~~~~~~-~~~~~~~~~~~~~~-~~~~~~~~~~~ 197 (197)
T cd08449 160 PWPGVRFIPLKQA-ISADLYAVYHPDSA-TPVIQAFLALL 197 (197)
T ss_pred CcCCeEEEECCCC-CcceEEEEECCCCC-CHHHHHHHhhC
Confidence 3457888888875 67899999999887 99999998864
No 78
>cd08486 PBP2_CbnR The C-terminal substrate binding domain of LysR-type transcriptional regulator, CbnR, involved in the chlorocatechol catabolism, contains the type 2 periplasmic binding fold. This CD represents the substrate binding domain of LysR-type regulator CbnR which is involved in the regulation of chlorocatechol breakdown. The chlorocatechol-degradative pathway is often found in bacteria that can use chlorinated aromatic compounds as carbon and energy sources. CbnR is found in the 3-chlorobenzoate degradative bacterium Ralstonia eutropha NH9 and forms a tetramer. CbnR activates the expression of the cbnABCD genes, which are responsible for the degradation of chlorocatechol converted from 3-chlorobenzoate and are transcribed divergently from cbnR. The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccha
Probab=99.96 E-value=2e-27 Score=183.65 Aligned_cols=195 Identities=12% Similarity=0.065 Sum_probs=172.6
Q ss_pred CcEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccCCCCCceeeccccceEEEEe
Q psy3760 93 GNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLISIPCYQWEYVIIV 172 (306)
Q Consensus 93 ~~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~~~~~~~~~l~~~~~~~v~ 172 (306)
|.|+||++.+++..++++++.+|.++||++.+++....+.++.+.|.+|++|++++... ...+++.+.+++++++++++
T Consensus 1 g~l~Ig~~~~~~~~~l~~~l~~f~~~~P~v~i~i~~~~~~~l~~~l~~g~~D~~~~~~~-~~~~~~~~~~l~~~~~~lv~ 79 (198)
T cd08486 1 GELSVAYFGTPIYRSLPLLLRAFLTSTPTATVSLTHMTKDEQVEGLLAGTIHVGFSRFF-PRHPGIEIVNIAQEDLYLAV 79 (198)
T ss_pred CeEEEEEechhhHHHHHHHHHHHHHhCCCeEEEEEECCHHHHHHHHHcCCceEEEecCC-CCCCceEEEEEeeccEEEEe
Confidence 57999999999999999999999999999999999999999999999999999998643 55678999999999999999
Q ss_pred cCCCCCCCCCCcChhhhcCCCeEeecCCC--CcHHHHHHHHHhCCCceeEEEEecCHHHHHHHHHhccceeeeecceecc
Q psy3760 173 PLDHPLLLLNSISLKEISNYPLITYDLSF--SGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMGIGIIASIAFDS 250 (306)
Q Consensus 173 ~~~~~l~~~~~i~~~dl~~~~~i~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~~~p~~~~~~ 250 (306)
+++||++.+..++++||.++|++.++.+. ..+..+..++...|+.++..+++++..++.+++.+|.|++++|.+....
T Consensus 80 ~~~h~l~~~~~i~~~dL~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~Gi~~lp~~~~~~ 159 (198)
T cd08486 80 HRSQSGKFGKTCKLADLRAVELTLFPRGGRPSFADEVIGLFKHAGIEPRIARVVEDATAALALTMAGAASSIVPASVAAI 159 (198)
T ss_pred cCCCccccCCcccHHHHcCCCeEeecCCcCchHHHHHHHHHHHcCCCcceEEEeccHHHHHHHHHcCceEEEcchhhccc
Confidence 99999998889999999999999987654 3677888999999999999999999999999999999999999977643
Q ss_pred cccCCceeeecCCCCccceEEEEEeCCccccHHHHHHHHH
Q psy3760 251 NRDKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKL 290 (306)
Q Consensus 251 ~~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~ 290 (306)
..+++..+++.+.....+++++|++++. ++.+++|+++
T Consensus 160 -~~~~l~~~~l~~~~~~~~~~~~~~~~~~-~~~~~~~~~~ 197 (198)
T cd08486 160 -RWPDIAFARIVGTRVKVPISCIFRKEKQ-PPILARFVEH 197 (198)
T ss_pred -CCCCeEEEECcCCCCCceEEEEEcCCCC-ChHHHHHHhh
Confidence 2346888888764556799999988874 6788888875
No 79
>cd08461 PBP2_DntR_like_3 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator similar to DntR, which is involved in the catabolism of dinitrotoluene; contains the type 2 periplasmic binding fold. This CD includes an uncharacterized LysR-type transcriptional regulator similar to DntR, NahR, and LinR, which are involved in the degradation of aromatic compounds. The transcription of the genes encoding enzymes involved in such degradation is regulated and expression of these enzymes is enhanced by inducers, which are either an intermediate in the metabolic pathway or compounds to be degraded. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytra
Probab=99.96 E-value=4.6e-28 Score=186.96 Aligned_cols=196 Identities=17% Similarity=0.176 Sum_probs=175.1
Q ss_pred cEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccCCCCCceeeccccceEEEEec
Q psy3760 94 NLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLISIPCYQWEYVIIVP 173 (306)
Q Consensus 94 ~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~~~~~~~~~l~~~~~~~v~~ 173 (306)
.++||++++++..++++++..|.++||++++++....++++.+.+.+|++|++|.... ...+++.+.++++++++++++
T Consensus 1 ~l~I~~~~~~~~~~l~~~l~~f~~~~P~v~i~i~~~~~~~~~~~l~~~~~Di~i~~~~-~~~~~~~~~~l~~~~~~lv~~ 79 (198)
T cd08461 1 TLVIAATDYAQKAILPPLLAALRQEAPGVRVAIRDLESDNLEAQLERGEVDLALTTPE-YAPDGLRSRPLFEERYVCVTR 79 (198)
T ss_pred CEEEEechHHHHHHhHHHHHHHHHHCCCcEEEEeeCCcccHHHHHhcCCCcEEEecCc-cCCccceeeeeecCcEEEEEc
Confidence 4899999999999999999999999999999999988888999999999999998643 456789999999999999999
Q ss_pred CCCCCCCCCCcChhhhcCCCeEeecC-CCCcHHHHHHHHHhCCCceeEEEEecCHHHHHHHHHhccceeeeecceecccc
Q psy3760 174 LDHPLLLLNSISLKEISNYPLITYDL-SFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMGIGIIASIAFDSNR 252 (306)
Q Consensus 174 ~~~~l~~~~~i~~~dl~~~~~i~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~~~p~~~~~~~~ 252 (306)
++||+.. ..+++++|.++|++.... +...+..+.+++...++.++..+++++..++++++.+|.|++++|...+...
T Consensus 80 ~~~p~~~-~~~~~~~L~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~Gi~~lp~~~~~~~- 157 (198)
T cd08461 80 RGHPLLQ-GPLSLDQFCALDHIVVSPSGGGFAGSTDEALAALGLTRNVVLSVPSFLVVPEILAATDMVAFVPSRLVPNL- 157 (198)
T ss_pred CCChhhc-CCCCHHHHhhCCcEEEecCCCCCCCHHHHHHHHcCCCCcEEEEcCchhhHHHHHhcCCeEEEchHHHHHhh-
Confidence 9999887 678999999999998765 4556677889999999988889999999999999999999999999887653
Q ss_pred cCCceeeecCCCCccceEEEEEeCCccccHHHHHHHHHHhH
Q psy3760 253 DKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLLSP 293 (306)
Q Consensus 253 ~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~ 293 (306)
++++.++++.......++++|++++..++.+++|++.+++
T Consensus 158 -~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 197 (198)
T cd08461 158 -EGLQEVELPLEPPGFDVVMAWHERTHRDPAHRWLRELLAA 197 (198)
T ss_pred -cCceeecCCCCCCCccEEEecChhhcCCHHHHHHHHHHhh
Confidence 6788888876556679999999998899999999998876
No 80
>cd08468 PBP2_Pa0477 The C-terminal substrate biniding domain of an uncharacterized LysR-like transcriptional regulator Pa0477 related to DntR, contains the type 2 periplasmic binding fold. LysR-type transcriptional regulator Pa0477 is related to DntR, which controls genes encoding enzymes for oxidative degradation of the nitro-aromatic compound 2,4-dinitrotoluene. The transcription of the genes encoding enzymes involved in such degradation is regulated and expression of these enzymes is enhanced by inducers, which are either an intermediate in the metabolic pathway or compounds to be degraded. The topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their spec
Probab=99.96 E-value=1.4e-27 Score=185.11 Aligned_cols=198 Identities=16% Similarity=0.091 Sum_probs=177.6
Q ss_pred cEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccC--CCCCceeeccccceEEEE
Q psy3760 94 NLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILS--PSDKLISIPCYQWEYVII 171 (306)
Q Consensus 94 ~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~--~~~~~~~~~l~~~~~~~v 171 (306)
+++||++++++..++++++..|.+.||++++++....+.++.+.|.+|++|++|+..+.. ..+++...++++++++++
T Consensus 1 ~~~Ig~~~~~~~~~l~~~l~~~~~~~P~v~i~~~~~~~~~~~~~l~~g~~Dl~i~~~~~~~~~~~~~~~~~l~~~~~~~~ 80 (202)
T cd08468 1 RFRFAVTDYTALAVMPRLMARLEELAPSVRLNLVHAEQKLPLDALLAGEIDFALGYSHDDGAEPRLIEERDWWEDTYVVI 80 (202)
T ss_pred CEEEEechHHHHHHhHHHHHHHHhhCCCCEEEEEECChHhHHHHHHCCCccEEEecccccccCCCCEEEEEEecCcEEEE
Confidence 489999999999999999999999999999999999999999999999999999864422 157899999999999999
Q ss_pred ecCCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCceeEEEEecCHHHHHHHHHhccceeeeecceeccc
Q psy3760 172 VPLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMGIGIIASIAFDSN 251 (306)
Q Consensus 172 ~~~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~~~p~~~~~~~ 251 (306)
++++||++. .++++||.++|++....+...+..+.++++..+..+++.+++++..++..++.+|.|++++|.+++...
T Consensus 81 ~~~~hpl~~--~~~~~~L~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~~~p~~~~~~~ 158 (202)
T cd08468 81 ASRDHPRLS--RLTLDAFLAERHLVVTPWNEDRGVVDQVLEKQGLEREIALQLPNVLNAPFIVASSDLLMTLPRQAARAL 158 (202)
T ss_pred EeCCCCCcC--CCCHHHHhhCCCeEEecCCCCCchHHHHHHHcCCCceEEEEcChhHhHHHHHhcCCeeeecHHHHHHHh
Confidence 999999976 799999999999999876666677888999999999999999999999999999999999999887665
Q ss_pred -ccCCceeeecCCCCccceEEEEEeCCccccHHHHHHHHHHhH
Q psy3760 252 -RDKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLLSP 293 (306)
Q Consensus 252 -~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~ 293 (306)
..++++.++++...+..+++++|++++..+++.++|++.+++
T Consensus 159 ~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~ 201 (202)
T cd08468 159 AEALPLELFDLPFDMPPYRLKLYSHRQHENSAANQWLIEQLDG 201 (202)
T ss_pred hhcCCcEEecCCCCCCceeEEeeEeccccCCHHHHHHHHHHhh
Confidence 556788888886666789999999999999999999998875
No 81
>cd08446 PBP2_Chlorocatechol The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in the chlorocatechol catabolism, contains the type 2 periplasmic binding fold. This CD includes the substrate binding domain of LysR-type regulators CbnR, ClcR and TfdR, which are involved in the regulation of chlorocatechol breakdown. The chlorocatechol-degradative pathway is often found in bacteria that can use chlorinated aromatic compounds as carbon and energy sources. CbnR is found in the 3-chlorobenzoate degradative bacterium Ralstonia eutropha NH9 and forms a tetramer. CbnR activates the expression of the cbnABCD genes, which are responsible for the degradation of chlorocatechol converted from 3-chlorobenzoate and are transcribed divergently from cbnR. In soil bacterium Pseudomonas putida, the 3-chlorocatechol-degradative pathway is encoded by clcABD operon, which requires the divergently transcribed clcR for activation. TfdR is involved in the activation of tf
Probab=99.96 E-value=2.5e-27 Score=182.88 Aligned_cols=195 Identities=17% Similarity=0.182 Sum_probs=170.6
Q ss_pred CcEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccCCCCCceeeccccceEEEEe
Q psy3760 93 GNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLISIPCYQWEYVIIV 172 (306)
Q Consensus 93 ~~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~~~~~~~~~l~~~~~~~v~ 172 (306)
|.++||++++++..++++++..|.++||++++++....+.++.+.|.+|++|++|+... ...+++...+++++++++++
T Consensus 1 g~l~ig~~~~~~~~~l~~~i~~~~~~~P~v~l~i~~~~~~~~~~~l~~~~~Dl~i~~~~-~~~~~~~~~~l~~~~~~~v~ 79 (198)
T cd08446 1 GELDVGYFGSAILDTVPRLLRAFLTARPDVTVSLHNMTKDEQIEALRAGRIHIGFGRFY-PVEPDIAVENVAQERLYLAV 79 (198)
T ss_pred CeEEEEechHHHHHHHHHHHHHHHHHCCCeEEEEeeCCHHHHHHHHHCCCccEEEEecC-CCCCCceeEEeeeccEEEEE
Confidence 57999999999999999999999999999999999988888999999999999998644 45678999999999999999
Q ss_pred cCCCCCCCCCCcChhhhcCCCeEeecCCC--CcHHHHHHHHHhCCCceeEEEEecCHHHHHHHHHhccceeeeecceecc
Q psy3760 173 PLDHPLLLLNSISLKEISNYPLITYDLSF--SGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMGIGIIASIAFDS 250 (306)
Q Consensus 173 ~~~~~l~~~~~i~~~dl~~~~~i~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~~~p~~~~~~ 250 (306)
+++||++.+..++++||.++|++.+..+. ..++.+..++...+..+++.+++++..++.+++.+|.|++++|.+.+..
T Consensus 80 ~~~~pl~~~~~~~~~~l~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~~~p~~~~~~ 159 (198)
T cd08446 80 PKSHPLAARPAVSLADLRNEPLILFPRGGRPSFADEVLGLFRRAGVEPRVAQEVEDVVAALALVAAGFGVCIVPESVAAL 159 (198)
T ss_pred eCCCCcccCCccCHHHHcCCCEEEeccccChHHHHHHHHHHHHCCCCCCcceecCCHHHHHHHHHcCCcEEEchhhhhcc
Confidence 99999987778999999999999976552 2455667788888988888899999999999999999999999988754
Q ss_pred cccCCceeeecCCCCccceEEEEEeCCccccHHHHHHHHH
Q psy3760 251 NRDKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKL 290 (306)
Q Consensus 251 ~~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~ 290 (306)
..+++..+|++.......++++|+++. .+++++.|+++
T Consensus 160 -~~~~l~~~~~~~~~~~~~~~l~~~~~~-~~~~~~~~~~~ 197 (198)
T cd08446 160 -RWPGVVFRPLADAEAKVPLSCIYRKDD-RSPILRAFLDV 197 (198)
T ss_pred -CCCCeEEEECCCCCcceeEEEEEcCCC-CCHHHHHHHhh
Confidence 245688888876555678999999888 79999999875
No 82
>cd08450 PBP2_HcaR The C-terminal substrate binding domain of LysR-type transcriptional regulator HcaR in involved in 3-phenylpropionic acid catabolism, contains the type2 periplasmic binding fold. HcaR, a member of the LysR family of transcriptional regulators, controls the expression of the hcA1, A2, B, C, and D operon, encoding for the 3-phenylpropionate dioxygenase complex and 3-phenylpropionate-2',3'-dihydrodiol dehydrogenase, that oxidizes 3-phenylpropionate to 3-(2,3-dihydroxyphenyl) propionate. Dioxygenases play an important role in protecting the cell against the toxic effects of dioxygen. The expression of hcaR is negatively auto-regulated, as for other members of the LysR family, and is strongly repressed in the presence of glucose. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, an
Probab=99.96 E-value=3.5e-27 Score=181.71 Aligned_cols=194 Identities=15% Similarity=0.124 Sum_probs=170.9
Q ss_pred cEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccCCCCCceeeccccceEEEEec
Q psy3760 94 NLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLISIPCYQWEYVIIVP 173 (306)
Q Consensus 94 ~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~~~~~~~~~l~~~~~~~v~~ 173 (306)
.++||++++++..++++++..|.++||++++++....+.++.+.|.+|++|++|+..+ ...+++...++++++++++++
T Consensus 1 ~l~Ig~~~~~~~~~l~~~l~~~~~~~P~i~l~i~~~~~~~~~~~l~~~~~Dl~i~~~~-~~~~~~~~~~l~~~~~~~~~~ 79 (196)
T cd08450 1 VLTIGFLPGAEVQWLPEVLPILREEHPDLDVELSSLFSPQLAEALMRGKLDVAFMRPE-IQSDGIDYQLLLKEPLIVVLP 79 (196)
T ss_pred CEEEEEehhhhhhhHHHHHHHHHhhCCCcEEEEEecChHHHHHHHhcCCccEEEEeCC-CCCCCcEEEEEEccceEEEec
Confidence 3899999999999999999999999999999999998889999999999999998654 446789999999999999999
Q ss_pred CCCCCCCCCCcChhhhcCCCeEeecCCCC-cHHHHHHHHHhCCCceeEEEEecCHHHHHHHHHhccceeeeecceecccc
Q psy3760 174 LDHPLLLLNSISLKEISNYPLITYDLSFS-GRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMGIGIIASIAFDSNR 252 (306)
Q Consensus 174 ~~~~l~~~~~i~~~dl~~~~~i~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~~~p~~~~~~~~ 252 (306)
++||++.+..++++||.++|++....+.. .++.+..++...|+.++..+++++..++..++.+|.|++++|...... .
T Consensus 80 ~~~pl~~~~~~~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~~~p~~~~~~-~ 158 (196)
T cd08450 80 ADHRLAGREKIPPQDLAGENFISPAPTAPVLQQVIENYAAQHNIQPNIIQEADNLLSAMSLVASTLGCALLPLYANNL-L 158 (196)
T ss_pred CCCCcccCceECHHHhCCCCeEeecCCCchHHHHHHHHHHHCCCCcEeeeeechHHHHHHHHhcCCcEEEeehhhhhc-c
Confidence 99999988889999999999999876644 466788899999999999999999999999999999999999986543 3
Q ss_pred cCCceeeecCCCCccceEEEEEeCCccccHHHHHHHHH
Q psy3760 253 DKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKL 290 (306)
Q Consensus 253 ~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~ 290 (306)
.+++..++++.......++++|+++. .++.++.|+++
T Consensus 159 ~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~ 195 (196)
T cd08450 159 PPSVVARPLSGETPTIDLVMGYNKAN-TSPLLKRFLSR 195 (196)
T ss_pred cCCeEEEEccCCCCceEEEEEEcCCC-CCHHHHHHHhc
Confidence 45688888876555679999998876 68999998864
No 83
>cd08457 PBP2_OccR The C-terminal substrate-domain of LysR-type transcriptional regulator, OccR, involved in the catabolism of octopine, contains the type 2 periplasmic binding fold. This CD includes the C-terminal substrate-domain of LysR-type transcriptional regulator OccR, which is involved in the catabolism of octopine. Opines are low molecular weight compounds found in plant crown gall tumors produced by the parasitic bacterium Agrobacterium. There are at least 30 different opines identified so far. Opines are utilized by tumor-colonizing bacteria as a source of carbon, nitrogen, and energy. In Agrobacterium tumefaciens, OccR protein activates the occQ operon of the Ti plasmid in response to octopine. This operon encodes proteins required for the uptake and catabolism of octopine, an arginine derivative. The occ operon also encodes the TraR protein, which is a quorum-sensing transcriptional regulator of the Ti plasmid tra regulon. This substrate-binding domain shows significant h
Probab=99.96 E-value=3.3e-27 Score=182.01 Aligned_cols=196 Identities=20% Similarity=0.220 Sum_probs=173.3
Q ss_pred cEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccCCCCCceeeccccceEEEEec
Q psy3760 94 NLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLISIPCYQWEYVIIVP 173 (306)
Q Consensus 94 ~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~~~~~~~~~l~~~~~~~v~~ 173 (306)
+++||++.+++..++++++..|.++||++++++....+.++.+.|.+|++|++|+..+ ...+++...++++++++++++
T Consensus 1 ~l~I~~~~~~~~~~l~~~l~~~~~~~P~i~l~~~~~~~~~~~~~l~~~~~Dl~i~~~~-~~~~~~~~~~l~~~~~~~~~~ 79 (196)
T cd08457 1 TLRIAAMPALANGFLPRFLAAFLRLRPNLHLSLMGLSSSQVLEAVASGRADLGIADGP-LEERQGFLIETRSLPAVVAVP 79 (196)
T ss_pred CEEEEeehhHhccccHHHHHHHHHHCCCeEEEEEecCcHHHHHHHHcCCccEEEeccC-CCCCCcEEEEeccCCeEEEee
Confidence 4899999999999999999999999999999999988889999999999999999654 446789999999999999999
Q ss_pred CCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCceeEEEEecCHHHHHHHHHhccceeeeecceeccccc
Q psy3760 174 LDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMGIGIIASIAFDSNRD 253 (306)
Q Consensus 174 ~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~~~p~~~~~~~~~ 253 (306)
++||++.+..++++||.++|+|.+..+...+..+.+++...++.+++.+++++..++.+++.+|.|++++|...+.....
T Consensus 80 ~~~~l~~~~~~~~~~l~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~Gi~~~p~~~~~~~~~ 159 (196)
T cd08457 80 MGHPLAQLDVVSPQDLAGERIITLENGYLFRMRVEVALGKIGVKRRPIIEVNLSHTALSLVREGLGIAIIDPATAIGLPL 159 (196)
T ss_pred CCCccccCCccCHHHhCCCceEecCCCccHHHHHHHHHHHcCCCCceEEEeccHHHHHHHHHcCCeEEEEChHHhhcccC
Confidence 99999988889999999999999887766677788899999999999999999999999999999999998766544334
Q ss_pred CCceeeecCCCCccceEEEEEeCCccccHHHHHHHHHH
Q psy3760 254 KNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLL 291 (306)
Q Consensus 254 ~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l 291 (306)
+++..++++. .....+|++|+++...++.++.|++++
T Consensus 160 ~~~~~~~~~~-~~~~~~~l~~~~~~~~~~~~~~~~~~~ 196 (196)
T cd08457 160 DGIVIRPFDT-FIDAGFLVVRAANGPPSTMVDRFIDEF 196 (196)
T ss_pred CCeEEEecCC-CCceeEEEEecCCCCCCHHHHHHHhhC
Confidence 5677888865 345789999999988999999999864
No 84
>cd08427 PBP2_LTTR_like_2 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator, contains the type 2 periplasmic binding fold. LysR-transcriptional regulators comprise the largest family of prokaryotic transcription factor. Homologs of some of LTTRs with similar domain organizations are also found in the archaea and eukaryotic organisms. The LTTRs are composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcriptional repressor undergoes a conformational change upon substrate binding which in turn changes the DNA binding affinity of the repressor. The genes controlled by the LTTRs have diverse functi
Probab=99.96 E-value=2.9e-27 Score=181.90 Aligned_cols=194 Identities=19% Similarity=0.244 Sum_probs=171.4
Q ss_pred cEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccCC-CCCceeeccccceEEEEe
Q psy3760 94 NLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSP-SDKLISIPCYQWEYVIIV 172 (306)
Q Consensus 94 ~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~-~~~~~~~~l~~~~~~~v~ 172 (306)
.++||++++++..++++++..|.+.||++++++....++++.+.+.+|++|++|+...... .+++.+.+++++++++++
T Consensus 1 ~l~Ig~~~~~~~~~l~~~l~~~~~~~P~i~l~~~~~~~~~~~~~l~~g~~Dl~i~~~~~~~~~~~~~~~~l~~~~~~~v~ 80 (195)
T cd08427 1 RLRLGAIATVLTGLLPRALARLRRRHPDLEVHIVPGLSAELLARVDAGELDAAIVVEPPFPLPKDLVWTPLVREPLVLIA 80 (195)
T ss_pred CEEEEeeHHHHHHHhHHHHHHHHHHCCCceEEEEeCCcHHHHHHHHCCCCCEEEEcCCCCccccCceEEEcccCcEEEEE
Confidence 4899999999999999999999999999999999998999999999999999999644333 578999999999999999
Q ss_pred cCCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCceeEEEEecCHHHHHHHHHhccceeeeecceecccc
Q psy3760 173 PLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMGIGIIASIAFDSNR 252 (306)
Q Consensus 173 ~~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~~~p~~~~~~~~ 252 (306)
+++||++. ..++|.++|++.+..+...+..+.+++...++.++..+++++...+.+++.+|.|++++|.+.+....
T Consensus 81 ~~~~p~~~----~~~~l~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gia~~p~~~~~~~~ 156 (195)
T cd08427 81 PAELAGDD----PRELLATQPFIRYDRSAWGGRLVDRFLRRQGIRVREVMELDSLEAIAAMVAQGLGVAIVPDIAVPLPA 156 (195)
T ss_pred CCCCCcch----HHHHhcCCCeEEecCCchHHHHHHHHHHHcCCCCCeEEEeccHHHHHHHHHhCCcEEEccHHHHhhhc
Confidence 99999753 35779999999987766667778889999999999999999999999999999999999998876335
Q ss_pred cCCceeeecCCCCccceEEEEEeCCccccHHHHHHHHHH
Q psy3760 253 DKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLL 291 (306)
Q Consensus 253 ~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l 291 (306)
.+++..++++......+++++|+++...+|.++.|+++|
T Consensus 157 ~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~ 195 (195)
T cd08427 157 GPRVRVLPLGDPAFSRRVGLLWRRSSPRSRLIQALLEAL 195 (195)
T ss_pred cCceEEEECCCCCceEEEEEEEeCCccCCHHHHHHHhhC
Confidence 678999998765567899999999988999999999864
No 85
>cd08445 PBP2_BenM_CatM_CatR The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in benzoate catabolism; contains the type 2 periplasmic binding fold. This CD includes the C-terminal of LysR-type transcription regulators, BenM, CatM, and CatR, which are involved in the benzoate catabolism. The BenM and CatM are paralogs with overlapping functions. BenM responds synergistically to two effectors, benzoate and cis,cis-muconate, to activate expression of the benABCDE operon which is involved in benzoate catabolism, while CatM responses only to muconate. BenM and CatM share high protein sequence identity and bind to the operator-promoter regions that have similar DNA sequences. In Pseudomonas species, phenolic compounds are converted by different enzymes to central intermediates, such as protocatechuate and catechols. Generally, unsubstituted compounds, such as benzoate, are metabolized by an ortho-cleavage pathway. The catBCA operon encodes three enzymes
Probab=99.96 E-value=4.9e-27 Score=182.09 Aligned_cols=198 Identities=18% Similarity=0.224 Sum_probs=172.1
Q ss_pred cEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccCCCCCceeeccccceEEEEec
Q psy3760 94 NLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLISIPCYQWEYVIIVP 173 (306)
Q Consensus 94 ~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~~~~~~~~~l~~~~~~~v~~ 173 (306)
.++||++++++..++++++..|.++||++++++....+.++.+.+.+|++|++|+..+ ...+++...++++++++++++
T Consensus 2 ~l~Ig~~~~~~~~~l~~~l~~~~~~~P~i~l~i~~~~~~~~~~~l~~~~~Dl~i~~~~-~~~~~~~~~~l~~~~~~~v~~ 80 (203)
T cd08445 2 TFSIGFVPSTLYGLLPELIRRFRQAAPDVEIELIEMTTVQQIEALKEGRIDVGFGRLR-IEDPAIRRIVLREEPLVVALP 80 (203)
T ss_pred eEEEEEehHHHHhHHHHHHHHHHHHCCCeEEEEEeCChHHHHHHHHcCCCcEEEecCC-CCCCCceeEEEEeccEEEEee
Confidence 6999999999999999999999999999999999998999999999999999998543 455789999999999999999
Q ss_pred CCCCCCCCC-CcChhhhcCCCeEeecCCC--CcHHHHHHHHHhCCCceeEEEEecCHHHHHHHHHhccceeeeecceecc
Q psy3760 174 LDHPLLLLN-SISLKEISNYPLITYDLSF--SGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMGIGIIASIAFDS 250 (306)
Q Consensus 174 ~~~~l~~~~-~i~~~dl~~~~~i~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~~~p~~~~~~ 250 (306)
++||++.+. +++++||.++|++.+..+. ..++.+..++...++.+++.+++++..++.+++.+|.|++++|.....
T Consensus 81 ~~hpl~~~~~~i~~~dL~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~~~p~~~~~- 159 (203)
T cd08445 81 AGHPLAQEKAPLTLAQLADEPLILYPASPRPSFADQVLSLFRDHGLRPRVIQEVRELQTALGLVAAGEGVTLVPASVQR- 159 (203)
T ss_pred CCCCCccCCCCcCHHHhcCCCEEecCcccChhHHHHHHHHHHHcCCCCceecccCCHHHHHHHHHcCCCeEEehHHhhc-
Confidence 999998766 7999999999999976542 234566778888898888899999999999999999999999998754
Q ss_pred cccCCceeeecCCCCccceEEEEEeCCccccHHHHHHHHHHhHH
Q psy3760 251 NRDKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLLSPK 294 (306)
Q Consensus 251 ~~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~ 294 (306)
...++++.+++++......++++|+++. .+|.+++|++.+++.
T Consensus 160 ~~~~~l~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~l~~~ 202 (203)
T cd08445 160 LRRDDVVYRPLLDPDATSPIIMSVRAGD-ESPYIALILQLIREL 202 (203)
T ss_pred cCCCCeEEEECCCCCCceEEEEEEcCCC-CChHHHHHHHHHHhh
Confidence 2466788889887555678899888775 489999999998763
No 86
>cd08430 PBP2_IlvY The C-terminal substrate binding of LysR-type transcriptional regulator IlvY, which activates the expression of ilvC gene that encoding acetohydroxy acid isomeroreductase for the biosynthesis of branched amino acids; contains the type 2 periplasmic binding fold. In Escherichia coli, IlvY is required for the regulation of ilvC gene expression that encodes acetohydroxy acid isomeroreductase (AHIR), a key enzyme in the biosynthesis of branched-chain amino acids (isoleucine, valine, and leucine). The ilvGMEDA operon genes encode remaining enzyme activities required for the biosynthesis of these amino acids. Activation of ilvC transcription by IlvY requires the additional binding of a co-inducer molecule (either alpha-acetolactate or alpha-acetohydoxybutyrate, the substrates for AHIR) to a preformed complex of IlvY protein-DNA. Like many other LysR-family members, IlvY negatively auto-regulates the transcription of its own divergently transcribed ilvY gene in an inducer-i
Probab=99.96 E-value=2e-27 Score=183.49 Aligned_cols=196 Identities=21% Similarity=0.306 Sum_probs=172.2
Q ss_pred cEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccCCCCCceeeccccceEEEEec
Q psy3760 94 NLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLISIPCYQWEYVIIVP 173 (306)
Q Consensus 94 ~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~~~~~~~~~l~~~~~~~v~~ 173 (306)
.|+||++.+++..++++++..|.++||++++++....+.++.+.+.+|++|++|+..+....+++.+.++++++++++++
T Consensus 1 ~l~ig~~~~~~~~~l~~~l~~~~~~~P~v~l~~~~~~~~~~~~~l~~g~~Dl~i~~~~~~~~~~l~~~~l~~~~~~~~~~ 80 (199)
T cd08430 1 ELSLYCSVTASYSFLPPILERFRAQHPQVEIKLHTGDPADAIDKVLNGEADIAIAARPDKLPARLAFLPLATSPLVFIAP 80 (199)
T ss_pred CeEEEeccccceeeccHHHHHHHHHCCCceEEEEeCCHHHHHHHHHCCCCCEEEEecCCCCCcccEEEeeccceEEEEEe
Confidence 48999999999999999999999999999999999989899999999999999986443334679999999999999999
Q ss_pred CCCCCCCC-CCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCceeEEEEecCHHHHHHHHHhccceeeeecceeccc-
Q psy3760 174 LDHPLLLL-NSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMGIGIIASIAFDSN- 251 (306)
Q Consensus 174 ~~~~l~~~-~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~~~p~~~~~~~- 251 (306)
++||++.+ ..++++||.++|++....+. .+..+..++...+..+++.+++++..++.+++.+|.|++++|..++...
T Consensus 81 ~~~~~~~~~~~~~~~~l~~~~~i~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gia~lp~~~~~~~~ 159 (199)
T cd08430 81 NIACAVTQQLSQGEIDWSRLPFILPERGL-ARERLDQWFRRRGIKPNIYAQVAGHEAIVSMVALGCGVGIVPELVLDNSP 159 (199)
T ss_pred CCchhhhhhccccccccccCCeEEccCCh-HHHHHHHHHHHcCCCCCeeEEEccHHHHHHHHHhCCeEEEccHHHhhhhh
Confidence 99998765 36789999999999877654 4667888999999989989999999999999999999999999888765
Q ss_pred ccCCceeeecCCCCccceEEEEEeCCccccHHHHHHHHH
Q psy3760 252 RDKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKL 290 (306)
Q Consensus 252 ~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~ 290 (306)
..++++.++++.......++++|+++...++.++.|++.
T Consensus 160 ~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~ 198 (199)
T cd08430 160 LKDKVRILEVQPELEPFEVGLCCLKKRLNEPLIKAFWQV 198 (199)
T ss_pred ccCcceEEEcCCCCCceEEEEEEccCcccChHHHHHHhh
Confidence 556799999875445679999999998889999999864
No 87
>cd08485 PBP2_ClcR The C-terminal substrate binding domain of LysR-type transcriptional regulator ClcR involved in the chlorocatechol catabolism, contains type 2 periplasmic binding fold. In soil bacterium Pseudomonas putida, the ortho-pathways of catechol and 3-chlorocatechol are central catabolic pathways that convert aromatic and chloroaromaric compounds to tricarboxylic acid (TCA) cycle intermediates. The 3-chlorocatechol-degradative pathway is encoded by clcABD operon, which requires the divergently transcribed clcR and an intermediate of the pathway, 2-chloromuconate, as an inducer for activation. The topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding th
Probab=99.96 E-value=6.6e-27 Score=180.72 Aligned_cols=196 Identities=14% Similarity=0.121 Sum_probs=171.3
Q ss_pred CcEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccCCCCCceeeccccceEEEEe
Q psy3760 93 GNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLISIPCYQWEYVIIV 172 (306)
Q Consensus 93 ~~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~~~~~~~~~l~~~~~~~v~ 172 (306)
|.|+||++.+++..++++++..|.+.||++++++....++++.+.|.+|++|++|+... ...+++...++.++++++++
T Consensus 1 g~l~ig~~~~~~~~~l~~~l~~~~~~~P~i~l~~~~~~~~~~~~~l~~~~~D~~i~~~~-~~~~~l~~~~l~~~~~~~~~ 79 (198)
T cd08485 1 GELRVAYFGTVVLHTLPLLLRQLLSVAPSATVSLTQMSKNRQIEALDAGTIDIGFGRFY-PYQEGVVVRNVTNERLFLGA 79 (198)
T ss_pred CeEEEEEeccchhHHHHHHHHHHHHhCCCcEEEEEECCHHHHHHHHHcCCccEEEecCC-CCCCCeEEEEeeccceEEEe
Confidence 57999999999999999999999999999999999998999999999999999998643 45678999999999999999
Q ss_pred cCCCCCCCCCCcChhhhcCCCeEeecCCC--CcHHHHHHHHHhCCCceeEEEEecCHHHHHHHHHhccceeeeecceecc
Q psy3760 173 PLDHPLLLLNSISLKEISNYPLITYDLSF--SGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMGIGIIASIAFDS 250 (306)
Q Consensus 173 ~~~~~l~~~~~i~~~dl~~~~~i~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~~~p~~~~~~ 250 (306)
+++||++....++++||.++|++.++.+. ..++.+.+++...++.++..+++++..++.+++.+|.|++++|..++..
T Consensus 80 ~~~~~~~~~~~v~~~~L~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~~~p~~~~~~ 159 (198)
T cd08485 80 QKSRARSFGEQVHCSALRNEPLILFPREGRPSFADEVIGVFKNARVEPKVVAIVEDVNAAMALALAGVGVTIVPETVAMI 159 (198)
T ss_pred CCCCccccCCCcCHHHHhcCCeEecCCCCCccHHHHHHHHHHHcCCCcceEEEcCcHHHHHHHHHcCCceEECcchhhcc
Confidence 99999876778999999999999986543 3466777889989999999999999999999999999999999987653
Q ss_pred cccCCceeeecCCCCccceEEEEEeCCccccHHHHHHHHHH
Q psy3760 251 NRDKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLL 291 (306)
Q Consensus 251 ~~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l 291 (306)
. .+++..+++.+.....+++++|+++. .++.++.|++++
T Consensus 160 ~-~~~~~~~~l~~~~~~~~~~~~~~~~~-~~~~~~~f~~~~ 198 (198)
T cd08485 160 S-WPDFGFTELVGSKATVPVSCIYRHDH-IAPILKTFLNLL 198 (198)
T ss_pred c-cCCeEEEeCCCCCCceeEEEEecccc-cChHHHHHHhhC
Confidence 2 34678888876556789999998865 699999999864
No 88
>cd08416 PBP2_MdcR The C-terminal substrate-binding domian of LysR-type transcriptional regulator MdcR, which involved in the malonate catabolism contains the type 2 periplasmic binding fold. This family includes the C-terminal substrate binding domain of LysR-type transcriptional regulator (LTTR) MdcR that controls the expression of the malonate decarboxylase (mdc) genes. Like other members of the LTTRs, MdcR is a positive regulatory protein for its target promoter and composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins (PBP2). The PBP2 are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these dom
Probab=99.96 E-value=7.2e-27 Score=180.37 Aligned_cols=197 Identities=14% Similarity=0.252 Sum_probs=171.6
Q ss_pred cEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEcccc-CCCCCceeeccccceEEEEe
Q psy3760 94 NLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEIL-SPSDKLISIPCYQWEYVIIV 172 (306)
Q Consensus 94 ~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~-~~~~~~~~~~l~~~~~~~v~ 172 (306)
.++||+++++...++++++..|.++||++++++....+.++.+.+.+|++|++|...+. ...+++...+++++++++++
T Consensus 1 ~l~ig~~~~~~~~~l~~~l~~~~~~~P~i~l~i~~~~~~~~~~~l~~~~~Dl~i~~~~~~~~~~~l~~~~l~~~~~~~v~ 80 (199)
T cd08416 1 RLRLGSLYSLTVNTVPRIIMGLKLRRPELDIELTLGSNKDLLKKLKDGELDAILVATPEGLNDPDFEVVPLFEDDIFLAV 80 (199)
T ss_pred CEEEEechHHHHhhhHHHHHHHHHhCCCeEEEEEEcCcHHHHHHHhCCCCCEEEEecCCcCCCCCeEEEEeecceEEEEE
Confidence 48999999999999999999999999999999999888889999999999999986542 24578999999999999999
Q ss_pred cCCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCceeEEEEecCHHHHHHHHHhccceeeeecceecccc
Q psy3760 173 PLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMGIGIIASIAFDSNR 252 (306)
Q Consensus 173 ~~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~~~p~~~~~~~~ 252 (306)
+++||++.+..++++||.+++++.+..+...+..+.+++...++.++..+++++...+.+++.+|.|++++|.+.+...
T Consensus 81 ~~~hp~~~~~~~~~~~L~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~~~p~~~~~~~- 159 (199)
T cd08416 81 PATSPLAASSEIDLRDLKDEKFVTLSEGFATYRGFDEAFEIAGFEPNVVMRVNDIFSLMSMVSGGVGYALLPGRIADVY- 159 (199)
T ss_pred CCCCcccccCccCHHHhcCCceEEecCCCcHHHHHHHHHHHcCCCCCceEEeCCHHHHHHHHHcCCcEEEechhhhhhc-
Confidence 9999998877899999999999998776656667788888899988899999999999999999999999999887543
Q ss_pred cCCceeeecCCC-CccceEEEEEeCCccccHHHHHHHHHH
Q psy3760 253 DKNLRSISASHL-FGTTISRVIIKQGTYLRSYVYSFIKLL 291 (306)
Q Consensus 253 ~~~l~~~~~~~~-~~~~~~~l~~~~~~~~~~~~~~~~~~l 291 (306)
.+.+..+++... ....+++++|++++..+|.++.|++++
T Consensus 160 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 199 (199)
T cd08416 160 EDKVQLIPLAEPYQIRQTIGLVFLRSRERDPNLLALAAEC 199 (199)
T ss_pred cCCeEEEECCcccCCceeEEEEEcCCCcCCHHHHHHHhhC
Confidence 345666666542 235689999999999999999999864
No 89
>cd08448 PBP2_LTTR_aromatics_like_2 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator similar to regulators involved in the catabolism of aromatic compounds, contains type 2 periplasmic binding fold. This CD represents the substrate binding domain of an uncharacterized LysR-type regulator similar to CbnR which is involved in the regulation of chlorocatechol breakdown. The transcription of the genes encoding enzymes involved in such degradation is regulated and expression of these enzymes is enhanced by inducers, which are either an intermediate in the metabolic pathway or compounds to be degraded. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Ve
Probab=99.96 E-value=7.3e-27 Score=179.90 Aligned_cols=195 Identities=16% Similarity=0.201 Sum_probs=170.9
Q ss_pred cEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccCCCCCceeeccccceEEEEec
Q psy3760 94 NLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLISIPCYQWEYVIIVP 173 (306)
Q Consensus 94 ~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~~~~~~~~~l~~~~~~~v~~ 173 (306)
+++||++++++..++++++..|.++||++++++....+.++.+.+.+|++|++|.... ...+++...++++++++++++
T Consensus 1 ~l~i~~~~~~~~~~l~~~l~~~~~~~P~i~i~i~~~~~~~~~~~l~~~~~Di~i~~~~-~~~~~~~~~~l~~~~~~~~~~ 79 (197)
T cd08448 1 RLRIGFVGSMLYRGLPRILRAFRAEYPGIEVALHEMSSAEQIEALLRGELDLGFVHSR-RLPAGLSARLLHREPFVCCLP 79 (197)
T ss_pred CeEEEEchhHHHHHHHHHHHHHHHHCCCCeEEEEeCCHHHHHHHHHcCCcceEEEeCC-CCCcCceEEEEecCcEEEEee
Confidence 4899999999999999999999999999999999998999999999999999998644 556889999999999999999
Q ss_pred CCCCCCCCCCcChhhhcCCCeEeecCCC--CcHHHHHHHHHhCCCceeEEEEecCHHHHHHHHHhccceeeeecceeccc
Q psy3760 174 LDHPLLLLNSISLKEISNYPLITYDLSF--SGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMGIGIIASIAFDSN 251 (306)
Q Consensus 174 ~~~~l~~~~~i~~~dl~~~~~i~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~~~p~~~~~~~ 251 (306)
++||++.++.++++||.++|++.+..+. ..++.+..++...+..++..+++++..++++++.+|.|++++|...+...
T Consensus 80 ~~hpl~~~~~~~~~~L~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~~~p~~~~~~~ 159 (197)
T cd08448 80 AGHPLAARRRIDLRELAGEPFVLFSREVSPDYYDQIIALCMDAGFHPKIRHEVRHWLTVVALVAAGMGVALVPRSLARAG 159 (197)
T ss_pred CCCCCcCCCCcCHHHhCCCcEEeeCcccChHHHHHHHHHHHHcCCceeeeeccccHHHHHHHHHcCCceEecchhhhhhc
Confidence 9999998888999999999999976543 24566778888888888888999999999999999999999999887653
Q ss_pred ccCCceeeecCCCCccceEEEEEeCCccccHHHHHHHHHH
Q psy3760 252 RDKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLL 291 (306)
Q Consensus 252 ~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l 291 (306)
..+++.+++++......++++|+++.. ++.++.|++++
T Consensus 160 -~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~ 197 (197)
T cd08448 160 -LAGVRFLPLKGATQRSELYAAWKASAP-NPALQAFLAAL 197 (197)
T ss_pred -cCceEEEECCCCCccEEEEEEEcCCCC-CHHHHHHHHhC
Confidence 345777777764456789999998877 99999998864
No 90
>cd08469 PBP2_PnbR The C-terminal substrate binding domain of LysR-type transcriptional regulator PnbR, which is involved in regulating the pnb genes encoding enzymes for 4-nitrobenzoate catabolism, contains the type 2 periplasmic binding fold. PnbR is the regulator of one or both of the two pnb genes that encoding enzymes for 4-nitrobenzoate catabolism. In Pseudomonas putida strain, pnbA encodes a 4-nitrobenzoate reductase, which is responsible for catalyzing the direct reduction of 4-nitrobenzoate to 4-hydroxylaminobenzoate, and pnbB encodes a 4-hydroxylaminobenzoate lyase, which catalyzes the conversion of 4-hydroxylaminobenzoate to 3, 4-dihydroxybenzoic acid and ammonium. The topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft bet
Probab=99.96 E-value=2.1e-27 Score=186.72 Aligned_cols=198 Identities=13% Similarity=0.157 Sum_probs=175.2
Q ss_pred cEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccCCCCCceeeccccceEEEEec
Q psy3760 94 NLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLISIPCYQWEYVIIVP 173 (306)
Q Consensus 94 ~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~~~~~~~~~l~~~~~~~v~~ 173 (306)
.++||+.++++..++++++..|.++||++++++...++.++.+.|.+|++|++|+..+ ...+++...++++++++++++
T Consensus 1 ~~~Ig~~~~~~~~~l~~~l~~f~~~~P~v~l~i~~~~~~~~~~~l~~g~~Di~i~~~~-~~~~~l~~~~l~~~~~~~v~~ 79 (221)
T cd08469 1 SFVIAANDYVTAVLLPALVRRLETEAPGIDLRIRPVTRLDLAEQLDLGRIDLVIGIFE-QIPPRFRRRTLFDEDEVWVMR 79 (221)
T ss_pred CEEEEEChHHHHHHHHHHHHHHHHHCCCcEEEEeeCChhhHHHHHHCCCccEEEecCC-CCCccceeeeeeccceEEEEe
Confidence 4899999999999999999999999999999999998889999999999999998654 456789999999999999999
Q ss_pred CCCCCCCCCCcChhhhcCCCeEeecCCCC---------------------cHHHHHHHHHhCCCceeEEEEecCHHHHHH
Q psy3760 174 LDHPLLLLNSISLKEISNYPLITYDLSFS---------------------GRIKLDREFSLQKLTPYIVLETINSDIIKT 232 (306)
Q Consensus 174 ~~~~l~~~~~i~~~dl~~~~~i~~~~~~~---------------------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 232 (306)
++||+.. ..++++||.++|++....+.. .++.+..+++..+..+++.+++++..++..
T Consensus 80 ~~~pl~~-~~~~~~dL~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 158 (221)
T cd08469 80 KDHPAAR-GALTIETLARYPHIVVSLGGEEEGAVSGFISERGLARQTEMFDRRALEEAFRESGLVPRVAVTVPHALAVPP 158 (221)
T ss_pred CCCcCCC-CCCCHHHHHhCCeEEEecCCCccchHHHHHHHcCCCcccccccchhhhhhhhhccccceEEEEcCcHHHHHH
Confidence 9999876 679999999999999865432 134466778888999999999999999999
Q ss_pred HHHhccceeeeecceeccc-ccCCceeeecCCCCccceEEEEEeCCccccHHHHHHHHHHhH
Q psy3760 233 YVELRMGIGIIASIAFDSN-RDKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLLSP 293 (306)
Q Consensus 233 ~v~~g~gi~~~p~~~~~~~-~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~ 293 (306)
++.+|.|++++|.+.+... ..++++.++++.......++++|+++...++.+++|++.+++
T Consensus 159 ~v~~g~gi~~~p~~~~~~~~~~~~l~~~~~~~~~~~~~~~lv~~~~~~~~~~~~~l~~~~~~ 220 (221)
T cd08469 159 LLADSDMLALLPRSLARAFAERGGLVMKEPPYPPPPVQIRAVWHERHDNDPAVAWLREMIRD 220 (221)
T ss_pred HHhCCchhhhHHHHHHHHHhhcCCcEEeCCCCCCCCceEEEEecccccCChHHHHHHHHHhh
Confidence 9999999999999888665 567899999876556789999999999999999999998875
No 91
>cd08429 PBP2_NhaR The C-terminal substrate binding domain of LysR-type transcriptional activator of the nhaA gene, encoding Na+/H+ antiporter, contains the type 2 periplasmic binding fold. NhaR is a positive regulator of the LysR family and is known to be an activator of the nhaA gene encoding a Na(+)/H(+) antiporter. In Escherichia coli, NhaA is the vital antiporter that protects against high sodium stress, and it is essential for growth in high sodium levels, while NhaB becomes essential only if NhaA is not available. The nhaA gene of nhaAR operon is induced by monovalent cations. The nhaR of the operon activates nhaAR, as well as the osmC transcription which is induced at elevated osmolarity. OsmC is transcribed from the two overlapping promoters (osmCp1 and osmP2) and that NhaR is shown to activate only the expression of osmCp1. NhaR also activates the transcription of the pgaABCD operon which is required for production of the biofilm adhesion, poly-beta-1,6-N-acetyl-d-glucosamine
Probab=99.96 E-value=3.5e-27 Score=183.11 Aligned_cols=198 Identities=14% Similarity=0.076 Sum_probs=172.5
Q ss_pred EEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccCC--CCCceeeccccceEEEEe
Q psy3760 95 LTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSP--SDKLISIPCYQWEYVIIV 172 (306)
Q Consensus 95 l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~--~~~~~~~~l~~~~~~~v~ 172 (306)
|+||+.++++..++++++..|.+.||++++++...++.++.+.|.+|++|++|...+... ..++...+++++++++++
T Consensus 2 l~ig~~~~~~~~~l~~~l~~f~~~~P~v~l~i~~~~~~~~~~~L~~~~~D~~i~~~~~~~~~~~~~~~~~l~~~~~~~~~ 81 (204)
T cd08429 2 FRVGVADAVPKSIAYRLLEPAMDLHEPIRLVCREGKLEQLLADLALHRLDMVLADRPMPSSLDVKGYSHRLGECGVSFFA 81 (204)
T ss_pred eeEEcchhhhHHHHHHHHHHHHHhCCCcEEEEEeCCHHHHHHHHHcCCccEEEecCCCccccchheeeccccccceEEEe
Confidence 799999999999999999999999999999999999999999999999999998644222 136778999999999999
Q ss_pred cCCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCceeEEEEecCHHHHHHHHHhccceeeeecceeccc-
Q psy3760 173 PLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMGIGIIASIAFDSN- 251 (306)
Q Consensus 173 ~~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~~~p~~~~~~~- 251 (306)
++.|+... .+++++||.++|+|.+..+...+..+.++++..|..++..+++++..++.+++.+|.|++++|...+...
T Consensus 82 ~~~~~~~~-~~~~~~dL~~~~~i~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~v~~G~Gv~~lp~~~~~~~~ 160 (204)
T cd08429 82 APPLAKRL-EKPFPASLDEAPLLLPGEDSALRRKLLQWFERQGLRPQIVGEFDDSALMKAFGQAGAGIFAAPTVIADEVA 160 (204)
T ss_pred cCCccccc-ccCCHhHhccCCeeecCCCCcHHHHHHHHHHHcCCCcceEEEeCCHHHHHHHHHcCCCeEeccHHHHHHHH
Confidence 98876432 4579999999999998887778888999999999999999999999999999999999999999887653
Q ss_pred ccCCceeeecCCCCccceEEEEEeCCccccHHHHHHHHHHhHH
Q psy3760 252 RDKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLLSPK 294 (306)
Q Consensus 252 ~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~ 294 (306)
..+.++.++... ...+.+|++|+++...++.++.|++.+++.
T Consensus 161 ~~~~l~~~~~~~-~~~~~~~l~~~~~~~~~~~~~~f~~~~~~~ 202 (204)
T cd08429 161 RQYGVVEIGRTD-EVVEEFYAISVERRITHPAVVAISEAARSA 202 (204)
T ss_pred hcCCeEeeccCc-cceeeEEEEeecccCCCHHHHHHHHhhccc
Confidence 456677765433 356789999999999999999999999875
No 92
>cd08451 PBP2_BudR The C-terminal substrate binding domain of LysR-type transcrptional regulator BudR, which is responsible for activation of the expression of the butanediol operon genes; contains the type 2 periplasmic binding fold. This CD represents the substrate binding domain of BudR regulator, which is responsible for induction of the butanediol formation pathway under fermentative growth conditions. Three enzymes are involved in the production of 1 mol of 2,3 butanediol from the condensation of 2 mol of pyruvate with acetolactate and acetoin as intermediates: acetolactate synthetase, acetolactate decarboxylase, and acetoin reductase. In Klebsiella terrigena, BudR regulates the expression of the budABC operon genes, encoding these three enzymes of the butanediol pathway. In many bacterial species, the use of this pathway can prevent intracellular acidification by diverting metabolism from acid production to the formation of neutral compounds (acetoin and butanediol). This substra
Probab=99.95 E-value=1.2e-26 Score=179.00 Aligned_cols=196 Identities=21% Similarity=0.255 Sum_probs=169.1
Q ss_pred cEEEEecccchh-hhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccCCCCCceeeccccceEEEEe
Q psy3760 94 NLTIATTHTQAR-YALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLISIPCYQWEYVIIV 172 (306)
Q Consensus 94 ~l~I~~~~~~~~-~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~~~~~~~~~l~~~~~~~v~ 172 (306)
+|+||++.+++. .++++++..|.+.||++.+++....+.++.+.+.+|++|++|+.......+++...+++++++++++
T Consensus 1 ~l~Ig~~~~~~~~~~l~~~l~~~~~~~P~i~l~i~~~~~~~~~~~l~~g~~Dl~i~~~~~~~~~~~~~~~l~~~~~~~v~ 80 (199)
T cd08451 1 RLRVGFTSSAAFHPLVPGLIRRFREAYPDVELTLEEANTAELLEALREGRLDAAFVRPPVARSDGLVLELLLEEPMLVAL 80 (199)
T ss_pred CeeEEeeeeeeeecccHHHHHHHHHHCCCcEEEEecCChHHHHHHHHCCCccEEEEecCCCCCCceeEEEeecccEEEEe
Confidence 489999998764 6999999999999999999999999989999999999999998644333678999999999999999
Q ss_pred cCCCCCCCCCCcChhhhcCCCeEeecCCC--CcHHHHHHHHHhCCCceeEEEEecCHHHHHHHHHhccceeeeecceecc
Q psy3760 173 PLDHPLLLLNSISLKEISNYPLITYDLSF--SGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMGIGIIASIAFDS 250 (306)
Q Consensus 173 ~~~~~l~~~~~i~~~dl~~~~~i~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~~~p~~~~~~ 250 (306)
+++||++.++.++++||.++|++....+. ..+..+.+++...+..+++.+++++..++.+++.+|.|++++|..++..
T Consensus 81 ~~~~~l~~~~~~~~~dL~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~~~p~~~~~~ 160 (199)
T cd08451 81 PAGHPLARERSIPLAALADEPFILFPRPVGPGLYDAIIAACRRAGFTPRIGQEAPQMASAINLVAAGLGVSIVPASMRQL 160 (199)
T ss_pred cCCCCCcccCccCHHHhcCCCEEEecCCcChhHHHHHHHHHHHcCCceeeEEehhhHHHHHHHHHcCCCEEEechHHHhh
Confidence 99999988778999999999999976543 3456778888888988889999999999999999999999999988754
Q ss_pred cccCCceeeecCCCCccceEEEEEeCCccccHHHHHHHHHH
Q psy3760 251 NRDKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLL 291 (306)
Q Consensus 251 ~~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l 291 (306)
. .+++..+++.+..+..+++++|+++.. ++.++.|++.+
T Consensus 161 ~-~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~ 199 (199)
T cd08451 161 Q-APGVVYRPLAGAPLTAPLALAYRRGER-SPAVRNFIALV 199 (199)
T ss_pred c-cCCeEEEEccCCCCCceEEEEEcCCCC-CHHHHHHHhhC
Confidence 2 346777888765566899999998876 99999998753
No 93
>cd05466 PBP2_LTTR_substrate The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily. This model and hierarchy represent the the substrate-binding domain of the LysR-type transcriptional regulators that form the largest family of prokaryotic transcription factor. Homologs of some of LTTRs with similar domain organizations are also found in the archaea and eukaryotic organisms. The LTTRs are composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcriptional repressor undergoes a conformational change upon substrate binding which in turn changes the DNA bin
Probab=99.95 E-value=1.7e-26 Score=177.21 Aligned_cols=196 Identities=29% Similarity=0.471 Sum_probs=177.6
Q ss_pred cEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccCCCCCceeeccccceEEEEec
Q psy3760 94 NLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLISIPCYQWEYVIIVP 173 (306)
Q Consensus 94 ~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~~~~~~~~~l~~~~~~~v~~ 173 (306)
+|+||+++++...++++++..|.+++|++++++....+.++.+.|.+|++|++|+... ...+++...++++++++++++
T Consensus 1 ~l~I~~~~~~~~~~l~~~i~~~~~~~p~i~i~~~~~~~~~~~~~l~~g~~D~~i~~~~-~~~~~~~~~~l~~~~~~~~~~ 79 (197)
T cd05466 1 TLRIGASPSIAAYLLPPLLAAFRQRYPGVELSLVEGGSSELLEALLEGELDLAIVALP-VDDPGLESEPLFEEPLVLVVP 79 (197)
T ss_pred CeEEEechhhHHHHhHHHHHHHHHHCCCCEEEEEECChHHHHHHHHcCCceEEEEcCC-CCCCcceEeeeeccceEEEec
Confidence 4899999999999999999999999999999999998889999999999999999755 466789999999999999999
Q ss_pred CCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCceeEEEEecCHHHHHHHHHhccceeeeecceeccc-c
Q psy3760 174 LDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMGIGIIASIAFDSN-R 252 (306)
Q Consensus 174 ~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~~~p~~~~~~~-~ 252 (306)
++||+..+..++++||.++|++.+..+......+..++...+..++..+.+++...+..++.+|.|++++|.+.+. . .
T Consensus 80 ~~~~~~~~~~~~~~~l~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~p~~~~~-~~~ 158 (197)
T cd05466 80 PDHPLAKRKSVTLADLADEPLILFERGSGLRRLLDRAFAEAGFTPNIALEVDSLEAIKALVAAGLGIALLPESAVE-ELA 158 (197)
T ss_pred CCCCcccCcEecHHHHcCCCEEEecCCchHHHHHHHHHHHcCCCceEEEEeccHHHHHHHHHhCCCEEEehHHHHh-hhh
Confidence 9999988777999999999999998876666677778888898888899999999999999999999999999877 4 6
Q ss_pred cCCceeeecCCCCccceEEEEEeCCccccHHHHHHHHHH
Q psy3760 253 DKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLL 291 (306)
Q Consensus 253 ~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l 291 (306)
.++++.++++......+++++|+++...++.+++|++++
T Consensus 159 ~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l 197 (197)
T cd05466 159 DGGLVVLPLEDPPLSRTIGLVWRKGRYLSPAARAFLELL 197 (197)
T ss_pred cCCeEEEEecCCcceEEEEEEEcCCCccCHHHHHHHhhC
Confidence 788999988865677899999999988899999999874
No 94
>cd08465 PBP2_ToxR The C-terminal substrate binding domain of LysR-type transcriptional regulator ToxR regulates the expression of the toxoflavin biosynthesis genes; contains the type 2 periplasmic bindinig fold. In soil bacterium Burkholderia glumae, ToxR regulates the toxABCDE and toxFGHI operons in the presence of toxoflavin as a coinducer. Additionally, the expression of both operons requires a transcriptional activator, ToxJ, whose expression is regulated by the TofI or TofR quorum-sensing system. The biosynthesis of toxoflavin is suggested to be synthesized in a pathway common to the synthesis of riboflavin. The topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After
Probab=99.95 E-value=6.6e-27 Score=181.00 Aligned_cols=198 Identities=12% Similarity=0.117 Sum_probs=173.4
Q ss_pred cEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccCCCCCceeeccccceEEEEec
Q psy3760 94 NLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLISIPCYQWEYVIIVP 173 (306)
Q Consensus 94 ~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~~~~~~~~~l~~~~~~~v~~ 173 (306)
+++||++++++..++++++..|.++||++++++...++.++.+.|.+|++|+||+..+ ...+++...++++++++++++
T Consensus 1 ~l~Ig~~~~~~~~~l~~~l~~f~~~~P~i~l~i~~~~~~~~~~~L~~g~~Dl~i~~~~-~~~~~~~~~~l~~~~~~lv~~ 79 (200)
T cd08465 1 VFRLAMSDYGARLVLPALMRQLRAEAPGIDLAVSQASREAMLAQVADGEIDLALGVFP-ELPEELHAETLFEERFVCLAD 79 (200)
T ss_pred CEEEEechhhHHHhhhHHHHHHHHHCCCcEEEEecCChHhHHHHHHCCCccEEEeccc-cCCcCeeEEEeeeccEEEEEe
Confidence 4899999999999999999999999999999999999999999999999999998654 345789999999999999999
Q ss_pred CCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCceeEEEEecCHHHHHHHHHh-ccceeeeecceecccc
Q psy3760 174 LDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVEL-RMGIGIIASIAFDSNR 252 (306)
Q Consensus 174 ~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~-g~gi~~~p~~~~~~~~ 252 (306)
++||. .+..+++++|.++|++.+..+...+..++.+++..++.+++.+++++..++.+++.+ |.|+++.|........
T Consensus 80 ~~h~~-~~~~i~~~~l~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~ 158 (200)
T cd08465 80 RATLP-ASGGLSLDAWLARPHVLVAMRGDAANEIDRALAARGLRRRVALTLPHWGVAPELIAGTDLILTVARRALDALRL 158 (200)
T ss_pred CCCCc-cCCCcCHHHHhhCCcEEEecCCCcCChHHHHHHHcCCceEEEEEcCcHHHHHHHHHcCChhhHhHHHHHHHhcc
Confidence 99965 456799999999999999877666778899999999999999999999999999998 5566777654443225
Q ss_pred cCCceeeecCCCCccceEEEEEeCCccccHHHHHHHHHHhH
Q psy3760 253 DKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLLSP 293 (306)
Q Consensus 253 ~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~ 293 (306)
.++++.++++...+..+++++|++++..+++.++|++.+++
T Consensus 159 ~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~l~~~i~~ 199 (200)
T cd08465 159 DERLAVFAPPFPIPPFAFQQIWHQRREGDPAHRWLRERIQE 199 (200)
T ss_pred cCCceEeCCCCCCCCceEEeeecccccCChHHHHHHHHHhh
Confidence 67899998887666789999999999999999999998875
No 95
>cd08452 PBP2_AlsR The C-terminal substrate binding domain of LysR-type trnascriptional regulator AlsR, which regulates acetoin formation under stationary phase growth conditions; contains the type 2 periplasmic binding fold. AlsR is responsible for activating the expression of the acetoin operon (alsSD) in response to inducing signals such as glucose and acetate. Like many other LysR family proteins, AlsR is transcribed divergently from the alsSD operon. The alsS gene encodes acetolactate synthase, an enzyme involved in the production of acetoin in cells of stationary-phase. AlsS catalyzes the conversion of two pyruvate molecules to acetolactate and carbon dioxide. Acetolactate is then converted to acetoin at low pH by acetolactate decarboxylase which encoded by the alsD gene. Acetoin is an important physiological metabolite excreted by many microorganisms grown on glucose or other fermentable carbon sources. This substrate-binding domain shows significant homology to the type 2 perip
Probab=99.95 E-value=2.1e-26 Score=177.73 Aligned_cols=193 Identities=18% Similarity=0.217 Sum_probs=170.0
Q ss_pred EEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccCCCCCceeeccccceEEEEecC
Q psy3760 95 LTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLISIPCYQWEYVIIVPL 174 (306)
Q Consensus 95 l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~~~~~~~~~l~~~~~~~v~~~ 174 (306)
|+||++++++..++++++..|+++||++++++....+.++.+.|.+|++|++|...+ ...+++...+++++++++++++
T Consensus 2 l~ig~~~~~~~~~l~~~l~~~~~~~P~v~i~i~~~~~~~~~~~l~~~~~Dl~i~~~~-~~~~~~~~~~l~~~~~~lv~~~ 80 (197)
T cd08452 2 LVIGFVGAAIYEFLPPIVREYRKKFPSVKVELRELSSPDQVEELLKGRIDIGFLHPP-IQHTALHIETVQSSPCVLALPK 80 (197)
T ss_pred EEEEEeHHHHHhHHHHHHHHHHHHCCCcEEEEEecChHHHHHHHHCCCccEEEeeCC-CCCCCeeEEEeeeccEEEEEeC
Confidence 799999999999999999999999999999999999999999999999999999644 5567899999999999999999
Q ss_pred CCCCCCCCCcChhhhcCCCeEeecCCC--CcHHHHHHHHHhCCCceeEEEEecCHHHHHHHHHhccceeeeecceecccc
Q psy3760 175 DHPLLLLNSISLKEISNYPLITYDLSF--SGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMGIGIIASIAFDSNR 252 (306)
Q Consensus 175 ~~~l~~~~~i~~~dl~~~~~i~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~~~p~~~~~~~~ 252 (306)
+||++.+.+++++||.++|++....+. ..++.+..++...+..+++.+++++.+++.+++.+|.|++++|...... .
T Consensus 81 ~hpl~~~~~~~~~~L~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gia~~p~~~~~~-~ 159 (197)
T cd08452 81 QHPLASKEEITIEDLRDEPIITVAREAWPTLYDEIIQLCEQAGFRPKIVQEATEYQTVIGLVSAGIGVTFVPSSAKKL-F 159 (197)
T ss_pred CCccccCCCCCHHHhcCCCEEeccCCcchhHHHHHHHHHHHcCCCccceeecccHHHHHHHHHcCCCEEEchHHHhhc-C
Confidence 999988778999999999999987653 2456777888989998999999999999999999999999999987533 3
Q ss_pred cCCceeeecCCCCccceEEEEEeCCccccHHHHHHHHH
Q psy3760 253 DKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKL 290 (306)
Q Consensus 253 ~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~ 290 (306)
.++++.+++.+......++++|+++.. +|.++.|++.
T Consensus 160 ~~~~~~~~l~~~~~~~~~~l~~~~~~~-~~~~~~f~~~ 196 (197)
T cd08452 160 NLEVAYRKIDQINLNAEWSIAYRKDNH-NPLLKHFIHI 196 (197)
T ss_pred CCCeEEEECCCCCcceeEEEEECCCCC-ChHHHHHHhc
Confidence 567888898775566799999988874 8989988763
No 96
>cd08447 PBP2_LTTR_aromatics_like_1 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator similar to regulators involved in the catabolism of aromatic compounds, contains type 2 periplasmic binding fold. This CD represents the substrate binding domain of an uncharacterized LysR-type regulator similar to CbnR which is involved in the regulation of chlorocatechol breakdown. The transcription of the genes encoding enzymes involved in such degradation is regulated and expression of these enzymes is enhanced by inducers, which are either an intermediate in the metabolic pathway or compounds to be degraded. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Ve
Probab=99.95 E-value=2.9e-26 Score=176.83 Aligned_cols=195 Identities=16% Similarity=0.185 Sum_probs=168.8
Q ss_pred cEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccCCCCCceeeccccceEEEEec
Q psy3760 94 NLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLISIPCYQWEYVIIVP 173 (306)
Q Consensus 94 ~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~~~~~~~~~l~~~~~~~v~~ 173 (306)
.++||++++++..++++++..|.++||++++++....+.++.+.+.+|++|++|+..+ ...+++....+++++++++++
T Consensus 1 ~l~Ig~~~~~~~~~l~~~l~~~~~~~P~i~v~~~~~~~~~~~~~l~~g~~D~~i~~~~-~~~~~~~~~~l~~~~~~~v~~ 79 (198)
T cd08447 1 SLRIGFTAASAYSFLPRLLAAARAALPDVDLVLREMVTTDQIEALESGRIDLGLLRPP-FARPGLETRPLVREPLVAAVP 79 (198)
T ss_pred CEEEEEehHHHHHHHHHHHHHHHHHCCCeEEEEEeCCHHHHHHHHHcCCceEEEecCC-CCCCCeeEEEeecCceEEEec
Confidence 4899999999999999999999999999999999999999999999999999999654 455789999999999999999
Q ss_pred CCCCCCCCCCcChhhhcCCCeEeecCCCC--cHHHHHHHHHhCCCceeEEEEecCHHHHHHHHHhccceeeeecceeccc
Q psy3760 174 LDHPLLLLNSISLKEISNYPLITYDLSFS--GRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMGIGIIASIAFDSN 251 (306)
Q Consensus 174 ~~~~l~~~~~i~~~dl~~~~~i~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~~~p~~~~~~~ 251 (306)
++||++.+..++++||.++|++.+..... .++.+..++...+..++..+++++..++.+++.+|.|++++|..++...
T Consensus 80 ~~~pl~~~~~~~~~~l~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~~~p~~~~~~~ 159 (198)
T cd08447 80 AGHPLAGAERLTLEDLDGQPFIMYSPTEARYFHDLVVRLFASAGVQPRYVQYLSQIHTMLALVRAGLGVALVPASASRLR 159 (198)
T ss_pred CCCchhhcCcccHHHhCCCeEEEeCCCCCchHHHHHHHHHHHcCCCCCceeecCCHHHHHHHHHcCCCeEEhhHHHhhcC
Confidence 99999887789999999999999865433 3567788898899888888999999999999999999999999877543
Q ss_pred ccCCceeeecCCC-CccceEEEEEeCCccccHHHHHHHHHH
Q psy3760 252 RDKNLRSISASHL-FGTTISRVIIKQGTYLRSYVYSFIKLL 291 (306)
Q Consensus 252 ~~~~l~~~~~~~~-~~~~~~~l~~~~~~~~~~~~~~~~~~l 291 (306)
...+..+++... ....+++++|+++. .++.+++|++++
T Consensus 160 -~~~~~~~~l~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~ 198 (198)
T cd08447 160 -FEGVVFRPLDLPRDVPVELHLAWRRDN-DNPALRALLDLI 198 (198)
T ss_pred -cCCeEEEECCCCCCCceEEEEEEcCCC-CCHHHHHHHhhC
Confidence 334566676553 35679999999875 589999998764
No 97
>cd08431 PBP2_HupR The C-terminal substrate binding domain of LysR-type transcriptional regulator, HupR, which regulates expression of the heme uptake receptor HupA; contains the type 2 periplasmic binding fold. HupR, a member of the LysR family, activates hupA transcription under low-iron conditions in the presence of hemin. The expression of many iron-uptake genes, such as hupA, is regulated at the transcriptional level by iron and an iron-binding repressor protein called Fur (ferric uptake regulation). Under iron-abundant conditions with heme, the active Fur repressor protein represses transcription of the iron-uptake gene hupA, and prevents transcriptional activation via HupR. Under low-iron conditions with heme, the Fur repressor is inactive and transcription of the hupA is allowed. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, p
Probab=99.94 E-value=1.3e-25 Score=172.86 Aligned_cols=192 Identities=16% Similarity=0.123 Sum_probs=160.7
Q ss_pred cEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccCCCCCceeeccccceEEEEec
Q psy3760 94 NLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLISIPCYQWEYVIIVP 173 (306)
Q Consensus 94 ~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~~~~~~~~~l~~~~~~~v~~ 173 (306)
+++||++++++..++++++..|.+.||++++++....++++.+.|.+|++|++|+.......+++...+++.++++++++
T Consensus 1 ~l~Ig~~~~~~~~~l~~~l~~~~~~~P~v~i~i~~~~~~~~~~~l~~g~~D~~i~~~~~~~~~~~~~~~l~~~~~~~v~~ 80 (195)
T cd08431 1 ELRIAIDTVLPLQPLYPLIAEFYQLNKATRIRLSEEVLGGTWDALASGRADLVIGATGELPPGGVKTRPLGEVEFVFAVA 80 (195)
T ss_pred CEEEEEccccChHHHHHHHHHHHHHCCCCceEEEEeccchHHHHHhCCCCCEEEEecCCCCCCceEEEecccceEEEEEc
Confidence 48999999999999999999999999999999999888899999999999999985433345689999999999999999
Q ss_pred CCCCCCCC-CCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCC-CceeEEEEecCHHHHHHHHHhccceeeeecceeccc
Q psy3760 174 LDHPLLLL-NSISLKEISNYPLITYDLSFSGRIKLDREFSLQK-LTPYIVLETINSDIIKTYVELRMGIGIIASIAFDSN 251 (306)
Q Consensus 174 ~~~~l~~~-~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~v~~g~gi~~~p~~~~~~~ 251 (306)
++||++.. ..+++++|.++|++.+..+...... ...+ ..++..+++++..++++++.+|.|++++|.+.+...
T Consensus 81 ~~hpl~~~~~~~~~~~L~~~~~i~~~~~~~~~~~-----~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~~lp~~~~~~~ 155 (195)
T cd08431 81 PNHPLAKLDGPLDASAIKQYPAIVVADTSRNLPP-----RSSGLLEGQDRIRVPTMQAKIDAQVLGLGVGYLPRHLAKPE 155 (195)
T ss_pred CCChhhhccCCCCHHHHhhCcEEEEcCCCccccc-----ccceeccCCCceEEcCHHHHHHHHHhCCceEecCHHHHHhh
Confidence 99999865 4799999999999998765432111 1112 245677889999999999999999999999887655
Q ss_pred -ccCCceeeecCCCCccceEEEEEeCCccccHHHHHHHHHH
Q psy3760 252 -RDKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLL 291 (306)
Q Consensus 252 -~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l 291 (306)
..+.++.+++.+.....+++++|+++. .++.+++|++.+
T Consensus 156 ~~~~~l~~~~~~~~~~~~~~~l~~~~~~-~~~~~~~~~~~~ 195 (195)
T cd08431 156 LASGELVEKALEDPRPPQELFLAWRKDQ-RGKALAWFVQRL 195 (195)
T ss_pred hhCCceEeeccCCCCCCceEEEEEecCC-CCHHHHHHHHhC
Confidence 567788888877566789999999886 688999988753
No 98
>cd08432 PBP2_GcdR_TrpI_HvrB_AmpR_like The C-terminal substrate domain of LysR-type GcdR, TrPI, HvR and beta-lactamase regulators, and that of other closely related homologs; contains the type 2 periplasmic binding fold. This CD includes the C-terminal substrate domain of LysR-type transcriptional regulators involved in controlling the expression of glutaryl-CoA dehydrogenase (GcdH), S-adenosyl-L-homocysteine hydrolase, cell division protein FtsW, tryptophan synthase, and beta-lactamase. The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex compris
Probab=99.93 E-value=1.3e-25 Score=172.52 Aligned_cols=192 Identities=14% Similarity=0.025 Sum_probs=161.7
Q ss_pred cEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccCCCCCceeeccccceEEEEec
Q psy3760 94 NLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLISIPCYQWEYVIIVP 173 (306)
Q Consensus 94 ~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~~~~~~~~~l~~~~~~~v~~ 173 (306)
+++||+.+++...++++++..|.+.||++++++.... ..+.|.+|++|++|+..+ ...+++.+.++++++++++++
T Consensus 1 ~l~Ig~~~~~~~~~l~~~l~~~~~~~P~v~i~~~~~~---~~~~l~~g~~D~~i~~~~-~~~~~~~~~~l~~~~~~~v~~ 76 (194)
T cd08432 1 VLTVSVTPSFAARWLIPRLARFQARHPDIDLRLSTSD---RLVDFAREGIDLAIRYGD-GDWPGLEAERLMDEELVPVCS 76 (194)
T ss_pred CEEEEccHHHHHHHHHHHhHHHHHHCCCeEEEEEecC---CccccccccccEEEEecC-CCCCCcceEEccCCcEEEecC
Confidence 4899999999999999999999999999999998765 457799999999998654 446789999999999999999
Q ss_pred CCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCceeEEEEecCHHHHHHHHHhccceeeeecceeccc-c
Q psy3760 174 LDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMGIGIIASIAFDSN-R 252 (306)
Q Consensus 174 ~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~~~p~~~~~~~-~ 252 (306)
++||.. ++.++++||.++|++....+...+..+.+.+...+..+++.+++++..++.+++.+|.|++++|...+... .
T Consensus 77 ~~~~~~-~~~i~~~~l~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~~lp~~~~~~~~~ 155 (194)
T cd08432 77 PALLAG-LPLLSPADLARHTLLHDATRPEAWQWWLWAAGVADVDARRGPRFDDSSLALQAAVAGLGVALAPRALVADDLA 155 (194)
T ss_pred HHHHHh-cCCCCHHHhhcCceEEecCcccccHHHHhcCCeeccccCCeEEECCHHHHHHHHHhCCCeEEeeHHHhhhhhc
Confidence 999854 45689999999999998766555666666677778888999999999999999999999999999887654 4
Q ss_pred cCCceeeecCC-CCccceEEEEEeCCccccHHHHHHHHHH
Q psy3760 253 DKNLRSISASH-LFGTTISRVIIKQGTYLRSYVYSFIKLL 291 (306)
Q Consensus 253 ~~~l~~~~~~~-~~~~~~~~l~~~~~~~~~~~~~~~~~~l 291 (306)
.+.+. .+++. .....+++++|++++..+|.+++|++++
T Consensus 156 ~~~l~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 194 (194)
T cd08432 156 AGRLV-RPFDLPLPSGGAYYLVYPPGRAESPAVAAFRDWL 194 (194)
T ss_pred CCceE-eccccccCCCCCEEEEeccccccchHHHHHHhhC
Confidence 55554 33333 3456799999999999999999998753
No 99
>cd08475 PBP2_CrgA_like_6 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold. This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 6. The LTTRs are acting as both auto-repressors and activators of target promoters, controlling operons involved in a wide variety of cellular processes such as amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to name a few. In contrast to the tetrameric form of other LTTRs, CrgA from Neisseria meningitides assembles into an octameric ring, which can bind up to four 63-bp DNA oligonucleotides. Phylogenetic cluster analysis showed that the CrgA-like regulators form a subclass of the LTTRs that function as octamers. The CrgA is an auto-repressor of its own gene a
Probab=99.93 E-value=1.7e-25 Score=172.66 Aligned_cols=196 Identities=15% Similarity=0.140 Sum_probs=160.2
Q ss_pred CcEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccCCCCCceeeccccceEEEEe
Q psy3760 93 GNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLISIPCYQWEYVIIV 172 (306)
Q Consensus 93 ~~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~~~~~~~~~l~~~~~~~v~ 172 (306)
|+++||++++++..++++++..|.++||++++++.. ..+..+.+.++ +|++|........+++.+.+++++++++++
T Consensus 1 g~l~Ig~~~~~~~~~l~~~l~~~~~~~P~v~i~i~~--~~~~~~~l~~~-~D~~i~~~~~~~~~~l~~~~l~~~~~~~v~ 77 (199)
T cd08475 1 GRLRIDLPVAFGRLCVAPLLLELARRHPELELELSF--SDRFVDLIEEG-IDLAVRIGELADSTGLVARRLGTQRMVLCA 77 (199)
T ss_pred CeEEEechHHHHHhhHHHHHHHHHHHCCCeEEEEEe--ccchhhHhhcC-ccEEEEeCCCCCCCCeEEEEcccceEEEEE
Confidence 579999999999999999999999999999999974 34567777655 999997544334467999999999999999
Q ss_pred cCCCCCCCCCCcChhhhcCCCeEeecCC-CCcH-HHHHHHHHhCCCceeEEEEecCHHHHHHHHHhccceeeeecceecc
Q psy3760 173 PLDHPLLLLNSISLKEISNYPLITYDLS-FSGR-IKLDREFSLQKLTPYIVLETINSDIIKTYVELRMGIGIIASIAFDS 250 (306)
Q Consensus 173 ~~~~~l~~~~~i~~~dl~~~~~i~~~~~-~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~~~p~~~~~~ 250 (306)
+++|+...+..++++||.++|++..... .... ..+...+...+..+++.+++++..++++++..|.|++++|.+++..
T Consensus 78 ~~~~~~~~~~~~~~~~l~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~~~p~~~~~~ 157 (199)
T cd08475 78 SPAYLARHGTPRTLEDLAEHQCIAYGRGGQPLPWRLADEQGRLVRFRPAPRLQFDDGEAIADAALAGLGIAQLPTWLVAD 157 (199)
T ss_pred CHHHHHhcCCCCCHHHHhhCCCEEecCCCCCCCeEEecCCCCeeeEeccCcEEECCHHHHHHHHHhCCCEEeeeHHHHHh
Confidence 9999876566799999999999998764 2221 2223334455677888999999999999999999999999988876
Q ss_pred c-ccCCceeeecCCCCccceEEEEEeCCccccHHHHHHHHHH
Q psy3760 251 N-RDKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLL 291 (306)
Q Consensus 251 ~-~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l 291 (306)
. ..+.++.++...+....+++++|+++...++.+++|++++
T Consensus 158 ~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l 199 (199)
T cd08475 158 HLQRGELVEVLPELAPEGLPIHAVWPRTRHLPPKVRAAVDAL 199 (199)
T ss_pred HhhcCcEEEecCCCcCCCccEEEEeCCcccCCHHHHHHHhhC
Confidence 5 5667777765544556799999999999999999999874
No 100
>cd08471 PBP2_CrgA_like_2 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold. This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 2. The LTTRs are acting as both auto-repressors and activators of target promoters, controlling operons involved in a wide variety of cellular processes such as amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to name a few. In contrast to the tetrameric form of other LTTRs, CrgA from Neisseria meningitides assembles into an octameric ring, which can bind up to four 63-bp DNA oligonucleotides. Phylogenetic cluster analysis showed that the CrgA-like regulators form a subclass of the LTTRs that function as octamers. The CrgA is an auto-repressor of its own gene a
Probab=99.93 E-value=2.1e-25 Score=172.42 Aligned_cols=198 Identities=13% Similarity=0.133 Sum_probs=158.5
Q ss_pred CcEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccCCCCCceeeccccceEEEEe
Q psy3760 93 GNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLISIPCYQWEYVIIV 172 (306)
Q Consensus 93 ~~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~~~~~~~~~l~~~~~~~v~ 172 (306)
|+|+||+.++++..++++++..|.+.||++++++.... ++.+ +.+|++|++|+..+ ...+++...+++++++++++
T Consensus 1 g~l~Ig~~~~~~~~~l~~~l~~~~~~~P~v~i~i~~~~--~~~~-~~~~~~Dl~i~~~~-~~~~~~~~~~l~~~~~~~v~ 76 (201)
T cd08471 1 GLLTVTAPVLFGRLHVLPIITDFLDAYPEVSVRLLLLD--RVVN-LLEEGVDVAVRIGH-LPDSSLVATRVGSVRRVVCA 76 (201)
T ss_pred CeEEEEccHHHHHHHHHHHHHHHHHHCCCcEEEEEEcC--ccch-hhcccccEEEEecC-CCCCCeEEEEccccceEEEE
Confidence 57999999999999999999999999999999998642 3443 56789999998644 45678999999999999999
Q ss_pred cCCCCCCCCCCcChhhhcCCCeEeecCCCCcHH-HHHHHHHhCCCceeEEEEecCHHHHHHHHHhccceeeeecceeccc
Q psy3760 173 PLDHPLLLLNSISLKEISNYPLITYDLSFSGRI-KLDREFSLQKLTPYIVLETINSDIIKTYVELRMGIGIIASIAFDSN 251 (306)
Q Consensus 173 ~~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~~~p~~~~~~~ 251 (306)
+++|+...+..++++||.++|++....+..... .+...+...++.+++.+++++..++.+++.+|.|++++|.+++...
T Consensus 77 ~~~~~~~~~~~v~~~~L~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~Gi~~~p~~~~~~~ 156 (201)
T cd08471 77 SPAYLARHGTPKHPDDLADHDCIAFTGLSPAPEWRFREGGKERSVRVRPRLTVNTVEAAIAAALAGLGLTRVLSYQVAEE 156 (201)
T ss_pred CHHHHHhcCCCCCHHHHhcCCeEEEecCCCCCceeEecCCcEEEEecCCcEEECCHHHHHHHHHcCCcEEEechhHHHHH
Confidence 999865555579999999999999876543211 1222333345667888999999999999999999999999876544
Q ss_pred -ccCCceeeecCCCCccceEEEEEeCCccccHHHHHHHHHHhHH
Q psy3760 252 -RDKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLLSPK 294 (306)
Q Consensus 252 -~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~ 294 (306)
..+.++.+..+.......++++|++++..++.++.|++++++.
T Consensus 157 ~~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~f~~~l~~~ 200 (201)
T cd08471 157 LAAGRLQRVLEDFEPPPLPVHLVHPEGRLAPAKVRAFVDFAVPR 200 (201)
T ss_pred hhcCceEEecccccCCCCcEEEEecCcccCCHHHHHHHHHHHhh
Confidence 5566776644433446799999999988999999999998764
No 101
>cd08478 PBP2_CrgA The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA, contains the type 2 periplasmic binding domain. This CD represents the substrate binding domain of LysR-type transcriptional regulator (LTTR) CrgA. The LTTRs are acting as both auto-repressors and activators of target promoters, controlling operons involved in a wide variety of cellular processes such as amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to name a few. In contrast to the tetrameric form of other LTTRs, CrgA from Neisseria meningitides assembles into an octameric ring, which can bind up to four 63-bp DNA oligonucleotides. Phylogenetic cluster analysis further showed that the CrgA-like regulators form a subclass of the LTTRs that function as octamers. The CrgA is an auto-repressor of its own gene and activates the expression of the mdaB gene wh
Probab=99.93 E-value=7.7e-26 Score=174.72 Aligned_cols=196 Identities=15% Similarity=0.156 Sum_probs=155.8
Q ss_pred CCcEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccCCCCCceeeccccceEEEE
Q psy3760 92 TGNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLISIPCYQWEYVII 171 (306)
Q Consensus 92 ~~~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~~~~~~~~~l~~~~~~~v 171 (306)
.|.|+||++++++..++++++..|.++||++++++.. ++.+. .+.+|++|++|+..+ ...+++...++++++++++
T Consensus 2 ~g~l~Ig~~~~~~~~~l~~~l~~f~~~~P~v~i~~~~--~~~~~-~l~~~~~D~~i~~~~-~~~~~l~~~~l~~~~~~~v 77 (199)
T cd08478 2 SGLLRVDAATPFVLHLLAPLIAKFRERYPDIELELVS--NEGII-DLIERKTDVAIRIGE-LTDSTLHARPLGKSRLRIL 77 (199)
T ss_pred CceEEEeCHHHHHHHHHHHHHHHHHHHCCCeEEEEEe--ccccc-cchhccccEEEEecC-CCCCCceEEEcccccEEEE
Confidence 4789999999999999999999999999999999973 33444 478899999998644 4567899999999999999
Q ss_pred ecCCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCceeEEEEecCHHHHHHHHHhccceeeeecceeccc
Q psy3760 172 VPLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMGIGIIASIAFDSN 251 (306)
Q Consensus 172 ~~~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~~~p~~~~~~~ 251 (306)
++++|+......++++||.++|+|.+..+...+......+...+..+++.+++++...++.++..|.|++++|.+++...
T Consensus 78 ~~~~~~~~~~~~~~~~~L~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~Gi~~~p~~~~~~~ 157 (199)
T cd08478 78 ASPDYLARHGTPQSIEDLAQHQLLGFTEPASLNTWPIKDADGNLLKIQPTITASSGETLRQLALSGCGIACLSDFMTDKD 157 (199)
T ss_pred ECHHHHHhcCCCCCHHHHHhChhhhccCCCCCCCceeeCCCCcEEeccceEEECCHHHHHHHHHhCCCEEeccHHHHHHH
Confidence 99999433334699999999999987665443322222233334566778899999999999999999999999887654
Q ss_pred -ccCCceeeecCC-CCccceEEEEEeCCccccHHHHHHHHHH
Q psy3760 252 -RDKNLRSISASH-LFGTTISRVIIKQGTYLRSYVYSFIKLL 291 (306)
Q Consensus 252 -~~~~l~~~~~~~-~~~~~~~~l~~~~~~~~~~~~~~~~~~l 291 (306)
..+.++.+.... ....++++++|++++..++.++.|++++
T Consensus 158 ~~~~~l~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~f~~~l 199 (199)
T cd08478 158 IAEGRLIPLFAEQTSDVRQPINAVYYRNTALSLRIRCFIDFL 199 (199)
T ss_pred HhCCCeEEeccccccCCCccEEEEECccccCChhhhhhhhhC
Confidence 456677664432 2346799999999999999999999864
No 102
>cd08422 PBP2_CrgA_like The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its related homologs, contains the type 2 periplasmic binding domain. This CD includes the substrate binding domain of LysR-type transcriptional regulator (LTTR) CrgA and its related homologs. The LTTRs are acting as both auto-repressors and activators of target promoters, controlling operons involved in a wide variety of cellular processes such as amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to name a few. In contrast to the tetrameric form of other LTTRs, CrgA from Neisseria meningitides assembles into an octameric ring, which can bind up to four 63-bp DNA oligonucleotides. Phylogenetic cluster analysis further showed that the CrgA-like regulators form a subclass of the LTTRs that function as octamers. The CrgA is an auto-repressor of its own
Probab=99.93 E-value=3e-25 Score=170.79 Aligned_cols=195 Identities=15% Similarity=0.187 Sum_probs=157.2
Q ss_pred CcEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccCCCCCceeeccccceEEEEe
Q psy3760 93 GNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLISIPCYQWEYVIIV 172 (306)
Q Consensus 93 ~~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~~~~~~~~~l~~~~~~~v~ 172 (306)
|+|+||++++++..++++++..|.++||++++++.... .+. .+.+|++|++|+..+ ...+++.+.+++++++++++
T Consensus 1 g~l~Ig~~~~~~~~~l~~~l~~~~~~~P~v~i~i~~~~--~~~-~l~~~~~D~~i~~~~-~~~~~~~~~~l~~~~~~~v~ 76 (197)
T cd08422 1 GRLRISAPVSFGRLHLAPLLAEFLARYPDVRLELVLSD--RLV-DLVEEGFDLAIRIGE-LPDSSLVARRLGPVRRVLVA 76 (197)
T ss_pred CeEEEEecHHHHHHHHHHHHHHHHHhCCceEEEEecCc--ccc-chhhcCccEEEEeCC-CCCcchhhhhhhccCcEEEE
Confidence 57999999999999999999999999999999998643 334 466788999998654 45678999999999999999
Q ss_pred cCCCCCCCCCCcChhhhcCCCeEeecCCCCc-HHHHHHHHHhCCCceeEEEEecCHHHHHHHHHhccceeeeecceeccc
Q psy3760 173 PLDHPLLLLNSISLKEISNYPLITYDLSFSG-RIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMGIGIIASIAFDSN 251 (306)
Q Consensus 173 ~~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~~~p~~~~~~~ 251 (306)
+++|+...+..++++||.++|++.+..+... ...+...+...+..+++.+++++..++++++.+|.|++++|.+.+...
T Consensus 77 ~~~~~~~~~~~~~~~~L~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~~~p~~~~~~~ 156 (197)
T cd08422 77 SPAYLARHGTPQTPEDLARHRCLGYRLPGRPLRWRFRRGGGEVEVRVRGRLVVNDGEALRAAALAGLGIALLPDFLVAED 156 (197)
T ss_pred CHHHHHhcCCCCCHHHHhcCCcEeecCccCcccceeecccCcccccccccEEEccHHHHHHHHHcCCcEEEecHHHHhhh
Confidence 9999654445689999999999998775221 112223333346778889999999999999999999999999887655
Q ss_pred -ccCCceeeecCCCCccceEEEEEeCCccccHHHHHHHHHH
Q psy3760 252 -RDKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLL 291 (306)
Q Consensus 252 -~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l 291 (306)
..+.++.++.+.......++++|++++..++.++.|++++
T Consensus 157 ~~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l 197 (197)
T cd08422 157 LASGRLVRVLPDWRPPPLPIYAVYPSRRHLPAKVRAFIDFL 197 (197)
T ss_pred ccCCeEEEecCcccCCCceEEEEEcccccCCHHHHHHHhhC
Confidence 5556666554434556899999999999999999998864
No 103
>cd08481 PBP2_GcdR_like The C-terminal substrate binding domain of LysR-type transcriptional regulators GcdR-like, contains the type 2 periplasmic binding fold. GcdR is involved in the glutaconate/glutarate-specific activation of the Pg promoter driving expression of a glutaryl-CoA dehydrogenase-encoding gene (gcdH). The GcdH protein is essential for the anaerobic catabolism of many aromatic compounds and some alicyclic and dicarboxylic acids. The structural topology of this substrate-binding domain is most similar to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplas
Probab=99.92 E-value=9.1e-25 Score=167.86 Aligned_cols=190 Identities=13% Similarity=0.041 Sum_probs=157.0
Q ss_pred cEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccCCCCCceeeccccceEEEEec
Q psy3760 94 NLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLISIPCYQWEYVIIVP 173 (306)
Q Consensus 94 ~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~~~~~~~~~l~~~~~~~v~~ 173 (306)
+|+||++.+++..++++++.+|.++||++++++...... +.+.+|++|++++..+ ...+++...++++++++++++
T Consensus 1 ~l~Ig~~~~~~~~~l~~~l~~f~~~~P~i~i~i~~~~~~---~~l~~~~~Dl~l~~~~-~~~~~~~~~~l~~~~~~~v~~ 76 (194)
T cd08481 1 TLELAVLPTFGTRWLIPRLPDFLARHPDITVNLVTRDEP---FDFSQGSFDAAIHFGD-PVWPGAESEYLMDEEVVPVCS 76 (194)
T ss_pred CEEEEecHHHHHHHHHhhhhHHHHHCCCceEEEEecccc---cCcccCCCCEEEEcCC-CCCCCccceecccCeeeecCC
Confidence 489999999999999999999999999999999976543 3688999999998644 456789999999999999999
Q ss_pred CCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCce---eEEEEecCHHHHHHHHHhccceeeeecceecc
Q psy3760 174 LDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTP---YIVLETINSDIIKTYVELRMGIGIIASIAFDS 250 (306)
Q Consensus 174 ~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~v~~g~gi~~~p~~~~~~ 250 (306)
++|| +.++.++++||.++|++...... ..+.+++...|..+ ...+++++...+.+++.+|.|++++|...+..
T Consensus 77 ~~~~-~~~~~~~~~dl~~~~~i~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~Gi~~~p~~~~~~ 152 (194)
T cd08481 77 PALL-AGRALAAPADLAHLPLLQQTTRP---EAWRDWFEEVGLEVPTAYRGMRFEQFSMLAQAAVAGLGVALLPRFLIEE 152 (194)
T ss_pred HHHH-hcCCCCcHHHHhhCceEecCCCC---cCHHHHHHHcCCCCCCccCceEeccHHHHHHHHHhCCCeEEecHHHHHH
Confidence 9997 55567899999999999865332 24577788887753 34578899999999999999999999988765
Q ss_pred c-ccCCceeeecCCCCccceEEEEEeCCccccHHHHHHHHHH
Q psy3760 251 N-RDKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLL 291 (306)
Q Consensus 251 ~-~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l 291 (306)
. ..+.++..+.+......+++++|+++...++.+++|++++
T Consensus 153 ~~~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~i 194 (194)
T cd08481 153 ELARGRLVVPFNLPLTSDKAYYLVYPEDKAESPPVQAFRDWL 194 (194)
T ss_pred HHHCCCEEeecCccccCCCeEEEEeCcccccCHHHHHHHhhC
Confidence 5 5566765544333346799999999999999999999864
No 104
>cd08474 PBP2_CrgA_like_5 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold. This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 5. The LTTRs are acting as both auto-repressors and activators of target promoters, controlling operons involved in a wide variety of cellular processes such as amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to name a few. In contrast to the tetrameric form of other LTTRs, CrgA from Neisseria meningitides assembles into an octameric ring, which can bind up to four 63-bp DNA oligonucleotides. Phylogenetic cluster analysis showed that the CrgA-like regulators form a subclass of the LTTRs that function as octamers. The CrgA is an auto-repressor of its own gene a
Probab=99.92 E-value=3.4e-25 Score=171.43 Aligned_cols=195 Identities=15% Similarity=0.144 Sum_probs=155.4
Q ss_pred CCcEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccCCCCCceeecccc-ceEEE
Q psy3760 92 TGNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLISIPCYQ-WEYVI 170 (306)
Q Consensus 92 ~~~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~~~~~~~~~l~~-~~~~~ 170 (306)
.|.|+||++++++..++++++..|.++||++++++...+. ...+.+|++|++|+... ...+++...+++. +++++
T Consensus 2 ~g~l~Ig~~~~~~~~~l~~~l~~~~~~~P~v~i~~~~~~~---~~~l~~g~~D~~i~~~~-~~~~~~~~~~l~~~~~~~~ 77 (202)
T cd08474 2 AGTLRINAPRVAARLLLAPLLARFLARYPDIRLELVVDDG---LVDIVAEGFDAGIRLGE-SVEKDMVAVPLGPPLRMAV 77 (202)
T ss_pred CcEEEEeCcHHHHHHHHHHHHHHHHHHCCCeEEEEEecCC---cccccccCccEEEEcCC-CCCCCeEEEEeccccceEE
Confidence 5789999999999999999999999999999999987542 45688999999998644 4467799999999 69999
Q ss_pred EecCCCCCCCCCCcChhhhcCCCeEeecCC-CC--cHHHHHHHHHhCCCceeEEEEecCHHHHHHHHHhccceeeeecce
Q psy3760 171 IVPLDHPLLLLNSISLKEISNYPLITYDLS-FS--GRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMGIGIIASIA 247 (306)
Q Consensus 171 v~~~~~~l~~~~~i~~~dl~~~~~i~~~~~-~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~~~p~~~ 247 (306)
+++++|+...+..++++||.++|++.+... .. ....+...+...++.+++.+++++..++.++|.+|.|++++|.+.
T Consensus 78 v~~~~~~~~~~~~i~~~~L~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~~lp~~~ 157 (202)
T cd08474 78 VASPAYLARHGTPEHPRDLLNHRCIRYRFPTSGALYRWEFERGGRELEVDVEGPLILNDSDLMLDAALDGLGIAYLFEDL 157 (202)
T ss_pred EeCHHHHHhcCCCCCHHHHhhCCeeeeeCCCCCcCcceEEecCCCeEEEecCCcEEECCHHHHHHHHHcCCCEEEeeHHH
Confidence 999998544445799999999999987643 21 222223333444556778899999999999999999999999988
Q ss_pred eccc-ccCCceeeecCCC-CccceEEEEEeCCccccHHHHHHHHHH
Q psy3760 248 FDSN-RDKNLRSISASHL-FGTTISRVIIKQGTYLRSYVYSFIKLL 291 (306)
Q Consensus 248 ~~~~-~~~~l~~~~~~~~-~~~~~~~l~~~~~~~~~~~~~~~~~~l 291 (306)
+... ..+.++.+ +.+. ....+++++|++++..+|.++.|++++
T Consensus 158 ~~~~~~~~~l~~~-~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~i 202 (202)
T cd08474 158 VAEHLASGRLVRV-LEDWSPPFPGGYLYYPSRRRVPPALRAFIDFL 202 (202)
T ss_pred HHHHHHCCCcEEe-CCcccCCCCCEEEEEeCCCCCCHHHHHHHhhC
Confidence 7654 55666654 3332 456799999999988999999999864
No 105
>cd08472 PBP2_CrgA_like_3 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold. This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 3. The LTTRs are acting as both auto-repressors and activators of target promoters, controlling operons involved in a wide variety of cellular processes such as amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to name a few. In contrast to the tetrameric form of other LTTRs, CrgA from Neisseria meningitides assembles into an octameric ring, which can bind up to four 63-bp DNA oligonucleotides. Phylogenetic cluster analysis showed that the CrgA-like regulators form a subclass of the LTTRs that function as octamers. The CrgA is an auto-repressor of its own gene a
Probab=99.92 E-value=9.7e-25 Score=168.84 Aligned_cols=196 Identities=13% Similarity=0.107 Sum_probs=157.8
Q ss_pred CcEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccCCCCCceeeccccceEEEEe
Q psy3760 93 GNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLISIPCYQWEYVIIV 172 (306)
Q Consensus 93 ~~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~~~~~~~~~l~~~~~~~v~ 172 (306)
|.|+||++++++..++++++..|.++||++++++... +++.+.+ .+++|++|+..+ ...+++...+++++++++++
T Consensus 1 g~l~Ig~~~~~~~~~l~~~l~~~~~~~P~i~v~~~~~--~~~~~~l-~~~~D~~i~~~~-~~~~~l~~~~l~~~~~~~v~ 76 (202)
T cd08472 1 GRLRVDVPGSLARLLLIPALPDFLARYPDIELDLGVS--DRPVDLI-REGVDCVIRVGE-LADSSLVARRLGELRMVTCA 76 (202)
T ss_pred CeEEEeccHHHHHHHHHHHHHHHHHHCCCcEEEEEEC--CCcchhh-cccccEEEEcCC-CCCccEEEEEccceeEEEEE
Confidence 5799999999999999999999999999999999753 3455544 567999998544 45678999999999999999
Q ss_pred cCCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCC----CceeEEEEecCHHHHHHHHHhccceeeeeccee
Q psy3760 173 PLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQK----LTPYIVLETINSDIIKTYVELRMGIGIIASIAF 248 (306)
Q Consensus 173 ~~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~----~~~~~~~~~~~~~~~~~~v~~g~gi~~~p~~~~ 248 (306)
+++|+...+..++++||.++|++.+..+.. ...+...+...+ +.+++.+++++...+++++..|.|++++|..++
T Consensus 77 ~~~~~~~~~~~~~~~~l~~~~~i~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~Gv~~lp~~~~ 155 (202)
T cd08472 77 SPAYLARHGTPRHPEDLERHRAVGYFSART-GRVLPWEFQRDGEEREVKLPSRVSVNDSEAYLAAALAGLGIIQVPRFMV 155 (202)
T ss_pred CHHHHHhCCCCCCHHHHhcCceEEEeccCC-CCccceEEecCCCceEEeccCeEEECCHHHHHHHHHcCCeEEECcHHHH
Confidence 999965545578999999999998765432 222333444445 567788999999999999999999999999887
Q ss_pred ccc-ccCCceeeecCCCCccceEEEEEeCCccccHHHHHHHHHHhH
Q psy3760 249 DSN-RDKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLLSP 293 (306)
Q Consensus 249 ~~~-~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~ 293 (306)
... ..+.++.++.........++++|+++...+|.++.|++++++
T Consensus 156 ~~~~~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~ 201 (202)
T cd08472 156 RPHLASGRLVEVLPDWRPPPLPVSLLYPHRRHLSPRVRVFVDWVAE 201 (202)
T ss_pred HHHHhcCccEEeeccccCCCCcEEEEecCcccCChhHHHHHHHHhh
Confidence 654 566777665443345679999999988889999999999875
No 106
>cd08477 PBP2_CrgA_like_8 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold. This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 8. The LTTRs are acting as both auto-repressors and activators of target promoters, controlling operons involved in a wide variety of cellular processes such as amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to name a few. In contrast to the tetrameric form of other LTTRs, CrgA from Neisseria meningitides assembles into an octameric ring, which can bind up to four 63-bp DNA oligonucleotides. Phylogenetic cluster analysis showed that the CrgA-like regulators form a subclass of the LTTRs that function as octamers. The CrgA is an auto-repressor of its own gene a
Probab=99.92 E-value=1.2e-24 Score=167.66 Aligned_cols=195 Identities=13% Similarity=0.168 Sum_probs=154.8
Q ss_pred CcEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccCCCCCceeeccccceEEEEe
Q psy3760 93 GNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLISIPCYQWEYVIIV 172 (306)
Q Consensus 93 ~~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~~~~~~~~~l~~~~~~~v~ 172 (306)
|.|+||++++++..++++++..|.++||++++++... ..+.+.+ +|++|++|...+ ...+++.+.+++++++++++
T Consensus 1 g~l~Ig~~~~~~~~~l~~~l~~~~~~~P~i~l~i~~~--~~~~~~~-~~~~D~~i~~~~-~~~~~~~~~~l~~~~~~~v~ 76 (197)
T cd08477 1 GKLRISAPVTFGSHVLTPALAEYLARYPDVRVDLVLS--DRLVDLV-EEGFDAAFRIGE-LADSSLVARPLAPYRMVLCA 76 (197)
T ss_pred CeEEEeCCHHHHHHHHHHHHHHHHHHCCCcEEEEEec--CCcchhh-hcCccEEEECCC-CCCCCeeEEEeeeeEEEEEE
Confidence 5799999999999999999999999999999999863 3455544 577999998644 45688999999999999999
Q ss_pred cCCCCCCCCCCcChhhhcCCCeEeecCCCCcHH-HHHHHHHhCCCceeEEEEecCHHHHHHHHHhccceeeeecceeccc
Q psy3760 173 PLDHPLLLLNSISLKEISNYPLITYDLSFSGRI-KLDREFSLQKLTPYIVLETINSDIIKTYVELRMGIGIIASIAFDSN 251 (306)
Q Consensus 173 ~~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~~~p~~~~~~~ 251 (306)
+++|+...+..++++||.++|++.+..+..... .........++.+++.+++++..+++.++.+|.|++++|.+.+...
T Consensus 77 ~~~~~~~~~~~~~~~~L~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~Gia~~p~~~~~~~ 156 (197)
T cd08477 77 SPDYLARHGTPTTPEDLARHECLGFSYWRARNRWRLEGPGGEVKVPVSGRLTVNSGQALRVAALAGLGIVLQPEALLAED 156 (197)
T ss_pred CHHHHhhCCCCCCHHHHhhCcceeecCCCCCccEEEecCCCceEEecCCcEEEcCHHHHHHHHHcCCceEechHHHHHHH
Confidence 999954444579999999999998876422111 1111122235677888999999999999999999999999887654
Q ss_pred -ccCCceeeecCCCCccceEEEEEeCCccccHHHHHHHHHH
Q psy3760 252 -RDKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLL 291 (306)
Q Consensus 252 -~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l 291 (306)
..+.++.+..........++++|++++..++.++.|++++
T Consensus 157 ~~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~f~~~l 197 (197)
T cd08477 157 LASGRLVELLPDYLPPPRPMHLLYPPDRRPTPKLRSFIDFL 197 (197)
T ss_pred HHcCCcEEeCCcccCCCCcEEEEecCCccccHHHHHHHhhC
Confidence 5677776654433456799999999988899999999864
No 107
>cd08479 PBP2_CrgA_like_9 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold. This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 9. The LTTRs are acting as both auto-repressors and activators of target promoters, controlling operons involved in a wide variety of cellular processes such as amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to name a few. In contrast to the tetrameric form of other LTTRs, CrgA from Neisseria meningitides assembles into an octameric ring, which can bind up to four 63-bp DNA oligonucleotides. Phylogenetic cluster analysis showed that the CrgA-like regulators form a subclass of the LTTRs that function as octamers. The CrgA is an auto-repressor of its own gene a
Probab=99.91 E-value=1.2e-24 Score=167.86 Aligned_cols=195 Identities=11% Similarity=0.064 Sum_probs=154.6
Q ss_pred CcEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccCCCCCceeeccccceEEEEe
Q psy3760 93 GNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLISIPCYQWEYVIIV 172 (306)
Q Consensus 93 ~~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~~~~~~~~~l~~~~~~~v~ 172 (306)
|.|+||++++++..++++++..|.++||++++++...+ ..+.+.+|++|++|+..+ ...+++.+.+++++++++++
T Consensus 1 g~l~Ig~~~~~~~~~l~~~l~~f~~~~P~i~i~~~~~~---~~~~l~~g~~Dl~i~~~~-~~~~~l~~~~l~~~~~~~~~ 76 (198)
T cd08479 1 GLLRVNASFGFGRRHIAPALSDFAKRYPELEVQLELTD---RPVDLVEEGFDLDIRVGD-LPDSSLIARKLAPNRRILCA 76 (198)
T ss_pred CcEEEeccHHHHHHHHHHHHHHHHHHCCCeEEEEEecC---ccccccccCccEEEEcCC-CCCccceeeeccCCceEEEE
Confidence 57999999999999999999999999999999998643 346899999999998543 45678999999999999999
Q ss_pred cCCCCCCCCCCcChhhhcCCCeEeecCCCCcHHH--HHHHHHhCCCceeEEEEecCHHHHHHHHHhccceeeeecceecc
Q psy3760 173 PLDHPLLLLNSISLKEISNYPLITYDLSFSGRIK--LDREFSLQKLTPYIVLETINSDIIKTYVELRMGIGIIASIAFDS 250 (306)
Q Consensus 173 ~~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~~~p~~~~~~ 250 (306)
+++|+......++++||.++|++.+......... +...+...+..++..+++++..+++.++.+|.|++++|...+..
T Consensus 77 ~~~~~~~~~~~~~~~~L~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~Gv~~~p~~~~~~ 156 (198)
T cd08479 77 SPAYLERHGAPASPEDLARHDCLVIRENDEDFGLWRLRNGDGEATVRVRGALSSNDGEVVLQWALDGHGIILRSEWDVAP 156 (198)
T ss_pred CHHHHHhCCCCCCHHHHhhCcCeEecccCCCccceEEecCCCeEEEeeCCeEEECCHHHHHHHHHcCCcEEeccHHHHHH
Confidence 9998654445799999999999987654322111 22223344566788899999999999999999999999977654
Q ss_pred c-ccCCceeeecCCCCccceEEEEEeCCccccHHHHHHHHHH
Q psy3760 251 N-RDKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLL 291 (306)
Q Consensus 251 ~-~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l 291 (306)
. ..+.++.+.........+++++|++++..++.++.|++++
T Consensus 157 ~~~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~f~~~l 198 (198)
T cd08479 157 YLRSGRLVRVLPDWQLPDADIWAVYPSRLSRSARVRVFVDFL 198 (198)
T ss_pred HHhCCceEEecCcccCCCCCEEEEccccccccHHHHHHHhhC
Confidence 4 4566665533222345799999999988999999999864
No 108
>cd08439 PBP2_LrhA_like The C-terminal substrate domain of LysR-like regulator LrhA (LysR homologue A) and that of closely related homologs, contains the type 2 periplasmic binding fold. This CD represents the LrhA subfamily of LysR-like bacterial transcriptional regulators, including LrhA, HexA, PecT, and DgdR. LrhA is involved in control of the transcription of flagellar, motility, and chemotaxis genes by regulating the synthesis and concentration of FlhD(2)C(2), the master regulator for the expression of flagellar and chemotaxis genes. The LrhA protein has strong homology to HexA and PecT from plant pathogenic bacteria, in which HexA and PecT act as repressors of motility and of virulence factors, such as exoenzymes required for lytic reactions. DgdR also shares similar characteristics to those of LrhA, HexA and PecT. The topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a vari
Probab=99.91 E-value=1.1e-22 Score=155.19 Aligned_cols=182 Identities=15% Similarity=0.165 Sum_probs=154.9
Q ss_pred cEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccCCCCCceeeccccceEEEEec
Q psy3760 94 NLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLISIPCYQWEYVIIVP 173 (306)
Q Consensus 94 ~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~~~~~~~~~l~~~~~~~v~~ 173 (306)
+++||+++++...++++++..|.++||++++++....+.++.+.|.+|++|++|+..+ .+++...+++.++++++++
T Consensus 1 ~l~i~~~~~~~~~~l~~~l~~~~~~~P~v~i~~~~~~~~~~~~~l~~~~~Dl~i~~~~---~~~~~~~~l~~~~~~~v~~ 77 (185)
T cd08439 1 TLRIGCPDDYADTILPFLLNRFASVYPRLAIEVVCKRTPRLMEMLERGEVDLALITHP---PPGASATILRRSPTVWYCA 77 (185)
T ss_pred CeEEEcchhHhHHHHHHHHHHHHHHCCCeEEEEEECChHHHHHHHHCCCCcEEEEecc---CCCCCceEEEEecCEEEEC
Confidence 4899999999999999999999999999999999998889999999999999998532 3568889999999999999
Q ss_pred CCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCceeEEEEecCHHHHHHHHHhccceeeeecceeccccc
Q psy3760 174 LDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMGIGIIASIAFDSNRD 253 (306)
Q Consensus 174 ~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~~~p~~~~~~~~~ 253 (306)
++||+..+.+ .|++....+...+..+..++...++.+++.+++++...+.+++.+|.|++++|...+..
T Consensus 78 ~~~~~~~~~~--------~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~~~p~~~~~~--- 146 (185)
T cd08439 78 AGYILAPGEP--------LPLALLDEPTLDRRAALAALDAAGIPWRIAYAASSLSGLRAAVRAGLGITARTQEMVPP--- 146 (185)
T ss_pred CCCccCcCCC--------ccEEEcCCCCcHHHHHHHHHHhcCCCceEEEEeCCHHHHHHHHHcCceeeecccCCCCc---
Confidence 9999775432 37888877666777888899999999999999999999999999999999999987643
Q ss_pred CCceeeecCC--C-CccceEEEEEeCCccccHHHHHHHHHH
Q psy3760 254 KNLRSISASH--L-FGTTISRVIIKQGTYLRSYVYSFIKLL 291 (306)
Q Consensus 254 ~~l~~~~~~~--~-~~~~~~~l~~~~~~~~~~~~~~~~~~l 291 (306)
++..+|+.. + .....++++|+++. .++.++.|+++|
T Consensus 147 -~l~~~~~~~~~~~~~~~~~~l~~~~~~-~~~~~~~f~~~~ 185 (185)
T cd08439 147 -DLRILGESEGLPPLPDTGYTLCLDPNR-PSELAQAFFEAL 185 (185)
T ss_pred -cceEeccccCCCCCCcceEEEEecCCC-ccHHHHHHHhhC
Confidence 577777753 1 23568999998655 588999998864
No 109
>cd08428 PBP2_IciA_ArgP The C-terminal substrate binding domain of LysR-type transcriptional regulator, ArgP (IciA), for arginine exporter (ArgO); contains the type 2 periplasmic binding fold. The inhibitor of chromosomal replication (iciA) protein encoded by Mycobacterium tuberculosis, which is implicated in chromosome replication initiation in vitro, has been identified as arginine permease (ArgP), a LysR-type transcriptional regulator for arginine outward transport, based on the same amino sequence and similar DNA binding targets. Arp has been shown to regulate various targets including DnaA (replication), ArgO (arginine export), dapB (lysine biosynthesis), and gdhA (glutamate biosynthesis). With abundant nutrition, ArgP activates the DnaA gene (to increase replication) and the ArgO (to export redundant molecules). However, when nutrition supply is limited, it is suggested that ArgP might function as an inhibitor of chromosome replication in order to slow replication. This substrate-
Probab=99.91 E-value=4.2e-23 Score=158.89 Aligned_cols=191 Identities=11% Similarity=0.132 Sum_probs=155.3
Q ss_pred cEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccCCCCCceeeccccceEEEEec
Q psy3760 94 NLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLISIPCYQWEYVIIVP 173 (306)
Q Consensus 94 ~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~~~~~~~~~l~~~~~~~v~~ 173 (306)
+|+||++.+....++++.+.+|.+++ ++++++...++.++.+.+.+|++|+++...+ ...+++...++++++++++++
T Consensus 1 ~l~Ig~~~~~~~~~l~~~l~~f~~~~-~v~l~l~~~~~~~~~~~l~~~~~D~~i~~~~-~~~~~~~~~~l~~~~~~~~~~ 78 (195)
T cd08428 1 TLPVAVNADSLATWFLPALAPVLKRE-RILLDLIVDDEDRTHDLLRDGEVVGCISTQA-QPMQGCRSDYLGSMDYLLVAS 78 (195)
T ss_pred CEEEEechhHHHHHhHHHHHHHHhCc-CeEEEEEeCCchhHHHHHHcCcceEEEEecC-CCCCCceeEEeeeeeEEEEEC
Confidence 48999997766677888999999995 9999999998889999999999999997544 455789999999999999999
Q ss_pred CCCCCCC-CCCcChhhhcCCCeEeecCCCCcH-HHHHHHHHhCCCceeEEEEecCHHHHHHHHHhccceeeeecceeccc
Q psy3760 174 LDHPLLL-LNSISLKEISNYPLITYDLSFSGR-IKLDREFSLQKLTPYIVLETINSDIIKTYVELRMGIGIIASIAFDSN 251 (306)
Q Consensus 174 ~~~~l~~-~~~i~~~dl~~~~~i~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~~~p~~~~~~~ 251 (306)
++|+... ...++++||.++|+|.+..+...+ ..+...+...+ .+++.+++++...+.+++.+|.|++++|...+...
T Consensus 79 ~~~~~~~~~~~i~~~~L~~~~~i~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~v~~G~Gi~~lp~~~~~~~ 157 (195)
T cd08428 79 PDFAARYFPNGLTREALLKAPAVAFNRKDDLHQSFLQQHFGLPP-GSYPCHYVPSSEAFVDLAAQGLAYGMIPELQIEPE 157 (195)
T ss_pred CcchhhcCCCCCCHHHHhcCcEEEEcCCCchhHHHHHHHhccCC-CCceEEEECCHHHHHHHHHhCCeeEeccHHHHHHH
Confidence 9998543 357999999999999988766553 23344443333 44567889999999999999999999999887654
Q ss_pred -ccCCceeeecCCCCccceEEEEEeCCccccHHHHHHHHH
Q psy3760 252 -RDKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKL 290 (306)
Q Consensus 252 -~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~ 290 (306)
..+.++.++ . ....+++++|++++..+++++.|++.
T Consensus 158 ~~~~~l~~l~--~-~~~~~~~l~~~~~~~~s~~~~~~~~~ 194 (195)
T cd08428 158 LASGELIDLA--P-GHLLRVTLYWHRWNLESGLMKRLSRA 194 (195)
T ss_pred hcCCCEEEcc--C-cccccceEEEecccccCHHHHHhhhc
Confidence 455565443 2 34579999999999999999999875
No 110
>cd08470 PBP2_CrgA_like_1 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding domain. This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 1. The LTTRs are acting as both auto-repressors and activators of target promoters, controlling operons involved in a wide variety of cellular processes such as amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to name a few. In contrast to the tetrameric form of other LTTRs, CrgA from Neisseria meningitides assembles into an octameric ring, which can bind up to four 63-bp DNA oligonucleotides. Phylogenetic cluster analysis showed that the CrgA-like regulators form a subclass of the LTTRs that function as octamers. The CrgA is an auto-repressor of its own gene
Probab=99.91 E-value=1.6e-24 Score=167.00 Aligned_cols=195 Identities=10% Similarity=0.054 Sum_probs=154.4
Q ss_pred CcEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccCCCCCceeeccccceEEEEe
Q psy3760 93 GNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLISIPCYQWEYVIIV 172 (306)
Q Consensus 93 ~~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~~~~~~~~~l~~~~~~~v~ 172 (306)
|.|+||++++++..++++++..|.++||++++++... ..+.+ +.++++|+||+..+ ...+++...+++++++++++
T Consensus 1 g~l~Ig~~~~~~~~~l~~~l~~f~~~~P~v~l~i~~~--~~~~~-~~~~~~D~~i~~~~-~~~~~~~~~~l~~~~~~~v~ 76 (197)
T cd08470 1 GLLRITCPVAYGERFIAPLVNDFMQRYPKLEVDIELT--NRVVD-LVSEGFDLAIRLGR-LTDSSLMARRLASRRHYVCA 76 (197)
T ss_pred CeEEEEcCHHHHHHHHHHHHHHHHHHCCCeEEEEEec--CCccc-hhccCccEEEEcCC-CCccchhhhhccCCceEEEE
Confidence 5799999999999999999999999999999999853 24455 55678999998544 45577999999999999999
Q ss_pred cCCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCceeEEEEecCHHHHHHHHHhccceeeeecceeccc-
Q psy3760 173 PLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMGIGIIASIAFDSN- 251 (306)
Q Consensus 173 ~~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~~~p~~~~~~~- 251 (306)
+++|+...+..++++||.++|++...... . .+.......+..+++.+++++..++++++.+|.|++++|.+.+...
T Consensus 77 ~~~~~~~~~~~~~~~~L~~~~~i~~~~~~-~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~Gi~~lp~~~~~~~~ 153 (197)
T cd08470 77 SPAYLERHGTPHSLADLDRHNCLLGTSDH-W--RFQENGRERSVRVQGRWRCNSGVALLDAALKGMGLAQLPDYYVDEHL 153 (197)
T ss_pred CHHHHHHcCCCCCHHHHhhCCceeccCcC-c--eEcCCCcEEEecCCCcEEECCHHHHHHHHHcCCcEEEechHHhHHHH
Confidence 99986544456899999999999854321 1 1111122235567778999999999999999999999999877654
Q ss_pred ccCCceeeecCCCCccceEEEEEeCCccccHHHHHHHHHHhHH
Q psy3760 252 RDKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLLSPK 294 (306)
Q Consensus 252 ~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~ 294 (306)
..+.++.++..+......++++|++++..++.++.|++++++.
T Consensus 154 ~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~ 196 (197)
T cd08470 154 AAGRLVPVLEDYRPPDEGIWALYPHNRHLSPKVRLLVDYLADA 196 (197)
T ss_pred HcCCcEEccccccCCCCcEEEEeCCchhccHHHHHHHHHHHhc
Confidence 5566776654434456799999999988899999999998764
No 111
>cd08473 PBP2_CrgA_like_4 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold. This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 4. The LTTRs are acting as both auto-repressors and activators of target promoters, controlling operons involved in a wide variety of cellular processes such as amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to name a few. In contrast to the tetrameric form of other LTTRs, CrgA from Neisseria meningitides assembles into an octameric ring, which can bind up to four 63-bp DNA oligonucleotides. Phylogenetic cluster analysis showed that the CrgA-like regulators form a subclass of the LTTRs that function as octamers. The CrgA is an auto-repressor of its own gene a
Probab=99.91 E-value=2.3e-24 Score=166.73 Aligned_cols=197 Identities=14% Similarity=0.096 Sum_probs=153.9
Q ss_pred CCcEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEcccc-CCCCCceeeccccceEEE
Q psy3760 92 TGNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEIL-SPSDKLISIPCYQWEYVI 170 (306)
Q Consensus 92 ~~~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~-~~~~~~~~~~l~~~~~~~ 170 (306)
.|+++||++++++..++++++..|.++||++++++..... .. .+.+|++|++|+.... ...+++.+.+++++++++
T Consensus 2 ~g~l~Ig~~~~~~~~~l~~~l~~~~~~~P~i~i~~~~~~~--~~-~~~~~~~D~~i~~~~~~~~~~~~~~~~l~~~~~~~ 78 (202)
T cd08473 2 RGTVRVSCPPALAQELLAPLLPRFMAAYPQVRLQLEATNR--RV-DLIEEGIDVALRVRFPPLEDSSLVMRVLGQSRQRL 78 (202)
T ss_pred CceEEEeccHHHHHHHHHHHHHHHHHHCCCeEEEEEEcCC--cc-cccccCccEEEEeCCCCCCCcceeEEeccCcceEE
Confidence 4789999999999999999999999999999999987543 23 3558899999974332 335789999999999999
Q ss_pred EecCCCCCCCCCCcChhhhcCCCeEeecCCCCc--HHHHHHHHHhCCCceeEEEEecCHHHHHHHHHhccceeeeeccee
Q psy3760 171 IVPLDHPLLLLNSISLKEISNYPLITYDLSFSG--RIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMGIGIIASIAF 248 (306)
Q Consensus 171 v~~~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~~~p~~~~ 248 (306)
+++++|+...+..++++||.++|++.+..+... +..+...+...+..+++.+++++...+++++.+|.|++++|.+.+
T Consensus 79 v~~~~~~~~~~~~~~~~~L~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~~~p~~~~ 158 (202)
T cd08473 79 VASPALLARLGRPRSPEDLAGLPTLSLGDVDGRHSWRLEGPDGESITVRHRPRLVTDDLLTLRQAALAGVGIALLPDHLC 158 (202)
T ss_pred EECHHHHHhCCCCCChHHHhhCCeEEEEccCCCCceEeecCCCcEEEecCCCcEEECCHHHHHHHHHhCCCeeeccHHHH
Confidence 999998543334479999999999998765322 111222233345556778899999999999999999999999887
Q ss_pred ccc-ccCCceeeecCCCCccceEEEEEeCCccccHHHHHHHHHH
Q psy3760 249 DSN-RDKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLL 291 (306)
Q Consensus 249 ~~~-~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l 291 (306)
... ..+.++.+..........++++|++++..+++++.|++++
T Consensus 159 ~~~~~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~f~~~l 202 (202)
T cd08473 159 REALRAGRLVRVLPDWTPPRGIVHAVFPSRRGLLPAVRALIDFL 202 (202)
T ss_pred HHHHHcCcEEEeccCCcCCCccEEEEecCCCCCCHHHhhHHhhC
Confidence 654 5666765543333345689999999999999999999864
No 112
>cd08476 PBP2_CrgA_like_7 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold. This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 7. The LTTRs are acting as both auto-repressors and activators of target promoters, controlling operons involved in a wide variety of cellular processes such as amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to name a few. In contrast to the tetrameric form of other LTTRs, CrgA from Neisseria meningitides assembles into an octameric ring, which can bind up to four 63-bp DNA oligonucleotides. Phylogenetic cluster analysis showed that the CrgA-like regulators form a subclass of the LTTRs that function as octamers. The CrgA is an auto-repressor of its own gene a
Probab=99.91 E-value=4.8e-24 Score=164.15 Aligned_cols=193 Identities=14% Similarity=0.179 Sum_probs=149.1
Q ss_pred CcEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccCCCCCceeeccccceEEEEe
Q psy3760 93 GNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLISIPCYQWEYVIIV 172 (306)
Q Consensus 93 ~~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~~~~~~~~~l~~~~~~~v~ 172 (306)
|+|+||++ . ...++++++..|.++||++++++.. +.++.+.+.+ ++|++|+..+ ...+++...++.++++++++
T Consensus 1 g~l~ig~~-~-~~~~l~~~l~~~~~~~P~v~i~~~~--~~~~~~~l~~-~~D~~i~~~~-~~~~~~~~~~l~~~~~~~v~ 74 (197)
T cd08476 1 GRLRVSLP-L-VGGLLLPVLAAFMQRYPEIELDLDF--SDRLVDVIDE-GFDAVIRTGE-LPDSRLMSRRLGSFRMVLVA 74 (197)
T ss_pred CeEEEEec-c-hHHHHHHHHHHHHHHCCCeEEEEEe--cCCccccccc-CeeEEEEeCC-CCCCCeeEEEeecccEEEEE
Confidence 57999998 4 5678889999999999999999964 3455665655 4999998644 45678999999999999999
Q ss_pred cCCCCCCCCCCcChhhhcCCCeEeecCCCC-cHHHH--HHHHHhCCCceeEEEEecCHHHHHHHHHhccceeeeecceec
Q psy3760 173 PLDHPLLLLNSISLKEISNYPLITYDLSFS-GRIKL--DREFSLQKLTPYIVLETINSDIIKTYVELRMGIGIIASIAFD 249 (306)
Q Consensus 173 ~~~~~l~~~~~i~~~dl~~~~~i~~~~~~~-~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~~~p~~~~~ 249 (306)
+++|+...+..++++||.++|++.+..... ....+ ...+...+..++..+++++...+.+++.+|.|++++|...+.
T Consensus 75 ~~~~~~~~~~~~~~~~L~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~Gi~ilp~~~~~ 154 (197)
T cd08476 75 SPDYLARHGTPETPADLAEHACLRYRFPTTGKLEPWPLRGDGGDPELRLPTALVCNNIEALIEFALQGLGIACLPDFSVR 154 (197)
T ss_pred CHHHHHhCCCCCCHHHHhcCceEEeeccCCCCCcceEEecCCceEEEecCCceEECCHHHHHHHHHhCCeEEEcCHHHHH
Confidence 999964444578999999999998754322 11111 112233356678889999999999999999999999998776
Q ss_pred cc-ccCCceeeecCCCCccceEEEEEeCCccccHHHHHHHHHH
Q psy3760 250 SN-RDKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLL 291 (306)
Q Consensus 250 ~~-~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l 291 (306)
.. ..+.++.++..+.....+++++|++++..++.++.|++++
T Consensus 155 ~~~~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~f~~~l 197 (197)
T cd08476 155 EALADGRLVTVLDDYVEERGQFRLLWPSSRHLSPKLRVFVDFM 197 (197)
T ss_pred HHhhcCCeEEccccccCCCCCEEEEecccccCCHHHHHHHhhC
Confidence 54 5566776654443456789999999998999999999864
No 113
>TIGR00637 ModE_repress ModE molybdate transport repressor domain. ModE is a molybdate-activated repressor of the molybdate transport operon in E. coli. It consists of the domain represented by this model and two tandem copies of mop-like domain, where Mop proteins are a family of 68-residue molybdenum-pterin binding proteins of Clostridium pasteurianum. This model also represents the full length of a pair of archaeal proteins that lack Mop-like domains. PSI-BLAST analysis shows similarity to helix-turn-helix regulatory proteins.
Probab=99.90 E-value=1.6e-23 Score=139.18 Aligned_cols=83 Identities=16% Similarity=0.167 Sum_probs=77.4
Q ss_pred CchhhHHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEec-----CCCccccCHhHHHHHHHHHHHHH
Q psy3760 1 MNLHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRH-----GKRIRGLTKPGQAILRSIEIIMQ 75 (306)
Q Consensus 1 m~~~~l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~-----~~~~~~lT~~G~~l~~~a~~il~ 75 (306)
|+.+++++|.+|+++| ||++||+.||+|||++|++|++||+.||.+||+|+ ++|+ +||++|+.|++.++++.+
T Consensus 2 ~~~~~l~~~~av~~~g-Sis~AA~~L~iS~stvs~~I~~LE~~lg~~Lf~R~~~g~~~~g~-~lT~~G~~l~~~~~~~~~ 79 (99)
T TIGR00637 2 ADPRRVALLKAIARMG-SISQAAKDAGISYKSAWDYIRAMNNLSGEPLVERATGGKGGGGA-VLTEYGQRLIQLYDLLER 79 (99)
T ss_pred CCHHHHHHHHHHHHhC-CHHHHHHHHCCCHHHHHHHHHHHHHHhCCCeEEecCCCCCCCCe-eECHHHHHHHHHHHHHHH
Confidence 6889999999999999 99999999999999999999999999999999998 4588 799999999999999999
Q ss_pred HHHHHHHHHH
Q psy3760 76 EIEGLKKIGK 85 (306)
Q Consensus 76 ~~~~~~~~~~ 85 (306)
.++.+.+...
T Consensus 80 ~~~~~~~~~~ 89 (99)
T TIGR00637 80 ILEKAFSVLE 89 (99)
T ss_pred HHHHHHHHhh
Confidence 9988886443
No 114
>cd08483 PBP2_HvrB The C-terminal substrate-binding domain of LysR-type transcriptional regulator HvrB, an activator of S-adenosyl-L-homocysteine hydrolase expression, contains the type 2 periplasmic binding fold. The transcriptional regulator HvrB of the LysR family is required for the light-dependent activation of both ahcY, which encoding the enzyme S-adenosyl-L-homocysteine hydrolase (AdoHcyase) that responsible for the reversible hydrolysis of AdoHcy to adenosine and homocysteine, and orf5, a gene of unknown. The topology of this C-terminal domain of HvrB is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transp
Probab=99.90 E-value=2.3e-23 Score=159.60 Aligned_cols=187 Identities=18% Similarity=0.170 Sum_probs=153.9
Q ss_pred cEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccCCCCCceeeccccceEEEEec
Q psy3760 94 NLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLISIPCYQWEYVIIVP 173 (306)
Q Consensus 94 ~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~~~~~~~~~l~~~~~~~v~~ 173 (306)
.|+||++++++..++++++..|.++||++++++.... ....+.+|++|++|+..+ ...+++...++++++++++++
T Consensus 1 ~l~Ig~~~~~~~~~l~~~l~~~~~~~P~i~l~~~~~~---~~~~l~~g~~Dl~i~~~~-~~~~~~~~~~l~~~~~~~v~~ 76 (190)
T cd08483 1 PLTVTLTPSFASNWLMPRLGSFWAKHPEIELSLLPSA---DLVDLRPDGIDVAIRYGN-GDWPGLESEPLTAAPFVVVAA 76 (190)
T ss_pred CeEEEeCcHHHHhhHHhhHHHHHHHCCCceEEEEecC---CcCCCCCCCcCEEEEecC-CCCCCcEEEeecccceEeeeC
Confidence 3899999999999999999999999999999997532 356799999999999643 456789999999999999999
Q ss_pred CCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCcee--EEEEecCHHHHHHHHHhccceeeeecceeccc
Q psy3760 174 LDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPY--IVLETINSDIIKTYVELRMGIGIIASIAFDSN 251 (306)
Q Consensus 174 ~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~v~~g~gi~~~p~~~~~~~ 251 (306)
++| ++.+..++++||.++|++..... ..+..++...|..++ ..+++++...+.+++.+|.|++++|...+...
T Consensus 77 ~~~-~~~~~~~~~~~L~~~~~i~~~~~----~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~Gi~~~p~~~~~~~ 151 (190)
T cd08483 77 PGL-LGDRKVDSLADLAGLPWLQERGT----NEQRVWLASMGVVPDLERGVTFLPGQLVLEAARAGLGLSIQARALVEPD 151 (190)
T ss_pred HHH-HhhCCCCCHHHHhcCceeccCCc----hHHHHHHHHcCCCcccccCceeCcHHHHHHHHHcCCcEEeecHHhhHHH
Confidence 997 56666799999999999985422 345678888888765 46889999999999999999999999887654
Q ss_pred -ccCCceeeecCCCCccceEEEEEeCCccccHHHHHHHHHH
Q psy3760 252 -RDKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLL 291 (306)
Q Consensus 252 -~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l 291 (306)
..+.++.++... .....++++|+++. .++.++.|++++
T Consensus 152 ~~~~~l~~~~~~~-~~~~~~~l~~~~~~-~~~~~~~f~~~l 190 (190)
T cd08483 152 IAAGRLTVLFEEE-EEGLGYHIVTRPGV-LRPAAKAFVRWL 190 (190)
T ss_pred HHCCCcccccccc-CCCCcEEEEecCCC-CCHHHHHHhhhC
Confidence 456676665442 34578999998875 689999998864
No 115
>PF00126 HTH_1: Bacterial regulatory helix-turn-helix protein, lysR family; InterPro: IPR000847 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. One such family, the lysR family, groups together a range of proteins, including ampR, catM, catR, cynR, cysB, gltC, iciA, ilvY, irgB, lysR, metR, mkaC, mleR, nahR, nhaR, nodD, nolR, oxyR, pssR, rbcR, syrM, tcbR, tfdS and trpI [, , , , ]. The majority of these proteins appear to be transcription activators and most are known to negatively regulate their own expression. All possess a potential HTH DNA-binding motif towards their N-termini.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 3T1B_D 3SZP_A 1O7L_C 1B9N_A 1B9M_A 3FZJ_J 3FXR_B 3FXQ_A 3FXU_A 2IJL_B ....
Probab=99.90 E-value=7.2e-24 Score=128.53 Aligned_cols=60 Identities=37% Similarity=0.588 Sum_probs=56.4
Q ss_pred hhhHHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCCccccCHhHH
Q psy3760 3 LHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKPGQ 64 (306)
Q Consensus 3 ~~~l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~~~lT~~G~ 64 (306)
|++|++|++++++| |+++||+.||+|||++|++|++||++||++||+|+++++ .||++|+
T Consensus 1 l~~l~~f~~v~~~g-s~~~AA~~l~is~~~vs~~i~~LE~~lg~~Lf~r~~~~~-~lT~~G~ 60 (60)
T PF00126_consen 1 LRQLRYFLAVAETG-SISAAAEELGISQSAVSRQIKQLEEELGVPLFERSGRGL-RLTEAGE 60 (60)
T ss_dssp HHHHHHHHHHHHHS-SHHHHHHHCTSSHHHHHHHHHHHHHHHTS-SEEECSSSE-EE-HHHH
T ss_pred ChHHHHHHHHHHhC-CHHHHHHHhhccchHHHHHHHHHHHHhCCeEEEECCCCe-eEChhhC
Confidence 68999999999999 999999999999999999999999999999999999998 7999996
No 116
>TIGR02136 ptsS_2 phosphate binding protein. Members of this family are phosphate-binding proteins. Most are found in phosphate ABC-transporter operons, but some are found in phosphate regulatory operons. This model separates members of the current family from the phosphate ABC transporter phosphate binding protein described by TIGRFAMs model TIGR00975.
Probab=99.90 E-value=1.7e-22 Score=163.84 Aligned_cols=211 Identities=15% Similarity=0.164 Sum_probs=164.0
Q ss_pred CCCcEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccCC---------CCCceee
Q psy3760 91 DTGNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSP---------SDKLISI 161 (306)
Q Consensus 91 ~~~~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~---------~~~~~~~ 161 (306)
.+..|+||+++++.. ++++++..|.++||++++++....+.++++.|.+|++|++++..+... ..++...
T Consensus 34 ~~~~lrig~s~s~~~-~lp~~l~~f~~~~P~i~v~i~~~~s~~l~~~L~~G~iDlai~~~~~~~~~~~~~~~~~~~l~~~ 112 (287)
T TIGR02136 34 GSSTITIDGSTTVAP-LAEAAAEEFQKIHPGVSVTVQGAGSGTGIKALINGTVDIGNSSRPIKDEELQKDKQKGIKLIEH 112 (287)
T ss_pred ccceEEEeccchHHH-HHHHHHHHHHhhCCCceEEEccCCchHHHHHHHcCCCchhhccCCCCHHHHHHHhhcCCCceEE
Confidence 456899999999764 899999999999999999999999999999999999999998643221 1248899
Q ss_pred ccccceEEEEecCCC-CCCCC-----------CCcCh----hhhcCCCeEeec--CCCCcHHHHHHHH-HhCCCceeEEE
Q psy3760 162 PCYQWEYVIIVPLDH-PLLLL-----------NSISL----KEISNYPLITYD--LSFSGRIKLDREF-SLQKLTPYIVL 222 (306)
Q Consensus 162 ~l~~~~~~~v~~~~~-~l~~~-----------~~i~~----~dl~~~~~i~~~--~~~~~~~~~~~~~-~~~~~~~~~~~ 222 (306)
+++.++++++++++| |++.. ...++ +||.++|++... .+...+..+.+++ ...+..++..
T Consensus 113 ~l~~~~l~lvv~~~h~pl~~~~~~~L~~l~~~~~~s~~~l~~dL~~~pli~~~~~~~~~~~~~~~~~l~~~~~~~~~~~- 191 (287)
T TIGR02136 113 KVAVDGLAVVVNKKNVPVDDLTVEQLKKIYSGEITNWKEVGGDLPNKPIVVVGRNAGSGTRDTFEEEVMGKAKIKPGKN- 191 (287)
T ss_pred EEEEeeEEEEECCCCCccccCCHHHHHHHhcCCcCcHhhcCCCCCCCceEEEecCCCCChHHHHHHHhccccccCccce-
Confidence 999999999999998 98753 23466 455689998854 4445777777765 4556666554
Q ss_pred EecCHHHHHHHHHhcc-ceeeeecceeccc-ccCCceeee-----cCC--CCccceEEEEEeCCccccHHHHHHHHHHhH
Q psy3760 223 ETINSDIIKTYVELRM-GIGIIASIAFDSN-RDKNLRSIS-----ASH--LFGTTISRVIIKQGTYLRSYVYSFIKLLSP 293 (306)
Q Consensus 223 ~~~~~~~~~~~v~~g~-gi~~~p~~~~~~~-~~~~l~~~~-----~~~--~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~ 293 (306)
++++.++++++|..|. |++++|...+... ....+..++ +.. ....++++++|++++..++.++.|++++++
T Consensus 192 ~~~s~~~i~~~V~~g~~gia~lp~~~v~~~~~~~~l~~~~~~~~~i~~~~~~~~~~l~L~~~~~~~~~~~~~~f~~~l~~ 271 (287)
T TIGR02136 192 EQESNGAVVSIVSSNPGAIGYLGLGYVDDSVKTLKVNGVEPSKENIANGSYPLSRPLFMYVNGKPKKPELVAEFIDFVLS 271 (287)
T ss_pred ecCCcHHHHHHHhcCCCceEEeehHHhhCCcceEEECCccCCHHHHhCCCccceeeEEEEEcCCCCCcHHHHHHHHHHhC
Confidence 9999999999999997 8999999887653 211111111 111 135779999999999999999999999988
Q ss_pred Hh-hHHHHHhh
Q psy3760 294 KL-NRKFINKI 303 (306)
Q Consensus 294 ~~-~~~~~~~~ 303 (306)
.- .+...++.
T Consensus 272 ~~~~~~~~~~~ 282 (287)
T TIGR02136 272 DDGGERIVEEL 282 (287)
T ss_pred chHhhHHHHHc
Confidence 77 56655554
No 117
>cd08480 PBP2_CrgA_like_10 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold. This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 10. The LTTRs are acting as both auto-repressors and activators of target promoters, controlling operons involved in a wide variety of cellular processes such as amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to name a few. In contrast to the tetrameric form of other LTTRs, CrgA from Neisseria meningitides assembles into an octameric ring, which can bind up to four 63-bp DNA oligonucleotides. Phylogenetic cluster analysis showed that the CrgA-like regulators form a subclass of the LTTRs that function as octamers. The CrgA is an auto-repressor of its own gene
Probab=99.89 E-value=2.1e-23 Score=161.04 Aligned_cols=191 Identities=12% Similarity=0.157 Sum_probs=149.7
Q ss_pred CcEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccCCCCCceeeccccceEEEEe
Q psy3760 93 GNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLISIPCYQWEYVIIV 172 (306)
Q Consensus 93 ~~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~~~~~~~~~l~~~~~~~v~ 172 (306)
|.|+||++.+++..++++++..|.++||++++++... .+..+ +.+|++|++|+..+ ...+++.+.+++++++++++
T Consensus 1 g~l~Ig~~~~~~~~~l~~~l~~~~~~~P~i~i~i~~~--~~~~~-~~~~~~D~~i~~~~-~~~~~~~~~~l~~~~~~~~~ 76 (198)
T cd08480 1 GRLRVNASVPFGTHFLLPLLPAFLARYPEILVDLSLT--DEVVD-LLAERTDVAIRVGP-LPDSSLVARKLGESRRVIVA 76 (198)
T ss_pred CeEEEEccHHHHhHhhHHHHHHHHHHCCCeEEEEEec--CCccc-cccccccEEEEeCC-CCCCCeEEEEcccceEEEEE
Confidence 5799999999999999999999999999999999742 34444 55899999998644 45578999999999999999
Q ss_pred cCCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHH-HHhCCCc----eeEEEEecCHHHHHHHHHhccceeeeecce
Q psy3760 173 PLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDRE-FSLQKLT----PYIVLETINSDIIKTYVELRMGIGIIASIA 247 (306)
Q Consensus 173 ~~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~-~~~~~~~----~~~~~~~~~~~~~~~~v~~g~gi~~~p~~~ 247 (306)
+++|+......++++||.++|+|....... +..+ +...+.. ++..+++++..++++++..|.|++++|...
T Consensus 77 ~~~~~~~~~~~~~~~~l~~~~~i~~~~~~~----~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~Gi~~~p~~~ 152 (198)
T cd08480 77 SPSYLARHGTPLTPQDLARHNCLGFNFRRA----LPDWPFRDGGRIVALPVSGNILVNDGEALRRLALAGAGLARLALFH 152 (198)
T ss_pred CHHHHHhcCCCCCHHHHHhCcceeecccCc----ccCeeEcCCCcEEEEEecCcEEECCHHHHHHHHHcCCeEEeccHHH
Confidence 999964444678999999999997643221 2233 3434432 344678999999999999999999999977
Q ss_pred eccc-ccCCceeeecC-CCCccceEEEEEeCCccccHHHHHHHHHH
Q psy3760 248 FDSN-RDKNLRSISAS-HLFGTTISRVIIKQGTYLRSYVYSFIKLL 291 (306)
Q Consensus 248 ~~~~-~~~~l~~~~~~-~~~~~~~~~l~~~~~~~~~~~~~~~~~~l 291 (306)
+... ..+.++.+... .+.....++++|+++...++.++.|++++
T Consensus 153 ~~~~~~~~~l~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~f~~~l 198 (198)
T cd08480 153 VADDIAAGRLVPVLEEYNPGDREPIHAVYVGGGRLPARVRAFLDFL 198 (198)
T ss_pred HHHHHhcCCeEEeCCCCCCCCCccEEEEEcCcccCChhhhhhhhcC
Confidence 6543 55667755322 22345789999999999999999999864
No 118
>cd08482 PBP2_TrpI The C-terminal substrate binding domain of LysR-type transcriptional regulator TrpI, which is involved in control of tryptophan synthesis, contains type 2 periplasmic binding fold. TrpI and indoleglycerol phosphate (InGP), are required to activate transcription of the trpBA, the genes for tryptophan synthase. The trpBA is induced by the InGp substrate, rather than by tryptophan, but the exact mechanism of the activation event is not known. This substrate-binding domain of TrpI shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cy
Probab=99.89 E-value=2.6e-22 Score=154.51 Aligned_cols=190 Identities=12% Similarity=0.017 Sum_probs=151.5
Q ss_pred cEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccCCCCCceeeccccceEEEEec
Q psy3760 94 NLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLISIPCYQWEYVIIVP 173 (306)
Q Consensus 94 ~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~~~~~~~~~l~~~~~~~v~~ 173 (306)
.|+||++.+++..++++++..|.++||++++++...+. ..+ +..+++|++|+..+....+++...++.+++++++++
T Consensus 1 ~l~Ig~~~~~~~~~l~~~i~~f~~~~P~v~i~~~~~~~--~~~-~~~~~~Dl~i~~~~~~~~~~~~~~~l~~~~~~~v~~ 77 (195)
T cd08482 1 PLVLSCSGSLLMRWLIPRLPAFQAALPDIDLQLSASDG--PVD-SLRDGIDAAIRFNDAPWPAGMQVIELFPERVGPVCS 77 (195)
T ss_pred CeEEEecHHHHHHHHHhhHHHHHHHCCCceEEEEecCC--ccc-cccCCcCEEEEcCCCCCCCCceEEEeecCcEEeeeC
Confidence 38999999999999999999999999999999987542 333 455789999986543335789999999999999999
Q ss_pred CCCCCCCC-CCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCc---eeEEEEecCHHHHHHHHHhccceeeeecceec
Q psy3760 174 LDHPLLLL-NSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLT---PYIVLETINSDIIKTYVELRMGIGIIASIAFD 249 (306)
Q Consensus 174 ~~~~l~~~-~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~v~~g~gi~~~p~~~~~ 249 (306)
++||++.+ ..++++||.++|++..... ...+..++...|.. ++..+++++...+.+++..|.|++++|...+.
T Consensus 78 ~~~~~~~~~~~~~l~~L~~~~~i~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~G~Gv~~lp~~~~~ 154 (195)
T cd08482 78 PSLAPTVPLRQAPAAALLGAPLLHTRSR---PQAWPDWAAAQGLAPEKLGTGQSFEHFYYLLEAAVAGLGVAIAPWPLVR 154 (195)
T ss_pred HHHHhhCCCCCCCHHHHhcCceeccCCC---HHHHHHHHHHcCCCcCCcccCceeCchHHHHHHHHcCCceEeccHHhhH
Confidence 99998765 4689999999999986432 13456677777764 35678999999999999999999999998876
Q ss_pred cc-ccCCceeeecCCCCccceEEEEEeCCccccHHHHHHHHHH
Q psy3760 250 SN-RDKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLL 291 (306)
Q Consensus 250 ~~-~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l 291 (306)
.. ..+.++. +++. ......+++|++++..++.++.|++++
T Consensus 155 ~~~~~~~l~~-~~~~-~~~~~~~~i~~~~~~~~~~~~~~~~~~ 195 (195)
T cd08482 155 DDLASGRLVA-PWGF-IETGSHYVLLRPARLRDSRAGALADWL 195 (195)
T ss_pred HHHhCCCeec-cCCc-CcCCCceEEEeccccCChHHHHHhhhC
Confidence 54 5666664 4543 334567778877776789999999864
No 119
>cd08488 PBP2_AmpR The C-terminal substrate domain of LysR-type transcriptional regulator AmpR that involved in control of the expression of beta-lactamase gene ampC, contains the type 2 periplasmic binding fold. AmpR acts as a transcriptional activator by binding to a DNA region immediately upstream of the ampC promoter. In the absence of a beta-lactam inducer, AmpR represses the synthesis of beta-lactamase, whereas expression is induced in the presence of a beta-lactam inducer. The AmpD, AmpG, and AmpR proteins are involved in the induction of AmpC-type beta-lactamase (class C) which produced by enterobacterial strains and many other gram-negative bacilli. The activation of ampC by AmpR requires ampG for induction or high-level expression of AmpC. It is probable that the AmpD and AmpG work together to modulate the ability of AmpR to activate ampC expression. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsibl
Probab=99.89 E-value=2.5e-22 Score=154.10 Aligned_cols=186 Identities=12% Similarity=0.018 Sum_probs=150.8
Q ss_pred cEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccCCCCCceeeccccceEEEEec
Q psy3760 94 NLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLISIPCYQWEYVIIVP 173 (306)
Q Consensus 94 ~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~~~~~~~~~l~~~~~~~v~~ 173 (306)
.|+||++.+++..++++++.+|.++||++++++...+.. ..+.+|++|++|+..+ ...+++...++++++++++++
T Consensus 1 ~l~Ig~~~~~~~~~l~~~l~~f~~~~P~v~i~~~~~~~~---~~l~~~~~D~~i~~~~-~~~~~~~~~~l~~~~~~~v~~ 76 (191)
T cd08488 1 VLHVGAVGTFAVGWLLPRLADFQNRHPFIDLRLSTNNNR---VDIAAEGLDYAIRFGS-GAWHGIDATRLFEAPLSPLCT 76 (191)
T ss_pred CEEEEecHHHHHHHHHhHHHHHHHHCCCcEEEEEecCCc---cccCCCCccEEEEecC-CCCCCcEEEEccCCcEEEEeC
Confidence 389999999999999999999999999999999876543 2566889999998644 456789999999999999999
Q ss_pred CCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCce----eEEEEecCHHHHHHHHHhccceeeeecceec
Q psy3760 174 LDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTP----YIVLETINSDIIKTYVELRMGIGIIASIAFD 249 (306)
Q Consensus 174 ~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~~~~~~~~~~v~~g~gi~~~p~~~~~ 249 (306)
+++ +. ..++++||.++|++..... ..+.+++...+..+ ...+++++...+.+++.+|.|++++|.+++.
T Consensus 77 ~~l--~~-~~~~~~dL~~~~~i~~~~~----~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~Gi~~lp~~~~~ 149 (191)
T cd08488 77 PEL--AR-QLREPADLARHTLLRSYRA----DEWPQWFEAAGVGHPCGLPNSIMFDSSLGMMEAALQGLGVALAPPSMFS 149 (191)
T ss_pred HHH--hc-ccCCHHHHhhCcEEecCCc----cHHHHHHHHcCCCCccccccccccCchHHHHHHHHhCCCeEEechHhhH
Confidence 873 33 4689999999999974322 24567788777654 3456789999999999999999999998775
Q ss_pred cc-ccCCceeeecCCCCccceEEEEEeCCccccHHHHHHHHHH
Q psy3760 250 SN-RDKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLL 291 (306)
Q Consensus 250 ~~-~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l 291 (306)
.. ..+.++ +++........++++|++++..++.++.|++++
T Consensus 150 ~~~~~~~l~-~~l~~~~~~~~~~l~~~~~~~~~~~~~~f~~~~ 191 (191)
T cd08488 150 RQLASGALV-QPFATTLSTGSYWLTRLQSRPETPAMSAFSAWL 191 (191)
T ss_pred HHHHCCCee-ccccccccCCcEEEEeccccCCCHHHHHHHhhC
Confidence 44 444454 677654456689999999999999999999874
No 120
>cd08487 PBP2_BlaA The C-terminal substrate-binding domain of LysR-type trnascriptional regulator BlaA which involved in control of the beta-lactamase gene expression; contains the type 2 periplasmic binding fold. This CD represents the C-terminal substrate binding domain of LysR-type transcriptional regulator, BlaA, that involved in control of the expression of beta-lactamase genes, blaA and blaB. Beta-lactamases are responsible for bacterial resistance to beta-lactam antibiotics such as penicillins. The blaA gene is located just upstream of blaB in the opposite direction and regulates the expression of the blaB. BlaA also negatively auto-regulates the expression of its own gene, blaA. BlaA (a constitutive class A penicllinase) belongs to the LysR family of transcriptional regulators, whereas BlaB (an inducible class C cephalosporinase or AmpC) can be referred to as a penicillin binding protein but it does not act as a beta-lactamase. The topology of this substrate-binding domain is
Probab=99.89 E-value=3.9e-22 Score=152.68 Aligned_cols=186 Identities=13% Similarity=0.057 Sum_probs=149.6
Q ss_pred cEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccCCCCCceeeccccceEEEEec
Q psy3760 94 NLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLISIPCYQWEYVIIVP 173 (306)
Q Consensus 94 ~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~~~~~~~~~l~~~~~~~v~~ 173 (306)
.|+||+.++++..++++.+..|.++||++++++.... .+.+ +.+|++|++|+..+ ...+++...++++++++++++
T Consensus 1 ~l~Ig~~~~~~~~~l~~~l~~f~~~~P~i~l~i~~~~--~~~~-~~~~~~Dl~i~~~~-~~~~~~~~~~l~~~~~~~v~~ 76 (189)
T cd08487 1 VLTVGAVGTFAVGWLLPRLAEFRQLHPFIELRLRTNN--NVVD-LATEGLDFAIRFGE-GLWPATHNERLLDAPLSVLCS 76 (189)
T ss_pred CeEEEecHHHHHHHHhHHHHHHHHHCCCceEEeeecC--Cccc-cccCCcCEEEEecC-CCCCCceeeeeccCceeeeeC
Confidence 4899999999999999999999999999999998653 3444 66678999998644 445789999999999999999
Q ss_pred CCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCceeEE--EEecCHHHHHHHHHhccceeeeecceeccc
Q psy3760 174 LDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIV--LETINSDIIKTYVELRMGIGIIASIAFDSN 251 (306)
Q Consensus 174 ~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~v~~g~gi~~~p~~~~~~~ 251 (306)
++|+ ...++++||.++|++.... .+.+.+++...|..++.. .++++..++..++.+|.|++++|...+...
T Consensus 77 ~~~~---~~~~~~~~l~~~~~i~~~~----~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~Gi~~~p~~~~~~~ 149 (189)
T cd08487 77 PEIA---KRLSHPADLINETLLRSYR----TDEWLQWFEAANMPPIKIRGPVFDSSRLMVEAAMQGAGVALAPAKMFSRE 149 (189)
T ss_pred HHHh---ccCCCHHHHhcCceeecCC----chHHHHHHHHcCCCCccccCCccccHHHHHHHHHhCCCeEeehHHHHHHH
Confidence 9984 2468999999999996422 123556788888776542 578999999999999999999999877554
Q ss_pred -ccCCceeeecCCCCccceEEEEEeCCccccHHHHHHHHHH
Q psy3760 252 -RDKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLL 291 (306)
Q Consensus 252 -~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l 291 (306)
..+.++ .+++.......++++|++++..+|.+++|++++
T Consensus 150 ~~~~~l~-~~l~~~~~~~~~~~~~~~~~~~~~~~~~f~~~~ 189 (189)
T cd08487 150 IENGQLV-QPFKIEVETGSYWLTWLKSKPMTPAMELFRQWI 189 (189)
T ss_pred HhCCCEE-cccCcccCCCcEEEEecccccCCHHHHHHHhhC
Confidence 444444 466654456789999999999999999999874
No 121
>cd08484 PBP2_LTTR_beta_lactamase The C-terminal substrate-domain of LysR-type transcriptional regulators for beta-lactamase genes, contains the type 2 periplasmic binding fold. This CD includes the C-terminal substrate binding domain of LysR-type transcriptional regulators, BlaA and AmpR, that are involved in control of the expression of beta-lactamase genes. Beta-lactamases are responsible for bacterial resistance to beta-lactam antibiotics such as penicillins. BlaA (a constitutive class A penicillinase) belongs to the LysR family of transcriptional regulators, while BlaB (an inducible class C cephalosporinase or AmpC) can be referred to as a penicillin-binding protein, but it does not act as a beta-lactamase. AmpR regulates the expression of beta-lactamases in many enterobacterial strains and many other gram-negative bacilli. In contrast to BlaA, AmpR acts an activator only in the presence of the beta-lactam inducer. In the absence of the inducer, AmpR acts as a repressor. The topol
Probab=99.88 E-value=5.3e-22 Score=151.99 Aligned_cols=186 Identities=14% Similarity=0.027 Sum_probs=149.2
Q ss_pred cEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccCCCCCceeeccccceEEEEec
Q psy3760 94 NLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLISIPCYQWEYVIIVP 173 (306)
Q Consensus 94 ~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~~~~~~~~~l~~~~~~~v~~ 173 (306)
.|+||++++++..++++++..|.++||++++++...+. ..+ +.++++|++|+..+ ...+++...++++++++++++
T Consensus 1 ~l~Ig~~~~~~~~~l~~~l~~f~~~~P~i~l~~~~~~~--~~~-~~~~~~D~~i~~~~-~~~~~l~~~~l~~~~~~~v~~ 76 (189)
T cd08484 1 VLTVGAVGTFAVGWLLPRLAEFRQLHPFIDLRLSTNNN--RVD-IAAEGLDFAIRFGE-GAWPGTDATRLFEAPLSPLCT 76 (189)
T ss_pred CEEEEecHHHHHHHHHhhhHHHHHHCCCceEEEecccC--ccc-cccCCccEEEEecC-CCCCCceEEEccCCceEEeeC
Confidence 38999999999999999999999999999999987543 334 44556999999644 456789999999999999999
Q ss_pred CCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCceeE--EEEecCHHHHHHHHHhccceeeeecceeccc
Q psy3760 174 LDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYI--VLETINSDIIKTYVELRMGIGIIASIAFDSN 251 (306)
Q Consensus 174 ~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~v~~g~gi~~~p~~~~~~~ 251 (306)
+++ + ...++++||.++|++..... ..+.+++...+..+.. .+++++...+.+++.+|.|++++|...+...
T Consensus 77 ~~~--~-~~~~~~~~L~~~~~i~~~~~----~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~Gi~~lp~~~~~~~ 149 (189)
T cd08484 77 PEL--A-RRLSEPADLANETLLRSYRA----DEWPQWFEAAGVPPPPINGPVFDSSLLMVEAALQGAGVALAPPSMFSRE 149 (189)
T ss_pred HHH--h-cccCChhHhhcCceEecCCC----chHHHHHHHcCCCCCcccCcccccHHHHHHHHHhCCCeEEecHHhHHHH
Confidence 885 2 24689999999999964321 2356678878877544 4788999999999999999999999877654
Q ss_pred -ccCCceeeecCCCCccceEEEEEeCCccccHHHHHHHHHH
Q psy3760 252 -RDKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLL 291 (306)
Q Consensus 252 -~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l 291 (306)
..+.+. .+++.....++++++|+++...++.++.|++++
T Consensus 150 ~~~~~l~-~~~~~~~~~~~~~l~~~~~~~~~~~~~~f~~~l 189 (189)
T cd08484 150 LASGALV-QPFKITVSTGSYWLTRLKSKPETPAMSAFSQWL 189 (189)
T ss_pred HHCCCEE-eecccccCCCCEEEEeccccccchhhHHHHhhC
Confidence 445554 466654456789999999999999999999864
No 122
>PRK14498 putative molybdopterin biosynthesis protein MoeA/LysR substrate binding-domain-containing protein; Provisional
Probab=99.83 E-value=9.5e-20 Score=163.05 Aligned_cols=186 Identities=17% Similarity=0.172 Sum_probs=162.5
Q ss_pred CCcEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccC--------------CCCC
Q psy3760 92 TGNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILS--------------PSDK 157 (306)
Q Consensus 92 ~~~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~--------------~~~~ 157 (306)
.++|+||++.+++..++++++.. |++++++...++.++++.|.+|++|+|++..... ..++
T Consensus 416 ~~~L~Ig~~~~~~~~~Lp~~l~~-----P~v~i~v~~~~s~~vl~~L~~GeiDlai~~~~~~~~~~~~~~~~~~~~~~~~ 490 (633)
T PRK14498 416 PPTLVIIGSHDPGLDLLLDLLAR-----RGLRLRSLHVGSMGGLMALKRGEADIAGIHLLDPETGEYNIPYIKKYLLGED 490 (633)
T ss_pred ccceEEEccCchHHHHHHHHhhc-----cCCceeEEecCCHHHHHHHHcCCceEEEEcccCcccccccHHHHHhhcCCCC
Confidence 58999999999999999998887 9999999999999999999999999999864321 1335
Q ss_pred ceeeccccceEEEEecCCCCCCCCCCcChhhhcCC--CeEeecCCCCcHHHHHHHHHhCCCceeE----EEEecCHHHHH
Q psy3760 158 LISIPCYQWEYVIIVPLDHPLLLLNSISLKEISNY--PLITYDLSFSGRIKLDREFSLQKLTPYI----VLETINSDIIK 231 (306)
Q Consensus 158 ~~~~~l~~~~~~~v~~~~~~l~~~~~i~~~dl~~~--~~i~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~~~~~~ 231 (306)
+.+.++++++++++++++||++ .++++||.++ ||+....+...+..++++|.+.|+.++. .+++++.+++.
T Consensus 491 l~~~~l~~d~lvlvvp~~hPl~---~isl~dL~~~~~plI~~~~gs~~r~~le~~l~~~Gi~~~~i~~~~~e~~s~~~i~ 567 (633)
T PRK14498 491 AVLVKGYRREQGLVVRKGNPKG---IEGIEDLVRKDVRFVNRQRGSGTRILLDYHLKELAIDPERINGYDREEKTHMAVA 567 (633)
T ss_pred EEEEEEEEEeEEEEECCCCCCC---CCCHHHhccCCcEEEecCCCchHHHHHHHHHHHcCCCHHHCCCcccccCCHHHHH
Confidence 8999999999999999999975 4899999999 9999999988999999999999999874 68999999999
Q ss_pred HHHHhc---cceeeeecceecccccCCceeeecCCCCccceEEEEEeCCccccHHHHHHHHHHhHH
Q psy3760 232 TYVELR---MGIGIIASIAFDSNRDKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLLSPK 294 (306)
Q Consensus 232 ~~v~~g---~gi~~~p~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~ 294 (306)
.+|.+| .|+++++. . . ..++..++++. ..++++|++++..++++++|++++++.
T Consensus 568 ~~V~~G~~d~Gi~i~~~--~-~--~~~l~~i~l~~----~~~~l~~~~~~~~s~a~~aFl~~l~~~ 624 (633)
T PRK14498 568 AAVAQGRADAGLGIRAA--A-K--ALGLDFIPLAE----EEYDLLIPKERLEKPAVRAFLEALKSP 624 (633)
T ss_pred HHHHcCCCcchHhHHHH--H-H--HcCCCCeeeee----EEEEEEEEhhHccCHHHHHHHHHHcCH
Confidence 999999 89999985 1 1 23577777763 268999999999999999999999764
No 123
>PRK10676 DNA-binding transcriptional regulator ModE; Provisional
Probab=99.81 E-value=2.4e-19 Score=141.80 Aligned_cols=98 Identities=14% Similarity=0.164 Sum_probs=83.1
Q ss_pred chhhHHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEec-----CCCccccCHhHHHHHHHHHHHHHH
Q psy3760 2 NLHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRH-----GKRIRGLTKPGQAILRSIEIIMQE 76 (306)
Q Consensus 2 ~~~~l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~-----~~~~~~lT~~G~~l~~~a~~il~~ 76 (306)
+++++++|.+|+++| ||++||+.||+|||++|++|++||+++|.+||+|. ++|+ +||++|+.|+ ++++.
T Consensus 18 ~~~~l~~l~~v~~~g-S~s~AA~~l~~s~~a~s~~i~~le~~lg~~L~~r~~gg~~g~~~-~lT~~G~~l~----~~~~~ 91 (263)
T PRK10676 18 DPRRISLLKQIALTG-SISQGAKLAGISYKSAWDAINEMNQLSEHILVERATGGKGGGGA-VLTRYGERLI----QLYDL 91 (263)
T ss_pred CHHHHHHHHHHHHHC-CHHHHHHHhCCCHHHHHHHHHHHHHHhCCCeEEEecCCCCCCCc-EECHHHHHHH----HHHHH
Confidence 689999999999999 99999999999999999999999999999999998 8888 7999999999 57777
Q ss_pred HHHHHHHHHhhccCCCCcEEEEecccchhhhhHHHHHHH
Q psy3760 77 IEGLKKIGKEFSAYDTGNLTIATTHTQARYALPKIIKEF 115 (306)
Q Consensus 77 ~~~~~~~~~~~~~~~~~~l~I~~~~~~~~~~l~~~l~~~ 115 (306)
++++...+.+... ........+++++..|
T Consensus 92 ~~~~~~~~~~~~~----------~~~~~~~~l~~~l~~~ 120 (263)
T PRK10676 92 LAQIQQKAFDVLD----------DDALPLDSLLAAISRF 120 (263)
T ss_pred HHHHHHHHHHHhh----------hcccchHHHHHHHHHh
Confidence 7776666555432 3334556677777777
No 124
>PF12727 PBP_like: PBP superfamily domain; InterPro: IPR024370 This entry represents members of the periplasmic binding domain superfamily []. It is often associated with a helix-turn-helix domain.
Probab=99.44 E-value=1e-11 Score=94.09 Aligned_cols=171 Identities=16% Similarity=0.169 Sum_probs=141.8
Q ss_pred HHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccCCC--------------CCceeeccccceEEEEecCCCCC
Q psy3760 113 KEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPS--------------DKLISIPCYQWEYVIIVPLDHPL 178 (306)
Q Consensus 113 ~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~~--------------~~~~~~~l~~~~~~~v~~~~~~l 178 (306)
..|.+++|++.+.+...++...+..|.+|.+|++.++...... ..+....++.....+++++++|+
T Consensus 2 e~~~~~~~~~~v~~~~~gS~~gl~~L~~g~~~iAg~h~~~~~~~~~n~~~~~~~l~g~~~v~v~~~~r~~Gl~v~~~np~ 81 (193)
T PF12727_consen 2 EEFARREPGVRVAVQYTGSRAGLSALARGEADIAGIHLPDPESGEYNIPFVRRLLPGIEVVLVRLARREQGLIVRPGNPK 81 (193)
T ss_pred hHHHhhCCCCeEEEEecCCHHHHHHHHCCCceEEEecCCCCcccccchHHHHHhcCCCcEEEEeeeEEeeeEEEeCCCCc
Confidence 4688899999999999999999999999999999986432211 24667888888999999999985
Q ss_pred CCCCCcChhhh--cCCCeEeecCCCCcHHHHHHHHHhCCCcee----EEEEecCHHHHHHHHHhc-cceeeeecceeccc
Q psy3760 179 LLLNSISLKEI--SNYPLITYDLSFSGRIKLDREFSLQKLTPY----IVLETINSDIIKTYVELR-MGIGIIASIAFDSN 251 (306)
Q Consensus 179 ~~~~~i~~~dl--~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~~~~~~~~~v~~g-~gi~~~p~~~~~~~ 251 (306)
...+++|| .+..+|..+.+++.+..+++++...++.+. ..-+..+...+..+|..| .-+++.....+..
T Consensus 82 ---~i~~~~dL~~~~~r~vnR~~GSGtR~l~d~~l~~~gi~~~~i~gy~~~~~th~~vA~aVa~G~AD~G~g~~~~A~~- 157 (193)
T PF12727_consen 82 ---GITSLEDLADPGLRFVNRQPGSGTRILFDQLLAEEGIDPEDIPGYAQEANTHLAVAAAVASGKADAGIGIRAAAEE- 157 (193)
T ss_pred ---cCCCHHHhccCCcEEEECCCCCHHHHHHHHHHHHcCCChhhCCCccccccChHHHHHHHHcCCCCEEeehHHHHHh-
Confidence 45689999 677899999999999999999999988752 235788999999999999 5677766666543
Q ss_pred ccCCceeeecCCCCccceEEEEEeCCccccHHHHHHHHHHh
Q psy3760 252 RDKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLLS 292 (306)
Q Consensus 252 ~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~ 292 (306)
-.+|.++|+.. ..+.++.+++....|.+++|+++++
T Consensus 158 -~~gL~Fvpl~~----E~~dlv~~~~~~~~~~vq~ll~~l~ 193 (193)
T PF12727_consen 158 -FYGLDFVPLAE----ERYDLVIRREDLEDPAVQALLDFLQ 193 (193)
T ss_pred -hcCCCcEEccc----cceEEEEEhhHcCCHHHHHHHHHhC
Confidence 35899999987 3788999999999999999999885
No 125
>PRK11553 alkanesulfonate transporter substrate-binding subunit; Provisional
Probab=99.33 E-value=7.7e-11 Score=97.53 Aligned_cols=201 Identities=12% Similarity=0.059 Sum_probs=133.0
Q ss_pred cCCCCcEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeC-ChhHHHHHHHcCCeeEEEEccccC---CCCCceeec--
Q psy3760 89 AYDTGNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQG-NPKQITEMIRNDQADIAIVTEILS---PSDKLISIP-- 162 (306)
Q Consensus 89 ~~~~~~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~-~~~~~~~~l~~~~~Di~i~~~~~~---~~~~~~~~~-- 162 (306)
....++||||+.++....+++..+..|.+.+|++++++... +...+.+.|.+|++|+++...... ...++....
T Consensus 23 ~~~~~~lrIg~~~~~~~~~l~~~~~~~~~~~p~v~ie~~~~~~~~~~~~aL~~G~iDia~~~~~~~~~~~~~g~~~~~v~ 102 (314)
T PRK11553 23 ESSPEALRIGYQKGSIGLVLAKSHQLLEKRFPQTKISWVEFPAGPQMLEALNVGSIDLGSTGDIPPIFAQAAGADLVYVG 102 (314)
T ss_pred cCCCCeEEEEeCCCchHHHHHHhhCHHHHhCCCCeeEEEECCCcHHHHHHHHcCCCCEEccCCHHHHHHHhCCCCEEEEE
Confidence 44678999999998888889999999999999999999987 456899999999999999742111 123343333
Q ss_pred ---cccceEEEEecCCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCceeE-EEEecCHHHHHHHHHhcc
Q psy3760 163 ---CYQWEYVIIVPLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYI-VLETINSDIIKTYVELRM 238 (306)
Q Consensus 163 ---l~~~~~~~v~~~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~v~~g~ 238 (306)
......+++++++|++. +++||.+.++.. ..+...+..+..+++..|+.+.. .....+...+..++.+|.
T Consensus 103 ~~~~~~~~~~lvv~~~s~i~-----s~~dL~Gk~I~~-~~gs~~~~~l~~~l~~~g~~~~dv~~v~~~~~~~~~al~~G~ 176 (314)
T PRK11553 103 VEPPKPKAEVILVAENSPIK-----TVADLKGHKVAF-QKGSSSHNLLLRALRKAGLKFTDIQPTYLTPADARAAFQQGN 176 (314)
T ss_pred EecCCCcceEEEEeCCCCCC-----CHHHhCCCEEee-cCCCcHHHHHHHHHHHcCCCHHHeEEEecChHHHHHHHHcCC
Confidence 33345789999999864 899999999554 55666777888899999987633 234446666778888884
Q ss_pred ceee-eecceeccc-ccCCceeeecCC-CCccceEEEEEeC-CccccHHHHHHHHHHhHHh
Q psy3760 239 GIGI-IASIAFDSN-RDKNLRSISASH-LFGTTISRVIIKQ-GTYLRSYVYSFIKLLSPKL 295 (306)
Q Consensus 239 gi~~-~p~~~~~~~-~~~~l~~~~~~~-~~~~~~~~l~~~~-~~~~~~~~~~~~~~l~~~~ 295 (306)
.=++ +.+...... ..+....+.... ......++++..+ ....+..+++|++.+.+..
T Consensus 177 vDa~~~~ep~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~v~~~l~a~~~A~ 237 (314)
T PRK11553 177 VDAWAIWDPYYSAALLQGGVRVLKDGTDLNQTGSFYLAARPYAEKNGAFIQQVLATLTEAD 237 (314)
T ss_pred CCEEEEcCcHHHHHHhcCCcEEeecCcccCcCceEEEEcHHHHHHCHHHHHHHHHHHHHHH
Confidence 3333 333332222 233444332222 1222233333322 1345678888888876653
No 126
>PRK00489 hisG ATP phosphoribosyltransferase; Reviewed
Probab=99.20 E-value=1.8e-10 Score=93.46 Aligned_cols=166 Identities=15% Similarity=0.188 Sum_probs=123.6
Q ss_pred HHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccCC-----CCCceeeccccceEEEEecCCCCCCCCCCcChhh
Q psy3760 114 EFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSP-----SDKLISIPCYQWEYVIIVPLDHPLLLLNSISLKE 188 (306)
Q Consensus 114 ~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~-----~~~~~~~~l~~~~~~~v~~~~~~l~~~~~i~~~d 188 (306)
.|...+|++.+++....+.++...|.+|++|++++...... ...+....+....++++++++|++. +++|
T Consensus 36 ~~~~~~p~~~ie~~~~~~~~i~~~L~sG~vDlgi~g~~~~~er~~~v~~~~~l~~~~~~lvvvvp~~~~i~-----sl~D 110 (287)
T PRK00489 36 SLIATDEDNPIEVLFLRPDDIPGYVADGVVDLGITGEDLLEESGADVEELLDLGFGKCRLVLAVPEDSDWQ-----GVED 110 (287)
T ss_pred ceEeecCCCCEEEEEECcHHHHHHHHcCCCCEEEcchHHHHHCCCCceEeeeccCCceEEEEEEECCCCCC-----ChHH
Confidence 47788999999999999999999999999999998522111 2233344577889999999999864 4899
Q ss_pred hcCCCeEeecCCCCcHHHHHHHHHhCCCceeEEEEecCHHHHHHHHHhccceeeeecceeccc-ccCCceeeecCCCCcc
Q psy3760 189 ISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMGIGIIASIAFDSN-RDKNLRSISASHLFGT 267 (306)
Q Consensus 189 l~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~~~p~~~~~~~-~~~~l~~~~~~~~~~~ 267 (306)
|.+..... .....+.+++.+.|+.++++...++.+. ++..|.+.++++....... ..++++.+ + ....
T Consensus 111 L~Gk~ia~-----~~~~~~~~~l~~~gi~~~iv~~~gs~ea---a~~~G~aDaivd~~~~~~~l~~~~L~~v--~-~~~~ 179 (287)
T PRK00489 111 LAGKRIAT-----SYPNLTRRYLAEKGIDAEVVELSGAVEV---APRLGLADAIVDVVSTGTTLRANGLKIV--E-VILR 179 (287)
T ss_pred hCCCEEEE-----cCcHHHHHHHHHcCCceEEEECCCchhh---hhcCCcccEEEeeHHHHHHHHHCCCEEE--E-eeee
Confidence 98885544 2346778899999998887777777775 4556999999986544333 44567776 2 3345
Q ss_pred ceEEEEEeCCccccHHHHHHHHHHhHHhh
Q psy3760 268 TISRVIIKQGTYLRSYVYSFIKLLSPKLN 296 (306)
Q Consensus 268 ~~~~l~~~~~~~~~~~~~~~~~~l~~~~~ 296 (306)
...++++++ ++.++..+.|++.+...++
T Consensus 180 ~~~~li~~k-~~~~~~~~~~i~~~l~~l~ 207 (287)
T PRK00489 180 SEAVLIARK-GWLDPEKQEKIDQLLTRLQ 207 (287)
T ss_pred eeEEEEEcc-cccChhHHHHHHHHHHHHH
Confidence 578999998 6678888888887776663
No 127
>COG2005 ModE N-terminal domain of molybdenum-binding protein [General function prediction only]
Probab=99.19 E-value=3.7e-10 Score=77.41 Aligned_cols=83 Identities=19% Similarity=0.184 Sum_probs=72.6
Q ss_pred chhhHHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecC-----CCccccCHhHHHHHHHHHHHHHH
Q psy3760 2 NLHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHG-----KRIRGLTKPGQAILRSIEIIMQE 76 (306)
Q Consensus 2 ~~~~l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~-----~~~~~lT~~G~~l~~~a~~il~~ 76 (306)
+...++.+.+|.++| |++.||+.++||.-..+..|+.+|+-+|.+|+++.. +|- .||+.|+++++....+-..
T Consensus 18 g~g~~~LL~~I~etG-SIs~AAk~~GiSYk~AW~~i~~~n~~~~~plVe~~rGGk~gGga-~LT~~g~~ll~~y~~l~~~ 95 (130)
T COG2005 18 GPGRIELLKAIAETG-SISAAAKAAGISYKSAWDYIKALNRLLGEPLVERRRGGKGGGGA-VLTDFGERLLEEYRLLEKE 95 (130)
T ss_pred CchHHHHHHHHHHhC-CHHHHHHHcCCCHHHHHHHHHHHHHHhCCCeeeeccCCCCCCcc-hhHHHHHHHHHHHHHHHHH
Confidence 446788999999999 999999999999999999999999999999999762 334 7999999999999999888
Q ss_pred HHHHHHHHHh
Q psy3760 77 IEGLKKIGKE 86 (306)
Q Consensus 77 ~~~~~~~~~~ 86 (306)
+++.......
T Consensus 96 ~~~~~~~~~~ 105 (130)
T COG2005 96 IEEALRKLED 105 (130)
T ss_pred HHHHHHHHhh
Confidence 8887764443
No 128
>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=99.02 E-value=1.9e-08 Score=78.15 Aligned_cols=185 Identities=14% Similarity=0.128 Sum_probs=119.9
Q ss_pred hhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccCC--CCC-ceeeccccceEEEEecCCCCCCCCC
Q psy3760 106 YALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSP--SDK-LISIPCYQWEYVIIVPLDHPLLLLN 182 (306)
Q Consensus 106 ~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~--~~~-~~~~~l~~~~~~~v~~~~~~l~~~~ 182 (306)
.+...++..+.++.+ +++++...+..+..+.|.+|++|+++....... ... .-..++....++++++++++..
T Consensus 23 G~~~~~~~~~~~~~g-~~~~~~~~~~~~~~~~l~~g~~D~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--- 98 (218)
T cd00134 23 GFDVDLAKAIAKELG-VKVKFVEVDWDGLITALKSGKVDLIAAGMTITPERAKQVDFSDPYYKSGQVILVKKGSPIK--- 98 (218)
T ss_pred eeeHHHHHHHHHHhC-CeEEEEeCCHHHHHHHHhcCCcCEEeecCcCCHHHHhhccCcccceeccEEEEEECCCCCC---
Confidence 455689999999886 999999999999999999999999998531111 111 2344788889999999998743
Q ss_pred CcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCceeEEEEecCHHHHHHHHHhccceeeeecc-eeccc-cc--CCcee
Q psy3760 183 SISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMGIGIIASI-AFDSN-RD--KNLRS 258 (306)
Q Consensus 183 ~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~~~p~~-~~~~~-~~--~~l~~ 258 (306)
+++||.+.++... .+......+.+.+. ......+++...++.++..|.+-+++... ..... .. ..+..
T Consensus 99 --~~~dl~g~~i~~~-~~~~~~~~~~~~~~-----~~~~~~~~~~~~~~~~l~~g~~d~~~~~~~~~~~~~~~~~~~l~~ 170 (218)
T cd00134 99 --SVKDLKGKKVAVQ-KGSTAEKYLKKALP-----EAKVVSYDDNAEALAALENGRADAVIVDEIALAALLKKHPPELKI 170 (218)
T ss_pred --ChHHhCCCEEEEE-cCchHHHHHHHhCC-----cccEEEeCCHHHHHHHHHcCCccEEEeccHHHHHHHHhcCCCcEE
Confidence 8999999988877 33333333333322 23455788899999999999766655543 32222 22 56777
Q ss_pred eecCCCCccceEEEEEeCCccccHHHHHHHHHHhHHhhHHHHHhhh
Q psy3760 259 ISASHLFGTTISRVIIKQGTYLRSYVYSFIKLLSPKLNRKFINKIL 304 (306)
Q Consensus 259 ~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~ 304 (306)
++.........+.+..++. .......|-+++.+.-+....+.+.
T Consensus 171 ~~~~~~~~~~~~~~~~~~~--~~~l~~~~~~~l~~~~~~g~~~~i~ 214 (218)
T cd00134 171 VGPSIDLEPLGFGVAVGKD--NKELLDAVNKALKELRADGELKKIS 214 (218)
T ss_pred eccccCCCccceEEEEcCC--CHHHHHHHHHHHHHHHhCccHHHHH
Confidence 6665333333444443333 2355666666665554444445444
No 129
>TIGR02122 TRAP_TAXI TRAP transporter solute receptor, TAXI family. This family is one of at least three major families of extracytoplasmic solute receptor (ESR) for TRAP (Tripartite ATP-independent Periplasmic Transporter) transporters. The others are the DctP (TIGR00787) and SmoM (pfam03480) families. These transporters are secondary (driven by an ion gradient) but composed of three polypeptides, although in some species the 4-TM and 12-TM integral membrane proteins are fused. Substrates for this transporter family are not fully characterized but, besides C4 dicarboxylates, may include mannitol and other compounds.
Probab=99.01 E-value=1.9e-08 Score=83.59 Aligned_cols=167 Identities=16% Similarity=0.133 Sum_probs=115.7
Q ss_pred CCCCcEEEEecccchhh-hhHHHH-HHHHHhCCCcEEEEEe-CChhHHHHHHHcCCeeEEEEcccc--------------
Q psy3760 90 YDTGNLTIATTHTQARY-ALPKII-KEFTIQFPKVKLSLLQ-GNPKQITEMIRNDQADIAIVTEIL-------------- 152 (306)
Q Consensus 90 ~~~~~l~I~~~~~~~~~-~l~~~l-~~~~~~~p~~~i~~~~-~~~~~~~~~l~~~~~Di~i~~~~~-------------- 152 (306)
...+.|+||+..+...+ .++..+ ..+.+.+|++++++.. .++.+.++.|.+|++|+++.....
T Consensus 27 ~~~~~l~Ig~~~~~~~~~~~~~~la~~~~~~~~~i~v~~~~~~~~~~~~~~l~~G~~D~~~~~~~~~~~~~~~~~~~~~~ 106 (320)
T TIGR02122 27 GEPTFVTIGTGGTGGVYYPIGGAIAQLINKKSGKLRVRVQSTGGSVENVNLLEAGEADLAIVQSDVAYYAYEGDGEFEFE 106 (320)
T ss_pred CCCceEEEEeCCCCCChHHHHHHHHHHHhccCCCeeEEEEeCcchHHHHHHHhCCCCcEEEEcchhHHHHhcCcCccccC
Confidence 55679999998776664 444444 5567888999999998 566688999999999999985221
Q ss_pred CCCCCce-eeccccceEEEEecCCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCceeEE--EEecCHHH
Q psy3760 153 SPSDKLI-SIPCYQWEYVIIVPLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIV--LETINSDI 229 (306)
Q Consensus 153 ~~~~~~~-~~~l~~~~~~~v~~~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~ 229 (306)
....++. ...++.+.+++++++++++. +++||.+.+++....+...+..+..+++..|+.+... +...+...
T Consensus 107 ~~~~~~~~v~~~~~~~~~lvv~~d~~i~-----sl~dL~gk~v~~~~~~s~~~~~~~~~l~~~G~~~~~~~~v~~~~~~~ 181 (320)
T TIGR02122 107 GPVEKLRALASLYPEYIQIVVRKDSGIK-----TVADLKGKRVAVGAPGSGTELNARAVLKAAGLTYDDVKKVEYLGYAE 181 (320)
T ss_pred CCCccHHhHHHhccccEEEEEECCCCCC-----cHHHcCCCEEecCCCCcchHHHHHHHHHHcCCCHHHccchhcCCHHH
Confidence 0123333 34677888899999998753 8899999998887666666667788888889876432 34456677
Q ss_pred HHHHHHhccceeee-----ecceeccc-ccCCceeeec
Q psy3760 230 IKTYVELRMGIGII-----ASIAFDSN-RDKNLRSISA 261 (306)
Q Consensus 230 ~~~~v~~g~gi~~~-----p~~~~~~~-~~~~l~~~~~ 261 (306)
+...+.+|..=+++ |...+... ..++++.+++
T Consensus 182 ~~~al~~G~vDa~~~~~~~~~~~~~~~~~~~~l~~l~~ 219 (320)
T TIGR02122 182 AADALKDGKIDAAFYTAGTPTAAITELATSLDIRIVPI 219 (320)
T ss_pred HHHHHHCCCccEEEEecCCChHHHHHHHhcCCeEEEeC
Confidence 78888888332222 11122233 5567766665
No 130
>TIGR01728 SsuA_fam ABC transporter, substrate-binding protein, aliphatic sulfonates family. Members of this family are substrate-binding periplasmic proteins of ABC transporters. This subfamily includes SsuA, a member of a transporter operon needed to obtain sulfur from aliphatic sulfonates. Related proteins outside the scope of this model include taurine (NH2-CH2-CH2-S03H) binding proteins, the probable sulfate ester binding protein AtsR, and the probable aromatic sulfonate binding protein AsfC. All these families make sulfur available when Cys and sulfate levels are low. Please note that phylogenetic analysis by neighbor-joining suggests that a number of sequences belonging to this family have been excluded because of scoring lower than taurine-binding proteins.
Probab=98.90 E-value=1.2e-07 Score=77.49 Aligned_cols=195 Identities=11% Similarity=0.031 Sum_probs=126.6
Q ss_pred EEEEecc-cchhhhhHHHHHHHHHhCCCcEEEEEeC-ChhHHHHHHHcCCeeEEEEccccC-----CCCCceeecccc--
Q psy3760 95 LTIATTH-TQARYALPKIIKEFTIQFPKVKLSLLQG-NPKQITEMIRNDQADIAIVTEILS-----PSDKLISIPCYQ-- 165 (306)
Q Consensus 95 l~I~~~~-~~~~~~l~~~l~~~~~~~p~~~i~~~~~-~~~~~~~~l~~~~~Di~i~~~~~~-----~~~~~~~~~l~~-- 165 (306)
||||+.+ +....+++.....|.+..|++++++... +..+..+.|.+|++|+++...... ....+.......
T Consensus 1 l~vg~~~~~~~~~~~a~~~g~f~~~g~~l~v~~~~~~~~~~~~~~l~~G~~D~~~~~~~~~~~~~~~g~~~~~i~~~~~~ 80 (288)
T TIGR01728 1 VRIGYQKNGHSALALAKEKGLLEKELGKTKVEWVEFPAGPPALEALGAGSLDFGYIGPGPALFAYAAGADIKAVGLVSDN 80 (288)
T ss_pred CeEEecCCCchHHHHHHHhCHHHHhhCCceEEEEecCCCcHHHHHHhcCCccccccCCcHHHHHHhcCCCEEEEEEecCC
Confidence 6899988 6677788999999999999899999885 556889999999999998642111 112344333322
Q ss_pred ceEEEEecCCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCceeE-EEEecCHHHHHHHHHhc-cceeee
Q psy3760 166 WEYVIIVPLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYI-VLETINSDIIKTYVELR-MGIGII 243 (306)
Q Consensus 166 ~~~~~v~~~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~v~~g-~gi~~~ 243 (306)
....++++++++.. +++||.+.++.. ..+......+...+...|+.+.. .....+...+..++.+| ..++++
T Consensus 81 ~~~~~v~~~~~~i~-----s~~dL~Gk~i~~-~~~~~~~~~~~~~l~~~G~~~~~v~~~~~~~~~~~~al~~g~vda~~~ 154 (288)
T TIGR01728 81 KATAIVVIKGSPIR-----TVADLKGKRIAV-PKGGSGHDLLLRALLKAGLSGDDVTILYLGPSDARAAFAAGQVDAWAI 154 (288)
T ss_pred CceEEEECCCCCCC-----CHHHcCCCEEEe-cCCccHHHHHHHHHHHcCCCccceeEEecCcHHHHHHHHCCCCCEEEe
Confidence 36778888776532 789999988554 44555566777888888987643 33435567788899998 666667
Q ss_pred ecceeccc-ccCCceeee-cCCCCccc-eEEEEEeCC--ccccHHHHHHHHHHhHHh
Q psy3760 244 ASIAFDSN-RDKNLRSIS-ASHLFGTT-ISRVIIKQG--TYLRSYVYSFIKLLSPKL 295 (306)
Q Consensus 244 p~~~~~~~-~~~~l~~~~-~~~~~~~~-~~~l~~~~~--~~~~~~~~~~~~~l~~~~ 295 (306)
+....... ..+..+.+. ..+..... ...++.+++ ...+..++.|++.+.+..
T Consensus 155 ~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~a~~~a~ 211 (288)
T TIGR01728 155 WEPWGSALVEEGGARVLANGEGIGLPGQPGFLVVRREFAEAHPEQVQRVLKVLVKAR 211 (288)
T ss_pred ccchHhHHhhccCCEEEEcCCccCCCCcceEEEECHHHHHHCHHHHHHHHHHHHHHH
Confidence 76555444 334444332 22211111 233444443 224566788887775554
No 131
>PRK09729 hypothetical protein; Provisional
Probab=98.87 E-value=1e-08 Score=62.81 Aligned_cols=62 Identities=11% Similarity=0.118 Sum_probs=56.1
Q ss_pred HHHHhccceeeeecceecccccCCceeeecCCCCccceEEEEEeCCccccHHHHHHHHHHhHHh
Q psy3760 232 TYVELRMGIGIIASIAFDSNRDKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLLSPKL 295 (306)
Q Consensus 232 ~~v~~g~gi~~~p~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~ 295 (306)
.||++|.|++++|+..... ..++++.+|++ +.+.+.++++|+++...+++++.|++++.+..
T Consensus 2 ~mV~~GLGIsIlP~l~l~~-~~~~v~~~~L~-~~~~R~IgLa~~~~~~~s~Aa~~f~~~l~~~~ 63 (68)
T PRK09729 2 NFIRQGLGIALQPELTLKS-IAGELCSVPLE-PTFYRQISLLAKEKPVEGSPLFLLQTCTEQLV 63 (68)
T ss_pred hHHHcCCcEEEchHHHhcc-CCCCEEEEECC-CCceEEEEEEEeCCCCCCHHHHHHHHHHHHHh
Confidence 6899999999999999876 46899999996 57889999999999999999999999998764
No 132
>smart00062 PBPb Bacterial periplasmic substrate-binding proteins. bacterial proteins, eukaryotic ones are in PBPe
Probab=98.82 E-value=4.9e-07 Score=70.12 Aligned_cols=184 Identities=12% Similarity=0.117 Sum_probs=112.3
Q ss_pred hhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccCC--CC-CceeeccccceEEEEecCCCCCCCCC
Q psy3760 106 YALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSP--SD-KLISIPCYQWEYVIIVPLDHPLLLLN 182 (306)
Q Consensus 106 ~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~--~~-~~~~~~l~~~~~~~v~~~~~~l~~~~ 182 (306)
.+...++..+.++. ++.+++...+..++.+.+.+|++|+++....... .. -....++.....+++++++++
T Consensus 24 G~~~~~~~~~~~~~-g~~~~~~~~~~~~~~~~l~~g~~D~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----- 97 (219)
T smart00062 24 GFDVDLAKAIAKEL-GLKVEFVEVSFDNLLTALKSGKIDVVAAGMTITPERAKQVDFSDPYYKSGQVILVRKDSP----- 97 (219)
T ss_pred cchHHHHHHHHHHh-CCeEEEEeccHHHHHHHHHCCcccEEeccccCCHHHHhheeeccceeeceeEEEEecCCC-----
Confidence 34555788888876 5999999988999999999999999998532111 11 224567777888999999886
Q ss_pred CcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCceeEEEEecCHHHHHHHHHhcc-ceeeeecceeccc-cc---CCce
Q psy3760 183 SISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRM-GIGIIASIAFDSN-RD---KNLR 257 (306)
Q Consensus 183 ~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~-gi~~~p~~~~~~~-~~---~~l~ 257 (306)
..+++||.+.++.... +..... ++...+... .....++...+..++.+|. ..++++....... .. ..+.
T Consensus 98 ~~~~~dL~g~~i~~~~-g~~~~~----~~~~~~~~~-~~~~~~~~~~~~~~l~~g~~d~~~~~~~~~~~~~~~~~~~~~~ 171 (219)
T smart00062 98 IKSLEDLKGKKVAVVA-GTTGEE----LLKKLYPEA-KIVSYDSQAEALAALKAGRADAAVADAPALAALVKQHGLPELK 171 (219)
T ss_pred CCChHHhCCCEEEEec-CccHHH----HHHHhCCCc-eEEEcCCHHHHHHHhhcCcccEEEeccHHHHHHHHhcCCCcee
Confidence 3588999888777665 333322 333222222 3445667788888888884 4455555543332 12 2344
Q ss_pred eeecCCCCccceEEEEEeCCccccHHHHHHHHHHhHHhhHHHHHhhh
Q psy3760 258 SISASHLFGTTISRVIIKQGTYLRSYVYSFIKLLSPKLNRKFINKIL 304 (306)
Q Consensus 258 ~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~ 304 (306)
.++... .....++++.+++.. .....+-+.+...-+....+++.
T Consensus 172 ~~~~~~-~~~~~~~~~~~~~~~--~~~~~~~~~l~~~~~~~~~~~i~ 215 (219)
T smart00062 172 IVGDPL-DTPEGYAFAVRKGDP--ELLDKINKALKELKADGTLKKIY 215 (219)
T ss_pred eccCCC-CCCcceEEEEECCCH--HHHHHHHHHHHHHHhCchHHHHH
Confidence 332222 222577888777742 33444444444433444455544
No 133
>PF13531 SBP_bac_11: Bacterial extracellular solute-binding protein; PDB: 2HXW_B 3FJG_C 3FJM_B 3FJ7_B 3FIR_B 3AXF_C 1WOD_A 1AMF_A 3R26_A 1SBP_A ....
Probab=98.79 E-value=1.8e-06 Score=68.23 Aligned_cols=200 Identities=15% Similarity=0.112 Sum_probs=138.7
Q ss_pred EEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcC-CeeEEEEccccC------CCCCc--eeecccc
Q psy3760 95 LTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRND-QADIAIVTEILS------PSDKL--ISIPCYQ 165 (306)
Q Consensus 95 l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~-~~Di~i~~~~~~------~~~~~--~~~~l~~ 165 (306)
|+|.+...+ ...+.++...| +++|++++++...++.++.+.|..| +.|+.+...... ..... ...++..
T Consensus 1 L~V~~~~~~-~~~~~~l~~~f-~~~~g~~v~v~~~~s~~~~~~l~~g~~~Dv~~~~~~~~~~~l~~~g~~~~~~~~~~~~ 78 (230)
T PF13531_consen 1 LTVYAASGL-APALEELAEAF-EKQPGIKVEVSFGGSGELVRRLQAGKKPDVFIPASSEWLERLAAAGLVDPGSPAPLAR 78 (230)
T ss_dssp EEEEEEGGG-HHHHHHHHHHH-HHHHCEEEEEEEECHHHHHHHHHTT-S-SEEEESSHHHHHHHHHTTTCSGGGEEEEEE
T ss_pred CEEEEcccH-HHHHHHHHHHH-HhccCCeEEEEECChHHHHHHHhcCCCceEEEECCHHHHHHHHhcccccCCccccccc
Confidence 577777764 55788899999 5589999999999999999999987 899999863211 11222 5788999
Q ss_pred ceEEEEecCCCCCCCCCCcChhhhcCC--CeEeecCCC-CcHHHHHHHHHhCC---C----ceeEEEEecCHHHHHHHHH
Q psy3760 166 WEYVIIVPLDHPLLLLNSISLKEISNY--PLITYDLSF-SGRIKLDREFSLQK---L----TPYIVLETINSDIIKTYVE 235 (306)
Q Consensus 166 ~~~~~v~~~~~~l~~~~~i~~~dl~~~--~~i~~~~~~-~~~~~~~~~~~~~~---~----~~~~~~~~~~~~~~~~~v~ 235 (306)
.+++++++++.|. ...+|+||.+- .+...++.. .....+...+...+ . ..+.....++...+...+.
T Consensus 79 ~~~vl~~~~~~~~---~~~~~~dL~~~~~~i~~~dP~~s~~g~~~~~~l~~~g~~~~~~~l~~~~~~~~~~~~~~~~~v~ 155 (230)
T PF13531_consen 79 SPLVLAVPKGNPK---GIRSWADLAQPGLRIAIPDPSTSPSGLAALQVLAAAGGQELLDALQKNIVQYVPSTSQVLSAVA 155 (230)
T ss_dssp EEEEEEEETTSTT---STTCHHHHCSTT--EEEE-TTTTHHHHHHHHHHHHHTHCHHHHHHHHTEEEEESSHHHHHHHHH
T ss_pred CceEEEeccCccc---ccCCHHHHhhccCEEEecCcccChhhHHHHHHHHHcccHHHHHHHHHhCcccccchHHHHHHHH
Confidence 9999999999864 34579999764 455555433 33445556666655 2 2466667888888888888
Q ss_pred hc-cceeeeecceeccc-ccCCceeeecCCCCc--cceEEEEEeCCccccHHHHHHHHHHhHHhhHHH
Q psy3760 236 LR-MGIGIIASIAFDSN-RDKNLRSISASHLFG--TTISRVIIKQGTYLRSYVYSFIKLLSPKLNRKF 299 (306)
Q Consensus 236 ~g-~gi~~~p~~~~~~~-~~~~l~~~~~~~~~~--~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~ 299 (306)
.| .-+++++...+... ....+..+++++... ...+.+...++....++.+.|+++|++.=.++.
T Consensus 156 ~g~~d~~~~~~s~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~a~~f~~~L~s~~~q~~ 223 (230)
T PF13531_consen 156 SGEADAGIVYESQAIFARQGDPLSYVYPPDGVNSPPIDYPIAILKNAPHPEAARAFIDFLLSPEGQQI 223 (230)
T ss_dssp TTSSSEEEEEHHHHHHCTSHTTEEEEE-STTTSSSEEEEEEEEBTTCTTHHHHHHHHHHHTSHHHHHH
T ss_pred cCCCcceeeHHHHHHHhhcCCCeEEEECCchhcCCCEEEEEEEecCCCCHHHHHHHHHHHCCHHHHHH
Confidence 88 44555555554321 456777777776444 356667666777778999999999987543333
No 134
>PF12849 PBP_like_2: PBP superfamily domain; InterPro: IPR024370 This entry represents members of the periplasmic binding domain superfamily []. It is often associated with a helix-turn-helix domain.; PDB: 1QUL_A 1OIB_A 1A54_A 1IXH_A 1A40_A 1QUJ_A 1A55_A 1IXI_A 2ABH_A 1QUK_A ....
Probab=98.61 E-value=6.1e-07 Score=73.13 Aligned_cols=202 Identities=17% Similarity=0.174 Sum_probs=130.8
Q ss_pred CCCcEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccCC---------------C
Q psy3760 91 DTGNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSP---------------S 155 (306)
Q Consensus 91 ~~~~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~---------------~ 155 (306)
..+.|+++.+.++ ..++..+...|.+.+|++++.+...++...+..|.+|.+|++++..+... .
T Consensus 8 ~~~~i~~~GS~~~-~~~~~~~~~~~~~~~~~~~v~v~~~gS~~g~~~l~~g~~di~~~sr~l~~~e~~~~~~~~~~~~~~ 86 (281)
T PF12849_consen 8 GSGTIRIAGSSTV-APIMEALAEAFERQYPGVKVTVESSGSGAGIQALINGKVDIAISSRPLTAAEIASEGYNAKGQKWG 86 (281)
T ss_dssp EE-EEEEEEHSTT-HHHHHHHHHHHHHHSTTBEEEEEEE-HHHHHHHHHTTSSSEEEESSHHHHHHHHHHTCCCCCHHHH
T ss_pred ceeEEEEEecCHH-HHHHHHHHHHHHHHCCCcEEEEEeCCCHHHHHHHHhCCCEEEEeCCCCcHHHHhHhhhhhcccccc
Confidence 3467999999885 66888899999999999999999999999999999999999999733221 1
Q ss_pred CCceeeccccceEEEEecCCCCCCC-----------CCCcChhhhc---CCC--eEeecCCCCcHHHHHHHHHhCCCcee
Q psy3760 156 DKLISIPCYQWEYVIIVPLDHPLLL-----------LNSISLKEIS---NYP--LITYDLSFSGRIKLDREFSLQKLTPY 219 (306)
Q Consensus 156 ~~~~~~~l~~~~~~~v~~~~~~l~~-----------~~~i~~~dl~---~~~--~i~~~~~~~~~~~~~~~~~~~~~~~~ 219 (306)
.++...+++.+.+++++++++|+.. .+..+|.|+. +.| ++....+.+.+..+.+++........
T Consensus 87 ~~~~~~~va~d~i~iv~n~~np~~~Lt~~ql~~I~~G~It~W~~~~~~~~~~I~~~~r~~~Sgt~~~f~~~l~~~~~~~~ 166 (281)
T PF12849_consen 87 GGLVQIPVARDAIVIVVNKDNPLNNLTREQLRDIFSGEITNWSDLGGGPDRPIKVVGRSDGSGTREFFTNYLLGGSPWTA 166 (281)
T ss_dssp CTEEEEEEEEEEEEEEEETTTTTEEETHHHHHHHHCTS--BGGGTTTCHSSB-EEEEESSTSHHHHHHHHHHHHHHHHHT
T ss_pred cccEEEEEEEeeEEEEEcCCCccccccHHHHHHHHhhhhhcccccccCCCCceEEEeCCCCCcHHHHHHHHHhccCCccc
Confidence 5678899999999999999998762 2233566652 334 44445555666677766655411111
Q ss_pred EEEEecCHHHHHHHHHhccceeeeecceecc-----cc-----------------cCCcee----------eec------
Q psy3760 220 IVLETINSDIIKTYVELRMGIGIIASIAFDS-----NR-----------------DKNLRS----------ISA------ 261 (306)
Q Consensus 220 ~~~~~~~~~~~~~~v~~g~gi~~~p~~~~~~-----~~-----------------~~~l~~----------~~~------ 261 (306)
..+.......+...+..-.+++++....... .. ...+.. .|.
T Consensus 167 ~~~~~~~~~~v~~~~~~~~~ig~v~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~l~~l~~~~~~~~v~p~~~~i~~ 246 (281)
T PF12849_consen 167 KAIGANGSEGVAQAVSTPGAIGYVSLSYALSNRAASIADLPNAIGYFVLPTTANVQKALKALSINPGDGSVAPTQENIAS 246 (281)
T ss_dssp TTEEESHHHHHHHHHHCTTEECCCCHHHHCSTCCEEEEEEEECCHHCCHHCHHHHCHCTECTHHT--TTTEEEEECHHST
T ss_pred cceeccCCccceeeccCCCceEEEecccccccccccccccccccccccccchhHHHHHHhhccccccceeeeecccCCcC
Confidence 1122233455555555555556655431110 00 111111 111
Q ss_pred CCCCccceEEEEEeCCccc-cHHHHHHHHHHhH
Q psy3760 262 SHLFGTTISRVIIKQGTYL-RSYVYSFIKLLSP 293 (306)
Q Consensus 262 ~~~~~~~~~~l~~~~~~~~-~~~~~~~~~~l~~ 293 (306)
...+..+.+|++++++... .+.++.|++|+.+
T Consensus 247 g~YPl~r~~y~~~~~~~~~~~~~~~~Fl~~~lS 279 (281)
T PF12849_consen 247 GSYPLSRPLYLYTNKDPLQPDPLVRAFLDFVLS 279 (281)
T ss_dssp TSSSCEEEEEEEEESTTSSHHHHHHHHHHHHHS
T ss_pred CCCCeEeEEEEEEECCCCCCcHHHHHHHHHHcC
Confidence 1234567889998887544 8999999999864
No 135
>COG2998 TupB ABC-type tungstate transport system, permease component [Coenzyme metabolism]
Probab=98.61 E-value=3.1e-05 Score=58.21 Aligned_cols=212 Identities=12% Similarity=0.117 Sum_probs=148.4
Q ss_pred ccCCCCcEEEEecccchhh-hhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccC------CCCCcee
Q psy3760 88 SAYDTGNLTIATTHTQARY-ALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILS------PSDKLIS 160 (306)
Q Consensus 88 ~~~~~~~l~I~~~~~~~~~-~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~------~~~~~~~ 160 (306)
.......||++++.+.-.. +|..++..|. +++++.+++...++...++.=++|++|+.|++.+.. ..-++..
T Consensus 25 ~sa~~~~LrmATTTSt~dtGLLd~l~p~fE-~~~g~~v~~vAvGTG~ALkmge~gdvDvv~vHapk~E~~fv~~G~gv~r 103 (280)
T COG2998 25 SSADAAELRMATTTSTEDTGLLDVLLPKFE-KYTGYDVQVVAVGTGKALKMGERGDVDVVIVHAPKAEKEFVKDGFGVDR 103 (280)
T ss_pred cCcccceEEEeeeccccccccHHHHHHhhh-hccCceEEEEEecchHHHhhhccCCcCEEEEeCcHHHHHHHHcCCCccC
Confidence 3556789999998876554 6666667776 789999999999999999999999999999974422 2346677
Q ss_pred eccccceEEEEecCCCCCCCCCCcC----hhhh--cCCCeEeecCCCCcHHHHHHHHHhCCCceeEE--EEe--cCHHHH
Q psy3760 161 IPCYQWEYVIIVPLDHPLLLLNSIS----LKEI--SNYPLITYDLSFSGRIKLDREFSLQKLTPYIV--LET--INSDII 230 (306)
Q Consensus 161 ~~l~~~~~~~v~~~~~~l~~~~~i~----~~dl--~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~--~~~~~~ 230 (306)
+++.-..|++|.|++.|.--+...+ ++.+ ...+||+..+.++....-...++..|+.|+.. +.. .-+...
T Consensus 104 ~~vmYNdFiiVgp~~dpA~~k~~kn~~e~fe~Ia~~ka~FvSRGD~SGT~~~E~~lWk~~g~~p~~~~wY~s~G~GMg~t 183 (280)
T COG2998 104 RPVMYNDFIIVGPADDPAGIKDAKNGKEAFEKIAEEKAKFVSRGDNSGTDSKELSLWKVTGIEPTVKGWYISAGQGMGDT 183 (280)
T ss_pred cceeeeeEEEECCcccchhcccchhHHHHHHHHHHcCCeeEecCCCCCccHHHHHHHHHcCCCCCCCcceeecCcchHHH
Confidence 8888889999999998855444333 2333 45789999888887777778888889887553 222 334566
Q ss_pred HHHHHhccceeeeecceeccc-ccCCceeeecCCCCccceEE--EEEeC--CccccHHHHHHHHHHhHHhhHHHH
Q psy3760 231 KTYVELRMGIGIIASIAFDSN-RDKNLRSISASHLFGTTISR--VIIKQ--GTYLRSYVYSFIKLLSPKLNRKFI 300 (306)
Q Consensus 231 ~~~v~~g~gi~~~p~~~~~~~-~~~~l~~~~~~~~~~~~~~~--l~~~~--~~~~~~~~~~~~~~l~~~~~~~~~ 300 (306)
+.+...-.++++..+...-.+ ..+.|+.+--.++...-.|. .+-++ ....-.....|++|+.+.-.++.+
T Consensus 184 L~~A~Ek~aytLtDrgTylaYr~r~~L~iv~~gd~~L~N~Ysvi~vNP~r~~~vny~~A~kfi~w~~s~~gq~~I 258 (280)
T COG2998 184 LNMANEKKAYTLTDRGTYLAYRNRPTLVIVLEGDPSLFNPYSVIAVNPKRVKGVNYTAATKFIEWLMSEKGQNLI 258 (280)
T ss_pred HHHhhhhceeEeeccceeeEecCccceEEEecCCccccCceeEEEEchhcCCCcCchHHHHHHHHHhhHHHHHHH
Confidence 777777788888887655555 66777776655533322333 33223 223456788999999776554444
No 136
>COG0725 ModA ABC-type molybdate transport system, periplasmic component [Inorganic ion transport and metabolism]
Probab=98.49 E-value=0.00012 Score=58.32 Aligned_cols=204 Identities=16% Similarity=0.131 Sum_probs=140.5
Q ss_pred CCCCcEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcC-CeeEEEEccccC-----C---CCCcee
Q psy3760 90 YDTGNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRND-QADIAIVTEILS-----P---SDKLIS 160 (306)
Q Consensus 90 ~~~~~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~-~~Di~i~~~~~~-----~---~~~~~~ 160 (306)
.....|+|....++.. -+..+..+|.+++ ++++.+..+++..+.+++.+| .+|+-++..... . ...-..
T Consensus 27 ~~~~~i~VfAAaSL~~-~l~~i~~~F~~~~-~~~V~~~f~gS~~l~~qIe~Ga~~D~fiSa~~~~~~~l~~~g~~~~~~~ 104 (258)
T COG0725 27 QEAATITVFAAASLTD-ALEEIAKQFEKET-GVKVEVEFGGSGALARQIEQGAPADLFISADDAYMDKLEDKGLIYADSR 104 (258)
T ss_pred ccCceEEEEEehhhHH-HHHHHHHHHHHHH-CCeEEEEecchHHHHHHHHcCCCcCEEEECCHHHHHHHHhcCCccCCce
Confidence 3456899999988755 5559999999999 999999999999999999997 799999863211 1 122246
Q ss_pred eccccceEEEEecCCCCCCCCCCcChhhhcCCC---eEeecC-CCCcHHHHHHHHHhCCCce---eEEEEecCHHHHHHH
Q psy3760 161 IPCYQWEYVIIVPLDHPLLLLNSISLKEISNYP---LITYDL-SFSGRIKLDREFSLQKLTP---YIVLETINSDIIKTY 233 (306)
Q Consensus 161 ~~l~~~~~~~v~~~~~~l~~~~~i~~~dl~~~~---~i~~~~-~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~ 233 (306)
..+....++++.+++.+.... .++++...+ +..-++ ..+....-.+.++..|+-. .......+...+...
T Consensus 105 ~~fa~n~lvl~~~~~~~~~~~---~~~~l~~~~~~~lai~~p~~~P~G~ya~~~l~~~g~~~~~~~k~v~~~~v~~~l~~ 181 (258)
T COG0725 105 IVFAGNRLVLAVPKGSKKKIE---SLEDLLERPDVRLAIGDPKTVPAGKYAKEALELLGLWYTLKDKLVLATNVRQALAY 181 (258)
T ss_pred EEeeCCeEEEEEeCCCccCcc---cHHHHhcCcCcEEEecCCCCCCchHHHHHHHHHhchhhhccccEEecCcHHHHHHH
Confidence 778889999999988764332 277777643 333332 3334556677777777753 355677888899999
Q ss_pred HHhc---cceeeeecceecccccCCceeeecCCC-CccceEEEEEeCCccccHHHHHHHHHHhHHhhHHHHH
Q psy3760 234 VELR---MGIGIIASIAFDSNRDKNLRSISASHL-FGTTISRVIIKQGTYLRSYVYSFIKLLSPKLNRKFIN 301 (306)
Q Consensus 234 v~~g---~gi~~~p~~~~~~~~~~~l~~~~~~~~-~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~~ 301 (306)
|..| .|+.+.++..... +.....+++.. .....+.+...++...++..++|++++.+.-.+...+
T Consensus 182 V~~G~ad~g~vy~sd~~~~~---~~~~~~~~~~~~~~Pi~y~iav~~~~~~~~~A~~f~~fl~s~~a~~il~ 250 (258)
T COG0725 182 VETGEADAGFVYVSDALLSK---KVKIVGVFPEDLHSPIVYPIAVLKNAKNPELAKEFVDFLLSPEAQEILE 250 (258)
T ss_pred HHcCCCCeEEEEEEhhhccC---CceEEEEcccccCCCeEEEEEEEcCCCCHHHHHHHHHHHhCHHHHHHHH
Confidence 9999 4444444333222 23333344432 2235667777788877899999999998855544443
No 137
>PRK11050 manganese transport regulator MntR; Provisional
Probab=98.48 E-value=6.9e-07 Score=65.09 Aligned_cols=61 Identities=21% Similarity=0.206 Sum_probs=52.7
Q ss_pred CHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEec-CCCccccCHhHHHHHHHHHHHHHHHHHHHH
Q psy3760 18 NLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRH-GKRIRGLTKPGQAILRSIEIIMQEIEGLKK 82 (306)
Q Consensus 18 s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~-~~~~~~lT~~G~~l~~~a~~il~~~~~~~~ 82 (306)
+.+..|+.+++|+|++|+.|++||+. | ++.|. ++++ .||+.|+.++..+......++.+..
T Consensus 53 t~~eLA~~l~is~stVsr~l~~Le~~-G--lI~r~~~~~v-~LT~~G~~l~~~~~~~~~~le~~l~ 114 (152)
T PRK11050 53 RQVDIAARLGVSQPTVAKMLKRLARD-G--LVEMRPYRGV-FLTPEGEKLAQESRERHQIVENFLL 114 (152)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHC-C--CEEEecCCce-EECchHHHHHHHHHHHHHHHHHHHH
Confidence 89999999999999999999999997 5 55554 5677 8999999999999988888877553
No 138
>TIGR01256 modA molybdenum ABC transporter, periplasmic molybdate-binding protein. The model 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 represent 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 the ModB, an integral membrane protein and ModC the ATP-binding subunit. Invariably almost all of them display a common beta/alpha folding motif and have similar tertiary structures consisting of two globular domains.
Probab=98.48 E-value=6.8e-05 Score=58.55 Aligned_cols=186 Identities=16% Similarity=0.093 Sum_probs=114.9
Q ss_pred hhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCC-eeEEEEccccC----CCCC----ceeeccccceEEEEecCC
Q psy3760 105 RYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQ-ADIAIVTEILS----PSDK----LISIPCYQWEYVIIVPLD 175 (306)
Q Consensus 105 ~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~-~Di~i~~~~~~----~~~~----~~~~~l~~~~~~~v~~~~ 175 (306)
...+..++..|.+++| +++++...++.++...+..|. +|+.+...... ...+ +....+....++++++++
T Consensus 5 ~~~~~~~~~~f~~~~g-i~V~~~~~gs~~l~~~l~~~~~aDv~~~~~~~~~~~l~~~g~~~~~~~~~~~~~~~~l~~~~~ 83 (216)
T TIGR01256 5 TDALKEIAKQFEKRTG-NKVVFSFGSSGTLYTQIENGAPADLFISADNKWPKKLVDKGLVVAGSRFTYAGNKLVLISPKN 83 (216)
T ss_pred HHHHHHHHHHHHHhhC-CeEEEEeCChHHHHHHHHcCCCCcEEEECCHHHHHHHHHCCCCCCCchheEEccEEEEEEECC
Confidence 3466778999999997 999999999999999999874 99999853211 0111 222336777888888776
Q ss_pred CCCCCCCCcChhhhc----CCCeEeecCCC-CcHHHHHHHHHhCC----CceeEEEEecCHHHHHHHHHhc-cceeeeec
Q psy3760 176 HPLLLLNSISLKEIS----NYPLITYDLSF-SGRIKLDREFSLQK----LTPYIVLETINSDIIKTYVELR-MGIGIIAS 245 (306)
Q Consensus 176 ~~l~~~~~i~~~dl~----~~~~i~~~~~~-~~~~~~~~~~~~~~----~~~~~~~~~~~~~~~~~~v~~g-~gi~~~p~ 245 (306)
. .+-+++||. +..++..++.. ........+++..+ +.++.. ...+...+..++..| ..+++...
T Consensus 84 ~-----~~~s~~dL~~~~~~~~i~~~~P~~~~~g~~~~~~~~~~g~~~~l~~n~~-~~~~~~~~~~~~~~Ge~~~~~~~~ 157 (216)
T TIGR01256 84 R-----VVDDLDILKKWVADKRVAIGDPKHAPYGAAAKEVLQKLGLWETLKKKLV-YGEDVRQALQFVETGNAPAGIVAL 157 (216)
T ss_pred C-----CcCcHHHHhhcccCCeEEecCCCcCcChHHHHHHHHHCCChhhhhhhee-ecCcHHHHHHHHHcCCCCEEeeeh
Confidence 2 234688884 23445544332 23334455555554 345544 455777888888888 45555554
Q ss_pred ceecccccCCceeeecCCC-CccceEEEEEeCCccccHHHHHHHHHHhHHhhHH
Q psy3760 246 IAFDSNRDKNLRSISASHL-FGTTISRVIIKQGTYLRSYVYSFIKLLSPKLNRK 298 (306)
Q Consensus 246 ~~~~~~~~~~l~~~~~~~~-~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~ 298 (306)
..+.... +....++++.. .....+.+...++.......++|++++.+.=.+.
T Consensus 158 ~~~~~~~-~~~~~~~~P~~~~~~~~~~~ai~k~a~~~~~A~~fi~fl~s~e~q~ 210 (216)
T TIGR01256 158 SDVIPSK-KVGSVATFPEDLYKPIRYPAVIVKGGKNNAAAKAFIDYLKSPEAKE 210 (216)
T ss_pred hhhcccC-CccEEEEeCccccCCccccEEEEECCCChHHHHHHHHHHcCHHHHH
Confidence 4333221 22233444432 2233445555566666889999999997654333
No 139
>COG1910 Periplasmic molybdate-binding protein/domain [Inorganic ion transport and metabolism]
Probab=98.47 E-value=6.4e-06 Score=61.61 Aligned_cols=153 Identities=20% Similarity=0.173 Sum_probs=116.2
Q ss_pred hhHHHHHHHcCCeeEEEEccccC-------------CCCCceeeccccceEEEEecCCCCCCCCCCcChhhhcCC--CeE
Q psy3760 131 PKQITEMIRNDQADIAIVTEILS-------------PSDKLISIPCYQWEYVIIVPLDHPLLLLNSISLKEISNY--PLI 195 (306)
Q Consensus 131 ~~~~~~~l~~~~~Di~i~~~~~~-------------~~~~~~~~~l~~~~~~~v~~~~~~l~~~~~i~~~dl~~~--~~i 195 (306)
+-.-+-.+..|++|++=..-.+. -.+.......+.-++.+++++++| +.--+++||... .+|
T Consensus 27 S~gG~~~i~~G~adiag~hlld~~~g~ynip~v~~~~~~~~~LI~g~~Re~Gl~v~~gnp---k~i~~~edl~~~d~~fV 103 (223)
T COG1910 27 SMGGLLAIKRGEADIAGIHLLDNESGTYNIPYVKKYLPGEAVLIRGYLREQGLMVQKGNP---KNISSLEDLLRKDLRFV 103 (223)
T ss_pred cccchHhhhhcccceeeeeeccCCCCceehhhhhhcCCCceEEEeeeeeeeeeEEecCCC---CccccHHHHhhcCcEEE
Confidence 33446679999999997641111 012244556666788999999997 334589999877 899
Q ss_pred eecCCCCcHHHHHHHHHhCCCceeE----EEEecCHHHHHHHHHhc-cceeeeecceecccccCCceeeecCCCCccceE
Q psy3760 196 TYDLSFSGRIKLDREFSLQKLTPYI----VLETINSDIIKTYVELR-MGIGIIASIAFDSNRDKNLRSISASHLFGTTIS 270 (306)
Q Consensus 196 ~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~~~~~~~~v~~g-~gi~~~p~~~~~~~~~~~l~~~~~~~~~~~~~~ 270 (306)
..+.+++.|..+++.+...+..|+. ..++.+...+...|++| .-+++--.+.+ ...+|.++|+... .|
T Consensus 104 NR~rGSGTR~LlD~~L~~~~~~~~~I~GY~~e~~th~avA~aVa~G~AD~GvGlr~~A---~~~gL~Fipl~~E----~Y 176 (223)
T COG1910 104 NRNRGSGTRILLDELLGELNILPDSIKGYSDEATTHDAVASAVASGRADAGVGLRHAA---EKYGLDFIPLGDE----EY 176 (223)
T ss_pred ecCCCccHHHHHHHHHHHcCcCchhcCCccccccccHHHHHHHHcCCCCccccHHHHH---HHcCCceEEcccc----eE
Confidence 9999999999999999999887643 36778888999999998 33444333443 3568999999872 78
Q ss_pred EEEEeCCccccHHHHHHHHHHhH
Q psy3760 271 RVIIKQGTYLRSYVYSFIKLLSP 293 (306)
Q Consensus 271 ~l~~~~~~~~~~~~~~~~~~l~~ 293 (306)
.++.+++....|.+++|++.|++
T Consensus 177 D~virke~~~~~~vr~fi~~L~s 199 (223)
T COG1910 177 DFVIRKERLDKPVVRAFIKALKS 199 (223)
T ss_pred EEEEehhHccCHHHHHHHHHhcc
Confidence 89999999999999999999985
No 140
>PF00497 SBP_bac_3: Bacterial extracellular solute-binding proteins, family 3; InterPro: IPR001638 Bacterial high affinity transport systems are involved in active transport of solutes across the cytoplasmic membrane. The protein components of these traffic systems include one or two transmembrane protein components, one or two membrane-associated ATP-binding proteins (ABC transporters; see IPR003439 from INTERPRO) and a high affinity periplasmic solute-binding protein. The latter are thought to bind the substrate in the vicinity of the inner membrane, and to transfer it to a complex of inner membrane proteins for concentration into the cytoplasm. In Gram-positive bacteria which are surrounded by a single membrane and have therefore no periplasmic region, the equivalent proteins are bound to the membrane via an N-terminal lipid anchor. These homologue proteins do not play an integral role in the transport process per se, but probably serve as receptors to trigger or initiate translocation of the solute throught the membrane by binding to external sites of the integral membrane proteins of the efflux system. In addition, at least some solute-binding proteins function in the initiation of sensory transduction pathways. On the basis of sequence similarities, the vast majority of these solute-binding proteins can be grouped [] into eight families or clusters, which generally correlate with the nature of the solute bound. Family 3 groups together specific amino acids and opine-binding periplasmic proteins and a periplasmic homologue with catalytic activity.; GO: 0005215 transporter activity, 0006810 transport, 0030288 outer membrane-bounded periplasmic space; PDB: 3N26_A 3QAX_A 3I6V_A 2VHA_B 2IA4_B 2Q89_A 2Q88_A 2YJP_C 1II5_A 1IIW_A ....
Probab=98.42 E-value=1.2e-05 Score=62.92 Aligned_cols=193 Identities=15% Similarity=0.094 Sum_probs=117.5
Q ss_pred hhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccc--cCCCCCce-eeccccceEEEEecCCCCCCC
Q psy3760 104 ARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEI--LSPSDKLI-SIPCYQWEYVIIVPLDHPLLL 180 (306)
Q Consensus 104 ~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~--~~~~~~~~-~~~l~~~~~~~v~~~~~~l~~ 180 (306)
...+...++..+.++. ++.+++...+...+...|.+|++|+++.... ......+. +.+++....+++++++.+...
T Consensus 21 ~~G~~~dl~~~i~~~~-g~~~~~~~~~~~~~~~~l~~g~~D~~~~~~~~~~~r~~~~~~s~p~~~~~~~~~~~~~~~~~~ 99 (225)
T PF00497_consen 21 PSGIDVDLLRAIAKRL-GIKIEFVPMPWSRLLEMLENGKADIIIGGLSITPERAKKFDFSDPYYSSPYVLVVRKGDAPPI 99 (225)
T ss_dssp EESHHHHHHHHHHHHH-TCEEEEEEEEGGGHHHHHHTTSSSEEESSEB-BHHHHTTEEEESESEEEEEEEEEETTSTCST
T ss_pred EEEEhHHHHHHHHhhc-ccccceeecccccccccccccccccccccccccccccccccccccccchhheeeecccccccc
Confidence 3457788888888876 8889998878889999999999999984211 11122333 558999999999997642111
Q ss_pred CCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCceeEEEEecCHHHHHHHHHhccc-eeeeecceeccc-ccCCce-
Q psy3760 181 LNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMG-IGIIASIAFDSN-RDKNLR- 257 (306)
Q Consensus 181 ~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~g-i~~~p~~~~~~~-~~~~l~- 257 (306)
...-+++||.+.++..... ......+.+.... ..++ ..+++...++.++.+|.. ..+.+...+... ......
T Consensus 100 ~~~~~~~dl~~~~i~~~~g-~~~~~~l~~~~~~---~~~~-~~~~~~~~~~~~l~~g~~d~~i~~~~~~~~~~~~~~~~~ 174 (225)
T PF00497_consen 100 KTIKSLDDLKGKRIGVVRG-SSYADYLKQQYPS---NINI-VEVDSPEEALEALLSGRIDAFIVDESTAEYLLKRHPLEN 174 (225)
T ss_dssp SSHSSGGGGTTSEEEEETT-SHHHHHHHHHTHH---TSEE-EEESSHHHHHHHHHTTSSSEEEEEHHHHHHHHHHTTTCE
T ss_pred ccccchhhhcCcccccccc-hhHHHHhhhhccc---hhhh-cccccHHHHHHHHhcCCeeeeeccchhhhhhhhhccccc
Confidence 1222567897776666554 3333344443322 2233 368999999999999966 555555555443 222222
Q ss_pred eeecCCCCccceEEEEEeCCccccHHHHHHHHHHhHHhhHHHHHhhh
Q psy3760 258 SISASHLFGTTISRVIIKQGTYLRSYVYSFIKLLSPKLNRKFINKIL 304 (306)
Q Consensus 258 ~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~ 304 (306)
............++++.+++. +...+.|-+.|.+.-+...++++.
T Consensus 175 ~~~~~~~~~~~~~~~~~~~~~--~~l~~~~n~~i~~l~~~G~~~~i~ 219 (225)
T PF00497_consen 175 IVVIPPPISPSPVYFAVRKKN--PELLEIFNKAIRELKQSGEIQKIL 219 (225)
T ss_dssp EEEEEEEEEEEEEEEEEETTT--HHHHHHHHHHHHHHHHTTHHHHHH
T ss_pred ccccccccccceeEEeecccc--cHHHHHHHHHHHHHHhCcHHHHHH
Confidence 222122233446666666542 455555655565555554555554
No 141
>PRK10677 modA molybdate transporter periplasmic protein; Provisional
Probab=98.41 E-value=0.00026 Score=56.71 Aligned_cols=199 Identities=15% Similarity=0.128 Sum_probs=123.8
Q ss_pred CCCCcEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCC-eeEEEEccccC----CCCCc----ee
Q psy3760 90 YDTGNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQ-ADIAIVTEILS----PSDKL----IS 160 (306)
Q Consensus 90 ~~~~~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~-~Di~i~~~~~~----~~~~~----~~ 160 (306)
.....|+|.+..++. ..+..+...|.+++ ++++.+...++..+.+++..|. +|+.+...... ...++ ..
T Consensus 24 ~~~~~l~v~~a~~~~-~~~~~l~~~Fe~~~-g~~v~~~~~~Sg~l~~qi~~g~~~Dv~~~a~~~~~~~l~~~gl~~~~~~ 101 (257)
T PRK10677 24 ADEGKITVFAAASLT-NALQDIAAQYKKEK-GVDVVSSFASSSTLARQIEQGAPADLFISADQKWMDYAVDKKAIDTATR 101 (257)
T ss_pred ccCCcEEEEEecChH-HHHHHHHHHHHhhh-CCeEEEEecccHHHHHHHHcCCCCCEEEECCHHHHHHHHHCCCCCCcch
Confidence 344579999998764 68888999999886 9999999999999999999887 99999853111 01111 13
Q ss_pred eccccceEEEEecCCCCCCCC---CCcChhhhcCC-CeEeecCC-CCcHHHHHHHHHhCCCc----eeEEEEecCHHHHH
Q psy3760 161 IPCYQWEYVIIVPLDHPLLLL---NSISLKEISNY-PLITYDLS-FSGRIKLDREFSLQKLT----PYIVLETINSDIIK 231 (306)
Q Consensus 161 ~~l~~~~~~~v~~~~~~l~~~---~~i~~~dl~~~-~~i~~~~~-~~~~~~~~~~~~~~~~~----~~~~~~~~~~~~~~ 231 (306)
..+....++++++++.|.... .+-+|+||.+- .+...++. .+........++..|+- .+ ....++...+.
T Consensus 102 ~~~a~n~lvl~~~~~~~~~~i~~~~~~~~~dLl~~~~iai~dP~~~p~G~~a~~~l~~~g~~~~l~~k-~~~~~~v~~~~ 180 (257)
T PRK10677 102 YTLLGNSLVVVAPKASEQKDFTIDKKTDWKSLLNGGRLAVGDPDHVPAGIYAKEALQKLGAWDTLSPK-LARAEDVRGAL 180 (257)
T ss_pred heeecCEEEEEEECCCccccccccCccCHHHhcCCCeEEEcCCCCChHHHHHHHHHHHcCCHHHHHhh-hcccccHHHHH
Confidence 468888999999998765431 23468888653 34444443 23444555666666541 12 22346677788
Q ss_pred HHHHhc-cceeeeecceecccccCCceee-ecCC-CCccceEEEEEeCCccccHHHHHHHHHHhHH
Q psy3760 232 TYVELR-MGIGIIASIAFDSNRDKNLRSI-SASH-LFGTTISRVIIKQGTYLRSYVYSFIKLLSPK 294 (306)
Q Consensus 232 ~~v~~g-~gi~~~p~~~~~~~~~~~l~~~-~~~~-~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~ 294 (306)
.++..| .-+++...+.+.. ..++..+ .++. ......+.+...++.. ++..++|++++.+.
T Consensus 181 ~~v~~G~ad~gi~~~s~a~~--~~~~~~~~~~P~e~~~~i~~~~avlk~~~-~~~Ak~Fi~fl~S~ 243 (257)
T PRK10677 181 ALVERNEAPLGIVYGSDAVA--SKKVKVVGTFPEDSHKPVEYPMAIVKGHN-NATVKAFYDYLKGP 243 (257)
T ss_pred HHHHcCCCCEEEEEeeeeec--cCCCeEEEECCcccCCcceeeEEEEcCCC-CHHHHHHHHHHcCH
Confidence 899888 3334443333222 2223322 2222 2223344444445544 57899999999654
No 142
>TIGR02337 HpaR homoprotocatechuate degradation operon regulator, HpaR. This Helix-Turn-Helix transcriptional regulator is a member of the MarR family (pfam01047) and is found in association with operons for the degradation of 4-hydroxyphenylacetic acid via homoprotocatechuate.
Probab=98.40 E-value=2.6e-06 Score=59.51 Aligned_cols=76 Identities=25% Similarity=0.350 Sum_probs=62.4
Q ss_pred CchhhHHHHHHHHHhcCC--HHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecC-------CCccccCHhHHHHHHHHH
Q psy3760 1 MNLHQFRFVREAVRQNFN--LTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHG-------KRIRGLTKPGQAILRSIE 71 (306)
Q Consensus 1 m~~~~l~~f~~v~~~~~s--~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~-------~~~~~lT~~G~~l~~~a~ 71 (306)
|+..++.++..+.+.+ . .+.-|+.++++++++|+.|++||+. -|+.|.. ..+ .||+.|+.+++.+.
T Consensus 26 lt~~q~~iL~~l~~~~-~~t~~ela~~~~~~~~tvs~~l~~Le~~---GlI~r~~~~~D~R~~~v-~LT~~G~~~~~~~~ 100 (118)
T TIGR02337 26 LTEQQWRILRILAEQG-SMEFTQLANQACILRPSLTGILARLERD---GLVTRLKASNDQRRVYI-SLTPKGQALYASLS 100 (118)
T ss_pred CCHHHHHHHHHHHHcC-CcCHHHHHHHhCCCchhHHHHHHHHHHC---CCEEeccCCCCCCeeEE-EECHhHHHHHHHhh
Confidence 4567888888888766 5 7899999999999999999999997 5666632 244 89999999999999
Q ss_pred HHHHHHHHHH
Q psy3760 72 IIMQEIEGLK 81 (306)
Q Consensus 72 ~il~~~~~~~ 81 (306)
+.........
T Consensus 101 ~~~~~~~~~~ 110 (118)
T TIGR02337 101 PQIEEIYAAI 110 (118)
T ss_pred HHHHHHHHHH
Confidence 9888776643
No 143
>smart00529 HTH_DTXR Helix-turn-helix diphteria tox regulatory element. iron dependent repressor
Probab=98.39 E-value=2.3e-06 Score=57.39 Aligned_cols=60 Identities=23% Similarity=0.309 Sum_probs=51.2
Q ss_pred HHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecC-CCccccCHhHHHHHHHHHHHHHHHHHHHH
Q psy3760 19 LTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHG-KRIRGLTKPGQAILRSIEIIMQEIEGLKK 82 (306)
Q Consensus 19 ~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~-~~~~~lT~~G~~l~~~a~~il~~~~~~~~ 82 (306)
++..|+.+++|+|++|+.++.||+. -|+.|.+ +++ .||+.|..+++.+......++....
T Consensus 2 ~~ela~~l~is~stvs~~l~~L~~~---glI~r~~~~~~-~lT~~g~~~~~~~~~~~~~~~~~l~ 62 (96)
T smart00529 2 TSEIAERLNVSPPTVTQMLKKLEKD---GLVEYEPYRGI-TLTEKGRRLARRLLRKHRLLERFLV 62 (96)
T ss_pred HHHHHHHhCCChHHHHHHHHHHHHC---CCEEEcCCCce-EechhHHHHHHHHHHHHHHHHHHHH
Confidence 4688999999999999999999996 5888887 466 8999999999888887776666554
No 144
>TIGR00975 3a0107s03 phosphate ABC transporter, phosphate-binding protein. This family represents one type of (periplasmic, in Gram-negative bacteria) phosphate-binding protein found in phosphate ABC (ATP-binding cassette) transporters. This protein is accompanied, generally in the same operon, by an ATP binding protein and (usually) two permease proteins.
Probab=98.37 E-value=4.4e-05 Score=62.97 Aligned_cols=152 Identities=12% Similarity=-0.001 Sum_probs=98.9
Q ss_pred EEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccCCC------CCceeeccccceEE
Q psy3760 96 TIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPS------DKLISIPCYQWEYV 169 (306)
Q Consensus 96 ~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~~------~~~~~~~l~~~~~~ 169 (306)
+++.+.+ ...++..+...|.+.||++++.+...++...++.+.+|.+||+....+..+. .++...++..+.++
T Consensus 2 ~~~GStt-~~pl~~~~~~~y~~~~~~v~v~v~~~GSg~Gi~~l~~g~~dia~ssr~l~~~E~~~~~~~~~~~pva~dai~ 80 (314)
T TIGR00975 2 TGAGSTF-PYPLYTKWFPDYQKSNPGVTINYQGIGSGAGIAQFAAGTVDFGASDAPLSEADLASRGSGLLQFPTVIGAIV 80 (314)
T ss_pred eeeccCc-HHHHHHHHHHHHHHhCCCceEEEecCCCHHHHHHHHcCCCCEEecCCCCCHHHHHhhcCCcEEeeEEeeeEE
Confidence 3444444 4668888899999999999999999999999999999999999997554322 25677888888999
Q ss_pred EEecC-CCC-----CCC--------CCCcChhh-----------hcCCCe--EeecCCCCcHHHHHHHHHhC--------
Q psy3760 170 IIVPL-DHP-----LLL--------LNSISLKE-----------ISNYPL--ITYDLSFSGRIKLDREFSLQ-------- 214 (306)
Q Consensus 170 ~v~~~-~~~-----l~~--------~~~i~~~d-----------l~~~~~--i~~~~~~~~~~~~~~~~~~~-------- 214 (306)
+++++ +.+ |.. .+.-+|+| +.+.|. +....+.+.+..+.+++...
T Consensus 81 vivn~~~~~~~~l~Lt~~~L~~If~G~It~W~d~~i~~~np~~~~p~~~I~vv~R~~~SGT~~~f~~~l~~~~~~~~~~~ 160 (314)
T TIGR00975 81 VTYNLPGVSKGELKLDGPVLAKIFLGKIKTWNDPAIAALNPGVKLPGTAITVVHRSDGSGTTFNFTNYLSKVSPEWKEKV 160 (314)
T ss_pred EEEeCCCCCccccccCHHHHHHHhCCCCcccCchhhhhcCCCCCCCCCceEEEeCCCCCchHHHHHHHHHhhChhhhhcc
Confidence 99985 322 110 22334665 122443 34455556777777665321
Q ss_pred --CC--ceeEEEEecCHHHHHHHHHhc-cceeeeeccee
Q psy3760 215 --KL--TPYIVLETINSDIIKTYVELR-MGIGIIASIAF 248 (306)
Q Consensus 215 --~~--~~~~~~~~~~~~~~~~~v~~g-~gi~~~p~~~~ 248 (306)
+. .........+...+.+.|... .+|+++....+
T Consensus 161 ~~~~~~~~~~~~~~~~~~~v~~~V~~~p~aIGY~~~~~~ 199 (314)
T TIGR00975 161 GAGTTVQWPAGVGGKGNDGVVAGVKQTPGAIGYVEWSYA 199 (314)
T ss_pred CCCceecCCcccccCCCHHHHHHHhcCCCceEEeeHHHH
Confidence 10 001123444556667777654 89999876544
No 145
>PRK11917 bifunctional adhesin/ABC transporter aspartate/glutamate-binding protein; Reviewed
Probab=98.29 E-value=0.00025 Score=56.99 Aligned_cols=179 Identities=13% Similarity=0.087 Sum_probs=111.2
Q ss_pred CCCcEEEEecccchh------------hhhHHHHHHHHHhC--CCcEEEEEeCChhHHHHHHHcCCeeEEEEcccc--CC
Q psy3760 91 DTGNLTIATTHTQAR------------YALPKIIKEFTIQF--PKVKLSLLQGNPKQITEMIRNDQADIAIVTEIL--SP 154 (306)
Q Consensus 91 ~~~~l~I~~~~~~~~------------~~l~~~l~~~~~~~--p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~--~~ 154 (306)
.+|.|+||+...... .+-..++..+.++- .++.+++...........|.+|++|+++..... ..
T Consensus 36 ~~g~l~vg~~~~~pP~~~~~~~~g~~~G~~vdl~~~ia~~llg~~~~~~~~~~~~~~~~~~l~~g~~D~~~~~~~~t~eR 115 (259)
T PRK11917 36 SKGQLIVGVKNDVPHYALLDQATGEIKGFEIDVAKLLAKSILGDDKKIKLVAVNAKTRGPLLDNGSVDAVIATFTITPER 115 (259)
T ss_pred hCCEEEEEECCCCCCceeeeCCCCceeEeeHHHHHHHHHHhcCCCccEEEEEcChhhHHHHHHCCCccEEEecccCChhh
Confidence 367999999753221 35567788888863 346777777776677789999999999874221 22
Q ss_pred CCCce-eeccccceEEEEecCCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCceeEEEEecCHHHHHHH
Q psy3760 155 SDKLI-SIPCYQWEYVIIVPLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTY 233 (306)
Q Consensus 155 ~~~~~-~~~l~~~~~~~v~~~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 233 (306)
...+. +.+++.....++++++.+ .-+++||.+.+.... .+......+.+.++..+... .....++.....++
T Consensus 116 ~~~~~fs~py~~~~~~lvv~~~~~-----~~s~~dL~g~~V~v~-~gs~~~~~l~~~~~~~~~~~-~~~~~~~~~~~~~~ 188 (259)
T PRK11917 116 KRIYNFSEPYYQDAIGLLVLKEKN-----YKSLADMKGANIGVA-QAATTKKAIGEAAKKIGIDV-KFSEFPDYPSIKAA 188 (259)
T ss_pred hheeeeccCceeeceEEEEECCCC-----CCCHHHhCCCeEEEe-cCCcHHHHHHHhhHhcCCce-eEEecCCHHHHHHH
Confidence 23343 457888899999998864 247899998885554 44444455566666555432 23456788888899
Q ss_pred HHhccceeeeec-ceecccccCCceeeecCCCCccceEEEEEeCCc
Q psy3760 234 VELRMGIGIIAS-IAFDSNRDKNLRSISASHLFGTTISRVIIKQGT 278 (306)
Q Consensus 234 v~~g~gi~~~p~-~~~~~~~~~~l~~~~~~~~~~~~~~~l~~~~~~ 278 (306)
+.+|..=+++-. .....+.......+ .......+++++.+++.
T Consensus 189 l~~GrvDa~~~d~~~~~~~~~~~~~~~--~~~~~~~~~~~a~~k~~ 232 (259)
T PRK11917 189 LDAKRVDAFSVDKSILLGYVDDKSEIL--PDSFEPQSYGIVTKKDD 232 (259)
T ss_pred HHcCCCcEEEecHHHHHHhhhcCCeec--CCcCCCCceEEEEeCCC
Confidence 999965444433 32223222222222 22222335667767663
No 146
>PRK03902 manganese transport transcriptional regulator; Provisional
Probab=98.26 E-value=8.8e-06 Score=58.80 Aligned_cols=74 Identities=16% Similarity=0.218 Sum_probs=53.2
Q ss_pred hHHHHHHHHHhc--CCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCCccccCHhHHHHHHHHHHHHHHHHHHH
Q psy3760 5 QFRFVREAVRQN--FNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKPGQAILRSIEIIMQEIEGLK 81 (306)
Q Consensus 5 ~l~~f~~v~~~~--~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~~~lT~~G~~l~~~a~~il~~~~~~~ 81 (306)
-|+.+..+.+.+ .+++..|+.|++|+|++|+.|++|++. |.-... ..+++ +||+.|+.+......--..++.+.
T Consensus 9 yL~~I~~l~~~~~~~~~~ela~~l~vs~~svs~~l~~L~~~-Gli~~~-~~~~i-~LT~~G~~~a~~~~~~h~~~e~~l 84 (142)
T PRK03902 9 YIEQIYLLIEEKGYARVSDIAEALSVHPSSVTKMVQKLDKD-EYLIYE-KYRGL-VLTPKGKKIGKRLVYRHELLEQFL 84 (142)
T ss_pred HHHHHHHHHhcCCCcCHHHHHHHhCCChhHHHHHHHHHHHC-CCEEEe-cCceE-EECHHHHHHHHHHHHHHHHHHHHH
Confidence 355555555442 166778999999999999999999999 764333 35777 899999998777654444444444
No 147
>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein.
Probab=98.22 E-value=1.8e-05 Score=53.55 Aligned_cols=76 Identities=21% Similarity=0.274 Sum_probs=60.9
Q ss_pred CchhhHHHHHHHHHhc-CCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecC-------CCccccCHhHHHHHHHHHH
Q psy3760 1 MNLHQFRFVREAVRQN-FNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHG-------KRIRGLTKPGQAILRSIEI 72 (306)
Q Consensus 1 m~~~~l~~f~~v~~~~-~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~-------~~~~~lT~~G~~l~~~a~~ 72 (306)
|+...+.+|..+.+.+ .+.+..|+.+++|++++++.|++|++. .++.+.. ..+ .+|+.|..++..+..
T Consensus 8 l~~~~~~il~~l~~~~~~~~~~la~~~~~s~~~i~~~l~~L~~~---g~v~~~~~~~~~r~~~~-~lT~~g~~~~~~~~~ 83 (101)
T smart00347 8 LTPTQFLVLRILYEEGPLSVSELAKRLGVSPSTVTRVLDRLEKK---GLIRRLPSPEDRRSVLV-SLTEEGRELIEELLE 83 (101)
T ss_pred CCHHHHHHHHHHHHcCCcCHHHHHHHHCCCchhHHHHHHHHHHC---CCeEecCCCCCCCeEEE-EECHhHHHHHHHHHH
Confidence 4667888999998764 377888999999999999999999996 4444332 245 799999999999998
Q ss_pred HHHHHHHH
Q psy3760 73 IMQEIEGL 80 (306)
Q Consensus 73 il~~~~~~ 80 (306)
.+..+...
T Consensus 84 ~~~~~~~~ 91 (101)
T smart00347 84 ARHETLAE 91 (101)
T ss_pred HHHHHHHH
Confidence 88876653
No 148
>TIGR03730 tungstate_WtpA tungstate ABC transporter binding protein WtpA. Members of this protein family are tungstate (and, more weakly, molybdate) binding proteins of tungstate(/molybdate) ABC transporters, as first characterized in Pyrococcus furiosus. Model seed members and cutoffs, pending experimental evidence for more distant homologs, were chosen such that this model identifies select archaeal proteins, excluding weaker archaeal and all bacterial homologs. Note that this family is homologous to molybdate transporters, and that at least one other family of tungstate transporter binding protein, TupA, also exists.
Probab=98.20 E-value=0.00081 Score=54.08 Aligned_cols=194 Identities=13% Similarity=0.039 Sum_probs=120.4
Q ss_pred cEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHH-c-CCeeEEEEccccC----CCCCc--eeecccc
Q psy3760 94 NLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIR-N-DQADIAIVTEILS----PSDKL--ISIPCYQ 165 (306)
Q Consensus 94 ~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~-~-~~~Di~i~~~~~~----~~~~~--~~~~l~~ 165 (306)
+|+|.+..++ ...+..+...|.+++|++++++...++..+..++. + ..+|+.++..... ...++ ....+..
T Consensus 2 ~L~V~aAasL-~~~~~ei~~~Fe~~~~gvkv~~~~~gSg~L~~Qi~e~Gap~DVfisAd~~~~~~L~~~g~~~~~~~~a~ 80 (273)
T TIGR03730 2 KLKIFHAGSL-SVPFEEMEKEFEAKHPNVDVQREAAGSVAAVRKITELGKPADILASADYTLIPQMMIPNYADWYIMFAT 80 (273)
T ss_pred eEEEEEccCc-HHHHHHHHHHHHhhCCCceEEEEeCcHHHHHHHHHHcCCCeeEEEeCCHHHHHHHHhCCCcCceeeEEc
Confidence 4788888886 45777899999999999999999999999999995 4 5899999863211 11222 3457889
Q ss_pred ceEEEEecCCCCCCCC-CCcCh-hhhcC--CCeEeecCC-CCcH-------HHHHHHHHhCC------------------
Q psy3760 166 WEYVIIVPLDHPLLLL-NSISL-KEISN--YPLITYDLS-FSGR-------IKLDREFSLQK------------------ 215 (306)
Q Consensus 166 ~~~~~v~~~~~~l~~~-~~i~~-~dl~~--~~~i~~~~~-~~~~-------~~~~~~~~~~~------------------ 215 (306)
.+++++++++.++... ..-++ ++|.+ ..+...++. .... ..-.+.+...|
T Consensus 81 n~LVL~~~~~~~~~~~~~~~~~~~~L~~~~~rIai~dP~~~P~G~~a~~~~~~A~~~l~~~gl~~~l~~~~~~~~~~~~~ 160 (273)
T TIGR03730 81 NEIVLAYTDKSKYADEINSDNWYEILQRPDVRWGFSDPNDDPCGYRSLMVIQLAELYYNDPTIFDNLLLKNTNITVEENN 160 (273)
T ss_pred ccEEEEEeCCCCcccccCcchHHHHhcCCCcEEEEcCCCCCCchHHHHHHHHHHHHHhcCCCHHHHHhhhcccccccccC
Confidence 9999999887654321 11244 44532 234444433 2222 12233322222
Q ss_pred ------------CceeEEEEecCHHHHHHHHHhc-cceeeeecceecccccCCceeeecCC-------------------
Q psy3760 216 ------------LTPYIVLETINSDIIKTYVELR-MGIGIIASIAFDSNRDKNLRSISASH------------------- 263 (306)
Q Consensus 216 ------------~~~~~~~~~~~~~~~~~~v~~g-~gi~~~p~~~~~~~~~~~l~~~~~~~------------------- 263 (306)
..++..+...+...+...+.+| .-++++..+.+.. .++.++.+++
T Consensus 161 ~~~~~~~~~~~~~~~~k~~~~~~v~~~~~~v~sG~aD~g~vY~S~A~~---~~~~~~~lP~~~n~~~~~~~~~y~~v~~~ 237 (273)
T TIGR03730 161 GTYLIHVPKEIDVNRSKIFIRPKEVELLSLLESGEIDYAFIYKSVAVQ---HGLKYIELPDEINLGDYSYADFYKKVSVE 237 (273)
T ss_pred CcccccCcccccccccceeecCchHhHHHHHHCCCCcEEEEEeeeccc---CCCceEECChhccCCChhhhcccceEEEE
Confidence 1124566777889999999998 4444444443322 2344444443
Q ss_pred --------CCccceEEEEEeCCccccHHHHHHHHHH
Q psy3760 264 --------LFGTTISRVIIKQGTYLRSYVYSFIKLL 291 (306)
Q Consensus 264 --------~~~~~~~~l~~~~~~~~~~~~~~~~~~l 291 (306)
....+.+.+...++....+..++|+++|
T Consensus 238 ~~~~~~~~~~~pi~y~~ai~~~~~~~~~a~~F~~fl 273 (273)
T TIGR03730 238 LGGGKKTITGKPIVYGITVPKNAPNREEAIEFLKFL 273 (273)
T ss_pred ecCCCceEecCCEEEEEeccCCCCCHHHHHHHHhhC
Confidence 1123455566667776678899999875
No 149
>PRK04168 molybdate ABC transporter periplasmic substrate-binding protein; Provisional
Probab=98.03 E-value=0.001 Score=55.31 Aligned_cols=203 Identities=16% Similarity=0.093 Sum_probs=122.8
Q ss_pred CCCcEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHH--cCCeeEEEEccccC----CCCCc--eeec
Q psy3760 91 DTGNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIR--NDQADIAIVTEILS----PSDKL--ISIP 162 (306)
Q Consensus 91 ~~~~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~--~~~~Di~i~~~~~~----~~~~~--~~~~ 162 (306)
....|+|.+..++ ...+..+...|.+++|++++++...++..+..++. ...+|+.++..... ...++ ....
T Consensus 30 ~~~~l~V~aA~sl-~~~l~~i~~~fe~~~~gv~v~~~~~gSg~L~~QI~e~Gap~DVfisAd~~~~~~l~~~g~~~~~~~ 108 (334)
T PRK04168 30 PKGKLKIFHAGSL-SVPFEEYEKEFEAYHPNVDVQREAGGSVKCVRKITELGKKADIMASADYTLIPKMMMPDYADWYVR 108 (334)
T ss_pred CCccEEEEeCCch-HHHHHHHHHHHHHhCCCeeEEEEeCcHHHHHHHHHhcCCCCCEEEECchhHHHHHhccCccceeEE
Confidence 4567999999885 45677899999999999999999999999999995 45899999863211 11222 3457
Q ss_pred cccceEEEEecCCCCCCC-CCCcChhhhc-C--CCeEeecCC-CCcHHHHHHHH-------HhCCCc-------------
Q psy3760 163 CYQWEYVIIVPLDHPLLL-LNSISLKEIS-N--YPLITYDLS-FSGRIKLDREF-------SLQKLT------------- 217 (306)
Q Consensus 163 l~~~~~~~v~~~~~~l~~-~~~i~~~dl~-~--~~~i~~~~~-~~~~~~~~~~~-------~~~~~~------------- 217 (306)
+...+++++.+++.+... ..+.+|.++. + ..+...++. .+....-.+.| ...|+-
T Consensus 109 fa~n~lVl~~~~~~~~~~~~~~~~~~~lL~~~~~~Iai~~P~~~P~G~~a~~~l~~a~~~l~~~gl~~~l~~~~~~~~~~ 188 (334)
T PRK04168 109 FATNEIVLAYTDKSKYADEINSDNWYEILQRPDVKFGFSDPNDDPCGYRSLMVLQLAELYYNDPTIYDKLIAKNTNIKVN 188 (334)
T ss_pred EEcccEEEEEcCCChhhhhcccccHHHHhcCCCcEEEcCCCCCCCchHHHHHHHHHHHHHhCCchHHHHHHhhccccccc
Confidence 888999999988765432 1223466633 2 234444432 22222111111 111110
Q ss_pred ------e-------eEEEEecCHHHHHHHHHhc-cceeeeecceecccccCCceeeecCCCC------------------
Q psy3760 218 ------P-------YIVLETINSDIIKTYVELR-MGIGIIASIAFDSNRDKNLRSISASHLF------------------ 265 (306)
Q Consensus 218 ------~-------~~~~~~~~~~~~~~~v~~g-~gi~~~p~~~~~~~~~~~l~~~~~~~~~------------------ 265 (306)
+ +..+...+...+...+..| .-++++..+.+.. .++.++.+++..
T Consensus 189 ~~~~~~~~~~~~~~~k~~~~~~~~~~~~~v~~G~aDagivy~S~a~~---~~~~~i~lP~~~n~~~~~~~~~y~~~~~~~ 265 (334)
T PRK04168 189 ENLIISPKEIEVNTDKVFVRPKEVELLSLLETGNMDYAFIYKSVAVQ---HNLKYIELPDEINLGNYKYADFYKKVSVTV 265 (334)
T ss_pred cccccCcccccccccceeecccchhhHHHHhcCCccEEEEEeeehhh---CCCCeeECchhhcCCChhhhhhhhEEEEEe
Confidence 0 0133445566888888888 4455555444332 245555555421
Q ss_pred ---------ccceEEEEEeCCccccHHHHHHHHHHhHHhhH
Q psy3760 266 ---------GTTISRVIIKQGTYLRSYVYSFIKLLSPKLNR 297 (306)
Q Consensus 266 ---------~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~ 297 (306)
....+.+...++.......++|++++.+.-.+
T Consensus 266 ~~~~~~~~~~pi~y~~ai~~~s~n~e~A~~Fi~fl~S~e~q 306 (334)
T PRK04168 266 TGTGKTITAKPIVYGITVPKNAPNREAAIEFLKYLLSEPGG 306 (334)
T ss_pred cCCCccccCceeeeeeeeecCCCCHHHHHHHHHHHcCHHHH
Confidence 12344455566666677899999999765333
No 150
>PRK11260 cystine transporter subunit; Provisional
Probab=97.92 E-value=0.0013 Score=53.17 Aligned_cols=175 Identities=13% Similarity=0.038 Sum_probs=105.2
Q ss_pred CCCcEEEEecccc-----------hhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccc--cCCCCC
Q psy3760 91 DTGNLTIATTHTQ-----------ARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEI--LSPSDK 157 (306)
Q Consensus 91 ~~~~l~I~~~~~~-----------~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~--~~~~~~ 157 (306)
..+.|+||+.... ...+...++..+.++. ++++++...+..++.+.+.+|++|+++.... ......
T Consensus 39 ~~~~l~v~~~~~~~P~~~~~~~g~~~G~~~dl~~~i~~~l-g~~~e~~~~~~~~~~~~l~~G~~D~~~~~~~~~~~r~~~ 117 (266)
T PRK11260 39 ERGTLLVGLEGTYPPFSFQGEDGKLTGFEVEFAEALAKHL-GVKASLKPTKWDGMLASLDSKRIDVVINQVTISDERKKK 117 (266)
T ss_pred cCCeEEEEeCCCcCCceEECCCCCEEEehHHHHHHHHHHH-CCeEEEEeCCHHHHHHHHhcCCCCEEEeccccCHHHHhc
Confidence 4578999985321 1345677777777764 7889999889999999999999999975211 112222
Q ss_pred c-eeeccccceEEEEecCCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCceeEEEEecCHHHHHHHHHh
Q psy3760 158 L-ISIPCYQWEYVIIVPLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVEL 236 (306)
Q Consensus 158 ~-~~~~l~~~~~~~v~~~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~ 236 (306)
+ -+.++....++++++++.+. ..-+++||.+..+... .+... ..+++..... .....+++...++.++.+
T Consensus 118 ~~fs~p~~~~~~~~~~~~~~~~---~~~~~~dL~g~~Igv~-~G~~~----~~~l~~~~~~-~~i~~~~~~~~~l~~L~~ 188 (266)
T PRK11260 118 YDFSTPYTVSGIQALVKKGNEG---TIKTAADLKGKKVGVG-LGTNY----EQWLRQNVQG-VDVRTYDDDPTKYQDLRV 188 (266)
T ss_pred cccCCceeecceEEEEEcCCcC---CCCCHHHcCCCEEEEe-cCCcH----HHHHHHhCCC-CceEecCCHHHHHHHHHc
Confidence 2 25567777788888876542 2346788877765553 33332 3344443222 234567788888999999
Q ss_pred ccceee-eecceeccc--ccCC-ceeeecCCCCccceEEEEEeCC
Q psy3760 237 RMGIGI-IASIAFDSN--RDKN-LRSISASHLFGTTISRVIIKQG 277 (306)
Q Consensus 237 g~gi~~-~p~~~~~~~--~~~~-l~~~~~~~~~~~~~~~l~~~~~ 277 (306)
|..=++ .+......+ ..+. +... .......++++..+++
T Consensus 189 GrvD~~i~d~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~v~~~ 231 (266)
T PRK11260 189 GRIDAILVDRLAALDLVKKTNDTLAVA--GEAFSRQESGVALRKG 231 (266)
T ss_pred CCCCEEEechHHHHHHHHhCCCcceec--CCccccCceEEEEeCC
Confidence 944443 344333322 2222 2221 1222234677777765
No 151
>PF13556 HTH_30: PucR C-terminal helix-turn-helix domain; PDB: 3ONQ_B.
Probab=97.85 E-value=3.3e-05 Score=46.23 Aligned_cols=43 Identities=23% Similarity=0.362 Sum_probs=32.5
Q ss_pred HHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCcee
Q psy3760 6 FRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDI 48 (306)
Q Consensus 6 l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~L 48 (306)
++++.+..++++|.++||+.|++-..|+.++|+++|+.+|..+
T Consensus 2 ~~TL~~yl~~~~n~~~tA~~L~iHrNTl~yRl~ki~~l~g~dl 44 (59)
T PF13556_consen 2 LETLRAYLENNGNISKTARALHIHRNTLRYRLKKIEELLGLDL 44 (59)
T ss_dssp --HHHHHHHTTT-HHHHHHHHTS-HHHHHHHHHHHHHHHS--T
T ss_pred hhHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCcCC
Confidence 3455666666459999999999999999999999999999876
No 152
>PRK09495 glnH glutamine ABC transporter periplasmic protein; Reviewed
Probab=97.82 E-value=0.0031 Score=50.31 Aligned_cols=199 Identities=10% Similarity=0.055 Sum_probs=116.2
Q ss_pred CCCCcEEEEecccch----------hhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEcccc--CCCCC
Q psy3760 90 YDTGNLTIATTHTQA----------RYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEIL--SPSDK 157 (306)
Q Consensus 90 ~~~~~l~I~~~~~~~----------~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~--~~~~~ 157 (306)
...+.|+||+..... ..+...++..+.+.- ++.++++..+...+++.+.+|++|+++..... .....
T Consensus 22 ~~~~~l~v~~~~~~~P~~~~~~g~~~G~~vdl~~~ia~~l-g~~~~~~~~~~~~~~~~l~~G~vDi~~~~~~~t~~R~~~ 100 (247)
T PRK09495 22 AADKKLVVATDTAFVPFEFKQGDKYVGFDIDLWAAIAKEL-KLDYTLKPMDFSGIIPALQTKNVDLALAGITITDERKKA 100 (247)
T ss_pred ccCCeEEEEeCCCCCCeeecCCCceEEEeHHHHHHHHHHh-CCceEEEeCCHHHHHHHHhCCCcCEEEecCccCHHHHhh
Confidence 346789999863211 134556777777764 68888888889999999999999998753211 11122
Q ss_pred c-eeeccccceEEEEecCCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCceeEEEEecCHHHHHHHHHh
Q psy3760 158 L-ISIPCYQWEYVIIVPLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVEL 236 (306)
Q Consensus 158 ~-~~~~l~~~~~~~v~~~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~ 236 (306)
+ -+.+++...+.++++++++ ..-+++||.+.+..... +... ..++....... .....++...+..++.+
T Consensus 101 ~~fs~p~~~~~~~~~~~~~~~----~~~~~~dL~g~~I~v~~-g~~~----~~~l~~~~~~~-~i~~~~~~~~~~~~L~~ 170 (247)
T PRK09495 101 IDFSDGYYKSGLLVMVKANNN----DIKSVKDLDGKVVAVKS-GTGS----VDYAKANIKTK-DLRQFPNIDNAYLELGT 170 (247)
T ss_pred ccccchheecceEEEEECCCC----CCCChHHhCCCEEEEec-CchH----HHHHHhcCCCC-ceEEcCCHHHHHHHHHc
Confidence 2 2457778888888887764 23488999988865544 3222 23333332222 23457788889999999
Q ss_pred ccceeeeecc-eec----ccccCCceeeecCCCCccceEEEEEeCCccccHHHHHHHHHHhHHhhHHHHHhhh
Q psy3760 237 RMGIGIIASI-AFD----SNRDKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLLSPKLNRKFINKIL 304 (306)
Q Consensus 237 g~gi~~~p~~-~~~----~~~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~ 304 (306)
|..=+++... ... ....+.+...+.. .....+++..+++. .....|=+.+++.-.....+++.
T Consensus 171 grvDa~i~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~a~~~~~---~l~~~~n~al~~~~~~g~~~~i~ 238 (247)
T PRK09495 171 GRADAVLHDTPNILYFIKTAGNGQFKAVGDS--LEAQQYGIAFPKGS---ELREKVNGALKTLKENGTYAEIY 238 (247)
T ss_pred CceeEEEeChHHHHHHHHhCCCCceEEecCc--ccccceEEEEcCcH---HHHHHHHHHHHHHHHCCcHHHHH
Confidence 9655544332 221 1112334443322 22335667666654 34444444444443333344443
No 153
>TIGR00363 lipoprotein, YaeC family. This family of putative lipoproteins contains a consensus site for lipoprotein signal sequence cleavage. Included in this family is the E. coli hypothetical protein yaeC. About half of the proteins between the noise and trusted cutoffs contain the consensus lipoprotein signature and may belong to this family.
Probab=97.80 E-value=0.01 Score=47.45 Aligned_cols=200 Identities=8% Similarity=0.004 Sum_probs=112.4
Q ss_pred CcEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeC-ChhHHHHHHHcCCeeEEEEccccC-----CCCCceeeccccc
Q psy3760 93 GNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQG-NPKQITEMIRNDQADIAIVTEILS-----PSDKLISIPCYQW 166 (306)
Q Consensus 93 ~~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~-~~~~~~~~l~~~~~Di~i~~~~~~-----~~~~~~~~~l~~~ 166 (306)
.+||||+........+......+.+. .++++++... +..+..+.|.+|++|+.+..+.+. ...++....++..
T Consensus 18 ~~l~vG~~~~~~~~~~~~~~~~~~~~-~G~~Ve~~~f~d~~~~~~Al~~G~ID~~~~q~~~~l~~~~~~~g~~lv~v~~~ 96 (258)
T TIGR00363 18 LHIKVGVISGAEQQVAEVAAKVAKEK-YGLDVELVEFNDYALPNEAVSKGDLDANAFQHKPYLDQDAKAKGYKLVAVGNT 96 (258)
T ss_pred CcEEEEeCCCChHHHHHHHHHHHHHh-cCCEEEEEEeCCcHHHHHHHHcCCCCeEecCCHHHHHHHHHhCCCcEEEEeee
Confidence 46999998765555554444443332 3677777653 456788999999999997643321 1234444444432
Q ss_pred eEEEEecCCCCCCCCCCcChhhhc-CCCeEeecCCCCcHHHHHHHHHhCCCc------------------e-eEEEEecC
Q psy3760 167 EYVIIVPLDHPLLLLNSISLKEIS-NYPLITYDLSFSGRIKLDREFSLQKLT------------------P-YIVLETIN 226 (306)
Q Consensus 167 ~~~~v~~~~~~l~~~~~i~~~dl~-~~~~i~~~~~~~~~~~~~~~~~~~~~~------------------~-~~~~~~~~ 226 (306)
.. .+-+ +...+--+++||. +..... +.+..........|+..|+. | ++.+.--+
T Consensus 97 ~~---~p~~--~ys~~~~sl~dlk~G~~IAi-p~d~~n~~raL~~L~~aGLi~l~~~~~~~~t~~DI~~n~~~v~~vel~ 170 (258)
T TIGR00363 97 FV---YPLA--GYSKKIKNVNELQDGAKVAV-PNDPTNLGRALLLLQKQGLIKLKDGNGLLPTVLDIVENPKKLNITELE 170 (258)
T ss_pred EE---eccc--ccCcCCCCHHHcCCCCEEEE-eCCcchHHHHHHHHHHcCCceecCCCCCcCChhhhhcCCCCCEEEEcC
Confidence 21 2111 1223455899997 555554 44434444555689998883 3 34454445
Q ss_pred HHHHHHHHHhc-cceeeeec-ceecccccC--CceeeecCCCCccceEEEEEeCCccccHHHHHHHHHHhHHhhHHHHH
Q psy3760 227 SDIIKTYVELR-MGIGIIAS-IAFDSNRDK--NLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLLSPKLNRKFIN 301 (306)
Q Consensus 227 ~~~~~~~v~~g-~gi~~~p~-~~~~~~~~~--~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~~ 301 (306)
...+.+.+.+| ...+++.. +........ +-....-.+ ...-..++++.+...++.++.|++.+++.=-+..++
T Consensus 171 ~~~~~~al~~g~vDaa~v~~~~~~~agl~~~~~~i~~e~~~--~~~~n~l~~r~~~~~~~~~~~lv~~~~s~~v~~~i~ 247 (258)
T TIGR00363 171 TSQLPRALDDPKVDLAVINTTYAGQVGLNPQDDGVFVEDKD--SPYVNIIVSREDNKDAENVKDFIQSYQSEEVYQAAQ 247 (258)
T ss_pred HHHHHHHhhcccccEEEEChHHHHHcCCCcCcCceeecCCC--CCeeEEEEEcCCccCCHHHHHHHHHHcCHHHHHHHH
Confidence 55566777775 34444444 443331111 112222111 122345667777778999999999987654444443
No 154
>PRK13777 transcriptional regulator Hpr; Provisional
Probab=97.80 E-value=0.0002 Score=53.74 Aligned_cols=78 Identities=18% Similarity=0.139 Sum_probs=60.5
Q ss_pred CchhhHHHHHHHHHhc-CCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEe-----cCCCccccCHhHHHHHHHHHHHH
Q psy3760 1 MNLHQFRFVREAVRQN-FNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIR-----HGKRIRGLTKPGQAILRSIEIIM 74 (306)
Q Consensus 1 m~~~~l~~f~~v~~~~-~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R-----~~~~~~~lT~~G~~l~~~a~~il 74 (306)
++..++.++..+.+.+ -|.+.-|+.+++++||+|+.|++||+. |.--..+ ....+ .||+.|+.+++.+.+..
T Consensus 43 Lt~~q~~iL~~L~~~~~itq~eLa~~l~l~~sTvtr~l~rLE~k-GlI~R~~~~~DrR~~~I-~LTekG~~l~~~l~~~~ 120 (185)
T PRK13777 43 LNINEHHILWIAYHLKGASISEIAKFGVMHVSTAFNFSKKLEER-GYLTFSKKEDDKRNTYI-ELTEKGEELLLETMEEY 120 (185)
T ss_pred CCHHHHHHHHHHHhCCCcCHHHHHHHHCCCHhhHHHHHHHHHHC-CCEEecCCCCCCCeeEE-EECHHHHHHHHHHHHHH
Confidence 3556788888888764 247888999999999999999999997 5544432 23344 79999999999998887
Q ss_pred HHHHHH
Q psy3760 75 QEIEGL 80 (306)
Q Consensus 75 ~~~~~~ 80 (306)
...+..
T Consensus 121 ~~~e~~ 126 (185)
T PRK13777 121 DPENNS 126 (185)
T ss_pred HHHHHH
Confidence 776653
No 155
>TIGR01096 3A0103s03R lysine-arginine-ornithine-binding periplasmic protein.
Probab=97.78 E-value=0.0035 Score=50.07 Aligned_cols=140 Identities=14% Similarity=0.100 Sum_probs=92.9
Q ss_pred CcEEEEecccc-----------hhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccC--CCCC-c
Q psy3760 93 GNLTIATTHTQ-----------ARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILS--PSDK-L 158 (306)
Q Consensus 93 ~~l~I~~~~~~-----------~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~--~~~~-~ 158 (306)
+.|++|+.... ...+...++..+.+.. +++++++..+..+.+..+.+|++|+++...... .... .
T Consensus 24 ~~l~v~~~~~~~P~~~~~~~g~~~G~~~dl~~~i~~~l-g~~~~~~~~~~~~~~~~l~~G~~D~~~~~~~~~~~r~~~~~ 102 (250)
T TIGR01096 24 GSVRIGTETGYPPFESKDANGKLVGFDVDLAKALCKRM-KAKCKFVEQNFDGLIPSLKAKKVDAIMATMSITPKRQKQID 102 (250)
T ss_pred CeEEEEECCCCCCceEECCCCCEEeehHHHHHHHHHHh-CCeEEEEeCCHHHHHHHHhCCCcCEEEecCccCHHHhhccc
Confidence 68999986321 1246677887777664 588899888999999999999999997532111 1122 2
Q ss_pred eeeccccceEEEEecCCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCceeEEEEecCHHHHHHHHHhcc
Q psy3760 159 ISIPCYQWEYVIIVPLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRM 238 (306)
Q Consensus 159 ~~~~l~~~~~~~v~~~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~ 238 (306)
-+.+++.....++++++.+. .-+++||.+.+..... +......+.+.+.. +. + ...+.+...++.++.+|.
T Consensus 103 ~s~p~~~~~~~~~~~~~~~~----~~~~~dl~g~~i~~~~-g~~~~~~l~~~~~~-~~--~-~~~~~s~~~~~~~L~~g~ 173 (250)
T TIGR01096 103 FSDPYYATGQGFVVKKGSDL----AKTLEDLDGKTVGVQS-GTTHEQYLKDYFKP-GV--D-IVEYDSYDNANMDLKAGR 173 (250)
T ss_pred cccchhcCCeEEEEECCCCc----CCChHHcCCCEEEEec-CchHHHHHHHhccC-Cc--E-EEEcCCHHHHHHHHHcCC
Confidence 36778888899999887653 2378889877665543 33333333333321 21 2 345688999999999994
Q ss_pred ceee
Q psy3760 239 GIGI 242 (306)
Q Consensus 239 gi~~ 242 (306)
.=++
T Consensus 174 vD~~ 177 (250)
T TIGR01096 174 IDAV 177 (250)
T ss_pred CCEE
Confidence 4443
No 156
>COG0226 PstS ABC-type phosphate transport system, periplasmic component [Inorganic ion transport and metabolism]
Probab=97.77 E-value=0.0033 Score=52.09 Aligned_cols=204 Identities=15% Similarity=0.113 Sum_probs=134.9
Q ss_pred CCCcEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHH-HHHcCCeeEEEEccccCC---------CCCcee
Q psy3760 91 DTGNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITE-MIRNDQADIAIVTEILSP---------SDKLIS 160 (306)
Q Consensus 91 ~~~~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~-~l~~~~~Di~i~~~~~~~---------~~~~~~ 160 (306)
..+.|+++.+.+ ...+...+...|.+.||++.+.+...++..-.. .+..+ +||+-+..+..+ ...+..
T Consensus 41 ~~~~l~~~GStt-v~p~~~~~a~~~~~~~~~~~v~~q~~GSg~G~~~~~~~~-vDig~ss~p~~~~e~~~~~~~~~~l~~ 118 (318)
T COG0226 41 ASGSLTIAGSTT-VAPLMEAWAEEFQKAYPNVKVNVQAGGSGAGIKQALAGG-VDIGASSRPLKDSEKEADAKAGKKLVE 118 (318)
T ss_pred ccceEEEeccCc-HHHHHHHHHHHHHHHCCCeeEEEecCCChHHHHHHhcCC-CccccCCCCCCcchHHHHHhcCCCceE
Confidence 467899988877 577899999999999999999999988888777 55555 999998654331 124778
Q ss_pred eccccceEEEEecCCCC-CCC-----------CCCcChhhhcC----CC--eEeecCCCCcHHHHHHHHHh------CC-
Q psy3760 161 IPCYQWEYVIIVPLDHP-LLL-----------LNSISLKEISN----YP--LITYDLSFSGRIKLDREFSL------QK- 215 (306)
Q Consensus 161 ~~l~~~~~~~v~~~~~~-l~~-----------~~~i~~~dl~~----~~--~i~~~~~~~~~~~~~~~~~~------~~- 215 (306)
.++..+-+++++.++.+ ... .+..+|.|+.. .+ .+..+.+++.+..+..++.. .+
T Consensus 119 ~pva~d~i~vi~N~~~~~~~~Lt~~~l~~If~G~it~W~d~~~~~~n~~I~vv~R~~~SGT~~~F~~~l~~~~~~~~~g~ 198 (318)
T COG0226 119 FPVAIDAIVVIVNLPNPDVLNLTKDQLADIFSGKITNWNDVGGQLLNPGITVVGRSDGSGTTETFTEYLLGWKKKVGAGK 198 (318)
T ss_pred eeEEeeeEEEEEcCCCccccccCHHHHHHHhcCCCccccccCcccCCCCceEEecCCCCchHHHHHHHHHhhhhccccCc
Confidence 99999999999999988 222 23335564432 23 34444456677777777764 12
Q ss_pred -CceeEEEEecCHHHHHHHHHhc-cceeeeecceeccc-cc-----CCc--e---eeec------CCC-CccceEEEEEe
Q psy3760 216 -LTPYIVLETINSDIIKTYVELR-MGIGIIASIAFDSN-RD-----KNL--R---SISA------SHL-FGTTISRVIIK 275 (306)
Q Consensus 216 -~~~~~~~~~~~~~~~~~~v~~g-~gi~~~p~~~~~~~-~~-----~~l--~---~~~~------~~~-~~~~~~~l~~~ 275 (306)
..-...........+...|.+. .+|+++-...+..- .. ... + .-|. ... +..+..|++++
T Consensus 199 ~~~~~~~~~~~~n~~v~~~v~~tp~aIGYv~~~y~~~n~~~~~~~~~~~~~~~~~v~p~~~~i~~~~y~Pi~~~~~~~v~ 278 (318)
T COG0226 199 TVDWPAAVGGKGNEGVVAAVSQTPGAIGYVGYAYAVQNNLKLAALANKAGGVGPTVEPTAENIANGKYSPIVRPLFIYVN 278 (318)
T ss_pred ccccCccccCCCcHHHHHHHhcCCCceEEEeehhhhcccchhhhhhcccCCcCccccCHHHHHhcCCccccceeeEEEEc
Confidence 1111244556667777878765 88888877665431 00 011 0 1111 112 44567788877
Q ss_pred CCcc--ccHHHHHHHHHHhHHhh
Q psy3760 276 QGTY--LRSYVYSFIKLLSPKLN 296 (306)
Q Consensus 276 ~~~~--~~~~~~~~~~~l~~~~~ 296 (306)
++.. ..+.+++|++++...=+
T Consensus 279 ~~~~~~~~~~~~~Fi~~~~~~~~ 301 (318)
T COG0226 279 KNPKDTKAPAVKAFLDWALSPGG 301 (318)
T ss_pred CCccccchHHHHHHHHHHhcccc
Confidence 6654 58999999988865433
No 157
>TIGR02995 ectoine_ehuB ectoine/hydroxyectoine ABC transporter solute-binding protein. Members of this family are the extracellular solute-binding proteins of ABC transporters that closely resemble amino acid transporters. The member from Sinorhizobium 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=97.76 E-value=0.003 Score=51.36 Aligned_cols=204 Identities=9% Similarity=0.019 Sum_probs=118.2
Q ss_pred CCCcEEEEecccch----------hhhhHHHHHHHHHhCCCcE-EEEEeCChhHHHHHHHcCCeeEEEEccc--cCCCCC
Q psy3760 91 DTGNLTIATTHTQA----------RYALPKIIKEFTIQFPKVK-LSLLQGNPKQITEMIRNDQADIAIVTEI--LSPSDK 157 (306)
Q Consensus 91 ~~~~l~I~~~~~~~----------~~~l~~~l~~~~~~~p~~~-i~~~~~~~~~~~~~l~~~~~Di~i~~~~--~~~~~~ 157 (306)
.+|.|++|+....+ ..+...++..+.+.. ++. +.+...+..+++..+.+|++|+++.... ......
T Consensus 31 ~~~~l~v~~~~~pP~~~~~~~g~~~G~~~dl~~~i~~~l-g~~~~~~~~~~w~~~~~~l~~G~~Di~~~~~~~t~eR~~~ 109 (275)
T TIGR02995 31 EQGFARIAIANEPPFTYVGADGKVSGAAPDVARAIFKRL-GIADVNASITEYGALIPGLQAGRFDAIAAGLFIKPERCKQ 109 (275)
T ss_pred hCCcEEEEccCCCCceeECCCCceecchHHHHHHHHHHh-CCCceeeccCCHHHHHHHHHCCCcCEEeecccCCHHHHhc
Confidence 35789998864322 245567888887774 453 6777788889999999999999765211 112222
Q ss_pred c-eeeccccceEEEEecCCCCCCCCCCcChhhhcC---CCeEeecCCCCcHHHHHHHHHhCCCceeEEEEecCHHHHHHH
Q psy3760 158 L-ISIPCYQWEYVIIVPLDHPLLLLNSISLKEISN---YPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTY 233 (306)
Q Consensus 158 ~-~~~~l~~~~~~~v~~~~~~l~~~~~i~~~dl~~---~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 233 (306)
+ -+.+++...+.++++++++.. .-+++||.+ ..+.. ..+.. ..++++..+........+++...++.+
T Consensus 110 ~~fs~py~~~~~~~~~~~~~~~~---i~~~~dl~~~~g~~Igv-~~g~~----~~~~l~~~~~~~~~i~~~~~~~~~i~~ 181 (275)
T TIGR02995 110 VAFTQPILCDAEALLVKKGNPKG---LKSYKDIAKNPDAKIAA-PGGGT----EEKLAREAGVKREQIIVVPDGQSGLKM 181 (275)
T ss_pred cccccceeecceeEEEECCCCCC---CCCHHHhccCCCceEEE-eCCcH----HHHHHHHcCCChhhEEEeCCHHHHHHH
Confidence 2 356788888999999987532 236778864 34443 33322 245565555443345577899999999
Q ss_pred HHhccceeeeecce-eccc-c---cCCceee-ecCCCCccceEEEEEeCCccccHHHHHHHHHHhHHhhHHHHHhhhc
Q psy3760 234 VELRMGIGIIASIA-FDSN-R---DKNLRSI-SASHLFGTTISRVIIKQGTYLRSYVYSFIKLLSPKLNRKFINKILN 305 (306)
Q Consensus 234 v~~g~gi~~~p~~~-~~~~-~---~~~l~~~-~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~ 305 (306)
+..|..=+++-... .... . .+.+..+ ++...+....+++..+++ .......|=+.|++..+....+++.+
T Consensus 182 L~~grvDa~i~d~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~l~~~~n~~l~~~~~sG~~~~i~~ 257 (275)
T TIGR02995 182 VQDGRADAYSLTVLTINDLASKAGDPNVEVLAPFKDAPVRYYGGAAFRPE--DKELRDAFNVELAKLKESGEFAKIIA 257 (275)
T ss_pred HHcCCCCEEecChHHHHHHHHhCCCCCceeecCccCCccccceeEEECCC--CHHHHHHHHHHHHHHHhChHHHHHHH
Confidence 99996655544322 2211 1 2233332 222211112224444443 34555555555665555555555543
No 158
>PRK14165 winged helix-turn-helix domain-containing protein/riboflavin kinase; Provisional
Probab=97.76 E-value=0.00014 Score=55.75 Aligned_cols=101 Identities=19% Similarity=0.202 Sum_probs=63.8
Q ss_pred CHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEec----CCCccccCHhHHHHHHHHHHHHHHHHHHHHHHHhhccCCCC
Q psy3760 18 NLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRH----GKRIRGLTKPGQAILRSIEIIMQEIEGLKKIGKEFSAYDTG 93 (306)
Q Consensus 18 s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~----~~~~~~lT~~G~~l~~~a~~il~~~~~~~~~~~~~~~~~~~ 93 (306)
|.+.-|+.|++|++|+|+.|++||+. -|+.|. +..+ .+|+.|+.+++ +....+..+... .......|
T Consensus 23 S~~eLA~~L~iS~~Tvsr~Lk~LEe~---GlI~R~~~~r~~~v-~LTekG~~ll~---~~~~d~~~if~~--~~ei~l~G 93 (217)
T PRK14165 23 SSSEFANHTGTSSKTAARILKQLEDE---GYITRTIVPRGQLI-TITEKGLDVLY---NEYADYSRIFSI--KDNLELEG 93 (217)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHC---CCEEEEEcCCceEE-EECHHHHHHHH---HHHHHHHHHhcc--cccceehh
Confidence 47799999999999999999999986 566665 4455 89999999884 444444444422 11123345
Q ss_pred cEEEEecccchhhhhHHHHHHHHHh-----CCCc-EEEEE
Q psy3760 94 NLTIATTHTQARYALPKIIKEFTIQ-----FPKV-KLSLL 127 (306)
Q Consensus 94 ~l~I~~~~~~~~~~l~~~l~~~~~~-----~p~~-~i~~~ 127 (306)
.+.=|...+--..-++....+|.+. ||+. ++.+.
T Consensus 94 ~v~sGlGeG~~y~~~~~Y~~~f~~~lGf~PypGTLNv~l~ 133 (217)
T PRK14165 94 NVVKGLGEGKYYINIKGYKIQFEEKLGFIPYPGTLNVKLD 133 (217)
T ss_pred hhhhccCCccEEEeCHHHHHHHHHHhCCcCCCCcEEEEec
Confidence 5555555542222344566666655 5543 55553
No 159
>TIGR03871 ABC_peri_MoxJ_2 quinoprotein dehydrogenase-associated probable ABC transporter substrate-binding protein. This protein family, a sister family to TIGR03870, is found more broadly. It occurs a range of PQQ-biosynthesizing species, not just in known methanotrophs. Interpretation of evidence by homology and by direct experimental work suggest two different roles. By homology, this family appears to be the periplasmic substrate-binding protein of an ABC transport family. However, mutational studies and direct characterization for some sequences related to this family suggests this family may act as a maturation chaperone or additional subunit of a methanol dehydrogenase-like enzyme.
Probab=97.74 E-value=0.01 Score=46.71 Aligned_cols=185 Identities=12% Similarity=0.090 Sum_probs=102.9
Q ss_pred hhhhHHHHHHHHHhCCCcEEEEEeC--ChhHHHHHHHcCCeeEEEEccccCCCCCce-eeccccceEEEEecCCCCCCCC
Q psy3760 105 RYALPKIIKEFTIQFPKVKLSLLQG--NPKQITEMIRNDQADIAIVTEILSPSDKLI-SIPCYQWEYVIIVPLDHPLLLL 181 (306)
Q Consensus 105 ~~~l~~~l~~~~~~~p~~~i~~~~~--~~~~~~~~l~~~~~Di~i~~~~~~~~~~~~-~~~l~~~~~~~v~~~~~~l~~~ 181 (306)
..+-..++..+.++ -++++++... ........+.+|++|+++.. + .....+. +.+++...++++++++++.
T Consensus 19 ~G~~~el~~~i~~~-~g~~i~~~~~~~~~~~~~~~l~~g~~Di~~~~-~-~r~~~~~fs~py~~~~~~lv~~~~~~~--- 92 (232)
T TIGR03871 19 EGFENKIAQLLADD-LGLPLEYTWFPQRRGFVRNTLNAGRCDVVIGV-P-AGYEMVLTTRPYYRSTYVFVTRKDSLL--- 92 (232)
T ss_pred CchHHHHHHHHHHH-cCCceEEEecCcchhhHHHHHhcCCccEEEec-c-CccccccccCCcEeeeEEEEEeCCCcc---
Confidence 34677788888776 4677776643 34445678999999998774 2 2223333 4578888999999988642
Q ss_pred CCcChhh--hcCCCeEeecCCCCcHHHHHHHHHhCCCceeEE---EE-----ecCHHHHHHHHHhccc-eeeeecceecc
Q psy3760 182 NSISLKE--ISNYPLITYDLSFSGRIKLDREFSLQKLTPYIV---LE-----TINSDIIKTYVELRMG-IGIIASIAFDS 250 (306)
Q Consensus 182 ~~i~~~d--l~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~---~~-----~~~~~~~~~~v~~g~g-i~~~p~~~~~~ 250 (306)
..-+++| +.+.++.... +... .+.+...+...+.. .. ..+...+++++.+|.. .++.....+..
T Consensus 93 ~~~~~~d~~l~g~~V~v~~-g~~~----~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~G~~Da~i~~~~~~~~ 167 (232)
T TIGR03871 93 DVKSLDDPRLKKLRIGVFA-GTPP----AHWLARHGLVENVVGYSLFGDYRPESPPGRMVEDLAAGEIDVAIVWGPIAGY 167 (232)
T ss_pred cccchhhhhhcCCeEEEEc-CChH----HHHHHhcCcccccccccccccccccCCHHHHHHHHHcCCcCEEEeccHHHHH
Confidence 2236666 7777765544 3222 33344444332211 11 2367889999999966 44444433322
Q ss_pred c---ccCCceeeecCC----CCccceEEEEEeCCccccHHHHHHHHHHhHHhhHHHHHhhh
Q psy3760 251 N---RDKNLRSISASH----LFGTTISRVIIKQGTYLRSYVYSFIKLLSPKLNRKFINKIL 304 (306)
Q Consensus 251 ~---~~~~l~~~~~~~----~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~ 304 (306)
. ..+.+...+... ......+++..+++. +...+.|-+++.+. .+ ..+++.
T Consensus 168 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~l~~~~n~~l~~~-~~-~~~~i~ 224 (232)
T TIGR03871 168 FAKQAGPPLVVVPLLPEDGGIPFDYRIAMGVRKGD--KAWKDELNAVLDRR-QA-EIDAIL 224 (232)
T ss_pred HHHhCCCCceeeccccCCCCCCccceEEEEEecCC--HHHHHHHHHHHHHH-HH-HHHHHH
Confidence 1 122343333221 112234455556543 45566666666553 22 345444
No 160
>PRK11512 DNA-binding transcriptional repressor MarR; Provisional
Probab=97.72 E-value=0.00032 Score=50.83 Aligned_cols=70 Identities=19% Similarity=0.198 Sum_probs=55.0
Q ss_pred CchhhHHHHHHHHHhc-CCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEec-------CCCccccCHhHHHHHHHHHH
Q psy3760 1 MNLHQFRFVREAVRQN-FNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRH-------GKRIRGLTKPGQAILRSIEI 72 (306)
Q Consensus 1 m~~~~l~~f~~v~~~~-~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~-------~~~~~~lT~~G~~l~~~a~~ 72 (306)
++..++.++..+.+.+ -+.+.-|+.+++++|++|+.|++||+. -|+.|. ...+ .||+.|+.+++.+..
T Consensus 38 lt~~q~~vL~~l~~~~~~t~~eLa~~l~i~~~tvsr~l~~Le~~---GlI~R~~~~~DrR~~~l-~LT~~G~~~~~~~~~ 113 (144)
T PRK11512 38 ITAAQFKVLCSIRCAACITPVELKKVLSVDLGALTRMLDRLVCK---GWVERLPNPNDKRGVLV-KLTTSGAAICEQCHQ 113 (144)
T ss_pred CCHHHHHHHHHHHHcCCCCHHHHHHHHCCCHHHHHHHHHHHHHC---CCEEeccCcccCCeeEe-EEChhHHHHHHHHHH
Confidence 3556778888887655 247899999999999999999999984 455543 3444 899999999998876
Q ss_pred HH
Q psy3760 73 IM 74 (306)
Q Consensus 73 il 74 (306)
..
T Consensus 114 ~~ 115 (144)
T PRK11512 114 LV 115 (144)
T ss_pred HH
Confidence 64
No 161
>PRK10797 glutamate and aspartate transporter subunit; Provisional
Probab=97.70 E-value=0.0089 Score=49.25 Aligned_cols=147 Identities=6% Similarity=0.070 Sum_probs=94.6
Q ss_pred CCcEEEEecccch-----------hhhhHHHHHHH----HHhC--CCcEEEEEeCChhHHHHHHHcCCeeEEEEcc--cc
Q psy3760 92 TGNLTIATTHTQA-----------RYALPKIIKEF----TIQF--PKVKLSLLQGNPKQITEMIRNDQADIAIVTE--IL 152 (306)
Q Consensus 92 ~~~l~I~~~~~~~-----------~~~l~~~l~~~----~~~~--p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~--~~ 152 (306)
+|.|++|+..... ..+-..++..+ .+.. +++++++........+..|.+|++|+++... ..
T Consensus 39 ~g~L~Vg~~~~~pP~~f~~~~g~~~G~didl~~~ia~~l~~~lg~~~~~~~~v~~~~~~~i~~L~~G~~Di~~~~~~~t~ 118 (302)
T PRK10797 39 NGVIVVGHRESSVPFSYYDNQQKVVGYSQDYSNAIVEAVKKKLNKPDLQVKLIPITSQNRIPLLQNGTFDFECGSTTNNL 118 (302)
T ss_pred CCeEEEEEcCCCCCcceECCCCCEeeecHHHHHHHHHHHHHhhCCCCceEEEEEcChHhHHHHHHCCCccEEecCCccCc
Confidence 5789998864321 12334444433 3333 3789999998888889999999999987532 11
Q ss_pred CCCCCce-eeccccceEEEEecCCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCceeEEEEecCHHHHH
Q psy3760 153 SPSDKLI-SIPCYQWEYVIIVPLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIK 231 (306)
Q Consensus 153 ~~~~~~~-~~~l~~~~~~~v~~~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 231 (306)
.....+. +.|++.....++++++.+ .-+++||.+...... .+......+..+... +...-....+++....+
T Consensus 119 eR~~~~~fS~Py~~~~~~lv~r~~~~-----i~sl~dL~Gk~V~v~-~gs~~~~~l~~~~~~-~~~~~~i~~~~~~~~~l 191 (302)
T PRK10797 119 ERQKQAAFSDTIFVVGTRLLTKKGGD-----IKDFADLKGKAVVVT-SGTTSEVLLNKLNEE-QKMNMRIISAKDHGDSF 191 (302)
T ss_pred chhhcceecccEeeccEEEEEECCCC-----CCChHHcCCCEEEEe-CCCcHHHHHHHHhhh-cCCceEEEEeCCHHHHH
Confidence 2333444 457778888999988753 347899988875554 443433444443332 21123456778999999
Q ss_pred HHHHhccceeeeec
Q psy3760 232 TYVELRMGIGIIAS 245 (306)
Q Consensus 232 ~~v~~g~gi~~~p~ 245 (306)
.++.+|..=+++-+
T Consensus 192 ~~L~~GrvDa~i~d 205 (302)
T PRK10797 192 RTLESGRAVAFMMD 205 (302)
T ss_pred HHHHcCCceEEEcc
Confidence 99999977776554
No 162
>TIGR01098 3A0109s03R phosphate/phosphite/phosphonate ABC transporters, periplasmic binding protein. A subset of this model in which nearly all members exhibit genomic context with elements of phosphonate metabolism, particularly the C-P lyase system has been built (TIGR03431) as an equivalog. Nevertheless, there are members of this subfamily (TIGR01098) which show up sporadically on a phylogenetic tree that also show phosphonate context and are most likely competent to transport phosphonates.
Probab=97.70 E-value=0.011 Score=47.35 Aligned_cols=180 Identities=17% Similarity=0.127 Sum_probs=103.6
Q ss_pred CCCcEEEEecccchhhhh----HHHHHHHHHhCCCcEEEEEe-CChhHHHHHHHcCCeeEEEEccccC----CCCC-ce-
Q psy3760 91 DTGNLTIATTHTQARYAL----PKIIKEFTIQFPKVKLSLLQ-GNPKQITEMIRNDQADIAIVTEILS----PSDK-LI- 159 (306)
Q Consensus 91 ~~~~l~I~~~~~~~~~~l----~~~l~~~~~~~p~~~i~~~~-~~~~~~~~~l~~~~~Di~i~~~~~~----~~~~-~~- 159 (306)
..+.|+||+.+......+ ..+...+.++. ++++++.. .+..+.++.+.+|++|+++...... ...+ ..
T Consensus 30 ~~~~l~vg~~~~~~~~~~~~~~~~l~~~l~~~~-g~~v~~~~~~~~~~~~~~l~~g~~Di~~~~~~~~~~~~~~~~~~~~ 108 (254)
T TIGR01098 30 VPKELNFGILPGENASNLTRRWEPLADYLEKKL-GIKVQLFVATDYSAVIEAMRFGRVDIAWFGPSSYVLAHYRANAEVF 108 (254)
T ss_pred CCCceEEEECCCCCHHHHHHHHHHHHHHHHHHh-CCcEEEEeCCCHHHHHHHHHcCCccEEEECcHHHHHHHHhcCCceE
Confidence 457899999876554332 34555555553 78888876 4667899999999999999642110 1111 11
Q ss_pred eeccc-c-----ceEEEEecCCCCCCCCCCcChhhhcCCCeEeecCCCCc-HHHHHHHHH-hCCCce----eEEEEecCH
Q psy3760 160 SIPCY-Q-----WEYVIIVPLDHPLLLLNSISLKEISNYPLITYDLSFSG-RIKLDREFS-LQKLTP----YIVLETINS 227 (306)
Q Consensus 160 ~~~l~-~-----~~~~~v~~~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~-~~~~~~~~~-~~~~~~----~~~~~~~~~ 227 (306)
..+.. . ....++++++++. -+++||.+.......++... ......++. ..+..+ ..+....+.
T Consensus 109 ~~~~~~~~~~~~~~~~lvv~~d~~i-----~~~~dL~gk~I~~~~~~s~~~~~~~~~~l~~~~~~~~~~~~~~i~~~~~~ 183 (254)
T TIGR01098 109 ALTAVSTDGSPGYYSVIIVKADSPI-----KSLKDLKGKTFAFGDPASTSGYLVPRYQLKKEGGLDADGFFSEVVFSGSH 183 (254)
T ss_pred EeeccccCCCCceEEEEEEECCCCC-----CChHHhcCCEEEeeCCCCccchHhHHHHHHHhcCCChHHhhhheeecCch
Confidence 11111 1 2357888888753 37899988877766543322 222233343 344332 233455667
Q ss_pred HHHHHHHHhccc-eeeeecceeccc-cc-----CCceeeecCCCCccceEEEEEeCCc
Q psy3760 228 DIIKTYVELRMG-IGIIASIAFDSN-RD-----KNLRSISASHLFGTTISRVIIKQGT 278 (306)
Q Consensus 228 ~~~~~~v~~g~g-i~~~p~~~~~~~-~~-----~~l~~~~~~~~~~~~~~~l~~~~~~ 278 (306)
..+.+++..|.. .++.+......+ .. .++..+......+ ...++.+++.
T Consensus 184 ~~~~~al~~G~~Da~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~ 239 (254)
T TIGR01098 184 DASALAVANGKVDAATNNSSAIGRLKKRGPSDMKKVRVIWKSPLIP--NDPIAVRKDL 239 (254)
T ss_pred HHHHHHHHcCCCCeEEecHHHHHHHHHhCccchhheEEEEecCCCC--CCCEEEECCC
Confidence 788899999854 555665444332 11 2455555433222 3456666663
No 163
>PRK03573 transcriptional regulator SlyA; Provisional
Probab=97.68 E-value=0.00037 Score=50.54 Aligned_cols=75 Identities=20% Similarity=0.360 Sum_probs=59.4
Q ss_pred CchhhHHHHHHHHHhc--CCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEec-------CCCccccCHhHHHHHHHHH
Q psy3760 1 MNLHQFRFVREAVRQN--FNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRH-------GKRIRGLTKPGQAILRSIE 71 (306)
Q Consensus 1 m~~~~l~~f~~v~~~~--~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~-------~~~~~~lT~~G~~l~~~a~ 71 (306)
++..++.++..+.+.+ .+.+.-|+.+++++||+|+.|++||+. -|+.|. ...+ .||+.|+.++..+.
T Consensus 29 lt~~q~~vL~~l~~~~~~~t~~eLa~~l~~~~~tvt~~v~~Le~~---GlV~r~~~~~DrR~~~l-~LT~~G~~~~~~~~ 104 (144)
T PRK03573 29 LTQTHWVTLHNIHQLPPEQSQIQLAKAIGIEQPSLVRTLDQLEEK---GLISRQTCASDRRAKRI-KLTEKAEPLISEVE 104 (144)
T ss_pred CCHHHHHHHHHHHHcCCCCCHHHHHHHhCCChhhHHHHHHHHHHC---CCEeeecCCCCcCeeee-EEChHHHHHHHHHH
Confidence 3566788888888642 267899999999999999999999984 445543 2344 79999999999999
Q ss_pred HHHHHHHH
Q psy3760 72 IIMQEIEG 79 (306)
Q Consensus 72 ~il~~~~~ 79 (306)
+....+.+
T Consensus 105 ~~~~~~~~ 112 (144)
T PRK03573 105 AVINKTRA 112 (144)
T ss_pred HHHHHHHH
Confidence 88877665
No 164
>PRK10859 membrane-bound lytic transglycosylase F; Provisional
Probab=97.65 E-value=0.0035 Score=55.24 Aligned_cols=177 Identities=15% Similarity=0.061 Sum_probs=105.0
Q ss_pred CCcEEEEecccch---------hhhhHHHHHHHHHhCCCcEEEEE-eCChhHHHHHHHcCCeeEEEEccccC--CCCCce
Q psy3760 92 TGNLTIATTHTQA---------RYALPKIIKEFTIQFPKVKLSLL-QGNPKQITEMIRNDQADIAIVTEILS--PSDKLI 159 (306)
Q Consensus 92 ~~~l~I~~~~~~~---------~~~l~~~l~~~~~~~p~~~i~~~-~~~~~~~~~~l~~~~~Di~i~~~~~~--~~~~~~ 159 (306)
.|.|+||+..... ..+-..++..+.+. -+++++++ ..+.++++..|.+|++|+++...... ....+.
T Consensus 42 ~g~LrVg~~~~P~~~~~~~~~~~G~~~DLl~~ia~~-LGv~~e~v~~~~~~~ll~aL~~G~iDi~~~~lt~T~eR~~~~~ 120 (482)
T PRK10859 42 RGELRVGTINSPLTYYIGNDGPTGFEYELAKRFADY-LGVKLEIKVRDNISQLFDALDKGKADLAAAGLTYTPERLKQFR 120 (482)
T ss_pred CCEEEEEEecCCCeeEecCCCcccHHHHHHHHHHHH-hCCcEEEEecCCHHHHHHHHhCCCCCEEeccCcCChhhhccCc
Confidence 5789999864321 23556788888776 37888887 45788999999999999876432111 122222
Q ss_pred -eeccccceEEEEecCCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCceeE-EEEecCHHHHHHHHHhc
Q psy3760 160 -SIPCYQWEYVIIVPLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYI-VLETINSDIIKTYVELR 237 (306)
Q Consensus 160 -~~~l~~~~~~~v~~~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~v~~g 237 (306)
+.++.....+++++++.+ ..-+++||.+..+..... ......+........ ..+. .....+.+.++.++.+|
T Consensus 121 FS~Py~~~~~~lv~r~~~~----~i~~l~dL~Gk~I~V~~g-S~~~~~L~~l~~~~p-~i~~~~~~~~s~~e~l~aL~~G 194 (482)
T PRK10859 121 FGPPYYSVSQQLVYRKGQP----RPRSLGDLKGGTLTVAAG-SSHVETLQELKKKYP-ELSWEESDDKDSEELLEQVAEG 194 (482)
T ss_pred ccCCceeeeEEEEEeCCCC----CCCCHHHhCCCeEEEECC-CcHHHHHHHHHHhCC-CceEEecCCCCHHHHHHHHHCC
Confidence 456777888889888763 234789999888766543 333334443333221 1111 22346889999999999
Q ss_pred cceeeeec-ceeccc--ccCCceeeecCCCCccceEEEEEeCC
Q psy3760 238 MGIGIIAS-IAFDSN--RDKNLRSISASHLFGTTISRVIIKQG 277 (306)
Q Consensus 238 ~gi~~~p~-~~~~~~--~~~~l~~~~~~~~~~~~~~~l~~~~~ 277 (306)
..=+++-+ ..+... ..+++...... ....+++++.+++
T Consensus 195 ~iDa~v~d~~~~~~~~~~~p~l~v~~~l--~~~~~~~~av~k~ 235 (482)
T PRK10859 195 KIDYTIADSVEISLNQRYHPELAVAFDL--TDEQPVAWALPPS 235 (482)
T ss_pred CCCEEEECcHHHHHHHHhCCCceeeeec--CCCceeEEEEeCC
Confidence 55444433 222111 23445432211 1234566777763
No 165
>PF13379 NMT1_2: NMT1-like family; PDB: 2G29_A 3UN6_A 2I4C_A 2I49_A 2I4B_A 2I48_A 3QSL_A.
Probab=97.60 E-value=0.006 Score=48.86 Aligned_cols=202 Identities=12% Similarity=0.055 Sum_probs=111.1
Q ss_pred CCCcEEEEecccchhhhhHHHH-HHHHHhCCCcEEEEEe-CChhHHHHHHHcCCeeEEEEccccC-----C-----CCCc
Q psy3760 91 DTGNLTIATTHTQARYALPKII-KEFTIQFPKVKLSLLQ-GNPKQITEMIRNDQADIAIVTEILS-----P-----SDKL 158 (306)
Q Consensus 91 ~~~~l~I~~~~~~~~~~l~~~l-~~~~~~~p~~~i~~~~-~~~~~~~~~l~~~~~Di~i~~~~~~-----~-----~~~~ 158 (306)
...+||||+.+.....-+.-.. ..+.+++ +++++++. .+..++.+.+.+|++|++.+ .... . ...+
T Consensus 4 ~~~~l~ig~~~~~~~~p~~~a~~~g~f~~~-G~~ve~~~~~~g~~~~~al~~G~iD~a~~-~~~~~~~~~~g~~~~~~~~ 81 (252)
T PF13379_consen 4 EPTTLRIGYLPGPDYAPLYVAQEKGLFEKE-GLDVEWVQFASGADILEALAAGEIDIAFV-LAPALIAIAKGAGGPDVDI 81 (252)
T ss_dssp SESEEEEEETSSGGGHHHHHHHHTTHHHHT-TSCEEEEEESSHHHHHHHHHCTSSSEEEE-CTHHHHHHHTTTTT----E
T ss_pred CCcEEEEEeecchHHHHHHHHHHcChHHHc-CCEEEEEEcCCHHHHHHHHHcCCCCEEEe-chHHHHHHHcCCCCcccce
Confidence 3568999998875433221111 2244444 55566655 35668999999999999999 2210 1 1122
Q ss_pred e-eeccccceEEEEecCCCCCCCCCCcChhhh-------cCCCeEeecCCCCcHHHHHHHHHhCCCce--eEEEEecCHH
Q psy3760 159 I-SIPCYQWEYVIIVPLDHPLLLLNSISLKEI-------SNYPLITYDLSFSGRIKLDREFSLQKLTP--YIVLETINSD 228 (306)
Q Consensus 159 ~-~~~l~~~~~~~v~~~~~~l~~~~~i~~~dl-------~~~~~i~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~ 228 (306)
. ...+..+...++++++.... ...-+++|| .+..+.....++...-.+..++++.|+.+ .+.+..-+..
T Consensus 82 ~~~~~~~~~g~~lvv~~~~~~~-~~~~~~~dl~~~~~~~kGk~i~~~~~gs~~~~~l~~~l~~~Gl~~~~dv~~~~~~~~ 160 (252)
T PF13379_consen 82 VVLAGLSQNGNALVVRNDLKDA-SDIKSLADLIKKRKAQKGKKIAVPFPGSTHDMLLRYLLKKAGLDPKDDVTLVNVPPP 160 (252)
T ss_dssp EEEEECSBSSEEEEECGGGTTC-STTCCGHHHHHTCCSCSTEEEEESSTTSHHHHHHHHHHHHTT--TTTSSEEEE--GH
T ss_pred EEeeccCCCceEEEEcCccccC-CCccCHHHHHhhhcccCCcEEEEcCCCCHHHHHHHHHHHhCCCCcccceEEEecCHH
Confidence 2 22344556677777653111 234578999 66677776666555556778999999987 3344444448
Q ss_pred HHHHHHHhc-cceeeeecceeccc-ccCC-ceeeecCCCCccceEE-EEEeCCc--cccHHHHHHHHHHhHHh
Q psy3760 229 IIKTYVELR-MGIGIIASIAFDSN-RDKN-LRSISASHLFGTTISR-VIIKQGT--YLRSYVYSFIKLLSPKL 295 (306)
Q Consensus 229 ~~~~~v~~g-~gi~~~p~~~~~~~-~~~~-l~~~~~~~~~~~~~~~-l~~~~~~--~~~~~~~~~~~~l~~~~ 295 (306)
.+..++++| .-.++++....... ..+. -..+...+.....+.+ ++.+++- ..+..+++|++.+.+..
T Consensus 161 ~~~~al~~g~iDa~~~~eP~~~~~~~~g~g~~v~~~~~~~~~~p~~~~~~~~~~~~~~p~~v~~~~~a~~~A~ 233 (252)
T PF13379_consen 161 EMVAALRAGEIDAAVLWEPFASQAEAKGIGKIVADSGDVWGNHPCCVIVARRDFLEENPEAVKAFLEALQEAQ 233 (252)
T ss_dssp HHHHHHHTTS-SEEEEETTHHHHHHHTTS-EEEEEHHHCSTT-B-EEEEEEHHHHHH-HHHHHHHHHHHHHHH
T ss_pred HHHHHHhCCCcCEEEecCCHHHHHHhccCCeEEEEeccccCCCCeEEEEECHHHHHHCHHHHHHHHHHHHHHH
Confidence 888888888 33333445444333 2332 3333333322222333 3444432 23567888888876654
No 166
>PRK10918 phosphate ABC transporter periplasmic substrate-binding protein PstS; Provisional
Probab=97.58 E-value=0.017 Score=48.31 Aligned_cols=151 Identities=14% Similarity=0.043 Sum_probs=101.0
Q ss_pred CcEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccCCC----CCceeeccccceE
Q psy3760 93 GNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPS----DKLISIPCYQWEY 168 (306)
Q Consensus 93 ~~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~~----~~~~~~~l~~~~~ 168 (306)
..|+++.+.+ ...++..+...|.+. +++++++...++..-+..+.+|.+||+-+..+..+. .++...++.-+.+
T Consensus 27 ~~i~~~GSt~-~~pl~~~~a~~y~~~-~~v~v~~~~~GSG~Gi~~~~~g~vd~a~ssr~l~~~E~~~~~~~~~pva~daI 104 (346)
T PRK10918 27 ASLTGAGATF-PAPVYAKWADTYQKE-TGNKVNYQGIGSSGGVKQIIANTVDFGASDAPLSDEKLAQEGLFQFPTVIGGV 104 (346)
T ss_pred ceEEEEccCh-HHHHHHHHHHHHHhh-cCCEEEEecCccHHHHHHHHhCCCcEEecCccCCHHHHhhcCCeeeeEEEEEE
Confidence 4688777766 566888888999764 789999999999999999999999999996543322 2466788888899
Q ss_pred EEEec-CCCCCC---C----------CCCcChhh-----------hcCCCeEee--cCCCCcHHHHHHHHHhCCC-----
Q psy3760 169 VIIVP-LDHPLL---L----------LNSISLKE-----------ISNYPLITY--DLSFSGRIKLDREFSLQKL----- 216 (306)
Q Consensus 169 ~~v~~-~~~~l~---~----------~~~i~~~d-----------l~~~~~i~~--~~~~~~~~~~~~~~~~~~~----- 216 (306)
+++++ ++.+.. . .+..+|.| +.+.|...+ ..+++.+..+.+.+....-
T Consensus 105 aivvN~~~~~~~~Ltl~~~~L~~If~G~It~W~d~~I~~~NP~~~lpd~~I~vv~R~d~SGTt~~Ft~~l~~~~~~w~~~ 184 (346)
T PRK10918 105 VLAVNIPGLKSGELVLDGKTLGDIYLGKIKKWNDEAIAKLNPGVKLPSQNIAVVRRADGSGTSFVFTSYLAKVNEEWKSK 184 (346)
T ss_pred EEEEeCCCCCccceeeCHHHHHHHhcCCCCCCCchhhhccCCCCCCCCCCeEEEECCCCCchHHHHHHHHHhcChhhhhc
Confidence 99998 555521 1 23335777 445555544 4456677777777643210
Q ss_pred --------ceeEEEEecCHHHHHHHHHhc-cceeeeecc
Q psy3760 217 --------TPYIVLETINSDIIKTYVELR-MGIGIIASI 246 (306)
Q Consensus 217 --------~~~~~~~~~~~~~~~~~v~~g-~gi~~~p~~ 246 (306)
-|. .........+...|.+. .+|+++...
T Consensus 185 ~~~g~~~~~p~-~~~~~gn~~v~~~V~~~p~aIGYv~~~ 222 (346)
T PRK10918 185 VGAGSTVNWPT-GLGGKGNDGIAAFVQRLPGAIGYVEYA 222 (346)
T ss_pred cCcCccccCcc-ccccCCCHHHHHHHhcCCCceEeeeHH
Confidence 011 12333444666777665 788888653
No 167
>PRK11063 metQ DL-methionine transporter substrate-binding subunit; Provisional
Probab=97.58 E-value=0.027 Score=45.45 Aligned_cols=201 Identities=7% Similarity=0.047 Sum_probs=112.7
Q ss_pred CcEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeC-ChhHHHHHHHcCCeeEEEEccccCC-----CCCceeeccccc
Q psy3760 93 GNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQG-NPKQITEMIRNDQADIAIVTEILSP-----SDKLISIPCYQW 166 (306)
Q Consensus 93 ~~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~-~~~~~~~~l~~~~~Di~i~~~~~~~-----~~~~~~~~l~~~ 166 (306)
..|+||+..+... .+..++....+..-++++++... +.....+.|.+|++|+.+..+...- ..+.....++.
T Consensus 31 ~~I~IG~~~~~~~-~~~~~~~~~l~~~~G~~Vel~~f~~~~~~~~ALa~GdID~~~~qh~~~l~~~~~~~g~~l~~~~~- 108 (271)
T PRK11063 31 NHIKVGVIVGAEQ-QVAEVAQKVAKEKYGLDVELVTFNDYVLPNEALSKGDIDANAFQHKPYLDQQIKDRGYKLVAVGN- 108 (271)
T ss_pred CcEEEEeCCCChH-HHHHHHHHHHHHhcCCeEEEEEecCcHHHHHHHHcCCcceecccCHHHHHHHHHHcCCcEEEEeE-
Confidence 4699999876444 34556666655555788888874 4478899999999999775432111 12333333322
Q ss_pred eEEEEecCCCCCCCCCCcChhhhc-CCCeEeecCCCCcHHHHHHHHHhCCC------------------ce-eEEEEecC
Q psy3760 167 EYVIIVPLDHPLLLLNSISLKEIS-NYPLITYDLSFSGRIKLDREFSLQKL------------------TP-YIVLETIN 226 (306)
Q Consensus 167 ~~~~v~~~~~~l~~~~~i~~~dl~-~~~~i~~~~~~~~~~~~~~~~~~~~~------------------~~-~~~~~~~~ 226 (306)
..++|.+ +...+--+++||. +.....+... ........+|+..|+ .| ++.+.--+
T Consensus 109 --~~vvp~~--~ys~~i~si~DL~~Gk~IAip~d~-~n~~r~L~lL~~~Gli~l~~~~~~~~t~~di~~n~~~v~~v~~~ 183 (271)
T PRK11063 109 --TFVYPIA--GYSKKIKSLDELQDGSQVAVPNDP-TNLGRSLLLLQKVGLIKLKDGVGLLPTVLDIVENPKNLKIVELE 183 (271)
T ss_pred --EEEEEee--ccccCCCCHHHhcCCCEEEecCCC-ccHHHHHHHHHHCCCEEecCCCCCCCCHHHHhcCCCCCEEEECc
Confidence 2223322 1122345899998 5555454433 333344447888777 22 34444445
Q ss_pred HHHHHHHHHhc-cceeeeecceeccc--cc-CCceeeecCCCCccceEEEEEeCCccccHHHHHHHHHHhHHhhHHHHHh
Q psy3760 227 SDIIKTYVELR-MGIGIIASIAFDSN--RD-KNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLLSPKLNRKFINK 302 (306)
Q Consensus 227 ~~~~~~~v~~g-~gi~~~p~~~~~~~--~~-~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~ 302 (306)
...+.+...+| .-.++++...+... .. .+-....-.+ . .+-..++.++....++.++.+++.+++-=-+..+++
T Consensus 184 ~~~~~~al~~g~vDaa~i~~~~a~~a~~~~~~~~l~~e~~~-~-~~~~~~~v~~~~~~~~~~~~l~~a~~s~~v~~~i~~ 261 (271)
T PRK11063 184 APQLPRSLDDAQIALAVINTTYASQIGLTPAKDGIFVEDKD-S-PYVNLIVAREDNKDAENVKKFVQAYQSDEVYEAANK 261 (271)
T ss_pred HHHHHHhcccccccEEEEChHHHHHcCCCCCCCeeEECCCC-C-CeEEEEEECCcccCCHHHHHHHHHHcCHHHHHHHHH
Confidence 55666666764 33444554443332 11 1222222222 2 233456667777789999999998876544444443
No 168
>TIGR01889 Staph_reg_Sar staphylococcal accessory regulator family. This model represents a family of transcriptional regulatory proteins in Staphylococcus aureus and Staphylococcus epidermidis. Some members contain two tandem copies of this region. This family is related to the MarR transcriptional regulator family described by pfam model pfam01047.
Probab=97.57 E-value=0.00064 Score=46.58 Aligned_cols=72 Identities=14% Similarity=0.255 Sum_probs=54.2
Q ss_pred chhhHHHHHHHH----Hh-cCCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEec-----CCCc-cccCHhHHHHHHHH
Q psy3760 2 NLHQFRFVREAV----RQ-NFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRH-----GKRI-RGLTKPGQAILRSI 70 (306)
Q Consensus 2 ~~~~l~~f~~v~----~~-~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~-----~~~~-~~lT~~G~~l~~~a 70 (306)
+..++.++..+. .. +-+.+.-|+.+++++|++|+.|++||+. -++.|. +|.+ +.||+.|+.+++.+
T Consensus 24 s~~q~~vL~~l~~~~~~~~~~t~~eL~~~l~~~~stvs~~i~~Le~k---g~I~r~~~~~D~R~~~i~lT~~G~~~~~~~ 100 (109)
T TIGR01889 24 SLEELLILYYLGKLENNEGKLTLKEIIKEILIKQSALVKIIKKLSKK---GYLSKERSEDDERKVIISINKEQRSKIESL 100 (109)
T ss_pred CHHHHHHHHHHHhhhccCCcCcHHHHHHHHCCCHHHHHHHHHHHHHC---CCEeccCCcccCCeEEEEECHHHHHHHHHH
Confidence 456777787777 22 1379999999999999999999999984 455543 1221 37999999999888
Q ss_pred HHHHHH
Q psy3760 71 EIIMQE 76 (306)
Q Consensus 71 ~~il~~ 76 (306)
..-++.
T Consensus 101 ~~~~~~ 106 (109)
T TIGR01889 101 ISEIEQ 106 (109)
T ss_pred HHHHHH
Confidence 776654
No 169
>COG1321 TroR Mn-dependent transcriptional regulator [Transcription]
Probab=97.55 E-value=0.00064 Score=49.40 Aligned_cols=62 Identities=19% Similarity=0.199 Sum_probs=49.1
Q ss_pred HHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCCccccCHhHHHHHHHHHHHHHHHHHHHHH
Q psy3760 19 LTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKPGQAILRSIEIIMQEIEGLKKI 83 (306)
Q Consensus 19 ~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~~~lT~~G~~l~~~a~~il~~~~~~~~~ 83 (306)
.+.-|+.|+|++||+|..+++|++ .|.--+++ .+|+ +||+.|+.+.....+.-..++.+...
T Consensus 27 ~~diA~~L~Vsp~sVt~ml~rL~~-~GlV~~~~-y~gi-~LT~~G~~~a~~~~r~hrlle~fL~~ 88 (154)
T COG1321 27 TKDIAERLKVSPPSVTEMLKRLER-LGLVEYEP-YGGV-TLTEKGREKAKELLRKHRLLERFLVD 88 (154)
T ss_pred HHHHHHHhCCCcHHHHHHHHHHHH-CCCeEEec-CCCe-EEChhhHHHHHHHHHHHHHHHHHHHH
Confidence 466799999999999999999986 35444443 4666 89999999888888777777777654
No 170
>COG1846 MarR Transcriptional regulators [Transcription]
Probab=97.54 E-value=0.00032 Score=49.38 Aligned_cols=73 Identities=19% Similarity=0.280 Sum_probs=59.2
Q ss_pred CchhhHHHHHHHHHhcCCH--HHHHHHhCCCchHHHHHHHHHHHHcCceeEEecC-------CCccccCHhHHHHHHHHH
Q psy3760 1 MNLHQFRFVREAVRQNFNL--TEAAKALYTSQPGVSKAIIELEEELSIDIFIRHG-------KRIRGLTKPGQAILRSIE 71 (306)
Q Consensus 1 m~~~~l~~f~~v~~~~~s~--~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~-------~~~~~lT~~G~~l~~~a~ 71 (306)
++..++.++..+.+.+ .. +.-|+.+++++|++|+.|++||+. -|+.|.. ..+ .+|+.|+.++..+.
T Consensus 20 lt~~q~~~L~~l~~~~-~~~~~~la~~l~i~~~~vt~~l~~Le~~---glv~r~~~~~DrR~~~l-~lT~~G~~~~~~~~ 94 (126)
T COG1846 20 LTPPQYQVLLALYEAG-GITVKELAERLGLDRSTVTRLLKRLEDK---GLIERLRDPEDRRAVLV-RLTEKGRELLEQLL 94 (126)
T ss_pred CCHHHHHHHHHHHHhC-CCcHHHHHHHHCCCHHHHHHHHHHHHHC---CCeeecCCccccceeeE-EECccHHHHHHHhc
Confidence 3567889999999999 77 899999999999999999999985 3555442 233 89999999999999
Q ss_pred HHHHHHH
Q psy3760 72 IIMQEIE 78 (306)
Q Consensus 72 ~il~~~~ 78 (306)
.......
T Consensus 95 ~~~~~~~ 101 (126)
T COG1846 95 PAAQELL 101 (126)
T ss_pred cHHHHHH
Confidence 8444433
No 171
>PRK09861 cytoplasmic membrane lipoprotein-28; Provisional
Probab=97.53 E-value=0.014 Score=47.01 Aligned_cols=205 Identities=6% Similarity=0.004 Sum_probs=114.1
Q ss_pred CcEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChh-HHHHHHHcCCeeEEEEccccC-----CCCCceeeccccc
Q psy3760 93 GNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPK-QITEMIRNDQADIAIVTEILS-----PSDKLISIPCYQW 166 (306)
Q Consensus 93 ~~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~-~~~~~l~~~~~Di~i~~~~~~-----~~~~~~~~~l~~~ 166 (306)
..|+||+..+... -+..+...+.+..+++++++...+.. ...+.|.+|++|+.+..+.+. ...+.....+.
T Consensus 32 ~tLkVG~~~~~~~-~~~e~a~~~~k~~~G~~Velv~fsd~~~~n~AL~~G~ID~n~~qh~~yl~~~~~~~g~~lv~~~-- 108 (272)
T PRK09861 32 KHIKVGVINGAEQ-DVAEVAKKVAKEKYGLDVELVGFSGSLLPNDATNHGELDANVFQHRPFLEQDNQAHGYKLVAVG-- 108 (272)
T ss_pred CcEEEEEcCCchH-HHHHHHHHHHHHcCCCeEEEEecCchhhHHHHHHcCCcceehhhhHHHHHHHHHhcCCCeEEEe--
Confidence 4799999887655 45556777766656899999865433 445899999999998643211 11222222222
Q ss_pred eEEEEecCCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCC---------Cc----------eeEEEEecCH
Q psy3760 167 EYVIIVPLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQK---------LT----------PYIVLETINS 227 (306)
Q Consensus 167 ~~~~v~~~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~---------~~----------~~~~~~~~~~ 227 (306)
..+++|-+ +...+--+++||.+-.-|..+.+.....+....++..| .. .+..+.--..
T Consensus 109 -~~~~~P~~--~Ys~~iksl~DL~~Ga~IAipnd~~n~~ral~lL~~agli~l~~~~g~~~t~~di~~np~~l~~ve~~~ 185 (272)
T PRK09861 109 -NTFVFPMA--GYSKKIKTVAQIKEGATVAIPNDPTNLGRALLLLQKEKLITLKEGKGLLPTALDITDNPRHLQIMELEG 185 (272)
T ss_pred -EEEEEeee--ccccCCCCHHHcCCCCEEEEeCCCccHHHHHHHHHHCCCEEEcCCCCCCCCHhHHhcCCCCCEEEEcCH
Confidence 23333322 22334458999995555555543343344455555544 22 1344444555
Q ss_pred HHHHHHHHhc--cceeeeecceecccccCCceeeecCCCCccceEEEEEeCCccccHHHHHHHHHHhHHhhHHHHHhh
Q psy3760 228 DIIKTYVELR--MGIGIIASIAFDSNRDKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLLSPKLNRKFINKI 303 (306)
Q Consensus 228 ~~~~~~v~~g--~gi~~~p~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~ 303 (306)
..+...+..| +++.+-..+....-..+.-..+-.+.....+-..++++.+...++.+++|++.+++.--+..+++.
T Consensus 186 ~q~~~al~dg~vD~a~i~~~~~~~ag~~~~~~~l~~e~~~~~~~n~~~~r~~~~~~~~~~~lv~~~~s~~v~~~i~~~ 263 (272)
T PRK09861 186 AQLPRVLDDPKVDVAIISTTYIQQTGLSPVHDSVFIEDKNSPYVNILVAREDNKNAENVKEFLQSYQSPEVAKAAETI 263 (272)
T ss_pred HHhHhhccCcccCEEEEchhHHHHcCCCcccceeEEcCCCCCeEEEEEEcCCccCCHHHHHHHHHHcCHHHHHHHHHH
Confidence 5666767774 444444444433211110011211211112344566787888899999999998776555555443
No 172
>PRK10870 transcriptional repressor MprA; Provisional
Probab=97.48 E-value=0.00076 Score=50.57 Aligned_cols=73 Identities=22% Similarity=0.201 Sum_probs=56.7
Q ss_pred chhhHHHHHHHHHh--cCCH--HHHHHHhCCCchHHHHHHHHHHHHcCceeEEec-------CCCccccCHhHHHHHHHH
Q psy3760 2 NLHQFRFVREAVRQ--NFNL--TEAAKALYTSQPGVSKAIIELEEELSIDIFIRH-------GKRIRGLTKPGQAILRSI 70 (306)
Q Consensus 2 ~~~~l~~f~~v~~~--~~s~--~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~-------~~~~~~lT~~G~~l~~~a 70 (306)
+..++.++..+.+. + ++ +.-|+.+++++|++|+.|++||+. -|+.|. ...+ .||+.|+.+++.+
T Consensus 54 t~~q~~iL~~L~~~~~~-~it~~eLa~~l~l~~~tvsr~v~rLe~k---GlV~R~~~~~DrR~~~v-~LT~~G~~~~~~i 128 (176)
T PRK10870 54 NETLFMALITLESQENH-SIQPSELSCALGSSRTNATRIADELEKR---GWIERRESDNDRRCLHL-QLTEKGHEFLREV 128 (176)
T ss_pred CHHHHHHHHHHhcCCCC-CcCHHHHHHHHCCCHHHHHHHHHHHHHC---CCEEecCCCCCCCeeEE-EECHHHHHHHHHH
Confidence 44567788888753 4 44 788999999999999999999984 455653 1233 8999999999999
Q ss_pred HHHHHHHHH
Q psy3760 71 EIIMQEIEG 79 (306)
Q Consensus 71 ~~il~~~~~ 79 (306)
.+.......
T Consensus 129 ~~~~~~~~~ 137 (176)
T PRK10870 129 LPPQHNCLH 137 (176)
T ss_pred HHHHHHHHH
Confidence 887776654
No 173
>PF02954 HTH_8: Bacterial regulatory protein, Fis family; InterPro: IPR002197 The Factor for Inversion Stimulation (FIS) protein is a regulator of bacterial functions, and binds specifically to weakly related DNA sequences [,]. It activates ribosomal RNA transcription, and is involved in upstream activation of rRNA promoters. The protein has been shown to play a role in the regulation of virulence factors in both Salmonella typhimurium and Escherichia coli []. Some of its functions include inhibition of the initiation of DNA replication from the OriC site, and promotion of Hin-mediated DNA inversion. In its C-terminal extremity, FIS encodes a helix-turn-helix (HTH) DNA- binding motif, which shares a high degree of similarity with other HTH motifs of more primitive bacterial transcriptional regulators, such as the nitrogen assimilation regulatory proteins (NtrC) from species like Azobacter, Rhodobacter and Rhizobium. This has led to speculation that both evolved from a single common ancestor []. The 3-dimensional structure of the E. coli FIS DNA-binding protein has been determined by means of X-ray diffraction to 2.0A resolution [,]. FIS is composed of four alpha-helices tightly intertwined to form a globular dimer with two protruding HTH motifs. The 24 N-terminal amino acids are poorly defined, indicating that they might act as `feelers' suitable for DNA or protein (invertase) recognition []. Other proteins belonging to this subfamily include: E. coli: atoC, hydG, ntrC, fhlA, tyrR, Rhizobium spp.: ntrC, nifA, dctD ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 1NTC_A 3JRH_A 3JRB_A 3IV5_A 3JRI_A 1ETQ_A 1ETW_B 1ETY_A 3JRF_A 3JRA_A ....
Probab=97.47 E-value=0.00032 Score=38.62 Aligned_cols=32 Identities=19% Similarity=0.155 Sum_probs=24.8
Q ss_pred HHHHHHHhcCCHHHHHHHhCCCchHHHHHHHH
Q psy3760 8 FVREAVRQNFNLTEAAKALYTSQPGVSKAIIE 39 (306)
Q Consensus 8 ~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~ 39 (306)
+-.++.+++++.++||+.||||++|+.+.|++
T Consensus 10 i~~aL~~~~gn~~~aA~~Lgisr~tL~~klkk 41 (42)
T PF02954_consen 10 IRQALERCGGNVSKAARLLGISRRTLYRKLKK 41 (42)
T ss_dssp HHHHHHHTTT-HHHHHHHHTS-HHHHHHHHHH
T ss_pred HHHHHHHhCCCHHHHHHHHCCCHHHHHHHHHh
Confidence 33455566669999999999999999999986
No 174
>PF13601 HTH_34: Winged helix DNA-binding domain; PDB: 1UB9_A.
Probab=97.40 E-value=0.0017 Score=41.54 Aligned_cols=65 Identities=23% Similarity=0.311 Sum_probs=44.7
Q ss_pred HHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCcee---E-EecCCCccccCHhHHHHHHHHHHHHHHH
Q psy3760 12 AVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDI---F-IRHGKRIRGLTKPGQAILRSIEIIMQEI 77 (306)
Q Consensus 12 v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~L---f-~R~~~~~~~lT~~G~~l~~~a~~il~~~ 77 (306)
..+.- +|+.=.+.|++|.+++|++++.||+.==++- | .|.++..+++|+.|+..++.-...++++
T Consensus 11 ~~~~~-~f~~L~~~l~lt~g~Ls~hL~~Le~~GyV~~~k~~~~~~p~t~~~lT~~Gr~~~~~~~~~L~~~ 79 (80)
T PF13601_consen 11 ANEEA-TFSELKEELGLTDGNLSKHLKKLEEAGYVEVEKEFEGRRPRTWYSLTDKGREAFERYVAALREI 79 (80)
T ss_dssp HHSEE-EHHHHHHHTT--HHHHHHHHHHHHHTTSEEEEEE-SSS--EEEEEE-HHHHHHHHHHHHHHHHH
T ss_pred hcCCC-CHHHHHHHhCcCHHHHHHHHHHHHHCCCEEEEEeccCCCCeEEEEECHHHHHHHHHHHHHHHHh
Confidence 34566 8999999999999999999999998632222 1 1223334589999999988877776653
No 175
>TIGR02285 conserved hypothetical protein. Members of this family are found in several Proteobacteria, including Pseudomonas putida KT2440, Bdellovibrio bacteriovorus HD100 (three members), Aeromonas hydrophila, and Chromobacterium violaceum ATCC 12472. The function is unknown.
Probab=97.37 E-value=0.029 Score=45.34 Aligned_cols=212 Identities=11% Similarity=0.032 Sum_probs=118.5
Q ss_pred CCcEEEEecccch----------hhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEcccc--CCCCCce
Q psy3760 92 TGNLTIATTHTQA----------RYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEIL--SPSDKLI 159 (306)
Q Consensus 92 ~~~l~I~~~~~~~----------~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~--~~~~~~~ 159 (306)
..+|+++..+..+ ..+...++..+.+..+++++++...+...++..+ +|+.|.++..... .....+.
T Consensus 17 ~~~l~~~~~~~pPf~~~~~~~~~~G~~~~i~~~i~~~~~~~~~~~~~~pw~r~l~~l-~~~~d~~~~~~~~t~eR~~~~~ 95 (268)
T TIGR02285 17 KEAITWIVNDFPPFFIFSGPSKGRGVFDVILQEIRRALPQYEHRFVRVSFARSLKEL-QGKGGVCTVNLLRTPEREKFLI 95 (268)
T ss_pred cceeEEEecccCCeeEeCCCCCCCChHHHHHHHHHHHcCCCceeEEECCHHHHHHHH-hcCCCeEEeeccCCcchhhcee
Confidence 3577877754222 1234556677888777889999999999999999 6666666532221 2223333
Q ss_pred -eeccc-cceEEEEecCCCCCCCC----CCcChhhh---cCCCeEeecCCCCcHHHHHHHHHhCCCceeE-EEEecCHHH
Q psy3760 160 -SIPCY-QWEYVIIVPLDHPLLLL----NSISLKEI---SNYPLITYDLSFSGRIKLDREFSLQKLTPYI-VLETINSDI 229 (306)
Q Consensus 160 -~~~l~-~~~~~~v~~~~~~l~~~----~~i~~~dl---~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~ 229 (306)
+.|+. ....+++++++.+..-. .++++.++ .+.. +....+......+++.+...+..+.. ....++...
T Consensus 96 Fs~P~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~l~~l~g~~-vgv~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 174 (268)
T TIGR02285 96 FSDPTLRALPVGLVLRKELTAGVRDEQDGDVDLKKLLASKKKR-LGVIASRSYGQQIDDILSDSGYQHNTRIIGNAAMGN 174 (268)
T ss_pred ecCCccccCCceEEEccchhhhccccCCCCccHHHHhcCCCeE-EEEecceeccHHHHHHHHhCCcccceeeeccchHHH
Confidence 34555 35788888887642211 13455544 4433 44444444444566777666544332 344567777
Q ss_pred HHHHHHhccceeeeec-ceeccc-c-----cCCceeeecCCCCccceEEEEEeCCccccHHHHHHHHHHhHHhhHHHHHh
Q psy3760 230 IKTYVELRMGIGIIAS-IAFDSN-R-----DKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLLSPKLNRKFINK 302 (306)
Q Consensus 230 ~~~~v~~g~gi~~~p~-~~~~~~-~-----~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~ 302 (306)
+.+++..|..=+++-+ ..+..+ . ...+...++........+++..+++.........|=+.|++..+....++
T Consensus 175 ~~~~L~~GrvD~~v~d~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~k~~~~~~l~~~in~~L~~l~~dG~~~~ 254 (268)
T TIGR02285 175 LFKMLEKGRVNYTLAYPPEKTYYEELNNGALPPLKFLPVAGMPAHISVWVACPKTEWGRKVIADIDQALSELNVDPKYYK 254 (268)
T ss_pred HHHHHHcCCccEEEeCcHHHHHHHHhccCCcCCeeEeecCCCccceEEEEEeCCCHHHHHHHHHHHHHHHHHhhCHHHHH
Confidence 8999999955554433 322222 1 12355555443222335677777653223455555555555555555666
Q ss_pred hhc
Q psy3760 303 ILN 305 (306)
Q Consensus 303 ~~~ 305 (306)
+.+
T Consensus 255 i~~ 257 (268)
T TIGR02285 255 YFD 257 (268)
T ss_pred HHH
Confidence 543
No 176
>PRK15010 ABC transporter lysine/arginine/ornithine binding periplasmic protein; Provisional
Probab=97.36 E-value=0.012 Score=47.42 Aligned_cols=203 Identities=11% Similarity=0.062 Sum_probs=115.3
Q ss_pred CCCcEEEEecc-cch----------hhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccC--CCCC
Q psy3760 91 DTGNLTIATTH-TQA----------RYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILS--PSDK 157 (306)
Q Consensus 91 ~~~~l~I~~~~-~~~----------~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~--~~~~ 157 (306)
....|+||+.. ..+ ..+...++..+.+. -++++++...+..++++.+..|++|+++...... ....
T Consensus 24 ~~~~l~v~~~~~~pPf~~~~~~g~~~G~~vdl~~~ia~~-lg~~~~~~~~~~~~~~~~l~~g~~Di~~~~~~~t~eR~~~ 102 (260)
T PRK15010 24 LPETVRIGTDTTYAPFSSKDAKGDFVGFDIDLGNEMCKR-MQVKCTWVASDFDALIPSLKAKKIDAIISSLSITDKRQQE 102 (260)
T ss_pred cCCeEEEEecCCcCCceeECCCCCEEeeeHHHHHHHHHH-hCCceEEEeCCHHHHHHHHHCCCCCEEEecCcCCHHHHhh
Confidence 34678999863 111 13556778787776 4788888888888999999999999987532211 2222
Q ss_pred ce-eeccccceEEEEecCCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCceeEEEEecCHHHHHHHHHh
Q psy3760 158 LI-SIPCYQWEYVIIVPLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVEL 236 (306)
Q Consensus 158 ~~-~~~l~~~~~~~v~~~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~ 236 (306)
+. +.++.....+++++++.+.. .+++||.+.+.-. ..+..........+...+. + ....++...++.++.+
T Consensus 103 ~~fs~p~~~~~~~~~~~~~~~~~----~~~~dl~g~~Igv-~~gs~~~~~~~~~~~~~~~--~-~~~~~~~~~~~~~l~~ 174 (260)
T PRK15010 103 IAFSDKLYAADSRLIAAKGSPIQ----PTLDSLKGKHVGV-LQGSTQEAYANETWRSKGV--D-VVAYANQDLVYSDLAA 174 (260)
T ss_pred cccccceEeccEEEEEECCCCCC----CChhHcCCCEEEE-ecCchHHHHHHHhcccCCc--e-EEecCCHHHHHHHHHc
Confidence 32 56777888999999887532 2678998877444 4443322222222222232 2 3346788888999999
Q ss_pred ccceeeeec-ceecc-c-c---cCCceeeecCCC---CccceEEEEEeCCccccHHHHHHHHHHhHHhhHHHHHhhh
Q psy3760 237 RMGIGIIAS-IAFDS-N-R---DKNLRSISASHL---FGTTISRVIIKQGTYLRSYVYSFIKLLSPKLNRKFINKIL 304 (306)
Q Consensus 237 g~gi~~~p~-~~~~~-~-~---~~~l~~~~~~~~---~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~ 304 (306)
|..=+++-+ ..... + . ...+...+.... .....+++..+++ .......|=+.|++.-+....+++.
T Consensus 175 griDa~i~d~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~--~~~L~~~ln~~l~~l~~~G~~~~i~ 249 (260)
T PRK15010 175 GRLDAALQDEVAASEGFLKQPAGKDFAFAGPSVKDKKYFGDGTGVGLRKD--DAELTAAFNKALGELRQDGTYDKMA 249 (260)
T ss_pred CCccEEEeCcHHHHHHHHhCCCCCceEEecCccccccccCCceEEEEeCC--CHHHHHHHHHHHHHHHhCCcHHHHH
Confidence 955444433 22211 1 1 123333322111 1112344555543 2445555555555554444555554
No 177
>TIGR00122 birA_repr_reg BirA biotin operon repressor domain. This model may recognize some other putative repressor proteins, such as DnrO of Streptomyces peucetius with scores below the noise cutoff but with significance shown by low E-value.
Probab=97.33 E-value=0.00064 Score=42.23 Aligned_cols=56 Identities=29% Similarity=0.402 Sum_probs=42.4
Q ss_pred CchhhHHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCCccccCHh
Q psy3760 1 MNLHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKP 62 (306)
Q Consensus 1 m~~~~l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~~~lT~~ 62 (306)
||.+-++.+ .+...|.+.-|+.+++|.+++++.|+.||+ .|.++..+ ++|. .+.+.
T Consensus 1 ~~~~il~~L---~~~~~~~~eLa~~l~vS~~tv~~~l~~L~~-~g~~i~~~-~~g~-~l~~~ 56 (69)
T TIGR00122 1 MPLRLLALL---ADNPFSGEKLGEALGMSRTAVNKHIQTLRE-WGVDVLTV-GKGY-RLPPP 56 (69)
T ss_pred ChHHHHHHH---HcCCcCHHHHHHHHCCCHHHHHHHHHHHHH-CCCeEEec-CCce-EecCc
Confidence 555555553 333338899999999999999999999986 59998877 6776 56443
No 178
>PF13412 HTH_24: Winged helix-turn-helix DNA-binding; PDB: 1I1G_B 2IA0_B 3I4P_A 2GQQ_A 2L4A_A 2CFX_B 2DBB_B 2EFO_A 2EFQ_A 2PN6_A ....
Probab=97.32 E-value=0.00076 Score=38.44 Aligned_cols=43 Identities=21% Similarity=0.223 Sum_probs=34.1
Q ss_pred CchhhHHHHHHHHHhc-CCHHHHHHHhCCCchHHHHHHHHHHHH
Q psy3760 1 MNLHQFRFVREAVRQN-FNLTEAAKALYTSQPGVSKAIIELEEE 43 (306)
Q Consensus 1 m~~~~l~~f~~v~~~~-~s~~~aA~~l~isq~~~s~~i~~LE~~ 43 (306)
||-.+.+++..+.+.+ -|.+..|+.+|+|.+++++.|++|++.
T Consensus 1 l~~~~~~Il~~l~~~~~~t~~ela~~~~is~~tv~~~l~~L~~~ 44 (48)
T PF13412_consen 1 LDETQRKILNYLRENPRITQKELAEKLGISRSTVNRYLKKLEEK 44 (48)
T ss_dssp --HHHHHHHHHHHHCTTS-HHHHHHHHTS-HHHHHHHHHHHHHT
T ss_pred CCHHHHHHHHHHHHcCCCCHHHHHHHhCCCHHHHHHHHHHHHHC
Confidence 6778888888888866 367788999999999999999999874
No 179
>TIGR01729 taurine_ABC_bnd taurine ABC transporter, periplasmic binding protein. This model identifies a cluster of ABC transporter periplasmic substrate binding proteins, apparently specific for taurine. Transport systems for taurine (NH2-CH2-CH2-SO3H), sulfonates, and sulfate esters import sulfur when sulfate levels are low. The most closely related proteins outside this family are putative aliphatic sulfonate binding proteins (TIGR01728).
Probab=97.30 E-value=0.02 Score=47.23 Aligned_cols=192 Identities=9% Similarity=0.024 Sum_probs=103.7
Q ss_pred EEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCC-hhHHHHHHHcCCeeEEEEccccC---CCCCceeecc-----cc
Q psy3760 95 LTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGN-PKQITEMIRNDQADIAIVTEILS---PSDKLISIPC-----YQ 165 (306)
Q Consensus 95 l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~-~~~~~~~l~~~~~Di~i~~~~~~---~~~~~~~~~l-----~~ 165 (306)
++||+........+...-..|.+++ ++++++.... ...+.+.|.+|++|+++...... ...+.....+ ..
T Consensus 1 ~~~~~~~~~~p~~va~~~G~~~k~~-Gl~Ve~~~~~~~~~~~~al~~G~iD~~~~~~~~~~~a~~~g~~~~~v~~~~~~~ 79 (300)
T TIGR01729 1 VTVGYQTIVEPFKVAQADGAAAKEA-GATIDWRKFDSGADISTALASGNVPIGVIGSSPLAAAASRGVPIELFWILDNIG 79 (300)
T ss_pred CEEEecCCCCHHHHHHHcCchHHhc-CCeeEEEecCcHHHHHHHHHcCCCCEeccCCCHHHHHHHCCCCeEEEEEeccCC
Confidence 5788877654445555444555443 7778877764 45788999999999998632111 1122221111 11
Q ss_pred ceEEEEecCCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCceeEE-EEecCHHHHHHHHHhc-cceeee
Q psy3760 166 WEYVIIVPLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIV-LETINSDIIKTYVELR-MGIGII 243 (306)
Q Consensus 166 ~~~~~v~~~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~v~~g-~gi~~~ 243 (306)
....++++++.+ .-+++||.+.++... .+......+..++...|+.+..+ +..-....+..++.+| .-.+++
T Consensus 80 ~~~~lv~~~~s~-----I~s~~DLkGK~Igv~-~~s~~~~~l~~~L~~~Gl~~~dv~~v~~~~~~~~~al~~G~vDa~~~ 153 (300)
T TIGR01729 80 KSEALVAREGSG-----IEKPEDLKGKNVAVP-FVSTTHYSLLAALKHWKTDPREVNILNLKPPQIVAAWQRGDIDAAYV 153 (300)
T ss_pred ccceEEecCCCC-----CCChhHcCCCEEEeC-CCCcHHHHHHHHHHHcCCChhheEEEecCcHHHHHHHHcCCcCEEEE
Confidence 234566665543 237899999886654 33344556677888888876432 3323455677778887 223334
Q ss_pred ecceeccc-ccCCceeeecCCC---CccceEEEEEeCCc--cccHHHHHHHHHHhHH
Q psy3760 244 ASIAFDSN-RDKNLRSISASHL---FGTTISRVIIKQGT--YLRSYVYSFIKLLSPK 294 (306)
Q Consensus 244 p~~~~~~~-~~~~l~~~~~~~~---~~~~~~~l~~~~~~--~~~~~~~~~~~~l~~~ 294 (306)
+....... ..+.+..-..... .+. ...++.+++- ..+..+++|++.+.+.
T Consensus 154 ~~p~~~~~~~~g~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~p~~~~~~~~a~~~a 209 (300)
T TIGR01729 154 WPPALSELLKSGKVISDSEQVGAWGAPT-FDGWVVRKDFAEKNPEFVAAFTKVLADA 209 (300)
T ss_pred ecHHHHHHHhcCcEEecchhccccCCCc-eeEEEECHHHHHHCHHHHHHHHHHHHHH
Confidence 44333333 3332221110100 111 1234444331 2467788888777654
No 180
>TIGR01884 cas_HTH CRISPR locus-related DNA-binding protein. 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=97.30 E-value=0.00058 Score=52.59 Aligned_cols=58 Identities=26% Similarity=0.354 Sum_probs=45.7
Q ss_pred chhhHHHHHHHHHhc-CCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEec---CCCccccCHhH
Q psy3760 2 NLHQFRFVREAVRQN-FNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRH---GKRIRGLTKPG 63 (306)
Q Consensus 2 ~~~~l~~f~~v~~~~-~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~---~~~~~~lT~~G 63 (306)
+.++++++..+.+.| .+.+..|+.+++|+||+++.|++||+. | +..|. ++.+ .+|+.|
T Consensus 142 s~~~~~IL~~l~~~g~~s~~eia~~l~is~stv~r~L~~Le~~-G--lI~r~~~r~~~~-~lT~~G 203 (203)
T TIGR01884 142 SREELKVLEVLKAEGEKSVKNIAKKLGKSLSTISRHLRELEKK-G--LVEQKGRKGKRY-SLTKLG 203 (203)
T ss_pred CHHHHHHHHHHHHcCCcCHHHHHHHHCcCHHHHHHHHHHHHHC-C--CEEEEcCCccEE-EeCCCC
Confidence 456778888888744 278999999999999999999999976 4 44444 3555 799876
No 181
>PF01022 HTH_5: Bacterial regulatory protein, arsR family; InterPro: IPR001845 Bacterial transcription regulatory proteins that bind DNA via a helix-turn-helix (HTH) motif can be grouped into families on the basis of sequence similarities. One such group, termed arsR, includes several proteins that appear to dissociate from DNA in the presence of metal ions: arsR, which functions as a transcriptional repressor of an arsenic resistance operon; smtB from Synechococcus sp. (strain PCC 7942), which acts as a transcriptional repressor of the smtA gene that codes for a metallothionein; cadC, a protein required for cadmium-resistance; and hypothetical protein yqcJ from Bacillus subtilis. The HTH motif is thought to be located in the central part of these proteins []. The motif is characterised by a number of well-conserved residues: at its N-terminal extremity is a cysteine residue; a second Cys is found in arsR and cadC, but not in smtA; and at the C terminus lie one or two histidines. These residues may be involved in metal-binding (Zn in smtB; metal-oxyanions such as arsenite, antimonite and arsenate for arsR; and cadmium for cadC) []. It is believed that binding of a metal ion could induce a conformational change that would prevent the protein from binding DNA []. The crystal structure of the cyanobacterial smtB shows a fold of five alpha-helices (H) and a pair of antiparallel beta-strands (B) in the topology H1-H2-H3-H4-B1-B2-H5. Helices 3 and 4 comprise the helix-turn-helix motif and the beta-sheet is called the wing as in other wHTH, such as the dtxR-type or the merR-type. Helix 4 is termed the recognition helix, like in other HTHs where it binds the DNA major groove. Most arsR/smtB-like metalloregulators form homodimers []. The dimer interface is formed by helix 5 and an N-terminal part []. Two distinct metal-binding sites have been identified. The first site comprises cysteine thiolates located in the HTH in helix 3 and for some cases in the N terminus, called the alpha3(N) site []. The second metal-binding site is located in helix 5 (and C terminus) and is called the alpha5(C) site. The alpha3N site binds large thiophilic, toxic metals including Cd, Pb, and Bi, as in S. aureus cadC. ArsR lacks the N-terminal arm and its alpha3 site coordinates smaller thiophilic ions like As and Sb. The alpha5 site contains carboxylate and imidazole ligands and interacts preferentially with biologically required metal ions including Zn, Co, and Ni. ArsR-type metalloregulators contain one of these sites, both, or other potential metal-binding sites [, ]. Binding of metal ions to these sites leads to allosteric changes that can derepress the operator/promotor DNA. The metal-inducible operons contain one or two imperfect 12-2-12 inverted repeats, which can be recognised by multimeric arsR-type metalloregulators. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3CUO_A 1U2W_C 3F72_C 3F6V_A 3JTH_B 2P4W_B 1KU9_B 2LKP_B 1SMT_A 1R22_B ....
Probab=97.30 E-value=0.00041 Score=39.34 Aligned_cols=40 Identities=25% Similarity=0.309 Sum_probs=32.1
Q ss_pred hhHHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHH
Q psy3760 4 HQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEE 43 (306)
Q Consensus 4 ~~l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~ 43 (306)
..++++..+.+...++..-|+.+++|||++|++++.|++.
T Consensus 3 ~R~~Il~~L~~~~~~~~el~~~l~~s~~~vs~hL~~L~~~ 42 (47)
T PF01022_consen 3 TRLRILKLLSEGPLTVSELAEELGLSQSTVSHHLKKLREA 42 (47)
T ss_dssp HHHHHHHHHTTSSEEHHHHHHHHTS-HHHHHHHHHHHHHT
T ss_pred HHHHHHHHHHhCCCchhhHHHhccccchHHHHHHHHHHHC
Confidence 4566666666655588999999999999999999999873
No 182
>PF12802 MarR_2: MarR family; PDB: 3ECO_B 2QWW_B 3KP6_B 3KP4_B 3KP2_A 3KP5_A 3KP3_B 3KP7_A 3NQO_B 3K0L_B ....
Probab=97.29 E-value=0.00069 Score=41.06 Aligned_cols=43 Identities=28% Similarity=0.321 Sum_probs=37.4
Q ss_pred CchhhHHHHHHHHHhcC---CHHHHHHHhCCCchHHHHHHHHHHHH
Q psy3760 1 MNLHQFRFVREAVRQNF---NLTEAAKALYTSQPGVSKAIIELEEE 43 (306)
Q Consensus 1 m~~~~l~~f~~v~~~~~---s~~~aA~~l~isq~~~s~~i~~LE~~ 43 (306)
|+..++.++..+.+.+. +.+.-|+.+++++|++|+.|++||+.
T Consensus 3 lt~~q~~vL~~l~~~~~~~~t~~~la~~l~~~~~~vs~~v~~L~~~ 48 (62)
T PF12802_consen 3 LTPSQFRVLMALARHPGEELTQSELAERLGISKSTVSRIVKRLEKK 48 (62)
T ss_dssp STHHHHHHHHHHHHSTTSGEEHHHHHHHHTS-HHHHHHHHHHHHHT
T ss_pred cCHHHHHHHHHHHHCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence 56778899999999884 68999999999999999999999974
No 183
>PF13463 HTH_27: Winged helix DNA-binding domain; PDB: 3GFL_A 2YR2_B 3GFM_A 3GFJ_A 3GF2_A 3GEZ_A 2GXG_A 3GFI_A 2EB7_A.
Probab=97.28 E-value=0.00057 Score=42.32 Aligned_cols=60 Identities=25% Similarity=0.257 Sum_probs=40.1
Q ss_pred chhhHHHHHHHH---HhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEec---CC-CccccCHhH
Q psy3760 2 NLHQFRFVREAV---RQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRH---GK-RIRGLTKPG 63 (306)
Q Consensus 2 ~~~~l~~f~~v~---~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~---~~-~~~~lT~~G 63 (306)
+..++.++..+. +.- +.+.-|+.++++++++|+.|++|++. |.---.++ ++ ..++||++|
T Consensus 2 t~~q~~vL~~l~~~~~~~-t~~~l~~~~~~~~~~vs~~i~~L~~~-glv~~~~~~~d~R~~~~~LT~~G 68 (68)
T PF13463_consen 2 TRPQWQVLRALAHSDGPM-TQSDLAERLGISKSTVSRIIKKLEEK-GLVEKERDPHDKRSKRYRLTPAG 68 (68)
T ss_dssp -HHHHHHHHHHT--TS-B-EHHHHHHHTT--HHHHHHHHHHHHHT-TSEEEEEESSCTTSEEEEE-HHH
T ss_pred CHHHHHHHHHHHccCCCc-CHHHHHHHHCcCHHHHHHHHHHHHHC-CCEEecCCCCcCCeeEEEeCCCC
Confidence 456777888887 444 88999999999999999999999986 33322222 23 223899998
No 184
>PF12974 Phosphonate-bd: ABC transporter, phosphonate, periplasmic substrate-binding protein ; PDB: 3N5L_B 3QUJ_C 3P7I_A 3QK6_A 3S4U_A.
Probab=97.27 E-value=0.0087 Score=47.63 Aligned_cols=177 Identities=17% Similarity=0.155 Sum_probs=101.2
Q ss_pred HHHHHHHHHhCCCcEEEEEeC-ChhHHHHHHHcCCeeEEEEccccC----CCCCceee--ccc-----cceEEEEecCCC
Q psy3760 109 PKIIKEFTIQFPKVKLSLLQG-NPKQITEMIRNDQADIAIVTEILS----PSDKLISI--PCY-----QWEYVIIVPLDH 176 (306)
Q Consensus 109 ~~~l~~~~~~~p~~~i~~~~~-~~~~~~~~l~~~~~Di~i~~~~~~----~~~~~~~~--~l~-----~~~~~~v~~~~~ 176 (306)
.++...+.+.. ++.+++... +..+..+.+.+|++|+++...... ...++... ... ....+++++++.
T Consensus 17 ~~l~~~L~~~~-g~~v~~~~~~~~~~~~~~l~~g~~D~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~~~~ivv~~ds 95 (243)
T PF12974_consen 17 APLADYLSKQL-GVPVELVPADDYAEFIEALRSGEIDLAFMGPLPYVQARQRAGVEPLATPVGPDGSPSYRSVIVVRADS 95 (243)
T ss_dssp HHHHHHHHHHH-TSEEEEE--SSHHHHHHHHHTTS-SEEE--HHHHHHHHHHSSEEEEEEEEETTT-SCEEEEEEEETTS
T ss_pred HHHHHHHHHHh-CCCEEEEEcCCHHHHHHHHHcCCccEEEECcHHHHHHhhcCcEEEEEEecccCCCcceeEEEEEECCC
Confidence 34555555544 788888886 468899999999999999851100 01122211 111 346788888887
Q ss_pred CCCCCCCcChhhhcCCCeEeecCCCCc-HHHHHHHH-HhCCCce----eEEEEecCHHHHHHHHHhc-cceeeeecceec
Q psy3760 177 PLLLLNSISLKEISNYPLITYDLSFSG-RIKLDREF-SLQKLTP----YIVLETINSDIIKTYVELR-MGIGIIASIAFD 249 (306)
Q Consensus 177 ~l~~~~~i~~~dl~~~~~i~~~~~~~~-~~~~~~~~-~~~~~~~----~~~~~~~~~~~~~~~v~~g-~gi~~~p~~~~~ 249 (306)
+. -+++||.+..+....+.+.. .-.-...+ ++.|+.+ ..+ .+.+...++.++.+| .-++.++.....
T Consensus 96 ~i-----~~l~dL~Gk~v~~~~~~s~sg~l~~~~~L~~~~Gl~~~~~~~~~-~~~~~~~~~~~l~~G~~Da~~~~~~~~~ 169 (243)
T PF12974_consen 96 PI-----TSLADLKGKRVAFPDPSSTSGYLIPRYELLREAGLDPGDDFKQV-FVGSHDAVLEALLNGKADAAAIPSDAFE 169 (243)
T ss_dssp S-------SHHHHGGSEEEEE-TT-TTTTHHHHHHTCCCCT--HHHHSSEE-EEE-HHHHHHHHHTTSSSEEEEEHHHHH
T ss_pred CC-----CChhhcCCCEEEEecCCccHHHHHHHHHHHHHcCCChhHceeEE-EeCCHHHHHHHHHcCCccEEEEechhHH
Confidence 52 37999999999988776543 23344556 6788874 445 777999999999998 556667776665
Q ss_pred cc-c-----cCCceeeecCCCCccceEEEEEeCCccccHHHHHHHHHHhHHh
Q psy3760 250 SN-R-----DKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLLSPKL 295 (306)
Q Consensus 250 ~~-~-----~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~ 295 (306)
.. . ..+++.+--..+.+ ...++.+++- .....+++.+.+.+.-
T Consensus 170 ~~~~~~~~~~~~~rvl~~s~~~p--~~~~~~~~~~-~~~~~~~l~~al~~~~ 218 (243)
T PF12974_consen 170 RLEAEGPDIPSQLRVLWTSPPYP--NWPLVASPDL-PPELRQRLRDALLSLS 218 (243)
T ss_dssp HHHHH-HHHHTTEEEEEEEEEEE----EEEEETTS--HHHHHHHHHHHHHTT
T ss_pred HHHHccCcccccEEEEEEeCCCC--CcEEEEeCCC-CHHHHHHHHHHHHcCC
Confidence 54 2 23566665443222 2234445553 2344556666665543
No 185
>PF12840 HTH_20: Helix-turn-helix domain; PDB: 1ULY_A 2CWE_A 1Y0U_B 2QUF_B 2QLZ_C 2OQG_B 2ZKZ_C 3PQK_A 3PQJ_D 3F6O_B ....
Probab=97.24 E-value=0.0014 Score=39.54 Aligned_cols=49 Identities=29% Similarity=0.302 Sum_probs=36.1
Q ss_pred hhHHHHHHH-HHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecC
Q psy3760 4 HQFRFVREA-VRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHG 53 (306)
Q Consensus 4 ~~l~~f~~v-~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~ 53 (306)
..++++..+ ...+.|++..|+.++++++++|++|+.||+ .|.-=-.|.|
T Consensus 11 ~R~~Il~~L~~~~~~t~~ela~~l~~~~~t~s~hL~~L~~-aGli~~~~~g 60 (61)
T PF12840_consen 11 TRLRILRLLASNGPMTVSELAEELGISQSTVSYHLKKLEE-AGLIEVEREG 60 (61)
T ss_dssp HHHHHHHHHHHCSTBEHHHHHHHHTS-HHHHHHHHHHHHH-TTSEEEEEET
T ss_pred HHHHHHHHHhcCCCCCHHHHHHHHCCCHHHHHHHHHHHHH-CCCeEEeccC
Confidence 345666666 444459999999999999999999999998 5654444443
No 186
>TIGR03414 ABC_choline_bnd choline ABC transporter, periplasmic binding protein. Partial phylogenetic profiling (PubMed:16930487) vs. the genome property of glycine betaine biosynthesis from choline consistently reveals a member of this ABC transporter periplasmic binding protein as the best match, save for the betaine biosynthesis enzymes themselves. Genomes often carry several paralogs, one encoded together with the permease and ATP-binding components and another encoded next to a choline-sulfatase gene, suggesting that different members of this protein family interact with shared components and give some flexibility in substrate. Of two members from Sinorhizobium meliloti 1021, one designated ChoX has been shown experimentally to bind choline (though not various related compounds such as betaine) and to be required for about 60 % of choline uptake. Members of this protein have an invariant Cys residue near the N-terminus and likely are lipoproteins.
Probab=97.22 E-value=0.075 Score=43.48 Aligned_cols=197 Identities=10% Similarity=0.033 Sum_probs=120.4
Q ss_pred CCcEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccCC---------CCCceee-
Q psy3760 92 TGNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSP---------SDKLISI- 161 (306)
Q Consensus 92 ~~~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~---------~~~~~~~- 161 (306)
...|+||....-...++..++..+.+.. +..+++...++..+.+.|.+|++|+....-.+.. ..++...
T Consensus 7 ~~~I~ig~~~w~~~~~~~~i~~~iLE~~-Gy~Ve~~~~~~~~~~~al~~GdiD~~~e~W~p~~~~~~~~~~~~~~l~~lg 85 (290)
T TIGR03414 7 CKTVRFADVGWTDITATTALASVLLEGL-GYQPKVTLLSVPVTYAGLKDGDLDVFLGNWMPAMEPDIKPYLESGSVEVLG 85 (290)
T ss_pred CCeEEEeeCCcchHHHHHHHHHHHHHHc-CCcceeEEccHHHHHHHHHcCCceEeccccCCcCHHHHHhhccCCeEEEec
Confidence 4569999999988889999998888865 7777888888888999999999999886522111 1123321
Q ss_pred c-cccceEEEEecCCCCCCCCCCcChhhhcCC------CeEeecCCCCcHHHHHHHHH--hCCCceeEEEEecCHHHH--
Q psy3760 162 P-CYQWEYVIIVPLDHPLLLLNSISLKEISNY------PLITYDLSFSGRIKLDREFS--LQKLTPYIVLETINSDII-- 230 (306)
Q Consensus 162 ~-l~~~~~~~v~~~~~~l~~~~~i~~~dl~~~------~~i~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~-- 230 (306)
+ .....+.+++|+.-. ...--+++||.++ .++..+++......+.+..+ ..|+. .......+...+
T Consensus 86 ~~~~~~~~g~~Vp~y~a--e~~i~sisDL~~~a~~f~g~~~g~~~g~~~~~~~~~~~~~~~ygL~-~~~~~~~s~~a~~a 162 (290)
T TIGR03414 86 PNLEGAKYTLAVPTYVA--DAGLKSFADIAKFKDKLDGKIYGIEPGNDGNRLIQKMIDKNAFGLG-GFKLVESSEAGMLA 162 (290)
T ss_pred ccCCCceEEEEEChhhh--hcCCCCHHHHhhHHHhcCCEEEcccCChhHHHHHHHHHhhccCCCC-CceEeecCHHHHHH
Confidence 2 234467888887643 2234478888653 23444544443334444555 44554 122222333343
Q ss_pred --HHHHHhccc---eeeeecceecccccCCceeeecCCCC-----ccceEEEEEeCCcc-ccHHHHHHHHHHhHHh
Q psy3760 231 --KTYVELRMG---IGIIASIAFDSNRDKNLRSISASHLF-----GTTISRVIIKQGTY-LRSYVYSFIKLLSPKL 295 (306)
Q Consensus 231 --~~~v~~g~g---i~~~p~~~~~~~~~~~l~~~~~~~~~-----~~~~~~l~~~~~~~-~~~~~~~~~~~l~~~~ 295 (306)
.+.+++|.. .+.-|+++... .+++.+..+... +..+++.+.+++-. ..|.+.+|++-+.-..
T Consensus 163 ~~~~A~~~~e~~v~~~w~P~w~~~~---~dl~~LeD~~~~~g~~~~~~~i~~v~~~~~~~~~P~~~~~L~~~~~~~ 235 (290)
T TIGR03414 163 QVARAVKRKEWVVFLGWEPHPMNTN---FKMTYLTGGDDYFGPNYGGATVYTNTRKGYAAECPNVGKLLTNLTFTL 235 (290)
T ss_pred HHHHHHHCCCCEEEEEecCchhhhc---cceeECCCCccccCCCCCCCeEEEEeccchHHHChHHHHHHHhCCcCH
Confidence 577788844 45567777654 356666553311 12355666666543 3588888887765444
No 187
>COG1654 BirA Biotin operon repressor [Transcription]
Probab=97.17 E-value=0.00087 Score=42.26 Aligned_cols=43 Identities=30% Similarity=0.213 Sum_probs=38.1
Q ss_pred CHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCCccccCHh
Q psy3760 18 NLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKP 62 (306)
Q Consensus 18 s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~~~lT~~ 62 (306)
|-.+-|++||+|..||+++|++|+ +.|++.+.+.++|. +|...
T Consensus 21 SGe~La~~LgiSRtaVwK~Iq~Lr-~~G~~I~s~~~kGY-~L~~~ 63 (79)
T COG1654 21 SGEKLAEELGISRTAVWKHIQQLR-EEGVDIESVRGKGY-LLPQL 63 (79)
T ss_pred cHHHHHHHHCccHHHHHHHHHHHH-HhCCceEecCCCce-eccCc
Confidence 668899999999999999999999 88999999998887 56543
No 188
>TIGR01276 thiB thiamine ABC transporter, periplasmic binding protein. This model finds the thiamine (and thiamine pyrophosphate) ABC transporter periplasmic binding protein ThiB in proteobacteria. Completed genomes having this protein (E. coli, Vibrio cholera, Haemophilus influenzae) also have the permease ThiP, described by TIGRFAMs equivalog model TIGR01253.
Probab=97.08 E-value=0.1 Score=43.23 Aligned_cols=199 Identities=14% Similarity=0.024 Sum_probs=109.0
Q ss_pred CcEEEEecccchhhhh--HHHHHHHHHhCCCcEEEEEeC-ChhHHHHHHHc----CCeeEEEEccccC----CCCC----
Q psy3760 93 GNLTIATTHTQARYAL--PKIIKEFTIQFPKVKLSLLQG-NPKQITEMIRN----DQADIAIVTEILS----PSDK---- 157 (306)
Q Consensus 93 ~~l~I~~~~~~~~~~l--~~~l~~~~~~~p~~~i~~~~~-~~~~~~~~l~~----~~~Di~i~~~~~~----~~~~---- 157 (306)
+.|+|.+-.++...+. +.++..|.+ .+++++++... ++.++...|.. ..+|+++...... ...+
T Consensus 2 ~~l~vy~~~~~~~~~~~~~~~~~~Fe~-~~gi~V~~~~~~s~~~l~~kl~~e~~~~~~DVv~~~~~~~~~~~~~~gll~p 80 (309)
T TIGR01276 2 PVLTVYTYDSFAADWGPGPVVKKAFEA-DCNCELKLVALEDGVSLLNRLRLEGKNSKADVVLGLDNNLLDAASKTGLFAK 80 (309)
T ss_pred CeEEEEEccccccCCCCchHHHHHHHH-HHCCEEEEEecCcHHHHHHHHHHcCCCCCCCEEEecCcHHHHHHHHCCCccc
Confidence 5688887666555444 357788875 46999999986 57778988875 4799998631110 0000
Q ss_pred ----------------ceeeccccceEEEEecCCCCCCCCCCcChhhhcCC----CeEeecCCC-CcHH-HHHHHHHhCC
Q psy3760 158 ----------------LISIPCYQWEYVIIVPLDHPLLLLNSISLKEISNY----PLITYDLSF-SGRI-KLDREFSLQK 215 (306)
Q Consensus 158 ----------------~~~~~l~~~~~~~v~~~~~~l~~~~~i~~~dl~~~----~~i~~~~~~-~~~~-~~~~~~~~~~ 215 (306)
-.+.++....++++.+++.. ...+-+|+||.+- .+.+.++.. .... .+.......|
T Consensus 81 ~~~~~~~~~~~~~~~~~~~~p~~~~~~~i~yn~~~~--~~~P~sw~DL~~~~~~g~i~~~~p~~s~~g~~~~~~~~~~~g 158 (309)
T TIGR01276 81 SGVAADAVNVPGGWNNDTFVPFDYGYFAFVYDKNKL--KNPPQSLKELVESDQNWRVIYQDPRTSTPGLGLLLWMQKVYG 158 (309)
T ss_pred CCCChhhccCCccccCCeEEEEeeEEEEEEECcccc--CCCCCCHHHHhccccCCeEEeeCCCCCcHHHHHHHHHHHHcC
Confidence 12456666678888888764 2345689999772 222323221 2111 1111111111
Q ss_pred ---------CceeEEEEecCHHHHHHHHHhcc-ceeeeecc--eeccc--ccCCceeeecCCCCccceEEEEEeCCcccc
Q psy3760 216 ---------LTPYIVLETINSDIIKTYVELRM-GIGIIASI--AFDSN--RDKNLRSISASHLFGTTISRVIIKQGTYLR 281 (306)
Q Consensus 216 ---------~~~~~~~~~~~~~~~~~~v~~g~-gi~~~p~~--~~~~~--~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~ 281 (306)
+..+......+......++.+|. .+++.... ..... ....+..+.+++........+...++.+..
T Consensus 159 ~~~~~~~~~L~~~~~~~~~~~~~~~~~~~~Ge~~i~i~~~~~~~~~~~~~~~~~~~~~~~~eG~~~~~~~~ai~k~a~n~ 238 (309)
T TIGR01276 159 DDAPQAWQKLAKKTVTVTKGWSEAYGLFLKGESDLVLSYTTSPAYHILEEKKDNYAAANFSEGHYLQVEVAARTAASKQP 238 (309)
T ss_pred ccHHHHHHHHHHcCceeCCChHHHHHHHHcCCcCEEEecCCcHHHHhhcccCcccceEecCCCCEeEEEEEEEeCCCCCH
Confidence 11122223334445667888884 44544432 11111 112233333333333334455557787788
Q ss_pred HHHHHHHHHHhHH
Q psy3760 282 SYVYSFIKLLSPK 294 (306)
Q Consensus 282 ~~~~~~~~~l~~~ 294 (306)
..+++|++++.+.
T Consensus 239 e~A~~Fidflls~ 251 (309)
T TIGR01276 239 ELAQKFLQFLVSP 251 (309)
T ss_pred HHHHHHHHHHcCH
Confidence 9999999998654
No 189
>PRK15437 histidine ABC transporter substrate-binding protein HisJ; Provisional
Probab=97.07 E-value=0.074 Score=42.74 Aligned_cols=205 Identities=8% Similarity=0.036 Sum_probs=115.2
Q ss_pred CCCCcEEEEecccchh-----------hhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccC--CCC
Q psy3760 90 YDTGNLTIATTHTQAR-----------YALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILS--PSD 156 (306)
Q Consensus 90 ~~~~~l~I~~~~~~~~-----------~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~--~~~ 156 (306)
...+.|++|+.+.... .+...++..+.++. ++++++...+...++..+++|++|+++...... ...
T Consensus 23 a~~~~l~v~~~~~~~P~~~~~~~g~~~G~~vdi~~~ia~~l-g~~i~~~~~pw~~~~~~l~~g~~D~~~~~~~~t~eR~~ 101 (259)
T PRK15437 23 AIPQNIRIGTDPTYAPFESKNSQGELVGFDIDLAKELCKRI-NTQCTFVENPLDALIPSLKAKKIDAIMSSLSITEKRQQ 101 (259)
T ss_pred ccCCeEEEEeCCCCCCcceeCCCCCEEeeeHHHHHHHHHHc-CCceEEEeCCHHHHHHHHHCCCCCEEEecCCCCHHHhh
Confidence 3457899998642111 24677888877764 678888888899999999999999887532211 122
Q ss_pred Cc-eeeccccceEEEEecCCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCceeEEEEecCHHHHHHHHH
Q psy3760 157 KL-ISIPCYQWEYVIIVPLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVE 235 (306)
Q Consensus 157 ~~-~~~~l~~~~~~~v~~~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~ 235 (306)
.+ -+.+++.....++++++++.. .+++||.+.+..... +..........+...+ ......++...++.++.
T Consensus 102 ~~~fs~p~~~~~~~~~~~~~~~~~----~~~~dl~g~~Igv~~-g~~~~~~~~~~~~~~~---~~~~~~~~~~~~i~~L~ 173 (259)
T PRK15437 102 EIAFTDKLYAADSRLVVAKNSDIQ----PTVESLKGKRVGVLQ-GTTQETFGNEHWAPKG---IEIVSYQGQDNIYSDLT 173 (259)
T ss_pred hccccchhhcCceEEEEECCCCCC----CChHHhCCCEEEEec-CcHHHHHHHhhccccC---ceEEecCCHHHHHHHHH
Confidence 22 256778888999999887643 267899888754443 3322222222111111 12346678888899999
Q ss_pred hcccee-eeecceecc--ccc---CCceee--ecCC-CCccceEEEEEeCCccccHHHHHHHHHHhHHhhHHHHHhhhc
Q psy3760 236 LRMGIG-IIASIAFDS--NRD---KNLRSI--SASH-LFGTTISRVIIKQGTYLRSYVYSFIKLLSPKLNRKFINKILN 305 (306)
Q Consensus 236 ~g~gi~-~~p~~~~~~--~~~---~~l~~~--~~~~-~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~ 305 (306)
+|..=+ +........ ... ..+... .+.. .....++++..+++ .......|=+.+.+.-+....+++.+
T Consensus 174 ~grvD~~v~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~ia~~~~--~~~l~~~~n~~l~~~~~~G~~~~i~~ 250 (259)
T PRK15437 174 AGRIDAAFQDEVAASEGFLKQPVGKDYKFGGPSVKDEKLFGVGTGMGLRKE--DNELREALNKAFAEMRADGTYEKLAK 250 (259)
T ss_pred cCCccEEEechHHHHHHHHhCCCCCceEEecCccccccccCcceEEEEeCC--CHHHHHHHHHHHHHHHHCCcHHHHHH
Confidence 985544 333322211 111 122221 1221 11122344555543 34455555555555545555666543
No 190
>PRK10141 DNA-binding transcriptional repressor ArsR; Provisional
Probab=97.05 E-value=0.015 Score=40.10 Aligned_cols=64 Identities=20% Similarity=0.200 Sum_probs=46.6
Q ss_pred hhHHHHHHHHHhc-CCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCCcc-ccCHhHHHHHH
Q psy3760 4 HQFRFVREAVRQN-FNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIR-GLTKPGQAILR 68 (306)
Q Consensus 4 ~~l~~f~~v~~~~-~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~~-~lT~~G~~l~~ 68 (306)
..++++..+.+.| .+...-|+.+++||||+|++|+.|++ .|.---+|.|+... ++.+....+..
T Consensus 17 tRl~IL~~L~~~~~~~v~ela~~l~lsqstvS~HL~~L~~-AGLV~~~r~Gr~~~Y~l~~~~~~~~~ 82 (117)
T PRK10141 17 TRLGIVLLLRESGELCVCDLCTALDQSQPKISRHLALLRE-SGLLLDRKQGKWVHYRLSPHIPAWAA 82 (117)
T ss_pred HHHHHHHHHHHcCCcCHHHHHHHHCcCHHHHHHHHHHHHH-CCceEEEEEcCEEEEEECchHHHHHH
Confidence 4567777776532 27899999999999999999999985 56666677766532 67776544333
No 191
>PRK15007 putative ABC transporter arginine-biding protein; Provisional
Probab=97.04 E-value=0.089 Score=41.75 Aligned_cols=199 Identities=6% Similarity=-0.018 Sum_probs=110.7
Q ss_pred CCCCcEEEEecccc-h----------hhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccc--cCCCC
Q psy3760 90 YDTGNLTIATTHTQ-A----------RYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEI--LSPSD 156 (306)
Q Consensus 90 ~~~~~l~I~~~~~~-~----------~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~--~~~~~ 156 (306)
...+.|++|+.... + ..+...++..+.+. -++.+++...+..++.+.+.+|++|+++.... .....
T Consensus 18 ~~~~~l~v~~~~~~~P~~~~~~~g~~~G~~~dl~~~i~~~-lg~~~~~~~~~~~~~~~~l~~g~~D~~~~~~~~~~~r~~ 96 (243)
T PRK15007 18 TAAETIRFATEASYPPFESIDANNQIVGFDVDLAQALCKE-IDATCTFSNQAFDSLIPSLKFRRVEAVMAGMDITPEREK 96 (243)
T ss_pred ccCCcEEEEeCCCCCCceeeCCCCCEEeeeHHHHHHHHHH-hCCcEEEEeCCHHHHhHHHhCCCcCEEEEcCccCHHHhc
Confidence 34578999986321 1 23556777777775 47888888888889999999999998875311 11122
Q ss_pred Cc-eeeccccceEEEEecCCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCceeEEEEecCHHHHHHHHH
Q psy3760 157 KL-ISIPCYQWEYVIIVPLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVE 235 (306)
Q Consensus 157 ~~-~~~~l~~~~~~~v~~~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~ 235 (306)
.+ -+.+++....+++.+.++ .-+++||.+..+.... +.. ..+++.......+ ....++......++.
T Consensus 97 ~~~fs~p~~~~~~~~v~~~~~------~~~~~dL~g~~Igv~~-g~~----~~~~l~~~~~~~~-~~~~~~~~~~~~~L~ 164 (243)
T PRK15007 97 QVLFTTPYYDNSALFVGQQGK------YTSVDQLKGKKVGVQN-GTT----HQKFIMDKHPEIT-TVPYDSYQNAKLDLQ 164 (243)
T ss_pred ccceecCccccceEEEEeCCC------CCCHHHhCCCeEEEec-CcH----HHHHHHHhCCCCe-EEEcCCHHHHHHHHH
Confidence 23 245666666777766553 2468999888775543 322 2234443322222 345678888888999
Q ss_pred hccc-eeeeecceeccc--ccCCceeee--cCC-CCccceEEEEEeCCccccHHHHHHHHHHhHHhhHHHHHhh
Q psy3760 236 LRMG-IGIIASIAFDSN--RDKNLRSIS--ASH-LFGTTISRVIIKQGTYLRSYVYSFIKLLSPKLNRKFINKI 303 (306)
Q Consensus 236 ~g~g-i~~~p~~~~~~~--~~~~l~~~~--~~~-~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~ 303 (306)
+|.. ..+.+......+ ..+++..+. +.. ......+.+..+++. .+....|=+.|.+..+....+++
T Consensus 165 ~grvDa~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~l~~~ln~~l~~l~~~g~~~~i 236 (243)
T PRK15007 165 NGRIDAVFGDTAVVTEWLKDNPKLAAVGDKVTDKDYFGTGLGIAVRQGN--TELQQKLNTALEKVKKDGTYETI 236 (243)
T ss_pred cCCCCEEEeCHHHHHHHHhcCCCceeecCcccccccCCcceEEEEeCCC--HHHHHHHHHHHHHHHhCCcHHHH
Confidence 9954 444444333222 234444332 111 111234556666542 33444444444443333334443
No 192
>PF09048 Cro: Cro; InterPro: IPR000655 Bacteriophage lambda encodes two repressors: the Cro repressor that acts to turn off early gene transcription during the lytic cycle, and the lambda or cI repressor that is required to maintain lysogenic growth. Together the Cro and cI repressors form a helix-turn-helix (HTH) superfamily. The lambda Cro repressor binds to DNA as a highly flexible dimer. The crystal structure of the lambda Cro repressor [] reveals a HTH DNA-binding protein with an alpha/beta fold that differs from other Cro family members, possibly by an evolutionary fold change []. Most Cro proteins, such as Enterobacteria phage P22 Cro and Bacteriophage 434 Cro, have an all-alpha structure that is thought to be ancestral to lambda Cro, where the fourth and fifth helices are replaced by a beta-sheet, possibly as a result of secondary structure switching rather than by nonhomologous replacement []. This entry represents the lambda-type Cro repressor with an alpha/beta topology.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 5CRO_A 2ECS_A 2OVG_A 6CRO_A 1D1L_A 2ORC_A 1D1M_B 3ORC_A 1ORC_A 2A63_A ....
Probab=97.03 E-value=0.00056 Score=39.61 Aligned_cols=28 Identities=36% Similarity=0.484 Sum_probs=21.4
Q ss_pred HHHHHHHhCCCchHHHHHHHHHHHHcCceeEEe
Q psy3760 19 LTEAAKALYTSQPGVSKAIIELEEELSIDIFIR 51 (306)
Q Consensus 19 ~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R 51 (306)
=.+||+.||++|+||||+|+. |-.+|..
T Consensus 15 Q~kaA~~lGV~Q~AIsKAlr~-----gR~I~v~ 42 (59)
T PF09048_consen 15 QAKAARALGVTQSAISKALRA-----GRNIFVT 42 (59)
T ss_dssp HHHHHHHHTS-HHHHHHHHHC-----T-EEEEE
T ss_pred hHHHHHHcCCcHHHHHHHHHc-----CCcEEEE
Confidence 489999999999999999974 5555553
No 193
>COG4742 Predicted transcriptional regulator [Transcription]
Probab=97.03 E-value=0.0084 Score=47.19 Aligned_cols=80 Identities=16% Similarity=0.256 Sum_probs=67.9
Q ss_pred hHHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCCccccCHhHHHHHHHHHHHHHHHHHHHHHH
Q psy3760 5 QFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKPGQAILRSIEIIMQEIEGLKKIG 84 (306)
Q Consensus 5 ~l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~~~lT~~G~~l~~~a~~il~~~~~~~~~~ 84 (306)
.-..++.+.+..+|+..--..|++|.+++..||++|++ .-|+.++++.. +||+-|+.+...++++++.++-+.+..
T Consensus 15 Rk~lLllL~egPkti~EI~~~l~vs~~ai~pqiKkL~~---~~LV~~~~~~Y-~LS~~G~iiv~km~~ll~tl~v~e~n~ 90 (260)
T COG4742 15 RKDLLLLLKEGPKTIEEIKNELNVSSSAILPQIKKLKD---KGLVVQEGDRY-SLSSLGKIIVEKMEPLLDTLEVFEENY 90 (260)
T ss_pred HHHHHHHHHhCCCCHHHHHHHhCCCcHHHHHHHHHHhh---CCCEEecCCEE-EecchHHHHHHHHHHHHHHHHHHHhhh
Confidence 34566777775559999999999999999999999987 56899998887 899999999999999999999888754
Q ss_pred Hhhc
Q psy3760 85 KEFS 88 (306)
Q Consensus 85 ~~~~ 88 (306)
.--.
T Consensus 91 dyW~ 94 (260)
T COG4742 91 DYWS 94 (260)
T ss_pred hHHh
Confidence 4433
No 194
>TIGR03261 phnS2 putative 2-aminoethylphosphonate ABC transporter, periplasmic 2-aminoethylphosphonate-binding protein. 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=97.01 E-value=0.12 Score=43.36 Aligned_cols=203 Identities=13% Similarity=0.098 Sum_probs=110.2
Q ss_pred CCCCcEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHH----cCCeeEEEEccccC----CCCC----
Q psy3760 90 YDTGNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIR----NDQADIAIVTEILS----PSDK---- 157 (306)
Q Consensus 90 ~~~~~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~----~~~~Di~i~~~~~~----~~~~---- 157 (306)
...++|+|.... .......++..|.++||++++++...++.++...+. +..+|+.+...... ...+
T Consensus 19 ~~~~~l~vy~~~--~~~~~~~l~~~Fe~~~pgi~V~~~~~~s~~~~~kl~ae~~~~~~Dvv~~~~~~~~~~~~~~gll~~ 96 (334)
T TIGR03261 19 KANTELTVYTAI--EDELIAKYKDAFEKVNPDIKINWVRDSTGIITAKLLAEKNNPQADVVWGLAASSLALLDKEGMLKP 96 (334)
T ss_pred ccCCeEEEEEec--cHHHHHHHHHHHHHHCCCceEEEEECChHHHHHHHHHHhhCCCCCEEEecCchHHHhhhhcccccc
Confidence 345789988663 356788999999999999999998888878877763 34689986521100 0011
Q ss_pred ------------c-------eeeccccceEEEEecCCCCCCC--CCCcChhhhcCC----CeEeecCCC-Cc-HHHHHHH
Q psy3760 158 ------------L-------ISIPCYQWEYVIIVPLDHPLLL--LNSISLKEISNY----PLITYDLSF-SG-RIKLDRE 210 (306)
Q Consensus 158 ------------~-------~~~~l~~~~~~~v~~~~~~l~~--~~~i~~~dl~~~----~~i~~~~~~-~~-~~~~~~~ 210 (306)
+ ......-...+++.+++..-.. ..+-+++||.+. .+.+.++.. +. ...+..+
T Consensus 97 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~yN~~~~~~~g~~~P~sw~dL~~p~~~g~i~~~dp~~s~~~~~~~~~~ 176 (334)
T TIGR03261 97 YKPKGLDALNPKFRDAKNPPHWVGMDAWMAAICFNTVEAKKKGLPKPTSWEDLTKPEYKGHIVMPNPASSGTGFLDVSAW 176 (334)
T ss_pred CCCcChhhcCHhhhCCCCCCceEeeeeeEEEEEEehHHHHhcCCCCCCChHHhcCHHhcCCEecCCCccchHHHHHHHHH
Confidence 0 0111212244555555431111 235689999763 233333322 21 1111222
Q ss_pred HHhCC----------CceeEEEEecCHHHHHHHHHhcc-ceeeeecceeccc-c-cCCceeeecCCCCccceEEEEEeCC
Q psy3760 211 FSLQK----------LTPYIVLETINSDIIKTYVELRM-GIGIIASIAFDSN-R-DKNLRSISASHLFGTTISRVIIKQG 277 (306)
Q Consensus 211 ~~~~~----------~~~~~~~~~~~~~~~~~~v~~g~-gi~~~p~~~~~~~-~-~~~l~~~~~~~~~~~~~~~l~~~~~ 277 (306)
+...| +.++......+.....+++.+|. .+++...+.+... . ...+..+-..+........+...++
T Consensus 177 ~~~~G~~~~~~~l~~l~~n~~~~~~s~~~~~~~v~~Ge~~i~~~~~~~~~~~~~~g~~v~~~~P~eG~~~~~~~~ai~k~ 256 (334)
T TIGR03261 177 LQMMGEDKGWDYMDKLHKNIAVYTHSGSKPCKLAGMGEFPIGISMAYRALKEKKKGAPIDVVFPKEGLGWDIEATAIIKG 256 (334)
T ss_pred HHHhChHHHHHHHHHHHhccCccCCCChHHHHHHhCCCceEEEEecHHHHHHHhCCCCeEEEecCCCCeeeeeeeEEEcC
Confidence 22222 12344344455566778888884 4444444332222 2 2334443333322222335555677
Q ss_pred ccccHHHHHHHHHHhHH
Q psy3760 278 TYLRSYVYSFIKLLSPK 294 (306)
Q Consensus 278 ~~~~~~~~~~~~~l~~~ 294 (306)
.+....+++|++++.+.
T Consensus 257 a~~~e~A~~fidfllS~ 273 (334)
T TIGR03261 257 SKNNDAAKKLVDWSISD 273 (334)
T ss_pred CCCHHHHHHHHHHHcCH
Confidence 77889999999999654
No 195
>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=96.98 E-value=0.0045 Score=39.10 Aligned_cols=68 Identities=26% Similarity=0.341 Sum_probs=48.4
Q ss_pred hhHHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecC-CCccccCHhHHHHHHHHHHH
Q psy3760 4 HQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHG-KRIRGLTKPGQAILRSIEII 73 (306)
Q Consensus 4 ~~l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~-~~~~~lT~~G~~l~~~a~~i 73 (306)
....++..+.+.+.+.+..|+.++++++++++.++.|++. |.---.+.+ .+..++|+ |..++..++.+
T Consensus 8 ~~~~il~~l~~~~~~~~ei~~~~~i~~~~i~~~l~~L~~~-g~i~~~~~~~~~~~~~~~-g~~~~~~~~~~ 76 (78)
T cd00090 8 TRLRILRLLLEGPLTVSELAERLGLSQSTVSRHLKKLEEA-GLVESRREGRRVYYSLTD-AERLLALLESL 76 (78)
T ss_pred HHHHHHHHHHHCCcCHHHHHHHHCcCHhHHHHHHHHHHHC-CCeEEEEeccEEEEEeCC-chHHHHHHHHh
Confidence 3455666666663489999999999999999999999774 433222222 22237999 99888887654
No 196
>PF03180 Lipoprotein_9: NLPA lipoprotein; InterPro: IPR004872 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 IPR001638 from INTERPRO which are solute binding proteins.; PDB: 4EF2_A 4EF1_B 3GXA_C 3IR1_D 3TQW_A 3K2D_B 3UP9_A 1XS5_A 1P99_A.
Probab=96.97 E-value=0.13 Score=40.62 Aligned_cols=197 Identities=12% Similarity=0.121 Sum_probs=117.3
Q ss_pred EEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeC-ChhHHHHHHHcCCeeEEEEccccC-------CCCCc-eeecccc
Q psy3760 95 LTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQG-NPKQITEMIRNDQADIAIVTEILS-------PSDKL-ISIPCYQ 165 (306)
Q Consensus 95 l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~-~~~~~~~~l~~~~~Di~i~~~~~~-------~~~~~-~~~~l~~ 165 (306)
||||+.+.....++-.+-..+.+. +++++++.. +..+.-..|.+|++|+-+..+... ....+ ...+.+-
T Consensus 1 ikIG~~~~~~~~i~~~v~~~~~~~--Gi~vevv~f~D~~~~N~AL~~G~iDaN~fQh~~yl~~~n~~~~~~L~~v~~~~~ 78 (237)
T PF03180_consen 1 IKIGVTPGPDAEILEAVKEKLKKK--GIDVEVVEFSDYVQPNEALADGEIDANFFQHIPYLEQFNKENGYNLVPVGPTYI 78 (237)
T ss_dssp EEEEEETTCHHHHHHHHHHHHHHT--TEEEEEEEESSTTHHHHHHHTTSSSEEEEEEHHHHHHHHHHHT--EEEEEEEEE
T ss_pred CEEEEeCCCHHHHHHHHHHHHHhc--CCeEEEEEecchhhcChHHHCCCcceeccCCHHHHHHHHHHCCCcEEEecceeE
Confidence 689999876676777444444444 588888774 667889999999999999863321 11122 2333444
Q ss_pred ceEEEEecCCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCc------------------e-eEEEEecC
Q psy3760 166 WEYVIIVPLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLT------------------P-YIVLETIN 226 (306)
Q Consensus 166 ~~~~~v~~~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~------------------~-~~~~~~~~ 226 (306)
.++.++. +. --+++|+.+---|..+.+.....+-...|+..|+- | +..+.--+
T Consensus 79 ~p~glYS-~k-------~~sl~~lp~Ga~VaIpnD~sN~~RaL~lLq~aGLI~Lk~~~~~~~t~~DI~~Npk~l~~~evd 150 (237)
T PF03180_consen 79 EPMGLYS-KK-------YKSLDDLPDGATVAIPNDPSNQARALKLLQEAGLITLKDGVGLTATVDDITENPKNLKFKEVD 150 (237)
T ss_dssp ---EEEE-SS-------SSSGGGS-TTEEEEEESSHHHHHHHHHHHHHTTSEEE-TT-GCC-SGGGEEEETTSEEEEEE-
T ss_pred EeEEEee-cc-------cCchhhcCCCCEEEEeCCccchhHHHHHHHhCCeEEEcCCCCCccChhhhhhcccCceEEEec
Confidence 4555553 23 34888888777777777666666667788888762 1 22233223
Q ss_pred HHHHHHHHHhccceeeeecceeccc--ccCCceeeecCCCCccceEEEEEeCCccccHHHHHHHHHHhHHhhHHHHHh
Q psy3760 227 SDIIKTYVELRMGIGIIASIAFDSN--RDKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLLSPKLNRKFINK 302 (306)
Q Consensus 227 ~~~~~~~v~~g~gi~~~p~~~~~~~--~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~ 302 (306)
...+.+.+..-++..+-+.++...- ....+...+... ...+-..++++.+...+|.++.+++.+++.=-+..+++
T Consensus 151 ~~~l~~~l~dvD~avi~~~~a~~agl~~~~~~~~~e~~~-~~~y~n~lv~r~~~~d~~~ik~l~ea~~s~~v~~~i~~ 227 (237)
T PF03180_consen 151 AAQLPRALDDVDAAVINGNYALDAGLDPKKDLLFEEPDA-DKPYANVLVVREDDKDDPWIKKLVEAYQSPEVKKFIEE 227 (237)
T ss_dssp GGGHHHHTTTSSEEEE-HHHHHHTT--CCCHSSEE-SSS-SCGGEEEEEEEGGGTTCHHHHHHHHHHTSHHHHHHHHH
T ss_pred HhhHHhhcccCCEEEecHhHHHHcCcCcccceeeeeccc-CcceeEEEEEECCccCCHHHHHHHHHHCCHHHHHHHHH
Confidence 4455555555455554455554332 222233333222 34567788889988899999999999886544444443
No 197
>PF14947 HTH_45: Winged helix-turn-helix; PDB: 1XSX_B 1R7J_A.
Probab=96.92 E-value=0.0055 Score=38.89 Aligned_cols=64 Identities=19% Similarity=0.253 Sum_probs=46.3
Q ss_pred HHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCCccccCHhHHHHHHHHHHHHHH
Q psy3760 9 VREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKPGQAILRSIEIIMQE 76 (306)
Q Consensus 9 f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~~~lT~~G~~l~~~a~~il~~ 76 (306)
+..+.+.+.+++.-+...|++.+++.+-|..|++. -|..+.++.. .+|+.|..+++..+.+.+-
T Consensus 12 L~~l~~~~~~~t~i~~~~~L~~~~~~~yL~~L~~~---gLI~~~~~~Y-~lTekG~~~l~~l~~~~~~ 75 (77)
T PF14947_consen 12 LKILSKGGAKKTEIMYKANLNYSTLKKYLKELEEK---GLIKKKDGKY-RLTEKGKEFLEELEELIEL 75 (77)
T ss_dssp HHHH-TT-B-HHHHHTTST--HHHHHHHHHHHHHT---TSEEEETTEE-EE-HHHHHHHHHHHHHHHH
T ss_pred HHHHHcCCCCHHHHHHHhCcCHHHHHHHHHHHHHC---cCeeCCCCEE-EECccHHHHHHHHHHHHHH
Confidence 33342344499999999999999999999999974 3457766776 8999999999988877654
No 198
>PF13404 HTH_AsnC-type: AsnC-type helix-turn-helix domain; PDB: 2ZNY_E 2ZNZ_G 1RI7_A 2CYY_A 2E1C_A 2VC1_B 2QZ8_A 2W29_C 2IVM_B 2VBX_B ....
Probab=96.91 E-value=0.0039 Score=34.17 Aligned_cols=24 Identities=33% Similarity=0.339 Sum_probs=21.4
Q ss_pred CHHHHHHHhCCCchHHHHHHHHHH
Q psy3760 18 NLTEAAKALYTSQPGVSKAIIELE 41 (306)
Q Consensus 18 s~~~aA~~l~isq~~~s~~i~~LE 41 (306)
|+.+-|+.+|+|.+++.++|++||
T Consensus 19 s~~~la~~lglS~~~v~~Ri~rL~ 42 (42)
T PF13404_consen 19 SYAELAEELGLSESTVRRRIRRLE 42 (42)
T ss_dssp -HHHHHHHHTS-HHHHHHHHHHHH
T ss_pred cHHHHHHHHCcCHHHHHHHHHHhC
Confidence 899999999999999999999997
No 199
>PF09084 NMT1: NMT1/THI5 like; InterPro: IPR015168 This entry is found in the NMT1 and THI5 proteins. These proteins are proposed to be required for the biosynthesis of the pyrimidine moiety of thiamine [, , ]. They are regulated by thiamine []. ; PDB: 2X26_A 3E4R_A 3KSJ_A 3KSX_A 3UIF_A 4DDD_A 1US4_A 1US5_A 3IX1_B 2X7P_A ....
Probab=96.89 E-value=0.056 Score=42.02 Aligned_cols=183 Identities=11% Similarity=0.028 Sum_probs=105.1
Q ss_pred hhhhHHHHHHHHHhCCCcEEEEEeC-ChhHHHHHHHcCCeeEEEEccccC---CCCCceee----ccccceEEEEecCCC
Q psy3760 105 RYALPKIIKEFTIQFPKVKLSLLQG-NPKQITEMIRNDQADIAIVTEILS---PSDKLISI----PCYQWEYVIIVPLDH 176 (306)
Q Consensus 105 ~~~l~~~l~~~~~~~p~~~i~~~~~-~~~~~~~~l~~~~~Di~i~~~~~~---~~~~~~~~----~l~~~~~~~v~~~~~ 176 (306)
..++..-..-|.+. ++++++... +..+..+.|.+|++|+++...... ...+.... ...+....++++++.
T Consensus 6 p~~vA~~~G~f~~~--gl~ve~~~~~~~~~~~~~l~~G~~D~~~~~~~~~~~~~~~g~~~~~i~~~~~~~~~~l~~~~~s 83 (216)
T PF09084_consen 6 PLYVAQEKGYFKEE--GLDVEIVFFGGGGDVLEALASGKADIAVAGPDAVLFARAKGADIKIIAASYQSSPNALVVRKDS 83 (216)
T ss_dssp HHHHHHHTTHHHHT--TEEEEEEEESSHHHHHHHHHTTSHSEEEEECHHHHHHHHTTSTEEEEEEEEEECCEEEEEETTT
T ss_pred HHHHHHHcCCCccC--eEEEEEEEecChhHHHHHHhcCCceEEeccchHHHHHHhcCCeeEEEEEecCCCceEEEEeccC
Confidence 33444444445555 777777765 557899999999999999862211 11222222 222445677777776
Q ss_pred CCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCceeEE-EEecCHHHHHHHHHhc--ccee-eeecceeccc-
Q psy3760 177 PLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIV-LETINSDIIKTYVELR--MGIG-IIASIAFDSN- 251 (306)
Q Consensus 177 ~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~v~~g--~gi~-~~p~~~~~~~- 251 (306)
. .-+++||.+.++.... +......+..+++..|+.++.+ +...+......++.+| +++. ..|.+.....
T Consensus 84 ~-----i~~~~DLkGK~i~v~~-~s~~~~~~~~~l~~~g~~~~~v~~v~~~~~~~~~al~~g~vDa~~~~~~~~~~~~~~ 157 (216)
T PF09084_consen 84 G-----IKSPADLKGKKIGVSR-GSSSEYFLRALLKKNGIDPDDVKIVNLGPPELAQALLSGQVDAAILWYPPWEPYEIA 157 (216)
T ss_dssp S------SSGGGGTTSEEEEST-TSHHHHHHHHHHHHTTT-GGGSEEEES-HHHHHHHHHTTSSSEEEEEEECTCHHHHH
T ss_pred C-----CCCHHHhCCCEEEEec-CcchhHHHHHHHHHhccccccceeeeeehhhhhhhhhcCCCCEEEEccCChHHHHHH
Confidence 4 3489999998887766 6566678889999999976433 3333355555577777 4333 4444222221
Q ss_pred -ccCCceeeecCCCCc-cc-eEEEEEeCC--ccccHHHHHHHHHHhHHh
Q psy3760 252 -RDKNLRSISASHLFG-TT-ISRVIIKQG--TYLRSYVYSFIKLLSPKL 295 (306)
Q Consensus 252 -~~~~l~~~~~~~~~~-~~-~~~l~~~~~--~~~~~~~~~~~~~l~~~~ 295 (306)
....+.......... .. ...++.+++ ...+..++.|++.+.+..
T Consensus 158 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~pe~~~~f~~a~~~a~ 206 (216)
T PF09084_consen 158 SKGKKLRVLELSDYGPPNYPVSVLVARDEFLEKNPEAVKAFLKAYAKAI 206 (216)
T ss_dssp HCCSCEEEEEGGGCCGGCS-SEEEEEEHHHHHHSHHHHHHHHHHHHHHH
T ss_pred HcCCceeeeeccccCcccccceEEEEchHHHHHCHHHHHHHHHHHHHHH
Confidence 334455566554221 22 222333332 223567888887776653
No 200
>PHA00738 putative HTH transcription regulator
Probab=96.88 E-value=0.0028 Score=42.09 Aligned_cols=58 Identities=10% Similarity=0.118 Sum_probs=39.8
Q ss_pred hhHHHHHHHHHhc-CCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCCcc-ccCHh
Q psy3760 4 HQFRFVREAVRQN-FNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIR-GLTKP 62 (306)
Q Consensus 4 ~~l~~f~~v~~~~-~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~~-~lT~~ 62 (306)
..++++..+.+.+ .+...-|+.+++|||+||++|+.|++ .|.---.|.|+.+. ++.+.
T Consensus 13 tRr~IL~lL~~~e~~~V~eLae~l~lSQptVS~HLKvLre-AGLV~srK~Gr~vyY~Ln~~ 72 (108)
T PHA00738 13 LRRKILELIAENYILSASLISHTLLLSYTTVLRHLKILNE-QGYIELYKEGRTLYAKIREN 72 (108)
T ss_pred HHHHHHHHHHHcCCccHHHHHHhhCCCHHHHHHHHHHHHH-CCceEEEEECCEEEEEECCC
Confidence 3456666666631 27889999999999999999999986 34444444444432 44444
No 201
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=96.85 E-value=0.0042 Score=36.76 Aligned_cols=45 Identities=16% Similarity=0.121 Sum_probs=36.9
Q ss_pred chhhHHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCce
Q psy3760 2 NLHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSID 47 (306)
Q Consensus 2 ~~~~l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~ 47 (306)
+-++.+++..+.+.. |....|+.+++|.+++.+.++++.+.||++
T Consensus 5 ~~~e~~i~~~~~~g~-s~~eia~~l~is~~tv~~~~~~~~~kl~~~ 49 (58)
T smart00421 5 TPREREVLRLLAEGL-TNKEIAERLGISEKTVKTHLSNIMRKLGVR 49 (58)
T ss_pred CHHHHHHHHHHHcCC-CHHHHHHHHCCCHHHHHHHHHHHHHHHCCC
Confidence 345566666655555 999999999999999999999999999864
No 202
>PF04967 HTH_10: HTH DNA binding domain; InterPro: IPR007050 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. This entry represents the HTH DNA binding domain found in Halobacterium salinarium (Halobacterium halobium) and described as a putative bacterio-opsin activator.
Probab=96.85 E-value=0.0058 Score=35.29 Aligned_cols=43 Identities=26% Similarity=0.247 Sum_probs=35.0
Q ss_pred chhhHHHHHHHHHhc-------CCHHHHHHHhCCCchHHHHHHHHHHHHc
Q psy3760 2 NLHQFRFVREAVRQN-------FNLTEAAKALYTSQPGVSKAIIELEEEL 44 (306)
Q Consensus 2 ~~~~l~~f~~v~~~~-------~s~~~aA~~l~isq~~~s~~i~~LE~~l 44 (306)
+-+|.+++....+.| -|+..-|+.||||.||+|.+|++-|+.+
T Consensus 2 T~~Q~e~L~~A~~~GYfd~PR~~tl~elA~~lgis~st~~~~LRrae~kl 51 (53)
T PF04967_consen 2 TDRQREILKAAYELGYFDVPRRITLEELAEELGISKSTVSEHLRRAERKL 51 (53)
T ss_pred CHHHHHHHHHHHHcCCCCCCCcCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Confidence 346777777777765 2678999999999999999999998764
No 203
>TIGR03870 ABC_MoxJ methanol oxidation system protein MoxJ. This predicted periplasmic protein, called MoxJ or MxaJ, is required for methanol oxidation in Methylobacterium extorquens. Two differing lines of evidence suggest two different roles. Forming one view, homology suggests it is the substrate-binding protein of an ABC transporter associated with methanol oxidation. The gene, furthermore, is found regular in genomes with, and only two or three genes away from, a corresponding permease and ATP-binding cassette gene pair. The other view is that this protein is an accessory factor or additional subunit of methanol dehydrogenase itself. Mutational studies show a dependence on this protein for expression of the PQQ-dependent, two-subunit methanol dehydrogenase (MxaF and MxaI) in Methylobacterium extorquens, as if it is a chaperone for enzyme assembly or a third subunit. A homologous N-terminal sequence was found in Paracoccus denitrificans as a 32Kd third subunit. This protein may, in
Probab=96.80 E-value=0.19 Score=40.09 Aligned_cols=130 Identities=12% Similarity=0.093 Sum_probs=74.9
Q ss_pred hhHHHHHHHHHhCCCcEEEEEeCChhHHH---HHHHcCCeeEEEEccccCCCCCc-eeeccccceEEEEecCCCCCCCCC
Q psy3760 107 ALPKIIKEFTIQFPKVKLSLLQGNPKQIT---EMIRNDQADIAIVTEILSPSDKL-ISIPCYQWEYVIIVPLDHPLLLLN 182 (306)
Q Consensus 107 ~l~~~l~~~~~~~p~~~i~~~~~~~~~~~---~~l~~~~~Di~i~~~~~~~~~~~-~~~~l~~~~~~~v~~~~~~l~~~~ 182 (306)
+-..++..+.++. ++++++.....+.+. ..|.+|++|+++.. . ..+.++ -+.|......+++++++....
T Consensus 21 fdvdl~~~ia~~l-g~~~~~~~~~~~~~~~~~~~L~~g~~Dii~~~-~-~t~~r~~fS~PY~~~~~~~v~~k~~~~~--- 94 (246)
T TIGR03870 21 FENKIAAALAAAM-GRKVVFVWLAKPAIYLVRDGLDKKLCDVVLGL-D-TGDPRVLTTKPYYRSSYVFLTRKDRNLD--- 94 (246)
T ss_pred chHHHHHHHHHHh-CCCeEEEEeccchhhHHHHHHhcCCccEEEeC-C-CChHHHhcccCcEEeeeEEEEeCCCCCC---
Confidence 4456777777774 788888877755544 69999999998853 2 222333 367888888999999886321
Q ss_pred CcCh--hhhcCC-CeEeecCCCCcHHHHHHHHHh-CC---------Cc-eeEEEEecCHHHHHHHHHhccceeee
Q psy3760 183 SISL--KEISNY-PLITYDLSFSGRIKLDREFSL-QK---------LT-PYIVLETINSDIIKTYVELRMGIGII 243 (306)
Q Consensus 183 ~i~~--~dl~~~-~~i~~~~~~~~~~~~~~~~~~-~~---------~~-~~~~~~~~~~~~~~~~v~~g~gi~~~ 243 (306)
.-++ .+|.+. +.... .+......+.+.... .. .. +...+...+...+.+++.+|..=+.+
T Consensus 95 ~~~~~d~~L~g~~~vgv~-~gs~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~aL~~GrvDa~i 168 (246)
T TIGR03870 95 IKSWNDPRLKKVSKIGVI-FGSPAETMLKQIGRYEDNFAYLYSLVNFKSPRNQYTQIDPRKLVSEVATGKADLAV 168 (246)
T ss_pred CCCccchhhccCceEEEe-cCChHHHHHHhcCccccccccccccccccCcccccccCCHHHHHHHHHcCCCCEEE
Confidence 1233 357776 54444 343332222221100 00 00 11112222457788999999654443
No 204
>PF04069 OpuAC: Substrate binding domain of ABC-type glycine betaine transport system; InterPro: IPR007210 This domain is a 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. It is often found in integral membrane proteins or proteins 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 []. 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. This domain is found also in proteins binding l-proline (ProX), histidine (HisX) and taurine (TauA).; GO: 0005215 transporter activity, 0005488 binding, 0006810 transport; PDB: 3R6U_A 3TMG_C 3MAM_A 1SW5_C 1SW4_B 1SW1_A 1SW2_A 3O66_A 1R9Q_A 1R9L_A ....
Probab=96.79 E-value=0.018 Score=46.28 Aligned_cols=192 Identities=9% Similarity=-0.016 Sum_probs=123.8
Q ss_pred cEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCCh-hHHHHHHHcCCeeEEE-EccccCCC----------CCce--
Q psy3760 94 NLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNP-KQITEMIRNDQADIAI-VTEILSPS----------DKLI-- 159 (306)
Q Consensus 94 ~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~-~~~~~~l~~~~~Di~i-~~~~~~~~----------~~~~-- 159 (306)
+|+||........++..++..+.+.. +..+++...+. ..+.+.|.+|++|+.. ...+ ... ..+.
T Consensus 2 ~I~ig~~~w~~~~~~a~i~~~~Le~~-G~~v~~~~~~~~~~~~~al~~G~iD~~~~~w~~-~~~~~~~~~~~~~~~~~~l 79 (257)
T PF04069_consen 2 PIVIGSKNWTESQILAEIYAQLLEAA-GYVVEVVNLGSTPVIFAALASGDIDIYPEEWTP-TTYEAYKKALEEKLGVVWL 79 (257)
T ss_dssp EEEEEEESSHHHHHHHHHHHHHHHHT-TEEEEEEEESSHHHHHHHHHTTSSSEEEEEEET-TTHHHHHHHHHHHHEEEEE
T ss_pred eEEEecCCCcHHHHHHHHHHHHHHHC-CCeEEEecCCchHHHHHHHHCCCCeEEhhhcCc-hhHHHHHHhhhhcCccccC
Confidence 68999999999999999999999998 88999998887 8899999999999999 4322 211 1222
Q ss_pred eeccccceEEEEecCCCCCCCCCCcChhhhcCCC----------eEeecCCCCcHHHHHHHHHhCCCceeEEEEecCHH-
Q psy3760 160 SIPCYQWEYVIIVPLDHPLLLLNSISLKEISNYP----------LITYDLSFSGRIKLDREFSLQKLTPYIVLETINSD- 228 (306)
Q Consensus 160 ~~~l~~~~~~~v~~~~~~l~~~~~i~~~dl~~~~----------~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~- 228 (306)
....+.....+++++.-... ..--+++||.++. ++..+++..........++..|+. +......+..
T Consensus 80 ~~~~~~~~~g~~Vp~~~ae~-~~i~si~dL~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~ygl~-~~~~~~~s~~~ 157 (257)
T PF04069_consen 80 GPLGAGNTYGWAVPKYVAEK-PGIKSISDLAKPAEDLEFGGKGEFYGRPDGWGCTTFNEQLLKAYGLD-NFELFPGSEAA 157 (257)
T ss_dssp EEEEEEEEEEEEEEHHHHHH-HT-SBGGGGGTCGGGCEEEETTEEECSSTTHHHHHHHHHHHHHCTCT-TSEEESSEHHH
T ss_pred CccccCCEEEEEEecccccc-cCcccHHHHhhcccccccCCCCceeeCCCCcchhhHHHHHHHhcCCC-cceecccccch
Confidence 22344567788888764211 1234778886543 455555554556667888888984 3333223333
Q ss_pred ---HHHHHHHhccce---eeeecceecccccCCceeeecCCC-Ccc-ceEEEEEeCCcc-ccHHHHHHHHHHh
Q psy3760 229 ---IIKTYVELRMGI---GIIASIAFDSNRDKNLRSISASHL-FGT-TISRVIIKQGTY-LRSYVYSFIKLLS 292 (306)
Q Consensus 229 ---~~~~~v~~g~gi---~~~p~~~~~~~~~~~l~~~~~~~~-~~~-~~~~l~~~~~~~-~~~~~~~~~~~l~ 292 (306)
.+.+.+.+|..+ +.-|+++... .+++.+.-+.. .+. ..+..+++++-. ..|.+..+++.+.
T Consensus 158 ~~~~~~~A~~~~~~~v~~~w~p~~~~~~---~~l~~L~D~~~~~~~~~~~~~~~r~~~~~~~P~~~~~l~~~~ 227 (257)
T PF04069_consen 158 MDAALYAAYKRGEPIVFYAWSPDWMIAK---YDLVVLEDPKGFFPPAYNVVPVVRKGFAEDHPEAAEFLNRFS 227 (257)
T ss_dssp HHHHHHHHHHTTSSSEEEEETSSTHHHH---STEEE-BTTTCTSSSSEEEEEEEEHHHHHHSHHHHHHHHCTT
T ss_pred hHHHHHHHHHcCCCEEEEEecCChhhcc---CCeEEeecCCCCCCCCCEEEEEecHHHHhhChHHHHHHHhcC
Confidence 556666777443 3445555443 46777775542 222 566666665432 3566777777765
No 205
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=96.74 E-value=0.02 Score=37.67 Aligned_cols=63 Identities=17% Similarity=0.145 Sum_probs=43.6
Q ss_pred hHHHHHHHHHh--cCCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEec--CCCccccCHhHHHHHHHHH
Q psy3760 5 QFRFVREAVRQ--NFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRH--GKRIRGLTKPGQAILRSIE 71 (306)
Q Consensus 5 ~l~~f~~v~~~--~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~--~~~~~~lT~~G~~l~~~a~ 71 (306)
.+.++..+.+. +.|++..|+.++++++++++.|+.|++. | ++.+. +++. .+++....+-..+.
T Consensus 7 ~~~Il~~l~~~~~~~t~~~ia~~l~i~~~tv~r~l~~L~~~-g--~l~~~~~~~~y-~l~~~~~~~~~~~~ 73 (91)
T smart00346 7 GLAVLRALAEEPGGLTLAELAERLGLSKSTAHRLLNTLQEL-G--YVEQDGQNGRY-RLGPKVLELGQSYL 73 (91)
T ss_pred HHHHHHHHHhCCCCcCHHHHHHHhCCCHHHHHHHHHHHHHC-C--CeeecCCCCce-eecHHHHHHHHHHH
Confidence 34455555543 2489999999999999999999999874 3 34443 4445 68776655554443
No 206
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=96.71 E-value=0.0026 Score=35.38 Aligned_cols=34 Identities=24% Similarity=0.268 Sum_probs=22.7
Q ss_pred HHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHH
Q psy3760 6 FRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIE 39 (306)
Q Consensus 6 l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~ 39 (306)
-.....+.+.|.|+.+-|+.||+|++||++-|++
T Consensus 10 R~~I~~l~~~G~s~~~IA~~lg~s~sTV~relkR 43 (44)
T PF13936_consen 10 RNQIEALLEQGMSIREIAKRLGRSRSTVSRELKR 43 (44)
T ss_dssp --HHHHHHCS---HHHHHHHTT--HHHHHHHHHH
T ss_pred HHHHHHHHHcCCCHHHHHHHHCcCcHHHHHHHhc
Confidence 3344455677889999999999999999999875
No 207
>PRK11480 tauA taurine transporter substrate binding subunit; Provisional
Probab=96.71 E-value=0.12 Score=42.97 Aligned_cols=192 Identities=9% Similarity=0.004 Sum_probs=104.3
Q ss_pred CCCcEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeC-ChhHHHHHHHcCCeeEEEEccccC-----CCCCceee---
Q psy3760 91 DTGNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQG-NPKQITEMIRNDQADIAIVTEILS-----PSDKLISI--- 161 (306)
Q Consensus 91 ~~~~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~-~~~~~~~~l~~~~~Di~i~~~~~~-----~~~~~~~~--- 161 (306)
....||||+..+....++...-..|.++ -++++++... +...+.+.+.+|++|+++...... ....+...
T Consensus 21 ~~~~v~~~y~~~~~~~~vA~~~g~f~~~-~Gl~Ve~~~~~~~~~~~~al~~G~~D~a~~~~~~~~~a~~~g~~~~~v~~~ 99 (320)
T PRK11480 21 QAVNVTVAYQTSAEPAKVAQADNTFAKE-SGATVDWRKFDSGASIVRALASGDVQIGNLGSSPLAVAASQQVPIEVFLLA 99 (320)
T ss_pred CCCeEEEEecCCCcHHHHHHHcCchHHH-cCCeeEEEEeCCHHHHHHHHHCCCCCEECcCchHHHHHHHCCCCeEEEEee
Confidence 4668999998765545555444445343 3667777554 456788999999999997632110 11112211
Q ss_pred ccccceEEEEecCCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCceeE-EEEecCHHHHHHHHHhc--c
Q psy3760 162 PCYQWEYVIIVPLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYI-VLETINSDIIKTYVELR--M 238 (306)
Q Consensus 162 ~l~~~~~~~v~~~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~v~~g--~ 238 (306)
........+++++ ..-+++||.+.++.... +......+..+++..|+.+.. .+.--....+..++.+| +
T Consensus 100 ~~~~~~~~lv~~~-------~I~s~~DLkGK~Iav~~-~s~~~~~l~~~L~~~Gl~~~dv~~v~~~~~~~~~Al~~G~VD 171 (320)
T PRK11480 100 SKLGNSEALVVKK-------TISKPEDLIGKRIAVPF-ISTTHYSLLAALKHWGIKPGQVEIVNLQPPAIIAAWQRGDID 171 (320)
T ss_pred ccCCcceEEEecC-------CCCChHHcCCCEEecCC-CCchHHHHHHHHHHcCCCHhheEEEECCcHHHHHHHHcCCcC
Confidence 1111223444432 13478999998877643 334445678889999998743 33333456677778887 4
Q ss_pred ceeeeecceeccc-ccCCceeeecCC-----CCccceEEEEEeCCc--cccHHHHHHHHHHhHHh
Q psy3760 239 GIGIIASIAFDSN-RDKNLRSISASH-----LFGTTISRVIIKQGT--YLRSYVYSFIKLLSPKL 295 (306)
Q Consensus 239 gi~~~p~~~~~~~-~~~~l~~~~~~~-----~~~~~~~~l~~~~~~--~~~~~~~~~~~~l~~~~ 295 (306)
++.+ ........ ..+. .+.-.. ..+.. ..++.+.+. ..+..++.|++.+.+..
T Consensus 172 Aa~~-~~p~~~~~~~~g~--~l~~~~~~~~~~~~~~-~~lv~~~~~i~~~p~~v~~f~~A~~~a~ 232 (320)
T PRK11480 172 GAYV-WAPAVNALEKDGK--VLTDSEQVGQWGAPTL-DVWVVRKDFAEKHPEVVKAFAKSAIDAQ 232 (320)
T ss_pred EEEE-cchHHHHHHhCCe--EEecchhhcccCCCce-EEEEECHHHHHHCHHHHHHHHHHHHHHH
Confidence 4333 33322222 2222 221111 01111 233444321 24678888888776553
No 208
>PF01047 MarR: MarR family; InterPro: IPR000835 The MarR-type HTH domain is a DNA-binding, winged helix-turn-helix (wHTH) domain of about 135 amino acids present in transcription regulators of the MarR/SlyA family, involved in the development of antibiotic resistance. This family of transcription regulators is named after Escherichia coli MarR, a repressor of genes which activate the multiple antibiotic resistance and oxidative stress regulons, and after slyA from Salmonella typhimurium and E. coli, a transcription regulator that is required for virulence and survival in the macrophage environment. Regulators with the MarR-type HTH domain are present in bacteria and archaea and control a variety of biological functions, including resistance to multiple antibiotics, household disinfectants, organic solvents, oxidative stress agents and regulation of the virulence factor synthesis in pathogens of humans and plants. Many of the MarR-like regulators respond to aromatic compounds [, , ]. The crystal structures of MarR, MexR and SlyA have been determined and show a winged HTH DNA-binding core flanked by helices involved in dimerisation. The DNA-binding domains are ascribed to the superfamily of winged helix proteins, containing a three (four)-helix (H) bundle and a three-stranded antiparallel beta-sheet (B) in the topology: H1-(H1')-H2-B1-H3-H4-B2-B3-H5-H6. Helices 3 and 4 comprise the helix-turn-helix motif and the beta-sheet is called the wing. Helix 4 is termed the recognition helix, like in other HTHs where it binds the DNA major groove. The helices 1, 5 and 6 are involved in dimerisation, as most MarR-like transcription regulators form dimers [, ]. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 1JGS_A 2NYX_D 2PEX_B 2PFB_A 3BPX_A 3BPV_A 2BV6_A 3BJA_A 3E6M_B 2ETH_A ....
Probab=96.69 E-value=0.0053 Score=36.68 Aligned_cols=43 Identities=28% Similarity=0.323 Sum_probs=35.8
Q ss_pred CchhhHHHHHHHHHhcC-CHHHHHHHhCCCchHHHHHHHHHHHH
Q psy3760 1 MNLHQFRFVREAVRQNF-NLTEAAKALYTSQPGVSKAIIELEEE 43 (306)
Q Consensus 1 m~~~~l~~f~~v~~~~~-s~~~aA~~l~isq~~~s~~i~~LE~~ 43 (306)
++..++.++..+.+.+. +.+.=|+.+++++|++|+.+++||+.
T Consensus 1 lt~~q~~iL~~l~~~~~~~~~~la~~~~~~~~~~t~~i~~L~~~ 44 (59)
T PF01047_consen 1 LTPSQFRILRILYENGGITQSELAEKLGISRSTVTRIIKRLEKK 44 (59)
T ss_dssp STHHHHHHHHHHHHHSSEEHHHHHHHHTS-HHHHHHHHHHHHHT
T ss_pred CCHHHHHHHHHHHHcCCCCHHHHHHHHCCChhHHHHHHHHHHHC
Confidence 46778888888888872 47788999999999999999999974
No 209
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=96.64 E-value=0.0071 Score=36.75 Aligned_cols=55 Identities=27% Similarity=0.195 Sum_probs=40.2
Q ss_pred HHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCC-CccccCH-hHHHHHHH
Q psy3760 13 VRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGK-RIRGLTK-PGQAILRS 69 (306)
Q Consensus 13 ~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~-~~~~lT~-~G~~l~~~ 69 (306)
.+.. +++..|+.+++|.+++++.|++|++. |.---.+.++ ....+|+ .|..++..
T Consensus 8 ~~~~-~~~~i~~~l~is~~~v~~~l~~L~~~-g~i~~~~~~~~~~~~~~~~~~~~~~~~ 64 (66)
T smart00418 8 EGEL-CVCELAEILGLSQSTVSHHLKKLREA-GLVESRREGKRVYYSLTDEKVADLLEE 64 (66)
T ss_pred cCCc-cHHHHHHHHCCCHHHHHHHHHHHHHC-CCeeeeecCCEEEEEEchHHHHHHHHh
Confidence 5566 99999999999999999999999975 4444333332 2236888 77766654
No 210
>TIGR00971 3a0106s03 sulfate/thiosulfate-binding protein. This model describes binding proteins functionally associated with the sulfate ABC transporter. In the model bacterium E. coli, two different members work with the same transporter; mutation analysis says each enables the uptake of both sulfate and thiosulfate. In many species, a single binding protein is found, and may be referred to in general terms as a sulfate ABC transporter sulfate-binding protein.
Probab=96.63 E-value=0.075 Score=44.06 Aligned_cols=196 Identities=13% Similarity=0.071 Sum_probs=103.4
Q ss_pred cEEEEecccchhhhhHHHHHHHHHh---CCCcE--EEEEeCChhHHHHHHHcC-CeeEEEEccccC----CCCCce----
Q psy3760 94 NLTIATTHTQARYALPKIIKEFTIQ---FPKVK--LSLLQGNPKQITEMIRND-QADIAIVTEILS----PSDKLI---- 159 (306)
Q Consensus 94 ~l~I~~~~~~~~~~l~~~l~~~~~~---~p~~~--i~~~~~~~~~~~~~l~~~-~~Di~i~~~~~~----~~~~~~---- 159 (306)
+|..+.- +.....+..+...|.++ .++++ +++..+++..+..++.+| .+|+.+...... ...++.
T Consensus 12 ~~~~~~~-~~~~~~~~~i~~~fe~~~~~~~g~~v~v~~~~g~Sg~l~~Qi~~Ga~~Dvf~sa~~~~~~~l~~~g~i~~~~ 90 (315)
T TIGR00971 12 QLLNVSY-DPTRELYEQYNKAFEAHWKQDTGDNVVIRQSHGGSGKQATSVINGIEADVVTLALAYDVDAIAERGRIDKDW 90 (315)
T ss_pred EEEeecc-cccHHHHHHHHHHHHHHHHhcCCCceEEEEecCCcHHHHHHHHcCCCcCEEecCCHHHHHHHHHCCCCCcch
Confidence 3443333 34577888899999885 57877 556889999999999996 789999853210 111221
Q ss_pred eeccccc------eEEEEecCCCCCCCCCCcChhhhcC--CCeEeecCCCC-c--HHHHHH---HHHhCC----------
Q psy3760 160 SIPCYQW------EYVIIVPLDHPLLLLNSISLKEISN--YPLITYDLSFS-G--RIKLDR---EFSLQK---------- 215 (306)
Q Consensus 160 ~~~l~~~------~~~~v~~~~~~l~~~~~i~~~dl~~--~~~i~~~~~~~-~--~~~~~~---~~~~~~---------- 215 (306)
...+... .+++++++++|.. .-+|+||.+ ..++..++... . ...+.. +....+
T Consensus 91 ~~~~~~n~~~~~~~lvl~v~k~~~~~---i~sw~dL~~~~~kiai~dp~~sg~~~~~~L~~~g~~~~~~~g~~~~a~~~l 167 (315)
T TIGR00971 91 IKRLPDNSAPYTSTIVFLVRKGNPKQ---IHDWNDLIKPGVSVITPNPKSSGGARWNYLAAWGYALHHNNGDQAKAQQFV 167 (315)
T ss_pred hhhCccCCCccceeEEEEEeCCCCCC---CCCHHHHhCCCcEEEeCChhhHHHHHHHHHHHHHHHhhhcCCCHHHHHHHH
Confidence 1122223 7999999998732 348999853 33343333221 1 111110 111101
Q ss_pred --CceeEEEE-ecCHHHHHHHHHhc-cceeeeecceeccc-c---cCCceeeecCCCCccceEEEEEeC----CccccHH
Q psy3760 216 --LTPYIVLE-TINSDIIKTYVELR-MGIGIIASIAFDSN-R---DKNLRSISASHLFGTTISRVIIKQ----GTYLRSY 283 (306)
Q Consensus 216 --~~~~~~~~-~~~~~~~~~~v~~g-~gi~~~p~~~~~~~-~---~~~l~~~~~~~~~~~~~~~l~~~~----~~~~~~~ 283 (306)
...++... .++...+..++.+| .-++++....+... . ...+..+-..+..+ ..+.+.+-+ .......
T Consensus 168 ~~l~~nv~~~~~~~~~~~~~~v~~Ge~dagivy~sda~~~~~~~~~~~i~iviP~e~~~-i~~~iavv~~~~~~~~~~e~ 246 (315)
T TIGR00971 168 TALLKNVEVLDSGARGATNTFVERGIGDVLIAWENEALLARKELGKDKFEIVTPSESIL-AEPTVSVVDKVVEKKGTKKV 246 (315)
T ss_pred HHHHhhccccCCCchHHHHHHHHcCceeEEEEEcHHHHHHHHhcCCCCeEEEECCCCcc-ccccEEEEEcccCCCCCHHH
Confidence 22344333 33355677778777 33344443332211 1 12454442222222 222233322 1233678
Q ss_pred HHHHHHHHhHH
Q psy3760 284 VYSFIKLLSPK 294 (306)
Q Consensus 284 ~~~~~~~l~~~ 294 (306)
.++|++++.+.
T Consensus 247 A~~FidfLlS~ 257 (315)
T TIGR00971 247 AEAYLKYLYSP 257 (315)
T ss_pred HHHHHHHhcCH
Confidence 99999999654
No 211
>COG2358 Imp TRAP-type uncharacterized transport system, periplasmic component [General function prediction only]
Probab=96.55 E-value=0.028 Score=45.95 Aligned_cols=168 Identities=10% Similarity=0.059 Sum_probs=109.2
Q ss_pred CCCcEEEEecccchhh-hhHHHHHHHHHh-CCCcEEEEEe-CChhHHHHHHHcCCeeEEEEccccC--------------
Q psy3760 91 DTGNLTIATTHTQARY-ALPKIIKEFTIQ-FPKVKLSLLQ-GNPKQITEMIRNDQADIAIVTEILS-------------- 153 (306)
Q Consensus 91 ~~~~l~I~~~~~~~~~-~l~~~l~~~~~~-~p~~~i~~~~-~~~~~~~~~l~~~~~Di~i~~~~~~-------------- 153 (306)
....++||+....+.+ -+..-+.+..+. .+++.+++.. ..+-+-++.+.+|++|++++.....
T Consensus 24 ~~~~itigTG~~~G~YY~ig~~ia~~~~~~~~~i~~~v~~tggSv~Nl~~i~~Ge~d~alvq~d~a~~ay~G~g~f~~~~ 103 (321)
T COG2358 24 EPKFITIGTGSTGGVYYPIGGGLAQLLNKDEKGIECSVVPTGGSVENLKLLASGEADLALVQSDVAYEAYNGTGSFEGKG 103 (321)
T ss_pred CceEEEEeecCCCceeeehHHHHHHHHhccCCCeEEEEeeccchHHHHHhHhcCccchhhhhHHHHHHHHhCcccccccc
Confidence 4557999997765544 334445555454 7888888877 4677789999999999999752110
Q ss_pred CCCCce-eeccccceEEEEecCCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCceeEEEEecCHH--HH
Q psy3760 154 PSDKLI-SIPCYQWEYVIIVPLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSD--II 230 (306)
Q Consensus 154 ~~~~~~-~~~l~~~~~~~v~~~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~ 230 (306)
..++++ .-.++.+.+.++++++.- --++.||.+.++-.-+++++.+-..+..+...|+.+...-..-.+. ..
T Consensus 104 ~~~~lr~v~~lype~~~vv~r~d~~-----Ikti~DL~GKrV~iG~~gSgt~~~a~~il~a~Gi~~~~~~~~~~~~~a~~ 178 (321)
T COG2358 104 KDENLRAVAALYPEPFHVVTRKDAG-----IKTIADLKGKRVAIGPPGSGTEATARQILEALGITYDDYELDLGLGDAES 178 (321)
T ss_pred cccchhhheecccceEEEEEecCCC-----cceehhcCCCEEeecCCCCccHHHHHHHHHHcCCCCcchhhhhhcCchhh
Confidence 112333 456777788888887753 4589999999999999999998889999999999865431111222 22
Q ss_pred HHHHHhc--cceee---eecceeccc-ccCCceeeecCC
Q psy3760 231 KTYVELR--MGIGI---IASIAFDSN-RDKNLRSISASH 263 (306)
Q Consensus 231 ~~~v~~g--~gi~~---~p~~~~~~~-~~~~l~~~~~~~ 263 (306)
.+++.+| ++..+ .|...+... ..-+++.+|+++
T Consensus 179 ~~~l~~g~iDA~~~~~G~p~~ai~el~~~~~i~lv~i~~ 217 (321)
T COG2358 179 ADALKNGTIDAAFYVAGVPNPAISELATTCDIVLVPISG 217 (321)
T ss_pred HHHhhCCcccEEEEecCCCCccHHHHHhhCCeEEEeCCH
Confidence 5556666 33222 334444333 334666666654
No 212
>PF00196 GerE: Bacterial regulatory proteins, luxR family; InterPro: IPR000792 This domain is a DNA-binding, helix-turn-helix (HTH) domain of about 65 amino acids, present in transcription regulators of the LuxR/FixJ family of response regulators. The domain is named after Vibrio fischeri luxR, a transcriptional activator for quorum-sensing control of luminescence. LuxR-type HTH domain proteins occur in a variety of organisms. The DNA-binding HTH domain is usually located in the C-terminal region; the N-terminal region often containing an autoinducer-binding domain or a response regulatory domain. Most luxR-type regulators act as transcription activators, but some can be repressors or have a dual role for different sites. LuxR-type HTH regulators control a wide variety of activities in various biological processes. The luxR-type, DNA-binding HTH domain forms a four-helical bundle structure. The HTH motif comprises the second and third helices, known as the scaffold and recognition helix, respectively. The HTH binds DNA in the major groove, where the N-terminal part of the recognition helix makes most of the DNA contacts. The fourth helix is involved in dimerisation of gerE and traR. Signalling events by one of the four activation mechanisms described below lead to multimerisation of the regulator. The regulators bind DNA as multimers [, , ]. LuxR-type HTH proteins can be activated by one of four different mechanisms: 1) Regulators which belong to a two-component sensory transduction system where the protein is activated by its phosphorylation, generally on an aspartate residue, by a transmembrane kinase [, ]. Some proteins that belong to this category are: Rhizobiaceae fixJ (global regulator inducing expression of nitrogen-fixation genes in microaerobiosis) Escherichia coli and Salmonella typhimurium uhpA (activates hexose phosphate transport gene uhpT) E. coli narL and narP (activate nitrate reductase operon) Enterobacteria rcsB (regulation of exopolysaccharide biosynthesis in enteric and plant pathogenesis) Bordetella pertussis bvgA (virulence factor) Bacillus subtilis coma (involved in expression of late-expressing competence genes) 2) Regulators which are activated, or in very rare cases repressed, when bound to N-acyl homoserine lactones, which are used as quorum sensing molecules in a variety of Gram-negative bacteria []: V. fischeri luxR (activates bioluminescence operon) Agrobacterium tumefaciens traR (regulation of Ti plasmid transfer) Erwinia carotovora carR (control of carbapenem antibiotics biosynthesis) E. carotovora expR (virulence factor for soft rot disease; activates plant tissue macerating enzyme genes) Pseudomonas aeruginosa lasR (activates elastase gene lasB) Erwinia chrysanthemi echR and Erwinia stewartii esaR Pseudomonas chlororaphis phzR (positive regulator of phenazine antibiotic production) Pseudomonas aeruginosa rhlR (activates rhlAB operon and lasB gene) 3) Autonomous effector domain regulators, without a regulatory domain, represented by gerE []. B. subtilis gerE (transcription activator and repressor for the regulation of spore formation) 4) Multiple ligand-binding regulators, exemplified by malT []. E. coli malT (activates maltose operon; MalT binds ATP and maltotriose); GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3SZT_A 3CLO_A 1H0M_A 1L3L_A 3C57_B 1ZLK_B 1ZLJ_H 3C3W_B 1RNL_A 1ZG1_A ....
Probab=96.54 E-value=0.0061 Score=36.28 Aligned_cols=45 Identities=16% Similarity=0.143 Sum_probs=38.7
Q ss_pred chhhHHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCce
Q psy3760 2 NLHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSID 47 (306)
Q Consensus 2 ~~~~l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~ 47 (306)
+-+.++++..+++-. |..+.|+.+++|..||..+++.+-+.||++
T Consensus 5 T~~E~~vl~~l~~G~-~~~eIA~~l~is~~tV~~~~~~i~~Kl~~~ 49 (58)
T PF00196_consen 5 TERELEVLRLLAQGM-SNKEIAEELGISEKTVKSHRRRIMKKLGVK 49 (58)
T ss_dssp -HHHHHHHHHHHTTS--HHHHHHHHTSHHHHHHHHHHHHHHHHT-S
T ss_pred CHHHHHHHHHHHhcC-CcchhHHhcCcchhhHHHHHHHHHHHhCCC
Confidence 446788999999888 999999999999999999999999999864
No 213
>PRK11119 proX glycine betaine transporter periplasmic subunit; Provisional
Probab=96.54 E-value=0.09 Score=43.83 Aligned_cols=202 Identities=6% Similarity=-0.029 Sum_probs=123.3
Q ss_pred cCCCCcEEEEecccchhhhhHHHHHHHHHhCCCcEE-EEEeCChhHHHHHHHcCCeeEEEEccccCCC-------C--Cc
Q psy3760 89 AYDTGNLTIATTHTQARYALPKIIKEFTIQFPKVKL-SLLQGNPKQITEMIRNDQADIAIVTEILSPS-------D--KL 158 (306)
Q Consensus 89 ~~~~~~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i-~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~~-------~--~~ 158 (306)
.+...+|+||....-.......++..+.+.. +.++ ++...+...+.+.|.+|++|+....-.+... . .+
T Consensus 25 ~~~~~~V~~~~~~W~~~~~~t~v~~~iLe~~-GY~V~e~~~~~~~~~~~ala~GdiDv~~~~W~P~~~~~~~~~~~~~~v 103 (331)
T PRK11119 25 PGKGITVQPAQSTIAEETFQTLLVSRALEKL-GYDVNKPKEVDYNVFYTSIANGDATFTAVNWFPLHDDMYEAAGGDKKF 103 (331)
T ss_pred CCCCeEEEEeecCccHHHHHHHHHHHHHHHc-CCceeeecccCcHHHHHHHHcCCCeEehhhcccccHHHHHHhhccCcE
Confidence 3456689999999888888888888888765 8888 7888888899999999999998854221110 1 11
Q ss_pred -eeec-cccceEEEEecCCCCCCCCCCcChhhhcC--CC------------eEeecCCCCcHHHHHHHHHhCCCceeEEE
Q psy3760 159 -ISIP-CYQWEYVIIVPLDHPLLLLNSISLKEISN--YP------------LITYDLSFSGRIKLDREFSLQKLTPYIVL 222 (306)
Q Consensus 159 -~~~~-l~~~~~~~v~~~~~~l~~~~~i~~~dl~~--~~------------~i~~~~~~~~~~~~~~~~~~~~~~~~~~~ 222 (306)
..-. +......+++|+.-.... .--+++||.+ +. ++..+++........+.++..|+.-+...
T Consensus 104 ~~~g~~~~~a~~G~~VP~yv~e~~-gI~Si~DL~~~~~a~~F~~e~~gkg~i~g~~~G~~~~~~~~~~l~~yGL~~~~~~ 182 (331)
T PRK11119 104 YREGVYVGGAAQGYLIDKKTADKY-NITNIAQLKDPKIAKLFDTNGDGKADLTGCNPGWGCEAVINHQLKAYGLEDTVTH 182 (331)
T ss_pred EeccccCCCcceeeeecHHHHHHc-CCCCHHHhCCcHHHHhcCCCCCCCcceECCCCCccccHHHHHHHHhcCCCcceeE
Confidence 1111 122356666665321010 2347888873 12 55566776666666777888888632333
Q ss_pred EecCHH----HHHHHHHhccceee---eecceeccc-ccCCceeeecCCC--------------------CccceEEEEE
Q psy3760 223 ETINSD----IIKTYVELRMGIGI---IASIAFDSN-RDKNLRSISASHL--------------------FGTTISRVII 274 (306)
Q Consensus 223 ~~~~~~----~~~~~v~~g~gi~~---~p~~~~~~~-~~~~l~~~~~~~~--------------------~~~~~~~l~~ 274 (306)
...+.. .+.+.++++..+.+ -|.++...+ ...+++.+..+.. .+...++.+.
T Consensus 183 ~~~S~aam~a~l~~A~~~~epiv~~~W~Phw~~~~~~~~~dl~~L~~P~~~~~~~~~~~~~~~~Dpk~~g~p~~~v~~v~ 262 (331)
T PRK11119 183 NQGNYAALMADTIARYKEGKPVLYYTWTPYWVSDVLKPGKDVVWLQVPFSSLPGDQKNADTKLPNGKNYGFPVNTMHIVA 262 (331)
T ss_pred CCCCHHHHHHHHHHHHHcCCCEEEEEecchhHHhhccCCCCeEEeccCCCCcccccccccCCCCCccccCCCcccEEEEE
Confidence 333333 45566677766555 566665554 3336776632210 1234566666
Q ss_pred eCC-ccccHHHHHHHHHHh
Q psy3760 275 KQG-TYLRSYVYSFIKLLS 292 (306)
Q Consensus 275 ~~~-~~~~~~~~~~~~~l~ 292 (306)
+++ ....|.+..|++-+.
T Consensus 263 r~~f~e~~Pea~~~L~~~~ 281 (331)
T PRK11119 263 NKAFAEKNPAAAKLFEIMK 281 (331)
T ss_pred chHHHHHChHHHHHHHhcC
Confidence 553 334678888876553
No 214
>PRK04172 pheS phenylalanyl-tRNA synthetase subunit alpha; Provisional
Probab=96.54 E-value=0.012 Score=51.83 Aligned_cols=77 Identities=18% Similarity=0.119 Sum_probs=57.7
Q ss_pred CchhhHHHHHHHHHhc-CCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecC---CCccccCHhHHHHHHHHHHHHHH
Q psy3760 1 MNLHQFRFVREAVRQN-FNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHG---KRIRGLTKPGQAILRSIEIIMQE 76 (306)
Q Consensus 1 m~~~~l~~f~~v~~~~-~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~---~~~~~lT~~G~~l~~~a~~il~~ 76 (306)
|+..+..++..+.+.+ .|.+.-|+.++++++++++.|+.||+. | |..|.. +.+ .||+.|+.++....+-...
T Consensus 4 Lt~~e~~vL~~L~~~~~~s~~eLA~~l~l~~~tVt~~i~~Le~k-G--lV~~~~~~~~~i-~LTeeG~~~~~~g~pE~rl 79 (489)
T PRK04172 4 LHPNEKKVLKALKELKEATLEELAEKLGLPPEAVMRAAEWLEEK-G--LVKVEERVEEVY-VLTEEGKKYAEEGLPERRL 79 (489)
T ss_pred CCHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHHHHhC-C--CEEEEeeeEEEE-EECHHHHHHHHhcCHHHHH
Confidence 3556778888887644 146778999999999999999999997 5 444433 345 8999999999877766555
Q ss_pred HHHHH
Q psy3760 77 IEGLK 81 (306)
Q Consensus 77 ~~~~~ 81 (306)
++.+.
T Consensus 80 ~~~l~ 84 (489)
T PRK04172 80 LNALK 84 (489)
T ss_pred HHhhH
Confidence 55444
No 215
>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein.
Probab=96.47 E-value=0.0059 Score=34.61 Aligned_cols=39 Identities=28% Similarity=0.337 Sum_probs=30.9
Q ss_pred CHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCCccccC
Q psy3760 18 NLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLT 60 (306)
Q Consensus 18 s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~~~lT 60 (306)
|....|+.+++|++++++.|++|++ ..++.+.++.+ .+|
T Consensus 10 s~~~la~~l~~s~~tv~~~l~~L~~---~g~l~~~~~~~-~i~ 48 (48)
T smart00419 10 TRQEIAELLGLTRETVSRTLKRLEK---EGLISREGGRI-VIL 48 (48)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHH---CCCEEEeCCEE-EEC
Confidence 6788999999999999999999998 44556665554 343
No 216
>PRK10852 thiosulfate transporter subunit; Provisional
Probab=96.46 E-value=0.26 Score=41.21 Aligned_cols=196 Identities=12% Similarity=0.067 Sum_probs=103.9
Q ss_pred cEEEEecccchhhhhHHHHHHHHH----hCCCcEEE--EEeCChhHHHHHHHcC-CeeEEEEccccC----CCCC-ce--
Q psy3760 94 NLTIATTHTQARYALPKIIKEFTI----QFPKVKLS--LLQGNPKQITEMIRND-QADIAIVTEILS----PSDK-LI-- 159 (306)
Q Consensus 94 ~l~I~~~~~~~~~~l~~~l~~~~~----~~p~~~i~--~~~~~~~~~~~~l~~~-~~Di~i~~~~~~----~~~~-~~-- 159 (306)
.+.+++.. ....+..+...|.+ ++|++.++ ...+++.....++.+| .+|+.+...... ...+ +.
T Consensus 28 ~~~~sy~~--~~e~~~~i~~~F~~~~~~~~~g~~v~i~~s~ggSg~~~~qi~~G~~ADV~~~A~~~~~d~l~~~g~li~~ 105 (338)
T PRK10852 28 LLNSSYDV--SRELFAALNPPFEQQWAKDNPGDKLTIKQSHAGSSKQALAILQGLKADVVTYNQVTDVQILHDKGKLIPA 105 (338)
T ss_pred EEeeeccC--CHHHHHHHHHHHHHHHHhhCCCCceEEEEcCCCcHHHHHHHhcCCCcCEEecCCHHHHHHHHHCCCCCCc
Confidence 34444443 46677788888876 67787774 5667777888888886 789998753111 0122 11
Q ss_pred -e-eccc------cceEEEEecCCCCCCCCCCcChhhhc--CCCeEeecCCCC-c--HHHHHHH---HHhCC--------
Q psy3760 160 -S-IPCY------QWEYVIIVPLDHPLLLLNSISLKEIS--NYPLITYDLSFS-G--RIKLDRE---FSLQK-------- 215 (306)
Q Consensus 160 -~-~~l~------~~~~~~v~~~~~~l~~~~~i~~~dl~--~~~~i~~~~~~~-~--~~~~~~~---~~~~~-------- 215 (306)
+ ..+. ...+++++++++| +.+-+|+||. +..+++.++... . +..+..+ ....|
T Consensus 106 ~~~~~~~~n~~p~~s~lV~vv~kgnp---k~i~sw~DL~~~~~kI~i~nP~tSg~g~~~~La~~~~~~~~~G~d~~~a~~ 182 (338)
T PRK10852 106 DWQSRLPNNSSPFYSTMAFLVRKGNP---KNIHDWNDLVRSDVKLIFPNPKTSGNARYTYLAAWGAADKADGGDKAKTEQ 182 (338)
T ss_pred chhhcccccCCcccceEEEEEECCCC---CCCCCHHHhcCCCcEEEECCCCcchHHHHHHHHHHHHHHHHcCCChHHHHH
Confidence 1 1222 2379999999998 3355899995 345666654322 2 1112211 11112
Q ss_pred ----CceeEE-EEecCHHHHHHHHHhcc-ceeeeecceecc----cccCCceeeecCCCC-ccceEEEEEeC--CccccH
Q psy3760 216 ----LTPYIV-LETINSDIIKTYVELRM-GIGIIASIAFDS----NRDKNLRSISASHLF-GTTISRVIIKQ--GTYLRS 282 (306)
Q Consensus 216 ----~~~~~~-~~~~~~~~~~~~v~~g~-gi~~~p~~~~~~----~~~~~l~~~~~~~~~-~~~~~~l~~~~--~~~~~~ 282 (306)
+..++. +..+........+..|. -+++....-+.. .....+..+...... ...++.++-.. +....+
T Consensus 183 ~l~~l~~Nv~v~~~~~~~a~~~~v~~Ge~Dvgi~yesda~~~~~~~~~~~~~iV~P~~~~~~~~pvAvv~k~~~~~~~~e 262 (338)
T PRK10852 183 FMTQFLKNVEVFDTGGRGATTTFAERGLGDVLISFESEVNNIRKQYEAQGYEVVVPKTNILAEFPVAWVDKNVQANGTEK 262 (338)
T ss_pred HHHHHHhcCCEecCCCcHHHHHHHHcCCccEEEEechHHHHHHHhcCCCCeEEEeCCCCceeeeeEEEEEeccccCCCHH
Confidence 112333 33455777788888773 334443332211 112333333223222 22233333211 234478
Q ss_pred HHHHHHHHHhHH
Q psy3760 283 YVYSFIKLLSPK 294 (306)
Q Consensus 283 ~~~~~~~~l~~~ 294 (306)
..++|+++|.+.
T Consensus 263 ~AkaFidfL~S~ 274 (338)
T PRK10852 263 AAKAYLNYLYSP 274 (338)
T ss_pred HHHHHHHHhcCH
Confidence 899999999654
No 217
>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=96.39 E-value=0.0055 Score=37.68 Aligned_cols=40 Identities=30% Similarity=0.380 Sum_probs=32.5
Q ss_pred CHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecC-CCccccCH
Q psy3760 18 NLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHG-KRIRGLTK 61 (306)
Q Consensus 18 s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~-~~~~~lT~ 61 (306)
|....|+.+++|++++++.|+.|++. .+..+.+ +++ .+||
T Consensus 27 s~~ela~~~g~s~~tv~r~l~~L~~~---g~i~~~~~~~~-~l~~ 67 (67)
T cd00092 27 TRQEIADYLGLTRETVSRTLKELEEE---GLISRRGRGKY-RVNP 67 (67)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHC---CCEEecCCCeE-EeCC
Confidence 78899999999999999999999996 4555555 555 5664
No 218
>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=96.38 E-value=0.014 Score=34.31 Aligned_cols=45 Identities=16% Similarity=0.144 Sum_probs=37.4
Q ss_pred chhhHHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCce
Q psy3760 2 NLHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSID 47 (306)
Q Consensus 2 ~~~~l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~ 47 (306)
+-++.++|....+.. |....|+.+++|.+++.++++++.+.+|.+
T Consensus 2 ~~~e~~i~~~~~~~~-s~~eia~~l~~s~~tv~~~~~~~~~~l~~~ 46 (57)
T cd06170 2 TPREREVLRLLAEGK-TNKEIADILGISEKTVKTHLRNIMRKLGVK 46 (57)
T ss_pred CHHHHHHHHHHHcCC-CHHHHHHHHCCCHHHHHHHHHHHHHHhCCC
Confidence 445666776666655 999999999999999999999998888763
No 219
>PF08279 HTH_11: HTH domain; InterPro: IPR013196 Winged helix DNA-binding proteins share a related winged helix-turn-helix DNA-binding motif, where the "wings", or loops, are small beta-sheets. The winged helix motif consists of two wings (W1, W2), three alpha helices (H1, H2, H3) and three beta-sheets (S1, S2, S3) arranged in the order H1-S1-H2-H3-S2-W1-S3-W2 []. The DNA-recognition helix makes sequence-specific DNA contacts with the major groove of DNA, while the wings make different DNA contacts, often with the minor groove or the backbone of DNA. Several winged-helix proteins display an exposed patch of hydrophobic residues thought to mediate protein-protein interactions. This entry represents a subset of the winged helix domain superfamily which is predominantly found in bacterial proteins, though there are also some archaeal and eukaryotic examples. This domain is commonly found in the biotin (vitamin H) repressor protein BirA which regulates transcription of the biotin operon []. It is also found in other proteins including regulators of amino acid biosynthsis such as LysM [], and regulators of carbohydrate metabolisms such as LicR and FrvR [, ].; PDB: 1HXD_B 2EWN_B 1BIA_A 1BIB_A 1J5Y_A 3V7S_A 3V7C_A 3RKW_A 3RIR_A 3RKX_A ....
Probab=96.36 E-value=0.019 Score=33.66 Aligned_cols=38 Identities=32% Similarity=0.267 Sum_probs=31.1
Q ss_pred CHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCCc
Q psy3760 18 NLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRI 56 (306)
Q Consensus 18 s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~ 56 (306)
|...-|+.|++|..||.+-|+.|++.+ .++-.+.++|.
T Consensus 17 t~~eLa~~l~vS~rTi~~~i~~L~~~~-~~I~~~~~~GY 54 (55)
T PF08279_consen 17 TAKELAEELGVSRRTIRRDIKELREWG-IPIESKRGKGY 54 (55)
T ss_dssp EHHHHHHHCTS-HHHHHHHHHHHHHTT--EEEEETTTEE
T ss_pred CHHHHHHHhCCCHHHHHHHHHHHHHCC-CeEEeeCCCCc
Confidence 788999999999999999999997776 88877777664
No 220
>PF13011 LZ_Tnp_IS481: leucine-zipper of insertion element IS481
Probab=96.32 E-value=0.033 Score=35.61 Aligned_cols=62 Identities=19% Similarity=0.206 Sum_probs=48.2
Q ss_pred HHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCCccccCHhHHHHH
Q psy3760 6 FRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKPGQAIL 67 (306)
Q Consensus 6 l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~~~lT~~G~~l~ 67 (306)
++....+++.|.++..||+..|||..|+.|.++...++=-.-|.+|+.+.--.|+.-.....
T Consensus 15 ~~lv~~vv~~g~~~a~aA~~~gVS~~Ta~kW~~Ryra~G~~GL~DRSSRP~~sP~~t~~~~~ 76 (85)
T PF13011_consen 15 LRLVRRVVEQGWPVAHAAAEFGVSRRTAYKWLARYRAEGEAGLQDRSSRPHRSPRRTPPEVE 76 (85)
T ss_pred HHHHHHHHHcCCcHHHHHHHhCCCHHHHHHHHHHHHHcCcccccccCCCCCCCCccCCHHHH
Confidence 44555677777799999999999999999999999988556689999766535665544433
No 221
>COG4623 Predicted soluble lytic transglycosylase fused to an ABC-type amino acid-binding protein [Cell envelope biogenesis, outer membrane]
Probab=96.25 E-value=0.16 Score=42.19 Aligned_cols=190 Identities=15% Similarity=0.198 Sum_probs=107.8
Q ss_pred CCcEEEEecccchhh---------hhHHHHHHHHHhCCCcEEEEEeCCh-hHHHHHHHcCCeeEEEEccccCCCCCceee
Q psy3760 92 TGNLTIATTHTQARY---------ALPKIIKEFTIQFPKVKLSLLQGNP-KQITEMIRNDQADIAIVTEILSPSDKLISI 161 (306)
Q Consensus 92 ~~~l~I~~~~~~~~~---------~l~~~l~~~~~~~p~~~i~~~~~~~-~~~~~~l~~~~~Di~i~~~~~~~~~~~~~~ 161 (306)
.|.|++++..+-.++ +=-.+..+|.+ |-++.+.+..... +++.+.|.+|+.|++-.. -.....++...
T Consensus 22 rGvLrV~tinsp~sy~~~~~~p~G~eYelak~Fa~-yLgV~Lki~~~~n~dqLf~aL~ng~~DL~Aag-l~~~~~~l~~~ 99 (473)
T COG4623 22 RGVLRVSTINSPLSYFEDKGGPTGLEYELAKAFAD-YLGVKLKIIPADNIDQLFDALDNGNADLAAAG-LLYNSERLKNF 99 (473)
T ss_pred cCeEEEEeecCccceeccCCCccchhHHHHHHHHH-HhCCeEEEEecCCHHHHHHHHhCCCcceeccc-ccCChhHhccc
Confidence 678999886543333 33566777766 5689999998755 899999999999998763 22332333322
Q ss_pred ---cc-ccceEEEEecCCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCceeEEEEe---cCHHHHHHHH
Q psy3760 162 ---PC-YQWEYVIIVPLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLET---INSDIIKTYV 234 (306)
Q Consensus 162 ---~l-~~~~~~~v~~~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~v 234 (306)
|. ...+..+|.+++.. .+-++++|.+..+......... .-...+++... |.-...+ -....++.+|
T Consensus 100 ~~gP~y~svs~qlVyRkG~~----Rp~~l~~L~g~~i~v~~gs~~~--~~l~~lk~~ky-P~l~~k~d~~~~~~dLle~v 172 (473)
T COG4623 100 QPGPTYYSVSQQLVYRKGQY----RPRSLGQLKGRQITVAKGSAHV--EDLKLLKETKY-PELIWKVDDKLGVEDLLEMV 172 (473)
T ss_pred CCCCceecccHHHHhhcCCC----CCCCHHHccCceeeccCCcHHH--HHHHHHHHhhc-chhhhhhcccccHHHHHHHH
Confidence 22 24456677777763 4678999988666555443211 11223333222 3323333 3567888889
Q ss_pred Hhc-cceeeeecceeccc--ccCCce-eeecCCCCccceEEEEEeCCccccHHHHHHHHHHhHH
Q psy3760 235 ELR-MGIGIIASIAFDSN--RDKNLR-SISASHLFGTTISRVIIKQGTYLRSYVYSFIKLLSPK 294 (306)
Q Consensus 235 ~~g-~gi~~~p~~~~~~~--~~~~l~-~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~ 294 (306)
..| .++++.....+... -.++|. .+.+.+. .++..+.+.+. .+.....+++++-+.
T Consensus 173 ~~Gkldytiads~~is~~q~i~P~laVafd~tde---~~v~Wy~~~~d-d~tL~a~ll~F~~~~ 232 (473)
T COG4623 173 AEGKLDYTIADSVEISLFQRVHPELAVAFDLTDE---QPVAWYLPRDD-DSTLSAALLDFLNEA 232 (473)
T ss_pred hcCCcceeeeccHHHHHHHHhCccceeeeecccc---cCceeeccCCc-hHHHHHHHHHHHHHh
Confidence 988 67777665444433 334444 3444442 23333334422 244444444444443
No 222
>COG1339 Transcriptional regulator of a riboflavin/FAD biosynthetic operon [Transcription / Coenzyme metabolism]
Probab=96.25 E-value=0.0097 Score=44.05 Aligned_cols=93 Identities=19% Similarity=0.254 Sum_probs=55.8
Q ss_pred CHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEec---CCCccccCHhHHHHHHHHHHHHHHHHHHHHHHHhhccCCCCc
Q psy3760 18 NLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRH---GKRIRGLTKPGQAILRSIEIIMQEIEGLKKIGKEFSAYDTGN 94 (306)
Q Consensus 18 s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~---~~~~~~lT~~G~~l~~~a~~il~~~~~~~~~~~~~~~~~~~~ 94 (306)
|.++.|+.|++|+++.+|.|++||++ .+..|. .+.++.+|+.|..++... ++.+..+...... -...|.
T Consensus 21 t~~ela~~l~~S~qta~R~l~~le~~---~~I~R~~~~~Gq~i~iTekG~~~L~~~---~~d~~r~~~~~~~--i~i~G~ 92 (214)
T COG1339 21 TSSELAKRLGVSSQTAARKLKELEDE---GYITRTISKRGQLITITEKGIDLLYKE---YEDLSRIFDSGGN--IVIEGE 92 (214)
T ss_pred cHHHHHHHhCcCcHHHHHHHHhhccC---CcEEEEecCCCcEEEehHhHHHHHHHH---HHHHHHHhcCCCc--eEEEEE
Confidence 67889999999999999999999974 455543 233348999999987643 2222222211110 122344
Q ss_pred EEEEecccchhhhhHHHHHHHHHh
Q psy3760 95 LTIATTHTQARYALPKIIKEFTIQ 118 (306)
Q Consensus 95 l~I~~~~~~~~~~l~~~l~~~~~~ 118 (306)
+.=|..+.--..-++....+|++.
T Consensus 93 V~SGlGEG~yyvS~~~Y~~qf~ek 116 (214)
T COG1339 93 VVSGLGEGRYYVSLPGYRRQFREK 116 (214)
T ss_pred EecccccceEEEecHHHHHHHHHH
Confidence 444544432111235666777665
No 223
>PF13518 HTH_28: Helix-turn-helix domain
Probab=96.24 E-value=0.013 Score=33.86 Aligned_cols=38 Identities=18% Similarity=0.169 Sum_probs=31.7
Q ss_pred HHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcC
Q psy3760 6 FRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELS 45 (306)
Q Consensus 6 l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg 45 (306)
+++...+.+.. |...+|+.+|||.++|.+.+++.++ -|
T Consensus 3 ~~iv~~~~~g~-s~~~~a~~~gis~~tv~~w~~~y~~-~G 40 (52)
T PF13518_consen 3 LQIVELYLEGE-SVREIAREFGISRSTVYRWIKRYRE-GG 40 (52)
T ss_pred HHHHHHHHcCC-CHHHHHHHHCCCHhHHHHHHHHHHh-cC
Confidence 44555666666 9999999999999999999999997 44
No 224
>PRK10434 srlR DNA-bindng transcriptional repressor SrlR; Provisional
Probab=96.24 E-value=0.066 Score=42.90 Aligned_cols=40 Identities=25% Similarity=0.287 Sum_probs=34.6
Q ss_pred CHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCCccccCH
Q psy3760 18 NLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTK 61 (306)
Q Consensus 18 s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~~~lT~ 61 (306)
++..-|+.+++|.+|+.|-|+.||++ .|+.|..+|. .+++
T Consensus 21 ~v~eLa~~l~VS~~TIRRDL~~Le~~---g~l~r~~Gga-~~~~ 60 (256)
T PRK10434 21 SVEELAQYFDTTGTTIRKDLVILEHA---GTVIRTYGGV-VLNK 60 (256)
T ss_pred EHHHHHHHHCCCHHHHHHHHHHHHHC---CCEEEEECCE-EcCC
Confidence 78899999999999999999999986 6788888887 4543
No 225
>PRK11205 tbpA thiamine transporter substrate binding subunit; Provisional
Probab=96.22 E-value=0.6 Score=39.08 Aligned_cols=199 Identities=14% Similarity=0.056 Sum_probs=108.6
Q ss_pred CCCcEEEEecccchhhh--hHHHHHHHHHhCCCcEEEEEeCChh-HHHHHHH----cCCeeEEEEccccC----CCCCc-
Q psy3760 91 DTGNLTIATTHTQARYA--LPKIIKEFTIQFPKVKLSLLQGNPK-QITEMIR----NDQADIAIVTEILS----PSDKL- 158 (306)
Q Consensus 91 ~~~~l~I~~~~~~~~~~--l~~~l~~~~~~~p~~~i~~~~~~~~-~~~~~l~----~~~~Di~i~~~~~~----~~~~~- 158 (306)
..++|+|.+..++...+ ...++..|.+++ ++++++...++. ++...+. ++.+|+.+...... ...++
T Consensus 21 ~~~~L~vy~~~~~~~~~~~~~~i~~~Fe~~t-gikV~~~~~~s~~~~~~kl~~e~~~~~~DV~~~~~~~~~~~l~~~gll 99 (330)
T PRK11205 21 AKPVLTVYTYDSFAAEWGPGPAVKKAFEAEC-GCELKFVALEDGVSLLNRLRLEGKNSKADVVLGLDNNLLAAAKQTGLF 99 (330)
T ss_pred CCCeEEEEEcccccccCCCchHHHHHHHHHH-CCEEEEEecCcHHHHHHHHHhcCCCCCCCEEEECCchHHHHHHHCCCc
Confidence 45789999976665543 357889998885 899999886664 7888777 36899998532100 00010
Q ss_pred -------------------eeeccccceEEEEecCCCCCCCCCCcChhhhcCC----CeEeecCCC-Cc-HHHHH-----
Q psy3760 159 -------------------ISIPCYQWEYVIIVPLDHPLLLLNSISLKEISNY----PLITYDLSF-SG-RIKLD----- 208 (306)
Q Consensus 159 -------------------~~~~l~~~~~~~v~~~~~~l~~~~~i~~~dl~~~----~~i~~~~~~-~~-~~~~~----- 208 (306)
...++....++++.+++.. ...+-+++||.+. .....++.. .. ...+.
T Consensus 100 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~yn~~~~--~~~P~sw~DL~~~~~~g~i~~~dp~~s~~~~~~~~~~~~~ 177 (330)
T PRK11205 100 APSGVDTSAVTVPGGWNDDTFVPYDYGYFAFVYDKEKL--KNPPKSLKELVESDQNWKVIYQDPRTSTPGLGLLLWMKKV 177 (330)
T ss_pred ccccCChhhccCcccccCCceeeEeeeeEEEEEccccc--CCCCCCHHHHhChhhcCCEEecCCCCCcHHHHHHHHHHHh
Confidence 0233444566677777653 2345689999752 233333221 11 11111
Q ss_pred ------HHHHhCCCceeEEEEecCHHHHHHHHHhcc-ceeeeecce--eccccc--CCceeeecCCCCccceEEEEEeCC
Q psy3760 209 ------REFSLQKLTPYIVLETINSDIIKTYVELRM-GIGIIASIA--FDSNRD--KNLRSISASHLFGTTISRVIIKQG 277 (306)
Q Consensus 209 ------~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~-gi~~~p~~~--~~~~~~--~~l~~~~~~~~~~~~~~~l~~~~~ 277 (306)
+.++. +..+..-...+.....+++.+|. .+++..... ...... ..+....+++......-++...++
T Consensus 178 ~g~~~~~~~~~--L~~~~~~~~~~~~~~~~~~~~Ge~~~~i~~~~~~~~~~~~~~~~~~~~~~~~eG~~~~~~~~ai~k~ 255 (330)
T PRK11205 178 YGDDAPQAWQK--LAKKTVTVTKGWSEAYGLFLKGEADLVLSYTTSPAYHIIAEKKDNYAAANFSEGHYLQVEVAARTAA 255 (330)
T ss_pred cCchHHHHHHH--HHhCCeeeCCChHHHHHHHHcCCccEEEeCCCcHHHHHhhccCCceeEEEcCCCCeEEEEEEEEeCC
Confidence 11111 11222222345567778888883 444443321 111111 133333333322222334555677
Q ss_pred ccccHHHHHHHHHHhHH
Q psy3760 278 TYLRSYVYSFIKLLSPK 294 (306)
Q Consensus 278 ~~~~~~~~~~~~~l~~~ 294 (306)
.+....+++|++++.+.
T Consensus 256 a~n~e~A~~Fi~fllS~ 272 (330)
T PRK11205 256 SKQPELAQKFLQFMVSP 272 (330)
T ss_pred CCCHHHHHHHHHHHcCH
Confidence 77788999999998654
No 226
>PF01638 HxlR: HxlR-like helix-turn-helix; InterPro: IPR002577 The hxlR-type HTH domain is a domain of ~90-100 amino acids present in putative transcription regulators with a winged helix-turn-helix (wHTH) structure. The domain is named after Bacillus subtilis hxlR, a transcription activator of the hxlAB operon involved in the detoxification of formaldehyde []. The hxlR-type domain forms the core of putative transcription regulators and of hypothetical proteins occurring in eubacteria as well as in archaea. The sequence and structure of hxlR-type proteins show similarities with the marR-type wHTH []. The crystal structure of ytfH resembles the DNA-binding domains of winged helix proteins, containing a three helix (H) bundle and a three-stranded antiparallel beta-sheet (B) in the topology: H1-H2-B1-H3-H4-B2-B3-H5-H6. This topology corresponds with that of the marR-type DNA-binding domain, wherein helices 3 and 4 comprise the helix-turn-helix motif and the beta-sheet is called the wing. ; PDB: 2F2E_B 3DF8_A 1Z7U_B 1YYV_A 4A5M_D 4A5N_B 2FSW_A 2HZT_D.
Probab=96.21 E-value=0.029 Score=36.87 Aligned_cols=68 Identities=24% Similarity=0.264 Sum_probs=49.1
Q ss_pred HHHHHHH-hcCCHHHHHHHh-CCCchHHHHHHHHHHHHcCceeEEecC-----C--CccccCHhHHHHHHHHHHHHHHHH
Q psy3760 8 FVREAVR-QNFNLTEAAKAL-YTSQPGVSKAIIELEEELSIDIFIRHG-----K--RIRGLTKPGQAILRSIEIIMQEIE 78 (306)
Q Consensus 8 ~f~~v~~-~~~s~~~aA~~l-~isq~~~s~~i~~LE~~lg~~Lf~R~~-----~--~~~~lT~~G~~l~~~a~~il~~~~ 78 (306)
++.++.. .. .|+.=.+.+ ++|+..++++++.||+. -|+.|.. . .. +||+.|+.|.+....+.+=.+
T Consensus 10 IL~~l~~g~~-rf~el~~~l~~is~~~L~~~L~~L~~~---GLv~r~~~~~~p~~v~Y-~LT~~G~~l~~~l~~l~~W~~ 84 (90)
T PF01638_consen 10 ILRALFQGPM-RFSELQRRLPGISPKVLSQRLKELEEA---GLVERRVYPEVPPRVEY-SLTEKGKELLPVLEALEEWGE 84 (90)
T ss_dssp HHHHHTTSSE-EHHHHHHHSTTS-HHHHHHHHHHHHHT---TSEEEEEESSSSSEEEE-EE-HHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHhCCC-cHHHHHHhcchhHHHHHHHHHHHHHHc---chhhcccccCCCCCCcc-CCCcCHHHHHHHHHHHHHHHH
Confidence 3444444 34 789999999 99999999999999984 4556541 1 24 899999999998888876655
Q ss_pred HH
Q psy3760 79 GL 80 (306)
Q Consensus 79 ~~ 80 (306)
+-
T Consensus 85 ~~ 86 (90)
T PF01638_consen 85 EH 86 (90)
T ss_dssp HH
T ss_pred HH
Confidence 43
No 227
>PF05225 HTH_psq: helix-turn-helix, Psq domain; InterPro: IPR007889 This DNA-binding motif is found in four copies in the pipsqueak protein of Drosophila melanogaster []. In pipsqueak this domain binds to GAGA sequence []. The pipsqueak family, which includes proteins from fungi, sea urchins, nematodes, insects, and vertebrates appear to be proteins essential for sequence-specific targeting of a polycomb group protein complex [].; GO: 0003677 DNA binding; PDB: 2COB_A.
Probab=96.18 E-value=0.017 Score=32.25 Aligned_cols=31 Identities=19% Similarity=0.250 Sum_probs=21.7
Q ss_pred HHHHHhc-CCHHHHHHHhCCCchHHHHHHHHH
Q psy3760 10 REAVRQN-FNLTEAAKALYTSQPGVSKAIIEL 40 (306)
Q Consensus 10 ~~v~~~~-~s~~~aA~~l~isq~~~s~~i~~L 40 (306)
+..++.| .|+.+||+..||+++||+++++.-
T Consensus 9 i~~v~~g~~S~r~AA~~ygVp~sTL~~r~~g~ 40 (45)
T PF05225_consen 9 IEAVKNGKMSIRKAAKKYGVPRSTLRRRLRGK 40 (45)
T ss_dssp HHHHHTTSS-HHHHHHHHT--HHHHHHHHHHT
T ss_pred HHHHHhCCCCHHHHHHHHCcCHHHHHHHHcCC
Confidence 3334444 699999999999999999988753
No 228
>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=96.18 E-value=0.56 Score=38.37 Aligned_cols=150 Identities=15% Similarity=0.069 Sum_probs=84.9
Q ss_pred CcEEEEecccchhh----hhHHHHHHHHHhCCCcEEEEEe-CChhHHHHHHHcCCeeEEEEccc-----cCCCCCce-ee
Q psy3760 93 GNLTIATTHTQARY----ALPKIIKEFTIQFPKVKLSLLQ-GNPKQITEMIRNDQADIAIVTEI-----LSPSDKLI-SI 161 (306)
Q Consensus 93 ~~l~I~~~~~~~~~----~l~~~l~~~~~~~p~~~i~~~~-~~~~~~~~~l~~~~~Di~i~~~~-----~~~~~~~~-~~ 161 (306)
..|+||+....... .+.++...+.++ .++++++.. .+....++.+.+|++|+++.... ........ ..
T Consensus 27 ~~l~vg~~~~~~~~~~~~~~~~l~~~l~~~-~g~~v~~~~~~~~~~~~~al~~g~~D~~~~~~~~~~~~~~~~~~~~~~~ 105 (288)
T TIGR03431 27 KELNFGIIPTENASDLKQRWEPLADYLSKK-LGVKVKLFFATDYAGVIEGMRFGKVDIAWYGPSSYAEAYQKANAEAFAI 105 (288)
T ss_pred CeEEEEEcCCCCHHHHHHHHHHHHHHHHHH-hCCcEEEEeCCCHHHHHHHHHcCCccEEEEChHHHHHHHHhcCCeEEEE
Confidence 57999997654332 233455556555 478888654 56778899999999999996411 01111100 00
Q ss_pred cc---ccc--eEEEEecCCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHH--HHHHHhCCCcee----EEEEecCHHHH
Q psy3760 162 PC---YQW--EYVIIVPLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKL--DREFSLQKLTPY----IVLETINSDII 230 (306)
Q Consensus 162 ~l---~~~--~~~~v~~~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~--~~~~~~~~~~~~----~~~~~~~~~~~ 230 (306)
.. +.. ..+++++++.+ .-+++||.+.......++......+ ....+..|.... .+....+...+
T Consensus 106 ~~~~~~~~~y~~~lvv~~ds~-----i~sl~DL~Gk~v~~~~~~s~~~~~~~~~~l~~~~g~~~~~~~~~v~~~~~~~~~ 180 (288)
T TIGR03431 106 EVNADGSTGYYSVLIVKKDSP-----IKSLEDLKGKTFGFVDPNSTSGFLVPSYYLFKKNGIKPKEYFKKVTFSGSHEAA 180 (288)
T ss_pred eccCCCCCceEEEEEEeCCCC-----CCcHHHhCCCEEEeeCCCcchhhHHHHHHHHHhcCCChHHhHHhheecCchHHH
Confidence 00 011 14667777754 3488999887766654443322222 223355565422 22233367788
Q ss_pred HHHHHhccc-eeeeeccee
Q psy3760 231 KTYVELRMG-IGIIASIAF 248 (306)
Q Consensus 231 ~~~v~~g~g-i~~~p~~~~ 248 (306)
...+.+|.. .++++...+
T Consensus 181 ~~al~~G~vDa~~~~~~~~ 199 (288)
T TIGR03431 181 ILAVANGTVDAATTNDENL 199 (288)
T ss_pred HHHHHcCCCCeEeccHHHH
Confidence 888898855 445555443
No 229
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=96.18 E-value=0.012 Score=35.08 Aligned_cols=36 Identities=31% Similarity=0.324 Sum_probs=28.6
Q ss_pred CHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCC
Q psy3760 18 NLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKR 55 (306)
Q Consensus 18 s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~ 55 (306)
|...-|+.+++|++++++.++.|+++ |. +-...++|
T Consensus 22 s~~~la~~~~vs~~tv~~~l~~L~~~-g~-i~~~~~~g 57 (60)
T smart00345 22 SERELAAQLGVSRTTVREALSRLEAE-GL-VQRRPGSG 57 (60)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHC-CC-EEEecCCe
Confidence 67788999999999999999999985 65 33333444
No 230
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=96.12 E-value=0.015 Score=39.68 Aligned_cols=43 Identities=26% Similarity=0.306 Sum_probs=35.8
Q ss_pred CchhhHHHHHHHHHhc-CCHHHHHHHhCCCchHHHHHHHHHHHH
Q psy3760 1 MNLHQFRFVREAVRQN-FNLTEAAKALYTSQPGVSKAIIELEEE 43 (306)
Q Consensus 1 m~~~~l~~f~~v~~~~-~s~~~aA~~l~isq~~~s~~i~~LE~~ 43 (306)
||-.+.+++..+.+.+ .|++.-|+.+|+|++++++++++|++.
T Consensus 1 ld~~D~~il~~L~~~~~~~~~~la~~l~~s~~tv~~~l~~L~~~ 44 (108)
T smart00344 1 LDEIDRKILEELQKDARISLAELAKKVGLSPSTVHNRVKRLEEE 44 (108)
T ss_pred CCHHHHHHHHHHHHhCCCCHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence 4556777777777643 289999999999999999999999995
No 231
>TIGR02702 SufR_cyano iron-sulfur cluster biosynthesis transcriptional regulator SufR. All members of this cyanobacterial protein family are the transcriptional regulator SufR and regulate the SUF system, which makes possible iron-sulfur cluster biosynthesis despite exposure to oxygen. In all cases, the sufR gene is encoded near SUF system genes but in the opposite direction. This DNA-binding protein belongs to the 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=96.09 E-value=0.018 Score=44.39 Aligned_cols=49 Identities=22% Similarity=0.320 Sum_probs=37.9
Q ss_pred CHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEec------CCC--ccccCHhHHHHHHH
Q psy3760 18 NLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRH------GKR--IRGLTKPGQAILRS 69 (306)
Q Consensus 18 s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~------~~~--~~~lT~~G~~l~~~ 69 (306)
|...-|+.+++|++|++++|++||+. | |+.|. ++. .+.||+.|...++.
T Consensus 17 t~~eLA~~lgis~~tV~~~L~~Le~~-G--lV~r~~~~~~~gRp~~~y~LT~~G~~~~~~ 73 (203)
T TIGR02702 17 TAAALAEALAISPQAVRRHLKDLETE-G--LIEYEAVVQGMGRPQYHYQLSRQGREQFPQ 73 (203)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHC-C--CeEEeecccCCCCCceEEEECcchhhhccc
Confidence 67788999999999999999999996 4 44433 121 12799999998765
No 232
>PRK09959 hybrid sensory histidine kinase in two-component regulatory system with EvgA; Provisional
Probab=96.07 E-value=0.27 Score=48.96 Aligned_cols=143 Identities=13% Similarity=0.092 Sum_probs=90.7
Q ss_pred CCcEEEEecccch------------hhhhHHHHHHHHHhCCCcEEEEEeC-ChhHHHHHHHcCCeeEEEEc--cccCCCC
Q psy3760 92 TGNLTIATTHTQA------------RYALPKIIKEFTIQFPKVKLSLLQG-NPKQITEMIRNDQADIAIVT--EILSPSD 156 (306)
Q Consensus 92 ~~~l~I~~~~~~~------------~~~l~~~l~~~~~~~p~~~i~~~~~-~~~~~~~~l~~~~~Di~i~~--~~~~~~~ 156 (306)
.+.|++|+..... ..+...++..+.+. -+++++++.. +++++++.|.+|++|+++.. .......
T Consensus 55 ~~~l~vgv~~~~~p~~~~~~~~g~~~G~~~D~l~~ia~~-lG~~~e~v~~~~~~~~l~~l~~g~iDl~~~~~~~~~~r~~ 133 (1197)
T PRK09959 55 KKNLVIAVHKSQTATLLHTDSQQRVRGINADYLNLLKRA-LNIKLTLREYADHQKAMDALEEGEVDIVLSHLVASPPLND 133 (1197)
T ss_pred CCeEEEEecCCCCCCceeecCCCccceecHHHHHHHHHh-cCCceEEEeCCCHHHHHHHHHcCCCcEecCcccccccccc
Confidence 4679999864321 22445566666554 5899999986 88999999999999997652 1112222
Q ss_pred Cc-eeeccccceEEEEecCCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCceeEEEEecCHHHHHHHHH
Q psy3760 157 KL-ISIPCYQWEYVIIVPLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVE 235 (306)
Q Consensus 157 ~~-~~~~l~~~~~~~v~~~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~ 235 (306)
.+ -+.|++....+++++++.. .-+++++.+....... +.... ..+++.. +--....+++...++.++.
T Consensus 134 ~~~fs~py~~~~~~~v~~~~~~-----~~~~~~l~~~~i~~~~-g~~~~----~~~~~~~-p~~~i~~~~s~~~al~av~ 202 (1197)
T PRK09959 134 DIAATKPLIITFPALVTTLHDS-----MRPLTSSKPVNIARVA-NYPPD----EVIHQSF-PKATIISFTNLYQALASVS 202 (1197)
T ss_pred chhcCCCccCCCceEEEeCCCC-----CCCcccccCeEEEEeC-CCCCH----HHHHHhC-CCCEEEeCCCHHHHHHHHH
Confidence 22 3557677777888877653 2345566555444433 33332 2333322 1123568899999999999
Q ss_pred hccceeeeecc
Q psy3760 236 LRMGIGIIASI 246 (306)
Q Consensus 236 ~g~gi~~~p~~ 246 (306)
.|..=+++...
T Consensus 203 ~G~~Da~i~~~ 213 (1197)
T PRK09959 203 AGQNDYFIGSN 213 (1197)
T ss_pred cCCCCEEEccH
Confidence 99877666553
No 233
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=95.97 E-value=0.032 Score=37.80 Aligned_cols=44 Identities=27% Similarity=0.343 Sum_probs=36.0
Q ss_pred hhhHHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCc
Q psy3760 3 LHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSI 46 (306)
Q Consensus 3 ~~~l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~ 46 (306)
-+++.........++|+...|+.||||.||+-.++.+|=+.+|.
T Consensus 36 ~E~~~Fi~~Fi~~rGnlKe~e~~lgiSYPTvR~rLd~ii~~lg~ 79 (113)
T PF09862_consen 36 PEQLEFIKLFIKNRGNLKEMEKELGISYPTVRNRLDKIIEKLGY 79 (113)
T ss_pred HHHHHHHHHHHHhcCCHHHHHHHHCCCcHHHHHHHHHHHHHhCC
Confidence 34555555555444499999999999999999999999999998
No 234
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=95.93 E-value=0.011 Score=33.84 Aligned_cols=36 Identities=25% Similarity=0.257 Sum_probs=23.3
Q ss_pred HHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHH
Q psy3760 6 FRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEE 42 (306)
Q Consensus 6 l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~ 42 (306)
+.++..+.+ |.|..++|+.+|+|++|+++.+++.++
T Consensus 8 ~~ii~l~~~-G~s~~~ia~~lgvs~~Tv~~w~kr~~~ 43 (50)
T PF13384_consen 8 AQIIRLLRE-GWSIREIAKRLGVSRSTVYRWIKRYRE 43 (50)
T ss_dssp --HHHHHHH-T--HHHHHHHHTS-HHHHHHHHT----
T ss_pred HHHHHHHHC-CCCHHHHHHHHCcCHHHHHHHHHHccc
Confidence 445555556 459999999999999999999998764
No 235
>PRK01905 DNA-binding protein Fis; Provisional
Probab=95.90 E-value=0.019 Score=36.44 Aligned_cols=30 Identities=17% Similarity=0.020 Sum_probs=24.7
Q ss_pred HHHHhcCCHHHHHHHhCCCchHHHHHHHHH
Q psy3760 11 EAVRQNFNLTEAAKALYTSQPGVSKAIIEL 40 (306)
Q Consensus 11 ~v~~~~~s~~~aA~~l~isq~~~s~~i~~L 40 (306)
++.+++.+.++||+.||||++++.+.++++
T Consensus 45 aL~~~~gn~s~aAr~LGIsrstL~rklkk~ 74 (77)
T PRK01905 45 VMEQAGGNQSLAAEYLGINRNTLRKKLQQH 74 (77)
T ss_pred HHHHcCCCHHHHHHHHCCCHHHHHHHHHHh
Confidence 334444389999999999999999999985
No 236
>COG0715 TauA ABC-type nitrate/sulfonate/bicarbonate transport systems, periplasmic components [Inorganic ion transport and metabolism]
Probab=95.87 E-value=0.23 Score=41.56 Aligned_cols=197 Identities=10% Similarity=0.002 Sum_probs=106.5
Q ss_pred CCcEEEEecccch--hhhhHHHHHHHHHhCCCc-EEEEEeC-ChhHHHHHHHcCCeeEEEEccccCC-----CC--Ccee
Q psy3760 92 TGNLTIATTHTQA--RYALPKIIKEFTIQFPKV-KLSLLQG-NPKQITEMIRNDQADIAIVTEILSP-----SD--KLIS 160 (306)
Q Consensus 92 ~~~l~I~~~~~~~--~~~l~~~l~~~~~~~p~~-~i~~~~~-~~~~~~~~l~~~~~Di~i~~~~~~~-----~~--~~~~ 160 (306)
.-.++++..+... ..++...-..|.+. ++ .+++... +.....+.|..|.+|++....+... .. .+..
T Consensus 30 ~~~~~~~~~~~~~~~~~~va~~kG~f~~~--Gl~~v~~~~~~~~~~~~~~l~~G~~D~a~~~~~~~~~~~~~~~g~pv~~ 107 (335)
T COG0715 30 KVTILLGWLPNPDHAPLYVAKEKGFFKKE--GLDDVELVEFTGGAPVLEALAAGALDFAVYYTGDTPLIAAGAAGAPVKV 107 (335)
T ss_pred ceeeeecccCchhHHHHHHHHHhChHhHh--CCCceEEEEcCCChHHHHHHhcCCcCccccccCchHHHHhhccCCCeEE
Confidence 4456666655311 22233333333443 34 4666554 5567889999999999964322111 11 1111
Q ss_pred --ecccc-ceEEEEecCCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCceeEE-EEecCHHHHHHHHHh
Q psy3760 161 --IPCYQ-WEYVIIVPLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIV-LETINSDIIKTYVEL 236 (306)
Q Consensus 161 --~~l~~-~~~~~v~~~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~v~~ 236 (306)
..... ....+++.++.+ ..+++||.+.++.....+....-.+..++...|+.+..+ +..-....+...+..
T Consensus 108 va~~~~~~~~~~i~~~~~~~-----i~~~adlkGk~vg~~~~~~~~~~~l~~~L~~~Gl~~~dv~~v~~~~~~~~~al~~ 182 (335)
T COG0715 108 VAALVQNGNGIALLVLKDSG-----IKSVADLKGKKVGVPFGGSTSDFLLRYALAKAGLDPDDVELVNLPPADAVAALAA 182 (335)
T ss_pred eeecccCCceeEEEeccCCC-----cccccCCCCceEEEeCCCchHHHHHHHHHHHcCCCcccceEEeeCcHHHHHHHhc
Confidence 11112 134555555543 235899999999888877545568889999999987443 333344456666655
Q ss_pred c-cceeeeecceeccc-ccCCceeeecCCCCc--cceEEEEEeCCcc--ccHHHHHHHHHHhHHh
Q psy3760 237 R-MGIGIIASIAFDSN-RDKNLRSISASHLFG--TTISRVIIKQGTY--LRSYVYSFIKLLSPKL 295 (306)
Q Consensus 237 g-~gi~~~p~~~~~~~-~~~~l~~~~~~~~~~--~~~~~l~~~~~~~--~~~~~~~~~~~l~~~~ 295 (306)
| .......+...... ..+.-+.+....... ....+++.++... ....+++|++.+.+..
T Consensus 183 g~vda~~~~ep~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~l~a~~~a~ 247 (335)
T COG0715 183 GQVDAFVVWEPWNAAAEGEGGGRVLLDGADLWGNHPELVLVVRKEFIEANPEAVKAFLKALAKAT 247 (335)
T ss_pred CCcceEEecCCchhhhhccCCeEEEEcchhhhccCchhhhhhHHHHHHHCHHHHHHHHHHHHHHH
Confidence 5 33344444443333 444444444433222 2233344443222 4778899988886654
No 237
>PF01325 Fe_dep_repress: Iron dependent repressor, N-terminal DNA binding domain; InterPro: IPR022687 The DtxR-type HTH domain is a DNA-binding, winged helix-turn-helix (wHTH) domain of about 65 residues present in metalloregulators of the DtxR/MntR family. The family is named after Corynebacterium diphtheriae DtxR, an iron-specific diphtheria toxin repressor, and Bacillus subtilis MntR, a manganese transport regulator. Iron-responsive metalloregulators such as DtxR and IdeR occur in Gram-positive bacteria of the high GC branch, while manganese-responsive metalloregulators like MntR are described in diverse genera of Gram-positive and Gram-negative bacteria and also in Archaea [].The metalloregulators like DtxR/MntR contain the DNA-binding DtxR-type HTH domain usually in the N-terminal part. The C-terminal part contains a dimerisation domain with two metal-binding sites, although the primary metal-binding site is less conserved in the Mn(II)-regulators. Fe(II)-regulated proteins contain an SH3-like domain as a C-terminal extension, which is absent in Mn(II)-regulated MntR [, ]. Metal-ion dependent regulators orchestrate the virulence of several important human pathogens. The DtxR protein regulates the expression of diphtheria toxinin response to environmental iron concentrations. Furthermore, DtxR and IdeR control iron uptake []. Homeostasis of manganese, which is an essential nutrient, is regulated by MntR. A typical DtxR-type metalloregulator binds two divalent metal effectors per monomer, upon which allosteric changes occur that moderate binding to the cognate DNA operators. Iron-bound DtxR homodimers bind to an interrupted palindrome of 19 bp, protecting a sequence of ~30 bp. The crystal structures of iron-regulated and manganese-regulated repressors show that the DNA binding domain contains three alpha-helices and a pair of antiparallel beta-strands. Helices 2 and 3 comprise the helix-turn-helix motif and the beta-strands are called the wing []. This wHTH topology is similar to the lysR-type HTH (see PDOC00043 from PROSITEDOC). Most DtxR-type metalloregulators bind as dimers to the DNA major groove. Several proteins are known to contain a DtxR-type HTH domain. These include- Corynebacterium diphtheriae DtxR, a diphtheria toxin repressor [], which regulates the expression of the high-affinity iron uptake system, other iron-sensitive genes, and the bacteriophage tox gene. Metal-bound DtxR represses transcription by binding the tox operator; if iron is limiting, conformational changes of the wHTH disrupt DNA-binding and the diphtheria toxin is produced. Mycobacterium tuberculosis IdeR, an iron-dependent regulator that is essential for this pathogen. The regulator represses genes for iron acquisition and activates iron storage genes, and is a positive regulator of oxidative stress responses []. Bacillus subtilis MntR, a manganese transport regulator, binds Mn2+ as an effector and is a transcriptional repressor of transporters for the import of manganese. Treponema pallidum troR, a metal-dependent transcriptional repressor. Archaeoglobus fulgidus MDR1 (troR), a metal-dependent transcriptional repressor, which negatively regulates its own transcription. This entry covers the entire DtxR-type HTH domain.; GO: 0005506 iron ion binding; PDB: 3HRT_B 3HRS_A 3HRU_B 2X4H_D 1ON1_B 2HYF_C 2F5E_A 3R60_B 1ON2_B 2F5F_A ....
Probab=95.83 E-value=0.011 Score=35.33 Aligned_cols=26 Identities=27% Similarity=0.358 Sum_probs=22.7
Q ss_pred CHHHHHHHhCCCchHHHHHHHHHHHH
Q psy3760 18 NLTEAAKALYTSQPGVSKAIIELEEE 43 (306)
Q Consensus 18 s~~~aA~~l~isq~~~s~~i~~LE~~ 43 (306)
+.+.-|+.|++|+||+|..+++|++.
T Consensus 24 ~~~~iA~~L~vs~~tvt~ml~~L~~~ 49 (60)
T PF01325_consen 24 RTKDIAERLGVSPPTVTEMLKRLAEK 49 (60)
T ss_dssp BHHHHHHHHTS-HHHHHHHHHHHHHT
T ss_pred cHHHHHHHHCCChHHHHHHHHHHHHC
Confidence 56788999999999999999999874
No 238
>PRK09959 hybrid sensory histidine kinase in two-component regulatory system with EvgA; Provisional
Probab=95.79 E-value=0.72 Score=46.00 Aligned_cols=193 Identities=8% Similarity=0.005 Sum_probs=107.8
Q ss_pred CCcEEEEecccch-----------hhhhHHHHHHHHHhCCCcEEEEEeCC-hhHHHHHHHcCCeeEEEEcccc-CCCCCc
Q psy3760 92 TGNLTIATTHTQA-----------RYALPKIIKEFTIQFPKVKLSLLQGN-PKQITEMIRNDQADIAIVTEIL-SPSDKL 158 (306)
Q Consensus 92 ~~~l~I~~~~~~~-----------~~~l~~~l~~~~~~~p~~~i~~~~~~-~~~~~~~l~~~~~Di~i~~~~~-~~~~~~ 158 (306)
.+.|++|+.+... ..+...++..+.+.- ++++++.... ..+....|.+|++|+....... .....+
T Consensus 301 ~~~l~v~~~~~~pP~~~~d~~g~~~G~~~Dll~~i~~~~-g~~~~~v~~~~~~~~~~~l~~g~~D~i~~~~~t~~r~~~~ 379 (1197)
T PRK09959 301 HPDLKVLENPYSPPYSMTDENGSVRGVMGDILNIITLQT-GLNFSPITVSHNIHAGTQLNPGGWDIIPGAIYSEDRENNV 379 (1197)
T ss_pred CCceEEEcCCCCCCeeEECCCCcEeeehHHHHHHHHHHH-CCeEEEEecCCHHHHHHHHHCCCceEeecccCCccccccc
Confidence 4689999875322 245566777776654 6888877754 4456778999999987653221 122223
Q ss_pred -eeeccccceEEEEecCCCCCCCCCCcChhhh-cCCCeEeecCCCCcHHHHHHHHHhCCCceeEEEEecCHHHHHHHHHh
Q psy3760 159 -ISIPCYQWEYVIIVPLDHPLLLLNSISLKEI-SNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVEL 236 (306)
Q Consensus 159 -~~~~l~~~~~~~v~~~~~~l~~~~~i~~~dl-~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~ 236 (306)
-+.|++..+++++++++... ..++ .+.. |....+... ..++...... .....+++...++.++.+
T Consensus 380 ~fs~py~~~~~~~v~~~~~~~-------~~~~~~g~~-vav~~g~~~----~~~~~~~~p~-~~~~~~~~~~~~l~av~~ 446 (1197)
T PRK09959 380 LFAEAFITTPYVFVMQKAPDS-------EQTLKKGMK-VAIPYYYEL----HSQLKEMYPE-VEWIKVDNASAAFHKVKE 446 (1197)
T ss_pred eeccccccCCEEEEEecCCCC-------ccccccCCE-EEEeCCcch----HHHHHHHCCC-cEEEEcCCHHHHHHHHHc
Confidence 36688888999888766421 1122 2333 333333322 2333333212 234678999999999999
Q ss_pred ccceeeeeccee-ccc-c---cCCceeeecCCCCccceEEEEEeCCccccHHHHHHHHHHhHHhhHHHHHh
Q psy3760 237 RMGIGIIASIAF-DSN-R---DKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLLSPKLNRKFINK 302 (306)
Q Consensus 237 g~gi~~~p~~~~-~~~-~---~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~ 302 (306)
|..=+++..... ..+ . .+.+..+..+. .....+++..+++. +.....++..-..+.+...++
T Consensus 447 G~~Da~i~~~~~~~~~~~~~~~~~l~~~~~~~-~~~~~~~~av~k~~---~~L~~~lnk~l~~i~~~~~~~ 513 (1197)
T PRK09959 447 GELDALVATQLNSRYMIDHYYPNELYHFLIPG-VPNASLSFAFPRGE---PELKDIINKALNAIPPSEVLR 513 (1197)
T ss_pred CCCCEEehhhHHHHHHHHhcccccceeeecCC-CCchheEEeeCCCC---HHHHHHHHHHHHhCCHHHHHH
Confidence 977666544322 222 1 13344444333 23346777777764 334444443333343334433
No 239
>PF07453 NUMOD1: NUMOD1 domain; InterPro: IPR010896 This helix-turn-helix-containing DNA-binding domain is found associated in homing nucleases [].
Probab=95.79 E-value=0.0075 Score=32.08 Aligned_cols=23 Identities=30% Similarity=0.335 Sum_probs=20.0
Q ss_pred HhcCCHHHHHHHhCCCchHHHHHH
Q psy3760 14 RQNFNLTEAAKALYTSQPGVSKAI 37 (306)
Q Consensus 14 ~~~~s~~~aA~~l~isq~~~s~~i 37 (306)
+-. |+++||+.||+++++|++.|
T Consensus 15 ~F~-Si~eAa~~l~i~~~~I~~~l 37 (37)
T PF07453_consen 15 SFD-SIREAARYLGISHSTISKYL 37 (37)
T ss_pred EEc-CHHHHHHHhCCCHHHHHHhC
Confidence 346 99999999999999999864
No 240
>COG1342 Predicted DNA-binding proteins [General function prediction only]
Probab=95.77 E-value=0.014 Score=37.63 Aligned_cols=50 Identities=10% Similarity=0.121 Sum_probs=41.7
Q ss_pred CchhhHHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEE
Q psy3760 1 MNLHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFI 50 (306)
Q Consensus 1 m~~~~l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~ 50 (306)
|+++-|+.+-.+--.+.+...||.+++||++|+++.+++-....-.-|++
T Consensus 34 lt~eElEAlRLvD~~~l~QeeAA~rMgISr~Tfwr~l~sAR~KvA~aLve 83 (99)
T COG1342 34 LTIEELEALRLVDYEGLTQEEAALRMGISRQTFWRLLTSARKKVADALVE 83 (99)
T ss_pred ecHHHHHHHHHHhHhhccHHHHHHHhcccHHHHHHHHHHHHHHHHHHHhc
Confidence 46677788777777777999999999999999999999988887666654
No 241
>PF02796 HTH_7: Helix-turn-helix domain of resolvase; InterPro: IPR006120 Site-specific recombination plays an important role in DNA rearrangement in prokaryotic organisms. Two types of site-specific recombination are known to occur: Recombination between inverted repeats resulting in the reversal of a DNA segment. Recombination between repeat sequences on two DNA molecules resulting in their cointegration, or between repeats on one DNA molecule resulting in the excision of a DNA fragment. Site-specific recombination is characterised by a strand exchange mechanism that requires no DNA synthesis or high energy cofactor; the phosphodiester bond energy is conserved in a phospho-protein linkage during strand cleavage and re-ligation. Two unrelated families of recombinases are currently known []. The first, called the 'phage integrase' family, groups a number of bacterial phage and yeast plasmid enzymes. The second [], called the 'resolvase' family, groups enzymes which share the following structural characteristics: an N-terminal catalytic and dimerization domain that contains a conserved serine residue involved in the transient covalent attachment to DNA IPR006119 from INTERPRO, and a C-terminal helix-turn-helix DNA-binding domain. ; GO: 0000150 recombinase activity, 0003677 DNA binding, 0006310 DNA recombination; PDB: 1ZR2_A 2GM4_B 1RES_A 1ZR4_A 1RET_A 1GDT_B 2R0Q_C 1JKP_C 1IJW_C 1JJ6_C ....
Probab=95.68 E-value=0.013 Score=32.71 Aligned_cols=36 Identities=19% Similarity=0.226 Sum_probs=28.3
Q ss_pred hhhHHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHH
Q psy3760 3 LHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAII 38 (306)
Q Consensus 3 ~~~l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~ 38 (306)
-++++....+.+.|.|+.+.|+.+|+|.+||-|-++
T Consensus 8 ~~~~~~i~~l~~~G~si~~IA~~~gvsr~TvyR~l~ 43 (45)
T PF02796_consen 8 KEQIEEIKELYAEGMSIAEIAKQFGVSRSTVYRYLN 43 (45)
T ss_dssp HCCHHHHHHHHHTT--HHHHHHHTTS-HHHHHHHHC
T ss_pred HHHHHHHHHHHHCCCCHHHHHHHHCcCHHHHHHHHh
Confidence 346777888889988999999999999999998764
No 242
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=95.66 E-value=0.028 Score=41.10 Aligned_cols=42 Identities=10% Similarity=0.073 Sum_probs=33.7
Q ss_pred chhhHHHHHHHHHhc-CCHHHHHHHhCCCchHHHHHHHHHHHH
Q psy3760 2 NLHQFRFVREAVRQN-FNLTEAAKALYTSQPGVSKAIIELEEE 43 (306)
Q Consensus 2 ~~~~l~~f~~v~~~~-~s~~~aA~~l~isq~~~s~~i~~LE~~ 43 (306)
|-.+.+++..+.+.| .|+++-|+++|+|++|+.++|++|++.
T Consensus 8 D~~D~~Il~~Lq~d~R~s~~eiA~~lglS~~tV~~Ri~rL~~~ 50 (153)
T PRK11179 8 DNLDRGILEALMENARTPYAELAKQFGVSPGTIHVRVEKMKQA 50 (153)
T ss_pred CHHHHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence 445566666665552 399999999999999999999999985
No 243
>PRK04217 hypothetical protein; Provisional
Probab=95.64 E-value=0.04 Score=37.39 Aligned_cols=51 Identities=18% Similarity=0.193 Sum_probs=40.3
Q ss_pred CchhhHHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEe
Q psy3760 1 MNLHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIR 51 (306)
Q Consensus 1 m~~~~l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R 51 (306)
|+-++.+.+......|.|+...|+.+++|.+||.+.+++..+.|-..|...
T Consensus 43 Lt~eereai~l~~~eGlS~~EIAk~LGIS~sTV~r~L~RArkkLre~L~~~ 93 (110)
T PRK04217 43 MTYEEFEALRLVDYEGLTQEEAGKRMGVSRGTVWRALTSARKKVAQMLVEG 93 (110)
T ss_pred CCHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHhc
Confidence 344566777777756669999999999999999999998888885555433
No 244
>PF09114 MotA_activ: Transcription factor MotA, activation domain; InterPro: IPR015198 Transcription factor MotA is required for the activation of middle promoters in Bacteriophage T4, in addition to phage T4 co-activator AsiA, and sigma-70-containing Escherichia coli RNA polymerase. Phage T4 middle promoters have the sigma70 -10 DNA element, but not the -35 element; instead, they have a MotA box at -30 to which the transcription factor MotA binds []. MotA and AsiA interact with the C-terminal of sigma70 (region 4), which normally binds the -35 element and the beta-flap, thereby diverting sigma70 away from host promoters that require -35 element-binding to phage T4 middle promoters. Transcription factor MotA has two domains: an N-terminal domain required for binding to sigma70, and a C-terminal domain required for binding to the -30 MotA box element in the phage T4 middle promoter. This entry represents the N-terminal (activation) domain of MotA factors that binds sigma70. The N-terminal domain adopts an almost completely alpha-helical topology, with five alpha-helices and a short, two-stranded, beta-ribbon. Four alpha helices (alpha1, alpha3, alpha4 and alpha5) are amphipathic and pack their hydrophobic surfaces around the central helix alpha2 [].; PDB: 1BJA_B 1I1S_A.
Probab=95.50 E-value=0.14 Score=32.64 Aligned_cols=73 Identities=16% Similarity=0.259 Sum_probs=55.8
Q ss_pred hhhHHHHHHHHHhcC-CHHHHHHHh--CCCchHHHHHHHHHHHHcCceeEEecCCCccccCHhHHHHHHHHHHHHHHHHH
Q psy3760 3 LHQFRFVREAVRQNF-NLTEAAKAL--YTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKPGQAILRSIEIIMQEIEG 79 (306)
Q Consensus 3 ~~~l~~f~~v~~~~~-s~~~aA~~l--~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~~~lT~~G~~l~~~a~~il~~~~~ 79 (306)
-+..-+|+.+++..| +.+..++.| .++.+.+-+.|..| +..-|.+++|-|++ .|..|..++..|-.+..+.+.
T Consensus 16 E~~~~ilI~v~Kk~Fit~~ev~e~l~~~~~~~~V~SNIGvL---IKkglIEKSGDGlv-~T~~g~~Ii~~AA~l~a~en~ 91 (96)
T PF09114_consen 16 ENAANILIQVAKKNFITASEVREALATEMNKASVNSNIGVL---IKKGLIEKSGDGLV-ITEEGMDIIIQAAELWAQENA 91 (96)
T ss_dssp HHHHHHHHHHHHSTTB-HHHHHH-T-TTS-HHHHHHHHHHH---HHTTSEEEETTEEE-E-HHHHHHHHHHHHHHHHHTH
T ss_pred HHHHHHHHHHHHHccCCHHHHHHHHHHHhhhhHHHHhHHHH---HHcCcccccCCceE-EechHHHHHHHHHHHHHhcCC
Confidence 355678888998776 667788877 68888888878776 44679999999995 999999999999988876543
No 245
>PF14549 P22_Cro: DNA-binding transcriptional regulator Cro; PDB: 1RZS_A 3BD1_A 3QWS_A 2HIN_B.
Probab=95.48 E-value=0.02 Score=34.13 Aligned_cols=25 Identities=28% Similarity=0.104 Sum_probs=21.3
Q ss_pred HHHHhcCCHHHHHHHhCCCchHHHHH
Q psy3760 11 EAVRQNFNLTEAAKALYTSQPGVSKA 36 (306)
Q Consensus 11 ~v~~~~~s~~~aA~~l~isq~~~s~~ 36 (306)
++.-.| |.++.|+.||||+++||+.
T Consensus 5 aI~~~G-~~~~lAkalGVs~~aVs~W 29 (60)
T PF14549_consen 5 AIKYFG-GQSKLAKALGVSPQAVSQW 29 (60)
T ss_dssp HHHHHS-SHHHHHHHHTS-HHHHHHH
T ss_pred HHHHHC-CHHHHHHHHCCCHHHHHHh
Confidence 455668 9999999999999999988
No 246
>PRK09834 DNA-binding transcriptional activator MhpR; Provisional
Probab=95.44 E-value=0.18 Score=40.63 Aligned_cols=62 Identities=13% Similarity=0.013 Sum_probs=45.0
Q ss_pred hHHHHHHHHHhc--CCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCCccccCHhHHHHHH
Q psy3760 5 QFRFVREAVRQN--FNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKPGQAILR 68 (306)
Q Consensus 5 ~l~~f~~v~~~~--~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~~~lT~~G~~l~~ 68 (306)
-+.++-.+.+.+ .|++.-|+.++++.||++|.|+.|++ .|.--....++.. +||+.+..+..
T Consensus 13 al~iL~~l~~~~~~ls~~eia~~lgl~kstv~RlL~tL~~-~g~v~~~~~~~~Y-~Lg~~~~~l~~ 76 (263)
T PRK09834 13 GLMVLRALNRLDGGATVGLLAELTGLHRTTVRRLLETLQE-EGYVRRSASDDSF-RLTLKVRQLSE 76 (263)
T ss_pred HHHHHHHHHhcCCCCCHHHHHHHHCcCHHHHHHHHHHHHH-CCCEEEecCCCcE-EEcHHHHHHHH
Confidence 345555555543 37999999999999999999999986 3544444446677 79987766543
No 247
>PRK13509 transcriptional repressor UlaR; Provisional
Probab=95.37 E-value=0.35 Score=38.65 Aligned_cols=48 Identities=10% Similarity=0.081 Sum_probs=36.2
Q ss_pred HHHHHHHHHhc-CCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCCc
Q psy3760 6 FRFVREAVRQN-FNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRI 56 (306)
Q Consensus 6 l~~f~~v~~~~-~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~ 56 (306)
-+++-.+.+.| .+....|+.+++|++|+.|-|++||++ .++.|.++|.
T Consensus 8 ~~Il~~l~~~~~~~~~ela~~l~vS~~TirRdL~~Le~~---g~i~r~~gga 56 (251)
T PRK13509 8 QILLELLAQLGFVTVEKVIERLGISPATARRDINKLDES---GKLKKVRNGA 56 (251)
T ss_pred HHHHHHHHHcCCcCHHHHHHHHCcCHHHHHHHHHHHHHC---CCEEEecCCc
Confidence 33444444433 267889999999999999999999974 5678887776
No 248
>PRK11886 bifunctional biotin--[acetyl-CoA-carboxylase] synthetase/biotin operon repressor; Provisional
Probab=95.35 E-value=0.043 Score=45.64 Aligned_cols=44 Identities=32% Similarity=0.372 Sum_probs=38.1
Q ss_pred CHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCCccccCHhH
Q psy3760 18 NLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKPG 63 (306)
Q Consensus 18 s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~~~lT~~G 63 (306)
|.+.-|+.+++|+++++++|+.|+ +.|..+..+.++|. .+.+..
T Consensus 20 s~~~LA~~lgvsr~tV~~~l~~L~-~~G~~i~~~~~~Gy-~L~~~~ 63 (319)
T PRK11886 20 SGEQLGEELGISRAAIWKHIQTLE-EWGLDIFSVKGKGY-RLAEPL 63 (319)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHH-HCCCceEEecCCeE-EecCcc
Confidence 778889999999999999999999 69999999887787 565543
No 249
>TIGR01481 ccpA catabolite control protein A. Catabolite control protein A is a LacI family global transcriptional regulator found in Gram-positive bacteria. CcpA is involved in repressing carbohydrate utilization genes [ex: alpha-amylase (amyE), acetyl-coenzyme A synthase (acsA)] and in activating genes involved in transporting excess carbon from the cell [ex: acetate kinase (ackA), alpha-acetolactate synthase (alsS)]. Additionally, disruption of CcpA in Bacillus megaterium, Staphylococcus xylosus, Lactobacillus casei and Lactocacillus pentosus also decreases growth rate, which suggests CcpA is involved in the regulation of other metabolic pathways.
Probab=95.35 E-value=0.48 Score=39.51 Aligned_cols=109 Identities=13% Similarity=0.182 Sum_probs=59.8
Q ss_pred CHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCCccccCHhHHHHHHHHHHHHHHHHHHHH----HHHhhccCCCC
Q psy3760 18 NLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKPGQAILRSIEIIMQEIEGLKK----IGKEFSAYDTG 93 (306)
Q Consensus 18 s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~~~lT~~G~~l~~~a~~il~~~~~~~~----~~~~~~~~~~~ 93 (306)
++...|+..|+|.+||||.|. ++.++ .+ +..+++++..+++-. ..+.+..+.++
T Consensus 3 ti~dIA~~agvS~~TVSrvLn-------------~~~~v---s~------~tr~rV~~~a~~lgY~pn~~a~~l~~~~~~ 60 (329)
T TIGR01481 3 TIYDVAREAGVSMATVSRVVN-------------GNPNV---KP------ATRKKVLEVIKRLDYRPNAVARGLASKRTT 60 (329)
T ss_pred cHHHHHHHhCCCHHHHHHHhC-------------CCCCC---CH------HHHHHHHHHHHHHCCCCCHHHHHHhhCCCC
Confidence 678899999999999999984 22232 22 222233333333321 11223333344
Q ss_pred cEEEEecccchhhhhHHHHHHHHHhCC--CcEEEEEeCC--h---hHHHHHHHcCCeeEEEEc
Q psy3760 94 NLTIATTHTQARYALPKIIKEFTIQFP--KVKLSLLQGN--P---KQITEMIRNDQADIAIVT 149 (306)
Q Consensus 94 ~l~I~~~~~~~~~~l~~~l~~~~~~~p--~~~i~~~~~~--~---~~~~~~l~~~~~Di~i~~ 149 (306)
.|-+-++. +...++..++..+.+... +..+.+.... . .+.++.+.++++|-.|..
T Consensus 61 ~Igvv~~~-~~~~f~~~l~~~i~~~~~~~g~~~~i~~~~~~~~~~~~~~~~l~~~~vdGiIi~ 122 (329)
T TIGR01481 61 TVGVIIPD-ISNIYYAELARGIEDIATMYKYNIILSNSDEDPEKEVQVLNTLLSKQVDGIIFM 122 (329)
T ss_pred EEEEEeCC-CCchhHHHHHHHHHHHHHHcCCEEEEEeCCCCHHHHHHHHHHHHhCCCCEEEEe
Confidence 55555543 344566666655544322 5566554332 1 134566778899998875
No 250
>COG1733 Predicted transcriptional regulators [Transcription]
Probab=95.34 E-value=0.11 Score=36.07 Aligned_cols=62 Identities=21% Similarity=0.192 Sum_probs=48.4
Q ss_pred HhcCCHHHHHHHhC-CCchHHHHHHHHHHHHcCceeEEecCCC------ccccCHhHHHHHHHHHHHHHHHHH
Q psy3760 14 RQNFNLTEAAKALY-TSQPGVSKAIIELEEELSIDIFIRHGKR------IRGLTKPGQAILRSIEIIMQEIEG 79 (306)
Q Consensus 14 ~~~~s~~~aA~~l~-isq~~~s~~i~~LE~~lg~~Lf~R~~~~------~~~lT~~G~~l~~~a~~il~~~~~ 79 (306)
... .|+.=-+.++ |||..+|+++++||+. -|+.|.-.. -.+||+.|+.|.+-...+.+=.+.
T Consensus 35 g~~-RF~eL~r~i~~Is~k~Ls~~Lk~Le~~---Glv~R~~~~~~PprveY~LT~~G~~L~~vl~~l~~Wg~~ 103 (120)
T COG1733 35 GPK-RFNELRRSIGGISPKMLSRRLKELEED---GLVERVVYPEEPPRVEYRLTEKGRDLLPVLLALADWGEK 103 (120)
T ss_pred CCC-cHHHHHHHccccCHHHHHHHHHHHHHC---CCEEeeecCCCCceeEEEEhhhHHHHHHHHHHHHHHHHH
Confidence 444 7999999999 9999999999999984 466776332 128999999999988887554443
No 251
>COG1609 PurR Transcriptional regulators [Transcription]
Probab=95.33 E-value=0.23 Score=41.66 Aligned_cols=137 Identities=12% Similarity=0.099 Sum_probs=76.2
Q ss_pred CHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCCccccCHhHHHHHHHHHHHHHHHHHH-HHHHHhhccCCCCcEE
Q psy3760 18 NLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKPGQAILRSIEIIMQEIEGL-KKIGKEFSAYDTGNLT 96 (306)
Q Consensus 18 s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~~~lT~~G~~l~~~a~~il~~~~~~-~~~~~~~~~~~~~~l~ 96 (306)
++...|+..|+|.+|+||.|.. ++. .+++= -+++.+..+++.-. ....+.+..+.++.|-
T Consensus 2 TikDVA~~AGVS~sTVSrvln~--------------~~~--Vs~eT---r~kV~~a~~elgY~pN~~Ar~L~~~~s~~Ig 62 (333)
T COG1609 2 TIKDVAKLAGVSKATVSRVLNG--------------SPY--VSEET---REKVLAAIKELGYRPNAVARSLRTGRTKTIG 62 (333)
T ss_pred CHHHHHHHhCCCHHHHHHHHcC--------------CCC--CCHHH---HHHHHHHHHHHCCCCCHHHHHHHhCCCCEEE
Confidence 5778999999999999998842 222 22211 22222233332222 1223444444555666
Q ss_pred EEecccchhhhhHHHHHHHHHhCC--CcEEEEEeCCh-----hHHHHHHHcCCeeEEEEccccCCCCCceeeccccceEE
Q psy3760 97 IATTHTQARYALPKIIKEFTIQFP--KVKLSLLQGNP-----KQITEMIRNDQADIAIVTEILSPSDKLISIPCYQWEYV 169 (306)
Q Consensus 97 I~~~~~~~~~~l~~~l~~~~~~~p--~~~i~~~~~~~-----~~~~~~l~~~~~Di~i~~~~~~~~~~~~~~~l~~~~~~ 169 (306)
+-++ .+...++..++..+.+..- +.++.+...+. .+..+.+.+.++|-.|........+......-...+++
T Consensus 63 ~i~p-~~~~~~~~~i~~gi~~~~~~~gy~~~l~~~~~~~~~e~~~~~~l~~~~vdGiIi~~~~~~~~~~~~l~~~~~P~V 141 (333)
T COG1609 63 LVVP-DITNPFFAEILKGIEEAAREAGYSLLLANTDDDPEKEREYLETLLQKRVDGLILLGERPNDSLLELLAAAGIPVV 141 (333)
T ss_pred EEeC-CCCCchHHHHHHHHHHHHHHcCCEEEEECCCCCHHHHHHHHHHHHHcCCCEEEEecCCCCHHHHHHHHhcCCCEE
Confidence 6555 3344677777777666543 55555555443 23578899999999999652222222223333345666
Q ss_pred EEecC
Q psy3760 170 IIVPL 174 (306)
Q Consensus 170 ~v~~~ 174 (306)
++-..
T Consensus 142 ~i~~~ 146 (333)
T COG1609 142 VIDRS 146 (333)
T ss_pred EEeCC
Confidence 66543
No 252
>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=95.31 E-value=0.074 Score=30.62 Aligned_cols=43 Identities=14% Similarity=0.102 Sum_probs=34.4
Q ss_pred chhhHHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHc
Q psy3760 2 NLHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEEL 44 (306)
Q Consensus 2 ~~~~l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~l 44 (306)
+-++.+.|...+..|.|....|+.+|+|++++.+.+.+..+.+
T Consensus 12 ~~~~~~~~~~~~~~~~~~~~ia~~~~~s~~~i~~~~~~~~~~l 54 (55)
T cd06171 12 PEREREVILLRFGEGLSYEEIAEILGISRSTVRQRLHRALKKL 54 (55)
T ss_pred CHHHHHHHHHHHhcCCCHHHHHHHHCcCHHHHHHHHHHHHHHc
Confidence 3455667777764445999999999999999999999887654
No 253
>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=95.26 E-value=0.046 Score=33.27 Aligned_cols=40 Identities=28% Similarity=0.258 Sum_probs=30.8
Q ss_pred CHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCCccccC
Q psy3760 18 NLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLT 60 (306)
Q Consensus 18 s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~~~lT 60 (306)
|...-|+.+++|.+++++.|++|++ -|. +....++|+ .+|
T Consensus 27 ~~~~la~~~~is~~~v~~~l~~L~~-~G~-i~~~~~~~~-~l~ 66 (66)
T cd07377 27 SERELAEELGVSRTTVREALRELEA-EGL-VERRPGRGT-FVA 66 (66)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHH-CCC-EEecCCCeE-EeC
Confidence 4778899999999999999999998 455 444445565 454
No 254
>COG3888 Predicted transcriptional regulator [Transcription]
Probab=95.26 E-value=0.11 Score=40.53 Aligned_cols=177 Identities=16% Similarity=0.104 Sum_probs=106.0
Q ss_pred HHHHHHHhCCCchHHHHHHHHHHHHcCceeEEec---C--CCccccCHhHHHHHHHHHHHHHHHHHHHHHHHhhccCCCC
Q psy3760 19 LTEAAKALYTSQPGVSKAIIELEEELSIDIFIRH---G--KRIRGLTKPGQAILRSIEIIMQEIEGLKKIGKEFSAYDTG 93 (306)
Q Consensus 19 ~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~---~--~~~~~lT~~G~~l~~~a~~il~~~~~~~~~~~~~~~~~~~ 93 (306)
=++-.+-+|.|.||+|-.++.||++ ..+.|. | +.++ |. +...--..+
T Consensus 23 Q~eIeel~GlSKStvSEaLs~LE~~---giv~RrkvsGKs~rVw-La------------------------ey~Py~d~~ 74 (321)
T COG3888 23 QTEIEELMGLSKSTVSEALSELEKQ---GIVKRRKVSGKSKRVW-LA------------------------EYSPYPDSR 74 (321)
T ss_pred HHHHHHHhCcchhHHHHHHHHHHhc---CeeeeeeecCcceEEe-ec------------------------ccCCCCCcc
Confidence 3567788999999999999999986 344443 1 2221 11 122334567
Q ss_pred cEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccCCCCCceeecccc---ceEE-
Q psy3760 94 NLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLISIPCYQ---WEYV- 169 (306)
Q Consensus 94 ~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~~~~~~~~~l~~---~~~~- 169 (306)
-+|||+-.+.....+.++...+.+.-=.+.+++... .-++...|-.|.+|+|...-- .+.++. -...
T Consensus 75 ~lRiGiLRatEYp~~i~aaKnl~e~ki~a~iR~Ydd-aisit~DLv~g~ld~~lSPii--------Tq~ifsi~~rni~I 145 (321)
T COG3888 75 FLRIGILRATEYPFFISAAKNLEERKISATIRFYDD-AISITRDLVEGKLDFGLSPII--------TQIIFSISYRNIRI 145 (321)
T ss_pred cEEEeeeecccchhHhHHHHhhhhccceEEEEEecc-HHHHHHHHHhhhhhhcccHHH--------HHHHHHHHhcceEE
Confidence 899999988777788888888887754455555544 447888999999999997411 111111 1111
Q ss_pred --EEecCCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCceeEEEEecCHHHHHHHHHhc--cceee
Q psy3760 170 --IIVPLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELR--MGIGI 242 (306)
Q Consensus 170 --~v~~~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g--~gi~~ 242 (306)
-|++.+.-+.. .. -...+.......+...+.++.+..++. . .-.+.+...++.-..+| .+|++
T Consensus 146 ~g~vAsgGgGi~~------n~--cn~~~~tsesSsmm~~~ref~~~egi~-~-I~yfs~p~~mid~l~~g~~r~IaI 212 (321)
T COG3888 146 IGGVASGGGGIIG------NT--CNRIASTSESSSMMWLFREFKNIEGIP-S-ISYFSDPESMIDFLEKGIVRYIAI 212 (321)
T ss_pred EeccccCCCceec------cc--cceeeeecccHHHHHHHHHHHhhcCCc-c-eeeecCHHHHHhHhhhcceeEEEE
Confidence 22222222111 11 112444444444444555555555554 3 44567788888888888 55555
No 255
>PF02001 DUF134: Protein of unknown function DUF134; InterPro: IPR002852 The bacterial and archaeal proteins in this family have no known function.
Probab=95.24 E-value=0.026 Score=37.85 Aligned_cols=48 Identities=13% Similarity=0.250 Sum_probs=41.0
Q ss_pred CchhhHHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCcee
Q psy3760 1 MNLHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDI 48 (306)
Q Consensus 1 m~~~~l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~L 48 (306)
|+++-++.+..+.-.|.|-..||+++|||++|+++.+.+-...+-.-|
T Consensus 42 L~~dElEAiRL~D~egl~QeeaA~~MgVSR~T~~ril~~ARkKiA~AL 89 (106)
T PF02001_consen 42 LTVDELEAIRLVDYEGLSQEEAAERMGVSRPTFQRILESARKKIADAL 89 (106)
T ss_pred eeHHHHHHHHHHHHcCCCHHHHHHHcCCcHHHHHHHHHHHHHHHHHHH
Confidence 456788888888888889999999999999999999998887774444
No 256
>PHA02591 hypothetical protein; Provisional
Probab=95.20 E-value=0.034 Score=34.25 Aligned_cols=31 Identities=23% Similarity=0.251 Sum_probs=27.2
Q ss_pred HHHHHHHhcCCHHHHHHHhCCCchHHHHHHH
Q psy3760 8 FVREAVRQNFNLTEAAKALYTSQPGVSKAII 38 (306)
Q Consensus 8 ~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~ 38 (306)
.-..+++.|+|..+-|+.||+||++|++-++
T Consensus 51 vA~eL~eqGlSqeqIA~~LGVsqetVrKYL~ 81 (83)
T PHA02591 51 VTHELARKGFTVEKIASLLGVSVRKVRRYLE 81 (83)
T ss_pred HHHHHHHcCCCHHHHHHHhCCCHHHHHHHHh
Confidence 3456889999999999999999999998765
No 257
>PRK00430 fis global DNA-binding transcriptional dual regulator Fis; Provisional
Probab=95.15 E-value=0.046 Score=36.18 Aligned_cols=26 Identities=23% Similarity=0.100 Sum_probs=23.1
Q ss_pred hcCCHHHHHHHhCCCchHHHHHHHHH
Q psy3760 15 QNFNLTEAAKALYTSQPGVSKAIIEL 40 (306)
Q Consensus 15 ~~~s~~~aA~~l~isq~~~s~~i~~L 40 (306)
++++.++||+.||||++|+.+.+++.
T Consensus 67 ~~gn~s~AAr~LGIsRsTL~rKLkr~ 92 (95)
T PRK00430 67 TRGNQTRAALMLGINRGTLRKKLKKY 92 (95)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHHHh
Confidence 43389999999999999999999975
No 258
>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=95.12 E-value=0.072 Score=34.96 Aligned_cols=43 Identities=21% Similarity=0.210 Sum_probs=38.1
Q ss_pred hhHHHHHHHHHhcCCHHHHHHHhC-CCchHHHHHHHHHHHHcCc
Q psy3760 4 HQFRFVREAVRQNFNLTEAAKALY-TSQPGVSKAIIELEEELSI 46 (306)
Q Consensus 4 ~~l~~f~~v~~~~~s~~~aA~~l~-isq~~~s~~i~~LE~~lg~ 46 (306)
+++-.+++....|.|++..|+.+| .+.|||++.++++|+.+..
T Consensus 32 R~ia~yl~~~~~~~s~~~Ig~~fg~r~hStV~~a~~ri~~~~~~ 75 (90)
T cd06571 32 RQIAMYLARELTGLSLPEIGRAFGGRDHSTVLHAVRKIEELLEE 75 (90)
T ss_pred HHHHHHHHHHHhCCCHHHHHHHhCCCCHhHHHHHHHHHHHHHHh
Confidence 567777888887889999999999 9999999999999998853
No 259
>COG1522 Lrp Transcriptional regulators [Transcription]
Probab=95.10 E-value=0.052 Score=39.72 Aligned_cols=36 Identities=33% Similarity=0.367 Sum_probs=28.8
Q ss_pred HHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHH
Q psy3760 6 FRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEE 43 (306)
Q Consensus 6 l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~ 43 (306)
|+.+..=++ . |++.-|+.+|+|+++++++|++||+.
T Consensus 14 L~~L~~d~r-~-~~~eia~~lglS~~~v~~Ri~~L~~~ 49 (154)
T COG1522 14 LRLLQEDAR-I-SNAELAERVGLSPSTVLRRIKRLEEE 49 (154)
T ss_pred HHHHHHhCC-C-CHHHHHHHHCCCHHHHHHHHHHHHHC
Confidence 333333333 4 79999999999999999999999985
No 260
>COG2522 Predicted transcriptional regulator [General function prediction only]
Probab=95.07 E-value=0.03 Score=38.40 Aligned_cols=28 Identities=25% Similarity=0.252 Sum_probs=24.4
Q ss_pred HHHHhcCCHHHHHHHhCCCchHHHHHHH
Q psy3760 11 EAVRQNFNLTEAAKALYTSQPGVSKAII 38 (306)
Q Consensus 11 ~v~~~~~s~~~aA~~l~isq~~~s~~i~ 38 (306)
.+.+.|.|-.+.|+-||+||||||+=|+
T Consensus 17 ~L~eeG~Sq~~iA~LLGltqaAVS~Yls 44 (119)
T COG2522 17 ELIEEGLSQYRIAKLLGLTQAAVSQYLS 44 (119)
T ss_pred HHHHcCCcHHHHHHHhCCCHHHHHHHHc
Confidence 4566688999999999999999998775
No 261
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=94.97 E-value=0.039 Score=40.93 Aligned_cols=42 Identities=14% Similarity=0.122 Sum_probs=33.2
Q ss_pred chhhHHHHHHHHHhc-CCHHHHHHHhCCCchHHHHHHHHHHHH
Q psy3760 2 NLHQFRFVREAVRQN-FNLTEAAKALYTSQPGVSKAIIELEEE 43 (306)
Q Consensus 2 ~~~~l~~f~~v~~~~-~s~~~aA~~l~isq~~~s~~i~~LE~~ 43 (306)
|--+.+++..+.+.+ .|++.-|+++|+|++|+.++|++||+.
T Consensus 13 D~~D~~IL~~Lq~d~R~s~~eiA~~lglS~~tv~~Ri~rL~~~ 55 (164)
T PRK11169 13 DRIDRNILNELQKDGRISNVELSKRVGLSPTPCLERVRRLERQ 55 (164)
T ss_pred HHHHHHHHHHhccCCCCCHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence 334566666665543 388999999999999999999999985
No 262
>PF02621 VitK2_biosynth: Menaquinone biosynthesis; InterPro: IPR003773 This entry describes proteins of unknown function, which appear to be putative periplasmic binding proteins.; PDB: 3A3U_A 2CZL_A 1ZBM_A 2NXO_C 2I6E_E.
Probab=94.96 E-value=0.74 Score=36.82 Aligned_cols=183 Identities=13% Similarity=0.127 Sum_probs=89.7
Q ss_pred EEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEcccc--CCCCCceeec------cccc
Q psy3760 95 LTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEIL--SPSDKLISIP------CYQW 166 (306)
Q Consensus 95 l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~--~~~~~~~~~~------l~~~ 166 (306)
+|||..+.+.... +.-.+ ...+...++++.....++.+.+.+|++|++.++... ...+++...+ .+..
T Consensus 1 lrig~i~y~N~~P---l~~~l-~~~~~~~~~~~~~~P~~Ln~~l~~g~~Dv~~iSs~~y~~~~~~y~ilp~~~i~s~g~v 76 (251)
T PF02621_consen 1 LRIGRIPYLNDLP---LFYGL-IKGEPFDFEIVRGVPSELNQMLLEGELDVALISSIEYARNADDYLILPDLSISSDGPV 76 (251)
T ss_dssp EEEEEESSHHHHH---HHHHH-HCTSSCCEEEEEE-HHHHHHHHHTTS-SEEEEEHHHHCTCTTTEEEESCECEEECCSS
T ss_pred CEEEecCCCCccc---eeehh-hcCCCCceEEEECCHHHHHHHHHcCCCCEEEcCHHHHHHhhhhheecCCcEEEEcCCc
Confidence 5788887654433 33333 333467788999999999999999999999987221 1223333332 1111
Q ss_pred eEEEEecCCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCceeEEEEecCHHHHHHHHHhc-cceeeeec
Q psy3760 167 EYVIIVPLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELR-MGIGIIAS 245 (306)
Q Consensus 167 ~~~~v~~~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g-~gi~~~p~ 245 (306)
.=+++.+ + .+++++.+.+. ..+..+.....+.+.+-.....|..+.. . .....++.+| ++.-++-+
T Consensus 77 ~Sv~l~s-~--------~p~~~l~~~~i-al~~~S~TS~~Llrill~~~~~p~~~~~--~-~~~~~~~~~~~da~LlIGD 143 (251)
T PF02621_consen 77 YSVLLFS-K--------VPIEELDGKKI-ALTGESTTSVALLRILLEEFYKPEYVPM--P-DDIPPAMLAGADAALLIGD 143 (251)
T ss_dssp SSEEEEE-S--------S-CCC-TTSEE-EESTTTSHHHHHHHHHHCCTT--EEEEE----CGHHHHHHTTSSEEEEECH
T ss_pred cceEEEE-C--------CChHHcCCCeE-EcCCCCHHHHHHHHHHHHhccccceeec--C-chhhHHhhcCCCEEEEEch
Confidence 1122222 2 23344444444 4444445545555555444444443333 3 4555555555 45445544
Q ss_pred ceecccccCCceeeecC-------CCCccceEEEEEeCCccccHHHHHHHHHHhHHhh
Q psy3760 246 IAFDSNRDKNLRSISAS-------HLFGTTISRVIIKQGTYLRSYVYSFIKLLSPKLN 296 (306)
Q Consensus 246 ~~~~~~~~~~l~~~~~~-------~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~ 296 (306)
........+......+. +.+...-.| +.+++... ..+..+.+.+++...
T Consensus 144 ~Al~~~~~~~~~v~DLg~~W~~~tGlPfvfa~~-~vrk~~~~-~~~~~~~~~l~~s~~ 199 (251)
T PF02621_consen 144 EALTYKSQGLPYVYDLGEEWYELTGLPFVFAVW-VVRKDLPE-EEIKELVQALRKSKQ 199 (251)
T ss_dssp HHHHGGGGTTEEEEEHHHHHHHHHSS-EEEEEE-EEETTSHH-HHHHHHHHHHHHHHH
T ss_pred HHcCCccCCCcEEEEHHHHHHHHHCCCceeEEE-EEecccCH-HHHHHHHHHHHHHHH
Confidence 43322123344555543 222222222 23555432 566677777766654
No 263
>TIGR03427 ABC_peri_uca ABC transporter periplasmic binding protein, urea carboxylase region. Members of this family are ABC transporter periplasmic binding proteins associated with the urea carboxylase/allophanate hydrolase pathway, an alternative to urease for urea degradation. The protein is restricted to bacteria with the pathway, with its gene close to the urea carboxylase and allophanate hydrolase genes. The substrate for this transporter therefore is likely to be urea or a compound from which urea is easily derived.
Probab=94.96 E-value=1.9 Score=36.10 Aligned_cols=189 Identities=6% Similarity=-0.042 Sum_probs=99.9
Q ss_pred CcEEEEecccchhhhhHHHH----HHHHHhC--CCcEEEEEeC-ChhHHHHHHHcCCeeEEEEccccC----CCCCce--
Q psy3760 93 GNLTIATTHTQARYALPKII----KEFTIQF--PKVKLSLLQG-NPKQITEMIRNDQADIAIVTEILS----PSDKLI-- 159 (306)
Q Consensus 93 ~~l~I~~~~~~~~~~l~~~l----~~~~~~~--p~~~i~~~~~-~~~~~~~~l~~~~~Di~i~~~~~~----~~~~~~-- 159 (306)
..+|||++.+.+ +.|-.+ .-|.+.+ -++++++... +..+.++.+.+|++|++....... ...+..
T Consensus 2 ~~~~i~~~~w~G--~~p~~lA~~~G~fe~~l~~~Gl~Ve~~~f~~~~~~l~Al~aG~iD~~~~g~~~~~~~~~a~g~~~~ 79 (328)
T TIGR03427 2 DKFKVCWSIYAG--WMPWGYAAQQGIVDKWADKYGITIEVVQINDYVESINQYTAGKFDGCTMTNMDALTIPAAGGVDTT 79 (328)
T ss_pred CceEEEecCCcc--HHHHHHHHHcCchhhhHHHcCCeEEEEECCChHHHHHHHHcCCCCEEeecCHHHHHHHHhCCCCeE
Confidence 469999998654 333333 2222111 2567777764 456778889999999986542110 122222
Q ss_pred eeccc---cceEEEEecCCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCcee-EEEEecCHHHHHHHHH
Q psy3760 160 SIPCY---QWEYVIIVPLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPY-IVLETINSDIIKTYVE 235 (306)
Q Consensus 160 ~~~l~---~~~~~~v~~~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~v~ 235 (306)
..-+. .....+++++ .-+++||.+.+..... +......+...++..|+.+. +.+.--+...+..+..
T Consensus 80 iv~v~~~~~g~~~ivv~~--------i~svaDLKGKkIav~~-gs~~~~ll~~aL~~aGL~~~DV~~v~~~~~d~~aAl~ 150 (328)
T TIGR03427 80 ALIVGDFSNGNDGIVLKG--------GKSLADLKGQKVNLVE-LSVSHYLLARALESVGLSEKDVKVVNTSDADIVAAFI 150 (328)
T ss_pred EEEEEccCCCceEEEECC--------CCCHHHcCCCEEeccC-CChHHHHHHHHHHHcCCCHHHeEEEeCChHHHHHHHh
Confidence 11111 1123344432 3589999999887644 44445677889999999863 3333334466677788
Q ss_pred hc--cceeeeecceeccc-ccCCceeeecCCCCcc-ceEEEEEeCC--ccccHHHHHHHHHHhH
Q psy3760 236 LR--MGIGIIASIAFDSN-RDKNLRSISASHLFGT-TISRVIIKQG--TYLRSYVYSFIKLLSP 293 (306)
Q Consensus 236 ~g--~gi~~~p~~~~~~~-~~~~l~~~~~~~~~~~-~~~~l~~~~~--~~~~~~~~~~~~~l~~ 293 (306)
+| ++++ +++...... ..++.+.+.-....+. ...+++.+.+ ...+..++.|++...+
T Consensus 151 ~G~VDAa~-~~eP~~s~~~~~~g~~~l~~~~~~~~~~~~~lv~~~~~l~~~pe~v~~~~~a~~k 213 (328)
T TIGR03427 151 TKDVTAVV-TWNPQLSEIKAQPGANEVFDSSQIPGEILDLMVVNTQTLKANPNLGKALTGAWYE 213 (328)
T ss_pred cCCCcEEE-EcCchHHHHHhCCCcEEecccccCCCcceEEEEECHHHHHHCHHHHHHHHHHHHH
Confidence 77 4443 444333222 3344444422221221 1223343332 1134567777665544
No 264
>smart00497 IENR1 Intron encoded nuclease repeat motif. Repeat of unknown function, but possibly DNA-binding via helix-turn-helix motif (Ponting, unpublished).
Probab=94.91 E-value=0.029 Score=32.53 Aligned_cols=25 Identities=32% Similarity=0.287 Sum_probs=22.6
Q ss_pred HhcCCHHHHHHHhCCCchHHHHHHHH
Q psy3760 14 RQNFNLTEAAKALYTSQPGVSKAIIE 39 (306)
Q Consensus 14 ~~~~s~~~aA~~l~isq~~~s~~i~~ 39 (306)
+-. |+++||+.|++++++|++.++.
T Consensus 16 ~f~-S~~eAa~~lg~~~~~I~~~~~~ 40 (53)
T smart00497 16 EFS-SIREAAKYLGISHSSISKYLNT 40 (53)
T ss_pred Eec-CHHHHHHHhCCCHHHHHHHHhC
Confidence 446 9999999999999999999886
No 265
>COG2508 Regulator of polyketide synthase expression [Signal transduction mechanisms / Secondary metabolites biosynthesis, transport, and catabolism]
Probab=94.86 E-value=0.056 Score=46.90 Aligned_cols=44 Identities=23% Similarity=0.360 Sum_probs=37.6
Q ss_pred hHHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCcee
Q psy3760 5 QFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDI 48 (306)
Q Consensus 5 ~l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~L 48 (306)
.++++.+-.+++.++++||++|+|=+-|+-++|+++|+.+|..|
T Consensus 355 Ll~TL~~yl~~~~ni~~tAk~L~iHRNTL~YRi~kieEltg~dL 398 (421)
T COG2508 355 LLETLRAYLKNNGNISATAKRLFVHRNTLRYRLKKIEELTGIDL 398 (421)
T ss_pred HHHHHHHHHHhcCCHHHHHHHhcccHHHHHHHHHHHHHHhCCCC
Confidence 45555555555559999999999999999999999999999988
No 266
>COG0834 HisJ ABC-type amino acid transport/signal transduction systems, periplasmic component/domain [Amino acid transport and metabolism / Signal transduction mechanisms]
Probab=94.86 E-value=1.7 Score=35.03 Aligned_cols=189 Identities=11% Similarity=0.053 Sum_probs=109.4
Q ss_pred hhHHHHHHHHHhCCCc-EEEEEeCChhHHHHHHHcCCeeEEEEccccCC----CCCceeeccccceEEEEecCCCCCCCC
Q psy3760 107 ALPKIIKEFTIQFPKV-KLSLLQGNPKQITEMIRNDQADIAIVTEILSP----SDKLISIPCYQWEYVIIVPLDHPLLLL 181 (306)
Q Consensus 107 ~l~~~l~~~~~~~p~~-~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~----~~~~~~~~l~~~~~~~v~~~~~~l~~~ 181 (306)
+-..+...+.+..... .+.+.....+.++..+.+|++|+++......+ .-.+ +.|.+.....+++.++.+..
T Consensus 61 ~dvdl~~~ia~~l~~~~~~~~~~~~~~~~~~~l~~g~~D~~~~~~~~t~er~~~~~f-s~py~~~~~~~~~~~~~~~~-- 137 (275)
T COG0834 61 FDVDLAKAIAKRLGGDKKVEFVPVAWDGLIPALKAGKVDIIIAGMTITPERKKKVDF-SDPYYYSGQVLLVKKDSDIG-- 137 (275)
T ss_pred eeHHHHHHHHHHhCCcceeEEeccchhhhhHHHhcCCcCEEEeccccCHHHhccccc-cccccccCeEEEEECCCCcC--
Confidence 3455666666665544 47777778889999999999999998622222 2234 78888889999998876532
Q ss_pred CCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCceeEEEEecCHHHHHHHHHhccceeeeecce-ecc--c--ccCCc
Q psy3760 182 NSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMGIGIIASIA-FDS--N--RDKNL 256 (306)
Q Consensus 182 ~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~~~p~~~-~~~--~--~~~~l 256 (306)
.-+.+||.+.......... .....+..... ........++...+..++.+|..=+++-+.. ... . .....
T Consensus 138 -~~~~~DL~gk~v~v~~gt~---~~~~~~~~~~~-~~~~~~~~~~~~~~~~al~~Gr~Da~~~d~~~~~~~~~~~~~~~~ 212 (275)
T COG0834 138 -IKSLEDLKGKKVGVQLGTT---DEAEEKAKKPG-PNAKIVAYDSNAEALLALKNGRADAVVSDSAVLAGLKLLKKNPGL 212 (275)
T ss_pred -cCCHHHhCCCEEEEEcCcc---hhHHHHHhhcc-CCceEEeeCCHHHHHHHHHcCCccEEEcchHhhhhhhhhhcCCCC
Confidence 3478999996666655433 22333333332 2234567788889999999996666654432 222 1 12222
Q ss_pred eeeecCCCCccceEEEEEeCCccccHHHHHHHHHHhHHhhHHHHHhhh
Q psy3760 257 RSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLLSPKLNRKFINKIL 304 (306)
Q Consensus 257 ~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~ 304 (306)
.............+.+..+++. .......+-..+.+..+....+++.
T Consensus 213 ~~~~~~~~~~~~~~~~~~~~~~-~~~l~~~in~~l~~l~~~G~~~~i~ 259 (275)
T COG0834 213 YVLLVFPGLSVEYLGIALRKGD-DPELLEAVNKALKELKADGTLQKIS 259 (275)
T ss_pred ceeeeccCCCcceeEEEeccCC-cHHHHHHHHHHHHHHHhCccHHHHH
Confidence 2222211111135555666662 2334444444444444444444443
No 267
>PF00325 Crp: Bacterial regulatory proteins, crp family; InterPro: IPR001808 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. This family groups together a range of proteins, including anr, crp, clp, cysR, fixK, flp, fnr, fnrN, hlyX and ntcA [, ]. Within this family, the HTH motif is situated towards the C terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 2OZ6_A 1CGP_B 2GZW_C 1O3T_B 3ROU_A 2CGP_A 3RDI_A 1I5Z_A 3IYD_H 3FWE_B ....
Probab=94.84 E-value=0.035 Score=28.21 Aligned_cols=24 Identities=25% Similarity=0.304 Sum_probs=20.6
Q ss_pred HHHHHHhCCCchHHHHHHHHHHHH
Q psy3760 20 TEAAKALYTSQPGVSKAIIELEEE 43 (306)
Q Consensus 20 ~~aA~~l~isq~~~s~~i~~LE~~ 43 (306)
..-|..+|.|.-++||.+++||++
T Consensus 6 ~diA~~lG~t~ETVSR~l~~l~~~ 29 (32)
T PF00325_consen 6 QDIADYLGLTRETVSRILKKLERQ 29 (32)
T ss_dssp HHHHHHHTS-HHHHHHHHHHHHHT
T ss_pred HHHHHHhCCcHHHHHHHHHHHHHc
Confidence 466899999999999999999974
No 268
>PRK09413 IS2 repressor TnpA; Reviewed
Probab=94.81 E-value=0.55 Score=32.79 Aligned_cols=38 Identities=8% Similarity=0.062 Sum_probs=31.5
Q ss_pred HHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHH
Q psy3760 6 FRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEE 43 (306)
Q Consensus 6 l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~ 43 (306)
++....+.+.|.|+..+|++++||.+++.+.+++.++.
T Consensus 19 ~~aV~~~~~~g~sv~evA~e~gIs~~tl~~W~r~y~~~ 56 (121)
T PRK09413 19 IAIVQQSFEPGMTVSLVARQHGVAASQLFLWRKQYQEG 56 (121)
T ss_pred HHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHhhc
Confidence 34455556667799999999999999999999999764
No 269
>PRK10906 DNA-binding transcriptional repressor GlpR; Provisional
Probab=94.79 E-value=0.35 Score=38.67 Aligned_cols=36 Identities=17% Similarity=0.287 Sum_probs=31.8
Q ss_pred CHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCCc
Q psy3760 18 NLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRI 56 (306)
Q Consensus 18 s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~ 56 (306)
+....|+.+++|..|+.|-|+.||++ -+..|..+|.
T Consensus 21 ~~~ela~~l~vS~~TiRRdL~~Le~~---g~l~r~~GGa 56 (252)
T PRK10906 21 STEELVEHFSVSPQTIRRDLNDLAEQ---NKILRHHGGA 56 (252)
T ss_pred eHHHHHHHhCCCHHHHHHHHHHHHHC---CCEEEecCCE
Confidence 67899999999999999999999995 4568887886
No 270
>TIGR01610 phage_O_Nterm phage replication protein O, N-terminal domain. This model represents the N-terminal region of the phage lambda replication protein O and homologous regions of other phage proteins.
Probab=94.79 E-value=0.087 Score=34.97 Aligned_cols=42 Identities=26% Similarity=0.249 Sum_probs=33.7
Q ss_pred chhhHHHHHHHHH---------hcCCHHHHHHHhCCCchHHHHHHHHHHHH
Q psy3760 2 NLHQFRFVREAVR---------QNFNLTEAAKALYTSQPGVSKAIIELEEE 43 (306)
Q Consensus 2 ~~~~l~~f~~v~~---------~~~s~~~aA~~l~isq~~~s~~i~~LE~~ 43 (306)
+-++.++++.+++ ...|-+.-|+.+|+|++++||.|++||+.
T Consensus 24 ~~r~~~vLl~L~~~~~G~~~~~~~is~~eLa~~~g~sr~tVsr~L~~Le~~ 74 (95)
T TIGR01610 24 SGREFRVLLAIIRLTYGWNKKQDRVTATVIAELTGLSRTHVSDAIKSLARR 74 (95)
T ss_pred CHHHHHHHHHHHHHHhCccccCCccCHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence 4467788888774 12356778999999999999999999985
No 271
>PF09339 HTH_IclR: IclR helix-turn-helix domain; InterPro: IPR005471 The many bacterial transcription regulation proteins which bind DNA through a 'helix-turn-helix' motif can be classified into subfamilies on the basis of sequence similarities. One of these subfamilies, called 'iclR', groups several proteins including: gylR, a possible activator protein for the gylABX glycerol operon in Streptomyces. iclR, the repressor of the acetate operon (also known as glyoxylate bypass operon) in Escherichia coli and Salmonella typhimurium. These proteins have a Helix-Turn-Helix motif at the N terminus that is similar to that of other DNA-binding proteins [].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1MKM_A 3MQ0_A 3R4K_A 2G7U_C 2O0Y_C 2XRO_F 2XRN_B 2IA2_D.
Probab=94.71 E-value=0.07 Score=30.84 Aligned_cols=40 Identities=25% Similarity=0.302 Sum_probs=31.4
Q ss_pred hhHHHHHHHHHhcC--CHHHHHHHhCCCchHHHHHHHHHHHH
Q psy3760 4 HQFRFVREAVRQNF--NLTEAAKALYTSQPGVSKAIIELEEE 43 (306)
Q Consensus 4 ~~l~~f~~v~~~~~--s~~~aA~~l~isq~~~s~~i~~LE~~ 43 (306)
+-+.++-.+++.+. +++.-|+.++++.|++.|.++.|++.
T Consensus 4 ral~iL~~l~~~~~~~t~~eia~~~gl~~stv~r~L~tL~~~ 45 (52)
T PF09339_consen 4 RALRILEALAESGGPLTLSEIARALGLPKSTVHRLLQTLVEE 45 (52)
T ss_dssp HHHHHHHCHHCTBSCEEHHHHHHHHTS-HHHHHHHHHHHHHT
T ss_pred HHHHHHHHHHcCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence 34566666666662 49999999999999999999999874
No 272
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=94.62 E-value=0.067 Score=30.77 Aligned_cols=37 Identities=22% Similarity=0.272 Sum_probs=30.0
Q ss_pred CCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCCc
Q psy3760 17 FNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRI 56 (306)
Q Consensus 17 ~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~ 56 (306)
.+...-|+.+++|++++++.|+.|++. .++.+..+|+
T Consensus 15 ~s~~~l~~~l~~s~~tv~~~l~~L~~~---g~i~~~~~~~ 51 (53)
T smart00420 15 VSVEELAELLGVSEMTIRRDLNKLEEQ---GLLTRVHGGA 51 (53)
T ss_pred cCHHHHHHHHCCCHHHHHHHHHHHHHC---CCEEEeecCc
Confidence 478888999999999999999999986 3455555553
No 273
>TIGR01254 sfuA ABC transporter periplasmic binding protein, thiB subfamily. The model describes thiamine ABC transporter, periplasmic protein in bacteria and archae. The protein belongs to the larger ABC transport system. It consists of at least three components: the thiamine binding periplasmic protein; an inner membrane permease; an ATP-binding subunit. It has been experimentally demonstrated that the mutants in the various steps in the de novo synthesis of the thiamine and the biologically active form, namely thiamine pyrophosphate can be exogenously supplemented with thiamine, thiamine monophosphate (TMP) or thiamine pyrophosphate (TPP).
Probab=94.49 E-value=2.3 Score=35.05 Aligned_cols=197 Identities=15% Similarity=0.036 Sum_probs=105.0
Q ss_pred CcEEEEecccch--hhhhHHHHHHHHHhCCCcEEEEEeCC-hhHHHHHHHc----CCeeEEEEcccc--------C---C
Q psy3760 93 GNLTIATTHTQA--RYALPKIIKEFTIQFPKVKLSLLQGN-PKQITEMIRN----DQADIAIVTEIL--------S---P 154 (306)
Q Consensus 93 ~~l~I~~~~~~~--~~~l~~~l~~~~~~~p~~~i~~~~~~-~~~~~~~l~~----~~~Di~i~~~~~--------~---~ 154 (306)
++|+|.+-.+.. ...+..+...|.+ ++++++++...+ ..++++.+.. +.+|+.+..... . +
T Consensus 2 ~~l~v~~~~~~~~~~~~~~~i~~~Fe~-~~gi~V~~~~~~~~~~~~~~l~~~~~~~~~Dv~~~~~~~~~~~~~~~gll~~ 80 (304)
T TIGR01254 2 PVVTVYTYDSFAADWGLGPVVEKAFEA-DCNCKVKFVALEDAGELLNRLRLEGKNPKADVVLGLDNNLLEAASKTGLLAP 80 (304)
T ss_pred CEEEEEEcccccCcccchHHHHHHHhh-hcCcEEEEEECCCHHHHHHHHHhcCCCCCCCEEEEeCHHHHHHHHHcCCccc
Confidence 578999866633 3477788888987 689999998875 4678788764 468999852110 0 0
Q ss_pred -CCCc------------eeeccccceEEEEecCCCCCCCCCCcChhhhcCCC----eEeecCCC-Cc-HHHHH-------
Q psy3760 155 -SDKL------------ISIPCYQWEYVIIVPLDHPLLLLNSISLKEISNYP----LITYDLSF-SG-RIKLD------- 208 (306)
Q Consensus 155 -~~~~------------~~~~l~~~~~~~v~~~~~~l~~~~~i~~~dl~~~~----~i~~~~~~-~~-~~~~~------- 208 (306)
.+.. ...++.-..++++.+++.. ...+-+++||.+-. ..+..+.. .. ...+.
T Consensus 81 ~~~~~~~~~~~~~~~~~~~~p~~~~~~~i~yn~~~~--~~~P~sw~dL~~~~~~g~i~~~~p~~~~~~~~~~~~~~~~~g 158 (304)
T TIGR01254 81 SGVALDKVNVPGGWNNATFLPFDYGYVAFVYDKNKL--QNPPQSLKELVEPEQDLLVIYQDPRTSSPGLGLLLWMQSVYG 158 (304)
T ss_pred CCccccccccccccCCCeEEEEeeeeEEEEEchHHh--cCCCCCHHHHhCHHhcCcEEecCCCCChhHHHHHHHHHHhcC
Confidence 0000 1134444566777777643 22356899986532 22222211 11 11111
Q ss_pred -----HHHHhCCCceeEEEEecCHHHHHHHHHhcc-ceeeeec--ceeccc--ccCCceeeecCCCCccceEEEEEeCCc
Q psy3760 209 -----REFSLQKLTPYIVLETINSDIIKTYVELRM-GIGIIAS--IAFDSN--RDKNLRSISASHLFGTTISRVIIKQGT 278 (306)
Q Consensus 209 -----~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~-gi~~~p~--~~~~~~--~~~~l~~~~~~~~~~~~~~~l~~~~~~ 278 (306)
++++... .+......+......++.+|. .+++.-. ...... ....+..+.+++........+...++.
T Consensus 159 ~~~~~~~~~~L~--~~~~~~~~~~~~~~~~~~~Ge~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~ai~k~a 236 (304)
T TIGR01254 159 EDDAPQAWKQLR--KKTVTVTKGWSEAYGTFLGGEYDLVLSYATSPAYHVLFEKKDNYAALNFSEGHYLQVEGAARLKGA 236 (304)
T ss_pred hHHHHHHHHHHH--hCCeecCCCCHHHHHHHhcCCccEEEEeccchhhhhhhccCCceeEEecCCCCEEEEEEEEEECCC
Confidence 2222111 111112233345567788884 3444322 111111 123455445444322223355556777
Q ss_pred cccHHHHHHHHHHhHH
Q psy3760 279 YLRSYVYSFIKLLSPK 294 (306)
Q Consensus 279 ~~~~~~~~~~~~l~~~ 294 (306)
.....+++|++++.+.
T Consensus 237 ~n~e~A~~fi~fllsp 252 (304)
T TIGR01254 237 KQPELADKFVQFLLSP 252 (304)
T ss_pred CCHHHHHHHHHHHcCH
Confidence 7889999999998544
No 274
>PRK00118 putative DNA-binding protein; Validated
Probab=94.38 E-value=0.15 Score=34.20 Aligned_cols=42 Identities=21% Similarity=0.249 Sum_probs=33.7
Q ss_pred hhHHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcC
Q psy3760 4 HQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELS 45 (306)
Q Consensus 4 ~~l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg 45 (306)
++-++|......|.|++..|+.+|+|.+|+.+++.+....+.
T Consensus 21 kqRevl~L~y~eg~S~~EIAe~lGIS~~TV~r~L~RArkkLr 62 (104)
T PRK00118 21 KQRNYMELYYLDDYSLGEIAEEFNVSRQAVYDNIKRTEKLLE 62 (104)
T ss_pred HHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHH
Confidence 445566665666679999999999999999999987776663
No 275
>COG1732 OpuBC Periplasmic glycine betaine/choline-binding (lipo)protein of an ABC-type transport system (osmoprotectant binding protein) [Cell envelope biogenesis, outer membrane]
Probab=94.25 E-value=1.9 Score=34.98 Aligned_cols=210 Identities=11% Similarity=0.126 Sum_probs=128.5
Q ss_pred CCCCcEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEe--CChhHHHHHHHcCCeeEEEEc--------cccCC----C
Q psy3760 90 YDTGNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQ--GNPKQITEMIRNDQADIAIVT--------EILSP----S 155 (306)
Q Consensus 90 ~~~~~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~--~~~~~~~~~l~~~~~Di~i~~--------~~~~~----~ 155 (306)
....+|+||.-..-...++..++..+.+.+ ++.+.... +++.-....|.+|++|+-.-+ ....+ +
T Consensus 30 ~~~~~I~VgsK~~tE~~IL~~m~~~lle~~-~~kv~~~~~lG~t~v~~~Al~~G~IDiYpEYTGt~~~~~lk~~~~~~~d 108 (300)
T COG1732 30 SAAKTIVVGSKIFTEQYILGNILKQLLEKN-GIKVEDKTGLGGTAVVRNALKSGDIDIYPEYTGTALFSFLKKDPPASKD 108 (300)
T ss_pred ccCCCEEEecCCCcHHHHHHHHHHHHHHhc-CCceeeccCCCchHHHHHHHHcCCCCeEeeecchhhhhhcccCccccCC
Confidence 457799999999889999999999999998 88777766 355567899999999998643 11000 0
Q ss_pred C---------------Cceeecc--ccceEEEEecCCCCCCCCCCcChhhhcCCCe-EeecCCCCc---HHHHHHHHHhC
Q psy3760 156 D---------------KLISIPC--YQWEYVIIVPLDHPLLLLNSISLKEISNYPL-ITYDLSFSG---RIKLDREFSLQ 214 (306)
Q Consensus 156 ~---------------~~~~~~l--~~~~~~~v~~~~~~l~~~~~i~~~dl~~~~~-i~~~~~~~~---~~~~~~~~~~~ 214 (306)
+ .+.+..- +...+.+.++++.... ..--++.||..+.= +....+..+ .+.+...-+..
T Consensus 109 p~~~y~~vK~~~~k~~~l~wl~p~~~nNTyA~av~~~~A~~-~~i~TiSDLak~~~~l~~g~~~eF~~R~DG~~~l~k~Y 187 (300)
T COG1732 109 PKKVYETVKKLDAKQFKLVWLKPAGFNNTYALAVRKDVAEK-YNLETISDLAKHSNQLKLGADSEFAERADGLPALQKAY 187 (300)
T ss_pred HHHHHHHHHHHHHhcCCEEEecccCCCcceEEEecHHHHHH-hCCccHHHHHHhhhhceecCChhhhccccccHHHHHHh
Confidence 0 1221111 2345666666664211 22347888876532 222222222 13344455566
Q ss_pred CCceeEEEEecCHHHHHHHHHhccceeeeecceeccc-ccCCceeeecCC-CCccceEEEEEeCC-ccccHHHHHHHHHH
Q psy3760 215 KLTPYIVLETINSDIIKTYVELRMGIGIIASIAFDSN-RDKNLRSISASH-LFGTTISRVIIKQG-TYLRSYVYSFIKLL 291 (306)
Q Consensus 215 ~~~~~~~~~~~~~~~~~~~v~~g~gi~~~p~~~~~~~-~~~~l~~~~~~~-~~~~~~~~l~~~~~-~~~~~~~~~~~~~l 291 (306)
|+.++..+..-+.....+++.+|. +-...-+..+.. ...+|+++.-+- ..|.+....+.+.+ ....|.++..++-+
T Consensus 188 g~~~~~~~~~m~~gl~y~Al~~g~-~d~~~~YsTDg~I~~~~L~VLkDDK~~fP~Y~~apvvre~vlk~~Pel~~~l~~l 266 (300)
T COG1732 188 GFDFKPDLRTMDGGLTYQALKNGT-VDAADAYSTDGRIAAYGLKVLKDDKGFFPPYQAAPVVREEVLKKHPELKTILNKL 266 (300)
T ss_pred CCccCCCceecCchHHHHHHHcCC-CCeEeeccccccccccCcEEEecCCcCCCCCcccceecHHHHhHCHHHHHHHHHH
Confidence 777665244445558899999985 222333333322 456788887664 34455555565554 33467888888888
Q ss_pred hHHhhHHHHHh
Q psy3760 292 SPKLNRKFINK 302 (306)
Q Consensus 292 ~~~~~~~~~~~ 302 (306)
...+.....+.
T Consensus 267 ~~kid~~tMq~ 277 (300)
T COG1732 267 SGKIDTETMQA 277 (300)
T ss_pred hccCCHHHHHH
Confidence 77776666554
No 276
>PF04545 Sigma70_r4: Sigma-70, region 4; InterPro: IPR007630 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 recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors is 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.; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2P7V_B 3IYD_F 1TLH_B 1KU7_A 1RIO_H 3N97_A 1KU3_A 1RP3_C 1SC5_A 1NR3_A ....
Probab=94.23 E-value=0.2 Score=28.59 Aligned_cols=37 Identities=19% Similarity=0.160 Sum_probs=27.1
Q ss_pred HHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHH
Q psy3760 6 FRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEE 42 (306)
Q Consensus 6 l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~ 42 (306)
-+++....-.+.|+...|+.+|+|.+++++..++-=+
T Consensus 10 r~vi~~~y~~~~t~~eIa~~lg~s~~~V~~~~~~al~ 46 (50)
T PF04545_consen 10 REVIRLRYFEGLTLEEIAERLGISRSTVRRILKRALK 46 (50)
T ss_dssp HHHHHHHHTST-SHHHHHHHHTSCHHHHHHHHHHHHH
T ss_pred HHHHHHHhcCCCCHHHHHHHHCCcHHHHHHHHHHHHH
Confidence 3444444444459999999999999999998876543
No 277
>PRK01686 hisG ATP phosphoribosyltransferase catalytic subunit; Reviewed
Probab=94.17 E-value=1.7 Score=33.62 Aligned_cols=159 Identities=11% Similarity=0.101 Sum_probs=91.0
Q ss_pred EEEEeCChhHHHHHHHcCCeeEEEEccccCCCC-----CceeeccccceEEEEecCCCCCCCCCCcChhhhcCCCeEeec
Q psy3760 124 LSLLQGNPKQITEMIRNDQADIAIVTEILSPSD-----KLISIPCYQWEYVIIVPLDHPLLLLNSISLKEISNYPLITYD 198 (306)
Q Consensus 124 i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~~~-----~~~~~~l~~~~~~~v~~~~~~l~~~~~i~~~dl~~~~~i~~~ 198 (306)
+++.-.-..++...+..|.+|+||+..+..... .+.-..++.-++++.+|++.+... ..+.....-|..
T Consensus 47 i~~~~~r~~DIp~yV~~G~~DlGItG~D~l~E~~~~v~~l~dLgfG~crl~vAvp~~~~~~~-----~~~~~~~~rIAT- 120 (215)
T PRK01686 47 VRFLLVRATDVPTYVEHGAADLGIVGKDVLLEHGKDLYEPLDLGIGKCRMSVAVPPGFDYAP-----AVKQGPRLRVAT- 120 (215)
T ss_pred EEEEEECHHHHHHHHhCCCccEEEeeeeEeeecCCCeEEEecCCccCEEEEEEEECcccccc-----hhhccCCCEEEe-
Confidence 444444567899999999999999853222111 122344567789999998876321 112111122222
Q ss_pred CCCCcHHHHHHHHHhCCCceeEEEEecCHHHHHHHHHhccceeeeeccee-cccccCCceeeecCCCCccceEEEEEeCC
Q psy3760 199 LSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMGIGIIASIAF-DSNRDKNLRSISASHLFGTTISRVIIKQG 277 (306)
Q Consensus 199 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~~~p~~~~-~~~~~~~l~~~~~~~~~~~~~~~l~~~~~ 277 (306)
.+.+...++|...|+...++....+.+.+ ..-|.+=+++.-... ..++..+|+.+. .....+..++.++.
T Consensus 121 ---kYp~it~~yf~~~gv~~~iv~l~GsvE~a---P~~GlAD~IvDivsTG~TLr~NgL~~ie---~Il~s~A~LI~n~~ 191 (215)
T PRK01686 121 ---KYPNIARRYFAEKGEQVEIIKLYGSVELA---PLVGLADAIVDIVETGNTLRANGLVEVE---EIMDISARLIVNRA 191 (215)
T ss_pred ---CCHHHHHHHHHHcCCeEEEEECcCceeec---cccCCccEEEEeecChHHHHHCcCEEee---EEEeeEEEEEEecc
Confidence 23467788999999876655444555442 222322222221111 112456777775 24456778888776
Q ss_pred cc--ccHHHHHHHHHHhHHhhH
Q psy3760 278 TY--LRSYVYSFIKLLSPKLNR 297 (306)
Q Consensus 278 ~~--~~~~~~~~~~~l~~~~~~ 297 (306)
.. ..+.++.+++.+++.+..
T Consensus 192 s~~~k~~~i~~l~~~l~~~~~a 213 (215)
T PRK01686 192 SLKLKREEIRPLIEKLREAVES 213 (215)
T ss_pred cchhhHHHHHHHHHHHHHHHhc
Confidence 43 346788888888776543
No 278
>PRK15201 fimbriae regulatory protein FimW; Provisional
Probab=94.16 E-value=0.16 Score=37.42 Aligned_cols=45 Identities=13% Similarity=0.166 Sum_probs=40.9
Q ss_pred CchhhHHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCc
Q psy3760 1 MNLHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSI 46 (306)
Q Consensus 1 m~~~~l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~ 46 (306)
++-+..++|.-+++-. |...-|+.|++|..||...++++=+.||+
T Consensus 134 LSpRErEVLrLLAqGk-TnKEIAe~L~IS~rTVkth~srImkKLgV 178 (198)
T PRK15201 134 FSVTERHLLKLIASGY-HLSETAALLSLSEEQTKSLRRSIMRKLHV 178 (198)
T ss_pred CCHHHHHHHHHHHCCC-CHHHHHHHhCCCHHHHHHHHHHHHHHhCC
Confidence 3557788999999877 99999999999999999999999999987
No 279
>TIGR00721 tfx DNA-binding protein, Tfx family. Tfx from Methanobacterium thermoautotrophicum is associated with the operon for molybdenum formyl-methanofuran dehydrogenase and binds a DNA sequence near its promoter.
Probab=94.13 E-value=0.31 Score=34.61 Aligned_cols=77 Identities=17% Similarity=0.164 Sum_probs=51.7
Q ss_pred chhhHHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCc-----eeEEecCCCccccCHhHHHHHHHHHHHHHH
Q psy3760 2 NLHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSI-----DIFIRHGKRIRGLTKPGQAILRSIEIIMQE 76 (306)
Q Consensus 2 ~~~~l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~-----~Lf~R~~~~~~~lT~~G~~l~~~a~~il~~ 76 (306)
+-++.+++....+. .|..+.|+.||+|++++++..++.-+.|.. .|.....-.+.-.-+.|..++.-...++..
T Consensus 8 te~qr~VL~Lr~~G-lTq~EIAe~LgiS~stV~~~e~ra~kkLr~a~~~~~l~~~~~a~~~~~~~~g~~~~~~~~~v~~~ 86 (137)
T TIGR00721 8 TERQIKVLELREKG-LSQKEIAKELKTTRANVSAIEKRAMENIEKARNTLDFVKFIKSPVRILCRRGDDLDEIPKRLFKK 86 (137)
T ss_pred CHHHHHHHHHHHcC-CCHHHHHHHHCcCHHHHHHHHHhHHHHHHHHhhHHHHHHHhcCCEEEEecCCCcHHHhHHHHHHH
Confidence 34566666665554 499999999999999999777776666653 233322323212557778888877777776
Q ss_pred HHH
Q psy3760 77 IEG 79 (306)
Q Consensus 77 ~~~ 79 (306)
.++
T Consensus 87 ~d~ 89 (137)
T TIGR00721 87 ADE 89 (137)
T ss_pred HhH
Confidence 554
No 280
>PF13730 HTH_36: Helix-turn-helix domain
Probab=94.09 E-value=0.08 Score=30.96 Aligned_cols=26 Identities=42% Similarity=0.405 Sum_probs=24.2
Q ss_pred CHHHHHHHhCCCchHHHHHHHHHHHH
Q psy3760 18 NLTEAAKALYTSQPGVSKAIIELEEE 43 (306)
Q Consensus 18 s~~~aA~~l~isq~~~s~~i~~LE~~ 43 (306)
|...-|+.+|+|..||.+.|++||+.
T Consensus 27 S~~~la~~~g~s~~Tv~~~i~~L~~~ 52 (55)
T PF13730_consen 27 SQETLAKDLGVSRRTVQRAIKELEEK 52 (55)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence 78999999999999999999999973
No 281
>COG4190 Predicted transcriptional regulator [Transcription]
Probab=94.08 E-value=0.29 Score=33.87 Aligned_cols=56 Identities=14% Similarity=0.245 Sum_probs=44.6
Q ss_pred hhHHHHHHHHHhc-CCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCCccccCH
Q psy3760 4 HQFRFVREAVRQN-FNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTK 61 (306)
Q Consensus 4 ~~l~~f~~v~~~~-~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~~~lT~ 61 (306)
+.++.+-.+++++ .|++++|+..+--.+.+++-++.|+ .+|+--|+++++.. .|+-
T Consensus 65 ~nleLl~~Ia~~~P~Si~ElAe~vgRdv~nvhr~Ls~l~-~~GlI~fe~~gq~k-~P~~ 121 (144)
T COG4190 65 RNLELLELIAQEEPASINELAELVGRDVKNVHRTLSTLA-DLGLIFFEEDGQRK-QPVV 121 (144)
T ss_pred hHHHHHHHHHhcCcccHHHHHHHhCcchHHHHHHHHHHH-hcCeEEEecCCccc-Ccee
Confidence 4556666665542 3999999999999999999999997 48999999987665 5653
No 282
>PF08281 Sigma70_r4_2: Sigma-70, region 4; InterPro: IPR013249 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 recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 promoter element via a helix-turn-helix motif [].; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2LFW_A 1OR7_B 2H27_D 2O8X_B.
Probab=94.07 E-value=0.17 Score=29.40 Aligned_cols=40 Identities=18% Similarity=0.120 Sum_probs=28.1
Q ss_pred hhHHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHH
Q psy3760 4 HQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEE 43 (306)
Q Consensus 4 ~~l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~ 43 (306)
++=++|.-..-.|.|+.+.|+.+|+|.+++-+++.+--+.
T Consensus 14 ~~r~i~~l~~~~g~s~~eIa~~l~~s~~~v~~~l~ra~~~ 53 (54)
T PF08281_consen 14 RQREIFLLRYFQGMSYAEIAEILGISESTVKRRLRRARKK 53 (54)
T ss_dssp HHHHHHHHHHTS---HHHHHHHCTS-HHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHCcCHHHHHHHHCcCHHHHHHHHHHHHhh
Confidence 3445566666677799999999999999999999875543
No 283
>smart00351 PAX Paired Box domain.
Probab=94.06 E-value=0.17 Score=35.55 Aligned_cols=35 Identities=20% Similarity=0.193 Sum_probs=29.1
Q ss_pred HHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHH
Q psy3760 9 VREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEE 43 (306)
Q Consensus 9 f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~ 43 (306)
++.+++.|.|..++|+.+++|.+++++.+++..++
T Consensus 26 iv~~~~~G~s~~~iA~~~gvs~~tV~kwi~r~~~~ 60 (125)
T smart00351 26 IVELAQNGVRPCDISRQLCVSHGCVSKILGRYYET 60 (125)
T ss_pred HHHHHHcCCCHHHHHHHHCcCHHHHHHHHHHHHHc
Confidence 34444556699999999999999999999998764
No 284
>PRK05638 threonine synthase; Validated
Probab=94.05 E-value=0.13 Score=44.86 Aligned_cols=63 Identities=27% Similarity=0.330 Sum_probs=45.1
Q ss_pred hHHHHHHHHHhcCCHHHHHHHhC--CCchHHHHHHHHHHHHcCceeEE---ecCCC-ccccCHhHHHHHHHH
Q psy3760 5 QFRFVREAVRQNFNLTEAAKALY--TSQPGVSKAIIELEEELSIDIFI---RHGKR-IRGLTKPGQAILRSI 70 (306)
Q Consensus 5 ~l~~f~~v~~~~~s~~~aA~~l~--isq~~~s~~i~~LE~~lg~~Lf~---R~~~~-~~~lT~~G~~l~~~a 70 (306)
.+.++..+.+...+...-++.++ +|+++++++|++||+. | |.. +.++. ..+||+.|+.++...
T Consensus 373 r~~IL~~L~~~~~~~~el~~~l~~~~s~~~v~~hL~~Le~~-G--LV~~~~~~g~~~~Y~Lt~~g~~~l~~~ 441 (442)
T PRK05638 373 KLEILKILSEREMYGYEIWKALGKPLKYQAVYQHIKELEEL-G--LIEEAYRKGRRVYYKLTEKGRRLLENL 441 (442)
T ss_pred HHHHHHHHhhCCccHHHHHHHHcccCCcchHHHHHHHHHHC-C--CEEEeecCCCcEEEEECcHHHHHHHhc
Confidence 34555555554447899999998 9999999999999976 2 332 22333 238999999988753
No 285
>TIGR03227 PhnS 2-aminoethylphosphonate ABC transporter, periplasmic 2-aminoethylphosphonate binding protein. This ABC transporter periplasmic substrate binding protein component is found in a region of the salmonella typhimurium LT2 genome responsible for the catabolism of 2-aminoethylphosphonate via the phnWX pathway (GenProp0238). The protein contains a match to pfam01547 for the "Bacterial extracellular solute-binding protein" domain.
Probab=94.03 E-value=3.4 Score=35.20 Aligned_cols=200 Identities=10% Similarity=0.058 Sum_probs=106.6
Q ss_pred CCcEEEEecccchh---hhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHH----cCCeeEEEEccccC-----------
Q psy3760 92 TGNLTIATTHTQAR---YALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIR----NDQADIAIVTEILS----------- 153 (306)
Q Consensus 92 ~~~l~I~~~~~~~~---~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~----~~~~Di~i~~~~~~----------- 153 (306)
.+.|+|.+..++.. .++..++..|.++ +++++++...++.++...+. ++.+|+++......
T Consensus 35 ~~~L~Vy~~~g~~~~~~~~~~~i~~~Fe~~-~Gi~V~~~~~~s~~~~~rl~~e~~~~~~DVv~~~~~~~~~~~~~Gll~~ 113 (367)
T TIGR03227 35 AAVVLVYSADGLEDGDNSLYQDQFDAFEKA-EGIKVNIVEAGGGEVVERAAKEKGNPKADVIVTAPPFIQQAAAEGLLAN 113 (367)
T ss_pred CCeEEEEecCcccccchHHHHHHHHHHHHH-HCCEEEEEeCChHHHHHHHHhhccCCCCCEEEeCcHHHHHHHHCCCccC
Confidence 46799999877653 5788899999988 49999999988888777665 35799988631100
Q ss_pred -CCCCc------------eeeccccceEEEEecCCCCCCCCCCcChhhhcCCC----eEeecCC-CCc-HHHHHHHHHhC
Q psy3760 154 -PSDKL------------ISIPCYQWEYVIIVPLDHPLLLLNSISLKEISNYP----LITYDLS-FSG-RIKLDREFSLQ 214 (306)
Q Consensus 154 -~~~~~------------~~~~l~~~~~~~v~~~~~~l~~~~~i~~~dl~~~~----~i~~~~~-~~~-~~~~~~~~~~~ 214 (306)
+.+.. .+.++....++++..++.. ...+-+|+||.+-. +...++. ... ...+.......
T Consensus 114 ~~~~~~~~~~~~~~~~~g~~~p~~~~~~~i~YN~d~~--~~~P~sw~DL~~p~~~Gki~~~~p~~s~~~~~~l~~~~~~~ 191 (367)
T TIGR03227 114 FNSDAAKAIPAIAKAADGLWAPFVKNYFSFAINPKLL--KSAPASFADLLDADFKGKLAYSNPAQAADGMAVIILAFALF 191 (367)
T ss_pred CCCcccccCchhhcCCCCeEEEEeeceeEEEEchhhc--CCCCCCHHHHhChhccCCEeecCCCcCccHHHHHHHHHHHc
Confidence 00110 1123333344666666642 23467899997632 2222221 111 11111111111
Q ss_pred C-----------CceeEEEEecCHHHHHHHHHhccce-eeeecce-eccc-ccC-Cceee-ecCCC-----CccceEEEE
Q psy3760 215 K-----------LTPYIVLETINSDIIKTYVELRMGI-GIIASIA-FDSN-RDK-NLRSI-SASHL-----FGTTISRVI 273 (306)
Q Consensus 215 ~-----------~~~~~~~~~~~~~~~~~~v~~g~gi-~~~p~~~-~~~~-~~~-~l~~~-~~~~~-----~~~~~~~l~ 273 (306)
| +.++.....++......++.+|... +..+... .... ..+ .+..+ |-+.. .......+.
T Consensus 192 G~~d~a~~~l~~l~~n~~~~~~~~~~~~~~~~~Gev~i~~g~~~~~~~~~~~~g~~i~~~~P~~g~g~~~~~~~~~~~~~ 271 (367)
T TIGR03227 192 GSEDAAFAYLAKLEANNKFHSAGTGKLNALLNKGEIAVANGDLQMDLADAEHGGLNIKIFFPAADAGEPPSAFAIPYAIG 271 (367)
T ss_pred CCchHHHHHHHHHHhcCCccCCCchhHHHHHhcCceEEEccHHHHHHHHHHhcCCCeEEEeecCCCCCCCcccccceeEE
Confidence 1 1234433344555666777777533 2111111 1111 112 34433 22110 112233455
Q ss_pred EeCCccccHHHHHHHHHHhHH
Q psy3760 274 IKQGTYLRSYVYSFIKLLSPK 294 (306)
Q Consensus 274 ~~~~~~~~~~~~~~~~~l~~~ 294 (306)
..++.+.....++|++++.+.
T Consensus 272 I~k~a~n~e~A~~Fidfllsp 292 (367)
T TIGR03227 272 LVKGAPNQDAGKKLIDFLLSA 292 (367)
T ss_pred EecCCCCHHHHHHHHHHHcCH
Confidence 567777889999999998654
No 286
>PF01379 Porphobil_deam: Porphobilinogen deaminase, dipyromethane cofactor binding domain; InterPro: IPR022417 Tetrapyrroles are large macrocyclic compounds derived from a common biosynthetic pathway []. The end-product, uroporphyrinogen III, is used to synthesise a number of important molecules, including vitamin B12, haem, sirohaem, chlorophyll, coenzyme F430 and phytochromobilin []. The first stage in tetrapyrrole synthesis is the synthesis of 5-aminoaevulinic acid ALA via two possible routes: (1) condensation of succinyl CoA and glycine (C4 pathway) using ALA synthase (2.3.1.37 from EC), or (2) decarboxylation of glutamate (C5 pathway) via three different enzymes, glutamyl-tRNA synthetase (6.1.1.17 from EC) to charge a tRNA with glutamate, glutamyl-tRNA reductase (1.2.1.70 from EC) to reduce glutamyl-tRNA to glutamate-1-semialdehyde (GSA), and GSA aminotransferase (5.4.3.8 from EC) to catalyse a transamination reaction to produce ALA. The second stage is to convert ALA to uroporphyrinogen III, the first macrocyclic tetrapyrrolic structure in the pathway. This is achieved by the action of three enzymes in one common pathway: porphobilinogen (PBG) synthase (or ALA dehydratase, 4.2.1.24 from EC) to condense two ALA molecules to generate porphobilinogen; hydroxymethylbilane synthase (or PBG deaminase, 2.5.1.61 from EC) to polymerise four PBG molecules into preuroporphyrinogen (tetrapyrrole structure); and uroporphyrinogen III synthase (4.2.1.75 from EC) to link two pyrrole units together (rings A and D) to yield uroporphyrinogen III. Uroporphyrinogen III is the first branch point of the pathway. To synthesise cobalamin (vitamin B12), sirohaem, and coenzyme F430, uroporphyrinogen III needs to be converted into precorrin-2 by the action of uroporphyrinogen III methyltransferase (2.1.1.107 from EC). To synthesise haem and chlorophyll, uroporphyrinogen III needs to be decarboxylated into coproporphyrinogen III by the action of uroporphyrinogen III decarboxylase (4.1.1.37 from EC) []. Porphobilinogen deaminase (also known as hydroxymethylbilane synthase, 2.5.1.61 from EC) functions during the second stage of tetrapyrrole biosynthesis. This enzyme catalyses the polymerisation of four PBG molecules into the tetrapyrrole structure, preuroporphyrinogen, with the concomitant release of four molecules of ammonia. This enzyme uses a unique dipyrro-methane cofactor made from two molecules of PBG, which is covalently attached to a cysteine side chain. The tetrapyrrole product is synthesized in an ordered, sequential fashion, by initial attachment of the first pyrrole unit (ring A) to the cofactor, followed by subsequent additions of the remaining pyrrole units (rings B, C, D) to the growing pyrrole chain []. The link between the pyrrole ring and the cofactor is broken once all the pyrroles have been added. This enzyme is folded into three distinct domains that enclose a single, large active site that makes use of an aspartic acid as its one essential catalytic residue, acting as a general acid/base during catalysis [, ]. A deficiency of hydroxymethylbilane synthase is implicated in the neuropathic disease, Acute Intermittent Porphyria (AIP) []. This entry represents the N-terminal domains 1 and 2 of porphobilinogen deaminase, an enzyme involved in tetrapyrrole biosynthesis. The structure of this domain consists of a duplication of two similar intertwined domains with three layers of (a/b/a) each. Porphobilinogen deaminase has a three-domain structure. Domains 1 (N-terminal) and 2 are duplications with the same structure, resembling the transferrins and periplasmic binding proteins. The dipyrromethane cofactor is covalently linked to domain 3 (C-terminal), but is bound by extensive salt-bridges and hydrogen-bonds within the cleft between domains 1 and 2, at a position corresponding to the binding sites for small-molecule ligands in the analogous proteins []. The enzyme has a single catalytic site, and the flexibility between domains is thought to aid elongation of the polypyrrole product in the active-site cleft of the enzyme.; GO: 0033014 tetrapyrrole biosynthetic process; PDB: 1GTK_A 1AH5_A 2YPN_A 1PDA_A 1YPN_A 3EQ1_B 3ECR_A.
Probab=94.01 E-value=2.2 Score=32.97 Aligned_cols=175 Identities=14% Similarity=0.116 Sum_probs=86.0
Q ss_pred cEEEEeccc-chhhhhHHHHHHHHHhCCCcEEEEEeCC--------------------hhHHHHHHHcCCeeEEEEcccc
Q psy3760 94 NLTIATTHT-QARYALPKIIKEFTIQFPKVKLSLLQGN--------------------PKQITEMIRNDQADIAIVTEIL 152 (306)
Q Consensus 94 ~l~I~~~~~-~~~~~l~~~l~~~~~~~p~~~i~~~~~~--------------------~~~~~~~l~~~~~Di~i~~~~~ 152 (306)
.|+||+-.+ ++..-...+...+.+.+|++++++.... ..++.+.|.+|++|+++.+...
T Consensus 1 ~irIGtR~S~LAl~Qa~~V~~~L~~~~P~~~~ei~~i~T~GD~~~~~~L~~~ggkg~Ftkele~aLl~g~iDiAVHSlKD 80 (215)
T PF01379_consen 1 KIRIGTRGSKLALAQAEMVIDRLKKAFPDLEFEIVTIKTTGDRDLDRPLSKIGGKGLFTKELEEALLDGEIDIAVHSLKD 80 (215)
T ss_dssp -EEEEEESSHHHHHHHHHHHHHHHHHSTTSEEEEEEE--CCHH--------TT--HCCCHHHHHHHHTTS-SEEEEEGGG
T ss_pred CEEEEeCCCHHHHHHHHHHHHHHHHhCCCceEEEEEccCCCCcccccchhhcCCccHHHHHHHHHHHcCCccEEEecccc
Confidence 478998665 4444556666888889999999886521 4578899999999999987432
Q ss_pred C---CCCCcee--eccccceEEEEecCCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCceeEEEEecCH
Q psy3760 153 S---PSDKLIS--IPCYQWEYVIIVPLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINS 227 (306)
Q Consensus 153 ~---~~~~~~~--~~l~~~~~~~v~~~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 227 (306)
- .++++.. .+=..++.-+++.+++ ...++++|.....|..+ +.+. ...+.......++.-.-.|+
T Consensus 81 lP~~l~~gl~iaav~~R~dprD~Lv~~~~-----~~~~l~~Lp~ga~IGTs---S~RR--~aql~~~~pdl~~~~iRGNv 150 (215)
T PF01379_consen 81 LPTELPEGLVIAAVLKREDPRDVLVSRGR-----DGKSLEDLPKGARIGTS---SLRR--RAQLKRLRPDLEVVPIRGNV 150 (215)
T ss_dssp S-SS--TTEEEEEE-------EEEEE-GC-----TTSSCCCS-TT-EEE------HHH--HHHHHHH-TTSEEE---S-H
T ss_pred CCCCCCCCceEeccCCCCCCccEEEEecC-----CCCChHHCccccccCCC---CHHH--HHHHHHhccCCeEEEecCCH
Confidence 2 2344432 2222233333333221 12356666555555443 2332 22222233345666667899
Q ss_pred HHHHHHHHhccceee-eecceeccc-ccCCce-eeecCC---CCccceEEEEEeCCc
Q psy3760 228 DIIKTYVELRMGIGI-IASIAFDSN-RDKNLR-SISASH---LFGTTISRVIIKQGT 278 (306)
Q Consensus 228 ~~~~~~v~~g~gi~~-~p~~~~~~~-~~~~l~-~~~~~~---~~~~~~~~l~~~~~~ 278 (306)
++-+.-+..|..=++ +..--.... ....+. .++.+. .+-+.-+.+-++++.
T Consensus 151 ~TRL~KL~~g~~daiiLA~AGL~RLgl~~~~~~~l~~~~~~PA~gQGalave~r~~d 207 (215)
T PF01379_consen 151 DTRLRKLDEGEYDAIILAAAGLKRLGLEDRISEILDPEEMLPAPGQGALAVECRKDD 207 (215)
T ss_dssp HHHHHHHHCTS-SEEEEEHHHHHHCT-GGGESEEE-TTTS-B-TTTT-EEEEEETT-
T ss_pred HHHHHHhcccCCCEEEhhhChhhhccccceeeeecCchhcCCCCCCeEEEEEEecCc
Confidence 999999998843333 333222222 222222 244443 122567777777763
No 287
>PRK09744 DNA-binding transcriptional regulator DicC; Provisional
Probab=93.96 E-value=0.08 Score=32.45 Aligned_cols=21 Identities=19% Similarity=-0.015 Sum_probs=19.8
Q ss_pred hcCCHHHHHHHhCCCchHHHHH
Q psy3760 15 QNFNLTEAAKALYTSQPGVSKA 36 (306)
Q Consensus 15 ~~~s~~~aA~~l~isq~~~s~~ 36 (306)
-| |.++.|+.||||++|||+.
T Consensus 10 FG-s~~kvA~aLGIs~~AVsQW 30 (75)
T PRK09744 10 FG-SKTKLANAAGVRLASVAAW 30 (75)
T ss_pred hC-cHHHHHHHHCCCHHHHHHH
Confidence 48 9999999999999999987
No 288
>PF08280 HTH_Mga: M protein trans-acting positive regulator (MGA) HTH domain; InterPro: IPR013199 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 [].; PDB: 2WTE_A 3SQN_A.
Probab=93.96 E-value=0.12 Score=30.79 Aligned_cols=50 Identities=26% Similarity=0.230 Sum_probs=37.2
Q ss_pred hhHHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCC
Q psy3760 4 HQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKR 55 (306)
Q Consensus 4 ~~l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~ 55 (306)
+-|.++.. -+.= ++...|+.+|+|..++-+-|.+|.+.|+..+.....+|
T Consensus 9 ~Ll~~L~~-~~~~-~~~ela~~l~~S~rti~~~i~~L~~~f~~~~~i~~~k~ 58 (59)
T PF08280_consen 9 KLLELLLK-NKWI-TLKELAKKLNISERTIKNDINELNEFFPENISITIQKG 58 (59)
T ss_dssp HHHHHHHH-HTSB-BHHHHHHHCTS-HHHHHHHHHHHHTT--TCCCCEEECT
T ss_pred HHHHHHHc-CCCC-cHHHHHHHHCCCHHHHHHHHHHHHHHhhhhceeeeecC
Confidence 34555666 4454 89999999999999999999999999988877665444
No 289
>PF01634 HisG: ATP phosphoribosyltransferase; InterPro: IPR013820 ATP phosphoribosyltransferase (2.4.2.17 from EC) is the enzyme that catalyzes the first step in the biosynthesis of histidine in bacteria, fungi and plants as shown below. It is a member of the larger phosphoribosyltransferase superfamily of enzymes which catalyse the condensation of 5-phospho-alpha-D-ribose 1-diphosphate with nitrogenous bases in the presence of divalent metal ions []. ATP + 5-phospho-alpha-D-ribose 1-diphosphate = 1-(5-phospho-D-ribosyl)-ATP + diphosphate Histidine biosynthesis is an energetically expensive process and ATP phosphoribosyltransferase activity is subject to control at several levels. Transcriptional regulation is based primarily on nutrient conditions and determines the amount of enzyme present in the cell, while feedback inihibition rapidly modulates activity in response to cellular conditions. The enzyme has been shown to be inhibited by 1-(5-phospho-D-ribosyl)-ATP, histidine, ppGpp (a signal associated with adverse environmental conditions) and ADP and AMP (which reflect the overall energy status of the cell). As this pathway of histidine biosynthesis is present only in prokayrotes, plants and fungi, this enzyme is a promising target for the development of novel antimicrobial compounds and herbicides. ATP phosphoribosyltransferase is found in two distinct forms: a long form containing two catalytic domains and a C-terminal regulatory domain, and a short form in which the regulatory domain is missing. The long form is catalytically competent, but in organisms with the short form, a histidyl-tRNA synthetase paralogue, HisZ, is required for enzyme activity []. This entry represents the catalytic region of this enzyme. The structures of the long form enzymes from Escherichia coli (P60757 from SWISSPROT) and Mycobacterium tuberculosis (P60759 from SWISSPROT) have been determined [, ]. The enzyme itself exists in equilibrium between an active dimeric form, an inactive hexameric form and higher aggregates. Interconversion between the various forms is largely reversible and is influenced by the binding of the natural substrates and inhibitors of the enzyme. The two catalytic domains are linked by a two-stranded beta-sheet and togther form a "periplasmic binding protein fold". A crevice between these domains contains the active site. The C-terminal domain is not directly involved in catalysis but appears to be involved the formation of hexamers, induced by the binding of inhibitors such as histidine to the enzyme, thus regulating activity.; GO: 0003879 ATP phosphoribosyltransferase activity, 0000105 histidine biosynthetic process, 0005737 cytoplasm; PDB: 1VE4_A 2VD3_B 1NH7_A 1NH8_A 1Z7N_G 1Z7M_E 1O64_A 1O63_A 1USY_F 1Q1K_A ....
Probab=93.80 E-value=1.8 Score=31.86 Aligned_cols=149 Identities=16% Similarity=0.213 Sum_probs=89.9
Q ss_pred hhHHHHHHHcCCeeEEEEccccC--------CCCCceeeccccceEEEEecCCCCCCCCCCcChhhhcCCCeEeecCCCC
Q psy3760 131 PKQITEMIRNDQADIAIVTEILS--------PSDKLISIPCYQWEYVIIVPLDHPLLLLNSISLKEISNYPLITYDLSFS 202 (306)
Q Consensus 131 ~~~~~~~l~~~~~Di~i~~~~~~--------~~~~~~~~~l~~~~~~~v~~~~~~l~~~~~i~~~dl~~~~~i~~~~~~~ 202 (306)
..++...+..|.+|+||+..... +-..+.-..++.-++++.+|.+.+. -+++++....-|.. .
T Consensus 3 ~~DIp~yV~~G~~DlGI~G~D~l~E~~~~~~~v~~~~dL~fg~crl~vAvp~~~~~-----~~~~~l~~~~rIAT----k 73 (163)
T PF01634_consen 3 PQDIPTYVEDGIADLGITGKDVLLESGLGRADVEELLDLGFGKCRLVVAVPEDWPY-----KSVEDLKAGLRIAT----K 73 (163)
T ss_dssp GGHHHHHHHTTSSSEEEEEHHHHHHHTHH-SSEEEEEEESCSEEEEEEEEETTSCG-----CCGGGGSSTEEEEE----S
T ss_pred hHHHHHHHHCCCCcEEEeehheeccCCCCccceEEEeecccccEEEEEEEECCcCC-----CCHHHhccCCEEEE----C
Confidence 45778899999999999852111 1122345566778899999988762 35667764333332 3
Q ss_pred cHHHHHHHHHhCCCceeEEEEecCHHHHHHHHHhccceeeeeccee-cccccCCceeeecCCCCccceEEEEEeCCcc--
Q psy3760 203 GRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMGIGIIASIAF-DSNRDKNLRSISASHLFGTTISRVIIKQGTY-- 279 (306)
Q Consensus 203 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~~~p~~~~-~~~~~~~l~~~~~~~~~~~~~~~l~~~~~~~-- 279 (306)
+.+...++|.+.|+...++....+.+.. ...|.+=+++---.. ..++..+|+.+ +.....+..|+.++...
T Consensus 74 yp~l~~~yf~~~g~~~~ii~l~GsvE~a---p~~glAD~IvDiv~TG~TLr~NgL~~i---~~i~~s~a~LI~n~~~~~~ 147 (163)
T PF01634_consen 74 YPNLTRRYFAEKGINVEIIKLSGSVELA---PPLGLADAIVDIVETGTTLRANGLKEI---ETILESSARLIANKASLKE 147 (163)
T ss_dssp -HHHHHHHHHHCT-EEEEEE-SS-TTHH---HHTTSSSEEEEEESSSHHHHHTTEEEE---EEEEEEEEEEEEEHHHHHH
T ss_pred CHHHHHHHHHHcCCcEEEEEccCCcccc---CCCCCCCEEEEeccCcHHHHHCCCEEe---EEEEEEEEEEEEcCccchh
Confidence 4567789999999887777666666655 445533344332111 11245677777 33445678888877653
Q ss_pred ccHHHHHHHHHHhHH
Q psy3760 280 LRSYVYSFIKLLSPK 294 (306)
Q Consensus 280 ~~~~~~~~~~~l~~~ 294 (306)
..+.++.+++.|+..
T Consensus 148 k~~~i~~l~~~l~~v 162 (163)
T PF01634_consen 148 KEEKIDELVTRLRGV 162 (163)
T ss_dssp CHHHHHHHHHHHHHH
T ss_pred hHHHHHHHHHHHHhh
Confidence 344566666666553
No 290
>PRK10411 DNA-binding transcriptional activator FucR; Provisional
Probab=93.78 E-value=1.2 Score=35.28 Aligned_cols=36 Identities=19% Similarity=0.291 Sum_probs=28.9
Q ss_pred CHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCCc
Q psy3760 18 NLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRI 56 (306)
Q Consensus 18 s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~ 56 (306)
+....|+.|++|+.|+.|-|++||+. .+..|..+|.
T Consensus 20 ~~~eLa~~l~VS~~TiRRdL~~L~~~---~~l~r~~Gga 55 (240)
T PRK10411 20 TTEALAEQLNVSKETIRRDLNELQTQ---GKILRNHGRA 55 (240)
T ss_pred cHHHHHHHHCcCHHHHHHHHHHHHHC---CCEEEecCeE
Confidence 66788999999999999999999994 2345665554
No 291
>COG0040 HisG ATP phosphoribosyltransferase [Amino acid transport and metabolism]
Probab=93.77 E-value=2.7 Score=34.01 Aligned_cols=162 Identities=14% Similarity=0.164 Sum_probs=100.7
Q ss_pred EEEEeCChhHHHHHHHcCCeeEEEEccccCCCC--------CceeeccccceEEEEecCCCCCCCCCCcChhhhcCCCeE
Q psy3760 124 LSLLQGNPKQITEMIRNDQADIAIVTEILSPSD--------KLISIPCYQWEYVIIVPLDHPLLLLNSISLKEISNYPLI 195 (306)
Q Consensus 124 i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~~~--------~~~~~~l~~~~~~~v~~~~~~l~~~~~i~~~dl~~~~~i 195 (306)
+++.-....++..-+..|.+|+||+....-... .+.-..++.-++++.+|++.+ ..+.+++.+-.-|
T Consensus 45 I~~~~vR~~DIP~yV~~G~~DlGItG~D~l~E~~~~~~~v~~l~dL~fG~crl~vAvp~~~~-----~~~~~~l~~~~rI 119 (290)
T COG0040 45 IELLLVRAQDIPTYVEDGVADLGITGEDVLRESGLDDASVEELLDLGFGGCRLVVAVPEESD-----YTSPEDLKGRLRI 119 (290)
T ss_pred eEEEEEChHHhhHHHhcCceeeeeechhhhhhcccCccCceehccCCCCcEEEEEEecCCcC-----ccChhHhcCCceE
Confidence 455555567899999999999999953322222 233556778899999999875 2345555433233
Q ss_pred eecCCCCcHHHHHHHHHhCCCceeEEEEecCHHHHHHHHHhccceeeeeccee-cccccCCceeeecCCCCccceEEEEE
Q psy3760 196 TYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMGIGIIASIAF-DSNRDKNLRSISASHLFGTTISRVII 274 (306)
Q Consensus 196 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~~~p~~~~-~~~~~~~l~~~~~~~~~~~~~~~l~~ 274 (306)
.. .+.+...++|+..|....++.-..+.+.+ ...|.+=+++.-... ..++..+|+.+. .....+-+++.
T Consensus 120 AT----kYp~l~~~yf~~~g~~~~Ii~l~GsvE~a---P~~GlADaIvDivsTG~TLkaNgL~~id---~i~~ssa~LI~ 189 (290)
T COG0040 120 AT----KYPNLARKYFAEKGIDVEIIKLSGSVELA---PALGLADAIVDIVSTGTTLKANGLKEIE---VIYDSSARLIV 189 (290)
T ss_pred EE----ccHHHHHHHHHHcCceEEEEEccCcEeec---cccCccceEEEeecCCHhHHHCCCEEEE---EEEeeEEEEEe
Confidence 32 24567788999999988777666665543 344544444433221 122456677762 23455777777
Q ss_pred e-C--CccccHHHHHHHHHHhHHhhHHHH
Q psy3760 275 K-Q--GTYLRSYVYSFIKLLSPKLNRKFI 300 (306)
Q Consensus 275 ~-~--~~~~~~~~~~~~~~l~~~~~~~~~ 300 (306)
+ + .+...+.++.++..++..++.+..
T Consensus 190 n~~~~~~~k~~~i~~l~~rl~gvi~a~~~ 218 (290)
T COG0040 190 NAKASLKDKQELIDQLVTRLKGVIEARGS 218 (290)
T ss_pred ccccccchhHHHHHHHHHHHHHHHhhcce
Confidence 7 2 223345688888888887766544
No 292
>PRK11477 carbohydrate diacid transcriptional activator CdaR; Provisional
Probab=93.60 E-value=0.15 Score=43.73 Aligned_cols=42 Identities=19% Similarity=0.280 Sum_probs=37.0
Q ss_pred HHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCcee
Q psy3760 7 RFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDI 48 (306)
Q Consensus 7 ~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~L 48 (306)
+++.+-.++++|+++||++|++-+-|+.++|+++|+.+|..+
T Consensus 325 ~TL~~y~~~~~ni~~tA~~L~iHrNTL~YRL~kI~eltG~d~ 366 (385)
T PRK11477 325 RTLAAWFRHNVQPLATSKALFIHRNTLEYRLNRISELTGLDL 366 (385)
T ss_pred HHHHHHHHcCCCHHHHHHHhCCCHhhHHHHHHHHHHHhCcCc
Confidence 466666676559999999999999999999999999999886
No 293
>PF13613 HTH_Tnp_4: Helix-turn-helix of DDE superfamily endonuclease
Probab=93.58 E-value=0.12 Score=30.04 Aligned_cols=39 Identities=18% Similarity=-0.055 Sum_probs=31.4
Q ss_pred HHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCce
Q psy3760 8 FVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSID 47 (306)
Q Consensus 8 ~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~ 47 (306)
++.-+-..- ++..-|...|||+||+|+.++.+++.|...
T Consensus 12 ~L~~LR~~~-~~~~La~~FgIs~stvsri~~~~~~~L~~~ 50 (53)
T PF13613_consen 12 TLMYLRLNL-TFQDLAYRFGISQSTVSRIFHEWIPLLYQV 50 (53)
T ss_pred HHHHHHcCC-cHhHHhhheeecHHHHHHHHHHHHHHHHHh
Confidence 344444444 999999999999999999999999887544
No 294
>cd00131 PAX Paired Box domain
Probab=93.52 E-value=0.79 Score=32.34 Aligned_cols=38 Identities=24% Similarity=0.171 Sum_probs=31.6
Q ss_pred HHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCce
Q psy3760 10 REAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSID 47 (306)
Q Consensus 10 ~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~ 47 (306)
+.+++.|.|...+|+.+++|+++|++.+++.+++=.+.
T Consensus 27 v~~~~~G~s~~~iA~~~~Vs~~tV~r~i~r~~e~G~v~ 64 (128)
T cd00131 27 VELAQSGIRPCDISRQLRVSHGCVSKILNRYYETGSIR 64 (128)
T ss_pred HHHHHcCCCHHHHHHHHCcCHHHHHHHHHHHHHcCCcC
Confidence 34455666999999999999999999999999865444
No 295
>PRK14987 gluconate operon transcriptional regulator; Provisional
Probab=93.50 E-value=1.1 Score=37.44 Aligned_cols=112 Identities=13% Similarity=0.122 Sum_probs=60.2
Q ss_pred CHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCCccccCHhHHHHHHHHHHHHHHHHHHHH-HHHhhccCCCCcEE
Q psy3760 18 NLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKPGQAILRSIEIIMQEIEGLKK-IGKEFSAYDTGNLT 96 (306)
Q Consensus 18 s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~~~lT~~G~~l~~~a~~il~~~~~~~~-~~~~~~~~~~~~l~ 96 (306)
++..-|+..|+|.+||||.|. .+.++ . + ..-+++.++.+++.-.-+ ..+.+..+.+..|-
T Consensus 7 ti~dIA~~agVS~~TVSrvLn-------------~~~~v-s--~---~tr~rV~~~a~elgY~pn~~a~~l~~~~~~~Ig 67 (331)
T PRK14987 7 VLQDVADRVGVTKMTVSRFLR-------------NPEQV-S--V---ALRGKIAAALDELGYIPNRAPDILSNATSRAIG 67 (331)
T ss_pred cHHHHHHHhCCCHHHhhhhhC-------------CCCCC-C--H---HHHHHHHHHHHHhCCCccHHHHHHhhCCCCEEE
Confidence 788999999999999999984 22233 2 2 222233333333321111 11222333334444
Q ss_pred EEecccchhhhhHHHHHHHHHhCC--CcEEEEEeCC--h---hHHHHHHHcCCeeEEEEc
Q psy3760 97 IATTHTQARYALPKIIKEFTIQFP--KVKLSLLQGN--P---KQITEMIRNDQADIAIVT 149 (306)
Q Consensus 97 I~~~~~~~~~~l~~~l~~~~~~~p--~~~i~~~~~~--~---~~~~~~l~~~~~Di~i~~ 149 (306)
+-++. +...++..++..+.+..- ++.+.+...+ . .+.++.+.+..+|-+|..
T Consensus 68 vi~~~-~~~~~~~~~~~gi~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~vdgiI~~ 126 (331)
T PRK14987 68 VLLPS-LTNQVFAEVLRGIESVTDAHGYQTMLAHYGYKPEMEQERLESMLSWNIDGLILT 126 (331)
T ss_pred EEeCC-CcchhHHHHHHHHHHHHHHCCCEEEEecCCCCHHHHHHHHHHHHhcCCCEEEEc
Confidence 44432 445566666665544432 5566554332 2 134566778889999985
No 296
>COG1349 GlpR Transcriptional regulators of sugar metabolism [Transcription / Carbohydrate transport and metabolism]
Probab=93.48 E-value=1.1 Score=36.00 Aligned_cols=58 Identities=14% Similarity=0.166 Sum_probs=42.4
Q ss_pred hhHHHHHHHHHhc-CCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCCccccCHhHH
Q psy3760 4 HQFRFVREAVRQN-FNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKPGQ 64 (306)
Q Consensus 4 ~~l~~f~~v~~~~-~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~~~lT~~G~ 64 (306)
++-+++-.|.+.| -++...|+.+++|..||-|=|.+||++ -+..|.++|.+.+.....
T Consensus 6 R~~~Il~~l~~~g~v~v~eLa~~~~VS~~TIRRDL~~Le~~---g~l~R~hGGa~~~~~~~~ 64 (253)
T COG1349 6 RHQKILELLKEKGKVSVEELAELFGVSEMTIRRDLNELEEQ---GLLLRVHGGAVLPDSESE 64 (253)
T ss_pred HHHHHHHHHHHcCcEEHHHHHHHhCCCHHHHHHhHHHHHHC---CcEEEEeCCEecCCCccc
Confidence 4445555666655 146789999999999999999999986 467888888743344343
No 297
>PF13551 HTH_29: Winged helix-turn helix
Probab=93.44 E-value=0.24 Score=33.89 Aligned_cols=44 Identities=16% Similarity=0.113 Sum_probs=33.5
Q ss_pred HHHHHHHHhcCC-HHHHHHHhCCCchHHHHHHHHHHHHcC-ceeEEec
Q psy3760 7 RFVREAVRQNFN-LTEAAKALYTSQPGVSKAIIELEEELS-IDIFIRH 52 (306)
Q Consensus 7 ~~f~~v~~~~~s-~~~aA~~l~isq~~~s~~i~~LE~~lg-~~Lf~R~ 52 (306)
.++..+.+-. + ..++|+.+|+|.+|+.+.+++.++ -| ..|..|.
T Consensus 3 ~~l~l~~~g~-~~~~~ia~~lg~s~~Tv~r~~~~~~~-~G~~~l~~~~ 48 (112)
T PF13551_consen 3 QILLLLAEGV-STIAEIARRLGISRRTVYRWLKRYRE-GGIEGLLPRK 48 (112)
T ss_pred HHHHHHHcCC-CcHHHHHHHHCcCHHHHHHHHHHHHc-ccHHHHHhcc
Confidence 4455555554 7 999999999999999999999984 44 3565643
No 298
>TIGR02719 repress_PhaQ poly-beta-hydroxybutyrate-responsive repressor. 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 (see pfam03551).
Probab=93.41 E-value=0.36 Score=34.38 Aligned_cols=57 Identities=21% Similarity=0.240 Sum_probs=37.4
Q ss_pred hCCCchHHHHHHHHHHHH--cCceeEEec---CCCccccCHhHHHHHHHHHHHHHHHHHHHH
Q psy3760 26 LYTSQPGVSKAIIELEEE--LSIDIFIRH---GKRIRGLTKPGQAILRSIEIIMQEIEGLKK 82 (306)
Q Consensus 26 l~isq~~~s~~i~~LE~~--lg~~Lf~R~---~~~~~~lT~~G~~l~~~a~~il~~~~~~~~ 82 (306)
..++++++...|++||+. +-...-.-. .+.+.++|+.|+..+.....-...+....+
T Consensus 53 ~~v~~GtLYp~L~RLE~~GlI~~~~~~~~~gp~RK~Y~LTe~Gr~~L~~~~~~w~~~~~~l~ 114 (138)
T TIGR02719 53 SSVDQGNVYRTLRKLEKDNLISSQWDTSAEGPAKRIYSLTDAGEQYLSMCANSFEHYQNMLD 114 (138)
T ss_pred CCCCcChHHHHHHHHHHCCCEEEEeeecCCCCCcEEEEECHHHHHHHHHHHHHHHHHHHHHH
Confidence 479999999999999986 222211111 133348999999988776655555444433
No 299
>PF08220 HTH_DeoR: DeoR-like helix-turn-helix domain; InterPro: IPR001034 The deoR-type HTH domain is a DNA-binding, helix-turn-helix (HTH) domain of about 50-60 amino acids present in transcription regulators of the deoR family, involved in sugar catabolism. This family of prokaryotic regulators is named after the Escherichia coli protein DeoR, a repressor of the deo operon, which encodes nucleotide and deoxyribonucleotide catabolic enzymes. DeoR also negatively regulates the expression of nupG and tsx, a nucleoside-specific transport protein and a channel-forming protein, respectively. DeoR-like transcription repressors occur in diverse bacteria as regulators of sugar and nucleoside metabolic systems. The effector molecules for deoR-like regulators are generally phosphorylated intermediates of the relevant metabolic pathway. The DNA-binding deoR-type HTH domain occurs usually in the N-terminal part. The C-terminal part can contain an effector-binding domain and/or an oligomerisation domain. DeoR occurs as an octamer, whilst glpR and agaR are tetramers. Several operators may be bound simultaneously, which could facilitate DNA looping [, ].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular
Probab=93.26 E-value=0.23 Score=29.32 Aligned_cols=43 Identities=14% Similarity=0.135 Sum_probs=34.7
Q ss_pred HHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCCc
Q psy3760 10 REAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRI 56 (306)
Q Consensus 10 ~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~ 56 (306)
+.-...= |+...|+.+++|..|+.|-|..||+.= +..|..+|.
T Consensus 9 l~~~~~~-s~~ela~~~~VS~~TiRRDl~~L~~~g---~i~r~~GG~ 51 (57)
T PF08220_consen 9 LKEKGKV-SVKELAEEFGVSEMTIRRDLNKLEKQG---LIKRTHGGA 51 (57)
T ss_pred HHHcCCE-EHHHHHHHHCcCHHHHHHHHHHHHHCC---CEEEEcCEE
Confidence 3334444 788999999999999999999999864 478887776
No 300
>PRK03975 tfx putative transcriptional regulator; Provisional
Probab=93.23 E-value=0.87 Score=32.57 Aligned_cols=77 Identities=19% Similarity=0.183 Sum_probs=50.5
Q ss_pred chhhHHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHH----HHHHcCceeEEec-CCCccccCHhHHHHHHHHHHHHHH
Q psy3760 2 NLHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIE----LEEELSIDIFIRH-GKRIRGLTKPGQAILRSIEIIMQE 76 (306)
Q Consensus 2 ~~~~l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~----LE~~lg~~Lf~R~-~~~~~~lT~~G~~l~~~a~~il~~ 76 (306)
+-++.++|.... .|.|..+.|+.||+|++++++..+. |++...+-.|.+. +..+.-.=++|..++.-.+.++..
T Consensus 8 t~rqreVL~lr~-~GlTq~EIAe~LGiS~~tVs~ie~ra~kkLr~~~~tl~~~~~l~a~~~v~~~~G~d~~~ip~~v~~~ 86 (141)
T PRK03975 8 TERQIEVLRLRE-RGLTQQEIADILGTSRANVSSIEKRARENIEKARETLAFAETLNAPVRVTIPAGTDLFDIPKRIYKE 86 (141)
T ss_pred CHHHHHHHHHHH-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCeEEEecCCCcHHHhHHHHHHH
Confidence 446677776654 5559999999999999999877665 4433333333332 333212557788888877777766
Q ss_pred HHH
Q psy3760 77 IEG 79 (306)
Q Consensus 77 ~~~ 79 (306)
.++
T Consensus 87 ~d~ 89 (141)
T PRK03975 87 ADE 89 (141)
T ss_pred hhH
Confidence 444
No 301
>PF04297 UPF0122: Putative helix-turn-helix protein, YlxM / p13 like; InterPro: IPR007394 Members of this family are predicted to contain a helix-turn-helix motif, for example residues 37-55 in Mycoplasma mycoides p13 (O05290 from SWISSPROT). 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 [].; PDB: 1S7O_A 1XSV_B.
Probab=93.23 E-value=0.17 Score=33.72 Aligned_cols=41 Identities=24% Similarity=0.280 Sum_probs=30.4
Q ss_pred hhHHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHc
Q psy3760 4 HQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEEL 44 (306)
Q Consensus 4 ~~l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~l 44 (306)
+|-++|-.-.....|++.-|+.+|||..||+..|++-++.|
T Consensus 21 kQ~~~l~lyy~eDlSlsEIAe~~~iSRqaV~d~ikr~~~~L 61 (101)
T PF04297_consen 21 KQREILELYYEEDLSLSEIAEELGISRQAVYDSIKRAEKKL 61 (101)
T ss_dssp HHHHHHHHHCTS---HHHHHHHCTS-HHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHccCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 55566666666667999999999999999999999877655
No 302
>PF01710 HTH_Tnp_IS630: Transposase; InterPro: IPR002622 Transposase proteins are necessary for efficient DNA transposition. This entry includes insertion sequences from Synechocystis sp. (strain PCC 6803) three of which are characterised as homologous to bacterial IS5- and IS4- and to several members of the IS630-Tc1-mariner superfamily []. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=93.22 E-value=0.13 Score=35.77 Aligned_cols=43 Identities=19% Similarity=0.181 Sum_probs=35.4
Q ss_pred CchhhHHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHc
Q psy3760 1 MNLHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEEL 44 (306)
Q Consensus 1 m~~~~l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~l 44 (306)
+|.+.|+.++.-.-.- ++.+-|+.+++|+++|++.+++|--..
T Consensus 57 id~~~L~~~v~~~pd~-tl~Ela~~l~Vs~~ti~~~Lkrlg~t~ 99 (119)
T PF01710_consen 57 IDRDELKALVEENPDA-TLRELAERLGVSPSTIWRALKRLGITR 99 (119)
T ss_pred ccHHHHHHHHHHCCCc-CHHHHHHHcCCCHHHHHHHHHHcCchh
Confidence 3566777777777777 889999999999999999999886544
No 303
>PRK10423 transcriptional repressor RbsR; Provisional
Probab=93.19 E-value=0.8 Score=38.11 Aligned_cols=110 Identities=14% Similarity=0.175 Sum_probs=55.5
Q ss_pred HHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCCccccCHhHHHHHHHHHHHHHHHHHHHH-HHHhhccCCCCcEEEE
Q psy3760 20 TEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKPGQAILRSIEIIMQEIEGLKK-IGKEFSAYDTGNLTIA 98 (306)
Q Consensus 20 ~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~~~lT~~G~~l~~~a~~il~~~~~~~~-~~~~~~~~~~~~l~I~ 98 (306)
..-|+..|+|.+||||.|.. +.++ .+ ..-+++.+..+++.-.-+ ..+.+..+..+.|-+-
T Consensus 2 ~dIA~~agVS~~TVSrvLn~-------------~~~v---s~---~tr~rV~~~a~~lgY~pn~~a~~l~~~~~~~Igvi 62 (327)
T PRK10423 2 KDVARLAGVSTSTVSHVINK-------------DRFV---SE---AITAKVEAAIKELNYAPSALARSLKLNQTRTIGML 62 (327)
T ss_pred hhHHHHhCCcHHHHHHHhCC-------------CCCC---CH---HHHHHHHHHHHHHCCCccHHHHHHhhCCCCeEEEE
Confidence 45799999999999999961 2232 22 222222222222221111 1122233334445444
Q ss_pred ecccchhhhhHHHHHHHHHhC--CCcEEEEEeCC--h---hHHHHHHHcCCeeEEEEc
Q psy3760 99 TTHTQARYALPKIIKEFTIQF--PKVKLSLLQGN--P---KQITEMIRNDQADIAIVT 149 (306)
Q Consensus 99 ~~~~~~~~~l~~~l~~~~~~~--p~~~i~~~~~~--~---~~~~~~l~~~~~Di~i~~ 149 (306)
++. +...++..++..+.+.. -+..+.+.... . .+.++.+.++++|-.|+.
T Consensus 63 ~~~-~~~~~~~~~~~gi~~~~~~~g~~~~~~~~~~~~~~~~~~~~~l~~~~vdGiI~~ 119 (327)
T PRK10423 63 ITA-STNPFYSELVRGVERSCFERGYSLVLCNTEGDEQRMNRNLETLMQKRVDGLLLL 119 (327)
T ss_pred eCC-CCCCcHHHHHHHHHHHHHHcCCEEEEEeCCCCHHHHHHHHHHHHHcCCCEEEEe
Confidence 443 23344555554443332 24565554332 2 234566778889988875
No 304
>COG3221 PhnD ABC-type phosphate/phosphonate transport system, periplasmic component [Inorganic ion transport and metabolism]
Probab=93.17 E-value=4.2 Score=33.48 Aligned_cols=194 Identities=15% Similarity=0.091 Sum_probs=112.4
Q ss_pred CcEEEEecccchhhhh----HHHHHHHHHhCCCcEEEEEe-CChhHHHHHHHcCCeeEEEEccccC--------CCCCce
Q psy3760 93 GNLTIATTHTQARYAL----PKIIKEFTIQFPKVKLSLLQ-GNPKQITEMIRNDQADIAIVTEILS--------PSDKLI 159 (306)
Q Consensus 93 ~~l~I~~~~~~~~~~l----~~~l~~~~~~~p~~~i~~~~-~~~~~~~~~l~~~~~Di~i~~~~~~--------~~~~~~ 159 (306)
..+++|+.++-...-+ .++...+.++ -++.++... .+...+++.+..|++|++....... ....+.
T Consensus 35 ~~l~~gi~p~e~~~~~~~~~~pl~~~L~~~-lG~~V~~~~a~dy~~vieal~~g~~D~A~~~~~a~~~a~~~~~~~e~~~ 113 (299)
T COG3221 35 KELRVGIVPTENPTNLIPAWAPLADYLEKE-LGIPVEFFVATDYAAVIEALRAGQVDIAWLGPSAYVEAVDRALAGEPLA 113 (299)
T ss_pred cceEEEEcCCCChHHHHHHHHHHHHHHHHH-hCCceEEEecccHHHHHHHHhCCCeeEEecCchhHHHHHhhccccccee
Confidence 4699999887555443 3444444443 466676666 4677899999999999998742100 011111
Q ss_pred ee--ccc--cceEEEEecCCCCCCCCCCcChhhhcCCCeEeecCCCCc-HHHHHHHHHhCC-Cc----eeEEEEecCHHH
Q psy3760 160 SI--PCY--QWEYVIIVPLDHPLLLLNSISLKEISNYPLITYDLSFSG-RIKLDREFSLQK-LT----PYIVLETINSDI 229 (306)
Q Consensus 160 ~~--~l~--~~~~~~v~~~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~-~~~~~~~~~~~~-~~----~~~~~~~~~~~~ 229 (306)
.. .=+ ...=++++.++.|+ -+++|+.+..+...++.+.- .-.-..++...| .. ...+....+++.
T Consensus 114 ~~~~~dg~~~Y~S~~i~~~ds~i-----~sl~dlkgk~~af~d~~StSG~l~P~~~L~~~g~~d~~~~f~~v~~~G~H~~ 188 (299)
T COG3221 114 QTVQKDGSPGYYSVIIVRADSPI-----KSLEDLKGKRFAFGDPDSTSGYLFPLYYLAKEGGIDPDKFFGEVIFSGGHDA 188 (299)
T ss_pred eeeccCCCcceeEEEEEeCCCCc-----chHHHhcCCeEeccCCCcchhhHhHHHHHHHhcCCChhhhhceeeccChHHH
Confidence 11 001 11345666777663 46779999999998876543 223345566666 43 245556676889
Q ss_pred HHHHHHhc-cceeeeecceeccc----cc---CCceeeecCCCCccceEEEEEeCCccccHHHHHHHHHHhHHh
Q psy3760 230 IKTYVELR-MGIGIIASIAFDSN----RD---KNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLLSPKL 295 (306)
Q Consensus 230 ~~~~v~~g-~gi~~~p~~~~~~~----~~---~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~ 295 (306)
.+..|.+| .-++.+........ .. .+++.+-..++.+. .-++|+++.. ....+++.+.+.+.-
T Consensus 189 a~~aV~nG~vDva~~~~~~~~~~~~~~~~~~~~~l~vi~~S~~iP~--~pi~vr~~L~-~~~k~kl~~af~~l~ 259 (299)
T COG3221 189 AVLAVANGQVDVAAVNSSARGLLKKAAPEGVAEKLRVIWKSPLIPN--DPIAVRSDLP-ADLKEKLRDAFLDLA 259 (299)
T ss_pred HHHHHHcCCceEEeccHHHHhhhhhcccccchhhceEEEecCCCCC--CCEEEeCCCC-HHHHHHHHHHHHhcC
Confidence 99999988 33333333222221 22 35666655554333 3456666643 555666666665553
No 305
>TIGR03433 padR_acidobact transcriptional regulator, Acidobacterial, PadR-family. Members of this protein family are putative transcriptional regulators of the PadR family, as found in species of the Acidobacteria. This family of proteins has expanded greatly in this lineage, and where it regularly is found in the vicinity of a putative transporter protein
Probab=93.06 E-value=0.44 Score=31.96 Aligned_cols=55 Identities=15% Similarity=0.095 Sum_probs=41.5
Q ss_pred HhCCCchHHHHHHHHHHHHcCceeEEe----c----CCCccccCHhHHHHHHHHHHHHHHHHHHHH
Q psy3760 25 ALYTSQPGVSKAIIELEEELSIDIFIR----H----GKRIRGLTKPGQAILRSIEIIMQEIEGLKK 82 (306)
Q Consensus 25 ~l~isq~~~s~~i~~LE~~lg~~Lf~R----~----~~~~~~lT~~G~~l~~~a~~il~~~~~~~~ 82 (306)
.+.++++++...|++||++= |..+ . .+..+++|+.|+.++.......+.+.+...
T Consensus 34 ~~~i~~gtlY~~L~rLe~~G---lI~~~~~~~~~~~~rk~y~iT~~Gr~~l~~~~~~~~~~~~~i~ 96 (100)
T TIGR03433 34 VLQVEEGSLYPALHRLERRG---WIAAEWGESENNRRAKFYRLTAAGRKQLAAETESWARLSAAIA 96 (100)
T ss_pred ccccCCCcHHHHHHHHHHCC---CeEEEeeecCCCCCceEEEECHHHHHHHHHHHHHHHHHHHHHH
Confidence 46899999999999999862 4443 1 123348999999999999888777766554
No 306
>PF05344 DUF746: Domain of Unknown Function (DUF746); InterPro: IPR008008 This is a short conserved region found in some transposons.
Probab=93.05 E-value=0.29 Score=29.36 Aligned_cols=40 Identities=20% Similarity=0.161 Sum_probs=34.8
Q ss_pred hHHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHc
Q psy3760 5 QFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEEL 44 (306)
Q Consensus 5 ~l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~l 44 (306)
.++.|+.+.-...|+..||+.||+++.++.+.+......+
T Consensus 2 ~~~~fIrlLs~~~s~~~Aa~~lG~~~~~v~~wv~~fR~wl 41 (65)
T PF05344_consen 2 KARAFIRLLSQQISVAQAADRLGTDPGTVRRWVRMFRQWL 41 (65)
T ss_pred cHHHHHHHhcccccHHHHHHHHCcCHHHHHHHHHHHHHHH
Confidence 4567777777777999999999999999999999988776
No 307
>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=92.97 E-value=0.25 Score=25.77 Aligned_cols=33 Identities=18% Similarity=0.189 Sum_probs=24.9
Q ss_pred hHHHHHHHHHhcCCHHHHHHHhCCCchHHHHHH
Q psy3760 5 QFRFVREAVRQNFNLTEAAKALYTSQPGVSKAI 37 (306)
Q Consensus 5 ~l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i 37 (306)
....+....+.+.|....|+.+++|.+++++.+
T Consensus 10 ~~~~i~~~~~~~~s~~~ia~~~~is~~tv~~~~ 42 (42)
T cd00569 10 QIEEARRLLAAGESVAEIARRLGVSRSTLYRYL 42 (42)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHhC
Confidence 344455555555599999999999999998753
No 308
>COG4189 Predicted transcriptional regulator [Transcription]
Probab=92.91 E-value=0.22 Score=38.20 Aligned_cols=27 Identities=37% Similarity=0.370 Sum_probs=25.1
Q ss_pred CCHHHHHHHhCCCchHHHHHHHHHHHH
Q psy3760 17 FNLTEAAKALYTSQPGVSKAIIELEEE 43 (306)
Q Consensus 17 ~s~~~aA~~l~isq~~~s~~i~~LE~~ 43 (306)
.++++.|+.|+++||++|..|+.||+-
T Consensus 38 lNvneiAe~lgLpqst~s~~ik~Le~a 64 (308)
T COG4189 38 LNVNEIAEALGLPQSTMSANIKVLEKA 64 (308)
T ss_pred CCHHHHHHHhCCchhhhhhhHHHHHhc
Confidence 479999999999999999999999973
No 309
>COG2771 CsgD DNA-binding HTH domain-containing proteins [Transcription]
Probab=92.88 E-value=0.43 Score=28.77 Aligned_cols=45 Identities=16% Similarity=0.183 Sum_probs=39.5
Q ss_pred chhhHHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCce
Q psy3760 2 NLHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSID 47 (306)
Q Consensus 2 ~~~~l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~ 47 (306)
+.+..++...+++-. |..+-|..|++|..|+..+++.+...+|+.
T Consensus 6 t~rE~~v~~l~~~G~-s~~eia~~l~is~~tV~~h~~~i~~Kl~~~ 50 (65)
T COG2771 6 TPREREILRLVAQGK-SNKEIARILGISEETVKTHLRNIYRKLGVK 50 (65)
T ss_pred CHHHHHHHHHHHCCC-CHHHHHHHHCCCHHHHHHHHHHHHHHHCCC
Confidence 446677777888877 999999999999999999999999999874
No 310
>PRK10163 DNA-binding transcriptional repressor AllR; Provisional
Probab=92.83 E-value=0.62 Score=37.77 Aligned_cols=57 Identities=4% Similarity=-0.106 Sum_probs=39.3
Q ss_pred hHHHHHHHHHhc--CCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCCccccCHhH
Q psy3760 5 QFRFVREAVRQN--FNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKPG 63 (306)
Q Consensus 5 ~l~~f~~v~~~~--~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~~~lT~~G 63 (306)
-+.++-.+.+.+ .+++.-|+.++++.||+.|-++.|++. |.--.+..++.. .|+..-
T Consensus 27 ~l~IL~~~~~~~~~~tl~eIa~~lglpkStv~RlL~tL~~~-G~l~~~~~~~~Y-~lG~~l 85 (271)
T PRK10163 27 GIAILQYLEKSGGSSSVSDISLNLDLPLSTTFRLLKVLQAA-DFVYQDSQLGWW-HIGLGV 85 (271)
T ss_pred HHHHHHHHHhCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHC-CCEEEcCCCCeE-EecHHH
Confidence 344455555432 379999999999999999999999874 554444344555 566543
No 311
>PHA00542 putative Cro-like protein
Probab=92.78 E-value=0.25 Score=31.71 Aligned_cols=32 Identities=22% Similarity=0.279 Sum_probs=25.7
Q ss_pred HHHHHHHHHhcCCHHHHHHHhCCCchHHHHHH
Q psy3760 6 FRFVREAVRQNFNLTEAAKALYTSQPGVSKAI 37 (306)
Q Consensus 6 l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i 37 (306)
.+....+.+.|.|..++|+.+|||+++||+..
T Consensus 21 ~~l~~~l~~~glTq~elA~~lgIs~~tIsr~e 52 (82)
T PHA00542 21 DELVCALIRAGWSQEQIADATDVSQPTICRIY 52 (82)
T ss_pred HHHHHHHHHCCCCHHHHHHHHCcCHHHHHHHH
Confidence 34445556667799999999999999999865
No 312
>COG0181 HemC Porphobilinogen deaminase [Coenzyme metabolism]
Probab=92.62 E-value=4.8 Score=32.80 Aligned_cols=141 Identities=16% Similarity=0.120 Sum_probs=81.8
Q ss_pred CcEEEEeccc-chhhhhHHHHHHHHHhCCCcEEEEEeC--------------------ChhHHHHHHHcCCeeEEEEccc
Q psy3760 93 GNLTIATTHT-QARYALPKIIKEFTIQFPKVKLSLLQG--------------------NPKQITEMIRNDQADIAIVTEI 151 (306)
Q Consensus 93 ~~l~I~~~~~-~~~~~l~~~l~~~~~~~p~~~i~~~~~--------------------~~~~~~~~l~~~~~Di~i~~~~ 151 (306)
..|+||+-.| ++..-...+...+++.||++.++++.. ...++.+.|.+|++|+|+.+..
T Consensus 2 ~~irIgTR~S~LAl~Qa~~V~~~L~~~~p~~~~ei~~i~T~GD~i~d~pL~~iGgkGlFtkEle~all~g~~DiAVHSlK 81 (307)
T COG0181 2 MKLRIGTRGSKLALAQANEVIERLKAAYPDLEVEIVTIKTKGDRILDKPLSKIGGKGLFTKELEQALLEGEIDIAVHSLK 81 (307)
T ss_pred CceEEecCCCHHHHHHHHHHHHHHHHhCCCceEEEEEEecccchhccchHHHcCCcEEEHHHHHHHHHcCCCCEEEeecc
Confidence 3688998665 444455566678888899888887432 2456788899999999998743
Q ss_pred cCCCCCceeeccccceEEEEecCCCCCCC---CCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCceeEEEEecCHH
Q psy3760 152 LSPSDKLISIPCYQWEYVIIVPLDHPLLL---LNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSD 228 (306)
Q Consensus 152 ~~~~~~~~~~~l~~~~~~~v~~~~~~l~~---~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 228 (306)
.-+ ..+ =..-.++.+..+.+|... ....++++|..-..|..+ +.|. ...++.......+..--.|++
T Consensus 82 DvP-~~~----p~gL~laai~~R~dprDalVs~~~~~l~~LP~Ga~VGTS---SlRR--~aql~~~rPdl~i~~lRGNVd 151 (307)
T COG0181 82 DVP-TEL----PEGLVLAAIPEREDPRDALVSRDGYDLEELPEGAVVGTS---SLRR--QAQLKALRPDLKIEPLRGNVD 151 (307)
T ss_pred cCC-ccC----CCCceEEEecCCCChhheEEECCCCchhhCCCCCccccc---hHHH--HHHHHHhCCCCeEEeccCcHH
Confidence 222 110 011233444444444221 122245666554455432 3333 223333443445555668888
Q ss_pred HHHHHHHhccceeee
Q psy3760 229 IIKTYVELRMGIGII 243 (306)
Q Consensus 229 ~~~~~v~~g~gi~~~ 243 (306)
+=++-+..|..=+++
T Consensus 152 TRL~KL~~g~yDAII 166 (307)
T COG0181 152 TRLRKLDEGEYDAII 166 (307)
T ss_pred HHHHHhhcCCccHHH
Confidence 888888888555543
No 313
>PF00356 LacI: Bacterial regulatory proteins, lacI family; InterPro: IPR000843 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. One such family groups together a range of proteins, including ascG, ccpA, cytR, ebgR, fruR, galR, galS, lacI, malI, opnR, purF, rafR, rbtR and scrR [, ]. Within this family, the HTH motif is situated towards the N terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3KJX_C 1ZAY_A 1VPW_A 2PUA_A 1QQA_A 1PNR_A 1JFT_A 1QP4_A 2PUD_A 1JH9_A ....
Probab=92.61 E-value=0.15 Score=28.55 Aligned_cols=21 Identities=19% Similarity=0.265 Sum_probs=18.5
Q ss_pred CHHHHHHHhCCCchHHHHHHH
Q psy3760 18 NLTEAAKALYTSQPGVSKAII 38 (306)
Q Consensus 18 s~~~aA~~l~isq~~~s~~i~ 38 (306)
++..-|+.+|+|.+|+|+.|.
T Consensus 1 Ti~dIA~~agvS~~TVSr~ln 21 (46)
T PF00356_consen 1 TIKDIAREAGVSKSTVSRVLN 21 (46)
T ss_dssp CHHHHHHHHTSSHHHHHHHHT
T ss_pred CHHHHHHHHCcCHHHHHHHHh
Confidence 467889999999999999874
No 314
>PRK10752 sulfate transporter subunit; Provisional
Probab=92.60 E-value=3.6 Score=34.45 Aligned_cols=101 Identities=16% Similarity=0.162 Sum_probs=63.2
Q ss_pred cEEEEecccchhhhhHHHHHHHHHhCC---CcEEEEEe--CChhHHHHHHHcC-CeeEEEEccccC----CCCCce----
Q psy3760 94 NLTIATTHTQARYALPKIIKEFTIQFP---KVKLSLLQ--GNPKQITEMIRND-QADIAIVTEILS----PSDKLI---- 159 (306)
Q Consensus 94 ~l~I~~~~~~~~~~l~~~l~~~~~~~p---~~~i~~~~--~~~~~~~~~l~~~-~~Di~i~~~~~~----~~~~~~---- 159 (306)
.+.++++.+ ......+...|.+.|+ ++.+++.. .++.++..++.+| .+|+.+...... ...++.
T Consensus 24 ~~~v~~~~~--~~~~~~~~~~f~~~~~~~tG~~V~v~~s~ggSg~l~~qI~~g~~aDV~~~a~~~~~~~l~~~gli~~~~ 101 (329)
T PRK10752 24 LLNVSYDPT--RELYEQYNKAFSAHWKQQTGDNVVIRQSHGGSGKQATSVINGIEADVVTLALAYDVDAIAERGRIDKNW 101 (329)
T ss_pred EEecccCch--HHHHHHHHHHHHHHHHhccCCceEEEeCCCChHHHHHHHHcCCCCCEEEeCCHHHHHHHHHCCCCCCcc
Confidence 455565554 4455667777776553 77777755 8999999999976 799998853111 111221
Q ss_pred eeccccc------eEEEEecCCCCCCCCCCcChhhhcC--CCeEeecC
Q psy3760 160 SIPCYQW------EYVIIVPLDHPLLLLNSISLKEISN--YPLITYDL 199 (306)
Q Consensus 160 ~~~l~~~------~~~~v~~~~~~l~~~~~i~~~dl~~--~~~i~~~~ 199 (306)
...+... .+++++++++|. .+-+++||.+ ..+++.++
T Consensus 102 ~~~l~~n~~~~~~~lviiv~~gnp~---~i~~w~DL~~~~~~I~i~dP 146 (329)
T PRK10752 102 IKRLPDNSAPYTSTIVFLVRKGNPK---QIHDWNDLIKPGVSVITPNP 146 (329)
T ss_pred hhhhhccccccceeEEEEEECCCCC---CCCCHHHhcCCCcEEEECCC
Confidence 1223333 788999999883 3348999854 34444444
No 315
>PF05043 Mga: Mga helix-turn-helix domain; InterPro: IPR007737 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 []. The family also contains VirR like proteins which match only at the C terminus of the alignment.; PDB: 3SQN_A.
Probab=92.57 E-value=0.17 Score=32.87 Aligned_cols=44 Identities=20% Similarity=0.298 Sum_probs=32.1
Q ss_pred HHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHc---CceeEEecCCCccccC
Q psy3760 12 AVRQNFNLTEAAKALYTSQPGVSKAIIELEEEL---SIDIFIRHGKRIRGLT 60 (306)
Q Consensus 12 v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~l---g~~Lf~R~~~~~~~lT 60 (306)
--+.- |+..-|+.+++|.||+.+.|+++++.| |.+| .++|+ .++
T Consensus 27 ~~~~~-s~~~la~~~~iS~sti~~~i~~l~~~l~~~~l~i---~~~~~-~l~ 73 (87)
T PF05043_consen 27 NNEYV-SIEDLAEELFISRSTIYRDIKKLNKYLKKYGLKI---SKKGY-RLE 73 (87)
T ss_dssp H-SEE-EHHHHHHHHT--HHHHHHHHHHHHHHHHCCT-EE----SSEE-EEE
T ss_pred cCCCc-CHHHHHHHHCCCHHHHHHHHHHHHHHHHHcCeEE---eCCCe-EEE
Confidence 34455 999999999999999999999999877 8888 44555 455
No 316
>PRK09802 DNA-binding transcriptional regulator AgaR; Provisional
Probab=92.57 E-value=1.9 Score=34.96 Aligned_cols=36 Identities=14% Similarity=0.127 Sum_probs=30.4
Q ss_pred CHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCCc
Q psy3760 18 NLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRI 56 (306)
Q Consensus 18 s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~ 56 (306)
+...-|+.+++|..|+-|-|..||++ | +..|..+|.
T Consensus 33 tv~eLa~~l~VS~~TIRRDL~~Le~~-G--~l~r~~GGa 68 (269)
T PRK09802 33 QVNDLSALYGVSTVTIRNDLAFLEKQ-G--IAVRAYGGA 68 (269)
T ss_pred eHHHHHHHHCCCHHHHHHHHHHHHhC-C--CeEEEeCCE
Confidence 78889999999999999999999886 4 445776666
No 317
>PRK15320 transcriptional activator SprB; Provisional
Probab=92.34 E-value=0.42 Score=35.89 Aligned_cols=45 Identities=16% Similarity=0.061 Sum_probs=40.4
Q ss_pred chhhHHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCce
Q psy3760 2 NLHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSID 47 (306)
Q Consensus 2 ~~~~l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~ 47 (306)
+-+.++++..+++-. |-.+-|++|++|.+|||+..++|-+.||.+
T Consensus 166 SdREIEVL~LLAkG~-SNKEIAekL~LS~KTVSTYKnRLLeKLgAk 210 (251)
T PRK15320 166 TQAKYALLILLSSGH-PAIELAKKFGLGTKTVSIYRKKVMYRLGMD 210 (251)
T ss_pred CHHHHHHHHHHHcCC-CHHHHHHHhccchhhHHHHHHHHHHHcCCC
Confidence 346788899999887 999999999999999999999999999864
No 318
>PF08222 HTH_CodY: CodY helix-turn-helix domain; InterPro: IPR013198 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 [].; PDB: 2B0L_C.
Probab=92.26 E-value=0.21 Score=28.89 Aligned_cols=25 Identities=16% Similarity=0.202 Sum_probs=20.8
Q ss_pred HHHHHHHhCCCchHHHHHHHHHHHH
Q psy3760 19 LTEAAKALYTSQPGVSKAIIELEEE 43 (306)
Q Consensus 19 ~~~aA~~l~isq~~~s~~i~~LE~~ 43 (306)
-++-|.+.|+|.|.+-.++++||.-
T Consensus 7 as~iAd~~GiTRSvIVNALRKleSa 31 (61)
T PF08222_consen 7 ASKIADRVGITRSVIVNALRKLESA 31 (61)
T ss_dssp HHHHHHHHT--HHHHHHHHHHHHHT
T ss_pred HHHHHHHhCccHHHHHHHHHHHHhc
Confidence 4788999999999999999999973
No 319
>TIGR00498 lexA SOS regulatory protein LexA. LexA acts as a homodimer to repress a number of genes involved in the response to DNA damage (SOS response), including itself and RecA. RecA, in the presence of single-stranded DNA, acts as a co-protease to activate a latent autolytic protease activity (EC 3.4.21.88) of LexA, where the active site Ser is part of LexA. The autolytic cleavage site is an Ala-Gly bond in LexA (at position 84-85 in E. coli LexA; this sequence is replaced by Gly-Gly in Synechocystis). The cleavage leads to derepression of the SOS regulon and eventually to DNA repair. LexA in Bacillus subtilis is called DinR. LexA is much less broadly distributed than RecA.
Probab=92.25 E-value=0.37 Score=37.04 Aligned_cols=41 Identities=15% Similarity=0.144 Sum_probs=34.8
Q ss_pred chhhHHHHHHHHHh-------cCCHHHHHHHhCCC-chHHHHHHHHHHHH
Q psy3760 2 NLHQFRFVREAVRQ-------NFNLTEAAKALYTS-QPGVSKAIIELEEE 43 (306)
Q Consensus 2 ~~~~l~~f~~v~~~-------~~s~~~aA~~l~is-q~~~s~~i~~LE~~ 43 (306)
+-.|.+++..+.+. - |.+.-|+.++++ .+|++++|++||+.
T Consensus 5 t~~q~~iL~~l~~~~~~~~~~~-~~~ela~~~~~~s~~tv~~~l~~L~~~ 53 (199)
T TIGR00498 5 TARQQEVLDLIRAHIESTGYPP-SIREIARAVGLRSPSAAEEHLKALERK 53 (199)
T ss_pred CHHHHHHHHHHHHHHHhcCCCC-cHHHHHHHhCCCChHHHHHHHHHHHHC
Confidence 55677777777754 5 788999999998 99999999999986
No 320
>COG1497 Predicted transcriptional regulator [Transcription]
Probab=92.16 E-value=1.4 Score=34.26 Aligned_cols=60 Identities=27% Similarity=0.242 Sum_probs=44.4
Q ss_pred hHHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCCccccCHhHHHHH
Q psy3760 5 QFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKPGQAIL 67 (306)
Q Consensus 5 ~l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~~~lT~~G~~l~ 67 (306)
|+-.++.+.+=..+-..-|++|++|..++|.+|++|-++ -|.+..|++-.+.|..|..++
T Consensus 14 qIL~ei~~~qp~v~q~eIA~~lgiT~QaVsehiK~Lv~e---G~i~~~gR~~Y~iTkkG~e~l 73 (260)
T COG1497 14 QILSEIAVRQPRVKQKEIAKKLGITLQAVSEHIKELVKE---GLIEKEGRGEYEITKKGAEWL 73 (260)
T ss_pred HHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHHHhc---cceeecCCeeEEEehhHHHHH
Confidence 444555555333367889999999999999999999875 466666664448999997754
No 321
>TIGR02431 pcaR_pcaU beta-ketoadipate pathway transcriptional regulators, PcaR/PcaU/PobR family. Member of this family are IclR-type transcriptional regulators with similar DNA binding sites, able to bind at least three different metabolites related to protocatechuate metabolism. Beta-ketoadipate is the inducer for PcaR, p-hydroxybenzoate for PobR, and protocatechuate for PcaU.
Probab=92.14 E-value=0.72 Score=36.85 Aligned_cols=54 Identities=19% Similarity=0.215 Sum_probs=38.3
Q ss_pred HHHHHHHHH--hcCCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCCccccCHhH
Q psy3760 6 FRFVREAVR--QNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKPG 63 (306)
Q Consensus 6 l~~f~~v~~--~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~~~lT~~G 63 (306)
|.++-.+.+ .+.|++.-|+.++++.||+.|-++.|++ .|. ..|++++. +|++.-
T Consensus 12 l~IL~~l~~~~~~~~l~eia~~lglpksT~~RlL~tL~~-~G~--l~~~~~~Y-~lG~~~ 67 (248)
T TIGR02431 12 LAVIEAFGAERPRLTLTDVAEATGLTRAAARRFLLTLVE-LGY--VTSDGRLF-WLTPRV 67 (248)
T ss_pred HHHHHHHhcCCCCCCHHHHHHHHCcCHHHHHHHHHHHHH-CCC--EEeCCCEE-EecHHH
Confidence 344444443 2348999999999999999999999975 453 45666666 676653
No 322
>PRK10727 DNA-binding transcriptional regulator GalR; Provisional
Probab=92.05 E-value=1.6 Score=36.66 Aligned_cols=109 Identities=14% Similarity=0.106 Sum_probs=57.2
Q ss_pred CHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCCccccCHhHHHHHHHHHHHHHHHHHHHH----HHHhhccCCCC
Q psy3760 18 NLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKPGQAILRSIEIIMQEIEGLKK----IGKEFSAYDTG 93 (306)
Q Consensus 18 s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~~~lT~~G~~l~~~a~~il~~~~~~~~----~~~~~~~~~~~ 93 (306)
++...|+..|+|.+||||.|. +++. .+++ .-+++++..+++-. ..+.++.+..+
T Consensus 3 ti~dIA~~aGVS~~TVSrvLn--------------~~~~--Vs~~------tr~rV~~~a~elgY~pn~~ar~l~~~~~~ 60 (343)
T PRK10727 3 TIKDVARLAGVSVATVSRVIN--------------NSPK--ASEA------SRLAVHSAMESLSYHPNANARALAQQSTE 60 (343)
T ss_pred CHHHHHHHhCCCHHHHHHHhC--------------CCCC--CCHH------HHHHHHHHHHHHCCCCCHHHHhhhhCCCC
Confidence 678899999999999999984 2232 2222 22233333333321 11222232333
Q ss_pred cEEEEecccchhhhhHHHHHHHHHhCC--CcEEEEEeCC--h---hHHHHHHHcCCeeEEEEc
Q psy3760 94 NLTIATTHTQARYALPKIIKEFTIQFP--KVKLSLLQGN--P---KQITEMIRNDQADIAIVT 149 (306)
Q Consensus 94 ~l~I~~~~~~~~~~l~~~l~~~~~~~p--~~~i~~~~~~--~---~~~~~~l~~~~~Di~i~~ 149 (306)
.|-+-++ .+...++..++..+.+..- +..+.+.... . .+.++.+.+.++|-+|+.
T Consensus 61 ~Igvi~~-~~~~~f~~~~~~gi~~~~~~~g~~~~~~~~~~~~~~~~~~i~~l~~~~vdgiIi~ 122 (343)
T PRK10727 61 TVGLVVG-DVSDPFFGAMVKAVEQVAYHTGNFLLIGNGYHNEQKERQAIEQLIRHRCAALVVH 122 (343)
T ss_pred eEEEEeC-CCCcchHHHHHHHHHHHHHHcCCEEEEEeCCCCHHHHHHHHHHHHhcCCCEEEEe
Confidence 3333333 3344566666655544322 3444443322 1 135667778889988875
No 323
>PRK00082 hrcA heat-inducible transcription repressor; Provisional
Probab=91.92 E-value=0.31 Score=40.80 Aligned_cols=50 Identities=16% Similarity=0.058 Sum_probs=39.1
Q ss_pred CHHHHHHH--hCCCchHHHHHHHHHHHHcCceeEEecCCCccccCHhHHHHHHH
Q psy3760 18 NLTEAAKA--LYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKPGQAILRS 69 (306)
Q Consensus 18 s~~~aA~~--l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~~~lT~~G~~l~~~ 69 (306)
+-..-|+. +++|.+|+-+-++.||+. |.--=..++.|.| ||+.|-++|-.
T Consensus 27 ~s~~l~~~~~l~~S~aTIR~dm~~Le~~-G~l~~~h~sagrI-PT~kGYR~YVd 78 (339)
T PRK00082 27 GSKTLSKRYGLGVSSATIRNDMADLEEL-GLLEKPHTSSGRI-PTDKGYRYFVD 78 (339)
T ss_pred CHHHHHHHhCCCCChHHHHHHHHHHHhC-CCcCCCcCCCCCC-cCHHHHHHHHH
Confidence 55667766 999999999999999887 6533334456665 99999999876
No 324
>PF14424 Toxin-deaminase: The BURPS668_1122 family of deaminases
Probab=91.82 E-value=1.1 Score=31.79 Aligned_cols=36 Identities=19% Similarity=0.463 Sum_probs=31.6
Q ss_pred CcEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeC
Q psy3760 93 GNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQG 129 (306)
Q Consensus 93 ~~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~ 129 (306)
|+|.+.+.-..+..... ++.+|...||++.+.+...
T Consensus 97 G~i~l~te~~pC~SC~~-vi~qF~~~~pni~~~v~~~ 132 (133)
T PF14424_consen 97 GTIDLFTELPPCESCSN-VIEQFKKDFPNIKVNVVYN 132 (133)
T ss_pred ceEEEEecCCcChhHHH-HHHHHHHHCCCcEEEEecC
Confidence 89999998887777666 9999999999999998754
No 325
>PRK10840 transcriptional regulator RcsB; Provisional
Probab=91.63 E-value=0.48 Score=36.83 Aligned_cols=45 Identities=20% Similarity=0.107 Sum_probs=40.5
Q ss_pred chhhHHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCce
Q psy3760 2 NLHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSID 47 (306)
Q Consensus 2 ~~~~l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~ 47 (306)
+-+..+++..+++-. |-.+-|++|++|..||..+++++=..||++
T Consensus 152 t~rE~evl~~~~~G~-s~~eIA~~l~iS~~TV~~h~~~i~~Kl~v~ 196 (216)
T PRK10840 152 SPKESEVLRLFAEGF-LVTEIAKKLNRSIKTISSQKKSAMMKLGVE 196 (216)
T ss_pred CHHHHHHHHHHHCCC-CHHHHHHHHCCCHHHHHHHHHHHHHHcCCC
Confidence 456778888888876 999999999999999999999999999975
No 326
>TIGR03879 near_KaiC_dom probable regulatory domain. This model describes a common domain shared by two different families of proteins, each of which occurs regularly next to its corresponding partner family, a probable regulatory with homology to KaiC. By implication, this protein family likely is also involved in sensory transduction and/or regulation.
Probab=91.57 E-value=0.29 Score=30.39 Aligned_cols=28 Identities=14% Similarity=0.088 Sum_probs=24.6
Q ss_pred hcCCHHHHHHHhCCCchHHHHHHHHHHH
Q psy3760 15 QNFNLTEAAKALYTSQPGVSKAIIELEE 42 (306)
Q Consensus 15 ~~~s~~~aA~~l~isq~~~s~~i~~LE~ 42 (306)
.|.|+...|+.||+|.+|+..+++.++.
T Consensus 31 eGlS~kEIAe~LGIS~~TVk~~l~~~~~ 58 (73)
T TIGR03879 31 AGKTASEIAEELGRTEQTVRNHLKGETK 58 (73)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHhcCcc
Confidence 4459999999999999999999987654
No 327
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=91.55 E-value=0.57 Score=28.80 Aligned_cols=36 Identities=17% Similarity=0.157 Sum_probs=28.7
Q ss_pred HHHHHHHhc---CCHHHHHHHhCCCchHHHHHHHHHHHH
Q psy3760 8 FVREAVRQN---FNLTEAAKALYTSQPGVSKAIIELEEE 43 (306)
Q Consensus 8 ~f~~v~~~~---~s~~~aA~~l~isq~~~s~~i~~LE~~ 43 (306)
++..+.+.| .+...-|+.||++.+++.|+|..||++
T Consensus 11 IL~~L~~~g~~~~ta~eLa~~lgl~~~~v~r~L~~L~~~ 49 (68)
T smart00550 11 ILEFLENSGDETSTALQLAKNLGLPKKEVNRVLYSLEKK 49 (68)
T ss_pred HHHHHHHCCCCCcCHHHHHHHHCCCHHHHHHHHHHHHHC
Confidence 344444543 267889999999999999999999987
No 328
>COG4197 Uncharacterized protein conserved in bacteria, prophage-related [Function unknown]
Probab=91.50 E-value=0.38 Score=30.99 Aligned_cols=33 Identities=18% Similarity=0.136 Sum_probs=30.1
Q ss_pred HHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHH
Q psy3760 6 FRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIE 39 (306)
Q Consensus 6 l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~ 39 (306)
+..|++..-.| .=.++|..|++|+|.+++.++-
T Consensus 3 ls~~va~~vvg-~q~a~a~LLgvsp~~vnQw~~g 35 (96)
T COG4197 3 LSIFVACAVVG-GQKALARLLGVSPPSVNQWIKG 35 (96)
T ss_pred hhHHHHHHHHc-cHHHHHHHHccCchHHHHHhhh
Confidence 67899999999 9999999999999999998864
No 329
>TIGR02531 yecD_yerC TrpR-related protein YerC/YecD. This model represents a protein subfamily found mostly in the Firmicutes (Bacillus and allies). This family is similar in sequence to the trp operon repressor TrpR described by TIGR01321, and represents a distinct clade within the broader family described by pfam01371. At least one species, Xylella fastidiosa, in the Proteobacteria, has a member of both this family and TIGR01321. Several genomes with a member of this family do not synthesize tryptophan, and members of this family should not be considered trp operon repressors without new evidence.
Probab=91.37 E-value=0.41 Score=31.10 Aligned_cols=32 Identities=6% Similarity=0.071 Sum_probs=25.4
Q ss_pred HHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHH
Q psy3760 6 FRFVREAVRQNFNLTEAAKALYTSQPGVSKAII 38 (306)
Q Consensus 6 l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~ 38 (306)
.+++..+.+-. |.++.|+.+|+|.+||++..+
T Consensus 41 ~~I~~ll~~G~-S~~eIA~~LgISrsTIyRi~R 72 (88)
T TIGR02531 41 LQVAKMLKQGK-TYSDIEAETGASTATISRVKR 72 (88)
T ss_pred HHHHHHHHCCC-CHHHHHHHHCcCHHHHHHHHH
Confidence 45555566655 999999999999999999443
No 330
>PRK10703 DNA-binding transcriptional repressor PurR; Provisional
Probab=91.33 E-value=1.8 Score=36.27 Aligned_cols=112 Identities=14% Similarity=0.154 Sum_probs=58.1
Q ss_pred CHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCCccccCHhHHHHHHHHHHHHHHHHHHHH-HHHhhccCCCCcEE
Q psy3760 18 NLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKPGQAILRSIEIIMQEIEGLKK-IGKEFSAYDTGNLT 96 (306)
Q Consensus 18 s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~~~lT~~G~~l~~~a~~il~~~~~~~~-~~~~~~~~~~~~l~ 96 (306)
++..-|+..|+|.+||||.|.. +.+ ..++-+ +.+.++.+++.-.-+ ..+.+..+.+..|-
T Consensus 3 Ti~dIA~~agVS~~TVSrvLn~-------------~~~---vs~~tr---~~V~~~a~elgY~pn~~a~~l~~~~~~~i~ 63 (341)
T PRK10703 3 TIKDVAKRAGVSTTTVSHVINK-------------TRF---VAEETR---NAVWAAIKELHYSPSAVARSLKVNHTKSIG 63 (341)
T ss_pred CHHHHHHHhCCCHHHHHHHHcC-------------CCC---CCHHHH---HHHHHHHHHHCCCcCHHHHHHhhCCCCeEE
Confidence 6788899999999999999853 122 233322 222222222221111 11222333334444
Q ss_pred EEecccchhhhhHHHHHHHHHhCC--CcEEEEEeCC--h---hHHHHHHHcCCeeEEEEc
Q psy3760 97 IATTHTQARYALPKIIKEFTIQFP--KVKLSLLQGN--P---KQITEMIRNDQADIAIVT 149 (306)
Q Consensus 97 I~~~~~~~~~~l~~~l~~~~~~~p--~~~i~~~~~~--~---~~~~~~l~~~~~Di~i~~ 149 (306)
+-++. ....++..++..+.+... +.++.+.... . .+.++.+.++.+|-.|+.
T Consensus 64 vi~~~-~~~~~~~~~~~gi~~~~~~~g~~~~~~~~~~~~~~~~~~i~~l~~~~vdgiii~ 122 (341)
T PRK10703 64 LLATS-SEAPYFAEIIEAVEKNCYQKGYTLILCNAWNNLEKQRAYLSMLAQKRVDGLLVM 122 (341)
T ss_pred EEeCC-CCCchHHHHHHHHHHHHHHCCCEEEEEeCCCCHHHHHHHHHHHHHcCCCEEEEe
Confidence 44433 234455555555544322 4555554322 2 245667888889988774
No 331
>PRK10401 DNA-binding transcriptional regulator GalS; Provisional
Probab=91.30 E-value=2.1 Score=35.99 Aligned_cols=109 Identities=10% Similarity=0.166 Sum_probs=57.5
Q ss_pred CHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCCccccCHhHHHHHHHHHHHHHHHHHHH----HHHHhhccCCCC
Q psy3760 18 NLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKPGQAILRSIEIIMQEIEGLK----KIGKEFSAYDTG 93 (306)
Q Consensus 18 s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~~~lT~~G~~l~~~a~~il~~~~~~~----~~~~~~~~~~~~ 93 (306)
++..-|+..|+|++||||.|.. +.++ . + +.-+++++..+++- ...+.+..+...
T Consensus 3 ti~dIA~~aGVS~~TVSrvLn~-------------~~~V-s--~------~tr~kV~~~a~elgY~pn~~a~~l~~~~~~ 60 (346)
T PRK10401 3 TIRDVARQAGVSVATVSRVLNN-------------SALV-S--A------DTREAVMKAVSELGYRPNANAQALATQVSD 60 (346)
T ss_pred CHHHHHHHhCCCHHHHHHHHCC-------------CCCC-C--H------HHHHHHHHHHHHHCCCCCHHHHHhhcCCCC
Confidence 6788999999999999999852 1233 1 1 11222333333221 112233333344
Q ss_pred cEEEEecccchhhhhHHHHHHHHHhCC--CcEEEEEeCC--h---hHHHHHHHcCCeeEEEEc
Q psy3760 94 NLTIATTHTQARYALPKIIKEFTIQFP--KVKLSLLQGN--P---KQITEMIRNDQADIAIVT 149 (306)
Q Consensus 94 ~l~I~~~~~~~~~~l~~~l~~~~~~~p--~~~i~~~~~~--~---~~~~~~l~~~~~Di~i~~ 149 (306)
.|-+-++. +...++..++..+.+... +..+.+.... . .+.++.+.++.+|-+|..
T Consensus 61 ~Igvi~~~-~~~~f~~~l~~gi~~~~~~~gy~~~~~~~~~~~~~~~~~i~~l~~~~vdGiIi~ 122 (346)
T PRK10401 61 TIGVVVMD-VSDAFFGALVKAVDLVAQQHQKYVLIGNSYHEAEKERHAIEVLIRQRCNALIVH 122 (346)
T ss_pred EEEEEeCC-CCCccHHHHHHHHHHHHHHCCCEEEEEcCCCChHHHHHHHHHHHhcCCCEEEEe
Confidence 55554443 344455555544433322 4455443322 1 135667778889988875
No 332
>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=91.19 E-value=0.53 Score=37.15 Aligned_cols=44 Identities=11% Similarity=0.068 Sum_probs=39.4
Q ss_pred chhhHHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCc
Q psy3760 2 NLHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSI 46 (306)
Q Consensus 2 ~~~~l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~ 46 (306)
+-+..+++..+++-+ |....|+.|++|..|+..++++..+.||+
T Consensus 173 t~re~evl~~~a~G~-t~~eIa~~l~is~~Tv~~~l~~~~~kl~~ 216 (232)
T TIGR03541 173 SEREREVLAWTALGR-RQADIAAILGISERTVENHLRSARRKLGV 216 (232)
T ss_pred CHHHHHHHHHHHCCC-CHHHHHHHHCcCHHHHHHHHHHHHHHHCC
Confidence 457788888888766 99999999999999999999999999985
No 333
>PF13542 HTH_Tnp_ISL3: Helix-turn-helix domain of transposase family ISL3
Probab=91.19 E-value=0.53 Score=26.98 Aligned_cols=31 Identities=13% Similarity=0.140 Sum_probs=25.8
Q ss_pred HHHHHHHhcCCHHHHHHHhCCCchHHHHHHHH
Q psy3760 8 FVREAVRQNFNLTEAAKALYTSQPGVSKAIIE 39 (306)
Q Consensus 8 ~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~ 39 (306)
++..+.+.. |++..|+.+|+|..+|.+.+++
T Consensus 20 i~~~~~~~~-s~~~vA~~~~vs~~TV~ri~~~ 50 (52)
T PF13542_consen 20 ILKLLRESR-SFKDVARELGVSWSTVRRIFDR 50 (52)
T ss_pred HHHHHhhcC-CHHHHHHHHCCCHHHHHHHHHh
Confidence 445566667 9999999999999999998765
No 334
>PF03444 HrcA_DNA-bdg: Winged helix-turn-helix transcription repressor, HrcA DNA-binding; InterPro: IPR005104 Prokaryotic cells have a defence mechanism against a sudden heat-shock stress. Commonly, they induce a set of proteins that protect cellular proteins from being denatured by heat. Among such proteins are the GroE and DnaK chaperones whose transcription is regulated by a heat-shock repressor protein HrcA. HrcA is a winged helix-turn-helix repressor that negatively regulates the transcription of dnaK and groE operons by binding the upstream CIRCE (controlling inverted repeat of chaperone expression) element. In Bacillus subtilis this element is a perfect 9 base pair inverted repeat separated by a 9 base pair spacer. The crystal structure of a heat-inducible transcriptional repressor, HrcA, from Thermotoga maritima has been reported at 2.2A resolution. HrcA is composed of three domains: an N-terminal winged helix-turn-helix domain (WHTH), a GAF-like domain, and an inserted dimerizing domain (IDD). The IDD shows a unique structural fold with an anti-parallel beta-sheet composed of three beta-strands sided by four alpha-helices. HrcA crystallises as a dimer, which is formed through hydrophobic contact between the IDDs and a limited contact that involves conserved residues between the GAF-like domains []. The structural studies suggest that the inactive form of HrcA is the dimer and this is converted to its DNA-binding form by interaction with GroEL, which binds to a conserved C-terminal sequence region [, ]. Comparison of the HrcA-CIRCE complexes from B. subtilis and Bacillus thermoglucosidasius (Geobacillus thermoglucosidasius), which grow at vastly different ranges of temperature shows that the thermostability profiles were consistent with the difference in the growth temperatures suggesting that HrcA can function as a thermosensor to detect temperature changes in cells []. Any increase in temperature causes the dissociation of the HrcA from the CIRCE complex with the concomitant activation of transcription of the groE and dnaK operons. This domain represents the winged helix-turn-helix DNA-binding domain which is located close to the N terminus of HrcA. This domain is also found at the N terminus of a set of uncharacterised proteins that have two C-terminal CBS domains. ; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent
Probab=91.15 E-value=1.9 Score=27.15 Aligned_cols=61 Identities=18% Similarity=0.130 Sum_probs=43.7
Q ss_pred chhhHHHHHHHHHh--------cCCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEe---cCCCccccCHhHHHHHH
Q psy3760 2 NLHQFRFVREAVRQ--------NFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIR---HGKRIRGLTKPGQAILR 68 (306)
Q Consensus 2 ~~~~l~~f~~v~~~--------~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R---~~~~~~~lT~~G~~l~~ 68 (306)
+-++-++|.++++. | |= .-|+.+++|..||-..++.||+ +| |++. ...|. .||..|-+++.
T Consensus 3 t~rq~~IL~alV~~Y~~~~~PVg-Sk-~ia~~l~~s~aTIRN~M~~Le~-lG--lve~~p~~s~Gr-iPT~~aYr~~~ 74 (78)
T PF03444_consen 3 TERQREILKALVELYIETGEPVG-SK-TIAEELGRSPATIRNEMADLEE-LG--LVESQPHPSGGR-IPTDKAYRALN 74 (78)
T ss_pred CHHHHHHHHHHHHHHHhcCCCcC-HH-HHHHHHCCChHHHHHHHHHHHH-CC--CccCCCCCCCCC-CcCHHHHHHHc
Confidence 34566666666653 3 33 3456799999999999999986 55 6653 24666 49999998774
No 335
>PRK10188 DNA-binding transcriptional activator SdiA; Provisional
Probab=91.11 E-value=0.58 Score=37.16 Aligned_cols=45 Identities=11% Similarity=0.084 Sum_probs=41.0
Q ss_pred chhhHHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCce
Q psy3760 2 NLHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSID 47 (306)
Q Consensus 2 ~~~~l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~ 47 (306)
+-+..+++..+++-+ |-...|+.|++|..||..+|+++-+.||+.
T Consensus 181 T~rE~evl~~~a~G~-t~~eIa~~l~is~~TV~~h~~~~~~KL~~~ 225 (240)
T PRK10188 181 SKREKEILKWTAEGK-TSAEIAMILSISENTVNFHQKNMQKKFNAP 225 (240)
T ss_pred CHHHHHHHHHHHcCC-CHHHHHHHhCCCHHHHHHHHHHHHHHhCCC
Confidence 557788999999877 999999999999999999999999999953
No 336
>PF01978 TrmB: Sugar-specific transcriptional regulator TrmB; InterPro: IPR002831 TrmB, is a protein of 38,800 apparent molecular weight, that is involved in the maltose-specific regulation of the trehalose/maltose ABC transport operon in Thermococcus litoralis. TrmB has been shown to be a maltose-specific repressor, and this inhibition is counteracted by maltose and trehalose. TrmB binds maltose and trehalose half-maximally at 20 uM and 0.5 mM sugar concentration, respectively []. Other members of this family are annotated as either transcriptional regulators or hypothetical proteins. ; PDB: 2D1H_A 3QPH_A 1SFX_A.
Probab=91.10 E-value=0.3 Score=30.02 Aligned_cols=39 Identities=23% Similarity=0.249 Sum_probs=29.8
Q ss_pred hHHHHHHHHHhc-CCHHHHHHHhCCCchHHHHHHHHHHHH
Q psy3760 5 QFRFVREAVRQN-FNLTEAAKALYTSQPGVSKAIIELEEE 43 (306)
Q Consensus 5 ~l~~f~~v~~~~-~s~~~aA~~l~isq~~~s~~i~~LE~~ 43 (306)
..+++..+.+.| .+...-|+.++++++++++.|++|++.
T Consensus 10 E~~vy~~Ll~~~~~t~~eIa~~l~i~~~~v~~~L~~L~~~ 49 (68)
T PF01978_consen 10 EAKVYLALLKNGPATAEEIAEELGISRSTVYRALKSLEEK 49 (68)
T ss_dssp HHHHHHHHHHHCHEEHHHHHHHHTSSHHHHHHHHHHHHHT
T ss_pred HHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence 345555554322 377889999999999999999999974
No 337
>PF04218 CENP-B_N: CENP-B N-terminal DNA-binding domain; InterPro: IPR006695 Centromere Protein B (CENP-B) is a DNA-binding protein localized to the centromere. Within the N-terminal 125 residues, there is a DNA-binding region, which binds to a corresponding 17bp CENP-B box sequence. CENP-B dimers either bind two separate DNA molecules or alternatively, they may bind two CENP-B boxes on one DNA molecule, with the intervening stretch of DNA forming a loop structure. The CENP-B DNA-binding domain consists of two repeating domains, RP1 and RP2. This family corresponds to RP1 has been shown to consist of four helices in a helix-turn-helix structure [].; GO: 0003677 DNA binding, 0000775 chromosome, centromeric region; PDB: 1BW6_A 1HLV_A 2ELH_A.
Probab=91.07 E-value=0.74 Score=26.66 Aligned_cols=36 Identities=11% Similarity=0.232 Sum_probs=24.4
Q ss_pred HHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHH
Q psy3760 6 FRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEE 42 (306)
Q Consensus 6 l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~ 42 (306)
+++... ++.|.|....|+.+|++++||+..++.=++
T Consensus 13 ~~iI~~-~e~g~s~~~ia~~fgv~~sTv~~I~K~k~~ 48 (53)
T PF04218_consen 13 LEIIKR-LEEGESKRDIAREFGVSRSTVSTILKNKDK 48 (53)
T ss_dssp HHHHHH-HHCTT-HHHHHHHHT--CCHHHHHHHCHHH
T ss_pred HHHHHH-HHcCCCHHHHHHHhCCCHHHHHHHHHhHHH
Confidence 344444 445559999999999999999998886444
No 338
>TIGR00070 hisG ATP phosphoribosyltransferase. Members of this family from B. subtilis, Aquifex aeolicus, and Synechocystis PCC6803 (and related taxa) lack the C-terminal third of the sequence. The sole homolog from Archaeoglobus fulgidus lacks the N-terminal 50 residues (as reported) and is otherwise atypical of the rest of the family. This model excludes the C-terminal extension.
Probab=91.02 E-value=2 Score=32.26 Aligned_cols=95 Identities=15% Similarity=0.182 Sum_probs=60.8
Q ss_pred EEEEeCChhHHHHHHHcCCeeEEEEccccCCCCC--c---eeeccccceEEEEecCCCCCCCCCCcChhhhcCCCeEeec
Q psy3760 124 LSLLQGNPKQITEMIRNDQADIAIVTEILSPSDK--L---ISIPCYQWEYVIIVPLDHPLLLLNSISLKEISNYPLITYD 198 (306)
Q Consensus 124 i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~~~~--~---~~~~l~~~~~~~v~~~~~~l~~~~~i~~~dl~~~~~i~~~ 198 (306)
+++...-..++...+.+|.+|++|+..+.....+ + .-..++.-+++++++++.+. -+.+++.+....+-
T Consensus 42 i~~~~~r~~Dip~yV~~G~aDlGI~G~D~l~E~~~~v~~~~dL~fg~crl~vA~p~~~~~-----~~~~~l~~~rIATk- 115 (182)
T TIGR00070 42 IEFLLLRPQDIPTYVEHGAADLGITGYDVLLESGADVYELLDLGFGKCRLVLAVPQESDI-----SSVEDLKGKRIATK- 115 (182)
T ss_pred EEEEEEccchhHHHHhCCCccEEEecchhhhhCCCCEEEEeecCcCceEEEEEEECCCCC-----CChHHhCCCEEEEC-
Confidence 4444445668899999999999997533222222 2 12345678999999998752 25677765554442
Q ss_pred CCCCcHHHHHHHHHhCCCceeEEEEecCHH
Q psy3760 199 LSFSGRIKLDREFSLQKLTPYIVLETINSD 228 (306)
Q Consensus 199 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 228 (306)
+.+...++|.+.|+...++..-.+.+
T Consensus 116 ----yp~i~~~~f~~~Gi~v~ii~l~GsvE 141 (182)
T TIGR00070 116 ----YPNLARRYFEKKGIDVEIIKLNGSVE 141 (182)
T ss_pred ----CHHHHHHHHHHcCCeEEEEECcceee
Confidence 23577889999998765544444443
No 339
>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=90.98 E-value=1.2 Score=27.20 Aligned_cols=53 Identities=13% Similarity=0.020 Sum_probs=34.8
Q ss_pred CCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCCccccCHhHHHHHHHHHHH
Q psy3760 17 FNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKPGQAILRSIEII 73 (306)
Q Consensus 17 ~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~~~lT~~G~~l~~~a~~i 73 (306)
++++.+|+.+|||.+++. ..|++.|..-..|+.+|.-.-|..=-.-+...+.+
T Consensus 1 ~~i~e~A~~~gVs~~tlr----~ye~~~gl~~~~r~~~g~R~yt~~di~~l~~i~~l 53 (68)
T cd04763 1 YTIGEVALLTGIKPHVLR----AWEREFGLLKPQRSDGGHRLFNDADIDRILEIKRW 53 (68)
T ss_pred CCHHHHHHHHCcCHHHHH----HHHHhcCCCCCCcCCCCCcccCHHHHHHHHHHHHH
Confidence 478999999999999876 45777776556676444313565544444444443
No 340
>PRK11569 transcriptional repressor IclR; Provisional
Probab=90.76 E-value=1.9 Score=35.07 Aligned_cols=55 Identities=7% Similarity=0.081 Sum_probs=36.9
Q ss_pred HHHHHHHHHh--cCCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCCccccCHh
Q psy3760 6 FRFVREAVRQ--NFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKP 62 (306)
Q Consensus 6 l~~f~~v~~~--~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~~~lT~~ 62 (306)
|.++-.+.+. +.+++.-|+.+|++.||+.|.++.|++. |.--.+-.+++. +|.+.
T Consensus 31 l~IL~~l~~~~~~~~lseia~~lglpksTv~RlL~tL~~~-G~l~~~~~~~~Y-~lG~~ 87 (274)
T PRK11569 31 LKLLEWIAESNGSVALTELAQQAGLPNSTTHRLLTTMQQQ-GFVRQVGELGHW-AIGAH 87 (274)
T ss_pred HHHHHHHHhCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHC-CCEEEcCCCCeE-ecCHH
Confidence 3444444442 2389999999999999999999999863 444333234555 56443
No 341
>PLN02245 ATP phosphoribosyl transferase
Probab=90.71 E-value=7.1 Score=33.35 Aligned_cols=171 Identities=15% Similarity=0.099 Sum_probs=91.9
Q ss_pred EEEEeCChhHHHHHHHcCCeeEEEEccccCCCC-----Cce----eeccccceEEEEecCCCCCCCCCCcChhhhcCCCe
Q psy3760 124 LSLLQGNPKQITEMIRNDQADIAIVTEILSPSD-----KLI----SIPCYQWEYVIIVPLDHPLLLLNSISLKEISNYPL 194 (306)
Q Consensus 124 i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~~~-----~~~----~~~l~~~~~~~v~~~~~~l~~~~~i~~~dl~~~~~ 194 (306)
+++.-.-..++...+.+|.+|+||+..+..... ... -..++.-++++.+|++.-. ...-+++||.+.+.
T Consensus 113 iev~flR~~DIp~yV~~G~~DlGItG~D~l~E~~~~~~~~v~~l~~LgFG~crlvvAvP~~~~~--~~~~s~~dL~g~~~ 190 (403)
T PLN02245 113 LEVWFQRPKDIVRKLLSGDLDLGIVGYDMLREYGQGNEDLVIVHDALGFGDCHLSIAIPKYGIF--ENINSLKELAQMPQ 190 (403)
T ss_pred eEEEEECHHHHHHHHhCCCccEEEeeeeeeeccCCCccceEEEeecCCCCceEEEEEEEccCCc--cccCCHHHhccccc
Confidence 444445567899999999999999853322221 111 2234678899999976200 11346788876331
Q ss_pred Eee----cCCCCcHHHHHHHHHhCCCc-eeEEEEecCHHHHHHHHHhccceeeeecc-eecccccCCceeeecCCCCccc
Q psy3760 195 ITY----DLSFSGRIKLDREFSLQKLT-PYIVLETINSDIIKTYVELRMGIGIIASI-AFDSNRDKNLRSISASHLFGTT 268 (306)
Q Consensus 195 i~~----~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~v~~g~gi~~~p~~-~~~~~~~~~l~~~~~~~~~~~~ 268 (306)
... .-...+-+...++|.+.|+. ..++....+.+. +..-|.+=+++.-- .-..++..+|+.+.-.. ....
T Consensus 191 ~~~~~~~RIATkYp~ltr~ff~~~Gv~~v~Iv~l~GAvE~---AP~lGlADaIvDIVsTGtTLraNgLk~i~~~~-Il~S 266 (403)
T PLN02245 191 WTEERPLRVVTGFTYLGPKFMKDNGFKHVTFSTADGALEA---APAMGIADAILDLVSSGTTLRENNLKEIEGGV-VLES 266 (403)
T ss_pred ccccCceEEEeCCHHHHHHHHHHcCCCeEEEEECcCceec---ccccCchhhhcchhccHHHHHHCCCEEccCce-EEEE
Confidence 111 00112446778899999985 455444444443 22233221222110 00112345677764212 3345
Q ss_pred eEEEEEeCCcc-----ccHHHHHHHHHHhHHhhHHHH
Q psy3760 269 ISRVIIKQGTY-----LRSYVYSFIKLLSPKLNRKFI 300 (306)
Q Consensus 269 ~~~l~~~~~~~-----~~~~~~~~~~~l~~~~~~~~~ 300 (306)
+..|+.++... ....++.+++.|+..+.++..
T Consensus 267 ~A~LIan~~sl~~~~~~~~~i~~ll~rl~~vl~A~~~ 303 (403)
T PLN02245 267 QAVLVASRRALLERKGALEVVHEILERLEAHLRAEGQ 303 (403)
T ss_pred EEEEEEecchhhcchhHHHHHHHHHHHHHHHHhhhcE
Confidence 77788776632 233677777777776654443
No 342
>COG1464 NlpA ABC-type metal ion transport system, periplasmic component/surface antigen [Inorganic ion transport and metabolism]
Probab=90.67 E-value=7.5 Score=31.10 Aligned_cols=204 Identities=9% Similarity=0.008 Sum_probs=114.6
Q ss_pred CcEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeC-ChhHHHHHHHcCCeeEEEEccccCC-----CCCceeeccccc
Q psy3760 93 GNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQG-NPKQITEMIRNDQADIAIVTEILSP-----SDKLISIPCYQW 166 (306)
Q Consensus 93 ~~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~-~~~~~~~~l~~~~~Di~i~~~~~~~-----~~~~~~~~l~~~ 166 (306)
..|+||+++.--..++-.......+. -++.+.+++. +...--..|.+|++|+=...+.+.- ..+.....++..
T Consensus 29 ~~I~vg~~~~p~a~ile~~~k~~~~k-~Gi~l~i~~FtDY~~PN~AL~~gdiDaN~FQH~pyL~~~~k~~~~~Lv~vg~~ 107 (268)
T COG1464 29 KTIKVGATPGPHAEILEVVVKPALKK-KGLDLKIVEFTDYVQPNEALADGDIDANAFQHKPYLDQFNKEHGGKLVAVGNT 107 (268)
T ss_pred CcEEEeecCCchHHHHHHHHHHHHHh-cCceEEEEEecCCcchhHHHhcCCccchhhhchHHHHHHHHHcCCCEEEEeeE
Confidence 58999999887777777666666554 3788888774 5556778999999999877543211 112222233322
Q ss_pred eEEEEecCCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCc-eeEE------------------EEecCH
Q psy3760 167 EYVIIVPLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLT-PYIV------------------LETINS 227 (306)
Q Consensus 167 ~~~~v~~~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~-~~~~------------------~~~~~~ 227 (306)
++.-+ + +..++--+++||.+---|..+.+.....+-...|++.|+- .+.. +.-=+.
T Consensus 108 ~i~Pm---g--~YSkk~ksl~el~~GatIaiPNDpsN~gRAL~lL~~aGLIkLk~~~~~~aT~~DI~eNPK~lki~EldA 182 (268)
T COG1464 108 HIEPM---G--LYSKKYKSLAELKDGATIAIPNDPTNEGRALLLLQKAGLIKLKDGVNLLATPKDITENPKNLKIKELEA 182 (268)
T ss_pred Eeccc---e--ecchhcCcHhhCCCCCEEECCCCCCchhHHHHHHHHCCcEEEcCCCcccCCHHHHhhCcccCeEEEcch
Confidence 21111 1 1123345788888777777776666666777788888762 1110 110111
Q ss_pred HHHHHHHHhccceeeeecceecccccC--CceeeecCCCCccceEEEEEeCCccccHHHHHHHHHHhHHhhHHHHHhh
Q psy3760 228 DIIKTYVELRMGIGIIASIAFDSNRDK--NLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLLSPKLNRKFINKI 303 (306)
Q Consensus 228 ~~~~~~v~~g~gi~~~p~~~~~~~~~~--~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~ 303 (306)
..+-+.+...++..+-+.+....--++ +....+... ...+--.++.++....++.++.|++.+++---+.++++.
T Consensus 183 aqlpRaLddvD~AvIN~nyA~~AgL~p~kdai~~e~~~-~spY~Niivvr~~d~d~~~ik~lv~a~qs~evk~~i~k~ 259 (268)
T COG1464 183 AQLPRALDDVDAAVINTNYALQAGLNPKKDALFEEDKD-SSPYVNIIVVREEDKDDPAVKKLVEAYQSDEVKAFIEKK 259 (268)
T ss_pred HhccccccccCEEEEcchHHHHcCCCccccceeccccc-CCcceEEEEEcccccCCHHHHHHHHHHcCHHHHHHHHHH
Confidence 122222233333333333333332111 222333212 233455677788888999999999998776555555543
No 343
>PRK11303 DNA-binding transcriptional regulator FruR; Provisional
Probab=90.64 E-value=3.2 Score=34.52 Aligned_cols=111 Identities=19% Similarity=0.207 Sum_probs=58.7
Q ss_pred CHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecC-CCccccCHhHHHHHHHHHHHHHHHHHHHH----HHHhhccCCC
Q psy3760 18 NLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHG-KRIRGLTKPGQAILRSIEIIMQEIEGLKK----IGKEFSAYDT 92 (306)
Q Consensus 18 s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~-~~~~~lT~~G~~l~~~a~~il~~~~~~~~----~~~~~~~~~~ 92 (306)
++...|+..|+|.+||||.|.. +.+ +++ .++ .-+++++..+++-. ..+.+..+..
T Consensus 2 ti~dIA~~aGVS~~TVSrvLn~-----------~~~~~~V---s~~------tr~rV~~~a~elgY~pn~~a~~l~~~~~ 61 (328)
T PRK11303 2 KLDEIARLAGVSRTTASYVING-----------KAKQYRV---SDK------TVEKVMAVVREHNYHPNAVAAGLRAGRT 61 (328)
T ss_pred CHHHHHHHhCCCHHHHHHHHcC-----------CCCCCCc---CHH------HHHHHHHHHHHhCCCCCHHHHHhhcCCC
Confidence 5778899999999999999951 110 122 222 22233333333321 1222333334
Q ss_pred CcEEEEecccchhhhhHHHHHHHHHhC--CCcEEEEEeCC--h---hHHHHHHHcCCeeEEEEc
Q psy3760 93 GNLTIATTHTQARYALPKIIKEFTIQF--PKVKLSLLQGN--P---KQITEMIRNDQADIAIVT 149 (306)
Q Consensus 93 ~~l~I~~~~~~~~~~l~~~l~~~~~~~--p~~~i~~~~~~--~---~~~~~~l~~~~~Di~i~~ 149 (306)
+.|-+-++. +...++..++..+.+.. -+..+.+.... . .+.++.+.++.+|-+|..
T Consensus 62 ~~Igvv~~~-~~~~~~~~l~~gi~~~~~~~g~~~~~~~~~~~~~~~~~~~~~l~~~~vdgiIi~ 124 (328)
T PRK11303 62 RSIGLIIPD-LENTSYARIAKYLERQARQRGYQLLIACSDDQPDNEMRCAEHLLQRQVDALIVS 124 (328)
T ss_pred ceEEEEeCC-CCCchHHHHHHHHHHHHHHcCCEEEEEeCCCCHHHHHHHHHHHHHcCCCEEEEc
Confidence 445544443 33445555555554432 24555554321 2 235667778899988774
No 344
>PRK11475 DNA-binding transcriptional activator BglJ; Provisional
Probab=90.59 E-value=0.73 Score=35.62 Aligned_cols=44 Identities=11% Similarity=0.139 Sum_probs=40.1
Q ss_pred chhhHHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCc
Q psy3760 2 NLHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSI 46 (306)
Q Consensus 2 ~~~~l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~ 46 (306)
+-+..+++..+++-. |-..-|++|++|..|+..+++++=+.||+
T Consensus 136 T~RE~eVL~ll~~G~-snkeIA~~L~iS~~TV~~h~~~I~~KLgv 179 (207)
T PRK11475 136 SPTEREILRFMSRGY-SMPQIAEQLERNIKTIRAHKFNVMSKLGV 179 (207)
T ss_pred CHHHHHHHHHHHCCC-CHHHHHHHHCCCHHHHHHHHHHHHHHcCC
Confidence 456788888999877 99999999999999999999999999996
No 345
>PRK15411 rcsA colanic acid capsular biosynthesis activation protein A; Provisional
Probab=90.57 E-value=0.7 Score=35.75 Aligned_cols=44 Identities=7% Similarity=0.057 Sum_probs=40.3
Q ss_pred chhhHHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCc
Q psy3760 2 NLHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSI 46 (306)
Q Consensus 2 ~~~~l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~ 46 (306)
+-+..+++..+++-. |-.+-|++|++|..|+..+++++=+.||+
T Consensus 139 T~RE~eVL~lla~G~-snkeIA~~L~iS~~TVk~h~~~I~~KL~v 182 (207)
T PRK15411 139 SRTESSMLRMWMAGQ-GTIQISDQMNIKAKTVSSHKGNIKRKIKT 182 (207)
T ss_pred CHHHHHHHHHHHcCC-CHHHHHHHcCCCHHHHHHHHHHHHHHhCC
Confidence 456788999999877 99999999999999999999999999997
No 346
>PRK13719 conjugal transfer transcriptional regulator TraJ; Provisional
Probab=90.49 E-value=0.79 Score=35.26 Aligned_cols=44 Identities=14% Similarity=-0.089 Sum_probs=40.0
Q ss_pred chhhHHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCc
Q psy3760 2 NLHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSI 46 (306)
Q Consensus 2 ~~~~l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~ 46 (306)
+-+..++|..+++-. |-..-|++|++|..|+.++++++=+.||+
T Consensus 145 S~RE~eVL~Lia~G~-SnkEIA~~L~IS~~TVk~hvs~I~~KLgv 188 (217)
T PRK13719 145 TKYQNDVFILYSFGF-SHEYIAQLLNITVGSSKNKISEILKFFGI 188 (217)
T ss_pred CHHHHHHHHHHHCCC-CHHHHHHHhCCCHHHHHHHHHHHHHHhCC
Confidence 456788888899866 99999999999999999999999999997
No 347
>COG3355 Predicted transcriptional regulator [Transcription]
Probab=90.48 E-value=0.84 Score=31.78 Aligned_cols=46 Identities=17% Similarity=0.231 Sum_probs=34.8
Q ss_pred hhHHHHHHHH--HhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEec
Q psy3760 4 HQFRFVREAV--RQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRH 52 (306)
Q Consensus 4 ~~l~~f~~v~--~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~ 52 (306)
.+.++|.++. +.+.+...-|+.||.|.||+.|++++|.+ .=|.+|.
T Consensus 28 ~Dv~v~~~LL~~~~~~tvdelae~lnr~rStv~rsl~~L~~---~GlV~Re 75 (126)
T COG3355 28 LDVEVYKALLEENGPLTVDELAEILNRSRSTVYRSLQNLLE---AGLVERE 75 (126)
T ss_pred HHHHHHHHHHhhcCCcCHHHHHHHHCccHHHHHHHHHHHHH---cCCeeee
Confidence 3456666666 34457889999999999999999999975 3455554
No 348
>TIGR02417 fruct_sucro_rep D-fructose-responsive transcription factor. Members of this family belong the lacI helix-turn-helix family (pfam00356) of DNA-binding transcriptional regulators. All members are from the proteobacteria. Characterized members act as positive and negative transcriptional regulators of fructose and sucrose transport and metabolism. Sucrose is a disaccharide composed of fructose and glucose; D-fructose-1-phosphate rather than an intact sucrose moiety has been shown to act as the inducer.
Probab=90.09 E-value=3 Score=34.65 Aligned_cols=110 Identities=23% Similarity=0.288 Sum_probs=58.2
Q ss_pred CHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCC--CccccCHhHHHHHHHHHHHHHHHHHHH---H-HHHhhccCC
Q psy3760 18 NLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGK--RIRGLTKPGQAILRSIEIIMQEIEGLK---K-IGKEFSAYD 91 (306)
Q Consensus 18 s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~--~~~~lT~~G~~l~~~a~~il~~~~~~~---~-~~~~~~~~~ 91 (306)
++..-|+..|+|.+||||.|. ..++ ++ .+ +.-+++++..+++- + ..+.+..+.
T Consensus 1 ti~dIA~~aGVS~~TVSrvLn------------~~~~~~~v---s~------~tr~rV~~~a~~lgY~pn~~a~~l~~~~ 59 (327)
T TIGR02417 1 TLSDIAKLAGVSKTTASYVIN------------GKAKEYRI---SQ------ETVERVMAVVREQGYQPNIHAASLRAGR 59 (327)
T ss_pred CHHHHHHHhCCCHHHHHHHHc------------CCCCCCcc---CH------HHHHHHHHHHHHhCCCCCHHHHHhhcCC
Confidence 467789999999999999995 1111 23 22 22233333333321 1 112233333
Q ss_pred CCcEEEEecccchhhhhHHHHHHHHHhC--CCcEEEEEeCC--h---hHHHHHHHcCCeeEEEEc
Q psy3760 92 TGNLTIATTHTQARYALPKIIKEFTIQF--PKVKLSLLQGN--P---KQITEMIRNDQADIAIVT 149 (306)
Q Consensus 92 ~~~l~I~~~~~~~~~~l~~~l~~~~~~~--p~~~i~~~~~~--~---~~~~~~l~~~~~Di~i~~ 149 (306)
...|-+-++. +...++..++..+.+.. -++.+.+...+ . ...++.+.+..+|-+|..
T Consensus 60 ~~~Igvi~~~-~~~~~~~~~~~~i~~~~~~~gy~~~i~~~~~~~~~~~~~~~~l~~~~vdgiIi~ 123 (327)
T TIGR02417 60 SRTIGLVIPD-LENYSYARIAKELEQQCREAGYQLLIACSDDNPDQEKVVIENLLARQVDALIVA 123 (327)
T ss_pred CceEEEEeCC-CCCccHHHHHHHHHHHHHHCCCEEEEEeCCCCHHHHHHHHHHHHHcCCCEEEEe
Confidence 3444444432 33445555555554332 35666665432 1 235667788889988875
No 349
>COG1414 IclR Transcriptional regulator [Transcription]
Probab=90.08 E-value=3.6 Score=32.80 Aligned_cols=57 Identities=16% Similarity=0.039 Sum_probs=40.0
Q ss_pred hHHHHHHHHHhcCC--HHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecC--CCccccCHhHHH
Q psy3760 5 QFRFVREAVRQNFN--LTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHG--KRIRGLTKPGQA 65 (306)
Q Consensus 5 ~l~~f~~v~~~~~s--~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~--~~~~~lT~~G~~ 65 (306)
-|.++-.+++...+ ++.-|+++|++.||+.|.+..|++. -+..+++ +.. +|++.--.
T Consensus 6 al~iL~~l~~~~~~l~l~ela~~~glpksT~~RlL~tL~~~---G~v~~d~~~g~Y-~Lg~~~~~ 66 (246)
T COG1414 6 ALAILDLLAEGPGGLSLAELAERLGLPKSTVHRLLQTLVEL---GYVEQDPEDGRY-RLGPRLLE 66 (246)
T ss_pred HHHHHHHHHhCCCCCCHHHHHHHhCcCHHHHHHHHHHHHHC---CCEEEcCCCCcE-eehHHHHH
Confidence 34455555544435 9999999999999999999999873 4566665 345 67664433
No 350
>COG2739 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=89.97 E-value=0.47 Score=31.17 Aligned_cols=40 Identities=20% Similarity=0.249 Sum_probs=30.7
Q ss_pred hHHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHc
Q psy3760 5 QFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEEL 44 (306)
Q Consensus 5 ~l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~l 44 (306)
|-.||-.=...-.|++.-|+..+||.+||.-.|++-|+.|
T Consensus 22 Q~~Y~~lyy~dDlSl~EIAee~~VSRqAIyDnIKr~~~~L 61 (105)
T COG2739 22 QKNYLELYYLDDLSLSEIAEEFNVSRQAIYDNIKRTEKIL 61 (105)
T ss_pred HHHHHHHHHHhhccHHHHHHHhCccHHHHHHHHHHHHHHH
Confidence 3334433333335999999999999999999999998876
No 351
>PF01527 HTH_Tnp_1: Transposase; InterPro: IPR002514 Transposase proteins are necessary for efficient DNA transposition. This family consists of various Escherichia coli insertion elements and other bacterial transposases some of which are members of the IS3 family. This region includes a helix-turn-helix motif (HTH) at the N terminus followed by a leucine zipper (LZ) motif. The LZ motif has been shown to mediate oligomerisation of the transposase components in IS911 []. More information about these proteins can be found at Protein of the Month: Transposase [].; GO: 0003677 DNA binding, 0004803 transposase activity, 0006313 transposition, DNA-mediated; PDB: 2JN6_A 2RN7_A.
Probab=89.92 E-value=0.6 Score=29.29 Aligned_cols=36 Identities=17% Similarity=0.132 Sum_probs=27.8
Q ss_pred HHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHH
Q psy3760 6 FRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELE 41 (306)
Q Consensus 6 l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE 41 (306)
+.+...+.+.|.|+...|+.+||++++|++.+++..
T Consensus 13 ~~~v~~~~~~g~sv~~va~~~gi~~~~l~~W~~~~~ 48 (76)
T PF01527_consen 13 LQAVREYLESGESVSEVAREYGISPSTLYNWRKQYR 48 (76)
T ss_dssp HHHHHHHHHHHCHHHHHHHHHTS-HHHHHHHHHHHH
T ss_pred HHHHHHHHHCCCceEeeecccccccccccHHHHHHh
Confidence 344444434455999999999999999999999996
No 352
>PRK06474 hypothetical protein; Provisional
Probab=89.87 E-value=0.97 Score=33.99 Aligned_cols=41 Identities=12% Similarity=0.184 Sum_probs=33.3
Q ss_pred hhhHHHHHHHHHhc--CCHHHHHHHh-CCCchHHHHHHHHHHHH
Q psy3760 3 LHQFRFVREAVRQN--FNLTEAAKAL-YTSQPGVSKAIIELEEE 43 (306)
Q Consensus 3 ~~~l~~f~~v~~~~--~s~~~aA~~l-~isq~~~s~~i~~LE~~ 43 (306)
-..++++..+.+.+ .|....++.+ +++++|++++|+.|++.
T Consensus 11 p~R~~Il~~L~~~~~~~ta~el~~~l~~is~aTvYrhL~~L~e~ 54 (178)
T PRK06474 11 PVRMKICQVLMRNKEGLTPLELVKILKDVPQATLYRHLQTMVDS 54 (178)
T ss_pred HHHHHHHHHHHhCCCCCCHHHHHHHhcCCCHHHHHHHHHHHHHC
Confidence 34567777777755 3788889999 89999999999999874
No 353
>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=89.85 E-value=0.38 Score=26.89 Aligned_cols=22 Identities=27% Similarity=0.218 Sum_probs=20.3
Q ss_pred CHHHHHHHhCCCchHHHHHHHH
Q psy3760 18 NLTEAAKALYTSQPGVSKAIIE 39 (306)
Q Consensus 18 s~~~aA~~l~isq~~~s~~i~~ 39 (306)
|..++|+.+++|.+++.+.+++
T Consensus 2 s~~e~a~~lgvs~~tl~~~~~~ 23 (49)
T cd04762 2 TTKEAAELLGVSPSTLRRWVKE 23 (49)
T ss_pred CHHHHHHHHCcCHHHHHHHHHc
Confidence 7889999999999999998886
No 354
>PRK09483 response regulator; Provisional
Probab=89.70 E-value=0.87 Score=35.12 Aligned_cols=44 Identities=14% Similarity=0.170 Sum_probs=38.4
Q ss_pred chhhHHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCc
Q psy3760 2 NLHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSI 46 (306)
Q Consensus 2 ~~~~l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~ 46 (306)
+-+..+++..+++-. |..+-|+.|++|..||..+++++-..||+
T Consensus 150 t~rE~~vl~~~~~G~-~~~~Ia~~l~is~~TV~~~~~~i~~Kl~v 193 (217)
T PRK09483 150 SERELQIMLMITKGQ-KVNEISEQLNLSPKTVNSYRYRMFSKLNI 193 (217)
T ss_pred CHHHHHHHHHHHCCC-CHHHHHHHhCCCHHHHHHHHHHHHHHcCC
Confidence 345667777777766 99999999999999999999999999996
No 355
>PRK01066 porphobilinogen deaminase; Provisional
Probab=89.66 E-value=8.4 Score=30.13 Aligned_cols=183 Identities=15% Similarity=0.064 Sum_probs=94.3
Q ss_pred CCcEEEEecccchhhh-hHHHHHHHHHhCCCcEEEEEe----CC----------------hhHHHHHHHcCCeeEEEEcc
Q psy3760 92 TGNLTIATTHTQARYA-LPKIIKEFTIQFPKVKLSLLQ----GN----------------PKQITEMIRNDQADIAIVTE 150 (306)
Q Consensus 92 ~~~l~I~~~~~~~~~~-l~~~l~~~~~~~p~~~i~~~~----~~----------------~~~~~~~l~~~~~Di~i~~~ 150 (306)
...|+||+-.+-...+ ...+...+.+.+|++.+++.. ++ ..++.+.|.+|++|+|+-+.
T Consensus 15 ~~~irIgTR~S~LAl~Qa~~v~~~L~~~~p~~~~ei~~i~T~GD~~~~~~L~~iGgkGlFtkele~aLl~g~iDiAVHSl 94 (231)
T PRK01066 15 KRPLRIASRQSSLAVAQVHECLRLLRSFFPKLWFQISTTTTQGDLDQKTPLHLVENTGFFTDDVDFLVLSGQCDLAIHSA 94 (231)
T ss_pred CceEEEEeCCCHHHHHHHHHHHHHHHHhCCCCcEEEEEEeccCcccccccHHHcCCceeeHHHHHHHHHcCCCCEEEecC
Confidence 3469999977644444 444456666778988888753 11 33778899999999999873
Q ss_pred ccCC-CCCceeeccccceEEEEecCCCCCC---CCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCceeEEEEecC
Q psy3760 151 ILSP-SDKLISIPCYQWEYVIIVPLDHPLL---LLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETIN 226 (306)
Q Consensus 151 ~~~~-~~~~~~~~l~~~~~~~v~~~~~~l~---~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 226 (306)
..-+ ++++. +.++.++..|-. .+...++++|..--.|... +.+.. .+ +.......++.-.-.|
T Consensus 95 KDlPt~~gl~--------l~av~~RedprDvLv~~~~~~l~~Lp~ga~IGTS---S~RR~-aq-l~~~rPdl~v~~iRGN 161 (231)
T PRK01066 95 KDLPEPPKLT--------VVAITAGLDPRDLLVYAEKYLSQPLPRRPRIGSS---SLRRE-EL-LKLLFPSGIILDIRGT 161 (231)
T ss_pred CcCCCCCCCE--------EEEEcCCCCCceEEEECCCCchhhCCCCCEEeCC---hHHHH-HH-HHHHCCCCEEEeCcCC
Confidence 3211 33333 222333333211 0111345555444444332 23322 22 2222233455555688
Q ss_pred HHHHHHHHHhccceeeee-cceeccc-ccCCc-eeeecCCCCccceEEEEEeCCccccHHHHHHHHH
Q psy3760 227 SDIIKTYVELRMGIGIIA-SIAFDSN-RDKNL-RSISASHLFGTTISRVIIKQGTYLRSYVYSFIKL 290 (306)
Q Consensus 227 ~~~~~~~v~~g~gi~~~p-~~~~~~~-~~~~l-~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~ 290 (306)
+.+=+.-+..|..=+++- .--...+ ....+ ..++.+..+-+.-+.+.++++ +..+..+++.
T Consensus 162 V~TRL~KL~~ge~DaiiLA~AGL~RLgl~~~~~~~l~~~~A~gQGalaie~R~~---d~~~~~ll~~ 225 (231)
T PRK01066 162 IEERLKLLEEKKYDAIVVAKAAVLRLGLRLPYTKELPPPYHPLQGRLAITASKH---IRSWKGLFLP 225 (231)
T ss_pred HHHHHHHhcCCCCCchhhHHHHHHhcCCcccceeECCCCCCCCCCeEEEEEecC---CHHHHHHHHH
Confidence 888888887774333322 2111222 11112 234444434466777877765 3334444443
No 356
>PRK09775 putative DNA-binding transcriptional regulator; Provisional
Probab=89.59 E-value=0.44 Score=41.40 Aligned_cols=26 Identities=27% Similarity=0.201 Sum_probs=24.0
Q ss_pred HhcCCHHHHHHHhCCCchHHHHHHHHH
Q psy3760 14 RQNFNLTEAAKALYTSQPGVSKAIIEL 40 (306)
Q Consensus 14 ~~~~s~~~aA~~l~isq~~~s~~i~~L 40 (306)
... |.+.=|+.|++|||++||+|+.|
T Consensus 12 g~~-~~~eL~~~l~~sq~~~s~~L~~L 37 (442)
T PRK09775 12 GPL-SAAELAARLGVSQATLSRLLAAL 37 (442)
T ss_pred CCC-CHHHHHHHhCCCHHHHHHHHHHh
Confidence 345 99999999999999999999999
No 357
>PRK13870 transcriptional regulator TraR; Provisional
Probab=89.53 E-value=0.93 Score=35.83 Aligned_cols=45 Identities=11% Similarity=0.099 Sum_probs=41.4
Q ss_pred chhhHHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCce
Q psy3760 2 NLHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSID 47 (306)
Q Consensus 2 ~~~~l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~ 47 (306)
+-+..+++.-+++-+ |-...|..|+||..||..+|++.-+.||+.
T Consensus 175 T~RE~E~L~W~A~GK-T~~EIa~ILgISe~TV~~Hl~na~~KLga~ 219 (234)
T PRK13870 175 DPKEATYLRWIAVGK-TMEEIADVEGVKYNSVRVKLREAMKRFDVR 219 (234)
T ss_pred CHHHHHHHHHHHcCC-CHHHHHHHHCCCHHHHHHHHHHHHHHcCCC
Confidence 457889999999988 999999999999999999999999999874
No 358
>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=89.49 E-value=1.8 Score=26.32 Aligned_cols=53 Identities=15% Similarity=0.260 Sum_probs=33.3
Q ss_pred CCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCCccccCHhHHHHHHHHHHHH
Q psy3760 17 FNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKPGQAILRSIEIIM 74 (306)
Q Consensus 17 ~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~~~lT~~G~~l~~~a~~il 74 (306)
+|+..+|+.+|+|++|+- ..|++.|.. +.|+.+|.-.-|+.--.-+..++.+.
T Consensus 1 ~~i~evA~~~gvs~~tlR----~~~~~g~l~-~~~~~~g~R~y~~~~l~~l~~i~~l~ 53 (67)
T cd04764 1 YTIKEVSEIIGVKPHTLR----YYEKEFNLY-IPRTENGRRYYTDEDIELLKKIKTLL 53 (67)
T ss_pred CCHHHHHHHHCcCHHHHH----HHHHhcCCC-CCCCCCCceeeCHHHHHHHHHHHHHH
Confidence 378899999999999876 456665554 55654443135555555444444443
No 359
>PRK10014 DNA-binding transcriptional repressor MalI; Provisional
Probab=89.45 E-value=5.7 Score=33.24 Aligned_cols=112 Identities=18% Similarity=0.176 Sum_probs=57.1
Q ss_pred CHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCCccccCHhHHHHHHHHHHHHHHHHHHHH-HHHhhccCCCCcEE
Q psy3760 18 NLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKPGQAILRSIEIIMQEIEGLKK-IGKEFSAYDTGNLT 96 (306)
Q Consensus 18 s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~~~lT~~G~~l~~~a~~il~~~~~~~~-~~~~~~~~~~~~l~ 96 (306)
++..-|+..|+|++||||.|. .++++ =-+..++..+.++++ .-..+ ..+.+..+....|-
T Consensus 8 Ti~dIA~~agVS~~TVSr~Ln-------------~~~~v--s~~tr~~V~~~a~el----gY~p~~~a~~l~~~~~~~Ig 68 (342)
T PRK10014 8 TIHDVALAAGVSVSTVSLVLS-------------GKGRI--STATGERVNQAIEEL----GFVRNRQASALRGGQSGVIG 68 (342)
T ss_pred cHHHHHHHhCCCHHHHHHHHC-------------CCCCC--CHHHHHHHHHHHHHh----CCCcCHHHHhhccCCCCEEE
Confidence 788999999999999999974 11222 122223333333222 21111 11222333334454
Q ss_pred EEecccchhhhhHHHHHHHHHhCC--CcEEEEEeC--Ch---hHHHHHHHcCCeeEEEEc
Q psy3760 97 IATTHTQARYALPKIIKEFTIQFP--KVKLSLLQG--NP---KQITEMIRNDQADIAIVT 149 (306)
Q Consensus 97 I~~~~~~~~~~l~~~l~~~~~~~p--~~~i~~~~~--~~---~~~~~~l~~~~~Di~i~~ 149 (306)
+-++. +...++..++..+.+..- +..+.+... +. .+.++.+.+..+|-.|..
T Consensus 69 vv~~~-~~~~~~~~i~~gi~~~a~~~g~~~~~~~~~~~~~~~~~~~~~l~~~~vdgiIi~ 127 (342)
T PRK10014 69 LIVRD-LSAPFYAELTAGLTEALEAQGRMVFLLQGGKDGEQLAQRFSTLLNQGVDGVVIA 127 (342)
T ss_pred EEeCC-CccchHHHHHHHHHHHHHHcCCEEEEEeCCCCHHHHHHHHHHHHhCCCCEEEEe
Confidence 44443 234455555444333221 345444332 22 245667778889998885
No 360
>PF01726 LexA_DNA_bind: LexA DNA binding domain; InterPro: IPR006199 This is the DNA binding domain of the LexA SOS regulon repressor which prevents expression of DNA repair proteins in bacteria. The aligned region contains a variant form of the helix-turn-helix DNA binding motif []. This domain usually at the N terminus is found associated with IPR006198 from INTERPRO the auto-proteolytic domain of LexA 3.4.21.88 from EC.; GO: 0004252 serine-type endopeptidase activity, 0006508 proteolysis; PDB: 1LEA_A 1JHH_A 3JSP_A 1JHF_A 3JSO_B 1LEB_A 3K2Z_A.
Probab=89.42 E-value=0.6 Score=28.41 Aligned_cols=25 Identities=28% Similarity=0.311 Sum_probs=22.7
Q ss_pred CHHHHHHHhCCC-chHHHHHHHHHHH
Q psy3760 18 NLTEAAKALYTS-QPGVSKAIIELEE 42 (306)
Q Consensus 18 s~~~aA~~l~is-q~~~s~~i~~LE~ 42 (306)
|+..-|+.+|++ .+++.++|+.||+
T Consensus 27 t~rEIa~~~g~~S~~tv~~~L~~Le~ 52 (65)
T PF01726_consen 27 TVREIAEALGLKSTSTVQRHLKALER 52 (65)
T ss_dssp -HHHHHHHHTSSSHHHHHHHHHHHHH
T ss_pred CHHHHHHHhCCCChHHHHHHHHHHHH
Confidence 788999999997 9999999999995
No 361
>PRK00072 hemC porphobilinogen deaminase; Reviewed
Probab=89.35 E-value=11 Score=30.92 Aligned_cols=183 Identities=14% Similarity=0.127 Sum_probs=95.4
Q ss_pred CcEEEEecccchh-hhhHHHHHHHHHhCCCcEEEEEeC----C----------------hhHHHHHHHcCCeeEEEEccc
Q psy3760 93 GNLTIATTHTQAR-YALPKIIKEFTIQFPKVKLSLLQG----N----------------PKQITEMIRNDQADIAIVTEI 151 (306)
Q Consensus 93 ~~l~I~~~~~~~~-~~l~~~l~~~~~~~p~~~i~~~~~----~----------------~~~~~~~l~~~~~Di~i~~~~ 151 (306)
..++||+-.+-.. .-...+...+.+.+|++++++... + ..++.+.|.+|++|+++.+..
T Consensus 3 ~~irIGtR~S~LAl~Qt~~V~~~L~~~~p~~~~ei~~i~T~GD~~~~~~L~~iggkG~Ftkele~aLl~g~iDiAVHSlK 82 (295)
T PRK00072 3 RKIRIGTRGSKLALWQAEWVKDRLKAAHPGLEVELVPIKTKGDKILDVPLAKIGGKGLFVKELEEALLEGEIDIAVHSLK 82 (295)
T ss_pred ccEEEEeCCCHHHHHHHHHHHHHHHHHCCCCeEEEEEeeccCcccccccHHHcCCcceeHHHHHHHHHcCCCCEEEeccC
Confidence 3589999766433 344555566777789888887541 2 236778999999999999743
Q ss_pred cCC---CCCceeeccccceEEEEecCCCCCC---CCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCceeEEEEec
Q psy3760 152 LSP---SDKLISIPCYQWEYVIIVPLDHPLL---LLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETI 225 (306)
Q Consensus 152 ~~~---~~~~~~~~l~~~~~~~v~~~~~~l~---~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 225 (306)
.-+ ++++. +..+.+++.|-. .++.-++++|..-..|... +.|.. . .+.......+++-.-.
T Consensus 83 DlP~~l~~gl~--------i~avl~R~dprDvlv~~~~~~l~~Lp~ga~IGTs---S~RR~-a-ql~~~~Pdl~~~~iRG 149 (295)
T PRK00072 83 DVPTELPEGLV--------LAAIPEREDPRDALVSRDYKSLDDLPEGAVVGTS---SLRRQ-A-QLLALRPDLEIKPLRG 149 (295)
T ss_pred cCCCCCCCCcE--------EEEEecCCCCceEEEECCCCChhHCCCCCEEecC---cHHHH-H-HHHHHCcCCEEEECcc
Confidence 222 23333 233333333311 1112366776554444432 33332 2 2222222234444458
Q ss_pred CHHHHHHHHHhccceeee-ecceeccc-ccCCc-eeeecCC---CCccceEEEEEeCCccccHHHHHHHHHH
Q psy3760 226 NSDIIKTYVELRMGIGII-ASIAFDSN-RDKNL-RSISASH---LFGTTISRVIIKQGTYLRSYVYSFIKLL 291 (306)
Q Consensus 226 ~~~~~~~~v~~g~gi~~~-p~~~~~~~-~~~~l-~~~~~~~---~~~~~~~~l~~~~~~~~~~~~~~~~~~l 291 (306)
|+++=+.-+.+|..=+++ ..--.... ....+ ..++.+. .+-+.-+.+.++++ +..+..+++.|
T Consensus 150 NV~TRL~KL~~g~~DaivLA~AGL~RLgl~~~~~~~l~~~~~~PA~gQGaiave~r~~---d~~~~~~l~~i 218 (295)
T PRK00072 150 NVDTRLRKLDEGEYDAIILAAAGLKRLGLEDRITEYLDPEEMLPAPGQGALGIECRAD---DEEILELLAPL 218 (295)
T ss_pred CHHHHHHHhhCCCCCEeehHhhHHHHcCCccccceecChhhcCCcccccceeeeeecC---CHHHHHHHHHc
Confidence 999999999888443332 22222222 11112 2344333 12244566666654 45555665555
No 362
>TIGR01764 excise DNA binding domain, excisionase family. An excisionase, or Xis protein, is a small protein that binds and promotes excisive recombination; it is not enzymatically active. This model 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 model 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 (pfam00376).
Probab=89.29 E-value=0.44 Score=26.71 Aligned_cols=22 Identities=36% Similarity=0.303 Sum_probs=19.9
Q ss_pred CHHHHHHHhCCCchHHHHHHHH
Q psy3760 18 NLTEAAKALYTSQPGVSKAIIE 39 (306)
Q Consensus 18 s~~~aA~~l~isq~~~s~~i~~ 39 (306)
|+.+||+.||+|.+++.+.+++
T Consensus 3 t~~e~a~~lgis~~ti~~~~~~ 24 (49)
T TIGR01764 3 TVEEAAEYLGVSKDTVYRLIHE 24 (49)
T ss_pred CHHHHHHHHCCCHHHHHHHHHc
Confidence 7899999999999999998864
No 363
>COG2512 Predicted membrane-associated trancriptional regulator [Transcription]
Probab=89.26 E-value=0.91 Score=36.27 Aligned_cols=58 Identities=21% Similarity=0.125 Sum_probs=44.3
Q ss_pred hhhHHHHHHHHHhcCCHHHH--HHHhCCCchHHHHHHHHHHHHcCceeEEecCCCccccC
Q psy3760 3 LHQFRFVREAVRQNFNLTEA--AKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLT 60 (306)
Q Consensus 3 ~~~l~~f~~v~~~~~s~~~a--A~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~~~lT 60 (306)
-+..+++..+.+.|+-++++ .+++|.|.+|+||++++||+.==++++.+.+...++|.
T Consensus 195 ~~e~~il~~i~~~GGri~Q~eL~r~lglsktTvsR~L~~LEk~GlIe~~K~G~~n~V~l~ 254 (258)
T COG2512 195 EDEKEILDLIRERGGRITQAELRRALGLSKTTVSRILRRLEKRGLIEKEKKGRTNIVELR 254 (258)
T ss_pred HHHHHHHHHHHHhCCEEeHHHHHHhhCCChHHHHHHHHHHHhCCceEEEEeCCeeEEEEe
Confidence 45677888888988336555 58999999999999999998765677777666554443
No 364
>PRK09954 putative kinase; Provisional
Probab=89.20 E-value=0.8 Score=38.90 Aligned_cols=54 Identities=26% Similarity=0.207 Sum_probs=39.1
Q ss_pred CchhhHHHHHHHHHhc-CCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCCccccC
Q psy3760 1 MNLHQFRFVREAVRQN-FNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLT 60 (306)
Q Consensus 1 m~~~~l~~f~~v~~~~-~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~~~lT 60 (306)
||-++.+++..+-+.+ .|.+.-|+.|++|++++.++|++|++ -|.. .+++. .+.
T Consensus 1 ~~~~~~~il~~l~~~~~~s~~~la~~l~~s~~~v~~~i~~L~~-~g~i----~~~~~-~l~ 55 (362)
T PRK09954 1 MNNREKEILAILRRNPLIQQNEIADILQISRSRVAAHIMDLMR-KGRI----KGKGY-ILT 55 (362)
T ss_pred CChHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHHH-CCCc----CCcEE-EEc
Confidence 5556666666666653 26777899999999999999999997 4543 34555 354
No 365
>PF12728 HTH_17: Helix-turn-helix domain
Probab=89.18 E-value=0.43 Score=27.26 Aligned_cols=22 Identities=32% Similarity=0.261 Sum_probs=19.8
Q ss_pred CHHHHHHHhCCCchHHHHHHHH
Q psy3760 18 NLTEAAKALYTSQPGVSKAIIE 39 (306)
Q Consensus 18 s~~~aA~~l~isq~~~s~~i~~ 39 (306)
|..+||+.|++|.+++.+.+++
T Consensus 3 t~~e~a~~l~is~~tv~~~~~~ 24 (51)
T PF12728_consen 3 TVKEAAELLGISRSTVYRWIRQ 24 (51)
T ss_pred CHHHHHHHHCcCHHHHHHHHHc
Confidence 7889999999999999988863
No 366
>cd00494 HMBS Hydroxymethylbilane synthase (HMBS), also known as porphobilinogen deaminase (PBGD), is an intermediate enzyme in the biosynthetic pathway of tetrapyrrolic ring systems, such as heme, chlorophylls, and vitamin B12. HMBS catalyzes the conversion of porphobilinogen (PBG) into hydroxymethylbilane (HMB). HMBS consists of three domains, and is believed to bind substrate through a hinge-bending motion of domains I and II. HMBS is found in all organisms except viruses.
Probab=89.12 E-value=11 Score=30.79 Aligned_cols=181 Identities=16% Similarity=0.179 Sum_probs=92.2
Q ss_pred EEEEecccchhh-hhHHHHHHHHHhCCCcEEEEEeC----C----------------hhHHHHHHHcCCeeEEEEccccC
Q psy3760 95 LTIATTHTQARY-ALPKIIKEFTIQFPKVKLSLLQG----N----------------PKQITEMIRNDQADIAIVTEILS 153 (306)
Q Consensus 95 l~I~~~~~~~~~-~l~~~l~~~~~~~p~~~i~~~~~----~----------------~~~~~~~l~~~~~Di~i~~~~~~ 153 (306)
|+||+-.|-... -...+...+.+.+|++++++... + ..++.+.|.+|++|+++.+...-
T Consensus 1 irIgtR~S~LAl~Qa~~V~~~L~~~~p~~~~ei~~i~T~GD~~~~~~L~~iggkG~Ftkele~aLl~g~iDiAVHSlKDl 80 (292)
T cd00494 1 IRIGTRKSKLALIQTNKVIEKLKELCPGIEVEIVIIKTTGDKILDKPLAKIGGKGLFTKELEEALLNGEIDLAVHSLKDV 80 (292)
T ss_pred CEEEcCCCHHHHHHHHHHHHHHHHhCCCCeEEEEEEEecCcccccccHHHcCCcceeHHHHHHHHHcCCCCEEEeccccC
Confidence 467775553333 33334455666688887777441 1 22677899999999999874322
Q ss_pred C---CCCceeeccccceEEEEecCCCCCC---CCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCceeEEEEecCH
Q psy3760 154 P---SDKLISIPCYQWEYVIIVPLDHPLL---LLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINS 227 (306)
Q Consensus 154 ~---~~~~~~~~l~~~~~~~v~~~~~~l~---~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 227 (306)
+ ++++. +..+.++..|-. .+...++++|..-..|... +.|.. ..+.......+++-.-.|+
T Consensus 81 P~~lp~gl~--------i~av~~RedprDvlv~~~~~~l~~Lp~ga~IGTs---S~RR~--aql~~~rpdl~~~~iRGNV 147 (292)
T cd00494 81 PTELPEGLV--------LGAIPKREDPRDALVSRNGSSLEDLPAGSVVGTS---SLRRQ--AQLKRKRPDLKFEPLRGNV 147 (292)
T ss_pred CCCCCCCcE--------EEEEecCCCCceEEEECCCCChhHCCCCCEEecC---CHHHH--HHHHHHCCCCEEEEcCCCH
Confidence 2 23333 223333333211 1112366777655545432 33332 2233333334555566899
Q ss_pred HHHHHHHHhccceeee-ecceeccc-ccCCc-eeeecCC---CCccceEEEEEeCCccccHHHHHHHHHH
Q psy3760 228 DIIKTYVELRMGIGII-ASIAFDSN-RDKNL-RSISASH---LFGTTISRVIIKQGTYLRSYVYSFIKLL 291 (306)
Q Consensus 228 ~~~~~~v~~g~gi~~~-p~~~~~~~-~~~~l-~~~~~~~---~~~~~~~~l~~~~~~~~~~~~~~~~~~l 291 (306)
.+=+.-+.+|..=+++ ..--.... ....+ ..++.+. .+-+.-+.+-++++ +..+..+++.|
T Consensus 148 ~TRL~KL~~ge~DaiiLA~AGL~RLgl~~~~~~~l~~~~~~PA~gQGalave~r~~---d~~~~~ll~~i 214 (292)
T cd00494 148 DTRLRKLDEGEYDAIILAAAGLKRLGLEDRITQYLSPEVMLPAVGQGALAIECRKG---DEELLALLKPL 214 (292)
T ss_pred HHHHHHhcCCCCCEeehHhhHHHHcCCcccCccccCccccCCccccceEEEEEecC---CHHHHHHHHHC
Confidence 9999989888433332 22212222 11112 2333332 12245666666655 34455555555
No 367
>TIGR01321 TrpR trp operon repressor, proteobacterial. This model represents TrpR, the repressor of the trp operon. It is found so far only in the gamma subdivision of the proteobacteria and in Chlamydia trachomatis. All members belong to species capable of tryptophan biosynthesis.
Probab=89.01 E-value=0.7 Score=30.29 Aligned_cols=33 Identities=24% Similarity=0.264 Sum_probs=25.1
Q ss_pred HHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHH
Q psy3760 6 FRFVREAVRQNFNLTEAAKALYTSQPGVSKAII 38 (306)
Q Consensus 6 l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~ 38 (306)
+.++-.+.+.+.|-.+.|+.+|||+++|||-=+
T Consensus 45 ~~i~~~Ll~~~~tQrEIa~~lGiS~atIsR~sn 77 (94)
T TIGR01321 45 IRIVNELLNGNMSQREIASKLGVSIATITRGSN 77 (94)
T ss_pred HHHHHHHHhCCCCHHHHHHHhCCChhhhhHHHh
Confidence 445555655444999999999999999997543
No 368
>PF08461 HTH_12: Ribonuclease R winged-helix domain; InterPro: IPR013668 This domain is found at the amino terminus of Ribonuclease R and a number of presumed transcriptional regulatory proteins from archaea.
Probab=88.92 E-value=0.44 Score=29.11 Aligned_cols=37 Identities=19% Similarity=0.261 Sum_probs=27.9
Q ss_pred CCCchHHHHHHHHHHHHcCceeEEecCCCccccCHhHHHH
Q psy3760 27 YTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKPGQAI 66 (306)
Q Consensus 27 ~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~~~lT~~G~~l 66 (306)
.+|..||.++++.||+. | +..|.+++...+|+.|..+
T Consensus 29 ~~se~avRrrLr~me~~-G--lt~~~g~~G~~iT~~G~~~ 65 (66)
T PF08461_consen 29 ELSEEAVRRRLRAMERD-G--LTRKVGRQGRIITEKGLDE 65 (66)
T ss_pred hhhHHHHHHHHHHHHHC-C--CccccCCcccccCHHHHhh
Confidence 56779999999999987 4 5555544333699999875
No 369
>PRK15046 2-aminoethylphosphonate ABC transporter substrate-binding protein; Provisional
Probab=88.88 E-value=13 Score=31.36 Aligned_cols=98 Identities=11% Similarity=0.142 Sum_probs=63.7
Q ss_pred CCCCcEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHc----CCeeEEEEccccC----------C-
Q psy3760 90 YDTGNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRN----DQADIAIVTEILS----------P- 154 (306)
Q Consensus 90 ~~~~~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~----~~~Di~i~~~~~~----------~- 154 (306)
...+.|+|.+.... ..++..++..|.+++ +++|++...++.++...+.. +.+|+++...... +
T Consensus 32 ~~~~~L~v~~~~~~-~~~~~~ii~~Fe~~~-gikV~~~~~~s~~~~~kl~~~~~~~~~DVv~~~~~~~~~~~~~Gll~~~ 109 (349)
T PRK15046 32 WAADAVTVYSADGL-EDWYQDVFPAFTKAT-GIKVNYVEAGSGEVVNRAAKEKSNPQADVLVTLPPFIQQAAAEGLLQPY 109 (349)
T ss_pred ccCCcEEEEeccch-HHHHHHHHHHHHhhh-CcEEEEEeCChHHHHHHHHhhhcCCCCCEEEeCcHHHHHHHhCCCcccc
Confidence 34467999987554 357889999998875 89999999888888877753 4799987531100 0
Q ss_pred -CCC---c---------eeeccccceEEEEecCCCCCCCCCCcChhhhcC
Q psy3760 155 -SDK---L---------ISIPCYQWEYVIIVPLDHPLLLLNSISLKEISN 191 (306)
Q Consensus 155 -~~~---~---------~~~~l~~~~~~~v~~~~~~l~~~~~i~~~dl~~ 191 (306)
..+ + .+.++....++++..++.. ...+-+|+||.+
T Consensus 110 ~~~~~~~i~~~~~d~~g~~~~~~~~~~~l~Yn~~~~--~~~P~sw~dL~~ 157 (349)
T PRK15046 110 SSVNAKAVPAIAKDADGTYAPFVNNYLSFIYNPKVL--KTAPATWADLLD 157 (349)
T ss_pred CccchhcCchhhcCCCCCEEeeecceeEEEEchhhc--cCCCCCHHHHhC
Confidence 000 0 1233444455677777653 234678999976
No 370
>PF13744 HTH_37: Helix-turn-helix domain; PDB: 2A6C_B 2O38_A.
Probab=88.61 E-value=0.41 Score=30.54 Aligned_cols=24 Identities=33% Similarity=0.297 Sum_probs=17.0
Q ss_pred hcCCHHHHHHHhCCCchHHHHHHH
Q psy3760 15 QNFNLTEAAKALYTSQPGVSKAII 38 (306)
Q Consensus 15 ~~~s~~~aA~~l~isq~~~s~~i~ 38 (306)
.|.|=..+|+.+|+|||.||+-.+
T Consensus 30 ~~ltQ~e~A~~lgisq~~vS~l~~ 53 (80)
T PF13744_consen 30 RGLTQAELAERLGISQPRVSRLEN 53 (80)
T ss_dssp CT--HHHHHHHHTS-HHHHHHHHT
T ss_pred cCCCHHHHHHHHCCChhHHHHHHc
Confidence 334567899999999999998653
No 371
>COG1568 Predicted methyltransferases [General function prediction only]
Probab=88.44 E-value=1.7 Score=34.70 Aligned_cols=57 Identities=18% Similarity=0.198 Sum_probs=50.2
Q ss_pred HHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCCccccCHhHHHHHH
Q psy3760 7 RFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKPGQAILR 68 (306)
Q Consensus 7 ~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~~~lT~~G~~l~~ 68 (306)
.++.++..++ |+-+-+..-..+-|.++.-+..||++ .+..++.+++ ++|+.|+.|.+
T Consensus 26 ~vl~ail~~~-d~wkIvd~s~~plp~v~~i~~~l~~e---giv~~~~g~v-~~TekG~E~~e 82 (354)
T COG1568 26 NVLSAILATN-DFWKIVDYSDLPLPLVASILEILEDE---GIVKIEEGGV-ELTEKGEELAE 82 (354)
T ss_pred HHHHHHHcCc-chHhhhhhccCCchHHHHHHHHHHhc---CcEEEecCcE-eehhhhHHHHH
Confidence 3677889999 99999999999999999999999985 5777788887 99999999865
No 372
>TIGR02405 trehalos_R_Ecol trehalose operon repressor, proteobacterial. This family consists of repressors of the LacI family typically associated with trehalose utilization operons. Trehalose is imported as trehalose-6-phosphate and then hydrolyzed by alpha,alpha-phosphotrehalase to glucose and glucose-6-P. This family includes repressors mostly from Gammaproteobacteria and does not include the GntR family TreR of Bacillus subtilis
Probab=88.41 E-value=13 Score=30.68 Aligned_cols=21 Identities=14% Similarity=0.218 Sum_probs=19.2
Q ss_pred CHHHHHHHhCCCchHHHHHHH
Q psy3760 18 NLTEAAKALYTSQPGVSKAII 38 (306)
Q Consensus 18 s~~~aA~~l~isq~~~s~~i~ 38 (306)
++..-|+..|+|++||||.|.
T Consensus 3 ti~dIA~~agVS~sTVSr~Ln 23 (311)
T TIGR02405 3 TIKDIARLAGVGKSTVSRVLN 23 (311)
T ss_pred cHHHHHHHhCCCHHHHHHHhC
Confidence 678899999999999999993
No 373
>PRK00215 LexA repressor; Validated
Probab=88.37 E-value=1.2 Score=34.28 Aligned_cols=42 Identities=21% Similarity=0.178 Sum_probs=32.4
Q ss_pred chhhHHHHHHHHH----hcC--CHHHHHHHhCC-CchHHHHHHHHHHHH
Q psy3760 2 NLHQFRFVREAVR----QNF--NLTEAAKALYT-SQPGVSKAIIELEEE 43 (306)
Q Consensus 2 ~~~~l~~f~~v~~----~~~--s~~~aA~~l~i-sq~~~s~~i~~LE~~ 43 (306)
+-+|.+++..+.+ .+. |++.-|+.+++ |+||+++.|+.||+.
T Consensus 3 t~~q~~il~~i~~~~~~~~~~~s~~ela~~~~~~~~~tv~~~l~~L~~~ 51 (205)
T PRK00215 3 TKRQQEILDFIRDHIEETGYPPSRREIADALGLRSPSAVHEHLKALERK 51 (205)
T ss_pred CHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCChHHHHHHHHHHHHC
Confidence 4456666655543 232 68899999999 999999999999985
No 374
>COG1910 Periplasmic molybdate-binding protein/domain [Inorganic ion transport and metabolism]
Probab=88.14 E-value=0.27 Score=37.52 Aligned_cols=48 Identities=15% Similarity=0.147 Sum_probs=40.8
Q ss_pred ChhHHHHHHHcCCeeEEEEccccCCCCCceeeccccceEEEEecCCCC
Q psy3760 130 NPKQITEMIRNDQADIAIVTEILSPSDKLISIPCYQWEYVIIVPLDHP 177 (306)
Q Consensus 130 ~~~~~~~~l~~~~~Di~i~~~~~~~~~~~~~~~l~~~~~~~v~~~~~~ 177 (306)
........+.+|++|++++.......-++.++||.++++-++++++..
T Consensus 138 th~avA~aVa~G~AD~GvGlr~~A~~~gL~Fipl~~E~YD~virke~~ 185 (223)
T COG1910 138 THDAVASAVASGRADAGVGLRHAAEKYGLDFIPLGDEEYDFVIRKERL 185 (223)
T ss_pred ccHHHHHHHHcCCCCccccHHHHHHHcCCceEEcccceEEEEEehhHc
Confidence 345678899999999999975555668899999999999999999873
No 375
>PF03401 TctC: Tripartite tricarboxylate transporter family receptor; InterPro: IPR005064 Bordetella pertussis, the causative agent of human whooping cough (pertussis), is an obligate human pathogen with diverse high-affinity transport systems for the assimilation of iron, a biometal that is essential for growth []. Periplasmic binding proteins of a new family, particularly well represented in this organism (and more generally in beta-proteobacteria), have been called Bug receptors []. They adopt a characteristic Venus flytrap fold with two globular domains bisected by a ligand-binding cleft. The family is specific for carboxylated solutes, with a characteristic mode of binding involving two highly conserved beta strand-beta turn-alpha helix motifs originating from each domain. These two motifs form hydrogen bonds with a carboxylate group of the ligand, both directly and via conserved water molecules, and have thus been termed the carboxylate pincers. Domain 1 recognises the ligand and the carboxylate group serves as an initial anchoring point. Domain 2 discriminates between productively and non-productively bound ligands as proper interactions with this domain is needed for the of the closed conformation []. BugE has a glutamate bound ligand. No charged residues are involved in glutamate binding by BugE, unlike what has been described for all glutamate receptors reported so far. The Bug architecture is highly conserved despite limited sequence identity [].; GO: 0030288 outer membrane-bounded periplasmic space; PDB: 2QPQ_C 2DVZ_A 2F5X_A.
Probab=88.05 E-value=8.7 Score=31.23 Aligned_cols=137 Identities=12% Similarity=0.009 Sum_probs=69.3
Q ss_pred ccccceEEEEecCCCCCCCCCCcChhhh----cCCC--eEeecCCC-CcHHHH-HHHHHhCCCceeEEEEecCHHHHHHH
Q psy3760 162 PCYQWEYVIIVPLDHPLLLLNSISLKEI----SNYP--LITYDLSF-SGRIKL-DREFSLQKLTPYIVLETINSDIIKTY 233 (306)
Q Consensus 162 ~l~~~~~~~v~~~~~~l~~~~~i~~~dl----~~~~--~i~~~~~~-~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~ 233 (306)
.+..++.+++++++.|. -+++|| ...| +..-..+. ...+.. ..+.+..|+..+.+- .+.....+..
T Consensus 74 ~~~~~~~vl~v~~dsp~-----~t~~eli~~ak~~p~~~~~g~~g~g~~~hl~~~~l~~~~G~~~~~Vp-y~G~~~~~~a 147 (274)
T PF03401_consen 74 RIASDPNVLVVRADSPY-----KTLEELIEYAKANPGKLTFGSSGPGSSDHLAAALLAKAAGIKFTHVP-YDGGAEALTA 147 (274)
T ss_dssp EEEEEEEEEEEETTSS------SSHHHHHHHHHCSCCC-EEEESSTTSHHHHHHHHHHHHHT---EEEE--SSHHHHHHH
T ss_pred hhhccceEEEEeCCCcc-----ccHHHHHHHHHhCCCCeEEEecCCCchHHHHHHHHHHHhCCceEEEE-eCCccHHHHH
Confidence 35567889999999874 366666 2323 33222222 223333 344566688766553 4455555555
Q ss_pred HHhc-cceeeeecceeccc-ccCCceeeec--------------------CCCCccceEEEEEeCCccccHHHHHHHHHH
Q psy3760 234 VELR-MGIGIIASIAFDSN-RDKNLRSISA--------------------SHLFGTTISRVIIKQGTYLRSYVYSFIKLL 291 (306)
Q Consensus 234 v~~g-~gi~~~p~~~~~~~-~~~~l~~~~~--------------------~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l 291 (306)
+..| .-+++.....+..+ +.++++.+-. ++.....-..++.+++.+ ...+..+.+.+
T Consensus 148 llgG~vd~~~~~~~~~~~~~~~G~~k~Lav~~~~r~~~~pdvPT~~E~G~~d~~~~~~~g~~~p~gtp-~~~~~~l~~a~ 226 (274)
T PF03401_consen 148 LLGGHVDAAFGSPGEALPYVEAGDLKPLAVFSDERSPALPDVPTFKEQGYPDIVFGSWRGLFAPKGTP-DEIVDKLADAI 226 (274)
T ss_dssp HHTTSSSEEEEEHHHHHHHHHTTSEEEEEECSSS-BTTCTTS-BTTTTT-TTG--EEEEEEEEETTS--HHHHHHHHHHH
T ss_pred HhCCeeeEEeecHHHHHHHHhCCCceEEEEecCccccccCCCCCHHHhCccceeeeeeeeeecCCCCC-HHHHHHHHHHH
Confidence 5555 33333333222233 5555554311 010111122355577775 77888888999
Q ss_pred hHHhhHHHHHhhhc
Q psy3760 292 SPKLNRKFINKILN 305 (306)
Q Consensus 292 ~~~~~~~~~~~~~~ 305 (306)
++.++.....+.++
T Consensus 227 ~~~~~~pe~~~~~~ 240 (274)
T PF03401_consen 227 KKALEDPEFQEFLE 240 (274)
T ss_dssp HHHHT-HHHHHHHH
T ss_pred HHHhCCHHHHHHHH
Confidence 98887777766543
No 376
>PRK09526 lacI lac repressor; Reviewed
Probab=88.01 E-value=15 Score=30.79 Aligned_cols=112 Identities=13% Similarity=0.138 Sum_probs=57.1
Q ss_pred CHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCCccccCHhHHHHHHHHHHHHHHHHHHHH-HHHhhccCCCCcEE
Q psy3760 18 NLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKPGQAILRSIEIIMQEIEGLKK-IGKEFSAYDTGNLT 96 (306)
Q Consensus 18 s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~~~lT~~G~~l~~~a~~il~~~~~~~~-~~~~~~~~~~~~l~ 96 (306)
++..-|+..|+|++||||.|.. +.++ .+ .--+++.++.+++.-.-+ ..+.++.+..+.|-
T Consensus 7 ti~dIA~~aGVS~~TVSrvLn~-------------~~~v---s~---~tr~rV~~~a~elgY~pn~~a~~l~~~~~~~Ig 67 (342)
T PRK09526 7 TLYDVARYAGVSYQTVSRVLNQ-------------ASHV---SA---KTREKVEAAMAELNYVPNRVAQQLAGKQSLTIG 67 (342)
T ss_pred cHHHHHHHhCCCHHHHHHHhcC-------------CCCC---CH---HHHHHHHHHHHHHCCCcCHHHHHhhcCCCceEE
Confidence 7889999999999999999831 1222 11 112222222222221111 11223333344444
Q ss_pred EEecccchhhhhHHHHHHHHHhC--CCcEEEEEeCC--h----hHHHHHHHcCCeeEEEEc
Q psy3760 97 IATTHTQARYALPKIIKEFTIQF--PKVKLSLLQGN--P----KQITEMIRNDQADIAIVT 149 (306)
Q Consensus 97 I~~~~~~~~~~l~~~l~~~~~~~--p~~~i~~~~~~--~----~~~~~~l~~~~~Di~i~~ 149 (306)
+-++. +...+...++..+.+.. -++.+.+...+ . .+.++.+.+..+|-+|+.
T Consensus 68 vv~~~-~~~~~~~~~~~gi~~~a~~~g~~~~i~~~~~~~~~~~~~~l~~l~~~~vdGiii~ 127 (342)
T PRK09526 68 LATTS-LALHAPSQIAAAIKSRADQLGYSVVISMVERSGVEACQAAVNELLAQRVSGVIIN 127 (342)
T ss_pred EEeCC-CCcccHHHHHHHHHHHHHHCCCEEEEEeCCCChHHHHHHHHHHHHhcCCCEEEEe
Confidence 44443 22333344444443321 25666664322 1 245677888899988874
No 377
>PRK15090 DNA-binding transcriptional regulator KdgR; Provisional
Probab=87.96 E-value=4.5 Score=32.50 Aligned_cols=45 Identities=13% Similarity=0.155 Sum_probs=33.9
Q ss_pred CCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEec--CCCccccCHhHHH
Q psy3760 17 FNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRH--GKRIRGLTKPGQA 65 (306)
Q Consensus 17 ~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~--~~~~~~lT~~G~~ 65 (306)
.|++.-|+.++++.||+.|-++.|++. |. ..|. ++.. +|++.-..
T Consensus 29 l~l~eia~~lgl~kstv~Rll~tL~~~-G~--l~~~~~~~~Y-~lG~~~~~ 75 (257)
T PRK15090 29 IGITELSQRVMMSKSTVYRFLQTMKTL-GY--VAQEGESEKY-SLTLKLFE 75 (257)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHHHHHC-CC--EEEcCCCCcE-EecHHHHH
Confidence 389999999999999999999999863 44 4443 4555 67765433
No 378
>PF07022 Phage_CI_repr: Bacteriophage CI repressor helix-turn-helix domain; InterPro: IPR010744 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 [].; GO: 0003677 DNA binding, 0045892 negative regulation of transcription, DNA-dependent; PDB: 2FJR_B.
Probab=87.55 E-value=0.35 Score=29.56 Aligned_cols=32 Identities=22% Similarity=0.113 Sum_probs=23.7
Q ss_pred HHHHHHHHHhcCCHHHHHHHhCCCchHHH-HHHH
Q psy3760 6 FRFVREAVRQNFNLTEAAKALYTSQPGVS-KAII 38 (306)
Q Consensus 6 l~~f~~v~~~~~s~~~aA~~l~isq~~~s-~~i~ 38 (306)
|+-+..+...+ +-..-|+.|+||++++| ...+
T Consensus 3 i~rl~~~~g~~-~~~~lA~~lgis~st~s~~~~~ 35 (66)
T PF07022_consen 3 IERLKEALGVK-SDKELAERLGISKSTLSNNWKK 35 (66)
T ss_dssp HHHHHHHHT-S-SCHHHHCCTT--HHHHH-HHHH
T ss_pred HHHHHHHhCCC-CHHHHHHHhCcCHHHhhHHHHh
Confidence 56677788888 88999999999999999 5543
No 379
>PRK10100 DNA-binding transcriptional regulator CsgD; Provisional
Probab=87.39 E-value=1.6 Score=34.05 Aligned_cols=44 Identities=14% Similarity=0.218 Sum_probs=39.6
Q ss_pred chhhHHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCc
Q psy3760 2 NLHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSI 46 (306)
Q Consensus 2 ~~~~l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~ 46 (306)
+-+..++|..+++-. |...-|+.|++|..|+..+++++=..+|+
T Consensus 157 t~rE~~Vl~l~~~G~-s~~eIA~~L~iS~~TVk~~~~~i~~Kl~v 200 (216)
T PRK10100 157 THREKEILNKLRIGA-SNNEIARSLFISENTVKTHLYNLFKKIAV 200 (216)
T ss_pred CHHHHHHHHHHHcCC-CHHHHHHHhCCCHHHHHHHHHHHHHHhCC
Confidence 456788999999855 99999999999999999999999888886
No 380
>PF05732 RepL: Firmicute plasmid replication protein (RepL); InterPro: IPR008813 This entry consists of proteins thought to be involved in plasmid replication. ; GO: 0006260 DNA replication, 0006276 plasmid maintenance
Probab=87.36 E-value=0.68 Score=34.24 Aligned_cols=42 Identities=33% Similarity=0.345 Sum_probs=32.8
Q ss_pred CHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCCccccCHh
Q psy3760 18 NLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKP 62 (306)
Q Consensus 18 s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~~~lT~~ 62 (306)
|...-|+.+++|.||+++.|+.||+. .++.|.+.|...+.|.
T Consensus 77 t~~~ia~~l~iS~~Tv~r~ik~L~e~---~iI~k~~~G~Y~iNP~ 118 (165)
T PF05732_consen 77 TQKEIAEKLGISKPTVSRAIKELEEK---NIIKKIRNGAYMINPN 118 (165)
T ss_pred eHHHHHHHhCCCHHHHHHHHHHHHhC---CcEEEccCCeEEECcH
Confidence 56778999999999999999999984 3455555554468876
No 381
>PF12727 PBP_like: PBP superfamily domain; InterPro: IPR024370 This entry represents members of the periplasmic binding domain superfamily []. It is often associated with a helix-turn-helix domain.
Probab=87.10 E-value=0.57 Score=35.76 Aligned_cols=50 Identities=12% Similarity=0.141 Sum_probs=41.6
Q ss_pred EeCChhHHHHHHHcCCeeEEEEccccCCC-CCceeeccccceEEEEecCCC
Q psy3760 127 LQGNPKQITEMIRNDQADIAIVTEILSPS-DKLISIPCYQWEYVIIVPLDH 176 (306)
Q Consensus 127 ~~~~~~~~~~~l~~~~~Di~i~~~~~~~~-~~~~~~~l~~~~~~~v~~~~~ 176 (306)
...+..++...+.+|.+|++++....... .++.+.|+..+++.++++++.
T Consensus 129 ~~~th~~vA~aVa~G~AD~G~g~~~~A~~~~gL~Fvpl~~E~~dlv~~~~~ 179 (193)
T PF12727_consen 129 EANTHLAVAAAVASGKADAGIGIRAAAEEFYGLDFVPLAEERYDLVIRRED 179 (193)
T ss_pred cccChHHHHHHHHcCCCCEEeehHHHHHhhcCCCcEEccccceEEEEEhhH
Confidence 34456688999999999999997553434 699999999999999999876
No 382
>TIGR02684 dnstrm_HI1420 probable addiction module antidote protein. gene pairs, when found on the bacterial chromosome, are located often with prophage regions, but also both in integrated plasmid regions and in housekeeping gene regions. Analysis suggests that the gene pair may serve as an addiction module.
Probab=87.09 E-value=1.2 Score=29.14 Aligned_cols=30 Identities=20% Similarity=0.187 Sum_probs=26.0
Q ss_pred HHHHHHHHhcCCHHHHHHHhCCCchHHHHHH
Q psy3760 7 RFVREAVRQNFNLTEAAKALYTSQPGVSKAI 37 (306)
Q Consensus 7 ~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i 37 (306)
..+..+.+.. .+++.|+..|||++++++..
T Consensus 35 ~~l~~~r~~~-glSqLAe~~GIs~stLs~iE 64 (89)
T TIGR02684 35 HALGYIARAR-GMTQLARKTGLSRESLYKAL 64 (89)
T ss_pred HHHHHHHHHC-ChHHHHHHHCCCHHHHHHHH
Confidence 4567888898 99999999999999999753
No 383
>PRK10651 transcriptional regulator NarL; Provisional
Probab=87.01 E-value=1.6 Score=33.37 Aligned_cols=43 Identities=7% Similarity=0.060 Sum_probs=38.2
Q ss_pred hhhHHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCc
Q psy3760 3 LHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSI 46 (306)
Q Consensus 3 ~~~l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~ 46 (306)
-+..++|..+++.. +-..-|+.|++|..||..++++|-..||.
T Consensus 158 ~rE~~vl~~l~~g~-~~~~ia~~l~is~~tV~~~~~~l~~Kl~~ 200 (216)
T PRK10651 158 PRERDILKLIAQGL-PNKMIARRLDITESTVKVHVKHMLKKMKL 200 (216)
T ss_pred HHHHHHHHHHHcCC-CHHHHHHHcCCCHHHHHHHHHHHHHHcCC
Confidence 46677888888776 99999999999999999999999999986
No 384
>PF13309 HTH_22: HTH domain
Probab=86.93 E-value=0.37 Score=29.21 Aligned_cols=20 Identities=20% Similarity=0.154 Sum_probs=18.0
Q ss_pred CHHHHHHHhCCCchHHHHHH
Q psy3760 18 NLTEAAKALYTSQPGVSKAI 37 (306)
Q Consensus 18 s~~~aA~~l~isq~~~s~~i 37 (306)
+...+|+.||+|.+||-+-|
T Consensus 44 av~~vA~~L~iS~~TVY~YL 63 (64)
T PF13309_consen 44 AVEYVAEKLGISRATVYRYL 63 (64)
T ss_pred HHHHHHHHHCCCHHHHHHHc
Confidence 77899999999999998765
No 385
>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=86.88 E-value=3.5 Score=25.06 Aligned_cols=53 Identities=15% Similarity=0.056 Sum_probs=31.9
Q ss_pred CCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCCccccCHhHHHHHHHHHHH
Q psy3760 17 FNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKPGQAILRSIEII 73 (306)
Q Consensus 17 ~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~~~lT~~G~~l~~~a~~i 73 (306)
+|+..+|+.+|+|++++.+..++ .|..--.|+.+|.-..|+.=-.-+..++.+
T Consensus 1 ~s~~eva~~~gvs~~tlr~w~~~----~g~~~~~r~~~~~r~yt~~~v~~l~~i~~l 53 (68)
T cd01104 1 YTIGAVARLTGVSPDTLRAWERR----YGLPAPQRTDGGHRLYSEADVARLRLIRRL 53 (68)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHh----CCCCCCCcCCCCCeecCHHHHHHHHHHHHH
Confidence 47889999999999999986543 344333454333214566544444444433
No 386
>COG1458 Predicted DNA-binding protein containing PIN domain [General function prediction only]
Probab=86.82 E-value=1 Score=33.61 Aligned_cols=93 Identities=16% Similarity=0.226 Sum_probs=65.5
Q ss_pred hCCCchHHHHHHHHHHHHcCce----------eEEecCCCccccCHhHHHHHHHHHHHHHHHHHHHHHHHhhccCCCC-c
Q psy3760 26 LYTSQPGVSKAIIELEEELSID----------IFIRHGKRIRGLTKPGQAILRSIEIIMQEIEGLKKIGKEFSAYDTG-N 94 (306)
Q Consensus 26 l~isq~~~s~~i~~LE~~lg~~----------Lf~R~~~~~~~lT~~G~~l~~~a~~il~~~~~~~~~~~~~~~~~~~-~ 94 (306)
.+|. |++-+-+...=+.-|++ +..+.++.. +++-.+..||++++.+-+.+++-.......--.... .
T Consensus 49 cyiP-PsVY~El~~fm~r~gc~~e~~~ki~twivkKtPnry-evkiPa~ifyeyV~diR~RinkGlRvAE~~i~eA~~~~ 126 (221)
T COG1458 49 CYIP-PSVYRELMGFMERNGCPEEVIAKIETWIVKKTPNRY-EVKIPAAIFYEYVEDIRERINKGLRVAEEAIREASIEC 126 (221)
T ss_pred EEeC-hHHHHHHHHHHHhCCCcHHHHHhhheeeEecCCCce-eecCcHHHHHHHHHHHHHHHHhhhhhHHHHHHHHHHHH
Confidence 3455 88888888777766666 788888998 899999999999999999988776544433111111 0
Q ss_pred EEEEecccchhhhhHHHHHHHHHhCCC
Q psy3760 95 LTIATTHTQARYALPKIIKEFTIQFPK 121 (306)
Q Consensus 95 l~I~~~~~~~~~~l~~~l~~~~~~~p~ 121 (306)
..+- ...+....+..++..|++.|-.
T Consensus 127 ~~~~-~~~i~~e~igk~I~~lR~KYR~ 152 (221)
T COG1458 127 YELE-KEEIIREVVGKIIRKLREKYRE 152 (221)
T ss_pred HHhh-hhhHHHHHHHHHHHHHHHHHHH
Confidence 1111 3455677888899999888743
No 387
>PF01418 HTH_6: Helix-turn-helix domain, rpiR family; InterPro: IPR000281 This domain contains a helix-turn-helix motif []. Every member of this family is N-terminal to a SIS domain IPR001347 from INTERPRO. Members of this family are probably regulators of genes involved in phosphosugar metobolism.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 2O3F_B 3IWF_B.
Probab=86.53 E-value=0.56 Score=29.66 Aligned_cols=25 Identities=16% Similarity=0.090 Sum_probs=20.1
Q ss_pred hcCCHHHHHHHhCCCchHHHHHHHHH
Q psy3760 15 QNFNLTEAAKALYTSQPGVSKAIIEL 40 (306)
Q Consensus 15 ~~~s~~~aA~~l~isq~~~s~~i~~L 40 (306)
.- |++.-|+..|+|++||+|-.++|
T Consensus 34 ~~-si~elA~~~~vS~sti~Rf~kkL 58 (77)
T PF01418_consen 34 FM-SISELAEKAGVSPSTIVRFCKKL 58 (77)
T ss_dssp T---HHHHHHHCTS-HHHHHHHHHHC
T ss_pred Hc-cHHHHHHHcCCCHHHHHHHHHHh
Confidence 56 99999999999999999988875
No 388
>PRK13325 bifunctional biotin--[acetyl-CoA-carboxylase] ligase/pantothenate kinase; Reviewed
Probab=86.45 E-value=2 Score=39.00 Aligned_cols=50 Identities=8% Similarity=0.072 Sum_probs=36.6
Q ss_pred hHHHHHHHHHhcC-CHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCCc
Q psy3760 5 QFRFVREAVRQNF-NLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRI 56 (306)
Q Consensus 5 ~l~~f~~v~~~~~-s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~ 56 (306)
+...+..++.-+| |-..=|+.|++|.++|+++++.|+ ++|..++ .+++|.
T Consensus 8 ~~~ll~~L~dg~~hSge~l~~~lgisr~av~~~~~~~~-~~~~~i~-v~g~GY 58 (592)
T PRK13325 8 HWRVLAELADGLPQHVSQLARMADMKPQQLNGFWQQMP-AHIRGLL-RQHDGY 58 (592)
T ss_pred HHHHHHHHhCCCccCHHHHHHHhCCCHHHHHHHHHHHH-HhCcEEE-EcCCCh
Confidence 3444444554333 779999999999999999999999 5556776 455664
No 389
>COG1725 Predicted transcriptional regulators [Transcription]
Probab=86.35 E-value=6.6 Score=27.44 Aligned_cols=67 Identities=28% Similarity=0.326 Sum_probs=47.2
Q ss_pred hcCCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCCccccCHhHHHHHHHH--HHHHHHHHHHHHHHH
Q psy3760 15 QNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKPGQAILRSI--EIIMQEIEGLKKIGK 85 (306)
Q Consensus 15 ~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~~~lT~~G~~l~~~a--~~il~~~~~~~~~~~ 85 (306)
.- |...=|..+++.+-|++|.-+.||.+ | -++.+.|.|.+ .|+.|......- ..+-+.++.+...+.
T Consensus 35 LP-SvRelA~~~~VNpnTv~raY~eLE~e-G-~i~t~rg~G~f-V~~~~~~~~~~~~~~~~~~~l~~~I~~~~ 103 (125)
T COG1725 35 LP-SVRELAKDLGVNPNTVQRAYQELERE-G-IVETKRGKGTF-VTEDAKEILDQLKRELAEEELEEFIEEAK 103 (125)
T ss_pred CC-cHHHHHHHhCCCHHHHHHHHHHHHHC-C-CEEEecCeeEE-EcCCchhhHHHHHHHHHHHHHHHHHHHHH
Confidence 45 88999999999999999999999986 3 45666778884 998888644322 223333444444444
No 390
>PHA02943 hypothetical protein; Provisional
Probab=86.33 E-value=10 Score=27.33 Aligned_cols=52 Identities=15% Similarity=0.026 Sum_probs=39.8
Q ss_pred HHHHHhc-CCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCCccccCH
Q psy3760 10 REAVRQN-FNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTK 61 (306)
Q Consensus 10 ~~v~~~~-~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~~~lT~ 61 (306)
+++.+.| .|.++-|+.||+|.+.+...|.-||.+=-++=..|+...++.+.+
T Consensus 17 LE~Lk~G~~TtseIAkaLGlS~~qa~~~LyvLErEG~VkrV~~G~~tyw~l~~ 69 (165)
T PHA02943 17 LRLLADGCKTTSRIANKLGVSHSMARNALYQLAKEGMVLKVEIGRAAIWCLDE 69 (165)
T ss_pred HHHHhcCCccHHHHHHHHCCCHHHHHHHHHHHHHcCceEEEeecceEEEEECh
Confidence 3333444 267899999999999999999999998666666666666656777
No 391
>PRK13583 hisG ATP phosphoribosyltransferase catalytic subunit; Provisional
Probab=86.29 E-value=14 Score=28.94 Aligned_cols=148 Identities=11% Similarity=0.033 Sum_probs=78.6
Q ss_pred EEEEeCChhHHHHHHHcCCeeEEEEccccCCCC---------CceeeccccceEEEEecCCCCCCCCCCcChhhhcCCCe
Q psy3760 124 LSLLQGNPKQITEMIRNDQADIAIVTEILSPSD---------KLISIPCYQWEYVIIVPLDHPLLLLNSISLKEISNYPL 194 (306)
Q Consensus 124 i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~~~---------~~~~~~l~~~~~~~v~~~~~~l~~~~~i~~~dl~~~~~ 194 (306)
+++.-.-..++...+..|.+|+||+........ .+.-..++.-++++++|+++. ..-+++||.+...
T Consensus 47 i~~~~vR~~DIp~yV~~G~~DlGI~G~D~l~E~~~~~~~~v~elldLgfG~crl~vA~p~~~~----~~~~~~dl~~~~~ 122 (228)
T PRK13583 47 VELLFLSASEIPRELGAGRVDLGVTGEDLVREKLADWDKRVEIVARLGFGHADLVVAVPEIWI----DVDTMADLDDVAA 122 (228)
T ss_pred eEEEEECHHHHHHHHhCCCCcEEEeeeeeeecccccCCCCeEEEecCCCCceEEEEEEECccc----ccCCHHHhhhhhh
Confidence 444444567899999999999999853222211 122334567788999987743 1235666652221
Q ss_pred Ee-------ecCCCCcHHHHHHHHHhCCCce-eEEEEecCHHHHHHHHHhccceeeeecce-ecccccCCceeeecCCCC
Q psy3760 195 IT-------YDLSFSGRIKLDREFSLQKLTP-YIVLETINSDIIKTYVELRMGIGIIASIA-FDSNRDKNLRSISASHLF 265 (306)
Q Consensus 195 i~-------~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~v~~g~gi~~~p~~~-~~~~~~~~l~~~~~~~~~ 265 (306)
.. ..-...+.+...++|.+.|+.. .++....+.+.+ ..-|.+=+++--.. -..++..+|+.+.-.. .
T Consensus 123 ~~~~~~g~~~RIATkYp~it~~yf~~~Gv~~~~Iv~l~GsvEla---P~~GlAD~IvDivsTG~TLr~NgL~~i~~~~-I 198 (228)
T PRK13583 123 DFRARHGRRLRIATKYWRLTQQFLSQKGVQDYRIVESLGATEGA---PANGSAEIIVDITSTGETLRANHLKILSDGV-I 198 (228)
T ss_pred hhhhccCCceEEEeCCHHHHHHHHHHcCCceeEEEECCCceecc---cccCcchhhhhhhchhHHHHHCCCEEecCce-E
Confidence 10 0011124467788999999884 665544555432 11121111111100 0112345677664111 3
Q ss_pred ccceEEEEEeCCcc
Q psy3760 266 GTTISRVIIKQGTY 279 (306)
Q Consensus 266 ~~~~~~l~~~~~~~ 279 (306)
...+..++.++...
T Consensus 199 l~SsA~LI~n~~s~ 212 (228)
T PRK13583 199 LRSQACLVRARKAD 212 (228)
T ss_pred EEEEEEEEEecccc
Confidence 34577888877753
No 392
>PF02042 RWP-RK: RWP-RK domain; InterPro: IPR003035 This domain is named RWP-RK after a conserved motif at the C terminus of the domain. The domain is found in algal minus dominance proteins as well as plant proteins involved in nitrogen-controlled development [].
Probab=86.21 E-value=1 Score=25.85 Aligned_cols=22 Identities=27% Similarity=0.217 Sum_probs=19.0
Q ss_pred CHHHHHHHhCCCchHHHHHHHH
Q psy3760 18 NLTEAAKALYTSQPGVSKAIIE 39 (306)
Q Consensus 18 s~~~aA~~l~isq~~~s~~i~~ 39 (306)
.+..||+.|||+.+++-+.-++
T Consensus 17 p~~eAA~~Lgv~~T~LKr~CR~ 38 (52)
T PF02042_consen 17 PIKEAAKELGVSVTTLKRRCRR 38 (52)
T ss_pred CHHHHHHHhCCCHHHHHHHHHH
Confidence 7899999999999888777663
No 393
>PF02376 CUT: CUT domain; InterPro: IPR003350 A class, also called ONECUT, of homeodomain proteins. The CUT domain is a DNA-binding motif which can bind independently or in cooperation with the homeodomain (IPR001356 from INTERPRO), often found downstream of the CUT domain. Proteins display two modes of DNA binding, which hinge on the homeodomain and on the linker that separates it from the cut domain, and two modes of transcriptional stimulation, which hinge on the homeodomain [].; GO: 0003677 DNA binding; PDB: 1WH6_A 2D5V_A 2CSF_A 1X2L_A 2O49_A 2O4A_A 1YSE_A 1S7E_A 1WIZ_A 1WH8_A.
Probab=86.16 E-value=1.2 Score=28.90 Aligned_cols=49 Identities=20% Similarity=0.067 Sum_probs=39.0
Q ss_pred HHHHhCCCchHHHHHHHHHHHHcCceeEEecCCCccccCHhHHHHHHHHHHHHHHHHHHHHH
Q psy3760 22 AAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKPGQAILRSIEIIMQEIEGLKKI 83 (306)
Q Consensus 22 aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~~~lT~~G~~l~~~a~~il~~~~~~~~~ 83 (306)
|...||.||.++|.-++ .++..-.||+.|+..|......++.-+.....
T Consensus 33 a~~vL~rsqgtlsdlL~-------------~PKpW~~L~~~gre~y~RM~nWL~~~e~~r~~ 81 (87)
T PF02376_consen 33 AKKVLNRSQGTLSDLLR-------------KPKPWNKLKPKGREPYIRMYNWLSLPEEERME 81 (87)
T ss_dssp HHHTTSS-HHHHHHHHH-------------SCCTTCHHHHHHHHHHHHHHHHHCSTHHHHHH
T ss_pred HHHHhccChhHHHHHhC-------------CCCCHHHcCccccHHHHHHHHHhcCCHHHHHH
Confidence 57889999999998877 55665479999999999999998876665543
No 394
>TIGR02277 PaaX_trns_reg phenylacetic acid degradation operon negative regulatory protein PaaX. This transcriptional regulator is always found in association with operons believed to be involved in the degradation of phenylacetic acid. The gene product has been shown to bind to the promoter sites and repress their transcription.
Probab=85.96 E-value=1.9 Score=35.06 Aligned_cols=78 Identities=13% Similarity=0.036 Sum_probs=51.9
Q ss_pred hcCCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCCccccCHhHHHHHHHHHHHHHHHHHHHHHHHhhccCCCCc
Q psy3760 15 QNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKPGQAILRSIEIIMQEIEGLKKIGKEFSAYDTGN 94 (306)
Q Consensus 15 ~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~~~lT~~G~~l~~~a~~il~~~~~~~~~~~~~~~~~~~~ 94 (306)
.+ ++-+..+.++|+.+++--.+++|+++==..=-.+.+++..+||+.|+..+..+.+-+-. .-...-.|.
T Consensus 20 ~~-~Li~l~~~~gi~~~~vr~al~RL~~~G~l~~~~~grr~~Y~LT~~g~~~l~~~~~rIy~---------~~~~~WdG~ 89 (280)
T TIGR02277 20 LG-SLIEFLAGLGINERLVRTAVSRLVAQGWLQSERKGRRSFYSLTDKGRRRFAAAAQRIYD---------PPAPAWDGK 89 (280)
T ss_pred HH-HHHHHHHhcCCCcchHHHHHHHHHHCCCEEeeecCCCCEEEECHHHHHHHHHHhhhhcC---------CCCCCCCCc
Confidence 46 78899999999999999999999986322222222233348999999888775544321 112334667
Q ss_pred EEEEeccc
Q psy3760 95 LTIATTHT 102 (306)
Q Consensus 95 l~I~~~~~ 102 (306)
..+.+...
T Consensus 90 W~lv~~~~ 97 (280)
T TIGR02277 90 WRLLLLSG 97 (280)
T ss_pred eEEEEeCC
Confidence 77766543
No 395
>cd04761 HTH_MerR-SF Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily. Helix-turn-helix (HTH) transcription regulator MerR superfamily, N-terminal domain. The MerR family transcription regulators have been shown to mediate responses to stress including exposure to heavy metals, drugs, or oxygen radicals in eubacterial and some archaeal species. They regulate transcription of multidrug/metal ion transporter genes and oxidative stress regulons by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=85.81 E-value=0.88 Score=25.56 Aligned_cols=21 Identities=19% Similarity=0.077 Sum_probs=18.1
Q ss_pred CCHHHHHHHhCCCchHHHHHH
Q psy3760 17 FNLTEAAKALYTSQPGVSKAI 37 (306)
Q Consensus 17 ~s~~~aA~~l~isq~~~s~~i 37 (306)
+|.+++|+.+|+|.++|.+.+
T Consensus 1 ~~~~e~a~~~gv~~~tlr~~~ 21 (49)
T cd04761 1 YTIGELAKLTGVSPSTLRYYE 21 (49)
T ss_pred CcHHHHHHHHCcCHHHHHHHH
Confidence 478999999999999988664
No 396
>PRK09492 treR trehalose repressor; Provisional
Probab=85.66 E-value=8.4 Score=31.79 Aligned_cols=21 Identities=14% Similarity=0.203 Sum_probs=19.6
Q ss_pred CHHHHHHHhCCCchHHHHHHH
Q psy3760 18 NLTEAAKALYTSQPGVSKAII 38 (306)
Q Consensus 18 s~~~aA~~l~isq~~~s~~i~ 38 (306)
++..-|+..|+|++||||.|.
T Consensus 6 ti~dIA~~agVS~~TVSrvLn 26 (315)
T PRK09492 6 TIKDIARLSGVGKSTVSRVLN 26 (315)
T ss_pred cHHHHHHHhCCCHHHHhHHhC
Confidence 788999999999999999984
No 397
>PRK12423 LexA repressor; Provisional
Probab=85.51 E-value=2.4 Score=32.63 Aligned_cols=41 Identities=20% Similarity=0.143 Sum_probs=32.8
Q ss_pred chhhHHHHHHHHH-------hcCCHHHHHHHhC-CCchHHHHHHHHHHHH
Q psy3760 2 NLHQFRFVREAVR-------QNFNLTEAAKALY-TSQPGVSKAIIELEEE 43 (306)
Q Consensus 2 ~~~~l~~f~~v~~-------~~~s~~~aA~~l~-isq~~~s~~i~~LE~~ 43 (306)
+-++-+++..+.+ .. |..+-|+.+| +|+++++++|+.|++.
T Consensus 5 t~~q~~il~~l~~~i~~~g~~P-s~~eia~~~g~~s~~~v~~~l~~L~~~ 53 (202)
T PRK12423 5 TPKRAAILAFIRERIAQAGQPP-SLAEIAQAFGFASRSVARKHVQALAEA 53 (202)
T ss_pred CHHHHHHHHHHHHHHHHcCCCC-CHHHHHHHhCCCChHHHHHHHHHHHHC
Confidence 3455666666665 35 8999999999 5999999999999984
No 398
>TIGR02944 suf_reg_Xantho FeS assembly SUF system regulator, gammaproteobacterial. The SUF system is an oxygen-resistant iron-sulfur cluster assembly system found in both aerobes and facultative anaerobes. Its presence appears to be a marker of oxygen tolerance; strict anaerobes and microaerophiles tend to have different FeS cluster biosynthesis systems. Members of this protein family belong to the rrf2 family of transcriptional regulators and are found, typically, as the first gene of a SUF operon. It is found only in a subset of genomes that encode the SUF system, including the genus Xanthomonas. The conserved location suggests an autoregulatory role.
Probab=85.10 E-value=2.2 Score=30.10 Aligned_cols=37 Identities=19% Similarity=0.222 Sum_probs=29.6
Q ss_pred HHHHHHHHHhc---CCHHHHHHHhCCCchHHHHHHHHHHH
Q psy3760 6 FRFVREAVRQN---FNLTEAAKALYTSQPGVSKAIIELEE 42 (306)
Q Consensus 6 l~~f~~v~~~~---~s~~~aA~~l~isq~~~s~~i~~LE~ 42 (306)
++.+..+++.+ -|...-|+.+++|++++++.++.|++
T Consensus 12 l~~l~~la~~~~~~~s~~eia~~l~is~~~v~~~l~~L~~ 51 (130)
T TIGR02944 12 TLVLTTLAQNDSQPYSAAEIAEQTGLNAPTVSKILKQLSL 51 (130)
T ss_pred HHHHHHHHhCCCCCccHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 44555555432 37888999999999999999999998
No 399
>COG3877 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=85.05 E-value=5 Score=26.64 Aligned_cols=46 Identities=26% Similarity=0.285 Sum_probs=35.9
Q ss_pred chhhHHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCce
Q psy3760 2 NLHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSID 47 (306)
Q Consensus 2 ~~~~l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~ 47 (306)
+-++|+......++++|+...-+.||+|.||+.-.+.++=..+|..
T Consensus 43 t~d~LeFv~lf~r~RGnlKEvEr~lg~sYptvR~kld~vlramgy~ 88 (122)
T COG3877 43 TSDQLEFVELFLRCRGNLKEVERELGISYPTVRTKLDEVLRAMGYN 88 (122)
T ss_pred CHhHhHHHHHHHHHccCHHHHHHHHCCccHHHHHHHHHHHHHcCCC
Confidence 3456665555555545999999999999999999998888777753
No 400
>PRK15369 two component system sensor kinase SsrB; Provisional
Probab=84.98 E-value=2.4 Score=32.16 Aligned_cols=43 Identities=12% Similarity=0.119 Sum_probs=36.9
Q ss_pred hhhHHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCc
Q psy3760 3 LHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSI 46 (306)
Q Consensus 3 ~~~l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~ 46 (306)
.+..++|.-+++.. |....|+.+++|..|+..+++++-..+|+
T Consensus 152 ~~e~~vl~l~~~g~-~~~~Ia~~l~~s~~tv~~~~~~~~~kl~~ 194 (211)
T PRK15369 152 PRERQILKLITEGY-TNRDIAEQLSISIKTVETHRLNMMRKLDV 194 (211)
T ss_pred HHHHHHHHHHHCCC-CHHHHHHHhCCCHHHHHHHHHHHHHHhCC
Confidence 34566676677766 99999999999999999999999999985
No 401
>PRK10681 DNA-binding transcriptional repressor DeoR; Provisional
Probab=84.75 E-value=12 Score=29.93 Aligned_cols=38 Identities=16% Similarity=0.141 Sum_probs=28.7
Q ss_pred hHHHHHHHHHhcC-CHHHHHHHhCCCchHHHHHHHHHHH
Q psy3760 5 QFRFVREAVRQNF-NLTEAAKALYTSQPGVSKAIIELEE 42 (306)
Q Consensus 5 ~l~~f~~v~~~~~-s~~~aA~~l~isq~~~s~~i~~LE~ 42 (306)
+-++.-.+.+.|+ +...-|+.+++|..|+-|=|+.||+
T Consensus 9 ~~~I~~~l~~~~~v~v~eLa~~~~VS~~TIRRDL~~Le~ 47 (252)
T PRK10681 9 IGQLLQALKRSDKLHLKDAAALLGVSEMTIRRDLNAHSA 47 (252)
T ss_pred HHHHHHHHHHcCCCcHHHHHHHhCCCHHHHHHHHHHhhc
Confidence 3344444444441 6788999999999999999999995
No 402
>PF13545 HTH_Crp_2: Crp-like helix-turn-helix domain; PDB: 3LA2_A 3LA3_B 3LA7_A 3B02_A 3E97_A 2H6C_B 1OMI_A 2BGC_H 2BEO_A 2GAU_A ....
Probab=84.74 E-value=1.5 Score=27.36 Aligned_cols=41 Identities=27% Similarity=0.300 Sum_probs=32.4
Q ss_pred CHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCCccccCHh
Q psy3760 18 NLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKP 62 (306)
Q Consensus 18 s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~~~lT~~ 62 (306)
|-..-|..+|+|..++++.+++|+++ -++..+++.+ .+++.
T Consensus 30 t~~~iA~~~g~sr~tv~r~l~~l~~~---g~I~~~~~~i-~I~d~ 70 (76)
T PF13545_consen 30 TQEEIADMLGVSRETVSRILKRLKDE---GIIEVKRGKI-IILDP 70 (76)
T ss_dssp SHHHHHHHHTSCHHHHHHHHHHHHHT---TSEEEETTEE-EESSH
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHC---CCEEEcCCEE-EECCH
Confidence 56778999999999999999999986 3566666776 45543
No 403
>PF01316 Arg_repressor: Arginine repressor, DNA binding domain; InterPro: IPR020900 The arginine dihydrolase (AD) pathway is found in many prokaryotes and some primitive eukaryotes, an example of the latter being Giardia lamblia (Giardia intestinalis) []. 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 10% of 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 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0006525 arginine metabolic process; PDB: 1AOY_A 3V4G_A 3LAJ_D 3FHZ_A 3LAP_B 3ERE_D 2P5L_C 1F9N_D 2P5K_A 1B4A_A ....
Probab=84.68 E-value=1.6 Score=27.03 Aligned_cols=17 Identities=24% Similarity=0.368 Sum_probs=11.9
Q ss_pred hCCCchHHHHHHHHHHH
Q psy3760 26 LYTSQPGVSKAIIELEE 42 (306)
Q Consensus 26 l~isq~~~s~~i~~LE~ 42 (306)
..+||+||||-|++|..
T Consensus 34 i~vTQaTiSRDLkeL~~ 50 (70)
T PF01316_consen 34 IEVTQATISRDLKELGA 50 (70)
T ss_dssp -T--HHHHHHHHHHHT-
T ss_pred CCcchhHHHHHHHHcCc
Confidence 57999999999998853
No 404
>PRK09333 30S ribosomal protein S19e; Provisional
Probab=84.65 E-value=2.4 Score=30.53 Aligned_cols=40 Identities=20% Similarity=0.283 Sum_probs=31.9
Q ss_pred CchHHHHHHHHHHHHcCceeEEecCCCccccCHhHHHHHHHHHH
Q psy3760 29 SQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKPGQAILRSIEI 72 (306)
Q Consensus 29 sq~~~s~~i~~LE~~lg~~Lf~R~~~~~~~lT~~G~~l~~~a~~ 72 (306)
|-+-+-+.|++||+ ..|++.+.+|- .+|+.|+.++.....
T Consensus 94 sg~iiR~~LqqLE~---~glVek~~~GR-~lT~~G~~~LD~iA~ 133 (150)
T PRK09333 94 SGSIIRKILQQLEK---AGLVEKTKKGR-VITPKGRSLLDNLAA 133 (150)
T ss_pred ccHHHHHHHHHHHH---CCCeeeCCCCC-EeCHHHHHHHHHHHH
Confidence 34558899999997 46788888888 699999999887653
No 405
>COG3388 Predicted transcriptional regulator [Transcription]
Probab=84.53 E-value=7.5 Score=25.28 Aligned_cols=68 Identities=13% Similarity=0.134 Sum_probs=53.8
Q ss_pred hhHHHHHHHHHhcCCH--HHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCCccccCHhHHHHHHHHHHHHHH
Q psy3760 4 HQFRFVREAVRQNFNL--TEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKPGQAILRSIEIIMQE 76 (306)
Q Consensus 4 ~~l~~f~~v~~~~~s~--~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~~~lT~~G~~l~~~a~~il~~ 76 (306)
+++.++-.|++.+ -+ -+-|...||.---+.++++-||++ -+..-+..|.+ +|+++-.+.+....=++.
T Consensus 15 RHl~Vl~~v~eeq-PiGI~klS~~TGmp~HKVRYSLRVLEq~---~iI~PS~~GAi-~td~~~e~ie~i~~dl~e 84 (101)
T COG3388 15 RHLSVLKVVLEEQ-PIGIIKLSDETGMPEHKVRYSLRVLEQE---NIISPSRQGAI-LTDDFPEFIEEIIGDLSE 84 (101)
T ss_pred HHHHHHHHHHHhC-CceeEeechhcCCchhhhhhhhhhhhhc---CccCccccCCc-cCccHHHHHHHHHHHHHH
Confidence 6788888899887 65 478899999999999999999985 46677788885 999987777655443333
No 406
>PRK10403 transcriptional regulator NarP; Provisional
Probab=84.47 E-value=2.6 Score=32.19 Aligned_cols=44 Identities=18% Similarity=0.188 Sum_probs=38.4
Q ss_pred chhhHHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCc
Q psy3760 2 NLHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSI 46 (306)
Q Consensus 2 ~~~~l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~ 46 (306)
+-+..+++..+++.- |-..-|+.+++|..||..+++++-+.+|+
T Consensus 155 t~~e~~vl~~~~~g~-s~~~ia~~l~~s~~tv~~~~~~i~~kl~~ 198 (215)
T PRK10403 155 TERELDVLHELAQGL-SNKQIASVLNISEQTVKVHIRNLLRKLNV 198 (215)
T ss_pred CHHHHHHHHHHHCCC-CHHHHHHHcCCCHHHHHHHHHHHHHHcCC
Confidence 446677788888776 99999999999999999999999999875
No 407
>smart00094 TR_FER Transferrin.
Probab=84.44 E-value=21 Score=29.98 Aligned_cols=75 Identities=9% Similarity=0.118 Sum_probs=44.0
Q ss_pred CcEEEEEe-CChhHHHHHHHcCCeeEEEEccccC--CCCCceeecccc------------ceEEEEecCCCCCCCCCCcC
Q psy3760 121 KVKLSLLQ-GNPKQITEMIRNDQADIAIVTEILS--PSDKLISIPCYQ------------WEYVIIVPLDHPLLLLNSIS 185 (306)
Q Consensus 121 ~~~i~~~~-~~~~~~~~~l~~~~~Di~i~~~~~~--~~~~~~~~~l~~------------~~~~~v~~~~~~l~~~~~i~ 185 (306)
...++++. .+..+.++.+.+|++|+++...... ........++.. ..-++|+.++.+ ..+
T Consensus 26 ~~~v~Cv~~~s~~~Ci~~I~~g~AD~a~ldg~~~y~A~~~~~l~pi~~E~~~~~~~~~~~Y~aVaVVkk~S~-----i~s 100 (332)
T smart00094 26 VPALECVSASSTEECIKAIQKGEADAVTLDGGDVYTAGKPYNLVPVFAENYGSEEEPETGYYAVAVVKKGSA-----IFT 100 (332)
T ss_pred CCceEEEEcCCHHHHHHHHHCCCCCEEEECcHHHHhhcccCCceEEEEEeeccCCCCCceeEEEEEEECCCC-----CCC
Confidence 34555554 3567899999999999999731111 111111222221 123566666654 367
Q ss_pred hhhhcCCCeEeecCC
Q psy3760 186 LKEISNYPLITYDLS 200 (306)
Q Consensus 186 ~~dl~~~~~i~~~~~ 200 (306)
++||.+...-....+
T Consensus 101 l~dLkGKksChtg~~ 115 (332)
T smart00094 101 WNQLRGKKSCHTGVG 115 (332)
T ss_pred HHHhCCCceecCCCC
Confidence 889988776665554
No 408
>PF14502 HTH_41: Helix-turn-helix domain
Probab=84.35 E-value=3.5 Score=23.14 Aligned_cols=38 Identities=21% Similarity=0.174 Sum_probs=33.3
Q ss_pred CHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCC
Q psy3760 18 NLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKR 55 (306)
Q Consensus 18 s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~ 55 (306)
+++.=|+++++|..+|-.+|+-||+.=-+.|-.|...|
T Consensus 8 tI~e~~~~~~vs~GtiQ~Alk~Le~~gaI~Le~rGh~G 45 (48)
T PF14502_consen 8 TISEYSEKFGVSRGTIQNALKFLEENGAIKLESRGHLG 45 (48)
T ss_pred CHHHHHHHhCcchhHHHHHHHHHHHCCcEEeeecCcCc
Confidence 78888999999999999999999999888886666555
No 409
>COG2197 CitB Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]
Probab=84.19 E-value=3 Score=32.41 Aligned_cols=45 Identities=16% Similarity=0.178 Sum_probs=39.0
Q ss_pred chhhHHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCce
Q psy3760 2 NLHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSID 47 (306)
Q Consensus 2 ~~~~l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~ 47 (306)
+-+..+++..+++-. |-..-|++|++|..||+.+++++=..||+.
T Consensus 150 T~RE~eVL~lla~G~-snkeIA~~L~iS~~TVk~h~~~i~~KL~v~ 194 (211)
T COG2197 150 TPRELEVLRLLAEGL-SNKEIAEELNLSEKTVKTHVSNILRKLGVR 194 (211)
T ss_pred CHHHHHHHHHHHCCC-CHHHHHHHHCCCHhHHHHHHHHHHHHcCCC
Confidence 346777888888765 999999999999999999999999988863
No 410
>COG1510 Predicted transcriptional regulators [Transcription]
Probab=84.14 E-value=1.3 Score=32.43 Aligned_cols=35 Identities=29% Similarity=0.297 Sum_probs=28.2
Q ss_pred CHHHHHHHhCCCchHHHHHHHHHHHHc-CceeEEec
Q psy3760 18 NLTEAAKALYTSQPGVSKAIIELEEEL-SIDIFIRH 52 (306)
Q Consensus 18 s~~~aA~~l~isq~~~s~~i~~LE~~l-g~~Lf~R~ 52 (306)
+++.-++.+|+|.|.+|..+++|++.= =.+-|.++
T Consensus 43 tl~Ei~E~lg~Sks~vS~~lkkL~~~~lV~~~~~~G 78 (177)
T COG1510 43 TLDEIAEALGMSKSNVSMGLKKLQDWNLVKKVFEKG 78 (177)
T ss_pred cHHHHHHHHCCCcchHHHHHHHHHhcchHHhhhccC
Confidence 778899999999999999999999753 33445553
No 411
>PF09012 FeoC: FeoC like transcriptional regulator; InterPro: IPR015102 This entry contains several transcriptional regulators, including FeoC, which contain a HTH motif. FeoC acts as a [Fe-S] dependent transcriptional repressor []. ; PDB: 1XN7_A 2K02_A.
Probab=83.80 E-value=1.7 Score=26.73 Aligned_cols=39 Identities=21% Similarity=0.172 Sum_probs=30.2
Q ss_pred hhhHHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHH
Q psy3760 3 LHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEE 42 (306)
Q Consensus 3 ~~~l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~ 42 (306)
|.+|+-++.--..= |+..-|+++++|+++|...|..|+.
T Consensus 2 L~~i~~~l~~~~~~-S~~eLa~~~~~s~~~ve~mL~~l~~ 40 (69)
T PF09012_consen 2 LQEIRDYLRERGRV-SLAELAREFGISPEAVEAMLEQLIR 40 (69)
T ss_dssp CHHHHHHHHHS-SE-EHHHHHHHTT--HHHHHHHHHHHHC
T ss_pred HHHHHHHHHHcCCc-CHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 45666677766666 8999999999999999999999985
No 412
>PRK13182 racA polar chromosome segregation protein; Reviewed
Probab=83.65 E-value=3.4 Score=30.89 Aligned_cols=54 Identities=17% Similarity=0.119 Sum_probs=40.8
Q ss_pred CHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCCccccCHhHHHHHHHHHHHHHH
Q psy3760 18 NLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKPGQAILRSIEIIMQE 76 (306)
Q Consensus 18 s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~~~lT~~G~~l~~~a~~il~~ 76 (306)
+++.+|+.+|+|.+||.+..+ ..|.+ +.|+.+|.-.-|+.--..+...+.+.+.
T Consensus 2 ti~evA~~lGVS~~TLRrw~k----~g~L~-~~R~~~G~R~y~~~dl~~L~~I~~l~~~ 55 (175)
T PRK13182 2 KTPFVAKKLGVSPKTVQRWVK----QLNLP-CEKNEYGHYIFTEEDLQLLEYVKSQIEE 55 (175)
T ss_pred CHHHHHHHHCcCHHHHHHHHH----cCCCC-CCcCCCCCEEECHHHHHHHHHHHHHHHc
Confidence 688999999999999876655 56677 5887555325788877777777777664
No 413
>COG4588 AcfC Accessory colonization factor AcfC, contains ABC-type periplasmic domain [General function prediction only]
Probab=83.57 E-value=18 Score=27.71 Aligned_cols=198 Identities=13% Similarity=0.061 Sum_probs=117.0
Q ss_pred CCCCcEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEcccc----------CCCCCce
Q psy3760 90 YDTGNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEIL----------SPSDKLI 159 (306)
Q Consensus 90 ~~~~~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~----------~~~~~~~ 159 (306)
.....|++..+.+. ...+..+...|.+. -+..+.+..++.. ....=..+++|+.++.... ..-....
T Consensus 18 ~~~adinlYGpGGP-htaL~~vA~~~~ek-tg~kVnvt~GPq~-tW~~kAkknADilfgaseqsalaia~~~~~~fs~~~ 94 (252)
T COG4588 18 AANADINLYGPGGP-HTALKDVAKKYEEK-TGIKVNVTAGPQA-TWNEKAKKNADILFGASEQSALAIAEDHKDSFSEKN 94 (252)
T ss_pred hhcceEEEecCCCC-cHHHHHHHHHHHHH-hCeEEEEecCCcc-hhhhhhhccCceeecccHHHHHHHHHhccccccccc
Confidence 34567888888774 44566666666654 5777777776553 3445567789999985211 1112334
Q ss_pred eeccccceEEEEecCCCCCCCCCCcChhhhcCCC--eEeecCCCC-----cHHHHHHHHHh-------CCCceeEEEEec
Q psy3760 160 SIPCYQWEYVIIVPLDHPLLLLNSISLKEISNYP--LITYDLSFS-----GRIKLDREFSL-------QKLTPYIVLETI 225 (306)
Q Consensus 160 ~~~l~~~~~~~v~~~~~~l~~~~~i~~~dl~~~~--~i~~~~~~~-----~~~~~~~~~~~-------~~~~~~~~~~~~ 225 (306)
..||+--+-.+++.+++|. ..-.++||.... .+.. ++.+ -...|+...-+ ..++-|++....
T Consensus 95 i~ply~R~aiIlvkkgNPk---nIk~~eDll~~gi~ivV~-dGaG~sntsgtgvwED~agr~~~ie~v~afR~NI~~fap 170 (252)
T COG4588 95 IQPLYLRPAIILVKKGNPK---NIKGFEDLLKPGIGIVVN-DGAGVSNTSGTGVWEDIAGRKGNIETVAAFRKNIVAFAP 170 (252)
T ss_pred cceeeeeceEEEecCCCcc---ccccHHHHhcCCceEEEe-CCCcccCCCCceehHhhhcccccHHHHHHHHhceEEEcc
Confidence 5677766778889999984 445789987643 4443 3322 11122322211 133457888888
Q ss_pred CHHHHHHHHHhcc---ceeeeecceecccccCCceeeecCC-CCccceEEEEEeCCccccHHHHHHHHHHhHHhhHH
Q psy3760 226 NSDIIKTYVELRM---GIGIIASIAFDSNRDKNLRSISASH-LFGTTISRVIIKQGTYLRSYVYSFIKLLSPKLNRK 298 (306)
Q Consensus 226 ~~~~~~~~v~~g~---gi~~~p~~~~~~~~~~~l~~~~~~~-~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~ 298 (306)
+..+...+-.++. .+-.=+++....-..+.++ +++. ....+++.++..++ .++..+.|+++|++.=++.
T Consensus 171 nSgaArkaf~~~~~aDawItW~dWa~snpdig~~v--~~~~d~vIyRd~nv~~~~~--a~~ea~~F~dyl~S~EAq~ 243 (252)
T COG4588 171 NSGAARKAFENQPDADAWITWADWAKSNPDIGDAV--EIEKDYVIYRDFNVALAKD--ANKEARDFADYLQSDEAQK 243 (252)
T ss_pred CCchHHHHHhcCCCCceEEEecchhhhCCchhcee--ecccceEEeeecceeecCC--CCHHHHHHHHHHhhHHHHH
Confidence 8888888887753 3333334443221333333 4433 23455666666666 5899999999998654333
No 414
>COG3415 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=83.51 E-value=6 Score=28.25 Aligned_cols=54 Identities=24% Similarity=0.190 Sum_probs=40.3
Q ss_pred HHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEE--ecCCCccccCHh
Q psy3760 7 RFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFI--RHGKRIRGLTKP 62 (306)
Q Consensus 7 ~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~--R~~~~~~~lT~~ 62 (306)
.+|..+.-.|.|..+||+.+++|-+|+-+.+++.+++=.. |.- +.|+.- .+++.
T Consensus 12 ~~~~~~~~~G~S~re~Ak~~gvs~sTvy~wv~r~~e~G~~-l~~~~~~GrP~-kl~~~ 67 (138)
T COG3415 12 RVVDAVVGEGLSCREAAKRFGVSISTVYRWVRRYRETGLD-LPPKPRKGRPR-KLSEE 67 (138)
T ss_pred HHHHHHHHcCccHHHHHHHhCccHHHHHHHHHHhcccccc-ccCccCCCCCc-ccCHH
Confidence 4566665566699999999999999999999999986544 433 445554 56654
No 415
>COG2345 Predicted transcriptional regulator [Transcription]
Probab=83.51 E-value=9.6 Score=29.61 Aligned_cols=49 Identities=24% Similarity=0.297 Sum_probs=35.9
Q ss_pred CHHHHHHHhCCCchHHHHHHHHHHHHc--CceeEEecCCC----ccccCHhHHHHH
Q psy3760 18 NLTEAAKALYTSQPGVSKAIIELEEEL--SIDIFIRHGKR----IRGLTKPGQAIL 67 (306)
Q Consensus 18 s~~~aA~~l~isq~~~s~~i~~LE~~l--g~~Lf~R~~~~----~~~lT~~G~~l~ 67 (306)
|....|++|+||..++-++|..||++= ... +.+.|.| +++||..|...+
T Consensus 27 sa~elA~~Lgis~~avR~HL~~Le~~Glv~~~-~~~~g~GRP~~~y~Lt~~g~~~f 81 (218)
T COG2345 27 SADELAEELGISPMAVRRHLDDLEAEGLVEVE-RQQGGRGRPAKLYRLTEKGREQF 81 (218)
T ss_pred cHHHHHHHhCCCHHHHHHHHHHHHhCcceeee-eccCCCCCCceeeeecccchhhc
Confidence 778899999999999999999999873 333 3333222 137888887743
No 416
>PF13343 SBP_bac_6: Bacterial extracellular solute-binding protein; PDB: 2QRY_D 1XVX_A 1SI1_A 1SI0_A 1Q35_A 1Y9U_A 2OWS_A 2OWT_A 2VP1_A 2VOZ_A ....
Probab=83.43 E-value=10 Score=29.89 Aligned_cols=136 Identities=13% Similarity=-0.023 Sum_probs=79.6
Q ss_pred eeccccceEEEEecCCCCCCCC-CCcChhhhcCCC----eEeecCCCCcHHHHHHHHHh-CC----------CceeEEEE
Q psy3760 160 SIPCYQWEYVIIVPLDHPLLLL-NSISLKEISNYP----LITYDLSFSGRIKLDREFSL-QK----------LTPYIVLE 223 (306)
Q Consensus 160 ~~~l~~~~~~~v~~~~~~l~~~-~~i~~~dl~~~~----~i~~~~~~~~~~~~~~~~~~-~~----------~~~~~~~~ 223 (306)
+.++.-..++++..++-- ... -+.+|+||.+-. +...++.......+...+.. .| +..+.. .
T Consensus 49 ~~~~~~~~~~i~yN~~~~-~~~~~P~sw~dL~~p~~~g~i~~~~~~~~~~~~~~~~~~~~~g~~~~~~~l~~l~~n~~-~ 126 (242)
T PF13343_consen 49 WVPYGYGPVVIAYNTDKL-KERDLPTSWADLLDPKYKGKIALPDPNSDTGLAFLLALAEAYGEDAGWEWLRELKANGA-T 126 (242)
T ss_dssp SEEEEEEEEEEEEETTTS-SSGGTTSSGGGGGSGGGTTTEEEETTTSHHHHHHHHHHHHHHHHHHHHHHHHHHHHCBS-S
T ss_pred EEEEEEEEEEEEEEhhhc-CCCCCCccHHHHHHHHhCCCEEECCccHHHHHHHHHHHHHHhhHHHHHHHHHHHHhhcc-c
Confidence 447778888999988763 222 157999998643 44444432222211111111 00 001111 1
Q ss_pred ecCHHHHHHHHHhc-cceeeeecceeccc--ccC-CceeeecCCCCccceEEEEEeCCccccHHHHHHHHHHhHHhhHH
Q psy3760 224 TINSDIIKTYVELR-MGIGIIASIAFDSN--RDK-NLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLLSPKLNRK 298 (306)
Q Consensus 224 ~~~~~~~~~~v~~g-~gi~~~p~~~~~~~--~~~-~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~ 298 (306)
.. .....+.+..| ..+++.+.+..... ... .+..+...+.......++...++......++.|++++.+.-.+.
T Consensus 127 ~~-~~~~~~~~~~Ge~~~~i~~~~~~~~~~~~~~~~i~~v~P~eG~~~~~~~~~i~k~a~~~~~A~~fi~~lls~e~q~ 204 (242)
T PF13343_consen 127 FS-SSQAAQAVASGEGAVAIGISWYSRAAQAKEKGPIKFVYPEEGTVVWPDGIAIVKGAPNPEAAKKFINFLLSPEAQK 204 (242)
T ss_dssp SC-HHHHHHHHHTTSCSEEEEEHHHHHHHHHCTTTTEEEE-TTTGBEEEEEEEEEBTT-STHHHHHHHHHHHTSHHHHH
T ss_pred cc-chhhhhHhhCCCceEEEEEehHHHHHHhhhcCCeEEEecCCCcEEEEEEEEEeCCCCCHHHHHHHHHHHCCHHHHH
Confidence 11 77888899999 56677776555443 221 66666666645555667777888888999999999997654333
No 417
>PRK09958 DNA-binding transcriptional activator EvgA; Provisional
Probab=83.21 E-value=3.3 Score=31.44 Aligned_cols=43 Identities=19% Similarity=0.227 Sum_probs=37.6
Q ss_pred hhhHHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCc
Q psy3760 3 LHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSI 46 (306)
Q Consensus 3 ~~~l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~ 46 (306)
-+..+++..+++.. |...-|+.+++|..||..++++|.+.||.
T Consensus 146 ~~E~~vl~~l~~g~-~~~~I~~~l~~s~~tv~~~~~~l~~Kl~~ 188 (204)
T PRK09958 146 KQEISVMRYILDGK-DNNDIAEKMFISNKTVSTYKSRLMEKLEC 188 (204)
T ss_pred HHHHHHHHHHHcCC-CHHHHHHHhCCCHHHHHHHHHHHHHHcCC
Confidence 35566777778776 99999999999999999999999999984
No 418
>PF11972 HTH_13: HTH DNA binding domain; InterPro: IPR021068 The proteins in this entry have not been characterised. They contain a C-terminal helix-turn-helix DNA binding domain.
Probab=83.10 E-value=1.9 Score=24.89 Aligned_cols=25 Identities=24% Similarity=0.190 Sum_probs=21.6
Q ss_pred CHHHHHHHhCCCchHHHHHHHHHHH
Q psy3760 18 NLTEAAKALYTSQPGVSKAIIELEE 42 (306)
Q Consensus 18 s~~~aA~~l~isq~~~s~~i~~LE~ 42 (306)
|...+|++|++|+.+..+.|++|..
T Consensus 15 sa~mva~~L~vT~~~A~~li~eLg~ 39 (54)
T PF11972_consen 15 SAPMVAKELGVTPQAAQRLIAELGL 39 (54)
T ss_pred cHHHHHHHhCCCHHHHHHHHHHhhc
Confidence 6778999999999999999866554
No 419
>PF01710 HTH_Tnp_IS630: Transposase; InterPro: IPR002622 Transposase proteins are necessary for efficient DNA transposition. This entry includes insertion sequences from Synechocystis sp. (strain PCC 6803) three of which are characterised as homologous to bacterial IS5- and IS4- and to several members of the IS630-Tc1-mariner superfamily []. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=83.08 E-value=1.8 Score=30.11 Aligned_cols=34 Identities=21% Similarity=0.125 Sum_probs=26.7
Q ss_pred HHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCc
Q psy3760 10 REAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSI 46 (306)
Q Consensus 10 ~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~ 46 (306)
-.+.+.+ |+++||+..+||.+|+.+.++ ..+.|.
T Consensus 13 ~~~~~g~-s~~eaa~~F~VS~~Tv~~W~k--~~~~G~ 46 (119)
T PF01710_consen 13 AYIEKGK-SIREAAKRFGVSRNTVYRWLK--RKETGD 46 (119)
T ss_pred HHHHccc-hHHHHHHHhCcHHHHHHHHHH--hccccc
Confidence 3444445 999999999999999999999 344554
No 420
>PRK09416 lstR lineage-specific thermal regulator protein; Provisional
Probab=82.34 E-value=3.2 Score=29.35 Aligned_cols=54 Identities=17% Similarity=0.180 Sum_probs=36.6
Q ss_pred hCCCchHHHHHHHHHHHH--cCceeEEecCCCccccCHhHHHHHHHHHHHHHHHHHH
Q psy3760 26 LYTSQPGVSKAIIELEEE--LSIDIFIRHGKRIRGLTKPGQAILRSIEIIMQEIEGL 80 (306)
Q Consensus 26 l~isq~~~s~~i~~LE~~--lg~~Lf~R~~~~~~~lT~~G~~l~~~a~~il~~~~~~ 80 (306)
..++.++|-..|++||+. +-...-.+ ++.+.++|+.|+..+....+--......
T Consensus 73 ~~~s~GtIYp~L~RLE~~GlI~s~~~~~-~RK~Y~ITe~Gre~L~e~~~~~~~~~~~ 128 (135)
T PRK09416 73 FEGNEGSLYTLLHRLEQNRFIQSSWDHE-GAKYYQLTDKGNKMLRKAEKNATKARFI 128 (135)
T ss_pred ccCCCccHHHHHHHHHHCCCeEEeecCC-CceEEEECHHHHHHHHHHHhCHHHhHHH
Confidence 357899999999999976 22111122 3444489999999998887644444433
No 421
>PF00392 GntR: Bacterial regulatory proteins, gntR family; InterPro: IPR000524 Many bacterial transcription regulation proteins bind DNA through a helix-turn-helix (HTH) motif, which can be classified into subfamilies on the basis of sequence similarities. The HTH GntR family has many members distributed among diverse bacterial groups that regulate various biological processes. It was named GntR after the Bacillus subtilis repressor of the gluconate operon []. Family members include GntR, HutC, KorA, NtaR, FadR, ExuR, FarR, DgoR and PhnF. The crystal structure of the FadR protein has been determined []. In general, these proteins contain a DNA-binding HTH domain at the N terminus, and an effector-binding or oligomerisation domain at the C terminus (IPR011711 from INTERPRO). The DNA-binding domain is well conserved in structure for the whole of the GntR family, consisting of a 3-helical bundle core with a small beta-sheet (wing); the GntR winged helix structure is similar to that found in several other transcriptional regulator families. The regions outside the DNA-binding domain are more variable and are consequently used to define GntR subfamilies []. This entry represents the N-terminal DNA-binding domain of the GntR family.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 1HW1_B 1H9T_A 1HW2_A 1H9G_A 1E2X_A 3IHU_A 3C7J_A 2RA5_A 3BY6_C 3IC7_A ....
Probab=82.15 E-value=2.1 Score=25.84 Aligned_cols=26 Identities=31% Similarity=0.268 Sum_probs=22.2
Q ss_pred CHHHHHHHhCCCchHHHHHHHHHHHH
Q psy3760 18 NLTEAAKALYTSQPGVSKAIIELEEE 43 (306)
Q Consensus 18 s~~~aA~~l~isq~~~s~~i~~LE~~ 43 (306)
|...=|+.+++|.+++.++++.|+++
T Consensus 26 s~~~la~~~~vsr~tvr~al~~L~~~ 51 (64)
T PF00392_consen 26 SERELAERYGVSRTTVREALRRLEAE 51 (64)
T ss_dssp -HHHHHHHHTS-HHHHHHHHHHHHHT
T ss_pred CHHHHHHHhccCCcHHHHHHHHHHHC
Confidence 66788999999999999999999985
No 422
>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=82.09 E-value=0.9 Score=25.95 Aligned_cols=17 Identities=29% Similarity=0.302 Sum_probs=14.9
Q ss_pred HHHHHhCCCchHHHHHH
Q psy3760 21 EAAKALYTSQPGVSKAI 37 (306)
Q Consensus 21 ~aA~~l~isq~~~s~~i 37 (306)
..|+.+|+|+++||+.+
T Consensus 2 ~lA~~~gvs~~tvs~~l 18 (52)
T cd01392 2 DIARAAGVSVATVSRVL 18 (52)
T ss_pred cHHHHHCcCHHHHHHHH
Confidence 36899999999999876
No 423
>PF12116 SpoIIID: Stage III sporulation protein D; InterPro: IPR014208 Members of this entry represent the transcriptional regulator SpoIIID, or stage III sporulation protein D. It is present in genomes if, and only if, the species is capable of endospore formation. In Bacillus subtilis SpoIIID is a DNA binding protein that is involved in gene repression as well as activation [].; PDB: 2L0K_A.
Probab=81.68 E-value=4 Score=25.72 Aligned_cols=33 Identities=18% Similarity=0.232 Sum_probs=22.2
Q ss_pred HHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHH
Q psy3760 6 FRFVREAVRQNFNLTEAAKALYTSQPGVSKAII 38 (306)
Q Consensus 6 l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~ 38 (306)
++.---+++++-++.+||+..|+|.||+-+-+.
T Consensus 9 i~i~~yIi~~~aTVR~~Ak~FGvSKSTVHkDvt 41 (82)
T PF12116_consen 9 IEIANYIIETKATVRQAAKVFGVSKSTVHKDVT 41 (82)
T ss_dssp HHHHHHHHHH---HHHHHHHHTS-HHHHHHHHT
T ss_pred HHHHHHHHHcccHHHHHHHHHCCcHHHHHHHHH
Confidence 333344555555999999999999999998774
No 424
>TIGR00331 hrcA heat shock gene repressor HrcA. In Bacillus subtilis, hrcA is the first gene of the dnaK operon and so is itself a heat shock gene.
Probab=81.46 E-value=3.1 Score=34.92 Aligned_cols=48 Identities=15% Similarity=0.108 Sum_probs=38.3
Q ss_pred CHHHHHHH--hCCCchHHHHHHHHHHHHcCceeEEec--CCCccccCHhHHHHHHH
Q psy3760 18 NLTEAAKA--LYTSQPGVSKAIIELEEELSIDIFIRH--GKRIRGLTKPGQAILRS 69 (306)
Q Consensus 18 s~~~aA~~--l~isq~~~s~~i~~LE~~lg~~Lf~R~--~~~~~~lT~~G~~l~~~ 69 (306)
+....|+. +++|.+|+-+-|++||+ .| ++.|. +-|. -||+.|-++|..
T Consensus 23 ~s~~l~~~~~~~vS~aTiR~d~~~Le~-~G--~l~~~h~sagr-ipt~kGYR~yv~ 74 (337)
T TIGR00331 23 GSKTLLEKYNLGLSSATIRNDMADLED-LG--FIEKPHTSSGR-IPTDKGYRYYVD 74 (337)
T ss_pred CHHHHHhhcCCCCChHHHHHHHHHHHH-CC--CccCCCCCCCc-CcChhHHHHHHH
Confidence 66788999 99999999999999999 33 34444 4555 499999998874
No 425
>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=81.28 E-value=7.5 Score=25.96 Aligned_cols=55 Identities=16% Similarity=0.104 Sum_probs=37.9
Q ss_pred CCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCCccccCHhHHHHHHHHHHHHH
Q psy3760 17 FNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKPGQAILRSIEIIMQ 75 (306)
Q Consensus 17 ~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~~~lT~~G~~l~~~a~~il~ 75 (306)
.+++.+|+.+|||.+|+.+ .|+++|..=..|+.+|.-.-|+.--..+..++.++.
T Consensus 1 yti~EvA~~~gVs~~tLR~----ye~~~gli~p~r~~~g~R~Yt~~di~~l~~I~~llr 55 (99)
T cd04765 1 FSIGEVAEILGLPPHVLRY----WETEFPQLKPVKRAGGRRYYRPKDVELLLLIKHLLY 55 (99)
T ss_pred CCHHHHHHHHCcCHHHHHH----HHHHcCCCCCcCCCCCCeeeCHHHHHHHHHHHHHHH
Confidence 3789999999999998765 566666544456544431477777777777766554
No 426
>PF01381 HTH_3: Helix-turn-helix; InterPro: IPR001387 This is large family of DNA binding helix-turn helix proteins that include a bacterial plasmid copy control protein, bacterial methylases, various bacteriophage transcription control proteins and a vegetative specific protein from Dictyostelium discoideum (Slime mould).; GO: 0043565 sequence-specific DNA binding; PDB: 2AXU_A 2AWI_D 2AXV_D 2AXZ_C 2AW6_A 3KXA_C 3BS3_A 2CRO_A 1ZUG_A 3CRO_R ....
Probab=81.26 E-value=1.7 Score=25.15 Aligned_cols=25 Identities=20% Similarity=0.181 Sum_probs=19.2
Q ss_pred HhcCCHHHHHHHhCCCchHHHHHHH
Q psy3760 14 RQNFNLTEAAKALYTSQPGVSKAII 38 (306)
Q Consensus 14 ~~~~s~~~aA~~l~isq~~~s~~i~ 38 (306)
+.|.|....|+.+|+|++++|+.++
T Consensus 7 ~~gls~~~la~~~gis~~~i~~~~~ 31 (55)
T PF01381_consen 7 EKGLSQKELAEKLGISRSTISRIEN 31 (55)
T ss_dssp HTTS-HHHHHHHHTS-HHHHHHHHT
T ss_pred HcCCCHHHHHHHhCCCcchhHHHhc
Confidence 4455888999999999999998764
No 427
>COG3432 Predicted transcriptional regulator [Transcription]
Probab=81.22 E-value=6.4 Score=25.93 Aligned_cols=56 Identities=20% Similarity=0.208 Sum_probs=39.6
Q ss_pred CHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCC---ccccCHhHHHHHHHHHHHHHH
Q psy3760 18 NLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKR---IRGLTKPGQAILRSIEIIMQE 76 (306)
Q Consensus 18 s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~---~~~lT~~G~~l~~~a~~il~~ 76 (306)
..++-.-..|++.....+-|+.|++. | |+.++.+| .+++|+.|+.|++...++-..
T Consensus 33 ~~Tri~y~aNlny~~~~~yi~~L~~~-G--li~~~~~~~~~~y~lT~KG~~fle~y~~i~~~ 91 (95)
T COG3432 33 GITRIIYGANLNYKRAQKYIEMLVEK-G--LIIKQDNGRRKVYELTEKGKRFLEKYSEIREL 91 (95)
T ss_pred CceeeeeecCcCHHHHHHHHHHHHhC-C--CEEeccCCccceEEEChhHHHHHHHHHHHHHH
Confidence 34555556677777777777777654 4 77766555 238999999998887777654
No 428
>PF04703 FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A.
Probab=81.18 E-value=2.1 Score=25.68 Aligned_cols=38 Identities=24% Similarity=0.155 Sum_probs=28.6
Q ss_pred HHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHc
Q psy3760 6 FRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEEL 44 (306)
Q Consensus 6 l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~l 44 (306)
|.++.....-- +-...|+.+++|..++.+-+..||++=
T Consensus 6 l~~i~~~~~p~-~T~eiA~~~gls~~~aR~yL~~Le~eG 43 (62)
T PF04703_consen 6 LEYIKEQNGPL-KTREIADALGLSIYQARYYLEKLEKEG 43 (62)
T ss_dssp HHHHHHHTS-E-EHHHHHHHHTS-HHHHHHHHHHHHHCT
T ss_pred HHHHHHcCCCC-CHHHHHHHhCCCHHHHHHHHHHHHHCC
Confidence 44444444444 788999999999999999999999874
No 429
>PRK09863 putative frv operon regulatory protein; Provisional
Probab=81.15 E-value=2.4 Score=38.67 Aligned_cols=42 Identities=21% Similarity=0.161 Sum_probs=32.9
Q ss_pred CHHHHHHHhCCCchHHHHHHHHHHHHcC--ceeEEecCCCccccC
Q psy3760 18 NLTEAAKALYTSQPGVSKAIIELEEELS--IDIFIRHGKRIRGLT 60 (306)
Q Consensus 18 s~~~aA~~l~isq~~~s~~i~~LE~~lg--~~Lf~R~~~~~~~lT 60 (306)
++..=|+.|++|.+|+++-|+++++.++ ..|..|.+.|+ .+.
T Consensus 94 ~~~~La~~l~vS~sTi~~dl~~v~~~l~~~l~l~~k~~~Gi-~i~ 137 (584)
T PRK09863 94 PMAQLASALNLSRTWVAERLPRLNQRYERICCIASRPGLGH-FID 137 (584)
T ss_pred cHHHHHHHhCCCHHHHHHHHHHHHHhhhcccEEEecCCceE-EEE
Confidence 6778888888888888888888888887 77766666666 443
No 430
>PF01371 Trp_repressor: Trp repressor protein; InterPro: IPR000831 The Trp repressor (TrpR) binds to at least five operators in the Escherichia coli genome, repressing gene expression. The operators at which it binds vary considerably in DNA sequence and location within the promoter; when bound to the Trp operon it recognises the sequence 5'-ACTAGT-3' and acts to prevent the initiation of transcription. The TrpR controls the trpEDCBA (trpO) operon and the genes for trpR, aroH, mtr and aroL, which are involved in the biosynthesis and uptake of the amino acid tryptophan []. The repressor binds to the operators only in the presence of L-tryptophan, thereby controlling the intracellular level of its effector; the complex also regulates Trp repressor biosynthesis by binding to its own regulatory region. TrpR acts as a dimer that is composed of identical 6-helical subunits, where four of the helices form the core of the protein and intertwine with the corresponding helices from the other subunit.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3FRW_H 3KOR_A 3SSW_N 1P6Z_N 1CO0_B 1JHG_A 1WRT_S 1WRS_R 1WRP_R 1RCS_B ....
Probab=80.97 E-value=7.4 Score=25.26 Aligned_cols=38 Identities=13% Similarity=0.144 Sum_probs=30.1
Q ss_pred hHHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHH
Q psy3760 5 QFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEE 42 (306)
Q Consensus 5 ~l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~ 42 (306)
.++++..+.+.|.|..+-|+.+|+|-.||||-=+.|..
T Consensus 38 R~~va~~lL~~g~syreIa~~tgvS~aTItRvsr~Lk~ 75 (87)
T PF01371_consen 38 RWQVAKELLDEGKSYREIAEETGVSIATITRVSRCLKY 75 (87)
T ss_dssp HHHHHHHHHHTTSSHHHHHHHHTSTHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHCCCCHHHHHHHhCCCHHHHHHHHHHHHc
Confidence 45667645555559999999999999999988777754
No 431
>PF01090 Ribosomal_S19e: Ribosomal protein S19e; InterPro: IPR001266 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This family includes a number of eukaryotic and archaebacterial ribosomal proteins; mammalian S19, Drosophila S19, Ascaris lumbricoides S19g (ALEP-1) and S19s, yeast YS16 (RP55A and RP55B), Aspergillus S16 and Haloarcula marismortui HS12.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 3IZ6_S 3U5G_T 3U5C_T 3O30_M 3O2Z_M 3IZB_S 2XZN_T 2XZM_T 2V7F_A.
Probab=80.62 E-value=2.1 Score=30.44 Aligned_cols=36 Identities=25% Similarity=0.245 Sum_probs=27.4
Q ss_pred hHHHHHHHHHHHHcCceeEEec-CCCccccCHhHHHHHHHH
Q psy3760 31 PGVSKAIIELEEELSIDIFIRH-GKRIRGLTKPGQAILRSI 70 (306)
Q Consensus 31 ~~~s~~i~~LE~~lg~~Lf~R~-~~~~~~lT~~G~~l~~~a 70 (306)
+-+-+.+++||+ ..|+++. ++|- .+|+.|+.++..+
T Consensus 95 ~iiR~~LqqLE~---~glv~k~~~~GR-~lT~~G~~~lD~i 131 (139)
T PF01090_consen 95 SIIRKILQQLEK---AGLVEKDPKGGR-RLTPKGQRDLDRI 131 (139)
T ss_dssp HHHHHHHHHHHH---TTSEEEETTTEE-EE-HHHHHHHHHH
T ss_pred HHHHHHHHHHHH---CCCEEecCCCCC-EECHHHHHHHHHH
Confidence 456778899997 5788888 6666 6999999988764
No 432
>TIGR00635 ruvB Holliday junction DNA helicase, RuvB subunit. RuvA specifically binds Holliday junctions as a sandwich of two tetramers and maintains the configuration of the junction. It forms a complex with two hexameric rings of RuvB, the subunit that contains helicase activity. The complex drives ATP-dependent branch migration of the Holliday junction recombination intermediate. The endonuclease RuvC resolves junctions.
Probab=80.61 E-value=3.9 Score=33.74 Aligned_cols=62 Identities=16% Similarity=0.071 Sum_probs=45.1
Q ss_pred hhHHHHHHHHH--hc--CCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCCccccCHhHHHHHH
Q psy3760 4 HQFRFVREAVR--QN--FNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKPGQAILR 68 (306)
Q Consensus 4 ~~l~~f~~v~~--~~--~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~~~lT~~G~~l~~ 68 (306)
.+..|+.++.+ .| .+...+|+.||++++++++.+.. .-+..-|+++.++|- ..|+.|..++.
T Consensus 239 ~~~~~L~al~~~~~~~~~~~~~ia~~lg~~~~~~~~~~e~--~Li~~~li~~~~~g~-~~~~~~~~~~~ 304 (305)
T TIGR00635 239 IDRKLLSVLIEQFQGGPVGLKTLAAALGEDADTIEDVYEP--YLLQIGFLQRTPRGR-IATELAYEHLG 304 (305)
T ss_pred HHHHHHHHHHHHhCCCcccHHHHHHHhCCCcchHHHhhhH--HHHHcCCcccCCchh-hhhHHHHHHhC
Confidence 34445655543 21 37899999999999999987741 234556678999998 59999998763
No 433
>PRK12527 RNA polymerase sigma factor; Reviewed
Probab=79.92 E-value=5.7 Score=29.02 Aligned_cols=45 Identities=13% Similarity=-0.011 Sum_probs=33.6
Q ss_pred hhhHHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCce
Q psy3760 3 LHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSID 47 (306)
Q Consensus 3 ~~~l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~ 47 (306)
.++-++|....-.|.|+...|+.||+|.+|+..+|.+--+.|-..
T Consensus 108 ~~~r~v~~l~~~~~~s~~eIA~~lgis~~tv~~~l~ra~~~Lr~~ 152 (159)
T PRK12527 108 PACRDSFLLRKLEGLSHQQIAEHLGISRSLVEKHIVNAMKHCRVR 152 (159)
T ss_pred HHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 345566666543444999999999999999999988777666443
No 434
>PF00165 HTH_AraC: Bacterial regulatory helix-turn-helix proteins, AraC family; PDB: 1WPK_A 1ZGW_A 1U8B_A.
Probab=79.79 E-value=2.6 Score=22.82 Aligned_cols=22 Identities=18% Similarity=0.072 Sum_probs=18.1
Q ss_pred CHHHHHHHhCCCchHHHHHHHH
Q psy3760 18 NLTEAAKALYTSQPGVSKAIIE 39 (306)
Q Consensus 18 s~~~aA~~l~isq~~~s~~i~~ 39 (306)
++...|+.+|+|++.++|..++
T Consensus 10 ~l~~iA~~~g~S~~~f~r~Fk~ 31 (42)
T PF00165_consen 10 TLEDIAEQAGFSPSYFSRLFKK 31 (42)
T ss_dssp -HHHHHHHHTS-HHHHHHHHHH
T ss_pred CHHHHHHHHCCCHHHHHHHHHH
Confidence 8899999999999999988765
No 435
>PF00376 MerR: MerR family regulatory protein; InterPro: IPR000551 The many bacterial transcription regulation proteins which bind DNA through a 'helix-turn-helix' motif can be classified into subfamilies on the basis of sequence similarities. One of these is the MerR subfamily. MerR, which is found in many bacterial species mediates the mercuric-dependent induction of the mercury resistance operon. In the absence of mercury merR represses transcription by binding tightly, as a dimer, to the 'mer' operator region; when mercury is present the dimeric complex binds a single ion and becomes a potent transcriptional activator, while remaining bound to the mer site. Members of the family include the mercuric resistance operon regulatory protein merR; Bacillus subtilis bltR and bmrR; Bacillus glnR; Streptomyces coelicolor hspR; Bradyrhizobium japonicum nolA; Escherichia coli superoxide response regulator soxR; and Streptomyces lividans transcriptional activator tipA [, , , , , ]. Other members include hypothetical proteins from E. coli, B. subtilis and Haemophilus influenzae. Within this family, the HTH motif is situated towards the N terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 3HH0_A 2DG6_A 1R8D_B 1JBG_A 2VZ4_A 2ZHH_A 2ZHG_A 1Q07_A 1Q06_A 1Q05_B ....
Probab=79.61 E-value=1.2 Score=23.64 Aligned_cols=22 Identities=32% Similarity=0.256 Sum_probs=16.1
Q ss_pred CHHHHHHHhCCCchHHHHHHHHHHHH
Q psy3760 18 NLTEAAKALYTSQPGVSKAIIELEEE 43 (306)
Q Consensus 18 s~~~aA~~l~isq~~~s~~i~~LE~~ 43 (306)
|+.++|+.+|+|..||- -.|++
T Consensus 1 ti~e~A~~~gvs~~tlR----~ye~~ 22 (38)
T PF00376_consen 1 TIGEVAKLLGVSPRTLR----YYERE 22 (38)
T ss_dssp EHHHHHHHHTS-HHHHH----HHHHT
T ss_pred CHHHHHHHHCCCHHHHH----HHHHC
Confidence 57899999999998765 45554
No 436
>smart00354 HTH_LACI helix_turn _helix lactose operon repressor.
Probab=79.57 E-value=1.8 Score=26.76 Aligned_cols=20 Identities=20% Similarity=0.318 Sum_probs=17.7
Q ss_pred CHHHHHHHhCCCchHHHHHH
Q psy3760 18 NLTEAAKALYTSQPGVSKAI 37 (306)
Q Consensus 18 s~~~aA~~l~isq~~~s~~i 37 (306)
++..-|+.+|+|.++||+.+
T Consensus 2 t~~~iA~~~gvS~~TVSr~l 21 (70)
T smart00354 2 TIKDVARLAGVSKATVSRVL 21 (70)
T ss_pred CHHHHHHHHCCCHHHHHHHH
Confidence 56788999999999999976
No 437
>COG2963 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=79.34 E-value=18 Score=24.88 Aligned_cols=45 Identities=18% Similarity=0.087 Sum_probs=35.3
Q ss_pred HHHHHHHHHhcCCHHHHHHHhCC-CchHHHHHHHHHHHHcCceeEE
Q psy3760 6 FRFVREAVRQNFNLTEAAKALYT-SQPGVSKAIIELEEELSIDIFI 50 (306)
Q Consensus 6 l~~f~~v~~~~~s~~~aA~~l~i-sq~~~s~~i~~LE~~lg~~Lf~ 50 (306)
+++.....+.|-|++++|++++| +++++.+.++++.+.-+...-.
T Consensus 14 ~~iv~~~~~~g~sv~~vAr~~gv~~~~~l~~W~~~~~~~~~~~~~~ 59 (116)
T COG2963 14 LEAVALYLRGGDTVSEVAREFGIVSATQLYKWRIQLQKGGGLAFSG 59 (116)
T ss_pred HHHHHHHHhcCccHHHHHHHhCCCChHHHHHHHHHHHHcccccccC
Confidence 45555666666469999999996 9999999999999987655433
No 438
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=79.31 E-value=6.1 Score=28.85 Aligned_cols=44 Identities=16% Similarity=0.108 Sum_probs=33.9
Q ss_pred hHHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCcee
Q psy3760 5 QFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDI 48 (306)
Q Consensus 5 ~l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~L 48 (306)
+-++|.-..-.|+|+...|+.||+|.+||..++.+--+.|-..|
T Consensus 111 ~r~v~~l~~~~g~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l 154 (161)
T PRK09047 111 QREAFLLRYWEDMDVAETAAAMGCSEGSVKTHCSRATHALAKAL 154 (161)
T ss_pred HHHHHHHHHHhcCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 34455554444559999999999999999999988877775554
No 439
>PF03551 PadR: Transcriptional regulator PadR-like family; InterPro: IPR005149 Phenolic acids, also called substituted hydroxycinnamic acids, are abundant in the plant kingdom because they are involved in the structure of plant cell walls and are present in some vacuoles. In plant-soil ecosystems they are released as free acids by hemicellulases produced by several fungi and bacteria. Of these weak acids, the most abundant are p-coumaric, ferulic, and caffeic acids, considered to be natural toxins that inhibit the growth of microorganisms, especially at low pHs. In spite of this chemical stress, some bacteria can use phenolic acids as a sole source of carbon. For other microorganisms, these compounds induce a specific response by which the organism adapts to its environment. The ubiquitous lactic acid bacterium Lactobacillus plantarum exhibits an inducible phenolic acid decarboxylase (PAD) activity which converts these substrates into less-toxic vinyl phenol derivatives. PadR acts as a repressor of padA gene expression in the phenolic acid stress response [].; PDB: 1XMA_B 2ESH_A 2DQL_B 3L9F_C 3ELK_B 4EJO_B 3L7W_A 3HHH_A 1YG2_A 3F8B_A ....
Probab=79.17 E-value=3.4 Score=25.84 Aligned_cols=43 Identities=26% Similarity=0.230 Sum_probs=30.2
Q ss_pred hCCCchHHHHHHHHHHHHcCceeEEec-----CCCccccCHhHHHHHH
Q psy3760 26 LYTSQPGVSKAIIELEEELSIDIFIRH-----GKRIRGLTKPGQAILR 68 (306)
Q Consensus 26 l~isq~~~s~~i~~LE~~lg~~Lf~R~-----~~~~~~lT~~G~~l~~ 68 (306)
..++.++|...|++||++==+.-.... ++.+.++|++|+..++
T Consensus 27 ~~i~~g~lY~~L~~Le~~gli~~~~~~~~~~~~rk~Y~iT~~G~~~l~ 74 (75)
T PF03551_consen 27 WKISPGSLYPALKRLEEEGLIESRWEEEGNGRPRKYYRITEKGREELR 74 (75)
T ss_dssp EETTHHHHHHHHHHHHHTTSEEEEEEEETTSSEEEEEEESHHHHHHHH
T ss_pred cccChhHHHHHHHHHHhCCCEEEeeeccCCCCCCEEEEECHHHHHHhc
Confidence 469999999999999987422222222 2333489999998765
No 440
>TIGR00212 hemC porphobilinogen deaminase. Biosynthesis of cofactors, prosthetic groups, and carriers: Heme and porphyrin
Probab=79.00 E-value=34 Score=28.04 Aligned_cols=181 Identities=14% Similarity=0.117 Sum_probs=92.1
Q ss_pred EEEEecccchhhh-hHHHHHHHHHhCCCcEEEEEe----CC----------------hhHHHHHHHcCCeeEEEEccccC
Q psy3760 95 LTIATTHTQARYA-LPKIIKEFTIQFPKVKLSLLQ----GN----------------PKQITEMIRNDQADIAIVTEILS 153 (306)
Q Consensus 95 l~I~~~~~~~~~~-l~~~l~~~~~~~p~~~i~~~~----~~----------------~~~~~~~l~~~~~Di~i~~~~~~ 153 (306)
|+||+-.|-...+ ...+...+.+.||++.+++.. ++ ..++.+.|.+|++|+++.+...-
T Consensus 1 i~IgTR~S~LAl~Qa~~V~~~L~~~~p~~~~ei~~i~T~GD~~~~~~L~~iGgkGlFtkele~aLl~g~iDiAVHSlKDl 80 (292)
T TIGR00212 1 LRIGTRGSKLALAQANLVREQLKAVYPELDTEIVIIKTTGDKIQDKPLYDIGGKGLFTKELEQALLDGEIDLAVHSLKDV 80 (292)
T ss_pred CEEEcCCCHHHHHHHHHHHHHHHHhCCCceEEEEEEeeeCcccccCcHHHcCCceeeHHHHHHHHhcCCCCEEEeccccC
Confidence 4677765533333 334445666668888887753 22 12677899999999999874322
Q ss_pred C---CCCceeeccccceEEEEecCCCCCC---CCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCceeEEEEecCH
Q psy3760 154 P---SDKLISIPCYQWEYVIIVPLDHPLL---LLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINS 227 (306)
Q Consensus 154 ~---~~~~~~~~l~~~~~~~v~~~~~~l~---~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 227 (306)
+ ++++. +..+.++..|.. .+...++++|..--.|..+ +.|+. .++ .......+++-.-.|+
T Consensus 81 Pt~lp~gl~--------i~av~~RedprD~lv~~~~~~l~~Lp~ga~VGTs---S~RR~-aql-~~~rPdl~i~~iRGNV 147 (292)
T TIGR00212 81 PTVLPEGLE--------IAAVLKREDPRDVLVSRKYLSLDSLPQGAKVGTS---SLRRK-AQL-KAIRPDLKIEPLRGNI 147 (292)
T ss_pred CCCCCCCcE--------EEEEecCCCCceEEEECCCCChhHCCCCCEeccC---CHHHH-HHH-HHHCCCCEEEECcCCH
Confidence 2 23332 233333333311 1112356666655444432 33332 222 2222234555556899
Q ss_pred HHHHHHHHhccceeeeec-ceeccccc-CCc-eeeecCC---CCccceEEEEEeCCccccHHHHHHHHHH
Q psy3760 228 DIIKTYVELRMGIGIIAS-IAFDSNRD-KNL-RSISASH---LFGTTISRVIIKQGTYLRSYVYSFIKLL 291 (306)
Q Consensus 228 ~~~~~~v~~g~gi~~~p~-~~~~~~~~-~~l-~~~~~~~---~~~~~~~~l~~~~~~~~~~~~~~~~~~l 291 (306)
++=+.-+.+|..=+++-. --...+.. ..+ ..++.+. .+-+.-+.+-++++ +..+..+++.+
T Consensus 148 ~TRL~KL~~g~~DaiiLA~AGL~RLgl~~~i~~~l~~~~~~PA~gQGalaIe~r~~---d~~~~~ll~~l 214 (292)
T TIGR00212 148 DTRLRKLDEGEYDAIILAEAGLKRLGLEDVITEVLDPEVMLPAPGQGAIAVECRKD---DTEIKEILKEI 214 (292)
T ss_pred HHHHHHhcCCCCCEeehHhhHHHhCCCccccccccChhhcCCccccceEEEEEecC---CHHHHHHHHHc
Confidence 999888888844444322 11122211 112 2334332 12255666766655 44455555544
No 441
>PF06322 Phage_NinH: Phage NinH protein; InterPro: IPR010454 This entry is represented by Bacteriophage 933W, NinH. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=78.94 E-value=4.5 Score=23.86 Aligned_cols=32 Identities=22% Similarity=0.128 Sum_probs=27.0
Q ss_pred HHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHc
Q psy3760 12 AVRQNFNLTEAAKALYTSQPGVSKAIIELEEEL 44 (306)
Q Consensus 12 v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~l 44 (306)
+-..| +.+++|+.|+.+..||.|=+...+.+-
T Consensus 13 i~~~G-nqtEvaR~l~c~R~TVrKY~~D~~a~~ 44 (64)
T PF06322_consen 13 IETYG-NQTEVARRLGCNRATVRKYSRDKDAKR 44 (64)
T ss_pred HHHhC-cHHHHHHHhcccHHHHHHHhcccccce
Confidence 34568 999999999999999999888777654
No 442
>PRK12546 RNA polymerase sigma factor; Provisional
Probab=78.86 E-value=3.7 Score=31.17 Aligned_cols=49 Identities=14% Similarity=0.010 Sum_probs=35.4
Q ss_pred hhHHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEec
Q psy3760 4 HQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRH 52 (306)
Q Consensus 4 ~~l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~ 52 (306)
++-++|....-.|.|....|+.||+|.+++-.++.+--..|...|-.+.
T Consensus 117 ~~r~v~~L~~~~g~s~~EIA~~LgiS~~tVk~~l~Rar~~Lr~~l~~~~ 165 (188)
T PRK12546 117 EQREALILVGASGFSYEEAAEMCGVAVGTVKSRANRARARLAELLQLEE 165 (188)
T ss_pred HHhHHhhhHHhcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHhccc
Confidence 3445666654445599999999999999998888777777655554433
No 443
>COG3835 CdaR Sugar diacid utilization regulator [Transcription / Signal transduction mechanisms]
Probab=78.65 E-value=3.2 Score=34.33 Aligned_cols=36 Identities=19% Similarity=0.335 Sum_probs=32.6
Q ss_pred HHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCcee
Q psy3760 12 AVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDI 48 (306)
Q Consensus 12 v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~L 48 (306)
.++.| ++..+|+.|||=.-|+-+++.++|+.-|..+
T Consensus 322 f~~N~-~l~~tA~~L~IHrNTLrYRL~kIe~iTGL~~ 357 (376)
T COG3835 322 FAHNG-QLNATAEALFIHRNTLRYRLEKIEEITGLDL 357 (376)
T ss_pred HHhcC-CHHHHHHHhccchhhHHHHHHHHHHHhCCCc
Confidence 35678 9999999999999999999999999988765
No 444
>PRK09935 transcriptional regulator FimZ; Provisional
Probab=78.52 E-value=5.8 Score=30.15 Aligned_cols=43 Identities=21% Similarity=0.172 Sum_probs=36.4
Q ss_pred hhHHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCce
Q psy3760 4 HQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSID 47 (306)
Q Consensus 4 ~~l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~ 47 (306)
+....+..+++.- |...-|+.|++|..|+..+++++...||++
T Consensus 153 re~~vl~~l~~g~-s~~eIa~~l~~s~~tv~~~~~~~~~kl~~~ 195 (210)
T PRK09935 153 REVTILRYLVSGL-SNKEIADQLLLSNKTVSAHKSNIYGKLGLH 195 (210)
T ss_pred HHHHHHHHHHcCC-CHHHHHHHhCCCHHHHHHHHHHHHHHcCCC
Confidence 4455566666666 999999999999999999999999999964
No 445
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=77.69 E-value=4 Score=24.34 Aligned_cols=27 Identities=11% Similarity=0.137 Sum_probs=18.9
Q ss_pred HHHhcCCHHHHHHHhCCCchHHHHHHH
Q psy3760 12 AVRQNFNLTEAAKALYTSQPGVSKAII 38 (306)
Q Consensus 12 v~~~~~s~~~aA~~l~isq~~~s~~i~ 38 (306)
+.+.|.|...-|+..|+|++++++.++
T Consensus 6 m~~~~it~~~La~~~gis~~tl~~~~~ 32 (63)
T PF13443_consen 6 MAERGITQKDLARKTGISRSTLSRILN 32 (63)
T ss_dssp HHHTT--HHHHHHHHT--HHHHHHHHT
T ss_pred HHHcCCCHHHHHHHHCcCHHHHHHHHh
Confidence 445556888999999999999998765
No 446
>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=77.59 E-value=2.3 Score=29.16 Aligned_cols=26 Identities=31% Similarity=0.185 Sum_probs=22.2
Q ss_pred HHhcCCHHHHHHHhCCCchHHHHHHHH
Q psy3760 13 VRQNFNLTEAAKALYTSQPGVSKAIIE 39 (306)
Q Consensus 13 ~~~~~s~~~aA~~l~isq~~~s~~i~~ 39 (306)
.... |+..||+.|+++.++||+.+..
T Consensus 78 ~~F~-S~~EAar~lgi~~~tIs~~~~~ 103 (113)
T cd00283 78 GIFD-STTEAARFLKVHSGTISKNIKS 103 (113)
T ss_pred EEeC-CHHHHHHHHCCCcchhHHHHCC
Confidence 3456 9999999999999999998654
No 447
>PRK11564 stationary phase inducible protein CsiE; Provisional
Probab=77.25 E-value=3.8 Score=35.72 Aligned_cols=42 Identities=10% Similarity=0.075 Sum_probs=35.5
Q ss_pred CHHHHHHHhCCCchHHHHHHHHHHHHc----CceeEEecCCCccccC
Q psy3760 18 NLTEAAKALYTSQPGVSKAIIELEEEL----SIDIFIRHGKRIRGLT 60 (306)
Q Consensus 18 s~~~aA~~l~isq~~~s~~i~~LE~~l----g~~Lf~R~~~~~~~lT 60 (306)
++..=|+.|+||.+|+++=|+++++.| |..|..+.++|+ .+.
T Consensus 32 ~l~~Lae~l~VSrsTi~~DLk~l~~~L~~y~~L~L~~~~~~Gi-~I~ 77 (426)
T PRK11564 32 TLETFSQLNGVDDDTARQDIAETGREIQRYHRLTLTTGADGSY-RIE 77 (426)
T ss_pred cHHHHHHHhCCCHHHHHHHHHHHHHHHHHhcCceEEEecCCeE-EEE
Confidence 688999999999999999999998876 688877777775 444
No 448
>PF06056 Terminase_5: Putative ATPase subunit of terminase (gpP-like); InterPro: IPR010332 This family of proteins are annotated as ATPase subunits of phage terminase after []. Terminases are viral proteins that are involved in packaging viral DNA into the capsid.; GO: 0005524 ATP binding, 0019069 viral capsid assembly
Probab=77.24 E-value=6.3 Score=23.31 Aligned_cols=31 Identities=16% Similarity=0.083 Sum_probs=25.3
Q ss_pred HHHHhcCCHHHHHHHhCCCchHHHHHHHHHH
Q psy3760 11 EAVRQNFNLTEAAKALYTSQPGVSKAIIELE 41 (306)
Q Consensus 11 ~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE 41 (306)
.++-.|.+...-|+.||++.+||....++=+
T Consensus 8 ~LY~~G~~~~eIA~~Lg~~~~TV~~W~~r~~ 38 (58)
T PF06056_consen 8 SLYLQGWSIKEIAEELGVPRSTVYSWKDRYK 38 (58)
T ss_pred HHHHcCCCHHHHHHHHCCChHHHHHHHHhhC
Confidence 3445677999999999999999998887543
No 449
>PF07750 GcrA: GcrA cell cycle regulator; InterPro: IPR011681 GcrA, together with CtrA (see IPR001789 from INTERPRO and IPR001867 from INTERPRO), form a master cell cycle regulator. These bacterial regulators are involved in controlling the progression and asymmetric polar morphogenesis []. During this process, there are temporal and spatial variations in the concentrations of GcrA and CtrA. The variation in concentration produces time and space dependent transcriptional regulation of modular functions that implement cell-cycle processes []. More specifically, GcrA acts as an activator of components of the replisome and the segregation machinery [].
Probab=77.05 E-value=4.1 Score=30.07 Aligned_cols=37 Identities=16% Similarity=0.168 Sum_probs=33.3
Q ss_pred hhHHHHHHHHHhcCCHHHHHHHhC-CCchHHHHHHHHH
Q psy3760 4 HQFRFVREAVRQNFNLTEAAKALY-TSQPGVSKAIIEL 40 (306)
Q Consensus 4 ~~l~~f~~v~~~~~s~~~aA~~l~-isq~~~s~~i~~L 40 (306)
+.++.+..+-..|.|.++.|++|| +|..+|.=.+.+|
T Consensus 6 e~~~~L~~lw~~G~SasqIA~~lg~vsRnAViGk~hRl 43 (162)
T PF07750_consen 6 ERVERLRKLWAEGLSASQIARQLGGVSRNAVIGKAHRL 43 (162)
T ss_pred HHHHHHHHHHHcCCCHHHHHHHhCCcchhhhhhhhhcc
Confidence 567788888999999999999999 9999999888876
No 450
>PRK09590 celB cellobiose phosphotransferase system IIB component; Reviewed
Probab=76.98 E-value=18 Score=24.40 Aligned_cols=55 Identities=11% Similarity=0.079 Sum_probs=43.2
Q ss_pred cEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEc
Q psy3760 94 NLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVT 149 (306)
Q Consensus 94 ~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~ 149 (306)
.+-+.|..++++.++..-+.++.+.+ ++.+++...+..++.+.+...++|+.++.
T Consensus 3 kILlvCg~G~STSlla~k~k~~~~e~-gi~~~i~a~~~~e~~~~~~~~~~DvIll~ 57 (104)
T PRK09590 3 KALIICAAGMSSSMMAKKTTEYLKEQ-GKDIEVDAITATEGEKAIAAAEYDLYLVS 57 (104)
T ss_pred EEEEECCCchHHHHHHHHHHHHHHHC-CCceEEEEecHHHHHHhhccCCCCEEEEC
Confidence 35677778888888888888887764 77888888888777776666789999984
No 451
>PRK10344 DNA-binding transcriptional regulator Nlp; Provisional
Probab=76.93 E-value=5.5 Score=25.73 Aligned_cols=36 Identities=8% Similarity=0.154 Sum_probs=30.0
Q ss_pred chhhHHHHHHHHHhcCCHHHHHHHhCCCchHHHHHH
Q psy3760 2 NLHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAI 37 (306)
Q Consensus 2 ~~~~l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i 37 (306)
|+..-.+..++-+.|.|+.+-|++.|+|++|+...+
T Consensus 7 DWH~adI~AaL~KrG~sLa~lsr~~Gls~~TL~nAL 42 (92)
T PRK10344 7 DWHPADIIAGLRKKGTSMAAESRRNGLSSSTLANAL 42 (92)
T ss_pred CCCHHHHHHHHHHcCCcHHHHHHHcCCChHHHHHHH
Confidence 344456677888888899999999999999999776
No 452
>PHA01976 helix-turn-helix protein
Probab=76.91 E-value=5.7 Score=24.02 Aligned_cols=22 Identities=5% Similarity=0.024 Sum_probs=18.3
Q ss_pred hcCCHHHHHHHhCCCchHHHHH
Q psy3760 15 QNFNLTEAAKALYTSQPGVSKA 36 (306)
Q Consensus 15 ~~~s~~~aA~~l~isq~~~s~~ 36 (306)
.|.|..+.|+.+++|++++|+.
T Consensus 14 ~glt~~~lA~~~gvs~~~v~~~ 35 (67)
T PHA01976 14 RAWSAPELSRRAGVRHSLIYDF 35 (67)
T ss_pred cCCCHHHHHHHhCCCHHHHHHH
Confidence 3447789999999999999964
No 453
>PLN02691 porphobilinogen deaminase
Probab=76.81 E-value=45 Score=28.16 Aligned_cols=184 Identities=12% Similarity=0.087 Sum_probs=96.1
Q ss_pred CCcEEEEecccchhh-hhHHHHHHHHHhCCCc----EEEEEe----CC----------------hhHHHHHHHcCCeeEE
Q psy3760 92 TGNLTIATTHTQARY-ALPKIIKEFTIQFPKV----KLSLLQ----GN----------------PKQITEMIRNDQADIA 146 (306)
Q Consensus 92 ~~~l~I~~~~~~~~~-~l~~~l~~~~~~~p~~----~i~~~~----~~----------------~~~~~~~l~~~~~Di~ 146 (306)
...|+||+-.+-... -...+...+.+.+|++ +++++. ++ ..++.+.|.+|++|+|
T Consensus 41 ~~~irIGTR~S~LAl~Qt~~V~~~L~~~~p~~~~~~~~eiv~i~T~GD~~~d~pL~~iGgkGlFtkele~aLl~g~iDiA 120 (351)
T PLN02691 41 VAPIRIGTRGSPLALAQAYETRDLLKAAHPELAEEGALEIVIIKTTGDKILDQPLADIGGKGLFTKEIDDALLSGRIDIA 120 (351)
T ss_pred CceEEEEeCCcHHHHHHHHHHHHHHHHhCCCcCCCCCEEEEEEeecCCccccchHHHcCCceEeHHHHHHHHHcCCCCEE
Confidence 358999997764443 4444556667778876 555532 11 1267889999999999
Q ss_pred EEccccCC---CCCceeeccccceEEEEecCCCCCC---CCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCceeE
Q psy3760 147 IVTEILSP---SDKLISIPCYQWEYVIIVPLDHPLL---LLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYI 220 (306)
Q Consensus 147 i~~~~~~~---~~~~~~~~l~~~~~~~v~~~~~~l~---~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~ 220 (306)
+-+...-+ ++++ .+..+.+++.|-. .+...++++|..-..|..+ +.+.. . .+.......++
T Consensus 121 VHSlKDlP~~l~~gl--------~i~Avl~RedprDvLv~~~~~~L~~Lp~ga~IGTS---S~RR~-a-ql~~~rPdl~v 187 (351)
T PLN02691 121 VHSMKDVPTYLPEGT--------ILPCNLPREDVRDAFISLKAKSLAELPAGSVVGTA---SLRRQ-S-QILHKYPHLKV 187 (351)
T ss_pred EeccccCCCCCCCCc--------EEEEEcCCCCCceEEEECCCCChhHCCCCCEeccC---cHHHH-H-HHHHHCCCCEE
Confidence 98743222 2333 2333333333311 1122467777554444332 33332 2 22222233455
Q ss_pred EEEecCHHHHHHHHHhccceeeeec-ceecccccCC--ceeeecCC---CCccceEEEEEeCCccccHHHHHHHHHH
Q psy3760 221 VLETINSDIIKTYVELRMGIGIIAS-IAFDSNRDKN--LRSISASH---LFGTTISRVIIKQGTYLRSYVYSFIKLL 291 (306)
Q Consensus 221 ~~~~~~~~~~~~~v~~g~gi~~~p~-~~~~~~~~~~--l~~~~~~~---~~~~~~~~l~~~~~~~~~~~~~~~~~~l 291 (306)
+-.-.|+++=+.-+..|..=+++-. --+..+...+ -..++.+. .+-+.-+.+-++++ ++.+..+++.|
T Consensus 188 ~~iRGNVdTRL~KL~~geyDaiILA~AGL~RLgl~~~i~~~l~~~~~~PA~gQGaLaVe~r~~---d~~~~~ll~~i 261 (351)
T PLN02691 188 VNFRGNVQTRLRKLQEGVVDATLLALAGLKRLDMTEHATSILSTDEMLPAVAQGAIGIACRTD---DDKMLEYLASL 261 (351)
T ss_pred EeccCCHHHHHHHhcCCCCCeeehHHHHHHhCCCcccccEecchhhcCCccccceEEEEEecC---CHHHHHHHHHC
Confidence 5566888888888888744443322 1122221111 12333332 22355666766765 45566666555
No 454
>COG0640 ArsR Predicted transcriptional regulators [Transcription]
Probab=76.79 E-value=18 Score=23.62 Aligned_cols=50 Identities=24% Similarity=0.278 Sum_probs=38.7
Q ss_pred hHHHHHHHHHh-cCCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCC
Q psy3760 5 QFRFVREAVRQ-NFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKR 55 (306)
Q Consensus 5 ~l~~f~~v~~~-~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~ 55 (306)
.++++..+.+. ..++..-++.+++++++++++++.|++.--+.. .+.++.
T Consensus 27 r~~il~~l~~~~~~~~~~l~~~~~~~~~~v~~hL~~L~~~glv~~-~~~~~~ 77 (110)
T COG0640 27 RLEILSLLAEGGELTVGELAEALGLSQSTVSHHLKVLREAGLVEL-RREGRL 77 (110)
T ss_pred HHHHHHHHHhcCCccHHHHHHHHCCChhHHHHHHHHHHHCCCeEE-EecccE
Confidence 45666667762 327889999999999999999999999887777 444444
No 455
>TIGR02960 SigX5 RNA polymerase sigma-70 factor, TIGR02960 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family.
Probab=76.63 E-value=31 Score=28.70 Aligned_cols=68 Identities=15% Similarity=-0.005 Sum_probs=40.4
Q ss_pred HHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEe--cCCCccccCHhHHHHHHHHHHHHH
Q psy3760 7 RFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIR--HGKRIRGLTKPGQAILRSIEIIMQ 75 (306)
Q Consensus 7 ~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R--~~~~~~~lT~~G~~l~~~a~~il~ 75 (306)
++|.--.-.|.|+...|+.||+|.+|+.+++.+-.+.|-..|=.. ...+. .+.+..+.++...-..++
T Consensus 149 ~v~~L~~~~g~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~~~~~~~~~~-~~~~~~~~~v~~~~~a~~ 218 (324)
T TIGR02960 149 AVLLLRDVLGWRAAETAELLGTSTASVNSALQRARATLDEVGPSARDDQLAQ-PPSPEEQDLLERYIAAFE 218 (324)
T ss_pred hHhhhHHHhCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHhcccccccccCC-CCCHHHHHHHHHHHHHHH
Confidence 344443333459999999999999999888877777665544211 11123 255555544444444433
No 456
>TIGR03697 NtcA_cyano global nitrogen regulator NtcA, cyanobacterial. Members of this protein family, found in the cyanobacteria, are the global nitrogen regulator NtcA. This DNA-binding transcriptional regulator is required for expressing many different ammonia-repressible genes. The consensus NtcA-binding site is G T A N(8)T A C.
Probab=76.59 E-value=2.1 Score=32.46 Aligned_cols=40 Identities=15% Similarity=0.287 Sum_probs=31.3
Q ss_pred CHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCCccccCH
Q psy3760 18 NLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTK 61 (306)
Q Consensus 18 s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~~~lT~ 61 (306)
+-..-|..+|+|+.++||.+++|+++ -++..+++.+ ...+
T Consensus 145 t~~~iA~~lG~tretvsR~l~~l~~~---g~I~~~~~~i-~I~d 184 (193)
T TIGR03697 145 SHQAIAEAIGSTRVTITRLLGDLRKK---KLISIHKKKI-TVHD 184 (193)
T ss_pred CHHHHHHHhCCcHHHHHHHHHHHHHC---CCEEecCCEE-EEeC
Confidence 55788999999999999999999985 4556566666 3443
No 457
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=76.50 E-value=8.2 Score=28.19 Aligned_cols=43 Identities=9% Similarity=-0.089 Sum_probs=31.0
Q ss_pred HHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCcee
Q psy3760 6 FRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDI 48 (306)
Q Consensus 6 l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~L 48 (306)
=.+|....-.|.|+...|+.||+|.+||..++.+--..|-..|
T Consensus 112 r~v~~l~~~~g~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l 154 (160)
T PRK09642 112 RDVVLAHYLEEKSYQEIALQEKIEVKTVEMKLYRARKWIKKHW 154 (160)
T ss_pred HHHHHHHHHhCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 3455444444559999999999999999777777666654443
No 458
>PLN02853 Probable phenylalanyl-tRNA synthetase alpha chain
Probab=76.45 E-value=9.5 Score=33.61 Aligned_cols=62 Identities=11% Similarity=-0.073 Sum_probs=46.6
Q ss_pred HHHHHHHHHhc--CCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEec-CCCccccCHhHHHHHHH
Q psy3760 6 FRFVREAVRQN--FNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRH-GKRIRGLTKPGQAILRS 69 (306)
Q Consensus 6 l~~f~~v~~~~--~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~-~~~~~~lT~~G~~l~~~ 69 (306)
.+++..+.+.+ .+-...|+.++++..++-+.++.|++. |.-=+++. .... .||+.|+..+..
T Consensus 6 ~~iL~~l~~~~~~~~~~~la~~~g~~~~~v~~~~~~L~~k-g~v~~~~~~~~~~-~LT~eG~~~l~~ 70 (492)
T PLN02853 6 EALLGALSNNEEISDSGQFAASHGLDHNEVVGVIKSLHGF-RYVDAQDIKRETW-VLTEEGKKYAAE 70 (492)
T ss_pred HHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHHHhC-CCEEEEEEEEEEE-EECHHHHHHHHc
Confidence 34555555533 156788999999999999999999998 65444444 4555 899999998874
No 459
>PRK08359 transcription factor; Validated
Probab=76.24 E-value=4.3 Score=30.33 Aligned_cols=39 Identities=15% Similarity=0.208 Sum_probs=32.8
Q ss_pred HhcCCHHHHHHHhCCCchHHHHH-----------HHHHHHHcCceeEEec
Q psy3760 14 RQNFNLTEAAKALYTSQPGVSKA-----------IIELEEELSIDIFIRH 52 (306)
Q Consensus 14 ~~~~s~~~aA~~l~isq~~~s~~-----------i~~LE~~lg~~Lf~R~ 52 (306)
+.|.|-..-|+.+|+++++|++. +.+|++.||+.|..+.
T Consensus 96 ~kglSQeeLA~~lgvs~stI~~iE~G~~~Ps~~~l~kLak~l~VsL~e~~ 145 (176)
T PRK08359 96 KSGLSYEELSHEVGLSVNDLRRIAHGEYEPTIKEAKKLERYFKIKLIERV 145 (176)
T ss_pred HcCCCHHHHHHHhCCCHHHHHHHHCCCcCCCHHHHHHHHHHhCCcccccc
Confidence 34567788999999999999854 8899999999998865
No 460
>PTZ00326 phenylalanyl-tRNA synthetase alpha chain; Provisional
Probab=76.20 E-value=10 Score=33.55 Aligned_cols=62 Identities=19% Similarity=0.135 Sum_probs=46.8
Q ss_pred hHHHHHHHHH---hcCCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEec-CCCccccCHhHHHHHHH
Q psy3760 5 QFRFVREAVR---QNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRH-GKRIRGLTKPGQAILRS 69 (306)
Q Consensus 5 ~l~~f~~v~~---~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~-~~~~~~lT~~G~~l~~~ 69 (306)
..+++..+.+ .- +-...|+.++++..++-+.++.|++. |.-=+++. .... .||+.|+..+..
T Consensus 8 e~~iL~~l~~~~~~~-~~~~la~~~~~~~~~v~~~~~~L~~k-g~v~~~~~~~~~~-~LT~eG~~~~~~ 73 (494)
T PTZ00326 8 ENTILSKLESENEIV-NSLALAESLNIDHQKVVGAIKSLESA-NYITTEMKKSNTW-TLTEEGEDYLKN 73 (494)
T ss_pred HHHHHHHHHhcCCCC-CHHHHHHHcCCCHHHHHHHHHHHHhC-CCEEEEEEEEEEE-EECHHHHHHHHc
Confidence 3455555655 23 56688999999999999999999997 65544444 4555 899999998876
No 461
>COG2113 ProX ABC-type proline/glycine betaine transport systems, periplasmic components [Amino acid transport and metabolism]
Probab=75.77 E-value=44 Score=27.64 Aligned_cols=197 Identities=10% Similarity=0.033 Sum_probs=118.5
Q ss_pred cCCCCcEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccCC---------CCCce
Q psy3760 89 AYDTGNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSP---------SDKLI 159 (306)
Q Consensus 89 ~~~~~~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~---------~~~~~ 159 (306)
....++|+|+....-.......++....+.+ ++++++...++.-..+.|.+|++|+....-.+.. ...+.
T Consensus 27 ~~~~~tV~~a~~~W~s~~~~t~v~~~iLk~~-Gy~v~~~~~~~~~~~~sla~gd~D~~~~~W~p~~~~~~~~~~~~~~v~ 105 (302)
T COG2113 27 AEAGKTVRIADVGWTSGTATTNVAKKILKGL-GYTVELVTLDTAVMYQSLAKGDLDVFPEAWLPTTPDDYKKAVKDKKVE 105 (302)
T ss_pred cccCCeeEEeecCccHHHHHHHHHHHHHHhC-CCcceeeeccHHHHHHHHHcCCCccccceecCCChHHHHHHhccCcee
Confidence 3457799999988877778888888888655 7778999999999999999999999987522111 11222
Q ss_pred ee--ccccceEEEEecCCCCCCCCCCcChhhhcC---CC---eEeecCCCCcHHHHHHHHHhCCCcee--EEEEecCHHH
Q psy3760 160 SI--PCYQWEYVIIVPLDHPLLLLNSISLKEISN---YP---LITYDLSFSGRIKLDREFSLQKLTPY--IVLETINSDI 229 (306)
Q Consensus 160 ~~--~l~~~~~~~v~~~~~~l~~~~~i~~~dl~~---~~---~i~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~ 229 (306)
.. -+..-...+++|+--.... .-+++|+.. .- +...+++........+.+...++..+ ..++.+...+
T Consensus 106 ~~~~~~~Ga~~g~~vp~y~~d~~--iksi~D~~~~~d~~~g~i~g~~pG~g~~~~~~~~~k~y~~~~~~~~lv~~s~~am 183 (302)
T COG2113 106 LGGTNLEGAKQGWAVPKYVADAG--IKSIADLAKFKDKFGGKIYGIEPGWGCMRVIEDAIKAYGLGLKGFELVESSEAAM 183 (302)
T ss_pred ecccccCCceEEEEeceehhhcc--ccchhhHHhccCCCCCcEEccCCCCchhHHHHHHHhhccccccceEEecCcHHHH
Confidence 22 2224556677776543221 223444433 22 77888888888888899998887433 3344444444
Q ss_pred HHHHHH---hcccee---eeecceecccccCCceeeecCCC---C--ccceEEEEEeCC-ccccHHHHHHHHHH
Q psy3760 230 IKTYVE---LRMGIG---IIASIAFDSNRDKNLRSISASHL---F--GTTISRVIIKQG-TYLRSYVYSFIKLL 291 (306)
Q Consensus 230 ~~~~v~---~g~gi~---~~p~~~~~~~~~~~l~~~~~~~~---~--~~~~~~l~~~~~-~~~~~~~~~~~~~l 291 (306)
+...++ .+..+. -.|+++.. ..+++++..+++ . ....++.+.++. ....|.+.+|++-+
T Consensus 184 l~~~~~a~~~~~piv~~~WsPh~m~~---k~~l~~L~~~~~~~~~~~g~~~v~t~~~kg~~~~~p~v~~~l~~~ 254 (302)
T COG2113 184 LAAAIRAAKRKEPIVFYGWSPHWMFG---KYDLKYLEDPGPPKGANGGWETVHTVVRKGFAEEAPNVAKLLANF 254 (302)
T ss_pred HHHHHHHHhcCCCEEEEEeCchhhhh---ccceeeecCCCcccCCCCcceeeehhhhhhhhHhCchHHHHHHHc
Confidence 444443 343333 35555543 346666665421 1 113445444443 22355666665544
No 462
>PRK12511 RNA polymerase sigma factor; Provisional
Probab=75.69 E-value=8.4 Score=29.03 Aligned_cols=40 Identities=18% Similarity=0.047 Sum_probs=28.5
Q ss_pred hHHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHc
Q psy3760 5 QFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEEL 44 (306)
Q Consensus 5 ~l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~l 44 (306)
+-++|.--.-.|.|+...|+.||+|.+|+..++.+--..|
T Consensus 116 ~R~v~~L~~~eg~s~~EIA~~lgis~~tV~~~l~Rar~~L 155 (182)
T PRK12511 116 QRAALHLVAIEGLSYQEAAAVLGIPIGTLMSRIGRARAAL 155 (182)
T ss_pred HHHHHHHHHHcCCCHHHHHHHhCcCHHHHHHHHHHHHHHH
Confidence 3345555333445999999999999999988876554444
No 463
>KOG2892|consensus
Probab=75.67 E-value=41 Score=27.16 Aligned_cols=58 Identities=16% Similarity=0.307 Sum_probs=42.7
Q ss_pred CCcEEEEeccc-chhhhhHHHHHHHHHhCCCcEEEEEeC--------------------ChhHHHHHHHcCCeeEEEEc
Q psy3760 92 TGNLTIATTHT-QARYALPKIIKEFTIQFPKVKLSLLQG--------------------NPKQITEMIRNDQADIAIVT 149 (306)
Q Consensus 92 ~~~l~I~~~~~-~~~~~l~~~l~~~~~~~p~~~i~~~~~--------------------~~~~~~~~l~~~~~Di~i~~ 149 (306)
...++||.-.+ ++..--..+...+.+.||+..+.+... -+.++.+.|.+|++||++-+
T Consensus 5 ~~~irIGtRKSkLAvIQs~~v~~~Lek~YP~l~f~I~t~~T~GDkIl~k~L~~ig~KsLfTkELE~aL~~~~~divVHS 83 (320)
T KOG2892|consen 5 TAVIRIGTRKSKLAVIQSYHVREKLEKKYPELAFEIITMSTTGDKILSKPLAKIGGKSLFTKELEDALINGHVDIVVHS 83 (320)
T ss_pred ceEEEecCcccchhhhhHHHHHHHHHhhCCCceeEEEEecccchHHhhchHhhhcccchhHHHHHHHHhcCCccEEEEe
Confidence 34688888665 333344556678888899988888543 24578899999999999986
No 464
>TIGR02959 SigZ RNA polymerase sigma factor, SigZ family. This family of RNA polymerase sigma factors is a member of the Sigma-70 subfamily (TIGR02937). One of these is designated as SigZ in B. subtilis (Swiss_Prot: SIGZ_BACSU). Interestingly, this group has a very sporatic distribution, B. subtilis, for instance, being the only sequenced strain of Bacilli with a member. Dechloromonas aromatica RCB appears to have two of these sigma factors. A member appears on a plasmid found in Photobacterium profundum SS9 and Vibrio fischeri ES114 (where a second one is chromosomally encoded).
Probab=75.17 E-value=9.4 Score=28.33 Aligned_cols=43 Identities=16% Similarity=0.094 Sum_probs=31.0
Q ss_pred hhHHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCc
Q psy3760 4 HQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSI 46 (306)
Q Consensus 4 ~~l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~ 46 (306)
++-.+|....-.|.|+.+.|+.||+|.++|-.++.+.-+.|..
T Consensus 104 ~~r~v~~l~~~~g~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~ 146 (170)
T TIGR02959 104 EYREAIRLTELEGLSQQEIAEKLGLSLSGAKSRVQRGRKKLKE 146 (170)
T ss_pred HHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 3445555544445599999999999999998877766655543
No 465
>PTZ00095 40S ribosomal protein S19; Provisional
Probab=74.95 E-value=7.1 Score=28.70 Aligned_cols=39 Identities=18% Similarity=0.139 Sum_probs=28.9
Q ss_pred CchHHHHHHHHHHHHcCceeEEecC--CCccccCHhHHHHHHHHH
Q psy3760 29 SQPGVSKAIIELEEELSIDIFIRHG--KRIRGLTKPGQAILRSIE 71 (306)
Q Consensus 29 sq~~~s~~i~~LE~~lg~~Lf~R~~--~~~~~lT~~G~~l~~~a~ 71 (306)
|-+-+-+.+++||+ ..|++... +|- .+|+.|+.++..+-
T Consensus 118 Sg~iiR~~LQqLE~---~glVek~~~~~GR-~lT~~Gr~~LD~iA 158 (169)
T PTZ00095 118 SGKILRWICQQLEK---LGLVEQGPKKKGR-RLTRKGCNFANAFA 158 (169)
T ss_pred chHHHHHHHHHHHH---CCCEEecCCCCCC-EECHhHHHHHHHHH
Confidence 34457778899986 46777663 577 69999999987654
No 466
>PRK00441 argR arginine repressor; Provisional
Probab=74.85 E-value=4.6 Score=29.33 Aligned_cols=29 Identities=31% Similarity=0.266 Sum_probs=23.0
Q ss_pred HHhcCCHHHHHHHh-----CCCchHHHHHHHHHHH
Q psy3760 13 VRQNFNLTEAAKAL-----YTSQPGVSKAIIELEE 42 (306)
Q Consensus 13 ~~~~~s~~~aA~~l-----~isq~~~s~~i~~LE~ 42 (306)
.... +-..-++.| ++||+|+||-|++|+-
T Consensus 16 ~~~~-~q~eL~~~L~~~G~~vSqaTisRDl~~L~l 49 (149)
T PRK00441 16 KEIE-TQEELAEELKKMGFDVTQATVSRDIKELKL 49 (149)
T ss_pred cCCC-cHHHHHHHHHhcCCCcCHHHHHHHHHHcCc
Confidence 3345 667778887 9999999999998863
No 467
>PRK06704 RNA polymerase factor sigma-70; Validated
Probab=74.83 E-value=9 Score=30.16 Aligned_cols=43 Identities=14% Similarity=0.118 Sum_probs=32.3
Q ss_pred hHHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCce
Q psy3760 5 QFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSID 47 (306)
Q Consensus 5 ~l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~ 47 (306)
+-.+|....-.|.|+...|+.||+|.+|+..++.+--+.|...
T Consensus 121 ~R~v~lL~~~eg~S~~EIAe~LgiS~~tVksrL~Rark~Lr~~ 163 (228)
T PRK06704 121 QSAILLLKDVFQYSIADIAKVCSVSEGAVKASLFRSRNRLKTV 163 (228)
T ss_pred HhhHhhhHHhhCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 3345555443455999999999999999998888877777543
No 468
>PRK03341 arginine repressor; Provisional
Probab=74.82 E-value=4.6 Score=29.99 Aligned_cols=25 Identities=28% Similarity=0.268 Sum_probs=20.9
Q ss_pred CHHHHHHHh-----CCCchHHHHHHHHHHH
Q psy3760 18 NLTEAAKAL-----YTSQPGVSKAIIELEE 42 (306)
Q Consensus 18 s~~~aA~~l-----~isq~~~s~~i~~LE~ 42 (306)
+-..-++.| .+||+||||-|++|+.
T Consensus 31 tQ~eL~~~L~~~Gi~vTQaTiSRDl~eL~~ 60 (168)
T PRK03341 31 SQAELAALLADEGIEVTQATLSRDLDELGA 60 (168)
T ss_pred cHHHHHHHHHHcCCcccHHHHHHHHHHhcC
Confidence 445667788 9999999999999874
No 469
>PRK12516 RNA polymerase sigma factor; Provisional
Probab=74.74 E-value=9.1 Score=28.98 Aligned_cols=42 Identities=14% Similarity=0.065 Sum_probs=30.4
Q ss_pred hhHHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcC
Q psy3760 4 HQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELS 45 (306)
Q Consensus 4 ~~l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg 45 (306)
++-++|....-.|.|+...|+.||+|.+||-.++.+--..|-
T Consensus 120 ~~r~i~~L~~~~g~s~~EIA~~Lgis~~tVk~~l~Rar~~Lr 161 (187)
T PRK12516 120 DQREAIILVGASGFAYEEAAEICGCAVGTIKSRVNRARQRLQ 161 (187)
T ss_pred HHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 344566554445569999999999999998777666555553
No 470
>TIGR00738 rrf2_super rrf2 family protein (putative transcriptional regulator). This model represents a superfamily of probable transcriptional regulators. One member, RRF2 of Desulfovibrio vulgaris is an apparent regulatory protein experimentally (MEDLINE:97293189). The N-terminal region appears related to the DNA-binding biotin repressor region of the BirA bifunctional according to results after three rounds of PSI-BLAST with a fairly high stringency.
Probab=74.74 E-value=15 Score=25.91 Aligned_cols=47 Identities=21% Similarity=0.241 Sum_probs=35.9
Q ss_pred CHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEec-CCCccccCHhHHHH
Q psy3760 18 NLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRH-GKRIRGLTKPGQAI 66 (306)
Q Consensus 18 s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~-~~~~~~lT~~G~~l 66 (306)
|...-|+.++++++++.+.++.|++ .|.---.+. ++|. .|+...+.+
T Consensus 27 s~~eia~~~~i~~~~v~~il~~L~~-~gli~~~~g~~ggy-~l~~~~~~i 74 (132)
T TIGR00738 27 SVKEIAERQGISRSYLEKILRTLRR-AGLVESVRGPGGGY-RLARPPEEI 74 (132)
T ss_pred cHHHHHHHHCcCHHHHHHHHHHHHH-CCcEEeccCCCCCc-cCCCCHHHC
Confidence 8889999999999999999999996 565222222 2466 798888765
No 471
>TIGR02787 codY_Gpos GTP-sensing transcriptional pleiotropic repressor CodY. This model represents the full length of CodY, a pleiotropic repressor in Bacillus subtilis and other Firmicutes (low-GC Gram-positive bacteria) that responds to intracellular levels of GTP and branched chain amino acids. The C-terminal helix-turn-helix DNA-binding region is modeled by pfam08222 in Pfam.
Probab=74.68 E-value=4.1 Score=31.94 Aligned_cols=48 Identities=13% Similarity=0.086 Sum_probs=34.9
Q ss_pred CHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecC-CCccccCHhHHHHH
Q psy3760 18 NLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHG-KRIRGLTKPGQAIL 67 (306)
Q Consensus 18 s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~-~~~~~lT~~G~~l~ 67 (306)
|.++-|+++|+|.+++..++++||+. |+--....| +|. ...+....|+
T Consensus 200 se~eLAerlGVSRs~ireAlrkLE~a-GvIe~r~LG~kGt-~V~~l~~~~~ 248 (251)
T TIGR02787 200 VASKIADRVGITRSVIVNALRKLESA-GVIESRSLGMKGT-YIKVLNDKLI 248 (251)
T ss_pred cHHHHHHHHCCCHHHHHHHHHHHHHC-CCEEeccCCCCcc-EeCCCChhhh
Confidence 67888999999999999999999974 555544324 465 4555555554
No 472
>PF02082 Rrf2: Transcriptional regulator; InterPro: IPR000944 The following uncharacterised bacterial proteins have been shown to be evolutionary related, Desulfovibrio vulgaris protein Rrf2; Escherichia coli hypothetical proteins yfhP and yjeB; Bacillus subtilis hypothetical proteins yhdE, yrzC and ywgB; Mycobacterium tuberculosis hypothetical protein Rv1287; and Synechocystis sp. (strain PCC 6803) hypothetical protein slr0846. These are small proteins of 12 to 18kDa which seem to contain a signal sequence, and may represent a family of probable transcriptional regulators.; PDB: 3T8T_A 3T8R_A 3K69_A 3LWF_C 1XD7_A 2Y75_E 1YLF_C.
Probab=74.48 E-value=7.6 Score=24.83 Aligned_cols=55 Identities=20% Similarity=0.171 Sum_probs=35.8
Q ss_pred HHHHHHHHHhc----CCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecC-CCccccCHh
Q psy3760 6 FRFVREAVRQN----FNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHG-KRIRGLTKP 62 (306)
Q Consensus 6 l~~f~~v~~~~----~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~-~~~~~lT~~ 62 (306)
++.++.++..+ -|...-|+.++++++.+.+-+++|++ -|.-=-.|.. +|. .|+..
T Consensus 11 l~~l~~la~~~~~~~~s~~eiA~~~~i~~~~l~kil~~L~~-~Gli~s~~G~~GGy-~L~~~ 70 (83)
T PF02082_consen 11 LRILLYLARHPDGKPVSSKEIAERLGISPSYLRKILQKLKK-AGLIESSRGRGGGY-RLARP 70 (83)
T ss_dssp HHHHHHHHCTTTSC-BEHHHHHHHHTS-HHHHHHHHHHHHH-TTSEEEETSTTSEE-EESS-
T ss_pred HHHHHHHHhCCCCCCCCHHHHHHHHCcCHHHHHHHHHHHhh-CCeeEecCCCCCce-eecCC
Confidence 44555555443 26889999999999999999999998 5653222332 344 56543
No 473
>TIGR03070 couple_hipB transcriptional regulator, y4mF family. Members of this family belong to a clade of helix-turn-helix DNA-binding proteins, among the larger family pfam01381 (HTH_3; Helix-turn-helix). Members are similar in sequence to the HipB protein of E. coli. Genes for members of the seed alignment for this protein family were found to be closely linked to genes encoding proteins related to HipA. The HibBA operon appears to have some features in common with toxin-antitoxin post-segregational killing systems.
Probab=74.41 E-value=3.1 Score=24.11 Aligned_cols=24 Identities=4% Similarity=-0.119 Sum_probs=19.4
Q ss_pred HhcCCHHHHHHHhCCCchHHHHHH
Q psy3760 14 RQNFNLTEAAKALYTSQPGVSKAI 37 (306)
Q Consensus 14 ~~~~s~~~aA~~l~isq~~~s~~i 37 (306)
+.|.|....|+.+++|++++|+..
T Consensus 13 ~~gltq~~lA~~~gvs~~~vs~~e 36 (58)
T TIGR03070 13 ALGLTQADLADLAGVGLRFIRDVE 36 (58)
T ss_pred HcCCCHHHHHHHhCCCHHHHHHHH
Confidence 344577889999999999999754
No 474
>PF13560 HTH_31: Helix-turn-helix domain; PDB: 3F51_C 3F52_A 3PXP_A 2OFY_A.
Probab=74.40 E-value=2.9 Score=25.15 Aligned_cols=22 Identities=27% Similarity=0.253 Sum_probs=16.9
Q ss_pred hcCCHHHHHHHhCCCchHHHHH
Q psy3760 15 QNFNLTEAAKALYTSQPGVSKA 36 (306)
Q Consensus 15 ~~~s~~~aA~~l~isq~~~s~~ 36 (306)
.|.|....|+.+|+|++++++.
T Consensus 13 ~gls~~~lA~~~g~s~s~v~~i 34 (64)
T PF13560_consen 13 AGLSQAQLADRLGVSQSTVSRI 34 (64)
T ss_dssp HTS-HHHHHHHHTS-HHHHHHH
T ss_pred cCCCHHHHHHHHCcCHHHHHHH
Confidence 3468899999999999999864
No 475
>PRK12524 RNA polymerase sigma factor; Provisional
Probab=74.27 E-value=9.3 Score=29.14 Aligned_cols=43 Identities=14% Similarity=-0.011 Sum_probs=33.3
Q ss_pred hHHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCce
Q psy3760 5 QFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSID 47 (306)
Q Consensus 5 ~l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~ 47 (306)
+=++|....-.|.|+...|+.||+|.+||..++.+-.+.|-..
T Consensus 141 ~r~i~~L~~~~g~s~~eIA~~lgis~~tV~~~l~Ra~~~Lr~~ 183 (196)
T PRK12524 141 QRQAVVLRHIEGLSNPEIAEVMEIGVEAVESLTARGKRALAAL 183 (196)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 3345655544556999999999999999999999887777443
No 476
>PRK10622 pheA bifunctional chorismate mutase/prephenate dehydratase; Provisional
Probab=74.15 E-value=57 Score=28.13 Aligned_cols=147 Identities=12% Similarity=0.034 Sum_probs=71.1
Q ss_pred cEEEEecccchhhhhHHHHHHHHHh-CCCcEEEEEeCChhHHHHHHHcCCeeEEEEccccCCCCCce-e-eccccceEE-
Q psy3760 94 NLTIATTHTQARYALPKIIKEFTIQ-FPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLI-S-IPCYQWEYV- 169 (306)
Q Consensus 94 ~l~I~~~~~~~~~~l~~~l~~~~~~-~p~~~i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~~~~~~-~-~~l~~~~~~- 169 (306)
..+||+.... ..+-..+...+... +++. ..+-..+..++++.+.+|++|+|++.-.......+. . .-|...++.
T Consensus 103 ~~~va~lGp~-GtfSh~Aa~~~~~~~~~~~-~~~~~~s~~~v~~av~~g~~d~gVvPiENS~~G~V~~t~DlL~~~~l~I 180 (386)
T PRK10622 103 SARIAFLGPK-GSYSHLAARQYAARHFEQF-IESGCAKFADIFNQVETGQADYAVLPIENTSSGAINDVYDLLQHTSLSI 180 (386)
T ss_pred cceEEEECCC-CcHHHHHHHHhhccccccc-cccCCCCHHHHHHHHHCCCCCEEEEEEecCCceehHHHHHHHhcCCCEE
Confidence 4667776443 23444444443221 1222 111345677899999999999999863211110000 0 001111111
Q ss_pred ---EEecCCCCCCCCCCcChhhhcCCCeEeecCCCCcHHHHHHHHHhCCCcee-EEEEecCHHHHHHHHHhcc---ceee
Q psy3760 170 ---IIVPLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPY-IVLETINSDIIKTYVELRM---GIGI 242 (306)
Q Consensus 170 ---~v~~~~~~l~~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~v~~g~---gi~~ 242 (306)
++.+-.|-|......+++++ ..|..++. ...+..+|++.+ |+ ....++|...+..++..+. ..++
T Consensus 181 ~~E~~l~I~h~Ll~~~~~~l~~I---~~V~SHpq--al~QC~~fL~~~---p~~~~~~~~sTa~Aa~~v~~~~~~~~AAI 252 (386)
T PRK10622 181 VGEMTLPIDHCVLVSGTTDLSTI---ETVYSHPQ--PFQQCSQFLNRY---PHWKIEYTESTAAAMEKVAQANSPHVAAL 252 (386)
T ss_pred EEEEEEEEEEEEecCCCCCHHHC---eEEEEehH--HHHHHHHHHHHC---CCceEEEcCChHHHHHHHHhcCCCCEEEE
Confidence 11222333332222344444 33444432 235667777765 22 2344677777777776542 2577
Q ss_pred eecceecc
Q psy3760 243 IASIAFDS 250 (306)
Q Consensus 243 ~p~~~~~~ 250 (306)
.|...+..
T Consensus 253 ~s~~aa~~ 260 (386)
T PRK10622 253 GSEAGGAL 260 (386)
T ss_pred CCHHHHHH
Confidence 77766554
No 477
>PRK12520 RNA polymerase sigma factor; Provisional
Probab=74.11 E-value=9.6 Score=28.88 Aligned_cols=44 Identities=9% Similarity=-0.030 Sum_probs=33.2
Q ss_pred hHHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCcee
Q psy3760 5 QFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDI 48 (306)
Q Consensus 5 ~l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~L 48 (306)
+=++|....-.|.|+...|+.||+|.+||-.++.+--+.|...|
T Consensus 136 ~r~v~~l~~~~g~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l 179 (191)
T PRK12520 136 TGRVFMMREWLELETEEICQELQITATNAWVLLYRARMRLRECL 179 (191)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 33455554434459999999999999999999998888774433
No 478
>PRK15431 ferrous iron transport protein FeoC; Provisional
Probab=74.07 E-value=12 Score=23.70 Aligned_cols=41 Identities=22% Similarity=0.233 Sum_probs=35.9
Q ss_pred chhhHHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHH
Q psy3760 2 NLHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEE 43 (306)
Q Consensus 2 ~~~~l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~ 43 (306)
++.+++-+++....- |...-|.++++++++|--.+..|+..
T Consensus 3 ~L~qlRd~l~~~gr~-s~~~Ls~~~~~p~~~VeaMLe~l~~k 43 (78)
T PRK15431 3 SLIQVRDLLALRGRM-EAAQISQTLNTPQPMINAMLQQLESM 43 (78)
T ss_pred cHHHHHHHHHHcCcc-cHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence 466788888888887 99999999999999999999999864
No 479
>TIGR02844 spore_III_D sporulation transcriptional regulator SpoIIID. Members of this protein are the transcriptional regulator SpoIIID, or stage III sporulation protein D. It is present in genomes if and only if the species is capable of endospore formation as occurs in the model species Bacillus subtilis. SpoIIID is a DNA binding protein that, in B. subtilis, downregulates many genes but also turns on ten genes.
Probab=73.93 E-value=6.9 Score=24.95 Aligned_cols=34 Identities=21% Similarity=0.226 Sum_probs=23.4
Q ss_pred hhHHHHHHHHHhcCCHHHHHHHhCCCchHHHHHH
Q psy3760 4 HQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAI 37 (306)
Q Consensus 4 ~~l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i 37 (306)
++.++.-.+.+...++..-|+.+|+|.+|||+.+
T Consensus 7 R~~~I~e~l~~~~~ti~dvA~~~gvS~~TVsr~L 40 (80)
T TIGR02844 7 RVLEIGKYIVETKATVRETAKVFGVSKSTVHKDV 40 (80)
T ss_pred HHHHHHHHHHHCCCCHHHHHHHhCCCHHHHHHHh
Confidence 3444444445412256778999999999999966
No 480
>PF04552 Sigma54_DBD: Sigma-54, DNA binding domain; InterPro: IPR007634 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 [].; PDB: 2AHQ_A 2O9L_A 2O8K_A.
Probab=73.90 E-value=1 Score=33.04 Aligned_cols=22 Identities=23% Similarity=0.309 Sum_probs=0.0
Q ss_pred CHHHHHHHhCCCchHHHHHHHH
Q psy3760 18 NLTEAAKALYTSQPGVSKAIIE 39 (306)
Q Consensus 18 s~~~aA~~l~isq~~~s~~i~~ 39 (306)
++...|+.||++.|||||.++.
T Consensus 51 t~~~iA~~lgl~~STVSRav~~ 72 (160)
T PF04552_consen 51 TMKDIADELGLHESTVSRAVKN 72 (160)
T ss_dssp ----------------------
T ss_pred CHHHHHHHhCCCHhHHHHHHcC
Confidence 6788999999999999999973
No 481
>PRK07377 hypothetical protein; Provisional
Probab=73.76 E-value=28 Score=26.09 Aligned_cols=57 Identities=7% Similarity=0.200 Sum_probs=37.7
Q ss_pred CCCcEEEEecc------cchhhhhHHHHHHHHHhCCCcEEEEEe-CChhHHHHHHHcCCeeEEEEc
Q psy3760 91 DTGNLTIATTH------TQARYALPKIIKEFTIQFPKVKLSLLQ-GNPKQITEMIRNDQADIAIVT 149 (306)
Q Consensus 91 ~~~~l~I~~~~------~~~~~~l~~~l~~~~~~~p~~~i~~~~-~~~~~~~~~l~~~~~Di~i~~ 149 (306)
.+..+|+|+-. .... -+.+.++.+.++| +.++++.. .+...+.+.+.+|++|++...
T Consensus 73 ss~~~Rlgv~~~~~~~~~~~~-~l~~~l~~~~~~y-~~rlElv~y~~~~~l~~aL~~~eVh~~c~~ 136 (184)
T PRK07377 73 SSLVMRLGVLEIETETSSVFD-QLIDQLRTILDKY-HLRLELVVYPDLQALEQALRDKEVHAICLE 136 (184)
T ss_pred hccEEEEEEEeccccccccHH-HHHHHHHHHHHHh-CceeeEEecCCHHHHHHHHhcCCccEEecC
Confidence 35689999733 1222 2334445566654 66677666 466778999999999988763
No 482
>PRK12533 RNA polymerase sigma factor; Provisional
Probab=73.76 E-value=8.5 Score=30.01 Aligned_cols=45 Identities=9% Similarity=-0.014 Sum_probs=33.1
Q ss_pred hhHHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCcee
Q psy3760 4 HQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDI 48 (306)
Q Consensus 4 ~~l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~L 48 (306)
++-++|....-.|.|+.+.|+.||+|.++|.++|.+.-..|-..|
T Consensus 138 ~~R~v~~L~y~eg~s~~EIAe~LgiS~~tVk~~L~RAr~~Lr~~l 182 (216)
T PRK12533 138 EYREVLVLRELEDMSYREIAAIADVPVGTVMSRLARARRRLAALL 182 (216)
T ss_pred HHHhHhhhHHhcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 344555554434559999999999999999888877666665554
No 483
>TIGR02607 antidote_HigA addiction module antidote protein, HigA family. Members of this family form a distinct clade within the larger family HTH_3 of helix-turn-helix proteins, described by Pfam model pfam01381. Members of this clade are strictly bacterial and nearly always shorter than 110 amino acids. This family includes the characterized 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 uncoded by the upstream member of the gene pair.
Probab=73.44 E-value=4.6 Score=25.34 Aligned_cols=24 Identities=25% Similarity=0.241 Sum_probs=20.1
Q ss_pred HHhcCCHHHHHHHhCCCchHHHHH
Q psy3760 13 VRQNFNLTEAAKALYTSQPGVSKA 36 (306)
Q Consensus 13 ~~~~~s~~~aA~~l~isq~~~s~~ 36 (306)
.+.|.+....|+.+|+|++++|+.
T Consensus 15 ~~~~~t~~~lA~~~gis~~tis~~ 38 (78)
T TIGR02607 15 EPLGLSIRALAKALGVSRSTLSRI 38 (78)
T ss_pred HHcCCCHHHHHHHhCCCHHHHHHH
Confidence 444558999999999999999974
No 484
>PF00292 PAX: 'Paired box' domain; InterPro: IPR001523 The paired box is a conserved 124 amino acid N-terminal domain of unknown function that usually, but not always, precedes a homeobox domain (see IPR001356 from INTERPRO) [, ]. Paired box genes are expressed in alternate segments of the developing fruit fly, the observed grouping of segments into pairs depending on the position of the segment in the segmental array, and not on the identity of the segment as in the case of homeotic genes. This implies that the genes affect different processes from those altered by homeotic genes.; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 6PAX_A 1K78_E 1MDM_A 2K27_A 1PDN_C.
Probab=73.41 E-value=8.5 Score=26.90 Aligned_cols=61 Identities=15% Similarity=0.007 Sum_probs=34.3
Q ss_pred HHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEec--CCCccccCHhHHHHHHHHH
Q psy3760 9 VREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRH--GKRIRGLTKPGQAILRSIE 71 (306)
Q Consensus 9 f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~--~~~~~~lT~~G~~l~~~a~ 71 (306)
.+.+++.|-+-...|++|.+|++.+||-|.+..+ -|.---..- .+.- ..||+-.......+
T Consensus 26 Ivela~~G~rp~~Isr~l~Vs~gcVsKIl~Ry~e-TGsi~Pg~iGGskpr-v~tp~v~~~I~~~k 88 (125)
T PF00292_consen 26 IVELAKEGVRPCDISRQLRVSHGCVSKILSRYRE-TGSIRPGPIGGSKPR-VATPEVVEKIEQYK 88 (125)
T ss_dssp HHHHHHTT--HHHHHHHHT--HHHHHHHHHHHHH-HS-SS----S----S-SS-HCHHHHHHHHH
T ss_pred HHHHhhhcCCHHHHHHHHccchhHHHHHHHHHHH-hcccCcccccCCCCC-CCChHHHHHHHHHH
Confidence 4567777778889999999999999999999954 443333322 1233 36776554444433
No 485
>COG1427 Predicted periplasmic solute-binding protein [General function prediction only]
Probab=73.33 E-value=45 Score=26.61 Aligned_cols=113 Identities=14% Similarity=0.195 Sum_probs=61.7
Q ss_pred EEEEeCChhHHHHHHHcCCeeEEEEccccCCCCCceeec------cccceEEEEecCCCCCCCCCCcChhhhcCCCeEee
Q psy3760 124 LSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLISIP------CYQWEYVIIVPLDHPLLLLNSISLKEISNYPLITY 197 (306)
Q Consensus 124 i~~~~~~~~~~~~~l~~~~~Di~i~~~~~~~~~~~~~~~------l~~~~~~~v~~~~~~l~~~~~i~~~dl~~~~~i~~ 197 (306)
+++....+.++.+.|.+|++|+|+++.-..-..++...+ .+.. +.+.+-...| +.+.+-+..
T Consensus 25 ~~v~~~~P~el~~~ll~Grid~a~VSs~~~~~~~l~~l~~~~I~s~g~v-lSV~L~s~~~-----------~~~~~~vAv 92 (252)
T COG1427 25 ERVVKAVPSELNELLLSGRIDAALVSSVAYAEDDLKLLPGLGIASNGKV-LSVLLFSNRP-----------LDEGRRVAV 92 (252)
T ss_pred eEEEecCCHHHHHHHHhCccceeeechHHHhhcccccCCCceEEecCce-EEEEEEecCC-----------cccCcceec
Confidence 677778788999999999999999873222222222222 1111 1111111111 222233333
Q ss_pred cCCCCc-HHHHHHHHHhCCCceeEEEEecCHHHHHHHHHhccceeeeecceecc
Q psy3760 198 DLSFSG-RIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMGIGIIASIAFDS 250 (306)
Q Consensus 198 ~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~~~p~~~~~~ 250 (306)
...+.. ...+.-.+.+.+ -+++...+ +....-++.+.-+|.-++.+-..+.
T Consensus 93 T~~S~TS~~LLkvL~~~~~-~~~v~~~~-~~~~~~~~le~~d~~LlIGDeAL~~ 144 (252)
T COG1427 93 TKESATSVALLKVLLEKLG-ISNVLVET-DTTDAEELLEEADGALLIGDEALRA 144 (252)
T ss_pred CccchhHHHHHHHHHHHhC-Ccceeeec-ccCcHhHHhhcCCceEEecHHHHHh
Confidence 443333 334444455556 34544444 4446677778888888888766663
No 486
>PRK09647 RNA polymerase sigma factor SigE; Reviewed
Probab=73.24 E-value=11 Score=29.11 Aligned_cols=44 Identities=16% Similarity=0.010 Sum_probs=33.2
Q ss_pred hHHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCcee
Q psy3760 5 QFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDI 48 (306)
Q Consensus 5 ~l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~L 48 (306)
+=.+|....-.|+|+...|+.||+|.++|..++.+-.+.|-..|
T Consensus 143 ~r~v~~L~~~~g~s~~EIA~~Lgis~~tV~~~l~RArk~Lr~~l 186 (203)
T PRK09647 143 FRAAVVLCDIEGLSYEEIAATLGVKLGTVRSRIHRGRQQLRAAL 186 (203)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 33455454434459999999999999999998888887775544
No 487
>PRK12540 RNA polymerase sigma factor; Provisional
Probab=72.84 E-value=11 Score=28.48 Aligned_cols=41 Identities=12% Similarity=0.038 Sum_probs=28.7
Q ss_pred hhHHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHc
Q psy3760 4 HQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEEL 44 (306)
Q Consensus 4 ~~l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~l 44 (306)
++-++|..-.-.|+|..+.|+.|++|.+++-.++.+-.+.|
T Consensus 115 ~~R~v~~L~~~~g~s~~EIA~~Lgis~~tV~~~l~RAr~~L 155 (182)
T PRK12540 115 DQREALILVGASGFSYEDAAAICGCAVGTIKSRVNRARSKL 155 (182)
T ss_pred HHHHHhhHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 34455555444555999999999999999876665544444
No 488
>PRK12542 RNA polymerase sigma factor; Provisional
Probab=72.81 E-value=11 Score=28.47 Aligned_cols=45 Identities=13% Similarity=0.117 Sum_probs=33.9
Q ss_pred hhHHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCcee
Q psy3760 4 HQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDI 48 (306)
Q Consensus 4 ~~l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~L 48 (306)
++-++|....-.|.|+...|+.||+|.+||-.++.+--+.|-..|
T Consensus 126 ~~r~i~~l~~~~g~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~l 170 (185)
T PRK12542 126 SNRQVFKYKVFYNLTYQEISSVMGITEANVRKQFERARKRVQNMI 170 (185)
T ss_pred HHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 344556554444559999999999999999999888877774433
No 489
>PRK12545 RNA polymerase sigma factor; Provisional
Probab=72.57 E-value=11 Score=28.98 Aligned_cols=44 Identities=11% Similarity=0.049 Sum_probs=34.2
Q ss_pred hHHHHHHHHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCcee
Q psy3760 5 QFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDI 48 (306)
Q Consensus 5 ~l~~f~~v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~L 48 (306)
+=++|....-.|+|+...|+.||+|.+||..++.+-...|-..|
T Consensus 144 ~r~v~~L~~~eg~s~~EIA~~lgis~~tVk~~l~RAr~~Lr~~l 187 (201)
T PRK12545 144 IGRVFMMREFLDFEIDDICTELTLTANHCSVLLYRARTRLRTCL 187 (201)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 33455554444559999999999999999999988888886555
No 490
>PRK09391 fixK transcriptional regulator FixK; Provisional
Probab=72.10 E-value=4.3 Score=31.96 Aligned_cols=40 Identities=23% Similarity=0.298 Sum_probs=30.7
Q ss_pred CHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecC-CCccccCH
Q psy3760 18 NLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHG-KRIRGLTK 61 (306)
Q Consensus 18 s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~-~~~~~lT~ 61 (306)
+-..-|..||+|+.++||.+++|+++ -++...+ +.+ ++.+
T Consensus 181 t~~~IA~~lGisretlsR~L~~L~~~---GlI~~~~~~~i-~I~D 221 (230)
T PRK09391 181 SRRDIADYLGLTIETVSRALSQLQDR---GLIGLSGARQI-ELRN 221 (230)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHC---CcEEecCCceE-EEcC
Confidence 34689999999999999999999985 3556554 456 4554
No 491
>smart00422 HTH_MERR helix_turn_helix, mercury resistance.
Probab=72.09 E-value=19 Score=21.79 Aligned_cols=51 Identities=20% Similarity=0.075 Sum_probs=32.5
Q ss_pred CCHHHHHHHhCCCchHHHHHHHHHHHHcCceeE-Eec-CCCccccCHhHHHHHHHHHHH
Q psy3760 17 FNLTEAAKALYTSQPGVSKAIIELEEELSIDIF-IRH-GKRIRGLTKPGQAILRSIEII 73 (306)
Q Consensus 17 ~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf-~R~-~~~~~~lT~~G~~l~~~a~~i 73 (306)
.|.+.+|+.+|+|++++.+..+ -|.--. .|. ++.. ..|+.--.-+..+..+
T Consensus 1 ~s~~eva~~~gvs~~tlr~~~~-----~gli~~~~~~~~g~r-~y~~~dl~~l~~i~~l 53 (70)
T smart00422 1 YTIGEVAKLAGVSVRTLRYYER-----IGLLPPPIRTEGGYR-LYSDEDLERLRFIKRL 53 (70)
T ss_pred CCHHHHHHHHCcCHHHHHHHHH-----CCCCCCCccCCCCCE-ecCHHHHHHHHHHHHH
Confidence 3788999999999999987754 333222 243 3333 4666666655555555
No 492
>TIGR02647 DNA conserved hypothetical protein TIGR02647. Members of this family are found, so far, only in the Gammaproteobacteria. The function is unknown. The location on the chromosome usually is not far from housekeeping genes rather than in what is clearly, say, a prophage region. Some members have been annotated in public databases as DNA-binding protein inhibitor Id-2-related protein, putative transcriptional regulator, or hypothetical DNA binding protein.
Probab=71.90 E-value=9.9 Score=23.68 Aligned_cols=59 Identities=12% Similarity=0.143 Sum_probs=44.5
Q ss_pred CCHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCCccccCHhHHHHHHHHHHHHHHH
Q psy3760 17 FNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKPGQAILRSIEIIMQEI 77 (306)
Q Consensus 17 ~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~~~lT~~G~~l~~~a~~il~~~ 77 (306)
|.++.+++-+-|-+.|-...+..+..-+..-|...--+| + ||+.|..-.++++.++..+
T Consensus 17 F~~~S~~~GIKvH~dA~p~~i~a~~RLheKGLI~~pdGg-y-LT~~G~~~aEhaq~ll~iL 75 (77)
T TIGR02647 17 FNLSSTQEGIKVHSTASPAAVAAAARLHEKGLTTQPDGG-Y-LTSLGLEAAEHAQKLLTIL 75 (77)
T ss_pred CCchhhhcCccccccCCHHHHHHHHHHHHcCCccCCCCC-E-ecHHHHHHHHHHHHHHHHH
Confidence 456666666667677777777777777777777765555 4 9999999999999988754
No 493
>cd02395 SF1_like-KH Splicing factor 1 (SF1) K homology RNA-binding domain (KH). Splicing factor 1 (SF1) specifically recognizes the intron branch point sequence (BPS) UACUAAC in the pre-mRNA transcripts during spliceosome assembly. We show that the KH-QUA2 region of SF1 defines an enlarged KH (hnRNP K) fold which is necessary and sufficient for BPS binding. KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=71.84 E-value=6.7 Score=27.30 Aligned_cols=20 Identities=30% Similarity=0.356 Sum_probs=17.5
Q ss_pred HHHHHHHHHcCceeEEecCC
Q psy3760 35 KAIIELEEELSIDIFIRHGK 54 (306)
Q Consensus 35 ~~i~~LE~~lg~~Lf~R~~~ 54 (306)
+.|++||++.|+++..|..+
T Consensus 26 ~tiK~i~~eTg~kI~Irg~g 45 (120)
T cd02395 26 NTLKQLEKETGAKISIRGKG 45 (120)
T ss_pred hHHHHHHHHHCCEEEEecCc
Confidence 46899999999999999753
No 494
>PRK09644 RNA polymerase sigma factor SigM; Provisional
Probab=71.67 E-value=12 Score=27.57 Aligned_cols=44 Identities=14% Similarity=0.037 Sum_probs=35.3
Q ss_pred hhHHHHHH-HHHhcCCHHHHHHHhCCCchHHHHHHHHHHHHcCcee
Q psy3760 4 HQFRFVRE-AVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDI 48 (306)
Q Consensus 4 ~~l~~f~~-v~~~~~s~~~aA~~l~isq~~~s~~i~~LE~~lg~~L 48 (306)
++-++|.. ..+.. |+.+.|+.||+|.+|+..+|.+.-+.|...|
T Consensus 112 ~~r~v~~l~~~~g~-s~~eIA~~lgis~~tv~~~l~Rar~~Lr~~l 156 (165)
T PRK09644 112 IEAQAILLCDVHEL-TYEEAASVLDLKLNTYKSHLFRGRKRLKALL 156 (165)
T ss_pred HHHHHHHhHHHhcC-CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 44456664 45666 9999999999999999999999988885544
No 495
>PF07900 DUF1670: Protein of unknown function (DUF1670); InterPro: IPR012872 The hypothetical eukaryotic proteins found in this family are of unknown function.
Probab=71.20 E-value=7.4 Score=30.02 Aligned_cols=48 Identities=27% Similarity=0.197 Sum_probs=38.3
Q ss_pred hHHHHHHHHHhcC--CHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEec
Q psy3760 5 QFRFVREAVRQNF--NLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRH 52 (306)
Q Consensus 5 ~l~~f~~v~~~~~--s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~ 52 (306)
-+|+|-+..+.|. +-+..|--|++|.+|||+.|+.+|++-|.-|=.|.
T Consensus 92 IvRl~~EAy~QgglLT~~Dla~LL~~S~~TI~~~i~~yq~e~g~vvPtrG 141 (220)
T PF07900_consen 92 IVRLTNEAYDQGGLLTQEDLAMLLGISPRTISKDIKEYQKEHGVVVPTRG 141 (220)
T ss_pred HHHHHHHHHHcCCcccHHHHHHHHCCCHHHHHHHHHHHHHHcCceeccCC
Confidence 3567777777762 23456889999999999999999999988886665
No 496
>COG1570 XseA Exonuclease VII, large subunit [DNA replication, recombination, and repair]
Probab=71.14 E-value=19 Score=31.27 Aligned_cols=95 Identities=19% Similarity=0.298 Sum_probs=67.2
Q ss_pred CCCcEEEEecccchhhhhHHHHHHHHHhCCCcEEEEEe------CChhHHHHHHHc----CCeeEEEEccccCC------
Q psy3760 91 DTGNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQ------GNPKQITEMIRN----DQADIAIVTEILSP------ 154 (306)
Q Consensus 91 ~~~~l~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~------~~~~~~~~~l~~----~~~Di~i~~~~~~~------ 154 (306)
+...=+||+-.+.....+-.++..+.+++|.+.+.+.+ ....++.+.|.. +++|+.|+......
T Consensus 132 P~~p~~IGVITS~tgAairDIl~~~~rR~P~~~viv~pt~VQG~~A~~eIv~aI~~an~~~~~DvlIVaRGGGSiEDLW~ 211 (440)
T COG1570 132 PFFPKKIGVITSPTGAALRDILHTLSRRFPSVEVIVYPTLVQGEGAAEEIVEAIERANQRGDVDVLIVARGGGSIEDLWA 211 (440)
T ss_pred CCCCCeEEEEcCCchHHHHHHHHHHHhhCCCCeEEEEeccccCCCcHHHHHHHHHHhhccCCCCEEEEecCcchHHHHhc
Confidence 44556899988888999999999999999999998866 234456555543 56999998632221
Q ss_pred -CCCceeeccccceEEEEecCCCCCCCCCCcChhhh
Q psy3760 155 -SDKLISIPCYQWEYVIIVPLDHPLLLLNSISLKEI 189 (306)
Q Consensus 155 -~~~~~~~~l~~~~~~~v~~~~~~l~~~~~i~~~dl 189 (306)
++....+.++..+.=++..-+|. .-.++.|+
T Consensus 212 FNdE~vaRAi~~s~iPvISAVGHE----tD~tL~Df 243 (440)
T COG1570 212 FNDEIVARAIAASRIPVISAVGHE----TDFTLADF 243 (440)
T ss_pred cChHHHHHHHHhCCCCeEeecccC----CCccHHHh
Confidence 34445567777777777778884 23455555
No 497
>COG2238 RPS19A Ribosomal protein S19E (S16A) [Translation, ribosomal structure and biogenesis]
Probab=71.07 E-value=8.8 Score=27.13 Aligned_cols=46 Identities=28% Similarity=0.354 Sum_probs=33.7
Q ss_pred CchHHHHHHHHHHHHcCceeEEecCCCccccCHhHHHHHHHH-HHHHHHHH
Q psy3760 29 SQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKPGQAILRSI-EIIMQEIE 78 (306)
Q Consensus 29 sq~~~s~~i~~LE~~lg~~Lf~R~~~~~~~lT~~G~~l~~~a-~~il~~~~ 78 (306)
|-+-+-+.+++||+. =|+++..+|- .+|+.|+.|+..+ .++.+++.
T Consensus 94 sgsI~RkilqqLE~~---G~V~k~~~GR-~ltp~GrsllD~~a~ei~eel~ 140 (147)
T COG2238 94 SGSIIRKVLQQLEKA---GLVEKTPKGR-VLTPKGRSLLDRIATEIKEELE 140 (147)
T ss_pred CchHHHHHHHHHHHC---CceeecCCCc-eeCccchhHHHHHHHHHHHHhc
Confidence 455667788899873 4778888888 6999999999764 44444444
No 498
>COG5625 Predicted transcription regulator containing HTH domain [Transcription]
Probab=71.04 E-value=20 Score=23.72 Aligned_cols=83 Identities=24% Similarity=0.174 Sum_probs=61.4
Q ss_pred hHHHHHHHHHhcC--CHHHHHHHhCCCchHHHHHHHHHH--HHcCceeEEecCCCcc-ccCHhHHHHHHHHHHHHHHHHH
Q psy3760 5 QFRFVREAVRQNF--NLTEAAKALYTSQPGVSKAIIELE--EELSIDIFIRHGKRIR-GLTKPGQAILRSIEIIMQEIEG 79 (306)
Q Consensus 5 ~l~~f~~v~~~~~--s~~~aA~~l~isq~~~s~~i~~LE--~~lg~~Lf~R~~~~~~-~lT~~G~~l~~~a~~il~~~~~ 79 (306)
.+++.--+++.++ -++.-+++|++|+-++-.+++.|= --+-.+|.+..==|.+ ..|+.=+-+-+.=+.++.++++
T Consensus 23 eI~IY~lLve~~~~mri~ei~rEl~is~rtvr~~v~~l~rrGll~relvqkgWvGYiya~~~P~k~leei~~~i~keiEe 102 (113)
T COG5625 23 EIRIYSLLVEKGRGMRIREIQRELGISERTVRAAVAVLLRRGLLARELVQKGWVGYIYATTPPPKPLEEIEEEIMKEIEE 102 (113)
T ss_pred hhhhhhHHHHhcCCchHHHHHHHHhHHHHHHHHHHHHHHHhhHHHHHHHhccceeeEecCCCCchHHHHHHHHHHHHHHH
Confidence 3555566666652 268899999999999999999886 5566666665522222 6778888888888889999999
Q ss_pred HHHHHHhh
Q psy3760 80 LKKIGKEF 87 (306)
Q Consensus 80 ~~~~~~~~ 87 (306)
++.++++.
T Consensus 103 lEk~~k~e 110 (113)
T COG5625 103 LEKEFKNE 110 (113)
T ss_pred HHHHHHhh
Confidence 99888764
No 499
>PRK13918 CRP/FNR family transcriptional regulator; Provisional
Probab=71.03 E-value=5 Score=30.65 Aligned_cols=41 Identities=27% Similarity=0.173 Sum_probs=31.3
Q ss_pred CHHHHHHHhCCCchHHHHHHHHHHHHcCceeEEecCCCccccCHh
Q psy3760 18 NLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKP 62 (306)
Q Consensus 18 s~~~aA~~l~isq~~~s~~i~~LE~~lg~~Lf~R~~~~~~~lT~~ 62 (306)
|-..-|..+|+|+.++||.+++|+++ -++.+.++.+ ++.+.
T Consensus 151 t~~~iA~~lG~tretvsR~l~~l~~~---g~I~~~~~~i-~I~d~ 191 (202)
T PRK13918 151 THDELAAAVGSVRETVTKVIGELSRE---GYIRSGYGKI-QLLDL 191 (202)
T ss_pred CHHHHHHHhCccHHHHHHHHHHHHHC---CCEEcCCCEE-EEECH
Confidence 45678999999999999999999963 4556665666 45443
No 500
>PF06970 RepA_N: Replication initiator protein A (RepA) N-terminus; InterPro: IPR010724 This entry represents the N terminus (approximately 80 residues) of replication initiator protein A (RepA), a DNA replication initiator in plasmids []. Most proteins in this entry are bacterial, but archaeal and eukaryotic members are also included.
Probab=70.62 E-value=3.5 Score=25.99 Aligned_cols=24 Identities=38% Similarity=0.390 Sum_probs=21.2
Q ss_pred CCHHHHHHHhCCCchHHHHHHHHH
Q psy3760 17 FNLTEAAKALYTSQPGVSKAIIEL 40 (306)
Q Consensus 17 ~s~~~aA~~l~isq~~~s~~i~~L 40 (306)
+|....++.||+|.+++.+..++|
T Consensus 53 ~s~eel~~~L~~s~~tv~~~~keL 76 (76)
T PF06970_consen 53 FSIEELMELLNCSKSTVIKAKKEL 76 (76)
T ss_pred eeHHHHHHHHCCCHHHHHHHHHcC
Confidence 367889999999999999998875
Done!