Query 018854
Match_columns 349
No_of_seqs 161 out of 1138
Neff 4.8
Searched_HMMs 46136
Date Fri Mar 29 04:35:59 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/018854.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/018854hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PLN02245 ATP phosphoribosyl tr 100.0 2.4E-90 5.3E-95 686.4 30.1 327 15-349 7-335 (403)
2 COG0040 HisG ATP phosphoribosy 100.0 1.1E-75 2.4E-80 561.2 23.8 243 82-349 1-244 (290)
3 PRK13583 hisG ATP phosphoribos 100.0 3.2E-71 6.9E-76 516.6 21.0 223 82-309 1-228 (228)
4 PRK01686 hisG ATP phosphoribos 100.0 9.3E-71 2E-75 509.9 22.6 212 81-315 1-214 (215)
5 PRK13584 hisG ATP phosphoribos 100.0 4.5E-67 9.8E-72 481.3 20.6 198 83-313 1-202 (204)
6 TIGR00070 hisG ATP phosphoribo 100.0 7.1E-65 1.5E-69 460.3 19.6 182 84-286 1-182 (182)
7 PF01634 HisG: ATP phosphoribo 100.0 7.8E-58 1.7E-62 408.1 11.4 163 132-312 1-163 (163)
8 KOG2831 ATP phosphoribosyltran 100.0 2.7E-58 5.8E-63 428.1 2.1 257 79-349 6-262 (308)
9 PRK00489 hisG ATP phosphoribos 100.0 1.3E-48 2.8E-53 372.4 24.0 240 81-349 2-241 (287)
10 TIGR03455 HisG_C-term ATP phos 99.1 6.8E-11 1.5E-15 98.5 5.4 55 287-349 1-55 (100)
11 PF08029 HisG_C: HisG, C-termi 98.4 2.2E-07 4.8E-12 73.9 2.5 31 313-349 1-31 (75)
12 TIGR01728 SsuA_fam ABC transpo 97.5 0.00049 1.1E-08 63.1 8.8 159 134-310 39-209 (288)
13 smart00062 PBPb Bacterial peri 97.0 0.0074 1.6E-07 50.6 9.7 142 128-289 42-190 (219)
14 PF09084 NMT1: NMT1/THI5 like; 96.9 0.0015 3.2E-08 58.4 5.3 168 127-311 23-205 (216)
15 PRK11480 tauA taurine transpor 96.9 0.0062 1.3E-07 58.9 10.0 163 127-310 53-230 (320)
16 PRK11553 alkanesulfonate trans 96.8 0.0072 1.6E-07 57.7 9.8 161 134-311 66-236 (314)
17 TIGR01729 taurine_ABC_bnd taur 96.8 0.0066 1.4E-07 57.6 9.3 166 127-310 29-208 (300)
18 TIGR03427 ABC_peri_uca ABC tra 95.2 0.18 3.9E-06 50.0 10.7 154 134-309 45-212 (328)
19 PF03466 LysR_substrate: LysR 95.0 0.32 7E-06 41.1 10.4 166 125-312 33-208 (209)
20 cd00134 PBPb Bacterial peripla 94.4 0.51 1.1E-05 39.7 10.2 128 127-273 40-172 (218)
21 PRK11917 bifunctional adhesin/ 94.2 0.8 1.7E-05 43.0 12.0 160 127-310 83-248 (259)
22 PRK11063 metQ DL-methionine tr 93.8 0.2 4.3E-06 48.4 7.3 103 83-187 130-236 (271)
23 PF13379 NMT1_2: NMT1-like fam 93.8 0.18 3.9E-06 46.8 6.7 205 80-312 4-233 (252)
24 COG0715 TauA ABC-type nitrate/ 93.1 0.42 9.2E-06 45.7 8.2 161 133-310 70-245 (335)
25 PF12974 Phosphonate-bd: ABC t 91.9 0.59 1.3E-05 43.0 7.3 135 127-273 31-186 (243)
26 TIGR00363 lipoprotein, YaeC fa 90.7 1.1 2.4E-05 43.1 8.0 78 83-162 117-199 (258)
27 PF00497 SBP_bac_3: Bacterial 90.5 4.4 9.5E-05 35.0 10.9 149 127-290 40-195 (225)
28 cd08417 PBP2_Nitroaromatics_li 87.6 3.6 7.8E-05 34.3 8.1 92 124-231 26-122 (200)
29 cd08418 PBP2_TdcA The C-termin 86.6 4.7 0.0001 33.5 8.3 165 125-309 27-199 (201)
30 TIGR01096 3A0103s03R lysine-ar 86.6 8.2 0.00018 34.8 10.4 123 128-267 66-191 (250)
31 PRK09861 cytoplasmic membrane 86.2 3.6 7.9E-05 39.8 8.4 78 83-162 131-213 (272)
32 PRK12682 transcriptional regul 85.7 10 0.00022 35.9 11.1 164 125-310 120-293 (309)
33 cd08436 PBP2_LTTR_like_3 The C 83.8 14 0.00031 30.3 9.8 90 125-231 27-124 (194)
34 TIGR02122 TRAP_TAXI TRAP trans 83.3 2 4.4E-05 40.5 5.1 110 135-257 72-197 (320)
35 cd08421 PBP2_LTTR_like_1 The C 83.0 17 0.00036 30.2 10.0 102 125-245 27-136 (198)
36 cd08464 PBP2_DntR_like_2 The C 82.3 14 0.00031 30.6 9.4 163 125-309 27-198 (200)
37 TIGR01098 3A0109s03R phosphate 82.3 6.6 0.00014 35.8 7.9 123 134-268 74-212 (254)
38 PRK15007 putative ABC transpor 81.0 20 0.00044 32.2 10.6 112 132-263 67-180 (243)
39 cd08442 PBP2_YofA_SoxR_like Th 80.2 5 0.00011 33.1 5.8 105 124-245 26-132 (193)
40 cd08437 PBP2_MleR The substrat 80.2 6.4 0.00014 32.9 6.6 104 125-245 27-138 (198)
41 cd08468 PBP2_Pa0477 The C-term 79.6 7.4 0.00016 33.0 6.8 110 125-246 27-138 (202)
42 cd05466 PBP2_LTTR_substrate Th 78.2 33 0.00072 27.5 10.5 143 128-290 32-184 (197)
43 cd08467 PBP2_SyrM The C-termin 78.2 9.2 0.0002 32.4 7.0 91 125-231 27-122 (200)
44 PRK11260 cystine transporter s 78.0 20 0.00043 33.3 9.7 118 127-261 82-201 (266)
45 PRK10797 glutamate and asparta 77.8 13 0.00028 35.9 8.7 102 135-255 96-203 (302)
46 PRK09495 glnH glutamine ABC tr 77.7 22 0.00047 32.5 9.8 122 129-268 67-191 (247)
47 cd08450 PBP2_HcaR The C-termin 77.6 10 0.00022 31.5 6.9 92 124-231 26-124 (196)
48 cd08463 PBP2_DntR_like_4 The C 77.2 14 0.00031 31.6 8.0 164 124-309 26-201 (203)
49 cd08466 PBP2_LeuO The C-termin 76.8 37 0.0008 28.2 10.2 90 125-230 27-120 (200)
50 cd08460 PBP2_DntR_like_1 The C 76.7 13 0.00028 31.3 7.5 103 124-243 26-132 (200)
51 cd08459 PBP2_DntR_NahR_LinR_li 76.3 9.3 0.0002 32.0 6.4 164 125-310 27-199 (201)
52 cd08458 PBP2_NocR The C-termin 75.7 5.6 0.00012 33.5 4.9 91 125-231 27-123 (196)
53 cd08449 PBP2_XapR The C-termin 75.7 7.4 0.00016 32.2 5.6 94 124-231 26-126 (197)
54 cd08453 PBP2_IlvR The C-termin 75.6 7 0.00015 32.7 5.5 112 124-245 26-141 (200)
55 PRK11063 metQ DL-methionine tr 75.4 25 0.00053 34.0 9.8 79 135-230 70-154 (271)
56 cd08440 PBP2_LTTR_like_4 TThe 75.0 5.9 0.00013 32.5 4.8 104 125-245 27-136 (197)
57 PRK11139 DNA-binding transcrip 74.7 18 0.00038 34.0 8.5 116 80-230 92-209 (297)
58 cd08435 PBP2_GbpR The C-termin 74.2 7.8 0.00017 32.1 5.4 95 125-231 27-125 (201)
59 PRK11242 DNA-binding transcrip 74.2 34 0.00074 31.7 10.2 162 125-313 118-292 (296)
60 cd08451 PBP2_BudR The C-termin 73.8 13 0.00028 30.8 6.6 105 125-245 28-140 (199)
61 cd08461 PBP2_DntR_like_3 The C 73.0 22 0.00049 29.5 7.9 92 124-231 26-123 (198)
62 cd08416 PBP2_MdcR The C-termin 72.4 16 0.00034 30.4 6.8 104 124-244 26-137 (199)
63 PRK11151 DNA-binding transcrip 71.8 36 0.00078 32.0 9.9 69 124-202 117-189 (305)
64 PRK10341 DNA-binding transcrip 71.6 21 0.00046 33.9 8.3 165 127-316 128-302 (312)
65 cd08429 PBP2_NhaR The C-termin 71.5 31 0.00068 29.8 8.8 109 125-245 27-138 (204)
66 cd08434 PBP2_GltC_like The sub 71.5 9.3 0.0002 31.3 5.2 102 125-245 27-136 (195)
67 cd08426 PBP2_LTTR_like_5 The C 71.2 11 0.00023 31.4 5.6 107 124-245 26-136 (199)
68 cd08462 PBP2_NodD The C-termin 70.4 21 0.00046 30.1 7.3 104 125-245 27-135 (200)
69 cd08438 PBP2_CidR The C-termin 70.1 22 0.00049 29.2 7.2 104 125-245 27-136 (197)
70 cd08456 PBP2_LysR The C-termin 69.6 10 0.00023 31.4 5.1 102 125-243 27-134 (196)
71 cd08465 PBP2_ToxR The C-termin 69.0 21 0.00046 30.2 7.0 151 124-291 26-185 (200)
72 cd08423 PBP2_LTTR_like_6 The C 68.8 16 0.00035 30.1 6.1 105 125-244 27-140 (200)
73 cd08433 PBP2_Nac The C-teminal 68.3 21 0.00046 29.6 6.8 103 124-244 26-135 (198)
74 PRK09861 cytoplasmic membrane 67.1 39 0.00084 32.8 9.1 150 139-310 75-253 (272)
75 PF03180 Lipoprotein_9: NLPA l 67.1 14 0.00031 35.3 6.0 101 82-187 96-202 (237)
76 cd08448 PBP2_LTTR_aromatics_li 67.1 11 0.00024 31.1 4.7 103 125-244 27-137 (197)
77 PRK11062 nhaR transcriptional 66.3 38 0.00083 31.9 8.8 149 125-291 120-277 (296)
78 PRK10216 DNA-binding transcrip 66.2 24 0.00051 33.7 7.4 113 125-244 124-240 (319)
79 cd08425 PBP2_CynR The C-termin 66.0 20 0.00044 29.7 6.2 104 125-245 28-138 (197)
80 cd08457 PBP2_OccR The C-termin 66.0 18 0.00038 30.3 5.9 105 124-245 26-136 (196)
81 cd08413 PBP2_CysB_like The C-t 63.4 22 0.00049 30.0 6.1 93 124-231 26-124 (198)
82 TIGR02424 TF_pcaQ pca operon t 63.4 13 0.00028 34.8 5.0 91 125-231 120-218 (300)
83 TIGR03431 PhnD phosphonate ABC 62.8 18 0.00039 34.0 5.9 119 135-266 70-204 (288)
84 PF13379 NMT1_2: NMT1-like fam 62.8 17 0.00038 33.6 5.7 61 82-156 120-181 (252)
85 cd08483 PBP2_HvrB The C-termin 62.4 24 0.00051 29.1 5.9 89 124-231 26-115 (190)
86 cd08427 PBP2_LTTR_like_2 The C 61.8 27 0.00059 28.7 6.2 55 125-187 27-83 (195)
87 cd08486 PBP2_CbnR The C-termin 60.8 17 0.00036 30.9 4.8 103 124-243 27-137 (198)
88 COG0725 ModA ABC-type molybdat 60.2 43 0.00094 32.3 8.0 88 84-187 136-226 (258)
89 TIGR02995 ectoine_ehuB ectoine 59.8 66 0.0014 30.0 9.1 128 129-269 76-206 (275)
90 PF03480 SBP_bac_7: Bacterial 59.4 30 0.00064 32.9 6.7 142 131-293 40-218 (286)
91 cd08443 PBP2_CysB The C-termin 59.3 59 0.0013 27.4 8.0 104 124-245 26-137 (198)
92 cd08419 PBP2_CbbR_RubisCO_like 59.3 21 0.00045 29.4 5.0 149 125-290 26-184 (197)
93 PRK15010 ABC transporter lysin 58.1 31 0.00068 31.8 6.5 111 129-257 69-183 (260)
94 PRK15243 transcriptional regul 57.7 38 0.00083 32.9 7.3 165 124-313 118-293 (297)
95 PF12727 PBP_like: PBP superfa 57.2 64 0.0014 29.5 8.3 162 127-308 13-192 (193)
96 PRK10837 putative DNA-binding 54.8 98 0.0021 28.5 9.2 100 127-245 120-224 (290)
97 cd08444 PBP2_Cbl The C-termina 54.1 44 0.00096 28.1 6.3 91 125-231 27-124 (198)
98 cd08414 PBP2_LTTR_aromatics_li 53.7 48 0.001 27.2 6.3 91 125-231 27-125 (197)
99 PRK09906 DNA-binding transcrip 53.2 1.3E+02 0.0028 27.9 9.9 100 125-243 117-226 (296)
100 cd08481 PBP2_GcdR_like The C-t 52.6 38 0.00082 27.8 5.5 88 125-231 27-116 (194)
101 CHL00180 rbcR LysR transcripti 51.8 37 0.0008 32.1 6.0 89 128-231 127-221 (305)
102 PRK12681 cysB transcriptional 51.3 1.2E+02 0.0027 29.2 9.6 164 125-312 120-295 (324)
103 PRK09791 putative DNA-binding 50.2 51 0.0011 30.9 6.7 91 128-231 127-218 (302)
104 PRK10859 membrane-bound lytic 48.2 1.7E+02 0.0037 30.3 10.6 110 133-261 89-206 (482)
105 PRK15421 DNA-binding transcrip 47.9 1.8E+02 0.0038 28.0 10.1 99 128-244 121-223 (317)
106 cd08412 PBP2_PAO1_like The C-t 47.9 61 0.0013 26.6 6.1 102 125-245 27-135 (198)
107 COG4521 TauA ABC-type taurine 47.5 16 0.00035 36.1 2.8 91 135-239 68-165 (334)
108 PRK12683 transcriptional regul 47.4 40 0.00087 32.2 5.5 88 127-231 124-217 (309)
109 PRK11233 nitrogen assimilation 47.2 55 0.0012 31.0 6.4 88 125-231 119-212 (305)
110 cd08484 PBP2_LTTR_beta_lactama 46.6 47 0.001 27.5 5.2 87 125-231 27-113 (189)
111 PRK09508 leuO leucine transcri 46.5 1.2E+02 0.0026 28.8 8.6 92 124-231 138-233 (314)
112 TIGR03414 ABC_choline_bnd chol 46.2 17 0.00037 35.3 2.8 223 83-334 9-257 (290)
113 COG0834 HisJ ABC-type amino ac 46.1 1.4E+02 0.0031 26.9 8.7 120 127-263 79-202 (275)
114 cd08441 PBP2_MetR The C-termin 45.5 1.1E+02 0.0023 25.4 7.3 93 125-231 27-123 (198)
115 PRK15437 histidine ABC transpo 44.3 2.6E+02 0.0056 25.7 10.3 110 135-261 75-187 (259)
116 PRK11013 DNA-binding transcrip 44.2 38 0.00083 32.1 4.8 101 127-244 125-229 (309)
117 cd08445 PBP2_BenM_CatM_CatR Th 43.3 44 0.00096 28.1 4.6 67 125-201 28-99 (203)
118 TIGR03339 phn_lysR aminoethylp 41.5 50 0.0011 30.1 5.0 95 131-244 119-219 (279)
119 TIGR00363 lipoprotein, YaeC fa 41.1 1.2E+02 0.0025 29.3 7.6 151 134-310 56-239 (258)
120 PRK12680 transcriptional regul 40.8 66 0.0014 31.2 6.0 105 124-244 119-230 (327)
121 cd08488 PBP2_AmpR The C-termin 40.6 51 0.0011 27.5 4.6 73 140-231 41-113 (191)
122 cd08431 PBP2_HupR The C-termin 40.4 40 0.00086 28.0 3.8 68 125-201 27-99 (195)
123 cd08487 PBP2_BlaA The C-termin 39.5 66 0.0014 26.5 5.0 87 125-231 27-113 (189)
124 cd08430 PBP2_IlvY The C-termin 39.2 37 0.0008 28.0 3.4 55 125-188 27-83 (199)
125 PF03401 TctC: Tripartite tric 39.1 63 0.0014 31.0 5.5 77 176-257 76-159 (274)
126 PRK10677 modA molybdate transp 37.7 70 0.0015 30.3 5.5 147 48-230 4-162 (257)
127 cd08480 PBP2_CrgA_like_10 The 35.5 36 0.00079 28.6 2.9 66 125-201 28-95 (198)
128 TIGR01729 taurine_ABC_bnd taur 34.3 58 0.0013 30.8 4.4 60 83-158 100-160 (300)
129 PRK12684 transcriptional regul 34.1 1.3E+02 0.0028 28.7 6.7 90 125-231 120-217 (313)
130 PRK14498 putative molybdopteri 32.8 1.1E+02 0.0024 32.9 6.6 92 127-231 443-549 (633)
131 TIGR03871 ABC_peri_MoxJ_2 quin 32.5 2.3E+02 0.005 25.2 7.7 108 139-267 51-172 (232)
132 TIGR01256 modA molybdenum ABC 31.4 60 0.0013 29.0 3.8 92 128-229 24-123 (216)
133 PF13531 SBP_bac_11: Bacterial 31.1 33 0.00071 30.9 2.0 95 126-229 27-128 (230)
134 PRK04168 molybdate ABC transpo 30.8 78 0.0017 31.5 4.8 23 136-158 213-235 (334)
135 PRK11074 putative DNA-binding 29.9 97 0.0021 29.1 5.1 99 80-202 90-193 (300)
136 cd08447 PBP2_LTTR_aromatics_li 27.7 43 0.00093 27.7 2.0 92 124-231 26-125 (198)
137 COG1464 NlpA ABC-type metal io 27.4 2.1E+02 0.0046 28.3 6.9 80 82-164 127-210 (268)
138 PRK12679 cbl transcriptional r 27.2 1.3E+02 0.0029 28.6 5.6 160 125-310 120-293 (316)
139 PRK03601 transcriptional regul 27.1 56 0.0012 30.5 2.9 51 127-187 120-170 (275)
140 PRK11482 putative DNA-binding 27.0 60 0.0013 31.2 3.2 67 125-201 144-211 (317)
141 PF11823 DUF3343: Protein of u 26.1 86 0.0019 24.1 3.3 51 220-273 16-68 (73)
142 PF09084 NMT1: NMT1/THI5 like; 25.9 1.1E+02 0.0023 27.1 4.3 67 220-289 11-82 (216)
143 cd08411 PBP2_OxyR The C-termin 24.9 50 0.0011 27.4 1.9 94 124-231 27-124 (200)
144 cd08428 PBP2_IciA_ArgP The C-t 24.3 1.3E+02 0.0028 24.9 4.4 65 127-201 30-97 (195)
145 PRK11716 DNA-binding transcrip 24.3 67 0.0014 29.0 2.8 54 125-187 94-149 (269)
146 COG2358 Imp TRAP-type uncharac 24.2 68 0.0015 32.4 3.0 88 138-238 71-169 (321)
147 cd08478 PBP2_CrgA The C-termin 24.2 67 0.0015 26.7 2.6 68 124-202 29-98 (199)
148 TIGR03427 ABC_peri_uca ABC tra 24.1 90 0.0019 31.0 3.8 66 76-157 99-165 (328)
149 PRK09959 hybrid sensory histid 23.9 5.5E+02 0.012 29.4 10.4 117 127-264 341-462 (1197)
150 PRK11480 tauA taurine transpor 23.7 1.2E+02 0.0027 29.2 4.7 61 82-158 121-182 (320)
151 cd08439 PBP2_LrhA_like The C-t 23.5 59 0.0013 26.9 2.1 51 125-187 27-79 (185)
152 PRK10094 DNA-binding transcrip 23.5 1.7E+02 0.0036 27.9 5.4 70 125-202 120-194 (308)
153 COG1022 FAA1 Long-chain acyl-C 22.9 88 0.0019 34.2 3.7 56 221-281 369-427 (613)
154 PRK10222 PTS system L-ascorbat 22.8 1.7E+02 0.0036 23.5 4.5 41 221-264 7-48 (85)
155 PRK09959 hybrid sensory histid 22.6 3.5E+02 0.0075 30.9 8.5 122 127-267 96-223 (1197)
156 KOG0186 Proline oxidase [Amino 22.3 48 0.001 35.3 1.6 59 176-273 400-458 (506)
157 cd08475 PBP2_CrgA_like_6 The C 21.6 1E+02 0.0023 25.3 3.2 67 125-201 28-96 (199)
158 cd08476 PBP2_CrgA_like_7 The C 21.6 89 0.0019 25.5 2.8 66 125-201 26-93 (197)
159 COG1040 ComFC Predicted amidop 21.3 52 0.0011 31.1 1.4 14 253-266 188-202 (225)
160 TIGR01256 modA molybdenum ABC 21.2 1.2E+02 0.0027 26.9 3.8 59 84-156 99-160 (216)
161 PF00156 Pribosyltran: Phospho 21.0 44 0.00096 27.1 0.8 14 253-266 92-106 (125)
162 TIGR03298 argP transcriptional 20.4 3E+02 0.0064 25.6 6.3 66 127-202 120-188 (292)
No 1
>PLN02245 ATP phosphoribosyl transferase
Probab=100.00 E-value=2.4e-90 Score=686.43 Aligned_cols=327 Identities=76% Similarity=1.121 Sum_probs=296.8
Q ss_pred cccCCCCCCCcccccCCcccceeeccCCCccCCCcccceeeeeccccccccceeeecCCcCCC--CCCCCceEEEecCCC
Q 018854 15 RQCPSLSPSGLSFFCPLSSFHISVASGPTTATNKPAAAVTCCVSSSQQFESHVSVVNGNIDNR--ISERDEIRLGLPSKG 92 (349)
Q Consensus 15 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~LrIALP~KG 92 (349)
.+|++..||++++|+|.++.+++.+. |++ .|++..++|.++.++. .+.+.....+ ++++.+|||||||||
T Consensus 7 ~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~---~~~~~~~~~~~~~~~~----~~~~~~~~~~~~~~~~~~LriAlPsKG 78 (403)
T PLN02245 7 SPSLSSLPSSSPLLSPPSSRASRLIA-PRR---RCLRLATACVSQVQSS----VVAGSTDSASSVVSSRTQIRLGLPSKG 78 (403)
T ss_pred ccccCCccccccccCCCCcCceeeec-chh---hhhhhheeeecccchh----hhcccccccCccccCCceEEEEECCCC
Confidence 44555678999999999998888887 888 7989999998887772 2223333333 688899999999999
Q ss_pred CchHHHHHHHHHCCCccCCCCCCceEEecCCCCCeEEEeecCCchhhhcccCceeeeeeccceecccCCCCccceeecCC
Q 018854 93 RMAADTLDLLKDCQLSVKQVNPRQYVAQIPQLSNLEVWFQRPKDIVRKLLSGDLDLGIVGLDTVSEFGQGNEDLIIVHDA 172 (349)
Q Consensus 93 RL~e~t~~LL~~aGi~~~~~~~R~L~~~~~~~p~vev~~vR~~DIP~yV~~G~aDlGIvG~DvL~E~~~~~~~lv~~l~d 172 (349)
||+|++++||++|||++...++|+|++.+++.|+++|+|+||+|||+||++|.+|+||||+|||.|++.+..+++++++|
T Consensus 79 RL~e~t~~LL~~aGl~~~~~~~R~L~~~~~~~~~iev~flR~~DIp~yV~~G~~DlGItG~D~l~E~~~~~~~~v~~l~~ 158 (403)
T PLN02245 79 RMAEDTLDLLKDCQLSVKKVNPRQYVAEIPQLPNLEVWFQRPKDIVRKLLSGDLDLGIVGYDMLREYGQGNEDLVIVHDA 158 (403)
T ss_pred ccHHHHHHHHHHcCCCCCCCCCceeEEEcCCCCceEEEEECHHHHHHHHhCCCccEEEeeeeeeeccCCCccceEEEeec
Confidence 99999999999999999876569999998777889999999999999999999999999999999998776778888889
Q ss_pred CCcccEEEEEEEeCCCccCcccchHHhhcCCccCCCCCcEEEcCCCccHHHHHHhcCCceEEEEecCCccccccCCCcce
Q 018854 173 LDYGDCRLSLAIPKYGIFENINSLRELAQMPQWTAEKPLRVATGFTYLGPKFMKDNGLKHVVFSTADGALEAAPAMGIAD 252 (349)
Q Consensus 173 LgfG~CRLvvAvP~~~~~~dv~sl~dL~~~~~~~~~~~lRVATkYPnlar~yf~~~Gi~~v~Ii~l~GSvElAP~lGlAD 252 (349)
||||+|||+||+|++..|.++++++||++...|..++++||||||||||++||+++|+++++|++++||||+||.+|+||
T Consensus 159 LgFG~crlvvAvP~~~~~~~~~s~~dL~g~~~~~~~~~~RIATkYp~ltr~ff~~~Gv~~v~Iv~l~GAvE~AP~lGlAD 238 (403)
T PLN02245 159 LGFGDCHLSIAIPKYGIFENINSLKELAQMPQWTEERPLRVVTGFTYLGPKFMKDNGFKHVTFSTADGALEAAPAMGIAD 238 (403)
T ss_pred CCCCceEEEEEEEccCCccccCCHHHhcccccccccCceEEEeCCHHHHHHHHHHcCCCeEEEEECcCceecccccCchh
Confidence 99999999999999866889999999998777777888999999999999999999997699999999999999999999
Q ss_pred eeeecccchhhHhhCCcEEecCceEEEEEEEEEeecchhhhhcCchhHHHHHHHHHHHHHhhcCeeEEEEecCCCCHHHH
Q 018854 253 AILDLVSSGTTLRENNLKEIEGGVVLESQAVLVASRKSLIRRKGVLDATHEILERLEAHLRASGQFTVTANMRGNSAEEV 332 (349)
Q Consensus 253 ~IVDIVsTGtTLraNgLk~ie~g~IleSsA~LIaN~~s~~~k~~~~~~i~~li~rl~~vl~Ar~~~~v~~N~p~~~l~~v 332 (349)
+||||||||+|||+|||++++||+||+|+|+||+|+.+++.++++++.|++|++||+++++|++|+||+||+|++++++|
T Consensus 239 aIvDIVsTGtTLraNgLk~i~~~~Il~S~A~LIan~~sl~~~~~~~~~i~~ll~rl~~vl~A~~~~~v~~Nvp~~~le~v 318 (403)
T PLN02245 239 AILDLVSSGTTLRENNLKEIEGGVVLESQAVLVASRRALLERKGALEVVHEILERLEAHLRAEGQFTVTANMRGSSAEEV 318 (403)
T ss_pred hhcchhccHHHHHHCCCEEccCceEEEEEEEEEEecchhhcchhHHHHHHHHHHHHHHHHhhhcEEEEEecCChhhHHHH
Confidence 99999999999999999999889999999999999999876555667999999999999999999999999999999999
Q ss_pred HHHhcccccCCCCCCCC
Q 018854 333 AERILSQTSFSGLQGPT 349 (349)
Q Consensus 333 ~~~~~~~~~lpgl~~PT 349 (349)
++++.+++.+||++|||
T Consensus 319 ~~~~~~~~~lPG~~~PT 335 (403)
T PLN02245 319 AERVLSQPSLSGLQGPT 335 (403)
T ss_pred HHhhhccccCCCCCCCc
Confidence 99999999999999999
No 2
>COG0040 HisG ATP phosphoribosyltransferase [Amino acid transport and metabolism]
Probab=100.00 E-value=1.1e-75 Score=561.23 Aligned_cols=243 Identities=34% Similarity=0.600 Sum_probs=221.3
Q ss_pred CceEEEecCCCCchHHHHHHHHHCCCccCCCCCCceEEecCCCCCeEEEeecCCchhhhcccCceeeeeeccceecccCC
Q 018854 82 DEIRLGLPSKGRMAADTLDLLKDCQLSVKQVNPRQYVAQIPQLSNLEVWFQRPKDIVRKLLSGDLDLGIVGLDTVSEFGQ 161 (349)
Q Consensus 82 ~~LrIALP~KGRL~e~t~~LL~~aGi~~~~~~~R~L~~~~~~~p~vev~~vR~~DIP~yV~~G~aDlGIvG~DvL~E~~~ 161 (349)
+||||||||||||.|++++||++|||++.....|+|++..++ ++++++|+||+|||+||++|++|+||||+|+|.|++.
T Consensus 1 ~~l~iAip~KGRL~e~~~~lL~~aG~~~~~~~~r~l~~~~~~-~~I~~~~vR~~DIP~yV~~G~~DlGItG~D~l~E~~~ 79 (290)
T COG0040 1 DMLRIALPKKGRLSEPALELLAKAGIKISALDSRKLIAETEN-PPIELLLVRAQDIPTYVEDGVADLGITGEDVLRESGL 79 (290)
T ss_pred CceEEEecCCCccchHHHHHHHHcCCCccCCCCcceEEecCC-CCeEEEEEChHHhhHHHhcCceeeeeechhhhhhccc
Confidence 589999999999999999999999999996457999999876 4599999999999999999999999999999999985
Q ss_pred CCccceeecCCCCcccEEEEEEEeCCCccCcccchHHhhcCCccCCCCCcEEEcCCCccHHHHHHhcCCceEEEEecCCc
Q 018854 162 GNEDLIIVHDALDYGDCRLSLAIPKYGIFENINSLRELAQMPQWTAEKPLRVATGFTYLGPKFMKDNGLKHVVFSTADGA 241 (349)
Q Consensus 162 ~~~~lv~~l~dLgfG~CRLvvAvP~~~~~~dv~sl~dL~~~~~~~~~~~lRVATkYPnlar~yf~~~Gi~~v~Ii~l~GS 241 (349)
+..++ +.+.||+||+|||+||+|+++ ++++.+||.+ + +||||||||+|++||+++|++ ++||+++||
T Consensus 80 ~~~~v-~~l~dL~fG~crl~vAvp~~~---~~~~~~~l~~-------~-~rIATkYp~l~~~yf~~~g~~-~~Ii~l~Gs 146 (290)
T COG0040 80 DDASV-EELLDLGFGGCRLVVAVPEES---DYTSPEDLKG-------R-LRIATKYPNLARKYFAEKGID-VEIIKLSGS 146 (290)
T ss_pred CccCc-eehccCCCCcEEEEEEecCCc---CccChhHhcC-------C-ceEEEccHHHHHHHHHHcCce-EEEEEccCc
Confidence 52343 344599999999999999994 4456666542 3 799999999999999999996 999999999
Q ss_pred cccccCCCcceeeeecccchhhHhhCCcEEecCceEEEEEEEEEee-cchhhhhcCchhHHHHHHHHHHHHHhhcCeeEE
Q 018854 242 LEAAPAMGIADAILDLVSSGTTLRENNLKEIEGGVVLESQAVLVAS-RKSLIRRKGVLDATHEILERLEAHLRASGQFTV 320 (349)
Q Consensus 242 vElAP~lGlAD~IVDIVsTGtTLraNgLk~ie~g~IleSsA~LIaN-~~s~~~k~~~~~~i~~li~rl~~vl~Ar~~~~v 320 (349)
||+||.+|+||+||||||||+|||+|||+++| +|++|+|+||+| +.+++++. +.|++|+++|++++.|++++|+
T Consensus 147 vE~aP~~GlADaIvDivsTG~TLkaNgL~~id--~i~~ssa~LI~n~~~~~~~k~---~~i~~l~~rl~gvi~a~~~~~i 221 (290)
T COG0040 147 VELAPALGLADAIVDIVSTGTTLKANGLKEIE--VIYDSSARLIVNAKASLKDKQ---ELIDQLVTRLKGVIEARGSKYI 221 (290)
T ss_pred EeeccccCccceEEEeecCCHhHHHCCCEEEE--EEEeeEEEEEeccccccchhH---HHHHHHHHHHHHHHhhcceeEE
Confidence 99999999999999999999999999999998 999999999999 66766543 6899999999999999999999
Q ss_pred EEecCCCCHHHHHHHhcccccCCCCCCCC
Q 018854 321 TANMRGNSAEEVAERILSQTSFSGLQGPT 349 (349)
Q Consensus 321 ~~N~p~~~l~~v~~~~~~~~~lpgl~~PT 349 (349)
|||+|++++++|.+ +|||+++||
T Consensus 222 ~~n~p~~~ld~v~~------llpg~~~pT 244 (290)
T COG0040 222 MLNAPRERLDEVTA------LLPGMEGPT 244 (290)
T ss_pred EeeCCHHHHHHHHH------hccCCCCCc
Confidence 99999999999999 599999998
No 3
>PRK13583 hisG ATP phosphoribosyltransferase catalytic subunit; Provisional
Probab=100.00 E-value=3.2e-71 Score=516.63 Aligned_cols=223 Identities=31% Similarity=0.497 Sum_probs=195.4
Q ss_pred CceEEEecCCCCchHHHHHHHHHCCCccCCC-CCCceEEecCCCCCeEEEeecCCchhhhcccCceeeeeeccceecccC
Q 018854 82 DEIRLGLPSKGRMAADTLDLLKDCQLSVKQV-NPRQYVAQIPQLSNLEVWFQRPKDIVRKLLSGDLDLGIVGLDTVSEFG 160 (349)
Q Consensus 82 ~~LrIALP~KGRL~e~t~~LL~~aGi~~~~~-~~R~L~~~~~~~p~vev~~vR~~DIP~yV~~G~aDlGIvG~DvL~E~~ 160 (349)
.||||||||||||++++++||++|||++... ++|+|++.+.+.|+++|+|+||+|||+||++|.+|+||||+|||.|++
T Consensus 1 ~~l~iAlP~KGRL~e~t~~ll~~aGl~~~~~~~~R~L~~~~~~~~~i~~~~vR~~DIp~yV~~G~~DlGI~G~D~l~E~~ 80 (228)
T PRK13583 1 MTITLGLPSKGRLKEKTFAWFEKAGLTLVRTGSDREYRGRVEGEDDVELLFLSASEIPRELGAGRVDLGVTGEDLVREKL 80 (228)
T ss_pred CcEEEEeCCCCccHHHHHHHHHHcCCCcccCCCCcccEeEcCCCCceEEEEECHHHHHHHHhCCCCcEEEeeeeeeeccc
Confidence 3799999999999999999999999998874 259999998767889999999999999999999999999999999987
Q ss_pred CCC-ccceeecCCCCcccEEEEEEEeCCCccCcccchHHhhcCCccC---CCCCcEEEcCCCccHHHHHHhcCCceEEEE
Q 018854 161 QGN-EDLIIVHDALDYGDCRLSLAIPKYGIFENINSLRELAQMPQWT---AEKPLRVATGFTYLGPKFMKDNGLKHVVFS 236 (349)
Q Consensus 161 ~~~-~~lv~~l~dLgfG~CRLvvAvP~~~~~~dv~sl~dL~~~~~~~---~~~~lRVATkYPnlar~yf~~~Gi~~v~Ii 236 (349)
.+. .+++ .+.|||||+|||+||+|++ |.++++++||.+...+. +++++||||||||||++||+++|++.++||
T Consensus 81 ~~~~~~v~-elldLgfG~crl~vA~p~~--~~~~~~~~dl~~~~~~~~~~~g~~~RIATkYp~it~~yf~~~Gv~~~~Iv 157 (228)
T PRK13583 81 ADWDKRVE-IVARLGFGHADLVVAVPEI--WIDVDTMADLDDVAADFRARHGRRLRIATKYWRLTQQFLSQKGVQDYRIV 157 (228)
T ss_pred ccCCCCeE-EEecCCCCceEEEEEEECc--ccccCCHHHhhhhhhhhhhccCCceEEEeCCHHHHHHHHHHcCCceeEEE
Confidence 532 3344 4459999999999999998 77889999987543322 234589999999999999999999745999
Q ss_pred ecCCccccccCCCcceeeeecccchhhHhhCCcEEecCceEEEEEEEEEeecchhhhhcCchhHHHHHHHHHH
Q 018854 237 TADGALEAAPAMGIADAILDLVSSGTTLRENNLKEIEGGVVLESQAVLVASRKSLIRRKGVLDATHEILERLE 309 (349)
Q Consensus 237 ~l~GSvElAP~lGlAD~IVDIVsTGtTLraNgLk~ie~g~IleSsA~LIaN~~s~~~k~~~~~~i~~li~rl~ 309 (349)
+++||+|+||.+|+||+||||||||+|||+|||++++||+||+|+|+||+|+.++... +.+.++.|++||+
T Consensus 158 ~l~GsvElaP~~GlAD~IvDivsTG~TLr~NgL~~i~~~~Il~SsA~LI~n~~s~~~~--~~~~~~~l~~r~~ 228 (228)
T PRK13583 158 ESLGATEGAPANGSAEIIVDITSTGETLRANHLKILSDGVILRSQACLVRARKADWSE--TEARVQAIAARIR 228 (228)
T ss_pred ECCCceecccccCcchhhhhhhchhHHHHHCCCEEecCceEEEEEEEEEEecccccch--hHHHHHHHHHhhC
Confidence 9999999999999999999999999999999999998789999999999999986532 2267888888874
No 4
>PRK01686 hisG ATP phosphoribosyltransferase catalytic subunit; Reviewed
Probab=100.00 E-value=9.3e-71 Score=509.93 Aligned_cols=212 Identities=31% Similarity=0.519 Sum_probs=190.4
Q ss_pred CCceEEEecCCCCchHHHHHHHHHCCCccCCC--CCCceEEecCCCCCeEEEeecCCchhhhcccCceeeeeeccceecc
Q 018854 81 RDEIRLGLPSKGRMAADTLDLLKDCQLSVKQV--NPRQYVAQIPQLSNLEVWFQRPKDIVRKLLSGDLDLGIVGLDTVSE 158 (349)
Q Consensus 81 ~~~LrIALP~KGRL~e~t~~LL~~aGi~~~~~--~~R~L~~~~~~~p~vev~~vR~~DIP~yV~~G~aDlGIvG~DvL~E 158 (349)
|+||||||| ||||++++++||++|||++... ++|+|++.+. .++++|+|+||+|||+||++|.+|+||||+|||.|
T Consensus 1 ~~~l~iAlp-KGRL~e~t~~ll~~aG~~~~~~~~~~R~L~~~~~-~~~i~~~~~r~~DIp~yV~~G~~DlGItG~D~l~E 78 (215)
T PRK01686 1 MDMLTIALP-KGRILEETLPLLAKAGIDPSEDPDKSRKLIFPTP-EPDVRFLLVRATDVPTYVEHGAADLGIVGKDVLLE 78 (215)
T ss_pred CCcEEEEec-CcccHHHHHHHHHHcCCCcccCCCCCcceEeecC-CCCEEEEEECHHHHHHHHhCCCccEEEeeeeEeee
Confidence 578999999 9999999999999999998875 3699999865 47899999999999999999999999999999999
Q ss_pred cCCCCccceeecCCCCcccEEEEEEEeCCCccCcccchHHhhcCCccCCCCCcEEEcCCCccHHHHHHhcCCceEEEEec
Q 018854 159 FGQGNEDLIIVHDALDYGDCRLSLAIPKYGIFENINSLRELAQMPQWTAEKPLRVATGFTYLGPKFMKDNGLKHVVFSTA 238 (349)
Q Consensus 159 ~~~~~~~lv~~l~dLgfG~CRLvvAvP~~~~~~dv~sl~dL~~~~~~~~~~~lRVATkYPnlar~yf~~~Gi~~v~Ii~l 238 (349)
++.+ ++++ .|||||+|||+||+|+++.| .+.++ ..+++||||||||||++||+++|++ ++||++
T Consensus 79 ~~~~---v~~l-~dLgfG~crl~vAvp~~~~~---~~~~~--------~~~~~rIATkYp~it~~yf~~~gv~-~~iv~l 142 (215)
T PRK01686 79 HGKD---LYEP-LDLGIGKCRMSVAVPPGFDY---APAVK--------QGPRLRVATKYPNIARRYFAEKGEQ-VEIIKL 142 (215)
T ss_pred cCCC---eEEE-ecCCccCEEEEEEEECcccc---cchhh--------ccCCCEEEeCCHHHHHHHHHHcCCe-EEEEEC
Confidence 9844 4444 48999999999999998432 22222 1246899999999999999999996 999999
Q ss_pred CCccccccCCCcceeeeecccchhhHhhCCcEEecCceEEEEEEEEEeecchhhhhcCchhHHHHHHHHHHHHHhhc
Q 018854 239 DGALEAAPAMGIADAILDLVSSGTTLRENNLKEIEGGVVLESQAVLVASRKSLIRRKGVLDATHEILERLEAHLRAS 315 (349)
Q Consensus 239 ~GSvElAP~lGlAD~IVDIVsTGtTLraNgLk~ie~g~IleSsA~LIaN~~s~~~k~~~~~~i~~li~rl~~vl~Ar 315 (349)
+||||+||.+|+||+||||||||+|||+|||++++ +||+|+|+||+|+.+++.|+ +.|++|+++|++++.|+
T Consensus 143 ~GsvE~aP~~GlAD~IvDivsTG~TLr~NgL~~ie--~Il~s~A~LI~n~~s~~~k~---~~i~~l~~~l~~~~~a~ 214 (215)
T PRK01686 143 YGSVELAPLVGLADAIVDIVETGNTLRANGLVEVE--EIMDISARLIVNRASLKLKR---EEIRPLIEKLREAVESR 214 (215)
T ss_pred cCceeeccccCCccEEEEeecChHHHHHCcCEEee--EEEeeEEEEEEecccchhhH---HHHHHHHHHHHHHHhcc
Confidence 99999999999999999999999999999999999 99999999999999987544 68999999999999886
No 5
>PRK13584 hisG ATP phosphoribosyltransferase catalytic subunit; Provisional
Probab=100.00 E-value=4.5e-67 Score=481.32 Aligned_cols=198 Identities=22% Similarity=0.407 Sum_probs=177.8
Q ss_pred ceEEEecCCCCchHHHHHHHHHCCCccCCC----CCCceEEecCCCCCeEEEeecCCchhhhcccCceeeeeeccceecc
Q 018854 83 EIRLGLPSKGRMAADTLDLLKDCQLSVKQV----NPRQYVAQIPQLSNLEVWFQRPKDIVRKLLSGDLDLGIVGLDTVSE 158 (349)
Q Consensus 83 ~LrIALP~KGRL~e~t~~LL~~aGi~~~~~----~~R~L~~~~~~~p~vev~~vR~~DIP~yV~~G~aDlGIvG~DvL~E 158 (349)
||||||| ||||++++++||++|||.+... .+|+|++.. ++++|+|+||+|||+||++|.+|+||||+|||.|
T Consensus 1 ~l~iAlp-KGRL~e~~~~ll~~aG~~~~~~~~~~~~R~L~~~~---~~i~~~~~r~~DIp~yV~~G~aDlGI~G~D~l~E 76 (204)
T PRK13584 1 MLRIAIA-KGRLMDSLINYLDVIEYTTLSETLKNRERQLLLSV---DNIECILVKGSDVPIYVEQGMADIGIVGSDILDE 76 (204)
T ss_pred CEEEEec-CcccHHHHHHHHHHcCCCcccccCccCCcceeccC---CCeEEEEECHHHHHHHHhCCCccEEEeeeeEeec
Confidence 6899999 9999999999999999987332 359998873 3699999999999999999999999999999999
Q ss_pred cCCCCccceeecCCCCcccEEEEEEEeCCCccCcccchHHhhcCCccCCCCCcEEEcCCCccHHHHHHhcCCceEEEEec
Q 018854 159 FGQGNEDLIIVHDALDYGDCRLSLAIPKYGIFENINSLRELAQMPQWTAEKPLRVATGFTYLGPKFMKDNGLKHVVFSTA 238 (349)
Q Consensus 159 ~~~~~~~lv~~l~dLgfG~CRLvvAvP~~~~~~dv~sl~dL~~~~~~~~~~~lRVATkYPnlar~yf~~~Gi~~v~Ii~l 238 (349)
++.+ ++++ .|||||+|||+||+|++ +. +.+||||||||||++||+++|++ ++||++
T Consensus 77 ~~~~---v~el-~dLgfG~crl~vA~p~~--~~-----------------~~~rVATkyp~it~~yf~~~Gi~-~~ii~l 132 (204)
T PRK13584 77 RQYN---VNNL-LNMPFGACHFAVAAKPE--TT-----------------NYRKIATSYVHTAETYFKSKGID-VELIKL 132 (204)
T ss_pred cCCC---eEEE-ecCCCCcEEEEEEEEcC--CC-----------------CceEEEeCcHHHHHHHHHHcCCe-EEEEEC
Confidence 9854 4444 48999999999999875 11 13799999999999999999995 999999
Q ss_pred CCccccccCCCcceeeeecccchhhHhhCCcEEecCceEEEEEEEEEeecchhhhhcCchhHHHHHHHHHHHHHh
Q 018854 239 DGALEAAPAMGIADAILDLVSSGTTLRENNLKEIEGGVVLESQAVLVASRKSLIRRKGVLDATHEILERLEAHLR 313 (349)
Q Consensus 239 ~GSvElAP~lGlAD~IVDIVsTGtTLraNgLk~ie~g~IleSsA~LIaN~~s~~~k~~~~~~i~~li~rl~~vl~ 313 (349)
+||+|+||.+|+||+||||||||+|||+|||++++ +|++|+|+||+|+.+++.++ ++|++|+++|+-.++
T Consensus 133 ~GsvElaP~~GlAD~IvDiv~TG~TLr~NgL~~~e--~I~~ssa~LI~n~~s~~~k~---~~i~~l~~~l~~~~~ 202 (204)
T PRK13584 133 NGSVELACVVDMVDGIVDIVQTGTTLKANGLVEKQ--HISDINARLITNKAAYFKKS---QLIEQFIRSLEVSIA 202 (204)
T ss_pred CCceeeccccCCccEEEEEECccHHHHHCCCEEEE--EEEeeEEEEEEccccchhhH---HHHHHHHHHHHHHhh
Confidence 99999999999999999999999999999999999 99999999999999987654 689999999986553
No 6
>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=100.00 E-value=7.1e-65 Score=460.32 Aligned_cols=182 Identities=42% Similarity=0.709 Sum_probs=168.8
Q ss_pred eEEEecCCCCchHHHHHHHHHCCCccCCCCCCceEEecCCCCCeEEEeecCCchhhhcccCceeeeeeccceecccCCCC
Q 018854 84 IRLGLPSKGRMAADTLDLLKDCQLSVKQVNPRQYVAQIPQLSNLEVWFQRPKDIVRKLLSGDLDLGIVGLDTVSEFGQGN 163 (349)
Q Consensus 84 LrIALP~KGRL~e~t~~LL~~aGi~~~~~~~R~L~~~~~~~p~vev~~vR~~DIP~yV~~G~aDlGIvG~DvL~E~~~~~ 163 (349)
|||||| ||||+|++++||++|||.+...++|+|++...+ ++++|+|+||+|||+||++|.+|+||||+||+.|++.+
T Consensus 1 l~iAlp-KGRl~~~t~~ll~~aG~~~~~~~~R~l~~~~~~-~~i~~~~~r~~Dip~yV~~G~aDlGI~G~D~l~E~~~~- 77 (182)
T TIGR00070 1 LRIALP-KGRLLEDTLKLLEKAGLKVSREDSRKLIARDPD-EGIEFLLLRPQDIPTYVEHGAADLGITGYDVLLESGAD- 77 (182)
T ss_pred CeEEec-CcccHHHHHHHHHHcCCCCCCCCCcceEeEcCC-CCEEEEEEccchhHHHHhCCCccEEEecchhhhhCCCC-
Confidence 689999 999999999999999999988556999998765 67999999999999999999999999999999999854
Q ss_pred ccceeecCCCCcccEEEEEEEeCCCccCcccchHHhhcCCccCCCCCcEEEcCCCccHHHHHHhcCCceEEEEecCCccc
Q 018854 164 EDLIIVHDALDYGDCRLSLAIPKYGIFENINSLRELAQMPQWTAEKPLRVATGFTYLGPKFMKDNGLKHVVFSTADGALE 243 (349)
Q Consensus 164 ~~lv~~l~dLgfG~CRLvvAvP~~~~~~dv~sl~dL~~~~~~~~~~~lRVATkYPnlar~yf~~~Gi~~v~Ii~l~GSvE 243 (349)
++++ .|||||+|||++|+|++ .++.+++||. ++||||||||+|++||+++|++ ++||+++||+|
T Consensus 78 --v~~~-~dL~fg~crl~vA~p~~---~~~~~~~~l~---------~~rIATkyp~i~~~~f~~~Gi~-v~ii~l~GsvE 141 (182)
T TIGR00070 78 --VYEL-LDLGFGKCRLVLAVPQE---SDISSVEDLK---------GKRIATKYPNLARRYFEKKGID-VEIIKLNGSVE 141 (182)
T ss_pred --EEEE-eecCcCceEEEEEEECC---CCCCChHHhC---------CCEEEECCHHHHHHHHHHcCCe-EEEEECcceee
Confidence 4444 48999999999999998 3677888876 3799999999999999999995 99999999999
Q ss_pred cccCCCcceeeeecccchhhHhhCCcEEecCceEEEEEEEEEe
Q 018854 244 AAPAMGIADAILDLVSSGTTLRENNLKEIEGGVVLESQAVLVA 286 (349)
Q Consensus 244 lAP~lGlAD~IVDIVsTGtTLraNgLk~ie~g~IleSsA~LIa 286 (349)
+||.+|+||+||||||||+|||+|||++++ +||+|+|+||+
T Consensus 142 ~aP~~GlaD~IvDiv~TG~TL~~NgL~~ie--~i~~s~a~LI~ 182 (182)
T TIGR00070 142 LAPLLGLADAIVDIVSTGTTLRENGLRIIE--VILESSARLIA 182 (182)
T ss_pred cccCCCceeEEEEEeCCHHHHHHCCCEEee--EEEeeEEEEEC
Confidence 999999999999999999999999999998 99999999996
No 7
>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=100.00 E-value=7.8e-58 Score=408.06 Aligned_cols=163 Identities=39% Similarity=0.639 Sum_probs=142.4
Q ss_pred ecCCchhhhcccCceeeeeeccceecccCCCCccceeecCCCCcccEEEEEEEeCCCccCcccchHHhhcCCccCCCCCc
Q 018854 132 QRPKDIVRKLLSGDLDLGIVGLDTVSEFGQGNEDLIIVHDALDYGDCRLSLAIPKYGIFENINSLRELAQMPQWTAEKPL 211 (349)
Q Consensus 132 vR~~DIP~yV~~G~aDlGIvG~DvL~E~~~~~~~lv~~l~dLgfG~CRLvvAvP~~~~~~dv~sl~dL~~~~~~~~~~~l 211 (349)
+||+|||+||++|.+|+||||+|||.|++.+..+++ .+.|||||+|||++|+|+++ ++.+++||.. ++
T Consensus 1 vR~~DIp~yV~~G~~DlGI~G~D~l~E~~~~~~~v~-~~~dL~fg~crl~vAvp~~~---~~~~~~~l~~--------~~ 68 (163)
T PF01634_consen 1 VRPQDIPTYVEDGIADLGITGKDVLLESGLGRADVE-ELLDLGFGKCRLVVAVPEDW---PYKSVEDLKA--------GL 68 (163)
T ss_dssp E-GGHHHHHHHTTSSSEEEEEHHHHHHHTHH-SSEE-EEEEESCSEEEEEEEEETTS---CGCCGGGGSS--------TE
T ss_pred CChHHHHHHHHCCCCcEEEeehheeccCCCCccceE-EEeecccccEEEEEEEECCc---CCCCHHHhcc--------CC
Confidence 699999999999999999999999999984223444 44599999999999999983 3677777663 48
Q ss_pred EEEcCCCccHHHHHHhcCCceEEEEecCCccccccCCCcceeeeecccchhhHhhCCcEEecCceEEEEEEEEEeecchh
Q 018854 212 RVATGFTYLGPKFMKDNGLKHVVFSTADGALEAAPAMGIADAILDLVSSGTTLRENNLKEIEGGVVLESQAVLVASRKSL 291 (349)
Q Consensus 212 RVATkYPnlar~yf~~~Gi~~v~Ii~l~GSvElAP~lGlAD~IVDIVsTGtTLraNgLk~ie~g~IleSsA~LIaN~~s~ 291 (349)
||||||||+|++||+++|++ ++|++++||+|+||.+|+||+||||||||+|||+|||++++ +||+|+|+||+|+.++
T Consensus 69 rIATkyp~l~~~yf~~~g~~-~~ii~l~GsvE~ap~~glAD~IvDiv~TG~TLr~NgL~~i~--~i~~s~a~LI~n~~~~ 145 (163)
T PF01634_consen 69 RIATKYPNLTRRYFAEKGIN-VEIIKLSGSVELAPPLGLADAIVDIVETGTTLRANGLKEIE--TILESSARLIANKASL 145 (163)
T ss_dssp EEEES-HHHHHHHHHHCT-E-EEEEE-SS-TTHHHHTTSSSEEEEEESSSHHHHHTTEEEEE--EEEEEEEEEEEEHHHH
T ss_pred EEEECCHHHHHHHHHHcCCc-EEEEEccCCccccCCCCCCCEEEEeccCcHHHHHCCCEEeE--EEEEEEEEEEEcCccc
Confidence 99999999999999999996 89999999999999999999999999999999999999998 9999999999999999
Q ss_pred hhhcCchhHHHHHHHHHHHHH
Q 018854 292 IRRKGVLDATHEILERLEAHL 312 (349)
Q Consensus 292 ~~k~~~~~~i~~li~rl~~vl 312 (349)
+.++ +.|++|++||++++
T Consensus 146 ~~k~---~~i~~l~~~l~~vi 163 (163)
T PF01634_consen 146 KEKE---EKIDELVTRLRGVI 163 (163)
T ss_dssp HHCH---HHHHHHHHHHHHHH
T ss_pred hhhH---HHHHHHHHHHHhhC
Confidence 7654 68999999999985
No 8
>KOG2831 consensus ATP phosphoribosyltransferase [Amino acid transport and metabolism]
Probab=100.00 E-value=2.7e-58 Score=428.14 Aligned_cols=257 Identities=54% Similarity=0.857 Sum_probs=234.2
Q ss_pred CCCCceEEEecCCCCchHHHHHHHHHCCCccCCCCCCceEEecCCCCCeEEEeecCCchhhhcccCceeeeeeccceecc
Q 018854 79 SERDEIRLGLPSKGRMAADTLDLLKDCQLSVKQVNPRQYVAQIPQLSNLEVWFQRPKDIVRKLLSGDLDLGIVGLDTVSE 158 (349)
Q Consensus 79 ~~~~~LrIALP~KGRL~e~t~~LL~~aGi~~~~~~~R~L~~~~~~~p~vev~~vR~~DIP~yV~~G~aDlGIvG~DvL~E 158 (349)
..+++|++|+||||||++++.++|+.|.|.+++ ++|.+++.+++.|+..+||. +.|||++|..|.+|+||||.|.+.|
T Consensus 6 hl~DrllfalPkKGRly~~~v~lLkg~di~f~r-npRldiAli~~LP~alVflp-aaDIprfvgsG~~dLGItG~Dql~E 83 (308)
T KOG2831|consen 6 HLRDRLLFALPKKGRLYADAVDLLKGCDIFFKR-NPRLDIALIPQLPNALVFLP-AADIPRFVGSGDLDLGITGLDQLSE 83 (308)
T ss_pred hhhhheeeccCcccchHHHHHHHhcCCceEEee-CcccceecccCCCceEEecc-hhhcchhhccCcccccccchHHHHH
Confidence 578999999999999999999999999999999 89999999999997766555 9999999999999999999999999
Q ss_pred cCCCCccceeecCCCCcccEEEEEEEeCCCccCcccchHHhhcCCccCCCCCcEEEcCCCccHHHHHHhcCCceEEEEec
Q 018854 159 FGQGNEDLIIVHDALDYGDCRLSLAIPKYGIFENINSLRELAQMPQWTAEKPLRVATGFTYLGPKFMKDNGLKHVVFSTA 238 (349)
Q Consensus 159 ~~~~~~~lv~~l~dLgfG~CRLvvAvP~~~~~~dv~sl~dL~~~~~~~~~~~lRVATkYPnlar~yf~~~Gi~~v~Ii~l 238 (349)
++.+..++++++.||.||.|+|.|++|++++|++++++.+++.+.+|++.++++.||-|...--++..+.||+ .+|...
T Consensus 84 ~~~~n~~~i~~~~dLqFG~CkLqvqvP~~G~~~~i~qL~g~~ivtsf~~l~~~yf~~~~~~a~~eg~~~~gik-t~i~fv 162 (308)
T KOG2831|consen 84 YGQENEDLIIVHEDLQFGDCKLQVQVPNYGIFENINQLKGLAIVTSFSELRPLYFATGFTYAGPEGMKENGIK-TVIFFV 162 (308)
T ss_pred hhccchhhhhhhhhcccCCeeEEEEcCCcccccCHHHhhceeccchHHHHHHHHHhhcccccCcccceecCce-EEEEEe
Confidence 9988777888999999999999999999988888877777766667777777777777777777777889997 488888
Q ss_pred CCccccccCCCcceeeeecccchhhHhhCCcEEecCceEEEEEEEEEeecchhhhhcCchhHHHHHHHHHHHHHhhcCee
Q 018854 239 DGALEAAPAMGIADAILDLVSSGTTLRENNLKEIEGGVVLESQAVLVASRKSLIRRKGVLDATHEILERLEAHLRASGQF 318 (349)
Q Consensus 239 ~GSvElAP~lGlAD~IVDIVsTGtTLraNgLk~ie~g~IleSsA~LIaN~~s~~~k~~~~~~i~~li~rl~~vl~Ar~~~ 318 (349)
+||+|++|.+|+||+|||+||+|.|||+|||++|+ ++|++||.||+++.. +.++...++++++||++++.|++|+
T Consensus 163 sGsvEAscAlGIaDAivDLVeSGeTmra~gLk~Ie--tVlstsA~Lv~S~N~---~s~~~~lv~tI~~Rieg~l~Aq~~v 237 (308)
T KOG2831|consen 163 SGSVEASCALGIADAIVDLVESGETMRANGLKEIE--TVLSTSAALVASRNE---RSGALNLVHTILERIEGHLKAQGQV 237 (308)
T ss_pred ccceecchhcchHHHHHHHHhcchhHHhcCCeehh--hhhhhhHHHHhccCc---ccchhhHHHHHHHHHHHheecceEE
Confidence 99999999999999999999999999999999999 899999999998854 4455678999999999999999999
Q ss_pred EEEEecCCCCHHHHHHHhcccccCCCCCCCC
Q 018854 319 TVTANMRGNSAEEVAERILSQTSFSGLQGPT 349 (349)
Q Consensus 319 ~v~~N~p~~~l~~v~~~~~~~~~lpgl~~PT 349 (349)
.+.||++++.+.++.+ +.||+++||
T Consensus 238 ~vvyN~~~~~lpe~lk------~tPG~raPT 262 (308)
T KOG2831|consen 238 TVVYNMRAQELPERLK------STPGLRAPT 262 (308)
T ss_pred EEEecCchHHhhHHhh------cCCCccCCc
Confidence 9999999999999999 699999998
No 9
>PRK00489 hisG ATP phosphoribosyltransferase; Reviewed
Probab=100.00 E-value=1.3e-48 Score=372.42 Aligned_cols=240 Identities=35% Similarity=0.592 Sum_probs=219.8
Q ss_pred CCceEEEecCCCCchHHHHHHHHHCCCccCCCCCCceEEecCCCCCeEEEeecCCchhhhcccCceeeeeeccceecccC
Q 018854 81 RDEIRLGLPSKGRMAADTLDLLKDCQLSVKQVNPRQYVAQIPQLSNLEVWFQRPKDIVRKLLSGDLDLGIVGLDTVSEFG 160 (349)
Q Consensus 81 ~~~LrIALP~KGRL~e~t~~LL~~aGi~~~~~~~R~L~~~~~~~p~vev~~vR~~DIP~yV~~G~aDlGIvG~DvL~E~~ 160 (349)
++||||||||||||+|++++||++|||++.. ++|+|....++ .++++.+++++||+.||..|.+|+||+|.|++.|++
T Consensus 2 ~~~l~~a~p~kg~l~~~~~~ll~~~g~~~~~-~~r~~~~~~p~-~~ie~~~~~~~~i~~~L~sG~vDlgi~g~~~~~er~ 79 (287)
T PRK00489 2 STMLRIAVPNKGRLSEPALELLAEAGLKIRR-DSRSLIATDED-NPIEVLFLRPDDIPGYVADGVVDLGITGEDLLEESG 79 (287)
T ss_pred CccEEEEECCCCccHHHHHHHHHHcCCCCCC-CCcceEeecCC-CCEEEEEECcHHHHHHHHcCCCCEEEcchHHHHHCC
Confidence 5789999999999999999999999999998 67999998876 469999999999999999999999999999999986
Q ss_pred CCCccceeecCCCCcccEEEEEEEeCCCccCcccchHHhhcCCccCCCCCcEEEcCCCccHHHHHHhcCCceEEEEecCC
Q 018854 161 QGNEDLIIVHDALDYGDCRLSLAIPKYGIFENINSLRELAQMPQWTAEKPLRVATGFTYLGPKFMKDNGLKHVVFSTADG 240 (349)
Q Consensus 161 ~~~~~lv~~l~dLgfG~CRLvvAvP~~~~~~dv~sl~dL~~~~~~~~~~~lRVATkYPnlar~yf~~~Gi~~v~Ii~l~G 240 (349)
.+ +..+..++|++|++++++|++ .++.+++||.+ +||||+|++++++||+++|++ ++++..+|
T Consensus 80 ~~----v~~~~~l~~~~~~lvvvvp~~---~~i~sl~DL~G---------k~ia~~~~~~~~~~l~~~gi~-~~iv~~~g 142 (287)
T PRK00489 80 AD----VEELLDLGFGKCRLVLAVPED---SDWQGVEDLAG---------KRIATSYPNLTRRYLAEKGID-AEVVELSG 142 (287)
T ss_pred CC----ceEeeeccCCceEEEEEEECC---CCCCChHHhCC---------CEEEEcCcHHHHHHHHHcCCc-eEEEECCC
Confidence 54 233457999999999999998 56788999875 699999999999999999995 89999999
Q ss_pred ccccccCCCcceeeeecccchhhHhhCCcEEecCceEEEEEEEEEeecchhhhhcCchhHHHHHHHHHHHHHhhcCeeEE
Q 018854 241 ALEAAPAMGIADAILDLVSSGTTLRENNLKEIEGGVVLESQAVLVASRKSLIRRKGVLDATHEILERLEAHLRASGQFTV 320 (349)
Q Consensus 241 SvElAP~lGlAD~IVDIVsTGtTLraNgLk~ie~g~IleSsA~LIaN~~s~~~k~~~~~~i~~li~rl~~vl~Ar~~~~v 320 (349)
++|++|.+|.+|+|+|.+++|+||++|||++++ ++++++++||+|+ .+.. +.+++.|+.++.+|+++++++.++++
T Consensus 143 s~eaa~~~G~aDaivd~~~~~~~l~~~~L~~v~--~~~~~~~~li~~k-~~~~-~~~~~~i~~~l~~l~g~l~a~~~k~~ 218 (287)
T PRK00489 143 AVEVAPRLGLADAIVDVVSTGTTLRANGLKIVE--VILRSEAVLIARK-GWLD-PEKQEKIDQLLTRLQGVLRARESKYL 218 (287)
T ss_pred chhhhhcCCcccEEEeeHHHHHHHHHCCCEEEE--eeeeeeEEEEEcc-cccC-hhHHHHHHHHHHHHHHHHHhhceEEE
Confidence 999999999999999999999999999999995 9999999999999 5443 23457899999999999999999999
Q ss_pred EEecCCCCHHHHHHHhcccccCCCCCCCC
Q 018854 321 TANMRGNSAEEVAERILSQTSFSGLQGPT 349 (349)
Q Consensus 321 ~~N~p~~~l~~v~~~~~~~~~lpgl~~PT 349 (349)
++|+|++++++|++ +|||+++||
T Consensus 219 ~~~~~~~~~~~~~~------~~p~~~~pt 241 (287)
T PRK00489 219 MMNAPKEKLDAVIA------LLPGLESPT 241 (287)
T ss_pred EEeCCHHHHHHHHH------hCCCCCCCc
Confidence 99999999999999 599999998
No 10
>TIGR03455 HisG_C-term ATP phosphoribosyltransferase, C-terminal domain. This domain corresponds to the C-terminal third of the HisG protein. It is absent in many lineages.
Probab=99.13 E-value=6.8e-11 Score=98.47 Aligned_cols=55 Identities=29% Similarity=0.485 Sum_probs=48.5
Q ss_pred ecchhhhhcCchhHHHHHHHHHHHHHhhcCeeEEEEecCCCCHHHHHHHhcccccCCCCCCCC
Q 018854 287 SRKSLIRRKGVLDATHEILERLEAHLRASGQFTVTANMRGNSAEEVAERILSQTSFSGLQGPT 349 (349)
Q Consensus 287 N~~s~~~k~~~~~~i~~li~rl~~vl~Ar~~~~v~~N~p~~~l~~v~~~~~~~~~lpgl~~PT 349 (349)
|+.++.+ .+++.++.|++||+++++|++|+||+||+|+++++++.+ +|||++|||
T Consensus 1 ~~~~~~~--~~~~~~~~l~~ri~gvl~A~~~~~v~~Nvp~~~l~~v~~------ilPg~~~PT 55 (100)
T TIGR03455 1 NKRSLDD--EKREKIEQLLTRLQGVLAARGKVLLMMNVPRDNLDEVRA------LLPGLEGPT 55 (100)
T ss_pred CCcchhh--HHHHHHHHHHHHHHHHHHHhheeEEEEeCChhhHHHHHH------hcCCCCCCC
Confidence 4555554 234789999999999999999999999999999999999 599999999
No 11
>PF08029 HisG_C: HisG, C-terminal domain; InterPro: IPR013115 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. This entry represents the C-terminal portion of ATP phosphoribosyltransferase. 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. This domain is not directly involved in catalysis but appears to be responsible for the formation of hexamers induced by the binding of inhibitors to the enzyme, thus regulating activity.; GO: 0000287 magnesium ion binding, 0003879 ATP phosphoribosyltransferase activity, 0000105 histidine biosynthetic process, 0005737 cytoplasm; PDB: 1Q1K_A 1H3D_A 2VD3_B 1NH7_A 1NH8_A.
Probab=98.36 E-value=2.2e-07 Score=73.89 Aligned_cols=31 Identities=35% Similarity=0.493 Sum_probs=26.6
Q ss_pred hhcCeeEEEEecCCCCHHHHHHHhcccccCCCCCCCC
Q 018854 313 RASGQFTVTANMRGNSAEEVAERILSQTSFSGLQGPT 349 (349)
Q Consensus 313 ~Ar~~~~v~~N~p~~~l~~v~~~~~~~~~lpgl~~PT 349 (349)
.||+|++|+||+|++++++|.+ +|||++|||
T Consensus 1 ~A~~~~~l~~Nvp~~~l~~v~~------ilPg~~~PT 31 (75)
T PF08029_consen 1 TARGYVLLMMNVPRESLEEVIK------ILPGLKSPT 31 (75)
T ss_dssp HCCCEEEEEEEEECCCHHHHHH------HS--SSS-E
T ss_pred CcccceEEEEeCCHHHHHHHHH------hCCCCCCCc
Confidence 4899999999999999999999 599999998
No 12
>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=97.50 E-value=0.00049 Score=63.12 Aligned_cols=159 Identities=20% Similarity=0.209 Sum_probs=96.4
Q ss_pred CCchhhhcccCceeeeeeccceec-ccCCCCccceeecCCCCcccEEEEEEEeCCCccCcccchHHhhcCCccCCCCCcE
Q 018854 134 PKDIVRKLLSGDLDLGIVGLDTVS-EFGQGNEDLIIVHDALDYGDCRLSLAIPKYGIFENINSLRELAQMPQWTAEKPLR 212 (349)
Q Consensus 134 ~~DIP~yV~~G~aDlGIvG~DvL~-E~~~~~~~lv~~l~dLgfG~CRLvvAvP~~~~~~dv~sl~dL~~~~~~~~~~~lR 212 (349)
..++...|..|.+|+|++|..... ..... .++. .+.-... .....++++.+ .++++++||.+ ++
T Consensus 39 ~~~~~~~l~~G~~D~~~~~~~~~~~~~~~g-~~~~-~i~~~~~-~~~~~~v~~~~---~~i~s~~dL~G---------k~ 103 (288)
T TIGR01728 39 GPPALEALGAGSLDFGYIGPGPALFAYAAG-ADIK-AVGLVSD-NKATAIVVIKG---SPIRTVADLKG---------KR 103 (288)
T ss_pred CcHHHHHHhcCCccccccCCcHHHHHHhcC-CCEE-EEEEecC-CCceEEEECCC---CCCCCHHHcCC---------CE
Confidence 367889999999999999887322 22111 2222 1111222 13556677766 67889999885 46
Q ss_pred EEc----CCCccHHHHHHhcCCce--EEEEecC-CccccccCCCcceeeeecccchhhHhhC-CcEEec-CceEEEE--E
Q 018854 213 VAT----GFTYLGPKFMKDNGLKH--VVFSTAD-GALEAAPAMGIADAILDLVSSGTTLREN-NLKEIE-GGVVLES--Q 281 (349)
Q Consensus 213 VAT----kYPnlar~yf~~~Gi~~--v~Ii~l~-GSvElAP~lGlAD~IVDIVsTGtTLraN-gLk~ie-~g~IleS--s 281 (349)
|++ ....+..++|++.|+.. ++++.+. +....+-.-|-+|+++---..++.+..+ +.+.+. .+.+... .
T Consensus 104 i~~~~~~~~~~~~~~~l~~~G~~~~~v~~~~~~~~~~~~al~~g~vda~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~ 183 (288)
T TIGR01728 104 IAVPKGGSGHDLLLRALLKAGLSGDDVTILYLGPSDARAAFAAGQVDAWAIWEPWGSALVEEGGARVLANGEGIGLPGQP 183 (288)
T ss_pred EEecCCccHHHHHHHHHHHcCCCccceeEEecCcHHHHHHHHCCCCCEEEeccchHhHHhhccCCEEEEcCCccCCCCcc
Confidence 764 44557778999999842 4444433 3444567788899998766666665444 344432 1122222 3
Q ss_pred EEEEeecchhhhhcCchhHHHHHHHHHHH
Q 018854 282 AVLVASRKSLIRRKGVLDATHEILERLEA 310 (349)
Q Consensus 282 A~LIaN~~s~~~k~~~~~~i~~li~rl~~ 310 (349)
..+++|+..++.++ +.++.+++.+..
T Consensus 184 ~~~~~~~~~~~~~p---~~~~~~~~a~~~ 209 (288)
T TIGR01728 184 GFLVVRREFAEAHP---EQVQRVLKVLVK 209 (288)
T ss_pred eEEEECHHHHHHCH---HHHHHHHHHHHH
Confidence 67888888776655 456666555543
No 13
>smart00062 PBPb Bacterial periplasmic substrate-binding proteins. bacterial proteins, eukaryotic ones are in PBPe
Probab=96.96 E-value=0.0074 Score=50.65 Aligned_cols=142 Identities=20% Similarity=0.154 Sum_probs=93.1
Q ss_pred EEEeecCCchhhhcccCceeeeeeccceecccCCCCccceeecCCCCcccEEEEEEEeCCCccCcccchHHhhcCCccCC
Q 018854 128 EVWFQRPKDIVRKLLSGDLDLGIVGLDTVSEFGQGNEDLIIVHDALDYGDCRLSLAIPKYGIFENINSLRELAQMPQWTA 207 (349)
Q Consensus 128 ev~~vR~~DIP~yV~~G~aDlGIvG~DvL~E~~~~~~~lv~~l~dLgfG~CRLvvAvP~~~~~~dv~sl~dL~~~~~~~~ 207 (349)
++......++...+..|.+|+++.+..+..|.... +. .-..+...++++.++.+ .++.+++||++
T Consensus 42 ~~~~~~~~~~~~~l~~g~~D~~~~~~~~~~~~~~~----~~--~~~~~~~~~~~~~~~~~---~~~~~~~dL~g------ 106 (219)
T smart00062 42 EFVEVSFDNLLTALKSGKIDVVAAGMTITPERAKQ----VD--FSDPYYKSGQVILVRKD---SPIKSLEDLKG------ 106 (219)
T ss_pred EEEeccHHHHHHHHHCCcccEEeccccCCHHHHhh----ee--eccceeeceeEEEEecC---CCCCChHHhCC------
Confidence 34444567888999999999999988765554311 11 12456666788889887 56788999864
Q ss_pred CCCcEEEcCCCccHHHHHHhcCCceEEEEecCCcccc--ccCCCcceeeeecccchhhHhhC----CcEEecCceEEE-E
Q 018854 208 EKPLRVATGFTYLGPKFMKDNGLKHVVFSTADGALEA--APAMGIADAILDLVSSGTTLREN----NLKEIEGGVVLE-S 280 (349)
Q Consensus 208 ~~~lRVATkYPnlar~yf~~~Gi~~v~Ii~l~GSvEl--AP~lGlAD~IVDIVsTGtTLraN----gLk~ie~g~Ile-S 280 (349)
++|++-.-.....+|.+.+. ..+++......++ +-.-|-+|+++--......+..+ +++++.. .... .
T Consensus 107 ---~~i~~~~g~~~~~~~~~~~~-~~~~~~~~~~~~~~~~l~~g~~d~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~ 181 (219)
T smart00062 107 ---KKVAVVAGTTGEELLKKLYP-EAKIVSYDSQAEALAALKAGRADAAVADAPALAALVKQHGLPELKIVGD-PLDTPE 181 (219)
T ss_pred ---CEEEEecCccHHHHHHHhCC-CceEEEcCCHHHHHHHhhcCcccEEEeccHHHHHHHHhcCCCceeeccC-CCCCCc
Confidence 57887766777788877643 2566666655553 45667889988887777766544 4666542 1222 4
Q ss_pred EEEEEeecc
Q 018854 281 QAVLVASRK 289 (349)
Q Consensus 281 sA~LIaN~~ 289 (349)
...++.++.
T Consensus 182 ~~~~~~~~~ 190 (219)
T smart00062 182 GYAFAVRKG 190 (219)
T ss_pred ceEEEEECC
Confidence 455555555
No 14
>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=96.91 E-value=0.0015 Score=58.36 Aligned_cols=168 Identities=23% Similarity=0.240 Sum_probs=102.3
Q ss_pred eEEEeecC-CchhhhcccCceeeeeeccceecccCCCCccceeecCCCCcccEEEEEEEeCCCccCcccchHHhhcCCcc
Q 018854 127 LEVWFQRP-KDIVRKLLSGDLDLGIVGLDTVSEFGQGNEDLIIVHDALDYGDCRLSLAIPKYGIFENINSLRELAQMPQW 205 (349)
Q Consensus 127 vev~~vR~-~DIP~yV~~G~aDlGIvG~DvL~E~~~~~~~lv~~l~dLgfG~CRLvvAvP~~~~~~dv~sl~dL~~~~~~ 205 (349)
+++....+ .+....+..|.+|+|+++.+.+.-......++..+. .+ +..+...+.++++ .+|++++||++
T Consensus 23 ve~~~~~~~~~~~~~l~~G~~D~~~~~~~~~~~~~~~g~~~~~i~-~~-~~~~~~~l~~~~~---s~i~~~~DLkG---- 93 (216)
T PF09084_consen 23 VEIVFFGGGGDVLEALASGKADIAVAGPDAVLFARAKGADIKIIA-AS-YQSSPNALVVRKD---SGIKSPADLKG---- 93 (216)
T ss_dssp EEEEEESSHHHHHHHHHTTSHSEEEEECHHHHHHHHTTSTEEEEE-EE-EEECCEEEEEETT---TS-SSGGGGTT----
T ss_pred EEEEEecChhHHHHHHhcCCceEEeccchHHHHHHhcCCeeEEEE-Ee-cCCCceEEEEecc---CCCCCHHHhCC----
Confidence 44444433 789999999999999999997774332223332221 11 1122345666666 67899999885
Q ss_pred CCCCCcEEEcCCC----ccHHHHHHhcCC--ceEEEEecCCcccc-ccCCCcceeeeecccc--hhhHhhCCcEE--ecC
Q 018854 206 TAEKPLRVATGFT----YLGPKFMKDNGL--KHVVFSTADGALEA-APAMGIADAILDLVSS--GTTLRENNLKE--IEG 274 (349)
Q Consensus 206 ~~~~~lRVATkYP----nlar~yf~~~Gi--~~v~Ii~l~GSvEl-AP~lGlAD~IVDIVsT--GtTLraNgLk~--ie~ 274 (349)
+||+..-- .+.++++++.|+ +.++++.+.+.... |-.-|-.|+++..... ..+++..|-.. ...
T Consensus 94 -----K~i~v~~~s~~~~~~~~~l~~~g~~~~~v~~v~~~~~~~~~al~~g~vDa~~~~~~~~~~~~~~~~~~~~~~~~~ 168 (216)
T PF09084_consen 94 -----KKIGVSRGSSSEYFLRALLKKNGIDPDDVKIVNLGPPELAQALLSGQVDAAILWYPPWEPYEIASKGKKLRVLEL 168 (216)
T ss_dssp -----SEEEESTTSHHHHHHHHHHHHTTT-GGGSEEEES-HHHHHHHHHTTSSSEEEEEEECTCHHHHHHCCSCEEEEEG
T ss_pred -----CEEEEecCcchhHHHHHHHHHhccccccceeeeeehhhhhhhhhcCCCCEEEEccCChHHHHHHHcCCceeeeec
Confidence 68876551 266788888998 46888887644332 5667889999966654 45544444322 110
Q ss_pred ceE---EEEEEEEEeecchhhhhcCchhHHHHHHHHHHHH
Q 018854 275 GVV---LESQAVLVASRKSLIRRKGVLDATHEILERLEAH 311 (349)
Q Consensus 275 g~I---leSsA~LIaN~~s~~~k~~~~~~i~~li~rl~~v 311 (349)
... --...++++++...+.++ +.++.++..+...
T Consensus 169 ~~~~~~~~~~~~~~~~~~~~~~~p---e~~~~f~~a~~~a 205 (216)
T PF09084_consen 169 SDYGPPNYPVSVLVARDEFLEKNP---EAVKAFLKAYAKA 205 (216)
T ss_dssp GGCCGGCS-SEEEEEEHHHHHHSH---HHHHHHHHHHHHH
T ss_pred cccCcccccceEEEEchHHHHHCH---HHHHHHHHHHHHH
Confidence 011 113457888888887766 5677776655543
No 15
>PRK11480 tauA taurine transporter substrate binding subunit; Provisional
Probab=96.91 E-value=0.0062 Score=58.87 Aligned_cols=163 Identities=18% Similarity=0.182 Sum_probs=95.6
Q ss_pred eEEEee-cCCchhhhcccCceeeeeeccceecc---cCCCCccceeecCCCCcccEEEEEEEeCCCccCcccchHHhhcC
Q 018854 127 LEVWFQ-RPKDIVRKLLSGDLDLGIVGLDTVSE---FGQGNEDLIIVHDALDYGDCRLSLAIPKYGIFENINSLRELAQM 202 (349)
Q Consensus 127 vev~~v-R~~DIP~yV~~G~aDlGIvG~DvL~E---~~~~~~~lv~~l~dLgfG~CRLvvAvP~~~~~~dv~sl~dL~~~ 202 (349)
+++... -..++...+..|.+|+|++|.+.+.- .+.+. .++-.....+ +...+.++. +|++++||++
T Consensus 53 Ve~~~~~~~~~~~~al~~G~~D~a~~~~~~~~~a~~~g~~~-~~v~~~~~~~---~~~~lv~~~-----~I~s~~DLkG- 122 (320)
T PRK11480 53 VDWRKFDSGASIVRALASGDVQIGNLGSSPLAVAASQQVPI-EVFLLASKLG---NSEALVVKK-----TISKPEDLIG- 122 (320)
T ss_pred eEEEEeCCHHHHHHHHHCCCCCEECcCchHHHHHHHCCCCe-EEEEeeccCC---cceEEEecC-----CCCChHHcCC-
Confidence 555433 34688899999999999998875432 33221 1111111122 222333442 4788999885
Q ss_pred CccCCCCCcEEEcCCC----ccHHHHHHhcCCc--eEEEEecCCc-cccccCCCcceeeeecccchhhHhhCCcEEecCc
Q 018854 203 PQWTAEKPLRVATGFT----YLGPKFMKDNGLK--HVVFSTADGA-LEAAPAMGIADAILDLVSSGTTLRENNLKEIEGG 275 (349)
Q Consensus 203 ~~~~~~~~lRVATkYP----nlar~yf~~~Gi~--~v~Ii~l~GS-vElAP~lGlAD~IVDIVsTGtTLraNgLk~ie~g 275 (349)
+|||+-.. .+..+++++.|++ .|+++.+... .-.|=.-|-.|+++--.-..+.++.+|-.+.+..
T Consensus 123 --------K~Iav~~~s~~~~~l~~~L~~~Gl~~~dv~~v~~~~~~~~~Al~~G~VDAa~~~~p~~~~~~~~g~~l~~~~ 194 (320)
T PRK11480 123 --------KRIAVPFISTTHYSLLAALKHWGIKPGQVEIVNLQPPAIIAAWQRGDIDGAYVWAPAVNALEKDGKVLTDSE 194 (320)
T ss_pred --------CEEecCCCCchHHHHHHHHHHcCCCHhheEEEECCcHHHHHHHHcCCcCEEEEcchHHHHHHhCCeEEecch
Confidence 68886432 3567789999983 4777776532 2223345778887754445566766664333211
Q ss_pred eEE----EEEEEEEeecchhhhhcCchhHHHHHHHHHHH
Q 018854 276 VVL----ESQAVLVASRKSLIRRKGVLDATHEILERLEA 310 (349)
Q Consensus 276 ~Il----eSsA~LIaN~~s~~~k~~~~~~i~~li~rl~~ 310 (349)
.+- .+...++++....++++ +.+..++..+..
T Consensus 195 ~~~~~~~~~~~~lv~~~~~i~~~p---~~v~~f~~A~~~ 230 (320)
T PRK11480 195 QVGQWGAPTLDVWVVRKDFAEKHP---EVVKAFAKSAID 230 (320)
T ss_pred hhcccCCCceEEEEECHHHHHHCH---HHHHHHHHHHHH
Confidence 221 23357888888777765 566777665443
No 16
>PRK11553 alkanesulfonate transporter substrate-binding subunit; Provisional
Probab=96.85 E-value=0.0072 Score=57.69 Aligned_cols=161 Identities=19% Similarity=0.186 Sum_probs=91.6
Q ss_pred CCchhhhcccCceeeeeeccce-ecccCCCCccceeecCCCCcccEEEEEEEeCCCccCcccchHHhhcCCccCCCCCcE
Q 018854 134 PKDIVRKLLSGDLDLGIVGLDT-VSEFGQGNEDLIIVHDALDYGDCRLSLAIPKYGIFENINSLRELAQMPQWTAEKPLR 212 (349)
Q Consensus 134 ~~DIP~yV~~G~aDlGIvG~Dv-L~E~~~~~~~lv~~l~dLgfG~CRLvvAvP~~~~~~dv~sl~dL~~~~~~~~~~~lR 212 (349)
..++...+..|.+|+|++|... +...... .++..+. ...+....+++.++.+ .++.+++||++ ++
T Consensus 66 ~~~~~~aL~~G~iDia~~~~~~~~~~~~~g-~~~~~v~-~~~~~~~~~~lvv~~~---s~i~s~~dL~G---------k~ 131 (314)
T PRK11553 66 GPQMLEALNVGSIDLGSTGDIPPIFAQAAG-ADLVYVG-VEPPKPKAEVILVAEN---SPIKTVADLKG---------HK 131 (314)
T ss_pred cHHHHHHHHcCCCCEEccCCHHHHHHHhCC-CCEEEEE-EecCCCcceEEEEeCC---CCCCCHHHhCC---------CE
Confidence 4689999999999999998432 2211111 2222111 1223334467778877 56789999885 45
Q ss_pred EEcC----CCccHHHHHHhcCCc--eEEEEecCCc-cccccCCCcceeeeecccchhh-HhhCCcEEecCce-EEEEEEE
Q 018854 213 VATG----FTYLGPKFMKDNGLK--HVVFSTADGA-LEAAPAMGIADAILDLVSSGTT-LRENNLKEIEGGV-VLESQAV 283 (349)
Q Consensus 213 VATk----YPnlar~yf~~~Gi~--~v~Ii~l~GS-vElAP~lGlAD~IVDIVsTGtT-LraNgLk~ie~g~-IleSsA~ 283 (349)
|++. ...+..++|++.|+. .++++.+... .-.|-.-|-+|+++=--...+. +++.+.+++.++. +-.....
T Consensus 132 I~~~~gs~~~~~l~~~l~~~g~~~~dv~~v~~~~~~~~~al~~G~vDa~~~~ep~~~~~~~~~~~~~~~~~~~~~~~~~~ 211 (314)
T PRK11553 132 VAFQKGSSSHNLLLRALRKAGLKFTDIQPTYLTPADARAAFQQGNVDAWAIWDPYYSAALLQGGVRVLKDGTDLNQTGSF 211 (314)
T ss_pred EeecCCCcHHHHHHHHHHHcCCCHHHeEEEecChHHHHHHHHcCCCCEEEEcCcHHHHHHhcCCcEEeecCcccCcCceE
Confidence 6643 335667788888873 3566655322 2234456888887632222333 2334555443222 2223346
Q ss_pred EEeecchhhhhcCchhHHHHHHHHHHHH
Q 018854 284 LVASRKSLIRRKGVLDATHEILERLEAH 311 (349)
Q Consensus 284 LIaN~~s~~~k~~~~~~i~~li~rl~~v 311 (349)
+++++...+.++ +.++.++..+...
T Consensus 212 ~~~~~~~~~~~p---~~v~~~l~a~~~A 236 (314)
T PRK11553 212 YLAARPYAEKNG---AFIQQVLATLTEA 236 (314)
T ss_pred EEEcHHHHHHCH---HHHHHHHHHHHHH
Confidence 777776555544 5677776666553
No 17
>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=96.84 E-value=0.0066 Score=57.56 Aligned_cols=166 Identities=16% Similarity=0.106 Sum_probs=95.1
Q ss_pred eEEEeec-CCchhhhcccCceeeeeeccceecccCCCCccceeecCCC-CcccEEEEEEEeCCCccCcccchHHhhcCCc
Q 018854 127 LEVWFQR-PKDIVRKLLSGDLDLGIVGLDTVSEFGQGNEDLIIVHDAL-DYGDCRLSLAIPKYGIFENINSLRELAQMPQ 204 (349)
Q Consensus 127 vev~~vR-~~DIP~yV~~G~aDlGIvG~DvL~E~~~~~~~lv~~l~dL-gfG~CRLvvAvP~~~~~~dv~sl~dL~~~~~ 204 (349)
+++.... ..++...+..|.+|+|++|.....-......++..+. -+ .++.+ ..+.++++ .+|++++||++
T Consensus 29 Ve~~~~~~~~~~~~al~~G~iD~~~~~~~~~~~a~~~g~~~~~v~-~~~~~~~~-~~lv~~~~---s~I~s~~DLkG--- 100 (300)
T TIGR01729 29 IDWRKFDSGADISTALASGNVPIGVIGSSPLAAAASRGVPIELFW-ILDNIGKS-EALVAREG---SGIEKPEDLKG--- 100 (300)
T ss_pred eEEEecCcHHHHHHHHHcCCCCEeccCCCHHHHHHHCCCCeEEEE-EeccCCcc-ceEEecCC---CCCCChhHcCC---
Confidence 4554443 4588899999999999998765532211112221111 11 12333 24556665 67889999885
Q ss_pred cCCCCCcEEEcCCC----ccHHHHHHhcCCc--eEEEEecCCcccc--ccCCCcceeeeecccchhhHhhCCcEEecCce
Q 018854 205 WTAEKPLRVATGFT----YLGPKFMKDNGLK--HVVFSTADGALEA--APAMGIADAILDLVSSGTTLRENNLKEIEGGV 276 (349)
Q Consensus 205 ~~~~~~lRVATkYP----nlar~yf~~~Gi~--~v~Ii~l~GSvEl--AP~lGlAD~IVDIVsTGtTLraNgLk~ie~g~ 276 (349)
++||.... .+..++|++.|++ .|+++.+. ..+. |=.-|-.|+++=---..+.+.+.|-.+.+...
T Consensus 101 ------K~Igv~~~s~~~~~l~~~L~~~Gl~~~dv~~v~~~-~~~~~~al~~G~vDa~~~~~p~~~~~~~~g~~~~~~~~ 173 (300)
T TIGR01729 101 ------KNVAVPFVSTTHYSLLAALKHWKTDPREVNILNLK-PPQIVAAWQRGDIDAAYVWPPALSELLKSGKVISDSEQ 173 (300)
T ss_pred ------CEEEeCCCCcHHHHHHHHHHHcCCChhheEEEecC-cHHHHHHHHcCCcCEEEEecHHHHHHHhcCcEEecchh
Confidence 57886433 3455788888874 36666642 2232 23457778776544455566666633332112
Q ss_pred EE----EEEEEEEeecchhhhhcCchhHHHHHHHHHHH
Q 018854 277 VL----ESQAVLVASRKSLIRRKGVLDATHEILERLEA 310 (349)
Q Consensus 277 Il----eSsA~LIaN~~s~~~k~~~~~~i~~li~rl~~ 310 (349)
+- .+...+++++...++++ +.++.|+..+..
T Consensus 174 ~~~~~~~~~~~~~~~~~~~~~~p---~~~~~~~~a~~~ 208 (300)
T TIGR01729 174 VGAWGAPTFDGWVVRKDFAEKNP---EFVAAFTKVLAD 208 (300)
T ss_pred ccccCCCceeEEEECHHHHHHCH---HHHHHHHHHHHH
Confidence 21 12357888887777655 466666655544
No 18
>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=95.17 E-value=0.18 Score=49.95 Aligned_cols=154 Identities=14% Similarity=0.132 Sum_probs=91.7
Q ss_pred CCchhhhcccCceeeeeecccee----cccCCCCccceeecCCCCcccEEEEEEEeCCCccCcccchHHhhcCCccCCCC
Q 018854 134 PKDIVRKLLSGDLDLGIVGLDTV----SEFGQGNEDLIIVHDALDYGDCRLSLAIPKYGIFENINSLRELAQMPQWTAEK 209 (349)
Q Consensus 134 ~~DIP~yV~~G~aDlGIvG~DvL----~E~~~~~~~lv~~l~dLgfG~CRLvvAvP~~~~~~dv~sl~dL~~~~~~~~~~ 209 (349)
..|.-..+..|.+|+|..|.+-. .-.+.+. .++ ...+-..|.-- +.+++ +++++||++
T Consensus 45 ~~~~l~Al~aG~iD~~~~g~~~~~~~~~a~g~~~-~iv-~v~~~~~g~~~--ivv~~------i~svaDLKG-------- 106 (328)
T TIGR03427 45 YVESINQYTAGKFDGCTMTNMDALTIPAAGGVDT-TAL-IVGDFSNGNDG--IVLKG------GKSLADLKG-------- 106 (328)
T ss_pred hHHHHHHHHcCCCCEEeecCHHHHHHHHhCCCCe-EEE-EEEccCCCceE--EEECC------CCCHHHcCC--------
Confidence 34555556699999999887532 2333221 122 22233333322 22332 588999885
Q ss_pred CcEEEcCCC----ccHHHHHHhcCCc--eEEEEecCCc-cccccCCCcceeeeecccchhhHhh-CCcEEecCceEE--E
Q 018854 210 PLRVATGFT----YLGPKFMKDNGLK--HVVFSTADGA-LEAAPAMGIADAILDLVSSGTTLRE-NNLKEIEGGVVL--E 279 (349)
Q Consensus 210 ~lRVATkYP----nlar~yf~~~Gi~--~v~Ii~l~GS-vElAP~lGlAD~IVDIVsTGtTLra-NgLk~ie~g~Il--e 279 (349)
+|||+..- .+..+.+++.|++ .|+++.+.-+ ...|=.-|-.|+.+----..+.+++ .|.+++-++.-+ .
T Consensus 107 -KkIav~~gs~~~~ll~~aL~~aGL~~~DV~~v~~~~~d~~aAl~~G~VDAa~~~eP~~s~~~~~~g~~~l~~~~~~~~~ 185 (328)
T TIGR03427 107 -QKVNLVELSVSHYLLARALESVGLSEKDVKVVNTSDADIVAAFITKDVTAVVTWNPQLSEIKAQPGANEVFDSSQIPGE 185 (328)
T ss_pred -CEEeccCCChHHHHHHHHHHHcCCCHHHeEEEeCChHHHHHHHhcCCCcEEEEcCchHHHHHhCCCcEEecccccCCCc
Confidence 68886432 3455788888985 5899987632 2234445778888754445666765 477777543222 1
Q ss_pred EEEEEEeecchhhhhcCchhHHHHHHHHHH
Q 018854 280 SQAVLVASRKSLIRRKGVLDATHEILERLE 309 (349)
Q Consensus 280 SsA~LIaN~~s~~~k~~~~~~i~~li~rl~ 309 (349)
+..+|+++....+.++ +.++.+++...
T Consensus 186 ~~~~lv~~~~~l~~~p---e~v~~~~~a~~ 212 (328)
T TIGR03427 186 ILDLMVVNTQTLKANP---NLGKALTGAWY 212 (328)
T ss_pred ceEEEEECHHHHHHCH---HHHHHHHHHHH
Confidence 4578999998888766 45666654444
No 19
>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=94.99 E-value=0.32 Score=41.10 Aligned_cols=166 Identities=19% Similarity=0.192 Sum_probs=99.1
Q ss_pred CCeEEE--eecCCchhhhcccCceeeeeeccceecccCCCCccceeecCCCCcccEEEEEEEeCCCccCc--ccchHHhh
Q 018854 125 SNLEVW--FQRPKDIVRKLLSGDLDLGIVGLDTVSEFGQGNEDLIIVHDALDYGDCRLSLAIPKYGIFEN--INSLRELA 200 (349)
Q Consensus 125 p~vev~--~vR~~DIP~yV~~G~aDlGIvG~DvL~E~~~~~~~lv~~l~dLgfG~CRLvvAvP~~~~~~d--v~sl~dL~ 200 (349)
|++++. .....++...+.+|.+|+||+.... +. .++. -..++..+++++++.+..+.. --+++||.
T Consensus 33 P~i~i~~~~~~~~~~~~~l~~g~~Dl~i~~~~~--~~----~~~~----~~~l~~~~~~~~~~~~~pl~~~~~i~~~dL~ 102 (209)
T PF03466_consen 33 PNIRIEIREGDSDELIEALRSGELDLAITFGPP--PP----PGLE----SEPLGEEPLVLVVSPDHPLAQKKPITLEDLA 102 (209)
T ss_dssp TTEEEEEEEESHHHHHHHHHTTSSSEEEESSSS--SS----TTEE----EEEEEEEEEEEEEETTSGGGTTSSSSGGGGT
T ss_pred CCcEEEEEeccchhhhHHHhcccccEEEEEeec--cc----cccc----cccccceeeeeeeeccccccccccchhhhhh
Confidence 445444 4455699999999999999998776 11 2222 234678999999998842221 12566666
Q ss_pred cCCccCCCCCcEEE--cCCCccHHHHHHhcCCceEEEEecCCcccccc---CCCcceeeeecccchhhHhhCCcEEecCc
Q 018854 201 QMPQWTAEKPLRVA--TGFTYLGPKFMKDNGLKHVVFSTADGALEAAP---AMGIADAILDLVSSGTTLRENNLKEIEGG 275 (349)
Q Consensus 201 ~~~~~~~~~~lRVA--TkYPnlar~yf~~~Gi~~v~Ii~l~GSvElAP---~lGlAD~IVDIVsTGtTLraNgLk~ie~g 275 (349)
..+. +... +.+-....++|++.|+. ..++.-..+.+.+- .-|.+=+|+---....-++..+|+.+.-.
T Consensus 103 ~~~~------i~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~v~~g~gi~~~p~~~~~~~~~~~~l~~~~~~ 175 (209)
T PF03466_consen 103 DYPL------ILLSPGSPYRDQLDRWLREHGFS-PNIVIEVDSFESILSLVASGDGIAILPDSLAQDELESGELVFLPLP 175 (209)
T ss_dssp TSEE------EEESTTTSHHHHHHHHHHHTTEE-EEEEEEESSHHHHHHHHHTTSEBEEEEHHHHHHHHHCTTEEEEEES
T ss_pred hccc------ccccccccccccccccccccccc-ccccccccchhhhccccccccceeecCcccccccccCCCEEEEECC
Confidence 4210 1111 23556777888888985 45544456665552 22333344444333455667788843311
Q ss_pred e-EEEEEEEEEeecchhhhhcCchhHHHHHHHHHHHHH
Q 018854 276 V-VLESQAVLVASRKSLIRRKGVLDATHEILERLEAHL 312 (349)
Q Consensus 276 ~-IleSsA~LIaN~~s~~~k~~~~~~i~~li~rl~~vl 312 (349)
. -+.-+-.|+.++..... ..++.+++.|+.++
T Consensus 176 ~~~~~~~~~l~~~~~~~~~-----~~~~~~~~~l~~~~ 208 (209)
T PF03466_consen 176 DPPLPRPIYLVWRKDRPLS-----PAIQWFIDLLREHF 208 (209)
T ss_dssp SSTEEEEEEEEEETTGTTH-----HHHHHHHHHHHHHH
T ss_pred CCCCceEEEEEEECCCCCC-----HHHHHHHHHHHHHh
Confidence 2 34477788887766432 35778888887764
No 20
>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=94.43 E-value=0.51 Score=39.68 Aligned_cols=128 Identities=20% Similarity=0.150 Sum_probs=81.3
Q ss_pred eEEEeecCCchhhhcccCceeeeeeccceecccCCCCccceeecCCCCcccEEEEEEEeCCCccCcccchHHhhcCCccC
Q 018854 127 LEVWFQRPKDIVRKLLSGDLDLGIVGLDTVSEFGQGNEDLIIVHDALDYGDCRLSLAIPKYGIFENINSLRELAQMPQWT 206 (349)
Q Consensus 127 vev~~vR~~DIP~yV~~G~aDlGIvG~DvL~E~~~~~~~lv~~l~dLgfG~CRLvvAvP~~~~~~dv~sl~dL~~~~~~~ 206 (349)
+++......+.-..+.+|.+|+++.+.....+... .+. .-..|....+++.++.+ ..+.+++||.+
T Consensus 40 ~~~~~~~~~~~~~~l~~g~~D~~~~~~~~~~~~~~----~~~--~~~~~~~~~~~~~~~~~---~~~~~~~dl~g----- 105 (218)
T cd00134 40 VKFVEVDWDGLITALKSGKVDLIAAGMTITPERAK----QVD--FSDPYYKSGQVILVKKG---SPIKSVKDLKG----- 105 (218)
T ss_pred EEEEeCCHHHHHHHHhcCCcCEEeecCcCCHHHHh----hcc--CcccceeccEEEEEECC---CCCCChHHhCC-----
Confidence 34444445778899999999999998733333221 111 12367777888999887 45568888874
Q ss_pred CCCCcEEEcCCCccHHHHHHhcCCceEEEEecCCccccc--cCCCcceeeeecccchhhHhh---CCcEEec
Q 018854 207 AEKPLRVATGFTYLGPKFMKDNGLKHVVFSTADGALEAA--PAMGIADAILDLVSSGTTLRE---NNLKEIE 273 (349)
Q Consensus 207 ~~~~lRVATkYPnlar~yf~~~Gi~~v~Ii~l~GSvElA--P~lGlAD~IVDIVsTGtTLra---NgLk~ie 273 (349)
+||+.-.......++.+..- ...++...+.-++. -.-|-+|+++--..+...+.+ .+|+++.
T Consensus 106 ----~~i~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~l~~g~~d~~~~~~~~~~~~~~~~~~~l~~~~ 172 (218)
T cd00134 106 ----KKVAVQKGSTAEKYLKKALP-EAKVVSYDDNAEALAALENGRADAVIVDEIALAALLKKHPPELKIVG 172 (218)
T ss_pred ----CEEEEEcCchHHHHHHHhCC-cccEEEeCCHHHHHHHHHcCCccEEEeccHHHHHHHHhcCCCcEEec
Confidence 46766544455666666542 24566655544433 356788988877777666554 4577775
No 21
>PRK11917 bifunctional adhesin/ABC transporter aspartate/glutamate-binding protein; Reviewed
Probab=94.18 E-value=0.8 Score=42.96 Aligned_cols=160 Identities=14% Similarity=0.037 Sum_probs=91.4
Q ss_pred eEEEeecCCchhhhcccCceeeeeeccceecccCCCCccceeecCCCCcccEEEEEEEeCCCccCcccchHHhhcCCccC
Q 018854 127 LEVWFQRPKDIVRKLLSGDLDLGIVGLDTVSEFGQGNEDLIIVHDALDYGDCRLSLAIPKYGIFENINSLRELAQMPQWT 206 (349)
Q Consensus 127 vev~~vR~~DIP~yV~~G~aDlGIvG~DvL~E~~~~~~~lv~~l~dLgfG~CRLvvAvP~~~~~~dv~sl~dL~~~~~~~ 206 (349)
+++..+.+.+....|..|.+|+.+.+..+=.|.... +. + --+|-....++.++.+ .++++++||.+
T Consensus 83 ~~~~~~~~~~~~~~l~~g~~D~~~~~~~~t~eR~~~----~~-f-s~py~~~~~~lvv~~~---~~~~s~~dL~g----- 148 (259)
T PRK11917 83 IKLVAVNAKTRGPLLDNGSVDAVIATFTITPERKRI----YN-F-SEPYYQDAIGLLVLKE---KNYKSLADMKG----- 148 (259)
T ss_pred EEEEEcChhhHHHHHHCCCccEEEecccCChhhhhe----ee-e-ccCceeeceEEEEECC---CCCCCHHHhCC-----
Confidence 455555556666789999999999887665554321 21 1 2356677888888887 45788999875
Q ss_pred CCCCcEEEcCC----CccHHHHHHhcCCceEEEEecCCcccc--ccCCCcceeeeecccchhhHhhCCcEEecCceEEEE
Q 018854 207 AEKPLRVATGF----TYLGPKFMKDNGLKHVVFSTADGALEA--APAMGIADAILDLVSSGTTLRENNLKEIEGGVVLES 280 (349)
Q Consensus 207 ~~~~lRVATkY----Pnlar~yf~~~Gi~~v~Ii~l~GSvEl--AP~lGlAD~IVDIVsTGtTLraNgLk~ie~g~IleS 280 (349)
+|||.-. -....+++++++++ +.++......++ +-.-|-+|+++---.+..++..+..+++. ..+-..
T Consensus 149 ----~~V~v~~gs~~~~~l~~~~~~~~~~-~~~~~~~~~~~~~~~l~~GrvDa~~~d~~~~~~~~~~~~~~~~-~~~~~~ 222 (259)
T PRK11917 149 ----ANIGVAQAATTKKAIGEAAKKIGID-VKFSEFPDYPSIKAALDAKRVDAFSVDKSILLGYVDDKSEILP-DSFEPQ 222 (259)
T ss_pred ----CeEEEecCCcHHHHHHHhhHhcCCc-eeEEecCCHHHHHHHHHcCCCcEEEecHHHHHHhhhcCCeecC-CcCCCC
Confidence 4665532 22234555566764 566665554433 34568888875433334455555566554 223223
Q ss_pred EEEEEeecchhhhhcCchhHHHHHHHHHHH
Q 018854 281 QAVLVASRKSLIRRKGVLDATHEILERLEA 310 (349)
Q Consensus 281 sA~LIaN~~s~~~k~~~~~~i~~li~rl~~ 310 (349)
...++..+.... ..+.++..++.+++
T Consensus 223 ~~~~a~~k~~~~----l~~~ln~~l~~~~~ 248 (259)
T PRK11917 223 SYGIVTKKDDPA----FAKYVDDFVKEHKN 248 (259)
T ss_pred ceEEEEeCCCHH----HHHHHHHHHHHHHH
Confidence 334444433211 12455555555543
No 22
>PRK11063 metQ DL-methionine transporter substrate-binding subunit; Provisional
Probab=93.82 E-value=0.2 Score=48.38 Aligned_cols=103 Identities=17% Similarity=0.148 Sum_probs=69.7
Q ss_pred ceEEEecCCCCchHHHHHHHHHCCCccCCCCC--CceEEec-CCCCCeEEEeecCCchhhhcccCceeeeeeccceeccc
Q 018854 83 EIRLGLPSKGRMAADTLDLLKDCQLSVKQVNP--RQYVAQI-PQLSNLEVWFQRPKDIVRKLLSGDLDLGIVGLDTVSEF 159 (349)
Q Consensus 83 ~LrIALP~KGRL~e~t~~LL~~aGi~~~~~~~--R~L~~~~-~~~p~vev~~vR~~DIP~yV~~G~aDlGIvG~DvL~E~ 159 (349)
==+||+|++..-....+.+|+++|+.--..+. ..-...+ .+..+++|+-+.+.++|+-+.+|.+|.+++..+|..+.
T Consensus 130 Gk~IAip~d~~n~~r~L~lL~~~Gli~l~~~~~~~~t~~di~~n~~~v~~v~~~~~~~~~al~~g~vDaa~i~~~~a~~a 209 (271)
T PRK11063 130 GSQVAVPNDPTNLGRSLLLLQKVGLIKLKDGVGLLPTVLDIVENPKNLKIVELEAPQLPRSLDDAQIALAVINTTYASQI 209 (271)
T ss_pred CCEEEecCCCccHHHHHHHHHHCCCEEecCCCCCCCCHHHHhcCCCCCEEEECcHHHHHHhcccccccEEEEChHHHHHc
Confidence 36799998899999999999999993332111 1001111 12236999999999999999999999999999999987
Q ss_pred CCCC-ccceeecCCCCcccEEEEEEEeCC
Q 018854 160 GQGN-EDLIIVHDALDYGDCRLSLAIPKY 187 (349)
Q Consensus 160 ~~~~-~~lv~~l~dLgfG~CRLvvAvP~~ 187 (349)
+.+. .+-+ ..++...-.|. ++++.++
T Consensus 210 ~~~~~~~~l-~~e~~~~~~~~-~~~v~~~ 236 (271)
T PRK11063 210 GLTPAKDGI-FVEDKDSPYVN-LIVARED 236 (271)
T ss_pred CCCCCCCee-EECCCCCCeEE-EEEECCc
Confidence 6543 2212 22344444554 4444443
No 23
>PF13379 NMT1_2: NMT1-like family; PDB: 2G29_A 3UN6_A 2I4C_A 2I49_A 2I4B_A 2I48_A 3QSL_A.
Probab=93.75 E-value=0.18 Score=46.76 Aligned_cols=205 Identities=24% Similarity=0.274 Sum_probs=114.3
Q ss_pred CCCceEEEecCCCCchHHH-----HHHHHHCCCccCCCCCCceEEecCCCCCeEE-EeecCCchhhhcccCceeeeeecc
Q 018854 80 ERDEIRLGLPSKGRMAADT-----LDLLKDCQLSVKQVNPRQYVAQIPQLSNLEV-WFQRPKDIVRKLLSGDLDLGIVGL 153 (349)
Q Consensus 80 ~~~~LrIALP~KGRL~e~t-----~~LL~~aGi~~~~~~~R~L~~~~~~~p~vev-~~vR~~DIP~yV~~G~aDlGIvG~ 153 (349)
+...||||.. .+--.-.. ..+|++.|+++ ++ .|.-..|+..-+..|.+|+|.+-.
T Consensus 4 ~~~~l~ig~~-~~~~~~p~~~a~~~g~f~~~G~~v------------------e~~~~~~g~~~~~al~~G~iD~a~~~~ 64 (252)
T PF13379_consen 4 EPTTLRIGYL-PGPDYAPLYVAQEKGLFEKEGLDV------------------EWVQFASGADILEALAAGEIDIAFVLA 64 (252)
T ss_dssp SESEEEEEET-SSGGGHHHHHHHHTTHHHHTTSCE------------------EEEEESSHHHHHHHHHCTSSSEEEECT
T ss_pred CCcEEEEEee-cchHHHHHHHHHHcChHHHcCCEE------------------EEEEcCCHHHHHHHHHcCCCCEEEech
Confidence 4457999987 44433332 12444444432 22 244568999999999999999922
Q ss_pred cee--cccCC-C-CccceeecCCCCcccEEEEEEEeCC-CccCcccchHHhhcCCccCCCCCcEEEcCCCc-----cHHH
Q 018854 154 DTV--SEFGQ-G-NEDLIIVHDALDYGDCRLSLAIPKY-GIFENINSLRELAQMPQWTAEKPLRVATGFTY-----LGPK 223 (349)
Q Consensus 154 DvL--~E~~~-~-~~~lv~~l~dLgfG~CRLvvAvP~~-~~~~dv~sl~dL~~~~~~~~~~~lRVATkYPn-----lar~ 223 (349)
..+ ...+. . ..+++ .+..+..+.- .+.+.++ ....++++++||....... ++++||+-.+. +.+.
T Consensus 65 ~~~~~~~~g~~~~~~~~~-~~~~~~~~g~--~lvv~~~~~~~~~~~~~~dl~~~~~~~--kGk~i~~~~~gs~~~~~l~~ 139 (252)
T PF13379_consen 65 PALIAIAKGAGGPDVDIV-VLAGLSQNGN--ALVVRNDLKDASDIKSLADLIKKRKAQ--KGKKIAVPFPGSTHDMLLRY 139 (252)
T ss_dssp HHHHHHHTTTTT----EE-EEEECSBSSE--EEEECGGGTTCSTTCCGHHHHHTCCSC--STEEEEESSTTSHHHHHHHH
T ss_pred HHHHHHHcCCCCcccceE-EeeccCCCce--EEEEcCccccCCCccCHHHHHhhhccc--CCcEEEEcCCCCHHHHHHHH
Confidence 222 22332 0 11333 3334554432 3333332 0115788899985421111 56899996653 4667
Q ss_pred HHHhcCCce---EEEEecCCccccc--cCCCcceeeeecccchhhHhhCCc--EEecCceEEE--EEEEEEeecchhhhh
Q 018854 224 FMKDNGLKH---VVFSTADGALEAA--PAMGIADAILDLVSSGTTLRENNL--KEIEGGVVLE--SQAVLVASRKSLIRR 294 (349)
Q Consensus 224 yf~~~Gi~~---v~Ii~l~GSvElA--P~lGlAD~IVDIVsTGtTLraNgL--k~ie~g~Ile--SsA~LIaN~~s~~~k 294 (349)
+|++.|++. ++++.+.. .++. -.-|-.|+++=.--..+.+.+.|. .+++.++++. ...++++++.....+
T Consensus 140 ~l~~~Gl~~~~dv~~~~~~~-~~~~~al~~g~iDa~~~~eP~~~~~~~~g~g~~v~~~~~~~~~~p~~~~~~~~~~~~~~ 218 (252)
T PF13379_consen 140 LLKKAGLDPKDDVTLVNVPP-PEMVAALRAGEIDAAVLWEPFASQAEAKGIGKIVADSGDVWGNHPCCVIVARRDFLEEN 218 (252)
T ss_dssp HHHHTT--TTTSSEEEE--G-HHHHHHHHTTS-SEEEEETTHHHHHHHTTS-EEEEEHHHCSTT-B-EEEEEEHHHHHH-
T ss_pred HHHhCCCCcccceEEEecCH-HHHHHHHhCCCcCEEEecCCHHHHHHhccCCeEEEEeccccCCCCeEEEEECHHHHHHC
Confidence 888889854 78887666 4433 445777888776677888888876 4443333422 345578888887776
Q ss_pred cCchhHHHHHHHHHHHHH
Q 018854 295 KGVLDATHEILERLEAHL 312 (349)
Q Consensus 295 ~~~~~~i~~li~rl~~vl 312 (349)
+ +.++.+++.+....
T Consensus 219 p---~~v~~~~~a~~~A~ 233 (252)
T PF13379_consen 219 P---EAVKAFLEALQEAQ 233 (252)
T ss_dssp H---HHHHHHHHHHHHHH
T ss_pred H---HHHHHHHHHHHHHH
Confidence 6 56667665555433
No 24
>COG0715 TauA ABC-type nitrate/sulfonate/bicarbonate transport systems, periplasmic components [Inorganic ion transport and metabolism]
Probab=93.08 E-value=0.42 Score=45.67 Aligned_cols=161 Identities=20% Similarity=0.183 Sum_probs=97.2
Q ss_pred cCCchhhhcccCceeee--eeccceecccCCCCccceeecCCCCccc-EEEEEEEeCCCccCcccchHHhhcCCccCCCC
Q 018854 133 RPKDIVRKLLSGDLDLG--IVGLDTVSEFGQGNEDLIIVHDALDYGD-CRLSLAIPKYGIFENINSLRELAQMPQWTAEK 209 (349)
Q Consensus 133 R~~DIP~yV~~G~aDlG--IvG~DvL~E~~~~~~~lv~~l~dLgfG~-CRLvvAvP~~~~~~dv~sl~dL~~~~~~~~~~ 209 (349)
...++...+..|.+|+| +.|.-...=.+.....+. .+.-+..+. .... .++.+ ..+.+++||++
T Consensus 70 ~~~~~~~~l~~G~~D~a~~~~~~~~~~~~~~~g~pv~-~va~~~~~~~~~~i-~~~~~---~~i~~~adlkG-------- 136 (335)
T COG0715 70 GGAPVLEALAAGALDFAVYYTGDTPLIAAGAAGAPVK-VVAALVQNGNGIAL-LVLKD---SGIKSVADLKG-------- 136 (335)
T ss_pred CChHHHHHHhcCCcCccccccCchHHHHhhccCCCeE-EeeecccCCceeEE-EeccC---CCcccccCCCC--------
Confidence 55788899999999999 444333222221112333 333466664 4444 44444 56777888764
Q ss_pred CcEEEcCCCc-----cHHHHHHhcCCc--eEEEEecCCccccc-cCCCcceeeeecccchhhHhhCCcE--EecCceEEE
Q 018854 210 PLRVATGFTY-----LGPKFMKDNGLK--HVVFSTADGALEAA-PAMGIADAILDLVSSGTTLRENNLK--EIEGGVVLE 279 (349)
Q Consensus 210 ~lRVATkYPn-----lar~yf~~~Gi~--~v~Ii~l~GSvElA-P~lGlAD~IVDIVsTGtTLraNgLk--~ie~g~Ile 279 (349)
+|||..++. +.+.++++.|++ .++++.+..+-..+ =.-|-.|+++-----...+...|.. +.++..+..
T Consensus 137 -k~vg~~~~~~~~~~~l~~~L~~~Gl~~~dv~~v~~~~~~~~~al~~g~vda~~~~ep~~~~~~~~~~~~~~~~~~~~~~ 215 (335)
T COG0715 137 -KKVGVPFGGSTSDFLLRYALAKAGLDPDDVELVNLPPADAVAALAAGQVDAFVVWEPWNAAAEGEGGGRVLLDGADLWG 215 (335)
T ss_pred -ceEEEeCCCchHHHHHHHHHHHcCCCcccceEEeeCcHHHHHHHhcCCcceEEecCCchhhhhccCCeEEEEcchhhhc
Confidence 789888775 467788888984 46777777763332 2367788766655555665555532 333334442
Q ss_pred --EEEEEEeecchhhhhcCchhHHHHHHHHHHH
Q 018854 280 --SQAVLVASRKSLIRRKGVLDATHEILERLEA 310 (349)
Q Consensus 280 --SsA~LIaN~~s~~~k~~~~~~i~~li~rl~~ 310 (349)
...++++++.....++ +.+..|+..+..
T Consensus 216 ~~~~~~~~~~~~~~~~~p---~~~~~~l~a~~~ 245 (335)
T COG0715 216 NHPELVLVVRKEFIEANP---EAVKAFLKALAK 245 (335)
T ss_pred cCchhhhhhHHHHHHHCH---HHHHHHHHHHHH
Confidence 4566667766665555 566777666554
No 25
>PF12974 Phosphonate-bd: ABC transporter, phosphonate, periplasmic substrate-binding protein ; PDB: 3N5L_B 3QUJ_C 3P7I_A 3QK6_A 3S4U_A.
Probab=91.94 E-value=0.59 Score=42.96 Aligned_cols=135 Identities=21% Similarity=0.173 Sum_probs=75.6
Q ss_pred eEEEeecC-CchhhhcccCceeeeeeccceecccCCC-CccceeecCC-CCcccEEEEEEEeCCCccCcccchHHhhcCC
Q 018854 127 LEVWFQRP-KDIVRKLLSGDLDLGIVGLDTVSEFGQG-NEDLIIVHDA-LDYGDCRLSLAIPKYGIFENINSLRELAQMP 203 (349)
Q Consensus 127 vev~~vR~-~DIP~yV~~G~aDlGIvG~DvL~E~~~~-~~~lv~~l~d-LgfG~CRLvvAvP~~~~~~dv~sl~dL~~~~ 203 (349)
+++...+. .+....+.+|.+|+++++-......... ....+..... =|--..+-++.++.+ .++++++||++
T Consensus 31 v~~~~~~~~~~~~~~l~~g~~D~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~~~~ivv~~d---s~i~~l~dL~G-- 105 (243)
T PF12974_consen 31 VELVPADDYAEFIEALRSGEIDLAFMGPLPYVQARQRAGVEPLATPVGPDGSPSYRSVIVVRAD---SPITSLADLKG-- 105 (243)
T ss_dssp EEEE--SSHHHHHHHHHTTS-SEEE--HHHHHHHHHHSSEEEEEEEEETTT-SCEEEEEEEETT---SS--SHHHHGG--
T ss_pred EEEEEcCCHHHHHHHHHcCCccEEEECcHHHHHHhhcCcEEEEEEecccCCCcceeEEEEEECC---CCCCChhhcCC--
Confidence 33433332 6667778999999999987765554311 1222211111 112266778889988 78999999986
Q ss_pred ccCCCCCcEEEcCCCc------cHHHHH-HhcCCc-----eEEEEecCCccccccCCCcceeeeecccchhhHhhCC---
Q 018854 204 QWTAEKPLRVATGFTY------LGPKFM-KDNGLK-----HVVFSTADGALEAAPAMGIADAILDLVSSGTTLRENN--- 268 (349)
Q Consensus 204 ~~~~~~~lRVATkYPn------lar~yf-~~~Gi~-----~v~Ii~l~GSvElAP~lGlAD~IVDIVsTGtTLraNg--- 268 (349)
+|||.-=|. +.+.+| ++.|++ ......-+.++=.+-.-|-+|+-+=-..+-..+.++|
T Consensus 106 -------k~v~~~~~~s~sg~l~~~~~L~~~~Gl~~~~~~~~~~~~~~~~~~~~l~~G~~Da~~~~~~~~~~~~~~~~~~ 178 (243)
T PF12974_consen 106 -------KRVAFPDPSSTSGYLIPRYELLREAGLDPGDDFKQVFVGSHDAVLEALLNGKADAAAIPSDAFERLEAEGPDI 178 (243)
T ss_dssp -------SEEEEE-TT-TTTTHHHHHHTCCCCT--HHHHSSEEEEE-HHHHHHHHHTTSSSEEEEEHHHHHHHHHH-HHH
T ss_pred -------CEEEEecCCccHHHHHHHHHHHHHcCCChhHceeEEEeCCHHHHHHHHHcCCccEEEEechhHHHHHHccCcc
Confidence 577754443 345557 688874 1223333343334566799998887777777887765
Q ss_pred ---cEEec
Q 018854 269 ---LKEIE 273 (349)
Q Consensus 269 ---Lk~ie 273 (349)
++++.
T Consensus 179 ~~~~rvl~ 186 (243)
T PF12974_consen 179 PSQLRVLW 186 (243)
T ss_dssp HTTEEEEE
T ss_pred cccEEEEE
Confidence 77665
No 26
>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=90.69 E-value=1.1 Score=43.09 Aligned_cols=78 Identities=17% Similarity=0.209 Sum_probs=59.6
Q ss_pred ceEEEecCCCCchHHHHHHHHHCCCc-cCCCCC----CceEEecCCCCCeEEEeecCCchhhhcccCceeeeeeccceec
Q 018854 83 EIRLGLPSKGRMAADTLDLLKDCQLS-VKQVNP----RQYVAQIPQLSNLEVWFQRPKDIVRKLLSGDLDLGIVGLDTVS 157 (349)
Q Consensus 83 ~LrIALP~KGRL~e~t~~LL~~aGi~-~~~~~~----R~L~~~~~~~p~vev~~vR~~DIP~yV~~G~aDlGIvG~DvL~ 157 (349)
--+||+|+..--....+.+|+++|+. +....+ =+.+.. +..+++++-+.+.++|.-+.+|.+|++++...++.
T Consensus 117 G~~IAip~d~~n~~raL~~L~~aGLi~l~~~~~~~~t~~DI~~--n~~~v~~vel~~~~~~~al~~g~vDaa~v~~~~~~ 194 (258)
T TIGR00363 117 GAKVAVPNDPTNLGRALLLLQKQGLIKLKDGNGLLPTVLDIVE--NPKKLNITELETSQLPRALDDPKVDLAVINTTYAG 194 (258)
T ss_pred CCEEEEeCCcchHHHHHHHHHHcCCceecCCCCCcCChhhhhc--CCCCCEEEEcCHHHHHHHhhcccccEEEEChHHHH
Confidence 46899996666778888899999995 332111 011222 23469999999999999999999999999999999
Q ss_pred ccCCC
Q 018854 158 EFGQG 162 (349)
Q Consensus 158 E~~~~ 162 (349)
..+.+
T Consensus 195 ~agl~ 199 (258)
T TIGR00363 195 QVGLN 199 (258)
T ss_pred HcCCC
Confidence 88754
No 27
>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=90.45 E-value=4.4 Score=35.00 Aligned_cols=149 Identities=19% Similarity=0.154 Sum_probs=87.0
Q ss_pred eEEEeecCCchhhhcccCceeeeeeccceecccCCCCccceeecCCCCcccEEEEEEEeCCC--ccCcccchHHhhcCCc
Q 018854 127 LEVWFQRPKDIVRKLLSGDLDLGIVGLDTVSEFGQGNEDLIIVHDALDYGDCRLSLAIPKYG--IFENINSLRELAQMPQ 204 (349)
Q Consensus 127 vev~~vR~~DIP~yV~~G~aDlGIvG~DvL~E~~~~~~~lv~~l~dLgfG~CRLvvAvP~~~--~~~dv~sl~dL~~~~~ 204 (349)
+++..+.-.++-..+..|.+|+++.+.-+-.|.... +.. --.+..-..++.++.+. ....+++++||.+
T Consensus 40 ~~~~~~~~~~~~~~l~~g~~D~~~~~~~~~~~r~~~----~~~--s~p~~~~~~~~~~~~~~~~~~~~~~~~~dl~~--- 110 (225)
T PF00497_consen 40 IEFVPMPWSRLLEMLENGKADIIIGGLSITPERAKK----FDF--SDPYYSSPYVLVVRKGDAPPIKTIKSLDDLKG--- 110 (225)
T ss_dssp EEEEEEEGGGHHHHHHTTSSSEEESSEB-BHHHHTT----EEE--ESESEEEEEEEEEETTSTCSTSSHSSGGGGTT---
T ss_pred cceeeccccccccccccccccccccccccccccccc----ccc--cccccchhheeeeccccccccccccchhhhcC---
Confidence 344445667888899999999999776555554321 211 23566678888888541 2345666777753
Q ss_pred cCCCCCcEEEcCCCccHHHHHHhcCCceEEEEecCCcccc--ccCCCcceeeeecc-cchhhHhhCCcEEecC--ceEEE
Q 018854 205 WTAEKPLRVATGFTYLGPKFMKDNGLKHVVFSTADGALEA--APAMGIADAILDLV-SSGTTLRENNLKEIEG--GVVLE 279 (349)
Q Consensus 205 ~~~~~~lRVATkYPnlar~yf~~~Gi~~v~Ii~l~GSvEl--AP~lGlAD~IVDIV-sTGtTLraNgLk~ie~--g~Ile 279 (349)
+||++--=....++|++..-...+++.....-|+ +-.-|-+|+++.-. .--..++.+++....- .....
T Consensus 111 ------~~i~~~~g~~~~~~l~~~~~~~~~~~~~~~~~~~~~~l~~g~~d~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~ 184 (225)
T PF00497_consen 111 ------KRIGVVRGSSYADYLKQQYPSNINIVEVDSPEEALEALLSGRIDAFIVDESTAEYLLKRHPLENIVVIPPPISP 184 (225)
T ss_dssp ------SEEEEETTSHHHHHHHHHTHHTSEEEEESSHHHHHHHHHTTSSSEEEEEHHHHHHHHHHTTTCEEEEEEEEEEE
T ss_pred ------cccccccchhHHHHhhhhccchhhhcccccHHHHHHHHhcCCeeeeeccchhhhhhhhhccccccccccccccc
Confidence 5777666566777777642102345543333332 25678889876544 4445666666665541 12445
Q ss_pred EEEEEEeecch
Q 018854 280 SQAVLVASRKS 290 (349)
Q Consensus 280 SsA~LIaN~~s 290 (349)
....+..++..
T Consensus 185 ~~~~~~~~~~~ 195 (225)
T PF00497_consen 185 SPVYFAVRKKN 195 (225)
T ss_dssp EEEEEEEETTT
T ss_pred ceeEEeecccc
Confidence 55556666543
No 28
>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=87.57 E-value=3.6 Score=34.31 Aligned_cols=92 Identities=18% Similarity=0.164 Sum_probs=54.7
Q ss_pred CCCeEEEee--cCCchhhhcccCceeeeeeccceecccCCCCccceeecCCCCcccEEEEEEEeCCCccC-cccchHHhh
Q 018854 124 LSNLEVWFQ--RPKDIVRKLLSGDLDLGIVGLDTVSEFGQGNEDLIIVHDALDYGDCRLSLAIPKYGIFE-NINSLRELA 200 (349)
Q Consensus 124 ~p~vev~~v--R~~DIP~yV~~G~aDlGIvG~DvL~E~~~~~~~lv~~l~dLgfG~CRLvvAvP~~~~~~-dv~sl~dL~ 200 (349)
.|++++.+. ...++...+.+|.+|+||+....- . .++. ...+++.++++++|.+.... ..-+++||.
T Consensus 26 ~P~i~l~~~~~~~~~~~~~l~~g~~D~~i~~~~~~---~---~~~~----~~~l~~~~~~~v~~~~~~~~~~~~~~~~L~ 95 (200)
T cd08417 26 APGVRLRFVPLDRDDLEEALESGEIDLAIGVFPEL---P---PGLR----SQPLFEDRFVCVARKDHPLAGGPLTLEDYL 95 (200)
T ss_pred CCCeEEEeccCCHHHHHHHHHcCCCCEEEeecccC---C---Cccc----hhhhhcCceEEEecCCCcccccccCHHHHh
Confidence 355655554 345689999999999999854321 1 1221 23467788898888764221 223567776
Q ss_pred cCCccCCCCCcEEE--cCCCccHHHHHHhcCCc
Q 018854 201 QMPQWTAEKPLRVA--TGFTYLGPKFMKDNGLK 231 (349)
Q Consensus 201 ~~~~~~~~~~lRVA--TkYPnlar~yf~~~Gi~ 231 (349)
+.+. .... +.+.+...+||.+.|+.
T Consensus 96 ~~~~------i~~~~~~~~~~~~~~~~~~~~~~ 122 (200)
T cd08417 96 AAPH------VLVSPRGRGHGLVDDALAELGLS 122 (200)
T ss_pred CCCe------EEeccccchHHHHHHHHHHcCcc
Confidence 5311 1111 23445667888888874
No 29
>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=86.64 E-value=4.7 Score=33.53 Aligned_cols=165 Identities=15% Similarity=0.128 Sum_probs=79.2
Q ss_pred CCeEEEee--cCCchhhhcccCceeeeeeccceecccCCCCccceeecCCCCcccEEEEEEEeCCCccCcccchHHhhcC
Q 018854 125 SNLEVWFQ--RPKDIVRKLLSGDLDLGIVGLDTVSEFGQGNEDLIIVHDALDYGDCRLSLAIPKYGIFENINSLRELAQM 202 (349)
Q Consensus 125 p~vev~~v--R~~DIP~yV~~G~aDlGIvG~DvL~E~~~~~~~lv~~l~dLgfG~CRLvvAvP~~~~~~dv~sl~dL~~~ 202 (349)
|++++.+. ...|+-..+.+|.+|+||+....-. .. .++. ...+++.+++++++.+.....-.+++||...
T Consensus 27 P~i~l~i~~~~~~~~~~~l~~g~~Dl~i~~~~~~~-~~---~~~~----~~~l~~~~~~~v~~~~~~~~~~~~~~~l~~~ 98 (201)
T cd08418 27 PDVQISIYEGQLSSLLPELRDGRLDFAIGTLPDEM-YL---KELI----SEPLFESDFVVVARKDHPLQGARSLEELLDA 98 (201)
T ss_pred CCceEEEEeCcHHHHHHHHHcCCCcEEEEecCCCC-CC---ccee----EEeecCCceEEEeCCCCccccCCCHHHHcCC
Confidence 44444444 4568999999999999997532111 00 1222 1334667788888776433223467777642
Q ss_pred CccCCCCCcEEE--cCCCccHHHHHHhcCCceEEEEecCCccccc---cCCCcceeeeecccchhhHhhCCcEEecC-ce
Q 018854 203 PQWTAEKPLRVA--TGFTYLGPKFMKDNGLKHVVFSTADGALEAA---PAMGIADAILDLVSSGTTLRENNLKEIEG-GV 276 (349)
Q Consensus 203 ~~~~~~~~lRVA--TkYPnlar~yf~~~Gi~~v~Ii~l~GSvElA---P~lGlAD~IVDIVsTGtTLraNgLk~ie~-g~ 276 (349)
+. +... +.+.....++|.+.|+. .++..-..+.+.. ..-|..=+|+--...-..++.++|+++.- ..
T Consensus 99 ~~------i~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~v~~g~gi~~~p~~~~~~~~~~~~l~~~~~~~~ 171 (201)
T cd08418 99 SW------VLPGTRMGYYNNLLEALRRLGYN-PRVAVRTDSIVSIINLVEKADFLTILSRDMGRGPLDSFRLITIPVEEP 171 (201)
T ss_pred CC------EecCCCCCHHHHHHHHHHHcCCC-CCceEEecCHHHHHHHHHhCCEEEEeEHHHhhhhhhcCCEEEecCCCC
Confidence 11 1110 12223456688888864 2332222333332 11122112222111112345567887641 12
Q ss_pred EEEEEEEEEeecchhhhhcCchhHHHHHHHHHH
Q 018854 277 VLESQAVLVASRKSLIRRKGVLDATHEILERLE 309 (349)
Q Consensus 277 IleSsA~LIaN~~s~~~k~~~~~~i~~li~rl~ 309 (349)
.....-.++.++..... ..++.+++.++
T Consensus 172 ~~~~~~~l~~~~~~~~~-----~~~~~~~~~l~ 199 (201)
T cd08418 172 LPSADYYLIYRKKSRLT-----PLAEQLVELFR 199 (201)
T ss_pred CCCCceEEEEecCCCCC-----HHHHHHHHHHH
Confidence 23345556665543221 24555655554
No 30
>TIGR01096 3A0103s03R lysine-arginine-ornithine-binding periplasmic protein.
Probab=86.56 E-value=8.2 Score=34.82 Aligned_cols=123 Identities=15% Similarity=0.031 Sum_probs=67.7
Q ss_pred EEEeecCCchhhhcccCceeeeeeccceecccCCCCccceeecCCCCcccEEEEEEEeCCCccCcccchHHhhcCCccCC
Q 018854 128 EVWFQRPKDIVRKLLSGDLDLGIVGLDTVSEFGQGNEDLIIVHDALDYGDCRLSLAIPKYGIFENINSLRELAQMPQWTA 207 (349)
Q Consensus 128 ev~~vR~~DIP~yV~~G~aDlGIvG~DvL~E~~~~~~~lv~~l~dLgfG~CRLvvAvP~~~~~~dv~sl~dL~~~~~~~~ 207 (349)
++......+.-..+..|.+|+++.+..+-.|.... +. ---+|..-...+.++.+.. ...+++||.+
T Consensus 66 ~~~~~~~~~~~~~l~~G~~D~~~~~~~~~~~r~~~----~~--~s~p~~~~~~~~~~~~~~~--~~~~~~dl~g------ 131 (250)
T TIGR01096 66 KFVEQNFDGLIPSLKAKKVDAIMATMSITPKRQKQ----ID--FSDPYYATGQGFVVKKGSD--LAKTLEDLDG------ 131 (250)
T ss_pred EEEeCCHHHHHHHHhCCCcCEEEecCccCHHHhhc----cc--cccchhcCCeEEEEECCCC--cCCChHHcCC------
Confidence 33334446777889999999998765444443211 11 1235566667777777632 2356777663
Q ss_pred CCCcEEEcCCCccHHHHHHhcCCceEEEEecCCcccc--ccCCCcceeeeecccchhh-HhhC
Q 018854 208 EKPLRVATGFTYLGPKFMKDNGLKHVVFSTADGALEA--APAMGIADAILDLVSSGTT-LREN 267 (349)
Q Consensus 208 ~~~lRVATkYPnlar~yf~~~Gi~~v~Ii~l~GSvEl--AP~lGlAD~IVDIVsTGtT-LraN 267 (349)
+||++---.....|+.+..-..++++...+.-|+ +-.-|-+|+++.-...... ++++
T Consensus 132 ---~~i~~~~g~~~~~~l~~~~~~~~~~~~~~s~~~~~~~L~~g~vD~~v~~~~~~~~~~~~~ 191 (250)
T TIGR01096 132 ---KTVGVQSGTTHEQYLKDYFKPGVDIVEYDSYDNANMDLKAGRIDAVFTDASVLAEGFLKP 191 (250)
T ss_pred ---CEEEEecCchHHHHHHHhccCCcEEEEcCCHHHHHHHHHcCCCCEEEeCHHHHHHHHHhC
Confidence 5777543333344554431102455555444443 2456889987775555443 3443
No 31
>PRK09861 cytoplasmic membrane lipoprotein-28; Provisional
Probab=86.23 E-value=3.6 Score=39.81 Aligned_cols=78 Identities=15% Similarity=0.215 Sum_probs=59.7
Q ss_pred ceEEEecCCCCchHHHHHHHHHCCC-ccCCCCC----CceEEecCCCCCeEEEeecCCchhhhcccCceeeeeeccceec
Q 018854 83 EIRLGLPSKGRMAADTLDLLKDCQL-SVKQVNP----RQYVAQIPQLSNLEVWFQRPKDIVRKLLSGDLDLGIVGLDTVS 157 (349)
Q Consensus 83 ~LrIALP~KGRL~e~t~~LL~~aGi-~~~~~~~----R~L~~~~~~~p~vev~~vR~~DIP~yV~~G~aDlGIvG~DvL~ 157 (349)
--+||+|++-.=....+.||+.+|+ +++.... -+-+.. |-.+++|..+-+.++|+-+.+|.+|+.++..+...
T Consensus 131 Ga~IAipnd~~n~~ral~lL~~agli~l~~~~g~~~t~~di~~--np~~l~~ve~~~~q~~~al~dg~vD~a~i~~~~~~ 208 (272)
T PRK09861 131 GATVAIPNDPTNLGRALLLLQKEKLITLKEGKGLLPTALDITD--NPRHLQIMELEGAQLPRVLDDPKVDVAIISTTYIQ 208 (272)
T ss_pred CCEEEEeCCCccHHHHHHHHHHCCCEEEcCCCCCCCCHhHHhc--CCCCCEEEEcCHHHhHhhccCcccCEEEEchhHHH
Confidence 4689999766777889999999995 3332111 111222 22469999999999999999999999999999999
Q ss_pred ccCCC
Q 018854 158 EFGQG 162 (349)
Q Consensus 158 E~~~~ 162 (349)
+.+.+
T Consensus 209 ~ag~~ 213 (272)
T PRK09861 209 QTGLS 213 (272)
T ss_pred HcCCC
Confidence 98765
No 32
>PRK12682 transcriptional regulator CysB-like protein; Reviewed
Probab=85.73 E-value=10 Score=35.89 Aligned_cols=164 Identities=18% Similarity=0.273 Sum_probs=84.5
Q ss_pred CCeEEEe--ecCCchhhhcccCceeeeeeccceecccCCCCccceeecCCCCcccEEEEEEEeCCCccC--cccchHHhh
Q 018854 125 SNLEVWF--QRPKDIVRKLLSGDLDLGIVGLDTVSEFGQGNEDLIIVHDALDYGDCRLSLAIPKYGIFE--NINSLRELA 200 (349)
Q Consensus 125 p~vev~~--vR~~DIP~yV~~G~aDlGIvG~DvL~E~~~~~~~lv~~l~dLgfG~CRLvvAvP~~~~~~--dv~sl~dL~ 200 (349)
|++++.+ ....++...+..|.+|+||+..+.... .++. ...++..++++++|.+.... ..-+++||.
T Consensus 120 P~i~i~i~~~~~~~~~~~l~~g~~D~~i~~~~~~~~-----~~l~----~~~l~~~~~~~~~~~~~pl~~~~~~~~~~L~ 190 (309)
T PRK12682 120 PKVNLSLHQGSPDEIARMVISGEADIGIATESLADD-----PDLA----TLPCYDWQHAVIVPPDHPLAQEERITLEDLA 190 (309)
T ss_pred CCeEEEEecCCHHHHHHHHHcCCccEEEecCcccCC-----Ccce----EEEeeeeeEEEEecCCCccccCCCcCHHHHh
Confidence 5555444 345688899999999999986543211 1221 34578899999998874221 223567776
Q ss_pred cCCccCCCCCcEEEcCCC--ccHHHHHHhcCCceEEEEecCCccccccC---CCcceeeeecccchhhHhhCCcEEecC-
Q 018854 201 QMPQWTAEKPLRVATGFT--YLGPKFMKDNGLKHVVFSTADGALEAAPA---MGIADAILDLVSSGTTLRENNLKEIEG- 274 (349)
Q Consensus 201 ~~~~~~~~~~lRVATkYP--nlar~yf~~~Gi~~v~Ii~l~GSvElAP~---lGlAD~IVDIVsTGtTLraNgLk~ie~- 274 (349)
..+. +.....++ +....+|.+.|+. .++..-..+.+..-. -|..=+|+.-. .-..++.++|+.+.-
T Consensus 191 ~~~~------i~~~~~~~~~~~~~~~~~~~g~~-~~~~~~~~~~~~~~~~v~~g~Gi~~lp~~-~~~~~~~~~l~~~~~~ 262 (309)
T PRK12682 191 EYPL------ITYHPGFTGRSRIDRAFAAAGLQ-PDIVLEAIDSDVIKTYVRLGLGVGIVAEM-AYRPDRDGDLVALPAG 262 (309)
T ss_pred cCCc------eeeCCCccHHHHHHHHHHHcCCC-CcEEEEeCCHHHHHHHHHhCCceEEehhh-hhhhccCCcEEEeeCC
Confidence 4211 11112232 2345678888875 343322233333211 12211333321 112255677887541
Q ss_pred ceEEEEEEEEEeecchhhhhcCchhHHHHHHHHHHH
Q 018854 275 GVVLESQAVLVASRKSLIRRKGVLDATHEILERLEA 310 (349)
Q Consensus 275 g~IleSsA~LIaN~~s~~~k~~~~~~i~~li~rl~~ 310 (349)
+....-.-.++.++..... ..+..+++.|+.
T Consensus 263 ~~~~~~~~~l~~~~~~~~~-----~~~~~f~~~l~~ 293 (309)
T PRK12682 263 HLFGPNTAWVALKRGAYLR-----NYVYKFIELCAP 293 (309)
T ss_pred CCCcceeEEEeeecCCcCC-----HHHHHHHHHHHH
Confidence 1222345567766665433 245556655554
No 33
>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=83.76 E-value=14 Score=30.31 Aligned_cols=90 Identities=17% Similarity=0.187 Sum_probs=50.6
Q ss_pred CCeEEEee--cCCchhhhcccCceeeeeeccceecccCCCCccceeecCCCCcccEEEEEEEeCCCccC--cccchHHhh
Q 018854 125 SNLEVWFQ--RPKDIVRKLLSGDLDLGIVGLDTVSEFGQGNEDLIIVHDALDYGDCRLSLAIPKYGIFE--NINSLRELA 200 (349)
Q Consensus 125 p~vev~~v--R~~DIP~yV~~G~aDlGIvG~DvL~E~~~~~~~lv~~l~dLgfG~CRLvvAvP~~~~~~--dv~sl~dL~ 200 (349)
|++++.+. ...++-..+.+|.+|+||+.... +.. .++. -..++..+++++++.+.... +.-+++||.
T Consensus 27 P~v~i~i~~~~~~~~~~~l~~~~~Dl~i~~~~~--~~~---~~~~----~~~l~~~~~~~~~~~~~~l~~~~~~~~~~L~ 97 (194)
T cd08436 27 PGVDIRLRQAGSDDLLAAVREGRLDLAFVGLPE--RRP---PGLA----SRELAREPLVAVVAPDHPLAGRRRVALADLA 97 (194)
T ss_pred CCcEEEEecCCHHHHHHHHHcCCccEEEEecCC--CCC---CCcE----EEEeecceEEEEecCCCcccCCCccCHHHHh
Confidence 45555444 45778889999999999986432 111 1222 12346667787777764222 223667776
Q ss_pred cCCccCCCCCcEEEcCCC----ccHHHHHHhcCCc
Q 018854 201 QMPQWTAEKPLRVATGFT----YLGPKFMKDNGLK 231 (349)
Q Consensus 201 ~~~~~~~~~~lRVATkYP----nlar~yf~~~Gi~ 231 (349)
+. .-|..+.. ....+++++.|+.
T Consensus 98 ~~--------~~i~~~~~~~~~~~~~~~~~~~~~~ 124 (194)
T cd08436 98 DE--------PFVDFPPGTGARRQVDRAFAAAGVR 124 (194)
T ss_pred CC--------CeEEecCcccHHHHHHHHHHHcCCC
Confidence 42 12222222 3445677777764
No 34
>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=83.30 E-value=2 Score=40.47 Aligned_cols=110 Identities=25% Similarity=0.198 Sum_probs=61.9
Q ss_pred CchhhhcccCceeeeeeccceeccc--CC-------CCccceeecCCCCcccEEEEEEEeCCCccCcccchHHhhcCCcc
Q 018854 135 KDIVRKLLSGDLDLGIVGLDTVSEF--GQ-------GNEDLIIVHDALDYGDCRLSLAIPKYGIFENINSLRELAQMPQW 205 (349)
Q Consensus 135 ~DIP~yV~~G~aDlGIvG~DvL~E~--~~-------~~~~lv~~l~dLgfG~CRLvvAvP~~~~~~dv~sl~dL~~~~~~ 205 (349)
.+....|..|.+|+|+++.+..... +. ...++ ..+. .+-.-.++++++.+ .++++++||.+.
T Consensus 72 ~~~~~~l~~G~~D~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~v~--~~~~~~~~lvv~~d---~~i~sl~dL~gk--- 142 (320)
T TIGR02122 72 VENVNLLEAGEADLAIVQSDVAYYAYEGDGEFEFEGPVEKL-RALA--SLYPEYIQIVVRKD---SGIKTVADLKGK--- 142 (320)
T ss_pred HHHHHHHhCCCCcEEEEcchhHHHHhcCcCccccCCCCccH-HhHH--HhccccEEEEEECC---CCCCcHHHcCCC---
Confidence 4788899999999999997764321 10 00111 1011 11222356888887 567889998742
Q ss_pred CCCCCcEEEc---CCCccHHHHHHhcCCce--EEEEecCCccccc--cCCCcceeeeec
Q 018854 206 TAEKPLRVAT---GFTYLGPKFMKDNGLKH--VVFSTADGALEAA--PAMGIADAILDL 257 (349)
Q Consensus 206 ~~~~~lRVAT---kYPnlar~yf~~~Gi~~--v~Ii~l~GSvElA--P~lGlAD~IVDI 257 (349)
++.+.+ .+-.+.++++++.|++. +..+.-.|.-|+. -.-|-+|+++.-
T Consensus 143 ----~v~~~~~~s~~~~~~~~~l~~~G~~~~~~~~v~~~~~~~~~~al~~G~vDa~~~~ 197 (320)
T TIGR02122 143 ----RVAVGAPGSGTELNARAVLKAAGLTYDDVKKVEYLGYAEAADALKDGKIDAAFYT 197 (320)
T ss_pred ----EEecCCCCcchHHHHHHHHHHcCCCHHHccchhcCCHHHHHHHHHCCCccEEEEe
Confidence 222221 12235578899888741 2223334444543 234778887765
No 35
>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=83.00 E-value=17 Score=30.19 Aligned_cols=102 Identities=18% Similarity=0.215 Sum_probs=55.9
Q ss_pred CCeEEEee--cCCchhhhcccCceeeeeeccceecccCCCCccceeecCCCCcccEEEEEEEeCCCccC--cccchHHhh
Q 018854 125 SNLEVWFQ--RPKDIVRKLLSGDLDLGIVGLDTVSEFGQGNEDLIIVHDALDYGDCRLSLAIPKYGIFE--NINSLRELA 200 (349)
Q Consensus 125 p~vev~~v--R~~DIP~yV~~G~aDlGIvG~DvL~E~~~~~~~lv~~l~dLgfG~CRLvvAvP~~~~~~--dv~sl~dL~ 200 (349)
|++++.+. ...|+-..+.+|.+|+||+..... . .++.. -.++..+++++++++.... +.-+++||.
T Consensus 27 P~i~i~~~~~~~~~~~~~l~~~~~D~~i~~~~~~---~---~~~~~----~~l~~~~~~~v~~~~~pl~~~~~~~~~~l~ 96 (198)
T cd08421 27 PDVRIDLEERLSADIVRAVAEGRADLGIVAGNVD---A---AGLET----RPYRTDRLVVVVPRDHPLAGRASVAFADTL 96 (198)
T ss_pred CCceEEEEecCcHHHHHHHhcCCceEEEEecCCC---C---CCcEE----EEeecCcEEEEeCCCCCccccCCCCHHHhc
Confidence 45555443 568889999999999999854421 1 12221 2345677888887763221 223567766
Q ss_pred cCCccCCCCCcEEEcC----CCccHHHHHHhcCCceEEEEecCCccccc
Q 018854 201 QMPQWTAEKPLRVATG----FTYLGPKFMKDNGLKHVVFSTADGALEAA 245 (349)
Q Consensus 201 ~~~~~~~~~~lRVATk----YPnlar~yf~~~Gi~~v~Ii~l~GSvElA 245 (349)
..+ -|... +.+...++|.+.|++ ..+..-..+.+++
T Consensus 97 ~~~--------~i~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~ 136 (198)
T cd08421 97 DHD--------FVGLPAGSALHTFLREAAARLGRR-LRLRVQVSSFDAV 136 (198)
T ss_pred CCc--------eEeecCCcchHHHHHHHHHHcCCC-ceEEEEECCHHHH
Confidence 421 12211 223445677777875 3443323444443
No 36
>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=82.34 E-value=14 Score=30.64 Aligned_cols=163 Identities=13% Similarity=0.020 Sum_probs=79.2
Q ss_pred CCeEEEee--cCCchhhhcccCceeeeeeccceecccCCCCccceeecCCCCcccEEEEEEEeCCCcc-CcccchHHhhc
Q 018854 125 SNLEVWFQ--RPKDIVRKLLSGDLDLGIVGLDTVSEFGQGNEDLIIVHDALDYGDCRLSLAIPKYGIF-ENINSLRELAQ 201 (349)
Q Consensus 125 p~vev~~v--R~~DIP~yV~~G~aDlGIvG~DvL~E~~~~~~~lv~~l~dLgfG~CRLvvAvP~~~~~-~dv~sl~dL~~ 201 (349)
|++++-+. ...++-..+.+|.+|+||+..+.. . .++. ...++.-+++++++.+... ...-+++||.+
T Consensus 27 P~v~l~i~~~~~~~~~~~l~~g~~D~~i~~~~~~-~-----~~~~----~~~l~~~~~~~v~~~~~~~~~~~~~~~~l~~ 96 (200)
T cd08464 27 PGVRLVFRQVDPFNVGDMLDRGEIDLAIGVFGEL-P-----AWLK----REVLYTEGYACLFDPQQLSLSAPLTLEDYVA 96 (200)
T ss_pred CCcEEEEecCCcccHHHHHhcCcccEEEecCCCC-c-----ccce----eeeecccceEEEEeCCCccccCCCCHHHHhc
Confidence 45554444 456788899999999999865421 1 1221 2344566677777665311 11235677664
Q ss_pred CCccCCCCCcEE--EcCCCccHHHHHHhcCCceEEEEecCCcccccc---CCCcceeeeecccchhhHhhCCcEEecC-c
Q 018854 202 MPQWTAEKPLRV--ATGFTYLGPKFMKDNGLKHVVFSTADGALEAAP---AMGIADAILDLVSSGTTLRENNLKEIEG-G 275 (349)
Q Consensus 202 ~~~~~~~~~lRV--ATkYPnlar~yf~~~Gi~~v~Ii~l~GSvElAP---~lGlAD~IVDIVsTGtTLraNgLk~ie~-g 275 (349)
.+. ... .+.+.+..+++|.+.|+. .++..-..+.+..- .-|..=+|+.-.-.-..++..+|+.+.- .
T Consensus 97 ~~~------i~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~v~~g~gi~~~p~~~~~~~~~~~~l~~~~~~~ 169 (200)
T cd08464 97 RPH------VLVSYRGGLRGFVDDALAELGRS-RRVVASTPHFAALPALLRGTPLIATVPARLARAWAAALGLRASPPPL 169 (200)
T ss_pred CCc------EEecCCCCCcchHHHHHHHcCCC-cceEEEcCchhhHHHHHcCCCceeecHHHHHHHhhhcCCceeecCCC
Confidence 211 111 123445677889988875 33332233333331 1122112222111112234456876531 0
Q ss_pred eEEEEEEEEEeecchhhhhcCchhHHHHHHHHHH
Q 018854 276 VVLESQAVLVASRKSLIRRKGVLDATHEILERLE 309 (349)
Q Consensus 276 ~IleSsA~LIaN~~s~~~k~~~~~~i~~li~rl~ 309 (349)
......-.++.++..... ..++.+++.|+
T Consensus 170 ~~~~~~~~l~~~~~~~~~-----~~~~~l~~~~~ 198 (200)
T cd08464 170 DLPEFPISLLWHARTDND-----PALVWLREQIV 198 (200)
T ss_pred CCCCceEEEEEcccccCC-----chHHHHHHHHh
Confidence 122344556665544322 24566666554
No 37
>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=82.33 E-value=6.6 Score=35.75 Aligned_cols=123 Identities=16% Similarity=0.114 Sum_probs=73.1
Q ss_pred CCchhhhcccCceeeeeeccceeccc--CCCCccceee-cCCCCcccEEEEEEEeCCCccCcccchHHhhcCCccCCCCC
Q 018854 134 PKDIVRKLLSGDLDLGIVGLDTVSEF--GQGNEDLIIV-HDALDYGDCRLSLAIPKYGIFENINSLRELAQMPQWTAEKP 210 (349)
Q Consensus 134 ~~DIP~yV~~G~aDlGIvG~DvL~E~--~~~~~~lv~~-l~dLgfG~CRLvvAvP~~~~~~dv~sl~dL~~~~~~~~~~~ 210 (349)
..++-..+..|.+|+++.|.....+. +.+...+... ...-|+-....++.++.+ ..+++++||.+
T Consensus 74 ~~~~~~~l~~g~~Di~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lvv~~d---~~i~~~~dL~g--------- 141 (254)
T TIGR01098 74 YSAVIEAMRFGRVDIAWFGPSSYVLAHYRANAEVFALTAVSTDGSPGYYSVIIVKAD---SPIKSLKDLKG--------- 141 (254)
T ss_pred HHHHHHHHHcCCccEEEECcHHHHHHHHhcCCceEEeeccccCCCCceEEEEEEECC---CCCCChHHhcC---------
Confidence 35677889999999999998776643 1111111110 001121234567888887 56888999874
Q ss_pred cEEEcCCC------ccHHHHHHhc-CCc----eEEEEecCCccc--cccCCCcceeeeecccchhhHhhCC
Q 018854 211 LRVATGFT------YLGPKFMKDN-GLK----HVVFSTADGALE--AAPAMGIADAILDLVSSGTTLRENN 268 (349)
Q Consensus 211 lRVATkYP------nlar~yf~~~-Gi~----~v~Ii~l~GSvE--lAP~lGlAD~IVDIVsTGtTLraNg 268 (349)
+||+.--| .+..+++.+. |++ .+.++...+..+ .+-.-|-+|+.+---.+-..+.++|
T Consensus 142 k~I~~~~~~s~~~~~~~~~~l~~~~~~~~~~~~~~i~~~~~~~~~~~al~~G~~Da~~~~~~~~~~~~~~~ 212 (254)
T TIGR01098 142 KTFAFGDPASTSGYLVPRYQLKKEGGLDADGFFSEVVFSGSHDASALAVANGKVDAATNNSSAIGRLKKRG 212 (254)
T ss_pred CEEEeeCCCCccchHhHHHHHHHhcCCChHHhhhheeecCchHHHHHHHHcCCCCeEEecHHHHHHHHHhC
Confidence 57775322 2334556554 432 146666554433 3567799998887666666666565
No 38
>PRK15007 putative ABC transporter arginine-biding protein; Provisional
Probab=81.04 E-value=20 Score=32.25 Aligned_cols=112 Identities=17% Similarity=0.111 Sum_probs=64.1
Q ss_pred ecCCchhhhcccCceeeeeeccceecccCCCCccceeecCCCCcccEEEEEEEeCCCccCcccchHHhhcCCccCCCCCc
Q 018854 132 QRPKDIVRKLLSGDLDLGIVGLDTVSEFGQGNEDLIIVHDALDYGDCRLSLAIPKYGIFENINSLRELAQMPQWTAEKPL 211 (349)
Q Consensus 132 vR~~DIP~yV~~G~aDlGIvG~DvL~E~~~~~~~lv~~l~dLgfG~CRLvvAvP~~~~~~dv~sl~dL~~~~~~~~~~~l 211 (349)
+...++-..+..|.+|+.+.|...-.|.... ... -=.|-....++...++ .+++++||.+ +
T Consensus 67 ~~~~~~~~~l~~g~~D~~~~~~~~~~~r~~~-~~f-----s~p~~~~~~~~v~~~~----~~~~~~dL~g---------~ 127 (243)
T PRK15007 67 QAFDSLIPSLKFRRVEAVMAGMDITPEREKQ-VLF-----TTPYYDNSALFVGQQG----KYTSVDQLKG---------K 127 (243)
T ss_pred CCHHHHhHHHhCCCcCEEEEcCccCHHHhcc-cce-----ecCccccceEEEEeCC----CCCCHHHhCC---------C
Confidence 3345677789999999988886655554321 110 0123333455666654 3567788764 5
Q ss_pred EEEcCCCccHHHHHHhcCCceEEEEecCCcccc--ccCCCcceeeeecccchhh
Q 018854 212 RVATGFTYLGPKFMKDNGLKHVVFSTADGALEA--APAMGIADAILDLVSSGTT 263 (349)
Q Consensus 212 RVATkYPnlar~yf~~~Gi~~v~Ii~l~GSvEl--AP~lGlAD~IVDIVsTGtT 263 (349)
+||.---.....|+++..- .++++.....-++ +-.-|-+|+++.-..+...
T Consensus 128 ~Igv~~g~~~~~~l~~~~~-~~~~~~~~~~~~~~~~L~~grvDa~i~~~~~~~~ 180 (243)
T PRK15007 128 KVGVQNGTTHQKFIMDKHP-EITTVPYDSYQNAKLDLQNGRIDAVFGDTAVVTE 180 (243)
T ss_pred eEEEecCcHHHHHHHHhCC-CCeEEEcCCHHHHHHHHHcCCCCEEEeCHHHHHH
Confidence 7776433344567776543 3566665444443 2567888987744444443
No 39
>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=80.18 E-value=5 Score=33.13 Aligned_cols=105 Identities=14% Similarity=0.107 Sum_probs=57.1
Q ss_pred CCCeEEEee--cCCchhhhcccCceeeeeeccceecccCCCCccceeecCCCCcccEEEEEEEeCCCccCcccchHHhhc
Q 018854 124 LSNLEVWFQ--RPKDIVRKLLSGDLDLGIVGLDTVSEFGQGNEDLIIVHDALDYGDCRLSLAIPKYGIFENINSLRELAQ 201 (349)
Q Consensus 124 ~p~vev~~v--R~~DIP~yV~~G~aDlGIvG~DvL~E~~~~~~~lv~~l~dLgfG~CRLvvAvP~~~~~~dv~sl~dL~~ 201 (349)
.|++++.+. ...++...+.+|.+|+||+....- . .++. . -.++..+++++++++..+ ..+++||..
T Consensus 26 ~P~i~l~i~~~~~~~~~~~l~~g~~Dl~i~~~~~~---~---~~~~-~---~~l~~~~~~~v~~~~~~~--~~~~~~l~~ 93 (193)
T cd08442 26 YPKVDLSLSTGTTGALIQAVLEGRLDGAFVAGPVE---H---PRLE-Q---EPVFQEELVLVSPKGHPP--VSRAEDLAG 93 (193)
T ss_pred CCCceEEEEeCCcHHHHHHHHCCCccEEEEeCCCC---C---CCcE-E---EEeecCcEEEEecCCCcc--cccHHHhCC
Confidence 355555444 556889999999999999864321 1 1222 1 123456677777776332 235677664
Q ss_pred CCccCCCCCcEEEcCCCccHHHHHHhcCCceEEEEecCCccccc
Q 018854 202 MPQWTAEKPLRVATGFTYLGPKFMKDNGLKHVVFSTADGALEAA 245 (349)
Q Consensus 202 ~~~~~~~~~lRVATkYPnlar~yf~~~Gi~~v~Ii~l~GSvElA 245 (349)
.+-.... -.+.+.+...+||.+.|+. .+++.-..+.+.+
T Consensus 94 ~~~i~~~----~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~ 132 (193)
T cd08442 94 STLLAFR----AGCSYRRRLEDWLAEEGVS-PGKIMEFGSYHAI 132 (193)
T ss_pred CceEEec----CCCcHHHHHHHHHHHcCCC-cceEEecCCHHHH
Confidence 3110000 0122445567788888875 3433223445443
No 40
>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=80.17 E-value=6.4 Score=32.91 Aligned_cols=104 Identities=12% Similarity=0.099 Sum_probs=58.4
Q ss_pred CCeEEEee--cCCchhhhcccCceeeeeeccceecccCCCCccceeecCCCCcccEEEEEEEeCCCccC--cccchHHhh
Q 018854 125 SNLEVWFQ--RPKDIVRKLLSGDLDLGIVGLDTVSEFGQGNEDLIIVHDALDYGDCRLSLAIPKYGIFE--NINSLRELA 200 (349)
Q Consensus 125 p~vev~~v--R~~DIP~yV~~G~aDlGIvG~DvL~E~~~~~~~lv~~l~dLgfG~CRLvvAvP~~~~~~--dv~sl~dL~ 200 (349)
|++++-+. ...++...+..|.+|+||+....-.+. .++. ---++..+++++++.+..+. ..-+++||.
T Consensus 27 P~v~i~~~~~~~~~~~~~l~~g~~Dl~i~~~~~~~~~----~~l~----~~~l~~~~~~~~~~~~hpl~~~~~i~~~dL~ 98 (198)
T cd08437 27 LMIQIDTYEGGSAELLEQLLQGDLDIALLGSLTPLEN----SALH----SKIIKTQHFMIIVSKDHPLAKAKKVNFADLK 98 (198)
T ss_pred CceEEEEEEcCHHHHHHHHHcCCCCEEEecCCCCCCc----ccce----EEEeecceEEEEecCCCcccccCcccHHHHc
Confidence 44544443 567889999999999999864211111 1221 12356788899888764222 123567776
Q ss_pred cCCccCCCCCcEEEcC----CCccHHHHHHhcCCceEEEEecCCccccc
Q 018854 201 QMPQWTAEKPLRVATG----FTYLGPKFMKDNGLKHVVFSTADGALEAA 245 (349)
Q Consensus 201 ~~~~~~~~~~lRVATk----YPnlar~yf~~~Gi~~v~Ii~l~GSvElA 245 (349)
+.+ -|... +.....++|.+.|+. .+++.-.++.+..
T Consensus 99 ~~~--------~i~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~ 138 (198)
T cd08437 99 KEN--------FILLNEHFVHPKAFDSLCQQANFQ-PNIVYRTNDIHIL 138 (198)
T ss_pred CCC--------eEEecccchHHHHHHHHHHHcCCC-ccEEEEeCcHHHH
Confidence 531 12211 224556788888875 3444334555444
No 41
>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=79.57 E-value=7.4 Score=32.97 Aligned_cols=110 Identities=10% Similarity=0.007 Sum_probs=59.3
Q ss_pred CCeEEEee--cCCchhhhcccCceeeeeeccceecccCCCCccceeecCCCCcccEEEEEEEeCCCccCcccchHHhhcC
Q 018854 125 SNLEVWFQ--RPKDIVRKLLSGDLDLGIVGLDTVSEFGQGNEDLIIVHDALDYGDCRLSLAIPKYGIFENINSLRELAQM 202 (349)
Q Consensus 125 p~vev~~v--R~~DIP~yV~~G~aDlGIvG~DvL~E~~~~~~~lv~~l~dLgfG~CRLvvAvP~~~~~~dv~sl~dL~~~ 202 (349)
|++++-+. ...++...+.+|.+|+||+..+...-.. .++.. ...+.-+++++++.+......-+++||...
T Consensus 27 P~v~i~~~~~~~~~~~~~l~~g~~Dl~i~~~~~~~~~~---~~~~~----~~l~~~~~~~~~~~~hpl~~~~~~~~L~~~ 99 (202)
T cd08468 27 PSVRLNLVHAEQKLPLDALLAGEIDFALGYSHDDGAEP---RLIEE----RDWWEDTYVVIASRDHPRLSRLTLDAFLAE 99 (202)
T ss_pred CCCEEEEEECChHhHHHHHHCCCccEEEecccccccCC---CCEEE----EEEecCcEEEEEeCCCCCcCCCCHHHHhhC
Confidence 44544444 5689999999999999998653210000 12211 123344567777665332223466776642
Q ss_pred CccCCCCCcEEEcCCCccHHHHHHhcCCceEEEEecCCcccccc
Q 018854 203 PQWTAEKPLRVATGFTYLGPKFMKDNGLKHVVFSTADGALEAAP 246 (349)
Q Consensus 203 ~~~~~~~~lRVATkYPnlar~yf~~~Gi~~v~Ii~l~GSvElAP 246 (349)
+... ..-...+....+++|++.|+. .++.--.++++...
T Consensus 100 ~~i~----~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~ 138 (202)
T cd08468 100 RHLV----VTPWNEDRGVVDQVLEKQGLE-REIALQLPNVLNAP 138 (202)
T ss_pred CCeE----EecCCCCCchHHHHHHHcCCC-ceEEEEcChhHhHH
Confidence 1100 001122345567788888875 45554456666553
No 42
>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=78.24 E-value=33 Score=27.45 Aligned_cols=143 Identities=22% Similarity=0.217 Sum_probs=70.9
Q ss_pred EEEeecCCchhhhcccCceeeeeeccceecccCCCCccceeecCCCCcccEEEEEEEeCCCccCc--ccchHHhhcCCcc
Q 018854 128 EVWFQRPKDIVRKLLSGDLDLGIVGLDTVSEFGQGNEDLIIVHDALDYGDCRLSLAIPKYGIFEN--INSLRELAQMPQW 205 (349)
Q Consensus 128 ev~~vR~~DIP~yV~~G~aDlGIvG~DvL~E~~~~~~~lv~~l~dLgfG~CRLvvAvP~~~~~~d--v~sl~dL~~~~~~ 205 (349)
++......|+...+.+|.+|+||+-.+. .+ .++. --.++..+++++++.+..... .-+++||...+
T Consensus 32 ~~~~~~~~~~~~~l~~g~~D~~i~~~~~-~~-----~~~~----~~~l~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~-- 99 (197)
T cd05466 32 SLVEGGSSELLEALLEGELDLAIVALPV-DD-----PGLE----SEPLFEEPLVLVVPPDHPLAKRKSVTLADLADEP-- 99 (197)
T ss_pred EEEECChHHHHHHHHcCCceEEEEcCCC-CC-----Ccce----EeeeeccceEEEecCCCCcccCcEecHHHHcCCC--
Confidence 3333345689999999999999986553 11 1221 133566788888887632111 12567765421
Q ss_pred CCCCCcEEEcCC----CccHHHHHHhcCCceEEEEecCCccccc---cCCCcceeeeecccchhhHhhCCcEEecC-ceE
Q 018854 206 TAEKPLRVATGF----TYLGPKFMKDNGLKHVVFSTADGALEAA---PAMGIADAILDLVSSGTTLRENNLKEIEG-GVV 277 (349)
Q Consensus 206 ~~~~~lRVATkY----Pnlar~yf~~~Gi~~v~Ii~l~GSvElA---P~lGlAD~IVDIVsTGtTLraNgLk~ie~-g~I 277 (349)
-|.... .....+++++.|.. .....-..+.+.+ -.-|.+=+++.---.- -++..+|+.+.- +..
T Consensus 100 ------~i~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~g~~~~p~~~~~-~~~~~~l~~~~~~~~~ 171 (197)
T cd05466 100 ------LILFERGSGLRRLLDRAFAEAGFT-PNIALEVDSLEAIKALVAAGLGIALLPESAVE-ELADGGLVVLPLEDPP 171 (197)
T ss_pred ------EEEecCCchHHHHHHHHHHHcCCC-ceEEEEeccHHHHHHHHHhCCCEEEehHHHHh-hhhcCCeEEEEecCCc
Confidence 122221 12234467777864 2333223344333 1223332333321111 246667776641 123
Q ss_pred EEEEEEEEeecch
Q 018854 278 LESQAVLVASRKS 290 (349)
Q Consensus 278 leSsA~LIaN~~s 290 (349)
....-.++.++..
T Consensus 172 ~~~~~~~~~~~~~ 184 (197)
T cd05466 172 LSRTIGLVWRKGR 184 (197)
T ss_pred ceEEEEEEEcCCC
Confidence 3445555655443
No 43
>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=78.21 E-value=9.2 Score=32.40 Aligned_cols=91 Identities=15% Similarity=0.103 Sum_probs=53.5
Q ss_pred CCeEEEee--cCCchhhhcccCceeeeeeccceecccCCCCccceeecCCCCcccEEEEEEEeCCCccCc-ccchHHhhc
Q 018854 125 SNLEVWFQ--RPKDIVRKLLSGDLDLGIVGLDTVSEFGQGNEDLIIVHDALDYGDCRLSLAIPKYGIFEN-INSLRELAQ 201 (349)
Q Consensus 125 p~vev~~v--R~~DIP~yV~~G~aDlGIvG~DvL~E~~~~~~~lv~~l~dLgfG~CRLvvAvP~~~~~~d-v~sl~dL~~ 201 (349)
|++++-+. ...++...+.+|.+|+||+-.... . .++. -..++..+++++++++..+.. --+++||..
T Consensus 27 P~i~l~~~~~~~~~~~~~l~~g~~D~~i~~~~~~-~-----~~~~----~~~l~~~~~~~v~~~~h~l~~~~~~~~dL~~ 96 (200)
T cd08467 27 PGLDLRLCPIGDDLAERGLEQGTIDLAVGRFAVP-P-----DGLV----VRRLYDDGFACLVRHGHPALAQEWTLDDFAT 96 (200)
T ss_pred CCCEEEEecCCcccHHHHhhCCCcCEEEecCCCC-C-----ccce----eEEeeeccEEEEEcCCCccccCCCCHHHHhC
Confidence 45555444 556899999999999999632211 1 1221 234667788888877632211 136677765
Q ss_pred CCccCCCCCcEE--EcCCCccHHHHHHhcCCc
Q 018854 202 MPQWTAEKPLRV--ATGFTYLGPKFMKDNGLK 231 (349)
Q Consensus 202 ~~~~~~~~~lRV--ATkYPnlar~yf~~~Gi~ 231 (349)
.+. ... .+.+.+...++|++.|++
T Consensus 97 ~~~------i~~~~~~~~~~~~~~~~~~~~~~ 122 (200)
T cd08467 97 LRH------VAIAPPGRLFGGIYKRLENLGLK 122 (200)
T ss_pred CCC------EEEcCCCCCCchHHHHHHhcCCc
Confidence 311 111 133445667888888875
No 44
>PRK11260 cystine transporter subunit; Provisional
Probab=78.03 E-value=20 Score=33.27 Aligned_cols=118 Identities=17% Similarity=0.090 Sum_probs=68.1
Q ss_pred eEEEeecCCchhhhcccCceeeeeeccceecccCCCCccceeecCCCCcccEEEEEEEeCCCccCcccchHHhhcCCccC
Q 018854 127 LEVWFQRPKDIVRKLLSGDLDLGIVGLDTVSEFGQGNEDLIIVHDALDYGDCRLSLAIPKYGIFENINSLRELAQMPQWT 206 (349)
Q Consensus 127 vev~~vR~~DIP~yV~~G~aDlGIvG~DvL~E~~~~~~~lv~~l~dLgfG~CRLvvAvP~~~~~~dv~sl~dL~~~~~~~ 206 (349)
+++......+.-..+.+|.+|+++.+..+-.|.... +.. --+|..-.+++.++.+. ...+++++||.+
T Consensus 82 ~e~~~~~~~~~~~~l~~G~~D~~~~~~~~~~~r~~~----~~f--s~p~~~~~~~~~~~~~~-~~~~~~~~dL~g----- 149 (266)
T PRK11260 82 ASLKPTKWDGMLASLDSKRIDVVINQVTISDERKKK----YDF--STPYTVSGIQALVKKGN-EGTIKTAADLKG----- 149 (266)
T ss_pred EEEEeCCHHHHHHHHhcCCCCEEEeccccCHHHHhc----ccc--CCceeecceEEEEEcCC-cCCCCCHHHcCC-----
Confidence 444444556677889999999998765444444321 111 23444445667777653 235677888764
Q ss_pred CCCCcEEEcCCCccHHHHHHhcCCceEEEEecCCcccc--ccCCCcceeeeecccch
Q 018854 207 AEKPLRVATGFTYLGPKFMKDNGLKHVVFSTADGALEA--APAMGIADAILDLVSSG 261 (349)
Q Consensus 207 ~~~~lRVATkYPnlar~yf~~~Gi~~v~Ii~l~GSvEl--AP~lGlAD~IVDIVsTG 261 (349)
++|+.---.....|+.+... ..++......-|+ +-.-|-+|++++-...+
T Consensus 150 ----~~Igv~~G~~~~~~l~~~~~-~~~i~~~~~~~~~l~~L~~GrvD~~i~d~~~~ 201 (266)
T PRK11260 150 ----KKVGVGLGTNYEQWLRQNVQ-GVDVRTYDDDPTKYQDLRVGRIDAILVDRLAA 201 (266)
T ss_pred ----CEEEEecCCcHHHHHHHhCC-CCceEecCCHHHHHHHHHcCCCCEEEechHHH
Confidence 46765332333667776543 3455555544442 34568899877644433
No 45
>PRK10797 glutamate and aspartate transporter subunit; Provisional
Probab=77.75 E-value=13 Score=35.87 Aligned_cols=102 Identities=15% Similarity=0.068 Sum_probs=61.2
Q ss_pred CchhhhcccCceeeeeeccceecccCCCCccceeecCCCCcccEEEEEEEeCCCccCcccchHHhhcCCccCCCCCcEEE
Q 018854 135 KDIVRKLLSGDLDLGIVGLDTVSEFGQGNEDLIIVHDALDYGDCRLSLAIPKYGIFENINSLRELAQMPQWTAEKPLRVA 214 (349)
Q Consensus 135 ~DIP~yV~~G~aDlGIvG~DvL~E~~~~~~~lv~~l~dLgfG~CRLvvAvP~~~~~~dv~sl~dL~~~~~~~~~~~lRVA 214 (349)
...-..+..|.+|+.+.|.=+-.|.... +. + --+|..-..++.++.+ .++.+++||.+ +|||
T Consensus 96 ~~~i~~L~~G~~Di~~~~~~~t~eR~~~----~~-f-S~Py~~~~~~lv~r~~---~~i~sl~dL~G---------k~V~ 157 (302)
T PRK10797 96 QNRIPLLQNGTFDFECGSTTNNLERQKQ----AA-F-SDTIFVVGTRLLTKKG---GDIKDFADLKG---------KAVV 157 (302)
T ss_pred HhHHHHHHCCCccEEecCCccCcchhhc----ce-e-cccEeeccEEEEEECC---CCCCChHHcCC---------CEEE
Confidence 3456888999999988775554444321 21 1 2356677788889887 46788999875 3554
Q ss_pred c----CCCccHHHHHHhcCCceEEEEecCCccc--cccCCCcceeee
Q 018854 215 T----GFTYLGPKFMKDNGLKHVVFSTADGALE--AAPAMGIADAIL 255 (349)
Q Consensus 215 T----kYPnlar~yf~~~Gi~~v~Ii~l~GSvE--lAP~lGlAD~IV 255 (349)
. .|....+++..+... +++++....-.| .+-..|-+|+++
T Consensus 158 v~~gs~~~~~l~~~~~~~~~-~~~i~~~~~~~~~l~~L~~GrvDa~i 203 (302)
T PRK10797 158 VTSGTTSEVLLNKLNEEQKM-NMRIISAKDHGDSFRTLESGRAVAFM 203 (302)
T ss_pred EeCCCcHHHHHHHHhhhcCC-ceEEEEeCCHHHHHHHHHcCCceEEE
Confidence 3 333344444443332 356666444322 235578889854
No 46
>PRK09495 glnH glutamine ABC transporter periplasmic protein; Reviewed
Probab=77.73 E-value=22 Score=32.45 Aligned_cols=122 Identities=19% Similarity=0.150 Sum_probs=69.0
Q ss_pred EEeecCCchhhhcccCceeeeeeccceecccCCCCccceeecCCCCcccEEEEEEEeCCCccCcccchHHhhcCCccCCC
Q 018854 129 VWFQRPKDIVRKLLSGDLDLGIVGLDTVSEFGQGNEDLIIVHDALDYGDCRLSLAIPKYGIFENINSLRELAQMPQWTAE 208 (349)
Q Consensus 129 v~~vR~~DIP~yV~~G~aDlGIvG~DvL~E~~~~~~~lv~~l~dLgfG~CRLvvAvP~~~~~~dv~sl~dL~~~~~~~~~ 208 (349)
+.......+-.++..|.+|+++.|.-+-.|... .+ .+ .-+|-...+.+.++.+. ..+++++||.+
T Consensus 67 ~~~~~~~~~~~~l~~G~vDi~~~~~~~t~~R~~----~~-~f-s~p~~~~~~~~~~~~~~--~~~~~~~dL~g------- 131 (247)
T PRK09495 67 LKPMDFSGIIPALQTKNVDLALAGITITDERKK----AI-DF-SDGYYKSGLLVMVKANN--NDIKSVKDLDG------- 131 (247)
T ss_pred EEeCCHHHHHHHHhCCCcCEEEecCccCHHHHh----hc-cc-cchheecceEEEEECCC--CCCCChHHhCC-------
Confidence 333345667789999999999888644344321 11 01 12455667777787662 34788888774
Q ss_pred CCcEEEcCCCccHHHHHHhcCCceEEEEecCCcccc--ccCCCcceeeeecccc-hhhHhhCC
Q 018854 209 KPLRVATGFTYLGPKFMKDNGLKHVVFSTADGALEA--APAMGIADAILDLVSS-GTTLRENN 268 (349)
Q Consensus 209 ~~lRVATkYPnlar~yf~~~Gi~~v~Ii~l~GSvEl--AP~lGlAD~IVDIVsT-GtTLraNg 268 (349)
+|||..=-.....|+.+.. ...+++.....-++ +-.-|-+|+++.-..+ -..+++++
T Consensus 132 --~~I~v~~g~~~~~~l~~~~-~~~~i~~~~~~~~~~~~L~~grvDa~i~~~~~~~~~~~~~~ 191 (247)
T PRK09495 132 --KVVAVKSGTGSVDYAKANI-KTKDLRQFPNIDNAYLELGTGRADAVLHDTPNILYFIKTAG 191 (247)
T ss_pred --CEEEEecCchHHHHHHhcC-CCCceEEcCCHHHHHHHHHcCceeEEEeChHHHHHHHHhCC
Confidence 5776432223456666653 23455553322221 2446889987754333 33455543
No 47
>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=77.61 E-value=10 Score=31.47 Aligned_cols=92 Identities=12% Similarity=0.165 Sum_probs=54.0
Q ss_pred CCCeEEEee--cCCchhhhcccCceeeeeeccceecccCCCCccceeecCCCCcccEEEEEEEeCCCccC--cccchHHh
Q 018854 124 LSNLEVWFQ--RPKDIVRKLLSGDLDLGIVGLDTVSEFGQGNEDLIIVHDALDYGDCRLSLAIPKYGIFE--NINSLREL 199 (349)
Q Consensus 124 ~p~vev~~v--R~~DIP~yV~~G~aDlGIvG~DvL~E~~~~~~~lv~~l~dLgfG~CRLvvAvP~~~~~~--dv~sl~dL 199 (349)
.|++++.+. ...++-..+.+|.+|+||+....- + .++. .-.++..+++++++.+.... ..-+++||
T Consensus 26 ~P~i~l~i~~~~~~~~~~~l~~~~~Dl~i~~~~~~-~-----~~~~----~~~l~~~~~~~~~~~~~pl~~~~~~~~~dl 95 (196)
T cd08450 26 HPDLDVELSSLFSPQLAEALMRGKLDVAFMRPEIQ-S-----DGID----YQLLLKEPLIVVLPADHRLAGREKIPPQDL 95 (196)
T ss_pred CCCcEEEEEecChHHHHHHHhcCCccEEEEeCCCC-C-----CCcE----EEEEEccceEEEecCCCCcccCceECHHHh
Confidence 456666555 457888999999999999753211 1 1222 12356778888887763221 22356777
Q ss_pred hcCCccCCCCCcEEEcC---CCccHHHHHHhcCCc
Q 018854 200 AQMPQWTAEKPLRVATG---FTYLGPKFMKDNGLK 231 (349)
Q Consensus 200 ~~~~~~~~~~~lRVATk---YPnlar~yf~~~Gi~ 231 (349)
.+.+ + +..... +.+...++|++.|+.
T Consensus 96 ~~~~-~-----i~~~~~~~~~~~~~~~~~~~~~~~ 124 (196)
T cd08450 96 AGEN-F-----ISPAPTAPVLQQVIENYAAQHNIQ 124 (196)
T ss_pred CCCC-e-----EeecCCCchHHHHHHHHHHHCCCC
Confidence 6531 1 122211 234567788888875
No 48
>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=77.24 E-value=14 Score=31.64 Aligned_cols=164 Identities=15% Similarity=0.035 Sum_probs=87.2
Q ss_pred CCCeEEEeec---CCchhhhcccCceeeeeeccceecccCCCCccceeecCCCCcccEEEEEEEeCCCccCcc--cchHH
Q 018854 124 LSNLEVWFQR---PKDIVRKLLSGDLDLGIVGLDTVSEFGQGNEDLIIVHDALDYGDCRLSLAIPKYGIFENI--NSLRE 198 (349)
Q Consensus 124 ~p~vev~~vR---~~DIP~yV~~G~aDlGIvG~DvL~E~~~~~~~lv~~l~dLgfG~CRLvvAvP~~~~~~dv--~sl~d 198 (349)
.|++++-+.- ..++-..+..|.+|+||...+... .++. -..+++-+++++++.+..+..- -+++|
T Consensus 26 ~P~~~v~~~~~~~~~~l~~~L~~g~lDl~i~~~~~~~------~~l~----~~~l~~~~~~lv~~~~h~l~~~~~i~~~~ 95 (203)
T cd08463 26 APGARLEIHPLGPDFDYERALASGELDLVIGNWPEPP------EHLH----LSPLFSDEIVCLMRADHPLARRGLMTLDD 95 (203)
T ss_pred CCCCEEEEEeCCcchhHHHHHhcCCeeEEEeccccCC------CCcE----EeEeecCceEEEEeCCCCcccCCCCCHHH
Confidence 4666666663 368999999999999998543211 1221 1345667778888877433221 24677
Q ss_pred hhcCCccCCCCCcEEEc---CCCccHHHHHHhcCCceEEEEecCCccccccCC-Ccceeeeecccchhh--HhhCCcEEe
Q 018854 199 LAQMPQWTAEKPLRVAT---GFTYLGPKFMKDNGLKHVVFSTADGALEAAPAM-GIADAILDLVSSGTT--LRENNLKEI 272 (349)
Q Consensus 199 L~~~~~~~~~~~lRVAT---kYPnlar~yf~~~Gi~~v~Ii~l~GSvElAP~l-GlAD~IVDIVsTGtT--LraNgLk~i 272 (349)
|.+.+ -+.... .+-....++|.+.|+. .++..-..+++....+ .-.|+|+=+...-.. .+..+|+.+
T Consensus 96 l~~~~------~i~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~i~~~v~~~~~i~~~p~~~~~~~~~~~~l~~~ 168 (203)
T cd08463 96 YLEAP------HLAPTPYSVGQRGVIDSHLARLGLK-RNIVVTVPYFGLAPYMLAQSDLVFTTGRHFAEHYAKLLPLAVV 168 (203)
T ss_pred HhhCC------cEEEEcCCCCCCchHHHHHHHcCCC-ceEEEEeChHHHHHHHHhCCCeeEecHHHHHHHhhhhcCceEe
Confidence 76531 122222 2446677899999975 3444334565554321 112444333332221 223356655
Q ss_pred c-CceEEEEEEEEEeecchhhhhcCchhHHHHHHHHHH
Q 018854 273 E-GGVVLESQAVLVASRKSLIRRKGVLDATHEILERLE 309 (349)
Q Consensus 273 e-~g~IleSsA~LIaN~~s~~~k~~~~~~i~~li~rl~ 309 (349)
. +.......-.++.++..... .....|++.+.
T Consensus 169 ~~~~~~~~~~~~l~~~~~~~~~-----~~~~~l~~~~~ 201 (203)
T cd08463 169 DAPIEFPRMRYYQLWHERSHRS-----PEHRWLRRLVA 201 (203)
T ss_pred CCCCCCCCeeEEEeecccccCC-----hHHHHHHHHHh
Confidence 3 11223466777776655432 23455555554
No 49
>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=76.76 E-value=37 Score=28.24 Aligned_cols=90 Identities=12% Similarity=-0.019 Sum_probs=51.0
Q ss_pred CCeEEEee--cCCchhhhcccCceeeeeeccceecccCCCCccceeecCCCCcccEEEEEEEeCCCccC-cccchHHhhc
Q 018854 125 SNLEVWFQ--RPKDIVRKLLSGDLDLGIVGLDTVSEFGQGNEDLIIVHDALDYGDCRLSLAIPKYGIFE-NINSLRELAQ 201 (349)
Q Consensus 125 p~vev~~v--R~~DIP~yV~~G~aDlGIvG~DvL~E~~~~~~~lv~~l~dLgfG~CRLvvAvP~~~~~~-dv~sl~dL~~ 201 (349)
|++++.+. ...++...+.+|.+|+||+....- . .++. .-.++.-+++++++.+.... .--+++||..
T Consensus 27 P~v~l~~~~~~~~~~~~~l~~g~~Dl~i~~~~~~---~---~~~~----~~~l~~~~~~lv~~~~~~~~~~~~~~~~L~~ 96 (200)
T cd08466 27 PNISLRESPSSEEDLFEDLRLQEVDLVIDYVPFR---D---PSFK----SELLFEDELVCVARKDHPRIQGSLSLEQYLA 96 (200)
T ss_pred CCCEEEEecCchHhHHHHHHcCCccEEEecccCC---C---CCce----eeeecccceEEEEeCCCCCCCCCcCHHHHhh
Confidence 44544443 456899999999999999743211 1 1221 22345678888888764221 1125777764
Q ss_pred CCccCCCCCcEE-EcCCCccHHHHHHhcCC
Q 018854 202 MPQWTAEKPLRV-ATGFTYLGPKFMKDNGL 230 (349)
Q Consensus 202 ~~~~~~~~~lRV-ATkYPnlar~yf~~~Gi 230 (349)
.. + ..+ ...+.....++|.+.|+
T Consensus 97 ~~-~-----i~~~~~~~~~~~~~~~~~~~~ 120 (200)
T cd08466 97 EK-H-----VVLSLRRGNLSALDLLTEEVL 120 (200)
T ss_pred CC-c-----EEecCCCCcchHHHHHHHhcC
Confidence 21 1 111 12233456778888886
No 50
>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=76.71 E-value=13 Score=31.30 Aligned_cols=103 Identities=14% Similarity=0.062 Sum_probs=56.3
Q ss_pred CCCeEEEee-cCCchhhhcccCceeeeeeccceecccCCCCccceeecCCCCcccEEEEEEEeCCCccCc-ccchHHhhc
Q 018854 124 LSNLEVWFQ-RPKDIVRKLLSGDLDLGIVGLDTVSEFGQGNEDLIIVHDALDYGDCRLSLAIPKYGIFEN-INSLRELAQ 201 (349)
Q Consensus 124 ~p~vev~~v-R~~DIP~yV~~G~aDlGIvG~DvL~E~~~~~~~lv~~l~dLgfG~CRLvvAvP~~~~~~d-v~sl~dL~~ 201 (349)
.|++++.+. ...+....+..|.+|+||+..+... .++. .-.++.=+++++++.+..+.. --+++||..
T Consensus 26 ~P~v~v~l~~~~~~~~~~l~~g~~D~~i~~~~~~~------~~~~----~~~l~~~~~~~v~~~~hpl~~~~~~l~dl~~ 95 (200)
T cd08460 26 APGVRLRFVPESDKDVDALREGRIDLEIGVLGPTG------PEIR----VQTLFRDRFVGVVRAGHPLARGPITPERYAA 95 (200)
T ss_pred CCCCEEEEecCchhHHHHHHCCCccEEEecCCCCC------cchh----eeeeeccceEEEEeCCCCCCCCCCCHHHHhc
Confidence 355555554 2238889999999999998544311 1111 122344566777777643211 126788765
Q ss_pred CCccCCCCCcEE--EcCCCccHHHHHHhcCCceEEEEecCCccc
Q 018854 202 MPQWTAEKPLRV--ATGFTYLGPKFMKDNGLKHVVFSTADGALE 243 (349)
Q Consensus 202 ~~~~~~~~~lRV--ATkYPnlar~yf~~~Gi~~v~Ii~l~GSvE 243 (349)
.+. +.. .+.+.....++|++.|+. .+++.--++.+
T Consensus 96 ~~~------i~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~ 132 (200)
T cd08460 96 APH------VSVSRRGRLHGPIDDALAALGLT-RRVVAVVPTFA 132 (200)
T ss_pred CCC------EEEecCCCCcchHHHHHHhcCCc-eeEEEEcCcHH
Confidence 321 111 122345678899998875 34433234443
No 51
>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=76.28 E-value=9.3 Score=32.02 Aligned_cols=164 Identities=12% Similarity=-0.008 Sum_probs=79.5
Q ss_pred CCeEEEee--cCCchhhhcccCceeeeeeccceecccCCCCccceeecCCCCcccEEEEEEEeCCCccCcc-cchHHhhc
Q 018854 125 SNLEVWFQ--RPKDIVRKLLSGDLDLGIVGLDTVSEFGQGNEDLIIVHDALDYGDCRLSLAIPKYGIFENI-NSLRELAQ 201 (349)
Q Consensus 125 p~vev~~v--R~~DIP~yV~~G~aDlGIvG~DvL~E~~~~~~~lv~~l~dLgfG~CRLvvAvP~~~~~~dv-~sl~dL~~ 201 (349)
|++++-+. ...++...+.+|.+|+||+-.+.. . .++. .-.+++-++++++|.+.....- -+++||.+
T Consensus 27 P~v~v~i~~~~~~~~~~~l~~g~~D~~i~~~~~~-~-----~~l~----~~~l~~~~~~~v~~~~~~l~~~~i~~~~L~~ 96 (201)
T cd08459 27 PGVRIETVRLPVDELEEALESGEIDLAIGYLPDL-G-----AGFF----QQRLFRERYVCLVRKDHPRIGSTLTLEQFLA 96 (201)
T ss_pred CCCeEEEEecCccCHHHHhhCCCceEEEEcCCCC-c-----ccce----EEEeecCceEEEEcCCCccccCCcCHHHHhh
Confidence 44444443 446888999999999999754321 1 1221 1234566777787776422211 26778765
Q ss_pred CCccCCCCCcEEE--cCCCccHHHHHHhcCCceEEEEecCCccccc---cCCCcceeeeecccchhhHhhCCcEEecC-c
Q 018854 202 MPQWTAEKPLRVA--TGFTYLGPKFMKDNGLKHVVFSTADGALEAA---PAMGIADAILDLVSSGTTLRENNLKEIEG-G 275 (349)
Q Consensus 202 ~~~~~~~~~lRVA--TkYPnlar~yf~~~Gi~~v~Ii~l~GSvElA---P~lGlAD~IVDIVsTGtTLraNgLk~ie~-g 275 (349)
.+. +... +.+....++++.+.|+. ..+..-.++.+.. -.-|..=+++--...=...+..+|+.+.= .
T Consensus 97 ~~~------i~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~v~~g~gi~~lp~~~~~~~~~~~~l~~~~~~~ 169 (201)
T cd08459 97 ARH------VVVSASGTGHGLVEQALREAGIR-RRIALRVPHFLALPLIVAQTDLVATVPERLARLFARAGGLRIVPLPF 169 (201)
T ss_pred CCc------EEEccCCCCcchHHHHHHHhCcc-ccEEEEcCcHHHHHHHHhcCCEEEecHHHHHHHHhhcCCeeEecCCC
Confidence 311 1111 23445667889888875 3333223444433 12222212222110001123455766530 1
Q ss_pred eEEEEEEEEEeecchhhhhcCchhHHHHHHHHHHH
Q 018854 276 VVLESQAVLVASRKSLIRRKGVLDATHEILERLEA 310 (349)
Q Consensus 276 ~IleSsA~LIaN~~s~~~k~~~~~~i~~li~rl~~ 310 (349)
....-.-.++.++..... ..+..+++.++.
T Consensus 170 ~~~~~~~~~~~~~~~~~~-----~~~~~~~~~~~~ 199 (201)
T cd08459 170 PLPPFEVKLYWHRRFHRD-----PGNRWLRQLVAE 199 (201)
T ss_pred CCCCceEEEEEccccCCC-----hHHHHHHHHHHh
Confidence 122345556666544322 235556555553
No 52
>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=75.71 E-value=5.6 Score=33.54 Aligned_cols=91 Identities=13% Similarity=0.142 Sum_probs=50.8
Q ss_pred CCeEEEee--cCCchhhhcccCceeeeeeccceecccCCCCccceeecCCCCcccEEEEEEEeCCCccCcc--cchHHhh
Q 018854 125 SNLEVWFQ--RPKDIVRKLLSGDLDLGIVGLDTVSEFGQGNEDLIIVHDALDYGDCRLSLAIPKYGIFENI--NSLRELA 200 (349)
Q Consensus 125 p~vev~~v--R~~DIP~yV~~G~aDlGIvG~DvL~E~~~~~~~lv~~l~dLgfG~CRLvvAvP~~~~~~dv--~sl~dL~ 200 (349)
|++++.+. ...|+...+..|.+|+||+-.+. ... ++. .-.+++-++++++|.+..+..- -+++||.
T Consensus 27 P~v~i~~~~~~~~~~~~~l~~g~~Dl~i~~~~~-~~~-----~~~----~~~l~~~~~~~v~~~~hpl~~~~~i~~~dL~ 96 (196)
T cd08458 27 PDVSVYLDTVPSQTVLELVSLQHYDLGISILAG-DYP-----GLT----TEPVPSFRAVCLLPPGHRLEDKETVHATDLE 96 (196)
T ss_pred CCcEEEEeccChHHHHHHHHcCCCCEEEEeccC-CCC-----Cce----EEEeccCceEEEecCCCccccCCccCHHHhC
Confidence 44444443 44568899999999999985432 111 121 1223556678888776433222 2567776
Q ss_pred cCCccCCCCCcEEEcC--CCccHHHHHHhcCCc
Q 018854 201 QMPQWTAEKPLRVATG--FTYLGPKFMKDNGLK 231 (349)
Q Consensus 201 ~~~~~~~~~~lRVATk--YPnlar~yf~~~Gi~ 231 (349)
+.+ + +..... +-....+||++.|+.
T Consensus 97 ~~~-~-----i~~~~~~~~~~~~~~~~~~~~~~ 123 (196)
T cd08458 97 GES-L-----ICLSPVSLLRMQTDAALDSCGVH 123 (196)
T ss_pred CCc-c-----EEecCCCcHHHHHHHHHHHcCCC
Confidence 531 1 111111 234567788888874
No 53
>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=75.71 E-value=7.4 Score=32.19 Aligned_cols=94 Identities=20% Similarity=0.245 Sum_probs=53.6
Q ss_pred CCCeEEEee--cCCchhhhcccCceeeeeeccceecccCCCCccceeecCCCCcccEEEEEEEeCCCccCc--ccchHHh
Q 018854 124 LSNLEVWFQ--RPKDIVRKLLSGDLDLGIVGLDTVSEFGQGNEDLIIVHDALDYGDCRLSLAIPKYGIFEN--INSLREL 199 (349)
Q Consensus 124 ~p~vev~~v--R~~DIP~yV~~G~aDlGIvG~DvL~E~~~~~~~lv~~l~dLgfG~CRLvvAvP~~~~~~d--v~sl~dL 199 (349)
.|++++.+. ...++-..+.+|.+|+||+-.....+ . .++. .-.++..+++++++.+..+.. .-+++||
T Consensus 26 ~P~i~i~~~~~~~~~~~~~l~~~~~Dl~i~~~~~~~~-~---~~~~----~~~l~~~~~~~v~~~~~~~~~~~~~~~~~L 97 (197)
T cd08449 26 YPNVTVRFHELSPEAQKAALLSKRIDLGFVRFADTLN-D---PPLA----SELLWREPMVVALPEEHPLAGRKSLTLADL 97 (197)
T ss_pred CCCeEEEEEECCHHHHHHHHhCCCccEEEecccccCC-C---CCce----EEEEEEeeEEEEecCCCCCCCCCCCCHHHH
Confidence 355655554 45778899999999999964321110 1 1222 123567788888877643222 2367787
Q ss_pred hcCCccCCCCCcEE---EcCCCccHHHHHHhcCCc
Q 018854 200 AQMPQWTAEKPLRV---ATGFTYLGPKFMKDNGLK 231 (349)
Q Consensus 200 ~~~~~~~~~~~lRV---ATkYPnlar~yf~~~Gi~ 231 (349)
...+. +.. .+.+.+...++|++.|+.
T Consensus 98 ~~~~~------i~~~~~~~~~~~~~~~~~~~~~~~ 126 (197)
T cd08449 98 RDEPF------VFLRLANSRFADFLINCCLQAGFT 126 (197)
T ss_pred CCCCE------EEecCCCchHHHHHHHHHHhCCCC
Confidence 65311 111 123345566788888874
No 54
>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=75.59 E-value=7 Score=32.74 Aligned_cols=112 Identities=19% Similarity=0.181 Sum_probs=58.4
Q ss_pred CCCeEEEee--cCCchhhhcccCceeeeeeccceecccCCCCccceeecCCCCcccEEEEEEEeCCCccCc--ccchHHh
Q 018854 124 LSNLEVWFQ--RPKDIVRKLLSGDLDLGIVGLDTVSEFGQGNEDLIIVHDALDYGDCRLSLAIPKYGIFEN--INSLREL 199 (349)
Q Consensus 124 ~p~vev~~v--R~~DIP~yV~~G~aDlGIvG~DvL~E~~~~~~~lv~~l~dLgfG~CRLvvAvP~~~~~~d--v~sl~dL 199 (349)
.|++++.+. ...++...+..|.+|+||+-.+.-.+.. .++. ...+++.+++++++.+..+.. .-+++||
T Consensus 26 ~P~i~l~i~~~~~~~~~~~l~~g~~D~~i~~~~~~~~~~---~~~~----~~~l~~~~~~~v~~~~hp~~~~~~i~~~~L 98 (200)
T cd08453 26 YPDVELQLREATSDVQLEALLAGEIDAGIVIPPPGASAP---PALA----YRPLLSEPLVLAVPAAWAAEGGAPLALAAV 98 (200)
T ss_pred CCCceEEEEeCCHHHHHHHHHcCCCCEEEEecCcccCCC---ccee----EEEeeeCceEEEEECCCccccCCCCCHHHh
Confidence 355555554 4568999999999999997544321111 1111 233456677788877643221 2356777
Q ss_pred hcCCccCCCCCcEEEcCCCccHHHHHHhcCCceEEEEecCCccccc
Q 018854 200 AQMPQWTAEKPLRVATGFTYLGPKFMKDNGLKHVVFSTADGALEAA 245 (349)
Q Consensus 200 ~~~~~~~~~~~lRVATkYPnlar~yf~~~Gi~~v~Ii~l~GSvElA 245 (349)
.+.+-..... .-...+-+...++|++.|+. .++..-..+.+++
T Consensus 99 ~~~~~i~~~~--~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~ 141 (200)
T cd08453 99 AAEPLVIFPR--RIAPAFHDAVTGYYRAAGQT-PRIAQEAIQMQTI 141 (200)
T ss_pred ccCCEEeccC--CcCCcHHHHHHHHHHHcCCC-CceeeccccHHHH
Confidence 6531100000 00012234566788888875 3444334444433
No 55
>PRK11063 metQ DL-methionine transporter substrate-binding subunit; Provisional
Probab=75.45 E-value=25 Score=34.02 Aligned_cols=79 Identities=24% Similarity=0.234 Sum_probs=46.3
Q ss_pred CchhhhcccCceeeeeeccceecccCCC--CccceeecCCCCcccEEEEEEEeCCCccCcccchHHhhcCCccCCCCCcE
Q 018854 135 KDIVRKLLSGDLDLGIVGLDTVSEFGQG--NEDLIIVHDALDYGDCRLSLAIPKYGIFENINSLRELAQMPQWTAEKPLR 212 (349)
Q Consensus 135 ~DIP~yV~~G~aDlGIvG~DvL~E~~~~--~~~lv~~l~dLgfG~CRLvvAvP~~~~~~dv~sl~dL~~~~~~~~~~~lR 212 (349)
.+.-..++.|.+|++..+..-.++.... ..++. -..-..++|.+.....++|++||.+ +++
T Consensus 70 ~~~~~ALa~GdID~~~~qh~~~l~~~~~~~g~~l~---------~~~~~~vvp~~~ys~~i~si~DL~~--------Gk~ 132 (271)
T PRK11063 70 VLPNEALSKGDIDANAFQHKPYLDQQIKDRGYKLV---------AVGNTFVYPIAGYSKKIKSLDELQD--------GSQ 132 (271)
T ss_pred HHHHHHHHcCCcceecccCHHHHHHHHHHcCCcEE---------EEeEEEEEEeeccccCCCCHHHhcC--------CCE
Confidence 4566789999999988877544432100 01211 1122345666432245899999974 379
Q ss_pred EEcC--CCccHHH--HHHhcCC
Q 018854 213 VATG--FTYLGPK--FMKDNGL 230 (349)
Q Consensus 213 VATk--YPnlar~--yf~~~Gi 230 (349)
||+. .-|..|. +|++.|+
T Consensus 133 IAip~d~~n~~r~L~lL~~~Gl 154 (271)
T PRK11063 133 VAVPNDPTNLGRSLLLLQKVGL 154 (271)
T ss_pred EEecCCCccHHHHHHHHHHCCC
Confidence 9988 3444443 5567665
No 56
>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=75.05 E-value=5.9 Score=32.48 Aligned_cols=104 Identities=19% Similarity=0.241 Sum_probs=57.3
Q ss_pred CCeEEEee--cCCchhhhcccCceeeeeeccceecccCCCCccceeecCCCCcccEEEEEEEeCCCccC--cccchHHhh
Q 018854 125 SNLEVWFQ--RPKDIVRKLLSGDLDLGIVGLDTVSEFGQGNEDLIIVHDALDYGDCRLSLAIPKYGIFE--NINSLRELA 200 (349)
Q Consensus 125 p~vev~~v--R~~DIP~yV~~G~aDlGIvG~DvL~E~~~~~~~lv~~l~dLgfG~CRLvvAvP~~~~~~--dv~sl~dL~ 200 (349)
|++++.+. ...++...+.+|.+|+||+..... . .++. --.+++.+++++++.+.... ..-+++||.
T Consensus 27 p~v~i~i~~~~~~~~~~~l~~g~~D~~i~~~~~~---~---~~~~----~~~l~~~~~~~~~~~~~pl~~~~~~~~~~l~ 96 (197)
T cd08440 27 PGIRVRLRDVSAEQVIEAVRSGEVDFGIGSEPEA---D---PDLE----FEPLLRDPFVLVCPKDHPLARRRSVTWAELA 96 (197)
T ss_pred CCcEEEEEeCChHHHHHHHHcCCccEEEEeCCCC---C---CCee----EEEeecccEEEEecCCCCcccCCccCHHHHc
Confidence 55555544 567889999999999999854321 1 1221 12356778888888764221 123567776
Q ss_pred cCCccCCCCCcEE--EcCCCccHHHHHHhcCCceEEEEecCCccccc
Q 018854 201 QMPQWTAEKPLRV--ATGFTYLGPKFMKDNGLKHVVFSTADGALEAA 245 (349)
Q Consensus 201 ~~~~~~~~~~lRV--ATkYPnlar~yf~~~Gi~~v~Ii~l~GSvElA 245 (349)
..+ + +.. .+.+.....++|++.|+. .+++.-..+.+..
T Consensus 97 ~~~-~-----i~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~ 136 (197)
T cd08440 97 GYP-L-----IALGRGSGVRALIDRALAAAGLT-LRPAYEVSHMSTA 136 (197)
T ss_pred cCC-E-----EecCCCccHHHHHHHHHHHcCCC-cceEEEeccHHHH
Confidence 421 1 111 112334556677888875 3333333444443
No 57
>PRK11139 DNA-binding transcriptional activator GcvA; Provisional
Probab=74.68 E-value=18 Score=33.96 Aligned_cols=116 Identities=13% Similarity=0.078 Sum_probs=61.5
Q ss_pred CCCceEEEecCCCCchHHHHHHHHHCCCccCCCCCCceEEecCCCCCeEEEeecCCchhhhcccCceeeeeeccceeccc
Q 018854 80 ERDEIRLGLPSKGRMAADTLDLLKDCQLSVKQVNPRQYVAQIPQLSNLEVWFQRPKDIVRKLLSGDLDLGIVGLDTVSEF 159 (349)
Q Consensus 80 ~~~~LrIALP~KGRL~e~t~~LL~~aGi~~~~~~~R~L~~~~~~~p~vev~~vR~~DIP~yV~~G~aDlGIvG~DvL~E~ 159 (349)
..+.||||++ -+-...-..+++++ + . + ..|++++-+.. .|....+..|.+|+||+....
T Consensus 92 ~~g~l~I~~~-~~~~~~~l~~~l~~--f--~----~-------~~p~i~i~l~~-~~~~~~l~~g~~Dl~i~~~~~---- 150 (297)
T PRK11139 92 AKGALTVSLL-PSFAIQWLVPRLSS--F--N----E-------AHPDIDVRLKA-VDRLEDFLRDDVDVAIRYGRG---- 150 (297)
T ss_pred CCceEEEecC-hHHHHHHHHHHHHH--H--H----H-------HCCCceEEEEe-CCChhhhccCCCCEEEEeCCC----
Confidence 4578999998 22222222333332 1 0 1 13455554433 455678899999999986421
Q ss_pred CCCCccceeecCCCCcccEEEEEEEeCCCc--cCcccchHHhhcCCccCCCCCcEEEcCCCccHHHHHHhcCC
Q 018854 160 GQGNEDLIIVHDALDYGDCRLSLAIPKYGI--FENINSLRELAQMPQWTAEKPLRVATGFTYLGPKFMKDNGL 230 (349)
Q Consensus 160 ~~~~~~lv~~l~dLgfG~CRLvvAvP~~~~--~~dv~sl~dL~~~~~~~~~~~lRVATkYPnlar~yf~~~Gi 230 (349)
.. .++. .-.++...++++++.+.. ....-+++||.+.+ -|...-.+...+||...|+
T Consensus 151 ~~--~~l~----~~~l~~~~~~~~~~~~~~~~~~~~i~~~dL~~~p--------~i~~~~~~~~~~~~~~~~~ 209 (297)
T PRK11139 151 NW--PGLR----VEKLLDEYLLPVCSPALLNGGKPLKTPEDLARHT--------LLHDDSREDWRAWFRAAGL 209 (297)
T ss_pred CC--CCce----EEEeccceeEEEeCHHHhcccCCCCCHHHhhcCc--------eEeecCcccHHHHHHHhCC
Confidence 11 1222 234556666776665421 12334677776531 2222223456778888776
No 58
>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=74.19 E-value=7.8 Score=32.07 Aligned_cols=95 Identities=21% Similarity=0.213 Sum_probs=52.7
Q ss_pred CCeEEEee--cCCchhhhcccCceeeeeeccceecccCCCCccceeecCCCCcccEEEEEEEeCCCccC--cccchHHhh
Q 018854 125 SNLEVWFQ--RPKDIVRKLLSGDLDLGIVGLDTVSEFGQGNEDLIIVHDALDYGDCRLSLAIPKYGIFE--NINSLRELA 200 (349)
Q Consensus 125 p~vev~~v--R~~DIP~yV~~G~aDlGIvG~DvL~E~~~~~~~lv~~l~dLgfG~CRLvvAvP~~~~~~--dv~sl~dL~ 200 (349)
|++++-+. ...++...+.+|.+|+||+..+.-... .++. ...+++.+++++++.+..+. +.-+++||.
T Consensus 27 P~v~i~i~~~~~~~~~~~l~~~~~Dl~i~~~~~~~~~----~~~~----~~~l~~~~~~~~~~~~~~l~~~~~~~~~dL~ 98 (201)
T cd08435 27 PRLTVRVVEGTSDELLEGLRAGELDLAIGRLADDEQP----PDLA----SEELADEPLVVVARPGHPLARRARLTLADLA 98 (201)
T ss_pred CCeEEEEEeCCHHHHHHHHHcCCccEEEEecCcccCC----CCcE----EEEcccCcEEEEEeCCCcCcccCCcCHHHHh
Confidence 55555544 567888999999999999754321101 1221 13456788888888764322 223567776
Q ss_pred cCCccCCCCCcEEEcCCCccHHHHHHhcCCc
Q 018854 201 QMPQWTAEKPLRVATGFTYLGPKFMKDNGLK 231 (349)
Q Consensus 201 ~~~~~~~~~~lRVATkYPnlar~yf~~~Gi~ 231 (349)
..+.-.... ...+....+++|++.|+.
T Consensus 99 ~~~~i~~~~----~~~~~~~~~~~~~~~~~~ 125 (201)
T cd08435 99 DYPWVLPPP----GTPLRQRLEQLFAAAGLP 125 (201)
T ss_pred cCCEEecCC----CCcHHHHHHHHHHHcCCC
Confidence 531100000 011224556778877763
No 59
>PRK11242 DNA-binding transcriptional regulator CynR; Provisional
Probab=74.19 E-value=34 Score=31.72 Aligned_cols=162 Identities=15% Similarity=0.110 Sum_probs=80.7
Q ss_pred CCeEEE--eecCCchhhhcccCceeeeeeccceecccCCCCccceeecCCCCcccEEEEEEEeCCCccCc---ccchHHh
Q 018854 125 SNLEVW--FQRPKDIVRKLLSGDLDLGIVGLDTVSEFGQGNEDLIIVHDALDYGDCRLSLAIPKYGIFEN---INSLREL 199 (349)
Q Consensus 125 p~vev~--~vR~~DIP~yV~~G~aDlGIvG~DvL~E~~~~~~~lv~~l~dLgfG~CRLvvAvP~~~~~~d---v~sl~dL 199 (349)
|++.+. .....++...+..|.+|+||+..+.- ..++. --.++.-+++++++.+..... .-+++||
T Consensus 118 p~~~i~~~~~~~~~~~~~l~~g~~Dl~i~~~~~~------~~~l~----~~~l~~~~~~~~~~~~~pl~~~~~~i~~~~L 187 (296)
T PRK11242 118 PGITLTIREMSQERIEALLADDELDVGIAFAPVH------SPEIE----AQPLFTETLALVVGRHHPLAARRKALTLDEL 187 (296)
T ss_pred CCCEEEEEeCCHHHHHHHHHCCCCcEEEEecCCC------Cccee----EEEeeeccEEEEEcCCCcccccCCCcCHHHH
Confidence 444444 34567788899999999999743321 12222 234677888988887643221 1356777
Q ss_pred hcCCccCCCCCcEEEcCCC----ccHHHHHHhcCCceEEEEecCCcccccc---CCCcceeeeecccchhhHhhCCcEEe
Q 018854 200 AQMPQWTAEKPLRVATGFT----YLGPKFMKDNGLKHVVFSTADGALEAAP---AMGIADAILDLVSSGTTLRENNLKEI 272 (349)
Q Consensus 200 ~~~~~~~~~~~lRVATkYP----nlar~yf~~~Gi~~v~Ii~l~GSvElAP---~lGlAD~IVDIVsTGtTLraNgLk~i 272 (349)
... .-|..... +.-..+|++.|+. .++..-..+.+++. .-|..=+++--.-.. +..+|+.+
T Consensus 188 ~~~--------~~i~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~v~~g~gi~~~p~~~~~---~~~~l~~~ 255 (296)
T PRK11242 188 ADE--------PLVLLSAEFATREQIDRYFRRHGVT-PRVAIEANSISAVLEIVRRGRLATLLPAAIAR---EHDGLCAI 255 (296)
T ss_pred hCC--------CcEeeCCCccHHHHHHHHHHHcCCC-ccEEEEeccHHHHHHHHHhCCeEEEeehhhcc---cCCCeEEE
Confidence 642 12222222 2335677778875 34433344554432 122222232211111 12456653
Q ss_pred cC-ceEEEEEEEEEeecchhhhhcCchhHHHHHHHHHHHHHh
Q 018854 273 EG-GVVLESQAVLVASRKSLIRRKGVLDATHEILERLEAHLR 313 (349)
Q Consensus 273 e~-g~IleSsA~LIaN~~s~~~k~~~~~~i~~li~rl~~vl~ 313 (349)
.- .......-.++.++..... ..++.+++.|+....
T Consensus 256 ~~~~~~~~~~~~l~~~~~~~~~-----~~~~~~~~~l~~~~~ 292 (296)
T PRK11242 256 PLDPPLPQRTAALLRRKGAYRS-----AAARAFIELALERRA 292 (296)
T ss_pred ECCCCCccceEEEEEeCCCCCC-----HHHHHHHHHHHHhhh
Confidence 20 0122334566666544322 245666666665543
No 60
>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=73.77 E-value=13 Score=30.77 Aligned_cols=105 Identities=14% Similarity=0.142 Sum_probs=55.0
Q ss_pred CCeEEEee--cCCchhhhcccCceeeeeeccceecccCCCCccceeecCCCCcccEEEEEEEeCCCccC--cccchHHhh
Q 018854 125 SNLEVWFQ--RPKDIVRKLLSGDLDLGIVGLDTVSEFGQGNEDLIIVHDALDYGDCRLSLAIPKYGIFE--NINSLRELA 200 (349)
Q Consensus 125 p~vev~~v--R~~DIP~yV~~G~aDlGIvG~DvL~E~~~~~~~lv~~l~dLgfG~CRLvvAvP~~~~~~--dv~sl~dL~ 200 (349)
|++++-+. ...++...+.+|.+|+||+..+.... .++. .-.++..+++++++.+.... +.-+++||.
T Consensus 28 P~i~l~i~~~~~~~~~~~l~~g~~Dl~i~~~~~~~~-----~~~~----~~~l~~~~~~~v~~~~~~l~~~~~~~~~dL~ 98 (199)
T cd08451 28 PDVELTLEEANTAELLEALREGRLDAAFVRPPVARS-----DGLV----LELLLEEPMLVALPAGHPLARERSIPLAALA 98 (199)
T ss_pred CCcEEEEecCChHHHHHHHHCCCccEEEEecCCCCC-----Ccee----EEEeecccEEEEecCCCCCcccCccCHHHhc
Confidence 44444333 45678899999999999975432111 1222 12245667777776653221 223677776
Q ss_pred cCCccCCCCCcEEEcCCC----ccHHHHHHhcCCceEEEEecCCccccc
Q 018854 201 QMPQWTAEKPLRVATGFT----YLGPKFMKDNGLKHVVFSTADGALEAA 245 (349)
Q Consensus 201 ~~~~~~~~~~lRVATkYP----nlar~yf~~~Gi~~v~Ii~l~GSvElA 245 (349)
+.+ -+......+ +...+||.+.|.. .++..-.++.+..
T Consensus 99 ~~~------~i~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~ 140 (199)
T cd08451 99 DEP------FILFPRPVGPGLYDAIIAACRRAGFT-PRIGQEAPQMASA 140 (199)
T ss_pred CCC------EEEecCCcChhHHHHHHHHHHHcCCc-eeeEEehhhHHHH
Confidence 521 122222221 2344567777864 3444334555543
No 61
>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=73.04 E-value=22 Score=29.49 Aligned_cols=92 Identities=15% Similarity=0.183 Sum_probs=53.5
Q ss_pred CCCeEEEee--cCCchhhhcccCceeeeeeccceecccCCCCccceeecCCCCcccEEEEEEEeCCCccC-cccchHHhh
Q 018854 124 LSNLEVWFQ--RPKDIVRKLLSGDLDLGIVGLDTVSEFGQGNEDLIIVHDALDYGDCRLSLAIPKYGIFE-NINSLRELA 200 (349)
Q Consensus 124 ~p~vev~~v--R~~DIP~yV~~G~aDlGIvG~DvL~E~~~~~~~lv~~l~dLgfG~CRLvvAvP~~~~~~-dv~sl~dL~ 200 (349)
.|++++-+. ...++...+.+|.+|+||+.... .. .++. ...+++-+++++++.+.... ..-+++||.
T Consensus 26 ~P~v~i~i~~~~~~~~~~~l~~~~~Di~i~~~~~-~~-----~~~~----~~~l~~~~~~lv~~~~~p~~~~~~~~~~L~ 95 (198)
T cd08461 26 APGVRVAIRDLESDNLEAQLERGEVDLALTTPEY-AP-----DGLR----SRPLFEERYVCVTRRGHPLLQGPLSLDQFC 95 (198)
T ss_pred CCCcEEEEeeCCcccHHHHHhcCCCcEEEecCcc-CC-----ccce----eeeeecCcEEEEEcCCChhhcCCCCHHHHh
Confidence 455655554 45678999999999999974221 11 1121 23345667788887763211 223667776
Q ss_pred cCCccCCCCCcEE---EcCCCccHHHHHHhcCCc
Q 018854 201 QMPQWTAEKPLRV---ATGFTYLGPKFMKDNGLK 231 (349)
Q Consensus 201 ~~~~~~~~~~lRV---ATkYPnlar~yf~~~Gi~ 231 (349)
..+. +.. .+.+.....+||.+.|++
T Consensus 96 ~~~~------i~~~~~~~~~~~~~~~~~~~~~~~ 123 (198)
T cd08461 96 ALDH------IVVSPSGGGFAGSTDEALAALGLT 123 (198)
T ss_pred hCCc------EEEecCCCCCCCHHHHHHHHcCCC
Confidence 5311 111 123445678899998874
No 62
>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=72.42 E-value=16 Score=30.38 Aligned_cols=104 Identities=17% Similarity=0.162 Sum_probs=56.0
Q ss_pred CCCeEEEee--cCCchhhhcccCceeeeeeccceecccCCCCccceeecCCCCcccEEEEEEEeCCCccC--cccchHHh
Q 018854 124 LSNLEVWFQ--RPKDIVRKLLSGDLDLGIVGLDTVSEFGQGNEDLIIVHDALDYGDCRLSLAIPKYGIFE--NINSLREL 199 (349)
Q Consensus 124 ~p~vev~~v--R~~DIP~yV~~G~aDlGIvG~DvL~E~~~~~~~lv~~l~dLgfG~CRLvvAvP~~~~~~--dv~sl~dL 199 (349)
.|++++.+. ...++...+.+|.+|+||+.... +.. ..++. ...+++.++++++|++..+. ..-+++||
T Consensus 26 ~P~i~l~i~~~~~~~~~~~l~~~~~Dl~i~~~~~--~~~--~~~l~----~~~l~~~~~~~v~~~~hp~~~~~~~~~~~L 97 (199)
T cd08416 26 RPELDIELTLGSNKDLLKKLKDGELDAILVATPE--GLN--DPDFE----VVPLFEDDIFLAVPATSPLAASSEIDLRDL 97 (199)
T ss_pred CCCeEEEEEEcCcHHHHHHHhCCCCCEEEEecCC--cCC--CCCeE----EEEeecceEEEEECCCCcccccCccCHHHh
Confidence 355555554 44567889999999999987432 100 11222 23456778888888764222 12356777
Q ss_pred hcCCccCCCCCcEEEcCC----CccHHHHHHhcCCceEEEEecCCcccc
Q 018854 200 AQMPQWTAEKPLRVATGF----TYLGPKFMKDNGLKHVVFSTADGALEA 244 (349)
Q Consensus 200 ~~~~~~~~~~~lRVATkY----Pnlar~yf~~~Gi~~v~Ii~l~GSvEl 244 (349)
.+.. -|.... ....+++|.+.|++ .++..-..+.+.
T Consensus 98 ~~~~--------~i~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~ 137 (199)
T cd08416 98 KDEK--------FVTLSEGFATYRGFDEAFEIAGFE-PNVVMRVNDIFS 137 (199)
T ss_pred cCCc--------eEEecCCCcHHHHHHHHHHHcCCC-CCceEEeCCHHH
Confidence 6431 122111 12345577777864 233332344443
No 63
>PRK11151 DNA-binding transcriptional regulator OxyR; Provisional
Probab=71.76 E-value=36 Score=31.98 Aligned_cols=69 Identities=25% Similarity=0.344 Sum_probs=45.0
Q ss_pred CCCeEEEee--cCCchhhhcccCceeeeeeccceecccCCCCccceeecCCCCcccEEEEEEEeCCCccC--cccchHHh
Q 018854 124 LSNLEVWFQ--RPKDIVRKLLSGDLDLGIVGLDTVSEFGQGNEDLIIVHDALDYGDCRLSLAIPKYGIFE--NINSLREL 199 (349)
Q Consensus 124 ~p~vev~~v--R~~DIP~yV~~G~aDlGIvG~DvL~E~~~~~~~lv~~l~dLgfG~CRLvvAvP~~~~~~--dv~sl~dL 199 (349)
.|++++.+. ..+++...+..|.+|+||+..+... .++. -..+|.-+++++++++.... +.-+++||
T Consensus 117 ~P~v~i~~~~~~~~~~~~~l~~g~~Dl~i~~~~~~~------~~l~----~~~l~~~~~~~~~~~~hpl~~~~~i~~~~L 186 (305)
T PRK11151 117 FPKLEMYLHEAQTHQLLAQLDSGKLDCAILALVKES------EAFI----EVPLFDEPMLLAVYEDHPWANRDRVPMSDL 186 (305)
T ss_pred CCCcEEEEEeCCHHHHHHHHHcCCccEEEEecCCCC------CCeE----EEEeccCcEEEEecCCCCcccCCccCHHHh
Confidence 355665555 5789999999999999998655321 1222 24567778888888764321 23367777
Q ss_pred hcC
Q 018854 200 AQM 202 (349)
Q Consensus 200 ~~~ 202 (349)
...
T Consensus 187 ~~~ 189 (305)
T PRK11151 187 AGE 189 (305)
T ss_pred cCC
Confidence 653
No 64
>PRK10341 DNA-binding transcriptional activator TdcA; Provisional
Probab=71.56 E-value=21 Score=33.86 Aligned_cols=165 Identities=16% Similarity=0.148 Sum_probs=82.3
Q ss_pred eEEEeecCCchhhhcccCceeeeeeccceecccCCCCccceeecCCCCcccEEEEEEEeCCCccCcccchHHhhcCCccC
Q 018854 127 LEVWFQRPKDIVRKLLSGDLDLGIVGLDTVSEFGQGNEDLIIVHDALDYGDCRLSLAIPKYGIFENINSLRELAQMPQWT 206 (349)
Q Consensus 127 vev~~vR~~DIP~yV~~G~aDlGIvG~DvL~E~~~~~~~lv~~l~dLgfG~CRLvvAvP~~~~~~dv~sl~dL~~~~~~~ 206 (349)
+++......++...|.+|.+|+||+...--.+. .++. --.+++.+++++++.+......-+++||.+.+
T Consensus 128 i~~~~~~~~~~~~~l~~g~~Dl~i~~~~~~~~~----~~l~----~~~l~~~~~~lv~~~~~pl~~~i~~~dL~~~~--- 196 (312)
T PRK10341 128 VSMYEAQLSSFLPAIRDGRLDFAIGTLSNEMKL----QDLH----VEPLFESEFVLVASKSRTCTGTTTLESLKNEQ--- 196 (312)
T ss_pred EEEEeCCHHHHHHHHHcCCCcEEEecCCccccc----CCee----EEEEecccEEEEEcCCCchhccCCHHHHhCCC---
Confidence 344444678999999999999999742110111 1221 23456778888888764333334577776531
Q ss_pred CCCCcEEEc----CCCccHHHHHHhcCCceEEEEecCCcccccc---CCCcceeee--ecccchhhHhhCCcEEecCc-e
Q 018854 207 AEKPLRVAT----GFTYLGPKFMKDNGLKHVVFSTADGALEAAP---AMGIADAIL--DLVSSGTTLRENNLKEIEGG-V 276 (349)
Q Consensus 207 ~~~~lRVAT----kYPnlar~yf~~~Gi~~v~Ii~l~GSvElAP---~lGlAD~IV--DIVsTGtTLraNgLk~ie~g-~ 276 (349)
-|.. .|-+...++|.+.|+. .+++.--.+.+..- .-|..=+++ .... .++.++|+.+.-. .
T Consensus 197 -----~i~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~v~~g~gi~~~p~~~~~---~~~~~~l~~i~l~~~ 267 (312)
T PRK10341 197 -----WVLPQTNMGYYSELLTTLQRNGIS-IENIVKTDSVVTIYNLVLNADFLTVIPCDMTS---PFGSNQFITIPIEET 267 (312)
T ss_pred -----eEccCCCCcHHHHHHHHHHHcCcC-CCceEEecCHHHHHHHHHhCCcEEEeeHHhcC---ccccCcEEEEecCCC
Confidence 1211 1212233567777764 23222223333221 112111222 1111 1234567776411 1
Q ss_pred EEEEEEEEEeecchhhhhcCchhHHHHHHHHHHHHHhhcC
Q 018854 277 VLESQAVLVASRKSLIRRKGVLDATHEILERLEAHLRASG 316 (349)
Q Consensus 277 IleSsA~LIaN~~s~~~k~~~~~~i~~li~rl~~vl~Ar~ 316 (349)
.....-.++.++..... ..++.+++.++....+++
T Consensus 268 ~~~~~~~l~~~~~~~~~-----~~~~~~~~~l~~~~~~~~ 302 (312)
T PRK10341 268 LPVAQYAAVWSKNYRIK-----KAASVLVELAKEYSSYNG 302 (312)
T ss_pred CCCCcEEEEEecCCCCC-----HHHHHHHHHHHHHhhhcc
Confidence 12234455665543222 356778888887776655
No 65
>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=71.52 E-value=31 Score=29.82 Aligned_cols=109 Identities=9% Similarity=0.051 Sum_probs=57.5
Q ss_pred CCeEEEee--cCCchhhhcccCceeeeeeccceecccCCCCccceeecCCCCcccEEEEEEEeCCCccC-cccchHHhhc
Q 018854 125 SNLEVWFQ--RPKDIVRKLLSGDLDLGIVGLDTVSEFGQGNEDLIIVHDALDYGDCRLSLAIPKYGIFE-NINSLRELAQ 201 (349)
Q Consensus 125 p~vev~~v--R~~DIP~yV~~G~aDlGIvG~DvL~E~~~~~~~lv~~l~dLgfG~CRLvvAvP~~~~~~-dv~sl~dL~~ 201 (349)
|++++.+. ...++-..|.+|.+|+||+-.+.- ... ..++. .-.++..+++++++...... .-.+++||.+
T Consensus 27 P~v~l~i~~~~~~~~~~~L~~~~~D~~i~~~~~~--~~~-~~~~~----~~~l~~~~~~~~~~~~~~~~~~~~~~~dL~~ 99 (204)
T cd08429 27 EPIRLVCREGKLEQLLADLALHRLDMVLADRPMP--SSL-DVKGY----SHRLGECGVSFFAAPPLAKRLEKPFPASLDE 99 (204)
T ss_pred CCcEEEEEeCCHHHHHHHHHcCCccEEEecCCCc--ccc-chhee----eccccccceEEEecCCcccccccCCHhHhcc
Confidence 44444443 556888999999999999744311 100 01111 12345666666665443221 1236677765
Q ss_pred CCccCCCCCcEEEcCCCccHHHHHHhcCCceEEEEecCCccccc
Q 018854 202 MPQWTAEKPLRVATGFTYLGPKFMKDNGLKHVVFSTADGALEAA 245 (349)
Q Consensus 202 ~~~~~~~~~lRVATkYPnlar~yf~~~Gi~~v~Ii~l~GSvElA 245 (349)
.+--.. .-.+.+-....+||++.|+. .+++.-..+.|..
T Consensus 100 ~~~i~~----~~~~~~~~~~~~~~~~~g~~-~~~~~~~~~~~~~ 138 (204)
T cd08429 100 APLLLP----GEDSALRRKLLQWFERQGLR-PQIVGEFDDSALM 138 (204)
T ss_pred CCeeec----CCCCcHHHHHHHHHHHcCCC-cceEEEeCCHHHH
Confidence 321000 00123335577889999975 3444445666655
No 66
>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=71.47 E-value=9.3 Score=31.32 Aligned_cols=102 Identities=19% Similarity=0.211 Sum_probs=55.4
Q ss_pred CCeEEEee--cCCchhhhcccCceeeeeeccceecccCCCCccceeecCCCCcccEEEEEEEeCCCccC--cccchHHhh
Q 018854 125 SNLEVWFQ--RPKDIVRKLLSGDLDLGIVGLDTVSEFGQGNEDLIIVHDALDYGDCRLSLAIPKYGIFE--NINSLRELA 200 (349)
Q Consensus 125 p~vev~~v--R~~DIP~yV~~G~aDlGIvG~DvL~E~~~~~~~lv~~l~dLgfG~CRLvvAvP~~~~~~--dv~sl~dL~ 200 (349)
|++++.+. ...++...+..|.+|+||+....- + .++. -..++..+++++++.+.... ..-+++||.
T Consensus 27 P~i~i~i~~~~~~~~~~~l~~~~~Dl~i~~~~~~-~-----~~l~----~~~l~~~~~~~v~~~~~~l~~~~~~~~~~l~ 96 (195)
T cd08434 27 PNVTFELHQGSTDELLDDLKNGELDLALCSPVPD-E-----PDIE----WIPLFTEELVLVVPKDHPLAGRDSVDLAELA 96 (195)
T ss_pred CCeEEEEecCcHHHHHHHHHcCCccEEEEccCCC-C-----CCee----EEEeecceEEEEecCCCccccCCccCHHHhc
Confidence 55555444 356678899999999999864321 1 1221 13356778888887763221 123667776
Q ss_pred cCCccCCCCCcEEEcC----CCccHHHHHHhcCCceEEEEecCCccccc
Q 018854 201 QMPQWTAEKPLRVATG----FTYLGPKFMKDNGLKHVVFSTADGALEAA 245 (349)
Q Consensus 201 ~~~~~~~~~~lRVATk----YPnlar~yf~~~Gi~~v~Ii~l~GSvElA 245 (349)
..+ -|... +....++++.+.|+. .++..-.++.+.+
T Consensus 97 ~~~--------~i~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~ 136 (195)
T cd08434 97 DEP--------FVLLSPGFGLRPIVDELCAAAGFT-PKIAFEGEEDSTI 136 (195)
T ss_pred CCc--------eEEecCCccHHHHHHHHHHHcCCc-cceEEEEccHHHH
Confidence 421 12211 223446788887764 3433223444433
No 67
>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=71.23 E-value=11 Score=31.38 Aligned_cols=107 Identities=13% Similarity=0.141 Sum_probs=56.9
Q ss_pred CCCeEEEee--cCCchhhhcccCceeeeeeccceecccCCCCccceeecCCCCcccEEEEEEEeCCCccC--cccchHHh
Q 018854 124 LSNLEVWFQ--RPKDIVRKLLSGDLDLGIVGLDTVSEFGQGNEDLIIVHDALDYGDCRLSLAIPKYGIFE--NINSLREL 199 (349)
Q Consensus 124 ~p~vev~~v--R~~DIP~yV~~G~aDlGIvG~DvL~E~~~~~~~lv~~l~dLgfG~CRLvvAvP~~~~~~--dv~sl~dL 199 (349)
.|++++.+. ...++...+.+|.+|+||+....-. .++. . -.++.-+++++++.+..+. +.-+++||
T Consensus 26 ~P~i~l~i~~~~~~~~~~~l~~~~~D~~i~~~~~~~------~~~~-~---~~l~~~~~~~v~~~~hpl~~~~~~~~~~l 95 (199)
T cd08426 26 YPGVFFTVDVASTADVLEAVLSGEADIGLAFSPPPE------PGIR-V---HSRQPAPIGAVVPPGHPLARQPSVTLAQL 95 (199)
T ss_pred CCCeEEEEEeCCcHHHHHHHHCCCccEEEecCCCCC------CCeE-E---EeeccCcEEEEecCCCCcccCCccCHHHH
Confidence 355555554 4578999999999999997543211 1221 1 2345667788887764222 22346777
Q ss_pred hcCCccCCCCCcEEEcCCCccHHHHHHhcCCceEEEEecCCccccc
Q 018854 200 AQMPQWTAEKPLRVATGFTYLGPKFMKDNGLKHVVFSTADGALEAA 245 (349)
Q Consensus 200 ~~~~~~~~~~~lRVATkYPnlar~yf~~~Gi~~v~Ii~l~GSvElA 245 (349)
.+.+.... .-.+.+.....+++.+.|+. ..+..-..+.+.+
T Consensus 96 ~~~~~i~~----~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~ 136 (199)
T cd08426 96 AGYPLALP----PPSFSLRQILDAAFARAGVQ-LEPVLISNSIETL 136 (199)
T ss_pred hCCCeEec----CCcchHHHHHHHHHHHcCCC-cceEEecCCHHHH
Confidence 64211000 00112234556788888875 3433324444443
No 68
>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=70.39 E-value=21 Score=30.09 Aligned_cols=104 Identities=10% Similarity=-0.021 Sum_probs=55.9
Q ss_pred CCeEEEee-cCCchhhhcccCceeeeeeccceecccCCCCccceeecCCCCcccEEEEEEEeCCCccC-cccchHHhhcC
Q 018854 125 SNLEVWFQ-RPKDIVRKLLSGDLDLGIVGLDTVSEFGQGNEDLIIVHDALDYGDCRLSLAIPKYGIFE-NINSLRELAQM 202 (349)
Q Consensus 125 p~vev~~v-R~~DIP~yV~~G~aDlGIvG~DvL~E~~~~~~~lv~~l~dLgfG~CRLvvAvP~~~~~~-dv~sl~dL~~~ 202 (349)
|++++-+. ...|+-..|.+|.+|+||+..... +. ++. --.++.-+++++++.+..+. ..-+++||.+.
T Consensus 27 P~i~l~i~~~~~~~~~~l~~g~~D~~i~~~~~~-~~-----~~~----~~~l~~~~~~~v~~~~hpl~~~~~~~~~l~~~ 96 (200)
T cd08462 27 PGVRFELLPPDDQPHELLERGEVDLLIAPERFM-SD-----GHP----SEPLFEEEFVCVVWADNPLVGGELTAEQYFSA 96 (200)
T ss_pred CCCEEEEecCChhHHHHHhcCCeeEEEecCCCC-CC-----Cce----eeeeeccceEEEEcCCCCccCCCCCHHHHhhC
Confidence 44544444 234999999999999999854321 11 111 12455677788877764321 22356777642
Q ss_pred CccCCCCCcEEEc--CC-CccHHHHHHhcCCceEEEEecCCccccc
Q 018854 203 PQWTAEKPLRVAT--GF-TYLGPKFMKDNGLKHVVFSTADGALEAA 245 (349)
Q Consensus 203 ~~~~~~~~lRVAT--kY-Pnlar~yf~~~Gi~~v~Ii~l~GSvElA 245 (349)
+ .+.+.. .+ ..+.+.|+++.|+. .++.--..+++..
T Consensus 97 ~------~i~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~ 135 (200)
T cd08462 97 G------HVVVRFGRNRRPSFEDWFLNEYGLK-RRVEVVTPSFSSI 135 (200)
T ss_pred C------CEEEecCCCCCccHHHHHHHHcCCc-ceEEEEeChHHHH
Confidence 1 111111 11 23445667888875 4544334555443
No 69
>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=70.11 E-value=22 Score=29.17 Aligned_cols=104 Identities=20% Similarity=0.252 Sum_probs=57.5
Q ss_pred CCeEEEee--cCCchhhhcccCceeeeeeccceecccCCCCccceeecCCCCcccEEEEEEEeCCCccC--cccchHHhh
Q 018854 125 SNLEVWFQ--RPKDIVRKLLSGDLDLGIVGLDTVSEFGQGNEDLIIVHDALDYGDCRLSLAIPKYGIFE--NINSLRELA 200 (349)
Q Consensus 125 p~vev~~v--R~~DIP~yV~~G~aDlGIvG~DvL~E~~~~~~~lv~~l~dLgfG~CRLvvAvP~~~~~~--dv~sl~dL~ 200 (349)
|++++-+. ...++-..+.+|.+|+||+.... .. .++. --.+++.+++++++.+..+. ..-+++||.
T Consensus 27 p~v~i~i~~~~~~~~~~~L~~~~~Dl~i~~~~~-~~-----~~~~----~~~l~~~~~~~v~~~~~~l~~~~~~~~~~l~ 96 (197)
T cd08438 27 PNIELELVEYGGKKVEQAVLNGELDVGITVLPV-DE-----EEFD----SQPLCNEPLVAVLPRGHPLAGRKTVSLADLA 96 (197)
T ss_pred cCeEEEEEEcCcHHHHHHHHcCCCCEEEEeccc-cc-----CCce----eEEeccccEEEEecCCCChhhccccCHHHHc
Confidence 45555544 45678899999999999986432 11 1222 12356788888888774322 233567776
Q ss_pred cCCccCCCCCcEEEcCC--CccHHHHHHhcCCceEEEEecCCccccc
Q 018854 201 QMPQWTAEKPLRVATGF--TYLGPKFMKDNGLKHVVFSTADGALEAA 245 (349)
Q Consensus 201 ~~~~~~~~~~lRVATkY--Pnlar~yf~~~Gi~~v~Ii~l~GSvElA 245 (349)
..+ -+.....+ -....+++++.|+. .++..-..+.+++
T Consensus 97 ~~~------~i~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~ 136 (197)
T cd08438 97 DEP------FILFNEDFALHDRIIDACQQAGFT-PNIAARSSQWDFI 136 (197)
T ss_pred CCC------eEEECCCccHHHHHHHHHHHcCCC-CCEEEeeCCHHHH
Confidence 421 11222222 12334677777875 3444434555543
No 70
>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=69.56 E-value=10 Score=31.36 Aligned_cols=102 Identities=12% Similarity=0.116 Sum_probs=53.0
Q ss_pred CCeEEEee--cCCchhhhcccCceeeeeeccceecccCCCCccceeecCCCCcccEEEEEEEeCCCccC--cccchHHhh
Q 018854 125 SNLEVWFQ--RPKDIVRKLLSGDLDLGIVGLDTVSEFGQGNEDLIIVHDALDYGDCRLSLAIPKYGIFE--NINSLRELA 200 (349)
Q Consensus 125 p~vev~~v--R~~DIP~yV~~G~aDlGIvG~DvL~E~~~~~~~lv~~l~dLgfG~CRLvvAvP~~~~~~--dv~sl~dL~ 200 (349)
|++++.+. ...++-..+.+|.+|+||+..... + .++. -..++.-+++++++.+..+. +.-+++||.
T Consensus 27 P~i~~~i~~~~~~~~~~~l~~g~~Dl~i~~~~~~-~-----~~~~----~~~l~~~~~~~~~~~~~~l~~~~~~~~~~l~ 96 (196)
T cd08456 27 PDVTISIHTRDSPTVEQWLSAQQCDLGLVSTLHE-P-----PGIE----RERLLRIDGVCVLPPGHRLAVKKVLTPSDLE 96 (196)
T ss_pred CCcEEEEEeCCHHHHHHHHHcCCccEEEEecCCC-C-----CCee----EEEeeccCeEEEecCCCchhccCccCHHHcC
Confidence 34444443 445677889999999999854321 1 1222 12345667777777653222 223567766
Q ss_pred cCCccCCCCCcEEE--cCCCccHHHHHHhcCCceEEEEecCCccc
Q 018854 201 QMPQWTAEKPLRVA--TGFTYLGPKFMKDNGLKHVVFSTADGALE 243 (349)
Q Consensus 201 ~~~~~~~~~~lRVA--TkYPnlar~yf~~~Gi~~v~Ii~l~GSvE 243 (349)
..+ + +... +.+.....++|.+.|++ .++..-..+.+
T Consensus 97 ~~~-~-----i~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~ 134 (196)
T cd08456 97 GEP-F-----ISLARTDGTRQRVDALFEQAGVK-RRIVVETSYAA 134 (196)
T ss_pred CCc-E-----EEecCCcchHHHHHHHHHHCCCC-cceEEEEccHH
Confidence 421 0 1111 12333456778888864 34433234443
No 71
>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=68.97 E-value=21 Score=30.24 Aligned_cols=151 Identities=13% Similarity=0.086 Sum_probs=75.8
Q ss_pred CCCeEEEee--cCCchhhhcccCceeeeeeccceecccCCCCccceeecCCCCcccEEEEEEEeCCCcc-CcccchHHhh
Q 018854 124 LSNLEVWFQ--RPKDIVRKLLSGDLDLGIVGLDTVSEFGQGNEDLIIVHDALDYGDCRLSLAIPKYGIF-ENINSLRELA 200 (349)
Q Consensus 124 ~p~vev~~v--R~~DIP~yV~~G~aDlGIvG~DvL~E~~~~~~~lv~~l~dLgfG~CRLvvAvP~~~~~-~dv~sl~dL~ 200 (349)
.|++++-+. ...++-..+.+|.+|+||+-.+.. + .++. . ..++.-+++++++.+... .+--+++||.
T Consensus 26 ~P~i~l~i~~~~~~~~~~~L~~g~~Dl~i~~~~~~-~-----~~~~-~---~~l~~~~~~lv~~~~h~~~~~~i~~~~l~ 95 (200)
T cd08465 26 APGIDLAVSQASREAMLAQVADGEIDLALGVFPEL-P-----EELH-A---ETLFEERFVCLADRATLPASGGLSLDAWL 95 (200)
T ss_pred CCCcEEEEecCChHhHHHHHHCCCccEEEeccccC-C-----cCee-E---EEeeeccEEEEEeCCCCccCCCcCHHHHh
Confidence 355555443 568999999999999999743321 1 1222 1 223344567777666311 1123567776
Q ss_pred cCCccCCCCCcEEE--cCCCccHHHHHHhcCCceEEEEecCCccccccCCCcc-eeeeecccchhh--HhhCCcEEec-C
Q 018854 201 QMPQWTAEKPLRVA--TGFTYLGPKFMKDNGLKHVVFSTADGALEAAPAMGIA-DAILDLVSSGTT--LRENNLKEIE-G 274 (349)
Q Consensus 201 ~~~~~~~~~~lRVA--TkYPnlar~yf~~~Gi~~v~Ii~l~GSvElAP~lGlA-D~IVDIVsTGtT--LraNgLk~ie-~ 274 (349)
+.+. .... +.+-....++|++.|+. .++.--.++.+..-.+=.+ ++++=++..... .+..+|+++. +
T Consensus 96 ~~~~------i~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~~l~~~~~~ 168 (200)
T cd08465 96 ARPH------VLVAMRGDAANEIDRALAARGLR-RRVALTLPHWGVAPELIAGTDLILTVARRALDALRLDERLAVFAPP 168 (200)
T ss_pred hCCc------EEEecCCCcCChHHHHHHHcCCc-eEEEEEcCcHHHHHHHHHcCChhhHhHHHHHHHhcccCCceEeCCC
Confidence 5311 1111 12335677889999986 4554434555544221111 333222222111 1234576664 1
Q ss_pred ceEEEEEEEEEeecchh
Q 018854 275 GVVLESQAVLVASRKSL 291 (349)
Q Consensus 275 g~IleSsA~LIaN~~s~ 291 (349)
+......-.++.++...
T Consensus 169 ~~~~~~~~~l~~~~~~~ 185 (200)
T cd08465 169 FPIPPFAFQQIWHQRRE 185 (200)
T ss_pred CCCCCceEEeeeccccc
Confidence 12334566666666554
No 72
>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=68.77 E-value=16 Score=30.10 Aligned_cols=105 Identities=20% Similarity=0.212 Sum_probs=56.2
Q ss_pred CCeEEEee--cCCchhhhcccCceeeeeeccce-ecccCCCCccceeecCCCCcccEEEEEEEeCCCccCc--ccchHHh
Q 018854 125 SNLEVWFQ--RPKDIVRKLLSGDLDLGIVGLDT-VSEFGQGNEDLIIVHDALDYGDCRLSLAIPKYGIFEN--INSLREL 199 (349)
Q Consensus 125 p~vev~~v--R~~DIP~yV~~G~aDlGIvG~Dv-L~E~~~~~~~lv~~l~dLgfG~CRLvvAvP~~~~~~d--v~sl~dL 199 (349)
|++++.+. ...++...+.+|.+|+||+.... ..+.. ..++. -..+++.+++++++.+..+.. .-+++||
T Consensus 27 P~i~i~~~~~~~~~~~~~l~~~~~Dl~i~~~~~~~~~~~--~~~~~----~~~l~~~~~~~~~~~~~p~~~~~~~~~~~l 100 (200)
T cd08423 27 PGLEVRLREAEPPESLDALRAGELDLAVVFDYPVTPPPD--DPGLT----RVPLLDDPLDLVLPADHPLAGREEVALADL 100 (200)
T ss_pred CCCeEEEEeCCHHHHHHHHhcCCccEEEEeccccccCCC--CCCcE----EEEeccCcEEEEecCCCCccccCCCCHHHh
Confidence 44555544 34688999999999999985421 00000 02222 123567888888877643221 3466777
Q ss_pred hcCCccCCCCCcEEEcCCC----ccHHHHHHhcCCceEEEEecCCcccc
Q 018854 200 AQMPQWTAEKPLRVATGFT----YLGPKFMKDNGLKHVVFSTADGALEA 244 (349)
Q Consensus 200 ~~~~~~~~~~~lRVATkYP----nlar~yf~~~Gi~~v~Ii~l~GSvEl 244 (349)
.+.+ -|..... ....+++++.|+. .++..-..+.+.
T Consensus 101 ~~~~--------~i~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~ 140 (200)
T cd08423 101 ADEP--------WIAGCPGSPCHRWLVRACRAAGFT-PRIAHEADDYAT 140 (200)
T ss_pred cCCc--------eEEecCCchHHHHHHHHHHHcCCC-CCeeeeeccHHH
Confidence 6431 2222222 2334567777764 343333444443
No 73
>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=68.34 E-value=21 Score=29.63 Aligned_cols=103 Identities=18% Similarity=0.164 Sum_probs=57.0
Q ss_pred CCCeEEEee--cCCchhhhcccCceeeeeeccceecccCCCCccceeecCCCCcccEEEEEEEeCCCccC--cccchHHh
Q 018854 124 LSNLEVWFQ--RPKDIVRKLLSGDLDLGIVGLDTVSEFGQGNEDLIIVHDALDYGDCRLSLAIPKYGIFE--NINSLREL 199 (349)
Q Consensus 124 ~p~vev~~v--R~~DIP~yV~~G~aDlGIvG~DvL~E~~~~~~~lv~~l~dLgfG~CRLvvAvP~~~~~~--dv~sl~dL 199 (349)
.|++++-+. ...++...+.+|.+|+||+....- . .++. -..++..+++++++.+.... ..-+++||
T Consensus 26 ~P~i~i~~~~~~~~~~~~~l~~~~~D~~i~~~~~~---~---~~~~----~~~l~~~~~~~~~~~~~~~~~~~~~~~~~l 95 (198)
T cd08433 26 YPGIRLRIVEGLSGHLLEWLLNGRLDLALLYGPPP---I---PGLS----TEPLLEEDLFLVGPADAPLPRGAPVPLAEL 95 (198)
T ss_pred CCCcEEEEEecCcHHHHHHHhCCCCcEEEEeCCCC---C---CCee----EEEeccccEEEEecCCCccccCCCCCHHHh
Confidence 355555543 456888999999999999853211 1 1222 23456778888887764221 22356777
Q ss_pred hcCCccCCCCCcEEEcC---CCccHHHHHHhcCCceEEEEecCCcccc
Q 018854 200 AQMPQWTAEKPLRVATG---FTYLGPKFMKDNGLKHVVFSTADGALEA 244 (349)
Q Consensus 200 ~~~~~~~~~~~lRVATk---YPnlar~yf~~~Gi~~v~Ii~l~GSvEl 244 (349)
.+.+ .-+-+. +.....+||++.|+. .++..-.++.++
T Consensus 96 ~~~~-------~i~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~ 135 (198)
T cd08433 96 ARLP-------LILPSRGHGLRRLVDEAAARAGLT-LNVVVEIDSVAT 135 (198)
T ss_pred CCCc-------eEEcCCCCcHHHHHHHHHHHcCCC-ceeEEEeCcHHH
Confidence 6531 111111 223456778888875 333332344443
No 74
>PRK09861 cytoplasmic membrane lipoprotein-28; Provisional
Probab=67.12 E-value=39 Score=32.78 Aligned_cols=150 Identities=17% Similarity=0.261 Sum_probs=81.5
Q ss_pred hhcccCceeeeeeccceecccCCCCccceeecCCCCcccEEEEEEEeCCCccCcccchHHhhcCCccCCCCCcEEEcCC-
Q 018854 139 RKLLSGDLDLGIVGLDTVSEFGQGNEDLIIVHDALDYGDCRLSLAIPKYGIFENINSLRELAQMPQWTAEKPLRVATGF- 217 (349)
Q Consensus 139 ~yV~~G~aDlGIvG~DvL~E~~~~~~~lv~~l~dLgfG~CRLvvAvP~~~~~~dv~sl~dL~~~~~~~~~~~lRVATkY- 217 (349)
.-++.|.+|+++.+.--.++.-.. + ....+-.+.-.+++|.+..-..++|++||.+ +.+||---
T Consensus 75 ~AL~~G~ID~n~~qh~~yl~~~~~--~-----~g~~lv~~~~~~~~P~~~Ys~~iksl~DL~~--------Ga~IAipnd 139 (272)
T PRK09861 75 DATNHGELDANVFQHRPFLEQDNQ--A-----HGYKLVAVGNTFVFPMAGYSKKIKTVAQIKE--------GATVAIPND 139 (272)
T ss_pred HHHHcCCcceehhhhHHHHHHHHH--h-----cCCCeEEEeEEEEEeeeccccCCCCHHHcCC--------CCEEEEeCC
Confidence 679999999999754444443211 0 0223333445777887532245999999884 36888543
Q ss_pred -CccHHHHH--HhcC---------C-----------ceEEEEecCCccccccCCCcceeeeeccc-chhhHhhCCcEEec
Q 018854 218 -TYLGPKFM--KDNG---------L-----------KHVVFSTADGALEAAPAMGIADAILDLVS-SGTTLRENNLKEIE 273 (349)
Q Consensus 218 -Pnlar~yf--~~~G---------i-----------~~v~Ii~l~GSvElAP~lGlAD~IVDIVs-TGtTLraNgLk~ie 273 (349)
-|.+|.++ ++.| . ++++++.+.-+- +.- -+.|.=||..- .|+=..+.||+.+.
T Consensus 140 ~~n~~ral~lL~~agli~l~~~~g~~~t~~di~~np~~l~~ve~~~~q-~~~--al~dg~vD~a~i~~~~~~~ag~~~~~ 216 (272)
T PRK09861 140 PTNLGRALLLLQKEKLITLKEGKGLLPTALDITDNPRHLQIMELEGAQ-LPR--VLDDPKVDVAIISTTYIQQTGLSPVH 216 (272)
T ss_pred CccHHHHHHHHHHCCCEEEcCCCCCCCCHhHHhcCCCCCEEEEcCHHH-hHh--hccCcccCEEEEchhHHHHcCCCccc
Confidence 45566544 3444 1 235555543322 111 13332233333 45555578998876
Q ss_pred CceEEE----EEEEEEeecchhhhhcCchhHHHHHHHHHHH
Q 018854 274 GGVVLE----SQAVLVASRKSLIRRKGVLDATHEILERLEA 310 (349)
Q Consensus 274 ~g~Ile----SsA~LIaN~~s~~~k~~~~~~i~~li~rl~~ 310 (349)
++..++ ..+.+|+-+..-+ ..+.+++|+++++.
T Consensus 217 ~~l~~e~~~~~~~n~~~~r~~~~----~~~~~~~lv~~~~s 253 (272)
T PRK09861 217 DSVFIEDKNSPYVNILVAREDNK----NAENVKEFLQSYQS 253 (272)
T ss_pred ceeEEcCCCCCeEEEEEEcCCcc----CCHHHHHHHHHHcC
Confidence 544444 2445555443221 23578888887763
No 75
>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=67.08 E-value=14 Score=35.31 Aligned_cols=101 Identities=16% Similarity=0.176 Sum_probs=65.2
Q ss_pred CceEEEecCCCCchHHHHHHHHHCCC-ccCCCCC----CceEEecCCCCCeEEEeecCCchhhhcccCceeeeeecccee
Q 018854 82 DEIRLGLPSKGRMAADTLDLLKDCQL-SVKQVNP----RQYVAQIPQLSNLEVWFQRPKDIVRKLLSGDLDLGIVGLDTV 156 (349)
Q Consensus 82 ~~LrIALP~KGRL~e~t~~LL~~aGi-~~~~~~~----R~L~~~~~~~p~vev~~vR~~DIP~yV~~G~aDlGIvG~DvL 156 (349)
+--+||||+.-.=+.-.+.+|+++|+ +++...+ =.-+... -.+++|.-+.+..+|+.+.+ +|++++.-+..
T Consensus 96 ~Ga~VaIpnD~sN~~RaL~lLq~aGLI~Lk~~~~~~~t~~DI~~N--pk~l~~~evd~~~l~~~l~d--vD~avi~~~~a 171 (237)
T PF03180_consen 96 DGATVAIPNDPSNQARALKLLQEAGLITLKDGVGLTATVDDITEN--PKNLKFKEVDAAQLPRALDD--VDAAVINGNYA 171 (237)
T ss_dssp TTEEEEEESSHHHHHHHHHHHHHTTSEEE-TT-GCC-SGGGEEEE--TTSEEEEEE-GGGHHHHTTT--SSEEEE-HHHH
T ss_pred CCCEEEEeCCccchhHHHHHHHhCCeEEEcCCCCCccChhhhhhc--ccCceEEEecHhhHHhhccc--CCEEEecHhHH
Confidence 34789999888888899999999998 3332111 1223332 34799999999999999988 99999999999
Q ss_pred cccCCCCcc-ceeecCCCCcccEEEEEEEeCC
Q 018854 157 SEFGQGNED-LIIVHDALDYGDCRLSLAIPKY 187 (349)
Q Consensus 157 ~E~~~~~~~-lv~~l~dLgfG~CRLvvAvP~~ 187 (349)
.+.|.+..+ ++ ..++..-..--.++++.++
T Consensus 172 ~~agl~~~~~~~-~~e~~~~~~y~n~lv~r~~ 202 (237)
T PF03180_consen 172 LDAGLDPKKDLL-FEEPDADKPYANVLVVRED 202 (237)
T ss_dssp HHTT--CCCHSS-EE-SSSSCGGEEEEEEEGG
T ss_pred HHcCcCccccee-eeecccCcceeEEEEEECC
Confidence 998866433 22 1121223444456666553
No 76
>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=67.07 E-value=11 Score=31.05 Aligned_cols=103 Identities=20% Similarity=0.192 Sum_probs=54.8
Q ss_pred CCeEEEee--cCCchhhhcccCceeeeeeccceecccCCCCccceeecCCCCcccEEEEEEEeCCCccCc--ccchHHhh
Q 018854 125 SNLEVWFQ--RPKDIVRKLLSGDLDLGIVGLDTVSEFGQGNEDLIIVHDALDYGDCRLSLAIPKYGIFEN--INSLRELA 200 (349)
Q Consensus 125 p~vev~~v--R~~DIP~yV~~G~aDlGIvG~DvL~E~~~~~~~lv~~l~dLgfG~CRLvvAvP~~~~~~d--v~sl~dL~ 200 (349)
|++++.+. ...++...+..|.+|+||+.... .. .++. --.++..+++++++.+..+.. .-+++||.
T Consensus 27 P~i~i~i~~~~~~~~~~~l~~~~~Di~i~~~~~---~~---~~~~----~~~l~~~~~~~~~~~~hpl~~~~~~~~~~L~ 96 (197)
T cd08448 27 PGIEVALHEMSSAEQIEALLRGELDLGFVHSRR---LP---AGLS----ARLLHREPFVCCLPAGHPLAARRRIDLRELA 96 (197)
T ss_pred CCCeEEEEeCCHHHHHHHHHcCCcceEEEeCCC---CC---cCce----EEEEecCcEEEEeeCCCCCcCCCCcCHHHhC
Confidence 44554443 57789999999999999974321 11 1221 123456667777777642221 23567776
Q ss_pred cCCccCCCCCcEEE----cCCCccHHHHHHhcCCceEEEEecCCcccc
Q 018854 201 QMPQWTAEKPLRVA----TGFTYLGPKFMKDNGLKHVVFSTADGALEA 244 (349)
Q Consensus 201 ~~~~~~~~~~lRVA----TkYPnlar~yf~~~Gi~~v~Ii~l~GSvEl 244 (349)
..+. +... +.+.+....+|++.|+. .++..-..+.+.
T Consensus 97 ~~~~------i~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~ 137 (197)
T cd08448 97 GEPF------VLFSREVSPDYYDQIIALCMDAGFH-PKIRHEVRHWLT 137 (197)
T ss_pred CCcE------EeeCcccChHHHHHHHHHHHHcCCc-eeeeeccccHHH
Confidence 4211 1111 11223444677788875 344333344443
No 77
>PRK11062 nhaR transcriptional activator NhaR; Provisional
Probab=66.27 E-value=38 Score=31.88 Aligned_cols=149 Identities=11% Similarity=0.092 Sum_probs=76.2
Q ss_pred CCeEEEee--cCCchhhhcccCceeeeeeccceecccCCCCccceeecCCCCcccEEEEEEEeCCCccCcccchHHhhcC
Q 018854 125 SNLEVWFQ--RPKDIVRKLLSGDLDLGIVGLDTVSEFGQGNEDLIIVHDALDYGDCRLSLAIPKYGIFENINSLRELAQM 202 (349)
Q Consensus 125 p~vev~~v--R~~DIP~yV~~G~aDlGIvG~DvL~E~~~~~~~lv~~l~dLgfG~CRLvvAvP~~~~~~dv~sl~dL~~~ 202 (349)
|++++.+. -..++...+.+|.+|+||+.... +. ....++ ....++.+++++.++.+. .....+++|.+.
T Consensus 120 P~i~l~~~~~~~~~~~~~l~~g~~D~~i~~~~~--~~-~~~~~l----~~~~l~~~~~~~~~~~~~--~~~~~~~~l~~~ 190 (296)
T PRK11062 120 ESIHLRCFESTHEMLLEQLSQHKLDMILSDCPV--DS-TQQEGL----FSKKLGECGVSFFCTNPL--PEKPFPACLEER 190 (296)
T ss_pred CceEEEEEeCCHHHHHHHHHcCCCCEEEecCCC--cc-ccccch----hhhhhhccCcceEecCCC--ccccChHHHhcC
Confidence 55555443 34678899999999999974321 10 011122 235667888877776552 222356776642
Q ss_pred CccCCCCCcEEEcC----CCccHHHHHHhcCCceEEEEecCCccccccCCCcce---eeeecccchhhHhhCCcEEecCc
Q 018854 203 PQWTAEKPLRVATG----FTYLGPKFMKDNGLKHVVFSTADGALEAAPAMGIAD---AILDLVSSGTTLRENNLKEIEGG 275 (349)
Q Consensus 203 ~~~~~~~~lRVATk----YPnlar~yf~~~Gi~~v~Ii~l~GSvElAP~lGlAD---~IVDIVsTGtTLraNgLk~ie~g 275 (349)
.-|... +.+...+||.+.|+. .++..-..+.+....+-.+. +++.-..--..++..+|+.+...
T Consensus 191 --------~~i~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~v~~g~Gi~~lp~~~~~~~~~~~~l~~l~~~ 261 (296)
T PRK11062 191 --------RLLIPGRRTMLGRKLLNWFNSQGLN-VEILGEFDDAALMKAFGAYHDAIFVAPSLYAQDFYADHSVVEIGRV 261 (296)
T ss_pred --------CeeecCCCchHHHHHHHHHHHcCCC-ceeeeeeCcHHHHHHHHHcCCceEECCHHHHHHHHHcCCeEEcCCc
Confidence 123222 234556788888874 34332234444332111111 12211111223455668888532
Q ss_pred eEEEEEEEEEeecchh
Q 018854 276 VVLESQAVLVASRKSL 291 (349)
Q Consensus 276 ~IleSsA~LIaN~~s~ 291 (349)
......-.|+.++...
T Consensus 262 ~~~~~~~~lv~~~~~~ 277 (296)
T PRK11062 262 DNVKEEYHVIFAERMI 277 (296)
T ss_pred cccceEEEEEEecCCC
Confidence 3345566677766543
No 78
>PRK10216 DNA-binding transcriptional regulator YidZ; Provisional
Probab=66.19 E-value=24 Score=33.69 Aligned_cols=113 Identities=12% Similarity=0.067 Sum_probs=58.1
Q ss_pred CCeEEEee-cCCchhhhcccCceeeeeeccceecccCCCCccceeecCCCCcccEEEEEEEeCCCccC-cccchHHhhcC
Q 018854 125 SNLEVWFQ-RPKDIVRKLLSGDLDLGIVGLDTVSEFGQGNEDLIIVHDALDYGDCRLSLAIPKYGIFE-NINSLRELAQM 202 (349)
Q Consensus 125 p~vev~~v-R~~DIP~yV~~G~aDlGIvG~DvL~E~~~~~~~lv~~l~dLgfG~CRLvvAvP~~~~~~-dv~sl~dL~~~ 202 (349)
|++++.+. ...|+...+.+|.+|+||++.....+........-..+.-..+...++++.+|.+..+. .--+++||.+.
T Consensus 124 P~v~v~i~~~~~~~~~~l~~g~~D~~i~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~v~~~~hp~~~~~~~~~dL~~~ 203 (319)
T PRK10216 124 PQATIKLRNWDYDSLDAITRGEVDIGFTGRESHPRSRELLSLLPLAIDFEVLFSDLPCVWLRKDHPALHEEWNLDTFLRY 203 (319)
T ss_pred CCCEEEEEeCCcchHHHHhcCCccEEEecCCCCccccccccccccccceeeeeecceEEEEeCCCCccCCCCCHHHHhhC
Confidence 44444433 23467899999999999986433221100000000001123455677788888764221 11246777653
Q ss_pred CccCCCCCcEE--EcCCCccHHHHHHhcCCceEEEEecCCcccc
Q 018854 203 PQWTAEKPLRV--ATGFTYLGPKFMKDNGLKHVVFSTADGALEA 244 (349)
Q Consensus 203 ~~~~~~~~lRV--ATkYPnlar~yf~~~Gi~~v~Ii~l~GSvEl 244 (349)
+ | +.. ...+.....++|.+.|+. ..+.--.++.+.
T Consensus 204 ~-~-----i~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~ 240 (319)
T PRK10216 204 P-H-----ISICWEQSDTWALDDVLQELGRE-RTIALSLPEFEQ 240 (319)
T ss_pred C-C-----eEecCCCCCcchHHHHHHHhCCc-cceEEECCcHHH
Confidence 1 1 111 123445668889898875 344333455554
No 79
>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=66.05 E-value=20 Score=29.72 Aligned_cols=104 Identities=21% Similarity=0.254 Sum_probs=55.3
Q ss_pred CCeEEEee--cCCchhhhcccCceeeeeeccceecccCCCCccceeecCCCCcccEEEEEEEeCCCccCc---ccchHHh
Q 018854 125 SNLEVWFQ--RPKDIVRKLLSGDLDLGIVGLDTVSEFGQGNEDLIIVHDALDYGDCRLSLAIPKYGIFEN---INSLREL 199 (349)
Q Consensus 125 p~vev~~v--R~~DIP~yV~~G~aDlGIvG~DvL~E~~~~~~~lv~~l~dLgfG~CRLvvAvP~~~~~~d---v~sl~dL 199 (349)
|++++.+. ...++-..|.+|.+|+||+-...-. .++. --.++..+++++++.+..+.. .-+++||
T Consensus 28 P~v~i~i~~~~~~~~~~~l~~g~~Dl~i~~~~~~~------~~~~----~~~l~~~~~~~v~~~~~pl~~~~~~~~~~dL 97 (197)
T cd08425 28 PGIALSLREMPQERIEAALADDRLDLGIAFAPVRS------PDID----AQPLFDERLALVVGATHPLAQRRTALTLDDL 97 (197)
T ss_pred CCcEEEEEECcHHHHHHHHHcCCccEEEEecCCCC------CCcE----EEEeccccEEEEecCCCchhHhcccCCHHHH
Confidence 55555444 4567888999999999997543211 1221 123566777777776632211 2456777
Q ss_pred hcCCccCCCCCcEEEcCC--CccHHHHHHhcCCceEEEEecCCccccc
Q 018854 200 AQMPQWTAEKPLRVATGF--TYLGPKFMKDNGLKHVVFSTADGALEAA 245 (349)
Q Consensus 200 ~~~~~~~~~~~lRVATkY--Pnlar~yf~~~Gi~~v~Ii~l~GSvElA 245 (349)
...+. +.....+ .+...++|++.|+. .++..-..+.+..
T Consensus 98 ~~~~~------i~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~ 138 (197)
T cd08425 98 AAEPL------ALLSPDFATRQHIDRYFQKQGIK-PRIAIEANSISAV 138 (197)
T ss_pred hcCCc------EecCCCccHHHHHHHHHHHcCCC-eeeEEeeCcHHHH
Confidence 64211 1111111 12346678888875 3443323444443
No 80
>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=66.05 E-value=18 Score=30.27 Aligned_cols=105 Identities=18% Similarity=0.177 Sum_probs=55.7
Q ss_pred CCCeEEEee--cCCchhhhcccCceeeeeeccceecccCCCCccceeecCCCCcccEEEEEEEeCCCccCc--ccchHHh
Q 018854 124 LSNLEVWFQ--RPKDIVRKLLSGDLDLGIVGLDTVSEFGQGNEDLIIVHDALDYGDCRLSLAIPKYGIFEN--INSLREL 199 (349)
Q Consensus 124 ~p~vev~~v--R~~DIP~yV~~G~aDlGIvG~DvL~E~~~~~~~lv~~l~dLgfG~CRLvvAvP~~~~~~d--v~sl~dL 199 (349)
.|++++-+. ...++...+..|.+|+||+-... + . .++.. -.++.-+++++++.+..+.. --+++||
T Consensus 26 ~P~i~l~~~~~~~~~~~~~l~~~~~Dl~i~~~~~--~-~---~~~~~----~~l~~~~~~~~~~~~~~l~~~~~~~~~~l 95 (196)
T cd08457 26 RPNLHLSLMGLSSSQVLEAVASGRADLGIADGPL--E-E---RQGFL----IETRSLPAVVAVPMGHPLAQLDVVSPQDL 95 (196)
T ss_pred CCCeEEEEEecCcHHHHHHHHcCCccEEEeccCC--C-C---CCcEE----EEeccCCeEEEeeCCCccccCCccCHHHh
Confidence 355555444 34688899999999999975331 1 1 12221 12356677788776532221 2356777
Q ss_pred hcCCccCCCCCcEEEcC--CCccHHHHHHhcCCceEEEEecCCccccc
Q 018854 200 AQMPQWTAEKPLRVATG--FTYLGPKFMKDNGLKHVVFSTADGALEAA 245 (349)
Q Consensus 200 ~~~~~~~~~~~lRVATk--YPnlar~yf~~~Gi~~v~Ii~l~GSvElA 245 (349)
.+.+- +..... +.....+++.+.|+. .++.-...+.+.+
T Consensus 96 ~~~~~------i~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~ 136 (196)
T cd08457 96 AGERI------ITLENGYLFRMRVEVALGKIGVK-RRPIIEVNLSHTA 136 (196)
T ss_pred CCCce------EecCCCccHHHHHHHHHHHcCCC-CceEEEeccHHHH
Confidence 65311 111111 223456778888875 2333334555544
No 81
>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=63.43 E-value=22 Score=29.96 Aligned_cols=93 Identities=19% Similarity=0.245 Sum_probs=50.8
Q ss_pred CCCeEEEee--cCCchhhhcccCceeeeeeccceecccCCCCccceeecCCCCcccEEEEEEEeCCCccC--cccchHHh
Q 018854 124 LSNLEVWFQ--RPKDIVRKLLSGDLDLGIVGLDTVSEFGQGNEDLIIVHDALDYGDCRLSLAIPKYGIFE--NINSLREL 199 (349)
Q Consensus 124 ~p~vev~~v--R~~DIP~yV~~G~aDlGIvG~DvL~E~~~~~~~lv~~l~dLgfG~CRLvvAvP~~~~~~--dv~sl~dL 199 (349)
.|++++.+. ...++-..+.+|.+|+||+....-.+. ++. ...+.+=+++++++.+..+. ..-+++||
T Consensus 26 ~P~i~v~~~~~~~~~~~~~l~~g~~D~~i~~~~~~~~~-----~~~----~~~l~~~~~~~v~~~~hpl~~~~~i~~~~l 96 (198)
T cd08413 26 YPKVKLSLHQGTPSQIAEMVLKGEADIAIATEALDDHP-----DLV----TLPCYRWNHCVIVPPGHPLADLGPLTLEDL 96 (198)
T ss_pred CCceEEEEEeCCHHHHHHHHHcCCCCEEEEccCCCCCC-----CcE----EEEeeeeeEEEEecCCCcccccCCCCHHHH
Confidence 355555554 346788999999999999754221111 121 12234557777777764322 22356777
Q ss_pred hcCCccCCCCCcEEEcC--CCccHHHHHHhcCCc
Q 018854 200 AQMPQWTAEKPLRVATG--FTYLGPKFMKDNGLK 231 (349)
Q Consensus 200 ~~~~~~~~~~~lRVATk--YPnlar~yf~~~Gi~ 231 (349)
....- +..... +....+++|++.|+.
T Consensus 97 ~~~~~------i~~~~~~~~~~~~~~~~~~~~~~ 124 (198)
T cd08413 97 AQYPL------ITYDFGFTGRSSIDRAFARAGLE 124 (198)
T ss_pred hcCCE------EECCCCccHHHHHHHHHHHcCCC
Confidence 65311 111111 123456778888874
No 82
>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=63.39 E-value=13 Score=34.77 Aligned_cols=91 Identities=15% Similarity=0.120 Sum_probs=52.6
Q ss_pred CCeEEE--eecCCchhhhcccCceeeeeeccceecccCCCCccceeecCCCCcccEEEEEEEeCCCccCcc--cchHHhh
Q 018854 125 SNLEVW--FQRPKDIVRKLLSGDLDLGIVGLDTVSEFGQGNEDLIIVHDALDYGDCRLSLAIPKYGIFENI--NSLRELA 200 (349)
Q Consensus 125 p~vev~--~vR~~DIP~yV~~G~aDlGIvG~DvL~E~~~~~~~lv~~l~dLgfG~CRLvvAvP~~~~~~dv--~sl~dL~ 200 (349)
|++++. .....|+...+..|.+|+||+..+.-.+ ..++. --.+|+.+++++++++.....- -+++||.
T Consensus 120 P~~~i~~~~~~~~~~~~~l~~g~~D~~i~~~~~~~~----~~~~~----~~~l~~~~~~~~~~~~hpl~~~~~i~~~dL~ 191 (300)
T TIGR02424 120 PRLRVRIMTGPNAYLLDQLRVGALDLVVGRLGAPET----MQGLS----FEHLYNEPVVFVVRAGHPLLAAPSLPVASLA 191 (300)
T ss_pred CCcEEEEEeCchHHHHHHHHCCCCCEEEEecCCccc----cccee----eeeecCCceEEEEcCCCccccCCCCCHHHHh
Confidence 444444 4466778899999999999964321111 01221 2356788889998877422211 1567776
Q ss_pred cCCccCCCCCcEEEcC----CCccHHHHHHhcCCc
Q 018854 201 QMPQWTAEKPLRVATG----FTYLGPKFMKDNGLK 231 (349)
Q Consensus 201 ~~~~~~~~~~lRVATk----YPnlar~yf~~~Gi~ 231 (349)
+.+ -|... +-+...+||.+.|+.
T Consensus 192 ~~~--------~i~~~~~~~~~~~~~~~~~~~~~~ 218 (300)
T TIGR02424 192 DYP--------VLLPPEGSAIRPLAERLFIACGIP 218 (300)
T ss_pred CCC--------EEecCCCCchHHHHHHHHHHCCCC
Confidence 531 12221 224456788888864
No 83
>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=62.79 E-value=18 Score=34.01 Aligned_cols=119 Identities=22% Similarity=0.183 Sum_probs=62.0
Q ss_pred CchhhhcccCceeeeeeccceecc--cCCCCccceeecCCCCcccE-EEEEEEeCCCccCcccchHHhhcCCccCCCCCc
Q 018854 135 KDIVRKLLSGDLDLGIVGLDTVSE--FGQGNEDLIIVHDALDYGDC-RLSLAIPKYGIFENINSLRELAQMPQWTAEKPL 211 (349)
Q Consensus 135 ~DIP~yV~~G~aDlGIvG~DvL~E--~~~~~~~lv~~l~dLgfG~C-RLvvAvP~~~~~~dv~sl~dL~~~~~~~~~~~l 211 (349)
.+.-..+..|.+|+++.+.-.... .+.....+.... ...++.+ ..++.++.+ .++++++||.+ +
T Consensus 70 ~~~~~al~~g~~D~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~y~~~lvv~~d---s~i~sl~DL~G---------k 136 (288)
T TIGR03431 70 AGVIEGMRFGKVDIAWYGPSSYAEAYQKANAEAFAIEV-NADGSTGYYSVLIVKKD---SPIKSLEDLKG---------K 136 (288)
T ss_pred HHHHHHHHcCCccEEEEChHHHHHHHHhcCCeEEEEec-cCCCCCceEEEEEEeCC---CCCCcHHHhCC---------C
Confidence 455667889999999977422211 221111111111 1222221 146677776 67889999864 5
Q ss_pred EEEcCCCc------cHHHHH-HhcCCce---EEEEecCCcccc---ccCCCcceeeeecccchhhHhh
Q 018854 212 RVATGFTY------LGPKFM-KDNGLKH---VVFSTADGALEA---APAMGIADAILDLVSSGTTLRE 266 (349)
Q Consensus 212 RVATkYPn------lar~yf-~~~Gi~~---v~Ii~l~GSvEl---AP~lGlAD~IVDIVsTGtTLra 266 (349)
|||.--|. +...++ ++.|+.. +..+...|+.+. +-.-|-+|+++.-..+-..+.+
T Consensus 137 ~v~~~~~~s~~~~~~~~~~l~~~~g~~~~~~~~~v~~~~~~~~~~~al~~G~vDa~~~~~~~~~~~~~ 204 (288)
T TIGR03431 137 TFGFVDPNSTSGFLVPSYYLFKKNGIKPKEYFKKVTFSGSHEAAILAVANGTVDAATTNDENLDRMIR 204 (288)
T ss_pred EEEeeCCCcchhhHHHHHHHHHhcCCChHHhHHhheecCchHHHHHHHHcCCCCeEeccHHHHHHHHH
Confidence 77753222 223334 5567531 123333444332 4567899988854444444544
No 84
>PF13379 NMT1_2: NMT1-like family; PDB: 2G29_A 3UN6_A 2I4C_A 2I49_A 2I4B_A 2I48_A 3QSL_A.
Probab=62.75 E-value=17 Score=33.57 Aligned_cols=61 Identities=20% Similarity=0.288 Sum_probs=47.0
Q ss_pred CceEEEecCCCCchHHHHH-HHHHCCCccCCCCCCceEEecCCCCCeEEEeecCCchhhhcccCceeeeeecccee
Q 018854 82 DEIRLGLPSKGRMAADTLD-LLKDCQLSVKQVNPRQYVAQIPQLSNLEVWFQRPKDIVRKLLSGDLDLGIVGLDTV 156 (349)
Q Consensus 82 ~~LrIALP~KGRL~e~t~~-LL~~aGi~~~~~~~R~L~~~~~~~p~vev~~vR~~DIP~yV~~G~aDlGIvG~DvL 156 (349)
.-.|||+|..|...+-.+. +|++.|++. ..++++..+.+.+++..+..|.+|...+..-+.
T Consensus 120 kGk~i~~~~~gs~~~~~l~~~l~~~Gl~~--------------~~dv~~~~~~~~~~~~al~~g~iDa~~~~eP~~ 181 (252)
T PF13379_consen 120 KGKKIAVPFPGSTHDMLLRYLLKKAGLDP--------------KDDVTLVNVPPPEMVAALRAGEIDAAVLWEPFA 181 (252)
T ss_dssp STEEEEESSTTSHHHHHHHHHHHHTT--T--------------TTSSEEEE--GHHHHHHHHTTS-SEEEEETTHH
T ss_pred CCcEEEEcCCCCHHHHHHHHHHHhCCCCc--------------ccceEEEecCHHHHHHHHhCCCcCEEEecCCHH
Confidence 5689999889999988775 899999963 124778888889999999999999999977774
No 85
>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=62.43 E-value=24 Score=29.13 Aligned_cols=89 Identities=13% Similarity=0.071 Sum_probs=48.3
Q ss_pred CCCeEEEeecCCchhhhcccCceeeeeeccceecccCCCCccceeecCCCCcccEEEEEEEeCCCc-cCcccchHHhhcC
Q 018854 124 LSNLEVWFQRPKDIVRKLLSGDLDLGIVGLDTVSEFGQGNEDLIIVHDALDYGDCRLSLAIPKYGI-FENINSLRELAQM 202 (349)
Q Consensus 124 ~p~vev~~vR~~DIP~yV~~G~aDlGIvG~DvL~E~~~~~~~lv~~l~dLgfG~CRLvvAvP~~~~-~~dv~sl~dL~~~ 202 (349)
.|++++-+.. .+....+..|.+|+||+....- + .++. ..-+++-+++++++.+.. -...-+++||.+.
T Consensus 26 ~P~i~l~~~~-~~~~~~l~~g~~Dl~i~~~~~~-~-----~~~~----~~~l~~~~~~~v~~~~~~~~~~~~~~~~L~~~ 94 (190)
T cd08483 26 HPEIELSLLP-SADLVDLRPDGIDVAIRYGNGD-W-----PGLE----SEPLTAAPFVVVAAPGLLGDRKVDSLADLAGL 94 (190)
T ss_pred CCCceEEEEe-cCCcCCCCCCCcCEEEEecCCC-C-----CCcE----EEeecccceEeeeCHHHHhhCCCCCHHHHhcC
Confidence 3555555543 4445789999999999853311 1 1121 122445666777766420 0123466777653
Q ss_pred CccCCCCCcEEEcCCCccHHHHHHhcCCc
Q 018854 203 PQWTAEKPLRVATGFTYLGPKFMKDNGLK 231 (349)
Q Consensus 203 ~~~~~~~~lRVATkYPnlar~yf~~~Gi~ 231 (349)
+ -|.........++|.+.|+.
T Consensus 95 ~--------~i~~~~~~~~~~~~~~~~~~ 115 (190)
T cd08483 95 P--------WLQERGTNEQRVWLASMGVV 115 (190)
T ss_pred c--------eeccCCchHHHHHHHHcCCC
Confidence 1 22233234456788888864
No 86
>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=61.76 E-value=27 Score=28.71 Aligned_cols=55 Identities=24% Similarity=0.245 Sum_probs=33.6
Q ss_pred CCeEEEee--cCCchhhhcccCceeeeeeccceecccCCCCccceeecCCCCcccEEEEEEEeCC
Q 018854 125 SNLEVWFQ--RPKDIVRKLLSGDLDLGIVGLDTVSEFGQGNEDLIIVHDALDYGDCRLSLAIPKY 187 (349)
Q Consensus 125 p~vev~~v--R~~DIP~yV~~G~aDlGIvG~DvL~E~~~~~~~lv~~l~dLgfG~CRLvvAvP~~ 187 (349)
|++++.+. ...++-..+.+|.+|+||+........ .++. --.++..+++++++++
T Consensus 27 P~i~l~~~~~~~~~~~~~l~~g~~Dl~i~~~~~~~~~----~~~~----~~~l~~~~~~~v~~~~ 83 (195)
T cd08427 27 PDLEVHIVPGLSAELLARVDAGELDAAIVVEPPFPLP----KDLV----WTPLVREPLVLIAPAE 83 (195)
T ss_pred CCceEEEEeCCcHHHHHHHHCCCCCEEEEcCCCCccc----cCce----EEEcccCcEEEEECCC
Confidence 45554443 456788899999999999864321101 1221 1224566778888776
No 87
>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=60.77 E-value=17 Score=30.94 Aligned_cols=103 Identities=14% Similarity=0.134 Sum_probs=58.2
Q ss_pred CCCeEEEee--cCCchhhhcccCceeeeeeccceecccCCCCccceeecCCCCcccEEEEEEEeCCCccC--cccchHHh
Q 018854 124 LSNLEVWFQ--RPKDIVRKLLSGDLDLGIVGLDTVSEFGQGNEDLIIVHDALDYGDCRLSLAIPKYGIFE--NINSLREL 199 (349)
Q Consensus 124 ~p~vev~~v--R~~DIP~yV~~G~aDlGIvG~DvL~E~~~~~~~lv~~l~dLgfG~CRLvvAvP~~~~~~--dv~sl~dL 199 (349)
+|++++-+. ...++...+..|.+|+||+..... + .++. -..+.+=++++++|++.... ..-+++||
T Consensus 27 ~P~v~i~i~~~~~~~l~~~l~~g~~D~~~~~~~~~-~-----~~~~----~~~l~~~~~~lv~~~~h~l~~~~~i~~~dL 96 (198)
T cd08486 27 TPTATVSLTHMTKDEQVEGLLAGTIHVGFSRFFPR-H-----PGIE----IVNIAQEDLYLAVHRSQSGKFGKTCKLADL 96 (198)
T ss_pred CCCeEEEEEECCHHHHHHHHHcCCceEEEecCCCC-C-----CceE----EEEEeeccEEEEecCCCccccCCcccHHHH
Confidence 355555544 567899999999999999754221 1 1111 12234557788888763211 12356777
Q ss_pred hcCCccCCCCCcEEE----cCCCccHHHHHHhcCCceEEEEecCCccc
Q 018854 200 AQMPQWTAEKPLRVA----TGFTYLGPKFMKDNGLKHVVFSTADGALE 243 (349)
Q Consensus 200 ~~~~~~~~~~~lRVA----TkYPnlar~yf~~~Gi~~v~Ii~l~GSvE 243 (349)
.+.+- +... ..|.+...++|++.|+. .++..-..+.+
T Consensus 97 ~~~~~------i~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~ 137 (198)
T cd08486 97 RAVEL------TLFPRGGRPSFADEVIGLFKHAGIE-PRIARVVEDAT 137 (198)
T ss_pred cCCCe------EeecCCcCchHHHHHHHHHHHcCCC-cceEEEeccHH
Confidence 65311 1111 12556788899999975 44433334444
No 88
>COG0725 ModA ABC-type molybdate transport system, periplasmic component [Inorganic ion transport and metabolism]
Probab=60.15 E-value=43 Score=32.30 Aligned_cols=88 Identities=17% Similarity=0.159 Sum_probs=48.8
Q ss_pred eEEEe--cCCCCchHHHHHHHHHCCCccCCCCCCceEEecCCCCCeEEEeecCCchhhhcccCceeeeeeccceecccCC
Q 018854 84 IRLGL--PSKGRMAADTLDLLKDCQLSVKQVNPRQYVAQIPQLSNLEVWFQRPKDIVRKLLSGDLDLGIVGLDTVSEFGQ 161 (349)
Q Consensus 84 LrIAL--P~KGRL~e~t~~LL~~aGi~~~~~~~R~L~~~~~~~p~vev~~vR~~DIP~yV~~G~aDlGIvG~DvL~E~~~ 161 (349)
.|||+ |+.-=.-.-+.+.|+.+|+--.- ..++... ++++ +.-.||+.|.+|+||+......-..
T Consensus 136 ~~lai~~p~~~P~G~ya~~~l~~~g~~~~~--~~k~v~~----~~v~-------~~l~~V~~G~ad~g~vy~sd~~~~~- 201 (258)
T COG0725 136 VRLAIGDPKTVPAGKYAKEALELLGLWYTL--KDKLVLA----TNVR-------QALAYVETGEADAGFVYVSDALLSK- 201 (258)
T ss_pred cEEEecCCCCCCchHHHHHHHHHhchhhhc--cccEEec----CcHH-------HHHHHHHcCCCCeEEEEEEhhhccC-
Confidence 44444 43333345566667777764222 2233221 2232 8899999999999999995443332
Q ss_pred CCccceeecCCCCcc-cEEEEEEEeCC
Q 018854 162 GNEDLIIVHDALDYG-DCRLSLAIPKY 187 (349)
Q Consensus 162 ~~~~lv~~l~dLgfG-~CRLvvAvP~~ 187 (349)
. ...+..+ +-... .-...+|++.+
T Consensus 202 ~-~~~~~~~-~~~~~~Pi~y~iav~~~ 226 (258)
T COG0725 202 K-VKIVGVF-PEDLHSPIVYPIAVLKN 226 (258)
T ss_pred C-ceEEEEc-ccccCCCeEEEEEEEcC
Confidence 1 1223333 22222 47777888776
No 89
>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=59.82 E-value=66 Score=30.05 Aligned_cols=128 Identities=15% Similarity=0.055 Sum_probs=75.4
Q ss_pred EEeecCCchhhhcccCceeeeeeccceecccCCCCccceeecCCCCcccEEEEEEEeCCCccCcccchHHhhcCCccCCC
Q 018854 129 VWFQRPKDIVRKLLSGDLDLGIVGLDTVSEFGQGNEDLIIVHDALDYGDCRLSLAIPKYGIFENINSLRELAQMPQWTAE 208 (349)
Q Consensus 129 v~~vR~~DIP~yV~~G~aDlGIvG~DvL~E~~~~~~~lv~~l~dLgfG~CRLvvAvP~~~~~~dv~sl~dL~~~~~~~~~ 208 (349)
+.++.-.+.-..+..|.+|+.+.|.=.-.|.... +. + --+|-.-..++.++++.. .++.+++||.+.
T Consensus 76 ~~~~~w~~~~~~l~~G~~Di~~~~~~~t~eR~~~----~~-f-s~py~~~~~~~~~~~~~~-~~i~~~~dl~~~------ 142 (275)
T TIGR02995 76 ASITEYGALIPGLQAGRFDAIAAGLFIKPERCKQ----VA-F-TQPILCDAEALLVKKGNP-KGLKSYKDIAKN------ 142 (275)
T ss_pred eccCCHHHHHHHHHCCCcCEEeecccCCHHHHhc----cc-c-ccceeecceeEEEECCCC-CCCCCHHHhccC------
Confidence 3444445667889999999877764332333211 10 0 113334455677777632 346777887531
Q ss_pred CCcEEEcCCCccHHHHHHhcCCceEEEEecCCcccc--ccCCCcceeeeecccchhh-HhhCCc
Q 018854 209 KPLRVATGFTYLGPKFMKDNGLKHVVFSTADGALEA--APAMGIADAILDLVSSGTT-LRENNL 269 (349)
Q Consensus 209 ~~lRVATkYPnlar~yf~~~Gi~~v~Ii~l~GSvEl--AP~lGlAD~IVDIVsTGtT-LraNgL 269 (349)
..+||+.---....+|+++.|+...+++.....-|+ +-.-|-+|+++.-..+... ++++++
T Consensus 143 ~g~~Igv~~g~~~~~~l~~~~~~~~~i~~~~~~~~~i~~L~~grvDa~i~d~~~~~~~~~~~~~ 206 (275)
T TIGR02995 143 PDAKIAAPGGGTEEKLAREAGVKREQIIVVPDGQSGLKMVQDGRADAYSLTVLTINDLASKAGD 206 (275)
T ss_pred CCceEEEeCCcHHHHHHHHcCCChhhEEEeCCHHHHHHHHHcCCCCEEecChHHHHHHHHhCCC
Confidence 136888777777788999887654566655543333 3567889988776655444 344443
No 90
>PF03480 SBP_bac_7: Bacterial extracellular solute-binding protein, family 7; InterPro: IPR018389 This family of proteins are involved in binding extracellular solutes for transport across the bacterial cytoplasmic membrane. This family includes a C4-dicarboxylate-binding protein DctP [, ] and the sialic acid-binding protein SiaP. The structure of the SiaP receptor has revealed an overall topology similar to ATP binding cassette ESR (extracytoplasmic solute receptors) proteins []. Upon binding of sialic acid, SiaP undergoes domain closure about a hinge region and kinking of an alpha-helix hinge component [].; GO: 0006810 transport, 0030288 outer membrane-bounded periplasmic space; PDB: 2HZK_C 2HZL_B 2HPG_C 2XWI_A 2XWK_A 2WX9_A 2CEY_A 2WYP_A 3B50_A 2CEX_B ....
Probab=59.42 E-value=30 Score=32.85 Aligned_cols=142 Identities=15% Similarity=0.102 Sum_probs=76.6
Q ss_pred eecCCchhhhcccCceeeeeeccceecccCCCCccceeecCCCCcc--------------------------cEEEEEE-
Q 018854 131 FQRPKDIVRKLLSGDLDLGIVGLDTVSEFGQGNEDLIIVHDALDYG--------------------------DCRLSLA- 183 (349)
Q Consensus 131 ~vR~~DIP~yV~~G~aDlGIvG~DvL~E~~~~~~~lv~~l~dLgfG--------------------------~CRLvvA- 183 (349)
+..+.|+...|..|.+|++++.-..+...... ..+ .+|+|. ..++.-.
T Consensus 40 lg~~~e~~~~v~~G~vdm~~~~~~~~~~~~p~-~~~----~~lP~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~L~~~ 114 (286)
T PF03480_consen 40 LGKEAEVLEAVQDGAVDMAVVSPSYLAGFVPE-FGV----FDLPFLFRDYEELDRVMDSGYGPELREELEEKGIKLLGWF 114 (286)
T ss_dssp SSSHHHHHHHHHTTSSSEEEEEGGGGTTTSGG-GGG----GGSTTTSSSHHHHHHHHHSHHHHHHHHHHHHTTEEEEEEE
T ss_pred cCCHHHHHHHHhCCCccEEeecchhhhhhchh-hee----eeCCCCCCCHHHHHHHHhCcHHHHHHHHHHhhceEEEEEe
Confidence 45667888888888888888877665544211 000 012111 1111100
Q ss_pred --EeCCCc--cCcccchHHhhcCCccCCCCCcEEEcCCCccHHHHHHhcCCceEEEEecCCccccccC--CCcceeeeec
Q 018854 184 --IPKYGI--FENINSLRELAQMPQWTAEKPLRVATGFTYLGPKFMKDNGLKHVVFSTADGALEAAPA--MGIADAILDL 257 (349)
Q Consensus 184 --vP~~~~--~~dv~sl~dL~~~~~~~~~~~lRVATkYPnlar~yf~~~Gi~~v~Ii~l~GSvElAP~--lGlAD~IVDI 257 (349)
.|.... -.+|.+++||++ +||-|-.-.+..++|+..|.. -+.+..+ |+.+. -|..|+..--
T Consensus 115 ~~g~~~~~~~~~pi~s~~DlkG---------~kiR~~~~~~~~~~~~~lGa~---pv~ip~~-evy~aLq~G~vDg~~~~ 181 (286)
T PF03480_consen 115 PGGPRQFFSTKKPIRSPEDLKG---------LKIRVPGSPVMSDFFEALGAS---PVPIPWS-EVYQALQQGVVDGAENS 181 (286)
T ss_dssp EEEEEEEEESSS--SSGGGGTT---------EEEEETSSHHHHHHHHHCTSE---EEE-TGG-GHHHHHHTTSSSEEEEE
T ss_pred cCCceEEEecccCCccHhhHhh---------CeEEecCCHHHHHHHHHcCCe---eecCcHH-HHHHHHhcCCcCeEecC
Confidence 111000 168899999886 455554457889999999963 3333433 66553 3555555544
Q ss_pred ccchhhHhhCCcEEecC----ceEEEEEEEEEeecchhhh
Q 018854 258 VSSGTTLRENNLKEIEG----GVVLESQAVLVASRKSLIR 293 (349)
Q Consensus 258 VsTGtTLraNgLk~ie~----g~IleSsA~LIaN~~s~~~ 293 (349)
..++.+ +++-++-. -...-+...++.|+..|..
T Consensus 182 ~~~~~~---~~~~ev~~y~~~~~~~~~~~~~~~n~~~w~~ 218 (286)
T PF03480_consen 182 ASSIYS---LGLYEVAKYFTDTNHGWSPYAVIMNKDWWDS 218 (286)
T ss_dssp HHHHHH---TTGGGTSSEEEEEEEEEEEEEEEEEHHHHHH
T ss_pred HHHHHh---cChhhhCCeeEeecccCcceEEEEcHHHHhc
Confidence 444444 44443321 0234466677889988764
No 91
>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=59.32 E-value=59 Score=27.42 Aligned_cols=104 Identities=16% Similarity=0.134 Sum_probs=55.7
Q ss_pred CCCeEEEee--cCCchhhhcccCceeeeeeccceecccCCCCccceeecCCCCcccEEEEEEEeCCCccC--cccchHHh
Q 018854 124 LSNLEVWFQ--RPKDIVRKLLSGDLDLGIVGLDTVSEFGQGNEDLIIVHDALDYGDCRLSLAIPKYGIFE--NINSLREL 199 (349)
Q Consensus 124 ~p~vev~~v--R~~DIP~yV~~G~aDlGIvG~DvL~E~~~~~~~lv~~l~dLgfG~CRLvvAvP~~~~~~--dv~sl~dL 199 (349)
.|++++.+. ...++-..+..|.+|+||+-... +.. .++. ...+...+++++++.+..+. .--+++||
T Consensus 26 ~P~~~i~i~~~~~~~~~~~l~~g~~Dl~i~~~~~--~~~---~~~~----~~~l~~~~~~~v~~~~hpl~~~~~i~~~~l 96 (198)
T cd08443 26 YPRVSLQMHQGSPTQIAEMVSKGLVDFAIATEAL--HDY---DDLI----TLPCYHWNRCVVVKRDHPLADKQSISIEEL 96 (198)
T ss_pred CCCeEEEEEeCCHHHHHHHHHCCCccEEEEeccc--ccc---CCce----EeeeeeceEEEEEcCCCccccCCCCCHHHH
Confidence 355555544 44688999999999999963211 011 1221 23456677888887664322 12356776
Q ss_pred hcCCccCCCCCcEEEcCCC----ccHHHHHHhcCCceEEEEecCCccccc
Q 018854 200 AQMPQWTAEKPLRVATGFT----YLGPKFMKDNGLKHVVFSTADGALEAA 245 (349)
Q Consensus 200 ~~~~~~~~~~~lRVATkYP----nlar~yf~~~Gi~~v~Ii~l~GSvElA 245 (349)
.+. .-|....+ +...++|++.|+. .++.--.++.+..
T Consensus 97 ~~~--------~~i~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~ 137 (198)
T cd08443 97 ATY--------PIVTYTFGFTGRSELDTAFNRAGLT-PNIVLTATDADVI 137 (198)
T ss_pred hcC--------CEEEecCCccHHHHHHHHHHHcCCC-ceEEEEECCHHHH
Confidence 642 12332222 3345677777875 3433223455443
No 92
>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=59.29 E-value=21 Score=29.39 Aligned_cols=149 Identities=21% Similarity=0.277 Sum_probs=72.1
Q ss_pred CCeEEE--eecCCchhhhcccCceeeeeeccceecccCCCCccceeecCCCCcccEEEEEEEeCCCccC--cccchHHhh
Q 018854 125 SNLEVW--FQRPKDIVRKLLSGDLDLGIVGLDTVSEFGQGNEDLIIVHDALDYGDCRLSLAIPKYGIFE--NINSLRELA 200 (349)
Q Consensus 125 p~vev~--~vR~~DIP~yV~~G~aDlGIvG~DvL~E~~~~~~~lv~~l~dLgfG~CRLvvAvP~~~~~~--dv~sl~dL~ 200 (349)
|++++. .....++...+.+|.+|+||+.... .+ .++. --.++..+++++++.+..+. +.-+++||.
T Consensus 26 P~i~l~i~~~~~~~~~~~l~~g~~Dl~i~~~~~-~~-----~~~~----~~~l~~~~~~~~~~~~~~l~~~~~~~~~~l~ 95 (197)
T cd08419 26 PGVEVSLRVGNREQVLERLADNEDDLAIMGRPP-ED-----LDLV----AEPFLDNPLVVIAPPDHPLAGQKRIPLERLA 95 (197)
T ss_pred CCceEEEEECCHHHHHHHHhcCCccEEEecCCC-CC-----CCeE----EEEeccCCEEEEecCCCCCcCCCCcCHHHHh
Confidence 444443 3456678889999999999975322 11 1222 12345667788877664222 123577776
Q ss_pred cCCccCCCCCcEEE--cCCCccHHHHHHhcCCceEEEEecCCcccccc---CCCcceeeeecccchhhHhhCCcEEecCc
Q 018854 201 QMPQWTAEKPLRVA--TGFTYLGPKFMKDNGLKHVVFSTADGALEAAP---AMGIADAILDLVSSGTTLRENNLKEIEGG 275 (349)
Q Consensus 201 ~~~~~~~~~~lRVA--TkYPnlar~yf~~~Gi~~v~Ii~l~GSvElAP---~lGlAD~IVDIVsTGtTLraNgLk~ie~g 275 (349)
+.+ + +... +.+-+...++|++.|+. .++.--..+.+.+. .-|..=+++--..--..+..++|+.+.-.
T Consensus 96 ~~~-~-----i~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~v~~g~gi~~~p~~~~~~~~~~~~l~~~~~~ 168 (197)
T cd08419 96 REP-F-----LLREPGSGTRLAMERFFAEHGVT-LRVRMELGSNEAIKQAVMAGLGLSVLSLHTLALELATGRLAVLDVE 168 (197)
T ss_pred CCC-c-----EEecCCCcHHHHHHHHHHHCCCC-cceEEEECCHHHHHHHHHhCCceEeecHHHHHHHHhhCCeEEEEcC
Confidence 531 1 1111 11224466788888875 23332234444331 11211122221111123455668876421
Q ss_pred e-EEEEEEEEEeecch
Q 018854 276 V-VLESQAVLVASRKS 290 (349)
Q Consensus 276 ~-IleSsA~LIaN~~s 290 (349)
. -....-.++.++..
T Consensus 169 ~~~~~~~~~~~~~~~~ 184 (197)
T cd08419 169 GFPIRRQWYVVHRKGK 184 (197)
T ss_pred CcceEEEEEEEEcCCC
Confidence 1 23344556665543
No 93
>PRK15010 ABC transporter lysine/arginine/ornithine binding periplasmic protein; Provisional
Probab=58.13 E-value=31 Score=31.81 Aligned_cols=111 Identities=15% Similarity=0.000 Sum_probs=59.0
Q ss_pred EEeecCCchhhhcccCceeeeeeccceecccCCCCccceeecCCCCcccEEEEEEEeCCCccCcccchHHhhcCCccCCC
Q 018854 129 VWFQRPKDIVRKLLSGDLDLGIVGLDTVSEFGQGNEDLIIVHDALDYGDCRLSLAIPKYGIFENINSLRELAQMPQWTAE 208 (349)
Q Consensus 129 v~~vR~~DIP~yV~~G~aDlGIvG~DvL~E~~~~~~~lv~~l~dLgfG~CRLvvAvP~~~~~~dv~sl~dL~~~~~~~~~ 208 (349)
+....-.++-..+..|.+|+.+.+...-.|.... ... --.|-.-+.++.++++.. ...+++||.+
T Consensus 69 ~~~~~~~~~~~~l~~g~~Di~~~~~~~t~eR~~~-~~f-----s~p~~~~~~~~~~~~~~~--~~~~~~dl~g------- 133 (260)
T PRK15010 69 WVASDFDALIPSLKAKKIDAIISSLSITDKRQQE-IAF-----SDKLYAADSRLIAAKGSP--IQPTLDSLKG------- 133 (260)
T ss_pred EEeCCHHHHHHHHHCCCCCEEEecCcCCHHHHhh-ccc-----ccceEeccEEEEEECCCC--CCCChhHcCC-------
Confidence 3333335677788999999988765554554321 110 123334456777777632 1225677653
Q ss_pred CCcEEEcCCCccHHHHHHhcCC-ceEEEEecCCccc---cccCCCcceeeeec
Q 018854 209 KPLRVATGFTYLGPKFMKDNGL-KHVVFSTADGALE---AAPAMGIADAILDL 257 (349)
Q Consensus 209 ~~lRVATkYPnlar~yf~~~Gi-~~v~Ii~l~GSvE---lAP~lGlAD~IVDI 257 (349)
+||+...=.....|+.++.. .++.++... +.| -+-..|-+|+++.-
T Consensus 134 --~~Igv~~gs~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~l~~griDa~i~d 183 (260)
T PRK15010 134 --KHVGVLQGSTQEAYANETWRSKGVDVVAYA-NQDLVYSDLAAGRLDAALQD 183 (260)
T ss_pred --CEEEEecCchHHHHHHHhcccCCceEEecC-CHHHHHHHHHcCCccEEEeC
Confidence 68887544433445543211 113454433 222 23557888987743
No 94
>PRK15243 transcriptional regulator SpvR; Provisional
Probab=57.70 E-value=38 Score=32.90 Aligned_cols=165 Identities=13% Similarity=0.045 Sum_probs=88.1
Q ss_pred CCCeEEEee--cCCchhhhcccCceeeeeeccceecccCCCCccceeecCCCCcccEEEEEEEeCCCccCcccchHHhhc
Q 018854 124 LSNLEVWFQ--RPKDIVRKLLSGDLDLGIVGLDTVSEFGQGNEDLIIVHDALDYGDCRLSLAIPKYGIFENINSLRELAQ 201 (349)
Q Consensus 124 ~p~vev~~v--R~~DIP~yV~~G~aDlGIvG~DvL~E~~~~~~~lv~~l~dLgfG~CRLvvAvP~~~~~~dv~sl~dL~~ 201 (349)
.|++++.+. ..+.+-..+..|. |+||+..+...+ .++. -..+..=.+++++|.+..|..-.+++||.+
T Consensus 118 ~P~v~i~~~~~~~~~~~~~l~~~~-~i~i~~~~~~~~-----~~l~----~~~l~~e~lvlv~~~~hpla~~~~l~~l~~ 187 (297)
T PRK15243 118 GQKTNIMGRAVNSQIIEELCQTNN-CIVISARNYFHR-----ESLV----CRTSVEGGVMLFIPKKFFLCGKPDINRLAG 187 (297)
T ss_pred CCceEEEEecCCHHHHHHHHcCCC-cEEEecCCCCCC-----CCee----EEEeccCCEEEEEcCCCccccCCCHHHHhc
Confidence 466766543 3445555666665 699974221111 1111 134455677888888866543346788865
Q ss_pred CCccCCCCCcEEEcCC-CccHHHHHHh-cCCceEEEEecCCccccccC-------CCcceeeeecccchhhHhhCCcEEe
Q 018854 202 MPQWTAEKPLRVATGF-TYLGPKFMKD-NGLKHVVFSTADGALEAAPA-------MGIADAILDLVSSGTTLRENNLKEI 272 (349)
Q Consensus 202 ~~~~~~~~~lRVATkY-Pnlar~yf~~-~Gi~~v~Ii~l~GSvElAP~-------lGlAD~IVDIVsTGtTLraNgLk~i 272 (349)
.+--. ....+.| -.+..++|++ .|+. .++--.+++|+.-. +|+| ++-+.+. .-+....|+.+
T Consensus 188 ~p~il----~~~~~~~~r~~~~~~~~~~~gi~--~~~~e~~s~e~i~~lv~v~~glGia-~lp~~~~--~~~~~~~L~~~ 258 (297)
T PRK15243 188 TPVLF----HEGAKNFNLDTIYHFFEQTLGIT--NPAFSFDNVDLFSSLYRLQQGLAML-LIPVRVC--RALGLSTDHAL 258 (297)
T ss_pred CCeEE----ecCCCccHHHHHHHHHHHhcCCC--hhheecccHHHHHHHHHHhcCCeee-cccHHHH--HHHhhCceEEe
Confidence 42111 1122333 3478899996 9984 34444777776532 2333 1111111 24555567766
Q ss_pred cCceEEEEEEEEEeecchhhhhcCchhHHHHHHHHHHHHHh
Q 018854 273 EGGVVLESQAVLVASRKSLIRRKGVLDATHEILERLEAHLR 313 (349)
Q Consensus 273 e~g~IleSsA~LIaN~~s~~~k~~~~~~i~~li~rl~~vl~ 313 (349)
.=.. +..+..+|.++..+.. ...+.+++.+++.+.
T Consensus 259 ~i~~-~~~~~~lv~~k~~~ls-----~~~~~f~~~~~~~~~ 293 (297)
T PRK15243 259 HIKG-VALCTSLYYPTKKRET-----PDYRKAIKLIQQELK 293 (297)
T ss_pred ccCc-CceeEEEEecCCCCCC-----hhHHHHHHHHHHHHh
Confidence 4101 4445588887776643 234566666665543
No 95
>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=57.17 E-value=64 Score=29.51 Aligned_cols=162 Identities=21% Similarity=0.194 Sum_probs=96.9
Q ss_pred eEEEeecCCchhhhcccCceeeeeeccceecccC-CCCccceeecCC-----CCcccEEEEEEEeCCCccCcccchHHhh
Q 018854 127 LEVWFQRPKDIVRKLLSGDLDLGIVGLDTVSEFG-QGNEDLIIVHDA-----LDYGDCRLSLAIPKYGIFENINSLRELA 200 (349)
Q Consensus 127 vev~~vR~~DIP~yV~~G~aDlGIvG~DvL~E~~-~~~~~lv~~l~d-----LgfG~CRLvvAvP~~~~~~dv~sl~dL~ 200 (349)
+.+.+.-..+=-..+..|.+|++-+.. +..|.+ .+...+...+.. +.+-+=..-++++.+.. .+|.+++||.
T Consensus 13 v~~~~~gS~~gl~~L~~g~~~iAg~h~-~~~~~~~~n~~~~~~~l~g~~~v~v~~~~r~~Gl~v~~~np-~~i~~~~dL~ 90 (193)
T PF12727_consen 13 VAVQYTGSRAGLSALARGEADIAGIHL-PDPESGEYNIPFVRRLLPGIEVVLVRLARREQGLIVRPGNP-KGITSLEDLA 90 (193)
T ss_pred EEEEecCCHHHHHHHHCCCceEEEecC-CCCcccccchHHHHHhcCCCcEEEEeeeEEeeeEEEeCCCC-ccCCCHHHhc
Confidence 555666777778889999999988876 333232 111111000000 22333344566776654 4789999985
Q ss_pred cCCccCCCCCcEEEcCCCcc-----HHHHHHhcCCce------EEEEecCCccccccCCCcceeeeecccchhhHhh-CC
Q 018854 201 QMPQWTAEKPLRVATGFTYL-----GPKFMKDNGLKH------VVFSTADGALEAAPAMGIADAILDLVSSGTTLRE-NN 268 (349)
Q Consensus 201 ~~~~~~~~~~lRVATkYPnl-----ar~yf~~~Gi~~------v~Ii~l~GSvElAP~lGlAD~IVDIVsTGtTLra-Ng 268 (349)
. +++|++.-=+.- -.+.+.+.|+.. -.....+.++=.+..-|.||+=+= +...-++ +|
T Consensus 91 ~-------~~~r~vnR~~GSGtR~l~d~~l~~~gi~~~~i~gy~~~~~th~~vA~aVa~G~AD~G~g---~~~~A~~~~g 160 (193)
T PF12727_consen 91 D-------PGLRFVNRQPGSGTRILFDQLLAEEGIDPEDIPGYAQEANTHLAVAAAVASGKADAGIG---IRAAAEEFYG 160 (193)
T ss_pred c-------CCcEEEECCCCCHHHHHHHHHHHHcCCChhhCCCccccccChHHHHHHHHcCCCCEEee---hHHHHHhhcC
Confidence 3 246776655543 334444445432 134444555555678889997652 3444444 89
Q ss_pred cEEecCceEEEEEEEEEeecchhhhhcCchhHHHHHHHHH
Q 018854 269 LKEIEGGVVLESQAVLVASRKSLIRRKGVLDATHEILERL 308 (349)
Q Consensus 269 Lk~ie~g~IleSsA~LIaN~~s~~~k~~~~~~i~~li~rl 308 (349)
|.-+. +.+-.--|+.++..+.. +.+++|++-|
T Consensus 161 L~Fvp---l~~E~~dlv~~~~~~~~-----~~vq~ll~~l 192 (193)
T PF12727_consen 161 LDFVP---LAEERYDLVIRREDLED-----PAVQALLDFL 192 (193)
T ss_pred CCcEE---ccccceEEEEEhhHcCC-----HHHHHHHHHh
Confidence 99985 88888888888888643 3567776654
No 96
>PRK10837 putative DNA-binding transcriptional regulator; Provisional
Probab=54.78 E-value=98 Score=28.53 Aligned_cols=100 Identities=16% Similarity=0.180 Sum_probs=55.3
Q ss_pred eEEEeecCCchhhhcccCceeeeeeccceecccCCCCccceeecCCCCcccEEEEEEEeCCCccC-cccchHHhhcCCcc
Q 018854 127 LEVWFQRPKDIVRKLLSGDLDLGIVGLDTVSEFGQGNEDLIIVHDALDYGDCRLSLAIPKYGIFE-NINSLRELAQMPQW 205 (349)
Q Consensus 127 vev~~vR~~DIP~yV~~G~aDlGIvG~DvL~E~~~~~~~lv~~l~dLgfG~CRLvvAvP~~~~~~-dv~sl~dL~~~~~~ 205 (349)
+++...-..++...+.+|.+|+||+.... ...++. ...+++.+++++++.+.... ..-+++||...+
T Consensus 120 i~v~~~~~~~~~~~l~~g~~Di~i~~~~~------~~~~~~----~~~l~~~~~~lv~~~~hpl~~~~i~~~~L~~~~-- 187 (290)
T PRK10837 120 LELSVGNSQDVINAVLDFRVDIGLIEGPC------HSPELI----SEPWLEDELVVFAAPDSPLARGPVTLEQLAAAP-- 187 (290)
T ss_pred EEEEECCHHHHHHHHHhCCceEEEecCCC------CCCcee----EEEeecceEEEEEcCCChhhcCCCCHHHHhcCC--
Confidence 34434455778999999999999974321 112222 24557888999998874221 123567776531
Q ss_pred CCCCCcEEEcC----CCccHHHHHHhcCCceEEEEecCCccccc
Q 018854 206 TAEKPLRVATG----FTYLGPKFMKDNGLKHVVFSTADGALEAA 245 (349)
Q Consensus 206 ~~~~~lRVATk----YPnlar~yf~~~Gi~~v~Ii~l~GSvElA 245 (349)
-|... +.+...++|.+.|.. .++..-..+.+..
T Consensus 188 ------~i~~~~~~~~~~~l~~~~~~~~~~-~~~~~~~~~~~~~ 224 (290)
T PRK10837 188 ------WILRERGSGTREIVDYLLLSHLPR-FELAMELGNSEAI 224 (290)
T ss_pred ------eEEecCCCcHHHHHHHHHHHcCCC-CceEEEeCCHHHH
Confidence 12211 223445667776764 3443333444433
No 97
>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=54.09 E-value=44 Score=28.12 Aligned_cols=91 Identities=18% Similarity=0.249 Sum_probs=47.7
Q ss_pred CCeEEEee--cCCchhhhcccCceeeeeeccceecccCCCCccceeecCCCCcccEEEEEEEeCCCccC--cccchHHhh
Q 018854 125 SNLEVWFQ--RPKDIVRKLLSGDLDLGIVGLDTVSEFGQGNEDLIIVHDALDYGDCRLSLAIPKYGIFE--NINSLRELA 200 (349)
Q Consensus 125 p~vev~~v--R~~DIP~yV~~G~aDlGIvG~DvL~E~~~~~~~lv~~l~dLgfG~CRLvvAvP~~~~~~--dv~sl~dL~ 200 (349)
|++++.+. ...++...+.+|.+|+||+-.....+. ++. -..++.-+++++++.+..+. ..-+++||.
T Consensus 27 P~v~l~i~~~~~~~~~~~l~~g~~Dl~i~~~~~~~~~-----~~~----~~~l~~~~~~~~~~~~hpl~~~~~~~~~~l~ 97 (198)
T cd08444 27 PNVHLVLHQGSPEEIASMLANGQADIGIATEALENHP-----ELV----SFPYYDWHHHIIVPVGHPLESITPLTIETIA 97 (198)
T ss_pred CCeEEEEEeCCHHHHHHHHHCCCccEEEeccccCCCc-----CcE----EeeccccceeEEecCCCccccCCCcCHHHHh
Confidence 44544443 455788999999999999742211111 221 12234456667766653222 223567766
Q ss_pred cCCccCCCCCcEEEc---CCCccHHHHHHhcCCc
Q 018854 201 QMPQWTAEKPLRVAT---GFTYLGPKFMKDNGLK 231 (349)
Q Consensus 201 ~~~~~~~~~~lRVAT---kYPnlar~yf~~~Gi~ 231 (349)
+. +.-.-. .+-....+||.+.|+.
T Consensus 98 ~~-------~~i~~~~~~~~~~~~~~~~~~~~~~ 124 (198)
T cd08444 98 KW-------PIITYHGGFTGRSRIDRAFSRAELT 124 (198)
T ss_pred CC-------CEEEecCCCchHHHHHHHHHHcCCC
Confidence 42 111111 1223446688888874
No 98
>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=53.65 E-value=48 Score=27.19 Aligned_cols=91 Identities=19% Similarity=0.184 Sum_probs=50.6
Q ss_pred CCeEEEee--cCCchhhhcccCceeeeeeccceecccCCCCccceeecCCCCcccEEEEEEEeCCCccC--cccchHHhh
Q 018854 125 SNLEVWFQ--RPKDIVRKLLSGDLDLGIVGLDTVSEFGQGNEDLIIVHDALDYGDCRLSLAIPKYGIFE--NINSLRELA 200 (349)
Q Consensus 125 p~vev~~v--R~~DIP~yV~~G~aDlGIvG~DvL~E~~~~~~~lv~~l~dLgfG~CRLvvAvP~~~~~~--dv~sl~dL~ 200 (349)
|++++-+. ...++...+.+|.+|+||+....- . .++. --.++.-+++++++.+.... +.-+++||.
T Consensus 27 p~i~i~i~~~~~~~~~~~l~~~~~Dl~i~~~~~~--~----~~~~----~~~l~~~~~~~v~~~~~~l~~~~~~~~~~L~ 96 (197)
T cd08414 27 PDVELELREMTTAEQLEALRAGRLDVGFVRPPPD--P----PGLA----SRPLLREPLVVALPADHPLAARESVSLADLA 96 (197)
T ss_pred CCcEEEEecCChHHHHHHHHcCCccEEEEcCCCC--C----CCee----EEEEeeccEEEEecCCCccccCCccCHHHhc
Confidence 44555444 357899999999999999854321 1 1221 12345667777777653221 223566766
Q ss_pred cCCccCCCCCcEEEcC----CCccHHHHHHhcCCc
Q 018854 201 QMPQWTAEKPLRVATG----FTYLGPKFMKDNGLK 231 (349)
Q Consensus 201 ~~~~~~~~~~lRVATk----YPnlar~yf~~~Gi~ 231 (349)
..+ -+..... +.+...++|++.|+.
T Consensus 97 ~~~------~i~~~~~~~~~~~~~~~~~~~~~~~~ 125 (197)
T cd08414 97 DEP------FVLFPREPGPGLYDQILALCRRAGFT 125 (197)
T ss_pred cCC------EEEecCCcchhHHHHHHHHHHHcCCC
Confidence 421 1222221 224456778887764
No 99
>PRK09906 DNA-binding transcriptional regulator HcaR; Provisional
Probab=53.24 E-value=1.3e+02 Score=27.94 Aligned_cols=100 Identities=12% Similarity=0.129 Sum_probs=58.2
Q ss_pred CCeEEEee--cCCchhhhcccCceeeeeeccceecccCCCCccceeecCCCCcccEEEEEEEeCCCccC--cccchHHhh
Q 018854 125 SNLEVWFQ--RPKDIVRKLLSGDLDLGIVGLDTVSEFGQGNEDLIIVHDALDYGDCRLSLAIPKYGIFE--NINSLRELA 200 (349)
Q Consensus 125 p~vev~~v--R~~DIP~yV~~G~aDlGIvG~DvL~E~~~~~~~lv~~l~dLgfG~CRLvvAvP~~~~~~--dv~sl~dL~ 200 (349)
|++++.+. ...++...+.+|.+|+||+..+.. . .++. .-.++..+++++++++.... +.-+++||.
T Consensus 117 p~v~i~~~~~~~~~~~~~l~~~~~D~~i~~~~~~-~-----~~l~----~~~l~~~~~~~v~~~~~pl~~~~~i~~~~L~ 186 (296)
T PRK09906 117 PDTLIELVSLITTQQEEKLRRGELDVGFMRHPVY-S-----DEID----YLELLDEPLVVVLPVDHPLAHEKEITAAQLD 186 (296)
T ss_pred CCeEEEEEeCCcHHHHHHHHcCCeeEEEecCCCC-C-----CCce----EEEEecccEEEEecCCCccccCCCcCHHHHc
Confidence 45554443 567899999999999999866531 1 1222 23467778888888763211 223567776
Q ss_pred cCCccCCCCCcEEEcC------CCccHHHHHHhcCCceEEEEecCCccc
Q 018854 201 QMPQWTAEKPLRVATG------FTYLGPKFMKDNGLKHVVFSTADGALE 243 (349)
Q Consensus 201 ~~~~~~~~~~lRVATk------YPnlar~yf~~~Gi~~v~Ii~l~GSvE 243 (349)
+.+ -|... +.....+|+.+.|+. .++..-..+.+
T Consensus 187 ~~~--------~i~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~ 226 (296)
T PRK09906 187 GVN--------FISTDPAYSGSLAPIIKAWFAQHNSQ-PNIVQVATNIL 226 (296)
T ss_pred CCC--------EEeccCCCCchHHHHHHHHHHHcCCC-cceEEEeccHH
Confidence 531 12211 124456788888875 34433334443
No 100
>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=52.60 E-value=38 Score=27.80 Aligned_cols=88 Identities=15% Similarity=0.074 Sum_probs=46.8
Q ss_pred CCeEEEeecCCchhhhcccCceeeeeeccceecccCCCCccceeecCCCCcccEEEEEEEeCCCcc-CcccchHHhhcCC
Q 018854 125 SNLEVWFQRPKDIVRKLLSGDLDLGIVGLDTVSEFGQGNEDLIIVHDALDYGDCRLSLAIPKYGIF-ENINSLRELAQMP 203 (349)
Q Consensus 125 p~vev~~vR~~DIP~yV~~G~aDlGIvG~DvL~E~~~~~~~lv~~l~dLgfG~CRLvvAvP~~~~~-~dv~sl~dL~~~~ 203 (349)
|++++.+.... -...+.+|.+|+||+..+.-. .++. .-.+++-+++++++.+... .+.-+++||.+.+
T Consensus 27 P~i~i~i~~~~-~~~~l~~~~~Dl~l~~~~~~~------~~~~----~~~l~~~~~~~v~~~~~~~~~~~~~~~dl~~~~ 95 (194)
T cd08481 27 PDITVNLVTRD-EPFDFSQGSFDAAIHFGDPVW------PGAE----SEYLMDEEVVPVCSPALLAGRALAAPADLAHLP 95 (194)
T ss_pred CCceEEEEecc-cccCcccCCCCEEEEcCCCCC------CCcc----ceecccCeeeecCCHHHHhcCCCCcHHHHhhCc
Confidence 55555544322 234689999999997543211 1111 2234566777777654210 1223677776531
Q ss_pred ccCCCCCcEEE-cCCCccHHHHHHhcCCc
Q 018854 204 QWTAEKPLRVA-TGFTYLGPKFMKDNGLK 231 (349)
Q Consensus 204 ~~~~~~~lRVA-TkYPnlar~yf~~~Gi~ 231 (349)
-|. ...+...+++|.+.|..
T Consensus 96 --------~i~~~~~~~~~~~~~~~~~~~ 116 (194)
T cd08481 96 --------LLQQTTRPEAWRDWFEEVGLE 116 (194)
T ss_pred --------eEecCCCCcCHHHHHHHcCCC
Confidence 222 22234567888888863
No 101
>CHL00180 rbcR LysR transcriptional regulator; Provisional
Probab=51.81 E-value=37 Score=32.07 Aligned_cols=89 Identities=20% Similarity=0.310 Sum_probs=51.0
Q ss_pred EEEeecCCchhhhcccCceeeeeeccceecccCCCCccceeecCCCCcccEEEEEEEeCCCccC--cccchHHhhcCCcc
Q 018854 128 EVWFQRPKDIVRKLLSGDLDLGIVGLDTVSEFGQGNEDLIIVHDALDYGDCRLSLAIPKYGIFE--NINSLRELAQMPQW 205 (349)
Q Consensus 128 ev~~vR~~DIP~yV~~G~aDlGIvG~DvL~E~~~~~~~lv~~l~dLgfG~CRLvvAvP~~~~~~--dv~sl~dL~~~~~~ 205 (349)
++......++...+.+|.+|+||++.+.-.+.. ..+. ...++.-++++++|.+..+. ..-+++||...+
T Consensus 127 ~~~~~~~~~~~~~l~~g~~Dl~i~~~~~~~~~~---~~~~----~~~l~~~~~~~v~~~~~pl~~~~~i~~~dL~~~~-- 197 (305)
T CHL00180 127 QLQVHSTRRIAWNVANGQIDIAIVGGEVPTELK---KILE----ITPYVEDELALIIPKSHPFAKLKKIQKEDLYRLN-- 197 (305)
T ss_pred EEEeCCHHHHHHHHHcCCccEEEEcCccCcccc---ccee----EEEeccCcEEEEECCCCccccCCccCHHHHccCC--
Confidence 333335677888999999999998654322111 1121 24566778899988764222 122566766421
Q ss_pred CCCCCcEEEcC----CCccHHHHHHhcCCc
Q 018854 206 TAEKPLRVATG----FTYLGPKFMKDNGLK 231 (349)
Q Consensus 206 ~~~~~lRVATk----YPnlar~yf~~~Gi~ 231 (349)
-|... +.....++|++.|+.
T Consensus 198 ------~i~~~~~~~~~~~~~~~~~~~~~~ 221 (305)
T CHL00180 198 ------FITLDSNSTIRKVIDNILIQNGID 221 (305)
T ss_pred ------ceEecCCCcHHHHHHHHHHHcCCC
Confidence 12222 234455678887864
No 102
>PRK12681 cysB transcriptional regulator CysB; Reviewed
Probab=51.29 E-value=1.2e+02 Score=29.21 Aligned_cols=164 Identities=18% Similarity=0.235 Sum_probs=79.5
Q ss_pred CCeEEEee--cCCchhhhcccCceeeeeeccceecccCCCCccceeecCCCCcccEEEEEEEeCCCccC--cccchHHhh
Q 018854 125 SNLEVWFQ--RPKDIVRKLLSGDLDLGIVGLDTVSEFGQGNEDLIIVHDALDYGDCRLSLAIPKYGIFE--NINSLRELA 200 (349)
Q Consensus 125 p~vev~~v--R~~DIP~yV~~G~aDlGIvG~DvL~E~~~~~~~lv~~l~dLgfG~CRLvvAvP~~~~~~--dv~sl~dL~ 200 (349)
|++++.+. ...++-..+.+|.+|+||+-.+.- .. .++.. ..++.=.+++.++.+..+. ..-+++||.
T Consensus 120 P~i~i~i~~~~~~~~~~~L~~g~iDl~i~~~~~~--~~---~~l~~----~~l~~~~~~~v~~~~hpl~~~~~~~~~~L~ 190 (324)
T PRK12681 120 PRVSLHMHQGSPTQIAEAAAKGNADFAIATEALH--LY---DDLIM----LPCYHWNRSVVVPPDHPLAKKKKLTIEELA 190 (324)
T ss_pred CCcEEEEEeCCHHHHHHHHHcCCCCEEEecCccc--CC---CCeEE----EEeccceeEEEeCCCChhhcCCCcCHHHHh
Confidence 44555443 456788899999999999732110 00 12211 2234444566666553222 223556766
Q ss_pred cCCccCCCCCcEEEcC----CCccHHHHHHhcCCceEEEEecCCccccccC---CCcceeeeecccchhhHhhCCcEEec
Q 018854 201 QMPQWTAEKPLRVATG----FTYLGPKFMKDNGLKHVVFSTADGALEAAPA---MGIADAILDLVSSGTTLRENNLKEIE 273 (349)
Q Consensus 201 ~~~~~~~~~~lRVATk----YPnlar~yf~~~Gi~~v~Ii~l~GSvElAP~---lGlAD~IVDIVsTGtTLraNgLk~ie 273 (349)
..+ -|... +.....++|++.|+. ..+..-.++.+..-. -|+.=+++-- ..-......+|+.+.
T Consensus 191 ~~~--------~i~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~s~~~~~~~v~~g~Gi~~lp~-~~~~~~~~~~l~~~~ 260 (324)
T PRK12681 191 QYP--------LVTYVFGFTGRSELDTAFNRAGLT-PRIVFTATDADVIKTYVRLGLGVGVIAS-MAVDPVADPDLVAID 260 (324)
T ss_pred CCC--------eEeccCCCchHHHHHHHHHHcCCC-CceEEEeCCHHHHHHHHHhCCCEEEeeh-hhcccccCCceEEee
Confidence 421 23222 223445677777874 343322345554321 1221122210 011112335677664
Q ss_pred C-ceEEEEEEEEEeecchhhhhcCchhHHHHHHHHHHHHH
Q 018854 274 G-GVVLESQAVLVASRKSLIRRKGVLDATHEILERLEAHL 312 (349)
Q Consensus 274 ~-g~IleSsA~LIaN~~s~~~k~~~~~~i~~li~rl~~vl 312 (349)
- +.....+-.|+.++..... ..++.+++.+...+
T Consensus 261 ~~~~~~~~~~~l~~~~~~~~~-----~~~~~fi~~~~~~~ 295 (324)
T PRK12681 261 ASHLFSHSTTKIGFRRGTFLR-----SYMYDFIERFAPHL 295 (324)
T ss_pred cCCCCCceEEEEEEECCchhh-----HHHHHHHHHHHHHH
Confidence 1 1234567777877776543 24556666665543
No 103
>PRK09791 putative DNA-binding transcriptional regulator; Provisional
Probab=50.23 E-value=51 Score=30.90 Aligned_cols=91 Identities=10% Similarity=0.058 Sum_probs=51.9
Q ss_pred EEEeecCCchhhhcccCceeeeeecc-ceecccCCCCccceeecCCCCcccEEEEEEEeCCCccCcccchHHhhcCCccC
Q 018854 128 EVWFQRPKDIVRKLLSGDLDLGIVGL-DTVSEFGQGNEDLIIVHDALDYGDCRLSLAIPKYGIFENINSLRELAQMPQWT 206 (349)
Q Consensus 128 ev~~vR~~DIP~yV~~G~aDlGIvG~-DvL~E~~~~~~~lv~~l~dLgfG~CRLvvAvP~~~~~~dv~sl~dL~~~~~~~ 206 (349)
++......|+...+..|.+|+||+.. +.... .++. --.++..+++++++.+.....-.+++||...+--.
T Consensus 127 ~~~~~~~~~~~~~l~~g~~Di~i~~~~~~~~~-----~~~~----~~~l~~~~~~l~~~~~~~~~~~~~~~~l~~~~~i~ 197 (302)
T PRK09791 127 RIMEGQLVSMINELRQGELDFTINTYYQGPYD-----HEFT----FEKLLEKQFAVFCRPGHPAIGARSLKQLLDYSWTM 197 (302)
T ss_pred EEEeCChHHHHHHHHCCCccEEEEecCCcccc-----ccee----EEEeccceEEEEEcCCCCcCCCCCHHHHhcCCeec
Confidence 33344567999999999999999842 21111 1221 13467899999998875443334577776531100
Q ss_pred CCCCcEEEcCCCccHHHHHHhcCCc
Q 018854 207 AEKPLRVATGFTYLGPKFMKDNGLK 231 (349)
Q Consensus 207 ~~~~lRVATkYPnlar~yf~~~Gi~ 231 (349)
..-.+.+-....++|.+.|+.
T Consensus 198 ----~~~~~~~~~~~~~~~~~~~~~ 218 (302)
T PRK09791 198 ----PTPHGSYYKQLSELLDDQAQT 218 (302)
T ss_pred ----CCCCCcHHHHHHHHHHhcCCC
Confidence 000111234446677777753
No 104
>PRK10859 membrane-bound lytic transglycosylase F; Provisional
Probab=48.25 E-value=1.7e+02 Score=30.33 Aligned_cols=110 Identities=18% Similarity=0.061 Sum_probs=61.2
Q ss_pred cCCchhhhcccCceeeeeeccceecccCCCCccceeecCCCCcccEEEEEEEeCCCccCcccchHHhhcCCccCCCCCcE
Q 018854 133 RPKDIVRKLLSGDLDLGIVGLDTVSEFGQGNEDLIIVHDALDYGDCRLSLAIPKYGIFENINSLRELAQMPQWTAEKPLR 212 (349)
Q Consensus 133 R~~DIP~yV~~G~aDlGIvG~DvL~E~~~~~~~lv~~l~dLgfG~CRLvvAvP~~~~~~dv~sl~dL~~~~~~~~~~~lR 212 (349)
...++-..+..|.+|+.+.|.-.-.|.... + .+ --.|-....++.+..+. ..+.+++||.+ ++
T Consensus 89 ~~~~ll~aL~~G~iDi~~~~lt~T~eR~~~----~-~F-S~Py~~~~~~lv~r~~~--~~i~~l~dL~G---------k~ 151 (482)
T PRK10859 89 NISQLFDALDKGKADLAAAGLTYTPERLKQ----F-RF-GPPYYSVSQQLVYRKGQ--PRPRSLGDLKG---------GT 151 (482)
T ss_pred CHHHHHHHHhCCCCCEEeccCcCChhhhcc----C-cc-cCCceeeeEEEEEeCCC--CCCCCHHHhCC---------Ce
Confidence 346777889999999988887655554321 1 01 12455677788888763 45788888875 46
Q ss_pred EEcCCCccHHHHHHh----c-CCceEEEEecCCcccc---ccCCCcceeeeecccch
Q 018854 213 VATGFTYLGPKFMKD----N-GLKHVVFSTADGALEA---APAMGIADAILDLVSSG 261 (349)
Q Consensus 213 VATkYPnlar~yf~~----~-Gi~~v~Ii~l~GSvEl---AP~lGlAD~IVDIVsTG 261 (349)
|+..--.....++++ . ++. ++++. ..+.|- +-.-|-+|+++.-..+.
T Consensus 152 I~V~~gS~~~~~L~~l~~~~p~i~-~~~~~-~~s~~e~l~aL~~G~iDa~v~d~~~~ 206 (482)
T PRK10859 152 LTVAAGSSHVETLQELKKKYPELS-WEESD-DKDSEELLEQVAEGKIDYTIADSVEI 206 (482)
T ss_pred EEEECCCcHHHHHHHHHHhCCCce-EEecC-CCCHHHHHHHHHCCCCCEEEECcHHH
Confidence 654332333333332 2 221 23222 223332 24568889776543333
No 105
>PRK15421 DNA-binding transcriptional regulator MetR; Provisional
Probab=47.92 E-value=1.8e+02 Score=27.99 Aligned_cols=99 Identities=14% Similarity=0.028 Sum_probs=55.1
Q ss_pred EEEeecCCchhhhcccCceeeeeeccceecccCCCCccceeecCCCCcccEEEEEEEeCCCccCc--ccchHHhhcCCcc
Q 018854 128 EVWFQRPKDIVRKLLSGDLDLGIVGLDTVSEFGQGNEDLIIVHDALDYGDCRLSLAIPKYGIFEN--INSLRELAQMPQW 205 (349)
Q Consensus 128 ev~~vR~~DIP~yV~~G~aDlGIvG~DvL~E~~~~~~~lv~~l~dLgfG~CRLvvAvP~~~~~~d--v~sl~dL~~~~~~ 205 (349)
++......|+-..+..|.+|+||+.... . ..++. --.+++.+++++++.+..+.. --+++||...+ +
T Consensus 121 ~~~~~~~~~~~~~L~~g~~Dl~i~~~~~--~----~~~~~----~~~l~~~~~~lv~~~~hpl~~~~~i~~~~L~~~p-~ 189 (317)
T PRK15421 121 DFKSGVTFDPQPALQQGELDLVMTSDIL--P----RSGLH----YSPMFDYEVRLVLAPDHPLAAKTRITPEDLASET-L 189 (317)
T ss_pred EEEeCccHHHHHHHHCCCcCEEEecCcc--c----CCCce----EEEeccceEEEEEcCCCCccccCcCCHHHhCCCc-E
Confidence 3333456788899999999999975321 1 11222 234678899999987743321 23567776531 1
Q ss_pred CCCCCcEEEc--CCCccHHHHHHhcCCceEEEEecCCcccc
Q 018854 206 TAEKPLRVAT--GFTYLGPKFMKDNGLKHVVFSTADGALEA 244 (349)
Q Consensus 206 ~~~~~lRVAT--kYPnlar~yf~~~Gi~~v~Ii~l~GSvEl 244 (349)
+-... ......+.||++.|++ ..++. .++.+.
T Consensus 190 -----i~~~~~~~~~~~~~~~~~~~~~~-~~~~~-~~~~~~ 223 (317)
T PRK15421 190 -----LIYPVQRSRLDVWRHFLQPAGVS-PSLKS-VDNTLL 223 (317)
T ss_pred -----EecCCchhhHHHHHHHHHHhCCC-Cceee-cCCHHH
Confidence 11111 1123455678888875 34442 355443
No 106
>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=47.92 E-value=61 Score=26.64 Aligned_cols=102 Identities=20% Similarity=0.175 Sum_probs=54.9
Q ss_pred CCeEEEe--ecCCchhhhcccCceeeeeeccceecccCCCCccceeecCCCCcccEEEEEEEeCCCccC--cccchHHhh
Q 018854 125 SNLEVWF--QRPKDIVRKLLSGDLDLGIVGLDTVSEFGQGNEDLIIVHDALDYGDCRLSLAIPKYGIFE--NINSLRELA 200 (349)
Q Consensus 125 p~vev~~--vR~~DIP~yV~~G~aDlGIvG~DvL~E~~~~~~~lv~~l~dLgfG~CRLvvAvP~~~~~~--dv~sl~dL~ 200 (349)
|++++-+ ....|+...+.+|.+|+||+..... . .++. ...++.-+++++++.+.... ..-+++||.
T Consensus 27 P~i~l~i~~~~~~~~~~~l~~~~~D~~i~~~~~~-~-----~~~~----~~~l~~~~~~~~~~~~~~l~~~~~~~~~~l~ 96 (198)
T cd08412 27 PGVEVRVVEGNQEELEEGLRSGELDLALTYDLDL-P-----EDIA----FEPLARLPPYVWLPADHPLAGKDEVSLADLA 96 (198)
T ss_pred CCcEEEEEECCHHHHHHHHHcCCCcEEEEcCCCC-C-----cccc----eeeeeccceEEEecCCCCCCCCCcCCHHHHc
Confidence 4444444 3567888999999999999854321 1 1221 23345666777776653211 123567776
Q ss_pred cCCccCCCCCcEEEcC---CCccHHHHHHhcCCceEEEEecCCccccc
Q 018854 201 QMPQWTAEKPLRVATG---FTYLGPKFMKDNGLKHVVFSTADGALEAA 245 (349)
Q Consensus 201 ~~~~~~~~~~lRVATk---YPnlar~yf~~~Gi~~v~Ii~l~GSvElA 245 (349)
+.+ -|... ..+...++|.+.|+. ..+..-.++.+.+
T Consensus 97 ~~~--------~i~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~ 135 (198)
T cd08412 97 AEP--------LILLDLPHSREYFLSLFAAAGLT-PRIAYRTSSFEAV 135 (198)
T ss_pred CCc--------EEecCchhHHHHHHHHHHHcCCC-ccEEEEeCcHHHH
Confidence 531 11111 223456688888875 3433323444443
No 107
>COG4521 TauA ABC-type taurine transport system, periplasmic component [Inorganic ion transport and metabolism]
Probab=47.47 E-value=16 Score=36.12 Aligned_cols=91 Identities=25% Similarity=0.323 Sum_probs=58.1
Q ss_pred CchhhhcccCceeeeeeccceecccCCCCccceeec-CCCCcccEEEEEEEeCCCccCcccchHHhhcCCccCCCCCcEE
Q 018854 135 KDIVRKLLSGDLDLGIVGLDTVSEFGQGNEDLIIVH-DALDYGDCRLSLAIPKYGIFENINSLRELAQMPQWTAEKPLRV 213 (349)
Q Consensus 135 ~DIP~yV~~G~aDlGIvG~DvL~E~~~~~~~lv~~l-~dLgfG~CRLvvAvP~~~~~~dv~sl~dL~~~~~~~~~~~lRV 213 (349)
.||.+-+++|.+++|..|.-=+.-.....-. ++++ ..=.+|... .+.+.++ ..|+.++||.+ +||
T Consensus 68 ~~vv~AlASGdvqiG~iGSsplaaAaSr~vp-ie~f~~~~~ig~sE-ALVvr~g---sgI~kpeDL~G---------K~i 133 (334)
T COG4521 68 ASIVRALASGDVQIGNIGSSPLAAAASRQVP-IEVFLLASQIGNSE-ALVVRKG---SGIEKPEDLIG---------KRI 133 (334)
T ss_pred hHHHHHHhcCCccccccCCchhhHHhhcCCc-eEEeehhhhcCccc-eeeeecC---CCcCChHHhcc---------Cee
Confidence 6899999999999999999877655332111 2221 112345544 2445565 67899999985 688
Q ss_pred EcCCCccHHH----HHHhcCCc--eEEEEecC
Q 018854 214 ATGFTYLGPK----FMKDNGLK--HVVFSTAD 239 (349)
Q Consensus 214 ATkYPnlar~----yf~~~Gi~--~v~Ii~l~ 239 (349)
|+-|...+-- -++..|++ .|+|+.|.
T Consensus 134 avPFvSTtHysLLaaLkhw~idp~~V~IlNl~ 165 (334)
T COG4521 134 AVPFVSTTHYSLLAALKHWGIDPGQVEILNLQ 165 (334)
T ss_pred ccceeehhHHHHHHHHHHcCCCccceeEeccC
Confidence 8877554432 13445653 47777664
No 108
>PRK12683 transcriptional regulator CysB-like protein; Reviewed
Probab=47.43 E-value=40 Score=32.17 Aligned_cols=88 Identities=22% Similarity=0.281 Sum_probs=50.5
Q ss_pred eEEEeecCCchhhhcccCceeeeeeccceecccCCCCccceeecCCCCcccEEEEEEEeCCCccC--cccchHHhhcCCc
Q 018854 127 LEVWFQRPKDIVRKLLSGDLDLGIVGLDTVSEFGQGNEDLIIVHDALDYGDCRLSLAIPKYGIFE--NINSLRELAQMPQ 204 (349)
Q Consensus 127 vev~~vR~~DIP~yV~~G~aDlGIvG~DvL~E~~~~~~~lv~~l~dLgfG~CRLvvAvP~~~~~~--dv~sl~dL~~~~~ 204 (349)
+++......|+...|.+|.+|+||+..+.-.+.+ +. ...++.=++++.+|.+..+. .--+++||...+
T Consensus 124 l~~~~~~~~~~~~~L~~~~~D~~i~~~~~~~~~~-----l~----~~~l~~~~~~~v~~~~hpl~~~~~~~~~~L~~~~- 193 (309)
T PRK12683 124 LALRQGSPQEIAEMLLNGEADIGIATEALDREPD-----LV----SFPYYSWHHVVVVPKGHPLTGRENLTLEAIAEYP- 193 (309)
T ss_pred EEEEeCCHHHHHHHHHcCCccEEEecCCCCCCCC-----ce----EEEcccCeEEEEecCCCCcccCCccCHHHHhcCC-
Confidence 3444446689999999999999997543222221 11 12234446677777664331 224567776531
Q ss_pred cCCCCCcEEEcC----CCccHHHHHHhcCCc
Q 018854 205 WTAEKPLRVATG----FTYLGPKFMKDNGLK 231 (349)
Q Consensus 205 ~~~~~~lRVATk----YPnlar~yf~~~Gi~ 231 (349)
-|... +.....++|.+.|+.
T Consensus 194 -------~i~~~~~~~~~~~~~~~~~~~~~~ 217 (309)
T PRK12683 194 -------IITYDQGFTGRSRIDQAFAEAGLV 217 (309)
T ss_pred -------eEeccCCCcHHHHHHHHHHHCCCC
Confidence 22221 234456788888875
No 109
>PRK11233 nitrogen assimilation transcriptional regulator; Provisional
Probab=47.15 E-value=55 Score=30.96 Aligned_cols=88 Identities=15% Similarity=0.109 Sum_probs=51.5
Q ss_pred CCeEEEee--cCCchhhhcccCceeeeeeccceecccCCCCccceeecCCCCcccEEEEEEEeCCCccCcccchHHhhcC
Q 018854 125 SNLEVWFQ--RPKDIVRKLLSGDLDLGIVGLDTVSEFGQGNEDLIIVHDALDYGDCRLSLAIPKYGIFENINSLRELAQM 202 (349)
Q Consensus 125 p~vev~~v--R~~DIP~yV~~G~aDlGIvG~DvL~E~~~~~~~lv~~l~dLgfG~CRLvvAvP~~~~~~dv~sl~dL~~~ 202 (349)
|++++.+. ...++...+..|.+|+||+.... .+ .++. --.++..+++++++.+.. ...-+++||...
T Consensus 119 p~i~l~~~~~~~~~~~~~l~~g~~Di~i~~~~~-~~-----~~~~----~~~l~~~~~~lv~~~~~~-~~~~~~~~l~~~ 187 (305)
T PRK11233 119 PGIVLYLHENSGATLNEKLMNGQLDMAVIYEHS-PV-----AGLS----SQPLLKEDLFLVGTQDCP-GQSVDLAAVAQM 187 (305)
T ss_pred CCcEEEEEECCcHHHHHHHHCCCCCEEEEcCCc-CC-----CCcE----EEEEeeeeEEEEEcCccC-CCCcCHHHHhCC
Confidence 45555443 45788899999999999975321 11 1222 124567778888877632 334466777653
Q ss_pred CccCCCCCcEEEcC----CCccHHHHHHhcCCc
Q 018854 203 PQWTAEKPLRVATG----FTYLGPKFMKDNGLK 231 (349)
Q Consensus 203 ~~~~~~~~lRVATk----YPnlar~yf~~~Gi~ 231 (349)
+ -|... +.....++|.+.|+.
T Consensus 188 ~--------~i~~~~~~~~~~~~~~~~~~~g~~ 212 (305)
T PRK11233 188 N--------LFLPRDYSAVRLRVDEAFSLRRLT 212 (305)
T ss_pred C--------eecCCCCccHHHHHHHHHHHcCCC
Confidence 1 11111 123456678888875
No 110
>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=46.58 E-value=47 Score=27.48 Aligned_cols=87 Identities=13% Similarity=0.029 Sum_probs=42.7
Q ss_pred CCeEEEeecCCchhhhcccCceeeeeeccceecccCCCCccceeecCCCCcccEEEEEEEeCCCccCcccchHHhhcCCc
Q 018854 125 SNLEVWFQRPKDIVRKLLSGDLDLGIVGLDTVSEFGQGNEDLIIVHDALDYGDCRLSLAIPKYGIFENINSLRELAQMPQ 204 (349)
Q Consensus 125 p~vev~~vR~~DIP~yV~~G~aDlGIvG~DvL~E~~~~~~~lv~~l~dLgfG~CRLvvAvP~~~~~~dv~sl~dL~~~~~ 204 (349)
|++++.+.-..+....+.. .+|+||+..... . .++. -..+++=+++++++.+.. ...-+++||.+.
T Consensus 27 P~i~l~~~~~~~~~~~~~~-~~D~~i~~~~~~-~-----~~l~----~~~l~~~~~~~v~~~~~~-~~~~~~~~L~~~-- 92 (189)
T cd08484 27 PFIDLRLSTNNNRVDIAAE-GLDFAIRFGEGA-W-----PGTD----ATRLFEAPLSPLCTPELA-RRLSEPADLANE-- 92 (189)
T ss_pred CCceEEEecccCccccccC-CccEEEEecCCC-C-----CCce----EEEccCCceEEeeCHHHh-cccCChhHhhcC--
Confidence 4555554433444445555 499999854321 1 1221 122445566666665421 112356777652
Q ss_pred cCCCCCcEEEcCCCccHHHHHHhcCCc
Q 018854 205 WTAEKPLRVATGFTYLGPKFMKDNGLK 231 (349)
Q Consensus 205 ~~~~~~lRVATkYPnlar~yf~~~Gi~ 231 (349)
+ -|.......-+++|++.|+.
T Consensus 93 -----~-~i~~~~~~~~~~~~~~~~~~ 113 (189)
T cd08484 93 -----T-LLRSYRADEWPQWFEAAGVP 113 (189)
T ss_pred -----c-eEecCCCchHHHHHHHcCCC
Confidence 1 23221112345688888864
No 111
>PRK09508 leuO leucine transcriptional activator; Reviewed
Probab=46.51 E-value=1.2e+02 Score=28.83 Aligned_cols=92 Identities=13% Similarity=0.084 Sum_probs=54.6
Q ss_pred CCCeEEEee--cCCchhhhcccCceeeeeeccceecccCCCCccceeecCCCCcccEEEEEEEeCCCcc-CcccchHHhh
Q 018854 124 LSNLEVWFQ--RPKDIVRKLLSGDLDLGIVGLDTVSEFGQGNEDLIIVHDALDYGDCRLSLAIPKYGIF-ENINSLRELA 200 (349)
Q Consensus 124 ~p~vev~~v--R~~DIP~yV~~G~aDlGIvG~DvL~E~~~~~~~lv~~l~dLgfG~CRLvvAvP~~~~~-~dv~sl~dL~ 200 (349)
.|++++-+. -..++...|..|.+|+||+..+.-. .++. .-.++.+++++.++.+... ...-+++||.
T Consensus 138 ~P~i~l~i~~~~~~~~~~~l~~g~~Di~i~~~~~~~------~~l~----~~~l~~~~~~lv~~~~hpl~~~~~~~~~L~ 207 (314)
T PRK09508 138 APNIHVVFKSSLNQNIEHQLRYQETEFVISYEEFDR------PEFT----SVPLFKDELVLVASKNHPRIKGPITEEQLY 207 (314)
T ss_pred CCCcEEEEEeCcchhHHHHHhcCCccEEEecCCCCc------cccc----eeeeecCceEEEEcCCCCccCCCCCHHHHh
Confidence 456666655 3578899999999999998654311 1222 2345778888888876321 1223567776
Q ss_pred cCCccCCCCCcEEE-cCCCccHHHHHHhcCCc
Q 018854 201 QMPQWTAEKPLRVA-TGFTYLGPKFMKDNGLK 231 (349)
Q Consensus 201 ~~~~~~~~~~lRVA-TkYPnlar~yf~~~Gi~ 231 (349)
.... ..+. ..+-....++|.+.|+.
T Consensus 208 ~~~~------~~~~~~~~~~~~~~~~~~~g~~ 233 (314)
T PRK09508 208 NEQH------AVVSLDRFASFSQPWYDTVDKQ 233 (314)
T ss_pred hCCC------EEecCCCCccHHHHHHHhcCcC
Confidence 4211 1222 12233456788888874
No 112
>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=46.20 E-value=17 Score=35.26 Aligned_cols=223 Identities=13% Similarity=0.052 Sum_probs=114.6
Q ss_pred ceEEEecC--CCCchHHHH-HHHHHCCCccCCCCCCceEEecCCCCCeEEEeecCCchhhhcccCceeeeeeccceeccc
Q 018854 83 EIRLGLPS--KGRMAADTL-DLLKDCQLSVKQVNPRQYVAQIPQLSNLEVWFQRPKDIVRKLLSGDLDLGIVGLDTVSEF 159 (349)
Q Consensus 83 ~LrIALP~--KGRL~e~t~-~LL~~aGi~~~~~~~R~L~~~~~~~p~vev~~vR~~DIP~yV~~G~aDlGIvG~DvL~E~ 159 (349)
.|+||.++ -+.+..... .+|++.|+++.. . .. -...+-.-++.|.+|+-.-. |+-.+
T Consensus 9 ~I~ig~~~w~~~~~~~~i~~~iLE~~Gy~Ve~----~-~~-------------~~~~~~~al~~GdiD~~~e~--W~p~~ 68 (290)
T TIGR03414 9 TVRFADVGWTDITATTALASVLLEGLGYQPKV----T-LL-------------SVPVTYAGLKDGDLDVFLGN--WMPAM 68 (290)
T ss_pred eEEEeeCCcchHHHHHHHHHHHHHHcCCccee----E-Ec-------------cHHHHHHHHHcCCceEeccc--cCCcC
Confidence 48888862 011112222 577777886532 1 01 11234456778888876644 33221
Q ss_pred C------CCCccceeecCCCCcccEEEEEEEeCCCccCcccchHHhhcCCccCCCCCcEEEcCC-Ccc---HHHHHH--h
Q 018854 160 G------QGNEDLIIVHDALDYGDCRLSLAIPKYGIFENINSLRELAQMPQWTAEKPLRVATGF-TYL---GPKFMK--D 227 (349)
Q Consensus 160 ~------~~~~~lv~~l~dLgfG~CRLvvAvP~~~~~~dv~sl~dL~~~~~~~~~~~lRVATkY-Pnl---ar~yf~--~ 227 (349)
. .+... +..+..+++| -+.-++||+...-.+|+|++||........ +.-++-.- +.. +.++++ .
T Consensus 69 ~~~~~~~~~~~~-l~~lg~~~~~-~~~g~~Vp~y~ae~~i~sisDL~~~a~~f~--g~~~g~~~g~~~~~~~~~~~~~~~ 144 (290)
T TIGR03414 69 EPDIKPYLESGS-VEVLGPNLEG-AKYTLAVPTYVADAGLKSFADIAKFKDKLD--GKIYGIEPGNDGNRLIQKMIDKNA 144 (290)
T ss_pred HHHHHhhccCCe-EEEecccCCC-ceEEEEEChhhhhcCCCCHHHHhhHHHhcC--CEEEcccCChhHHHHHHHHHhhcc
Confidence 1 00112 3344456675 677999998742137999999975322111 11111100 111 223444 3
Q ss_pred cCCceEEEEecCC-----ccccccCCCcceeeeecccchhhHhhCCcEEecC-ceEE-----EEEEEEEeecchhhhhcC
Q 018854 228 NGLKHVVFSTADG-----ALEAAPAMGIADAILDLVSSGTTLRENNLKEIEG-GVVL-----ESQAVLVASRKSLIRRKG 296 (349)
Q Consensus 228 ~Gi~~v~Ii~l~G-----SvElAP~lGlAD~IVDIVsTGtTLraNgLk~ie~-g~Il-----eSsA~LIaN~~s~~~k~~ 296 (349)
-|+..++.+..++ .+.-|-.-|-. .++-.=+|=-.+.+-+|+.++| ..++ .+..+.++|+......+
T Consensus 145 ygL~~~~~~~~s~~a~~a~~~~A~~~~e~-~v~~~w~P~w~~~~~dl~~LeD~~~~~g~~~~~~~i~~v~~~~~~~~~P- 222 (290)
T TIGR03414 145 FGLGGFKLVESSEAGMLAQVARAVKRKEW-VVFLGWEPHPMNTNFKMTYLTGGDDYFGPNYGGATVYTNTRKGYAAECP- 222 (290)
T ss_pred CCCCCceEeecCHHHHHHHHHHHHHCCCC-EEEEEecCchhhhccceeECCCCccccCCCCCCCeEEEEeccchHHHCh-
Confidence 4664455554111 11122222322 2333444555567788999987 3333 15566788888665544
Q ss_pred chhHHHHHHHHHHHHHhhcCeeEEEEecCCCCHHHHHH
Q 018854 297 VLDATHEILERLEAHLRASGQFTVTANMRGNSAEEVAE 334 (349)
Q Consensus 297 ~~~~i~~li~rl~~vl~Ar~~~~v~~N~p~~~l~~v~~ 334 (349)
.+.+++++|..-+......+-.+...+...++|++
T Consensus 223 ---~~~~~L~~~~~~~~~~~~l~~~~~~~~~~p~~vA~ 257 (290)
T TIGR03414 223 ---NVGKLLTNLTFTLDMENQIMGAILNDGKDPEAAAR 257 (290)
T ss_pred ---HHHHHHHhCCcCHHHHHHHHHHHHhcCCCHHHHHH
Confidence 56777777776555544444444555667777755
No 113
>COG0834 HisJ ABC-type amino acid transport/signal transduction systems, periplasmic component/domain [Amino acid transport and metabolism / Signal transduction mechanisms]
Probab=46.05 E-value=1.4e+02 Score=26.88 Aligned_cols=120 Identities=19% Similarity=0.123 Sum_probs=76.9
Q ss_pred eEEEeecCCchhhhcccCceeeeeeccceecccCCCCccceeecCCCCcccEEEEEEEeCCCccCcccchHHhhcCCccC
Q 018854 127 LEVWFQRPKDIVRKLLSGDLDLGIVGLDTVSEFGQGNEDLIIVHDALDYGDCRLSLAIPKYGIFENINSLRELAQMPQWT 206 (349)
Q Consensus 127 vev~~vR~~DIP~yV~~G~aDlGIvG~DvL~E~~~~~~~lv~~l~dLgfG~CRLvvAvP~~~~~~dv~sl~dL~~~~~~~ 206 (349)
+++..+.-+..-..+..|.+|+.+.+..+..|.... +. . .-+|..-...+.++.+.. ..+.+.+||.+
T Consensus 79 ~~~~~~~~~~~~~~l~~g~~D~~~~~~~~t~er~~~---~~--f-s~py~~~~~~~~~~~~~~-~~~~~~~DL~g----- 146 (275)
T COG0834 79 VEFVPVAWDGLIPALKAGKVDIIIAGMTITPERKKK---VD--F-SDPYYYSGQVLLVKKDSD-IGIKSLEDLKG----- 146 (275)
T ss_pred eEEeccchhhhhHHHhcCCcCEEEeccccCHHHhcc---cc--c-cccccccCeEEEEECCCC-cCcCCHHHhCC-----
Confidence 445566678888999999999999996666665422 11 1 245566666777776632 22568899885
Q ss_pred CCCCcEEEcCCCcc--HHHHHHhcCCceEEEEecCCc--cccccCCCcceeeeecccchhh
Q 018854 207 AEKPLRVATGFTYL--GPKFMKDNGLKHVVFSTADGA--LEAAPAMGIADAILDLVSSGTT 263 (349)
Q Consensus 207 ~~~~lRVATkYPnl--ar~yf~~~Gi~~v~Ii~l~GS--vElAP~lGlAD~IVDIVsTGtT 263 (349)
+||+..-=-. ...+....+- .++++..... .-.+-.-|-+|+++.--.+...
T Consensus 147 ----k~v~v~~gt~~~~~~~~~~~~~-~~~~~~~~~~~~~~~al~~Gr~Da~~~d~~~~~~ 202 (275)
T COG0834 147 ----KKVGVQLGTTDEAEEKAKKPGP-NAKIVAYDSNAEALLALKNGRADAVVSDSAVLAG 202 (275)
T ss_pred ----CEEEEEcCcchhHHHHHhhccC-CceEEeeCCHHHHHHHHHcCCccEEEcchHhhhh
Confidence 4666544322 4445444443 4678887776 3334678999999865555555
No 114
>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=45.47 E-value=1.1e+02 Score=25.44 Aligned_cols=93 Identities=18% Similarity=0.131 Sum_probs=50.3
Q ss_pred CCeEEEee--cCCchhhhcccCceeeeeeccceecccCCCCccceeecCCCCcccEEEEEEEeCCCccC--cccchHHhh
Q 018854 125 SNLEVWFQ--RPKDIVRKLLSGDLDLGIVGLDTVSEFGQGNEDLIIVHDALDYGDCRLSLAIPKYGIFE--NINSLRELA 200 (349)
Q Consensus 125 p~vev~~v--R~~DIP~yV~~G~aDlGIvG~DvL~E~~~~~~~lv~~l~dLgfG~CRLvvAvP~~~~~~--dv~sl~dL~ 200 (349)
|++++-+. ...++...+.+|.+|+||.-.+. . . .++. ..-++...++++++.+..+. ..-+++||.
T Consensus 27 P~i~i~i~~~~~~~~~~~l~~g~~Dl~i~~~~~-~--~---~~~~----~~~l~~~~~~~~~~~~~~l~~~~~~~~~~l~ 96 (198)
T cd08441 27 PDVELDLSSGFHFDPLPALLRGELDLVITSDPL-P--L---PGIA----YEPLFDYEVVLVVAPDHPLAAKEFITPEDLA 96 (198)
T ss_pred CCeEEEEEeCCchhHHHHHHcCCceEEEecCCc-C--C---CCcE----EEEccCCcEEEEEcCCCChHHcccCCHHHhc
Confidence 55555444 44688999999999999963221 1 1 1222 23356677777777663221 123566665
Q ss_pred cCCccCCCCCcEEEcCCCccHHHHHHhcCCc
Q 018854 201 QMPQWTAEKPLRVATGFTYLGPKFMKDNGLK 231 (349)
Q Consensus 201 ~~~~~~~~~~lRVATkYPnlar~yf~~~Gi~ 231 (349)
..+-... .-.+.+.....+||++.|+.
T Consensus 97 ~~~~i~~----~~~~~~~~~~~~~~~~~~~~ 123 (198)
T cd08441 97 DETLITY----PVERERLDVFRHFLQPAGIE 123 (198)
T ss_pred CCceEEe----cCCccHHHHHHHHHHhcCCC
Confidence 4211000 00112334556788888864
No 115
>PRK15437 histidine ABC transporter substrate-binding protein HisJ; Provisional
Probab=44.29 E-value=2.6e+02 Score=25.71 Aligned_cols=110 Identities=15% Similarity=0.081 Sum_probs=59.2
Q ss_pred CchhhhcccCceeeeeeccceecccCCCCccceeecCCCCcccEEEEEEEeCCCccCcccchHHhhcCCccCCCCCcEEE
Q 018854 135 KDIVRKLLSGDLDLGIVGLDTVSEFGQGNEDLIIVHDALDYGDCRLSLAIPKYGIFENINSLRELAQMPQWTAEKPLRVA 214 (349)
Q Consensus 135 ~DIP~yV~~G~aDlGIvG~DvL~E~~~~~~~lv~~l~dLgfG~CRLvvAvP~~~~~~dv~sl~dL~~~~~~~~~~~lRVA 214 (349)
..+-..++.|.+|+.+.+...-.|.... +.. .=.+..-..++.++.+..+ ..+++||.+ +|||
T Consensus 75 ~~~~~~l~~g~~D~~~~~~~~t~eR~~~----~~f--s~p~~~~~~~~~~~~~~~~--~~~~~dl~g---------~~Ig 137 (259)
T PRK15437 75 DALIPSLKAKKIDAIMSSLSITEKRQQE----IAF--TDKLYAADSRLVVAKNSDI--QPTVESLKG---------KRVG 137 (259)
T ss_pred HHHHHHHHCCCCCEEEecCCCCHHHhhh----ccc--cchhhcCceEEEEECCCCC--CCChHHhCC---------CEEE
Confidence 4466778999999888776555554321 100 1123344566777776321 236777663 5777
Q ss_pred cCCCccHHHHHHhcCC-ceEEEEecCCcccc--ccCCCcceeeeecccch
Q 018854 215 TGFTYLGPKFMKDNGL-KHVVFSTADGALEA--APAMGIADAILDLVSSG 261 (349)
Q Consensus 215 TkYPnlar~yf~~~Gi-~~v~Ii~l~GSvEl--AP~lGlAD~IVDIVsTG 261 (349)
..-=....+|+++... .+++++...+.-++ +-..|-+|+++---.++
T Consensus 138 v~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~L~~grvD~~v~~~~~~ 187 (259)
T PRK15437 138 VLQGTTQETFGNEHWAPKGIEIVSYQGQDNIYSDLTAGRIDAAFQDEVAA 187 (259)
T ss_pred EecCcHHHHHHHhhccccCceEEecCCHHHHHHHHHcCCccEEEechHHH
Confidence 6443334556555321 12455654443321 23568889866443344
No 116
>PRK11013 DNA-binding transcriptional regulator LysR; Provisional
Probab=44.19 E-value=38 Score=32.09 Aligned_cols=101 Identities=12% Similarity=0.092 Sum_probs=55.3
Q ss_pred eEEEeecCCchhhhcccCceeeeeeccceecccCCCCccceeecCCCCcccEEEEEEEeCCCccC--cccchHHhhcCCc
Q 018854 127 LEVWFQRPKDIVRKLLSGDLDLGIVGLDTVSEFGQGNEDLIIVHDALDYGDCRLSLAIPKYGIFE--NINSLRELAQMPQ 204 (349)
Q Consensus 127 vev~~vR~~DIP~yV~~G~aDlGIvG~DvL~E~~~~~~~lv~~l~dLgfG~CRLvvAvP~~~~~~--dv~sl~dL~~~~~ 204 (349)
+++......++-..+.+|.+|+||+..+.. +.+ +. ---++...+++++|.+.... +.-+++||...+.
T Consensus 125 i~i~~~~~~~~~~~l~~~~~Dl~i~~~~~~-~~~-----~~----~~~l~~~~~~~~~~~~~pl~~~~~i~~~dL~~~~~ 194 (309)
T PRK11013 125 LNIVPQESPLLEEWLSAQRHDLGLTETLHT-PAG-----TE----RTELLTLDEVCVLPAGHPLAAKKVLTPDDFAGENF 194 (309)
T ss_pred EEEEeCCHHHHHHHHHcCCCCEEEEcCCCC-CCC-----ce----eeeecceeEEEEEcCCCccccCCccCHHHHCCCcE
Confidence 344444566778899999999999865532 222 11 11234455677777653211 2235677765311
Q ss_pred cCCCCCcEE--EcCCCccHHHHHHhcCCceEEEEecCCcccc
Q 018854 205 WTAEKPLRV--ATGFTYLGPKFMKDNGLKHVVFSTADGALEA 244 (349)
Q Consensus 205 ~~~~~~lRV--ATkYPnlar~yf~~~Gi~~v~Ii~l~GSvEl 244 (349)
+.. .+.|..+..+||.+.|+. -.++.-..+.+.
T Consensus 195 ------i~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~ 229 (309)
T PRK11013 195 ------ISLSRTDSYRQLLDQLFAEHGVK-RRMVVETHSAAS 229 (309)
T ss_pred ------EeecCCCcHHHHHHHHHHHcCCC-cceEEEeccHHH
Confidence 111 123445678899999985 344433344443
No 117
>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=43.27 E-value=44 Score=28.07 Aligned_cols=67 Identities=18% Similarity=0.274 Sum_probs=39.5
Q ss_pred CCeEEEee--cCCchhhhcccCceeeeeeccceecccCCCCccceeecCCCCcccEEEEEEEeCCCccCc---ccchHHh
Q 018854 125 SNLEVWFQ--RPKDIVRKLLSGDLDLGIVGLDTVSEFGQGNEDLIIVHDALDYGDCRLSLAIPKYGIFEN---INSLREL 199 (349)
Q Consensus 125 p~vev~~v--R~~DIP~yV~~G~aDlGIvG~DvL~E~~~~~~~lv~~l~dLgfG~CRLvvAvP~~~~~~d---v~sl~dL 199 (349)
|++++-+. ...++-..+.+|.+|+||+... ... .++. ...++..+++++++++..... .-+++||
T Consensus 28 P~i~l~i~~~~~~~~~~~l~~~~~Dl~i~~~~-~~~-----~~~~----~~~l~~~~~~~v~~~~hpl~~~~~~i~~~dL 97 (203)
T cd08445 28 PDVEIELIEMTTVQQIEALKEGRIDVGFGRLR-IED-----PAIR----RIVLREEPLVVALPAGHPLAQEKAPLTLAQL 97 (203)
T ss_pred CCeEEEEEeCChHHHHHHHHcCCCcEEEecCC-CCC-----CCce----eEEEEeccEEEEeeCCCCCccCCCCcCHHHh
Confidence 45554444 5678999999999999996321 111 1222 123456677888877632211 2356777
Q ss_pred hc
Q 018854 200 AQ 201 (349)
Q Consensus 200 ~~ 201 (349)
.+
T Consensus 98 ~~ 99 (203)
T cd08445 98 AD 99 (203)
T ss_pred cC
Confidence 65
No 118
>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=41.49 E-value=50 Score=30.09 Aligned_cols=95 Identities=16% Similarity=0.126 Sum_probs=52.0
Q ss_pred eecCCchhhhcccCceeeeeeccceecccCCCCccceeecCCCCcccEEEEEEEeCCCccCcc--cchHHhhcCCccCCC
Q 018854 131 FQRPKDIVRKLLSGDLDLGIVGLDTVSEFGQGNEDLIIVHDALDYGDCRLSLAIPKYGIFENI--NSLRELAQMPQWTAE 208 (349)
Q Consensus 131 ~vR~~DIP~yV~~G~aDlGIvG~DvL~E~~~~~~~lv~~l~dLgfG~CRLvvAvP~~~~~~dv--~sl~dL~~~~~~~~~ 208 (349)
.-...++...+..|.+|+||+..+.- . .++. . -.++.=+++++++.+..+..- -+++||...+
T Consensus 119 ~~~~~~~~~~l~~g~~Dl~i~~~~~~---~---~~~~-~---~~l~~~~~~lv~s~~~pl~~~~~i~~~~L~~~~----- 183 (279)
T TIGR03339 119 IGNSQEVLQALQSYRVDVAVSSEVVD---D---PRLD-R---VVLGNDPLVAVVHRQHPLAERESVTLEELAGQP----- 183 (279)
T ss_pred ECCHHHHHHHHHcCCCcEEEEecccC---C---CceE-E---EEcCCceEEEEECCCCccccCCCcCHHHHhCCC-----
Confidence 33556788999999999999864421 1 1221 1 234455778888766433221 2566776531
Q ss_pred CCcEEEcC----CCccHHHHHHhcCCceEEEEecCCcccc
Q 018854 209 KPLRVATG----FTYLGPKFMKDNGLKHVVFSTADGALEA 244 (349)
Q Consensus 209 ~~lRVATk----YPnlar~yf~~~Gi~~v~Ii~l~GSvEl 244 (349)
-|... +.....+||++.|+. .....-.++.+.
T Consensus 184 ---~i~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~ 219 (279)
T TIGR03339 184 ---LLMREPGSVTRQTTEEALAAAGVA-PRPALEIGSREA 219 (279)
T ss_pred ---eEEecCCCChHHHHHHHHHHcCCC-ccEEEEeCCHHH
Confidence 12211 123456788888875 233322344443
No 119
>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=41.07 E-value=1.2e+02 Score=29.30 Aligned_cols=151 Identities=16% Similarity=0.228 Sum_probs=77.1
Q ss_pred CCchhhhcccCceeeeeeccce-ecccCCC-CccceeecCCCCcccEEEEEEEeCCCccCcccchHHhhcCCccCCCCCc
Q 018854 134 PKDIVRKLLSGDLDLGIVGLDT-VSEFGQG-NEDLIIVHDALDYGDCRLSLAIPKYGIFENINSLRELAQMPQWTAEKPL 211 (349)
Q Consensus 134 ~~DIP~yV~~G~aDlGIvG~Dv-L~E~~~~-~~~lv~~l~dLgfG~CRLvvAvP~~~~~~dv~sl~dL~~~~~~~~~~~l 211 (349)
..+.-.-+..|.+|+++.+..- +.....+ ..+++. .| .. ...|-+.....+++++||.. +.
T Consensus 56 ~~~~~~Al~~G~ID~~~~q~~~~l~~~~~~~g~~lv~----v~--~~---~~~p~~~ys~~~~sl~dlk~--------G~ 118 (258)
T TIGR00363 56 YALPNEAVSKGDLDANAFQHKPYLDQDAKAKGYKLVA----VG--NT---FVYPLAGYSKKIKNVNELQD--------GA 118 (258)
T ss_pred cHHHHHHHHcCCCCeEecCCHHHHHHHHHhCCCcEEE----Ee--ee---EEecccccCcCCCCHHHcCC--------CC
Confidence 3456678999999999876654 4422111 123321 11 11 12222222356889999863 36
Q ss_pred EEEcC--CCccHH--HHHHhcCCc--------------------eEEEEecCCccccccCCCc--ceeeeecccchhhHh
Q 018854 212 RVATG--FTYLGP--KFMKDNGLK--------------------HVVFSTADGALEAAPAMGI--ADAILDLVSSGTTLR 265 (349)
Q Consensus 212 RVATk--YPnlar--~yf~~~Gi~--------------------~v~Ii~l~GSvElAP~lGl--AD~IVDIVsTGtTLr 265 (349)
+||.. .-|..| +.|++.|+- +++++.+.-+- +...+.- .|+.+ -.+.-+.
T Consensus 119 ~IAip~d~~n~~raL~~L~~aGLi~l~~~~~~~~t~~DI~~n~~~v~~vel~~~~-~~~al~~g~vDaa~---v~~~~~~ 194 (258)
T TIGR00363 119 KVAVPNDPTNLGRALLLLQKQGLIKLKDGNGLLPTVLDIVENPKKLNITELETSQ-LPRALDDPKVDLAV---INTTYAG 194 (258)
T ss_pred EEEEeCCcchHHHHHHHHHHcCCceecCCCCCcCChhhhhcCCCCCEEEEcCHHH-HHHHhhcccccEEE---EChHHHH
Confidence 89864 222233 357887761 36666655432 2222222 33322 2445566
Q ss_pred hCCcEEecCceEEEE----EEEEE-eecchhhhhcCchhHHHHHHHHHHH
Q 018854 266 ENNLKEIEGGVVLES----QAVLV-ASRKSLIRRKGVLDATHEILERLEA 310 (349)
Q Consensus 266 aNgLk~ie~g~IleS----sA~LI-aN~~s~~~k~~~~~~i~~li~rl~~ 310 (349)
+.||...+++.++++ .+.++ ++.. +...+.+..|+++++.
T Consensus 195 ~agl~~~~~~i~~e~~~~~~~n~l~~r~~-----~~~~~~~~~lv~~~~s 239 (258)
T TIGR00363 195 QVGLNPQDDGVFVEDKDSPYVNIIVSRED-----NKDAENVKDFIQSYQS 239 (258)
T ss_pred HcCCCcCcCceeecCCCCCeeEEEEEcCC-----ccCCHHHHHHHHHHcC
Confidence 677776544444443 22333 4442 1123577888877653
No 120
>PRK12680 transcriptional regulator CysB-like protein; Reviewed
Probab=40.84 E-value=66 Score=31.17 Aligned_cols=105 Identities=16% Similarity=0.141 Sum_probs=56.5
Q ss_pred CCCeEEEee--cCCchhhhcccCceeeeeeccceecccCCCCccceeecCCCCcccEEEEEEEeCCCccC---cccchHH
Q 018854 124 LSNLEVWFQ--RPKDIVRKLLSGDLDLGIVGLDTVSEFGQGNEDLIIVHDALDYGDCRLSLAIPKYGIFE---NINSLRE 198 (349)
Q Consensus 124 ~p~vev~~v--R~~DIP~yV~~G~aDlGIvG~DvL~E~~~~~~~lv~~l~dLgfG~CRLvvAvP~~~~~~---dv~sl~d 198 (349)
.|++++.+. ...++-..+..|.+|+||+......+. +.+ ...++.-++++++|.+..+. ..-+++|
T Consensus 119 ~P~v~i~l~~~~~~~~~~~l~~g~~Dl~i~~~~~~~~~-----~~~----~~~l~~~~~~l~~~~~hpl~~~~~~~~~~d 189 (327)
T PRK12680 119 YPQVSVHLQQAAESAALDLLGQGDADIAIVSTAGGEPS-----AGI----AVPLYRWRRLVVVPRGHALDTPRRAPDMAA 189 (327)
T ss_pred CCCcEEEEEeCChHHHHHHHHCCCCcEEEEecCCCCCC-----cce----EEEeeccceEEEEeCCChhhccCCCCCHHH
Confidence 355555443 567899999999999999754321111 111 12344566677777653322 2235677
Q ss_pred hhcCCccCCCCCcEEEc--CCCccHHHHHHhcCCceEEEEecCCcccc
Q 018854 199 LAQMPQWTAEKPLRVAT--GFTYLGPKFMKDNGLKHVVFSTADGALEA 244 (349)
Q Consensus 199 L~~~~~~~~~~~lRVAT--kYPnlar~yf~~~Gi~~v~Ii~l~GSvEl 244 (349)
|.+.+- +.... .+-....++|++.|+. ..+..-..+.+.
T Consensus 190 l~~~~~------i~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~ 230 (327)
T PRK12680 190 LAEHPL------ISYESSTRPGSSLQRAFAQLGLE-PSIALTALDADL 230 (327)
T ss_pred HhcCCE------EEecCCCchHHHHHHHHHHCCCC-CcEEEEECCHHH
Confidence 765321 11111 1224567788888874 233333344443
No 121
>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=40.65 E-value=51 Score=27.47 Aligned_cols=73 Identities=14% Similarity=0.036 Sum_probs=38.8
Q ss_pred hcccCceeeeeeccceecccCCCCccceeecCCCCcccEEEEEEEeCCCccCcccchHHhhcCCccCCCCCcEEEcCCCc
Q 018854 140 KLLSGDLDLGIVGLDTVSEFGQGNEDLIIVHDALDYGDCRLSLAIPKYGIFENINSLRELAQMPQWTAEKPLRVATGFTY 219 (349)
Q Consensus 140 yV~~G~aDlGIvG~DvL~E~~~~~~~lv~~l~dLgfG~CRLvvAvP~~~~~~dv~sl~dL~~~~~~~~~~~lRVATkYPn 219 (349)
.+..|.+|+||+..... . .++. .-.+++-+++++++.+.. ...-+++||.+.+ -|.....+
T Consensus 41 ~l~~~~~D~~i~~~~~~-~-----~~~~----~~~l~~~~~~~v~~~~l~-~~~~~~~dL~~~~--------~i~~~~~~ 101 (191)
T cd08488 41 DIAAEGLDYAIRFGSGA-W-----HGID----ATRLFEAPLSPLCTPELA-RQLREPADLARHT--------LLRSYRAD 101 (191)
T ss_pred ccCCCCccEEEEecCCC-C-----CCcE----EEEccCCcEEEEeCHHHh-cccCCHHHHhhCc--------EEecCCcc
Confidence 46679999999743211 1 1111 122345566666665421 1224678877531 23322223
Q ss_pred cHHHHHHhcCCc
Q 018854 220 LGPKFMKDNGLK 231 (349)
Q Consensus 220 lar~yf~~~Gi~ 231 (349)
..++||.+.|..
T Consensus 102 ~~~~~~~~~~~~ 113 (191)
T cd08488 102 EWPQWFEAAGVG 113 (191)
T ss_pred HHHHHHHHcCCC
Confidence 567889888863
No 122
>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=40.35 E-value=40 Score=27.99 Aligned_cols=68 Identities=13% Similarity=0.104 Sum_probs=38.9
Q ss_pred CCeEEEee--cCCchhhhcccCceeeeeeccceecccCCCCccceeecCCCCcccEEEEEEEeCCCccC---cccchHHh
Q 018854 125 SNLEVWFQ--RPKDIVRKLLSGDLDLGIVGLDTVSEFGQGNEDLIIVHDALDYGDCRLSLAIPKYGIFE---NINSLREL 199 (349)
Q Consensus 125 p~vev~~v--R~~DIP~yV~~G~aDlGIvG~DvL~E~~~~~~~lv~~l~dLgfG~CRLvvAvP~~~~~~---dv~sl~dL 199 (349)
|++++.+. ...++...+..|.+|+||+....... .++. -..++...++++++.+.... .--+++||
T Consensus 27 P~v~i~i~~~~~~~~~~~l~~g~~D~~i~~~~~~~~-----~~~~----~~~l~~~~~~~v~~~~hpl~~~~~~~~~~~L 97 (195)
T cd08431 27 KATRIRLSEEVLGGTWDALASGRADLVIGATGELPP-----GGVK----TRPLGEVEFVFAVAPNHPLAKLDGPLDASAI 97 (195)
T ss_pred CCCceEEEEeccchHHHHHhCCCCCEEEEecCCCCC-----CceE----EEecccceEEEEEcCCChhhhccCCCCHHHH
Confidence 44444443 45688899999999999975321111 1222 23345667787777663211 12356676
Q ss_pred hc
Q 018854 200 AQ 201 (349)
Q Consensus 200 ~~ 201 (349)
..
T Consensus 98 ~~ 99 (195)
T cd08431 98 KQ 99 (195)
T ss_pred hh
Confidence 64
No 123
>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=39.48 E-value=66 Score=26.50 Aligned_cols=87 Identities=14% Similarity=0.074 Sum_probs=44.3
Q ss_pred CCeEEEeecCCchhhhcccCceeeeeeccceecccCCCCccceeecCCCCcccEEEEEEEeCCCccCcccchHHhhcCCc
Q 018854 125 SNLEVWFQRPKDIVRKLLSGDLDLGIVGLDTVSEFGQGNEDLIIVHDALDYGDCRLSLAIPKYGIFENINSLRELAQMPQ 204 (349)
Q Consensus 125 p~vev~~vR~~DIP~yV~~G~aDlGIvG~DvL~E~~~~~~~lv~~l~dLgfG~CRLvvAvP~~~~~~dv~sl~dL~~~~~ 204 (349)
|++++.+.-..++.. +..|.+|+||+..... . .++. .-.+++.+++++++.+.. ...-+++||.+.+
T Consensus 27 P~i~l~i~~~~~~~~-~~~~~~Dl~i~~~~~~---~---~~~~----~~~l~~~~~~~v~~~~~~-~~~~~~~~l~~~~- 93 (189)
T cd08487 27 PFIELRLRTNNNVVD-LATEGLDFAIRFGEGL---W---PATH----NERLLDAPLSVLCSPEIA-KRLSHPADLINET- 93 (189)
T ss_pred CCceEEeeecCCccc-cccCCcCEEEEecCCC---C---CCce----eeeeccCceeeeeCHHHh-ccCCCHHHHhcCc-
Confidence 455554443344555 4556799999753211 1 1221 123456677777776521 1223567776421
Q ss_pred cCCCCCcEEEcCCCccHHHHHHhcCCc
Q 018854 205 WTAEKPLRVATGFTYLGPKFMKDNGLK 231 (349)
Q Consensus 205 ~~~~~~lRVATkYPnlar~yf~~~Gi~ 231 (349)
. |.....+...++|.+.|+.
T Consensus 94 ------~-i~~~~~~~~~~~~~~~~~~ 113 (189)
T cd08487 94 ------L-LRSYRTDEWLQWFEAANMP 113 (189)
T ss_pred ------e-eecCCchHHHHHHHHcCCC
Confidence 1 2211113456788888864
No 124
>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=39.20 E-value=37 Score=28.02 Aligned_cols=55 Identities=22% Similarity=0.374 Sum_probs=33.2
Q ss_pred CCeEEEee--cCCchhhhcccCceeeeeeccceecccCCCCccceeecCCCCcccEEEEEEEeCCC
Q 018854 125 SNLEVWFQ--RPKDIVRKLLSGDLDLGIVGLDTVSEFGQGNEDLIIVHDALDYGDCRLSLAIPKYG 188 (349)
Q Consensus 125 p~vev~~v--R~~DIP~yV~~G~aDlGIvG~DvL~E~~~~~~~lv~~l~dLgfG~CRLvvAvP~~~ 188 (349)
|++++.+. ...++-..+.+|.+|+||+....-.+ .++. -..++.-++++++|.+.
T Consensus 27 P~v~l~~~~~~~~~~~~~l~~g~~Dl~i~~~~~~~~-----~~l~----~~~l~~~~~~~~~~~~~ 83 (199)
T cd08430 27 PQVEIKLHTGDPADAIDKVLNGEADIAIAARPDKLP-----ARLA----FLPLATSPLVFIAPNIA 83 (199)
T ss_pred CCceEEEEeCCHHHHHHHHHCCCCCEEEEecCCCCC-----cccE----EEeeccceEEEEEeCCc
Confidence 44544443 45677888999999999986432111 1121 12245667788888763
No 125
>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=39.10 E-value=63 Score=30.98 Aligned_cols=77 Identities=21% Similarity=0.190 Sum_probs=46.0
Q ss_pred ccEEEEEEEeCCCccCcccchHHhhcCCccCCCCCcEEEcC----CCccH-HHHHHhcCCceEEEEecCCcccccc--CC
Q 018854 176 GDCRLSLAIPKYGIFENINSLRELAQMPQWTAEKPLRVATG----FTYLG-PKFMKDNGLKHVVFSTADGALEAAP--AM 248 (349)
Q Consensus 176 G~CRLvvAvP~~~~~~dv~sl~dL~~~~~~~~~~~lRVATk----YPnla-r~yf~~~Gi~~v~Ii~l~GSvElAP--~l 248 (349)
..--.+++++.+ .++++++||-... ..+++.+++|+. .++++ ..++++.|++ ++.|+-.|+-|+.. +=
T Consensus 76 ~~~~~vl~v~~d---sp~~t~~eli~~a-k~~p~~~~~g~~g~g~~~hl~~~~l~~~~G~~-~~~Vpy~G~~~~~~allg 150 (274)
T PF03401_consen 76 ASDPNVLVVRAD---SPYKTLEELIEYA-KANPGKLTFGSSGPGSSDHLAAALLAKAAGIK-FTHVPYDGGAEALTALLG 150 (274)
T ss_dssp EEEEEEEEEETT---SS-SSHHHHHHHH-HCSCCC-EEEESSTTSHHHHHHHHHHHHHT----EEEE-SSHHHHHHHHHT
T ss_pred hccceEEEEeCC---CccccHHHHHHHH-HhCCCCeEEEecCCCchHHHHHHHHHHHhCCc-eEEEEeCCccHHHHHHhC
Confidence 344568888888 5667788875421 233456899885 34555 4456677996 89999999888753 33
Q ss_pred Ccceeeeec
Q 018854 249 GIADAILDL 257 (349)
Q Consensus 249 GlAD~IVDI 257 (349)
|-.|+.+.-
T Consensus 151 G~vd~~~~~ 159 (274)
T PF03401_consen 151 GHVDAAFGS 159 (274)
T ss_dssp TSSSEEEEE
T ss_pred CeeeEEeec
Confidence 666765543
No 126
>PRK10677 modA molybdate transporter periplasmic protein; Provisional
Probab=37.72 E-value=70 Score=30.34 Aligned_cols=147 Identities=15% Similarity=0.133 Sum_probs=77.4
Q ss_pred CcccceeeeeccccccccceeeecCCcCCCCCCCCceEEEecCCCCchHHHHHHHHHCCCccCCCCCCceEEecCCCCCe
Q 018854 48 KPAAAVTCCVSSSQQFESHVSVVNGNIDNRISERDEIRLGLPSKGRMAADTLDLLKDCQLSVKQVNPRQYVAQIPQLSNL 127 (349)
Q Consensus 48 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~LrIALP~KGRL~e~t~~LL~~aGi~~~~~~~R~L~~~~~~~p~v 127 (349)
+-+|...-|+.+...-. .....++.|+|+-. |-+.+...++.++ + . ++. +. .+
T Consensus 4 ~~~~~~~~~~~~~~~~~-----------~~~~~~~~l~v~~a--~~~~~~~~~l~~~--F--e----~~~-----g~-~v 56 (257)
T PRK10677 4 KWLRLFAGAVLSFAVAG-----------NALADEGKITVFAA--ASLTNALQDIAAQ--Y--K----KEK-----GV-DV 56 (257)
T ss_pred hHHHHHHHHHHHhhccc-----------cccccCCcEEEEEe--cChHHHHHHHHHH--H--H----hhh-----CC-eE
Confidence 45666777776543310 01134456899887 5554433333222 1 0 110 11 24
Q ss_pred EEEeecCCchhhhcccCc-eeeeeeccceecccCCCCccceeecCCCCcccEEEEEEEeCCCccCc-----ccchHHhhc
Q 018854 128 EVWFQRPKDIVRKLLSGD-LDLGIVGLDTVSEFGQGNEDLIIVHDALDYGDCRLSLAIPKYGIFEN-----INSLRELAQ 201 (349)
Q Consensus 128 ev~~vR~~DIP~yV~~G~-aDlGIvG~DvL~E~~~~~~~lv~~l~dLgfG~CRLvvAvP~~~~~~d-----v~sl~dL~~ 201 (349)
.+.+-....+...++.|. +|+.+.+..-..+.-.. ..++.......|..-+|++++|++..... .++++||..
T Consensus 57 ~~~~~~Sg~l~~qi~~g~~~Dv~~~a~~~~~~~l~~-~gl~~~~~~~~~a~n~lvl~~~~~~~~~~i~~~~~~~~~dLl~ 135 (257)
T PRK10677 57 VSSFASSSTLARQIEQGAPADLFISADQKWMDYAVD-KKAIDTATRYTLLGNSLVVVAPKASEQKDFTIDKKTDWKSLLN 135 (257)
T ss_pred EEEecccHHHHHHHHcCCCCCEEEECCHHHHHHHHH-CCCCCCcchheeecCEEEEEEECCCccccccccCccCHHHhcC
Confidence 455556667778888888 89999986332222100 11111101235788899999998732211 235666642
Q ss_pred CCccCCCCCcEEEcCCCc------cHHHHHHhcCC
Q 018854 202 MPQWTAEKPLRVATGFTY------LGPKFMKDNGL 230 (349)
Q Consensus 202 ~~~~~~~~~lRVATkYPn------lar~yf~~~Gi 230 (349)
..|||--.|. -++..|++.|+
T Consensus 136 --------~~~iai~dP~~~p~G~~a~~~l~~~g~ 162 (257)
T PRK10677 136 --------GGRLAVGDPDHVPAGIYAKEALQKLGA 162 (257)
T ss_pred --------CCeEEEcCCCCChHHHHHHHHHHHcCC
Confidence 1356555554 45667777775
No 127
>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=35.53 E-value=36 Score=28.58 Aligned_cols=66 Identities=17% Similarity=0.170 Sum_probs=37.6
Q ss_pred CCeEEEeecCCchhhhcccCceeeeeeccceecccCCCCccceeecCCCCcccEEEEEEEeCCCcc--CcccchHHhhc
Q 018854 125 SNLEVWFQRPKDIVRKLLSGDLDLGIVGLDTVSEFGQGNEDLIIVHDALDYGDCRLSLAIPKYGIF--ENINSLRELAQ 201 (349)
Q Consensus 125 p~vev~~vR~~DIP~yV~~G~aDlGIvG~DvL~E~~~~~~~lv~~l~dLgfG~CRLvvAvP~~~~~--~dv~sl~dL~~ 201 (349)
|++++-+.-.+++... ..|.+|+||+..+. .. .++. ...++..+++++++.+... .+.-+++||.+
T Consensus 28 P~i~i~i~~~~~~~~~-~~~~~D~~i~~~~~-~~-----~~~~----~~~l~~~~~~~~~~~~~~~~~~~~~~~~~l~~ 95 (198)
T cd08480 28 PEILVDLSLTDEVVDL-LAERTDVAIRVGPL-PD-----SSLV----ARKLGESRRVIVASPSYLARHGTPLTPQDLAR 95 (198)
T ss_pred CCeEEEEEecCCcccc-ccccccEEEEeCCC-CC-----CCeE----EEEcccceEEEEECHHHHHhcCCCCCHHHHHh
Confidence 5555555445566654 47999999975331 11 1221 2446678888888765211 12235677765
No 128
>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=34.35 E-value=58 Score=30.79 Aligned_cols=60 Identities=22% Similarity=0.275 Sum_probs=43.2
Q ss_pred ceEEEecCCCCchH-HHHHHHHHCCCccCCCCCCceEEecCCCCCeEEEeecCCchhhhcccCceeeeeeccceecc
Q 018854 83 EIRLGLPSKGRMAA-DTLDLLKDCQLSVKQVNPRQYVAQIPQLSNLEVWFQRPKDIVRKLLSGDLDLGIVGLDTVSE 158 (349)
Q Consensus 83 ~LrIALP~KGRL~e-~t~~LL~~aGi~~~~~~~R~L~~~~~~~p~vev~~vR~~DIP~yV~~G~aDlGIvG~DvL~E 158 (349)
--|||++ +|...+ -...+|++.|++.. +++++.+.+.|....+..|.+|..++...+..+
T Consensus 100 GK~Igv~-~~s~~~~~l~~~L~~~Gl~~~---------------dv~~v~~~~~~~~~al~~G~vDa~~~~~p~~~~ 160 (300)
T TIGR01729 100 GKNVAVP-FVSTTHYSLLAALKHWKTDPR---------------EVNILNLKPPQIVAAWQRGDIDAAYVWPPALSE 160 (300)
T ss_pred CCEEEeC-CCCcHHHHHHHHHHHcCCChh---------------heEEEecCcHHHHHHHHcCCcCEEEEecHHHHH
Confidence 3579998 565444 45567888887421 244555677899999999999999998876544
No 129
>PRK12684 transcriptional regulator CysB-like protein; Reviewed
Probab=34.07 E-value=1.3e+02 Score=28.67 Aligned_cols=90 Identities=22% Similarity=0.279 Sum_probs=51.5
Q ss_pred CCeEEEe--ecCCchhhhcccCceeeeeeccceecccCCCCccceeecCCCCcccEEEEEEEeCCCccC--cccchHHhh
Q 018854 125 SNLEVWF--QRPKDIVRKLLSGDLDLGIVGLDTVSEFGQGNEDLIIVHDALDYGDCRLSLAIPKYGIFE--NINSLRELA 200 (349)
Q Consensus 125 p~vev~~--vR~~DIP~yV~~G~aDlGIvG~DvL~E~~~~~~~lv~~l~dLgfG~CRLvvAvP~~~~~~--dv~sl~dL~ 200 (349)
|++++.+ ....++-..+..|.+|+||+..+.... .++. ...+++-.+++.+|.+..+. ..-+++||.
T Consensus 120 p~i~l~~~~~~~~~~~~~L~~g~~D~~i~~~~~~~~-----~~l~----~~~l~~~~~~~v~~~~~pl~~~~~i~~~dL~ 190 (313)
T PRK12684 120 PKVRLSILQGSPTQIAEMVLHGQADLAIATEAIADY-----KELV----SLPCYQWNHCVVVPPDHPLLERKPLTLEDLA 190 (313)
T ss_pred CCceEEEEeCChHHHHHHHHCCCcCEEEeecCCCCC-----CCce----EEEeccceEEEEeCCCCccccCCCcCHHHHh
Confidence 4444443 355688899999999999986432111 1221 24566677788888764332 123567776
Q ss_pred cCCccCCCCCcEEEcCC----CccHHHHHHhcCCc
Q 018854 201 QMPQWTAEKPLRVATGF----TYLGPKFMKDNGLK 231 (349)
Q Consensus 201 ~~~~~~~~~~lRVATkY----Pnlar~yf~~~Gi~ 231 (349)
+.+ -|.... .....++|++.|+.
T Consensus 191 ~~~--------~i~~~~~~~~~~~~~~~~~~~~~~ 217 (313)
T PRK12684 191 QYP--------LITYDFAFAGRSKINKAFALRGLK 217 (313)
T ss_pred cCC--------cEecCCCCcHHHHHHHHHHHcCCC
Confidence 531 222221 23456678788875
No 130
>PRK14498 putative molybdopterin biosynthesis protein MoeA/LysR substrate binding-domain-containing protein; Provisional
Probab=32.77 E-value=1.1e+02 Score=32.92 Aligned_cols=92 Identities=18% Similarity=0.152 Sum_probs=56.8
Q ss_pred eEEEeecCCchhhhcccCceeeeeeccceecccCC----------CCccceeecCCCCcccEEEEEEEeCCCccCcccch
Q 018854 127 LEVWFQRPKDIVRKLLSGDLDLGIVGLDTVSEFGQ----------GNEDLIIVHDALDYGDCRLSLAIPKYGIFENINSL 196 (349)
Q Consensus 127 vev~~vR~~DIP~yV~~G~aDlGIvG~DvL~E~~~----------~~~~lv~~l~dLgfG~CRLvvAvP~~~~~~dv~sl 196 (349)
+++......++-..|..|.+|+||+.... .+.+. +..+ + .-..+..=++++++|.+..|. .-++
T Consensus 443 i~v~~~~s~~vl~~L~~GeiDlai~~~~~-~~~~~~~~~~~~~~~~~~~-l---~~~~l~~d~lvlvvp~~hPl~-~isl 516 (633)
T PRK14498 443 LRSLHVGSMGGLMALKRGEADIAGIHLLD-PETGEYNIPYIKKYLLGED-A---VLVKGYRREQGLVVRKGNPKG-IEGI 516 (633)
T ss_pred eeEEecCCHHHHHHHHcCCceEEEEcccC-cccccccHHHHHhhcCCCC-E---EEEEEEEEeEEEEECCCCCCC-CCCH
Confidence 55666789999999999999999975432 11110 0001 1 113455668899999986553 4588
Q ss_pred HHhhcCCccCCCCCcEE-E----cCCCccHHHHHHhcCCc
Q 018854 197 RELAQMPQWTAEKPLRV-A----TGFTYLGPKFMKDNGLK 231 (349)
Q Consensus 197 ~dL~~~~~~~~~~~lRV-A----TkYPnlar~yf~~~Gi~ 231 (349)
+||.+. .+++ . +.+-.+..++|++.|+.
T Consensus 517 ~dL~~~-------~~plI~~~~gs~~r~~le~~l~~~Gi~ 549 (633)
T PRK14498 517 EDLVRK-------DVRFVNRQRGSGTRILLDYHLKELAID 549 (633)
T ss_pred HHhccC-------CcEEEecCCCchHHHHHHHHHHHcCCC
Confidence 888763 0121 1 12235667778888875
No 131
>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=32.45 E-value=2.3e+02 Score=25.19 Aligned_cols=108 Identities=19% Similarity=0.155 Sum_probs=60.9
Q ss_pred hhcccCceeeeeeccceecccCCCCccceeecCCCCcccEEEEEEEeCCCccCcccchHH--hhcCCccCCCCCcEEEcC
Q 018854 139 RKLLSGDLDLGIVGLDTVSEFGQGNEDLIIVHDALDYGDCRLSLAIPKYGIFENINSLRE--LAQMPQWTAEKPLRVATG 216 (349)
Q Consensus 139 ~yV~~G~aDlGIvG~DvL~E~~~~~~~lv~~l~dLgfG~CRLvvAvP~~~~~~dv~sl~d--L~~~~~~~~~~~lRVATk 216 (349)
..+..|.+|+.+ +. .|.. .. + .. --.|..-..++.++++.. .++++++| |. ++|||.-
T Consensus 51 ~~l~~g~~Di~~-~~---~~r~---~~-~-~f-s~py~~~~~~lv~~~~~~-~~~~~~~d~~l~---------g~~V~v~ 110 (232)
T TIGR03871 51 NTLNAGRCDVVI-GV---PAGY---EM-V-LT-TRPYYRSTYVFVTRKDSL-LDVKSLDDPRLK---------KLRIGVF 110 (232)
T ss_pred HHHhcCCccEEE-ec---cCcc---cc-c-cc-cCCcEeeeEEEEEeCCCc-ccccchhhhhhc---------CCeEEEE
Confidence 357889999964 31 2221 11 1 11 235666778888887632 35667776 44 3688887
Q ss_pred CCccHHHHHHhcCCceEEEEec--C---------CccccccCCCcceeee-ecccchhhHhhC
Q 018854 217 FTYLGPKFMKDNGLKHVVFSTA--D---------GALEAAPAMGIADAIL-DLVSSGTTLREN 267 (349)
Q Consensus 217 YPnlar~yf~~~Gi~~v~Ii~l--~---------GSvElAP~lGlAD~IV-DIVsTGtTLraN 267 (349)
.-.....|+++.|.. ..+... . -..-.+-.-|-+|+++ |.......++.+
T Consensus 111 ~g~~~~~~l~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~l~~G~~Da~i~~~~~~~~~~~~~ 172 (232)
T TIGR03871 111 AGTPPAHWLARHGLV-ENVVGYSLFGDYRPESPPGRMVEDLAAGEIDVAIVWGPIAGYFAKQA 172 (232)
T ss_pred cCChHHHHHHhcCcc-cccccccccccccccCCHHHHHHHHHcCCcCEEEeccHHHHHHHHhC
Confidence 777888999887753 222211 1 1111234568888865 444444445544
No 132
>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=31.45 E-value=60 Score=28.95 Aligned_cols=92 Identities=22% Similarity=0.328 Sum_probs=51.4
Q ss_pred EEEeecCCchhhhcccCc-eeeeeeccce-ecccCCCCccceeecCCCCcccEEEEEEEeCCCccCcccchHHhhcCCcc
Q 018854 128 EVWFQRPKDIVRKLLSGD-LDLGIVGLDT-VSEFGQGNEDLIIVHDALDYGDCRLSLAIPKYGIFENINSLRELAQMPQW 205 (349)
Q Consensus 128 ev~~vR~~DIP~yV~~G~-aDlGIvG~Dv-L~E~~~~~~~lv~~l~dLgfG~CRLvvAvP~~~~~~dv~sl~dL~~~~~~ 205 (349)
++.+.-..++...+..|. +|+.+.+... +.+... ..++.....-.|+.-+++++++.+ ..+++++||.. |
T Consensus 24 ~~~~~gs~~l~~~l~~~~~aDv~~~~~~~~~~~l~~--~g~~~~~~~~~~~~~~~~l~~~~~---~~~~s~~dL~~---~ 95 (216)
T TIGR01256 24 VFSFGSSGTLYTQIENGAPADLFISADNKWPKKLVD--KGLVVAGSRFTYAGNKLVLISPKN---RVVDDLDILKK---W 95 (216)
T ss_pred EEEeCChHHHHHHHHcCCCCcEEEECCHHHHHHHHH--CCCCCCCchheEEccEEEEEEECC---CCcCcHHHHhh---c
Confidence 334444456666777665 9999998542 222111 111211112236667899999887 45678888852 2
Q ss_pred CCCCCcEEEcCCCcc------HHHHHHhcC
Q 018854 206 TAEKPLRVATGFTYL------GPKFMKDNG 229 (349)
Q Consensus 206 ~~~~~lRVATkYPnl------ar~yf~~~G 229 (349)
.. ..||+.-.|+. +..+++..|
T Consensus 96 ~~--~~~i~~~~P~~~~~g~~~~~~~~~~g 123 (216)
T TIGR01256 96 VA--DKRVAIGDPKHAPYGAAAKEVLQKLG 123 (216)
T ss_pred cc--CCeEEecCCCcCcChHHHHHHHHHCC
Confidence 10 24788766653 344555555
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=31.12 E-value=33 Score=30.92 Aligned_cols=95 Identities=26% Similarity=0.254 Sum_probs=59.8
Q ss_pred CeEEEeecCCchhhhcccC-ceeeeeeccceecccCCCCccceeecCCCCcccEEEEEEEeCCCccCcccchHHhhcCCc
Q 018854 126 NLEVWFQRPKDIVRKLLSG-DLDLGIVGLDTVSEFGQGNEDLIIVHDALDYGDCRLSLAIPKYGIFENINSLRELAQMPQ 204 (349)
Q Consensus 126 ~vev~~vR~~DIP~yV~~G-~aDlGIvG~DvL~E~~~~~~~lv~~l~dLgfG~CRLvvAvP~~~~~~dv~sl~dL~~~~~ 204 (349)
++++.+....++...+..| ..|+-|.+.+...|.-.. ...+..-..-.|..-.++++++++.. .++.+++||...
T Consensus 27 ~v~v~~~~s~~~~~~l~~g~~~Dv~~~~~~~~~~~l~~-~g~~~~~~~~~~~~~~~vl~~~~~~~-~~~~~~~dL~~~-- 102 (230)
T PF13531_consen 27 KVEVSFGGSGELVRRLQAGKKPDVFIPASSEWLERLAA-AGLVDPGSPAPLARSPLVLAVPKGNP-KGIRSWADLAQP-- 102 (230)
T ss_dssp EEEEEEECHHHHHHHHHTT-S-SEEEESSHHHHHHHHH-TTTCSGGGEEEEEEEEEEEEEETTST-TSTTCHHHHCST--
T ss_pred eEEEEECChHHHHHHHhcCCCceEEEECCHHHHHHHHh-cccccCCcccccccCceEEEeccCcc-cccCCHHHHhhc--
Confidence 3678888899999999988 789999987533332100 01111001234667779999999853 478889998741
Q ss_pred cCCCCCcEEEcCCCcc------HHHHHHhcC
Q 018854 205 WTAEKPLRVATGFTYL------GPKFMKDNG 229 (349)
Q Consensus 205 ~~~~~~lRVATkYPnl------ar~yf~~~G 229 (349)
.+|||+-.|.. +..+|.+.|
T Consensus 103 -----~~~i~~~dP~~s~~g~~~~~~l~~~g 128 (230)
T PF13531_consen 103 -----GLRIAIPDPSTSPSGLAALQVLAAAG 128 (230)
T ss_dssp -----T--EEEE-TTTTHHHHHHHHHHHHHT
T ss_pred -----cCEEEecCcccChhhHHHHHHHHHcc
Confidence 35899998853 455566655
No 134
>PRK04168 molybdate ABC transporter periplasmic substrate-binding protein; Provisional
Probab=30.82 E-value=78 Score=31.51 Aligned_cols=23 Identities=13% Similarity=0.346 Sum_probs=19.3
Q ss_pred chhhhcccCceeeeeeccceecc
Q 018854 136 DIVRKLLSGDLDLGIVGLDTVSE 158 (349)
Q Consensus 136 DIP~yV~~G~aDlGIvG~DvL~E 158 (349)
++-.||+.|.+|+||+-.-....
T Consensus 213 ~~~~~v~~G~aDagivy~S~a~~ 235 (334)
T PRK04168 213 ELLSLLETGNMDYAFIYKSVAVQ 235 (334)
T ss_pred hhHHHHhcCCccEEEEEeeehhh
Confidence 78999999999999997665443
No 135
>PRK11074 putative DNA-binding transcriptional regulator; Provisional
Probab=29.89 E-value=97 Score=29.14 Aligned_cols=99 Identities=16% Similarity=0.180 Sum_probs=55.2
Q ss_pred CCCceEEEecCCCCchHHHHHHHHHCCCccCCCCCCceEEecCCCCCeEEEe--ecCCchhhhcccCceeeeeeccceec
Q 018854 80 ERDEIRLGLPSKGRMAADTLDLLKDCQLSVKQVNPRQYVAQIPQLSNLEVWF--QRPKDIVRKLLSGDLDLGIVGLDTVS 157 (349)
Q Consensus 80 ~~~~LrIALP~KGRL~e~t~~LL~~aGi~~~~~~~R~L~~~~~~~p~vev~~--vR~~DIP~yV~~G~aDlGIvG~DvL~ 157 (349)
..+.++||++ ..-...-..+++...- + ..|++++.+ -...|+...|..|.+|+||+......
T Consensus 90 ~~g~l~Ig~~-~~~~~~~l~~~l~~~~--------~-------~~p~i~i~i~~~~~~~~~~~l~~g~~Dl~i~~~~~~~ 153 (300)
T PRK11074 90 WRGQLSIAVD-NIVRPDRTRQLIVDFY--------R-------HFDDVELIIRQEVFNGVWDALADGRVDIAIGATRAIP 153 (300)
T ss_pred CCceEEEEEc-CccchhHHHHHHHHHH--------H-------hCCCceEEEEehhhhHHHHHHHCCCCCEEEecCccCC
Confidence 4567888887 3333333333333310 0 124444433 34678999999999999997432111
Q ss_pred ccCCCCccceeecCCCCcccEEEEEEEeCCCccCc---ccchHHhhcC
Q 018854 158 EFGQGNEDLIIVHDALDYGDCRLSLAIPKYGIFEN---INSLRELAQM 202 (349)
Q Consensus 158 E~~~~~~~lv~~l~dLgfG~CRLvvAvP~~~~~~d---v~sl~dL~~~ 202 (349)
.. .++. ...+++.++++.++++..+.. .-+++||...
T Consensus 154 -~~---~~l~----~~~l~~~~~~~v~~~~hpl~~~~~~~~~~dl~~~ 193 (300)
T PRK11074 154 -VG---GRFA----FRDMGMLSWACVVSSDHPLASMDGPLSDDELRPY 193 (300)
T ss_pred -cc---cccc----eeecccceEEEEEcCCCcccccCCCCCHHHHhhC
Confidence 00 1121 234678888888887753322 2466777753
No 136
>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=27.71 E-value=43 Score=27.69 Aligned_cols=92 Identities=20% Similarity=0.260 Sum_probs=50.4
Q ss_pred CCCeEEEee--cCCchhhhcccCceeeeeeccceecccCCCCccceeecCCCCcccEEEEEEEeCCCccC--cccchHHh
Q 018854 124 LSNLEVWFQ--RPKDIVRKLLSGDLDLGIVGLDTVSEFGQGNEDLIIVHDALDYGDCRLSLAIPKYGIFE--NINSLREL 199 (349)
Q Consensus 124 ~p~vev~~v--R~~DIP~yV~~G~aDlGIvG~DvL~E~~~~~~~lv~~l~dLgfG~CRLvvAvP~~~~~~--dv~sl~dL 199 (349)
.|++++-+. ...|+...+.+|.+|+||+..+.. . .++. ...+++.+++++++.+..+. ..-+++||
T Consensus 26 ~P~i~v~~~~~~~~~~~~~l~~g~~D~~i~~~~~~---~---~~~~----~~~l~~~~~~~v~~~~~pl~~~~~~~~~~l 95 (198)
T cd08447 26 LPDVDLVLREMVTTDQIEALESGRIDLGLLRPPFA---R---PGLE----TRPLVREPLVAAVPAGHPLAGAERLTLEDL 95 (198)
T ss_pred CCCeEEEEEeCCHHHHHHHHHcCCceEEEecCCCC---C---CCee----EEEeecCceEEEecCCCchhhcCcccHHHh
Confidence 355655554 567899999999999999854321 1 1222 12244566677777653221 12356676
Q ss_pred hcCCccCCCCCcEEEcC----CCccHHHHHHhcCCc
Q 018854 200 AQMPQWTAEKPLRVATG----FTYLGPKFMKDNGLK 231 (349)
Q Consensus 200 ~~~~~~~~~~~lRVATk----YPnlar~yf~~~Gi~ 231 (349)
...+ -+..... +.+...++|.+.|+.
T Consensus 96 ~~~~------~i~~~~~~~~~~~~~~~~~~~~~~~~ 125 (198)
T cd08447 96 DGQP------FIMYSPTEARYFHDLVVRLFASAGVQ 125 (198)
T ss_pred CCCe------EEEeCCCCCchHHHHHHHHHHHcCCC
Confidence 5421 1111111 123456777788864
No 137
>COG1464 NlpA ABC-type metal ion transport system, periplasmic component/surface antigen [Inorganic ion transport and metabolism]
Probab=27.42 E-value=2.1e+02 Score=28.28 Aligned_cols=80 Identities=18% Similarity=0.220 Sum_probs=59.6
Q ss_pred CceEEEecCCCCchHHHHHHHHHCCCccCCCCCCceEE---ec-CCCCCeEEEeecCCchhhhcccCceeeeeeccceec
Q 018854 82 DEIRLGLPSKGRMAADTLDLLKDCQLSVKQVNPRQYVA---QI-PQLSNLEVWFQRPKDIVRKLLSGDLDLGIVGLDTVS 157 (349)
Q Consensus 82 ~~LrIALP~KGRL~e~t~~LL~~aGi~~~~~~~R~L~~---~~-~~~p~vev~~vR~~DIP~yV~~G~aDlGIvG~DvL~ 157 (349)
+--+||+|++-.=.--++.+|+++|+---.... .+.+ ++ .|-.+++|.-+.+.=.|+-+.+ +|+.|.-.++..
T Consensus 127 ~GatIaiPNDpsN~gRAL~lL~~aGLIkLk~~~-~~~aT~~DI~eNPK~lki~EldAaqlpRaLdd--vD~AvIN~nyA~ 203 (268)
T COG1464 127 DGATIAIPNDPTNEGRALLLLQKAGLIKLKDGV-NLLATPKDITENPKNLKIKELEAAQLPRALDD--VDAAVINTNYAL 203 (268)
T ss_pred CCCEEECCCCCCchhHHHHHHHHCCcEEEcCCC-cccCCHHHHhhCcccCeEEEcchHhccccccc--cCEEEEcchHHH
Confidence 346899999888888999999999984332221 2211 11 1234688888899999999988 799999999999
Q ss_pred ccCCCCc
Q 018854 158 EFGQGNE 164 (349)
Q Consensus 158 E~~~~~~ 164 (349)
+.|.+..
T Consensus 204 ~AgL~p~ 210 (268)
T COG1464 204 QAGLNPK 210 (268)
T ss_pred HcCCCcc
Confidence 9987643
No 138
>PRK12679 cbl transcriptional regulator Cbl; Reviewed
Probab=27.24 E-value=1.3e+02 Score=28.61 Aligned_cols=160 Identities=19% Similarity=0.225 Sum_probs=77.6
Q ss_pred CCeEEEee--cCCchhhhcccCceeeeeeccceecccCCCCccceeecCCCCcccEEEEEEEeCCCccCc--ccchHHhh
Q 018854 125 SNLEVWFQ--RPKDIVRKLLSGDLDLGIVGLDTVSEFGQGNEDLIIVHDALDYGDCRLSLAIPKYGIFEN--INSLRELA 200 (349)
Q Consensus 125 p~vev~~v--R~~DIP~yV~~G~aDlGIvG~DvL~E~~~~~~~lv~~l~dLgfG~CRLvvAvP~~~~~~d--v~sl~dL~ 200 (349)
|++++.+. ...++...+.+|.+|+||+..+.... .++. .-.++.=++++.+|.+..+.. .-+++||.
T Consensus 120 P~i~l~l~~~~~~~~~~~L~~g~~Dl~i~~~~~~~~-----~~l~----~~~l~~~~~~~v~~~~hpl~~~~~i~~~~L~ 190 (316)
T PRK12679 120 PEVRLELIQGTPQEIATLLQNGEADIGIASERLSND-----PQLV----AFPWFRWHHSLLVPHDHPLTQITPLTLESIA 190 (316)
T ss_pred CCeEEEEecCCHHHHHHHHHcCCCCEEEecccCCCC-----CCce----EEEccCCcEEEEecCCCccccCCCCCHHHHh
Confidence 55555544 34578899999999999974321111 1221 123455566777776633221 22567766
Q ss_pred cCCccCCCCCcEEEc----CCCccHHHHHHhcCCceEEEEecCCccccc---cC--CCcceeeeecccchhhHhhCCcEE
Q 018854 201 QMPQWTAEKPLRVAT----GFTYLGPKFMKDNGLKHVVFSTADGALEAA---PA--MGIADAILDLVSSGTTLRENNLKE 271 (349)
Q Consensus 201 ~~~~~~~~~~lRVAT----kYPnlar~yf~~~Gi~~v~Ii~l~GSvElA---P~--lGlAD~IVDIVsTGtTLraNgLk~ 271 (349)
..+ -|-. .......++|.+.|+. -.+..-..+.+.. .. +|+| .+-..+. ..++..+|+.
T Consensus 191 ~~~--------~i~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~s~~~~~~~v~~g~Gi~-~lp~~~~--~~~~~~~L~~ 258 (316)
T PRK12679 191 KWP--------LITYRQGITGRSRIDDAFARKGLL-ADIVLSAQDSDVIKTYVALGLGIG-LVAEQSS--GEQEESNLIR 258 (316)
T ss_pred CCC--------eEEecCCCcHHHHHHHHHHHcCCC-ceEEEEeccHHHHHHHHHcCCcEE-Eeccccc--ccccCCcEEE
Confidence 421 1221 1223456778888875 2433323444432 11 2332 1111121 1344455776
Q ss_pred ecCc-eEEEEEEEEEeecchhhhhcCchhHHHHHHHHHHH
Q 018854 272 IEGG-VVLESQAVLVASRKSLIRRKGVLDATHEILERLEA 310 (349)
Q Consensus 272 ie~g-~IleSsA~LIaN~~s~~~k~~~~~~i~~li~rl~~ 310 (349)
+.-+ ......-.++.++..... ..++.+++.++.
T Consensus 259 ~~~~~~~~~~~~~l~~~~~~~~~-----~~~~~f~~~~~~ 293 (316)
T PRK12679 259 LDTRHLFDANTVWLGLKRGQLQR-----NYVWRFLELCNA 293 (316)
T ss_pred EECcccCCCceEEEEEeCCchhh-----HHHHHHHHHHhc
Confidence 6411 222334556666554332 235555555544
No 139
>PRK03601 transcriptional regulator HdfR; Provisional
Probab=27.12 E-value=56 Score=30.46 Aligned_cols=51 Identities=20% Similarity=0.268 Sum_probs=35.7
Q ss_pred eEEEeecCCchhhhcccCceeeeeeccceecccCCCCccceeecCCCCcccEEEEEEEeCC
Q 018854 127 LEVWFQRPKDIVRKLLSGDLDLGIVGLDTVSEFGQGNEDLIIVHDALDYGDCRLSLAIPKY 187 (349)
Q Consensus 127 vev~~vR~~DIP~yV~~G~aDlGIvG~DvL~E~~~~~~~lv~~l~dLgfG~CRLvvAvP~~ 187 (349)
+++..-...|+-..+.+|.+|+||++...- . .++ ....++.+++++++|.+
T Consensus 120 v~~~~~~~~~~~~~l~~g~~Dl~i~~~~~~--~----~~l----~~~~l~~~~~~~v~~~~ 170 (275)
T PRK03601 120 FEARIAQRQSLVKQLHERQLDLLITTEAPK--M----DEF----SSQLLGHFTLALYTSAP 170 (275)
T ss_pred EEEEECChHHHHHHHHcCCCCEEEEcCCCc--c----CCc----cEEEecceeEEEEecCc
Confidence 334455677889999999999999864321 1 122 13457789999999876
No 140
>PRK11482 putative DNA-binding transcriptional regulator; Provisional
Probab=27.00 E-value=60 Score=31.18 Aligned_cols=67 Identities=12% Similarity=-0.103 Sum_probs=42.9
Q ss_pred CCeEEEeecCCchhhhcccCceeeeeeccceecccCCCCccceeecCCCCcccEEEEEEEeCCCccC-cccchHHhhc
Q 018854 125 SNLEVWFQRPKDIVRKLLSGDLDLGIVGLDTVSEFGQGNEDLIIVHDALDYGDCRLSLAIPKYGIFE-NINSLRELAQ 201 (349)
Q Consensus 125 p~vev~~vR~~DIP~yV~~G~aDlGIvG~DvL~E~~~~~~~lv~~l~dLgfG~CRLvvAvP~~~~~~-dv~sl~dL~~ 201 (349)
|++++.+....++...|.+|.+|+||+...... .++. .-.++.-.++++++.+..+. .--+++||..
T Consensus 144 P~i~i~~~~~~~~~~~l~~g~~Dl~i~~~~~~~------~~~~----~~~l~~~~~~lv~~~~hpl~~~~~~~~dL~~ 211 (317)
T PRK11482 144 PQLLLRNIPISDAENQLSQFQTDLIIDTHSCSN------RTIQ----HHVLFTDNVVLVCRQGHPLLSLEDDEETLDN 211 (317)
T ss_pred CCCEEEEecchhHHHHHHCCCcCEEEeccCCCC------CceE----EEEEecCcEEEEEeCCCCccCCCCCHHHHhh
Confidence 556665566678999999999999998755321 1221 12345677788888764221 1236788775
No 141
>PF11823 DUF3343: Protein of unknown function (DUF3343); InterPro: IPR021778 This family of proteins are functionally uncharacterised. This protein is found in bacteria and archaea. Proteins in this family are typically between 78 to 102 amino acids in length.
Probab=26.09 E-value=86 Score=24.11 Aligned_cols=51 Identities=25% Similarity=0.291 Sum_probs=38.5
Q ss_pred cHHHHHHhcCCceEEEEecCCccccccCCCcceee--eecccchhhHhhCCcEEec
Q 018854 220 LGPKFMKDNGLKHVVFSTADGALEAAPAMGIADAI--LDLVSSGTTLRENNLKEIE 273 (349)
Q Consensus 220 lar~yf~~~Gi~~v~Ii~l~GSvElAP~lGlAD~I--VDIVsTGtTLraNgLk~ie 273 (349)
-++++++++|++ +++++.-..+-... |+|=.+ -|.-.--..|++||+.+-.
T Consensus 16 ~~ek~lk~~gi~-~~liP~P~~i~~~C--G~al~~~~~d~~~i~~~l~~~~i~~~~ 68 (73)
T PF11823_consen 16 KAEKLLKKNGIP-VRLIPTPREISAGC--GLALRFEPEDLEKIKEILEENGIEYEG 68 (73)
T ss_pred HHHHHHHHCCCc-EEEeCCChhccCCC--CEEEEEChhhHHHHHHHHHHCCCCeeE
Confidence 467899999996 89999988887666 554233 4666677889999988653
No 142
>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=25.89 E-value=1.1e+02 Score=27.12 Aligned_cols=67 Identities=22% Similarity=0.210 Sum_probs=44.0
Q ss_pred cHHHHHHhcCCceEEEEecCCccccc--cCCCcceeeeecccchhhHhhCCc--EEecCceEEE-EEEEEEeecc
Q 018854 220 LGPKFMKDNGLKHVVFSTADGALEAA--PAMGIADAILDLVSSGTTLRENNL--KEIEGGVVLE-SQAVLVASRK 289 (349)
Q Consensus 220 lar~yf~~~Gi~~v~Ii~l~GSvElA--P~lGlAD~IVDIVsTGtTLraNgL--k~ie~g~Ile-SsA~LIaN~~ 289 (349)
..+-||++.|++ |+++...|..+.. -.-|-+|+.+.-...----+++|. +.+- .+.. ..-.+++.+.
T Consensus 11 ~~~G~f~~~gl~-ve~~~~~~~~~~~~~l~~G~~D~~~~~~~~~~~~~~~g~~~~~i~--~~~~~~~~~l~~~~~ 82 (216)
T PF09084_consen 11 QEKGYFKEEGLD-VEIVFFGGGGDVLEALASGKADIAVAGPDAVLFARAKGADIKIIA--ASYQSSPNALVVRKD 82 (216)
T ss_dssp HHTTHHHHTTEE-EEEEEESSHHHHHHHHHTTSHSEEEEECHHHHHHHHTTSTEEEEE--EEEEECCEEEEEETT
T ss_pred HHcCCCccCeEE-EEEEEecChhHHHHHHhcCCceEEeccchHHHHHHhcCCeeEEEE--EecCCCceEEEEecc
Confidence 345699999996 9999998866655 445778877665555554577776 4443 3342 3345666554
No 143
>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=24.85 E-value=50 Score=27.43 Aligned_cols=94 Identities=20% Similarity=0.245 Sum_probs=49.5
Q ss_pred CCCeEEEee--cCCchhhhcccCceeeeeeccceecccCCCCccceeecCCCCcccEEEEEEEeCCCccC--cccchHHh
Q 018854 124 LSNLEVWFQ--RPKDIVRKLLSGDLDLGIVGLDTVSEFGQGNEDLIIVHDALDYGDCRLSLAIPKYGIFE--NINSLREL 199 (349)
Q Consensus 124 ~p~vev~~v--R~~DIP~yV~~G~aDlGIvG~DvL~E~~~~~~~lv~~l~dLgfG~CRLvvAvP~~~~~~--dv~sl~dL 199 (349)
.|++++.+. ...++...+..|.+|+||+....- + .++. ...++.=+++++++.+..+. ..-+++||
T Consensus 27 ~P~i~i~i~~~~~~~~~~~l~~~~~Dl~i~~~~~~-~-----~~~~----~~~l~~~~~~~v~~~~~pl~~~~~~~~~~l 96 (200)
T cd08411 27 YPKLRLYLREDQTERLLEKLRSGELDAALLALPVD-E-----PGLE----EEPLFDEPFLLAVPKDHPLAKRKSVTPEDL 96 (200)
T ss_pred CCCcEEEEEeCcHHHHHHHHHcCCccEEEEeccCC-C-----CCce----EEEeeccceEEEecCCCCccccCccCHHHH
Confidence 355555554 467888999999999999753211 1 1221 12234556677776653221 22367777
Q ss_pred hcCCccCCCCCcEEEcCCCccHHHHHHhcCCc
Q 018854 200 AQMPQWTAEKPLRVATGFTYLGPKFMKDNGLK 231 (349)
Q Consensus 200 ~~~~~~~~~~~lRVATkYPnlar~yf~~~Gi~ 231 (349)
...+-..... .+.+.....++|.+.|+.
T Consensus 97 ~~~~~i~~~~----~~~~~~~~~~~~~~~~~~ 124 (200)
T cd08411 97 AGERLLLLEE----GHCLRDQALELCRLAGAR 124 (200)
T ss_pred cCCceEecCC----CCcHHHHHHHHHHHcCCC
Confidence 6532110000 012233445567777764
No 144
>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=24.33 E-value=1.3e+02 Score=24.92 Aligned_cols=65 Identities=12% Similarity=-0.018 Sum_probs=39.3
Q ss_pred eEEEeecCCchhhhcccCceeeeeeccceecccCCCCccceeecCCCCcccEEEEEEEeCCCccC---cccchHHhhc
Q 018854 127 LEVWFQRPKDIVRKLLSGDLDLGIVGLDTVSEFGQGNEDLIIVHDALDYGDCRLSLAIPKYGIFE---NINSLRELAQ 201 (349)
Q Consensus 127 vev~~vR~~DIP~yV~~G~aDlGIvG~DvL~E~~~~~~~lv~~l~dLgfG~CRLvvAvP~~~~~~---dv~sl~dL~~ 201 (349)
+++......++...++.|.+|+||..... +. .++. ...++..+++++++.+.... ..-+++||.+
T Consensus 30 l~l~~~~~~~~~~~l~~~~~D~~i~~~~~--~~----~~~~----~~~l~~~~~~~~~~~~~~~~~~~~~i~~~~L~~ 97 (195)
T cd08428 30 LDLIVDDEDRTHDLLRDGEVVGCISTQAQ--PM----QGCR----SDYLGSMDYLLVASPDFAARYFPNGLTREALLK 97 (195)
T ss_pred EEEEeCCchhHHHHHHcCcceEEEEecCC--CC----CCce----eEEeeeeeEEEEECCcchhhcCCCCCCHHHHhc
Confidence 45555556689999999999999965431 11 1221 23456778888887653111 2235677765
No 145
>PRK11716 DNA-binding transcriptional regulator IlvY; Provisional
Probab=24.32 E-value=67 Score=28.99 Aligned_cols=54 Identities=22% Similarity=0.253 Sum_probs=34.6
Q ss_pred CCeEEEe--ecCCchhhhcccCceeeeeeccceecccCCCCccceeecCCCCcccEEEEEEEeCC
Q 018854 125 SNLEVWF--QRPKDIVRKLLSGDLDLGIVGLDTVSEFGQGNEDLIIVHDALDYGDCRLSLAIPKY 187 (349)
Q Consensus 125 p~vev~~--vR~~DIP~yV~~G~aDlGIvG~DvL~E~~~~~~~lv~~l~dLgfG~CRLvvAvP~~ 187 (349)
|++++.+ ....|+...+..|.+|+||+....-. . .++. ...++..++++++|.+
T Consensus 94 p~i~l~i~~~~~~~~~~~l~~~~~D~~i~~~~~~~--~---~~~~----~~~l~~~~~~~v~~~~ 149 (269)
T PRK11716 94 PLVEIKLTTGDAADAVEKVQSGEADLAIAAKPETL--P---ASVA----FSPIDEIPLVLIAPAL 149 (269)
T ss_pred CCeEEEEEECCHHHHHHHHHCCCccEEEEecCCCC--C---cceE----EEEcccceEEEEEcCC
Confidence 4444443 35568899999999999997643211 1 1221 2345778888888876
No 146
>COG2358 Imp TRAP-type uncharacterized transport system, periplasmic component [General function prediction only]
Probab=24.24 E-value=68 Score=32.37 Aligned_cols=88 Identities=20% Similarity=0.151 Sum_probs=54.1
Q ss_pred hhhcccCceeeeeeccceecccCCC--Ccc---ceeecCCCC-cccEEEEEEEeCCCccCcccchHHhhcCCccCCCCCc
Q 018854 138 VRKLLSGDLDLGIVGLDTVSEFGQG--NED---LIIVHDALD-YGDCRLSLAIPKYGIFENINSLRELAQMPQWTAEKPL 211 (349)
Q Consensus 138 P~yV~~G~aDlGIvG~DvL~E~~~~--~~~---lv~~l~dLg-fG~CRLvvAvP~~~~~~dv~sl~dL~~~~~~~~~~~l 211 (349)
-..+.+|.+|+|++=.|+..|.-.. ..+ ..+.+..+. +=.=-+-+.+.++ .+|++++||++ +
T Consensus 71 l~~i~~Ge~d~alvq~d~a~~ay~G~g~f~~~~~~~~lr~v~~lype~~~vv~r~d---~~Ikti~DL~G---------K 138 (321)
T COG2358 71 LKLLASGEADLALVQSDVAYEAYNGTGSFEGKGKDENLRAVAALYPEPFHVVTRKD---AGIKTIADLKG---------K 138 (321)
T ss_pred HHhHhcCccchhhhhHHHHHHHHhCcccccccccccchhhheecccceEEEEEecC---CCcceehhcCC---------C
Confidence 3478899999999999998875211 000 000011111 0011233445555 67999999885 7
Q ss_pred EEEcCCCcc-----HHHHHHhcCCceEEEEec
Q 018854 212 RVATGFTYL-----GPKFMKDNGLKHVVFSTA 238 (349)
Q Consensus 212 RVATkYPnl-----ar~yf~~~Gi~~v~Ii~l 238 (349)
||++-=|.- +++-|+..|+. .+.+++
T Consensus 139 rV~iG~~gSgt~~~a~~il~a~Gi~-~~~~~~ 169 (321)
T COG2358 139 RVAIGPPGSGTEATARQILEALGIT-YDDYEL 169 (321)
T ss_pred EEeecCCCCccHHHHHHHHHHcCCC-Ccchhh
Confidence 999887764 67888999996 344444
No 147
>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=24.21 E-value=67 Score=26.69 Aligned_cols=68 Identities=21% Similarity=0.247 Sum_probs=39.1
Q ss_pred CCCeEEEeecCCchhhhcccCceeeeeeccceecccCCCCccceeecCCCCcccEEEEEEEeCCCcc--CcccchHHhhc
Q 018854 124 LSNLEVWFQRPKDIVRKLLSGDLDLGIVGLDTVSEFGQGNEDLIIVHDALDYGDCRLSLAIPKYGIF--ENINSLRELAQ 201 (349)
Q Consensus 124 ~p~vev~~vR~~DIP~yV~~G~aDlGIvG~DvL~E~~~~~~~lv~~l~dLgfG~CRLvvAvP~~~~~--~dv~sl~dL~~ 201 (349)
.|++++.+....++.. +.+|.+|+||+-... .+ .++. --.+...++++++|.+... ...-+++||.+
T Consensus 29 ~P~v~i~~~~~~~~~~-l~~~~~D~~i~~~~~-~~-----~~l~----~~~l~~~~~~~v~~~~~~~~~~~~~~~~~L~~ 97 (199)
T cd08478 29 YPDIELELVSNEGIID-LIERKTDVAIRIGEL-TD-----STLH----ARPLGKSRLRILASPDYLARHGTPQSIEDLAQ 97 (199)
T ss_pred CCCeEEEEEecccccc-chhccccEEEEecCC-CC-----CCce----EEEcccccEEEEECHHHHHhcCCCCCHHHHHh
Confidence 4666666665566665 778999999974321 11 1221 1234567788888765210 11235677765
Q ss_pred C
Q 018854 202 M 202 (349)
Q Consensus 202 ~ 202 (349)
.
T Consensus 98 ~ 98 (199)
T cd08478 98 H 98 (199)
T ss_pred C
Confidence 3
No 148
>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=24.13 E-value=90 Score=31.02 Aligned_cols=66 Identities=15% Similarity=0.154 Sum_probs=48.5
Q ss_pred CCCCCCCceEEEecCCCCchHHH-HHHHHHCCCccCCCCCCceEEecCCCCCeEEEeecCCchhhhcccCceeeeeeccc
Q 018854 76 NRISERDEIRLGLPSKGRMAADT-LDLLKDCQLSVKQVNPRQYVAQIPQLSNLEVWFQRPKDIVRKLLSGDLDLGIVGLD 154 (349)
Q Consensus 76 ~~~~~~~~LrIALP~KGRL~e~t-~~LL~~aGi~~~~~~~R~L~~~~~~~p~vev~~vR~~DIP~yV~~G~aDlGIvG~D 154 (349)
.++.+..==|||++ +|...+-. ...|+++|++. .+++++.+.+.|.+..+..|.+|..++-.-
T Consensus 99 ~svaDLKGKkIav~-~gs~~~~ll~~aL~~aGL~~---------------~DV~~v~~~~~d~~aAl~~G~VDAa~~~eP 162 (328)
T TIGR03427 99 KSLADLKGQKVNLV-ELSVSHYLLARALESVGLSE---------------KDVKVVNTSDADIVAAFITKDVTAVVTWNP 162 (328)
T ss_pred CCHHHcCCCEEecc-CCChHHHHHHHHHHHcCCCH---------------HHeEEEeCChHHHHHHHhcCCCcEEEEcCc
Confidence 33433333589998 78876644 45788888842 147788888999999999999999998766
Q ss_pred eec
Q 018854 155 TVS 157 (349)
Q Consensus 155 vL~ 157 (349)
++.
T Consensus 163 ~~s 165 (328)
T TIGR03427 163 QLS 165 (328)
T ss_pred hHH
Confidence 653
No 149
>PRK09959 hybrid sensory histidine kinase in two-component regulatory system with EvgA; Provisional
Probab=23.95 E-value=5.5e+02 Score=29.37 Aligned_cols=117 Identities=16% Similarity=0.103 Sum_probs=64.7
Q ss_pred eEEEeecCCc---hhhhcccCceeeeeeccceecccCCCCccceeecCCCCcccEEEEEEEeCCCccCcccchHHhhcCC
Q 018854 127 LEVWFQRPKD---IVRKLLSGDLDLGIVGLDTVSEFGQGNEDLIIVHDALDYGDCRLSLAIPKYGIFENINSLRELAQMP 203 (349)
Q Consensus 127 vev~~vR~~D---IP~yV~~G~aDlGIvG~DvL~E~~~~~~~lv~~l~dLgfG~CRLvvAvP~~~~~~dv~sl~dL~~~~ 203 (349)
++|.++...+ ....+..|.+|+-.... .-.|.. +.+ .+ --+|-...+++.+..+. .... ++.
T Consensus 341 ~~~~~v~~~~~~~~~~~l~~g~~D~i~~~~-~t~~r~----~~~-~f-s~py~~~~~~~v~~~~~--~~~~---~~~--- 405 (1197)
T PRK09959 341 LNFSPITVSHNIHAGTQLNPGGWDIIPGAI-YSEDRE----NNV-LF-AEAFITTPYVFVMQKAP--DSEQ---TLK--- 405 (1197)
T ss_pred CeEEEEecCCHHHHHHHHHCCCceEeeccc-CCcccc----ccc-ee-ccccccCCEEEEEecCC--CCcc---ccc---
Confidence 4444444332 34568899999744332 222222 111 11 23566777777777652 2111 111
Q ss_pred ccCCCCCcEEEcCCCccHHHHHHhcCCceEEEEecCCcccc--ccCCCcceeeeecccchhhH
Q 018854 204 QWTAEKPLRVATGFTYLGPKFMKDNGLKHVVFSTADGALEA--APAMGIADAILDLVSSGTTL 264 (349)
Q Consensus 204 ~~~~~~~lRVATkYPnlar~yf~~~Gi~~v~Ii~l~GSvEl--AP~lGlAD~IVDIVsTGtTL 264 (349)
+++|||-..-....+|+.++.- .++++.....-|+ +-.-|-||+.++-..+..-+
T Consensus 406 -----~g~~vav~~g~~~~~~~~~~~p-~~~~~~~~~~~~~l~av~~G~~Da~i~~~~~~~~~ 462 (1197)
T PRK09959 406 -----KGMKVAIPYYYELHSQLKEMYP-EVEWIKVDNASAAFHKVKEGELDALVATQLNSRYM 462 (1197)
T ss_pred -----cCCEEEEeCCcchHHHHHHHCC-CcEEEEcCCHHHHHHHHHcCCCCEEehhhHHHHHH
Confidence 2467777655566778877643 4677766554443 46679999987766555554
No 150
>PRK11480 tauA taurine transporter substrate binding subunit; Provisional
Probab=23.75 E-value=1.2e+02 Score=29.18 Aligned_cols=61 Identities=21% Similarity=0.210 Sum_probs=43.7
Q ss_pred CceEEEecCCCCch-HHHHHHHHHCCCccCCCCCCceEEecCCCCCeEEEeecCCchhhhcccCceeeeeeccceecc
Q 018854 82 DEIRLGLPSKGRMA-ADTLDLLKDCQLSVKQVNPRQYVAQIPQLSNLEVWFQRPKDIVRKLLSGDLDLGIVGLDTVSE 158 (349)
Q Consensus 82 ~~LrIALP~KGRL~-e~t~~LL~~aGi~~~~~~~R~L~~~~~~~p~vev~~vR~~DIP~yV~~G~aDlGIvG~DvL~E 158 (349)
.=-|||+| .|... .-...+|++.|++.. +++++.+.+.+...-+..|.+|..++..-+..+
T Consensus 121 kGK~Iav~-~~s~~~~~l~~~L~~~Gl~~~---------------dv~~v~~~~~~~~~Al~~G~VDAa~~~~p~~~~ 182 (320)
T PRK11480 121 IGKRIAVP-FISTTHYSLLAALKHWGIKPG---------------QVEIVNLQPPAIIAAWQRGDIDGAYVWAPAVNA 182 (320)
T ss_pred CCCEEecC-CCCchHHHHHHHHHHcCCCHh---------------heEEEECCcHHHHHHHHcCCcCEEEEcchHHHH
Confidence 33589998 55544 345668889998521 255566678899999999999999887665543
No 151
>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=23.51 E-value=59 Score=26.93 Aligned_cols=51 Identities=14% Similarity=0.075 Sum_probs=32.4
Q ss_pred CCeEEEee--cCCchhhhcccCceeeeeeccceecccCCCCccceeecCCCCcccEEEEEEEeCC
Q 018854 125 SNLEVWFQ--RPKDIVRKLLSGDLDLGIVGLDTVSEFGQGNEDLIIVHDALDYGDCRLSLAIPKY 187 (349)
Q Consensus 125 p~vev~~v--R~~DIP~yV~~G~aDlGIvG~DvL~E~~~~~~~lv~~l~dLgfG~CRLvvAvP~~ 187 (349)
|++++-+. ...++...+.+|.+|+||+..+. . +.. ...++..+++++++.+
T Consensus 27 P~v~i~~~~~~~~~~~~~l~~~~~Dl~i~~~~~---~-----~~~----~~~l~~~~~~~v~~~~ 79 (185)
T cd08439 27 PRLAIEVVCKRTPRLMEMLERGEVDLALITHPP---P-----GAS----ATILRRSPTVWYCAAG 79 (185)
T ss_pred CCeEEEEEECChHHHHHHHHCCCCcEEEEeccC---C-----CCC----ceEEEEecCEEEECCC
Confidence 45554443 45788999999999999985431 1 111 1224456777777776
No 152
>PRK10094 DNA-binding transcriptional activator AllS; Provisional
Probab=23.45 E-value=1.7e+02 Score=27.89 Aligned_cols=70 Identities=14% Similarity=0.045 Sum_probs=41.7
Q ss_pred CCeEEEe--ecCCchhhhcccCceeeeeeccceecccCCCCccceeecCCCCcccEEEEEEEeCCCccCc---ccchHHh
Q 018854 125 SNLEVWF--QRPKDIVRKLLSGDLDLGIVGLDTVSEFGQGNEDLIIVHDALDYGDCRLSLAIPKYGIFEN---INSLREL 199 (349)
Q Consensus 125 p~vev~~--vR~~DIP~yV~~G~aDlGIvG~DvL~E~~~~~~~lv~~l~dLgfG~CRLvvAvP~~~~~~d---v~sl~dL 199 (349)
|++++.+ ....|+..-+.+|.+|+||.-.+. +.. ..++. .-.++.-+++++++.+..+.. .-+++||
T Consensus 120 P~i~l~l~~~~~~~~~~~l~~g~~D~~i~~~~~--~~~--~~~l~----~~~l~~~~~~~v~~~~hpl~~~~~~~~~~~L 191 (308)
T PRK10094 120 PFTQFHISRQIYMGVWDSLLYEGFSLAIGVTGT--EAL--ANTFS----LDPLGSVQWRFVMAADHPLANVEEPLTEAQL 191 (308)
T ss_pred CCcEEEEEeehhhhHHHHHhCCCccEEEecccC--ccc--cCCee----EEEecceeEEEEECCCCCCcCCCCCCCHHHH
Confidence 4444443 356789999999999999963111 110 12221 235677888888887743322 3466777
Q ss_pred hcC
Q 018854 200 AQM 202 (349)
Q Consensus 200 ~~~ 202 (349)
.+.
T Consensus 192 ~~~ 194 (308)
T PRK10094 192 RRF 194 (308)
T ss_pred HhC
Confidence 653
No 153
>COG1022 FAA1 Long-chain acyl-CoA synthetases (AMP-forming) [Lipid metabolism]
Probab=22.94 E-value=88 Score=34.17 Aligned_cols=56 Identities=20% Similarity=0.289 Sum_probs=41.4
Q ss_pred HHHHHHhcCCceEEEEecCCccccccCCCcc---eeeeecccchhhHhhCCcEEecCceEEEEE
Q 018854 221 GPKFMKDNGLKHVVFSTADGALEAAPAMGIA---DAILDLVSSGTTLRENNLKEIEGGVVLESQ 281 (349)
Q Consensus 221 ar~yf~~~Gi~~v~Ii~l~GSvElAP~lGlA---D~IVDIVsTGtTLraNgLk~ie~g~IleSs 281 (349)
+..||...|+ .|..-+|-+|.+|..-.- +...|.| |.-+--+-.|+.|+|+|+-=.
T Consensus 369 ~~~f~~~lGi---~i~eGYGlTEts~~~~v~~~~~~~~gtv--G~p~p~~evKI~d~GEilVRG 427 (613)
T COG1022 369 LLHFFRSLGI---PILEGYGLTETSAVVSVNPPDRFVLGTV--GKPLPGIEVKIADDGEILVRG 427 (613)
T ss_pred HHHHHHHcCC---CeEEEecccccccceEEccccCcccCCc--CCcCCCceEEEccCceEEEec
Confidence 4669999995 566779999988754332 4555555 888888889999999886533
No 154
>PRK10222 PTS system L-ascorbate-specific transporter subunit IIB; Provisional
Probab=22.83 E-value=1.7e+02 Score=23.52 Aligned_cols=41 Identities=15% Similarity=0.209 Sum_probs=26.3
Q ss_pred HHHHHHhcCCceEEEEecCCcc-ccccCCCcceeeeecccchhhH
Q 018854 221 GPKFMKDNGLKHVVFSTADGAL-EAAPAMGIADAILDLVSSGTTL 264 (349)
Q Consensus 221 ar~yf~~~Gi~~v~Ii~l~GSv-ElAP~lGlAD~IVDIVsTGtTL 264 (349)
.+++++++|++ +++. +.++ |+...++-||+||=.+.--..+
T Consensus 7 Ik~~L~e~Gi~-~~ve--~~diss~~~~~~~aDiiVtt~~l~~~~ 48 (85)
T PRK10222 7 VDQFLTQSNID-HTVN--SCAVGEYKSELSGADIIIASTHIAGEI 48 (85)
T ss_pred HHHHHHHcCCC-eEEE--EeehhhcccCCCCCCEEEECccchhhh
Confidence 57899999996 6766 3333 4445555677777555544454
No 155
>PRK09959 hybrid sensory histidine kinase in two-component regulatory system with EvgA; Provisional
Probab=22.63 E-value=3.5e+02 Score=30.91 Aligned_cols=122 Identities=11% Similarity=0.110 Sum_probs=66.3
Q ss_pred eEEEeecC---CchhhhcccCceeeeeeccceecccCCCCccceeecCCCCcccEEEEEEEeCCCccCcccchHHhhcCC
Q 018854 127 LEVWFQRP---KDIVRKLLSGDLDLGIVGLDTVSEFGQGNEDLIIVHDALDYGDCRLSLAIPKYGIFENINSLRELAQMP 203 (349)
Q Consensus 127 vev~~vR~---~DIP~yV~~G~aDlGIvG~DvL~E~~~~~~~lv~~l~dLgfG~CRLvvAvP~~~~~~dv~sl~dL~~~~ 203 (349)
++|-|+.- ++.-..+..|.+|+.+.+...-.|... . + ..--+|..-..++.++.+ .++.+++++.+
T Consensus 96 ~~~e~v~~~~~~~~l~~l~~g~iDl~~~~~~~~~~r~~---~-~--~fs~py~~~~~~~v~~~~---~~~~~~~~l~~-- 164 (1197)
T PRK09959 96 IKLTLREYADHQKAMDALEEGEVDIVLSHLVASPPLND---D-I--AATKPLIITFPALVTTLH---DSMRPLTSSKP-- 164 (1197)
T ss_pred CceEEEeCCCHHHHHHHHHcCCCcEecCcccccccccc---c-h--hcCCCccCCCceEEEeCC---CCCCCcccccC--
Confidence 44555443 466688999999997666443333321 1 1 012344445556666665 34555555543
Q ss_pred ccCCCCCcEEEcCCCccHHHHHHhcCCceEEEEecCCcccc--ccCCCcceeeeecccc-hhhHhhC
Q 018854 204 QWTAEKPLRVATGFTYLGPKFMKDNGLKHVVFSTADGALEA--APAMGIADAILDLVSS-GTTLREN 267 (349)
Q Consensus 204 ~~~~~~~lRVATkYPnlar~yf~~~Gi~~v~Ii~l~GSvEl--AP~lGlAD~IVDIVsT-GtTLraN 267 (349)
++||.-=-.....+++++. ..++++......|+ |-.-|-||++++-..+ ...++.+
T Consensus 165 -------~~i~~~~g~~~~~~~~~~~-p~~~i~~~~s~~~al~av~~G~~Da~i~~~~~~~~~i~~~ 223 (1197)
T PRK09959 165 -------VNIARVANYPPDEVIHQSF-PKATIISFTNLYQALASVSAGQNDYFIGSNIITSSMISRY 223 (1197)
T ss_pred -------eEEEEeCCCCCHHHHHHhC-CCCEEEeCCCHHHHHHHHHcCCCCEEEccHHHHHHHHhcc
Confidence 4555311112344555543 34677776655553 3678999988776543 3345543
No 156
>KOG0186 consensus Proline oxidase [Amino acid transport and metabolism]
Probab=22.34 E-value=48 Score=35.27 Aligned_cols=59 Identities=15% Similarity=0.322 Sum_probs=43.4
Q ss_pred ccEEEEEEEeCCCccCcccchHHhhcCCccCCCCCcEEEcCCCccHHHHHHhcCCceEEEEecCCccccccCCCcceeee
Q 018854 176 GDCRLSLAIPKYGIFENINSLRELAQMPQWTAEKPLRVATGFTYLGPKFMKDNGLKHVVFSTADGALEAAPAMGIADAIL 255 (349)
Q Consensus 176 G~CRLvvAvP~~~~~~dv~sl~dL~~~~~~~~~~~lRVATkYPnlar~yf~~~Gi~~v~Ii~l~GSvElAP~lGlAD~IV 255 (349)
++|.++||..++ .. . .++-+-++++||+ +.+|.++.+=++|+||.|-
T Consensus 400 ~~~~vmVASHN~---dS------------------~-------r~a~nlm~elgi~-----~~~~~i~fgQLlGM~D~vS 446 (506)
T KOG0186|consen 400 SKAHVMVASHNE---DS------------------V-------RLATNLMEELGIN-----PAKGKIYFGQLLGMCDQVS 446 (506)
T ss_pred CceeEEEEecch---HH------------------H-------HHHHHHHHHhCCC-----cccceEeHHHhhcchhhhc
Confidence 589999998775 11 1 4555678899984 5799999999999999763
Q ss_pred ecccchhhHhhCCcEEec
Q 018854 256 DLVSSGTTLRENNLKEIE 273 (349)
Q Consensus 256 DIVsTGtTLraNgLk~ie 273 (349)
=-|.+.|..|+.
T Consensus 447 ------f~L~qagf~V~K 458 (506)
T KOG0186|consen 447 ------FALGQAGFNVYK 458 (506)
T ss_pred ------hhhccCCceeEE
Confidence 234567777664
No 157
>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=21.61 E-value=1e+02 Score=25.26 Aligned_cols=67 Identities=21% Similarity=0.254 Sum_probs=35.0
Q ss_pred CCeEEEeecCCchhhhcccCceeeeeeccceecccCCCCccceeecCCCCcccEEEEEEEeCCCcc--CcccchHHhhc
Q 018854 125 SNLEVWFQRPKDIVRKLLSGDLDLGIVGLDTVSEFGQGNEDLIIVHDALDYGDCRLSLAIPKYGIF--ENINSLRELAQ 201 (349)
Q Consensus 125 p~vev~~vR~~DIP~yV~~G~aDlGIvG~DvL~E~~~~~~~lv~~l~dLgfG~CRLvvAvP~~~~~--~dv~sl~dL~~ 201 (349)
|++++-+....++...+..| +|+||........ .++. -..+++-+++++++.+... ...-+++||..
T Consensus 28 P~v~i~i~~~~~~~~~l~~~-~D~~i~~~~~~~~-----~~l~----~~~l~~~~~~~v~~~~~~~~~~~~~~~~~l~~ 96 (199)
T cd08475 28 PELELELSFSDRFVDLIEEG-IDLAVRIGELADS-----TGLV----ARRLGTQRMVLCASPAYLARHGTPRTLEDLAE 96 (199)
T ss_pred CCeEEEEEeccchhhHhhcC-ccEEEEeCCCCCC-----CCeE----EEEcccceEEEEECHHHHHhcCCCCCHHHHhh
Confidence 55555554456677777766 9999963221111 1121 1234566777777654211 11235677664
No 158
>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=21.58 E-value=89 Score=25.54 Aligned_cols=66 Identities=17% Similarity=0.202 Sum_probs=36.9
Q ss_pred CCeEEEeecCCchhhhcccCceeeeeeccceecccCCCCccceeecCCCCcccEEEEEEEeCCCcc--CcccchHHhhc
Q 018854 125 SNLEVWFQRPKDIVRKLLSGDLDLGIVGLDTVSEFGQGNEDLIIVHDALDYGDCRLSLAIPKYGIF--ENINSLRELAQ 201 (349)
Q Consensus 125 p~vev~~vR~~DIP~yV~~G~aDlGIvG~DvL~E~~~~~~~lv~~l~dLgfG~CRLvvAvP~~~~~--~dv~sl~dL~~ 201 (349)
|++++.+.-..++...+..| +|+||+.... .+ .++. -..+++.++++++|++... ...-+++||.+
T Consensus 26 P~v~i~~~~~~~~~~~l~~~-~D~~i~~~~~-~~-----~~~~----~~~l~~~~~~~v~~~~~~~~~~~~~~~~~L~~ 93 (197)
T cd08476 26 PEIELDLDFSDRLVDVIDEG-FDAVIRTGEL-PD-----SRLM----SRRLGSFRMVLVASPDYLARHGTPETPADLAE 93 (197)
T ss_pred CCeEEEEEecCCcccccccC-eeEEEEeCCC-CC-----CCee----EEEeecccEEEEECHHHHHhCCCCCCHHHHhc
Confidence 45555554456777777766 9999974321 11 1221 1234677888888765211 11235677764
No 159
>COG1040 ComFC Predicted amidophosphoribosyltransferases [General function prediction only]
Probab=21.34 E-value=52 Score=31.10 Aligned_cols=14 Identities=36% Similarity=0.757 Sum_probs=10.7
Q ss_pred eee-ecccchhhHhh
Q 018854 253 AIL-DLVSSGTTLRE 266 (349)
Q Consensus 253 ~IV-DIVsTGtTLra 266 (349)
++| ||+-||+||++
T Consensus 188 lLvDDV~TTGaTl~~ 202 (225)
T COG1040 188 LLVDDVYTTGATLKE 202 (225)
T ss_pred EEEecccccHHHHHH
Confidence 455 89999999654
No 160
>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=21.17 E-value=1.2e+02 Score=26.91 Aligned_cols=59 Identities=19% Similarity=0.305 Sum_probs=33.7
Q ss_pred eEEEec--CCCCchHHHHHHHHHCCCccCCCCCCceEEecCCCCCeEEEeecC-CchhhhcccCceeeeeecccee
Q 018854 84 IRLGLP--SKGRMAADTLDLLKDCQLSVKQVNPRQYVAQIPQLSNLEVWFQRP-KDIVRKLLSGDLDLGIVGLDTV 156 (349)
Q Consensus 84 LrIALP--~KGRL~e~t~~LL~~aGi~~~~~~~R~L~~~~~~~p~vev~~vR~-~DIP~yV~~G~aDlGIvG~DvL 156 (349)
-+|++| ...-....+..+|+..|+- . ++. +++. .... .++-.+|..|.+|+||+-....
T Consensus 99 ~~i~~~~P~~~~~g~~~~~~~~~~g~~-~-----~l~------~n~~--~~~~~~~~~~~~~~Ge~~~~~~~~~~~ 160 (216)
T TIGR01256 99 KRVAIGDPKHAPYGAAAKEVLQKLGLW-E-----TLK------KKLV--YGEDVRQALQFVETGNAPAGIVALSDV 160 (216)
T ss_pred CeEEecCCCcCcChHHHHHHHHHCCCh-h-----hhh------hhee--ecCcHHHHHHHHHcCCCCEEeeehhhh
Confidence 467765 2233345567777776751 1 110 1221 2222 4677799999999999865443
No 161
>PF00156 Pribosyltran: Phosphoribosyl transferase domain; InterPro: IPR000836 The name PRT comes from phosphoribosyltransferase (PRTase) enzymes, which carry out phosphoryl transfer reactions on 5-phosphoribosyl-alpha1-pyrophosphate PRPP, an activated form of ribose-5-phosphate. Members of Phosphoribosyltransferase (PRT) are catalytic and are regulatory proteins involved in nucleotide synthesis and salvage []. This includes a range of diverse phosphoribosyl transferase enzymes including adenine phosphoribosyltransferase (2.4.2.7 from EC); hypoxanthine-guanine-xanthine phosphoribosyltransferase; hypoxanthine phosphoribosyltransferase (2.4.2.8 from EC); ribose-phosphate pyrophosphokinase (2.7.6.1 from EC); amidophosphoribosyltransferase (2.4.2.14 from EC); orotate phosphoribosyltransferase (2.4.2.10 from EC);uracil phosphoribosyltransferase (2.4.2.9 from EC); and xanthine-guanine phosphoribosyltransferase (2.4.2.22 from EC). Not all PRT proteins are enzymes. For example, in some bacteria PRT proteins regulate the expression of purine and pyrimidine synthetic genes. Members of PRT are defined by the protein fold and by a short 13-residue sequence motif, The motif consists of four hydrophobic amino acids, two acidic amino acids and seven amino acids of variable character, usually including glycine and threonine. The motif has been predicted to be a PRPP-binding site in advance of structural information [, ]. Apart of this motif, different PRT proteins have a low level of sequence identity, less than 15%. The PRT sequence motif is only found in PRTases from the nucleotide synthesis and salvage pathways. Other PRTases, from the tryptophan, histidine and nicotinamide synthetic and salvage pathways, lack the PRT sequence motif and appear to be unrelated to each other and unrelated to the PRT family.; GO: 0009116 nucleoside metabolic process; PDB: 2JBH_A 1Y0B_D 2FXV_B 1GPH_1 1AO0_D 1ORO_B 1VCH_C 2WNS_A 2PRZ_B 2PS1_A ....
Probab=20.96 E-value=44 Score=27.09 Aligned_cols=14 Identities=43% Similarity=0.821 Sum_probs=11.2
Q ss_pred eeee-cccchhhHhh
Q 018854 253 AILD-LVSSGTTLRE 266 (349)
Q Consensus 253 ~IVD-IVsTGtTLra 266 (349)
+||| ++.||+||++
T Consensus 92 liVDDvi~tG~Tl~~ 106 (125)
T PF00156_consen 92 LIVDDVIDTGGTLKE 106 (125)
T ss_dssp EEEEEEESSSHHHHH
T ss_pred EEEeeeEcccHHHHH
Confidence 5665 9999999865
No 162
>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=20.38 E-value=3e+02 Score=25.55 Aligned_cols=66 Identities=12% Similarity=0.047 Sum_probs=40.8
Q ss_pred eEEEeecCCchhhhcccCceeeeeeccceecccCCCCccceeecCCCCcccEEEEEEEeCCCccC---cccchHHhhcC
Q 018854 127 LEVWFQRPKDIVRKLLSGDLDLGIVGLDTVSEFGQGNEDLIIVHDALDYGDCRLSLAIPKYGIFE---NINSLRELAQM 202 (349)
Q Consensus 127 vev~~vR~~DIP~yV~~G~aDlGIvG~DvL~E~~~~~~~lv~~l~dLgfG~CRLvvAvP~~~~~~---dv~sl~dL~~~ 202 (349)
+++....+.++...+.+|.+|+||...+.-. .++. -..+++=+++++++.+.... .--+++||.+.
T Consensus 120 i~l~~~~~~~~~~~l~~g~~d~~i~~~~~~~------~~l~----~~~l~~~~~~~v~~~~~~~~~~~~~i~~~dL~~~ 188 (292)
T TIGR03298 120 LDLVVEDQDHTAELLRSGEVLGAVTTQAKPV------QGCR----VVPLGAMRYLAVASPAFAARYFPDGVTAEALARA 188 (292)
T ss_pred EEEEeCcchhHHHHHhCCCceEEEecCCCCC------CCce----EEecCCceEEEEECchhhhhccCCCCCHHHhcCC
Confidence 4555556678999999999999998754321 1222 13456667777777652101 22367887753
Done!