Query gi|254780779|ref|YP_003065192.1| 30S ribosomal protein S2 [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 278
No_of_seqs 150 out of 1435
Neff 5.3
Searched_HMMs 39220
Date Sun May 29 19:08:50 2011
Command /home/congqian_1/programs/hhpred/hhsearch -i 254780779.hhm -d /home/congqian_1/database/cdd/Cdd.hhm
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 TIGR01011 rpsB_bact ribosomal 100.0 0 0 790.0 19.7 223 5-227 1-226 (227)
2 PRK12311 rpsB 30S ribosomal pr 100.0 0 0 694.3 23.7 246 1-246 1-247 (332)
3 COG0052 RpsB Ribosomal protein 100.0 0 0 656.7 21.2 228 3-230 1-228 (252)
4 PRK05299 rpsB 30S ribosomal pr 100.0 0 0 652.6 22.1 230 3-232 1-231 (255)
5 CHL00067 rps2 ribosomal protei 100.0 0 0 611.4 21.9 225 3-227 1-226 (227)
6 pfam00318 Ribosomal_S2 Ribosom 100.0 0 0 541.6 18.2 205 11-226 1-205 (205)
7 cd01425 RPS2 Ribosomal protein 100.0 0 0 497.6 17.1 193 11-224 1-193 (193)
8 PRK04020 rps2P 30S ribosomal p 100.0 0 0 467.3 15.3 183 5-236 9-192 (204)
9 PTZ00254 40S ribosomal protein 100.0 0 0 450.6 16.3 188 1-236 8-196 (242)
10 KOG0832 consensus 100.0 0 0 438.1 15.1 202 4-232 46-247 (251)
11 TIGR01012 Sa_S2_E_A ribosomal 100.0 7.6E-43 0 297.6 13.4 181 5-233 3-184 (197)
12 KOG0830 consensus 99.9 5.1E-26 1.3E-30 189.0 11.9 159 26-230 2-161 (254)
13 PRK00414 gmhA phosphoheptose i 97.3 0.012 3.2E-07 38.0 12.6 155 44-224 22-188 (192)
14 PRK13938 phosphoheptose isomer 97.0 0.039 9.9E-07 34.8 13.4 157 42-224 21-189 (196)
15 PRK13936 phosphoheptose isomer 96.8 0.038 9.7E-07 34.8 11.2 153 45-224 22-190 (197)
16 PRK13937 phosphoheptose isomer 96.7 0.067 1.7E-06 33.3 13.6 151 47-224 23-186 (192)
17 cd05006 SIS_GmhA Phosphoheptos 95.9 0.17 4.3E-06 30.7 13.5 148 49-222 16-175 (177)
18 PRK10886 DnaA initiator-associ 95.1 0.33 8.4E-06 28.8 13.8 151 46-224 21-188 (196)
19 PRK13608 diacylglycerol glucos 93.8 0.65 1.6E-05 26.9 8.9 139 63-210 2-161 (391)
20 cd05013 SIS_RpiR RpiR-like pro 93.0 0.87 2.2E-05 26.1 9.5 48 159-206 61-114 (139)
21 PRK00726 murG N-acetylglucosam 92.7 0.96 2.4E-05 25.8 8.2 29 67-95 91-119 (359)
22 TIGR00113 queA S-adenosylmethi 92.1 0.15 3.7E-06 31.1 3.1 72 41-113 241-327 (364)
23 cd05007 SIS_Etherase N-acetylm 92.0 1.2 3E-05 25.2 12.5 156 45-224 28-201 (257)
24 cd03805 GT1_ALG2_like This fam 91.9 0.78 2E-05 26.4 6.6 73 134-207 260-353 (392)
25 pfam04007 DUF354 Protein of un 91.8 1.2 3.2E-05 25.1 9.0 102 51-192 12-114 (335)
26 cd03785 GT1_MurG MurG is an N- 91.3 1.4 3.5E-05 24.8 7.8 25 70-94 92-116 (350)
27 cd06305 PBP1_methylthioribose_ 91.0 0.72 1.8E-05 26.6 5.7 14 173-186 72-85 (273)
28 cd06317 PBP1_ABC_sugar_binding 91.0 0.81 2.1E-05 26.3 5.9 44 157-201 55-100 (275)
29 PRK05636 replicative DNA helic 88.7 2.2 5.7E-05 23.4 9.4 159 16-195 246-431 (507)
30 cd06271 PBP1_AglR_RafR_like Li 88.7 2.2 5.7E-05 23.4 7.5 63 156-218 179-251 (268)
31 pfam10087 DUF2325 Uncharacteri 88.6 2.3 5.8E-05 23.4 6.7 75 68-187 1-79 (96)
32 cd06267 PBP1_LacI_sugar_bindin 88.5 1.5 3.9E-05 24.5 5.7 33 157-189 176-214 (264)
33 PRK06904 replicative DNA helic 88.5 2.3 5.9E-05 23.3 8.6 164 31-210 213-403 (472)
34 COG0279 GmhA Phosphoheptose is 88.4 2.4 6E-05 23.3 9.6 134 46-205 21-164 (176)
35 PRK08506 replicative DNA helic 88.2 2.4 6.1E-05 23.2 10.5 146 45-208 204-370 (473)
36 COG0707 MurG UDP-N-acetylgluco 88.2 2.4 6.2E-05 23.2 7.0 51 45-95 69-119 (357)
37 PRK12446 N-acetylglucosaminyl 87.8 2.6 6.6E-05 23.0 7.8 28 67-94 91-118 (352)
38 cd06307 PBP1_uncharacterized_s 87.5 2.5 6.5E-05 23.1 6.4 29 159-187 59-89 (275)
39 PRK02858 germination protease; 87.3 2.7 6.9E-05 22.9 9.3 162 28-227 65-268 (367)
40 cd01538 PBP1_ABC_xylose_bindin 86.5 2.8 7E-05 22.8 6.1 40 56-95 45-85 (288)
41 cd06302 PBP1_LsrB_Quorum_Sensi 85.7 1.2 2.9E-05 25.3 3.8 46 157-203 55-102 (298)
42 PRK13396 3-deoxy-7-phosphohept 85.6 3.4 8.6E-05 22.3 7.5 145 7-169 120-280 (352)
43 cd06299 PBP1_LacI_like_13 Liga 85.5 2.6 6.6E-05 23.0 5.5 63 157-219 174-246 (265)
44 cd01575 PBP1_GntR Ligand-bindi 85.5 3.4 8.6E-05 22.3 7.6 63 157-219 176-248 (268)
45 PRK10355 xylF D-xylose transpo 85.0 1.4 3.5E-05 24.8 3.9 61 158-221 81-143 (330)
46 cd06277 PBP1_LacI_like_1 Ligan 84.4 3.8 9.7E-05 21.9 6.7 64 155-218 174-247 (268)
47 PRK00941 acetyl-CoA decarbonyl 84.3 0.84 2.2E-05 26.2 2.6 36 157-192 301-336 (779)
48 PRK05441 murQ N-acetylmuramic 83.9 4 0.0001 21.8 12.6 155 45-227 37-213 (273)
49 PTZ00286 6-phospho-1-fructokin 83.9 1.2 3.1E-05 25.1 3.3 45 159-209 188-238 (486)
50 cd06312 PBP1_ABC_sugar_binding 83.7 4 0.0001 21.8 6.3 37 157-194 56-94 (271)
51 cd01139 TroA_f Periplasmic bin 83.7 1.8 4.7E-05 24.0 4.1 51 159-219 92-146 (342)
52 cd01141 TroA_d Periplasmic bin 83.6 1.5 3.9E-05 24.5 3.7 31 159-189 70-100 (186)
53 cd01916 ACS_1 Acetyl-CoA synth 82.8 1 2.7E-05 25.6 2.6 36 157-192 264-299 (731)
54 cd06296 PBP1_CatR_like Ligand- 82.6 4.5 0.00011 21.5 6.5 63 156-218 176-248 (270)
55 cd06315 PBP1_ABC_sugar_binding 82.4 1.2 3.2E-05 25.1 2.8 38 157-195 55-94 (280)
56 PRK13609 diacylglycerol glucos 82.1 4.7 0.00012 21.4 9.7 49 158-207 104-158 (388)
57 cd06308 PBP1_sensor_kinase_lik 82.0 2.3 6E-05 23.3 4.1 39 57-95 47-86 (270)
58 cd06322 PBP1_ABC_sugar_binding 81.3 2 5.1E-05 23.7 3.5 31 159-189 180-213 (267)
59 cd06300 PBP1_ABC_sugar_binding 80.7 5.1 0.00013 21.1 5.5 35 60-94 54-89 (272)
60 cd06313 PBP1_ABC_sugar_binding 80.4 4.4 0.00011 21.5 5.0 14 81-94 71-84 (272)
61 cd01539 PBP1_GGBP Periplasmic 80.4 1.9 4.7E-05 24.0 3.1 13 173-185 74-86 (303)
62 cd06278 PBP1_LacI_like_2 Ligan 80.2 3.5 8.9E-05 22.2 4.5 62 157-218 173-245 (266)
63 cd01544 PBP1_GalR Ligand-bindi 80.1 5.4 0.00014 20.9 9.1 63 156-218 177-249 (270)
64 cd06310 PBP1_ABC_sugar_binding 80.0 2.7 6.9E-05 22.9 3.9 39 159-200 184-226 (273)
65 PRK06830 diphosphate--fructose 80.0 0.98 2.5E-05 25.7 1.6 44 159-208 172-221 (442)
66 PRK12570 N-acetylmuramic acid- 79.7 5.6 0.00014 20.8 11.7 160 43-226 35-212 (296)
67 PRK05724 acetyl-CoA carboxylas 78.7 3.7 9.5E-05 22.0 4.2 20 173-192 142-161 (318)
68 cd06295 PBP1_CelR Ligand bindi 78.4 4.2 0.00011 21.6 4.5 63 157-219 185-257 (275)
69 COG1609 PurR Transcriptional r 78.1 6.3 0.00016 20.5 7.8 61 159-219 238-308 (333)
70 cd06274 PBP1_FruR Ligand bindi 78.1 3.8 9.7E-05 21.9 4.2 63 156-218 176-248 (264)
71 cd06318 PBP1_ABC_sugar_binding 77.8 2.5 6.4E-05 23.1 3.1 36 59-94 48-84 (282)
72 TIGR03590 PseG pseudaminic aci 77.6 6.5 0.00016 20.4 9.9 47 159-205 82-128 (280)
73 cd00764 Eukaryotic_PFK Phospho 77.6 6.5 0.00017 20.4 6.4 174 26-224 316-544 (762)
74 PRK00758 GMP synthase subunit 77.5 6.5 0.00017 20.4 6.8 31 159-189 42-75 (184)
75 cd06309 PBP1_YtfQ_like Peripla 77.4 6.5 0.00017 20.4 5.8 24 158-181 185-208 (273)
76 pfam01380 SIS SIS domain. SIS 77.1 6.7 0.00017 20.3 6.3 48 159-206 54-107 (131)
77 cd06323 PBP1_ribose_binding Pe 77.0 6.7 0.00017 20.3 6.0 34 158-191 181-217 (268)
78 cd06311 PBP1_ABC_sugar_binding 76.8 3.5 8.8E-05 22.2 3.6 12 172-183 202-213 (274)
79 cd06273 PBP1_GntR_like_1 This 76.2 7.1 0.00018 20.2 7.8 63 156-218 176-248 (268)
80 COG4069 Uncharacterized protei 75.6 2.8 7.2E-05 22.8 2.9 200 3-209 60-327 (367)
81 TIGR02858 spore_III_AA stage I 75.2 4.1 0.00011 21.7 3.7 52 125-190 187-240 (282)
82 TIGR03600 phage_DnaB phage rep 75.1 7.6 0.00019 20.0 9.5 135 45-196 205-359 (421)
83 cd06321 PBP1_ABC_sugar_binding 74.9 3.4 8.6E-05 22.3 3.2 29 159-187 182-213 (271)
84 PRK05749 3-deoxy-D-manno-octul 74.9 5.7 0.00014 20.8 4.3 27 159-185 124-150 (423)
85 cd01571 NAPRTase_B Nicotinate 74.1 6 0.00015 20.6 4.3 22 55-78 101-122 (302)
86 KOG2754 consensus 73.9 2.7 6.9E-05 22.9 2.5 84 9-96 44-131 (443)
87 cd06288 PBP1_sucrose_transcrip 73.9 8.1 0.00021 19.8 6.1 64 156-219 175-249 (269)
88 pfam04413 Glycos_transf_N 3-De 73.7 8.2 0.00021 19.8 8.4 92 49-187 31-124 (186)
89 cd01545 PBP1_SalR Ligand-bindi 73.5 8.3 0.00021 19.8 7.4 35 156-190 177-217 (270)
90 PRK06749 replicative DNA helic 73.1 8.4 0.00021 19.7 9.6 145 32-196 189-355 (428)
91 cd06283 PBP1_RegR_EndR_KdgR_li 72.3 7.8 0.0002 19.9 4.5 62 157-218 177-248 (267)
92 PRK12362 germination protease; 72.3 8.8 0.00022 19.6 9.3 156 28-221 56-250 (324)
93 TIGR01815 TrpE-clade3 anthrani 72.0 9 0.00023 19.5 5.9 95 44-188 503-603 (726)
94 cd05014 SIS_Kpsf KpsF-like pro 72.0 6.9 0.00018 20.3 4.2 46 159-204 48-99 (128)
95 PRK11316 bifunctional heptose 71.3 4.1 0.0001 21.7 2.9 154 29-202 21-194 (473)
96 LOAD_uvrC_endov consensus 70.2 5.6 0.00014 20.8 3.4 35 156-190 78-116 (123)
97 cd05298 GH4_GlvA_pagL_like Gly 69.9 9.9 0.00025 19.3 4.6 47 159-206 135-196 (437)
98 PRK00025 lpxB lipid-A-disaccha 69.6 10 0.00026 19.2 4.6 56 40-95 58-119 (382)
99 PRK11337 DNA-binding transcrip 69.6 10 0.00026 19.2 5.1 51 159-209 189-247 (293)
100 cd01536 PBP1_ABC_sugar_binding 69.5 10 0.00026 19.2 5.5 33 158-190 181-217 (267)
101 cd01540 PBP1_arabinose_binding 69.3 8 0.0002 19.8 4.0 40 56-95 44-84 (289)
102 TIGR02639 ClpA ATP-dependent C 69.2 10 0.00026 19.2 4.5 189 25-236 491-722 (774)
103 PRK08694 consensus 69.1 10 0.00026 19.1 9.7 161 32-208 211-397 (468)
104 PRK10936 periplasmic sensory p 68.9 10 0.00027 19.1 4.8 58 139-204 90-147 (340)
105 PRK09701 D-allose transporter 68.4 4 0.0001 21.8 2.3 37 157-194 81-119 (311)
106 cd05005 SIS_PHI Hexulose-6-pho 68.3 11 0.00027 19.0 9.0 73 159-231 76-168 (179)
107 PRK05562 precorrin-2 dehydroge 68.1 11 0.00028 19.0 6.4 126 56-220 15-157 (222)
108 pfam02350 Epimerase_2 UDP-N-ac 67.9 11 0.00027 19.0 4.5 26 171-196 267-292 (346)
109 PRK05973 replicative DNA helic 67.8 11 0.00028 19.0 8.9 119 46-206 76-208 (237)
110 cd06294 PBP1_ycjW_transcriptio 67.5 11 0.00028 18.9 6.2 63 156-218 181-253 (270)
111 cd06314 PBP1_tmGBP Periplasmic 67.4 5 0.00013 21.2 2.7 40 157-199 176-221 (271)
112 cd01743 GATase1_Anthranilate_S 67.2 11 0.00029 18.9 5.5 31 159-189 43-79 (184)
113 TIGR03127 RuMP_HxlB 6-phospho 67.0 11 0.00029 18.9 10.1 136 45-230 8-164 (179)
114 cd06320 PBP1_allose_binding Pe 66.4 4.3 0.00011 21.6 2.2 24 159-182 183-206 (275)
115 PRK00558 uvrC excinuclease ABC 66.1 12 0.0003 18.8 6.3 37 155-191 458-498 (609)
116 pfam02056 Glyco_hydro_4 Family 65.8 8 0.0002 19.9 3.5 129 39-190 30-169 (183)
117 cd06291 PBP1_Qymf_like Ligand 65.7 8.9 0.00023 19.6 3.7 61 158-218 173-243 (265)
118 cd06279 PBP1_LacI_like_3 Ligan 65.5 12 0.00031 18.7 4.9 63 156-218 193-264 (283)
119 PRK11148 cyclic 3',5'-adenosin 65.0 8.7 0.00022 19.6 3.5 54 48-104 38-96 (275)
120 TIGR01457 HAD-SF-IIA-hyp2 HAD- 65.0 4.6 0.00012 21.4 2.1 57 41-97 4-66 (251)
121 COG1737 RpiR Transcriptional r 64.9 12 0.00032 18.6 6.5 45 159-203 178-228 (281)
122 cd06298 PBP1_CcpA_like Ligand- 64.3 13 0.00033 18.5 6.1 62 157-218 176-247 (268)
123 TIGR00888 guaA_Nterm GMP synth 63.8 7.4 0.00019 20.1 3.0 31 158-188 41-77 (195)
124 cd06338 PBP1_ABC_ligand_bindin 63.5 13 0.00034 18.4 9.7 38 158-195 196-236 (345)
125 PRK10727 DNA-binding transcrip 63.4 13 0.00034 18.4 7.7 62 156-217 235-306 (342)
126 pfam02684 LpxB Lipid-A-disacch 63.3 13 0.00034 18.4 4.6 58 41-98 56-120 (373)
127 PRK12306 uvrC excinuclease ABC 63.0 14 0.00034 18.4 6.1 72 156-227 432-510 (519)
128 TIGR01133 murG undecaprenyldip 62.5 14 0.00035 18.3 5.6 57 39-95 69-127 (368)
129 PRK02947 hypothetical protein; 62.5 14 0.00035 18.3 12.3 116 48-189 23-142 (247)
130 PRK12319 acetyl-CoA carboxylas 61.9 4.2 0.00011 21.6 1.4 17 174-190 91-107 (256)
131 cd06280 PBP1_LacI_like_4 Ligan 61.6 14 0.00036 18.2 7.1 63 156-218 170-242 (263)
132 cd06306 PBP1_TorT-like TorT-li 61.4 11 0.00027 19.0 3.4 39 157-195 56-95 (268)
133 cd06292 PBP1_LacI_like_10 Liga 61.3 14 0.00037 18.2 4.3 34 157-190 180-219 (273)
134 PRK07188 nicotinate phosphorib 60.4 9.5 0.00024 19.4 3.0 15 63-77 132-146 (355)
135 cd06328 PBP1_SBP_like_2 Peripl 60.2 15 0.00039 18.1 9.5 95 53-191 126-226 (333)
136 pfam08459 UvrC_HhH_N UvrC Heli 59.7 8.2 0.00021 19.8 2.6 35 156-190 76-113 (154)
137 PRK05748 replicative DNA helic 59.0 16 0.0004 17.9 10.1 161 16-195 182-369 (448)
138 TIGR03191 benz_CoA_bzdO benzoy 58.3 16 0.00042 17.9 6.3 57 158-223 111-169 (430)
139 cd01542 PBP1_TreR_like Ligand- 58.2 16 0.00042 17.8 6.2 62 157-218 172-243 (259)
140 cd01537 PBP1_Repressors_Sugar_ 58.2 16 0.00042 17.8 6.4 61 158-218 178-248 (264)
141 PRK08662 nicotinate phosphorib 57.9 6.9 0.00018 20.3 2.0 16 63-78 124-139 (343)
142 cd06285 PBP1_LacI_like_7 Ligan 57.4 17 0.00043 17.8 6.6 63 156-218 173-245 (265)
143 cd01149 HutB Hemin binding pro 57.1 15 0.00038 18.1 3.6 32 62-94 54-85 (235)
144 pfam02900 LigB Catalytic LigB 56.8 15 0.00038 18.1 3.5 26 51-78 29-54 (265)
145 CHL00198 accA acetyl-CoA carbo 56.8 7.8 0.0002 19.9 2.1 134 41-192 7-165 (322)
146 cd06335 PBP1_ABC_ligand_bindin 56.8 17 0.00044 17.7 7.8 37 158-195 193-232 (347)
147 PRK03379 vitamin B12-transport 56.7 14 0.00037 18.2 3.4 27 159-185 78-104 (265)
148 PRK11557 putative DNA-binding 56.2 18 0.00045 17.6 5.2 44 159-202 180-229 (282)
149 pfam03418 Peptidase_A25 Germin 55.7 5.9 0.00015 20.7 1.3 161 29-227 53-256 (355)
150 PRK08840 replicative DNA helic 55.6 18 0.00046 17.6 10.6 148 32-195 210-383 (464)
151 PRK11006 phoR phosphate regulo 55.6 18 0.00046 17.6 5.6 86 135-226 243-334 (431)
152 CHL00197 carA carbamoyl-phosph 55.4 6.7 0.00017 20.3 1.6 31 158-188 235-273 (383)
153 COG1879 RbsB ABC-type sugar tr 55.1 18 0.00047 17.5 5.2 65 157-223 90-156 (322)
154 COG1152 CdhA CO dehydrogenase/ 55.0 9.6 0.00024 19.3 2.3 49 157-205 300-358 (772)
155 pfam01497 Peripla_BP_2 Peripla 54.7 16 0.0004 18.0 3.4 33 62-95 56-88 (236)
156 cd06281 PBP1_LacI_like_5 Ligan 54.4 19 0.00048 17.4 7.8 63 156-218 174-246 (269)
157 PRK09732 hypothetical protein; 54.2 8 0.0002 19.9 1.8 41 172-215 18-59 (134)
158 PRK04308 murD UDP-N-acetylmura 54.2 19 0.00048 17.4 5.9 26 67-92 111-138 (445)
159 pfam03345 DDOST_48kD Oligosacc 54.0 19 0.00049 17.4 4.9 91 10-104 38-130 (439)
160 COG0825 AccA Acetyl-CoA carbox 53.5 7.7 0.0002 20.0 1.6 15 174-188 181-195 (317)
161 TIGR00314 cdhA CO dehydrogenas 53.2 11 0.00029 18.9 2.4 49 156-204 303-361 (795)
162 cd06289 PBP1_MalI_like Ligand- 52.9 20 0.00051 17.3 7.8 63 157-219 177-249 (268)
163 cd01143 YvrC Periplasmic bindi 52.5 20 0.00051 17.3 3.6 28 159-187 61-88 (195)
164 pfam01866 Diphthamide_syn Puta 52.0 21 0.00052 17.2 4.9 53 14-77 48-102 (300)
165 pfam00117 GATase Glutamine ami 51.9 12 0.0003 18.7 2.4 31 159-189 42-79 (187)
166 PRK10653 D-ribose transporter 51.8 21 0.00053 17.2 4.4 14 173-186 99-112 (295)
167 TIGR01265 tyr_nico_aTase tyros 51.4 11 0.00028 19.0 2.1 39 147-186 172-222 (424)
168 cd05008 SIS_GlmS_GlmD_1 SIS (S 51.4 21 0.00054 17.1 4.3 48 158-205 46-99 (126)
169 cd06284 PBP1_LacI_like_6 Ligan 51.1 21 0.00054 17.1 6.1 63 156-218 174-246 (267)
170 PRK09165 replicative DNA helic 51.1 21 0.00054 17.1 10.9 150 45-209 216-399 (484)
171 cd01543 PBP1_XylR Ligand-bindi 51.0 21 0.00054 17.1 8.4 61 158-218 171-242 (265)
172 cd06316 PBP1_ABC_sugar_binding 50.9 21 0.00054 17.1 5.4 38 57-94 47-85 (294)
173 pfam03033 Glyco_transf_28 Glyc 50.9 21 0.00054 17.1 8.1 117 48-198 8-124 (136)
174 PTZ00295 glucosamine-fructose- 50.8 21 0.00055 17.1 3.9 61 161-221 425-494 (691)
175 cd06290 PBP1_LacI_like_9 Ligan 50.5 22 0.00055 17.1 6.8 62 157-218 175-246 (265)
176 PRK07004 replicative DNA helic 50.0 22 0.00056 17.0 9.0 147 31-195 205-378 (460)
177 PRK11070 ssDNA exonuclease Rec 49.9 22 0.00056 17.0 9.8 57 49-105 51-115 (574)
178 cd04795 SIS SIS domain. SIS (S 49.2 18 0.00047 17.5 3.0 30 159-188 48-81 (87)
179 PRK11303 DNA-binding transcrip 49.1 23 0.00058 16.9 7.7 62 157-218 237-308 (330)
180 PRK10339 DNA-binding transcrip 49.1 23 0.00058 16.9 8.4 65 156-220 232-306 (327)
181 TIGR02634 xylF D-xylose ABC tr 48.5 17 0.00043 17.8 2.7 51 157-208 53-105 (307)
182 PRK11041 DNA-binding transcrip 48.3 23 0.0006 16.8 8.6 64 155-218 242-315 (341)
183 smart00481 POLIIIAc DNA polyme 48.3 11 0.00027 19.0 1.7 21 172-192 19-39 (67)
184 PRK09492 treR trehalose repres 48.3 23 0.0006 16.8 6.4 60 157-216 231-297 (315)
185 KOG2062 consensus 48.1 23 0.00058 16.9 3.3 47 157-215 740-786 (929)
186 cd05710 SIS_1 A subgroup of th 48.0 24 0.0006 16.8 5.8 47 159-205 48-100 (120)
187 PRK08605 D-lactate dehydrogena 48.0 24 0.0006 16.8 4.4 27 66-92 146-172 (332)
188 PRK10703 DNA-binding transcrip 47.9 17 0.00043 17.7 2.6 64 156-219 237-310 (335)
189 PRK09526 lacI lac repressor; R 47.2 15 0.00038 18.1 2.3 63 156-218 238-310 (342)
190 COG0809 QueA S-adenosylmethion 46.7 12 0.0003 18.8 1.7 59 53-113 236-306 (348)
191 cd06324 PBP1_ABC_sugar_binding 46.1 21 0.00054 17.1 2.9 37 59-95 49-87 (305)
192 PRK12838 carbamoyl phosphate s 46.1 13 0.00032 18.6 1.8 30 159-188 209-244 (356)
193 PRK07765 para-aminobenzoate sy 45.4 26 0.00066 16.5 6.2 25 68-92 2-26 (221)
194 cd06275 PBP1_PurR Ligand-bindi 45.4 26 0.00066 16.5 4.6 63 156-218 176-248 (269)
195 cd06293 PBP1_LacI_like_11 Liga 44.8 26 0.00067 16.5 6.1 29 156-184 175-203 (269)
196 cd01574 PBP1_LacI Ligand-bindi 44.5 27 0.00068 16.5 7.3 61 158-218 174-244 (264)
197 PRK11302 DNA-binding transcrip 44.5 27 0.00068 16.5 4.8 46 159-204 176-226 (284)
198 cd06286 PBP1_CcpB_like Ligand- 44.4 27 0.00068 16.5 7.8 36 155-190 172-213 (260)
199 TIGR00065 ftsZ cell division p 43.7 28 0.0007 16.4 7.4 101 50-195 91-216 (365)
200 TIGR03573 WbuX N-acetyl sugar 43.3 28 0.00071 16.3 5.0 129 43-189 36-168 (343)
201 cd01744 GATase1_CPSase Small c 43.3 19 0.00049 17.4 2.3 31 159-189 40-77 (178)
202 TIGR02482 PFKA_ATP 6-phosphofr 42.9 28 0.00072 16.3 4.5 83 126-227 70-154 (302)
203 pfam05511 ATP-synt_F6 Mitochon 42.9 28 0.00072 16.3 4.0 49 114-162 43-96 (99)
204 COG4800 Predicted transcriptio 42.9 18 0.00046 17.6 2.2 49 82-130 32-81 (170)
205 COG2071 Predicted glutamine am 42.6 12 0.0003 18.8 1.2 25 165-189 88-115 (243)
206 cd01147 HemV-2 Metal binding p 42.5 29 0.00073 16.3 3.6 54 61-118 69-122 (262)
207 TIGR01533 lipo_e_P4 5'-nucleot 42.4 29 0.00073 16.3 4.1 113 54-204 147-263 (295)
208 cd05296 GH4_P_beta_glucosidase 42.2 29 0.00074 16.2 4.1 47 159-206 136-196 (419)
209 TIGR00694 thiM hydroxyethylthi 41.8 18 0.00046 17.6 2.0 33 152-185 43-83 (282)
210 pfam00857 Isochorismatase Isoc 41.7 29 0.00075 16.2 3.1 37 159-195 110-149 (172)
211 TIGR01082 murC UDP-N-acetylmur 41.5 26 0.00065 16.6 2.7 27 159-185 66-94 (491)
212 cd00984 DnaB_C DnaB helicase C 41.4 30 0.00076 16.2 10.2 142 32-196 16-178 (242)
213 KOG2544 consensus 41.3 30 0.00076 16.1 4.1 108 94-202 415-561 (711)
214 PRK08006 replicative DNA helic 40.2 31 0.00079 16.0 11.8 147 45-209 235-404 (471)
215 KOG3818 consensus 40.1 31 0.00078 16.1 3.0 133 40-179 193-341 (525)
216 cd00904 Ferritin Ferritin iron 40.1 31 0.0008 16.0 4.5 115 39-167 38-160 (160)
217 pfam06636 DUF1157 Protein of u 40.0 31 0.0008 16.0 3.4 65 140-204 59-125 (370)
218 cd06337 PBP1_ABC_ligand_bindin 39.9 31 0.0008 16.0 4.9 41 157-197 202-245 (357)
219 TIGR00597 rad10 DNA repair pro 39.4 16 0.0004 18.0 1.4 36 139-182 61-97 (117)
220 PRK12564 carbamoyl phosphate s 39.3 19 0.00049 17.4 1.8 30 159-188 213-249 (355)
221 pfam03796 DnaB_C DnaB-like hel 39.2 32 0.00082 15.9 9.5 55 32-94 22-77 (186)
222 cd01745 GATase1_2 Subgroup of 39.0 11 0.00029 18.9 0.6 20 170-189 89-108 (189)
223 TIGR00979 fumC_II fumarate hyd 39.0 32 0.00083 15.9 5.7 168 41-228 202-391 (459)
224 cd03786 GT1_UDP-GlcNAc_2-Epime 38.9 32 0.00082 15.9 2.9 33 174-206 289-323 (363)
225 cd01742 GATase1_GMP_Synthase T 38.6 32 0.00082 16.0 2.9 30 159-188 42-77 (181)
226 pfam00532 Peripla_BP_1 family. 38.0 34 0.00086 15.8 5.6 63 157-219 181-262 (281)
227 TIGR03639 cas1_NMENI CRISPR-as 37.9 34 0.00086 15.8 5.9 50 160-210 36-87 (278)
228 COG0614 FepB ABC-type Fe3+-hyd 37.6 34 0.00087 15.8 4.6 31 159-190 116-146 (319)
229 COG2503 Predicted secreted aci 37.5 34 0.00087 15.8 4.1 44 53-96 125-170 (274)
230 cd00354 FBPase Fructose-1,6-bi 37.3 2.3 5.9E-05 23.3 -3.1 49 43-91 12-74 (315)
231 COG1648 CysG Siroheme synthase 37.2 35 0.00088 15.7 6.3 124 63-222 9-147 (210)
232 cd06287 PBP1_LacI_like_8 Ligan 37.2 35 0.00088 15.7 6.0 62 158-219 178-249 (269)
233 PRK07591 threonine synthase; V 37.1 35 0.00088 15.7 6.5 51 59-109 178-229 (422)
234 PRK05638 threonine synthase; V 36.9 35 0.00089 15.7 6.3 56 58-113 151-207 (443)
235 pfam08672 APC2 Anaphase promot 36.8 30 0.00075 16.2 2.5 24 98-123 1-24 (60)
236 PRK11617 endonuclease V; Provi 36.0 23 0.00058 16.9 1.8 37 154-190 92-133 (223)
237 TIGR00287 cas1 CRISPR-associat 35.8 36 0.00091 15.7 2.8 45 159-204 37-88 (353)
238 pfam00743 FMO-like Flavin-bind 35.4 36 0.00092 15.6 2.7 35 63-97 180-214 (532)
239 CHL00101 trpG anthranilate syn 35.4 37 0.00094 15.6 6.3 31 68-98 1-31 (190)
240 KOG0256 consensus 35.2 22 0.00055 17.1 1.5 42 171-219 214-256 (471)
241 PRK00421 murC UDP-N-acetylmura 35.1 37 0.00095 15.5 2.9 86 8-107 46-149 (459)
242 cd06270 PBP1_GalS_like Ligand 34.8 38 0.00096 15.5 6.3 63 156-218 175-247 (268)
243 PRK10416 cell division protein 34.6 38 0.00097 15.5 6.4 148 30-193 294-451 (499)
244 pfam10609 ParA ParA/MinD ATPas 34.5 31 0.00079 16.1 2.3 33 158-190 25-62 (81)
245 cd06559 Endonuclease_V Endonuc 34.4 25 0.00064 16.7 1.8 36 155-190 90-130 (208)
246 COG2984 ABC-type uncharacteriz 34.2 39 0.00099 15.4 5.6 142 42-187 64-245 (322)
247 TIGR02638 lactal_redase lactal 34.0 24 0.00062 16.7 1.7 48 181-228 168-237 (380)
248 PRK09375 quinolinate synthetas 34.0 39 0.00099 15.4 3.9 22 158-179 208-229 (323)
249 cd03819 GT1_WavL_like This fam 33.9 39 0.001 15.4 3.5 34 171-205 278-316 (355)
250 PRK00073 pgk phosphoglycerate 33.4 40 0.001 15.3 7.0 25 6-30 41-71 (391)
251 PRK13545 tagH teichoic acids e 32.9 41 0.001 15.3 7.2 90 39-142 163-256 (549)
252 cd00763 Bacterial_PFK Phosphof 32.8 41 0.001 15.3 6.7 45 159-209 93-137 (317)
253 PRK08673 3-deoxy-7-phosphohept 32.8 41 0.001 15.3 7.8 141 8-169 113-271 (335)
254 TIGR00313 cobQ cobyric acid sy 32.7 26 0.00067 16.5 1.7 41 185-225 276-318 (502)
255 pfam01039 Carboxyl_trans Carbo 32.7 22 0.00055 17.1 1.2 44 149-192 283-338 (487)
256 pfam00977 His_biosynth Histidi 32.2 39 0.00098 15.4 2.4 32 76-111 59-90 (229)
257 PRK10423 transcriptional repre 32.2 42 0.0011 15.2 8.4 64 156-219 233-306 (327)
258 cd06272 PBP1_hexuronate_repres 31.9 42 0.0011 15.2 7.3 63 156-218 170-242 (261)
259 COG1515 Nfi Deoxyinosine 3'end 31.8 34 0.00087 15.8 2.1 36 155-190 92-132 (212)
260 PRK11366 puuD gamma-glutamyl-g 31.6 21 0.00053 17.2 1.0 37 55-91 28-64 (254)
261 TIGR01318 gltD_gamma_fam gluta 31.6 41 0.001 15.3 2.5 43 59-105 136-184 (480)
262 PRK00994 F420-dependent methyl 31.5 43 0.0011 15.2 3.4 33 158-190 59-95 (276)
263 TIGR00441 gmhA phosphoheptose 31.2 43 0.0011 15.1 9.6 136 48-209 21-169 (186)
264 PRK10637 cysG siroheme synthas 31.0 43 0.0011 15.1 5.8 25 64-88 10-34 (457)
265 cd06329 PBP1_SBP_like_3 Peripl 30.9 44 0.0011 15.1 8.2 80 66-186 143-232 (342)
266 TIGR01918 various_sel_PB selen 30.9 43 0.0011 15.1 2.5 71 130-208 318-402 (433)
267 PRK00147 queA S-adenosylmethio 30.7 44 0.0011 15.1 5.0 14 62-75 243-256 (345)
268 PRK08250 glutamine amidotransf 30.4 17 0.00044 17.7 0.4 25 53-77 71-95 (235)
269 TIGR01279 DPOR_bchN light-inde 30.4 24 0.00061 16.8 1.1 183 32-227 46-255 (458)
270 cd05197 GH4_glycoside_hydrolas 30.3 45 0.0011 15.0 6.2 46 159-205 135-195 (425)
271 PRK12778 putative bifunctional 30.2 45 0.0011 15.0 6.4 30 93-122 236-265 (760)
272 PRK00331 glucosamine--fructose 30.1 45 0.0011 15.0 6.9 57 160-216 337-402 (604)
273 PRK07263 consensus 30.0 45 0.0012 15.0 10.7 143 32-196 206-369 (453)
274 TIGR00513 accA acetyl-CoA carb 29.9 30 0.00076 16.2 1.6 20 174-193 152-171 (329)
275 PRK01021 lpxB lipid-A-disaccha 29.9 45 0.0012 15.0 4.6 15 76-90 320-334 (607)
276 TIGR01368 CPSaseIIsmall carbam 29.4 46 0.0012 14.9 2.8 30 159-188 238-275 (383)
277 TIGR03669 urea_ABC_arch urea A 29.3 46 0.0012 14.9 9.3 27 158-184 188-217 (374)
278 COG0126 Pgk 3-phosphoglycerate 29.3 47 0.0012 14.9 2.6 193 6-221 43-309 (395)
279 TIGR03659 IsdE heme ABC transp 29.2 47 0.0012 14.9 5.4 27 159-186 92-118 (289)
280 cd06331 PBP1_AmiC_like Type I 29.1 47 0.0012 14.9 8.8 86 54-182 122-212 (333)
281 pfam06925 MGDG_synth Monogalac 28.8 47 0.0012 14.9 4.2 52 158-209 89-150 (169)
282 PRK07053 glutamine amidotransf 28.7 26 0.00066 16.6 1.1 29 49-77 66-94 (235)
283 COG0560 SerB Phosphoserine pho 28.6 48 0.0012 14.8 6.6 46 163-208 138-190 (212)
284 TIGR01108 oadA oxaloacetate de 28.3 36 0.00093 15.6 1.8 58 26-106 236-302 (616)
285 PRK05670 anthranilate synthase 28.1 49 0.0012 14.8 5.7 31 159-189 44-80 (192)
286 cd06332 PBP1_aromatic_compound 28.1 49 0.0012 14.8 10.0 30 158-187 186-220 (333)
287 PRK07226 fructose-bisphosphate 27.9 30 0.00075 16.2 1.3 16 173-188 131-146 (266)
288 cd06334 PBP1_ABC_ligand_bindin 27.8 49 0.0013 14.7 8.5 43 53-95 53-95 (351)
289 cd00223 TOPRIM_TopoIIB_SPO TOP 27.8 28 0.00072 16.3 1.1 17 180-198 50-66 (160)
290 PRK11382 frlB fructoselysine-6 27.8 49 0.0013 14.7 3.2 53 161-213 102-160 (347)
291 COG2093 DNA-directed RNA polym 27.7 30 0.00076 16.2 1.3 24 159-186 34-57 (64)
292 PRK09922 UDP-D-galactose:(gluc 27.5 50 0.0013 14.7 3.4 58 161-220 261-326 (361)
293 PRK10401 DNA-binding transcrip 27.5 50 0.0013 14.7 7.5 63 156-218 235-307 (346)
294 cd01968 Nitrogenase_NifE_I Nit 27.4 50 0.0013 14.7 7.2 32 162-193 291-322 (410)
295 TIGR00083 ribF riboflavin bios 27.2 13 0.00033 18.5 -0.7 61 15-75 9-110 (296)
296 PRK10530 phosphotransferase; P 27.0 51 0.0013 14.7 6.0 41 156-196 185-230 (272)
297 PRK08760 replicative DNA helic 27.0 51 0.0013 14.7 9.7 157 32-206 222-404 (476)
298 PRK02231 ppnK inorganic polyph 27.0 51 0.0013 14.7 2.5 70 36-106 10-83 (272)
299 cd06282 PBP1_GntR_like_2 Ligan 26.7 51 0.0013 14.6 4.6 62 157-218 175-246 (266)
300 pfam04493 Endonuclease_5 Endon 26.5 39 0.001 15.4 1.7 36 155-190 85-125 (205)
301 PRK02769 histidine decarboxyla 26.1 53 0.0013 14.6 5.2 14 45-58 116-129 (380)
302 COG3384 Aromatic ring-opening 25.7 54 0.0014 14.5 2.7 40 35-76 15-54 (268)
303 cd01541 PBP1_AraR Ligand-bindi 25.7 54 0.0014 14.5 6.0 63 156-218 181-253 (273)
304 COG3193 GlcG Uncharacterized p 25.7 43 0.0011 15.1 1.8 53 171-226 18-71 (141)
305 TIGR01182 eda 2-dehydro-3-deox 25.5 54 0.0014 14.5 6.8 92 49-188 16-109 (205)
306 pfam01973 MAF_flag10 Protein o 25.1 55 0.0014 14.4 4.5 85 64-198 22-108 (169)
307 COG2072 TrkA Predicted flavopr 25.0 55 0.0014 14.4 3.4 44 54-97 163-206 (443)
308 LOAD_php consensus 24.8 39 0.00099 15.4 1.4 22 170-191 177-198 (206)
309 COG1518 CRISPR-associated prot 24.7 56 0.0014 14.4 5.9 40 167-207 48-87 (327)
310 PRK00771 signal recognition pa 24.5 56 0.0014 14.4 8.0 142 26-190 92-242 (433)
311 PRK10201 G/U mismatch-specific 24.4 43 0.0011 15.1 1.6 31 59-95 2-32 (168)
312 cd01014 nicotinamidase_related 24.4 57 0.0014 14.3 2.8 38 159-196 99-139 (155)
313 PRK09293 fructose-1,6-bisphosp 24.4 3.6 9.2E-05 22.1 -4.0 63 29-91 6-84 (328)
314 PRK06393 rpoE DNA-directed RNA 24.2 39 0.001 15.4 1.3 23 159-185 33-55 (64)
315 TIGR00959 ffh signal recogniti 24.1 58 0.0015 14.3 5.2 132 46-190 114-255 (439)
316 pfam01488 Shikimate_DH Shikima 23.7 58 0.0015 14.3 3.4 34 64-97 10-44 (134)
317 TIGR00612 ispG_gcpE 4-hydroxy- 23.7 59 0.0015 14.3 2.9 79 12-90 88-184 (633)
318 TIGR00009 L28 ribosomal protei 23.5 33 0.00084 15.9 0.8 19 14-32 29-48 (70)
319 PRK13530 arsenate reductase; P 23.1 60 0.0015 14.2 3.2 22 65-86 2-23 (133)
320 PRK10966 exonuclease subunit S 23.0 60 0.0015 14.2 3.4 27 50-76 58-84 (402)
321 TIGR01364 serC_1 phosphoserine 22.9 25 0.00063 16.7 0.1 25 176-208 238-262 (391)
322 cd06333 PBP1_ABC-type_HAAT_lik 22.7 61 0.0016 14.1 8.7 38 157-195 187-227 (312)
323 pfam03928 DUF336 Domain of unk 22.6 56 0.0014 14.4 1.8 23 172-194 14-37 (132)
324 COG3854 SpoIIIAA ncharacterize 22.5 62 0.0016 14.1 2.5 44 152-197 214-259 (308)
325 TIGR01737 FGAM_synth_I phospho 22.5 49 0.0012 14.8 1.5 25 53-77 80-104 (264)
326 PRK09065 glutamine amidotransf 22.3 45 0.0011 15.0 1.3 40 33-77 62-101 (238)
327 cd01056 Euk_Ferritin eukaryoti 22.2 63 0.0016 14.1 6.3 106 45-166 44-159 (161)
328 TIGR01135 glmS glucosamine--fr 22.1 63 0.0016 14.1 3.0 70 159-228 353-433 (628)
329 TIGR03407 urea_ABC_UrtA urea A 22.1 63 0.0016 14.1 9.7 87 54-182 123-214 (359)
330 cd06297 PBP1_LacI_like_12 Liga 22.1 63 0.0016 14.1 5.9 35 156-190 178-218 (269)
331 pfam12044 Metallopep Putative 22.0 22 0.00057 17.0 -0.3 16 39-54 179-194 (419)
332 cd01979 Pchlide_reductase_N Pc 22.0 63 0.0016 14.1 4.5 147 33-222 59-218 (396)
333 TIGR02637 RhaS rhamnose ABC tr 21.9 60 0.0015 14.2 1.9 64 159-225 57-123 (307)
334 PRK06719 precorrin-2 dehydroge 21.9 64 0.0016 14.0 2.7 34 64-97 11-44 (157)
335 pfam10186 DUF2355 Predicted co 21.8 50 0.0013 14.7 1.5 22 78-99 56-77 (216)
336 PRK12440 acetate kinase; Revie 21.8 52 0.0013 14.6 1.6 40 184-223 272-312 (397)
337 pfam10893 DUF2724 Protein of u 21.6 40 0.001 15.3 1.0 17 13-29 16-38 (68)
338 COG0196 RibF FAD synthase [Coe 21.6 23 0.00058 16.9 -0.3 13 125-137 96-108 (304)
339 PRK01368 murD UDP-N-acetylmura 21.6 64 0.0016 14.0 5.8 26 67-92 105-132 (450)
340 cd05297 GH4_alpha_glucosidase_ 21.5 64 0.0016 14.0 4.4 142 39-203 31-194 (423)
341 TIGR00658 orni_carb_tr ornithi 21.5 65 0.0016 14.0 7.8 108 56-195 61-203 (341)
342 cd06355 PBP1_FmdD_like Peripla 21.5 65 0.0016 14.0 9.9 91 55-187 123-223 (348)
343 TIGR00644 recJ single-stranded 21.5 65 0.0017 14.0 8.5 114 41-193 30-149 (705)
344 PRK07449 2-succinyl-6-hydroxy- 21.3 60 0.0015 14.2 1.8 42 52-96 204-246 (548)
345 PRK05595 replicative DNA helic 21.2 65 0.0017 14.0 10.1 145 46-208 213-378 (444)
346 COG3577 Predicted aspartyl pro 21.2 64 0.0016 14.0 1.9 36 160-205 116-153 (215)
347 cd06358 PBP1_NHase Type I peri 21.1 66 0.0017 13.9 9.0 90 52-183 119-213 (333)
348 COG2193 Bfr Bacterioferritin ( 21.1 51 0.0013 14.6 1.4 27 80-110 13-39 (157)
349 TIGR01487 SPP-like SPP-like hy 20.9 45 0.0012 15.0 1.1 55 53-107 23-90 (223)
350 COG2103 Predicted sugar phosph 20.9 66 0.0017 13.9 7.8 161 44-231 38-219 (298)
351 PRK08351 DNA-directed RNA poly 20.9 49 0.0013 14.7 1.3 23 159-185 31-53 (61)
352 pfam04035 consensus 20.9 50 0.0013 14.7 1.3 22 159-184 30-51 (60)
353 cd06327 PBP1_SBP_like_1 Peripl 20.9 67 0.0017 13.9 9.2 77 65-182 134-215 (334)
354 pfam01522 Polysacc_deac_1 Poly 20.3 68 0.0017 13.8 6.0 17 168-184 106-122 (123)
355 PRK00784 cobyric acid synthase 20.2 69 0.0017 13.8 2.8 51 52-104 113-174 (492)
356 PRK10014 DNA-binding transcrip 20.2 69 0.0018 13.8 8.3 60 157-220 119-179 (342)
357 PRK03202 6-phosphofructokinase 20.2 69 0.0018 13.8 5.6 45 159-209 95-140 (323)
358 COG2513 PrpB PEP phosphonomuta 20.1 69 0.0018 13.8 3.3 134 6-187 97-233 (289)
No 1
>TIGR01011 rpsB_bact ribosomal protein S2; InterPro: IPR005706 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites , . About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many of ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome , . This family describes the bacterial, mitochondrial and chloroplast forms of ribosomal protein S2.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0015935 small ribosomal subunit.
Probab=100.00 E-value=0 Score=790.01 Aligned_cols=223 Identities=50% Similarity=0.884 Sum_probs=219.9
Q ss_pred CCCHHHHHHCCCCCCCCCCCCCCCCCCCCCCCC-CCEEEECHHHHHHHHHHHHHHHHHHHCCCCEEEEEECC-HHHHHHH
Q ss_conf 245899986088607547765788562102001-88167538999999999999999861078816996078-2357999
Q gi|254780779|r 5 QFTIRQLLESGVQFGHRNFLWNPKMERYIFCER-NNTHIIDLSQTVPMLQKALQVISDTVARGGRILFVATK-SQASDCV 82 (278)
Q Consensus 5 ~~t~~~Ll~ag~H~Gh~~~~wnPkM~~yI~g~r-ngihIIdL~kT~~~L~~A~~~i~~i~~~gg~ILFVgTk-~~~~~~i 82 (278)
.|||++||+||||||||||||||||++|||++| ||+|||||+||+..|+.|++||++++.+||+||||||| +||+++|
T Consensus 1 ~vsmk~LleaGvHFGHqtRRWNPkMk~fIf~eRKngihIIDL~kT~~~~~~Ay~~v~~~~~~gg~iLFVGTKNkQA~~~i 80 (227)
T TIGR01011 1 VVSMKDLLEAGVHFGHQTRRWNPKMKPFIFGERKNGIHIIDLQKTLQLLEEAYNFVREVVANGGKILFVGTKNKQAKEII 80 (227)
T ss_pred CCCHHHHHHCCCCCCCEECCCCCCCCCCCCCCCCCCCEEECHHHHHHHHHHHHHHHHHHHHCCCEEEEEECHHHHHHHHH
T ss_conf 97657686388543754223688898855320127851225789999999999999999981995888516588999999
Q ss_pred HHHHHHCCCEECCCCCCCCCCCCHHHHHHHHHHHHHHHHHH-HCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCE
Q ss_conf 99986339831423345873234266655567789988763-01212677467887665567776434433221135957
Q gi|254780779|r 83 MEAAKRSAQYCVNSKWLGGMMTNWKTVSQSIQKLRDLEELL-NKENQGFTKKERLNIERKRDKLKRALDGIRDMGGLPDL 161 (278)
Q Consensus 83 ~~~A~~~~~~yV~~RWlGG~LTN~~ti~~si~~l~~l~~~~-~~~~~~~tkKe~~~~~r~~~kl~k~lgGi~~m~~lP~~ 161 (278)
+++|++||+||||+||||||||||+||++||+||++||++. ++.|+.|||||.+++.||++||+++|||||+|+++||+
T Consensus 81 ~~~A~r~g~~YVn~RWLGGMLTNf~TirkSi~kL~~lE~~~~~g~~~~LtKKE~~~L~Re~~KL~k~LgGIk~M~~lPd~ 160 (227)
T TIGR01011 81 KEEAERCGMFYVNQRWLGGMLTNFKTIRKSIKKLKKLEKMEEDGTFDVLTKKEILMLSREKEKLEKNLGGIKDMKKLPDL 160 (227)
T ss_pred HHHHHHCCCCEECCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCE
T ss_conf 99998748962113334640024799999999999999877613312477000776789999986553002545316970
Q ss_pred EEEECCCCCCHHHHHHHHCCCEEEEECCCCCCCHHCCCEEEECCCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf 999438877123212343398145403677670011520321577268999999999999999999
Q gi|254780779|r 162 MFVVDTNREKLAIQEARRLRIPIVAVVDTNSNPDLVDYVIPGNDDSSRSIALFCDLVASAAIDGIA 227 (278)
Q Consensus 162 iiv~d~~~e~~Av~EA~kl~IPvIaivDTn~dp~~idypIP~NDds~~si~l~~~~i~~ai~~g~~ 227 (278)
|||+||.+|+|||.||++|||||||+|||||||+.|||||||||||+|||.|||+.+++||+||+.
T Consensus 161 l~viD~~~E~IAv~EA~kLgIPvvA~vDTNCdPd~vD~~IPgNDDairSi~L~~~~~AdAv~Eg~~ 226 (227)
T TIGR01011 161 LFVIDPRKEKIAVAEARKLGIPVVAIVDTNCDPDVVDYPIPGNDDAIRSIRLLTSLIADAVLEGKQ 226 (227)
T ss_pred EEEECCCCCHHHHHHHHHCCCCEEEEECCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHC
T ss_conf 899748210689999733799789870478888866502579730589999999999999986514
No 2
>PRK12311 rpsB 30S ribosomal protein S2; Provisional
Probab=100.00 E-value=0 Score=694.31 Aligned_cols=246 Identities=61% Similarity=1.053 Sum_probs=238.5
Q ss_pred CCCCCCCHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCEEEECHHHHHHHHHHHHHHHHHHHCCCCEEEEEECCHHHHH
Q ss_conf 98662458999860886075477657885621020018816753899999999999999986107881699607823579
Q gi|254780779|r 1 MALPQFTIRQLLESGVQFGHRNFLWNPKMERYIFCERNNTHIIDLSQTVPMLQKALQVISDTVARGGRILFVATKSQASD 80 (278)
Q Consensus 1 m~m~~~t~~~Ll~ag~H~Gh~~~~wnPkM~~yI~g~rngihIIdL~kT~~~L~~A~~~i~~i~~~gg~ILFVgTk~~~~~ 80 (278)
|+||.+||++||+||||||||+++|||+|+|||||.|||+|||||+||+.+|++|++|+++++++||+|||||||+|+++
T Consensus 1 m~~p~~t~~~LLeAGvHfGHqt~rWNPkM~pYIyg~RngIHIIDL~qT~~~L~~A~~~v~~ia~~Gg~ILFVGTK~qa~~ 80 (332)
T PRK12311 1 MALPDFSMRQLLEAGVHFGHQSHRWNPKMAPYIFGARNNIHIIDLAQTVPLLHRALQAVSDTVAKGGRVLFVGTKRQAQD 80 (332)
T ss_pred CCCCCCCHHHHHHHCCCCCCCCCCCCCCCCCHHHCCCCCCEEECHHHHHHHHHHHHHHHHHHHHCCCEEEEEECCHHHHH
T ss_conf 99860369999971886788788559896230012408978986999999999999999999966997999868788999
Q ss_pred HHHHHHHHCCCEECCCCCCCCCCCCHHHHHHHHHHHHHHHHHH-HCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCC
Q ss_conf 9999986339831423345873234266655567789988763-012126774678876655677764344332211359
Q gi|254780779|r 81 CVMEAAKRSAQYCVNSKWLGGMMTNWKTVSQSIQKLRDLEELL-NKENQGFTKKERLNIERKRDKLKRALDGIRDMGGLP 159 (278)
Q Consensus 81 ~i~~~A~~~~~~yV~~RWlGG~LTN~~ti~~si~~l~~l~~~~-~~~~~~~tkKe~~~~~r~~~kl~k~lgGi~~m~~lP 159 (278)
+|++.|++|+|||||+||||||||||+||++||+||++|+++. ++.+.+|||||++.+.||++||+++||||++|+++|
T Consensus 81 ~V~~~A~r~~~~YVn~RWLGGtLTN~~TI~~sI~rL~~le~~~~~g~~~~ltKKE~l~l~Re~~KL~k~lgGIk~M~~lP 160 (332)
T PRK12311 81 AVADAAKRSAQYFVNSRWLGGTLTNWKTISGSIKRLRKLDEVLSSGDAGAYTKKERLTLQRERDKLDRSLGGIKDMGGLP 160 (332)
T ss_pred HHHHHHHHCCCCEEECCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCC
T ss_conf 99999998399657340027635559999999999999999861265233587889999879999998546254205599
Q ss_pred CEEEEECCCCCCHHHHHHHHCCCEEEEECCCCCCCHHCCCEEEECCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCC
Q ss_conf 57999438877123212343398145403677670011520321577268999999999999999999744310111101
Q gi|254780779|r 160 DLMFVVDTNREKLAIQEARRLRIPIVAVVDTNSNPDLVDYVIPGNDDSSRSIALFCDLVASAAIDGIARQHSYMGADTKS 239 (278)
Q Consensus 160 ~~iiv~d~~~e~~Av~EA~kl~IPvIaivDTn~dp~~idypIP~NDds~~si~l~~~~i~~ai~~g~~~~~~~~~~~~~~ 239 (278)
|+|||+||++|++||+||++|||||||||||||||++|||||||||||+|||.|||+++++||++|.....+..+.|.++
T Consensus 161 DlvfViD~~kE~iAV~EA~kLgIPvIaIvDTN~dP~~IdYpIPgNDDairsI~L~c~lia~A~l~G~~~~~~~~g~d~g~ 240 (332)
T PRK12311 161 DLIFVIDTNKEDIAIQEAQRLGIPVAAIVDTNCDPKGITYLVPGNDDAGRAIALYCDLIARAAIDGISRAQGDLGIDIGA 240 (332)
T ss_pred CEEEEECCCCCHHHHHHHHHCCCCEEEEEECCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCC
T ss_conf 98999689733899999998097989997389998657756848655899999999999999999998752002667554
Q ss_pred CCCCCHH
Q ss_conf 1221001
Q gi|254780779|r 240 AGETVVH 246 (278)
Q Consensus 240 ~~~~~~~ 246 (278)
.+++..+
T Consensus 241 ~~~~~~~ 247 (332)
T PRK12311 241 SEAPLAE 247 (332)
T ss_pred CCCCCHH
T ss_conf 3467311
No 3
>COG0052 RpsB Ribosomal protein S2 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=0 Score=656.72 Aligned_cols=228 Identities=50% Similarity=0.858 Sum_probs=223.4
Q ss_pred CCCCCHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCEEEECHHHHHHHHHHHHHHHHHHHCCCCEEEEEECCHHHHHHH
Q ss_conf 66245899986088607547765788562102001881675389999999999999998610788169960782357999
Q gi|254780779|r 3 LPQFTIRQLLESGVQFGHRNFLWNPKMERYIFCERNNTHIIDLSQTVPMLQKALQVISDTVARGGRILFVATKSQASDCV 82 (278)
Q Consensus 3 m~~~t~~~Ll~ag~H~Gh~~~~wnPkM~~yI~g~rngihIIdL~kT~~~L~~A~~~i~~i~~~gg~ILFVgTk~~~~~~i 82 (278)
|+.+||++||+|||||||||++|||+|+|||||.|||+|||||+||+..|+.|++|++.++.+||+|||||||+|++++|
T Consensus 1 m~~vsm~~lLeAGvHfGhqtr~wnpkm~~fIf~~RngihIIDL~kT~~~l~~A~~~v~~~~~~~g~ILfVgTK~~a~~~V 80 (252)
T COG0052 1 MAVVSMKQLLEAGVHFGHQTRRWNPKMKPFIFGERNGIHIIDLQKTLERLREAYKFLRRIAANGGKILFVGTKKQAQEPV 80 (252)
T ss_pred CCCCCHHHHHHCCCCCCCCCCCCCCCCCCCCEEECCCCEEEEHHHHHHHHHHHHHHHHHHHCCCCEEEEEECHHHHHHHH
T ss_conf 98578999987385116542324876466500002771798799989999999999999972899799995208878999
Q ss_pred HHHHHHCCCEECCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCEE
Q ss_conf 99986339831423345873234266655567789988763012126774678876655677764344332211359579
Q gi|254780779|r 83 MEAAKRSAQYCVNSKWLGGMMTNWKTVSQSIQKLRDLEELLNKENQGFTKKERLNIERKRDKLKRALDGIRDMGGLPDLM 162 (278)
Q Consensus 83 ~~~A~~~~~~yV~~RWlGG~LTN~~ti~~si~~l~~l~~~~~~~~~~~tkKe~~~~~r~~~kl~k~lgGi~~m~~lP~~i 162 (278)
+++|++||+||||+||||||||||+||++||++|++|+.+...+|+.|||||.+++.|+++||+++||||++|+++||++
T Consensus 81 ~~~A~r~g~~yV~~RwLgG~LTN~~ti~~si~rl~~lE~~~~~~~~~~tKkE~l~l~re~~kL~k~lgGIk~m~~~Pd~l 160 (252)
T COG0052 81 KEFAERTGAYYVNGRWLGGMLTNFKTIRKSIKRLKELEKMEEDGFDGLTKKEALMLTRELEKLEKSLGGIKDMKGLPDVL 160 (252)
T ss_pred HHHHHHHCCCEECCCCCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHCCHHHCCCCCCEE
T ss_conf 99999959951327643742447405888999999999876414321007888877778999987401411126799989
Q ss_pred EEECCCCCCHHHHHHHHCCCEEEEECCCCCCCHHCCCEEEECCCCHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 99438877123212343398145403677670011520321577268999999999999999999744
Q gi|254780779|r 163 FVVDTNREKLAIQEARRLRIPIVAVVDTNSNPDLVDYVIPGNDDSSRSIALFCDLVASAAIDGIARQH 230 (278)
Q Consensus 163 iv~d~~~e~~Av~EA~kl~IPvIaivDTn~dp~~idypIP~NDds~~si~l~~~~i~~ai~~g~~~~~ 230 (278)
||+||..|++||.||++|||||||+|||||||+.|||||||||||+|||.|+++++++||++|+....
T Consensus 161 ~ViDp~~e~iAv~EA~klgIPVvAlvDTn~dpd~VD~~IP~Ndda~rsi~Li~~~lA~ai~e~r~~~~ 228 (252)
T COG0052 161 FVIDPRKEKIAVKEANKLGIPVVALVDTNCDPDGVDYVIPGNDDAIRSIALIYWLLARAILEGRGGAL 228 (252)
T ss_pred EEECCCHHHHHHHHHHHCCCCEEEEECCCCCCCCCCEEECCCCHHHHHHHHHHHHHHHHHHHHHCCCC
T ss_conf 99688176899999997599989984189997657655228870898999999999999998743654
No 4
>PRK05299 rpsB 30S ribosomal protein S2; Provisional
Probab=100.00 E-value=0 Score=652.64 Aligned_cols=230 Identities=51% Similarity=0.877 Sum_probs=223.8
Q ss_pred CCCCCHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCEEEECHHHHHHHHHHHHHHHHHHHCCCCEEEEEECCHHHHHHH
Q ss_conf 66245899986088607547765788562102001881675389999999999999998610788169960782357999
Q gi|254780779|r 3 LPQFTIRQLLESGVQFGHRNFLWNPKMERYIFCERNNTHIIDLSQTVPMLQKALQVISDTVARGGRILFVATKSQASDCV 82 (278)
Q Consensus 3 m~~~t~~~Ll~ag~H~Gh~~~~wnPkM~~yI~g~rngihIIdL~kT~~~L~~A~~~i~~i~~~gg~ILFVgTk~~~~~~i 82 (278)
|+.||+++||+|||||||++++|||+|+|||||.|||+|||||++|+.+|++|++|+++++.+||+|||||||+|++++|
T Consensus 1 ~~~iti~~Ll~aGvH~GH~~~~WNPkM~~yIyg~r~gihIIDL~kT~~~L~~A~~~l~~~~~~gg~iLFVgTk~q~~~~V 80 (255)
T PRK05299 1 MAVVSMKQLLEAGVHFGHQTRRWNPKMKPYIFGERNGIHIIDLQKTVPMLDEAYNFVRDVAANGGKILFVGTKKQAQEII 80 (255)
T ss_pred CCCCCHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCEEECHHHHHHHHHHHHHHHHHHHHCCCCEEEEECCHHHHHHH
T ss_conf 99488999998087058887867999746011455992788499999999999999999997699369996658789999
Q ss_pred HHHHHHCCCEECCCCCCCCCCCCHHHHHHHHHHHHHHHHH-HHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCE
Q ss_conf 9998633983142334587323426665556778998876-301212677467887665567776434433221135957
Q gi|254780779|r 83 MEAAKRSAQYCVNSKWLGGMMTNWKTVSQSIQKLRDLEEL-LNKENQGFTKKERLNIERKRDKLKRALDGIRDMGGLPDL 161 (278)
Q Consensus 83 ~~~A~~~~~~yV~~RWlGG~LTN~~ti~~si~~l~~l~~~-~~~~~~~~tkKe~~~~~r~~~kl~k~lgGi~~m~~lP~~ 161 (278)
+++|.+||+|||++||+|||||||+||++||++|++|+.+ .++.+++|||||.+.+.|+++||+++||||++|+++||+
T Consensus 81 ~~~A~~~~~~yV~~RWlGG~LTN~~tI~~~i~~l~~l~~~~~~~~~~~~tKKE~~~~~r~~~kL~k~~~Gi~~m~~lPd~ 160 (255)
T PRK05299 81 AEEAERCGQPYVNHRWLGGMLTNFKTIRKSIKRLKELEKMEEDGTFEKLTKKEALMLTRELEKLEKSLGGIKDMGGLPDA 160 (255)
T ss_pred HHHHHHCCCCEECCCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCE
T ss_conf 99999839970438727865337888877999999999887234054455899998877788899865405324319987
Q ss_pred EEEECCCCCCHHHHHHHHCCCEEEEECCCCCCCHHCCCEEEECCCCHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 99943887712321234339814540367767001152032157726899999999999999999974431
Q gi|254780779|r 162 MFVVDTNREKLAIQEARRLRIPIVAVVDTNSNPDLVDYVIPGNDDSSRSIALFCDLVASAAIDGIARQHSY 232 (278)
Q Consensus 162 iiv~d~~~e~~Av~EA~kl~IPvIaivDTn~dp~~idypIP~NDds~~si~l~~~~i~~ai~~g~~~~~~~ 232 (278)
|||+||..|++||+||.+|||||||||||||||++|||||||||||++||.|||+.+++||++|++.+...
T Consensus 161 viv~d~~~e~~AV~EA~kl~IPvI~ivDTn~dP~~idypIP~NDDs~~SI~li~~~l~~ai~~g~~~~~~~ 231 (255)
T PRK05299 161 LFVVDPNKEHIAVKEARKLGIPVVAIVDTNCDPDGVDYPIPGNDDAIRSIKLYTSKLADAILEGRGEVAAE 231 (255)
T ss_pred EEEECCCCCHHHHHHHHHCCCCEEEEECCCCCCCCCCEEECCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 99847853379999999759988876248999665865533775289999999999999999988787666
No 5
>CHL00067 rps2 ribosomal protein S2
Probab=100.00 E-value=0 Score=611.37 Aligned_cols=225 Identities=41% Similarity=0.689 Sum_probs=220.7
Q ss_pred CCCCCHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCEEEECHHHHHHHHHHHHHHHHHHHCCCCEEEEEECCHHHHHHH
Q ss_conf 66245899986088607547765788562102001881675389999999999999998610788169960782357999
Q gi|254780779|r 3 LPQFTIRQLLESGVQFGHRNFLWNPKMERYIFCERNNTHIIDLSQTVPMLQKALQVISDTVARGGRILFVATKSQASDCV 82 (278)
Q Consensus 3 m~~~t~~~Ll~ag~H~Gh~~~~wnPkM~~yI~g~rngihIIdL~kT~~~L~~A~~~i~~i~~~gg~ILFVgTk~~~~~~i 82 (278)
|.++|+++||+|||||||++++|||+|+|||||.|||+|||||++|+.+|++|++||++++++||+||||||++|++++|
T Consensus 1 m~~i~i~~Ll~agvH~Gh~~~~wnp~m~~yIyg~rngihIIdL~kT~~~L~~A~~~i~~~~~~~g~ILfVgTk~~~~~~i 80 (227)
T CHL00067 1 MWNINLEEMLEAGVHFGHQTRKWNPKMAPYIYAKRKGIHIINLTQTARFLSEACDLVFDAASRGKKFLFVGTKKQAADLV 80 (227)
T ss_pred CCCCCHHHHHHCCCCCCCCCCCCCCCCCCHHHCCCCCCEEECHHHHHHHHHHHHHHHHHHHHCCCEEEEEECCHHHHHHH
T ss_conf 99788999997084058787837999600433155992798599999999999999999985499479997658789999
Q ss_pred HHHHHHCCCEECCCCCCCCCCCCHHHHHHHHHHHHHHHHH-HHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCE
Q ss_conf 9998633983142334587323426665556778998876-301212677467887665567776434433221135957
Q gi|254780779|r 83 MEAAKRSAQYCVNSKWLGGMMTNWKTVSQSIQKLRDLEEL-LNKENQGFTKKERLNIERKRDKLKRALDGIRDMGGLPDL 161 (278)
Q Consensus 83 ~~~A~~~~~~yV~~RWlGG~LTN~~ti~~si~~l~~l~~~-~~~~~~~~tkKe~~~~~r~~~kl~k~lgGi~~m~~lP~~ 161 (278)
+++|.+||+|||++||+|||||||+||++|+++|++++.+ .++.++.+||||.+.+.|++.||+++||||++|+++||+
T Consensus 81 ~~~A~~~~~~yV~~rWlgG~LTN~~ti~k~i~~l~~l~~~~~~~~~~~~~KKe~~~~~~~~~kL~k~~~Gi~~m~~lPd~ 160 (227)
T CHL00067 81 ASAAIRARCHYVNKKWLGGMLTNWSTTKTRLKKLRDLRMEEKTGLFNRLPKKEAAILKRQLSRLQKYLGGIKYMTKLPDI 160 (227)
T ss_pred HHHHHHHCCCEEECCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCE
T ss_conf 99999819971537642874447899977999999999976245231020789998888898999875315456208976
Q ss_pred EEEECCCCCCHHHHHHHHCCCEEEEECCCCCCCHHCCCEEEECCCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf 999438877123212343398145403677670011520321577268999999999999999999
Q gi|254780779|r 162 MFVVDTNREKLAIQEARRLRIPIVAVVDTNSNPDLVDYVIPGNDDSSRSIALFCDLVASAAIDGIA 227 (278)
Q Consensus 162 iiv~d~~~e~~Av~EA~kl~IPvIaivDTn~dp~~idypIP~NDds~~si~l~~~~i~~ai~~g~~ 227 (278)
|||+||..|++||+||++|||||||||||||||+.|||||||||||++||+|+++.+++||++|+.
T Consensus 161 iii~d~~~e~~ai~Ea~kL~IPvIaivDTn~~p~~idypIP~NDds~~SI~li~~~l~~ai~~Gk~ 226 (227)
T CHL00067 161 VIIVDQQEEYTALRECIKLGIPTISIVDTNCDPDLADIPIPANDDAIASIRLILNKLVTAICEGRS 226 (227)
T ss_pred EEEECCCCCHHHHHHHHHCCCCEEEEEECCCCCCCCCEEEECCCCHHHHHHHHHHHHHHHHHHHCC
T ss_conf 999677533799999987599989996389997757767537866699999999999999997533
No 6
>pfam00318 Ribosomal_S2 Ribosomal protein S2.
Probab=100.00 E-value=0 Score=541.56 Aligned_cols=205 Identities=55% Similarity=0.927 Sum_probs=201.6
Q ss_pred HHHCCCCCCCCCCCCCCCCCCCCCCCCCCEEEECHHHHHHHHHHHHHHHHHHHCCCCEEEEEECCHHHHHHHHHHHHHCC
Q ss_conf 98608860754776578856210200188167538999999999999999861078816996078235799999986339
Q gi|254780779|r 11 LLESGVQFGHRNFLWNPKMERYIFCERNNTHIIDLSQTVPMLQKALQVISDTVARGGRILFVATKSQASDCVMEAAKRSA 90 (278)
Q Consensus 11 Ll~ag~H~Gh~~~~wnPkM~~yI~g~rngihIIdL~kT~~~L~~A~~~i~~i~~~gg~ILFVgTk~~~~~~i~~~A~~~~ 90 (278)
||+||+||||++++|||+|+|||||.|||+|||||++|+.+|++|++|+++++++||+||||||+++++++|+++|++||
T Consensus 1 ll~ag~H~Gh~~~~wnp~m~~yIy~~r~gi~IidL~~T~~~L~~A~~~i~~i~~~~~~iLfVgTk~~~~~~v~~~a~~~~ 80 (205)
T pfam00318 1 LLEAGVHFGHQTRRWNPKMKPYIYGERNGIHIIDLEKTLEKLRKAANFIKEIAAKGGKILFVGTKKQAQEAVKKFAKRTG 80 (205)
T ss_pred CCCCCEECCCCCCCCCCCCHHHHHCCCCCCEEEEHHHHHHHHHHHHHHHHHHHHCCCEEEEEECCHHHHHHHHHHHHHHC
T ss_conf 97766534777773799812010144599279729999999999999999999669828999777899999999999839
Q ss_pred CEECCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCEEEEECCCCC
Q ss_conf 83142334587323426665556778998876301212677467887665567776434433221135957999438877
Q gi|254780779|r 91 QYCVNSKWLGGMMTNWKTVSQSIQKLRDLEELLNKENQGFTKKERLNIERKRDKLKRALDGIRDMGGLPDLMFVVDTNRE 170 (278)
Q Consensus 91 ~~yV~~RWlGG~LTN~~ti~~si~~l~~l~~~~~~~~~~~tkKe~~~~~r~~~kl~k~lgGi~~m~~lP~~iiv~d~~~e 170 (278)
+|||++||+|||||||+|+++++++|++ ++|||.+.+.|++.||+++|||+++|+++||+|||+||..|
T Consensus 81 ~~yv~~rWigG~LTN~~~i~~~~~~l~~-----------~~kk~~~~~~~~~~kl~k~~~Gi~~~~~~Pd~vii~d~~~~ 149 (205)
T pfam00318 81 QFYVNGRWLGGTLTNWKTIKKSIKKLEE-----------LSKKEALKLKRELEKLEKYLGGIKNMKKLPDLVIVVDPNKE 149 (205)
T ss_pred CCCCCCCCCCCCCCCHHHHHHHHHHHHH-----------HHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCEEEEECCCCC
T ss_conf 9743164338723669999888877776-----------54788888888999999845435445008986998578645
Q ss_pred CHHHHHHHHCCCEEEEECCCCCCCHHCCCEEEECCCCHHHHHHHHHHHHHHHHHHH
Q ss_conf 12321234339814540367767001152032157726899999999999999999
Q gi|254780779|r 171 KLAIQEARRLRIPIVAVVDTNSNPDLVDYVIPGNDDSSRSIALFCDLVASAAIDGI 226 (278)
Q Consensus 171 ~~Av~EA~kl~IPvIaivDTn~dp~~idypIP~NDds~~si~l~~~~i~~ai~~g~ 226 (278)
++||+||.++||||||||||||||++|||||||||||++||+||++.+++||++|+
T Consensus 150 ~~ai~Ea~~l~IP~I~ivDTn~~p~~idypIP~Ndds~~si~li~~~l~~ai~~g~ 205 (205)
T pfam00318 150 HIAIKEASKLGIPVIAIVDTNCDPDLIDYPIPGNDDSIRSIALILWLLARAILEGR 205 (205)
T ss_pred HHHHHHHHHCCCCEEEECCCCCCCCCCCEEEECCCCHHHHHHHHHHHHHHHHHHCC
T ss_conf 38999998759975654059999543877885788709899999999999998049
No 7
>cd01425 RPS2 Ribosomal protein S2 (RPS2), involved in formation of the translation initiation complex, where it might contact the messenger RNA and several components of the ribosome. It has been shown that in Escherichia coli RPS2 is essential for the binding of ribosomal protein S1 to the 30s ribosomal subunit. In humans, most likely in all vertebrates, and perhaps in all metazoans, the protein also functions as the 67 kDa laminin receptor (LAMR1 or 67LR), which is formed from a 37 kDa precursor, and is overexpressed in many tumors. 67LR is a cell surface receptor which interacts with a variety of ligands, laminin-1 and others. It is assumed that the ligand interactions are mediated via the conserved C-terminus, which becomes extracellular as the protein undergoes conformational changes which are not well understood. Specifically, a conserved palindromic motif, LMWWML, may participate in the interactions. 67LR plays essential roles in the adhesion of cells to the basement membrane an
Probab=100.00 E-value=0 Score=497.62 Aligned_cols=193 Identities=53% Similarity=0.903 Sum_probs=188.1
Q ss_pred HHHCCCCCCCCCCCCCCCCCCCCCCCCCCEEEECHHHHHHHHHHHHHHHHHHHCCCCEEEEEECCHHHHHHHHHHHHHCC
Q ss_conf 98608860754776578856210200188167538999999999999999861078816996078235799999986339
Q gi|254780779|r 11 LLESGVQFGHRNFLWNPKMERYIFCERNNTHIIDLSQTVPMLQKALQVISDTVARGGRILFVATKSQASDCVMEAAKRSA 90 (278)
Q Consensus 11 Ll~ag~H~Gh~~~~wnPkM~~yI~g~rngihIIdL~kT~~~L~~A~~~i~~i~~~gg~ILFVgTk~~~~~~i~~~A~~~~ 90 (278)
||+||+||||++++|||+|+|||||.|||+|||||++|+.+|++|++|+++++.+||+||||||+++++++|+++|++++
T Consensus 1 ll~ag~h~G~~~~~wnp~m~~yI~g~r~g~~IidL~~T~~~L~~A~~~i~~~~~~~g~ILfVgtk~~~~~~v~~~a~~~~ 80 (193)
T cd01425 1 LLEAGVHLGHKTRRWNPKMKPYIYGERNGIHIIDLEKTLEKLRLALNFIANIAAKGGKILFVGTKPQAQRAVKKFAERTG 80 (193)
T ss_pred CCCCCEECCCCCCCCCCCCCCHHHCCCCCCEEEEHHHHHHHHHHHHHHHHHHHHCCCEEEEEECCHHHHHHHHHHHHHCC
T ss_conf 97766534667775798720022245198199779999999999999999999759959999757899999999999839
Q ss_pred CEECCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCEEEEECCCCC
Q ss_conf 83142334587323426665556778998876301212677467887665567776434433221135957999438877
Q gi|254780779|r 91 QYCVNSKWLGGMMTNWKTVSQSIQKLRDLEELLNKENQGFTKKERLNIERKRDKLKRALDGIRDMGGLPDLMFVVDTNRE 170 (278)
Q Consensus 91 ~~yV~~RWlGG~LTN~~ti~~si~~l~~l~~~~~~~~~~~tkKe~~~~~r~~~kl~k~lgGi~~m~~lP~~iiv~d~~~e 170 (278)
+|||++||+|||||||+++++++.+++.++. .|++++|+|+++|.++||+|||+||..|
T Consensus 81 ~~yv~~rWigG~LTN~~~~~~~i~~~~~~~~---------------------~k~~~~~~g~~~~~~~Pdliiv~d~~~~ 139 (193)
T cd01425 81 SFYVNGRWLGGTLTNWKTIRKSIKRLKKLEK---------------------EKLEKNLGGIKDMFRLPDLVIVLDPRKE 139 (193)
T ss_pred CEEECCEECCCCCCCHHHHHHHHHHHHHHHH---------------------HHHHHHCCCHHHCCCCCCEEEEECCCCC
T ss_conf 9454485758772488888668998887542---------------------2566520340101669998999889841
Q ss_pred CHHHHHHHHCCCEEEEECCCCCCCHHCCCEEEECCCCHHHHHHHHHHHHHHHHH
Q ss_conf 123212343398145403677670011520321577268999999999999999
Q gi|254780779|r 171 KLAIQEARRLRIPIVAVVDTNSNPDLVDYVIPGNDDSSRSIALFCDLVASAAID 224 (278)
Q Consensus 171 ~~Av~EA~kl~IPvIaivDTn~dp~~idypIP~NDds~~si~l~~~~i~~ai~~ 224 (278)
++||+||.++||||||||||||||++|||||||||||++||.|+++++++||++
T Consensus 140 ~~ai~Ea~~l~IPvI~i~Dtn~~p~~idypIP~Ndds~~si~li~~~l~~ai~~ 193 (193)
T cd01425 140 HQAIREASKLGIPVIAIVDTNCDPDLIDYPIPANDDSIRSIALILWLLARAILE 193 (193)
T ss_pred HHHHHHHHHHCCCEEEEECCCCCCCCCCEEEECCCCCHHHHHHHHHHHHHHHHC
T ss_conf 689999986187557885089996658778758887188999999999999829
No 8
>PRK04020 rps2P 30S ribosomal protein S2; Provisional
Probab=100.00 E-value=0 Score=467.32 Aligned_cols=183 Identities=25% Similarity=0.397 Sum_probs=167.0
Q ss_pred CCCHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCC-CEEEECHHHHHHHHHHHHHHHHHHHCCCCEEEEEECCHHHHHHHH
Q ss_conf 2458999860886075477657885621020018-816753899999999999999986107881699607823579999
Q gi|254780779|r 5 QFTIRQLLESGVQFGHRNFLWNPKMERYIFCERN-NTHIIDLSQTVPMLQKALQVISDTVARGGRILFVATKSQASDCVM 83 (278)
Q Consensus 5 ~~t~~~Ll~ag~H~Gh~~~~wnPkM~~yI~g~rn-gihIIdL~kT~~~L~~A~~~i~~i~~~gg~ILFVgTk~~~~~~i~ 83 (278)
-||+++||+|||||| +++|||+|+|||||.|+ |+|||||+||+.+|+.|++|++.+ .++.|||||||+|++++|+
T Consensus 9 lvsi~~ll~AgvHfG--t~~~np~M~~yIy~~R~~GihIIDL~kT~~~L~~A~~~l~~~--~~~~ILfVgtk~qa~~~v~ 84 (204)
T PRK04020 9 LVPLEEYLAAGVHIG--TQQKTKDMEKFIYRVRPDGLYVLDVRKTDERIRIAAKFLSRY--EPEKILVVSSRQYGQKPVK 84 (204)
T ss_pred EEEHHHHHHCCEEEC--CCCCCCCCHHHCCCCCCCCEEEECHHHHHHHHHHHHHHHHHC--CCCEEEEEECCHHHHHHHH
T ss_conf 588999986095657--776998723221476899758973999999999999999960--7984999979899999999
Q ss_pred HHHHHCCCEECCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCEEE
Q ss_conf 99863398314233458732342666555677899887630121267746788766556777643443322113595799
Q gi|254780779|r 84 EAAKRSAQYCVNSKWLGGMMTNWKTVSQSIQKLRDLEELLNKENQGFTKKERLNIERKRDKLKRALDGIRDMGGLPDLMF 163 (278)
Q Consensus 84 ~~A~~~~~~yV~~RWlGG~LTN~~ti~~si~~l~~l~~~~~~~~~~~tkKe~~~~~r~~~kl~k~lgGi~~m~~lP~~ii 163 (278)
++|++||+|||++||+||||||.. ++ +| + -||++|
T Consensus 85 ~~A~~~g~~yv~~RWlgG~LTN~~--------l~-----------~~------------------~--------ePdlli 119 (204)
T PRK04020 85 KFAEVVGAKAITGRFIPGTLTNPS--------LK-----------GY------------------I--------EPDVLV 119 (204)
T ss_pred HHHHHHCCEEECCCCCCCCCCCHH--------HC-----------CC------------------C--------CCCEEE
T ss_conf 999996990682622798656831--------30-----------25------------------6--------899899
Q ss_pred EECCCCCCHHHHHHHHCCCEEEEECCCCCCCHHCCCEEEECCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCC
Q ss_conf 9438877123212343398145403677670011520321577268999999999999999999744310111
Q gi|254780779|r 164 VVDTNREKLAIQEARRLRIPIVAVVDTNSNPDLVDYVIPGNDDSSRSIALFCDLVASAAIDGIARQHSYMGAD 236 (278)
Q Consensus 164 v~d~~~e~~Av~EA~kl~IPvIaivDTn~dp~~idypIP~NDds~~si~l~~~~i~~ai~~g~~~~~~~~~~~ 236 (278)
|+||..|++||+||.++||||||||||||||++|||||||||||++||.|++++|+++|++|++......+.+
T Consensus 120 V~Dp~~e~~AV~EA~~l~IPvIaivDTn~dp~~Vdy~IP~NDds~~SI~Li~~lLa~ail~~kg~~~~~~~~~ 192 (204)
T PRK04020 120 VTDPRGDAQAVKEAIEIGIPVVALCDTDNLTSNVDLVIPTNNKGRKALALIYWLLAREILRERGEIKPDEDLP 192 (204)
T ss_pred EECCCCCHHHHHHHHHCCCCEEEEECCCCCCHHCCEEEECCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCC
T ss_conf 9788630489999987699989982799891115736516883073899999999999999739777666887
No 9
>PTZ00254 40S ribosomal protein SA; Provisional
Probab=100.00 E-value=0 Score=450.56 Aligned_cols=188 Identities=23% Similarity=0.370 Sum_probs=171.6
Q ss_pred CCCCCCCHHHHHHCCCCCCCCCCCCCCCCCCCCCCCC-CCEEEECHHHHHHHHHHHHHHHHHHHCCCCEEEEEECCHHHH
Q ss_conf 9866245899986088607547765788562102001-881675389999999999999998610788169960782357
Q gi|254780779|r 1 MALPQFTIRQLLESGVQFGHRNFLWNPKMERYIFCER-NNTHIIDLSQTVPMLQKALQVISDTVARGGRILFVATKSQAS 79 (278)
Q Consensus 1 m~m~~~t~~~Ll~ag~H~Gh~~~~wnPkM~~yI~g~r-ngihIIdL~kT~~~L~~A~~~i~~i~~~gg~ILFVgTk~~~~ 79 (278)
|+|.+.++++||+|||||| +++|||+|+|||||.| ||+|||||+||+++|+.|++|+..+ ++++.|||||||++++
T Consensus 8 l~~~e~di~~lL~AgvH~G--t~~~np~Mk~YIy~~r~dGihIIdL~kT~e~L~~Aa~~i~~i-~~~~~Il~V~tr~~~q 84 (242)
T PTZ00254 8 LSPKEDDIQKLLACKCHIG--TKNLENAMKKYVYKRTKEGVHIINLAKTWEKIKLAARVIAAV-ENPADVVVVSSRPYGQ 84 (242)
T ss_pred CCCCHHHHHHHHHCCEEEC--CCCCCCCCCCCCCCCCCCCCEEEEHHHHHHHHHHHHHHHHHH-CCCCCEEEEECCHHHH
T ss_conf 5878788999997295137--672898870421354689917967999999999999999986-4799779998388987
Q ss_pred HHHHHHHHHCCCEECCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCC
Q ss_conf 99999986339831423345873234266655567789988763012126774678876655677764344332211359
Q gi|254780779|r 80 DCVMEAAKRSAQYCVNSKWLGGMMTNWKTVSQSIQKLRDLEELLNKENQGFTKKERLNIERKRDKLKRALDGIRDMGGLP 159 (278)
Q Consensus 80 ~~i~~~A~~~~~~yV~~RWlGG~LTN~~ti~~si~~l~~l~~~~~~~~~~~tkKe~~~~~r~~~kl~k~lgGi~~m~~lP 159 (278)
++|.++|.+||++||++||+||||||+.+ + .| ..|
T Consensus 85 ~aV~kfA~~tG~~~i~~Rw~pGtlTN~i~--~-----------------~f--------------------------~eP 119 (242)
T PTZ00254 85 RAILKFSQYTGASFIAGRFTPGTFTNQIQ--K-----------------KF--------------------------QEP 119 (242)
T ss_pred HHHHHHHHHHCCCEEECCCCCCCCCCHHH--H-----------------CC--------------------------CCC
T ss_conf 99999999979942405127866468766--5-----------------24--------------------------688
Q ss_pred CEEEEECCCCCCHHHHHHHHCCCEEEEECCCCCCCHHCCCEEEECCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCC
Q ss_conf 57999438877123212343398145403677670011520321577268999999999999999999744310111
Q gi|254780779|r 160 DLMFVVDTNREKLAIQEARRLRIPIVAVVDTNSNPDLVDYVIPGNDDSSRSIALFCDLVASAAIDGIARQHSYMGAD 236 (278)
Q Consensus 160 ~~iiv~d~~~e~~Av~EA~kl~IPvIaivDTn~dp~~idypIP~NDds~~si~l~~~~i~~ai~~g~~~~~~~~~~~ 236 (278)
+++||+||..|++||+||.++||||||||||||||+.|||||||||||++||.|++++|+++|+++++......+.+
T Consensus 120 ~lliV~DP~~d~~AV~EA~~~nIPvIal~DTds~p~~VD~~IP~Ndds~~SI~Li~~lLArevl~~rG~i~r~~~w~ 196 (242)
T PTZ00254 120 RLLIVTDPRTDHQAIREASYVNIPVIALCDTDAPLEYVDIAIPCNNRGKKSIAMMYWLLAREVLRLRGTIPRSEPWD 196 (242)
T ss_pred CEEEEECCCCCHHHHHHHHHCCCCEEEEECCCCCCCCCCEEEECCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCC
T ss_conf 88999667544089999998599889861699995326567656883076899999999999998368878889866
No 10
>KOG0832 consensus
Probab=100.00 E-value=0 Score=438.06 Aligned_cols=202 Identities=36% Similarity=0.633 Sum_probs=183.2
Q ss_pred CCCCHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCEEEECHHHHHHHHHHHHHHHHHHHCCCCEEEEEECCHHHHHHHH
Q ss_conf 62458999860886075477657885621020018816753899999999999999986107881699607823579999
Q gi|254780779|r 4 PQFTIRQLLESGVQFGHRNFLWNPKMERYIFCERNNTHIIDLSQTVPMLQKALQVISDTVARGGRILFVATKSQASDCVM 83 (278)
Q Consensus 4 ~~~t~~~Ll~ag~H~Gh~~~~wnPkM~~yI~g~rngihIIdL~kT~~~L~~A~~~i~~i~~~gg~ILFVgTk~~~~~~i~ 83 (278)
..+++++||.|||||||.++.|||.|+|||||+|+|+|||||++|..+|++|++|+..++..||.||||||++.+.++|+
T Consensus 46 ~~~~v~~L~~agvHlGh~t~~wn~~m~pyiyG~R~Gi~IIdLdqT~~~Lr~A~~fVa~vA~r~GiILFv~tn~~~~~~ve 125 (251)
T KOG0832 46 ELISVEELFNAGVHLGHKTGKWNPRMKPYIYGKRLGIHIIDLDQTASYLRRALNFVAHVAHRGGIILFVGTNNGFKDLVE 125 (251)
T ss_pred HHCCHHHHHHCCCCCCCCCCCCCCCCCHHHCCCCCCCEEEECHHHHHHHHHHHHHHHHHHHCCCEEEEEECCCCHHHHHH
T ss_conf 55029999741241355446568665510102326727984288999999999999989845984999945842678999
Q ss_pred HHHHHCCCEECCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCEEE
Q ss_conf 99863398314233458732342666555677899887630121267746788766556777643443322113595799
Q gi|254780779|r 84 EAAKRSAQYCVNSKWLGGMMTNWKTVSQSIQKLRDLEELLNKENQGFTKKERLNIERKRDKLKRALDGIRDMGGLPDLMF 163 (278)
Q Consensus 84 ~~A~~~~~~yV~~RWlGG~LTN~~ti~~si~~l~~l~~~~~~~~~~~tkKe~~~~~r~~~kl~k~lgGi~~m~~lP~~ii 163 (278)
.+|.+++.||++.||+|||||||.++..+..+ +.+++-....+.. +-.||+|+
T Consensus 126 ~aA~r~~gy~~~~~w~~G~lTN~~~l~g~~~~------------~~~~~pd~~~f~~---------------t~~~D~vv 178 (251)
T KOG0832 126 RAARRAGGYSHNRKWLGGLLTNARELFGALVR------------KFLSLPDALCFLP---------------TLTPDLVV 178 (251)
T ss_pred HHHHHHCCCEEEEEECCCEEECCHHHCCCCCC------------CCCCCCCCEEECC---------------CCCCCEEE
T ss_conf 99998467214201215523240665064245------------5457875202535---------------57866267
Q ss_pred EECCCCCCHHHHHHHHCCCEEEEECCCCCCCHHCCCEEEECCCCHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 943887712321234339814540367767001152032157726899999999999999999974431
Q gi|254780779|r 164 VVDTNREKLAIQEARRLRIPIVAVVDTNSNPDLVDYVIPGNDDSSRSIALFCDLVASAAIDGIARQHSY 232 (278)
Q Consensus 164 v~d~~~e~~Av~EA~kl~IPvIaivDTn~dp~~idypIP~NDds~~si~l~~~~i~~ai~~g~~~~~~~ 232 (278)
|+|+..++.||+||.|++||+||||||||||++|||||||||||.+|+.|+|+++..||.+|++++...
T Consensus 179 vln~~e~~sAilEA~K~~IPTIgIVDtN~~P~liTYpVPaNDDs~~sv~f~~~l~k~ai~~g~~~ri~q 247 (251)
T KOG0832 179 VLNPEENHSAILEAAKMAIPTIGIVDTNCNPELITYPVPANDDSPASVEFILNLLKRAIARGKQKRIQQ 247 (251)
T ss_pred ECCCCCCCHHHHHHHHHCCCEEEEECCCCCCCCEEECCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 627544318999999707985888669998100531158888759999999999999999999999876
No 11
>TIGR01012 Sa_S2_E_A ribosomal protein S2; InterPro: IPR005707 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites , . About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many of ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome , . This family describes the ribosomal protein of the eukaryotic cytosol and of Archaea, homologous to S2 of bacteria. It is designated typically as Sa in eukaryotes and Sa or S2 in the archaea. ; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0015935 small ribosomal subunit.
Probab=100.00 E-value=7.6e-43 Score=297.56 Aligned_cols=181 Identities=27% Similarity=0.382 Sum_probs=165.0
Q ss_pred CCCHHHHHHCCCCCCCCCCCCCCCCCCCCCCCC-CCEEEECHHHHHHHHHHHHHHHHHHHCCCCEEEEEECCHHHHHHHH
Q ss_conf 245899986088607547765788562102001-8816753899999999999999986107881699607823579999
Q gi|254780779|r 5 QFTIRQLLESGVQFGHRNFLWNPKMERYIFCER-NNTHIIDLSQTVPMLQKALQVISDTVARGGRILFVATKSQASDCVM 83 (278)
Q Consensus 5 ~~t~~~Ll~ag~H~Gh~~~~wnPkM~~yI~g~r-ngihIIdL~kT~~~L~~A~~~i~~i~~~gg~ILFVgTk~~~~~~i~ 83 (278)
.+-..++++||||+| |...+-.|++|||..| +|+||+|+.||++.|+-|++||... +++.+|+.|+.+..++.+|+
T Consensus 3 lvp~~~ylaAGvh~G--T~~~t~~M~~fiyk~r~DG~Y~ld~~K~dErL~~AAk~l~~~-ENP~~I~vvS~R~Yg~~pV~ 79 (197)
T TIGR01012 3 LVPVDKYLAAGVHIG--TQNKTKDMEKFIYKVRSDGLYVLDLRKTDERLRVAAKFLSRF-ENPEDILVVSARIYGQKPVL 79 (197)
T ss_pred CCCHHHHHHCCCCCC--CCCCCCCCCEEEEEECCCCEEEECCHHHHHHHHHHHHHHHHH-CCCCCEEEEECCHHHHHHHH
T ss_conf 576667754122006--632243322125566478707870113408999999998742-48211134401522246899
Q ss_pred HHHHHCCCEECCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCEEE
Q ss_conf 99863398314233458732342666555677899887630121267746788766556777643443322113595799
Q gi|254780779|r 84 EAAKRSAQYCVNSKWLGGMMTNWKTVSQSIQKLRDLEELLNKENQGFTKKERLNIERKRDKLKRALDGIRDMGGLPDLMF 163 (278)
Q Consensus 84 ~~A~~~~~~yV~~RWlGG~LTN~~ti~~si~~l~~l~~~~~~~~~~~tkKe~~~~~r~~~kl~k~lgGi~~m~~lP~~ii 163 (278)
++|+.+|.-+|.+|++||||||- - ...|. =|++||
T Consensus 80 ~f~~~tG~~~I~GRf~PGT~TNp--------~-----------~~~f~--------------------------EP~vv~ 114 (197)
T TIGR01012 80 KFAEVTGARAIAGRFIPGTFTNP--------A-----------LKEFR--------------------------EPEVVV 114 (197)
T ss_pred HHHHHCCCCCCCCCCCCCCCCCH--------H-----------HHCCC--------------------------CCEEEE
T ss_conf 99876088745665437776402--------3-----------31367--------------------------873799
Q ss_pred EECCCCCCHHHHHHHHCCCEEEEECCCCCCCHHCCCEEEECCCCHHHHHHHHHHHHHHHHHHHHHHHHHC
Q ss_conf 9438877123212343398145403677670011520321577268999999999999999999744310
Q gi|254780779|r 164 VVDTNREKLAIQEARRLRIPIVAVVDTNSNPDLVDYVIPGNDDSSRSIALFCDLVASAAIDGIARQHSYM 233 (278)
Q Consensus 164 v~d~~~e~~Av~EA~kl~IPvIaivDTn~dp~~idypIP~NDds~~si~l~~~~i~~ai~~g~~~~~~~~ 233 (278)
|.||.-||+||+||...|||||||||||+.-..||..||+|+...+|+.|++|+|++.|+.-|+.-....
T Consensus 115 vtDPR~D~Qa~~EA~~vgiP~vALcDTd~~~~~vDl~IP~NNKG~~s~al~yWlLaRe~L~~RG~i~~~~ 184 (197)
T TIGR01012 115 VTDPRADHQALKEASEVGIPIVALCDTDNSLRYVDLVIPTNNKGRRSLALIYWLLAREILRMRGVISADE 184 (197)
T ss_pred ECCCCCCCCHHHHHHCCCCCEEEEECCCCCCCCCCEEECCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCC
T ss_conf 7588766212120001589668987588750002401079861368999999999999997537404798
No 12
>KOG0830 consensus
Probab=99.94 E-value=5.1e-26 Score=188.95 Aligned_cols=159 Identities=22% Similarity=0.353 Sum_probs=146.7
Q ss_pred CCCCCCCCCCCC-CCEEEECHHHHHHHHHHHHHHHHHHHCCCCEEEEEECCHHHHHHHHHHHHHCCCEECCCCCCCCCCC
Q ss_conf 788562102001-8816753899999999999999986107881699607823579999998633983142334587323
Q gi|254780779|r 26 NPKMERYIFCER-NNTHIIDLSQTVPMLQKALQVISDTVARGGRILFVATKSQASDCVMEAAKRSAQYCVNSKWLGGMMT 104 (278)
Q Consensus 26 nPkM~~yI~g~r-ngihIIdL~kT~~~L~~A~~~i~~i~~~gg~ILFVgTk~~~~~~i~~~A~~~~~~yV~~RWlGG~LT 104 (278)
|..|.+|+|+.| +|+|||||.+|++.|..|...|..+ .+.+.|-.++++...++.|.++|..+|.--+..|+++|++|
T Consensus 2 ~~~~~~y~~~~~~d~~~i~~~~~twekl~~aar~i~ai-enp~dv~v~ssr~~gqravlkfa~~tgatpiag~ftpg~ft 80 (254)
T KOG0830 2 NFQMEQYIYKRRSDGIYIINLGRTWEKLLLAARAIVAI-ENPADVSVISSRNTGQRAVLKFAAATGATPIAGRFTPGTFT 80 (254)
T ss_pred CCCCCCCCCCCCCCCEEEEECCCCHHHHHHHHHHHHHC-CCCCCEEEECCCCCCHHHHHHHHHHHCCCCCCCCCCCCCCC
T ss_conf 74343234355677447840463089888888877513-68320578704775346899878770887434521466243
Q ss_pred CHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCEEEEECCCCCCHHHHHHHHCCCEE
Q ss_conf 42666555677899887630121267746788766556777643443322113595799943887712321234339814
Q gi|254780779|r 105 NWKTVSQSIQKLRDLEELLNKENQGFTKKERLNIERKRDKLKRALDGIRDMGGLPDLMFVVDTNREKLAIQEARRLRIPI 184 (278)
Q Consensus 105 N~~ti~~si~~l~~l~~~~~~~~~~~tkKe~~~~~r~~~kl~k~lgGi~~m~~lP~~iiv~d~~~e~~Av~EA~kl~IPv 184 (278)
| +|+++. +-|.+++|.||.-+|.++.|+...|+||
T Consensus 81 n--~iq~~f-------------------------------------------~epr~lvvtdpr~d~q~~~E~s~~n~p~ 115 (254)
T KOG0830 81 N--QIQAAF-------------------------------------------REPRLLVVTDPRADHQPLTEASYVNLPT 115 (254)
T ss_pred C--HHHHHH-------------------------------------------CCCCEEEECCCCCCCHHHHHHHHCCCCE
T ss_conf 0--777753-------------------------------------------3773046217533310344442047744
Q ss_pred EEECCCCCCCHHCCCEEEECCCCHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 5403677670011520321577268999999999999999999744
Q gi|254780779|r 185 VAVVDTNSNPDLVDYVIPGNDDSSRSIALFCDLVASAAIDGIARQH 230 (278)
Q Consensus 185 IaivDTn~dp~~idypIP~NDds~~si~l~~~~i~~ai~~g~~~~~ 230 (278)
|+||||++....||..||||+.+..||.++.+++++.|+.-+....
T Consensus 116 ialcnTDSpL~~VDIAIPcNNKG~hSVgl~ww~LareVLrmrgtis 161 (254)
T KOG0830 116 IALCNTDSPLCYVDIAIPCNNKGAHSVGVMWWMLAREVLRMRGTIS 161 (254)
T ss_pred EEEECCCCCCCEEEEEEECCCCCCCCCHHHHHHHHHHHHHHHHHHH
T ss_conf 8874488841001333113788752200144541279999875434
No 13
>PRK00414 gmhA phosphoheptose isomerase; Reviewed
Probab=97.32 E-value=0.012 Score=37.98 Aligned_cols=155 Identities=15% Similarity=0.247 Sum_probs=95.5
Q ss_pred CHHHHHHHHHHHHHHHHHHHCCCCEEEEEECCHHHHHHHHHHHHHCCCEECCCCCCCCC-CCCHHHHHHHHHHHHHHHHH
Q ss_conf 38999999999999999861078816996078235799999986339831423345873-23426665556778998876
Q gi|254780779|r 44 DLSQTVPMLQKALQVISDTVARGGRILFVATKSQASDCVMEAAKRSAQYCVNSKWLGGM-MTNWKTVSQSIQKLRDLEEL 122 (278)
Q Consensus 44 dL~kT~~~L~~A~~~i~~i~~~gg~ILFVgTk~~~~~~i~~~A~~~~~~yV~~RWlGG~-LTN~~ti~~si~~l~~l~~~ 122 (278)
+-+.-+..+.+|...+.+...+||+|+|.|..-.+...-.-.+.-++.|.....=++.. |||-.++. .+..
T Consensus 22 ~~~~~~~~I~~aa~~i~~~~~~g~kI~~cGNGGSaa~A~Hfa~dl~~~~~~~r~~l~ai~Lsd~s~lT-a~~N------- 93 (192)
T PRK00414 22 KDDANIHAIQRAAVLIADSFKAGGKVLSCGNGGSHCDAMHFAEELTGRYRENRPGYPAIAISDVSHLS-CVSN------- 93 (192)
T ss_pred HCHHHHHHHHHHHHHHHHHHHCCCEEEEEECCHHHHHHHHHHHHHHCCCCCCCCCCCEEECCCHHHHH-HHCC-------
T ss_conf 15644999999999999999879979999685889999999998746314466654325327677750-1007-------
Q ss_pred HHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCEEEEECCCCCCH----HHHHHHHCCCEEEEECCCCCCC--HH
Q ss_conf 30121267746788766556777643443322113595799943887712----3212343398145403677670--01
Q gi|254780779|r 123 LNKENQGFTKKERLNIERKRDKLKRALDGIRDMGGLPDLMFVVDTNREKL----AIQEARRLRIPIVAVVDTNSNP--DL 196 (278)
Q Consensus 123 ~~~~~~~~tkKe~~~~~r~~~kl~k~lgGi~~m~~lP~~iiv~d~~~e~~----Av~EA~kl~IPvIaivDTn~dp--~~ 196 (278)
+-+|+. .+.|| ++.+.+.-|++|++.+..++- |++.|++.|+.+|+++--+... ..
T Consensus 94 -D~g~e~-------iF~~Q----------l~~~~~~gDvLi~iS~SGnS~Nii~A~~~Ak~~g~~~i~ltG~~GG~l~~l 155 (192)
T PRK00414 94 -DFGYDY-------VFSRY----------VEAVGREGDVLLGISTSGNSGNIIKAIEAAREKGMKVITLTGKDGGKMAGL 155 (192)
T ss_pred -CCCHHH-------HHHHH----------HHHHCCCCCEEEEECCCCCCHHHHHHHHHHHHCCCEEEEEECCCCHHHHHH
T ss_conf -664889-------99999----------998178999999976899999999999999988998999977996147760
Q ss_pred CCC--EEEECCCC--HHHHHH-HHHHHHHHHHH
Q ss_conf 152--03215772--689999-99999999999
Q gi|254780779|r 197 VDY--VIPGNDDS--SRSIAL-FCDLVASAAID 224 (278)
Q Consensus 197 idy--pIP~NDds--~~si~l-~~~~i~~ai~~ 224 (278)
.|+ .||..|++ ++-+.+ +...|++-|..
T Consensus 156 ~D~~i~Vps~~~~~riqE~Hl~i~H~i~elIe~ 188 (192)
T PRK00414 156 ADIEIRVPHFGYADRIQEIHIKVIHILIQLIEK 188 (192)
T ss_pred CCEEEEECCCCCCHHHHHHHHHHHHHHHHHHHH
T ss_conf 897999189997379999999999999999999
No 14
>PRK13938 phosphoheptose isomerase; Provisional
Probab=96.99 E-value=0.039 Score=34.80 Aligned_cols=157 Identities=15% Similarity=0.248 Sum_probs=96.6
Q ss_pred EECHHHHHHHHHHHHHHHHHHHCCCCEEEEEECCHHHHHHHHHHHHHCCCEECCCCCCCC-CC-CCHHHHHHHHHHHHHH
Q ss_conf 753899999999999999986107881699607823579999998633983142334587-32-3426665556778998
Q gi|254780779|r 42 IIDLSQTVPMLQKALQVISDTVARGGRILFVATKSQASDCVMEAAKRSAQYCVNSKWLGG-MM-TNWKTVSQSIQKLRDL 119 (278)
Q Consensus 42 IIdL~kT~~~L~~A~~~i~~i~~~gg~ILFVgTk~~~~~~i~~~A~~~~~~yV~~RWlGG-~L-TN~~ti~~si~~l~~l 119 (278)
|++-+.-...+..+...+.+...+||+|++.|..-.+...-.-.++-.+-+....+=+|. .| +|-.++. .+..
T Consensus 21 ~~~~~~~~~~i~~~~~~i~~~~~~g~kI~~cGNGGSaa~A~Hfa~el~~~~~~~R~~lpaiaL~~n~s~lT-AiaN---- 95 (196)
T PRK13938 21 ILNDRVLLEAARAIGDRLIAGYRAGARVFMCGNGGSAADAQHFAAELTGHLIFDRPPLGAEALHANSSHLT-AVAN---- 95 (196)
T ss_pred HHHCHHHHHHHHHHHHHHHHHHHCCCEEEEEECCHHHHHHHHHHHHHHHHCCCCCCCCCEEECCCCCHHHH-HHHC----
T ss_conf 98252209999999999999998799899996868899999999998633357899847454478807888-8762----
Q ss_pred HHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCEEEEECCCCCC----HHHHHHHHCCCEEEEECCCCCCC-
Q ss_conf 8763012126774678876655677764344332211359579994388771----23212343398145403677670-
Q gi|254780779|r 120 EELLNKENQGFTKKERLNIERKRDKLKRALDGIRDMGGLPDLMFVVDTNREK----LAIQEARRLRIPIVAVVDTNSNP- 194 (278)
Q Consensus 120 ~~~~~~~~~~~tkKe~~~~~r~~~kl~k~lgGi~~m~~lP~~iiv~d~~~e~----~Av~EA~kl~IPvIaivDTn~dp- 194 (278)
|-+|+. .+.|| ++.+.+--|+++++.+..++ .|++.|++.|+.+|++.--+..+
T Consensus 96 ----D~gye~-------vF~rQ----------l~al~~~gDvLi~iStSGnS~NIi~A~~~Ak~~g~~~i~ltG~~gg~l 154 (196)
T PRK13938 96 ----DYDYDT-------VFARA----------LEGSARPGDTLFAISTSGNSMSVLRAAKTARELGVTVVAMTGESGGQL 154 (196)
T ss_pred ----CCCHHH-------HHHHH----------HHHCCCCCCEEEEECCCCCCHHHHHHHHHHHHCCCEEEEEECCCCCHH
T ss_conf ----478999-------99999----------997168999899977999999999999999987998999988996317
Q ss_pred -HHCCCEEEECCCCHHHHH----HHHHHHHHHHHH
Q ss_conf -011520321577268999----999999999999
Q gi|254780779|r 195 -DLVDYVIPGNDDSSRSIA----LFCDLVASAAID 224 (278)
Q Consensus 195 -~~idypIP~NDds~~si~----l~~~~i~~ai~~ 224 (278)
...|+.|-.+.+...-|+ +++..|++.|..
T Consensus 155 ~~l~D~~i~vps~~~~~IqE~Hl~i~H~lceliE~ 189 (196)
T PRK13938 155 AEFADFLINVPSRDTGRIQESHIVFIHAISEHVEH 189 (196)
T ss_pred HHCCCEEEEECCCCCHHHHHHHHHHHHHHHHHHHH
T ss_conf 75489899938998479999999999999999999
No 15
>PRK13936 phosphoheptose isomerase; Provisional
Probab=96.83 E-value=0.038 Score=34.84 Aligned_cols=153 Identities=18% Similarity=0.270 Sum_probs=86.6
Q ss_pred HHHHHHHHHHHHHHHHHHHCCCCEEEEEECCHHHHHHHHHHHHHCCCEECCCC-CCCC-CCC-CHHHHHHHHHHHHHHHH
Q ss_conf 89999999999999998610788169960782357999999863398314233-4587-323-42666555677899887
Q gi|254780779|r 45 LSQTVPMLQKALQVISDTVARGGRILFVATKSQASDCVMEAAKRSAQYCVNSK-WLGG-MMT-NWKTVSQSIQKLRDLEE 121 (278)
Q Consensus 45 L~kT~~~L~~A~~~i~~i~~~gg~ILFVgTk~~~~~~i~~~A~~~~~~yV~~R-WlGG-~LT-N~~ti~~si~~l~~l~~ 121 (278)
++.....+..|...+.+...+||+|++.|..-.+...-.-.++-.+.| ..+| =++- .|+ |-.++. .+..
T Consensus 22 ~~~~~~~i~~aa~~i~~~~~~g~ki~~~GNGgSaa~A~h~a~el~~~~-~~~r~~lpai~L~~d~~~lT-ai~N------ 93 (197)
T PRK13936 22 MEVLAPPIAQAVELMVQALLNEGKILACGNGGSAADAQHFSSELLNRF-ERERPSLPAIALTTDSSTLT-AIAN------ 93 (197)
T ss_pred HHHHHHHHHHHHHHHHHHHHCCCEEEEEECCHHHHHHHHHHHHHHCHH-HCCCCCCCEEEECCCCHHHH-CCCC------
T ss_conf 997099999999999999987998999968789999999999986654-12788875576436740110-1027------
Q ss_pred HHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCEEEEECCCCCCH----HHHHHHHCCCEEEEECCCCCCC--H
Q ss_conf 630121267746788766556777643443322113595799943887712----3212343398145403677670--0
Q gi|254780779|r 122 LLNKENQGFTKKERLNIERKRDKLKRALDGIRDMGGLPDLMFVVDTNREKL----AIQEARRLRIPIVAVVDTNSNP--D 195 (278)
Q Consensus 122 ~~~~~~~~~tkKe~~~~~r~~~kl~k~lgGi~~m~~lP~~iiv~d~~~e~~----Av~EA~kl~IPvIaivDTn~dp--~ 195 (278)
+.+|+ -.+.|| ++...+.-|++|++.+..++- |++.|+..|++||+++-.+... .
T Consensus 94 --D~g~~-------~vf~rQ----------l~a~~~~gDili~iS~SGnS~Nii~A~~~A~~~g~~~i~ltG~dgg~l~~ 154 (197)
T PRK13936 94 --DYSYN-------EVFSKQ----------VRALGQPGDVLLAISTSGNSANVIQAIQAAHEREMHVVALTGRDGGKMAS 154 (197)
T ss_pred --CCCHH-------HHHHHH----------HHHHCCCCCEEEEEECCCCCHHHHHHHHHHHHCCCEEEEEECCCCHHHHH
T ss_conf --87899-------999999----------99838999989999699999899999999998599599998168535675
Q ss_pred H---CCCEEEECCCCHHHHH----HHHHHHHHHHHH
Q ss_conf 1---1520321577268999----999999999999
Q gi|254780779|r 196 L---VDYVIPGNDDSSRSIA----LFCDLVASAAID 224 (278)
Q Consensus 196 ~---idypIP~NDds~~si~----l~~~~i~~ai~~ 224 (278)
. -|+.|-.+.++..-|+ ++...|++.|.+
T Consensus 155 l~~~~Di~i~vps~~~~~iqe~Hl~i~H~Lc~lie~ 190 (197)
T PRK13936 155 LLLPEDVEIRVPHDRTARIQEVHLLAIHCLCDLIDS 190 (197)
T ss_pred HCCCCCEEEECCCCCHHHHHHHHHHHHHHHHHHHHH
T ss_conf 256689899819997079999999999999999999
No 16
>PRK13937 phosphoheptose isomerase; Provisional
Probab=96.69 E-value=0.067 Score=33.26 Aligned_cols=151 Identities=17% Similarity=0.309 Sum_probs=88.2
Q ss_pred HHHHHHHHHHHHHHHHHCCCCEEEEEECCHHHHHHHHHHHHHCCCEECCCC-CCCC-CCC-CHHHHHHHHHHHHHHHHHH
Q ss_conf 999999999999998610788169960782357999999863398314233-4587-323-4266655567789988763
Q gi|254780779|r 47 QTVPMLQKALQVISDTVARGGRILFVATKSQASDCVMEAAKRSAQYCVNSK-WLGG-MMT-NWKTVSQSIQKLRDLEELL 123 (278)
Q Consensus 47 kT~~~L~~A~~~i~~i~~~gg~ILFVgTk~~~~~~i~~~A~~~~~~yV~~R-WlGG-~LT-N~~ti~~si~~l~~l~~~~ 123 (278)
.-...+.++...+.+...+||+|++.|..-.+...-.-.+.-.+.+ ..+| =++- .|+ |-.++. .+..
T Consensus 23 ~~~~~I~~~a~~i~~~~~~g~kI~~~GNGGSaa~A~Hfa~dl~~~~-~~~r~~lpaisL~~d~~~lT-A~~N-------- 92 (192)
T PRK13937 23 SLLAAIAKIAEALIEALASGGKLLLCGNGGSAADAQHIAAELVGRY-KKERPALPAIALTTDTSALT-AIGN-------- 92 (192)
T ss_pred HHHHHHHHHHHHHHHHHHCCCEEEEEECCHHHHHHHHHHHHHHCCC-CCCCCCCCEEECCCCHHHHH-HHHC--------
T ss_conf 8499999999999999987998999968631888999999996413-55789853577678828777-6427--------
Q ss_pred HCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCEEEEECCCCCC----HHHHHHHHCCCEEEEECCCCCCC--HHC
Q ss_conf 012126774678876655677764344332211359579994388771----23212343398145403677670--011
Q gi|254780779|r 124 NKENQGFTKKERLNIERKRDKLKRALDGIRDMGGLPDLMFVVDTNREK----LAIQEARRLRIPIVAVVDTNSNP--DLV 197 (278)
Q Consensus 124 ~~~~~~~tkKe~~~~~r~~~kl~k~lgGi~~m~~lP~~iiv~d~~~e~----~Av~EA~kl~IPvIaivDTn~dp--~~i 197 (278)
+.+|+. .+.|+ ++.+.+--|++|++.+..++ .|++.|++.|+.||+++-.+... ...
T Consensus 93 D~g~~~-------if~~q----------l~~~~~~gDili~iS~SGnS~Nii~A~~~A~~~g~~~i~ltG~~gg~l~~~~ 155 (192)
T PRK13937 93 DYGYER-------VFARQ----------VEALGRPGDVLIGISTSGNSPNVLAALEKARELGMTTIGLTGRDGGKMKELC 155 (192)
T ss_pred CCCHHH-------HHHHH----------HHHCCCCCCEEEEECCCCCCHHHHHHHHHHHHCCCEEEEEECCCCHHHHHHC
T ss_conf 787899-------99999----------9955788988999779999979999999999879979999888960578839
Q ss_pred CCEEEECCCCHHHH----HHHHHHHHHHHHH
Q ss_conf 52032157726899----9999999999999
Q gi|254780779|r 198 DYVIPGNDDSSRSI----ALFCDLVASAAID 224 (278)
Q Consensus 198 dypIP~NDds~~si----~l~~~~i~~ai~~ 224 (278)
|+.|-.+.++..-| -+++..|++.|..
T Consensus 156 D~~i~vps~~~~~iee~H~~i~H~lc~lIe~ 186 (192)
T PRK13937 156 DLLLIVPSDDTPRIQEIHITIGHILCDLVER 186 (192)
T ss_pred CEEEEECCCCCHHHHHHHHHHHHHHHHHHHH
T ss_conf 9899958998589999999999999999999
No 17
>cd05006 SIS_GmhA Phosphoheptose isomerase is a member of the SIS (Sugar ISomerase) superfamily. Phosphoheptose isomerase catalyzes the isomerization of sedoheptulose 7-phosphate into D-glycero-D-mannoheptose 7-phosphate. This is the first step of the biosynthesis of gram-negative bacteria inner core lipopolysaccharide precursor, L-glycero-D-mannoheptose (Gmh).
Probab=95.95 E-value=0.17 Score=30.65 Aligned_cols=148 Identities=17% Similarity=0.273 Sum_probs=84.7
Q ss_pred HHHHHHHHHHHHHHHCCCCEEEEEECCHHHHHHHHHHHHHCCCEECCCCCCCCC-CC-CHHHHHHHHHHHHHHHHHHHCC
Q ss_conf 999999999999861078816996078235799999986339831423345873-23-4266655567789988763012
Q gi|254780779|r 49 VPMLQKALQVISDTVARGGRILFVATKSQASDCVMEAAKRSAQYCVNSKWLGGM-MT-NWKTVSQSIQKLRDLEELLNKE 126 (278)
Q Consensus 49 ~~~L~~A~~~i~~i~~~gg~ILFVgTk~~~~~~i~~~A~~~~~~yV~~RWlGG~-LT-N~~ti~~si~~l~~l~~~~~~~ 126 (278)
...+.+|...+.+...+||+|++.|....+...=.-.+.-.+.+-...++++-. |+ |-..++ .+. -+-+
T Consensus 16 ~~~i~~~~~~i~~~~~~g~kI~~~GNGgSa~~A~H~a~dl~~~~~~~r~~l~aisL~~~~~~~t-a~~--------ND~~ 86 (177)
T cd05006 16 AEAIEQAAQLLAEALLNGGKILICGNGGSAADAQHFAAELVKRFEKERPGLPAIALTTDTSILT-AIA--------NDYG 86 (177)
T ss_pred HHHHHHHHHHHHHHHHCCCEEEEEECCHHHHHHHHHHHHHHCCCCCCCCCEEEEECCCCHHHHH-HHH--------CCCC
T ss_conf 8999999999999998799899996874088899999987357666888701797678778888-875--------6532
Q ss_pred CCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCEEEEECCCCCC----HHHHHHHHCCCEEEEECCCCCCC--HHCCCE
Q ss_conf 126774678876655677764344332211359579994388771----23212343398145403677670--011520
Q gi|254780779|r 127 NQGFTKKERLNIERKRDKLKRALDGIRDMGGLPDLMFVVDTNREK----LAIQEARRLRIPIVAVVDTNSNP--DLVDYV 200 (278)
Q Consensus 127 ~~~~tkKe~~~~~r~~~kl~k~lgGi~~m~~lP~~iiv~d~~~e~----~Av~EA~kl~IPvIaivDTn~dp--~~idyp 200 (278)
|+ ..+.|+ ++.+-+.-|++|++....++ .|++.|++.|+.+|+++-.+..+ ..-|+.
T Consensus 87 ~~-------~if~~q----------l~~~~~~gDili~iS~sG~s~nii~a~~~ak~~g~~~i~ltg~~gg~l~~~~D~~ 149 (177)
T cd05006 87 YE-------EVFSRQ----------VEALGQPGDVLIGISTSGNSPNVLKALEAAKERGMKTIALTGRDGGKLLELADIE 149 (177)
T ss_pred HH-------HHHHHH----------HHHHCCCCCEEEEECCCCCCHHHHHHHHHHHHCCCEEEEEECCCCCHHHHHCCEE
T ss_conf 99-------999999----------9974468988999818999989999999999879989999878986167619989
Q ss_pred EEECCCCHHHHHH----HHHHHHHHH
Q ss_conf 3215772689999----999999999
Q gi|254780779|r 201 IPGNDDSSRSIAL----FCDLVASAA 222 (278)
Q Consensus 201 IP~NDds~~si~l----~~~~i~~ai 222 (278)
|-.+.+...-|+= ++..+++.|
T Consensus 150 i~vps~~~~~vee~Hl~i~H~l~~~i 175 (177)
T cd05006 150 IHVPSDDTPRIQEVHLLIGHILCELV 175 (177)
T ss_pred EEECCCCCHHHHHHHHHHHHHHHHHH
T ss_conf 99699985899999999999999986
No 18
>PRK10886 DnaA initiator-associating protein DiaA; Provisional
Probab=95.12 E-value=0.33 Score=28.77 Aligned_cols=151 Identities=17% Similarity=0.252 Sum_probs=89.5
Q ss_pred HHHHHHHHHHHHHHHHHHCCCCEEEEEECCHHHHHHHHHHHHHCCCEECCCCCCCCC-C-CCHHHHHHHHHHHHHHHHHH
Q ss_conf 999999999999999861078816996078235799999986339831423345873-2-34266655567789988763
Q gi|254780779|r 46 SQTVPMLQKALQVISDTVARGGRILFVATKSQASDCVMEAAKRSAQYCVNSKWLGGM-M-TNWKTVSQSIQKLRDLEELL 123 (278)
Q Consensus 46 ~kT~~~L~~A~~~i~~i~~~gg~ILFVgTk~~~~~~i~~~A~~~~~~yV~~RWlGG~-L-TN~~ti~~si~~l~~l~~~~ 123 (278)
+.-...+..|...+.....+||+|++.|..-.+...=.-.++-++.|-...+=++-. | ||-.++. .+..
T Consensus 21 e~l~~~I~~aa~~i~~~l~~g~ki~~cGNGGSaa~A~Hfa~el~~~f~~~R~~lpai~L~~d~s~lT-ai~N-------- 91 (196)
T PRK10886 21 EALPDAISRAAMTLVQSLLNGNKILCCGNGTSAANAQHFAASMINRFETERPSLPAIALNTDNVVLT-AIAN-------- 91 (196)
T ss_pred HHHHHHHHHHHHHHHHHHHCCCEEEEEECCHHHHHHHHHHHHHHCCCCCCCCCCEEEEECCCCHHHH-HHHC--------
T ss_conf 8719999999999999998799799986847488999999999646556898840566326705654-3116--------
Q ss_pred HCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCEEEEECCCCCC----HHHHHHHHCCCEEEEECCCCCCC-----
Q ss_conf 012126774678876655677764344332211359579994388771----23212343398145403677670-----
Q gi|254780779|r 124 NKENQGFTKKERLNIERKRDKLKRALDGIRDMGGLPDLMFVVDTNREK----LAIQEARRLRIPIVAVVDTNSNP----- 194 (278)
Q Consensus 124 ~~~~~~~tkKe~~~~~r~~~kl~k~lgGi~~m~~lP~~iiv~d~~~e~----~Av~EA~kl~IPvIaivDTn~dp----- 194 (278)
+.+|+ ..+.|| ++.+.+.-|++|++.+..++ .|++.|++.|+++|++.-.+..-
T Consensus 92 D~~~~-------~vF~rQ----------l~alg~~gDiLi~iStSGnS~Nii~Ai~~A~~~g~~~i~ltG~~gg~l~~l~ 154 (196)
T PRK10886 92 DRLHD-------EVYAKQ----------VRALGHAGDVLLAISTRGNSRDIVKAVEAAVTRDMTIVALTGYDGGELAGLL 154 (196)
T ss_pred CCCHH-------HHHHHH----------HHHHCCCCCEEEEEECCCCCHHHHHHHHHHHHCCCEEEEEECCCCHHHHHHC
T ss_conf 67799-------999999----------9985679998999948999989999999999889989999768862366515
Q ss_pred --HHCCCEEEECCCCHHHHH----HHHHHHHHHHHH
Q ss_conf --011520321577268999----999999999999
Q gi|254780779|r 195 --DLVDYVIPGNDDSSRSIA----LFCDLVASAAID 224 (278)
Q Consensus 195 --~~idypIP~NDds~~si~----l~~~~i~~ai~~ 224 (278)
..+..-||.++ ...|+ +++..|++.|..
T Consensus 155 ~~~Di~I~vps~~--t~rIqE~Hl~i~H~lcelIe~ 188 (196)
T PRK10886 155 GPQDVEIRIPSHR--SARIQEMHMLTVNCLCDLIDN 188 (196)
T ss_pred CCCCEEEECCCCC--CHHHHHHHHHHHHHHHHHHHH
T ss_conf 7679899869998--118999999999999999999
No 19
>PRK13608 diacylglycerol glucosyltransferase; Provisional
Probab=93.84 E-value=0.65 Score=26.90 Aligned_cols=139 Identities=14% Similarity=0.179 Sum_probs=67.5
Q ss_pred HCCCCEEEEEECC-----HHHHHHHHHHHHHCCCE--ECC--CCC--CCCCCCCH--HHHHHHHHHHHHHHHHHHCCCCC
Q ss_conf 1078816996078-----23579999998633983--142--334--58732342--66655567789988763012126
Q gi|254780779|r 63 VARGGRILFVATK-----SQASDCVMEAAKRSAQY--CVN--SKW--LGGMMTNW--KTVSQSIQKLRDLEELLNKENQG 129 (278)
Q Consensus 63 ~~~gg~ILFVgTk-----~~~~~~i~~~A~~~~~~--yV~--~RW--lGG~LTN~--~ti~~si~~l~~l~~~~~~~~~~ 129 (278)
+.++++||++... .++.+.+++...+.+.. .|. .=| ..-.+..+ ..-.+++++... ....-+..
T Consensus 2 ~~~~KKVLILtas~G~GH~~AA~AL~~~l~~~~~~~~~v~~~D~~~~~~p~~~~~~~~~Yl~~~k~~p~---ly~~~Y~~ 78 (391)
T PRK13608 2 VTQNKKILIITGSFGNGHMQVTQSIVNQLNDMNLDHLSVIEHDLFMEAHPILTSICKKWYINSFKYFRN---MYKGFYYS 78 (391)
T ss_pred CCCCCEEEEEECCCCHHHHHHHHHHHHHHHHHCCCCEEEEEECHHHHCCCHHHHHHHHHHHHHHHHHHH---HHHHHHHC
T ss_conf 988887999968988379999999999998509996699991378764841888899999999999999---99989854
Q ss_pred CCHHHHHHHHH--HHHHHHHHHHHHHHHCCCCCEEEEECCCCCCHHHHHHHHCCCEEEEECCCCC--CCH----HCCCEE
Q ss_conf 77467887665--5677764344332211359579994388771232123433981454036776--700----115203
Q gi|254780779|r 130 FTKKERLNIER--KRDKLKRALDGIRDMGGLPDLMFVVDTNREKLAIQEARRLRIPIVAVVDTNS--NPD----LVDYVI 201 (278)
Q Consensus 130 ~tkKe~~~~~r--~~~kl~k~lgGi~~m~~lP~~iiv~d~~~e~~Av~EA~kl~IPvIaivDTn~--dp~----~idypI 201 (278)
-+++-.-.+.+ -..||.+. |.. ..||+||.+-|..-...+++...++||+++++ ||- .+. .+|+.+
T Consensus 79 ~~~~~~~~~~~~~~~~kl~~~---L~~--~kPDvII~T~P~~~~s~lk~~~~~~iP~~tVi-TD~~~H~~W~~~~~D~y~ 152 (391)
T PRK13608 79 RPDKLDKCFYKYYGLNKLINL---LIK--EKPDLILLTFPTPVMSVLTEQFNINIPVATVM-TDYRLHKNWITPYSTRYY 152 (391)
T ss_pred CCHHHHHHHHHHHHHHHHHHH---HHH--HCCCEEEECCHHHHHHHHHHHCCCCCCEEEEE-CCHHHHHHHCCCCCCEEE
T ss_conf 840677999999889999999---998--49299999982899999998249999889995-871332303689999799
Q ss_pred EECCCCHHH
Q ss_conf 215772689
Q gi|254780779|r 202 PGNDDSSRS 210 (278)
Q Consensus 202 P~NDds~~s 210 (278)
-++++..+.
T Consensus 153 Va~~~~~~~ 161 (391)
T PRK13608 153 VATKETKQD 161 (391)
T ss_pred ECCHHHHHH
T ss_conf 699999999
No 20
>cd05013 SIS_RpiR RpiR-like protein. RpiR contains a SIS (Sugar ISomerase) domain, which is found in many phosphosugar isomerases and phosphosugar binding proteins. In E. coli, rpiR negatively regulates the expression of rpiB gene. Both rpiB and rpiA are ribose phosphate isomerases that catalyze the reversible reactions of ribose 5-phosphate into ribulose 5-phosphate.
Probab=93.03 E-value=0.87 Score=26.07 Aligned_cols=48 Identities=21% Similarity=0.347 Sum_probs=35.4
Q ss_pred CCEEEEECCCCC----CHHHHHHHHCCCEEEEECCCCCCC--HHCCCEEEECCC
Q ss_conf 957999438877----123212343398145403677670--011520321577
Q gi|254780779|r 159 PDLMFVVDTNRE----KLAIQEARRLRIPIVAVVDTNSNP--DLVDYVIPGNDD 206 (278)
Q Consensus 159 P~~iiv~d~~~e----~~Av~EA~kl~IPvIaivDTn~dp--~~idypIP~NDd 206 (278)
-|++|++....+ .-+++.|++.|+|+|+|.|...+| ...|+.+++..+
T Consensus 61 ~d~~i~iS~sg~~~~~~~~~~~ak~~g~~ii~IT~~~~s~l~~~ad~~l~~~~~ 114 (139)
T cd05013 61 GDVVIAISFSGETKETVEAAEIAKERGAKVIAITDSANSPLAKLADIVLLVSSE 114 (139)
T ss_pred CCEEEEECCCCCCHHHHHHHHHHHHCCCEEEEEECCCCCHHHHHCCEEEECCCC
T ss_conf 999999768636378999999999869979999799999779969999982886
No 21
>PRK00726 murG N-acetylglucosaminyl transferase; Provisional
Probab=92.72 E-value=0.96 Score=25.79 Aligned_cols=29 Identities=17% Similarity=-0.154 Sum_probs=18.2
Q ss_pred CEEEEEECCHHHHHHHHHHHHHCCCEECC
Q ss_conf 81699607823579999998633983142
Q gi|254780779|r 67 GRILFVATKSQASDCVMEAAKRSAQYCVN 95 (278)
Q Consensus 67 g~ILFVgTk~~~~~~i~~~A~~~~~~yV~ 95 (278)
+--+.||+--..+-++--.|...+.|++-
T Consensus 91 kPd~Vig~GGY~s~P~~laA~l~~iP~ii 119 (359)
T PRK00726 91 KPDVVVGFGGYVSGPAGLAARLLGIPLVI 119 (359)
T ss_pred CCCEEEECCCHHHHHHHHHHHHCCCCEEE
T ss_conf 99999978974128999999982998699
No 22
>TIGR00113 queA S-adenosylmethionine:tRNA ribosyltransferase-isomerase; InterPro: IPR003699 Queuosine is a hypermodified nucleoside that usually occurs in the first position of the anticodon of tRNAs specifying the amino acids asparagine, aspartate, histidine, and tyrosine. The hypermodified nucleoside is found in bacteria and eukaryotes . Queuosine is synthesized de novo exclusively in bacteria; for eukaryotes the compound is a nutrient factor. Queuosine biosynthesis protein, or S-adenosylmethionine:tRNA -ribosyltransferase-isomerase, is required for the synthesis of the queuosine precursor (oQ). ; GO: 0003824 catalytic activity, 0008616 queuosine biosynthetic process.
Probab=92.09 E-value=0.15 Score=31.06 Aligned_cols=72 Identities=21% Similarity=0.358 Sum_probs=49.7
Q ss_pred EEECHHHHHHHHHHHHHHHHHHHCCCCEEEEEECCHH------------HHHHHHHHHHHCCCE-ECCCCC--CCCCCCC
Q ss_conf 6753899999999999999986107881699607823------------579999998633983-142334--5873234
Q gi|254780779|r 41 HIIDLSQTVPMLQKALQVISDTVARGGRILFVATKSQ------------ASDCVMEAAKRSAQY-CVNSKW--LGGMMTN 105 (278)
Q Consensus 41 hIIdL~kT~~~L~~A~~~i~~i~~~gg~ILFVgTk~~------------~~~~i~~~A~~~~~~-yV~~RW--lGG~LTN 105 (278)
|++--|.. ..=...++.|.+.-++||+|+=|||--. ..+.++.++..|..| |--..| +-|++||
T Consensus 241 H~mH~E~~-~vp~~~~~~~~k~~~~G~Ri~aVGTTsvRslE~~a~~~~~~~~~~~~~~~~T~iFiYPG~~~~~Vd~LiTN 319 (364)
T TIGR00113 241 HVMHAEYL-EVPQETVEALEKTRESGGRIIAVGTTSVRSLESAAQEADEPRDLLEPFFGDTDIFIYPGYQFKVVDGLITN 319 (364)
T ss_pred CCCCCHHE-ECCHHHHHHHHHHHHCCCEEEEECCCHHHHHHHHHHHHCCCCCHHHHHCCCCCEEECCCCEEEEEEEEECC
T ss_conf 64200001-26878999999999709839998761477798887630477100201116743676067404534000206
Q ss_pred HHHHHHHH
Q ss_conf 26665556
Q gi|254780779|r 106 WKTVSQSI 113 (278)
Q Consensus 106 ~~ti~~si 113 (278)
|.==+.|+
T Consensus 320 FHLPkSsL 327 (364)
T TIGR00113 320 FHLPKSSL 327 (364)
T ss_pred CCCCHHHH
T ss_conf 62702679
No 23
>cd05007 SIS_Etherase N-acetylmuramic acid 6-phosphate etherase. Members of this family contain the SIS (Sugar ISomerase) domain. The SIS domain is found in many phosphosugar isomerases and phosphosugar binding proteins. The bacterial cell wall sugar N-acetylmuramic acid carries a unique D-lactyl ether substituent at the C3 position. The etherase catalyzes the cleavage of the lactyl ether bond of N-acetylmuramic acid 6-phosphate.
Probab=92.01 E-value=1.2 Score=25.23 Aligned_cols=156 Identities=14% Similarity=0.262 Sum_probs=96.0
Q ss_pred HHHHHHHHHHHHHHHHHHHCCCCEEEEEECCHHHHHHHHHHHHHCCCEECCCCCCCCCCCC-HHHHHHHHHHHHHHHHHH
Q ss_conf 8999999999999999861078816996078235799999986339831423345873234-266655567789988763
Q gi|254780779|r 45 LSQTVPMLQKALQVISDTVARGGRILFVATKSQASDCVMEAAKRSAQYCVNSKWLGGMMTN-WKTVSQSIQKLRDLEELL 123 (278)
Q Consensus 45 L~kT~~~L~~A~~~i~~i~~~gg~ILFVgTk~~~~~~i~~~A~~~~~~yV~~RWlGG~LTN-~~ti~~si~~l~~l~~~~ 123 (278)
+.+.+..+..|...+.+-..+||++.++|.--...-.+...++-..-|-+...++-|.+-. |..+.+++....+...
T Consensus 28 v~~~lp~I~~~i~~~~~~l~~gGRl~Y~GAGTSGrlgvlDa~E~~PTFg~~~~~v~gliAGG~~al~~~~E~aED~~~-- 105 (257)
T cd05007 28 VEAALPQIARAVDAAAERLRAGGRLIYVGAGTSGRLGVLDASELPPTFGTPPERVVGLIAGGEPALTRAVEGAEDDEE-- 105 (257)
T ss_pred HHHHHHHHHHHHHHHHHHHHCCCCEEEECCCHHHHHHHHHHHHCCCCCCCCHHHHEEEEECCHHHHHHCHHCCCCCHH--
T ss_conf 999899999999999999965982899878605889998899739877999899110243889999645311256689--
Q ss_pred HCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCEEEEECCC----CCCHHHHHHHHCCCEEEEECCCCCCC--HHC
Q ss_conf 012126774678876655677764344332211359579994388----77123212343398145403677670--011
Q gi|254780779|r 124 NKENQGFTKKERLNIERKRDKLKRALDGIRDMGGLPDLMFVVDTN----REKLAIQEARRLRIPIVAVVDTNSNP--DLV 197 (278)
Q Consensus 124 ~~~~~~~tkKe~~~~~r~~~kl~k~lgGi~~m~~lP~~iiv~d~~----~e~~Av~EA~kl~IPvIaivDTn~dp--~~i 197 (278)
.+.. ...++ ++ .--|+||-+-.. .=.-++++|+++|.++|+|+..-..| ...
T Consensus 106 -~g~~------------dl~~~-----~~----~~~DvVIgIsaSG~TPyv~~aL~~A~~~ga~ti~I~~n~~s~~~~~a 163 (257)
T cd05007 106 -AGAA------------DLQAI-----NL----TERDVVIGIAASGRTPYVLGALRYARARGALTIGIACNPGSPLLQLA 163 (257)
T ss_pred -HHHH------------HHHHC-----CC----CCCCEEEEEECCCCCHHHHHHHHHHHHCCCCEEEEECCCCCCCCCCC
T ss_conf -9999------------99980-----89----96458999946999859999999999869957876438863100027
Q ss_pred CCEEEECCC-----------CHHHHHHHHHHHHHHHHH
Q ss_conf 520321577-----------268999999999999999
Q gi|254780779|r 198 DYVIPGNDD-----------SSRSIALFCDLVASAAID 224 (278)
Q Consensus 198 dypIP~NDd-----------s~~si~l~~~~i~~ai~~ 224 (278)
|++|.-.-- |--+-++++|.|+...--
T Consensus 164 d~~I~~~tGpEvi~GSTRmkaGTaqK~iLNmiST~~mi 201 (257)
T cd05007 164 DIAIALITGPEVVAGSTRLKAGTAQKLALNMLSTAVMI 201 (257)
T ss_pred CEEEEECCCCEEEECCCCCCHHHHHHHHHHHHHHHHHH
T ss_conf 84687268850022354202257899999998899999
No 24
>cd03805 GT1_ALG2_like This family is most closely related to the GT1 family of glycosyltransferases. ALG2, a 1,3-mannosyltransferase, in yeast catalyzes the mannosylation of Man(2)GlcNAc(2)-dolichol diphosphate and Man(1)GlcNAc(2)-dolichol diphosphate to form Man(3)GlcNAc(2)-dolichol diphosphate. A deficiency of this enzyme causes an abnormal accumulation of Man1GlcNAc2-PP-dolichol and Man2GlcNAc2-PP-dolichol, which is associated with a type of congenital disorders of glycosylation (CDG), designated CDG-Ii, in humans.
Probab=91.93 E-value=0.78 Score=26.37 Aligned_cols=73 Identities=14% Similarity=0.205 Sum_probs=41.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHH----HCCCC----------CEEEEECCCCC--CHHHHHHHHCCCEEEEECCCCCCCHHC
Q ss_conf 788766556777643443322----11359----------57999438877--123212343398145403677670011
Q gi|254780779|r 134 ERLNIERKRDKLKRALDGIRD----MGGLP----------DLMFVVDTNRE--KLAIQEARRLRIPIVAVVDTNSNPDLV 197 (278)
Q Consensus 134 e~~~~~r~~~kl~k~lgGi~~----m~~lP----------~~iiv~d~~~e--~~Av~EA~kl~IPvIaivDTn~dp~~i 197 (278)
|.....+++.+|...+.|+.+ +...| .-+||.-+..| -+++-||--.|.|||| .|+...|+.|
T Consensus 260 e~~~y~~eL~~l~~~~~~l~~~V~Flg~~~~~~~~~l~~~ad~~v~~s~~Egfg~v~lEAma~G~PVVa-sd~gG~~E~I 338 (392)
T cd03805 260 ENVEYLEELQRLAEELLLLEDQVIFLPSISDSQKELLLSSARALLYTPSNEHFGIVPLEAMYAGKPVIA-CNSGGPLETV 338 (392)
T ss_pred HHHHHHHHHHHHHHHHCCCCCEEEECCCCCHHHHHHHHHHCCEEEECCCCCCCCHHHHHHHHCCCCEEE-ECCCCCHHHE
T ss_conf 018999999999998259878599988899699999998597999887434666079999977999999-4899867664
Q ss_pred C-----CEEEECCCC
Q ss_conf 5-----203215772
Q gi|254780779|r 198 D-----YVIPGNDDS 207 (278)
Q Consensus 198 d-----ypIP~NDds 207 (278)
. |.+|+|+++
T Consensus 339 ~~g~~G~Lv~~d~~~ 353 (392)
T cd03805 339 VDGETGFLCEPTPEE 353 (392)
T ss_pred ECCCEEEEECCCHHH
T ss_conf 579669995959999
No 25
>pfam04007 DUF354 Protein of unknown function (DUF354). Members of this family are around 350 amino acids in length. They are found in archaebacteria and have no known function.
Probab=91.77 E-value=1.2 Score=25.06 Aligned_cols=102 Identities=19% Similarity=0.209 Sum_probs=60.9
Q ss_pred HHHHHHHHHHHHHCCCCEEEEEECCHHHHHHHHHHHHHCCCEEC-CCCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCC
Q ss_conf 99999999998610788169960782357999999863398314-23345873234266655567789988763012126
Q gi|254780779|r 51 MLQKALQVISDTVARGGRILFVATKSQASDCVMEAAKRSAQYCV-NSKWLGGMMTNWKTVSQSIQKLRDLEELLNKENQG 129 (278)
Q Consensus 51 ~L~~A~~~i~~i~~~gg~ILFVgTk~~~~~~i~~~A~~~~~~yV-~~RWlGG~LTN~~ti~~si~~l~~l~~~~~~~~~~ 129 (278)
+..-...+|.++-.+|-.|++...+. +.+.+.++..|.+|. -.++ |+++.. -+..++.|..+|-+
T Consensus 12 hvhfFk~iI~eL~k~GheV~iTaR~~---~~~~~LL~~y~i~~~~iG~~-g~s~~~--Kl~~~~~R~~~L~~-------- 77 (335)
T pfam04007 12 HVHFFKPIISELEKEGYEVLLTCRKF---GELPELLRSLGFQVKSIGKH-GATLIK--KLLSSAERVYLLTK-------- 77 (335)
T ss_pred HHHHHHHHHHHHHHCCCEEEEEEECC---CHHHHHHHHCCCCEEEECCC-CCCHHH--HHHHHHHHHHHHHH--------
T ss_conf 88889999999986898899999613---51999999769976997588-888899--99999999999999--------
Q ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCEEEEECCCCCCHHHHHHHHCCCEEEEECCCCC
Q ss_conf 774678876655677764344332211359579994388771232123433981454036776
Q gi|254780779|r 130 FTKKERLNIERKRDKLKRALDGIRDMGGLPDLMFVVDTNREKLAIQEARRLRIPIVAVVDTNS 192 (278)
Q Consensus 130 ~tkKe~~~~~r~~~kl~k~lgGi~~m~~lP~~iiv~d~~~e~~Av~EA~kl~IPvIaivDTn~ 192 (278)
... +..||+.+-..-.. |.+=|.-||||.|.++||.-
T Consensus 78 ------------------~~~-----~~~PDv~is~~S~~---a~~va~~LgipsI~f~Dteh 114 (335)
T pfam04007 78 ------------------LIP-----EKKPDVAIMKNSME---LPRVAFGLRIPSIIVLDNEH 114 (335)
T ss_pred ------------------HHH-----HHCCCEEEECCCHH---HHHHHHHCCCCEEEEECCHH
T ss_conf ------------------988-----62997899448801---99999882998799947755
No 26
>cd03785 GT1_MurG MurG is an N-acetylglucosaminyltransferase, the last enzyme involved in the intracellular phase of peptidoglycan biosynthesis. It transfers N-acetyl-D-glucosamine (GlcNAc) from UDP-GlcNAc to the C4 hydroxyl of a lipid-linked N-acetylmuramoyl pentapeptide (NAM). The resulting disaccharide is then transported across the cell membrane, where it is polymerized into NAG-NAM cell-wall repeat structure. MurG belongs to the GT-B structural superfamily of glycoslytransferases, which have characteristic N- and C-terminal domains, each containing a typical Rossmann fold. The two domains have high structural homology despite minimal sequence homology. The large cleft that separates the two domains includes the catalytic center and permits a high degree of flexibility.
Probab=91.31 E-value=1.4 Score=24.76 Aligned_cols=25 Identities=28% Similarity=-0.015 Sum_probs=14.5
Q ss_pred EEEECCHHHHHHHHHHHHHCCCEEC
Q ss_conf 9960782357999999863398314
Q gi|254780779|r 70 LFVATKSQASDCVMEAAKRSAQYCV 94 (278)
Q Consensus 70 LFVgTk~~~~~~i~~~A~~~~~~yV 94 (278)
+.||+--..+-.+--.|...+.|.+
T Consensus 92 ~vi~~GGY~s~P~~laA~~~~iP~~ 116 (350)
T cd03785 92 VVVGFGGYVSGPVGLAAKLLGIPLV 116 (350)
T ss_pred EEEECCCCHHHHHHHHHHHCCCCCE
T ss_conf 9998898103899999997299855
No 27
>cd06305 PBP1_methylthioribose_binding_like Methylthioribose-binding protein-like of ABC-type transport systems that belong to a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein (PBP1) superfamily. Methylthioribose-binding protein-like of ABC-type transport systems that belong to a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein (PBP1) superfamily, which consists of two alpha/beta globular domains connected by a three-stranded hinge. This Venus flytrap-like domain undergoes transition from an open to a closed conformational state upon ligand binding. The sugar-binding domain of the periplasmic proteins in this group is also homologous to the ligand-binding domain of eukaryotic receptors such as metabotropic glutamate receptor (mGluR), DNA-binding transcriptional repressors such as LacI and GalR.
Probab=90.98 E-value=0.72 Score=26.61 Aligned_cols=14 Identities=36% Similarity=0.468 Sum_probs=5.5
Q ss_pred HHHHHHHCCCEEEE
Q ss_conf 32123433981454
Q gi|254780779|r 173 AIQEARRLRIPIVA 186 (278)
Q Consensus 173 Av~EA~kl~IPvIa 186 (278)
++++|..-|||||.
T Consensus 72 ~l~~a~~aGIPVV~ 85 (273)
T cd06305 72 WVKRALDAGIPVVA 85 (273)
T ss_pred HHHHHHHCCCCEEE
T ss_conf 99999985997899
No 28
>cd06317 PBP1_ABC_sugar_binding_like_8 Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems. Pperiplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily, which consists of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis.
Probab=90.98 E-value=0.81 Score=26.26 Aligned_cols=44 Identities=16% Similarity=0.255 Sum_probs=24.1
Q ss_pred CCCCEEEEE--CCCCCCHHHHHHHHCCCEEEEECCCCCCCHHCCCEE
Q ss_conf 359579994--388771232123433981454036776700115203
Q gi|254780779|r 157 GLPDLMFVV--DTNREKLAIQEARRLRIPIVAVVDTNSNPDLVDYVI 201 (278)
Q Consensus 157 ~lP~~iiv~--d~~~e~~Av~EA~kl~IPvIaivDTn~dp~~idypI 201 (278)
+-+|+|++. |+..-..++++|...|||||. +|+..+....+|..
T Consensus 55 ~~vd~Iii~p~d~~~~~~~i~~a~~agIpVv~-~d~~~~~~~~~~~~ 100 (275)
T cd06317 55 QKVDGIILWPTDGQAYIPGLRKAKQAGIPVVI-TNSNISEKGFEFIK 100 (275)
T ss_pred CCCCEEEEECCCCHHHHHHHHHHHHCCCEEEE-ECCCCCCCCCCEEE
T ss_conf 59999999678712457999999986994999-76888766775289
No 29
>PRK05636 replicative DNA helicase; Provisional
Probab=88.70 E-value=2.2 Score=23.41 Aligned_cols=159 Identities=17% Similarity=0.294 Sum_probs=85.0
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCC-EEEEC----HHHHHHHHHHHHHHHHHHH-CCCCEEEEEECCHHHHHHHHHHH-HH
Q ss_conf 860754776578856210200188-16753----8999999999999999861-07881699607823579999998-63
Q gi|254780779|r 16 VQFGHRNFLWNPKMERYIFCERNN-THIID----LSQTVPMLQKALQVISDTV-ARGGRILFVATKSQASDCVMEAA-KR 88 (278)
Q Consensus 16 ~H~Gh~~~~wnPkM~~yI~g~rng-ihIId----L~kT~~~L~~A~~~i~~i~-~~gg~ILFVgTk~~~~~~i~~~A-~~ 88 (278)
.-.|..|... ..-.++-|.+.| +.||= .-||...|.-| ..++ .+|+.++|.+---...+++..+. ..
T Consensus 246 ~~~Gi~TGf~--~LD~~t~Gl~~G~LiIiAARPsmGKTalAlnia----~n~A~~~g~~v~~fSLEMs~~ql~~Rlla~~ 319 (507)
T PRK05636 246 IATGIPTGFK--DLDDLTNGLRGGQMIIVAARPGVGKSTIALDFM----RSASIKNNKASVIFSLEMSKSEIVMRLLSAE 319 (507)
T ss_pred CCEEEECCCH--HHHHHHCCCCCCCEEEEEECCCCCHHHHHHHHH----HHHHHHCCCCEEEEECCCCHHHHHHHHHHHH
T ss_conf 9525658808--899755088835679997378786689999999----9999876993799715699899999999984
Q ss_pred CCCEECCCCCCCCCCCC--HHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCEEEEEC
Q ss_conf 39831423345873234--2666555677899887630121267746788766556777643443322113595799943
Q gi|254780779|r 89 SAQYCVNSKWLGGMMTN--WKTVSQSIQKLRDLEELLNKENQGFTKKERLNIERKRDKLKRALDGIRDMGGLPDLMFVVD 166 (278)
Q Consensus 89 ~~~~yV~~RWlGG~LTN--~~ti~~si~~l~~l~~~~~~~~~~~tkKe~~~~~r~~~kl~k~lgGi~~m~~lP~~iiv~d 166 (278)
++.++ +++-.|.||. |..+...+.++.++.-..+ .-..+|--+.....| |+.+.. | .++||| |
T Consensus 320 s~V~~--~~ir~g~l~~~~~~~l~~a~~~l~~~pl~Id-D~~~lti~~Ira~aR---rlk~~~-~-------l~livV-D 384 (507)
T PRK05636 320 AEVRL--ADMRGGKMDEDAWEKLVQRLGKIAQAPIFID-DSANLTMMEIRSKAR---RLKQKH-D-------LKMIVV-D 384 (507)
T ss_pred CCCCH--HHHHCCCCCHHHHHHHHHHHHHHHHCCEEEE-CCCCCCHHHHHHHHH---HHHHHC-C-------CCEEEE-E
T ss_conf 79887--8885588788999999999999861988998-499976999999999---998617-9-------998998-4
Q ss_pred ------C-C---CCCHHHHH--------HHHCCCEEEEECCCCCCCH
Q ss_conf ------8-8---77123212--------3433981454036776700
Q gi|254780779|r 167 ------T-N---REKLAIQE--------ARRLRIPIVAVVDTNSNPD 195 (278)
Q Consensus 167 ------~-~---~e~~Av~E--------A~kl~IPvIaivDTn~dp~ 195 (278)
+ . .....|.| |+.|+||||+++--|=..+
T Consensus 385 YLQLm~~~~~~~~R~~ev~~ISr~LK~lAkel~vpVi~LsQLnR~~E 431 (507)
T PRK05636 385 YLQLMSSGKRVESRQQEVSEFSRQLKLLAKELDVPLIAISQLNRGPE 431 (507)
T ss_pred HHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCEEEECCCCCCCC
T ss_conf 58845688887668999999999999999997998899712684423
No 30
>cd06271 PBP1_AglR_RafR_like Ligand-binding domain of DNA transcription repressors specific for raffinose (RafR) and alpha-glucosides (AglR) which are members of the LacI-GalR family of bacterial transcription regulators. Ligand-binding domain of DNA transcription repressors specific for raffinose (RafR) and alpha-glucosides (AglR) which are members of the LacI-GalR family of bacterial transcription regulators. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the represso
Probab=88.69 E-value=2.2 Score=23.40 Aligned_cols=63 Identities=11% Similarity=0.054 Sum_probs=41.9
Q ss_pred CCCCCEEEEECCCCCCHHHHHHHHCCCE------EEEECCCC----CCCHHCCCEEEECCCCHHHHHHHHHHH
Q ss_conf 1359579994388771232123433981------45403677----670011520321577268999999999
Q gi|254780779|r 156 GGLPDLMFVVDTNREKLAIQEARRLRIP------IVAVVDTN----SNPDLVDYVIPGNDDSSRSIALFCDLV 218 (278)
Q Consensus 156 ~~lP~~iiv~d~~~e~~Av~EA~kl~IP------vIaivDTn----~dp~~idypIP~NDds~~si~l~~~~i 218 (278)
...|+++|+.+-.--.-+++.++++|+. |+|+=|+. +.|.+-+.-.|...=+..++++++..|
T Consensus 179 ~~~p~Ai~~~nD~~A~g~l~~l~~~g~~vP~DisvigfD~~~~~~~~~p~LTti~~~~~~~g~~A~~~Ll~~i 251 (268)
T cd06271 179 PDRPTAIVCSSELMALGVLAALAEAGLRPGRDVSVVGFDDSPPLLFFSPPLTTVRSDLRAAGRRLAELLLARI 251 (268)
T ss_pred CCCCCEEEECCHHHHHHHHHHHHHCCCCCCCCEEEEEECCCHHHHHCCCCEEEEECCHHHHHHHHHHHHHHHH
T ss_conf 9998689977779999999999982999899979999788289982789808998099999999999999997
No 31
>pfam10087 DUF2325 Uncharacterized protein conserved in bacteria (DUF2325). Members of this family of hypothetical bacterial proteins have no known function.
Probab=88.63 E-value=2.3 Score=23.39 Aligned_cols=75 Identities=17% Similarity=0.201 Sum_probs=47.0
Q ss_pred EEEEEECCHHHHHHHHHHHHHCCCEECCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHH
Q ss_conf 16996078235799999986339831423345873234266655567789988763012126774678876655677764
Q gi|254780779|r 68 RILFVATKSQASDCVMEAAKRSAQYCVNSKWLGGMMTNWKTVSQSIQKLRDLEELLNKENQGFTKKERLNIERKRDKLKR 147 (278)
Q Consensus 68 ~ILFVgTk~~~~~~i~~~A~~~~~~yV~~RWlGG~LTN~~ti~~si~~l~~l~~~~~~~~~~~tkKe~~~~~r~~~kl~k 147 (278)
+||.||-+.....-++...++.|.-.+.+ | ||.=.+ ..+|+.
T Consensus 1 svLiIGG~~~~~~~~~~~~~~~G~~~~~h-~-~g~~~~------------------------------------~~~l~~ 42 (96)
T pfam10087 1 SVLIVGGRDDRLGHYRKLLEKYGGEFIVH-D-GGREKK------------------------------------KKKIPA 42 (96)
T ss_pred CEEEECCCHHHHHHHHHHHHHCCCEEEEE-C-CCCCCH------------------------------------HHHHHH
T ss_conf 99999585567899999999839989996-5-898733------------------------------------556775
Q ss_pred HHHHHHHHCCCCCEEEEECCCCCCH----HHHHHHHCCCEEEEE
Q ss_conf 3443322113595799943887712----321234339814540
Q gi|254780779|r 148 ALDGIRDMGGLPDLMFVVDTNREKL----AIQEARRLRIPIVAV 187 (278)
Q Consensus 148 ~lgGi~~m~~lP~~iiv~d~~~e~~----Av~EA~kl~IPvIai 187 (278)
.-+-+|+||++--.-.|. +-++|++.|||++-+
T Consensus 43 -------~i~~aDlVI~~td~vsH~~~~~vK~~akk~~~p~v~~ 79 (96)
T pfam10087 43 -------LLKKADLVIVFTDCVSHDAMWRVKEEAKKRGIPVVFS 79 (96)
T ss_pred -------CCCCCCEEEEECCCCCHHHHHHHHHHHHHHCCCEEEE
T ss_conf -------0589888999717668799999999999849978997
No 32
>cd06267 PBP1_LacI_sugar_binding_like Ligand binding domain of the LacI tanscriptional regulator family belonging to the type I periplasmic-binding fold protein superfamily. Ligand binding domain of the LacI tanscriptional regulator family belonging to the type I periplasmic-binding fold protein superfamily. In most cases, ligands are monosaccharide including lactose, ribose, fructose, xylose, arabinose, galactose/glucose, and other sugars. The LacI family of proteins consists of transcriptional regulators related to the lac repressor. In this case, the domain sugar binding changes the DNA binding activity of the repressor domain.
Probab=88.48 E-value=1.5 Score=24.48 Aligned_cols=33 Identities=21% Similarity=0.289 Sum_probs=22.2
Q ss_pred CCCCEEEEECCCCCCHHHHHHHHCCCE------EEEECC
Q ss_conf 359579994388771232123433981------454036
Q gi|254780779|r 157 GLPDLMFVVDTNREKLAIQEARRLRIP------IVAVVD 189 (278)
Q Consensus 157 ~lP~~iiv~d~~~e~~Av~EA~kl~IP------vIaivD 189 (278)
..|++||+.+-.--.-+++.+...|+. |+|+=|
T Consensus 176 ~~~~ai~~~~D~~A~g~~~~l~~~g~~iP~di~Iig~d~ 214 (264)
T cd06267 176 ERPTAIFAANDLMAIGALRALRELGLRVPEDVSVVGFDD 214 (264)
T ss_pred CCCCEEEECCHHHHHHHHHHHHHCCCCCCCCEEEEEECC
T ss_conf 999899878879999999999982999999779999998
No 33
>PRK06904 replicative DNA helicase; Validated
Probab=88.48 E-value=2.3 Score=23.31 Aligned_cols=164 Identities=21% Similarity=0.275 Sum_probs=82.7
Q ss_pred CCCCCCCCC-EEEEC----HHHHHHHHHHHHHHHHHHHCCCCEEEEEECCHHHHHHHHH-HHHHCCCEECCCCCCCC-CC
Q ss_conf 210200188-16753----8999999999999999861078816996078235799999-98633983142334587-32
Q gi|254780779|r 31 RYIFCERNN-THIID----LSQTVPMLQKALQVISDTVARGGRILFVATKSQASDCVME-AAKRSAQYCVNSKWLGG-MM 103 (278)
Q Consensus 31 ~yI~g~rng-ihIId----L~kT~~~L~~A~~~i~~i~~~gg~ILFVgTk~~~~~~i~~-~A~~~~~~yV~~RWlGG-~L 103 (278)
..+-|.+.| .-||= .-||...|.-|.+... ..++.|+|..---...++... .|..++.++ +++--| .+
T Consensus 213 ~~t~Gl~~g~LiViAaRPsmGKTa~alnia~n~A~---~~~~~V~~fSLEM~~~~l~~R~ls~~s~v~~--~~i~~g~~l 287 (472)
T PRK06904 213 KKTAGLQPSDLIIVAARPSMGKTTFAMNLCENAAM---ASEKPVLVFSLEMPAEQIMMRMLASLSRVDQ--TKIRTGQNL 287 (472)
T ss_pred HHHCCCCCCCEEEEEECCCCCHHHHHHHHHHHHHH---HCCCCEEEECCCCCHHHHHHHHHHHHCCCCH--HHHHCCCCC
T ss_conf 44158875757999737987568999999999999---5599579977879999999999998649998--886468856
Q ss_pred CC--HHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCEEEEEC-------CC---CCC
Q ss_conf 34--2666555677899887630121267746788766556777643443322113595799943-------88---771
Q gi|254780779|r 104 TN--WKTVSQSIQKLRDLEELLNKENQGFTKKERLNIERKRDKLKRALDGIRDMGGLPDLMFVVD-------TN---REK 171 (278)
Q Consensus 104 TN--~~ti~~si~~l~~l~~~~~~~~~~~tkKe~~~~~r~~~kl~k~lgGi~~m~~lP~~iiv~d-------~~---~e~ 171 (278)
++ |..+.+.+..+.++....-..-.++|--+... ...++.+.-+| .++| |+| +. ...
T Consensus 288 ~~~e~~~~~~~~~~l~~~~~l~idd~~~~t~~~i~~---~~r~~~~~~~~-------l~~v-vIDYLqL~~~~~~~~~r~ 356 (472)
T PRK06904 288 DQQDWAKISSTVGMFKQKPNLYIDDSSGLTPTELRS---RARRVYRENGG-------LSLI-MVDYLQLMRAPGFEDNRT 356 (472)
T ss_pred HHHHHHHHHHHHHHHHCCCCEEEECCCCCCHHHHHH---HHHHHHHHCCC-------CCEE-EEEHHHHCCCCCCCCCHH
T ss_conf 099999999999998468981684699999999999---99999987389-------9789-963886604888777788
Q ss_pred HHHHH--------HHHCCCEEEEECCCCCCCHHCCCEEEECCCCHHH
Q ss_conf 23212--------3433981454036776700115203215772689
Q gi|254780779|r 172 LAIQE--------ARRLRIPIVAVVDTNSNPDLVDYVIPGNDDSSRS 210 (278)
Q Consensus 172 ~Av~E--------A~kl~IPvIaivDTn~dp~~idypIP~NDds~~s 210 (278)
..|.| |+.|+||||+++-=|=.++.=+=.-|.-.|-.-|
T Consensus 357 ~ei~~isr~LK~lAkel~ipvi~LsQLnR~~e~R~dkrP~lsDLReS 403 (472)
T PRK06904 357 LEIAEISRSLKALAKELKVPVVALSQLNRTLENRGDKRPVNSDLRES 403 (472)
T ss_pred HHHHHHHHHHHHHHHHHCCCEEEECCCCCCCCCCCCCCCCCCCCCCC
T ss_conf 99999999999999997998899732684311279998860202252
No 34
>COG0279 GmhA Phosphoheptose isomerase [Carbohydrate transport and metabolism]
Probab=88.40 E-value=2.4 Score=23.28 Aligned_cols=134 Identities=16% Similarity=0.301 Sum_probs=92.8
Q ss_pred HHHHHHHHHHHHHHHHHHCCCCEEEEEECCHHHHHHHHHHHHHCCCEECCCCCCCCCC-C-CHHHHHHHHHHHHHHHHHH
Q ss_conf 9999999999999998610788169960782357999999863398314233458732-3-4266655567789988763
Q gi|254780779|r 46 SQTVPMLQKALQVISDTVARGGRILFVATKSQASDCVMEAAKRSAQYCVNSKWLGGMM-T-NWKTVSQSIQKLRDLEELL 123 (278)
Q Consensus 46 ~kT~~~L~~A~~~i~~i~~~gg~ILFVgTk~~~~~~i~~~A~~~~~~yV~~RWlGG~L-T-N~~ti~~si~~l~~l~~~~ 123 (278)
+.-...+..|...+.....+|++||.-|.-..+.+...-.|+-+|-|.-..+=+|+.. | |-+.+. +|..
T Consensus 21 ~~l~~~I~~aa~~i~~~l~~G~Kvl~cGNGgSaadAqHfaaEl~gRf~~eR~~lpaIaLt~dsS~lT-ai~N-------- 91 (176)
T COG0279 21 EALIEAIERAAQLLVQSLLNGNKVLACGNGGSAADAQHFAAELTGRFEKERPSLPAIALSTDSSVLT-AIAN-------- 91 (176)
T ss_pred HHHHHHHHHHHHHHHHHHHCCCEEEEECCCCCHHHHHHHHHHHHHHHHHCCCCCCEEEEECCCHHHH-HHHC--------
T ss_conf 9869999999999999997699799976985245189999998607875278987368642637776-5650--------
Q ss_pred HCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCEEEEECCCCCC----HHHHHHHHCCCEEEEECCCCCCC--HHC
Q ss_conf 012126774678876655677764344332211359579994388771----23212343398145403677670--011
Q gi|254780779|r 124 NKENQGFTKKERLNIERKRDKLKRALDGIRDMGGLPDLMFVVDTNREK----LAIQEARRLRIPIVAVVDTNSNP--DLV 197 (278)
Q Consensus 124 ~~~~~~~tkKe~~~~~r~~~kl~k~lgGi~~m~~lP~~iiv~d~~~e~----~Av~EA~kl~IPvIaivDTn~dp--~~i 197 (278)
+-+|+ ..+.|+. ....+.-|+++=+.|..++ .|+..|+.+|+-||++.--|..- ...
T Consensus 92 Dy~yd-------~vFsRqv----------eA~g~~GDvLigISTSGNS~nVi~Ai~~Ak~~gm~vI~ltG~~GG~~~~~~ 154 (176)
T COG0279 92 DYGYD-------EVFSRQV----------EALGQPGDVLIGISTSGNSKNVLKAIEAAKEKGMTVIALTGKDGGKLAGLL 154 (176)
T ss_pred CCCHH-------HHHHHHH----------HHCCCCCCEEEEEECCCCCHHHHHHHHHHHHCCCEEEEEECCCCCCCCCCC
T ss_conf 45588-------9999999----------952788878999817999778999999998769879999558875000113
Q ss_pred C--CEEEECC
Q ss_conf 5--2032157
Q gi|254780779|r 198 D--YVIPGND 205 (278)
Q Consensus 198 d--ypIP~ND 205 (278)
| ..||..+
T Consensus 155 D~~i~VPs~~ 164 (176)
T COG0279 155 DVEIRVPSTD 164 (176)
T ss_pred CEEEECCCCC
T ss_conf 1578658886
No 35
>PRK08506 replicative DNA helicase; Provisional
Probab=88.25 E-value=2.4 Score=23.22 Aligned_cols=146 Identities=21% Similarity=0.314 Sum_probs=81.0
Q ss_pred HHHHHHHHHHHHHHHHHHHCCCCEEEEEECCHHHHHHHHHH-HHHCCCEECCCCCCCCCCC--CHHHHHHHHHHHHHHHH
Q ss_conf 89999999999999998610788169960782357999999-8633983142334587323--42666555677899887
Q gi|254780779|r 45 LSQTVPMLQKALQVISDTVARGGRILFVATKSQASDCVMEA-AKRSAQYCVNSKWLGGMMT--NWKTVSQSIQKLRDLEE 121 (278)
Q Consensus 45 L~kT~~~L~~A~~~i~~i~~~gg~ILFVgTk~~~~~~i~~~-A~~~~~~yV~~RWlGG~LT--N~~ti~~si~~l~~l~~ 121 (278)
.-||...|.-|.+. +.+|+.|+|..---...+++..+ |..++.++ +++--|-|| .|..+...+.+|..+.-
T Consensus 204 mGKTAfAlniA~~~----a~~~~~V~~FSLEMs~~ql~~Rlls~~s~V~~--~~lr~g~l~~~e~~~~~~a~~~l~~~~l 277 (473)
T PRK08506 204 MGKTTLVLNMVLKA----LNQGKGVAFFSLEMPAEQLMLRMLSAKTSIPL--QNLRTGDLDDDEWENLSDACDELSQKKL 277 (473)
T ss_pred CCHHHHHHHHHHHH----HHCCCCEEEEECCCCHHHHHHHHHHHHCCCCC--CCCCCCCCCHHHHHHHHHHHHHHHCCCE
T ss_conf 86789999999999----96599658982247999999999997288783--1000689999999999999999865988
Q ss_pred HHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCEEEEEC------CC-C--C-CHHHHH--------HHHCCCE
Q ss_conf 630121267746788766556777643443322113595799943------88-7--7-123212--------3433981
Q gi|254780779|r 122 LLNKENQGFTKKERLNIERKRDKLKRALDGIRDMGGLPDLMFVVD------TN-R--E-KLAIQE--------ARRLRIP 183 (278)
Q Consensus 122 ~~~~~~~~~tkKe~~~~~r~~~kl~k~lgGi~~m~~lP~~iiv~d------~~-~--e-~~Av~E--------A~kl~IP 183 (278)
.. ..-.++|=-+ +.-...|+.+..||+ ++ +|+| +. . + ...|.| |+.|+||
T Consensus 278 ~I-dD~~~lti~~---Ira~~Rr~k~~~~~l-------~l-ivIDYLQLm~~~~~~~~R~~ev~~ISr~LK~lAkEl~vP 345 (473)
T PRK08506 278 FV-YDSGYVNIHQ---VRAQLRKLKSQHPEI-------GL-AVIDYLQLMSGSKNFKDRHLQISEISRGLKLLARELDIP 345 (473)
T ss_pred EE-ECCCCCCHHH---HHHHHHHHHHHCCCC-------CE-EEEEHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCC
T ss_conf 99-8899999999---999999999976998-------78-996367554688875308899999999999999996997
Q ss_pred EEEECCCCCCCHHCCCEEEECCCCH
Q ss_conf 4540367767001152032157726
Q gi|254780779|r 184 IVAVVDTNSNPDLVDYVIPGNDDSS 208 (278)
Q Consensus 184 vIaivDTn~dp~~idypIP~NDds~ 208 (278)
||+++-=|=.++.=.---|---|-+
T Consensus 346 ViaLSQLnR~vE~R~dkrP~lSDLR 370 (473)
T PRK08506 346 IIALSQLNRSLESRADKRPMLSDLR 370 (473)
T ss_pred EEEECCCCCCCCCCCCCCCCCCCCC
T ss_conf 9997036876555789987600113
No 36
>COG0707 MurG UDP-N-acetylglucosamine:LPS N-acetylglucosamine transferase [Cell envelope biogenesis, outer membrane]
Probab=88.20 E-value=2.4 Score=23.20 Aligned_cols=51 Identities=18% Similarity=-0.022 Sum_probs=32.4
Q ss_pred HHHHHHHHHHHHHHHHHHHCCCCEEEEEECCHHHHHHHHHHHHHCCCEECC
Q ss_conf 899999999999999986107881699607823579999998633983142
Q gi|254780779|r 45 LSQTVPMLQKALQVISDTVARGGRILFVATKSQASDCVMEAAKRSAQYCVN 95 (278)
Q Consensus 45 L~kT~~~L~~A~~~i~~i~~~gg~ILFVgTk~~~~~~i~~~A~~~~~~yV~ 95 (278)
+.++...+..+..-...+.++-.--+.+||--..+-..--.|..++.|-+.
T Consensus 69 ~~~~~~~~~~~~~~a~~il~~~kPd~vig~Ggyvs~P~~~Aa~~~~iPv~i 119 (357)
T COG0707 69 LLKAPFKLLKGVLQARKILKKLKPDVVIGTGGYVSGPVGIAAKLLGIPVII 119 (357)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHCCCEEEECCCCCCCHHHHHHHHCCCCEEE
T ss_conf 788699999999999999997099899957986346499998616998799
No 37
>PRK12446 N-acetylglucosaminyl transferase; Reviewed
Probab=87.76 E-value=2.6 Score=23.03 Aligned_cols=28 Identities=7% Similarity=-0.159 Sum_probs=16.5
Q ss_pred CEEEEEECCHHHHHHHHHHHHHCCCEEC
Q ss_conf 8169960782357999999863398314
Q gi|254780779|r 67 GRILFVATKSQASDCVMEAAKRSAQYCV 94 (278)
Q Consensus 67 g~ILFVgTk~~~~~~i~~~A~~~~~~yV 94 (278)
+--+.||+--.++-++--.|...+.|.+
T Consensus 91 kPd~Vig~GGY~S~P~~lAA~ll~iP~~ 118 (352)
T PRK12446 91 KPDVIFSKGGFVSVPVVIGGWLNRVPVL 118 (352)
T ss_pred CCCEEEECCCHHHHHHHHHHHHCCCCEE
T ss_conf 9999997498777999999998599969
No 38
>cd06307 PBP1_uncharacterized_sugar_binding Periplasmic sugar-binding domain of uncharacterized transport systems. Periplasmic sugar-binding domain of uncharacterized transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein (PBP1) superfamily. The members of this group are predicted to be involved in the transport of sugar-containing molecules across cellular and organellar membranes.
Probab=87.51 E-value=2.5 Score=23.07 Aligned_cols=29 Identities=17% Similarity=0.340 Sum_probs=13.5
Q ss_pred CCEEEEECCCCC--CHHHHHHHHCCCEEEEE
Q ss_conf 957999438877--12321234339814540
Q gi|254780779|r 159 PDLMFVVDTNRE--KLAIQEARRLRIPIVAV 187 (278)
Q Consensus 159 P~~iiv~d~~~e--~~Av~EA~kl~IPvIai 187 (278)
+|.+++.-+... .-+|++|..-|||||.+
T Consensus 59 vDgiii~~~d~~~~~~~i~~a~~~GIPVV~~ 89 (275)
T cd06307 59 SDGVALVAPDHPQVRAAVARLAAAGVPVVTL 89 (275)
T ss_pred CCEEEEECCCCHHHHHHHHHHHHCCCEEEEE
T ss_conf 9889998998177899999999879849997
No 39
>PRK02858 germination protease; Provisional
Probab=87.33 E-value=2.7 Score=22.87 Aligned_cols=162 Identities=21% Similarity=0.262 Sum_probs=87.6
Q ss_pred CCCCCCCCCCCCEEEECHHHHHHHHHHHHHHHHHHH-----CCCCEEEEEECCHHHHHHHHHHHHHCCCEECCCCCCCCC
Q ss_conf 856210200188167538999999999999999861-----078816996078235799999986339831423345873
Q gi|254780779|r 28 KMERYIFCERNNTHIIDLSQTVPMLQKALQVISDTV-----ARGGRILFVATKSQASDCVMEAAKRSAQYCVNSKWLGGM 102 (278)
Q Consensus 28 kM~~yI~g~rngihIIdL~kT~~~L~~A~~~i~~i~-----~~gg~ILFVgTk~~~~~~i~~~A~~~~~~yV~~RWlGG~ 102 (278)
.+..||-=+-.++.--|-+.--...+..++.++.+. ....++|.||--.. .|+--=||=.
T Consensus 65 p~G~YITiEap~l~~~D~~~~~~v~~~la~~l~~ll~~~~i~~~~~vLVVGLGN~---------------~vTPDALGP~ 129 (367)
T PRK02858 65 KPGNYLTLEVQGIRQQDTELQQKVERIFAKEFSAFLEELGITKEASCLIVGLGNW---------------NVTPDALGPI 129 (367)
T ss_pred CCCCEEEEECCCCCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCEEEEEECCCC---------------CCCCCCCCHH
T ss_conf 9851799945876656778999999999999999998528998880899967887---------------7786552624
Q ss_pred CCCHHHHHHHHHHHHHHH-HHH----------HCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCEEEEECCC---
Q ss_conf 234266655567789988-763----------012126774678876655677764344332211359579994388---
Q gi|254780779|r 103 MTNWKTVSQSIQKLRDLE-ELL----------NKENQGFTKKERLNIERKRDKLKRALDGIRDMGGLPDLMFVVDTN--- 168 (278)
Q Consensus 103 LTN~~ti~~si~~l~~l~-~~~----------~~~~~~~tkKe~~~~~r~~~kl~k~lgGi~~m~~lP~~iiv~d~~--- 168 (278)
....--+.. +|.++. ... ..+.-+.|-=|...+-+ ||.. +-.||+|+++|.-
T Consensus 130 vv~~l~VTR---HL~~~~p~~~~~g~r~VsaiaPGVmg~TGiET~EIIk----------gIVe-k~kPD~VIaIDALAaR 195 (367)
T PRK02858 130 VVENVLVTR---HLFQLQPESVEEGFRPVSAIAPGVMGITGIETSDIIY----------GIIE-KTKPDFVIAIDALAAR 195 (367)
T ss_pred HHHCEEEEH---HHHHHCCHHHCCCCCEEEEECCCCCCCCCCCHHHHHH----------HHHH-HHCCCEEEEEHHHHCC
T ss_conf 220141134---3655371434057630247757743044403999999----------9987-5089889996031227
Q ss_pred -----------------------CCCHHHHHHHHCCCEEEEECCCCCCCHHCCCEEEECCCCHHHHHHHHHHHHHHHHHH
Q ss_conf -----------------------771232123433981454036776700115203215772689999999999999999
Q gi|254780779|r 169 -----------------------REKLAIQEARRLRIPIVAVVDTNSNPDLVDYVIPGNDDSSRSIALFCDLVASAAIDG 225 (278)
Q Consensus 169 -----------------------~e~~Av~EA~kl~IPvIaivDTn~dp~~idypIP~NDds~~si~l~~~~i~~ai~~g 225 (278)
+...++.| ..|||||||| .=|+.||-+.-+|| +|.+++..+.+...++
T Consensus 196 s~~Rln~TIQIsDTGI~PGSGVGN~R~~i~~-etLGVPVIAI----GVPTVVdAatI~~D----tid~~l~~~~~~~~e~ 266 (367)
T PRK02858 196 SIERVNSTIQISDTGIHPGSGVGNKRKELSK-ETLGIPVIAI----GVPTVVDAVSITSD----TIDFILKHFGREMKEG 266 (367)
T ss_pred CHHHCCCEEEECCCCCCCCCCCCCCCCCCCH-HHCCCCEEEE----CCCCEEEHHHHHHH----HHHHHHHHHHHHHHCC
T ss_conf 5676267578546786888775644442688-7729987996----58817504998899----9999999875543113
Q ss_pred HH
Q ss_conf 99
Q gi|254780779|r 226 IA 227 (278)
Q Consensus 226 ~~ 227 (278)
..
T Consensus 267 ~~ 268 (367)
T PRK02858 267 NK 268 (367)
T ss_pred CC
T ss_conf 56
No 40
>cd01538 PBP1_ABC_xylose_binding Periplasmic xylose-binding component of the ABC-type transport systems that belong to a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein (PBP1) superfamily. Periplasmic xylose-binding component of the ABC-type transport systems that belong to a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein (PBP1) superfamily, which consists of two alpha/beta globular domains connected by a three-stranded hinge. This Venus flytrap-like domain undergoes a transition from an open to a closed conformational state upon ligand binding. Moreover, the periplasmic xylose-binding protein is homologous to the ligand-binding domain of eukaryotic receptors such as glutamate receptor (GluR) and DNA-binding transcriptional repressors such as LacI and GalR.
Probab=86.48 E-value=2.8 Score=22.83 Aligned_cols=40 Identities=20% Similarity=0.334 Sum_probs=17.3
Q ss_pred HHHHHHHHCCCCEEEEEE-CCHHHHHHHHHHHHHCCCEECC
Q ss_conf 999998610788169960-7823579999998633983142
Q gi|254780779|r 56 LQVISDTVARGGRILFVA-TKSQASDCVMEAAKRSAQYCVN 95 (278)
Q Consensus 56 ~~~i~~i~~~gg~ILFVg-Tk~~~~~~i~~~A~~~~~~yV~ 95 (278)
...|..++.++-..++|. +...+....-+.|...|.|.|.
T Consensus 45 ~~~i~~lia~~vD~Iii~p~d~~a~~~~l~~a~~agIPVV~ 85 (288)
T cd01538 45 ISQIENMIAKGVDVLVIAPVDGEALASAVEKAADAGIPVIA 85 (288)
T ss_pred HHHHHHHHHCCCCEEEECCCCHHHHHHHHHHHHHCCCEEEE
T ss_conf 99999999849989998677534439999999975999999
No 41
>cd06302 PBP1_LsrB_Quorum_Sensing Periplasmic binding domain of autoinducer-2 (AI-2) receptor LsrB from Salmonella typhimurium and its close homologs. Periplasmic binding domain of autoinducer-2 (AI-2) receptor LsrB from Salmonella typhimurium and its close homologs from other bacteria. The members of this group are homologous to a family of periplasmic pentose/hexose sugar-binding proteins that function as the primary receptors for chemotaxis and transporters of many sugar based solutes in bacteria and archaea and that are a member of the type I periplasmic binding protein superfamily. LsrB binds a chemically distinct form of the AI-2 signal that lacks boron, in contrast to the Vibrio harveyi AI-2 signaling molecule that has an unusual furanosyl borate diester. Hence, many bacteria coordinate their gene expression according to the local density of their population by producing species specific AI-2. This process of quorum sensing allows LsrB to function as a periplasmic AI-2 binding p
Probab=85.69 E-value=1.2 Score=25.28 Aligned_cols=46 Identities=28% Similarity=0.373 Sum_probs=31.9
Q ss_pred CCCCEEEEECCCCCC--HHHHHHHHCCCEEEEECCCCCCCHHCCCEEEE
Q ss_conf 359579994388771--23212343398145403677670011520321
Q gi|254780779|r 157 GLPDLMFVVDTNREK--LAIQEARRLRIPIVAVVDTNSNPDLVDYVIPG 203 (278)
Q Consensus 157 ~lP~~iiv~d~~~e~--~Av~EA~kl~IPvIaivDTn~dp~~idypIP~ 203 (278)
+-||+|++.-...+. .++++|..-|||||.+ |+..+++..++.+-.
T Consensus 55 ~gvDaIii~p~d~~a~~~~i~~A~~aGIpVv~~-Ds~~~~~~~~~~v~~ 102 (298)
T cd06302 55 QGVDAIAVVPNDPDALEPVLKKAREAGIKVVTH-DSDVQPDNRDYDIEQ 102 (298)
T ss_pred CCCCEEEEECCCHHHHHHHHHHHHHCCCEEEEE-CCCCCCCCEEEEEEC
T ss_conf 399889990687788899999998679869982-687887780599971
No 42
>PRK13396 3-deoxy-7-phosphoheptulonate synthase; Provisional
Probab=85.56 E-value=3.4 Score=22.28 Aligned_cols=145 Identities=14% Similarity=0.275 Sum_probs=85.2
Q ss_pred CHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCEEEECHHHHHHHHHHHHHH--------------HHHHHCCCCEEEEE
Q ss_conf 5899986088607547765788562102001881675389999999999999--------------99861078816996
Q gi|254780779|r 7 TIRQLLESGVQFGHRNFLWNPKMERYIFCERNNTHIIDLSQTVPMLQKALQV--------------ISDTVARGGRILFV 72 (278)
Q Consensus 7 t~~~Ll~ag~H~Gh~~~~wnPkM~~yI~g~rngihIIdL~kT~~~L~~A~~~--------------i~~i~~~gg~ILFV 72 (278)
+-+.+-++|+++- +-.-|-|+..||=|- |.- ++-+..|.+|.+- +.. +.+-..+|-|
T Consensus 120 ~A~~vk~~Ga~~l-RgGa~KPRTsPysFq---GlG----eeGL~~L~~ak~e~GLpvvTEV~~~~~ve~-v~~~~DilQI 190 (352)
T PRK13396 120 TAKRVKAAGAKFL-RGGAYKPRTSPYAFQ---GHG----ESALELLAAAREATGLGIITEVMDAADLDK-IAEVADVIQV 190 (352)
T ss_pred HHHHHHHCCCCEE-CCCCCCCCCCCCCCC---CCC----HHHHHHHHHHHHHHCCCEEEEECCHHHHHH-HHHHCCEEEE
T ss_conf 9999998399878-265024789985435---870----879999999999869972688679999999-9865888998
Q ss_pred ECCHHHHHHHHHHHHHCCCEECCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCC--CCHHHHHHHHHHHHHHHHHHH
Q ss_conf 078235799999986339831423345873234266655567789988763012126--774678876655677764344
Q gi|254780779|r 73 ATKSQASDCVMEAAKRSAQYCVNSKWLGGMMTNWKTVSQSIQKLRDLEELLNKENQG--FTKKERLNIERKRDKLKRALD 150 (278)
Q Consensus 73 gTk~~~~~~i~~~A~~~~~~yV~~RWlGG~LTN~~ti~~si~~l~~l~~~~~~~~~~--~tkKe~~~~~r~~~kl~k~lg 150 (278)
|++.-.+..+.+.+-+++-|-.-.|=+..++--|--. . +.....+... ++-+-...+...+.|..--+.
T Consensus 191 GARn~qNf~LL~~~g~t~kPVllKrg~~~ti~ewl~A---a------Eyi~~~Gn~~viLcERGirtfe~~~~RntlDl~ 261 (352)
T PRK13396 191 GARNMQNFSLLKKVGAQDKPVLLKRGMSATIDEWLMA---A------EYILAAGNPNVILCERGIRTFDRQYTRNTLDLS 261 (352)
T ss_pred CCHHHCCHHHHHHHHCCCCEEEECCCCCCCHHHHHHH---H------HHHHHCCCCCEEEEECCCCCCCCCCCCCCCCHH
T ss_conf 9254059999999854698079737888999999869---9------999976998589994897756676546775578
Q ss_pred HHHHHCCCCCEEEEECCCC
Q ss_conf 3322113595799943887
Q gi|254780779|r 151 GIRDMGGLPDLMFVVDTNR 169 (278)
Q Consensus 151 Gi~~m~~lP~~iiv~d~~~ 169 (278)
.|--|++++.+-+|+||.+
T Consensus 262 aip~~k~~thlPVi~DPSH 280 (352)
T PRK13396 262 VIPVLRSLTHLPIMIDPSH 280 (352)
T ss_pred HHHHHHHCCCCCEEECCCC
T ss_conf 8799974899988978986
No 43
>cd06299 PBP1_LacI_like_13 Ligand-binding domain of DNA-binding regulatory protein from Corynebacterium glutamicum which has a unique ability to produce significant amounts of L-glutamate directly from cheap sugar and ammonia. This group includes the ligand-binding domain of DNA-binding regulatory protein from Corynebacterium glutamicum which has a unique ability to produce significant amounts of L-glutamate directly from cheap sugar and ammonia. This regulatory protein is a member of the LacI-GalR family of bacterial transcription repressors. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial trans
Probab=85.49 E-value=2.6 Score=23.03 Aligned_cols=63 Identities=14% Similarity=0.124 Sum_probs=40.1
Q ss_pred CCCCEEEEECCCCCCHHHHHHHHCCC--E----EEEECCCC----CCCHHCCCEEEECCCCHHHHHHHHHHHH
Q ss_conf 35957999438877123212343398--1----45403677----6700115203215772689999999999
Q gi|254780779|r 157 GLPDLMFVVDTNREKLAIQEARRLRI--P----IVAVVDTN----SNPDLVDYVIPGNDDSSRSIALFCDLVA 219 (278)
Q Consensus 157 ~lP~~iiv~d~~~e~~Av~EA~kl~I--P----vIaivDTn----~dp~~idypIP~NDds~~si~l~~~~i~ 219 (278)
.-|+++|+.+-.--.-+++.+..+|+ | |+|+=|+. +.|.+-+.-.|.-.=+..++++++..+.
T Consensus 174 ~~p~ai~~~nD~~A~g~~~~l~~~g~~vP~dvsvvgfd~~~~~~~~~p~lTTv~~~~~~~g~~A~~~L~~~i~ 246 (265)
T cd06299 174 QGATAIIAGDSMMTIGAIRAIHDAGLVIGEDISLIGFDDLPVFRLQTPPLTVIDQQVEQMGKRAVDMLLSLIA 246 (265)
T ss_pred CCCCEEECCCCHHHHHHHHHHHHHCCCCCCCEEEEEECCHHHHHHCCCCEEEEECCHHHHHHHHHHHHHHHHC
T ss_conf 3998545068588999999999838999993499999975889853998399980999999999999999962
No 44
>cd01575 PBP1_GntR Ligand-binding domain of DNA transcription repressor GntR specific for gluconate, a member of the LacI-GalR family of bacterial transcription regulators. This group represents the ligand-binding domain of DNA transcription repressor GntR specific for gluconate, a member of the LacI-GalR family of bacterial transcription regulators. The ligand-binding domain of GntR is structurally homologous to the periplasmic sugar-binding domain of ABC-type transporters and both domains contain the type I periplasmic binding protein-like fold. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the type I periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding,
Probab=85.49 E-value=3.4 Score=22.26 Aligned_cols=63 Identities=22% Similarity=0.210 Sum_probs=40.5
Q ss_pred CCCCEEEEECCCCCCHHHHHHHHCCCE------EEEECCC----CCCCHHCCCEEEECCCCHHHHHHHHHHHH
Q ss_conf 359579994388771232123433981------4540367----76700115203215772689999999999
Q gi|254780779|r 157 GLPDLMFVVDTNREKLAIQEARRLRIP------IVAVVDT----NSNPDLVDYVIPGNDDSSRSIALFCDLVA 219 (278)
Q Consensus 157 ~lP~~iiv~d~~~e~~Av~EA~kl~IP------vIaivDT----n~dp~~idypIP~NDds~~si~l~~~~i~ 219 (278)
..||++|+.+-.--.-+++.+..+|+. +||+=|+ -.+|..-+.-.|...=+.+++++++..+.
T Consensus 176 ~~~dai~~~nD~~A~g~~~~l~~~g~~iP~disvigfdd~~~~~~~~p~ltti~~~~~~~g~~a~~~l~~~i~ 248 (268)
T cd01575 176 PDLDAVFCSNDDLALGALFECQRRGISVPEDIAIAGFGDLEIAAALPPALTTVRTPRREIGRRAAELLLARLA 248 (268)
T ss_pred CCCCEEEECCHHHHHHHHHHHHHHCCCCCCCEEEEEECCHHHHHCCCCCCEEEEECHHHHHHHHHHHHHHHHC
T ss_conf 9983799878899999999999838999997799998973899616899679996999999999999999976
No 45
>PRK10355 xylF D-xylose transporter subunit XylF; Provisional
Probab=84.98 E-value=1.4 Score=24.79 Aligned_cols=61 Identities=18% Similarity=0.196 Sum_probs=32.0
Q ss_pred CCCEEEEEC--CCCCCHHHHHHHHCCCEEEEECCCCCCCHHCCCEEEECCCCHHHHHHHHHHHHHH
Q ss_conf 595799943--8877123212343398145403677670011520321577268999999999999
Q gi|254780779|r 158 LPDLMFVVD--TNREKLAIQEARRLRIPIVAVVDTNSNPDLVDYVIPGNDDSSRSIALFCDLVASA 221 (278)
Q Consensus 158 lP~~iiv~d--~~~e~~Av~EA~kl~IPvIaivDTn~dp~~idypIP~NDds~~si~l~~~~i~~a 221 (278)
-+|+|+|.- +..=..+|.+|..-|||||.+ |+..+...++|.|-.| ..+.=++....+.+.
T Consensus 81 gvdaIiv~p~D~~al~~~v~~A~~aGIPVI~~-D~~i~~~~~~~~V~~D--n~~~G~~~a~~l~~~ 143 (330)
T PRK10355 81 GVDVLVIIPYNGQVLSNVIKEAKQEGIKVLAY-DRMINNADIDFYISFD--NEKVGELQAKALVDI 143 (330)
T ss_pred CCCEEEEECCCHHHHHHHHHHHHHCCCEEEEE-CCCCCCCCCEEEEEEC--HHHHHHHHHHHHHHH
T ss_conf 99999996998788899999999879949995-7877888811999867--899999999999974
No 46
>cd06277 PBP1_LacI_like_1 Ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. This group includes the ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.
Probab=84.37 E-value=3.8 Score=21.93 Aligned_cols=64 Identities=14% Similarity=0.257 Sum_probs=40.7
Q ss_pred HCCCCCEEEEECCCCCCHHHHHHHHCCC------EEEEECCCC----CCCHHCCCEEEECCCCHHHHHHHHHHH
Q ss_conf 1135957999438877123212343398------145403677----670011520321577268999999999
Q gi|254780779|r 155 MGGLPDLMFVVDTNREKLAIQEARRLRI------PIVAVVDTN----SNPDLVDYVIPGNDDSSRSIALFCDLV 218 (278)
Q Consensus 155 m~~lP~~iiv~d~~~e~~Av~EA~kl~I------PvIaivDTn----~dp~~idypIP~NDds~~si~l~~~~i 218 (278)
+...|+++|+.+-.--.-+++.++.+|+ -+||+=|+. ..|.+-+.-.|...=+..++++++..+
T Consensus 174 ~~~~ptAi~~~nD~~A~g~~~~l~~~g~~vP~Disivgfdd~~~~~~~~P~LTtv~~~~~~~G~~A~~~Ll~~i 247 (268)
T cd06277 174 LKPLPTAFFCSNDGVAFLLIKVLKEMGIRVPEDVSVIGFDDIEYATIFTPPLTTVRVDKEEMGKLAVKRLLEKL 247 (268)
T ss_pred CCCCCCEEEECCHHHHHHHHHHHHHCCCCCCCCCEEEEECCHHHHHHCCCCEEEEEECHHHHHHHHHHHHHHHH
T ss_conf 78899879968859999999999985999998628999788789984489808999299999999999999996
No 47
>PRK00941 acetyl-CoA decarbonylase/synthase complex subunit alpha; Validated
Probab=84.33 E-value=0.84 Score=26.15 Aligned_cols=36 Identities=31% Similarity=0.558 Sum_probs=30.2
Q ss_pred CCCCEEEEECCCCCCHHHHHHHHCCCEEEEECCCCC
Q ss_conf 359579994388771232123433981454036776
Q gi|254780779|r 157 GLPDLMFVVDTNREKLAIQEARRLRIPIVAVVDTNS 192 (278)
Q Consensus 157 ~lP~~iiv~d~~~e~~Av~EA~kl~IPvIaivDTn~ 192 (278)
++||+|++-.+--..-.+.||++++||+||-.|-.|
T Consensus 301 Gi~DViVvDEQCvr~Dileea~k~~~pvIAt~dK~~ 336 (779)
T PRK00941 301 GIPDVIVVDEQCVRTDILEEAKKLGIPVIATNDKIC 336 (779)
T ss_pred CCCCEEEECCCCCCHHHHHHHHHCCCCEEEECHHHH
T ss_conf 699579964532212189999863994898263654
No 48
>PRK05441 murQ N-acetylmuramic acid-6-phosphate etherase; Reviewed
Probab=83.94 E-value=4 Score=21.82 Aligned_cols=155 Identities=14% Similarity=0.271 Sum_probs=94.2
Q ss_pred HHHHHHHHHHHHHHHHHHHCCCCEEEEEECCHHHHHHHHHHHHHCCCEECCCCCCCCCCCC-HHHHHHHHHHHHHHHHHH
Q ss_conf 8999999999999999861078816996078235799999986339831423345873234-266655567789988763
Q gi|254780779|r 45 LSQTVPMLQKALQVISDTVARGGRILFVATKSQASDCVMEAAKRSAQYCVNSKWLGGMMTN-WKTVSQSIQKLRDLEELL 123 (278)
Q Consensus 45 L~kT~~~L~~A~~~i~~i~~~gg~ILFVgTk~~~~~~i~~~A~~~~~~yV~~RWlGG~LTN-~~ti~~si~~l~~l~~~~ 123 (278)
+.+.+..+..|...+..-..+||++.+||.--..+--|...++-..-|-+...++-|.+-- ...+.+++.-- +
T Consensus 37 v~~~lp~I~~~v~~~~~~l~~gGRL~YvGAGTSGRlgvlDa~E~~PTFg~~~~~v~~liAGG~~Al~~~~Ega------E 110 (273)
T PRK05441 37 VEKALPQIAAAVDAIAAALRSGGRLIYIGAGTSGRLGVLDASECPPTFGVPPELVVGLIAGGEKALTKAVEGA------E 110 (273)
T ss_pred HHHHHHHHHHHHHHHHHHHHCCCEEEEECCCHHHHHHHHHHHHCCCCCCCCHHHHEEEEECCHHHHHHCHHCC------C
T ss_conf 9998789999999999999759829997476158899988986487668998991446768899986361102------4
Q ss_pred HCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCC----CCCEEEEECCC----CCCHHHHHHHHCCCEEEEEC-CCCCCC
Q ss_conf 0121267746788766556777643443322113----59579994388----77123212343398145403-677670
Q gi|254780779|r 124 NKENQGFTKKERLNIERKRDKLKRALDGIRDMGG----LPDLMFVVDTN----REKLAIQEARRLRIPIVAVV-DTNSNP 194 (278)
Q Consensus 124 ~~~~~~~tkKe~~~~~r~~~kl~k~lgGi~~m~~----lP~~iiv~d~~----~e~~Av~EA~kl~IPvIaiv-DTn~dp 194 (278)
|.. -.|..++.. --|+||-+-.. +=.-|++.|++.|+++++|+ +.++..
T Consensus 111 D~~----------------------~~g~~dl~~~~~~~~DvvIgIaASG~TPyv~~al~~A~~~ga~ti~I~~n~~s~l 168 (273)
T PRK05441 111 DDA----------------------ELGAADLKAINLTAKDVVVGIAASGRTPYVIGALEYAREIGALTIAISCNPGSPI 168 (273)
T ss_pred CCH----------------------HHHHHHHHHHCCCCCCEEEEEECCCCCHHHHHHHHHHHHCCCCEEEEECCCCCCH
T ss_conf 688----------------------8999999982899657899993688971899999999986995799853896200
Q ss_pred -HHCCCEEEECCC-----------CHHHHHHHHHHHHHHHHHHHH
Q ss_conf -011520321577-----------268999999999999999999
Q gi|254780779|r 195 -DLVDYVIPGNDD-----------SSRSIALFCDLVASAAIDGIA 227 (278)
Q Consensus 195 -~~idypIP~NDd-----------s~~si~l~~~~i~~ai~~g~~ 227 (278)
...|+||-..-- |=-+-++++|.|+..+--...
T Consensus 169 ~~~ad~~I~~~tGpEvitGSTRmKAGTAqK~iLNmiST~~mi~lG 213 (273)
T PRK05441 169 SKEADIAIEVVVGPEVLTGSTRMKAGTAQKLVLNMISTGVMIKLG 213 (273)
T ss_pred HHHCCEEEEECCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHCC
T ss_conf 010681375178843002666545225999999999899999808
No 49
>PTZ00286 6-phospho-1-fructokinase; Provisional
Probab=83.86 E-value=1.2 Score=25.09 Aligned_cols=45 Identities=24% Similarity=0.372 Sum_probs=29.6
Q ss_pred CCEEEEECCCCC---CHHH-HHH--HHCCCEEEEECCCCCCCHHCCCEEEECCCCHH
Q ss_conf 957999438877---1232-123--43398145403677670011520321577268
Q gi|254780779|r 159 PDLMFVVDTNRE---KLAI-QEA--RRLRIPIVAVVDTNSNPDLVDYVIPGNDDSSR 209 (278)
Q Consensus 159 P~~iiv~d~~~e---~~Av-~EA--~kl~IPvIaivDTn~dp~~idypIP~NDds~~ 209 (278)
=|++|++.-..- ..+| .|+ +.++|+|||| |.-||-=||.-|.|.-
T Consensus 188 Id~LfvIGGDGTlrgA~~I~~e~~~Rgl~I~VVGI------PKTIDNDI~~~D~TFG 238 (486)
T PTZ00286 188 INILFTVGGDGTQRGALKIYEEAKRRGENIAVFGV------PKTIDNDLAFSHRTFG 238 (486)
T ss_pred CCEEEEECCCCHHHHHHHHHHHHHHHCCCCEEEEC------CCCCCCCCCCHHCCCC
T ss_conf 99899978846688999999999971788506646------8543576410010024
No 50
>cd06312 PBP1_ABC_sugar_binding_like_4 Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems. Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily, which consists of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis.
Probab=83.73 E-value=4 Score=21.76 Aligned_cols=37 Identities=22% Similarity=0.296 Sum_probs=25.8
Q ss_pred CCCCEEEEEC--CCCCCHHHHHHHHCCCEEEEECCCCCCC
Q ss_conf 3595799943--8877123212343398145403677670
Q gi|254780779|r 157 GLPDLMFVVD--TNREKLAIQEARRLRIPIVAVVDTNSNP 194 (278)
Q Consensus 157 ~lP~~iiv~d--~~~e~~Av~EA~kl~IPvIaivDTn~dp 194 (278)
+-||+|++.- +..-.-++++|...|||||.+ ||+.+.
T Consensus 56 ~~vDaIii~p~~~~~~~~~i~~a~~agIpVv~~-ds~~~~ 94 (271)
T cd06312 56 AKPDGIVVTIPDPDALDPAIKRAVAAGIPVISF-NAGDPK 94 (271)
T ss_pred CCCCEEEEECCCCCHHHHHHHHHHHCCCEEEEE-ECCCCC
T ss_conf 599989993788300269999999659869999-478864
No 51
>cd01139 TroA_f Periplasmic binding protein TroA_f. These proteins are predicted to function as initial receptors in the ABC metal ion uptake in eubacteria and archaea. They belong to the TroA superfamily of helical backbone metal receptor proteins that share a distinct fold and ligand binding mechanism. A typical TroA protein is comprised of two globular subdomains connected by a single helix and can bind their ligands in the cleft between these domains.
Probab=83.72 E-value=1.8 Score=23.99 Aligned_cols=51 Identities=24% Similarity=0.372 Sum_probs=26.9
Q ss_pred CCEEEEE----CCCCCCHHHHHHHHCCCEEEEECCCCCCCHHCCCEEEECCCCHHHHHHHHHHHH
Q ss_conf 9579994----388771232123433981454036776700115203215772689999999999
Q gi|254780779|r 159 PDLMFVV----DTNREKLAIQEARRLRIPIVAVVDTNSNPDLVDYVIPGNDDSSRSIALFCDLVA 219 (278)
Q Consensus 159 P~~iiv~----d~~~e~~Av~EA~kl~IPvIaivDTn~dp~~idypIP~NDds~~si~l~~~~i~ 219 (278)
||+||+. +...+.-++..-.++|||||.+ |.+.+ .-+|..++|.++-.++.
T Consensus 92 PDvVi~~~~~~~~~~~~~~~~~l~~~GIpVv~~-~~~~~---------~~e~~~~~i~~lG~ilg 146 (342)
T cd01139 92 PDLVILNIWAKTTAEESGILEKLEQAGIPVVFV-DFRQK---------PLKNTTPSMRLLGKALG 146 (342)
T ss_pred CCEEEEECCCCCCCCCHHHHHHHHHCCCCEEEE-ECCCC---------HHHHHHHHHHHHHHHHC
T ss_conf 988999443456544567999999719988999-46875---------08889999999999829
No 52
>cd01141 TroA_d Periplasmic binding protein TroA_d. These proteins are predicted to function as initial receptors in the ABC metal ion uptake in eubacteria and archaea. They belong to the TroA superfamily of helical backbone metal receptor proteins that share a distinct fold and ligand binding mechanism. A typical TroA protein is comprised of two globular subdomains connected by a single helix and can bind their ligands in the cleft between these domains.
Probab=83.60 E-value=1.5 Score=24.52 Aligned_cols=31 Identities=23% Similarity=0.465 Sum_probs=24.1
Q ss_pred CCEEEEECCCCCCHHHHHHHHCCCEEEEECC
Q ss_conf 9579994388771232123433981454036
Q gi|254780779|r 159 PDLMFVVDTNREKLAIQEARRLRIPIVAVVD 189 (278)
Q Consensus 159 P~~iiv~d~~~e~~Av~EA~kl~IPvIaivD 189 (278)
||+||..+.....-.+.....+|||++.+-+
T Consensus 70 PDlVi~~~~~~~~~~~~~L~~~gI~v~~~~~ 100 (186)
T cd01141 70 PDLVILYGGFQAQTILDKLEQLGIPVLYVNE 100 (186)
T ss_pred CCEEEEECCCCCHHHHHHHHHCCCCEEEEEC
T ss_conf 9999995887867899999964995799606
No 53
>cd01916 ACS_1 Acetyl-CoA synthase (ACS), also known as acetyl-CoA decarbonylase, is found in acetogenic and methanogenic organisms and is responsible for the synthesis and breakdown of acetyl-CoA. ACS forms a heterotetramer with carbon monoxide dehydrogenase (CODH) consisting of two ACS and two CODH subunits. CODH reduces carbon dioxide to carbon monoxide and ACS then synthesizes acetyl-CoA from carbon monoxide, CoA, and a methyl group donated by another protein (CoFeSP). ACS has three structural domains, an N-terminal rossman fold domain with a helical region at its N-terminus which interacts with CODH, and two alpha + beta fold domains. A Ni-Fe-S center referred to as the A-cluster is located in the C-terminal domain. A large cavity exists between the three domains which may bind CoA.
Probab=82.84 E-value=1 Score=25.55 Aligned_cols=36 Identities=28% Similarity=0.449 Sum_probs=30.0
Q ss_pred CCCCEEEEECCCCCCHHHHHHHHCCCEEEEECCCCC
Q ss_conf 359579994388771232123433981454036776
Q gi|254780779|r 157 GLPDLMFVVDTNREKLAIQEARRLRIPIVAVVDTNS 192 (278)
Q Consensus 157 ~lP~~iiv~d~~~e~~Av~EA~kl~IPvIaivDTn~ 192 (278)
++||+|++-.+--..-.+.||++++||+||-.|-.|
T Consensus 264 Gi~DViVvDEQCir~Dileea~k~~~pvIAt~dK~~ 299 (731)
T cd01916 264 GIADVVVVDEQCIRADILEEAQKLGIPVIATNDKIM 299 (731)
T ss_pred CCCCEEEECCCCCCHHHHHHHHHCCCCEEEECHHHH
T ss_conf 699579964532212189999863994898263654
No 54
>cd06296 PBP1_CatR_like Ligand-binding domain of a LacI-like transcriptional regulator, CatR which is involved in catechol degradation. This group includes the ligand-binding domain of a LacI-like transcriptional regulator, CatR which is involved in catechol degradation. This group belongs to the the LacI-GalR family repressors that are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.
Probab=82.57 E-value=4.5 Score=21.47 Aligned_cols=63 Identities=17% Similarity=0.195 Sum_probs=37.8
Q ss_pred CCCCCEEEEECCCCCCHHHHHHHHCCCE------EEEECCCC----CCCHHCCCEEEECCCCHHHHHHHHHHH
Q ss_conf 1359579994388771232123433981------45403677----670011520321577268999999999
Q gi|254780779|r 156 GGLPDLMFVVDTNREKLAIQEARRLRIP------IVAVVDTN----SNPDLVDYVIPGNDDSSRSIALFCDLV 218 (278)
Q Consensus 156 ~~lP~~iiv~d~~~e~~Av~EA~kl~IP------vIaivDTn----~dp~~idypIP~NDds~~si~l~~~~i 218 (278)
...|+++|+.+-.--.-+++.++.+||. +||+=|+. +.|.+-+.-+|...=+..++++++..+
T Consensus 176 ~~~~~aii~~~D~~A~g~~~~l~~~gi~vP~di~iigfd~~~~~~~~~p~lttI~~~~~~~g~~a~~~ll~~i 248 (270)
T cd06296 176 PERPTAIFAGNDLMALGVYEAARERGLRIPEDLSVVGFDDLPEARWVSPPLTTVRQPLREMGRAAVRLLLRLI 248 (270)
T ss_pred CCCCCCEEECCCHHHHHHHHHHHHCCCCCCCCCEEEEECCHHHHHHCCCCEEEEEECHHHHHHHHHHHHHHHH
T ss_conf 9988620347868999999999986999999887999788789985289838998299999999999999996
No 55
>cd06315 PBP1_ABC_sugar_binding_like_6 Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems. Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily, which consists of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis.
Probab=82.42 E-value=1.2 Score=25.06 Aligned_cols=38 Identities=21% Similarity=0.334 Sum_probs=25.6
Q ss_pred CCCCEEEEE--CCCCCCHHHHHHHHCCCEEEEECCCCCCCH
Q ss_conf 359579994--388771232123433981454036776700
Q gi|254780779|r 157 GLPDLMFVV--DTNREKLAIQEARRLRIPIVAVVDTNSNPD 195 (278)
Q Consensus 157 ~lP~~iiv~--d~~~e~~Av~EA~kl~IPvIaivDTn~dp~ 195 (278)
..||+|++. |+..-..++++|++.|||+|+. +...+|.
T Consensus 55 ~k~D~Iii~~~D~~~~~~~l~~A~~agIPvv~~-~~~~~pg 94 (280)
T cd06315 55 LKPDGIVLGGVDAAELQAELELAQKAGIPVVGW-HAGPEPG 94 (280)
T ss_pred CCCCEEEECCCCHHHHHHHHHHHHHCCCCEEEE-CCCCCCC
T ss_conf 399999999829788789999999879978962-4778899
No 56
>PRK13609 diacylglycerol glucosyltransferase; Provisional
Probab=82.13 E-value=4.7 Score=21.37 Aligned_cols=49 Identities=18% Similarity=0.204 Sum_probs=28.2
Q ss_pred CCCEEEEECCCCCCHHHHHHHHCCCEEEEECCCCCCC------HHCCCEEEECCCC
Q ss_conf 5957999438877123212343398145403677670------0115203215772
Q gi|254780779|r 158 LPDLMFVVDTNREKLAIQEARRLRIPIVAVVDTNSNP------DLVDYVIPGNDDS 207 (278)
Q Consensus 158 lP~~iiv~d~~~e~~Av~EA~kl~IPvIaivDTn~dp------~~idypIP~NDds 207 (278)
.||+||.+-|..--..+++...+.+|++.++ ||-.+ ..+|+.+-++++.
T Consensus 104 kPDvII~T~P~~~l~~lk~~~~~~iP~~tVi-TD~~~H~~Wi~~~~D~y~Vase~~ 158 (388)
T PRK13609 104 KPDIVINTFPIIAVPELKKQTGISIPVYNVL-TDFCVHKIWIHREVDRYFVATDHV 158 (388)
T ss_pred CCCEEEECCCHHHHHHHHHHCCCCCCEEEEE-CCCCCHHHHCCCCCCEEEECCHHH
T ss_conf 9599998887899999998459999889994-785204645578999799398999
No 57
>cd06308 PBP1_sensor_kinase_like Periplasmic binding domain of two-component sensor kinase signaling systems. Periplasmic binding domain of two-component sensor kinase signaling systems, some of which are fused with a C-terminal histidine kinase A domain (HisK) and/or a signal receiver domain (REC). Members of this group share homology with a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily and are predicted to be involved in sensing of environmental stimuli; their substrate specificities, however, are not known in detail.
Probab=81.99 E-value=2.3 Score=23.28 Aligned_cols=39 Identities=18% Similarity=0.235 Sum_probs=14.6
Q ss_pred HHHHHHHCCCCEEEEEECC-HHHHHHHHHHHHHCCCEECC
Q ss_conf 9999861078816996078-23579999998633983142
Q gi|254780779|r 57 QVISDTVARGGRILFVATK-SQASDCVMEAAKRSAQYCVN 95 (278)
Q Consensus 57 ~~i~~i~~~gg~ILFVgTk-~~~~~~i~~~A~~~~~~yV~ 95 (278)
..|..+..++=..|+|... ..+....-+.|...|.|.|.
T Consensus 47 ~~ie~li~~~vD~iiv~p~d~~~~~~~l~~a~~agIPVV~ 86 (270)
T cd06308 47 ADIENFIRQGVDLLIISPNEAAPLTPVVEEAYRAGIPVIL 86 (270)
T ss_pred HHHHHHHHCCCCEEEEECCCCCHHHHHHHHHHHCCCCEEE
T ss_conf 9999999849999999648852008999999985991999
No 58
>cd06322 PBP1_ABC_sugar_binding_like_12 Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems. This group includes the periplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily, which consist of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis.
Probab=81.27 E-value=2 Score=23.75 Aligned_cols=31 Identities=16% Similarity=0.204 Sum_probs=13.7
Q ss_pred CCEEEEECCCCCCHHH---HHHHHCCCEEEEECC
Q ss_conf 9579994388771232---123433981454036
Q gi|254780779|r 159 PDLMFVVDTNREKLAI---QEARRLRIPIVAVVD 189 (278)
Q Consensus 159 P~~iiv~d~~~e~~Av---~EA~kl~IPvIaivD 189 (278)
|++||..+-.--.-|+ +++.+-.|.++|+=|
T Consensus 180 ~~aI~~~nD~~A~Ga~~al~~~g~~di~vvGfD~ 213 (267)
T cd06322 180 LDGIFAFGDDAALGAVSAIKAAGRDNVKVIGFDG 213 (267)
T ss_pred CCEEEECCCHHHHHHHHHHHHCCCCCCEEEEECC
T ss_conf 7489981879999999999975999988999949
No 59
>cd06300 PBP1_ABC_sugar_binding_like_1 Periplasmic sugar-binding component of uncharacterized ABC-type transport systems that are members of the pentose/hexose sugar-binding protein family of the type I periplasmic binding protein superfamily. Periplasmic sugar-binding component of uncharacterized ABC-type transport systems that are members of the pentose/hexose sugar-binding protein family of the type I periplasmic binding protein superfamily, which consists of two alpha/beta globular domains connected by a three-stranded hinge. This Venus flytrap-like domain undergoes transition from an open to a closed conformational state upon ligand binding. Members of this group are predicted to be involved in the transport of sugar-containing molecules across cellular and organellar membranes; however their substrate specificity is not known in detail.
Probab=80.66 E-value=5.1 Score=21.09 Aligned_cols=35 Identities=20% Similarity=0.249 Sum_probs=13.7
Q ss_pred HHHHCCCCEEEEEEC-CHHHHHHHHHHHHHCCCEEC
Q ss_conf 986107881699607-82357999999863398314
Q gi|254780779|r 60 SDTVARGGRILFVAT-KSQASDCVMEAAKRSAQYCV 94 (278)
Q Consensus 60 ~~i~~~gg~ILFVgT-k~~~~~~i~~~A~~~~~~yV 94 (278)
..++.+|=..++|.. ...+....-+.|...|.|-|
T Consensus 54 e~~I~qgvD~Iiv~p~d~~a~~~~l~~A~~aGIpVV 89 (272)
T cd06300 54 RNLIAQGVDAIIINPASPTALNPVIEEACEAGIPVV 89 (272)
T ss_pred HHHHHCCCCEEEEECCCHHHHHHHHHHHHHCCCEEE
T ss_conf 999985999999978976788999999998599699
No 60
>cd06313 PBP1_ABC_sugar_binding_like_5 Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems. Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily, which consists of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis.
Probab=80.36 E-value=4.4 Score=21.54 Aligned_cols=14 Identities=7% Similarity=-0.043 Sum_probs=5.6
Q ss_pred HHHHHHHHCCCEEC
Q ss_conf 99999863398314
Q gi|254780779|r 81 CVMEAAKRSAQYCV 94 (278)
Q Consensus 81 ~i~~~A~~~~~~yV 94 (278)
..-+.|...|.|.|
T Consensus 71 ~~~~~A~~aGIpVV 84 (272)
T cd06313 71 EAVQKAIARGIPVI 84 (272)
T ss_pred HHHHHHHHCCCEEE
T ss_conf 99999998699899
No 61
>cd01539 PBP1_GGBP Periplasmic glucose/galactose-binding protein (GGBP) involved in chemotaxis towards, and active transport of, glucose and galactose in various bacterial species. Periplasmic glucose/galactose-binding protein (GGBP) involved in chemotaxis towards, and active transport of, glucose and galactose in various bacterial species. GGBP is a member of the pentose/hexose sugar-binding protein family of the type I periplasmic binding protein superfamily which consists of two alpha/beta globular domains connected by a three-stranded hinge. This Venus flytrap-like domain undergoes transition from an open to a closed conformational state upon ligand binding. Moreover, the periplasmic GGBP is homologous to the ligand-binding domain of eukaryotic receptors such as glutamate receptor (GluR) and DNA-binding transcriptional repressors such as LacI and GalR.
Probab=80.36 E-value=1.9 Score=23.95 Aligned_cols=13 Identities=31% Similarity=0.733 Sum_probs=4.8
Q ss_pred HHHHHHHCCCEEE
Q ss_conf 3212343398145
Q gi|254780779|r 173 AIQEARRLRIPIV 185 (278)
Q Consensus 173 Av~EA~kl~IPvI 185 (278)
+|++|..-|||||
T Consensus 74 ~i~~A~~agIPVI 86 (303)
T cd01539 74 VINKAKQKNIPVI 86 (303)
T ss_pred HHHHHHHCCCEEE
T ss_conf 9999996698499
No 62
>cd06278 PBP1_LacI_like_2 Ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. This group includes the ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.
Probab=80.19 E-value=3.5 Score=22.18 Aligned_cols=62 Identities=16% Similarity=0.224 Sum_probs=37.8
Q ss_pred CCCCEEEEECCCCCCHHHHHHH-HCC--CE----EEEECCCC----CCCHHCCCEEEECCCCHHHHHHHHHHH
Q ss_conf 3595799943887712321234-339--81----45403677----670011520321577268999999999
Q gi|254780779|r 157 GLPDLMFVVDTNREKLAIQEAR-RLR--IP----IVAVVDTN----SNPDLVDYVIPGNDDSSRSIALFCDLV 218 (278)
Q Consensus 157 ~lP~~iiv~d~~~e~~Av~EA~-kl~--IP----vIaivDTn----~dp~~idypIP~NDds~~si~l~~~~i 218 (278)
..|+++|+.+-.--.-+++.++ ++| || |||+=|+. +.|.+-+.-.|...=+..++++++..+
T Consensus 173 ~~ptAi~~~nD~~A~g~l~~l~~~~g~~vP~disvvgfD~~~~~~~~~p~LTtv~~~~~~~g~~A~~~Ll~~i 245 (266)
T cd06278 173 PRPDAIFCANDLLAIGVMDAARQEGGLRVPEDVSVIGFDDIPMAAWPSYQLTTVRQPVDRMAEEAVDLLEARI 245 (266)
T ss_pred CCCCCCEECCHHHHHHHHHHHHHHCCCCCCCCEEEEEECCHHHHHCCCCCEEEEECCHHHHHHHHHHHHHHHH
T ss_conf 9988625077899999999999735888888669998788089854499848998399999999999999997
No 63
>cd01544 PBP1_GalR Ligand-binding domain of DNA transcription repressor GalR which is one of two regulatory proteins involved in galactose transport and metabolism. Ligand-binding domain of DNA transcription repressor GalR which is one of two regulatory proteins involved in galactose transport and metabolism. Transcription of the galactose regulon genes is regulated by Gal iso-repressor (GalS) and Gal repressor (GalR) in different ways, but both repressors recognize the same DNA binding site in the absence of D-galactose. GalR is a dimeric protein like GalS and is exclusively involved in the regulation of galactose permease, the low-affinity galactose transporter. GalS is involved in regulating expression of the high-affinity galactose transporter encoded by the mgl operon. GalS and GalR are members of the LacI-GalR family of transcription regulators and both contain the type I periplasmic binding protein-like fold. Hence, they are structurally homologous to the periplasmic sugar bindi
Probab=80.12 E-value=5.4 Score=20.93 Aligned_cols=63 Identities=16% Similarity=0.293 Sum_probs=46.9
Q ss_pred CCCCCEEEEECCCCCCHHHHHHHHCCCE------EEEECCCC----CCCHHCCCEEEECCCCHHHHHHHHHHH
Q ss_conf 1359579994388771232123433981------45403677----670011520321577268999999999
Q gi|254780779|r 156 GGLPDLMFVVDTNREKLAIQEARRLRIP------IVAVVDTN----SNPDLVDYVIPGNDDSSRSIALFCDLV 218 (278)
Q Consensus 156 ~~lP~~iiv~d~~~e~~Av~EA~kl~IP------vIaivDTn----~dp~~idypIP~NDds~~si~l~~~~i 218 (278)
...|+++|+.+-.--.-+++.|+.+|+. |||+=|+. +.|.+-+.-.|...=+.+++.+++..+
T Consensus 177 ~~~ptAi~~~nD~~A~g~l~~l~~~gl~VP~DisviGfDd~~~~~~~~P~LTTV~q~~~~iG~~A~~~Ll~~i 249 (270)
T cd01544 177 DNLPTAFFIASDPMAIGALRALQEAGIKVPEDVSVISFNDIEVAKYVSPPLSTVKIDTEEMGETAVDLLLERI 249 (270)
T ss_pred CCCCCEEEECCCHHHHHHHHHHHHCCCCCCCCEEEEEECCHHHHHHCCCCCEEEECCHHHHHHHHHHHHHHHH
T ss_conf 7899789982318899999999987998877659999778078982689936998299999999999999996
No 64
>cd06310 PBP1_ABC_sugar_binding_like_2 Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems. Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily, which consists of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis.
Probab=80.01 E-value=2.7 Score=22.89 Aligned_cols=39 Identities=15% Similarity=0.346 Sum_probs=15.9
Q ss_pred CCEEEEECCCCC---CHHHHHHHHCC-CEEEEECCCCCCCHHCCCE
Q ss_conf 957999438877---12321234339-8145403677670011520
Q gi|254780779|r 159 PDLMFVVDTNRE---KLAIQEARRLR-IPIVAVVDTNSNPDLVDYV 200 (278)
Q Consensus 159 P~~iiv~d~~~e---~~Av~EA~kl~-IPvIaivDTn~dp~~idyp 200 (278)
+++||..+-.-- ..|++++.+-+ |.++|+ |++|..+++.
T Consensus 184 i~ai~~~nd~~a~ga~~al~~~g~~~~i~vvg~---D~~~~~~~~i 226 (273)
T cd06310 184 LKGIFGANEGSAVGAARAVRQAGKAGKVKVVGF---DASPEQIDAL 226 (273)
T ss_pred CCEEEECCCHHHHHHHHHHHHCCCCCCEEEEEE---CCCHHHHHHH
T ss_conf 757984384899999999997799999399998---9869999999
No 65
>PRK06830 diphosphate--fructose-6-phosphate 1-phosphotransferase; Provisional
Probab=79.98 E-value=0.98 Score=25.73 Aligned_cols=44 Identities=30% Similarity=0.450 Sum_probs=28.8
Q ss_pred CCEEEEECCCCCC---HHHH-HH--HHCCCEEEEECCCCCCCHHCCCEEEECCCCH
Q ss_conf 9579994388771---2321-23--4339814540367767001152032157726
Q gi|254780779|r 159 PDLMFVVDTNREK---LAIQ-EA--RRLRIPIVAVVDTNSNPDLVDYVIPGNDDSS 208 (278)
Q Consensus 159 P~~iiv~d~~~e~---~Av~-EA--~kl~IPvIaivDTn~dp~~idypIP~NDds~ 208 (278)
=|++|++.-..-. .+|. |+ +.|+|+|||| |.-||--||+-|-|.
T Consensus 172 id~L~~IGGDGTl~gA~~i~~e~~~rgl~I~VvGI------PKTIDNDi~~~d~sf 221 (442)
T PRK06830 172 INILFVIGGDGTLKGALKIAEEIARRNLKISVVGI------PKTIDNDINFIQKSF 221 (442)
T ss_pred CCEEEEECCCHHHHHHHHHHHHHHHCCCCCEEEEC------CCCCCCCCCCCCCEE
T ss_conf 99899948802789999999999963899407745------643347754303131
No 66
>PRK12570 N-acetylmuramic acid-6-phosphate etherase; Reviewed
Probab=79.70 E-value=5.6 Score=20.84 Aligned_cols=160 Identities=16% Similarity=0.297 Sum_probs=95.0
Q ss_pred ECHHHHHHHHHHHHHHHHHHHCCCCEEEEEECCHHHHHHHHHHHHHCCCEECCCCCCCCCC-CCHHHHHHHHHHHHHHHH
Q ss_conf 5389999999999999998610788169960782357999999863398314233458732-342666555677899887
Q gi|254780779|r 43 IDLSQTVPMLQKALQVISDTVARGGRILFVATKSQASDCVMEAAKRSAQYCVNSKWLGGMM-TNWKTVSQSIQKLRDLEE 121 (278)
Q Consensus 43 IdL~kT~~~L~~A~~~i~~i~~~gg~ILFVgTk~~~~~~i~~~A~~~~~~yV~~RWlGG~L-TN~~ti~~si~~l~~l~~ 121 (278)
.-+.+.+..+..|...+.....+||++.+||.--...--+...++-..-|-+....+-|.+ --|..+.+++.--.+-.+
T Consensus 35 ~Av~~~l~~I~~av~~~~~~l~~gGRL~YvGAGTSGRlgvlDa~E~~PTfg~~~~~v~~liAGG~~Al~~~vEgaED~~~ 114 (296)
T PRK12570 35 LAVEKVLPQIAQAVDKIVAAFKQGGRLIYMGAGTSGRLGVLDASECPPTFSVSPEMVIGLIAGGPDAMLTAIEGAEDDPE 114 (296)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHCCCEEEEECCCHHHHHHHHHHHHCCCCCCCCHHHEEEEEECCHHHHHHHHCCCCCCHH
T ss_conf 99999999999999999999965983999778705899999998727865899899676763889998640302666699
Q ss_pred HHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCEEEEEC----CCCCCHHHHHHHHCCCEEEEECCCCCCC--H
Q ss_conf 630121267746788766556777643443322113595799943----8877123212343398145403677670--0
Q gi|254780779|r 122 LLNKENQGFTKKERLNIERKRDKLKRALDGIRDMGGLPDLMFVVD----TNREKLAIQEARRLRIPIVAVVDTNSNP--D 195 (278)
Q Consensus 122 ~~~~~~~~~tkKe~~~~~r~~~kl~k~lgGi~~m~~lP~~iiv~d----~~~e~~Av~EA~kl~IPvIaivDTn~dp--~ 195 (278)
.-.+ +..++ ++ + --|+|+-+- +..-.-|++.|+++|.++|+++.....| .
T Consensus 115 --------~g~~-------dl~~~-----~~---~-~~DvVIgiaASG~TPyv~~al~~A~~~Ga~ti~i~~n~~s~l~~ 170 (296)
T PRK12570 115 --------LGAQ-------DLKAI-----GL---T-SDDVVVGIAASGRTPYVIGALEYAKQIGATTVALSCNPDSPIAQ 170 (296)
T ss_pred --------HHHH-------HHHHC-----CC---C-CCCEEEEEECCCCCHHHHHHHHHHHHCCCCEEEEECCCCHHHHH
T ss_conf --------9999-------99980-----89---9-54479998468885149999999998599679862488324566
Q ss_pred HCCCEEEECC-----------CCHHHHHHHHHHHHHHHHHHH
Q ss_conf 1152032157-----------726899999999999999999
Q gi|254780779|r 196 LVDYVIPGND-----------DSSRSIALFCDLVASAAIDGI 226 (278)
Q Consensus 196 ~idypIP~ND-----------ds~~si~l~~~~i~~ai~~g~ 226 (278)
..|+||-..- .|--+-++++|.|+..+--..
T Consensus 171 ~ad~~I~~~tGpEvi~GSTRmKAGTAqK~vLNmiST~~mi~l 212 (296)
T PRK12570 171 LADIAISPVVGPEVLTGSTRLKSGTAQKMVLNMLSTASMIRL 212 (296)
T ss_pred HCCEEEECCCCCHHHHCCCCCCCHHHHHHHHHHHHHHHHHHC
T ss_conf 267525407880676367542105699999999889999981
No 67
>PRK05724 acetyl-CoA carboxylase carboxyltransferase subunit alpha; Validated
Probab=78.67 E-value=3.7 Score=22.00 Aligned_cols=20 Identities=30% Similarity=0.625 Sum_probs=15.1
Q ss_pred HHHHHHHCCCEEEEECCCCC
Q ss_conf 32123433981454036776
Q gi|254780779|r 173 AIQEARRLRIPIVAVVDTNS 192 (278)
Q Consensus 173 Av~EA~kl~IPvIaivDTn~ 192 (278)
..+-|.|.++|||.++||-.
T Consensus 142 lm~lAekf~~Pvit~IDTpG 161 (318)
T PRK05724 142 LMEMAERFGLPIITFIDTPG 161 (318)
T ss_pred HHHHHHHCCCCEEEEECCCC
T ss_conf 99999970997799934897
No 68
>cd06295 PBP1_CelR Ligand binding domain of a transcription regulator of cellulose genes, CelR, which is highly homologous to the LacI-GalR family of bacterial transcription regulators. This group includes the ligand binding domain of a transcription regulator of cellulose genes, CelR, which is highly homologous to the LacI-GalR family of bacterial transcription regulators. The binding of CelR to the celE promoter is inhibited specifically by cellobiose. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn chang
Probab=78.44 E-value=4.2 Score=21.63 Aligned_cols=63 Identities=17% Similarity=0.131 Sum_probs=42.7
Q ss_pred CCCCEEEEECCCCCCHHHHHHHHCCCE------EEEECCCC----CCCHHCCCEEEECCCCHHHHHHHHHHHH
Q ss_conf 359579994388771232123433981------45403677----6700115203215772689999999999
Q gi|254780779|r 157 GLPDLMFVVDTNREKLAIQEARRLRIP------IVAVVDTN----SNPDLVDYVIPGNDDSSRSIALFCDLVA 219 (278)
Q Consensus 157 ~lP~~iiv~d~~~e~~Av~EA~kl~IP------vIaivDTn----~dp~~idypIP~NDds~~si~l~~~~i~ 219 (278)
..|++||+.+-.-=.-+++.|+++||- ++|+-|+. .+|.+-+.-+|.-.=+..++++++..+.
T Consensus 185 ~~~~ai~~~nD~~A~g~~~~~~~~g~~iP~disIigfd~~~~~~~~~P~LTtI~~~~~~ig~~A~~~Ll~~i~ 257 (275)
T cd06295 185 PDFDAVFAASDLMALGALRALREAGRRVPEDVAVVGFDDIPLAAYADPPLTTVRQDIEEAGRLLVDLLLALIA 257 (275)
T ss_pred CCCCEEEECCCHHHHHHHHHHHHCCCCCCCCEEEEEECCHHHHHHCCCCEEEEEECHHHHHHHHHHHHHHHHC
T ss_conf 9987034147587899999999749998985699996786899834898699980999999999999999967
No 69
>COG1609 PurR Transcriptional regulators [Transcription]
Probab=78.05 E-value=6.3 Score=20.52 Aligned_cols=61 Identities=18% Similarity=0.282 Sum_probs=40.7
Q ss_pred CCEEEEECCCCCCHHHHHHHHCCCE------EEEECCCC----CCCHHCCCEEEECCCCHHHHHHHHHHHH
Q ss_conf 9579994388771232123433981------45403677----6700115203215772689999999999
Q gi|254780779|r 159 PDLMFVVDTNREKLAIQEARRLRIP------IVAVVDTN----SNPDLVDYVIPGNDDSSRSIALFCDLVA 219 (278)
Q Consensus 159 P~~iiv~d~~~e~~Av~EA~kl~IP------vIaivDTn----~dp~~idypIP~NDds~~si~l~~~~i~ 219 (278)
|++||+.+-.--.-++++|..+||. |||+=|+. ..|.+-+.-+|--.=+.+++++++..+.
T Consensus 238 ptAif~~nD~~Alg~l~~~~~~g~~vP~disviGfDd~~~~~~~~P~LTTv~~~~~~~G~~A~~~Ll~~i~ 308 (333)
T COG1609 238 PTAIFCANDLMALGALRALRELGLRVPEDLSVIGFDDIELARFLTPPLTTVRQPIEELGRRAAELLLERIN 308 (333)
T ss_pred CCEEEECCCHHHHHHHHHHHHCCCCCCCCEEEEEECCHHHHHHCCCCEEEEECCHHHHHHHHHHHHHHHHH
T ss_conf 97899878099999999999808999987899998884776515898069950999999999999998743
No 70
>cd06274 PBP1_FruR Ligand binding domain of DNA transcription repressor specific for fructose (FruR) and its close homologs. Ligand binding domain of DNA transcription repressor specific for fructose (FruR) and its close homologs, all of which are a member of the LacI-GalR family of bacterial transcription regulators. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to members of the type I periplasmic binding protein superfamily. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor
Probab=78.05 E-value=3.8 Score=21.92 Aligned_cols=63 Identities=14% Similarity=0.066 Sum_probs=40.6
Q ss_pred CCCCCEEEEECCCCCCHHHHHHHHCCC--E----EEEECCCC----CCCHHCCCEEEECCCCHHHHHHHHHHH
Q ss_conf 135957999438877123212343398--1----45403677----670011520321577268999999999
Q gi|254780779|r 156 GGLPDLMFVVDTNREKLAIQEARRLRI--P----IVAVVDTN----SNPDLVDYVIPGNDDSSRSIALFCDLV 218 (278)
Q Consensus 156 ~~lP~~iiv~d~~~e~~Av~EA~kl~I--P----vIaivDTn----~dp~~idypIP~NDds~~si~l~~~~i 218 (278)
.+.|+++|+.+-.-=.-+++.++.+|+ | |+|+=|+. ..|.+-+.-.|...=+.+++++++..|
T Consensus 176 ~~~p~ai~~~nd~~a~g~l~~l~~~g~~vP~disvvgfDd~~~a~~~~p~LTtv~q~~~~~g~~A~~lLl~~i 248 (264)
T cd06274 176 GRLPRALFTTSYTLLEGVLRFLRERPGLAPSDLRIATFDDHPLLDFLPFPVHSVPQDHEALAEAAFELALAAL 248 (264)
T ss_pred CCCCCCCCCCCHHHHHHHHHHHHHCCCCCCCCEEEEEECCHHHHHHCCCCCEEEECCHHHHHHHHHHHHHHHH
T ss_conf 6887422017699999999999985999999879999898689973799976996799999999999999986
No 71
>cd06318 PBP1_ABC_sugar_binding_like_9 Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems. Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily, which consists of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis.
Probab=77.76 E-value=2.5 Score=23.11 Aligned_cols=36 Identities=22% Similarity=0.306 Sum_probs=12.8
Q ss_pred HHHHHCCCCEEEEEEC-CHHHHHHHHHHHHHCCCEEC
Q ss_conf 9986107881699607-82357999999863398314
Q gi|254780779|r 59 ISDTVARGGRILFVAT-KSQASDCVMEAAKRSAQYCV 94 (278)
Q Consensus 59 i~~i~~~gg~ILFVgT-k~~~~~~i~~~A~~~~~~yV 94 (278)
|..++.+|-..++|.. ...+...+-+.|...|.|.|
T Consensus 48 i~~~i~~~vd~iii~~~d~~~~~~~~~~a~~aGIPVv 84 (282)
T cd06318 48 VEDLLTRGVNVLIINPVDPEGLVPAVAAAKAAGVPVV 84 (282)
T ss_pred HHHHHHCCCCEEEEECCCHHHHHHHHHHHHHCCCCEE
T ss_conf 9999976998799811680566999999997799889
No 72
>TIGR03590 PseG pseudaminic acid biosynthesis-associated protein PseG. This protein is found in association with enzymes involved in the biosynthesis of pseudaminic acid, a component of polysaccharide in certain Pseudomonas strains as well as a modification of flagellin in Campylobacter and Hellicobacter. The role of this protein is unclear, although it may participate in N-acetylation in conjunction with, or in the absence of PseH (TIGR03585) as it often scores above the trusted cutoff to pfam00583 representing a family of acetyltransferases.
Probab=77.63 E-value=6.5 Score=20.44 Aligned_cols=47 Identities=13% Similarity=0.135 Sum_probs=31.6
Q ss_pred CCEEEEECCCCCCHHHHHHHHCCCEEEEECCCCCCCHHCCCEEEECC
Q ss_conf 95799943887712321234339814540367767001152032157
Q gi|254780779|r 159 PDLMFVVDTNREKLAIQEARRLRIPIVAVVDTNSNPDLVDYVIPGND 205 (278)
Q Consensus 159 P~~iiv~d~~~e~~Av~EA~kl~IPvIaivDTn~dp~~idypIP~ND 205 (278)
||.+++=+-.-+..-.+..+..+++++.+-|.+.-|...|+.|..|-
T Consensus 82 ~d~vIiD~y~~~~~~~~~lk~~~~~~i~iDD~~~~~~~~d~vin~~~ 128 (280)
T TIGR03590 82 FDILIVDHYALDADWEKLIKHFGRKLLVIDDLADRPHDCDLLLDQNP 128 (280)
T ss_pred CCEEEEECCCCCHHHHHHHHHHCCEEEEEECCCCCCCCCCEEECCCC
T ss_conf 79999925999979999999839839999367654656142541454
No 73
>cd00764 Eukaryotic_PFK Phosphofructokinase, a key regulatory enzyme in glycolysis, catalyzes the phosphorylation of fructose-6-phosphate to fructose-1,6-biphosphate. The members belong to a subfamily of the PFKA family (cd00363) and include eukaryotic ATP-dependent phosphofructokinases. These have evolved from the bacterial PFKs by gene duplication and fusion events and exhibit complex allosteric behavior.
Probab=77.58 E-value=6.5 Score=20.44 Aligned_cols=174 Identities=16% Similarity=0.154 Sum_probs=87.1
Q ss_pred CCCCCCCCCCCC-CCEEEECHHHHHHHHHHHHHHHH-----------------------HHH---------CCCCE--EE
Q ss_conf 788562102001-88167538999999999999999-----------------------861---------07881--69
Q gi|254780779|r 26 NPKMERYIFCER-NNTHIIDLSQTVPMLQKALQVIS-----------------------DTV---------ARGGR--IL 70 (278)
Q Consensus 26 nPkM~~yI~g~r-ngihIIdL~kT~~~L~~A~~~i~-----------------------~i~---------~~gg~--IL 70 (278)
.|...+++.+.+ |.+.=..|-+.+..-+...+.+. .++ ...-+ ||
T Consensus 316 tp~t~~~~i~~~~n~i~r~pL~e~V~~t~~v~~a~~~k~f~~a~~lr~~~F~~~~~~~~~~~~~~~~~~~~~~~~rIaIl 395 (762)
T cd00764 316 TPDTPACVVSLNGNKAVRLPLMECVQLTKDVQKAMDEKRFDEAAALRGKSFDKNWNLYKLLAIELPQPLPEKTNLNIAIV 395 (762)
T ss_pred CCCCCCCEEEECCCEEEECCHHHHHHHHHHHHHHHHCCCHHHHHHHCCHHHHHHHHHHHHHCCCCCCCCCCCCCCEEEEE
T ss_conf 99998857996177568532899999999999999722789999743777899999999860347777886677069998
Q ss_pred EEECCH----HHHHHHHHHHHHCCC-EECCCCCCCCCCCCHHHHHHHHHHHHH--HHHHH-HCC-C----CCCCHHHHHH
Q ss_conf 960782----357999999863398-314233458732342666555677899--88763-012-1----2677467887
Q gi|254780779|r 71 FVATKS----QASDCVMEAAKRSAQ-YCVNSKWLGGMMTNWKTVSQSIQKLRD--LEELL-NKE-N----QGFTKKERLN 137 (278)
Q Consensus 71 FVgTk~----~~~~~i~~~A~~~~~-~yV~~RWlGG~LTN~~ti~~si~~l~~--l~~~~-~~~-~----~~~tkKe~~~ 137 (278)
-+|--- .+-+.+-.+|..-|. +|--++=..|++.+ .+..|.. ...+. .|+ + ..++++..
T Consensus 396 t~GgdapGMNAAiRA~Vr~~~~~G~~v~gI~~Gf~GL~~g------~i~~l~~~~V~g~~~~GGt~LgT~R~~p~~~~-- 467 (762)
T cd00764 396 NVGAPAAGMNAAVRSAVRYGLAHGHRPYAIYDGFEGLAKG------QIVELGWIDVGGWTGRGGSELGTKRTLPKKDL-- 467 (762)
T ss_pred CCCCCCHHHHHHHHHHHHHHHHCCCEEEEEECCHHHHHCC------CEEECCHHHHCCHHHCCCEEECCCCCCCCCCH--
T ss_conf 5688961477999999999998899999992584367479------86777845638866468803265788973449--
Q ss_pred HHHHHHHHHHHHHHHHHHCCCCCEEEEECCCCCCHH---HHHHH----HCCCEEEEECCCCCCCHHCCCEEEECCCCHHH
Q ss_conf 665567776434433221135957999438877123---21234----33981454036776700115203215772689
Q gi|254780779|r 138 IERKRDKLKRALDGIRDMGGLPDLMFVVDTNREKLA---IQEAR----RLRIPIVAVVDTNSNPDLVDYVIPGNDDSSRS 210 (278)
Q Consensus 138 ~~r~~~kl~k~lgGi~~m~~lP~~iiv~d~~~e~~A---v~EA~----kl~IPvIaivDTn~dp~~idypIP~NDds~~s 210 (278)
.+...+|. . .-=|+++|+.-..-..+ +.+++ .++||+|+| |--||-=|||.|-|+-+
T Consensus 468 -----~~~a~~l~---~--~~Id~LivIGG~gs~~ga~~L~~~r~~y~~~~IP~v~I------PaTIdNdv~GTd~siG~ 531 (762)
T cd00764 468 -----ETIAYNFQ---K--YGIDGLIIVGGFEAYKGLLQLREAREQYEEFCIPMVLI------PATVSNNVPGTDFSLGS 531 (762)
T ss_pred -----HHHHHHHH---H--CCCCEEEEECCCHHHHHHHHHHHHHHHCCCCCCCEEEE------ECCEECCCCCCCCCEEH
T ss_conf -----99999999---8--19988999668079999999997564243458867973------12130799786040158
Q ss_pred HHHHHHHHHHHHHH
Q ss_conf 99999999999999
Q gi|254780779|r 211 IALFCDLVASAAID 224 (278)
Q Consensus 211 i~l~~~~i~~ai~~ 224 (278)
.--++.+.++|-.
T Consensus 532 -DTAlN~i~~aiD~ 544 (762)
T cd00764 532 -DTALNALMKYCDR 544 (762)
T ss_pred -HHHHHHHHHHHHH
T ss_conf -8699999999987
No 74
>PRK00758 GMP synthase subunit A; Validated
Probab=77.48 E-value=6.5 Score=20.42 Aligned_cols=31 Identities=19% Similarity=0.297 Sum_probs=20.0
Q ss_pred CCEEEEEC-C--CCCCHHHHHHHHCCCEEEEECC
Q ss_conf 95799943-8--8771232123433981454036
Q gi|254780779|r 159 PDLMFVVD-T--NREKLAIQEARRLRIPIVAVVD 189 (278)
Q Consensus 159 P~~iiv~d-~--~~e~~Av~EA~kl~IPvIaivD 189 (278)
||.||+.. | .+...+..-...++||+.|||=
T Consensus 42 ~dgiilS~GP~~~~~~~~~~~i~~~~iPiLGICl 75 (184)
T PRK00758 42 PDGIILSGGPEIERAGNCEEYLLELDVPILGICL 75 (184)
T ss_pred CCEEEECCCCCCCCCCCHHHHHHHCCCCEEEEEH
T ss_conf 9989988999833322069999865998899717
No 75
>cd06309 PBP1_YtfQ_like Periplasmic binding domain of ABC-type YtfQ-like transport systems. Periplasmic binding domain of ABC-type YtfQ-like transport systems. The YtfQ protein from Escherichia coli is up-regulated under glucose-limited conditions and shares homology with a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily. Members of this group are predicted to be involved in the transport of sugar-containing molecules across cellular and organellar membranes; however their ligand specificity is not determined experimentally.
Probab=77.43 E-value=6.5 Score=20.41 Aligned_cols=24 Identities=17% Similarity=0.069 Sum_probs=10.5
Q ss_pred CCCEEEEECCCCCCHHHHHHHHCC
Q ss_conf 595799943887712321234339
Q gi|254780779|r 158 LPDLMFVVDTNREKLAIQEARRLR 181 (278)
Q Consensus 158 lP~~iiv~d~~~e~~Av~EA~kl~ 181 (278)
-|++||..+-.--.-|++.++..|
T Consensus 185 ~i~ai~~~nd~~a~Ga~~al~~~G 208 (273)
T cd06309 185 DIDAVYAHNDEMALGAIQAIKAAG 208 (273)
T ss_pred CCCEEEECCCHHHHHHHHHHHHCC
T ss_conf 888898678579999999999839
No 76
>pfam01380 SIS SIS domain. SIS (Sugar ISomerase) domains are found in many phosphosugar isomerases and phosphosugar binding proteins. SIS domains are also found in proteins that regulate the expression of genes involved in synthesis of phosphosugars. Presumably the SIS domains bind to the end-product of the pathway.
Probab=77.06 E-value=6.7 Score=20.34 Aligned_cols=48 Identities=21% Similarity=0.232 Sum_probs=34.3
Q ss_pred CCEEEEECCCCC----CHHHHHHHHCCCEEEEECCCCCCC--HHCCCEEEECCC
Q ss_conf 957999438877----123212343398145403677670--011520321577
Q gi|254780779|r 159 PDLMFVVDTNRE----KLAIQEARRLRIPIVAVVDTNSNP--DLVDYVIPGNDD 206 (278)
Q Consensus 159 P~~iiv~d~~~e----~~Av~EA~kl~IPvIaivDTn~dp--~~idypIP~NDd 206 (278)
=|++|++....+ ..++++|++.|+|+|+|.+...+| ...|+.|..+.+
T Consensus 54 ~d~vi~iS~sG~t~~~~~~~~~a~~~g~~~i~iT~~~~S~la~~ad~~l~~~~~ 107 (131)
T pfam01380 54 DDLVIAISQSGETRDLLEAAKLLKARGAKIIAITDSKGSPLAREADHVLYIIAG 107 (131)
T ss_pred CCEEEEECCCCCCHHHHHHHHHHHHCCCEEEEEECCCCCHHHHHCCEEEECCCC
T ss_conf 999999548986576898789999849969999899999789968998987998
No 77
>cd06323 PBP1_ribose_binding Periplasmic sugar-binding domain of the thermophilic Thermoanaerobacter tengcongensis ribose binding protein (ttRBP) and its mesophilic homologs. Periplasmic sugar-binding domain of the thermophilic Thermoanaerobacter tengcongensis ribose binding protein (ttRBP) and its mesophilic homologs. Members of this group are belonging to the type I periplasmic binding protein superfamily, whose members are involved in chemotaxis, ATP-binding cassette transport, and intercellular communication in central nervous system. The thermophilic and mesophilic ribose-binding proteins are structurally very similar, but differ substantially in thermal stability.
Probab=77.02 E-value=6.7 Score=20.33 Aligned_cols=34 Identities=15% Similarity=0.069 Sum_probs=17.0
Q ss_pred CCCEEEEECCCCCCHHHHHHHHCC---CEEEEECCCC
Q ss_conf 595799943887712321234339---8145403677
Q gi|254780779|r 158 LPDLMFVVDTNREKLAIQEARRLR---IPIVAVVDTN 191 (278)
Q Consensus 158 lP~~iiv~d~~~e~~Av~EA~kl~---IPvIaivDTn 191 (278)
-|++||+.+-.--.-|++.++..| |-+||+=+++
T Consensus 181 ~~~aI~~~nD~~A~ga~~al~~~g~~di~viGfD~~~ 217 (268)
T cd06323 181 DIKGVFAQNDEMALGAIEALKAAGKDDVKVVGFDGTP 217 (268)
T ss_pred CCCEEEECCCHHHHHHHHHHHHHCCCCEEEEEECCCH
T ss_conf 8858997783999999999997099982999888988
No 78
>cd06311 PBP1_ABC_sugar_binding_like_3 Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems. Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily, which consists of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis.
Probab=76.81 E-value=3.5 Score=22.20 Aligned_cols=12 Identities=42% Similarity=0.454 Sum_probs=5.0
Q ss_pred HHHHHHHHCCCE
Q ss_conf 232123433981
Q gi|254780779|r 172 LAIQEARRLRIP 183 (278)
Q Consensus 172 ~Av~EA~kl~IP 183 (278)
.|+++|.+.+++
T Consensus 202 ~Al~~aG~~~~~ 213 (274)
T cd06311 202 AAIKQAGRTDIK 213 (274)
T ss_pred HHHHHCCCCCCC
T ss_conf 999976999997
No 79
>cd06273 PBP1_GntR_like_1 This group includes the ligand-binding domain of putative DNA transcription repressors which are highly similar to that of the repressor specific for gluconate (GntR), a member of the LacI-GalR family of bacterial transcription regulators. This group includes the ligand-binding domain of putative DNA transcription repressors which are highly similar to that of the repressor specific for gluconate (GntR), a member of the LacI-GalR family of bacterial transcription regulators. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational
Probab=76.22 E-value=7.1 Score=20.19 Aligned_cols=63 Identities=22% Similarity=0.258 Sum_probs=36.0
Q ss_pred CCCCCEEEEECCCCCCHHHHHHHHCCCE------EEEECCCC----CCCHHCCCEEEECCCCHHHHHHHHHHH
Q ss_conf 1359579994388771232123433981------45403677----670011520321577268999999999
Q gi|254780779|r 156 GGLPDLMFVVDTNREKLAIQEARRLRIP------IVAVVDTN----SNPDLVDYVIPGNDDSSRSIALFCDLV 218 (278)
Q Consensus 156 ~~lP~~iiv~d~~~e~~Av~EA~kl~IP------vIaivDTn----~dp~~idypIP~NDds~~si~l~~~~i 218 (278)
...|+++|+.+-.--.-+++.+..+|+. ++|+=|+. +.|.+-+.-.|.-.=+.+++++++..+
T Consensus 176 ~~~~~ai~~~nd~~A~g~i~~l~~~g~~iP~disvigfd~~~~~~~~~p~lTti~~~~~~~g~~a~~~L~~~i 248 (268)
T cd06273 176 PPRPTAVICGNDVLALGALYEARRLGLSVPEDLSIVGFDDIDGSAELEPALTTVRVPAREIGRIAAEALLALL 248 (268)
T ss_pred CCCCCEEEECCHHHHHHHHHHHHHCCCCCCCCEEEEEECCHHHHHHHCCCCEEEEECHHHHHHHHHHHHHHHH
T ss_conf 9998489977879999999999963999999679999998288984189947999199999999999999996
No 80
>COG4069 Uncharacterized protein conserved in archaea [Function unknown]
Probab=75.59 E-value=2.8 Score=22.78 Aligned_cols=200 Identities=21% Similarity=0.287 Sum_probs=94.7
Q ss_pred CCCCCHHHHHH---------------CCCCCCCCCCCCCCCCCCCCCCCCC----CEEEECHHHHHHHHHHHHHHHHH--
Q ss_conf 66245899986---------------0886075477657885621020018----81675389999999999999998--
Q gi|254780779|r 3 LPQFTIRQLLE---------------SGVQFGHRNFLWNPKMERYIFCERN----NTHIIDLSQTVPMLQKALQVISD-- 61 (278)
Q Consensus 3 m~~~t~~~Ll~---------------ag~H~Gh~~~~wnPkM~~yI~g~rn----gihIIdL~kT~~~L~~A~~~i~~-- 61 (278)
||+-.++.|++ +|--||.+.-..+|.-+|.|--+|- |--|.==..-....++-.+.+.-
T Consensus 60 ~PS~ci~~l~e~~Dlv~LlN~Gks~~TG~~Fg~~V~sr~~~~kpliQiErPge~dG~lipwn~~~~~~aekls~~lgl~i 139 (367)
T COG4069 60 KPSACIEELFESNDLVCLLNHGKSRETGHTFGRIVVSRAPEKKPLIQIERPGEPDGELIPWNRAARPHAEKLSELLGLKI 139 (367)
T ss_pred CHHHHHHHHHCCCCEEEEECCCCCCCCCCCHHHEEEECCCCCCCEEEECCCCCCCCEEEECCCCCCHHHHHHHHHHCCCC
T ss_conf 90889998736687899803784311352130024204888997067227999997277323121278999989848724
Q ss_pred -----HHC--------CCCEE------EEEECCHHHHHHHHHHHHHCCCEECCCCCCCCCCCCHH--HH-HHHHHHHHHH
Q ss_conf -----610--------78816------99607823579999998633983142334587323426--66-5556778998
Q gi|254780779|r 62 -----TVA--------RGGRI------LFVATKSQASDCVMEAAKRSAQYCVNSKWLGGMMTNWK--TV-SQSIQKLRDL 119 (278)
Q Consensus 62 -----i~~--------~gg~I------LFVgTk~~~~~~i~~~A~~~~~~yV~~RWlGG~LTN~~--ti-~~si~~l~~l 119 (278)
... .|+++ .|.|-+-....+|--.|...+---|.+- |.||--. +| ..-|.+|+..
T Consensus 140 ~~p~~~~~~~~e~~~~~gk~~~Rri~gv~pgenIlVnGIvVGkA~S~~V~LVaEn---G~lt~i~GG~IKe~GiEkL~~V 216 (367)
T COG4069 140 SRPPLPVRNNGEICNQIGKRVVRRISGVFPGENILVNGIVVGKATSSEVELVAEN---GFLTDIEGGRIKEHGIEKLHRV 216 (367)
T ss_pred CCCCCHHHHCCCCCCCCCCEEEEEEECCCCCCCEEEEEEEEEEECCCCEEEEEEC---CEEEEEECCEECHHHHHHHCCC
T ss_conf 5787102314635676687157887402688636894179866515746999618---6799875555445355676056
Q ss_pred HHH----HHCCCCCCCHHHHHHHHHHHHHH-----------HHHHHHHHHHCCCCCEEEEECCCCCCHHHHHHHHCCCEE
Q ss_conf 876----30121267746788766556777-----------643443322113595799943887712321234339814
Q gi|254780779|r 120 EEL----LNKENQGFTKKERLNIERKRDKL-----------KRALDGIRDMGGLPDLMFVVDTNREKLAIQEARRLRIPI 184 (278)
Q Consensus 120 ~~~----~~~~~~~~tkKe~~~~~r~~~kl-----------~k~lgGi~~m~~lP~~iiv~d~~~e~~Av~EA~kl~IPv 184 (278)
+-. +.+....-+-+-.-...|+-... ++.+. |-+--++++-+.-..-.+|-.=-.++||||
T Consensus 217 dl~~avVKTg~lRrs~~~~k~~~~~~~~~~~~kvilidHaaE~~~e----l~~~~~lvvTvGDDTT~vagdIl~Rfgipi 292 (367)
T COG4069 217 DLARAVVKTGALRRSPDEPKKVKSRKENAHAVKVILIDHAAERSYE----LIEGAGLVVTVGDDTTEVAGDILYRFGIPI 292 (367)
T ss_pred CHHHHEEECCCCCCCCCCCCCCCCCCCCCCCEEEEEEECCHHHHHH----HHCCCCEEEEECCCCHHHHHHHHHHCCCCE
T ss_conf 7768334415201489865672347122564489997040467787----640586289976860357788898639807
Q ss_pred EEECCCCCCC----------HHCCCEEEECCCCHH
Q ss_conf 5403677670----------011520321577268
Q gi|254780779|r 185 VAVVDTNSNP----------DLVDYVIPGNDDSSR 209 (278)
Q Consensus 185 IaivDTn~dp----------~~idypIP~NDds~~ 209 (278)
|||.|-+||- +.|-..+|+-||-+-
T Consensus 293 iGItDgD~D~~~~~~~~~~gsvi~~l~~~~DDdvG 327 (367)
T COG4069 293 IGITDGDCDEVTREVNIAPGSVILLLKPGRDDDVG 327 (367)
T ss_pred EECCCCCHHHHHHHCCCCCCCEEEEECCCCCHHHH
T ss_conf 85356886776342023787389997177620788
No 81
>TIGR02858 spore_III_AA stage III sporulation protein AA; InterPro: IPR014217 Proteins in this entry include the stage III sporulation protein AA that is encoded by one of several genes in the spoIIIA locus. This protein is only found in species that are capable of endospore formation..
Probab=75.21 E-value=4.1 Score=21.70 Aligned_cols=52 Identities=25% Similarity=0.358 Sum_probs=42.4
Q ss_pred CCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCEEEEE--CCCCCCHHHHHHHHCCCEEEEECCC
Q ss_conf 12126774678876655677764344332211359579994--3887712321234339814540367
Q gi|254780779|r 125 KENQGFTKKERLNIERKRDKLKRALDGIRDMGGLPDLMFVV--DTNREKLAIQEARRLRIPIVAVVDT 190 (278)
Q Consensus 125 ~~~~~~tkKe~~~~~r~~~kl~k~lgGi~~m~~lP~~iiv~--d~~~e~~Av~EA~kl~IPvIaivDT 190 (278)
.-+++=||-|-++|. ||.|. |++|++= ...+|--|+.||.--|+-+|+=+--
T Consensus 187 DVLD~CPKAEGmMM~------------iRSMS--P~Viv~DEIGr~ED~~Al~eA~naGV~~I~TaHg 240 (282)
T TIGR02858 187 DVLDGCPKAEGMMML------------IRSMS--PDVIVVDEIGREEDVEALLEALNAGVSVIATAHG 240 (282)
T ss_pred EECCCCCHHHHHHHH------------HHCCC--CCEEEEECCCCHHHHHHHHHHHCCCCEEEEEECC
T ss_conf 751788537899999------------97069--8579981488953389999986167568876404
No 82
>TIGR03600 phage_DnaB phage replicative helicase, DnaB family, HK022 subfamily. Members of this family are phage (or prophage-region) homologs of the bacterial homohexameric replicative helicase DnaB. Some phage may rely on host DnaB, while others encode their own verions. This model describes the largest phage-specific clade among the close homologs of DnaB, but there are, or course, other DnaB homologs from phage that fall outside the scope of this model.
Probab=75.10 E-value=7.6 Score=20.01 Aligned_cols=135 Identities=21% Similarity=0.339 Sum_probs=70.1
Q ss_pred HHHHHHHHHHHHHHHHHHHCCCCEEEEEECCHHHHHHHHHH-HHHCCCEECCCCCCCCCCC--CHHHHHHHHHHHHHHHH
Q ss_conf 89999999999999998610788169960782357999999-8633983142334587323--42666555677899887
Q gi|254780779|r 45 LSQTVPMLQKALQVISDTVARGGRILFVATKSQASDCVMEA-AKRSAQYCVNSKWLGGMMT--NWKTVSQSIQKLRDLEE 121 (278)
Q Consensus 45 L~kT~~~L~~A~~~i~~i~~~gg~ILFVgTk~~~~~~i~~~-A~~~~~~yV~~RWlGG~LT--N~~ti~~si~~l~~l~~ 121 (278)
.-||...+.-|.+.. ..+|+.|||...--...++...+ |..++.++- ++--|.|| -|..+.+.+.++.++.-
T Consensus 205 mGKTafalnia~n~A---~~~g~~Vl~fSLEMs~eql~~R~la~~s~i~~~--~i~~g~l~~~~~~~~~~a~~~l~~~~l 279 (421)
T TIGR03600 205 MGKTTLALNIAENVA---LREGKPVLFFSLEMSAEQLGERLLASKSGINTG--NIRTGRFNDSDFNRLLNAVDRLSEKDL 279 (421)
T ss_pred CCHHHHHHHHHHHHH---HHCCCEEEEEECCCCHHHHHHHHHHHHCCCCHH--HHHCCCCCHHHHHHHHHHHHHHHCCCE
T ss_conf 874599999999999---866983899925799999999999985489776--665289998999999999998616878
Q ss_pred HHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCEEEEEC------CCC---CCHHHHH--------HHHCCCEE
Q ss_conf 630121267746788766556777643443322113595799943------887---7123212--------34339814
Q gi|254780779|r 122 LLNKENQGFTKKERLNIERKRDKLKRALDGIRDMGGLPDLMFVVD------TNR---EKLAIQE--------ARRLRIPI 184 (278)
Q Consensus 122 ~~~~~~~~~tkKe~~~~~r~~~kl~k~lgGi~~m~~lP~~iiv~d------~~~---e~~Av~E--------A~kl~IPv 184 (278)
.. .....+|=-+ +.-...++.+..+| +++|| +| +.. ....|.| |+.|+|||
T Consensus 280 ~i-~d~~~~ti~~---ir~~~r~~~~~~~~-------l~liv-IDYLqLi~~~~~~~r~~ei~~Isr~LK~lAkel~ipV 347 (421)
T TIGR03600 280 YI-DDTGGLTVAQ---IRSIARRIKRKKGG-------LDLIV-VDYIQLMAPTRGRDRNEELGGISRGLKALAKELDVPV 347 (421)
T ss_pred EE-ECCCCCCHHH---HHHHHHHHHHHCCC-------CCEEE-ECHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCE
T ss_conf 99-6699887678---99999999986289-------86999-7578653788888889999999999999999979978
Q ss_pred EEECCCCCCCHH
Q ss_conf 540367767001
Q gi|254780779|r 185 VAVVDTNSNPDL 196 (278)
Q Consensus 185 IaivDTn~dp~~ 196 (278)
|+++--|=+.+.
T Consensus 348 i~lsQLnR~~e~ 359 (421)
T TIGR03600 348 VLLAQLNRGSEK 359 (421)
T ss_pred EEECCCCCCCCC
T ss_conf 997057865233
No 83
>cd06321 PBP1_ABC_sugar_binding_like_11 Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems. This group includes the periplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily, which consist of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis.
Probab=74.95 E-value=3.4 Score=22.27 Aligned_cols=29 Identities=24% Similarity=0.205 Sum_probs=12.8
Q ss_pred CCEEEEECCCCCCHHHHHHHHCC---CEEEEE
Q ss_conf 95799943887712321234339---814540
Q gi|254780779|r 159 PDLMFVVDTNREKLAIQEARRLR---IPIVAV 187 (278)
Q Consensus 159 P~~iiv~d~~~e~~Av~EA~kl~---IPvIai 187 (278)
|++||..+-.--.-|++.++.+| |.++|+
T Consensus 182 ~~aifa~nD~~A~Ga~~a~~~~G~~~i~ivg~ 213 (271)
T cd06321 182 LDGVFAINDPTAIGADLAAKQAGRNDIKITSV 213 (271)
T ss_pred CCEEEECCCHHHHHHHHHHHHCCCCCCEEEEE
T ss_conf 77899778689999999999759799989999
No 84
>PRK05749 3-deoxy-D-manno-octulosonic-acid transferase; Reviewed
Probab=74.94 E-value=5.7 Score=20.82 Aligned_cols=27 Identities=33% Similarity=0.559 Sum_probs=11.9
Q ss_pred CCEEEEECCCCCCHHHHHHHHCCCEEE
Q ss_conf 957999438877123212343398145
Q gi|254780779|r 159 PDLMFVVDTNREKLAIQEARRLRIPIV 185 (278)
Q Consensus 159 P~~iiv~d~~~e~~Av~EA~kl~IPvI 185 (278)
|++++++...-=-+-+.+|.+.|||++
T Consensus 124 P~~~i~~E~EiWPnli~~~~~~~Ip~~ 150 (423)
T PRK05749 124 PKLLIIMETELWPNLIAEAKKRGIPLV 150 (423)
T ss_pred CCEEEEEECCCCHHHHHHHHHCCCCEE
T ss_conf 887998620310889999962788667
No 85
>cd01571 NAPRTase_B Nicotinate phosphoribosyltransferase (NAPRTase), subgroup B. Nicotinate phosphoribosyltransferase catalyses the formation of NAMN and PPi from 5-phosphoribosy -1-pyrophosphate (PRPP) and nicotinic acid, this is the first, and also rate limiting, reaction in the NAD salvage synthesis. This salvage pathway serves to recycle NAD degradation products.
Probab=74.06 E-value=6 Score=20.65 Aligned_cols=22 Identities=14% Similarity=0.120 Sum_probs=14.3
Q ss_pred HHHHHHHHHCCCCEEEEEECCHHH
Q ss_conf 999999861078816996078235
Q gi|254780779|r 55 ALQVISDTVARGGRILFVATKSQA 78 (278)
Q Consensus 55 A~~~i~~i~~~gg~ILFVgTk~~~ 78 (278)
|.+++. +..+..+++.|+++..
T Consensus 101 a~r~v~--aA~~~~v~~fg~Rr~~ 122 (302)
T cd01571 101 AARVKL--AAGDKPVISFGDRRDH 122 (302)
T ss_pred HHHHHH--HCCCCCEEEECCCCCC
T ss_conf 999999--7499938974453359
No 86
>KOG2754 consensus
Probab=73.93 E-value=2.7 Score=22.89 Aligned_cols=84 Identities=17% Similarity=0.265 Sum_probs=51.5
Q ss_pred HHHHHCCCCCCCCCCCCCCCCCCCCCCCC--CCEEEECHHHHHHHH--HHHHHHHHHHHCCCCEEEEEECCHHHHHHHHH
Q ss_conf 99986088607547765788562102001--881675389999999--99999999861078816996078235799999
Q gi|254780779|r 9 RQLLESGVQFGHRNFLWNPKMERYIFCER--NNTHIIDLSQTVPML--QKALQVISDTVARGGRILFVATKSQASDCVME 84 (278)
Q Consensus 9 ~~Ll~ag~H~Gh~~~~wnPkM~~yI~g~r--ngihIIdL~kT~~~L--~~A~~~i~~i~~~gg~ILFVgTk~~~~~~i~~ 84 (278)
+.|=+-|.-+-.+.. =+++.+=+-||+| +++-|+-. ..+.+ ..--+-|.+.+..||++|.++.- +..+.|++
T Consensus 44 ~sLkdRgf~L~~~~a-~dssl~L~~Ygq~LyDnlIifap--~~e~fgg~is~k~l~~Fvd~gGnvlv~ass-~~~d~iRe 119 (443)
T KOG2754 44 KSLKDRGFKLTYKLA-DDSSLALFKYGQRLYDNLIIFAP--SVENFGGSISVKSLAKFVDSGGNVLVAASS-AIGDAIRE 119 (443)
T ss_pred HHHHHCCCEEEEEEC-CCCHHHHHHHHHHHHCCEEEECC--CHHHCCCCCCHHHHHHHHHCCCCEEEECCC-CCCHHHHH
T ss_conf 458756940489743-77315788753576546799467--435407878989999998479848998477-66478999
Q ss_pred HHHHCCCEECCC
Q ss_conf 986339831423
Q gi|254780779|r 85 AAKRSAQYCVNS 96 (278)
Q Consensus 85 ~A~~~~~~yV~~ 96 (278)
+|..||+++--.
T Consensus 120 ~~~E~g~~~~e~ 131 (443)
T KOG2754 120 FASECGIEFDEE 131 (443)
T ss_pred HHHHHCCCCCCC
T ss_conf 999729650746
No 87
>cd06288 PBP1_sucrose_transcription_regulator Ligand-binding domain of DNA-binding regulatory proteins specific to sucrose that are members of the LacI-GalR family of bacterial transcription repressors. This group includes the ligand-binding domain of DNA-binding regulatory proteins specific to sucrose that are members of the LacI-GalR family of bacterial transcription repressors. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.
Probab=73.85 E-value=8.1 Score=19.81 Aligned_cols=64 Identities=16% Similarity=0.212 Sum_probs=42.7
Q ss_pred CCCCCEEEEECCCCCCHHHHHHHHCCC------EEEEECCCC-----CCCHHCCCEEEECCCCHHHHHHHHHHHH
Q ss_conf 135957999438877123212343398------145403677-----6700115203215772689999999999
Q gi|254780779|r 156 GGLPDLMFVVDTNREKLAIQEARRLRI------PIVAVVDTN-----SNPDLVDYVIPGNDDSSRSIALFCDLVA 219 (278)
Q Consensus 156 ~~lP~~iiv~d~~~e~~Av~EA~kl~I------PvIaivDTn-----~dp~~idypIP~NDds~~si~l~~~~i~ 219 (278)
...||++|+.+-.--.-+++.++.+|| -+||+=|+. +.|..-+.-+|...=+.+++++++..+.
T Consensus 175 ~~~~dai~~~~d~~A~g~~~~l~~~gi~vP~di~iigfD~~~~~~~~~~P~lTti~q~~~~~g~~A~~~l~~~i~ 249 (269)
T cd06288 175 DDRPTAIFCGNDRMAMGAYQALLERGLRIPQDVSVVGFDNQEIIAEHLRPPLTTVALPHYEMGRWAVELLLDGIE 249 (269)
T ss_pred CCCCCEECCCCHHHHHHHHHHHHHCCCCCCCCEEEEEECCCHHHHHHCCCCCEEEEECHHHHHHHHHHHHHHHHC
T ss_conf 899861014778999999999998599999988999988868999637899649980999999999999999975
No 88
>pfam04413 Glycos_transf_N 3-Deoxy-D-manno-octulosonic-acid transferase (kdotransferase). Members of this family transfer activated sugars to a variety of substrates, including glycogen, fructose-6-phosphate and lipopolysaccharides. Members of the family transfer UDP, ADP, GDP or CMP linked sugars. The Glycos_transf_N region is flanked at the N-terminus by a signal peptide and at the C-terminus by Glycos_transf_1 (pfam00534). The eukaryotic glycogen synthases may be distant members of this bacterial family.
Probab=73.65 E-value=8.2 Score=19.78 Aligned_cols=92 Identities=27% Similarity=0.303 Sum_probs=54.3
Q ss_pred HHHHHHHHHHHHHHHCC--CCEEEEEECCHHHHHHHHHHHHHCCCEECCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHCC
Q ss_conf 99999999999986107--8816996078235799999986339831423345873234266655567789988763012
Q gi|254780779|r 49 VPMLQKALQVISDTVAR--GGRILFVATKSQASDCVMEAAKRSAQYCVNSKWLGGMMTNWKTVSQSIQKLRDLEELLNKE 126 (278)
Q Consensus 49 ~~~L~~A~~~i~~i~~~--gg~ILFVgTk~~~~~~i~~~A~~~~~~yV~~RWlGG~LTN~~ti~~si~~l~~l~~~~~~~ 126 (278)
+-....|..+++++..+ +-.||+=.+-+.+.+.+++... .-+.+.++| +-....+++-+++
T Consensus 31 vGE~~~~~~li~~l~~~~p~~~iliT~~T~sg~~~~~~~~~----~~~~~~ylP--~D~~~~~~~fl~~----------- 93 (186)
T pfam04413 31 VGEVLAALPLIEALKARYPGLRILVTTTTPTGAELARKLLP----DRVIHQYLP--LDLPGAVRRFLKH----------- 93 (186)
T ss_pred HHHHHHHHHHHHHHHHHCCCCEEEEEECCCHHHHHHHHHCC----CCCEEEECC--CCCHHHHHHHHHH-----------
T ss_conf 89999999999999986899629998358169999998678----980799777--6777999999998-----------
Q ss_pred CCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCEEEEECCCCCCHHHHHHHHCCCEEEEE
Q ss_conf 1267746788766556777643443322113595799943887712321234339814540
Q gi|254780779|r 127 NQGFTKKERLNIERKRDKLKRALDGIRDMGGLPDLMFVVDTNREKLAIQEARRLRIPIVAV 187 (278)
Q Consensus 127 ~~~~tkKe~~~~~r~~~kl~k~lgGi~~m~~lP~~iiv~d~~~e~~Av~EA~kl~IPvIai 187 (278)
+ .|++++++...-=-+-+.+|.+.|||++=+
T Consensus 94 -------------------------~-----~P~~~i~~e~EiWPnli~~~~~~~ip~~li 124 (186)
T pfam04413 94 -------------------------W-----RPDLLVIVETELWPNLIAAAKKRGIPVVLV 124 (186)
T ss_pred -------------------------H-----CCCEEEEEECCHHHHHHHHHHHCCCCEEEE
T ss_conf -------------------------5-----998899986132099999999879999999
No 89
>cd01545 PBP1_SalR Ligand-binding domain of DNA transcription repressor SalR, a member of the LacI-GalR family of bacterial transcription regulators. Ligand-binding domain of DNA transcription repressor SalR, a member of the LacI-GalR family of bacterial transcription regulators. The SalR binds to glucose based compound Salicin which is chemically related to aspirin. The ligand-binding of SalR is structurally homologous to the periplasmic sugar-binding domain of ABC-transporters and both domains contain the type I periplasmic binding protein-like fold. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the type I periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand bind
Probab=73.50 E-value=8.3 Score=19.76 Aligned_cols=35 Identities=20% Similarity=0.266 Sum_probs=25.1
Q ss_pred CCCCCEEEEECCCCCCHHHHHHHHCCCE------EEEECCC
Q ss_conf 1359579994388771232123433981------4540367
Q gi|254780779|r 156 GGLPDLMFVVDTNREKLAIQEARRLRIP------IVAVVDT 190 (278)
Q Consensus 156 ~~lP~~iiv~d~~~e~~Av~EA~kl~IP------vIaivDT 190 (278)
...|+++|+.+-.--.-+++.++.+|+- |||+=|+
T Consensus 177 ~~~~tai~~~nD~~A~g~~~~l~~~g~~iP~dvsiigfD~~ 217 (270)
T cd01545 177 PDRPTAIFASNDDMAAGVLAVAHRRGLRVPDDLSVVGFDDT 217 (270)
T ss_pred CCCCCEEEECCHHHHHHHHHHHHHHCCCCCCCEEEEEECCH
T ss_conf 99985899788899999999999818999998699998885
No 90
>PRK06749 replicative DNA helicase; Provisional
Probab=73.13 E-value=8.4 Score=19.70 Aligned_cols=145 Identities=19% Similarity=0.239 Sum_probs=74.5
Q ss_pred CCCCCCCCEEEECHHHHHHHHHHHHHHHHHHHCCCCEEEEEECCHHHHHHHHHHH-HHCCCEECCCCCCCCCCCC--HHH
Q ss_conf 1020018816753899999999999999986107881699607823579999998-6339831423345873234--266
Q gi|254780779|r 32 YIFCERNNTHIIDLSQTVPMLQKALQVISDTVARGGRILFVATKSQASDCVMEAA-KRSAQYCVNSKWLGGMMTN--WKT 108 (278)
Q Consensus 32 yI~g~rngihIIdL~kT~~~L~~A~~~i~~i~~~gg~ILFVgTk~~~~~~i~~~A-~~~~~~yV~~RWlGG~LTN--~~t 108 (278)
+|.+-|-+ .-||...|.-|.+ ++.+|+.++|.+.--...++...+. ..++.++-.-|=--|+++. |..
T Consensus 189 iviaaRPs-----mGKTa~alnia~~----~a~~g~~v~~fSlEMs~~~l~~R~ls~~s~v~~~~i~~~~~~~~~~~~~~ 259 (428)
T PRK06749 189 VVLGARPS-----MGKTAFALNVGLH----AAKSGAAVGLFSLEMSSKQLLKRMASCVGEVSGGRLKNPKHRFAMEDWEK 259 (428)
T ss_pred EEEECCCC-----CCHHHHHHHHHHH----HHHCCCCEEEEECCCCHHHHHHHHHHHHCCCCHHHHHCCCCCCCHHHHHH
T ss_conf 99962798-----9768999999999----99649927998378999999999999754998888627767799999999
Q ss_pred HHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCEEEEEC--------CCCC---CHHHHH-
Q ss_conf 6555677899887630121267746788766556777643443322113595799943--------8877---123212-
Q gi|254780779|r 109 VSQSIQKLRDLEELLNKENQGFTKKERLNIERKRDKLKRALDGIRDMGGLPDLMFVVD--------TNRE---KLAIQE- 176 (278)
Q Consensus 109 i~~si~~l~~l~~~~~~~~~~~tkKe~~~~~r~~~kl~k~lgGi~~m~~lP~~iiv~d--------~~~e---~~Av~E- 176 (278)
+.+.+.++.++.-..+ ....+|=-+.... ..++.+..|. ...+||+| +... ...|.|
T Consensus 260 ~~~a~~~l~~~~l~i~-d~~~~ti~~i~~~---~r~~~~~~g~-------~~~livIDYlqLi~~~~~~~~~r~~ev~~i 328 (428)
T PRK06749 260 VSKAFAEIGELPLEIY-DNAGVTVQDIWMQ---TRKLKRKHGD-------KKVLIIVDYLQLITGDPKHKGNRFQEISEI 328 (428)
T ss_pred HHHHHHHHHCCCEEEE-CCCCCCHHHHHHH---HHHHHHHCCC-------CCEEEEEEHHHHCCCCCCCCCCHHHHHHHH
T ss_conf 9999999855965997-5899767999999---9999997499-------876999767765057877777899999999
Q ss_pred -------HHHCCCEEEEECCCCCCCHH
Q ss_conf -------34339814540367767001
Q gi|254780779|r 177 -------ARRLRIPIVAVVDTNSNPDL 196 (278)
Q Consensus 177 -------A~kl~IPvIaivDTn~dp~~ 196 (278)
|+.|+||||+++-=|=..+.
T Consensus 329 sr~lK~lAkel~vpvi~lsQLnR~~e~ 355 (428)
T PRK06749 329 SRKLKLLARELNVCVVALSQLSRSVES 355 (428)
T ss_pred HHHHHHHHHHHCCCEEEECCCCCCCCC
T ss_conf 999999999969989997137855233
No 91
>cd06283 PBP1_RegR_EndR_KdgR_like Ligand-binding domain of DNA transcription repressor RegR and other putative regulators such as KdgR and EndR. Ligand-binding domain of DNA transcription repressor RegR and other putative regulators such as KdgR and EndR, all of which are members of the LacI-GalR family of bacterial transcription regulators. RegR regulates bacterial competence and the expression of virulence factors, including hyaluronidase. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA b
Probab=72.30 E-value=7.8 Score=19.91 Aligned_cols=62 Identities=13% Similarity=0.179 Sum_probs=35.5
Q ss_pred CCCCEEEEECCCCCCHHHHHHHHCCCE------EEEECCC----CCCCHHCCCEEEECCCCHHHHHHHHHHH
Q ss_conf 359579994388771232123433981------4540367----7670011520321577268999999999
Q gi|254780779|r 157 GLPDLMFVVDTNREKLAIQEARRLRIP------IVAVVDT----NSNPDLVDYVIPGNDDSSRSIALFCDLV 218 (278)
Q Consensus 157 ~lP~~iiv~d~~~e~~Av~EA~kl~IP------vIaivDT----n~dp~~idypIP~NDds~~si~l~~~~i 218 (278)
..|+++|+.+-.-=.-+++.+...|+. |+|+=|+ -.+|.+-+.-+|...=+.+++++++..+
T Consensus 177 ~~~~aii~~~D~~A~g~~~~l~~~g~~vP~disVvg~dd~~~~~~~~p~lTtv~~~~~~~g~~av~~l~~~i 248 (267)
T cd06283 177 KKKTAIFAANGLILLEVLKALKELGIRIPEDVGLIGFDDTEWAELIGPGITTIAQPTYEMGKTAAELLLERI 248 (267)
T ss_pred CCCCEECCCCCHHHHHHHHHHHHCCCCCCCCCEEEEECCHHHHHHCCCCCEEEECCHHHHHHHHHHHHHHHH
T ss_conf 998642037709999999999982998898766885388699984299953998399999999999999997
No 92
>PRK12362 germination protease; Provisional
Probab=72.30 E-value=8.8 Score=19.58 Aligned_cols=156 Identities=21% Similarity=0.301 Sum_probs=81.5
Q ss_pred CCCCCCCCCCCCEEEECHHHHHHHHHHHHHHHHHHH--CCCCEEEEEECCHHHHHHHHHHHHHCCCEECCCCCCCCCCCC
Q ss_conf 856210200188167538999999999999999861--078816996078235799999986339831423345873234
Q gi|254780779|r 28 KMERYIFCERNNTHIIDLSQTVPMLQKALQVISDTV--ARGGRILFVATKSQASDCVMEAAKRSAQYCVNSKWLGGMMTN 105 (278)
Q Consensus 28 kM~~yI~g~rngihIIdL~kT~~~L~~A~~~i~~i~--~~gg~ILFVgTk~~~~~~i~~~A~~~~~~yV~~RWlGG~LTN 105 (278)
.+..||-=+-.++.--|-+.--...+..++.++.+. ...+++|.||--.. .|+--=||=....
T Consensus 56 p~G~YiTiE~p~l~~~D~~~~~~v~~~la~~L~~li~~~~~~~vLVVGLGN~---------------~vTPDALGP~vv~ 120 (324)
T PRK12362 56 PIGNYITIEAPELREYDGELHEEVSKILAKELKKLINLDEDMTVLVVGLGNW---------------NVTPDALGPKVVS 120 (324)
T ss_pred CCCCEEEEECCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCEEEEECCCC---------------CCCCCCCCHHEEC
T ss_conf 9863799846876656878999999999999999858998884899967887---------------7786563712000
Q ss_pred HHHHHHHHHHHHHHH-HHHH----------CCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCEEEEECCC------
Q ss_conf 266655567789988-7630----------12126774678876655677764344332211359579994388------
Q gi|254780779|r 106 WKTVSQSIQKLRDLE-ELLN----------KENQGFTKKERLNIERKRDKLKRALDGIRDMGGLPDLMFVVDTN------ 168 (278)
Q Consensus 106 ~~ti~~si~~l~~l~-~~~~----------~~~~~~tkKe~~~~~r~~~kl~k~lgGi~~m~~lP~~iiv~d~~------ 168 (278)
.--+.. +|.++. +... .+.-+.|-=|...+-| ||.. +-.||+|+++|.-
T Consensus 121 ~l~VTR---Hl~~~~p~~~~~g~r~VsaiaPGVmg~TGiET~EIIk----------giv~-k~kPd~VIaIDALAaRs~~ 186 (324)
T PRK12362 121 KIMVTR---HLKEYVPEQIDEGVRPVSAISPGVLGITGIETAEIIK----------GIVE-KIKPDLVIAIDALASRKVE 186 (324)
T ss_pred CEEEEH---HHHHHCCHHHCCCCCEEEEECCCCCCCCCCCHHHHHH----------HHHH-HHCCCEEEEEHHHHCCCHH
T ss_conf 251025---3676563544278731468858754044303999999----------9987-5089899996021137666
Q ss_pred --------------------CCCHHHHHHHHCCCEEEEECCCCCCCHHCCCEEEECCCCHHHHHHHHHHHHHH
Q ss_conf --------------------77123212343398145403677670011520321577268999999999999
Q gi|254780779|r 169 --------------------REKLAIQEARRLRIPIVAVVDTNSNPDLVDYVIPGNDDSSRSIALFCDLVASA 221 (278)
Q Consensus 169 --------------------~e~~Av~EA~kl~IPvIaivDTn~dp~~idypIP~NDds~~si~l~~~~i~~a 221 (278)
+...++.| ..|||||||| .=|+.||-..-+|| ++.+++..+.+.
T Consensus 187 Rln~TIQIsDTGI~PGSGVGN~R~~l~~-etLGVPVIAI----GVPTVVdAatI~~D----ti~~~~~~~~~~ 250 (324)
T PRK12362 187 RVNTTIQISDTGISPGSGVGNKRMGLNE-ETLGVPVIAI----GVPTVVDAATIAND----TIDMVLDELIKQ 250 (324)
T ss_pred HCCCEEEECCCCCCCCCCCCCCCCCCCH-HHCCCCEEEE----CCCEEECHHHHHHH----HHHHHHHHHHHH
T ss_conf 5367588657785899886754442698-7829988996----58816522999899----999999998640
No 93
>TIGR01815 TrpE-clade3 anthranilate synthase; InterPro: IPR010112 This entry represents a small clade of anthranilate synthases from alpha proteobacteria and Nostoc (a cyanobacterium). This enzyme is the first step in the pathway for the biosynthesis of tryprophan from chorismate.; GO: 0004049 anthranilate synthase activity, 0000162 tryptophan biosynthetic process.
Probab=71.96 E-value=9 Score=19.53 Aligned_cols=95 Identities=22% Similarity=0.319 Sum_probs=56.9
Q ss_pred CHHHHHHHHHHHHHHHHHHHCCCCEEEEEECCHHHHHHHHHHHHHCCCEECCCCCCCCCCCCHHHHHHHHHHHHHHHHHH
Q ss_conf 38999999999999999861078816996078235799999986339831423345873234266655567789988763
Q gi|254780779|r 44 DLSQTVPMLQKALQVISDTVARGGRILFVATKSQASDCVMEAAKRSAQYCVNSKWLGGMMTNWKTVSQSIQKLRDLEELL 123 (278)
Q Consensus 44 dL~kT~~~L~~A~~~i~~i~~~gg~ILFVgTk~~~~~~i~~~A~~~~~~yV~~RWlGG~LTN~~ti~~si~~l~~l~~~~ 123 (278)
|-.++.....+.-+++-+= ..|.+||.|--.-.+-.....+-.. .|-+.| |++.++.+
T Consensus 503 ~~a~~~~~~~~~gkylPdG-q~G~~iLLvDHeDSFVHTLAnY~Rq----------TGAsVT---TlRh~~ae-------- 560 (726)
T TIGR01815 503 DAAKEESAVAKVGKYLPDG-QEGKRILLVDHEDSFVHTLANYLRQ----------TGASVT---TLRHSFAE-------- 560 (726)
T ss_pred CCCCCCHHHHHHCCCCCCC-CCCCEEEEEECCCCHHHHHHHHHHH----------CCCEEE---ECCCHHHH--------
T ss_conf 7434501265520247886-2587799985475437777888763----------487553---04304789--------
Q ss_pred HCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCEEEEEC-CCC-----CCHHHHHHHHCCCEEEEEC
Q ss_conf 0121267746788766556777643443322113595799943-887-----7123212343398145403
Q gi|254780779|r 124 NKENQGFTKKERLNIERKRDKLKRALDGIRDMGGLPDLMFVVD-TNR-----EKLAIQEARRLRIPIVAVV 188 (278)
Q Consensus 124 ~~~~~~~tkKe~~~~~r~~~kl~k~lgGi~~m~~lP~~iiv~d-~~~-----e~~Av~EA~kl~IPvIaiv 188 (278)
..+. +..||+||+.- |.. -.--|.-|..++||++|+|
T Consensus 561 ------------~~fd----------------~~rPDLVVLSPGPGrP~dFdv~~Ti~aa~ar~lP~FGVC 603 (726)
T TIGR01815 561 ------------ELFD----------------EERPDLVVLSPGPGRPKDFDVKETIKAALARDLPVFGVC 603 (726)
T ss_pred ------------HHHH----------------CCCCCEEEECCCCCCCCCCCHHHHHHHHHHCCCCEEEEH
T ss_conf ------------9973----------------279988986873123875447889999997289857741
No 94
>cd05014 SIS_Kpsf KpsF-like protein. KpsF is an arabinose-5-phosphate isomerase which contains SIS (Sugar ISomerase) domains. SIS domains are found in many phosphosugar isomerases and phosphosugar binding proteins. KpsF catalyzes the reversible reaction of ribulose 5-phosphate to arabinose 5-phosphate. This is the second step in the CMP-Kdo biosynthesis pathway.
Probab=71.96 E-value=6.9 Score=20.27 Aligned_cols=46 Identities=20% Similarity=0.314 Sum_probs=31.8
Q ss_pred CCEEEEECCCCC----CHHHHHHHHCCCEEEEECCCCCCC--HHCCCEEEEC
Q ss_conf 957999438877----123212343398145403677670--0115203215
Q gi|254780779|r 159 PDLMFVVDTNRE----KLAIQEARRLRIPIVAVVDTNSNP--DLVDYVIPGN 204 (278)
Q Consensus 159 P~~iiv~d~~~e----~~Av~EA~kl~IPvIaivDTn~dp--~~idypIP~N 204 (278)
-|++|++....+ ..+++.|++.|+|+|+|.....+| ...||.|+.+
T Consensus 48 ~Dv~i~iS~SG~T~e~~~~~~~ak~~g~~vI~iT~~~~S~La~~ad~~l~~~ 99 (128)
T cd05014 48 GDVVIAISNSGETDELLNLLPHLKRRGAPIIAITGNPNSTLAKLSDVVLDLP 99 (128)
T ss_pred CCEEEEEECCCCCHHHHHHHHHHHHCCCCEEEEECCCCCHHHHHCCEEEECC
T ss_conf 9999999799998679999999986378589998799996799689899779
No 95
>PRK11316 bifunctional heptose 7-phosphate kinase/heptose 1-phosphate adenyltransferase; Provisional
Probab=71.30 E-value=4.1 Score=21.72 Aligned_cols=154 Identities=16% Similarity=0.275 Sum_probs=84.5
Q ss_pred CCCCCCCCCCC------EEEECHHHHHHHHHHHHHHHHHHHCCCCEEEEEE---CCHHHHHHHHHHHHHCCCEECCCCCC
Q ss_conf 56210200188------1675389999999999999998610788169960---78235799999986339831423345
Q gi|254780779|r 29 MERYIFCERNN------THIIDLSQTVPMLQKALQVISDTVARGGRILFVA---TKSQASDCVMEAAKRSAQYCVNSKWL 99 (278)
Q Consensus 29 M~~yI~g~rng------ihIIdL~kT~~~L~~A~~~i~~i~~~gg~ILFVg---Tk~~~~~~i~~~A~~~~~~yV~~RWl 99 (278)
.-.|+||.-+. +.+++...+...+-=|.+....+++-|+.+-||| .-.....+.... ...|. +..|+
T Consensus 21 LD~y~~G~v~RiSPEAPVPVv~v~~~~~~pGGAaNVA~NLa~LGa~v~lvg~vG~D~~G~~L~~~L-~~~gI---dt~~v 96 (473)
T PRK11316 21 LDRYWYGPTSRISPEAPVPVVKVNQIEERPGGAANVAMNIASLGAQARLVGLTGIDEAARALSKLL-AAVGV---KCDFV 96 (473)
T ss_pred EEEEEEEEECEECCCCCCCEEEECCEEECCCHHHHHHHHHHHCCCCEEEEEEECCCHHHHHHHHHH-HHCCC---CCCEE
T ss_conf 887687405738999983469843089518789999999996699389999967877799999999-87599---72348
Q ss_pred CCCCCCHHHHHH-HHHHH-HHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCEEEEECCCCC-----CH
Q ss_conf 873234266655-56778-998876301212677467887665567776434433221135957999438877-----12
Q gi|254780779|r 100 GGMMTNWKTVSQ-SIQKL-RDLEELLNKENQGFTKKERLNIERKRDKLKRALDGIRDMGGLPDLMFVVDTNRE-----KL 172 (278)
Q Consensus 100 GG~LTN~~ti~~-si~~l-~~l~~~~~~~~~~~tkKe~~~~~r~~~kl~k~lgGi~~m~~lP~~iiv~d~~~e-----~~ 172 (278)
...+..|+.| ++--- +.+-+ .+.+ +.++..+...+ ...++..+. -.|+|++.|-.+- ..
T Consensus 97 --~~~~~~T~~KtRiia~~qqllR-vD~E-~~~~~~~~~~l---~~~~~~~l~-------~~d~VIlSDY~KG~L~~~~~ 162 (473)
T PRK11316 97 --SVPTHPTITKLRVLSRNQQLIR-LDFE-EGFEGVDPQPL---LERIEQALP-------SIGALVLSDYAKGALASVQA 162 (473)
T ss_pred --ECCCCCCEEEEEEECCCCEEEE-ECCC-CCCCCCCHHHH---HHHHHHHHH-------HCCEEEEECCCCCHHHHHHH
T ss_conf --7189984487888538847999-5156-66775379999---999998762-------18889995556315677999
Q ss_pred HHHHHHHCCCEEEEECCCC-CCCH---HCCCEEE
Q ss_conf 3212343398145403677-6700---1152032
Q gi|254780779|r 173 AIQEARRLRIPIVAVVDTN-SNPD---LVDYVIP 202 (278)
Q Consensus 173 Av~EA~kl~IPvIaivDTn-~dp~---~idypIP 202 (278)
++..|++.|+||+ +|.. .|++ ++|+..|
T Consensus 163 iI~~Ar~~gipVi--VDPK~~d~~~y~ga~litP 194 (473)
T PRK11316 163 MIQLARKAGVPVL--IDPKGTDFERYRGATLLTP 194 (473)
T ss_pred HHHHHHHCCCCEE--EECCCCCHHHCCCCCCCCC
T ss_conf 9999997399799--9499867444179841267
No 96
>LOAD_uvrC_endov consensus
Probab=70.22 E-value=5.6 Score=20.83 Aligned_cols=35 Identities=26% Similarity=0.356 Sum_probs=21.4
Q ss_pred CCCCCEEEEECCCCCCHHHH----HHHHCCCEEEEECCC
Q ss_conf 13595799943887712321----234339814540367
Q gi|254780779|r 156 GGLPDLMFVVDTNREKLAIQ----EARRLRIPIVAVVDT 190 (278)
Q Consensus 156 ~~lP~~iiv~d~~~e~~Av~----EA~kl~IPvIaivDT 190 (278)
..+||+++|=.-..-+.+.. |...++||+||++-.
T Consensus 78 ~~~PDLilIDGg~~ql~~~~~~l~~lg~~~ip~iglAK~ 116 (123)
T LOAD_uvrC_endo 78 LKLPDLILVDGGGGQHPRALGVASHLGVLGIPVIGVAKN 116 (123)
T ss_pred CCCCCEEEECCCHHHHHHHHHHHHHCCCCCCCEEEEEEC
T ss_conf 889989998796778899999999869989858999808
No 97
>cd05298 GH4_GlvA_pagL_like Glycoside Hydrolases Family 4; GlvA- and pagL-like glycosidases. Bacillus subtilis GlvA and Clostridium acetobutylicum pagL are 6-phospho-alpha-glucosidase, catalyzing the hydrolysis of alpha-glucopyranoside bonds to release glucose from oligosaccharides. The substrate specificities of other members of this subgroup are unknown. Some bacteria simultaneously translocate and phosphorylate disaccharides via the phosphoenolpyruvate-dependent phosphotransferase system (PEP_PTS). After translocation, these phospho-disaccharides may be hydrolyzed by the GH4 glycoside hydrolases, which include 6-phospho-beta-glucosidases, 6-phospho-alpha-glucosidases, alpha-glucosidases/alpha-glucuronidases (only from Thermotoga), and alpha-galactosidases. Members of this subfamily are part of the NAD(P)-binding Rossmann fold superfamily, which includes a wide variety of protein families including the NAD(P)-binding domains of alcohol dehydrogenases, tyrosine-dependent oxidoreductas
Probab=69.93 E-value=9.9 Score=19.25 Aligned_cols=47 Identities=17% Similarity=0.202 Sum_probs=31.5
Q ss_pred CCEEEEECCCCCCHHHHHHHH---CCCEEEEECCC------------CCCCHHCCCEEEECCC
Q ss_conf 957999438877123212343---39814540367------------7670011520321577
Q gi|254780779|r 159 PDLMFVVDTNREKLAIQEARR---LRIPIVAVVDT------------NSNPDLVDYVIPGNDD 206 (278)
Q Consensus 159 P~~iiv~d~~~e~~Av~EA~k---l~IPvIaivDT------------n~dp~~idypIP~NDd 206 (278)
|+|.++ |-.+=...|.||-. -++++|||||+ +.+++.|+|-..|=+.
T Consensus 135 P~Awli-NytNP~~~vt~al~~~~~~~k~vGLCh~~~~~~~~la~~Lg~~~~~v~~~~aGlNH 196 (437)
T cd05298 135 PDAWIL-NYSNPAAIVAEALRRLFPNARILNICDMPIAIMDSMAAILGLDRKDLEPDYFGLNH 196 (437)
T ss_pred CCCEEE-ECCCHHHHHHHHHHHHCCCCCEEEECCCHHHHHHHHHHHHCCCHHHEEEEEEECCH
T ss_conf 992899-75787899999999748999889889788999999999958988991788961042
No 98
>PRK00025 lpxB lipid-A-disaccharide synthase; Reviewed
Probab=69.64 E-value=10 Score=19.21 Aligned_cols=56 Identities=9% Similarity=0.138 Sum_probs=29.9
Q ss_pred EEEECHHHHHHHHHHHHHHHHHHHC-CCCEEEEEECCHHHHHHHHHHHHHC--CC---EECC
Q ss_conf 1675389999999999999998610-7881699607823579999998633--98---3142
Q gi|254780779|r 40 THIIDLSQTVPMLQKALQVISDTVA-RGGRILFVATKSQASDCVMEAAKRS--AQ---YCVN 95 (278)
Q Consensus 40 ihIIdL~kT~~~L~~A~~~i~~i~~-~gg~ILFVgTk~~~~~~i~~~A~~~--~~---~yV~ 95 (278)
+-+++.-+.+..+.+..+.+.+.+. ..-.+++.---+.+.--+.+.+++. |. |||.
T Consensus 58 mG~~evl~~~~~~~~~~~~~~~~i~~~~Pd~vi~ID~pgFnlrlak~lkk~~~~ipvi~yv~ 119 (382)
T PRK00025 58 MGLVEVLPRLPRLLKIRKELKRLLLAEPPDVFILIDAPDFNLRLAKKLKKALPGIPIIHYVS 119 (382)
T ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHHHCCCCCEEEEEC
T ss_conf 01999997799999999999999986499999997783065999999997169998899947
No 99
>PRK11337 DNA-binding transcriptional repressor RpiR; Provisional
Probab=69.56 E-value=10 Score=19.19 Aligned_cols=51 Identities=24% Similarity=0.409 Sum_probs=35.9
Q ss_pred CCEEEEECCCCC----CHHHHHHHHCCCEEEEECCCCCCC--HHCCCEEE--ECCCCHH
Q ss_conf 957999438877----123212343398145403677670--01152032--1577268
Q gi|254780779|r 159 PDLMFVVDTNRE----KLAIQEARRLRIPIVAVVDTNSNP--DLVDYVIP--GNDDSSR 209 (278)
Q Consensus 159 P~~iiv~d~~~e----~~Av~EA~kl~IPvIaivDTn~dp--~~idypIP--~NDds~~ 209 (278)
-|++|++.-..+ --+++.|++.|+|||+|.|...+| ...||.+. .++...+
T Consensus 189 ~Dv~i~iS~sG~t~e~i~~~~~Ak~~Ga~vI~IT~~~~SpLa~~aD~vL~~~~~e~~~~ 247 (293)
T PRK11337 189 GDVVLVVSHSGRTSDVKAAVELAKQNGAKIICITHSYHSPIAKLADYIICSPAPETPLL 247 (293)
T ss_pred CCEEEEEECCCCCHHHHHHHHHHHHCCCEEEEECCCCCCHHHHHCCEEEECCCCCCCCC
T ss_conf 98899981899988999999999987994999769999846895899886488764434
No 100
>cd01536 PBP1_ABC_sugar_binding_like Periplasmic sugar-binding domain of active transport systems that are members of the type I periplasmic binding protein (PBP1) superfamily. Periplasmic sugar-binding domain of active transport systems that are members of the type I periplasmic binding protein (PBP1) superfamily. The members of this family function as the primary receptors for chemotaxis and transport of many sugar based solutes in bacteria and archaea. The sugar binding domain is also homologous to the ligand-binding domain of eukaryotic receptors such as glutamate receptor (GluR) and DNA-binding transcriptional repressors such as LacI and GalR. Moreover, this periplasmic binding domain, also known as Venus flytrap domain, undergoes transition from an open to a closed conformational state upon the binding of ligands such as lactose, ribose, fructose, xylose, arabinose, galactose/glucose, and other sugars. This family also includes the periplasmic binding domain of autoinducer-2 (AI-2
Probab=69.49 E-value=10 Score=19.18 Aligned_cols=33 Identities=18% Similarity=0.128 Sum_probs=23.8
Q ss_pred CCCEEEEECCCCCCHHHHHHHHCCCE----EEEECCC
Q ss_conf 59579994388771232123433981----4540367
Q gi|254780779|r 158 LPDLMFVVDTNREKLAIQEARRLRIP----IVAVVDT 190 (278)
Q Consensus 158 lP~~iiv~d~~~e~~Av~EA~kl~IP----vIaivDT 190 (278)
.|++||+.+-.--.-+++.++.+|+| +||+=|+
T Consensus 181 ~~~ai~~~nd~~a~g~~~al~~~g~~~di~viG~D~~ 217 (267)
T cd01536 181 DIDAIFAANDSMALGAVAALKAAGRKGDVKIVGVDGS 217 (267)
T ss_pred CCEEEEECCCHHHHHHHHHHHHCCCCCCEEEEEECCC
T ss_conf 8629997164999999999997699999399998983
No 101
>cd01540 PBP1_arabinose_binding Periplasmic L-arabinose-binding protein (ABP), a member of a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily. Periplasmic L-arabinose-binding protein (ABP), a member of a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily. ABP is only involved in transport contrary to other related sugar-binding proteins such as the glucose/galactose-binding protein (GGBP) and the ribose-binding protein (RBP), both of which are involved in chemotaxis as well as transport. The periplasmic ABP consists of two alpha/beta globular domains connected by a three-stranded hinge, a Venus flytrap-like domain, which undergoes a transition from an open to a closed conformational state upon ligand binding. Moreover, ABP is homologous to the ligand-binding domain of eukaryotic receptors such as metabotropic glutamate receptor (mGluR) and DNA-binding transcriptional repressors such a
Probab=69.27 E-value=8 Score=19.84 Aligned_cols=40 Identities=18% Similarity=0.239 Sum_probs=21.2
Q ss_pred HHHHHHHHCCCCEEEEEE-CCHHHHHHHHHHHHHCCCEECC
Q ss_conf 999998610788169960-7823579999998633983142
Q gi|254780779|r 56 LQVISDTVARGGRILFVA-TKSQASDCVMEAAKRSAQYCVN 95 (278)
Q Consensus 56 ~~~i~~i~~~gg~ILFVg-Tk~~~~~~i~~~A~~~~~~yV~ 95 (278)
...+..++.+|-..++|. +...+...+-+.|...|.|-|+
T Consensus 44 ~~~ie~~i~qgvd~iii~p~d~~~~~~~v~~A~~agIpVv~ 84 (289)
T cd01540 44 LSAIDNLGAQGAKGFVICVPDVKLGPAIVAKAKAYNMKVVA 84 (289)
T ss_pred HHHHHHHHHCCCCEEEECCCCCCHHHHHHHHHHHCCCEEEE
T ss_conf 99999999858988999278710018999999987986999
No 102
>TIGR02639 ClpA ATP-dependent Clp protease ATP-binding subunit ClpA; InterPro: IPR013461 Proteins in this entry are related to ClpA () from Escherichia coli. ClpA is an ATP-dependent chaperone and part of the ClpAP protease that participates in regulatory protein degradation and the dissolution and degradation of protein aggregates . ClpA recognises sequences in specific proteins, which it then unfolds in an ATP-dependent manner and transports into the degradation chamber of the associated ClpP protein , . A small adaptor-like protein, ClpS, modulates the activity of ClpA and is an important regulatory factor for this protein . It protects ClpA from autodegradation and appears to redirect its activity away from soluble proteins and toward aggregated proteins..
Probab=69.21 E-value=10 Score=19.20 Aligned_cols=189 Identities=14% Similarity=0.200 Sum_probs=104.8
Q ss_pred CCCCCCCCCCCCCCCEEEECHHHHHHHHHHHHHHHHHHHCCCCEEEEEECCHHH-HHHHHHHHHHC--------------
Q ss_conf 578856210200188167538999999999999999861078816996078235-79999998633--------------
Q gi|254780779|r 25 WNPKMERYIFCERNNTHIIDLSQTVPMLQKALQVISDTVARGGRILFVATKSQA-SDCVMEAAKRS-------------- 89 (278)
Q Consensus 25 wnPkM~~yI~g~rngihIIdL~kT~~~L~~A~~~i~~i~~~gg~ILFVgTk~~~-~~~i~~~A~~~-------------- 89 (278)
..+..+.=|||.=.- +++-+..++++..=+.+--+==|++||+|--=.. .++-++.|+..
T Consensus 491 L~~~L~~kIfGQD~A-----I~~lv~aiK~SrAGl~~~nkP~GSFLF~GPTGVGKTElak~LA~~LGv~l~RFDMSEYmE 565 (774)
T TIGR02639 491 LEKELKAKIFGQDEA-----IEQLVSAIKRSRAGLGEPNKPVGSFLFVGPTGVGKTELAKQLAEELGVHLLRFDMSEYME 565 (774)
T ss_pred HHHHHHCCCCCHHHH-----HHHHHHHHHHHHHHCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHCCHHCCCCCHHHHH
T ss_conf 447630131515899-----999999999987424778881688886479896257889999997082001046504468
Q ss_pred --------CCE--ECCCCCCCCCCCCHHHHHHHHH---HHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHC
Q ss_conf --------983--1423345873234266655567---789988763012126774678876655677764344332211
Q gi|254780779|r 90 --------AQY--CVNSKWLGGMMTNWKTVSQSIQ---KLRDLEELLNKENQGFTKKERLNIERKRDKLKRALDGIRDMG 156 (278)
Q Consensus 90 --------~~~--yV~~RWlGG~LTN~~ti~~si~---~l~~l~~~~~~~~~~~tkKe~~~~~r~~~kl~k~lgGi~~m~ 156 (278)
|+| ||=.- -||.||+ .|+|.=. -|-++|+--...++-| |+.+ .+..|-.+=|=-.+
T Consensus 566 KHTVsRLIGsPPGYVGfE-qGGLLT~--AvrK~P~cVLLLDEIEKAHpDI~NIL-----LQVM-D~AtLTDN~GrKaD-- 634 (774)
T TIGR02639 566 KHTVSRLIGSPPGYVGFE-QGGLLTD--AVRKHPHCVLLLDEIEKAHPDIYNIL-----LQVM-DYATLTDNNGRKAD-- 634 (774)
T ss_pred HHHHHHHHCCCCCCCCCC-CCCCCHH--HHCCCCCEEEHHHHHHHHHHHHHHHH-----HHHH-CCCEEECCCCCEEE--
T ss_conf 999987416888851316-7772122--33128853542346666313366678-----7663-35434058885763--
Q ss_pred CCCCEEEEECCCCCCHHHHHHHHCCCEEEEECCCCCC-C-----------H---HCCCEEEECCCCHHHHHHHHHHHHHH
Q ss_conf 3595799943887712321234339814540367767-0-----------0---11520321577268999999999999
Q gi|254780779|r 157 GLPDLMFVVDTNREKLAIQEARRLRIPIVAVVDTNSN-P-----------D---LVDYVIPGNDDSSRSIALFCDLVASA 221 (278)
Q Consensus 157 ~lP~~iiv~d~~~e~~Av~EA~kl~IPvIaivDTn~d-p-----------~---~idypIP~NDds~~si~l~~~~i~~a 221 (278)
.=.+|.|+=.|- =|+-.+=|.||+.+.+.. - . -+|=.||-||=+...+..|+....+.
T Consensus 635 -FRNVILIMTSNa------Ga~E~~~~~iGF~~~~~~~~~~~Aikk~F~PEFRNRLDaii~F~~L~~~~~~~i~~K~l~e 707 (774)
T TIGR02639 635 -FRNVILIMTSNA------GAREMSKNPIGFGGERVEDKSEKAIKKLFSPEFRNRLDAIIAFNDLSEEVAEKIVKKFLDE 707 (774)
T ss_pred -ECCEEEEECCCC------CCCCCCCCCCCCCCCCCHHHHHHHHHHHCCCCCCCCCCCEEECCCCCHHHHHHHHHHHHHH
T ss_conf -113688840370------0102367764425554123348889731587420133464416998899999999999999
Q ss_pred HHHHHHHHHHHCCCC
Q ss_conf 999999744310111
Q gi|254780779|r 222 AIDGIARQHSYMGAD 236 (278)
Q Consensus 222 i~~g~~~~~~~~~~~ 236 (278)
+...+..+.-.....
T Consensus 708 l~~~L~eK~v~l~l~ 722 (774)
T TIGR02639 708 LQKQLNEKNVELELT 722 (774)
T ss_pred HHHHHHHCCEEEEEC
T ss_conf 997553065378764
No 103
>PRK08694 consensus
Probab=69.06 E-value=10 Score=19.13 Aligned_cols=161 Identities=17% Similarity=0.221 Sum_probs=81.1
Q ss_pred CCCCCCCC-EEEEC----HHHHHHHHHHHHHHHHHHHCCCC-EEEEEECCHHHHHHHHHHHHHC-CCEECCCCCCCCCCC
Q ss_conf 10200188-16753----89999999999999998610788-1699607823579999998633-983142334587323
Q gi|254780779|r 32 YIFCERNN-THIID----LSQTVPMLQKALQVISDTVARGG-RILFVATKSQASDCVMEAAKRS-AQYCVNSKWLGGMMT 104 (278)
Q Consensus 32 yI~g~rng-ihIId----L~kT~~~L~~A~~~i~~i~~~gg-~ILFVgTk~~~~~~i~~~A~~~-~~~yV~~RWlGG~LT 104 (278)
.+-|.+.| +.||= .-||...|.-| ..++.+++ .|+|..---...+++..+.... +.+ .++.--|.||
T Consensus 211 ~t~Gl~~G~LiVIaaRPsmGKTalalnia----~~~a~~~~~~V~~fSLEMs~~~l~~Rlla~~s~v~--~~~i~~g~l~ 284 (468)
T PRK08694 211 KTSGLQPGDLIIVAGRPSMGKTAFSINIA----EHVAVEGKLPVAVFSMEMGGAQLVMRMLGSVGRLD--QSVLKTGRLE 284 (468)
T ss_pred HHCCCCCCCEEEEEECCCCCHHHHHHHHH----HHHHHHCCCCEEEECCCCCHHHHHHHHHHHHCCCC--HHHCCCCCCC
T ss_conf 64488878479996178653789999999----99998479847997788999999999999725986--3211048999
Q ss_pred C--HHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCEEEEE-----CC-CCC---CHH
Q ss_conf 4--266655567789988763012126774678876655677764344332211359579994-----38-877---123
Q gi|254780779|r 105 N--WKTVSQSIQKLRDLEELLNKENQGFTKKERLNIERKRDKLKRALDGIRDMGGLPDLMFVV-----DT-NRE---KLA 173 (278)
Q Consensus 105 N--~~ti~~si~~l~~l~~~~~~~~~~~tkKe~~~~~r~~~kl~k~lgGi~~m~~lP~~iiv~-----d~-~~e---~~A 173 (278)
. |..+...+.++.++.-.. .....+|--+.... ..++.+..|+ .+++|||= ++ .+. ...
T Consensus 285 ~~e~~~~~~a~~~l~~~pl~i-dd~~~~t~~~i~a~---~r~~~~~~~~------kl~~vvIDYLqLi~~~~~~~~r~~~ 354 (468)
T PRK08694 285 DEHWGRLNEAVVKLSDAPVYI-DETPGLTALELRAR---ARRLARQFNN------KLGLIVIDYLQLMAGSGRSDNRASE 354 (468)
T ss_pred HHHHHHHHHHHHHHHCCCEEE-ECCCCCCHHHHHHH---HHHHHHHHCC------CCCEEEEEHHHHCCCCCCCCCHHHH
T ss_conf 999999999999986299689-76999988799999---9999998389------8738997367541688876559999
Q ss_pred HHH--------HHHCCCEEEEECCCCCCCHHCCCEEEECCCCH
Q ss_conf 212--------34339814540367767001152032157726
Q gi|254780779|r 174 IQE--------ARRLRIPIVAVVDTNSNPDLVDYVIPGNDDSS 208 (278)
Q Consensus 174 v~E--------A~kl~IPvIaivDTn~dp~~idypIP~NDds~ 208 (278)
|.| |+.|+||||+++-=|=..+.=+=--|.-.|-.
T Consensus 355 i~~isr~LK~lAkel~ipvi~LsQLnR~~e~R~dkrP~lsDLR 397 (468)
T PRK08694 355 LGEISRSLKALAKELQVPIIALSQLSRTVESRTDKRPMMSDLR 397 (468)
T ss_pred HHHHHHHHHHHHHHHCCCEEEECCCCCCCCCCCCCCCCCCCCC
T ss_conf 9999999999999979989996326854233799998713012
No 104
>PRK10936 periplasmic sensory protein associated with the TorRS two-component regulatory system; Provisional
Probab=68.87 E-value=10 Score=19.10 Aligned_cols=58 Identities=12% Similarity=0.200 Sum_probs=32.6
Q ss_pred HHHHHHHHHHHHHHHHHCCCCCEEEEECCCCCCHHHHHHHHCCCEEEEECCCCCCCHHCCCEEEEC
Q ss_conf 655677764344332211359579994388771232123433981454036776700115203215
Q gi|254780779|r 139 ERKRDKLKRALDGIRDMGGLPDLMFVVDTNREKLAIQEARRLRIPIVAVVDTNSNPDLVDYVIPGN 204 (278)
Q Consensus 139 ~r~~~kl~k~lgGi~~m~~lP~~iiv~d~~~e~~Av~EA~kl~IPvIaivDTn~dp~~idypIP~N 204 (278)
.+|..-++.++ .+-+|+|++--+..+. +..++...|||||++++ ..|.+.+.=.|=.|
T Consensus 90 ~~Q~~qie~~i------~~~vDAIil~~vd~~a-~~~~~~~agIPVI~~dn-~i~~~~~~~~vg~d 147 (340)
T PRK10936 90 ATQQQQLEQCV------AWGADAILLGAVTPDG-PDLQLQAANIPVIALVN-GIDSPQVTTRVGVS 147 (340)
T ss_pred HHHHHHHHHHH------HCCCCEEEECCCCCCC-HHHHHHHCCCCEEEEEC-CCCCCCCCEEEECC
T ss_conf 99999999999------7599999986788341-15689858997899966-77777644488456
No 105
>PRK09701 D-allose transporter subunit; Provisional
Probab=68.36 E-value=4 Score=21.82 Aligned_cols=37 Identities=11% Similarity=0.036 Sum_probs=26.1
Q ss_pred CCCCEEEEE--CCCCCCHHHHHHHHCCCEEEEECCCCCCC
Q ss_conf 359579994--38877123212343398145403677670
Q gi|254780779|r 157 GLPDLMFVV--DTNREKLAIQEARRLRIPIVAVVDTNSNP 194 (278)
Q Consensus 157 ~lP~~iiv~--d~~~e~~Av~EA~kl~IPvIaivDTn~dp 194 (278)
+-||+|+|. |+..=..+|++|..-|||||. +|+.-|+
T Consensus 81 ~gvdaIii~p~d~~a~~~~i~~A~~aGIpVV~-~D~~v~~ 119 (311)
T PRK09701 81 KNYKGIAFAPLSSVNLVMPVARAWKKGIYLVN-LDEKIDM 119 (311)
T ss_pred CCCCEEEEECCCHHHHHHHHHHHHHCCCCEEE-CCCCCCC
T ss_conf 59999999189877889999999977991896-3676673
No 106
>cd05005 SIS_PHI Hexulose-6-phosphate isomerase (PHI). PHI is a member of the SIS (Sugar ISomerase domain) superfamily. In the ribulose monophosphate pathway of formaldehyde fixation, hexulose-6-phosphate synthase catalyzes the condensation of ribulose-5-phosphate with formadelhyde to become hexulose-6-phosphate, which is then isomerized to fructose-6-phosphate by PHI.
Probab=68.28 E-value=11 Score=19.02 Aligned_cols=73 Identities=22% Similarity=0.329 Sum_probs=40.8
Q ss_pred CCEEEEECCCCC----CHHHHHHHHCCCEEEEECCCCCCC--HHCC--CEEEECC-----CCHHHHH-------HHHHHH
Q ss_conf 957999438877----123212343398145403677670--0115--2032157-----7268999-------999999
Q gi|254780779|r 159 PDLMFVVDTNRE----KLAIQEARRLRIPIVAVVDTNSNP--DLVD--YVIPGND-----DSSRSIA-------LFCDLV 218 (278)
Q Consensus 159 P~~iiv~d~~~e----~~Av~EA~kl~IPvIaivDTn~dp--~~id--ypIP~ND-----ds~~si~-------l~~~~i 218 (278)
=|++|++.-..+ ..+++-|++.|++||+|.....+| ...| ..||+.. +...++. ..+..+
T Consensus 76 ~Dv~I~iS~SG~T~~~~~~~~~aK~~ga~iI~IT~~~~S~la~~aD~~l~ip~~~~~~~~~~~~s~~pm~s~~e~~~l~~ 155 (179)
T cd05005 76 GDLLIAISGSGETSSVVNAAEKAKKAGAKVVLITSNPDSPLAKLADVVVVIPAATKDDHGGEHKSIQPLGTLFEQSALVF 155 (179)
T ss_pred CCEEEEECCCCCCHHHHHHHHHHHHCCCEEEEEECCCCCHHHHHCCEEEECCCCCCCCCCCCCCCCCCCCCHHHHHHHHH
T ss_conf 99999981999956899999999987991999979899978995899998187431388889876575775999999999
Q ss_pred HHHHHHHHHHHHH
Q ss_conf 9999999997443
Q gi|254780779|r 219 ASAAIDGIARQHS 231 (278)
Q Consensus 219 ~~ai~~g~~~~~~ 231 (278)
.|++.-..-++..
T Consensus 156 ~Dal~~~lm~~~~ 168 (179)
T cd05005 156 LDAVIAKLMEELG 168 (179)
T ss_pred HHHHHHHHHHHCC
T ss_conf 9999999999809
No 107
>PRK05562 precorrin-2 dehydrogenase; Provisional
Probab=68.10 E-value=11 Score=19.00 Aligned_cols=126 Identities=17% Similarity=0.133 Sum_probs=64.8
Q ss_pred HHHHHHHHCCCCEEEEEECCHHHHHHHHHHHHHCCCEECCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHC--CCCCCCHH
Q ss_conf 9999986107881699607823579999998633983142334587323426665556778998876301--21267746
Q gi|254780779|r 56 LQVISDTVARGGRILFVATKSQASDCVMEAAKRSAQYCVNSKWLGGMMTNWKTVSQSIQKLRDLEELLNK--ENQGFTKK 133 (278)
Q Consensus 56 ~~~i~~i~~~gg~ILFVgTk~~~~~~i~~~A~~~~~~yV~~RWlGG~LTN~~ti~~si~~l~~l~~~~~~--~~~~~tkK 133 (278)
+.||. +.++.-++|.||-.+.|.+-++...+..-.-.|-...+.- .+.+|.+...- ....|...
T Consensus 15 ~~~i~-l~s~klkvLVVGGG~VA~RKi~~Ll~agA~VtVVSP~~~~-------------el~~L~~~~~I~~i~r~y~~~ 80 (222)
T PRK05562 15 YSFIS-LLSNKIKVLVIGGGKAAFIKGKTFLKKGCYVEILSKEFSK-------------EFLDLKKYGNLKLIKGNYDKE 80 (222)
T ss_pred EEEEE-EECCCCEEEEECCCHHHHHHHHHHHHCCCEEEEECCCCCH-------------HHHHHHHCCCEEEEECCCCHH
T ss_conf 13324-3126766999998799999999998789989998786688-------------999999759869996867977
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHCCCCCEEEEE--CCCCCCHHHHHHHHCCCEEEEECCCCCCCHHCCCEEEEC-------
Q ss_conf 78876655677764344332211359579994--388771232123433981454036776700115203215-------
Q gi|254780779|r 134 ERLNIERKRDKLKRALDGIRDMGGLPDLMFVV--DTNREKLAIQEARRLRIPIVAVVDTNSNPDLVDYVIPGN------- 204 (278)
Q Consensus 134 e~~~~~r~~~kl~k~lgGi~~m~~lP~~iiv~--d~~~e~~Av~EA~kl~IPvIaivDTn~dp~~idypIP~N------- 204 (278)
.+.| ..+||.- |+.-+...-++|...||++....| |..-+|.+|+-
T Consensus 81 --------------dL~~-------~~LVIaATdd~~lN~~I~~~a~~~~ilvNvvdd----p~~~~fi~Paiv~Rg~L~ 135 (222)
T PRK05562 81 --------------FIKD-------KHLIIIATDDEELNNKIRKHCDRLYKLYIDCSD----FKKGLCVIPYQRSSKNMV 135 (222)
T ss_pred --------------HCCC-------CCEEEEECCCHHHHHHHHHHHHHHCCEEEECCC----CCCCCEEECEEEEECCEE
T ss_conf --------------8088-------739999479889999999999980998898578----876817977099728979
Q ss_pred ------CCCHHHHHHHHHHHHH
Q ss_conf ------7726899999999999
Q gi|254780779|r 205 ------DDSSRSIALFCDLVAS 220 (278)
Q Consensus 205 ------Dds~~si~l~~~~i~~ 220 (278)
--|+.--.++...+..
T Consensus 136 IAIST~G~SP~lAr~iR~klE~ 157 (222)
T PRK05562 136 FALNTKGGSPKTSVFIGEKVKN 157 (222)
T ss_pred EEEECCCCCHHHHHHHHHHHHH
T ss_conf 9998999897999999999999
No 108
>pfam02350 Epimerase_2 UDP-N-acetylglucosamine 2-epimerase. This family consists of UDP-N-acetylglucosamine 2-epimerases EC:5.1.3.14 this enzyme catalyses the production of UDP-ManNAc from UDP-GlcNAc. Note that some of the enzymes is this family are bifunctional, in this instance Pfam matches only the N-terminal half of the protein suggesting that the additional C-terminal part (when compared to mono-functional members of this family) is responsible for the UPD-N-acetylmannosamine kinase activity of these enzymes. This hypothesis is further supported by the assumption that the C-terminal part of rat bifunctional UDP-N-acetylglucosamine 2-epimerase/N-acetylmannosamine kinase is the kinase domain.
Probab=67.95 E-value=11 Score=19.02 Aligned_cols=26 Identities=27% Similarity=0.327 Sum_probs=17.3
Q ss_pred CHHHHHHHHCCCEEEEECCCCCCCHH
Q ss_conf 12321234339814540367767001
Q gi|254780779|r 171 KLAIQEARRLRIPIVAVVDTNSNPDL 196 (278)
Q Consensus 171 ~~Av~EA~kl~IPvIaivDTn~dp~~ 196 (278)
...+.||--+|+|+|-+=|+.-=|..
T Consensus 267 s~~~~Ea~~l~~P~iniR~~geRqeg 292 (346)
T pfam02350 267 GGIQEEAPSLGKPVLNLRDTTERPEG 292 (346)
T ss_pred CCHHHHHHHHCCCEEEECCCCCCHHH
T ss_conf 62166666508968982788888756
No 109
>PRK05973 replicative DNA helicase; Provisional
Probab=67.78 E-value=11 Score=18.96 Aligned_cols=119 Identities=16% Similarity=0.204 Sum_probs=58.7
Q ss_pred HHHHHHHHHHHHHHHHHHCCCCEEEEEECCHHHHHHHHHHHHHCCCEECCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHC
Q ss_conf 99999999999999986107881699607823579999998633983142334587323426665556778998876301
Q gi|254780779|r 46 SQTVPMLQKALQVISDTVARGGRILFVATKSQASDCVMEAAKRSAQYCVNSKWLGGMMTNWKTVSQSIQKLRDLEELLNK 125 (278)
Q Consensus 46 ~kT~~~L~~A~~~i~~i~~~gg~ILFVgTk~~~~~~i~~~A~~~~~~yV~~RWlGG~LTN~~ti~~si~~l~~l~~~~~~ 125 (278)
-||...|..|.+. +..|+.++|..---....++..+..-.-..--+.++. .++
T Consensus 76 GKTafaLnla~~A----~k~g~~v~fFSLEM~~~ql~~RL~~~~~~~~~~~~~~------------------~iD----- 128 (237)
T PRK05973 76 GKTLLGLELAVEA----MKSGRTGVFFTLEYTEKDVLDRLRALGVDRAQFADLF------------------EFD----- 128 (237)
T ss_pred CHHHHHHHHHHHH----HHHCCCEEEEEECCCHHHHHHHHHHCCCCHHHCCCCC------------------EEC-----
T ss_conf 7899999999999----9959966999615999999999997277833406751------------------003-----
Q ss_pred CCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCEEEEEC------CCCCCHHHHH--------HHHCCCEEEEECCCC
Q ss_conf 21267746788766556777643443322113595799943------8877123212--------343398145403677
Q gi|254780779|r 126 ENQGFTKKERLNIERKRDKLKRALDGIRDMGGLPDLMFVVD------TNREKLAIQE--------ARRLRIPIVAVVDTN 191 (278)
Q Consensus 126 ~~~~~tkKe~~~~~r~~~kl~k~lgGi~~m~~lP~~iiv~d------~~~e~~Av~E--------A~kl~IPvIaivDTn 191 (278)
.-+..+.-+. ..+|.+. -+.-++||| ..++...+.| |+.+|+|||+|.--|
T Consensus 129 ~sd~i~~~~i------~rrl~~~---------~~~~LIVIDYLQLM~~~r~~~eiseisRsLK~lAkEl~vPVvaLSQLn 193 (237)
T PRK05973 129 TSDAICADYI------IARLASA---------PRGTLVVIDYLQLLDQRREKPDLSVQVRALKSFARKRGVILVFISQID 193 (237)
T ss_pred CCHHHHHHHH------HHHHHHC---------CCCCEEEEECHHHHCCCCCCCCHHHHHHHHHHHHHHHCCCEEEEECCC
T ss_conf 8303339999------9998527---------899689997677526677886689999999999998699399940036
Q ss_pred CCCHHCCCEEEECCC
Q ss_conf 670011520321577
Q gi|254780779|r 192 SNPDLVDYVIPGNDD 206 (278)
Q Consensus 192 ~dp~~idypIP~NDd 206 (278)
=..+.-.=.-|...|
T Consensus 194 Rs~E~R~dKrP~lSD 208 (237)
T PRK05973 194 RSFDPASKPLPDIRD 208 (237)
T ss_pred CCCCCCCCCCCCCCC
T ss_conf 432235678997401
No 110
>cd06294 PBP1_ycjW_transcription_regulator_like Ligand-binding domain of uncharacterized transcription regulator ycjW which is a member of the LacI-GalR family repressors. This group includes the ligand-binding domain of uncharacterized transcription regulator ycjW which is a member of the LacI-GalR family repressors that are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.
Probab=67.46 E-value=11 Score=18.92 Aligned_cols=63 Identities=16% Similarity=0.195 Sum_probs=42.9
Q ss_pred CCCCCEEEEECCCCCCHHHHHHHHCCCE------EEEECCCC----CCCHHCCCEEEECCCCHHHHHHHHHHH
Q ss_conf 1359579994388771232123433981------45403677----670011520321577268999999999
Q gi|254780779|r 156 GGLPDLMFVVDTNREKLAIQEARRLRIP------IVAVVDTN----SNPDLVDYVIPGNDDSSRSIALFCDLV 218 (278)
Q Consensus 156 ~~lP~~iiv~d~~~e~~Av~EA~kl~IP------vIaivDTn----~dp~~idypIP~NDds~~si~l~~~~i 218 (278)
...|+++|+.+-.--.-+++.++.+|+. ++|+=|+. +.|.+-+.-.|...=+..++++++..+
T Consensus 181 ~~~~tai~~~nD~~A~g~~~al~~~g~~iP~disvvgfDd~~~~~~~~P~LTtv~q~~~~~G~~A~~~Ll~~i 253 (270)
T cd06294 181 HPRPTAIVATDDLLALGVLKVLNELGLKVPEDLSIIGFNNSILSELAHPPLTSVDINPRELGYEAAELLIDLI 253 (270)
T ss_pred CCCCCEEEECCHHHHHHHHHHHHHCCCCCCCCEEEEEECCHHHHHHCCCCCEEEECCHHHHHHHHHHHHHHHH
T ss_conf 9998489987749999999999983999999849999897289984289817997399999999999999996
No 111
>cd06314 PBP1_tmGBP Periplasmic sugar-binding domain of Thermotoga maritima glucose-binding protein (tmGBP) and its close homologs. Periplasmic sugar-binding domain of Thermotoga maritima glucose-binding protein (tmGBP) and its close homologs from other bacteria. They are a member of the type I periplasmic binding protein superfamily which consists of two domains connected by a three-stranded hinge. TmGBP is specific for glucose and its binding pocket is buried at the interface of the two domains. TmGBP also exhibits high thermostability and the highest structural similarity to E. coli glucose binding protein (ecGBP).
Probab=67.39 E-value=5 Score=21.16 Aligned_cols=40 Identities=30% Similarity=0.470 Sum_probs=17.6
Q ss_pred CCCCE--EEEECCCCC---CHHHHHHHHCC-CEEEEECCCCCCCHHCCC
Q ss_conf 35957--999438877---12321234339-814540367767001152
Q gi|254780779|r 157 GLPDL--MFVVDTNRE---KLAIQEARRLR-IPIVAVVDTNSNPDLVDY 199 (278)
Q Consensus 157 ~lP~~--iiv~d~~~e---~~Av~EA~kl~-IPvIaivDTn~dp~~idy 199 (278)
.-||+ +|..+...- ..|++++.+.+ |.++|+ |.+|+.+++
T Consensus 176 ~~pdi~~i~~~~~~~a~ga~~Al~~~g~~~~i~vvg~---D~~~~~~~~ 221 (271)
T cd06314 176 AHPDLKCMFGLYAYNGPAIAEAVKAAGKLGKVKIVGF---DEDPDTLQG 221 (271)
T ss_pred HCCCCCEEEEECCCCHHHHHHHHHHHCCCCCCEEEEE---CCCHHHHHH
T ss_conf 5899878998088516999999998475899679987---898999999
No 112
>cd01743 GATase1_Anthranilate_Synthase Type 1 glutamine amidotransferase (GATase1) domain found in Anthranilate synthase. Type 1 glutamine amidotransferase (GATase1) domain found in Anthranilate synthase (ASase). This group contains proteins similar to para-aminobenzoate (PABA) synthase and ASase. These enzymes catalyze similar reactions and produce similar products, PABA and ortho-aminobenzoate (anthranilate). Each enzyme is composed of non-identical subunits: a glutamine amidotransferase subunit (component II) and a subunit that produces an aminobenzoate products (component I). ASase catalyses the synthesis of anthranilate from chorismate and glutamine and is a tetrameric protein comprising two copies each of components I and II. Component II of ASase belongs to the family of triad GTases which hydrolyze glutamine and transfer nascent ammonia between the active sites. In some bacteria, such as Escherichia coli, component II can be much larger than in other organisms, due to the prese
Probab=67.16 E-value=11 Score=18.88 Aligned_cols=31 Identities=26% Similarity=0.367 Sum_probs=23.0
Q ss_pred CCEEEEEC-C---CC--CCHHHHHHHHCCCEEEEECC
Q ss_conf 95799943-8---87--71232123433981454036
Q gi|254780779|r 159 PDLMFVVD-T---NR--EKLAIQEARRLRIPIVAVVD 189 (278)
Q Consensus 159 P~~iiv~d-~---~~--e~~Av~EA~kl~IPvIaivD 189 (278)
||+||+.. | .. ....+.++.+.+||+.|||=
T Consensus 43 ~~giiLS~GPg~p~~~~~~~~~~~~l~~~iPiLGIC~ 79 (184)
T cd01743 43 PDAIVISPGPGHPEDAGISLEIIRALAGKVPILGVCL 79 (184)
T ss_pred CCEEEECCCCCCHHHCCCHHHHHHHHHCCCCEEEECH
T ss_conf 7999999999892561460999999846998999809
No 113
>TIGR03127 RuMP_HxlB 6-phospho 3-hexuloisomerase. Members of this protein family are 6-phospho 3-hexuloisomerase (PHI), or the PHI domain of a fusion protein. This enzyme is part of the ribulose monophosphate (RuMP) pathway, which in one direction removes the toxic metabolite formaldehyde by assimilation into fructose-6-phosphate. In the other direction, in species lacking a complete pentose phosphate pathway, the RuMP pathway yields ribulose-5-phosphate, necessary for nucleotide biosynthesis, at the cost of also yielding formaldehyde. These latter species tend usually have a formaldehyde-activating enzyme to attach formaldehyde to the C1 carrier tetrahydromethanopterin.
Probab=66.98 E-value=11 Score=18.86 Aligned_cols=136 Identities=18% Similarity=0.219 Sum_probs=68.3
Q ss_pred HHHHHHHHHH-HHHHHHHHHCCCCEEEEEECCHHHHHHHHHHHHHCCCEECCCCCCCCCCCCHHHHHHHHHHHHHHHHHH
Q ss_conf 8999999999-999999861078816996078235799999986339831423345873234266655567789988763
Q gi|254780779|r 45 LSQTVPMLQK-ALQVISDTVARGGRILFVATKSQASDCVMEAAKRSAQYCVNSKWLGGMMTNWKTVSQSIQKLRDLEELL 123 (278)
Q Consensus 45 L~kT~~~L~~-A~~~i~~i~~~gg~ILFVgTk~~~~~~i~~~A~~~~~~yV~~RWlGG~LTN~~ti~~si~~l~~l~~~~ 123 (278)
|++|...|.. .+.-+.+...+.++|.|.|..+..- +-+.++.+...--.+-.|+|-+.+. +
T Consensus 8 i~~t~~~id~~~i~~~v~~I~~a~~I~v~G~G~Sg~-ia~~~a~rL~~~G~~~~~~~d~~~~------~----------- 69 (179)
T TIGR03127 8 ISQVASRIDEEELDKLADKIIKAKRIFVAGAGRSGL-VGKAFAMRLMHLGFNVYVVGETTTP------S----------- 69 (179)
T ss_pred HHHHHHHCCHHHHHHHHHHHHCCCCEEEEEECCHHH-HHHHHHHHHHHCCCEEEEECCCCCC------C-----------
T ss_conf 999999669999999999997399099999554399-9999999998519757997644446------6-----------
Q ss_pred HCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCEEEEECCCCC----CHHHHHHHHCCCEEEEECCCCCCC--H--
Q ss_conf 01212677467887665567776434433221135957999438877----123212343398145403677670--0--
Q gi|254780779|r 124 NKENQGFTKKERLNIERKRDKLKRALDGIRDMGGLPDLMFVVDTNRE----KLAIQEARRLRIPIVAVVDTNSNP--D-- 195 (278)
Q Consensus 124 ~~~~~~~tkKe~~~~~r~~~kl~k~lgGi~~m~~lP~~iiv~d~~~e----~~Av~EA~kl~IPvIaivDTn~dp--~-- 195 (278)
+ +-=|++|++.-..+ ..+++-|++.|+|+|+|.....+| .
T Consensus 70 ------i--------------------------~~~Dv~I~iS~SGeT~e~~~~~~~aK~~ga~ii~IT~~~~S~Lak~a 117 (179)
T TIGR03127 70 ------I--------------------------KKGDLLIAISGSGETESLVTVAKKAKEIGATVAAITTNPESTLGKLA 117 (179)
T ss_pred ------C--------------------------CCCCEEEEECCCCCCHHHHHHHHHHHHCCCEEEEEECCCCCHHHHHC
T ss_conf ------9--------------------------99999999819999689999999999879929999798989779949
Q ss_pred HCCCEEEEC-----CCCHHHHH-------HHHHHHHHHHHHHHHHHH
Q ss_conf 115203215-----77268999-------999999999999999744
Q gi|254780779|r 196 LVDYVIPGN-----DDSSRSIA-------LFCDLVASAAIDGIARQH 230 (278)
Q Consensus 196 ~idypIP~N-----Dds~~si~-------l~~~~i~~ai~~g~~~~~ 230 (278)
.+...||+. ++...++. ..+-.+.|++.-..-+++
T Consensus 118 D~~l~ip~~~~~~~~~~~~~~~p~~s~~e~~~l~~~Dal~~~l~~~~ 164 (179)
T TIGR03127 118 DVVVEIPAATKKDSEGNYKSIQPLGSLFEQSLLLFLDAVILKLMKKK 164 (179)
T ss_pred CEEEEECCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHC
T ss_conf 99999068654577788566686674999999999999999999981
No 114
>cd06320 PBP1_allose_binding Periplasmic allose-binding domain of bacterial transport systems that function as a primary receptor of active transport and chemotaxis. Periplasmic allose-binding domain of bacterial transport systems that function as a primary receptor of active transport and chemotaxis. The members of this group are belonging to a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily. Like other periplasmic receptors of the ABC-type transport systems, the allose-binding protein consists of two alpha/beta domains connected by a three-stranded hinge. This Venus flytrap-like domain undergoes transition from an open to a closed conformational state upon ligand binding.
Probab=66.44 E-value=4.3 Score=21.61 Aligned_cols=24 Identities=0% Similarity=0.011 Sum_probs=10.3
Q ss_pred CCEEEEECCCCCCHHHHHHHHCCC
Q ss_conf 957999438877123212343398
Q gi|254780779|r 159 PDLMFVVDTNREKLAIQEARRLRI 182 (278)
Q Consensus 159 P~~iiv~d~~~e~~Av~EA~kl~I 182 (278)
+++||+.+-.--.-|++-++..|+
T Consensus 183 ~~ai~~~nD~~A~Ga~~al~~~g~ 206 (275)
T cd06320 183 LKAIYCNNDTMALGVVEAVKNAGK 206 (275)
T ss_pred CCEEEECCCHHHHHHHHHHHHCCC
T ss_conf 677996698899999999997699
No 115
>PRK00558 uvrC excinuclease ABC subunit C; Validated
Probab=66.15 E-value=12 Score=18.75 Aligned_cols=37 Identities=24% Similarity=0.469 Sum_probs=24.6
Q ss_pred HCCCCCEEEEECCCCCCHHHHHHHH---C-CCEEEEECCCC
Q ss_conf 1135957999438877123212343---3-98145403677
Q gi|254780779|r 155 MGGLPDLMFVVDTNREKLAIQEARR---L-RIPIVAVVDTN 191 (278)
Q Consensus 155 m~~lP~~iiv~d~~~e~~Av~EA~k---l-~IPvIaivDTn 191 (278)
-..+||+++|=+-..--.|+.++.+ + +||+|||+=-+
T Consensus 458 ~~~lPDLilIDGGkgQL~~a~~~l~~l~l~~i~viglaK~~ 498 (609)
T PRK00558 458 FAKLPDLILIDGGKGQLNAAKEVLEELGLDDIPVIGLAKGD 498 (609)
T ss_pred CCCCCCEEEECCCHHHHHHHHHHHHHCCCCCCCEEEEECCC
T ss_conf 89999889954977899999999997699986089997168
No 116
>pfam02056 Glyco_hydro_4 Family 4 glycosyl hydrolase.
Probab=65.81 E-value=8 Score=19.85 Aligned_cols=129 Identities=17% Similarity=0.191 Sum_probs=57.8
Q ss_pred CEEEECHHHHHHHHHHHHHHHHHHHCC-CCEEEEEECCHHHHHHHHHHHHHCCCEECCCCCCCCCCCCHHHHHHHHHHHH
Q ss_conf 816753899999999999999986107-8816996078235799999986339831423345873234266655567789
Q gi|254780779|r 39 NTHIIDLSQTVPMLQKALQVISDTVAR-GGRILFVATKSQASDCVMEAAKRSAQYCVNSKWLGGMMTNWKTVSQSIQKLR 117 (278)
Q Consensus 39 gihIIdL~kT~~~L~~A~~~i~~i~~~-gg~ILFVgTk~~~~~~i~~~A~~~~~~yV~~RWlGG~LTN~~ti~~si~~l~ 117 (278)
-+...|++. ..|+....+.+.+..+ |..+=|..|-.. +.| -.|.-||-.----|.+--|.. --.|..-.
T Consensus 30 ei~L~DId~--~rL~~~~~l~~~~~~~~~~~~~v~~ttd~------~eA-l~gADfVi~~irvG~~~~r~~-De~Iplk~ 99 (183)
T pfam02056 30 ELALYDIDE--ERLDAIQTACKKLVDEAGPDIKFEKTTDR------KEA-LTDADFVINAIRVGLLPAREL-DEKIPLRH 99 (183)
T ss_pred EEEEECCCH--HHHHHHHHHHHHHHHHCCCCEEEEEECCH------HHH-HCCCCEEEEEEEECCCHHHHH-HHHHHHHC
T ss_conf 999977999--99999999999999961998399997899------999-668999999864077148887-77679983
Q ss_pred HHHH--HHH---CC-CCCC-CHHHHHHHHHHHHHHHHHHHHHHHHCCCCCEEEEECCCCCCHHHHHHH-H--CCCEEEEE
Q ss_conf 9887--630---12-1267-746788766556777643443322113595799943887712321234-3--39814540
Q gi|254780779|r 118 DLEE--LLN---KE-NQGF-TKKERLNIERKRDKLKRALDGIRDMGGLPDLMFVVDTNREKLAIQEAR-R--LRIPIVAV 187 (278)
Q Consensus 118 ~l~~--~~~---~~-~~~~-tkKe~~~~~r~~~kl~k~lgGi~~m~~lP~~iiv~d~~~e~~Av~EA~-k--l~IPvIai 187 (278)
-+.. +.. ++ +..| |=...+.+-|..+++- |||.+ +|-.+-...|.||- + -++++|||
T Consensus 100 Gv~~~~~eT~G~GG~~~alRtip~~l~ia~~i~e~~------------P~Awl-iNytNP~~~vt~al~r~~~~~k~vGl 166 (183)
T pfam02056 100 GVVGTIQETVGPGGIFRGLRTIPVFFDIAKDIEELC------------PDAWV-LNYTNPAAMVTEAVYRRYPNIKAVGL 166 (183)
T ss_pred CCCCEECCCCCCCHHHHHHCCHHHHHHHHHHHHHHC------------CCCEE-EECCCHHHHHHHHHHHHCCCCCEEEE
T ss_conf 965323324572288877601899999999999979------------98389-98278889999999985899988996
Q ss_pred CCC
Q ss_conf 367
Q gi|254780779|r 188 VDT 190 (278)
Q Consensus 188 vDT 190 (278)
||+
T Consensus 167 Ch~ 169 (183)
T pfam02056 167 CHS 169 (183)
T ss_pred CCC
T ss_conf 987
No 117
>cd06291 PBP1_Qymf_like Ligand binding domain of the lacI-like transcription regulator from a novel metal-reducing bacterium Alkaliphilus Metalliredigens (strain Qymf) and its close homologs. This group includes the ligand binding domain of the lacI-like transcription regulator from a novel metal-reducing bacterium Alkaliphilus Metalliredigens (strain Qymf) and its close homologs. Qymf is a strict anaerobe that could be grown in the presence of borax and its cells are straight rods that produce endospores. This group is a member of the LacI-GalR family repressors that are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription
Probab=65.66 E-value=8.9 Score=19.55 Aligned_cols=61 Identities=20% Similarity=0.256 Sum_probs=38.1
Q ss_pred CCCEEEEECCCCCCHHHHHHHHCCCE------EEEECCCC----CCCHHCCCEEEECCCCHHHHHHHHHHH
Q ss_conf 59579994388771232123433981------45403677----670011520321577268999999999
Q gi|254780779|r 158 LPDLMFVVDTNREKLAIQEARRLRIP------IVAVVDTN----SNPDLVDYVIPGNDDSSRSIALFCDLV 218 (278)
Q Consensus 158 lP~~iiv~d~~~e~~Av~EA~kl~IP------vIaivDTn----~dp~~idypIP~NDds~~si~l~~~~i 218 (278)
.|++||+.+-.-=.-+++.++.+|+. |||+=|+. +.|.+-+.-.|...=+.+++++++..+
T Consensus 173 ~~~Ai~~~nD~~A~g~~~al~~~g~~vP~disvigfDd~~~~~~~~p~LTtv~~~~~~~g~~A~~~Ll~~i 243 (265)
T cd06291 173 DIDGIFASNDLTAILVLKEAQQRGIRVPEDLQIIGYDGTKLTRLYTPELTTIRQPIEEIAKTAVDLLIKQI 243 (265)
T ss_pred CCCEEECCCHHHHHHHHHHHHHCCCCCCCCEEEEEECCHHHHHHCCCCCEEEECCHHHHHHHHHHHHHHHH
T ss_conf 98843216689999999999981999999869999888099984399955997399999999999999996
No 118
>cd06279 PBP1_LacI_like_3 Ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. This group includes the ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.
Probab=65.51 E-value=12 Score=18.68 Aligned_cols=63 Identities=21% Similarity=0.264 Sum_probs=43.1
Q ss_pred CCCCCEEEEECCCCCCHHHHHHHHCCCE------EEEECCCC---CCCHHCCCEEEECCCCHHHHHHHHHHH
Q ss_conf 1359579994388771232123433981------45403677---670011520321577268999999999
Q gi|254780779|r 156 GGLPDLMFVVDTNREKLAIQEARRLRIP------IVAVVDTN---SNPDLVDYVIPGNDDSSRSIALFCDLV 218 (278)
Q Consensus 156 ~~lP~~iiv~d~~~e~~Av~EA~kl~IP------vIaivDTn---~dp~~idypIP~NDds~~si~l~~~~i 218 (278)
...|+++|+.+-.-=.-+++.++.+||. |||+=|+. ..|.+-+.-.|..+=+..++++++..+
T Consensus 193 ~~~ptai~~~nD~~A~g~~~~l~~~Gi~VP~DvsviGfDd~~~a~~~P~LTTI~q~~~~~G~~A~~~Ll~~i 264 (283)
T cd06279 193 SPRPTAILCMSDVLALGALQVARELGLRVPEDLSVVGFDGIPEARLRPGLTTVRQPSEEKGRLAARLLLDLL 264 (283)
T ss_pred CCCCCEEEECCHHHHHHHHHHHHHHCCCCCCCEEEEEECCCHHHHCCCCCEEEECCHHHHHHHHHHHHHHHH
T ss_conf 999966985772999999999998189999965999589888994589970896199999999999999996
No 119
>PRK11148 cyclic 3',5'-adenosine monophosphate phosphodiesterase; Provisional
Probab=65.01 E-value=8.7 Score=19.62 Aligned_cols=54 Identities=20% Similarity=0.212 Sum_probs=22.7
Q ss_pred HHHHHHHHHHHHHHHHCCCCEEEEEEC-----CHHHHHHHHHHHHHCCCEECCCCCCCCCCC
Q ss_conf 999999999999986107881699607-----823579999998633983142334587323
Q gi|254780779|r 48 TVPMLQKALQVISDTVARGGRILFVAT-----KSQASDCVMEAAKRSAQYCVNSKWLGGMMT 104 (278)
Q Consensus 48 T~~~L~~A~~~i~~i~~~gg~ILFVgT-----k~~~~~~i~~~A~~~~~~yV~~RWlGG~LT 104 (278)
|...|+.+..-|.......--|++-|- .+.+-..+.+...+.+.|+ .|++|==-
T Consensus 38 t~~~l~~vl~~i~~~~~~~D~viiTGDLs~dgs~esY~~l~~~L~~l~~P~---~~lPGNHD 96 (275)
T PRK11148 38 TWESYQAVLEAIRAEQHEFDLIVATGDLAQDHSAEAYQHFAEGIAPLRKPC---VWLPGNHD 96 (275)
T ss_pred HHHHHHHHHHHHHHCCCCCCEEEECCCCCCCCCHHHHHHHHHHHHHCCCCE---EEECCCCC
T ss_conf 899999999999845999889997640258999999999999997269998---99588762
No 120
>TIGR01457 HAD-SF-IIA-hyp2 HAD-superfamily subfamily IIA hydrolase, TIGR01457; InterPro: IPR006354 These sequences are all members of the Class IIA subfamily of the haloacid dehalogenase superfamily of aspartate-nucleophile hydrolases. The sequences are all from the Gram-positive (low-GC) bacteria..
Probab=65.00 E-value=4.6 Score=21.40 Aligned_cols=57 Identities=21% Similarity=0.292 Sum_probs=42.4
Q ss_pred EEECHHHHH----HHHHHHHHHHHHHHCCCCEEEEEECCHH-HHHHHHHHHHH-CCCEECCCC
Q ss_conf 675389999----9999999999986107881699607823-57999999863-398314233
Q gi|254780779|r 41 HIIDLSQTV----PMLQKALQVISDTVARGGRILFVATKSQ-ASDCVMEAAKR-SAQYCVNSK 97 (278)
Q Consensus 41 hIIdL~kT~----~~L~~A~~~i~~i~~~gg~ILFVgTk~~-~~~~i~~~A~~-~~~~yV~~R 97 (278)
++|||+=|. +.+..|+.|++++..++-.-|||-.|.. ..+.|+..-.. .+.|.-.+.
T Consensus 4 yLIDLDGT~Y~G~e~I~ea~~FV~~L~kr~~pYLFVTNNstrtPe~Va~~L~snfdipat~e~ 66 (251)
T TIGR01457 4 YLIDLDGTMYKGKEKIEEAVEFVKELKKRDVPYLFVTNNSTRTPESVAELLASNFDIPATKEQ 66 (251)
T ss_pred EEEECCCCEECCCCCHHHHHHHHHHHHHCCCCEEEEECCCCCCHHHHHHHHHHHCCCCCCCCH
T ss_conf 355157614358530167899999886479863687278888817999998751689997210
No 121
>COG1737 RpiR Transcriptional regulators [Transcription]
Probab=64.87 E-value=12 Score=18.60 Aligned_cols=45 Identities=20% Similarity=0.303 Sum_probs=31.3
Q ss_pred CCEEEEECCCCCC----HHHHHHHHCCCEEEEECCCCCCC--HHCCCEEEE
Q ss_conf 9579994388771----23212343398145403677670--011520321
Q gi|254780779|r 159 PDLMFVVDTNREK----LAIQEARRLRIPIVAVVDTNSNP--DLVDYVIPG 203 (278)
Q Consensus 159 P~~iiv~d~~~e~----~Av~EA~kl~IPvIaivDTn~dp--~~idypIP~ 203 (278)
=|++|++.-..+. .+++.|+.-|+|||+|.|+-.+| ...|+.++.
T Consensus 178 ~Dv~i~iS~sG~t~e~i~~a~~ak~~ga~vIaiT~~~~spla~~Ad~~L~~ 228 (281)
T COG1737 178 GDVVIAISFSGYTREIVEAAELAKERGAKVIAITDSADSPLAKLADIVLLV 228 (281)
T ss_pred CCEEEEEECCCCCHHHHHHHHHHHHCCCEEEEEECCCCCCHHHHCCEEEEE
T ss_conf 988999848999689999999999779929998399999366654778871
No 122
>cd06298 PBP1_CcpA_like Ligand-binding domain of the catabolite control protein A (CcpA), which functions as the major transcriptional regulator of carbon catabolite repression/regulation. Ligand-binding domain of the catabolite control protein A (CcpA), which functions as the major transcriptional regulator of carbon catabolite repression/regulation (CCR), a process in which enzymes necessary for the metabolism of alternative sugars are inhibited in the presence of glucose. In gram-positive bacteria, CCR is controlled by HPr, a phosphoenolpyruvate:sugar phsophotrasnferase system (PTS) and a transcriptional regulator CcpA. Moreover, CcpA can regulate sporulation and antibiotic resistance as well as play a role in virulence development of certain pathogens such as the group A streptococcus. The ligand binding domain of CcpA is a member of the LacI-GalR family of bacterial transcription regulators.
Probab=64.26 E-value=13 Score=18.53 Aligned_cols=62 Identities=23% Similarity=0.313 Sum_probs=38.9
Q ss_pred CCCCEEEEECCCCCCHHHHHHHHCCCE------EEEECCC----CCCCHHCCCEEEECCCCHHHHHHHHHHH
Q ss_conf 359579994388771232123433981------4540367----7670011520321577268999999999
Q gi|254780779|r 157 GLPDLMFVVDTNREKLAIQEARRLRIP------IVAVVDT----NSNPDLVDYVIPGNDDSSRSIALFCDLV 218 (278)
Q Consensus 157 ~lP~~iiv~d~~~e~~Av~EA~kl~IP------vIaivDT----n~dp~~idypIP~NDds~~si~l~~~~i 218 (278)
..|+++|+.+-.-=.-+++.++.+|+. |+|+=|+ -+.|.+-+.-.|...=+..++++++..+
T Consensus 176 ~~~~ai~~~nD~~A~g~l~~l~~~g~~vP~disvigfDd~~~a~~~~P~LTtv~~~~~~~G~~A~~~l~~~i 247 (268)
T cd06298 176 GKPTAAFVTDDELAIGILNAAQDAGLKVPEDFEIIGFNNTKLASMVRPQLTSVTQPLYDIGAVAMRLLTKLM 247 (268)
T ss_pred CCCCEEEECCHHHHHHHHHHHHHCCCCCCCCEEEEEECCHHHHHCCCCCCEEEECCHHHHHHHHHHHHHHHH
T ss_conf 999789966879999999999974999998749999788189971489976997299999999999999996
No 123
>TIGR00888 guaA_Nterm GMP synthase, N-terminal domain; InterPro: IPR004739 The N-terminal region of GMP synthase 6.3.5.2 from EC is recognised by this signature. GMP synthase catalyzes the synthesis of GMP from XMP , . ATP + xanthosine 5'-phosphate + L-glutamine + H(2)O = AMP + diphosphate + GMP + L-glutamate ; GO: 0003922 GMP synthase (glutamine-hydrolyzing) activity, 0005524 ATP binding, 0006177 GMP biosynthetic process.
Probab=63.78 E-value=7.4 Score=20.08 Aligned_cols=31 Identities=13% Similarity=0.255 Sum_probs=22.6
Q ss_pred CCCEEEEEC-C--CCCCHHHHHHH---HCCCEEEEEC
Q ss_conf 595799943-8--87712321234---3398145403
Q gi|254780779|r 158 LPDLMFVVD-T--NREKLAIQEAR---RLRIPIVAVV 188 (278)
Q Consensus 158 lP~~iiv~d-~--~~e~~Av~EA~---kl~IPvIaiv 188 (278)
.|.-||+.. | .++..|.+=+. .|||||.|||
T Consensus 41 ~P~GiILSGGP~sv~~~n~~~~~~~if~LgVPvLGIC 77 (195)
T TIGR00888 41 NPKGIILSGGPASVYAENAPEADEKIFELGVPVLGIC 77 (195)
T ss_pred CCCEEEEECCCCCCCCCCCHHHHHHHHHCCCCEEEEE
T ss_conf 9867997278876467885022488862799688762
No 124
>cd06338 PBP1_ABC_ligand_binding_like_5 Type I periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type active transport systems that are predicted to be involved in transport of amino acids, peptides, or inorganic ions. This subgroup includes the type I periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type active transport systems that are predicted to be involved in transport of amino acids, peptides, or inorganic ions. This subgroup has high sequence similarity to members of the family of hydrophobic amino acid transporters (HAAT); however their ligand specificity has not been determined experimentally.
Probab=63.47 E-value=13 Score=18.43 Aligned_cols=38 Identities=16% Similarity=0.201 Sum_probs=25.4
Q ss_pred CCCEEEEECCCCC-CHHHHHHHHCCC--EEEEECCCCCCCH
Q ss_conf 5957999438877-123212343398--1454036776700
Q gi|254780779|r 158 LPDLMFVVDTNRE-KLAIQEARRLRI--PIVAVVDTNSNPD 195 (278)
Q Consensus 158 lP~~iiv~d~~~e-~~Av~EA~kl~I--PvIaivDTn~dp~ 195 (278)
-||+||+.....+ ...+++++.+|+ |+++..+...++.
T Consensus 196 ~pd~i~~~~~~~~~~~~~~q~~~~G~~~~~~~~~~~~~~~~ 236 (345)
T cd06338 196 GPDAVVVAGHFPDAVLLVRQMKELGYNPKALYMTVGPAFPA 236 (345)
T ss_pred CCCEEEECCCCCHHHHHHHHHHHCCCCCCEEEEECCCCCHH
T ss_conf 99999990777159999999997699988899844667899
No 125
>PRK10727 DNA-binding transcriptional regulator GalR; Provisional
Probab=63.40 E-value=13 Score=18.43 Aligned_cols=62 Identities=15% Similarity=0.069 Sum_probs=41.5
Q ss_pred CCCCCEEEEECCCCCCHHHHHHHHCCCE------EEEECCC----CCCCHHCCCEEEECCCCHHHHHHHHHH
Q ss_conf 1359579994388771232123433981------4540367----767001152032157726899999999
Q gi|254780779|r 156 GGLPDLMFVVDTNREKLAIQEARRLRIP------IVAVVDT----NSNPDLVDYVIPGNDDSSRSIALFCDL 217 (278)
Q Consensus 156 ~~lP~~iiv~d~~~e~~Av~EA~kl~IP------vIaivDT----n~dp~~idypIP~NDds~~si~l~~~~ 217 (278)
...|+++|+.+-.-=.-+++.++.+|+- |||+=|+ -..|.+-+.-.|.-.=+..++++++..
T Consensus 235 ~~~~tAi~~~nD~~A~g~l~al~~~Gl~VP~DisViGfDd~~~~~~~~P~LTTV~~p~~e~g~~A~~lLl~~ 306 (342)
T PRK10727 235 GRNFTAVACYNDSMAAGAMGVLNDNGIDVPGEISLIGFDDVLVSRYVRPRLTTVRYPIVTMATQAAELALAL 306 (342)
T ss_pred CCCCCCCEECCHHHHHHHHHHHHHCCCCCCCCEEEEEECCHHHHHCCCCCCEEEECCHHHHHHHHHHHHHHH
T ss_conf 999774155469999999999998299999986999889718986488998589779999999999999998
No 126
>pfam02684 LpxB Lipid-A-disaccharide synthetase. This is a family of lipid-A-disaccharide synthetases, EC:2.4.2.128. These enzymes catalyse the reaction: UDP-2,3-bis(3-hydroxytetradecanoyl) glucosamine + 2,3-bis(3-hydroxytetradecanoyl)-beta-D-glucosaminyl 1-phosphate <= UDP + 2,3-bis(3-hydroxytetradecanoyl)-D-glucosaminyl-1,6 -beta-D-2,3-bis(3-hydroxytetradecanoyl)-beta-D-glucosaminyl 1-phosphate. These enzymes catalyse the fist disaccharide step in the synthesis of lipid-A-disaccharide.
Probab=63.30 E-value=13 Score=18.41 Aligned_cols=58 Identities=14% Similarity=0.172 Sum_probs=33.1
Q ss_pred EEECHHHHHHHHHHHHHHHHH-HHCCCCEEEEEECCHHHHHHHHHHHHHCCC-----EECC-CCC
Q ss_conf 675389999999999999998-610788169960782357999999863398-----3142-334
Q gi|254780779|r 41 HIIDLSQTVPMLQKALQVISD-TVARGGRILFVATKSQASDCVMEAAKRSAQ-----YCVN-SKW 98 (278)
Q Consensus 41 hIIdL~kT~~~L~~A~~~i~~-i~~~gg~ILFVgTk~~~~~~i~~~A~~~~~-----~yV~-~RW 98 (278)
-+++.-+-+..+.+..+-+.+ +....-.+++.---+.+.--+.+.+++.|. |||. +=|
T Consensus 56 G~~evl~~l~~l~~~~~~~~~~i~~~~PD~vIlID~pgFNlrlak~lkk~g~~ipvi~yV~PqvW 120 (373)
T pfam02684 56 GFIEVLGRLFKLLKIYQKVVKNILKKKPDTLILIDAPDFNLRLAKKLRKLGPKLKIIHYVSPSVW 120 (373)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHCCCCEEEEECCCCHHHHHHHHHHHCCCCCCEEEEECCCEE
T ss_conf 19999989999999999999987426998899971761559999999971999878999688422
No 127
>PRK12306 uvrC excinuclease ABC subunit C; Reviewed
Probab=63.01 E-value=14 Score=18.38 Aligned_cols=72 Identities=22% Similarity=0.265 Sum_probs=36.2
Q ss_pred CCCCCEEEEECCCCCCHHHHH---HHHCCCEEEEECCCCCC---CH-HCCCEEEECCCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf 135957999438877123212---34339814540367767---00-11520321577268999999999999999999
Q gi|254780779|r 156 GGLPDLMFVVDTNREKLAIQE---ARRLRIPIVAVVDTNSN---PD-LVDYVIPGNDDSSRSIALFCDLVASAAIDGIA 227 (278)
Q Consensus 156 ~~lP~~iiv~d~~~e~~Av~E---A~kl~IPvIaivDTn~d---p~-~idypIP~NDds~~si~l~~~~i~~ai~~g~~ 227 (278)
..+||+|+|=+-..--.|+.+ ...+.||+|||+--+-. |. .-.+.+|-|+.+...++-+-...-+-.+....
T Consensus 432 ~~lPDLilIDGGkgQl~~a~~vl~~l~~~i~viglaK~~e~i~~~~~~~~i~l~~~s~~l~lLq~iRDEaHRFAIt~HR 510 (519)
T PRK12306 432 SELPDLIIIDGGKGQLSSAFKELRKLKLKIPIISIAKREEEIYVPGIKNPLPIKKNEKASLFIQEIRDEAHRFAITYNR 510 (519)
T ss_pred CCCCCEEEECCCHHHHHHHHHHHHHCCCCCEEEEEEECCEEEECCCCCCEEECCCCCHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 9999989985999999999999997699932999980783896389986456599998999999999879887999898
No 128
>TIGR01133 murG undecaprenyldiphospho-muramoylpentapeptide beta-N-acetylglucosaminyltransferase; InterPro: IPR006009 The murG gene of Escherichia coli encodes the N-acetylglucosaminyltransferase, UDP-N-acetylglucosamine--N-acetylmuramyl-(pentapeptide) pyrophosphoryl-undecaprenol N-acetylglucosamine transferase, responsible for the final step in the formation of the lipid-linked disaccharide-pentapeptide subunit of peptidoglycan. The enzyme is peripherally associated with the inner face of the cytoplasmic membrane. Therefore, the peptidoglycan subunit is completely assembled before it traverses the cytoplasmic membrane .; GO: 0050511 undecaprenyldiphospho-muramoylpentapeptide beta-N-acetylglucosaminyltransferase activity, 0019277 UDP-N-acetylgalactosamine biosynthetic process, 0009276 1-2nm peptidoglycan-based cell wall.
Probab=62.52 E-value=14 Score=18.32 Aligned_cols=57 Identities=16% Similarity=-0.101 Sum_probs=27.5
Q ss_pred CEEEECHHHHHH-HHHHHHHHHHHHHCCCCEEEEEECCHHHHHHHHHHHHHCC-CEECC
Q ss_conf 816753899999-9999999999861078816996078235799999986339-83142
Q gi|254780779|r 39 NTHIIDLSQTVP-MLQKALQVISDTVARGGRILFVATKSQASDCVMEAAKRSA-QYCVN 95 (278)
Q Consensus 39 gihIIdL~kT~~-~L~~A~~~i~~i~~~gg~ILFVgTk~~~~~~i~~~A~~~~-~~yV~ 95 (278)
+....++-++.. .+-.|..-..++.++-.--+.||+-=.++-+.--.|..+| .|-+.
T Consensus 69 ~~~~~~~~~~~~~~~~~~~~~a~~~l~~~~p~~v~G~GGY~s~P~~~AA~l~g~iP~~~ 127 (368)
T TIGR01133 69 RKGSKKLLKLPLLKLLKAVLQARRILKKFKPDVVVGFGGYVSGPAGLAAKLLGRIPLIL 127 (368)
T ss_pred CCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCEEEECCCHHHHHHHHHHHHCCCCCEEE
T ss_conf 65510146788999999999999998600874798747367899999987667994898
No 129
>PRK02947 hypothetical protein; Provisional
Probab=62.51 E-value=14 Score=18.32 Aligned_cols=116 Identities=23% Similarity=0.338 Sum_probs=63.8
Q ss_pred HHHHHHHHHHHHHHHHCCCCEEEEEECCHHHHHHHHHHHHHCCCEECCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCC
Q ss_conf 99999999999998610788169960782357999999863398314233458732342666555677899887630121
Q gi|254780779|r 48 TVPMLQKALQVISDTVARGGRILFVATKSQASDCVMEAAKRSAQYCVNSKWLGGMMTNWKTVSQSIQKLRDLEELLNKEN 127 (278)
Q Consensus 48 T~~~L~~A~~~i~~i~~~gg~ILFVgTk~~~~~~i~~~A~~~~~~yV~~RWlGG~LTN~~ti~~si~~l~~l~~~~~~~~ 127 (278)
-...+.+|.+.+.+...+||.|-..||-... -+..+..-|.|.+.-.+..+---|+-+....++- .+|+.
T Consensus 23 q~~~I~~Aa~~ia~si~~gg~i~~fGtGHS~-~~a~E~f~RAGGla~~~pI~~~~l~~~~g~~~s~----~~ER~----- 92 (247)
T PRK02947 23 QADAIKQAADLVADSIANGGRIYVFGTGHSH-MAAEEVFYRAGGLAPFNPILEPSLMLHEGAVASS----YLERI----- 92 (247)
T ss_pred HHHHHHHHHHHHHHHHHCCCEEEEECCCCHH-HHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCC----HHHCC-----
T ss_conf 9999999999999999759979998885164-8999874114764331300341102547866653----12225-----
Q ss_pred CCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCEEEEEC-CCCCCHHH---HHHHHCCCEEEEECC
Q ss_conf 267746788766556777643443322113595799943-88771232---123433981454036
Q gi|254780779|r 128 QGFTKKERLNIERKRDKLKRALDGIRDMGGLPDLMFVVD-TNREKLAI---QEARRLRIPIVAVVD 189 (278)
Q Consensus 128 ~~~tkKe~~~~~r~~~kl~k~lgGi~~m~~lP~~iiv~d-~~~e~~Av---~EA~kl~IPvIaivD 189 (278)
.+|-+ ..+.+ -.| +--|+++|+. -..+...| .+|++.|.+|||+..
T Consensus 93 ~g~a~---~il~~---------~~i----~~~Dvlii~SnSG~N~~pVE~A~~ak~~G~~VIaiTS 142 (247)
T PRK02947 93 EGYAK---LILDR---------YPI----RPGDVLIIVSNSGRNAVPIEMALEAKERGAKVIAVTS 142 (247)
T ss_pred CCHHH---HHHHH---------CCC----CCCCEEEEEECCCCCHHHHHHHHHHHHCCCEEEEEEC
T ss_conf 50999---99986---------799----9998899996787776899999999986996999966
No 130
>PRK12319 acetyl-CoA carboxylase subunit alpha; Provisional
Probab=61.85 E-value=4.2 Score=21.64 Aligned_cols=17 Identities=24% Similarity=0.636 Sum_probs=8.9
Q ss_pred HHHHHHCCCEEEEECCC
Q ss_conf 21234339814540367
Q gi|254780779|r 174 IQEARRLRIPIVAVVDT 190 (278)
Q Consensus 174 v~EA~kl~IPvIaivDT 190 (278)
.+-|.|+|+|||.++||
T Consensus 91 m~lAekf~~PvitfIDT 107 (256)
T PRK12319 91 MKQAEKFGRPVVTFINT 107 (256)
T ss_pred HHHHHHHCCCEEEEECC
T ss_conf 99999809987999607
No 131
>cd06280 PBP1_LacI_like_4 Ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. This group includes the ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.
Probab=61.62 E-value=14 Score=18.22 Aligned_cols=63 Identities=10% Similarity=0.125 Sum_probs=44.0
Q ss_pred CCCCCEEEEECCCCCCHHHHHHHHCCCE------EEEECCCC----CCCHHCCCEEEECCCCHHHHHHHHHHH
Q ss_conf 1359579994388771232123433981------45403677----670011520321577268999999999
Q gi|254780779|r 156 GGLPDLMFVVDTNREKLAIQEARRLRIP------IVAVVDTN----SNPDLVDYVIPGNDDSSRSIALFCDLV 218 (278)
Q Consensus 156 ~~lP~~iiv~d~~~e~~Av~EA~kl~IP------vIaivDTn----~dp~~idypIP~NDds~~si~l~~~~i 218 (278)
...|+++|+.+-.-=.-+++.++.+|+- |+|+=|+. ..|.+-+.-.|...=+..++++++..+
T Consensus 170 ~~~~~ai~~~nD~~A~g~l~~l~~~g~~vP~disviGfDd~~~a~~~~P~LTTv~~~~~~~g~~A~~~Ll~~i 242 (263)
T cd06280 170 PERPEALVASNGLLLLGALRAVRAAGLRIPQDLALAGFDNDPWTELVGPGITVIEQPVEEIGRAAMSLLLERL 242 (263)
T ss_pred CCCCCEEEECCHHHHHHHHHHHHHHCCCCCCCCEEEEECCHHHHHCCCCCCEEEEECHHHHHHHHHHHHHHHH
T ss_conf 9999789967889999999999984899999878999778588861799977998099999999999999996
No 132
>cd06306 PBP1_TorT-like TorT-like proteins, a periplasmic binding protein family that activates induction of the Tor respiratory system upon trimethylamine N-oxide (TMAO) electron-acceptor binding in bacteria. TorT-like proteins, a periplasmic binding protein family that activates induction of the Tor respiratory system upon trimethylamine N-oxide (TMAO) electron-acceptor binding in bacteria. The Tor respiratory system is consists of three proteins (TorC, TorA, and TorD) and is induced in the presence of TMAO. The TMAO control is tightly regulated by three proteins: TorS, TorT, and TorR. Thus, the disruption of any of these proteins can abolish the Tor respiratory induction. TorT shares homology with the sugar-binding domain of the type I periplasmic binding proteins. The members of TorT-like family bind TMAO or related compounds and are predicted to be involved in signal transduction and/or substrate transport.
Probab=61.36 E-value=11 Score=19.01 Aligned_cols=39 Identities=21% Similarity=0.296 Sum_probs=18.5
Q ss_pred CCCCEEEEECCCCC-CHHHHHHHHCCCEEEEECCCCCCCH
Q ss_conf 35957999438877-1232123433981454036776700
Q gi|254780779|r 157 GLPDLMFVVDTNRE-KLAIQEARRLRIPIVAVVDTNSNPD 195 (278)
Q Consensus 157 ~lP~~iiv~d~~~e-~~Av~EA~kl~IPvIaivDTn~dp~ 195 (278)
+-+|+|++.-...+ ...+.+|..-|||||.+.+.-.++.
T Consensus 56 ~gvDaIii~p~d~~al~~~~~a~~agIPVV~~d~~i~~~~ 95 (268)
T cd06306 56 WGADAILLGAVSPDGLNEILQQVAASIPVIALVNDINSPD 95 (268)
T ss_pred CCCCEEEECCCCHHHHHHHHHHHHCCCEEEEEECCCCCCC
T ss_conf 3999999867986777899999986982999945778755
No 133
>cd06292 PBP1_LacI_like_10 Ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. This group includes the ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.
Probab=61.27 E-value=14 Score=18.18 Aligned_cols=34 Identities=24% Similarity=0.218 Sum_probs=24.9
Q ss_pred CCCCEEEEECCCCCCHHHHHHHHCCCE------EEEECCC
Q ss_conf 359579994388771232123433981------4540367
Q gi|254780779|r 157 GLPDLMFVVDTNREKLAIQEARRLRIP------IVAVVDT 190 (278)
Q Consensus 157 ~lP~~iiv~d~~~e~~Av~EA~kl~IP------vIaivDT 190 (278)
+-|+++|+.+-.--.-+++.++.+|+- |+|+=|+
T Consensus 180 ~~~~ai~~~nD~~A~g~~~~l~~~g~~ip~di~VigfD~~ 219 (273)
T cd06292 180 SGPTAIVAASDLMALGAIRAARRRGLRVPEDVSVVGYDDS 219 (273)
T ss_pred CCCCEEEECCCHHHHHHHHHHHHCCCCCCCCEEEEEECCH
T ss_conf 7996577458599999999999839989996599999985
No 134
>PRK07188 nicotinate phosphoribosyltransferase; Provisional
Probab=60.45 E-value=9.5 Score=19.35 Aligned_cols=15 Identities=13% Similarity=0.439 Sum_probs=12.3
Q ss_pred HCCCCEEEEEECCHH
Q ss_conf 107881699607823
Q gi|254780779|r 63 VARGGRILFVATKSQ 77 (278)
Q Consensus 63 ~~~gg~ILFVgTk~~ 77 (278)
+..+..+||-|.+.+
T Consensus 132 aA~~k~vl~fg~R~~ 146 (355)
T PRK07188 132 AANEKPVIFMGDRAD 146 (355)
T ss_pred HCCCCEEEECCCCCC
T ss_conf 649791882147565
No 135
>cd06328 PBP1_SBP_like_2 Periplasmic solute-binding domain of active transport proteins found in gram-negative and gram-positive bacteria. Periplasmic solute-binding domain of active transport proteins found in gram-negative and gram-positive bacteria. Members of this group are initial receptors in the process of active transport across cellular membrane, but their substrate specificities are not known in detail. However, they closely resemble the group of AmiC and active transport systems for short-chain amides and urea (FmdDEF), and thus are likely to exhibit a ligand-binding mode similar to that of the amide sensor protein AmiC from Pseudomonas aeruginosa. Moreover, this binding domain has high sequence identity to the family of hydrophobic amino acid transporters (HAAT), and thus it may also be involved in transport of amino acids.
Probab=60.23 E-value=15 Score=18.07 Aligned_cols=95 Identities=15% Similarity=0.156 Sum_probs=59.4
Q ss_pred HHHHHHHHHHHCCCCEEEEEECCHH----HHHHHHHHHHHCCCEECCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCC
Q ss_conf 9999999986107881699607823----579999998633983142334587323426665556778998876301212
Q gi|254780779|r 53 QKALQVISDTVARGGRILFVATKSQ----ASDCVMEAAKRSAQYCVNSKWLGGMMTNWKTVSQSIQKLRDLEELLNKENQ 128 (278)
Q Consensus 53 ~~A~~~i~~i~~~gg~ILFVgTk~~----~~~~i~~~A~~~~~~yV~~RWlGG~LTN~~ti~~si~~l~~l~~~~~~~~~ 128 (278)
..+..++. .+++++.+++..-. ....+++..+..|..-|.+.|.+.--|+|..+-..++.
T Consensus 126 ~a~~~~l~---~~~kkva~i~~d~~~g~~~~~~~~~~~~~~g~~iv~~~~~~~~~~Df~~~i~~i~~------------- 189 (333)
T cd06328 126 IAAAAALG---KPGKKIATLAQDYAFGRDGVAAFKAALEKLGAAIVTEEYAPTDTTDFTPYAQRLLD------------- 189 (333)
T ss_pred HHHHHHHH---HCCCEEEEEECCCHHHHHHHHHHHHHHHHCCCEEEEEEECCCCCCCHHHHHHHHHH-------------
T ss_conf 99999998---36988999967855769999999999997399699998268888777999999986-------------
Q ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCEEEEECCCCC--CHHHHHHHHCCCEEEEECCCC
Q ss_conf 677467887665567776434433221135957999438877--123212343398145403677
Q gi|254780779|r 129 GFTKKERLNIERKRDKLKRALDGIRDMGGLPDLMFVVDTNRE--KLAIQEARRLRIPIVAVVDTN 191 (278)
Q Consensus 129 ~~tkKe~~~~~r~~~kl~k~lgGi~~m~~lP~~iiv~d~~~e--~~Av~EA~kl~IPvIaivDTn 191 (278)
.-||+||+.-.... ..+++++...+........++
T Consensus 190 ----------------------------~~pd~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 226 (333)
T cd06328 190 ----------------------------ALKKVLFVIWAGAGGPWPKLQQMGVLGYGIEITLAGD 226 (333)
T ss_pred ----------------------------CCCCEEEEECCCCHHHHHHHHHHHHCCCCCEEEEECC
T ss_conf ----------------------------6999999935786269999999986599974998655
No 136
>pfam08459 UvrC_HhH_N UvrC Helix-hairpin-helix N-terminal. This domain is found in the C subunits of the bacterial and archaeal UvrABC system which catalyses nucleotide excision repair in a multi-step process. UvrC catalyses the first incision on the fourth or fifth phosphodiester bond 3' and on the eighth phosphodiester bond 5' from the damage that is to be excised. The domain described here is found to the N-terminus of a helix hairpin helix (pfam00633) motif and also co-occurs with the pfam01541 catalytic domain which is found at the N-terminus of the same proteins.
Probab=59.72 E-value=8.2 Score=19.77 Aligned_cols=35 Identities=26% Similarity=0.395 Sum_probs=21.3
Q ss_pred CCCCCEEEEECCCCCCHHHHHHH---HCCCEEEEECCC
Q ss_conf 13595799943887712321234---339814540367
Q gi|254780779|r 156 GGLPDLMFVVDTNREKLAIQEAR---RLRIPIVAVVDT 190 (278)
Q Consensus 156 ~~lP~~iiv~d~~~e~~Av~EA~---kl~IPvIaivDT 190 (278)
..+||+++|=+-..--.|+.++. .++||+|||+--
T Consensus 76 ~~~PDLilIDGGkgQl~~a~~~l~~~~~~i~vi~iaK~ 113 (154)
T pfam08459 76 LPLPDLILIDGGKGQLNAAKEVLEELGLDIPVIGLAKG 113 (154)
T ss_pred CCCCCEEEECCCHHHHHHHHHHHHHCCCCCEEEEEEEC
T ss_conf 89998899759989999999999985999529999735
No 137
>PRK05748 replicative DNA helicase; Provisional
Probab=58.96 E-value=16 Score=17.93 Aligned_cols=161 Identities=19% Similarity=0.303 Sum_probs=81.3
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCC-EEEEC----HHHHHHHHHHHHHHHHHHHCCCCEEEEEECCHHHHHHHHHH-HHHC
Q ss_conf 860754776578856210200188-16753----89999999999999998610788169960782357999999-8633
Q gi|254780779|r 16 VQFGHRNFLWNPKMERYIFCERNN-THIID----LSQTVPMLQKALQVISDTVARGGRILFVATKSQASDCVMEA-AKRS 89 (278)
Q Consensus 16 ~H~Gh~~~~wnPkM~~yI~g~rng-ihIId----L~kT~~~L~~A~~~i~~i~~~gg~ILFVgTk~~~~~~i~~~-A~~~ 89 (278)
-..|-.|..+. .-..+-|.+.| +.||= .-||...+..|.+... ..|..|+|.+.--...++...+ |..+
T Consensus 182 ~~~Gi~TG~~~--LD~~~~G~~~g~LiviaaRP~mGKTa~alnia~~~a~---~~~~~v~~fSlEM~~~~l~~R~la~~s 256 (448)
T PRK05748 182 DITGIPTGFRD--LDKMTSGLQPNDLIIVAARPSVGKTAFALNIAQNVAT---KTDKNVAIFSLEMGAESLVMRMLCAEG 256 (448)
T ss_pred CCCEEECCHHH--HHHHHCCCCCCCEEEEEECCCCCHHHHHHHHHHHHHH---HCCCEEEEEECCCCHHHHHHHHHHHHH
T ss_conf 97610578278--9998279886737999847998768999999999998---569808998177888899999999974
Q ss_pred CCEECCCCCCCCCCCC--HHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCEEEEEC-
Q ss_conf 9831423345873234--2666555677899887630121267746788766556777643443322113595799943-
Q gi|254780779|r 90 AQYCVNSKWLGGMMTN--WKTVSQSIQKLRDLEELLNKENQGFTKKERLNIERKRDKLKRALDGIRDMGGLPDLMFVVD- 166 (278)
Q Consensus 90 ~~~yV~~RWlGG~LTN--~~ti~~si~~l~~l~~~~~~~~~~~tkKe~~~~~r~~~kl~k~lgGi~~m~~lP~~iiv~d- 166 (278)
+.++ ++...|.||. |..+.+.+.++..+.-..+ .-..+|--+ +.-...++.+..+| +++ ||+|
T Consensus 257 ~v~~--~~i~~g~l~~~~~~~~~~a~~~l~~~~l~i~-d~~~~ti~~---i~~~~r~~~~~~~~-------~~~-vviDY 322 (448)
T PRK05748 257 RIDQ--QKLRTGQLTDEDWPKLTIAVGSLSDAPIYID-DTPGIKVTE---IRARCRRLAQEHGG-------LGL-IVIDY 322 (448)
T ss_pred CCCH--HHHHCCCCCHHHHHHHHHHHHHHHCCCEEEE-CCCCCCHHH---HHHHHHHHHHHCCC-------CCE-EEEEH
T ss_conf 6777--7776289999999999999999865983785-589886899---99999999997599-------889-99716
Q ss_pred ------CCC----CCHHHHH--------HHHCCCEEEEECCCCCCCH
Q ss_conf ------887----7123212--------3433981454036776700
Q gi|254780779|r 167 ------TNR----EKLAIQE--------ARRLRIPIVAVVDTNSNPD 195 (278)
Q Consensus 167 ------~~~----e~~Av~E--------A~kl~IPvIaivDTn~dp~ 195 (278)
+.. ....|.| |+.|+||||+++-=|=+.+
T Consensus 323 lqli~~~~~~~~~r~~ev~~isr~lK~lAkel~ipvi~lsQLnR~~e 369 (448)
T PRK05748 323 LQLIQGSGRSGENRQQEVSEISRSLKALAKELKVPVIALSQLSRGVE 369 (448)
T ss_pred HHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCEEEECCCCCCCC
T ss_conf 86447778776439999999999999999996998899702684322
No 138
>TIGR03191 benz_CoA_bzdO benzoyl-CoA reductase, bzd-type, O subunit. Members of this family are the O subunit of one of two related types of four-subunit ATP-dependent benzoyl-CoA reductase. This enzyme system catalyzes the dearomatization of benzoyl-CoA, a common intermediate in pathways for the degradation for a number of different aromatic compounds, such as phenol and toluene.
Probab=58.29 E-value=16 Score=17.85 Aligned_cols=57 Identities=14% Similarity=0.149 Sum_probs=32.8
Q ss_pred CCCEEEEECCCCCCHHH--HHHHHCCCEEEEECCCCCCCHHCCCEEEECCCCHHHHHHHHHHHHHHHH
Q ss_conf 59579994388771232--1234339814540367767001152032157726899999999999999
Q gi|254780779|r 158 LPDLMFVVDTNREKLAI--QEARRLRIPIVAVVDTNSNPDLVDYVIPGNDDSSRSIALFCDLVASAAI 223 (278)
Q Consensus 158 lP~~iiv~d~~~e~~Av--~EA~kl~IPvIaivDTn~dp~~idypIP~NDds~~si~l~~~~i~~ai~ 223 (278)
.||.|+..+....+.== .=|+.++||.|-| |+-- ..++ +-+-..|.++...+-++|.
T Consensus 111 kPDfl~~nniC~t~~KWye~~are~~IPlf~i-Dip~---~~~~-----e~~~~~i~Yv~~Q~~d~I~ 169 (430)
T TIGR03191 111 KPDFIFQTQICCSHAKWYQHVAKEEKIPDFYL-DVGV---GAYK-----DLTDARLDYVANQLHDGIE 169 (430)
T ss_pred CCCEEEECCCCCHHHHHHHHHHHHCCCCEEEE-ECCC---CCCC-----CCCHHHHHHHHHHHHHHHH
T ss_conf 99889664865038999999999719996998-2687---8888-----7798999999999999999
No 139
>cd01542 PBP1_TreR_like Ligand-binding domain of DNA transcription repressor specific for trehalose (TreR) which is a member of the LacI-GalR family of bacterial transcription regulators. Ligand-binding domain of DNA transcription repressor specific for trehalose (TreR) which is a member of the LacI-GalR family of bacterial transcription regulators. The ligand-binding domain of TreR is structurally homologous to the periplasmic sugar-binding domain of ABC-type transporters and both domains contain the type I periplasmic binding protein-like fold. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the type I periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding wh
Probab=58.19 E-value=16 Score=17.84 Aligned_cols=62 Identities=13% Similarity=0.153 Sum_probs=40.5
Q ss_pred CCCCEEEEECCCCCCHHHHHHHHCCCE------EEEECCCC----CCCHHCCCEEEECCCCHHHHHHHHHHH
Q ss_conf 359579994388771232123433981------45403677----670011520321577268999999999
Q gi|254780779|r 157 GLPDLMFVVDTNREKLAIQEARRLRIP------IVAVVDTN----SNPDLVDYVIPGNDDSSRSIALFCDLV 218 (278)
Q Consensus 157 ~lP~~iiv~d~~~e~~Av~EA~kl~IP------vIaivDTn----~dp~~idypIP~NDds~~si~l~~~~i 218 (278)
..|+++|+.+-.--.-+++.++.+|+. +||+-|+. ..|.+-+.-.|...=+..++++++..+
T Consensus 172 ~~~~Ai~~~nD~~A~g~~~~l~~~g~~vP~Disvigfdd~~~~~~~~P~LTtv~q~~~~~G~~A~~~Ll~~i 243 (259)
T cd01542 172 QPPDAIVCATDTIALGAMKYLQELGRRIPEDISVAGFGGYELSSVVTPSLTTVDFGYKEAGKKAAELLLQLI 243 (259)
T ss_pred CCCCCEEECCHHHHHHHHHHHHHCCCCCCCCEEEEEECCHHHHHHCCCCCEEEEECHHHHHHHHHHHHHHHH
T ss_conf 799832434589999999999981999999869999898299982689978999599999999999999996
No 140
>cd01537 PBP1_Repressors_Sugar_Binding_like Ligand-binding domain of the LacI-GalR family of transcription regulators and the sugar-binding domain of ABC-type transport systems. Ligand-binding domain of the LacI-GalR family of transcription regulators and the sugar-binding domain of ABC-type transport systems, all of which contain the type I periplasmic binding protein-like fold. Their specific ligands include lactose, ribose, fructose, xylose, arabinose, galactose/glucose, and other sugars. The LacI family of proteins consists of transcriptional regulators related to the lac repressor; in general the sugar binding domain in this family binds a sugar, which in turn changes the DNA binding activity of the repressor domain. The core structure of the periplasmic binding proteins is classified into two types and they differ in number and order of beta strands in each domain: type I, which has six beta strands, and type II, which has five beta strands. These two distinct structural arrangem
Probab=58.15 E-value=16 Score=17.84 Aligned_cols=61 Identities=16% Similarity=0.304 Sum_probs=32.9
Q ss_pred CCCEEEEECCCCCCHHHHHHHHCCCE------EEEECCCC----CCCHHCCCEEEECCCCHHHHHHHHHHH
Q ss_conf 59579994388771232123433981------45403677----670011520321577268999999999
Q gi|254780779|r 158 LPDLMFVVDTNREKLAIQEARRLRIP------IVAVVDTN----SNPDLVDYVIPGNDDSSRSIALFCDLV 218 (278)
Q Consensus 158 lP~~iiv~d~~~e~~Av~EA~kl~IP------vIaivDTn----~dp~~idypIP~NDds~~si~l~~~~i 218 (278)
.|+++|+.+-.--.-+++.++.+|+. |+|+=|+. ..|..-+.-.|...=+..++++++..+
T Consensus 178 ~~dai~~~~d~~A~gv~~al~~~g~~ip~di~ivg~d~~~~~~~~~p~ltti~~~~~~~g~~a~~~l~~~i 248 (264)
T cd01537 178 DPTAIFAANDDMALGALRALREAGLRVPDDISVIGFDGTPEALLAGPPLTTVRQPPDELGRAAVELLLELL 248 (264)
T ss_pred CCEEEEECCHHHHHHHHHHHHHCCCCCCCCEEEEEECCHHHHHHHCCCEEEEECCHHHHHHHHHHHHHHHH
T ss_conf 97699989869999999999974999999839999997499997199829998399999999999999996
No 141
>PRK08662 nicotinate phosphoribosyltransferase; Reviewed
Probab=57.92 E-value=6.9 Score=20.28 Aligned_cols=16 Identities=13% Similarity=0.111 Sum_probs=12.6
Q ss_pred HCCCCEEEEEECCHHH
Q ss_conf 1078816996078235
Q gi|254780779|r 63 VARGGRILFVATKSQA 78 (278)
Q Consensus 63 ~~~gg~ILFVgTk~~~ 78 (278)
+..+..+|+-|+++..
T Consensus 124 aA~~~~vl~fG~Rr~h 139 (343)
T PRK08662 124 AAGDKPVLSFGARHLH 139 (343)
T ss_pred HCCCCCEEECCCCCCC
T ss_conf 7599827815761238
No 142
>cd06285 PBP1_LacI_like_7 Ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. This group includes the ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.
Probab=57.35 E-value=17 Score=17.75 Aligned_cols=63 Identities=16% Similarity=0.168 Sum_probs=39.1
Q ss_pred CCCCCEEEEECCCCCCHHHHHHHHCC------CEEEEECCCC----CCCHHCCCEEEECCCCHHHHHHHHHHH
Q ss_conf 13595799943887712321234339------8145403677----670011520321577268999999999
Q gi|254780779|r 156 GGLPDLMFVVDTNREKLAIQEARRLR------IPIVAVVDTN----SNPDLVDYVIPGNDDSSRSIALFCDLV 218 (278)
Q Consensus 156 ~~lP~~iiv~d~~~e~~Av~EA~kl~------IPvIaivDTn----~dp~~idypIP~NDds~~si~l~~~~i 218 (278)
...|+++|+.+-.--.-+++-+..+| |.|||+=|+. +.|.+-+.-.|..+=+..++++++..+
T Consensus 173 ~~~~~ai~~~nD~~A~g~~~~l~~~g~~iP~di~iigfd~~~~~~~~~p~LTti~q~~~~ig~~A~~~ll~~i 245 (265)
T cd06285 173 DSPPTAIFAVNDFAAIGVMGAARDRGLRVPDDVALVGYNDIPLVARLPVPLTTVRSPFHQIGRTALRLLLETI 245 (265)
T ss_pred CCCCCCEECCCHHHHHHHHHHHHHCCCCCCCCEEEEEECCHHHHHHCCCCCEEEECCHHHHHHHHHHHHHHHH
T ss_conf 9998810037889999999999985999999879999878289970789957997299999999999999984
No 143
>cd01149 HutB Hemin binding protein HutB. These proteins have been shown to function as initial receptors in ABC transport of hemin and hemoproteins in many eubacterial species. They belong to the TroA superfamily of periplasmic metal binding proteins that share a distinct fold and ligand binding mechanism. A typical TroA protein is comprised of two globular subdomains connected by a single helix and can bind the metal ion in the cleft between these domains.
Probab=57.14 E-value=15 Score=18.12 Aligned_cols=32 Identities=3% Similarity=0.103 Sum_probs=11.8
Q ss_pred HHCCCCEEEEEECCHHHHHHHHHHHHHCCCEEC
Q ss_conf 610788169960782357999999863398314
Q gi|254780779|r 62 TVARGGRILFVATKSQASDCVMEAAKRSAQYCV 94 (278)
Q Consensus 62 i~~~gg~ILFVgTk~~~~~~i~~~A~~~~~~yV 94 (278)
+++-.-.+.|..........+. ..+..|.+.+
T Consensus 54 il~l~PDLVi~~~~~~~~~~~~-~L~~~gi~v~ 85 (235)
T cd01149 54 VLSLKPTLVIASDEAGPPEALD-QLRAAGVPVV 85 (235)
T ss_pred HHHCCCCEEEEECCCCHHHHHH-HHHHCCCCEE
T ss_conf 9737998899817768399999-9996299079
No 144
>pfam02900 LigB Catalytic LigB subunit of aromatic ring-opening dioxygenase.
Probab=56.81 E-value=15 Score=18.11 Aligned_cols=26 Identities=8% Similarity=0.084 Sum_probs=14.6
Q ss_pred HHHHHHHHHHHHHCCCCEEEEEECCHHH
Q ss_conf 9999999999861078816996078235
Q gi|254780779|r 51 MLQKALQVISDTVARGGRILFVATKSQA 78 (278)
Q Consensus 51 ~L~~A~~~i~~i~~~gg~ILFVgTk~~~ 78 (278)
.+++..+.+.. .+...|++|++.-+.
T Consensus 29 ~~~~~~~~l~~--~~Pd~IvVis~Hw~t 54 (265)
T pfam02900 29 GFAEIRARLRE--LRPDVIVVFSPHWET 54 (265)
T ss_pred HHHHHHHHHHH--CCCCEEEEECCCCCC
T ss_conf 99999998776--299999998998775
No 145
>CHL00198 accA acetyl-CoA carboxylase carboxyltransferase alpha subunit; Provisional
Probab=56.79 E-value=7.8 Score=19.93 Aligned_cols=134 Identities=12% Similarity=0.193 Sum_probs=58.6
Q ss_pred EEECHHHHHHHHHHHHHHHHHHHCCCCEEEEEECCHHHHHHHHHHHHHCCCEECCCCCCCCCCCCHHHHHHHH-----HH
Q ss_conf 6753899999999999999986107881699607823579999998633983142334587323426665556-----77
Q gi|254780779|r 41 HIIDLSQTVPMLQKALQVISDTVARGGRILFVATKSQASDCVMEAAKRSAQYCVNSKWLGGMMTNWKTVSQSI-----QK 115 (278)
Q Consensus 41 hIIdL~kT~~~L~~A~~~i~~i~~~gg~ILFVgTk~~~~~~i~~~A~~~~~~yV~~RWlGG~LTN~~ti~~si-----~~ 115 (278)
..+|.+|-+.-|..-..-++.+...++. ....+...+-++.......-| .-||-|..++-.= ..
T Consensus 7 ~yLdFEkpi~eLe~ki~eL~~~~~~~~~----~~~~ei~~Le~k~~~~~~~iy-------~nLt~wq~vq~aRhp~RP~~ 75 (322)
T CHL00198 7 PLLEFEKPLAELEQQIEELSKLAPKNDV----VVNNKLKSFQRKLTILKKEIF-------YGLTPLQKLQLARHPERPTT 75 (322)
T ss_pred CCCCCCCHHHHHHHHHHHHHHHCCCCCC----CHHHHHHHHHHHHHHHHHHHH-------HCCCHHHHHHHHHCCCCCCH
T ss_conf 8577410699999999999734104675----679999999999999999998-------57999999998628999988
Q ss_pred HHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCEEEEECCCCC--------------------CHHHH
Q ss_conf 8998876301212677467887665567776434433221135957999438877--------------------12321
Q gi|254780779|r 116 LRDLEELLNKENQGFTKKERLNIERKRDKLKRALDGIRDMGGLPDLMFVVDTNRE--------------------KLAIQ 175 (278)
Q Consensus 116 l~~l~~~~~~~~~~~tkKe~~~~~r~~~kl~k~lgGi~~m~~lP~~iiv~d~~~e--------------------~~Av~ 175 (278)
+..++...+ .|..|-- .|...-=..-+||+..+...|=+|+=..-.++ .-..+
T Consensus 76 ~dyi~~~~~-~f~elhG------DR~~~dD~aivgG~a~~~~~~v~vig~~KG~~t~e~i~rNFGm~~PeGYRKAlRlm~ 148 (322)
T CHL00198 76 LDYIPYILD-EWIELHG------DRGGSDDPALVGGIGKIDNRTVVFLGHQKGRNTKENVARNFGMPSPGGYRKALRLME 148 (322)
T ss_pred HHHHHHHHC-CCEEECC------CCCCCCCCCCEEEEEEECCCEEEEEEEECCCCCHHHHHHCCCCCCHHHHHHHHHHHH
T ss_conf 999999848-7857227------837788975178899998925899998479980776675189998599999999999
Q ss_pred HHHHCCCEEEEECCCCC
Q ss_conf 23433981454036776
Q gi|254780779|r 176 EARRLRIPIVAVVDTNS 192 (278)
Q Consensus 176 EA~kl~IPvIaivDTn~ 192 (278)
-|.|.++|||.++||-.
T Consensus 149 lAekf~~Pvit~IDTpG 165 (322)
T CHL00198 149 HANRFGLPILTFIDTPG 165 (322)
T ss_pred HHHHCCCCEEEEECCCC
T ss_conf 99970997799832898
No 146
>cd06335 PBP1_ABC_ligand_binding_like_2 Type I periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type active transport systems that are predicted to be involved in transport of amino acids, peptides, or inorganic ions. This subgroup includes the type I periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type active transport systems that are predicted to be involved in transport of amino acids, peptides, or inorganic ions. Members of this group are sequence-similar to members of the family of ABC-type hydrophobic amino acid transporters, such as leucine-isoleucine-valine-binding protein (LIVBP); however their ligand specificity has not been determined experimentally.
Probab=56.75 E-value=17 Score=17.69 Aligned_cols=37 Identities=19% Similarity=0.223 Sum_probs=24.3
Q ss_pred CCCEEEEECCCCC-CHHHHHHHHCC--CEEEEECCCCCCCH
Q ss_conf 5957999438877-12321234339--81454036776700
Q gi|254780779|r 158 LPDLMFVVDTNRE-KLAIQEARRLR--IPIVAVVDTNSNPD 195 (278)
Q Consensus 158 lP~~iiv~d~~~e-~~Av~EA~kl~--IPvIaivDTn~dp~ 195 (278)
-||+||+.....+ ...++.++.+| .|+++- +...+|.
T Consensus 193 ~pD~V~~~~~~~~~~~~~~q~~~~G~~~~~~g~-~~~~~~~ 232 (347)
T cd06335 193 GADAIIIVGNGPEGAQIANGMAKLGWKVPIISH-WGLSGGN 232 (347)
T ss_pred CCCEEEEECCCHHHHHHHHHHHHCCCCCCEEEE-CCCCCHH
T ss_conf 999999947761799999999971999767941-4777589
No 147
>PRK03379 vitamin B12-transporter protein BtuF; Provisional
Probab=56.68 E-value=14 Score=18.21 Aligned_cols=27 Identities=19% Similarity=0.375 Sum_probs=9.7
Q ss_pred CCEEEEECCCCCCHHHHHHHHCCCEEE
Q ss_conf 957999438877123212343398145
Q gi|254780779|r 159 PDLMFVVDTNREKLAIQEARRLRIPIV 185 (278)
Q Consensus 159 P~~iiv~d~~~e~~Av~EA~kl~IPvI 185 (278)
||+|+..+...-.-.+..-.++||||+
T Consensus 78 PDLVia~~~~~~~~~~~~L~~~GI~v~ 104 (265)
T PRK03379 78 PDLVLAWRGGNAERQVDQLASLGIKVM 104 (265)
T ss_pred CCEEEEECCCCCHHHHHHHHHCCCEEE
T ss_conf 998999568895899999981697588
No 148
>PRK11557 putative DNA-binding transcriptional regulator; Provisional
Probab=56.18 E-value=18 Score=17.63 Aligned_cols=44 Identities=23% Similarity=0.302 Sum_probs=31.3
Q ss_pred CCEEEEECCCCC----CHHHHHHHHCCCEEEEECCCCCCC--HHCCCEEE
Q ss_conf 957999438877----123212343398145403677670--01152032
Q gi|254780779|r 159 PDLMFVVDTNRE----KLAIQEARRLRIPIVAVVDTNSNP--DLVDYVIP 202 (278)
Q Consensus 159 P~~iiv~d~~~e----~~Av~EA~kl~IPvIaivDTn~dp--~~idypIP 202 (278)
-|++|++.-..+ ..+++.|++.|+|||+|.|...+| ...||.+.
T Consensus 180 ~Dv~I~iS~sG~t~~~~~~~~~Ak~~Ga~iIaIT~~~~spLa~~aD~~L~ 229 (282)
T PRK11557 180 DDLLLAISYSGERRELNLAADEALRVGGKVLAITGFTPNALQQRASHCLY 229 (282)
T ss_pred CCEEEEEECCCCCHHHHHHHHHHHHCCCEEEEECCCCCCCHHHHCCEEEE
T ss_conf 99899985999978999999999987993999729899815886999998
No 149
>pfam03418 Peptidase_A25 Germination protease.
Probab=55.65 E-value=5.9 Score=20.69 Aligned_cols=161 Identities=20% Similarity=0.265 Sum_probs=84.3
Q ss_pred CCCCCCCCCCCEEEECHHHHHHH-----HHHHHHHHHHH-HCCCCEEEEEECCHHHHHHHHHHHHHCCCEECCCCCCCCC
Q ss_conf 56210200188167538999999-----99999999986-1078816996078235799999986339831423345873
Q gi|254780779|r 29 MERYIFCERNNTHIIDLSQTVPM-----LQKALQVISDT-VARGGRILFVATKSQASDCVMEAAKRSAQYCVNSKWLGGM 102 (278)
Q Consensus 29 M~~yI~g~rngihIIdL~kT~~~-----L~~A~~~i~~i-~~~gg~ILFVgTk~~~~~~i~~~A~~~~~~yV~~RWlGG~ 102 (278)
+..||-=+-.++.--|-+.--.. -+....|++.+ .....++|.||--.. .|+--=||=.
T Consensus 53 ~G~YITiEap~l~~~D~~~~~e~v~~~~a~el~~l~~~~~~~~~~~vLVVGLGNw---------------nvTPDALGP~ 117 (355)
T pfam03418 53 EGRYLTLEAQGIRENDSEKQEEAMEAVFAEEFNAFIENLNIPDDASCLIVGLGNL---------------NVTPDALGPK 117 (355)
T ss_pred CCCEEEEECCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCEEEEECCCC---------------CCCCCCCCHH
T ss_conf 8627998557666568788999999999999999998517898872799966777---------------7787552602
Q ss_pred CCCHHHHHHHHHHHHHHH-HHHH----------CCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCEEEEECCC---
Q ss_conf 234266655567789988-7630----------12126774678876655677764344332211359579994388---
Q gi|254780779|r 103 MTNWKTVSQSIQKLRDLE-ELLN----------KENQGFTKKERLNIERKRDKLKRALDGIRDMGGLPDLMFVVDTN--- 168 (278)
Q Consensus 103 LTN~~ti~~si~~l~~l~-~~~~----------~~~~~~tkKe~~~~~r~~~kl~k~lgGi~~m~~lP~~iiv~d~~--- 168 (278)
....--+.. +|.++. +... .+.-+.|-=|...+-| ||.. +-.||+|+++|.-
T Consensus 118 vv~~l~VTR---HL~~~~pe~~~~g~r~VsaiaPGVmg~TGiET~eIi~----------giv~-~~kPd~vIaIDALAaR 183 (355)
T pfam03418 118 AVDNLLITR---HLFELQPENVQDGFRPVSAFAPGVMGITGIETSDIIF----------GVIE-KSKPDFIIAIDALAAR 183 (355)
T ss_pred HHHCCHHHH---HHHHHCCHHHCCCCCEEEEECCCCCCCCCCCHHHHHH----------HHHH-HCCCCEEEEEHHHHCC
T ss_conf 001030105---4666473122257504557757633154302999999----------9985-2089889996442306
Q ss_pred -----------------------CCCHHHHHHHHCCCEEEEECCCCCCCHHCCCEEEECCCCHHHHHHHHHHHHHHHHHH
Q ss_conf -----------------------771232123433981454036776700115203215772689999999999999999
Q gi|254780779|r 169 -----------------------REKLAIQEARRLRIPIVAVVDTNSNPDLVDYVIPGNDDSSRSIALFCDLVASAAIDG 225 (278)
Q Consensus 169 -----------------------~e~~Av~EA~kl~IPvIaivDTn~dp~~idypIP~NDds~~si~l~~~~i~~ai~~g 225 (278)
+...++.| ..|||||||| .=|+.||-..-+|| +|.+++..|++...++
T Consensus 184 s~~Rln~TIQisdTGI~PGSGVGN~R~~i~~-etLGVPVIAI----GVPTVVdAatI~~D----tid~~l~~f~~~~~~~ 254 (355)
T pfam03418 184 AIERVNATIQISDSGIHPGSGVGNKRKDISK-DTLGIPVIAI----GIPTVVDAVSIASD----TIDFILKHFGREMKDN 254 (355)
T ss_pred CHHHHCCEEEECCCCCCCCCCCCCCCCCCCH-HHCCCCEEEE----CCCEEEEHHHHHHH----HHHHHHHHHHHHHHCC
T ss_conf 4676167578436786888765643331588-6729977995----38807504998889----9999999876553103
Q ss_pred HH
Q ss_conf 99
Q gi|254780779|r 226 IA 227 (278)
Q Consensus 226 ~~ 227 (278)
.+
T Consensus 255 ~~ 256 (355)
T pfam03418 255 GK 256 (355)
T ss_pred CC
T ss_conf 56
No 150
>PRK08840 replicative DNA helicase; Provisional
Probab=55.62 E-value=18 Score=17.57 Aligned_cols=148 Identities=19% Similarity=0.300 Sum_probs=71.7
Q ss_pred CCCCCCCC-EEEEC----HHHHHHHHHHHHHHHHHHHCCCCEEEEEECCHHHHHHHHHH-HHHCCCEECCCCCCCCCCCC
Q ss_conf 10200188-16753----89999999999999998610788169960782357999999-86339831423345873234
Q gi|254780779|r 32 YIFCERNN-THIID----LSQTVPMLQKALQVISDTVARGGRILFVATKSQASDCVMEA-AKRSAQYCVNSKWLGGMMTN 105 (278)
Q Consensus 32 yI~g~rng-ihIId----L~kT~~~L~~A~~~i~~i~~~gg~ILFVgTk~~~~~~i~~~-A~~~~~~yV~~RWlGG~LTN 105 (278)
.+-|.+.| ..||= --||...|.-|.+... .+|+.|+|..---...++.... |..++.++ +++-.|.|+.
T Consensus 210 ~~~Gl~~G~LiviaaRPsmGKTalalnia~n~a~---~~~~~v~~fSlEMs~~ql~~Rlls~~s~i~~--~~ir~g~l~~ 284 (464)
T PRK08840 210 KTAGLQGSDLIIVAARPSMGKTTFAMNLCENAAM---DQDKPVLIFSLEMPAEQLMMRMLASLSRVDQ--TKIRTGQLDD 284 (464)
T ss_pred HCCCCCCCCEEEEEECCCCCHHHHHHHHHHHHHH---HCCCCEEEECCCCCHHHHHHHHHHHHCCCCC--CHHHCCCCCH
T ss_conf 5369875767999837987368999999999999---6599679976779989999999998538982--0111488899
Q ss_pred --HHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCEEEEEC-------CCCC---CHH
Q ss_conf --2666555677899887630121267746788766556777643443322113595799943-------8877---123
Q gi|254780779|r 106 --WKTVSQSIQKLRDLEELLNKENQGFTKKERLNIERKRDKLKRALDGIRDMGGLPDLMFVVD-------TNRE---KLA 173 (278)
Q Consensus 106 --~~ti~~si~~l~~l~~~~~~~~~~~tkKe~~~~~r~~~kl~k~lgGi~~m~~lP~~iiv~d-------~~~e---~~A 173 (278)
|..+...+..+.+.....-..-..+|--+. .-+..++.+..+| .++| |+| +... ...
T Consensus 285 ~e~~~i~~a~~~~~~~~~l~idd~~~~t~~~i---~a~~r~~~~~~~~-------l~lv-vIDYLqL~~~~~~~~~r~~~ 353 (464)
T PRK08840 285 EDWARISSTMGILMEKKNMYIDDSSGLTPTEV---RSRARRVAREHGG-------LSMI-MVDYLQLMRVPALQDNRTLE 353 (464)
T ss_pred HHHHHHHHHHHHHHHCCCEEEECCCCCCHHHH---HHHHHHHHHHCCC-------CCEE-EEEHHHHCCCCCCCCHHHHH
T ss_conf 99999999999998479958856998757999---9999999986489-------8789-96188660678864036789
Q ss_pred HHH--------HHHCCCEEEEECCCCCCCH
Q ss_conf 212--------3433981454036776700
Q gi|254780779|r 174 IQE--------ARRLRIPIVAVVDTNSNPD 195 (278)
Q Consensus 174 v~E--------A~kl~IPvIaivDTn~dp~ 195 (278)
|.| |+.|+||||+++.=|-..+
T Consensus 354 i~~isr~lK~lAkel~vpVv~lsQLnR~~e 383 (464)
T PRK08840 354 IAEISRSLKALAKELNVPVVALSQLNRSLE 383 (464)
T ss_pred HHHHHHHHHHHHHHHCCCEEEECCCCCCCC
T ss_conf 999999999999996998999631685311
No 151
>PRK11006 phoR phosphate regulon sensor protein; Provisional
Probab=55.59 E-value=18 Score=17.57 Aligned_cols=86 Identities=13% Similarity=0.146 Sum_probs=43.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHCCCCCEEE-----EECCCC-CCHHHHHHHHCCCEEEEECCCCCCCHHCCCEEEECCCCH
Q ss_conf 88766556777643443322113595799-----943887-712321234339814540367767001152032157726
Q gi|254780779|r 135 RLNIERKRDKLKRALDGIRDMGGLPDLMF-----VVDTNR-EKLAIQEARRLRIPIVAVVDTNSNPDLVDYVIPGNDDSS 208 (278)
Q Consensus 135 ~~~~~r~~~kl~k~lgGi~~m~~lP~~ii-----v~d~~~-e~~Av~EA~kl~IPvIaivDTn~dp~~idypIP~NDds~ 208 (278)
...+.++-.+|..-+.-+-++.++-..-. .+|... -.....++..+.-.-.. +..+++++ .++-|+.+
T Consensus 243 l~~i~~~~~Rm~~LI~dLL~lsrle~~~~~~~~~~vd~~~ll~~l~~~~~~l~~~~~~-i~~~~~~~---~~v~~D~~-- 316 (431)
T PRK11006 243 LHTMREQTQRMEGLVKQLLTLSKIEAAPTHLLNEKVDVPMMLRVLEREAQTLSQKKHT-ITFEVDDS---LKVLGNED-- 316 (431)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHCCC-CCCCCCCC---CEEEECHH--
T ss_conf 9999999999999999999997642587521365313999999999999999862566-65568998---27997899--
Q ss_pred HHHHHHHHHHHHHHHHHH
Q ss_conf 899999999999999999
Q gi|254780779|r 209 RSIALFCDLVASAAIDGI 226 (278)
Q Consensus 209 ~si~l~~~~i~~ai~~g~ 226 (278)
+--..+.|++..||.-..
T Consensus 317 ~L~qvl~NLi~NAikytp 334 (431)
T PRK11006 317 QLRSAISNLVYNAVNHTP 334 (431)
T ss_pred HHHHHHHHHHHHHHHHCC
T ss_conf 999999999998997479
No 152
>CHL00197 carA carbamoyl-phosphate synthase arginine-specific small subunit; Provisional
Probab=55.38 E-value=6.7 Score=20.33 Aligned_cols=31 Identities=23% Similarity=0.520 Sum_probs=21.0
Q ss_pred CCCEEEEEC----CCCCCHHHHHHHHC----CCEEEEEC
Q ss_conf 595799943----88771232123433----98145403
Q gi|254780779|r 158 LPDLMFVVD----TNREKLAIQEARRL----RIPIVAVV 188 (278)
Q Consensus 158 lP~~iiv~d----~~~e~~Av~EA~kl----~IPvIaiv 188 (278)
-||.||+.| |..-..+|.+.++| +||+.|||
T Consensus 235 ~PDGIfLSNGPGDP~~~~~~i~~i~~li~~~~iPifGIC 273 (383)
T CHL00197 235 QPDGILLSNGPGDPSTVHYGIKTVKKLIKKANIPIFGIC 273 (383)
T ss_pred CCCEEEECCCCCCHHHHHHHHHHHHHHHHCCCCCEEEEC
T ss_conf 888899789999978989999999999964899789955
No 153
>COG1879 RbsB ABC-type sugar transport system, periplasmic component [Carbohydrate transport and metabolism]
Probab=55.11 E-value=18 Score=17.52 Aligned_cols=65 Identities=23% Similarity=0.250 Sum_probs=40.5
Q ss_pred CCCCEEEE--ECCCCCCHHHHHHHHCCCEEEEECCCCCCCHHCCCEEEECCCCHHHHHHHHHHHHHHHH
Q ss_conf 35957999--43887712321234339814540367767001152032157726899999999999999
Q gi|254780779|r 157 GLPDLMFV--VDTNREKLAIQEARRLRIPIVAVVDTNSNPDLVDYVIPGNDDSSRSIALFCDLVASAAI 223 (278)
Q Consensus 157 ~lP~~iiv--~d~~~e~~Av~EA~kl~IPvIaivDTn~dp~~idypIP~NDds~~si~l~~~~i~~ai~ 223 (278)
+-||+|+| .|+..=.-+|++|..-|||||.+ |++.++.....+-.+. |...+=++....+.+..-
T Consensus 90 ~~~daIiv~~~d~~a~~~~v~~a~~aGIpVv~~-d~~~~~~~~~~~~vg~-dn~~~G~~~a~~l~~~~~ 156 (322)
T COG1879 90 QGVDAIIINPVDPDALTPAVKKAKAAGIPVVTV-DSDIPGPGDRVAYVGS-DNYKAGRLAAEYLAKALG 156 (322)
T ss_pred CCCCEEEEECCCHHHHHHHHHHHHHCCCEEEEE-CCCCCCCCCEEEEECC-CHHHHHHHHHHHHHHHHC
T ss_conf 599889992898075899999999779849996-1677766651489814-809999999999999717
No 154
>COG1152 CdhA CO dehydrogenase/acetyl-CoA synthase alpha subunit [Energy production and conversion]
Probab=54.99 E-value=9.6 Score=19.34 Aligned_cols=49 Identities=27% Similarity=0.514 Sum_probs=35.1
Q ss_pred CCCCEEEEECCCCCCHHHHHHHHCCCEEEEECC---------CCCCCH-HCCCEEEECC
Q ss_conf 359579994388771232123433981454036---------776700-1152032157
Q gi|254780779|r 157 GLPDLMFVVDTNREKLAIQEARRLRIPIVAVVD---------TNSNPD-LVDYVIPGND 205 (278)
Q Consensus 157 ~lP~~iiv~d~~~e~~Av~EA~kl~IPvIaivD---------Tn~dp~-~idypIP~ND 205 (278)
++||+++|-.+---.-.+.||+++|||+||-.| |+-|++ .|.+.+-+|+
T Consensus 300 G~aDViVvDEqCir~Dileea~k~g~~vIat~~k~~~gLpD~Td~~~d~iV~~L~sg~~ 358 (772)
T COG1152 300 GKADVIVVDEQCIREDILEEASKLGIPVIATNEKGMLGLPDVTDEDVDEIVESLVSGEP 358 (772)
T ss_pred CCCEEEEECCCCCCHHHHHHHHCCCCCEEECHHHHHCCCCCCCCCCHHHHHHHHHCCCC
T ss_conf 87518984000134137898754598166302677638985655789999999964898
No 155
>pfam01497 Peripla_BP_2 Periplasmic binding protein. This family includes bacterial periplasmic binding proteins. Several of which are involved in iron transport.
Probab=54.74 E-value=16 Score=17.96 Aligned_cols=33 Identities=9% Similarity=-0.119 Sum_probs=13.6
Q ss_pred HHCCCCEEEEEECCHHHHHHHHHHHHHCCCEECC
Q ss_conf 6107881699607823579999998633983142
Q gi|254780779|r 62 TVARGGRILFVATKSQASDCVMEAAKRSAQYCVN 95 (278)
Q Consensus 62 i~~~gg~ILFVgTk~~~~~~i~~~A~~~~~~yV~ 95 (278)
+..-.-.+.|+.+.......+. ...+.|.|.+.
T Consensus 56 i~~l~PDlVi~~~~~~~~~~~~-~~~~~gipvv~ 88 (236)
T pfam01497 56 LAALKPDLIIGSAGIGLTDKAY-ELLSLIIPTVI 88 (236)
T ss_pred HHHCCCCEEEEECCCCCHHHHH-HHHHCCCCEEE
T ss_conf 9715999899726767368999-99957997899
No 156
>cd06281 PBP1_LacI_like_5 Ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. This group includes the ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.
Probab=54.39 E-value=19 Score=17.45 Aligned_cols=63 Identities=11% Similarity=0.158 Sum_probs=43.4
Q ss_pred CCCCCEEEEECCCCCCHHHHHHHHCCCE------EEEECCCC----CCCHHCCCEEEECCCCHHHHHHHHHHH
Q ss_conf 1359579994388771232123433981------45403677----670011520321577268999999999
Q gi|254780779|r 156 GGLPDLMFVVDTNREKLAIQEARRLRIP------IVAVVDTN----SNPDLVDYVIPGNDDSSRSIALFCDLV 218 (278)
Q Consensus 156 ~~lP~~iiv~d~~~e~~Av~EA~kl~IP------vIaivDTn----~dp~~idypIP~NDds~~si~l~~~~i 218 (278)
...|+++|+.+-.--.-+++.++++|+. |||+=|+. ..|.+-+.-.|...=+.+++++++..|
T Consensus 174 ~~~p~ai~~~~d~~A~g~l~~l~~~g~~VP~disviGfD~~~~~~~~~P~LTTi~~~~~~~g~~A~~~Ll~~i 246 (269)
T cd06281 174 PDRPTAIIAGGTQVLVGVLRALREAGLRIPRDLSVISIGDSDLAELMDPPITALRRDREAVGRTAAELMLDRL 246 (269)
T ss_pred CCCCCEEEECCHHHHHHHHHHHHHCCCCCCCCEEEEEECCHHHHHHCCCCCEEEECCHHHHHHHHHHHHHHHH
T ss_conf 9999656512338899999999981999999869999888799983589967997499999999999999996
No 157
>PRK09732 hypothetical protein; Provisional
Probab=54.24 E-value=8 Score=19.86 Aligned_cols=41 Identities=15% Similarity=0.088 Sum_probs=24.5
Q ss_pred HHHHHHHHCCCEE-EEECCCCCCCHHCCCEEEECCCCHHHHHHHH
Q ss_conf 2321234339814-5403677670011520321577268999999
Q gi|254780779|r 172 LAIQEARRLRIPI-VAVVDTNSNPDLVDYVIPGNDDSSRSIALFC 215 (278)
Q Consensus 172 ~Av~EA~kl~IPv-IaivDTn~dp~~idypIP~NDds~~si~l~~ 215 (278)
.|+.+|.+.|+|+ |++||...++-.. .-..+-...|+++=.
T Consensus 18 aa~~~A~~~g~~v~IaVvD~~G~L~a~---~RmDgA~~~S~~iA~ 59 (134)
T PRK09732 18 AGQEEAQKNNWSVSIAVADDGGHLLAL---SRMDDCAPIAAYISQ 59 (134)
T ss_pred HHHHHHHHHCCCEEEEEECCCCCEEEE---EECCCCCCCCHHHHH
T ss_conf 999999983998799999899999888---754999424099999
No 158
>PRK04308 murD UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional
Probab=54.21 E-value=19 Score=17.43 Aligned_cols=26 Identities=8% Similarity=-0.012 Sum_probs=15.3
Q ss_pred CEEEEEECC--HHHHHHHHHHHHHCCCE
Q ss_conf 816996078--23579999998633983
Q gi|254780779|r 67 GRILFVATK--SQASDCVMEAAKRSAQY 92 (278)
Q Consensus 67 g~ILFVgTk--~~~~~~i~~~A~~~~~~ 92 (278)
..|-.-||+ -....++....+.+|..
T Consensus 111 ~~IaVTGTnGKTTTtsli~~iL~~~g~~ 138 (445)
T PRK04308 111 KVIAITGSNGKTTVTSLVGYLCIKCGLD 138 (445)
T ss_pred CEEEEECCCCCHHHHHHHHHHHHHCCCC
T ss_conf 5799948998377999999999975996
No 159
>pfam03345 DDOST_48kD Oligosaccharyltransferase 48 kDa subunit beta. Members of this family are involved in asparagine-linked protein glycosylation. In particular, dolichyl-diphosphooligosaccharide-protein glycosyltransferase (DDOST), also known as oligosaccharyltransferase EC:2.4.1.119, transfers the high-mannose sugar GlcNAc(2)-Man(9)-Glc(3) from a dolichol-linked donor to an asparagine acceptor in a consensus Asn-X-Ser/Thr motif. In most eukaryotes, the DDOST complex is composed of three subunits, which in humans are described as a 48kD subunit, ribophorin I, and ribophorin II. However, the yeast DDOST appears to consist of six subunits (alpha, beta, gamma, delta, epsilon, zeta). The yeast beta subunit is a 45kD polypeptide, previously discovered as the Wbp1 protein, with known sequence similarity to the human 48kD subunit and the other orthologues. This family includes the 48kD-like subunits from several eukaryotes; it also includes the yeast DDOST beta subunit Wbp1.
Probab=54.03 E-value=19 Score=17.41 Aligned_cols=91 Identities=14% Similarity=0.237 Sum_probs=58.0
Q ss_pred HHHHCCCCCCCCCCCCCCCCCCCCCCCCCCEEEECHHHHHHHHHHH--HHHHHHHHCCCCEEEEEECCHHHHHHHHHHHH
Q ss_conf 9986088607547765788562102001881675389999999999--99999861078816996078235799999986
Q gi|254780779|r 10 QLLESGVQFGHRNFLWNPKMERYIFCERNNTHIIDLSQTVPMLQKA--LQVISDTVARGGRILFVATKSQASDCVMEAAK 87 (278)
Q Consensus 10 ~Ll~ag~H~Gh~~~~wnPkM~~yI~g~rngihIIdL~kT~~~L~~A--~~~i~~i~~~gg~ILFVgTk~~~~~~i~~~A~ 87 (278)
.|-+.|-.+-.++- =+++..=|-||+|.==|+|=+.-+.+.+-.. .+-|.+-+.+||+||+++.-....+.++.+|.
T Consensus 38 ~L~~rG~~lt~~~~-~d~~l~L~~~Ge~lYDhlIlf~p~~k~~g~~ls~~~l~~Fid~GGNilva~s~~~~~~~ir~l~~ 116 (439)
T pfam03345 38 SLESRGYELTFKTP-KDESLSLFKYGERLYDHLILFPPKSKGLGPSLSPKKLLDFIDKGGNVLVALSSETTPDAIRELLS 116 (439)
T ss_pred HHHHCCCEEEEECC-CCCCCEEECCCCCCCCEEEEECCCHHHHCCCCCHHHHHHHHHCCCCEEEEECCCCCCHHHHHHHH
T ss_conf 99867964899558-88752200078300346999366414407778989999998689979999388767589999999
Q ss_pred HCCCEECCCCCCCCCCC
Q ss_conf 33983142334587323
Q gi|254780779|r 88 RSAQYCVNSKWLGGMMT 104 (278)
Q Consensus 88 ~~~~~yV~~RWlGG~LT 104 (278)
.||... ..| |..+.
T Consensus 117 E~gi~~-~~~--~~~vi 130 (439)
T pfam03345 117 ELGIEL-DER--NTVVV 130 (439)
T ss_pred HCCCEE-CCC--CCEEE
T ss_conf 859156-788--98677
No 160
>COG0825 AccA Acetyl-CoA carboxylase alpha subunit [Lipid metabolism]
Probab=53.50 E-value=7.7 Score=19.96 Aligned_cols=15 Identities=40% Similarity=0.964 Sum_probs=7.5
Q ss_pred HHHHHHCCCEEEEEC
Q ss_conf 212343398145403
Q gi|254780779|r 174 IQEARRLRIPIVAVV 188 (278)
Q Consensus 174 v~EA~kl~IPvIaiv 188 (278)
+.|+..|.+|+|++|
T Consensus 181 L~em~~LkvP~I~iV 195 (317)
T COG0825 181 LREMARLKVPIISIV 195 (317)
T ss_pred HHHHHCCCCCEEEEE
T ss_conf 999857999879999
No 161
>TIGR00314 cdhA CO dehydrogenase/acetyl-CoA synthase complex, epsilon subunit; InterPro: IPR004460 Acetyl-CoA decarbonylase/synthase (ACDS) is a multienzyme complex (carbon monoxide dehydrogenase is a synonym). The ACDS complex carries out an unusual reaction involving the reversible cleavage and synthesis of acetyl-CoA in methanogens. The family contains the 4Fe-4S ferredoxin domain [C-x(2)-C-x(2)-C-x(3)-C-[PEG]] between residues 448-462 of the model.; GO: 0018492 carbon-monoxide dehydrogenase (acceptor) activity, 0006084 acetyl-CoA metabolic process.
Probab=53.15 E-value=11 Score=18.88 Aligned_cols=49 Identities=33% Similarity=0.665 Sum_probs=35.0
Q ss_pred CCCCCEEEEECCCCCCHHHHHHHHCCCEEEEECCC---------CCCCHH-CCCEEEEC
Q ss_conf 13595799943887712321234339814540367---------767001-15203215
Q gi|254780779|r 156 GGLPDLMFVVDTNREKLAIQEARRLRIPIVAVVDT---------NSNPDL-VDYVIPGN 204 (278)
Q Consensus 156 ~~lP~~iiv~d~~~e~~Av~EA~kl~IPvIaivDT---------n~dp~~-idypIP~N 204 (278)
.++||+|||=-+---.=.+.|+.|+|||+||=-|- +.||+. |+|-|-||
T Consensus 303 aG~aDV~v~DEQCiRaD~Le~~~K~g~~~IaT~~k~~~gLpD~~~~~~~~Iv~~L~~g~ 361 (795)
T TIGR00314 303 AGVADVIVVDEQCIRADILEEVKKLGIPLIATNDKACLGLPDVSDEDPDKIVDYLLSGN 361 (795)
T ss_pred CCCCCEEEECCCCHHHHHHHHHHHCCCCEEECCHHHHHCCCCCCCCCHHHHHHHHHCCC
T ss_conf 17873799747301278999998658606734178851387777688778999985388
No 162
>cd06289 PBP1_MalI_like Ligand-binding domain of MalI, a transcription regulator of the maltose system of Escherichia coli and its close homologs from other bacteria. This group includes the ligand-binding domain of MalI, a transcription regulator of the maltose system of Escherichia coli and its close homologs from other bacteria. They are members of the LacI-GalR family of repressor proteins which are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.
Probab=52.91 E-value=20 Score=17.30 Aligned_cols=63 Identities=17% Similarity=0.181 Sum_probs=40.0
Q ss_pred CCCCEEEEECCCCCCHHHHHHHHCCC------EEEEECCC----CCCCHHCCCEEEECCCCHHHHHHHHHHHH
Q ss_conf 35957999438877123212343398------14540367----76700115203215772689999999999
Q gi|254780779|r 157 GLPDLMFVVDTNREKLAIQEARRLRI------PIVAVVDT----NSNPDLVDYVIPGNDDSSRSIALFCDLVA 219 (278)
Q Consensus 157 ~lP~~iiv~d~~~e~~Av~EA~kl~I------PvIaivDT----n~dp~~idypIP~NDds~~si~l~~~~i~ 219 (278)
..|+++|+.+-.--.-+++.+..+|| -++|+=|+ -..|.+-+.-+|...=+..++++++..+.
T Consensus 177 ~~~~aii~~~D~~A~g~l~~l~~~gi~vp~disiigfd~~~~~~~~~p~ltti~~~~~~~g~~a~~~l~~~i~ 249 (268)
T cd06289 177 PRPTAIVCFNDLVAFGAMSGLRRAGLTPGRDIAVVGFDDVAEAALATPALTTVSTDPREIGRRAAELLLRRIA 249 (268)
T ss_pred CCCCEECCCCHHHHHHHHHHHHHCCCCCCCCEEEEEECCHHHHHHCCCCEEEEEECHHHHHHHHHHHHHHHHC
T ss_conf 9986203576899999999999849999985499995787899722897169984999999999999999976
No 163
>cd01143 YvrC Periplasmic binding protein YvrC. These proteins are predicted to function as initial receptors in ABC transport of metal ions in eubacteria and archaea. They belong to the TroA superfamily of periplasmic metal binding proteins that share a distinct fold and ligand binding mechanism. A typical TroA protein is comprised of two globular subdomains connected by a single helix and can bind the metal ion in the cleft between these domains.
Probab=52.52 E-value=20 Score=17.30 Aligned_cols=28 Identities=25% Similarity=0.504 Sum_probs=20.8
Q ss_pred CCEEEEECCCCCCHHHHHHHHCCCEEEEE
Q ss_conf 95799943887712321234339814540
Q gi|254780779|r 159 PDLMFVVDTNREKLAIQEARRLRIPIVAV 187 (278)
Q Consensus 159 P~~iiv~d~~~e~~Av~EA~kl~IPvIai 187 (278)
||+||...-.. .-.+....++|||++.+
T Consensus 61 PDLVi~~~~~~-~~~~~~L~~~gi~v~~~ 88 (195)
T cd01143 61 PDLVIVSSSSL-AELLEKLKDAGIPVVVL 88 (195)
T ss_pred CCEEEEECCCC-HHHHHHHHHCCCEEEEE
T ss_conf 99999827874-77999986418859997
No 164
>pfam01866 Diphthamide_syn Putative diphthamide synthesis protein. Human DPHL2 is a candidate tumour suppressor gene. DPH2 from yeast, which confers resistance to diphtheria toxin has been found to be involved in diphthamide synthesis. Diphtheria toxin inhibits eukaryotic protein synthesis by ADP-ribosylating diphthamide, a posttranslationally modified histidine residue present in EF2. The exact function of the members of this family is unknown.
Probab=51.96 E-value=21 Score=17.20 Aligned_cols=53 Identities=25% Similarity=0.296 Sum_probs=30.1
Q ss_pred CCCCCCCCCCCC-CC-CCCCCCCCCCCCEEEECHHHHHHHHHHHHHHHHHHHCCCCEEEEEECCHH
Q ss_conf 088607547765-78-85621020018816753899999999999999986107881699607823
Q gi|254780779|r 14 SGVQFGHRNFLW-NP-KMERYIFCERNNTHIIDLSQTVPMLQKALQVISDTVARGGRILFVATKSQ 77 (278)
Q Consensus 14 ag~H~Gh~~~~w-nP-kM~~yI~g~rngihIIdL~kT~~~L~~A~~~i~~i~~~gg~ILFVgTk~~ 77 (278)
+=+||||.--.+ .+ -=--|||+..+ +|++.....++. ......+|.+++|-..
T Consensus 48 ~iVH~Ghscl~~~~~~~pv~yVf~~~~----~d~~~~~~~~~~-------~~~~~~~i~l~~t~qy 102 (300)
T pfam01866 48 LIVHYGHSCLVPVRYEIPVLYVFVEIK----IDVEHLLEKLKE-------NLPGYKRIGLVTTIQH 102 (300)
T ss_pred EEEEECCCCCCCCCCCCCEEEEECCCC----CCHHHHHHHHHH-------HCCCCCEEEEEEEHHH
T ss_conf 899937876786668898899945678----798999999998-------6689987999970777
No 165
>pfam00117 GATase Glutamine amidotransferase class-I.
Probab=51.88 E-value=12 Score=18.72 Aligned_cols=31 Identities=29% Similarity=0.426 Sum_probs=21.4
Q ss_pred CCEEEEEC----C---CCCCHHHHHHHHCCCEEEEECC
Q ss_conf 95799943----8---8771232123433981454036
Q gi|254780779|r 159 PDLMFVVD----T---NREKLAIQEARRLRIPIVAVVD 189 (278)
Q Consensus 159 P~~iiv~d----~---~~e~~Av~EA~kl~IPvIaivD 189 (278)
||.||+.. | ....-.++++...++|+.|||=
T Consensus 42 ~d~iilspGpg~p~~~~~~~~~i~~~~~~~~PiLGICl 79 (187)
T pfam00117 42 PDGIIISPGPGSPGDAGGAIEAIKELRENKIPILGICL 79 (187)
T ss_pred CCEEEECCCCCCHHHCCCHHHHHHHHHHCCCCEEEEEH
T ss_conf 99899919986110134589999999977998999988
No 166
>PRK10653 D-ribose transporter subunit RbsB; Provisional
Probab=51.78 E-value=21 Score=17.18 Aligned_cols=14 Identities=29% Similarity=0.636 Sum_probs=6.2
Q ss_pred HHHHHHHCCCEEEE
Q ss_conf 32123433981454
Q gi|254780779|r 173 AIQEARRLRIPIVA 186 (278)
Q Consensus 173 Av~EA~kl~IPvIa 186 (278)
++++|...|||+|.
T Consensus 99 ~~~~a~~~gIPvV~ 112 (295)
T PRK10653 99 AVKMANQANIPVIT 112 (295)
T ss_pred HHHHHHHCCCEEEE
T ss_conf 99999976981999
No 167
>TIGR01265 tyr_nico_aTase tyrosine/nicotianamine aminotransferases; InterPro: IPR005958 This entry describes tyrosine aminotransferase (2.6.1.5 from EC) as found in animals and Trypanosoma cruzi (Euglenozoa). It is the first enzyme of a pathway of tyrosine degradation via homogentisate. L-tyrosine + 2-oxoglutarate = 4-hydroxyphenylpyruvate + L-glutamate. Several plant enzyme designated as probable tyrosine aminotransferases are very closely related to an experimentally demonstrated nicotianamine aminotransferase, an enzyme in a siderophore (iron uptake chelator) biosynthesis pathway are included in this family. ; GO: 0008483 transaminase activity, 0030170 pyridoxal phosphate binding, 0006519 amino acid and derivative metabolic process.
Probab=51.39 E-value=11 Score=18.96 Aligned_cols=39 Identities=33% Similarity=0.580 Sum_probs=25.7
Q ss_pred HHHHHHHHHC-CCCCEEEEECCCC-----------CCHHHHHHHHCCCEEEE
Q ss_conf 4344332211-3595799943887-----------71232123433981454
Q gi|254780779|r 147 RALDGIRDMG-GLPDLMFVVDTNR-----------EKLAIQEARRLRIPIVA 186 (278)
Q Consensus 147 k~lgGi~~m~-~lP~~iiv~d~~~-----------e~~Av~EA~kl~IPvIa 186 (278)
--|.||..+. .-=-||+|+||.+ +.+ +.=|.||+|||||
T Consensus 172 iDL~~le~l~DekT~A~vv~NP~NPCGsVF~~~HL~k~-~~~A~kl~i~iIA 222 (424)
T TIGR01265 172 IDLDGLESLADEKTVAIVVINPSNPCGSVFSRDHLEKI-AEVARKLGIPIIA 222 (424)
T ss_pred ECHHHHHHHHCCCCEEEEEECCCCCCCCCCCHHHHHHH-HHHHHHHCCCEEE
T ss_conf 64789987632687699984756678888788889999-9999870982687
No 168
>cd05008 SIS_GlmS_GlmD_1 SIS (Sugar ISomerase) domain repeat 1 found in Glucosamine 6-phosphate synthase (GlmS) and Glucosamine-6-phosphate deaminase (GlmD). The SIS domain is found in many phosphosugar isomerases and phosphosugar binding proteins. GlmS contains a N-terminal glutaminase domain and two C-terminal SIS domains and catalyzes the first step in hexosamine metabolism, converting fructose 6-phosphate into glucosamine 6-phosphate using glutamine as nitrogen source. The glutaminase domain hydrolyzes glutamine to glutamate and ammonia. Ammonia is transferred through a channel to the isomerase domain for glucosamine 6-phosphate synthesis. The end product of the pathway is N-acetylglucosamine, which plays multiple roles in eukaryotic cells including being a building block of bacterial and fungal cell walls. In the absence of glutamine, GlmS catalyzes the isomerization of fructose 6-phosphate into glucose 6- phosphate (PGI-like activity). Glucosamine-6-phosphate deaminase (GlmD) cont
Probab=51.38 E-value=21 Score=17.14 Aligned_cols=48 Identities=19% Similarity=0.209 Sum_probs=34.4
Q ss_pred CCCEEEEECCCCC----CHHHHHHHHCCCEEEEECCCCCCC--HHCCCEEEECC
Q ss_conf 5957999438877----123212343398145403677670--01152032157
Q gi|254780779|r 158 LPDLMFVVDTNRE----KLAIQEARRLRIPIVAVVDTNSNP--DLVDYVIPGND 205 (278)
Q Consensus 158 lP~~iiv~d~~~e----~~Av~EA~kl~IPvIaivDTn~dp--~~idypIP~ND 205 (278)
-+|++|.+.+..+ .-|++-|++.|+|+|+++..-..| ...||.|+.+.
T Consensus 46 ~~~lvI~iS~SG~t~e~i~a~~~a~~~g~~~i~iT~~~~S~la~~ad~~i~~~~ 99 (126)
T cd05008 46 EDTLVIAISQSGETADTLAALRLAKEKGAKTVAITNVVGSTLAREADYVLYLRA 99 (126)
T ss_pred CCCEEEEECCCCCCCCHHHHHHHHHHCCCCEEEEECCCCCHHHHHCCEEEECCC
T ss_conf 985999986897980078899999982994898706999978996898798698
No 169
>cd06284 PBP1_LacI_like_6 Ligand-binding domain of an uncharacterized transcription regulator from Actinobacillus succinogenes and its close homologs from other bacteria. This group includes the ligand-binding domain of an uncharacterized transcription regulator from Actinobacillus succinogenes and its close homologs from other bacteria. This group belongs to the the LacI-GalR family repressors and are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding.
Probab=51.14 E-value=21 Score=17.12 Aligned_cols=63 Identities=19% Similarity=0.304 Sum_probs=35.4
Q ss_pred CCCCCEEEEECCCCCCHHHHHHHHCCCE------EEEECCCC----CCCHHCCCEEEECCCCHHHHHHHHHHH
Q ss_conf 1359579994388771232123433981------45403677----670011520321577268999999999
Q gi|254780779|r 156 GGLPDLMFVVDTNREKLAIQEARRLRIP------IVAVVDTN----SNPDLVDYVIPGNDDSSRSIALFCDLV 218 (278)
Q Consensus 156 ~~lP~~iiv~d~~~e~~Av~EA~kl~IP------vIaivDTn----~dp~~idypIP~NDds~~si~l~~~~i 218 (278)
...|+++|+.+-.--.-+++-++.+|+. +||+=|+. ..|..-+.-+|..+=+..++++++..+
T Consensus 174 ~~~~~ai~~~nD~~A~g~~~~l~~~g~~vP~di~vigfd~~~~~~~~~p~lttv~~~~~~~g~~a~~~ll~~i 246 (267)
T cd06284 174 PDRPTAIFCFSDEMAIGAISALKELGLRVPEDISVVGFDDIDFARMTTPPLTTIRQPRYEIGRTAAELLLDII 246 (267)
T ss_pred CCCCCEEEECCCHHHHHHHHHHHHCCCCCCCEEEEEEECCHHHHHHCCCCCEEEEECHHHHHHHHHHHHHHHH
T ss_conf 9999802657868899999999983999996279998778489982489833998599999999999999997
No 170
>PRK09165 replicative DNA helicase; Provisional
Probab=51.11 E-value=21 Score=17.11 Aligned_cols=150 Identities=20% Similarity=0.320 Sum_probs=81.4
Q ss_pred HHHHHHHHHHHHHHHHH-----------HHCCCCEEEEEECCHHHHHHHHHHH-HHCCCEECCCCCCCCCCC--CHHHHH
Q ss_conf 89999999999999998-----------6107881699607823579999998-633983142334587323--426665
Q gi|254780779|r 45 LSQTVPMLQKALQVISD-----------TVARGGRILFVATKSQASDCVMEAA-KRSAQYCVNSKWLGGMMT--NWKTVS 110 (278)
Q Consensus 45 L~kT~~~L~~A~~~i~~-----------i~~~gg~ILFVgTk~~~~~~i~~~A-~~~~~~yV~~RWlGG~LT--N~~ti~ 110 (278)
.-||...|.-|.+..+. ...+|+.|+|..---...+++..+. ..++.++ +++.-|.|| .|..+.
T Consensus 216 mGKTafaLniA~n~A~~~~~~~~~~~~~~~~~g~~V~~FSLEMs~~ql~~Rlls~~s~V~~--~~ir~g~l~~~e~~~i~ 293 (484)
T PRK09165 216 MGKTALATNIAFNAAKAYLREAQPDGSKKAVNGGVVGFFSLEMSAEQLATRILSEQSEISS--SKIRRGKISEEDFEKLV 293 (484)
T ss_pred CCHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCEEEEEECCCCHHHHHHHHHHHHHCCCH--HHHHCCCCCHHHHHHHH
T ss_conf 9778999999999998741022223321136898489994779999999999999726861--35544899999999999
Q ss_pred HHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCEEEEEC------CC-CC-----CHHHHH--
Q ss_conf 55677899887630121267746788766556777643443322113595799943------88-77-----123212--
Q gi|254780779|r 111 QSIQKLRDLEELLNKENQGFTKKERLNIERKRDKLKRALDGIRDMGGLPDLMFVVD------TN-RE-----KLAIQE-- 176 (278)
Q Consensus 111 ~si~~l~~l~~~~~~~~~~~tkKe~~~~~r~~~kl~k~lgGi~~m~~lP~~iiv~d------~~-~e-----~~Av~E-- 176 (278)
..+.+|..+.-..+ .-.++|=-+... ...++.+.. |+ + +||+| +. .. ...|.|
T Consensus 294 ~a~~~l~~~~l~Id-D~~~~ti~~Ira---~~Rr~k~~~-gl-------~-livIDYLqLi~~~~~~~~~~R~~ev~~Is 360 (484)
T PRK09165 294 DASQELQKLPLYID-DTPALSISALRA---RARRLKRQH-GL-------D-LLVIDYLQLIRGSSKRSQDNRVQEISEIT 360 (484)
T ss_pred HHHHHHHCCCEEEE-CCCCCCHHHHHH---HHHHHHHHH-CC-------C-EEEEECHHHCCCCCCCCCHHHHHHHHHHH
T ss_conf 99999971984897-799987999999---999999860-99-------8-89995176357888886121999999999
Q ss_pred ------HHHCCCEEEEECCCCCCCHHCCCEEEECCCCHH
Q ss_conf ------343398145403677670011520321577268
Q gi|254780779|r 177 ------ARRLRIPIVAVVDTNSNPDLVDYVIPGNDDSSR 209 (278)
Q Consensus 177 ------A~kl~IPvIaivDTn~dp~~idypIP~NDds~~ 209 (278)
|+.|+||||+++-=|-+.+.=+=--|..-|-.-
T Consensus 361 r~LK~lAkel~ipVi~LsQLnR~~E~R~dkrP~lsDLRe 399 (484)
T PRK09165 361 QGLKALAKELNIPVIALSQLSRQVEQRDDKRPQLSDLRE 399 (484)
T ss_pred HHHHHHHHHHCCCEEEECCCCCCCCCCCCCCCCCCCCCC
T ss_conf 999999999699699974578442347999976001035
No 171
>cd01543 PBP1_XylR Ligand-binding domain of DNA transcription repressor specific for xylose (XylR). Ligand-binding domain of DNA transcription repressor specific for xylose (XylR), a member of the LacI-GalR family of bacterial transcription regulators. The ligand-binding domain of XylR is structurally homologous to the periplasmic sugar-binding domain of ABC-type transporters and both domains contain the type I periplasmic binding protein-like fold. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the type I periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.
Probab=50.95 E-value=21 Score=17.10 Aligned_cols=61 Identities=20% Similarity=0.269 Sum_probs=41.1
Q ss_pred CCCEEEEECCCCCCHHHHHHHHCCCE------EEEECCCC-----CCCHHCCCEEEECCCCHHHHHHHHHHH
Q ss_conf 59579994388771232123433981------45403677-----670011520321577268999999999
Q gi|254780779|r 158 LPDLMFVVDTNREKLAIQEARRLRIP------IVAVVDTN-----SNPDLVDYVIPGNDDSSRSIALFCDLV 218 (278)
Q Consensus 158 lP~~iiv~d~~~e~~Av~EA~kl~IP------vIaivDTn-----~dp~~idypIP~NDds~~si~l~~~~i 218 (278)
.|++||+.+-.--.-+++.++.+||. |||+=|.. +.|.+-+.-.|.-.=+..++++++..+
T Consensus 171 ~ptAi~~~nD~~A~g~l~~l~~~Gi~VP~disViGfD~~~~~~~~~~P~LTtV~q~~~~mG~~Aa~lL~~~i 242 (265)
T cd01543 171 KPVGIFACTDARARQLLEACRRAGIAVPEEVAVLGVDNDELICELSRPPLSSVEQNAERIGYEAAKLLDRLM 242 (265)
T ss_pred CCEEEEECCHHHHHHHHHHHHHHHCCCCCCEEEEEECCCHHHHHHCCCCCCEEEECHHHHHHHHHHHHHHHH
T ss_conf 983999883699999999999832257775599998286888952799973396299999999999999996
No 172
>cd06316 PBP1_ABC_sugar_binding_like_7 Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems. Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily, which consists of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis.
Probab=50.95 E-value=21 Score=17.10 Aligned_cols=38 Identities=11% Similarity=0.142 Sum_probs=17.2
Q ss_pred HHHHHHHCCCCEEEEE-ECCHHHHHHHHHHHHHCCCEEC
Q ss_conf 9999861078816996-0782357999999863398314
Q gi|254780779|r 57 QVISDTVARGGRILFV-ATKSQASDCVMEAAKRSAQYCV 94 (278)
Q Consensus 57 ~~i~~i~~~gg~ILFV-gTk~~~~~~i~~~A~~~~~~yV 94 (278)
..|...+.+|-..+++ .+...+...+-+.|...|.|.|
T Consensus 47 ~~i~~~I~~gvDaIii~p~d~~a~~~~v~~A~~aGIpVv 85 (294)
T cd06316 47 ADIETTISQKPDIIISIPVDPVSTAAAYKKVAEAGIKLV 85 (294)
T ss_pred HHHHHHHHCCCCEEEEECCCHHHHHHHHHHHHHCCCCEE
T ss_conf 999999985999999938886787999999998199679
No 173
>pfam03033 Glyco_transf_28 Glycosyltransferase family 28 N-terminal domain. The glycosyltransferase family 28 includes monogalactosyldiacylglycerol synthase (EC 2.4.1.46) and UDP-N-acetylglucosamine transferase (EC 2.4.1.-). This N-terminal domain contains the acceptor binding site and likely membrane association site. This family also contains a large number of proteins that probably have quite distinct activities.
Probab=50.94 E-value=21 Score=17.10 Aligned_cols=117 Identities=21% Similarity=0.172 Sum_probs=65.0
Q ss_pred HHHHHHHHHHHHHHHHCCCCEEEEEECCHHHHHHHHHHHHHCCCEECCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCC
Q ss_conf 99999999999998610788169960782357999999863398314233458732342666555677899887630121
Q gi|254780779|r 48 TVPMLQKALQVISDTVARGGRILFVATKSQASDCVMEAAKRSAQYCVNSKWLGGMMTNWKTVSQSIQKLRDLEELLNKEN 127 (278)
Q Consensus 48 T~~~L~~A~~~i~~i~~~gg~ILFVgTk~~~~~~i~~~A~~~~~~yV~~RWlGG~LTN~~ti~~si~~l~~l~~~~~~~~ 127 (278)
|--++.-|..+..++..+|-.+. +||.+...+.+. ..|.+|+.- ..+|.-.+ .++.+..+-....+.
T Consensus 8 TGGHv~Palala~~L~~~g~~v~-igt~~~~e~~v~----~~~~~~~~i-~~~~~~~~------~~~~~~~~~~~~~~~- 74 (136)
T pfam03033 8 TRGHVFPAVALAWALRRRGHEVR-LGTPPGLEEFVE----EAGLPFVPI-GGDGLRRK------SLKNLKEPLEGGRAL- 74 (136)
T ss_pred CHHHHHHHHHHHHHHHHCCCEEE-ECCCCCHHHHHH----HCCCEEEEE-CCCCCCCC------HHHHHHHHHHHHHHH-
T ss_conf 57999999999999998599771-215802888875----359818996-27985467------599999999999999-
Q ss_pred CCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCEEEEECCCCCCHHHHHHHHCCCEEEEECCCCCCCHHCC
Q ss_conf 26774678876655677764344332211359579994388771232123433981454036776700115
Q gi|254780779|r 128 QGFTKKERLNIERKRDKLKRALDGIRDMGGLPDLMFVVDTNREKLAIQEARRLRIPIVAVVDTNSNPDLVD 198 (278)
Q Consensus 128 ~~~tkKe~~~~~r~~~kl~k~lgGi~~m~~lP~~iiv~d~~~e~~Av~EA~kl~IPvIaivDTn~dp~~id 198 (278)
.+.+.-++ +..||+++-+.---.--++-.|..++||++ +..-|+=|..++
T Consensus 75 ------------------~~~~~~l~--~~kp~~vig~GGy~s~p~~~aa~~~~ip~~-ihEqN~vpG~an 124 (136)
T pfam03033 75 ------------------RQAKEILK--EFKPDLVIGFGGYVAVPALIAAPLAGIPLI-VHEQNGIPGLVN 124 (136)
T ss_pred ------------------HHHHHHHH--HCCCCEEECCCCCCCHHHHHHHHHCCCCEE-EECCCCCHHHHH
T ss_conf ------------------99999998--569988974388542289999998399889-987986249999
No 174
>PTZ00295 glucosamine-fructose-6-phosphate aminotransferase; Provisional
Probab=50.80 E-value=21 Score=17.08 Aligned_cols=61 Identities=20% Similarity=0.192 Sum_probs=42.6
Q ss_pred EEEEECCCCC----CHHHHHHHHCCCEEEEECCCCCC--CHHCCCEEEECCC---CHHHHHHHHHHHHHH
Q ss_conf 7999438877----12321234339814540367767--0011520321577---268999999999999
Q gi|254780779|r 161 LMFVVDTNRE----KLAIQEARRLRIPIVAVVDTNSN--PDLVDYVIPGNDD---SSRSIALFCDLVASA 221 (278)
Q Consensus 161 ~iiv~d~~~e----~~Av~EA~kl~IPvIaivDTn~d--p~~idypIP~NDd---s~~si~l~~~~i~~a 221 (278)
+++.+.+..| ..|+++|++.|.+++|||+.-.. ....|+.|+.+-- ++.|-.-|+..++--
T Consensus 425 lvI~ISQSGETADTLaALr~AK~~G~~tlaIvNv~gSsiaReaD~~i~t~AGpEIgVASTKaFtsQl~~L 494 (691)
T PTZ00295 425 GVIFISQSGETRDVIKACKLAEDLGIPKLSVVNSVGSTIARMTGCGVYLNAGREVAVASTKAFSSQVSVL 494 (691)
T ss_pred EEEEECCCCCCHHHHHHHHHHHHCCCCEEEEECCCCCHHHEECCEEEEECCCCEEEEEECHHHHHHHHHH
T ss_conf 3999757788567999999999769938999547887253044632682477646787048999999999
No 175
>cd06290 PBP1_LacI_like_9 Ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. This group includes the ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.
Probab=50.53 E-value=22 Score=17.06 Aligned_cols=62 Identities=13% Similarity=0.084 Sum_probs=34.6
Q ss_pred CCCCEEEEECCCCCCHHHHHHHHCCCE------EEEECCC----CCCCHHCCCEEEECCCCHHHHHHHHHHH
Q ss_conf 359579994388771232123433981------4540367----7670011520321577268999999999
Q gi|254780779|r 157 GLPDLMFVVDTNREKLAIQEARRLRIP------IVAVVDT----NSNPDLVDYVIPGNDDSSRSIALFCDLV 218 (278)
Q Consensus 157 ~lP~~iiv~d~~~e~~Av~EA~kl~IP------vIaivDT----n~dp~~idypIP~NDds~~si~l~~~~i 218 (278)
..|+++|+.+-.--.-+++.|..+||- |||+=|+ -..|..-+.-+|.-.=+.+++++++..+
T Consensus 175 ~~~~ai~~~nD~~A~g~~~~~~~~g~~vP~di~vigfD~~~~~~~~~p~ltti~~~~~~~G~~A~~~L~~~i 246 (265)
T cd06290 175 PDFTAIFAANDQTAYGARLALYRRGLRVPEDVSLIGFDDLPLSAYTTPPLTTVRQPIEEMGQIAARALLALI 246 (265)
T ss_pred CCCCCCEECCHHHHHHHHHHHHHHCCCCCCCEEEEEECCHHHHHHCCCCEEEEEECHHHHHHHHHHHHHHHH
T ss_conf 998842105789999999999980999999879999998789973289828999599999999999999997
No 176
>PRK07004 replicative DNA helicase; Provisional
Probab=50.04 E-value=22 Score=17.01 Aligned_cols=147 Identities=16% Similarity=0.279 Sum_probs=76.4
Q ss_pred CCCCCCCCC-EEEE----CHHHHHHHHHHHHHHHHHHH-CCCCEEEEEECCHHHHHHHHHHHH-HCCCEECCCCCCCCCC
Q ss_conf 210200188-1675----38999999999999999861-078816996078235799999986-3398314233458732
Q gi|254780779|r 31 RYIFCERNN-THII----DLSQTVPMLQKALQVISDTV-ARGGRILFVATKSQASDCVMEAAK-RSAQYCVNSKWLGGMM 103 (278)
Q Consensus 31 ~yI~g~rng-ihII----dL~kT~~~L~~A~~~i~~i~-~~gg~ILFVgTk~~~~~~i~~~A~-~~~~~yV~~RWlGG~L 103 (278)
..+-|.+.| +.|| ---||...|.-|.+ ++ .+|..|+|.+.--...+++..+.. .++.+ .+++.-|.|
T Consensus 205 ~~t~Gl~~gdLiIIAARPsmGKTafAlniA~n----~A~~~g~~V~~FSLEMs~eql~~Rlls~~s~I~--~~~ir~g~l 278 (460)
T PRK07004 205 RMTSGMHGGELIIVAGRPSMGKTAFSMNIGEY----VAVEYGLPVAVFSMEMPGTQLAMRMLGSVGRLD--QHRMRTGRL 278 (460)
T ss_pred HHHCCCCCCCEEEEEECCCCCHHHHHHHHHHH----HHHHCCCCEEEECCCCCHHHHHHHHHHHCCCCC--CCHHHCCCC
T ss_conf 65238987757999736876426999999999----987258866998477999999999998606988--211007889
Q ss_pred CC--HHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCEEEEEC------CC----CCC
Q ss_conf 34--2666555677899887630121267746788766556777643443322113595799943------88----771
Q gi|254780779|r 104 TN--WKTVSQSIQKLRDLEELLNKENQGFTKKERLNIERKRDKLKRALDGIRDMGGLPDLMFVVD------TN----REK 171 (278)
Q Consensus 104 TN--~~ti~~si~~l~~l~~~~~~~~~~~tkKe~~~~~r~~~kl~k~lgGi~~m~~lP~~iiv~d------~~----~e~ 171 (278)
|. |..+...+.++.++.-..+ .-..++--+.. -...++.+..|+ .++|| +| +. ...
T Consensus 279 ~~~e~~~i~~a~~~l~~~~l~Id-D~~~lt~~~ir---a~~Rr~~~~~g~-------l~lvv-iDYlqli~~~~~~~~r~ 346 (460)
T PRK07004 279 TDEDWPKLTHAVQKMSEAQLFID-ETGGLNPMELR---SRARRLARQCGK-------LGLII-IDYLQLMSGSSQGENRA 346 (460)
T ss_pred CHHHHHHHHHHHHHHHCCCEEEE-CCCCCHHHHHH---HHHHHHHHHCCC-------CCEEE-EEHHHHCCCCCCCCCHH
T ss_conf 99999999999999855974896-89873078999---999999974358-------88998-50775447888888899
Q ss_pred HHHHH--------HHHCCCEEEEECCCCCCCH
Q ss_conf 23212--------3433981454036776700
Q gi|254780779|r 172 LAIQE--------ARRLRIPIVAVVDTNSNPD 195 (278)
Q Consensus 172 ~Av~E--------A~kl~IPvIaivDTn~dp~ 195 (278)
..|.| |+.|+||||+++-=|=+.+
T Consensus 347 ~ei~~isr~lK~lAkel~ipvi~lsQLnR~~e 378 (460)
T PRK07004 347 TEISEISRSLKSLAKELDVPVIALSQLNRGLE 378 (460)
T ss_pred HHHHHHHHHHHHHHHHHCCCEEEECCCCCCCC
T ss_conf 99999999999999996997899704684312
No 177
>PRK11070 ssDNA exonuclease RecJ; Provisional
Probab=49.89 E-value=22 Score=16.99 Aligned_cols=57 Identities=18% Similarity=0.300 Sum_probs=38.0
Q ss_pred HHHHHHHHHHHHHHHCCCCEEEEEECCHH----HHHHHHHHHHHCCC----EECCCCCCCCCCCC
Q ss_conf 99999999999986107881699607823----57999999863398----31423345873234
Q gi|254780779|r 49 VPMLQKALQVISDTVARGGRILFVATKSQ----ASDCVMEAAKRSAQ----YCVNSKWLGGMMTN 105 (278)
Q Consensus 49 ~~~L~~A~~~i~~i~~~gg~ILFVgTk~~----~~~~i~~~A~~~~~----~yV~~RWlGG~LTN 105 (278)
+.-+.+|..-|.+-..++.+|++.|---. +.-+...+-...|. ||+.+|.--|-=-|
T Consensus 51 l~dm~~Av~ri~~Ai~~~ekI~I~GDYDvDGiTstaiL~~~l~~~g~~~v~y~IP~R~~eGYGl~ 115 (574)
T PRK11070 51 LSGIEKAVEILYNAFREGTRIIVVGDFDADGATSTALSVLALRSLGCSNIDYLVPNRFEDGYGLS 115 (574)
T ss_pred CCCHHHHHHHHHHHHHCCCEEEEEECCCCHHHHHHHHHHHHHHHCCCCCEEEECCCCCCCCCCCC
T ss_conf 13999999999999987994999934786067999999999998699716997989876787979
No 178
>cd04795 SIS SIS domain. SIS (Sugar ISomerase) domains are found in many phosphosugar isomerases and phosphosugar binding proteins. SIS domains are also found in proteins that regulate the expression of genes involved in synthesis of phosphosugars.
Probab=49.19 E-value=18 Score=17.52 Aligned_cols=30 Identities=23% Similarity=0.457 Sum_probs=24.0
Q ss_pred CCEEEEECCCCC----CHHHHHHHHCCCEEEEEC
Q ss_conf 957999438877----123212343398145403
Q gi|254780779|r 159 PDLMFVVDTNRE----KLAIQEARRLRIPIVAVV 188 (278)
Q Consensus 159 P~~iiv~d~~~e----~~Av~EA~kl~IPvIaiv 188 (278)
=|+++++....+ ..+++.|++.|+|+|+|.
T Consensus 48 ~D~vi~iS~SG~t~e~~~~~~~ak~~g~~vi~IT 81 (87)
T cd04795 48 GDVVIALSYSGRTEELLAALEIAKELGIPVIAIT 81 (87)
T ss_pred CCEEEEEECCCCCHHHHHHHHHHHHCCCCEEEEE
T ss_conf 9989999799798899999999998799899983
No 179
>PRK11303 DNA-binding transcriptional regulator FruR; Provisional
Probab=49.15 E-value=23 Score=16.92 Aligned_cols=62 Identities=15% Similarity=0.104 Sum_probs=26.5
Q ss_pred CCCCEEEEECCCCCCHHHHHHHHCCC--E----EEEECCCC----CCCHHCCCEEEECCCCHHHHHHHHHHH
Q ss_conf 35957999438877123212343398--1----45403677----670011520321577268999999999
Q gi|254780779|r 157 GLPDLMFVVDTNREKLAIQEARRLRI--P----IVAVVDTN----SNPDLVDYVIPGNDDSSRSIALFCDLV 218 (278)
Q Consensus 157 ~lP~~iiv~d~~~e~~Av~EA~kl~I--P----vIaivDTn----~dp~~idypIP~NDds~~si~l~~~~i 218 (278)
..|+++|+.+-.-=.-+++.++.+|+ | |||+=|+. ..|.+-+.-.|...=+..++++++..|
T Consensus 237 ~~p~Ai~~~nD~~A~g~l~al~~~g~~VP~DvsvigfDd~~~~~~~~p~LTtv~q~~~~~g~~A~~~Ll~~i 308 (330)
T PRK11303 237 GMPDALFTTSYTLLQGVLDVLLERPGKLPSDLAIATFGDNELLDFLPCPVNAVAQQHRLIAERALELALAAL 308 (330)
T ss_pred CCCCEEEECCHHHHHHHHHHHHHCCCCCCCCEEEEEECCHHHHHCCCCCCEEEECCHHHHHHHHHHHHHHHH
T ss_conf 999779974899999999999985999999759999996288971799972996799999999999999996
No 180
>PRK10339 DNA-binding transcriptional repressor EbgR; Provisional
Probab=49.11 E-value=23 Score=16.91 Aligned_cols=65 Identities=15% Similarity=0.214 Sum_probs=42.6
Q ss_pred CCCCCEEEEECCCCCCHHHHHHHHCCCE------EEEECCC----CCCCHHCCCEEEECCCCHHHHHHHHHHHHH
Q ss_conf 1359579994388771232123433981------4540367----767001152032157726899999999999
Q gi|254780779|r 156 GGLPDLMFVVDTNREKLAIQEARRLRIP------IVAVVDT----NSNPDLVDYVIPGNDDSSRSIALFCDLVAS 220 (278)
Q Consensus 156 ~~lP~~iiv~d~~~e~~Av~EA~kl~IP------vIaivDT----n~dp~~idypIP~NDds~~si~l~~~~i~~ 220 (278)
...|+++|+.+-.-=.-+++.++.+||. |+|+=|+ -+.|.+-+.-+|...=+..++++++..+.+
T Consensus 232 ~~~p~ai~~~nD~~A~g~l~al~~~gi~VP~DisVigfdd~~~~~~~~P~LTtv~~~~~~~g~~Av~~Ll~~i~~ 306 (327)
T PRK10339 232 EDYPKALFVASDSIAIGVLRAIHERGLNIPQDISLISVNDIPTARFTFPPLSTVRIHSEMMGSQGVNLLYEKARD 306 (327)
T ss_pred CCCCCEEEECCHHHHHHHHHHHHHCCCCCCCCEEEEEECCHHHHHHCCCCCEEEECCHHHHHHHHHHHHHHHHHC
T ss_conf 999974897777999999999998299999975999989738898338995699869999999999999999738
No 181
>TIGR02634 xylF D-xylose ABC transporter, substrate-binding protein; InterPro: IPR013456 ABC transporters belong to the ATP-Binding Cassette (ABC) superfamily, which uses the hydrolysis of ATP to energize diverse biological systems. ABC transporters are minimally constituted of two conserved regions: a highly conserved ATP binding cassette (ABC) and a less conserved transmembrane domain (TMD). These regions can be found on the same protein or on two different ones. Most ABC transporters function as a dimer and therefore are constituted of four domains, two ABC modules and two TMDs. ABC transporters are involved in the export or import of a wide variety of substrates ranging from small ions to macromolecules. The major function of ABC import systems is to provide essential nutrients to bacteria. They are found only in prokaryotes and their four constitutive domains are usually encoded by independent polypeptides (two ABC proteins and two TMD proteins). Prokaryotic importers require additional extracytoplasmic binding proteins (one or more per systems) for function. In contrast, export systems are involved in the extrusion of noxious substances, the export of extracellular toxins and the targeting of membrane components. They are found in all living organisms and in general the TMD is fused to the ABC module in a variety of combinations. Some eukaryotic exporters encode the four domains on the same polypeptide chain . The ABC module (approximately two hundred amino acid residues) is known to bind and hydrolyze ATP, thereby coupling transport to ATP hydrolysis in a large number of biological processes. The cassette is duplicated in several subfamilies. Its primary sequence is highly conserved, displaying a typical phosphate-binding loop: Walker A, and a magnesium binding site: Walker B. Besides these two regions, three other conserved motifs are present in the ABC cassette: the switch region which contains a histidine loop, postulated to polarize the attaching water molecule for hydrolysis, the signature conserved motif (LSGGQ) specific to the ABC transporter, and the Q-motif (between Walker A and the signature), which interacts with the gamma phosphate through a water bond. The Walker A, Walker B, Q-loop and switch region form the nucleotide binding site , , . The 3D structure of a monomeric ABC module adopts a stubby L-shape with two distinct arms. ArmI (mainly beta-strand) contains Walker A and Walker B. The important residues for ATP hydrolysis and/or binding are located in the P-loop. The ATP-binding pocket is located at the extremity of armI. The perpendicular armII contains mostly the alpha helical subdomain with the signature motif. It only seems to be required for structural integrity of the ABC module. ArmII is in direct contact with the TMD. The hinge between armI and armII contains both the histidine loop and the Q-loop, making contact with the gamma phosphate of the ATP molecule. ATP hydrolysis leads to a conformational change that could facilitate ADP release. In the dimer the two ABC cassettes contact each other through hydrophobic interactions at the antiparallel beta-sheet of armI by a two-fold axis , , , , , . Proteins known to belong to this family are classified in several functional subfamilies depending on the substrate used (for further information see http://www.tcdb.org/tcdb/index.php?tc=3.A.1). This entry represents the D-xylose ABC transporter substrate-binding protein which is a periplasmic (when in Gram-negative bacteria) binding protein for D-xylose import by a high-affinity ATP-binding cassette (ABC) transporter..
Probab=48.46 E-value=17 Score=17.75 Aligned_cols=51 Identities=20% Similarity=0.277 Sum_probs=32.9
Q ss_pred CCCCEEEEECCCCC--CHHHHHHHHCCCEEEEECCCCCCCHHCCCEEEECCCCH
Q ss_conf 35957999438877--12321234339814540367767001152032157726
Q gi|254780779|r 157 GLPDLMFVVDTNRE--KLAIQEARRLRIPIVAVVDTNSNPDLVDYVIPGNDDSS 208 (278)
Q Consensus 157 ~lP~~iiv~d~~~e--~~Av~EA~kl~IPvIaivDTn~dp~~idypIP~NDds~ 208 (278)
+==++++|+-.+.+ ..+|.||.+-||||++-=--=.|+ .+||.|--.+.-+
T Consensus 53 ~gv~vlvi~~~~~~vl~~~~~~A~~~GI~V~aYDRLI~~a-D~~fY~sFDN~~V 105 (307)
T TIGR02634 53 RGVDVLVIIPYNGEVLSNAVQEAKKEGIKVLAYDRLIEDA-DIDFYLSFDNEKV 105 (307)
T ss_pred CCCCEEEEECCCCHHHHHHHHHHHHCCCEEEEEECCCCCC-CCCEEEEECHHHH
T ss_conf 7980999953686037889999987798088730111335-5200223043578
No 182
>PRK11041 DNA-binding transcriptional regulator CytR; Provisional
Probab=48.34 E-value=23 Score=16.84 Aligned_cols=64 Identities=17% Similarity=0.279 Sum_probs=39.5
Q ss_pred HCCCCCEEEEECCCCCCHHHHHHHHCCCE------EEEECCCC----CCCHHCCCEEEECCCCHHHHHHHHHHH
Q ss_conf 11359579994388771232123433981------45403677----670011520321577268999999999
Q gi|254780779|r 155 MGGLPDLMFVVDTNREKLAIQEARRLRIP------IVAVVDTN----SNPDLVDYVIPGNDDSSRSIALFCDLV 218 (278)
Q Consensus 155 m~~lP~~iiv~d~~~e~~Av~EA~kl~IP------vIaivDTn----~dp~~idypIP~NDds~~si~l~~~~i 218 (278)
+...|+++|+.+-.-=.-+++.++.+||- |||+-|+. +.|.+-+.-+|..+=+..++.+++..+
T Consensus 242 ~~~~ptAi~~~nD~~A~g~l~al~~~Gl~VP~DisViGfdd~~~~~~~~P~LTTV~~~~~~~g~~A~~~L~~~i 315 (341)
T PRK11041 242 LPQPPTAVFCHSDVMALGALSQAKRQGLKVPQDLSIIGFDNIDLAQFCDPPLTTIAQPRYEIGREAMLLLLDQL 315 (341)
T ss_pred CCCCCCEEEECCHHHHHHHHHHHHHHCCCCCCCEEEEEECCHHHHHCCCCCEEEEECCHHHHHHHHHHHHHHHH
T ss_conf 59998579876779999999999971898999659999888389852699836998199999999999999996
No 183
>smart00481 POLIIIAc DNA polymerase alpha chain like domain. DNA polymerase alpha chain like domain, incl. family of hypothetical proteins
Probab=48.31 E-value=11 Score=19.03 Aligned_cols=21 Identities=19% Similarity=0.401 Sum_probs=17.9
Q ss_pred HHHHHHHHCCCEEEEECCCCC
Q ss_conf 232123433981454036776
Q gi|254780779|r 172 LAIQEARRLRIPIVAVVDTNS 192 (278)
Q Consensus 172 ~Av~EA~kl~IPvIaivDTn~ 192 (278)
..++.|.+.|+|.+||+|.|+
T Consensus 19 ~lv~~a~~~g~~~vaiTDh~~ 39 (67)
T smart00481 19 ELVKRAKELGLKAIAITDHGN 39 (67)
T ss_pred HHHHHHHHCCCCEEEEECCCC
T ss_conf 999999987998899967886
No 184
>PRK09492 treR trehalose repressor; Provisional
Probab=48.30 E-value=23 Score=16.83 Aligned_cols=60 Identities=8% Similarity=-0.011 Sum_probs=24.7
Q ss_pred CCCCEEEEECCCCCCHHHHHHHHCCC---EEEEECCCC----CCCHHCCCEEEECCCCHHHHHHHHH
Q ss_conf 35957999438877123212343398---145403677----6700115203215772689999999
Q gi|254780779|r 157 GLPDLMFVVDTNREKLAIQEARRLRI---PIVAVVDTN----SNPDLVDYVIPGNDDSSRSIALFCD 216 (278)
Q Consensus 157 ~lP~~iiv~d~~~e~~Av~EA~kl~I---PvIaivDTn----~dp~~idypIP~NDds~~si~l~~~ 216 (278)
..|+++|+.+-.--.-+++.+..+|| .|+|+-|+. ..|.+-++-+|...=+..++++++.
T Consensus 231 ~~~~ai~~~~D~~A~g~~~~l~~~gi~disi~g~d~~~~~~~~~P~LTTi~~~~~~~g~~A~~~Ll~ 297 (315)
T PRK09492 231 PETTALVCATDTLALGASKYLQEQGRETLQVAGVGNTPLLKFLFPNIVSVDPGYAEAGRQAACQLIE 297 (315)
T ss_pred CCCCEEEEECHHHHHHHHHHHHHCCCCCEEEEEECCHHHHHHCCCCCEEEEECHHHHHHHHHHHHHH
T ss_conf 7998599956799999999999719998589998881889845899749985999999999999999
No 185
>KOG2062 consensus
Probab=48.11 E-value=23 Score=16.90 Aligned_cols=47 Identities=17% Similarity=0.376 Sum_probs=35.3
Q ss_pred CCCCEEEEECCCCCCHHHHHHHHCCCEEEEECCCCCCCHHCCCEEEECCCCHHHHHHHH
Q ss_conf 35957999438877123212343398145403677670011520321577268999999
Q gi|254780779|r 157 GLPDLMFVVDTNREKLAIQEARRLRIPIVAVVDTNSNPDLVDYVIPGNDDSSRSIALFC 215 (278)
Q Consensus 157 ~lP~~iiv~d~~~e~~Av~EA~kl~IPvIaivDTn~dp~~idypIP~NDds~~si~l~~ 215 (278)
-.|.++|.+|- -|.||.+-+. |++.|+...||-|.--.+.+.++-+-
T Consensus 740 f~PT~vigln~-----------dLk~Pk~e~~-s~ak~~~faYP~p~e~~~~k~~~Kv~ 786 (929)
T KOG2062 740 FTPTTVIGLNE-----------DLKIPKFEYI-SHAKPSLFAYPPPDEVKKAKEVEKVA 786 (929)
T ss_pred CCCCEEEEECC-----------CCCCCCEEEE-CCCCHHHCCCCCCCCCCHHHHHHCCC
T ss_conf 27606997645-----------5577513301-36780211689843341233331223
No 186
>cd05710 SIS_1 A subgroup of the SIS domain. SIS (Sugar ISomerase) domains are found in many phosphosugar isomerases and phosphosugar binding proteins. SIS domains are also found in proteins that regulate the expression of genes involved in synthesis of phosphosugars.
Probab=48.04 E-value=24 Score=16.81 Aligned_cols=47 Identities=19% Similarity=0.306 Sum_probs=34.2
Q ss_pred CCEEEEECCCCC----CHHHHHHHHCCCEEEEECCCCCCC--HHCCCEEEECC
Q ss_conf 957999438877----123212343398145403677670--01152032157
Q gi|254780779|r 159 PDLMFVVDTNRE----KLAIQEARRLRIPIVAVVDTNSNP--DLVDYVIPGND 205 (278)
Q Consensus 159 P~~iiv~d~~~e----~~Av~EA~kl~IPvIaivDTn~dp--~~idypIP~ND 205 (278)
-++++.+.+..+ -.|++.|+..|.++|||++....| ...||.|+.--
T Consensus 48 ~~lvi~iS~SG~T~e~i~a~~~ak~~g~~tiaiT~~~~S~la~~aD~~i~~g~ 100 (120)
T cd05710 48 KSVVILASHSGNTKETVAAAKFAKEKGATVIGLTDDEDSPLAKLADYVIVYGF 100 (120)
T ss_pred CCEEEEECCCCCCHHHHHHHHHHHHCCCEEEEEECCCCCHHHHHCCEEEECCC
T ss_conf 96999983798978999999999986995999989898987996798888899
No 187
>PRK08605 D-lactate dehydrogenase; Validated
Probab=47.99 E-value=24 Score=16.80 Aligned_cols=27 Identities=11% Similarity=-0.082 Sum_probs=14.0
Q ss_pred CCEEEEEECCHHHHHHHHHHHHHCCCE
Q ss_conf 881699607823579999998633983
Q gi|254780779|r 66 GGRILFVATKSQASDCVMEAAKRSAQY 92 (278)
Q Consensus 66 gg~ILFVgTk~~~~~~i~~~A~~~~~~ 92 (278)
|+++-+||..+-.+.+.+..|...||-
T Consensus 146 ~ktvGIiG~G~IG~~vak~~a~~fgm~ 172 (332)
T PRK08605 146 DLKVAVIGTGRIGLAVAKIFAKGYGCD 172 (332)
T ss_pred CCEEEEEEEEHHHHHHHHHHHHHCCCE
T ss_conf 778999974368899999998756982
No 188
>PRK10703 DNA-binding transcriptional repressor PurR; Provisional
Probab=47.87 E-value=17 Score=17.74 Aligned_cols=64 Identities=16% Similarity=0.215 Sum_probs=40.0
Q ss_pred CCCCCEEEEECCCCCCHHHHHHHHCCC--E----EEEECCCC----CCCHHCCCEEEECCCCHHHHHHHHHHHH
Q ss_conf 135957999438877123212343398--1----45403677----6700115203215772689999999999
Q gi|254780779|r 156 GGLPDLMFVVDTNREKLAIQEARRLRI--P----IVAVVDTN----SNPDLVDYVIPGNDDSSRSIALFCDLVA 219 (278)
Q Consensus 156 ~~lP~~iiv~d~~~e~~Av~EA~kl~I--P----vIaivDTn----~dp~~idypIP~NDds~~si~l~~~~i~ 219 (278)
...|+++|+.+-.-=.-+++.++.+|| | |||+-|+. +.|.+-+.-+|...=+..++.+++..+.
T Consensus 237 ~~~ptAi~~~nD~~A~g~~~~l~~~g~~VP~DisvigfDd~~~~~~~~P~LTtv~~~~~~~g~~A~~~Ll~~i~ 310 (335)
T PRK10703 237 EHRPTAVFCGGDIMAMGAICAADEMGLRVPQDISVIGYDNVRNARYFTPALTTIHQPKDRLGETAFNMLLDRIV 310 (335)
T ss_pred CCCCCEEEECCHHHHHHHHHHHHHCCCCCCCCEEEEEECCCHHHHHCCCCCEEEECCHHHHHHHHHHHHHHHHC
T ss_conf 99986689687599999999999719999997499998882899825898279982999999999999999961
No 189
>PRK09526 lacI lac repressor; Reviewed
Probab=47.20 E-value=15 Score=18.10 Aligned_cols=63 Identities=13% Similarity=0.107 Sum_probs=38.5
Q ss_pred CCCCCEEEEECCCCCCHHHHHHHHCCC--E----EEEECCCC----CCCHHCCCEEEECCCCHHHHHHHHHHH
Q ss_conf 135957999438877123212343398--1----45403677----670011520321577268999999999
Q gi|254780779|r 156 GGLPDLMFVVDTNREKLAIQEARRLRI--P----IVAVVDTN----SNPDLVDYVIPGNDDSSRSIALFCDLV 218 (278)
Q Consensus 156 ~~lP~~iiv~d~~~e~~Av~EA~kl~I--P----vIaivDTn----~dp~~idypIP~NDds~~si~l~~~~i 218 (278)
...|+++|+.+-.--.-+++.++.+|+ | |||+-|+. ..|.+-+.-+|.-.=+..++.+++..+
T Consensus 238 ~~~ptai~~~~D~~A~g~i~~l~~~g~~vP~DisIigfDd~~~~~~~~P~LTtv~~p~~~ig~~A~~~Ll~~i 310 (342)
T PRK09526 238 GPVFTAVLVANDQMALGVLRALHESGLRVPGDISVIGYDDTEDSSYFIPPLTTIKQDFRLLGKEAVDRLLSLS 310 (342)
T ss_pred CCCCCEEEECCHHHHHHHHHHHHHHCCCCCCCEEEEEECCCHHHHHCCCCEEEEEECHHHHHHHHHHHHHHHH
T ss_conf 9999758756779999999999980999999749999898089982489808998199999999999999986
No 190
>COG0809 QueA S-adenosylmethionine:tRNA-ribosyltransferase-isomerase (queuine synthetase) [Translation, ribosomal structure and biogenesis]
Probab=46.75 E-value=12 Score=18.78 Aligned_cols=59 Identities=25% Similarity=0.448 Sum_probs=37.9
Q ss_pred HHHHHHHHHHHCCCCEEEEEECCHHHHHHHHHHHHHCC---------CE-ECCCCC--CCCCCCCHHHHHHHH
Q ss_conf 99999999861078816996078235799999986339---------83-142334--587323426665556
Q gi|254780779|r 53 QKALQVISDTVARGGRILFVATKSQASDCVMEAAKRSA---------QY-CVNSKW--LGGMMTNWKTVSQSI 113 (278)
Q Consensus 53 ~~A~~~i~~i~~~gg~ILFVgTk~~~~~~i~~~A~~~~---------~~-yV~~RW--lGG~LTN~~ti~~si 113 (278)
...+..|...-++||+|.-|||-- -+.++..|...+ .| |--.+| .-+++|||.-=+.++
T Consensus 236 ~eta~~i~~~k~~GgRIiaVGTTs--~R~LEsa~~~~~~~~~sg~T~IFI~PGy~~~~vD~LiTNFHlPkSTL 306 (348)
T COG0809 236 QETADAINAAKARGGRIIAVGTTS--VRTLESAAREAGLKAFSGWTDIFIYPGYRFKVVDALITNFHLPKSTL 306 (348)
T ss_pred HHHHHHHHHHHHCCCEEEEECCHH--HHHHHHHHCCCCCCCCCCCCCEEECCCCCCEECCEEHCCCCCCCCHH
T ss_conf 999999999997398499981615--77788775137767676762178627985267011000476872389
No 191
>cd06324 PBP1_ABC_sugar_binding_like_13 Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems. This group includes the periplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily, which consists of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis.
Probab=46.14 E-value=21 Score=17.10 Aligned_cols=37 Identities=8% Similarity=0.057 Sum_probs=18.0
Q ss_pred HHHHHCC--CCEEEEEECCHHHHHHHHHHHHHCCCEECC
Q ss_conf 9986107--881699607823579999998633983142
Q gi|254780779|r 59 ISDTVAR--GGRILFVATKSQASDCVMEAAKRSAQYCVN 95 (278)
Q Consensus 59 i~~i~~~--gg~ILFVgTk~~~~~~i~~~A~~~~~~yV~ 95 (278)
+...+.+ +-..|++..-......+.+.|...|.|.|.
T Consensus 49 ie~~I~~~~~vd~Iii~p~~~~~~~~l~~A~~agIPVv~ 87 (305)
T cd06324 49 ARTILQRPDKPDALIFTNEKSVAPELLRLAEGAGVKLFL 87 (305)
T ss_pred HHHHHHCCCCCEEEEECCCCCCHHHHHHHHHHCCCEEEE
T ss_conf 999983637970999879620018999999976983999
No 192
>PRK12838 carbamoyl phosphate synthase small subunit; Reviewed
Probab=46.06 E-value=13 Score=18.56 Aligned_cols=30 Identities=17% Similarity=0.383 Sum_probs=17.8
Q ss_pred CCEEEEECCCCC----CHHHHHHHHC--CCEEEEEC
Q ss_conf 957999438877----1232123433--98145403
Q gi|254780779|r 159 PDLMFVVDTNRE----KLAIQEARRL--RIPIVAVV 188 (278)
Q Consensus 159 P~~iiv~d~~~e----~~Av~EA~kl--~IPvIaiv 188 (278)
||.||+.|--.+ ..+|...++| +||+.|||
T Consensus 209 pDGiflSNGPGDP~~~~~~i~~vr~l~~~~PifGIC 244 (356)
T PRK12838 209 PDGIVLSNGPGDPKELQPYLPTIKDLASSYPILGIC 244 (356)
T ss_pred CCEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEC
T ss_conf 748994389989688788999999997498889974
No 193
>PRK07765 para-aminobenzoate synthase component II; Provisional
Probab=45.37 E-value=26 Score=16.55 Aligned_cols=25 Identities=16% Similarity=0.025 Sum_probs=10.1
Q ss_pred EEEEEECCHHHHHHHHHHHHHCCCE
Q ss_conf 1699607823579999998633983
Q gi|254780779|r 68 RILFVATKSQASDCVMEAAKRSAQY 92 (278)
Q Consensus 68 ~ILFVgTk~~~~~~i~~~A~~~~~~ 92 (278)
+||+|-.--++...+...-...|.+
T Consensus 2 rILiIDn~DSFT~ni~~~lr~lg~~ 26 (221)
T PRK07765 2 RILVVDNYDSFVFNLVQYLGQLGVE 26 (221)
T ss_pred EEEEEECCCCHHHHHHHHHHHCCCE
T ss_conf 7999938893399999999877991
No 194
>cd06275 PBP1_PurR Ligand-binding domain of purine repressor, PurR, which functions as the master regulatory protein of de novo purine nucleotide biosynthesis in Escherichia coli. Ligand-binding domain of purine repressor, PurR, which functions as the master regulatory protein of de novo purine nucleotide biosynthesis in Escherichia coli. This dimeric PurR belongs to the LacI-GalR family of transcription regulators and is activated to bind to DNA operator sites by initially binding either of high affinity corepressors, hypoxanthine or guanine. PurR is composed of two functional domains: aan N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the purine transcription repressor undergoes a
Probab=45.35 E-value=26 Score=16.54 Aligned_cols=63 Identities=16% Similarity=0.219 Sum_probs=39.0
Q ss_pred CCCCCEEEEECCCCCCHHHHHHHHCCC--E----EEEECCCCC----CCHHCCCEEEECCCCHHHHHHHHHHH
Q ss_conf 135957999438877123212343398--1----454036776----70011520321577268999999999
Q gi|254780779|r 156 GGLPDLMFVVDTNREKLAIQEARRLRI--P----IVAVVDTNS----NPDLVDYVIPGNDDSSRSIALFCDLV 218 (278)
Q Consensus 156 ~~lP~~iiv~d~~~e~~Av~EA~kl~I--P----vIaivDTn~----dp~~idypIP~NDds~~si~l~~~~i 218 (278)
...|+++|+.+-.--.-+++.+..+|| | |+|+-|+.- .|..-+.-.|...=+..++++++..|
T Consensus 176 ~~~~~aii~~~d~~A~g~~~~l~~~gi~vP~di~vvgfd~~~~~~~~~p~ltti~q~~~~~g~~a~~~L~~~i 248 (269)
T cd06275 176 PKRPTAVFCGNDLMAMGALCAAQEAGLRVPQDLSIIGYDDIELARYFSPPLTTIHQPKDRLGELAVNMLLERI 248 (269)
T ss_pred CCCCCEEECCCHHHHHHHHHHHHHCCCCCCCCCEEEEECCHHHHHHCCCCEEEEECCHHHHHHHHHHHHHHHH
T ss_conf 8996612318749999999999980887899867998778799983389858996199999999999999996
No 195
>cd06293 PBP1_LacI_like_11 Ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. This group includes the ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.
Probab=44.82 E-value=26 Score=16.49 Aligned_cols=29 Identities=17% Similarity=0.258 Sum_probs=23.6
Q ss_pred CCCCCEEEEECCCCCCHHHHHHHHCCCEE
Q ss_conf 13595799943887712321234339814
Q gi|254780779|r 156 GGLPDLMFVVDTNREKLAIQEARRLRIPI 184 (278)
Q Consensus 156 ~~lP~~iiv~d~~~e~~Av~EA~kl~IPv 184 (278)
...|++||+.+-.--.-+++.|..+||-|
T Consensus 175 ~~~~~av~~~nD~~A~g~l~~l~~~gi~v 203 (269)
T cd06293 175 GDPPTAIFAASDEIAIGLLEVLRERGLSI 203 (269)
T ss_pred CCCCCEEEECCHHHHHHHHHHHHHCCCCC
T ss_conf 99985899688599999999999849999
No 196
>cd01574 PBP1_LacI Ligand-binding domain of DNA transcription repressor LacI specific for lactose, a member of the LacI-GalR family of bacterial transcription regulators. Ligand-binding domain of DNA transcription repressor LacI specific for lactose, a member of the LacI-GalR family of bacterial transcription regulators. The ligand-binding domain of LacI is structurally homologous to the periplasmic sugar-binding domain of ABC-type transporters and both domains contain the type I periplasmic binding protein-like fold. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the type I periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA b
Probab=44.52 E-value=27 Score=16.46 Aligned_cols=61 Identities=16% Similarity=0.173 Sum_probs=36.9
Q ss_pred CCCEEEEECCCCCCHHHHHHHHCCCE------EEEECCCC----CCCHHCCCEEEECCCCHHHHHHHHHHH
Q ss_conf 59579994388771232123433981------45403677----670011520321577268999999999
Q gi|254780779|r 158 LPDLMFVVDTNREKLAIQEARRLRIP------IVAVVDTN----SNPDLVDYVIPGNDDSSRSIALFCDLV 218 (278)
Q Consensus 158 lP~~iiv~d~~~e~~Av~EA~kl~IP------vIaivDTn----~dp~~idypIP~NDds~~si~l~~~~i 218 (278)
.|+++|+.+-.-=.-+++.+.+.|+- +||+=|+. ..|..-+.-+|.-.=+..++.+++..+
T Consensus 174 ~~~aii~~~D~~A~g~i~~l~~~g~~iP~di~iigfd~~~~~~~~~p~lTtI~~~~~~~g~~A~~~l~~~i 244 (264)
T cd01574 174 DPTAVFAANDQMALGVLRALHELGLRVPDDVSVVGFDDIPESAYFIPPLTTVRQDFAALGRRAVELLLALL 244 (264)
T ss_pred CCCEEEECCHHHHHHHHHHHHHHCCCCCCCCEEEEECCCHHHHHCCCCEEEEEECHHHHHHHHHHHHHHHH
T ss_conf 99689636429999999999982998898847998688178895089858998199999999999999997
No 197
>PRK11302 DNA-binding transcriptional regulator HexR; Provisional
Probab=44.52 E-value=27 Score=16.46 Aligned_cols=46 Identities=11% Similarity=0.112 Sum_probs=31.9
Q ss_pred CCEEEEECCCCC----CHHHHHHHHCCCEEEEECCCCCCC-HHCCCEEEEC
Q ss_conf 957999438877----123212343398145403677670-0115203215
Q gi|254780779|r 159 PDLMFVVDTNRE----KLAIQEARRLRIPIVAVVDTNSNP-DLVDYVIPGN 204 (278)
Q Consensus 159 P~~iiv~d~~~e----~~Av~EA~kl~IPvIaivDTn~dp-~~idypIP~N 204 (278)
-|++|++.-..+ --+++.|++.|+|||+|.+.+++. ..-||.+...
T Consensus 176 ~Dvvi~iS~sG~t~e~i~~~~~Ak~~ga~vIaIT~~~SpLa~~AD~~L~~~ 226 (284)
T PRK11302 176 GDVVVLISHTGRTKSLVELAQLARENGATVIGITAAGSPLAREATLALTLD 226 (284)
T ss_pred CCEEEEECCCCCCHHHHHHHHHHHHCCCCEEEECCCCCHHHHHCCEEEEEC
T ss_conf 888999737999879999999999879958997799981488689889846
No 198
>cd06286 PBP1_CcpB_like Ligand-binding domain of a novel transcription factor implicated in catabolite repression in Bacillus and Clostridium species. This group includes the ligand-binding domain of a novel transcription factor implicated in catabolite repression in Bacillus and Clostridium species. CcpB is 30% identical in sequence to CcpA which functions as the major transcriptional regulator of carbon catabolite repression/regulation (CCR), a process in which enzymes necessary for the metabolism of alternative sugars are inhibited in the presence of glucose. Like CcpA, the DNA-binding protein CcpB exerts its catabolite-repressing effect by a mechanism dependent on the presence of HPr(Ser-P), the small phosphocarrier proteins of the phosphoenolpyruvate-sugar phosphotransferase system, but with a less significant degree.
Probab=44.44 E-value=27 Score=16.45 Aligned_cols=36 Identities=25% Similarity=0.326 Sum_probs=24.5
Q ss_pred HCCCCCEEEEECCCCCCHHHHHHHHCCCE------EEEECCC
Q ss_conf 11359579994388771232123433981------4540367
Q gi|254780779|r 155 MGGLPDLMFVVDTNREKLAIQEARRLRIP------IVAVVDT 190 (278)
Q Consensus 155 m~~lP~~iiv~d~~~e~~Av~EA~kl~IP------vIaivDT 190 (278)
....|+++|+.+-.--.-+++.++.+|+. ++|+=|+
T Consensus 172 ~~~~p~ai~~~nd~~A~g~~~al~~~g~~vP~di~vigfdd~ 213 (260)
T cd06286 172 MKDRPDAIFTGSDEVAAGIITEAKKQGIRVPEDLAIIGFDNQ 213 (260)
T ss_pred CCCCCCEEEECCHHHHHHHHHHHHHCCCCCCCCEEEEEECCH
T ss_conf 499987367368999999999999729999997699998984
No 199
>TIGR00065 ftsZ cell division protein FtsZ; InterPro: IPR000158 In bacteria, FtsZ , , is an essential cell division protein which appears to be involved in the initiation of this event. It assembles into a cytokinetic ring on the inner surface of the cytoplasmic membrane at the place where division will occur. The ring serves as a scaffold that is disassembled when septation is completed. FtsZ ring formation is initiated at a single site on one side of the bacterium and appears to grow bidirectionally. In Escherichia coli, MinCD IPR005526 from INTERPRO, encoded by the MinB locus, form a complex which appears to block the formation of FtsZ rings at the cell poles, at the ancient mid cell division sites, whilst MinE, encoded at the same locus, specifically prevents the action of MinCD at mid cell. FtsZ is a GTP binding protein PDOC00199 from PROSITEDOC with a GTPase activity. It undergoes GTP-dependent polymerization into filaments (or tubules) that seem to form a cytoskeleton involved in septum synthesis. The structure and the properties of FtsZ clearly provide it with the capacity for the cytoskeletal, perhaps motor role, necessary for "contraction" along the division plane. In addition, however, the FtsZ ring structure provides the framework for the recruitment or assembly of the ten or so membrane and cytoplasmic proteins, uniquely required for cell division in E. coli or Bacillus subtilis, some of which are required for biogenesis of the new hemispherical poles of the two daughter cells. FtsZ can polymerize into various structures, for example a single linear polymer of FtsZ monomers, called a protofilament. Protofilaments can associate laterally to form pairs (sometimes called thick filaments, bundles (ill-defined linear associations of multiple protofilaments or thick filaments, sheets (parallel or anti-parallel two-dimensional associations of thick filaments and tubes (anti-parallel associations of thick filaments in a circular fashion to form a tubular structure). In addition, small circles of FtsZ monomers (a short protofilament bent around to join itself, apparently head to tail) have been observed and termed mini-rings. FtsZ is a protein of about 400 residues which is well conserved across bacterial species and which is also present in the chloroplast of plants as well as in archaebacteria . FtsZ shows structural similarity with eukaryotic tubulins. This similarity is probably both evolutionary and functionally significant.; GO: 0005525 GTP binding, 0005737 cytoplasm.
Probab=43.68 E-value=28 Score=16.38 Aligned_cols=101 Identities=17% Similarity=0.296 Sum_probs=66.8
Q ss_pred HHHHHHHHHHHHHHCCCCEEEEE------ECCHHHHHHHHHHHHHCC--------CEECCCCCCCCCCCCHHHHHHHHHH
Q ss_conf 99999999999861078816996------078235799999986339--------8314233458732342666555677
Q gi|254780779|r 50 PMLQKALQVISDTVARGGRILFV------ATKSQASDCVMEAAKRSA--------QYCVNSKWLGGMMTNWKTVSQSIQK 115 (278)
Q Consensus 50 ~~L~~A~~~i~~i~~~gg~ILFV------gTk~~~~~~i~~~A~~~~--------~~yV~~RWlGG~LTN~~ti~~si~~ 115 (278)
.+-+.+.+-|++. -+|-...|| ||---|...|.+.|+..| .||..++
T Consensus 91 ~AAees~d~i~~~-l~GaDmVFitAGmGGGTGTGAAPVvA~~AK~~GaLTvavVT~PF~~EG------------------ 151 (365)
T TIGR00065 91 KAAEESRDEIREL-LEGADMVFITAGMGGGTGTGAAPVVAKIAKELGALTVAVVTKPFKFEG------------------ 151 (365)
T ss_pred HHHHHHHHHHHHH-CCCCCEEEEEECCCCCCCCCCHHHHHHHHHHCCEEEEEEECCCCCCHH------------------
T ss_conf 9989889999997-038881899725866866663578999997579069998428741015------------------
Q ss_pred HHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCEEEEECC------CCCCHHHHHHHHC-----CCEE
Q ss_conf 8998876301212677467887665567776434433221135957999438------8771232123433-----9814
Q gi|254780779|r 116 LRDLEELLNKENQGFTKKERLNIERKRDKLKRALDGIRDMGGLPDLMFVVDT------NREKLAIQEARRL-----RIPI 184 (278)
Q Consensus 116 l~~l~~~~~~~~~~~tkKe~~~~~r~~~kl~k~lgGi~~m~~lP~~iiv~d~------~~e~~Av~EA~kl-----~IPv 184 (278)
+.|+++--.||..|++-=|-++|++= ..+...+.+|.++ .==|
T Consensus 152 --------------------------~kr~~~A~~Gl~~L~~~~Dt~ivIPNdkLL~v~p~~~p~~~AF~~AD~vL~~aV 205 (365)
T TIGR00065 152 --------------------------KKRRKKAEEGLERLKQAVDTLIVIPNDKLLEVVPNNLPLNDAFKVADDVLRRAV 205 (365)
T ss_pred --------------------------HHHHHHHHHHHHHHHHHCCEEEEECCHHHHHHCCCCCCHHHHHHHHHHHHHHHC
T ss_conf --------------------------899999998789876556847882664688860689888999999999999750
Q ss_pred EEECCCCCCCH
Q ss_conf 54036776700
Q gi|254780779|r 185 VAVVDTNSNPD 195 (278)
Q Consensus 185 IaivDTn~dp~ 195 (278)
=||.|.=.-|.
T Consensus 206 kGI~elIt~Pg 216 (365)
T TIGR00065 206 KGISELITKPG 216 (365)
T ss_pred CCHHHHHHCHH
T ss_conf 26478863200
No 200
>TIGR03573 WbuX N-acetyl sugar amidotransferase. This enzyme has been implicated in the formation of the acetamido moiety (sugar-NC(=NH)CH3) which is found on some exopolysaccharides and is positively charged at neutral pH. The reaction involves ligation of ammonia with a sugar N-acetyl group, displacing water. In E. coli (O145 strain) and Pseudomonas aeruginosa (O12 strain) this gene is known as wbuX and ifnA respectively and likely acts on sialic acid. In Campylobacter jejuni, the gene is known as pseA and acts on pseudaminic acid in the process of flagellin glycosylation. In other Pseudomonas strains and various organisms it is unclear what the identity of the sugar substrate is, and in fact, the phylogenetic tree of this family sports a considerably deep branching suggestive of possible major differences in substrate structure. Nevertheless, the family is characterized by a conserved tetracysteine motif (CxxC.....[GN]xCxxC) possibly indicative of a metal binding site, as well as an
Probab=43.29 E-value=28 Score=16.34 Aligned_cols=129 Identities=16% Similarity=0.079 Sum_probs=72.1
Q ss_pred ECHHHHHHHHHHHHHHHHHHHCCCC----EEEEEECCHHHHHHHHHHHHHCCCEECCCCCCCCCCCCHHHHHHHHHHHHH
Q ss_conf 5389999999999999998610788----169960782357999999863398314233458732342666555677899
Q gi|254780779|r 43 IDLSQTVPMLQKALQVISDTVARGG----RILFVATKSQASDCVMEAAKRSAQYCVNSKWLGGMMTNWKTVSQSIQKLRD 118 (278)
Q Consensus 43 IdL~kT~~~L~~A~~~i~~i~~~gg----~ILFVgTk~~~~~~i~~~A~~~~~~yV~~RWlGG~LTN~~ti~~si~~l~~ 118 (278)
||-.+-...|.+-+.-++ .+++ -|.-|+-.+-.+-.+.....+.|+--+.--|=+|+.|- .-.+.+.++-
T Consensus 36 i~w~~r~~~l~~l~~~~r---~~~~~~YDCiv~vSGGkDS~y~~~~l~~~~gl~pL~vt~d~~~~t~--~g~~Ni~~l~- 109 (343)
T TIGR03573 36 IDWDEREKELEELVDKIK---KKGGGRYDCIIGVSGGKDSTYQAHVLKKKLGLNPLLVTVDPGWNTE--LGVKNLNNLI- 109 (343)
T ss_pred CCHHHHHHHHHHHHHHHH---HCCCCCCCEEEECCCCHHHHHHHHHHHHHHCCCEEEEEECCCCCCH--HHHHHHHHHH-
T ss_conf 986889999999999997---1489988689868877289999999999829925999835987798--9999999999-
Q ss_pred HHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCEEEEECCCCCCHHHHHHHHCCCEEEEECC
Q ss_conf 88763012126774678876655677764344332211359579994388771232123433981454036
Q gi|254780779|r 119 LEELLNKENQGFTKKERLNIERKRDKLKRALDGIRDMGGLPDLMFVVDTNREKLAIQEARRLRIPIVAVVD 189 (278)
Q Consensus 119 l~~~~~~~~~~~tkKe~~~~~r~~~kl~k~lgGi~~m~~lP~~iiv~d~~~e~~Av~EA~kl~IPvIaivD 189 (278)
+ ..+++-.+-.---...|++.| ..+.+++|.-...+..--..+++-|.+.|||.|=--.
T Consensus 110 --~--~lgvD~i~~~~n~~~~k~l~k--------~~~~~~gd~~~~~~~~i~~~~~~iA~k~~IplIi~Ge 168 (343)
T TIGR03573 110 --K--KLGFDLHTITINPETFRKLQR--------AYFKKVGDPEWPQDHAIFASVYQVALKFNIPLIIWGE 168 (343)
T ss_pred --H--HCCCCEEEECCCHHHHHHHHH--------HHHHHCCCHHHHHHHHHHHHHHHHHHHCCCCEEEECC
T ss_conf --8--369985874699999999999--------9998668946999999999999999981999899756
No 201
>cd01744 GATase1_CPSase Small chain of the glutamine-dependent form of carbamoyl phosphate synthase, CPSase II. This group of sequences represents the small chain of the glutamine-dependent form of carbamoyl phosphate synthase, CPSase II. CPSase II catalyzes the production of carbomyl phosphate (CP) from bicarbonate, glutamine and two molecules of MgATP. The reaction is believed to proceed by a series of four biochemical reactions involving a minimum of three discrete highly reactive intermediates. The synthesis of CP is critical for the initiation of two separate biosynthetic pathways. In one CP is coupled to aspartate, its carbon and nitrogen nuclei ultimately incorporated into the aromatic moieties of pyrimidine nucleotides. In the second pathway CP is condensed with ornithine at the start of the urea cycle and is utilized for the detoxification of ammonia and biosynthesis of arginine. CPSases may be encoded by one or by several genes, depending on the species. The E.coli enzyme is
Probab=43.26 E-value=19 Score=17.39 Aligned_cols=31 Identities=19% Similarity=0.342 Sum_probs=21.0
Q ss_pred CCEEEEEC----CCC---CCHHHHHHHHCCCEEEEECC
Q ss_conf 95799943----887---71232123433981454036
Q gi|254780779|r 159 PDLMFVVD----TNR---EKLAIQEARRLRIPIVAVVD 189 (278)
Q Consensus 159 P~~iiv~d----~~~---e~~Av~EA~kl~IPvIaivD 189 (278)
|+.||+.. |.. ..-.+++....+||+.|||=
T Consensus 40 p~giIlS~GPg~p~~~~~~~~~~~~~~~~~iPILGICl 77 (178)
T cd01744 40 PDGIFLSNGPGDPALLDEAIKTVRKLLGKKIPIFGICL 77 (178)
T ss_pred CCEEEECCCCCCHHHHCCHHHHHHHHHHCCCCEEEECH
T ss_conf 99799899999957734449999999746998899812
No 202
>TIGR02482 PFKA_ATP 6-phosphofructokinase; InterPro: IPR012828 6-phosphofructokinase (2.7.1.11 from EC) catalyses the addition of phosphate from ATP to fructose 6-phosphate to give fructose 1,6-bisphosphate. This represents a key control step in glycolysis. This entry contains bacterial ATP-dependent 6-phosphofructokinases, which lack a beta-hairpin loop present in IPR012829 from INTERPRO family members. IPR012829 from INTERPRO contains members that are ATP-dependent as well as members that are pyrophosphate-dependent. IPR011183 from INTERPRO represents the pyrophosphate-dependent phosphofructokinase, diphosphate--fructose-6-phosphate 1-phosphotransferase (2.7.1.90 from EC).; GO: 0003872 6-phosphofructokinase activity, 0005524 ATP binding, 0006002 fructose 6-phosphate metabolic process, 0006096 glycolysis.
Probab=42.94 E-value=28 Score=16.31 Aligned_cols=83 Identities=16% Similarity=0.206 Sum_probs=55.3
Q ss_pred CCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCC-CCEEEEECCCCCCHHHHHHHHCC-CEEEEECCCCCCCHHCCCEEEE
Q ss_conf 212677467887665567776434433221135-95799943887712321234339-8145403677670011520321
Q gi|254780779|r 126 ENQGFTKKERLNIERKRDKLKRALDGIRDMGGL-PDLMFVVDTNREKLAIQEARRLR-IPIVAVVDTNSNPDLVDYVIPG 203 (278)
Q Consensus 126 ~~~~~tkKe~~~~~r~~~kl~k~lgGi~~m~~l-P~~iiv~d~~~e~~Av~EA~kl~-IPvIaivDTn~dp~~idypIP~ 203 (278)
-+..|.+.|.-..- +.+|+++ =|.+||+.=.--..==+-=.+++ ||+||| |--||==||+
T Consensus 70 R~~EFK~~evR~kA------------~~nLK~~GI~~LVViGGDGSy~GA~~L~~~gg~~~iGl------PGTIDNDI~~ 131 (302)
T TIGR02482 70 RCPEFKTEEVREKA------------VENLKKLGIEALVVIGGDGSYTGAQKLYEEGGIPVIGL------PGTIDNDIQG 131 (302)
T ss_pred CCCCCCCHHHHHHH------------HHHHHHHCCCEEEEECCCHHHHHHHHHHHHCCCCEEEE------CCCCCCCCCC
T ss_conf 78545687899999------------99988748866899868440688999997179847874------5850256664
Q ss_pred CCCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf 577268999999999999999999
Q gi|254780779|r 204 NDDSSRSIALFCDLVASAAIDGIA 227 (278)
Q Consensus 204 NDds~~si~l~~~~i~~ai~~g~~ 227 (278)
-|-.+ =.+-.||.+-+||-.=|.
T Consensus 132 TDyTI-GfDTALNTi~~avdKiRD 154 (302)
T TIGR02482 132 TDYTI-GFDTALNTILDAVDKIRD 154 (302)
T ss_pred CCHHH-HHHHHHHHHHHHHHHHHC
T ss_conf 32255-666674379987765421
No 203
>pfam05511 ATP-synt_F6 Mitochondrial ATP synthase coupling factor 6. Coupling factor 6 (F6) is a component of mitochondrial ATP synthase which is required for the interactions of the catalytic and proton-translocating segments.
Probab=42.87 E-value=28 Score=16.30 Aligned_cols=49 Identities=16% Similarity=0.243 Sum_probs=31.0
Q ss_pred HHHHHHHHHH--HCC-CCCCCHHHHHHHHHHHHHHHHHHHHHH--HHCCCCCEE
Q ss_conf 7789988763--012-126774678876655677764344332--211359579
Q gi|254780779|r 114 QKLRDLEELL--NKE-NQGFTKKERLNIERKRDKLKRALDGIR--DMGGLPDLM 162 (278)
Q Consensus 114 ~~l~~l~~~~--~~~-~~~~tkKe~~~~~r~~~kl~k~lgGi~--~m~~lP~~i 162 (278)
.++++|.... .++ .-.-+....-.+..++.||.+.+||=. +|++.|..-
T Consensus 43 dKiREY~~Ksk~~gGk~vD~~Pe~~kel~~el~kL~~~YGgg~~~DmtkFP~Fk 96 (99)
T pfam05511 43 DKIREYRQKSKSSGGKLVDAGPEYEKELKEELEKLAKQYGGGSGDDMTKFPKFK 96 (99)
T ss_pred HHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCHHHCCCCC
T ss_conf 999999986126799857899899999999999999995899878675588888
No 204
>COG4800 Predicted transcriptional regulator with an HTH domain [Transcription]
Probab=42.87 E-value=18 Score=17.55 Aligned_cols=49 Identities=22% Similarity=0.180 Sum_probs=40.8
Q ss_pred HHHHHHHCCCEECC-CCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCCC
Q ss_conf 99998633983142-33458732342666555677899887630121267
Q gi|254780779|r 82 VMEAAKRSAQYCVN-SKWLGGMMTNWKTVSQSIQKLRDLEELLNKENQGF 130 (278)
Q Consensus 82 i~~~A~~~~~~yV~-~RWlGG~LTN~~ti~~si~~l~~l~~~~~~~~~~~ 130 (278)
-.++|++.|.||-+ .+-+.|-=-|++|+.+-++.+..+++..+++|-.+
T Consensus 32 ~~eFak~anIP~StLYKil~G~dpr~~tl~~I~ktir~~ek~en~~fiA~ 81 (170)
T COG4800 32 PSEFAKRANIPLSTLYKILKGSDPRYDTLTRIFKTIRSYEKKENIGFIAL 81 (170)
T ss_pred HHHHHHHCCCCHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHCCCCCEEEE
T ss_conf 89998870998999999981799657789999999998875047784665
No 205
>COG2071 Predicted glutamine amidotransferases [General function prediction only]
Probab=42.63 E-value=12 Score=18.78 Aligned_cols=25 Identities=32% Similarity=0.428 Sum_probs=19.3
Q ss_pred ECCCC---CCHHHHHHHHCCCEEEEECC
Q ss_conf 43887---71232123433981454036
Q gi|254780779|r 165 VDTNR---EKLAIQEARRLRIPIVAVVD 189 (278)
Q Consensus 165 ~d~~~---e~~Av~EA~kl~IPvIaivD 189 (278)
.||.+ |...|++|...|||+.|||-
T Consensus 88 ~~p~RD~~E~aLi~~ALe~~iPILgICR 115 (243)
T COG2071 88 YDPERDAFELALIRAALERGIPILGICR 115 (243)
T ss_pred CCCCCCHHHHHHHHHHHHCCCCEEEECC
T ss_conf 8843007789999999976998899840
No 206
>cd01147 HemV-2 Metal binding protein HemV-2. These proteins are predicted to function as initial receptors in ABC transport of metal ions. They belong to the TroA superfamily of helical backbone metal receptor proteins that share a distinct fold and ligand binding mechanism. A typical TroA protein is comprised of two globular subdomains connected by a single helix and can bind the metal ion in the cleft between these domains. In addition, these proteins sometimes have a low complexity region containing a metal-binding histidine-rich motif (repetitive HDH sequence).
Probab=42.49 E-value=29 Score=16.26 Aligned_cols=54 Identities=11% Similarity=0.101 Sum_probs=22.0
Q ss_pred HHHCCCCEEEEEECCHHHHHHHHHHHHHCCCEECCCCCCCCCCCCHHHHHHHHHHHHH
Q ss_conf 8610788169960782357999999863398314233458732342666555677899
Q gi|254780779|r 61 DTVARGGRILFVATKSQASDCVMEAAKRSAQYCVNSKWLGGMMTNWKTVSQSIQKLRD 118 (278)
Q Consensus 61 ~i~~~gg~ILFVgTk~~~~~~i~~~A~~~~~~yV~~RWlGG~LTN~~ti~~si~~l~~ 118 (278)
.+.+-.-.+.|+..............+..|.|++.-.. + .++..+...+..+-+
T Consensus 69 ~i~al~PDlVi~~~~~~~~~~~~~~~~~~gip~v~~~~-~---~~~~~~~~~i~~lg~ 122 (262)
T cd01147 69 KIAALKPDVVIDVGSDDPTSIADDLQKKTGIPVVVLDG-G---DSLEDTPEQIRLLGK 122 (262)
T ss_pred HHHCCCCCEEEEECCCCCHHHHHHHHHHHCCCEEECCC-C---CCHHHHHHHHHHHHH
T ss_conf 99606998899846777067899999987997897489-9---999999999999999
No 207
>TIGR01533 lipo_e_P4 5'-nucleotidase, lipoprotein e(P4) family; InterPro: IPR006423 This group of sequences represents a set of bacterial lipoproteins belonging to a larger acid phosphatase family, which in turn belongs to the haloacid dehalogenase (HAD) superfamily of aspartate-dependent hydrolases. Members are found on the outer membrane of Gram-negative bacteria and the cytoplasmic membrane of Gram-positive bacteria. Most members have classic lipoprotein signal sequences. A critical role of this 5'-nucleotidase in Haemophilus influenzae is the degradation of external riboside in order to allow transport into the cell. An earlier suggested role in hemin transport is no longer current. This enzyme may also have other physiologically significant roles..
Probab=42.41 E-value=29 Score=16.26 Aligned_cols=113 Identities=18% Similarity=0.243 Sum_probs=66.4
Q ss_pred HHHHHHHHHHCCCCEEEEEECCH-HH-HHHHHHHHHHCCCEECCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCCCC
Q ss_conf 99999998610788169960782-35-79999998633983142334587323426665556778998876301212677
Q gi|254780779|r 54 KALQVISDTVARGGRILFVATKS-QA-SDCVMEAAKRSAQYCVNSKWLGGMMTNWKTVSQSIQKLRDLEELLNKENQGFT 131 (278)
Q Consensus 54 ~A~~~i~~i~~~gg~ILFVgTk~-~~-~~~i~~~A~~~~~~yV~~RWlGG~LTN~~ti~~si~~l~~l~~~~~~~~~~~t 131 (278)
=|+.|+...-.+|..|..|..|. +. .....+--++.|.|++.+-=+ | |.
T Consensus 147 GA~~Fl~ya~~kGv~iFYvsnR~~~~~~~aTl~nLk~~g~P~~~~~hl---l--------------------------ll 197 (295)
T TIGR01533 147 GALEFLNYANSKGVKIFYVSNRSDEKEKEATLENLKKKGFPQADEEHL---L--------------------------LL 197 (295)
T ss_pred CHHHHHHHHHHCCCEEEEEECCCCCHHHHHHHHHHHHCCCCCCCHHHE---E--------------------------EE
T ss_conf 078899999875925899656873012442079998638795550120---0--------------------------00
Q ss_pred HHHHHHHHHHHHHHHH-HHHHHHHHCCCCCEEEEECCCCCCHHHHHHH-HCCCEEEEECCCCCCCHHCCCEEEEC
Q ss_conf 4678876655677764-3443322113595799943887712321234-33981454036776700115203215
Q gi|254780779|r 132 KKERLNIERKRDKLKR-ALDGIRDMGGLPDLMFVVDTNREKLAIQEAR-RLRIPIVAVVDTNSNPDLVDYVIPGN 204 (278)
Q Consensus 132 kKe~~~~~r~~~kl~k-~lgGi~~m~~lP~~iiv~d~~~e~~Av~EA~-kl~IPvIaivDTn~dp~~idypIP~N 204 (278)
++....-.-.+.++++ -+ -=+++|=|.-.|...+.+.. +.+=-==|+|+++.+--+=.|.|==|
T Consensus 198 ~~d~k~KesRR~~v~kq~y---------~iVLl~GDNL~DF~~~~~~~a~e~~~~~Alv~~~~~~FG~~fIiLPN 263 (295)
T TIGR01533 198 KKDKKSKESRRQKVQKQDY---------EIVLLFGDNLLDFSDFFYKKAKESKERQALVLQNQEKFGKKFIILPN 263 (295)
T ss_pred CCCCCCCHHHHHHHHHCCC---------EEEEEECCCHHHHHHHHHHHHHCCCHHHHHHHHCCCCCCCEEEECCC
T ss_conf 3689972578887521571---------38998658722245765445430723467766310024874530678
No 208
>cd05296 GH4_P_beta_glucosidase Glycoside Hydrolases Family 4; Phospho-beta-glucosidase. Some bacteria simultaneously translocate and phosphorylate disaccharides via the phosphoenolpyruvate-dependent phosphotransferase system (PEP-PTS). After translocation, these phospho-disaccharides may be hydrolyzed by the GH4 glycoside hydrolases such as the phospho-beta-glucosidases. Other organisms (such as archaea and Thermotoga maritima ) lack the PEP-PTS system, but have several enzymes normally associated with the PEP-PTS operon. The 6-phospho-beta-glucosidase from Thermotoga maritima hydrolylzes cellobiose 6-phosphate (6P) into glucose-6P and glucose, in an NAD+ and Mn2+ dependent fashion. The Escherichia coli 6-phospho-beta-glucosidase (also called celF) hydrolyzes a variety of phospho-beta-glucosides including cellobiose-6P, salicin-6P, arbutin-6P, and gentobiose-6P. Phospho-beta-glucosidases are part of the NAD(P)-binding Rossmann fold superfamily, which includes a wide variety of protein
Probab=42.23 E-value=29 Score=16.24 Aligned_cols=47 Identities=21% Similarity=0.304 Sum_probs=29.2
Q ss_pred CCEEEEECCCCCCHHHHHH--HHCCCEEEEECCC------------CCCCHHCCCEEEECCC
Q ss_conf 9579994388771232123--4339814540367------------7670011520321577
Q gi|254780779|r 159 PDLMFVVDTNREKLAIQEA--RRLRIPIVAVVDT------------NSNPDLVDYVIPGNDD 206 (278)
Q Consensus 159 P~~iiv~d~~~e~~Av~EA--~kl~IPvIaivDT------------n~dp~~idypIP~NDd 206 (278)
|+|.++==++--.+ |.|| +..++++|||||+ +.+++.|+|-..|=+.
T Consensus 136 P~AwliNytNP~~i-vt~a~~r~~~~k~vGlCh~~~~~~~~la~~Lg~~~~~i~~~~~GlNH 196 (419)
T cd05296 136 PDAWLINFTNPAGI-VTEAVLRHTGDRVIGLCNVPIGLQRRIAELLGVDPEDVFIDYAGLNH 196 (419)
T ss_pred CCCEEEECCCHHHH-HHHHHHHCCCCCEEEECCCHHHHHHHHHHHHCCCHHHEEEEEEEECC
T ss_conf 98389973787999-99999966899889979777989999999958987990789986554
No 209
>TIGR00694 thiM hydroxyethylthiazole kinase; InterPro: IPR000417 Thiamine pyrophosphate (TPP), a required cofactor for many enzymes in the cell, is synthesised de novo in Salmonella typhimurium . Five kinase activities have been implicated in TPP synthesis, which involves joining a 4-methyl-5-(beta-hydroxyethyl)thiazole (THZ) moiety and a 4-amino-5- hydroxymethyl-2-methylpyrimidine (HMP) moiety , . THZ kinase (2.7.1.50 from EC) activity is involved in the salvage synthesis of TH-P from the thiazole: 2-methyl-4-amino-5-hydroxymethylpyrimidine diphosphate + 4-4-methyl-5-(2-phosphonooxyethyl)-thiazole = pyrophosphate + thiamin monophosphate Hydroxyethylthiazole kinase expression is regulated at the mRNA level by intracellular thiamin pyrophosphate .; GO: 0004417 hydroxyethylthiazole kinase activity, 0009228 thiamin biosynthetic process.
Probab=41.80 E-value=18 Score=17.59 Aligned_cols=33 Identities=24% Similarity=0.457 Sum_probs=25.2
Q ss_pred HHHHCCCCCEEEEEC--CCC------CCHHHHHHHHCCCEEE
Q ss_conf 322113595799943--887------7123212343398145
Q gi|254780779|r 152 IRDMGGLPDLMFVVD--TNR------EKLAIQEARRLRIPIV 185 (278)
Q Consensus 152 i~~m~~lP~~iiv~d--~~~------e~~Av~EA~kl~IPvI 185 (278)
+.+|-++|+++ |+| +-. =..|++-|+.+|.|||
T Consensus 43 ~~e~akIa~AL-viNIGTL~~~~~~a~~~A~~~ane~~~Pv~ 83 (282)
T TIGR00694 43 VSELAKIADAL-VINIGTLDEKAIEAMIAAVKSANELGKPVV 83 (282)
T ss_pred HHHHHHHCCCE-EEEEECCCHHHHHHHHHHHHHHHHCCCCEE
T ss_conf 99997520343-765421482899999999997654389568
No 210
>pfam00857 Isochorismatase Isochorismatase family. This family are hydrolase enzymes.
Probab=41.74 E-value=29 Score=16.19 Aligned_cols=37 Identities=14% Similarity=0.126 Sum_probs=28.1
Q ss_pred CCEEEEECCCCCC---HHHHHHHHCCCEEEEECCCCCCCH
Q ss_conf 9579994388771---232123433981454036776700
Q gi|254780779|r 159 PDLMFVVDTNREK---LAIQEARRLRIPIVAVVDTNSNPD 195 (278)
Q Consensus 159 P~~iiv~d~~~e~---~Av~EA~kl~IPvIaivDTn~dp~ 195 (278)
.+-|++.+...+. ..++.|..+|..++-+.|.-++++
T Consensus 110 i~~lii~G~~t~~CV~~Ta~~a~~~g~~v~vv~Da~~~~~ 149 (172)
T pfam00857 110 IDTLVLAGVATDVCVLSTARDAFDRGYEVVVVSDAVAALS 149 (172)
T ss_pred CCEEEEECCCCCCHHHHHHHHHHHCCCEEEEECCCCCCCC
T ss_conf 9999995036486999999999988987999575556899
No 211
>TIGR01082 murC UDP-N-acetylmuramate--alanine ligase; InterPro: IPR005758 The bacterial cell wall provides strength and rigidity to counteract internal osmotic pressure, and protection against the environment. The peptidoglycan layer gives the cell wall its strength, and helps maintain the overall shape of the cell. The basic peptidoglycan structure of both Gram-positive and Gram-negative bacteria is comprised of a sheet of glycan chains connected by short cross-linking polypeptides. Biosynthesis of peptidoglycan is a multi-step (11-12 steps) process comprising three main stages: (1) formation of UDP-N-acetylmuramic acid (UDPMurNAc) from N-acetylglucosamine (GlcNAc). (2) addition of a short polypeptide chain to the UDPMurNAc. (3) addition of a second GlcNAc to the disaccharide-pentapeptide building block and transport of this unit through the cytoplasmic membrane and incorporation into the growing peptidoglycan layer. Stage two involves four key Mur ligase enzymes: MurC (6.3.2.8 from EC) , MurD (6.3.2.9 from EC) , MurE (6.3.2.13 from EC) and MurF (6.3.2.10 from EC) . These four Mur ligases are responsible for the successive additions of L-alanine, D-glutamate, meso-diaminopimelate or L-lysine, and D-alanyl-D-alanine to UDP-N-acetylmuramic acid. All four Mur ligases are topologically similar to one another, even though they display low sequence identity. They are each composed of three domains: an N-terminal Rossmann-fold domain responsible for binding the UDPMurNAc substrate; a central domain (similar to ATP-binding domains of several ATPases and GTPases); and a C-terminal domain (similar to dihydrofolate reductase fold) that appears to be associated with binding the incoming amino acid. The conserved sequence motifs found in the four Mur enzymes also map to other members of the Mur ligase family, including folylpolyglutamate synthetase, cyanophycin synthetase and the capB enzyme from Bacillales . This entry represents UDP-N-acetylmuramate-alanine ligase (MurC). MurC is an essential, cytoplasmic peptidoglycan biosynthetic enzyme, catalyzes the ATP-dependent ligation of L-alanine (Ala) and UDP-N-acetylmuramic acid (UNAM) to form UDP-N-acetylmuramyl-L-alanine (UNAM-Ala). The enzyme is a nonribosomal peptide ligase which utilises ATP to form an amide bond between L-alanine and UNAM.1 Mechanistic studies on the Escherichia coli MurC enzyme using oxygen isotope analyses demonstrated that the enzyme-catalyzed reaction proceeds through an acyl phosphate UNAM intermediate prior to L-alanine addition.; GO: 0005524 ATP binding, 0008763 UDP-N-acetylmuramate-L-alanine ligase activity, 0008360 regulation of cell shape, 0009252 peptidoglycan biosynthetic process, 0009273 peptidoglycan-based cell wall biogenesis, 0051301 cell division, 0005737 cytoplasm.
Probab=41.47 E-value=26 Score=16.59 Aligned_cols=27 Identities=26% Similarity=0.477 Sum_probs=12.9
Q ss_pred CCEEEEE-C-CCCCCHHHHHHHHCCCEEE
Q ss_conf 9579994-3-8877123212343398145
Q gi|254780779|r 159 PDLMFVV-D-TNREKLAIQEARRLRIPIV 185 (278)
Q Consensus 159 P~~iiv~-d-~~~e~~Av~EA~kl~IPvI 185 (278)
||+|++. . .+.+..=|.||+..+|||+
T Consensus 66 ~~vVv~S~~Ai~~~NpEi~~A~~~~IPv~ 94 (491)
T TIGR01082 66 ADVVVVSAAAIKEDNPEIVEAKERGIPVI 94 (491)
T ss_pred CCEEEEEEECCCCCCHHHHHHHHCCCCEE
T ss_conf 43799864033788888999996488813
No 212
>cd00984 DnaB_C DnaB helicase C terminal domain. The hexameric helicase DnaB unwinds the DNA duplex at the chromosome replication fork. Although the mechanism by which DnaB both couples ATP hydrolysis to translocation along DNA and denatures the duplex is unknown, a change in the quaternary structure of the protein involving dimerization of the N-terminal domain has been observed and may occur during the enzymatic cycle. This C-terminal domain contains an ATP-binding site and is therefore probably the site of ATP hydrolysis.
Probab=41.44 E-value=30 Score=16.16 Aligned_cols=142 Identities=18% Similarity=0.368 Sum_probs=66.4
Q ss_pred CCCCCCCCEEEECHHHHHHHHHHHHHHHHHHHCCCCEEEEEECCHHHHHHHHHH-HHHCCCEECCCCCCCCCCCC--HHH
Q ss_conf 102001881675389999999999999998610788169960782357999999-86339831423345873234--266
Q gi|254780779|r 32 YIFCERNNTHIIDLSQTVPMLQKALQVISDTVARGGRILFVATKSQASDCVMEA-AKRSAQYCVNSKWLGGMMTN--WKT 108 (278)
Q Consensus 32 yI~g~rngihIIdL~kT~~~L~~A~~~i~~i~~~gg~ILFVgTk~~~~~~i~~~-A~~~~~~yV~~RWlGG~LTN--~~t 108 (278)
++++-+-| .-||...+..|+++.. .+|.+|+|+.---...++...+ +..++.++-. ...|.++. |..
T Consensus 16 ~vi~a~~g-----~GKS~~~~~la~~~a~---~~g~~V~~~SlEm~~~~~~~R~~s~~~~i~~~~--i~~~~~~~~~~~~ 85 (242)
T cd00984 16 IIIAARPS-----MGKTAFALNIAENIAK---KQGKPVLFFSLEMSKEQLLQRLLASESGISLSK--LRTGSLSDEDWER 85 (242)
T ss_pred EEEEECCC-----CCHHHHHHHHHHHHHH---HCCCCEEEEECCCCHHHHHHHHHHHHHCCCHHH--HHCCCCCHHHHHH
T ss_conf 99996899-----9999999999999999---779959999333538899999999982977455--3026522799999
Q ss_pred HHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCEEEEEC------CC--C--CCHHHHH--
Q ss_conf 6555677899887630121267746788766556777643443322113595799943------88--7--7123212--
Q gi|254780779|r 109 VSQSIQKLRDLEELLNKENQGFTKKERLNIERKRDKLKRALDGIRDMGGLPDLMFVVD------TN--R--EKLAIQE-- 176 (278)
Q Consensus 109 i~~si~~l~~l~~~~~~~~~~~tkKe~~~~~r~~~kl~k~lgGi~~m~~lP~~iiv~d------~~--~--e~~Av~E-- 176 (278)
+.+.+..+.+..-.. ......|--+ +.....++.+. .-|++||| | +. . +..++.+
T Consensus 86 ~~~~~~~~~~~~l~i-~d~~~~t~~~---i~~~ir~~~~~--------~~~~~vvv-Dylql~~~~~~~~~~~~~i~~i~ 152 (242)
T cd00984 86 LAEAIGELKELPIYI-DDSSSLTVSD---IRSRARRLKKE--------HGLGLIVI-DYLQLMSGSKKKGNRQQEVAEIS 152 (242)
T ss_pred HHHHHHHHCCCCEEE-ECCCCCCHHH---HHHHHHHHHHH--------CCCCEEEE-EHHHHCCCCCCCCCHHHHHHHHH
T ss_conf 999999861698899-6699999999---99999999883--------69989998-26985467776657999999999
Q ss_pred ------HHHCCCEEEEECCCCCCCHH
Q ss_conf ------34339814540367767001
Q gi|254780779|r 177 ------ARRLRIPIVAVVDTNSNPDL 196 (278)
Q Consensus 177 ------A~kl~IPvIaivDTn~dp~~ 196 (278)
|..++||||+++-.|-.+..
T Consensus 153 ~~Lk~lA~e~~v~Vi~~sQlnR~~~~ 178 (242)
T cd00984 153 RSLKLLAKELNVPVIALSQLSRGVES 178 (242)
T ss_pred HHHHHHHHHHCCEEEEEECCCCCCCC
T ss_conf 99999999979939998467866122
No 213
>KOG2544 consensus
Probab=41.33 E-value=30 Score=16.15 Aligned_cols=108 Identities=19% Similarity=0.300 Sum_probs=69.8
Q ss_pred CCCCCCCCCCCCHHHHHHHH----------------------HHHHHHHHHH-H-------CCCCCCCHHHHHHHHHHHH
Q ss_conf 42334587323426665556----------------------7789988763-0-------1212677467887665567
Q gi|254780779|r 94 VNSKWLGGMMTNWKTVSQSI----------------------QKLRDLEELL-N-------KENQGFTKKERLNIERKRD 143 (278)
Q Consensus 94 V~~RWlGG~LTN~~ti~~si----------------------~~l~~l~~~~-~-------~~~~~~tkKe~~~~~r~~~ 143 (278)
|-.|.++-.=|||.++++.. ..+.+...+. + |+...-+--.++.-.-|..
T Consensus 415 v~~R~l~~gd~~~~~~n~t~vMgIlN~TPDSFSDGGkf~~ids~l~~v~smi~dga~IiDiGgqSTrP~a~~iS~eEEir 494 (711)
T KOG2544 415 VIQRVLPIGDTLWDFSNKTYVMGILNLTPDSFSDGGKFQSIDSALSRVRSMISDGADIIDIGGQSTRPMASRISSEEEIR 494 (711)
T ss_pred CEEEEEECCCHHHHHCCCCEEEEEEECCCCCCCCCCCCCCHHHHHHHHHHHHCCCCEEEEECCCCCCCCCCCCCHHHHHH
T ss_conf 22577523650444157626999970587654777710007779999999860776289605755788866455388998
Q ss_pred HHHHHHHHHHHHCCCCCEEEEECCCCCCHHHHHHHHCCCEEE-----EECCCCCCCH----HCCCEEE
Q ss_conf 776434433221135957999438877123212343398145-----4036776700----1152032
Q gi|254780779|r 144 KLKRALDGIRDMGGLPDLMFVVDTNREKLAIQEARRLRIPIV-----AVVDTNSNPD----LVDYVIP 202 (278)
Q Consensus 144 kl~k~lgGi~~m~~lP~~iiv~d~~~e~~Av~EA~kl~IPvI-----aivDTn~dp~----~idypIP 202 (278)
|+--.+.-++.|..+|..++-+|+-+... -+||.+.|.-+| |+.|.|.-+- .|-|.|-
T Consensus 495 R~iP~ikavR~~~e~~~v~iSiDTy~S~V-AkeAI~~GadIiNDvsgG~~D~nM~~vvAe~~vpy~im 561 (711)
T KOG2544 495 RLIPVIKAVRGMTEMPQVLISIDTYNSEV-AKEAIKNGADIINDVSGGLLDENMHKVVAESEVPYMIM 561 (711)
T ss_pred HHHHHHHHHHCCCCCCCEEEEEECHHHHH-HHHHHHCCCHHEECCCCCCCCHHHHHHHHHCCCCEEEE
T ss_conf 77589999733454674468874144688-99998643201002546667613677776248878987
No 214
>PRK08006 replicative DNA helicase; Provisional
Probab=40.24 E-value=31 Score=16.04 Aligned_cols=147 Identities=19% Similarity=0.288 Sum_probs=71.5
Q ss_pred HHHHHHHHHHHHHHHHHHHCCCCEEEEEECCHHHHHHHHHH-HHHCCCEECCCCCCCCCCCCH--HHHHHHHHHHHHHHH
Q ss_conf 89999999999999998610788169960782357999999-863398314233458732342--666555677899887
Q gi|254780779|r 45 LSQTVPMLQKALQVISDTVARGGRILFVATKSQASDCVMEA-AKRSAQYCVNSKWLGGMMTNW--KTVSQSIQKLRDLEE 121 (278)
Q Consensus 45 L~kT~~~L~~A~~~i~~i~~~gg~ILFVgTk~~~~~~i~~~-A~~~~~~yV~~RWlGG~LTN~--~ti~~si~~l~~l~~ 121 (278)
.-||...|.-|.+... .+|+.++|.+---...+++... |..++.++ ++..-|.|+.- ..+...+..+ ++.
T Consensus 235 mGKTalalnia~~~a~---~~~~~V~~fSlEMs~~ql~~Rlla~~s~v~~--~~i~~g~l~~~e~~~l~~~~~~~--~~~ 307 (471)
T PRK08006 235 MGKTTFAMNLCENAAM---LQDKPVLIFSLEMPGEQIMMRMLASLSRVDQ--TRIRTGQLDDEDWARISGTMGIL--LEK 307 (471)
T ss_pred CCHHHHHHHHHHHHHH---HCCCCEEEEECCCCHHHHHHHHHHHHCCCCC--CCCCCCCCCHHHHHHHHHHHHHH--HHC
T ss_conf 8769999999999998---6699579981679999999999997447775--54536887999999999999999--751
Q ss_pred H--HHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCEEEEEC-------CC-C--CCHHHHH--------HHHCC
Q ss_conf 6--30121267746788766556777643443322113595799943-------88-7--7123212--------34339
Q gi|254780779|r 122 L--LNKENQGFTKKERLNIERKRDKLKRALDGIRDMGGLPDLMFVVD-------TN-R--EKLAIQE--------ARRLR 181 (278)
Q Consensus 122 ~--~~~~~~~~tkKe~~~~~r~~~kl~k~lgGi~~m~~lP~~iiv~d-------~~-~--e~~Av~E--------A~kl~ 181 (278)
. .-.....+|-- .+.-...++.+..+|+ ++| |+| +. . ....|.| |+.|+
T Consensus 308 ~~l~idd~~~~t~~---~i~a~~r~~~~~~~gl-------~lv-vIDYLqL~~~~~~~~~r~~ei~~isr~lK~lAkel~ 376 (471)
T PRK08006 308 RNMYIDDSSGLTPT---EVRSRARRIFREHGGL-------SLI-MIDYLQLMRVPSLSDNRTLEIAEISRSLKALAKELQ 376 (471)
T ss_pred CCEEEECCCCCCHH---HHHHHHHHHHHHCCCC-------CEE-EEEHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHHC
T ss_conf 88577368999899---9999999999864898-------689-963886616787441066899999999999999969
Q ss_pred CEEEEECCCCCCCHHCCCEEEECCCCHH
Q ss_conf 8145403677670011520321577268
Q gi|254780779|r 182 IPIVAVVDTNSNPDLVDYVIPGNDDSSR 209 (278)
Q Consensus 182 IPvIaivDTn~dp~~idypIP~NDds~~ 209 (278)
||||+++.=|-..+.=+=.-|.--|-.-
T Consensus 377 ipVi~LsQLnR~~e~R~dkrP~lsDLRe 404 (471)
T PRK08006 377 VPVVALSQLNRSLEQRADKRPVNSDLRE 404 (471)
T ss_pred CCEEEECCCCCCCCCCCCCCCCCCCCCC
T ss_conf 9689970168310016999987340224
No 215
>KOG3818 consensus
Probab=40.10 E-value=31 Score=16.08 Aligned_cols=133 Identities=18% Similarity=0.236 Sum_probs=69.3
Q ss_pred EEEECHHHHHHHHHHHHHHHHHHHCCCCEEEEEECCHHHHHHH-------HHHHHHCCCEECCCCCCCCC-CCCHHHHHH
Q ss_conf 1675389999999999999998610788169960782357999-------99986339831423345873-234266655
Q gi|254780779|r 40 THIIDLSQTVPMLQKALQVISDTVARGGRILFVATKSQASDCV-------MEAAKRSAQYCVNSKWLGGM-MTNWKTVSQ 111 (278)
Q Consensus 40 ihIIdL~kT~~~L~~A~~~i~~i~~~gg~ILFVgTk~~~~~~i-------~~~A~~~~~~yV~~RWlGG~-LTN~~ti~~ 111 (278)
.|+=|+.-++..=-.-+.|=..+.-.|--||+=|+-...--.| .+-++.+..+|=|.-|+||- -+++ +
T Consensus 193 ~~lEDpsgsVqlDlsqa~fh~glf~egC~VL~EG~f~~~vf~V~~lg~PP~E~~~~tr~~~gN~n~~Gg~~~~~~----k 268 (525)
T KOG3818 193 FHLEDPSGSVQLDLSQAKFHHGLFCEGCFVLVEGTFESGVFHVNELGFPPVERREVTRKELGNLNWLGGDSKIAF----K 268 (525)
T ss_pred EEEECCCCCEEEEECCCCCCCCEECCCEEEEEEEEEECCEEEEEECCCCCCCCCHHHHHHHCCCCCCCCCCHHHH----H
T ss_conf 787479873799621343356241065189995255135688730268988700548987345752378604556----7
Q ss_pred HHHHHHHHHHH-HHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCEEEEECC-------CCCCHHHHHHHH
Q ss_conf 56778998876-301212677467887665567776434433221135957999438-------877123212343
Q gi|254780779|r 112 SIQKLRDLEEL-LNKENQGFTKKERLNIERKRDKLKRALDGIRDMGGLPDLMFVVDT-------NREKLAIQEARR 179 (278)
Q Consensus 112 si~~l~~l~~~-~~~~~~~~tkKe~~~~~r~~~kl~k~lgGi~~m~~lP~~iiv~d~-------~~e~~Av~EA~k 179 (278)
.+.+|+++++. .+..|--+ .--.+...+-+.+|.+-|.|..+ -.|-++|..+. +....+.+++.+
T Consensus 269 ~sA~L~~lE~~~~d~~fVfL-SdV~LD~~~vm~aL~kifqgy~~--~pP~~iIlcG~FtS~p~~~~s~~~~k~~f~ 341 (525)
T KOG3818 269 CSARLRSLEAENTDTSFVFL-SDVFLDDKKVMEALRKIFQGYKD--APPTAIILCGSFTSSPRQTSSSDQLKDGFR 341 (525)
T ss_pred HHHHHHHHHHHCCCCEEEEE-EHHCCCCHHHHHHHHHHHHHCCC--CCCEEEEEECCCCCCCCCCCHHHHHHHHHH
T ss_conf 88999999974747449997-51103659999999999831568--998389995465566556536899998899
No 216
>cd00904 Ferritin Ferritin iron storage proteins. Ferritins are the primary iron storage proteins of most living organisms and members of a broad superfamily of ferritin-like diiron-carboxylate proteins. The iron-free (apoferritin) ferritin molecule is a protein shell composed of 24 protein chains arranged in 432 symmetry. Iron storage involves the uptake of iron (II) at the protein shell, its oxidation by molecular oxygen at the dinuclear ferroxidase centers, and the movement of iron (III) into the cavity for deposition as ferrihydrite; the protein shell can hold up to 4500 iron atoms. In vertebrates, two types of chains (subunits) have been characterized, H or M (fast) and L (slow), which differ in rates of iron uptake and mineralization. Bacterial non-heme ferritins are composed only of H chains. Fe(II) oxidation in the H/M subunits take place initially at the ferroxidase center, a carboxylate-bridged diiron center, located within the subunit four-helix bundle. In a complementary rol
Probab=40.07 E-value=31 Score=16.02 Aligned_cols=115 Identities=14% Similarity=0.152 Sum_probs=64.5
Q ss_pred CEEEECHHHHHHHHHHHHHHHHHHHCCCCEEEEEECCHHH----HHHHHHHHHHCCCEECCCCCCCCCCCCHHHHHHHHH
Q ss_conf 8167538999999999999999861078816996078235----799999986339831423345873234266655567
Q gi|254780779|r 39 NTHIIDLSQTVPMLQKALQVISDTVARGGRILFVATKSQA----SDCVMEAAKRSAQYCVNSKWLGGMMTNWKTVSQSIQ 114 (278)
Q Consensus 39 gihIIdL~kT~~~L~~A~~~i~~i~~~gg~ILFVgTk~~~----~~~i~~~A~~~~~~yV~~RWlGG~LTN~~ti~~si~ 114 (278)
|..=+=..+..+....|.+|+..+...||++.|-...+.. ..+..- +-..|.+.+++.++|.
T Consensus 38 Gfa~ff~~~a~EE~~Ha~~l~~Yl~~RGg~v~~~~i~~p~~~~~~s~~~~--------------~~~al~~Ek~vt~~i~ 103 (160)
T cd00904 38 GVAHFFKEQAQEEREHAEKFYKYQNERGGRVELQDIEKPPSDEWGGTLDA--------------MEAALKLEKFVNQALL 103 (160)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHCCCEEECCCCCCCCCCCCCCHHHH--------------HHHHHHHHHHHHHHHH
T ss_conf 69999999999999999999999997799233488678888777988999--------------9999999999999999
Q ss_pred HHHHHHHH-HHCCCCCCCHHHHHH-HHHHHHHHHHHHHHHHHHCCCC--CEEEEECC
Q ss_conf 78998876-301212677467887-6655677764344332211359--57999438
Q gi|254780779|r 115 KLRDLEEL-LNKENQGFTKKERLN-IERKRDKLKRALDGIRDMGGLP--DLMFVVDT 167 (278)
Q Consensus 115 ~l~~l~~~-~~~~~~~~tkKe~~~-~~r~~~kl~k~lgGi~~m~~lP--~~iiv~d~ 167 (278)
.|.++-.. .+.....|-.-+.+. -..+...+...+.-++.+..-+ -.++++|.
T Consensus 104 ~L~~~A~~~~D~~~~~fLe~~Fv~eQ~ee~~~~~~~l~~l~~~g~~~~glg~ylfDk 160 (160)
T cd00904 104 DLHELASEEKDPHLCDFLESHFLDEQVKEIKQVGDILTNLERLNGQQAGSGEYLFDR 160 (160)
T ss_pred HHHHHHHHCCCHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHCCCCCCCEEEEEECC
T ss_conf 999999886997599887165379999999999999999998089998703410086
No 217
>pfam06636 DUF1157 Protein of unknown function (DUF1157). This family consists of several uncharacterized proteins from Melanoplus sanguinipes entomopoxvirus (MsEPV). The function of this family is unknown.
Probab=40.00 E-value=31 Score=16.02 Aligned_cols=65 Identities=17% Similarity=0.332 Sum_probs=49.7
Q ss_pred HHHHHHHHHHHHHHHHCCCCCEEEEECCCCCCHHHHH--HHHCCCEEEEECCCCCCCHHCCCEEEEC
Q ss_conf 5567776434433221135957999438877123212--3433981454036776700115203215
Q gi|254780779|r 140 RKRDKLKRALDGIRDMGGLPDLMFVVDTNREKLAIQE--ARRLRIPIVAVVDTNSNPDLVDYVIPGN 204 (278)
Q Consensus 140 r~~~kl~k~lgGi~~m~~lP~~iiv~d~~~e~~Av~E--A~kl~IPvIaivDTn~dp~~idypIP~N 204 (278)
+|-.-+.++|.|++..+-.|..||.-+-..+.....+ -..|.-|+=-+..-..++=.=-|.|-+|
T Consensus 59 ~~n~i~~r~~dg~q~~k~iPtfvFl~N~~~~evi~yggfn~~l~fP~NNi~N~s~~WIygGwfi~~n 125 (370)
T pfam06636 59 YENVIIDRFFDGLQYLKNIPTFVFLNNFKTNEVIAYGGFNKSLTFPINNIINKSINWIYGGWFIVAN 125 (370)
T ss_pred HHHHHHHHHHHHHHHHCCCCEEEEEECCCHHHHHHCCCCHHCCCCCCCCCCCCCCCEEECCEEEEEC
T ss_conf 2324677777666663168639986012334443245520102476532235655546633799971
No 218
>cd06337 PBP1_ABC_ligand_binding_like_4 Type I periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type active transport systems that are predicted to be involved in transport of amino acids, peptides, or inorganic ions. This subgroup includes the type I periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type active transport systems that are predicted to be involved in transport of amino acids, peptides, or inorganic ions. Members of this group are sequence-similar to members of the family of ABC-type hydrophobic amino acid transporters, such as leucine-isoleucine-valine-binding protein (LIVBP); however their ligand specificity has not been determined experimentally.
Probab=39.93 E-value=31 Score=16.01 Aligned_cols=41 Identities=15% Similarity=0.080 Sum_probs=28.9
Q ss_pred CCCCEEEEECCCCCCHH-HHHHHHCCC--EEEEECCCCCCCHHC
Q ss_conf 35957999438877123-212343398--145403677670011
Q gi|254780779|r 157 GLPDLMFVVDTNREKLA-IQEARRLRI--PIVAVVDTNSNPDLV 197 (278)
Q Consensus 157 ~lP~~iiv~d~~~e~~A-v~EA~kl~I--PvIaivDTn~dp~~i 197 (278)
.-||+||+.....+..+ ++.++.+|+ |++++.+.-.+|..+
T Consensus 202 ~~pD~V~~~~~~~d~~~~~kQ~~~~G~~~~i~~~~~~~~~~~~~ 245 (357)
T cd06337 202 EGVDIVTGFAIPPDFATFWRQAAQAGFKPKIVTIAKALLFPEDV 245 (357)
T ss_pred CCCCEEEECCCCHHHHHHHHHHHHCCCCCCEEEECCCCCCHHHH
T ss_conf 59999998787468999999999759998758861454788899
No 219
>TIGR00597 rad10 DNA repair protein rad10; InterPro: IPR004579 All proteins in this family for which functions are known are components in a multiprotein endonuclease complex (usually made up of Rad1 and Rad10 homologs). This complex is used primarily for nucleotide excision repair but also for some aspects of recombination repair. In yeast, Rad10 works as a heterodimer with Rad1, and is involved in nucleotide excision repair of DNA damaged with UV light, bulky adducts or cross-linking agents. The complex forms an endonuclease which specifically degrades single-stranded DNA.; GO: 0003684 damaged DNA binding, 0004519 endonuclease activity, 0006281 DNA repair, 0005634 nucleus.
Probab=39.41 E-value=16 Score=17.97 Aligned_cols=36 Identities=31% Similarity=0.479 Sum_probs=27.9
Q ss_pred HHHHHHHHHHHHH-HHHHCCCCCEEEEECCCCCCHHHHHHHHCCC
Q ss_conf 6556777643443-3221135957999438877123212343398
Q gi|254780779|r 139 ERKRDKLKRALDG-IRDMGGLPDLMFVVDTNREKLAIQEARRLRI 182 (278)
Q Consensus 139 ~r~~~kl~k~lgG-i~~m~~lP~~iiv~d~~~e~~Av~EA~kl~I 182 (278)
.+.+++|-|++.- | ++|++|.++...+++|=.|+.|
T Consensus 61 ~~R~q~Lgkn~nlRi--------Ll~~VDv~n~~~~l~el~K~ci 97 (117)
T TIGR00597 61 SRRLQKLGKNFNLRI--------LLVLVDVKNSQDALKELTKLCI 97 (117)
T ss_pred HHHHHHCCCCCCCEE--------EEEEEECCCHHHHHHHHHHHHH
T ss_conf 763003022100447--------7889605885888999998877
No 220
>PRK12564 carbamoyl phosphate synthase small subunit; Reviewed
Probab=39.33 E-value=19 Score=17.41 Aligned_cols=30 Identities=27% Similarity=0.472 Sum_probs=15.5
Q ss_pred CCEEEEEC----CCCCCHHHHHHHH---CCCEEEEEC
Q ss_conf 95799943----8877123212343---398145403
Q gi|254780779|r 159 PDLMFVVD----TNREKLAIQEARR---LRIPIVAVV 188 (278)
Q Consensus 159 P~~iiv~d----~~~e~~Av~EA~k---l~IPvIaiv 188 (278)
||.||+.+ |..-..+|...++ -+||+.|||
T Consensus 213 pDGIflSNGPGDP~~~~~~i~~ik~li~~~~PifGIC 249 (355)
T PRK12564 213 PDGVFLSNGPGDPAALDYAIEMIKELLEGKIPIFGIC 249 (355)
T ss_pred CCEEEECCCCCCHHHHHHHHHHHHHHHCCCCCEEEEC
T ss_conf 8889967999996887999999999852698789988
No 221
>pfam03796 DnaB_C DnaB-like helicase C terminal domain. The hexameric helicase DnaB unwinds the DNA duplex at the Escherichia coli chromosome replication fork. Although the mechanism by which DnaB both couples ATP hydrolysis to translocation along DNA and denatures the duplex is unknown, a change in the quaternary structure of the protein involving dimerization of the N-terminal domain has been observed and may occur during the enzymatic cycle. This C-terminal domain contains an ATP-binding site and is therefore probably the site of ATP hydrolysis.
Probab=39.19 E-value=32 Score=15.94 Aligned_cols=55 Identities=16% Similarity=0.147 Sum_probs=34.8
Q ss_pred CCCCCCCCEEEECHHHHHHHHHHHHHHHHHHHCCCCEEEEEECCHHHHHHHHH-HHHHCCCEEC
Q ss_conf 10200188167538999999999999999861078816996078235799999-9863398314
Q gi|254780779|r 32 YIFCERNNTHIIDLSQTVPMLQKALQVISDTVARGGRILFVATKSQASDCVME-AAKRSAQYCV 94 (278)
Q Consensus 32 yI~g~rngihIIdL~kT~~~L~~A~~~i~~i~~~gg~ILFVgTk~~~~~~i~~-~A~~~~~~yV 94 (278)
++++-+-| .-||...+..|+++.. ..|..|||+..--...++... .|..++.++-
T Consensus 22 ~vi~g~pg-----~GKS~~~~~~a~~~a~---~~g~~Vl~~slEm~~~~~~~R~~a~~~~v~~~ 77 (186)
T pfam03796 22 IIIAARPS-----MGKTAFALNIARNAAL---KQDKPVLFFSLEMSAEQLAERLLSSESRISSS 77 (186)
T ss_pred EEEEECCC-----CCHHHHHHHHHHHHHH---HCCCCEEEECCCCCHHHHHHHHHHHHHCCCHH
T ss_conf 99996799-----9879999999999999---70996687547552999999999986267655
No 222
>cd01745 GATase1_2 Subgroup of proteins having the Type 1 glutamine amidotransferase (GATase1) domain. This group contains a subgroup of proteins having the Type 1 glutamine amidotransferase (GATase1) domain. GATase activity catalyses the transfer of ammonia from the amide side chain of glutamine to an acceptor substrate. Glutamine amidotransferases (GATase) includes the triad family of amidotransferases which have a conserved Cys-His-Glu catalytic triad in the glutaminase active site. In this subgroup this triad is conserved. GATase activity can be found in a range of biosynthetic enzymes, including: glutamine amidotransferase, formylglycinamide ribonucleotide, GMP synthetase , anthranilate synthase component II, glutamine-dependent carbamoyl phosphate synthase, cytidine triphosphate synthetase, gamma-glutamyl hydrolase, imidazole glycerol phosphate synthase and, cobyric acid synthase. Glutamine amidotransferase (GATase) domains can occur either as single polypeptides, as in glutamine
Probab=39.04 E-value=11 Score=18.88 Aligned_cols=20 Identities=20% Similarity=0.258 Sum_probs=14.1
Q ss_pred CCHHHHHHHHCCCEEEEECC
Q ss_conf 71232123433981454036
Q gi|254780779|r 170 EKLAIQEARRLRIPIVAVVD 189 (278)
Q Consensus 170 e~~Av~EA~kl~IPvIaivD 189 (278)
|...+++|.+.+||+.|||-
T Consensus 89 E~~l~~~a~~~~~PilGICR 108 (189)
T cd01745 89 ELALLRAALERGKPILGICR 108 (189)
T ss_pred HHHHHHHHHHHCCCCEEEHH
T ss_conf 99999999980987603505
No 223
>TIGR00979 fumC_II fumarate hydratase, class II; InterPro: IPR005677 Fumarase C catalyzes the stereospecific interconversion of fumarate to L-malate as part of the metabolic citric acid or Kreb's cycle. The recent three-dimensional structure of fumarase C from Escherichia coli has identified a binding site for anions which is generated by side chains from three of the four subunits within the tetramer. These same side chains are found in the three most highly conserved regions within the class II fumarate hydratase family. Putative fumarases from several species (Mycobacterium tuberculosis, Streptomyces coelicolor, Pseudomonas aeruginosa) branch deeply, although within the same branch of a phylogenetic tree rooted by aspartate ammonia-lyase sequences.; GO: 0004333 fumarate hydratase activity, 0006106 fumarate metabolic process, 0045239 tricarboxylic acid cycle enzyme complex.
Probab=38.99 E-value=32 Score=15.92 Aligned_cols=168 Identities=17% Similarity=0.164 Sum_probs=90.9
Q ss_pred EEECHHHHHHHHHHHHHHHHHHHCCCCEEEEEECCH----H-HHHHHHHHHHHCCCEECCCCCCCCCCCCHHHHHHHHHH
Q ss_conf 675389999999999999998610788169960782----3-57999999863398314233458732342666555677
Q gi|254780779|r 41 HIIDLSQTVPMLQKALQVISDTVARGGRILFVATKS----Q-ASDCVMEAAKRSAQYCVNSKWLGGMMTNWKTVSQSIQK 115 (278)
Q Consensus 41 hIIdL~kT~~~L~~A~~~i~~i~~~gg~ILFVgTk~----~-~~~~i~~~A~~~~~~yV~~RWlGG~LTN~~ti~~si~~ 115 (278)
|+--|+..++.+..++.-+..+ +.||+ =|||-- + ...++++.++.|+.||++--=-=--|++..-|-..-.-
T Consensus 202 Y~~qL~~~l~~i~~sL~~l~~L-A~GGT--AVGTGLN~~~~f~~Kv~~~~~~~T~~~F~~ApNKF~ALa~HDAiv~ahGa 278 (459)
T TIGR00979 202 YVAQLEHGLERIEESLPHLYEL-ALGGT--AVGTGLNTHPGFDEKVAEEIAKFTGLPFVTAPNKFEALAAHDAIVEAHGA 278 (459)
T ss_pred HHHHHHHHHHHHHHHHHHHHHH-HCCCC--EEECCCCCCHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHH
T ss_conf 9999999999999999999997-35773--23156688666788999999997378998996167786445899986478
Q ss_pred HHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHH-----HHHHHC---CCCCEEEE---ECC-CCCCHHHHHHHHCC-C
Q ss_conf 89988763012126774678876655677764344-----332211---35957999---438-87712321234339-8
Q gi|254780779|r 116 LRDLEELLNKENQGFTKKERLNIERKRDKLKRALD-----GIRDMG---GLPDLMFV---VDT-NREKLAIQEARRLR-I 182 (278)
Q Consensus 116 l~~l~~~~~~~~~~~tkKe~~~~~r~~~kl~k~lg-----Gi~~m~---~lP~~iiv---~d~-~~e~~Av~EA~kl~-I 182 (278)
|+.|- ..+.| .+.==|+|| ||=.+- -=|.--|. ||| +.|..---=|+.+| =
T Consensus 279 L~~LA---------------~sL~K-IAnD~R~LgSGPRCGlGEl~~PENEPGSSIMPGKVNPTQ~EalTMVC~QVmGNd 342 (459)
T TIGR00979 279 LKTLA---------------ASLMK-IANDIRWLGSGPRCGLGELFLPENEPGSSIMPGKVNPTQCEALTMVCVQVMGND 342 (459)
T ss_pred HHHHH---------------HHHHH-HHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHH
T ss_conf 99999---------------98877-987787850788642002567778757876978987104358899888773002
Q ss_pred EEEEECCCCCCCHH-CCCEEEECCCCHHHHHHHHH---HHHHHHHHHHHH
Q ss_conf 14540367767001-15203215772689999999---999999999997
Q gi|254780779|r 183 PIVAVVDTNSNPDL-VDYVIPGNDDSSRSIALFCD---LVASAAIDGIAR 228 (278)
Q Consensus 183 PvIaivDTn~dp~~-idypIP~NDds~~si~l~~~---~i~~ai~~g~~~ 228 (278)
-+|++.-|..+.++ |==|+=--| =.+||+|+.. .|.+-+..|.+-
T Consensus 343 ~tI~~agS~GnFELNVFkPViIyN-fLqS~~LLsDa~~SF~~hcv~Gi~p 391 (459)
T TIGR00979 343 ATIGFAGSQGNFELNVFKPVIIYN-FLQSVRLLSDAMESFREHCVVGIEP 391 (459)
T ss_pred HHHHHHHCCCCCCCCCCCHHHHHH-HHHHHHHHHHHHHHHHHHCCCCCCC
T ss_conf 454533204653123452589987-9989999998999888640124502
No 224
>cd03786 GT1_UDP-GlcNAc_2-Epimerase Bacterial members of the UDP-N-Acetylglucosamine (GlcNAc) 2-Epimerase family are known to catalyze the reversible interconversion of UDP-GlcNAc and UDP-N-acetylmannosamine (UDP-ManNAc). The enzyme serves to produce an activated form of ManNAc residues (UDP-ManNAc) for use in the biosynthesis of a variety of cell surface polysaccharides; The mammalian enzyme is bifunctional, catalyzing both the inversion of stereochemistry at C-2 and the hydrolysis of the UDP-sugar linkage to generate free ManNAc. It also catalyzes the phosphorylation of ManNAc to generate ManNAc 6-phosphate, a precursor to salic acids. In mammals, sialic acids are found at the termini of oligosaccharides in a large variety of cell surface glycoconjugates and are key mediators of cell-cell recognition events. Mutations in human members of this family have been associated with Sialuria, a rare disease caused by the disorders of sialic acid metabolism. This family belongs to the GT-B st
Probab=38.94 E-value=32 Score=15.95 Aligned_cols=33 Identities=24% Similarity=0.367 Sum_probs=23.0
Q ss_pred HHHHHHCCCEEEEECCCCCCCHHCCCEEE--ECCC
Q ss_conf 21234339814540367767001152032--1577
Q gi|254780779|r 174 IQEARRLRIPIVAVVDTNSNPDLVDYVIP--GNDD 206 (278)
Q Consensus 174 v~EA~kl~IPvIaivDTn~dp~~idypIP--~NDd 206 (278)
+.||.-+|+|+|-+-|..--|..++..+= +++|
T Consensus 289 ~Eea~~l~~P~i~ir~rqe~re~~~~~~~~~v~~~ 323 (363)
T cd03786 289 QEEASFLGVPVLNLRDRTERPETVESGTNVLVGTD 323 (363)
T ss_pred EEEECCCCCCEEEECCCCCCCEEHHCCEEEECCCC
T ss_conf 88502069878982687767342100548865899
No 225
>cd01742 GATase1_GMP_Synthase Type 1 glutamine amidotransferase (GATase1) domain found in GMP synthetase. Type 1 glutamine amidotransferase (GATase1) domain found in GMP synthetase. GMP synthetase is a glutamine amidotransferase from the de novo purine biosynthetic pathway. Glutamine amidotransferase (GATase) activity catalyse the transfer of ammonia from the amide side chain of glutamine to an acceptor substrate. GMP synthetase catalyses the amination of the nucleotide precursor xanthosine 5'-monophospahte to form GMP. GMP synthetase belongs to the triad family of amidotransferases having a conserved Cys-His-Glu catalytic triad in the glutaminase active site.
Probab=38.57 E-value=32 Score=15.95 Aligned_cols=30 Identities=13% Similarity=0.272 Sum_probs=20.1
Q ss_pred CCEEEEEC-CC-----CCCHHHHHHHHCCCEEEEEC
Q ss_conf 95799943-88-----77123212343398145403
Q gi|254780779|r 159 PDLMFVVD-TN-----REKLAIQEARRLRIPIVAVV 188 (278)
Q Consensus 159 P~~iiv~d-~~-----~e~~Av~EA~kl~IPvIaiv 188 (278)
||.||+.+ |. ....++++....++|+.|||
T Consensus 42 ~dgvils~GP~~~~~~~~~~~~~~i~~~~~PilGIC 77 (181)
T cd01742 42 PKGIILSGGPSSVYEEDAPRVDPEIFELGVPVLGIC 77 (181)
T ss_pred CCEEEECCCCCCCCCCCCCHHHHHHHHCCCCEEEEH
T ss_conf 898998999998555798333099984799999985
No 226
>pfam00532 Peripla_BP_1 family. This family includes the periplasmic binding proteins, and the LacI family transcriptional regulators. The periplasmic binding proteins are the primary receptors for chemotaxis and transport of many sugar based solutes. The LacI family of proteins consist of transcriptional regulators related to the lac repressor. In this case, generally the sugar binding domain binds a sugar which changes the DNA binding activity of the repressor domain (pfam00356).
Probab=38.01 E-value=34 Score=15.82 Aligned_cols=63 Identities=11% Similarity=0.110 Sum_probs=43.5
Q ss_pred CCCCEEEEECCCCCCHHHHHHHHCC---CE---------EEEECCCC-------CCCHHCCCEEEECCCCHHHHHHHHHH
Q ss_conf 3595799943887712321234339---81---------45403677-------67001152032157726899999999
Q gi|254780779|r 157 GLPDLMFVVDTNREKLAIQEARRLR---IP---------IVAVVDTN-------SNPDLVDYVIPGNDDSSRSIALFCDL 217 (278)
Q Consensus 157 ~lP~~iiv~d~~~e~~Av~EA~kl~---IP---------vIaivDTn-------~dp~~idypIP~NDds~~si~l~~~~ 217 (278)
..|++||+.+-.-=.-|++.++..| || +||+.|.+ .+|.+-+.-.|...=+.+++++++..
T Consensus 181 ~~~~Ai~~~nD~~A~G~~~al~~~G~~~vP~dv~i~~~svvg~d~~~~~~~~~~~~P~LTTV~qp~~~mG~~A~~~Ll~~ 260 (281)
T pfam00532 181 PTIDAIVAMNDEAAMGAVRALLKQGRVKIPDIVGIGINSVVGFDGLSKAQDTGLYLSPLTVIQLPRQLLGIKASDMVYQW 260 (281)
T ss_pred CCCEEEEECCHHHHHHHHHHHHHCCCCCCCCHHCCCCCCEEEEECCCHHHHHHCCCCCCEEEECCHHHHHHHHHHHHHHH
T ss_conf 99609997587999999999998299978831125777669990883256650389984379559999999999999998
Q ss_pred HH
Q ss_conf 99
Q gi|254780779|r 218 VA 219 (278)
Q Consensus 218 i~ 219 (278)
|.
T Consensus 261 I~ 262 (281)
T pfam00532 261 IP 262 (281)
T ss_pred HC
T ss_conf 67
No 227
>TIGR03639 cas1_NMENI CRISPR-associated protein Cas1, NMENI subtype. The CRISPR-associated protein Cas1 is virtually universal to CRISPR systems. CRISPR, an acronym for Clustered Regularly Interspaced Short Palindromic Repeats, is a prokaryotic immunity system for foreign DNA, mostly from phage. CRISPR systems belong to different subtypes, distinguished by both nature of the repeats, the makeup of the cohort of associated Cas proteins, and by molecular phylogeny within the more universal Cas proteins such as this one. This model is of type EXCEPTION and provides more specific information than the EQUIVALOG model TIGR00287. It describes the Cas1 variant of the NMENI subtype of CRISPR/Cas system.
Probab=37.94 E-value=34 Score=15.81 Aligned_cols=50 Identities=12% Similarity=0.157 Sum_probs=25.9
Q ss_pred CEEEEEC--CCCCCHHHHHHHHCCCEEEEECCCCCCCHHCCCEEEECCCCHHH
Q ss_conf 5799943--88771232123433981454036776700115203215772689
Q gi|254780779|r 160 DLMFVVD--TNREKLAIQEARRLRIPIVAVVDTNSNPDLVDYVIPGNDDSSRS 210 (278)
Q Consensus 160 ~~iiv~d--~~~e~~Av~EA~kl~IPvIaivDTn~dp~~idypIP~NDds~~s 210 (278)
+.|++.. ..-...++.+|.+-|||++ ++|.+..|.+.-+|..++..+.+-
T Consensus 36 ~~Ivi~~~~v~iss~ll~~l~~~~I~v~-f~~~~g~~~g~~~p~~~~~~~~~~ 87 (278)
T TIGR03639 36 DVILIENPQVTISSALLSALAENNIALI-FCDEKHLPVGQLLPFYGHHRSLKR 87 (278)
T ss_pred CEEEECCCCEEECHHHHHHHHHCCCEEE-EECCCCCEEEEEECCCCCCCHHHH
T ss_conf 8899968979987999999998799799-998999888999547788538999
No 228
>COG0614 FepB ABC-type Fe3+-hydroxamate transport system, periplasmic component [Inorganic ion transport and metabolism]
Probab=37.63 E-value=34 Score=15.78 Aligned_cols=31 Identities=26% Similarity=0.330 Sum_probs=18.9
Q ss_pred CCEEEEECCCCCCHHHHHHHHCCCEEEEECCC
Q ss_conf 95799943887712321234339814540367
Q gi|254780779|r 159 PDLMFVVDTNREKLAIQEARRLRIPIVAVVDT 190 (278)
Q Consensus 159 P~~iiv~d~~~e~~Av~EA~kl~IPvIaivDT 190 (278)
||+||..+. ...-.+.+-...++|+|.+-..
T Consensus 116 PDlIi~~~~-~~~~~~~~~~~~~~pvv~~~~~ 146 (319)
T COG0614 116 PDLIIASSS-SQDDLIYKLLSLGAPVVVVDYG 146 (319)
T ss_pred CCEEEEECC-CCCHHHHHHHHCCCCEEEECCC
T ss_conf 989997076-5541279998469978998887
No 229
>COG2503 Predicted secreted acid phosphatase [General function prediction only]
Probab=37.50 E-value=34 Score=15.77 Aligned_cols=44 Identities=20% Similarity=0.363 Sum_probs=31.4
Q ss_pred HHHHHHHHHHHCCCCEEEEEECCHHHH--HHHHHHHHHCCCEECCC
Q ss_conf 999999998610788169960782357--99999986339831423
Q gi|254780779|r 53 QKALQVISDTVARGGRILFVATKSQAS--DCVMEAAKRSAQYCVNS 96 (278)
Q Consensus 53 ~~A~~~i~~i~~~gg~ILFVgTk~~~~--~~i~~~A~~~~~~yV~~ 96 (278)
--|..|+..+-.+||.|.||..+.+-. ....+--.+.|.|-+.+
T Consensus 125 pGA~eFl~Yvn~~Gg~ifyiSNR~~~~~~~~T~~nLk~~g~~~~~~ 170 (274)
T COG2503 125 PGAVEFLNYVNSNGGKIFYISNRDQENEKDGTIENLKSEGLPQVLE 170 (274)
T ss_pred CCHHHHHHHHHHCCCEEEEEECCCHHHHCCHHHHHHHHHCCCCCCC
T ss_conf 5589999999855967999836541200110588898707654465
No 230
>cd00354 FBPase Fructose-1,6-bisphosphatase, an enzyme that catalyzes the hydrolysis of fructose-1,6-biphosphate into fructose-6-phosphate and is critical in gluconeogenesis pathway. The alignment model also includes chloroplastic FBPases and sedoheptulose-1,7-biphosphatases that play a role in pentose phosphate pathway (Calvin cycle).
Probab=37.31 E-value=2.3 Score=23.33 Aligned_cols=49 Identities=31% Similarity=0.300 Sum_probs=31.6
Q ss_pred ECHHHHHHHHHHHHHHHHHHHCCCCE---EEEEECC-H----------HHHHHHHHHHHHCCC
Q ss_conf 53899999999999999986107881---6996078-2----------357999999863398
Q gi|254780779|r 43 IDLSQTVPMLQKALQVISDTVARGGR---ILFVATK-S----------QASDCVMEAAKRSAQ 91 (278)
Q Consensus 43 IdL~kT~~~L~~A~~~i~~i~~~gg~---ILFVgTk-~----------~~~~~i~~~A~~~~~ 91 (278)
=||...+..|..||+.|...+++++. .=..|+. . .+.+++.+....++.
T Consensus 12 ~dl~~ll~~ia~a~k~Is~~v~~a~l~~~~g~~g~~N~~Ge~QkkLDv~an~~~~~aL~~~~~ 74 (315)
T cd00354 12 GDLTDLLSSLALACKEISRAVRRAGLAGLLGLAGSVNVQGDEQKKLDVLANDIFIEALKSSGV 74 (315)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHCCCC
T ss_conf 789999999999999999998631455565555562589758999999999999999861897
No 231
>COG1648 CysG Siroheme synthase (precorrin-2 oxidase/ferrochelatase domain) [Coenzyme metabolism]
Probab=37.24 E-value=35 Score=15.74 Aligned_cols=124 Identities=23% Similarity=0.258 Sum_probs=65.6
Q ss_pred HCCCCEEEEEECCHHHHHHHHHHHHHCCCEECCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHH
Q ss_conf 10788169960782357999999863398314233458732342666555677899887630121267746788766556
Q gi|254780779|r 63 VARGGRILFVATKSQASDCVMEAAKRSAQYCVNSKWLGGMMTNWKTVSQSIQKLRDLEELLNKENQGFTKKERLNIERKR 142 (278)
Q Consensus 63 ~~~gg~ILFVgTk~~~~~~i~~~A~~~~~~yV~~RWlGG~LTN~~ti~~si~~l~~l~~~~~~~~~~~tkKe~~~~~r~~ 142 (278)
--+|++||+||....+..-++.++..-...+|...=.. ..+..+.+...-.+
T Consensus 9 ~l~~k~VlvvGgG~va~rKa~~ll~~ga~v~Vvs~~~~-------------~el~~~~~~~~i~~--------------- 60 (210)
T COG1648 9 DLEGKKVLVVGGGSVALRKARLLLKAGADVTVVSPEFE-------------PELKALIEEGKIKW--------------- 60 (210)
T ss_pred ECCCCEEEEECCCHHHHHHHHHHHHCCCEEEEECCCCC-------------HHHHHHHHHCCCCH---------------
T ss_conf 81997799989989999999999746997999878744-------------99999998348531---------------
Q ss_pred HHHHHHHHHHHHHCCCCCEEEEE--CCCCCCHHHHHHHHCCCEEEEECCCCCCCHHCCCEEEE-------------CCCC
Q ss_conf 77764344332211359579994--38877123212343398145403677670011520321-------------5772
Q gi|254780779|r 143 DKLKRALDGIRDMGGLPDLMFVV--DTNREKLAIQEARRLRIPIVAVVDTNSNPDLVDYVIPG-------------NDDS 207 (278)
Q Consensus 143 ~kl~k~lgGi~~m~~lP~~iiv~--d~~~e~~Av~EA~kl~IPvIaivDTn~dp~~idypIP~-------------NDds 207 (278)
.+..|..- .... ++++|+- |+.-+.-..+.|...+||+-..=| |..-|+.+|+ +-.|
T Consensus 61 --~~~~~~~~-~~~~-~~lviaAt~d~~ln~~i~~~a~~~~i~vNv~D~----p~~~~f~~Pa~~~r~~l~iaIsT~G~s 132 (210)
T COG1648 61 --IEREFDAE-DLDD-AFLVIAATDDEELNERIAKAARERRILVNVVDD----PELCDFIFPAIVDRGPLQIAISTGGKS 132 (210)
T ss_pred --HHCCCCHH-HHCC-CEEEEEECCCHHHHHHHHHHHHHHCCCEEECCC----CCCCCEEECEEECCCCEEEEEECCCCC
T ss_conf --00223636-5368-249999169989999999999993993560488----465856601054358879999779977
Q ss_pred HHHHHHHHHHHHHHH
Q ss_conf 689999999999999
Q gi|254780779|r 208 SRSIALFCDLVASAA 222 (278)
Q Consensus 208 ~~si~l~~~~i~~ai 222 (278)
..--.++...|...+
T Consensus 133 P~la~~ir~~Ie~~l 147 (210)
T COG1648 133 PVLARLLREKIEALL 147 (210)
T ss_pred HHHHHHHHHHHHHHC
T ss_conf 499999999999975
No 232
>cd06287 PBP1_LacI_like_8 Ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. This group includes the ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.
Probab=37.19 E-value=35 Score=15.74 Aligned_cols=62 Identities=18% Similarity=0.131 Sum_probs=43.4
Q ss_pred CCCEEEEECCCCCCHHHHHHHHCCCE------EEEECCCC----CCCHHCCCEEEECCCCHHHHHHHHHHHH
Q ss_conf 59579994388771232123433981------45403677----6700115203215772689999999999
Q gi|254780779|r 158 LPDLMFVVDTNREKLAIQEARRLRIP------IVAVVDTN----SNPDLVDYVIPGNDDSSRSIALFCDLVA 219 (278)
Q Consensus 158 lP~~iiv~d~~~e~~Av~EA~kl~IP------vIaivDTn----~dp~~idypIP~NDds~~si~l~~~~i~ 219 (278)
.|++||+.+-.--.-+++.++.+|+. |||+-|+. .+|.+-+.-.|...=+.+++++++..+.
T Consensus 178 ~~~AI~~~nD~~A~g~l~al~~~Gl~VP~DvsVvgfdD~~~a~~~~P~LTtV~qp~~e~G~~A~~lLl~~i~ 249 (269)
T cd06287 178 DLDALCVPVDAFAVGAVRAATELGRAVPDQLRVVTRYDGLRARTSEPPLTAVDLHLDEVAEQAVDLLFAHLE 249 (269)
T ss_pred CCCEEEEECHHHHHHHHHHHHHHCCCCCCCCEEEEECCCHHHHCCCCCCEEEEECHHHHHHHHHHHHHHHHC
T ss_conf 997799827999999999999858877987669981592897345888548971999999999999999966
No 233
>PRK07591 threonine synthase; Validated
Probab=37.13 E-value=35 Score=15.73 Aligned_cols=51 Identities=18% Similarity=0.085 Sum_probs=30.0
Q ss_pred HHHHHCCCCEEEEEECC-HHHHHHHHHHHHHCCCEECCCCCCCCCCCCHHHH
Q ss_conf 99861078816996078-2357999999863398314233458732342666
Q gi|254780779|r 59 ISDTVARGGRILFVATK-SQASDCVMEAAKRSAQYCVNSKWLGGMMTNWKTV 109 (278)
Q Consensus 59 i~~i~~~gg~ILFVgTk-~~~~~~i~~~A~~~~~~yV~~RWlGG~LTN~~ti 109 (278)
+..+...|.+|+.|... ..+..+..+.+.+.|.+|+|.-|-+-.+--.+||
T Consensus 178 ~~q~~~yGA~vv~v~G~~dda~~~~~~~a~~~g~~~~n~~~~P~~iEG~KTi 229 (422)
T PRK07591 178 VVGTLVYGPTLVAVEGNYDDVNRLCSEVANTYGWGFVNINLRPYYSEGSKTL 229 (422)
T ss_pred HHHHHHCCCEEEEECCCHHHHHHHHHHHHHHCCCEEECCCCCCCHHHHHHHH
T ss_conf 9989856998999379888999999999986496221466782253326689
No 234
>PRK05638 threonine synthase; Validated
Probab=36.87 E-value=35 Score=15.71 Aligned_cols=56 Identities=20% Similarity=0.149 Sum_probs=41.9
Q ss_pred HHHHHHCCCCEEEEEE-CCHHHHHHHHHHHHHCCCEECCCCCCCCCCCCHHHHHHHH
Q ss_conf 9998610788169960-7823579999998633983142334587323426665556
Q gi|254780779|r 58 VISDTVARGGRILFVA-TKSQASDCVMEAAKRSAQYCVNSKWLGGMMTNWKTVSQSI 113 (278)
Q Consensus 58 ~i~~i~~~gg~ILFVg-Tk~~~~~~i~~~A~~~~~~yV~~RWlGG~LTN~~ti~~si 113 (278)
-+..+...|.+|..|+ +...+.....+.|...|.||++.-|-+-.+--.+||---|
T Consensus 151 Kl~q~~~yGA~vi~v~g~~d~a~~~a~~~a~~~g~~~~~~~~nP~~iEG~KTiayEI 207 (443)
T PRK05638 151 KLIQMIAFGAKIIRYGESVDEAIEYAEELAKLNGLYNVTPEDNIIGLEGQKTIAFEL 207 (443)
T ss_pred HHHHHHHCCCEEEEECCCHHHHHHHHHHHHHHCCEEEECCCCCCCHHHHHHHHHHHH
T ss_conf 999999649889997996799999999998656948825877722432123589999
No 235
>pfam08672 APC2 Anaphase promoting complex (APC) subunit 2. The anaphase promoting complex or cyclosome (APC2) is an E3 ubiquitin ligase which is part of the SCF family of ubiquitin ligases. Ubiquitin ligases catalyse the transfer of ubiquitin from the ubiquitin conjugating enzyme (E2), to the substrate protein.
Probab=36.82 E-value=30 Score=16.19 Aligned_cols=24 Identities=17% Similarity=0.545 Sum_probs=16.0
Q ss_pred CCCCCCCCHHHHHHHHHHHHHHHHHH
Q ss_conf 45873234266655567789988763
Q gi|254780779|r 98 WLGGMMTNWKTVSQSIQKLRDLEELL 123 (278)
Q Consensus 98 WlGG~LTN~~ti~~si~~l~~l~~~~ 123 (278)
++=|||||+.+ -.+.|.+.+-++.
T Consensus 1 yI~gMLtN~~s--lpl~RIh~mLkmf 24 (60)
T pfam08672 1 YIVGMLTNLGS--LPLERIHSMLKMF 24 (60)
T ss_pred CCCHHHHCCCC--CCHHHHHHHHHHH
T ss_conf 90208445787--8899999999974
No 236
>PRK11617 endonuclease V; Provisional
Probab=36.05 E-value=23 Score=16.91 Aligned_cols=37 Identities=24% Similarity=0.387 Sum_probs=27.8
Q ss_pred HHCCCCCEEEEEC-----CCCCCHHHHHHHHCCCEEEEECCC
Q ss_conf 2113595799943-----887712321234339814540367
Q gi|254780779|r 154 DMGGLPDLMFVVD-----TNREKLAIQEARRLRIPIVAVVDT 190 (278)
Q Consensus 154 ~m~~lP~~iiv~d-----~~~e~~Av~EA~kl~IPvIaivDT 190 (278)
.|+..||+++|=. |..=-+|-+=.-.+++|+||+.-+
T Consensus 92 ~L~~~PDvllvDG~Gi~HPRr~GlAsHlGV~l~~PTIGVAK~ 133 (223)
T PRK11617 92 QLSQKPDLVFVDGHGISHPRRLGVASHFGLLVDVPTIGVAKK 133 (223)
T ss_pred HCCCCCCEEEECCCCCCCCCCCCHHHEEEEECCCCCCCCCCC
T ss_conf 627799999987975437624161202455428783230053
No 237
>TIGR00287 cas1 CRISPR-associated protein Cas1; InterPro: IPR002729 This family of proteins are found in archaea and bacteria and are, as yet, functionally uncharacterised. It is one of four protein families in prokaryotic genomes that contain multiple CRISPR elements. CRISPR is an acronym for Clustered Regularly Interspaced Short Palindromic Repeats. The cas genes are found near the repeats . This protein is otherwise uncharacterised..
Probab=35.84 E-value=36 Score=15.65 Aligned_cols=45 Identities=20% Similarity=0.113 Sum_probs=35.0
Q ss_pred CCEEEE-ECCCCCCHHHHHHHHCCCEEEEECCCCCCCHHC------CCEEEEC
Q ss_conf 957999-438877123212343398145403677670011------5203215
Q gi|254780779|r 159 PDLMFV-VDTNREKLAIQEARRLRIPIVAVVDTNSNPDLV------DYVIPGN 204 (278)
Q Consensus 159 P~~iiv-~d~~~e~~Av~EA~kl~IPvIaivDTn~dp~~i------dypIP~N 204 (278)
=+.++. -.+.-.+-||++|.+.||||+ ++|.+++|-.= =||=+.+
T Consensus 37 ~~I~~~tg~~~~s~~ai~~l~~~~I~~~-F~~~~G~~~gr~~E~~~l~~~~~~ 88 (353)
T TIGR00287 37 DDIVIFTGGVSISSAAIRLLAKRGIDIV-FLDGDGNYLGRTDEVVFLYPQEEG 88 (353)
T ss_pred EEEEEECCCCCCCHHHHHHHHHCCCEEE-EECCCCCEEEECCEEEEEECCCCC
T ss_conf 1588970784025899999997597299-988887054404238997447888
No 238
>pfam00743 FMO-like Flavin-binding monooxygenase-like. This family includes FMO proteins and cyclohexanone monooxygenase.
Probab=35.44 E-value=36 Score=15.61 Aligned_cols=35 Identities=20% Similarity=0.373 Sum_probs=30.8
Q ss_pred HCCCCEEEEEECCHHHHHHHHHHHHHCCCEECCCC
Q ss_conf 10788169960782357999999863398314233
Q gi|254780779|r 63 VARGGRILFVATKSQASDCVMEAAKRSAQYCVNSK 97 (278)
Q Consensus 63 ~~~gg~ILFVgTk~~~~~~i~~~A~~~~~~yV~~R 97 (278)
...|++||.||....+.++..+.+..+.+-|+..|
T Consensus 180 ~f~GKrVlVVG~GnSg~DIA~els~~a~~V~ls~R 214 (532)
T pfam00743 180 GFQGKRVLVIGLGNSGGDIAVELSRTAAQVFLSTR 214 (532)
T ss_pred HCCCCEEEEECCCCCCCHHHHHHHHHCCEEEEEEE
T ss_conf 85997499978889841059999852786899970
No 239
>CHL00101 trpG anthranilate synthase component 2
Probab=35.37 E-value=37 Score=15.55 Aligned_cols=31 Identities=6% Similarity=0.007 Sum_probs=23.3
Q ss_pred EEEEEECCHHHHHHHHHHHHHCCCEECCCCC
Q ss_conf 1699607823579999998633983142334
Q gi|254780779|r 68 RILFVATKSQASDCVMEAAKRSAQYCVNSKW 98 (278)
Q Consensus 68 ~ILFVgTk~~~~~~i~~~A~~~~~~yV~~RW 98 (278)
.||+|-..-|+...|...-..+|.+..--||
T Consensus 1 mILiiD~~dsft~~i~r~lrelg~~~~v~~~ 31 (190)
T CHL00101 1 MILIIDNYDSFTYNLVQSLGELNSDLLVCRN 31 (190)
T ss_pred CEEEEECCCHHHHHHHHHHHHCCCEEEEECC
T ss_conf 9999978880899999999868998999869
No 240
>KOG0256 consensus
Probab=35.18 E-value=22 Score=17.07 Aligned_cols=42 Identities=26% Similarity=0.370 Sum_probs=26.2
Q ss_pred CHHHHHHHHCCCEEEEECCCC-CCCHHCCCEEEECCCCHHHHHHHHHHHH
Q ss_conf 123212343398145403677-6700115203215772689999999999
Q gi|254780779|r 171 KLAIQEARRLRIPIVAVVDTN-SNPDLVDYVIPGNDDSSRSIALFCDLVA 219 (278)
Q Consensus 171 ~~Av~EA~kl~IPvIaivDTn-~dp~~idypIP~NDds~~si~l~~~~i~ 219 (278)
..|.++|+++|++|=|++=|| +||-+.+| +...+..+++...
T Consensus 214 E~A~~~A~~~~~kVkGvlitNPsNPLG~~~-------~~e~L~~ll~Fa~ 256 (471)
T KOG0256 214 EAALNQARKLGLKVKGVLITNPSNPLGTTL-------SPEELISLLNFAS 256 (471)
T ss_pred HHHHHHHHHHCCCEEEEEEECCCCCCCCCC-------CHHHHHHHHHHHH
T ss_conf 999999998189524899827999777746-------9999999999886
No 241
>PRK00421 murC UDP-N-acetylmuramate--L-alanine ligase; Provisional
Probab=35.14 E-value=37 Score=15.53 Aligned_cols=86 Identities=12% Similarity=0.211 Sum_probs=43.0
Q ss_pred HHHHHHCCC--CCCCCCCCC--------CCCCC----CCCCCCCCCEEEECHHHHHHHHHHHHHHHHHHHCCCCEEEEEE
Q ss_conf 899986088--607547765--------78856----2102001881675389999999999999998610788169960
Q gi|254780779|r 8 IRQLLESGV--QFGHRNFLW--------NPKME----RYIFCERNNTHIIDLSQTVPMLQKALQVISDTVARGGRILFVA 73 (278)
Q Consensus 8 ~~~Ll~ag~--H~Gh~~~~w--------nPkM~----~yI~g~rngihIIdL~kT~~~L~~A~~~i~~i~~~gg~ILFVg 73 (278)
.++|.+.|+ +.||....+ .|... .+.+...+|+.|+.--. |+..+......|-+-|
T Consensus 46 ~~~L~~~Gi~v~~g~~~~~l~~~d~vV~Sp~I~~~~p~~~~a~~~gi~v~~~~e----------~l~~~~~~~~~IaVtG 115 (459)
T PRK00421 46 TQRLLELGAIIFIGHDAENIKGADVVVVSSAIKPDNPELVAARELGIPVVRRAE----------MLAELMRLRTSIAVAG 115 (459)
T ss_pred HHHHHHCCCEEECCCCHHHCCCCCEEEECCCCCCCCHHHHHHHHCCCCEEEHHH----------HHHHHHHCCCEEEEEC
T ss_conf 999997879997798979879999999899859989999999987997988999----------9999982596499977
Q ss_pred CC--HHHHHHHHHHHHHCCCE--ECCCCCCCCCCCCHH
Q ss_conf 78--23579999998633983--142334587323426
Q gi|254780779|r 74 TK--SQASDCVMEAAKRSAQY--CVNSKWLGGMMTNWK 107 (278)
Q Consensus 74 Tk--~~~~~~i~~~A~~~~~~--yV~~RWlGG~LTN~~ 107 (278)
|+ -....++....+.+|.. | ++||.+.|+.
T Consensus 116 TnGKTTtT~ll~~il~~~g~~~~~----~iGg~~~~~~ 149 (459)
T PRK00421 116 THGKTTTTSLLAHVLAEAGLDPTF----IIGGILNAAG 149 (459)
T ss_pred CCCCCHHHHHHHHHHHHCCCCCEE----EECCCCCCCC
T ss_conf 888611899999999976998748----8575335566
No 242
>cd06270 PBP1_GalS_like Ligand binding domain of DNA transcription iso-repressor GalS, which is one of two regulatory proteins involved in galactose transport and metabolism. Ligand binding domain of DNA transcription iso-repressor GalS, which is one of two regulatory proteins involved in galactose transport and metabolism. Transcription of the galactose regulon genes is regulated by Gal iso-repressor (GalS) and Gal repressor (GalR) in different ways, but both repressors recognize the same DNA binding site in the absence of D-galactose. GalS is a dimeric protein like GalR,and its major role is in regulating expression of the high-affinity galactose transporter encoded by the mgl operon, whereas GalR is the exclusive regulator of galactose permease, the low-affinity galactose transporter. GalS and GalR are members of the LacI-GalR family of transcription regulators and both contain the type I periplasmic binding protein-like fold. Hence, they are homologous to the periplasmic sugar bindi
Probab=34.82 E-value=38 Score=15.50 Aligned_cols=63 Identities=22% Similarity=0.214 Sum_probs=38.1
Q ss_pred CCCCCEEEEECCCCCCHHHHHHHHCCCE------EEEECCCC----CCCHHCCCEEEECCCCHHHHHHHHHHH
Q ss_conf 1359579994388771232123433981------45403677----670011520321577268999999999
Q gi|254780779|r 156 GGLPDLMFVVDTNREKLAIQEARRLRIP------IVAVVDTN----SNPDLVDYVIPGNDDSSRSIALFCDLV 218 (278)
Q Consensus 156 ~~lP~~iiv~d~~~e~~Av~EA~kl~IP------vIaivDTn----~dp~~idypIP~NDds~~si~l~~~~i 218 (278)
...|+++|+.+-.-=.-+++.++.+|+. |||+=|+. +.|.+-+.-.|...=+..++++++..+
T Consensus 175 ~~~~~ai~~~nD~~A~g~~~~l~~~g~~vP~disvigfdd~~~~~~~~P~LTti~~~~~~~g~~A~~~Ll~~i 247 (268)
T cd06270 175 GAPFTAVFCANDEMAAGAISALREHGISVPQDVSIIGFDDVLLARYLYPKLTTVHYPIEEMAQMAAKLALQLV 247 (268)
T ss_pred CCCCCEEEECCHHHHHHHHHHHHHCCCCCCCCEEEEEECCHHHHHHCCCCCEEEECCHHHHHHHHHHHHHHHH
T ss_conf 9998745533779999999999982999999769999898689971489954996499999999999999997
No 243
>PRK10416 cell division protein FtsY; Provisional
Probab=34.59 E-value=38 Score=15.47 Aligned_cols=148 Identities=14% Similarity=0.234 Sum_probs=80.4
Q ss_pred CCCCCCCC--CCEEEECHHHHHHHHHHHHHHHHHHHCCCCEEEEEECC---HHHHHHHHHHHHHCCCEECCCCCCCCCCC
Q ss_conf 62102001--88167538999999999999999861078816996078---23579999998633983142334587323
Q gi|254780779|r 30 ERYIFCER--NNTHIIDLSQTVPMLQKALQVISDTVARGGRILFVATK---SQASDCVMEAAKRSAQYCVNSKWLGGMMT 104 (278)
Q Consensus 30 ~~yI~g~r--ngihIIdL~kT~~~L~~A~~~i~~i~~~gg~ILFVgTk---~~~~~~i~~~A~~~~~~yV~~RWlGG~LT 104 (278)
+|||.-.- ||. -||-..-+.|..|- .+|++||++..- ..+.+-++..+.+.|.+++.+.- |. -
T Consensus 294 ~P~VIl~vGvNG~-----GKTTTigKLA~~~~----~~gkkVllaA~DTfRaAAieQL~~w~~r~~v~vi~~~~-g~--D 361 (499)
T PRK10416 294 TPFVILMVGVNGV-----GKTTTIGKLARQFE----QQGKSVMLAAGDTFRAAAVEQLQVWGQRNNIPVIAQHT-GA--D 361 (499)
T ss_pred CCEEEEEECCCCC-----CHHHHHHHHHHHHH----HCCCCEEEEEECCCCHHHHHHHHHHHCCCCCEEEECCC-CC--C
T ss_conf 9879999747878-----78989999999999----77995378840667568999999984245736983689-99--9
Q ss_pred CHHHHHHHHHHHHH--HHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCC-EEEEECCCCCCHHHHHHHHC-
Q ss_conf 42666555677899--887630121267746788766556777643443322113595-79994388771232123433-
Q gi|254780779|r 105 NWKTVSQSIQKLRD--LEELLNKENQGFTKKERLNIERKRDKLKRALDGIRDMGGLPD-LMFVVDTNREKLAIQEARRL- 180 (278)
Q Consensus 105 N~~ti~~si~~l~~--l~~~~~~~~~~~tkKe~~~~~r~~~kl~k~lgGi~~m~~lP~-~iiv~d~~~e~~Av~EA~kl- 180 (278)
--+-+...+...+. ++-..-..-..+.-|+ .++.|+.|+.+...-+ ...-|+ .++|+|...-.+|+.-|+..
T Consensus 362 pa~V~~dai~~a~~~~~DvviiDTAGRl~~~~--~LM~EL~ki~rvi~k~--~~~aP~e~lLVlDa~tGQna~~qak~F~ 437 (499)
T PRK10416 362 SASVIFDAIQAAKARNVDVLIADTAGRLQNKS--HLMEELKKIVRVMKKL--DVEAPHEVMLTIDASTGQNAVSQAKLFH 437 (499)
T ss_pred HHHHHHHHHHHHHHCCCCEEEEECCCCCCCCH--HHHHHHHHHHHHHHHC--CCCCCCEEEEEEECCCCHHHHHHHHHHH
T ss_conf 79999999999997299989985776432609--9999999999999723--7899974899977876778999999984
Q ss_pred -CCEEEEECCCCCC
Q ss_conf -9814540367767
Q gi|254780779|r 181 -RIPIVAVVDTNSN 193 (278)
Q Consensus 181 -~IPvIaivDTn~d 193 (278)
.+++=|++=|-+|
T Consensus 438 e~~~ltGiIlTKlD 451 (499)
T PRK10416 438 EAVGLTGITLTKLD 451 (499)
T ss_pred HCCCCCEEEEECCC
T ss_conf 42799759996567
No 244
>pfam10609 ParA ParA/MinD ATPase like. This family contains ATPases involved in plasmid partitioning. It also contains the cytosolic Fe-S cluster assembling factor NBP35 which is required for biogenesis and export of both ribosomal subunits.
Probab=34.49 E-value=31 Score=16.06 Aligned_cols=33 Identities=24% Similarity=0.482 Sum_probs=23.4
Q ss_pred CCCEEEEECCCCCCH-----HHHHHHHCCCEEEEECCC
Q ss_conf 595799943887712-----321234339814540367
Q gi|254780779|r 158 LPDLMFVVDTNREKL-----AIQEARRLRIPIVAVVDT 190 (278)
Q Consensus 158 lP~~iiv~d~~~e~~-----Av~EA~kl~IPvIaivDT 190 (278)
...+++|.-|+.-+. ++.=++++|||++|+|.-
T Consensus 25 ~~~~ivVTTP~~ls~~dv~r~i~~~~~~~i~ilGiVEN 62 (81)
T pfam10609 25 VDGAVIVTTPQDVALLDVRKAIDMFKKLNVPILGIVEN 62 (81)
T ss_pred CCCEEEEECCHHHHHHHHHHHHHHHHHCCCCEEEEEEC
T ss_conf 57769980985999999999999999849961899977
No 245
>cd06559 Endonuclease_V Endonuclease_V, a DNA repair enzyme that initiates repair of nitrosative deaminated purine bases. Endonuclease_V (EndoV) is an enzyme that can initiate repair of all possible deaminated DNA bases. EndoV cleaves the DNA strand containing lesions at the second phosphodiester bond 3' to the lesion using Mg2+ as a cofactor. EndoV homologs are conserved throughout all domains of life from bacteria to humans. EndoV is encoded by the nfi gene and nfi null mutant mice have a phenotype prone to cancer. The ability of endonuclease V to recognize mismatches and abnormal replicative DNA structures suggests that the enzyme plays an important role in DNA metabolism. The details of downstream processing for the EndoV pathway remain unknown.
Probab=34.36 E-value=25 Score=16.66 Aligned_cols=36 Identities=28% Similarity=0.392 Sum_probs=27.7
Q ss_pred HCCCCCEEEEEC-----CCCCCHHHHHHHHCCCEEEEECCC
Q ss_conf 113595799943-----887712321234339814540367
Q gi|254780779|r 155 MGGLPDLMFVVD-----TNREKLAIQEARRLRIPIVAVVDT 190 (278)
Q Consensus 155 m~~lP~~iiv~d-----~~~e~~Av~EA~kl~IPvIaivDT 190 (278)
+...||+++|=. |..--+|-.=.-.+|+|+||+.-+
T Consensus 90 l~~~PdlllvDG~Gi~HPR~~GlAsHlGv~l~~PtIGVAK~ 130 (208)
T cd06559 90 LKTKPDLLLVDGHGIAHPRRFGLASHLGVLLDLPTIGVAKS 130 (208)
T ss_pred CCCCCCEEEECCCCCCCCCCCCHHEEEEEECCCCCCCCCCC
T ss_conf 57799999986887526655470103455528783342154
No 246
>COG2984 ABC-type uncharacterized transport system, periplasmic component [General function prediction only]
Probab=34.16 E-value=39 Score=15.43 Aligned_cols=142 Identities=18% Similarity=0.218 Sum_probs=73.6
Q ss_pred EECHHHHHHHHHHHHHHHHHHHCCCCEEEEEECCHHHHHHHHHHHHHCCCEE----CC----CC----C--CCCCCCCHH
Q ss_conf 7538999999999999999861078816996078235799999986339831----42----33----4--587323426
Q gi|254780779|r 42 IIDLSQTVPMLQKALQVISDTVARGGRILFVATKSQASDCVMEAAKRSAQYC----VN----SK----W--LGGMMTNWK 107 (278)
Q Consensus 42 IIdL~kT~~~L~~A~~~i~~i~~~gg~ILFVgTk~~~~~~i~~~A~~~~~~y----V~----~R----W--lGG~LTN~~ 107 (278)
-||++...--+..|....+.+..++..+....+-+.++-++..... .|- |+ -+ | -||-.|-|+
T Consensus 64 ~i~~~na~~~~~~a~~iarql~~~~~dviv~i~tp~Aq~~~s~~~~---iPVV~aavtd~v~a~Lv~~~~~pg~NvTGvs 140 (322)
T COG2984 64 KIDYQNAQGDLGTAAQIARQLVGDKPDVIVAIATPAAQALVSATKT---IPVVFAAVTDPVGAKLVKSLEQPGGNVTGVS 140 (322)
T ss_pred EEEEECCCCCHHHHHHHHHHHHCCCCCEEEECCCHHHHHHHHHCCC---CCEEEECCCCHHHCCCCCCCCCCCCCEEECC
T ss_conf 8996247788578999999961479967996177899999984679---8879972576332358764447888436237
Q ss_pred HHHHHHHHHHHHHHHHHCC---C-CCCCHHHH--HHHHHHHHHHHHHHH----------------HHHHHCCCCCEEEEE
Q ss_conf 6655567789988763012---1-26774678--876655677764344----------------332211359579994
Q gi|254780779|r 108 TVSQSIQKLRDLEELLNKE---N-QGFTKKER--LNIERKRDKLKRALD----------------GIRDMGGLPDLMFVV 165 (278)
Q Consensus 108 ti~~si~~l~~l~~~~~~~---~-~~~tkKe~--~~~~r~~~kl~k~lg----------------Gi~~m~~lP~~iiv~ 165 (278)
-.. -+.+--+|-+..... . --|...|. ..+.++..+.-+..| -++.|.+.+|++++.
T Consensus 141 D~~-~v~q~i~lik~~~Pnak~Igv~Y~p~E~ns~~l~eelk~~A~~~Gl~vve~~v~~~ndi~~a~~~l~g~~d~i~~p 219 (322)
T COG2984 141 DLL-PVAQQIELIKALLPNAKSIGVLYNPGEANSVSLVEELKKEARKAGLEVVEAAVTSVNDIPRAVQALLGKVDVIYIP 219 (322)
T ss_pred CCC-HHHHHHHHHHHHCCCCEEEEEEECCCCCCCHHHHHHHHHHHHHCCCEEEEEECCCCCCCHHHHHHHCCCCCEEEEE
T ss_conf 751-6999999999867887069999579886608999999999987798899983476320089999734787679986
Q ss_pred CCCCC----CHHHHHHHHCCCEEEEE
Q ss_conf 38877----12321234339814540
Q gi|254780779|r 166 DTNRE----KLAIQEARRLRIPIVAV 187 (278)
Q Consensus 166 d~~~e----~~Av~EA~kl~IPvIai 187 (278)
.-+.. +..+.+|++-+||+|+=
T Consensus 220 ~dn~i~s~~~~l~~~a~~~kiPli~s 245 (322)
T COG2984 220 TDNLIVSAIESLLQVANKAKIPLIAS 245 (322)
T ss_pred CCHHHHHHHHHHHHHHHHHCCCEECC
T ss_conf 60677888999999988708973547
No 247
>TIGR02638 lactal_redase lactaldehyde reductase; InterPro: IPR013460 The proteins in this entry form a distinct clade of iron-containing alcohol dehydrogenases. The genes encoding these proteins are generally found in apparent operons for the catabolism of rhamnose or fucose. Catabolism of both of these monosaccharides results in the production of lactaldehydes, which are reduced by these enzymes to 1,2 propanediol . These enzymes are also sometimes called 1,2 propanediol oxidoreductases. They are active under anaerobic conditions in E. coli, while being inactivated by reactive oxygen species under aerobic conditions . Under aerobic conditions the lactaldehyde product of rhamnose and fucose catabolism is believed to be oxidized to lactate by a separate enzyme, lactaldehyde dehydrogenase..
Probab=34.03 E-value=24 Score=16.72 Aligned_cols=48 Identities=33% Similarity=0.444 Sum_probs=30.7
Q ss_pred CCEEEEECCCCCC---CHH---------CC-----CEEEEC----C-CCHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 9814540367767---001---------15-----203215----7-72689999999999999999997
Q gi|254780779|r 181 RIPIVAVVDTNSN---PDL---------VD-----YVIPGN----D-DSSRSIALFCDLVASAAIDGIAR 228 (278)
Q Consensus 181 ~IPvIaivDTn~d---p~~---------id-----ypIP~N----D-ds~~si~l~~~~i~~ai~~g~~~ 228 (278)
.||.||++|++-= |.. .| |.-+|- | -.+++|++|-..|..||..|+..
T Consensus 168 ~IP~vAv~D~~~M~~mP~~ltAATGmDALTHAiEgyiT~GAw~ltD~~~LkAIe~Ia~~L~~aV~~g~~~ 237 (380)
T TIGR02638 168 DIPDVAVVDAELMLSMPKSLTAATGMDALTHAIEGYITKGAWELTDMLHLKAIEIIARSLRSAVEDGKDL 237 (380)
T ss_pred CCCEEEEECHHHHHHCCHHHHHHHCHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHCCCCCH
T ss_conf 6780665473776215500000002017888898754243663054668999999998777751589862
No 248
>PRK09375 quinolinate synthetase; Provisional
Probab=33.95 E-value=39 Score=15.41 Aligned_cols=22 Identities=18% Similarity=0.144 Sum_probs=15.0
Q ss_pred CCCEEEEECCCCCCHHHHHHHH
Q ss_conf 5957999438877123212343
Q gi|254780779|r 158 LPDLMFVVDTNREKLAIQEARR 179 (278)
Q Consensus 158 lP~~iiv~d~~~e~~Av~EA~k 179 (278)
-|++.|++-|....-.+..|..
T Consensus 208 ~P~a~vlvHPEC~~eV~~~AD~ 229 (323)
T PRK09375 208 YPDAKVLVHPECPPEVVALADF 229 (323)
T ss_pred CCCCEEEECCCCCHHHHHHHHH
T ss_conf 8997598558888789988676
No 249
>cd03819 GT1_WavL_like This family is most closely related to the GT1 family of glycosyltransferases. WavL in Vibrio cholerae has been shown to be involved in the biosynthesis of the lipopolysaccharide core.
Probab=33.87 E-value=39 Score=15.40 Aligned_cols=34 Identities=24% Similarity=0.407 Sum_probs=23.7
Q ss_pred CHHHHHHHHCCCEEEEECCCCCCCHHC-----CCEEEECC
Q ss_conf 123212343398145403677670011-----52032157
Q gi|254780779|r 171 KLAIQEARRLRIPIVAVVDTNSNPDLV-----DYVIPGND 205 (278)
Q Consensus 171 ~~Av~EA~kl~IPvIaivDTn~dp~~i-----dypIP~ND 205 (278)
.+++-||--.|.|||+- |....++.| -|-+|.+|
T Consensus 278 ~~vllEAma~G~PvV~s-~~gg~~eii~~~~~G~l~~~~d 316 (355)
T cd03819 278 GRTAVEAQAMGRPVIAS-DHGGARETVRPGETGLLVPPGD 316 (355)
T ss_pred HHHHHHHHHCCCCEEEE-CCCCCHHHCCCCCCEEEECCCC
T ss_conf 07899999869989990-8999476615899789988999
No 250
>PRK00073 pgk phosphoglycerate kinase; Provisional
Probab=33.36 E-value=40 Score=15.35 Aligned_cols=25 Identities=28% Similarity=0.336 Sum_probs=17.6
Q ss_pred CCHHHHHHCCC------CCCCCCCCCCCCCC
Q ss_conf 45899986088------60754776578856
Q gi|254780779|r 6 FTIRQLLESGV------QFGHRNFLWNPKME 30 (278)
Q Consensus 6 ~t~~~Ll~ag~------H~Gh~~~~wnPkM~ 30 (278)
-||+.|++.|+ |+|+....+++++.
T Consensus 41 pTI~~l~~~gakvvi~SHlGRPkg~~~~~~S 71 (391)
T PRK00073 41 PTIKYLLEKGAKVILLSHLGRPKGEGDEEFS 71 (391)
T ss_pred HHHHHHHHCCCEEEEEECCCCCCCCCCCCCC
T ss_conf 9999999789989999368899999896568
No 251
>PRK13545 tagH teichoic acids export protein ATP-binding subunit; Provisional
Probab=32.86 E-value=41 Score=15.30 Aligned_cols=90 Identities=14% Similarity=0.352 Sum_probs=53.4
Q ss_pred CEEEECHHH---HHHHHHHHHHHHHHHHCCCCEEEEEECCHHHHHHHHHHHHHCCCEECCCCCC-CCCCCCHHHHHHHHH
Q ss_conf 816753899---9999999999999861078816996078235799999986339831423345-873234266655567
Q gi|254780779|r 39 NTHIIDLSQ---TVPMLQKALQVISDTVARGGRILFVATKSQASDCVMEAAKRSAQYCVNSKWL-GGMMTNWKTVSQSIQ 114 (278)
Q Consensus 39 gihIIdL~k---T~~~L~~A~~~i~~i~~~gg~ILFVgTk~~~~~~i~~~A~~~~~~yV~~RWl-GG~LTN~~ti~~si~ 114 (278)
.|-|||=-- ....-.++..-+.++..+|++|+||.-. -..|++++.|+ =|+ .|-+--+..+..-+.
T Consensus 163 DILIIDEaLSVGD~~F~~Kc~~rm~ef~e~gkTIvfVSHs---l~~Vk~~C~R~-------iWLe~G~vr~~G~~~eVv~ 232 (549)
T PRK13545 163 DILVIDEALSVGDQTFTKKCLDKMNEFKEQGKTIFFISHS---LSQVKSFCTKA-------LWLHYGQVKEYGDIKEIVD 232 (549)
T ss_pred CEEEEECCCCCCCHHHHHHHHHHHHHHHHCCCEEEEEECC---HHHHHHHCCEE-------EEEECCEEEEECCHHHHHH
T ss_conf 9999946200578999999999999999789889999588---89999857310-------6343866787488889999
Q ss_pred HHHHHHHHHHCCCCCCCHHHHHHHHHHH
Q ss_conf 7899887630121267746788766556
Q gi|254780779|r 115 KLRDLEELLNKENQGFTKKERLNIERKR 142 (278)
Q Consensus 115 ~l~~l~~~~~~~~~~~tkKe~~~~~r~~ 142 (278)
+|..+-+ .|++++|+|+-.+..|.
T Consensus 233 ~Ye~Flk----~~~~~sk~e~~~~~~e~ 256 (549)
T PRK13545 233 HYDEFLK----KYNQMSVEERKDLRKEQ 256 (549)
T ss_pred HHHHHHH----HHHHCCHHHHHHHHHHH
T ss_conf 9999999----98733999999999999
No 252
>cd00763 Bacterial_PFK Phosphofructokinase, a key regulatory enzyme in glycolysis, catalyzes the phosphorylation of fructose-6-phosphate to fructose-1,6-biphosphate. The members belong to a subfamily of the PFKA family (cd00363) and include bacterial ATP-dependent phosphofructokinases. These are allosrterically regulated homotetramers; the subunits are of about 320 amino acids.
Probab=32.82 E-value=41 Score=15.29 Aligned_cols=45 Identities=22% Similarity=0.364 Sum_probs=31.9
Q ss_pred CCEEEEECCCCCCHHHHHHHHCCCEEEEECCCCCCCHHCCCEEEECCCCHH
Q ss_conf 957999438877123212343398145403677670011520321577268
Q gi|254780779|r 159 PDLMFVVDTNREKLAIQEARRLRIPIVAVVDTNSNPDLVDYVIPGNDDSSR 209 (278)
Q Consensus 159 P~~iiv~d~~~e~~Av~EA~kl~IPvIaivDTn~dp~~idypIP~NDds~~ 209 (278)
=|++|++.-..-......-.+.+||+|++ |--||-=||+.|-++-
T Consensus 93 Id~Li~IGGdgS~~~a~~l~e~~i~vigI------PkTIDNDi~gtd~t~G 137 (317)
T cd00763 93 IDALVVIGGDGSYMGAMRLTEHGFPCVGL------PGTIDNDIPGTDYTIG 137 (317)
T ss_pred CCEEEEECCCHHHHHHHHHHHCCCCEEEE------CCCCCCCCCCCCCCCC
T ss_conf 99899956945899999999749977971------3544678888787868
No 253
>PRK08673 3-deoxy-7-phosphoheptulonate synthase; Reviewed
Probab=32.80 E-value=41 Score=15.29 Aligned_cols=141 Identities=15% Similarity=0.249 Sum_probs=78.5
Q ss_pred HHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCEEEECHHHHHHHHHHHHH--------------HHHHHHCCCCEEEEEE
Q ss_conf 89998608860754776578856210200188167538999999999999--------------9998610788169960
Q gi|254780779|r 8 IRQLLESGVQFGHRNFLWNPKMERYIFCERNNTHIIDLSQTVPMLQKALQ--------------VISDTVARGGRILFVA 73 (278)
Q Consensus 8 ~~~Ll~ag~H~Gh~~~~wnPkM~~yI~g~rngihIIdL~kT~~~L~~A~~--------------~i~~i~~~gg~ILFVg 73 (278)
-+.+-++|+++- +-.-|-|+..||=| .|.- +.-+..|.+|.. -+. .+.+.-.||-||
T Consensus 113 A~~vk~~ga~~l-RgGa~KPRTsPysF---qGlg----~eGL~~L~~~~~e~GlpvvTEV~~~~~ve-~v~~~vDilQIG 183 (335)
T PRK08673 113 ARAVKEAGAQIL-RGGAFKPRTSPYSF---QGLG----EEGLKLLAEAREETGLPIVTEVMDPRDVE-LVAEYADILQIG 183 (335)
T ss_pred HHHHHHCCCCEE-CCCCCCCCCCCCCC---CCCC----HHHHHHHHHHHHHHCCCEEEEECCHHHHH-HHHHHCCEEEEC
T ss_conf 999997799688-06665789998541---4551----66999999999986995289966899999-999649799989
Q ss_pred CCHHHHHHHHHHHHHCCCEECCCCCCCCCCCCHHHHHHHHHHHHHH--HHH--HHCCCCCCCHHHHHHHHHHHHHHHHHH
Q ss_conf 7823579999998633983142334587323426665556778998--876--301212677467887665567776434
Q gi|254780779|r 74 TKSQASDCVMEAAKRSAQYCVNSKWLGGMMTNWKTVSQSIQKLRDL--EEL--LNKENQGFTKKERLNIERKRDKLKRAL 149 (278)
Q Consensus 74 Tk~~~~~~i~~~A~~~~~~yV~~RWlGG~LTN~~ti~~si~~l~~l--~~~--~~~~~~~~tkKe~~~~~r~~~kl~k~l 149 (278)
++.-.+...-+.+-+++-|-.-.|=+..++--|-- +..++..- .+. .+-++..|.+.. +..--+
T Consensus 184 ARnmqN~~LL~evg~~~kPVllKrg~~~ti~ewl~---AaEyi~~~Gn~~ViLcERGirtfe~~t---------RntlDl 251 (335)
T PRK08673 184 ARNMQNFDLLKEVGKTNKPVLLKRGMSATIEEWLM---AAEYILAEGNPNVILCERGIRTFETAT---------RNTLDL 251 (335)
T ss_pred HHHHCCHHHHHHHHHHCCEEEECCCCCCCHHHHHH---HHHHHHHCCCCCEEEEECCCCCCCCCC---------CCCCCH
T ss_conf 15505999999999729948973788788999987---899999769986799934654567666---------787787
Q ss_pred HHHHHHCCCCCEEEEECCCC
Q ss_conf 43322113595799943887
Q gi|254780779|r 150 DGIRDMGGLPDLMFVVDTNR 169 (278)
Q Consensus 150 gGi~~m~~lP~~iiv~d~~~ 169 (278)
..|--|++++.+=+|+||.+
T Consensus 252 ~aip~~k~~thlPVI~DPSH 271 (335)
T PRK08673 252 SAVPVLKKLTHLPVIVDPSH 271 (335)
T ss_pred HHHHHHHHCCCCCEEECCCC
T ss_conf 88899971889888988822
No 254
>TIGR00313 cobQ cobyric acid synthase CobQ; InterPro: IPR004459 Cobyric acid synthase (CobQ) catalyses amidations at positions B, D, E, and G on adenosylcobyrinic A,C-diamide in the biosynthesis of cobalamin. NH(2) groups are provided by glutamine, and one molecule of ATP is hydrogenolysed for each amidation .; GO: 0003824 catalytic activity, 0009236 cobalamin biosynthetic process.
Probab=32.71 E-value=26 Score=16.52 Aligned_cols=41 Identities=22% Similarity=0.320 Sum_probs=27.5
Q ss_pred EEECCCCCCCHHCCC-EEEECCCCHHHHHHH-HHHHHHHHHHH
Q ss_conf 540367767001152-032157726899999-99999999999
Q gi|254780779|r 185 VAVVDTNSNPDLVDY-VIPGNDDSSRSIALF-CDLVASAAIDG 225 (278)
Q Consensus 185 IaivDTn~dp~~idy-pIP~NDds~~si~l~-~~~i~~ai~~g 225 (278)
|-++++|.+.+..|- .|||--++++-.+.+ -+-+++.|.+-
T Consensus 276 v~fl~l~~~L~~~d~vIiPGsk~ti~dl~~L~~~~~~~~i~~~ 318 (502)
T TIGR00313 276 VKFLELEDSLDGLDAVIIPGSKDTIADLKALKESGFAEEILDL 318 (502)
T ss_pred EEEECCCCCCCCCEEEEECCCCCHHHHHHHHHHCCCHHHHHHH
T ss_conf 9983268877884489967996578999999746866799999
No 255
>pfam01039 Carboxyl_trans Carboxyl transferase domain. All of the members in this family are biotin dependent carboxylases. The carboxyl transferase domain carries out the following reaction; transcarboxylation from biotin to an acceptor molecule. There are two recognized types of carboxyl transferase. One of them uses acyl-CoA and the other uses 2-oxoacid as the acceptor molecule of carbon dioxide. All of the members in this family utilize acyl-CoA as the acceptor molecule.
Probab=32.65 E-value=22 Score=17.07 Aligned_cols=44 Identities=23% Similarity=0.400 Sum_probs=29.5
Q ss_pred HHHHHHHCCCCCEEEEECCCC------------CCHHHHHHHHCCCEEEEECCCCC
Q ss_conf 443322113595799943887------------71232123433981454036776
Q gi|254780779|r 149 LDGIRDMGGLPDLMFVVDTNR------------EKLAIQEARRLRIPIVAVVDTNS 192 (278)
Q Consensus 149 lgGi~~m~~lP~~iiv~d~~~------------e~~Av~EA~kl~IPvIaivDTn~ 192 (278)
+.|+.-+.+.|-.|+=-||.. -.-.|+=|.+.|||+|.++||..
T Consensus 283 vtg~arl~G~~VGviAn~p~~~~G~l~~~aa~Kaarfi~lcd~~~iPlv~lvDtpG 338 (487)
T pfam01039 283 VTGFARLGGIPVGVVANQPRVLAGVLFIDSADKAARFIRLCDAFNIPLVILVDVPG 338 (487)
T ss_pred EEEEEEECCCEEEEECCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCCEEEEEECCC
T ss_conf 26678873854799833654346753045589999999986333997699984898
No 256
>pfam00977 His_biosynth Histidine biosynthesis protein. Proteins involved in steps 4 and 6 of the histidine biosynthesis pathway are contained in this family. Histidine is formed by several complex and distinct biochemical reactions catalysed by eight enzymes. The enzymes in this Pfam entry are called His6 and His7 in eukaryotes and HisA and HisF in prokaryotes. The structure of HisA is known to be a TIM barrel fold. In some archaeal HisA proteins the TIM barrel is composed of two tandem repeats of a half barrel. This family belong to the common phosphate binding site TIM barrel family.
Probab=32.19 E-value=39 Score=15.44 Aligned_cols=32 Identities=16% Similarity=0.144 Sum_probs=22.0
Q ss_pred HHHHHHHHHHHHHCCCEECCCCCCCCCCCCHHHHHH
Q ss_conf 235799999986339831423345873234266655
Q gi|254780779|r 76 SQASDCVMEAAKRSAQYCVNSKWLGGMMTNWKTVSQ 111 (278)
Q Consensus 76 ~~~~~~i~~~A~~~~~~yV~~RWlGG~LTN~~ti~~ 111 (278)
....+++++.++.|..|. |+||-+.+...+.+
T Consensus 59 ~~n~~~i~~i~~~~~~pi----~vgGGIrs~e~~~~ 90 (229)
T pfam00977 59 PVNLDLIEEIAEEVFIPV----QVGGGIRSLEDAER 90 (229)
T ss_pred HHHHHHHHHHHHHCCCCE----EEECCEEEHHHHHH
T ss_conf 106999999998669878----99645611899999
No 257
>PRK10423 transcriptional repressor RbsR; Provisional
Probab=32.16 E-value=42 Score=15.22 Aligned_cols=64 Identities=16% Similarity=0.189 Sum_probs=41.4
Q ss_pred CCCCCEEEEECCCCCCHHHHHHHHCCC--E----EEEECCCC----CCCHHCCCEEEECCCCHHHHHHHHHHHH
Q ss_conf 135957999438877123212343398--1----45403677----6700115203215772689999999999
Q gi|254780779|r 156 GGLPDLMFVVDTNREKLAIQEARRLRI--P----IVAVVDTN----SNPDLVDYVIPGNDDSSRSIALFCDLVA 219 (278)
Q Consensus 156 ~~lP~~iiv~d~~~e~~Av~EA~kl~I--P----vIaivDTn----~dp~~idypIP~NDds~~si~l~~~~i~ 219 (278)
...|+++|+.+-.--.-+++.++.+|+ | |||+=|+. ..|.+-+.-+|...=+..++++++..+.
T Consensus 233 ~~~ptAi~~~nD~~A~g~~~al~~~g~~iP~DisvigfDd~~~~~~~~P~LTTv~~~~~~~g~~A~~~Ll~~i~ 306 (327)
T PRK10423 233 PLRPQAVFTGNDAMAVGVYQALYQAGLQVPQDIAVIGYDDIELASYMTPPLTTIHQPKDELGELAIDVLIHRMA 306 (327)
T ss_pred CCCCCEEEECCCHHHHHHHHHHHHCCCCCCCCEEEEEECCCHHHHHCCCCCEEEECCHHHHHHHHHHHHHHHHC
T ss_conf 99998455178099999999999869999997599997582899826999379983999999999999999966
No 258
>cd06272 PBP1_hexuronate_repressor_like Ligand-binding domain of DNA transcription repressor for the hexuronate utilization operon from Bacillus species and its close homologs from other bacteria, all of which are a member of the LacI-GalR family of bacterial transcription regulators. Ligand-binding domain of DNA transcription repressor for the hexuronate utilization operon from Bacillus species and its close homologs from other bacteria, all of which are a member of the LacI-GalR family of bacterial transcription regulators. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor
Probab=31.94 E-value=42 Score=15.20 Aligned_cols=63 Identities=16% Similarity=0.259 Sum_probs=42.0
Q ss_pred CCCCCEEEEECCCCCCHHHHHHHHCCCE------EEEECCCC----CCCHHCCCEEEECCCCHHHHHHHHHHH
Q ss_conf 1359579994388771232123433981------45403677----670011520321577268999999999
Q gi|254780779|r 156 GGLPDLMFVVDTNREKLAIQEARRLRIP------IVAVVDTN----SNPDLVDYVIPGNDDSSRSIALFCDLV 218 (278)
Q Consensus 156 ~~lP~~iiv~d~~~e~~Av~EA~kl~IP------vIaivDTn----~dp~~idypIP~NDds~~si~l~~~~i 218 (278)
...|+++|+.+-.--.-+++.++.+|+. +||+=|+. ..|.+-+.-.|.-.=+.+++++++..+
T Consensus 170 ~~~p~Ai~~~nD~~A~g~~~~l~~~g~~vP~dvsviGfDd~~~~~~~~P~LTtv~q~~~~ig~~A~~~L~~~i 242 (261)
T cd06272 170 SDLPTAIICGSYDIALGVLSALNKQGISIPEDIEIISYDNIPQMAIIDPPLTAVDVPIEEIAKKSLELLLKLI 242 (261)
T ss_pred CCCCCCEEECCHHHHHHHHHHHHHHCCCCCCCEEEEEECCCHHHHHHCCCCEEEEECHHHHHHHHHHHHHHHH
T ss_conf 7898610127689999999999980999999559999888188995099847998099999999999999996
No 259
>COG1515 Nfi Deoxyinosine 3'endonuclease (endonuclease V) [DNA replication, recombination, and repair]
Probab=31.85 E-value=34 Score=15.79 Aligned_cols=36 Identities=28% Similarity=0.399 Sum_probs=29.2
Q ss_pred HCCCCCEEEEEC-----CCCCCHHHHHHHHCCCEEEEECCC
Q ss_conf 113595799943-----887712321234339814540367
Q gi|254780779|r 155 MGGLPDLMFVVD-----TNREKLAIQEARRLRIPIVAVVDT 190 (278)
Q Consensus 155 m~~lP~~iiv~d-----~~~e~~Av~EA~kl~IPvIaivDT 190 (278)
+...||+++|=. |..--+|-..+-.|+.|+||+.-+
T Consensus 92 l~~~~d~ilVDG~GiaHPR~~GlAsH~Gv~l~~PtIGVAK~ 132 (212)
T COG1515 92 LSVKPDLLLVDGHGIAHPRRLGLASHIGVLLDVPTIGVAKS 132 (212)
T ss_pred CCCCCCEEEECCCCEECCCCCCHHHEEEEEECCCCEEEEHH
T ss_conf 48888899986865145766673211344207871257643
No 260
>PRK11366 puuD gamma-glutamyl-gamma-aminobutyrate hydrolase; Provisional
Probab=31.64 E-value=21 Score=17.16 Aligned_cols=37 Identities=5% Similarity=0.066 Sum_probs=21.4
Q ss_pred HHHHHHHHHCCCCEEEEEECCHHHHHHHHHHHHHCCC
Q ss_conf 9999998610788169960782357999999863398
Q gi|254780779|r 55 ALQVISDTVARGGRILFVATKSQASDCVMEAAKRSAQ 91 (278)
Q Consensus 55 A~~~i~~i~~~gg~ILFVgTk~~~~~~i~~~A~~~~~ 91 (278)
...++..+...||.-+.+-.-....+.+.....++..
T Consensus 28 ~~~Y~~ai~~aGgiPvllP~~~~~~~~~~~~l~~lDG 64 (254)
T PRK11366 28 QEKYLNAIIHAGGLPIALPHALAEPSLLEQLLPKLDG 64 (254)
T ss_pred HHHHHHHHHHCCCEEEECCCCCCCHHHHHHHHHHCCE
T ss_conf 8999999998298589848887887899999987898
No 261
>TIGR01318 gltD_gamma_fam glutamate synthase, small subunit; InterPro: IPR006006 One pathway for the assimilation of ammonia and glutamate biosynthesis involves glutamate synthase (1.4.1.13 from EC) which transfers the amide group of glutamine to 2-oxoglutarate to yield two molecules of glutamate. 2 L-glutamate + NADP^+ = L-glutamine + 2-oxoglutarate + NADPH + H^+. This model describes both glutatate synthase small subunit and closely related paralogs of unknown function from a number of gamma and alpha subdivision Proteobacteria, including Escherichia coli. ; GO: 0016639 oxidoreductase activity acting on the CH-NH2 group of donors NAD or NADP as acceptor, 0006537 glutamate biosynthetic process.
Probab=31.59 E-value=41 Score=15.29 Aligned_cols=43 Identities=21% Similarity=0.414 Sum_probs=32.5
Q ss_pred HHHHHCCCCEEEEEECCHHH---HHHHHHHHHHCCC-EECCCCC--CCCCCCC
Q ss_conf 99861078816996078235---7999999863398-3142334--5873234
Q gi|254780779|r 59 ISDTVARGGRILFVATKSQA---SDCVMEAAKRSAQ-YCVNSKW--LGGMMTN 105 (278)
Q Consensus 59 i~~i~~~gg~ILFVgTk~~~---~~~i~~~A~~~~~-~yV~~RW--lGG~LTN 105 (278)
++++...+++|=+||.-|.. .++. .|.|- --|.-|+ +|||||=
T Consensus 136 ~S~V~~~g~rVAviGAGPAGLaCAD~L----~RaGV~v~VfDRhP~iGGLLtF 184 (480)
T TIGR01318 136 LSHVKPTGKRVAVIGAGPAGLACADIL----ARAGVQVVVFDRHPEIGGLLTF 184 (480)
T ss_pred CCCCCCCCCEEEEECCCCCHHHHHHHH----HHCCCEEEEEECCCCCCCCCCC
T ss_conf 877300782789977886025799987----5178559997477030760136
No 262
>PRK00994 F420-dependent methylenetetrahydromethanopterin dehydrogenase; Provisional
Probab=31.54 E-value=43 Score=15.16 Aligned_cols=33 Identities=24% Similarity=0.416 Sum_probs=24.4
Q ss_pred CCCEEEEECCCCC---CHHHHHHHH-CCCEEEEECCC
Q ss_conf 5957999438877---123212343-39814540367
Q gi|254780779|r 158 LPDLMFVVDTNRE---KLAIQEARR-LRIPIVAVVDT 190 (278)
Q Consensus 158 lP~~iiv~d~~~e---~~Av~EA~k-l~IPvIaivDT 190 (278)
-||.++++.|+-- ..+-||..+ .|||+|-|.|.
T Consensus 59 ~pDf~i~isPN~a~PGP~~ARE~l~~~~iP~IvI~D~ 95 (276)
T PRK00994 59 KPDFIIVISPNPAAPGPTKAREILSAAGIPCIVIGDA 95 (276)
T ss_pred CCCEEEEECCCCCCCCCHHHHHHHHHCCCCEEEECCC
T ss_conf 8998999789988999567999997569988997488
No 263
>TIGR00441 gmhA phosphoheptose isomerase; InterPro: IPR004515 Phosphoheptose isomerase is involved in lipopolysaccharide biosynthesis, and more specifically in the synthesis of glyceromannoheptose 7-phosphate. It may also have a role in virulence in Haemophilus ducreyi.; GO: 0008968 phosphoheptose isomerase activity, 0009244 lipopolysaccharide core region biosynthetic process, 0005737 cytoplasm.
Probab=31.15 E-value=43 Score=15.11 Aligned_cols=136 Identities=18% Similarity=0.357 Sum_probs=97.3
Q ss_pred HHHHHHHHHHHHHHHHCCCCEEEEEECCHHHHHHHHHHHHHCCCEECCCCCCCCC-CC-CHHHHHHHHHHHHHHHHHHHC
Q ss_conf 9999999999999861078816996078235799999986339831423345873-23-426665556778998876301
Q gi|254780779|r 48 TVPMLQKALQVISDTVARGGRILFVATKSQASDCVMEAAKRSAQYCVNSKWLGGM-MT-NWKTVSQSIQKLRDLEELLNK 125 (278)
Q Consensus 48 T~~~L~~A~~~i~~i~~~gg~ILFVgTk~~~~~~i~~~A~~~~~~yV~~RWlGG~-LT-N~~ti~~si~~l~~l~~~~~~ 125 (278)
-...+++|...|.+-..+||+||.-|.-..+.+.-.-.|+-+|=|-.+.+=||-- || |-+.++ +|.-
T Consensus 21 ~~~Ai~~aa~ll~~~l~~GgK~L~CGNGgSaadAqHFAaEl~GRf~~eR~glPAIAL~tD~S~Lt-ai~N---------- 89 (186)
T TIGR00441 21 LIEAIQRAALLLVQSLKNGGKILICGNGGSAADAQHFAAELVGRFKLERPGLPAIALNTDISILT-AIAN---------- 89 (186)
T ss_pred HHHHHHHHHHHHHHHHHCCCCEEEECCCCCHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHH-HCCC----------
T ss_conf 08899999999999998089089856850433588899987164000267764677762235323-2001----------
Q ss_pred CCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCEEEEECCCCCC----HHHHHHHHCCCEEEEECCCCC-------CC
Q ss_conf 2126774678876655677764344332211359579994388771----232123433981454036776-------70
Q gi|254780779|r 126 ENQGFTKKERLNIERKRDKLKRALDGIRDMGGLPDLMFVVDTNREK----LAIQEARRLRIPIVAVVDTNS-------NP 194 (278)
Q Consensus 126 ~~~~~tkKe~~~~~r~~~kl~k~lgGi~~m~~lP~~iiv~d~~~e~----~Av~EA~kl~IPvIaivDTn~-------dp 194 (278)
.|+-- ..|.|+ +.-+.+-=|+++=+.|.-++ -|+.-|+.+++.|||+.--|. -|
T Consensus 90 ---Dygyd--~vF~Rq----------VEAlG~~GDVL~GiSTSGNS~NvlkA~~~Ak~~gm~~i~L~G~dGGk~~~l~GP 154 (186)
T TIGR00441 90 ---DYGYD--EVFSRQ----------VEALGQEGDVLLGISTSGNSKNVLKAIEAAKDKGMKTIALTGKDGGKLAGLAGP 154 (186)
T ss_pred ---HHHHH--HHHHHH----------HHHCCCCCCEEEEEECCCCCHHHHHHHHHHHHCCCEEEEEECCCCCCCCCCCCC
T ss_conf ---10256--787777----------663288986888742476708899999988457966999721786311335788
Q ss_pred HHCCCEEEECCCCHH
Q ss_conf 011520321577268
Q gi|254780779|r 195 DLVDYVIPGNDDSSR 209 (278)
Q Consensus 195 ~~idypIP~NDds~~ 209 (278)
..+...||-+.|+.|
T Consensus 155 qD~~l~VP~~~~t~R 169 (186)
T TIGR00441 155 QDVELRVPSKRDTAR 169 (186)
T ss_pred CCEEEECCCCCCCCC
T ss_conf 860567678875840
No 264
>PRK10637 cysG siroheme synthase; Provisional
Probab=31.01 E-value=43 Score=15.10 Aligned_cols=25 Identities=16% Similarity=-0.004 Sum_probs=16.9
Q ss_pred CCCCEEEEEECCHHHHHHHHHHHHH
Q ss_conf 0788169960782357999999863
Q gi|254780779|r 64 ARGGRILFVATKSQASDCVMEAAKR 88 (278)
Q Consensus 64 ~~gg~ILFVgTk~~~~~~i~~~A~~ 88 (278)
-+|+++|+||..+-+.+-+....+.
T Consensus 10 L~gk~vLVVGGG~vA~rK~~~Ll~a 34 (457)
T PRK10637 10 LRDRDCLIVGGGDVAERKARLLLDA 34 (457)
T ss_pred CCCCEEEEECCCHHHHHHHHHHHHC
T ss_conf 3898699989989999999999878
No 265
>cd06329 PBP1_SBP_like_3 Periplasmic solute-binding domain of active transport proteins. Periplasmic solute-binding domain of active transport proteins found in bacteria and Archaea. Members of this group are initial receptors in the process of active transport across cellular membrane, but their substrate specificities are not known in detail. However, they closely resemble the group of AmiC and active transport systems for short-chain amides and urea (FmdDEF), and thus are likely to exhibit a ligand-binding mode similar to that of the amide sensor protein AmiC from Pseudomonas aeruginosa. Moreover, this binding domain has high sequence identity to the family of hydrophobic amino acid transporters (HAAT), and thus it may also be involved in transport of amino acids.
Probab=30.95 E-value=44 Score=15.09 Aligned_cols=80 Identities=10% Similarity=0.160 Sum_probs=39.2
Q ss_pred CCEEEEEECCHHH----HHHHHHHHHHC--CCEECCCCCCC-CCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHH
Q ss_conf 8816996078235----79999998633--98314233458-73234266655567789988763012126774678876
Q gi|254780779|r 66 GGRILFVATKSQA----SDCVMEAAKRS--AQYCVNSKWLG-GMMTNWKTVSQSIQKLRDLEELLNKENQGFTKKERLNI 138 (278)
Q Consensus 66 gg~ILFVgTk~~~----~~~i~~~A~~~--~~~yV~~RWlG-G~LTN~~ti~~si~~l~~l~~~~~~~~~~~tkKe~~~~ 138 (278)
.++|-+++.+-.. .+.+++..... +...|.+.|.+ |..|+|..+-.+++.
T Consensus 143 ~k~vai~~~d~~~g~~~~~~~~~~~~~~~~g~~vv~~~~~p~~~~~Df~~~i~~i~~----------------------- 199 (342)
T cd06329 143 GKKVYLINQDYSWGQDVAAAFKAMLAAKRPDIQIVGEDLHPLGKVKDFSPYVAKIKA----------------------- 199 (342)
T ss_pred CCEEEEECCCCHHHHHHHHHHHHHHHHHCCCCEEEEEEECCCCCCCCHHHHHHHHHH-----------------------
T ss_conf 976999369973769999999999998169958876785258887766999999986-----------------------
Q ss_pred HHHHHHHHHHHHHHHHHCCCCCEEEEECCCCC-CHHHHHHHHCCC--EEEE
Q ss_conf 65567776434433221135957999438877-123212343398--1454
Q gi|254780779|r 139 ERKRDKLKRALDGIRDMGGLPDLMFVVDTNRE-KLAIQEARRLRI--PIVA 186 (278)
Q Consensus 139 ~r~~~kl~k~lgGi~~m~~lP~~iiv~d~~~e-~~Av~EA~kl~I--PvIa 186 (278)
.-||+||+.....+ ...+++++.+|+ |+++
T Consensus 200 ------------------~~pd~v~~~~~~~~~~~~~kq~~~~g~~~~~~~ 232 (342)
T cd06329 200 ------------------SGADTVITGNWGNDLLLLVKQAADAGLKLPFYT 232 (342)
T ss_pred ------------------CCCCEEEECCCCHHHHHHHHHHHHCCCCCCEEE
T ss_conf ------------------699999993775569999999997699981899
No 266
>TIGR01918 various_sel_PB selenoprotein B, glycine/betaine/sarcosine/D-proline reductase family; InterPro: IPR010187 This entry represents selenoprotein B of glycine reductase, sarcosine reductase, betaine reductase, D-proline reductase, and perhaps others. All members are expected to contain an internal UGA codon, encoding selenocysteine, which may be misinterpreted as a stop codon.; GO: 0030699 glycine reductase activity, 0050485 oxidoreductase activity acting on X-H and Y-H to form an X-Y bond with a disulfide as acceptor, 0030700 glycine reductase complex.
Probab=30.89 E-value=43 Score=15.12 Aligned_cols=71 Identities=20% Similarity=0.179 Sum_probs=43.8
Q ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCEEEEEC-----CCCCCHHHHHHHHCCCEEEEECCC---------CCCCH
Q ss_conf 7746788766556777643443322113595799943-----887712321234339814540367---------76700
Q gi|254780779|r 130 FTKKERLNIERKRDKLKRALDGIRDMGGLPDLMFVVD-----TNREKLAIQEARRLRIPIVAVVDT---------NSNPD 195 (278)
Q Consensus 130 ~tkKe~~~~~r~~~kl~k~lgGi~~m~~lP~~iiv~d-----~~~e~~Av~EA~kl~IPvIaivDT---------n~dp~ 195 (278)
-+--+...+.+|..+ +-|..-=|+||+.. ++.-..-|+|--|-|||||.+|.- |-=--
T Consensus 318 T~~~~s~~~AkE~~~--------~L~~~~VDaVIlTST~GTCTRCGATMVKEIERaG~PvV~~C~~~Pia~TVGAN~IvP 389 (433)
T TIGR01918 318 TTVAESKQFAKEFVK--------ELLEGGVDAVILTSTKGTCTRCGATMVKEIERAGIPVVHMCTVIPIALTVGANRIVP 389 (433)
T ss_pred HHHHHHHHHHHHHHH--------HHHHCCCCEEEECCCCCCCCCCCCCHHHHHHHCCCCEEEECCEEEECCCCCCCCCCC
T ss_conf 557878889999999--------998279888998168885544556200012316987476402010000136442336
Q ss_pred HCCCEEEECCCCH
Q ss_conf 1152032157726
Q gi|254780779|r 196 LVDYVIPGNDDSS 208 (278)
Q Consensus 196 ~idypIP~NDds~ 208 (278)
-|..|-|--|=|.
T Consensus 390 tIaIP~PLGdPa~ 402 (433)
T TIGR01918 390 TIAIPHPLGDPAL 402 (433)
T ss_pred CEECCCCCCCCCC
T ss_conf 3253888878768
No 267
>PRK00147 queA S-adenosylmethionine:tRNA ribosyltransferase-isomerase; Provisional
Probab=30.74 E-value=44 Score=15.07 Aligned_cols=14 Identities=57% Similarity=0.854 Sum_probs=7.8
Q ss_pred HHCCCCEEEEEECC
Q ss_conf 61078816996078
Q gi|254780779|r 62 TVARGGRILFVATK 75 (278)
Q Consensus 62 i~~~gg~ILFVgTk 75 (278)
.-++||+|+-|||-
T Consensus 243 ak~~g~rIiAVGTT 256 (345)
T PRK00147 243 TKARGGRVIAVGTT 256 (345)
T ss_pred HHHCCCEEEEEECC
T ss_conf 88649869999252
No 268
>PRK08250 glutamine amidotransferase; Provisional
Probab=30.45 E-value=17 Score=17.67 Aligned_cols=25 Identities=16% Similarity=0.207 Sum_probs=13.3
Q ss_pred HHHHHHHHHHHCCCCEEEEEECCHH
Q ss_conf 9999999986107881699607823
Q gi|254780779|r 53 QKALQVISDTVARGGRILFVATKSQ 77 (278)
Q Consensus 53 ~~A~~~i~~i~~~gg~ILFVgTk~~ 77 (278)
+.-..+|++....+.-+|=|+---|
T Consensus 71 ~~E~~lir~a~~~~~PvlGIClG~Q 95 (235)
T PRK08250 71 KAEQHLINQAITARKAVVGVCLGSQ 95 (235)
T ss_pred HHHHHHHHHHHHCCCCEEEEEHHHH
T ss_conf 9999999999986998899816779
No 269
>TIGR01279 DPOR_bchN light-independent protochlorophyllide reductase, N subunit; InterPro: IPR005970 Synonym: dark protochlorophyllide reductase Protochlorophyllide reductase catalyzes the reductive formation of chlorophyllide from protochlorophyllide during biosynthesis of chlorophylls and bacteriochlorophylls. The light-independent (dark) form of protochlorophyllide reductase plays a key role in the ability of gymnosperms, algae, and photosynthetic bacteria to form chlorophyll in the dark. Genetic and sequence analyses have indicated that dark protochlorophyllide reductase consists of three protein subunits that exhibit significant sequence similarity to the three subunits of nitrogenase, which catalyzes the reductive formation of ammonia from dinitrogen. Dark protochlorophyllide reductase activity was shown to be dependent on the presence of all three subunits, ATP, and the reductant dithionite. This enzyme describes the N subunit of the dark form protochlorophyllide reductase, a nitrogenase-like enzyme . ; GO: 0016730 oxidoreductase activity acting on iron-sulfur proteins as donors, 0015995 chlorophyll biosynthetic process, 0019685 photosynthesis dark reaction.
Probab=30.39 E-value=24 Score=16.78 Aligned_cols=183 Identities=12% Similarity=0.179 Sum_probs=95.9
Q ss_pred CCCC-CCCCEEEEC------HHHHHHHHHHHHHHHHHHHCCCCEEEEEECCHH------HHHHHHHHHHHCC--CEECCC
Q ss_conf 1020-018816753------899999999999999986107881699607823------5799999986339--831423
Q gi|254780779|r 32 YIFC-ERNNTHIID------LSQTVPMLQKALQVISDTVARGGRILFVATKSQ------ASDCVMEAAKRSA--QYCVNS 96 (278)
Q Consensus 32 yI~g-~rngihIId------L~kT~~~L~~A~~~i~~i~~~gg~ILFVgTk~~------~~~~i~~~A~~~~--~~yV~~ 96 (278)
-||. -|-++.+|+ ...+.+.|.+.+.-|.+-.-+.+-|..|||-.. ...+-+....+.+ .|-+.-
T Consensus 46 MiFA~PRFa~A~lee~DLs~~~~~~eeL~~v~~~i~~~~P~p~vifllssCt~ev~K~Dl~~~A~~Ls~~~~Pr~PvL~~ 125 (458)
T TIGR01279 46 MIFAEPRFAVALLEESDLSSAAPAYEELKRVVEQIKRERPNPSVIFLLSSCTPEVIKMDLEGLAEQLSTEFGPRVPVLFA 125 (458)
T ss_pred EEEECCCCCEEEEECHHHHHCCCCHHHHHHHHHHHHHCCCCCEEEEEECCCCCCEEECCHHHHHHHHHCCCCCCEEEEEE
T ss_conf 15523652146652002321163078999999999850899649999616886225402677668730036895007873
Q ss_pred CCCCCCCCCHHHHHHHHHHHHHH----HH-HHHCCCC--CCCHHHHHHHHHHHH--HHHHHHHHHHHHCCCCCEEEEECC
Q ss_conf 34587323426665556778998----87-6301212--677467887665567--776434433221135957999438
Q gi|254780779|r 97 KWLGGMMTNWKTVSQSIQKLRDL----EE-LLNKENQ--GFTKKERLNIERKRD--KLKRALDGIRDMGGLPDLMFVVDT 167 (278)
Q Consensus 97 RWlGG~LTN~~ti~~si~~l~~l----~~-~~~~~~~--~~tkKe~~~~~r~~~--kl~k~lgGi~~m~~lP~~iiv~d~ 167 (278)
+ -.|.=++|.+-=-++ |.-| -+ .....-+ .-.+...+.+.|+-+ |.+....- -..|++++-
T Consensus 126 ~-asGlD~~FTQgED~V--L~AL~P~~P~sa~apa~e~~E~~~~~~~~FG~~~~~EKvese~~~-------~~~lv~~GS 195 (458)
T TIGR01279 126 P-ASGLDYTFTQGEDTV--LAALVPFCPKSAEAPAEEKVERKKQKLLSFGKKADKEKVESEAVD-------QRKLVLVGS 195 (458)
T ss_pred C-CCCCCCCCCCHHHHH--HHHHCCCCCCCCCCCCCCCHHHHCCHHHHCCCHHHHHHHHHHCCC-------CCCEEEEEC
T ss_conf 0-585310223427899--996312578877698987112212212113630112222100027-------865689943
Q ss_pred CCCCH---HHHHHHHCCCEEEEECCCCCCCHHCCCEEEECCCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf 87712---3212343398145403677670011520321577268999999999999999999
Q gi|254780779|r 168 NREKL---AIQEARRLRIPIVAVVDTNSNPDLVDYVIPGNDDSSRSIALFCDLVASAAIDGIA 227 (278)
Q Consensus 168 ~~e~~---Av~EA~kl~IPvIaivDTn~dp~~idypIP~NDds~~si~l~~~~i~~ai~~g~~ 227 (278)
..|.+ --.|+.+||||++++.=- -+.-+.|.=+-+--+--++=|++-.+.++..-|+
T Consensus 196 v~D~~~~~l~~e~~~LGi~~~~flPa---~~~~~lP~i~pgt~~a~~qPyL~~ta~~L~~eR~ 255 (458)
T TIGR01279 196 VNDIVADQLRLELKQLGIPVVGFLPA---SRFTELPVIGPGTVVAPLQPYLSDTATTLRRERG 255 (458)
T ss_pred CCCHHHHHHHHHHHHCCCCCCCCCCC---CCCCCCCCCCCCEEEEECCCHHHHHHHHHHHHCC
T ss_conf 55123677999998378864342774---3345576879861698337418899999985026
No 270
>cd05197 GH4_glycoside_hydrolases Glycoside Hydrases Family 4. Glycoside hydrolases cleave glycosidic bonds to release smaller sugars from oligo- or polysaccharides. Some bacteria simultaneously translocate and phosphorylate disaccharides via the phosphoenolpyruvate-dependent phosphotransferase system (PEP-PTS). After translocation, these phospho-disaccharides may be hydrolyzed by GH4 glycoside hydrolases. Other organisms (such as archaea and Thermotoga maritima) lack the PEP-PTS system, but have several enzymes normally associated with the PEP-PTS operon. GH4 family members include 6-phospho-beta-glucosidases, 6-phospho-alpha-glucosidases, alpha-glucosidases/alpha-glucuronidases (only from Thermotoga), and alpha-galactosidases. They require two cofactors, NAD+ and a divalent metal (Mn2+, Ni2+, Mg2+), for activity. Some also require reducing conditions. GH4 glycoside hydrolases are part of the NAD(P)-binding Rossmann fold superfamily, which includes a wide variety of protein families in
Probab=30.27 E-value=45 Score=15.02 Aligned_cols=46 Identities=24% Similarity=0.355 Sum_probs=30.8
Q ss_pred CCEEEEECCCCCCHHHHHHHH--C-CCEEEEECCC------------CCCCHHCCCEEEECC
Q ss_conf 957999438877123212343--3-9814540367------------767001152032157
Q gi|254780779|r 159 PDLMFVVDTNREKLAIQEARR--L-RIPIVAVVDT------------NSNPDLVDYVIPGND 205 (278)
Q Consensus 159 P~~iiv~d~~~e~~Av~EA~k--l-~IPvIaivDT------------n~dp~~idypIP~ND 205 (278)
|+|.++==++--. .|.||-. . ++++|||||+ +.+++.|+|-..|=+
T Consensus 135 P~AwliNytNP~~-ivt~al~~~~~~~k~vGLCh~~~~~~~~la~~lg~~~~~i~~~~~GlN 195 (425)
T cd05197 135 PDAWYLNFTNPAG-EVTEAVRRYVPPEKAVGLCNVPIGVMEIVAKLLGESEEKVDWQYAGLN 195 (425)
T ss_pred CCEEEEECCCHHH-HHHHHHHHHCCCCCEEEECCCHHHHHHHHHHHHCCCHHHCEEEEEEEC
T ss_conf 9808997378789-999999974888848985866799999999994998899679999766
No 271
>PRK12778 putative bifunctional 2-polyprenylphenol hydroxylase/glutamate synthase subunit beta; Provisional
Probab=30.19 E-value=45 Score=15.01 Aligned_cols=30 Identities=13% Similarity=0.399 Sum_probs=19.8
Q ss_pred ECCCCCCCCCCCCHHHHHHHHHHHHHHHHH
Q ss_conf 142334587323426665556778998876
Q gi|254780779|r 93 CVNSKWLGGMMTNWKTVSQSIQKLRDLEEL 122 (278)
Q Consensus 93 yV~~RWlGG~LTN~~ti~~si~~l~~l~~~ 122 (278)
.|..-|.-|-+-||...-+|...|+.-|+.
T Consensus 236 CvDGPeFd~h~Vd~d~~~~R~~~yk~~ek~ 265 (760)
T PRK12778 236 CVDGPEFDGHQVDFDEMLKRMGAFKTIERE 265 (760)
T ss_pred ECCCCCCCCEEECHHHHHHHHHHHHHHHHH
T ss_conf 562897566065799999998876888765
No 272
>PRK00331 glucosamine--fructose-6-phosphate aminotransferase; Reviewed
Probab=30.10 E-value=45 Score=15.00 Aligned_cols=57 Identities=18% Similarity=0.212 Sum_probs=39.4
Q ss_pred CEEEEECCCCC----CHHHHHHHHCCCEEEEECCCCCCC--HHCCCEEEECC---CCHHHHHHHHH
Q ss_conf 57999438877----123212343398145403677670--01152032157---72689999999
Q gi|254780779|r 160 DLMFVVDTNRE----KLAIQEARRLRIPIVAVVDTNSNP--DLVDYVIPGND---DSSRSIALFCD 216 (278)
Q Consensus 160 ~~iiv~d~~~e----~~Av~EA~kl~IPvIaivDTn~dp--~~idypIP~ND---ds~~si~l~~~ 216 (278)
+++|.+.+..| .-|++.|+..|.+++|||++-.++ ...|+.|+-|- -|+.|-+-|..
T Consensus 337 ~l~i~iSQSGET~Dtl~al~~ak~~ga~tiaIvNv~~Ssiar~sD~~i~~~aGpEi~VASTKafts 402 (604)
T PRK00331 337 TLVIAISQSGETADTLAALRLAKELGAKTLAICNVPGSTLARESDLVLYTHAGPEIGVASTKAFTT 402 (604)
T ss_pred EEEEEECCCCCCHHHHHHHHHHHHCCCCEEEEECCCCCCCCCCCCCEEEECCCCEEEECCCCHHHH
T ss_conf 389997578883789999999987799489860689953231458178855723574312303799
No 273
>PRK07263 consensus
Probab=30.04 E-value=45 Score=15.00 Aligned_cols=143 Identities=17% Similarity=0.262 Sum_probs=72.0
Q ss_pred CCCCCCCCEEEECHHHHHHHHHHHHHHHHHHHCCCCEEEEEECCHHHHHHHHHHH-HHCCCEECCCCCCCCCCCCH--HH
Q ss_conf 1020018816753899999999999999986107881699607823579999998-63398314233458732342--66
Q gi|254780779|r 32 YIFCERNNTHIIDLSQTVPMLQKALQVISDTVARGGRILFVATKSQASDCVMEAA-KRSAQYCVNSKWLGGMMTNW--KT 108 (278)
Q Consensus 32 yI~g~rngihIIdL~kT~~~L~~A~~~i~~i~~~gg~ILFVgTk~~~~~~i~~~A-~~~~~~yV~~RWlGG~LTN~--~t 108 (278)
.|.+-|-+ .-||...|.-|.++- ..+|+.|+|.+.--...+++..+. ..++.++ ++.-.|.||.. ..
T Consensus 206 iviaaRPs-----mGKTa~alnia~~iA---~~~~~~V~~fSlEMs~~ql~~R~la~~~~i~~--~~i~~g~l~~~e~~~ 275 (453)
T PRK07263 206 IILAARPA-----VGKTAFVLNIAQNVG---TKQKKTVAIFSLEMGAESLVDRMLAAEGMVDS--HSLRTGQLTDQDWNN 275 (453)
T ss_pred EEEEECCC-----CCHHHHHHHHHHHHH---HHCCCEEEEEECCCCHHHHHHHHHHHHCCCCH--HCCCCCCCCHHHHHH
T ss_conf 99972788-----847899999999999---85598289992469989999999998617331--033136524799999
Q ss_pred HHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHH-HHHHHHCCCCCEEEEEC-------CC--CCCHHHHH--
Q ss_conf 65556778998876301212677467887665567776434-43322113595799943-------88--77123212--
Q gi|254780779|r 109 VSQSIQKLRDLEELLNKENQGFTKKERLNIERKRDKLKRAL-DGIRDMGGLPDLMFVVD-------TN--REKLAIQE-- 176 (278)
Q Consensus 109 i~~si~~l~~l~~~~~~~~~~~tkKe~~~~~r~~~kl~k~l-gGi~~m~~lP~~iiv~d-------~~--~e~~Av~E-- 176 (278)
+.....++..+.-.. .....++--+. .-...|+.+.. +| .++ ||+| +. .....|.|
T Consensus 276 ~~~a~~~l~~~~l~i-dd~~~~~i~~i---~~~~r~~~~~~~~~-------l~l-ivIDYlqLi~~~~~~~r~~ev~~is 343 (453)
T PRK07263 276 VTIAQGALAEAPIYI-DDTPGIKITEI---RARSRKLSQEVDGG-------LGL-IVIDYLQLITGTKPENRQQEVSDIS 343 (453)
T ss_pred HHHHHHHHCCCCEEE-ECCCCCCHHHH---HHHHHHHHHHHCCC-------CCE-EEEEHHHHCCCCCCCCHHHHHHHHH
T ss_conf 999998740685899-78999998999---99999999860589-------868-9973676446888535999999999
Q ss_pred ------HHHCCCEEEEECCCCCCCHH
Q ss_conf ------34339814540367767001
Q gi|254780779|r 177 ------ARRLRIPIVAVVDTNSNPDL 196 (278)
Q Consensus 177 ------A~kl~IPvIaivDTn~dp~~ 196 (278)
|+.||||||+++-=|=+.+.
T Consensus 344 r~lK~lAkel~ipvi~lsQLnR~~e~ 369 (453)
T PRK07263 344 RQLKILAKELKVPVIALSQLSRGVEQ 369 (453)
T ss_pred HHHHHHHHHHCCCEEEECCCCCCCCC
T ss_conf 99999999879979997436843123
No 274
>TIGR00513 accA acetyl-CoA carboxylase, carboxyl transferase, alpha subunit; InterPro: IPR001095 This entry contains the alpha subunit the acetyl coenzyme A carboxylase complex (). It catalyzes the first step in the synthesis of long-chain fatty acids which involves the carboxylation of acetyl-CoA to malonyl-CoA. The acetyl-CoA carboxylase complex () is a heterohexamer of biotin carboxyl carrier protein, biotin carboxylase and two non-identical carboxyl transferase subunits (alpha and beta) in a 2:2 association . The reaction involves two steps: Biotin carrier protein + ATP + HCO_3^- -> Carboxybiotin carrier protein + ADP + P_i Carboxybiotin carrier protein + Acetyl-CoA -> Malonyl-CoA + Biotin carrier protein ; GO: 0003989 acetyl-CoA carboxylase activity, 0006633 fatty acid biosynthetic process, 0009317 acetyl-CoA carboxylase complex.
Probab=29.89 E-value=30 Score=16.16 Aligned_cols=20 Identities=30% Similarity=0.659 Sum_probs=14.6
Q ss_pred HHHHHHCCCEEEEECCCCCC
Q ss_conf 21234339814540367767
Q gi|254780779|r 174 IQEARRLRIPIVAVVDTNSN 193 (278)
Q Consensus 174 v~EA~kl~IPvIaivDTn~d 193 (278)
-+-|.|.|.|||.++||-.=
T Consensus 152 m~~AerF~~PIi~fiDT~GA 171 (329)
T TIGR00513 152 MKMAERFNLPIITFIDTPGA 171 (329)
T ss_pred HHHHHHCCCCEEEEECCCCC
T ss_conf 98777617985886538888
No 275
>PRK01021 lpxB lipid-A-disaccharide synthase; Reviewed
Probab=29.89 E-value=45 Score=14.98 Aligned_cols=15 Identities=0% Similarity=0.062 Sum_probs=6.0
Q ss_pred HHHHHHHHHHHHHCC
Q ss_conf 235799999986339
Q gi|254780779|r 76 SQASDCVMEAAKRSA 90 (278)
Q Consensus 76 ~~~~~~i~~~A~~~~ 90 (278)
|.+.-.+.+..++.|
T Consensus 320 PdFNlrlak~lkk~g 334 (607)
T PRK01021 320 PDFHFLLIKKLRKCG 334 (607)
T ss_pred CCCCHHHHHHHHHCC
T ss_conf 987889999999728
No 276
>TIGR01368 CPSaseIIsmall carbamoyl-phosphate synthase, small subunit; InterPro: IPR006274 Carbamoyl phosphate synthase (CPSase) is a heterodimeric enzyme composed of a small and a large subunit (with the exception of CPSase III, see below). CPSase catalyses the synthesis of carbamoyl phosphate from biocarbonate, ATP and glutamine (6.3.5.5 from EC) or ammonia (6.3.4.16 from EC), and represents the first committed step in pyrimidine and arginine biosynthesis in prokaryotes and eukaryotes, and in the urea cycle in most terrestrial vertebrates , . CPSase has three active sites, one in the small subunit and two in the large subunit. The small subunit contains the glutamine binding site and catalyses the hydrolysis of glutamine to glutamate and ammonia. The large subunit has two homologous carboxy phosphate domains, both of which have ATP-binding sites; however, the N-terminal carboxy phosphate domain catalyses the phosphorylation of biocarbonate, while the C-terminal domain catalyses the phosphorylation of the carbamate intermediate . The carboxy phosphate domain found duplicated in the large subunit of CPSase is also present as a single copy in the biotin-dependent enzymes acetyl-CoA carboxylase (6.4.1.2 from EC) (ACC), propionyl-CoA carboxylase (6.4.1.3 from EC) (PCCase), pyruvate carboxylase (6.4.1.1 from EC) (PC) and urea carboxylase (6.3.4.6 from EC). Most prokaryotes carry one form of CPSase that participates in both arginine and pyrimidine biosynthesis, however certain bacteria can have separate forms. The large subunit in bacterial CPSase has four structural domains: the carboxy phosphate domain 1, the oligomerisation domain, the carbamoyl phosphate domain 2 and the allosteric domain . CPSase heterodimers from Escherichia coli contain two molecular tunnels: an ammonia tunnel and a carbamate tunnel. These inter-domain tunnels connect the three distinct active sites, and function as conduits for the transport of unstable reaction intermediates (ammonia and carbamate) between successive active sites . The catalytic mechanism of CPSase involves the diffusion of carbamate through the interior of the enzyme from the site of synthesis within the N-terminal domain of the large subunit to the site of phosphorylation within the C-terminal domain. Eukaryotes have two distinct forms of CPSase: a mitochondrial enzyme (CPSase I) that participates in both arginine biosynthesis and the urea cycle; and a cytosolic enzyme (CPSase II) involved in pyrimidine biosynthesis. CPSase II occurs as part of a multi-enzyme complex along with aspartate transcarbamoylase and dihydroorotase; this complex is referred to as the CAD protein . The hepatic expression of CPSase is transcriptionally regulated by glucocorticoids and/or cAMP . There is a third form of the enzyme, CPSase III, found in fish, which uses glutamine as a nitrogen source instead of ammonia . CPSase III is closely related to CPSase I, and is composed of a single polypeptide that may have arisen from gene fusion of the glutaminase and synthetase domains . This entry represents the small subunit of the glutamine-dependent form (6.3.5.5 from EC) of carbamoyl phosphate synthase, CPSase II. The small subunit catalyses the hydrolysis of glutamine to ammonia, which in turn used by the large chain to synthesize carbamoyl phosphate. The C-terminal domain of the small subunit of CPSase has glutamine amidotransferase activity. Note that the sequence from the mammalian urea cycle form has lost the active site Cys, resulting in an ammonia-dependent form, CPSase I (6.3.4.16 from EC). CPSases of pyrimidine biosynthesis, arginine biosynthesis, and the urea cycle may be encoded by one or by several genes, depending on the species. ; GO: 0004086 carbamoyl-phosphate synthase activity, 0006807 nitrogen compound metabolic process.
Probab=29.39 E-value=46 Score=14.92 Aligned_cols=30 Identities=27% Similarity=0.520 Sum_probs=18.2
Q ss_pred CCEEEEECCCCCC-HHH-------HHHHHCCCEEEEEC
Q ss_conf 9579994388771-232-------12343398145403
Q gi|254780779|r 159 PDLMFVVDTNREK-LAI-------QEARRLRIPIVAVV 188 (278)
Q Consensus 159 P~~iiv~d~~~e~-~Av-------~EA~kl~IPvIaiv 188 (278)
||-||+.|=--|- -+| ||-..-.||+.|||
T Consensus 238 PDGiflSNGPGDPH~~~~~~i~~~~~l~~~~~P~fGIC 275 (383)
T TIGR01368 238 PDGIFLSNGPGDPHAAVEPAIETVRELLEAKIPIFGIC 275 (383)
T ss_pred CCEEEEECCCCCCHHHHHHHHHHHHHHHHCCCCCCCCC
T ss_conf 88899908798805678999999999984489710026
No 277
>TIGR03669 urea_ABC_arch urea ABC transporter, substrate-binding protein, archaeal type. Members of this protein family are identified as the substrate-binding protein of a urea ABC transport system by similarity to a known urea transporter from Corynebacterium glutamicum, operon structure, proximity of its operons to urease (urea-utilization protein) operons, and by Partial Phylogenetic Profiling vs. urea utilization.
Probab=29.29 E-value=46 Score=14.91 Aligned_cols=27 Identities=15% Similarity=0.342 Sum_probs=16.7
Q ss_pred CCCEEEEECCCCCCHH-HHHHHHCC--CEE
Q ss_conf 5957999438877123-21234339--814
Q gi|254780779|r 158 LPDLMFVVDTNREKLA-IQEARRLR--IPI 184 (278)
Q Consensus 158 lP~~iiv~d~~~e~~A-v~EA~kl~--IPv 184 (278)
-||+||......+... ++.++.+| +|+
T Consensus 188 ~pD~V~~~~~g~~~~~f~rq~~~~Gl~~p~ 217 (374)
T TIGR03669 188 DPDFVMSMLVGANHASFYEQAASANLNLPM 217 (374)
T ss_pred CCCEEEEECCCCCHHHHHHHHHHCCCCCCC
T ss_conf 999999905587479999999974999863
No 278
>COG0126 Pgk 3-phosphoglycerate kinase [Carbohydrate transport and metabolism]
Probab=29.26 E-value=47 Score=14.91 Aligned_cols=193 Identities=21% Similarity=0.254 Sum_probs=94.5
Q ss_pred CCHHHHHHCC------CCCCCCCCCCCCCCCCCCCCCC------CCEEEECHHHHHHHHHHHHHHHHHHHCCCCEEEEEE
Q ss_conf 4589998608------8607547765788562102001------881675389999999999999998610788169960
Q gi|254780779|r 6 FTIRQLLESG------VQFGHRNFLWNPKMERYIFCER------NNTHIIDLSQTVPMLQKALQVISDTVARGGRILFVA 73 (278)
Q Consensus 6 ~t~~~Ll~ag------~H~Gh~~~~wnPkM~~yI~g~r------ngihIIdL~kT~~~L~~A~~~i~~i~~~gg~ILFVg 73 (278)
-||+.|++.| .|+|+.+. +++++.=-....+ +.+...| .... ..|..-+.++ ..|.-+|+=+
T Consensus 43 pTIk~l~~~ga~Vvl~SHlGRPk~-~~~~~SL~pva~~Ls~ll~~~V~f~~---d~~g-~~a~~~v~~l-~~GevlLLEN 116 (395)
T COG0126 43 PTIKYLLEKGAKVVLLSHLGRPKE-YSDKTSLEPVAKRLSELLGKEVKFVD---DCVG-PEARQAVAEL-KDGEVLLLEN 116 (395)
T ss_pred HHHHHHHHCCCEEEEEECCCCCCC-CCCCCCHHHHHHHHHHHCCCCEEECC---CCCC-HHHHHHHHCC-CCCCEEEEEE
T ss_conf 899999958995999824789899-98764479999999986299618544---4468-7999999616-8986799863
Q ss_pred CCHHH----------HHHHHHHHHHCCCEECCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCC-CCCCHHHHHHHHHHH
Q ss_conf 78235----------7999999863398314233458732342666555677899887630121-267746788766556
Q gi|254780779|r 74 TKSQA----------SDCVMEAAKRSAQYCVNSKWLGGMMTNWKTVSQSIQKLRDLEELLNKEN-QGFTKKERLNIERKR 142 (278)
Q Consensus 74 Tk~~~----------~~~i~~~A~~~~~~yV~~RWlGG~LTN~~ti~~si~~l~~l~~~~~~~~-~~~tkKe~~~~~r~~ 142 (278)
|+-.. ..++++.|..+. .|||.- |.|...+-.-. -++ ..++.--...+.||+
T Consensus 117 ~RF~~~E~~~d~~~~~~l~k~la~l~D-vfVnDA--------FgtAHRahaS~--------~g~~~~lps~aG~LmekEl 179 (395)
T COG0126 117 VRFYSEEEKNDEEARTELVKKLASLGD-VFVNDA--------FGTAHRAHAST--------VGFAKFLPSAAGFLMEKEL 179 (395)
T ss_pred CCCCCCCCCCCHHHHHHHHHHHHHHCC-EEEECH--------HHHHHHHCCCH--------HHHHHHCHHHHHHHHHHHH
T ss_conf 331565568625568999999986469-887424--------57777625431--------2466644254518899999
Q ss_pred HHHHHHHH--------------------HHHHHCCCCCEEEEECC----------------CCCCHHHHHHH--------
Q ss_conf 77764344--------------------33221135957999438----------------87712321234--------
Q gi|254780779|r 143 DKLKRALD--------------------GIRDMGGLPDLMFVVDT----------------NREKLAIQEAR-------- 178 (278)
Q Consensus 143 ~kl~k~lg--------------------Gi~~m~~lP~~iiv~d~----------------~~e~~Av~EA~-------- 178 (278)
.-|.+-+. =|.++-+.-|.|++-.- ..|..-+..|+
T Consensus 180 ~~L~k~l~~p~rP~vaIlGGaKVsdki~vienLl~kaD~liigGgma~tFl~A~G~~vG~sl~E~~~~~~Ak~ll~k~~~ 259 (395)
T COG0126 180 DALGKALENPERPFVAILGGAKVSDKIGVIENLLKKADKLIIGGGMANTFLKAQGYDVGKSLVEFDLIDGAKELLEKAKD 259 (395)
T ss_pred HHHHHHHCCCCCCEEEEEECCCCCHHHHHHHHHHHHCCEEEECCHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHCC
T ss_conf 99999863999865999606500008999999997517588652689999998366501678889888899999997178
Q ss_pred HCCCEEEEECCCCCCCHHCCC---EEE----ECCCCHHHHHHHHHHHHHH
Q ss_conf 339814540367767001152---032----1577268999999999999
Q gi|254780779|r 179 RLRIPIVAVVDTNSNPDLVDY---VIP----GNDDSSRSIALFCDLVASA 221 (278)
Q Consensus 179 kl~IPvIaivDTn~dp~~idy---pIP----~NDds~~si~l~~~~i~~a 221 (278)
++-+|+=..|..+...+-..+ -|| +.|=..+|+.+|...|.+|
T Consensus 260 ~I~lPvD~~v~~~f~~~~~~~~~~~i~~~~~~lDIGp~Ti~~~~~~i~~A 309 (395)
T COG0126 260 KIVLPVDVVVAKEFSRDAPATVKLEIPDDLMILDIGPKTIELFAEIIKGA 309 (395)
T ss_pred CEECCCCEEECCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHC
T ss_conf 17776205870566666654334678887613156889999999998458
No 279
>TIGR03659 IsdE heme ABC transporter, heme-binding protein isdE. This family of ABC substrate-binding proteins is observed primarily in close proximity with proteins localized to the cell wall and bearing the NEAT (NEAr Transporter, pfam05031) heme-binding domain. IsdE has been shown to bind heme and is involved in the process of scavenging heme for the purpose of obtaining iron.
Probab=29.17 E-value=47 Score=14.90 Aligned_cols=27 Identities=22% Similarity=0.301 Sum_probs=10.7
Q ss_pred CCEEEEECCCCCCHHHHHHHHCCCEEEE
Q ss_conf 9579994388771232123433981454
Q gi|254780779|r 159 PDLMFVVDTNREKLAIQEARRLRIPIVA 186 (278)
Q Consensus 159 P~~iiv~d~~~e~~Av~EA~kl~IPvIa 186 (278)
||+||..+...+.+ .....+++||++.
T Consensus 92 PDLIi~~~~~~~~~-~~~l~~~~i~v~~ 118 (289)
T TIGR03659 92 PTVVLSVTTLEEDL-GPKFKQLGVEATF 118 (289)
T ss_pred CCEEEECCCCHHHH-HHHHHHCCCEEEE
T ss_conf 97899557425878-9999860975999
No 280
>cd06331 PBP1_AmiC_like Type I periplasmic components of amide-binding protein (AmiC) and the active transport system for short-chain and urea (FmdDEF). This group includes the type I periplasmic components of amide-binding protein (AmiC) and the active transport system for short-chain and urea (FmdDEF), found in bacteria and Archaea. AmiC controls expression of the amidase operon by a ligand-triggered conformational switch. In the absence of ligand or presence of butyramide (repressor), AmiC (the ligand sensor and negative regulator) adopts an open conformation and inhibits the transcription antitermination function of AmiR by direct protein-protein interaction. In the presence of inducing ligands such as acetamide, AmiC adopts a closed conformation which disrupts a silencing AmiC-AmiR complex and the expression of amidase and other genes of the operon is induced. FmdDEF is predicted to be an ATP-dependent transporter and closely resembles the periplasmic binding protein and the two t
Probab=29.07 E-value=47 Score=14.89 Aligned_cols=86 Identities=10% Similarity=0.184 Sum_probs=47.4
Q ss_pred HHHHHHHHHHCCCCEEEEEECCH----HHHHHHHHHHHHCCCEECCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCC
Q ss_conf 99999998610788169960782----35799999986339831423345873234266655567789988763012126
Q gi|254780779|r 54 KALQVISDTVARGGRILFVATKS----QASDCVMEAAKRSAQYCVNSKWLGGMMTNWKTVSQSIQKLRDLEELLNKENQG 129 (278)
Q Consensus 54 ~A~~~i~~i~~~gg~ILFVgTk~----~~~~~i~~~A~~~~~~yV~~RWlGG~LTN~~ti~~si~~l~~l~~~~~~~~~~ 129 (278)
.+..++.+ ..+++|-+|+..- ...+.+++.++..|.-.|.+-|.+---|+|..+-..++
T Consensus 122 ~~~~~~~~--~~~kkvai~~~d~~~G~~~~~~~~~~~~~~G~~vv~~~~~~~~~~Dfs~~l~~i~--------------- 184 (333)
T cd06331 122 PLIPYLME--KYGKRFYLIGSDYVWPRESNRIARALLEELGGEVVGEEYLPLGTSDFGSVIEKIK--------------- 184 (333)
T ss_pred HHHHHHHH--CCCCEEEEEECCCCHHHHHHHHHHHHHHHCCCEEEEEEEECCCCCCHHHHHHHHH---------------
T ss_conf 99999997--3798799994486178999999999999859949999970699724799999987---------------
Q ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCEEEEECCCCCCHH-HHHHHHCCC
Q ss_conf 77467887665567776434433221135957999438877123-212343398
Q gi|254780779|r 130 FTKKERLNIERKRDKLKRALDGIRDMGGLPDLMFVVDTNREKLA-IQEARRLRI 182 (278)
Q Consensus 130 ~tkKe~~~~~r~~~kl~k~lgGi~~m~~lP~~iiv~d~~~e~~A-v~EA~kl~I 182 (278)
..-||+||+.....+..+ +++++.+|+
T Consensus 185 --------------------------~~~pD~v~~~~~~~~~~~~~~q~~~~G~ 212 (333)
T cd06331 185 --------------------------AAGPDVVLSTLVGDSNVAFYRQFAAAGL 212 (333)
T ss_pred --------------------------HCCCCEEEEECCCCHHHHHHHHHHHCCC
T ss_conf --------------------------6599999993566039999999997599
No 281
>pfam06925 MGDG_synth Monogalactosyldiacylglycerol (MGDG) synthase. This family represents a conserved region of approximately 180 residues within plant and bacterial monogalactosyldiacylglycerol (MGDG) synthase (EC:2.4.1.46). In Arabidopsis, there are two types of MGDG synthase which differ in their N-terminal portion: type A and type B.
Probab=28.75 E-value=47 Score=14.85 Aligned_cols=52 Identities=17% Similarity=0.300 Sum_probs=34.9
Q ss_pred CCCEEEEECCCCCCHHH---HHHHHC-CCEEEEE-CCC-CCCCH----HCCCEEEECCCCHH
Q ss_conf 59579994388771232---123433-9814540-367-76700----11520321577268
Q gi|254780779|r 158 LPDLMFVVDTNREKLAI---QEARRL-RIPIVAV-VDT-NSNPD----LVDYVIPGNDDSSR 209 (278)
Q Consensus 158 lP~~iiv~d~~~e~~Av---~EA~kl-~IPvIai-vDT-n~dp~----~idypIP~NDds~~ 209 (278)
.||+|+.+-|---..++ ++-..+ .+|++++ .|- .|.+. .+|+.+-++++..+
T Consensus 89 ~PD~IV~Thp~~~~~~l~~lk~~~~~~~~p~~tViTD~~~~H~~W~~~~~D~y~Va~ee~~~ 150 (169)
T pfam06925 89 QPDIIISTHPLPAAVPLSVLKSKGLLKRVLVVTVVTDFRTCHPFWLHPEIDRYYVPSKEVKK 150 (169)
T ss_pred CCCEEEECCHHHHHHHHHHHHHCCCCCCCCEEEEECCCCCCCCCCCCCCCCEEEECCHHHHH
T ss_conf 93999999762667899999983878899789998988666578168999989979999999
No 282
>PRK07053 glutamine amidotransferase; Provisional
Probab=28.72 E-value=26 Score=16.57 Aligned_cols=29 Identities=21% Similarity=0.313 Sum_probs=22.0
Q ss_pred HHHHHHHHHHHHHHHCCCCEEEEEECCHH
Q ss_conf 99999999999986107881699607823
Q gi|254780779|r 49 VPMLQKALQVISDTVARGGRILFVATKSQ 77 (278)
Q Consensus 49 ~~~L~~A~~~i~~i~~~gg~ILFVgTk~~ 77 (278)
..-|..-..+|++....+.-||=|+---|
T Consensus 66 ~Pwl~~e~~lIr~a~~~~~PvLGIClG~Q 94 (235)
T PRK07053 66 YPFLAPEIALLRQRLAAGLPTLGICLGAQ 94 (235)
T ss_pred CCCHHHHHHHHHHHHHCCCCEEEECHHHH
T ss_conf 85589999999999986998899847389
No 283
>COG0560 SerB Phosphoserine phosphatase [Amino acid transport and metabolism]
Probab=28.56 E-value=48 Score=14.83 Aligned_cols=46 Identities=24% Similarity=0.213 Sum_probs=33.7
Q ss_pred EEECC-CCCCHHHHHHHHCCCE---EEEECCCCCCCH---HCCCEEEECCCCH
Q ss_conf 99438-8771232123433981---454036776700---1152032157726
Q gi|254780779|r 163 FVVDT-NREKLAIQEARRLRIP---IVAVVDTNSNPD---LVDYVIPGNDDSS 208 (278)
Q Consensus 163 iv~d~-~~e~~Av~EA~kl~IP---vIaivDTn~dp~---~idypIP~NDds~ 208 (278)
.+++. .+......=+.++||+ ++|.-|+..|-. .+++||..|.+..
T Consensus 138 ~~~~~~~K~~~l~~~~~~~g~~~~~~~a~gDs~nDlpml~~ag~~ia~n~~~~ 190 (212)
T COG0560 138 PICDGEGKAKALRELAAELGIPLEETVAYGDSANDLPMLEAAGLPIAVNPKPK 190 (212)
T ss_pred EECCCCCHHHHHHHHHHHCCCCHHHEEEECCCHHHHHHHHHCCCCEEECCCHH
T ss_conf 55267228999999999809896447887375613999996799869897779
No 284
>TIGR01108 oadA oxaloacetate decarboxylase alpha subunit; InterPro: IPR005776 This family describes the bacterial oxaloacetate decarboxylase alpha subunit and its equivalents in archaea . The oxaloacetate decarboxylase Na+ pump is the paradigm of the family of Na+ transport decarboxylases that present in bacteria and archaea. It a multi subunit enzyme consisting of a peripheral alpha-subunit and integral membrane subunits beta and gamma. The energy released by the decarboxylation reaction of oxaloacetate is coupled to Na+ ion pumping across the membrane.; GO: 0008948 oxaloacetate decarboxylase activity, 0006814 sodium ion transport.
Probab=28.26 E-value=36 Score=15.60 Aligned_cols=58 Identities=19% Similarity=0.259 Sum_probs=30.8
Q ss_pred CCCCCCCCCCCCC-CEEE-ECHHHHHHHHHHHHHHHHHHHCCCCEEEEEECCHHHHHHHHHHHHH--CCCEECCCC----
Q ss_conf 7885621020018-8167-5389999999999999998610788169960782357999999863--398314233----
Q gi|254780779|r 26 NPKMERYIFCERN-NTHI-IDLSQTVPMLQKALQVISDTVARGGRILFVATKSQASDCVMEAAKR--SAQYCVNSK---- 97 (278)
Q Consensus 26 nPkM~~yI~g~rn-gihI-IdL~kT~~~L~~A~~~i~~i~~~gg~ILFVgTk~~~~~~i~~~A~~--~~~~yV~~R---- 97 (278)
||-.+--+|.-|. |-.- +|+ ..|+++..+.+++- ++++.. ..+.|...|
T Consensus 236 HPptE~lv~~L~~~gyD~gld~----~~L~~i~~YFr~VR-------------------kKY~~fle~~~~~~D~RiLv~ 292 (616)
T TIGR01108 236 HPPTETLVAALRGTGYDTGLDI----ELLLEIADYFRKVR-------------------KKYSQFLESQLKGPDSRILVS 292 (616)
T ss_pred CCHHHHHHHHHHCCCCCCHHHH----HHHHHHHHHHHHHH-------------------HHHHHHCCCCCCCCCCEEEEE
T ss_conf 8747999999705787431027----99999999999999-------------------999886076777888448997
Q ss_pred -CCCCCCCCH
Q ss_conf -458732342
Q gi|254780779|r 98 -WLGGMMTNW 106 (278)
Q Consensus 98 -WlGG~LTN~ 106 (278)
=-||||||+
T Consensus 293 QvPGGM~SNL 302 (616)
T TIGR01108 293 QVPGGMLSNL 302 (616)
T ss_pred ECCCHHHHHH
T ss_conf 3688068899
No 285
>PRK05670 anthranilate synthase component II; Provisional
Probab=28.06 E-value=49 Score=14.78 Aligned_cols=31 Identities=19% Similarity=0.298 Sum_probs=18.1
Q ss_pred CCEEEEEC-C---CC--CCHHHHHHHHCCCEEEEECC
Q ss_conf 95799943-8---87--71232123433981454036
Q gi|254780779|r 159 PDLMFVVD-T---NR--EKLAIQEARRLRIPIVAVVD 189 (278)
Q Consensus 159 P~~iiv~d-~---~~--e~~Av~EA~kl~IPvIaivD 189 (278)
||.||+.. | .. ....+-+....+||+.|||=
T Consensus 44 pdgiiLS~GPg~P~~~~~~~~~i~~~~~~iPiLGICl 80 (192)
T PRK05670 44 PDAIVLSPGPGTPAEAGISLELIREFAGKVPILGVCL 80 (192)
T ss_pred CCEEEECCCCCCHHHCCCHHHHHHHHCCCCCEEEEEH
T ss_conf 8989999999993660554999997346997899847
No 286
>cd06332 PBP1_aromatic_compounds_like Type I periplasmic binding proteins of active transport systems that are predicted to be involved in transport of aromatic compounds such as 2-nitrobenzoic acid and alkylbenzenes. This group includes the type I periplasmic binding proteins of active transport systems that are predicted to be involved in transport of aromatic compounds such as 2-nitrobenzoic acid and alkylbenzenes; their substrate specificities are not well characterized, however. Members also exhibit close similarity to active transport systems for short chain amides and/or urea found in bacteria and archaea.
Probab=28.06 E-value=49 Score=14.78 Aligned_cols=30 Identities=17% Similarity=0.308 Sum_probs=20.8
Q ss_pred CCCEEEEECCCCCCH-HHHHHHHCCC----EEEEE
Q ss_conf 595799943887712-3212343398----14540
Q gi|254780779|r 158 LPDLMFVVDTNREKL-AIQEARRLRI----PIVAV 187 (278)
Q Consensus 158 lP~~iiv~d~~~e~~-Av~EA~kl~I----PvIai 187 (278)
-||+||+..+..+.. .+++++.+|+ |+++-
T Consensus 186 ~pD~v~~~~~~~~~~~~~~q~~~~g~~~~~~~~~~ 220 (333)
T cd06332 186 KPDAVFVFLPGGMAVNFVKQYDQAGLKKKIPLYGP 220 (333)
T ss_pred CCCEEEEECCCHHHHHHHHHHHHCCCCCCCCEEEE
T ss_conf 97999993575379999999997499878618986
No 287
>PRK07226 fructose-bisphosphate aldolase; Provisional
Probab=27.90 E-value=30 Score=16.18 Aligned_cols=16 Identities=19% Similarity=0.488 Sum_probs=12.7
Q ss_pred HHHHHHHCCCEEEEEC
Q ss_conf 3212343398145403
Q gi|254780779|r 173 AIQEARRLRIPIVAVV 188 (278)
Q Consensus 173 Av~EA~kl~IPvIaiv 188 (278)
.+.||.+.|+|+++.+
T Consensus 131 l~~ea~~~GlPll~~~ 146 (266)
T PRK07226 131 IARECEEWGMPLLAMM 146 (266)
T ss_pred HHHHHHHHCCCEEEEE
T ss_conf 9999998599569997
No 288
>cd06334 PBP1_ABC_ligand_binding_like_1 Type I periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type active transport systems that are predicted to be involved in transport of amino acids, peptides, or inorganic ions. This subgroup includes the type I periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type active transport systems that are predicted to be involved in transport of amino acids, peptides, or inorganic ions. Members of this group are sequence-similar to members of the family of ABC-type hydrophobic amino acid transporters, such as leucine-isoleucine-valine-binding protein (LIVBP); however their ligand specificity has not been determined experimentally.
Probab=27.79 E-value=49 Score=14.75 Aligned_cols=43 Identities=5% Similarity=0.128 Sum_probs=26.5
Q ss_pred HHHHHHHHHHHCCCCEEEEEECCHHHHHHHHHHHHHCCCEECC
Q ss_conf 9999999986107881699607823579999998633983142
Q gi|254780779|r 53 QKALQVISDTVARGGRILFVATKSQASDCVMEAAKRSAQYCVN 95 (278)
Q Consensus 53 ~~A~~~i~~i~~~gg~ILFVgTk~~~~~~i~~~A~~~~~~yV~ 95 (278)
.+|....++++.+.+-+.++|........+...+.+.+.|++.
T Consensus 53 ~~a~~~a~kLi~~d~V~~i~g~~s~~~~A~~~~~~~~~vp~i~ 95 (351)
T cd06334 53 PRGVECYERLKGEDGAVAFQGWSTGITEALIPKIAADKIPLMS 95 (351)
T ss_pred HHHHHHHHHHHHCCCEEEECCCCCHHHHHHHHHHHHHCCCEEE
T ss_conf 9999999999853982665688867899999999981992895
No 289
>cd00223 TOPRIM_TopoIIB_SPO TOPRIM_TopoIIB_SPO: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the type found in the type IIB family of DNA topoisomerases and Spo11. This subgroup contains proteins similar to Sulfolobus shibatae topoisomerase VI (TopoVI) and Saccharomyces cerevisiae meiotic recombination factor: Spo11. Type II DNA topoisomerases catalyze the ATP-dependent transport of one DNA duplex through another, in the process generating transient double strand breaks via covalent attachments to both DNA strands at the 5' positions. TopoVI enzymes are heterotetramers found in archaea and plants. Spo11 plays a role in generating the double strand breaks that initiate homologous recombination during meiosis. S. shibatae TopoVI relaxes both positive and negative supercoils, and in addition has a strong decatenase activity. The TOPRIM domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspart
Probab=27.77 E-value=28 Score=16.29 Aligned_cols=17 Identities=29% Similarity=0.624 Sum_probs=9.7
Q ss_pred CCCEEEEECCCCCCCHHCC
Q ss_conf 3981454036776700115
Q gi|254780779|r 180 LRIPIVAVVDTNSNPDLVD 198 (278)
Q Consensus 180 l~IPvIaivDTn~dp~~id 198 (278)
+++|+.+++| +||.+++
T Consensus 50 ~~lpv~~l~D--~DP~Gi~ 66 (160)
T cd00223 50 LDLPVYILVD--GDPYGIS 66 (160)
T ss_pred HCCCEEEEEC--CCCCCEE
T ss_conf 7898899975--8866106
No 290
>PRK11382 frlB fructoselysine-6-P-deglycase; Provisional
Probab=27.76 E-value=49 Score=14.74 Aligned_cols=53 Identities=17% Similarity=0.162 Sum_probs=37.7
Q ss_pred EEEEECCCCC----CHHHHHHHHCCCEEEEECCCCCCC--HHCCCEEEECCCCHHHHHH
Q ss_conf 7999438877----123212343398145403677670--0115203215772689999
Q gi|254780779|r 161 LMFVVDTNRE----KLAIQEARRLRIPIVAVVDTNSNP--DLVDYVIPGNDDSSRSIAL 213 (278)
Q Consensus 161 ~iiv~d~~~e----~~Av~EA~kl~IPvIaivDTn~dp--~~idypIP~NDds~~si~l 213 (278)
++|.+.+..| --|++.|++.|.++++|++.-..| ...|+.|+.+-....++..
T Consensus 102 lvI~ISQSGETaDtl~Al~~ak~~Ga~tiaitN~~~S~i~r~ad~~i~~~a~~~~~v~~ 160 (347)
T PRK11382 102 AVIGVSDYGKTEEVIKALELGRACGALTAAFTKRADSPITSAAEFSIDYQADCIWEIHL 160 (347)
T ss_pred EEEEEECCCCHHHHHHHHHHHHHCCCCEEEEECCCCCHHHHCCCHHHHHCCCHHHHHHH
T ss_conf 99999368472999999999998699679986799888887476247544667999999
No 291
>COG2093 DNA-directed RNA polymerase, subunit E'' [Transcription]
Probab=27.74 E-value=30 Score=16.16 Aligned_cols=24 Identities=29% Similarity=0.581 Sum_probs=18.5
Q ss_pred CCEEEEECCCCCCHHHHHHHHCCCEEEE
Q ss_conf 9579994388771232123433981454
Q gi|254780779|r 159 PDLMFVVDTNREKLAIQEARRLRIPIVA 186 (278)
Q Consensus 159 P~~iiv~d~~~e~~Av~EA~kl~IPvIa 186 (278)
-++++|+||.+..| |++|||++-|
T Consensus 34 ~G~~iIidpe~SeI----Akrlgi~~Pg 57 (64)
T COG2093 34 FGLLIIIDPEKSEI----AKRLGIKIPG 57 (64)
T ss_pred CCEEEEECCCHHHH----HHHHCCCCCC
T ss_conf 62799976717789----9995899875
No 292
>PRK09922 UDP-D-galactose:(glucosyl)lipopolysaccharide-1,6-D-galactosyltransferase; Provisional
Probab=27.54 E-value=50 Score=14.72 Aligned_cols=58 Identities=14% Similarity=0.281 Sum_probs=33.6
Q ss_pred EEEEECCCCC--CHHHHHHHHCCCEEEEECCCCCCCH-HC-----CCEEEECCCCHHHHHHHHHHHHH
Q ss_conf 7999438877--1232123433981454036776700-11-----52032157726899999999999
Q gi|254780779|r 161 LMFVVDTNRE--KLAIQEARRLRIPIVAVVDTNSNPD-LV-----DYVIPGNDDSSRSIALFCDLVAS 220 (278)
Q Consensus 161 ~iiv~d~~~e--~~Av~EA~kl~IPvIaivDTn~dp~-~i-----dypIP~NDds~~si~l~~~~i~~ 220 (278)
-+||+--..| .+++-||..+|.|||+ .|+-+-|. .| -|-+|-|| .-.-.+-+..++.+
T Consensus 261 difVl~S~~EGfp~vllEAma~G~PvIa-td~~~G~~EiI~dg~nG~Lv~~~d-~~~la~~i~~li~~ 326 (361)
T PRK09922 261 SALLLTSKFEGFPMTLLEAMSYGIPCIS-SDCMSGPRDIIKPGLNGELYTPGN-IDEFVGKLNKVISG 326 (361)
T ss_pred CEEEECCCCCCCCCHHHHHHHHCCCEEE-ECCCCCCHHHHCCCCCEEEECCCC-HHHHHHHHHHHHHC
T ss_conf 4999647556887289999995998999-759999088715898379977999-99999999999848
No 293
>PRK10401 DNA-binding transcriptional regulator GalS; Provisional
Probab=27.53 E-value=50 Score=14.72 Aligned_cols=63 Identities=16% Similarity=0.117 Sum_probs=42.5
Q ss_pred CCCCCEEEEECCCCCCHHHHHHHHCCCE------EEEECCCC----CCCHHCCCEEEECCCCHHHHHHHHHHH
Q ss_conf 1359579994388771232123433981------45403677----670011520321577268999999999
Q gi|254780779|r 156 GGLPDLMFVVDTNREKLAIQEARRLRIP------IVAVVDTN----SNPDLVDYVIPGNDDSSRSIALFCDLV 218 (278)
Q Consensus 156 ~~lP~~iiv~d~~~e~~Av~EA~kl~IP------vIaivDTn----~dp~~idypIP~NDds~~si~l~~~~i 218 (278)
...|+++|+.+-.-=.-+++.++.+||- |||+=|+. +.|.+-+.-.|.-.=+..++++++..+
T Consensus 235 ~~~~tAi~~~nD~~A~g~l~al~~~Gl~VP~DisViGfDd~~~a~~~~P~LTTV~~p~~~mg~~Av~lLl~~i 307 (346)
T PRK10401 235 NLQLTAVFAYNDNMAAGALTALKDNGIAIPLHLSIIGFDDIPIARYTDPQLTTVRYPIASMAKLATELALQGA 307 (346)
T ss_pred CCCCCCCEECCHHHHHHHHHHHHHCCCCCCCCEEEEEECCHHHHHCCCCCCCEEECCHHHHHHHHHHHHHHHH
T ss_conf 9998861444889999999999985998998728999898089852899987696099999999999999985
No 294
>cd01968 Nitrogenase_NifE_I Nitrogenase_NifE_I: a subgroup of the NifE subunit of the NifEN complex: NifE forms an alpha2beta2 tetramer with NifN. NifE and NifN are structurally homologous to nitrogenase MoFe protein alpha and beta subunits respectively. NifEN participates in the synthesis of the iron-molybdenum cofactor (FeMoco) of the MoFe protein. NifB-co (an iron and sulfur containing precursor of the FeMoco) from NifB is transferred to the NifEN complex where it is further processed to FeMoco. The NifEN bound precursor of FeMoco has been identified as a molybdenum-free, iron- and sulfur- containing analog of FeMoco. It has been suggested that this NifEN bound precursor also acts as a cofactor precursor in nitrogenase systems which require a cofactor other than FeMoco: i.e. iron-vanadium cofactor (FeVco) or iron only cofactor (FeFeco).
Probab=27.42 E-value=50 Score=14.71 Aligned_cols=32 Identities=9% Similarity=0.093 Sum_probs=12.6
Q ss_pred EEEECCCCCCHHHHHHHHCCCEEEEECCCCCC
Q ss_conf 99943887712321234339814540367767
Q gi|254780779|r 162 MFVVDTNREKLAIQEARRLRIPIVAVVDTNSN 193 (278)
Q Consensus 162 iiv~d~~~e~~Av~EA~kl~IPvIaivDTn~d 193 (278)
.+..|+..-....+-+.-||+-+++....+.+
T Consensus 291 ai~~~~~~~~~l~~~l~ElGm~vv~~~~~~~~ 322 (410)
T cd01968 291 ALYTGGVKSWSLVSALQDLGMEVVATGTQKGT 322 (410)
T ss_pred EEECCCHHHHHHHHHHHHCCCEEEEEECCCCC
T ss_conf 99648468899999999779989998157898
No 295
>TIGR00083 ribF riboflavin biosynthesis protein RibF; InterPro: IPR002606 Riboflavin is converted into catalytically active cofactors (FAD and FMN) by the actions of riboflavin kinase (2.7.1.26 from EC), which converts it into FMN, and FAD synthetase (2.7.7.2 from EC), which adenylates FMN to FAD. Eukaryotes usually have two separate enzymes, while most prokaryotes have a single bifunctional protein that can carry out both catalyses, although exceptions occur in both cases. While eukaryotic monofunctional riboflavin kinase is orthologous to the bifunctional prokaryotic enzyme , the monofunctional FAD synthetase differs from its prokaryotic counterpart, and is instead related to the PAPS-reductase family . The bacterial FAD synthetase that is part of the bifunctional enzyme has remote similarity to nucleotidyl transferases and, hence, it may be involved in the adenylylation reaction of FAD synthetases . This entry represents the bifunctional enzyme, FAD synthetase / riboflavin kinase.; GO: 0003919 FMN adenylyltransferase activity, 0008531 riboflavin kinase activity, 0009231 riboflavin biosynthetic process.
Probab=27.16 E-value=13 Score=18.53 Aligned_cols=61 Identities=18% Similarity=0.218 Sum_probs=32.9
Q ss_pred CCCCCCC-----CC------CCC-CCC------CCCCC--CCCCCEEEECHHHHHHHHHH-------------------H
Q ss_conf 8860754-----77------657-885------62102--00188167538999999999-------------------9
Q gi|254780779|r 15 GVQFGHR-----NF------LWN-PKM------ERYIF--CERNNTHIIDLSQTVPMLQK-------------------A 55 (278)
Q Consensus 15 g~H~Gh~-----~~------~wn-PkM------~~yI~--g~rngihIIdL~kT~~~L~~-------------------A 55 (278)
|+|.||| .+ ..+ |.| .|+-+ +...+..++-|+.=...+.. |
T Consensus 9 GlH~GHq~l~~~~~df~~A~e~~L~~avllf~~~P~~~~~~~~~P~rL~pL~~k~~~~~~~~~~~~~v~~Fd~~~a~l~A 88 (296)
T TIGR00083 9 GLHLGHQALLQELKDFQKAEEKGLPVAVLLFEPHPSEQFSGLKAPARLTPLEEKARQLEALGVEVLVVVKFDEEFANLSA 88 (296)
T ss_pred CCCHHHHHHHHHHHHHHHHHHCCCCEEEEEECCCCHHHHCCCCCCCCCCCCHHHHHHHHHHCCCEEEEEECCHHHHHCCH
T ss_conf 52368999998635567687619947999862887344046678864568489999999853773899962357652486
Q ss_pred HHHHHHHHCC--CCEEEEEECC
Q ss_conf 9999986107--8816996078
Q gi|254780779|r 56 LQVISDTVAR--GGRILFVATK 75 (278)
Q Consensus 56 ~~~i~~i~~~--gg~ILFVgTk 75 (278)
..|+..+..+ .=..|.||+-
T Consensus 89 ~~F~~~~~~~~L~~~~l~VG~D 110 (296)
T TIGR00083 89 KQFIDQLLVKHLRVKFLVVGDD 110 (296)
T ss_pred HHHHHHHHHCCCCCCEEEECCC
T ss_conf 5558987432677568886166
No 296
>PRK10530 phosphotransferase; Provisional
Probab=27.02 E-value=51 Score=14.66 Aligned_cols=41 Identities=10% Similarity=0.059 Sum_probs=25.9
Q ss_pred CCCCCEEEEECCCCC-CHHHHH-HHHCCCE---EEEECCCCCCCHH
Q ss_conf 135957999438877-123212-3433981---4540367767001
Q gi|254780779|r 156 GGLPDLMFVVDTNRE-KLAIQE-ARRLRIP---IVAVVDTNSNPDL 196 (278)
Q Consensus 156 ~~lP~~iiv~d~~~e-~~Av~E-A~kl~IP---vIaivDTn~dp~~ 196 (278)
...|+.+=|+.+.-+ -.|+++ |..+||+ |+|+-|...|-+.
T Consensus 185 ~s~~~~lei~~~g~sKg~al~~l~~~~gi~~~~viafGD~~NDl~M 230 (272)
T PRK10530 185 WSWHDQVDIARKGNSKGKRLTQWVEAQGWSMENVVAFGDNFNDISM 230 (272)
T ss_pred ECCCCCEEEECCCCCHHHHHHHHHHHHCCCHHHEEEECCCHHHHHH
T ss_conf 6178707975799989999999999829898997987685666999
No 297
>PRK08760 replicative DNA helicase; Provisional
Probab=27.02 E-value=51 Score=14.66 Aligned_cols=157 Identities=18% Similarity=0.249 Sum_probs=77.6
Q ss_pred CCCCCCCC-EEEEC----HHHHHHHHHHHHHHHHHHHCCCCEEEEEECCHHHHHHHHHH-HHHCCCEECCCCCCCCCCC-
Q ss_conf 10200188-16753----89999999999999998610788169960782357999999-8633983142334587323-
Q gi|254780779|r 32 YIFCERNN-THIID----LSQTVPMLQKALQVISDTVARGGRILFVATKSQASDCVMEA-AKRSAQYCVNSKWLGGMMT- 104 (278)
Q Consensus 32 yI~g~rng-ihIId----L~kT~~~L~~A~~~i~~i~~~gg~ILFVgTk~~~~~~i~~~-A~~~~~~yV~~RWlGG~LT- 104 (278)
++-|.+.| +.||= .-||...|..|.+... ..++.|+|...--...+++... |..++.+ .+++-.|.|+
T Consensus 222 ~t~Gl~~G~LiViaaRPsmGKTalalnia~~~A~---~~~~~V~~fSLEMs~~ql~~Rlls~~s~v~--~~~i~~g~l~~ 296 (476)
T PRK08760 222 MTAGLQPTDLIILAARPAMGKTTFALNIAEYAAI---KSKKGVAVFSMEMSASQLAMRLISSNGRIN--AQRLRTGALED 296 (476)
T ss_pred HHCCCCCCCEEEEEECCCCCHHHHHHHHHHHHHH---HCCCCEEEEECCCCHHHHHHHHHHHHCCCC--HHHHHCCCCCH
T ss_conf 4469987777999877887478999999999998---379978997036999999999999833897--67776489999
Q ss_pred -CHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCEEEEEC-------CC-C--CCHH
Q ss_conf -42666555677899887630121267746788766556777643443322113595799943-------88-7--7123
Q gi|254780779|r 105 -NWKTVSQSIQKLRDLEELLNKENQGFTKKERLNIERKRDKLKRALDGIRDMGGLPDLMFVVD-------TN-R--EKLA 173 (278)
Q Consensus 105 -N~~ti~~si~~l~~l~~~~~~~~~~~tkKe~~~~~r~~~kl~k~lgGi~~m~~lP~~iiv~d-------~~-~--e~~A 173 (278)
.|..+...+.++.++.-..+ .-..+|--+.-. +..++.+.. | +++|| +| +. . ....
T Consensus 297 ~e~~~~~~a~~~l~~~~l~id-D~~~~t~~~ir~---~~R~~k~~~-~-------l~lvv-IDYLqL~~~~~~~~~r~~~ 363 (476)
T PRK08760 297 EDWARVTGAIKMLKETKIFID-DTPGVSPEVLRS---KCRRLKREH-D-------LGLIV-IDYLQLMSVPGNSENRATE 363 (476)
T ss_pred HHHHHHHHHHHHHHHCCCEEE-CCCCCCHHHHHH---HHHHHHHHC-C-------CCEEE-EEHHHHCCCCCCCCCHHHH
T ss_conf 999999999999860881685-799999999999---999998727-9-------98799-9707641588887448899
Q ss_pred HHH--------HHHCCCEEEEECCCCCCCHHCCCEEEECCC
Q ss_conf 212--------343398145403677670011520321577
Q gi|254780779|r 174 IQE--------ARRLRIPIVAVVDTNSNPDLVDYVIPGNDD 206 (278)
Q Consensus 174 v~E--------A~kl~IPvIaivDTn~dp~~idypIP~NDd 206 (278)
|.| |+.|+||||+++-=|=..+.=.=.-|.--|
T Consensus 364 v~~isr~lK~lAkel~vpVi~LsQLnR~~e~R~dkrP~lsD 404 (476)
T PRK08760 364 ISEISRSLKGLAKELNVPVIALSQLNRSLETRTDKRPVMAD 404 (476)
T ss_pred HHHHHHHHHHHHHHHCCCEEEECCCCCCCCCCCCCCCCCCC
T ss_conf 99999999999999799789963157663447999986001
No 298
>PRK02231 ppnK inorganic polyphosphate/ATP-NAD kinase; Provisional
Probab=26.99 E-value=51 Score=14.66 Aligned_cols=70 Identities=7% Similarity=0.022 Sum_probs=27.3
Q ss_pred CCCCEEEECHHHHHHHHHHHHH---HHHHHHCCCCEEEEEECCHHHHHHHHHHHHHCCCEECCCC-CCCCCCCCH
Q ss_conf 0188167538999999999999---9998610788169960782357999999863398314233-458732342
Q gi|254780779|r 36 ERNNTHIIDLSQTVPMLQKALQ---VISDTVARGGRILFVATKSQASDCVMEAAKRSAQYCVNSK-WLGGMMTNW 106 (278)
Q Consensus 36 ~rngihIIdL~kT~~~L~~A~~---~i~~i~~~gg~ILFVgTk~~~~~~i~~~A~~~~~~yV~~R-WlGG~LTN~ 106 (278)
...|++++=-..+...|..+-. -+.++..+---++-+|--=..=...+.++ ..+.|.+--. =-=|.||.+
T Consensus 10 ~~~g~~v~l~~~~a~~l~~~~~~~~~~~e~~~~~Dlii~iGGDGT~L~a~r~~~-~~~iPilGiN~G~lGFL~~~ 83 (272)
T PRK02231 10 MERGYQVLVEKEVGETLELSFNHLASLEEIGQRAQLAIVIGGDGNMLGRARVLA-KYDIPLIGINRGNLGFLTDI 83 (272)
T ss_pred HHCCCEEEEEHHHHHHCCCCCCCCCCHHHHCCCCCEEEEECCCHHHHHHHHHHH-CCCCCEEEECCCCCEEEECC
T ss_conf 978999999779987649986664798897017789999787589999999860-05997896537886274225
No 299
>cd06282 PBP1_GntR_like_2 Ligand-binding domain of putative DNA transcription repressors highly similar to that of the repressor specific for gluconate (GntR) which is a member of the LacI-GalR family of bacterial transcription regulators. This group includes the ligand-binding domain of putative DNA transcription repressors highly similar to that of the repressor specific for gluconate (GntR) which is a member of the LacI-GalR family of bacterial transcription regulators. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding
Probab=26.73 E-value=51 Score=14.63 Aligned_cols=62 Identities=18% Similarity=0.261 Sum_probs=36.7
Q ss_pred CCCCEEEEECCCCCCHHHHHHHHCCCE------EEEECCCC----CCCHHCCCEEEECCCCHHHHHHHHHHH
Q ss_conf 359579994388771232123433981------45403677----670011520321577268999999999
Q gi|254780779|r 157 GLPDLMFVVDTNREKLAIQEARRLRIP------IVAVVDTN----SNPDLVDYVIPGNDDSSRSIALFCDLV 218 (278)
Q Consensus 157 ~lP~~iiv~d~~~e~~Av~EA~kl~IP------vIaivDTn----~dp~~idypIP~NDds~~si~l~~~~i 218 (278)
..|++||+.+-.--.-+++.++..|+. |+|+=|+. ++|.+-+.-.|.-.=+..++++++..|
T Consensus 175 ~~~~ai~~~nD~~A~g~l~al~~~g~~vP~disIigfd~~~~~~~~~P~lTti~q~~~~~g~~A~~~l~~~i 246 (266)
T cd06282 175 PAPTAIFCSNDLLALAVIRALRRLGLRVPDDLSVVGFDGIAIGRLLTPPLATVAQPNRDIGRQAVQRLLARI 246 (266)
T ss_pred CCCCEEEECCCHHHHHHHHHHHHCCCCCCCCEEEEEECCHHHHHCCCCCCEEEECCHHHHHHHHHHHHHHHH
T ss_conf 998479853888999999999984999999849999897089970799967998699999999999999997
No 300
>pfam04493 Endonuclease_5 Endonuclease V. Endonuclease V is specific for single-stranded DNA or for duplex DNA that contains uracil or that is damaged by a variety of agents.
Probab=26.46 E-value=39 Score=15.40 Aligned_cols=36 Identities=25% Similarity=0.328 Sum_probs=27.1
Q ss_pred HCCCCCEEEEEC-----CCCCCHHHHHHHHCCCEEEEECCC
Q ss_conf 113595799943-----887712321234339814540367
Q gi|254780779|r 155 MGGLPDLMFVVD-----TNREKLAIQEARRLRIPIVAVVDT 190 (278)
Q Consensus 155 m~~lP~~iiv~d-----~~~e~~Av~EA~kl~IPvIaivDT 190 (278)
+...||+++|=. |..=-+|-.=.-.+++|+||+.-+
T Consensus 85 L~~~PDvllvDG~Gi~HPR~~GlAsHlGV~l~~PTIGVAK~ 125 (205)
T pfam04493 85 LYDEPDVLLVDGNGIAHPRRFGLATHAGVLLDKPTIGVAKK 125 (205)
T ss_pred CCCCCCEEEECCCCCCCCCCCCHHEEEEEECCCCCCCCCCC
T ss_conf 57799999987876437624260103566528783230143
No 301
>PRK02769 histidine decarboxylase; Provisional
Probab=26.10 E-value=53 Score=14.55 Aligned_cols=14 Identities=14% Similarity=0.036 Sum_probs=5.2
Q ss_pred HHHHHHHHHHHHHH
Q ss_conf 89999999999999
Q gi|254780779|r 45 LSQTVPMLQKALQV 58 (278)
Q Consensus 45 L~kT~~~L~~A~~~ 58 (278)
.+.+-.++.+|+.+
T Consensus 116 Se~aHYSi~Kaa~l 129 (380)
T PRK02769 116 SKDTHYSVSKIARL 129 (380)
T ss_pred CCCCHHHHHHHHHH
T ss_conf 67322779999998
No 302
>COG3384 Aromatic ring-opening dioxygenase, catalytic LigB subunit related enzyme [Amino acid transport and metabolism]
Probab=25.71 E-value=54 Score=14.51 Aligned_cols=40 Identities=8% Similarity=0.077 Sum_probs=28.8
Q ss_pred CCCCCEEEECHHHHHHHHHHHHHHHHHHHCCCCEEEEEECCH
Q ss_conf 001881675389999999999999998610788169960782
Q gi|254780779|r 35 CERNNTHIIDLSQTVPMLQKALQVISDTVARGGRILFVATKS 76 (278)
Q Consensus 35 g~rngihIIdL~kT~~~L~~A~~~i~~i~~~gg~ILFVgTk~ 76 (278)
+.--+.++++.......+++--+.+.+ .....|+.|.+.=
T Consensus 15 shgsP~~~~~~n~~~~~l~~lG~~~~e--~rp~tIiV~SaHw 54 (268)
T COG3384 15 SHGSPMLALEDNAATRGLRELGRELPE--LRPDTIIVFSAHW 54 (268)
T ss_pred CCCCCCCCCCCCHHHHHHHHHHHHHHH--CCCCEEEEEECEE
T ss_conf 289812236840789999999776566--0898799983507
No 303
>cd01541 PBP1_AraR Ligand-binding domain of DNA transcription repressor specific for arabinose (AraR) which is a member of the LacI-GalR family of bacterial transcription regulators. Ligand-binding domain of DNA transcription repressor specific for arabinose (AraR) which is a member of the LacI-GalR family of bacterial transcription regulators. The ligand-binding domain of AraR is structurally homologous to the periplasmic sugar-binding domain of ABC-type transporters and both domains contain the type I periplasmic binding protein-like fold. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the type I periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which i
Probab=25.69 E-value=54 Score=14.51 Aligned_cols=63 Identities=13% Similarity=0.191 Sum_probs=41.0
Q ss_pred CCCCCEEEEECCCCCCHHHHHHHHCCCE------EEEECCC----CCCCHHCCCEEEECCCCHHHHHHHHHHH
Q ss_conf 1359579994388771232123433981------4540367----7670011520321577268999999999
Q gi|254780779|r 156 GGLPDLMFVVDTNREKLAIQEARRLRIP------IVAVVDT----NSNPDLVDYVIPGNDDSSRSIALFCDLV 218 (278)
Q Consensus 156 ~~lP~~iiv~d~~~e~~Av~EA~kl~IP------vIaivDT----n~dp~~idypIP~NDds~~si~l~~~~i 218 (278)
...|++||+.+-.--.-+++.+..+|+- +||+=|+ -+.|.+-+.-.|.-+=+.+++++++..|
T Consensus 181 ~~~~~av~~~~D~~A~g~~~~l~~~g~~vP~dvsIigfd~~~~~~~~~P~LTti~~~~~~~g~~A~~~L~~~i 253 (273)
T cd01541 181 PERPTAIVCYNDEIALRVIDLLKELGLKIPEDISVVGFDDSYLSVASEVKLTTVTHPKEQMGEDAAKMILKMI 253 (273)
T ss_pred CCCCCEEEECCHHHHHHHHHHHHHCCCCCCCCEEEEECCCHHHHHHCCCCEEEEEECHHHHHHHHHHHHHHHH
T ss_conf 9999569848889998899865314888887724761287788974389829999399999999999999997
No 304
>COG3193 GlcG Uncharacterized protein, possibly involved in utilization of glycolate and propanediol [General function prediction only]
Probab=25.65 E-value=43 Score=15.10 Aligned_cols=53 Identities=28% Similarity=0.271 Sum_probs=33.0
Q ss_pred CHHHHHHHHCCCEE-EEECCCCCCCHHCCCEEEECCCCHHHHHHHHHHHHHHHHHHH
Q ss_conf 12321234339814-540367767001152032157726899999999999999999
Q gi|254780779|r 171 KLAIQEARRLRIPI-VAVVDTNSNPDLVDYVIPGNDDSSRSIALFCDLVASAAIDGI 226 (278)
Q Consensus 171 ~~Av~EA~kl~IPv-IaivDTn~dp~~idypIP~NDds~~si~l~~~~i~~ai~~g~ 226 (278)
..|+.||++++.|+ |++||.+.++-- .+-..|-+.-|+++=...--.|+.-|+
T Consensus 18 ~aA~a~a~~~g~~VtvaVVD~~G~~~a---~~RmDga~~~s~eiA~~KA~tA~~~~~ 71 (141)
T COG3193 18 AAAVAEAQQLGVPVTVAVVDAGGHLVA---LERMDGASPLSAEIAFGKAYTAAALGR 71 (141)
T ss_pred HHHHHHHHHHCCCEEEEEECCCCCEEE---EEECCCCCCCCHHHHHHHHHHHHHHCC
T ss_conf 999999997398469999979997898---996489732305677778899998177
No 305
>TIGR01182 eda 2-dehydro-3-deoxyphosphogluconate aldolase/4-hydroxy-2-oxoglutarate aldolase; InterPro: IPR000887 4-Hydroxy-2-oxoglutarate aldolase (4.1.3.16 from EC) (KHG-aldolase) catalyzes the interconversion of 4-hydroxy-2-oxoglutarate into pyruvate and glyoxylate. Phospho-2-dehydro-3-deoxygluconate aldolase (4.1.2.14 from EC) (KDPG-aldolase) catalyzes the interconversion of 6-phospho-2-dehydro-3-deoxy-D-gluconate into pyruvate and glyceraldehyde 3-phosphate. These two enzymes are structurally and functionally related . They are both homotrimeric proteins of approximately 220 amino-acid residues. They are class I aldolases whose catalytic mechanism involves the formation of a Schiff-base intermediate between the substrate and the epsilon-amino group of a lysine residue. In both enzymes, an arginine is required for catalytic activity.; GO: 0003824 catalytic activity, 0008152 metabolic process.
Probab=25.46 E-value=54 Score=14.48 Aligned_cols=92 Identities=20% Similarity=0.253 Sum_probs=61.6
Q ss_pred HHHHHHHHHHHHHHHCCCCEEEEEECC-HHHHHHHHHHHHHCC-CEECCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHCC
Q ss_conf 999999999999861078816996078-235799999986339-831423345873234266655567789988763012
Q gi|254780779|r 49 VPMLQKALQVISDTVARGGRILFVATK-SQASDCVMEAAKRSA-QYCVNSKWLGGMMTNWKTVSQSIQKLRDLEELLNKE 126 (278)
Q Consensus 49 ~~~L~~A~~~i~~i~~~gg~ILFVgTk-~~~~~~i~~~A~~~~-~~yV~~RWlGG~LTN~~ti~~si~~l~~l~~~~~~~ 126 (278)
...+..|+...+.++..|=+++=|-=+ +++.+.|+..++++- ---| =-||.+|-.+..+..
T Consensus 16 ~~~~~~A~~lA~aL~egG~~~~EvTlRT~~A~~aI~~l~~~~P~~~~i----GAGTVL~~~Q~~~A~------------- 78 (205)
T TIGR01182 16 IDDVEDALPLAKALIEGGLRVLEVTLRTPVALEAIRALRKEVPKDALI----GAGTVLNPEQLRQAV------------- 78 (205)
T ss_pred ECCHHHHHHHHHHHHHCCCEEEEEEECCCCHHHHHHHHHHHCCCCCEE----CCCCCCCHHHHHHHH-------------
T ss_conf 267877789999998679808988514721689999999728233487----167648989999999-------------
Q ss_pred CCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCEEEEECCCCCCHHHHHHHHCCCEEEEEC
Q ss_conf 12677467887665567776434433221135957999438877123212343398145403
Q gi|254780779|r 127 NQGFTKKERLNIERKRDKLKRALDGIRDMGGLPDLMFVVDTNREKLAIQEARRLRIPIVAVV 188 (278)
Q Consensus 127 ~~~~tkKe~~~~~r~~~kl~k~lgGi~~m~~lP~~iiv~d~~~e~~Av~EA~kl~IPvIaiv 188 (278)
-=.|-|++-|.-+.-.++=|...+||+|==|
T Consensus 79 -------------------------------~AGA~F~vSPG~~p~l~~~~~~~~~P~iPGV 109 (205)
T TIGR01182 79 -------------------------------AAGAQFIVSPGLTPELAKHAKDKGIPIIPGV 109 (205)
T ss_pred -------------------------------HCCCCEEECCCCCHHHHHHHHHCCCCEECCC
T ss_conf -------------------------------7089578769788899999850888121777
No 306
>pfam01973 MAF_flag10 Protein of unknown function DUF115. This family of archaebacterial proteins has no known function.
Probab=25.13 E-value=55 Score=14.44 Aligned_cols=85 Identities=20% Similarity=0.364 Sum_probs=47.1
Q ss_pred CCCCEEEEEECCHHHHHHHHHHHHHCCCEECCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHH
Q ss_conf 07881699607823579999998633983142334587323426665556778998876301212677467887665567
Q gi|254780779|r 64 ARGGRILFVATKSQASDCVMEAAKRSAQYCVNSKWLGGMMTNWKTVSQSIQKLRDLEELLNKENQGFTKKERLNIERKRD 143 (278)
Q Consensus 64 ~~gg~ILFVgTk~~~~~~i~~~A~~~~~~yV~~RWlGG~LTN~~ti~~si~~l~~l~~~~~~~~~~~tkKe~~~~~r~~~ 143 (278)
.+|..+++||.-|...+-+...-+.-+..++-- . | .++..|.+
T Consensus 22 ~~g~~~~IvgaGPSL~~~i~~Lk~~~~~~~iia-----~--~-----~a~~~L~~------------------------- 64 (169)
T pfam01973 22 KKGKPAIIVGAGPSLDKHLPLLKKNRDKAVIIA-----A--D-----SALKALLK------------------------- 64 (169)
T ss_pred HCCCEEEEECCCCCHHHHHHHHHHHCCCEEEEE-----E--C-----HHHHHHHH-------------------------
T ss_conf 489719999568998999999997169839999-----6--6-----79999997-------------------------
Q ss_pred HHHHHHHHHHHHCCCCCEEEEECCCCCC-HHHHHHHHC-CCEEEEECCCCCCCHHCC
Q ss_conf 7764344332211359579994388771-232123433-981454036776700115
Q gi|254780779|r 144 KLKRALDGIRDMGGLPDLMFVVDTNREK-LAIQEARRL-RIPIVAVVDTNSNPDLVD 198 (278)
Q Consensus 144 kl~k~lgGi~~m~~lP~~iiv~d~~~e~-~Av~EA~kl-~IPvIaivDTn~dp~~id 198 (278)
-||+ ||.++.+|+.... .++.|.... .+|.+. .+-++|..+.
T Consensus 65 ------~gI~-----Pd~~v~~D~~~~~~~~~~~~~~~~~~~lv~--~~~~~~~~~~ 108 (169)
T pfam01973 65 ------HGIK-----PDIVVSLDRQEISYEFFKEAFKEGDIPLVH--AHGVNPELLE 108 (169)
T ss_pred ------CCCC-----CEEEEEECCCHHHHHHHHHHCCCCCEEEEE--ECCCCHHHHH
T ss_conf ------7998-----149999748645699986431258848999--7887999998
No 307
>COG2072 TrkA Predicted flavoprotein involved in K+ transport [Inorganic ion transport and metabolism]
Probab=25.01 E-value=55 Score=14.42 Aligned_cols=44 Identities=20% Similarity=0.247 Sum_probs=34.6
Q ss_pred HHHHHHHHHHCCCCEEEEEECCHHHHHHHHHHHHHCCCEECCCC
Q ss_conf 99999998610788169960782357999999863398314233
Q gi|254780779|r 54 KALQVISDTVARGGRILFVATKSQASDCVMEAAKRSAQYCVNSK 97 (278)
Q Consensus 54 ~A~~~i~~i~~~gg~ILFVgTk~~~~~~i~~~A~~~~~~yV~~R 97 (278)
.+..+-......|++|+.||+.-.+.+++.+.++....-++..|
T Consensus 163 HS~~~~~~~~~~GKrV~VIG~GaSA~di~~~l~~~ga~vt~~qR 206 (443)
T COG2072 163 HSADWPNPEDLRGKRVLVIGAGASAVDIAPELAEVGASVTLSQR 206 (443)
T ss_pred CCCCCCCHHHCCCCEEEEECCCCCHHHHHHHHHHCCCEEEEEEC
T ss_conf 41016961342788799989870399999999730671789851
No 308
>LOAD_php consensus
Probab=24.76 E-value=39 Score=15.42 Aligned_cols=22 Identities=36% Similarity=0.493 Sum_probs=16.2
Q ss_pred CCHHHHHHHHCCCEEEEECCCC
Q ss_conf 7123212343398145403677
Q gi|254780779|r 170 EKLAIQEARRLRIPIVAVVDTN 191 (278)
Q Consensus 170 e~~Av~EA~kl~IPvIaivDTn 191 (278)
+..+++=|.+.|||+|+--|.-
T Consensus 177 ~~~l~~la~~~~lp~vat~Dvh 198 (206)
T LOAD_php 177 EEALLKLAEELGLPIVAGSDAH 198 (206)
T ss_pred HHHHHHHHHHHCCCEEEECCCC
T ss_conf 9999999998099999987125
No 309
>COG1518 CRISPR-associated protein Cas1 [Defense mechanisms]
Probab=24.70 E-value=56 Score=14.39 Aligned_cols=40 Identities=20% Similarity=0.019 Sum_probs=17.2
Q ss_pred CCCCCHHHHHHHHCCCEEEEECCCCCCCHHCCCEEEECCCC
Q ss_conf 88771232123433981454036776700115203215772
Q gi|254780779|r 167 TNREKLAIQEARRLRIPIVAVVDTNSNPDLVDYVIPGNDDS 207 (278)
Q Consensus 167 ~~~e~~Av~EA~kl~IPvIaivDTn~dp~~idypIP~NDds 207 (278)
+.-.+-||+++.+.|||++ +||.+.-|...=||-+++-.+
T Consensus 48 ~siSs~av~~la~~gI~i~-f~~~~G~~~g~~~p~~~~~~~ 87 (327)
T COG1518 48 TSISSAALRLLAKRGIPIV-FFDQYGFYLGRLSPREGLGSG 87 (327)
T ss_pred CCCCHHHHHHHHHCCCEEE-EECCCCCEEEEEECCCCCCCH
T ss_conf 7407999999997698699-988998587998064346639
No 310
>PRK00771 signal recognition particle protein Srp54; Provisional
Probab=24.55 E-value=56 Score=14.37 Aligned_cols=142 Identities=13% Similarity=0.173 Sum_probs=78.3
Q ss_pred CCCCCCCCCCCCCCEEEECH---HHHHHHHHHHHHHHHHHHCCCCEEEEEECC---HHHHHHHHHHHHHCCCEECCCCCC
Q ss_conf 78856210200188167538---999999999999999861078816996078---235799999986339831423345
Q gi|254780779|r 26 NPKMERYIFCERNNTHIIDL---SQTVPMLQKALQVISDTVARGGRILFVATK---SQASDCVMEAAKRSAQYCVNSKWL 99 (278)
Q Consensus 26 nPkM~~yI~g~rngihIIdL---~kT~~~L~~A~~~i~~i~~~gg~ILFVgTk---~~~~~~i~~~A~~~~~~yV~~RWl 99 (278)
+|..+|++.- ++-| -||-.+-+.|..| + .+|.+++.|++- +.|.+-++..|++.+.||....--
T Consensus 92 ~~~~kP~Vim------~vGlqGsGKTTT~aKLA~~~-k---k~g~kv~lvaaDt~RpaA~eQL~~la~~~~v~~~~~~~~ 161 (433)
T PRK00771 92 EILLKPQTIL------LVGLQGSGKTTTAAKLARYF-Q---KKGLKVGVICADTWRPGAYEQLKQLCEKINVPFYGDPKE 161 (433)
T ss_pred CCCCCCEEEE------EECCCCCCHHHHHHHHHHHH-H---HCCCCEEEEECCCCCHHHHHHHHHHHHHCCCCCCCCCCC
T ss_conf 5668985899------97378897899999999999-9---779946785067883689999999998638873178899
Q ss_pred CCCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCC-EEEEECCCCCCHHH--HH
Q ss_conf 8732342666555677899887630121267746788766556777643443322113595-79994388771232--12
Q gi|254780779|r 100 GGMMTNWKTVSQSIQKLRDLEELLNKENQGFTKKERLNIERKRDKLKRALDGIRDMGGLPD-LMFVVDTNREKLAI--QE 176 (278)
Q Consensus 100 GG~LTN~~ti~~si~~l~~l~~~~~~~~~~~tkKe~~~~~r~~~kl~k~lgGi~~m~~lP~-~iiv~d~~~e~~Av--~E 176 (278)
.. --...+..+.+.+.++-..-..-..+...+. +..|+.++.+.. . |+ .+||+|...-..|+ .+
T Consensus 162 ~d---p~~i~~~a~~~~k~~DvviiDTAGRl~~d~~--Lm~El~~i~~~~-------~-P~e~llV~Da~~GQ~a~~~a~ 228 (433)
T PRK00771 162 KD---AVKIVKEGLEKLKKVDVIIVDTAGRHKLEKD--LIEEMKQIKEIT-------K-PDEVILVIDATIGQQASEQAK 228 (433)
T ss_pred CC---HHHHHHHHHHHHCCCCEEEEECCCCCCCCHH--HHHHHHHHHHHH-------C-CCEEEEEEECCCCHHHHHHHH
T ss_conf 99---9999999999845698899977652104099--999999998775-------7-976899865442267899999
Q ss_pred HHHCCCEEEEECCC
Q ss_conf 34339814540367
Q gi|254780779|r 177 ARRLRIPIVAVVDT 190 (278)
Q Consensus 177 A~kl~IPvIaivDT 190 (278)
+..-.+|+=|++=|
T Consensus 229 ~F~~~~~i~gvIlT 242 (433)
T PRK00771 229 AFKEAVGIGGIIIT 242 (433)
T ss_pred HHHHHCCCCEEEEE
T ss_conf 99875388737997
No 311
>PRK10201 G/U mismatch-specific DNA glycosylase; Provisional
Probab=24.38 E-value=43 Score=15.11 Aligned_cols=31 Identities=16% Similarity=0.264 Sum_probs=23.1
Q ss_pred HHHHHCCCCEEEEEECCHHHHHHHHHHHHHCCCEECC
Q ss_conf 9986107881699607823579999998633983142
Q gi|254780779|r 59 ISDTVARGGRILFVATKSQASDCVMEAAKRSAQYCVN 95 (278)
Q Consensus 59 i~~i~~~gg~ILFVgTk~~~~~~i~~~A~~~~~~yV~ 95 (278)
+.++...|=+|||||++|. ..+...|.+|-+
T Consensus 2 lpD~l~p~L~vlF~GiNPg------l~Sa~~g~~fA~ 32 (168)
T PRK10201 2 VEDILAPGLRVVFCGINPG------LSSAGTGFPFAH 32 (168)
T ss_pred CCCCCCCCCEEEEEEECCC------HHHHHCCCCCCC
T ss_conf 8754589984899974978------888853987789
No 312
>cd01014 nicotinamidase_related Nicotinamidase_ related amidohydrolases. Cysteine hydrolases of unknown function that share the catalytic triad with other amidohydrolases, like nicotinamidase, which converts nicotinamide to nicotinic acid and ammonia.
Probab=24.38 E-value=57 Score=14.35 Aligned_cols=38 Identities=21% Similarity=0.264 Sum_probs=28.3
Q ss_pred CCEEEEECCCCC---CHHHHHHHHCCCEEEEECCCCCCCHH
Q ss_conf 957999438877---12321234339814540367767001
Q gi|254780779|r 159 PDLMFVVDTNRE---KLAIQEARRLRIPIVAVVDTNSNPDL 196 (278)
Q Consensus 159 P~~iiv~d~~~e---~~Av~EA~kl~IPvIaivDTn~dp~~ 196 (278)
-+-|+|.+...+ ...+++|..+|-.|+-+-|..+..+.
T Consensus 99 i~~lii~Gi~T~~CV~~Ta~da~~~Gy~v~vv~Da~a~~~~ 139 (155)
T cd01014 99 IDHLVICGAMTEMCVDTTVRSAFDLGYDVTVVADACATFDL 139 (155)
T ss_pred CCEEEEEEECCCHHHHHHHHHHHHCCCEEEEECCCCCCCCC
T ss_conf 97089987101679999999999889979995835458981
No 313
>PRK09293 fructose-1,6-bisphosphatase; Provisional
Probab=24.37 E-value=3.6 Score=22.08 Aligned_cols=63 Identities=21% Similarity=0.318 Sum_probs=39.0
Q ss_pred CCCCCCCCCC--CEEEECHHHHHHHHHHHHHHHHHHHCCCCEEEEE---EC-CH----------HHHHHHHHHHHHCCC
Q ss_conf 5621020018--8167538999999999999999861078816996---07-82----------357999999863398
Q gi|254780779|r 29 MERYIFCERN--NTHIIDLSQTVPMLQKALQVISDTVARGGRILFV---AT-KS----------QASDCVMEAAKRSAQ 91 (278)
Q Consensus 29 M~~yI~g~rn--gihIIdL~kT~~~L~~A~~~i~~i~~~gg~ILFV---gT-k~----------~~~~~i~~~A~~~~~ 91 (278)
+..||..... .-+==||..-+..|..||+.|...+++++..=.. |+ +- .+.+++.+....++.
T Consensus 6 l~~fl~~~~~~~~~~~~dl~~ll~~Ia~A~k~Is~~v~~~~l~~~~G~~g~~N~~Gd~QkkLDv~an~~~~~~L~~~~~ 84 (328)
T PRK09293 6 LSEFLVEQQAEFPNATGELTALISAIALAAKIISRAVNKGGLADILGAAGTENVQGETQKKLDVLANEILKEALKASGH 84 (328)
T ss_pred HHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHCCCC
T ss_conf 9999999863079985789999999999999999998522455655655672799648888999999999999860897
No 314
>PRK06393 rpoE DNA-directed RNA polymerase subunit E''; Validated
Probab=24.25 E-value=39 Score=15.37 Aligned_cols=23 Identities=13% Similarity=0.258 Sum_probs=17.5
Q ss_pred CCEEEEECCCCCCHHHHHHHHCCCEEE
Q ss_conf 957999438877123212343398145
Q gi|254780779|r 159 PDLMFVVDTNREKLAIQEARRLRIPIV 185 (278)
Q Consensus 159 P~~iiv~d~~~e~~Av~EA~kl~IPvI 185 (278)
-+.|+|+||.+..+ |.+|||..-
T Consensus 33 ~G~viI~dPe~SeI----Ak~lgI~~p 55 (64)
T PRK06393 33 FGFLIITEPEGSAI----AKRAGITEP 55 (64)
T ss_pred CEEEEEECCHHHHH----HHHHCCCCC
T ss_conf 64899978606089----998299988
No 315
>TIGR00959 ffh signal recognition particle protein; InterPro: IPR004780 The signal recognition particle (SRP) is a multimeric protein, which along with its conjugate receptor (SR), is involved in targeting secretory proteins to the rough endoplasmic reticulum (RER) membrane in eukaryotes, or to the plasma membrane in prokaryotes , . SRP recognises the signal sequence of the nascent polypeptide on the ribosome, retards its elongation, and docks the SRP-ribosome-polypeptide complex to the RER membrane via the SR receptor. SRP consists of six polypeptides (SRP9, SRP14, SRP19, SRP54, SRP68 and SRP72) and a single 300 nucleotide 7S RNA molecule. The RNA component catalyses the interaction of SRP with its SR receptor . In higher eukaryotes, the SRP complex consists of the Alu domain and the S domain linked by the SRP RNA. The Alu domain consists of a heterodimer of SRP9 and SRP14 bound to the 5' and 3' terminal sequences of SRP RNA. This domain is necessary for retarding the elongation of the nascent polypeptide chain, which gives SRP time to dock the ribosome-polypeptide complex to the RER membrane. This entry represents various SRP subunits.; GO: 0008312 7S RNA binding, 0006614 SRP-dependent cotranslational protein targeting to membrane, 0048500 signal recognition particle.
Probab=24.09 E-value=58 Score=14.31 Aligned_cols=132 Identities=16% Similarity=0.196 Sum_probs=81.0
Q ss_pred HHHHHHHHHHHHHHHHHHCCCCEEEEEECC---HHHHHHHHHHHHHCCCEECCCCCCCCCCC--CHHHHHHHHHHHHHHH
Q ss_conf 999999999999999861078816996078---23579999998633983142334587323--4266655567789988
Q gi|254780779|r 46 SQTVPMLQKALQVISDTVARGGRILFVATK---SQASDCVMEAAKRSAQYCVNSKWLGGMMT--NWKTVSQSIQKLRDLE 120 (278)
Q Consensus 46 ~kT~~~L~~A~~~i~~i~~~gg~ILFVgTk---~~~~~~i~~~A~~~~~~yV~~RWlGG~LT--N~~ti~~si~~l~~l~ 120 (278)
-||-.|=+.|+.++.+ .+|.++|.|++- |.|.+=.+..++.+|-|+..| --+|-=- =-.|.+..+.+.+.-.
T Consensus 114 GKTTt~gKLA~~ll~k--k~~~kvLLva~D~yRPAA~~QL~~Lg~Q~gVpvf~h-~~~~~~p~~Pv~ia~~Al~~Ak~~~ 190 (439)
T TIGR00959 114 GKTTTAGKLALYLLKK--KEGKKVLLVACDLYRPAAIEQLKVLGEQVGVPVFAH-LGKGQSPDDPVEIARQALEEAKENG 190 (439)
T ss_pred CHHHHHHHHHHHHHHH--HCCCCEEEEEHHCCCHHHHHHHHHHHHHCCCCCCCC-CCCCCCCCCHHHHHHHHHHHHHHCC
T ss_conf 5788999999999998--638970340321034789999999767528871100-4788898877899999999999748
Q ss_pred HH---HHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCEEEEECCCCCCHHHHHHHH--CCCEEEEECCC
Q ss_conf 76---301212677467887665567776434433221135957999438877123212343--39814540367
Q gi|254780779|r 121 EL---LNKENQGFTKKERLNIERKRDKLKRALDGIRDMGGLPDLMFVVDTNREKLAIQEARR--LRIPIVAVVDT 190 (278)
Q Consensus 121 ~~---~~~~~~~~tkKe~~~~~r~~~kl~k~lgGi~~m~~lP~~iiv~d~~~e~~Av~EA~k--l~IPvIaivDT 190 (278)
-. .| .-.-|.==| .+..|+.. ||.-...-..+||+|.-.-.-||+=|+. =++=+=|+|=|
T Consensus 191 ~D~vI~D-TAGRL~ID~--~LM~EL~~-------iK~~~nP~EiLlVvDaM~GQdAvn~A~~F~e~lgltG~vlt 255 (439)
T TIGR00959 191 FDVVIVD-TAGRLQIDE--ELMEELAE-------IKEILNPDEILLVVDAMTGQDAVNTAKTFNERLGLTGVVLT 255 (439)
T ss_pred CCEEEEE-CCCCHHHHH--HHHHHHHH-------HHHHHCCCEEEECCHHCCHHHHHHHHHHHCCCCCCCEEEEE
T ss_conf 9789972-675125559--99999999-------98886887054122010216999999863660013547885
No 316
>pfam01488 Shikimate_DH Shikimate / quinate 5-dehydrogenase. This family contains both shikimate and quinate dehydrogenases. Shikimate 5-dehydrogenase catalyses the conversion of shikimate to 5-dehydroshikimate. This reaction is part of the shikimate pathway which is involved in the biosynthesis of aromatic amino acids. Quinate 5-dehydrogenase catalyses the conversion of quinate to 5-dehydroquinate. This reaction is part of the quinate pathway where quinic acid is exploited as a source of carbon in prokaryotes and microbial eukaryotes. Both the shikimate and quinate pathways share two common pathway metabolites 3-dehydroquinate and dehydroshikimate.
Probab=23.73 E-value=58 Score=14.27 Aligned_cols=34 Identities=9% Similarity=0.257 Sum_probs=25.0
Q ss_pred CCCCEEEEEECCHHHHHHHHHHHHHC-CCEECCCC
Q ss_conf 07881699607823579999998633-98314233
Q gi|254780779|r 64 ARGGRILFVATKSQASDCVMEAAKRS-AQYCVNSK 97 (278)
Q Consensus 64 ~~gg~ILFVgTk~~~~~~i~~~A~~~-~~~yV~~R 97 (278)
-.+.++|+||+...++.+++....+- ..-++.+|
T Consensus 10 l~~~~vlVIGaG~~~~~~~~~L~~~g~~~i~v~nR 44 (134)
T pfam01488 10 LKGKKVLLIGAGEMARLAAKHLLSKGAKKITIANR 44 (134)
T ss_pred CCCCEEEEECCCHHHHHHHHHHHHCCCCEEEEECC
T ss_conf 14898999996099999999999759988999547
No 317
>TIGR00612 ispG_gcpE 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase; InterPro: IPR004588 This protein previously of unknown biochemical function is essential in Escherichia coli. It has now been characterised as 1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate synthase, which converts 2C-methyl-D-erythritol 2,4-cyclodiphosphate (ME-2,4CPP) into 1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate in the sixth step of nonmevalonate terpenoid biosynthesis. The family is restricted to bacteria, where it is widely but not universally distributed. No homology can be detected between this family and other proteins.; GO: 0016114 terpenoid biosynthetic process.
Probab=23.70 E-value=59 Score=14.27 Aligned_cols=79 Identities=10% Similarity=0.149 Sum_probs=46.2
Q ss_pred HHCCCCC-CCCCCCCCCCCCCCCCCCC-C-CEEEE-------------CHHHHHHHHHHHHHHHHHHHCCCCEEEEEECC
Q ss_conf 8608860-7547765788562102001-8-81675-------------38999999999999999861078816996078
Q gi|254780779|r 12 LESGVQF-GHRNFLWNPKMERYIFCER-N-NTHII-------------DLSQTVPMLQKALQVISDTVARGGRILFVATK 75 (278)
Q Consensus 12 l~ag~H~-Gh~~~~wnPkM~~yI~g~r-n-gihII-------------dL~kT~~~L~~A~~~i~~i~~~gg~ILFVgTk 75 (278)
|=|-+|| ||+-++-.+.|+..+-+.| | |..+. .--+....+++-..-|-+-++..|+=+=+|-|
T Consensus 88 LVADiHf~Ghk~~~~~~~~~~~v~kvRINPGNig~k~~~~~~~~Y~~~~yA~~~~~~~e~v~~~Ve~ar~~G~a~RIGVN 167 (633)
T TIGR00612 88 LVADIHFAGHKYKKAALAVAKGVAKVRINPGNIGFKKKDAKRKIYSDAKYAEILLKVEERVRDVVEKARRHGKAMRIGVN 167 (633)
T ss_pred EEEEECCCCCCHHHHHHHHHHCCCEEEECCCCCCCCCCHHHCCCCCHHHHHHHHCCHHHHHHHHHHHHHHCCCCEEEECC
T ss_conf 48873025661468999986117825437876434670120045642578886300467889999999857896875035
Q ss_pred HHH--HHHHHHHHHHCC
Q ss_conf 235--799999986339
Q gi|254780779|r 76 SQA--SDCVMEAAKRSA 90 (278)
Q Consensus 76 ~~~--~~~i~~~A~~~~ 90 (278)
.-. +.+.+....+-|
T Consensus 168 ~GSL~~~~~~~ll~~Yg 184 (633)
T TIGR00612 168 HGSLEQVLKRRLLEKYG 184 (633)
T ss_pred CCCCHHHHHHHHHHHHC
T ss_conf 67660899999999715
No 318
>TIGR00009 L28 ribosomal protein L28; InterPro: IPR001383 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites , . About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many of ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome , . The ribosomal L28 protein family include proteins from bacteria and chloroplasts. The L24 protein from yeast, found in the large subunit of the mitochodrial ribosome, contains a region similar to the bacterial L28 protein.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome.
Probab=23.51 E-value=33 Score=15.87 Aligned_cols=19 Identities=11% Similarity=0.314 Sum_probs=13.9
Q ss_pred CCCCCCCCCCC-CCCCCCCC
Q ss_conf 08860754776-57885621
Q gi|254780779|r 14 SGVQFGHRNFL-WNPKMERY 32 (278)
Q Consensus 14 ag~H~Gh~~~~-wnPkM~~y 32 (278)
+|-|=.++|+| |+|.+..-
T Consensus 29 ~G~Hs~~~tkRrf~PNLq~~ 48 (70)
T TIGR00009 29 VGRHSHRKTKRRFKPNLQKV 48 (70)
T ss_pred CCCCCCCCCCEEECCCCCEE
T ss_conf 16010466322436662267
No 319
>PRK13530 arsenate reductase; Provisional
Probab=23.14 E-value=60 Score=14.20 Aligned_cols=22 Identities=18% Similarity=0.206 Sum_probs=17.1
Q ss_pred CCCEEEEEECCHHHHHHHHHHH
Q ss_conf 7881699607823579999998
Q gi|254780779|r 65 RGGRILFVATKSQASDCVMEAA 86 (278)
Q Consensus 65 ~gg~ILFVgTk~~~~~~i~~~A 86 (278)
+.++||||+|...++..+.+.-
T Consensus 2 ~kk~VLFvCt~Ns~RSqmAEal 23 (133)
T PRK13530 2 NKKTIYFLCTGNSCRSQMAEGW 23 (133)
T ss_pred CCCEEEEEECCCCHHHHHHHHH
T ss_conf 9887999959962788999999
No 320
>PRK10966 exonuclease subunit SbcD; Provisional
Probab=22.99 E-value=60 Score=14.18 Aligned_cols=27 Identities=7% Similarity=0.071 Sum_probs=15.1
Q ss_pred HHHHHHHHHHHHHHCCCCEEEEEECCH
Q ss_conf 999999999998610788169960782
Q gi|254780779|r 50 PMLQKALQVISDTVARGGRILFVATKS 76 (278)
Q Consensus 50 ~~L~~A~~~i~~i~~~gg~ILFVgTk~ 76 (278)
........|+.++...|-.++.++-|.
T Consensus 58 ~A~~l~~~fl~~l~~~~~~vvvIaGNH 84 (402)
T PRK10966 58 YARELYNRFVVNLQQTGCQLVVLAGNH 84 (402)
T ss_pred HHHHHHHHHHHHHHHCCCCEEEEECCC
T ss_conf 999999999999996699689994798
No 321
>TIGR01364 serC_1 phosphoserine aminotransferase; InterPro: IPR003248 Phosphoserine aminotransferases (2.6.1.52 from EC) catalyse the conversion of O-phospho-L-serine and oxoglutarate to 3-phosphonooxypyruvate and L-glutamate in the major phosphorylated serine biosynthesis pathway. In bacteria it is also equired for the biosynthesis of pyridoxine. The enzyme requires pyridoxal phosphate as a cofactor, and is part of the aminotransferase class-V family.; GO: 0006564 L-serine biosynthetic process.
Probab=22.86 E-value=25 Score=16.68 Aligned_cols=25 Identities=36% Similarity=0.752 Sum_probs=19.4
Q ss_pred HHHHCCCEEEEECCCCCCCHHCCCEEEECCCCH
Q ss_conf 234339814540367767001152032157726
Q gi|254780779|r 176 EARRLRIPIVAVVDTNSNPDLVDYVIPGNDDSS 208 (278)
Q Consensus 176 EA~kl~IPvIaivDTn~dp~~idypIP~NDds~ 208 (278)
|=-+||||++ |+-.||.|=+..||.
T Consensus 238 ~LH~L~vP~~--------P~~~~Y~~~~~~~Sm 262 (391)
T TIGR01364 238 ELHKLGVPIT--------PSMLNYKIHAENDSM 262 (391)
T ss_pred CHHHCCCCCC--------CCCCCHHHHHHCCCC
T ss_conf 0201666597--------841321898863887
No 322
>cd06333 PBP1_ABC-type_HAAT_like Type I periplasmic binding component of ABC (ATPase Binding Cassette)-type transport systems that are predicted to be involved in uptake of amino acids. This subgroup includes the type I periplasmic binding component of ABC (ATPase Binding Cassette)-type transport systems that are predicted to be involved in uptake of amino acids. Members of this subgroup are sequence-similar to members of the family of ABC-type hydrophobic amino acid transporters (HAAT), such as leucine-isoleucine-valine-binding protein (LIVBP); their ligand specificity has not been determined experimentally, however.
Probab=22.66 E-value=61 Score=14.14 Aligned_cols=38 Identities=18% Similarity=0.298 Sum_probs=23.9
Q ss_pred CCCCEEEEECCCCC-CHHHHHHHHCCCE--EEEECCCCCCCH
Q ss_conf 35957999438877-1232123433981--454036776700
Q gi|254780779|r 157 GLPDLMFVVDTNRE-KLAIQEARRLRIP--IVAVVDTNSNPD 195 (278)
Q Consensus 157 ~lP~~iiv~d~~~e-~~Av~EA~kl~IP--vIaivDTn~dp~ 195 (278)
.-||+||+.....+ ...++.++.+|+. +++- |.-.+|.
T Consensus 187 ~~pD~v~~~~~~~~~~~~~~q~~~~G~~~~~~~~-~~~~~~~ 227 (312)
T cd06333 187 ARPDAVLIWGSGTPAALPAKNLRERGYKGPIYQT-HGVASPD 227 (312)
T ss_pred CCCCEEEEECCCCHHHHHHHHHHHCCCCCCEEEC-CCCCCHH
T ss_conf 6989999945751699999999976998708812-7667879
No 323
>pfam03928 DUF336 Domain of unknown function (DUF336). This family contains uncharacterized sequences, including several GlcG proteins. The alignment contains many conserved motifs that are suggestive of cofactor binding and enzymatic activity.
Probab=22.63 E-value=56 Score=14.41 Aligned_cols=23 Identities=39% Similarity=0.544 Sum_probs=12.0
Q ss_pred HHHHHHHHCCCEE-EEECCCCCCC
Q ss_conf 2321234339814-5403677670
Q gi|254780779|r 172 LAIQEARRLRIPI-VAVVDTNSNP 194 (278)
Q Consensus 172 ~Av~EA~kl~IPv-IaivDTn~dp 194 (278)
.|+.+|++.|+|+ |++||.+.++
T Consensus 14 ~a~~~a~~~g~~vsvaVvD~~G~l 37 (132)
T pfam03928 14 AAVAAARELGVRVTVAVVDAGGHL 37 (132)
T ss_pred HHHHHHHHCCCCEEEEEECCCCCE
T ss_conf 999999981998899999899989
No 324
>COG3854 SpoIIIAA ncharacterized protein conserved in bacteria [Function unknown]
Probab=22.52 E-value=62 Score=14.12 Aligned_cols=44 Identities=30% Similarity=0.490 Sum_probs=32.6
Q ss_pred HHHHCCCCCEEEEE--CCCCCCHHHHHHHHCCCEEEEECCCCCCCHHC
Q ss_conf 32211359579994--38877123212343398145403677670011
Q gi|254780779|r 152 IRDMGGLPDLMFVV--DTNREKLAIQEARRLRIPIVAVVDTNSNPDLV 197 (278)
Q Consensus 152 i~~m~~lP~~iiv~--d~~~e~~Av~EA~kl~IPvIaivDTn~dp~~i 197 (278)
|++|. |++++|- .+..|..|++||.-.|+.+|+-.--|.=-+++
T Consensus 214 Irsm~--PEViIvDEIGt~~d~~A~~ta~~~GVkli~TaHG~~iedl~ 259 (308)
T COG3854 214 IRSMS--PEVIIVDEIGTEEDALAILTALHAGVKLITTAHGNGIEDLI 259 (308)
T ss_pred HHHCC--CCEEEEECCCCHHHHHHHHHHHHCCCEEEEEECCCCHHHHH
T ss_conf 99549--95799834364777999999985485899950441177765
No 325
>TIGR01737 FGAM_synth_I phosphoribosylformylglycinamidine synthase I; InterPro: IPR010075 In some species, phosphoribosylformylglycinamidine synthase is composed of a single polypeptide chain. This entry describes the PurQ protein of Bacillus subtilis (where PurL, PurQ, and PurS are required for phosphoribosylformylglycinamidine synthase activity) and functionally equivalent proteins from other bacteria and archaea.; GO: 0004642 phosphoribosylformylglycinamidine synthase activity, 0006189 'de novo' IMP biosynthetic process, 0005737 cytoplasm.
Probab=22.47 E-value=49 Score=14.78 Aligned_cols=25 Identities=16% Similarity=0.242 Sum_probs=14.3
Q ss_pred HHHHHHHHHHHCCCCEEEEEECCHH
Q ss_conf 9999999986107881699607823
Q gi|254780779|r 53 QKALQVISDTVARGGRILFVATKSQ 77 (278)
Q Consensus 53 ~~A~~~i~~i~~~gg~ILFVgTk~~ 77 (278)
..+..-|++.+.+|+-||=|+.--|
T Consensus 80 ~p~~~~V~~~A~~G~pVLGiCNGFQ 104 (264)
T TIGR01737 80 SPIMQEVREFAEKGKPVLGICNGFQ 104 (264)
T ss_pred HHHHHHHHHHHHCCCEEEEEECHHH
T ss_conf 0889999999955982899766479
No 326
>PRK09065 glutamine amidotransferase; Provisional
Probab=22.30 E-value=45 Score=15.01 Aligned_cols=40 Identities=18% Similarity=0.184 Sum_probs=27.6
Q ss_pred CCCCCCCEEEECHHHHHHHHHHHHHHHHHHHCCCCEEEEEECCHH
Q ss_conf 020018816753899999999999999986107881699607823
Q gi|254780779|r 33 IFCERNNTHIIDLSQTVPMLQKALQVISDTVARGGRILFVATKSQ 77 (278)
Q Consensus 33 I~g~rngihIIdL~kT~~~L~~A~~~i~~i~~~gg~ILFVgTk~~ 77 (278)
|.|.+.+++ | -..-+.....||++....+..+|=|+---|
T Consensus 62 itGS~~~v~--d---~~pWi~~l~~~ir~~~~~~~PilGICfGhQ 101 (238)
T PRK09065 62 ITGSHAMVT--D---RAPWSERTADWLRQAAAAGMPLLGICYGHQ 101 (238)
T ss_pred EECCCCCCC--C---CCHHHHHHHHHHHHHHHCCCCEEEEEHHHH
T ss_conf 979852057--9---988899999999999877999999817789
No 327
>cd01056 Euk_Ferritin eukaryotic ferritins. Eukaryotic Ferritin (Euk_Ferritin) domain. Ferritins are the primary iron storage proteins of most living organisms and members of a broad superfamily of ferritin-like diiron-carboxylate proteins. The iron-free (apoferritin) ferritin molecule is a protein shell composed of 24 protein chains arranged in 432 symmetry. Iron storage involves the uptake of iron (II) at the protein shell, its oxidation by molecular oxygen at the dinuclear ferroxidase centers, and the movement of iron (III) into the cavity for deposition as ferrihydrite; the protein shell can hold up to 4500 iron atoms. In vertebrates, two types of chains (subunits) have been characterized, H or M (fast) and L (slow), which differ in rates of iron uptake and mineralization. Fe(II) oxidation in the H/M subunits take place initially at the ferroxidase center, a carboxylate-bridged diiron center, located within the subunit four-helix bundle. In a complementary role, negatively charged r
Probab=22.15 E-value=63 Score=14.07 Aligned_cols=106 Identities=20% Similarity=0.226 Sum_probs=61.5
Q ss_pred HHHHHHHHHHHHHHHHHHHCCCCEEEEEECCHHHHHHHHHHHHHCCCEECCCCCCC------CCCCCHHHHHHHHHHHHH
Q ss_conf 89999999999999998610788169960782357999999863398314233458------732342666555677899
Q gi|254780779|r 45 LSQTVPMLQKALQVISDTVARGGRILFVATKSQASDCVMEAAKRSAQYCVNSKWLG------GMMTNWKTVSQSIQKLRD 118 (278)
Q Consensus 45 L~kT~~~L~~A~~~i~~i~~~gg~ILFVgTk~~~~~~i~~~A~~~~~~yV~~RWlG------G~LTN~~ti~~si~~l~~ 118 (278)
..+..+....|.+|+..+...||++.|-...+... .-|.. -.|...+++.++|..+.+
T Consensus 44 ~~~s~Ee~~ha~kl~~Yl~~RG~~v~~~~i~~p~~----------------~~~~s~l~~~~~al~~Ek~vt~~i~~L~~ 107 (161)
T cd01056 44 RKLSDEEREHAEKLIKYQNKRGGRVVLQDIKKPEK----------------DEWGSGLEALELALDLEKLVNQSLLDLHK 107 (161)
T ss_pred HHHHHHHHHHHHHHHHHHHHCCCEEECCCCCCCCC----------------CCCCCHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 99999999999999999998699202588688877----------------77799999999999999999999999999
Q ss_pred HHHH-HHCCCCCCCHHHHHH-HHHHHHHHHHHHHHHHHHCCCCCE--EEEEC
Q ss_conf 8876-301212677467887-665567776434433221135957--99943
Q gi|254780779|r 119 LEEL-LNKENQGFTKKERLN-IERKRDKLKRALDGIRDMGGLPDL--MFVVD 166 (278)
Q Consensus 119 l~~~-~~~~~~~~tkKe~~~-~~r~~~kl~k~lgGi~~m~~lP~~--iiv~d 166 (278)
+-.. .+.....|-.-+.+. -..+..++...+.-++.+..-+.. .+++|
T Consensus 108 ~A~~~~D~~~~~fLe~~fi~eQ~e~~~~~~~~l~~l~~~~~~~~glg~ylfD 159 (161)
T cd01056 108 LASEHNDPHLADFLESEFLEEQVESIKKLAGYITNLKRVGKPQSGLGEYLFD 159 (161)
T ss_pred HHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCC
T ss_conf 9987699669999988878999999999999999999847998650000348
No 328
>TIGR01135 glmS glucosamine--fructose-6-phosphate aminotransferase, isomerizing; InterPro: IPR005855 Glucosamine:fructose-6-phosphate aminotransferase (2.6.1.16 from EC) catalyses the formation of glucosamine 6-phosphate and is the first and rate-limiting enzyme of the hexosamine biosynthetic pathway. The final product of the hexosamine pathway, UDP-N-acetyl glucosamine, is an active precursor of numerous macromolecules containing amino sugars. This family of sequences belong to the MEROPS peptidase family C44 (clan PB(C)), and are classified as non-peptidase homologs.; GO: 0004360 glutamine-fructose-6-phosphate transaminase (isomerizing) activity, 0016051 carbohydrate biosynthetic process, 0005737 cytoplasm.
Probab=22.13 E-value=63 Score=14.07 Aligned_cols=70 Identities=14% Similarity=0.165 Sum_probs=52.0
Q ss_pred CCEEEEECCCCC----CHHHHHHHHCC--CEEEEECCCCCC--CHHCCCEEE---ECCCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf 957999438877----12321234339--814540367767--001152032---1577268999999999999999999
Q gi|254780779|r 159 PDLMFVVDTNRE----KLAIQEARRLR--IPIVAVVDTNSN--PDLVDYVIP---GNDDSSRSIALFCDLVASAAIDGIA 227 (278)
Q Consensus 159 P~~iiv~d~~~e----~~Av~EA~kl~--IPvIaivDTn~d--p~~idypIP---~NDds~~si~l~~~~i~~ai~~g~~ 227 (278)
=+++|.+-|..| .-|+++|+.+| -.++|||+...+ ++..|+.+= |===++.|-+=|+..++-..+-+..
T Consensus 353 ~~L~I~ISQSGETADTL~ALr~aK~~G~~~~~L~IcNv~gS~l~Re~D~~L~t~AGpEIGVAsTKaFt~Ql~~L~~L~~~ 432 (628)
T TIGR01135 353 KTLVIAISQSGETADTLEALRLAKELGLYAKTLGICNVPGSTLTREADHTLYTRAGPEIGVASTKAFTAQLTVLYLLALA 432 (628)
T ss_pred CCEEEEEECCCCHHHHHHHHHHHHHCCCCEEEEEEEECCCCCHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 76599997486108899999999847985158999836875335787787765069711145458899999999999999
Q ss_pred H
Q ss_conf 7
Q gi|254780779|r 228 R 228 (278)
Q Consensus 228 ~ 228 (278)
.
T Consensus 433 ~ 433 (628)
T TIGR01135 433 L 433 (628)
T ss_pred H
T ss_conf 9
No 329
>TIGR03407 urea_ABC_UrtA urea ABC transporter, urea binding protein. Members of this protein family are ABC transporter substrate-binding proteins associated with urea transport and metabolism. This protein is found in a conserved five-gene transport operon typically found adjacent to urease genes. It was shown in Cyanobacteria that disruption leads to the loss of high-affinity urea transport activity. Members of this protein family tend to have the twin-arginine signal for Sec-independent transport across the plasma membrane.
Probab=22.13 E-value=63 Score=14.07 Aligned_cols=87 Identities=14% Similarity=0.187 Sum_probs=51.0
Q ss_pred HHHHHHHHHHCCCCEEEEEECCH----HHHHHHHHHHHHCCCEECCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCC
Q ss_conf 99999998610788169960782----35799999986339831423345873234266655567789988763012126
Q gi|254780779|r 54 KALQVISDTVARGGRILFVATKS----QASDCVMEAAKRSAQYCVNSKWLGGMMTNWKTVSQSIQKLRDLEELLNKENQG 129 (278)
Q Consensus 54 ~A~~~i~~i~~~gg~ILFVgTk~----~~~~~i~~~A~~~~~~yV~~RWlGG~LTN~~ti~~si~~l~~l~~~~~~~~~~ 129 (278)
.+..++.+- ...+++-+++..- ...+.+++.+++.|.-.|.+.|.+---|.|+..-.+|+.
T Consensus 123 ~~~~~~~~~-~g~k~vaii~~d~~~g~~~~~~~~~~~~~~G~~vv~~~~~~~g~~Dfs~~l~kik~-------------- 187 (359)
T TIGR03407 123 PAVDYLLSK-KGAKRFFLLGSDYVFPRTANKIIKAYLKSLGGTVVGEDYTPLGHTDFQTIINKIKA-------------- 187 (359)
T ss_pred HHHHHHHHH-CCCCEEEEEECCCCCHHHHHHHHHHHHHHCCCCEEEEEECCCCCCCHHHHHHHHHH--------------
T ss_conf 999999985-69987999945873058999999999997599737788257987558999999997--------------
Q ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCEEEEECCCCCCH-HHHHHHHCCC
Q ss_conf 7746788766556777643443322113595799943887712-3212343398
Q gi|254780779|r 130 FTKKERLNIERKRDKLKRALDGIRDMGGLPDLMFVVDTNREKL-AIQEARRLRI 182 (278)
Q Consensus 130 ~tkKe~~~~~r~~~kl~k~lgGi~~m~~lP~~iiv~d~~~e~~-Av~EA~kl~I 182 (278)
.-||+||+.....+.. .+++++.+|+
T Consensus 188 ---------------------------a~pD~v~~~~~~~~~~~~~kq~~~~G~ 214 (359)
T TIGR03407 188 ---------------------------FKPDVVFNTLNGDSNVAFFKQLKNAGI 214 (359)
T ss_pred ---------------------------CCCCEEEEECCCCCHHHHHHHHHHHCC
T ss_conf ---------------------------699999993746205799999998289
No 330
>cd06297 PBP1_LacI_like_12 Ligand-binding domain of uncharacterized transcription regulators from Thermus thermophilus and close homologs. Ligand-binding domain of uncharacterized transcription regulators from Thermus thermophilus and close homologs from other bacteria. This group belongs to the the LacI-GalR family repressors that are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding.
Probab=22.10 E-value=63 Score=14.06 Aligned_cols=35 Identities=26% Similarity=0.296 Sum_probs=25.1
Q ss_pred CCCCCEEEEECCCCCCHHHHHHHHCCCE------EEEECCC
Q ss_conf 1359579994388771232123433981------4540367
Q gi|254780779|r 156 GGLPDLMFVVDTNREKLAIQEARRLRIP------IVAVVDT 190 (278)
Q Consensus 156 ~~lP~~iiv~d~~~e~~Av~EA~kl~IP------vIaivDT 190 (278)
...|++||+.+-.-=.-+++.++.+||. |||+=|+
T Consensus 178 ~~~p~Ai~~~nD~~A~g~l~~l~~~Gi~vP~DisviGfDd~ 218 (269)
T cd06297 178 ASPPLAVFASADQQALGALQEAVELGLTVGEDVRVVGFDDH 218 (269)
T ss_pred CCCCCEEEECCHHHHHHHHHHHHHCCCCCCCCEEEEEECCH
T ss_conf 99985899897899999999999839988996699998984
No 331
>pfam12044 Metallopep Putative peptidase family. This family of proteins is functionally uncharacterized. However, it does contain an HEXXH motif characteristic of metallopeptidases. This protein is found in bacteria and eukaryotes. Proteins in this family are typically between 625 to 773 amino acids in length.
Probab=22.05 E-value=22 Score=16.98 Aligned_cols=16 Identities=25% Similarity=0.457 Sum_probs=7.0
Q ss_pred CEEEECHHHHHHHHHH
Q ss_conf 8167538999999999
Q gi|254780779|r 39 NTHIIDLSQTVPMLQK 54 (278)
Q Consensus 39 gihIIdL~kT~~~L~~ 54 (278)
.+|||--++|+..++.
T Consensus 179 kvhv~rs~ktv~Elrd 194 (419)
T pfam12044 179 KIHVLRSDKTVAELRD 194 (419)
T ss_pred EEEEEECCCCHHHHHC
T ss_conf 6999947888999856
No 332
>cd01979 Pchlide_reductase_N Pchlide_reductase_N: N protein of the NB protein complex of Protochlorophyllide (Pchlide)_reductase. Pchlide reductase catalyzes the reductive formation of chlorophyllide (chlide) from protochlorophyllide (pchlide) during biosynthesis of chlorophylls and bacteriochlorophylls. This group contains both the light-independent Pchlide reductase (DPOR) and light-dependent Pchlide reductase (LPOR). Angiosperms contain only LPOR, cyanobacteria, algae and gymnosperms contain both DPOR and LPOR, primitive anoxygenic photosynthetic bacteria contain only DPOR. NB is structurally similar to the FeMo protein of nitrogenase, forming an N2B2 heterotetramer. N and B are homologous to the FeMo alpha and beta subunits respectively. Also in common with nitrogenase in vitro DPOR activity requires ATP hydrolysis and dithoionite or ferredoxin as electron donor. The NB protein complex may serve as a catalytic site for Pchlide reduction similar to MoFe for nitrogen reduction.
Probab=22.01 E-value=63 Score=14.05 Aligned_cols=147 Identities=14% Similarity=0.154 Sum_probs=70.6
Q ss_pred CCCCCCCEEEECHHHHHHHHHHHHHHHHHHHCCCCEEEEEECCHHH--H----HHHHHHHHHCCCEECCCCCCCCCCCCH
Q ss_conf 0200188167538999999999999999861078816996078235--7----999999863398314233458732342
Q gi|254780779|r 33 IFCERNNTHIIDLSQTVPMLQKALQVISDTVARGGRILFVATKSQA--S----DCVMEAAKRSAQYCVNSKWLGGMMTNW 106 (278)
Q Consensus 33 I~g~rngihIIdL~kT~~~L~~A~~~i~~i~~~gg~ILFVgTk~~~--~----~~i~~~A~~~~~~yV~~RWlGG~LTN~ 106 (278)
+..+++=.-+.|-+ ..|++++.-|..- ++...|..|||-+.- . .+-++...+.|.+-|+.+ -.|.=|||
T Consensus 59 ~leE~Dl~~~~~~~---~eL~r~v~~i~~~-r~p~~iFlvgtCpseVIk~DLe~~A~rls~~~~v~Vv~vs-~sGiettF 133 (396)
T cd01979 59 ELEEGDLSALLNDY---AELDRVVTQIKRD-RNPSVIFLIGSCTTEVIKMDLEGAAPRLSAEIGVPILVAS-ASGLDYTF 133 (396)
T ss_pred CCCCHHHHHCCCCH---HHHHHHHHHHHHH-CCCCEEEEECCCCHHHHHHHHHHHHHHHHHCCCCEEEEEE-CCCCCCCH
T ss_conf 04620554236966---9999999999974-8994799972585777752499998875326795599952-68754757
Q ss_pred HHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCEEEEECC--CCCCHHHHHHHHCCCEE
Q ss_conf 6665556778998876301212677467887665567776434433221135957999438--87712321234339814
Q gi|254780779|r 107 KTVSQSIQKLRDLEELLNKENQGFTKKERLNIERKRDKLKRALDGIRDMGGLPDLMFVVDT--NREKLAIQEARRLRIPI 184 (278)
Q Consensus 107 ~ti~~si~~l~~l~~~~~~~~~~~tkKe~~~~~r~~~kl~k~lgGi~~m~~lP~~iiv~d~--~~e~~Av~EA~kl~IPv 184 (278)
.+--... |.-+ ...+++.. ..-|.++++=+. .-+....++-.++||++
T Consensus 134 TQGEDa~--LaAl-------vp~~P~~~---------------------~~~~~LvlvGsl~d~vedq~~~ll~~lGI~v 183 (396)
T cd01979 134 TQGEDTV--LAAL-------VPRCPEKP---------------------SPERSLVLVGSLPDIVEDQLRRELEQLGIPV 183 (396)
T ss_pred HHHHHHH--HHHH-------HHHCCCCC---------------------CCCCCEEEEEECCCHHHHHHHHHHHHCCCCE
T ss_conf 6799999--9999-------86474323---------------------7888648997058168999999999769924
Q ss_pred EEECCCCCCCH-----HCCCEEEECCCCHHHHHHHHHHHHHHH
Q ss_conf 54036776700-----115203215772689999999999999
Q gi|254780779|r 185 VAVVDTNSNPD-----LVDYVIPGNDDSSRSIALFCDLVASAA 222 (278)
Q Consensus 185 IaivDTn~dp~-----~idypIP~NDds~~si~l~~~~i~~ai 222 (278)
++..-....-+ .=+|.+++|. |++..+++.
T Consensus 184 v~~LP~~~~~eLp~vg~~t~v~l~qP--------fL~~TA~~L 218 (396)
T cd01979 184 VGFLPPRRYTDLPVIGPGTYVLGIQP--------FLSRTATTL 218 (396)
T ss_pred EEECCCCCCCCCCCCCCCCEEEEECH--------HHHHHHHHH
T ss_conf 67758876110213588718998371--------799999999
No 333
>TIGR02637 RhaS rhamnose ABC transporter, rhamnose-binding protein; InterPro: IPR013459 ABC transporters belong to the ATP-Binding Cassette (ABC) superfamily, which uses the hydrolysis of ATP to energize diverse biological systems. ABC transporters are minimally constituted of two conserved regions: a highly conserved ATP binding cassette (ABC) and a less conserved transmembrane domain (TMD). These regions can be found on the same protein or on two different ones. Most ABC transporters function as a dimer and therefore are constituted of four domains, two ABC modules and two TMDs. ABC transporters are involved in the export or import of a wide variety of substrates ranging from small ions to macromolecules. The major function of ABC import systems is to provide essential nutrients to bacteria. They are found only in prokaryotes and their four constitutive domains are usually encoded by independent polypeptides (two ABC proteins and two TMD proteins). Prokaryotic importers require additional extracytoplasmic binding proteins (one or more per systems) for function. In contrast, export systems are involved in the extrusion of noxious substances, the export of extracellular toxins and the targeting of membrane components. They are found in all living organisms and in general the TMD is fused to the ABC module in a variety of combinations. Some eukaryotic exporters encode the four domains on the same polypeptide chain . The ABC module (approximately two hundred amino acid residues) is known to bind and hydrolyze ATP, thereby coupling transport to ATP hydrolysis in a large number of biological processes. The cassette is duplicated in several subfamilies. Its primary sequence is highly conserved, displaying a typical phosphate-binding loop: Walker A, and a magnesium binding site: Walker B. Besides these two regions, three other conserved motifs are present in the ABC cassette: the switch region which contains a histidine loop, postulated to polarize the attaching water molecule for hydrolysis, the signature conserved motif (LSGGQ) specific to the ABC transporter, and the Q-motif (between Walker A and the signature), which interacts with the gamma phosphate through a water bond. The Walker A, Walker B, Q-loop and switch region form the nucleotide binding site , , . The 3D structure of a monomeric ABC module adopts a stubby L-shape with two distinct arms. ArmI (mainly beta-strand) contains Walker A and Walker B. The important residues for ATP hydrolysis and/or binding are located in the P-loop. The ATP-binding pocket is located at the extremity of armI. The perpendicular armII contains mostly the alpha helical subdomain with the signature motif. It only seems to be required for structural integrity of the ABC module. ArmII is in direct contact with the TMD. The hinge between armI and armII contains both the histidine loop and the Q-loop, making contact with the gamma phosphate of the ATP molecule. ATP hydrolysis leads to a conformational change that could facilitate ADP release. In the dimer the two ABC cassettes contact each other through hydrophobic interactions at the antiparallel beta-sheet of armI by a two-fold axis , , , , , . Proteins known to belong to this family are classified in several functional subfamilies depending on the substrate used (for further information see http://www.tcdb.org/tcdb/index.php?tc=3.A.1). This sugar-binding component of ABC transporter complexes is found in rhamnose catabolism operon contexts. Mutation of the gene in Rhizobium leguminosarum abolishes rhamnose transport and prevents growth on rhamnose as a carbon source..
Probab=21.93 E-value=60 Score=14.20 Aligned_cols=64 Identities=17% Similarity=0.184 Sum_probs=40.1
Q ss_pred CCEEEEE--CCCCCCHHHHHHHHCCCEEEEECCCCCCCHHCCCE-EEECCCCHHHHHHHHHHHHHHHHHH
Q ss_conf 9579994--38877123212343398145403677670011520-3215772689999999999999999
Q gi|254780779|r 159 PDLMFVV--DTNREKLAIQEARRLRIPIVAVVDTNSNPDLVDYV-IPGNDDSSRSIALFCDLVASAAIDG 225 (278)
Q Consensus 159 P~~iiv~--d~~~e~~Av~EA~kl~IPvIaivDTn~dp~~idyp-IP~NDds~~si~l~~~~i~~ai~~g 225 (278)
=|+|-|. ||.-=-.|++-|.+-||+||.. ||..+|+.=... =|+..+.+- +.++.++++-|..+
T Consensus 57 V~AIaiSAnDpdAlvpalkkA~~rgI~Vv~~-DS~v~pegR~l~~n~a~~~~IG--~~~vql~A~~~~~~ 123 (307)
T TIGR02637 57 VDAIAISANDPDALVPALKKAMKRGIKVVTW-DSGVAPEGRKLFLNQADAELIG--RTQVQLAAEQLEEG 123 (307)
T ss_pred EEEEEECCCCCCHHHHHHHHHHHCCCEEEEE-CCCCCCCCCEEEECCCCHHHHH--HHHHHHHHHHHCCC
T ss_conf 0069970278522789999998569829985-2788813454422646831288--99999999971789
No 334
>PRK06719 precorrin-2 dehydrogenase; Validated
Probab=21.87 E-value=64 Score=14.04 Aligned_cols=34 Identities=12% Similarity=-0.021 Sum_probs=23.5
Q ss_pred CCCCEEEEEECCHHHHHHHHHHHHHCCCEECCCC
Q ss_conf 0788169960782357999999863398314233
Q gi|254780779|r 64 ARGGRILFVATKSQASDCVMEAAKRSAQYCVNSK 97 (278)
Q Consensus 64 ~~gg~ILFVgTk~~~~~~i~~~A~~~~~~yV~~R 97 (278)
-+|++||+||-.+.+.+-++...+....-.|-..
T Consensus 11 l~~k~vLVvGGG~VA~rK~~~Ll~~ga~VtVvsp 44 (157)
T PRK06719 11 LHNKVVVIIGGGKIAYRKASGLKDTGAFVTVVSP 44 (157)
T ss_pred CCCCEEEEECCCHHHHHHHHHHHHCCCEEEEECC
T ss_conf 5998799988989999999999878796999999
No 335
>pfam10186 DUF2355 Predicted coiled-coil protein (DUF2355). This is a predicted coiled-coil containing region of approximately 200 residues of a family of proteins conserved from nematodes to humans. The exact function is not known.
Probab=21.84 E-value=50 Score=14.70 Aligned_cols=22 Identities=27% Similarity=0.431 Sum_probs=19.9
Q ss_pred HHHHHHHHHHHCCCEECCCCCC
Q ss_conf 5799999986339831423345
Q gi|254780779|r 78 ASDCVMEAAKRSAQYCVNSKWL 99 (278)
Q Consensus 78 ~~~~i~~~A~~~~~~yV~~RWl 99 (278)
.++.|.+.|+..+-.||.+||+
T Consensus 56 ~~~tvs~LaEA~rTsYvrGrWV 77 (216)
T pfam10186 56 TSSTVSALAEATRTTYVRGKWV 77 (216)
T ss_pred CHHHHHHHHHHHCCCEEEEEEE
T ss_conf 2789999997651444603688
No 336
>PRK12440 acetate kinase; Reviewed
Probab=21.83 E-value=52 Score=14.61 Aligned_cols=40 Identities=15% Similarity=0.213 Sum_probs=20.9
Q ss_pred EEEECCCCCCCHHC-CCEEEECCCCHHHHHHHHHHHHHHHH
Q ss_conf 45403677670011-52032157726899999999999999
Q gi|254780779|r 184 IVAVVDTNSNPDLV-DYVIPGNDDSSRSIALFCDLVASAAI 223 (278)
Q Consensus 184 vIaivDTn~dp~~i-dypIP~NDds~~si~l~~~~i~~ai~ 223 (278)
..|+....+|-..+ .-.=-+|.+|.-++++|+..+++.|-
T Consensus 272 LlGlSG~s~DmR~l~~~~~~g~~~A~lA~d~f~yri~k~IG 312 (397)
T PRK12440 272 FLGVSGLTSDARGILEAMEEGHEGATLAFQVFTYRVAKYIA 312 (397)
T ss_pred CEECCCCCCCHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
T ss_conf 33603787659999999878898799999999999999999
No 337
>pfam10893 DUF2724 Protein of unknown function (DUF2724). This is a family of proteins with unknown function.
Probab=21.65 E-value=40 Score=15.33 Aligned_cols=17 Identities=24% Similarity=0.667 Sum_probs=11.9
Q ss_pred HCCCCCCCC------CCCCCCCC
Q ss_conf 608860754------77657885
Q gi|254780779|r 13 ESGVQFGHR------NFLWNPKM 29 (278)
Q Consensus 13 ~ag~H~Gh~------~~~wnPkM 29 (278)
.-+.|+||- -+||||--
T Consensus 16 SPaMHyGHGWI~gkdgkrWHPc~ 38 (68)
T pfam10893 16 SPAMHYGHGWIAGKDGKRWHPCR 38 (68)
T ss_pred CCCCCCCCCEEECCCCCCCCCCC
T ss_conf 85422476546647888468786
No 338
>COG0196 RibF FAD synthase [Coenzyme metabolism]
Probab=21.62 E-value=23 Score=16.93 Aligned_cols=13 Identities=15% Similarity=0.156 Sum_probs=6.9
Q ss_pred CCCCCCCHHHHHH
Q ss_conf 1212677467887
Q gi|254780779|r 125 KENQGFTKKERLN 137 (278)
Q Consensus 125 ~~~~~~tkKe~~~ 137 (278)
..|..++-.+.+.
T Consensus 96 ~~fa~ls~~~Fv~ 108 (304)
T COG0196 96 LEFANLSAEEFVE 108 (304)
T ss_pred HHHHHCCHHHHHH
T ss_conf 6576399789999
No 339
>PRK01368 murD UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional
Probab=21.59 E-value=64 Score=14.00 Aligned_cols=26 Identities=8% Similarity=0.024 Sum_probs=12.4
Q ss_pred CEEEEEECCH--HHHHHHHHHHHHCCCE
Q ss_conf 8169960782--3579999998633983
Q gi|254780779|r 67 GRILFVATKS--QASDCVMEAAKRSAQY 92 (278)
Q Consensus 67 g~ILFVgTk~--~~~~~i~~~A~~~~~~ 92 (278)
.-|-+-||+= ....++......+|..
T Consensus 105 ~~IaITGTnGKTTTt~li~~iL~~~g~~ 132 (450)
T PRK01368 105 KFIAITGTNGKSTTTALISHILNSNGLD 132 (450)
T ss_pred CEEEEECCCCCHHHHHHHHHHHHHCCCC
T ss_conf 7799968999748999999999975996
No 340
>cd05297 GH4_alpha_glucosidase_galactosidase Glycoside Hydrolases Family 4; Alpha-glucosidases and alpha-galactosidases. linked to 3D####ucture
Probab=21.55 E-value=64 Score=13.99 Aligned_cols=142 Identities=19% Similarity=0.162 Sum_probs=67.9
Q ss_pred CEEEECHHHHHHHHHHHHHHHHHHHCCCC-EEEEEECCHHHHHHHHHHHHHCCCEECCCCCCCCCCCCHHHHHHHHHHHH
Q ss_conf 81675389999999999999998610788-16996078235799999986339831423345873234266655567789
Q gi|254780779|r 39 NTHIIDLSQTVPMLQKALQVISDTVARGG-RILFVATKSQASDCVMEAAKRSAQYCVNSKWLGGMMTNWKTVSQSIQKLR 117 (278)
Q Consensus 39 gihIIdL~kT~~~L~~A~~~i~~i~~~gg-~ILFVgTk~~~~~~i~~~A~~~~~~yV~~RWlGG~LTN~~ti~~si~~l~ 117 (278)
-+...|++. ..|.....+.+.++...| .+=|..|--. +.|.. |.-||..--.-|-+--|..= -+|..-.
T Consensus 31 ei~L~Did~--erl~~v~~l~~~~~~~~~~~~~v~~Ttd~------~eAl~-gADfV~~~irvGg~~~r~~D-e~Iplk~ 100 (423)
T cd05297 31 TIALMDIDE--ERLETVEILAKKIVEELGAPLKIEATTDR------REALD-GADFVINTIQVGGHEYTETD-FEIPEKY 100 (423)
T ss_pred EEEEECCCH--HHHHHHHHHHHHHHHHHCCCEEEEEECCH------HHHHC-CCCEEEEEEEECCCHHHHHH-HHHHHHC
T ss_conf 899988999--99999999999999851998189996899------99846-89999998774682488988-8489883
Q ss_pred HHHHH--HH---CC-CCCC-CHHHHHHHHHHHHHHHHHHHHHHHHCCCCCEEEEECCCCCCHHHHHHHH--CCCEEEEEC
Q ss_conf 98876--30---12-1267-7467887665567776434433221135957999438877123212343--398145403
Q gi|254780779|r 118 DLEEL--LN---KE-NQGF-TKKERLNIERKRDKLKRALDGIRDMGGLPDLMFVVDTNREKLAIQEARR--LRIPIVAVV 188 (278)
Q Consensus 118 ~l~~~--~~---~~-~~~~-tkKe~~~~~r~~~kl~k~lgGi~~m~~lP~~iiv~d~~~e~~Av~EA~k--l~IPvIaiv 188 (278)
-+.++ .. |+ +..| |-.-.+.+-+..+++ -|+|.++==++-- ..|.||-. .++.+||||
T Consensus 101 Gv~~~vGET~G~GG~~~alRtIPv~leia~~i~e~------------~P~AwiiNytNP~-~ivteal~r~~~~k~iGlC 167 (423)
T cd05297 101 GYYQTVGDTSGPGGIFRALRTIPVLLDIARDIEEL------------CPDAWLLNYANPM-AELTWALNRYTPIKTVGLC 167 (423)
T ss_pred CCCEEECCCCCHHHHHHHHCCHHHHHHHHHHHHHH------------CCCCEEEECCCHH-HHHHHHHHHHCCCCEEEEC
T ss_conf 96604456547758999862289999999999987------------9983899767888-9999999973899789879
Q ss_pred CC------------CCCCHHCCCEEEE
Q ss_conf 67------------7670011520321
Q gi|254780779|r 189 DT------------NSNPDLVDYVIPG 203 (278)
Q Consensus 189 DT------------n~dp~~idypIP~ 203 (278)
|+ .++++.++|-..|
T Consensus 168 ~~p~~~~~~la~~l~~~~~~v~~~~~G 194 (423)
T cd05297 168 HGVQGTAEQLAKLLGEPPEEVDYQVAG 194 (423)
T ss_pred CCHHHHHHHHHHHHCCCHHHCEEEEEC
T ss_conf 776999999999829988991899950
No 341
>TIGR00658 orni_carb_tr ornithine carbamoyltransferase; InterPro: IPR002292 The ornithine carbamoyltransferases are a family of enzymes that catalyse the production of citrulline from carbamoyl-phosphate and ornithine . This reaction is part of the arginine biosynthetic pathway, and in some organisms the reaction is also part of the arginine deaminase pathway . In most prokaryotes, and some lower eukaryotes, the enzyme is found in the cytoplasm, but in higher eukaryotes, such as mammals, the enzyme is found in the mitochondrial matrix and functions as part of the urea cycle. In most organisms analysed to date, the enzyme has been shown to consist of a trimer of identical or nonidentical subunits . Extensive similarity has been found within the ornithine carbamoyltransferase family, some of the conserved areas being important in catalysis . The C-terminal region of these enzymes shows a degree of similarity to the aspartate carbamoyltransferases, which are also known to bind carbamoyl- phosphate . This region contains a highly conserved Cys residue (in a His-Cys-Lys-Pro motif) implicated in ornithine binding . ; GO: 0004585 ornithine carbamoyltransferase activity, 0006520 amino acid metabolic process, 0009348 ornithine carbamoyltransferase complex.
Probab=21.55 E-value=65 Score=13.99 Aligned_cols=108 Identities=18% Similarity=0.251 Sum_probs=65.3
Q ss_pred HHHHHHHHCCCCEEEEEECCH---------------------------HHHHHHHHHHHHCCCEECCCCCCCCCCCCHHH
Q ss_conf 999998610788169960782---------------------------35799999986339831423345873234266
Q gi|254780779|r 56 LQVISDTVARGGRILFVATKS---------------------------QASDCVMEAAKRSAQYCVNSKWLGGMMTNWKT 108 (278)
Q Consensus 56 ~~~i~~i~~~gg~ILFVgTk~---------------------------~~~~~i~~~A~~~~~~yV~~RWlGG~LTN~~t 108 (278)
+.|=-.....||+.||.|-+- ..++.|+++|+.++.|-+|. |||..=
T Consensus 61 vSFEvA~y~lGg~~lyL~~~~~QlG~gEsi~DTARVLsRyVD~I~~R~~~h~~v~~lA~yasVPVINg------LtD~~H 134 (341)
T TIGR00658 61 VSFEVAAYQLGGQPLYLNPSDLQLGRGESIKDTARVLSRYVDGIMARVYKHEDVEELAKYASVPVING------LTDLFH 134 (341)
T ss_pred CCHHHHHHHCCCCEEECCCCCCEECCCCCCCCHHHHHCCEEEEEEEECCCHHHHHHHHHHCCCCEECC------CCCCCC
T ss_conf 00779998649821224875320036887000110203156567773255378999985489854605------568552
Q ss_pred HHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHH--HHHHH----CCCCCEEEEECCCCC--CHHHHHHHHC
Q ss_conf 655567789988763012126774678876655677764344--33221----135957999438877--1232123433
Q gi|254780779|r 109 VSQSIQKLRDLEELLNKENQGFTKKERLNIERKRDKLKRALD--GIRDM----GGLPDLMFVVDTNRE--KLAIQEARRL 180 (278)
Q Consensus 109 i~~si~~l~~l~~~~~~~~~~~tkKe~~~~~r~~~kl~k~lg--Gi~~m----~~lP~~iiv~d~~~e--~~Av~EA~kl 180 (278)
-.+-|- .+.-+.=++| .++++ ...=.+++|=|.++| +..+-=|-++
T Consensus 135 ---PcQ~LA-----------------------DllTI~E~~g~~~l~g~nkGinsklk~vy~GDgRNNVcnSL~la~a~~ 188 (341)
T TIGR00658 135 ---PCQALA-----------------------DLLTIKEHFGEKKLKGVNKGINSKLKVVYVGDGRNNVCNSLLLAAAKL 188 (341)
T ss_pred ---HHHHHH-----------------------HHHHHHHHCCCCCCCHHCCCCCCCCEEEEECCCCHHHHHHHHHHHHHH
T ss_conf ---379999-----------------------988898746795600000352442168997378512688999999972
Q ss_pred CCEEEEECCCCCCCH
Q ss_conf 981454036776700
Q gi|254780779|r 181 RIPIVAVVDTNSNPD 195 (278)
Q Consensus 181 ~IPvIaivDTn~dp~ 195 (278)
|+-+.-.+=-++.|+
T Consensus 189 Gm~~~v~tP~gyeP~ 203 (341)
T TIGR00658 189 GMDVVVATPEGYEPD 203 (341)
T ss_pred CCEEEEECCCCCCCC
T ss_conf 854788788888878
No 342
>cd06355 PBP1_FmdD_like Periplasmic component (FmdD) of an active transport system for short-chain amides and urea (FmdDEF). This group includes the periplasmic component (FmdD) of an active transport system for short-chain amides and urea (FmdDEF), found in Methylophilus methylotrophus, and its homologs from other bacteria. FmdD, a type I periplasmic binding protein, is induced by short-chain amides and urea and repressed by excess ammonia, while FmdE and FmdF are hydrophobic transmembrane proteins. FmdDEF is predicted to be an ATP-dependent transporter and closely resembles the periplasmic binding protein and the two transmembrane proteins present in various hydrophobic amino acid-binding transport systems.
Probab=21.51 E-value=65 Score=13.99 Aligned_cols=91 Identities=14% Similarity=0.262 Sum_probs=53.6
Q ss_pred HHHHHHHHHCCCCEEEEEECCH----HHHHHHHHHHHHCCCEECCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCCC
Q ss_conf 9999998610788169960782----357999999863398314233458732342666555677899887630121267
Q gi|254780779|r 55 ALQVISDTVARGGRILFVATKS----QASDCVMEAAKRSAQYCVNSKWLGGMMTNWKTVSQSIQKLRDLEELLNKENQGF 130 (278)
Q Consensus 55 A~~~i~~i~~~gg~ILFVgTk~----~~~~~i~~~A~~~~~~yV~~RWlGG~LTN~~ti~~si~~l~~l~~~~~~~~~~~ 130 (278)
+..++.+- ...+++-+++..- ...+.++..++..|.--|.+.|.+---|.|...-.+|+.
T Consensus 123 ~~~~~~~~-~g~k~vaii~~d~~~g~~~~~~~~~~~~~~G~~vv~~~~~~~g~~Dfs~~l~ki~~--------------- 186 (348)
T cd06355 123 AVDWLMSN-KGGKRFYLVGSDYVYPRTANKILKAQLESLGGEVVGEEYLPLGHTDFQSIINKIKA--------------- 186 (348)
T ss_pred HHHHHHHH-CCCCEEEEEECCCHHHHHHHHHHHHHHHHCCCEEEEEEECCCCCCCHHHHHHHHHH---------------
T ss_conf 99999984-79987999916851348999999999998599899998137997567999999997---------------
Q ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHCCCCCEEEEECCCCCCH-HHHHHHHCCC-----EEEEE
Q ss_conf 746788766556777643443322113595799943887712-3212343398-----14540
Q gi|254780779|r 131 TKKERLNIERKRDKLKRALDGIRDMGGLPDLMFVVDTNREKL-AIQEARRLRI-----PIVAV 187 (278)
Q Consensus 131 tkKe~~~~~r~~~kl~k~lgGi~~m~~lP~~iiv~d~~~e~~-Av~EA~kl~I-----PvIai 187 (278)
.-||+||+.....+.. .+++++.+|+ |+++.
T Consensus 187 --------------------------a~pD~v~~~~~g~~~~~~~~q~~~~G~~~~~~~~~~~ 223 (348)
T cd06355 187 --------------------------AKPDVVVSTVNGDSNVAFFKQLKAAGITASKVPVLSF 223 (348)
T ss_pred --------------------------CCCCEEEEECCCCCHHHHHHHHHHHCCCCCCCEEEEE
T ss_conf --------------------------6999999947651248999999981787667358884
No 343
>TIGR00644 recJ single-stranded-DNA-specific exonuclease RecJ; InterPro: IPR004610 All proteins in this family are 5'-3' single-strand DNA exonucleases. These proteins are used in some aspects of mismatch repair, recombination, and recombinational repair. RecJ is a single-stranded DNA-specific endonuclease which is required for many types of recombination events, although the stringency of the requirement for RecJ appears to vary with the type of recombinational event monitored, and the other recombination gene products which are available.; GO: 0008409 5'-3' exonuclease activity, 0006281 DNA repair, 0006310 DNA recombination.
Probab=21.46 E-value=65 Score=13.98 Aligned_cols=114 Identities=19% Similarity=0.278 Sum_probs=69.5
Q ss_pred EEECHHHHHHHHHHHHHHHHHHHCCCCEEEEEECCHH----HHHHHHHHHHHCCCEECCCCC-CCCCCCCHHHHHHHHHH
Q ss_conf 6753899999999999999986107881699607823----579999998633983142334-58732342666555677
Q gi|254780779|r 41 HIIDLSQTVPMLQKALQVISDTVARGGRILFVATKSQ----ASDCVMEAAKRSAQYCVNSKW-LGGMMTNWKTVSQSIQK 115 (278)
Q Consensus 41 hIIdL~kT~~~L~~A~~~i~~i~~~gg~ILFVgTk~~----~~~~i~~~A~~~~~~yV~~RW-lGG~LTN~~ti~~si~~ 115 (278)
|+-|--.-+.-+++|..-|.+-..++.+||++|=.-. +.-+..++-...|. |+.-+| +|.-+|-.--
T Consensus 30 ~l~~~p~~l~dm~kAv~ri~~A~~~~eki~i~GDyDvDGiTSt~~l~~~L~~lGp-~~~~~~~IPnR~~egYG------- 101 (705)
T TIGR00644 30 HLHDPPFLLKDMEKAVERIIEAIENNEKILIFGDYDVDGITSTAILVEFLRELGP-YVQVDYYIPNRFTEGYG------- 101 (705)
T ss_pred CCCCCCHHCCCHHHHHHHHHHHHHCCCCEEEEECCCCCHHHHHHHHHHHHHHCCC-CCEEEEEECCCCCCCCC-------
T ss_conf 8878702114368999999999972893899961752268999999999995099-73246662663577778-------
Q ss_pred HHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCEEEEECCC-CCCHHHHHHHHCCCEEEEECCCCCC
Q ss_conf 89988763012126774678876655677764344332211359579994388-7712321234339814540367767
Q gi|254780779|r 116 LRDLEELLNKENQGFTKKERLNIERKRDKLKRALDGIRDMGGLPDLMFVVDTN-REKLAIQEARRLRIPIVAVVDTNSN 193 (278)
Q Consensus 116 l~~l~~~~~~~~~~~tkKe~~~~~r~~~kl~k~lgGi~~m~~lP~~iiv~d~~-~e~~Av~EA~kl~IPvIaivDTn~d 193 (278)
+.++.+.-..+. | =++||-+|.. ..+-+|+-|+.+||.|| +.|=.|.
T Consensus 102 ---------------~~~~~~~~~~~~--------G-------~~LiiTVD~Gi~a~~e~~~a~~~G~dVI-VtDHHC~ 149 (705)
T TIGR00644 102 ---------------LSPEALRELKEN--------G-------VSLIITVDNGISAHEEIEYAKELGIDVI-VTDHHCL 149 (705)
T ss_pred ---------------CCHHHHHHHHHC--------C-------CEEEEECCCCHHHHHHHHHHHHCCCEEE-EECCCCC
T ss_conf ---------------898999999866--------9-------8399982687426999999986698199-9725679
No 344
>PRK07449 2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylic acid synthase/2-oxoglutarate decarboxylase; Validated
Probab=21.34 E-value=60 Score=14.20 Aligned_cols=42 Identities=2% Similarity=-0.023 Sum_probs=26.4
Q ss_pred HHHHHHHHHHHHCCCCEEEEEECC-HHHHHHHHHHHHHCCCEECCC
Q ss_conf 999999999861078816996078-235799999986339831423
Q gi|254780779|r 52 LQKALQVISDTVARGGRILFVATK-SQASDCVMEAAKRSAQYCVNS 96 (278)
Q Consensus 52 L~~A~~~i~~i~~~gg~ILFVgTk-~~~~~~i~~~A~~~~~~yV~~ 96 (278)
+.++...+. ...+-++++|.. ..+.+.+.++|+++|.|.+..
T Consensus 204 ~~~~~~~l~---~a~rpvIiaG~~~~~a~~~l~~lae~l~~PVv~~ 246 (548)
T PRK07449 204 WLREAVDLD---LSKRGVVIAGRMPAEEAQAAAALAQLLGWPLLAD 246 (548)
T ss_pred HHHHHHHHH---HCCCEEEEECCCCHHHHHHHHHHHHHHCCCEEEE
T ss_conf 999999997---4799099986897789999999999829989983
No 345
>PRK05595 replicative DNA helicase; Provisional
Probab=21.23 E-value=65 Score=13.95 Aligned_cols=145 Identities=14% Similarity=0.234 Sum_probs=72.9
Q ss_pred HHHHHHHHHHHHHHHHHHCCCCEEEEEECCHHHHHHHHHH-HHHCCCEECCCCCCCCCCCC--HHHHHHHHHHHHHHHHH
Q ss_conf 9999999999999998610788169960782357999999-86339831423345873234--26665556778998876
Q gi|254780779|r 46 SQTVPMLQKALQVISDTVARGGRILFVATKSQASDCVMEA-AKRSAQYCVNSKWLGGMMTN--WKTVSQSIQKLRDLEEL 122 (278)
Q Consensus 46 ~kT~~~L~~A~~~i~~i~~~gg~ILFVgTk~~~~~~i~~~-A~~~~~~yV~~RWlGG~LTN--~~ti~~si~~l~~l~~~ 122 (278)
-||...|.-|.+.. ..+|+.|+|.+.--...+++..+ |..++.++- ++-.|.|+. |..+.+....+..+.-.
T Consensus 213 GKTa~alnia~~~a---~~~g~~V~~fSlEMs~~ql~~R~ls~~s~i~~~--~i~~g~l~~~~~~~~~~a~~~l~~~~l~ 287 (444)
T PRK05595 213 GKTTFALNIAEYAA---LREGKSVVIFSLEMSKEQLAYKLLCSEANVDML--RLRTGNLEDKDWENIARASGPLAAAKIY 287 (444)
T ss_pred CCHHHHHHHHHHHH---HHCCCCEEEEECCCCHHHHHHHHHHHHCCCCCC--CCCCCCCCHHHHHHHHHHHHHHHCCCCC
T ss_conf 80799999999999---866993799958899999999999964698844--2326897999999999999998548970
Q ss_pred HHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCEEEEEC------CC-C---CCHHHHH--------HHHCCCEE
Q ss_conf 30121267746788766556777643443322113595799943------88-7---7123212--------34339814
Q gi|254780779|r 123 LNKENQGFTKKERLNIERKRDKLKRALDGIRDMGGLPDLMFVVD------TN-R---EKLAIQE--------ARRLRIPI 184 (278)
Q Consensus 123 ~~~~~~~~tkKe~~~~~r~~~kl~k~lgGi~~m~~lP~~iiv~d------~~-~---e~~Av~E--------A~kl~IPv 184 (278)
.+ ...++|=-+.-.. ..++.+. .-+++||| | +. . ...+|.| |+.|+|||
T Consensus 288 i~-d~~~~ti~~i~~~---~r~~~~~--------~~~~liii-DYlqLi~~~~~~~~r~~ev~~isr~LK~lAkel~ipv 354 (444)
T PRK05595 288 ID-DTAGVSVMEMRSK---CRRLKIE--------HGIDLILI-DYLQLMSGGKSSESRQQEVSEISRSIKALAKEMECPV 354 (444)
T ss_pred CC-CCCCCCHHHHHHH---HHHHHHH--------CCCCEEEE-EHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCE
T ss_conf 54-8999648999999---9999987--------39998998-2376357898888899999999999999999969979
Q ss_pred EEECCCCCCCHHCCCEEEECCCCH
Q ss_conf 540367767001152032157726
Q gi|254780779|r 185 VAVVDTNSNPDLVDYVIPGNDDSS 208 (278)
Q Consensus 185 IaivDTn~dp~~idypIP~NDds~ 208 (278)
|+++-=|=+.+.=.=.-|.--|-.
T Consensus 355 i~lsQLnR~~e~R~dkrP~lsDLR 378 (444)
T PRK05595 355 IALSQLSRAPEQRADHRPMLSDLR 378 (444)
T ss_pred EEECCCCCCCCCCCCCCCCCCCCC
T ss_conf 997026854112799997610101
No 346
>COG3577 Predicted aspartyl protease [General function prediction only]
Probab=21.19 E-value=64 Score=14.03 Aligned_cols=36 Identities=39% Similarity=0.599 Sum_probs=26.7
Q ss_pred CEEEEECCCCCCHHHHH--HHHCCCEEEEECCCCCCCHHCCCEEEECC
Q ss_conf 57999438877123212--34339814540367767001152032157
Q gi|254780779|r 160 DLMFVVDTNREKLAIQE--ARRLRIPIVAVVDTNSNPDLVDYVIPGND 205 (278)
Q Consensus 160 ~~iiv~d~~~e~~Av~E--A~kl~IPvIaivDTn~dp~~idypIP~ND 205 (278)
.+=|++|+.--+.|+.| |+++|| |+...+|+||.+.
T Consensus 116 ~v~fLVDTGATsVal~~~dA~RlGi----------d~~~l~y~~~v~T 153 (215)
T COG3577 116 KVDFLVDTGATSVALNEEDARRLGI----------DLNSLDYTITVST 153 (215)
T ss_pred EEEEEEECCCCEEECCHHHHHHHCC----------CCCCCCCCEEEEC
T ss_conf 8899994585326537879998488----------6555688368881
No 347
>cd06358 PBP1_NHase Type I periplasmic-binding protein of the nitrile hydratase (NHase) system that selectively converts nitriles to corresponding amides. This group includes the type I periplasmic-binding protein of the nitrile hydratase (NHase) system that selectively converts nitriles to corresponding amides, which are subsequently converted by amidases to yield free carboxylic acids and ammonia. NHases from bacteria and fungi have been purified and characterized. In Rhodococcus sp., the nitrile hydratase operon consists of six genes encoding NHase regulator 2, NHase regulator 1, amidase, NHase alpha subunit, NHase beta subunit, and NHase activator. The operon produces a constitutive hydratase that has a broad substrate spectrum: aliphatic and aromatic nitriles, mononitriles and dinitriles, hydroxynitriles and amino-nitriles, and a constitutive amidase of equally low substrate specificity. NHases are metalloenzymes containing either cobalt or iron, and therefore can be classified int
Probab=21.14 E-value=66 Score=13.94 Aligned_cols=90 Identities=9% Similarity=0.086 Sum_probs=53.9
Q ss_pred HHHHHHHHHHHHCCCCEEEEEECCH----HHHHHHHHHHHHCCCEECCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCC
Q ss_conf 9999999998610788169960782----357999999863398314233458732342666555677899887630121
Q gi|254780779|r 52 LQKALQVISDTVARGGRILFVATKS----QASDCVMEAAKRSAQYCVNSKWLGGMMTNWKTVSQSIQKLRDLEELLNKEN 127 (278)
Q Consensus 52 L~~A~~~i~~i~~~gg~ILFVgTk~----~~~~~i~~~A~~~~~~yV~~RWlGG~LTN~~ti~~si~~l~~l~~~~~~~~ 127 (278)
...+..++.+. ...+++.+|+..- ...+.+++.+++.|.-.|.+-|.+---|.|..+-.+++.
T Consensus 119 ~~~~~~~~~~~-~g~k~vavi~~d~~~G~~~~~~~~~~~~~~G~~vv~~~~~~~~~~Dfs~~l~~i~~------------ 185 (333)
T cd06358 119 LAPAIPWLAEE-KGARRWYLIGNDYVWPRGSLAAAKRYIAELGGEVVGEEYVPLGTTDFTSVLERIAA------------ 185 (333)
T ss_pred HHHHHHHHHHH-CCCCEEEEEECCCHHHHHHHHHHHHHHHHCCCEEEEEEECCCCCCCHHHHHHHHHH------------
T ss_conf 99999999983-79978999926834658899999999997498599998279999789999999997------------
Q ss_pred CCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCEEEEECCCCCCH-HHHHHHHCCCE
Q ss_conf 267746788766556777643443322113595799943887712-32123433981
Q gi|254780779|r 128 QGFTKKERLNIERKRDKLKRALDGIRDMGGLPDLMFVVDTNREKL-AIQEARRLRIP 183 (278)
Q Consensus 128 ~~~tkKe~~~~~r~~~kl~k~lgGi~~m~~lP~~iiv~d~~~e~~-Av~EA~kl~IP 183 (278)
.-||+||+.....+.. .+++++.+|+.
T Consensus 186 -----------------------------~~pD~v~~~~~~~~~~~~~~q~~~~G~~ 213 (333)
T cd06358 186 -----------------------------SGADAVLSTLVGQDAVAFNRQFAAAGLR 213 (333)
T ss_pred -----------------------------CCCCEEEECCCCCHHHHHHHHHHHCCCC
T ss_conf -----------------------------4989999937772399999999976999
No 348
>COG2193 Bfr Bacterioferritin (cytochrome b1) [Inorganic ion transport and metabolism]
Probab=21.12 E-value=51 Score=14.64 Aligned_cols=27 Identities=22% Similarity=0.395 Sum_probs=15.9
Q ss_pred HHHHHHHHHCCCEECCCCCCCCCCCCHHHHH
Q ss_conf 9999998633983142334587323426665
Q gi|254780779|r 80 DCVMEAAKRSAQYCVNSKWLGGMMTNWKTVS 110 (278)
Q Consensus 80 ~~i~~~A~~~~~~yV~~RWlGG~LTN~~ti~ 110 (278)
.+....-...+|||...| |++||.-.+
T Consensus 13 ~~L~~EL~ainQYflHsr----M~~~WG~~~ 39 (157)
T COG2193 13 EALGLELAAINQYFLHSR----MYKNWGLTK 39 (157)
T ss_pred HHHHHHHHHHHHHHHHHH----HHHCCCHHH
T ss_conf 999989999999999999----981647478
No 349
>TIGR01487 SPP-like SPP-like hydrolase, Archaeal; InterPro: IPR006382 This group of Archaeal sequences is most closely related to the sucrose-phosphate phosphatases (SPP) from plants and cyanobacteria. If it should be shown that the proteins in this family possess sucrose-phosphatase activity then SPP would represent a broad family of functionally related proteins..
Probab=20.94 E-value=45 Score=14.99 Aligned_cols=55 Identities=11% Similarity=0.083 Sum_probs=30.2
Q ss_pred HHHHHHHHHHHCCCCEEEEEECC-HHHHHHHHHHHHHCCCE---------EC---CCCCCCCCCCCHH
Q ss_conf 99999999861078816996078-23579999998633983---------14---2334587323426
Q gi|254780779|r 53 QKALQVISDTVARGGRILFVATK-SQASDCVMEAAKRSAQY---------CV---NSKWLGGMMTNWK 107 (278)
Q Consensus 53 ~~A~~~i~~i~~~gg~ILFVgTk-~~~~~~i~~~A~~~~~~---------yV---~~RWlGG~LTN~~ 107 (278)
.+|..+|+....+|=.|..|.-| .++-+....+-.-.|.. |= -.+.++-+-++|-
T Consensus 23 ~~A~e~iRk~~k~GI~V~LvtGN~~~f~~al~~~i~~~G~v~~ENGg~~~~~~~~~~~~~~~~~~~~~ 90 (223)
T TIGR01487 23 LRAIEAIRKAEKKGIKVSLVTGNVVPFARALAVLIGVSGPVVAENGGVVFFNDDSEDIFLSNEEKESF 90 (223)
T ss_pred HHHHHHHHHHHHCCCEEEEEECCHHHHHHHHHHHHCCCCCEEEECCCEEEECCCCEEEEEECCCHHHH
T ss_conf 88999998675278369998088279988888750688868962683899757980353202321456
No 350
>COG2103 Predicted sugar phosphate isomerase [General function prediction only]
Probab=20.94 E-value=66 Score=13.91 Aligned_cols=161 Identities=16% Similarity=0.323 Sum_probs=92.6
Q ss_pred CHHHHHHHHHHHHHHHHHHHCCCCEEEEEECCHHHHHHHHHHHHHCCCEECCCCCCCCCCCCHHHHHHHHHHHHHHHHHH
Q ss_conf 38999999999999999861078816996078235799999986339831423345873234266655567789988763
Q gi|254780779|r 44 DLSQTVPMLQKALQVISDTVARGGRILFVATKSQASDCVMEAAKRSAQYCVNSKWLGGMMTNWKTVSQSIQKLRDLEELL 123 (278)
Q Consensus 44 dL~kT~~~L~~A~~~i~~i~~~gg~ILFVgTk~~~~~~i~~~A~~~~~~yV~~RWlGG~LTN~~ti~~si~~l~~l~~~~ 123 (278)
-.++.+..+..|.+.+..-..+||+..++|.--...--|...++-..-|-+..--.=|.+---. ..+.+.. +..+
T Consensus 38 AV~~alp~Ia~Av~~~~~~l~~GGRLiY~GAGTSGRLGvlDAsEcPPTfgv~~e~ViglIAGG~---~A~~~av--EGaE 112 (298)
T COG2103 38 AVEAALPQIAAAVDIIAAALKQGGRLIYIGAGTSGRLGVLDASECPPTFGVPPELVIGLIAGGE---EAILKAV--EGAE 112 (298)
T ss_pred HHHHHHHHHHHHHHHHHHHHHCCCEEEEECCCCCCCHHCCCHHHCCCCCCCCHHHEEEEECCCH---HHHHHHH--CCCC
T ss_conf 9999768899999999999972984999747765420103251178976888668565643878---9999763--3754
Q ss_pred HCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHC-CCCCEEEEEC----CCCCCHHHHHHHHCCCEEEEECCCCCCCH---
Q ss_conf 012126774678876655677764344332211-3595799943----88771232123433981454036776700---
Q gi|254780779|r 124 NKENQGFTKKERLNIERKRDKLKRALDGIRDMG-GLPDLMFVVD----TNREKLAIQEARRLRIPIVAVVDTNSNPD--- 195 (278)
Q Consensus 124 ~~~~~~~tkKe~~~~~r~~~kl~k~lgGi~~m~-~lP~~iiv~d----~~~e~~Av~EA~kl~IPvIaivDTn~dp~--- 195 (278)
+..- + .++ -+++.. .--|+|+=+- +.+=.-|+++|++.|..+|+|. |||+
T Consensus 113 D~~~--~--------g~~---------dl~~~~lt~~DvvvgIaASGrTPYvigal~yAr~~Ga~Ti~ia---cNp~s~i 170 (298)
T COG2103 113 DDEE--L--------GEA---------DLKNIGLTAKDVVVGIAASGRTPYVIGALEYARQRGATTIGIA---CNPGSAI 170 (298)
T ss_pred CCHH--H--------HHH---------HHHHCCCCCCCEEEEEECCCCCCHHHHHHHHHHHCCCEEEEEE---CCCCCHH
T ss_conf 4487--8--------999---------9997499967779998507998303588999886497489960---4899634
Q ss_pred --HCCCEEEEC---------C--CCHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf --115203215---------7--72689999999999999999997443
Q gi|254780779|r 196 --LVDYVIPGN---------D--DSSRSIALFCDLVASAAIDGIARQHS 231 (278)
Q Consensus 196 --~idypIP~N---------D--ds~~si~l~~~~i~~ai~~g~~~~~~ 231 (278)
..|++|--- . .|=-.-++++|.|+.+.--+..+--.
T Consensus 171 ~~~Ad~~I~~~vGPEvltGSTRlKaGTAQKlvLNMlST~~Mi~lGKvy~ 219 (298)
T COG2103 171 SRIADIAIEPVVGPEVLTGSTRLKAGTAQKLVLNMLSTGVMIKLGKVYG 219 (298)
T ss_pred HHHCCCCEEECCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCC
T ss_conf 5536833252558401036643345329999999998999997221105
No 351
>PRK08351 DNA-directed RNA polymerase subunit E''; Validated
Probab=20.92 E-value=49 Score=14.75 Aligned_cols=23 Identities=17% Similarity=0.484 Sum_probs=17.3
Q ss_pred CCEEEEECCCCCCHHHHHHHHCCCEEE
Q ss_conf 957999438877123212343398145
Q gi|254780779|r 159 PDLMFVVDTNREKLAIQEARRLRIPIV 185 (278)
Q Consensus 159 P~~iiv~d~~~e~~Av~EA~kl~IPvI 185 (278)
-+.|+|+||.+..+ |++|||..-
T Consensus 31 ~G~viI~dPe~SeI----Ak~lgi~~p 53 (61)
T PRK08351 31 FDLVIIIDVENSEI----AKKIGAKVP 53 (61)
T ss_pred CEEEEEECCHHHHH----HHHHCCCCC
T ss_conf 45999968416189----998499988
No 352
>pfam04035 consensus
Probab=20.91 E-value=50 Score=14.72 Aligned_cols=22 Identities=27% Similarity=0.563 Sum_probs=16.3
Q ss_pred CCEEEEECCCCCCHHHHHHHHCCCEE
Q ss_conf 95799943887712321234339814
Q gi|254780779|r 159 PDLMFVVDTNREKLAIQEARRLRIPI 184 (278)
Q Consensus 159 P~~iiv~d~~~e~~Av~EA~kl~IPv 184 (278)
-+.|+|+||.+..+ |++|||..
T Consensus 30 ~G~viI~dpe~SeI----Ak~l~i~~ 51 (60)
T pfam04035 30 FGLVIIIDPEKSEI----AKRLGAKI 51 (60)
T ss_pred CEEEEEECCHHHHH----HHHHCCCC
T ss_conf 35999967707799----99849998
No 353
>cd06327 PBP1_SBP_like_1 Periplasmic solute-binding domain of active transport proteins that belong to the type I periplasmic binding fold protein family. Periplasmic solute-binding domain of active transport proteins that belong to the type I periplasmic binding fold protein family. Solute binding proteins are the primary specific receptors that initiate uptake of a broad range of solutes, including amino acids, peptides and inorganic ions. The members are predicted to have a similar function to an active transport system for short chain amides and urea by sequence comparison and phylogenetic analysis. Moreover, this binding domain has high sequence identity to the family of hydrophobic amino acid transporters (HAAT), and thus may also be involved in transport of amino acids.
Probab=20.89 E-value=67 Score=13.91 Aligned_cols=77 Identities=12% Similarity=0.150 Sum_probs=42.0
Q ss_pred CCCEEEEEECCH----HHHHHHHHHHHHCCCEECCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHH
Q ss_conf 788169960782----3579999998633983142334587323426665556778998876301212677467887665
Q gi|254780779|r 65 RGGRILFVATKS----QASDCVMEAAKRSAQYCVNSKWLGGMMTNWKTVSQSIQKLRDLEELLNKENQGFTKKERLNIER 140 (278)
Q Consensus 65 ~gg~ILFVgTk~----~~~~~i~~~A~~~~~~yV~~RWlGG~LTN~~ti~~si~~l~~l~~~~~~~~~~~tkKe~~~~~r 140 (278)
.++++-+|+.+- ...+.+++..++.|.-.|...+.+---|+|..+-..+
T Consensus 134 ~~kkva~i~~d~~~G~~~~~~~~~~~~~~G~~vv~~~~~~~~~~Dfs~~l~~i--------------------------- 186 (334)
T cd06327 134 GGKKWFFLTADYAFGHSLERDARKVVKANGGKVVGSVRHPLGTSDFSSYLLQA--------------------------- 186 (334)
T ss_pred CCCEEEEEECCCHHHHHHHHHHHHHHHHCCCEEEEEEECCCCCCCHHHHHHHH---------------------------
T ss_conf 79879999537456699999999999965987999996289975568999887---------------------------
Q ss_pred HHHHHHHHHHHHHHHCCCCCEEEEECCCCCC-HHHHHHHHCCC
Q ss_conf 5677764344332211359579994388771-23212343398
Q gi|254780779|r 141 KRDKLKRALDGIRDMGGLPDLMFVVDTNREK-LAIQEARRLRI 182 (278)
Q Consensus 141 ~~~kl~k~lgGi~~m~~lP~~iiv~d~~~e~-~Av~EA~kl~I 182 (278)
+ ..-||+||+.....+. ..++.++.+|+
T Consensus 187 ------------~--~~~pD~v~~~~~~~~~~~~~~q~~~~G~ 215 (334)
T cd06327 187 ------------Q--ASGADVLVLANAGADTVNAIKQAAEFGL 215 (334)
T ss_pred ------------H--HCCCCEEEEECCCHHHHHHHHHHHHCCC
T ss_conf ------------7--5599999991665479999999997499
No 354
>pfam01522 Polysacc_deac_1 Polysaccharide deacetylase. This domain is found in polysaccharide deacetylase. This family of polysaccharide deacetylases includes NodB (nodulation protein B from Rhizobium) which is a chitooligosaccharide deacetylase. It also includes chitin deacetylase from yeast, and endoxylanases which hydrolyses glucosidic bonds in xylan.
Probab=20.33 E-value=68 Score=13.83 Aligned_cols=17 Identities=12% Similarity=0.110 Sum_probs=8.9
Q ss_pred CCCCHHHHHHHHCCCEE
Q ss_conf 87712321234339814
Q gi|254780779|r 168 NREKLAIQEARRLRIPI 184 (278)
Q Consensus 168 ~~e~~Av~EA~kl~IPv 184 (278)
..+...++-++++|...
T Consensus 106 ~~~~~~~~~~~~~Gy~~ 122 (123)
T pfam01522 106 SYNDDTLAIAKKLGYRY 122 (123)
T ss_pred CCCHHHHHHHHHCCCCC
T ss_conf 87999999999864908
No 355
>PRK00784 cobyric acid synthase; Provisional
Probab=20.24 E-value=69 Score=13.82 Aligned_cols=51 Identities=20% Similarity=0.275 Sum_probs=25.5
Q ss_pred HHHHHHHHHHHHCCCCEEEEEECCHHH------HHHH-HHHHHHCCCEEC----CCCCCCCCCC
Q ss_conf 999999999861078816996078235------7999-999863398314----2334587323
Q gi|254780779|r 52 LQKALQVISDTVARGGRILFVATKSQA------SDCV-MEAAKRSAQYCV----NSKWLGGMMT 104 (278)
Q Consensus 52 L~~A~~~i~~i~~~gg~ILFVgTk~~~------~~~i-~~~A~~~~~~yV----~~RWlGG~LT 104 (278)
+..+..-+..+..+..-|..=|.-..+ .+++ -..|+.++.|-+ -.| ||.+.
T Consensus 113 ~~~v~~a~~~L~~~~d~iV~EGAGSpaEiNL~~~Di~Nm~~A~~~~apviLV~DIdR--GGvfA 174 (492)
T PRK00784 113 LEAVLESLDRLAAEYDLVVVEGAGSPAEINLRDRDIANMGFAEAADAPVILVADIDR--GGVFA 174 (492)
T ss_pred HHHHHHHHHHHHHHCCEEEEECCCCCCCCCCCHHHHHHHHHHHHCCCCEEEEEECCC--CCHHH
T ss_conf 999999999988658899993589820026522002428999865998899997567--64268
No 356
>PRK10014 DNA-binding transcriptional repressor MalI; Provisional
Probab=20.19 E-value=69 Score=13.81 Aligned_cols=60 Identities=20% Similarity=0.166 Sum_probs=32.3
Q ss_pred CCCCEEEEECCC-CCCHHHHHHHHCCCEEEEECCCCCCCHHCCCEEEECCCCHHHHHHHHHHHHH
Q ss_conf 359579994388-7712321234339814540367767001152032157726899999999999
Q gi|254780779|r 157 GLPDLMFVVDTN-REKLAIQEARRLRIPIVAVVDTNSNPDLVDYVIPGNDDSSRSIALFCDLVAS 220 (278)
Q Consensus 157 ~lP~~iiv~d~~-~e~~Av~EA~kl~IPvIaivDTn~dp~~idypIP~NDds~~si~l~~~~i~~ 220 (278)
+..|.+++.... .+..-+......+||+|.+ |.+.+...+++..+- ...+.++....|.+
T Consensus 119 ~~vdgiIi~~~~~~~~~~~~~~~~~~iP~V~~-~~~~~~~~~~~V~~D---~~~~~~~a~~~L~~ 179 (342)
T PRK10014 119 QGVDGVVIAGAAGSSDDLRRMAEEKAIPVVFA-SRASYLDDVDTVRPD---NMQAAQLLTEHLIR 179 (342)
T ss_pred CCCCEEEEECCCCCCHHHHHHHHHCCCCEEEE-CCCCCCCCCCEEEEC---HHHHHHHHHHHHHH
T ss_conf 39888999578778889999998559979995-687788999889857---69999999999987
No 357
>PRK03202 6-phosphofructokinase; Provisional
Probab=20.18 E-value=69 Score=13.81 Aligned_cols=45 Identities=18% Similarity=0.305 Sum_probs=25.2
Q ss_pred CCEEEEECCCCCCHH-HHHHHHCCCEEEEECCCCCCCHHCCCEEEECCCCHH
Q ss_conf 957999438877123-212343398145403677670011520321577268
Q gi|254780779|r 159 PDLMFVVDTNREKLA-IQEARRLRIPIVAVVDTNSNPDLVDYVIPGNDDSSR 209 (278)
Q Consensus 159 P~~iiv~d~~~e~~A-v~EA~kl~IPvIaivDTn~dp~~idypIP~NDds~~ 209 (278)
=|++|++.-..-... -+=+...+||+|+| |.-||-=||+.|-++-
T Consensus 95 Id~Li~IGGdgS~~~a~~L~~~~~i~vigI------PkTIDNDl~~tD~t~G 140 (323)
T PRK03202 95 IDALVVIGGDGSYDGAKKLSEEYGIPCIGI------PKTIDNDLAGTDYTIG 140 (323)
T ss_pred CCEEEEECCCHHHHHHHHHHHCCCCCEEEE------CCCCCCCCCCCCCCCC
T ss_conf 999999379469999999984379748972------1444689877767888
No 358
>COG2513 PrpB PEP phosphonomutase and related enzymes [Carbohydrate transport and metabolism]
Probab=20.13 E-value=69 Score=13.80 Aligned_cols=134 Identities=16% Similarity=0.194 Sum_probs=73.8
Q ss_pred CCHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCEEEECHHHHHHHHHHHHHHHHHHHCCCCEEEEEECCHHHHHHHHHH
Q ss_conf 45899986088607547765788562102001881675389999999999999998610788169960782357999999
Q gi|254780779|r 6 FTIRQLLESGVQFGHRNFLWNPKMERYIFCERNNTHIIDLSQTVPMLQKALQVISDTVARGGRILFVATKSQASDCVMEA 85 (278)
Q Consensus 6 ~t~~~Ll~ag~H~Gh~~~~wnPkM~~yI~g~rngihIIdL~kT~~~L~~A~~~i~~i~~~gg~ILFVgTk~~~~~~i~~~ 85 (278)
-|+++|.++|+-=.|---+-.||+ +|.++|-.|++++.-+..++-|..--.. .-+|+.-+-.+ ..
T Consensus 97 rtV~~~~~aG~agi~iEDq~~pk~----cgh~~gk~l~~~~e~v~rIkAa~~a~~~------~~fvi~ARTda-~~---- 161 (289)
T COG2513 97 RTVRELEQAGAAGIHIEDQVGPKR----CGHLPGKELVSIDEMVDRIKAAVEARRD------PDFVIIARTDA-LL---- 161 (289)
T ss_pred HHHHHHHHCCCCEEEEEECCCCHH----CCCCCCCCCCCHHHHHHHHHHHHHHCCC------CCEEEEEEHHH-HH----
T ss_conf 999999975862664532255021----2788898767899999999999971558------88599961487-77----
Q ss_pred HHHCCCEECCCCCCCCCCCCHHHHHHHHHHHHHHHHHH-HCCC-CCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCEEE
Q ss_conf 86339831423345873234266655567789988763-0121-267746788766556777643443322113595799
Q gi|254780779|r 86 AKRSAQYCVNSKWLGGMMTNWKTVSQSIQKLRDLEELL-NKEN-QGFTKKERLNIERKRDKLKRALDGIRDMGGLPDLMF 163 (278)
Q Consensus 86 A~~~~~~yV~~RWlGG~LTN~~ti~~si~~l~~l~~~~-~~~~-~~~tkKe~~~~~r~~~kl~k~lgGi~~m~~lP~~ii 163 (278)
.|| +-.-|+|.+-|.+-- +..| ..++..|.+.-..+ .+ +.|=.+-
T Consensus 162 -------------~~~-------ld~AI~Ra~AY~eAGAD~if~~al~~~e~i~~f~~---------av----~~pl~~N 208 (289)
T COG2513 162 -------------VEG-------LDDAIERAQAYVEAGADAIFPEALTDLEEIRAFAE---------AV----PVPLPAN 208 (289)
T ss_pred -------------HCC-------HHHHHHHHHHHHHCCCCEECCCCCCCHHHHHHHHH---------HC----CCCCEEE
T ss_conf -------------524-------79999999999975976871366799999999998---------46----8770268
Q ss_pred EEC-CCCCCHHHHHHHHCCCEEEEE
Q ss_conf 943-887712321234339814540
Q gi|254780779|r 164 VVD-TNREKLAIQEARRLRIPIVAV 187 (278)
Q Consensus 164 v~d-~~~e~~Av~EA~kl~IPvIai 187 (278)
++- ...-..-+.|=..+|+-.|..
T Consensus 209 ~t~~g~tp~~~~~~L~~~Gv~~V~~ 233 (289)
T COG2513 209 ITEFGKTPLLTVAELAELGVKRVSY 233 (289)
T ss_pred EECCCCCCCCCHHHHHHCCCEEEEE
T ss_conf 6324898876899999669649997
Done!