Query 025329
Match_columns 254
No_of_seqs 150 out of 1075
Neff 4.6
Searched_HMMs 46136
Date Fri Mar 29 04:45:08 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/025329.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/025329hhsearch_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 1.8E-61 3.8E-66 460.4 20.7 232 15-254 7-240 (403)
2 PRK13583 hisG ATP phosphoribos 100.0 2.7E-54 6E-59 386.0 16.8 170 82-254 1-175 (228)
3 PRK01686 hisG ATP phosphoribos 100.0 9.1E-53 2E-57 373.3 15.7 156 81-254 1-158 (215)
4 TIGR00070 hisG ATP phosphoribo 100.0 4.8E-52 1E-56 360.7 14.8 152 84-254 1-152 (182)
5 COG0040 HisG ATP phosphoribosy 100.0 3E-50 6.4E-55 370.1 14.6 159 82-254 1-159 (290)
6 PRK13584 hisG ATP phosphoribos 100.0 4.5E-50 9.8E-55 353.7 14.4 144 83-254 1-148 (204)
7 PF01634 HisG: ATP phosphoribo 100.0 4E-39 8.7E-44 275.6 4.2 110 132-254 1-110 (163)
8 KOG2831 ATP phosphoribosyltran 100.0 6.1E-37 1.3E-41 275.3 1.1 173 79-254 6-178 (308)
9 PRK00489 hisG ATP phosphoribos 100.0 8.3E-32 1.8E-36 244.9 14.8 155 81-254 2-156 (287)
10 TIGR01728 SsuA_fam ABC transpo 95.9 0.0087 1.9E-07 52.0 4.1 105 134-253 39-151 (288)
11 PRK11063 metQ DL-methionine tr 95.9 0.027 5.8E-07 51.7 7.2 102 83-187 130-236 (271)
12 PF09084 NMT1: NMT1/THI5 like; 95.4 0.015 3.2E-07 49.2 3.6 100 127-240 23-129 (216)
13 smart00062 PBPb Bacterial peri 95.3 0.059 1.3E-06 42.7 6.4 97 128-243 42-138 (219)
14 PRK11553 alkanesulfonate trans 94.4 0.11 2.5E-06 47.0 6.5 91 134-238 66-163 (314)
15 PRK11480 tauA taurine transpor 93.8 0.13 2.8E-06 47.3 5.7 95 127-239 53-157 (320)
16 TIGR00363 lipoprotein, YaeC fa 93.2 0.35 7.7E-06 44.3 7.5 78 83-162 117-199 (258)
17 TIGR01729 taurine_ABC_bnd taur 92.4 0.31 6.7E-06 43.9 5.9 96 127-238 29-134 (300)
18 PRK09861 cytoplasmic membrane 91.2 0.96 2.1E-05 41.7 7.8 79 83-163 131-214 (272)
19 PF03466 LysR_substrate: LysR 90.8 0.86 1.9E-05 36.4 6.4 102 125-243 33-140 (209)
20 cd08442 PBP2_YofA_SoxR_like Th 89.0 1.2 2.7E-05 34.8 5.8 89 125-231 27-119 (193)
21 cd08468 PBP2_Pa0477 The C-term 88.5 2.1 4.5E-05 34.4 7.0 109 125-245 27-137 (202)
22 cd08467 PBP2_SyrM The C-termin 87.9 2.8 6.1E-05 33.7 7.4 91 125-231 27-122 (200)
23 cd08437 PBP2_MleR The substrat 87.7 2.5 5.4E-05 33.5 6.9 102 125-243 27-136 (198)
24 cd08418 PBP2_TdcA The C-termin 87.4 1.3 2.8E-05 35.0 5.0 93 125-231 27-123 (201)
25 cd08440 PBP2_LTTR_like_4 TThe 86.8 2 4.3E-05 33.4 5.8 91 125-231 27-123 (197)
26 cd08453 PBP2_IlvR The C-termin 86.8 2.1 4.5E-05 34.0 6.0 109 125-243 27-139 (200)
27 cd00134 PBPb Bacterial peripla 86.6 2.2 4.7E-05 33.9 5.9 95 127-240 40-134 (218)
28 cd08417 PBP2_Nitroaromatics_li 86.3 2.2 4.9E-05 33.6 5.8 91 125-231 27-122 (200)
29 cd08450 PBP2_HcaR The C-termin 86.0 2.3 4.9E-05 33.5 5.7 91 125-231 27-124 (196)
30 cd08459 PBP2_DntR_NahR_LinR_li 85.9 3.3 7.2E-05 32.9 6.7 91 125-231 27-122 (201)
31 cd08451 PBP2_BudR The C-termin 85.7 3.4 7.3E-05 32.5 6.6 95 133-243 38-138 (199)
32 cd08460 PBP2_DntR_like_1 The C 85.7 5.1 0.00011 32.0 7.7 95 125-236 27-125 (200)
33 cd08463 PBP2_DntR_like_4 The C 85.4 6.8 0.00015 31.9 8.5 103 124-243 26-136 (203)
34 cd08461 PBP2_DntR_like_3 The C 85.4 6.6 0.00014 31.0 8.2 91 125-231 27-123 (198)
35 cd08449 PBP2_XapR The C-termin 85.4 2.8 6E-05 32.9 6.0 93 125-231 27-126 (197)
36 cd08435 PBP2_GbpR The C-termin 85.3 2.8 6.1E-05 32.9 5.9 69 125-201 27-99 (201)
37 cd08464 PBP2_DntR_like_2 The C 85.2 4.3 9.3E-05 32.0 7.0 91 125-231 27-122 (200)
38 cd08436 PBP2_LTTR_like_3 The C 84.5 5.6 0.00012 31.0 7.3 68 125-201 27-98 (194)
39 cd08416 PBP2_MdcR The C-termin 84.2 5.1 0.00011 31.6 7.0 69 125-201 27-99 (199)
40 cd08426 PBP2_LTTR_like_5 The C 84.1 2.8 6.1E-05 33.0 5.5 93 125-231 27-123 (199)
41 cd08456 PBP2_LysR The C-termin 84.1 2.5 5.4E-05 33.2 5.2 91 125-231 27-123 (196)
42 cd08465 PBP2_ToxR The C-termin 83.9 6 0.00013 31.9 7.4 102 125-243 27-133 (200)
43 cd08434 PBP2_GltC_like The sub 83.4 3.4 7.4E-05 32.1 5.6 89 125-231 27-123 (195)
44 cd08433 PBP2_Nac The C-teminal 83.4 6.7 0.00015 30.9 7.4 90 125-231 27-123 (198)
45 cd08462 PBP2_NodD The C-termin 83.1 8.1 0.00018 30.9 7.9 102 125-243 27-133 (200)
46 cd08421 PBP2_LTTR_like_1 The C 82.8 5.1 0.00011 31.5 6.5 67 125-201 27-97 (198)
47 cd08448 PBP2_LTTR_aromatics_li 82.7 3.2 6.9E-05 32.5 5.2 67 125-201 27-97 (197)
48 cd08438 PBP2_CidR The C-termin 82.4 8.5 0.00019 30.0 7.6 67 125-201 27-97 (197)
49 TIGR02122 TRAP_TAXI TRAP trans 82.0 4 8.7E-05 36.4 6.3 84 135-231 72-167 (320)
50 cd08458 PBP2_NocR The C-termin 81.3 2.4 5.1E-05 33.9 4.1 91 125-231 27-123 (196)
51 PF12974 Phosphonate-bd: ABC t 80.9 1.3 2.7E-05 38.7 2.5 93 127-231 31-133 (243)
52 cd08486 PBP2_CbnR The C-termin 80.7 4.4 9.6E-05 32.7 5.6 94 125-235 28-129 (198)
53 PRK11917 bifunctional adhesin/ 80.6 9.9 0.00022 33.8 8.2 95 127-240 83-181 (259)
54 cd08427 PBP2_LTTR_like_2 The C 80.2 7.3 0.00016 30.4 6.5 55 125-187 27-83 (195)
55 cd08425 PBP2_CynR The C-termin 80.0 8.2 0.00018 30.4 6.8 91 125-231 28-125 (197)
56 COG4521 TauA ABC-type taurine 79.8 3.9 8.5E-05 38.7 5.5 90 135-239 68-165 (334)
57 COG0715 TauA ABC-type nitrate/ 79.7 4.1 8.8E-05 36.9 5.5 95 133-241 70-174 (335)
58 PF03180 Lipoprotein_9: NLPA l 79.7 5.4 0.00012 36.3 6.3 100 83-187 97-202 (237)
59 cd08457 PBP2_OccR The C-termin 79.2 7 0.00015 31.0 6.2 91 125-231 27-123 (196)
60 PF13379 NMT1_2: NMT1-like fam 78.7 6.1 0.00013 34.7 6.2 61 82-156 120-181 (252)
61 PF13379 NMT1_2: NMT1-like fam 78.5 5.1 0.00011 35.2 5.6 103 132-240 43-159 (252)
62 cd05466 PBP2_LTTR_substrate Th 77.9 16 0.00034 27.8 7.6 64 127-200 31-96 (197)
63 cd08413 PBP2_CysB_like The C-t 77.6 9 0.0002 30.7 6.4 92 125-231 27-124 (198)
64 cd08411 PBP2_OxyR The C-termin 77.3 7.1 0.00015 30.8 5.7 67 125-201 28-98 (200)
65 cd08419 PBP2_CbbR_RubisCO_like 77.2 6.7 0.00014 30.6 5.4 88 128-231 31-122 (197)
66 TIGR03427 ABC_peri_uca ABC tra 75.6 8.9 0.00019 36.2 6.7 87 134-239 45-141 (328)
67 PRK11242 DNA-binding transcrip 75.3 11 0.00025 33.1 7.0 67 125-201 118-189 (296)
68 PRK10216 DNA-binding transcrip 75.0 13 0.00029 33.6 7.5 101 125-231 124-228 (319)
69 PRK12682 transcriptional regul 75.0 8.6 0.00019 34.6 6.2 92 125-231 120-217 (309)
70 cd08423 PBP2_LTTR_like_6 The C 74.7 10 0.00022 29.7 5.8 71 125-201 27-102 (200)
71 PF00497 SBP_bac_3: Bacterial 74.5 7.7 0.00017 31.7 5.3 86 128-228 41-128 (225)
72 cd08443 PBP2_CysB The C-termin 74.4 26 0.00056 28.1 8.3 90 125-231 27-124 (198)
73 TIGR01098 3A0109s03R phosphate 74.1 11 0.00023 32.7 6.3 95 134-240 74-182 (254)
74 cd08445 PBP2_BenM_CatM_CatR Th 73.9 10 0.00022 30.3 5.8 67 125-201 28-99 (203)
75 PRK15007 putative ABC transpor 73.2 13 0.00028 31.8 6.6 87 132-238 67-153 (243)
76 TIGR02424 TF_pcaQ pca operon t 73.1 8.3 0.00018 34.2 5.6 91 125-231 120-218 (300)
77 cd08483 PBP2_HvrB The C-termin 72.5 9.9 0.00021 29.7 5.3 87 125-231 27-115 (190)
78 cd08429 PBP2_NhaR The C-termin 72.5 19 0.00041 29.6 7.2 107 125-243 27-136 (204)
79 PRK11151 DNA-binding transcrip 72.3 7.2 0.00016 34.8 5.0 67 125-201 118-188 (305)
80 PRK09791 putative DNA-binding 71.7 7.8 0.00017 34.5 5.1 65 128-201 127-192 (302)
81 cd08466 PBP2_LeuO The C-termin 71.2 20 0.00044 28.2 6.9 90 125-230 27-120 (200)
82 cd08444 PBP2_Cbl The C-termina 71.2 17 0.00037 29.0 6.6 91 125-231 27-124 (198)
83 PRK11063 metQ DL-methionine tr 70.9 13 0.00028 34.2 6.4 79 135-230 70-154 (271)
84 cd08414 PBP2_LTTR_aromatics_li 70.6 21 0.00045 27.8 6.7 91 125-231 27-125 (197)
85 cd08415 PBP2_LysR_opines_like 70.5 20 0.00043 28.0 6.6 67 125-201 27-97 (196)
86 cd08452 PBP2_AlsR The C-termin 69.7 25 0.00054 28.0 7.2 67 125-201 27-97 (197)
87 cd08412 PBP2_PAO1_like The C-t 68.6 18 0.00038 28.3 6.0 91 125-231 27-122 (198)
88 PRK10341 DNA-binding transcrip 68.5 11 0.00023 34.1 5.3 67 127-201 128-194 (312)
89 PRK11062 nhaR transcriptional 66.8 8 0.00017 34.6 4.1 90 125-231 120-215 (296)
90 PRK11260 cystine transporter s 66.0 21 0.00045 31.4 6.5 96 127-239 82-177 (266)
91 COG0725 ModA ABC-type molybdat 65.6 39 0.00085 31.0 8.4 77 136-230 177-254 (258)
92 PRK09508 leuO leucine transcri 65.3 48 0.0011 29.8 8.9 91 125-231 139-233 (314)
93 PRK12683 transcriptional regul 64.7 17 0.00037 32.9 5.9 88 127-231 124-217 (309)
94 PRK09495 glnH glutamine ABC tr 64.3 30 0.00065 29.9 7.1 91 129-237 67-157 (247)
95 PRK09906 DNA-binding transcrip 63.8 24 0.00053 31.1 6.5 89 125-231 117-215 (296)
96 cd08481 PBP2_GcdR_like The C-t 63.6 17 0.00037 28.3 5.0 87 125-230 27-115 (194)
97 PRK11233 nitrogen assimilation 63.1 30 0.00066 31.0 7.1 90 125-231 119-212 (305)
98 TIGR03339 phn_lysR aminoethylp 62.3 21 0.00045 30.9 5.7 88 128-231 116-207 (279)
99 TIGR01096 3A0103s03R lysine-ar 61.1 31 0.00068 29.4 6.6 84 128-228 66-149 (250)
100 PRK10677 modA molybdate transp 61.0 23 0.0005 31.9 6.0 147 48-230 4-162 (257)
101 PRK10837 putative DNA-binding 59.8 18 0.00039 31.7 4.9 65 127-201 120-185 (290)
102 cd08446 PBP2_Chlorocatechol Th 59.8 36 0.00078 26.7 6.3 67 125-201 28-98 (198)
103 PF13531 SBP_bac_11: Bacterial 58.7 8.5 0.00018 33.0 2.6 95 126-229 27-128 (230)
104 PRK12680 transcriptional regul 58.7 32 0.0007 31.7 6.6 92 125-231 120-218 (327)
105 PRK10797 glutamate and asparta 58.1 37 0.0008 31.1 6.9 64 128-200 89-152 (302)
106 cd08430 PBP2_IlvY The C-termin 57.7 17 0.00036 28.5 4.0 54 125-187 27-82 (199)
107 PRK12684 transcriptional regul 56.4 45 0.00096 30.2 7.1 68 125-201 120-191 (313)
108 PRK11013 DNA-binding transcrip 56.1 22 0.00048 32.0 5.0 89 127-231 125-217 (309)
109 COG1464 NlpA ABC-type metal io 55.9 42 0.0009 31.7 6.8 101 83-187 128-234 (268)
110 PF09084 NMT1: NMT1/THI5 like; 55.8 12 0.00026 31.5 3.0 60 77-152 87-147 (216)
111 cd08431 PBP2_HupR The C-termin 55.1 20 0.00044 28.2 4.1 68 125-201 27-99 (195)
112 cd08447 PBP2_LTTR_aromatics_li 55.0 16 0.00035 28.6 3.5 66 125-200 27-96 (198)
113 cd08439 PBP2_LrhA_like The C-t 52.4 21 0.00046 28.0 3.8 29 125-153 27-57 (185)
114 PRK14498 putative molybdopteri 52.4 48 0.001 33.9 7.2 92 127-231 443-549 (633)
115 PRK04168 molybdate ABC transpo 52.3 27 0.00059 33.1 5.1 24 136-159 213-236 (334)
116 cd08441 PBP2_MetR The C-termin 52.0 18 0.00039 28.5 3.4 93 125-231 27-123 (198)
117 cd08484 PBP2_LTTR_beta_lactama 51.2 36 0.00078 26.7 5.0 87 125-231 27-113 (189)
118 CHL00180 rbcR LysR transcripti 51.1 52 0.0011 29.4 6.5 89 128-231 127-221 (305)
119 cd08487 PBP2_BlaA The C-termin 49.1 43 0.00093 26.1 5.1 86 125-231 27-113 (189)
120 TIGR03431 PhnD phosphonate ABC 48.7 54 0.0012 29.2 6.2 69 135-216 70-141 (288)
121 PRK11074 putative DNA-binding 47.0 49 0.0011 29.5 5.7 99 80-202 90-193 (300)
122 PRK11139 DNA-binding transcrip 46.9 63 0.0014 28.6 6.4 87 125-230 121-209 (297)
123 PRK15421 DNA-binding transcrip 46.6 39 0.00085 30.8 5.1 92 128-236 121-216 (317)
124 TIGR01729 taurine_ABC_bnd taur 45.3 66 0.0014 28.8 6.3 66 77-158 94-160 (300)
125 TIGR01256 modA molybdenum ABC 45.0 36 0.00078 28.9 4.3 94 127-229 23-123 (216)
126 PRK12679 cbl transcriptional r 44.6 60 0.0013 29.4 5.9 90 125-231 120-217 (316)
127 cd08480 PBP2_CrgA_like_10 The 43.3 31 0.00067 27.4 3.5 66 125-201 28-95 (198)
128 PRK03601 transcriptional regul 43.0 29 0.00062 30.8 3.5 51 127-187 120-170 (275)
129 cd08488 PBP2_AmpR The C-termin 42.7 71 0.0015 25.2 5.5 72 140-230 41-112 (191)
130 KOG0186 Proline oxidase [Amino 42.5 16 0.00035 37.0 2.0 46 176-254 400-445 (506)
131 PRK11482 putative DNA-binding 42.4 35 0.00075 31.2 4.1 67 125-201 144-211 (317)
132 TIGR03427 ABC_peri_uca ABC tra 42.1 41 0.00089 31.8 4.6 66 76-157 99-165 (328)
133 TIGR03730 tungstate_WtpA tungs 42.1 47 0.001 30.8 4.9 24 134-157 184-207 (273)
134 COG0834 HisJ ABC-type amino ac 41.4 89 0.0019 26.7 6.3 98 127-241 79-178 (275)
135 PF03401 TctC: Tripartite tric 40.5 55 0.0012 29.8 5.0 66 175-245 75-145 (274)
136 cd08420 PBP2_CysL_like C-termi 40.5 40 0.00086 26.1 3.6 64 128-201 32-97 (201)
137 PRK11480 tauA taurine transpor 39.7 63 0.0014 29.6 5.4 68 76-159 115-183 (320)
138 TIGR02995 ectoine_ehuB ectoine 39.7 1E+02 0.0022 27.3 6.5 98 129-239 76-173 (275)
139 cd08469 PBP2_PnbR The C-termin 39.2 57 0.0012 26.4 4.5 67 125-201 27-96 (221)
140 PRK11716 DNA-binding transcrip 38.9 33 0.00071 29.4 3.2 54 125-187 94-149 (269)
141 TIGR01256 modA molybdenum ABC 36.8 57 0.0012 27.6 4.3 22 135-156 139-160 (216)
142 cd08475 PBP2_CrgA_like_6 The C 36.6 42 0.0009 26.2 3.2 67 125-201 28-96 (199)
143 COG2358 Imp TRAP-type uncharac 36.0 37 0.0008 32.7 3.3 88 138-238 71-169 (321)
144 PRK12681 cysB transcriptional 35.8 1.4E+02 0.0031 27.3 7.1 28 125-152 120-149 (324)
145 TIGR03298 argP transcriptional 35.7 1.5E+02 0.0032 26.1 6.9 65 127-201 120-187 (292)
146 PRK15243 transcriptional regul 35.4 59 0.0013 30.0 4.5 105 124-244 118-226 (297)
147 PRK10094 DNA-binding transcrip 35.2 1.1E+02 0.0024 27.7 6.1 69 125-201 120-193 (308)
148 PF12727 PBP_like: PBP superfa 34.1 52 0.0011 28.6 3.7 85 82-187 92-178 (193)
149 PRK11553 alkanesulfonate trans 33.7 92 0.002 28.1 5.4 63 77-155 123-186 (314)
150 TIGR03871 ABC_peri_MoxJ_2 quin 33.6 2.5E+02 0.0054 23.6 7.8 72 139-230 51-124 (232)
151 COG0715 TauA ABC-type nitrate/ 31.9 1.9E+02 0.004 26.1 7.0 71 73-158 126-197 (335)
152 cd08478 PBP2_CrgA The C-termin 31.8 41 0.00088 26.5 2.4 67 124-201 29-97 (199)
153 TIGR01728 SsuA_fam ABC transpo 31.0 1.2E+02 0.0026 26.0 5.5 65 78-157 96-160 (288)
154 PRK10859 membrane-bound lytic 30.6 1.7E+02 0.0036 28.9 6.9 60 133-200 89-148 (482)
155 cd08428 PBP2_IciA_ArgP The C-t 30.5 85 0.0018 24.6 4.1 65 127-201 30-97 (195)
156 PRK15010 ABC transporter lysin 29.6 1.6E+02 0.0036 25.6 6.1 81 129-226 69-149 (260)
157 cd08476 PBP2_CrgA_like_7 The C 28.5 51 0.0011 25.5 2.5 66 125-201 26-93 (197)
158 cd08472 PBP2_CrgA_like_3 The C 27.9 74 0.0016 24.9 3.3 66 125-201 28-95 (202)
159 cd08485 PBP2_ClcR The C-termin 27.7 52 0.0011 26.3 2.4 28 125-152 28-57 (198)
160 smart00094 TR_FER Transferrin. 27.4 2.2E+02 0.0047 27.3 6.9 71 125-201 27-106 (332)
161 cd08479 PBP2_CrgA_like_9 The C 24.2 63 0.0014 25.3 2.3 27 125-152 28-54 (198)
162 TIGR00787 dctP tripartite ATP- 23.8 2.2E+02 0.0048 25.2 5.9 32 191-231 126-157 (257)
163 PRK15437 histidine ABC transpo 22.3 4.1E+02 0.009 23.1 7.3 76 135-227 75-150 (259)
164 cd08432 PBP2_GcdR_TrpI_HvrB_Am 21.7 78 0.0017 24.5 2.4 28 125-153 27-54 (194)
165 PF09047 MEF2_binding: MEF2 bi 20.6 58 0.0013 21.5 1.1 19 88-107 4-22 (35)
166 PRK09861 cytoplasmic membrane 20.3 1.7E+02 0.0037 27.0 4.6 76 139-229 75-154 (272)
167 PF07927 YcfA: YcfA-like prote 20.3 1.4E+02 0.003 20.3 3.1 46 96-143 2-50 (56)
168 PF03460 NIR_SIR_ferr: Nitrite 20.3 90 0.0019 22.1 2.2 54 83-142 11-64 (69)
169 PRK10329 glutaredoxin-like pro 20.0 89 0.0019 23.4 2.2 24 219-243 15-38 (81)
No 1
>PLN02245 ATP phosphoribosyl transferase
Probab=100.00 E-value=1.8e-61 Score=460.37 Aligned_cols=232 Identities=69% Similarity=1.072 Sum_probs=205.9
Q ss_pred cccCCCCCCCcccccCCccceeeeccCCcccCCCcccceeeeecccccccceeeeecCcccCC--CCCCCceEEEecCCC
Q 025329 15 RQCPSLSPSGLSFFCPLSSFHISVASGPTTATNKPAAAVTCCVSSSQQFESHVSVVNGNIDNR--ISERDEIRLGLPSKG 92 (254)
Q Consensus 15 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~LrIALPsKG 92 (254)
.+|++.+||++++++|.++.+++.+. |++ .|++..++|.++.++. .+.+.....+ +.++.+|||||||||
T Consensus 7 ~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~---~~~~~~~~~~~~~~~~----~~~~~~~~~~~~~~~~~~LriAlPsKG 78 (403)
T PLN02245 7 SPSLSSLPSSSPLLSPPSSRASRLIA-PRR---RCLRLATACVSQVQSS----VVAGSTDSASSVVSSRTQIRLGLPSKG 78 (403)
T ss_pred ccccCCccccccccCCCCcCceeeec-chh---hhhhhheeeecccchh----hhcccccccCccccCCceEEEEECCCC
Confidence 34445688999999999998888887 888 8999999999888772 2223333333 688889999999999
Q ss_pred CChHHHHHHHHhCCCccCCCCCCceEeecCCCCCeEEEeecCcchhhhhhcCceeeeeeccceeecccCCCcceeeecCC
Q 025329 93 RMAADTLDLLKDCQLSVKQVNPRQYVAQIPQLSNLEVWFQRPKDIVRKLLSGDLDLGIVGLDTVSEFGQGNEDLIIVHDA 172 (254)
Q Consensus 93 RL~e~tl~LL~~aGi~v~~~~~R~L~~~~~~~p~iev~~vRp~DIp~yV~~G~aDlGIvG~DvL~E~~~d~~~l~~~l~d 172 (254)
||+|++++||++|||++...++|+|++.+.+.|+++|+|+||+|||+||++|.+|+||||+|||.|++.+..+++++++|
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 99999999999999999876569999998877889999999999999999999999999999999998776778888889
Q ss_pred CCcccEEEEEEEeCCCccccccchHHhhcCCcccCCCCcEEEcCCCccHHHHHHHcCCceEEEEEcCCceecccCCCccc
Q 025329 173 LDYGDCRLSLAIPKYGIFENINSLRELAQMPQWTAEKPLRVATGFTYLGPKFMKDNGLKHVVFSTADGALEAAPAVRITH 252 (254)
Q Consensus 173 LgfG~CRLvVAvP~~~~~~dv~sl~dL~~~~~~~~~r~lRVATkYPnLarkyf~~~Gi~~veIi~l~GSvElAP~lGlAD 252 (254)
||||+|||+||+|+++.|.++++++||+++..|..++++||||||||||++||+++|+++++|++++||||+||.+|+||
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 99999999999999866888999999997777777888999999999999999999996699999999999999999999
Q ss_pred cC
Q 025329 253 LL 254 (254)
Q Consensus 253 aI 254 (254)
+|
T Consensus 239 aI 240 (403)
T PLN02245 239 AI 240 (403)
T ss_pred hh
Confidence 98
No 2
>PRK13583 hisG ATP phosphoribosyltransferase catalytic subunit; Provisional
Probab=100.00 E-value=2.7e-54 Score=385.96 Aligned_cols=170 Identities=27% Similarity=0.467 Sum_probs=149.0
Q ss_pred CceEEEecCCCCChHHHHHHHHhCCCccCCC-CCCceEeecCCCCCeEEEeecCcchhhhhhcCceeeeeeccceeeccc
Q 025329 82 DEIRLGLPSKGRMAADTLDLLKDCQLSVKQV-NPRQYVAQIPQLSNLEVWFQRPKDIVRKLLSGDLDLGIVGLDTVSEFG 160 (254)
Q Consensus 82 ~~LrIALPsKGRL~e~tl~LL~~aGi~v~~~-~~R~L~~~~~~~p~iev~~vRp~DIp~yV~~G~aDlGIvG~DvL~E~~ 160 (254)
.||||||||||||++++++||++|||++... ++|+|++.+.+.|+++++|+||+|||+||++|.+|+||||+|||.|++
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 3699999999999999999999999998775 359999998777889999999999999999999999999999999987
Q ss_pred CCC-cceeeecCCCCcccEEEEEEEeCCCccccccchHHhhcCCcc---cCCCCcEEEcCCCccHHHHHHHcCCceEEEE
Q 025329 161 QGN-EDLIIVHDALDYGDCRLSLAIPKYGIFENINSLRELAQMPQW---TAEKPLRVATGFTYLGPKFMKDNGLKHVVFS 236 (254)
Q Consensus 161 ~d~-~~l~~~l~dLgfG~CRLvVAvP~~~~~~dv~sl~dL~~~~~~---~~~r~lRVATkYPnLarkyf~~~Gi~~veIi 236 (254)
.+. .++++ ++|||||+|||+||+|++ |.++++++||.+...+ .+++++||||||||||++||+++|++.++|+
T Consensus 81 ~~~~~~v~e-lldLgfG~crl~vA~p~~--~~~~~~~~dl~~~~~~~~~~~g~~~RIATkYp~it~~yf~~~Gv~~~~Iv 157 (228)
T PRK13583 81 ADWDKRVEI-VARLGFGHADLVVAVPEI--WIDVDTMADLDDVAADFRARHGRRLRIATKYWRLTQQFLSQKGVQDYRIV 157 (228)
T ss_pred ccCCCCeEE-EecCCCCceEEEEEEECc--ccccCCHHHhhhhhhhhhhccCCceEEEeCCHHHHHHHHHHcCCceeEEE
Confidence 542 23554 459999999999999998 7788999998744332 1234589999999999999999999635999
Q ss_pred EcCCceecccCCCccccC
Q 025329 237 TADGALEAAPAVRITHLL 254 (254)
Q Consensus 237 ~l~GSvElAP~lGlADaI 254 (254)
+++||+|+||.+|+||+|
T Consensus 158 ~l~GsvElaP~~GlAD~I 175 (228)
T PRK13583 158 ESLGATEGAPANGSAEII 175 (228)
T ss_pred ECCCceecccccCcchhh
Confidence 999999999999999987
No 3
>PRK01686 hisG ATP phosphoribosyltransferase catalytic subunit; Reviewed
Probab=100.00 E-value=9.1e-53 Score=373.33 Aligned_cols=156 Identities=28% Similarity=0.474 Sum_probs=138.2
Q ss_pred CCceEEEecCCCCChHHHHHHHHhCCCccCCC--CCCceEeecCCCCCeEEEeecCcchhhhhhcCceeeeeeccceeec
Q 025329 81 RDEIRLGLPSKGRMAADTLDLLKDCQLSVKQV--NPRQYVAQIPQLSNLEVWFQRPKDIVRKLLSGDLDLGIVGLDTVSE 158 (254)
Q Consensus 81 ~~~LrIALPsKGRL~e~tl~LL~~aGi~v~~~--~~R~L~~~~~~~p~iev~~vRp~DIp~yV~~G~aDlGIvG~DvL~E 158 (254)
|+||||||| ||||++++++||++|||.+... ++|+|++.+.+ ++++|+|+||+|||+||++|.+|+||||+|||.|
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-KGRILEETLPLLAKAGIDPSEDPDKSRKLIFPTPE-PDVRFLLVRATDVPTYVEHGAADLGIVGKDVLLE 78 (215)
T ss_pred CCcEEEEec-CcccHHHHHHHHHHcCCCcccCCCCCcceEeecCC-CCEEEEEECHHHHHHHHhCCCccEEEeeeeEeee
Confidence 578999999 9999999999999999998875 47999999765 6899999999999999999999999999999999
Q ss_pred ccCCCcceeeecCCCCcccEEEEEEEeCCCccccccchHHhhcCCcccCCCCcEEEcCCCccHHHHHHHcCCceEEEEEc
Q 025329 159 FGQGNEDLIIVHDALDYGDCRLSLAIPKYGIFENINSLRELAQMPQWTAEKPLRVATGFTYLGPKFMKDNGLKHVVFSTA 238 (254)
Q Consensus 159 ~~~d~~~l~~~l~dLgfG~CRLvVAvP~~~~~~dv~sl~dL~~~~~~~~~r~lRVATkYPnLarkyf~~~Gi~~veIi~l 238 (254)
++.+ ++++ .|||||+|||+||+|+++.| .+.++ +.+++||||||||||++||+++|++ ++|+++
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 9865 4544 38999999999999999432 22222 2347999999999999999999995 999999
Q ss_pred CCceecccCCCccccC
Q 025329 239 DGALEAAPAVRITHLL 254 (254)
Q Consensus 239 ~GSvElAP~lGlADaI 254 (254)
+||||+||.+|+||+|
T Consensus 143 ~GsvE~aP~~GlAD~I 158 (215)
T PRK01686 143 YGSVELAPLVGLADAI 158 (215)
T ss_pred cCceeeccccCCccEE
Confidence 9999999999999987
No 4
>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=4.8e-52 Score=360.71 Aligned_cols=152 Identities=34% Similarity=0.623 Sum_probs=139.6
Q ss_pred eEEEecCCCCChHHHHHHHHhCCCccCCCCCCceEeecCCCCCeEEEeecCcchhhhhhcCceeeeeeccceeecccCCC
Q 025329 84 IRLGLPSKGRMAADTLDLLKDCQLSVKQVNPRQYVAQIPQLSNLEVWFQRPKDIVRKLLSGDLDLGIVGLDTVSEFGQGN 163 (254)
Q Consensus 84 LrIALPsKGRL~e~tl~LL~~aGi~v~~~~~R~L~~~~~~~p~iev~~vRp~DIp~yV~~G~aDlGIvG~DvL~E~~~d~ 163 (254)
|||||| ||||++++++||++|||.+...++|+|++.+.+ ++++++++||+|||+||++|.+|+||||+|||.|++.+
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 999999999999999999988656999999876 67999999999999999999999999999999999866
Q ss_pred cceeeecCCCCcccEEEEEEEeCCCccccccchHHhhcCCcccCCCCcEEEcCCCccHHHHHHHcCCceEEEEEcCCcee
Q 025329 164 EDLIIVHDALDYGDCRLSLAIPKYGIFENINSLRELAQMPQWTAEKPLRVATGFTYLGPKFMKDNGLKHVVFSTADGALE 243 (254)
Q Consensus 164 ~~l~~~l~dLgfG~CRLvVAvP~~~~~~dv~sl~dL~~~~~~~~~r~lRVATkYPnLarkyf~~~Gi~~veIi~l~GSvE 243 (254)
+++++ |||||+|||++|+|++ | ++++++||+ ++||||||||+|++||+++|++ ++|++++||+|
T Consensus 78 --v~~~~-dL~fg~crl~vA~p~~--~-~~~~~~~l~---------~~rIATkyp~i~~~~f~~~Gi~-v~ii~l~GsvE 141 (182)
T TIGR00070 78 --VYELL-DLGFGKCRLVLAVPQE--S-DISSVEDLK---------GKRIATKYPNLARRYFEKKGID-VEIIKLNGSVE 141 (182)
T ss_pred --EEEEe-ecCcCceEEEEEEECC--C-CCCChHHhC---------CCEEEECCHHHHHHHHHHcCCe-EEEEECcceee
Confidence 55443 8999999999999999 4 577888875 5899999999999999999995 99999999999
Q ss_pred cccCCCccccC
Q 025329 244 AAPAVRITHLL 254 (254)
Q Consensus 244 lAP~lGlADaI 254 (254)
+||.+|+||+|
T Consensus 142 ~aP~~GlaD~I 152 (182)
T TIGR00070 142 LAPLLGLADAI 152 (182)
T ss_pred cccCCCceeEE
Confidence 99999999987
No 5
>COG0040 HisG ATP phosphoribosyltransferase [Amino acid transport and metabolism]
Probab=100.00 E-value=3e-50 Score=370.06 Aligned_cols=159 Identities=30% Similarity=0.547 Sum_probs=142.0
Q ss_pred CceEEEecCCCCChHHHHHHHHhCCCccCCCCCCceEeecCCCCCeEEEeecCcchhhhhhcCceeeeeeccceeecccC
Q 025329 82 DEIRLGLPSKGRMAADTLDLLKDCQLSVKQVNPRQYVAQIPQLSNLEVWFQRPKDIVRKLLSGDLDLGIVGLDTVSEFGQ 161 (254)
Q Consensus 82 ~~LrIALPsKGRL~e~tl~LL~~aGi~v~~~~~R~L~~~~~~~p~iev~~vRp~DIp~yV~~G~aDlGIvG~DvL~E~~~ 161 (254)
+||||||||||||.+++++||++|||++....+|+|++...+ ++++++|+||+|||+||++|.+|+||||+|+|.|++.
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 489999999999999999999999999986557999999877 5599999999999999999999999999999999986
Q ss_pred CCcceeeecCCCCcccEEEEEEEeCCCccccccchHHhhcCCcccCCCCcEEEcCCCccHHHHHHHcCCceEEEEEcCCc
Q 025329 162 GNEDLIIVHDALDYGDCRLSLAIPKYGIFENINSLRELAQMPQWTAEKPLRVATGFTYLGPKFMKDNGLKHVVFSTADGA 241 (254)
Q Consensus 162 d~~~l~~~l~dLgfG~CRLvVAvP~~~~~~dv~sl~dL~~~~~~~~~r~lRVATkYPnLarkyf~~~Gi~~veIi~l~GS 241 (254)
+..+++ .+.||+||+|||+||+|+++. +++.+||. ++ +||||||||+|++||+++|++ ++|++++||
T Consensus 80 ~~~~v~-~l~dL~fG~crl~vAvp~~~~---~~~~~~l~-------~~-~rIATkYp~l~~~yf~~~g~~-~~Ii~l~Gs 146 (290)
T COG0040 80 DDASVE-ELLDLGFGGCRLVVAVPEESD---YTSPEDLK-------GR-LRIATKYPNLARKYFAEKGID-VEIIKLSGS 146 (290)
T ss_pred CccCce-ehccCCCCcEEEEEEecCCcC---ccChhHhc-------CC-ceEEEccHHHHHHHHHHcCce-EEEEEccCc
Confidence 533444 445899999999999999944 45566653 24 799999999999999999995 999999999
Q ss_pred eecccCCCccccC
Q 025329 242 LEAAPAVRITHLL 254 (254)
Q Consensus 242 vElAP~lGlADaI 254 (254)
||+||.+|+||+|
T Consensus 147 vE~aP~~GlADaI 159 (290)
T COG0040 147 VELAPALGLADAI 159 (290)
T ss_pred EeeccccCccceE
Confidence 9999999999997
No 6
>PRK13584 hisG ATP phosphoribosyltransferase catalytic subunit; Provisional
Probab=100.00 E-value=4.5e-50 Score=353.67 Aligned_cols=144 Identities=21% Similarity=0.365 Sum_probs=128.6
Q ss_pred ceEEEecCCCCChHHHHHHHHhCCCccCCC----CCCceEeecCCCCCeEEEeecCcchhhhhhcCceeeeeeccceeec
Q 025329 83 EIRLGLPSKGRMAADTLDLLKDCQLSVKQV----NPRQYVAQIPQLSNLEVWFQRPKDIVRKLLSGDLDLGIVGLDTVSE 158 (254)
Q Consensus 83 ~LrIALPsKGRL~e~tl~LL~~aGi~v~~~----~~R~L~~~~~~~p~iev~~vRp~DIp~yV~~G~aDlGIvG~DvL~E 158 (254)
||||||| ||||++++++||++|||.+... .+|+|++.. ++++++|+||+|||+||++|.+|+||||+|||+|
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 9999999999999999976332 359999873 4699999999999999999999999999999999
Q ss_pred ccCCCcceeeecCCCCcccEEEEEEEeCCCccccccchHHhhcCCcccCCCCcEEEcCCCccHHHHHHHcCCceEEEEEc
Q 025329 159 FGQGNEDLIIVHDALDYGDCRLSLAIPKYGIFENINSLRELAQMPQWTAEKPLRVATGFTYLGPKFMKDNGLKHVVFSTA 238 (254)
Q Consensus 159 ~~~d~~~l~~~l~dLgfG~CRLvVAvP~~~~~~dv~sl~dL~~~~~~~~~r~lRVATkYPnLarkyf~~~Gi~~veIi~l 238 (254)
++.+ +++++ |||||+|||+||+|++ +. +.+||||||||||++||+++|++ ++|+++
T Consensus 77 ~~~~---v~el~-dLgfG~crl~vA~p~~--~~-----------------~~~rVATkyp~it~~yf~~~Gi~-~~ii~l 132 (204)
T PRK13584 77 RQYN---VNNLL-NMPFGACHFAVAAKPE--TT-----------------NYRKIATSYVHTAETYFKSKGID-VELIKL 132 (204)
T ss_pred cCCC---eEEEe-cCCCCcEEEEEEEEcC--CC-----------------CceEEEeCcHHHHHHHHHHcCCe-EEEEEC
Confidence 9866 44443 8999999999999876 11 14899999999999999999995 999999
Q ss_pred CCceecccCCCccccC
Q 025329 239 DGALEAAPAVRITHLL 254 (254)
Q Consensus 239 ~GSvElAP~lGlADaI 254 (254)
+||+|+||.+|+||+|
T Consensus 133 ~GsvElaP~~GlAD~I 148 (204)
T PRK13584 133 NGSVELACVVDMVDGI 148 (204)
T ss_pred CCceeeccccCCccEE
Confidence 9999999999999987
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=4e-39 Score=275.60 Aligned_cols=110 Identities=32% Similarity=0.568 Sum_probs=92.1
Q ss_pred ecCcchhhhhhcCceeeeeeccceeecccCCCcceeeecCCCCcccEEEEEEEeCCCccccccchHHhhcCCcccCCCCc
Q 025329 132 QRPKDIVRKLLSGDLDLGIVGLDTVSEFGQGNEDLIIVHDALDYGDCRLSLAIPKYGIFENINSLRELAQMPQWTAEKPL 211 (254)
Q Consensus 132 vRp~DIp~yV~~G~aDlGIvG~DvL~E~~~d~~~l~~~l~dLgfG~CRLvVAvP~~~~~~dv~sl~dL~~~~~~~~~r~l 211 (254)
+||+|||+||++|.+|+||||+|||.|++.+..++++ +.|||||+|||++|+|++ |. +++++||.. ++
T Consensus 1 vR~~DIp~yV~~G~~DlGI~G~D~l~E~~~~~~~v~~-~~dL~fg~crl~vAvp~~--~~-~~~~~~l~~--------~~ 68 (163)
T PF01634_consen 1 VRPQDIPTYVEDGIADLGITGKDVLLESGLGRADVEE-LLDLGFGKCRLVVAVPED--WP-YKSVEDLKA--------GL 68 (163)
T ss_dssp E-GGHHHHHHHTTSSSEEEEEHHHHHHHTHH-SSEEE-EEEESCSEEEEEEEEETT--SC-GCCGGGGSS--------TE
T ss_pred CChHHHHHHHHCCCCcEEEeehheeccCCCCccceEE-EeecccccEEEEEEEECC--cC-CCCHHHhcc--------CC
Confidence 6999999999999999999999999999842233554 448999999999999999 33 677777742 69
Q ss_pred EEEcCCCccHHHHHHHcCCceEEEEEcCCceecccCCCccccC
Q 025329 212 RVATGFTYLGPKFMKDNGLKHVVFSTADGALEAAPAVRITHLL 254 (254)
Q Consensus 212 RVATkYPnLarkyf~~~Gi~~veIi~l~GSvElAP~lGlADaI 254 (254)
||||||||+|++||+++|++ ++|++++||+|+||.+|+||+|
T Consensus 69 rIATkyp~l~~~yf~~~g~~-~~ii~l~GsvE~ap~~glAD~I 110 (163)
T PF01634_consen 69 RIATKYPNLTRRYFAEKGIN-VEIIKLSGSVELAPPLGLADAI 110 (163)
T ss_dssp EEEES-HHHHHHHHHHCT-E-EEEEE-SS-TTHHHHTTSSSEE
T ss_pred EEEECCHHHHHHHHHHcCCc-EEEEEccCCccccCCCCCCCEE
Confidence 99999999999999999995 9999999999999999999997
No 8
>KOG2831 consensus ATP phosphoribosyltransferase [Amino acid transport and metabolism]
Probab=100.00 E-value=6.1e-37 Score=275.31 Aligned_cols=173 Identities=51% Similarity=0.858 Sum_probs=160.6
Q ss_pred CCCCceEEEecCCCCChHHHHHHHHhCCCccCCCCCCceEeecCCCCCeEEEeecCcchhhhhhcCceeeeeeccceeec
Q 025329 79 SERDEIRLGLPSKGRMAADTLDLLKDCQLSVKQVNPRQYVAQIPQLSNLEVWFQRPKDIVRKLLSGDLDLGIVGLDTVSE 158 (254)
Q Consensus 79 ~~~~~LrIALPsKGRL~e~tl~LL~~aGi~v~~~~~R~L~~~~~~~p~iev~~vRp~DIp~yV~~G~aDlGIvG~DvL~E 158 (254)
..+++|++|+||||||++++.++|+.|.|.+++ ++|.+++.++++|+..+||. |.|||++|..|.+|+||||.|.+.|
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 456889999999999999999999999999998 89999999999998777766 9999999999999999999999999
Q ss_pred ccCCCcceeeecCCCCcccEEEEEEEeCCCccccccchHHhhcCCcccCCCCcEEEcCCCccHHHHHHHcCCceEEEEEc
Q 025329 159 FGQGNEDLIIVHDALDYGDCRLSLAIPKYGIFENINSLRELAQMPQWTAEKPLRVATGFTYLGPKFMKDNGLKHVVFSTA 238 (254)
Q Consensus 159 ~~~d~~~l~~~l~dLgfG~CRLvVAvP~~~~~~dv~sl~dL~~~~~~~~~r~lRVATkYPnLarkyf~~~Gi~~veIi~l 238 (254)
.+.+++++++++.||.||.|+|.|++|+++.|.+++++.+++.+.+|.+.++++.||-|...-.++.++.|++ -+|...
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 9988878888999999999999999999999999988888887778888888899999999999999999997 588888
Q ss_pred CCceecccCCCccccC
Q 025329 239 DGALEAAPAVRITHLL 254 (254)
Q Consensus 239 ~GSvElAP~lGlADaI 254 (254)
+||+|++|++|+||+|
T Consensus 163 sGsvEAscAlGIaDAi 178 (308)
T KOG2831|consen 163 SGSVEASCALGIADAI 178 (308)
T ss_pred ccceecchhcchHHHH
Confidence 9999999999999987
No 9
>PRK00489 hisG ATP phosphoribosyltransferase; Reviewed
Probab=99.97 E-value=8.3e-32 Score=244.91 Aligned_cols=155 Identities=30% Similarity=0.562 Sum_probs=140.5
Q ss_pred CCceEEEecCCCCChHHHHHHHHhCCCccCCCCCCceEeecCCCCCeEEEeecCcchhhhhhcCceeeeeeccceeeccc
Q 025329 81 RDEIRLGLPSKGRMAADTLDLLKDCQLSVKQVNPRQYVAQIPQLSNLEVWFQRPKDIVRKLLSGDLDLGIVGLDTVSEFG 160 (254)
Q Consensus 81 ~~~LrIALPsKGRL~e~tl~LL~~aGi~v~~~~~R~L~~~~~~~p~iev~~vRp~DIp~yV~~G~aDlGIvG~DvL~E~~ 160 (254)
++||||||||||||+|++++||++|||++.. ++|+|....++. ++++.+++++||+.+|..|.+|+||+|.|++.|.+
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-DSRSLIATDEDN-PIEVLFLRPDDIPGYVADGVVDLGITGEDLLEESG 79 (287)
T ss_pred CccEEEEECCCCccHHHHHHHHHHcCCCCCC-CCcceEeecCCC-CEEEEEECcHHHHHHHHcCCCCEEEcchHHHHHCC
Confidence 5789999999999999999999999999988 679999998874 69999999999999999999999999999999986
Q ss_pred CCCcceeeecCCCCcccEEEEEEEeCCCccccccchHHhhcCCcccCCCCcEEEcCCCccHHHHHHHcCCceEEEEEcCC
Q 025329 161 QGNEDLIIVHDALDYGDCRLSLAIPKYGIFENINSLRELAQMPQWTAEKPLRVATGFTYLGPKFMKDNGLKHVVFSTADG 240 (254)
Q Consensus 161 ~d~~~l~~~l~dLgfG~CRLvVAvP~~~~~~dv~sl~dL~~~~~~~~~r~lRVATkYPnLarkyf~~~Gi~~veIi~l~G 240 (254)
.+. ..+..++|++|++++++|++. ++++++||+ ++||||+|++++++||+++|++ ++++..+|
T Consensus 80 ~~v----~~~~~l~~~~~~lvvvvp~~~---~i~sl~DL~---------Gk~ia~~~~~~~~~~l~~~gi~-~~iv~~~g 142 (287)
T PRK00489 80 ADV----EELLDLGFGKCRLVLAVPEDS---DWQGVEDLA---------GKRIATSYPNLTRRYLAEKGID-AEVVELSG 142 (287)
T ss_pred CCc----eEeeeccCCceEEEEEEECCC---CCCChHHhC---------CCEEEEcCcHHHHHHHHHcCCc-eEEEECCC
Confidence 543 233479999999999999994 577889986 4699999999999999999995 99999999
Q ss_pred ceecccCCCccccC
Q 025329 241 ALEAAPAVRITHLL 254 (254)
Q Consensus 241 SvElAP~lGlADaI 254 (254)
++|++|..|.+|+|
T Consensus 143 s~eaa~~~G~aDai 156 (287)
T PRK00489 143 AVEVAPRLGLADAI 156 (287)
T ss_pred chhhhhcCCcccEE
Confidence 99999999999986
No 10
>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=95.93 E-value=0.0087 Score=51.98 Aligned_cols=105 Identities=20% Similarity=0.210 Sum_probs=61.3
Q ss_pred CcchhhhhhcCceeeeeeccceee-cccCCCcceeeecCCCCcccEEEEEEEeCCCccccccchHHhhcCCcccCCCCcE
Q 025329 134 PKDIVRKLLSGDLDLGIVGLDTVS-EFGQGNEDLIIVHDALDYGDCRLSLAIPKYGIFENINSLRELAQMPQWTAEKPLR 212 (254)
Q Consensus 134 p~DIp~yV~~G~aDlGIvG~DvL~-E~~~d~~~l~~~l~dLgfG~CRLvVAvP~~~~~~dv~sl~dL~~~~~~~~~r~lR 212 (254)
..++...|..|.+|+|++|..... ..... .++..+. -... .....++++.+ .++++++||+ ++|
T Consensus 39 ~~~~~~~l~~G~~D~~~~~~~~~~~~~~~g-~~~~~i~-~~~~-~~~~~~v~~~~---~~i~s~~dL~---------Gk~ 103 (288)
T TIGR01728 39 GPPALEALGAGSLDFGYIGPGPALFAYAAG-ADIKAVG-LVSD-NKATAIVVIKG---SPIRTVADLK---------GKR 103 (288)
T ss_pred CcHHHHHHhcCCccccccCCcHHHHHHhcC-CCEEEEE-EecC-CCceEEEECCC---CCCCCHHHcC---------CCE
Confidence 367889999999999999886322 21111 1222111 1121 13456666666 4678899986 356
Q ss_pred EEc----CCCccHHHHHHHcCCc--eEEEEEcC-CceecccCCCcccc
Q 025329 213 VAT----GFTYLGPKFMKDNGLK--HVVFSTAD-GALEAAPAVRITHL 253 (254)
Q Consensus 213 VAT----kYPnLarkyf~~~Gi~--~veIi~l~-GSvElAP~lGlADa 253 (254)
|++ ....+..++|++.|++ .++++.+. +....+-.-|-+|+
T Consensus 104 i~~~~~~~~~~~~~~~l~~~G~~~~~v~~~~~~~~~~~~al~~g~vda 151 (288)
T TIGR01728 104 IAVPKGGSGHDLLLRALLKAGLSGDDVTILYLGPSDARAAFAAGQVDA 151 (288)
T ss_pred EEecCCccHHHHHHHHHHHcCCCccceeEEecCcHHHHHHHHCCCCCE
Confidence 774 3445777899999984 24444332 33334444555553
No 11
>PRK11063 metQ DL-methionine transporter substrate-binding subunit; Provisional
Probab=95.89 E-value=0.027 Score=51.75 Aligned_cols=102 Identities=16% Similarity=0.159 Sum_probs=70.4
Q ss_pred ceEEEecCCCCChHHHHHHHHhCCCccCCCCC--CceEeecC-CCCCeEEEeecCcchhhhhhcCceeeeeeccceeecc
Q 025329 83 EIRLGLPSKGRMAADTLDLLKDCQLSVKQVNP--RQYVAQIP-QLSNLEVWFQRPKDIVRKLLSGDLDLGIVGLDTVSEF 159 (254)
Q Consensus 83 ~LrIALPsKGRL~e~tl~LL~~aGi~v~~~~~--R~L~~~~~-~~p~iev~~vRp~DIp~yV~~G~aDlGIvG~DvL~E~ 159 (254)
-=+||+|++..-....+.+|+++|+.--+... +.-...+. +-.+++|.-+.+.++|+-+.+|.+|.+++..+|..+.
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 36899998899999999999999993333211 11111111 2236999999999999999999999999999999987
Q ss_pred cCCC-cc-eeeecCCCCcccEEEEEEEeCC
Q 025329 160 GQGN-ED-LIIVHDALDYGDCRLSLAIPKY 187 (254)
Q Consensus 160 ~~d~-~~-l~~~l~dLgfG~CRLvVAvP~~ 187 (254)
+.+. .+ ++ .++...-.|. ++++.++
T Consensus 210 ~~~~~~~~l~--~e~~~~~~~~-~~~v~~~ 236 (271)
T PRK11063 210 GLTPAKDGIF--VEDKDSPYVN-LIVARED 236 (271)
T ss_pred CCCCCCCeeE--ECCCCCCeEE-EEEECCc
Confidence 7553 22 33 2344444554 4444444
No 12
>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=95.45 E-value=0.015 Score=49.22 Aligned_cols=100 Identities=23% Similarity=0.298 Sum_probs=62.7
Q ss_pred eEEEeecC-cchhhhhhcCceeeeeeccceeecccCCCcceeeecCCCCcccEEEEEEEeCCCccccccchHHhhcCCcc
Q 025329 127 LEVWFQRP-KDIVRKLLSGDLDLGIVGLDTVSEFGQGNEDLIIVHDALDYGDCRLSLAIPKYGIFENINSLRELAQMPQW 205 (254)
Q Consensus 127 iev~~vRp-~DIp~yV~~G~aDlGIvG~DvL~E~~~d~~~l~~~l~dLgfG~CRLvVAvP~~~~~~dv~sl~dL~~~~~~ 205 (254)
+++....+ .+....+..|.+|+|+++.+.+.-......++..+. .+-- ..-..+.++++ .++++++||+
T Consensus 23 ve~~~~~~~~~~~~~l~~G~~D~~~~~~~~~~~~~~~g~~~~~i~-~~~~-~~~~~l~~~~~---s~i~~~~DLk----- 92 (216)
T PF09084_consen 23 VEIVFFGGGGDVLEALASGKADIAVAGPDAVLFARAKGADIKIIA-ASYQ-SSPNALVVRKD---SGIKSPADLK----- 92 (216)
T ss_dssp EEEEEESSHHHHHHHHHTTSHSEEEEECHHHHHHHHTTSTEEEEE-EEEE-ECCEEEEEETT---TS-SSGGGGT-----
T ss_pred EEEEEecChhHHHHHHhcCCceEEeccchHHHHHHhcCCeeEEEE-EecC-CCceEEEEecc---CCCCCHHHhC-----
Confidence 34444433 789999999999999999997774322222333221 1111 22245566666 4588999986
Q ss_pred cCCCCcEEEcCCC----ccHHHHHHHcCC--ceEEEEEcCC
Q 025329 206 TAEKPLRVATGFT----YLGPKFMKDNGL--KHVVFSTADG 240 (254)
Q Consensus 206 ~~~r~lRVATkYP----nLarkyf~~~Gi--~~veIi~l~G 240 (254)
++||+..-- .+.++++++.|+ ++++++.+.+
T Consensus 93 ----GK~i~v~~~s~~~~~~~~~l~~~g~~~~~v~~v~~~~ 129 (216)
T PF09084_consen 93 ----GKKIGVSRGSSSEYFLRALLKKNGIDPDDVKIVNLGP 129 (216)
T ss_dssp ----TSEEEESTTSHHHHHHHHHHHHTTT-GGGSEEEES-H
T ss_pred ----CCEEEEecCcchhHHHHHHHHHhccccccceeeeeeh
Confidence 478886651 266778889998 5688887754
No 13
>smart00062 PBPb Bacterial periplasmic substrate-binding proteins. bacterial proteins, eukaryotic ones are in PBPe
Probab=95.31 E-value=0.059 Score=42.70 Aligned_cols=97 Identities=20% Similarity=0.155 Sum_probs=65.2
Q ss_pred EEEeecCcchhhhhhcCceeeeeeccceeecccCCCcceeeecCCCCcccEEEEEEEeCCCccccccchHHhhcCCcccC
Q 025329 128 EVWFQRPKDIVRKLLSGDLDLGIVGLDTVSEFGQGNEDLIIVHDALDYGDCRLSLAIPKYGIFENINSLRELAQMPQWTA 207 (254)
Q Consensus 128 ev~~vRp~DIp~yV~~G~aDlGIvG~DvL~E~~~d~~~l~~~l~dLgfG~CRLvVAvP~~~~~~dv~sl~dL~~~~~~~~ 207 (254)
++......++...+..|.+|+++.+..+..|.... +. .-..+...++++.++.+. ++++++||+
T Consensus 42 ~~~~~~~~~~~~~l~~g~~D~~~~~~~~~~~~~~~---~~---~~~~~~~~~~~~~~~~~~---~~~~~~dL~------- 105 (219)
T smart00062 42 EFVEVSFDNLLTALKSGKIDVVAAGMTITPERAKQ---VD---FSDPYYKSGQVILVRKDS---PIKSLEDLK------- 105 (219)
T ss_pred EEEeccHHHHHHHHHCCcccEEeccccCCHHHHhh---ee---eccceeeceeEEEEecCC---CCCChHHhC-------
Confidence 34444557889999999999999987764444221 11 123566667888888884 478889985
Q ss_pred CCCcEEEcCCCccHHHHHHHcCCceEEEEEcCCcee
Q 025329 208 EKPLRVATGFTYLGPKFMKDNGLKHVVFSTADGALE 243 (254)
Q Consensus 208 ~r~lRVATkYPnLarkyf~~~Gi~~veIi~l~GSvE 243 (254)
+++|++-.-.....++.+.+. ..+++......+
T Consensus 106 --g~~i~~~~g~~~~~~~~~~~~-~~~~~~~~~~~~ 138 (219)
T smart00062 106 --GKKVAVVAGTTGEELLKKLYP-EAKIVSYDSQAE 138 (219)
T ss_pred --CCEEEEecCccHHHHHHHhCC-CceEEEcCCHHH
Confidence 367888777777888877643 256665554444
No 14
>PRK11553 alkanesulfonate transporter substrate-binding subunit; Provisional
Probab=94.39 E-value=0.11 Score=46.99 Aligned_cols=91 Identities=20% Similarity=0.211 Sum_probs=55.2
Q ss_pred CcchhhhhhcCceeeeeeccce-eecccCCCcceeeecCCCCcccEEEEEEEeCCCccccccchHHhhcCCcccCCCCcE
Q 025329 134 PKDIVRKLLSGDLDLGIVGLDT-VSEFGQGNEDLIIVHDALDYGDCRLSLAIPKYGIFENINSLRELAQMPQWTAEKPLR 212 (254)
Q Consensus 134 p~DIp~yV~~G~aDlGIvG~Dv-L~E~~~d~~~l~~~l~dLgfG~CRLvVAvP~~~~~~dv~sl~dL~~~~~~~~~r~lR 212 (254)
..++...+..|.+|+|++|... +.....+ .++..+. ...+..-.+++.++.+ .++++++||++ ++
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 1222111 1223334467777877 35778999863 45
Q ss_pred EEcC----CCccHHHHHHHcCCc--eEEEEEc
Q 025329 213 VATG----FTYLGPKFMKDNGLK--HVVFSTA 238 (254)
Q Consensus 213 VATk----YPnLarkyf~~~Gi~--~veIi~l 238 (254)
|++. ...+..++|++.|++ +++++.+
T Consensus 132 I~~~~gs~~~~~l~~~l~~~g~~~~dv~~v~~ 163 (314)
T PRK11553 132 VAFQKGSSSHNLLLRALRKAGLKFTDIQPTYL 163 (314)
T ss_pred EeecCCCcHHHHHHHHHHHcCCCHHHeEEEec
Confidence 6653 335566778888873 4666654
No 15
>PRK11480 tauA taurine transporter substrate binding subunit; Provisional
Probab=93.82 E-value=0.13 Score=47.35 Aligned_cols=95 Identities=22% Similarity=0.279 Sum_probs=57.5
Q ss_pred eEEEee-cCcchhhhhhcCceeeeeeccceeec---ccCCCcceeeecCCCCcccEEEEEEEeCCCccccccchHHhhcC
Q 025329 127 LEVWFQ-RPKDIVRKLLSGDLDLGIVGLDTVSE---FGQGNEDLIIVHDALDYGDCRLSLAIPKYGIFENINSLRELAQM 202 (254)
Q Consensus 127 iev~~v-Rp~DIp~yV~~G~aDlGIvG~DvL~E---~~~d~~~l~~~l~dLgfG~CRLvVAvP~~~~~~dv~sl~dL~~~ 202 (254)
+++... -..++...+..|.+|+|++|.+.+.- .+.+. .++-.....+ ....+.+++ +|++++||+
T Consensus 53 Ve~~~~~~~~~~~~al~~G~~D~a~~~~~~~~~a~~~g~~~-~~v~~~~~~~---~~~~lv~~~-----~I~s~~DLk-- 121 (320)
T PRK11480 53 VDWRKFDSGASIVRALASGDVQIGNLGSSPLAVAASQQVPI-EVFLLASKLG---NSEALVVKK-----TISKPEDLI-- 121 (320)
T ss_pred eEEEEeCCHHHHHHHHHCCCCCEECcCchHHHHHHHCCCCe-EEEEeeccCC---cceEEEecC-----CCCChHHcC--
Confidence 444433 34688899999999999999875432 33321 1111111112 222333443 378999986
Q ss_pred CcccCCCCcEEEcCCC----ccHHHHHHHcCC--ceEEEEEcC
Q 025329 203 PQWTAEKPLRVATGFT----YLGPKFMKDNGL--KHVVFSTAD 239 (254)
Q Consensus 203 ~~~~~~r~lRVATkYP----nLarkyf~~~Gi--~~veIi~l~ 239 (254)
++|||+-.. .+..+++++.|+ ++++++.+.
T Consensus 122 -------GK~Iav~~~s~~~~~l~~~L~~~Gl~~~dv~~v~~~ 157 (320)
T PRK11480 122 -------GKRIAVPFISTTHYSLLAALKHWGIKPGQVEIVNLQ 157 (320)
T ss_pred -------CCEEecCCCCchHHHHHHHHHHcCCCHhheEEEECC
Confidence 478886432 356678999998 357777655
No 16
>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=93.23 E-value=0.35 Score=44.28 Aligned_cols=78 Identities=17% Similarity=0.225 Sum_probs=59.5
Q ss_pred ceEEEecCCCCChHHHHHHHHhCCCc-cCCCCCCceEe---ecC-CCCCeEEEeecCcchhhhhhcCceeeeeeccceee
Q 025329 83 EIRLGLPSKGRMAADTLDLLKDCQLS-VKQVNPRQYVA---QIP-QLSNLEVWFQRPKDIVRKLLSGDLDLGIVGLDTVS 157 (254)
Q Consensus 83 ~LrIALPsKGRL~e~tl~LL~~aGi~-v~~~~~R~L~~---~~~-~~p~iev~~vRp~DIp~yV~~G~aDlGIvG~DvL~ 157 (254)
--|||+|+..--....+.+|+++|+. ++.. ..+.. ++. +..++++.-+.+.++|.-+.+|.+|++++...++.
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 GAKVAVPNDPTNLGRALLLLQKQGLIKLKDG--NGLLPTVLDIVENPKKLNITELETSQLPRALDDPKVDLAVINTTYAG 194 (258)
T ss_pred CCEEEEeCCcchHHHHHHHHHHcCCceecCC--CCCcCChhhhhcCCCCCEEEEcCHHHHHHHhhcccccEEEEChHHHH
Confidence 36899996666778888999999995 3321 11211 111 22469999999999999999999999999999999
Q ss_pred cccCC
Q 025329 158 EFGQG 162 (254)
Q Consensus 158 E~~~d 162 (254)
..+.+
T Consensus 195 ~agl~ 199 (258)
T TIGR00363 195 QVGLN 199 (258)
T ss_pred HcCCC
Confidence 88765
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=92.38 E-value=0.31 Score=43.88 Aligned_cols=96 Identities=21% Similarity=0.243 Sum_probs=57.7
Q ss_pred eEEEeec-CcchhhhhhcCceeeeeeccceeec---ccCCCcceeeecCCCCcccEEEEEEEeCCCccccccchHHhhcC
Q 025329 127 LEVWFQR-PKDIVRKLLSGDLDLGIVGLDTVSE---FGQGNEDLIIVHDALDYGDCRLSLAIPKYGIFENINSLRELAQM 202 (254)
Q Consensus 127 iev~~vR-p~DIp~yV~~G~aDlGIvG~DvL~E---~~~d~~~l~~~l~dLgfG~CRLvVAvP~~~~~~dv~sl~dL~~~ 202 (254)
+++.... ..++...+..|.+|+|++|...+.- .+.+. .++-... .++.+ ..+.++++ .++++++||+
T Consensus 29 Ve~~~~~~~~~~~~al~~G~iD~~~~~~~~~~~a~~~g~~~-~~v~~~~--~~~~~-~~lv~~~~---s~I~s~~DLk-- 99 (300)
T TIGR01729 29 IDWRKFDSGADISTALASGNVPIGVIGSSPLAAAASRGVPI-ELFWILD--NIGKS-EALVAREG---SGIEKPEDLK-- 99 (300)
T ss_pred eEEEecCcHHHHHHHHHcCCCCEeccCCCHHHHHHHCCCCe-EEEEEec--cCCcc-ceEEecCC---CCCCChhHcC--
Confidence 4444443 3588999999999999998765532 23221 1111111 22333 24555555 4688999986
Q ss_pred CcccCCCCcEEEcCCC----ccHHHHHHHcCCc--eEEEEEc
Q 025329 203 PQWTAEKPLRVATGFT----YLGPKFMKDNGLK--HVVFSTA 238 (254)
Q Consensus 203 ~~~~~~r~lRVATkYP----nLarkyf~~~Gi~--~veIi~l 238 (254)
++|||.... .+..++|++.|++ +++++.+
T Consensus 100 -------GK~Igv~~~s~~~~~l~~~L~~~Gl~~~dv~~v~~ 134 (300)
T TIGR01729 100 -------GKNVAVPFVSTTHYSLLAALKHWKTDPREVNILNL 134 (300)
T ss_pred -------CCEEEeCCCCcHHHHHHHHHHHcCCChhheEEEec
Confidence 468886443 3445688888873 4666654
No 18
>PRK09861 cytoplasmic membrane lipoprotein-28; Provisional
Probab=91.16 E-value=0.96 Score=41.72 Aligned_cols=79 Identities=16% Similarity=0.250 Sum_probs=60.3
Q ss_pred ceEEEecCCCCChHHHHHHHHhCCC-ccCCCCCCceEe---ecC-CCCCeEEEeecCcchhhhhhcCceeeeeeccceee
Q 025329 83 EIRLGLPSKGRMAADTLDLLKDCQL-SVKQVNPRQYVA---QIP-QLSNLEVWFQRPKDIVRKLLSGDLDLGIVGLDTVS 157 (254)
Q Consensus 83 ~LrIALPsKGRL~e~tl~LL~~aGi-~v~~~~~R~L~~---~~~-~~p~iev~~vRp~DIp~yV~~G~aDlGIvG~DvL~ 157 (254)
-=+||+|++-.=....+.||+++|+ +++.. -.+.. ++. |-.+++|..+-+.++|+-+.+|.+|+.++..+...
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 GATVAIPNDPTNLGRALLLLQKEKLITLKEG--KGLLPTALDITDNPRHLQIMELEGAQLPRVLDDPKVDVAIISTTYIQ 208 (272)
T ss_pred CCEEEEeCCCccHHHHHHHHHHCCCEEEcCC--CCCCCCHhHHhcCCCCCEEEEcCHHHhHhhccCcccCEEEEchhHHH
Confidence 4689999766777889999999995 33321 11211 111 22369999999999999999999999999999999
Q ss_pred cccCCC
Q 025329 158 EFGQGN 163 (254)
Q Consensus 158 E~~~d~ 163 (254)
+.+.+.
T Consensus 209 ~ag~~~ 214 (272)
T PRK09861 209 QTGLSP 214 (272)
T ss_pred HcCCCc
Confidence 988763
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=90.81 E-value=0.86 Score=36.43 Aligned_cols=102 Identities=18% Similarity=0.252 Sum_probs=62.1
Q ss_pred CCeEE--EeecCcchhhhhhcCceeeeeeccceeecccCCCcceeeecCCCCcccEEEEEEEeCCCcccc--ccchHHhh
Q 025329 125 SNLEV--WFQRPKDIVRKLLSGDLDLGIVGLDTVSEFGQGNEDLIIVHDALDYGDCRLSLAIPKYGIFEN--INSLRELA 200 (254)
Q Consensus 125 p~iev--~~vRp~DIp~yV~~G~aDlGIvG~DvL~E~~~d~~~l~~~l~dLgfG~CRLvVAvP~~~~~~d--v~sl~dL~ 200 (254)
|++++ ......++...+.+|.+|+||+.... .. .++. -..++..+++++++.+.++.. --+++||.
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 44444 44455699999999999999998766 11 2222 235678999999998843222 22567775
Q ss_pred cCCcccCCCCcEEE--cCCCccHHHHHHHcCCceEEEEEcCCcee
Q 025329 201 QMPQWTAEKPLRVA--TGFTYLGPKFMKDNGLKHVVFSTADGALE 243 (254)
Q Consensus 201 ~~~~~~~~r~lRVA--TkYPnLarkyf~~~Gi~~veIi~l~GSvE 243 (254)
..+- +... +.+-....++|++.|+. ..++--..+.+
T Consensus 103 ~~~~------i~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~ 140 (209)
T PF03466_consen 103 DYPL------ILLSPGSPYRDQLDRWLREHGFS-PNIVIEVDSFE 140 (209)
T ss_dssp TSEE------EEESTTTSHHHHHHHHHHHTTEE-EEEEEEESSHH
T ss_pred hccc------ccccccccccccccccccccccc-ccccccccchh
Confidence 3210 1111 23556677788888884 45543344443
No 20
>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=89.03 E-value=1.2 Score=34.81 Aligned_cols=89 Identities=16% Similarity=0.165 Sum_probs=51.0
Q ss_pred CCeEEEee--cCcchhhhhhcCceeeeeeccceeecccCCCcceeeecCCCCcccEEEEEEEeCCCccccccchHHhhcC
Q 025329 125 SNLEVWFQ--RPKDIVRKLLSGDLDLGIVGLDTVSEFGQGNEDLIIVHDALDYGDCRLSLAIPKYGIFENINSLRELAQM 202 (254)
Q Consensus 125 p~iev~~v--Rp~DIp~yV~~G~aDlGIvG~DvL~E~~~d~~~l~~~l~dLgfG~CRLvVAvP~~~~~~dv~sl~dL~~~ 202 (254)
|++++.+. ...++...+.+|.+|+||+....- . .++.. -..+.-+++++++++.+. ..+++||...
T Consensus 27 P~i~l~i~~~~~~~~~~~l~~g~~Dl~i~~~~~~---~---~~~~~----~~l~~~~~~~v~~~~~~~--~~~~~~l~~~ 94 (193)
T cd08442 27 PKVDLSLSTGTTGALIQAVLEGRLDGAFVAGPVE---H---PRLEQ----EPVFQEELVLVSPKGHPP--VSRAEDLAGS 94 (193)
T ss_pred CCceEEEEeCCcHHHHHHHHCCCccEEEEeCCCC---C---CCcEE----EEeecCcEEEEecCCCcc--cccHHHhCCC
Confidence 45544444 566899999999999999864321 1 11221 134456667777776332 3457777532
Q ss_pred CcccCCCCcEE--EcCCCccHHHHHHHcCCc
Q 025329 203 PQWTAEKPLRV--ATGFTYLGPKFMKDNGLK 231 (254)
Q Consensus 203 ~~~~~~r~lRV--ATkYPnLarkyf~~~Gi~ 231 (254)
+- +.. .+.+.+...+||++.|+.
T Consensus 95 ~~------i~~~~~~~~~~~~~~~~~~~~~~ 119 (193)
T cd08442 95 TL------LAFRAGCSYRRRLEDWLAEEGVS 119 (193)
T ss_pred ce------EEecCCCcHHHHHHHHHHHcCCC
Confidence 11 111 122345566788888874
No 21
>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=88.53 E-value=2.1 Score=34.43 Aligned_cols=109 Identities=9% Similarity=-0.016 Sum_probs=57.8
Q ss_pred CCeEEEee--cCcchhhhhhcCceeeeeeccceeecccCCCcceeeecCCCCcccEEEEEEEeCCCccccccchHHhhcC
Q 025329 125 SNLEVWFQ--RPKDIVRKLLSGDLDLGIVGLDTVSEFGQGNEDLIIVHDALDYGDCRLSLAIPKYGIFENINSLRELAQM 202 (254)
Q Consensus 125 p~iev~~v--Rp~DIp~yV~~G~aDlGIvG~DvL~E~~~d~~~l~~~l~dLgfG~CRLvVAvP~~~~~~dv~sl~dL~~~ 202 (254)
|++++.+. ...++...|.+|.+|+||+......-.. .++.. ...+.-+++++++++.+....-+++||...
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 44444444 5789999999999999998643210000 11221 123344556666665332223367787532
Q ss_pred CcccCCCCcEEEcCCCccHHHHHHHcCCceEEEEEcCCceecc
Q 025329 203 PQWTAEKPLRVATGFTYLGPKFMKDNGLKHVVFSTADGALEAA 245 (254)
Q Consensus 203 ~~~~~~r~lRVATkYPnLarkyf~~~Gi~~veIi~l~GSvElA 245 (254)
+... ..-...+.....+++++.|+. .++.--.+++|+.
T Consensus 100 ~~i~----~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~ 137 (202)
T cd08468 100 RHLV----VTPWNEDRGVVDQVLEKQGLE-REIALQLPNVLNA 137 (202)
T ss_pred CCeE----EecCCCCCchHHHHHHHcCCC-ceEEEEcChhHhH
Confidence 1100 001122345567788888874 4554445555544
No 22
>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=87.92 E-value=2.8 Score=33.70 Aligned_cols=91 Identities=15% Similarity=0.103 Sum_probs=53.0
Q ss_pred CCeEEEee--cCcchhhhhhcCceeeeeeccceeecccCCCcceeeecCCCCcccEEEEEEEeCCCcccc-ccchHHhhc
Q 025329 125 SNLEVWFQ--RPKDIVRKLLSGDLDLGIVGLDTVSEFGQGNEDLIIVHDALDYGDCRLSLAIPKYGIFEN-INSLRELAQ 201 (254)
Q Consensus 125 p~iev~~v--Rp~DIp~yV~~G~aDlGIvG~DvL~E~~~d~~~l~~~l~dLgfG~CRLvVAvP~~~~~~d-v~sl~dL~~ 201 (254)
|++++.+. ...++...|.+|.+|+||+-.... + .++. -..++..+++++++++.+... --+++||..
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 44555444 566899999999999999632211 1 1122 235667788888877632211 136778764
Q ss_pred CCcccCCCCcEE--EcCCCccHHHHHHHcCCc
Q 025329 202 MPQWTAEKPLRV--ATGFTYLGPKFMKDNGLK 231 (254)
Q Consensus 202 ~~~~~~~r~lRV--ATkYPnLarkyf~~~Gi~ 231 (254)
.+- ... .+.+.+...++|++.|++
T Consensus 97 ~~~------i~~~~~~~~~~~~~~~~~~~~~~ 122 (200)
T cd08467 97 LRH------VAIAPPGRLFGGIYKRLENLGLK 122 (200)
T ss_pred CCC------EEEcCCCCCCchHHHHHHhcCCc
Confidence 311 111 133445667788888874
No 23
>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=87.73 E-value=2.5 Score=33.53 Aligned_cols=102 Identities=12% Similarity=0.110 Sum_probs=56.4
Q ss_pred CCeEEEe--ecCcchhhhhhcCceeeeeeccceeecccCCCcceeeecCCCCcccEEEEEEEeCCCccc--cccchHHhh
Q 025329 125 SNLEVWF--QRPKDIVRKLLSGDLDLGIVGLDTVSEFGQGNEDLIIVHDALDYGDCRLSLAIPKYGIFE--NINSLRELA 200 (254)
Q Consensus 125 p~iev~~--vRp~DIp~yV~~G~aDlGIvG~DvL~E~~~d~~~l~~~l~dLgfG~CRLvVAvP~~~~~~--dv~sl~dL~ 200 (254)
|++++-+ ....++...+.+|.+|+||+......+. .++. ---++..+++++++.+.+.. ..-+++||.
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 4444444 3567899999999999999864211111 1122 12456788888888764322 123567776
Q ss_pred cCCcccCCCCcEEEcC----CCccHHHHHHHcCCceEEEEEcCCcee
Q 025329 201 QMPQWTAEKPLRVATG----FTYLGPKFMKDNGLKHVVFSTADGALE 243 (254)
Q Consensus 201 ~~~~~~~~r~lRVATk----YPnLarkyf~~~Gi~~veIi~l~GSvE 243 (254)
+.+ -|... +.....++|++.|+. .+++--..+.+
T Consensus 99 ~~~--------~i~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~ 136 (198)
T cd08437 99 KEN--------FILLNEHFVHPKAFDSLCQQANFQ-PNIVYRTNDIH 136 (198)
T ss_pred CCC--------eEEecccchHHHHHHHHHHHcCCC-ccEEEEeCcHH
Confidence 421 12211 224456778888874 34433334433
No 24
>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=87.35 E-value=1.3 Score=34.95 Aligned_cols=93 Identities=17% Similarity=0.255 Sum_probs=51.0
Q ss_pred CCeEEEee--cCcchhhhhhcCceeeeeeccceeecccCCCcceeeecCCCCcccEEEEEEEeCCCccccccchHHhhcC
Q 025329 125 SNLEVWFQ--RPKDIVRKLLSGDLDLGIVGLDTVSEFGQGNEDLIIVHDALDYGDCRLSLAIPKYGIFENINSLRELAQM 202 (254)
Q Consensus 125 p~iev~~v--Rp~DIp~yV~~G~aDlGIvG~DvL~E~~~d~~~l~~~l~dLgfG~CRLvVAvP~~~~~~dv~sl~dL~~~ 202 (254)
|++++.+. ...++-..+.+|.+|+||+....-. .. .++. -..+++.+++++++.+.+.....+++||...
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 44444443 4568999999999999997532110 00 1122 1244667788888776433333467777532
Q ss_pred CcccCCCCcEEE--cCCCccHHHHHHHcCCc
Q 025329 203 PQWTAEKPLRVA--TGFTYLGPKFMKDNGLK 231 (254)
Q Consensus 203 ~~~~~~r~lRVA--TkYPnLarkyf~~~Gi~ 231 (254)
+ + +... +.+.....++|++.|+.
T Consensus 99 ~-~-----i~~~~~~~~~~~~~~~~~~~~~~ 123 (201)
T cd08418 99 S-W-----VLPGTRMGYYNNLLEALRRLGYN 123 (201)
T ss_pred C-C-----EecCCCCCHHHHHHHHHHHcCCC
Confidence 1 0 1100 12223455677777763
No 25
>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=86.84 E-value=2 Score=33.37 Aligned_cols=91 Identities=21% Similarity=0.283 Sum_probs=51.9
Q ss_pred CCeEEEee--cCcchhhhhhcCceeeeeeccceeecccCCCcceeeecCCCCcccEEEEEEEeCCCccc--cccchHHhh
Q 025329 125 SNLEVWFQ--RPKDIVRKLLSGDLDLGIVGLDTVSEFGQGNEDLIIVHDALDYGDCRLSLAIPKYGIFE--NINSLRELA 200 (254)
Q Consensus 125 p~iev~~v--Rp~DIp~yV~~G~aDlGIvG~DvL~E~~~d~~~l~~~l~dLgfG~CRLvVAvP~~~~~~--dv~sl~dL~ 200 (254)
|++++.+. ...++...+.+|.+|+||+..... . .++. --.++..+++++++.+.+.. ..-+++||.
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 45555544 568899999999999999854321 1 1122 12456778888888764321 123567775
Q ss_pred cCCcccCCCCcEE--EcCCCccHHHHHHHcCCc
Q 025329 201 QMPQWTAEKPLRV--ATGFTYLGPKFMKDNGLK 231 (254)
Q Consensus 201 ~~~~~~~~r~lRV--ATkYPnLarkyf~~~Gi~ 231 (254)
..+ + +.. .+.+.....++|++.|+.
T Consensus 97 ~~~-~-----i~~~~~~~~~~~~~~~~~~~~~~ 123 (197)
T cd08440 97 GYP-L-----IALGRGSGVRALIDRALAAAGLT 123 (197)
T ss_pred cCC-E-----EecCCCccHHHHHHHHHHHcCCC
Confidence 321 1 111 112334455677777774
No 26
>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=86.83 E-value=2.1 Score=34.04 Aligned_cols=109 Identities=19% Similarity=0.185 Sum_probs=56.6
Q ss_pred CCeEEEee--cCcchhhhhhcCceeeeeeccceeecccCCCcceeeecCCCCcccEEEEEEEeCCCccc--cccchHHhh
Q 025329 125 SNLEVWFQ--RPKDIVRKLLSGDLDLGIVGLDTVSEFGQGNEDLIIVHDALDYGDCRLSLAIPKYGIFE--NINSLRELA 200 (254)
Q Consensus 125 p~iev~~v--Rp~DIp~yV~~G~aDlGIvG~DvL~E~~~d~~~l~~~l~dLgfG~CRLvVAvP~~~~~~--dv~sl~dL~ 200 (254)
|++++.+. ...++...+.+|.+|+||+-.+.-.+... ++. ...++..+++++++.+.++. +.-+++||.
T Consensus 27 P~i~l~i~~~~~~~~~~~l~~g~~D~~i~~~~~~~~~~~---~~~----~~~l~~~~~~~v~~~~hp~~~~~~i~~~~L~ 99 (200)
T cd08453 27 PDVELQLREATSDVQLEALLAGEIDAGIVIPPPGASAPP---ALA----YRPLLSEPLVLAVPAAWAAEGGAPLALAAVA 99 (200)
T ss_pred CCceEEEEeCCHHHHHHHHHcCCCCEEEEecCcccCCCc---cee----EEEeeeCceEEEEECCCccccCCCCCHHHhc
Confidence 55555554 45689999999999999975443211111 111 12345667777777764322 123677876
Q ss_pred cCCcccCCCCcEEEcCCCccHHHHHHHcCCceEEEEEcCCcee
Q 025329 201 QMPQWTAEKPLRVATGFTYLGPKFMKDNGLKHVVFSTADGALE 243 (254)
Q Consensus 201 ~~~~~~~~r~lRVATkYPnLarkyf~~~Gi~~veIi~l~GSvE 243 (254)
+.+-..... .-...+-+...++|++.|+. .++..-..+.+
T Consensus 100 ~~~~i~~~~--~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~ 139 (200)
T cd08453 100 AEPLVIFPR--RIAPAFHDAVTGYYRAAGQT-PRIAQEAIQMQ 139 (200)
T ss_pred cCCEEeccC--CcCCcHHHHHHHHHHHcCCC-CceeeccccHH
Confidence 431100000 00012234556788888874 44433334433
No 27
>cd00134 PBPb Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and inorganic ions. PBPs have two cell-membrane translocation functions: bind substrate, and interact with the membrane bound complex. A diverse group of periplasmic transport receptors for lysine/arginine/ornithine (LAO), glutamine, histidine, sulfate, phosphate, molybdate, and methanol are included in the PBPb CD.
Probab=86.55 E-value=2.2 Score=33.87 Aligned_cols=95 Identities=18% Similarity=0.152 Sum_probs=58.1
Q ss_pred eEEEeecCcchhhhhhcCceeeeeeccceeecccCCCcceeeecCCCCcccEEEEEEEeCCCccccccchHHhhcCCccc
Q 025329 127 LEVWFQRPKDIVRKLLSGDLDLGIVGLDTVSEFGQGNEDLIIVHDALDYGDCRLSLAIPKYGIFENINSLRELAQMPQWT 206 (254)
Q Consensus 127 iev~~vRp~DIp~yV~~G~aDlGIvG~DvL~E~~~d~~~l~~~l~dLgfG~CRLvVAvP~~~~~~dv~sl~dL~~~~~~~ 206 (254)
+++......+.-..+.+|.+|+++.+.....+.. + .+.. -..+....+++.++.+. .+.+++||+
T Consensus 40 ~~~~~~~~~~~~~~l~~g~~D~~~~~~~~~~~~~-~---~~~~--~~~~~~~~~~~~~~~~~---~~~~~~dl~------ 104 (218)
T cd00134 40 VKFVEVDWDGLITALKSGKVDLIAAGMTITPERA-K---QVDF--SDPYYKSGQVILVKKGS---PIKSVKDLK------ 104 (218)
T ss_pred EEEEeCCHHHHHHHHhcCCcCEEeecCcCCHHHH-h---hccC--cccceeccEEEEEECCC---CCCChHHhC------
Confidence 3444444578889999999999999873322221 1 1111 23677778888888874 345788875
Q ss_pred CCCCcEEEcCCCccHHHHHHHcCCceEEEEEcCC
Q 025329 207 AEKPLRVATGFTYLGPKFMKDNGLKHVVFSTADG 240 (254)
Q Consensus 207 ~~r~lRVATkYPnLarkyf~~~Gi~~veIi~l~G 240 (254)
++||+.-.......++.+..- ..+++...+
T Consensus 105 ---g~~i~~~~~~~~~~~~~~~~~-~~~~~~~~~ 134 (218)
T cd00134 105 ---GKKVAVQKGSTAEKYLKKALP-EAKVVSYDD 134 (218)
T ss_pred ---CCEEEEEcCchHHHHHHHhCC-cccEEEeCC
Confidence 357776544455666666543 245554444
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=86.27 E-value=2.2 Score=33.64 Aligned_cols=91 Identities=19% Similarity=0.170 Sum_probs=54.2
Q ss_pred CCeEEEee--cCcchhhhhhcCceeeeeeccceeecccCCCcceeeecCCCCcccEEEEEEEeCCCccc-cccchHHhhc
Q 025329 125 SNLEVWFQ--RPKDIVRKLLSGDLDLGIVGLDTVSEFGQGNEDLIIVHDALDYGDCRLSLAIPKYGIFE-NINSLRELAQ 201 (254)
Q Consensus 125 p~iev~~v--Rp~DIp~yV~~G~aDlGIvG~DvL~E~~~d~~~l~~~l~dLgfG~CRLvVAvP~~~~~~-dv~sl~dL~~ 201 (254)
|++++.+. ...++...+.+|.+|+||+....- . .++. ...+++.+++++++.+.+.. ..-+++||.+
T Consensus 27 P~i~l~~~~~~~~~~~~~l~~g~~D~~i~~~~~~---~---~~~~----~~~l~~~~~~~v~~~~~~~~~~~~~~~~L~~ 96 (200)
T cd08417 27 PGVRLRFVPLDRDDLEEALESGEIDLAIGVFPEL---P---PGLR----SQPLFEDRFVCVARKDHPLAGGPLTLEDYLA 96 (200)
T ss_pred CCeEEEeccCCHHHHHHHHHcCCCCEEEeecccC---C---Cccc----hhhhhcCceEEEecCCCcccccccCHHHHhC
Confidence 55555554 445789999999999999854321 1 1122 23567788888888774321 2235677764
Q ss_pred CCcccCCCCcEEE--cCCCccHHHHHHHcCCc
Q 025329 202 MPQWTAEKPLRVA--TGFTYLGPKFMKDNGLK 231 (254)
Q Consensus 202 ~~~~~~~r~lRVA--TkYPnLarkyf~~~Gi~ 231 (254)
.+- +... +.+.+...+||++.|+.
T Consensus 97 ~~~------i~~~~~~~~~~~~~~~~~~~~~~ 122 (200)
T cd08417 97 APH------VLVSPRGRGHGLVDDALAELGLS 122 (200)
T ss_pred CCe------EEeccccchHHHHHHHHHHcCcc
Confidence 211 1111 23445667788888874
No 29
>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=85.97 E-value=2.3 Score=33.49 Aligned_cols=91 Identities=12% Similarity=0.147 Sum_probs=53.1
Q ss_pred CCeEEEee--cCcchhhhhhcCceeeeeeccceeecccCCCcceeeecCCCCcccEEEEEEEeCCCccc--cccchHHhh
Q 025329 125 SNLEVWFQ--RPKDIVRKLLSGDLDLGIVGLDTVSEFGQGNEDLIIVHDALDYGDCRLSLAIPKYGIFE--NINSLRELA 200 (254)
Q Consensus 125 p~iev~~v--Rp~DIp~yV~~G~aDlGIvG~DvL~E~~~d~~~l~~~l~dLgfG~CRLvVAvP~~~~~~--dv~sl~dL~ 200 (254)
|++++.+. ...++-..+.+|.+|+||+....- . .++. .-.++..+++++++++.+.. ..-+++||.
T Consensus 27 P~i~l~i~~~~~~~~~~~l~~~~~Dl~i~~~~~~---~---~~~~----~~~l~~~~~~~~~~~~~pl~~~~~~~~~dl~ 96 (196)
T cd08450 27 PDLDVELSSLFSPQLAEALMRGKLDVAFMRPEIQ---S---DGID----YQLLLKEPLIVVLPADHRLAGREKIPPQDLA 96 (196)
T ss_pred CCcEEEEEecChHHHHHHHhcCCccEEEEeCCCC---C---CCcE----EEEEEccceEEEecCCCCcccCceECHHHhC
Confidence 55666555 467888999999999999753211 1 1122 12456778888887763221 233577876
Q ss_pred cCCcccCCCCcEEEcC---CCccHHHHHHHcCCc
Q 025329 201 QMPQWTAEKPLRVATG---FTYLGPKFMKDNGLK 231 (254)
Q Consensus 201 ~~~~~~~~r~lRVATk---YPnLarkyf~~~Gi~ 231 (254)
+.+ -+..... +.+...++|++.|++
T Consensus 97 ~~~------~i~~~~~~~~~~~~~~~~~~~~~~~ 124 (196)
T cd08450 97 GEN------FISPAPTAPVLQQVIENYAAQHNIQ 124 (196)
T ss_pred CCC------eEeecCCCchHHHHHHHHHHHCCCC
Confidence 421 1122211 234556788888874
No 30
>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=85.89 E-value=3.3 Score=32.89 Aligned_cols=91 Identities=14% Similarity=0.093 Sum_probs=51.8
Q ss_pred CCeEEEee--cCcchhhhhhcCceeeeeeccceeecccCCCcceeeecCCCCcccEEEEEEEeCCCccccc-cchHHhhc
Q 025329 125 SNLEVWFQ--RPKDIVRKLLSGDLDLGIVGLDTVSEFGQGNEDLIIVHDALDYGDCRLSLAIPKYGIFENI-NSLRELAQ 201 (254)
Q Consensus 125 p~iev~~v--Rp~DIp~yV~~G~aDlGIvG~DvL~E~~~d~~~l~~~l~dLgfG~CRLvVAvP~~~~~~dv-~sl~dL~~ 201 (254)
|++++.+. ...++...+.+|.+|+||+-.+.. . .++. .-.++.-+++++++.+.+...- -+++||.+
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 456889999999999999754321 1 1122 1245566677777776432211 26788864
Q ss_pred CCcccCCCCcEEE--cCCCccHHHHHHHcCCc
Q 025329 202 MPQWTAEKPLRVA--TGFTYLGPKFMKDNGLK 231 (254)
Q Consensus 202 ~~~~~~~r~lRVA--TkYPnLarkyf~~~Gi~ 231 (254)
.+ + +... +.+....++++++.|++
T Consensus 97 ~~-~-----i~~~~~~~~~~~~~~~~~~~~~~ 122 (201)
T cd08459 97 AR-H-----VVVSASGTGHGLVEQALREAGIR 122 (201)
T ss_pred CC-c-----EEEccCCCCcchHHHHHHHhCcc
Confidence 31 1 1111 23445567888888874
No 31
>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=85.74 E-value=3.4 Score=32.47 Aligned_cols=95 Identities=14% Similarity=0.109 Sum_probs=50.4
Q ss_pred cCcchhhhhhcCceeeeeeccceeecccCCCcceeeecCCCCcccEEEEEEEeCCCccc--cccchHHhhcCCcccCCCC
Q 025329 133 RPKDIVRKLLSGDLDLGIVGLDTVSEFGQGNEDLIIVHDALDYGDCRLSLAIPKYGIFE--NINSLRELAQMPQWTAEKP 210 (254)
Q Consensus 133 Rp~DIp~yV~~G~aDlGIvG~DvL~E~~~d~~~l~~~l~dLgfG~CRLvVAvP~~~~~~--dv~sl~dL~~~~~~~~~r~ 210 (254)
...++...+.+|.+|+||+....... .++. .-.++..+++++++.+.+.. +.-+++||.+.+ -
T Consensus 38 ~~~~~~~~l~~g~~Dl~i~~~~~~~~-----~~~~----~~~l~~~~~~~v~~~~~~l~~~~~~~~~dL~~~~------~ 102 (199)
T cd08451 38 NTAELLEALREGRLDAAFVRPPVARS-----DGLV----LELLLEEPMLVALPAGHPLARERSIPLAALADEP------F 102 (199)
T ss_pred ChHHHHHHHHCCCccEEEEecCCCCC-----Ccee----EEEeecccEEEEecCCCCCcccCccCHHHhcCCC------E
Confidence 55678899999999999975432111 1122 12345667777776653221 224678876421 1
Q ss_pred cEEEcCCC----ccHHHHHHHcCCceEEEEEcCCcee
Q 025329 211 LRVATGFT----YLGPKFMKDNGLKHVVFSTADGALE 243 (254)
Q Consensus 211 lRVATkYP----nLarkyf~~~Gi~~veIi~l~GSvE 243 (254)
+......+ +...+|+.+.|.. .++.--.++.+
T Consensus 103 i~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~ 138 (199)
T cd08451 103 ILFPRPVGPGLYDAIIAACRRAGFT-PRIGQEAPQMA 138 (199)
T ss_pred EEecCCcChhHHHHHHHHHHHcCCc-eeeEEehhhHH
Confidence 22222221 2334567777764 44443334444
No 32
>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=85.71 E-value=5.1 Score=32.01 Aligned_cols=95 Identities=15% Similarity=0.075 Sum_probs=53.0
Q ss_pred CCeEEEee-cCcchhhhhhcCceeeeeeccceeecccCCCcceeeecCCCCcccEEEEEEEeCCCcccc-ccchHHhhcC
Q 025329 125 SNLEVWFQ-RPKDIVRKLLSGDLDLGIVGLDTVSEFGQGNEDLIIVHDALDYGDCRLSLAIPKYGIFEN-INSLRELAQM 202 (254)
Q Consensus 125 p~iev~~v-Rp~DIp~yV~~G~aDlGIvG~DvL~E~~~d~~~l~~~l~dLgfG~CRLvVAvP~~~~~~d-v~sl~dL~~~ 202 (254)
|++++.+. ...+....+..|.+|+||+..+... .++. .-.++.-+++++++.+.+... --+++||...
T Consensus 27 P~v~v~l~~~~~~~~~~l~~g~~D~~i~~~~~~~------~~~~----~~~l~~~~~~~v~~~~hpl~~~~~~l~dl~~~ 96 (200)
T cd08460 27 PGVRLRFVPESDKDVDALREGRIDLEIGVLGPTG------PEIR----VQTLFRDRFVGVVRAGHPLARGPITPERYAAA 96 (200)
T ss_pred CCCEEEEecCchhHHHHHHCCCccEEEecCCCCC------cchh----eeeeeccceEEEEeCCCCCCCCCCCHHHHhcC
Confidence 55555554 2238889999999999998544311 1111 122344456777776633211 1267888643
Q ss_pred CcccCCCCcEE--EcCCCccHHHHHHHcCCceEEEE
Q 025329 203 PQWTAEKPLRV--ATGFTYLGPKFMKDNGLKHVVFS 236 (254)
Q Consensus 203 ~~~~~~r~lRV--ATkYPnLarkyf~~~Gi~~veIi 236 (254)
+- +.. .+.+.....++|++.|+. .++.
T Consensus 97 ~~------i~~~~~~~~~~~~~~~~~~~~~~-~~~~ 125 (200)
T cd08460 97 PH------VSVSRRGRLHGPIDDALAALGLT-RRVV 125 (200)
T ss_pred CC------EEEecCCCCcchHHHHHHhcCCc-eeEE
Confidence 21 111 122345678899998874 4443
No 33
>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=85.42 E-value=6.8 Score=31.93 Aligned_cols=103 Identities=17% Similarity=0.080 Sum_probs=59.7
Q ss_pred CCCeEEEeec---CcchhhhhhcCceeeeeeccceeecccCCCcceeeecCCCCcccEEEEEEEeCCCccccc--cchHH
Q 025329 124 LSNLEVWFQR---PKDIVRKLLSGDLDLGIVGLDTVSEFGQGNEDLIIVHDALDYGDCRLSLAIPKYGIFENI--NSLRE 198 (254)
Q Consensus 124 ~p~iev~~vR---p~DIp~yV~~G~aDlGIvG~DvL~E~~~d~~~l~~~l~dLgfG~CRLvVAvP~~~~~~dv--~sl~d 198 (254)
.|++++.+.- ..++-..+..|.+|+||...+... .++. -..++.-+++++++++.++..- -+++|
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 3566666662 368999999999999998543211 1122 1345666778887777433221 25677
Q ss_pred hhcCCcccCCCCcEEEc---CCCccHHHHHHHcCCceEEEEEcCCcee
Q 025329 199 LAQMPQWTAEKPLRVAT---GFTYLGPKFMKDNGLKHVVFSTADGALE 243 (254)
Q Consensus 199 L~~~~~~~~~r~lRVAT---kYPnLarkyf~~~Gi~~veIi~l~GSvE 243 (254)
|.+.+ -+...+ .+-....++|++.|+. .++.--..+++
T Consensus 96 l~~~~------~i~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~ 136 (203)
T cd08463 96 YLEAP------HLAPTPYSVGQRGVIDSHLARLGLK-RNIVVTVPYFG 136 (203)
T ss_pred HhhCC------cEEEEcCCCCCCchHHHHHHHcCCC-ceEEEEeChHH
Confidence 76421 122222 2446677889998874 34432233443
No 34
>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=85.42 E-value=6.6 Score=30.97 Aligned_cols=91 Identities=15% Similarity=0.181 Sum_probs=53.0
Q ss_pred CCeEEEee--cCcchhhhhhcCceeeeeeccceeecccCCCcceeeecCCCCcccEEEEEEEeCCCccc-cccchHHhhc
Q 025329 125 SNLEVWFQ--RPKDIVRKLLSGDLDLGIVGLDTVSEFGQGNEDLIIVHDALDYGDCRLSLAIPKYGIFE-NINSLRELAQ 201 (254)
Q Consensus 125 p~iev~~v--Rp~DIp~yV~~G~aDlGIvG~DvL~E~~~d~~~l~~~l~dLgfG~CRLvVAvP~~~~~~-dv~sl~dL~~ 201 (254)
|++++.+. ...++...+.+|.+|+||+.... .. .++. ..-+++-+++++++.+.+.. ..-+++||..
T Consensus 27 P~v~i~i~~~~~~~~~~~l~~~~~Di~i~~~~~-~~-----~~~~----~~~l~~~~~~lv~~~~~p~~~~~~~~~~L~~ 96 (198)
T cd08461 27 PGVRVAIRDLESDNLEAQLERGEVDLALTTPEY-AP-----DGLR----SRPLFEERYVCVTRRGHPLLQGPLSLDQFCA 96 (198)
T ss_pred CCcEEEEeeCCcccHHHHHhcCCCcEEEecCcc-CC-----ccce----eeeeecCcEEEEEcCCChhhcCCCCHHHHhh
Confidence 55555554 45679999999999999974221 11 1121 22455667788877763211 2346777764
Q ss_pred CCcccCCCCcEE---EcCCCccHHHHHHHcCCc
Q 025329 202 MPQWTAEKPLRV---ATGFTYLGPKFMKDNGLK 231 (254)
Q Consensus 202 ~~~~~~~r~lRV---ATkYPnLarkyf~~~Gi~ 231 (254)
.+ -+.. .+.+.....+||++.|++
T Consensus 97 ~~------~i~~~~~~~~~~~~~~~~~~~~~~~ 123 (198)
T cd08461 97 LD------HIVVSPSGGGFAGSTDEALAALGLT 123 (198)
T ss_pred CC------cEEEecCCCCCCCHHHHHHHHcCCC
Confidence 21 1111 123445677889888874
No 35
>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=85.39 E-value=2.8 Score=32.89 Aligned_cols=93 Identities=20% Similarity=0.270 Sum_probs=52.7
Q ss_pred CCeEEEee--cCcchhhhhhcCceeeeeeccceeecccCCCcceeeecCCCCcccEEEEEEEeCCCcccc--ccchHHhh
Q 025329 125 SNLEVWFQ--RPKDIVRKLLSGDLDLGIVGLDTVSEFGQGNEDLIIVHDALDYGDCRLSLAIPKYGIFEN--INSLRELA 200 (254)
Q Consensus 125 p~iev~~v--Rp~DIp~yV~~G~aDlGIvG~DvL~E~~~d~~~l~~~l~dLgfG~CRLvVAvP~~~~~~d--v~sl~dL~ 200 (254)
|++++.+. ...++-..+.+|.+|+||+-.....+ . .++. .-.++..+++++++.+..+.. .-+++||.
T Consensus 27 P~i~i~~~~~~~~~~~~~l~~~~~Dl~i~~~~~~~~-~---~~~~----~~~l~~~~~~~v~~~~~~~~~~~~~~~~~L~ 98 (197)
T cd08449 27 PNVTVRFHELSPEAQKAALLSKRIDLGFVRFADTLN-D---PPLA----SELLWREPMVVALPEEHPLAGRKSLTLADLR 98 (197)
T ss_pred CCeEEEEEECCHHHHHHHHhCCCccEEEecccccCC-C---CCce----EEEEEEeeEEEEecCCCCCCCCCCCCHHHHC
Confidence 55555554 45788899999999999964321110 1 1122 123567788888877643321 23678886
Q ss_pred cCCcccCCCCcEE---EcCCCccHHHHHHHcCCc
Q 025329 201 QMPQWTAEKPLRV---ATGFTYLGPKFMKDNGLK 231 (254)
Q Consensus 201 ~~~~~~~~r~lRV---ATkYPnLarkyf~~~Gi~ 231 (254)
..+ + +.. .+.+.+...++|++.|+.
T Consensus 99 ~~~-~-----i~~~~~~~~~~~~~~~~~~~~~~~ 126 (197)
T cd08449 99 DEP-F-----VFLRLANSRFADFLINCCLQAGFT 126 (197)
T ss_pred CCC-E-----EEecCCCchHHHHHHHHHHhCCCC
Confidence 421 1 111 123335556778888874
No 36
>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=85.29 E-value=2.8 Score=32.88 Aligned_cols=69 Identities=23% Similarity=0.263 Sum_probs=42.0
Q ss_pred CCeEEEee--cCcchhhhhhcCceeeeeeccceeecccCCCcceeeecCCCCcccEEEEEEEeCCCccc--cccchHHhh
Q 025329 125 SNLEVWFQ--RPKDIVRKLLSGDLDLGIVGLDTVSEFGQGNEDLIIVHDALDYGDCRLSLAIPKYGIFE--NINSLRELA 200 (254)
Q Consensus 125 p~iev~~v--Rp~DIp~yV~~G~aDlGIvG~DvL~E~~~d~~~l~~~l~dLgfG~CRLvVAvP~~~~~~--dv~sl~dL~ 200 (254)
|++++.+. ...++...+.+|.+|+||+..+.-.. . .++. ...++..+++++++++.++. +.-+++||.
T Consensus 27 P~v~i~i~~~~~~~~~~~l~~~~~Dl~i~~~~~~~~-~---~~~~----~~~l~~~~~~~~~~~~~~l~~~~~~~~~dL~ 98 (201)
T cd08435 27 PRLTVRVVEGTSDELLEGLRAGELDLAIGRLADDEQ-P---PDLA----SEELADEPLVVVARPGHPLARRARLTLADLA 98 (201)
T ss_pred CCeEEEEEeCCHHHHHHHHHcCCccEEEEecCcccC-C---CCcE----EEEcccCcEEEEEeCCCcCcccCCcCHHHHh
Confidence 55555544 56789999999999999975432110 0 1122 23456788888888774321 223567776
Q ss_pred c
Q 025329 201 Q 201 (254)
Q Consensus 201 ~ 201 (254)
.
T Consensus 99 ~ 99 (201)
T cd08435 99 D 99 (201)
T ss_pred c
Confidence 4
No 37
>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=85.17 E-value=4.3 Score=31.99 Aligned_cols=91 Identities=14% Similarity=0.123 Sum_probs=51.2
Q ss_pred CCeEEEee--cCcchhhhhhcCceeeeeeccceeecccCCCcceeeecCCCCcccEEEEEEEeCCCcc-ccccchHHhhc
Q 025329 125 SNLEVWFQ--RPKDIVRKLLSGDLDLGIVGLDTVSEFGQGNEDLIIVHDALDYGDCRLSLAIPKYGIF-ENINSLRELAQ 201 (254)
Q Consensus 125 p~iev~~v--Rp~DIp~yV~~G~aDlGIvG~DvL~E~~~d~~~l~~~l~dLgfG~CRLvVAvP~~~~~-~dv~sl~dL~~ 201 (254)
|++++.+. ...++-..+.+|.+|+||+..+.. . .++. ...++.-+++++++.+..- ...-+++||.+
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 44444444 466788999999999999865421 1 1121 2344556666666655211 11235677764
Q ss_pred CCcccCCCCcEE--EcCCCccHHHHHHHcCCc
Q 025329 202 MPQWTAEKPLRV--ATGFTYLGPKFMKDNGLK 231 (254)
Q Consensus 202 ~~~~~~~r~lRV--ATkYPnLarkyf~~~Gi~ 231 (254)
.+. .-. .+.+.+..+++|++.|+.
T Consensus 97 ~~~------i~~~~~~~~~~~~~~~~~~~~~~ 122 (200)
T cd08464 97 RPH------VLVSYRGGLRGFVDDALAELGRS 122 (200)
T ss_pred CCc------EEecCCCCCcchHHHHHHHcCCC
Confidence 211 111 123445677889888874
No 38
>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=84.45 E-value=5.6 Score=30.97 Aligned_cols=68 Identities=19% Similarity=0.288 Sum_probs=40.4
Q ss_pred CCeEEEee--cCcchhhhhhcCceeeeeeccceeecccCCCcceeeecCCCCcccEEEEEEEeCCCccc--cccchHHhh
Q 025329 125 SNLEVWFQ--RPKDIVRKLLSGDLDLGIVGLDTVSEFGQGNEDLIIVHDALDYGDCRLSLAIPKYGIFE--NINSLRELA 200 (254)
Q Consensus 125 p~iev~~v--Rp~DIp~yV~~G~aDlGIvG~DvL~E~~~d~~~l~~~l~dLgfG~CRLvVAvP~~~~~~--dv~sl~dL~ 200 (254)
|++++.+. ...++-..+.+|.+|+||+.... +.. .++. -..++..+++++++.+.+.. +.-+++||.
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 44555544 45788899999999999986432 111 1122 12346667777777663221 223677775
Q ss_pred c
Q 025329 201 Q 201 (254)
Q Consensus 201 ~ 201 (254)
.
T Consensus 98 ~ 98 (194)
T cd08436 98 D 98 (194)
T ss_pred C
Confidence 3
No 39
>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=84.21 E-value=5.1 Score=31.55 Aligned_cols=69 Identities=23% Similarity=0.360 Sum_probs=41.6
Q ss_pred CCeEEEee--cCcchhhhhhcCceeeeeeccceeecccCCCcceeeecCCCCcccEEEEEEEeCCCccc--cccchHHhh
Q 025329 125 SNLEVWFQ--RPKDIVRKLLSGDLDLGIVGLDTVSEFGQGNEDLIIVHDALDYGDCRLSLAIPKYGIFE--NINSLRELA 200 (254)
Q Consensus 125 p~iev~~v--Rp~DIp~yV~~G~aDlGIvG~DvL~E~~~d~~~l~~~l~dLgfG~CRLvVAvP~~~~~~--dv~sl~dL~ 200 (254)
|++++.+. ...++...+.+|.+|+||+.... +. ...++. ...+++.++++++|++.++. ..-+++||.
T Consensus 27 P~i~l~i~~~~~~~~~~~l~~~~~Dl~i~~~~~--~~--~~~~l~----~~~l~~~~~~~v~~~~hp~~~~~~~~~~~L~ 98 (199)
T cd08416 27 PELDIELTLGSNKDLLKKLKDGELDAILVATPE--GL--NDPDFE----VVPLFEDDIFLAVPATSPLAASSEIDLRDLK 98 (199)
T ss_pred CCeEEEEEEcCcHHHHHHHhCCCCCEEEEecCC--cC--CCCCeE----EEEeecceEEEEECCCCcccccCccCHHHhc
Confidence 55555554 45667889999999999986432 00 011222 23456777888888764322 123567775
Q ss_pred c
Q 025329 201 Q 201 (254)
Q Consensus 201 ~ 201 (254)
+
T Consensus 99 ~ 99 (199)
T cd08416 99 D 99 (199)
T ss_pred C
Confidence 3
No 40
>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=84.13 E-value=2.8 Score=33.03 Aligned_cols=93 Identities=13% Similarity=0.147 Sum_probs=50.6
Q ss_pred CCeEEEee--cCcchhhhhhcCceeeeeeccceeecccCCCcceeeecCCCCcccEEEEEEEeCCCccc--cccchHHhh
Q 025329 125 SNLEVWFQ--RPKDIVRKLLSGDLDLGIVGLDTVSEFGQGNEDLIIVHDALDYGDCRLSLAIPKYGIFE--NINSLRELA 200 (254)
Q Consensus 125 p~iev~~v--Rp~DIp~yV~~G~aDlGIvG~DvL~E~~~d~~~l~~~l~dLgfG~CRLvVAvP~~~~~~--dv~sl~dL~ 200 (254)
|++++.+. ...++...+.+|.+|+||+....-. .++. --.++.-+++++++++.++. +.-+++||.
T Consensus 27 P~i~l~i~~~~~~~~~~~l~~~~~D~~i~~~~~~~------~~~~----~~~l~~~~~~~v~~~~hpl~~~~~~~~~~l~ 96 (199)
T cd08426 27 PGVFFTVDVASTADVLEAVLSGEADIGLAFSPPPE------PGIR----VHSRQPAPIGAVVPPGHPLARQPSVTLAQLA 96 (199)
T ss_pred CCeEEEEEeCCcHHHHHHHHCCCccEEEecCCCCC------CCeE----EEeeccCcEEEEecCCCCcccCCccCHHHHh
Confidence 55555544 4578999999999999997543211 1122 12345667777777763322 223577775
Q ss_pred cCCcccCCCCcEEEcCCCccHHHHHHHcCCc
Q 025329 201 QMPQWTAEKPLRVATGFTYLGPKFMKDNGLK 231 (254)
Q Consensus 201 ~~~~~~~~r~lRVATkYPnLarkyf~~~Gi~ 231 (254)
..+-... .-.+.+.+...+++++.|+.
T Consensus 97 ~~~~i~~----~~~~~~~~~~~~~~~~~~~~ 123 (199)
T cd08426 97 GYPLALP----PPSFSLRQILDAAFARAGVQ 123 (199)
T ss_pred CCCeEec----CCcchHHHHHHHHHHHcCCC
Confidence 3211000 00112234456677777764
No 41
>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=84.06 E-value=2.5 Score=33.24 Aligned_cols=91 Identities=13% Similarity=0.128 Sum_probs=48.6
Q ss_pred CCeEEEee--cCcchhhhhhcCceeeeeeccceeecccCCCcceeeecCCCCcccEEEEEEEeCCCccc--cccchHHhh
Q 025329 125 SNLEVWFQ--RPKDIVRKLLSGDLDLGIVGLDTVSEFGQGNEDLIIVHDALDYGDCRLSLAIPKYGIFE--NINSLRELA 200 (254)
Q Consensus 125 p~iev~~v--Rp~DIp~yV~~G~aDlGIvG~DvL~E~~~d~~~l~~~l~dLgfG~CRLvVAvP~~~~~~--dv~sl~dL~ 200 (254)
|++++.+. ...++-..+.+|.+|+||+..... + .++. -..++.-+++++++.+.++. +.-+++||.
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 33444433 456778889999999999854321 1 1122 12345667777777653221 223567775
Q ss_pred cCCcccCCCCcEEE--cCCCccHHHHHHHcCCc
Q 025329 201 QMPQWTAEKPLRVA--TGFTYLGPKFMKDNGLK 231 (254)
Q Consensus 201 ~~~~~~~~r~lRVA--TkYPnLarkyf~~~Gi~ 231 (254)
..+ -+... +.+.+...++|.+.|++
T Consensus 97 ~~~------~i~~~~~~~~~~~~~~~~~~~~~~ 123 (196)
T cd08456 97 GEP------FISLARTDGTRQRVDALFEQAGVK 123 (196)
T ss_pred CCc------EEEecCCcchHHHHHHHHHHCCCC
Confidence 321 11111 12333445677777764
No 42
>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=83.86 E-value=6 Score=31.89 Aligned_cols=102 Identities=13% Similarity=0.099 Sum_probs=55.6
Q ss_pred CCeEEEee--cCcchhhhhhcCceeeeeeccceeecccCCCcceeeecCCCCcccEEEEEEEeCCCcc-ccccchHHhhc
Q 025329 125 SNLEVWFQ--RPKDIVRKLLSGDLDLGIVGLDTVSEFGQGNEDLIIVHDALDYGDCRLSLAIPKYGIF-ENINSLRELAQ 201 (254)
Q Consensus 125 p~iev~~v--Rp~DIp~yV~~G~aDlGIvG~DvL~E~~~d~~~l~~~l~dLgfG~CRLvVAvP~~~~~-~dv~sl~dL~~ 201 (254)
|++++.+. ...++-..+.+|.+|+||+-.+.. + .++.. ..++.-+++++++++-.. ..--+++||..
T Consensus 27 P~i~l~i~~~~~~~~~~~L~~g~~Dl~i~~~~~~-~-----~~~~~----~~l~~~~~~lv~~~~h~~~~~~i~~~~l~~ 96 (200)
T cd08465 27 PGIDLAVSQASREAMLAQVADGEIDLALGVFPEL-P-----EELHA----ETLFEERFVCLADRATLPASGGLSLDAWLA 96 (200)
T ss_pred CCcEEEEecCChHhHHHHHHCCCccEEEeccccC-C-----cCeeE----EEeeeccEEEEEeCCCCccCCCcCHHHHhh
Confidence 45555443 578999999999999999743321 1 11221 123344566666665311 11235777764
Q ss_pred CCcccCCCCcEEE--cCCCccHHHHHHHcCCceEEEEEcCCcee
Q 025329 202 MPQWTAEKPLRVA--TGFTYLGPKFMKDNGLKHVVFSTADGALE 243 (254)
Q Consensus 202 ~~~~~~~r~lRVA--TkYPnLarkyf~~~Gi~~veIi~l~GSvE 243 (254)
.+ .+... +.+-....++|++.|++ .++.--.++.+
T Consensus 97 ~~------~i~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~ 133 (200)
T cd08465 97 RP------HVLVAMRGDAANEIDRALAARGLR-RRVALTLPHWG 133 (200)
T ss_pred CC------cEEEecCCCcCChHHHHHHHcCCc-eEEEEEcCcHH
Confidence 31 11111 12335677888999985 55543334433
No 43
>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=83.44 E-value=3.4 Score=32.10 Aligned_cols=89 Identities=21% Similarity=0.272 Sum_probs=49.8
Q ss_pred CCeEEEee--cCcchhhhhhcCceeeeeeccceeecccCCCcceeeecCCCCcccEEEEEEEeCCCccc--cccchHHhh
Q 025329 125 SNLEVWFQ--RPKDIVRKLLSGDLDLGIVGLDTVSEFGQGNEDLIIVHDALDYGDCRLSLAIPKYGIFE--NINSLRELA 200 (254)
Q Consensus 125 p~iev~~v--Rp~DIp~yV~~G~aDlGIvG~DvL~E~~~d~~~l~~~l~dLgfG~CRLvVAvP~~~~~~--dv~sl~dL~ 200 (254)
|++++.+. ...++...+.+|.+|+||+....- + .++. -..++..+++++++.+.+.. ..-+++||.
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 44554444 456788999999999999864321 1 1122 12456777788877663221 123667775
Q ss_pred cCCcccCCCCcEEEcC----CCccHHHHHHHcCCc
Q 025329 201 QMPQWTAEKPLRVATG----FTYLGPKFMKDNGLK 231 (254)
Q Consensus 201 ~~~~~~~~r~lRVATk----YPnLarkyf~~~Gi~ 231 (254)
..+ -|... +.+..++++.+.|+.
T Consensus 97 ~~~--------~i~~~~~~~~~~~~~~~~~~~~~~ 123 (195)
T cd08434 97 DEP--------FVLLSPGFGLRPIVDELCAAAGFT 123 (195)
T ss_pred CCc--------eEEecCCccHHHHHHHHHHHcCCc
Confidence 321 12211 223345677777764
No 44
>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=83.40 E-value=6.7 Score=30.92 Aligned_cols=90 Identities=22% Similarity=0.221 Sum_probs=51.1
Q ss_pred CCeEEEee--cCcchhhhhhcCceeeeeeccceeecccCCCcceeeecCCCCcccEEEEEEEeCCCccc--cccchHHhh
Q 025329 125 SNLEVWFQ--RPKDIVRKLLSGDLDLGIVGLDTVSEFGQGNEDLIIVHDALDYGDCRLSLAIPKYGIFE--NINSLRELA 200 (254)
Q Consensus 125 p~iev~~v--Rp~DIp~yV~~G~aDlGIvG~DvL~E~~~d~~~l~~~l~dLgfG~CRLvVAvP~~~~~~--dv~sl~dL~ 200 (254)
|++++-+. ...++...+.+|.+|+||+....- . .++. -..++..+++++++.+.... ..-+++||.
T Consensus 27 P~i~i~~~~~~~~~~~~~l~~~~~D~~i~~~~~~---~---~~~~----~~~l~~~~~~~~~~~~~~~~~~~~~~~~~l~ 96 (198)
T cd08433 27 PGIRLRIVEGLSGHLLEWLLNGRLDLALLYGPPP---I---PGLS----TEPLLEEDLFLVGPADAPLPRGAPVPLAELA 96 (198)
T ss_pred CCcEEEEEecCcHHHHHHHhCCCCcEEEEeCCCC---C---CCee----EEEeccccEEEEecCCCccccCCCCCHHHhC
Confidence 55555543 557889999999999999853211 1 1222 23456678888887764221 223567775
Q ss_pred cCCcccCCCCcEEEc---CCCccHHHHHHHcCCc
Q 025329 201 QMPQWTAEKPLRVAT---GFTYLGPKFMKDNGLK 231 (254)
Q Consensus 201 ~~~~~~~~r~lRVAT---kYPnLarkyf~~~Gi~ 231 (254)
+.+ .-+-+ .+.....+||++.|++
T Consensus 97 ~~~-------~i~~~~~~~~~~~~~~~~~~~~~~ 123 (198)
T cd08433 97 RLP-------LILPSRGHGLRRLVDEAAARAGLT 123 (198)
T ss_pred CCc-------eEEcCCCCcHHHHHHHHHHHcCCC
Confidence 421 11111 1223355677777774
No 45
>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=83.08 E-value=8.1 Score=30.89 Aligned_cols=102 Identities=10% Similarity=-0.023 Sum_probs=54.7
Q ss_pred CCeEEEee-cCcchhhhhhcCceeeeeeccceeecccCCCcceeeecCCCCcccEEEEEEEeCCCccc-cccchHHhhcC
Q 025329 125 SNLEVWFQ-RPKDIVRKLLSGDLDLGIVGLDTVSEFGQGNEDLIIVHDALDYGDCRLSLAIPKYGIFE-NINSLRELAQM 202 (254)
Q Consensus 125 p~iev~~v-Rp~DIp~yV~~G~aDlGIvG~DvL~E~~~d~~~l~~~l~dLgfG~CRLvVAvP~~~~~~-dv~sl~dL~~~ 202 (254)
|++++-+. ...|+-..|.+|.+|+||+..... +. ++. --.++.-+++++++.+-++. ..-+++||.+.
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 12455667788777664321 23457777642
Q ss_pred CcccCCCCcEEEc--CC-CccHHHHHHHcCCceEEEEEcCCcee
Q 025329 203 PQWTAEKPLRVAT--GF-TYLGPKFMKDNGLKHVVFSTADGALE 243 (254)
Q Consensus 203 ~~~~~~r~lRVAT--kY-PnLarkyf~~~Gi~~veIi~l~GSvE 243 (254)
+ .+.+.. .+ ..+.+.++++.|+. .++.--..+++
T Consensus 97 ~------~i~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~ 133 (200)
T cd08462 97 G------HVVVRFGRNRRPSFEDWFLNEYGLK-RRVEVVTPSFS 133 (200)
T ss_pred C------CEEEecCCCCCccHHHHHHHHcCCc-ceEEEEeChHH
Confidence 1 111111 11 23445667888874 45432234433
No 46
>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=82.84 E-value=5.1 Score=31.52 Aligned_cols=67 Identities=22% Similarity=0.320 Sum_probs=40.3
Q ss_pred CCeEEEee--cCcchhhhhhcCceeeeeeccceeecccCCCcceeeecCCCCcccEEEEEEEeCCCccc--cccchHHhh
Q 025329 125 SNLEVWFQ--RPKDIVRKLLSGDLDLGIVGLDTVSEFGQGNEDLIIVHDALDYGDCRLSLAIPKYGIFE--NINSLRELA 200 (254)
Q Consensus 125 p~iev~~v--Rp~DIp~yV~~G~aDlGIvG~DvL~E~~~d~~~l~~~l~dLgfG~CRLvVAvP~~~~~~--dv~sl~dL~ 200 (254)
|++++.+. ...|+-..+.+|.+|+||+..... . .++.. -.++..+++++++++.+.. +.-+++||.
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 44555443 568899999999999999854421 1 11221 1345667788877763221 233567775
Q ss_pred c
Q 025329 201 Q 201 (254)
Q Consensus 201 ~ 201 (254)
.
T Consensus 97 ~ 97 (198)
T cd08421 97 D 97 (198)
T ss_pred C
Confidence 3
No 47
>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=82.67 E-value=3.2 Score=32.47 Aligned_cols=67 Identities=27% Similarity=0.306 Sum_probs=40.0
Q ss_pred CCeEEEee--cCcchhhhhhcCceeeeeeccceeecccCCCcceeeecCCCCcccEEEEEEEeCCCccc--cccchHHhh
Q 025329 125 SNLEVWFQ--RPKDIVRKLLSGDLDLGIVGLDTVSEFGQGNEDLIIVHDALDYGDCRLSLAIPKYGIFE--NINSLRELA 200 (254)
Q Consensus 125 p~iev~~v--Rp~DIp~yV~~G~aDlGIvG~DvL~E~~~d~~~l~~~l~dLgfG~CRLvVAvP~~~~~~--dv~sl~dL~ 200 (254)
|++++.+. ...++...+.+|.+|+||+.... .. .++. --.++..+++++++++.+.. +.-+++||.
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 44444443 67889999999999999974321 11 1122 12455666777777764322 123577776
Q ss_pred c
Q 025329 201 Q 201 (254)
Q Consensus 201 ~ 201 (254)
.
T Consensus 97 ~ 97 (197)
T cd08448 97 G 97 (197)
T ss_pred C
Confidence 3
No 48
>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=82.36 E-value=8.5 Score=29.99 Aligned_cols=67 Identities=27% Similarity=0.376 Sum_probs=41.3
Q ss_pred CCeEEEee--cCcchhhhhhcCceeeeeeccceeecccCCCcceeeecCCCCcccEEEEEEEeCCCccc--cccchHHhh
Q 025329 125 SNLEVWFQ--RPKDIVRKLLSGDLDLGIVGLDTVSEFGQGNEDLIIVHDALDYGDCRLSLAIPKYGIFE--NINSLRELA 200 (254)
Q Consensus 125 p~iev~~v--Rp~DIp~yV~~G~aDlGIvG~DvL~E~~~d~~~l~~~l~dLgfG~CRLvVAvP~~~~~~--dv~sl~dL~ 200 (254)
|++++.+. ...++-..+.+|.+|+||+.... .. .++. --.++..+++++++.+.++. ..-+++||.
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 44555544 45678899999999999986432 11 1222 12456778888888774322 223567775
Q ss_pred c
Q 025329 201 Q 201 (254)
Q Consensus 201 ~ 201 (254)
.
T Consensus 97 ~ 97 (197)
T cd08438 97 D 97 (197)
T ss_pred C
Confidence 3
No 49
>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=82.04 E-value=4 Score=36.44 Aligned_cols=84 Identities=23% Similarity=0.234 Sum_probs=48.1
Q ss_pred cchhhhhhcCceeeeeeccceeecc--cC-------CCcceeeecCCCCcccEEEEEEEeCCCccccccchHHhhcCCcc
Q 025329 135 KDIVRKLLSGDLDLGIVGLDTVSEF--GQ-------GNEDLIIVHDALDYGDCRLSLAIPKYGIFENINSLRELAQMPQW 205 (254)
Q Consensus 135 ~DIp~yV~~G~aDlGIvG~DvL~E~--~~-------d~~~l~~~l~dLgfG~CRLvVAvP~~~~~~dv~sl~dL~~~~~~ 205 (254)
.+....|..|.+|+|+++.+..... +. ...++. .+. .+-.-.++++++.+. .+++++||+.
T Consensus 72 ~~~~~~l~~G~~D~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~v~--~~~~~~~~lvv~~d~---~i~sl~dL~g---- 141 (320)
T TIGR02122 72 VENVNLLEAGEADLAIVQSDVAYYAYEGDGEFEFEGPVEKLR-ALA--SLYPEYIQIVVRKDS---GIKTVADLKG---- 141 (320)
T ss_pred HHHHHHHhCCCCcEEEEcchhHHHHhcCcCccccCCCCccHH-hHH--HhccccEEEEEECCC---CCCcHHHcCC----
Confidence 4788899999999999997654311 10 001111 011 122233567888883 4678899862
Q ss_pred cCCCCcEEEcC---CCccHHHHHHHcCCc
Q 025329 206 TAEKPLRVATG---FTYLGPKFMKDNGLK 231 (254)
Q Consensus 206 ~~~r~lRVATk---YPnLarkyf~~~Gi~ 231 (254)
+++.+.+. +-.+..+++++.|++
T Consensus 142 ---k~v~~~~~~s~~~~~~~~~l~~~G~~ 167 (320)
T TIGR02122 142 ---KRVAVGAPGSGTELNARAVLKAAGLT 167 (320)
T ss_pred ---CEEecCCCCcchHHHHHHHHHHcCCC
Confidence 12223211 223557888888874
No 50
>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=81.29 E-value=2.4 Score=33.94 Aligned_cols=91 Identities=13% Similarity=0.142 Sum_probs=50.2
Q ss_pred CCeEEEee--cCcchhhhhhcCceeeeeeccceeecccCCCcceeeecCCCCcccEEEEEEEeCCCccccc--cchHHhh
Q 025329 125 SNLEVWFQ--RPKDIVRKLLSGDLDLGIVGLDTVSEFGQGNEDLIIVHDALDYGDCRLSLAIPKYGIFENI--NSLRELA 200 (254)
Q Consensus 125 p~iev~~v--Rp~DIp~yV~~G~aDlGIvG~DvL~E~~~d~~~l~~~l~dLgfG~CRLvVAvP~~~~~~dv--~sl~dL~ 200 (254)
|++++.+. ...|+...+..|.+|+||+-.+. .+. ++. .-.+++-+++++++.+.++..- -+++||.
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 44444433 45678899999999999985432 111 121 1233455678887776433222 2567775
Q ss_pred cCCcccCCCCcEEEcC--CCccHHHHHHHcCCc
Q 025329 201 QMPQWTAEKPLRVATG--FTYLGPKFMKDNGLK 231 (254)
Q Consensus 201 ~~~~~~~~r~lRVATk--YPnLarkyf~~~Gi~ 231 (254)
+.+ + +..... +-....+||++.|++
T Consensus 97 ~~~-~-----i~~~~~~~~~~~~~~~~~~~~~~ 123 (196)
T cd08458 97 GES-L-----ICLSPVSLLRMQTDAALDSCGVH 123 (196)
T ss_pred CCc-c-----EEecCCCcHHHHHHHHHHHcCCC
Confidence 421 1 111111 224566788888874
No 51
>PF12974 Phosphonate-bd: ABC transporter, phosphonate, periplasmic substrate-binding protein ; PDB: 3N5L_B 3QUJ_C 3P7I_A 3QK6_A 3S4U_A.
Probab=80.86 E-value=1.3 Score=38.71 Aligned_cols=93 Identities=19% Similarity=0.186 Sum_probs=50.1
Q ss_pred eEEEeecC-cchhhhhhcCceeeeeeccceeecccCC-CcceeeecCC-CCcccEEEEEEEeCCCccccccchHHhhcCC
Q 025329 127 LEVWFQRP-KDIVRKLLSGDLDLGIVGLDTVSEFGQG-NEDLIIVHDA-LDYGDCRLSLAIPKYGIFENINSLRELAQMP 203 (254)
Q Consensus 127 iev~~vRp-~DIp~yV~~G~aDlGIvG~DvL~E~~~d-~~~l~~~l~d-LgfG~CRLvVAvP~~~~~~dv~sl~dL~~~~ 203 (254)
+++...+. .+....+.+|.+|+++++-......... ..+++..... =|--..+-++.++.+ .++++++||+
T Consensus 31 v~~~~~~~~~~~~~~l~~g~~D~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~~~~ivv~~d---s~i~~l~dL~--- 104 (243)
T PF12974_consen 31 VELVPADDYAEFIEALRSGEIDLAFMGPLPYVQARQRAGVEPLATPVGPDGSPSYRSVIVVRAD---SPITSLADLK--- 104 (243)
T ss_dssp EEEE--SSHHHHHHHHHTTS-SEEE--HHHHHHHHHHSSEEEEEEEEETTT-SCEEEEEEEETT---SS--SHHHHG---
T ss_pred EEEEEcCCHHHHHHHHHcCCccEEEECcHHHHHHhhcCcEEEEEEecccCCCcceeEEEEEECC---CCCCChhhcC---
Confidence 34444432 6677789999999999987766554311 1222211111 112267778888888 4689999996
Q ss_pred cccCCCCcEEEcCCCc------cHHHHH-HHcCCc
Q 025329 204 QWTAEKPLRVATGFTY------LGPKFM-KDNGLK 231 (254)
Q Consensus 204 ~~~~~r~lRVATkYPn------Larkyf-~~~Gi~ 231 (254)
++|||.-=|. +.+.+| +++|++
T Consensus 105 ------Gk~v~~~~~~s~sg~l~~~~~L~~~~Gl~ 133 (243)
T PF12974_consen 105 ------GKRVAFPDPSSTSGYLIPRYELLREAGLD 133 (243)
T ss_dssp ------GSEEEEE-TT-TTTTHHHHHHTCCCCT--
T ss_pred ------CCEEEEecCCccHHHHHHHHHHHHHcCCC
Confidence 3677764444 244556 688874
No 52
>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=80.72 E-value=4.4 Score=32.68 Aligned_cols=94 Identities=16% Similarity=0.178 Sum_probs=54.3
Q ss_pred CCeEEEee--cCcchhhhhhcCceeeeeeccceeecccCCCcceeeecCCCCcccEEEEEEEeCCCccc--cccchHHhh
Q 025329 125 SNLEVWFQ--RPKDIVRKLLSGDLDLGIVGLDTVSEFGQGNEDLIIVHDALDYGDCRLSLAIPKYGIFE--NINSLRELA 200 (254)
Q Consensus 125 p~iev~~v--Rp~DIp~yV~~G~aDlGIvG~DvL~E~~~d~~~l~~~l~dLgfG~CRLvVAvP~~~~~~--dv~sl~dL~ 200 (254)
|++++.+. ...++...|..|.+|+||+..... +.+ +. -..+.+=++++++|++.... ..-+++||.
T Consensus 28 P~v~i~i~~~~~~~l~~~l~~g~~D~~~~~~~~~-~~~-----~~----~~~l~~~~~~lv~~~~h~l~~~~~i~~~dL~ 97 (198)
T cd08486 28 PTATVSLTHMTKDEQVEGLLAGTIHVGFSRFFPR-HPG-----IE----IVNIAQEDLYLAVHRSQSGKFGKTCKLADLR 97 (198)
T ss_pred CCeEEEEEECCHHHHHHHHHcCCceEEEecCCCC-CCc-----eE----EEEEeeccEEEEecCCCccccCCcccHHHHc
Confidence 55555544 667899999999999999754221 111 11 12344457788887763211 223567776
Q ss_pred cCCcccCCCCcEEE----cCCCccHHHHHHHcCCceEEE
Q 025329 201 QMPQWTAEKPLRVA----TGFTYLGPKFMKDNGLKHVVF 235 (254)
Q Consensus 201 ~~~~~~~~r~lRVA----TkYPnLarkyf~~~Gi~~veI 235 (254)
+.+- +... ..|.+...++|++.|+. .++
T Consensus 98 ~~~~------i~~~~~~~~~~~~~~~~~~~~~~~~-~~~ 129 (198)
T cd08486 98 AVEL------TLFPRGGRPSFADEVIGLFKHAGIE-PRI 129 (198)
T ss_pred CCCe------EeecCCcCchHHHHHHHHHHHcCCC-cce
Confidence 4311 1111 12556778888998874 444
No 53
>PRK11917 bifunctional adhesin/ABC transporter aspartate/glutamate-binding protein; Reviewed
Probab=80.57 E-value=9.9 Score=33.82 Aligned_cols=95 Identities=18% Similarity=0.101 Sum_probs=58.7
Q ss_pred eEEEeecCcchhhhhhcCceeeeeeccceeecccCCCcceeeecCCCCcccEEEEEEEeCCCccccccchHHhhcCCccc
Q 025329 127 LEVWFQRPKDIVRKLLSGDLDLGIVGLDTVSEFGQGNEDLIIVHDALDYGDCRLSLAIPKYGIFENINSLRELAQMPQWT 206 (254)
Q Consensus 127 iev~~vRp~DIp~yV~~G~aDlGIvG~DvL~E~~~d~~~l~~~l~dLgfG~CRLvVAvP~~~~~~dv~sl~dL~~~~~~~ 206 (254)
+++..+.+.+....|..|.+|+.+.+..+=.|.... +. . --.|-....++.++.+. ++++++||+
T Consensus 83 ~~~~~~~~~~~~~~l~~g~~D~~~~~~~~t~eR~~~----~~-f-s~py~~~~~~lvv~~~~---~~~s~~dL~------ 147 (259)
T PRK11917 83 IKLVAVNAKTRGPLLDNGSVDAVIATFTITPERKRI----YN-F-SEPYYQDAIGLLVLKEK---NYKSLADMK------ 147 (259)
T ss_pred EEEEEcChhhHHHHHHCCCccEEEecccCChhhhhe----ee-e-ccCceeeceEEEEECCC---CCCCHHHhC------
Confidence 555555666667789999999998876553443221 21 1 23566777888888873 467889986
Q ss_pred CCCCcEEEcCCCc----cHHHHHHHcCCceEEEEEcCC
Q 025329 207 AEKPLRVATGFTY----LGPKFMKDNGLKHVVFSTADG 240 (254)
Q Consensus 207 ~~r~lRVATkYPn----Larkyf~~~Gi~~veIi~l~G 240 (254)
++|||.-.-. ...+++++++++ ++++....
T Consensus 148 ---g~~V~v~~gs~~~~~l~~~~~~~~~~-~~~~~~~~ 181 (259)
T PRK11917 148 ---GANIGVAQAATTKKAIGEAAKKIGID-VKFSEFPD 181 (259)
T ss_pred ---CCeEEEecCCcHHHHHHHhhHhcCCc-eeEEecCC
Confidence 3567653322 223455556764 66665443
No 54
>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=80.25 E-value=7.3 Score=30.44 Aligned_cols=55 Identities=24% Similarity=0.258 Sum_probs=33.5
Q ss_pred CCeEEEee--cCcchhhhhhcCceeeeeeccceeecccCCCcceeeecCCCCcccEEEEEEEeCC
Q 025329 125 SNLEVWFQ--RPKDIVRKLLSGDLDLGIVGLDTVSEFGQGNEDLIIVHDALDYGDCRLSLAIPKY 187 (254)
Q Consensus 125 p~iev~~v--Rp~DIp~yV~~G~aDlGIvG~DvL~E~~~d~~~l~~~l~dLgfG~CRLvVAvP~~ 187 (254)
|++++.+. ..+++-..+.+|.+|+||+......+ . .++. ---++..+++++++++
T Consensus 27 P~i~l~~~~~~~~~~~~~l~~g~~Dl~i~~~~~~~~-~---~~~~----~~~l~~~~~~~v~~~~ 83 (195)
T cd08427 27 PDLEVHIVPGLSAELLARVDAGELDAAIVVEPPFPL-P---KDLV----WTPLVREPLVLIAPAE 83 (195)
T ss_pred CCceEEEEeCCcHHHHHHHHCCCCCEEEEcCCCCcc-c---cCce----EEEcccCcEEEEECCC
Confidence 44544443 46778899999999999986432110 1 1121 1234566778888776
No 55
>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=80.00 E-value=8.2 Score=30.40 Aligned_cols=91 Identities=23% Similarity=0.272 Sum_probs=49.4
Q ss_pred CCeEEEee--cCcchhhhhhcCceeeeeeccceeecccCCCcceeeecCCCCcccEEEEEEEeCCCcccc---ccchHHh
Q 025329 125 SNLEVWFQ--RPKDIVRKLLSGDLDLGIVGLDTVSEFGQGNEDLIIVHDALDYGDCRLSLAIPKYGIFEN---INSLREL 199 (254)
Q Consensus 125 p~iev~~v--Rp~DIp~yV~~G~aDlGIvG~DvL~E~~~d~~~l~~~l~dLgfG~CRLvVAvP~~~~~~d---v~sl~dL 199 (254)
|++++.+. ...++-..|.+|.+|+||+-...-. .++. ---++..+++++++.+.++.. ..+++||
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 44555443 4578889999999999997543211 1122 123556677777776632211 2467777
Q ss_pred hcCCcccCCCCcEEEcCC--CccHHHHHHHcCCc
Q 025329 200 AQMPQWTAEKPLRVATGF--TYLGPKFMKDNGLK 231 (254)
Q Consensus 200 ~~~~~~~~~r~lRVATkY--PnLarkyf~~~Gi~ 231 (254)
...+ -+.....+ .+...++|++.|+.
T Consensus 98 ~~~~------~i~~~~~~~~~~~~~~~~~~~~~~ 125 (197)
T cd08425 98 AAEP------LALLSPDFATRQHIDRYFQKQGIK 125 (197)
T ss_pred hcCC------cEecCCCccHHHHHHHHHHHcCCC
Confidence 6321 11111111 12345677788874
No 56
>COG4521 TauA ABC-type taurine transport system, periplasmic component [Inorganic ion transport and metabolism]
Probab=79.79 E-value=3.9 Score=38.69 Aligned_cols=90 Identities=22% Similarity=0.326 Sum_probs=58.5
Q ss_pred cchhhhhhcCceeeeeeccceeecccCC-C-cceeeecCCCCcccEEEEEEEeCCCccccccchHHhhcCCcccCCCCcE
Q 025329 135 KDIVRKLLSGDLDLGIVGLDTVSEFGQG-N-EDLIIVHDALDYGDCRLSLAIPKYGIFENINSLRELAQMPQWTAEKPLR 212 (254)
Q Consensus 135 ~DIp~yV~~G~aDlGIvG~DvL~E~~~d-~-~~l~~~l~dLgfG~CRLvVAvP~~~~~~dv~sl~dL~~~~~~~~~r~lR 212 (254)
.||.+-+++|.++||..|.-=|.-.... . -++.-+. =.+|...- +.+.++ ..|..++||. ++|
T Consensus 68 ~~vv~AlASGdvqiG~iGSsplaaAaSr~vpie~f~~~--~~ig~sEA-LVvr~g---sgI~kpeDL~---------GK~ 132 (334)
T COG4521 68 ASIVRALASGDVQIGNIGSSPLAAAASRQVPIEVFLLA--SQIGNSEA-LVVRKG---SGIEKPEDLI---------GKR 132 (334)
T ss_pred hHHHHHHhcCCccccccCCchhhHHhhcCCceEEeehh--hhcCccce-eeeecC---CCcCChHHhc---------cCe
Confidence 6999999999999999998877654322 1 1222222 25565553 344555 4688899986 478
Q ss_pred EEcCCCccHHHH----HHHcCCc--eEEEEEcC
Q 025329 213 VATGFTYLGPKF----MKDNGLK--HVVFSTAD 239 (254)
Q Consensus 213 VATkYPnLarky----f~~~Gi~--~veIi~l~ 239 (254)
||+-|...+.-. ++..|++ +|+|+.|.
T Consensus 133 iavPFvSTtHysLLaaLkhw~idp~~V~IlNl~ 165 (334)
T COG4521 133 IAVPFVSTTHYSLLAALKHWGIDPGQVEILNLQ 165 (334)
T ss_pred eccceeehhHHHHHHHHHHcCCCccceeEeccC
Confidence 998876544322 4566773 57777654
No 57
>COG0715 TauA ABC-type nitrate/sulfonate/bicarbonate transport systems, periplasmic components [Inorganic ion transport and metabolism]
Probab=79.74 E-value=4.1 Score=36.93 Aligned_cols=95 Identities=22% Similarity=0.188 Sum_probs=58.6
Q ss_pred cCcchhhhhhcCceeeee-eccceeecc-cCCCcceeeecCCCCccc-EEEEEEEeCCCccccccchHHhhcCCcccCCC
Q 025329 133 RPKDIVRKLLSGDLDLGI-VGLDTVSEF-GQGNEDLIIVHDALDYGD-CRLSLAIPKYGIFENINSLRELAQMPQWTAEK 209 (254)
Q Consensus 133 Rp~DIp~yV~~G~aDlGI-vG~DvL~E~-~~d~~~l~~~l~dLgfG~-CRLvVAvP~~~~~~dv~sl~dL~~~~~~~~~r 209 (254)
...++...+..|.+|+|. .+.+++.=. +.....+.. +--+..+. ....+ ++.+ ..+++++||+
T Consensus 70 ~~~~~~~~l~~G~~D~a~~~~~~~~~~~~~~~g~pv~~-va~~~~~~~~~~i~-~~~~---~~i~~~adlk--------- 135 (335)
T COG0715 70 GGAPVLEALAAGALDFAVYYTGDTPLIAAGAAGAPVKV-VAALVQNGNGIALL-VLKD---SGIKSVADLK--------- 135 (335)
T ss_pred CChHHHHHHhcCCcCccccccCchHHHHhhccCCCeEE-eeecccCCceeEEE-eccC---CCcccccCCC---------
Confidence 457888999999999994 333444222 111113332 33455664 44444 4444 3577778875
Q ss_pred CcEEEcCCCc-----cHHHHHHHcCC--ceEEEEEcCCc
Q 025329 210 PLRVATGFTY-----LGPKFMKDNGL--KHVVFSTADGA 241 (254)
Q Consensus 210 ~lRVATkYPn-----Larkyf~~~Gi--~~veIi~l~GS 241 (254)
++|||..++. +.+.++++.|+ ++++++.+..+
T Consensus 136 Gk~vg~~~~~~~~~~~l~~~L~~~Gl~~~dv~~v~~~~~ 174 (335)
T COG0715 136 GKKVGVPFGGSTSDFLLRYALAKAGLDPDDVELVNLPPA 174 (335)
T ss_pred CceEEEeCCCchHHHHHHHHHHHcCCCcccceEEeeCcH
Confidence 5789988876 46777888998 34666766554
No 58
>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=79.74 E-value=5.4 Score=36.32 Aligned_cols=100 Identities=15% Similarity=0.165 Sum_probs=64.7
Q ss_pred ceEEEecCCCCChHHHHHHHHhCCC-ccCCCCC----CceEeecCCCCCeEEEeecCcchhhhhhcCceeeeeeccceee
Q 025329 83 EIRLGLPSKGRMAADTLDLLKDCQL-SVKQVNP----RQYVAQIPQLSNLEVWFQRPKDIVRKLLSGDLDLGIVGLDTVS 157 (254)
Q Consensus 83 ~LrIALPsKGRL~e~tl~LL~~aGi-~v~~~~~----R~L~~~~~~~p~iev~~vRp~DIp~yV~~G~aDlGIvG~DvL~ 157 (254)
--+||||+.-.-..-.+.+|+++|+ +++...+ =.-+... -.+++|.-+.+.-+|+.+.+ +|++++.-+...
T Consensus 97 Ga~VaIpnD~sN~~RaL~lLq~aGLI~Lk~~~~~~~t~~DI~~N--pk~l~~~evd~~~l~~~l~d--vD~avi~~~~a~ 172 (237)
T PF03180_consen 97 GATVAIPNDPSNQARALKLLQEAGLITLKDGVGLTATVDDITEN--PKNLKFKEVDAAQLPRALDD--VDAAVINGNYAL 172 (237)
T ss_dssp TEEEEEESSHHHHHHHHHHHHHTTSEEE-TT-GCC-SGGGEEEE--TTSEEEEEE-GGGHHHHTTT--SSEEEE-HHHHH
T ss_pred CCEEEEeCCccchhHHHHHHHhCCeEEEcCCCCCccChhhhhhc--ccCceEEEecHhhHHhhccc--CCEEEecHhHHH
Confidence 3689999887888889999999998 3333211 1122222 24799999999999999988 999999999999
Q ss_pred cccCCCcc-eeeecCCCCcccEEEEEEEeCC
Q 025329 158 EFGQGNED-LIIVHDALDYGDCRLSLAIPKY 187 (254)
Q Consensus 158 E~~~d~~~-l~~~l~dLgfG~CRLvVAvP~~ 187 (254)
+.|.+..+ ++. .++..-..--.++++..+
T Consensus 173 ~agl~~~~~~~~-~e~~~~~~y~n~lv~r~~ 202 (237)
T PF03180_consen 173 DAGLDPKKDLLF-EEPDADKPYANVLVVRED 202 (237)
T ss_dssp HTT--CCCHSSE-E-SSSSCGGEEEEEEEGG
T ss_pred HcCcCcccceee-eecccCcceeEEEEEECC
Confidence 98877543 332 221223444456666554
No 59
>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=79.19 E-value=7 Score=30.96 Aligned_cols=91 Identities=20% Similarity=0.259 Sum_probs=49.0
Q ss_pred CCeEEEee--cCcchhhhhhcCceeeeeeccceeecccCCCcceeeecCCCCcccEEEEEEEeCCCcccc--ccchHHhh
Q 025329 125 SNLEVWFQ--RPKDIVRKLLSGDLDLGIVGLDTVSEFGQGNEDLIIVHDALDYGDCRLSLAIPKYGIFEN--INSLRELA 200 (254)
Q Consensus 125 p~iev~~v--Rp~DIp~yV~~G~aDlGIvG~DvL~E~~~d~~~l~~~l~dLgfG~CRLvVAvP~~~~~~d--v~sl~dL~ 200 (254)
|++++-+. ...++...+..|.+|+||+-... + . .++.. -.++.-+++++++.+..+.. --+++||.
T Consensus 27 P~i~l~~~~~~~~~~~~~l~~~~~Dl~i~~~~~--~-~---~~~~~----~~l~~~~~~~~~~~~~~l~~~~~~~~~~l~ 96 (196)
T cd08457 27 PNLHLSLMGLSSSQVLEAVASGRADLGIADGPL--E-E---RQGFL----IETRSLPAVVAVPMGHPLAQLDVVSPQDLA 96 (196)
T ss_pred CCeEEEEEecCcHHHHHHHHcCCccEEEeccCC--C-C---CCcEE----EEeccCCeEEEeeCCCccccCCccCHHHhC
Confidence 44555443 44788899999999999975331 1 1 11221 12345667777776532221 23567776
Q ss_pred cCCcccCCCCcEEEcC--CCccHHHHHHHcCCc
Q 025329 201 QMPQWTAEKPLRVATG--FTYLGPKFMKDNGLK 231 (254)
Q Consensus 201 ~~~~~~~~r~lRVATk--YPnLarkyf~~~Gi~ 231 (254)
+.+ + +..... +.....+++++.|++
T Consensus 97 ~~~-~-----i~~~~~~~~~~~~~~~~~~~~~~ 123 (196)
T cd08457 97 GER-I-----ITLENGYLFRMRVEVALGKIGVK 123 (196)
T ss_pred CCc-e-----EecCCCccHHHHHHHHHHHcCCC
Confidence 421 1 111111 223455677777774
No 60
>PF13379 NMT1_2: NMT1-like family; PDB: 2G29_A 3UN6_A 2I4C_A 2I49_A 2I4B_A 2I48_A 3QSL_A.
Probab=78.71 E-value=6.1 Score=34.72 Aligned_cols=61 Identities=20% Similarity=0.308 Sum_probs=46.9
Q ss_pred CceEEEecCCCCChHHHHH-HHHhCCCccCCCCCCceEeecCCCCCeEEEeecCcchhhhhhcCceeeeeecccee
Q 025329 82 DEIRLGLPSKGRMAADTLD-LLKDCQLSVKQVNPRQYVAQIPQLSNLEVWFQRPKDIVRKLLSGDLDLGIVGLDTV 156 (254)
Q Consensus 82 ~~LrIALPsKGRL~e~tl~-LL~~aGi~v~~~~~R~L~~~~~~~p~iev~~vRp~DIp~yV~~G~aDlGIvG~DvL 156 (254)
.-.|||+|..|...+-.+. +|++.|++. . .++++..+.+.+++..+..|.+|...+..-+.
T Consensus 120 kGk~i~~~~~gs~~~~~l~~~l~~~Gl~~-------------~-~dv~~~~~~~~~~~~al~~g~iDa~~~~eP~~ 181 (252)
T PF13379_consen 120 KGKKIAVPFPGSTHDMLLRYLLKKAGLDP-------------K-DDVTLVNVPPPEMVAALRAGEIDAAVLWEPFA 181 (252)
T ss_dssp STEEEEESSTTSHHHHHHHHHHHHTT--T-------------T-TSSEEEE--GHHHHHHHHTTS-SEEEEETTHH
T ss_pred CCcEEEEcCCCCHHHHHHHHHHHhCCCCc-------------c-cceEEEecCHHHHHHHHhCCCcCEEEecCCHH
Confidence 5689999889998888765 899999964 1 24788888889999999999999999977764
No 61
>PF13379 NMT1_2: NMT1-like family; PDB: 2G29_A 3UN6_A 2I4C_A 2I49_A 2I4B_A 2I48_A 3QSL_A.
Probab=78.53 E-value=5.1 Score=35.24 Aligned_cols=103 Identities=23% Similarity=0.299 Sum_probs=56.9
Q ss_pred ecCcchhhhhhcCceeeeeecccee--ecccC-C-CcceeeecCCCCcccEEEEEEEeCCC-ccccccchHHhhcCCccc
Q 025329 132 QRPKDIVRKLLSGDLDLGIVGLDTV--SEFGQ-G-NEDLIIVHDALDYGDCRLSLAIPKYG-IFENINSLRELAQMPQWT 206 (254)
Q Consensus 132 vRp~DIp~yV~~G~aDlGIvG~DvL--~E~~~-d-~~~l~~~l~dLgfG~CRLvVAvP~~~-~~~dv~sl~dL~~~~~~~ 206 (254)
--..|+..-+..|.+|+|.+-...+ ...+. + ..+++ .+..+..+.-. +.+.++. ...++++++||....
T Consensus 43 ~~g~~~~~al~~G~iD~a~~~~~~~~~~~~g~~~~~~~~~-~~~~~~~~g~~--lvv~~~~~~~~~~~~~~dl~~~~--- 116 (252)
T PF13379_consen 43 ASGADILEALAAGEIDIAFVLAPALIAIAKGAGGPDVDIV-VLAGLSQNGNA--LVVRNDLKDASDIKSLADLIKKR--- 116 (252)
T ss_dssp SSHHHHHHHHHCTSSSEEEECTHHHHHHHTTTTT----EE-EEEECSBSSEE--EEECGGGTTCSTTCCGHHHHHTC---
T ss_pred CCHHHHHHHHHcCCCCEEEechHHHHHHHcCCCCcccceE-EeeccCCCceE--EEEcCccccCCCccCHHHHHhhh---
Confidence 3458999999999999999922222 23333 0 11233 33345544432 3333320 015688999984321
Q ss_pred CC-CCcEEEcCCCc-----cHHHHHHHcCCce---EEEEEcCC
Q 025329 207 AE-KPLRVATGFTY-----LGPKFMKDNGLKH---VVFSTADG 240 (254)
Q Consensus 207 ~~-r~lRVATkYPn-----Larkyf~~~Gi~~---veIi~l~G 240 (254)
.. +++|||+-.+. +.+.+|+++|++. ++++.+..
T Consensus 117 ~~~kGk~i~~~~~gs~~~~~l~~~l~~~Gl~~~~dv~~~~~~~ 159 (252)
T PF13379_consen 117 KAQKGKKIAVPFPGSTHDMLLRYLLKKAGLDPKDDVTLVNVPP 159 (252)
T ss_dssp CSCSTEEEEESSTTSHHHHHHHHHHHHTT--TTTSSEEEE--G
T ss_pred cccCCcEEEEcCCCCHHHHHHHHHHHhCCCCcccceEEEecCH
Confidence 11 57999996653 4567788889843 67765543
No 62
>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=77.94 E-value=16 Score=27.75 Aligned_cols=64 Identities=27% Similarity=0.344 Sum_probs=38.9
Q ss_pred eEEEeecCcchhhhhhcCceeeeeeccceeecccCCCcceeeecCCCCcccEEEEEEEeCCCcccc--ccchHHhh
Q 025329 127 LEVWFQRPKDIVRKLLSGDLDLGIVGLDTVSEFGQGNEDLIIVHDALDYGDCRLSLAIPKYGIFEN--INSLRELA 200 (254)
Q Consensus 127 iev~~vRp~DIp~yV~~G~aDlGIvG~DvL~E~~~d~~~l~~~l~dLgfG~CRLvVAvP~~~~~~d--v~sl~dL~ 200 (254)
+++......|+...+.+|.+|+||+-.+. .+ .++. -..++..+++++++.+.+... .-+++||.
T Consensus 31 i~~~~~~~~~~~~~l~~g~~D~~i~~~~~-~~-----~~~~----~~~l~~~~~~~~~~~~~~~~~~~~~~~~~l~ 96 (197)
T cd05466 31 LSLVEGGSSELLEALLEGELDLAIVALPV-DD-----PGLE----SEPLFEEPLVLVVPPDHPLAKRKSVTLADLA 96 (197)
T ss_pred EEEEECChHHHHHHHHcCCceEEEEcCCC-CC-----Ccce----EeeeeccceEEEecCCCCcccCcEecHHHHc
Confidence 33434456689999999999999986553 11 1122 124566778888877642111 12567775
No 63
>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=77.64 E-value=9 Score=30.68 Aligned_cols=92 Identities=18% Similarity=0.231 Sum_probs=50.0
Q ss_pred CCeEEEee--cCcchhhhhhcCceeeeeeccceeecccCCCcceeeecCCCCcccEEEEEEEeCCCccc--cccchHHhh
Q 025329 125 SNLEVWFQ--RPKDIVRKLLSGDLDLGIVGLDTVSEFGQGNEDLIIVHDALDYGDCRLSLAIPKYGIFE--NINSLRELA 200 (254)
Q Consensus 125 p~iev~~v--Rp~DIp~yV~~G~aDlGIvG~DvL~E~~~d~~~l~~~l~dLgfG~CRLvVAvP~~~~~~--dv~sl~dL~ 200 (254)
|++++.+. ...++-..+.+|.+|+||+....-.+.+ +. ...+..-+++++++.+.++. ..-+++||.
T Consensus 27 P~i~v~~~~~~~~~~~~~l~~g~~D~~i~~~~~~~~~~-----~~----~~~l~~~~~~~v~~~~hpl~~~~~i~~~~l~ 97 (198)
T cd08413 27 PKVKLSLHQGTPSQIAEMVLKGEADIAIATEALDDHPD-----LV----TLPCYRWNHCVIVPPGHPLADLGPLTLEDLA 97 (198)
T ss_pred CceEEEEEeCCHHHHHHHHHcCCCCEEEEccCCCCCCC-----cE----EEEeeeeeEEEEecCCCcccccCCCCHHHHh
Confidence 55555544 4467889999999999997532111111 21 12344557777777764322 223567776
Q ss_pred cCCcccCCCCcEEEcC--CCccHHHHHHHcCCc
Q 025329 201 QMPQWTAEKPLRVATG--FTYLGPKFMKDNGLK 231 (254)
Q Consensus 201 ~~~~~~~~r~lRVATk--YPnLarkyf~~~Gi~ 231 (254)
..+- +..... +....+++|++.|++
T Consensus 98 ~~~~------i~~~~~~~~~~~~~~~~~~~~~~ 124 (198)
T cd08413 98 QYPL------ITYDFGFTGRSSIDRAFARAGLE 124 (198)
T ss_pred cCCE------EECCCCccHHHHHHHHHHHcCCC
Confidence 4211 111111 123456678888874
No 64
>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=77.29 E-value=7.1 Score=30.84 Aligned_cols=67 Identities=25% Similarity=0.345 Sum_probs=38.9
Q ss_pred CCeEEEee--cCcchhhhhhcCceeeeeeccceeecccCCCcceeeecCCCCcccEEEEEEEeCCCccc--cccchHHhh
Q 025329 125 SNLEVWFQ--RPKDIVRKLLSGDLDLGIVGLDTVSEFGQGNEDLIIVHDALDYGDCRLSLAIPKYGIFE--NINSLRELA 200 (254)
Q Consensus 125 p~iev~~v--Rp~DIp~yV~~G~aDlGIvG~DvL~E~~~d~~~l~~~l~dLgfG~CRLvVAvP~~~~~~--dv~sl~dL~ 200 (254)
|++++.+. ...++...+..|.+|+||+....- + .++. -..++.-+++++++.+.++. ..-+++||.
T Consensus 28 P~i~i~i~~~~~~~~~~~l~~~~~Dl~i~~~~~~-~-----~~~~----~~~l~~~~~~~v~~~~~pl~~~~~~~~~~l~ 97 (200)
T cd08411 28 PKLRLYLREDQTERLLEKLRSGELDAALLALPVD-E-----PGLE----EEPLFDEPFLLAVPKDHPLAKRKSVTPEDLA 97 (200)
T ss_pred CCcEEEEEeCcHHHHHHHHHcCCccEEEEeccCC-C-----CCce----EEEeeccceEEEecCCCCccccCccCHHHHc
Confidence 55555554 567889999999999999753211 1 1121 12344555666666653221 223677776
Q ss_pred c
Q 025329 201 Q 201 (254)
Q Consensus 201 ~ 201 (254)
+
T Consensus 98 ~ 98 (200)
T cd08411 98 G 98 (200)
T ss_pred C
Confidence 4
No 65
>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=77.21 E-value=6.7 Score=30.61 Aligned_cols=88 Identities=22% Similarity=0.344 Sum_probs=48.4
Q ss_pred EEEeecCcchhhhhhcCceeeeeeccceeecccCCCcceeeecCCCCcccEEEEEEEeCCCccc--cccchHHhhcCCcc
Q 025329 128 EVWFQRPKDIVRKLLSGDLDLGIVGLDTVSEFGQGNEDLIIVHDALDYGDCRLSLAIPKYGIFE--NINSLRELAQMPQW 205 (254)
Q Consensus 128 ev~~vRp~DIp~yV~~G~aDlGIvG~DvL~E~~~d~~~l~~~l~dLgfG~CRLvVAvP~~~~~~--dv~sl~dL~~~~~~ 205 (254)
++......++...+.+|.+|+||+.... .+ .++. --.++..+++++++.+.+.. +.-+++||.+.+ +
T Consensus 31 ~i~~~~~~~~~~~l~~g~~Dl~i~~~~~-~~-----~~~~----~~~l~~~~~~~~~~~~~~l~~~~~~~~~~l~~~~-~ 99 (197)
T cd08419 31 SLRVGNREQVLERLADNEDDLAIMGRPP-ED-----LDLV----AEPFLDNPLVVIAPPDHPLAGQKRIPLERLAREP-F 99 (197)
T ss_pred EEEECCHHHHHHHHhcCCccEEEecCCC-CC-----CCeE----EEEeccCCEEEEecCCCCCcCCCCcCHHHHhCCC-c
Confidence 3333456778889999999999975322 11 1222 12455667777777663222 123577876421 1
Q ss_pred cCCCCcEEE--cCCCccHHHHHHHcCCc
Q 025329 206 TAEKPLRVA--TGFTYLGPKFMKDNGLK 231 (254)
Q Consensus 206 ~~~r~lRVA--TkYPnLarkyf~~~Gi~ 231 (254)
+... +.+.+...++|++.|++
T Consensus 100 -----i~~~~~~~~~~~~~~~~~~~~~~ 122 (197)
T cd08419 100 -----LLREPGSGTRLAMERFFAEHGVT 122 (197)
T ss_pred -----EEecCCCcHHHHHHHHHHHCCCC
Confidence 1111 11223456678888874
No 66
>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=75.57 E-value=8.9 Score=36.24 Aligned_cols=87 Identities=15% Similarity=0.159 Sum_probs=51.6
Q ss_pred CcchhhhhhcCceeeeeecccee----ecccCCCcceeeecCCCCcccEEEEEEEeCCCccccccchHHhhcCCcccCCC
Q 025329 134 PKDIVRKLLSGDLDLGIVGLDTV----SEFGQGNEDLIIVHDALDYGDCRLSLAIPKYGIFENINSLRELAQMPQWTAEK 209 (254)
Q Consensus 134 p~DIp~yV~~G~aDlGIvG~DvL----~E~~~d~~~l~~~l~dLgfG~CRLvVAvP~~~~~~dv~sl~dL~~~~~~~~~r 209 (254)
..|.-..+..|.+|+|..|.+-. .-.+.+. .++ ...+-.-|.--+ .+++ +++++||+
T Consensus 45 ~~~~l~Al~aG~iD~~~~g~~~~~~~~~a~g~~~-~iv-~v~~~~~g~~~i--vv~~------i~svaDLK--------- 105 (328)
T TIGR03427 45 YVESINQYTAGKFDGCTMTNMDALTIPAAGGVDT-TAL-IVGDFSNGNDGI--VLKG------GKSLADLK--------- 105 (328)
T ss_pred hHHHHHHHHcCCCCEEeecCHHHHHHHHhCCCCe-EEE-EEEccCCCceEE--EECC------CCCHHHcC---------
Confidence 34555566699999999887532 2333321 122 222333333222 2232 68999986
Q ss_pred CcEEEcCCC----ccHHHHHHHcCCc--eEEEEEcC
Q 025329 210 PLRVATGFT----YLGPKFMKDNGLK--HVVFSTAD 239 (254)
Q Consensus 210 ~lRVATkYP----nLarkyf~~~Gi~--~veIi~l~ 239 (254)
++|||+..- .+..+.|++.|++ +|+++.+.
T Consensus 106 GKkIav~~gs~~~~ll~~aL~~aGL~~~DV~~v~~~ 141 (328)
T TIGR03427 106 GQKVNLVELSVSHYLLARALESVGLSEKDVKVVNTS 141 (328)
T ss_pred CCEEeccCCChHHHHHHHHHHHcCCCHHHeEEEeCC
Confidence 578986432 3455778889984 68998775
No 67
>PRK11242 DNA-binding transcriptional regulator CynR; Provisional
Probab=75.31 E-value=11 Score=33.06 Aligned_cols=67 Identities=19% Similarity=0.157 Sum_probs=41.4
Q ss_pred CCeEEE--eecCcchhhhhhcCceeeeeeccceeecccCCCcceeeecCCCCcccEEEEEEEeCCCcccc---ccchHHh
Q 025329 125 SNLEVW--FQRPKDIVRKLLSGDLDLGIVGLDTVSEFGQGNEDLIIVHDALDYGDCRLSLAIPKYGIFEN---INSLREL 199 (254)
Q Consensus 125 p~iev~--~vRp~DIp~yV~~G~aDlGIvG~DvL~E~~~d~~~l~~~l~dLgfG~CRLvVAvP~~~~~~d---v~sl~dL 199 (254)
|++++. .....++...+.+|.+|+||+..+.- ..++. --.++.-+++++++.+.+... .-+++||
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 44667888999999999999743321 12232 235667888888887643221 1456777
Q ss_pred hc
Q 025329 200 AQ 201 (254)
Q Consensus 200 ~~ 201 (254)
..
T Consensus 188 ~~ 189 (296)
T PRK11242 188 AD 189 (296)
T ss_pred hC
Confidence 64
No 68
>PRK10216 DNA-binding transcriptional regulator YidZ; Provisional
Probab=75.02 E-value=13 Score=33.57 Aligned_cols=101 Identities=12% Similarity=0.075 Sum_probs=51.7
Q ss_pred CCeEEEee-cCcchhhhhhcCceeeeeeccceeecccCCCcceeeecCCCCcccEEEEEEEeCCCccc-cccchHHhhcC
Q 025329 125 SNLEVWFQ-RPKDIVRKLLSGDLDLGIVGLDTVSEFGQGNEDLIIVHDALDYGDCRLSLAIPKYGIFE-NINSLRELAQM 202 (254)
Q Consensus 125 p~iev~~v-Rp~DIp~yV~~G~aDlGIvG~DvL~E~~~d~~~l~~~l~dLgfG~CRLvVAvP~~~~~~-dv~sl~dL~~~ 202 (254)
|++++.+. ...|+...+.+|.+|+||+......+........-..+.-..+..-++++++|++-++. .--+++||.+.
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 34444333 23468899999999999986432211100000000001123445667778888764321 11246777642
Q ss_pred CcccCCCCcEE--EcCCCccHHHHHHHcCCc
Q 025329 203 PQWTAEKPLRV--ATGFTYLGPKFMKDNGLK 231 (254)
Q Consensus 203 ~~~~~~r~lRV--ATkYPnLarkyf~~~Gi~ 231 (254)
+ | +.. .+.+.....++|++.|+.
T Consensus 204 ~-~-----i~~~~~~~~~~~~~~~~~~~~~~ 228 (319)
T PRK10216 204 P-H-----ISICWEQSDTWALDDVLQELGRE 228 (319)
T ss_pred C-C-----eEecCCCCCcchHHHHHHHhCCc
Confidence 2 1 111 123444567888888874
No 69
>PRK12682 transcriptional regulator CysB-like protein; Reviewed
Probab=74.98 E-value=8.6 Score=34.55 Aligned_cols=92 Identities=24% Similarity=0.383 Sum_probs=53.7
Q ss_pred CCeEEEe--ecCcchhhhhhcCceeeeeeccceeecccCCCcceeeecCCCCcccEEEEEEEeCCCccc--cccchHHhh
Q 025329 125 SNLEVWF--QRPKDIVRKLLSGDLDLGIVGLDTVSEFGQGNEDLIIVHDALDYGDCRLSLAIPKYGIFE--NINSLRELA 200 (254)
Q Consensus 125 p~iev~~--vRp~DIp~yV~~G~aDlGIvG~DvL~E~~~d~~~l~~~l~dLgfG~CRLvVAvP~~~~~~--dv~sl~dL~ 200 (254)
|++++.+ ....++...+..|.+|+||+..+..... ++. ...++..++++++|.+.+.. ..-+++||.
T Consensus 120 P~i~i~i~~~~~~~~~~~l~~g~~D~~i~~~~~~~~~-----~l~----~~~l~~~~~~~~~~~~~pl~~~~~~~~~~L~ 190 (309)
T PRK12682 120 PKVNLSLHQGSPDEIARMVISGEADIGIATESLADDP-----DLA----TLPCYDWQHAVIVPPDHPLAQEERITLEDLA 190 (309)
T ss_pred CCeEEEEecCCHHHHHHHHHcCCccEEEecCcccCCC-----cce----EEEeeeeeEEEEecCCCccccCCCcCHHHHh
Confidence 4554444 3456899999999999999865431111 122 34678889999998874221 223567775
Q ss_pred cCCcccCCCCcEEEcCCC--ccHHHHHHHcCCc
Q 025329 201 QMPQWTAEKPLRVATGFT--YLGPKFMKDNGLK 231 (254)
Q Consensus 201 ~~~~~~~~r~lRVATkYP--nLarkyf~~~Gi~ 231 (254)
..+ -+.....++ +...++|.+.|+.
T Consensus 191 ~~~------~i~~~~~~~~~~~~~~~~~~~g~~ 217 (309)
T PRK12682 191 EYP------LITYHPGFTGRSRIDRAFAAAGLQ 217 (309)
T ss_pred cCC------ceeeCCCccHHHHHHHHHHHcCCC
Confidence 321 111112222 2345677788874
No 70
>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=74.69 E-value=10 Score=29.65 Aligned_cols=71 Identities=25% Similarity=0.309 Sum_probs=41.2
Q ss_pred CCeEEEee--cCcchhhhhhcCceeeeeeccce-eecccCCCcceeeecCCCCcccEEEEEEEeCCCccc--cccchHHh
Q 025329 125 SNLEVWFQ--RPKDIVRKLLSGDLDLGIVGLDT-VSEFGQGNEDLIIVHDALDYGDCRLSLAIPKYGIFE--NINSLREL 199 (254)
Q Consensus 125 p~iev~~v--Rp~DIp~yV~~G~aDlGIvG~Dv-L~E~~~d~~~l~~~l~dLgfG~CRLvVAvP~~~~~~--dv~sl~dL 199 (254)
|++++.+. ...++...+.+|.+|+||+.... ..+.. ..++. -..++..+++++++.+.++. ..-+++||
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 44545444 45688999999999999985421 00000 11222 12456778888887764322 13467777
Q ss_pred hc
Q 025329 200 AQ 201 (254)
Q Consensus 200 ~~ 201 (254)
.+
T Consensus 101 ~~ 102 (200)
T cd08423 101 AD 102 (200)
T ss_pred cC
Confidence 53
No 71
>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=74.49 E-value=7.7 Score=31.68 Aligned_cols=86 Identities=20% Similarity=0.157 Sum_probs=54.8
Q ss_pred EEEeecCcchhhhhhcCceeeeeeccceeecccCCCcceeeecCCCCcccEEEEEEEeCCC--ccccccchHHhhcCCcc
Q 025329 128 EVWFQRPKDIVRKLLSGDLDLGIVGLDTVSEFGQGNEDLIIVHDALDYGDCRLSLAIPKYG--IFENINSLRELAQMPQW 205 (254)
Q Consensus 128 ev~~vRp~DIp~yV~~G~aDlGIvG~DvL~E~~~d~~~l~~~l~dLgfG~CRLvVAvP~~~--~~~dv~sl~dL~~~~~~ 205 (254)
++..+.-.++-..+.+|.+|+++.+.-+-.|.... +. . --.+..-..++.++.+. .+..+++++||.
T Consensus 41 ~~~~~~~~~~~~~l~~g~~D~~~~~~~~~~~r~~~---~~-~--s~p~~~~~~~~~~~~~~~~~~~~~~~~~dl~----- 109 (225)
T PF00497_consen 41 EFVPMPWSRLLEMLENGKADIIIGGLSITPERAKK---FD-F--SDPYYSSPYVLVVRKGDAPPIKTIKSLDDLK----- 109 (225)
T ss_dssp EEEEEEGGGHHHHHHTTSSSEEESSEB-BHHHHTT---EE-E--ESESEEEEEEEEEETTSTCSTSSHSSGGGGT-----
T ss_pred ceeeccccccccccccccccccccccccccccccc---cc-c--cccccchhheeeeccccccccccccchhhhc-----
Confidence 34444557888899999999998765544444221 11 1 12566778888888542 345666777774
Q ss_pred cCCCCcEEEcCCCccHHHHHHHc
Q 025329 206 TAEKPLRVATGFTYLGPKFMKDN 228 (254)
Q Consensus 206 ~~~r~lRVATkYPnLarkyf~~~ 228 (254)
++||++--=....++|++.
T Consensus 110 ----~~~i~~~~g~~~~~~l~~~ 128 (225)
T PF00497_consen 110 ----GKRIGVVRGSSYADYLKQQ 128 (225)
T ss_dssp ----TSEEEEETTSHHHHHHHHH
T ss_pred ----CcccccccchhHHHHhhhh
Confidence 3578776656677777774
No 72
>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=74.38 E-value=26 Score=28.08 Aligned_cols=90 Identities=19% Similarity=0.178 Sum_probs=49.6
Q ss_pred CCeEEEee--cCcchhhhhhcCceeeeeeccceeecccCCCcceeeecCCCCcccEEEEEEEeCCCccc--cccchHHhh
Q 025329 125 SNLEVWFQ--RPKDIVRKLLSGDLDLGIVGLDTVSEFGQGNEDLIIVHDALDYGDCRLSLAIPKYGIFE--NINSLRELA 200 (254)
Q Consensus 125 p~iev~~v--Rp~DIp~yV~~G~aDlGIvG~DvL~E~~~d~~~l~~~l~dLgfG~CRLvVAvP~~~~~~--dv~sl~dL~ 200 (254)
|++++.+. ...++-..+.+|.+|+||+-... +.. .++. ...+...+++++++.+.++. ..-+++||.
T Consensus 27 P~~~i~i~~~~~~~~~~~l~~g~~Dl~i~~~~~--~~~---~~~~----~~~l~~~~~~~v~~~~hpl~~~~~i~~~~l~ 97 (198)
T cd08443 27 PRVSLQMHQGSPTQIAEMVSKGLVDFAIATEAL--HDY---DDLI----TLPCYHWNRCVVVKRDHPLADKQSISIEELA 97 (198)
T ss_pred CCeEEEEEeCCHHHHHHHHHCCCccEEEEeccc--ccc---CCce----EeeeeeceEEEEEcCCCccccCCCCCHHHHh
Confidence 55555544 45688999999999999963211 011 1122 23456667788877664321 223567775
Q ss_pred cCCcccCCCCcEEEcCC----CccHHHHHHHcCCc
Q 025329 201 QMPQWTAEKPLRVATGF----TYLGPKFMKDNGLK 231 (254)
Q Consensus 201 ~~~~~~~~r~lRVATkY----PnLarkyf~~~Gi~ 231 (254)
+. .-|.... .+...++|++.|++
T Consensus 98 ~~--------~~i~~~~~~~~~~~~~~~~~~~~~~ 124 (198)
T cd08443 98 TY--------PIVTYTFGFTGRSELDTAFNRAGLT 124 (198)
T ss_pred cC--------CEEEecCCccHHHHHHHHHHHcCCC
Confidence 32 1232222 23345677777874
No 73
>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=74.12 E-value=11 Score=32.65 Aligned_cols=95 Identities=14% Similarity=0.107 Sum_probs=53.5
Q ss_pred CcchhhhhhcCceeeeeeccceeecc--cCCCcceeeecC-CCCcccEEEEEEEeCCCccccccchHHhhcCCcccCCCC
Q 025329 134 PKDIVRKLLSGDLDLGIVGLDTVSEF--GQGNEDLIIVHD-ALDYGDCRLSLAIPKYGIFENINSLRELAQMPQWTAEKP 210 (254)
Q Consensus 134 p~DIp~yV~~G~aDlGIvG~DvL~E~--~~d~~~l~~~l~-dLgfG~CRLvVAvP~~~~~~dv~sl~dL~~~~~~~~~r~ 210 (254)
..++-..+..|.+|+++.|.....+. ..+...+..... .-|.-....+++++.+ ..+++++||. +
T Consensus 74 ~~~~~~~l~~g~~Di~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lvv~~d---~~i~~~~dL~---------g 141 (254)
T TIGR01098 74 YSAVIEAMRFGRVDIAWFGPSSYVLAHYRANAEVFALTAVSTDGSPGYYSVIIVKAD---SPIKSLKDLK---------G 141 (254)
T ss_pred HHHHHHHHHcCCccEEEECcHHHHHHHHhcCCceEEeeccccCCCCceEEEEEEECC---CCCCChHHhc---------C
Confidence 35678889999999999998776643 111111111000 1121234567888887 3578889985 3
Q ss_pred cEEEcCCC------ccHHHHHHHc-CCc----eEEEEEcCC
Q 025329 211 LRVATGFT------YLGPKFMKDN-GLK----HVVFSTADG 240 (254)
Q Consensus 211 lRVATkYP------nLarkyf~~~-Gi~----~veIi~l~G 240 (254)
+||+.--| .+..+++.++ |++ .++++...+
T Consensus 142 k~I~~~~~~s~~~~~~~~~~l~~~~~~~~~~~~~~i~~~~~ 182 (254)
T TIGR01098 142 KTFAFGDPASTSGYLVPRYQLKKEGGLDADGFFSEVVFSGS 182 (254)
T ss_pred CEEEeeCCCCccchHhHHHHHHHhcCCChHHhhhheeecCc
Confidence 67775322 2335566554 432 145655543
No 74
>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=73.91 E-value=10 Score=30.30 Aligned_cols=67 Identities=18% Similarity=0.256 Sum_probs=39.4
Q ss_pred CCeEEEee--cCcchhhhhhcCceeeeeeccceeecccCCCcceeeecCCCCcccEEEEEEEeCCCcccc---ccchHHh
Q 025329 125 SNLEVWFQ--RPKDIVRKLLSGDLDLGIVGLDTVSEFGQGNEDLIIVHDALDYGDCRLSLAIPKYGIFEN---INSLREL 199 (254)
Q Consensus 125 p~iev~~v--Rp~DIp~yV~~G~aDlGIvG~DvL~E~~~d~~~l~~~l~dLgfG~CRLvVAvP~~~~~~d---v~sl~dL 199 (254)
|++++-+. ...++-..|.+|.+|+||+.... .. .++. ...++..+++++++++-+... .-+++||
T Consensus 28 P~i~l~i~~~~~~~~~~~l~~~~~Dl~i~~~~~-~~-----~~~~----~~~l~~~~~~~v~~~~hpl~~~~~~i~~~dL 97 (203)
T cd08445 28 PDVEIELIEMTTVQQIEALKEGRIDVGFGRLRI-ED-----PAIR----RIVLREEPLVVALPAGHPLAQEKAPLTLAQL 97 (203)
T ss_pred CCeEEEEEeCChHHHHHHHHcCCCcEEEecCCC-CC-----CCce----eEEEEeccEEEEeeCCCCCccCCCCcCHHHh
Confidence 45555444 56789999999999999963211 11 1222 123456677788777632211 2356787
Q ss_pred hc
Q 025329 200 AQ 201 (254)
Q Consensus 200 ~~ 201 (254)
.+
T Consensus 98 ~~ 99 (203)
T cd08445 98 AD 99 (203)
T ss_pred cC
Confidence 64
No 75
>PRK15007 putative ABC transporter arginine-biding protein; Provisional
Probab=73.25 E-value=13 Score=31.82 Aligned_cols=87 Identities=15% Similarity=0.129 Sum_probs=49.2
Q ss_pred ecCcchhhhhhcCceeeeeeccceeecccCCCcceeeecCCCCcccEEEEEEEeCCCccccccchHHhhcCCcccCCCCc
Q 025329 132 QRPKDIVRKLLSGDLDLGIVGLDTVSEFGQGNEDLIIVHDALDYGDCRLSLAIPKYGIFENINSLRELAQMPQWTAEKPL 211 (254)
Q Consensus 132 vRp~DIp~yV~~G~aDlGIvG~DvL~E~~~d~~~l~~~l~dLgfG~CRLvVAvP~~~~~~dv~sl~dL~~~~~~~~~r~l 211 (254)
+...++-..+..|.+|+.+.|...-.|.... +. .- =.|-....+++.+.+ .+++++||. ++
T Consensus 67 ~~~~~~~~~l~~g~~D~~~~~~~~~~~r~~~---~~-fs--~p~~~~~~~~v~~~~----~~~~~~dL~---------g~ 127 (243)
T PRK15007 67 QAFDSLIPSLKFRRVEAVMAGMDITPEREKQ---VL-FT--TPYYDNSALFVGQQG----KYTSVDQLK---------GK 127 (243)
T ss_pred CCHHHHhHHHhCCCcCEEEEcCccCHHHhcc---cc-ee--cCccccceEEEEeCC----CCCCHHHhC---------CC
Confidence 3345677789999999988775554443221 11 00 123333445556554 256778875 35
Q ss_pred EEEcCCCccHHHHHHHcCCceEEEEEc
Q 025329 212 RVATGFTYLGPKFMKDNGLKHVVFSTA 238 (254)
Q Consensus 212 RVATkYPnLarkyf~~~Gi~~veIi~l 238 (254)
|||.---....+|+++..- +++++..
T Consensus 128 ~Igv~~g~~~~~~l~~~~~-~~~~~~~ 153 (243)
T PRK15007 128 KVGVQNGTTHQKFIMDKHP-EITTVPY 153 (243)
T ss_pred eEEEecCcHHHHHHHHhCC-CCeEEEc
Confidence 7776433344567776554 3566553
No 76
>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=73.11 E-value=8.3 Score=34.17 Aligned_cols=91 Identities=15% Similarity=0.115 Sum_probs=51.8
Q ss_pred CCeEEE--eecCcchhhhhhcCceeeeeeccceeecccCCCcceeeecCCCCcccEEEEEEEeCCCccccc--cchHHhh
Q 025329 125 SNLEVW--FQRPKDIVRKLLSGDLDLGIVGLDTVSEFGQGNEDLIIVHDALDYGDCRLSLAIPKYGIFENI--NSLRELA 200 (254)
Q Consensus 125 p~iev~--~vRp~DIp~yV~~G~aDlGIvG~DvL~E~~~d~~~l~~~l~dLgfG~CRLvVAvP~~~~~~dv--~sl~dL~ 200 (254)
|++++. .....|+...+..|.+|+||+..+.-.+ . .++. --.+|+.+++++++++-+...- -+++||.
T Consensus 120 P~~~i~~~~~~~~~~~~~l~~g~~D~~i~~~~~~~~-~---~~~~----~~~l~~~~~~~~~~~~hpl~~~~~i~~~dL~ 191 (300)
T TIGR02424 120 PRLRVRIMTGPNAYLLDQLRVGALDLVVGRLGAPET-M---QGLS----FEHLYNEPVVFVVRAGHPLLAAPSLPVASLA 191 (300)
T ss_pred CCcEEEEEeCchHHHHHHHHCCCCCEEEEecCCccc-c---ccee----eeeecCCceEEEEcCCCccccCCCCCHHHHh
Confidence 444444 4466788999999999999964321111 0 1222 2357788888888877432211 1567776
Q ss_pred cCCcccCCCCcEEEcC----CCccHHHHHHHcCCc
Q 025329 201 QMPQWTAEKPLRVATG----FTYLGPKFMKDNGLK 231 (254)
Q Consensus 201 ~~~~~~~~r~lRVATk----YPnLarkyf~~~Gi~ 231 (254)
+.+ -|... +-+....||++.|+.
T Consensus 192 ~~~--------~i~~~~~~~~~~~~~~~~~~~~~~ 218 (300)
T TIGR02424 192 DYP--------VLLPPEGSAIRPLAERLFIACGIP 218 (300)
T ss_pred CCC--------EEecCCCCchHHHHHHHHHHCCCC
Confidence 421 12111 223446678887763
No 77
>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=72.55 E-value=9.9 Score=29.74 Aligned_cols=87 Identities=14% Similarity=0.081 Sum_probs=46.7
Q ss_pred CCeEEEeecCcchhhhhhcCceeeeeeccceeecccCCCcceeeecCCCCcccEEEEEEEeCCCcc--ccccchHHhhcC
Q 025329 125 SNLEVWFQRPKDIVRKLLSGDLDLGIVGLDTVSEFGQGNEDLIIVHDALDYGDCRLSLAIPKYGIF--ENINSLRELAQM 202 (254)
Q Consensus 125 p~iev~~vRp~DIp~yV~~G~aDlGIvG~DvL~E~~~d~~~l~~~l~dLgfG~CRLvVAvP~~~~~--~dv~sl~dL~~~ 202 (254)
|++++.+.. .+....+.+|.+|+||+....- +. ++. ..-+++-+++++++.+- + ...-+++||.+.
T Consensus 27 P~i~l~~~~-~~~~~~l~~g~~Dl~i~~~~~~-~~-----~~~----~~~l~~~~~~~v~~~~~-~~~~~~~~~~~L~~~ 94 (190)
T cd08483 27 PEIELSLLP-SADLVDLRPDGIDVAIRYGNGD-WP-----GLE----SEPLTAAPFVVVAAPGL-LGDRKVDSLADLAGL 94 (190)
T ss_pred CCceEEEEe-cCCcCCCCCCCcCEEEEecCCC-CC-----CcE----EEeecccceEeeeCHHH-HhhCCCCCHHHHhcC
Confidence 455555543 3445789999999999853311 11 111 12344566677776541 1 123467777642
Q ss_pred CcccCCCCcEEEcCCCccHHHHHHHcCCc
Q 025329 203 PQWTAEKPLRVATGFTYLGPKFMKDNGLK 231 (254)
Q Consensus 203 ~~~~~~r~lRVATkYPnLarkyf~~~Gi~ 231 (254)
+ -|.........+||++.|+.
T Consensus 95 ~--------~i~~~~~~~~~~~~~~~~~~ 115 (190)
T cd08483 95 P--------WLQERGTNEQRVWLASMGVV 115 (190)
T ss_pred c--------eeccCCchHHHHHHHHcCCC
Confidence 1 12222223456788887763
No 78
>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=72.55 E-value=19 Score=29.57 Aligned_cols=107 Identities=9% Similarity=0.058 Sum_probs=54.6
Q ss_pred CCeEEEee--cCcchhhhhhcCceeeeeeccceeecccCCCcceeeecCCCCcccEEEEEEEeCCCccc-cccchHHhhc
Q 025329 125 SNLEVWFQ--RPKDIVRKLLSGDLDLGIVGLDTVSEFGQGNEDLIIVHDALDYGDCRLSLAIPKYGIFE-NINSLRELAQ 201 (254)
Q Consensus 125 p~iev~~v--Rp~DIp~yV~~G~aDlGIvG~DvL~E~~~d~~~l~~~l~dLgfG~CRLvVAvP~~~~~~-dv~sl~dL~~ 201 (254)
|++++.+. ...++-..|.+|.+|+||+-.+.- ... ..++. .-.++..+++++++...... .-.+++||.+
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 44444444 556899999999999999744311 100 00111 12445566666655442221 1236778764
Q ss_pred CCcccCCCCcEEEcCCCccHHHHHHHcCCceEEEEEcCCcee
Q 025329 202 MPQWTAEKPLRVATGFTYLGPKFMKDNGLKHVVFSTADGALE 243 (254)
Q Consensus 202 ~~~~~~~r~lRVATkYPnLarkyf~~~Gi~~veIi~l~GSvE 243 (254)
.+--.. .-.+.+-....+||+++|+. .+++.-..+.|
T Consensus 100 ~~~i~~----~~~~~~~~~~~~~~~~~g~~-~~~~~~~~~~~ 136 (204)
T cd08429 100 APLLLP----GEDSALRRKLLQWFERQGLR-PQIVGEFDDSA 136 (204)
T ss_pred CCeeec----CCCCcHHHHHHHHHHHcCCC-cceEEEeCCHH
Confidence 321000 00123335567788999984 34433334444
No 79
>PRK11151 DNA-binding transcriptional regulator OxyR; Provisional
Probab=72.33 E-value=7.2 Score=34.84 Aligned_cols=67 Identities=25% Similarity=0.354 Sum_probs=44.0
Q ss_pred CCeEEEee--cCcchhhhhhcCceeeeeeccceeecccCCCcceeeecCCCCcccEEEEEEEeCCCccc--cccchHHhh
Q 025329 125 SNLEVWFQ--RPKDIVRKLLSGDLDLGIVGLDTVSEFGQGNEDLIIVHDALDYGDCRLSLAIPKYGIFE--NINSLRELA 200 (254)
Q Consensus 125 p~iev~~v--Rp~DIp~yV~~G~aDlGIvG~DvL~E~~~d~~~l~~~l~dLgfG~CRLvVAvP~~~~~~--dv~sl~dL~ 200 (254)
|++++.+. ..+++...+..|.+|+||+..+... .++. -..++.-+++++++++.+.. ..-+++||.
T Consensus 118 P~v~i~~~~~~~~~~~~~l~~g~~Dl~i~~~~~~~------~~l~----~~~l~~~~~~~~~~~~hpl~~~~~i~~~~L~ 187 (305)
T PRK11151 118 PKLEMYLHEAQTHQLLAQLDSGKLDCAILALVKES------EAFI----EVPLFDEPMLLAVYEDHPWANRDRVPMSDLA 187 (305)
T ss_pred CCcEEEEEeCCHHHHHHHHHcCCccEEEEecCCCC------CCeE----EEEeccCcEEEEecCCCCcccCCccCHHHhc
Confidence 55655555 5789999999999999998654321 1222 23667778888887764321 223677876
Q ss_pred c
Q 025329 201 Q 201 (254)
Q Consensus 201 ~ 201 (254)
.
T Consensus 188 ~ 188 (305)
T PRK11151 188 G 188 (305)
T ss_pred C
Confidence 4
No 80
>PRK09791 putative DNA-binding transcriptional regulator; Provisional
Probab=71.66 E-value=7.8 Score=34.54 Aligned_cols=65 Identities=12% Similarity=0.108 Sum_probs=41.8
Q ss_pred EEEeecCcchhhhhhcCceeeeeecc-ceeecccCCCcceeeecCCCCcccEEEEEEEeCCCccccccchHHhhc
Q 025329 128 EVWFQRPKDIVRKLLSGDLDLGIVGL-DTVSEFGQGNEDLIIVHDALDYGDCRLSLAIPKYGIFENINSLRELAQ 201 (254)
Q Consensus 128 ev~~vRp~DIp~yV~~G~aDlGIvG~-DvL~E~~~d~~~l~~~l~dLgfG~CRLvVAvP~~~~~~dv~sl~dL~~ 201 (254)
++......|+...+..|.+|+||+.. +...+. ++. --.++..+++++++.+.+...-.+++||..
T Consensus 127 ~~~~~~~~~~~~~l~~g~~Di~i~~~~~~~~~~-----~~~----~~~l~~~~~~l~~~~~~~~~~~~~~~~l~~ 192 (302)
T PRK09791 127 RIMEGQLVSMINELRQGELDFTINTYYQGPYDH-----EFT----FEKLLEKQFAVFCRPGHPAIGARSLKQLLD 192 (302)
T ss_pred EEEeCChHHHHHHHHCCCccEEEEecCCccccc-----cee----EEEeccceEEEEEcCCCCcCCCCCHHHHhc
Confidence 34444568999999999999999842 211111 122 135678899999988754333345777764
No 81
>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=71.20 E-value=20 Score=28.22 Aligned_cols=90 Identities=12% Similarity=-0.019 Sum_probs=50.8
Q ss_pred CCeEEEee--cCcchhhhhhcCceeeeeeccceeecccCCCcceeeecCCCCcccEEEEEEEeCCCccc-cccchHHhhc
Q 025329 125 SNLEVWFQ--RPKDIVRKLLSGDLDLGIVGLDTVSEFGQGNEDLIIVHDALDYGDCRLSLAIPKYGIFE-NINSLRELAQ 201 (254)
Q Consensus 125 p~iev~~v--Rp~DIp~yV~~G~aDlGIvG~DvL~E~~~d~~~l~~~l~dLgfG~CRLvVAvP~~~~~~-dv~sl~dL~~ 201 (254)
|++++.+. ...++...+.+|.+|+||+....- . .++. .-.++.-+++++++++.+.. .--+++||..
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 44444443 456899999999999999743211 1 1122 22455667888887764321 1125788753
Q ss_pred CCcccCCCCcEE-EcCCCccHHHHHHHcCC
Q 025329 202 MPQWTAEKPLRV-ATGFTYLGPKFMKDNGL 230 (254)
Q Consensus 202 ~~~~~~~r~lRV-ATkYPnLarkyf~~~Gi 230 (254)
.. + ..+ ...+.....++|++.|+
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 82
>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=71.15 E-value=17 Score=29.02 Aligned_cols=91 Identities=18% Similarity=0.241 Sum_probs=47.1
Q ss_pred CCeEEEe--ecCcchhhhhhcCceeeeeeccceeecccCCCcceeeecCCCCcccEEEEEEEeCCCccc--cccchHHhh
Q 025329 125 SNLEVWF--QRPKDIVRKLLSGDLDLGIVGLDTVSEFGQGNEDLIIVHDALDYGDCRLSLAIPKYGIFE--NINSLRELA 200 (254)
Q Consensus 125 p~iev~~--vRp~DIp~yV~~G~aDlGIvG~DvL~E~~~d~~~l~~~l~dLgfG~CRLvVAvP~~~~~~--dv~sl~dL~ 200 (254)
|++++.+ ....++...+.+|.+|+||+-.....+. ++. -..++.-+++++++.+.+.. ..-+++||.
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 4444444 3456789999999999999742211111 122 12334455666666553222 223567775
Q ss_pred cCCcccCCCCcEEEc---CCCccHHHHHHHcCCc
Q 025329 201 QMPQWTAEKPLRVAT---GFTYLGPKFMKDNGLK 231 (254)
Q Consensus 201 ~~~~~~~~r~lRVAT---kYPnLarkyf~~~Gi~ 231 (254)
+.+ .-.-+ .+-....+||++.|+.
T Consensus 98 ~~~-------~i~~~~~~~~~~~~~~~~~~~~~~ 124 (198)
T cd08444 98 KWP-------IITYHGGFTGRSRIDRAFSRAELT 124 (198)
T ss_pred CCC-------EEEecCCCchHHHHHHHHHHcCCC
Confidence 321 11111 1223346678887874
No 83
>PRK11063 metQ DL-methionine transporter substrate-binding subunit; Provisional
Probab=70.86 E-value=13 Score=34.21 Aligned_cols=79 Identities=25% Similarity=0.280 Sum_probs=46.8
Q ss_pred cchhhhhhcCceeeeeeccceeeccc-CC-CcceeeecCCCCcccEEEEEEEeCCCccccccchHHhhcCCcccCCCCcE
Q 025329 135 KDIVRKLLSGDLDLGIVGLDTVSEFG-QG-NEDLIIVHDALDYGDCRLSLAIPKYGIFENINSLRELAQMPQWTAEKPLR 212 (254)
Q Consensus 135 ~DIp~yV~~G~aDlGIvG~DvL~E~~-~d-~~~l~~~l~dLgfG~CRLvVAvP~~~~~~dv~sl~dL~~~~~~~~~r~lR 212 (254)
.+.-..+..|.+|+...+..-.++.. .+ ..++. .+| -..++|.+.....++|++||.. +++
T Consensus 70 ~~~~~ALa~GdID~~~~qh~~~l~~~~~~~g~~l~------~~~---~~~vvp~~~ys~~i~si~DL~~--------Gk~ 132 (271)
T PRK11063 70 VLPNEALSKGDIDANAFQHKPYLDQQIKDRGYKLV------AVG---NTFVYPIAGYSKKIKSLDELQD--------GSQ 132 (271)
T ss_pred HHHHHHHHcCCcceecccCHHHHHHHHHHcCCcEE------EEe---EEEEEEeeccccCCCCHHHhcC--------CCE
Confidence 46667899999999888775544321 00 01121 111 1344565431245899999963 579
Q ss_pred EEcC--CCccHHH--HHHHcCC
Q 025329 213 VATG--FTYLGPK--FMKDNGL 230 (254)
Q Consensus 213 VATk--YPnLark--yf~~~Gi 230 (254)
||+. .-|..|. .|++.|+
T Consensus 133 IAip~d~~n~~r~L~lL~~~Gl 154 (271)
T PRK11063 133 VAVPNDPTNLGRSLLLLQKVGL 154 (271)
T ss_pred EEecCCCccHHHHHHHHHHCCC
Confidence 9988 4444443 5677776
No 84
>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=70.62 E-value=21 Score=27.79 Aligned_cols=91 Identities=19% Similarity=0.196 Sum_probs=49.9
Q ss_pred CCeEEEee--cCcchhhhhhcCceeeeeeccceeecccCCCcceeeecCCCCcccEEEEEEEeCCCccc--cccchHHhh
Q 025329 125 SNLEVWFQ--RPKDIVRKLLSGDLDLGIVGLDTVSEFGQGNEDLIIVHDALDYGDCRLSLAIPKYGIFE--NINSLRELA 200 (254)
Q Consensus 125 p~iev~~v--Rp~DIp~yV~~G~aDlGIvG~DvL~E~~~d~~~l~~~l~dLgfG~CRLvVAvP~~~~~~--dv~sl~dL~ 200 (254)
|++++.+. ...++...+.+|.+|+||+....- . .++. --.++.-+++++++++.+.. +.-+++||.
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 44555544 457899999999999999854321 1 1122 12345667777776663221 223567775
Q ss_pred cCCcccCCCCcEEEcC----CCccHHHHHHHcCCc
Q 025329 201 QMPQWTAEKPLRVATG----FTYLGPKFMKDNGLK 231 (254)
Q Consensus 201 ~~~~~~~~r~lRVATk----YPnLarkyf~~~Gi~ 231 (254)
..+ -+..... +.+...++|++.|++
T Consensus 97 ~~~------~i~~~~~~~~~~~~~~~~~~~~~~~~ 125 (197)
T cd08414 97 DEP------FVLFPREPGPGLYDQILALCRRAGFT 125 (197)
T ss_pred cCC------EEEecCCcchhHHHHHHHHHHHcCCC
Confidence 321 1222211 224456677777763
No 85
>cd08415 PBP2_LysR_opines_like The C-terminal substrate-domain of LysR-type transcriptional regulators involved in the catabolism of opines and that of related regulators, contains the type 2 periplasmic binding fold. This CD includes the C-terminal substrate-domain of LysR-type transcriptional regulators, OccR and NocR, involved in the catabolism of opines and that of LysR for lysine biosynthesis which clustered together in phylogenetic trees. Opines, such as octopine and nopaline, are low molecular weight compounds found in plant crown gall tumors that are produced by the parasitic bacterium Agrobacterium. There are at least 30 different opines identified so far. Opines are utilized by tumor-colonizing bacteria as a source of carbon, nitrogen, and energy. NocR and OccR belong to the family of LysR-type transcriptional regulators that positively regulates the catabolism of nopaline and octopine, respectively. Both nopaline and octopalin are arginine derivatives. In Agrobacterium tumefa
Probab=70.55 E-value=20 Score=27.96 Aligned_cols=67 Identities=19% Similarity=0.287 Sum_probs=40.2
Q ss_pred CCeEEEee--cCcchhhhhhcCceeeeeeccceeecccCCCcceeeecCCCCcccEEEEEEEeCCCccc--cccchHHhh
Q 025329 125 SNLEVWFQ--RPKDIVRKLLSGDLDLGIVGLDTVSEFGQGNEDLIIVHDALDYGDCRLSLAIPKYGIFE--NINSLRELA 200 (254)
Q Consensus 125 p~iev~~v--Rp~DIp~yV~~G~aDlGIvG~DvL~E~~~d~~~l~~~l~dLgfG~CRLvVAvP~~~~~~--dv~sl~dL~ 200 (254)
|++++.+. ...++...+.+|.+|+||+-...- . .++. --.++..+++++++.+.+.. ..-+++||.
T Consensus 27 P~i~l~i~~~~~~~~~~~l~~~~~Dl~i~~~~~~---~---~~~~----~~~l~~~~~~~v~~~~~~l~~~~~~~~~~l~ 96 (196)
T cd08415 27 PDVRISLHTLSSSTVVEAVLSGQADLGLASLPLD---H---PGLE----SEPLASGRAVCVLPPGHPLARKDVVTPADLA 96 (196)
T ss_pred CCcEEEEEecchHHHHHHHHcCCccEEEEeCCCC---C---Ccce----eeeecccceEEEEcCCCChHhcCccCHHHhc
Confidence 44444444 557899999999999999754321 1 1122 23456677888887764221 223567775
Q ss_pred c
Q 025329 201 Q 201 (254)
Q Consensus 201 ~ 201 (254)
.
T Consensus 97 ~ 97 (196)
T cd08415 97 G 97 (196)
T ss_pred C
Confidence 3
No 86
>cd08452 PBP2_AlsR The C-terminal substrate binding domain of LysR-type trnascriptional regulator AlsR, which regulates acetoin formation under stationary phase growth conditions; contains the type 2 periplasmic binding fold. AlsR is responsible for activating the expression of the acetoin operon (alsSD) in response to inducing signals such as glucose and acetate. Like many other LysR family proteins, AlsR is transcribed divergently from the alsSD operon. The alsS gene encodes acetolactate synthase, an enzyme involved in the production of acetoin in cells of stationary-phase. AlsS catalyzes the conversion of two pyruvate molecules to acetolactate and carbon dioxide. Acetolactate is then converted to acetoin at low pH by acetolactate decarboxylase which encoded by the alsD gene. Acetoin is an important physiological metabolite excreted by many microorganisms grown on glucose or other fermentable carbon sources. This substrate-binding domain shows significant homology to the type 2 perip
Probab=69.72 E-value=25 Score=27.96 Aligned_cols=67 Identities=21% Similarity=0.278 Sum_probs=38.7
Q ss_pred CCeEEEe--ecCcchhhhhhcCceeeeeeccceeecccCCCcceeeecCCCCcccEEEEEEEeCCCccc--cccchHHhh
Q 025329 125 SNLEVWF--QRPKDIVRKLLSGDLDLGIVGLDTVSEFGQGNEDLIIVHDALDYGDCRLSLAIPKYGIFE--NINSLRELA 200 (254)
Q Consensus 125 p~iev~~--vRp~DIp~yV~~G~aDlGIvG~DvL~E~~~d~~~l~~~l~dLgfG~CRLvVAvP~~~~~~--dv~sl~dL~ 200 (254)
|++++.+ ....++...|.+|.+|+||+-...- . .++. .-.+..-+++++++.+.+.. +.-+++||.
T Consensus 27 P~v~i~i~~~~~~~~~~~l~~~~~Dl~i~~~~~~-~-----~~~~----~~~l~~~~~~lv~~~~hpl~~~~~~~~~~L~ 96 (197)
T cd08452 27 PSVKVELRELSSPDQVEELLKGRIDIGFLHPPIQ-H-----TALH----IETVQSSPCVLALPKQHPLASKEEITIEDLR 96 (197)
T ss_pred CCcEEEEEecChHHHHHHHHCCCccEEEeeCCCC-C-----CCee----EEEeeeccEEEEEeCCCccccCCCCCHHHhc
Confidence 4555544 3678899999999999999743221 1 1121 11234456677776653221 123577776
Q ss_pred c
Q 025329 201 Q 201 (254)
Q Consensus 201 ~ 201 (254)
+
T Consensus 97 ~ 97 (197)
T cd08452 97 D 97 (197)
T ss_pred C
Confidence 4
No 87
>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=68.55 E-value=18 Score=28.30 Aligned_cols=91 Identities=20% Similarity=0.178 Sum_probs=48.9
Q ss_pred CCeEEEe--ecCcchhhhhhcCceeeeeeccceeecccCCCcceeeecCCCCcccEEEEEEEeCCCccc--cccchHHhh
Q 025329 125 SNLEVWF--QRPKDIVRKLLSGDLDLGIVGLDTVSEFGQGNEDLIIVHDALDYGDCRLSLAIPKYGIFE--NINSLRELA 200 (254)
Q Consensus 125 p~iev~~--vRp~DIp~yV~~G~aDlGIvG~DvL~E~~~d~~~l~~~l~dLgfG~CRLvVAvP~~~~~~--dv~sl~dL~ 200 (254)
|++++.+ ....|+...+.+|.+|+||+..... . .++. ...++.-+++++++.+.+.. ..-+++||.
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 4444443 3567889999999999999854321 1 1122 22445566676666553221 123577776
Q ss_pred cCCcccCCCCcEEE-cCCCccHHHHHHHcCCc
Q 025329 201 QMPQWTAEKPLRVA-TGFTYLGPKFMKDNGLK 231 (254)
Q Consensus 201 ~~~~~~~~r~lRVA-TkYPnLarkyf~~~Gi~ 231 (254)
..+- +... +...+...++|++.|+.
T Consensus 97 ~~~~------i~~~~~~~~~~~~~~~~~~~~~ 122 (198)
T cd08412 97 AEPL------ILLDLPHSREYFLSLFAAAGLT 122 (198)
T ss_pred CCcE------EecCchhHHHHHHHHHHHcCCC
Confidence 4211 1100 11223455678888874
No 88
>PRK10341 DNA-binding transcriptional activator TdcA; Provisional
Probab=68.49 E-value=11 Score=34.09 Aligned_cols=67 Identities=16% Similarity=0.201 Sum_probs=41.4
Q ss_pred eEEEeecCcchhhhhhcCceeeeeeccceeecccCCCcceeeecCCCCcccEEEEEEEeCCCccccccchHHhhc
Q 025329 127 LEVWFQRPKDIVRKLLSGDLDLGIVGLDTVSEFGQGNEDLIIVHDALDYGDCRLSLAIPKYGIFENINSLRELAQ 201 (254)
Q Consensus 127 iev~~vRp~DIp~yV~~G~aDlGIvG~DvL~E~~~d~~~l~~~l~dLgfG~CRLvVAvP~~~~~~dv~sl~dL~~ 201 (254)
+++......++...|.+|.+|+||+...--.+ ..++. --.++..+++++++.+.+..+.-+++||.+
T Consensus 128 i~~~~~~~~~~~~~l~~g~~Dl~i~~~~~~~~----~~~l~----~~~l~~~~~~lv~~~~~pl~~~i~~~dL~~ 194 (312)
T PRK10341 128 VSMYEAQLSSFLPAIRDGRLDFAIGTLSNEMK----LQDLH----VEPLFESEFVLVASKSRTCTGTTTLESLKN 194 (312)
T ss_pred EEEEeCCHHHHHHHHHcCCCcEEEecCCcccc----cCCee----EEEEecccEEEEEcCCCchhccCCHHHHhC
Confidence 34444467899999999999999974211000 01122 235666788888877744333346778764
No 89
>PRK11062 nhaR transcriptional activator NhaR; Provisional
Probab=66.82 E-value=8 Score=34.63 Aligned_cols=90 Identities=13% Similarity=0.180 Sum_probs=51.2
Q ss_pred CCeEEEee--cCcchhhhhhcCceeeeeeccceeecccCCCcceeeecCCCCcccEEEEEEEeCCCccccccchHHhhcC
Q 025329 125 SNLEVWFQ--RPKDIVRKLLSGDLDLGIVGLDTVSEFGQGNEDLIIVHDALDYGDCRLSLAIPKYGIFENINSLRELAQM 202 (254)
Q Consensus 125 p~iev~~v--Rp~DIp~yV~~G~aDlGIvG~DvL~E~~~d~~~l~~~l~dLgfG~CRLvVAvP~~~~~~dv~sl~dL~~~ 202 (254)
|++++.+. -..++...+.+|.+|+||+.... +. ....++. ...++.+++++.++.+ +....+++||.+.
T Consensus 120 P~i~l~~~~~~~~~~~~~l~~g~~D~~i~~~~~--~~-~~~~~l~----~~~l~~~~~~~~~~~~--~~~~~~~~~l~~~ 190 (296)
T PRK11062 120 ESIHLRCFESTHEMLLEQLSQHKLDMILSDCPV--DS-TQQEGLF----SKKLGECGVSFFCTNP--LPEKPFPACLEER 190 (296)
T ss_pred CceEEEEEeCCHHHHHHHHHcCCCCEEEecCCC--cc-ccccchh----hhhhhccCcceEecCC--CccccChHHHhcC
Confidence 45555443 34688999999999999974321 10 0011222 3466788887776655 2223456777532
Q ss_pred CcccCCCCcEEEcC----CCccHHHHHHHcCCc
Q 025329 203 PQWTAEKPLRVATG----FTYLGPKFMKDNGLK 231 (254)
Q Consensus 203 ~~~~~~r~lRVATk----YPnLarkyf~~~Gi~ 231 (254)
.-|... +.+...+||.+.|+.
T Consensus 191 --------~~i~~~~~~~~~~~~~~~~~~~~~~ 215 (296)
T PRK11062 191 --------RLLIPGRRTMLGRKLLNWFNSQGLN 215 (296)
T ss_pred --------CeeecCCCchHHHHHHHHHHHcCCC
Confidence 123222 234456778888874
No 90
>PRK11260 cystine transporter subunit; Provisional
Probab=65.98 E-value=21 Score=31.39 Aligned_cols=96 Identities=16% Similarity=0.096 Sum_probs=53.8
Q ss_pred eEEEeecCcchhhhhhcCceeeeeeccceeecccCCCcceeeecCCCCcccEEEEEEEeCCCccccccchHHhhcCCccc
Q 025329 127 LEVWFQRPKDIVRKLLSGDLDLGIVGLDTVSEFGQGNEDLIIVHDALDYGDCRLSLAIPKYGIFENINSLRELAQMPQWT 206 (254)
Q Consensus 127 iev~~vRp~DIp~yV~~G~aDlGIvG~DvL~E~~~d~~~l~~~l~dLgfG~CRLvVAvP~~~~~~dv~sl~dL~~~~~~~ 206 (254)
+++......+.-..|.+|.+|+++.+..+-.|.... +.. --.|..-.+++.++.+.. ..+++++||.
T Consensus 82 ~e~~~~~~~~~~~~l~~G~~D~~~~~~~~~~~r~~~----~~f--s~p~~~~~~~~~~~~~~~-~~~~~~~dL~------ 148 (266)
T PRK11260 82 ASLKPTKWDGMLASLDSKRIDVVINQVTISDERKKK----YDF--STPYTVSGIQALVKKGNE-GTIKTAADLK------ 148 (266)
T ss_pred EEEEeCCHHHHHHHHhcCCCCEEEeccccCHHHHhc----ccc--CCceeecceEEEEEcCCc-CCCCCHHHcC------
Confidence 344444456777889999999998765433343221 111 124444456667776532 3567788875
Q ss_pred CCCCcEEEcCCCccHHHHHHHcCCceEEEEEcC
Q 025329 207 AEKPLRVATGFTYLGPKFMKDNGLKHVVFSTAD 239 (254)
Q Consensus 207 ~~r~lRVATkYPnLarkyf~~~Gi~~veIi~l~ 239 (254)
+++|+.---....+|+++... +.++....
T Consensus 149 ---g~~Igv~~G~~~~~~l~~~~~-~~~i~~~~ 177 (266)
T PRK11260 149 ---GKKVGVGLGTNYEQWLRQNVQ-GVDVRTYD 177 (266)
T ss_pred ---CCEEEEecCCcHHHHHHHhCC-CCceEecC
Confidence 356765332333667766543 24555443
No 91
>COG0725 ModA ABC-type molybdate transport system, periplasmic component [Inorganic ion transport and metabolism]
Probab=65.58 E-value=39 Score=31.04 Aligned_cols=77 Identities=14% Similarity=0.170 Sum_probs=44.5
Q ss_pred chhhhhhcCceeeeeeccceeecccCCCcceeeecCCCCcc-cEEEEEEEeCCCccccccchHHhhcCCcccCCCCcEEE
Q 025329 136 DIVRKLLSGDLDLGIVGLDTVSEFGQGNEDLIIVHDALDYG-DCRLSLAIPKYGIFENINSLRELAQMPQWTAEKPLRVA 214 (254)
Q Consensus 136 DIp~yV~~G~aDlGIvG~DvL~E~~~d~~~l~~~l~dLgfG-~CRLvVAvP~~~~~~dv~sl~dL~~~~~~~~~r~lRVA 214 (254)
++-.||+.|.+|+||+......-... ...+... +-... .-...+|++.+. .+-+...++-. -+.
T Consensus 177 ~~l~~V~~G~ad~g~vy~sd~~~~~~--~~~~~~~-~~~~~~Pi~y~iav~~~~--~~~~~A~~f~~----------fl~ 241 (258)
T COG0725 177 QALAYVETGEADAGFVYVSDALLSKK--VKIVGVF-PEDLHSPIVYPIAVLKNA--KNPELAKEFVD----------FLL 241 (258)
T ss_pred HHHHHHHcCCCCeEEEEEEhhhccCC--ceEEEEc-ccccCCCeEEEEEEEcCC--CCHHHHHHHHH----------HHh
Confidence 89999999999999999954333321 1122222 22222 577788888874 22222233221 011
Q ss_pred cCCCccHHHHHHHcCC
Q 025329 215 TGFTYLGPKFMKDNGL 230 (254)
Q Consensus 215 TkYPnLarkyf~~~Gi 230 (254)
+ .-++++|++.|.
T Consensus 242 s---~~a~~il~~~Gf 254 (258)
T COG0725 242 S---PEAQEILEKYGF 254 (258)
T ss_pred C---HHHHHHHHHcCC
Confidence 1 457788888886
No 92
>PRK09508 leuO leucine transcriptional activator; Reviewed
Probab=65.26 E-value=48 Score=29.85 Aligned_cols=91 Identities=13% Similarity=0.081 Sum_probs=54.3
Q ss_pred CCeEEEee--cCcchhhhhhcCceeeeeeccceeecccCCCcceeeecCCCCcccEEEEEEEeCCCcc-ccccchHHhhc
Q 025329 125 SNLEVWFQ--RPKDIVRKLLSGDLDLGIVGLDTVSEFGQGNEDLIIVHDALDYGDCRLSLAIPKYGIF-ENINSLRELAQ 201 (254)
Q Consensus 125 p~iev~~v--Rp~DIp~yV~~G~aDlGIvG~DvL~E~~~d~~~l~~~l~dLgfG~CRLvVAvP~~~~~-~dv~sl~dL~~ 201 (254)
|++++-+. -..++...|.+|.+|+||+..+.-. .++. --.++..++++.++.+.+. ...-+++||..
T Consensus 139 P~i~l~i~~~~~~~~~~~l~~g~~Di~i~~~~~~~------~~l~----~~~l~~~~~~lv~~~~hpl~~~~~~~~~L~~ 208 (314)
T PRK09508 139 PNIHVVFKSSLNQNIEHQLRYQETEFVISYEEFDR------PEFT----SVPLFKDELVLVASKNHPRIKGPITEEQLYN 208 (314)
T ss_pred CCcEEEEEeCcchhHHHHHhcCCccEEEecCCCCc------cccc----eeeeecCceEEEEcCCCCccCCCCCHHHHhh
Confidence 55666555 4678899999999999998654311 1122 2346678888888877322 12345778764
Q ss_pred CCcccCCCCcEEE-cCCCccHHHHHHHcCCc
Q 025329 202 MPQWTAEKPLRVA-TGFTYLGPKFMKDNGLK 231 (254)
Q Consensus 202 ~~~~~~~r~lRVA-TkYPnLarkyf~~~Gi~ 231 (254)
.+ ...+. ..+-....+++.+.|++
T Consensus 209 ~~------~~~~~~~~~~~~~~~~~~~~g~~ 233 (314)
T PRK09508 209 EQ------HAVVSLDRFASFSQPWYDTVDKQ 233 (314)
T ss_pred CC------CEEecCCCCccHHHHHHHhcCcC
Confidence 21 11122 12233456778888874
No 93
>PRK12683 transcriptional regulator CysB-like protein; Reviewed
Probab=64.69 E-value=17 Score=32.92 Aligned_cols=88 Identities=22% Similarity=0.277 Sum_probs=49.5
Q ss_pred eEEEeecCcchhhhhhcCceeeeeeccceeecccCCCcceeeecCCCCcccEEEEEEEeCCCccc--cccchHHhhcCCc
Q 025329 127 LEVWFQRPKDIVRKLLSGDLDLGIVGLDTVSEFGQGNEDLIIVHDALDYGDCRLSLAIPKYGIFE--NINSLRELAQMPQ 204 (254)
Q Consensus 127 iev~~vRp~DIp~yV~~G~aDlGIvG~DvL~E~~~d~~~l~~~l~dLgfG~CRLvVAvP~~~~~~--dv~sl~dL~~~~~ 204 (254)
+++.....+|+...|.+|.+|+||+..+.-.+.+ +. ...++.=++++++|.+.++. ..-+++||...+
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 4444456789999999999999997543211221 11 11233446677777664331 224577776421
Q ss_pred ccCCCCcEEEc----CCCccHHHHHHHcCCc
Q 025329 205 WTAEKPLRVAT----GFTYLGPKFMKDNGLK 231 (254)
Q Consensus 205 ~~~~r~lRVAT----kYPnLarkyf~~~Gi~ 231 (254)
-|.. .+.+...++|++.|+.
T Consensus 194 -------~i~~~~~~~~~~~~~~~~~~~~~~ 217 (309)
T PRK12683 194 -------IITYDQGFTGRSRIDQAFAEAGLV 217 (309)
T ss_pred -------eEeccCCCcHHHHHHHHHHHCCCC
Confidence 1222 1234456678888874
No 94
>PRK09495 glnH glutamine ABC transporter periplasmic protein; Reviewed
Probab=64.28 E-value=30 Score=29.91 Aligned_cols=91 Identities=18% Similarity=0.133 Sum_probs=52.5
Q ss_pred EEeecCcchhhhhhcCceeeeeeccceeecccCCCcceeeecCCCCcccEEEEEEEeCCCccccccchHHhhcCCcccCC
Q 025329 129 VWFQRPKDIVRKLLSGDLDLGIVGLDTVSEFGQGNEDLIIVHDALDYGDCRLSLAIPKYGIFENINSLRELAQMPQWTAE 208 (254)
Q Consensus 129 v~~vRp~DIp~yV~~G~aDlGIvG~DvL~E~~~d~~~l~~~l~dLgfG~CRLvVAvP~~~~~~dv~sl~dL~~~~~~~~~ 208 (254)
+.......+-..+..|.+|+++.|.-+-.|.. + .+. . .-+|-...+.+.++.+. ..+++++||.
T Consensus 67 ~~~~~~~~~~~~l~~G~vDi~~~~~~~t~~R~-~---~~~-f-s~p~~~~~~~~~~~~~~--~~~~~~~dL~-------- 130 (247)
T PRK09495 67 LKPMDFSGIIPALQTKNVDLALAGITITDERK-K---AID-F-SDGYYKSGLLVMVKANN--NDIKSVKDLD-------- 130 (247)
T ss_pred EEeCCHHHHHHHHhCCCcCEEEecCccCHHHH-h---hcc-c-cchheecceEEEEECCC--CCCCChHHhC--------
Confidence 33344567789999999999988754333332 1 111 1 12455667777777763 3477888875
Q ss_pred CCcEEEcCCCccHHHHHHHcCCceEEEEE
Q 025329 209 KPLRVATGFTYLGPKFMKDNGLKHVVFST 237 (254)
Q Consensus 209 r~lRVATkYPnLarkyf~~~Gi~~veIi~ 237 (254)
++|||..=-.....|+++..- +.+++.
T Consensus 131 -g~~I~v~~g~~~~~~l~~~~~-~~~i~~ 157 (247)
T PRK09495 131 -GKVVAVKSGTGSVDYAKANIK-TKDLRQ 157 (247)
T ss_pred -CCEEEEecCchHHHHHHhcCC-CCceEE
Confidence 356764322334556655433 245544
No 95
>PRK09906 DNA-binding transcriptional regulator HcaR; Provisional
Probab=63.76 E-value=24 Score=31.13 Aligned_cols=89 Identities=13% Similarity=0.165 Sum_probs=53.6
Q ss_pred CCeEEEe--ecCcchhhhhhcCceeeeeeccceeecccCCCcceeeecCCCCcccEEEEEEEeCCCccc--cccchHHhh
Q 025329 125 SNLEVWF--QRPKDIVRKLLSGDLDLGIVGLDTVSEFGQGNEDLIIVHDALDYGDCRLSLAIPKYGIFE--NINSLRELA 200 (254)
Q Consensus 125 p~iev~~--vRp~DIp~yV~~G~aDlGIvG~DvL~E~~~d~~~l~~~l~dLgfG~CRLvVAvP~~~~~~--dv~sl~dL~ 200 (254)
|++++.+ ....++...+.+|.+|+||+..+.. . .++. .-.++..+++++++++.+.. +.-+++||.
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 4454444 4578899999999999999866531 1 1122 23567778888888763221 223567776
Q ss_pred cCCcccCCCCcEEEcC------CCccHHHHHHHcCCc
Q 025329 201 QMPQWTAEKPLRVATG------FTYLGPKFMKDNGLK 231 (254)
Q Consensus 201 ~~~~~~~~r~lRVATk------YPnLarkyf~~~Gi~ 231 (254)
+.+ -|... +.....+|+++.|++
T Consensus 187 ~~~--------~i~~~~~~~~~~~~~~~~~~~~~~~~ 215 (296)
T PRK09906 187 GVN--------FISTDPAYSGSLAPIIKAWFAQHNSQ 215 (296)
T ss_pred CCC--------EEeccCCCCchHHHHHHHHHHHcCCC
Confidence 421 12211 124456788888874
No 96
>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=63.60 E-value=17 Score=28.28 Aligned_cols=87 Identities=15% Similarity=0.070 Sum_probs=45.3
Q ss_pred CCeEEEeecCcchhhhhhcCceeeeeeccceeecccCCCcceeeecCCCCcccEEEEEEEeCCCcc-ccccchHHhhcCC
Q 025329 125 SNLEVWFQRPKDIVRKLLSGDLDLGIVGLDTVSEFGQGNEDLIIVHDALDYGDCRLSLAIPKYGIF-ENINSLRELAQMP 203 (254)
Q Consensus 125 p~iev~~vRp~DIp~yV~~G~aDlGIvG~DvL~E~~~d~~~l~~~l~dLgfG~CRLvVAvP~~~~~-~dv~sl~dL~~~~ 203 (254)
|++++.+.... -...+.+|.+|+||+..+.-. .++. .--++.-+++++++.+-.. .+.-+++||.+.+
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 45555544322 234689999999997543211 1111 1234566777777554210 1223677776421
Q ss_pred cccCCCCcEEE-cCCCccHHHHHHHcCC
Q 025329 204 QWTAEKPLRVA-TGFTYLGPKFMKDNGL 230 (254)
Q Consensus 204 ~~~~~r~lRVA-TkYPnLarkyf~~~Gi 230 (254)
-|. +..+...+++|++.|.
T Consensus 96 --------~i~~~~~~~~~~~~~~~~~~ 115 (194)
T cd08481 96 --------LLQQTTRPEAWRDWFEEVGL 115 (194)
T ss_pred --------eEecCCCCcCHHHHHHHcCC
Confidence 122 1123445778888876
No 97
>PRK11233 nitrogen assimilation transcriptional regulator; Provisional
Probab=63.14 E-value=30 Score=31.03 Aligned_cols=90 Identities=14% Similarity=0.112 Sum_probs=50.8
Q ss_pred CCeEEEee--cCcchhhhhhcCceeeeeeccceeecccCCCcceeeecCCCCcccEEEEEEEeCCCccccccchHHhhcC
Q 025329 125 SNLEVWFQ--RPKDIVRKLLSGDLDLGIVGLDTVSEFGQGNEDLIIVHDALDYGDCRLSLAIPKYGIFENINSLRELAQM 202 (254)
Q Consensus 125 p~iev~~v--Rp~DIp~yV~~G~aDlGIvG~DvL~E~~~d~~~l~~~l~dLgfG~CRLvVAvP~~~~~~dv~sl~dL~~~ 202 (254)
|++++.+. ...++...+..|.+|+||+.... .+ .++. --.++..+++++++.+.+ ...-+++||...
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 44555443 55789999999999999975321 11 1222 124566777888777632 333467787642
Q ss_pred CcccCCCCcEEEc--CCCccHHHHHHHcCCc
Q 025329 203 PQWTAEKPLRVAT--GFTYLGPKFMKDNGLK 231 (254)
Q Consensus 203 ~~~~~~r~lRVAT--kYPnLarkyf~~~Gi~ 231 (254)
+ + +.... .+.....++|++.|+.
T Consensus 188 ~-~-----i~~~~~~~~~~~~~~~~~~~g~~ 212 (305)
T PRK11233 188 N-L-----FLPRDYSAVRLRVDEAFSLRRLT 212 (305)
T ss_pred C-e-----ecCCCCccHHHHHHHHHHHcCCC
Confidence 1 1 10000 1123345677778874
No 98
>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=62.30 E-value=21 Score=30.89 Aligned_cols=88 Identities=17% Similarity=0.186 Sum_probs=48.4
Q ss_pred EEEeecCcchhhhhhcCceeeeeeccceeecccCCCcceeeecCCCCcccEEEEEEEeCCCcccc--ccchHHhhcCCcc
Q 025329 128 EVWFQRPKDIVRKLLSGDLDLGIVGLDTVSEFGQGNEDLIIVHDALDYGDCRLSLAIPKYGIFEN--INSLRELAQMPQW 205 (254)
Q Consensus 128 ev~~vRp~DIp~yV~~G~aDlGIvG~DvL~E~~~d~~~l~~~l~dLgfG~CRLvVAvP~~~~~~d--v~sl~dL~~~~~~ 205 (254)
++..-...++-..+.+|.+|+||+..+.- . .++. --.++.-+++++++.+.++.+ --+++||...+
T Consensus 116 ~i~~~~~~~~~~~l~~g~~Dl~i~~~~~~-~-----~~~~----~~~l~~~~~~lv~s~~~pl~~~~~i~~~~L~~~~-- 183 (279)
T TIGR03339 116 SVRIGNSQEVLQALQSYRVDVAVSSEVVD-D-----PRLD----RVVLGNDPLVAVVHRQHPLAERESVTLEELAGQP-- 183 (279)
T ss_pred EEEECCHHHHHHHHHcCCCcEEEEecccC-C-----CceE----EEEcCCceEEEEECCCCccccCCCcCHHHHhCCC--
Confidence 33334556888999999999999864421 1 1122 123445677888776643322 12567776421
Q ss_pred cCCCCcEEEcC--CCccHHHHHHHcCCc
Q 025329 206 TAEKPLRVATG--FTYLGPKFMKDNGLK 231 (254)
Q Consensus 206 ~~~r~lRVATk--YPnLarkyf~~~Gi~ 231 (254)
-+..... +.....+||++.|++
T Consensus 184 ----~i~~~~~~~~~~~~~~~~~~~~~~ 207 (279)
T TIGR03339 184 ----LLMREPGSVTRQTTEEALAAAGVA 207 (279)
T ss_pred ----eEEecCCCChHHHHHHHHHHcCCC
Confidence 1111111 123456778888874
No 99
>TIGR01096 3A0103s03R lysine-arginine-ornithine-binding periplasmic protein.
Probab=61.10 E-value=31 Score=29.39 Aligned_cols=84 Identities=13% Similarity=0.074 Sum_probs=47.9
Q ss_pred EEEeecCcchhhhhhcCceeeeeeccceeecccCCCcceeeecCCCCcccEEEEEEEeCCCccccccchHHhhcCCcccC
Q 025329 128 EVWFQRPKDIVRKLLSGDLDLGIVGLDTVSEFGQGNEDLIIVHDALDYGDCRLSLAIPKYGIFENINSLRELAQMPQWTA 207 (254)
Q Consensus 128 ev~~vRp~DIp~yV~~G~aDlGIvG~DvL~E~~~d~~~l~~~l~dLgfG~CRLvVAvP~~~~~~dv~sl~dL~~~~~~~~ 207 (254)
++......+.-..+..|.+|+++.+..+-.|.... +.. --.|..-...+.++.+.. ...+++||.
T Consensus 66 ~~~~~~~~~~~~~l~~G~~D~~~~~~~~~~~r~~~----~~~--s~p~~~~~~~~~~~~~~~--~~~~~~dl~------- 130 (250)
T TIGR01096 66 KFVEQNFDGLIPSLKAKKVDAIMATMSITPKRQKQ----IDF--SDPYYATGQGFVVKKGSD--LAKTLEDLD------- 130 (250)
T ss_pred EEEeCCHHHHHHHHhCCCcCEEEecCccCHHHhhc----ccc--ccchhcCCeEEEEECCCC--cCCChHHcC-------
Confidence 33334446777889999999998765433333211 111 235566667777777642 235677764
Q ss_pred CCCcEEEcCCCccHHHHHHHc
Q 025329 208 EKPLRVATGFTYLGPKFMKDN 228 (254)
Q Consensus 208 ~r~lRVATkYPnLarkyf~~~ 228 (254)
++||++---.....|+.+.
T Consensus 131 --g~~i~~~~g~~~~~~l~~~ 149 (250)
T TIGR01096 131 --GKTVGVQSGTTHEQYLKDY 149 (250)
T ss_pred --CCEEEEecCchHHHHHHHh
Confidence 3577764333334555543
No 100
>PRK10677 modA molybdate transporter periplasmic protein; Provisional
Probab=61.03 E-value=23 Score=31.94 Aligned_cols=147 Identities=14% Similarity=0.114 Sum_probs=78.3
Q ss_pred CcccceeeeecccccccceeeeecCcccCCCCCCCceEEEecCCCCChHHHHHHHHhCCCccCCCCCCceEeecCCCCCe
Q 025329 48 KPAAAVTCCVSSSQQFESHVSVVNGNIDNRISERDEIRLGLPSKGRMAADTLDLLKDCQLSVKQVNPRQYVAQIPQLSNL 127 (254)
Q Consensus 48 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~LrIALPsKGRL~e~tl~LL~~aGi~v~~~~~R~L~~~~~~~p~i 127 (254)
+-+|...-|+.+...- +. ....++.|+|+-. |-+.+-.-++.+. + .++. + -.+
T Consensus 4 ~~~~~~~~~~~~~~~~-------~~----~~~~~~~l~v~~a--~~~~~~~~~l~~~--F------e~~~-----g-~~v 56 (257)
T PRK10677 4 KWLRLFAGAVLSFAVA-------GN----ALADEGKITVFAA--ASLTNALQDIAAQ--Y------KKEK-----G-VDV 56 (257)
T ss_pred hHHHHHHHHHHHhhcc-------cc----ccccCCcEEEEEe--cChHHHHHHHHHH--H------Hhhh-----C-CeE
Confidence 4566677777654331 01 1134456889887 5554333332222 1 0111 1 124
Q ss_pred EEEeecCcchhhhhhcCc-eeeeeeccceeecccCCCcceeeecCCCCcccEEEEEEEeCCCcccc-----ccchHHhhc
Q 025329 128 EVWFQRPKDIVRKLLSGD-LDLGIVGLDTVSEFGQGNEDLIIVHDALDYGDCRLSLAIPKYGIFEN-----INSLRELAQ 201 (254)
Q Consensus 128 ev~~vRp~DIp~yV~~G~-aDlGIvG~DvL~E~~~d~~~l~~~l~dLgfG~CRLvVAvP~~~~~~d-----v~sl~dL~~ 201 (254)
.+.+-....+...+++|. +|+.+.+..-..+.-.. ..++.......|+.-+|++++|.+..... .++++||..
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 555556677888888888 99999986332322111 01111101235788899999998753222 246677742
Q ss_pred CCcccCCCCcEEEcCCCc------cHHHHHHHcCC
Q 025329 202 MPQWTAEKPLRVATGFTY------LGPKFMKDNGL 230 (254)
Q Consensus 202 ~~~~~~~r~lRVATkYPn------Larkyf~~~Gi 230 (254)
..|||--.|. .+++.|++.|+
T Consensus 136 --------~~~iai~dP~~~p~G~~a~~~l~~~g~ 162 (257)
T PRK10677 136 --------GGRLAVGDPDHVPAGIYAKEALQKLGA 162 (257)
T ss_pred --------CCeEEEcCCCCChHHHHHHHHHHHcCC
Confidence 1355555554 45666776665
No 101
>PRK10837 putative DNA-binding transcriptional regulator; Provisional
Probab=59.83 E-value=18 Score=31.71 Aligned_cols=65 Identities=18% Similarity=0.253 Sum_probs=40.5
Q ss_pred eEEEeecCcchhhhhhcCceeeeeeccceeecccCCCcceeeecCCCCcccEEEEEEEeCCCccc-cccchHHhhc
Q 025329 127 LEVWFQRPKDIVRKLLSGDLDLGIVGLDTVSEFGQGNEDLIIVHDALDYGDCRLSLAIPKYGIFE-NINSLRELAQ 201 (254)
Q Consensus 127 iev~~vRp~DIp~yV~~G~aDlGIvG~DvL~E~~~d~~~l~~~l~dLgfG~CRLvVAvP~~~~~~-dv~sl~dL~~ 201 (254)
+++...-..++...+.+|.+|+||+.... +..++. ...+++.+++++++++-+.. ..-+++||..
T Consensus 120 i~v~~~~~~~~~~~l~~g~~Di~i~~~~~------~~~~~~----~~~l~~~~~~lv~~~~hpl~~~~i~~~~L~~ 185 (290)
T PRK10837 120 LELSVGNSQDVINAVLDFRVDIGLIEGPC------HSPELI----SEPWLEDELVVFAAPDSPLARGPVTLEQLAA 185 (290)
T ss_pred EEEEECCHHHHHHHHHhCCceEEEecCCC------CCCcee----EEEeecceEEEEEcCCChhhcCCCCHHHHhc
Confidence 34444456789999999999999974321 111232 24567788899988774321 1235677764
No 102
>cd08446 PBP2_Chlorocatechol The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in the chlorocatechol catabolism, contains the type 2 periplasmic binding fold. This CD includes the substrate binding domain of LysR-type regulators CbnR, ClcR and TfdR, which are involved in the regulation of chlorocatechol breakdown. The chlorocatechol-degradative pathway is often found in bacteria that can use chlorinated aromatic compounds as carbon and energy sources. CbnR is found in the 3-chlorobenzoate degradative bacterium Ralstonia eutropha NH9 and forms a tetramer. CbnR activates the expression of the cbnABCD genes, which are responsible for the degradation of chlorocatechol converted from 3-chlorobenzoate and are transcribed divergently from cbnR. In soil bacterium Pseudomonas putida, the 3-chlorocatechol-degradative pathway is encoded by clcABD operon, which requires the divergently transcribed clcR for activation. TfdR is involved in the activation of tf
Probab=59.78 E-value=36 Score=26.70 Aligned_cols=67 Identities=21% Similarity=0.311 Sum_probs=38.2
Q ss_pred CCeEEEee--cCcchhhhhhcCceeeeeeccceeecccCCCcceeeecCCCCcccEEEEEEEeCCCcc--ccccchHHhh
Q 025329 125 SNLEVWFQ--RPKDIVRKLLSGDLDLGIVGLDTVSEFGQGNEDLIIVHDALDYGDCRLSLAIPKYGIF--ENINSLRELA 200 (254)
Q Consensus 125 p~iev~~v--Rp~DIp~yV~~G~aDlGIvG~DvL~E~~~d~~~l~~~l~dLgfG~CRLvVAvP~~~~~--~dv~sl~dL~ 200 (254)
|++++.+. ...++...+.+|.+|+||+.... . . .++. ...+++-+++++++.+.+. .+.-+++||.
T Consensus 28 P~v~l~i~~~~~~~~~~~l~~~~~Dl~i~~~~~-~--~---~~~~----~~~l~~~~~~~v~~~~~pl~~~~~~~~~~l~ 97 (198)
T cd08446 28 PDVTVSLHNMTKDEQIEALRAGRIHIGFGRFYP-V--E---PDIA----VENVAQERLYLAVPKSHPLAARPAVSLADLR 97 (198)
T ss_pred CCeEEEEeeCCHHHHHHHHHCCCccEEEEecCC-C--C---CCce----eEEeeeccEEEEEeCCCCcccCCccCHHHHc
Confidence 45555444 35678899999999999964321 1 1 1121 1234566677777665322 1234567775
Q ss_pred c
Q 025329 201 Q 201 (254)
Q Consensus 201 ~ 201 (254)
+
T Consensus 98 ~ 98 (198)
T cd08446 98 N 98 (198)
T ss_pred C
Confidence 3
No 103
>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=58.74 E-value=8.5 Score=32.97 Aligned_cols=95 Identities=26% Similarity=0.254 Sum_probs=60.1
Q ss_pred CeEEEeecCcchhhhhhcC-ceeeeeeccceeecccCCCcceeeecCCCCcccEEEEEEEeCCCccccccchHHhhcCCc
Q 025329 126 NLEVWFQRPKDIVRKLLSG-DLDLGIVGLDTVSEFGQGNEDLIIVHDALDYGDCRLSLAIPKYGIFENINSLRELAQMPQ 204 (254)
Q Consensus 126 ~iev~~vRp~DIp~yV~~G-~aDlGIvG~DvL~E~~~d~~~l~~~l~dLgfG~CRLvVAvP~~~~~~dv~sl~dL~~~~~ 204 (254)
++++.+....++...+..| ..|+-|.+.+..+|.... ......-..-.+..-.++++++++.+ .++.+++||...
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 899999997544332111 01111001245677789999999863 478889998631
Q ss_pred ccCCCCcEEEcCCCcc------HHHHHHHcC
Q 025329 205 WTAEKPLRVATGFTYL------GPKFMKDNG 229 (254)
Q Consensus 205 ~~~~r~lRVATkYPnL------arkyf~~~G 229 (254)
.+|||+-.|.. +..+|.+.|
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 46899998853 344555544
No 104
>PRK12680 transcriptional regulator CysB-like protein; Reviewed
Probab=58.67 E-value=32 Score=31.66 Aligned_cols=92 Identities=18% Similarity=0.183 Sum_probs=50.4
Q ss_pred CCeEEEee--cCcchhhhhhcCceeeeeeccceeecccCCCcceeeecCCCCcccEEEEEEEeCCCccc---cccchHHh
Q 025329 125 SNLEVWFQ--RPKDIVRKLLSGDLDLGIVGLDTVSEFGQGNEDLIIVHDALDYGDCRLSLAIPKYGIFE---NINSLREL 199 (254)
Q Consensus 125 p~iev~~v--Rp~DIp~yV~~G~aDlGIvG~DvL~E~~~d~~~l~~~l~dLgfG~CRLvVAvP~~~~~~---dv~sl~dL 199 (254)
|++++.+. ...++-..|..|.+|+||+......+. +.+ ...++.-++++++|.+.++. ..-+++||
T Consensus 120 P~v~i~l~~~~~~~~~~~l~~g~~Dl~i~~~~~~~~~-----~~~----~~~l~~~~~~l~~~~~hpl~~~~~~~~~~dl 190 (327)
T PRK12680 120 PQVSVHLQQAAESAALDLLGQGDADIAIVSTAGGEPS-----AGI----AVPLYRWRRLVVVPRGHALDTPRRAPDMAAL 190 (327)
T ss_pred CCcEEEEEeCChHHHHHHHHCCCCcEEEEecCCCCCC-----cce----EEEeeccceEEEEeCCChhhccCCCCCHHHH
Confidence 55555443 568899999999999999754321111 111 12344556677777654322 12356777
Q ss_pred hcCCcccCCCCcEEEc--CCCccHHHHHHHcCCc
Q 025329 200 AQMPQWTAEKPLRVAT--GFTYLGPKFMKDNGLK 231 (254)
Q Consensus 200 ~~~~~~~~~r~lRVAT--kYPnLarkyf~~~Gi~ 231 (254)
.+.+- +.... .+-+...++|++.|+.
T Consensus 191 ~~~~~------i~~~~~~~~~~~~~~~~~~~~~~ 218 (327)
T PRK12680 191 AEHPL------ISYESSTRPGSSLQRAFAQLGLE 218 (327)
T ss_pred hcCCE------EEecCCCchHHHHHHHHHHCCCC
Confidence 64311 11111 1224566788888863
No 105
>PRK10797 glutamate and aspartate transporter subunit; Provisional
Probab=58.10 E-value=37 Score=31.12 Aligned_cols=64 Identities=14% Similarity=0.068 Sum_probs=40.6
Q ss_pred EEEeecCcchhhhhhcCceeeeeeccceeecccCCCcceeeecCCCCcccEEEEEEEeCCCccccccchHHhh
Q 025329 128 EVWFQRPKDIVRKLLSGDLDLGIVGLDTVSEFGQGNEDLIIVHDALDYGDCRLSLAIPKYGIFENINSLRELA 200 (254)
Q Consensus 128 ev~~vRp~DIp~yV~~G~aDlGIvG~DvL~E~~~d~~~l~~~l~dLgfG~CRLvVAvP~~~~~~dv~sl~dL~ 200 (254)
++.-......-..|..|.+|+.+.|.=+-.|.... +.. --.|..-..++.++.+. ++++++||.
T Consensus 89 ~~v~~~~~~~i~~L~~G~~Di~~~~~~~t~eR~~~----~~f--S~Py~~~~~~lv~r~~~---~i~sl~dL~ 152 (302)
T PRK10797 89 KLIPITSQNRIPLLQNGTFDFECGSTTNNLERQKQ----AAF--SDTIFVVGTRLLTKKGG---DIKDFADLK 152 (302)
T ss_pred EEEEcChHhHHHHHHCCCccEEecCCccCcchhhc----cee--cccEeeccEEEEEECCC---CCCChHHcC
Confidence 33333334466889999999988775443443221 211 23566777888888873 578899986
No 106
>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=57.68 E-value=17 Score=28.48 Aligned_cols=54 Identities=22% Similarity=0.364 Sum_probs=32.5
Q ss_pred CCeEEEee--cCcchhhhhhcCceeeeeeccceeecccCCCcceeeecCCCCcccEEEEEEEeCC
Q 025329 125 SNLEVWFQ--RPKDIVRKLLSGDLDLGIVGLDTVSEFGQGNEDLIIVHDALDYGDCRLSLAIPKY 187 (254)
Q Consensus 125 p~iev~~v--Rp~DIp~yV~~G~aDlGIvG~DvL~E~~~d~~~l~~~l~dLgfG~CRLvVAvP~~ 187 (254)
|++++.+. ...++-..+.+|.+|+||+....-.+. ++. -..++.-++++++|.+
T Consensus 27 P~v~l~~~~~~~~~~~~~l~~g~~Dl~i~~~~~~~~~-----~l~----~~~l~~~~~~~~~~~~ 82 (199)
T cd08430 27 PQVEIKLHTGDPADAIDKVLNGEADIAIAARPDKLPA-----RLA----FLPLATSPLVFIAPNI 82 (199)
T ss_pred CCceEEEEeCCHHHHHHHHHCCCCCEEEEecCCCCCc-----ccE----EEeeccceEEEEEeCC
Confidence 44444443 456788899999999999864321111 121 1234556677777776
No 107
>PRK12684 transcriptional regulator CysB-like protein; Reviewed
Probab=56.44 E-value=45 Score=30.21 Aligned_cols=68 Identities=21% Similarity=0.263 Sum_probs=40.9
Q ss_pred CCeEEE--eecCcchhhhhhcCceeeeeeccceeecccCCCcceeeecCCCCcccEEEEEEEeCCCccc--cccchHHhh
Q 025329 125 SNLEVW--FQRPKDIVRKLLSGDLDLGIVGLDTVSEFGQGNEDLIIVHDALDYGDCRLSLAIPKYGIFE--NINSLRELA 200 (254)
Q Consensus 125 p~iev~--~vRp~DIp~yV~~G~aDlGIvG~DvL~E~~~d~~~l~~~l~dLgfG~CRLvVAvP~~~~~~--dv~sl~dL~ 200 (254)
|++++. .....++-..+.+|.+|+||+..+... . .++. ...+++-.+++.+|.+.++. ..-+++||.
T Consensus 120 p~i~l~~~~~~~~~~~~~L~~g~~D~~i~~~~~~~--~---~~l~----~~~l~~~~~~~v~~~~~pl~~~~~i~~~dL~ 190 (313)
T PRK12684 120 PKVRLSILQGSPTQIAEMVLHGQADLAIATEAIAD--Y---KELV----SLPCYQWNHCVVVPPDHPLLERKPLTLEDLA 190 (313)
T ss_pred CCceEEEEeCChHHHHHHHHCCCcCEEEeecCCCC--C---CCce----EEEeccceEEEEeCCCCccccCCCcCHHHHh
Confidence 444444 345678899999999999998643211 1 1122 24566677777777774332 123567776
Q ss_pred c
Q 025329 201 Q 201 (254)
Q Consensus 201 ~ 201 (254)
+
T Consensus 191 ~ 191 (313)
T PRK12684 191 Q 191 (313)
T ss_pred c
Confidence 4
No 108
>PRK11013 DNA-binding transcriptional regulator LysR; Provisional
Probab=56.07 E-value=22 Score=31.99 Aligned_cols=89 Identities=13% Similarity=0.135 Sum_probs=50.3
Q ss_pred eEEEeecCcchhhhhhcCceeeeeeccceeecccCCCcceeeecCCCCcccEEEEEEEeCCCccc--cccchHHhhcCCc
Q 025329 127 LEVWFQRPKDIVRKLLSGDLDLGIVGLDTVSEFGQGNEDLIIVHDALDYGDCRLSLAIPKYGIFE--NINSLRELAQMPQ 204 (254)
Q Consensus 127 iev~~vRp~DIp~yV~~G~aDlGIvG~DvL~E~~~d~~~l~~~l~dLgfG~CRLvVAvP~~~~~~--dv~sl~dL~~~~~ 204 (254)
+++......++-..+.+|.+|+||+..+.. +.+ +.. --++...+++++|.+.+.. +.-+++||...+
T Consensus 125 i~i~~~~~~~~~~~l~~~~~Dl~i~~~~~~-~~~-----~~~----~~l~~~~~~~~~~~~~pl~~~~~i~~~dL~~~~- 193 (309)
T PRK11013 125 LNIVPQESPLLEEWLSAQRHDLGLTETLHT-PAG-----TER----TELLTLDEVCVLPAGHPLAAKKVLTPDDFAGEN- 193 (309)
T ss_pred EEEEeCCHHHHHHHHHcCCCCEEEEcCCCC-CCC-----cee----eeecceeEEEEEcCCCccccCCccCHHHHCCCc-
Confidence 444444667788899999999999865532 222 111 1233455666777664321 223567776321
Q ss_pred ccCCCCcEE--EcCCCccHHHHHHHcCCc
Q 025329 205 WTAEKPLRV--ATGFTYLGPKFMKDNGLK 231 (254)
Q Consensus 205 ~~~~r~lRV--ATkYPnLarkyf~~~Gi~ 231 (254)
+ +.. .+.|..+..+||++.|+.
T Consensus 194 ~-----i~~~~~~~~~~~~~~~~~~~~~~ 217 (309)
T PRK11013 194 F-----ISLSRTDSYRQLLDQLFAEHGVK 217 (309)
T ss_pred E-----EeecCCCcHHHHHHHHHHHcCCC
Confidence 1 111 123445677888888874
No 109
>COG1464 NlpA ABC-type metal ion transport system, periplasmic component/surface antigen [Inorganic ion transport and metabolism]
Probab=55.92 E-value=42 Score=31.66 Aligned_cols=101 Identities=15% Similarity=0.177 Sum_probs=68.7
Q ss_pred ceEEEecCCCCChHHHHHHHHhCCCccCCCCCCceEe---ecC-CCCCeEEEeecCcchhhhhhcCceeeeeeccceeec
Q 025329 83 EIRLGLPSKGRMAADTLDLLKDCQLSVKQVNPRQYVA---QIP-QLSNLEVWFQRPKDIVRKLLSGDLDLGIVGLDTVSE 158 (254)
Q Consensus 83 ~LrIALPsKGRL~e~tl~LL~~aGi~v~~~~~R~L~~---~~~-~~p~iev~~vRp~DIp~yV~~G~aDlGIvG~DvL~E 158 (254)
--+||+|++-.=..-.+.+|+++|+---+.. ..+.+ +|. |-.+++|.-+.+.=.|+-+.+ +|+.|+-.++.++
T Consensus 128 GatIaiPNDpsN~gRAL~lL~~aGLIkLk~~-~~~~aT~~DI~eNPK~lki~EldAaqlpRaLdd--vD~AvIN~nyA~~ 204 (268)
T COG1464 128 GATIAIPNDPTNEGRALLLLQKAGLIKLKDG-VNLLATPKDITENPKNLKIKELEAAQLPRALDD--VDAAVINTNYALQ 204 (268)
T ss_pred CCEEECCCCCCchhHHHHHHHHCCcEEEcCC-CcccCCHHHHhhCcccCeEEEcchHhccccccc--cCEEEEcchHHHH
Confidence 3679999988888889999999998332221 12322 111 224678888899999999988 7999999999999
Q ss_pred ccCCCc-ceeeecCCCC-cccEEEEEEEeCC
Q 025329 159 FGQGNE-DLIIVHDALD-YGDCRLSLAIPKY 187 (254)
Q Consensus 159 ~~~d~~-~l~~~l~dLg-fG~CRLvVAvP~~ 187 (254)
.|.+.. +.+. .++.. -=...+.++-+.+
T Consensus 205 AgL~p~kdai~-~e~~~~spY~Niivvr~~d 234 (268)
T COG1464 205 AGLNPKKDALF-EEDKDSSPYVNIIVVREED 234 (268)
T ss_pred cCCCcccccee-cccccCCcceEEEEEcccc
Confidence 998753 3332 22222 3345555555544
No 110
>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=55.77 E-value=12 Score=31.46 Aligned_cols=60 Identities=20% Similarity=0.325 Sum_probs=41.1
Q ss_pred CCCCCCceEEEecCCCCChH-HHHHHHHhCCCccCCCCCCceEeecCCCCCeEEEeecCcchhhhhhcCceeeeeec
Q 025329 77 RISERDEIRLGLPSKGRMAA-DTLDLLKDCQLSVKQVNPRQYVAQIPQLSNLEVWFQRPKDIVRKLLSGDLDLGIVG 152 (254)
Q Consensus 77 ~~~~~~~LrIALPsKGRL~e-~tl~LL~~aGi~v~~~~~R~L~~~~~~~p~iev~~vRp~DIp~yV~~G~aDlGIvG 152 (254)
++.+..-=|||++. |...+ -...+|++.|++.. +++++-+.+.++...+..|.+|.++.+
T Consensus 87 ~~~DLkGK~i~v~~-~s~~~~~~~~~l~~~g~~~~---------------~v~~v~~~~~~~~~al~~g~vDa~~~~ 147 (216)
T PF09084_consen 87 SPADLKGKKIGVSR-GSSSEYFLRALLKKNGIDPD---------------DVKIVNLGPPELAQALLSGQVDAAILW 147 (216)
T ss_dssp SGGGGTTSEEEEST-TSHHHHHHHHHHHHTTT-GG---------------GSEEEES-HHHHHHHHHTTSSSEEEEE
T ss_pred CHHHhCCCEEEEec-CcchhHHHHHHHHHhccccc---------------cceeeeeehhhhhhhhhcCCCCEEEEc
Confidence 44544456999995 76655 45568889898432 244555556788889999999999943
No 111
>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=55.08 E-value=20 Score=28.18 Aligned_cols=68 Identities=13% Similarity=0.104 Sum_probs=38.5
Q ss_pred CCeEEEee--cCcchhhhhhcCceeeeeeccceeecccCCCcceeeecCCCCcccEEEEEEEeCCCccc---cccchHHh
Q 025329 125 SNLEVWFQ--RPKDIVRKLLSGDLDLGIVGLDTVSEFGQGNEDLIIVHDALDYGDCRLSLAIPKYGIFE---NINSLREL 199 (254)
Q Consensus 125 p~iev~~v--Rp~DIp~yV~~G~aDlGIvG~DvL~E~~~d~~~l~~~l~dLgfG~CRLvVAvP~~~~~~---dv~sl~dL 199 (254)
|++++.+. ...++...+..|.+|+||+....... .++. -.-++...++++++.+.+.. ..-+++||
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 46788899999999999974321111 1222 12345567777776653221 12356777
Q ss_pred hc
Q 025329 200 AQ 201 (254)
Q Consensus 200 ~~ 201 (254)
..
T Consensus 98 ~~ 99 (195)
T cd08431 98 KQ 99 (195)
T ss_pred hh
Confidence 53
No 112
>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=54.99 E-value=16 Score=28.62 Aligned_cols=66 Identities=20% Similarity=0.237 Sum_probs=39.2
Q ss_pred CCeEEEee--cCcchhhhhhcCceeeeeeccceeecccCCCcceeeecCCCCcccEEEEEEEeCCCccc--cccchHHhh
Q 025329 125 SNLEVWFQ--RPKDIVRKLLSGDLDLGIVGLDTVSEFGQGNEDLIIVHDALDYGDCRLSLAIPKYGIFE--NINSLRELA 200 (254)
Q Consensus 125 p~iev~~v--Rp~DIp~yV~~G~aDlGIvG~DvL~E~~~d~~~l~~~l~dLgfG~CRLvVAvP~~~~~~--dv~sl~dL~ 200 (254)
|++++-+. ...|+...+.+|.+|+||+..+.. . .++. ...+++-+++++++.+.+.. ..-+++||.
T Consensus 27 P~i~v~~~~~~~~~~~~~l~~g~~D~~i~~~~~~---~---~~~~----~~~l~~~~~~~v~~~~~pl~~~~~~~~~~l~ 96 (198)
T cd08447 27 PDVDLVLREMVTTDQIEALESGRIDLGLLRPPFA---R---PGLE----TRPLVREPLVAAVPAGHPLAGAERLTLEDLD 96 (198)
T ss_pred CCeEEEEEeCCHHHHHHHHHcCCceEEEecCCCC---C---CCee----EEEeecCceEEEecCCCchhhcCcccHHHhC
Confidence 55555554 567999999999999999854321 1 1122 12345566677776653221 123567765
No 113
>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=52.42 E-value=21 Score=28.05 Aligned_cols=29 Identities=21% Similarity=0.388 Sum_probs=21.9
Q ss_pred CCeEEEee--cCcchhhhhhcCceeeeeecc
Q 025329 125 SNLEVWFQ--RPKDIVRKLLSGDLDLGIVGL 153 (254)
Q Consensus 125 p~iev~~v--Rp~DIp~yV~~G~aDlGIvG~ 153 (254)
|++++.+. ...++...+.+|.+|+||+..
T Consensus 27 P~v~i~~~~~~~~~~~~~l~~~~~Dl~i~~~ 57 (185)
T cd08439 27 PRLAIEVVCKRTPRLMEMLERGEVDLALITH 57 (185)
T ss_pred CCeEEEEEECChHHHHHHHHCCCCcEEEEec
Confidence 44544443 567889999999999999854
No 114
>PRK14498 putative molybdopterin biosynthesis protein MoeA/LysR substrate binding-domain-containing protein; Provisional
Probab=52.38 E-value=48 Score=33.86 Aligned_cols=92 Identities=18% Similarity=0.161 Sum_probs=57.6
Q ss_pred eEEEeecCcchhhhhhcCceeeeeeccceeeccc-C---------CCcceeeecCCCCcccEEEEEEEeCCCccccccch
Q 025329 127 LEVWFQRPKDIVRKLLSGDLDLGIVGLDTVSEFG-Q---------GNEDLIIVHDALDYGDCRLSLAIPKYGIFENINSL 196 (254)
Q Consensus 127 iev~~vRp~DIp~yV~~G~aDlGIvG~DvL~E~~-~---------d~~~l~~~l~dLgfG~CRLvVAvP~~~~~~dv~sl 196 (254)
+++......++-..|..|.+|+||+.... .+.+ . +...+- -..+..=++++++|.+.++. .-++
T Consensus 443 i~v~~~~s~~vl~~L~~GeiDlai~~~~~-~~~~~~~~~~~~~~~~~~~l~----~~~l~~d~lvlvvp~~hPl~-~isl 516 (633)
T PRK14498 443 LRSLHVGSMGGLMALKRGEADIAGIHLLD-PETGEYNIPYIKKYLLGEDAV----LVKGYRREQGLVVRKGNPKG-IEGI 516 (633)
T ss_pred eeEEecCCHHHHHHHHcCCceEEEEcccC-cccccccHHHHHhhcCCCCEE----EEEEEEEeEEEEECCCCCCC-CCCH
Confidence 56667789999999999999999975432 1111 0 000111 13455678899999986653 4588
Q ss_pred HHhhcCCcccCCCCcEEE-----cCCCccHHHHHHHcCCc
Q 025329 197 RELAQMPQWTAEKPLRVA-----TGFTYLGPKFMKDNGLK 231 (254)
Q Consensus 197 ~dL~~~~~~~~~r~lRVA-----TkYPnLarkyf~~~Gi~ 231 (254)
+||.+. .+++. +.+-.+..++|++.|+.
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 998743 01221 22335667788888884
No 115
>PRK04168 molybdate ABC transporter periplasmic substrate-binding protein; Provisional
Probab=52.26 E-value=27 Score=33.07 Aligned_cols=24 Identities=13% Similarity=0.331 Sum_probs=19.7
Q ss_pred chhhhhhcCceeeeeeccceeecc
Q 025329 136 DIVRKLLSGDLDLGIVGLDTVSEF 159 (254)
Q Consensus 136 DIp~yV~~G~aDlGIvG~DvL~E~ 159 (254)
++-.||+.|.+|+||+-.-.....
T Consensus 213 ~~~~~v~~G~aDagivy~S~a~~~ 236 (334)
T PRK04168 213 ELLSLLETGNMDYAFIYKSVAVQH 236 (334)
T ss_pred hhHHHHhcCCccEEEEEeeehhhC
Confidence 789999999999999976654443
No 116
>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=51.99 E-value=18 Score=28.53 Aligned_cols=93 Identities=17% Similarity=0.140 Sum_probs=49.5
Q ss_pred CCeEEEee--cCcchhhhhhcCceeeeeeccceeecccCCCcceeeecCCCCcccEEEEEEEeCCCccc--cccchHHhh
Q 025329 125 SNLEVWFQ--RPKDIVRKLLSGDLDLGIVGLDTVSEFGQGNEDLIIVHDALDYGDCRLSLAIPKYGIFE--NINSLRELA 200 (254)
Q Consensus 125 p~iev~~v--Rp~DIp~yV~~G~aDlGIvG~DvL~E~~~d~~~l~~~l~dLgfG~CRLvVAvP~~~~~~--dv~sl~dL~ 200 (254)
|++++.+. ...++...+.+|.+|+||.-.+. . . .++. ..-++...++++++.+.++. ..-+++||.
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 45555443 45689999999999999963221 1 1 1222 23456667777777663221 123566765
Q ss_pred cCCcccCCCCcEEEcCCCccHHHHHHHcCCc
Q 025329 201 QMPQWTAEKPLRVATGFTYLGPKFMKDNGLK 231 (254)
Q Consensus 201 ~~~~~~~~r~lRVATkYPnLarkyf~~~Gi~ 231 (254)
..+ +-. ..-.+.+.....+||++.|+.
T Consensus 97 ~~~-~i~---~~~~~~~~~~~~~~~~~~~~~ 123 (198)
T cd08441 97 DET-LIT---YPVERERLDVFRHFLQPAGIE 123 (198)
T ss_pred CCc-eEE---ecCCccHHHHHHHHHHhcCCC
Confidence 321 100 000112234456678777763
No 117
>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=51.15 E-value=36 Score=26.65 Aligned_cols=87 Identities=13% Similarity=0.029 Sum_probs=41.5
Q ss_pred CCeEEEeecCcchhhhhhcCceeeeeeccceeecccCCCcceeeecCCCCcccEEEEEEEeCCCccccccchHHhhcCCc
Q 025329 125 SNLEVWFQRPKDIVRKLLSGDLDLGIVGLDTVSEFGQGNEDLIIVHDALDYGDCRLSLAIPKYGIFENINSLRELAQMPQ 204 (254)
Q Consensus 125 p~iev~~vRp~DIp~yV~~G~aDlGIvG~DvL~E~~~d~~~l~~~l~dLgfG~CRLvVAvP~~~~~~dv~sl~dL~~~~~ 204 (254)
|++++.+.-..+....+.. .+|+||+..... . .++. -..++.=+++++++.+-. ...-+++||.+.+
T Consensus 27 P~i~l~~~~~~~~~~~~~~-~~D~~i~~~~~~-~-----~~l~----~~~l~~~~~~~v~~~~~~-~~~~~~~~L~~~~- 93 (189)
T cd08484 27 PFIDLRLSTNNNRVDIAAE-GLDFAIRFGEGA-W-----PGTD----ATRLFEAPLSPLCTPELA-RRLSEPADLANET- 93 (189)
T ss_pred CCceEEEecccCccccccC-CccEEEEecCCC-C-----CCce----EEEccCCceEEeeCHHHh-cccCChhHhhcCc-
Confidence 4455554433344444555 499999854321 1 1111 123445556666665411 1123567776421
Q ss_pred ccCCCCcEEEcCCCccHHHHHHHcCCc
Q 025329 205 WTAEKPLRVATGFTYLGPKFMKDNGLK 231 (254)
Q Consensus 205 ~~~~r~lRVATkYPnLarkyf~~~Gi~ 231 (254)
-|.......-+++|+++|+.
T Consensus 94 -------~i~~~~~~~~~~~~~~~~~~ 113 (189)
T cd08484 94 -------LLRSYRADEWPQWFEAAGVP 113 (189)
T ss_pred -------eEecCCCchHHHHHHHcCCC
Confidence 13211112345688888863
No 118
>CHL00180 rbcR LysR transcriptional regulator; Provisional
Probab=51.08 E-value=52 Score=29.45 Aligned_cols=89 Identities=20% Similarity=0.310 Sum_probs=50.7
Q ss_pred EEEeecCcchhhhhhcCceeeeeeccceeecccCCCcceeeecCCCCcccEEEEEEEeCCCccc--cccchHHhhcCCcc
Q 025329 128 EVWFQRPKDIVRKLLSGDLDLGIVGLDTVSEFGQGNEDLIIVHDALDYGDCRLSLAIPKYGIFE--NINSLRELAQMPQW 205 (254)
Q Consensus 128 ev~~vRp~DIp~yV~~G~aDlGIvG~DvL~E~~~d~~~l~~~l~dLgfG~CRLvVAvP~~~~~~--dv~sl~dL~~~~~~ 205 (254)
++......++...|.+|.+|+||++.+.-.+.. ..+. ...++.-++++++|.+.+.. ..-+++||...+
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 343335677888999999999998654222111 1122 24566778899988764322 122567775321
Q ss_pred cCCCCcEEEcC----CCccHHHHHHHcCCc
Q 025329 206 TAEKPLRVATG----FTYLGPKFMKDNGLK 231 (254)
Q Consensus 206 ~~~r~lRVATk----YPnLarkyf~~~Gi~ 231 (254)
-|... +.....++|++.|+.
T Consensus 198 ------~i~~~~~~~~~~~~~~~~~~~~~~ 221 (305)
T CHL00180 198 ------FITLDSNSTIRKVIDNILIQNGID 221 (305)
T ss_pred ------ceEecCCCcHHHHHHHHHHHcCCC
Confidence 12222 223455677777763
No 119
>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=49.07 E-value=43 Score=26.12 Aligned_cols=86 Identities=14% Similarity=0.085 Sum_probs=43.4
Q ss_pred CCeEEEeecCcchhhhhhcCceeeeeeccceeecccCCCcceeeecCCCCcccEEEEEEEeCCCccccccchHHhhcCCc
Q 025329 125 SNLEVWFQRPKDIVRKLLSGDLDLGIVGLDTVSEFGQGNEDLIIVHDALDYGDCRLSLAIPKYGIFENINSLRELAQMPQ 204 (254)
Q Consensus 125 p~iev~~vRp~DIp~yV~~G~aDlGIvG~DvL~E~~~d~~~l~~~l~dLgfG~CRLvVAvP~~~~~~dv~sl~dL~~~~~ 204 (254)
|++++.+.-..++.. +..|.+|+||+..... . .++. .-.+++.+++++++++.. ...-+++||...+
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 445555443344555 5556799999753211 1 1111 123456667777766521 1123567775321
Q ss_pred ccCCCCcEEE-cCCCccHHHHHHHcCCc
Q 025329 205 WTAEKPLRVA-TGFTYLGPKFMKDNGLK 231 (254)
Q Consensus 205 ~~~~r~lRVA-TkYPnLarkyf~~~Gi~ 231 (254)
. |. +. .+...++|++.|+.
T Consensus 94 ------~-i~~~~-~~~~~~~~~~~~~~ 113 (189)
T cd08487 94 ------L-LRSYR-TDEWLQWFEAANMP 113 (189)
T ss_pred ------e-eecCC-chHHHHHHHHcCCC
Confidence 1 21 11 13456788888864
No 120
>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=48.69 E-value=54 Score=29.22 Aligned_cols=69 Identities=19% Similarity=0.170 Sum_probs=37.6
Q ss_pred cchhhhhhcCceeeeeeccceeec--ccCCCcceeeecCCCCcccE-EEEEEEeCCCccccccchHHhhcCCcccCCCCc
Q 025329 135 KDIVRKLLSGDLDLGIVGLDTVSE--FGQGNEDLIIVHDALDYGDC-RLSLAIPKYGIFENINSLRELAQMPQWTAEKPL 211 (254)
Q Consensus 135 ~DIp~yV~~G~aDlGIvG~DvL~E--~~~d~~~l~~~l~dLgfG~C-RLvVAvP~~~~~~dv~sl~dL~~~~~~~~~r~l 211 (254)
.+.-..+..|.+|+++.+.-.+.. .+.+...+.... ...++.. ..++.++.+ .++++++||+ ++
T Consensus 70 ~~~~~al~~g~~D~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~y~~~lvv~~d---s~i~sl~DL~---------Gk 136 (288)
T TIGR03431 70 AGVIEGMRFGKVDIAWYGPSSYAEAYQKANAEAFAIEV-NADGSTGYYSVLIVKKD---SPIKSLEDLK---------GK 136 (288)
T ss_pred HHHHHHHHcCCccEEEEChHHHHHHHHhcCCeEEEEec-cCCCCCceEEEEEEeCC---CCCCcHHHhC---------CC
Confidence 456677899999999977422211 222211121111 1222211 146667777 4578899985 46
Q ss_pred EEEcC
Q 025329 212 RVATG 216 (254)
Q Consensus 212 RVATk 216 (254)
|||+-
T Consensus 137 ~v~~~ 141 (288)
T TIGR03431 137 TFGFV 141 (288)
T ss_pred EEEee
Confidence 78754
No 121
>PRK11074 putative DNA-binding transcriptional regulator; Provisional
Probab=46.97 E-value=49 Score=29.51 Aligned_cols=99 Identities=15% Similarity=0.161 Sum_probs=54.7
Q ss_pred CCCceEEEecCCCCChHHHHHHHHhCCCccCCCCCCceEeecCCCCCeEEEe--ecCcchhhhhhcCceeeeeeccceee
Q 025329 80 ERDEIRLGLPSKGRMAADTLDLLKDCQLSVKQVNPRQYVAQIPQLSNLEVWF--QRPKDIVRKLLSGDLDLGIVGLDTVS 157 (254)
Q Consensus 80 ~~~~LrIALPsKGRL~e~tl~LL~~aGi~v~~~~~R~L~~~~~~~p~iev~~--vRp~DIp~yV~~G~aDlGIvG~DvL~ 157 (254)
..+.|+||++ ..-...-..+++...- . ..|++++.+ -...|+...|.+|.+|+||+......
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 3467888887 3433333333333310 0 124444433 34678999999999999997432111
Q ss_pred cccCCCcceeeecCCCCcccEEEEEEEeCCCccc---cccchHHhhcC
Q 025329 158 EFGQGNEDLIIVHDALDYGDCRLSLAIPKYGIFE---NINSLRELAQM 202 (254)
Q Consensus 158 E~~~d~~~l~~~l~dLgfG~CRLvVAvP~~~~~~---dv~sl~dL~~~ 202 (254)
.. .++. -..++..+++++++++-++. ..-+++||...
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 1122 23567778888887764332 12467787643
No 122
>PRK11139 DNA-binding transcriptional activator GcvA; Provisional
Probab=46.88 E-value=63 Score=28.64 Aligned_cols=87 Identities=15% Similarity=0.094 Sum_probs=47.4
Q ss_pred CCeEEEeecCcchhhhhhcCceeeeeeccceeecccCCCcceeeecCCCCcccEEEEEEEeCCCc--cccccchHHhhcC
Q 025329 125 SNLEVWFQRPKDIVRKLLSGDLDLGIVGLDTVSEFGQGNEDLIIVHDALDYGDCRLSLAIPKYGI--FENINSLRELAQM 202 (254)
Q Consensus 125 p~iev~~vRp~DIp~yV~~G~aDlGIvG~DvL~E~~~d~~~l~~~l~dLgfG~CRLvVAvP~~~~--~~dv~sl~dL~~~ 202 (254)
|++++-+.. .+....+..|.+|+||+.... .. .++. .-.++...++++++.+-. ....-+++||.+.
T Consensus 121 p~i~i~l~~-~~~~~~l~~g~~Dl~i~~~~~----~~--~~l~----~~~l~~~~~~~~~~~~~~~~~~~~i~~~dL~~~ 189 (297)
T PRK11139 121 PDIDVRLKA-VDRLEDFLRDDVDVAIRYGRG----NW--PGLR----VEKLLDEYLLPVCSPALLNGGKPLKTPEDLARH 189 (297)
T ss_pred CCceEEEEe-CCChhhhccCCCCEEEEeCCC----CC--CCce----EEEeccceeEEEeCHHHhcccCCCCCHHHhhcC
Confidence 445554443 455678999999999986421 11 1122 234556666766655421 1223467787642
Q ss_pred CcccCCCCcEEEcCCCccHHHHHHHcCC
Q 025329 203 PQWTAEKPLRVATGFTYLGPKFMKDNGL 230 (254)
Q Consensus 203 ~~~~~~r~lRVATkYPnLarkyf~~~Gi 230 (254)
+ =|...-.+...+||.+.|.
T Consensus 190 p--------~i~~~~~~~~~~~~~~~~~ 209 (297)
T PRK11139 190 T--------LLHDDSREDWRAWFRAAGL 209 (297)
T ss_pred c--------eEeecCcccHHHHHHHhCC
Confidence 1 1222223445678877776
No 123
>PRK15421 DNA-binding transcriptional regulator MetR; Provisional
Probab=46.60 E-value=39 Score=30.82 Aligned_cols=92 Identities=15% Similarity=0.050 Sum_probs=51.9
Q ss_pred EEEeecCcchhhhhhcCceeeeeeccceeecccCCCcceeeecCCCCcccEEEEEEEeCCCcccc--ccchHHhhcCCcc
Q 025329 128 EVWFQRPKDIVRKLLSGDLDLGIVGLDTVSEFGQGNEDLIIVHDALDYGDCRLSLAIPKYGIFEN--INSLRELAQMPQW 205 (254)
Q Consensus 128 ev~~vRp~DIp~yV~~G~aDlGIvG~DvL~E~~~d~~~l~~~l~dLgfG~CRLvVAvP~~~~~~d--v~sl~dL~~~~~~ 205 (254)
++......|+-..|..|.+|+||+....- ..++. --.+++.+++++++.+.++.. .-+++||...+ +
T Consensus 121 ~~~~~~~~~~~~~L~~g~~Dl~i~~~~~~------~~~~~----~~~l~~~~~~lv~~~~hpl~~~~~i~~~~L~~~p-~ 189 (317)
T PRK15421 121 DFKSGVTFDPQPALQQGELDLVMTSDILP------RSGLH----YSPMFDYEVRLVLAPDHPLAAKTRITPEDLASET-L 189 (317)
T ss_pred EEEeCccHHHHHHHHCCCcCEEEecCccc------CCCce----EEEeccceEEEEEcCCCCccccCcCCHHHhCCCc-E
Confidence 33334567888999999999999753211 11222 235678899999887743321 23567775421 1
Q ss_pred cCCCCcEEEc--CCCccHHHHHHHcCCceEEEE
Q 025329 206 TAEKPLRVAT--GFTYLGPKFMKDNGLKHVVFS 236 (254)
Q Consensus 206 ~~~r~lRVAT--kYPnLarkyf~~~Gi~~veIi 236 (254)
+-... ......+.||++.|++ .+++
T Consensus 190 -----i~~~~~~~~~~~~~~~~~~~~~~-~~~~ 216 (317)
T PRK15421 190 -----LIYPVQRSRLDVWRHFLQPAGVS-PSLK 216 (317)
T ss_pred -----EecCCchhhHHHHHHHHHHhCCC-Ccee
Confidence 11111 1123345677788874 3443
No 124
>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=45.32 E-value=66 Score=28.82 Aligned_cols=66 Identities=20% Similarity=0.257 Sum_probs=46.7
Q ss_pred CCCCCCceEEEecCCCCChH-HHHHHHHhCCCccCCCCCCceEeecCCCCCeEEEeecCcchhhhhhcCceeeeeeccce
Q 025329 77 RISERDEIRLGLPSKGRMAA-DTLDLLKDCQLSVKQVNPRQYVAQIPQLSNLEVWFQRPKDIVRKLLSGDLDLGIVGLDT 155 (254)
Q Consensus 77 ~~~~~~~LrIALPsKGRL~e-~tl~LL~~aGi~v~~~~~R~L~~~~~~~p~iev~~vRp~DIp~yV~~G~aDlGIvG~Dv 155 (254)
++.+-.--|||++ +|...+ -...+|++.|++.. +++++.+.+.|....+..|.+|..++...+
T Consensus 94 s~~DLkGK~Igv~-~~s~~~~~l~~~L~~~Gl~~~---------------dv~~v~~~~~~~~~al~~G~vDa~~~~~p~ 157 (300)
T TIGR01729 94 KPEDLKGKNVAVP-FVSTTHYSLLAALKHWKTDPR---------------EVNILNLKPPQIVAAWQRGDIDAAYVWPPA 157 (300)
T ss_pred ChhHcCCCEEEeC-CCCcHHHHHHHHHHHcCCChh---------------heEEEecCcHHHHHHHHcCCcCEEEEecHH
Confidence 4444445689998 565544 34567888887431 245555677899999999999999998877
Q ss_pred eec
Q 025329 156 VSE 158 (254)
Q Consensus 156 L~E 158 (254)
..+
T Consensus 158 ~~~ 160 (300)
T TIGR01729 158 LSE 160 (300)
T ss_pred HHH
Confidence 644
No 125
>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=45.05 E-value=36 Score=28.85 Aligned_cols=94 Identities=21% Similarity=0.288 Sum_probs=52.9
Q ss_pred eEEEeecCcchhhhhhcCc-eeeeeeccceeecccCCCcceeeecCCCCcccEEEEEEEeCCCccccccchHHhhcCCcc
Q 025329 127 LEVWFQRPKDIVRKLLSGD-LDLGIVGLDTVSEFGQGNEDLIIVHDALDYGDCRLSLAIPKYGIFENINSLRELAQMPQW 205 (254)
Q Consensus 127 iev~~vRp~DIp~yV~~G~-aDlGIvG~DvL~E~~~d~~~l~~~l~dLgfG~CRLvVAvP~~~~~~dv~sl~dL~~~~~~ 205 (254)
+++.+--..++...+..|. +|+.+.+.....+.-.+ ..++.....-.|+.-+++++++.+ ..+++++||. + |
T Consensus 23 V~~~~~gs~~l~~~l~~~~~aDv~~~~~~~~~~~l~~-~g~~~~~~~~~~~~~~~~l~~~~~---~~~~s~~dL~--~-~ 95 (216)
T TIGR01256 23 VVFSFGSSGTLYTQIENGAPADLFISADNKWPKKLVD-KGLVVAGSRFTYAGNKLVLISPKN---RVVDDLDILK--K-W 95 (216)
T ss_pred EEEEeCChHHHHHHHHcCCCCcEEEECCHHHHHHHHH-CCCCCCCchheEEccEEEEEEECC---CCcCcHHHHh--h-c
Confidence 3344445567777777775 99999986432222110 111211112246677899999887 4567889985 1 2
Q ss_pred cCCCCcEEEcCCCcc------HHHHHHHcC
Q 025329 206 TAEKPLRVATGFTYL------GPKFMKDNG 229 (254)
Q Consensus 206 ~~~r~lRVATkYPnL------arkyf~~~G 229 (254)
.. ..||+.-.|+. +..+++..|
T Consensus 96 ~~--~~~i~~~~P~~~~~g~~~~~~~~~~g 123 (216)
T TIGR01256 96 VA--DKRVAIGDPKHAPYGAAAKEVLQKLG 123 (216)
T ss_pred cc--CCeEEecCCCcCcChHHHHHHHHHCC
Confidence 11 24788766553 344555555
No 126
>PRK12679 cbl transcriptional regulator Cbl; Reviewed
Probab=44.57 E-value=60 Score=29.43 Aligned_cols=90 Identities=19% Similarity=0.254 Sum_probs=48.8
Q ss_pred CCeEEEee--cCcchhhhhhcCceeeeeeccceeecccCCCcceeeecCCCCcccEEEEEEEeCCCccc--cccchHHhh
Q 025329 125 SNLEVWFQ--RPKDIVRKLLSGDLDLGIVGLDTVSEFGQGNEDLIIVHDALDYGDCRLSLAIPKYGIFE--NINSLRELA 200 (254)
Q Consensus 125 p~iev~~v--Rp~DIp~yV~~G~aDlGIvG~DvL~E~~~d~~~l~~~l~dLgfG~CRLvVAvP~~~~~~--dv~sl~dL~ 200 (254)
|++++.+. ..+++...+.+|.+|+||+....... .++. .-.++.=+++++++.+.+.. ..-+++||.
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 34588899999999999974321111 1122 12345556677777663321 122567775
Q ss_pred cCCcccCCCCcEEEc----CCCccHHHHHHHcCCc
Q 025329 201 QMPQWTAEKPLRVAT----GFTYLGPKFMKDNGLK 231 (254)
Q Consensus 201 ~~~~~~~~r~lRVAT----kYPnLarkyf~~~Gi~ 231 (254)
..+ -|-. .......++|++.|+.
T Consensus 191 ~~~--------~i~~~~~~~~~~~~~~~~~~~~~~ 217 (316)
T PRK12679 191 KWP--------LITYRQGITGRSRIDDAFARKGLL 217 (316)
T ss_pred CCC--------eEEecCCCcHHHHHHHHHHHcCCC
Confidence 321 1211 1223456677777874
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=43.32 E-value=31 Score=27.43 Aligned_cols=66 Identities=17% Similarity=0.170 Sum_probs=36.7
Q ss_pred CCeEEEeecCcchhhhhhcCceeeeeeccceeecccCCCcceeeecCCCCcccEEEEEEEeCCCcc--ccccchHHhhc
Q 025329 125 SNLEVWFQRPKDIVRKLLSGDLDLGIVGLDTVSEFGQGNEDLIIVHDALDYGDCRLSLAIPKYGIF--ENINSLRELAQ 201 (254)
Q Consensus 125 p~iev~~vRp~DIp~yV~~G~aDlGIvG~DvL~E~~~d~~~l~~~l~dLgfG~CRLvVAvP~~~~~--~dv~sl~dL~~ 201 (254)
|++++.+.-.+++... ..|.+|+||+..+. .. .++. ...++..+++++++.+-.. .+.-+++||.+
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 4555555444556554 47999999975331 11 1122 2346677888888765211 12235677754
No 128
>PRK03601 transcriptional regulator HdfR; Provisional
Probab=43.00 E-value=29 Score=30.76 Aligned_cols=51 Identities=20% Similarity=0.272 Sum_probs=35.6
Q ss_pred eEEEeecCcchhhhhhcCceeeeeeccceeecccCCCcceeeecCCCCcccEEEEEEEeCC
Q 025329 127 LEVWFQRPKDIVRKLLSGDLDLGIVGLDTVSEFGQGNEDLIIVHDALDYGDCRLSLAIPKY 187 (254)
Q Consensus 127 iev~~vRp~DIp~yV~~G~aDlGIvG~DvL~E~~~d~~~l~~~l~dLgfG~CRLvVAvP~~ 187 (254)
+++..-...|+-..|.+|.+|+||++... +. .++. ...++.++++++++++
T Consensus 120 v~~~~~~~~~~~~~l~~g~~Dl~i~~~~~--~~----~~l~----~~~l~~~~~~~v~~~~ 170 (275)
T PRK03601 120 FEARIAQRQSLVKQLHERQLDLLITTEAP--KM----DEFS----SQLLGHFTLALYTSAP 170 (275)
T ss_pred EEEEECChHHHHHHHHcCCCCEEEEcCCC--cc----CCcc----EEEecceeEEEEecCc
Confidence 34445567889999999999999986432 11 1122 3467789999998876
No 129
>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=42.71 E-value=71 Score=25.15 Aligned_cols=72 Identities=14% Similarity=0.041 Sum_probs=37.6
Q ss_pred hhhcCceeeeeeccceeecccCCCcceeeecCCCCcccEEEEEEEeCCCccccccchHHhhcCCcccCCCCcEEEcCCCc
Q 025329 140 KLLSGDLDLGIVGLDTVSEFGQGNEDLIIVHDALDYGDCRLSLAIPKYGIFENINSLRELAQMPQWTAEKPLRVATGFTY 219 (254)
Q Consensus 140 yV~~G~aDlGIvG~DvL~E~~~d~~~l~~~l~dLgfG~CRLvVAvP~~~~~~dv~sl~dL~~~~~~~~~r~lRVATkYPn 219 (254)
.+..|.+|+||+..... . .++. .-..++-+++++++.+-. ....+++||.+.+ -|.....+
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 123344566666665421 1234678886431 12222223
Q ss_pred cHHHHHHHcCC
Q 025329 220 LGPKFMKDNGL 230 (254)
Q Consensus 220 Larkyf~~~Gi 230 (254)
..++||.+.|.
T Consensus 102 ~~~~~~~~~~~ 112 (191)
T cd08488 102 EWPQWFEAAGV 112 (191)
T ss_pred HHHHHHHHcCC
Confidence 56788888876
No 130
>KOG0186 consensus Proline oxidase [Amino acid transport and metabolism]
Probab=42.50 E-value=16 Score=37.04 Aligned_cols=46 Identities=13% Similarity=0.256 Sum_probs=36.0
Q ss_pred ccEEEEEEEeCCCccccccchHHhhcCCcccCCCCcEEEcCCCccHHHHHHHcCCceEEEEEcCCceecccCCCccccC
Q 025329 176 GDCRLSLAIPKYGIFENINSLRELAQMPQWTAEKPLRVATGFTYLGPKFMKDNGLKHVVFSTADGALEAAPAVRITHLL 254 (254)
Q Consensus 176 G~CRLvVAvP~~~~~~dv~sl~dL~~~~~~~~~r~lRVATkYPnLarkyf~~~Gi~~veIi~l~GSvElAP~lGlADaI 254 (254)
++|.++||..++. . . .++-+-++++|++ +.+|.++.|=++|+||.|
T Consensus 400 ~~~~vmVASHN~d---S------------------~-------r~a~nlm~elgi~-----~~~~~i~fgQLlGM~D~v 445 (506)
T KOG0186|consen 400 SKAHVMVASHNED---S------------------V-------RLATNLMEELGIN-----PAKGKIYFGQLLGMCDQV 445 (506)
T ss_pred CceeEEEEecchH---H------------------H-------HHHHHHHHHhCCC-----cccceEeHHHhhcchhhh
Confidence 5888999887761 0 1 3555678899984 579999999999999975
No 131
>PRK11482 putative DNA-binding transcriptional regulator; Provisional
Probab=42.40 E-value=35 Score=31.18 Aligned_cols=67 Identities=12% Similarity=-0.088 Sum_probs=42.6
Q ss_pred CCeEEEeecCcchhhhhhcCceeeeeeccceeecccCCCcceeeecCCCCcccEEEEEEEeCCCcc-ccccchHHhhc
Q 025329 125 SNLEVWFQRPKDIVRKLLSGDLDLGIVGLDTVSEFGQGNEDLIIVHDALDYGDCRLSLAIPKYGIF-ENINSLRELAQ 201 (254)
Q Consensus 125 p~iev~~vRp~DIp~yV~~G~aDlGIvG~DvL~E~~~d~~~l~~~l~dLgfG~CRLvVAvP~~~~~-~dv~sl~dL~~ 201 (254)
|++++......++...|.+|.+|+||+......+ ++. --.++.-.++++++.+.+. ..-.+++||..
T Consensus 144 P~i~i~~~~~~~~~~~l~~g~~Dl~i~~~~~~~~------~~~----~~~l~~~~~~lv~~~~hpl~~~~~~~~dL~~ 211 (317)
T PRK11482 144 PQLLLRNIPISDAENQLSQFQTDLIIDTHSCSNR------TIQ----HHVLFTDNVVLVCRQGHPLLSLEDDEETLDN 211 (317)
T ss_pred CCCEEEEecchhHHHHHHCCCcCEEEeccCCCCC------ceE----EEEEecCcEEEEEeCCCCccCCCCCHHHHhh
Confidence 5566655666789999999999999987553211 122 1234566778888766432 11236788864
No 132
>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=42.09 E-value=41 Score=31.79 Aligned_cols=66 Identities=15% Similarity=0.154 Sum_probs=50.0
Q ss_pred CCCCCCCceEEEecCCCCChHHH-HHHHHhCCCccCCCCCCceEeecCCCCCeEEEeecCcchhhhhhcCceeeeeeccc
Q 025329 76 NRISERDEIRLGLPSKGRMAADT-LDLLKDCQLSVKQVNPRQYVAQIPQLSNLEVWFQRPKDIVRKLLSGDLDLGIVGLD 154 (254)
Q Consensus 76 ~~~~~~~~LrIALPsKGRL~e~t-l~LL~~aGi~v~~~~~R~L~~~~~~~p~iev~~vRp~DIp~yV~~G~aDlGIvG~D 154 (254)
.++.+-.==|||++ +|...+-. ...|+++|++. .+++++.+.+.|.+..+..|.+|..++-.-
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 45555544599998 89876644 35788888842 147788888899999999999999998776
Q ss_pred eee
Q 025329 155 TVS 157 (254)
Q Consensus 155 vL~ 157 (254)
++.
T Consensus 163 ~~s 165 (328)
T TIGR03427 163 QLS 165 (328)
T ss_pred hHH
Confidence 653
No 133
>TIGR03730 tungstate_WtpA tungstate ABC transporter binding protein WtpA. Members of this protein family are tungstate (and, more weakly, molybdate) binding proteins of tungstate(/molybdate) ABC transporters, as first characterized in Pyrococcus furiosus. Model seed members and cutoffs, pending experimental evidence for more distant homologs, were chosen such that this model identifies select archaeal proteins, excluding weaker archaeal and all bacterial homologs. Note that this family is homologous to molybdate transporters, and that at least one other family of tungstate transporter binding protein, TupA, also exists.
Probab=42.08 E-value=47 Score=30.76 Aligned_cols=24 Identities=17% Similarity=0.295 Sum_probs=18.9
Q ss_pred CcchhhhhhcCceeeeeeccceee
Q 025329 134 PKDIVRKLLSGDLDLGIVGLDTVS 157 (254)
Q Consensus 134 p~DIp~yV~~G~aDlGIvG~DvL~ 157 (254)
-.++-.||+.|.+|+||+-.-...
T Consensus 184 v~~~~~~v~sG~aD~g~vY~S~A~ 207 (273)
T TIGR03730 184 EVELLSLLESGEIDYAFIYKSVAV 207 (273)
T ss_pred hHhHHHHHHCCCCcEEEEEeeecc
Confidence 357789999999999999754433
No 134
>COG0834 HisJ ABC-type amino acid transport/signal transduction systems, periplasmic component/domain [Amino acid transport and metabolism / Signal transduction mechanisms]
Probab=41.37 E-value=89 Score=26.68 Aligned_cols=98 Identities=18% Similarity=0.155 Sum_probs=61.7
Q ss_pred eEEEeecCcchhhhhhcCceeeeeeccceeecccCCCcceeeecCCCCcccEEEEEEEeCCCccccccchHHhhcCCccc
Q 025329 127 LEVWFQRPKDIVRKLLSGDLDLGIVGLDTVSEFGQGNEDLIIVHDALDYGDCRLSLAIPKYGIFENINSLRELAQMPQWT 206 (254)
Q Consensus 127 iev~~vRp~DIp~yV~~G~aDlGIvG~DvL~E~~~d~~~l~~~l~dLgfG~CRLvVAvP~~~~~~dv~sl~dL~~~~~~~ 206 (254)
+++..+.-+..-..+..|.+|+.+.+-.+..|.... +. . .-+|..-...+.++.+..+ .+.+++||.
T Consensus 79 ~~~~~~~~~~~~~~l~~g~~D~~~~~~~~t~er~~~---~~--f-s~py~~~~~~~~~~~~~~~-~~~~~~DL~------ 145 (275)
T COG0834 79 VEFVPVAWDGLIPALKAGKVDIIIAGMTITPERKKK---VD--F-SDPYYYSGQVLLVKKDSDI-GIKSLEDLK------ 145 (275)
T ss_pred eEEeccchhhhhHHHhcCCcCEEEeccccCHHHhcc---cc--c-cccccccCeEEEEECCCCc-CcCCHHHhC------
Confidence 455566678889999999999999996665554322 11 1 2366666667777766432 256888986
Q ss_pred CCCCcEEEcCCCcc--HHHHHHHcCCceEEEEEcCCc
Q 025329 207 AEKPLRVATGFTYL--GPKFMKDNGLKHVVFSTADGA 241 (254)
Q Consensus 207 ~~r~lRVATkYPnL--arkyf~~~Gi~~veIi~l~GS 241 (254)
++||+..-=-. ...+.++..- .++++.....
T Consensus 146 ---gk~v~v~~gt~~~~~~~~~~~~~-~~~~~~~~~~ 178 (275)
T COG0834 146 ---GKKVGVQLGTTDEAEEKAKKPGP-NAKIVAYDSN 178 (275)
T ss_pred ---CCEEEEEcCcchhHHHHHhhccC-CceEEeeCCH
Confidence 35666554333 4555555443 3677766655
No 135
>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=40.51 E-value=55 Score=29.84 Aligned_cols=66 Identities=20% Similarity=0.214 Sum_probs=38.7
Q ss_pred cccEEEEEEEeCCCccccccchHHhhcCCcccCCCCcEEEcC----CCccHHH-HHHHcCCceEEEEEcCCceecc
Q 025329 175 YGDCRLSLAIPKYGIFENINSLRELAQMPQWTAEKPLRVATG----FTYLGPK-FMKDNGLKHVVFSTADGALEAA 245 (254)
Q Consensus 175 fG~CRLvVAvP~~~~~~dv~sl~dL~~~~~~~~~r~lRVATk----YPnLark-yf~~~Gi~~veIi~l~GSvElA 245 (254)
+..--.+++++.+.+| +|++||... ...+++.+++||. ..+++.. ++++.|++ ++.|.-.|+-|+.
T Consensus 75 ~~~~~~vl~v~~dsp~---~t~~eli~~-ak~~p~~~~~g~~g~g~~~hl~~~~l~~~~G~~-~~~Vpy~G~~~~~ 145 (274)
T PF03401_consen 75 IASDPNVLVVRADSPY---KTLEELIEY-AKANPGKLTFGSSGPGSSDHLAAALLAKAAGIK-FTHVPYDGGAEAL 145 (274)
T ss_dssp EEEEEEEEEEETTSS----SSHHHHHHH-HHCSCCC-EEEESSTTSHHHHHHHHHHHHHT----EEEE-SSHHHHH
T ss_pred hhccceEEEEeCCCcc---ccHHHHHHH-HHhCCCCeEEEecCCCchHHHHHHHHHHHhCCc-eEEEEeCCccHHH
Confidence 3445568888888654 566776431 1233457999985 3456644 55677996 8999988887653
No 136
>cd08420 PBP2_CysL_like C-terminal substrate binding domain of LysR-type transcriptional regulator CysL, which activates the transcription of the cysJI operon encoding sulfite reductase, contains the type 2 periplasmic binding fold. CysL, also known as YwfK, is a regular of sulfur metabolism in Bacillus subtilis. Sulfur is required for the synthesis of proteins and essential cofactors in all living organism. Sulfur can be assimilated either from inorganic sources (sulfate and thiosulfate), or from organic sources (sulfate esters, sulfamates, and sulfonates). CysL activates the transcription of the cysJI operon encoding sulfite reductase, which reduces sulfite to sulfide. Both cysL mutant and cysJI mutant are unable to grow using sulfate or sulfite as the sulfur source. Like other LysR-type regulators, CysL also negatively regulates its own transcription. In Escherichia coli, three LysR-type activators are involved in the regulation of sulfur metabolism: CysB, Cbl and MetR. The topology
Probab=40.45 E-value=40 Score=26.06 Aligned_cols=64 Identities=25% Similarity=0.394 Sum_probs=38.5
Q ss_pred EEEeecCcchhhhhhcCceeeeeeccceeecccCCCcceeeecCCCCcccEEEEEEEeCCCccc--cccchHHhhc
Q 025329 128 EVWFQRPKDIVRKLLSGDLDLGIVGLDTVSEFGQGNEDLIIVHDALDYGDCRLSLAIPKYGIFE--NINSLRELAQ 201 (254)
Q Consensus 128 ev~~vRp~DIp~yV~~G~aDlGIvG~DvL~E~~~d~~~l~~~l~dLgfG~CRLvVAvP~~~~~~--dv~sl~dL~~ 201 (254)
++......|+...+.+|.+|+||+..+.- ..++. ...++..+++++++++.+.. +.-+++||.+
T Consensus 32 ~~~~~~~~~~~~~l~~g~~D~~i~~~~~~------~~~~~----~~~l~~~~~~~v~~~~~~~~~~~~i~~~~l~~ 97 (201)
T cd08420 32 SLTIGNTEEIAERVLDGEIDLGLVEGPVD------HPDLI----VEPFAEDELVLVVPPDHPLAGRKEVTAEELAA 97 (201)
T ss_pred EEEeCCcHHHHHHHHCCCccEEEecCCCC------CcceE----EEeecCccEEEEecCCCCccccCccCHHHHhc
Confidence 33334557889999999999999854321 11222 12456677888887764322 1224677753
No 137
>PRK11480 tauA taurine transporter substrate binding subunit; Provisional
Probab=39.72 E-value=63 Score=29.63 Aligned_cols=68 Identities=19% Similarity=0.214 Sum_probs=48.0
Q ss_pred CCCCCCCceEEEecCCCCChH-HHHHHHHhCCCccCCCCCCceEeecCCCCCeEEEeecCcchhhhhhcCceeeeeeccc
Q 025329 76 NRISERDEIRLGLPSKGRMAA-DTLDLLKDCQLSVKQVNPRQYVAQIPQLSNLEVWFQRPKDIVRKLLSGDLDLGIVGLD 154 (254)
Q Consensus 76 ~~~~~~~~LrIALPsKGRL~e-~tl~LL~~aGi~v~~~~~R~L~~~~~~~p~iev~~vRp~DIp~yV~~G~aDlGIvG~D 154 (254)
.++.+..--|||+| .|.... -...+|++.|++.. +++++.+.+.+...-+..|.+|..++..-
T Consensus 115 ~s~~DLkGK~Iav~-~~s~~~~~l~~~L~~~Gl~~~---------------dv~~v~~~~~~~~~Al~~G~VDAa~~~~p 178 (320)
T PRK11480 115 SKPEDLIGKRIAVP-FISTTHYSLLAALKHWGIKPG---------------QVEIVNLQPPAIIAAWQRGDIDGAYVWAP 178 (320)
T ss_pred CChHHcCCCEEecC-CCCchHHHHHHHHHHcCCCHh---------------heEEEECCcHHHHHHHHcCCcCEEEEcch
Confidence 34555555689998 565443 45668899998531 24556667889999999999999988776
Q ss_pred eeecc
Q 025329 155 TVSEF 159 (254)
Q Consensus 155 vL~E~ 159 (254)
+..+.
T Consensus 179 ~~~~~ 183 (320)
T PRK11480 179 AVNAL 183 (320)
T ss_pred HHHHH
Confidence 65433
No 138
>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=39.69 E-value=1e+02 Score=27.35 Aligned_cols=98 Identities=14% Similarity=0.090 Sum_probs=57.6
Q ss_pred EEeecCcchhhhhhcCceeeeeeccceeecccCCCcceeeecCCCCcccEEEEEEEeCCCccccccchHHhhcCCcccCC
Q 025329 129 VWFQRPKDIVRKLLSGDLDLGIVGLDTVSEFGQGNEDLIIVHDALDYGDCRLSLAIPKYGIFENINSLRELAQMPQWTAE 208 (254)
Q Consensus 129 v~~vRp~DIp~yV~~G~aDlGIvG~DvL~E~~~d~~~l~~~l~dLgfG~CRLvVAvP~~~~~~dv~sl~dL~~~~~~~~~ 208 (254)
+.++.-.+.-..+..|.+|+.+.|.=.-.|.... +. . --.|-.-..++.++.+.. .++++++||...
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 4444445677889999999877664222222111 10 0 013334445666777642 346778887521
Q ss_pred CCcEEEcCCCccHHHHHHHcCCceEEEEEcC
Q 025329 209 KPLRVATGFTYLGPKFMKDNGLKHVVFSTAD 239 (254)
Q Consensus 209 r~lRVATkYPnLarkyf~~~Gi~~veIi~l~ 239 (254)
.++||+.---....+++++.+..+.+++...
T Consensus 143 ~g~~Igv~~g~~~~~~l~~~~~~~~~i~~~~ 173 (275)
T TIGR02995 143 PDAKIAAPGGGTEEKLAREAGVKREQIIVVP 173 (275)
T ss_pred CCceEEEeCCcHHHHHHHHcCCChhhEEEeC
Confidence 2478888777777889988876444555443
No 139
>cd08469 PBP2_PnbR The C-terminal substrate binding domain of LysR-type transcriptional regulator PnbR, which is involved in regulating the pnb genes encoding enzymes for 4-nitrobenzoate catabolism, contains the type 2 periplasmic binding fold. PnbR is the regulator of one or both of the two pnb genes that encoding enzymes for 4-nitrobenzoate catabolism. In Pseudomonas putida strain, pnbA encodes a 4-nitrobenzoate reductase, which is responsible for catalyzing the direct reduction of 4-nitrobenzoate to 4-hydroxylaminobenzoate, and pnbB encodes a 4-hydroxylaminobenzoate lyase, which catalyzes the conversion of 4-hydroxylaminobenzoate to 3, 4-dihydroxybenzoic acid and ammonium. The topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft bet
Probab=39.22 E-value=57 Score=26.38 Aligned_cols=67 Identities=15% Similarity=0.121 Sum_probs=39.1
Q ss_pred CCeEEEee--cCcchhhhhhcCceeeeeeccceeecccCCCcceeeecCCCCcccEEEEEEEeCCCccc-cccchHHhhc
Q 025329 125 SNLEVWFQ--RPKDIVRKLLSGDLDLGIVGLDTVSEFGQGNEDLIIVHDALDYGDCRLSLAIPKYGIFE-NINSLRELAQ 201 (254)
Q Consensus 125 p~iev~~v--Rp~DIp~yV~~G~aDlGIvG~DvL~E~~~d~~~l~~~l~dLgfG~CRLvVAvP~~~~~~-dv~sl~dL~~ 201 (254)
|++++-+. ...++...+.+|.+|+||+..... + .++. --.++.-+++++++.+.+.. ..-+++||..
T Consensus 27 P~v~l~i~~~~~~~~~~~l~~g~~Di~i~~~~~~-~-----~~l~----~~~l~~~~~~~v~~~~~pl~~~~~~~~dL~~ 96 (221)
T cd08469 27 PGIDLRIRPVTRLDLAEQLDLGRIDLVIGIFEQI-P-----PRFR----RRTLFDEDEVWVMRKDHPAARGALTIETLAR 96 (221)
T ss_pred CCcEEEEeeCChhhHHHHHHCCCccEEEecCCCC-C-----ccce----eeeeeccceEEEEeCCCcCCCCCCCHHHHHh
Confidence 44444444 456789999999999999854321 1 1122 12335566677777663221 2236788864
No 140
>PRK11716 DNA-binding transcriptional regulator IlvY; Provisional
Probab=38.90 E-value=33 Score=29.38 Aligned_cols=54 Identities=22% Similarity=0.227 Sum_probs=34.5
Q ss_pred CCeEEE--eecCcchhhhhhcCceeeeeeccceeecccCCCcceeeecCCCCcccEEEEEEEeCC
Q 025329 125 SNLEVW--FQRPKDIVRKLLSGDLDLGIVGLDTVSEFGQGNEDLIIVHDALDYGDCRLSLAIPKY 187 (254)
Q Consensus 125 p~iev~--~vRp~DIp~yV~~G~aDlGIvG~DvL~E~~~d~~~l~~~l~dLgfG~CRLvVAvP~~ 187 (254)
|++++. .....|+...+.+|.+|+||+....-. . .++. ...++..++++++|++
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 444444 345678999999999999997643111 1 1122 2345778888888777
No 141
>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=36.78 E-value=57 Score=27.58 Aligned_cols=22 Identities=27% Similarity=0.477 Sum_probs=17.6
Q ss_pred cchhhhhhcCceeeeeecccee
Q 025329 135 KDIVRKLLSGDLDLGIVGLDTV 156 (254)
Q Consensus 135 ~DIp~yV~~G~aDlGIvG~DvL 156 (254)
.++-.+|..|.+|+||+-....
T Consensus 139 ~~~~~~~~~Ge~~~~~~~~~~~ 160 (216)
T TIGR01256 139 RQALQFVETGNAPAGIVALSDV 160 (216)
T ss_pred HHHHHHHHcCCCCEEeeehhhh
Confidence 4677899999999999865443
No 142
>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=36.62 E-value=42 Score=26.17 Aligned_cols=67 Identities=21% Similarity=0.254 Sum_probs=34.6
Q ss_pred CCeEEEeecCcchhhhhhcCceeeeeeccceeecccCCCcceeeecCCCCcccEEEEEEEeCCCcc--ccccchHHhhc
Q 025329 125 SNLEVWFQRPKDIVRKLLSGDLDLGIVGLDTVSEFGQGNEDLIIVHDALDYGDCRLSLAIPKYGIF--ENINSLRELAQ 201 (254)
Q Consensus 125 p~iev~~vRp~DIp~yV~~G~aDlGIvG~DvL~E~~~d~~~l~~~l~dLgfG~CRLvVAvP~~~~~--~dv~sl~dL~~ 201 (254)
|++++.+....++...+..| +|+||.......+ .++. -.-+++-+++++++.+... ...-+++||..
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 45555554456777777766 9999963221111 1121 1234556677777554211 11235677753
No 143
>COG2358 Imp TRAP-type uncharacterized transport system, periplasmic component [General function prediction only]
Probab=36.04 E-value=37 Score=32.66 Aligned_cols=88 Identities=22% Similarity=0.176 Sum_probs=52.8
Q ss_pred hhhhhcCceeeeeeccceeecc--cCCCcc---eeeecCCCCcc-cEEEEEEEeCCCccccccchHHhhcCCcccCCCCc
Q 025329 138 VRKLLSGDLDLGIVGLDTVSEF--GQGNED---LIIVHDALDYG-DCRLSLAIPKYGIFENINSLRELAQMPQWTAEKPL 211 (254)
Q Consensus 138 p~yV~~G~aDlGIvG~DvL~E~--~~d~~~---l~~~l~dLgfG-~CRLvVAvP~~~~~~dv~sl~dL~~~~~~~~~r~l 211 (254)
-..+.+|.+|+|++=.|+-.|. |....+ ..+-+..+..= .=-+-+.+.++ .+|++++||+ +|
T Consensus 71 l~~i~~Ge~d~alvq~d~a~~ay~G~g~f~~~~~~~~lr~v~~lype~~~vv~r~d---~~Ikti~DL~---------GK 138 (321)
T COG2358 71 LKLLASGEADLALVQSDVAYEAYNGTGSFEGKGKDENLRAVAALYPEPFHVVTRKD---AGIKTIADLK---------GK 138 (321)
T ss_pred HHhHhcCccchhhhhHHHHHHHHhCcccccccccccchhhheecccceEEEEEecC---CCcceehhcC---------CC
Confidence 4578899999999999998875 111100 00000001100 11123444455 5689999986 58
Q ss_pred EEEcCCCcc-----HHHHHHHcCCceEEEEEc
Q 025329 212 RVATGFTYL-----GPKFMKDNGLKHVVFSTA 238 (254)
Q Consensus 212 RVATkYPnL-----arkyf~~~Gi~~veIi~l 238 (254)
||++-=|.- +++-|+..|+. .+-+++
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 999988875 56778889995 444444
No 144
>PRK12681 cysB transcriptional regulator CysB; Reviewed
Probab=35.80 E-value=1.4e+02 Score=27.25 Aligned_cols=28 Identities=18% Similarity=0.412 Sum_probs=20.9
Q ss_pred CCeEEEee--cCcchhhhhhcCceeeeeec
Q 025329 125 SNLEVWFQ--RPKDIVRKLLSGDLDLGIVG 152 (254)
Q Consensus 125 p~iev~~v--Rp~DIp~yV~~G~aDlGIvG 152 (254)
|++++.+. ...++-..+.+|.+|+||+-
T Consensus 120 P~i~i~i~~~~~~~~~~~L~~g~iDl~i~~ 149 (324)
T PRK12681 120 PRVSLHMHQGSPTQIAEAAAKGNADFAIAT 149 (324)
T ss_pred CCcEEEEEeCCHHHHHHHHHcCCCCEEEec
Confidence 44555443 45688899999999999974
No 145
>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=35.68 E-value=1.5e+02 Score=26.14 Aligned_cols=65 Identities=12% Similarity=0.051 Sum_probs=40.6
Q ss_pred eEEEeecCcchhhhhhcCceeeeeeccceeecccCCCcceeeecCCCCcccEEEEEEEeCCCccc---cccchHHhhc
Q 025329 127 LEVWFQRPKDIVRKLLSGDLDLGIVGLDTVSEFGQGNEDLIIVHDALDYGDCRLSLAIPKYGIFE---NINSLRELAQ 201 (254)
Q Consensus 127 iev~~vRp~DIp~yV~~G~aDlGIvG~DvL~E~~~d~~~l~~~l~dLgfG~CRLvVAvP~~~~~~---dv~sl~dL~~ 201 (254)
+++....+.++...|.+|.+|+||+..+.-. .++. -..+++=+++++++++-... ..-+++||.+
T Consensus 120 i~l~~~~~~~~~~~l~~g~~d~~i~~~~~~~------~~l~----~~~l~~~~~~~v~~~~~~~~~~~~~i~~~dL~~ 187 (292)
T TIGR03298 120 LDLVVEDQDHTAELLRSGEVLGAVTTQAKPV------QGCR----VVPLGAMRYLAVASPAFAARYFPDGVTAEALAR 187 (292)
T ss_pred EEEEeCcchhHHHHHhCCCceEEEecCCCCC------CCce----EEecCCceEEEEECchhhhhccCCCCCHHHhcC
Confidence 5555556788999999999999998754321 1122 13456667777776652101 2236788864
No 146
>PRK15243 transcriptional regulator SpvR; Provisional
Probab=35.38 E-value=59 Score=30.04 Aligned_cols=105 Identities=13% Similarity=0.036 Sum_probs=57.0
Q ss_pred CCCeEEEee--cCcchhhhhhcCceeeeeeccceeecccCCCcceeeecCCCCcccEEEEEEEeCCCccccccchHHhhc
Q 025329 124 LSNLEVWFQ--RPKDIVRKLLSGDLDLGIVGLDTVSEFGQGNEDLIIVHDALDYGDCRLSLAIPKYGIFENINSLRELAQ 201 (254)
Q Consensus 124 ~p~iev~~v--Rp~DIp~yV~~G~aDlGIvG~DvL~E~~~d~~~l~~~l~dLgfG~CRLvVAvP~~~~~~dv~sl~dL~~ 201 (254)
.|++++.+. ..+.+-..+..|. |+||+..+...+.+ +. -..+..=.+++++|++.++..-.+++||.+
T Consensus 118 ~P~v~i~~~~~~~~~~~~~l~~~~-~i~i~~~~~~~~~~-----l~----~~~l~~e~lvlv~~~~hpla~~~~l~~l~~ 187 (297)
T PRK15243 118 GQKTNIMGRAVNSQIIEELCQTNN-CIVISARNYFHRES-----LV----CRTSVEGGVMLFIPKKFFLCGKPDINRLAG 187 (297)
T ss_pred CCceEEEEecCCHHHHHHHHcCCC-cEEEecCCCCCCCC-----ee----EEEeccCCEEEEEcCCCccccCCCHHHHhc
Confidence 366666543 3445555555554 79997422111111 11 124455567888888866643347888875
Q ss_pred CCcccCCCCcEEEcCC-CccHHHHHHH-cCCceEEEEEcCCceec
Q 025329 202 MPQWTAEKPLRVATGF-TYLGPKFMKD-NGLKHVVFSTADGALEA 244 (254)
Q Consensus 202 ~~~~~~~r~lRVATkY-PnLarkyf~~-~Gi~~veIi~l~GSvEl 244 (254)
.+-.. ....+.+ -.+..++|++ .|+. .++--.+++|+
T Consensus 188 ~p~il----~~~~~~~~r~~~~~~~~~~~gi~--~~~~e~~s~e~ 226 (297)
T PRK15243 188 TPVLF----HEGAKNFNLDTIYHFFEQTLGIT--NPAFSFDNVDL 226 (297)
T ss_pred CCeEE----ecCCCccHHHHHHHHHHHhcCCC--hhheecccHHH
Confidence 43111 1122343 3478899996 9984 34434556554
No 147
>PRK10094 DNA-binding transcriptional activator AllS; Provisional
Probab=35.21 E-value=1.1e+02 Score=27.68 Aligned_cols=69 Identities=14% Similarity=0.038 Sum_probs=40.8
Q ss_pred CCeEEEe--ecCcchhhhhhcCceeeeeeccceeecccCCCcceeeecCCCCcccEEEEEEEeCCCcccc---ccchHHh
Q 025329 125 SNLEVWF--QRPKDIVRKLLSGDLDLGIVGLDTVSEFGQGNEDLIIVHDALDYGDCRLSLAIPKYGIFEN---INSLREL 199 (254)
Q Consensus 125 p~iev~~--vRp~DIp~yV~~G~aDlGIvG~DvL~E~~~d~~~l~~~l~dLgfG~CRLvVAvP~~~~~~d---v~sl~dL 199 (254)
|++++.+ ....|+..-+.+|.+|+||.-.+. +.. ..++. .-.++.-+++++++.+-++.. .-+++||
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 4444444 356789999999999999963111 110 11222 235677788888877643321 3466777
Q ss_pred hc
Q 025329 200 AQ 201 (254)
Q Consensus 200 ~~ 201 (254)
.+
T Consensus 192 ~~ 193 (308)
T PRK10094 192 RR 193 (308)
T ss_pred Hh
Confidence 64
No 148
>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=34.14 E-value=52 Score=28.64 Aligned_cols=85 Identities=19% Similarity=0.214 Sum_probs=51.0
Q ss_pred CceEEEecCCCCChHHHHH-HHHhCCCccCCCCCCceEeecCCCCCeEEEeecCcchhhhhhcCceeeeeeccceeec-c
Q 025329 82 DEIRLGLPSKGRMAADTLD-LLKDCQLSVKQVNPRQYVAQIPQLSNLEVWFQRPKDIVRKLLSGDLDLGIVGLDTVSE-F 159 (254)
Q Consensus 82 ~~LrIALPsKGRL~e~tl~-LL~~aGi~v~~~~~R~L~~~~~~~p~iev~~vRp~DIp~yV~~G~aDlGIvG~DvL~E-~ 159 (254)
..+|+.--.+|.=....++ +|++.|+..... +.|.- ..-...|+..+|+.|.+|+||+=...-.+ +
T Consensus 92 ~~~r~vnR~~GSGtR~l~d~~l~~~gi~~~~i--~gy~~----------~~~th~~vA~aVa~G~AD~G~g~~~~A~~~~ 159 (193)
T PF12727_consen 92 PGLRFVNRQPGSGTRILFDQLLAEEGIDPEDI--PGYAQ----------EANTHLAVAAAVASGKADAGIGIRAAAEEFY 159 (193)
T ss_pred CCcEEEECCCCCHHHHHHHHHHHHcCCChhhC--CCccc----------cccChHHHHHHHHcCCCCEEeehHHHHHhhc
Confidence 4678877778876655555 566677754332 33322 22234789999999999999954333333 2
Q ss_pred cCCCcceeeecCCCCcccEEEEEEEeCC
Q 025329 160 GQGNEDLIIVHDALDYGDCRLSLAIPKY 187 (254)
Q Consensus 160 ~~d~~~l~~~l~dLgfG~CRLvVAvP~~ 187 (254)
+.++ .+.+.=++-+++|.+
T Consensus 160 gL~F---------vpl~~E~~dlv~~~~ 178 (193)
T PF12727_consen 160 GLDF---------VPLAEERYDLVIRRE 178 (193)
T ss_pred CCCc---------EEccccceEEEEEhh
Confidence 4432 122334566677666
No 149
>PRK11553 alkanesulfonate transporter substrate-binding subunit; Provisional
Probab=33.74 E-value=92 Score=28.10 Aligned_cols=63 Identities=14% Similarity=0.250 Sum_probs=44.7
Q ss_pred CCCCCCceEEEecCCCCChHH-HHHHHHhCCCccCCCCCCceEeecCCCCCeEEEeecCcchhhhhhcCceeeeeeccce
Q 025329 77 RISERDEIRLGLPSKGRMAAD-TLDLLKDCQLSVKQVNPRQYVAQIPQLSNLEVWFQRPKDIVRKLLSGDLDLGIVGLDT 155 (254)
Q Consensus 77 ~~~~~~~LrIALPsKGRL~e~-tl~LL~~aGi~v~~~~~R~L~~~~~~~p~iev~~vRp~DIp~yV~~G~aDlGIvG~Dv 155 (254)
++.+..-.+|+++ .|...+. ..++|++.|++.. ++++.++.+.|...-+..|.+|..++..-+
T Consensus 123 s~~dL~Gk~I~~~-~gs~~~~~l~~~l~~~g~~~~---------------dv~~v~~~~~~~~~al~~G~vDa~~~~ep~ 186 (314)
T PRK11553 123 TVADLKGHKVAFQ-KGSSSHNLLLRALRKAGLKFT---------------DIQPTYLTPADARAAFQQGNVDAWAIWDPY 186 (314)
T ss_pred CHHHhCCCEEeec-CCCcHHHHHHHHHHHcCCCHH---------------HeEEEecChHHHHHHHHcCCCCEEEEcCcH
Confidence 4555556789998 5665544 4567888887531 244566677899999999999999886544
No 150
>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=33.61 E-value=2.5e+02 Score=23.61 Aligned_cols=72 Identities=19% Similarity=0.266 Sum_probs=45.1
Q ss_pred hhhhcCceeeeeeccceeecccCCCcceeeecCCCCcccEEEEEEEeCCCccccccchHH--hhcCCcccCCCCcEEEcC
Q 025329 139 RKLLSGDLDLGIVGLDTVSEFGQGNEDLIIVHDALDYGDCRLSLAIPKYGIFENINSLRE--LAQMPQWTAEKPLRVATG 216 (254)
Q Consensus 139 ~yV~~G~aDlGIvG~DvL~E~~~d~~~l~~~l~dLgfG~CRLvVAvP~~~~~~dv~sl~d--L~~~~~~~~~r~lRVATk 216 (254)
..+..|.+|+.+ +. .|.. . .+. . --.|..-..++.++.+.. .++++++| |. ++|||.-
T Consensus 51 ~~l~~g~~Di~~-~~---~~r~-~---~~~-f-s~py~~~~~~lv~~~~~~-~~~~~~~d~~l~---------g~~V~v~ 110 (232)
T TIGR03871 51 NTLNAGRCDVVI-GV---PAGY-E---MVL-T-TRPYYRSTYVFVTRKDSL-LDVKSLDDPRLK---------KLRIGVF 110 (232)
T ss_pred HHHhcCCccEEE-ec---cCcc-c---ccc-c-cCCcEeeeEEEEEeCCCc-ccccchhhhhhc---------CCeEEEE
Confidence 367899999965 41 2211 1 111 1 225666778888888732 35667776 43 4688887
Q ss_pred CCccHHHHHHHcCC
Q 025329 217 FTYLGPKFMKDNGL 230 (254)
Q Consensus 217 YPnLarkyf~~~Gi 230 (254)
.-....+|++++|.
T Consensus 111 ~g~~~~~~l~~~~~ 124 (232)
T TIGR03871 111 AGTPPAHWLARHGL 124 (232)
T ss_pred cCChHHHHHHhcCc
Confidence 77778888888775
No 151
>COG0715 TauA ABC-type nitrate/sulfonate/bicarbonate transport systems, periplasmic components [Inorganic ion transport and metabolism]
Probab=31.86 E-value=1.9e+02 Score=26.12 Aligned_cols=71 Identities=18% Similarity=0.156 Sum_probs=48.7
Q ss_pred cccCCCCCCCceEEEecCCCCChHH-HHHHHHhCCCccCCCCCCceEeecCCCCCeEEEeecCcchhhhhhcCceeeeee
Q 025329 73 NIDNRISERDEIRLGLPSKGRMAAD-TLDLLKDCQLSVKQVNPRQYVAQIPQLSNLEVWFQRPKDIVRKLLSGDLDLGIV 151 (254)
Q Consensus 73 ~~~~~~~~~~~LrIALPsKGRL~e~-tl~LL~~aGi~v~~~~~R~L~~~~~~~p~iev~~vRp~DIp~yV~~G~aDlGIv 151 (254)
..-.++.+..--|||++..|...+- ...+|+++|++..+ ++++.+.+.|++..+..|.+|...+
T Consensus 126 ~~i~~~adlkGk~vg~~~~~~~~~~~l~~~L~~~Gl~~~d---------------v~~v~~~~~~~~~al~~g~vda~~~ 190 (335)
T COG0715 126 SGIKSVADLKGKKVGVPFGGSTSDFLLRYALAKAGLDPDD---------------VELVNLPPADAVAALAAGQVDAFVV 190 (335)
T ss_pred CCcccccCCCCceEEEeCCCchHHHHHHHHHHHcCCCccc---------------ceEEeeCcHHHHHHHhcCCcceEEe
Confidence 3334466766789999955543444 45589999997543 2244455569999999999999777
Q ss_pred ccceeec
Q 025329 152 GLDTVSE 158 (254)
Q Consensus 152 G~DvL~E 158 (254)
+.-|...
T Consensus 191 ~ep~~~~ 197 (335)
T COG0715 191 WEPWNAA 197 (335)
T ss_pred cCCchhh
Confidence 7666544
No 152
>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=31.76 E-value=41 Score=26.51 Aligned_cols=67 Identities=21% Similarity=0.243 Sum_probs=37.5
Q ss_pred CCCeEEEeecCcchhhhhhcCceeeeeeccceeecccCCCcceeeecCCCCcccEEEEEEEeCCCcc--ccccchHHhhc
Q 025329 124 LSNLEVWFQRPKDIVRKLLSGDLDLGIVGLDTVSEFGQGNEDLIIVHDALDYGDCRLSLAIPKYGIF--ENINSLRELAQ 201 (254)
Q Consensus 124 ~p~iev~~vRp~DIp~yV~~G~aDlGIvG~DvL~E~~~d~~~l~~~l~dLgfG~CRLvVAvP~~~~~--~dv~sl~dL~~ 201 (254)
.|++++.+...+++.. +.+|.+|+||+-... .+. ++. --.+...++++++|++... ...-+++||.+
T Consensus 29 ~P~v~i~~~~~~~~~~-l~~~~~D~~i~~~~~-~~~-----~l~----~~~l~~~~~~~v~~~~~~~~~~~~~~~~~L~~ 97 (199)
T cd08478 29 YPDIELELVSNEGIID-LIERKTDVAIRIGEL-TDS-----TLH----ARPLGKSRLRILASPDYLARHGTPQSIEDLAQ 97 (199)
T ss_pred CCCeEEEEEecccccc-chhccccEEEEecCC-CCC-----Cce----EEEcccccEEEEECHHHHHhcCCCCCHHHHHh
Confidence 3566666665566665 778999999974321 111 121 1234566778888765210 11235667653
No 153
>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=31.05 E-value=1.2e+02 Score=26.05 Aligned_cols=65 Identities=18% Similarity=0.214 Sum_probs=42.4
Q ss_pred CCCCCceEEEecCCCCChHHHHHHHHhCCCccCCCCCCceEeecCCCCCeEEEeecCcchhhhhhcCceeeeeeccceee
Q 025329 78 ISERDEIRLGLPSKGRMAADTLDLLKDCQLSVKQVNPRQYVAQIPQLSNLEVWFQRPKDIVRKLLSGDLDLGIVGLDTVS 157 (254)
Q Consensus 78 ~~~~~~LrIALPsKGRL~e~tl~LL~~aGi~v~~~~~R~L~~~~~~~p~iev~~vRp~DIp~yV~~G~aDlGIvG~DvL~ 157 (254)
+.+-.--+||++..+-...-...+|++.|++.. ++++.+..+.+....+..|.+|++++...+..
T Consensus 96 ~~dL~Gk~i~~~~~~~~~~~~~~~l~~~G~~~~---------------~v~~~~~~~~~~~~al~~g~vda~~~~~p~~~ 160 (288)
T TIGR01728 96 VADLKGKRIAVPKGGSGHDLLLRALLKAGLSGD---------------DVTILYLGPSDARAAFAAGQVDAWAIWEPWGS 160 (288)
T ss_pred HHHcCCCEEEecCCccHHHHHHHHHHHcCCCcc---------------ceeEEecCcHHHHHHHHCCCCCEEEeccchHh
Confidence 333333479998433344445578888887421 13344455578899999999999998766543
No 154
>PRK10859 membrane-bound lytic transglycosylase F; Provisional
Probab=30.56 E-value=1.7e+02 Score=28.91 Aligned_cols=60 Identities=22% Similarity=0.165 Sum_probs=39.5
Q ss_pred cCcchhhhhhcCceeeeeeccceeecccCCCcceeeecCCCCcccEEEEEEEeCCCccccccchHHhh
Q 025329 133 RPKDIVRKLLSGDLDLGIVGLDTVSEFGQGNEDLIIVHDALDYGDCRLSLAIPKYGIFENINSLRELA 200 (254)
Q Consensus 133 Rp~DIp~yV~~G~aDlGIvG~DvL~E~~~d~~~l~~~l~dLgfG~CRLvVAvP~~~~~~dv~sl~dL~ 200 (254)
..+++-..+.+|.+|+.+.|.-.-.|.... +. . --.|-....++.+..+. ..+++++||.
T Consensus 89 ~~~~ll~aL~~G~iDi~~~~lt~T~eR~~~----~~-F-S~Py~~~~~~lv~r~~~--~~i~~l~dL~ 148 (482)
T PRK10859 89 NISQLFDALDKGKADLAAAGLTYTPERLKQ----FR-F-GPPYYSVSQQLVYRKGQ--PRPRSLGDLK 148 (482)
T ss_pred CHHHHHHHHhCCCCCEEeccCcCChhhhcc----Cc-c-cCCceeeeEEEEEeCCC--CCCCCHHHhC
Confidence 346788899999999988776554443221 11 1 12455677788888763 4577888886
No 155
>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=30.48 E-value=85 Score=24.65 Aligned_cols=65 Identities=12% Similarity=-0.018 Sum_probs=39.3
Q ss_pred eEEEeecCcchhhhhhcCceeeeeeccceeecccCCCcceeeecCCCCcccEEEEEEEeCCCccc---cccchHHhhc
Q 025329 127 LEVWFQRPKDIVRKLLSGDLDLGIVGLDTVSEFGQGNEDLIIVHDALDYGDCRLSLAIPKYGIFE---NINSLRELAQ 201 (254)
Q Consensus 127 iev~~vRp~DIp~yV~~G~aDlGIvG~DvL~E~~~d~~~l~~~l~dLgfG~CRLvVAvP~~~~~~---dv~sl~dL~~ 201 (254)
+++......++...+++|.+|+||..... +. .++. ...++..+++++++.+-... ..-+++||.+
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 55555566789999999999999965431 11 1121 23455677788877652111 2335677753
No 156
>PRK15010 ABC transporter lysine/arginine/ornithine binding periplasmic protein; Provisional
Probab=29.63 E-value=1.6e+02 Score=25.62 Aligned_cols=81 Identities=14% Similarity=-0.002 Sum_probs=44.4
Q ss_pred EEeecCcchhhhhhcCceeeeeeccceeecccCCCcceeeecCCCCcccEEEEEEEeCCCccccccchHHhhcCCcccCC
Q 025329 129 VWFQRPKDIVRKLLSGDLDLGIVGLDTVSEFGQGNEDLIIVHDALDYGDCRLSLAIPKYGIFENINSLRELAQMPQWTAE 208 (254)
Q Consensus 129 v~~vRp~DIp~yV~~G~aDlGIvG~DvL~E~~~d~~~l~~~l~dLgfG~CRLvVAvP~~~~~~dv~sl~dL~~~~~~~~~ 208 (254)
+....-.++-..+..|.+|+.+.+...-.|.... +.. --.|-.-+.++.++.+... ..+++||.
T Consensus 69 ~~~~~~~~~~~~l~~g~~Di~~~~~~~t~eR~~~----~~f--s~p~~~~~~~~~~~~~~~~--~~~~~dl~-------- 132 (260)
T PRK15010 69 WVASDFDALIPSLKAKKIDAIISSLSITDKRQQE----IAF--SDKLYAADSRLIAAKGSPI--QPTLDSLK-------- 132 (260)
T ss_pred EEeCCHHHHHHHHHCCCCCEEEecCcCCHHHHhh----ccc--ccceEeccEEEEEECCCCC--CCChhHcC--------
Confidence 3333335778889999999988765443443221 100 1133344567777776321 22566764
Q ss_pred CCcEEEcCCCccHHHHHH
Q 025329 209 KPLRVATGFTYLGPKFMK 226 (254)
Q Consensus 209 r~lRVATkYPnLarkyf~ 226 (254)
++||+...=.....|+.
T Consensus 133 -g~~Igv~~gs~~~~~~~ 149 (260)
T PRK15010 133 -GKHVGVLQGSTQEAYAN 149 (260)
T ss_pred -CCEEEEecCchHHHHHH
Confidence 46788754444444554
No 157
>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=28.52 E-value=51 Score=25.52 Aligned_cols=66 Identities=17% Similarity=0.202 Sum_probs=35.8
Q ss_pred CCeEEEeecCcchhhhhhcCceeeeeeccceeecccCCCcceeeecCCCCcccEEEEEEEeCCCcc--ccccchHHhhc
Q 025329 125 SNLEVWFQRPKDIVRKLLSGDLDLGIVGLDTVSEFGQGNEDLIIVHDALDYGDCRLSLAIPKYGIF--ENINSLRELAQ 201 (254)
Q Consensus 125 p~iev~~vRp~DIp~yV~~G~aDlGIvG~DvL~E~~~d~~~l~~~l~dLgfG~CRLvVAvP~~~~~--~dv~sl~dL~~ 201 (254)
|++++.+.-.+++...+..| +|+||+.... .+ .++. -..++..++++++|++... ...-+++||.+
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 1121 1234667778888665211 11235677753
No 158
>cd08472 PBP2_CrgA_like_3 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold. This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 3. The LTTRs are acting as both auto-repressors and activators of target promoters, controlling operons involved in a wide variety of cellular processes such as amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to name a few. In contrast to the tetrameric form of other LTTRs, CrgA from Neisseria meningitides assembles into an octameric ring, which can bind up to four 63-bp DNA oligonucleotides. Phylogenetic cluster analysis showed that the CrgA-like regulators form a subclass of the LTTRs that function as octamers. The CrgA is an auto-repressor of its own gene a
Probab=27.88 E-value=74 Score=24.90 Aligned_cols=66 Identities=14% Similarity=0.117 Sum_probs=34.7
Q ss_pred CCeEEEeecCcchhhhhhcCceeeeeeccceeecccCCCcceeeecCCCCcccEEEEEEEeCCCcc--ccccchHHhhc
Q 025329 125 SNLEVWFQRPKDIVRKLLSGDLDLGIVGLDTVSEFGQGNEDLIIVHDALDYGDCRLSLAIPKYGIF--ENINSLRELAQ 201 (254)
Q Consensus 125 p~iev~~vRp~DIp~yV~~G~aDlGIvG~DvL~E~~~d~~~l~~~l~dLgfG~CRLvVAvP~~~~~--~dv~sl~dL~~ 201 (254)
|++++-+....++...+. |.+|+||+..+. .+ .++. ...++..+++++++.+-.. ...-+++||.+
T Consensus 28 P~i~v~~~~~~~~~~~l~-~~~D~~i~~~~~-~~-----~~l~----~~~l~~~~~~~v~~~~~~~~~~~~~~~~~l~~ 95 (202)
T cd08472 28 PDIELDLGVSDRPVDLIR-EGVDCVIRVGEL-AD-----SSLV----ARRLGELRMVTCASPAYLARHGTPRHPEDLER 95 (202)
T ss_pred CCcEEEEEECCCcchhhc-ccccEEEEcCCC-CC-----ccEE----EEEccceeEEEEECHHHHHhCCCCCCHHHHhc
Confidence 445554444455666665 559999974321 11 1122 2345667788777654211 12236777764
No 159
>cd08485 PBP2_ClcR The C-terminal substrate binding domain of LysR-type transcriptional regulator ClcR involved in the chlorocatechol catabolism, contains type 2 periplasmic binding fold. In soil bacterium Pseudomonas putida, the ortho-pathways of catechol and 3-chlorocatechol are central catabolic pathways that convert aromatic and chloroaromaric compounds to tricarboxylic acid (TCA) cycle intermediates. The 3-chlorocatechol-degradative pathway is encoded by clcABD operon, which requires the divergently transcribed clcR and an intermediate of the pathway, 2-chloromuconate, as an inducer for activation. The topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding th
Probab=27.66 E-value=52 Score=26.28 Aligned_cols=28 Identities=18% Similarity=0.291 Sum_probs=21.7
Q ss_pred CCeEEEee--cCcchhhhhhcCceeeeeec
Q 025329 125 SNLEVWFQ--RPKDIVRKLLSGDLDLGIVG 152 (254)
Q Consensus 125 p~iev~~v--Rp~DIp~yV~~G~aDlGIvG 152 (254)
|++++-+. -.+|+...+.+|.+|+||+-
T Consensus 28 P~i~l~~~~~~~~~~~~~l~~~~~D~~i~~ 57 (198)
T cd08485 28 PSATVSLTQMSKNRQIEALDAGTIDIGFGR 57 (198)
T ss_pred CCcEEEEEECCHHHHHHHHHcCCccEEEec
Confidence 55555544 56789999999999999974
No 160
>smart00094 TR_FER Transferrin.
Probab=27.44 E-value=2.2e+02 Score=27.31 Aligned_cols=71 Identities=21% Similarity=0.265 Sum_probs=41.7
Q ss_pred CCeEEEeecC-cchhhhhhcCceeeeee-ccceeecccCCCcceeeecCCCCcc------cEEEEEE-EeCCCccccccc
Q 025329 125 SNLEVWFQRP-KDIVRKLLSGDLDLGIV-GLDTVSEFGQGNEDLIIVHDALDYG------DCRLSLA-IPKYGIFENINS 195 (254)
Q Consensus 125 p~iev~~vRp-~DIp~yV~~G~aDlGIv-G~DvL~E~~~d~~~l~~~l~dLgfG------~CRLvVA-vP~~~~~~dv~s 195 (254)
+.++++..+. .|.-..+.+|.||+.+. |.++..-. .. ..+.-++ .--++ ...-+|| |+.+ .++.+
T Consensus 27 ~~v~Cv~~~s~~~Ci~~I~~g~AD~a~ldg~~~y~A~-~~-~~l~pi~-~E~~~~~~~~~~~Y~aVaVVkk~---S~i~s 100 (332)
T smart00094 27 PALECVSASSTEECIKAIQKGEADAVTLDGGDVYTAG-KP-YNLVPVF-AENYGSEEEPETGYYAVAVVKKG---SAIFT 100 (332)
T ss_pred CceEEEEcCCHHHHHHHHHCCCCCEEEECcHHHHhhc-cc-CCceEEE-EEeeccCCCCCceeEEEEEEECC---CCCCC
Confidence 4566665543 68999999999999999 77766432 21 2221111 11122 1344444 5666 35678
Q ss_pred hHHhhc
Q 025329 196 LRELAQ 201 (254)
Q Consensus 196 l~dL~~ 201 (254)
++||++
T Consensus 101 l~dLkG 106 (332)
T smart00094 101 WNQLRG 106 (332)
T ss_pred HHHhCC
Confidence 889864
No 161
>cd08479 PBP2_CrgA_like_9 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold. This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 9. The LTTRs are acting as both auto-repressors and activators of target promoters, controlling operons involved in a wide variety of cellular processes such as amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to name a few. In contrast to the tetrameric form of other LTTRs, CrgA from Neisseria meningitides assembles into an octameric ring, which can bind up to four 63-bp DNA oligonucleotides. Phylogenetic cluster analysis showed that the CrgA-like regulators form a subclass of the LTTRs that function as octamers. The CrgA is an auto-repressor of its own gene a
Probab=24.18 E-value=63 Score=25.28 Aligned_cols=27 Identities=30% Similarity=0.310 Sum_probs=18.1
Q ss_pred CCeEEEeecCcchhhhhhcCceeeeeec
Q 025329 125 SNLEVWFQRPKDIVRKLLSGDLDLGIVG 152 (254)
Q Consensus 125 p~iev~~vRp~DIp~yV~~G~aDlGIvG 152 (254)
|++++.+.- .+....+..|.+|+||+-
T Consensus 28 P~i~i~~~~-~~~~~~l~~g~~Dl~i~~ 54 (198)
T cd08479 28 PELEVQLEL-TDRPVDLVEEGFDLDIRV 54 (198)
T ss_pred CCeEEEEEe-cCccccccccCccEEEEc
Confidence 445554442 234468899999999974
No 162
>TIGR00787 dctP tripartite ATP-independent periplasmic transporter solute receptor, DctP family. TRAP-T (Tripartite ATP-independent Periplasmic Transporter) family proteins generally consist of three components, and these systems have so far been found in Gram-negative bacteria, Gram-postive bacteria and archaea. The best characterized example is the DctPQM system of Rhodobacter capsulatus, a C4 dicarboxylate (malate, fumarate, succinate) transporter. This model represents the DctP family, one of at least three major families of extracytoplasmic solute receptor for TRAP family transporters. Other are the SnoM family (see pfam03480) and TAXI (TRAP-associated extracytoplasmic immunogenic) family.
Probab=23.84 E-value=2.2e+02 Score=25.23 Aligned_cols=32 Identities=16% Similarity=0.183 Sum_probs=22.1
Q ss_pred ccccchHHhhcCCcccCCCCcEEEcCCCccHHHHHHHcCCc
Q 025329 191 ENINSLRELAQMPQWTAEKPLRVATGFTYLGPKFMKDNGLK 231 (254)
Q Consensus 191 ~dv~sl~dL~~~~~~~~~r~lRVATkYPnLarkyf~~~Gi~ 231 (254)
..|++++||+ ++||.+---.+..++++..|..
T Consensus 126 ~~i~s~~Dl~---------G~kir~~~~~~~~~~~~~~Ga~ 157 (257)
T TIGR00787 126 KPITKPEDLK---------GLKIRIPNSPMNEAQFKALGAN 157 (257)
T ss_pred CccCChHHhC---------CCEEecCCCHHHHHHHHHcCCc
Confidence 4588999986 3556554334678888888864
No 163
>PRK15437 histidine ABC transporter substrate-binding protein HisJ; Provisional
Probab=22.26 E-value=4.1e+02 Score=23.05 Aligned_cols=76 Identities=14% Similarity=0.083 Sum_probs=41.4
Q ss_pred cchhhhhhcCceeeeeeccceeecccCCCcceeeecCCCCcccEEEEEEEeCCCccccccchHHhhcCCcccCCCCcEEE
Q 025329 135 KDIVRKLLSGDLDLGIVGLDTVSEFGQGNEDLIIVHDALDYGDCRLSLAIPKYGIFENINSLRELAQMPQWTAEKPLRVA 214 (254)
Q Consensus 135 ~DIp~yV~~G~aDlGIvG~DvL~E~~~d~~~l~~~l~dLgfG~CRLvVAvP~~~~~~dv~sl~dL~~~~~~~~~r~lRVA 214 (254)
..+-..++.|.+|+.+.+...=.|.... +... =.+..-..++.++.+..+ ..+++||. ++|||
T Consensus 75 ~~~~~~l~~g~~D~~~~~~~~t~eR~~~----~~fs--~p~~~~~~~~~~~~~~~~--~~~~~dl~---------g~~Ig 137 (259)
T PRK15437 75 DALIPSLKAKKIDAIMSSLSITEKRQQE----IAFT--DKLYAADSRLVVAKNSDI--QPTVESLK---------GKRVG 137 (259)
T ss_pred HHHHHHHHCCCCCEEEecCCCCHHHhhh----cccc--chhhcCceEEEEECCCCC--CCChHHhC---------CCEEE
Confidence 4566779999999887765443443221 1111 133344556667776432 23577764 35777
Q ss_pred cCCCccHHHHHHH
Q 025329 215 TGFTYLGPKFMKD 227 (254)
Q Consensus 215 TkYPnLarkyf~~ 227 (254)
..-=....+|+++
T Consensus 138 v~~g~~~~~~~~~ 150 (259)
T PRK15437 138 VLQGTTQETFGNE 150 (259)
T ss_pred EecCcHHHHHHHh
Confidence 6443333445544
No 164
>cd08432 PBP2_GcdR_TrpI_HvrB_AmpR_like The C-terminal substrate domain of LysR-type GcdR, TrPI, HvR and beta-lactamase regulators, and that of other closely related homologs; contains the type 2 periplasmic binding fold. This CD includes the C-terminal substrate domain of LysR-type transcriptional regulators involved in controlling the expression of glutaryl-CoA dehydrogenase (GcdH), S-adenosyl-L-homocysteine hydrolase, cell division protein FtsW, tryptophan synthase, and beta-lactamase. The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex compris
Probab=21.74 E-value=78 Score=24.48 Aligned_cols=28 Identities=11% Similarity=0.176 Sum_probs=19.0
Q ss_pred CCeEEEeecCcchhhhhhcCceeeeeecc
Q 025329 125 SNLEVWFQRPKDIVRKLLSGDLDLGIVGL 153 (254)
Q Consensus 125 p~iev~~vRp~DIp~yV~~G~aDlGIvG~ 153 (254)
|++++-+.-.. ....+.+|.+|+||+..
T Consensus 27 P~v~i~~~~~~-~~~~l~~g~~D~~i~~~ 54 (194)
T cd08432 27 PDIDLRLSTSD-RLVDFAREGIDLAIRYG 54 (194)
T ss_pred CCeEEEEEecC-CccccccccccEEEEec
Confidence 45555554333 45678999999999753
No 165
>PF09047 MEF2_binding: MEF2 binding; InterPro: IPR015134 The myocyte enhancer factor-2 (MEF2) binding domain, predominantly found in the calcineurin-binding protein CABIN 1, adopts an amphipathic alpha-helical structure, which allows it to bind a hydrophobic groove on the MEF2S domain, forming a triple-helical interaction. Interaction of this domain with MEF2 causes repression of transcription []. ; PDB: 1N6J_G.
Probab=20.60 E-value=58 Score=21.51 Aligned_cols=19 Identities=37% Similarity=0.543 Sum_probs=11.8
Q ss_pred ecCCCCChHHHHHHHHhCCC
Q 025329 88 LPSKGRMAADTLDLLKDCQL 107 (254)
Q Consensus 88 LPsKGRL~e~tl~LL~~aGi 107 (254)
-| ||.+.|++-+-|+.+=+
T Consensus 4 sp-kgsiseetkqklk~~il 22 (35)
T PF09047_consen 4 SP-KGSISEETKQKLKSAIL 22 (35)
T ss_dssp ---SS---HHHHHHHHHHHH
T ss_pred CC-CCcccHHHHHHHHHHHh
Confidence 36 99999999999988644
No 166
>PRK09861 cytoplasmic membrane lipoprotein-28; Provisional
Probab=20.31 E-value=1.7e+02 Score=26.98 Aligned_cols=76 Identities=16% Similarity=0.203 Sum_probs=45.6
Q ss_pred hhhhcCceeeeeeccceeecccCCCcceeeecCCCCcccEEEEEEEeCCCccccccchHHhhcCCcccCCCCcEEEcCC-
Q 025329 139 RKLLSGDLDLGIVGLDTVSEFGQGNEDLIIVHDALDYGDCRLSLAIPKYGIFENINSLRELAQMPQWTAEKPLRVATGF- 217 (254)
Q Consensus 139 ~yV~~G~aDlGIvG~DvL~E~~~d~~~l~~~l~dLgfG~CRLvVAvP~~~~~~dv~sl~dL~~~~~~~~~r~lRVATkY- 217 (254)
.-++.|.+|+++.+.--.++.-... ....+-.+.-.+++|.+..-..++|++||.. +.+||---
T Consensus 75 ~AL~~G~ID~n~~qh~~yl~~~~~~-------~g~~lv~~~~~~~~P~~~Ys~~iksl~DL~~--------Ga~IAipnd 139 (272)
T PRK09861 75 DATNHGELDANVFQHRPFLEQDNQA-------HGYKLVAVGNTFVFPMAGYSKKIKTVAQIKE--------GATVAIPND 139 (272)
T ss_pred HHHHcCCcceehhhhHHHHHHHHHh-------cCCCeEEEeEEEEEeeeccccCCCCHHHcCC--------CCEEEEeCC
Confidence 6799999999997554444431110 0223333445677777432245999999863 46888544
Q ss_pred -CccHHHHH--HHcC
Q 025329 218 -TYLGPKFM--KDNG 229 (254)
Q Consensus 218 -PnLarkyf--~~~G 229 (254)
-|.+|..+ ++.|
T Consensus 140 ~~n~~ral~lL~~ag 154 (272)
T PRK09861 140 PTNLGRALLLLQKEK 154 (272)
T ss_pred CccHHHHHHHHHHCC
Confidence 55666544 4555
No 167
>PF07927 YcfA: YcfA-like protein; InterPro: IPR012933 This entry represents UPF0395, which contains viral, archaeal and bacterial proteins. It includes YncN of Escherichia coli K12. Most of these proteins are hypothetical proteins of unknown function. ; GO: 0016788 hydrolase activity, acting on ester bonds; PDB: 1WHZ_A.
Probab=20.30 E-value=1.4e+02 Score=20.32 Aligned_cols=46 Identities=11% Similarity=0.103 Sum_probs=23.4
Q ss_pred HHHHHHHHhCCCccCCCCCCceEeecCCCCCeEEEeec---Ccchhhhhhc
Q 025329 96 ADTLDLLKDCQLSVKQVNPRQYVAQIPQLSNLEVWFQR---PKDIVRKLLS 143 (254)
Q Consensus 96 e~tl~LL~~aGi~v~~~~~R~L~~~~~~~p~iev~~vR---p~DIp~yV~~ 143 (254)
++...+|++.|+.+.+......++.-++.+. .+.+. .+||+.+...
T Consensus 2 ~el~k~L~~~G~~~~r~~GSH~~~~~~~~~~--~~~vp~h~~~ei~~~~~k 50 (56)
T PF07927_consen 2 RELIKLLEKAGFEEVRQKGSHHIFRHPGGRK--IVTVPPHPGKEIKPGTVK 50 (56)
T ss_dssp HHHHHHHHHTT-EEEEEETTEEEEE-TTS-E---EEEE-SSS-S--HHHHH
T ss_pred hHHHHHHHHCCCEEecCCCCEEEEEeCCCCc--ceEeCCCCccccCHHHHH
Confidence 5788999999998776433334444333222 23433 2578877654
No 168
>PF03460 NIR_SIR_ferr: Nitrite/Sulfite reductase ferredoxin-like half domain; InterPro: IPR005117 Sulphite reductases (SiRs) and related nitrite reductases (NiRs) catalyse the six-electron reduction reactions of sulphite to sulphide, and nitrite to ammonia, respectively. The Escherichia coli SiR enzyme is a complex composed of two proteins, a flavoprotein alpha-component (SiR-FP) and a hemoprotein beta-component (SiR-HP), and has an alpha(8)beta(4) quaternary structure []. SiR-FP contains both FAD and FMN, while SiR-HP contains a Fe(4)S(4) cluster coupled to a sirohaem through a cysteine bridge. Electrons are transferred from NADPH to FAD, and on to FMN in SiR-FP, from which they are transferred to the metal centre of SiR-HP, where they reduce the siroheme-bound sulphite. SiR-HP has a two-fold symmetry, which generates a distinctive three-domain alpha/beta fold that controls assembly and reactivity []. This entry describes the ferrodoxin-like (alpha/beta sandwich) domain, which consists of a duplication containing two subdomains of this fold.; GO: 0016491 oxidoreductase activity, 0055114 oxidation-reduction process; PDB: 3B0H_A 4GEP_A 2GEP_A 2AOP_A 5AOP_A 6GEP_A 4AOP_A 1AOP_A 3AOP_A 8GEP_A ....
Probab=20.28 E-value=90 Score=22.13 Aligned_cols=54 Identities=17% Similarity=0.279 Sum_probs=35.6
Q ss_pred ceEEEecCCCCChHHHHHHHHhCCCccCCCCCCceEeecCCCCCeEEEeecCcchhhhhh
Q 025329 83 EIRLGLPSKGRMAADTLDLLKDCQLSVKQVNPRQYVAQIPQLSNLEVWFQRPKDIVRKLL 142 (254)
Q Consensus 83 ~LrIALPsKGRL~e~tl~LL~~aGi~v~~~~~R~L~~~~~~~p~iev~~vRp~DIp~yV~ 142 (254)
++++-+| -|++..+-+..|.+. - +++..-.+.+... .++.+.-+++.++|...+
T Consensus 11 ~v~~~~~-~G~i~~~~l~~la~i--a-~~yg~~~irlT~~--Q~l~l~~v~~~~~~~i~~ 64 (69)
T PF03460_consen 11 MVRIRIP-GGRISAEQLRALAEI--A-EKYGDGEIRLTTR--QNLQLRGVPEENLPAIFE 64 (69)
T ss_dssp EEEEB-G-GGEEEHHHHHHHHHH--H-HHHSTSEEEEETT--SCEEEEEEEGGGHHHHHH
T ss_pred EEEEeCC-CEEECHHHHHHHHHH--H-HHhCCCeEEECCC--CeEEEeCCCHHHHHHHHH
Confidence 6999999 699988877766652 1 1112223444433 479999999999987653
No 169
>PRK10329 glutaredoxin-like protein; Provisional
Probab=20.02 E-value=89 Score=23.38 Aligned_cols=24 Identities=17% Similarity=0.202 Sum_probs=18.7
Q ss_pred ccHHHHHHHcCCceEEEEEcCCcee
Q 025329 219 YLGPKFMKDNGLKHVVFSTADGALE 243 (254)
Q Consensus 219 nLarkyf~~~Gi~~veIi~l~GSvE 243 (254)
+-+++||+++|+. ++.+.++..-|
T Consensus 15 ~~ak~~L~~~gI~-~~~idi~~~~~ 38 (81)
T PRK10329 15 HATKRAMESRGFD-FEMINVDRVPE 38 (81)
T ss_pred HHHHHHHHHCCCc-eEEEECCCCHH
Confidence 4588999999995 88888875443
Done!