Query gi|254781049|ref|YP_003065462.1| succinyl-CoA synthetase subunit beta [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 398
No_of_seqs 206 out of 1932
Neff 6.1
Searched_HMMs 39220
Date Mon May 30 06:50:53 2011
Command /home/congqian_1/programs/hhpred/hhsearch -i 254781049.hhm -d /home/congqian_1/database/cdd/Cdd.hhm
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 TIGR01016 sucCoAbeta succinyl- 100.0 0 0 1126.3 39.0 386 1-396 1-389 (389)
2 PRK00696 sucC succinyl-CoA syn 100.0 0 0 1038.7 44.0 388 1-398 1-388 (388)
3 COG0045 SucC Succinyl-CoA synt 100.0 0 0 970.9 42.5 384 1-397 1-386 (387)
4 KOG1447 consensus 100.0 0 0 788.6 29.5 391 1-394 20-410 (412)
5 KOG2799 consensus 100.0 0 0 765.2 18.4 393 1-396 23-422 (434)
6 pfam08442 ATP-grasp_2 ATP-gras 100.0 0 0 458.0 21.6 201 2-212 1-201 (202)
7 pfam00549 Ligase_CoA CoA-ligas 100.0 1.2E-27 3.1E-32 201.7 11.5 119 272-392 1-126 (128)
8 KOG1254 consensus 99.7 4.4E-19 1.1E-23 145.4 1.2 313 37-373 76-464 (600)
9 COG1042 Acyl-CoA synthetase (N 99.5 4.5E-14 1.2E-18 112.4 5.1 361 2-396 23-449 (598)
10 COG1042 Acyl-CoA synthetase (N 99.5 4.6E-14 1.2E-18 112.3 4.6 117 2-148 470-586 (598)
11 TIGR02717 AcCoA-syn-alpha acet 99.4 4.5E-12 1.1E-16 99.2 11.8 187 185-395 218-454 (457)
12 TIGR01369 CPSaseII_lrg carbamo 99.4 1.5E-11 3.8E-16 95.8 11.9 95 10-130 133-227 (1089)
13 pfam01071 GARS_A Phosphoribosy 99.3 3.1E-11 8E-16 93.7 12.4 99 6-127 4-102 (193)
14 pfam02222 ATP-grasp ATP-grasp 99.3 5.4E-10 1.4E-14 85.5 14.8 88 12-128 1-88 (171)
15 PRK02186 argininosuccinate lya 99.3 5.5E-10 1.4E-14 85.5 14.6 92 5-124 108-199 (892)
16 PRK12815 carB carbamoyl phosph 99.2 1E-10 2.6E-15 90.3 8.4 116 9-154 133-248 (1068)
17 pfam02786 CPSase_L_D2 Carbamoy 99.2 7.1E-10 1.8E-14 84.7 11.4 107 6-135 3-111 (211)
18 PRK05294 carB carbamoyl phosph 99.1 2.6E-10 6.7E-15 87.6 8.1 139 9-180 133-278 (1063)
19 PRK01372 ddl D-alanine--D-alan 99.1 1.4E-08 3.4E-13 76.3 16.0 166 5-223 99-265 (304)
20 PRK09288 purT phosphoribosylgl 99.1 5E-09 1.3E-13 79.1 13.7 95 8-126 117-212 (395)
21 TIGR00877 purD phosphoribosyla 99.1 1.2E-09 3E-14 83.3 10.3 211 8-265 112-346 (459)
22 PRK00885 phosphoribosylamine-- 99.1 3E-09 7.7E-14 80.6 11.6 199 7-253 105-307 (424)
23 PRK13789 phosphoribosylamine-- 99.1 2.7E-09 6.9E-14 80.9 10.8 212 7-265 111-328 (426)
24 TIGR02068 cya_phycin_syn cyano 99.0 1.4E-09 3.7E-14 82.7 7.9 121 8-164 222-350 (876)
25 PRK13790 phosphoribosylamine-- 99.0 6.1E-09 1.5E-13 78.6 11.1 197 7-253 106-305 (415)
26 COG0151 PurD Phosphoribosylami 99.0 6.6E-09 1.7E-13 78.3 10.8 195 7-253 106-308 (428)
27 PRK07206 hypothetical protein; 99.0 2.4E-07 6.1E-12 68.1 17.6 97 5-123 109-208 (415)
28 pfam07478 Dala_Dala_lig_C D-al 98.9 1.8E-07 4.5E-12 68.9 15.6 159 11-223 1-168 (201)
29 PRK12767 carbamoyl phosphate s 98.9 1.3E-08 3.3E-13 76.4 8.4 92 5-129 112-204 (325)
30 pfam08443 RimK RimK-like ATP-g 98.8 5.6E-08 1.4E-12 72.2 10.9 93 6-126 5-100 (190)
31 PRK01966 ddl D-alanyl-alanine 98.8 5.8E-07 1.5E-11 65.5 15.9 166 5-224 133-308 (344)
32 PRK05586 biotin carboxylase; V 98.8 9E-07 2.3E-11 64.3 16.8 107 6-135 117-225 (447)
33 PRK08462 biotin carboxylase; V 98.8 1E-07 2.6E-12 70.6 11.4 107 6-135 119-227 (446)
34 PRK08654 pyruvate carboxylase 98.8 4.1E-08 1.1E-12 73.1 9.4 167 6-212 117-292 (497)
35 PRK07178 acetyl-CoA carboxylas 98.8 3E-07 7.7E-12 67.4 13.4 165 6-210 116-289 (471)
36 PRK08591 acetyl-CoA carboxylas 98.8 3.8E-07 9.7E-12 66.8 13.8 107 6-135 117-225 (449)
37 TIGR01369 CPSaseII_lrg carbamo 98.8 4.1E-08 1E-12 73.2 8.6 331 9-391 694-1088(1089)
38 PRK06111 acetyl-CoA carboxylas 98.8 1.6E-06 4.1E-11 62.6 16.7 107 6-135 117-225 (449)
39 TIGR00514 accC acetyl-CoA carb 98.8 1.2E-07 2.9E-12 70.2 10.3 106 7-135 118-226 (451)
40 COG0458 CarB Carbamoylphosphat 98.7 2.2E-07 5.6E-12 68.3 11.0 101 7-134 119-219 (400)
41 PRK08463 acetyl-CoA carboxylas 98.7 3.8E-06 9.7E-11 60.2 16.4 107 6-135 116-225 (478)
42 TIGR02144 LysX_arch Lysine bio 98.7 7.9E-08 2E-12 71.2 7.2 81 7-113 91-173 (289)
43 PRK06019 phosphoribosylaminoim 98.6 8.5E-07 2.2E-11 64.4 11.7 93 6-127 107-199 (377)
44 TIGR02712 urea_carbox urea car 98.6 9.7E-07 2.5E-11 64.1 12.0 255 6-328 116-426 (1226)
45 COG0439 AccC Biotin carboxylas 98.6 1.1E-06 2.7E-11 63.8 11.9 101 5-127 116-218 (449)
46 PRK12999 pyruvate carboxylase; 98.6 9.6E-06 2.5E-10 57.5 16.4 108 6-136 121-230 (1147)
47 TIGR01161 purK phosphoribosyla 98.6 9.7E-07 2.5E-11 64.1 11.1 121 5-162 103-227 (386)
48 COG0026 PurK Phosphoribosylami 98.6 5.4E-06 1.4E-10 59.1 14.6 119 6-162 101-219 (375)
49 TIGR01205 D_ala_D_alaTIGR D-al 98.6 1.3E-06 3.4E-11 63.1 10.7 153 5-198 150-316 (375)
50 PRK12833 acetyl-CoA carboxylas 98.6 5.2E-06 1.3E-10 59.3 13.7 107 6-136 120-228 (458)
51 PRK06395 phosphoribosylamine-- 98.5 9.7E-07 2.5E-11 64.1 9.7 196 7-253 108-312 (435)
52 KOG0237 consensus 98.5 1.2E-06 3.2E-11 63.4 9.9 106 7-134 111-216 (788)
53 KOG0238 consensus 98.5 1.6E-05 4.1E-10 56.1 15.3 107 6-135 113-221 (670)
54 COG4770 Acetyl/propionyl-CoA c 98.5 5.1E-05 1.3E-09 52.7 16.9 108 6-136 117-226 (645)
55 PRK05294 carB carbamoyl phosph 98.4 0.00019 4.9E-09 48.9 24.0 329 9-393 673-1049(1063)
56 PRK10446 ribosomal protein S6 98.4 8.6E-06 2.2E-10 57.8 12.2 80 6-113 101-181 (300)
57 PRK12815 carB carbamoyl phosph 98.4 5E-05 1.3E-09 52.8 16.0 326 9-393 674-1049(1068)
58 pfam02655 ATP-grasp_3 ATP-gras 98.4 2.4E-06 6E-11 61.5 9.0 80 5-127 4-83 (160)
59 TIGR03103 trio_acet_GNAT GNAT- 98.2 1.2E-05 3E-10 56.9 9.2 109 8-148 301-415 (547)
60 TIGR00768 rimK_fam alpha-L-glu 98.2 1.5E-05 3.8E-10 56.3 8.7 83 7-113 116-209 (321)
61 PRK05784 phosphoribosylamine-- 98.1 1.7E-05 4.3E-10 55.9 8.2 214 7-265 112-342 (485)
62 COG0027 PurT Formate-dependent 98.0 3.2E-05 8.1E-10 54.1 7.7 84 13-120 123-206 (394)
63 COG0189 RimK Glutathione synth 97.8 0.0003 7.6E-09 47.7 10.3 93 6-125 121-215 (318)
64 PRK02471 bifunctional glutamat 97.8 0.00023 5.7E-09 48.5 8.9 89 6-123 491-583 (753)
65 COG1038 PycA Pyruvate carboxyl 97.8 0.0016 4.2E-08 42.8 12.9 128 6-171 123-259 (1149)
66 pfam06263 consensus 97.8 0.0011 2.7E-08 44.1 11.9 129 267-397 339-509 (514)
67 TIGR01235 pyruv_carbox pyruvat 97.8 0.00062 1.6E-08 45.6 10.7 167 7-212 122-298 (1169)
68 PRK06091 membrane protein FdrA 97.5 0.0029 7.4E-08 41.2 10.9 129 267-397 331-495 (555)
69 PRK05678 succinyl-CoA syntheta 97.4 0.0059 1.5E-07 39.1 11.7 125 262-395 141-288 (289)
70 PTZ00187 succinyl-CoA syntheta 97.3 0.005 1.3E-07 39.6 10.8 127 263-395 158-305 (309)
71 COG1181 DdlA D-alanine-D-alani 97.3 0.0014 3.6E-08 43.3 7.3 94 5-127 104-201 (317)
72 KOG0369 consensus 96.9 0.042 1.1E-06 33.5 13.0 106 7-135 150-257 (1176)
73 KOG0370 consensus 96.7 0.0012 3E-08 43.8 2.6 90 13-130 507-596 (1435)
74 PRK06849 hypothetical protein; 96.4 0.036 9.3E-07 34.0 8.6 95 8-135 120-214 (387)
75 KOG0368 consensus 96.3 0.026 6.7E-07 34.9 7.6 88 23-137 223-310 (2196)
76 cd07022 S49_Sppa_36K_type Sign 96.3 0.033 8.5E-07 34.2 8.1 24 178-201 146-169 (214)
77 PRK13277 5-formaminoimidazole- 96.2 0.043 1.1E-06 33.5 8.4 97 10-135 129-225 (363)
78 PRK13278 purP 5-formaminoimida 96.1 0.04 1E-06 33.7 7.7 94 9-135 126-219 (356)
79 cd01540 PBP1_arabinose_binding 96.0 0.14 3.5E-06 30.2 11.9 107 282-393 152-266 (289)
80 COG1759 5-formaminoimidazole-4 95.9 0.081 2.1E-06 31.7 8.7 95 9-134 129-223 (361)
81 cd07014 S49_SppA Signal peptid 95.9 0.078 2E-06 31.8 8.4 71 297-370 16-89 (177)
82 COG0074 SucD Succinyl-CoA synt 95.6 0.2 5E-06 29.1 11.5 132 257-395 134-289 (293)
83 cd06287 PBP1_LacI_like_8 Ligan 95.6 0.2 5.1E-06 29.1 12.0 117 268-395 120-244 (269)
84 TIGR01142 purT phosphoribosylg 95.6 0.075 1.9E-06 31.9 7.3 107 11-136 111-217 (407)
85 cd07019 S49_SppA_1 Signal pept 95.2 0.19 4.7E-06 29.3 8.3 24 178-201 142-165 (211)
86 cd06283 PBP1_RegR_EndR_KdgR_li 95.1 0.29 7.5E-06 28.0 9.5 105 281-395 138-244 (267)
87 cd06300 PBP1_ABC_sugar_binding 95.1 0.29 7.5E-06 28.0 13.4 104 282-395 147-251 (272)
88 pfam06263 consensus 95.0 0.3 7.6E-06 27.9 10.8 120 266-397 191-316 (514)
89 cd07023 S49_Sppa_N_C Signal pe 94.9 0.17 4.2E-06 29.6 7.3 24 178-201 139-162 (208)
90 COG3919 Predicted ATP-grasp en 94.8 0.08 2.1E-06 31.7 5.6 94 13-135 123-222 (415)
91 cd06319 PBP1_ABC_sugar_binding 94.7 0.36 9.1E-06 27.4 14.5 85 302-395 166-252 (277)
92 cd06318 PBP1_ABC_sugar_binding 94.6 0.4 1E-05 27.1 13.3 86 301-395 170-257 (282)
93 cd06298 PBP1_CcpA_like Ligand- 94.5 0.41 1E-05 27.0 8.8 105 282-395 139-243 (268)
94 cd06284 PBP1_LacI_like_6 Ligan 94.3 0.45 1.2E-05 26.7 10.0 104 283-395 138-242 (267)
95 cd06321 PBP1_ABC_sugar_binding 94.2 0.46 1.2E-05 26.7 12.1 90 298-395 158-249 (271)
96 cd06285 PBP1_LacI_like_7 Ligan 94.1 0.49 1.2E-05 26.5 8.8 103 284-395 138-241 (265)
97 PRK06091 membrane protein FdrA 94.1 0.49 1.3E-05 26.5 10.6 121 266-397 193-318 (555)
98 cd06292 PBP1_LacI_like_10 Liga 93.8 0.57 1.4E-05 26.1 9.3 105 281-395 143-247 (273)
99 cd06291 PBP1_Qymf_like Ligand 93.6 0.59 1.5E-05 26.0 10.1 103 282-395 135-239 (265)
100 cd06313 PBP1_ABC_sugar_binding 93.6 0.61 1.6E-05 25.9 14.7 86 301-395 163-249 (272)
101 PRK10401 DNA-binding transcrip 93.4 0.64 1.6E-05 25.7 9.9 106 280-394 196-302 (346)
102 cd01539 PBP1_GGBP Periplasmic 93.4 0.65 1.7E-05 25.7 12.9 89 299-396 178-274 (303)
103 TIGR00706 SppA_dom signal pept 93.3 0.39 1E-05 27.2 6.6 22 179-200 150-171 (224)
104 cd06317 PBP1_ABC_sugar_binding 93.2 0.71 1.8E-05 25.5 13.5 88 299-395 164-254 (275)
105 PRK10355 xylF D-xylose transpo 93.1 0.71 1.8E-05 25.5 9.8 87 300-395 189-278 (330)
106 cd06308 PBP1_sensor_kinase_lik 93.1 0.71 1.8E-05 25.4 14.1 91 300-397 161-256 (270)
107 cd06270 PBP1_GalS_like Ligand 92.9 0.77 2E-05 25.2 9.8 104 283-395 139-243 (268)
108 cd06273 PBP1_GntR_like_1 This 92.8 0.8 2E-05 25.1 9.5 102 285-395 142-244 (268)
109 cd06289 PBP1_MalI_like Ligand- 92.8 0.8 2E-05 25.1 9.7 87 299-395 156-244 (268)
110 PRK04308 murD UDP-N-acetylmura 92.5 0.86 2.2E-05 24.9 8.3 103 284-397 299-412 (445)
111 cd06310 PBP1_ABC_sugar_binding 92.5 0.87 2.2E-05 24.9 13.6 85 301-394 163-249 (273)
112 PRK10423 transcriptional repre 92.3 0.92 2.4E-05 24.7 8.8 105 281-395 195-301 (327)
113 cd06311 PBP1_ABC_sugar_binding 92.3 0.93 2.4E-05 24.7 13.7 90 299-397 163-259 (274)
114 cd01537 PBP1_Repressors_Sugar_ 92.2 0.93 2.4E-05 24.7 13.0 99 283-395 141-244 (264)
115 cd06286 PBP1_CcpB_like Ligand- 92.2 0.94 2.4E-05 24.6 10.3 103 282-395 136-239 (260)
116 cd01574 PBP1_LacI Ligand-bindi 92.2 0.94 2.4E-05 24.6 9.3 82 301-395 155-240 (264)
117 cd06294 PBP1_ycjW_transcriptio 91.9 1 2.6E-05 24.4 11.0 104 282-395 144-249 (270)
118 cd01575 PBP1_GntR Ligand-bindi 91.9 1 2.6E-05 24.4 12.4 103 282-394 138-242 (268)
119 cd06295 PBP1_CelR Ligand bindi 91.7 1.1 2.7E-05 24.3 9.0 103 283-395 148-252 (275)
120 cd06267 PBP1_LacI_sugar_bindin 91.7 1.1 2.7E-05 24.3 9.2 101 283-395 139-243 (264)
121 cd06275 PBP1_PurR Ligand-bindi 91.7 1.1 2.8E-05 24.2 8.2 83 301-395 158-244 (269)
122 cd06320 PBP1_allose_binding Pe 91.6 1.1 2.8E-05 24.2 11.6 88 299-395 160-249 (275)
123 PRK09701 D-allose transporter 91.4 1.1 2.9E-05 24.1 13.8 85 301-394 196-282 (311)
124 cd06271 PBP1_AglR_RafR_like Li 91.4 1.2 2.9E-05 24.1 9.1 104 283-395 143-247 (268)
125 cd06303 PBP1_LuxPQ_Quorum_Sens 91.3 1.2 3E-05 24.0 11.7 86 299-393 168-258 (280)
126 cd06293 PBP1_LacI_like_11 Liga 91.2 1.2 3.1E-05 23.9 11.0 103 282-394 138-242 (269)
127 cd06272 PBP1_hexuronate_repres 90.9 1.3 3.3E-05 23.7 9.2 103 283-395 134-238 (261)
128 cd01538 PBP1_ABC_xylose_bindin 90.8 1.3 3.4E-05 23.7 12.2 86 301-395 169-257 (288)
129 cd06296 PBP1_CatR_like Ligand- 90.8 1.3 3.4E-05 23.7 8.9 101 283-395 140-244 (270)
130 cd06301 PBP1_rhizopine_binding 90.5 1.4 3.5E-05 23.5 12.2 86 301-395 163-251 (272)
131 cd06316 PBP1_ABC_sugar_binding 90.3 1.5 3.7E-05 23.4 13.5 88 300-396 165-258 (294)
132 cd01542 PBP1_TreR_like Ligand- 90.2 1.5 3.8E-05 23.4 9.8 102 282-395 137-239 (259)
133 cd06297 PBP1_LacI_like_12 Liga 90.0 1.5 3.9E-05 23.3 10.7 102 282-395 141-244 (269)
134 cd06309 PBP1_YtfQ_like Peripla 89.8 1.6 4E-05 23.2 12.7 86 300-395 163-253 (273)
135 PRK10727 DNA-binding transcrip 89.7 1.6 4.1E-05 23.1 8.7 107 280-395 196-303 (342)
136 cd06274 PBP1_FruR Ligand bindi 89.5 1.7 4.2E-05 23.0 10.3 103 283-395 139-244 (264)
137 cd07018 S49_SppA_67K_type Sign 89.3 1.7 4.4E-05 22.9 7.5 24 178-201 152-175 (222)
138 PRK02472 murD UDP-N-acetylmura 89.3 1.7 4.4E-05 22.9 8.8 90 296-397 325-414 (450)
139 pfam00532 Peripla_BP_1 family. 89.2 1.7 4.4E-05 22.9 10.7 105 281-394 142-256 (281)
140 PRK03815 murD UDP-N-acetylmura 89.1 1.8 4.6E-05 22.8 8.7 106 282-397 252-368 (401)
141 cd06281 PBP1_LacI_like_5 Ligan 89.0 1.8 4.6E-05 22.8 11.1 102 283-395 139-242 (269)
142 cd06288 PBP1_sucrose_transcrip 88.4 2 5E-05 22.5 9.8 88 299-395 155-244 (269)
143 PRK10653 D-ribose transporter 88.3 2 5.1E-05 22.5 12.5 86 301-395 187-273 (295)
144 TIGR00705 SppA_67K signal pept 88.3 2 5.1E-05 22.5 7.2 251 75-364 117-404 (614)
145 PRK11303 DNA-binding transcrip 88.0 2.1 5.3E-05 22.4 10.8 103 281-395 200-304 (330)
146 cd06324 PBP1_ABC_sugar_binding 87.7 2.2 5.5E-05 22.3 14.5 79 301-388 182-264 (305)
147 PRK10703 DNA-binding transcrip 87.2 2.3 5.9E-05 22.0 9.0 106 280-395 198-305 (335)
148 cd06290 PBP1_LacI_like_9 Ligan 87.1 2.3 6E-05 22.0 8.5 85 301-395 156-242 (265)
149 pfam03709 OKR_DC_1_N Orn/Lys/A 87.1 1.8 4.7E-05 22.7 5.4 82 308-396 26-109 (111)
150 PRK02705 murD UDP-N-acetylmura 87.0 2.4 6.1E-05 22.0 9.0 91 296-397 328-420 (459)
151 cd06279 PBP1_LacI_like_3 Ligan 86.9 2.4 6.2E-05 21.9 10.5 102 282-395 155-260 (283)
152 PRK02006 murD UDP-N-acetylmura 86.7 2.5 6.4E-05 21.9 7.6 91 296-397 370-460 (501)
153 cd06302 PBP1_LsrB_Quorum_Sensi 86.6 2.5 6.4E-05 21.8 13.7 123 266-397 123-258 (298)
154 PRK11041 DNA-binding transcrip 86.1 2.7 6.8E-05 21.7 10.6 105 281-395 205-311 (341)
155 pfam02955 GSH-S_ATP Prokaryoti 85.9 2.7 6.9E-05 21.6 10.9 69 18-114 11-80 (176)
156 cd06282 PBP1_GntR_like_2 Ligan 85.6 2.8 7.1E-05 21.5 8.8 100 285-395 142-242 (266)
157 cd06323 PBP1_ribose_binding Pe 84.6 3.1 7.9E-05 21.2 12.5 84 303-395 163-247 (268)
158 pfam01740 STAS STAS domain. Th 84.5 2.7 6.9E-05 21.6 5.3 81 304-387 23-106 (106)
159 cd06305 PBP1_methylthioribose_ 84.5 3.2 8E-05 21.2 10.6 86 303-395 163-252 (273)
160 COG1609 PurR Transcriptional r 84.0 3.3 8.4E-05 21.0 10.6 117 268-395 177-303 (333)
161 cd01545 PBP1_SalR Ligand-bindi 83.6 3.4 8.7E-05 21.0 9.2 85 301-394 159-244 (270)
162 cd01536 PBP1_ABC_sugar_binding 83.4 3.5 8.9E-05 20.9 11.1 86 301-395 161-248 (267)
163 cd06299 PBP1_LacI_like_13 Liga 83.0 3.6 9.2E-05 20.8 10.2 84 301-395 157-241 (265)
164 PRK10669 putative cation:proto 82.6 3.7 9.5E-05 20.7 8.5 89 291-396 460-548 (558)
165 cd01544 PBP1_GalR Ligand-bindi 82.1 3.9 1E-04 20.6 9.6 106 280-395 137-245 (270)
166 PRK10339 DNA-binding transcrip 81.4 4.1 0.00011 20.4 9.1 102 283-395 197-300 (327)
167 TIGR01124 ilvA_2Cterm threonin 81.0 3.6 9.3E-05 20.8 4.8 54 21-87 68-134 (508)
168 TIGR01859 fruc_bis_ald_ fructo 80.7 4.4 0.00011 20.2 5.1 41 161-202 254-299 (339)
169 cd06312 PBP1_ABC_sugar_binding 80.2 4.5 0.00012 20.1 10.5 82 305-395 167-250 (271)
170 TIGR01768 GGGP-family geranylg 79.8 3.2 8.1E-05 21.2 4.2 57 291-349 159-220 (242)
171 cd06322 PBP1_ABC_sugar_binding 79.0 4.9 0.00013 19.9 15.2 83 304-395 162-246 (267)
172 cd01543 PBP1_XylR Ligand-bindi 78.9 5 0.00013 19.9 9.8 106 281-395 129-238 (265)
173 KOG1255 consensus 77.9 5.3 0.00014 19.7 5.4 108 261-370 171-280 (329)
174 TIGR02086 IPMI_arch 3-isopropy 76.9 5.6 0.00014 19.5 4.7 165 10-208 6-198 (431)
175 PRK06241 phosphoenolpyruvate s 76.7 5.7 0.00015 19.5 9.9 110 11-130 25-198 (870)
176 cd06307 PBP1_uncharacterized_s 76.3 5.9 0.00015 19.4 14.3 85 301-395 166-252 (275)
177 PRK03803 murD UDP-N-acetylmura 75.5 6.2 0.00016 19.3 9.5 95 295-397 320-414 (448)
178 TIGR00097 HMP-P_kinase phospho 75.3 6.2 0.00016 19.2 7.4 111 74-197 50-165 (264)
179 TIGR01481 ccpA catabolite cont 72.4 7.3 0.00019 18.8 5.1 43 305-354 224-266 (332)
180 TIGR00470 sepS O-phosphoseryl- 72.4 3.8 9.6E-05 20.7 2.9 97 211-341 238-351 (558)
181 cd01391 Periplasmic_Binding_Pr 70.4 8.1 0.00021 18.5 7.8 72 284-365 147-222 (269)
182 PRK10949 protease 4; Provision 69.9 8.3 0.00021 18.4 7.1 247 75-366 130-410 (618)
183 cd06280 PBP1_LacI_like_4 Ligan 68.0 9 0.00023 18.2 8.7 83 304-395 155-238 (263)
184 cd06277 PBP1_LacI_like_1 Ligan 66.5 9.7 0.00025 18.0 9.5 79 305-395 164-243 (268)
185 pfam08886 GshA Glutamate-cyste 64.9 10 0.00026 17.8 4.5 29 115-144 108-137 (404)
186 KOG3432 consensus 64.8 10 0.00027 17.8 6.7 64 292-363 34-97 (121)
187 PRK01390 murD UDP-N-acetylmura 64.6 11 0.00027 17.7 8.3 87 296-396 332-418 (457)
188 PRK09526 lacI lac repressor; R 63.7 11 0.00028 17.6 9.9 101 280-395 201-306 (342)
189 TIGR01019 sucCoAalpha succinyl 62.3 12 0.00029 17.5 6.2 104 261-370 140-245 (288)
190 PTZ00294 glycerol kinase; Prov 61.7 12 0.0003 17.4 4.9 92 294-394 373-478 (510)
191 pfam10281 Ish1 Putative stress 61.6 10 0.00026 17.8 3.4 32 4-37 5-36 (38)
192 TIGR00417 speE spermidine synt 61.3 4.8 0.00012 20.0 1.6 51 106-161 59-109 (284)
193 PRK00683 murD UDP-N-acetylmura 60.5 12 0.00032 17.3 8.4 103 283-397 268-381 (418)
194 cd06278 PBP1_LacI_like_2 Ligan 60.4 12 0.00032 17.3 10.5 101 283-395 138-241 (266)
195 KOG1663 consensus 58.4 7.8 0.0002 18.6 2.3 28 309-336 208-235 (237)
196 cd01820 PAF_acetylesterase_lik 57.2 14 0.00036 16.9 6.4 19 201-219 165-183 (214)
197 PRK12412 pyridoxal kinase; Rev 57.1 14 0.00036 16.9 7.8 17 274-290 209-225 (268)
198 TIGR01320 mal_quin_oxido malat 56.5 14 0.00037 16.8 3.8 21 68-88 263-284 (487)
199 cd01541 PBP1_AraR Ligand-bindi 52.5 17 0.00043 16.4 9.8 82 304-395 166-249 (273)
200 TIGR02584 cas_NE0113 CRISPR-as 52.5 14 0.00034 17.0 2.7 67 60-143 134-200 (224)
201 TIGR02049 gshA_ferroox glutama 52.1 17 0.00043 16.4 3.6 75 21-114 237-319 (436)
202 PRK04531 acetylglutamate kinas 51.5 17 0.00044 16.3 6.5 60 333-395 345-412 (421)
203 TIGR01087 murD UDP-N-acetylmur 50.6 18 0.00046 16.2 7.6 109 279-397 317-442 (476)
204 TIGR00326 eubact_ribD riboflav 50.5 18 0.00046 16.2 3.4 37 308-346 305-341 (393)
205 PRK09585 anmK anhydro-N-acetyl 50.4 9.9 0.00025 17.9 1.8 119 271-392 181-335 (366)
206 pfam07364 DUF1485 Protein of u 49.9 18 0.00047 16.2 6.6 75 302-392 208-291 (292)
207 COG0821 gcpE 1-hydroxy-2-methy 49.7 18 0.00047 16.1 3.9 10 269-278 297-306 (361)
208 COG0069 GltB Glutamate synthas 49.0 4.2 0.00011 20.3 -0.3 117 229-345 274-396 (485)
209 COG0769 MurE UDP-N-acetylmuram 48.5 19 0.00049 16.0 7.6 100 293-397 333-438 (475)
210 TIGR00017 cmk cytidylate kinas 48.5 19 0.00049 16.0 3.8 76 139-240 83-165 (223)
211 PRK12483 threonine dehydratase 48.2 19 0.0005 16.0 5.2 13 74-86 139-151 (521)
212 pfam11379 DUF3182 Protein of u 46.5 21 0.00053 15.8 6.9 54 18-86 113-168 (355)
213 pfam03702 UPF0075 Uncharacteri 46.1 11 0.00027 17.7 1.4 119 271-392 180-332 (363)
214 PRK03562 glutathione-regulated 45.5 21 0.00055 15.7 8.1 111 257-395 420-530 (615)
215 PRK04169 geranylgeranylglycery 45.2 22 0.00055 15.7 3.6 50 290-345 154-206 (229)
216 pfam01990 ATP-synt_F ATP synth 45.1 22 0.00055 15.7 7.3 52 303-362 24-75 (92)
217 COG2115 XylA Xylose isomerase 44.7 14 0.00034 17.0 1.7 128 257-393 257-415 (438)
218 PRK09224 threonine dehydratase 44.5 22 0.00056 15.6 5.4 18 70-87 117-135 (504)
219 cd00616 AHBA_syn 3-amino-5-hyd 43.9 23 0.00058 15.6 6.1 14 339-352 282-295 (352)
220 pfam00462 Glutaredoxin Glutare 43.7 23 0.00058 15.5 3.9 43 6-52 13-56 (60)
221 PRK09084 aspartate kinase III; 43.4 23 0.00059 15.5 4.6 20 328-347 389-409 (447)
222 PRK03659 glutathione-regulated 43.0 23 0.00059 15.5 10.1 112 256-395 420-531 (602)
223 PRK10638 glutaredoxin 3; Provi 43.0 23 0.00059 15.5 4.0 46 6-54 16-61 (83)
224 TIGR03628 arch_S11P archaeal r 42.6 24 0.0006 15.4 5.4 47 337-383 50-105 (114)
225 cd07016 S14_ClpP_1 Caseinolyti 42.5 24 0.0006 15.4 8.0 14 26-39 15-28 (160)
226 cd02066 GRX_family Glutaredoxi 42.4 24 0.00061 15.4 3.6 45 6-53 14-58 (72)
227 PRK03806 murD UDP-N-acetylmura 42.3 24 0.00061 15.4 6.4 91 295-397 314-404 (438)
228 COG0771 MurD UDP-N-acetylmuram 42.2 24 0.00061 15.4 8.5 106 281-397 297-413 (448)
229 KOG2519 consensus 42.1 22 0.00057 15.6 2.5 27 294-320 305-331 (449)
230 PRK06253 O-phosphoseryl-tRNA s 41.8 24 0.00062 15.3 6.1 17 334-350 368-384 (527)
231 cd03419 GRX_GRXh_1_2_like Glut 41.5 23 0.00058 15.6 2.5 47 6-54 14-62 (82)
232 TIGR00612 ispG_gcpE 4-hydroxy- 41.1 13 0.00033 17.2 1.2 52 276-328 479-531 (633)
233 PRK10014 DNA-binding transcrip 41.1 25 0.00064 15.3 9.7 106 280-395 202-318 (342)
234 cd03027 GRX_DEP Glutaredoxin ( 40.7 25 0.00064 15.2 3.4 46 6-54 15-60 (73)
235 PRK06382 threonine dehydratase 39.9 26 0.00066 15.2 5.4 25 266-290 293-317 (400)
236 PRK10936 periplasmic sensory p 39.8 26 0.00066 15.1 10.3 117 268-397 171-300 (340)
237 cd01844 SGNH_hydrolase_like_6 39.8 26 0.00066 15.1 5.1 28 15-42 5-34 (177)
238 cd03418 GRX_GRXb_1_3_like Glut 39.5 26 0.00067 15.1 4.2 34 6-39 14-47 (75)
239 pfam03411 Peptidase_M74 Penici 39.4 26 0.00067 15.1 4.4 52 306-360 124-181 (240)
240 TIGR00273 TIGR00273 iron-sulfu 39.4 26 0.00067 15.1 10.1 122 70-220 67-201 (450)
241 cd06306 PBP1_TorT-like TorT-li 38.8 27 0.00069 15.0 10.6 84 301-394 164-249 (268)
242 KOG3857 consensus 38.4 13 0.00034 17.1 0.9 37 7-43 89-131 (465)
243 PRK01077 cobyrinic acid a,c-di 38.3 27 0.0007 15.0 6.6 15 10-24 26-40 (451)
244 PRK09607 rps11p 30S ribosomal 38.3 28 0.0007 15.0 5.3 49 336-384 53-110 (129)
245 cd00394 Clp_protease_like Case 38.1 28 0.00071 15.0 6.4 11 189-199 113-123 (161)
246 PRK04663 murD UDP-N-acetylmura 37.8 28 0.00071 14.9 7.2 90 295-397 315-404 (438)
247 PRK08190 bifunctional enoyl-Co 37.7 18 0.00046 16.2 1.5 72 326-397 303-388 (465)
248 PRK06464 phosphoenolpyruvate s 37.6 16 0.00042 16.5 1.3 55 74-129 148-211 (794)
249 PRK08198 threonine dehydratase 37.5 28 0.00072 14.9 5.2 25 266-290 298-322 (406)
250 COG4789 EscV Type III secretor 36.8 15 0.00038 16.7 1.0 14 3-16 90-103 (689)
251 COG1646 Predicted phosphate-bi 36.4 29 0.00075 14.8 3.2 51 291-347 164-214 (240)
252 pfam08981 consensus 36.2 30 0.00075 14.8 7.0 17 29-45 15-31 (181)
253 PRK08526 threonine dehydratase 35.8 30 0.00077 14.7 5.3 24 267-290 296-319 (403)
254 COG1058 CinA Predicted nucleot 35.6 30 0.00077 14.7 5.9 63 10-77 28-95 (255)
255 pfam02195 ParBc ParB-like nucl 35.4 30 0.00078 14.7 3.9 55 342-397 26-89 (90)
256 PRK03995 hypothetical protein; 34.8 31 0.00079 14.6 5.3 40 340-379 219-262 (264)
257 PRK04690 murD UDP-N-acetylmura 34.4 32 0.0008 14.6 8.6 91 295-394 324-418 (468)
258 PTZ00317 malic enzyme; Provisi 34.1 32 0.00081 14.6 7.3 22 340-362 396-417 (570)
259 PRK05878 pyruvate phosphate di 33.8 22 0.00055 15.7 1.4 32 104-135 192-227 (529)
260 cd03364 TOPRIM_DnaG_primases T 33.7 32 0.00082 14.5 3.8 54 340-393 7-61 (79)
261 PRK08928 consensus 33.7 32 0.00082 14.5 5.8 25 304-328 358-382 (861)
262 pfam00411 Ribosomal_S11 Riboso 33.6 33 0.00083 14.5 5.9 49 335-383 45-94 (109)
263 TIGR03632 bact_S11 30S ribosom 33.4 33 0.00083 14.5 5.8 49 335-383 45-94 (108)
264 COG1879 RbsB ABC-type sugar tr 33.4 33 0.00084 14.5 12.5 120 267-395 159-286 (322)
265 PRK00536 speE spermidine synth 33.2 27 0.0007 15.0 1.8 39 120-160 65-103 (262)
266 CHL00041 rps11 ribosomal prote 32.3 34 0.00087 14.4 5.7 49 335-383 58-107 (116)
267 COG0281 SfcA Malic enzyme [Ene 32.2 34 0.00087 14.4 3.7 28 269-296 200-228 (432)
268 TIGR02903 spore_lon_C ATP-depe 31.7 3.3 8.3E-05 21.1 -3.1 58 294-351 480-546 (616)
269 PRK11660 putative sulfate tran 31.7 35 0.00089 14.3 8.7 84 304-393 476-565 (567)
270 PRK07334 threonine dehydratase 31.6 35 0.00089 14.3 5.1 23 268-290 294-316 (399)
271 PRK09492 treR trehalose repres 31.5 35 0.0009 14.3 9.8 98 281-395 197-295 (315)
272 pfam09840 DUF2067 Uncharacteri 31.5 35 0.0009 14.3 3.4 20 183-202 114-133 (190)
273 PRK13529 malate dehydrogenase; 31.3 35 0.0009 14.3 6.2 14 73-86 129-142 (563)
274 pfam01341 Glyco_hydro_6 Glycos 31.0 36 0.00091 14.2 8.0 67 292-358 154-230 (295)
275 COG0646 MetH Methionine syntha 31.0 36 0.00091 14.2 9.8 159 183-378 47-223 (311)
276 TIGR00962 atpA ATP synthase F1 30.9 22 0.00056 15.6 1.0 49 75-133 124-177 (520)
277 COG0272 Lig NAD-dependent DNA 30.2 37 0.00094 14.2 3.6 35 4-38 237-272 (667)
278 COG2759 MIS1 Formyltetrahydrof 30.2 37 0.00094 14.1 4.9 14 280-293 326-339 (554)
279 TIGR01418 PEP_synth phosphoeno 29.8 17 0.00044 16.3 0.3 95 275-371 564-673 (877)
280 pfam01949 DUF99 Protein of unk 29.0 39 0.00099 14.0 7.7 20 354-373 139-158 (185)
281 TIGR00644 recJ single-stranded 28.9 39 0.00099 14.0 7.1 14 73-86 422-435 (705)
282 COG2379 GckA Putative glycerat 28.9 17 0.00043 16.4 0.1 54 129-197 113-166 (422)
283 TIGR01746 Thioester-redct thio 28.8 39 0.00099 14.0 2.6 62 332-393 257-327 (405)
284 PRK02255 putrescine carbamoylt 28.8 39 0.001 14.0 6.7 15 31-45 61-75 (341)
285 COG0616 SppA Periplasmic serin 28.7 39 0.001 14.0 8.3 24 178-201 201-224 (317)
286 TIGR01828 pyru_phos_dikin pyru 28.7 27 0.00068 15.1 1.1 46 261-317 519-564 (920)
287 PRK05309 30S ribosomal protein 28.5 39 0.001 14.0 5.7 48 336-383 62-110 (126)
288 COG1405 SUA7 Transcription ini 28.4 25 0.00063 15.3 0.9 17 170-186 104-120 (285)
289 pfam02571 CbiJ Precorrin-6x re 28.4 40 0.001 13.9 5.3 62 288-359 162-223 (246)
290 pfam04223 CitF Citrate lyase, 28.1 40 0.001 13.9 6.9 66 282-349 216-284 (466)
291 PRK09466 metL bifunctional asp 27.6 41 0.001 13.9 4.4 23 293-315 419-448 (810)
292 TIGR01091 upp uracil phosphori 27.3 41 0.0011 13.8 4.8 33 260-292 117-157 (213)
293 cd03028 GRX_PICOT_like Glutare 27.1 42 0.0011 13.8 2.6 45 6-54 27-72 (90)
294 PRK09429 mepA penicillin-insen 26.9 42 0.0011 13.8 4.4 54 305-361 153-212 (270)
295 cd04258 AAK_AKiii-LysC-EC AAK_ 26.7 42 0.0011 13.8 4.5 41 262-302 188-228 (292)
296 PRK12861 malic enzyme; Reviewe 26.5 43 0.0011 13.7 6.8 38 279-316 617-660 (762)
297 TIGR00575 dnlj DNA ligase, NAD 25.9 44 0.0011 13.7 4.2 36 3-38 240-279 (706)
298 TIGR00416 sms DNA repair prote 25.8 44 0.0011 13.6 3.8 163 183-357 219-422 (481)
299 PRK09902 hypothetical protein; 25.7 40 0.001 13.9 1.6 17 187-203 137-153 (216)
300 pfam00730 HhH-GPD HhH-GPD supe 25.7 42 0.0011 13.8 1.7 35 8-42 18-52 (144)
301 pfam06714 Gp5_OB Gp5 N-termina 24.6 46 0.0012 13.5 2.9 28 117-145 48-75 (144)
302 TIGR02181 GRX_bact glutaredoxi 24.5 47 0.0012 13.5 3.6 44 7-52 14-59 (82)
303 PRK00766 hypothetical protein; 24.4 47 0.0012 13.5 7.6 21 354-374 146-166 (194)
304 cd05147 RIO1_euk RIO kinase fa 24.1 47 0.0012 13.4 2.4 36 187-224 123-161 (190)
305 TIGR00593 pola DNA polymerase 23.5 48 0.0012 13.4 3.2 39 8-46 92-133 (1005)
306 pfam04414 tRNA_deacylase D-ami 22.9 50 0.0013 13.3 5.1 38 341-379 172-212 (214)
307 TIGR02665 molyb_mobA molybdopt 22.9 45 0.0011 13.6 1.4 120 48-218 4-136 (202)
308 TIGR02291 rimK_rel_E_lig alpha 22.8 50 0.0013 13.3 3.6 99 7-115 40-145 (320)
309 pfam01163 RIO1 RIO1 family. Th 22.7 50 0.0013 13.3 2.4 38 185-224 107-147 (186)
310 PRK06740 histidinol-phosphatas 22.4 51 0.0013 13.2 3.6 89 279-378 218-317 (338)
311 cd06314 PBP1_tmGBP Periplasmic 22.3 51 0.0013 13.2 10.9 84 303-395 161-246 (271)
312 TIGR03470 HpnH hopanoid biosyn 22.2 51 0.0013 13.2 4.2 71 26-126 59-133 (318)
313 PRK00286 xseA exodeoxyribonucl 22.2 51 0.0013 13.2 10.1 90 265-359 134-232 (443)
314 COG1486 CelF Alpha-galactosida 21.8 52 0.0013 13.1 5.1 39 7-53 51-89 (442)
315 pfam11094 UL11 Membrane-associ 21.6 53 0.0013 13.1 1.6 16 209-225 16-31 (39)
316 TIGR02392 rpoH_proteo alternat 21.5 17 0.00043 16.4 -1.0 22 163-184 139-160 (279)
317 cd08025 RNR_PFL_like_DUF711 Un 21.4 53 0.0014 13.1 2.0 23 7-29 55-77 (400)
318 PRK01368 murD UDP-N-acetylmura 21.3 53 0.0014 13.1 7.8 89 295-397 321-409 (450)
319 PRK09271 flavodoxin; Provision 21.0 54 0.0014 13.0 3.3 13 75-87 13-25 (160)
320 PRK03992 proteasome-activating 21.0 54 0.0014 13.0 3.9 49 130-178 126-191 (390)
321 PRK07679 pyrroline-5-carboxyla 20.7 28 0.00071 14.9 -0.0 38 359-397 234-271 (279)
322 cd05119 RIO RIO kinase family, 20.4 56 0.0014 13.0 2.3 37 187-225 120-159 (187)
323 cd02812 PcrB_like PcrB_like pr 20.4 56 0.0014 13.0 6.3 60 279-345 137-196 (219)
324 PRK11706 TDP-4-oxo-6-deoxy-D-g 20.3 56 0.0014 12.9 6.4 14 340-353 303-316 (375)
325 TIGR01063 gyrA DNA gyrase, A s 20.0 57 0.0014 12.9 1.5 37 100-141 550-586 (864)
No 1
>TIGR01016 sucCoAbeta succinyl-CoA synthetase, beta subunit; InterPro: IPR005809 There are four different enzymes that share a similar catalytic mechanism which involves the phosphorylation by ATP (or GTP) of a specific histidine residue in the active site. These enzymes are: ATP citrate-lyase (4.1.3.8 from EC) , the primary enzyme responsible for the synthesis of cytosolic acetyl-CoA in many tissues, catalyzes the formation of acetyl-CoA and oxaloacetate from citrate and CoA with the concomitant hydrolysis of ATP to ADP and phosphate. ATP-citrate lyase is a tetramer of identical subunits; Succinyl-CoA ligase (GDP-forming) (6.2.1.4 from EC) is a mitochondrial enzyme that catalyzes the substrate level phosphorylation step of the tricarboxylic acid cycle: the formation of succinyl-CoA from succinate with a concomitant hydrolysis of GTP to GDP and phosphate. This enzyme is a dimer composed of an alpha and a beta subunits; Succinyl-CoA ligase (ADP-forming) (6.2.1.5 from EC) is a bacterial enzyme that during aerobic metabolism functions in the citric acid cycle, coupling the hydrolysis of succinyl-CoA to the synthesis of ATP. It can also function in the other direction for anabolic purposes. This enzyme is a tetramer composed of two alpha and two beta subunits; and Malate-CoA ligase (6.2.1.9 from EC) (malyl-CoA synthetase) , is a bacterial enzyme that forms malyl-CoA from malate and CoA with the concomitant hydrolysis of ATP to ADP and phosphate. Malate-CoA ligase is composed of two different subunits. This entry corresponds to a conserved region located in the first half of ATP citrate lyase and in the beta subunits of succinyl-CoA ligases and malate-CoA ligase. ; GO: 0003824 catalytic activity, 0008152 metabolic process.
Probab=100.00 E-value=0 Score=1126.33 Aligned_cols=386 Identities=51% Similarity=0.845 Sum_probs=382.7
Q ss_pred CCCCHHHHHHHHHHCCCCCCCCEEECCHHHHHHHHHHCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHH
Q ss_conf 98657999999998689888815747999999999872998699971213687656565567777777079958999999
Q gi|254781049|r 1 MNIHEYQAKALLRKYNVPVAKGVVISSVHAAESAIKTLPGPLYVVKSQIHAGGRGKGRFKELPADSKGGVRVESSLKSVI 80 (398)
Q Consensus 1 M~L~EyqaK~lL~~~GIpvp~g~~a~s~~ea~~~a~~ig~p~~VvKaQV~aGgRGKa~~~~~hk~~~GGV~l~~s~~ea~ 80 (398)
|||||||||+||++||||||+|.+|+|++|+..++.++|...||||||||+|||||| |||++++|++|+.
T Consensus 1 M~LHEYqAK~if~~YGiPvp~g~v~~s~~e~~~~~~~~g~~~~VvKaQVhaGGRGKA----------GGv~~a~s~ee~~ 70 (389)
T TIGR01016 1 MKLHEYQAKEIFAKYGIPVPEGEVATSVEEVEEIAEELGEGKVVVKAQVHAGGRGKA----------GGVKVAKSKEEAL 70 (389)
T ss_pred CCCCHHHHHHHHHHCCCCCCCCCEEECHHHHHHHHHHCCCCCEEEEEEEEECCCCCC----------CCEEEEECHHHHH
T ss_conf 986435589999847896788600416789999999707997899987732671121----------5768970879999
Q ss_pred HHHHHHCCCCCCCCCCCCCCCCCCCEEECCCCCCCEEEEEEEEEECCCCCEEEEEECCCCCCHHHHHHHCHHHHEEEECC
Q ss_conf 99998618765442122222443301103455565058999998347780489984478840245557483122033214
Q gi|254781049|r 81 SDIREILGSTLITKQTGPTGSRVNCVYVEDGADILRELYLSLLVDRTSGMVAFIASTQGGMDIEEVAKDYPQKIFKLLID 160 (398)
Q Consensus 81 ~~a~~ilg~~l~t~qt~~~G~~v~~vLVEe~v~~~~E~ylgi~~Dr~~~~~vii~S~~GGvdIE~va~~~p~~I~~~~id 160 (398)
++|.+|||+.+.|+||++.|++|++||||++++|.||||+|+++||+.++|++|+|++||||||++|+++||+|++.+||
T Consensus 71 ~~a~~llg~~l~t~Qt~~~g~~VnkiliE~~~~I~kEyY~s~v~DR~~~~pv~maS~eGGvdIEEvA~~~Pe~I~k~~id 150 (389)
T TIGR01016 71 KAAEKLLGKELKTFQTDPLGQPVNKILIEEKIDIDKEYYLSIVIDRSAKKPVIMASTEGGVDIEEVAEKSPEKIIKVAID 150 (389)
T ss_pred HHHHHHHCCEEEEEECCCCCCEEEEEEECCCCCCCCEEEEEEEEEECCCCCEEEEECCCCCCHHHHHHCCCCCEEEEEEC
T ss_conf 99998708915786407888634478732677412001477999804787179970677841789952195716888717
Q ss_pred CCCCCCHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCEEEECCCCCEEEEEEEEEECCCHHHHHHHHH
Q ss_conf 44578957888788751988899885999999998999955975102326799059967994001321573556410278
Q gi|254781049|r 161 PLIGVTSEDVASLCDMLELQGQARIDGGDLFPNLYKAFCDKDMSLLEINPLIIMKNGRLRVLDSKISFDDNALYRHLDIQ 240 (398)
Q Consensus 161 ~~~gl~~~~~~~l~~~lg~~~~~~~~~~~ii~~L~~~f~e~Da~liEINPLvvt~dg~vvAlDAKi~iDDnA~fR~~~~~ 240 (398)
|..++.+||+|.++++++|++..+.++.+++.+||++|.++|++|+||||||+|+||.++|||||+++||||+|||||+.
T Consensus 151 p~~~~~pYq~R~~a~~~~l~~~~~~~~~~i~~~Ly~~F~e~Da~L~EINPLViT~~G~L~alDAKl~~DDnALFRH~~l~ 230 (389)
T TIGR01016 151 PLTGLLPYQARELAKKLGLEGELIKQVASIIKKLYQIFLEKDASLVEINPLVITKDGNLVALDAKLTIDDNALFRHPDLE 230 (389)
T ss_pred CCCCCCCHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCEEEECCEEECCCCCEEEEEEECCCCCCHHCCCCCHH
T ss_conf 77777878999999970897057788999999999988753710254526368789888998332244655100671168
Q ss_pred HHHCCCCCCHHHHHHHHCCCCEEECCCCEEEEECCCHHHHHHHHHHHHCCCCCCEEEECCCCCCHHHHHHHHHHHHCCCC
Q ss_conf 63100015622245775398644228817999555036899999999658996248842788898999999999861998
Q gi|254781049|r 241 ELRDVSEEDSREIEAKQHNLSYIALDGNIGCMVNGAGLAMATMDIIKLYGGAPANFLDVGGGADQDKVAAAFKIITSDSS 320 (398)
Q Consensus 241 ~~~d~~~~~~~E~~A~~~~l~yv~LdG~Ig~~vnGaGlamatmD~i~~~Gg~pANFlD~gG~a~~e~~~~a~~~il~~~~ 320 (398)
+|||++|+|++|.+|++.|||||+||||||||||||||||+|||+|+.|||+||||||||||||.|+|++||++|||||+
T Consensus 231 ~~~D~~~~~~~e~~A~~~gL~Yv~LdGnIGc~vNGAGLAMaTMDIiKl~GG~PANFLDvGGGA~~e~v~eA~~~vLsD~~ 310 (389)
T TIGR01016 231 EMEDYTQEDQLEVEAKQLGLNYVKLDGNIGCMVNGAGLAMATMDIIKLYGGKPANFLDVGGGASEERVKEALKLVLSDKS 310 (389)
T ss_pred HHCCCCCCCHHHHHHHHHCCCEEEECCCEEEECCCHHHHHHHHHHHHHHCCCCCEECCCCCCCCHHHHHHHHHHHHCCCC
T ss_conf 76388877733799986188368854770797043567899999999718895302245878898999999898735998
Q ss_pred CCEEEEECCCCHHHHHHHHHHHHHHHHHCCCCCCEEEECCCCCHHHHHHHHHHCC---CCEEEECCHHHHHHHHHHHHH
Q ss_conf 6589996358613289999999999997299987999748985899999999769---958994998999999999850
Q gi|254781049|r 321 VKGILINIFGGIMRCDVLVKGILSAVKEVKINIPLVMRLEGANVDIGNRLIAESG---LNVITAIDLDDAAQKIVHAVK 396 (398)
Q Consensus 321 vk~iliNifGGI~~cd~vA~gii~a~~~~~~~~pivvRl~Gtn~~~g~~il~~~g---~~~~~~~~~~~A~~~~v~~~k 396 (398)
||+|||||||||||||.||+|||.|+++.+.++|+||||.|||+|+|++||+||| +|+++++||++||+|+|++++
T Consensus 311 VKvvfiNIFGGI~RCD~vA~G~v~A~~~~~~~VP~VvRL~GTN~E~G~~iL~e~gkdr~ni~~~~sm~~aA~kaV~~~~ 389 (389)
T TIGR01016 311 VKVVFINIFGGITRCDEVAKGLVEALKDVGVNVPVVVRLEGTNVEEGKKILQESGKDRLNIIFATSMEEAAEKAVELAK 389 (389)
T ss_pred CEEEEEEECCCEECHHHHHHHHHHHHHCCCCCCCEEEECCCCCHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHHHC
T ss_conf 2089997068600187887889999831885368789815788788889999727677886322687889999999839
No 2
>PRK00696 sucC succinyl-CoA synthetase subunit beta; Provisional
Probab=100.00 E-value=0 Score=1038.67 Aligned_cols=388 Identities=59% Similarity=0.939 Sum_probs=385.4
Q ss_pred CCCCHHHHHHHHHHCCCCCCCCEEECCHHHHHHHHHHCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHH
Q ss_conf 98657999999998689888815747999999999872998699971213687656565567777777079958999999
Q gi|254781049|r 1 MNIHEYQAKALLRKYNVPVAKGVVISSVHAAESAIKTLPGPLYVVKSQIHAGGRGKGRFKELPADSKGGVRVESSLKSVI 80 (398)
Q Consensus 1 M~L~EyqaK~lL~~~GIpvp~g~~a~s~~ea~~~a~~ig~p~~VvKaQV~aGgRGKa~~~~~hk~~~GGV~l~~s~~ea~ 80 (398)
|||||||||+||++||||||+|.+++|++|+.++++++++|+||||||||+|||||| ||||+++|++|+.
T Consensus 1 M~LhEyqaKell~~~gIpvp~g~v~~~~~ea~~~~~~l~~~~~VvKAQV~aGGRGKa----------GGVk~~~s~~ea~ 70 (388)
T PRK00696 1 MNLHEYQAKELLAEYGVPVPRGYVAFTPEEAVEAAEELGGPVWVVKAQVHAGGRGKA----------GGVKVAKSKEEVR 70 (388)
T ss_pred CCHHHHHHHHHHHHCCCCCCCCEEECCHHHHHHHHHHHCCCCEEEEEEECCCCCCCC----------CEEEEECCHHHHH
T ss_conf 963489999999986998999737799999999999829995899980545888868----------6079908999999
Q ss_pred HHHHHHCCCCCCCCCCCCCCCCCCCEEECCCCCCCEEEEEEEEEECCCCCEEEEEECCCCCCHHHHHHHCHHHHEEEECC
Q ss_conf 99998618765442122222443301103455565058999998347780489984478840245557483122033214
Q gi|254781049|r 81 SDIREILGSTLITKQTGPTGSRVNCVYVEDGADILRELYLSLLVDRTSGMVAFIASTQGGMDIEEVAKDYPQKIFKLLID 160 (398)
Q Consensus 81 ~~a~~ilg~~l~t~qt~~~G~~v~~vLVEe~v~~~~E~ylgi~~Dr~~~~~vii~S~~GGvdIE~va~~~p~~I~~~~id 160 (398)
+.+++|||++|+|+||+++|++|++|||||++++.+|||+|+++||++++|++|+|.+||||||++|+++|++|++.++|
T Consensus 71 ~~a~~ilg~~lvT~QTg~~G~~V~~vlvee~~~i~~E~Ylsi~~DR~~~~~~~i~S~~GG~dIEevA~~~Pe~I~k~~id 150 (388)
T PRK00696 71 AAAEEILGKDLVTHQTGPEGQPVNRLLIEEGADIAKELYLSAVVDRATRRVVFMASTEGGMEIEEVAEETPEKIHKVAVD 150 (388)
T ss_pred HHHHHHHCCCCCEECCCCCCCEEEEEEEEECCCHHHHEEEEEEEECCCCCEEEEEECCCCCCHHHHHHHCHHHEEEEECC
T ss_conf 99999856774210158888444799987516612406899998647785799998887987999865291238999757
Q ss_pred CCCCCCHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCEEEECCCCCEEEEEEEEEECCCHHHHHHHHH
Q ss_conf 44578957888788751988899885999999998999955975102326799059967994001321573556410278
Q gi|254781049|r 161 PLIGVTSEDVASLCDMLELQGQARIDGGDLFPNLYKAFCDKDMSLLEINPLIIMKNGRLRVLDSKISFDDNALYRHLDIQ 240 (398)
Q Consensus 161 ~~~gl~~~~~~~l~~~lg~~~~~~~~~~~ii~~L~~~f~e~Da~liEINPLvvt~dg~vvAlDAKi~iDDnA~fR~~~~~ 240 (398)
|..|++++++|.+++.+|++++...++.+++.+||++|.++||+|+|||||++|+||+++|||||++|||||+||||+|.
T Consensus 151 p~~gl~~~~~r~i~~~lgl~~~~~~~~~~ii~~Ly~~F~~~Da~LvEINPLv~t~dg~~ialDaKv~iDDNAlfR~~~i~ 230 (388)
T PRK00696 151 PLVGLQPYQAREIAFKLGLPGEQVKQAVKIFMGLYKAFVEKDASLVEINPLVVTKDGDLLALDAKITFDDNALFRHPDIA 230 (388)
T ss_pred CCCCCCHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCEEECCCEEECCCCCEEEEEEEEECCCCHHHCCHHHH
T ss_conf 77798999999999982999999999999999999999965974256124268689978998889841675233186667
Q ss_pred HHHCCCCCCHHHHHHHHCCCCEEECCCCEEEEECCCHHHHHHHHHHHHCCCCCCEEEECCCCCCHHHHHHHHHHHHCCCC
Q ss_conf 63100015622245775398644228817999555036899999999658996248842788898999999999861998
Q gi|254781049|r 241 ELRDVSEEDSREIEAKQHNLSYIALDGNIGCMVNGAGLAMATMDIIKLYGGAPANFLDVGGGADQDKVAAAFKIITSDSS 320 (398)
Q Consensus 241 ~~~d~~~~~~~E~~A~~~~l~yv~LdG~Ig~~vnGaGlamatmD~i~~~Gg~pANFlD~gG~a~~e~~~~a~~~il~~~~ 320 (398)
++||+++++|+|.+|+++|||||+||||||||||||||||||||+|+++||+||||||+||+|+.|+|++||+++++||+
T Consensus 231 ~~rd~~~ed~~E~~A~~~~lnyv~LdG~IG~mvNGAGLaMaTmD~i~~~Gg~pANFLDvGG~a~~e~v~~a~~ii~~d~~ 310 (388)
T PRK00696 231 ALRDPSQEDPREAEASKFDLNYVALDGNIGCMVNGAGLAMATMDIIKLHGGEPANFLDVGGGATKERVTEAFKIILSDPN 310 (388)
T ss_pred HCCCCCCCCHHHHHHHHCCCCEEEECCEEEEEECCCCCCCHHHHHHHHCCCCCCEEEECCCCCCHHHHHHHHHHHHCCCC
T ss_conf 32687648978999988697359745769999747644413589999759985425634899889999999999866999
Q ss_pred CCEEEEECCCCHHHHHHHHHHHHHHHHHCCCCCCEEEECCCCCHHHHHHHHHHCCCCEEEECCHHHHHHHHHHHHHCC
Q ss_conf 658999635861328999999999999729998799974898589999999976995899499899999999985069
Q gi|254781049|r 321 VKGILINIFGGIMRCDVLVKGILSAVKEVKINIPLVMRLEGANVDIGNRLIAESGLNVITAIDLDDAAQKIVHAVKGV 398 (398)
Q Consensus 321 vk~iliNifGGI~~cd~vA~gii~a~~~~~~~~pivvRl~Gtn~~~g~~il~~~g~~~~~~~~~~~A~~~~v~~~k~v 398 (398)
||+|||||||||+|||+||+||++|+++.++++|+||||+|||+++|++||+++|+++++++||+|||+++|+++||.
T Consensus 311 vk~IliNIfGGI~rcd~vA~giv~A~~~~~~~~PiVvRl~Gtn~e~g~~iL~~sgl~i~~~~~l~eAa~~aV~~~~g~ 388 (388)
T PRK00696 311 VKAILVNIFGGIMRCDVIAEGIVAAVKEVGVKVPLVVRLEGTNVELGKKILAESGLPIIAADSLMDAAQKVVAAVAGK 388 (388)
T ss_pred CEEEEEEECCCCCCHHHHHHHHHHHHHHCCCCCCEEEEECCCCHHHHHHHHHHCCCCEEEECCHHHHHHHHHHHHCCC
T ss_conf 509999936882439999999999999649998789990678879999999978997487078999999999973489
No 3
>COG0045 SucC Succinyl-CoA synthetase, beta subunit [Energy production and conversion]
Probab=100.00 E-value=0 Score=970.94 Aligned_cols=384 Identities=55% Similarity=0.879 Sum_probs=377.8
Q ss_pred CCCCHHHHHHHHHHCCCCCCCCEEECCHHHHHHHHHHCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHH
Q ss_conf 98657999999998689888815747999999999872998699971213687656565567777777079958999999
Q gi|254781049|r 1 MNIHEYQAKALLRKYNVPVAKGVVISSVHAAESAIKTLPGPLYVVKSQIHAGGRGKGRFKELPADSKGGVRVESSLKSVI 80 (398)
Q Consensus 1 M~L~EyqaK~lL~~~GIpvp~g~~a~s~~ea~~~a~~ig~p~~VvKaQV~aGgRGKa~~~~~hk~~~GGV~l~~s~~ea~ 80 (398)
|||||||||+||++||||||+|.+++|++|+..++.++|.++||+|||||+|||||| ||||+++|++|++
T Consensus 1 M~lhEYqaKelf~~~GiPvp~g~v~~s~eea~~~a~~lg~~~~VvKaQV~aGGRGKa----------GGVk~~~s~~ea~ 70 (387)
T COG0045 1 MNLHEYQAKELFAKYGIPVPPGYVATSPEEAEEAAKELGGGPVVVKAQVHAGGRGKA----------GGVKLAKSPEEAK 70 (387)
T ss_pred CCHHHHHHHHHHHHCCCCCCCCEEEECHHHHHHHHHHHCCCCEEEEEEEEECCCCCC----------CCEEEECCHHHHH
T ss_conf 967888899899972998999545408999999999818996799922530576666----------7668838989999
Q ss_pred HHHHHHCCCCCCCCCCCCCCCCCCCEEECCCCCCC-EEEEEEEEEECCCCCEEEEEECCCCCCHHHHHHHCHHHHEEEEC
Q ss_conf 99998618765442122222443301103455565-05899999834778048998447884024555748312203321
Q gi|254781049|r 81 SDIREILGSTLITKQTGPTGSRVNCVYVEDGADIL-RELYLSLLVDRTSGMVAFIASTQGGMDIEEVAKDYPQKIFKLLI 159 (398)
Q Consensus 81 ~~a~~ilg~~l~t~qt~~~G~~v~~vLVEe~v~~~-~E~ylgi~~Dr~~~~~vii~S~~GGvdIE~va~~~p~~I~~~~i 159 (398)
+++++|||++ +||+++|++|++||||+++++. +|||+|+++||+.++|++|+|++||||||++++++|++|++.++
T Consensus 71 ~~a~~~lg~~---~q~~~~G~~v~~vlvee~~~~~~~E~Ylsiv~DR~~~~p~~~~S~eGGmDIEeVa~~~PekI~~~~i 147 (387)
T COG0045 71 EAAEEILGKN---YQTDIKGEPVNKVLVEEAVDIIKKEYYLSIVLDRSSRRPVLMASTEGGMDIEEVAEKTPEKIVKVSV 147 (387)
T ss_pred HHHHHHHCCC---CCCCCCCCEEEEEEEEECCCCCCCEEEEEEEEECCCCCEEEEEECCCCCCHHHHHHHCHHHEEEEEE
T ss_conf 9999984866---5457688454289997467776433799999973778379999667795189950028345268974
Q ss_pred CCCCCCCHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCEEEECCCC-CEEEEEEEEEECCCHHHHHHH
Q ss_conf 4445789578887887519888998859999999989999559751023267990599-679940013215735564102
Q gi|254781049|r 160 DPLIGVTSEDVASLCDMLELQGQARIDGGDLFPNLYKAFCDKDMSLLEINPLIIMKNG-RLRVLDSKISFDDNALYRHLD 238 (398)
Q Consensus 160 d~~~gl~~~~~~~l~~~lg~~~~~~~~~~~ii~~L~~~f~e~Da~liEINPLvvt~dg-~vvAlDAKi~iDDnA~fR~~~ 238 (398)
||..|+++|++|.+++.+|+++....++++++.+||++|.++|++|+|||||++|+++ +++|||||++|||||+||||+
T Consensus 148 dp~~g~~~~~aR~la~~lgl~~~~~~~~~~ii~~ly~~f~~~Da~lvEINPLvvt~~~g~v~aLDaKi~~DdnAlfRHp~ 227 (387)
T COG0045 148 DPLTGLRPYQARELAFKLGLEGELVKQVADIIKKLYKLFVEKDATLVEINPLVVTPDGGDVLALDAKITLDDNALFRHPD 227 (387)
T ss_pred CCCCCCCHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCEEEEECCEEECCCCCEEEEEEEEECCCCCCCCCCC
T ss_conf 77668787799999997499878999999999999999997587678752508817998089976454036764346834
Q ss_pred HHHHHCCCCCCHHHHHHHHCCCCEEECCCCEEEEECCCHHHHHHHHHHHHCCCCCCEEEECCCCCCHHHHHHHHHHHHCC
Q ss_conf 78631000156222457753986442288179995550368999999996589962488427888989999999998619
Q gi|254781049|r 239 IQELRDVSEEDSREIEAKQHNLSYIALDGNIGCMVNGAGLAMATMDIIKLYGGAPANFLDVGGGADQDKVAAAFKIITSD 318 (398)
Q Consensus 239 ~~~~~d~~~~~~~E~~A~~~~l~yv~LdG~Ig~~vnGaGlamatmD~i~~~Gg~pANFlD~gG~a~~e~~~~a~~~il~~ 318 (398)
+.++||.++++|+|.+|++++||||+||||||||+|||||+|+|||+|+++||+||||||+||+||.|++++||++|++|
T Consensus 228 ~~~~~d~~~ed~~e~~a~~~~l~yV~LdG~IG~ivNGAGLaMaTmDii~~~Gg~PANFLDvGGgA~~e~v~~a~~~il~d 307 (387)
T COG0045 228 LAELRDESEEDPREAEASGYGLNYVELDGNIGCIVNGAGLAMATMDIVKLYGGKPANFLDVGGGATAERVKEAFKLILSD 307 (387)
T ss_pred HHHHHCCCCCCHHHHHHHHCCCCEEEECCCEEEEECCHHHHHHHHHHHHHCCCCCCCEEECCCCCCHHHHHHHHHHHHCC
T ss_conf 45553233358557876127875188638378996272699999999998089974144148999988999999998459
Q ss_pred CCCCEEEEECCCCHHHHHHHHHHHHHHHHHCCCCCCEEEECCCCCHHHHHHHHHHCCCCEEEECCHHHHHHHHHHHHHC
Q ss_conf 9865899963586132899999999999972999879997489858999999997699589949989999999998506
Q gi|254781049|r 319 SSVKGILINIFGGIMRCDVLVKGILSAVKEVKINIPLVMRLEGANVDIGNRLIAESGLNVITAIDLDDAAQKIVHAVKG 397 (398)
Q Consensus 319 ~~vk~iliNifGGI~~cd~vA~gii~a~~~~~~~~pivvRl~Gtn~~~g~~il~~~g~~~~~~~~~~~A~~~~v~~~k~ 397 (398)
|+||+|||||||||||||.||+||++|+++.+.++|+||||.|||+|+|++||++||++++++++|++|++++|+++++
T Consensus 308 ~~vk~IfVNIfGGI~rcD~vA~GIi~Al~e~~~~vPlVVRL~GtN~e~Gk~iL~esg~~i~~~~~l~~aa~k~v~~~~~ 386 (387)
T COG0045 308 PNVKAIFVNIFGGITRCDEVAEGIIAALKEVGVNVPLVVRLEGTNVEEGKRILAESGLNIIAADDLDEAAEKAVELAKG 386 (387)
T ss_pred CCCCEEEEEECCCCCCCHHHHHHHHHHHHHCCCCCCEEEECCCCCHHHHHHHHHHCCCCEEECCCHHHHHHHHHHHHHC
T ss_conf 9854899997168675089999999999852988888998678878999999997399407624688999999998514
No 4
>KOG1447 consensus
Probab=100.00 E-value=0 Score=788.57 Aligned_cols=391 Identities=47% Similarity=0.735 Sum_probs=384.2
Q ss_pred CCCCHHHHHHHHHHCCCCCCCCEEECCHHHHHHHHHHCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHH
Q ss_conf 98657999999998689888815747999999999872998699971213687656565567777777079958999999
Q gi|254781049|r 1 MNIHEYQAKALLRKYNVPVAKGVVISSVHAAESAIKTLPGPLYVVKSQIHAGGRGKGRFKELPADSKGGVRVESSLKSVI 80 (398)
Q Consensus 1 M~L~EyqaK~lL~~~GIpvp~g~~a~s~~ea~~~a~~ig~p~~VvKaQV~aGgRGKa~~~~~hk~~~GGV~l~~s~~ea~ 80 (398)
+||.|||||+||++||+.|.+..++++..|+.++++.++.|.+|+||||++|||||+.+....| |||++.+++.++.
T Consensus 20 LNLqEfQSK~~l~k~Gv~vQ~F~Va~n~kea~E~~k~f~~~EyVvKAQILAGGRGKG~F~nG~K---GGVhiTk~k~~vl 96 (412)
T KOG1447 20 LNLQEFQSKEILSKNGVRVQRFFVADNAKEALEAAKRFNAKEYVVKAQILAGGRGKGVFNNGLK---GGVHITKDKNVVL 96 (412)
T ss_pred CCHHHHHHHHHHHHCCEEEEEEEEECCCHHHHHHHHHCCCCCEEEEEEEEECCCCCCEECCCCC---CEEEEECCHHHHH
T ss_conf 1288766678898649058999970670778999985499223776443106765542447765---4068744874999
Q ss_pred HHHHHHCCCCCCCCCCCCCCCCCCCEEECCCCCCCEEEEEEEEEECCCCCEEEEEECCCCCCHHHHHHHCHHHHEEEECC
Q ss_conf 99998618765442122222443301103455565058999998347780489984478840245557483122033214
Q gi|254781049|r 81 SDIREILGSTLITKQTGPTGSRVNCVYVEDGADILRELYLSLLVDRTSGMVAFIASTQGGMDIEEVAKDYPQKIFKLLID 160 (398)
Q Consensus 81 ~~a~~ilg~~l~t~qt~~~G~~v~~vLVEe~v~~~~E~ylgi~~Dr~~~~~vii~S~~GGvdIE~va~~~p~~I~~~~id 160 (398)
+.+++|+|++++|+||+..|.+|++|+|.+.++|.+|.||+|++||+..+|++++|++||||||.+|+++|++|.+.|+|
T Consensus 97 ~l~~qMIG~rL~TKQTpkeGv~VnKVMvAe~~dI~RETYLaiLmDRe~NGPVlvaSP~GGmDIEaVAe~tPE~Ifk~piD 176 (412)
T KOG1447 97 QLAKQMIGYRLATKQTPKEGVKVNKVMVAEALDISRETYLAILMDRECNGPVLVASPQGGMDIEAVAESTPELIFKEPID 176 (412)
T ss_pred HHHHHHHHHHHHHCCCCCCCEEEEEEEEEECCCCCHHEEEEEEECCCCCCCEEEECCCCCCCHHHHHHHCHHHHCCCCCH
T ss_conf 99999874533204488556265558873003611240014355145689779856998865999865395765144620
Q ss_pred CCCCCCHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCEEEECCCCCEEEEEEEEEECCCHHHHHHHHH
Q ss_conf 44578957888788751988899885999999998999955975102326799059967994001321573556410278
Q gi|254781049|r 161 PLIGVTSEDVASLCDMLELQGQARIDGGDLFPNLYKAFCDKDMSLLEINPLIIMKNGRLRVLDSKISFDDNALYRHLDIQ 240 (398)
Q Consensus 161 ~~~gl~~~~~~~l~~~lg~~~~~~~~~~~ii~~L~~~f~e~Da~liEINPLvvt~dg~vvAlDAKi~iDDnA~fR~~~~~ 240 (398)
...++.+.++.+++..|+|.|....+.++-|.+||.+|..-|++.+|||||..|++|+++|+|||++|||||.|||+|++
T Consensus 177 I~~gi~esq~l~~Ak~L~F~G~l~~~aA~eI~kLY~LF~avDAtQvEiNPl~ET~~G~V~cvDAK~NFDDnA~fRQKdIF 256 (412)
T KOG1447 177 IFEGIKESQALRMAKNLGFVGPLKSQAADEITKLYNLFLAVDATQVEINPLGETPEGQVVCVDAKINFDDNAEFRQKDIF 256 (412)
T ss_pred HCCCCCHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHCCEEEEECCCCCCCCCEEEEEEEECCCCCHHHHHHCCEE
T ss_conf 13688668899999844666707778999999999999651212787325665898608998501067841766423312
Q ss_pred HHHCCCCCCHHHHHHHHCCCCEEECCCCEEEEECCCHHHHHHHHHHHHCCCCCCEEEECCCCCCHHHHHHHHHHHHCCCC
Q ss_conf 63100015622245775398644228817999555036899999999658996248842788898999999999861998
Q gi|254781049|r 241 ELRDVSEEDSREIEAKQHNLSYIALDGNIGCMVNGAGLAMATMDIIKLYGGAPANFLDVGGGADQDKVAAAFKIITSDSS 320 (398)
Q Consensus 241 ~~~d~~~~~~~E~~A~~~~l~yv~LdG~Ig~~vnGaGlamatmD~i~~~Gg~pANFlD~gG~a~~e~~~~a~~~il~~~~ 320 (398)
.+.+.++++|+|.+|.+++||||.|||||+|+||||||+|||||+|+++||+||||||+||+.+.+++++||+++++||+
T Consensus 257 amd~~eE~dPrEveAakynLnYigmDGNIaClVNGAGLAMATmDiIkLnGGePANFLDvGGgV~EdqV~~Af~ilTaDPk 336 (412)
T KOG1447 257 AMDDKEENDPREVEAAKYNLNYIGMDGNIACLVNGAGLAMATMDIIKLNGGEPANFLDVGGGVKEDQVYQAFKILTADPK 336 (412)
T ss_pred ECCCCCCCCCHHHHHHHCCCCEEECCCCEEEEECCCHHHHHEEEEEEECCCCCCCEEECCCCCCHHHHHHHHHHHCCCCC
T ss_conf 10454435811334554474146316826888746314312010588549987530422676038899777643125884
Q ss_pred CCEEEEECCCCHHHHHHHHHHHHHHHHHCCCCCCEEEECCCCCHHHHHHHHHHCCCCEEEECCHHHHHHHHHHH
Q ss_conf 65899963586132899999999999972999879997489858999999997699589949989999999998
Q gi|254781049|r 321 VKGILINIFGGIMRCDVLVKGILSAVKEVKINIPLVMRLEGANVDIGNRLIAESGLNVITAIDLDDAAQKIVHA 394 (398)
Q Consensus 321 vk~iliNifGGI~~cd~vA~gii~a~~~~~~~~pivvRl~Gtn~~~g~~il~~~g~~~~~~~~~~~A~~~~v~~ 394 (398)
||+|||||||||++|..+|+||+.|+++++.++|+||||+|||.+++++||++||+|+.++.||++|++|+|..
T Consensus 337 Vk~iLvNiFGGIVNCAtIANGiv~A~~kl~LnVPlVVRLEGTNV~~A~~Ilk~SGLpI~tA~dLddAA~KAVas 410 (412)
T KOG1447 337 VKAILVNIFGGIVNCATIANGIVKACRKLELNVPLVVRLEGTNVQEAQKILKKSGLPITTAIDLDDAAKKAVAS 410 (412)
T ss_pred EEEEEEEHHCCEEHHHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHHHHCCCCEEECCCHHHHHHHHHHC
T ss_conf 03999830046311476765799998862578757999757777899999873698502213367899977643
No 5
>KOG2799 consensus
Probab=100.00 E-value=0 Score=765.17 Aligned_cols=393 Identities=46% Similarity=0.737 Sum_probs=382.5
Q ss_pred CCCCHHHHHHHHHHCCCCCCCCEEECCHHHHHHHHHHCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHH
Q ss_conf 98657999999998689888815747999999999872998699971213687656565567777777079958999999
Q gi|254781049|r 1 MNIHEYQAKALLRKYNVPVAKGVVISSVHAAESAIKTLPGPLYVVKSQIHAGGRGKGRFKELPADSKGGVRVESSLKSVI 80 (398)
Q Consensus 1 M~L~EyqaK~lL~~~GIpvp~g~~a~s~~ea~~~a~~ig~p~~VvKaQV~aGgRGKa~~~~~hk~~~GGV~l~~s~~ea~ 80 (398)
+.+|||++-+||++||+.+|++.++.|||||.++++++|...+|+|||+++|||||+.|+. +-.|||+++.+|+|++
T Consensus 23 L~~hey~~~~ll~~~Gv~vp~g~vA~speEA~~~akklg~kdlVikAQ~lAgGRgKGtF~S---glkgGV~iVf~p~Eak 99 (434)
T KOG2799 23 LGIHEYRSAALLRKYGINVPLGYVAKSPEEAFAIAKKLGSKDLVIKAQVLAGGRGKGTFDS---GLKGGVKIVFSPQEAK 99 (434)
T ss_pred HHHHHHHHHHHHHHCCCCCCCCCCCCCHHHHHHHHHHHCCCCEEEEEEECCCCCCCCCCCC---CCCCCEEEEECHHHHH
T ss_conf 4689988999999718788877556887899999997088645997520105766677376---7678637976758888
Q ss_pred HHHHHHCCCCCCCCCCCCCCCCCCCEEECCCCCCCEEEEEEEEEECCCCCEEEEEECCCCCCHHHHHHHCHHHHEEEECC
Q ss_conf 99998618765442122222443301103455565058999998347780489984478840245557483122033214
Q gi|254781049|r 81 SDIREILGSTLITKQTGPTGSRVNCVYVEDGADILRELYLSLLVDRTSGMVAFIASTQGGMDIEEVAKDYPQKIFKLLID 160 (398)
Q Consensus 81 ~~a~~ilg~~l~t~qt~~~G~~v~~vLVEe~v~~~~E~ylgi~~Dr~~~~~vii~S~~GGvdIE~va~~~p~~I~~~~id 160 (398)
+.+.+|+|++|+|+||++.|+.|+.|+|.+.....+|+|+||++||.+.+|++++|.+||++||++++++|++|.+.|+|
T Consensus 100 ~va~qmiG~kLiTKQtG~~gk~c~~v~iC~Rk~~~~e~yFsil~dr~~k~pliIas~kgg~~ie~vae~~pdai~k~pi~ 179 (434)
T KOG2799 100 AVASQMIGKKLITKQTGPAGKACSEVYICERKHTRAEYYFSILMDRHTKGPLIIASSKGGVNIEEVAEDTPDAIIKKPID 179 (434)
T ss_pred HHHHHHHCCEEEEECCCCCCCCCCEEEEEEECCHHHHHHHHHHHHCCCCCCEEEEECCCCCCHHHHHHHCCCCHHCCCCC
T ss_conf 88997634020433347888843069985101305678899987304579779982457762898865582411104555
Q ss_pred CCCCCCHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCEEEECCCC-CEEEEEEEEEECCCHHHHHHHH
Q ss_conf 445789578887887519888998859999999989999559751023267990599-6799400132157355641027
Q gi|254781049|r 161 PLIGVTSEDVASLCDMLELQGQARIDGGDLFPNLYKAFCDKDMSLLEINPLIIMKNG-RLRVLDSKISFDDNALYRHLDI 239 (398)
Q Consensus 161 ~~~gl~~~~~~~l~~~lg~~~~~~~~~~~ii~~L~~~f~e~Da~liEINPLvvt~dg-~vvAlDAKi~iDDnA~fR~~~~ 239 (398)
...|+++.++..++..||++.....+..+.+.+||++|...|++++|||||+.+.++ +++|.|||+.+||||.|||.++
T Consensus 180 ~~~Gls~~~a~~v~~~lgfs~~~~~~a~~~~~kly~vf~~~dat~veinpl~e~t~d~~v~c~dak~~fd~na~fRq~~i 259 (434)
T KOG2799 180 NNTGLSPEIACLVADKLGFSPDGIRKAAKAVPKLYKVFHKSDATQVEINPLAEITSDHKVTCMDAKLNFDDNAAFRQKKI 259 (434)
T ss_pred CCCCCCHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHCCCEEEEECCHHHCCCCCEEEECHHHHCCCCCHHHHHHHH
T ss_conf 66898888899998610889301799999999999998634642688522222156866661002323665578886455
Q ss_pred HHHHCCCCCCHHHHHHHHCCCCEEECCCCEEEEECCCHHHHHHHHHHHHCCCCCCEEEECCCCCCHHHHHHHHHHHHCCC
Q ss_conf 86310001562224577539864422881799955503689999999965899624884278889899999999986199
Q gi|254781049|r 240 QELRDVSEEDSREIEAKQHNLSYIALDGNIGCMVNGAGLAMATMDIIKLYGGAPANFLDVGGGADQDKVAAAFKIITSDS 319 (398)
Q Consensus 240 ~~~~d~~~~~~~E~~A~~~~l~yv~LdG~Ig~~vnGaGlamatmD~i~~~Gg~pANFlD~gG~a~~e~~~~a~~~il~~~ 319 (398)
+.+||.+||||+|..|++++|||+.||||||||||||||+|||||+|+++||.||||||+||+|+.|.+.++|++|++||
T Consensus 260 F~~rd~~QEd~re~~aak~~ln~igldG~igC~vngaglamaTmdiiklhgg~panfldVGg~Atve~v~eaf~litsd~ 339 (434)
T KOG2799 260 FLLRDLSQEDPREVTAAKVDLNYIGLDGNIGCLVNGAGLAMATMDIIKLHGGTPANFLDVGGGATVEQVREAFSLITSDK 339 (434)
T ss_pred HHCCCHHHCCCHHHHHHHHCCCEECCCCCCCEEECCCHHHHHHEEEEEECCCCCCCEEEECCCCCHHHHHHHHHHHHCCH
T ss_conf 40036000484056687721000125776460004305543120024304899852144079876778988888872580
Q ss_pred CCCEEEEECCCCHHHHHHHHHHHHHHHHHCCCCCCEEEECCCCCHHHHHHHHHHCCCCEEEECCHHHHHHHH------HH
Q ss_conf 865899963586132899999999999972999879997489858999999997699589949989999999------99
Q gi|254781049|r 320 SVKGILINIFGGIMRCDVLVKGILSAVKEVKINIPLVMRLEGANVDIGNRLIAESGLNVITAIDLDDAAQKI------VH 393 (398)
Q Consensus 320 ~vk~iliNifGGI~~cd~vA~gii~a~~~~~~~~pivvRl~Gtn~~~g~~il~~~g~~~~~~~~~~~A~~~~------v~ 393 (398)
+|.+||+||||||+|||.+|.||+.|.+++..++|||+||+|||.+.|+.++.+||+.+.+++++++|++++ |+
T Consensus 340 kv~ailvnifGgi~rCDvia~Giv~aar~l~~~ipiv~rlqgt~v~~ak~~i~~sgmri~~~deldeaa~~~v~~S~ive 419 (434)
T KOG2799 340 KVMAILVNIFGGIMRCDVIAFGIVLAARELELNIPIVVRLQGTRVEAAKPIINTSGMRIRSFDELDEAAKKAVGGSTIVE 419 (434)
T ss_pred HHHHHHHHHHCCEEECCCEECCHHHHHHHHHCCCCEEEEECCCCHHHHHHHHHHCCCEEEECHHHHHHHHHHCCCCHHHH
T ss_conf 49999999865720033010013356566523787899965776234146675257367741345688632216414988
Q ss_pred HHH
Q ss_conf 850
Q gi|254781049|r 394 AVK 396 (398)
Q Consensus 394 ~~k 396 (398)
+++
T Consensus 420 la~ 422 (434)
T KOG2799 420 LAS 422 (434)
T ss_pred HHH
T ss_conf 766
No 6
>pfam08442 ATP-grasp_2 ATP-grasp domain.
Probab=100.00 E-value=0 Score=458.03 Aligned_cols=201 Identities=48% Similarity=0.740 Sum_probs=199.1
Q ss_pred CCCHHHHHHHHHHCCCCCCCCEEECCHHHHHHHHHHCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHH
Q ss_conf 86579999999986898888157479999999998729986999712136876565655677777770799589999999
Q gi|254781049|r 2 NIHEYQAKALLRKYNVPVAKGVVISSVHAAESAIKTLPGPLYVVKSQIHAGGRGKGRFKELPADSKGGVRVESSLKSVIS 81 (398)
Q Consensus 2 ~L~EyqaK~lL~~~GIpvp~g~~a~s~~ea~~~a~~ig~p~~VvKaQV~aGgRGKa~~~~~hk~~~GGV~l~~s~~ea~~ 81 (398)
||||||||+||++||||||+|.+++|++||.+++++||+|+||+|||||+|||||+ |||++++|++|+++
T Consensus 1 nlhEyqaK~ll~~~gIpvp~g~~~~~~~ea~~~~~~l~~~~~VvKaQv~aGGRGKa----------GGVk~~~~~~ea~~ 70 (202)
T pfam08442 1 NLHEYQAKEILAKYGVPVPRGEVAFSPEEAEEIAKKLGGKVYVVKAQVLAGGRGKA----------GGVKLAKSPEEAKE 70 (202)
T ss_pred CCCHHHHHHHHHHCCCCCCCEEEECCHHHHHHHHHHHCCCEEEEEEEECCCCCCCC----------CEEEEECCHHHHHH
T ss_conf 95388999999985998999159699999999999809986999874235888767----------73899789999999
Q ss_pred HHHHHCCCCCCCCCCCCCCCCCCCEEECCCCCCCEEEEEEEEEECCCCCEEEEEECCCCCCHHHHHHHCHHHHEEEECCC
Q ss_conf 99986187654421222224433011034555650589999983477804899844788402455574831220332144
Q gi|254781049|r 82 DIREILGSTLITKQTGPTGSRVNCVYVEDGADILRELYLSLLVDRTSGMVAFIASTQGGMDIEEVAKDYPQKIFKLLIDP 161 (398)
Q Consensus 82 ~a~~ilg~~l~t~qt~~~G~~v~~vLVEe~v~~~~E~ylgi~~Dr~~~~~vii~S~~GGvdIE~va~~~p~~I~~~~id~ 161 (398)
++++|||++|+|+||++.|++|++|||||++++.+|||+|+++||++++|++|+|.+||||||++|+++|++|.+.+|||
T Consensus 71 ~a~~~lg~~l~T~QTg~~G~~V~~vlvee~~~i~~E~Ylsi~~DR~~~~~~ii~S~~GG~dIEeVa~~~Pe~I~k~~id~ 150 (202)
T pfam08442 71 AAKEMLGKNLVTKQTGPEGKPVNKVLVEEAVDIAREYYLSIVLDRASRGPVVIASSEGGVDIEEVAAKNPEAIIKVPIDP 150 (202)
T ss_pred HHHHHCCCEEEEEECCCCCCEEEEEEEEECCCCCCEEEEEEEECCCCCCEEEEEECCCCCCHHHHHCCCHHHEEEEEECC
T ss_conf 99987297787550278896233899985154010079999975777844789726788509997300955729997187
Q ss_pred CCCCCHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCEEE
Q ss_conf 457895788878875198889988599999999899995597510232679
Q gi|254781049|r 162 LIGVTSEDVASLCDMLELQGQARIDGGDLFPNLYKAFCDKDMSLLEINPLI 212 (398)
Q Consensus 162 ~~gl~~~~~~~l~~~lg~~~~~~~~~~~ii~~L~~~f~e~Da~liEINPLv 212 (398)
..|++++++|++++.+|+++....++.+++.+||++|.++||+|+|||||+
T Consensus 151 ~~gl~~~~~r~~~~~lg~~~~~~~~~~~~i~~Ly~~f~~~Da~llEINPLV 201 (202)
T pfam08442 151 AKGLTPYQAREIAFKLGLEGELVKQAADIIKKLYKLFVEYDATLVEINPLV 201 (202)
T ss_pred CCCCCHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCEEEECCCC
T ss_conf 879899999999998499989999999999999999996698289756887
No 7
>pfam00549 Ligase_CoA CoA-ligase. This family includes the CoA ligases Succinyl-CoA synthetase alpha and beta chains, malate CoA ligase and ATP-citrate lyase. Some members of the family utilize ATP others use GTP.
Probab=99.95 E-value=1.2e-27 Score=201.73 Aligned_cols=119 Identities=38% Similarity=0.598 Sum_probs=108.7
Q ss_pred EECCCHHHHHHHHHHHHCCCCCCEEEECCCCC-CHHHHHHHHHHHHCCCCCCEEEEECCCCHHHHHHHHHHHHHHHHHCC
Q ss_conf 95550368999999996589962488427888-98999999999861998658999635861328999999999999729
Q gi|254781049|r 272 MVNGAGLAMATMDIIKLYGGAPANFLDVGGGA-DQDKVAAAFKIITSDSSVKGILINIFGGIMRCDVLVKGILSAVKEVK 350 (398)
Q Consensus 272 ~vnGaGlamatmD~i~~~Gg~pANFlD~gG~a-~~e~~~~a~~~il~~~~vk~iliNifGGI~~cd~vA~gii~a~~~~~ 350 (398)
|+|||||+|+|||+++++|++|+||+|+||++ +.+.+.++|+++++||++|+||||+|+||.+||++|.++++|+++.+
T Consensus 1 ~~nGggL~~et~~~l~~~G~~~a~~ldiGGd~~~~~~~~e~l~~~~~Dp~tk~Ili~~~~G~g~~e~~A~~~v~a~~~~~ 80 (128)
T pfam00549 1 LVNGGTLAMEAMDLIKLAGGGPHNFIDLGGDAFTPTTRIDALKLEAADPEVKVILLDIVLGYGACEDPAGGLLKAIKEAR 80 (128)
T ss_pred CCCCHHHHHHHHHHHHHCCCCCCEEEEECCCCCCCHHHHHHHHHHHCCCCCEEEEEEEEEECCCHHHHHHHHHHHHHHHC
T ss_conf 94538699999999998599832588837999863379999999957888629999987743626999999999999846
Q ss_pred -CCCCEEEECCCCCHHHH-----HHHHHHCCCCEEEECCHHHHHHHHH
Q ss_conf -99879997489858999-----9999976995899499899999999
Q gi|254781049|r 351 -INIPLVMRLEGANVDIG-----NRLIAESGLNVITAIDLDDAAQKIV 392 (398)
Q Consensus 351 -~~~pivvRl~Gtn~~~g-----~~il~~~g~~~~~~~~~~~A~~~~v 392 (398)
.++|||+|+.|||++.+ .+.|.++|.+.. .+..+|+++|.
T Consensus 81 ~~~~PvVa~i~Gt~a~~~~~~ghagal~~~G~~~~--~sk~~A~~~Ag 126 (128)
T pfam00549 81 ARELPVVARVCGTEADPQGRSGQAKALAESGVLIA--SSNNQALRAAG 126 (128)
T ss_pred CCCCCEEEEEEECCCCCCCCHHHHHHHHHCCCCCH--HHHHHHHHHCC
T ss_conf 99875899993026996553378789997799643--01999999769
No 8
>KOG1254 consensus
Probab=99.73 E-value=4.4e-19 Score=145.40 Aligned_cols=313 Identities=17% Similarity=0.088 Sum_probs=224.1
Q ss_pred HCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCEEECCCCCC--
Q ss_conf 729986999712136876565655677777770799589999999999861876544212222244330110345556--
Q gi|254781049|r 37 TLPGPLYVVKSQIHAGGRGKGRFKELPADSKGGVRVESSLKSVISDIREILGSTLITKQTGPTGSRVNCVYVEDGADI-- 114 (398)
Q Consensus 37 ~ig~p~~VvKaQV~aGgRGKa~~~~~hk~~~GGV~l~~s~~ea~~~a~~ilg~~l~t~qt~~~G~~v~~vLVEe~v~~-- 114 (398)
|+..-..|.|+..+++.|||. |-|.+..+..+..++.+.+.+.+... + .-.| +...+.||+.+.+
T Consensus 76 ~faS~rsv~k~~m~~~k~~ki----------~lvAiiAegvpe~~~~kl~~~a~~k~-~-~iiG-PaTvggVePg~fkig 142 (600)
T KOG1254 76 WFASTRSVAKPDMLALKRGKI----------GLVAIIAEGVPEADTRKLRAGAEVKG-V-GIIG-PATVGGVEPGVFKIG 142 (600)
T ss_pred CHHHHHHHCCCHHHHHHCCCC----------CEEEEECCCCCHHHHHHHHHCCCCCC-C-EEEE-EEEECCCCCCCCCCC
T ss_conf 144434320334777635764----------18999715880778999874311236-3-6873-002211557865668
Q ss_pred ----CEEEEEEEEEECCCCCEEEEEECCCCCCHHHHHHHCHHHHEEEECCCCCC----CCHHHHHHHHHHCCCCHHHHHH
Q ss_conf ----50589999983477804899844788402455574831220332144457----8957888788751988899885
Q gi|254781049|r 115 ----LRELYLSLLVDRTSGMVAFIASTQGGMDIEEVAKDYPQKIFKLLIDPLIG----VTSEDVASLCDMLELQGQARID 186 (398)
Q Consensus 115 ----~~E~ylgi~~Dr~~~~~vii~S~~GGvdIE~va~~~p~~I~~~~id~~~g----l~~~~~~~l~~~lg~~~~~~~~ 186 (398)
-.|+|+.+.++|... ++.+|..|||++|+++.. .+...-|..+ -+.+-...+..++ +-.+...
T Consensus 143 nt~g~~dnil~~klyR~Gs--v~~vS~sGGmsnE~nn~i-----srtt~g~~egiaiggd~~pgSTl~dhi--~r~q~~~ 213 (600)
T KOG1254 143 NTGGMMDNILNSKLYRPGS--VIYVSRSGGMSNELNNII-----SRTTDGPYEGIAIGGDRYPGSTLIDHI--PREQHDP 213 (600)
T ss_pred CCCCCHHHHHHHCCCCCCC--EEEEECCCCCCHHHHHHH-----HHEECCCEEEEEECCCCCCCCHHHHHH--HHHHCCC
T ss_conf 8774245422110137865--799944788641221134-----401034113222056776681176520--3552367
Q ss_pred HHHHHHHHHHHHHHCCCCCCCCC-------EEEECCCCC---EEEEEEEEEECCCHHHHHHH-HH----HHHCCCCCCHH
Q ss_conf 99999999899995597510232-------679905996---79940013215735564102-78----63100015622
Q gi|254781049|r 187 GGDLFPNLYKAFCDKDMSLLEIN-------PLIIMKNGR---LRVLDSKISFDDNALYRHLD-IQ----ELRDVSEEDSR 251 (398)
Q Consensus 187 ~~~ii~~L~~~f~e~Da~liEIN-------PLvvt~dg~---vvAlDAKi~iDDnA~fR~~~-~~----~~~d~~~~~~~ 251 (398)
..++|..|+.++-+.+.+++|+| ||+.-.-|. ++-+|.....|+.|.|-.-+ |. .+|+--..-|.
T Consensus 214 ~vk~Iv~Lgevgg~~ey~~~e~~k~g~~tkPlVaw~~gtcA~~F~~evqfghagtaa~~~~eka~akn~al~~ag~~vpe 293 (600)
T KOG1254 214 LVKFIVVLGEVGGDEEYTFLEANKEGKITKPLVAWCIGTCADMFPLEVQFGHAGTAAFKNGEKAAAKNQALRDAGATVPE 293 (600)
T ss_pred CCCEEEEEHHHCCCCEEEHHHHHHCCCCCCCEEEEECCCCCCCCCHHHHCCCCCHHHHCCHHHHHHCCHHHHHCCCCCCC
T ss_conf 01068873222663315454454147766887999467522024034421334122211156666403135541565763
Q ss_pred ----------------------------------HHHHHHCCCCEEECCCCEEEEECCC-HHHHHHHHHHHHCCC--CCC
Q ss_conf ----------------------------------2457753986442288179995550-368999999996589--962
Q gi|254781049|r 252 ----------------------------------EIEAKQHNLSYIALDGNIGCMVNGA-GLAMATMDIIKLYGG--APA 294 (398)
Q Consensus 252 ----------------------------------E~~A~~~~l~yv~LdG~Ig~~vnGa-GlamatmD~i~~~Gg--~pA 294 (398)
|-.+....|..+.-.|+|||++.|. |....+.|+....|. +-+
T Consensus 294 sf~~l~~~i~~~~e~lv~~Grvvp~~Ev~pp~lp~d~saalklgllr~p~~i~t~Ia~~rGaeviYA~~p~~~~~a~elG 373 (600)
T KOG1254 294 SFDALGADIQETYEFLVPFGRVVPKTEVPPPGLPEDTSAALKLGLLRKPGRIWTSIAGGRGAEVIYADVPISLGYASELG 373 (600)
T ss_pred CHHHHHHHHCCCHHCCCCCCEECCCCCCCCCCCCHHHHHHHHCCCCCCCCEEEEEECCCCCCEEEECCCHHHHHHHHHCC
T ss_conf 13344333234201115354454575579999871446676502305786389985179874036558605555676506
Q ss_pred EEEECCCCCCHHHHHHHHHHHH-------CCCCCCEEEEECCCCHHHHHHHH---HHHHHHHHHCCC----CCCEEEECC
Q ss_conf 4884278889899999999986-------19986589996358613289999---999999997299----987999748
Q gi|254781049|r 295 NFLDVGGGADQDKVAAAFKIIT-------SDSSVKGILINIFGGIMRCDVLV---KGILSAVKEVKI----NIPLVMRLE 360 (398)
Q Consensus 295 NFlD~gG~a~~e~~~~a~~~il-------~~~~vk~iliNifGGI~~cd~vA---~gii~a~~~~~~----~~pivvRl~ 360 (398)
|+..+||-+...++.++.+.++ .|-+.++.+ +.|||+++...+ .+|+.++.+.+. .+-+.+|.-
T Consensus 374 ~gg~~Sllw~~~~lp~Ya~kfie~~~m~~aDhgp~Vsg--a~ntI~~~ra~kdl~sslv~gLltigdRfggald~aaR~f 451 (600)
T KOG1254 374 NGGVYSLLWFQRRLPQYARKFIEICTMLTADHGPAVSG--AGNTIANFRAGKDLFSSLVRGLLTIGDRFGGALDIAARRF 451 (600)
T ss_pred CCCEECCCCCCCCCHHHHHHHHHHHHHCCCCCCCEEEE--CCCCEEEECCHHHHHHHHHHHHHHHHHHHCCHHHHHHHHC
T ss_conf 66057144134411789999999884216898854674--1671687325899999999988551012143226998861
Q ss_pred CCCHHHHHHHHHH
Q ss_conf 9858999999997
Q gi|254781049|r 361 GANVDIGNRLIAE 373 (398)
Q Consensus 361 Gtn~~~g~~il~~ 373 (398)
|+|+++|+.-++.
T Consensus 452 ~~ayd~GL~~m~f 464 (600)
T KOG1254 452 GPAYDKGLAPMRF 464 (600)
T ss_pred CHHHHCCCHHHHH
T ss_conf 8454346607887
No 9
>COG1042 Acyl-CoA synthetase (NDP forming) [Energy production and conversion]
Probab=99.47 E-value=4.5e-14 Score=112.36 Aligned_cols=361 Identities=16% Similarity=0.120 Sum_probs=223.0
Q ss_pred CCCHHHHHHHHHHCC----CCCCCCE------EECCHHHHHHHHHHCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCEEE
Q ss_conf 865799999999868----9888815------747999999999872998699971213687656565567777777079
Q gi|254781049|r 2 NIHEYQAKALLRKYN----VPVAKGV------VISSVHAAESAIKTLPGPLYVVKSQIHAGGRGKGRFKELPADSKGGVR 71 (398)
Q Consensus 2 ~L~EyqaK~lL~~~G----Ipvp~g~------~a~s~~ea~~~a~~ig~p~~VvKaQV~aGgRGKa~~~~~hk~~~GGV~ 71 (398)
...+|+.++.|.+|| +||++.. .|.+.......+.++++++ |.+.. .+.+.|+...+||+
T Consensus 23 ~~vg~~i~~nL~~~g~g~i~PVnp~~~~v~G~~ay~s~~~lp~~~dlav~~-v~~~~---------~~~i~~~~~~kGv~ 92 (598)
T COG1042 23 GKLGYEILRNLLEYGQGKIYPVNPKYDEVLGVKAYTSVADLPDAPDLAVIV-VPAKV---------VPEIVHELGEKGVK 92 (598)
T ss_pred CHHHHHHHHHHHHCCCCCEEECCCCCCCCCCCCCCCHHHHCCCCCCCEEEE-ECHHH---------HHHHHHHHCCCCCC
T ss_conf 215799999998568885574276532336631464075578887706898-52445---------68999872005873
Q ss_pred E-ECCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCEEECCCCCCCEEEEEE--EEEECCCCCEEEEEECCCCCCHHHHHH
Q ss_conf 9-5899999999998618765442122222443301103455565058999--998347780489984478840245557
Q gi|254781049|r 72 V-ESSLKSVISDIREILGSTLITKQTGPTGSRVNCVYVEDGADILRELYLS--LLVDRTSGMVAFIASTQGGMDIEEVAK 148 (398)
Q Consensus 72 l-~~s~~ea~~~a~~ilg~~l~t~qt~~~G~~v~~vLVEe~v~~~~E~ylg--i~~Dr~~~~~vii~S~~GGvdIE~va~ 148 (398)
. +.......++.+++. .+.+.+.. ....-...++.+++....+...+ .+.++.+..- + .-|+..+++...
T Consensus 93 ~~i~is~gf~e~~~~~~--~~e~~~~~-~a~~~~~rligPn~~G~~~~~~glna~f~p~~~~~---~-~g~~afvsqsga 165 (598)
T COG1042 93 GAIVISAGFREAGEEGM--ELEKELVE-AARKYGMRIIGPNCLGLINPIIGLNATFDPVFGLG---R-GGGGAFVSQSGA 165 (598)
T ss_pred EEEEECHHHHHHHHHHH--HHHHHHHH-HHHHCCCEEECCCCCCCCCCCCCCCCCCCCCCCCC---C-CCCEEEEEECHH
T ss_conf 58996245678877676--77889999-98855963862332453112236563126532334---7-887379995257
Q ss_pred HCHHHHEEEECCCCCCCCHHHHHHHHHHCCCCHHHHHHHHHHHHH--------HHHHHHHCCC-CCCCCCEEEECCCCC-
Q ss_conf 483122033214445789578887887519888998859999999--------9899995597-510232679905996-
Q gi|254781049|r 149 DYPQKIFKLLIDPLIGVTSEDVASLCDMLELQGQARIDGGDLFPN--------LYKAFCDKDM-SLLEINPLIIMKNGR- 218 (398)
Q Consensus 149 ~~p~~I~~~~id~~~gl~~~~~~~l~~~lg~~~~~~~~~~~ii~~--------L~~~f~e~Da-~liEINPLvvt~dg~- 218 (398)
-. ..-.++....+ ..+...-.+|. ....+..+++.. ...+|.|..- -...+||.-....++
T Consensus 166 v~---~~il~~~~~~~----~g~s~~vs~gn--~ad~~~~d~~~~~~~D~~tk~i~Ly~E~~~~~r~fl~~a~~~~~~kp 236 (598)
T COG1042 166 VS---FAILDWANEDG----MGFSIKVSLGN--AADRDESDLLEYLADDPRTKAIGLYIEGVKDGRKFLNAARAAERKKP 236 (598)
T ss_pred HH---HHCCCHHHHCC----CCEEEEEEECC--HHHCCCHHHHHHHHHCCCCEEEEEEECCCHHHHHHHHHHHHHHCCCC
T ss_conf 88---76165234268----75369996142--54338446677775276530799984254427999889998735787
Q ss_pred EEEEEEEEEECCCHHH------------------HHHHHHHHHCCCCCCHHHH-HHHHCCCCEEECCC-CEEEEECCCHH
Q ss_conf 7994001321573556------------------4102786310001562224-57753986442288-17999555036
Q gi|254781049|r 219 LRVLDSKISFDDNALY------------------RHLDIQELRDVSEEDSREI-EAKQHNLSYIALDG-NIGCMVNGAGL 278 (398)
Q Consensus 219 vvAlDAKi~iDDnA~f------------------R~~~~~~~~d~~~~~~~E~-~A~~~~l~yv~LdG-~Ig~~vnGaGl 278 (398)
++++|+..+.-....+ ||-.+ ...++..|. ++.+....+..+.| ++..+.||+|.
T Consensus 237 ii~lk~gr~~~~akAa~shTgslag~~~~y~Aa~~~agv-----ir~~~~~elf~~~k~l~~~~~~~g~~~~ivtn~Gg~ 311 (598)
T COG1042 237 IIALKAGRSEAGAKAAASHTGSLAGSDEAYDAAFKQAGV-----IRVESIEELFDAAKALSHQPPPAGDRVAIITNGGGP 311 (598)
T ss_pred EEEEECCCCHHHHHHHHCCCCCCCCCCCCCHHHHHHCCC-----EECCCHHHHHHHHHHHCCCCCCCCCCEEEEECCCCC
T ss_conf 799963478788899860261103642002798864072-----231674999999998624899987654789548876
Q ss_pred HHHHHHHHHHCCCCC---------------------CEEEECCCCCCHHHHHHHHHHHHCCCCCCEEEE-ECCCCHHHHH
Q ss_conf 899999999658996---------------------248842788898999999999861998658999-6358613289
Q gi|254781049|r 279 AMATMDIIKLYGGAP---------------------ANFLDVGGGADQDKVAAAFKIITSDSSVKGILI-NIFGGIMRCD 336 (398)
Q Consensus 279 amatmD~i~~~Gg~p---------------------ANFlD~gG~a~~e~~~~a~~~il~~~~vk~ili-NifGGI~~cd 336 (398)
+.-..|.+...|++. +|=+|+-|.++.++-.++++.++.++++..+++ .+.+..+--.
T Consensus 312 gvla~D~l~~~g~~l~~~~~~~~~~l~~~Lp~~~~~~NPvD~~~~a~~e~y~~~~~~~~~~~~~~~llvi~~~~~~~~~~ 391 (598)
T COG1042 312 GVLAADALEERGLKLAELSEETIEKLRSRLPPHASVKNPVDLTGDADAERYKKTLEILLRDENVDALLVIVLPPASADPE 391 (598)
T ss_pred CCCCHHHHHHCCCCCCCCCHHHHHHHHHCCCCCCCCCCCEEEECCCCHHHHHHHHHHHHHCCCCCEEEEEECCCCCCCCH
T ss_conf 53225579872887678998999999860695124468734206785788999999986065775589996378778841
Q ss_pred HHHHHHHHHHHHCCCCCC-EEEECCCCCHHHHHHHHHHCCCCEEEECCHHHHHHHHHHHHH
Q ss_conf 999999999997299987-999748985899999999769958994998999999999850
Q gi|254781049|r 337 VLVKGILSAVKEVKINIP-LVMRLEGANVDIGNRLIAESGLNVITAIDLDDAAQKIVHAVK 396 (398)
Q Consensus 337 ~vA~gii~a~~~~~~~~p-ivvRl~Gtn~~~g~~il~~~g~~~~~~~~~~~A~~~~v~~~k 396 (398)
..|+.|+.+ .....++| ++.-++|.+++.+.+++.+.|++.+ .+.+.|++....+++
T Consensus 392 ~~a~~~~~~-~~~~~~k~~v~~~~gg~~~~~~~~~l~~~gip~~--~~pe~a~~a~~~l~~ 449 (598)
T COG1042 392 ETAEAIIRA-TAKKRGKPVVVSSMGGESSEKARRLLEEAGIPTY--PTPERAVKALSALAR 449 (598)
T ss_pred HHHHHHHHH-HHHHCCCCEEEEECCCCCHHHHHHHHHHCCCCCC--CCHHHHHHHHHHHHH
T ss_conf 456788777-7661697659996677652667877641588766--680777889999998
No 10
>COG1042 Acyl-CoA synthetase (NDP forming) [Energy production and conversion]
Probab=99.47 E-value=4.6e-14 Score=112.33 Aligned_cols=117 Identities=26% Similarity=0.374 Sum_probs=103.2
Q ss_pred CCCHHHHHHHHHHCCCCCCCCEEECCHHHHHHHHHHCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHH
Q ss_conf 86579999999986898888157479999999998729986999712136876565655677777770799589999999
Q gi|254781049|r 2 NIHEYQAKALLRKYNVPVAKGVVISSVHAAESAIKTLPGPLYVVKSQIHAGGRGKGRFKELPADSKGGVRVESSLKSVIS 81 (398)
Q Consensus 2 ~L~EyqaK~lL~~~GIpvp~g~~a~s~~ea~~~a~~ig~p~~VvKaQV~aGgRGKa~~~~~hk~~~GGV~l~~s~~ea~~ 81 (398)
.+.|+++|++++.|||++|++ ++.+++|+..+++.++ |. .++++.||++.|||.+..+..++.+
T Consensus 470 ~~~~~e~~~~l~~~gi~~~~~-~~~~~~ea~~~a~~~~------Kl---------~s~~i~hksev~gv~l~~~~~~v~~ 533 (598)
T COG1042 470 TLDEPEAKELLEAYGIPVPAT-IASTLDEAVHIAESIG------KL---------RSPDIDHKSEVGGVMLNRTADAVEK 533 (598)
T ss_pred CCCCHHHHHHHHHHCCCCCCC-CCCCHHHHHHHHHHHH------HC---------CCCCCCHHHHCCCEEECCCHHHHHH
T ss_conf 157431455799846865654-5679899999999741------20---------4674211342166042673999999
Q ss_pred HHHHHCCCCCCCCCCCCCCCCCCCEEECCCCCCCEEEEEEEEEECCCCCEEEEEECCCCCCHHHHHH
Q ss_conf 9998618765442122222443301103455565058999998347780489984478840245557
Q gi|254781049|r 82 DIREILGSTLITKQTGPTGSRVNCVYVEDGADILRELYLSLLVDRTSGMVAFIASTQGGMDIEEVAK 148 (398)
Q Consensus 82 ~a~~ilg~~l~t~qt~~~G~~v~~vLVEe~v~~~~E~ylgi~~Dr~~~~~vii~S~~GGvdIE~va~ 148 (398)
++..++.+ + ..+.+++||+|.. .|+++++..|+.|+ |+++++ +||+.+|.+-+
T Consensus 534 a~~~~~~~--------p--a~i~g~lvq~m~~--~E~~vgv~~dp~fg-p~i~~G-~Gg~~ve~l~d 586 (598)
T COG1042 534 AADDILAR--------P--ARIAGVLVQTMAK--LELIVGVKNDPTFG-PLILFG-EGGIEVEVLKD 586 (598)
T ss_pred HHHHHHCC--------C--CHHHEEEHHHHHH--CCCEEECCCCCCCH-HHHHHC-CCCEEEEEECC
T ss_conf 99877506--------5--5002001576640--04122113888603-698853-78648884226
No 11
>TIGR02717 AcCoA-syn-alpha acetyl coenzyme A synthetase (ADP forming), alpha domain; InterPro: IPR014089 This group of ADP-dependent acetyl-CoA synthetases (ACS) act in the direction of acetate and ATP production in the organisms in which they have been characterised , , . In most species this protein is bifunctional, existing as fused alpha-beta domains. In Pyrococcus and related species, however, the domains exist as separate polypeptides. This entry represents the alpha (N-terminal) domain. In Pyrococcus and related species there appears to have been the development of a paralogous family such that four other proteins are close relatives. One of these (along with its beta-domain partner) was characterised as ACS-II showing specificity for phenylacetyl-CoA . This entry excludes non-ACS-I paralogs. .
Probab=99.41 E-value=4.5e-12 Score=99.21 Aligned_cols=187 Identities=24% Similarity=0.396 Sum_probs=134.6
Q ss_pred HHHHHHHHHHHHHHHHCCCCCCCCCEEEECCCCCEE----EEE--------EEEEECCCHHHHHH------HHHHHHCCC
Q ss_conf 859999999989999559751023267990599679----940--------01321573556410------278631000
Q gi|254781049|r 185 IDGGDLFPNLYKAFCDKDMSLLEINPLIIMKNGRLR----VLD--------SKISFDDNALYRHL------DIQELRDVS 246 (398)
Q Consensus 185 ~~~~~ii~~L~~~f~e~Da~liEINPLvvt~dg~vv----AlD--------AKi~iDDnA~fR~~------~~~~~~d~~ 246 (398)
.+-.+++.+...+-.. -|.++.+.|+=- |.- .-..+| |.|||- .+.+|.|.+
T Consensus 218 ~DG~~Fl~~A~~~s~~--------KPiv~lKsG~s~~GakAA~SHTGaLAGs~~~y~--aaf~q~G~iRa~~~~ELfd~A 287 (457)
T TIGR02717 218 KDGRKFLKTAKEISKK--------KPIVVLKSGTSEAGAKAASSHTGALAGSDEAYD--AAFKQAGVIRADSIEELFDLA 287 (457)
T ss_pred CCHHHHHHHHHHHHHC--------CCEEEEECCCCHHHHHHHHHCCCHHHHHHHHHH--HHHCCCCEEEEECHHHHHHHH
T ss_conf 0416899998886305--------988999368883456765210231336689999--874301438870177889999
Q ss_pred CCCHHHHHHHHCCCCEEEC--CC-CEEEEECCCHHHHHHHHHHHHCCCCCCEEE---------------------ECCC-
Q ss_conf 1562224577539864422--88-179995550368999999996589962488---------------------4278-
Q gi|254781049|r 247 EEDSREIEAKQHNLSYIAL--DG-NIGCMVNGAGLAMATMDIIKLYGGAPANFL---------------------DVGG- 301 (398)
Q Consensus 247 ~~~~~E~~A~~~~l~yv~L--dG-~Ig~~vnGaGlamatmD~i~~~Gg~pANFl---------------------D~gG- 301 (398)
+ -|++-.+ +| ||+++.||+|....|.|.+.++|.+-|+|. |+-|
T Consensus 288 ~-----------~L~~~~~~~~g~~~~IiTN~GG~Gvia~D~~~~~Gl~L~~~~~~t~~~L~~~LP~~as~~NPVD~~Gs 356 (457)
T TIGR02717 288 R-----------LLSNQPLPPKGNRVAIITNAGGPGVIATDACEEVGLELAELSEKTKEKLRNILPPEASIKNPVDVLGS 356 (457)
T ss_pred H-----------HHHCCCCCCCCCEEEEEECCCCHHHHHHHHHHHCCCEEECCCHHHHHHHHHHCCCCCCCCCCCEEEEC
T ss_conf 9-----------98358989988769999789616778765677749745558589999999747611477875125522
Q ss_pred CCCHHHHHHHHHHHHCCCCCCEEEEECCCC--HHH-HHHHHHHHHHHHHHCCCC---CCEEE-ECCCCCHHHHHHHHHHC
Q ss_conf 889899999999986199865899963586--132-899999999999972999---87999-74898589999999976
Q gi|254781049|r 302 GADQDKVAAAFKIITSDSSVKGILINIFGG--IMR-CDVLVKGILSAVKEVKIN---IPLVM-RLEGANVDIGNRLIAES 374 (398)
Q Consensus 302 ~a~~e~~~~a~~~il~~~~vk~iliNifGG--I~~-cd~vA~gii~a~~~~~~~---~pivv-Rl~Gtn~~~g~~il~~~ 374 (398)
.||+++-++++++++.|+||+++++ |+.- .++ |++||++||+..++.+.+ +|+|+ -+.|..+..+.++|+++
T Consensus 357 DA~~~~Y~~~l~~v~eD~nVd~~~v-v~~~~a~~~~~~~va~~~~~~~~~~~~k~~~Kpvv~~~~gG~~~~~a~~~L~~~ 435 (457)
T TIGR02717 357 DATAERYAKALKIVAEDENVDGVVV-VLTPTAMTDKPEEVAKGIIEVAKKSNEKKRDKPVVAGFVGGKSVKEAKRILEEN 435 (457)
T ss_pred CCCHHHHHHHHHHHHCCCCCCEEEE-EEECCCHHHHHHHHHHHHHHHHCCCCCCCCCCCEEEEEECCCCCCHHHHHHHHC
T ss_conf 7898999999999834888888999-642530246799999988754303674212474489984673220156622315
Q ss_pred CCCEEEECCHHHHHHHHHHHH
Q ss_conf 995899499899999999985
Q gi|254781049|r 375 GLNVITAIDLDDAAQKIVHAV 395 (398)
Q Consensus 375 g~~~~~~~~~~~A~~~~v~~~ 395 (398)
|+|.++ +-+.||+-.-.+-
T Consensus 436 giP~Y~--~Pe~AV~Al~~l~ 454 (457)
T TIGR02717 436 GIPNYT--FPERAVKALSALY 454 (457)
T ss_pred CCCCCC--CHHHHHHHHHHHH
T ss_conf 887647--9688999999861
No 12
>TIGR01369 CPSaseII_lrg carbamoyl-phosphate synthase, large subunit; InterPro: IPR006275 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 glutamine-dependent CPSase (6.3.5.5 from EC) from prokaryotes and eukaryotes (CPSase II). ; GO: 0004086 carbamoyl-phosphate synthase activity, 0006807 nitrogen compound metabolic process.
Probab=99.36 E-value=1.5e-11 Score=95.79 Aligned_cols=95 Identities=24% Similarity=0.401 Sum_probs=44.3
Q ss_pred HHHHHCCCCCCCCEEECCHHHHHHHHHHCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHHHHHHHCCC
Q ss_conf 99998689888815747999999999872998699971213687656565567777777079958999999999986187
Q gi|254781049|r 10 ALLRKYNVPVAKGVVISSVHAAESAIKTLPGPLYVVKSQIHAGGRGKGRFKELPADSKGGVRVESSLKSVISDIREILGS 89 (398)
Q Consensus 10 ~lL~~~GIpvp~g~~a~s~~ea~~~a~~ig~p~~VvKaQV~aGgRGKa~~~~~hk~~~GGV~l~~s~~ea~~~a~~ilg~ 89 (398)
++|++-|.|||++..++|.+||.++++++|||+ +|-+==-=||+| || ++.|.+|+++-+++=|..
T Consensus 133 ~~M~ei~~pvp~S~~~~~~eEA~~~a~~~GyPv-iVRpAftLGG~G------------gG--iA~n~eEL~~~~~~aL~~ 197 (1089)
T TIGR01369 133 EAMKEIGEPVPKSEIVHSVEEALKAAKEIGYPV-IVRPAFTLGGTG------------GG--IASNEEELKEIVERALSA 197 (1089)
T ss_pred HHHHHCCCCCCCCCCCCCHHHHHHHHHHCCCCE-EECCCHHCCCCC------------CC--EECCHHHHHHHHHHHHHH
T ss_conf 999973899881100278899999996268968-981003238899------------85--225778999999988630
Q ss_pred CCCCCCCCCCCCCCCCEEECCCCCCCEEEEEEEEEECCCCC
Q ss_conf 65442122222443301103455565058999998347780
Q gi|254781049|r 90 TLITKQTGPTGSRVNCVYVEDGADILRELYLSLLVDRTSGM 130 (398)
Q Consensus 90 ~l~t~qt~~~G~~v~~vLVEe~v~~~~E~ylgi~~Dr~~~~ 130 (398)
. ++++|||||-+.+.||+=.=+.+|+...+
T Consensus 198 S-----------pI~qvL~EkSl~GWKE~EYEVmRD~~dNC 227 (1089)
T TIGR01369 198 S-----------PINQVLVEKSLAGWKEIEYEVMRDSKDNC 227 (1089)
T ss_pred C-----------CCCEEEEEEECCCCEEEEEEEEEECCCCE
T ss_conf 8-----------88557501100331788988986268788
No 13
>pfam01071 GARS_A Phosphoribosylglycinamide synthetase, ATP-grasp (A) domain. Phosphoribosylglycinamide synthetase catalyses the second step in the de novo biosynthesis of purine. The reaction catalysed by Phosphoribosylglycinamide synthetase is the ATP- dependent addition of 5-phosphoribosylamine to glycine to form 5'phosphoribosylglycinamide. This domain is related to the ATP-grasp domain of biotin carboxylase/carbamoyl phosphate synthetase (see pfam02786).
Probab=99.34 E-value=3.1e-11 Score=93.66 Aligned_cols=99 Identities=26% Similarity=0.283 Sum_probs=80.9
Q ss_pred HHHHHHHHHCCCCCCCCEEECCHHHHHHHHHHCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHHHHHH
Q ss_conf 99999999868988881574799999999987299869997121368765656556777777707995899999999998
Q gi|254781049|r 6 YQAKALLRKYNVPVAKGVVISSVHAAESAIKTLPGPLYVVKSQIHAGGRGKGRFKELPADSKGGVRVESSLKSVISDIRE 85 (398)
Q Consensus 6 yqaK~lL~~~GIpvp~g~~a~s~~ea~~~a~~ig~p~~VvKaQV~aGgRGKa~~~~~hk~~~GGV~l~~s~~ea~~~a~~ 85 (398)
..+|++|+++|||+|++..++|.+|+.++++++|||+ |||+--.+|+| ||+++.|.+|+..++++
T Consensus 4 ~~~r~~l~~~gip~p~~~~~~~~~ea~~~~~~~g~P~-VvKp~~~~gs~--------------Gv~~v~~~~e~~~a~~~ 68 (193)
T pfam01071 4 SFAKDFMKRHGIPTAEYETFTDPEEAKSYIREAGFPA-VVKADGLAAGK--------------GVIVAMDNEEAIKAVDE 68 (193)
T ss_pred HHHHHHHHHCCCCCCCEEEECCHHHHHHHHHHCCCCE-EEEECCCCCCC--------------CEEEECCHHHHHHHHHH
T ss_conf 9999999986989999078789999999999769988-99974346788--------------37995458999999999
Q ss_pred HCCCCCCCCCCCCCCCCCCCEEECCCCCCCEEEEEEEEEECC
Q ss_conf 618765442122222443301103455565058999998347
Q gi|254781049|r 86 ILGSTLITKQTGPTGSRVNCVYVEDGADILRELYLSLLVDRT 127 (398)
Q Consensus 86 ilg~~l~t~qt~~~G~~v~~vLVEe~v~~~~E~ylgi~~Dr~ 127 (398)
++.... .+..-..|||||+++ +.|+-+....|..
T Consensus 69 ~~~~~~-------~~~~~~~vlvEefl~-G~E~sv~~~~dg~ 102 (193)
T pfam01071 69 ILEQKK-------FGEAGEPVVIEEFLE-GEEVSVLAFVDGK 102 (193)
T ss_pred HHHHCC-------CCCCCCCEEEEEECC-CCEEEEEEEEECC
T ss_conf 985230-------357899789987205-7165578984099
No 14
>pfam02222 ATP-grasp ATP-grasp domain. This family does not contain all known ATP-grasp domain members. This family includes a diverse set of enzymes that possess ATP-dependent carboxylate-amine ligase activity.
Probab=99.25 E-value=5.4e-10 Score=85.50 Aligned_cols=88 Identities=24% Similarity=0.240 Sum_probs=70.0
Q ss_pred HHHCCCCCCCCEEECCHHHHHHHHHHCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHHHHHHHCCCCC
Q ss_conf 99868988881574799999999987299869997121368765656556777777707995899999999998618765
Q gi|254781049|r 12 LRKYNVPVAKGVVISSVHAAESAIKTLPGPLYVVKSQIHAGGRGKGRFKELPADSKGGVRVESSLKSVISDIREILGSTL 91 (398)
Q Consensus 12 L~~~GIpvp~g~~a~s~~ea~~~a~~ig~p~~VvKaQV~aGgRGKa~~~~~hk~~~GGV~l~~s~~ea~~~a~~ilg~~l 91 (398)
|++.|||+|++.+++|.+|+.++++++|||+ |||+- ..|.-| .|+.++++.+|+.++.+...+
T Consensus 1 l~~~Giptp~~~~i~~~~d~~~~~~~iGyP~-vvKp~-~~G~~g------------~G~~~v~~~~el~~a~~~~~~--- 63 (171)
T pfam02222 1 LQKLGLPTPRFMAAESLEELIEAGQELGYPC-VLKAR-RGGYDG------------KGQYVVRSEADIPQAWEELGG--- 63 (171)
T ss_pred CHHCCCCCCCCEEECCHHHHHHHHHHCCCCE-EEEEC-CCCCCC------------CCCEEECCHHHHHHHHHHCCC---
T ss_conf 9020989999549899999999999709978-99961-102589------------852898899999999985589---
Q ss_pred CCCCCCCCCCCCCCEEECCCCCCCEEEEEEEEEECCC
Q ss_conf 4421222224433011034555650589999983477
Q gi|254781049|r 92 ITKQTGPTGSRVNCVYVEDGADILRELYLSLLVDRTS 128 (398)
Q Consensus 92 ~t~qt~~~G~~v~~vLVEe~v~~~~E~ylgi~~Dr~~ 128 (398)
..+++|+.++..+|+-+-..+|.+.
T Consensus 64 ------------~~~liE~~I~~~~Ei~~~~~r~~~g 88 (171)
T pfam02222 64 ------------GPVIVEEFVPFDKELSVLVVRSVDG 88 (171)
T ss_pred ------------CCEEEEEECCCCEEEEEEEEECCCC
T ss_conf ------------9579986046757999874344999
No 15
>PRK02186 argininosuccinate lyase; Provisional
Probab=99.25 E-value=5.5e-10 Score=85.47 Aligned_cols=92 Identities=20% Similarity=0.218 Sum_probs=73.6
Q ss_pred HHHHHHHHHHCCCCCCCCEEECCHHHHHHHHHHCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHHHHH
Q ss_conf 79999999986898888157479999999998729986999712136876565655677777770799589999999999
Q gi|254781049|r 5 EYQAKALLRKYNVPVAKGVVISSVHAAESAIKTLPGPLYVVKSQIHAGGRGKGRFKELPADSKGGVRVESSLKSVISDIR 84 (398)
Q Consensus 5 EyqaK~lL~~~GIpvp~g~~a~s~~ea~~~a~~ig~p~~VvKaQV~aGgRGKa~~~~~hk~~~GGV~l~~s~~ea~~~a~ 84 (398)
-+.-++.|.++|+|+|++.++++.+++..++.+||||+ |||+-..+| .-||++|.|.+|+.+++.
T Consensus 108 K~~~Rq~L~~aGVp~P~~~lv~~~~e~~~aAa~IGfPv-VVKP~dgSG--------------S~GVrLc~s~aEL~e~~~ 172 (892)
T PRK02186 108 KKRLARTLRDHGIDVPRTHALALDAVALDALDGLTYPV-VVKPRMGSG--------------SVGVRLCASVAEAAAHCA 172 (892)
T ss_pred HHHHHHHHHHCCCCCCCEEEECCHHHHHHHHHHCCCCE-EECCCCCCC--------------CCCEEEECCHHHHHHHHH
T ss_conf 99999999966999995688358878999998479998-971688887--------------768587689999999999
Q ss_pred HHCCCCCCCCCCCCCCCCCCCEEECCCCCCCEEEEEEEEE
Q ss_conf 8618765442122222443301103455565058999998
Q gi|254781049|r 85 EILGSTLITKQTGPTGSRVNCVYVEDGADILRELYLSLLV 124 (398)
Q Consensus 85 ~ilg~~l~t~qt~~~G~~v~~vLVEe~v~~~~E~ylgi~~ 124 (398)
.+.+.. ...+||||+++.. ||-+-...
T Consensus 173 ~l~~~r------------~~~vLVEEFieGp-EYSVEt~s 199 (892)
T PRK02186 173 ALRRAG------------TRAALVQAYVEGD-EYSVETLT 199 (892)
T ss_pred HHHHCC------------CCCEEEEECCCCC-EEEEEEEE
T ss_conf 997154------------8866999715688-78999999
No 16
>PRK12815 carB carbamoyl phosphate synthase large subunit; Reviewed
Probab=99.19 E-value=1e-10 Score=90.32 Aligned_cols=116 Identities=19% Similarity=0.348 Sum_probs=85.3
Q ss_pred HHHHHHCCCCCCCCEEECCHHHHHHHHHHCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHHHHHHHCC
Q ss_conf 99999868988881574799999999987299869997121368765656556777777707995899999999998618
Q gi|254781049|r 9 KALLRKYNVPVAKGVVISSVHAAESAIKTLPGPLYVVKSQIHAGGRGKGRFKELPADSKGGVRVESSLKSVISDIREILG 88 (398)
Q Consensus 9 K~lL~~~GIpvp~g~~a~s~~ea~~~a~~ig~p~~VvKaQV~aGgRGKa~~~~~hk~~~GGV~l~~s~~ea~~~a~~ilg 88 (398)
++++.+.|+|+|++..+++.+||..+++++|||+ ++.+--.-|||| || ++.|.+|+.+.+++-+.
T Consensus 133 ~~~m~~ig~~~~~s~~~~s~~ea~~~a~~ig~Pv-ivRps~~lGg~g------------~~--i~~n~~eL~~~~~~~~~ 197 (1068)
T PRK12815 133 RALMKELGEPVPESEIVDSEEEALRFAEKIGFPI-IVRPAYTLGGDG------------GG--IAENEEELEQLARQGLQ 197 (1068)
T ss_pred HHHHHHCCCCCCCCHHCCCHHHHHHHHHHCCCCE-EEEECCCCCCCC------------CE--EECCHHHHHHHHHHHHH
T ss_conf 9999976999997052199999999998669989-998361066896------------50--44599999999999996
Q ss_pred CCCCCCCCCCCCCCCCCEEECCCCCCCEEEEEEEEEECCCCCEEEEEECCCCCCHHHHHHHCHHHH
Q ss_conf 765442122222443301103455565058999998347780489984478840245557483122
Q gi|254781049|r 89 STLITKQTGPTGSRVNCVYVEDGADILRELYLSLLVDRTSGMVAFIASTQGGMDIEEVAKDYPQKI 154 (398)
Q Consensus 89 ~~l~t~qt~~~G~~v~~vLVEe~v~~~~E~ylgi~~Dr~~~~~vii~S~~GGvdIE~va~~~p~~I 154 (398)
.. +++.+|||+.+...+|+-+-+.+|.... .+++++.+ ++|.+.-.+-|.+
T Consensus 198 ~S-----------~~~~vlie~sl~gwkEie~ev~RD~~~n-~i~vc~mE---nidP~GIHTGDSi 248 (1068)
T PRK12815 198 AS-----------PIHQCLLEESIAGWKEIEYEVMRDRNDN-CVTVCNME---NIDPVGVHTGDSI 248 (1068)
T ss_pred HC-----------CCCCEEEEHHCCCCEEEEEEEEEECCCC-EEEEEECC---CCCCCCCCCCCCC
T ss_conf 39-----------9985786501179769999999988989-79985412---3544543567745
No 17
>pfam02786 CPSase_L_D2 Carbamoyl-phosphate synthase L chain, ATP binding domain. Carbamoyl-phosphate synthase catalyses the ATP-dependent synthesis of carbamyl-phosphate from glutamine or ammonia and bicarbonate. This important enzyme initiates both the urea cycle and the biosynthesis of arginine and/or pyrimidines. The carbamoyl-phosphate synthase (CPS) enzyme in prokaryotes is a heterodimer of a small and large chain. The small chain promotes the hydrolysis of glutamine to ammonia, which is used by the large chain to synthesize carbamoyl phosphate. See pfam00988. The small chain has a GATase domain in the carboxyl terminus. See pfam00117. The ATP binding domain (this one) has an ATP-grasp fold.
Probab=99.16 E-value=7.1e-10 Score=84.72 Aligned_cols=107 Identities=20% Similarity=0.270 Sum_probs=81.3
Q ss_pred HHHHHHHHHCCCCCCCCE--EECCHHHHHHHHHHCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHHHH
Q ss_conf 999999998689888815--747999999999872998699971213687656565567777777079958999999999
Q gi|254781049|r 6 YQAKALLRKYNVPVAKGV--VISSVHAAESAIKTLPGPLYVVKSQIHAGGRGKGRFKELPADSKGGVRVESSLKSVISDI 83 (398)
Q Consensus 6 yqaK~lL~~~GIpvp~g~--~a~s~~ea~~~a~~ig~p~~VvKaQV~aGgRGKa~~~~~hk~~~GGV~l~~s~~ea~~~a 83 (398)
...|++|++.|||+|++. .++|.+|+.+++++||||+ |||+- . ||-|+ |+.++++.+|+.+++
T Consensus 3 ~~~k~~l~~~GvP~~~~~~~~~~s~ee~~~~a~~iG~Pv-vvKp~-~-~g~g~------------G~~~v~~~~eL~~a~ 67 (211)
T pfam02786 3 VLFKAAMKEAGVPTVPGTAGPVETEEEALAAAKEIGYPV-IIKAA-F-GGGGL------------GMGIARNEEELAELF 67 (211)
T ss_pred HHHHHHHHHCCCCCCCCCCCCCCCHHHHHHHHHHHCCCE-EEECC-C-CCCCC------------CCEEEHHHHHHHHHH
T ss_conf 999999998698919987888799999999999859978-99737-7-78998------------751241277899999
Q ss_pred HHHCCCCCCCCCCCCCCCCCCCEEECCCCCCCEEEEEEEEEECCCCCEEEEE
Q ss_conf 9861876544212222244330110345556505899999834778048998
Q gi|254781049|r 84 REILGSTLITKQTGPTGSRVNCVYVEDGADILRELYLSLLVDRTSGMVAFIA 135 (398)
Q Consensus 84 ~~ilg~~l~t~qt~~~G~~v~~vLVEe~v~~~~E~ylgi~~Dr~~~~~vii~ 135 (398)
++.+... .....-..+++|++++..+|+=+.+..|.... .+.++
T Consensus 68 ~~a~~~a-------~~~~~~~~vlvEe~i~g~~ei~v~v~~d~~~~-~~~~~ 111 (211)
T pfam02786 68 ALALAEA-------PAAFGNPQVLVEKSLKGPKHIEYQVLRDAHGN-CITVC 111 (211)
T ss_pred HHHHHHH-------HHCCCCCCEEEEECCCCCEEEEEEEEEECCCC-EEEEE
T ss_conf 9998751-------43169983899740477658999999827998-99999
No 18
>PRK05294 carB carbamoyl phosphate synthase large subunit; Reviewed
Probab=99.13 E-value=2.6e-10 Score=87.59 Aligned_cols=139 Identities=14% Similarity=0.272 Sum_probs=91.9
Q ss_pred HHHHHHCCCCCCCCEEECCHHHHHHHHHHCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHHHHHHHCC
Q ss_conf 99999868988881574799999999987299869997121368765656556777777707995899999999998618
Q gi|254781049|r 9 KALLRKYNVPVAKGVVISSVHAAESAIKTLPGPLYVVKSQIHAGGRGKGRFKELPADSKGGVRVESSLKSVISDIREILG 88 (398)
Q Consensus 9 K~lL~~~GIpvp~g~~a~s~~ea~~~a~~ig~p~~VvKaQV~aGgRGKa~~~~~hk~~~GGV~l~~s~~ea~~~a~~ilg 88 (398)
+++|.+.|+|+|++..++|.+||.++++++|||+ ++.+----||||- | ++.|.+|+.+....-+.
T Consensus 133 ~~~l~~i~~p~~~s~~~~s~~ea~~~a~~igyPv-ivRps~~LGG~g~------------~--i~~n~~eL~~~~~~~~~ 197 (1063)
T PRK05294 133 KEAMKKIGLPVPRSGIAHTMEEALEVAEEIGYPV-IIRPSFTLGGTGG------------G--IAYNREELEEIVERGLD 197 (1063)
T ss_pred HHHHHHCCCCCCCCHHCCCHHHHHHHHHHCCCCE-EEEECCCCCCCCC------------E--EECCHHHHHHHHHHHHH
T ss_conf 9999976999997253099999999998659988-9984421678764------------0--43499999999999996
Q ss_pred CCCCCCCCCCCCCCCCCEEECCCCCCCEEEEEEEEEECCCCCEEEEEECCCCCCHHHHHHHCHHHHEEEECCCCCCCCHH
Q ss_conf 76544212222244330110345556505899999834778048998447884024555748312203321444578957
Q gi|254781049|r 89 STLITKQTGPTGSRVNCVYVEDGADILRELYLSLLVDRTSGMVAFIASTQGGMDIEEVAKDYPQKIFKLLIDPLIGVTSE 168 (398)
Q Consensus 89 ~~l~t~qt~~~G~~v~~vLVEe~v~~~~E~ylgi~~Dr~~~~~vii~S~~GGvdIE~va~~~p~~I~~~~id~~~gl~~~ 168 (398)
.. +++.+|||+.+...+|+-+-+.+|..... +++++.+ ++|.+.-.+-|.+.. -|...+++.
T Consensus 198 ~S-----------~~~qvLie~sl~gwkEie~ev~rD~~~n~-i~v~~mE---nidp~GIHtGDSi~v---aP~qTL~d~ 259 (1063)
T PRK05294 198 LS-----------PTTEVLIEESLLGWKEYEMEVMRDKADNC-IIVCSIE---NIDPMGVHTGDSITV---APAQTLTDK 259 (1063)
T ss_pred HC-----------CCCCEEEEHHCCCCEEEEEEEEEECCCCE-EEEEEEC---CCCCCCCCCCCCCEE---CCCCCCCHH
T ss_conf 19-----------99868966111798899999998189998-9995411---354564566672535---688658989
Q ss_pred -------HHHHHHHHCCCC
Q ss_conf -------888788751988
Q gi|254781049|r 169 -------DVASLCDMLELQ 180 (398)
Q Consensus 169 -------~~~~l~~~lg~~ 180 (398)
.+.+++..||+.
T Consensus 260 e~q~lR~~a~kI~~~L~iv 278 (1063)
T PRK05294 260 EYQMLRDASIAILREIGVE 278 (1063)
T ss_pred HHHHHHHHHHHHHHHCCCC
T ss_conf 9999999999999982957
No 19
>PRK01372 ddl D-alanine--D-alanine ligase; Reviewed
Probab=99.10 E-value=1.4e-08 Score=76.30 Aligned_cols=166 Identities=23% Similarity=0.249 Sum_probs=107.6
Q ss_pred HHHHHHHHHHCCCCCCCCEEECCHHHHHHHHHHCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHHHHH
Q ss_conf 79999999986898888157479999999998729986999712136876565655677777770799589999999999
Q gi|254781049|r 5 EYQAKALLRKYNVPVAKGVVISSVHAAESAIKTLPGPLYVVKSQIHAGGRGKGRFKELPADSKGGVRVESSLKSVISDIR 84 (398)
Q Consensus 5 EyqaK~lL~~~GIpvp~g~~a~s~~ea~~~a~~ig~p~~VvKaQV~aGgRGKa~~~~~hk~~~GGV~l~~s~~ea~~~a~ 84 (398)
-+.+|++|+++|||+|++.+.+..++.......+++|+ +||+ ... | |. =||.++++.+|+.++.+
T Consensus 99 K~~tK~i~~~~gI~tp~~~~~~~~~~~~~~~~~l~~P~-iVKP-~~~-G-----------SS-iGv~~V~~~~el~~ai~ 163 (304)
T PRK01372 99 KLRTKLVWQAAGLPTAPWVVLTRAEDLLAAIDKLGLPL-VVKP-ARE-G-----------SS-VGVTKVKEADELPAALE 163 (304)
T ss_pred HHHHHHHHHHCCCCCCCEEEECCCHHHHHHHHHHCCCE-EEEE-CCC-C-----------CC-CCEEEECCHHHHHHHHH
T ss_conf 89999999986999898499865313999987618987-9976-688-8-----------66-65389669889999999
Q ss_pred HHCCCCCCCCCCCCCCCCCCCEEECCCCCCCEEEEEEEEEECCCCCEEEEEECCCCC-CHHHHHHHCHHHHEEEECCCCC
Q ss_conf 861876544212222244330110345556505899999834778048998447884-0245557483122033214445
Q gi|254781049|r 85 EILGSTLITKQTGPTGSRVNCVYVEDGADILRELYLSLLVDRTSGMVAFIASTQGGM-DIEEVAKDYPQKIFKLLIDPLI 163 (398)
Q Consensus 85 ~ilg~~l~t~qt~~~G~~v~~vLVEe~v~~~~E~ylgi~~Dr~~~~~vii~S~~GGv-dIE~va~~~p~~I~~~~id~~~ 163 (398)
..+.. + +.+|||+.++. +|+-+++.-|+... ++-+. +.++. |-|. +.++.
T Consensus 164 ~a~~~----------~---~~vLvE~~I~G-rEitv~Vlg~~~lp-~~eI~-~~~~fyDy~a--KY~~~----------- 214 (304)
T PRK01372 164 LAFKY----------D---DEVLVEKYIKG-RELTVAVLGGKALP-VIRIV-PPGEFYDYEA--KYLAG----------- 214 (304)
T ss_pred HHHHC----------C---CCCEEEEEECC-EEEEEEEECCCCCC-EEEEE-CCCCCCCHHH--CCCCC-----------
T ss_conf 98744----------8---86254502565-69999998997775-38994-5998757766--12557-----------
Q ss_pred CCCHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCEEEECCCCCEEEEE
Q ss_conf 789578887887519888998859999999989999559751023267990599679940
Q gi|254781049|r 164 GVTSEDVASLCDMLELQGQARIDGGDLFPNLYKAFCDKDMSLLEINPLIIMKNGRLRVLD 223 (398)
Q Consensus 164 gl~~~~~~~l~~~lg~~~~~~~~~~~ii~~L~~~f~e~Da~liEINPLvvt~dg~vvAlD 223 (398)
..+. ..-..++.+..+.+.++..++|+++--.+..-++ +.++++|+++.+.
T Consensus 215 -----~s~~-~~Pa~l~~~~~~~i~~~a~~~~~aLg~~g~aRvD---f~~~~~g~~~~lE 265 (304)
T PRK01372 215 -----DTQY-LCPAGLPAELEAELQALALRAYKALGCRGWGRVD---FMLDEDGKPYLLE 265 (304)
T ss_pred -----CCCE-ECCCCCCHHHHHHHHHHHHHHHHHHCCCCEEEEE---EEEECCCCEEEEE
T ss_conf -----7411-0068999999999999999999984997369889---9990799789998
No 20
>PRK09288 purT phosphoribosylglycinamide formyltransferase 2; Validated
Probab=99.10 E-value=5e-09 Score=79.14 Aligned_cols=95 Identities=21% Similarity=0.200 Sum_probs=69.7
Q ss_pred HHHHH-HHCCCCCCCCEEECCHHHHHHHHHHCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHHHHHHH
Q ss_conf 99999-98689888815747999999999872998699971213687656565567777777079958999999999986
Q gi|254781049|r 8 AKALL-RKYNVPVAKGVVISSVHAAESAIKTLPGPLYVVKSQIHAGGRGKGRFKELPADSKGGVRVESSLKSVISDIREI 86 (398)
Q Consensus 8 aK~lL-~~~GIpvp~g~~a~s~~ea~~~a~~ig~p~~VvKaQV~aGgRGKa~~~~~hk~~~GGV~l~~s~~ea~~~a~~i 86 (398)
-|+++ .++|||+|++..+++.+|+..+++++|||+ |+|+. .|+-|| |+.+++|.+|+.++.+..
T Consensus 117 ~k~~~~~~lgIPt~~f~~v~s~~el~~~~~~lG~P~-vlK~~--~G~DGK------------Gq~~v~~~~dl~~a~~~a 181 (395)
T PRK09288 117 IRRLAAEELGLPTSPYRFADSLEELRAAVEEIGYPC-VVKPV--MSSSGK------------GQSVVRSPEDIEAAWEYA 181 (395)
T ss_pred HHHHHHHHCCCCCCCCEEECCHHHHHHHHHHHCCCE-EEECC--CCCCCC------------CEEEECCHHHHHHHHHHH
T ss_conf 999999746999999547089999999999829875-87224--157887------------528966878889999999
Q ss_pred CCCCCCCCCCCCCCCCCCCEEECCCCCCCEEEEEEEEEEC
Q ss_conf 1876544212222244330110345556505899999834
Q gi|254781049|r 87 LGSTLITKQTGPTGSRVNCVYVEDGADILRELYLSLLVDR 126 (398)
Q Consensus 87 lg~~l~t~qt~~~G~~v~~vLVEe~v~~~~E~ylgi~~Dr 126 (398)
+... .+ ....+++|++++..+|+=+-+.++.
T Consensus 182 ~~~~--------~~-~~~~~ivE~~v~f~~E~Svi~aR~~ 212 (395)
T PRK09288 182 QEGG--------RG-GAGRVIVEEFIDFDYEITLLTVRAV 212 (395)
T ss_pred HHHC--------CC-CCCCEEEEEEECCCEEEEEEEEECC
T ss_conf 8507--------57-8970899888536179999999969
No 21
>TIGR00877 purD phosphoribosylamine--glycine ligase; InterPro: IPR000115 Phosphoribosylglycinamide synthetase (6.3.4.13 from EC) (GARS) (phosphoribosylamine glycine ligase) catalyzes the second step in the de novo biosynthesis of purine: ATP + 5-phosphoribosylamine + glycine = ADP + P_i + 5'-phosphoribosylglycinamide In bacteria, GARS is a monofunctional enzyme (encoded by the purD gene). In yeast, GARS is part of a bifunctional enzyme (encoded by the ADE5/7 gene) in conjunction with phosphoribosylformylglycinamidine cyclo-ligase (AIRS) (IPR000728 from INTERPRO). In higher eukaryotes, GARS is part of a trifunctional enzyme in conjunction with AIRS (IPR000728 from INTERPRO) and with phosphoribosylglycinamide formyltransferase (GART) (), forming GARS-AIRS-GART.; GO: 0004637 phosphoribosylamine-glycine ligase activity, 0009113 purine base biosynthetic process.
Probab=99.10 E-value=1.2e-09 Score=83.28 Aligned_cols=211 Identities=24% Similarity=0.297 Sum_probs=133.5
Q ss_pred HHHHHHHCCCC-CCCCEEECCHHHHHHHHHHCCCC-EEEEECCCCCCCCCCCCCCCCCCCCCCEEEEE----CCHHHHHH
Q ss_conf 99999986898-88815747999999999872998-69997121368765656556777777707995----89999999
Q gi|254781049|r 8 AKALLRKYNVP-VAKGVVISSVHAAESAIKTLPGP-LYVVKSQIHAGGRGKGRFKELPADSKGGVRVE----SSLKSVIS 81 (398)
Q Consensus 8 aK~lL~~~GIp-vp~g~~a~s~~ea~~~a~~ig~p-~~VvKaQV~aGgRGKa~~~~~hk~~~GGV~l~----~s~~ea~~ 81 (398)
+|++|++|||| ++.+...++++||.+..++.+.| .+|||+.=||+|- ||.++ .|.+||.+
T Consensus 112 aK~fm~~~gIPGta~Y~~Ft~~eea~~y~~~~g~PA~~VVKadGLAAGK--------------GV~V~Ge~L~~~eEA~~ 177 (459)
T TIGR00877 112 AKDFMKRYGIPGTAEYEVFTDPEEAKSYIQEKGAPAEIVVKADGLAAGK--------------GVIVAGEQLKTNEEAIK 177 (459)
T ss_pred HHHHHHHCCCCCCEEEECCCCHHHHHHHHHHCCCCCCEEEECCCCCCCC--------------CCEEECCCCCCHHHHHH
T ss_conf 9999996489832221000898999999984188974898056665798--------------62684760274789999
Q ss_pred HHHHHCCCCCCCCCCCCCCCCCCCEEECCCCCCCEEEEEEEEEECCCCCEEEEEECCCCCCHHHHHHHCHHHHEEEECCC
Q ss_conf 99986187654421222224433011034555650589999983477804899844788402455574831220332144
Q gi|254781049|r 82 DIREILGSTLITKQTGPTGSRVNCVYVEDGADILRELYLSLLVDRTSGMVAFIASTQGGMDIEEVAKDYPQKIFKLLIDP 161 (398)
Q Consensus 82 ~a~~ilg~~l~t~qt~~~G~~v~~vLVEe~v~~~~E~ylgi~~Dr~~~~~vii~S~~GGvdIE~va~~~p~~I~~~~id~ 161 (398)
++++||... +-+..+ ++|+|||+++. .|+=+-.+.|..+--||..+ | ++|. -+|-
T Consensus 178 ~~~~~~~~~----~FG~a~---~~VVIEEfL~G-~E~S~~~~~DG~~v~Plp~a--Q----------DhKR-----~~eg 232 (459)
T TIGR00877 178 AVEEILEQK----AFGEAG---ERVVIEEFLEG-EEVSLLAFVDGKTVIPLPPA--Q----------DHKR-----ALEG 232 (459)
T ss_pred HHHHHHHCC----CCCCCC---CCEEEEECCCC-CCEEEEEEECCCEEEECCCC--C----------CCCC-----CCCC
T ss_conf 999998547----656668---82589642488-00899999748667705421--5----------7650-----4668
Q ss_pred CC-CC-----CHHHHHHHHHHCCCCHHH-HHHHHHHHHHHHHHHHHCC-----CCCCCCCEEEECCCCCEEEEEEEEEEC
Q ss_conf 45-78-----957888788751988899-8859999999989999559-----751023267990599679940013215
Q gi|254781049|r 162 LI-GV-----TSEDVASLCDMLELQGQA-RIDGGDLFPNLYKAFCDKD-----MSLLEINPLIIMKNGRLRVLDSKISFD 229 (398)
Q Consensus 162 ~~-gl-----~~~~~~~l~~~lg~~~~~-~~~~~~ii~~L~~~f~e~D-----a~liEINPLvvt~dg~vvAlDAKi~iD 229 (398)
.. |+ -.|--.+ ..|-+..+. .+....|++.--+.+.+-. ..+.. |+++++|+. |=-|| |+
T Consensus 233 D~~GpNTGGMGAYsP~p--hlL~~~~e~~~~~~~~I~~pt~~~l~~eG~~y~GvLYag---lMl~~~G~~--L~PkV-lE 304 (459)
T TIGR00877 233 DKKGPNTGGMGAYSPAP--HLLVFTEEVEKRIAEEIVEPTVKALRKEGTPYKGVLYAG---LMLTKEGGV--LVPKV-LE 304 (459)
T ss_pred CCCCCCCCCCCCCCCCC--CCEECCCHHHHHHHHHHHHHHHHHHHHCCCCEEEEEEEE---EEEECCCCE--EEEEE-EE
T ss_conf 88788557863302787--844237178999987778999999985289724787413---899768988--64478-89
Q ss_pred CCHHHHHHHHHHHHCCCC--CCHHHH--HHHHCCCC--EEEC
Q ss_conf 735564102786310001--562224--57753986--4422
Q gi|254781049|r 230 DNALYRHLDIQELRDVSE--EDSREI--EAKQHNLS--YIAL 265 (398)
Q Consensus 230 DnA~fR~~~~~~~~d~~~--~~~~E~--~A~~~~l~--yv~L 265 (398)
=|+.|==|+=.......+ .|-.|+ .+-+..|. .+++
T Consensus 305 fN~RFGDPEtq~vL~lL~dqsdL~e~~~a~~eg~L~d~~~~~ 346 (459)
T TIGR00877 305 FNVRFGDPETQAVLPLLKDQSDLLEVCLAAVEGKLDDSEVEL 346 (459)
T ss_pred ECCCCCCHHHHHHHHHHCCCCCHHHHHHHHHCCCCCCCEEEE
T ss_conf 705278853444645423888889999998456665641124
No 22
>PRK00885 phosphoribosylamine--glycine ligase; Provisional
Probab=99.08 E-value=3e-09 Score=80.60 Aligned_cols=199 Identities=21% Similarity=0.247 Sum_probs=121.0
Q ss_pred HHHHHHHHCCCCCCCCEEECCHHHHHHHHHHCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHHHHHHH
Q ss_conf 99999998689888815747999999999872998699971213687656565567777777079958999999999986
Q gi|254781049|r 7 QAKALLRKYNVPVAKGVVISSVHAAESAIKTLPGPLYVVKSQIHAGGRGKGRFKELPADSKGGVRVESSLKSVISDIREI 86 (398)
Q Consensus 7 qaK~lL~~~GIpvp~g~~a~s~~ea~~~a~~ig~p~~VvKaQV~aGgRGKa~~~~~hk~~~GGV~l~~s~~ea~~~a~~i 86 (398)
-+|+++++|+||++++...++.++|.+..++.++| +|+|+.=|++|. ||.++.|.+|+.++.+++
T Consensus 105 faK~~m~~~~IPTa~~~~f~~~~~A~~~l~~~~~p-~VIKaDGLAaGK--------------GV~V~~~~~ea~~al~~i 169 (424)
T PRK00885 105 FAKDFMARYGIPTAAYEVFTDAEEAKAYLDEQGAP-IVVKADGLAAGK--------------GVVVAMTLEEAEAAVDDM 169 (424)
T ss_pred HHHHHHHHCCCCCCCEEEECCHHHHHHHHHHCCCC-EEEECCCCCCCC--------------CEEEECCHHHHHHHHHHH
T ss_conf 99999998298987548868999999999857998-899617656777--------------517637899999999998
Q ss_pred CCCCCCCCCCCCCCCCCCCEEECCCCCCCEEEEEEEEEECCCCCEEEEEECCCCCCHHHHHHHCHHHHEEEECCCCCC-C
Q ss_conf 187654421222224433011034555650589999983477804899844788402455574831220332144457-8
Q gi|254781049|r 87 LGSTLITKQTGPTGSRVNCVYVEDGADILRELYLSLLVDRTSGMVAFIASTQGGMDIEEVAKDYPQKIFKLLIDPLIG-V 165 (398)
Q Consensus 87 lg~~l~t~qt~~~G~~v~~vLVEe~v~~~~E~ylgi~~Dr~~~~~vii~S~~GGvdIE~va~~~p~~I~~~~id~~~g-l 165 (398)
|..+. .+..| ++|+|||++.. .|+=+-...|...-.|+-.+ + ++ .++..-..-|..| +
T Consensus 170 ~~~~~----fg~ag---~~VvIEE~L~G-~E~S~~a~~DG~~~~~lp~a--q----------Dh-KR~~dgD~GPNTGGM 228 (424)
T PRK00885 170 LAGNK----FGDAG---ARVVIEEFLDG-EEASFFALVDGENVLPLPTA--Q----------DH-KRAGDGDTGPNTGGM 228 (424)
T ss_pred HCCCC----CCCCC---CEEEEEECCCC-CEEEEEEEECCCCCCCCCCC--C----------CC-CCCCCCCCCCCCCCC
T ss_conf 50332----34568---72899970588-31799999789972647021--1----------47-505689999889988
Q ss_pred CHHHHHHHHHHCCCCHHHHHHH-HHHHHHHHHHHHHCCCCCCCC--CEEEECCCCCEEEEEEEEEECCCHHHHHHHHHHH
Q ss_conf 9578887887519888998859-999999989999559751023--2679905996799400132157355641027863
Q gi|254781049|r 166 TSEDVASLCDMLELQGQARIDG-GDLFPNLYKAFCDKDMSLLEI--NPLIIMKNGRLRVLDSKISFDDNALYRHLDIQEL 242 (398)
Q Consensus 166 ~~~~~~~l~~~lg~~~~~~~~~-~~ii~~L~~~f~e~Da~liEI--NPLvvt~dg~vvAlDAKi~iDDnA~fR~~~~~~~ 242 (398)
-.+.-.. -+..+..+.+ .+++....+.+.+......=| ==|.+|++| .. .|.=|+.|=-|+...+
T Consensus 229 Ga~sP~p-----~~~~~~~~~i~~~Ii~pt~~~l~~eg~~y~GiLy~GlMit~~G-pk------VlEyN~RfGDPE~qvl 296 (424)
T PRK00885 229 GAYSPAP-----VVTEEVHDRVMEEIIEPTVKGMAAEGIPYTGVLYAGLMITKDG-PK------VIEFNCRFGDPETQVV 296 (424)
T ss_pred CCCCCCC-----CCCHHHHHHHHHHHHHHHHHHHHHCCCCEEEEEEEEEEEECCC-CE------EEEEECCCCCHHHHHH
T ss_conf 5667886-----7999999999998799999999857984799987799986797-55------8986313488588899
Q ss_pred HCCCCCCHHHH
Q ss_conf 10001562224
Q gi|254781049|r 243 RDVSEEDSREI 253 (398)
Q Consensus 243 ~d~~~~~~~E~ 253 (398)
....+.|-.++
T Consensus 297 lp~L~~dl~~l 307 (424)
T PRK00885 297 LPRLKSDLVEL 307 (424)
T ss_pred HHHCCCCHHHH
T ss_conf 87523619999
No 23
>PRK13789 phosphoribosylamine--glycine ligase; Provisional
Probab=99.06 E-value=2.7e-09 Score=80.91 Aligned_cols=212 Identities=21% Similarity=0.260 Sum_probs=123.5
Q ss_pred HHHHHHHHCCCCCCCCEEECCHHHHHHHHHHCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHHHHHHH
Q ss_conf 99999998689888815747999999999872998699971213687656565567777777079958999999999986
Q gi|254781049|r 7 QAKALLRKYNVPVAKGVVISSVHAAESAIKTLPGPLYVVKSQIHAGGRGKGRFKELPADSKGGVRVESSLKSVISDIREI 86 (398)
Q Consensus 7 qaK~lL~~~GIpvp~g~~a~s~~ea~~~a~~ig~p~~VvKaQV~aGgRGKa~~~~~hk~~~GGV~l~~s~~ea~~~a~~i 86 (398)
-+|+++++||||++++...++.++|.+..++.++|+ |||+.=||+|. ||.++.+.+|+.++.++|
T Consensus 111 faK~fm~~~~IPTa~~~~f~~~~~A~~~l~~~~~P~-VIKaDGLAaGK--------------GV~V~~~~~eA~~al~~i 175 (426)
T PRK13789 111 FAKSLMKEAKIPTASYKTFTEYSSSLSYLESEMLPI-VIKADGLAAGK--------------GVTVATEKKMAKRALKEI 175 (426)
T ss_pred HHHHHHHHCCCCCCEEEEECCHHHHHHHHHHCCCCE-EEECCCCCCCC--------------CEEEECCHHHHHHHHHHH
T ss_conf 999999972999760157368999999998579988-99678768999--------------669539999999999997
Q ss_pred CCCCCCCCCCCCCCCCCCCEEECCCCCCCEEEEEEEEEECCCCCEEEEEECCCCCCHHHHHHHCHHHHEEEECCCCC-CC
Q ss_conf 18765442122222443301103455565058999998347780489984478840245557483122033214445-78
Q gi|254781049|r 87 LGSTLITKQTGPTGSRVNCVYVEDGADILRELYLSLLVDRTSGMVAFIASTQGGMDIEEVAKDYPQKIFKLLIDPLI-GV 165 (398)
Q Consensus 87 lg~~l~t~qt~~~G~~v~~vLVEe~v~~~~E~ylgi~~Dr~~~~~vii~S~~GGvdIE~va~~~p~~I~~~~id~~~-gl 165 (398)
|.... -+..| ++|+|||++.. .|+=+-...|...- +.|-+.+ ++ .++..-..-|.. |+
T Consensus 176 ~~~~~----fg~ag---~~VvIEE~L~G-~E~S~~a~~dG~~~--~~lp~aQ----------Dh-KR~~dgD~GPNTGGM 234 (426)
T PRK13789 176 FKDKK----FGQSG---NQVVIEEFMEG-QEASIFAISDGDSY--FLLPAAQ----------DH-KRAFDGDQGPNTGGM 234 (426)
T ss_pred HHHHH----HHCCC---CEEEEEECCCC-CCEEEEEEECCCEE--EECCCCC----------CC-CCCCCCCCCCCCCCC
T ss_conf 54423----30358---75999974589-84479999729977--8688644----------44-213379999999987
Q ss_pred CHHHHHHHHHHCCCCHHHHHHHH-HHHHHHHHHHHHCCCCCCCC--CEEEECCCCCEEEEEEEEEECCCHHHHHHHHHHH
Q ss_conf 95788878875198889988599-99999989999559751023--2679905996799400132157355641027863
Q gi|254781049|r 166 TSEDVASLCDMLELQGQARIDGG-DLFPNLYKAFCDKDMSLLEI--NPLIIMKNGRLRVLDSKISFDDNALYRHLDIQEL 242 (398)
Q Consensus 166 ~~~~~~~l~~~lg~~~~~~~~~~-~ii~~L~~~f~e~Da~liEI--NPLvvt~dg~vvAlDAKi~iDDnA~fR~~~~~~~ 242 (398)
-.+--. --+.....+.+. .++....+.+.+......=| ==|.+|++|++..+ .=|+.|--|+...+
T Consensus 235 GaysP~-----p~~~~~~~~~i~~~ii~pt~~~l~~~g~~y~GvLy~GlMlt~~G~pkVl------EfN~RfGDPE~q~i 303 (426)
T PRK13789 235 GAYCPA-----PVITEAILQKVKERIFDPMFDDFRKKGHPYRGLLYAGLMISPEGEPKVV------EFNCRFGDPETQCV 303 (426)
T ss_pred CCCCCC-----CCCCHHHHHHHHHHHHHHHHHHHHHCCCCCEEEEEEEEEECCCCCEEEE------EEEEECCCCHHHHH
T ss_conf 677778-----6689999999998604899999985899988676532899269976999------98853189168889
Q ss_pred HCCCCCCHHHH--HHHHCCCCEEEC
Q ss_conf 10001562224--577539864422
Q gi|254781049|r 243 RDVSEEDSREI--EAKQHNLSYIAL 265 (398)
Q Consensus 243 ~d~~~~~~~E~--~A~~~~l~yv~L 265 (398)
....+.|-.++ .+.+..|+-+.+
T Consensus 304 Lp~L~~dl~~~~~a~~~g~L~~~~~ 328 (426)
T PRK13789 304 LAMLDGDLLELLYAASTGKIKVVNL 328 (426)
T ss_pred HHHHHCCHHHHHHHHHHCCCCCCCC
T ss_conf 8874154999999997088664544
No 24
>TIGR02068 cya_phycin_syn cyanophycin synthetase; InterPro: IPR011810 Cyanophycin is an insoluble storage polymer for carbon, nitrogen, and energy, found in most Cyanobacteria. The polymer has a backbone of L-aspartic acid, with most Asp side chain carboxyl groups attached to L-arginine. The polymer is made by this enzyme, cyanophycin synthetase, and degraded by cyanophycinase. Heterologously expressed cyanophycin synthetase in Escherichia coli produces a closely related, water-soluble polymer with some Arg replaced by Lys. It is unclear whether enzymes that produce soluble cyanophycin-like polymers in vivo in non-Cyanobacterial species should be designated as cyanophycin synthetase itself or as a related enzyme. Cyanophycin synthesis is analogous to polyhydroxyalkanoic acid (PHA) biosynthesis, except that PHA polymers lack nitrogen and may be made under nitrogen-limiting conditions .; GO: 0005524 ATP binding, 0016874 ligase activity, 0009059 macromolecule biosynthetic process.
Probab=99.01 E-value=1.4e-09 Score=82.70 Aligned_cols=121 Identities=27% Similarity=0.354 Sum_probs=79.3
Q ss_pred HHHHHHHCCCCCCCCEEECCHHHHHHHHHHCC-CCEEEEECCCCCCCCCCCCCCCCCCCCCCEEEE-ECCHHHHHHHHHH
Q ss_conf 99999986898888157479999999998729-986999712136876565655677777770799-5899999999998
Q gi|254781049|r 8 AKALLRKYNVPVAKGVVISSVHAAESAIKTLP-GPLYVVKSQIHAGGRGKGRFKELPADSKGGVRV-ESSLKSVISDIRE 85 (398)
Q Consensus 8 aK~lL~~~GIpvp~g~~a~s~~ea~~~a~~ig-~p~~VvKaQV~aGgRGKa~~~~~hk~~~GGV~l-~~s~~ea~~~a~~ 85 (398)
-|+||+.+|+|||+|.++.+.+||..+++++| ||+ |+|+- =|-.|| ||.+ .+|.+|+..+++.
T Consensus 222 TK~iL~~~GvPVP~G~~~~~~~~a~~aa~~~GG~Pv-ViKP~--DGn~Gr------------Gv~~ni~~r~e~e~AY~~ 286 (876)
T TIGR02068 222 TKKILKAAGVPVPEGTVVQSAEEAWEAAEDLGGYPV-VIKPY--DGNHGR------------GVTINIETRDEIESAYEA 286 (876)
T ss_pred HHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHCCCCE-EEEEC--CCCCCC------------EEEECCCCHHHHHHHHHH
T ss_conf 999998478988887366778999999997189968-99517--799874------------378407774889999999
Q ss_pred HCCCCCCCCCCCCCCCCCCCEEECCCCCCCEEEEEEEEEEC----CCC-CEEEEEECCCCCCHHHHHHHCHHHH-EEEEC
Q ss_conf 61876544212222244330110345556505899999834----778-0489984478840245557483122-03321
Q gi|254781049|r 86 ILGSTLITKQTGPTGSRVNCVYVEDGADILRELYLSLLVDR----TSG-MVAFIASTQGGMDIEEVAKDYPQKI-FKLLI 159 (398)
Q Consensus 86 ilg~~l~t~qt~~~G~~v~~vLVEe~v~~~~E~ylgi~~Dr----~~~-~~vii~S~~GGvdIE~va~~~p~~I-~~~~i 159 (398)
=- +. + ..+.|+||.++... ||=|=++-++ +.+ ++-+++ -|==-|||+ | ..+.-
T Consensus 287 A~-------~~---S-k~~~ViVEr~i~G~-dhRlLVVg~k~VAvA~R~PA~ViG--DG~hTi~eL-------iG~~~N~ 345 (876)
T TIGR02068 287 AK-------EE---S-KTSEVIVERYIKGR-DHRLLVVGGKLVAVAERVPAHVIG--DGVHTIEEL-------IGEQINK 345 (876)
T ss_pred HH-------HC---C-CCCEEEEEEEECCC-CEEEEEECCEEEEEECCCCCEEEC--CCCCHHHHH-------HHHHHCC
T ss_conf 98-------60---7-86606898764276-238999989689986188886883--872007664-------0576467
Q ss_pred CCCCC
Q ss_conf 44457
Q gi|254781049|r 160 DPLIG 164 (398)
Q Consensus 160 d~~~g 164 (398)
||..|
T Consensus 346 DP~RG 350 (876)
T TIGR02068 346 DPLRG 350 (876)
T ss_pred CCCCC
T ss_conf 77888
No 25
>PRK13790 phosphoribosylamine--glycine ligase; Provisional
Probab=99.01 E-value=6.1e-09 Score=78.59 Aligned_cols=197 Identities=22% Similarity=0.264 Sum_probs=117.4
Q ss_pred HHHHHHHHCCCCCCCCEEECCHHHHHHHHHHCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHHHHHHH
Q ss_conf 99999998689888815747999999999872998699971213687656565567777777079958999999999986
Q gi|254781049|r 7 QAKALLRKYNVPVAKGVVISSVHAAESAIKTLPGPLYVVKSQIHAGGRGKGRFKELPADSKGGVRVESSLKSVISDIREI 86 (398)
Q Consensus 7 qaK~lL~~~GIpvp~g~~a~s~~ea~~~a~~ig~p~~VvKaQV~aGgRGKa~~~~~hk~~~GGV~l~~s~~ea~~~a~~i 86 (398)
-+|+++++||||++++..+++.++|.+..++.++|. |||+.=||+|. ||.++.|.+|+.++.++|
T Consensus 106 faK~~m~~~~IPTa~~~~f~~~~~A~~~l~~~~~p~-VIKaDGLAaGK--------------GV~V~~~~~eA~~al~~i 170 (415)
T PRK13790 106 FAKKIMEKYNIPTADYKEVERKKDALTYIENCELPV-VVKKDGLAAGK--------------GVIIADTIEAARSAIEIM 170 (415)
T ss_pred HHHHHHHHCCCCCCCEEEECCHHHHHHHHHHCCCCE-EEECCCCCCCC--------------CEEEECCHHHHHHHHHHH
T ss_conf 999999982979777255087999999986179988-99668667899--------------569979999999999998
Q ss_pred CCCCCCCCCCCCCCCCCCCEEECCCCCCCEEEEEEEEEECCCCCEEEEEECCCCCCHHHHHHHCHHHHEEEECCCCCCCC
Q ss_conf 18765442122222443301103455565058999998347780489984478840245557483122033214445789
Q gi|254781049|r 87 LGSTLITKQTGPTGSRVNCVYVEDGADILRELYLSLLVDRTSGMVAFIASTQGGMDIEEVAKDYPQKIFKLLIDPLIGVT 166 (398)
Q Consensus 87 lg~~l~t~qt~~~G~~v~~vLVEe~v~~~~E~ylgi~~Dr~~~~~vii~S~~GGvdIE~va~~~p~~I~~~~id~~~gl~ 166 (398)
|..+. .| .|+|||++.. .|+=+-...|.... +.+.+. +.+ ++--.|-..|..
T Consensus 171 ~~~~~-------~g----~VvIEE~L~G-~E~S~~a~~DG~~~--~p~~~~---------aQD-----hKR~~dgD~GPN 222 (415)
T PRK13790 171 YGDEE-------EG----TVVFETFLEG-EEFSLMTFVNGDLA--VPFDCI---------AQD-----HKRAFDHDEGPN 222 (415)
T ss_pred HCCCC-------CC----EEEEEEECCC-CCEEEEEEECCCEE--EECCCC---------CCC-----CCCCCCCCCCCC
T ss_conf 55554-------76----5999871578-63489999739979--957754---------321-----202468999999
Q ss_pred HHHHHHHHHHCCCCHHHHHHH-HHHHHHHHHHHHHCCCCCCCC--CEEEECCCCCEEEEEEEEEECCCHHHHHHHHHHHH
Q ss_conf 578887887519888998859-999999989999559751023--26799059967994001321573556410278631
Q gi|254781049|r 167 SEDVASLCDMLELQGQARIDG-GDLFPNLYKAFCDKDMSLLEI--NPLIIMKNGRLRVLDSKISFDDNALYRHLDIQELR 243 (398)
Q Consensus 167 ~~~~~~l~~~lg~~~~~~~~~-~~ii~~L~~~f~e~Da~liEI--NPLvvt~dg~vvAlDAKi~iDDnA~fR~~~~~~~~ 243 (398)
.--.-...-.--++.+..+.+ ..++....+.+.+......=| ==|.+|++| +.. |.=|+.|--|+...+.
T Consensus 223 TGGMGaysp~p~~~~~~~~~~~~~I~~p~~~~l~~eg~~y~GvLy~GlMlt~~G-pkV------lEyN~RfGDPE~q~iL 295 (415)
T PRK13790 223 TGGMGAYCPVPHISDDVLKLTNETIAQPIAKAMLNEGYQFFGVLYIGAILTKDG-PKV------IEFNARFGDPEAQVLL 295 (415)
T ss_pred CCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCEEEEEEEEEEECCC-CEE------EEEEEECCCCHHHHHH
T ss_conf 998756677744698999999987089999999855998489988779986898-669------9987411892288898
Q ss_pred CCCCCCHHHH
Q ss_conf 0001562224
Q gi|254781049|r 244 DVSEEDSREI 253 (398)
Q Consensus 244 d~~~~~~~E~ 253 (398)
...+.|-.|+
T Consensus 296 p~L~~Dl~~~ 305 (415)
T PRK13790 296 SRMESDLMQH 305 (415)
T ss_pred HHCCCHHHHH
T ss_conf 7605519999
No 26
>COG0151 PurD Phosphoribosylamine-glycine ligase [Nucleotide transport and metabolism]
Probab=99.00 E-value=6.6e-09 Score=78.34 Aligned_cols=195 Identities=23% Similarity=0.263 Sum_probs=117.4
Q ss_pred HHHHHHHHCCCCCCCCEEECCHHHHHHHHHHCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHHHHHHH
Q ss_conf 99999998689888815747999999999872998699971213687656565567777777079958999999999986
Q gi|254781049|r 7 QAKALLRKYNVPVAKGVVISSVHAAESAIKTLPGPLYVVKSQIHAGGRGKGRFKELPADSKGGVRVESSLKSVISDIREI 86 (398)
Q Consensus 7 qaK~lL~~~GIpvp~g~~a~s~~ea~~~a~~ig~p~~VvKaQV~aGgRGKa~~~~~hk~~~GGV~l~~s~~ea~~~a~~i 86 (398)
-+|+++++||||++.+...+++++|.+..++.|.|+ |||+.=|++|. ||+++.+.+|+.+++++|
T Consensus 106 faK~fm~k~~IPta~y~~f~~~e~a~ayi~~~g~pi-VVKadGLaaGK--------------GV~V~~~~eeA~~a~~~~ 170 (428)
T COG0151 106 FAKDFMKKYGIPTAEYEVFTDPEEAKAYIDEKGAPI-VVKADGLAAGK--------------GVIVAMTLEEAEAAVDEM 170 (428)
T ss_pred HHHHHHHHCCCCCCCCEECCCHHHHHHHHHHCCCCE-EEECCCCCCCC--------------CEEECCCHHHHHHHHHHH
T ss_conf 999999981999641110089899999999729988-99345446789--------------859827799999999999
Q ss_pred CCCCCCCCCCCCCCCCCCCEEECCCCCCCEEEEEEEEEECCCCCEEEEEECCCCCCHHHHHHHCHHHHEEEECCCCCC--
Q ss_conf 187654421222224433011034555650589999983477804899844788402455574831220332144457--
Q gi|254781049|r 87 LGSTLITKQTGPTGSRVNCVYVEDGADILRELYLSLLVDRTSGMVAFIASTQGGMDIEEVAKDYPQKIFKLLIDPLIG-- 164 (398)
Q Consensus 87 lg~~l~t~qt~~~G~~v~~vLVEe~v~~~~E~ylgi~~Dr~~~~~vii~S~~GGvdIE~va~~~p~~I~~~~id~~~g-- 164 (398)
|.... -|....+|+|||+++. .|+=+=.+.|..+-.|+..+ + ++ +--.|-..|
T Consensus 171 l~~~~-------fg~~g~~VVIEEfL~G-eE~S~~a~~DG~~v~p~p~a--Q----------Dh-----Kra~dgD~GPN 225 (428)
T COG0151 171 LEGNA-------FGSAGARVVIEEFLDG-EEFSLQAFVDGKTVIPMPTA--Q----------DH-----KRAYDGDTGPN 225 (428)
T ss_pred HHHCC-------CCCCCCCEEEEECCCC-EEEEEEEEECCCEEEECCCC--C----------CC-----CCCCCCCCCCC
T ss_conf 74000-------1478874899853346-17999999769867878531--4----------56-----43348998998
Q ss_pred ---CCHHHHHHHHHHCCCCHHHHHHHH-HHHHHHHHHHHHCCCCCCC--CCEEEECCCCCEEEEEEEEEECCCHHHHHHH
Q ss_conf ---895788878875198889988599-9999998999955975102--3267990599679940013215735564102
Q gi|254781049|r 165 ---VTSEDVASLCDMLELQGQARIDGG-DLFPNLYKAFCDKDMSLLE--INPLIIMKNGRLRVLDSKISFDDNALYRHLD 238 (398)
Q Consensus 165 ---l~~~~~~~l~~~lg~~~~~~~~~~-~ii~~L~~~f~e~Da~liE--INPLvvt~dg~vvAlDAKi~iDDnA~fR~~~ 238 (398)
+-.|.-.. =++.+..+... +++..-.+.+.+......= --=|.+|++| .. .|.=|+.|--|+
T Consensus 226 TGGMGaysp~P-----~~t~e~~~~~~~~Iv~ptv~gm~~EG~~f~GvLy~glMlt~~G-Pk------ViEfN~RFGDPE 293 (428)
T COG0151 226 TGGMGAYSPAP-----FITDEVVERAVEEIVEPTVEGMAKEGYPFRGVLYAGLMLTADG-PK------VIEFNARFGDPE 293 (428)
T ss_pred CCCCCCCCCCC-----CCCHHHHHHHHHHHHHHHHHHHHHCCCCCEEEEEEEEEECCCC-CE------EEEEECCCCCHH
T ss_conf 88877777988-----7998999999999999999999971898147887678982899-67------999856668835
Q ss_pred HHHHHCCCCCCHHHH
Q ss_conf 786310001562224
Q gi|254781049|r 239 IQELRDVSEEDSREI 253 (398)
Q Consensus 239 ~~~~~d~~~~~~~E~ 253 (398)
-.......+.|-.|+
T Consensus 294 tq~vL~~l~sdl~~~ 308 (428)
T COG0151 294 TQVVLPLLESDLVEL 308 (428)
T ss_pred HHHHHHHCCCCHHHH
T ss_conf 777787602609999
No 27
>PRK07206 hypothetical protein; Provisional
Probab=98.96 E-value=2.4e-07 Score=68.09 Aligned_cols=97 Identities=20% Similarity=0.233 Sum_probs=77.7
Q ss_pred HHHHHHHHHHCCCCCCCCEEECCHHHHHHHHHH---CCCCEEEEECCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHH
Q ss_conf 799999999868988881574799999999987---29986999712136876565655677777770799589999999
Q gi|254781049|r 5 EYQAKALLRKYNVPVAKGVVISSVHAAESAIKT---LPGPLYVVKSQIHAGGRGKGRFKELPADSKGGVRVESSLKSVIS 81 (398)
Q Consensus 5 EyqaK~lL~~~GIpvp~g~~a~s~~ea~~~a~~---ig~p~~VvKaQV~aGgRGKa~~~~~hk~~~GGV~l~~s~~ea~~ 81 (398)
-|.-++.|++.|+|+|+...+++.+|+...+++ ++||+ |||+---+|. -||++|.|.+|+++
T Consensus 109 K~~m~~~L~~aGl~~~~~~~~~~~~e~~~~~~~~~~~~~Pv-VvKP~~gagS--------------~gV~~c~~~~el~~ 173 (415)
T PRK07206 109 KYEMINALANAGLPAIRQIDTADWEEASAWIRVNNLWDSPV-VIKPLESAGS--------------DGVFFCPDKQDAYH 173 (415)
T ss_pred HHHHHHHHHHCCCCCCCEEECCCHHHHHHHHHHCCCCCCCE-EEECCCCCCC--------------CCEEEECCHHHHHH
T ss_conf 99999999975998553885299999999998605579998-9958999987--------------99899799999999
Q ss_pred HHHHHCCCCCCCCCCCCCCCCCCCEEECCCCCCCEEEEEEEE
Q ss_conf 999861876544212222244330110345556505899999
Q gi|254781049|r 82 DIREILGSTLITKQTGPTGSRVNCVYVEDGADILRELYLSLL 123 (398)
Q Consensus 82 ~a~~ilg~~l~t~qt~~~G~~v~~vLVEe~v~~~~E~ylgi~ 123 (398)
++.+++++.- ..|..-+.+||||+++ +.||.+-.+
T Consensus 174 a~~~i~~~~n------~~g~~~~~vLveEyl~-G~EysVe~v 208 (415)
T PRK07206 174 AFNAILGKAN------KLGLVNESVLVQEFLI-GTEYVVNTV 208 (415)
T ss_pred HHHHHHCCCC------CCCCCCCCEEEEECCC-CCEEEEEEE
T ss_conf 9999856654------3578675388754146-857899999
No 28
>pfam07478 Dala_Dala_lig_C D-ala D-ala ligase C-terminus. This family represents the C-terminal, catalytic domain of the D-alanine--D-alanine ligase enzyme EC:6.3.2.4. D-Alanine is one of the central molecules of the cross-linking step of peptidoglycan assembly. There are three enzymes involved in the D-alanine branch of peptidoglycan biosynthesis: the pyridoxal phosphate-dependent D-alanine racemase (Alr), the ATP-dependent D-alanine:D-alanine ligase (Ddl), and the ATP-dependent D-alanine:D-alanine-adding enzyme (MurF).
Probab=98.92 E-value=1.8e-07 Score=68.95 Aligned_cols=159 Identities=21% Similarity=0.285 Sum_probs=94.3
Q ss_pred HHHHCCCCCCCCEEECCHH----HHHHHHHHCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHHHHHHH
Q ss_conf 9998689888815747999----999999872998699971213687656565567777777079958999999999986
Q gi|254781049|r 11 LLRKYNVPVAKGVVISSVH----AAESAIKTLPGPLYVVKSQIHAGGRGKGRFKELPADSKGGVRVESSLKSVISDIREI 86 (398)
Q Consensus 11 lL~~~GIpvp~g~~a~s~~----ea~~~a~~ig~p~~VvKaQV~aGgRGKa~~~~~hk~~~GGV~l~~s~~ea~~~a~~i 86 (398)
||+++|||+|++.++++.+ ++.++..++|||+ |+|+- .||-| =||.+++|.+|+.++.+..
T Consensus 1 ll~~~Giptp~~~~v~~~~~~~~~~~~i~~~lg~P~-vvKP~--~~gss------------~Gv~~v~~~~el~~~i~~~ 65 (201)
T pfam07478 1 LLKAAGIPVAPFIVLTREDWVLATIEKVEEKLGYPV-FVKPA--NLGSS------------VGISKVTSREELQSAIEEA 65 (201)
T ss_pred CHHHCCCCCCCEEEEECCCCCHHHHHHHHHHCCCCE-EEEEC--CCCCC------------CCEEEECCHHHHHHHHHHH
T ss_conf 955659999990898253234357999998659988-99989--99986------------6879995846879999998
Q ss_pred CCCCCCCCCCCCCCCCCCCEEECCCCCCCEEEEEEEEEECCCCCEEEEE----ECCCCC-CHHHHHHHCHHHHEEEECCC
Q ss_conf 1876544212222244330110345556505899999834778048998----447884-02455574831220332144
Q gi|254781049|r 87 LGSTLITKQTGPTGSRVNCVYVEDGADILRELYLSLLVDRTSGMVAFIA----STQGGM-DIEEVAKDYPQKIFKLLIDP 161 (398)
Q Consensus 87 lg~~l~t~qt~~~G~~v~~vLVEe~v~~~~E~ylgi~~Dr~~~~~vii~----S~~GGv-dIE~va~~~p~~I~~~~id~ 161 (398)
+... +.+|||++++ ++|+-+++..|.. +.++. ...+|+ +.+.-. .+.. .
T Consensus 66 ~~~~-------------~~vlVEefi~-G~E~~v~vl~~~~---~~~~~~~e~~~~~~~~~~~~k~--~~~~--~----- 119 (201)
T pfam07478 66 FQYD-------------NKVLIEEAIE-GREIECAVLGNED---LEVSPVGEIRLSGGFYDYEAKY--ILSS--A----- 119 (201)
T ss_pred HHCC-------------CCEEEEECCC-CCEEEEEEEECCC---EEEEEEEEEECCCCEEEHHHEE--CCCC--C-----
T ss_conf 7459-------------8079998566-9679999970898---0898758994377502676801--3687--2-----
Q ss_pred CCCCCHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCEEEECCCCCEEEEE
Q ss_conf 45789578887887519888998859999999989999559751023267990599679940
Q gi|254781049|r 162 LIGVTSEDVASLCDMLELQGQARIDGGDLFPNLYKAFCDKDMSLLEINPLIIMKNGRLRVLD 223 (398)
Q Consensus 162 ~~gl~~~~~~~l~~~lg~~~~~~~~~~~ii~~L~~~f~e~Da~liEINPLvvt~dg~vvAlD 223 (398)
....-..++......+.++..+.+++.--.+..-+|. .++++|+++.+.
T Consensus 120 ----------~~~~Pa~l~~~~~~~i~~~A~~~~~aLg~~g~~rvD~---~~d~~g~~~vlE 168 (201)
T pfam07478 120 ----------QIIVPADLPEEVEEQIQELALKAYKALGCRGLARIDF---FLTEDGEIYLNE 168 (201)
T ss_pred ----------EEEECCCCCHHHHHHHHHHHHHHHHHHCCCCCEEEEE---EECCCCCEEEEE
T ss_conf ----------3761566859999999999999999848876057999---996899499999
No 29
>PRK12767 carbamoyl phosphate synthase-like protein; Provisional
Probab=98.87 E-value=1.3e-08 Score=76.40 Aligned_cols=92 Identities=15% Similarity=0.156 Sum_probs=72.1
Q ss_pred HHHHHHHHHHCCCCCCCCEEECCHHHHHH-HHHHCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHHHH
Q ss_conf 79999999986898888157479999999-99872998699971213687656565567777777079958999999999
Q gi|254781049|r 5 EYQAKALLRKYNVPVAKGVVISSVHAAES-AIKTLPGPLYVVKSQIHAGGRGKGRFKELPADSKGGVRVESSLKSVISDI 83 (398)
Q Consensus 5 EyqaK~lL~~~GIpvp~g~~a~s~~ea~~-~a~~ig~p~~VvKaQV~aGgRGKa~~~~~hk~~~GGV~l~~s~~ea~~~a 83 (398)
-+..+++|+++|||+|++...++.+++.. .+++++||+ |+|+-.-+|+ -|+.+++|.+|+..+.
T Consensus 112 K~~~~~~l~~~gip~P~t~~~~~~~~~~~~~~~~~~fP~-vvKP~~g~gs--------------~Gv~~i~~~~el~~~~ 176 (325)
T PRK12767 112 KWLTYEFLKENGINTPKSYLPEDLEDLLKALAEELGFPL-IVKPRDGSGS--------------IGVFKVNNREELEFLL 176 (325)
T ss_pred HHHHHHHHHHCCCCCCCCCCCCCHHHHHHHHHHHCCCCE-EEEECCCCCC--------------CCEEEECCHHHHHHHH
T ss_conf 999999999759998982055899999999986569966-9853567887--------------7549979999999999
Q ss_pred HHHCCCCCCCCCCCCCCCCCCCEEECCCCCCCEEEEEEEEEECCCC
Q ss_conf 9861876544212222244330110345556505899999834778
Q gi|254781049|r 84 REILGSTLITKQTGPTGSRVNCVYVEDGADILRELYLSLLVDRTSG 129 (398)
Q Consensus 84 ~~ilg~~l~t~qt~~~G~~v~~vLVEe~v~~~~E~ylgi~~Dr~~~ 129 (398)
++. ..++|||.++ ++||-+.+..|++..
T Consensus 177 ~~~-----------------~~~ivqe~i~-G~E~tvdv~~d~~g~ 204 (325)
T PRK12767 177 RYN-----------------PNLIIQEFIE-GQEYTVDVLCDLNGE 204 (325)
T ss_pred HHC-----------------CCEEEEECCC-CCEEEEEEEEECCCC
T ss_conf 748-----------------9749870348-988999999978999
No 30
>pfam08443 RimK RimK-like ATP-grasp domain. This ATP-grasp domain is found in the ribosomal S6 modification enzyme RimK.
Probab=98.84 E-value=5.6e-08 Score=72.21 Aligned_cols=93 Identities=24% Similarity=0.224 Sum_probs=71.5
Q ss_pred HHHHHHHHHCCCCCCCCEEECCHHHHHHHHHHC-CCCEEEEECCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHHHHH
Q ss_conf 999999998689888815747999999999872-9986999712136876565655677777770799589999999999
Q gi|254781049|r 6 YQAKALLRKYNVPVAKGVVISSVHAAESAIKTL-PGPLYVVKSQIHAGGRGKGRFKELPADSKGGVRVESSLKSVISDIR 84 (398)
Q Consensus 6 yqaK~lL~~~GIpvp~g~~a~s~~ea~~~a~~i-g~p~~VvKaQV~aGgRGKa~~~~~hk~~~GGV~l~~s~~ea~~~a~ 84 (398)
+.+|++|+++|||+|++.++.+++++.+.++++ |||+ |+|+- .|+.|+ ||.++++.+++.++.+
T Consensus 5 ~~tk~ll~~~Gip~P~~~~~~~~~~~~~~~~~~~g~Pv-VvKP~--~g~~g~------------gV~~v~~~~el~~~~~ 69 (190)
T pfam08443 5 AKSHQLLAKHGIPVPNTGLAWSPEDAEKFIEQIKGFPV-VVKSV--FGSQGI------------GVFLAEDEQSLEQLLE 69 (190)
T ss_pred HHHHHHHHHCCCCCCCEEEECCHHHHHHHHHHHCCCCE-EEECC--CCCCCC------------CEEEEECHHHHHHHHH
T ss_conf 99999999879797998998899999999998089838-99678--899984------------5588606377778888
Q ss_pred HHCCCCCCCCCCCCCCCCCCCEEECCCCCC--CEEEEEEEEEEC
Q ss_conf 861876544212222244330110345556--505899999834
Q gi|254781049|r 85 EILGSTLITKQTGPTGSRVNCVYVEDGADI--LRELYLSLLVDR 126 (398)
Q Consensus 85 ~ilg~~l~t~qt~~~G~~v~~vLVEe~v~~--~~E~ylgi~~Dr 126 (398)
...... ..+|+|++++. .+|+=+.+.-+.
T Consensus 70 ~~~~~~-------------~~vlvqefI~~~~~~dirv~vi~~~ 100 (190)
T pfam08443 70 AFKWLK-------------NQILVQEFIAEAGNRDIRCLVVGGE 100 (190)
T ss_pred HHHHCC-------------CCEEEEEEEECCCCCEEEEEEECCC
T ss_conf 886348-------------7377555660478854899996063
No 31
>PRK01966 ddl D-alanyl-alanine synthetase A; Reviewed
Probab=98.84 E-value=5.8e-07 Score=65.53 Aligned_cols=166 Identities=17% Similarity=0.168 Sum_probs=101.4
Q ss_pred HHHHHHHHHHCCCCCCCCEEECCHH---HHHHHHHHCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHH
Q ss_conf 7999999998689888815747999---9999998729986999712136876565655677777770799589999999
Q gi|254781049|r 5 EYQAKALLRKYNVPVAKGVVISSVH---AAESAIKTLPGPLYVVKSQIHAGGRGKGRFKELPADSKGGVRVESSLKSVIS 81 (398)
Q Consensus 5 EyqaK~lL~~~GIpvp~g~~a~s~~---ea~~~a~~ig~p~~VvKaQV~aGgRGKa~~~~~hk~~~GGV~l~~s~~ea~~ 81 (398)
-+.+|.+|+++|||+|++.+.+..+ ........+++|+ +||+ ...| |. =||.++++.+|+.+
T Consensus 133 K~~tK~i~~~~gI~tp~~~~~~~~~~~~~~~~~~~~l~~P~-iVKP-~~~G------------SS-iGvs~v~~~~el~~ 197 (344)
T PRK01966 133 KILTKRLLAAAGIPQAPYVVLTRSRREEAIAEVEEKLGLPV-FVKP-ANLG------------SS-VGISKVKNEEELEA 197 (344)
T ss_pred HHHHHHHHHHCCCCCCCEEEEECCCCHHHHHHHHHHCCCCE-EEEC-CCCC------------CC-CCEEEECCHHHHHH
T ss_conf 99999999987999898399816662345899998618987-9932-8996------------34-32599689999999
Q ss_pred HHHHHCCCCCCCCCCCCCCCCCCCEEECCCCCCCEEEEEEEEEECCCCCEEEEEECCCCCCHHHHHHHCHHHHEEEECCC
Q ss_conf 99986187654421222224433011034555650589999983477804899844788402455574831220332144
Q gi|254781049|r 82 DIREILGSTLITKQTGPTGSRVNCVYVEDGADILRELYLSLLVDRTSGMVAFIASTQGGMDIEEVAKDYPQKIFKLLIDP 161 (398)
Q Consensus 82 ~a~~ilg~~l~t~qt~~~G~~v~~vLVEe~v~~~~E~ylgi~~Dr~~~~~vii~S~~GGvdIE~va~~~p~~I~~~~id~ 161 (398)
+.+..+.. + +.+||||+++ ++|+-+|+.-. .+.|..+. -+ +|. +
T Consensus 198 ai~~a~~~----------~---~~vlvEefI~-GrE~tv~vl~~--~~~~~~l~--~~--Ei~----------------~ 241 (344)
T PRK01966 198 ALDLAFEY----------D---RKVLVEQGIK-GREIECAVLGY--NDEPVASV--PG--EIV----------------K 241 (344)
T ss_pred HHHHHHHC----------C---CCCEEECCCC-CEEEEEEEECC--CCCEEEEC--CE--EEC----------------C
T ss_conf 99999863----------9---7505751244-48999999748--99467731--15--871----------------7
Q ss_pred CCCCCHHHHHHHH-------HHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCEEEECCCCCEEEEEE
Q ss_conf 4578957888788-------75198889988599999999899995597510232679905996799400
Q gi|254781049|r 162 LIGVTSEDVASLC-------DMLELQGQARIDGGDLFPNLYKAFCDKDMSLLEINPLIIMKNGRLRVLDS 224 (398)
Q Consensus 162 ~~gl~~~~~~~l~-------~~lg~~~~~~~~~~~ii~~L~~~f~e~Da~liEINPLvvt~dg~vvAlDA 224 (398)
..++.+|+..... .-..++.+..+.+.++..+.|++.--.+..-++. .++++|+++.+..
T Consensus 242 ~~~fydy~~KY~~~~~~~~~~Pa~l~~~~~~~i~~~a~~~~~~lg~rg~~RiDf---~~d~~g~~y~lEv 308 (344)
T PRK01966 242 DNDFYDYEAKYIDDSGATLVIPADLSEELTEQIRELAIKAFKALGCSGLARVDF---FLTEDGEIYLNEI 308 (344)
T ss_pred CCCCCCHHHCCCCCCCCEEECCCCCCHHHHHHHHHHHHHHHHHHCCCCEEEEEE---EEECCCCEEEEEE
T ss_conf 987514888104689716966788999999999999999999819972798989---9908998899982
No 32
>PRK05586 biotin carboxylase; Validated
Probab=98.83 E-value=9e-07 Score=64.29 Aligned_cols=107 Identities=24% Similarity=0.410 Sum_probs=80.8
Q ss_pred HHHHHHHHHCCCCCCCCE--EECCHHHHHHHHHHCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHHHH
Q ss_conf 999999998689888815--747999999999872998699971213687656565567777777079958999999999
Q gi|254781049|r 6 YQAKALLRKYNVPVAKGV--VISSVHAAESAIKTLPGPLYVVKSQIHAGGRGKGRFKELPADSKGGVRVESSLKSVISDI 83 (398)
Q Consensus 6 yqaK~lL~~~GIpvp~g~--~a~s~~ea~~~a~~ig~p~~VvKaQV~aGgRGKa~~~~~hk~~~GGV~l~~s~~ea~~~a 83 (398)
-.+|++..+.|+|+.+|. .+++.+++.++++++|||+ ++||- +||-|| |.+++.+.+|+.+++
T Consensus 117 ~~ar~~a~~~gvPv~pg~~~~v~~~~ea~~~a~~iGyPv-~lKAa--~GGGGr------------Gmriv~~~~el~~~~ 181 (447)
T PRK05586 117 SNAREIMKKAGVPVVPGSEGEIENEEEALKIAEEIGYPV-MVKAS--AGGGGR------------GIRIVRSEEELIKAF 181 (447)
T ss_pred HHHHHHHHHCCCCCCCCCCCCCCCHHHHHHHHHHCCCCE-EEECC--CCCCCC------------EEEEECCHHHHHHHH
T ss_conf 999999998499765686888899999999998629823-76305--699977------------369989999999999
Q ss_pred HHHCCCCCCCCCCCCCCCCCCCEEECCCCCCCEEEEEEEEEECCCCCEEEEE
Q ss_conf 9861876544212222244330110345556505899999834778048998
Q gi|254781049|r 84 REILGSTLITKQTGPTGSRVNCVYVEDGADILRELYLSLLVDRTSGMVAFIA 135 (398)
Q Consensus 84 ~~ilg~~l~t~qt~~~G~~v~~vLVEe~v~~~~E~ylgi~~Dr~~~~~vii~ 135 (398)
+.-..-- ++. -| -..++||+.+...++.=+=+..|+... .+-++
T Consensus 182 ~~a~~ea----~~a-Fg--~~~v~vEk~i~~~RHIEVQvl~D~~Gn-~vhlg 225 (447)
T PRK05586 182 NTAKSEA----KAA-FG--DDSMYIEKFIENPRHIEFQILGDNYGN-VVHLG 225 (447)
T ss_pred HHHHHHH----HHH-CC--CCCEEEEEECCCCCEEEEEEEECCCCC-EEEEE
T ss_conf 9999999----982-79--984688772478717999999707998-88840
No 33
>PRK08462 biotin carboxylase; Validated
Probab=98.81 E-value=1e-07 Score=70.57 Aligned_cols=107 Identities=24% Similarity=0.370 Sum_probs=81.5
Q ss_pred HHHHHHHHHCCCCCCCCE--EECCHHHHHHHHHHCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHHHH
Q ss_conf 999999998689888815--747999999999872998699971213687656565567777777079958999999999
Q gi|254781049|r 6 YQAKALLRKYNVPVAKGV--VISSVHAAESAIKTLPGPLYVVKSQIHAGGRGKGRFKELPADSKGGVRVESSLKSVISDI 83 (398)
Q Consensus 6 yqaK~lL~~~GIpvp~g~--~a~s~~ea~~~a~~ig~p~~VvKaQV~aGgRGKa~~~~~hk~~~GGV~l~~s~~ea~~~a 83 (398)
-.+|++..+.|+|+++|. .+++.+|+.+++++||||+ +|||- +||-|| |.+++.+.+|+.+++
T Consensus 119 ~~ar~~a~~~gvPvvpg~~~~v~~~~ea~~~a~~iGyPV-~lKas--~GGGGr------------Gmriv~~~~el~~~~ 183 (446)
T PRK08462 119 SKAKQVMKRAGVPVIPGSDGALKSYEEAKKIAKEIGYPV-ILKAA--AGGGGR------------GMRVVEDESDLENLY 183 (446)
T ss_pred HHHHHHHHHCCCCCCCCCCCCCCCHHHHHHHHHHHCCCE-EEEEC--CCCCCC------------EEEEECCHHHHHHHH
T ss_conf 989999998599806786787799999999999729956-87632--789987------------428957679999999
Q ss_pred HHHCCCCCCCCCCCCCCCCCCCEEECCCCCCCEEEEEEEEEECCCCCEEEEE
Q ss_conf 9861876544212222244330110345556505899999834778048998
Q gi|254781049|r 84 REILGSTLITKQTGPTGSRVNCVYVEDGADILRELYLSLLVDRTSGMVAFIA 135 (398)
Q Consensus 84 ~~ilg~~l~t~qt~~~G~~v~~vLVEe~v~~~~E~ylgi~~Dr~~~~~vii~ 135 (398)
...-+.-. .-..-..+++|+.+...+++=+-+..|+. |..+.++
T Consensus 184 ~~a~~ea~-------~~fg~~~v~vEk~i~~~rHIEvQvl~D~~-Gn~ihl~ 227 (446)
T PRK08462 184 LAAESEAL-------SAFGDGTMYMEKFINNPRHIEVQILGDKH-GNVIHVG 227 (446)
T ss_pred HHHHHHHH-------HHCCCCCEEEEEEECCCEEEEEEEEECCC-CCEEEEE
T ss_conf 99987788-------60588866999850355078999885289-9888853
No 34
>PRK08654 pyruvate carboxylase subunit A; Validated
Probab=98.81 E-value=4.1e-08 Score=73.11 Aligned_cols=167 Identities=23% Similarity=0.370 Sum_probs=101.5
Q ss_pred HHHHHHHHHCCCCCCCCE--EECCHHHHHHHHHHCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHHHH
Q ss_conf 999999998689888815--747999999999872998699971213687656565567777777079958999999999
Q gi|254781049|r 6 YQAKALLRKYNVPVAKGV--VISSVHAAESAIKTLPGPLYVVKSQIHAGGRGKGRFKELPADSKGGVRVESSLKSVISDI 83 (398)
Q Consensus 6 yqaK~lL~~~GIpvp~g~--~a~s~~ea~~~a~~ig~p~~VvKaQV~aGgRGKa~~~~~hk~~~GGV~l~~s~~ea~~~a 83 (398)
-.+|++..+.|+|+.+|. .+++.+|+.+.+++||||+ ++||- +||-|| |.+++.+.+|+.+++
T Consensus 117 ~~ar~la~~~gVPvvPG~~~~v~~~~ea~~~A~~IGyPV-~iKAs--~GGGGr------------GmriV~~~~eL~~~~ 181 (497)
T PRK08654 117 INAKKLMKKAGVPVLPGTEEGIEDIEEAKEVAEEIGYPV-IIKAS--AGGGGI------------GMRVVYNEEELEEAI 181 (497)
T ss_pred HHHHHHHHHCCCCCCCCCCCCCCCHHHHHHHHHHCCCCE-EEEEC--CCCCCC------------CCEEEECCHHHHHHH
T ss_conf 999999998099868997566799999999998649845-87652--688888------------658996025689999
Q ss_pred HHHCCCCCCCCCCCCCCCCCCCEEECCCCCCCEEEEEEEEEECCCCCEEEEEECCCCCCHHHHHHHCHHHHEEEECCCCC
Q ss_conf 98618765442122222443301103455565058999998347780489984478840245557483122033214445
Q gi|254781049|r 84 REILGSTLITKQTGPTGSRVNCVYVEDGADILRELYLSLLVDRTSGMVAFIASTQGGMDIEEVAKDYPQKIFKLLIDPLI 163 (398)
Q Consensus 84 ~~ilg~~l~t~qt~~~G~~v~~vLVEe~v~~~~E~ylgi~~Dr~~~~~vii~S~~GGvdIE~va~~~p~~I~~~~id~~~ 163 (398)
..-..- .+.. -|- ..|+||+.+...+++=+-++.|.... .+-++...- .| -+.++..| ...|.-
T Consensus 182 ~~a~~e----A~~~-fgd--~~v~iEk~i~~~RHIEVQvl~D~~Gn-vihlgeRdC--Si---QRr~QKvI---EeaPap 245 (497)
T PRK08654 182 ESTQSI----AQSA-FGD--STVFIEKYLEKPRHIEIQVLADKHGN-VIHLGDREC--SI---QRRHQKLI---EEAPSP 245 (497)
T ss_pred HHHHHH----HHHH-CCC--CCEEEEEECCCCEEEEEEEEEECCCC-EEEECCEEC--CE---EECCCCEE---EECCCC
T ss_conf 999999----8874-599--84579884155537899999844797-867146023--43---62686369---978999
Q ss_pred CCCHH-------HHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCEEE
Q ss_conf 78957-------88878875198889988599999999899995597510232679
Q gi|254781049|r 164 GVTSE-------DVASLCDMLELQGQARIDGGDLFPNLYKAFCDKDMSLLEINPLI 212 (398)
Q Consensus 164 gl~~~-------~~~~l~~~lg~~~~~~~~~~~ii~~L~~~f~e~Da~liEINPLv 212 (398)
.+++. .+.+++..+|+.+....+| || .+.+.-++|+||=+
T Consensus 246 ~l~~~~r~~m~~~Av~la~~vgY~gaGTVEF------l~---d~g~fyFlEmNtRl 292 (497)
T PRK08654 246 IMTPELRERMGEAAVKAAKAINYENAGTVEF------LY---SNGNFYFLEMNTRL 292 (497)
T ss_pred CCCHHHHHHHHHHHHHHHHHHCEECCCEEEE------EE---ECCEEEEEEEECCC
T ss_conf 8988999999999999888734302332799------87---48839999612442
No 35
>PRK07178 acetyl-CoA carboxylase; Validated
Probab=98.80 E-value=3e-07 Score=67.42 Aligned_cols=165 Identities=18% Similarity=0.313 Sum_probs=101.5
Q ss_pred HHHHHHHHHCCCCCCCCE--EECCHHHHHHHHHHCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHHHH
Q ss_conf 999999998689888815--747999999999872998699971213687656565567777777079958999999999
Q gi|254781049|r 6 YQAKALLRKYNVPVAKGV--VISSVHAAESAIKTLPGPLYVVKSQIHAGGRGKGRFKELPADSKGGVRVESSLKSVISDI 83 (398)
Q Consensus 6 yqaK~lL~~~GIpvp~g~--~a~s~~ea~~~a~~ig~p~~VvKaQV~aGgRGKa~~~~~hk~~~GGV~l~~s~~ea~~~a 83 (398)
-.||++..+.|+|+.+|. .+++.+|+.+.++++|||+ ++|| -+||-|| |.+++.+++|+.+.+
T Consensus 116 ~~ar~~a~~~gvPv~pgs~~~v~~~eea~~~A~~iGyPV-~lKA--a~GGGGr------------Gmrvv~~~~el~~~~ 180 (471)
T PRK07178 116 TEARRSMIKAGVPVTPGSEGNLADIDEALAEAERIGYPV-MLKA--TSGGGGR------------GIRRCNSREELEQNF 180 (471)
T ss_pred HHHHHHHHHCCCCCCCCCCCCCCCHHHHHHHHHHCCCCE-EEEE--CCCCCCC------------CEEEECCCHHHHHHH
T ss_conf 989999998699826896886566999999998669815-8632--0268766------------449976605688999
Q ss_pred HHHCCCCCCCCCCCCCCCCCCCEEECCCCCCCEEEEEEEEEECCCCCEEEEEECCCCCCHHHHHHHCHHHHEEEECCCCC
Q ss_conf 98618765442122222443301103455565058999998347780489984478840245557483122033214445
Q gi|254781049|r 84 REILGSTLITKQTGPTGSRVNCVYVEDGADILRELYLSLLVDRTSGMVAFIASTQGGMDIEEVAKDYPQKIFKLLIDPLI 163 (398)
Q Consensus 84 ~~ilg~~l~t~qt~~~G~~v~~vLVEe~v~~~~E~ylgi~~Dr~~~~~vii~S~~GGvdIE~va~~~p~~I~~~~id~~~ 163 (398)
+....--. ....-..+++|+.+.-.++.=+-+.-|... ..+-++-..-- |. +.+. ++. ...|..
T Consensus 181 ~~~~~EA~-------~aFg~~~v~lEk~i~~~RHIEVQilgD~~G-nvihl~eRdCS--iQ---Rr~Q-KvI--EeaPa~ 244 (471)
T PRK07178 181 PRVISEAT-------KAFGSAEVFLEKCIVNPKHIEVQILADSFG-NVVHLFERDCS--IQ---RRNQ-KLI--EIAPSP 244 (471)
T ss_pred HHHHHHHH-------HHCCCCCEEEEEECCCCEEEEEEEEEECCC-CEEEEEEEECC--CC---CCCC-CEE--EECCCC
T ss_conf 99999999-------844997368766046762899999980789-88888412346--51---0787-327--876999
Q ss_pred CCCHHH-------HHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCE
Q ss_conf 789578-------88788751988899885999999998999955975102326
Q gi|254781049|r 164 GVTSED-------VASLCDMLELQGQARIDGGDLFPNLYKAFCDKDMSLLEINP 210 (398)
Q Consensus 164 gl~~~~-------~~~l~~~lg~~~~~~~~~~~ii~~L~~~f~e~Da~liEINP 210 (398)
.+++.. +.+++..+|+.+.-..+| | +.+.+.-++|+||
T Consensus 245 ~l~~~~r~~l~~~A~~la~~v~Y~gaGTvEF------l---v~~~~~yFlEvNt 289 (471)
T PRK07178 245 QLTPEQRAYIGDLAVRAAKAVGYENAGTVEF------L---LADGEVYFMEMNT 289 (471)
T ss_pred CCCHHHHHHHHHHHHHHHHHCCCCEEEEEEE------E---EECCCEEEEECCC
T ss_conf 8889999999889999999648650126999------9---8679479983246
No 36
>PRK08591 acetyl-CoA carboxylase biotin carboxylase subunit; Validated
Probab=98.79 E-value=3.8e-07 Score=66.76 Aligned_cols=107 Identities=24% Similarity=0.350 Sum_probs=79.4
Q ss_pred HHHHHHHHHCCCCCCCCE--EECCHHHHHHHHHHCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHHHH
Q ss_conf 999999998689888815--747999999999872998699971213687656565567777777079958999999999
Q gi|254781049|r 6 YQAKALLRKYNVPVAKGV--VISSVHAAESAIKTLPGPLYVVKSQIHAGGRGKGRFKELPADSKGGVRVESSLKSVISDI 83 (398)
Q Consensus 6 yqaK~lL~~~GIpvp~g~--~a~s~~ea~~~a~~ig~p~~VvKaQV~aGgRGKa~~~~~hk~~~GGV~l~~s~~ea~~~a 83 (398)
-.||++..+.|+|+.+|. .+++++++...+++||||+ ++|| -+||-|| |.+++.+++|+.+++
T Consensus 117 ~~ar~~a~~agVPvvpgs~~~~~~~~ea~~~a~~iGyPv-~iKA--~~GGGGr------------Gmrvv~~~~el~~~~ 181 (449)
T PRK08591 117 VTAKATMKKAGVPVVPGSDGPVDDEEEALAIAKEIGYPV-IIKA--TAGGGGR------------GMRVVRTEAELEKAF 181 (449)
T ss_pred HHHHHHHHHCCCCCCCCCCCCCCCHHHHHHHHHHCCCCE-EEEE--CCCCCCC------------EEEEECCHHHHHHHH
T ss_conf 999999998399978887665568999999998749966-9885--2689877------------699985678999999
Q ss_pred HHHCCCCCCCCCCCCCCCCCCCEEECCCCCCCEEEEEEEEEECCCCCEEEEE
Q ss_conf 9861876544212222244330110345556505899999834778048998
Q gi|254781049|r 84 REILGSTLITKQTGPTGSRVNCVYVEDGADILRELYLSLLVDRTSGMVAFIA 135 (398)
Q Consensus 84 ~~ilg~~l~t~qt~~~G~~v~~vLVEe~v~~~~E~ylgi~~Dr~~~~~vii~ 135 (398)
..--.-- + .-.--..+++|+.++..+..=+=+.-|.. |..+-++
T Consensus 182 ~~~~~Ea----~---~aFg~~~v~iEk~i~~~RHIEVQilgD~~-Gn~vhl~ 225 (449)
T PRK08591 182 SMARAEA----K---AAFGNPGVYMEKYLENPRHIEIQVLADGH-GNAIHLG 225 (449)
T ss_pred HHHHHHH----H---HHCCCCCEEEEEECCCCCEEEEEEEECCC-CCEEECC
T ss_conf 9999999----9---73799856787712565367899986389-9889874
No 37
>TIGR01369 CPSaseII_lrg carbamoyl-phosphate synthase, large subunit; InterPro: IPR006275 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 glutamine-dependent CPSase (6.3.5.5 from EC) from prokaryotes and eukaryotes (CPSase II). ; GO: 0004086 carbamoyl-phosphate synthase activity, 0006807 nitrogen compound metabolic process.
Probab=98.78 E-value=4.1e-08 Score=73.16 Aligned_cols=331 Identities=18% Similarity=0.235 Sum_probs=184.0
Q ss_pred HHHHHHCCCCCCCCEEECCHHHHHHHHHHCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHHHHHHHCC
Q ss_conf 99999868988881574799999999987299869997121368765656556777777707995899999999998618
Q gi|254781049|r 9 KALLRKYNVPVAKGVVISSVHAAESAIKTLPGPLYVVKSQIHAGGRGKGRFKELPADSKGGVRVESSLKSVISDIREILG 88 (398)
Q Consensus 9 K~lL~~~GIpvp~g~~a~s~~ea~~~a~~ig~p~~VvKaQV~aGgRGKa~~~~~hk~~~GGV~l~~s~~ea~~~a~~ilg 88 (398)
-++|.+-|||=|++..++|.|||..+|++||||++|==+-|+. ||+- .++.|.+|+.+..++-..
T Consensus 694 s~~l~~Lgi~QP~~~~a~s~eea~~~A~~iGYPvlvRPSYVLg-G~aM--------------~iv~~~eeL~~yl~~a~~ 758 (1089)
T TIGR01369 694 SELLDELGIPQPEWKIATSVEEAKEFASEIGYPVLVRPSYVLG-GRAM--------------EIVYNEEELARYLEEAVE 758 (1089)
T ss_pred HHHHHHCCCCCCCCCEECCHHHHHHHHHHCCCCEEECCCCCCC-CCCH--------------HEECCHHHHHHHHHHHHH
T ss_conf 9999715879898852728799999985469928981683003-3621--------------002678899999999997
Q ss_pred CCCCCCCCCCCCCCCCCEEECCCCCCCEEEEEEEEEECCCCCEEEEEECCCCC--CHHHHHHHCHHHHEEEECCCCCCCC
Q ss_conf 76544212222244330110345556505899999834778048998447884--0245557483122033214445789
Q gi|254781049|r 89 STLITKQTGPTGSRVNCVYVEDGADILRELYLSLLVDRTSGMVAFIASTQGGM--DIEEVAKDYPQKIFKLLIDPLIGVT 166 (398)
Q Consensus 89 ~~l~t~qt~~~G~~v~~vLVEe~v~~~~E~ylgi~~Dr~~~~~vii~S~~GGv--dIE~va~~~p~~I~~~~id~~~gl~ 166 (398)
-. .. +-|||.++++.+.|+=+=.+-|-. .+++ .|+ +||+-.-++=|...-.|- ..++
T Consensus 759 ~S--------~~---~PVlidky~e~A~E~dVD~v~Dg~--~v~i-----~gI~EHiE~AGVHSGDs~~~~Pp---~~L~ 817 (1089)
T TIGR01369 759 VS--------PE---HPVLIDKYLEDAVEIDVDAVSDGE--EVLI-----PGIMEHIEEAGVHSGDSTCVLPP---QTLS 817 (1089)
T ss_pred HC--------CC---CCEEEEEECCCCEEEEEEEEEECC--EEEE-----EEHHHHHHHCCCCCCCHHHCCCC---CCCC
T ss_conf 20--------89---976988852888899998997288--4899-----62312342136761305311769---7778
Q ss_pred HH-------HHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHH-CCCCCCCCCEEEECCCCCEEEEEEEEEECCCHHH--H-
Q ss_conf 57-------88878875198889988599999999899995-5975102326799059967994001321573556--4-
Q gi|254781049|r 167 SE-------DVASLCDMLELQGQARIDGGDLFPNLYKAFCD-KDMSLLEINPLIIMKNGRLRVLDSKISFDDNALY--R- 235 (398)
Q Consensus 167 ~~-------~~~~l~~~lg~~~~~~~~~~~ii~~L~~~f~e-~Da~liEINPLvvt~dg~vvAlDAKi~iDDnA~f--R- 235 (398)
.. ..+++|+.|.+.|--..|| +..+ .+.-.||.||= . .|=+..=.|++==+=|.. |
T Consensus 818 ~~~~~~i~~~~~~iA~~L~v~Gl~NiQf---------~~~~E~~~yVIE~NpR-A---SRtVPFvSKa~Gipl~~~A~~~ 884 (1089)
T TIGR01369 818 EDIVKRIKDIVRKIAKELNVKGLFNIQF---------VVKDEGEVYVIEVNPR-A---SRTVPFVSKATGIPLAKLAVRV 884 (1089)
T ss_pred HHHHHHHHHHHHHHHHHCCCCCCEEEEE---------EEECCCCEEEEEECCC-C---CCCCCCEEEECCCCHHHHHHHH
T ss_conf 8999999999999998706607222455---------5616996799997174-2---0665413210378879999999
Q ss_pred --HHHHHHHHC-C---CCCCHHHHHHHHCCCCEEECC-------------CCEEEEECCCHHHHHHHHHHHHCCC---CC
Q ss_conf --102786310-0---015622245775398644228-------------8179995550368999999996589---96
Q gi|254781049|r 236 --HLDIQELRD-V---SEEDSREIEAKQHNLSYIALD-------------GNIGCMVNGAGLAMATMDIIKLYGG---AP 293 (398)
Q Consensus 236 --~~~~~~~~d-~---~~~~~~E~~A~~~~l~yv~Ld-------------G~Ig~~vnGaGlamatmD~i~~~Gg---~p 293 (398)
=.++.++-. . .+..+.-.--|..-|+|.+|- |.++|+.-=-..|. .=.....|- +.
T Consensus 885 ~~G~~l~~~~~~~gv~~~~~~~~vavK~~vFSF~kL~g~Dp~LGpEMkSTGEvmg~g~d~~~A~--~Ka~~~~~~~~p~k 962 (1089)
T TIGR01369 885 MLGKKLEELGKDLGVGKEKESKYVAVKVPVFSFSKLAGVDPVLGPEMKSTGEVMGIGRDLEEAF--LKAMLSSGNRIPKK 962 (1089)
T ss_pred HHCCCCHHCCCCCCCCCCCCCCEEEEEEEECCCHHHCCCCEEECCCCCCCCEEEEECCCHHHHH--HHHHHHCCCCCCCC
T ss_conf 7088201027540112326887279964237712214887111775551322564127889999--99999818705788
Q ss_pred CEEEECCCCCCHHHHHHHHHHHHC----------------CCCCCEEEEE-CCCCHH--HHHHHHHHHHHHHHHCCCCCC
Q ss_conf 248842788898999999999861----------------9986589996-358613--289999999999997299987
Q gi|254781049|r 294 ANFLDVGGGADQDKVAAAFKIITS----------------DSSVKGILIN-IFGGIM--RCDVLVKGILSAVKEVKINIP 354 (398)
Q Consensus 294 ANFlD~gG~a~~e~~~~a~~~il~----------------~~~vk~iliN-ifGGI~--~cd~vA~gii~a~~~~~~~~p 354 (398)
..++=.++..+.+++...++.+.. +..++.-+|+ ++.+-. .|.- -.-|.+.+++-+.+.=
T Consensus 963 g~~~~~~~d~dk~~~~~~a~~L~~~G~~~yat~gT~~~L~e~gi~~~~v~~~~e~~~~~~C~~-~p~~~~~~~~~~~~~v 1041 (1089)
T TIGR01369 963 GSVLLSVRDKDKEELLDLAKKLAEKGYKIYATEGTAKFLEEAGIKAEVVLKVSEGREDDDCEA-QPNILELIKNGEIELV 1041 (1089)
T ss_pred CEEEEEECCCCHHHHHHHHHHHHHCCCEEEEECCHHHHHHHCCCCHHHEEEECCCCCCCCCCC-CHHHHHHHHHCCCEEE
T ss_conf 779998034434579999999986373788502026767651876332000037887888888-7158999970880699
Q ss_pred EEEECCCC-------CHHHHHHHHH---HCCCCEEEECCHHHHHHHH
Q ss_conf 99974898-------5899999999---7699589949989999999
Q gi|254781049|r 355 LVMRLEGA-------NVDIGNRLIA---ESGLNVITAIDLDDAAQKI 391 (398)
Q Consensus 355 ivvRl~Gt-------n~~~g~~il~---~~g~~~~~~~~~~~A~~~~ 391 (398)
|=.+-.|. ....|.++.+ +.++|+++.-++-+|.-+|
T Consensus 1042 IN~~~~~~~~~~~~~~~~~gy~iRR~A~~~~vp~~t~~~~~~~~~~a 1088 (1089)
T TIGR01369 1042 INLTSKGKEGVLLRETATDGYKIRREAVDYGVPLITTLETAEAFLEA 1088 (1089)
T ss_pred EECCCCCCCCEEECCCCCHHHHHHHHHHHCCCCEEECHHHHHHHHHH
T ss_conf 96578886631220245445899999996499778656899999980
No 38
>PRK06111 acetyl-CoA carboxylase biotin carboxylase subunit; Validated
Probab=98.78 E-value=1.6e-06 Score=62.61 Aligned_cols=107 Identities=20% Similarity=0.339 Sum_probs=78.5
Q ss_pred HHHHHHHHHCCCCCCCCE--EECCHHHHHHHHHHCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHHHH
Q ss_conf 999999998689888815--747999999999872998699971213687656565567777777079958999999999
Q gi|254781049|r 6 YQAKALLRKYNVPVAKGV--VISSVHAAESAIKTLPGPLYVVKSQIHAGGRGKGRFKELPADSKGGVRVESSLKSVISDI 83 (398)
Q Consensus 6 yqaK~lL~~~GIpvp~g~--~a~s~~ea~~~a~~ig~p~~VvKaQV~aGgRGKa~~~~~hk~~~GGV~l~~s~~ea~~~a 83 (398)
-.||++..+.|+|+.+|. ..++++++...+++||||+ ++|| -+||-|| |.+++++.+|+.+++
T Consensus 117 ~~ar~~a~~~gvPvvPG~~~~~~~~~ea~~~a~~iGyPv-liKA--a~GGGGr------------Gmriv~~~~el~~~~ 181 (449)
T PRK06111 117 IEARRAMQAAGVPVVPGITTALEDAEEAIAIARQIGYPV-MLKA--SAGGGGI------------GMQLVETEQELTKAF 181 (449)
T ss_pred HHHHHHHHHCCCCCCCCCCCCCCCHHHHHHHHHHCCCCE-EEEE--CCCCCCC------------CEEEECCHHHHHHHH
T ss_conf 999999998399855786777899999999998659802-6620--3589867------------208957999999999
Q ss_pred HHHCCCCCCCCCCCCCCCCCCCEEECCCCCCCEEEEEEEEEECCCCCEEEEE
Q ss_conf 9861876544212222244330110345556505899999834778048998
Q gi|254781049|r 84 REILGSTLITKQTGPTGSRVNCVYVEDGADILRELYLSLLVDRTSGMVAFIA 135 (398)
Q Consensus 84 ~~ilg~~l~t~qt~~~G~~v~~vLVEe~v~~~~E~ylgi~~Dr~~~~~vii~ 135 (398)
..--.. . +. .-| -..+++|+.++-.+..-+=+.-|. +|..+-++
T Consensus 182 ~~~~~e-A---~~-~Fg--~~~v~iEk~i~~~RHIEVQvl~D~-~Gn~vhlg 225 (449)
T PRK06111 182 ESNKKR-A---AN-FFG--NGEMYLEKYIEDARHIEIQLLADT-HGNTVYLW 225 (449)
T ss_pred HHHHHH-H---HH-HCC--CCCEEEEEECCCCCEEEEEEEECC-CCCEEEEE
T ss_conf 999999-9---98-639--960255441357733799999706-88888830
No 39
>TIGR00514 accC acetyl-CoA carboxylase, biotin carboxylase; InterPro: IPR004549 This family represents the biotin carboxylase subunit found usually as a component of acetyl-CoA carboxylase. Acetyl-CoA carboxylase (6.4.1.2 from EC) is a heterohexamer of biotin carboxyl carrier protein, biotin carboxylase (6.3.4.14 from EC), and two subunits of carboxyl transferase in a 2:2 complex. In the first step of long-chain fatty acid synthesis, biotin carboxylase catalyses the carboxylation of the carrier protein and then the transcarboxylase transfers the carboxyl group to form malonyl-coA. Homologous domains are found in eukaryotic forms of acetyl-CoA carboxylase and in a number of other carboxylases (e.g. pyruvate carboxylase). In some systems, the biotin carboxyl carrier protein and this protein (biotin carboxylase) may be shared by different carboxyltransferases. However, this model is not intended to identify the biotin carboxylase domain of propionyl-coA carboxylase. The model should hit the full length of proteins, except for chloroplast transit peptides in plants. If it hits a domain only of a longer protein, there may be a problem with the identification.; GO: 0016874 ligase activity.
Probab=98.76 E-value=1.2e-07 Score=70.17 Aligned_cols=106 Identities=25% Similarity=0.435 Sum_probs=82.2
Q ss_pred HHHHHHHHCCCCCCCC--E-EECCHHHHHHHHHHCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHHHH
Q ss_conf 9999999868988881--5-747999999999872998699971213687656565567777777079958999999999
Q gi|254781049|r 7 QAKALLRKYNVPVAKG--V-VISSVHAAESAIKTLPGPLYVVKSQIHAGGRGKGRFKELPADSKGGVRVESSLKSVISDI 83 (398)
Q Consensus 7 qaK~lL~~~GIpvp~g--~-~a~s~~ea~~~a~~ig~p~~VvKaQV~aGgRGKa~~~~~hk~~~GGV~l~~s~~ea~~~a 83 (398)
-||+..++.|+|+-|| . ++.+.+|+...|++||||+ ++||- +||=|+ |+|++++++|..+..
T Consensus 118 ~A~~~mKkaGVP~VPGS~GP~~~~~~e~~~~A~~IGyPv-~IKA~--AGGGGR------------GmR~vR~~~El~~~~ 182 (451)
T TIGR00514 118 TAKETMKKAGVPVVPGSDGPLVEDEEEAVRIAKEIGYPV-IIKAT--AGGGGR------------GMRVVREEDELVKLI 182 (451)
T ss_pred HHHHHHHHCCCCEECCCCCCCCCCHHHHHHHHHHCCCCE-EEEEE--CCCCCC------------EEEEECCHHHHHHHH
T ss_conf 999999748876623888863102788999997478968-99962--589972------------258862868999999
Q ss_pred HHHCCCCCCCCCCCCCCCCCCCEEECCCCCCCEEEEEEEEEECCCCCEEEEE
Q ss_conf 9861876544212222244330110345556505899999834778048998
Q gi|254781049|r 84 REILGSTLITKQTGPTGSRVNCVYVEDGADILRELYLSLLVDRTSGMVAFIA 135 (398)
Q Consensus 84 ~~ilg~~l~t~qt~~~G~~v~~vLVEe~v~~~~E~ylgi~~Dr~~~~~vii~ 135 (398)
+. |++-...+..=..||+|++++--|..=+=|+=| .+|..+-++
T Consensus 183 ~~-------a~~EA~AAF~N~~VYiEKfienPRH~E~QVLAD-~~GN~vyLg 226 (451)
T TIGR00514 183 KA-------ARAEAAAAFNNDGVYIEKFIENPRHVEIQVLAD-KYGNVVYLG 226 (451)
T ss_pred HH-------HHHHHHHCCCCCCEEEEEEECCCCEEEEEEEEC-CCCCEEEEC
T ss_conf 99-------999997402879627863336994079998751-788878971
No 40
>COG0458 CarB Carbamoylphosphate synthase large subunit (split gene in MJ) [Amino acid transport and metabolism / Nucleotide transport and metabolism]
Probab=98.73 E-value=2.2e-07 Score=68.31 Aligned_cols=101 Identities=22% Similarity=0.283 Sum_probs=82.4
Q ss_pred HHHHHHHHCCCCCCCCEEECCHHHHHHHHHHCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHHHHHHH
Q ss_conf 99999998689888815747999999999872998699971213687656565567777777079958999999999986
Q gi|254781049|r 7 QAKALLRKYNVPVAKGVVISSVHAAESAIKTLPGPLYVVKSQIHAGGRGKGRFKELPADSKGGVRVESSLKSVISDIREI 86 (398)
Q Consensus 7 qaK~lL~~~GIpvp~g~~a~s~~ea~~~a~~ig~p~~VvKaQV~aGgRGKa~~~~~hk~~~GGV~l~~s~~ea~~~a~~i 86 (398)
-.|+.|++.|+|+| +.++++.+++.+....+|||+ ++|+-.-.||. |.-++.|.+|+.+.....
T Consensus 119 ~fke~m~eigi~~P-~~~~~~~~e~~~~~~~ig~Pv-IVrP~~~lGG~--------------G~~i~~n~eel~~~~~~~ 182 (400)
T COG0458 119 LFKEAMREIGIPVP-SRIAHSVEEADEIADEIGYPV-IVKPSFGLGGS--------------GGGIAYNEEELEEIIEEG 182 (400)
T ss_pred HHHHHHHHCCCCCC-CCCCCCHHHHHHHHHHCCCCE-EEECCCCCCCC--------------CEEEEECHHHHHHHHHHC
T ss_conf 99999998399988-412356777765576369977-98068578887--------------516871899999998732
Q ss_pred CCCCCCCCCCCCCCCCCCCEEECCCCCCCEEEEEEEEEECCCCCEEEE
Q ss_conf 187654421222224433011034555650589999983477804899
Q gi|254781049|r 87 LGSTLITKQTGPTGSRVNCVYVEDGADILRELYLSLLVDRTSGMVAFI 134 (398)
Q Consensus 87 lg~~l~t~qt~~~G~~v~~vLVEe~v~~~~E~ylgi~~Dr~~~~~vii 134 (398)
+.. .+++.+|+|+.+...+|+..-+.+|......+..
T Consensus 183 l~~-----------s~~~~vl~eesi~G~ke~e~ev~rd~~~n~ivvc 219 (400)
T COG0458 183 LRA-----------SPVEEVLIEESIIGWKEFEYEVVRDGKDNCIVVC 219 (400)
T ss_pred CCC-----------CCCCCCEEEEEECCCEEEEEEEEEECCCCEEEEE
T ss_conf 244-----------7642001244216856999999983799879998
No 41
>PRK08463 acetyl-CoA carboxylase; Validated
Probab=98.70 E-value=3.8e-06 Score=60.18 Aligned_cols=107 Identities=19% Similarity=0.295 Sum_probs=78.7
Q ss_pred HHHHHHHHHCCCCCCCCE---EECCHHHHHHHHHHCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHHH
Q ss_conf 999999998689888815---74799999999987299869997121368765656556777777707995899999999
Q gi|254781049|r 6 YQAKALLRKYNVPVAKGV---VISSVHAAESAIKTLPGPLYVVKSQIHAGGRGKGRFKELPADSKGGVRVESSLKSVISD 82 (398)
Q Consensus 6 yqaK~lL~~~GIpvp~g~---~a~s~~ea~~~a~~ig~p~~VvKaQV~aGgRGKa~~~~~hk~~~GGV~l~~s~~ea~~~ 82 (398)
-+||++..+.|+||.+|. ...+++++..+++++|||+ ++|| -+||-|| |.+++.+.+|+.+.
T Consensus 116 ~~Ar~~a~~~gVPvvpg~~~~~~~~~~~~~~~a~~iGyPv-~lKA--~~GGGGr------------Gmrvv~~~~el~~~ 180 (478)
T PRK08463 116 NIARKLMAKNGIPIVPGTEKLNSESMEEIKIFARKIGYPV-ILKA--SGGGGGR------------GIRVVWKEEDLENA 180 (478)
T ss_pred HHHHHHHHHCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCE-EEEE--CCCCCCC------------EEEEECCHHHHHHH
T ss_conf 9999999983998466767788767999999998659804-7840--3599987------------11785578999999
Q ss_pred HHHHCCCCCCCCCCCCCCCCCCCEEECCCCCCCEEEEEEEEEECCCCCEEEEE
Q ss_conf 99861876544212222244330110345556505899999834778048998
Q gi|254781049|r 83 IREILGSTLITKQTGPTGSRVNCVYVEDGADILRELYLSLLVDRTSGMVAFIA 135 (398)
Q Consensus 83 a~~ilg~~l~t~qt~~~G~~v~~vLVEe~v~~~~E~ylgi~~Dr~~~~~vii~ 135 (398)
+.....-- + .-.--..|++|+.+...+..=+-++-|.. |..+-++
T Consensus 181 ~~~a~~ea----~---~~Fg~~~v~iEk~i~~~RHiEVQvlgD~~-Gnvi~l~ 225 (478)
T PRK08463 181 FESCKREA----K---AYFNNDEVFMEKYVVNPRHIEFQILGDNY-GNIIHLC 225 (478)
T ss_pred HHHHHHHH----H---HHCCCCCEEEEEEECCCEEEEEEEEEECC-CCEEEEE
T ss_conf 99999999----9---84699854788750245178999986179-9788963
No 42
>TIGR02144 LysX_arch Lysine biosynthesis enzyme LysX; InterPro: IPR011870 The family of proteins found in this family include the characterised LysX from Thermus thermophilus which is part of a well-organised lysine biosynthesis gene cluster . LysX is believed to carry out an ATP-dependent acylation of the amino group of alpha-aminoadipate in the prokaryotic version of the fungal AAA lysine biosynthesis pathway. No species having a sequence in this family contains the elements of the more common diaminopimelate lysine biosythesis pathway, and none has been shown to be a lysine auxotroph. These sequences have mainly recieved the name of the related enzyme, "ribosomal protein S6 modification protein RimK". RimK has been characterised in Escherichia coli, and acts by ATP-dependent condensation of S6 with glutamate residues .; GO: 0003824 catalytic activity, 0005524 ATP binding, 0009085 lysine biosynthetic process.
Probab=98.67 E-value=7.9e-08 Score=71.24 Aligned_cols=81 Identities=26% Similarity=0.278 Sum_probs=63.6
Q ss_pred HHHHHHHHCCCCCCCCEEECCHHHHHHHHHHCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHH--HHH
Q ss_conf 999999986898888157479999999998729986999712136876565655677777770799589999999--999
Q gi|254781049|r 7 QAKALLRKYNVPVAKGVVISSVHAAESAIKTLPGPLYVVKSQIHAGGRGKGRFKELPADSKGGVRVESSLKSVIS--DIR 84 (398)
Q Consensus 7 qaK~lL~~~GIpvp~g~~a~s~~ea~~~a~~ig~p~~VvKaQV~aGgRGKa~~~~~hk~~~GGV~l~~s~~ea~~--~a~ 84 (398)
-+.-.|+++|||+|++.++.+++.|..++++||||+ |+|+-+=|.||--+ +++|.+++.. ..+
T Consensus 91 ~T~~~L~~~gvP~P~t~~a~d~~~A~~~~e~lGYPv-V~KP~~GSWGRlV~--------------~~~d~~~~~~llEh~ 155 (289)
T TIGR02144 91 FTTLKLAKAGVPTPRTYIAFDREAALKAAEELGYPV-VLKPVIGSWGRLVS--------------KIRDKDELESLLEHK 155 (289)
T ss_pred HHHHHHHHCCCCCCCEEEEECHHHHHHHHHHCCCCE-EEECCCCCHHHHHH--------------HHCCHHHHHHHHHHH
T ss_conf 899999966788983589828689999999708988-97088884378876--------------403788988999999
Q ss_pred HHCCCCCCCCCCCCCCCCCCCEEECCCCC
Q ss_conf 86187654421222224433011034555
Q gi|254781049|r 85 EILGSTLITKQTGPTGSRVNCVYVEDGAD 113 (398)
Q Consensus 85 ~ilg~~l~t~qt~~~G~~v~~vLVEe~v~ 113 (398)
++++. ...+=.||||+++
T Consensus 156 e~~~~-----------~~~~~~y~QEfi~ 173 (289)
T TIGR02144 156 EVLGG-----------SQLKLYYVQEFIN 173 (289)
T ss_pred HHHCC-----------CCCCEEEEEEEEC
T ss_conf 98679-----------7633379998871
No 43
>PRK06019 phosphoribosylaminoimidazole carboxylase ATPase subunit; Reviewed
Probab=98.64 E-value=8.5e-07 Score=64.44 Aligned_cols=93 Identities=26% Similarity=0.298 Sum_probs=72.2
Q ss_pred HHHHHHHHHCCCCCCCCEEECCHHHHHHHHHHCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHHHHHH
Q ss_conf 99999999868988881574799999999987299869997121368765656556777777707995899999999998
Q gi|254781049|r 6 YQAKALLRKYNVPVAKGVVISSVHAAESAIKTLPGPLYVVKSQIHAGGRGKGRFKELPADSKGGVRVESSLKSVISDIRE 85 (398)
Q Consensus 6 yqaK~lL~~~GIpvp~g~~a~s~~ea~~~a~~ig~p~~VvKaQV~aGgRGKa~~~~~hk~~~GGV~l~~s~~ea~~~a~~ 85 (398)
+.=|++|++.|||+|++..++|.+|+..+.+++|||+ |+|+ ..-|=-|| |..+++|.+++.++...
T Consensus 107 ~~eK~~l~~lgiptapf~~v~s~~dl~~~~~~lg~P~-vlKt-~~~GYDGK------------Gq~~i~s~~dl~~a~~~ 172 (377)
T PRK06019 107 LTEKQFLDELGIPVAPFALVDSAEDLDAAIADLGLPA-VLKT-RRGGYDGK------------GQWVLRSEADLDAAWAA 172 (377)
T ss_pred HHHHHHHHHCCCCCCCEEEECCHHHHHHHHHHCCCCE-EEEC-CCCCCCCC------------CCEEECCHHHHHHHHHH
T ss_conf 9999999976999888067189999999999729976-9951-33461887------------01897788899999986
Q ss_pred HCCCCCCCCCCCCCCCCCCCEEECCCCCCCEEEEEEEEEECC
Q ss_conf 618765442122222443301103455565058999998347
Q gi|254781049|r 86 ILGSTLITKQTGPTGSRVNCVYVEDGADILRELYLSLLVDRT 127 (398)
Q Consensus 86 ilg~~l~t~qt~~~G~~v~~vLVEe~v~~~~E~ylgi~~Dr~ 127 (398)
+ +. ..+++|++++..+|+=+-+.+|.+
T Consensus 173 l-~~--------------~~~i~E~~i~f~~ElSvivaR~~~ 199 (377)
T PRK06019 173 L-GS--------------GPCILEEFVPFEREVSVIVARGRD 199 (377)
T ss_pred C-CC--------------CCEEEEEEECCEEEEEEEEEECCC
T ss_conf 5-69--------------988999654351899999998489
No 44
>TIGR02712 urea_carbox urea carboxylase; InterPro: IPR014084 Members of this family are ATP-dependent urea carboxylases, including characterised members from Oleomonas sagaranensis (alpha class Proteobacterium) and yeasts such as Saccharomyces cerevisiae (Baker's yeast). The allophanate hydrolase domain of the yeast enzyme is not included in this entry and is represented by an adjacent gene in Oleomonas sagaranensis. The fusion of urea carboxylase and allophanate hydrolase is designated urea amidolyase. The enzyme from O. sagaranensis was shown to be highly active on acetamide and formamide as well as urea..
Probab=98.64 E-value=9.7e-07 Score=64.08 Aligned_cols=255 Identities=20% Similarity=0.222 Sum_probs=142.2
Q ss_pred HHHHHHHHHCCCCCCCC-EEECCHHHHHHHHHHCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHHHHH
Q ss_conf 99999999868988881-57479999999998729986999712136876565655677777770799589999999999
Q gi|254781049|r 6 YQAKALLRKYNVPVAKG-VVISSVHAAESAIKTLPGPLYVVKSQIHAGGRGKGRFKELPADSKGGVRVESSLKSVISDIR 84 (398)
Q Consensus 6 yqaK~lL~~~GIpvp~g-~~a~s~~ea~~~a~~ig~p~~VvKaQV~aGgRGKa~~~~~hk~~~GGV~l~~s~~ea~~~a~ 84 (398)
|-|.+|=.+.|+|..+| -+..|.+||..+|++||||+ +|||= |||=|= |-..|.|.+|+.+++.
T Consensus 116 HtAR~lA~~aGVPL~PGTgLL~sl~eA~~~A~~IGYPV-MlKST--AGGGGI------------Gl~~c~~~~eL~~aFe 180 (1226)
T TIGR02712 116 HTARELAEAAGVPLLPGTGLLESLDEALEAAKEIGYPV-MLKST--AGGGGI------------GLQKCDNAAELAEAFE 180 (1226)
T ss_pred HHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHCCCCE-EEEEC--CCCCCC------------CCCCCCCHHHHHHHHH
T ss_conf 56899999668898885155877999999986469954-79870--787652------------4511189899999999
Q ss_pred HHCCCCCCCCCCCCCCCCCCCEEECCCCCCCEEEEEEEEEECCCCCEEEEEECCCCCCHHHHHHHCHHHHEEEECCCCCC
Q ss_conf 86187654421222224433011034555650589999983477804899844788402455574831220332144457
Q gi|254781049|r 85 EILGSTLITKQTGPTGSRVNCVYVEDGADILRELYLSLLVDRTSGMVAFIASTQGGMDIEEVAKDYPQKIFKLLIDPLIG 164 (398)
Q Consensus 85 ~ilg~~l~t~qt~~~G~~v~~vLVEe~v~~~~E~ylgi~~Dr~~~~~vii~S~~GGvdIE~va~~~p~~I~~~~id~~~g 164 (398)
.- +++- ..-.-=.+|.+|.+|+.+|..=+=|.=|.. |+.+.++-. |= ++=+.++..|--+|-+
T Consensus 181 ~V--krlg-----~~~F~daGVFlErfv~~ARHvEVQifGDG~-G~v~aLGeR----DC-SLQRRNQKVvEETPAP---- 243 (1226)
T TIGR02712 181 TV--KRLG-----ESFFGDAGVFLERFVENARHVEVQIFGDGK-GKVVALGER----DC-SLQRRNQKVVEETPAP---- 243 (1226)
T ss_pred HH--HHHH-----HHCCCCCCEEHHHHHCCCCEEEEEEEECCC-CCEEEEECC----CC-CCCCCCCCEEEECCCC----
T ss_conf 98--9988-----632363514340320378428998752697-336997116----75-4444566558727746----
Q ss_pred CCHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHH------------H--HCCCCCCCCCEEEECCCC---CEEEEE----
Q ss_conf 8957888788751988899885999999998999------------9--559751023267990599---679940----
Q gi|254781049|r 165 VTSEDVASLCDMLELQGQARIDGGDLFPNLYKAF------------C--DKDMSLLEINPLIIMKNG---RLRVLD---- 223 (398)
Q Consensus 165 l~~~~~~~l~~~lg~~~~~~~~~~~ii~~L~~~f------------~--e~Da~liEINPLvvt~dg---~vvAlD---- 223 (398)
+|+.+....+.+-..+|.+.. . .-++..+|+|-=.-.+.+ .|.=||
T Consensus 244 -------------~LP~~~R~~L~~AA~~Lg~~V~YrSAGTVEFiYD~~~d~FYFLEVNTRLQVEHPvTE~VtGlDLVEW 310 (1226)
T TIGR02712 244 -------------NLPEETRAALLAAAEKLGEAVNYRSAGTVEFIYDEARDEFYFLEVNTRLQVEHPVTEMVTGLDLVEW 310 (1226)
T ss_pred -------------CCCHHHHHHHHHHHHHHHHHHCCCCCCEEEEEECCCCCCEEEEEECCCCCCCCCCEEEEECCHHHHH
T ss_conf -------------8648999999999999999718763760477402210871211323411133573017846408989
Q ss_pred -EEEEECCCHHHHHHHHHHHHCC-----CC-------CCHHHHHHHH----CC-C----------CEEECCCCEEEEECC
Q ss_conf -0132157355641027863100-----01-------5622245775----39-8----------644228817999555
Q gi|254781049|r 224 -SKISFDDNALYRHLDIQELRDV-----SE-------EDSREIEAKQ----HN-L----------SYIALDGNIGCMVNG 275 (398)
Q Consensus 224 -AKi~iDDnA~fR~~~~~~~~d~-----~~-------~~~~E~~A~~----~~-l----------~yv~LdG~Ig~~vnG 275 (398)
-|+.=+ ..|++.++.-. .+ +-..|..++. .| | .-++.|++|-
T Consensus 311 M~r~AAg-----~~p~~~~~~~~~~~~l~p~G~aiEaRvYAEnP~k~F~PSpG~Lt~V~FP~~~G~~~RvDTWV~----- 380 (1226)
T TIGR02712 311 MVRIAAG-----ELPDFDSLNIEIFDNLTPRGAAIEARVYAENPAKNFQPSPGLLTEVQFPDDGGKAVRVDTWVE----- 380 (1226)
T ss_pred HHHHHCC-----CCCCHHHCCCCCCCCCCCCEEEEEEEEEEECCCCCCCCCCCEEEEEECCCCCCCEEEEECEEC-----
T ss_conf 9997168-----888852443000357887503899998440776777269860688772788895378702112-----
Q ss_pred CHHHHHHHHHHHHCCCCCCEEEE------CCCCCCHHHHHHHHHHHHCCCCCCEEEEEC
Q ss_conf 03689999999965899624884------278889899999999986199865899963
Q gi|254781049|r 276 AGLAMATMDIIKLYGGAPANFLD------VGGGADQDKVAAAFKIITSDSSVKGILINI 328 (398)
Q Consensus 276 aGlamatmD~i~~~Gg~pANFlD------~gG~a~~e~~~~a~~~il~~~~vk~iliNi 328 (398)
.|-+-.-|-| |--+++++.....|.-=|..-+|.+|.=|+
T Consensus 381 -------------~Gtevsp~YDPmlAKiIv~g~~R~~A~~kL~~AL~~T~v~Gi~TNL 426 (1226)
T TIGR02712 381 -------------TGTEVSPEYDPMLAKIIVHGKDREDAIAKLSQALDETRVYGIETNL 426 (1226)
T ss_pred -------------CCCEECCCCCCCEEEEEECCCCHHHHHHHHHHHHHHCCCEEEEECH
T ss_conf -------------7835677658742446643679789999999887301012354247
No 45
>COG0439 AccC Biotin carboxylase [Lipid metabolism]
Probab=98.63 E-value=1.1e-06 Score=63.78 Aligned_cols=101 Identities=25% Similarity=0.350 Sum_probs=75.4
Q ss_pred HHHHHHHHHHCCCCCCCCEE--ECCHHHHHHHHHHCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHHH
Q ss_conf 79999999986898888157--4799999999987299869997121368765656556777777707995899999999
Q gi|254781049|r 5 EYQAKALLRKYNVPVAKGVV--ISSVHAAESAIKTLPGPLYVVKSQIHAGGRGKGRFKELPADSKGGVRVESSLKSVISD 82 (398)
Q Consensus 5 EyqaK~lL~~~GIpvp~g~~--a~s~~ea~~~a~~ig~p~~VvKaQV~aGgRGKa~~~~~hk~~~GGV~l~~s~~ea~~~ 82 (398)
-+.+|+++.+.|+|+|++.- ..+.+|+.+.+++||||+ +||+---.||| |+++|.+.+|+.++
T Consensus 116 K~~ar~~~~~aGVP~vpgs~~~~~~~ee~~~~a~~iGyPV-ivKa~~GgGg~--------------G~r~v~~~~el~~a 180 (449)
T COG0439 116 KITARRLMAKAGVPVVPGSDGAVADNEEALAIAEEIGYPV-IVKAAAGGGGR--------------GMRVVRNEEELEAA 180 (449)
T ss_pred HHHHHHHHHHCCCCCCCCCCCCCCCHHHHHHHHHHCCCCE-EEEECCCCCCC--------------CEEEECCHHHHHHH
T ss_conf 8999999997499958997877688899999998719978-99977889965--------------47997999999999
Q ss_pred HHHHCCCCCCCCCCCCCCCCCCCEEECCCCCCCEEEEEEEEEECC
Q ss_conf 998618765442122222443301103455565058999998347
Q gi|254781049|r 83 IREILGSTLITKQTGPTGSRVNCVYVEDGADILRELYLSLLVDRT 127 (398)
Q Consensus 83 a~~ilg~~l~t~qt~~~G~~v~~vLVEe~v~~~~E~ylgi~~Dr~ 127 (398)
+....+-.- .- -|. ..+++|+.+...+-.-+-+.-|..
T Consensus 181 ~~~~~~ea~----~~-fg~--~~v~iEk~i~~~rhievqv~gD~~ 218 (449)
T COG0439 181 FEAARGEAE----AA-FGN--PRVYLEKFIEGPRHIEVQVLGDGH 218 (449)
T ss_pred HHHHHHHHH----HH-CCC--CCEEEEEECCCCCEEEEEEEECCC
T ss_conf 999998888----75-589--727863410588468999987686
No 46
>PRK12999 pyruvate carboxylase; Reviewed
Probab=98.61 E-value=9.6e-06 Score=57.51 Aligned_cols=108 Identities=24% Similarity=0.332 Sum_probs=79.9
Q ss_pred HHHHHHHHHCCCCCCCCE--EECCHHHHHHHHHHCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHHHH
Q ss_conf 999999998689888815--747999999999872998699971213687656565567777777079958999999999
Q gi|254781049|r 6 YQAKALLRKYNVPVAKGV--VISSVHAAESAIKTLPGPLYVVKSQIHAGGRGKGRFKELPADSKGGVRVESSLKSVISDI 83 (398)
Q Consensus 6 yqaK~lL~~~GIpvp~g~--~a~s~~ea~~~a~~ig~p~~VvKaQV~aGgRGKa~~~~~hk~~~GGV~l~~s~~ea~~~a 83 (398)
-+||++-.+.|+|+.+|. .+++.+++.+.++++|||+ .+||- +||-|+ |.+++.+.+|+.+++
T Consensus 121 ~~ar~~a~~~gvPvvpgs~~~~~~~~~~~~~a~~iGyPv-~iKA~--~GGGGr------------Gmrvv~~~~~l~~~~ 185 (1147)
T PRK12999 121 VAARNAAIKAGVPVIPGTEGPIDDLEEALEFAEEIGYPL-MLKAS--AGGGGR------------GMRIVRSEEELEEAF 185 (1147)
T ss_pred HHHHHHHHHCCCCCCCCCCCCCCCHHHHHHHHHHCCCCE-EEEEC--CCCCCC------------CEEEECCHHHHHHHH
T ss_conf 999999998398988898998899999999998719978-99977--789805------------148958989999999
Q ss_pred HHHCCCCCCCCCCCCCCCCCCCEEECCCCCCCEEEEEEEEEECCCCCEEEEEE
Q ss_conf 98618765442122222443301103455565058999998347780489984
Q gi|254781049|r 84 REILGSTLITKQTGPTGSRVNCVYVEDGADILRELYLSLLVDRTSGMVAFIAS 136 (398)
Q Consensus 84 ~~ilg~~l~t~qt~~~G~~v~~vLVEe~v~~~~E~ylgi~~Dr~~~~~vii~S 136 (398)
..--+- - + .-.--..+++|+.+...+..-+-|+-|. +|..+-++-
T Consensus 186 ~~a~~E-A---~---~aFG~~~v~~Ek~i~~~rHiEvQilgD~-~Gnvvhl~e 230 (1147)
T PRK12999 186 ERAKRE-A---K---AAFGNDEVYLEKYVENPRHIEVQILGDK-HGNVVHLYE 230 (1147)
T ss_pred HHHHHH-H---H---HHCCCCCEEEEEECCCCCEEEEEEEECC-CCCEEEECC
T ss_conf 999999-9---9---8369975688550367864799999628-898887147
No 47
>TIGR01161 purK phosphoribosylaminoimidazole carboxylase, ATPase subunit; InterPro: IPR005875 Phosphoribosylaminoimidazole carboxylase is a fusion protein in plants and fungi, but consists of two non-interacting proteins in bacteria, PurK and PurE. This family represents PurK, N5-carboxyaminoimidazole ribonucleotide (N5_CAIR) synthetase, which catalyzes the conversion of 5-aminoimidazole ribonucleotide (AIR), ATP, and bicarbonate to N5-CAIR, ADP, and Pi. PurE converts N5-CAIR to CAIR. In the presence of high concentrations of bicarbonate, PurE is reported able to convert AIR to CAIR directly and without ATP. PurK belongs to the ATP grasp superfamily of C-N ligase enzymes. Each subunit of PurK is composed of three domains (A, B, and C). The B domain contains a flexible, glycine-rich loop (B loop, T123-G130) that is disordered in the sulphate-PurK structure and becomes ordered in the MgADP-PurK structure. MgADP is wedged between the B and C domains, as with all members of the ATP grasp superfamily. Other enzymes in this superfamily contain a conserved Omega loop proposed to interact with the B loop, define the specificity of their nonnucleotide substrate, and protect the acyl phosphate intermediate formed from this substrate. PurK contains a minimal Omega loop without conserved residues. In the reaction catalyzed by PurK, carboxyphosphate is the putative acyl phosphate intermediate. The sulphate of the sulphate ion-liganded PurK interacts electrostatically with Arg 242 and the backbone amide group of Asn 245, components of the J loop of the C domain. This sulphate may reveal the location of the carboxyphosphate binding site. Conserved residues within the C-terminus of the C domain define a pocket that is proposed to bind AIR in collaboration with an N-terminal strand loop helix motif in the A domain (P loop, G8-L1). The P loop is proposed to bind the phosphate of AIR on the basis of similar binding sites observed in PurN and PurE and proposed in PurD and PurT, four other enzymes in the purine pathway .; GO: 0004638 phosphoribosylaminoimidazole carboxylase activity, 0006189 'de novo' IMP biosynthetic process, 0009320 phosphoribosylaminoimidazole carboxylase complex.
Probab=98.60 E-value=9.7e-07 Score=64.08 Aligned_cols=121 Identities=22% Similarity=0.278 Sum_probs=85.0
Q ss_pred HHHHHHHHHHCCCCCCCCEEEC--CHHHHHHHHHHCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHHH
Q ss_conf 7999999998689888815747--99999999987299869997121368765656556777777707995899999999
Q gi|254781049|r 5 EYQAKALLRKYNVPVAKGVVIS--SVHAAESAIKTLPGPLYVVKSQIHAGGRGKGRFKELPADSKGGVRVESSLKSVISD 82 (398)
Q Consensus 5 EyqaK~lL~~~GIpvp~g~~a~--s~~ea~~~a~~ig~p~~VvKaQV~aGgRGKa~~~~~hk~~~GGV~l~~s~~ea~~~ 82 (398)
=|.=|++|.++|+|||++.++. +.++......++|+|+ |||+-=+ += |-=|..++++.+++.++
T Consensus 103 k~~qK~~L~~~g~~vp~f~~~~~~~~~~~~~~~~~~g~p~-VlK~~~g-------GY------DGrGq~~i~~~~~~~~~ 168 (386)
T TIGR01161 103 KLTQKQFLQKLGLPVPPFVVIEIKDEEELDSALQELGFPV-VLKARRG-------GY------DGRGQFVIKSEADLPQA 168 (386)
T ss_pred HHHHHHHHHHCCCCCCCCCEEECCCHHHHHHHHHHCCCCE-EEEEEEC-------CC------CCCCCEEECCHHHHHHH
T ss_conf 5899999996689988412022368425789998739847-9984206-------52------77310897474328899
Q ss_pred HHHHCCCCCCCCCCCCCCCCCCCEEECCCCCCCEEEEEEEEEECCCCCEEEEEECCCCCCHHHHHHHCHH--HHEEEECC
Q ss_conf 9986187654421222224433011034555650589999983477804899844788402455574831--22033214
Q gi|254781049|r 83 IREILGSTLITKQTGPTGSRVNCVYVEDGADILRELYLSLLVDRTSGMVAFIASTQGGMDIEEVAKDYPQ--KIFKLLID 160 (398)
Q Consensus 83 a~~ilg~~l~t~qt~~~G~~v~~vLVEe~v~~~~E~ylgi~~Dr~~~~~vii~S~~GGvdIE~va~~~p~--~I~~~~id 160 (398)
++.+-... ..++||++|+..+|+=+=+.++ ..+-+..+ +- +|-+ ..| -|.+..+-
T Consensus 169 ~~~~~~~~-------------~~~~~E~fV~F~~Elsv~vaR~--~~G~~~~Y-P~----ven~---~~ddagIl~~~~a 225 (386)
T TIGR01161 169 LKELGDKE-------------EELIVEEFVPFERELSVIVARS--ADGEIAFY-PV----VENI---HQDDAGILRLVVA 225 (386)
T ss_pred HHHCCCCC-------------EEEEEEECCCCCEEEEEEEEEC--CCCCEEEC-CC----EEEE---EECCCCEEEEEEE
T ss_conf 98528884-------------0589852356200699999977--89748882-86----1235---6527787789863
Q ss_pred CC
Q ss_conf 44
Q gi|254781049|r 161 PL 162 (398)
Q Consensus 161 ~~ 162 (398)
|.
T Consensus 226 PA 227 (386)
T TIGR01161 226 PA 227 (386)
T ss_pred CC
T ss_conf 37
No 48
>COG0026 PurK Phosphoribosylaminoimidazole carboxylase (NCAIR synthetase) [Nucleotide transport and metabolism]
Probab=98.59 E-value=5.4e-06 Score=59.14 Aligned_cols=119 Identities=24% Similarity=0.246 Sum_probs=77.1
Q ss_pred HHHHHHHHHCCCCCCCCEEECCHHHHHHHHHHCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHHHHHH
Q ss_conf 99999999868988881574799999999987299869997121368765656556777777707995899999999998
Q gi|254781049|r 6 YQAKALLRKYNVPVAKGVVISSVHAAESAIKTLPGPLYVVKSQIHAGGRGKGRFKELPADSKGGVRVESSLKSVISDIRE 85 (398)
Q Consensus 6 yqaK~lL~~~GIpvp~g~~a~s~~ea~~~a~~ig~p~~VvKaQV~aGgRGKa~~~~~hk~~~GGV~l~~s~~ea~~~a~~ 85 (398)
+.=|++|.+.|||||++.++++.+|+..++.++|+|. |+|.-- -|=-| -|..++++.++....+..
T Consensus 101 ~~eK~~l~~~Gi~va~~~~v~~~~el~~~~~~~g~p~-VlKtr~-gGYDG------------kGQ~~i~~~~~~~~~~~~ 166 (375)
T COG0026 101 LVEKQFLDKAGLPVAPFQVVDSAEELDAAAADLGFPA-VLKTRR-GGYDG------------KGQWRIRSDADLELRAAG 166 (375)
T ss_pred HHHHHHHHHCCCCCCCEEEECCHHHHHHHHHHCCCCE-EEEECC-CCCCC------------CCEEEEECCCCCHHHHHH
T ss_conf 9999999976999998278579889999999759956-998322-65668------------870894070102356766
Q ss_pred HCCCCCCCCCCCCCCCCCCCEEECCCCCCCEEEEEEEEEECCCCCEEEEEECCCCCCHHHHHHHCHHHHEEEECCCC
Q ss_conf 61876544212222244330110345556505899999834778048998447884024555748312203321444
Q gi|254781049|r 86 ILGSTLITKQTGPTGSRVNCVYVEDGADILRELYLSLLVDRTSGMVAFIASTQGGMDIEEVAKDYPQKIFKLLIDPL 162 (398)
Q Consensus 86 ilg~~l~t~qt~~~G~~v~~vLVEe~v~~~~E~ylgi~~Dr~~~~~vii~S~~GGvdIE~va~~~p~~I~~~~id~~ 162 (398)
.. .+ ...++|++++..+|+ |+..-|+..+-+..+-. .|.+ +.+-|....+-|.
T Consensus 167 ~~-----------~~---~~~vlE~fV~F~~Ei--Svi~aR~~~G~~~~yP~-----~eN~---h~~gIl~~siaPa 219 (375)
T COG0026 167 LA-----------EG---GVPVLEEFVPFEREI--SVIVARSNDGEVAFYPV-----AENV---HRNGILRTSIAPA 219 (375)
T ss_pred HH-----------CC---CCEEEEEECCCCEEE--EEEEEECCCCCEEEECC-----CCEE---EECCEEEEEEECC
T ss_conf 51-----------36---863688603566489--99999858997898066-----2101---3367899997237
No 49
>TIGR01205 D_ala_D_alaTIGR D-alanine--D-alanine ligase; InterPro: IPR005905 D-alanine--D-alanine ligase (6.3.2.4 from EC) is a bacterial enzyme involved in cell-wall biosynthesis. It participates in forming UDP-N-acetylmuramoyl pentapeptide, the peptidoglycan precursor. These enzymes are proteins of 300 to 360 amino acids containing many conserved regions. The N-terminal Gly-rich region could be involved in ATP-binding. This family of enzymes represent chromosomal versions of species not specifically resistant to glycopeptide antibiotics such as vancomycin. The mechanism of glycopeptide antibiotic resistance involves the production of D-alanine-D-lactate (VanA and VanB families) or D-alanine-D-serine (VanC). This model attempts to exclude the VanA/VanB and VanC subfamilies while capturing most other D-Ala-D-Ala ligases above the trusted cut-off. However, changes in small numbers of amino acids, as demonstrated crystallographically, can alter specificity. In chlamydial species, this enzyme is found as a fusion protein with UDP-N-acetylmuramate--alanine ligase. ; GO: 0008716 D-alanine-D-alanine ligase activity, 0009252 peptidoglycan biosynthetic process, 0005737 cytoplasm.
Probab=98.55 E-value=1.3e-06 Score=63.14 Aligned_cols=153 Identities=20% Similarity=0.191 Sum_probs=98.8
Q ss_pred HHHHHHHHHHCCCCCCCCEEE--CCHHHHH-------HHHHHCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCEEEEECC
Q ss_conf 799999999868988881574--7999999-------9998729986999712136876565655677777770799589
Q gi|254781049|r 5 EYQAKALLRKYNVPVAKGVVI--SSVHAAE-------SAIKTLPGPLYVVKSQIHAGGRGKGRFKELPADSKGGVRVESS 75 (398)
Q Consensus 5 EyqaK~lL~~~GIpvp~g~~a--~s~~ea~-------~~a~~ig~p~~VvKaQV~aGgRGKa~~~~~hk~~~GGV~l~~s 75 (398)
=+-.|.++++.|||+|++... .+..... ....++|||+ +||+- + -.|.. ||..+.+
T Consensus 150 K~~tK~~~~~~Glp~~~y~~l~~~~~~~~~~~~~~~~~~~~~lg~P~-~VKPa-~------------~GSSv-G~~~V~~ 214 (375)
T TIGR01205 150 KLLTKLLLKSLGLPTPDYAVLRRKERSSEDEAECENVAVLEKLGFPV-FVKPA-R------------EGSSV-GISKVKS 214 (375)
T ss_pred HHHHHHHHHHCCCCCCCCEEEEECCCCCCHHHHHHHHHHHHHCCCCE-EEEEC-C------------CCCEE-EEEEECC
T ss_conf 89999999875797447046750454456134689999998368978-99734-6------------77757-7898467
Q ss_pred HHHHHHHHHHHCCCCCCCCCCCCCCCCCCCEEECCC---CCCCEEEEEEEEEECCCCCEEEEEECCCCCCHHHHHHHCHH
Q ss_conf 999999999861876544212222244330110345---55650589999983477804899844788402455574831
Q gi|254781049|r 76 LKSVISDIREILGSTLITKQTGPTGSRVNCVYVEDG---ADILRELYLSLLVDRTSGMVAFIASTQGGMDIEEVAKDYPQ 152 (398)
Q Consensus 76 ~~ea~~~a~~ilg~~l~t~qt~~~G~~v~~vLVEe~---v~~~~E~ylgi~~Dr~~~~~vii~S~~GGvdIE~va~~~p~ 152 (398)
.+|+..+.+.-|... ++|+||++ +. .+|+=+|++-+-. .-|.+ |. ++. + .++
T Consensus 215 ~~eL~~a~~~Af~~d-------------~~v~vE~~~~~i~-grEl~v~~L~~~~-~lp~~--~~-~~~-~------~~~ 269 (375)
T TIGR01205 215 EEELEAALDEAFKYD-------------ERVIVEEFKQRIK-GRELEVSILGNEE-ALPII--SI-VPE-I------EPD 269 (375)
T ss_pred HHHHHHHHHHHHCCC-------------CEEEEEECCCCCC-CCEEEEEEEECCC-CCEEE--EC-CCC-C------CCC
T ss_conf 789999999861559-------------6599981114789-8526898870797-43245--40-675-3------567
Q ss_pred HHEEEECCCCCCCCHHH-HHHHHHH-CCCCHHHHHHHHHHHHHHHHHH
Q ss_conf 22033214445789578-8878875-1988899885999999998999
Q gi|254781049|r 153 KIFKLLIDPLIGVTSED-VASLCDM-LELQGQARIDGGDLFPNLYKAF 198 (398)
Q Consensus 153 ~I~~~~id~~~gl~~~~-~~~l~~~-lg~~~~~~~~~~~ii~~L~~~f 198 (398)
-. ..-.|-........ .+.+... .+++.+..+.+.++..+.|+..
T Consensus 270 g~-~~FYDY~~KY~~~~g~~~~~pa~~~L~~~~~~~i~~~a~~ay~~~ 316 (375)
T TIGR01205 270 GG-SDFYDYEAKYLDGDGTEYVIPAPAGLDEELEEKIKELALKAYKAL 316 (375)
T ss_pred CC-CEECCHHHCCCCCCCCEEEECCCCCCCHHHHHHHHHHHHHHHHHC
T ss_conf 67-600002114277887326515656788899999999999999840
No 50
>PRK12833 acetyl-CoA carboxylase biotin carboxylase subunit; Provisional
Probab=98.55 E-value=5.2e-06 Score=59.27 Aligned_cols=107 Identities=24% Similarity=0.358 Sum_probs=77.6
Q ss_pred HHHHHHHHHCCCCCCCCE--EECCHHHHHHHHHHCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHHHH
Q ss_conf 999999998689888815--747999999999872998699971213687656565567777777079958999999999
Q gi|254781049|r 6 YQAKALLRKYNVPVAKGV--VISSVHAAESAIKTLPGPLYVVKSQIHAGGRGKGRFKELPADSKGGVRVESSLKSVISDI 83 (398)
Q Consensus 6 yqaK~lL~~~GIpvp~g~--~a~s~~ea~~~a~~ig~p~~VvKaQV~aGgRGKa~~~~~hk~~~GGV~l~~s~~ea~~~a 83 (398)
-++|++..+.|+|+.+|. .+++.+++...+++||||+ ++||- +||-|| |.+++.+.+|+.+.+
T Consensus 120 ~~ar~~a~~~gvPvvpgs~~~v~~~~ea~~~a~~iGyPv-~iKAs--~GGGGr------------Gmriv~~~~el~~~~ 184 (458)
T PRK12833 120 ARARETARRAGVPTVPGSDGVVASLDAALEVAARIGYPV-MIKAA--AGGGGR------------GIRVAHDAAQLAAEL 184 (458)
T ss_pred HHHHHHHHHCCCCCCCCCCCCCCCHHHHHHHHHHCCCHH-HHHHC--CCCCCC------------CEEEECCCCCHHHHH
T ss_conf 999999998499966896676677999999998659754-21332--589987------------107952641148999
Q ss_pred HHHCCCCCCCCCCCCCCCCCCCEEECCCCCCCEEEEEEEEEECCCCCEEEEEE
Q ss_conf 98618765442122222443301103455565058999998347780489984
Q gi|254781049|r 84 REILGSTLITKQTGPTGSRVNCVYVEDGADILRELYLSLLVDRTSGMVAFIAS 136 (398)
Q Consensus 84 ~~ilg~~l~t~qt~~~G~~v~~vLVEe~v~~~~E~ylgi~~Dr~~~~~vii~S 136 (398)
..--..- + .-..-..+++|+.++..+++=+=+.-|.. + .+-++.
T Consensus 185 ~~a~~ea----~---~~Fg~~~v~iEk~i~~~RHIEVQvl~D~~-~-~vhl~e 228 (458)
T PRK12833 185 PLAQREA----Q---AAFGDGGVYLERFIARARHIEVQILGDGE-N-VVHLFE 228 (458)
T ss_pred HHHHHHH----H---HHCCCCCEEEEEECCCCEEEEEEEEECCC-C-EEEEEE
T ss_conf 9999999----9---72699764787613675079999985478-7-699850
No 51
>PRK06395 phosphoribosylamine--glycine ligase; Provisional
Probab=98.54 E-value=9.7e-07 Score=64.08 Aligned_cols=196 Identities=21% Similarity=0.199 Sum_probs=108.1
Q ss_pred HHHHHHHHCCCC-CCCCEEECCHHHHHHHHHHCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCEEEEEC----CHHHHHH
Q ss_conf 999999986898-88815747999999999872998699971213687656565567777777079958----9999999
Q gi|254781049|r 7 QAKALLRKYNVP-VAKGVVISSVHAAESAIKTLPGPLYVVKSQIHAGGRGKGRFKELPADSKGGVRVES----SLKSVIS 81 (398)
Q Consensus 7 qaK~lL~~~GIp-vp~g~~a~s~~ea~~~a~~ig~p~~VvKaQV~aGgRGKa~~~~~hk~~~GGV~l~~----s~~ea~~ 81 (398)
-+|+++++|||| ++++..+.+.+++.......++|+ |||+.-|++| | ||.++. +.+++.+
T Consensus 108 FaK~fm~~~~IP~ta~~~~~~~~~ea~~~~~~~~~pi-VIKadGLAaG--K------------GV~V~~~~~~~~~ea~~ 172 (435)
T PRK06395 108 FMRYLMERHNIPGNINFNACFSEKDAARDYITSMKDV-AVKPIGLTGG--K------------GVKVTGEQLNSVDEAIR 172 (435)
T ss_pred HHHHHHHHCCCCCCCCCCCCCCHHHHHHHHHHCCCCE-EEEECCCCCC--C------------CEEEECCCHHHHHHHHH
T ss_conf 8999999809985664532399999999999709984-8973422578--9------------64895585778999999
Q ss_pred HHHHHCCCCCCCCCCCCCCCCCCCEEECCCCCCCEEEEEEEEEECCCCCEEEEEECCCCCCHHHHHHHCHHHHEEEECCC
Q ss_conf 99986187654421222224433011034555650589999983477804899844788402455574831220332144
Q gi|254781049|r 82 DIREILGSTLITKQTGPTGSRVNCVYVEDGADILRELYLSLLVDRTSGMVAFIASTQGGMDIEEVAKDYPQKIFKLLIDP 161 (398)
Q Consensus 82 ~a~~ilg~~l~t~qt~~~G~~v~~vLVEe~v~~~~E~ylgi~~Dr~~~~~vii~S~~GGvdIE~va~~~p~~I~~~~id~ 161 (398)
.+.+++.. + ..|+|||++. +.|+=+....|...-.|+-. .+ ++ .++..-.--|
T Consensus 173 ~~~~~~~~----------~---~~vvIEE~L~-G~E~S~~a~~dG~~~~~lp~--aq----------Dh-KR~~dgD~GP 225 (435)
T PRK06395 173 YAIEILDR----------D---GVVLIEKKMT-GEEFSLQAFSDGKHLSFMPI--VQ----------DY-KRAYEGDHGP 225 (435)
T ss_pred HHHHHHHC----------C---CEEEEEEEEE-CCEEEEEEEECCCEEEECCC--CC----------CC-CCCCCCCCCC
T ss_conf 99988734----------8---8599999984-41689999976995585873--01----------25-3344799999
Q ss_pred CC-CCCHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCC---CCCCEEEECCCCCEEEEEEEEEECCCHHHHHH
Q ss_conf 45-789578887887519888998859999999989999559751---02326799059967994001321573556410
Q gi|254781049|r 162 LI-GVTSEDVASLCDMLELQGQARIDGGDLFPNLYKAFCDKDMSL---LEINPLIIMKNGRLRVLDSKISFDDNALYRHL 237 (398)
Q Consensus 162 ~~-gl~~~~~~~l~~~lg~~~~~~~~~~~ii~~L~~~f~e~Da~l---iEINPLvvt~dg~vvAlDAKi~iDDnA~fR~~ 237 (398)
.. |+-.+.-.....- -+.....+....++....+...+..... +=+. |.+|++| +.. |.=|+.|--|
T Consensus 226 NTGGMGaysp~~~~~p-~l~~~~~e~~~~Ii~pti~~l~~eg~~y~GvLy~G-lMit~~g-pkV------lEyN~RfGDP 296 (435)
T PRK06395 226 NTGGMGSISDRDFSLP-FLSKDAPERAKHILNDIIRAMKDENNPFKGIMYGQ-FMDTPNG-VKV------IEINARFADP 296 (435)
T ss_pred CCCCCCCCCCCCCCCC-CCCHHHHHHHHHHHHHHHHHHHHCCCCEEEEEEEE-EEEECCC-CEE------EEEEECCCCC
T ss_conf 9998745688888874-32778999999999999999996499708998778-9850899-648------9986203880
Q ss_pred HHHHHHCCCCCCHHHH
Q ss_conf 2786310001562224
Q gi|254781049|r 238 DIQELRDVSEEDSREI 253 (398)
Q Consensus 238 ~~~~~~d~~~~~~~E~ 253 (398)
+..-+....+.|-.|+
T Consensus 297 E~QviLp~L~~Dl~~l 312 (435)
T PRK06395 297 EGINVLYLLKSDFVET 312 (435)
T ss_pred HHHHHHHHHCCCHHHH
T ss_conf 6888877600529999
No 52
>KOG0237 consensus
Probab=98.53 E-value=1.2e-06 Score=63.38 Aligned_cols=106 Identities=24% Similarity=0.241 Sum_probs=82.4
Q ss_pred HHHHHHHHCCCCCCCCEEECCHHHHHHHHHHCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHHHHHHH
Q ss_conf 99999998689888815747999999999872998699971213687656565567777777079958999999999986
Q gi|254781049|r 7 QAKALLRKYNVPVAKGVVISSVHAAESAIKTLPGPLYVVKSQIHAGGRGKGRFKELPADSKGGVRVESSLKSVISDIREI 86 (398)
Q Consensus 7 qaK~lL~~~GIpvp~g~~a~s~~ea~~~a~~ig~p~~VvKaQV~aGgRGKa~~~~~hk~~~GGV~l~~s~~ea~~~a~~i 86 (398)
-+|+++.+||||+.++...+++++|....+..++|.+|+||.=+|-| -||.+.+|.+|+.++.++|
T Consensus 111 fsK~fm~r~~IPTA~y~~ft~~e~a~sfi~~~~~~~~ViKAdGLAAG--------------KGViv~~~~~EA~eAv~sI 176 (788)
T KOG0237 111 FSKDFMHRHNIPTAKYKTFTDPEEAKSFIQSATDKALVIKADGLAAG--------------KGVIVAKSKEEAFEAVDSI 176 (788)
T ss_pred HHHHHHHHCCCCCCEEEEECCHHHHHHHHHHCCCCCEEEEECCCCCC--------------CCEEEECCHHHHHHHHHHH
T ss_conf 89988986399832026407879989999848985648960552457--------------7157405479999999999
Q ss_pred CCCCCCCCCCCCCCCCCCCEEECCCCCCCEEEEEEEEEECCCCCEEEE
Q ss_conf 187654421222224433011034555650589999983477804899
Q gi|254781049|r 87 LGSTLITKQTGPTGSRVNCVYVEDGADILRELYLSLLVDRTSGMVAFI 134 (398)
Q Consensus 87 lg~~l~t~qt~~~G~~v~~vLVEe~v~~~~E~ylgi~~Dr~~~~~vii 134 (398)
|... +-+..|+ +|.|||..+...=-.|.+ .|..+..++..
T Consensus 177 l~~~----~fg~AG~---tvViEE~LEGeEvS~laf-tDG~s~~~mp~ 216 (788)
T KOG0237 177 LVKK----VFGSAGK---TVVIEELLEGEEVSFLAF-TDGYSVRPLPP 216 (788)
T ss_pred HHHH----HHCCCCC---EEEHHHHCCCCEEEEEEE-ECCCCCCCCCC
T ss_conf 8544----4135664---586112307625789998-55730233885
No 53
>KOG0238 consensus
Probab=98.51 E-value=1.6e-05 Score=56.07 Aligned_cols=107 Identities=21% Similarity=0.310 Sum_probs=81.2
Q ss_pred HHHHHHHHHCCCCCCCC--EEECCHHHHHHHHHHCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHHHH
Q ss_conf 99999999868988881--5747999999999872998699971213687656565567777777079958999999999
Q gi|254781049|r 6 YQAKALLRKYNVPVAKG--VVISSVHAAESAIKTLPGPLYVVKSQIHAGGRGKGRFKELPADSKGGVRVESSLKSVISDI 83 (398)
Q Consensus 6 yqaK~lL~~~GIpvp~g--~~a~s~~ea~~~a~~ig~p~~VvKaQV~aGgRGKa~~~~~hk~~~GGV~l~~s~~ea~~~a 83 (398)
..||++.++.|+|+-+| ....+.+++.+.+.+||||+ .+|| -+||-|| |-+++.+++|..+..
T Consensus 113 ~~sk~im~~AgVp~vpG~~g~~qs~e~~~~~a~eIgyPv-MiKa--~~GGGGk------------GMria~~~~ef~~~~ 177 (670)
T KOG0238 113 STSKQIMKAAGVPLVPGYHGEDQSDEEAKKVAREIGYPV-MIKA--TAGGGGK------------GMRIAWSEEEFEEGL 177 (670)
T ss_pred HHHHHHHHHCCCCCCCCCCCCCCCHHHHHHHHHHCCCCE-EEEE--CCCCCCC------------CEEEECCHHHHHHHH
T ss_conf 778999986499613685643266799999998619857-9995--1578876------------317514868899999
Q ss_pred HHHCCCCCCCCCCCCCCCCCCCEEECCCCCCCEEEEEEEEEECCCCCEEEEE
Q ss_conf 9861876544212222244330110345556505899999834778048998
Q gi|254781049|r 84 REILGSTLITKQTGPTGSRVNCVYVEDGADILRELYLSLLVDRTSGMVAFIA 135 (398)
Q Consensus 84 ~~ilg~~l~t~qt~~~G~~v~~vLVEe~v~~~~E~ylgi~~Dr~~~~~vii~ 135 (398)
+.- .|...+-.--.++|+|.+++--+..-+-++-| .+|..+-++
T Consensus 178 ~~a-------k~Ea~~sFGdd~~llEkfi~npRHiEvQv~gD-~hGnav~l~ 221 (670)
T KOG0238 178 ESA-------KQEAAKSFGDDGMLLEKFIDNPRHIEVQVFGD-KHGNAVHLG 221 (670)
T ss_pred HHH-------HHHHHHHCCCCHHHHHHHCCCCCEEEEEEEEC-CCCCEEEEC
T ss_conf 988-------88887631864110777636875489999734-777688850
No 54
>COG4770 Acetyl/propionyl-CoA carboxylase, alpha subunit [Lipid metabolism]
Probab=98.46 E-value=5.1e-05 Score=52.74 Aligned_cols=108 Identities=23% Similarity=0.362 Sum_probs=79.9
Q ss_pred HHHHHHHHHCCCCCCCCEE--ECCHHHHHHHHHHCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHHHH
Q ss_conf 9999999986898888157--47999999999872998699971213687656565567777777079958999999999
Q gi|254781049|r 6 YQAKALLRKYNVPVAKGVV--ISSVHAAESAIKTLPGPLYVVKSQIHAGGRGKGRFKELPADSKGGVRVESSLKSVISDI 83 (398)
Q Consensus 6 yqaK~lL~~~GIpvp~g~~--a~s~~ea~~~a~~ig~p~~VvKaQV~aGgRGKa~~~~~hk~~~GGV~l~~s~~ea~~~a 83 (398)
-.||.+..+.|+|+-+|.. +.+.+++...+.+||||+ .+|| -+||-|| |.|++.+++|+.+..
T Consensus 117 ~~AK~l~~~AgVp~VPG~~g~~qd~~~~~~~A~eiGyPV-lIKA--saGGGGK------------GMRvv~~~~e~~e~l 181 (645)
T COG4770 117 IAAKKLAAEAGVPTVPGYHGPIQDAAELVAIAEEIGYPV-LIKA--SAGGGGK------------GMRVVETPEEFAEAL 181 (645)
T ss_pred HHHHHHHHHCCCCCCCCCCCCCCCHHHHHHHHHHCCCCE-EEEE--CCCCCCC------------CEEEECCHHHHHHHH
T ss_conf 999999997499806897874458999999998639858-9996--3689977------------537626889999999
Q ss_pred HHHCCCCCCCCCCCCCCCCCCCEEECCCCCCCEEEEEEEEEECCCCCEEEEEE
Q ss_conf 98618765442122222443301103455565058999998347780489984
Q gi|254781049|r 84 REILGSTLITKQTGPTGSRVNCVYVEDGADILRELYLSLLVDRTSGMVAFIAS 136 (398)
Q Consensus 84 ~~ilg~~l~t~qt~~~G~~v~~vLVEe~v~~~~E~ylgi~~Dr~~~~~vii~S 136 (398)
..-- +. -+..-| =..++||..++--+..-+-+.-| ++|..+.++-
T Consensus 182 ~sar-rE----A~asFG--ddrv~iEkyl~~PRHIEiQV~aD-~HGNvv~LgE 226 (645)
T COG4770 182 ESAR-RE----AKASFG--DDRVFIEKYLDKPRHIEIQVFAD-QHGNVVHLGE 226 (645)
T ss_pred HHHH-HH----HHHHCC--CCEEEHHHHCCCCCEEEEEEEEC-CCCCEEEEEC
T ss_conf 9999-99----885048--86476245517874489999862-7787888632
No 55
>PRK05294 carB carbamoyl phosphate synthase large subunit; Reviewed
Probab=98.45 E-value=0.00019 Score=48.94 Aligned_cols=329 Identities=19% Similarity=0.178 Sum_probs=176.2
Q ss_pred HHHHHHCCCCCCCCEEECCHHHHHHHHHHCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHHHHHHHCC
Q ss_conf 99999868988881574799999999987299869997121368765656556777777707995899999999998618
Q gi|254781049|r 9 KALLRKYNVPVAKGVVISSVHAAESAIKTLPGPLYVVKSQIHAGGRGKGRFKELPADSKGGVRVESSLKSVISDIREILG 88 (398)
Q Consensus 9 K~lL~~~GIpvp~g~~a~s~~ea~~~a~~ig~p~~VvKaQV~aGgRGKa~~~~~hk~~~GGV~l~~s~~ea~~~a~~ilg 88 (398)
+++|.+.||+.|++..++|.+||.++++++|||++|=-+-|+ |||| -.++.|.+|+.....+.+.
T Consensus 673 ~~~l~~l~i~qp~~~~a~s~~ea~~~a~~iGyPvlvRPSyVL-GG~~--------------M~iv~~~~eL~~yl~~a~~ 737 (1063)
T PRK05294 673 QKLLEKLGIKQPPNGTATSVEEALEIAEEIGYPVLVRPSYVL-GGRA--------------MEIVYDEEELERYMREAVK 737 (1063)
T ss_pred HHHHHHCCCCCCCCCEECCHHHHHHHHHHCCCCEEECCCCCC-CCCC--------------EEEECCHHHHHHHHHHHHH
T ss_conf 999986599999970766899999999864986684343102-5771--------------4785699999999999986
Q ss_pred CCCCCCCCCCCCCCCCCEEECCCCCCCEEEEEEEEEECCCCCEEEEEECCCCCCHHHHHHHCHHHHEEEECCCCCCCCHH
Q ss_conf 76544212222244330110345556505899999834778048998447884024555748312203321444578957
Q gi|254781049|r 89 STLITKQTGPTGSRVNCVYVEDGADILRELYLSLLVDRTSGMVAFIASTQGGMDIEEVAKDYPQKIFKLLIDPLIGVTSE 168 (398)
Q Consensus 89 ~~l~t~qt~~~G~~v~~vLVEe~v~~~~E~ylgi~~Dr~~~~~vii~S~~GGvdIE~va~~~p~~I~~~~id~~~gl~~~ 168 (398)
- . . -+.|||.+++...+|+=+-...|.. -+++.+-. =+||.-.-.+-|.+... |...++..
T Consensus 738 v-------s-~---~~pvlIdkfl~ga~E~eVDai~Dg~---~v~I~gIm--EHIE~AGVHSGDS~~V~---Pp~~Ls~~ 798 (1063)
T PRK05294 738 V-------S-P---DHPVLIDRFLEDAIEVDVDAICDGE---DVLIGGIM--EHIEEAGVHSGDSACSL---PPYTLSEE 798 (1063)
T ss_pred H-------C-C---CCCEEEEHHHHHCHHHHHHEEECCC---EEEEEEEE--EECCCCCCCCCCCEEEE---CCCCCCHH
T ss_conf 3-------8-9---9977863543202454430231488---48999987--20014575667842881---68558999
Q ss_pred HHH-------HHHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCEEEECCCCCEEEEEEEEEECCCHHHH-----H
Q ss_conf 888-------7887519888998859999999989999559751023267990599679940013215735564-----1
Q gi|254781049|r 169 DVA-------SLCDMLELQGQARIDGGDLFPNLYKAFCDKDMSLLEINPLIIMKNGRLRVLDSKISFDDNALYR-----H 236 (398)
Q Consensus 169 ~~~-------~l~~~lg~~~~~~~~~~~ii~~L~~~f~e~Da~liEINPLvvt~dg~vvAlDAKi~iDDnA~fR-----~ 236 (398)
..+ +++..|++.|-...|| +..+.+.-.+|+||=+ .+=++.=+|.+==+=|..- -
T Consensus 799 ~~~~i~~~t~~ia~~l~v~G~~NiQf---------~vk~~~vyVIE~NpRa----SRtvPfvSKatg~pl~~iAtk~~lG 865 (1063)
T PRK05294 799 IIDEIREQTKKLALELNVVGLMNVQF---------AVKDDEVYVIEVNPRA----SRTVPFVSKATGVPLAKIAARVMLG 865 (1063)
T ss_pred HHHHHHHHHHHHHHHCCCCCCCEEEE---------EECCCEEEEEEECCCC----CCCCHHHHHHCCCCHHHHHHHHHCC
T ss_conf 99999999999998556666420335---------5409838999944744----4530445764199799999999829
Q ss_pred HHHHHHHCCCCCCHHHHHHHHCCCCEEECCC----------CEE-EEECCCHHHHHHHHHHHHCCCCC----CEEEECCC
Q ss_conf 0278631000156222457753986442288----------179-99555036899999999658996----24884278
Q gi|254781049|r 237 LDIQELRDVSEEDSREIEAKQHNLSYIALDG----------NIG-CMVNGAGLAMATMDIIKLYGGAP----ANFLDVGG 301 (398)
Q Consensus 237 ~~~~~~~d~~~~~~~E~~A~~~~l~yv~LdG----------~Ig-~~vnGaGlamatmD~i~~~Gg~p----ANFlD~gG 301 (398)
..+.++.......+.-.--+..-++|-+|.| ..| +|+-|--+..|..-.....|.+- .=|+-++.
T Consensus 866 ~~l~~l~~~~~~~~~~v~VK~pvFsf~k~~g~d~~LGpEMkSTGEVmg~g~~~~eAl~Ka~~aag~~iP~~G~v~iSv~d 945 (1063)
T PRK05294 866 KKLAELGYTKEIIPPHVSVKEAVFPFNKFPGVDPLLGPEMKSTGEVMGIDRTFGEAFAKAQLAAGNRLPTSGTVLVSVRD 945 (1063)
T ss_pred CCHHHCCCCCCCCCCCEEEECCCCCHHHCCCCCCCCCCCCCCCCCCEEECCCHHHHHHHHHHHCCCCCCCCCEEEEEECC
T ss_conf 97344278877888828997564874334999988787724343415734999999999998669988988879999424
Q ss_pred CCCHHHHHHHHHHH----------------HCCCCCCEEEEECCCCHHHHHHHHHHHHHHHHHCCCCCCEEEEC--CCCC
Q ss_conf 88989999999998----------------61998658999635861328999999999999729998799974--8985
Q gi|254781049|r 302 GADQDKVAAAFKII----------------TSDSSVKGILINIFGGIMRCDVLVKGILSAVKEVKINIPLVMRL--EGAN 363 (398)
Q Consensus 302 ~a~~e~~~~a~~~i----------------l~~~~vk~iliNifGGI~~cd~vA~gii~a~~~~~~~~pivvRl--~Gtn 363 (398)
. +.+.+....+.+ |.+.++++-.|+-..- --.-|++.+++.+++ +|+-. ....
T Consensus 946 ~-dK~~~~~~a~~l~~lGf~i~AT~GTa~~L~~~GI~~~~V~Kv~e------~~p~i~d~i~~~~I~--lVINt~~~~~~ 1016 (1063)
T PRK05294 946 R-DKEEVVELAKRLLELGFKILATEGTAKFLEEAGIPVELVNKVHE------GRPHIVDLIKNGEID--LVINTPEGRQA 1016 (1063)
T ss_pred C-CHHHHHHHHHHHHHCCCEEEECHHHHHHHHHCCCCEEEECCCCC------CCCCHHHHHHCCCEE--EEEECCCCCCC
T ss_conf 2-57999999999997699899841789999976991599646578------992599999769826--99979999877
Q ss_pred HHHHHHHH---HHCCCCEEEECCHHHHHHHHHH
Q ss_conf 89999999---9769958994998999999999
Q gi|254781049|r 364 VDIGNRLI---AESGLNVITAIDLDDAAQKIVH 393 (398)
Q Consensus 364 ~~~g~~il---~~~g~~~~~~~~~~~A~~~~v~ 393 (398)
...|.+|- -+.++|+++.-+.-+|+-++.+
T Consensus 1017 ~~dg~~IRR~Av~~~IP~~Tsl~~A~a~v~al~ 1049 (1063)
T PRK05294 1017 IRDGFSIRRAALEYKVPYITTLAGARAAAEAIE 1049 (1063)
T ss_pred CCCCHHHHHHHHHHCCCEEECHHHHHHHHHHHH
T ss_conf 776299999999709998967999999999999
No 56
>PRK10446 ribosomal protein S6 modification protein; Provisional
Probab=98.42 E-value=8.6e-06 Score=57.82 Aligned_cols=80 Identities=20% Similarity=0.258 Sum_probs=61.3
Q ss_pred HHHHHHHHHCCCCCCCCEEECCHHHHHHHHHHC-CCCEEEEECCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHHHHH
Q ss_conf 999999998689888815747999999999872-9986999712136876565655677777770799589999999999
Q gi|254781049|r 6 YQAKALLRKYNVPVAKGVVISSVHAAESAIKTL-PGPLYVVKSQIHAGGRGKGRFKELPADSKGGVRVESSLKSVISDIR 84 (398)
Q Consensus 6 yqaK~lL~~~GIpvp~g~~a~s~~ea~~~a~~i-g~p~~VvKaQV~aGgRGKa~~~~~hk~~~GGV~l~~s~~ea~~~a~ 84 (398)
+.+-++|+++|||+|+..++.+++++.++.+.+ |+| +|+|. +.|-.|+ ||.++++.+++....+
T Consensus 101 l~t~qlL~~~gip~P~T~~~~~~~~~~~~i~~~gg~P-vViKp--l~Gs~G~------------GV~l~e~~~~~~~i~~ 165 (300)
T PRK10446 101 LRSMQLLARQGIDLPVTGIAHSPDDTSDLIDMVGGAP-LVVKL--VEGTQGI------------GVVLAETRQAAESVID 165 (300)
T ss_pred HHHHHHHHHCCCCCCCEEEECCHHHHHHHHHHHCCCC-EEEEE--CCCCCCC------------CEEEEECHHHHHHHHH
T ss_conf 9999999875979998898369999999999808997-89996--7898860------------3699737899999999
Q ss_pred HHCCCCCCCCCCCCCCCCCCCEEECCCCC
Q ss_conf 86187654421222224433011034555
Q gi|254781049|r 85 EILGSTLITKQTGPTGSRVNCVYVEDGAD 113 (398)
Q Consensus 85 ~ilg~~l~t~qt~~~G~~v~~vLVEe~v~ 113 (398)
.+.+.. ..+|++|+++
T Consensus 166 ~~~~~~-------------~~~~iQeyI~ 181 (300)
T PRK10446 166 AFRGLN-------------AHILVQEYIK 181 (300)
T ss_pred HHHHCC-------------CCEEEEEECC
T ss_conf 886228-------------7377522025
No 57
>PRK12815 carB carbamoyl phosphate synthase large subunit; Reviewed
Probab=98.42 E-value=5e-05 Score=52.78 Aligned_cols=326 Identities=18% Similarity=0.201 Sum_probs=164.3
Q ss_pred HHHHHHCCCCCCCCEEECCHHHHHHHHHHCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHHHHHHHCC
Q ss_conf 99999868988881574799999999987299869997121368765656556777777707995899999999998618
Q gi|254781049|r 9 KALLRKYNVPVAKGVVISSVHAAESAIKTLPGPLYVVKSQIHAGGRGKGRFKELPADSKGGVRVESSLKSVISDIREILG 88 (398)
Q Consensus 9 K~lL~~~GIpvp~g~~a~s~~ea~~~a~~ig~p~~VvKaQV~aGgRGKa~~~~~hk~~~GGV~l~~s~~ea~~~a~~ilg 88 (398)
+++|.+.||+.|++..++|.+||.++++++|||++|=-+-|+ |||+- .++.|.+|+....++-..
T Consensus 674 ~~ll~~l~i~~p~~~~~~~~~ea~~~a~~iGyPvlvRPSyvL-gG~~m--------------~iv~~~~eL~~y~~~a~~ 738 (1068)
T PRK12815 674 YQLLDELGLPHVPGLTATSEEEALAFAKRIGYPVLIRPSYVI-GGQGM--------------AVVYDEPALEAYLEENVQ 738 (1068)
T ss_pred HHHHHHCCCCCCCCCEECCHHHHHHHHHHCCCCEEECCCCCC-CCCEE--------------EEECCHHHHHHHHHHHCC
T ss_conf 999997389999963545667999999864997784244335-77423--------------897599999999985157
Q ss_pred CCCCCCCCCCCCCCCCCEEECCCCCCCEEEEEEEEEECCCCCEEEEEECCCCCCHHHHHHHCHHHHEEEECCCCCCCCHH
Q ss_conf 76544212222244330110345556505899999834778048998447884024555748312203321444578957
Q gi|254781049|r 89 STLITKQTGPTGSRVNCVYVEDGADILRELYLSLLVDRTSGMVAFIASTQGGMDIEEVAKDYPQKIFKLLIDPLIGVTSE 168 (398)
Q Consensus 89 ~~l~t~qt~~~G~~v~~vLVEe~v~~~~E~ylgi~~Dr~~~~~vii~S~~GGvdIE~va~~~p~~I~~~~id~~~gl~~~ 168 (398)
..+.|||.++++ ++|+=+-...|.. ..++-+..+ +||+-.-.+-|.+... |...++..
T Consensus 739 -------------~~~pvlIdkfl~-g~E~evDai~Dg~--~v~I~gImE---HIE~AGVHSGDS~~v~---Pp~~Ls~~ 796 (1068)
T PRK12815 739 -------------QLYPILIDQFID-GKEYEVDAISDGE--DVTIPGIIE---HIEQAGVHSGDSIAVL---PPQSLSPE 796 (1068)
T ss_pred -------------CCCCEEEEECCC-CCEEEEEEEECCC--CEEEEEEEE---CHHHCCCCCCCCEEEE---CCCCCCHH
T ss_conf -------------888556230005-4046889996499--559999642---1131466568854883---89878999
Q ss_pred HHH-------HHHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCEEEECCCCCEEEEEEEEEECCCHHH--H---H
Q ss_conf 888-------788751988899885999999998999955975102326799059967994001321573556--4---1
Q gi|254781049|r 169 DVA-------SLCDMLELQGQARIDGGDLFPNLYKAFCDKDMSLLEINPLIIMKNGRLRVLDSKISFDDNALY--R---H 236 (398)
Q Consensus 169 ~~~-------~l~~~lg~~~~~~~~~~~ii~~L~~~f~e~Da~liEINPLvvt~dg~vvAlDAKi~iDDnA~f--R---~ 236 (398)
..+ +++..|++.|-...+++ ..+.+.-.+|+||=+ .+=++.=+|.+==+=|.. | -
T Consensus 797 ~~~~i~~~t~kia~~L~v~Gl~NiQfa---------vk~~~vyVIEvNpRA----SRTvPFvSKatG~pl~~iAtkvmlG 863 (1068)
T PRK12815 797 QQAKIRDQAIKIAKKLGFRGIMNIQFL---------LAGDEIYVLEVNPRA----SRTVPFVSKATGVPLAKLATKVLLG 863 (1068)
T ss_pred HHHHHHHHHHHHHHHCEEECCEEEEEE---------EECCEEEEEEEECCC----CCCHHHHHHHCCCCHHHHHHHHHCC
T ss_conf 999999999999964835451269999---------979989999961875----5432667873298899999999849
Q ss_pred HHHHHHHCCCCCCH-HHH-HHHHCCCCEEECC-------------CCEEEEECCCHHHHHHHHHHHHCCCC-C---CEEE
Q ss_conf 02786310001562-224-5775398644228-------------81799955503689999999965899-6---2488
Q gi|254781049|r 237 LDIQELRDVSEEDS-REI-EAKQHNLSYIALD-------------GNIGCMVNGAGLAMATMDIIKLYGGA-P---ANFL 297 (398)
Q Consensus 237 ~~~~~~~d~~~~~~-~E~-~A~~~~l~yv~Ld-------------G~Ig~~vnGaGlamatmD~i~~~Gg~-p---ANFl 297 (398)
..+.++..+....| .+. --+..=++|-+|. |.+ |+-|.-+..|..-.....|.+ | .=|+
T Consensus 864 ~~L~~l~~~~~~~p~~~~~~VK~pvFsf~k~~g~d~~LGpEMkSTGEV--mgig~~~~eA~~Ka~~aag~~lP~~G~vfi 941 (1068)
T PRK12815 864 KSLAELGYPNELWPGSNFIHVKMPVFSFLRYPGVDNTLGPEMKSTGEV--MGIDKDLESALYKGYAASDLHIPTYGTIFI 941 (1068)
T ss_pred CCHHHCCCCCCCCCCCCCEEEECCCCCHHHCCCCCCCCCCCCCCCCCC--EEECCCHHHHHHHHHHHCCCCCCCCCEEEE
T ss_conf 975662886555778882899835487444389998778884223231--562499999999999966998898988999
Q ss_pred ECCCCCCHHHHHHHHHHH----------------HCCCCCCEEEEECCCCHHHHHHHHHHHHHHHHHCCCCCCEEEECCC
Q ss_conf 427888989999999998----------------6199865899963586132899999999999972999879997489
Q gi|254781049|r 298 DVGGGADQDKVAAAFKII----------------TSDSSVKGILINIFGGIMRCDVLVKGILSAVKEVKINIPLVMRLEG 361 (398)
Q Consensus 298 D~gG~a~~e~~~~a~~~i----------------l~~~~vk~iliNifGGI~~cd~vA~gii~a~~~~~~~~pivvRl~G 361 (398)
-++- .+.+.+....+.+ |...++.+-.||-..-- -.-|++.+++.++.+-+......
T Consensus 942 Sv~d-~DK~~~~~~a~~l~~lGf~i~AT~GTa~~L~~~GI~~~~V~Kv~eg------~p~i~d~i~~~~i~lViNt~~g~ 1014 (1068)
T PRK12815 942 SVRD-EDKEAVAELARRFEQLGFKLLATEGTANWLAEEGITTGVVEKVQEG------SPSLLERIKQHRIVLVVNTSLSD 1014 (1068)
T ss_pred EECC-CCHHHHHHHHHHHHHCCCEEEECHHHHHHHHHCCCEEEEEECCCCC------CCCHHHHHHCCCEEEEEECCCCC
T ss_conf 9610-0178999999999987998998658999999779836997136789------81299998679857999799998
Q ss_pred CCHHHHHHHH---HHCCCCEEEECCHHHHHHHHHH
Q ss_conf 8589999999---9769958994998999999999
Q gi|254781049|r 362 ANVDIGNRLI---AESGLNVITAIDLDDAAQKIVH 393 (398)
Q Consensus 362 tn~~~g~~il---~~~g~~~~~~~~~~~A~~~~v~ 393 (398)
.....|.+|- -+.++|+++.-+.-+|.-++.+
T Consensus 1015 ~~~~D~~~IRr~Av~~~IP~~Ttl~~A~a~v~al~ 1049 (1068)
T PRK12815 1015 SASEDAIKIRDEALTTHIPVFTSLETAQAFLDVLE 1049 (1068)
T ss_pred CCCCCHHHHHHHHHHHCCCEEECHHHHHHHHHHHH
T ss_conf 76654399999999829988927999999999999
No 58
>pfam02655 ATP-grasp_3 ATP-grasp domain. No functional information or experimental verification of function is known in this family. This family appears to be an ATP-grasp domain (Pers. obs. A Bateman).
Probab=98.41 E-value=2.4e-06 Score=61.54 Aligned_cols=80 Identities=21% Similarity=0.232 Sum_probs=59.5
Q ss_pred HHHHHHHHHHCCCCCCCCEEECCHHHHHHHHHHCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHHHHH
Q ss_conf 79999999986898888157479999999998729986999712136876565655677777770799589999999999
Q gi|254781049|r 5 EYQAKALLRKYNVPVAKGVVISSVHAAESAIKTLPGPLYVVKSQIHAGGRGKGRFKELPADSKGGVRVESSLKSVISDIR 84 (398)
Q Consensus 5 EyqaK~lL~~~GIpvp~g~~a~s~~ea~~~a~~ig~p~~VvKaQV~aGgRGKa~~~~~hk~~~GGV~l~~s~~ea~~~a~ 84 (398)
-|..+++|+++|||+|+.....++++ +.+|+ |+|+-.-+||| ||.++++.+++....
T Consensus 4 K~~t~~~l~~~gip~P~~~~~~~~~~-------~~~P~-VvKP~~g~gs~--------------Gv~~v~~~~~l~~~~- 60 (160)
T pfam02655 4 KLKTYKALKNAGVPTPETLSAEEPTE-------EEKKY-IVKPRDGCGGE--------------GVRFVENGREDEEFI- 60 (160)
T ss_pred HHHHHHHHHHCCCCCCCEEECCCHHH-------CCCCE-EEECCCCCCCC--------------CEEEEECHHHHHHHC-
T ss_conf 89999999987959999986578235-------59989-99808989873--------------189994899986532-
Q ss_pred HHCCCCCCCCCCCCCCCCCCCEEECCCCCCCEEEEEEEEEECC
Q ss_conf 8618765442122222443301103455565058999998347
Q gi|254781049|r 85 EILGSTLITKQTGPTGSRVNCVYVEDGADILRELYLSLLVDRT 127 (398)
Q Consensus 85 ~ilg~~l~t~qt~~~G~~v~~vLVEe~v~~~~E~ylgi~~Dr~ 127 (398)
..+++||+++ +.|+=+++..|..
T Consensus 61 -------------------~~~liqe~i~-G~e~sv~~l~~~~ 83 (160)
T pfam02655 61 -------------------ENVIIQEFIE-GEPLSVSLLSDGE 83 (160)
T ss_pred -------------------CCEEEEEEEE-CCEEEEEEEEECC
T ss_conf -------------------5658874794-4423899999899
No 59
>TIGR03103 trio_acet_GNAT GNAT-family acetyltransferase TIGR03103. Members of this protein family belong to the GNAT family of acetyltransferases. Each is part of a conserved three-gene cassette sparsely distributed across at least twenty different species known so far, including alpha, beta, and gamma Proteobacteria, Mycobacterium, and Prosthecochloris, which is a member of the Chlorobi. The other two members of the cassette are a probable protease and an asparagine synthetase family protein.
Probab=98.23 E-value=1.2e-05 Score=56.92 Aligned_cols=109 Identities=18% Similarity=0.213 Sum_probs=72.2
Q ss_pred HHHHHHHCCCCCCCCEEECCHHHHHHHHHHCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCEEEE-ECCHHHHHHHHHHH
Q ss_conf 99999986898888157479999999998729986999712136876565655677777770799-58999999999986
Q gi|254781049|r 8 AKALLRKYNVPVAKGVVISSVHAAESAIKTLPGPLYVVKSQIHAGGRGKGRFKELPADSKGGVRV-ESSLKSVISDIREI 86 (398)
Q Consensus 8 aK~lL~~~GIpvp~g~~a~s~~ea~~~a~~ig~p~~VvKaQV~aGgRGKa~~~~~hk~~~GGV~l-~~s~~ea~~~a~~i 86 (398)
.|+||++.|+|||.++++.+.+++.+++.+.| |+ |||+. -|-.|| ||-+ ..|.+++..++..-
T Consensus 301 T~rll~~AG~~VP~~~~~~~~~~~~~fl~~~G-~V-VVKP~--dGnqGr------------GVtvnl~t~eev~~A~~~A 364 (547)
T TIGR03103 301 TRRLVSEAGLQVPEQQLAGNGEAVEAFLAEHG-AV-VVKPV--RGEQGK------------GISVDVRTPDDLEAAIAKA 364 (547)
T ss_pred HHHHHHHCCCCCCCCCCCCCHHHHHHHHHHCC-CE-EECCC--CCCCCC------------CEEECCCCHHHHHHHHHHH
T ss_conf 99999973998999745699899999998739-99-97768--788886------------1587259999999999999
Q ss_pred CCCCCCCCCCCCCCCCCCCEEECCCCCCCEEEEEEEEEEC----CCC-CEEEEEECCCCCCHHHHHH
Q ss_conf 1876544212222244330110345556505899999834----778-0489984478840245557
Q gi|254781049|r 87 LGSTLITKQTGPTGSRVNCVYVEDGADILRELYLSLLVDR----TSG-MVAFIASTQGGMDIEEVAK 148 (398)
Q Consensus 87 lg~~l~t~qt~~~G~~v~~vLVEe~v~~~~E~ylgi~~Dr----~~~-~~vii~S~~GGvdIE~va~ 148 (398)
-.....|+||++++.. +|=+=+.-++ ..+ ++-+++ -|=-.|+++-+
T Consensus 365 -------------~~~~~~VIVE~fi~G~-D~RlLVIggkVVAAA~R~Pa~VvG--DG~sTI~eLIe 415 (547)
T TIGR03103 365 -------------RQFCDRVLLERYVPGE-DLRLVVIDFEVVAAAVRRPPEVIG--DGRSSIRDLIE 415 (547)
T ss_pred -------------HHHCCCEEEEEEECCC-CEEEEEECCEEEEEECCCCCEEEE--CCHHHHHHHHH
T ss_conf -------------9759957999840697-169999999999998147967984--86620999984
No 60
>TIGR00768 rimK_fam alpha-L-glutamate ligases, RimK family; InterPro: IPR004666 Escherichia coli RimK adds additional Glu residues to the native Glu-Glu C-terminus of ribosomal protein S6. Mutation of the Glu-Glu terminus to Lys-Glu blocked addition. S6 has the C-terminal sequence Glu-Glu in few species, suggesting the homolog of rimK may have a function other than S6 modification in those species. However, most species having a member of this protein subfamily do not have an S6 homolog ending in Glu-Glu.; GO: 0006464 protein modification process.
Probab=98.17 E-value=1.5e-05 Score=56.25 Aligned_cols=83 Identities=22% Similarity=0.290 Sum_probs=61.6
Q ss_pred HHHHHHHHCCCCCCCCEEEC--------CHHHHHHHHHHCC---CCEEEEECCCCCCCCCCCCCCCCCCCCCCEEEEECC
Q ss_conf 99999998689888815747--------9999999998729---986999712136876565655677777770799589
Q gi|254781049|r 7 QAKALLRKYNVPVAKGVVIS--------SVHAAESAIKTLP---GPLYVVKSQIHAGGRGKGRFKELPADSKGGVRVESS 75 (398)
Q Consensus 7 qaK~lL~~~GIpvp~g~~a~--------s~~ea~~~a~~ig---~p~~VvKaQV~aGgRGKa~~~~~hk~~~GGV~l~~s 75 (398)
-+-.+|+++|||+|++.++. ++++|...++++| ||. |+|+-. |-+|+ +|-++++
T Consensus 116 ~s~~~L~~~G~P~P~~~~~~PqnfDReW~~~~a~~~ie~~g~lEfP~-V~Kp~~--GS~G~------------~V~l~~D 180 (321)
T TIGR00768 116 LSHQLLAKAGVPLPRTGVAGPQNFDREWSPEEALKLIEEIGQLEFPV-VLKPVF--GSWGR------------LVSLARD 180 (321)
T ss_pred HHHHHHHHCCCCCCCEEEECCCCCCCCCCHHHHHHHHHHHCCCCCCE-EEECCC--CCCCC------------EEEEEEC
T ss_conf 99999995868987335736632243589889999998731764245-871785--63542------------6898506
Q ss_pred HHHHHHHHHHHCCCCCCCCCCCCCCCCCCCEEECCCCC
Q ss_conf 99999999986187654421222224433011034555
Q gi|254781049|r 76 LKSVISDIREILGSTLITKQTGPTGSRVNCVYVEDGAD 113 (398)
Q Consensus 76 ~~ea~~~a~~ilg~~l~t~qt~~~G~~v~~vLVEe~v~ 113 (398)
..++....... ++. +|..-+.+||+|.++
T Consensus 181 ~~~~~~~~e~~-------~~~--~~~~~~~~~~QeyI~ 209 (321)
T TIGR00768 181 KQAAETLLEHF-------EQL--NGPQYKVFLVQEYIK 209 (321)
T ss_pred HHHHHHHHHHH-------HHH--CCCCCCEEEEEEEEC
T ss_conf 78999999999-------721--883323578872011
No 61
>PRK05784 phosphoribosylamine--glycine ligase; Provisional
Probab=98.13 E-value=1.7e-05 Score=55.93 Aligned_cols=214 Identities=19% Similarity=0.172 Sum_probs=105.0
Q ss_pred HHHHHHHHCCCC-CCCCEEECCHHHHHHHHHHCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCEEEEECC-HHHHHH---
Q ss_conf 999999986898-888157479999999998729986999712136876565655677777770799589-999999---
Q gi|254781049|r 7 QAKALLRKYNVP-VAKGVVISSVHAAESAIKTLPGPLYVVKSQIHAGGRGKGRFKELPADSKGGVRVESS-LKSVIS--- 81 (398)
Q Consensus 7 qaK~lL~~~GIp-vp~g~~a~s~~ea~~~a~~ig~p~~VvKaQV~aGgRGKa~~~~~hk~~~GGV~l~~s-~~ea~~--- 81 (398)
-+|+++++|||| ++++...++.++|.+..+..+ | +|||+.=||+|. ||.++.+ .+.+.+
T Consensus 112 FaK~fm~~~~IPtta~~~~f~~~~~A~~~l~~~~-p-iVIKaDGLAaGK--------------GV~V~~~~~~~~~~~~~ 175 (485)
T PRK05784 112 FARSLMWKYGIPGRLRYGVFKDVEEAYSFAEYGG-S-VAIKPARQAGGK--------------GVKVIYDLQAYLSNEKD 175 (485)
T ss_pred HHHHHHHHCCCCCCCCCCCCCCHHHHHHHHHHCC-C-EEEECCHHCCCC--------------CEEEECCCHHHHHHHHH
T ss_conf 9999999728996640121389999999986489-8-499211330678--------------51882272777777899
Q ss_pred -----HHHHHCCCCCCCCCCCCCCCCCCCEEECCCCCCCEEEEEEEEEECCCCCEEEEEECCCCCCHHHHHHHCHHHHEE
Q ss_conf -----999861876544212222244330110345556505899999834778048998447884024555748312203
Q gi|254781049|r 82 -----DIREILGSTLITKQTGPTGSRVNCVYVEDGADILRELYLSLLVDRTSGMVAFIASTQGGMDIEEVAKDYPQKIFK 156 (398)
Q Consensus 82 -----~a~~ilg~~l~t~qt~~~G~~v~~vLVEe~v~~~~E~ylgi~~Dr~~~~~vii~S~~GGvdIE~va~~~p~~I~~ 156 (398)
.+.+++... .. -|.--++|+|||++. +.|+=+-...|...- +.|.+.+ ++ .++..
T Consensus 176 e~~~~~~~~~~~~~---~~---fg~ag~~VvIEEfL~-G~E~S~~a~~DG~~~--~~lp~aQ----------Dh-KR~~d 235 (485)
T PRK05784 176 EVLTKGAEEIKEQL---AS---YRDVEEKILVEEKVD-GVEYTVQVLTDGESV--FPLPPVQ----------DN-PHAYE 235 (485)
T ss_pred HHHHHHHHHHHHHH---HH---HCCCCCEEEEEECCC-CCEEEEEEEEECCEE--EECCCCC----------CC-CCCCC
T ss_conf 99999999999876---54---324687099996446-817999999829969--9892220----------57-65568
Q ss_pred EECCCCCC-CCHHHHHHHHHHCC-CCHHHHHHHHHHHHHHHHHHH-HCCCCCCC--CCEEEECCCCCEEEEEEEEEECCC
Q ss_conf 32144457-89578887887519-888998859999999989999-55975102--326799059967994001321573
Q gi|254781049|r 157 LLIDPLIG-VTSEDVASLCDMLE-LQGQARIDGGDLFPNLYKAFC-DKDMSLLE--INPLIIMKNGRLRVLDSKISFDDN 231 (398)
Q Consensus 157 ~~id~~~g-l~~~~~~~l~~~lg-~~~~~~~~~~~ii~~L~~~f~-e~Da~liE--INPLvvt~dg~vvAlDAKi~iDDn 231 (398)
-..-|..| +-.|--... .+. +.........+++....+... +......= -==|.+|++| ... +.=|
T Consensus 236 gD~GPNTGGMGAysP~~~--~~P~l~~~~~~~~~~Ii~pti~~l~~e~g~~y~GvLY~GlMit~~G-PkV------lEfN 306 (485)
T PRK05784 236 YGIGPETGGMGSVSGPGE--LLPFIEEEEYEEAVEIVKATVEAIRKETGERYVGVLSGQMMLTALG-PTV------IEYY 306 (485)
T ss_pred CCCCCCCCCCEECCCCCC--CCCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCEEEEEEEEEECCCC-CEE------EEEE
T ss_conf 999989998700678766--7754479999999874899999998616997278887678861898-489------9996
Q ss_pred HHHHHHHHHHHHCCCCCCHHHH--HHHHCCCCEEEC
Q ss_conf 5564102786310001562224--577539864422
Q gi|254781049|r 232 ALYRHLDIQELRDVSEEDSREI--EAKQHNLSYIAL 265 (398)
Q Consensus 232 A~fR~~~~~~~~d~~~~~~~E~--~A~~~~l~yv~L 265 (398)
+.|--|+...+....+.|-.++ .+.+..|+-+++
T Consensus 307 ~RfGDPEtQ~iLp~L~sDl~~l~~a~~~g~L~~~~~ 342 (485)
T PRK05784 307 SRLGDPEALNALYLYEGDFYELFELAATGKLHKAER 342 (485)
T ss_pred CCCCCCHHHHHHHHHHCCHHHHHHHHHCCCCCCCCE
T ss_conf 887883388899874263999999998199887870
No 62
>COG0027 PurT Formate-dependent phosphoribosylglycinamide formyltransferase (GAR transformylase) [Nucleotide transport and metabolism]
Probab=98.01 E-value=3.2e-05 Score=54.08 Aligned_cols=84 Identities=25% Similarity=0.295 Sum_probs=62.9
Q ss_pred HHCCCCCCCCEEECCHHHHHHHHHHCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHHHHHHHCCCCCC
Q ss_conf 98689888815747999999999872998699971213687656565567777777079958999999999986187654
Q gi|254781049|r 13 RKYNVPVAKGVVISSVHAAESAIKTLPGPLYVVKSQIHAGGRGKGRFKELPADSKGGVRVESSLKSVISDIREILGSTLI 92 (398)
Q Consensus 13 ~~~GIpvp~g~~a~s~~ea~~~a~~ig~p~~VvKaQV~aGgRGKa~~~~~hk~~~GGV~l~~s~~ea~~~a~~ilg~~l~ 92 (398)
.+.|+|+.++..++|.+|...++..||||+ |+|+-+-+-|.|.. ++++++++..+-+.-
T Consensus 123 eeLglpTs~Y~fa~s~~e~~~a~~~iGfPc-vvKPvMSSSGkGqs--------------vv~~~e~ve~AW~~A------ 181 (394)
T COG0027 123 EELGLPTSKYRFADSLEELRAAVEKIGFPC-VVKPVMSSSGKGQS--------------VVRSPEDVEKAWEYA------ 181 (394)
T ss_pred HHHCCCCCCCCCCCCHHHHHHHHHHCCCCE-ECCCCCCCCCCCCE--------------EECCHHHHHHHHHHH------
T ss_conf 972999766321355999999999749970-21332026889821--------------435987889999999------
Q ss_pred CCCCCCCCCCCCCEEECCCCCCCEEEEE
Q ss_conf 4212222244330110345556505899
Q gi|254781049|r 93 TKQTGPTGSRVNCVYVEDGADILRELYL 120 (398)
Q Consensus 93 t~qt~~~G~~v~~vLVEe~v~~~~E~yl 120 (398)
|.+..|. -.+|.||++++++-|.-+
T Consensus 182 --~~g~R~~-~~RVIVE~fv~fd~EITl 206 (394)
T COG0027 182 --QQGGRGG-SGRVIVEEFVKFDFEITL 206 (394)
T ss_pred --HHCCCCC-CCCEEEEEEECCEEEEEE
T ss_conf --7547888-871899987323279999
No 63
>COG0189 RimK Glutathione synthase/Ribosomal protein S6 modification enzyme (glutaminyl transferase) [Coenzyme metabolism / Translation, ribosomal structure and biogenesis]
Probab=97.85 E-value=0.0003 Score=47.69 Aligned_cols=93 Identities=22% Similarity=0.248 Sum_probs=64.4
Q ss_pred HHHHHHHHHCCCCCCCCEEECCHHHH-HHHHHHCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCEEEEECCHH-HHHHHH
Q ss_conf 99999999868988881574799999-9999872998699971213687656565567777777079958999-999999
Q gi|254781049|r 6 YQAKALLRKYNVPVAKGVVISSVHAA-ESAIKTLPGPLYVVKSQIHAGGRGKGRFKELPADSKGGVRVESSLK-SVISDI 83 (398)
Q Consensus 6 yqaK~lL~~~GIpvp~g~~a~s~~ea-~~~a~~ig~p~~VvKaQV~aGgRGKa~~~~~hk~~~GGV~l~~s~~-ea~~~a 83 (398)
..+-++|+..|+|+|+..++.+++++ ...++.+|+|+ |+|+---+||| ||.++++.+ ++.+..
T Consensus 121 ~~~~~~l~~~~ipvP~T~i~~~~~~~~~~~~~~~g~pv-VlKp~~Gs~G~--------------gV~~v~~~d~~l~~~~ 185 (318)
T COG0189 121 LYTTQLLAKAGIPVPPTLITRDPDEAAEFVAEHLGFPV-VLKPLDGSGGR--------------GVFLVEDADPELLSLL 185 (318)
T ss_pred HHHHHHHHHCCCCCCCEEEECCHHHHHHHHHHHCCCCE-EEEECCCCCCC--------------CEEEECCCCHHHHHHH
T ss_conf 99999999659999986896584788999997468988-99647888866--------------5599437765699999
Q ss_pred HHHCCCCCCCCCCCCCCCCCCCEEECCCCCCCEEEEEEEEEE
Q ss_conf 986187654421222224433011034555650589999983
Q gi|254781049|r 84 REILGSTLITKQTGPTGSRVNCVYVEDGADILRELYLSLLVD 125 (398)
Q Consensus 84 ~~ilg~~l~t~qt~~~G~~v~~vLVEe~v~~~~E~ylgi~~D 125 (398)
..+.+.. -+.++++|+++....-+..+++.
T Consensus 186 e~~~~~~------------~~~~ivQeyi~~~~~~~rrivv~ 215 (318)
T COG0189 186 ETLTQEG------------RKLIIVQEYIPKAKRDDRRVLVG 215 (318)
T ss_pred HHHHCCC------------CCEEEEECCCCCCCCCEEEEEEE
T ss_conf 9863455------------64298620347677873999998
No 64
>PRK02471 bifunctional glutamate--cysteine ligase/glutathione synthetase; Provisional
Probab=97.79 E-value=0.00023 Score=48.49 Aligned_cols=89 Identities=21% Similarity=0.244 Sum_probs=62.4
Q ss_pred HHHHHHHHHCCCCCCCCEEECCHHHHHHHHHHCCCCEEEEECCCCCCCCCCCCCCCCCCCCCC-EEEE---ECCHHHHHH
Q ss_conf 999999998689888815747999999999872998699971213687656565567777777-0799---589999999
Q gi|254781049|r 6 YQAKALLRKYNVPVAKGVVISSVHAAESAIKTLPGPLYVVKSQIHAGGRGKGRFKELPADSKG-GVRV---ESSLKSVIS 81 (398)
Q Consensus 6 yqaK~lL~~~GIpvp~g~~a~s~~ea~~~a~~ig~p~~VvKaQV~aGgRGKa~~~~~hk~~~G-GV~l---~~s~~ea~~ 81 (398)
.-+|++|+++|+|||+|.-.++.++|.++...+.....|||+. . +.-| ||-+ ..|.++..+
T Consensus 491 ~vtK~vl~~~g~~vp~g~~~~~~~~a~~~~~~~~~k~ivvKpk--------s-------tn~g~gi~if~~~~~~~~~~~ 555 (753)
T PRK02471 491 VVTKKILAEAGFPVPAGDEFTSLEEALADYSLFEDKAIVVKPK--------S-------TNFGLGISIFKEVASLEDYQK 555 (753)
T ss_pred HHHHHHHHHCCCCCCCCCEECCHHHHHHHHHHHCCCCEEECCC--------C-------CCCCCCEEEECCCCCHHHHHH
T ss_conf 9999999985998999874078999999999867996686807--------7-------778776598348999899999
Q ss_pred HHHHHCCCCCCCCCCCCCCCCCCCEEECCCCCCCEEEEEEEE
Q ss_conf 999861876544212222244330110345556505899999
Q gi|254781049|r 82 DIREILGSTLITKQTGPTGSRVNCVYVEDGADILRELYLSLL 123 (398)
Q Consensus 82 ~a~~ilg~~l~t~qt~~~G~~v~~vLVEe~v~~~~E~ylgi~ 123 (398)
+.+.-+.-. +.|+||++++. +||=+=+.
T Consensus 556 A~~~af~~d-------------~~VlVE~~i~G-~dyR~lVI 583 (753)
T PRK02471 556 ALEIAFKED-------------SSVLVEEFIVG-TEYRFFVL 583 (753)
T ss_pred HHHHHHHCC-------------CEEEEEEEECC-CCEEEEEE
T ss_conf 999998569-------------81899973168-70699999
No 65
>COG1038 PycA Pyruvate carboxylase [Energy production and conversion]
Probab=97.76 E-value=0.0016 Score=42.81 Aligned_cols=128 Identities=23% Similarity=0.319 Sum_probs=86.0
Q ss_pred HHHHHHHHHCCCCCCCCE--EECCHHHHHHHHHHCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHHHH
Q ss_conf 999999998689888815--747999999999872998699971213687656565567777777079958999999999
Q gi|254781049|r 6 YQAKALLRKYNVPVAKGV--VISSVHAAESAIKTLPGPLYVVKSQIHAGGRGKGRFKELPADSKGGVRVESSLKSVISDI 83 (398)
Q Consensus 6 yqaK~lL~~~GIpvp~g~--~a~s~~ea~~~a~~ig~p~~VvKaQV~aGgRGKa~~~~~hk~~~GGV~l~~s~~ea~~~a 83 (398)
-.|+.+-.+.|+||-++. .+.+.+|+.+.++++|||+ .+||----|||| -+++.+.+++.+.+
T Consensus 123 v~Ar~~A~~agvPvipgt~~~~~~~ee~~~fa~~~gyPv-miKA~~GGGGRG--------------MR~vr~~~~l~~~~ 187 (1149)
T COG1038 123 VKARNAAIKAGVPVIPGTDGPIETIEEALEFAEEYGYPV-MIKAAAGGGGRG--------------MRVVRSEADLAEAF 187 (1149)
T ss_pred HHHHHHHHHCCCCCCCCCCCCCCCHHHHHHHHHHCCCCE-EEEECCCCCCCC--------------EEEECCHHHHHHHH
T ss_conf 889999997599855699998212999999998669858-999714798665--------------26625888999999
Q ss_pred HH-------HCCCCCCCCCCCCCCCCCCCEEECCCCCCCEEEEEEEEEECCCCCEEEEEECCCCCCHHHHHHHCHHHHEE
Q ss_conf 98-------61876544212222244330110345556505899999834778048998447884024555748312203
Q gi|254781049|r 84 RE-------ILGSTLITKQTGPTGSRVNCVYVEDGADILRELYLSLLVDRTSGMVAFIASTQGGMDIEEVAKDYPQKIFK 156 (398)
Q Consensus 84 ~~-------ilg~~l~t~qt~~~G~~v~~vLVEe~v~~~~E~ylgi~~Dr~~~~~vii~S~~GGvdIE~va~~~p~~I~~ 156 (398)
.+ -||+ ..|+||..++-.+..-+-|+-| ..|.++-++- ---.|. +.++..
T Consensus 188 ~~AksEAkaAFG~--------------~eVyvEk~ve~pkHIEVQiLgD-~~GnvvHLfE--RDCSvQ---RRhQKV--- 244 (1149)
T COG1038 188 ERAKSEAKAAFGN--------------DEVYVEKLVENPKHIEVQILGD-THGNVVHLFE--RDCSVQ---RRHQKV--- 244 (1149)
T ss_pred HHHHHHHHHHCCC--------------CCEEHHHHHCCCCEEEEEEEEC-CCCCEEEEEE--CCCCHH---HCCCEE---
T ss_conf 9988999974189--------------8066565524865268998605-7787888862--355331---014403---
Q ss_pred EECCCCCCCCHHHHH
Q ss_conf 321444578957888
Q gi|254781049|r 157 LLIDPLIGVTSEDVA 171 (398)
Q Consensus 157 ~~id~~~gl~~~~~~ 171 (398)
+.+.|...+++..-.
T Consensus 245 VE~APa~~L~~~~R~ 259 (1149)
T COG1038 245 VEVAPAPYLSPELRD 259 (1149)
T ss_pred EEECCCCCCCHHHHH
T ss_conf 785688889999999
No 66
>pfam06263 consensus
Probab=97.75 E-value=0.0011 Score=44.06 Aligned_cols=129 Identities=17% Similarity=0.186 Sum_probs=85.9
Q ss_pred CCEEEEECCCHHHHHHHHHHHHCCC--------------------CCCEEEECCCCC----------CHHHHHHHHHHHH
Q ss_conf 8179995550368999999996589--------------------962488427888----------9899999999986
Q gi|254781049|r 267 GNIGCMVNGAGLAMATMDIIKLYGG--------------------APANFLDVGGGA----------DQDKVAAAFKIIT 316 (398)
Q Consensus 267 G~Ig~~vnGaGlamatmD~i~~~Gg--------------------~pANFlD~gG~a----------~~e~~~~a~~~il 316 (398)
+.|-=+-.|+-|+=-.|=++....+ .--.|+|+|-.. +++.=.+.+.--.
T Consensus 339 ~~irGLysGGTLa~EA~~l~~~~l~~~~sn~~~~g~~~L~d~~~s~gH~iiDlGDD~fT~GRPHPMIDPs~R~e~i~~~a 418 (514)
T pfam06263 339 KYIRGLYSGGTLADEAAMLLSEALGDVYSNIPLEGEMLLANIDKSQGHTIIDLGDDMFTVGRPHPMIDPTLRNERILQEA 418 (514)
T ss_pred CEEEEEECCHHHHHHHHHHHHHHCCCCCCCCCCCCHHCCCCCCCCCCCEEEECCCCCCCCCCCCCCCCHHHHHHHHHHHH
T ss_conf 74899954715999999999986087667888873002576333589568866774345789978868478999999971
Q ss_pred CCCCCCEEEEECCCCHHHHHHHHHHHHHHHHHC-------CCCCCEEEECCCCC-----HHHHHHHHHHCCCCEEEECCH
Q ss_conf 199865899963586132899999999999972-------99987999748985-----899999999769958994998
Q gi|254781049|r 317 SDSSVKGILINIFGGIMRCDVLVKGILSAVKEV-------KINIPLVMRLEGAN-----VDIGNRLIAESGLNVITAIDL 384 (398)
Q Consensus 317 ~~~~vk~iliNifGGI~~cd~vA~gii~a~~~~-------~~~~pivvRl~Gtn-----~~~g~~il~~~g~~~~~~~~~ 384 (398)
.||.+-+||+-+-=|-=...+.|..++.|+++. +..+++|+-.+||. .++..+.|+++| +..+++-
T Consensus 419 ~Dp~v~VILlDvVLGyGah~DPag~L~paI~~a~~~a~~~gr~l~vvatV~GT~~DPQ~~~~Q~~~L~~AG--v~V~~SN 496 (514)
T pfam06263 419 ADPEVAVILLDVVLGYGAHADPAGELLPAIEEARAIAKADGRELAVIATVCGTEADPQGRSEQIKILEEAG--VLVVSSN 496 (514)
T ss_pred CCCCCEEEEEEEEECCCCCCCHHHHHHHHHHHHHHHHHHCCCCEEEEEEECCCCCCCCCHHHHHHHHHHCC--EEEECCC
T ss_conf 49972289998532268999848999999999998887538970899997388989748999999999789--5997585
Q ss_pred HHHHHHHHHHHHC
Q ss_conf 9999999998506
Q gi|254781049|r 385 DDAAQKIVHAVKG 397 (398)
Q Consensus 385 ~~A~~~~v~~~k~ 397 (398)
.+|++.|.+++|.
T Consensus 497 a~A~~~A~~l~~~ 509 (514)
T pfam06263 497 AQAVRLAKKIAKL 509 (514)
T ss_pred HHHHHHHHHHHHH
T ss_conf 9999999999987
No 67
>TIGR01235 pyruv_carbox pyruvate carboxylase; InterPro: IPR005930 In the postabsorptive state, blood glucose concentration is kept constant by a combination of glycogenolysis and gluconeogenesis. During prolonged fasting, when hepatic glycogen is exhausted, gluconeogenesis becomes the only source of plasma glucose. Gluconeogenesis (the production of new glucose molecules) occurs mainly in liver and, to a small extent, in kidneys. Pyruvate carboxylase (6.4.1.1 from EC), a member of the biotin-dependent enzyme family, catalyses the ATP-dependent carboxylation of pyruvate to oxaloacetate, thus playing a crucial role in gluconeogenesis. ATP + pyruvate + HCO3- = ADP + phosphate + oxaloacetate Most well characterised forms of active enzyme consist of four identical subunits arranged in a tetrahedron-like structure. Each subunit contains three functional domains: the biotin carboxylation domain, the transcarboxylation domain and the biotin carboxyl carrier domain.; GO: 0004736 pyruvate carboxylase activity, 0006094 gluconeogenesis, 0005737 cytoplasm.
Probab=97.75 E-value=0.00062 Score=45.60 Aligned_cols=167 Identities=23% Similarity=0.332 Sum_probs=100.1
Q ss_pred HHHHHHHHCCCCCCCC--EEECCHHHHHHHHHHCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHHHHH
Q ss_conf 9999999868988881--57479999999998729986999712136876565655677777770799589999999999
Q gi|254781049|r 7 QAKALLRKYNVPVAKG--VVISSVHAAESAIKTLPGPLYVVKSQIHAGGRGKGRFKELPADSKGGVRVESSLKSVISDIR 84 (398)
Q Consensus 7 qaK~lL~~~GIpvp~g--~~a~s~~ea~~~a~~ig~p~~VvKaQV~aGgRGKa~~~~~hk~~~GGV~l~~s~~ea~~~a~ 84 (398)
.|.++=.+.||||-|| -.++|.+|+...++..|||+ ++||=-=-|||| -|++++.+|+.++++
T Consensus 122 ~AR~~A~~aGvPvvPgt~Gp~~t~eev~~f~~~~GYPv-i~KAs~GGGGRG--------------MRvvR~~~dv~~~~~ 186 (1169)
T TIGR01235 122 AARNLAIKAGVPVVPGTDGPVETLEEVLDFAKAIGYPV-IIKASYGGGGRG--------------MRVVRSEEDVADAFQ 186 (1169)
T ss_pred HHHHHHHHCCCCEECCCCCCHHHHHHHHHHHHHCCCCE-EEEECCCCCCCC--------------CEEECCHHHHHHHHH
T ss_conf 99988887788763688687525999999997569958-987216889720--------------168607567999988
Q ss_pred HHCCCCCCCCCCCCCCCCCCCEEECCCCCCCEEEEEEEEEECCCCCEEEEEECCCCCCHHHHHHHCHHHHEEEECCCCCC
Q ss_conf 86187654421222224433011034555650589999983477804899844788402455574831220332144457
Q gi|254781049|r 85 EILGSTLITKQTGPTGSRVNCVYVEDGADILRELYLSLLVDRTSGMVAFIASTQGGMDIEEVAKDYPQKIFKLLIDPLIG 164 (398)
Q Consensus 85 ~ilg~~l~t~qt~~~G~~v~~vLVEe~v~~~~E~ylgi~~Dr~~~~~vii~S~~GGvdIE~va~~~p~~I~~~~id~~~g 164 (398)
+= .+.-.+ .=|. ..++||+.++-.|..=+=++-| ..|.+|=+|=. -=. |-+.++.. +.+.|..-
T Consensus 187 rA-~sEA~A----AFGn--d~~yvEklie~pkHiEvQ~LGD-~~GNVVHLFER--DCS---VQRRhQKV---vE~APA~~ 250 (1169)
T TIGR01235 187 RA-KSEAKA----AFGN--DEVYVEKLIERPKHIEVQLLGD-KHGNVVHLFER--DCS---VQRRHQKV---VEVAPAPS 250 (1169)
T ss_pred HH-HHHHHH----CCCC--CEEEEEEECCCCCEEEEEEEEC-CCCCEEEEEEC--CCC---CEEECCEE---EEECCCCC
T ss_conf 87-688731----0489--8069851024882078987634-88987888750--776---20005507---88678877
Q ss_pred CCHHHH-------HHHHHHCCCCHHHHHHHHHHHHHHHHHHHHC-CCCCCCCCEEE
Q ss_conf 895788-------8788751988899885999999998999955-97510232679
Q gi|254781049|r 165 VTSEDV-------ASLCDMLELQGQARIDGGDLFPNLYKAFCDK-DMSLLEINPLI 212 (398)
Q Consensus 165 l~~~~~-------~~l~~~lg~~~~~~~~~~~ii~~L~~~f~e~-Da~liEINPLv 212 (398)
|+++.- -+||+..|+.+.--.+| |.. .+. .+-.|||||=+
T Consensus 251 Ls~e~Rd~~~~~AvkLAk~~nY~nAGTvEF------L~d--~~~G~FYFIEvNpRi 298 (1169)
T TIGR01235 251 LSREVRDEIAEYAVKLAKEVNYINAGTVEF------LVD--NDTGKFYFIEVNPRI 298 (1169)
T ss_pred CCHHHHHHHHHHHHHHHHHCCCCCCCCEEE------EEE--CCCCCEEEEEECCCE
T ss_conf 888899999999999987428988872488------555--488937789988800
No 68
>PRK06091 membrane protein FdrA; Validated
Probab=97.48 E-value=0.0029 Score=41.19 Aligned_cols=129 Identities=14% Similarity=0.182 Sum_probs=81.7
Q ss_pred CCEEEEECCCHHHHHHHHHHHHCCCCC---------------CEEEECCCCC----------CHHHHHHHHHHHHCCCCC
Q ss_conf 817999555036899999999658996---------------2488427888----------989999999998619986
Q gi|254781049|r 267 GNIGCMVNGAGLAMATMDIIKLYGGAP---------------ANFLDVGGGA----------DQDKVAAAFKIITSDSSV 321 (398)
Q Consensus 267 G~Ig~~vnGaGlamatmD~i~~~Gg~p---------------ANFlD~gG~a----------~~e~~~~a~~~il~~~~v 321 (398)
+.|-=+-.|+-|+=-.|=++...-+-| -.|+|+|-.. +++.=.+.+.--..||.+
T Consensus 331 ~~irGLysGGTLa~EA~~ll~~~l~~~~~~~~~~g~~l~s~gH~iiDlGDD~fT~GRPHPMIDPs~R~e~i~~~a~Dp~v 410 (555)
T PRK06091 331 GFICGLYTGGTLAAEAAGLLAGHLGVEADDEHHHGMMLDADGHQIIDLGDDFYTVGRPHPMIDPTLRNQLIADLGAKPQV 410 (555)
T ss_pred CEEEEEECCCHHHHHHHHHHHHHHCCCCCCCCCCCCHHHCCCCEEEECCCCCCCCCCCCCCCCHHHHHHHHHHHHCCCCC
T ss_conf 73799953712999999999987099888533544111058956986577423578988886827799999997349972
Q ss_pred CEEEEECCCCHHHHHHHHHHHHHHHHH------CCCCCCEEEECCCCC-----HHHHHHHHHHCCCCEEEECCHHHHHHH
Q ss_conf 589996358613289999999999997------299987999748985-----899999999769958994998999999
Q gi|254781049|r 322 KGILINIFGGIMRCDVLVKGILSAVKE------VKINIPLVMRLEGAN-----VDIGNRLIAESGLNVITAIDLDDAAQK 390 (398)
Q Consensus 322 k~iliNifGGI~~cd~vA~gii~a~~~------~~~~~pivvRl~Gtn-----~~~g~~il~~~g~~~~~~~~~~~A~~~ 390 (398)
-+||+-+-=|.=...+.|..++.|+++ -+..+++|+-..||. .++..+.|+++| +..+++-.+|++.
T Consensus 411 ~VILlDvVLGyGah~DPag~L~paI~~a~~a~~~gr~l~vVa~V~GT~~DPQ~~~~Q~~~L~~AG--v~V~~SNa~A~~~ 488 (555)
T PRK06091 411 RVLLLDVVIGFGATADPAASLVSAWQKACAARSDNQPLYAIATVTGTERDPQCRSQQIATLEDAG--IAVVSSLPEATLL 488 (555)
T ss_pred EEEEEEEEECCCCCCCHHHHHHHHHHHHHHHHHCCCCEEEEEEEECCCCCCCCHHHHHHHHHHCC--EEEECCCHHHHHH
T ss_conf 28999875326899984899999999999755338963899998078889738999999999689--5997573999999
Q ss_pred HHHHHHC
Q ss_conf 9998506
Q gi|254781049|r 391 IVHAVKG 397 (398)
Q Consensus 391 ~v~~~k~ 397 (398)
|+++.+.
T Consensus 489 A~~l~~~ 495 (555)
T PRK06091 489 AAALIRP 495 (555)
T ss_pred HHHHHCC
T ss_conf 9997088
No 69
>PRK05678 succinyl-CoA synthetase subunit alpha; Validated
Probab=97.40 E-value=0.0059 Score=39.14 Aligned_cols=125 Identities=16% Similarity=0.306 Sum_probs=92.6
Q ss_pred EEECCCCEEEEECCCHHHHHHHHHHHHCCCCCCEEEECCCCCCH-HHHHHHHHHHHCCCCCCEEEEECCCCHHHH--HHH
Q ss_conf 44228817999555036899999999658996248842788898-999999999861998658999635861328--999
Q gi|254781049|r 262 YIALDGNIGCMVNGAGLAMATMDIIKLYGGAPANFLDVGGGADQ-DKVAAAFKIITSDSSVKGILINIFGGIMRC--DVL 338 (398)
Q Consensus 262 yv~LdG~Ig~~vnGaGlamatmD~i~~~Gg~pANFlD~gG~a~~-e~~~~a~~~il~~~~vk~iliNifGGI~~c--d~v 338 (398)
++-..|+||++..-++|+-..+|.+...|.=-.-+.-+||.+-. ......++.+..||+.|+|++ +|-|--. ...
T Consensus 141 ~~~~pG~VgiiSrSGtLtye~~~~l~~~g~G~S~~VgiGgD~i~G~~f~d~L~~f~~Dp~T~~Ivl--iGEiGG~~E~~a 218 (289)
T PRK05678 141 HIHKKGRVGIVSRSGTLTYEAVAQLTDLGLGQSTCVGIGGDPINGTNFIDVLKAFEEDPETDAIVM--IGEIGGSAEEEA 218 (289)
T ss_pred CCCCCCCEEEEECCCCHHHHHHHHHHHCCCCEEEEEECCCCCCCCCCHHHHHHHHHCCCCCCEEEE--EECCCCHHHHHH
T ss_conf 247798689997776579999999997698669898527887678449999999742977327999--975598799999
Q ss_pred HHHHHHHHHHCCCCCCEEEECCCCCHHHHHH--------------------HHHHCCCCEEEECCHHHHHHHHHHHH
Q ss_conf 9999999997299987999748985899999--------------------99976995899499899999999985
Q gi|254781049|r 339 VKGILSAVKEVKINIPLVMRLEGANVDIGNR--------------------LIAESGLNVITAIDLDDAAQKIVHAV 395 (398)
Q Consensus 339 A~gii~a~~~~~~~~pivvRl~Gtn~~~g~~--------------------il~~~g~~~~~~~~~~~A~~~~v~~~ 395 (398)
|+- .++ ++++|||.-..|..+-+|++ -|+++|+. .+++..+-.+..-+..
T Consensus 219 a~~----i~~-~~~KPVva~iaG~~AP~gk~mGHAGAIi~~~~gta~~K~~al~~aGv~--Va~~p~~i~~~~~~~l 288 (289)
T PRK05678 219 AEW----IKA-NVTKPVVGYIAGVTAPPGKRMGHAGAIISGGKGTAEEKIEALEAAGVK--VARSPSEIGKTLKEVL 288 (289)
T ss_pred HHH----HHH-CCCCCEEEEEECCCCCCCCCCCCCCEECCCCCCCHHHHHHHHHHCCCE--ECCCHHHHHHHHHHHH
T ss_conf 999----985-589967999951458999723321222048988899999999987797--5799999999999984
No 70
>PTZ00187 succinyl-CoA synthetase alpha subunit; Provisional
Probab=97.34 E-value=0.005 Score=39.64 Aligned_cols=127 Identities=17% Similarity=0.320 Sum_probs=95.5
Q ss_pred EECCCCEEEEECCCHHHHHHHHHHHHCCCCCCEEEECCCCC-CHHHHHHHHHHHHCCCCCCEEEEECCCCHHHHHHHHHH
Q ss_conf 42288179995550368999999996589962488427888-98999999999861998658999635861328999999
Q gi|254781049|r 263 IALDGNIGCMVNGAGLAMATMDIIKLYGGAPANFLDVGGGA-DQDKVAAAFKIITSDSSVKGILINIFGGIMRCDVLVKG 341 (398)
Q Consensus 263 v~LdG~Ig~~vnGaGlamatmD~i~~~Gg~pANFlD~gG~a-~~e~~~~a~~~il~~~~vk~iliNifGGI~~cd~vA~g 341 (398)
+--.|+||++...+.|+--..+.+...|.=.--..-+||.+ .-....+++++...||+.|+|++ .|-|=-.++ +-
T Consensus 158 i~~pG~VGivSRSGTLTyE~~~~lt~~G~GqSt~VgIGGDpi~Gt~f~d~L~~f~~D~~T~aIVl--iGEIGG~~E--e~ 233 (309)
T PTZ00187 158 IHQKGKIGIVSRSGTLTYEAVAQTTAVGLGQSTCVGIGGDPFNGTNFIDCLKLFLNDPETEGIIL--IGEIGGTAE--EE 233 (309)
T ss_pred HCCCCCEEEEECCCCHHHHHHHHHHHCCCCEEEEEEECCCCCCCCCHHHHHHHHHCCCCCCEEEE--EECCCCHHH--HH
T ss_conf 55788358994477528999999986698669999846987589789999999862957658999--816598699--99
Q ss_pred HHHHHHHCCCCCCEEEECCCCCHHHHHHH--------------------HHHCCCCEEEECCHHHHHHHHHHHH
Q ss_conf 99999972999879997489858999999--------------------9976995899499899999999985
Q gi|254781049|r 342 ILSAVKEVKINIPLVMRLEGANVDIGNRL--------------------IAESGLNVITAIDLDDAAQKIVHAV 395 (398)
Q Consensus 342 ii~a~~~~~~~~pivvRl~Gtn~~~g~~i--------------------l~~~g~~~~~~~~~~~A~~~~v~~~ 395 (398)
..+.+++...++|+|.-+.|..+-.|+++ |+++|++ .+++..+-.+...++.
T Consensus 234 aA~~Ik~~~~~KPVva~IAG~~AP~gkrmGHAGAIi~~~~gta~~K~~al~~AGv~--Va~~p~ei~~~v~~~l 305 (309)
T PTZ00187 234 AADWIKNNPTKKPVVSFIAGITAPPGRRMGHAGAIVSGGKGTAKGKIEALRAAGVT--VSKSPAQLGKTMAEVM 305 (309)
T ss_pred HHHHHHHCCCCCCEEEEEEECCCCCCCCCCCHHEEECCCCCCHHHHHHHHHHCCCE--ECCCHHHHHHHHHHHH
T ss_conf 99999966999988999812568999704320001028988899999999988698--7899999999999999
No 71
>COG1181 DdlA D-alanine-D-alanine ligase and related ATP-grasp enzymes [Cell envelope biogenesis, outer membrane]
Probab=97.27 E-value=0.0014 Score=43.25 Aligned_cols=94 Identities=22% Similarity=0.202 Sum_probs=65.2
Q ss_pred HHHHHHHHHHCCCCCCCCEEECC----HHHHHHHHHHCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHH
Q ss_conf 79999999986898888157479----99999999872998699971213687656565567777777079958999999
Q gi|254781049|r 5 EYQAKALLRKYNVPVAKGVVISS----VHAAESAIKTLPGPLYVVKSQIHAGGRGKGRFKELPADSKGGVRVESSLKSVI 80 (398)
Q Consensus 5 EyqaK~lL~~~GIpvp~g~~a~s----~~ea~~~a~~ig~p~~VvKaQV~aGgRGKa~~~~~hk~~~GGV~l~~s~~ea~ 80 (398)
-...|.+++..|+|+++....+. ..........++||+ +||.- |. .| .=|+..+++.+|..
T Consensus 104 k~~~K~~~~~~g~~~a~~~~~~~~~~~~~~~e~~~~~l~~p~-~Vkp~-----~~--------gS-Svg~~~v~~~~d~~ 168 (317)
T COG1181 104 KIVTKRLFKAEGLPVAPYVALTRDEYSSVIVEEVEEGLGFPL-FVKPA-----RE--------GS-SVGRSPVNVEGDLQ 168 (317)
T ss_pred HHHHHHHHHHCCCCCCHHHHHHCCCCHHHHHHHHHCCCCCCE-EEECC-----CC--------EE-EEEEEECCEECCHH
T ss_conf 999988998678651235675334520478887741468878-99858-----73--------11-36799883504369
Q ss_pred HHHHHHCCCCCCCCCCCCCCCCCCCEEECCCCCCCEEEEEEEEEECC
Q ss_conf 99998618765442122222443301103455565058999998347
Q gi|254781049|r 81 SDIREILGSTLITKQTGPTGSRVNCVYVEDGADILRELYLSLLVDRT 127 (398)
Q Consensus 81 ~~a~~ilg~~l~t~qt~~~G~~v~~vLVEe~v~~~~E~ylgi~~Dr~ 127 (398)
.+.+..+... +.+++|+.+. .+|+-+++..+..
T Consensus 169 ~~~e~a~~~d-------------~~vl~e~~~~-~rei~v~vl~~~~ 201 (317)
T COG1181 169 SALELAFKYD-------------RDVLREQGIT-GREIEVGVLGNDY 201 (317)
T ss_pred HHHHHHHHHC-------------CCCEECCCCC-CCEEEEEECCCCC
T ss_conf 9999999847-------------8512003776-6558986358865
No 72
>KOG0369 consensus
Probab=96.87 E-value=0.042 Score=33.51 Aligned_cols=106 Identities=27% Similarity=0.377 Sum_probs=74.5
Q ss_pred HHHHHHHHCCCCCCCCE--EECCHHHHHHHHHHCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHHHHH
Q ss_conf 99999998689888815--7479999999998729986999712136876565655677777770799589999999999
Q gi|254781049|r 7 QAKALLRKYNVPVAKGV--VISSVHAAESAIKTLPGPLYVVKSQIHAGGRGKGRFKELPADSKGGVRVESSLKSVISDIR 84 (398)
Q Consensus 7 qaK~lL~~~GIpvp~g~--~a~s~~ea~~~a~~ig~p~~VvKaQV~aGgRGKa~~~~~hk~~~GGV~l~~s~~ea~~~a~ 84 (398)
.|..+--+.|+||-+|- -+++.+||.+.+++.|+|+ .+||----|||| .+++.+.+++.+.++
T Consensus 150 ~AR~~Ai~agVpvVPGTpgPitt~~EA~eF~k~yG~Pv-I~KAAyGGGGRG--------------mRvVr~~e~vee~f~ 214 (1176)
T KOG0369 150 AARAIAIEAGVPVVPGTPGPITTVEEALEFVKEYGLPV-IIKAAYGGGGRG--------------MRVVRSGEDVEEAFQ 214 (1176)
T ss_pred HHHHHHHHCCCCCCCCCCCCCCCHHHHHHHHHHCCCCE-EEEECCCCCCCC--------------EEEEECHHHHHHHHH
T ss_conf 88899997199715899997542999999998619838-996101689764--------------377502556999999
Q ss_pred HHCCCCCCCCCCCCCCCCCCCEEECCCCCCCEEEEEEEEEECCCCCEEEEE
Q ss_conf 861876544212222244330110345556505899999834778048998
Q gi|254781049|r 85 EILGSTLITKQTGPTGSRVNCVYVEDGADILRELYLSLLVDRTSGMVAFIA 135 (398)
Q Consensus 85 ~ilg~~l~t~qt~~~G~~v~~vLVEe~v~~~~E~ylgi~~Dr~~~~~vii~ 135 (398)
.--+-- ++. -| --.+.||.+++--+..-+-++-| ..|.++-++
T Consensus 215 Ra~SEA----~aa-FG--nG~~FvEkF~ekPrHIEvQllgD-~~GNvvHLy 257 (1176)
T KOG0369 215 RAYSEA----LAA-FG--NGTLFVEKFLEKPRHIEVQLLGD-KHGNVVHLY 257 (1176)
T ss_pred HHHHHH----HHH-CC--CCEEEHHHHHCCCCEEEEEEECC-CCCCEEEEE
T ss_conf 888999----986-17--86153786625865268987213-568789876
No 73
>KOG0370 consensus
Probab=96.67 E-value=0.0012 Score=43.77 Aligned_cols=90 Identities=19% Similarity=0.258 Sum_probs=55.2
Q ss_pred HHCCCCCCCCEEECCHHHHHHHHHHCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHHHHHHHCCCCCC
Q ss_conf 98689888815747999999999872998699971213687656565567777777079958999999999986187654
Q gi|254781049|r 13 RKYNVPVAKGVVISSVHAAESAIKTLPGPLYVVKSQIHAGGRGKGRFKELPADSKGGVRVESSLKSVISDIREILGSTLI 92 (398)
Q Consensus 13 ~~~GIpvp~g~~a~s~~ea~~~a~~ig~p~~VvKaQV~aGgRGKa~~~~~hk~~~GGV~l~~s~~ea~~~a~~ilg~~l~ 92 (398)
.+.+.++.++..+++.+||.++++.+|||+ ++.+----||-|-+ +++|.+|+.+-+.+-|.++
T Consensus 507 ~ei~e~ia~s~a~~sie~al~aae~l~ypv-ivRaayalgglgSg--------------fa~n~eeL~~l~~~a~a~s-- 569 (1435)
T KOG0370 507 NEINEKIAPSEAVSTIEEALEAAERLGYPV-IVRAAYALGGLGSG--------------FANNEEELQDLAAQALALS-- 569 (1435)
T ss_pred HHHCCCCCCHHHHHHHHHHHHHHHHCCCHH-HHHHHHHHCCCCCC--------------CCCCHHHHHHHHHHCCCCC--
T ss_conf 763150562566767999998888628289-99999985376643--------------3444899999976431258--
Q ss_pred CCCCCCCCCCCCCEEECCCCCCCEEEEEEEEEECCCCC
Q ss_conf 42122222443301103455565058999998347780
Q gi|254781049|r 93 TKQTGPTGSRVNCVYVEDGADILRELYLSLLVDRTSGM 130 (398)
Q Consensus 93 t~qt~~~G~~v~~vLVEe~v~~~~E~ylgi~~Dr~~~~ 130 (398)
.++|||+.....+|.-.-+++|.-..+
T Consensus 570 -----------~QilvekSlkGwkevEyevvrDa~~nc 596 (1435)
T KOG0370 570 -----------PQILVEKSLKGWKEVEYEVVRDAYDNC 596 (1435)
T ss_pred -----------CEEEEHHHHCCCCCEEEEEEECCCCCH
T ss_conf -----------615422332443434899980200040
No 74
>PRK06849 hypothetical protein; Provisional
Probab=96.35 E-value=0.036 Score=33.95 Aligned_cols=95 Identities=15% Similarity=0.087 Sum_probs=58.1
Q ss_pred HHHHHHHCCCCCCCCEEECCHHHHHHHHHHCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHHHHHHHC
Q ss_conf 99999986898888157479999999998729986999712136876565655677777770799589999999999861
Q gi|254781049|r 8 AKALLRKYNVPVAKGVVISSVHAAESAIKTLPGPLYVVKSQIHAGGRGKGRFKELPADSKGGVRVESSLKSVISDIREIL 87 (398)
Q Consensus 8 aK~lL~~~GIpvp~g~~a~s~~ea~~~a~~ig~p~~VvKaQV~aGgRGKa~~~~~hk~~~GGV~l~~s~~ea~~~a~~il 87 (398)
--++..+.|+|+|++.++++++++......-.++++|+|+ + .+|+. .+|....+.+++.. +
T Consensus 120 F~~~a~~lGl~vP~T~~i~s~edv~~~~~~~~~~~~ilKP-v--~~~~~-----------~~v~~~~~~~~l~~----l- 180 (387)
T PRK06849 120 FIQQARSLGLSAPKTYLITDPEAIINFDFKTPHTPYVLKP-I--YSRFV-----------RRVDLTKTKAAVLK----L- 180 (387)
T ss_pred HHHHHHHCCCCCCCEEEECCHHHHHHHHHCCCCCCEEECC-C--CCCCC-----------CEEEECCCHHHHHC----C-
T ss_conf 9999997499999889818999998655336689789823-7--66653-----------33652159778615----8-
Q ss_pred CCCCCCCCCCCCCCCCCCEEECCCCCCCEEEEEEEEEECCCCCEEEEE
Q ss_conf 876544212222244330110345556505899999834778048998
Q gi|254781049|r 88 GSTLITKQTGPTGSRVNCVYVEDGADILRELYLSLLVDRTSGMVAFIA 135 (398)
Q Consensus 88 g~~l~t~qt~~~G~~v~~vLVEe~v~~~~E~ylgi~~Dr~~~~~vii~ 135 (398)
++ +.+ +.++++|.++...-++.++..+ |.++...
T Consensus 181 --~~-s~~--------~p~v~Qe~I~G~~~ct~al~~~---Gkv~A~~ 214 (387)
T PRK06849 181 --PI-SHK--------SPWIMQEFIPGQEYCSYSIVRS---GELRAHS 214 (387)
T ss_pred --CC-CCC--------CCEEEEEECCCCEEEEEEEEEC---CEEEEEE
T ss_conf --87-667--------9828998716967589999789---9999999
No 75
>KOG0368 consensus
Probab=96.31 E-value=0.026 Score=34.90 Aligned_cols=88 Identities=24% Similarity=0.365 Sum_probs=64.7
Q ss_pred EEECCHHHHHHHHHHCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHHHHHHHCCCCCCCCCCCCCCCC
Q ss_conf 57479999999998729986999712136876565655677777770799589999999999861876544212222244
Q gi|254781049|r 23 VVISSVHAAESAIKTLPGPLYVVKSQIHAGGRGKGRFKELPADSKGGVRVESSLKSVISDIREILGSTLITKQTGPTGSR 102 (398)
Q Consensus 23 ~~a~s~~ea~~~a~~ig~p~~VvKaQV~aGgRGKa~~~~~hk~~~GGV~l~~s~~ea~~~a~~ilg~~l~t~qt~~~G~~ 102 (398)
..+.+++|+.++++.||||+ .+|| --||-|| |++-|.|.++....+++..+- -.|-+
T Consensus 223 acv~~~eegLeaae~IGfPv-MIKA--SEGGGGK------------GIRkv~n~ddF~~lf~qv~~E--------vPGSP 279 (2196)
T KOG0368 223 ACVRNVEEGLEAAEKIGFPV-MIKA--SEGGGGK------------GIRKVENEDDFKALFKQVQNE--------VPGSP 279 (2196)
T ss_pred HHCCCHHHHHHHHHHCCCCE-EEEE--CCCCCCC------------CEEECCCHHHHHHHHHHHHHH--------CCCCC
T ss_conf 43088889999998629836-9995--4578976------------613045667899999999855--------89995
Q ss_pred CCCEEECCCCCCCEEEEEEEEEECCCCCEEEEEEC
Q ss_conf 33011034555650589999983477804899844
Q gi|254781049|r 103 VNCVYVEDGADILRELYLSLLVDRTSGMVAFIAST 137 (398)
Q Consensus 103 v~~vLVEe~v~~~~E~ylgi~~Dr~~~~~vii~S~ 137 (398)
+.+-+-++..+.+-+-++-| +.|..+-++|.
T Consensus 280 ---IFlMK~a~~ARHlEVQlLaD-qYGn~IsLfgR 310 (2196)
T KOG0368 280 ---IFLMKLADQARHLEVQLLAD-QYGNVISLFGR 310 (2196)
T ss_pred ---EEHHHHCCCCCEEEEEHHHH-HHCCEEEEECC
T ss_conf ---55200336754021002245-30878777436
No 76
>cd07022 S49_Sppa_36K_type Signal peptide peptidase A (SppA) 36K type, a serine protease, has catalytic Ser-Lys dyad. Signal peptide peptidase A (SppA; Peptidase S49; Protease IV) 36K type: SppA is found in all three domains of life and is involved in the cleavage of signal peptides after their removal from the precursor proteins by signal peptidases. Members in this subfamily are all bacterial and include sohB peptidase and protein C. These are sometimes referred to as 36K type since they contain only one domain, unlike E. coli SppA that also contains an amino-terminal domain. Site-directed mutagenesis and sequence analysis have shown these SppAs to be serine proteases. The predicted active site serine for members in this family occurs in a transmembrane domain. Mutagenesis studies also suggest that the catalytic center comprises a Ser-Lys dyad and not the usual Ser-His-Asp catalytic triad found in the majority of serine proteases.
Probab=96.29 E-value=0.033 Score=34.21 Aligned_cols=24 Identities=25% Similarity=0.267 Sum_probs=16.9
Q ss_pred CCCHHHHHHHHHHHHHHHHHHHHC
Q ss_conf 988899885999999998999955
Q gi|254781049|r 178 ELQGQARIDGGDLFPNLYKAFCDK 201 (398)
Q Consensus 178 g~~~~~~~~~~~ii~~L~~~f~e~ 201 (398)
.++.+..+.+...+..+|+.|.+.
T Consensus 146 ~~s~e~~~~~q~~ld~~~~~F~~~ 169 (214)
T cd07022 146 PLSDEARARLQAEVDALYAMFVAA 169 (214)
T ss_pred CCCHHHHHHHHHHHHHHHHHHHHH
T ss_conf 568899999999999999999999
No 77
>PRK13277 5-formaminoimidazole-4-carboxamide-1-(beta)-D-ribofuranosyl 5'-monophosphate synthetase-like protein; Provisional
Probab=96.25 E-value=0.043 Score=33.47 Aligned_cols=97 Identities=13% Similarity=0.218 Sum_probs=66.2
Q ss_pred HHHHHCCCCCCCCEEECCHHHHHHHHHHCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHHHHHHHCCC
Q ss_conf 99998689888815747999999999872998699971213687656565567777777079958999999999986187
Q gi|254781049|r 10 ALLRKYNVPVAKGVVISSVHAAESAIKTLPGPLYVVKSQIHAGGRGKGRFKELPADSKGGVRVESSLKSVISDIREILGS 89 (398)
Q Consensus 10 ~lL~~~GIpvp~g~~a~s~~ea~~~a~~ig~p~~VvKaQV~aGgRGKa~~~~~hk~~~GGV~l~~s~~ea~~~a~~ilg~ 89 (398)
.||.+.|||.|+ ...+|+| |..|+ .||-+=-.|+-|+ |--+++|++|..+.+++++..
T Consensus 129 ~LLe~Agi~~Pk--~~~~Pee-------IDr~V-IVK~~gAkg~~gr------------GyF~a~s~~ef~~k~~~li~~ 186 (363)
T PRK13277 129 RLLEKAGIPRPR--TFKPPEE-------IDRPV-IVKLPEAKRRLER------------GFFIAASYKDFYEKSERLIKQ 186 (363)
T ss_pred HHHHHCCCCCCC--CCCCHHH-------CCCCE-EEEECCCCCCCCC------------EEEEECCHHHHHHHHHHHHHC
T ss_conf 999867999870--0599666-------78526-9974567787763------------589967989999999999875
Q ss_pred CCCCCCCCCCCCCCCCEEECCCCCCCEEEEEEEEEECCCCCEEEEE
Q ss_conf 6544212222244330110345556505899999834778048998
Q gi|254781049|r 90 TLITKQTGPTGSRVNCVYVEDGADILRELYLSLLVDRTSGMVAFIA 135 (398)
Q Consensus 90 ~l~t~qt~~~G~~v~~vLVEe~v~~~~E~ylgi~~Dr~~~~~vii~ 135 (398)
-+++. .-++...|||.+-. --||+-...+|-.+..=+++
T Consensus 187 G~I~~------e~l~~~~IeEyv~G-~~~~~~fFySpl~~~lEllg 225 (363)
T PRK13277 187 GVIDR------EDLEKARIEEYVIG-AHFNFNYFYSPIRDRVELLG 225 (363)
T ss_pred CCCCH------HHCCCCEEEEEECC-CEEEEEECCCCCCCCEEEEE
T ss_conf 87572------21444378998437-64665210253237503663
No 78
>PRK13278 purP 5-formaminoimidazole-4-carboxamide-1-(beta)-D-ribofuranosyl 5'-monophosphate synthetase; Provisional
Probab=96.11 E-value=0.04 Score=33.71 Aligned_cols=94 Identities=18% Similarity=0.280 Sum_probs=65.1
Q ss_pred HHHHHHCCCCCCCCEEECCHHHHHHHHHHCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHHHHHHHCC
Q ss_conf 99999868988881574799999999987299869997121368765656556777777707995899999999998618
Q gi|254781049|r 9 KALLRKYNVPVAKGVVISSVHAAESAIKTLPGPLYVVKSQIHAGGRGKGRFKELPADSKGGVRVESSLKSVISDIREILG 88 (398)
Q Consensus 9 K~lL~~~GIpvp~g~~a~s~~ea~~~a~~ig~p~~VvKaQV~aGgRGKa~~~~~hk~~~GGV~l~~s~~ea~~~a~~ilg 88 (398)
.+||.+.|||.|+ ...+|+| |..|+ .||.|=-.|||| --+++|++|..+.+++++.
T Consensus 126 ~~lLe~Agi~~Pk--~~~~Pee-------IDr~V-IVK~~gAkggrG--------------yF~a~s~~ef~~k~~~l~~ 181 (356)
T PRK13278 126 RKLLEGAGIRIPR--KYEDPED-------IDGPV-IVKLPGAKGGRG--------------YFIASSPEEFWEKIDRLKE 181 (356)
T ss_pred HHHHHHCCCCCCE--ECCCHHH-------CCCCE-EEEECCCCCCCE--------------EEEECCHHHHHHHHHHHHH
T ss_conf 9999867999871--1589555-------78526-997467777745--------------8995798999999999886
Q ss_pred CCCCCCCCCCCCCCCCCEEECCCCCCCEEEEEEEEEECCCCCEEEEE
Q ss_conf 76544212222244330110345556505899999834778048998
Q gi|254781049|r 89 STLITKQTGPTGSRVNCVYVEDGADILRELYLSLLVDRTSGMVAFIA 135 (398)
Q Consensus 89 ~~l~t~qt~~~G~~v~~vLVEe~v~~~~E~ylgi~~Dr~~~~~vii~ 135 (398)
.-++. ..+...|||.+-. --+|+....+|-.+..=+++
T Consensus 182 ~g~i~--------d~~~~~IeEyv~G-~~~~~~yFySpl~~~lEllg 219 (356)
T PRK13278 182 KGLIE--------DVEKYIIQEYVVG-VPYYIHYFYSPIKNRLELLG 219 (356)
T ss_pred CCCCC--------CCCCCEEEEEECC-CEEEHHHCCCCCCCCEEEEE
T ss_conf 27545--------5544279998347-41231220352006613663
No 79
>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=96.02 E-value=0.14 Score=30.18 Aligned_cols=107 Identities=19% Similarity=0.183 Sum_probs=68.3
Q ss_pred HHHHHHHCCCCCCEEEEC-CCCCCHHHHHHHHH-HHHCCCCCCEEEEECCCCHHHHHHHHHHHHHHHHHCCCC--CCEEE
Q ss_conf 999999658996248842-78889899999999-986199865899963586132899999999999972999--87999
Q gi|254781049|r 282 TMDIIKLYGGAPANFLDV-GGGADQDKVAAAFK-IITSDSSVKGILINIFGGIMRCDVLVKGILSAVKEVKIN--IPLVM 357 (398)
Q Consensus 282 tmD~i~~~Gg~pANFlD~-gG~a~~e~~~~a~~-~il~~~~vk~iliNifGGI~~cd~vA~gii~a~~~~~~~--~pivv 357 (398)
..|.++..|.+..+.++. -++.+.++-+++++ +|.++|+++.++| +...|.+|.|.++|+++.+.+ ..++|
T Consensus 152 f~~~l~~~g~p~~~vv~~~~~~~~~~~a~~~~~~~L~a~pdi~~~~i-----~a~ND~mAlGA~~Al~~aGl~~~~v~vv 226 (289)
T cd01540 152 ALEALKAPGFPEANIFQAPQKTTDTEGAFDAAASTLTKNPNVKNWII-----YGLNDETVLGAVRATEQSGIAAADVIGV 226 (289)
T ss_pred HHHHHHHCCCCCCEEEEECCCCCCHHHHHHHHHHHHHHCCCCCCEEE-----EECCCHHHHHHHHHHHHCCCCCCCEEEE
T ss_conf 99999635999607998456886699999999999975899884399-----9779668899999999749988976999
Q ss_pred ECCCCCHHHHHHHHHHCCCCEEEECCHH----HHHHHHHH
Q ss_conf 7489858999999997699589949989----99999999
Q gi|254781049|r 358 RLEGANVDIGNRLIAESGLNVITAIDLD----DAAQKIVH 393 (398)
Q Consensus 358 Rl~Gtn~~~g~~il~~~g~~~~~~~~~~----~A~~~~v~ 393 (398)
-+.|+..-...--..++++--....+-. .|++.+++
T Consensus 227 gidg~~~~~~~~~~~~~~~~atv~Q~p~~~G~~av~~~~~ 266 (289)
T cd01540 227 GINGSDAADEESKKQPTGFYGTVLISPTNHGYITAQNLYE 266 (289)
T ss_pred EEECCCHHHHHHHCCCCCEEEEEEECHHHHHHHHHHHHHH
T ss_conf 9728825999974336764899950889999999999999
No 80
>COG1759 5-formaminoimidazole-4-carboxamide-1-beta-D-ribofuranosyl 5'-monophosphate synthetase (purine biosynthesis) [Nucleotide transport and metabolism]
Probab=95.95 E-value=0.081 Score=31.67 Aligned_cols=95 Identities=20% Similarity=0.284 Sum_probs=65.5
Q ss_pred HHHHHHCCCCCCCCEEECCHHHHHHHHHHCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHHHHHHHCC
Q ss_conf 99999868988881574799999999987299869997121368765656556777777707995899999999998618
Q gi|254781049|r 9 KALLRKYNVPVAKGVVISSVHAAESAIKTLPGPLYVVKSQIHAGGRGKGRFKELPADSKGGVRVESSLKSVISDIREILG 88 (398)
Q Consensus 9 K~lL~~~GIpvp~g~~a~s~~ea~~~a~~ig~p~~VvKaQV~aGgRGKa~~~~~hk~~~GGV~l~~s~~ea~~~a~~ilg 88 (398)
.+||.+.||++|+ ..++|+| |..|+ .||-+---|||| --++.|++|..+.+++++.
T Consensus 129 ~~lLekAgi~~P~--~~~~Pee-------Idr~V-iVK~pgAkggRG--------------yFiA~s~eef~ek~erl~~ 184 (361)
T COG1759 129 YKLLEKAGLRIPK--KYKSPEE-------IDRPV-IVKLPGAKGGRG--------------YFIASSPEEFYEKAERLLK 184 (361)
T ss_pred HHHHHHCCCCCCC--CCCCHHH-------CCCCE-EEECCCCCCCCE--------------EEEECCHHHHHHHHHHHHH
T ss_conf 9999974999885--6699678-------68736-985577667743--------------7997698999999999987
Q ss_pred CCCCCCCCCCCCCCCCCEEECCCCCCCEEEEEEEEEECCCCCEEEE
Q ss_conf 7654421222224433011034555650589999983477804899
Q gi|254781049|r 89 STLITKQTGPTGSRVNCVYVEDGADILRELYLSLLVDRTSGMVAFI 134 (398)
Q Consensus 89 ~~l~t~qt~~~G~~v~~vLVEe~v~~~~E~ylgi~~Dr~~~~~vii 134 (398)
..++|.. ..+...|||.+- +.-||+.....+-....=++
T Consensus 185 ~gvi~~E------dlkna~IeEYv~-G~~f~~~yFyS~i~~~lEl~ 223 (361)
T COG1759 185 RGVITEE------DLKNARIEEYVV-GAPFYFHYFYSPIKDRLELL 223 (361)
T ss_pred CCCCCHH------HHHHCEEEEEEE-CCCEEEEEEECCCCCCEEEE
T ss_conf 2876534------432135447750-66013455202345704576
No 81
>cd07014 S49_SppA Signal peptide peptidase A. Signal peptide peptidase A (SppA; Peptidase S49; Protease IV): SppA is an intramembrane enzyme found in all three domains of life and is involved in the cleavage of signal peptides after their removal from the precursor proteins by signal peptidases. Unlike the eukaryotic functional homologs that are proposed to be aspartic proteases, site-directed mutagenesis and sequence analysis have shown these bacterial, archaeal and thylakoid SppAs to be ClpP-like serine proteases. The predicted active site serine for members in this family occurs in a transmembrane domain, cleaving peptide bonds in the plane of the lipid bilayer. Mutagenesis studies also suggest that the catalytic center comprises a Ser-Lys dyad (both residues absolutely conserved within bacteria, chloroplast and mitochondrial signal peptidase family members) and not the usual Ser-His-Asp catalytic triad found in the majority of serine proteases. In addition to the carboxyl-terminal p
Probab=95.90 E-value=0.078 Score=31.77 Aligned_cols=71 Identities=23% Similarity=0.336 Sum_probs=51.0
Q ss_pred EECCCCCCHHHHHHHHHHHHCCCCCCEEEEEC--CCCHH-HHHHHHHHHHHHHHHCCCCCCEEEECCCCCHHHHHHH
Q ss_conf 84278889899999999986199865899963--58613-2899999999999972999879997489858999999
Q gi|254781049|r 297 LDVGGGADQDKVAAAFKIITSDSSVKGILINI--FGGIM-RCDVLVKGILSAVKEVKINIPLVMRLEGANVDIGNRL 370 (398)
Q Consensus 297 lD~gG~a~~e~~~~a~~~il~~~~vk~iliNi--fGGI~-~cd~vA~gii~a~~~~~~~~pivvRl~Gtn~~~g~~i 370 (398)
.+..|+.+.+.+.+.++-...||+||+|++.| .||-+ -|+.+++.|-+ +++ .++|+++-+.+.-+.-|--+
T Consensus 16 ~~~~g~~~~~~i~~~l~~a~~d~~vkaIvL~InSPGGs~~~s~~i~~~I~~-~r~--~~KPV~a~~~~~aASg~Y~i 89 (177)
T cd07014 16 SDTQGNVSGDTTAAQIRDARLDPKVKAIVLRVNSPGGSVTASEVIRAELAA-ARA--AGKPVVASGGGNAASGGYWI 89 (177)
T ss_pred CCCCCCCCHHHHHHHHHHHHHCCCCCEEEEEEECCCCCHHHHHHHHHHHHH-HHH--CCCCEEEEECCCCCCHHHHH
T ss_conf 888887169999999999951999628999961898188999999999999-886--59989999778562057787
No 82
>COG0074 SucD Succinyl-CoA synthetase, alpha subunit [Energy production and conversion]
Probab=95.63 E-value=0.2 Score=29.14 Aligned_cols=132 Identities=17% Similarity=0.317 Sum_probs=93.8
Q ss_pred HCCC--CEEECCCCEEEEECCCHHHHHHHHHHHHCCCCCCEEEECCCCC-CHHHHHHHHHHHHCCCCCCEEEEECCCCHH
Q ss_conf 5398--6442288179995550368999999996589962488427888-989999999998619986589996358613
Q gi|254781049|r 257 QHNL--SYIALDGNIGCMVNGAGLAMATMDIIKLYGGAPANFLDVGGGA-DQDKVAAAFKIITSDSSVKGILINIFGGIM 333 (398)
Q Consensus 257 ~~~l--~yv~LdG~Ig~~vnGaGlamatmD~i~~~Gg~pANFlD~gG~a-~~e~~~~a~~~il~~~~vk~iliNifGGI~ 333 (398)
+.|+ +++-..|+||++.--+.|+--....+...|.-----.-+||.+ .-.....+++++..||..++|.+ .|-|-
T Consensus 134 kiGimp~~i~~~G~IGiVSrSGTLTyE~~~qlt~~G~GqS~~IGiGGDpi~Gt~fid~L~~fe~Dp~T~~ivm--iGEiG 211 (293)
T COG0074 134 KIGIMPGNIYKPGNIGIVSRSGTLTYEAVSQLTEAGLGQSTAIGIGGDPIPGTSFIDALEMFEADPETEAIVM--IGEIG 211 (293)
T ss_pred EEEECHHHHCCCCCEEEEECCCCHHHHHHHHHHHCCCCEEEEEEECCCCCCCCCHHHHHHHHHCCCCCEEEEE--EECCC
T ss_conf 3510523405788569996686639999999976388558999857887688159999998645867407999--92679
Q ss_pred -HHHHHHHHHHHHHHHCCCCCCEEEECCCCCHHHHHHH--------------------HHHCCCCEEEECCHHHHHHHHH
Q ss_conf -2899999999999972999879997489858999999--------------------9976995899499899999999
Q gi|254781049|r 334 -RCDVLVKGILSAVKEVKINIPLVMRLEGANVDIGNRL--------------------IAESGLNVITAIDLDDAAQKIV 392 (398)
Q Consensus 334 -~cd~vA~gii~a~~~~~~~~pivvRl~Gtn~~~g~~i--------------------l~~~g~~~~~~~~~~~A~~~~v 392 (398)
..+..|--.|++ .-..+|+|.-+.|.-+.+|+++ |+++|.++ .+++.+-.+...
T Consensus 212 G~aEe~AA~~i~~---~~~~KPVVa~iaG~tap~gkrmGhaGaiv~~~~gta~~Ki~al~~aGv~v--~etp~~l~~~l~ 286 (293)
T COG0074 212 GPAEEEAAEYIKA---NATRKPVVAYIAGRTAPEGKRMGHAGAIVSGGKGTAESKIAALEAAGVKV--AETPAELGELLL 286 (293)
T ss_pred CCHHHHHHHHHHH---HCCCCCEEEEEECCCCCCCCHHHHHHHHHCCCCCCHHHHHHHHHHCCCEE--CCCHHHHHHHHH
T ss_conf 9389999999996---34689869998436798233012103433078765899999999759741--179999999999
Q ss_pred HHH
Q ss_conf 985
Q gi|254781049|r 393 HAV 395 (398)
Q Consensus 393 ~~~ 395 (398)
+..
T Consensus 287 ~vl 289 (293)
T COG0074 287 EVL 289 (293)
T ss_pred HHH
T ss_conf 986
No 83
>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=95.60 E-value=0.2 Score=29.08 Aligned_cols=117 Identities=20% Similarity=0.231 Sum_probs=72.7
Q ss_pred CEEEEECCCHHHH------HHHHHHHHCCCCCCEEEECCCCCCHHHHHHHHHHHH-CCCCCCEEEEECCCCHHHHHHHHH
Q ss_conf 1799955503689------999999965899624884278889899999999986-199865899963586132899999
Q gi|254781049|r 268 NIGCMVNGAGLAM------ATMDIIKLYGGAPANFLDVGGGADQDKVAAAFKIIT-SDSSVKGILINIFGGIMRCDVLVK 340 (398)
Q Consensus 268 ~Ig~~vnGaGlam------atmD~i~~~Gg~pANFlD~gG~a~~e~~~~a~~~il-~~~~vk~iliNifGGI~~cd~vA~ 340 (398)
+|+++..-..... .+.+....+|..|.. ..+....+.+.-+++++-++ ..|.+.+|| ...|.+|-
T Consensus 120 rIa~i~g~~~~~~~~~R~~gy~~a~~~~gl~~~~-~~~~~~~~~~~g~~a~~~ll~~~~~~~AI~-------~~nD~~A~ 191 (269)
T cd06287 120 QIALIVGSARRNSYLEAEAAYRAFAAEHGMPPVV-LRVDEAGGEEAGYAACAQLLAQHPDLDALC-------VPVDAFAV 191 (269)
T ss_pred EEEEEECCCCCHHHHHHHHHHHHHHHHCCCCCCE-EEECCCCCHHHHHHHHHHHHCCCCCCCEEE-------EECHHHHH
T ss_conf 7999968986758999999999999877999847-997688985999999999971799997799-------82799999
Q ss_pred HHHHHHHHCCCCCCEEEECCC-CCHHHHHHHHHHCCCCEEEECCHHHHHHHHHHHH
Q ss_conf 999999972999879997489-8589999999976995899499899999999985
Q gi|254781049|r 341 GILSAVKEVKINIPLVMRLEG-ANVDIGNRLIAESGLNVITAIDLDDAAQKIVHAV 395 (398)
Q Consensus 341 gii~a~~~~~~~~pivvRl~G-tn~~~g~~il~~~g~~~~~~~~~~~A~~~~v~~~ 395 (398)
|+++|+++.++++|==+.+-| .+...+ + +....+.- ...+.++..++++++.
T Consensus 192 g~l~al~~~Gl~VP~DvsVvgfdD~~~a-~-~~~P~LTt-V~qp~~e~G~~A~~lL 244 (269)
T cd06287 192 GAVRAATELGRAVPDQLRVVTRYDGLRA-R-TSEPPLTA-VDLHLDEVAEQAVDLL 244 (269)
T ss_pred HHHHHHHHHCCCCCCCCEEEEECCCHHH-H-CCCCCCEE-EEECHHHHHHHHHHHH
T ss_conf 9999999858877987669981592897-3-45888548-9719999999999999
No 84
>TIGR01142 purT phosphoribosylglycinamide formyltransferase 2; InterPro: IPR005862 The formation of isosinate, a precursor of adenylate and guanylate, from 5-phosphoribosyl 1-pyrophosphate in the de novo purine biosynthesis pathway is basically composed of 10 steps of reactions . Phosphoribosylglycinamide formyltransferase 2 (2.1.2 from EC) is an alternative enzyme to phosphoribosylglycinamide formyltransferase that catalyzes the third step in the de novo purine biosynthesis pathway. ; GO: 0016742 hydroxymethyl- formyl- and related transferase activity, 0009113 purine base biosynthetic process.
Probab=95.58 E-value=0.075 Score=31.86 Aligned_cols=107 Identities=20% Similarity=0.190 Sum_probs=76.3
Q ss_pred HHHHCCCCCCCCEEECCHHHHHHHHHHCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHHHHHHHCCCC
Q ss_conf 99986898888157479999999998729986999712136876565655677777770799589999999999861876
Q gi|254781049|r 11 LLRKYNVPVAKGVVISSVHAAESAIKTLPGPLYVVKSQIHAGGRGKGRFKELPADSKGGVRVESSLKSVISDIREILGST 90 (398)
Q Consensus 11 lL~~~GIpvp~g~~a~s~~ea~~~a~~ig~p~~VvKaQV~aGgRGKa~~~~~hk~~~GGV~l~~s~~ea~~~a~~ilg~~ 90 (398)
...+.|+|+.++..+++.++.......+|+|+ ++|+-.-+.|+|.. ++++++++..+-+.-.|..
T Consensus 111 ~~~~~g~~~~~~~~~~~~~~~~~~~~~~g~p~-~~~p~~~~~g~g~~--------------~~~~~~~~~~~w~~~~g~~ 175 (407)
T TIGR01142 111 AAEELGLPTAPYEFADSLEELREAVEKIGFPC-VVKPVLSSSGKGQS--------------VVRGPEDLEKAWEYAKGHQ 175 (407)
T ss_pred HHHHHCCCCCCHHHHHHHHHHHHHHHHCCCCC-EEHHHHCCCCCCCE--------------EECCHHHHHHHHHHHHCCC
T ss_conf 67763254220011101788999998607750-00122114666530--------------0047345678876650431
Q ss_pred CCCCCCCCCCCCCCCEEECCCCCCCEEEEEEEEEECCCCCEEEEEE
Q ss_conf 5442122222443301103455565058999998347780489984
Q gi|254781049|r 91 LITKQTGPTGSRVNCVYVEDGADILRELYLSLLVDRTSGMVAFIAS 136 (398)
Q Consensus 91 l~t~qt~~~G~~v~~vLVEe~v~~~~E~ylgi~~Dr~~~~~vii~S 136 (398)
+ |.+..|. -.++++|+.++...|.-+-....-...+++..++
T Consensus 176 ~---~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~ 217 (407)
T TIGR01142 176 V---QEGGRGG-AGRVIVEEFIDFDYEITLLTVRAVDGNGPLTTFC 217 (407)
T ss_pred C---CCCCCCC-CCCEEEEECCCCHHHHHHHEEEECCCCCCEEEEC
T ss_conf 0---1134555-5624552001310211000000027777501101
No 85
>cd07019 S49_SppA_1 Signal peptide peptidase A (SppA), a serine protease, has catalytic Ser-Lys dyad. Signal peptide peptidase A (SppA; Peptidase S49; Protease IV): SppAs in this subfamily are found in all three domains of life and are involved in the cleavage of signal peptides after their removal from the precursor proteins by signal peptidases. Site-directed mutagenesis and sequence analysis have shown these bacterial, archaeal and thylakoid SppAs to be serine proteases. The predicted active site serine for members in this family occurs in a transmembrane domain. Mutagenesis studies also suggest that the catalytic center comprises a Ser-Lys dyad (both residues absolutely conserved within bacteria, chloroplast and mitochondrial signal peptidase family members) and not the usual Ser-His-Asp catalytic triad found in the majority of serine proteases. In addition to the carboxyl-terminal protease domain that is conserved in all the S49 family members, the E. coli SppA contains an amino-te
Probab=95.21 E-value=0.19 Score=29.29 Aligned_cols=24 Identities=25% Similarity=0.187 Sum_probs=19.0
Q ss_pred CCCHHHHHHHHHHHHHHHHHHHHC
Q ss_conf 988899885999999998999955
Q gi|254781049|r 178 ELQGQARIDGGDLFPNLYKAFCDK 201 (398)
Q Consensus 178 g~~~~~~~~~~~ii~~L~~~f~e~ 201 (398)
.++++....+...+..+|+.|.+.
T Consensus 142 ~lt~e~r~~~q~~vd~~~~~F~~~ 165 (211)
T cd07019 142 ALPPEAQLGLQLSIENGYKRFITL 165 (211)
T ss_pred CCCHHHHHHHHHHHHHHHHHHHHH
T ss_conf 999999999999999999999999
No 86
>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=95.07 E-value=0.29 Score=27.98 Aligned_cols=105 Identities=16% Similarity=0.238 Sum_probs=64.7
Q ss_pred HHHHHHHHCCCCC-CEEEECCCCCCHHHHHHHHHHHH-CCCCCCEEEEECCCCHHHHHHHHHHHHHHHHHCCCCCCEEEE
Q ss_conf 9999999658996-24884278889899999999986-199865899963586132899999999999972999879997
Q gi|254781049|r 281 ATMDIIKLYGGAP-ANFLDVGGGADQDKVAAAFKIIT-SDSSVKGILINIFGGIMRCDVLVKGILSAVKEVKINIPLVMR 358 (398)
Q Consensus 281 atmD~i~~~Gg~p-ANFlD~gG~a~~e~~~~a~~~il-~~~~vk~iliNifGGI~~cd~vA~gii~a~~~~~~~~pivvR 358 (398)
...+.++.+|... -.+.+. +..+.+..+++++-++ .+|.+.+|+ ...|.+|.|+++++++.+.++|==+.
T Consensus 138 g~~~a~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~l~~~~~~~aii-------~~~D~~A~g~~~~l~~~g~~vP~dis 209 (267)
T cd06283 138 GFKEALAEHGIGVNEELIEI-DDEDADELDERLRQLLNKPKKKTAIF-------AANGLILLEVLKALKELGIRIPEDVG 209 (267)
T ss_pred HHHHHHHHCCCCCCCEEEEE-CCCCHHHHHHHHHHHHHCCCCCCEEC-------CCCCHHHHHHHHHHHHCCCCCCCCCE
T ss_conf 99999997599765148983-35426779999999984799986420-------37709999999999982998898766
Q ss_pred CCCCCHHHHHHHHHHCCCCEEEECCHHHHHHHHHHHH
Q ss_conf 4898589999999976995899499899999999985
Q gi|254781049|r 359 LEGANVDIGNRLIAESGLNVITAIDLDDAAQKIVHAV 395 (398)
Q Consensus 359 l~Gtn~~~g~~il~~~g~~~~~~~~~~~A~~~~v~~~ 395 (398)
.-|-+-..--+.+ ...+.- ...+..+..+++|++.
T Consensus 210 Vvg~dd~~~~~~~-~p~lTt-v~~~~~~~g~~av~~l 244 (267)
T cd06283 210 LIGFDDTEWAELI-GPGITT-IAQPTYEMGKTAAELL 244 (267)
T ss_pred EEEECCHHHHHHC-CCCCEE-EECCHHHHHHHHHHHH
T ss_conf 8853886999842-999539-9839999999999999
No 87
>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=95.07 E-value=0.29 Score=27.98 Aligned_cols=104 Identities=22% Similarity=0.221 Sum_probs=65.2
Q ss_pred HHHHHHHCCCCCCEEEECCCCCCHHHHHHHHHHH-HCCCCCCEEEEECCCCHHHHHHHHHHHHHHHHHCCCCCCEEEECC
Q ss_conf 9999996589962488427888989999999998-619986589996358613289999999999997299987999748
Q gi|254781049|r 282 TMDIIKLYGGAPANFLDVGGGADQDKVAAAFKII-TSDSSVKGILINIFGGIMRCDVLVKGILSAVKEVKINIPLVMRLE 360 (398)
Q Consensus 282 tmD~i~~~Gg~pANFlD~gG~a~~e~~~~a~~~i-l~~~~vk~iliNifGGI~~cd~vA~gii~a~~~~~~~~pivvRl~ 360 (398)
.+|.+..+++- ---...-|+.+.++-++.++-+ .++|++++||-| |..|.|.++|+++.+.+.|+++=-.
T Consensus 147 f~~~l~~~p~i-~iv~~~~~~~~~~~a~~~~~~~L~~~pdid~I~~~--------d~~a~Ga~~Al~~aG~~~~~~~g~~ 217 (272)
T cd06300 147 AKEVLKEYPGI-KIVGEVYGDWDQAVAQKAVADFLASNPDVDGIWTQ--------GGDAVGAVQAFEQAGRDIPPVTGED 217 (272)
T ss_pred HHHHHHHCCCE-EEEEEECCCCCHHHHHHHHHHHHHHCCCCEEEEEC--------CCCHHHHHHHHHHCCCCCCEEEEEC
T ss_conf 99998641424-88655448888899999999999868996099977--------8218999999996699988699975
Q ss_pred CCCHHHHHHHHHHCCCCEEEECCHHHHHHHHHHHH
Q ss_conf 98589999999976995899499899999999985
Q gi|254781049|r 361 GANVDIGNRLIAESGLNVITAIDLDDAAQKIVHAV 395 (398)
Q Consensus 361 Gtn~~~g~~il~~~g~~~~~~~~~~~A~~~~v~~~ 395 (398)
++ ......++++.++....+.+-.+-.+.+|+.+
T Consensus 218 ~~-~~~~~~~~~~g~~~a~~~q~p~~~G~~av~~a 251 (272)
T cd06300 218 EN-GFLRWRLWKDKGLKGIAISNPPGQSAAALRAA 251 (272)
T ss_pred CC-HHHHHHHHCCCCEEEEEECCHHHHHHHHHHHH
T ss_conf 95-78999983489759999708599999999999
No 88
>pfam06263 consensus
Probab=95.04 E-value=0.3 Score=27.92 Aligned_cols=120 Identities=28% Similarity=0.379 Sum_probs=94.5
Q ss_pred CCCEEEEEC-CCHHHHHHHHHHHHCCCCCCEEEECCCCCCHHH-----HHHHHHHHHCCCCCCEEEEECCCCHHHHHHHH
Q ss_conf 881799955-503689999999965899624884278889899-----99999998619986589996358613289999
Q gi|254781049|r 266 DGNIGCMVN-GAGLAMATMDIIKLYGGAPANFLDVGGGADQDK-----VAAAFKIITSDSSVKGILINIFGGIMRCDVLV 339 (398)
Q Consensus 266 dG~Ig~~vn-GaGlamatmD~i~~~Gg~pANFlD~gG~a~~e~-----~~~a~~~il~~~~vk~iliNifGGI~~cd~vA 339 (398)
.|+||+++. |-|+- --+=+|..+|+---+-+-+||-.=.+. +..+++.+..||..++|.+ | .=--+..|+
T Consensus 191 ~G~IGiVgASGTG~Q-Evt~~Id~~G~GVshaIGtGGRDLs~eVGGisml~al~aL~~Dp~T~vIvl-I--SKPPa~eV~ 266 (514)
T pfam06263 191 RGDIGVVGASGTGIQ-EVTVIIDRLGGGISQAIGTGGRDLSAEVGGIMMLDALDALEQDEETKVIVL-I--SKPPAPEVA 266 (514)
T ss_pred CCCCEEEECCCCCHH-HHHHHHHHHCCCEEEEECCCCCHHHHHHCCHHHHHHHHHHHCCCCCEEEEE-E--CCCCCHHHH
T ss_conf 787117851664467-899999871787322203677402577534689999999855998329999-6--589978999
Q ss_pred HHHHHHHHHCCCCCCEEEECCCCCHHHHHHHHHHCCCCEEEECCHHHHHHHHHHHHHC
Q ss_conf 9999999972999879997489858999999997699589949989999999998506
Q gi|254781049|r 340 KGILSAVKEVKINIPLVMRLEGANVDIGNRLIAESGLNVITAIDLDDAAQKIVHAVKG 397 (398)
Q Consensus 340 ~gii~a~~~~~~~~pivvRl~Gtn~~~g~~il~~~g~~~~~~~~~~~A~~~~v~~~k~ 397 (398)
+-|++.++. ..+|+|+-+-|.+.+.- .+ -+++++.+++||++++|.++++
T Consensus 267 ~kVl~~~~~--~~KPVV~~FLG~~~~~~----~~--~nv~~a~tL~eAA~~Av~l~~~ 316 (514)
T pfam06263 267 EKILELLKA--SGKPVVVLFLGGDPTER----RE--GNVTFATTLEDAAQKAVALSNG 316 (514)
T ss_pred HHHHHHHHH--CCCCEEEEEECCCCCCC----CC--CCEEECCCHHHHHHHHHHHHCC
T ss_conf 999999984--29988999847998545----66--8825236789999999997168
No 89
>cd07023 S49_Sppa_N_C Signal peptide peptidase A (SppA), a serine protease, has catalytic Ser-Lys dyad. Signal peptide peptidase A (SppA; Peptidase S49; Protease IV): SppA is found in all three domains of life and is involved in the cleavage of signal peptides after their removal from the precursor proteins by signal peptidases. This subfamily contains members with either a single domain (sometimes referred to as 36K type), such as sohB peptidase, protein C and archaeal signal peptide peptidase, or an amino-terminal domain in addition to the carboxyl-terminal protease domain that is conserved in all the S49 family members (sometimes referred to as 67K type), similar to E. coli and Arabidopsis thaliana SppA peptidases. Site-directed mutagenesis and sequence analysis have shown these SppAs to be serine proteases. The predicted active site serine for members in this family occurs in a transmembrane domain. Mutagenesis studies also suggest that the catalytic center comprises a Ser-Lys dyad
Probab=94.90 E-value=0.17 Score=29.62 Aligned_cols=24 Identities=25% Similarity=0.353 Sum_probs=18.5
Q ss_pred CCCHHHHHHHHHHHHHHHHHHHHC
Q ss_conf 988899885999999998999955
Q gi|254781049|r 178 ELQGQARIDGGDLFPNLYKAFCDK 201 (398)
Q Consensus 178 g~~~~~~~~~~~ii~~L~~~f~e~ 201 (398)
.++.+..+.+...+..+|+.|.+.
T Consensus 139 ~~s~e~~~~~~~~ld~~~~~F~~~ 162 (208)
T cd07023 139 PLTEEERAILQALVDDIYDQFVDV 162 (208)
T ss_pred CCCHHHHHHHHHHHHHHHHHHHHH
T ss_conf 899999999999999999999999
No 90
>COG3919 Predicted ATP-grasp enzyme [General function prediction only]
Probab=94.82 E-value=0.08 Score=31.68 Aligned_cols=94 Identities=17% Similarity=0.129 Sum_probs=56.5
Q ss_pred HHCCCCCCCCEEECCHHHHHHHHHHCCCCEEEEECCC----CCCCCCCCCCCCCCCCCCCEEEEECCHHHHHHHHHHHCC
Q ss_conf 9868988881574799999999987299869997121----368765656556777777707995899999999998618
Q gi|254781049|r 13 RKYNVPVAKGVVISSVHAAESAIKTLPGPLYVVKSQI----HAGGRGKGRFKELPADSKGGVRVESSLKSVISDIREILG 88 (398)
Q Consensus 13 ~~~GIpvp~g~~a~s~~ea~~~a~~ig~p~~VvKaQV----~aGgRGKa~~~~~hk~~~GGV~l~~s~~ea~~~a~~ilg 88 (398)
.++|+|+|+...++|..++ .+.++.+|+ .+|+-. |.=+|.|+ ..+.+.+|.+.+...--+
T Consensus 123 ~elgl~~P~Ty~v~S~~d~--~~~el~FPv-ILKP~mgg~~~~~araKa-------------~~a~d~ee~k~a~~~a~e 186 (415)
T COG3919 123 EELGLPYPKTYLVNSEIDT--LVDELTFPV-ILKPGMGGSVHFEARAKA-------------FTAADNEEMKLALHRAYE 186 (415)
T ss_pred HHHCCCCCCEEEECCHHHH--HHHHEEEEE-EECCCCCCCCEEEHHHHE-------------EECCCHHHHHHHHHHHHH
T ss_conf 9819997606772314432--123144038-861788875100101001-------------431677999999999887
Q ss_pred CCCCCCCCCCCCCCCCCEEECCCCCCCEEEEEE--EEEECCCCCEEEEE
Q ss_conf 765442122222443301103455565058999--99834778048998
Q gi|254781049|r 89 STLITKQTGPTGSRVNCVYVEDGADILRELYLS--LLVDRTSGMVAFIA 135 (398)
Q Consensus 89 ~~l~t~qt~~~G~~v~~vLVEe~v~~~~E~ylg--i~~Dr~~~~~vii~ 135 (398)
.+ -...+.|+|+++.+-|=-.+ ...| .+.|+.++
T Consensus 187 ----------ei-gpDnvvvQe~IPGGgE~qfsyaAlw~--~g~pvaef 222 (415)
T COG3919 187 ----------EI-GPDNVVVQEFIPGGGENQFSYAALWD--KGHPVAEF 222 (415)
T ss_pred ----------HC-CCCCEEEEEECCCCCCCCCHHHHHHH--CCCCHHHH
T ss_conf ----------43-99725887705799822320988985--79834644
No 91
>cd06319 PBP1_ABC_sugar_binding_like_10 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=94.74 E-value=0.36 Score=27.41 Aligned_cols=85 Identities=12% Similarity=0.095 Sum_probs=55.8
Q ss_pred CCCHHHHHH-HHHHHHCCCCCCEEEEECCCCHHHHHHHHHHHHHHHHHCCCCC-CEEEECCCCCHHHHHHHHHHCCCCEE
Q ss_conf 889899999-9999861998658999635861328999999999999729998-79997489858999999997699589
Q gi|254781049|r 302 GADQDKVAA-AFKIITSDSSVKGILINIFGGIMRCDVLVKGILSAVKEVKINI-PLVMRLEGANVDIGNRLIAESGLNVI 379 (398)
Q Consensus 302 ~a~~e~~~~-a~~~il~~~~vk~iliNifGGI~~cd~vA~gii~a~~~~~~~~-pivvRl~Gtn~~~g~~il~~~g~~~~ 379 (398)
+.+.+..++ +-+++.++|++++||. ..|.+|.|.++|+++.+.+- ..++=..|+ .++.+.+++-.+...
T Consensus 166 ~~~~~~~~~~~~~~L~~~p~i~ai~~-------~~d~~a~Ga~~a~~~~G~~~~i~vvg~D~~--~~~~~~i~~G~~~~t 236 (277)
T cd06319 166 DFSYQETFDYTNDLLTANPDIRAIWL-------QGSDRYQGALDAIATAGKTGKVLLICFDAE--PEFIELLKSGALVGA 236 (277)
T ss_pred CCCHHHHHHHHHHHHHHCCCCCEEEE-------CCCHHHHHHHHHHHHCCCCCCEEEEECCCC--HHHHHHHHCCCCEEE
T ss_conf 99999999999999973899768996-------698899999999997599998589963797--999999875993699
Q ss_pred EECCHHHHHHHHHHHH
Q ss_conf 9499899999999985
Q gi|254781049|r 380 TAIDLDDAAQKIVHAV 395 (398)
Q Consensus 380 ~~~~~~~A~~~~v~~~ 395 (398)
...+..+-..++++.+
T Consensus 237 v~q~p~~~G~~av~~~ 252 (277)
T cd06319 237 GMQQPFLMGERAVETV 252 (277)
T ss_pred EECCHHHHHHHHHHHH
T ss_conf 9649999999999999
No 92
>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=94.55 E-value=0.4 Score=27.13 Aligned_cols=86 Identities=15% Similarity=0.151 Sum_probs=60.7
Q ss_pred CCCCHHHHHHHHH-HHHCCCCCCEEEEECCCCHHHHHHHHHHHHHHHHHCCCC-CCEEEECCCCCHHHHHHHHHHCCCCE
Q ss_conf 8889899999999-986199865899963586132899999999999972999-87999748985899999999769958
Q gi|254781049|r 301 GGADQDKVAAAFK-IITSDSSVKGILINIFGGIMRCDVLVKGILSAVKEVKIN-IPLVMRLEGANVDIGNRLIAESGLNV 378 (398)
Q Consensus 301 G~a~~e~~~~a~~-~il~~~~vk~iliNifGGI~~cd~vA~gii~a~~~~~~~-~pivvRl~Gtn~~~g~~il~~~g~~~ 378 (398)
|..+.+.-+++++ ++.++|++++||- .-|.+|.|.++|+++.+.. ...|+=..|+ .++++.+++-.+..
T Consensus 170 ~~~~~~~a~~~~~~~L~~~p~i~~i~~-------~nD~~a~Ga~~Al~~~G~~~~v~vvG~D~~--~~~~~~i~~g~~~~ 240 (282)
T cd06318 170 GDWTREGGLKAMEDLLVAHPDINVVYS-------ENDDMALGAMRVLAEAGKTDDVKVAAADGQ--KEALALIKGGKYGA 240 (282)
T ss_pred CCCCHHHHHHHHHHHHHHCCCCEEEEE-------CCCHHHHHHHHHHHHCCCCCCEEEEEECCC--HHHHHHHHCCCCEE
T ss_conf 897799999999999975899709998-------896799999999996699998299998988--99999998399649
Q ss_pred EEECCHHHHHHHHHHHH
Q ss_conf 99499899999999985
Q gi|254781049|r 379 ITAIDLDDAAQKIVHAV 395 (398)
Q Consensus 379 ~~~~~~~~A~~~~v~~~ 395 (398)
....+.....+.+|+++
T Consensus 241 tv~q~p~~~G~~av~~~ 257 (282)
T cd06318 241 TALNDPDLVARTAVEVA 257 (282)
T ss_pred EEECCHHHHHHHHHHHH
T ss_conf 99349999999999999
No 93
>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=94.48 E-value=0.41 Score=27.03 Aligned_cols=105 Identities=14% Similarity=0.106 Sum_probs=64.0
Q ss_pred HHHHHHHCCCCCCEEEECCCCCCHHHHHHHHHHHHCCCCCCEEEEECCCCHHHHHHHHHHHHHHHHHCCCCCCEEEECCC
Q ss_conf 99999965899624884278889899999999986199865899963586132899999999999972999879997489
Q gi|254781049|r 282 TMDIIKLYGGAPANFLDVGGGADQDKVAAAFKIITSDSSVKGILINIFGGIMRCDVLVKGILSAVKEVKINIPLVMRLEG 361 (398)
Q Consensus 282 tmD~i~~~Gg~pANFlD~gG~a~~e~~~~a~~~il~~~~vk~iliNifGGI~~cd~vA~gii~a~~~~~~~~pivvRl~G 361 (398)
..+.+..+|.++-+-.-.-+..+.+.-+++++-+++++++.+|+. ..|.+|.|+++++++.+.++|==+.+-|
T Consensus 139 f~~a~~~~g~~~~~~~i~~~~~~~~~~~~~~~~l~~~~~~~ai~~-------~nD~~A~g~l~~l~~~g~~vP~disvig 211 (268)
T cd06298 139 YKEALSEANIEFDESLIFEGDYTYESGYELAEELLEDGKPTAAFV-------TDDELAIGILNAAQDAGLKVPEDFEIIG 211 (268)
T ss_pred HHHHHHHCCCCCCHHHEECCCHHHHHHHHHHHHHHHCCCCCEEEE-------CCHHHHHHHHHHHHHCCCCCCCCEEEEE
T ss_conf 999999849997601200354037789999999983699978996-------6879999999999974999998749999
Q ss_pred CCHHHHHHHHHHCCCCEEEECCHHHHHHHHHHHH
Q ss_conf 8589999999976995899499899999999985
Q gi|254781049|r 362 ANVDIGNRLIAESGLNVITAIDLDDAAQKIVHAV 395 (398)
Q Consensus 362 tn~~~g~~il~~~g~~~~~~~~~~~A~~~~v~~~ 395 (398)
-.-..--+ +-...+.. ...+..+..+.|+++.
T Consensus 212 fDd~~~a~-~~~P~LTt-v~~~~~~~G~~A~~~l 243 (268)
T cd06298 212 FNNTKLAS-MVRPQLTS-VTQPLYDIGAVAMRLL 243 (268)
T ss_pred ECCHHHHH-CCCCCCEE-EECCHHHHHHHHHHHH
T ss_conf 78818997-14899769-9729999999999999
No 94
>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=94.27 E-value=0.45 Score=26.73 Aligned_cols=104 Identities=15% Similarity=0.095 Sum_probs=64.5
Q ss_pred HHHHHHCCCCCCEEEECCCCCCHHHHHHHHHHHH-CCCCCCEEEEECCCCHHHHHHHHHHHHHHHHHCCCCCCEEEECCC
Q ss_conf 9999965899624884278889899999999986-199865899963586132899999999999972999879997489
Q gi|254781049|r 283 MDIIKLYGGAPANFLDVGGGADQDKVAAAFKIIT-SDSSVKGILINIFGGIMRCDVLVKGILSAVKEVKINIPLVMRLEG 361 (398)
Q Consensus 283 mD~i~~~Gg~pANFlD~gG~a~~e~~~~a~~~il-~~~~vk~iliNifGGI~~cd~vA~gii~a~~~~~~~~pivvRl~G 361 (398)
++.++.+|..+-...-..+..+.+..+++++-++ ..+++.+|+ ...|.+|.|+++++++.+.++|==+.+-|
T Consensus 138 ~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~ai~-------~~nD~~A~g~~~~l~~~g~~vP~di~vig 210 (267)
T cd06284 138 RQALAEAGLPADEELIQEGDFSLESGYAAARRLLALPDRPTAIF-------CFSDEMAIGAISALKELGLRVPEDISVVG 210 (267)
T ss_pred HHHHHHCCCCCCCEEEECCCCCHHHHHHHHHHHHHCCCCCCEEE-------ECCCHHHHHHHHHHHHCCCCCCCEEEEEE
T ss_conf 99999839985512773278767778899999996599998026-------57868899999999983999996279998
Q ss_pred CCHHHHHHHHHHCCCCEEEECCHHHHHHHHHHHH
Q ss_conf 8589999999976995899499899999999985
Q gi|254781049|r 362 ANVDIGNRLIAESGLNVITAIDLDDAAQKIVHAV 395 (398)
Q Consensus 362 tn~~~g~~il~~~g~~~~~~~~~~~A~~~~v~~~ 395 (398)
-+-..--+++ ...+.. ...+..+..++|+++.
T Consensus 211 fd~~~~~~~~-~p~ltt-v~~~~~~~g~~a~~~l 242 (267)
T cd06284 211 FDDIDFARMT-TPPLTT-IRQPRYEIGRTAAELL 242 (267)
T ss_pred ECCHHHHHHC-CCCCEE-EEECHHHHHHHHHHHH
T ss_conf 7784899824-898339-9859999999999999
No 95
>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=94.23 E-value=0.46 Score=26.68 Aligned_cols=90 Identities=20% Similarity=0.188 Sum_probs=59.9
Q ss_pred ECCCCCCHHHHHHHHH-HHHCCCCCCEEEEECCCCHHHHHHHHHHHHHHHHHCCCCCCEEEECCCCCHHHHHHHHHHCCC
Q ss_conf 4278889899999999-986199865899963586132899999999999972999879997489858999999997699
Q gi|254781049|r 298 DVGGGADQDKVAAAFK-IITSDSSVKGILINIFGGIMRCDVLVKGILSAVKEVKINIPLVMRLEGANVDIGNRLIAESGL 376 (398)
Q Consensus 298 D~gG~a~~e~~~~a~~-~il~~~~vk~iliNifGGI~~cd~vA~gii~a~~~~~~~~pivvRl~Gtn~~~g~~il~~~g~ 376 (398)
...|..+.+.-+++++ ++.++|++++||- .-|.+|.|.++|+++.+.+.+.++-..|...-. ..+....+.
T Consensus 158 ~~~~~~~~~~~~~~~~~ll~~~p~~~aifa-------~nD~~A~Ga~~a~~~~G~~~i~ivg~dg~~~~~-~~~~~~~~~ 229 (271)
T cd06321 158 DQNGKGSRDGGLRVMQGLLTRFPKLDGVFA-------INDPTAIGADLAAKQAGRNDIKITSVDGAPDAE-KAILSGNSL 229 (271)
T ss_pred EECCCCCHHHHHHHHHHHHHCCCCCCEEEE-------CCCHHHHHHHHHHHHCCCCCCEEEEEECCHHHH-HHHHCCCCC
T ss_conf 722887899999999999850886778997-------786899999999997597999899996967999-998669997
Q ss_pred C-EEEECCHHHHHHHHHHHH
Q ss_conf 5-899499899999999985
Q gi|254781049|r 377 N-VITAIDLDDAAQKIVHAV 395 (398)
Q Consensus 377 ~-~~~~~~~~~A~~~~v~~~ 395 (398)
- -....+..+..+++++++
T Consensus 230 ~~~tv~Q~~~~mG~~av~~l 249 (271)
T cd06321 230 IIATAAQDPRAMARKAVEIG 249 (271)
T ss_pred CEEEEECCHHHHHHHHHHHH
T ss_conf 27998489999999999999
No 96
>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=94.11 E-value=0.49 Score=26.51 Aligned_cols=103 Identities=17% Similarity=0.105 Sum_probs=62.0
Q ss_pred HHHHHCCCCCCEEEECCCCCCHHHHHHHHHHHH-CCCCCCEEEEECCCCHHHHHHHHHHHHHHHHHCCCCCCEEEECCCC
Q ss_conf 999965899624884278889899999999986-1998658999635861328999999999999729998799974898
Q gi|254781049|r 284 DIIKLYGGAPANFLDVGGGADQDKVAAAFKIIT-SDSSVKGILINIFGGIMRCDVLVKGILSAVKEVKINIPLVMRLEGA 362 (398)
Q Consensus 284 D~i~~~Gg~pANFlD~gG~a~~e~~~~a~~~il-~~~~vk~iliNifGGI~~cd~vA~gii~a~~~~~~~~pivvRl~Gt 362 (398)
+.+..+|-+.....-+.+..+.+..+++++-++ +++.+.+|| ...|.+|.|+++++++.+.++|==+.+-|-
T Consensus 138 ~a~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~l~~~~~~~ai~-------~~nD~~A~g~~~~l~~~g~~iP~di~iigf 210 (265)
T cd06285 138 AALAEAGIEVPPERIVYSGFDIEGGEAAAEKLLRSDSPPTAIF-------AVNDFAAIGVMGAARDRGLRVPDDVALVGY 210 (265)
T ss_pred HHHHHCCCCCCHHHEECCCCCHHHHHHHHHHHHHCCCCCCCEE-------CCCHHHHHHHHHHHHHCCCCCCCCEEEEEE
T ss_conf 9999869998756601366215569999999985699988100-------378899999999999859999998799998
Q ss_pred CHHHHHHHHHHCCCCEEEECCHHHHHHHHHHHH
Q ss_conf 589999999976995899499899999999985
Q gi|254781049|r 363 NVDIGNRLIAESGLNVITAIDLDDAAQKIVHAV 395 (398)
Q Consensus 363 n~~~g~~il~~~g~~~~~~~~~~~A~~~~v~~~ 395 (398)
+--.-.+.+. ..+.. ...+..+-+++|+++.
T Consensus 211 d~~~~~~~~~-p~LTt-i~q~~~~ig~~A~~~l 241 (265)
T cd06285 211 NDIPLVARLP-VPLTT-VRSPFHQIGRTALRLL 241 (265)
T ss_pred CCHHHHHHCC-CCCEE-EECCHHHHHHHHHHHH
T ss_conf 7828997078-99579-9729999999999999
No 97
>PRK06091 membrane protein FdrA; Validated
Probab=94.10 E-value=0.49 Score=26.50 Aligned_cols=121 Identities=21% Similarity=0.257 Sum_probs=93.8
Q ss_pred CCCEEEEECCCHHHHHHHHHHHHCCCCCCEEEECCCCCCHHH-----HHHHHHHHHCCCCCCEEEEECCCCHHHHHHHHH
Q ss_conf 881799955503689999999965899624884278889899-----999999986199865899963586132899999
Q gi|254781049|r 266 DGNIGCMVNGAGLAMATMDIIKLYGGAPANFLDVGGGADQDK-----VAAAFKIITSDSSVKGILINIFGGIMRCDVLVK 340 (398)
Q Consensus 266 dG~Ig~~vnGaGlamatmD~i~~~Gg~pANFlD~gG~a~~e~-----~~~a~~~il~~~~vk~iliNifGGI~~cd~vA~ 340 (398)
.|+||+++.-+--.=--+=+|..+|+---+-+-+||-.=.+. +..+++.+..||..++|.+ | .=--+..|++
T Consensus 193 ~G~IGIVgASGTG~QEvs~~Id~~G~GVshaIGtGGRDLs~eVGGis~l~al~aL~~Dp~T~vIvl-I--SKPPa~eV~~ 269 (555)
T PRK06091 193 EGNIGVIGASGTGIQELCSQIALAGEGITHAIGLGGRDLSREVGGISALTALEMLSADEKSEVLAF-V--SKPPAEAVRL 269 (555)
T ss_pred CCCCEEEECCCCCHHHHHHHHHHHCCCEEEEECCCCCHHHHHHCCHHHHHHHHHHHCCCCCEEEEE-E--CCCCCHHHHH
T ss_conf 887127951665466899999871787322203777402567533789999999855998329999-6--5899789999
Q ss_pred HHHHHHHHCCCCCCEEEECCCCCHHHHHHHHHHCCCCEEEECCHHHHHHHHHHHHHC
Q ss_conf 999999972999879997489858999999997699589949989999999998506
Q gi|254781049|r 341 GILSAVKEVKINIPLVMRLEGANVDIGNRLIAESGLNVITAIDLDDAAQKIVHAVKG 397 (398)
Q Consensus 341 gii~a~~~~~~~~pivvRl~Gtn~~~g~~il~~~g~~~~~~~~~~~A~~~~v~~~k~ 397 (398)
-|++.++. ..+|+|+-+-|.+.+.. .+ -+++++.+++||++++|.+++.
T Consensus 270 kVl~~~~~--~~KPVV~~FLG~~p~~~----~e--~~~~~a~tL~eaA~~Av~l~~~ 318 (555)
T PRK06091 270 KIINAMKA--TGKPVVALFLGYTPAVA----RE--ENVWFASTLDEAARLACLLSRV 318 (555)
T ss_pred HHHHHHHH--CCCCEEEEEECCCCCCC----CC--CCEEHHHHHHHHHHHHHHHCCC
T ss_conf 99999984--29988999727997656----76--7641244299999998744055
No 98
>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=93.75 E-value=0.57 Score=26.09 Aligned_cols=105 Identities=14% Similarity=0.147 Sum_probs=69.0
Q ss_pred HHHHHHHHCCCCCCEEEECCCCCCHHHHHHHHHHHHCCCCCCEEEEECCCCHHHHHHHHHHHHHHHHHCCCCCCEEEECC
Q ss_conf 99999996589962488427888989999999998619986589996358613289999999999997299987999748
Q gi|254781049|r 281 ATMDIIKLYGGAPANFLDVGGGADQDKVAAAFKIITSDSSVKGILINIFGGIMRCDVLVKGILSAVKEVKINIPLVMRLE 360 (398)
Q Consensus 281 atmD~i~~~Gg~pANFlD~gG~a~~e~~~~a~~~il~~~~vk~iliNifGGI~~cd~vA~gii~a~~~~~~~~pivvRl~ 360 (398)
...+.++.+|..+-...-..+..+.+.-+++++-+++.+ ..+|| +..|.+|.|+++++++.+.++|==+.+-
T Consensus 143 G~~~a~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~l~~~-~~ai~-------~~nD~~A~g~~~~l~~~g~~ip~di~Vi 214 (273)
T cd06292 143 GFRAALEEAGLEPPEALVARGMFSVEGGQAAAVELLGSG-PTAIV-------AASDLMALGAIRAARRRGLRVPEDVSVV 214 (273)
T ss_pred HHHHHHHHCCCCCCCEEEEECCCCHHHHHHHHHHHHHCC-CCEEE-------ECCCHHHHHHHHHHHHCCCCCCCCEEEE
T ss_conf 999999984999771489716777788999999997479-96577-------4585999999999998399899965999
Q ss_pred CCCHHHHHHHHHHCCCCEEEECCHHHHHHHHHHHH
Q ss_conf 98589999999976995899499899999999985
Q gi|254781049|r 361 GANVDIGNRLIAESGLNVITAIDLDDAAQKIVHAV 395 (398)
Q Consensus 361 Gtn~~~g~~il~~~g~~~~~~~~~~~A~~~~v~~~ 395 (398)
|-+-..-.+++ ...+. ....+.++..++|+++.
T Consensus 215 gfD~~~~~~~~-~p~LT-tI~q~~~~~g~~a~~~l 247 (273)
T cd06292 215 GYDDSALMAFT-DPPLT-TVRQPVEEMAAAAVDRL 247 (273)
T ss_pred EECCHHHHHHC-CCCCE-EEECCHHHHHHHHHHHH
T ss_conf 99985899815-89967-99959999999999999
No 99
>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=93.64 E-value=0.59 Score=25.96 Aligned_cols=103 Identities=15% Similarity=0.229 Sum_probs=64.7
Q ss_pred HHHHHHHCCCCCCEEEECCCCCCHHHHHHHHHHH-HCCCCCCEEEEECCCCHHHHHHHHHHHHHHHHHCCCCCCEEEECC
Q ss_conf 9999996589962488427888989999999998-619986589996358613289999999999997299987999748
Q gi|254781049|r 282 TMDIIKLYGGAPANFLDVGGGADQDKVAAAFKII-TSDSSVKGILINIFGGIMRCDVLVKGILSAVKEVKINIPLVMRLE 360 (398)
Q Consensus 282 tmD~i~~~Gg~pANFlD~gG~a~~e~~~~a~~~i-l~~~~vk~iliNifGGI~~cd~vA~gii~a~~~~~~~~pivvRl~ 360 (398)
..+.++.+|.++. ...+.+..+.+..+++++-+ .+.|++.+|| ...|.+|-|+++++++.+.++|==+.+-
T Consensus 135 f~~al~~~g~~~~-~~~~~~~~~~~~~~~~~~~~l~~~~~~~Ai~-------~~nD~~A~g~~~al~~~g~~vP~disvi 206 (265)
T cd06291 135 FLDVLKENGLEVR-IIEIQENFDDAEKKEEIKELLEEYPDIDGIF-------ASNDLTAILVLKEAQQRGIRVPEDLQII 206 (265)
T ss_pred HHHHHHHCCCCCE-EEEECCCCCHHHHHHHHHHHHHCCCCCCEEE-------CCCHHHHHHHHHHHHHCCCCCCCCEEEE
T ss_conf 9999997699960-8997688986999999999985599988432-------1668999999999998199999986999
Q ss_pred CCCHHHHHHHHHHCCCCEE-EECCHHHHHHHHHHHH
Q ss_conf 9858999999997699589-9499899999999985
Q gi|254781049|r 361 GANVDIGNRLIAESGLNVI-TAIDLDDAAQKIVHAV 395 (398)
Q Consensus 361 Gtn~~~g~~il~~~g~~~~-~~~~~~~A~~~~v~~~ 395 (398)
|-+-. .+.+...-++. ...+..+..++|+++.
T Consensus 207 gfDd~---~~~~~~~p~LTtv~~~~~~~g~~A~~~L 239 (265)
T cd06291 207 GYDGT---KLTRLYTPELTTIRQPIEEIAKTAVDLL 239 (265)
T ss_pred EECCH---HHHHHCCCCCEEEECCHHHHHHHHHHHH
T ss_conf 98880---9998439995599739999999999999
No 100
>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=93.57 E-value=0.61 Score=25.88 Aligned_cols=86 Identities=10% Similarity=0.089 Sum_probs=64.4
Q ss_pred CCCCHHHHHHHHHH-HHCCCCCCEEEEECCCCHHHHHHHHHHHHHHHHHCCCCCCEEEECCCCCHHHHHHHHHHCCCCEE
Q ss_conf 88898999999999-86199865899963586132899999999999972999879997489858999999997699589
Q gi|254781049|r 301 GGADQDKVAAAFKI-ITSDSSVKGILINIFGGIMRCDVLVKGILSAVKEVKINIPLVMRLEGANVDIGNRLIAESGLNVI 379 (398)
Q Consensus 301 G~a~~e~~~~a~~~-il~~~~vk~iliNifGGI~~cd~vA~gii~a~~~~~~~~pivvRl~Gtn~~~g~~il~~~g~~~~ 379 (398)
++.+.++..+.++- +.++|++++|| ...|.+|.|.++|+++.+.+.-+|+-..|+.+ +++.+++-.+...
T Consensus 163 ~~~~~~~a~~~~~~~L~~~pdid~I~-------~~nD~~a~Ga~~Al~~aG~~~v~v~g~Dg~~~--~l~~I~~G~~~at 233 (272)
T cd06313 163 ANWDVSKAARIWETWLTKYPQLDGAF-------CHNDSMALAAYQIMKAAGRTKIVIGGVDGDPP--AIQAVSDGRMVAT 233 (272)
T ss_pred CCCCHHHHHHHHHHHHHHCCCCCEEE-------ECCCHHHHHHHHHHHHCCCCCCEEEEECCCHH--HHHHHHCCCCEEE
T ss_conf 68768999999999996499987899-------88847789999999976999868999789999--9999985991899
Q ss_pred EECCHHHHHHHHHHHH
Q ss_conf 9499899999999985
Q gi|254781049|r 380 TAIDLDDAAQKIVHAV 395 (398)
Q Consensus 380 ~~~~~~~A~~~~v~~~ 395 (398)
...+..+-.+.+|+.+
T Consensus 234 v~q~~~~~G~~av~~a 249 (272)
T cd06313 234 VRNPACRIHGGAIAAG 249 (272)
T ss_pred EECCHHHHHHHHHHHH
T ss_conf 8069999999999999
No 101
>PRK10401 DNA-binding transcriptional regulator GalS; Provisional
Probab=93.42 E-value=0.64 Score=25.73 Aligned_cols=106 Identities=18% Similarity=0.179 Sum_probs=69.8
Q ss_pred HHHHHHHHHCCCCCCEEEECCCCCCHHHHHHHHHHHH-CCCCCCEEEEECCCCHHHHHHHHHHHHHHHHHCCCCCCEEEE
Q ss_conf 9999999965899624884278889899999999986-199865899963586132899999999999972999879997
Q gi|254781049|r 280 MATMDIIKLYGGAPANFLDVGGGADQDKVAAAFKIIT-SDSSVKGILINIFGGIMRCDVLVKGILSAVKEVKINIPLVMR 358 (398)
Q Consensus 280 matmD~i~~~Gg~pANFlD~gG~a~~e~~~~a~~~il-~~~~vk~iliNifGGI~~cd~vA~gii~a~~~~~~~~pivvR 358 (398)
....+.+..+|..+..-+=.-+..+.+.-++++.-++ .++.+.+|| ...|.+|-|+++++++.++++|==+.
T Consensus 196 ~G~~~al~~~gl~~~~~~v~~~~~~~~~~~~~~~~ll~~~~~~tAi~-------~~nD~~A~g~l~al~~~Gl~VP~Dis 268 (346)
T PRK10401 196 AGWLSALKEQGIIPPESWIGTGTPDMQGGEAAMVELLGRNLQLTAVF-------AYNDNMAAGALTALKDNGIAIPLHLS 268 (346)
T ss_pred HHHHHHHHHCCCCCCHHEEEECCCCHHHHHHHHHHHHHCCCCCCCCE-------ECCHHHHHHHHHHHHHCCCCCCCCEE
T ss_conf 99999999849998701487268757889999999981599988614-------44889999999999985998998728
Q ss_pred CCCCCHHHHHHHHHHCCCCEEEECCHHHHHHHHHHH
Q ss_conf 489858999999997699589949989999999998
Q gi|254781049|r 359 LEGANVDIGNRLIAESGLNVITAIDLDDAAQKIVHA 394 (398)
Q Consensus 359 l~Gtn~~~g~~il~~~g~~~~~~~~~~~A~~~~v~~ 394 (398)
+-|-+-.. .--+-...|.-+ ..+.++..+.|+++
T Consensus 269 ViGfDd~~-~a~~~~P~LTTV-~~p~~~mg~~Av~l 302 (346)
T PRK10401 269 IIGFDDIP-IARYTDPQLTTV-RYPIASMAKLATEL 302 (346)
T ss_pred EEEECCHH-HHHCCCCCCCEE-ECCHHHHHHHHHHH
T ss_conf 99989808-985289998769-60999999999999
No 102
>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=93.39 E-value=0.65 Score=25.69 Aligned_cols=89 Identities=12% Similarity=0.134 Sum_probs=65.3
Q ss_pred CCCCCCHHHHHHHHHHHH-CCC-CCCEEEEECCCCHHHHHHHHHHHHHHHHHCCCC------CCEEEECCCCCHHHHHHH
Q ss_conf 278889899999999986-199-865899963586132899999999999972999------879997489858999999
Q gi|254781049|r 299 VGGGADQDKVAAAFKIIT-SDS-SVKGILINIFGGIMRCDVLVKGILSAVKEVKIN------IPLVMRLEGANVDIGNRL 370 (398)
Q Consensus 299 ~gG~a~~e~~~~a~~~il-~~~-~vk~iliNifGGI~~cd~vA~gii~a~~~~~~~------~pivvRl~Gtn~~~g~~i 370 (398)
.-+..+.+.-++.++-+| +.| ++++|| ...|.+|.|.++|+++.+.+ ...|+-..|+. ++++.
T Consensus 178 ~~~~w~~~~a~~~~e~~L~~~~d~id~I~-------a~ND~mAlGA~~Al~~aG~~~~~~~~~I~VvG~Dg~~--~~l~a 248 (303)
T cd01539 178 DTANWDRAQAKDKMDALLLKYGDKIEAVI-------ANNDAMALGAIEALQKYGYNKGDKSKNIPVVGVDALP--EALEL 248 (303)
T ss_pred EECCCCHHHHHHHHHHHHHHCCCCEEEEE-------ECCCHHHHHHHHHHHHCCCCCCCCCCCCEEEEECCCH--HHHHH
T ss_conf 71687889999999999985899735999-------7894779999999997598766678886799867999--99999
Q ss_pred HHHCCCCEEEECCHHHHHHHHHHHHH
Q ss_conf 99769958994998999999999850
Q gi|254781049|r 371 IAESGLNVITAIDLDDAAQKIVHAVK 396 (398)
Q Consensus 371 l~~~g~~~~~~~~~~~A~~~~v~~~k 396 (398)
+++-.+......+..+-.+.+|+++.
T Consensus 249 I~~G~~~aTv~Q~p~~~g~~av~~a~ 274 (303)
T cd01539 249 IKKGSMTGTVLNDPKGQAEAIYNLGM 274 (303)
T ss_pred HHCCCCEEEEECCHHHHHHHHHHHHH
T ss_conf 98399889995699999999999999
No 103
>TIGR00706 SppA_dom signal peptide peptidase SppA, 36K type; InterPro: IPR004635 Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes . They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Over 20 families (denoted S1 - S66) of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence . Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases . Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base . The geometric orientations of the catalytic residues are similar between families, despite different protein folds . The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) , . Peptidases are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry. Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. This group of serine peptidases belong to MEROPS peptidase family S49 (protease IV family, clan S-). The predicted active site serine for members of this family occurs in a transmembrane domain. This group of sequences represent both long and short forms of the bacterial SppA and homologs found in the archaea and plants. Signal peptides of secretory proteins seem to serve at least two important biological functions. First, they are required for protein targeting to and translocation across membranes, such as the eubacterial plasma membrane and the endoplasmic reticular membrane of eukaryotes. Second, in addition to their role as determinants for protein targeting and translocation, certain signal peptides have a signaling function. During or shortly after pre-protein translocation, the signal peptide is removed by signal peptidases. The integral membrane protein, SppA (protease IV), of Escherichia coli was shown experimentally to degrade signal peptides. The member of this family from Bacillus subtilis has only been shown to be required for efficient processing of pre-proteins under conditions of hyper-secretion . ; GO: 0008233 peptidase activity, 0006508 proteolysis.
Probab=93.27 E-value=0.39 Score=27.16 Aligned_cols=22 Identities=23% Similarity=0.255 Sum_probs=13.0
Q ss_pred CCHHHHHHHHHHHHHHHHHHHH
Q ss_conf 8889988599999999899995
Q gi|254781049|r 179 LQGQARIDGGDLFPNLYKAFCD 200 (398)
Q Consensus 179 ~~~~~~~~~~~ii~~L~~~f~e 200 (398)
+.++...-+..+|..-|+.|++
T Consensus 150 lt~eE~~~lQ~~v~~~Y~~F~~ 171 (224)
T TIGR00706 150 LTPEERKILQSLVNESYEQFVQ 171 (224)
T ss_pred HHHHHHHHHHHHHHHHHHHHHH
T ss_conf 6299999999988888757899
No 104
>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=93.17 E-value=0.71 Score=25.47 Aligned_cols=88 Identities=15% Similarity=0.200 Sum_probs=60.8
Q ss_pred CCCCCCHHHHHHHHHHHH-C-CCCCCEEEEECCCCHHHHHHHHHHHHHHHHHCCCC-CCEEEECCCCCHHHHHHHHHHCC
Q ss_conf 278889899999999986-1-99865899963586132899999999999972999-87999748985899999999769
Q gi|254781049|r 299 VGGGADQDKVAAAFKIIT-S-DSSVKGILINIFGGIMRCDVLVKGILSAVKEVKIN-IPLVMRLEGANVDIGNRLIAESG 375 (398)
Q Consensus 299 ~gG~a~~e~~~~a~~~il-~-~~~vk~iliNifGGI~~cd~vA~gii~a~~~~~~~-~pivvRl~Gtn~~~g~~il~~~g 375 (398)
.-++.+.+..++.++-+| + .+.+++|| ...|.+|.|.++|+++.+.+ ...|+=..|+ .++.+.+++-.
T Consensus 164 ~~~~~~~~~a~~~~~~lL~~~~~~i~~I~-------~~nd~~a~Ga~~Al~~~G~~~~v~vvg~d~~--~~~~~~i~~G~ 234 (275)
T cd06317 164 QPADWDREKAQVAMEALITKFGDDIDGVY-------AGDDNMARGALNAAKEAGLAGGIVIVGANNF--AVGYEAIRAGK 234 (275)
T ss_pred EECCCCHHHHHHHHHHHHHHCCCCCCEEE-------CCCCHHHHHHHHHHHHCCCCCCCEEEEECCC--HHHHHHHHCCC
T ss_conf 74147789999999999873457533440-------5895789999999997499899879987980--99999998599
Q ss_pred CCEEEECCHHHHHHHHHHHH
Q ss_conf 95899499899999999985
Q gi|254781049|r 376 LNVITAIDLDDAAQKIVHAV 395 (398)
Q Consensus 376 ~~~~~~~~~~~A~~~~v~~~ 395 (398)
+......+.......+++++
T Consensus 235 ~~~tv~q~p~~~G~~av~~~ 254 (275)
T cd06317 235 YYGTIYQSPVDDGEAALQTA 254 (275)
T ss_pred CEEEEECCHHHHHHHHHHHH
T ss_conf 83999259999999999999
No 105
>PRK10355 xylF D-xylose transporter subunit XylF; Provisional
Probab=93.15 E-value=0.71 Score=25.45 Aligned_cols=87 Identities=8% Similarity=0.095 Sum_probs=64.2
Q ss_pred CCCCCHHHHHHHHHH-HHCCCC-CCEEEEECCCCHHHHHHHHHHHHHHHHHCCCC-CCEEEECCCCCHHHHHHHHHHCCC
Q ss_conf 788898999999999-861998-65899963586132899999999999972999-879997489858999999997699
Q gi|254781049|r 300 GGGADQDKVAAAFKI-ITSDSS-VKGILINIFGGIMRCDVLVKGILSAVKEVKIN-IPLVMRLEGANVDIGNRLIAESGL 376 (398)
Q Consensus 300 gG~a~~e~~~~a~~~-il~~~~-vk~iliNifGGI~~cd~vA~gii~a~~~~~~~-~pivvRl~Gtn~~~g~~il~~~g~ 376 (398)
.++.++++-.+.++- +.++|+ +++|| ..-|.+|.|.++|+++.+.. ...|+=..|+. ++.+.+++-.+
T Consensus 189 ~~~w~~~~A~~~me~~L~a~~~~id~V~-------a~ND~mAlGA~~Al~~aG~~~~v~V~G~Dg~~--~al~~I~~G~~ 259 (330)
T PRK10355 189 VDGWLPENALKIMENALTANNNKIDAVV-------ASNDATAGGAIQALSAQGLSGKVAISGQDADL--AAIKRIVAGTQ 259 (330)
T ss_pred CCCCCHHHHHHHHHHHHHHCCCCEEEEE-------ECCCCHHHHHHHHHHHCCCCCCCEEECCCCCH--HHHHHHHCCCE
T ss_conf 5642288999999999960998516999-------89971489999999966999997699027998--99999974962
Q ss_pred CEEEECCHHHHHHHHHHHH
Q ss_conf 5899499899999999985
Q gi|254781049|r 377 NVITAIDLDDAAQKIVHAV 395 (398)
Q Consensus 377 ~~~~~~~~~~A~~~~v~~~ 395 (398)
....+.+..+-++.+++++
T Consensus 260 ~~Tv~q~~~~~g~~ave~a 278 (330)
T PRK10355 260 TMTVYKPITKLANTAAEIA 278 (330)
T ss_pred EEEEECCHHHHHHHHHHHH
T ss_conf 8998379999999999999
No 106
>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=93.13 E-value=0.71 Score=25.44 Aligned_cols=91 Identities=12% Similarity=0.150 Sum_probs=61.3
Q ss_pred CCCCCHHHHHHHHHHH-HCCCCCCEEEEECCCCHHHHHHHHHHHHHHHHHCCCC-CCEEEECCCCC-HHHHHHHHHHCCC
Q ss_conf 7888989999999998-6199865899963586132899999999999972999-87999748985-8999999997699
Q gi|254781049|r 300 GGGADQDKVAAAFKII-TSDSSVKGILINIFGGIMRCDVLVKGILSAVKEVKIN-IPLVMRLEGAN-VDIGNRLIAESGL 376 (398)
Q Consensus 300 gG~a~~e~~~~a~~~i-l~~~~vk~iliNifGGI~~cd~vA~gii~a~~~~~~~-~pivvRl~Gtn-~~~g~~il~~~g~ 376 (398)
-|..+.+..+++++-+ .++|.+++|| ..-|.+|.|.++|+++.+.. .-.|+-..|+. ..++.+.+++--+
T Consensus 161 ~~~~~~~~a~~~~~~~L~~~pdi~aI~-------a~nD~~A~Ga~~Al~~aG~~~~i~vvg~D~~~~~~~~l~~i~~g~~ 233 (270)
T cd06308 161 DGDWLKEKAEEKMEELLQANPDIDLVY-------AHNDPMALGAYLAAKRAGREKEIKFIGIDGLPGPGGGIEAVRDGEL 233 (270)
T ss_pred CCCCCHHHHHHHHHHHHHHCCCCCEEE-------ECCCHHHHHHHHHHHHCCCCCCCEEEEECCCCCHHHHHHHHHCCCC
T ss_conf 176679999999999985088888899-------7786589999999997699999589988899336999999873861
Q ss_pred CEEEE-CCH-HHHHHHHHHHHHC
Q ss_conf 58994-998-9999999998506
Q gi|254781049|r 377 NVITA-IDL-DDAAQKIVHAVKG 397 (398)
Q Consensus 377 ~~~~~-~~~-~~A~~~~v~~~k~ 397 (398)
..... ..+ ..|++.++.+.+|
T Consensus 234 ~~t~~~p~~G~~av~~a~~~l~G 256 (270)
T cd06308 234 DATFLYPTGGKEAIEVAMKILNG 256 (270)
T ss_pred EEEEECHHHHHHHHHHHHHHHCC
T ss_conf 69998837899999999999777
No 107
>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=92.91 E-value=0.77 Score=25.23 Aligned_cols=104 Identities=18% Similarity=0.214 Sum_probs=61.6
Q ss_pred HHHHHHCCCCCCEEEECCCCCCHHHHHHHHHHHH-CCCCCCEEEEECCCCHHHHHHHHHHHHHHHHHCCCCCCEEEECCC
Q ss_conf 9999965899624884278889899999999986-199865899963586132899999999999972999879997489
Q gi|254781049|r 283 MDIIKLYGGAPANFLDVGGGADQDKVAAAFKIIT-SDSSVKGILINIFGGIMRCDVLVKGILSAVKEVKINIPLVMRLEG 361 (398)
Q Consensus 283 mD~i~~~Gg~pANFlD~gG~a~~e~~~~a~~~il-~~~~vk~iliNifGGI~~cd~vA~gii~a~~~~~~~~pivvRl~G 361 (398)
.+.+..+|.++..-.-+-+..+.+.-+++++-++ +.|++.+|| +.-|.+|-|+++++++.+.++|==+.+-|
T Consensus 139 ~~al~~~gl~~~~~~i~~~~~~~~~g~~~~~~ll~~~~~~~ai~-------~~nD~~A~g~~~~l~~~g~~vP~disvig 211 (268)
T cd06270 139 RDALAEAGIALDESLIIEGDFTEEGGYAAMQELLARGAPFTAVF-------CANDEMAAGAISALREHGISVPQDVSIIG 211 (268)
T ss_pred HHHHHHCCCCCCCEEEEECCCCHHHHHHHHHHHHHCCCCCCEEE-------ECCHHHHHHHHHHHHHCCCCCCCCEEEEE
T ss_conf 99999859997800476167767889998899995699987455-------33779999999999982999999769999
Q ss_pred CCHHHHHHHHHHCCCCEEEECCHHHHHHHHHHHH
Q ss_conf 8589999999976995899499899999999985
Q gi|254781049|r 362 ANVDIGNRLIAESGLNVITAIDLDDAAQKIVHAV 395 (398)
Q Consensus 362 tn~~~g~~il~~~g~~~~~~~~~~~A~~~~v~~~ 395 (398)
-+-..--+++ ...+.. ...+.++..++|+++.
T Consensus 212 fdd~~~~~~~-~P~LTt-i~~~~~~~g~~A~~~L 243 (268)
T cd06270 212 FDDVLLARYL-YPKLTT-VHYPIEEMAQMAAKLA 243 (268)
T ss_pred ECCHHHHHHC-CCCCEE-EECCHHHHHHHHHHHH
T ss_conf 8986899714-899549-9649999999999999
No 108
>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=92.78 E-value=0.8 Score=25.11 Aligned_cols=102 Identities=14% Similarity=0.173 Sum_probs=61.7
Q ss_pred HHHHCCCCCCEEEECCCCCCHHHHHHHHHHHHC-CCCCCEEEEECCCCHHHHHHHHHHHHHHHHHCCCCCCEEEECCCCC
Q ss_conf 999658996248842788898999999999861-9986589996358613289999999999997299987999748985
Q gi|254781049|r 285 IIKLYGGAPANFLDVGGGADQDKVAAAFKIITS-DSSVKGILINIFGGIMRCDVLVKGILSAVKEVKINIPLVMRLEGAN 363 (398)
Q Consensus 285 ~i~~~Gg~pANFlD~gG~a~~e~~~~a~~~il~-~~~vk~iliNifGGI~~cd~vA~gii~a~~~~~~~~pivvRl~Gtn 363 (398)
.+..+|...-...-..+..+.+.-+++++-++. .++..+|| +..|.+|.|+++++++.+.++|==+.+-|-.
T Consensus 142 al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~ai~-------~~nd~~A~g~i~~l~~~g~~iP~disvigfd 214 (268)
T cd06273 142 ALAEAGLELPELWQVEAPYSIADGRAALRQLLEQPPRPTAVI-------CGNDVLALGALYEARRLGLSVPEDLSIVGFD 214 (268)
T ss_pred HHHHHCCCCCHHHEEECCCCHHHHHHHHHHHHHCCCCCCEEE-------ECCHHHHHHHHHHHHHCCCCCCCCEEEEEEC
T ss_conf 999809998714203157898999999999984799984899-------7787999999999996399999967999999
Q ss_pred HHHHHHHHHHCCCCEEEECCHHHHHHHHHHHH
Q ss_conf 89999999976995899499899999999985
Q gi|254781049|r 364 VDIGNRLIAESGLNVITAIDLDDAAQKIVHAV 395 (398)
Q Consensus 364 ~~~g~~il~~~g~~~~~~~~~~~A~~~~v~~~ 395 (398)
-..-.+++. ..+.. ...+.++..++|+++.
T Consensus 215 ~~~~~~~~~-p~lTt-i~~~~~~~g~~a~~~L 244 (268)
T cd06273 215 DIDGSAELE-PALTT-VRVPAREIGRIAAEAL 244 (268)
T ss_pred CHHHHHHHC-CCCEE-EEECHHHHHHHHHHHH
T ss_conf 828898418-99479-9919999999999999
No 109
>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=92.76 E-value=0.8 Score=25.10 Aligned_cols=87 Identities=13% Similarity=0.115 Sum_probs=56.9
Q ss_pred CCCCCCHHHHHHHHHHHHC-CCCCCEEEEECCCCHHHHHHHHHHHHHHHHHCCCCCCEEEECCCCCHHHHHHHHHHCCCC
Q ss_conf 2788898999999999861-998658999635861328999999999999729998799974898589999999976995
Q gi|254781049|r 299 VGGGADQDKVAAAFKIITS-DSSVKGILINIFGGIMRCDVLVKGILSAVKEVKINIPLVMRLEGANVDIGNRLIAESGLN 377 (398)
Q Consensus 299 ~gG~a~~e~~~~a~~~il~-~~~vk~iliNifGGI~~cd~vA~gii~a~~~~~~~~pivvRl~Gtn~~~g~~il~~~g~~ 377 (398)
+-+..+.+.-+.+++-++. +|.+.+|+ +..|.+|-|+++|+++.+.++|==+.+-|.+-. .+..-..-+
T Consensus 156 ~~~~~~~~~~~~~~~~~l~~~~~~~aii-------~~~D~~A~g~l~~l~~~gi~vp~disiigfd~~---~~~~~~~p~ 225 (268)
T cd06289 156 VEGPPSRQGGAEAVAQLLDLPPRPTAIV-------CFNDLVAFGAMSGLRRAGLTPGRDIAVVGFDDV---AEAALATPA 225 (268)
T ss_pred ECCCCCHHHHHHHHHHHHHCCCCCCEEC-------CCCHHHHHHHHHHHHHCCCCCCCCEEEEEECCH---HHHHHCCCC
T ss_conf 3168865569999999984699986203-------576899999999999849999985499995787---899722897
Q ss_pred EE-EECCHHHHHHHHHHHH
Q ss_conf 89-9499899999999985
Q gi|254781049|r 378 VI-TAIDLDDAAQKIVHAV 395 (398)
Q Consensus 378 ~~-~~~~~~~A~~~~v~~~ 395 (398)
+. ...+..+..++|+++.
T Consensus 226 ltti~~~~~~~g~~a~~~l 244 (268)
T cd06289 226 LTTVSTDPREIGRRAAELL 244 (268)
T ss_pred EEEEEECHHHHHHHHHHHH
T ss_conf 1699849999999999999
No 110
>PRK04308 murD UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional
Probab=92.54 E-value=0.86 Score=24.91 Aligned_cols=103 Identities=21% Similarity=0.303 Sum_probs=68.9
Q ss_pred HHHHHCCCCC-----------CEEEECCCCCCHHHHHHHHHHHHCCCCCCEEEEECCCCHHHHHHHHHHHHHHHHHCCCC
Q ss_conf 9999658996-----------24884278889899999999986199865899963586132899999999999972999
Q gi|254781049|r 284 DIIKLYGGAP-----------ANFLDVGGGADQDKVAAAFKIITSDSSVKGILINIFGGIMRCDVLVKGILSAVKEVKIN 352 (398)
Q Consensus 284 D~i~~~Gg~p-----------ANFlD~gG~a~~e~~~~a~~~il~~~~vk~iliNifGGI~~cd~vA~gii~a~~~~~~~ 352 (398)
+.++.|-|-| -.|.|=+=+++.+.+..|++-+ . + +.+| |.||..+-.+... +.+.+++.
T Consensus 299 ~aL~~F~Gl~hR~E~v~~~~GV~~iNDSKaTn~~at~~Al~~~-~--~-~i~l--I~GG~~Kg~d~~~-l~~~~~~~--- 368 (445)
T PRK04308 299 EHVKTFQGLPHRVEKIGEKNGVVFIDDSKGTNVGATAAAIAGL-Q--N-PLFV--ILGGMGKGQDFTP-LRDALAGK--- 368 (445)
T ss_pred HHHHHCCCCCCCEEEEEEECCEEEEECCCCCCHHHHHHHHHHC-C--C-CEEE--EECCCCCCCCHHH-HHHHHHHH---
T ss_conf 9987579999862899864898898079888889999999827-7--9-7799--9767667778699-99998752---
Q ss_pred CCEEEECCCCCHHHHHHHHHHCCCCEEEECCHHHHHHHHHHHHHC
Q ss_conf 879997489858999999997699589949989999999998506
Q gi|254781049|r 353 IPLVMRLEGANVDIGNRLIAESGLNVITAIDLDDAAQKIVHAVKG 397 (398)
Q Consensus 353 ~pivvRl~Gtn~~~g~~il~~~g~~~~~~~~~~~A~~~~v~~~k~ 397 (398)
+. -+-+-|.+.+.=.+.|+.+++++..+++|++|+++|.++++.
T Consensus 369 ~~-~v~~~G~~~~~i~~~l~~~~~~~~~~~~l~~Av~~a~~~a~~ 412 (445)
T PRK04308 369 AK-GVFLIGVDAPQIRRDLDGCGLNLTDCATLEEAVQTAYAQAEA 412 (445)
T ss_pred CE-EEEEECCCHHHHHHHHHHCCCCEEECCCHHHHHHHHHHHCCC
T ss_conf 56-999989799999998863798558768799999999974889
No 111
>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=92.49 E-value=0.87 Score=24.87 Aligned_cols=85 Identities=14% Similarity=0.119 Sum_probs=55.8
Q ss_pred CCCCHHHHHHHHH-HHHCCCCCCEEEEECCCCHHHHHHHHHHHHHHHHHCCCCCC-EEEECCCCCHHHHHHHHHHCCCCE
Q ss_conf 8889899999999-98619986589996358613289999999999997299987-999748985899999999769958
Q gi|254781049|r 301 GGADQDKVAAAFK-IITSDSSVKGILINIFGGIMRCDVLVKGILSAVKEVKINIP-LVMRLEGANVDIGNRLIAESGLNV 378 (398)
Q Consensus 301 G~a~~e~~~~a~~-~il~~~~vk~iliNifGGI~~cd~vA~gii~a~~~~~~~~p-ivvRl~Gtn~~~g~~il~~~g~~~ 378 (398)
+..+.+..++.++ ++.++|++++||. .+|.+|.|.++|+++.+.+-. .|+=..++ .+..+.+++--+..
T Consensus 163 ~~~~~~~~~~~~~~~L~~~pdi~ai~~-------~nd~~a~ga~~al~~~g~~~~i~vvg~D~~--~~~~~~i~~G~i~~ 233 (273)
T cd06310 163 SDSDYAKALDITEDLLTANPDLKGIFG-------ANEGSAVGAARAVRQAGKAGKVKVVGFDAS--PEQIDALREGVIQA 233 (273)
T ss_pred CCCHHHHHHHHHHHHHHHCCCCCEEEE-------CCCHHHHHHHHHHHHCCCCCCEEEEEECCC--HHHHHHHHCCCCEE
T ss_conf 652489999999999975898757984-------384899999999997799999399998986--99999998599859
Q ss_pred EEECCHHHHHHHHHHH
Q ss_conf 9949989999999998
Q gi|254781049|r 379 ITAIDLDDAAQKIVHA 394 (398)
Q Consensus 379 ~~~~~~~~A~~~~v~~ 394 (398)
....+-.+-...+|++
T Consensus 234 tv~q~p~~~G~~av~~ 249 (273)
T cd06310 234 LVVQNPYKMGYLGVKT 249 (273)
T ss_pred EECCCHHHHHHHHHHH
T ss_conf 9818999999999999
No 112
>PRK10423 transcriptional repressor RbsR; Provisional
Probab=92.27 E-value=0.92 Score=24.69 Aligned_cols=105 Identities=11% Similarity=0.114 Sum_probs=69.6
Q ss_pred HHHHHHHHCCCCCCEEEECCCCCCHHHHHHHHHHHHC-CCCCCEEEEECCCCHHHHHHHHHHHHHHHHHCCCCCCEEEEC
Q ss_conf 9999999658996248842788898999999999861-998658999635861328999999999999729998799974
Q gi|254781049|r 281 ATMDIIKLYGGAPANFLDVGGGADQDKVAAAFKIITS-DSSVKGILINIFGGIMRCDVLVKGILSAVKEVKINIPLVMRL 359 (398)
Q Consensus 281 atmD~i~~~Gg~pANFlD~gG~a~~e~~~~a~~~il~-~~~vk~iliNifGGI~~cd~vA~gii~a~~~~~~~~pivvRl 359 (398)
...+.+..+|.....-..+-+..+.+.-+++++-+++ .+.+.+|| ...|.+|.|+++|+++.++++|==+.+
T Consensus 195 gf~~al~~~gl~~~~~~~~~~~~~~~~g~~~~~~ll~~~~~ptAi~-------~~nD~~A~g~~~al~~~g~~iP~Disv 267 (327)
T PRK10423 195 GYRAAMKRAGLNIPDGYEVTGDFEFNGGFDAMQQLLAHPLRPQAVF-------TGNDAMAVGVYQALYQAGLQVPQDIAV 267 (327)
T ss_pred HHHHHHHHCCCCCCCCEEEECCCCHHHHHHHHHHHHHCCCCCCEEE-------ECCCHHHHHHHHHHHHCCCCCCCCEEE
T ss_conf 9999999859998843699604673789999999984799998455-------178099999999999869999997599
Q ss_pred CCCCHHHHHHHHHHCCCCEE-EECCHHHHHHHHHHHH
Q ss_conf 89858999999997699589-9499899999999985
Q gi|254781049|r 360 EGANVDIGNRLIAESGLNVI-TAIDLDDAAQKIVHAV 395 (398)
Q Consensus 360 ~Gtn~~~g~~il~~~g~~~~-~~~~~~~A~~~~v~~~ 395 (398)
-|-+-. .+.+-..-++. ...+.++..+.|+++.
T Consensus 268 igfDd~---~~~~~~~P~LTTv~~~~~~~g~~A~~~L 301 (327)
T PRK10423 268 IGYDDI---ELASYMTPPLTTIHQPKDELGELAIDVL 301 (327)
T ss_pred EEECCC---HHHHHCCCCCEEEECCHHHHHHHHHHHH
T ss_conf 997582---8998269993799839999999999999
No 113
>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=92.26 E-value=0.93 Score=24.68 Aligned_cols=90 Identities=16% Similarity=0.220 Sum_probs=58.3
Q ss_pred CCCCCCHHHHHHHHH-HHHCCCCCCEEEEECCCCHHHHHHHHHHHHHHHHHCCCC-CCEEEECCCCCHHHHHHHHHHCC-
Q ss_conf 278889899999999-986199865899963586132899999999999972999-87999748985899999999769-
Q gi|254781049|r 299 VGGGADQDKVAAAFK-IITSDSSVKGILINIFGGIMRCDVLVKGILSAVKEVKIN-IPLVMRLEGANVDIGNRLIAESG- 375 (398)
Q Consensus 299 ~gG~a~~e~~~~a~~-~il~~~~vk~iliNifGGI~~cd~vA~gii~a~~~~~~~-~pivvRl~Gtn~~~g~~il~~~g- 375 (398)
.-|+.+.+.-.+.++ +|.++|++++|| ...|.+|.|.++|+++.+.+ .++++=..|+. ++.+.+++-.
T Consensus 163 ~~~~~~~~~a~~~~~~~L~~~pdi~~If-------a~nD~ma~Ga~~Al~~aG~~~~~~vvG~Dg~~--~~~~~i~~G~~ 233 (274)
T cd06311 163 QYANWNRDDAFSVMQDLLTKFPKIDAVW-------AHDDDMAVGVLAAIKQAGRTDIKFVVGGAGSK--DMIKMIMDGDP 233 (274)
T ss_pred ECCCCCHHHHHHHHHHHHHCCCCCCEEE-------ECCCCHHHHHHHHHHHCCCCCCCEEEEECCCH--HHHHHHHCCCC
T ss_conf 0387568999999999984388888899-------88980589999999976999997899965998--99999976997
Q ss_pred -CCEEEECC---HHHHHHHHHHHHHC
Q ss_conf -95899499---89999999998506
Q gi|254781049|r 376 -LNVITAID---LDDAAQKIVHAVKG 397 (398)
Q Consensus 376 -~~~~~~~~---~~~A~~~~v~~~k~ 397 (398)
+......+ .-.|++.++.+.+|
T Consensus 234 ~~~atv~~~p~~~~~Av~~a~~~l~G 259 (274)
T cd06311 234 LIPADVLYPPSMIASAIDLTVALFQG 259 (274)
T ss_pred EEEEEEECCHHHHHHHHHHHHHHHCC
T ss_conf 48999808999999999999999779
No 114
>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=92.25 E-value=0.93 Score=24.68 Aligned_cols=99 Identities=20% Similarity=0.257 Sum_probs=60.2
Q ss_pred HHHHHHCCCCCCEEEECCCCCCHHHHHHHHHHH-HCCCCCCEEEEECCCCHHHHHHHHHHHHHHHHHCCCCCC---EEEE
Q ss_conf 999996589962488427888989999999998-619986589996358613289999999999997299987---9997
Q gi|254781049|r 283 MDIIKLYGGAPANFLDVGGGADQDKVAAAFKII-TSDSSVKGILINIFGGIMRCDVLVKGILSAVKEVKINIP---LVMR 358 (398)
Q Consensus 283 mD~i~~~Gg~pANFlD~gG~a~~e~~~~a~~~i-l~~~~vk~iliNifGGI~~cd~vA~gii~a~~~~~~~~p---ivvR 358 (398)
.+.+..+|..+..+... +..+.+..++.++-+ .+.|++.+|+ ...|.+|.|+++++++.+.++| -|+-
T Consensus 141 ~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~l~~~~~~dai~-------~~~d~~A~gv~~al~~~g~~ip~di~ivg 212 (264)
T cd01537 141 KDALKEAGPIEIVLVQE-GDWDAEKGYQAAEELLTAHPDPTAIF-------AANDDMALGALRALREAGLRVPDDISVIG 212 (264)
T ss_pred HHHHHHCCCCCCEEEEE-CCCCHHHHHHHHHHHHHHCCCCEEEE-------ECCHHHHHHHHHHHHHCCCCCCCCEEEEE
T ss_conf 99999779998537995-79998999999999985089976999-------89869999999999974999999839999
Q ss_pred CCCCCHHHHHHHHHHCCCCEE-EECCHHHHHHHHHHHH
Q ss_conf 489858999999997699589-9499899999999985
Q gi|254781049|r 359 LEGANVDIGNRLIAESGLNVI-TAIDLDDAAQKIVHAV 395 (398)
Q Consensus 359 l~Gtn~~~g~~il~~~g~~~~-~~~~~~~A~~~~v~~~ 395 (398)
..++ .... ..+-++. ...+.++..+.++++.
T Consensus 213 ~d~~--~~~~----~~~p~ltti~~~~~~~g~~a~~~l 244 (264)
T cd01537 213 FDGT--PEAL----LAGPPLTTVRQPPDELGRAAVELL 244 (264)
T ss_pred ECCH--HHHH----HHCCCEEEEECCHHHHHHHHHHHH
T ss_conf 9974--9999----719982999839999999999999
No 115
>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=92.21 E-value=0.94 Score=24.65 Aligned_cols=103 Identities=15% Similarity=0.187 Sum_probs=63.7
Q ss_pred HHHHHHHCCCCCCEEEECCCCCCHHHHHHHHHHHHC-CCCCCEEEEECCCCHHHHHHHHHHHHHHHHHCCCCCCEEEECC
Q ss_conf 999999658996248842788898999999999861-9986589996358613289999999999997299987999748
Q gi|254781049|r 282 TMDIIKLYGGAPANFLDVGGGADQDKVAAAFKIITS-DSSVKGILINIFGGIMRCDVLVKGILSAVKEVKINIPLVMRLE 360 (398)
Q Consensus 282 tmD~i~~~Gg~pANFlD~gG~a~~e~~~~a~~~il~-~~~vk~iliNifGGI~~cd~vA~gii~a~~~~~~~~pivvRl~ 360 (398)
..+.+..+|..+-.-+-+.+..+.+.-+++++.+++ .+++.++| +..|.+|.|+++|+++.+.++|==+.+-
T Consensus 136 f~~al~~~g~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~p~ai~-------~~nd~~A~g~~~al~~~g~~vP~di~vi 208 (260)
T cd06286 136 YKDALEEYGLTPDEEWIFEGCFTIEDGERIGHQLLKMKDRPDAIF-------TGSDEVAAGIITEAKKQGIRVPEDLAII 208 (260)
T ss_pred HHHHHHHCCCCCCCEEEECCCCCHHHHHHHHHHHHHCCCCCCEEE-------ECCHHHHHHHHHHHHHCCCCCCCCEEEE
T ss_conf 999999779997730364465206679999999984499987367-------3689999999999997299999976999
Q ss_pred CCCHHHHHHHHHHCCCCEEEECCHHHHHHHHHHHH
Q ss_conf 98589999999976995899499899999999985
Q gi|254781049|r 361 GANVDIGNRLIAESGLNVITAIDLDDAAQKIVHAV 395 (398)
Q Consensus 361 Gtn~~~g~~il~~~g~~~~~~~~~~~A~~~~v~~~ 395 (398)
|-+-.. +-+...+.. ...+..+..+.|+++.
T Consensus 209 gfdd~~---~~~~p~lTt-v~~~~~~~g~~A~~~l 239 (260)
T cd06286 209 GFDNQP---ISELLGITT-IDQPVKELGEKAFELL 239 (260)
T ss_pred EECCHH---HHCCCCCCE-EECCHHHHHHHHHHHH
T ss_conf 989849---982899758-9359999999999999
No 116
>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=92.20 E-value=0.94 Score=24.64 Aligned_cols=82 Identities=15% Similarity=0.188 Sum_probs=56.1
Q ss_pred CCCCHHHHHHHHHHHHCCCCCCEEEEECCCCHHHHHHHHHHHHHHHHHCCCCCC---EEEECCCCCHHHHHHHHHHCCCC
Q ss_conf 888989999999998619986589996358613289999999999997299987---99974898589999999976995
Q gi|254781049|r 301 GGADQDKVAAAFKIITSDSSVKGILINIFGGIMRCDVLVKGILSAVKEVKINIP---LVMRLEGANVDIGNRLIAESGLN 377 (398)
Q Consensus 301 G~a~~e~~~~a~~~il~~~~vk~iliNifGGI~~cd~vA~gii~a~~~~~~~~p---ivvRl~Gtn~~~g~~il~~~g~~ 377 (398)
|..+.+.-+++++.++++|.+.+|+. .-|.+|.|+++++++.+.++| -|+-+.++-. .....-+
T Consensus 155 ~~~~~~~~~~~~~~l~~~~~~~aii~-------~~D~~A~g~i~~l~~~g~~iP~di~iigfd~~~~------~~~~~p~ 221 (264)
T cd01574 155 GDWSAESGYRAGRELLREGDPTAVFA-------ANDQMALGVLRALHELGLRVPDDVSVVGFDDIPE------SAYFIPP 221 (264)
T ss_pred CCCCHHHHHHHHHHHHHCCCCCEEEE-------CCHHHHHHHHHHHHHHCCCCCCCCEEEEECCCHH------HHHCCCC
T ss_conf 68997999999999983799968963-------6429999999999982998898847998688178------8950898
Q ss_pred EE-EECCHHHHHHHHHHHH
Q ss_conf 89-9499899999999985
Q gi|254781049|r 378 VI-TAIDLDDAAQKIVHAV 395 (398)
Q Consensus 378 ~~-~~~~~~~A~~~~v~~~ 395 (398)
+. ...+..+..+.|+++.
T Consensus 222 lTtI~~~~~~~g~~A~~~l 240 (264)
T cd01574 222 LTTVRQDFAALGRRAVELL 240 (264)
T ss_pred EEEEEECHHHHHHHHHHHH
T ss_conf 5899819999999999999
No 117
>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=91.87 E-value=1 Score=24.39 Aligned_cols=104 Identities=14% Similarity=0.141 Sum_probs=68.7
Q ss_pred HHHHHHHCCCCCCEEEECCCCCCHHHHHHHHHHHHC-CCCCCEEEEECCCCHHHHHHHHHHHHHHHHHCCCCCCEEEECC
Q ss_conf 999999658996248842788898999999999861-9986589996358613289999999999997299987999748
Q gi|254781049|r 282 TMDIIKLYGGAPANFLDVGGGADQDKVAAAFKIITS-DSSVKGILINIFGGIMRCDVLVKGILSAVKEVKINIPLVMRLE 360 (398)
Q Consensus 282 tmD~i~~~Gg~pANFlD~gG~a~~e~~~~a~~~il~-~~~vk~iliNifGGI~~cd~vA~gii~a~~~~~~~~pivvRl~ 360 (398)
..+.++.+|..+-...-+.+..+.+.-+++++-+++ ++.+.+|| ...|.+|.|+++|+++.+.++|==+.+-
T Consensus 144 f~~al~~~g~~~~~~~~~~~~~~~~~~~~~~~~ll~~~~~~tai~-------~~nD~~A~g~~~al~~~g~~iP~disvv 216 (270)
T cd06294 144 YKQALEDHGIPDRNEVIISLDFSEEGGYKALKKLLEQHPRPTAIV-------ATDDLLALGVLKVLNELGLKVPEDLSII 216 (270)
T ss_pred HHHHHHHCCCCCCCCEEECCCCCHHHHHHHHHHHHHCCCCCCEEE-------ECCHHHHHHHHHHHHHCCCCCCCCEEEE
T ss_conf 999999869997733331377667889999999984699984899-------8774999999999998399999984999
Q ss_pred CCCHHHHHHHHHHCCCCEE-EECCHHHHHHHHHHHH
Q ss_conf 9858999999997699589-9499899999999985
Q gi|254781049|r 361 GANVDIGNRLIAESGLNVI-TAIDLDDAAQKIVHAV 395 (398)
Q Consensus 361 Gtn~~~g~~il~~~g~~~~-~~~~~~~A~~~~v~~~ 395 (398)
|-+-. .+.+-..-++. ...+.++..++|+++.
T Consensus 217 gfDd~---~~~~~~~P~LTtv~q~~~~~G~~A~~~L 249 (270)
T cd06294 217 GFNNS---ILSELAHPPLTSVDINPRELGYEAAELL 249 (270)
T ss_pred EECCH---HHHHHCCCCCEEEECCHHHHHHHHHHHH
T ss_conf 98972---8998428981799739999999999999
No 118
>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=91.85 E-value=1 Score=24.38 Aligned_cols=103 Identities=10% Similarity=0.055 Sum_probs=65.5
Q ss_pred HHHHHHHCCCCCCEEEECCCCCCHHHHHHHHHHHH-CCCCCCEEEEECCCCHHHHHHHHHHHHHHHHHCCCCCCEEEECC
Q ss_conf 99999965899624884278889899999999986-19986589996358613289999999999997299987999748
Q gi|254781049|r 282 TMDIIKLYGGAPANFLDVGGGADQDKVAAAFKIIT-SDSSVKGILINIFGGIMRCDVLVKGILSAVKEVKINIPLVMRLE 360 (398)
Q Consensus 282 tmD~i~~~Gg~pANFlD~gG~a~~e~~~~a~~~il-~~~~vk~iliNifGGI~~cd~vA~gii~a~~~~~~~~pivvRl~ 360 (398)
..+.++.+|..+.......+..+.+.-+++++-++ +.|++++||. ..|.+|.|+++++++.++++|==+.+-
T Consensus 138 ~~~al~~~g~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~dai~~-------~nD~~A~g~~~~l~~~g~~iP~disvi 210 (268)
T cd01575 138 FRAALRAAGLDPPLVVTTPEPSSFALGRELLAELLARWPDLDAVFC-------SNDDLALGALFECQRRGISVPEDIAIA 210 (268)
T ss_pred HHHHHHHCCCCCCEEEEECCCCCHHHHHHHHHHHHHCCCCCCEEEE-------CCHHHHHHHHHHHHHHCCCCCCCEEEE
T ss_conf 9999997698988089954899889999999999956999837998-------788999999999998389999977999
Q ss_pred CCCHHHHHHHHHHCCCCEE-EECCHHHHHHHHHHH
Q ss_conf 9858999999997699589-949989999999998
Q gi|254781049|r 361 GANVDIGNRLIAESGLNVI-TAIDLDDAAQKIVHA 394 (398)
Q Consensus 361 Gtn~~~g~~il~~~g~~~~-~~~~~~~A~~~~v~~ 394 (398)
|-+-. .+.+-..-++. ...+..+..++|+++
T Consensus 211 gfdd~---~~~~~~~p~ltti~~~~~~~g~~a~~~ 242 (268)
T cd01575 211 GFGDL---EIAAALPPALTTVRTPRREIGRRAAEL 242 (268)
T ss_pred EECCH---HHHHCCCCCCEEEEECHHHHHHHHHHH
T ss_conf 98973---899616899679996999999999999
No 119
>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=91.72 E-value=1.1 Score=24.29 Aligned_cols=103 Identities=17% Similarity=0.212 Sum_probs=67.0
Q ss_pred HHHHHHCCCCCCEEEECCCCCCHHHHHHHHHHHHC-CCCCCEEEEECCCCHHHHHHHHHHHHHHHHHCCCCCCEEEECCC
Q ss_conf 99999658996248842788898999999999861-99865899963586132899999999999972999879997489
Q gi|254781049|r 283 MDIIKLYGGAPANFLDVGGGADQDKVAAAFKIITS-DSSVKGILINIFGGIMRCDVLVKGILSAVKEVKINIPLVMRLEG 361 (398)
Q Consensus 283 mD~i~~~Gg~pANFlD~gG~a~~e~~~~a~~~il~-~~~vk~iliNifGGI~~cd~vA~gii~a~~~~~~~~pivvRl~G 361 (398)
.+.+..+|..+-.+.-+.+.-+.+..+++++-++. .|+.++||. .-|.+|.|+++++++.+.++|==+.+-|
T Consensus 148 ~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~ai~~-------~nD~~A~g~~~~~~~~g~~iP~disIig 220 (275)
T cd06295 148 REALAEAGLPLDPRLVAPGDFTEESGRAAMRALLERGPDFDAVFA-------ASDLMALGALRALREAGRRVPEDVAVVG 220 (275)
T ss_pred HHHHHHCCCCCCCCEEEECCCCHHHHHHHHHHHHHCCCCCCEEEE-------CCCHHHHHHHHHHHHCCCCCCCCEEEEE
T ss_conf 999998699999417996577668799998889854999870341-------4758789999999974999898569999
Q ss_pred CCHHHHHHHHHHCCCCEE-EECCHHHHHHHHHHHH
Q ss_conf 858999999997699589-9499899999999985
Q gi|254781049|r 362 ANVDIGNRLIAESGLNVI-TAIDLDDAAQKIVHAV 395 (398)
Q Consensus 362 tn~~~g~~il~~~g~~~~-~~~~~~~A~~~~v~~~ 395 (398)
-+-. .+.+-..-++. ...+..+..++|+++.
T Consensus 221 fd~~---~~~~~~~P~LTtI~~~~~~ig~~A~~~L 252 (275)
T cd06295 221 FDDI---PLAAYADPPLTTVRQDIEEAGRLLVDLL 252 (275)
T ss_pred ECCH---HHHHHCCCCEEEEEECHHHHHHHHHHHH
T ss_conf 6786---8998348986999809999999999999
No 120
>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=91.68 E-value=1.1 Score=24.26 Aligned_cols=101 Identities=16% Similarity=0.232 Sum_probs=60.4
Q ss_pred HHHHHHCCCCCCEEEECCCCCCHHHHHHHHHHHH-CCCCCCEEEEECCCCHHHHHHHHHHHHHHHHHCCCCCCE---EEE
Q ss_conf 9999965899624884278889899999999986-199865899963586132899999999999972999879---997
Q gi|254781049|r 283 MDIIKLYGGAPANFLDVGGGADQDKVAAAFKIIT-SDSSVKGILINIFGGIMRCDVLVKGILSAVKEVKINIPL---VMR 358 (398)
Q Consensus 283 mD~i~~~Gg~pANFlD~gG~a~~e~~~~a~~~il-~~~~vk~iliNifGGI~~cd~vA~gii~a~~~~~~~~pi---vvR 358 (398)
.+.++.+|.+.-...-..+..+.+..+++++-++ +.|++.+|| +..|.+|.|+++++++.+.++|= |+-
T Consensus 139 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~ai~-------~~~D~~A~g~~~~l~~~g~~iP~di~Iig 211 (264)
T cd06267 139 REALEEAGIPLDEELIVEGDFSEESGYEAARELLASGERPTAIF-------AANDLMAIGALRALRELGLRVPEDVSVVG 211 (264)
T ss_pred HHHHHHCCCCCCHHEEECCCCCHHHHHHHHHHHHHCCCCCCEEE-------ECCHHHHHHHHHHHHHCCCCCCCCEEEEE
T ss_conf 99999869998853075278977999999999996599998998-------78879999999999982999999779999
Q ss_pred CCCCCHHHHHHHHHHCCCCEEEECCHHHHHHHHHHHH
Q ss_conf 4898589999999976995899499899999999985
Q gi|254781049|r 359 LEGANVDIGNRLIAESGLNVITAIDLDDAAQKIVHAV 395 (398)
Q Consensus 359 l~Gtn~~~g~~il~~~g~~~~~~~~~~~A~~~~v~~~ 395 (398)
..++ +. .+. -...+.- ...+..+..++|+++.
T Consensus 212 ~d~~--~~-~~~-~~p~ltt-v~~~~~~ig~~a~~~l 243 (264)
T cd06267 212 FDDI--PL-AEL-LTPPLTT-VRQPIEEMGRAAAELL 243 (264)
T ss_pred ECCH--HH-HHC-CCCCCEE-EEECHHHHHHHHHHHH
T ss_conf 9984--89-853-4899479-9909999999999999
No 121
>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=91.65 E-value=1.1 Score=24.24 Aligned_cols=83 Identities=14% Similarity=0.252 Sum_probs=54.9
Q ss_pred CCCCHHHHHHHHHHHH-CCCCCCEEEEECCCCHHHHHHHHHHHHHHHHHCCCCCC---EEEECCCCCHHHHHHHHHHCCC
Q ss_conf 8889899999999986-19986589996358613289999999999997299987---9997489858999999997699
Q gi|254781049|r 301 GGADQDKVAAAFKIIT-SDSSVKGILINIFGGIMRCDVLVKGILSAVKEVKINIP---LVMRLEGANVDIGNRLIAESGL 376 (398)
Q Consensus 301 G~a~~e~~~~a~~~il-~~~~vk~iliNifGGI~~cd~vA~gii~a~~~~~~~~p---ivvRl~Gtn~~~g~~il~~~g~ 376 (398)
+..+.+..+++++-++ ..+.+.+|+ +..|.+|.|+++++++.++++| -|+=..++... +++. ..+
T Consensus 158 ~~~~~~~~~~~~~~~l~~~~~~~aii-------~~~d~~A~g~~~~l~~~gi~vP~di~vvgfd~~~~~---~~~~-p~l 226 (269)
T cd06275 158 GDFECEGGYEAMQRLLAQPKRPTAVF-------CGNDLMAMGALCAAQEAGLRVPQDLSIIGYDDIELA---RYFS-PPL 226 (269)
T ss_pred CCCCHHHHHHHHHHHHHHCCCCCEEE-------CCCHHHHHHHHHHHHHCCCCCCCCCEEEEECCHHHH---HHCC-CCE
T ss_conf 77776889999999997089966123-------187499999999999808878998679987787999---8338-985
Q ss_pred CEEEECCHHHHHHHHHHHH
Q ss_conf 5899499899999999985
Q gi|254781049|r 377 NVITAIDLDDAAQKIVHAV 395 (398)
Q Consensus 377 ~~~~~~~~~~A~~~~v~~~ 395 (398)
.. ...+..+..+.|+++.
T Consensus 227 tt-i~q~~~~~g~~a~~~L 244 (269)
T cd06275 227 TT-IHQPKDRLGELAVNML 244 (269)
T ss_pred EE-EECCHHHHHHHHHHHH
T ss_conf 89-9619999999999999
No 122
>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=91.65 E-value=1.1 Score=24.24 Aligned_cols=88 Identities=17% Similarity=0.175 Sum_probs=59.0
Q ss_pred CCCCCCHHHHHHHHH-HHHCCCCCCEEEEECCCCHHHHHHHHHHHHHHHHHCCCCCC-EEEECCCCCHHHHHHHHHHCCC
Q ss_conf 278889899999999-98619986589996358613289999999999997299987-9997489858999999997699
Q gi|254781049|r 299 VGGGADQDKVAAAFK-IITSDSSVKGILINIFGGIMRCDVLVKGILSAVKEVKINIP-LVMRLEGANVDIGNRLIAESGL 376 (398)
Q Consensus 299 ~gG~a~~e~~~~a~~-~il~~~~vk~iliNifGGI~~cd~vA~gii~a~~~~~~~~p-ivvRl~Gtn~~~g~~il~~~g~ 376 (398)
.-+..+.+.-+++++ ++.++|++++||. ..|.+|.|.++|+++.+..-. .|+=..|+ .++++.+++-.+
T Consensus 160 ~~~~~~~~~~~~~~~~~L~~~pd~~ai~~-------~nD~~A~Ga~~al~~~g~~~di~vvG~D~~--~~~~~~i~~g~~ 230 (275)
T cd06320 160 QPADWDREKAYDVATTILQRNPDLKAIYC-------NNDTMALGVVEAVKNAGKQGKVLVVGTDGI--PEAYKSIRAGEL 230 (275)
T ss_pred CCCCCHHHHHHHHHHHHHHHCCCCCEEEE-------CCCHHHHHHHHHHHHCCCCCCEEEEEECCC--HHHHHHHHCCCC
T ss_conf 15530389999999998862876677996-------698899999999997699998299998976--999999864996
Q ss_pred CEEEECCHHHHHHHHHHHH
Q ss_conf 5899499899999999985
Q gi|254781049|r 377 NVITAIDLDDAAQKIVHAV 395 (398)
Q Consensus 377 ~~~~~~~~~~A~~~~v~~~ 395 (398)
......+..+..+.+++++
T Consensus 231 ~~tv~q~~~~~G~~av~~l 249 (275)
T cd06320 231 TATVDSFPALIGEVAMEVM 249 (275)
T ss_pred EEEECCCHHHHHHHHHHHH
T ss_conf 6998179999999999999
No 123
>PRK09701 D-allose transporter subunit; Provisional
Probab=91.41 E-value=1.1 Score=24.08 Aligned_cols=85 Identities=15% Similarity=0.222 Sum_probs=59.2
Q ss_pred CCCCHHHHHHH-HHHHHCCCCCCEEEEECCCCHHHHHHHHHHHHHHHHHCCCC-CCEEEECCCCCHHHHHHHHHHCCCCE
Q ss_conf 88898999999-99986199865899963586132899999999999972999-87999748985899999999769958
Q gi|254781049|r 301 GGADQDKVAAA-FKIITSDSSVKGILINIFGGIMRCDVLVKGILSAVKEVKIN-IPLVMRLEGANVDIGNRLIAESGLNV 378 (398)
Q Consensus 301 G~a~~e~~~~a-~~~il~~~~vk~iliNifGGI~~cd~vA~gii~a~~~~~~~-~pivvRl~Gtn~~~g~~il~~~g~~~ 378 (398)
+..+.++-++. -.++.++|++++||- ..|.+|-|.++|+++.+.+ .-.++-..|+.+ +.+.+++-.+..
T Consensus 196 ~~~d~~~a~~~~~~~L~a~Pdi~~I~~-------~nd~~a~Ga~~Al~~aG~~~~i~vvG~D~~~~--~~~~I~~G~i~a 266 (311)
T PRK09701 196 ADWDRIKALDVATNVLQRNPNIKAIYC-------ANDTMAMGVAQAVANAGKTGKVLVVGTDGIPE--ARKMVEAGQMTA 266 (311)
T ss_pred CCCCHHHHHHHHHHHHHCCCCCCEEEE-------CCCHHHHHHHHHHHHCCCCCCEEEEEECCCHH--HHHHHHCCCCEE
T ss_conf 776587799999999954999768997-------79726899999999669999839999789999--999998598279
Q ss_pred EEECCHHHHHHHHHHH
Q ss_conf 9949989999999998
Q gi|254781049|r 379 ITAIDLDDAAQKIVHA 394 (398)
Q Consensus 379 ~~~~~~~~A~~~~v~~ 394 (398)
....+-.+.-.++|+.
T Consensus 267 tv~Q~P~~~G~~av~~ 282 (311)
T PRK09701 267 TVAQNPADIGATGLKL 282 (311)
T ss_pred EEEECHHHHHHHHHHH
T ss_conf 9973999999999999
No 124
>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=91.40 E-value=1.2 Score=24.07 Aligned_cols=104 Identities=15% Similarity=0.132 Sum_probs=61.7
Q ss_pred HHHHHHCCCCCCEEEECCCCCCHHHHHHHHHHHH-CCCCCCEEEEECCCCHHHHHHHHHHHHHHHHHCCCCCCEEEECCC
Q ss_conf 9999965899624884278889899999999986-199865899963586132899999999999972999879997489
Q gi|254781049|r 283 MDIIKLYGGAPANFLDVGGGADQDKVAAAFKIIT-SDSSVKGILINIFGGIMRCDVLVKGILSAVKEVKINIPLVMRLEG 361 (398)
Q Consensus 283 mD~i~~~Gg~pANFlD~gG~a~~e~~~~a~~~il-~~~~vk~iliNifGGI~~cd~vA~gii~a~~~~~~~~pivvRl~G 361 (398)
.+.++.+|.++-...-+-+..+.+.-+++++-++ +.+++.+|| +..|.+|.|+++++++.+.++|==+.+-|
T Consensus 143 ~~al~~~gl~~~~~~~~~~~~~~~~~~~~~~~ll~~~~~p~Ai~-------~~nD~~A~g~l~~l~~~g~~vP~Disvig 215 (268)
T cd06271 143 RRALAEAGLPLDPALIVSGDMTEEGGYAAAAELLALPDRPTAIV-------CSSELMALGVLAALAEAGLRPGRDVSVVG 215 (268)
T ss_pred HHHHHHCCCCCCCCEEEECCCCHHHHHHHHHHHHHCCCCCCEEE-------ECCHHHHHHHHHHHHHCCCCCCCCEEEEE
T ss_conf 99999839997711365068757779999999996599986899-------77779999999999982999899979999
Q ss_pred CCHHHHHHHHHHCCCCEEEECCHHHHHHHHHHHH
Q ss_conf 8589999999976995899499899999999985
Q gi|254781049|r 362 ANVDIGNRLIAESGLNVITAIDLDDAAQKIVHAV 395 (398)
Q Consensus 362 tn~~~g~~il~~~g~~~~~~~~~~~A~~~~v~~~ 395 (398)
-.-..--+++ ...+.. ...+.++..++|+++.
T Consensus 216 fD~~~~~~~~-~p~LTt-i~~~~~~~g~~A~~~L 247 (268)
T cd06271 216 FDDSPPLLFF-SPPLTT-VRSDLRAAGRRLAELL 247 (268)
T ss_pred ECCCHHHHHC-CCCEEE-EECCHHHHHHHHHHHH
T ss_conf 7882899827-898089-9809999999999999
No 125
>cd06303 PBP1_LuxPQ_Quorum_Sensing Periplasmic binding protein (LuxP) of autoinducer-2 (AI-2) receptor LuxPQ from Vibrio harveyi and its close homologs. Periplasmic binding protein (LuxP) of autoinducer-2 (AI-2) receptor LuxPQ from Vibrio harveyi and its close homologs from other bacteria. The members of this group are highly homologous to a family of periplasmic pentose/hexose sugar-binding proteins that function as the primary receptors for chemotaxis and transport of many sugar based solutes in bacteria and archaea, and that are members of the type I periplasmic binding protein superfamily. The Vibrio harveyi AI-2 receptor consists of two polypeptides, LuxP and LuxQ: LuxP is a periplasmic binding protein that binds AI-2 by clamping it between two domains, LuxQ is an integral membrane protein belonging to the two-component sensor kinase family. Unlike AI-2 bound to the LsrB receptor in Salmonella typhimurium, the Vibrio harveyi AI-2 signaling molecule has an unusual furanosyl borate
Probab=91.29 E-value=1.2 Score=24.00 Aligned_cols=86 Identities=19% Similarity=0.143 Sum_probs=62.9
Q ss_pred CCCCCCHHHHHHHHHH-HHCCCCCCEEEEECCCCHHHHHHHHHHHHHHHHHCCCC-CCEEEECCCCCHHHHHHHHHHCCC
Q ss_conf 2788898999999999-86199865899963586132899999999999972999-879997489858999999997699
Q gi|254781049|r 299 VGGGADQDKVAAAFKI-ITSDSSVKGILINIFGGIMRCDVLVKGILSAVKEVKIN-IPLVMRLEGANVDIGNRLIAESGL 376 (398)
Q Consensus 299 ~gG~a~~e~~~~a~~~-il~~~~vk~iliNifGGI~~cd~vA~gii~a~~~~~~~-~pivvRl~Gtn~~~g~~il~~~g~ 376 (398)
.-|..++++-+++.+- +.++|++++|| ...|.+|.|.++|+++.+.. .-+|+-..|+-.+ .+.+++-.+
T Consensus 168 ~~~~~~r~~a~~~a~~~L~~~Pdi~~I~-------a~nd~mAlGa~~Al~~ag~~~~i~vvG~dg~~~~--l~ai~~G~l 238 (280)
T cd06303 168 FYTDATRQKAYQATSDILSNNPDVDFIY-------ACSTDIALGASDALKELGREDDILINGWGGGSAE--LDAIQQGEL 238 (280)
T ss_pred ECCCCCHHHHHHHHHHHHHHCCCCCEEE-------ECCCHHHHHHHHHHHHCCCCCCEEEEEECCCHHH--HHHHHCCCC
T ss_conf 5277668999999999998698930999-------7894578999999997398788799972799999--999984998
Q ss_pred CEEE---ECCHHHHHHHHHH
Q ss_conf 5899---4998999999999
Q gi|254781049|r 377 NVIT---AIDLDDAAQKIVH 393 (398)
Q Consensus 377 ~~~~---~~~~~~A~~~~v~ 393 (398)
.... -+|+--|+.-|+.
T Consensus 239 ~aTv~r~~dd~g~~~aeaik 258 (280)
T cd06303 239 DVTVMRMNDDTGVAMAEAIK 258 (280)
T ss_pred EEEEEECCCCHHHHHHHHHH
T ss_conf 58984026642199999999
No 126
>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=91.21 E-value=1.2 Score=23.95 Aligned_cols=103 Identities=14% Similarity=0.048 Sum_probs=64.8
Q ss_pred HHHHHHHCCCCCCEEEECCCCCCHHHHHHHHHHHH-CCCCCCEEEEECCCCHHHHHHHHHHHHHHHHHCCCCCCEEEECC
Q ss_conf 99999965899624884278889899999999986-19986589996358613289999999999997299987999748
Q gi|254781049|r 282 TMDIIKLYGGAPANFLDVGGGADQDKVAAAFKIIT-SDSSVKGILINIFGGIMRCDVLVKGILSAVKEVKINIPLVMRLE 360 (398)
Q Consensus 282 tmD~i~~~Gg~pANFlD~gG~a~~e~~~~a~~~il-~~~~vk~iliNifGGI~~cd~vA~gii~a~~~~~~~~pivvRl~ 360 (398)
..+.+..+|...-.-.-+-|..+.+.-+++++-++ .+++..++| +..|.+|-|+.+++++.++++|==+.+-
T Consensus 138 ~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~av~-------~~nD~~A~g~l~~l~~~gi~vP~disii 210 (269)
T cd06293 138 YREALAEAHIPEVPEYVCFGDYTREFGRAAAAQLLARGDPPTAIF-------AASDEIAIGLLEVLRERGLSIPGDMSLV 210 (269)
T ss_pred HHHHHHHCCCCCCCEEEEECCCCHHHHHHHHHHHHHCCCCCCEEE-------ECCHHHHHHHHHHHHHCCCCCCCCEEEE
T ss_conf 999999769999934899556311359999999984799985899-------6885999999999998499999965999
Q ss_pred CCCHHHHHHHHHHCCCCEE-EECCHHHHHHHHHHH
Q ss_conf 9858999999997699589-949989999999998
Q gi|254781049|r 361 GANVDIGNRLIAESGLNVI-TAIDLDDAAQKIVHA 394 (398)
Q Consensus 361 Gtn~~~g~~il~~~g~~~~-~~~~~~~A~~~~v~~ 394 (398)
|-+-. .+.+...-++. ...+.++..++|+++
T Consensus 211 gfd~~---~~~~~~~P~lTti~q~~~~ig~~A~~~ 242 (269)
T cd06293 211 GFDDV---GPAHLFAPPLTTIRQPVRELGRRAVAL 242 (269)
T ss_pred EECCH---HHHHHCCCCEEEEECCHHHHHHHHHHH
T ss_conf 88880---999830898489965999999999999
No 127
>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=90.85 E-value=1.3 Score=23.73 Aligned_cols=103 Identities=17% Similarity=0.195 Sum_probs=61.0
Q ss_pred HHHHHHCCCCCC-EEEECCCCCCHHHHHHHHHHHHC-CCCCCEEEEECCCCHHHHHHHHHHHHHHHHHCCCCCCEEEECC
Q ss_conf 999996589962-48842788898999999999861-9986589996358613289999999999997299987999748
Q gi|254781049|r 283 MDIIKLYGGAPA-NFLDVGGGADQDKVAAAFKIITS-DSSVKGILINIFGGIMRCDVLVKGILSAVKEVKINIPLVMRLE 360 (398)
Q Consensus 283 mD~i~~~Gg~pA-NFlD~gG~a~~e~~~~a~~~il~-~~~vk~iliNifGGI~~cd~vA~gii~a~~~~~~~~pivvRl~ 360 (398)
.+.+..+|.... .+.. .+..+.+.-+++++-+++ .+.+.+|| ...|.+|.|+++++++.+.++|==+.+-
T Consensus 134 ~~al~~~g~~~~~~~i~-~~~~~~~~~~~~~~~ll~~~~~p~Ai~-------~~nD~~A~g~~~~l~~~g~~vP~dvsvi 205 (261)
T cd06272 134 LETCDENGISISDSHID-VDGLSAEGGDNAAKKLLKESDLPTAII-------CGSYDIALGVLSALNKQGISIPEDIEII 205 (261)
T ss_pred HHHHHHCCCCCCCEEEE-ECCCHHHHHHHHHHHHHHCCCCCCCEE-------ECCHHHHHHHHHHHHHHCCCCCCCEEEE
T ss_conf 99999859985513898-303103679999999985278986101-------2768999999999998099999955999
Q ss_pred CCCHHHHHHHHHHCCCCEEEECCHHHHHHHHHHHH
Q ss_conf 98589999999976995899499899999999985
Q gi|254781049|r 361 GANVDIGNRLIAESGLNVITAIDLDDAAQKIVHAV 395 (398)
Q Consensus 361 Gtn~~~g~~il~~~g~~~~~~~~~~~A~~~~v~~~ 395 (398)
|-+-..-.+++. ..+.- ...+.++..++|+++.
T Consensus 206 GfDd~~~~~~~~-P~LTt-v~q~~~~ig~~A~~~L 238 (261)
T cd06272 206 SYDNIPQMAIID-PPLTA-VDVPIEEIAKKSLELL 238 (261)
T ss_pred EECCCHHHHHHC-CCCEE-EEECHHHHHHHHHHHH
T ss_conf 988818899509-98479-9809999999999999
No 128
>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=90.78 E-value=1.3 Score=23.69 Aligned_cols=86 Identities=16% Similarity=0.183 Sum_probs=60.1
Q ss_pred CCCCHHHHHHHHHHHH-CCC-CCCEEEEECCCCHHHHHHHHHHHHHHHHHCCCC-CCEEEECCCCCHHHHHHHHHHCCCC
Q ss_conf 8889899999999986-199-865899963586132899999999999972999-8799974898589999999976995
Q gi|254781049|r 301 GGADQDKVAAAFKIIT-SDS-SVKGILINIFGGIMRCDVLVKGILSAVKEVKIN-IPLVMRLEGANVDIGNRLIAESGLN 377 (398)
Q Consensus 301 G~a~~e~~~~a~~~il-~~~-~vk~iliNifGGI~~cd~vA~gii~a~~~~~~~-~pivvRl~Gtn~~~g~~il~~~g~~ 377 (398)
++.+.+.-++.++-+| +.| ++++|| ...|.+|.|.++|+++.+.. ...|+=..|+. ++++.+++-.+.
T Consensus 169 ~~~~~~~a~~~~~~~L~~~~~~i~aI~-------a~nD~~A~Ga~~Al~~aG~~~~v~vvG~Dg~~--~~l~~I~~G~~~ 239 (288)
T cd01538 169 PDWDPETAQKRMENALTANYNKVDGVL-------AANDGTAGGAIAALKAAGLAGKPPVTGQDAEL--AAVQRIVEGTQT 239 (288)
T ss_pred CCCCHHHHHHHHHHHHHHCCCCCCEEE-------ECCCHHHHHHHHHHHHCCCCCCCEEEECCCCH--HHHHHHHCCCCE
T ss_conf 785778899999999984655575898-------55856779999999974999987398359989--999999739825
Q ss_pred EEEECCHHHHHHHHHHHH
Q ss_conf 899499899999999985
Q gi|254781049|r 378 VITAIDLDDAAQKIVHAV 395 (398)
Q Consensus 378 ~~~~~~~~~A~~~~v~~~ 395 (398)
.....+..+-..++|+++
T Consensus 240 ~tv~Q~p~~~G~~av~~a 257 (288)
T cd01538 240 MTVYKDIRELAEAAAELA 257 (288)
T ss_pred EEEECCHHHHHHHHHHHH
T ss_conf 999559999999999999
No 129
>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=90.77 E-value=1.3 Score=23.68 Aligned_cols=101 Identities=16% Similarity=0.168 Sum_probs=61.1
Q ss_pred HHHHHHCCCCCCEEEECCCCCCHHHHHHHHHHHHC-CCCCCEEEEECCCCHHHHHHHHHHHHHHHHHCCCCCC---EEEE
Q ss_conf 99999658996248842788898999999999861-9986589996358613289999999999997299987---9997
Q gi|254781049|r 283 MDIIKLYGGAPANFLDVGGGADQDKVAAAFKIITS-DSSVKGILINIFGGIMRCDVLVKGILSAVKEVKINIP---LVMR 358 (398)
Q Consensus 283 mD~i~~~Gg~pANFlD~gG~a~~e~~~~a~~~il~-~~~vk~iliNifGGI~~cd~vA~gii~a~~~~~~~~p---ivvR 358 (398)
.+.+..+|..+-.-.-+-|..+.+..+++++-++. ++++.+|+ +..|.+|-|+++++++.++++| -|+=
T Consensus 140 ~~a~~~~~~~~~~~~i~~~~~~~~~~~~~~~~ll~~~~~~~aii-------~~~D~~A~g~~~~l~~~gi~vP~di~iig 212 (270)
T cd06296 140 RAALAEAGIPVDPALVREGDFSTESGFRAAAELLALPERPTAIF-------AGNDLMALGVYEAARERGLRIPEDLSVVG 212 (270)
T ss_pred HHHHHHCCCCCCHHHEEECCCHHHHHHHHHHHHHHCCCCCCCEE-------ECCCHHHHHHHHHHHHCCCCCCCCCEEEE
T ss_conf 99999869998855533065017899999999995499886203-------47868999999999986999999887999
Q ss_pred CCCCCHHHHHHHHHHCCCCEEEECCHHHHHHHHHHHH
Q ss_conf 4898589999999976995899499899999999985
Q gi|254781049|r 359 LEGANVDIGNRLIAESGLNVITAIDLDDAAQKIVHAV 395 (398)
Q Consensus 359 l~Gtn~~~g~~il~~~g~~~~~~~~~~~A~~~~v~~~ 395 (398)
..++..- +++ ...+.. ...+..+..++|+++.
T Consensus 213 fd~~~~~---~~~-~p~ltt-I~~~~~~~g~~a~~~l 244 (270)
T cd06296 213 FDDLPEA---RWV-SPPLTT-VRQPLREMGRAAVRLL 244 (270)
T ss_pred ECCHHHH---HHC-CCCEEE-EEECHHHHHHHHHHHH
T ss_conf 7887899---852-898389-9829999999999999
No 130
>cd06301 PBP1_rhizopine_binding_like Periplasmic binding proteins specific to rhizopines. Periplasmic binding proteins specific to rhizopines, which are simple sugar-like compounds produced in the nodules induced by the symbiotic root nodule bacteria, such as Rhizobium and Sinorhizobium. Rhizopine-binding-like proteins from other bacteria are also included. Two inositol based rhizopine compounds are known to date: L-3-O-methly-scyllo-inosamine (3-O-MSI) and scyllo-inosamine. Bacterial strains that can metabolize rhizopine have a greater competitive advantage in nodulation and rhizopine synthesis is regulated by NifA/NtrA regulatory transcription activators which are maximally expressed at the onset of nitrogen fixation in bacteroids. The members of this group belong to the pentose/hexose sugar-binding protein family of the type I periplasmic binding protein superfamily.
Probab=90.53 E-value=1.4 Score=23.54 Aligned_cols=86 Identities=13% Similarity=0.172 Sum_probs=54.8
Q ss_pred CCCCHHHHHHHHH-HHHCCCCCCEEEEECCCCHHHHHHHHHHHHHHHHHCCCCC-C-EEEECCCCCHHHHHHHHHHCCCC
Q ss_conf 8889899999999-9861998658999635861328999999999999729998-7-99974898589999999976995
Q gi|254781049|r 301 GGADQDKVAAAFK-IITSDSSVKGILINIFGGIMRCDVLVKGILSAVKEVKINI-P-LVMRLEGANVDIGNRLIAESGLN 377 (398)
Q Consensus 301 G~a~~e~~~~a~~-~il~~~~vk~iliNifGGI~~cd~vA~gii~a~~~~~~~~-p-ivvRl~Gtn~~~g~~il~~~g~~ 377 (398)
|..+.+..++.++ ++.++|++++||- .-|.+|-|.++|+++.+..- . .|+=..|+ .++.+.+++-.+.
T Consensus 163 ~~~~~~~a~~~~~~~L~~~~~~~aI~~-------~nd~~a~Ga~~al~~~g~~~~~i~v~G~D~~--~~~~~~i~~g~~~ 233 (272)
T cd06301 163 ANWSRAEAMDLMENWLSSGGKIDAVVA-------NNDEMALGAIMALKAAGKSDKDVPVAGIDGT--PDALAAVKKGDLD 233 (272)
T ss_pred CCHHHHHHHHHHHHHHHHCCCCCEEEE-------CCCHHHHHHHHHHHHCCCCCCCEEEEEECCC--HHHHHHHHCCCCE
T ss_conf 312357899999999983677787995-------5827899999999986989998799998985--9999998749976
Q ss_pred EEEECCHHHHHHHHHHHH
Q ss_conf 899499899999999985
Q gi|254781049|r 378 VITAIDLDDAAQKIVHAV 395 (398)
Q Consensus 378 ~~~~~~~~~A~~~~v~~~ 395 (398)
.....+..+-.+.+|+++
T Consensus 234 ~tv~q~~~~~G~~av~~~ 251 (272)
T cd06301 234 VTVFQDAKGQGAGALDAA 251 (272)
T ss_pred EEEECCHHHHHHHHHHHH
T ss_conf 998069999999999999
No 131
>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=90.28 E-value=1.5 Score=23.40 Aligned_cols=88 Identities=17% Similarity=0.220 Sum_probs=53.5
Q ss_pred CCCCCHHHHHHH-HHHHHCCCCCCEEEEECCCCHHHHHHHHHHHHHHHHHCCCC-CCEEEECCCCCHHHHHHHHHHCCCC
Q ss_conf 788898999999-99986199865899963586132899999999999972999-8799974898589999999976995
Q gi|254781049|r 300 GGGADQDKVAAA-FKIITSDSSVKGILINIFGGIMRCDVLVKGILSAVKEVKIN-IPLVMRLEGANVDIGNRLIAESGLN 377 (398)
Q Consensus 300 gG~a~~e~~~~a-~~~il~~~~vk~iliNifGGI~~cd~vA~gii~a~~~~~~~-~pivvRl~Gtn~~~g~~il~~~g~~ 377 (398)
-+..+.++..+. -.++.++|++++||- ..|.+|.|.++|+++.+.+ ++|+ -..+ ..+.+.+++++--+.
T Consensus 165 ~~~~~~~~a~~~~~~~L~~~Pdi~~I~~-------~nd~~a~Ga~~Al~~aG~~~v~iv-g~d~-g~~~~~~~i~~G~~~ 235 (294)
T cd06316 165 KGIDGPSKAEDIANAMLTQNPDLKGIYA-------VWDVPAEGVIAALRAAGRDDIKVT-TVDL-GLNVALDMAKGGNVA 235 (294)
T ss_pred CCCCCHHHHHHHHHHHHHHCCCCCEEEE-------CCCHHHHHHHHHHHHCCCCCCEEE-EEEC-CCHHHHHHHHCCCCE
T ss_conf 3888889999999999973999888998-------686365999999998199983799-9958-968999999779977
Q ss_pred EEEECCHH----HHHHHHHHHHH
Q ss_conf 89949989----99999999850
Q gi|254781049|r 378 VITAIDLD----DAAQKIVHAVK 396 (398)
Q Consensus 378 ~~~~~~~~----~A~~~~v~~~k 396 (398)
.....+-. .+++.++.+.+
T Consensus 236 atv~q~p~~~G~~~v~~a~~~l~ 258 (294)
T cd06316 236 GIGAQRPYDQGVAEARLAALALI 258 (294)
T ss_pred EEEEECHHHHHHHHHHHHHHHHC
T ss_conf 99983889999999999999977
No 132
>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=90.18 E-value=1.5 Score=23.35 Aligned_cols=102 Identities=16% Similarity=0.276 Sum_probs=64.2
Q ss_pred HHHHHHHCCCCCCEEEECCCCCCHHHHHHHHHHHHCCCCCCEEEEECCCCHHHHHHHHHHHHHHHHHCCCCCCEEEECCC
Q ss_conf 99999965899624884278889899999999986199865899963586132899999999999972999879997489
Q gi|254781049|r 282 TMDIIKLYGGAPANFLDVGGGADQDKVAAAFKIITSDSSVKGILINIFGGIMRCDVLVKGILSAVKEVKINIPLVMRLEG 361 (398)
Q Consensus 282 tmD~i~~~Gg~pANFlD~gG~a~~e~~~~a~~~il~~~~vk~iliNifGGI~~cd~vA~gii~a~~~~~~~~pivvRl~G 361 (398)
..+.+..+|.++..+.. +..+.+.-+++++-+++...+.+|| ..-|.+|.|+++++++.+.++|==+.+-|
T Consensus 137 ~~~al~~~g~~~~~~~~--~~~~~~~~~~~~~~ll~~~~~~Ai~-------~~nD~~A~g~~~~l~~~g~~vP~Disvig 207 (259)
T cd01542 137 YLDALKEHGICPPNIVE--TDFSYESAYEAAQELLEPQPPDAIV-------CATDTIALGAMKYLQELGRRIPEDISVAG 207 (259)
T ss_pred HHHHHHHCCCCCCEEEE--CCCCHHHHHHHHHHHHHCCCCCCEE-------ECCHHHHHHHHHHHHHCCCCCCCCEEEEE
T ss_conf 99999976999635996--5787778999999997457998324-------34589999999999981999999869999
Q ss_pred C-CHHHHHHHHHHCCCCEEEECCHHHHHHHHHHHH
Q ss_conf 8-589999999976995899499899999999985
Q gi|254781049|r 362 A-NVDIGNRLIAESGLNVITAIDLDDAAQKIVHAV 395 (398)
Q Consensus 362 t-n~~~g~~il~~~g~~~~~~~~~~~A~~~~v~~~ 395 (398)
- |.+.+ +++ ...+.. ...+..+..++|+++.
T Consensus 208 fdd~~~~-~~~-~P~LTt-v~q~~~~~G~~A~~~L 239 (259)
T cd01542 208 FGGYELS-SVV-TPSLTT-VDFGYKEAGKKAAELL 239 (259)
T ss_pred ECCHHHH-HHC-CCCCEE-EEECHHHHHHHHHHHH
T ss_conf 8982999-826-899789-9959999999999999
No 133
>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=90.05 E-value=1.5 Score=23.28 Aligned_cols=102 Identities=15% Similarity=0.148 Sum_probs=65.8
Q ss_pred HHHHHHHCCCCCCEEEECCCCCCHHHHHHHHHHHHC-CCCCCEEEEECCCCHHHHHHHHHHHHHHHHHCCCCCCEEEECC
Q ss_conf 999999658996248842788898999999999861-9986589996358613289999999999997299987999748
Q gi|254781049|r 282 TMDIIKLYGGAPANFLDVGGGADQDKVAAAFKIITS-DSSVKGILINIFGGIMRCDVLVKGILSAVKEVKINIPLVMRLE 360 (398)
Q Consensus 282 tmD~i~~~Gg~pANFlD~gG~a~~e~~~~a~~~il~-~~~vk~iliNifGGI~~cd~vA~gii~a~~~~~~~~pivvRl~ 360 (398)
..+.++.+|.....-+-+.+..+.+.-+++++-+++ .+.+.+|| .-.|.+|-|+++++++.++++|==+.+-
T Consensus 141 f~~al~~~g~~~~~~~~~~~~~~~~~g~~~~~~ll~~~~~p~Ai~-------~~nD~~A~g~l~~l~~~Gi~vP~Disvi 213 (269)
T cd06297 141 FQQALKDAGRPFSPDLLAITDHSEEGGRLAMRHLLEKASPPLAVF-------ASADQQALGALQEAVELGLTVGEDVRVV 213 (269)
T ss_pred HHHHHHHCCCCCCCCEEECCCCCHHHHHHHHHHHHHCCCCCCEEE-------ECCHHHHHHHHHHHHHCCCCCCCCEEEE
T ss_conf 999999829986622341378636569999999983699985899-------8978999999999998399889966999
Q ss_pred CCCH-HHHHHHHHHCCCCEEEECCHHHHHHHHHHHH
Q ss_conf 9858-9999999976995899499899999999985
Q gi|254781049|r 361 GANV-DIGNRLIAESGLNVITAIDLDDAAQKIVHAV 395 (398)
Q Consensus 361 Gtn~-~~g~~il~~~g~~~~~~~~~~~A~~~~v~~~ 395 (398)
|-+- +.+ +..+|... ..+..+..++|+++.
T Consensus 214 GfDd~~~a----~~~~LTTv-~q~~~~~G~~A~~~L 244 (269)
T cd06297 214 GFDDHPFA----REAGLSTL-AQPVEAMGARAAQLL 244 (269)
T ss_pred EECCHHHH----HCCCCCEE-ECCHHHHHHHHHHHH
T ss_conf 98984897----24898679-639999999999999
No 134
>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=89.79 E-value=1.6 Score=23.15 Aligned_cols=86 Identities=12% Similarity=0.182 Sum_probs=58.8
Q ss_pred CCCCCHHHHHHHHHHHH-CCC-CCCEEEEECCCCHHHHHHHHHHHHHHHHHCCCCCC---EEEECCCCCHHHHHHHHHHC
Q ss_conf 78889899999999986-199-86589996358613289999999999997299987---99974898589999999976
Q gi|254781049|r 300 GGGADQDKVAAAFKIIT-SDS-SVKGILINIFGGIMRCDVLVKGILSAVKEVKINIP---LVMRLEGANVDIGNRLIAES 374 (398)
Q Consensus 300 gG~a~~e~~~~a~~~il-~~~-~vk~iliNifGGI~~cd~vA~gii~a~~~~~~~~p---ivvRl~Gtn~~~g~~il~~~ 374 (398)
.|..+.+.-+++++-+| ++| .+++|| ..-|.+|.|.++|+++.+.++| .|+-..|+ .++.+.+++-
T Consensus 163 ~~~~~~~~~~~~~~~~L~~~p~~i~ai~-------~~nd~~a~Ga~~al~~~G~~~~~di~ivg~D~~--~~~~~~i~~g 233 (273)
T cd06309 163 TGDFTRAKGKEVMEALLKAHGDDIDAVY-------AHNDEMALGAIQAIKAAGKKPGKDIKIVSIDGT--KDAFQAMADG 233 (273)
T ss_pred CCCCCHHHHHHHHHHHHHHCCCCCCEEE-------ECCCHHHHHHHHHHHHCCCCCCCCEEEEEECCC--HHHHHHHHCC
T ss_conf 2346889999999999972788888898-------678579999999999839999998699998999--9999998769
Q ss_pred CCCEEEECCHHHHHHHHHHHH
Q ss_conf 995899499899999999985
Q gi|254781049|r 375 GLNVITAIDLDDAAQKIVHAV 395 (398)
Q Consensus 375 g~~~~~~~~~~~A~~~~v~~~ 395 (398)
.+......+-. ..+++|+++
T Consensus 234 ~l~~~~~~~p~-~G~~Av~~l 253 (273)
T cd06309 234 KLNATVECNPL-FGPLAFDTL 253 (273)
T ss_pred CCEEEEECCHH-HHHHHHHHH
T ss_conf 97199978399-999999999
No 135
>PRK10727 DNA-binding transcriptional regulator GalR; Provisional
Probab=89.67 E-value=1.6 Score=23.09 Aligned_cols=107 Identities=14% Similarity=0.152 Sum_probs=69.2
Q ss_pred HHHHHHHHHCCCCCCEEEECCCCCCHHHHHHHHHHHHC-CCCCCEEEEECCCCHHHHHHHHHHHHHHHHHCCCCCCEEEE
Q ss_conf 99999999658996248842788898999999999861-99865899963586132899999999999972999879997
Q gi|254781049|r 280 MATMDIIKLYGGAPANFLDVGGGADQDKVAAAFKIITS-DSSVKGILINIFGGIMRCDVLVKGILSAVKEVKINIPLVMR 358 (398)
Q Consensus 280 matmD~i~~~Gg~pANFlD~gG~a~~e~~~~a~~~il~-~~~vk~iliNifGGI~~cd~vA~gii~a~~~~~~~~pivvR 358 (398)
-...+.+..+|..+-..+=.-+..+.+.-+++++-+++ .+.+.+|| .-.|.+|-|+++|+++.++++|==+.
T Consensus 196 ~g~~~al~~~gl~~~~~~i~~~~~~~~~~~~~~~~ll~~~~~~tAi~-------~~nD~~A~g~l~al~~~Gl~VP~Dis 268 (342)
T PRK10727 196 QGYYDALAESGIPANDRLVTFGEPDESGGEQAMTELLGRGRNFTAVA-------CYNDSMAAGAMGVLNDNGIDVPGEIS 268 (342)
T ss_pred HHHHHHHHHCCCCCCCCEEEECCCCHHHHHHHHHHHHHCCCCCCCCE-------ECCHHHHHHHHHHHHHCCCCCCCCEE
T ss_conf 99999999769999820588157877889999999985599977415-------54699999999999982999999869
Q ss_pred CCCCCHHHHHHHHHHCCCCEEEECCHHHHHHHHHHHH
Q ss_conf 4898589999999976995899499899999999985
Q gi|254781049|r 359 LEGANVDIGNRLIAESGLNVITAIDLDDAAQKIVHAV 395 (398)
Q Consensus 359 l~Gtn~~~g~~il~~~g~~~~~~~~~~~A~~~~v~~~ 395 (398)
+-|-+--.--+. -...|.- ...+.++..+.|+++.
T Consensus 269 ViGfDd~~~~~~-~~P~LTT-V~~p~~e~g~~A~~lL 303 (342)
T PRK10727 269 LIGFDDVLVSRY-VRPRLTT-VRYPIVTMATQAAELA 303 (342)
T ss_pred EEEECCHHHHHC-CCCCCEE-EECCHHHHHHHHHHHH
T ss_conf 998897189864-8899858-9779999999999999
No 136
>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=89.54 E-value=1.7 Score=23.03 Aligned_cols=103 Identities=12% Similarity=0.044 Sum_probs=64.0
Q ss_pred HHHHHHCCCCCCEEEECCCCCCHHHHHHHHHHHH-CCCC-CCEEEEECCCCHHHHHHHHHHHHHHHHHCCCCCCEEEECC
Q ss_conf 9999965899624884278889899999999986-1998-6589996358613289999999999997299987999748
Q gi|254781049|r 283 MDIIKLYGGAPANFLDVGGGADQDKVAAAFKIIT-SDSS-VKGILINIFGGIMRCDVLVKGILSAVKEVKINIPLVMRLE 360 (398)
Q Consensus 283 mD~i~~~Gg~pANFlD~gG~a~~e~~~~a~~~il-~~~~-vk~iliNifGGI~~cd~vA~gii~a~~~~~~~~pivvRl~ 360 (398)
.+.+..+|.....-+-+.+..+.+.-+++++-++ +.+. ..+|| +..|.+|.|+++++++.+.++|==+.+-
T Consensus 139 ~~al~~~g~~~~~~~i~~~~~~~~~g~~~~~~~l~~~~~~p~ai~-------~~nd~~a~g~l~~l~~~g~~vP~disvv 211 (264)
T cd06274 139 RQALADAGLPVQPDWIYAEGYSPESGYQLMAELLARLGRLPRALF-------TTSYTLLEGVLRFLRERPGLAPSDLRIA 211 (264)
T ss_pred HHHHHHCCCCCCCEEEEECCCCHHHHHHHHHHHHHHCCCCCCCCC-------CCCHHHHHHHHHHHHHCCCCCCCCEEEE
T ss_conf 999997799877407982688878999999999986568874220-------1769999999999998599999987999
Q ss_pred CCCHHHHHHHHHHCCCCEE-EECCHHHHHHHHHHHH
Q ss_conf 9858999999997699589-9499899999999985
Q gi|254781049|r 361 GANVDIGNRLIAESGLNVI-TAIDLDDAAQKIVHAV 395 (398)
Q Consensus 361 Gtn~~~g~~il~~~g~~~~-~~~~~~~A~~~~v~~~ 395 (398)
|-.-. .+.+-...++. ...+.++.+++|+++.
T Consensus 212 gfDd~---~~a~~~~p~LTtv~q~~~~~g~~A~~lL 244 (264)
T cd06274 212 TFDDH---PLLDFLPFPVHSVPQDHEALAEAAFELA 244 (264)
T ss_pred EECCH---HHHHHCCCCCEEEECCHHHHHHHHHHHH
T ss_conf 98986---8997379997699679999999999999
No 137
>cd07018 S49_SppA_67K_type Signal peptide peptidase A (SppA) 67K type, a serine protease, has catalytic Ser-Lys dyad. Signal peptide peptidase A (SppA; Peptidase S49; Protease IV) 67K type: SppA is found in all three domains of life and is involved in the cleavage of signal peptides after their removal from the precursor proteins by signal peptidases. Members in this subfamily contain an amino-terminal domain in addition to the carboxyl-terminal protease domain that is conserved in all the S49 family members (sometimes referred to as 67K type), similar to E. coli and Arabidopsis thaliana SppA peptidases. Unlike the eukaryotic functional homologs that are proposed to be aspartic proteases, site-directed mutagenesis and sequence analysis have shown that members in this subfamily, mostly bacterial, are serine proteases. The predicted active site serine for members in this family occurs in a transmembrane domain. Mutagenesis studies also suggest that the catalytic center comprises a Ser-Lys
Probab=89.32 E-value=1.7 Score=22.92 Aligned_cols=24 Identities=17% Similarity=0.378 Sum_probs=18.0
Q ss_pred CCCHHHHHHHHHHHHHHHHHHHHC
Q ss_conf 988899885999999998999955
Q gi|254781049|r 178 ELQGQARIDGGDLFPNLYKAFCDK 201 (398)
Q Consensus 178 g~~~~~~~~~~~ii~~L~~~f~e~ 201 (398)
.++.+..+.+..++..+|+.|.+.
T Consensus 152 ~~s~e~re~~~~~l~~~~~~f~~~ 175 (222)
T cd07018 152 DMSPEAREQTQALLDSLWDQYLAD 175 (222)
T ss_pred CCCHHHHHHHHHHHHHHHHHHHHH
T ss_conf 658999999999999999999999
No 138
>PRK02472 murD UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional
Probab=89.31 E-value=1.7 Score=22.92 Aligned_cols=90 Identities=17% Similarity=0.252 Sum_probs=59.3
Q ss_pred EEECCCCCCHHHHHHHHHHHHCCCCCCEEEEECCCCHHHHHHHHHHHHHHHHHCCCCCCEEEECCCCCHHHHHHHHHHCC
Q ss_conf 88427888989999999998619986589996358613289999999999997299987999748985899999999769
Q gi|254781049|r 296 FLDVGGGADQDKVAAAFKIITSDSSVKGILINIFGGIMRCDVLVKGILSAVKEVKINIPLVMRLEGANVDIGNRLIAESG 375 (398)
Q Consensus 296 FlD~gG~a~~e~~~~a~~~il~~~~vk~iliNifGGI~~cd~vA~gii~a~~~~~~~~pivvRl~Gtn~~~g~~il~~~g 375 (398)
|.|=+=.++.+.+..|++-. . . +.+| |.||..+-....+ +...++. +.-++ +-|.+.+.=.+.+++.+
T Consensus 325 ~iNDSKaTN~~at~~Al~~~-~-~--~iil--I~GG~~Kg~d~~~-l~~~~~~----vk~v~-~~G~~~~~i~~~~~~~~ 392 (450)
T PRK02472 325 FYNDSKATNILATQKALSGF-N-Q--PVIL--LAGGLDRGNEFDE-LIPYLKN----VKAMV-VFGETAPKLARAANKAG 392 (450)
T ss_pred EEECCCCCCHHHHHHHHHCC-C-C--CEEE--EEECCCCCCCHHH-HHHHHHC----CCEEE-EECCCHHHHHHHHHHCC
T ss_conf 98268888999999998458-9-9--8799--9915556888799-9999737----68999-96889999999997379
Q ss_pred CCEEEECCHHHHHHHHHHHHHC
Q ss_conf 9589949989999999998506
Q gi|254781049|r 376 LNVITAIDLDDAAQKIVHAVKG 397 (398)
Q Consensus 376 ~~~~~~~~~~~A~~~~v~~~k~ 397 (398)
++++.+++|++|+++|.+.++.
T Consensus 393 ~~~~~~~~l~~Av~~a~~~a~~ 414 (450)
T PRK02472 393 ITIVEADNVEDAVPKAYALSEP 414 (450)
T ss_pred CEEEECCCHHHHHHHHHHHCCC
T ss_conf 7189879999999999985889
No 139
>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=89.23 E-value=1.7 Score=22.88 Aligned_cols=105 Identities=19% Similarity=0.176 Sum_probs=67.4
Q ss_pred HHHHHHHHCCCCCCEEEECCCCCCHHHHHHHHHHHH-CCCCCCEEEEECCCCHHHHHHHHHHHHHHHHHCC-CCCCE---
Q ss_conf 999999965899624884278889899999999986-1998658999635861328999999999999729-99879---
Q gi|254781049|r 281 ATMDIIKLYGGAPANFLDVGGGADQDKVAAAFKIIT-SDSSVKGILINIFGGIMRCDVLVKGILSAVKEVK-INIPL--- 355 (398)
Q Consensus 281 atmD~i~~~Gg~pANFlD~gG~a~~e~~~~a~~~il-~~~~vk~iliNifGGI~~cd~vA~gii~a~~~~~-~~~pi--- 355 (398)
...+.++.+|.......=..|..+.+.-+++++-++ +.|.+.+|| ...|.+|-|.++++++.+ .++|=
T Consensus 142 Gf~~al~~~g~~~~~~~~~~~~~~~~~g~~~~~~ll~~~~~~~Ai~-------~~nD~~A~G~~~al~~~G~~~vP~dv~ 214 (281)
T pfam00532 142 GFMAALAAAGREVKIYHVATGDNDIPDAALAANAMLVSHPTIDAIV-------AMNDEAAMGAVRALLKQGRVKIPDIVG 214 (281)
T ss_pred HHHHHHHHCCCCCCCEEEEECCCCHHHHHHHHHHHHHCCCCCEEEE-------ECCHHHHHHHHHHHHHCCCCCCCCHHC
T ss_conf 9999999759999820688368888999999999985499960999-------758799999999999829997883112
Q ss_pred -----EEECCCCCHHHHHHHHHHCCCCEEEECCHHHHHHHHHHH
Q ss_conf -----997489858999999997699589949989999999998
Q gi|254781049|r 356 -----VMRLEGANVDIGNRLIAESGLNVITAIDLDDAAQKIVHA 394 (398)
Q Consensus 356 -----vvRl~Gtn~~~g~~il~~~g~~~~~~~~~~~A~~~~v~~ 394 (398)
|+-..|.....--.+ -...|.- ...+.++..++|+++
T Consensus 215 i~~~svvg~d~~~~~~~~~~-~~P~LTT-V~qp~~~mG~~A~~~ 256 (281)
T pfam00532 215 IGINSVVGFDGLSKAQDTGL-YLSPLTV-IQLPRQLLGIKASDM 256 (281)
T ss_pred CCCCCEEEEECCCHHHHHHC-CCCCCEE-EECCHHHHHHHHHHH
T ss_conf 57776699908832566503-8998437-955999999999999
No 140
>PRK03815 murD UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional
Probab=89.06 E-value=1.8 Score=22.80 Aligned_cols=106 Identities=19% Similarity=0.177 Sum_probs=67.1
Q ss_pred HHHHHHHCCCCC---C--------EEEECCCCCCHHHHHHHHHHHHCCCCCCEEEEECCCCHHHHHHHHHHHHHHHHHCC
Q ss_conf 999999658996---2--------48842788898999999999861998658999635861328999999999999729
Q gi|254781049|r 282 TMDIIKLYGGAP---A--------NFLDVGGGADQDKVAAAFKIITSDSSVKGILINIFGGIMRCDVLVKGILSAVKEVK 350 (398)
Q Consensus 282 tmD~i~~~Gg~p---A--------NFlD~gG~a~~e~~~~a~~~il~~~~vk~iliNifGGI~~cd~vA~gii~a~~~~~ 350 (398)
..+.++.+.|-| - .|.|=+=+++.+.+..|++-. .++ +.+| |.||..+-.+..+ +.+.+++.
T Consensus 252 ~~~~l~~F~gl~HRlE~v~~~~gv~fiNDSKATN~~At~~Al~~~-~~~--~iil--I~GG~~Kg~d~~~-L~~~i~~~- 324 (401)
T PRK03815 252 DYERLNAFVIEAHKLEEFRDKQGRLWVDDSKATNIDATIQALKRY-KDK--KIHL--ILGGDDKGVDLTP-LFEELKNF- 324 (401)
T ss_pred HHHHHHHCCCCCCCEEEEEEECCEEEECCCCCCCHHHHHHHHHHC-CCC--CEEE--EECCCCCCCCHHH-HHHHHHHH-
T ss_conf 899998489988853899984898996688789889999999837-678--6799--9637655678799-99997640-
Q ss_pred CCCCEEEECCCCCHHHHHHHHHHCCCCEEEECCHHHHHHHHHHHHHC
Q ss_conf 99879997489858999999997699589949989999999998506
Q gi|254781049|r 351 INIPLVMRLEGANVDIGNRLIAESGLNVITAIDLDDAAQKIVHAVKG 397 (398)
Q Consensus 351 ~~~pivvRl~Gtn~~~g~~il~~~g~~~~~~~~~~~A~~~~v~~~k~ 397 (398)
+ .-+-+-|.+.+.=.+.+++.+++++.+++|++|++.|-+.++.
T Consensus 325 --~-~~v~~~G~~~~~i~~~~~~~~~~~~~~~~l~eAv~~a~~~a~~ 368 (401)
T PRK03815 325 --D-IEIYAIGSNAEKILALAKEFNIKAQKCEFLEKAVNEIKKVLKQ 368 (401)
T ss_pred --C-EEEEEECCCHHHHHHHHHHCCCCEEECCCHHHHHHHHHHHCCC
T ss_conf --5-6999987899999999875698469828699999999985789
No 141
>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=88.96 E-value=1.8 Score=22.76 Aligned_cols=102 Identities=13% Similarity=0.071 Sum_probs=60.8
Q ss_pred HHHHHHCCCCCCEEEECCCCCCHHHHHHHHHHHH-CCCCCCEEEEECCCCHHHHHHHHHHHHHHHHHCCCCCCEEEECCC
Q ss_conf 9999965899624884278889899999999986-199865899963586132899999999999972999879997489
Q gi|254781049|r 283 MDIIKLYGGAPANFLDVGGGADQDKVAAAFKIIT-SDSSVKGILINIFGGIMRCDVLVKGILSAVKEVKINIPLVMRLEG 361 (398)
Q Consensus 283 mD~i~~~Gg~pANFlD~gG~a~~e~~~~a~~~il-~~~~vk~iliNifGGI~~cd~vA~gii~a~~~~~~~~pivvRl~G 361 (398)
.+.+..+|..+-...-..+. +.+..+++++-++ ..+.+.+|| ...|.+|.|+++++++.+.++|==+.+-|
T Consensus 139 ~~al~~~g~~~~~~~~~~~~-~~~~~~~~~~~ll~~~~~p~ai~-------~~~d~~A~g~l~~l~~~g~~VP~disviG 210 (269)
T cd06281 139 KAAFAAAGLPPDPALVRLST-PAASGFDATRALLALPDRPTAII-------AGGTQVLVGVLRALREAGLRIPRDLSVIS 210 (269)
T ss_pred HHHHHHCCCCCCCEEEECCC-CHHHHHHHHHHHHHCCCCCCEEE-------ECCHHHHHHHHHHHHHCCCCCCCCEEEEE
T ss_conf 99999779999943997799-74899999999980799996565-------12338899999999981999999869999
Q ss_pred CCHHHHHHHHHHCCCCEE-EECCHHHHHHHHHHHH
Q ss_conf 858999999997699589-9499899999999985
Q gi|254781049|r 362 ANVDIGNRLIAESGLNVI-TAIDLDDAAQKIVHAV 395 (398)
Q Consensus 362 tn~~~g~~il~~~g~~~~-~~~~~~~A~~~~v~~~ 395 (398)
-+-.. +.+...-++. ...+..+..++|+++.
T Consensus 211 fD~~~---~~~~~~P~LTTi~~~~~~~g~~A~~~L 242 (269)
T cd06281 211 IGDSD---LAELMDPPITALRRDREAVGRTAAELM 242 (269)
T ss_pred ECCHH---HHHHCCCCCEEEECCHHHHHHHHHHHH
T ss_conf 88879---998358996799749999999999999
No 142
>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=88.42 E-value=2 Score=22.53 Aligned_cols=88 Identities=20% Similarity=0.214 Sum_probs=54.9
Q ss_pred CCCCCCHHHHHHHHHHHHC-CCCCCEEEEECCCCHHHHHHHHHHHHHHHHHCCCCCCEEEECCCC-CHHHHHHHHHHCCC
Q ss_conf 2788898999999999861-998658999635861328999999999999729998799974898-58999999997699
Q gi|254781049|r 299 VGGGADQDKVAAAFKIITS-DSSVKGILINIFGGIMRCDVLVKGILSAVKEVKINIPLVMRLEGA-NVDIGNRLIAESGL 376 (398)
Q Consensus 299 ~gG~a~~e~~~~a~~~il~-~~~vk~iliNifGGI~~cd~vA~gii~a~~~~~~~~pivvRl~Gt-n~~~g~~il~~~g~ 376 (398)
+-+..+.+..+++++-+++ .+++.+|| ...|.+|-|+++++++.+.++|==+.+-|- |.+...+.+. .++
T Consensus 155 ~~~~~~~~~~~~~~~~ll~~~~~~dai~-------~~~d~~A~g~~~~l~~~gi~vP~di~iigfD~~~~~~~~~~-P~l 226 (269)
T cd06288 155 VHGDWSADDGYEAAAALLDLDDRPTAIF-------CGNDRMAMGAYQALLERGLRIPQDVSVVGFDNQEIIAEHLR-PPL 226 (269)
T ss_pred ECCCCCHHHHHHHHHHHHHCCCCCCEEC-------CCCHHHHHHHHHHHHHCCCCCCCCEEEEEECCCHHHHHHCC-CCC
T ss_conf 1267766777777799985589986101-------47789999999999985999999889999888689996378-996
Q ss_pred CEEEECCHHHHHHHHHHHH
Q ss_conf 5899499899999999985
Q gi|254781049|r 377 NVITAIDLDDAAQKIVHAV 395 (398)
Q Consensus 377 ~~~~~~~~~~A~~~~v~~~ 395 (398)
..+ ..+.++..++|+++.
T Consensus 227 Tti-~q~~~~~g~~A~~~l 244 (269)
T cd06288 227 TTV-ALPHYEMGRWAVELL 244 (269)
T ss_pred EEE-EECHHHHHHHHHHHH
T ss_conf 499-809999999999999
No 143
>PRK10653 D-ribose transporter subunit RbsB; Provisional
Probab=88.31 E-value=2 Score=22.48 Aligned_cols=86 Identities=19% Similarity=0.270 Sum_probs=58.6
Q ss_pred CCCCHHHHHHHHHH-HHCCCCCCEEEEECCCCHHHHHHHHHHHHHHHHHCCCCCCEEEECCCCCHHHHHHHHHHCCCCEE
Q ss_conf 88898999999999-86199865899963586132899999999999972999879997489858999999997699589
Q gi|254781049|r 301 GGADQDKVAAAFKI-ITSDSSVKGILINIFGGIMRCDVLVKGILSAVKEVKINIPLVMRLEGANVDIGNRLIAESGLNVI 379 (398)
Q Consensus 301 G~a~~e~~~~a~~~-il~~~~vk~iliNifGGI~~cd~vA~gii~a~~~~~~~~pivvRl~Gtn~~~g~~il~~~g~~~~ 379 (398)
+..+.+.-+++++- +.++|++++||- ..|.+|-|.++|+++.+++-..|+=..|+. ++...+++.-+...
T Consensus 187 ~~~~~~~g~~~~~~lL~~~p~~~aIf~-------~nD~~A~Ga~~al~~~G~~di~vvGfD~~~--~~~~~i~~g~~~~T 257 (295)
T PRK10653 187 ADFDRTKGLNVMQNLLTAHPDVQAVFA-------QNDEMALGALRALQTAGKSDVMVVGFDGTP--DGEKAVNDGKLAAT 257 (295)
T ss_pred CCCCHHHHHHHHHHHHHHCCCCCEEEE-------CCCHHHHHHHHHHHHCCCCCCEEEEECCCH--HHHHHHHCCCCEEE
T ss_conf 777899999999999960899778997-------797799999999998099983999289987--99999774996299
Q ss_pred EECCHHHHHHHHHHHH
Q ss_conf 9499899999999985
Q gi|254781049|r 380 TAIDLDDAAQKIVHAV 395 (398)
Q Consensus 380 ~~~~~~~A~~~~v~~~ 395 (398)
...+..+-.+.+|+++
T Consensus 258 v~Q~~~~~G~~av~~l 273 (295)
T PRK10653 258 IAQQPDQIGAKGVETA 273 (295)
T ss_pred EECCHHHHHHHHHHHH
T ss_conf 9279999999999999
No 144
>TIGR00705 SppA_67K signal peptide peptidase SppA, 67K type; InterPro: IPR004634 Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes . They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Over 20 families (denoted S1 - S66) of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence . Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases . Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base . The geometric orientations of the catalytic residues are similar between families, despite different protein folds . The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) , . Peptidases are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry. Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. This group of serine peptidases belong to MEROPS peptidase family S49 (protease IV family, clan S-). The predicted active site serine for members of this family occurs in a transmembrane domain. Signal peptides of secretory proteins seem to serve at least two important biological functions. First, they are required for protein targeting to and translocation across membranes, such as the eubacterial plasma membrane and the endoplasmic reticular membrane of eukaryotes. Second, in addition to their role as determinants for protein targeting and translocation, certain signal peptides have a signalling function. During or shortly after pre-protein translocation, the signal peptide is removed by signal peptidases. The integral membrane protein, SppA (protease IV), of Escherichia coli was shown experimentally to degrade signal peptides. The member of this family from Bacillus subtilis has only been shown to be required for efficient processing of pre-proteins under conditions of hyper-secretion . These enzymes have a molecular mass around 67 kDa and a duplication such that the N-terminal half shares extensive homology with the C-terminal half and was shown in E. coli to form homotetramers. E. coli SohB, which is most closely homologous to the C-terminal duplication of SppA, is predicted to perform a similar function of small peptide degradation, but in the periplasm. Many prokaryotes have a single SppA/SohB homolog that may perform the function of either or both. ; GO: 0009003 signal peptidase activity, 0006465 signal peptide processing, 0016021 integral to membrane.
Probab=88.31 E-value=2 Score=22.48 Aligned_cols=251 Identities=18% Similarity=0.256 Sum_probs=124.4
Q ss_pred CHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCEEECCCCCCCEEEEEEEEEECCCCCEEEEEECCCCCCHHHHHHHC---H
Q ss_conf 9999999999861876544212222244330110345556505899999834778048998447884024555748---3
Q gi|254781049|r 75 SLKSVISDIREILGSTLITKQTGPTGSRVNCVYVEDGADILRELYLSLLVDRTSGMVAFIASTQGGMDIEEVAKDY---P 151 (398)
Q Consensus 75 s~~ea~~~a~~ilg~~l~t~qt~~~G~~v~~vLVEe~v~~~~E~ylgi~~Dr~~~~~vii~S~~GGvdIE~va~~~---p 151 (398)
+..++..+..+- +| .|++| ++----.-.-.|||+-+=|. |+.++.|+|||.=.+.++ .
T Consensus 117 ~l~~~~~AL~~F-------k~---SgKpv---~ay~~nYS~~~YYLAsfAd~------I~L~p~G~Vdl~Gl~~~~Lfy~ 177 (614)
T TIGR00705 117 ALSEIGKALSEF-------KD---SGKPV---YAYGENYSQGQYYLASFADE------ILLNPMGSVDLHGLATETLFYK 177 (614)
T ss_pred CHHHHHHHHHHH-------HH---CCCEE---EEEECCCCCHHHHHHHHHHH------HHCCCCCCEECCCCCCCCCCHH
T ss_conf 279889999999-------85---69908---99852534023688765402------4036887245035244764088
Q ss_pred HHHEEEECCC---CCCCCHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHC----CCCCCCCCEEEECCCCCEEEEEE
Q ss_conf 1220332144---4578957888788751988899885999999998999955----97510232679905996799400
Q gi|254781049|r 152 QKIFKLLIDP---LIGVTSEDVASLCDMLELQGQARIDGGDLFPNLYKAFCDK----DMSLLEINPLIIMKNGRLRVLDS 224 (398)
Q Consensus 152 ~~I~~~~id~---~~gl~~~~~~~l~~~lg~~~~~~~~~~~ii~~L~~~f~e~----Da~liEINPLvvt~dg~vvAlDA 224 (398)
..+-|..|.+ -.|-..-.+..+.+. .++++........+-.||+-|+.. -..-++-.-++-..++ .+..|-
T Consensus 178 ~~l~K~~v~~~~~rvG~YKgavEpF~R~-d~SPe~r~~~q~~l~~lWq~YL~~Va~NRsl~~~~~~~~~~a~~-~L~~l~ 255 (614)
T TIGR00705 178 GMLDKLGVSVHVFRVGTYKGAVEPFLRE-DMSPEARENQQRWLGELWQNYLSSVAENRSLAIPKEQVLPSAQG-LLEALK 255 (614)
T ss_pred HHHHHHCCCCCEEEEECCCCCCCCCCCC-CCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHCCCHHH-HHHHHH
T ss_conf 7997612862168962102421423555-66888899999999999988888887031135708760211212-467877
Q ss_pred EEEECCCHHH-HHHHH-HHHH---CCCCCCHHHHH--HHHCCCCEEEC----------------CCCEEEEECCCHHHHH
Q ss_conf 1321573556-41027-8631---00015622245--77539864422----------------8817999555036899
Q gi|254781049|r 225 KISFDDNALY-RHLDI-QELR---DVSEEDSREIE--AKQHNLSYIAL----------------DGNIGCMVNGAGLAMA 281 (398)
Q Consensus 225 Ki~iDDnA~f-R~~~~-~~~~---d~~~~~~~E~~--A~~~~l~yv~L----------------dG~Ig~~vnGaGlama 281 (398)
|..=| .|.+ .+.++ .... +..-..+.+.+ -.+...++|.| +-.||++ |=+|
T Consensus 256 ~~~g~-~~~~a~~~~lV~~~~~~~~~~~~l~~~~e~~~~d~~~~~i~l~dY~~~~~~r~E~~~~~~~iaiv-~~~G---- 329 (614)
T TIGR00705 256 KLKGD-LAKYALEEKLVTAVVSQAEVEKALKELFEEDEEDKEKRLISLDDYARKRPQRLENYDVDDKIAIV-YLEG---- 329 (614)
T ss_pred HHCCH-HHHHHHHHHHHHHHHHHCCCCCCCHHHCCCCCCCCHHCCCCHHHHHHCCHHHHHHCCCCCCEEEE-EEEC----
T ss_conf 51354-78999876578998735175310444448872310003211466520132354422798816999-7006----
Q ss_pred HHHHHHHCCCCCCEEEECCCC-CCHHHHHHHHHHHHCCCCCCEEE--EECCCCHHHHHH-HHHHHHHHHHHCCCCCCEEE
Q ss_conf 999999658996248842788-89899999999986199865899--963586132899-99999999997299987999
Q gi|254781049|r 282 TMDIIKLYGGAPANFLDVGGG-ADQDKVAAAFKIITSDSSVKGIL--INIFGGIMRCDV-LVKGILSAVKEVKINIPLVM 357 (398)
Q Consensus 282 tmD~i~~~Gg~pANFlD~gG~-a~~e~~~~a~~~il~~~~vk~il--iNifGGI~~cd~-vA~gii~a~~~~~~~~pivv 357 (398)
.-+|==|.-++ +-.+++.+-++...+||+||+|. ||=-||=+..-+ |=+-+ ..++..+ ++||||
T Consensus 330 ----------~I~~G~~t~~nG~ggD~~a~lLr~a~~D~~iKAvvLRinSPGGsv~Ase~IR~e~-~~~~~~G-kKPViv 397 (614)
T TIGR00705 330 ----------SIVDGRDTEENGVGGDTVAALLRKARSDPDIKAVVLRINSPGGSVFASEIIRREL-ERLQARG-KKPVIV 397 (614)
T ss_pred ----------CEECCCCCCCCCCHHHHHHHHHHHHCCCCCCEEEEEEEECCCCCEEHHHHHHHHH-HHHHHCC-CCCEEE
T ss_conf ----------4235775667860036799999987079981289988638986342878999999-9998268-997898
Q ss_pred ECCCCCH
Q ss_conf 7489858
Q gi|254781049|r 358 RLEGANV 364 (398)
Q Consensus 358 Rl~Gtn~ 364 (398)
-|.+--+
T Consensus 398 SMG~~AA 404 (614)
T TIGR00705 398 SMGAMAA 404 (614)
T ss_pred ECCHHHH
T ss_conf 4350232
No 145
>PRK11303 DNA-binding transcriptional regulator FruR; Provisional
Probab=88.05 E-value=2.1 Score=22.37 Aligned_cols=103 Identities=13% Similarity=0.066 Sum_probs=69.1
Q ss_pred HHHHHHHHCCCCCCEEEECCCCCCHHHHHHHHHHHHC-CCCCCEEEEECCCCHHHHHHHHHHHHHHHHHCCCCCCEEEEC
Q ss_conf 9999999658996248842788898999999999861-998658999635861328999999999999729998799974
Q gi|254781049|r 281 ATMDIIKLYGGAPANFLDVGGGADQDKVAAAFKIITS-DSSVKGILINIFGGIMRCDVLVKGILSAVKEVKINIPLVMRL 359 (398)
Q Consensus 281 atmD~i~~~Gg~pANFlD~gG~a~~e~~~~a~~~il~-~~~vk~iliNifGGI~~cd~vA~gii~a~~~~~~~~pivvRl 359 (398)
...+.+..+|.++- + -+++..+.+.-+++++-+++ .+...+|| ...|.+|.|+++++++.++++|==+.+
T Consensus 200 Gf~~al~~~g~~~~-~-~~~~~~~~~~g~~~~~~ll~~~~~p~Ai~-------~~nD~~A~g~l~al~~~g~~VP~Dvsv 270 (330)
T PRK11303 200 GFRQALKDDPREVH-F-LYAESFSREAGAQLFEKWLETHGMPDALF-------TTSYTLLQGVLDVLLERPGKLPSDLAI 270 (330)
T ss_pred HHHHHHHHCCCCEE-E-EECCCCCHHHHHHHHHHHHHCCCCCCEEE-------ECCHHHHHHHHHHHHHCCCCCCCCEEE
T ss_conf 99999996799805-9-96488998999999999983799997799-------748999999999999859999997599
Q ss_pred CCCCHHHHHHHHHHCCCCEE-EECCHHHHHHHHHHHH
Q ss_conf 89858999999997699589-9499899999999985
Q gi|254781049|r 360 EGANVDIGNRLIAESGLNVI-TAIDLDDAAQKIVHAV 395 (398)
Q Consensus 360 ~Gtn~~~g~~il~~~g~~~~-~~~~~~~A~~~~v~~~ 395 (398)
-|-+-. .+..-...++. ...+.++.+++|+++.
T Consensus 271 igfDd~---~~~~~~~p~LTtv~q~~~~~g~~A~~~L 304 (330)
T PRK11303 271 ATFGDN---ELLDFLPCPVNAVAQQHRLIAERALELA 304 (330)
T ss_pred EEECCH---HHHHCCCCCCEEEECCHHHHHHHHHHHH
T ss_conf 999962---8897179997299679999999999999
No 146
>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=87.74 E-value=2.2 Score=22.26 Aligned_cols=79 Identities=19% Similarity=0.149 Sum_probs=54.9
Q ss_pred CCCCHHHHHHHHHH-HHCCCCCCEEEEECCCCHHHHHHHHHHHHHHHHHCCCCCC---EEEECCCCCHHHHHHHHHHCCC
Q ss_conf 88898999999999-8619986589996358613289999999999997299987---9997489858999999997699
Q gi|254781049|r 301 GGADQDKVAAAFKI-ITSDSSVKGILINIFGGIMRCDVLVKGILSAVKEVKINIP---LVMRLEGANVDIGNRLIAESGL 376 (398)
Q Consensus 301 G~a~~e~~~~a~~~-il~~~~vk~iliNifGGI~~cd~vA~gii~a~~~~~~~~p---ivvRl~Gtn~~~g~~il~~~g~ 376 (398)
++.+.++-+++++- |.++|++++|| ...|.+|.|.++|+++.+.+.| .|+-..|+ .++.+.+++-.+
T Consensus 182 ~~~~~~~a~~~~~~lL~~~Pdi~aI~-------~~ND~mAlGAv~Al~~aG~~~~~dv~IvG~Dg~--~~~~~~I~~G~~ 252 (305)
T cd06324 182 AGWSEDEAYEQAENLLKRYPDVRLIW-------AANDQMAFGALRAAKEAGRKPGRDVLFGGVNWS--PEALRAIKDGRL 252 (305)
T ss_pred CCCCHHHHHHHHHHHHHHCCCCCEEE-------ECCCHHHHHHHHHHHHCCCCCCCCEEEEEECCC--HHHHHHHHCCCE
T ss_conf 89878999999999997399998899-------788578999999999749987998899970698--999999984980
Q ss_pred CEEEECCHHHHH
Q ss_conf 589949989999
Q gi|254781049|r 377 NVITAIDLDDAA 388 (398)
Q Consensus 377 ~~~~~~~~~~A~ 388 (398)
............
T Consensus 253 ~~t~~~~~~~g~ 264 (305)
T cd06324 253 SVSAGGHFTEGG 264 (305)
T ss_pred EEEECCCHHHHH
T ss_conf 699728888999
No 147
>PRK10703 DNA-binding transcriptional repressor PurR; Provisional
Probab=87.19 E-value=2.3 Score=22.05 Aligned_cols=106 Identities=12% Similarity=0.089 Sum_probs=67.4
Q ss_pred HHHHHHHHHCCCCCCEEEECCCCCCHHHHHHHHHHHHC-CCCCCEEEEECCCCHHHHHHHHHHHHHHHHHCCCCCCEEEE
Q ss_conf 99999999658996248842788898999999999861-99865899963586132899999999999972999879997
Q gi|254781049|r 280 MATMDIIKLYGGAPANFLDVGGGADQDKVAAAFKIITS-DSSVKGILINIFGGIMRCDVLVKGILSAVKEVKINIPLVMR 358 (398)
Q Consensus 280 matmD~i~~~Gg~pANFlD~gG~a~~e~~~~a~~~il~-~~~vk~iliNifGGI~~cd~vA~gii~a~~~~~~~~pivvR 358 (398)
-...+.+..+|...-.-.=+-|..+.+.-+++++-++. .+.+.+|| ...|.+|-|+++++++.++++|==+.
T Consensus 198 ~gf~~al~~~gl~~~~~~i~~~~~~~~~g~~~~~~ll~~~~~ptAi~-------~~nD~~A~g~~~~l~~~g~~VP~Dis 270 (335)
T PRK10703 198 AGFMKAMEEANIKVPEEWIVQGDFEPESGYEAMQQILSQEHRPTAVF-------CGGDIMAMGAICAADEMGLRVPQDIS 270 (335)
T ss_pred HHHHHHHHHCCCCCCHHEEEECCCCHHHHHHHHHHHHHCCCCCCEEE-------ECCHHHHHHHHHHHHHCCCCCCCCEE
T ss_conf 99999999859998813289657885889999999995699986689-------68759999999999971999999749
Q ss_pred CCCCCHHHHHHHHHHCCCCEE-EECCHHHHHHHHHHHH
Q ss_conf 489858999999997699589-9499899999999985
Q gi|254781049|r 359 LEGANVDIGNRLIAESGLNVI-TAIDLDDAAQKIVHAV 395 (398)
Q Consensus 359 l~Gtn~~~g~~il~~~g~~~~-~~~~~~~A~~~~v~~~ 395 (398)
+-|-+-.. +.+...-++. ...+.++..+.|+++.
T Consensus 271 vigfDd~~---~~~~~~P~LTtv~~~~~~~g~~A~~~L 305 (335)
T PRK10703 271 VIGYDNVR---NARYFTPALTTIHQPKDRLGETAFNML 305 (335)
T ss_pred EEEECCCH---HHHHCCCCCEEEECCHHHHHHHHHHHH
T ss_conf 99988828---998258982799829999999999999
No 148
>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=87.14 E-value=2.3 Score=22.03 Aligned_cols=85 Identities=15% Similarity=0.162 Sum_probs=50.8
Q ss_pred CCCCHHHHHHHHH-HHHCCCCCCEEEEECCCCHHHHHHHHHHHHHHHHHCCCCCCEEEECCCCCHHHHHHHHHHCCCCEE
Q ss_conf 8889899999999-986199865899963586132899999999999972999879997489858999999997699589
Q gi|254781049|r 301 GGADQDKVAAAFK-IITSDSSVKGILINIFGGIMRCDVLVKGILSAVKEVKINIPLVMRLEGANVDIGNRLIAESGLNVI 379 (398)
Q Consensus 301 G~a~~e~~~~a~~-~il~~~~vk~iliNifGGI~~cd~vA~gii~a~~~~~~~~pivvRl~Gtn~~~g~~il~~~g~~~~ 379 (398)
|..+.+.-+++++ ++.+.|.+.+|| +..|.+|.|+++++++.+.++|==+.+-|-+-. .+..-..-++.
T Consensus 156 ~~~~~~~~~~~~~~~l~~~~~~~ai~-------~~nD~~A~g~~~~~~~~g~~vP~di~vigfD~~---~~~~~~~p~lt 225 (265)
T cd06290 156 GDFEEESGLEAVEELLQRGPDFTAIF-------AANDQTAYGARLALYRRGLRVPEDVSLIGFDDL---PLSAYTTPPLT 225 (265)
T ss_pred CCCCCHHHHHHHHHHHHHCCCCCCCE-------ECCHHHHHHHHHHHHHHCCCCCCCEEEEEECCH---HHHHHCCCCEE
T ss_conf 66771789999999997199988421-------057899999999999809999998799999987---89973289828
Q ss_pred -EECCHHHHHHHHHHHH
Q ss_conf -9499899999999985
Q gi|254781049|r 380 -TAIDLDDAAQKIVHAV 395 (398)
Q Consensus 380 -~~~~~~~A~~~~v~~~ 395 (398)
...+..+..++|+++.
T Consensus 226 ti~~~~~~~G~~A~~~L 242 (265)
T cd06290 226 TVRQPIEEMGQIAARAL 242 (265)
T ss_pred EEEECHHHHHHHHHHHH
T ss_conf 99959999999999999
No 149
>pfam03709 OKR_DC_1_N Orn/Lys/Arg decarboxylase, N-terminal domain. This domain has a flavodoxin-like fold, and is termed the "wing" domain because of its position in the overall 3D structure.
Probab=87.06 E-value=1.8 Score=22.73 Aligned_cols=82 Identities=15% Similarity=0.287 Sum_probs=57.0
Q ss_pred HHHHHHHHHCCCCCCEEEEECCCCHHHHHHHHHHHHHHHHHCCCCCCEEEECCC-CCHHHHHHHHHHC-CCCEEEECCHH
Q ss_conf 999999986199865899963586132899999999999972999879997489-8589999999976-99589949989
Q gi|254781049|r 308 VAAAFKIITSDSSVKGILINIFGGIMRCDVLVKGILSAVKEVKINIPLVMRLEG-ANVDIGNRLIAES-GLNVITAIDLD 385 (398)
Q Consensus 308 ~~~a~~~il~~~~vk~iliNifGGI~~cd~vA~gii~a~~~~~~~~pivvRl~G-tn~~~g~~il~~~-g~~~~~~~~~~ 385 (398)
...+..++-+++++-++++.+ |+...++++.+++.+.++||++=-.- +.++.-...|+.. |+=-...++-+
T Consensus 26 ~~d~~~~~~~~~~i~avil~~-------~~~~~~ll~~ir~~n~~lPvFl~~~~~~~~~vp~~~l~~i~gfi~l~edt~~ 98 (111)
T pfam03709 26 TDDLLSLIETFTDIAAVVLSW-------DDEARGLLDEIRRRNFDLPVFLLAETRTSEDVPLDVLREIDGFIELFEDTPE 98 (111)
T ss_pred HHHHHHHHHHCCCCCEEEEEE-------CHHHHHHHHHHHHHCCCCCEEEEECHHHHHCCCHHHHHHHHHHHHHHCCCHH
T ss_conf 899999998387876899984-------6068999999997478999898844125750999999988786736568989
Q ss_pred HHHHHHHHHHH
Q ss_conf 99999999850
Q gi|254781049|r 386 DAAQKIVHAVK 396 (398)
Q Consensus 386 ~A~~~~v~~~k 396 (398)
.-++++...++
T Consensus 99 fia~~I~~aa~ 109 (111)
T pfam03709 99 FIARQIEAAAR 109 (111)
T ss_pred HHHHHHHHHHH
T ss_conf 99999999986
No 150
>PRK02705 murD UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional
Probab=87.04 E-value=2.4 Score=22.00 Aligned_cols=91 Identities=22% Similarity=0.265 Sum_probs=60.9
Q ss_pred EEECCCCCCHHHHHHHHHHHHCCCCCCEEEEECCCCHHHHHHHHHHHHHHHHHCCCCCCEEEECCCCCHHHHHHHHHHCC
Q ss_conf 88427888989999999998619986589996358613289999999999997299987999748985899999999769
Q gi|254781049|r 296 FLDVGGGADQDKVAAAFKIITSDSSVKGILINIFGGIMRCDVLVKGILSAVKEVKINIPLVMRLEGANVDIGNRLIAESG 375 (398)
Q Consensus 296 FlD~gG~a~~e~~~~a~~~il~~~~vk~iliNifGGI~~cd~vA~gii~a~~~~~~~~pivvRl~Gtn~~~g~~il~~~g 375 (398)
|.|=+=+++.+.+..|++-. ++ +.|| |.||..+-.+..+ +...+++ ++.- |-+-|.+.+.=.+.+++++
T Consensus 328 fiNDSKaTN~~a~~~Al~~~---~~-~iil--I~GG~~K~~d~~~-l~~~~~~---~v~~-v~~~G~~~~~i~~~l~~~~ 396 (459)
T PRK02705 328 FINDSKATNYDAAEVGLKAV---PG-PIIL--IAGGEAKQGDDSA-WLKQIKA---KAAA-VLLFGEAAPELAQLLQESG 396 (459)
T ss_pred EECCCCCCCHHHHHHHHHHC---CC-CEEE--EECCCCCCCCHHH-HHHHHHH---CCEE-EEEECCCHHHHHHHHHHCC
T ss_conf 97278788989999999828---99-8699--9567666787399-9999864---0619-9998989999999997369
Q ss_pred C--CEEEECCHHHHHHHHHHHHHC
Q ss_conf 9--589949989999999998506
Q gi|254781049|r 376 L--NVITAIDLDDAAQKIVHAVKG 397 (398)
Q Consensus 376 ~--~~~~~~~~~~A~~~~v~~~k~ 397 (398)
+ ++..+++|++|+++|.++++.
T Consensus 397 ~~~~~~~~~~l~~Av~~a~~~a~~ 420 (459)
T PRK02705 397 YTGEIEIVETLDEAVNRAFELAKE 420 (459)
T ss_pred CCCCEEECCCHHHHHHHHHHHHHC
T ss_conf 987769859999999999998765
No 151
>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=86.89 E-value=2.4 Score=21.94 Aligned_cols=102 Identities=15% Similarity=0.231 Sum_probs=64.0
Q ss_pred HHHHHHHCCCCCCE--EEECCCCCCHHHHHHHHHHHHC-CCCCCEEEEECCCCHHHHHHHHHHHHHHHHHCCCCCCEEEE
Q ss_conf 99999965899624--8842788898999999999861-99865899963586132899999999999972999879997
Q gi|254781049|r 282 TMDIIKLYGGAPAN--FLDVGGGADQDKVAAAFKIITS-DSSVKGILINIFGGIMRCDVLVKGILSAVKEVKINIPLVMR 358 (398)
Q Consensus 282 tmD~i~~~Gg~pAN--FlD~gG~a~~e~~~~a~~~il~-~~~vk~iliNifGGI~~cd~vA~gii~a~~~~~~~~pivvR 358 (398)
..+.+..+|..+-. ..+ .|..+.+..+++++-+++ .+++.+|| ...|.+|-|+++++++.++++|==+.
T Consensus 155 ~~~al~~~gl~~~~~~i~~-~~~~~~~~g~~~~~~ll~~~~~ptai~-------~~nD~~A~g~~~~l~~~Gi~VP~Dvs 226 (283)
T cd06279 155 YLEALEEAGIDISDVPIWE-IPENDRASGEEAARELLDASPRPTAIL-------CMSDVLALGALQVARELGLRVPEDLS 226 (283)
T ss_pred HHHHHHHCCCCCCCEEEEE-CCCCCHHHHHHHHHHHHHCCCCCCEEE-------ECCHHHHHHHHHHHHHHCCCCCCCEE
T ss_conf 9999998599977205784-599999999999999995599996698-------57729999999999981899999659
Q ss_pred CCCCC-HHHHHHHHHHCCCCEEEECCHHHHHHHHHHHH
Q ss_conf 48985-89999999976995899499899999999985
Q gi|254781049|r 359 LEGAN-VDIGNRLIAESGLNVITAIDLDDAAQKIVHAV 395 (398)
Q Consensus 359 l~Gtn-~~~g~~il~~~g~~~~~~~~~~~A~~~~v~~~ 395 (398)
+-|-+ .+.+ .+ ...+..+ ..+..+..+.|+++.
T Consensus 227 viGfDd~~~a--~~-~P~LTTI-~q~~~~~G~~A~~~L 260 (283)
T cd06279 227 VVGFDGIPEA--RL-RPGLTTV-RQPSEEKGRLAARLL 260 (283)
T ss_pred EEEECCCHHH--HC-CCCCEEE-ECCHHHHHHHHHHHH
T ss_conf 9958988899--45-8997089-619999999999999
No 152
>PRK02006 murD UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional
Probab=86.65 E-value=2.5 Score=21.86 Aligned_cols=91 Identities=19% Similarity=0.285 Sum_probs=61.5
Q ss_pred EEECCCCCCHHHHHHHHHHHHCCCCCCEEEEECCCCHHHHHHHHHHHHHHHHHCCCCCCEEEECCCCCHHHHHHHHHHCC
Q ss_conf 88427888989999999998619986589996358613289999999999997299987999748985899999999769
Q gi|254781049|r 296 FLDVGGGADQDKVAAAFKIITSDSSVKGILINIFGGIMRCDVLVKGILSAVKEVKINIPLVMRLEGANVDIGNRLIAESG 375 (398)
Q Consensus 296 FlD~gG~a~~e~~~~a~~~il~~~~vk~iliNifGGI~~cd~vA~gii~a~~~~~~~~pivvRl~Gtn~~~g~~il~~~g 375 (398)
|-|=+=+++.+.+..|++-. ++ +.+| |.||..+-.+... +.+.+++. +.-++ +-|.+.+.=.+.+.+++
T Consensus 370 ~iNDSKaTN~~at~~Al~s~--~~--~iil--I~GG~~K~~d~~~-L~~~~~~~---~k~vi-l~G~~~~~i~~~l~~~~ 438 (501)
T PRK02006 370 YVDDSKGTNVGATVAALDGL--AQ--RVVL--IAGGDGKGQDFSP-LAAPVARW---ARAVV-LIGRDAPAIRAALADTG 438 (501)
T ss_pred EECCCCCCCHHHHHHHHHHC--CC--CEEE--EEECCCCCCCHHH-HHHHHHHH---CEEEE-EECCCHHHHHHHHHCCC
T ss_conf 97378778989999999707--89--7499--9805777779799-99999853---70999-98989999999975179
Q ss_pred CCEEEECCHHHHHHHHHHHHHC
Q ss_conf 9589949989999999998506
Q gi|254781049|r 376 LNVITAIDLDDAAQKIVHAVKG 397 (398)
Q Consensus 376 ~~~~~~~~~~~A~~~~v~~~k~ 397 (398)
++++.+.+|++|+++|.++++.
T Consensus 439 ~~~~~~~~l~~Av~~a~~~a~~ 460 (501)
T PRK02006 439 VPLVDAATLEEAVRAAAELAQP 460 (501)
T ss_pred CEEEECCCHHHHHHHHHHHCCC
T ss_conf 8079859999999999975789
No 153
>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=86.56 E-value=2.5 Score=21.83 Aligned_cols=123 Identities=17% Similarity=0.136 Sum_probs=69.7
Q ss_pred CCCEEEEECCCHHHHH------HHHHHHHCCCCCCEEEE-CCCCCCHHHHHHHHH-HHHCCCCCCEEEEECCCCHHHHHH
Q ss_conf 8817999555036899------99999965899624884-278889899999999-986199865899963586132899
Q gi|254781049|r 266 DGNIGCMVNGAGLAMA------TMDIIKLYGGAPANFLD-VGGGADQDKVAAAFK-IITSDSSVKGILINIFGGIMRCDV 337 (398)
Q Consensus 266 dG~Ig~~vnGaGlama------tmD~i~~~Gg~pANFlD-~gG~a~~e~~~~a~~-~il~~~~vk~iliNifGGI~~cd~ 337 (398)
.|+|.++..-.|-.-. ..|.++..+..--.-.+ .-+..+.++.++.++ ++.++|++++|| ...|.
T Consensus 123 ~g~v~i~~g~~~~~~~~~R~~g~~~~l~~~~~~~~~vv~~~~~~~~~~~a~~~~~~~L~~~Pdi~~I~-------~~nd~ 195 (298)
T cd06302 123 KGEYAIFVGSLTATNQNAWIDAAKAYQKEKYYPMLELVDRQYGDDDADKSYQTAQELLKAYPDLKGII-------GPTSV 195 (298)
T ss_pred CCCEEEEECCCCCHHHHHHHHHHHHHHHHCCCCCEEEEEEECCCCCHHHHHHHHHHHHHHCCCCCEEE-------ECCCH
T ss_conf 99589998588986799999999999863489987999861378748999999999997599912999-------78981
Q ss_pred HHHHHHHHHHHCCCCCC-EEEECCCCCHHHHHHHHHHCCCCEEEECCHHH----HHHHHHHHHHC
Q ss_conf 99999999997299987-99974898589999999976995899499899----99999998506
Q gi|254781049|r 338 LVKGILSAVKEVKINIP-LVMRLEGANVDIGNRLIAESGLNVITAIDLDD----AAQKIVHAVKG 397 (398)
Q Consensus 338 vA~gii~a~~~~~~~~p-ivvRl~Gtn~~~g~~il~~~g~~~~~~~~~~~----A~~~~v~~~k~ 397 (398)
+|.|.++|+++.+.+-. .|+=..++ +++.+.+++-.+......+-.. |++.++++.+|
T Consensus 196 ~a~Ga~~Al~~aG~~~~V~vvG~D~~--~~~~~~I~~G~i~atv~Q~P~~~G~~av~~a~~~~~G 258 (298)
T cd06302 196 GIPGAARAVEEAGLKGKVAVTGLGLP--NQMAPYVKSGAVKEFALWNPADLGYAAVYVAKALLEG 258 (298)
T ss_pred HHHHHHHHHHHCCCCCCEEEEEECCC--HHHHHHHHCCCCEEEEECCHHHHHHHHHHHHHHHHCC
T ss_conf 69999999996799998599996887--9999999859826999849999999999999999779
No 154
>PRK11041 DNA-binding transcriptional regulator CytR; Provisional
Probab=86.10 E-value=2.7 Score=21.67 Aligned_cols=105 Identities=14% Similarity=0.121 Sum_probs=67.5
Q ss_pred HHHHHHHHCCCCCCEEEECCCCCCHHHHHHHHHHHHC-CCCCCEEEEECCCCHHHHHHHHHHHHHHHHHCCCCCCEEEEC
Q ss_conf 9999999658996248842788898999999999861-998658999635861328999999999999729998799974
Q gi|254781049|r 281 ATMDIIKLYGGAPANFLDVGGGADQDKVAAAFKIITS-DSSVKGILINIFGGIMRCDVLVKGILSAVKEVKINIPLVMRL 359 (398)
Q Consensus 281 atmD~i~~~Gg~pANFlD~gG~a~~e~~~~a~~~il~-~~~vk~iliNifGGI~~cd~vA~gii~a~~~~~~~~pivvRl 359 (398)
...+.+..+|...-.-.-+-|..+.+.-+++++-++. .+.+.+|| ...|.+|-|+++++++.++++|==+.+
T Consensus 205 G~~~al~~~gl~~~~~~i~~~~~~~~~g~~~~~~ll~~~~~ptAi~-------~~nD~~A~g~l~al~~~Gl~VP~DisV 277 (341)
T PRK11041 205 GYVQALRRCGITVDPQYIARGDFTFEAGAKAMQQLLELPQPPTAVF-------CHSDVMALGALSQAKRQGLKVPQDLSI 277 (341)
T ss_pred HHHHHHHHCCCCCCCCEEEECCCCHHHHHHHHHHHHHCCCCCCEEE-------ECCHHHHHHHHHHHHHHCCCCCCCEEE
T ss_conf 9999999869999910489546767999999999995599985798-------767799999999999718989996599
Q ss_pred CCCCHHHHHHHHHHCCCCEEE-ECCHHHHHHHHHHHH
Q ss_conf 898589999999976995899-499899999999985
Q gi|254781049|r 360 EGANVDIGNRLIAESGLNVIT-AIDLDDAAQKIVHAV 395 (398)
Q Consensus 360 ~Gtn~~~g~~il~~~g~~~~~-~~~~~~A~~~~v~~~ 395 (398)
-|-+-.. +.+-..-++.+ ..+.++..+.|+++.
T Consensus 278 iGfdd~~---~~~~~~P~LTTV~~~~~~~g~~A~~~L 311 (341)
T PRK11041 278 IGFDNID---LAQFCDPPLTTIAQPRYEIGREAMLLL 311 (341)
T ss_pred EEECCHH---HHHCCCCCEEEEECCHHHHHHHHHHHH
T ss_conf 9988838---985269983699819999999999999
No 155
>pfam02955 GSH-S_ATP Prokaryotic glutathione synthetase, ATP-grasp domain.
Probab=85.92 E-value=2.7 Score=21.62 Aligned_cols=69 Identities=12% Similarity=0.087 Sum_probs=42.1
Q ss_pred CCCCCEEECCHHHHHHHHHHCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCEEE-EECCHHHHHHHHHHHCCCCCCCCCC
Q ss_conf 888815747999999999872998699971213687656565567777777079-9589999999999861876544212
Q gi|254781049|r 18 PVAKGVVISSVHAAESAIKTLPGPLYVVKSQIHAGGRGKGRFKELPADSKGGVR-VESSLKSVISDIREILGSTLITKQT 96 (398)
Q Consensus 18 pvp~g~~a~s~~ea~~~a~~ig~p~~VvKaQV~aGgRGKa~~~~~hk~~~GGV~-l~~s~~ea~~~a~~ilg~~l~t~qt 96 (398)
-+|+..++++++++.+..+..+ + +|+|+---+||| ||. +..+...+....+.+..
T Consensus 11 ~~P~T~vt~~~~~i~~f~~~~g-~-vVvKPl~Gs~G~--------------GV~~i~~~~~~~~~i~e~~~~-------- 66 (176)
T pfam02955 11 LIPPTLVTRDKEEIRAFLEEHG-D-IILKPLDGMGGA--------------GVFRIKKDDPNLNVILETLTQ-------- 66 (176)
T ss_pred CCCCEEEECCHHHHHHHHHHCC-C-EEEEECCCCCCC--------------CEEEECCCCHHHHHHHHHHHH--------
T ss_conf 0869479889999999999779-8-999957888876--------------759954783558999999984--------
Q ss_pred CCCCCCCCCEEECCCCCC
Q ss_conf 222244330110345556
Q gi|254781049|r 97 GPTGSRVNCVYVEDGADI 114 (398)
Q Consensus 97 ~~~G~~v~~vLVEe~v~~ 114 (398)
.+. ..++++|+++.
T Consensus 67 --~~~--~~ii~QeyI~~ 80 (176)
T pfam02955 67 --YGR--RPVMAQRYLPE 80 (176)
T ss_pred --CCC--CCEEEEECCCC
T ss_conf --688--83986431376
No 156
>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=85.65 E-value=2.8 Score=21.53 Aligned_cols=100 Identities=17% Similarity=0.252 Sum_probs=54.3
Q ss_pred HHHHCCCCCCEEEECCCCCCHHHHHHH-HHHHHCCCCCCEEEEECCCCHHHHHHHHHHHHHHHHHCCCCCCEEEECCCCC
Q ss_conf 999658996248842788898999999-9998619986589996358613289999999999997299987999748985
Q gi|254781049|r 285 IIKLYGGAPANFLDVGGGADQDKVAAA-FKIITSDSSVKGILINIFGGIMRCDVLVKGILSAVKEVKINIPLVMRLEGAN 363 (398)
Q Consensus 285 ~i~~~Gg~pANFlD~gG~a~~e~~~~a-~~~il~~~~vk~iliNifGGI~~cd~vA~gii~a~~~~~~~~pivvRl~Gtn 363 (398)
.+..+|.++-....... +.+..+++ .+++.+++.+.+|| ..-|.+|-|+++|+++.+.++|==+.+-|-+
T Consensus 142 a~~~~~~~~~~~~~~~~--~~~~~~~~~~~~l~~~~~~~ai~-------~~nD~~A~g~l~al~~~g~~vP~disIigfd 212 (266)
T cd06282 142 AMRAAGLAPLPPVEIPF--NTAALPSALLALLTAHPAPTAIF-------CSNDLLALAVIRALRRLGLRVPDDLSVVGFD 212 (266)
T ss_pred HHHHCCCCCCCEEEECC--CHHHHHHHHHHHHHCCCCCCEEE-------ECCCHHHHHHHHHHHHCCCCCCCCEEEEEEC
T ss_conf 99986999761799348--72689999999983799984798-------5388899999999998499999984999989
Q ss_pred HHHHHHHHHHCCCCEEEECCHHHHHHHHHHHH
Q ss_conf 89999999976995899499899999999985
Q gi|254781049|r 364 VDIGNRLIAESGLNVITAIDLDDAAQKIVHAV 395 (398)
Q Consensus 364 ~~~g~~il~~~g~~~~~~~~~~~A~~~~v~~~ 395 (398)
-..--++ -...+.. ...+.++..+.|+++.
T Consensus 213 ~~~~~~~-~~P~lTt-i~q~~~~~g~~A~~~l 242 (266)
T cd06282 213 GIAIGRL-LTPPLAT-VAQPNRDIGRQAVQRL 242 (266)
T ss_pred CHHHHHC-CCCCCEE-EECCHHHHHHHHHHHH
T ss_conf 7089970-7999679-9869999999999999
No 157
>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=84.63 E-value=3.1 Score=21.23 Aligned_cols=84 Identities=17% Similarity=0.219 Sum_probs=56.4
Q ss_pred CCHHHHHHHH-HHHHCCCCCCEEEEECCCCHHHHHHHHHHHHHHHHHCCCCCCEEEECCCCCHHHHHHHHHHCCCCEEEE
Q ss_conf 8989999999-998619986589996358613289999999999997299987999748985899999999769958994
Q gi|254781049|r 303 ADQDKVAAAF-KIITSDSSVKGILINIFGGIMRCDVLVKGILSAVKEVKINIPLVMRLEGANVDIGNRLIAESGLNVITA 381 (398)
Q Consensus 303 a~~e~~~~a~-~~il~~~~vk~iliNifGGI~~cd~vA~gii~a~~~~~~~~pivvRl~Gtn~~~g~~il~~~g~~~~~~ 381 (398)
.+.+.-+++. +++.++|++++|| ...|.+|.|.++|+++.+++-.-|+=..++... ...+...-+-....
T Consensus 163 ~~~~~~~~~~~~lL~~~~~~~aI~-------~~nD~~A~ga~~al~~~g~~di~viGfD~~~~~--~~~~~~~~~~~Ti~ 233 (268)
T cd06323 163 FDRAKGLNVMENILQAHPDIKGVF-------AQNDEMALGAIEALKAAGKDDVKVVGFDGTPDA--LKAIKAGKMAATVA 233 (268)
T ss_pred HHHHHHHHHHHHHHHCCCCCCEEE-------ECCCHHHHHHHHHHHHHCCCCEEEEEECCCHHH--HHHHHCCCCEEEEE
T ss_conf 027999999999986298885899-------778399999999999709998299988898899--99744599439990
Q ss_pred CCHHHHHHHHHHHH
Q ss_conf 99899999999985
Q gi|254781049|r 382 IDLDDAAQKIVHAV 395 (398)
Q Consensus 382 ~~~~~A~~~~v~~~ 395 (398)
.+..+..++++++.
T Consensus 234 q~~~~~g~~av~~l 247 (268)
T cd06323 234 QQPALMGRLAVETA 247 (268)
T ss_pred CCHHHHHHHHHHHH
T ss_conf 79999999999999
No 158
>pfam01740 STAS STAS domain. The STAS (after Sulphate Transporter and AntiSigma factor antagonist) domain is found in the C terminal region of Sulphate transporters and bacterial antisigma factor antagonists. It has been suggested that this domain may have a general NTP binding function.
Probab=84.55 E-value=2.7 Score=21.62 Aligned_cols=81 Identities=15% Similarity=0.315 Sum_probs=52.3
Q ss_pred CHHHHHHHHHHHHCCCCCCEEEEECCCCHHHHHHHHHHHHHHH-HHCCCCCCEEEECCCCCHHHHHHHHHHCCCC--EEE
Q ss_conf 9899999999986199865899963586132899999999999-9729998799974898589999999976995--899
Q gi|254781049|r 304 DQDKVAAAFKIITSDSSVKGILINIFGGIMRCDVLVKGILSAV-KEVKINIPLVMRLEGANVDIGNRLIAESGLN--VIT 380 (398)
Q Consensus 304 ~~e~~~~a~~~il~~~~vk~iliNifGGI~~cd~vA~gii~a~-~~~~~~~pivvRl~Gtn~~~g~~il~~~g~~--~~~ 380 (398)
+.+...+.+.-.+..+.++.+.++ |.++...|-.+-+.+..+ ++.. +.-+-+.+.|.+.+. +++++.+|+. +..
T Consensus 23 ~a~~~~~~l~~~~~~~~~~~vvlD-~~~v~~iDssgl~~l~~~~~~~~-~~g~~l~l~~~~~~v-~~~l~~~gl~~~~~i 99 (106)
T pfam01740 23 NAEAFRERLLRAIEEGEIRHVILD-LSGVPFIDSSGLGALLELYKELR-RRGVELVLVGPSPEV-RRTLEKTGLDDIIGI 99 (106)
T ss_pred HHHHHHHHHHHHHHCCCCCEEEEE-EECCCCCCCHHHHHHHHHHHHHH-HCCCEEEEECCCHHH-HHHHHHHCCCCEECC
T ss_conf 999999999999865899789999-70898889029999999999999-769909997699899-999998099866446
Q ss_pred ECCHHHH
Q ss_conf 4998999
Q gi|254781049|r 381 AIDLDDA 387 (398)
Q Consensus 381 ~~~~~~A 387 (398)
+.+.++|
T Consensus 100 ~~s~~eA 106 (106)
T pfam01740 100 FPTVEEA 106 (106)
T ss_pred CCCHHHC
T ss_conf 4995659
No 159
>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=84.48 E-value=3.2 Score=21.19 Aligned_cols=86 Identities=16% Similarity=0.050 Sum_probs=51.5
Q ss_pred CCHHHHHH-HHHHHHCCCCCCEEEEECCCCHHHHHHHHHHHHHHHHHCCCCCC-EEEECCCCCHHHHHHHHHH-CC-CCE
Q ss_conf 89899999-99998619986589996358613289999999999997299987-9997489858999999997-69-958
Q gi|254781049|r 303 ADQDKVAA-AFKIITSDSSVKGILINIFGGIMRCDVLVKGILSAVKEVKINIP-LVMRLEGANVDIGNRLIAE-SG-LNV 378 (398)
Q Consensus 303 a~~e~~~~-a~~~il~~~~vk~iliNifGGI~~cd~vA~gii~a~~~~~~~~p-ivvRl~Gtn~~~g~~il~~-~g-~~~ 378 (398)
.+.+..+. ...++.++|+.+...| +...|.+|.|.++|+++.+.+-. .|+=..|+. +..+.+++ .| +..
T Consensus 163 ~~~~~~~~~~~~~L~~~pd~~~~ai-----~~~nd~~a~Ga~~Al~~~G~~~~v~v~G~D~~~--~~~~~i~~~~g~~~a 235 (273)
T cd06305 163 NTAQDAAAQVEAVLKKYPKGGIDAI-----WAAWDEFAKGAKQALDEAGRTDEIKIYGVDISP--EDLQLMREPDSPWVA 235 (273)
T ss_pred CHHHHHHHHHHHHHHHCCCCCEEEE-----EECCCHHHHHHHHHHHHCCCCCCCEEEEECCCH--HHHHHHHCCCCCEEE
T ss_conf 6399999999999973888762799-----935857899999999976999994899978998--999999727995599
Q ss_pred EEECCHHHHHHHHHHHH
Q ss_conf 99499899999999985
Q gi|254781049|r 379 ITAIDLDDAAQKIVHAV 395 (398)
Q Consensus 379 ~~~~~~~~A~~~~v~~~ 395 (398)
....+..+-.+.+|+.+
T Consensus 236 tv~Q~p~~~G~~av~~~ 252 (273)
T cd06305 236 TAAQDPALIGKVAVRNV 252 (273)
T ss_pred EEECCHHHHHHHHHHHH
T ss_conf 99479999999999999
No 160
>COG1609 PurR Transcriptional regulators [Transcription]
Probab=83.97 E-value=3.3 Score=21.04 Aligned_cols=117 Identities=13% Similarity=0.155 Sum_probs=73.1
Q ss_pred CEEEEECCC-HHH-----HHHHHHHHHCCCCC-CEEEECCCCCCHHHHHHHHHHHHCCC-C-CCEEEEECCCCHHHHHHH
Q ss_conf 179995550-368-----99999999658996-24884278889899999999986199-8-658999635861328999
Q gi|254781049|r 268 NIGCMVNGA-GLA-----MATMDIIKLYGGAP-ANFLDVGGGADQDKVAAAFKIITSDS-S-VKGILINIFGGIMRCDVL 338 (398)
Q Consensus 268 ~Ig~~vnGa-Gla-----matmD~i~~~Gg~p-ANFlD~gG~a~~e~~~~a~~~il~~~-~-vk~iliNifGGI~~cd~v 338 (398)
+|+++..+. ..+ ....+....+|..+ ..+. .-|..+.+.-+++++-++... . +.+|| ...|.+
T Consensus 177 ~i~~i~~~~~~~~~~~R~~Gf~~al~~~~~~~~~~~i-~~~~~~~~~g~~~~~~ll~~~~~~ptAif-------~~nD~~ 248 (333)
T COG1609 177 RIAFIGGPLDSSASRERLEGYRAALREAGLPINPEWI-VEGDFSEESGYEAAERLLARGEPRPTAIF-------CANDLM 248 (333)
T ss_pred EEEEEECCCCCCCHHHHHHHHHHHHHHCCCCCCCCEE-EECCCCHHHHHHHHHHHHHCCCCCCCEEE-------ECCCHH
T ss_conf 5999967987721899999999999975999774236-61678878999999999854899997899-------878099
Q ss_pred HHHHHHHHHHCCCCCCEEEECCCCCHHHHHHHHHHCCCCEE-EECCHHHHHHHHHHHH
Q ss_conf 99999999972999879997489858999999997699589-9499899999999985
Q gi|254781049|r 339 VKGILSAVKEVKINIPLVMRLEGANVDIGNRLIAESGLNVI-TAIDLDDAAQKIVHAV 395 (398)
Q Consensus 339 A~gii~a~~~~~~~~pivvRl~Gtn~~~g~~il~~~g~~~~-~~~~~~~A~~~~v~~~ 395 (398)
|.|+++++++.++++|==+.+-|-+-. .+-+-..-++. ...+..+..++|+++.
T Consensus 249 Alg~l~~~~~~g~~vP~disviGfDd~---~~~~~~~P~LTTv~~~~~~~G~~A~~~L 303 (333)
T COG1609 249 ALGALRALRELGLRVPEDLSVIGFDDI---ELARFLTPPLTTVRQPIEELGRRAAELL 303 (333)
T ss_pred HHHHHHHHHHCCCCCCCCEEEEEECCH---HHHHHCCCCEEEEECCHHHHHHHHHHHH
T ss_conf 999999999808999987899998884---7765158980699509999999999999
No 161
>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=83.64 E-value=3.4 Score=20.96 Aligned_cols=85 Identities=13% Similarity=0.117 Sum_probs=51.4
Q ss_pred CCCCHHHHHHHHHHHH-CCCCCCEEEEECCCCHHHHHHHHHHHHHHHHHCCCCCCEEEECCCCCHHHHHHHHHHCCCCEE
Q ss_conf 8889899999999986-199865899963586132899999999999972999879997489858999999997699589
Q gi|254781049|r 301 GGADQDKVAAAFKIIT-SDSSVKGILINIFGGIMRCDVLVKGILSAVKEVKINIPLVMRLEGANVDIGNRLIAESGLNVI 379 (398)
Q Consensus 301 G~a~~e~~~~a~~~il-~~~~vk~iliNifGGI~~cd~vA~gii~a~~~~~~~~pivvRl~Gtn~~~g~~il~~~g~~~~ 379 (398)
|.-+.+.-+++.+.++ .+++..+|| +..|.+|.|+++++++.+.++|==|.+-|-+-..-.+++ ...+..
T Consensus 159 ~~~s~~~~~~~~~~ll~~~~~~tai~-------~~nD~~A~g~~~~l~~~g~~iP~dvsiigfD~~~~~~~~-~P~LTt- 229 (270)
T cd01545 159 GDFTFESGLEAAEALLALPDRPTAIF-------ASNDDMAAGVLAVAHRRGLRVPDDLSVVGFDDTPIATTI-WPPLTT- 229 (270)
T ss_pred CCCCCHHHHHHHHHHHHCCCCCCEEE-------ECCHHHHHHHHHHHHHHCCCCCCCEEEEEECCHHHHHHC-CCCCEE-
T ss_conf 65310269999999985599985899-------788899999999999818999998699998885999835-898249-
Q ss_pred EECCHHHHHHHHHHH
Q ss_conf 949989999999998
Q gi|254781049|r 380 TAIDLDDAAQKIVHA 394 (398)
Q Consensus 380 ~~~~~~~A~~~~v~~ 394 (398)
...+..+..++|++.
T Consensus 230 i~q~~~~~g~~A~~~ 244 (270)
T cd01545 230 VRQPIAEMARAAAEL 244 (270)
T ss_pred EECCHHHHHHHHHHH
T ss_conf 971999999999999
No 162
>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=83.44 E-value=3.5 Score=20.91 Aligned_cols=86 Identities=20% Similarity=0.245 Sum_probs=55.6
Q ss_pred CCCCHHHHHHHHHHHH-CCCCCCEEEEECCCCHHHHHHHHHHHHHHHHHCCCCCC-EEEECCCCCHHHHHHHHHHCCCCE
Q ss_conf 8889899999999986-19986589996358613289999999999997299987-999748985899999999769958
Q gi|254781049|r 301 GGADQDKVAAAFKIIT-SDSSVKGILINIFGGIMRCDVLVKGILSAVKEVKINIP-LVMRLEGANVDIGNRLIAESGLNV 378 (398)
Q Consensus 301 G~a~~e~~~~a~~~il-~~~~vk~iliNifGGI~~cd~vA~gii~a~~~~~~~~p-ivvRl~Gtn~~~g~~il~~~g~~~ 378 (398)
+..+.+..+++++-++ +.|++.+|| +.-|.+|.|+++|+++.+.+-. -|+=..++ ++....+.+..+-.
T Consensus 161 ~~~~~~~~~~~~~~~l~~~~~~~ai~-------~~nd~~a~g~~~al~~~g~~~di~viG~D~~--~~~~~~~~~~~~lt 231 (267)
T cd01536 161 GNWDREKALQAMEDLLQANPDIDAIF-------AANDSMALGAVAALKAAGRKGDVKIVGVDGS--PEALAAIKEGGILA 231 (267)
T ss_pred CCCCHHHHHHHHHHHHHCCCCCEEEE-------ECCCHHHHHHHHHHHHCCCCCCEEEEEECCC--HHHHHHHHCCCCEE
T ss_conf 01102578899997764179862999-------7164999999999997699999399998983--99999985599659
Q ss_pred EEECCHHHHHHHHHHHH
Q ss_conf 99499899999999985
Q gi|254781049|r 379 ITAIDLDDAAQKIVHAV 395 (398)
Q Consensus 379 ~~~~~~~~A~~~~v~~~ 395 (398)
....+..+..++++++.
T Consensus 232 tv~q~~~~~G~~a~~~l 248 (267)
T cd01536 232 TVAQDPYTQGYLAVEAA 248 (267)
T ss_pred EEECCHHHHHHHHHHHH
T ss_conf 99279999999999999
No 163
>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=83.04 E-value=3.6 Score=20.80 Aligned_cols=84 Identities=13% Similarity=0.167 Sum_probs=54.5
Q ss_pred CCCCHHHHHHHHHHHHCCCCCCEEEEECCCCHHHHHHHHHHHHHHHHHCCCCCCEEEECCCCCHHHHHHHHHHCCCCEEE
Q ss_conf 88898999999999861998658999635861328999999999999729998799974898589999999976995899
Q gi|254781049|r 301 GGADQDKVAAAFKIITSDSSVKGILINIFGGIMRCDVLVKGILSAVKEVKINIPLVMRLEGANVDIGNRLIAESGLNVIT 380 (398)
Q Consensus 301 G~a~~e~~~~a~~~il~~~~vk~iliNifGGI~~cd~vA~gii~a~~~~~~~~pivvRl~Gtn~~~g~~il~~~g~~~~~ 380 (398)
+..+.+.-+.+++.+++. ++.+|| ...|.+|.|+++++++.+.++|==+.+-|-+-.+ +.....-++.+
T Consensus 157 ~~~~~~~~~~~~~~~l~~-~p~ai~-------~~nD~~A~g~~~~l~~~g~~vP~dvsvvgfd~~~---~~~~~~p~lTT 225 (265)
T cd06299 157 GGYSQESGYAGATKLLDQ-GATAII-------AGDSMMTIGAIRAIHDAGLVIGEDISLIGFDDLP---VFRLQTPPLTV 225 (265)
T ss_pred ECCCHHHHHHHHHHHHHC-CCCEEE-------CCCCHHHHHHHHHHHHHCCCCCCCEEEEEECCHH---HHHHCCCCEEE
T ss_conf 403557899999999963-998545-------0685889999999998389999934999999758---89853998399
Q ss_pred -ECCHHHHHHHHHHHH
Q ss_conf -499899999999985
Q gi|254781049|r 381 -AIDLDDAAQKIVHAV 395 (398)
Q Consensus 381 -~~~~~~A~~~~v~~~ 395 (398)
..+..+..+.|+++.
T Consensus 226 v~~~~~~~g~~A~~~L 241 (265)
T cd06299 226 IDQQVEQMGKRAVDML 241 (265)
T ss_pred EECCHHHHHHHHHHHH
T ss_conf 9809999999999999
No 164
>PRK10669 putative cation:proton antiport protein; Provisional
Probab=82.62 E-value=3.7 Score=20.70 Aligned_cols=89 Identities=18% Similarity=0.292 Sum_probs=58.1
Q ss_pred CCCCEEEECCCCCCHHHHHHHHHHHHCCCCCCEEEEECCCCHHHHHHHHHHHHHHHHHCCCCCCEEEECCCCCHHHHHHH
Q ss_conf 99624884278889899999999986199865899963586132899999999999972999879997489858999999
Q gi|254781049|r 291 GAPANFLDVGGGADQDKVAAAFKIITSDSSVKGILINIFGGIMRCDVLVKGILSAVKEVKINIPLVMRLEGANVDIGNRL 370 (398)
Q Consensus 291 g~pANFlD~gG~a~~e~~~~a~~~il~~~~vk~iliNifGGI~~cd~vA~gii~a~~~~~~~~pivvRl~Gtn~~~g~~i 370 (398)
|.|+=| |.++.+.+-++..+ .+.|.+.+-+ .-+.-+.-++...++..+++||++|-. .++-.+.
T Consensus 460 g~~v~~----GDa~~~~~L~~agi----~~A~~vvit~-----~d~~~~~~iv~~~r~~~p~~~IiaRa~---~~~~~~~ 523 (558)
T PRK10669 460 GIRAVL----GNAANEEIMQLAHL----DCARWLLLTI-----PNGYEAGEIVASAREKNPDIEIIARAH---YDDEVAY 523 (558)
T ss_pred CCEEEE----ECCCCHHHHHHCCC----CCCCEEEEEE-----CCHHHHHHHHHHHHHHCCCCEEEEEEC---CHHHHHH
T ss_conf 997999----78998899985791----3249999981-----988999999999998786986999979---8999999
Q ss_pred HHHCCCCEEEECCHHHHHHHHHHHHH
Q ss_conf 99769958994998999999999850
Q gi|254781049|r 371 IAESGLNVITAIDLDDAAQKIVHAVK 396 (398)
Q Consensus 371 l~~~g~~~~~~~~~~~A~~~~v~~~k 396 (398)
|++.|.+.... +-.|++++.+++..
T Consensus 524 L~~aGA~~VV~-~~~e~a~~m~e~l~ 548 (558)
T PRK10669 524 ITERGANQVVM-GEREIARTMLELLE 548 (558)
T ss_pred HHHCCCCEEEC-CHHHHHHHHHHHHC
T ss_conf 99779998989-37899999999857
No 165
>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=82.05 E-value=3.9 Score=20.56 Aligned_cols=106 Identities=16% Similarity=0.161 Sum_probs=67.9
Q ss_pred HHHHHHHHHCCCCCCEEEECCCCCCHHHHHHHHHHHHCC---CCCCEEEEECCCCHHHHHHHHHHHHHHHHHCCCCCCEE
Q ss_conf 999999996589962488427888989999999998619---98658999635861328999999999999729998799
Q gi|254781049|r 280 MATMDIIKLYGGAPANFLDVGGGADQDKVAAAFKIITSD---SSVKGILINIFGGIMRCDVLVKGILSAVKEVKINIPLV 356 (398)
Q Consensus 280 matmD~i~~~Gg~pANFlD~gG~a~~e~~~~a~~~il~~---~~vk~iliNifGGI~~cd~vA~gii~a~~~~~~~~piv 356 (398)
-...+.+..+|.....+. +.|..+.+.-+++++-+++. ..+.+|| +..|.+|.|+++++++.++++|==
T Consensus 137 ~Gy~~al~~~g~~~~~~~-~~~~~~~~~g~~~~~~~l~~~~~~~ptAi~-------~~nD~~A~g~l~~l~~~gl~VP~D 208 (270)
T cd01544 137 TAFREYMKEKGLYDPELI-YIGDFTVESGYQLMKEALKSLGDNLPTAFF-------IASDPMAIGALRALQEAGIKVPED 208 (270)
T ss_pred HHHHHHHHHCCCCCCCEE-EECCCCHHHHHHHHHHHHHCCCCCCCCEEE-------ECCCHHHHHHHHHHHHCCCCCCCC
T ss_conf 999999998599996449-966899799999999999728878997899-------823188999999999879988776
Q ss_pred EECCCCCHHHHHHHHHHCCCCEEEECCHHHHHHHHHHHH
Q ss_conf 974898589999999976995899499899999999985
Q gi|254781049|r 357 MRLEGANVDIGNRLIAESGLNVITAIDLDDAAQKIVHAV 395 (398)
Q Consensus 357 vRl~Gtn~~~g~~il~~~g~~~~~~~~~~~A~~~~v~~~ 395 (398)
+.+-|-.-..-.+++ ...+.. ...+..+-.++|+++.
T Consensus 209 isviGfDd~~~~~~~-~P~LTT-V~q~~~~iG~~A~~~L 245 (270)
T cd01544 209 VSVISFNDIEVAKYV-SPPLST-VKIDTEEMGETAVDLL 245 (270)
T ss_pred EEEEEECCHHHHHHC-CCCCEE-EECCHHHHHHHHHHHH
T ss_conf 599997780789826-899369-9829999999999999
No 166
>PRK10339 DNA-binding transcriptional repressor EbgR; Provisional
Probab=81.36 E-value=4.1 Score=20.40 Aligned_cols=102 Identities=19% Similarity=0.190 Sum_probs=61.1
Q ss_pred HHHHHHCCC-CCCEEEECCCCCCHHHHHHHHHHHHCCCC-CCEEEEECCCCHHHHHHHHHHHHHHHHHCCCCCCEEEECC
Q ss_conf 999996589-96248842788898999999999861998-6589996358613289999999999997299987999748
Q gi|254781049|r 283 MDIIKLYGG-APANFLDVGGGADQDKVAAAFKIITSDSS-VKGILINIFGGIMRCDVLVKGILSAVKEVKINIPLVMRLE 360 (398)
Q Consensus 283 mD~i~~~Gg-~pANFlD~gG~a~~e~~~~a~~~il~~~~-vk~iliNifGGI~~cd~vA~gii~a~~~~~~~~pivvRl~ 360 (398)
.+.....|. .+.+.. -|..+.+.-+++.+-++..+. ..+|| ..+|.+|-|+++++++.++++|==+.+-
T Consensus 197 ~~~~~~~~~~~~~~i~--~~~~~~~~g~~~~~~ll~~~~~p~ai~-------~~nD~~A~g~l~al~~~gi~VP~DisVi 267 (327)
T PRK10339 197 AEYGRLKQVVREEDIW--RGGFSSSSGYELAKQMLAREDYPKALF-------VASDSIAIGVLRAIHERGLNIPQDISLI 267 (327)
T ss_pred HHHHHHCCCCCHHHEE--ECCCCHHHHHHHHHHHHHCCCCCCEEE-------ECCHHHHHHHHHHHHHCCCCCCCCEEEE
T ss_conf 9999875999737558--668986999999999984699997489-------7777999999999998299999975999
Q ss_pred CCCHHHHHHHHHHCCCCEEEECCHHHHHHHHHHHH
Q ss_conf 98589999999976995899499899999999985
Q gi|254781049|r 361 GANVDIGNRLIAESGLNVITAIDLDDAAQKIVHAV 395 (398)
Q Consensus 361 Gtn~~~g~~il~~~g~~~~~~~~~~~A~~~~v~~~ 395 (398)
|-+-..--+++ ...+.. ...+.++..+.||++.
T Consensus 268 gfdd~~~~~~~-~P~LTt-v~~~~~~~g~~Av~~L 300 (327)
T PRK10339 268 SVNDIPTARFT-FPPLST-VRIHSEMMGSQGVNLL 300 (327)
T ss_pred EECCHHHHHHC-CCCCEE-EECCHHHHHHHHHHHH
T ss_conf 98973889833-899569-9869999999999999
No 167
>TIGR01124 ilvA_2Cterm threonine ammonia-lyase, biosynthetic; InterPro: IPR005787 Serine and threonine dehydratases , are functionally and structurally related pyridoxal-phosphate dependent enzymes. L-serine dehydratase () and D-serine dehydratase () catalyze the dehydratation of L-serine (respectively D-serine) into ammonia and pyruvate. Threonine dehydratase () (TDH) catalyzes the dehydratation of threonine into alpha-ketobutarate and ammonia. In Escherichia coli and other microorganisms, two classes of TDH are known to exist. One is involved in the biosynthesis of isoleucine, the other in hydroxamino acid catabolism. Threonine synthase () is also a pyridoxal-phosphate enzyme, it catalyzes the transformation of homoserine-phosphate into threonine. It has been shown that threonine synthase is distantly related to the serine/threonine dehydratases. In all these enzymes, the pyridoxal-phosphate group is attached to a lysine residue. This family describes a form of threonine dehydratase, with two copies of the threonine dehydratase C-terminal domain IPR001721 from INTERPRO. Members with known function participate in isoleucine biosynthesis and are inhibited by isoleucine.; GO: 0004794 L-threonine ammonia-lyase activity, 0009097 isoleucine biosynthetic process.
Probab=80.97 E-value=3.6 Score=20.77 Aligned_cols=54 Identities=15% Similarity=0.169 Sum_probs=31.2
Q ss_pred CCEEECCH-HH---HHHHHHHCCCCEEE--------EECCCCCCCCCCCCCCCCCCCCCCEEEE-ECCHHHHHHHHHHHC
Q ss_conf 81574799-99---99999872998699--------9712136876565655677777770799-589999999999861
Q gi|254781049|r 21 KGVVISSV-HA---AESAIKTLPGPLYV--------VKSQIHAGGRGKGRFKELPADSKGGVRV-ESSLKSVISDIREIL 87 (398)
Q Consensus 21 ~g~~a~s~-~e---a~~~a~~ig~p~~V--------vKaQV~aGgRGKa~~~~~hk~~~GGV~l-~~s~~ea~~~a~~il 87 (398)
+|++|-|+ +. ..-.+++||-+-+. ||.|- -|+.-|-|.| -.|-+||...|.++-
T Consensus 68 ~GVIaASAGNHAQGVAlsa~~LG~~A~IVMP~tTP~IKV~A-------------Vk~~GgeVvLhG~~y~~A~~~A~eL~ 134 (508)
T TIGR01124 68 RGVIAASAGNHAQGVALSAEKLGLKAVIVMPETTPDIKVDA-------------VKAFGGEVVLHGDNYDDAKDHAIELA 134 (508)
T ss_pred CCEEECCCCCHHHHHHHHHHHCCCCEEEECCCCCCCCCHHH-------------EECCCCEEEEECCCHHHHHHHHHHHH
T ss_conf 82012024545789987663179726987888882200120-------------31269879973798579999999999
No 168
>TIGR01859 fruc_bis_ald_ fructose-1,6-bisphosphate aldolase, class II; InterPro: IPR011289 Fructose-1,6-bisphosphate (FBP) aldolases reversibly cleave FBP to two triose phosphates, glycerone phophate and D-glyceraldehyde 3-phosphate. They play a key role in both glycolysis (FBP cleavage) and gluconeogenesis (FBP synthesis). These enzymes can be divide into two classes based on their mode of catalysis. Class I FBP aldolases form a Schiff-base intermediate between glycerone phophate and an active site lysine residue, while the class II enzymes use a divalent cation such as Zn(2+) for catalysis . This entry represents class II FBP aldolases found in Gram-positive bacteria, a variety of Gram-negative baceria, and amitochondriate protists. These enzymes are homotetramers where each momomer forms a TIM barrel fold .; GO: 0004332 fructose-bisphosphate aldolase activity, 0008270 zinc ion binding, 0006096 glycolysis, 0030388 fructose 16-bisphosphate metabolic process.
Probab=80.67 E-value=4.4 Score=20.25 Aligned_cols=41 Identities=17% Similarity=0.266 Sum_probs=17.5
Q ss_pred CCCCCCHHHHHHHHHHCCC-----CHHHHHHHHHHHHHHHHHHHHCC
Q ss_conf 4457895788878875198-----88998859999999989999559
Q gi|254781049|r 161 PLIGVTSEDVASLCDMLEL-----QGQARIDGGDLFPNLYKAFCDKD 202 (398)
Q Consensus 161 ~~~gl~~~~~~~l~~~lg~-----~~~~~~~~~~ii~~L~~~f~e~D 202 (398)
-..|++..++++.+. ||. .-+....|..-++++.+=|...|
T Consensus 254 ds~GIP~e~ikkAi~-lGiaKiNidTe~riAf~~~~R~~l~dy~a~d 299 (339)
T TIGR01859 254 DSKGIPEEQIKKAIK-LGIAKINIDTECRIAFTAAIRKVLEDYEAKD 299 (339)
T ss_pred CCCCCCHHHHHHHHH-CCCCEEEECCHHHHHHHHHHHHHHHHCCCCC
T ss_conf 777686789999997-2914176581678999999999984114355
No 169
>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=80.20 E-value=4.5 Score=20.15 Aligned_cols=82 Identities=10% Similarity=-0.006 Sum_probs=58.6
Q ss_pred HHHHHHH-HHHHHCCCCCCEEEEECCCCHHHHHHHHHHHHHHHHHCCCC-CCEEEECCCCCHHHHHHHHHHCCCCEEEEC
Q ss_conf 8999999-99986199865899963586132899999999999972999-879997489858999999997699589949
Q gi|254781049|r 305 QDKVAAA-FKIITSDSSVKGILINIFGGIMRCDVLVKGILSAVKEVKIN-IPLVMRLEGANVDIGNRLIAESGLNVITAI 382 (398)
Q Consensus 305 ~e~~~~a-~~~il~~~~vk~iliNifGGI~~cd~vA~gii~a~~~~~~~-~pivvRl~Gtn~~~g~~il~~~g~~~~~~~ 382 (398)
.+...+. -.++.++|++++|| ...|.+|.|.++|+++.+.+ .-.|+=..++. +..+.+++-.+......
T Consensus 167 ~~~a~~~~~~~L~~~pdi~~I~-------~~nd~~a~ga~~Al~~ag~~~~i~vvg~D~~~--~~~~~i~~G~i~~tv~Q 237 (271)
T cd06312 167 PTEVASRIAAYLRANPDVDAVL-------TLGAPSAAPAAKALKQAGLKGKVKLGGFDLSP--ATLQAIKAGYIQFAIDQ 237 (271)
T ss_pred HHHHHHHHHHHHHHCCCCCEEE-------ECCCHHHHHHHHHHHHCCCCCCEEEEEECCCH--HHHHHHHCCCCEEEEEC
T ss_conf 9999999999998498988899-------88967899999999966999985999988999--99999986995599958
Q ss_pred CHHHHHHHHHHHH
Q ss_conf 9899999999985
Q gi|254781049|r 383 DLDDAAQKIVHAV 395 (398)
Q Consensus 383 ~~~~A~~~~v~~~ 395 (398)
+-.+--.++|+..
T Consensus 238 ~p~~~Gy~aV~~l 250 (271)
T cd06312 238 QPYLQGYLPVSLL 250 (271)
T ss_pred CHHHHHHHHHHHH
T ss_conf 9999999999999
No 170
>TIGR01768 GGGP-family geranylgeranylglyceryl phosphate synthase family protein; InterPro: IPR008205 This family contains prokaryotic proteins that are related to pcrB. Staphylococcus aureus chromosomal gene pcrA encodes a protein with significant similarity (40 0dentity) to two Escherichia coli helicases: the helicase II encoded by the uvrD gene and the Rep helicase. PcrB gene seems to belong to an operon containing at least one other gene, pcrBA, downstream from pcrB . The PcrB proteins often contain an FMN binding site although the function of these proteins is still unknown..
Probab=79.75 E-value=3.2 Score=21.16 Aligned_cols=57 Identities=26% Similarity=0.376 Sum_probs=44.2
Q ss_pred CCCCEEEECCCCCCH---HHHHHHHHHHHCC--CCCCEEEEECCCCHHHHHHHHHHHHHHHHHC
Q ss_conf 996248842788898---9999999998619--9865899963586132899999999999972
Q gi|254781049|r 291 GAPANFLDVGGGADQ---DKVAAAFKIITSD--SSVKGILINIFGGIMRCDVLVKGILSAVKEV 349 (398)
Q Consensus 291 g~pANFlD~gG~a~~---e~~~~a~~~il~~--~~vk~iliNifGGI~~cd~vA~gii~a~~~~ 349 (398)
+=|==||++||++.. ..+-...|-++++ -.-+..| ++||-.|+-+.|+-++.|.-+.
T Consensus 159 g~~~~YLEagsgap~pvpPE~va~vk~v~~~aGyGGe~~L--~vGGGIRs~E~A~~~a~AgAD~ 220 (242)
T TIGR01768 159 GMPIIYLEAGSGAPEPVPPELVAEVKKVLDKAGYGGEVKL--IVGGGIRSVEKARKLAEAGADV 220 (242)
T ss_pred CCCEEEEECCCCCCCCCCHHHHHHHHHHHHCCCCCCCEEE--EEECCCCCHHHHHHHHHCCCCE
T ss_conf 9968999637875479745899999987410478863257--8407647889999995345989
No 171
>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=78.98 E-value=4.9 Score=19.90 Aligned_cols=83 Identities=19% Similarity=0.229 Sum_probs=55.8
Q ss_pred CHHHHH-HHHHHHHCCCCCCEEEEECCCCHHHHHHHHHHHHHHHHHCCCCCCEEEECCCCCHHHHHHHHHHCCCCE-EEE
Q ss_conf 989999-999998619986589996358613289999999999997299987999748985899999999769958-994
Q gi|254781049|r 304 DQDKVA-AAFKIITSDSSVKGILINIFGGIMRCDVLVKGILSAVKEVKINIPLVMRLEGANVDIGNRLIAESGLNV-ITA 381 (398)
Q Consensus 304 ~~e~~~-~a~~~il~~~~vk~iliNifGGI~~cd~vA~gii~a~~~~~~~~pivvRl~Gtn~~~g~~il~~~g~~~-~~~ 381 (398)
+.+.-. .+-+++.++|++++||- .-|.+|.|.++|+++.+.+-.-|+-..|+ .+++..++..+... ...
T Consensus 162 ~~~~~~~~~~~~L~~~p~~~aI~~-------~nD~~A~Ga~~al~~~g~~di~vvGfD~~--~~a~~~i~~~~p~~ttv~ 232 (267)
T cd06322 162 TRAEALTAAQNILQANPDLDGIFA-------FGDDAALGAVSAIKAAGRDNVKVIGFDGM--PEARKAVDGEPPFVAVIR 232 (267)
T ss_pred CHHHHHHHHHHHHHHCCCCCEEEE-------CCCHHHHHHHHHHHHCCCCCCEEEEECCC--HHHHHHHHHCCCCEEEEE
T ss_conf 879999999999862877748998-------18799999999999759999889999494--999999970898789996
Q ss_pred CCHHHHHHHHHHHH
Q ss_conf 99899999999985
Q gi|254781049|r 382 IDLDDAAQKIVHAV 395 (398)
Q Consensus 382 ~~~~~A~~~~v~~~ 395 (398)
.+..+-.+++++++
T Consensus 233 Q~~~~~G~~av~~l 246 (267)
T cd06322 233 QYPDQMGKKAIDAA 246 (267)
T ss_pred CCHHHHHHHHHHHH
T ss_conf 89999999999999
No 172
>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=78.89 E-value=5 Score=19.88 Aligned_cols=106 Identities=12% Similarity=0.097 Sum_probs=62.2
Q ss_pred HHHHHHHHCCCCCC--EEEECCCCCCHHHHHHHHH-HHHCCCCCCEEEEECCCCHHHHHHHHHHHHHHHHHCCCCCCEEE
Q ss_conf 99999996589962--4884278889899999999-98619986589996358613289999999999997299987999
Q gi|254781049|r 281 ATMDIIKLYGGAPA--NFLDVGGGADQDKVAAAFK-IITSDSSVKGILINIFGGIMRCDVLVKGILSAVKEVKINIPLVM 357 (398)
Q Consensus 281 atmD~i~~~Gg~pA--NFlD~gG~a~~e~~~~a~~-~il~~~~vk~iliNifGGI~~cd~vA~gii~a~~~~~~~~pivv 357 (398)
...+.+..+|.++- .+.+.-...+.+...+.+. .+.+.|+..+||. ..|.+|-|+++++++.++++|==+
T Consensus 129 Gf~~al~~~g~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~ptAi~~-------~nD~~A~g~l~~l~~~Gi~VP~di 201 (265)
T cd01543 129 AFRQLVAEAGYECSFFYRGLSTDAQSWEEEQEELAQWLQSLPKPVGIFA-------CTDARARQLLEACRRAGIAVPEEV 201 (265)
T ss_pred HHHHHHHHCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHCCCCCEEEEE-------CCHHHHHHHHHHHHHHHCCCCCCE
T ss_conf 9999999779997634124544675399999999999835999839998-------836999999999998322577755
Q ss_pred ECCCCC-HHHHHHHHHHCCCCEEEECCHHHHHHHHHHHH
Q ss_conf 748985-89999999976995899499899999999985
Q gi|254781049|r 358 RLEGAN-VDIGNRLIAESGLNVITAIDLDDAAQKIVHAV 395 (398)
Q Consensus 358 Rl~Gtn-~~~g~~il~~~g~~~~~~~~~~~A~~~~v~~~ 395 (398)
.+-|-+ ......+. ...+.- ...+.++..++|+++.
T Consensus 202 sViGfD~~~~~~~~~-~P~LTt-V~q~~~~mG~~Aa~lL 238 (265)
T cd01543 202 AVLGVDNDELICELS-RPPLSS-VEQNAERIGYEAAKLL 238 (265)
T ss_pred EEEEECCCHHHHHHC-CCCCCE-EEECHHHHHHHHHHHH
T ss_conf 999982868889527-999733-9629999999999999
No 173
>KOG1255 consensus
Probab=77.89 E-value=5.3 Score=19.69 Aligned_cols=108 Identities=19% Similarity=0.328 Sum_probs=67.4
Q ss_pred CEEECCCCEEEEECCCHHHHHHHHHHHHCCCCCCEEEECCCCC-CHHHHHHHHHHHHCCCCCCEEE-EECCCCHHHHHHH
Q ss_conf 6442288179995550368999999996589962488427888-9899999999986199865899-9635861328999
Q gi|254781049|r 261 SYIALDGNIGCMVNGAGLAMATMDIIKLYGGAPANFLDVGGGA-DQDKVAAAFKIITSDSSVKGIL-INIFGGIMRCDVL 338 (398)
Q Consensus 261 ~yv~LdG~Ig~~vnGaGlamatmD~i~~~Gg~pANFlD~gG~a-~~e~~~~a~~~il~~~~vk~il-iNifGGI~~cd~v 338 (398)
.++.-.|.||++.--+-|+--..-.-...|.-..-..-+||.| +-..-..++++.|.||..++|. |-=.|| ..++-
T Consensus 171 g~Ihk~G~IGIVSRSGTLTYEaVhQTT~vglGQslcvGiGGDpFnGT~FID~L~vFl~D~~t~GIiliGEIGG--~AEe~ 248 (329)
T KOG1255 171 GHIHKRGKIGIVSRSGTLTYEAVHQTTQVGLGQSLCVGIGGDPFNGTNFIDCLEVFLEDPETEGIILIGEIGG--SAEEE 248 (329)
T ss_pred CCCCCCCEEEEEECCCCEEEHHHHHHCCCCCCCEEEEEECCCCCCCCCHHHHHHHHHCCCCCCEEEEEECCCC--HHHHH
T ss_conf 1146686268996587246004012041356634688614788899648999998825856341799961477--14688
Q ss_pred HHHHHHHHHHCCCCCCEEEECCCCCHHHHHHH
Q ss_conf 99999999972999879997489858999999
Q gi|254781049|r 339 VKGILSAVKEVKINIPLVMRLEGANVDIGNRL 370 (398)
Q Consensus 339 A~gii~a~~~~~~~~pivvRl~Gtn~~~g~~i 370 (398)
|--.++....-...+|+|--+.|.-+-.|+|+
T Consensus 249 AA~flk~~nSg~~~kPVvsFIAG~tAppGrRM 280 (329)
T KOG1255 249 AAEFLKEYNSGSTAKPVVSFIAGVTAPPGRRM 280 (329)
T ss_pred HHHHHHHHCCCCCCCCEEEEEECCCCCCCCCC
T ss_conf 99999984158988864578514657986534
No 174
>TIGR02086 IPMI_arch 3-isopropylmalate dehydratase, large subunit; InterPro: IPR011826 3-isopropylmalate dehydratase (or isopropylmalate isomerase; 4.2.1.33 from EC) catalyses the stereo-specific isomerisation of 2-isopropylmalate and 3-isopropylmalate, via the formation of 2-isopropylmaleate. This enzyme performs the second step in the biosynthesis of leucine, and is present in most prokaryotes and many fungal species. The prokaryotic enzyme is a heterodimer composed of a large (LeuC) and small (LeuD) subunit, while the fungal form is a monomeric enzyme. Both forms of isopropylmalate are related and are part of the larger aconitase family . Aconitases are mostly monomeric proteins which share four domains in common and contain a single, labile [4Fe-4S] cluster. Three structural domains (1, 2 and 3) are tightly packed around the iron-sulphur cluster, while a fourth domain (4) forms a deep active-site cleft. The prokaryotic enzyme is encoded by two adjacent genes, leuC and leuD, corresponding to aconitase domains 1-3 and 4 respectively , . LeuC does not bind an iron-sulphur cluster. It is thought that some prokaryotic isopropylamalate dehydrogenases can also function as homoaconitase 4.2.1.36 from EC, converting cis-homoaconitate to homoisocitric acid in lysine biosynthesis . Homoaconitase has been identified in higher fungi (mitochondria) and several archaea and one thermophilic species of bacteria, Thermus thermophilus . This entry represents the large subunit of 3-isopropylmalate dehydratase (LeuC), as well as homoaconitase enzymes, from prokaryotes. Homoaconitase, aconitase and 3-isopropylmalate dehydratase have similar overall structures and domain organisation . All are dehydratases that bind a [4Fe-4S]-cluster. Information about related proteins can be found at Protein of the Month: Aconitase .; GO: 0003861 3-isopropylmalate dehydratase activity, 0051539 4 iron 4 sulfur cluster binding, 0009098 leucine biosynthetic process.
Probab=76.87 E-value=5.6 Score=19.53 Aligned_cols=165 Identities=19% Similarity=0.167 Sum_probs=101.4
Q ss_pred HHHHHC-CCCCCCCEEEC-----------CHHHHHHHHHHCC---CCEEEEECCCCCCCCCCCCCCCCCCCCCCEEEEEC
Q ss_conf 999986-89888815747-----------9999999998729---98699971213687656565567777777079958
Q gi|254781049|r 10 ALLRKY-NVPVAKGVVIS-----------SVHAAESAIKTLP---GPLYVVKSQIHAGGRGKGRFKELPADSKGGVRVES 74 (398)
Q Consensus 10 ~lL~~~-GIpvp~g~~a~-----------s~~ea~~~a~~ig---~p~~VvKaQV~aGgRGKa~~~~~hk~~~GGV~l~~ 74 (398)
+||++. |-+|-+|.++. |.--+.+..++++ +|.-|.+.| |+..-+=|..-.--|+.++
T Consensus 6 KILS~kvG~~V~aGE~V~v~VD~am~hDGt~p~~i~~l~~~g~rGG~~~v~~p~-------k~v~~fDH~~P~~~v~~A~ 78 (431)
T TIGR02086 6 KILSEKVGRPVEAGEIVEVEVDLAMAHDGTGPLAIKALRELGERGGMAKVEDPE-------KIVIVFDHVVPAPTVEAAE 78 (431)
T ss_pred HHHHHHCCCCCCCCCEEEEECCEEEEECCCHHHHHHHHHHHHHCCCCCCCCCCC-------EEEEEEECCCCCCCHHHHH
T ss_conf 888985679878865799702599996487178999999997347867664686-------4899982688996567788
Q ss_pred CHHHHHHHHHHHCCCCCCC-CCCCCCCCCCCCEEECC-CCCCCEEEEEEE-EEECCCCCEEEEEECCCCCCHH------H
Q ss_conf 9999999999861876544-21222224433011034-555650589999-9834778048998447884024------5
Q gi|254781049|r 75 SLKSVISDIREILGSTLIT-KQTGPTGSRVNCVYVED-GADILRELYLSL-LVDRTSGMVAFIASTQGGMDIE------E 145 (398)
Q Consensus 75 s~~ea~~~a~~ilg~~l~t-~qt~~~G~~v~~vLVEe-~v~~~~E~ylgi-~~Dr~~~~~vii~S~~GGvdIE------~ 145 (398)
...+.+++++++ .|.. .+.+ .| .+++||+|+ .+...+ +.+|- ...+..|..-.++.+.|+.|+= +
T Consensus 79 ~Q~~~REF~K~~---gI~~f~~~g-~G-IcHQ~L~E~Gya~PG~-vvvG~DSHT~T~GA~GAFA~GmGATDvA~a~~~G~ 152 (431)
T TIGR02086 79 LQKEIREFAKRH---GIKVFFDVG-EG-ICHQVLVEKGYAEPGM-VVVGADSHTCTSGALGAFATGMGATDVAIALATGK 152 (431)
T ss_pred HHHHHHHHHHHC---CCCEEEECC-CE-EEEEEEEECCCCCCCE-EEEECCCCCCHHHCHHHEEECCCHHHHHHHHHHCC
T ss_conf 778999888766---870599879-80-2778865306247761-89952677400000023042578689999998286
Q ss_pred HHHHCHHHHEEEECC--CCCCCCHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCC--CCC
Q ss_conf 557483122033214--445789578887887519888998859999999989999559751--023
Q gi|254781049|r 146 VAKDYPQKIFKLLID--PLIGVTSEDVASLCDMLELQGQARIDGGDLFPNLYKAFCDKDMSL--LEI 208 (398)
Q Consensus 146 va~~~p~~I~~~~id--~~~gl~~~~~~~l~~~lg~~~~~~~~~~~ii~~L~~~f~e~Da~l--iEI 208 (398)
.|-+-|+.|. +.++ |....+ .+|++.++.+.+..-.++. +|+
T Consensus 153 ~W~~VPe~~~-V~~~G~l~~~v~--------------------AKDv~L~~~~~lg~~gatY~a~E~ 198 (431)
T TIGR02086 153 TWLKVPESIK-VVVEGKLEEGVT--------------------AKDVALEIVGELGADGATYMAIEF 198 (431)
T ss_pred CEEECCEEEE-EEEEECCCCCEE--------------------HHHHHHHHHHHHCCCCCCCCEEEE
T ss_conf 1364580899-998721698602--------------------248898999984878764016987
No 175
>PRK06241 phosphoenolpyruvate synthase; Validated
Probab=76.71 E-value=5.7 Score=19.48 Aligned_cols=110 Identities=17% Similarity=0.148 Sum_probs=59.9
Q ss_pred HHHHCCCCCCCCEEECCHH---------------------------------------------------HHHHHHHHCC
Q ss_conf 9998689888815747999---------------------------------------------------9999998729
Q gi|254781049|r 11 LLRKYNVPVAKGVVISSVH---------------------------------------------------AAESAIKTLP 39 (398)
Q Consensus 11 lL~~~GIpvp~g~~a~s~~---------------------------------------------------ea~~~a~~ig 39 (398)
-|.+.|+|||+|.++++.. +...+...++
T Consensus 25 ~l~~~G~pVP~gfvit~~a~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~i~~~~~~~~~p~~~~~~i~~~~~~~~ 104 (870)
T PRK06241 25 ELSKAGIPVPEGFCVTTEAYKKFIESNEELDELLDQLTLLKREDREQIGEISKKIREVIRAIEIPEDIKEAIAAALSKFG 104 (870)
T ss_pred HHHHCCCCCCCCEEEHHHHHHHHHHCCCCHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHC
T ss_conf 99978899999687519999999980885689999997267765777999999999999828998899999999999827
Q ss_pred --CCEEEEECCCCCCCCCCCCCCCCCCCCCCEEE--E-ECCHHHHHHHHHHHCCCC----CCCCCCCCCCCC----CCCE
Q ss_conf --98699971213687656565567777777079--9-589999999999861876----544212222244----3301
Q gi|254781049|r 40 --GPLYVVKSQIHAGGRGKGRFKELPADSKGGVR--V-ESSLKSVISDIREILGST----LITKQTGPTGSR----VNCV 106 (398)
Q Consensus 40 --~p~~VvKaQV~aGgRGKa~~~~~hk~~~GGV~--l-~~s~~ea~~~a~~ilg~~----l~t~qt~~~G~~----v~~v 106 (398)
.|+ .|.+--. ..+....|..|--- + +...+++.++.++.+.+- .+... ...|.. --.|
T Consensus 105 ~~~~~-aVRSSa~-------~ED~~~~sfAGq~dt~L~v~~~~~l~~ai~~c~aS~~~~ra~~YR-~~~~~~~~~~~maV 175 (870)
T PRK06241 105 EDHAY-AVRSSAT-------AEDLPTASFAGQQDTYLNVIGKEAILQHIRKCWASLFTDRAVIYR-LQNGFDHRKVSMSV 175 (870)
T ss_pred CCCCE-EEECCCC-------CCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHCCCCHHHHHHH-HHCCCCHHHHCCEE
T ss_conf 99878-9967661-------247977773544112068899899999999999706889999999-98499917744057
Q ss_pred EECCCCCCCEEEEEEEEEECCCCC
Q ss_conf 103455565058999998347780
Q gi|254781049|r 107 YVEDGADILRELYLSLLVDRTSGM 130 (398)
Q Consensus 107 LVEe~v~~~~E~ylgi~~Dr~~~~ 130 (398)
+|++|++... -=+.++.||.++.
T Consensus 176 vVQ~Mv~~~~-sGV~FT~dP~tg~ 198 (870)
T PRK06241 176 VVQKMVFPEA-SGILFTADPVTGN 198 (870)
T ss_pred EEEECCCCCC-CEEEEECCCCCCC
T ss_conf 8885114764-2699977888899
No 176
>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=76.28 E-value=5.9 Score=19.41 Aligned_cols=85 Identities=16% Similarity=0.235 Sum_probs=57.2
Q ss_pred CCCCHHHHHHHHH-HHHCCCCCCEEEEECCCCHHHHHHHHHHHHHHHHHCCCC-CCEEEECCCCCHHHHHHHHHHCCCCE
Q ss_conf 8889899999999-986199865899963586132899999999999972999-87999748985899999999769958
Q gi|254781049|r 301 GGADQDKVAAAFK-IITSDSSVKGILINIFGGIMRCDVLVKGILSAVKEVKIN-IPLVMRLEGANVDIGNRLIAESGLNV 378 (398)
Q Consensus 301 G~a~~e~~~~a~~-~il~~~~vk~iliNifGGI~~cd~vA~gii~a~~~~~~~-~pivvRl~Gtn~~~g~~il~~~g~~~ 378 (398)
+..+.+.-+++++ ++.++|++++||.. ++ .++ |+++|+++.+.. ...+|=..++ .+..+.|++-.+..
T Consensus 166 ~~~~~~~a~~~~~~lL~~~Pdi~ai~~~--~~-----~~~-ga~~Al~~~g~~~~v~vvg~D~~--~~~~~~l~~G~i~a 235 (275)
T cd06307 166 GLDDPARAYEATRKLLARHPDLVGIYNA--GG-----GNR-GVIRALREAGRAGKVVFVGHELT--PETRAALRDGTIDA 235 (275)
T ss_pred CCCCHHHHHHHHHHHHHHCCCCEEEEEC--CC-----CHH-HHHHHHHHCCCCCCEEEEECCCC--HHHHHHHHCCCCEE
T ss_conf 7886599999999999749996299984--87-----169-99999997399998699962799--89999998198379
Q ss_pred EEECCHHHHHHHHHHHH
Q ss_conf 99499899999999985
Q gi|254781049|r 379 ITAIDLDDAAQKIVHAV 395 (398)
Q Consensus 379 ~~~~~~~~A~~~~v~~~ 395 (398)
....+-.+-.+++|+++
T Consensus 236 ~v~Q~P~~~G~~Av~~l 252 (275)
T cd06307 236 VIDQDPGHLARSAVRVL 252 (275)
T ss_pred EEECCHHHHHHHHHHHH
T ss_conf 99359999999999999
No 177
>PRK03803 murD UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional
Probab=75.51 E-value=6.2 Score=19.27 Aligned_cols=95 Identities=17% Similarity=0.260 Sum_probs=59.7
Q ss_pred EEEECCCCCCHHHHHHHHHHHHCCCCCCEEEEECCCCHHHHHHHHHHHHHHHHHCCCCCCEEEECCCCCHHHHHHHHHHC
Q ss_conf 48842788898999999999861998658999635861328999999999999729998799974898589999999976
Q gi|254781049|r 295 NFLDVGGGADQDKVAAAFKIITSDSSVKGILINIFGGIMRCDVLVKGILSAVKEVKINIPLVMRLEGANVDIGNRLIAES 374 (398)
Q Consensus 295 NFlD~gG~a~~e~~~~a~~~il~~~~vk~iliNifGGI~~cd~vA~gii~a~~~~~~~~pivvRl~Gtn~~~g~~il~~~ 374 (398)
-|.|=+=+++.+.+..|++-+.+...=+.|| |.||..+-.+..+ +.+.+.+ ++.-++ +-|...+.=.+.+.+
T Consensus 320 ~fiNDSKaTN~~at~~Al~~~~~~~~~~iil--I~GG~~K~~d~~~-l~~~~~~---~v~~v~-l~G~~~~~i~~~l~~- 391 (448)
T PRK03803 320 RYYNDSKGTNVGATLAAIEGLGADIEGKLVL--IAGGQGKGADFSE-LREPVAK---YCRAVV-LIGRDAELIEQALGD- 391 (448)
T ss_pred EEEECCCCCCHHHHHHHHHHHHHHCCCCEEE--EECCCCCCCCHHH-HHHHHHH---CCEEEE-EECCCHHHHHHHHCC-
T ss_conf 9996899899789999999646523686899--9378666668799-9999973---660999-979599999997506-
Q ss_pred CCCEEEECCHHHHHHHHHHHHHC
Q ss_conf 99589949989999999998506
Q gi|254781049|r 375 GLNVITAIDLDDAAQKIVHAVKG 397 (398)
Q Consensus 375 g~~~~~~~~~~~A~~~~v~~~k~ 397 (398)
..+++.+.+|++|++.|.+.++.
T Consensus 392 ~~~~~~~~~l~~Av~~a~~~a~~ 414 (448)
T PRK03803 392 AVPLVRAATLEEAVTQAAELAQP 414 (448)
T ss_pred CCCEEECCCHHHHHHHHHHHCCC
T ss_conf 89879949999999999985789
No 178
>TIGR00097 HMP-P_kinase phosphomethylpyrimidine kinase; InterPro: IPR004399 Phosphomethylpyrimidine kinase (2.7.4.7 from EC), also known as HMP-phosphate kinase, catalyses the phosphorylation of HMP-P to HMP-PP in the reaction: ATP + 4-amino-2-methyl-5-phosphomethylpyrimidine = ADP + 4-amino-2-methyl-5-diphosphomethylpyrimidine during the biosynthesis of thiamine.; GO: 0008972 phosphomethylpyrimidine kinase activity, 0009228 thiamin biosynthetic process.
Probab=75.30 E-value=6.2 Score=19.24 Aligned_cols=111 Identities=19% Similarity=0.172 Sum_probs=49.1
Q ss_pred CCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCEEECCCCCCCEEEEE--EEEEECCCCCEEEEEECCCCCCHHHHHHHCH
Q ss_conf 89999999999861876544212222244330110345556505899--9998347780489984478840245557483
Q gi|254781049|r 74 SSLKSVISDIREILGSTLITKQTGPTGSRVNCVYVEDGADILRELYL--SLLVDRTSGMVAFIASTQGGMDIEEVAKDYP 151 (398)
Q Consensus 74 ~s~~ea~~~a~~ilg~~l~t~qt~~~G~~v~~vLVEe~v~~~~E~yl--gi~~Dr~~~~~vii~S~~GGvdIE~va~~~p 151 (398)
-.|+-+.+-.+..+. .+ ..+.-.-|...+.=+||-=+.--+||=+ -+++| |||+ |.-|....++-+-.
T Consensus 50 ipp~~V~aQl~aV~~-D~-~~~a~KtGML~saeIve~Va~~l~~y~~~~~~VvD-----PVMV-AksG~~Ll~~~a~~-- 119 (264)
T TIGR00097 50 IPPDFVEAQLDAVLS-DI-KVDAVKTGMLASAEIVEAVAKKLREYDVQIPIVVD-----PVMV-AKSGAALLEEEAVE-- 119 (264)
T ss_pred CCHHHHHHHHHHHHH-CC-CCCEEEECCCCCHHHHHHHHHHHHCCCCCEEEEEC-----CCEE-ECCCCCCCCHHHHH--
T ss_conf 587799999999861-08-96558862456707778667765404883038976-----7216-52875465478999--
Q ss_pred HHHEEE--ECCCCCCCCHHHHHHHHHHCCCCHHHHHHHHHHHHHHH-HH
Q ss_conf 122033--21444578957888788751988899885999999998-99
Q gi|254781049|r 152 QKIFKL--LIDPLIGVTSEDVASLCDMLELQGQARIDGGDLFPNLY-KA 197 (398)
Q Consensus 152 ~~I~~~--~id~~~gl~~~~~~~l~~~lg~~~~~~~~~~~ii~~L~-~~ 197 (398)
.+++. |+-...-+..+++..|+.. .+-+..+++.+-.++|+ ++
T Consensus 120 -~l~~~LLP~A~~~TPN~pEAe~L~g~--~~I~~~~dm~~AAk~l~~~l 165 (264)
T TIGR00097 120 -ALKKRLLPLATLVTPNLPEAEALLGA--TKIRTEEDMIKAAKKLREEL 165 (264)
T ss_pred -HHHHHHCCCEEEECCCHHHHHHHCCC--CCCCCHHHHHHHHHHHHHHH
T ss_conf -99997387114306897999998089--66589899999999998851
No 179
>TIGR01481 ccpA catabolite control protein A; InterPro: IPR006377 Catabolite control protein A is a LacI family global transcriptional regulator found in Gram-positive bacteria. CcpA is involved in repressing carbohydrate utilization genes [ex: alpha-amylase (amyE), acetyl-coenzyme A synthase (acsA)] and in activating genes involved in transporting excess carbon from the cell [e.g. acetate kinase (ackA), alpha-acetolactate synthase (alsS)]. Additionally, disruption of CcpA in Bacillus megaterium, Staphylococcus xylosus, Lactobacillus casei and Lactocacillus pentosus also decreases growth rate, which suggests CcpA is involved in the regulation of other metabolic pathways.; GO: 0030528 transcription regulator activity, 0045449 regulation of transcription.
Probab=72.44 E-value=7.3 Score=18.79 Aligned_cols=43 Identities=26% Similarity=0.444 Sum_probs=35.8
Q ss_pred HHHHHHHHHHHHCCCCCCEEEEECCCCHHHHHHHHHHHHHHHHHCCCCCC
Q ss_conf 89999999998619986589996358613289999999999997299987
Q gi|254781049|r 305 QDKVAAAFKIITSDSSVKGILINIFGGIMRCDVLVKGILSAVKEVKINIP 354 (398)
Q Consensus 305 ~e~~~~a~~~il~~~~vk~iliNifGGI~~cd~vA~gii~a~~~~~~~~p 354 (398)
.+-++-.-++.-+.|++.+||+ --|++|=||++|.-+.++++|
T Consensus 224 ~~G~K~~~~l~~s~p~~tAv~v-------~~DE~A~G~lnaa~D~Gi~VP 266 (332)
T TIGR01481 224 DAGVKLAAELLESSPKITAVVV-------ADDELAIGILNAALDAGIKVP 266 (332)
T ss_pred HHHHHHHHHHHHCCCCCCEEEE-------CCHHHHHHHHHHHHHCCCCCC
T ss_conf 4469999999853899658998-------182889999999985789887
No 180
>TIGR00470 sepS O-phosphoseryl-tRNA(Cys) synthetase; InterPro: IPR005246 The aminoacyl-tRNA synthetases (6.1.1. from EC) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction. These proteins differ widely in size and oligomeric state, and have limited sequence homology . The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric . Class II aminoacyl-tRNA synthetases share an anti-parallel beta-sheet fold flanked by alpha-helices , and are mostly dimeric or multimeric, containing at least three conserved regions , , . However, tRNA binding involves an alpha-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan and valine belong to class I synthetases; these synthetases are further divided into three subclasses, a, b and c, according to sequence homology. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, lysine, phenylalanine, proline, serine, and threonine belong to class-II synthetases . All known phenylalanyl-tRNA synthetases, excepting a monomeric mitochondrial form, have an alpha 2 beta 2 heterotetrameric structure. This family of archaeal proteins resembles known phenylalanyl-tRNA synthetase alpha chains but is longer and of unknown function; more generally, it resembles class 2 aminoacyl tRNA ligases. .
Probab=72.38 E-value=3.8 Score=20.68 Aligned_cols=97 Identities=21% Similarity=0.247 Sum_probs=50.2
Q ss_pred EEECCCCCEEEEEEEEEECC-----CHHHHHHHHHHHH---------CCCCCCHHHHHHHHCCCC--EEE-CCCCEEEEE
Q ss_conf 79905996799400132157-----3556410278631---------000156222457753986--442-288179995
Q gi|254781049|r 211 LIIMKNGRLRVLDSKISFDD-----NALYRHLDIQELR---------DVSEEDSREIEAKQHNLS--YIA-LDGNIGCMV 273 (398)
Q Consensus 211 Lvvt~dg~vvAlDAKi~iDD-----nA~fR~~~~~~~~---------d~~~~~~~E~~A~~~~l~--yv~-LdG~Ig~~v 273 (398)
|.-.-+-.+|.+|--+.+|| .+|-+|--+..+| ...+++..|+.|=.--|. -.+ -||+|=+
T Consensus 238 LmtYhSASCVvVdeevsvDdGKaVAEgLL~qfGF~~FrFrpDEKkSKYYiP~TQTEVyAyHPkL~GsstkysdeWiEv-- 315 (558)
T TIGR00470 238 LMTYHSASCVVVDEEVSVDDGKAVAEGLLEQFGFEKFRFRPDEKKSKYYIPDTQTEVYAYHPKLKGSSTKYSDEWIEV-- 315 (558)
T ss_pred CCCEEEEEEEEECCCCCCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCCCCCCCCCCCCEEE--
T ss_conf 011345466785771243642688999998708544750576464543578885056776264566644104764798--
Q ss_pred CCCHHHHHHHHHHHHCCCCCCEEEECCCCCCHHHHHHHHHHHHCCCCCCEEEEECCCCHHHHHHHHHH
Q ss_conf 55036899999999658996248842788898999999999861998658999635861328999999
Q gi|254781049|r 274 NGAGLAMATMDIIKLYGGAPANFLDVGGGADQDKVAAAFKIITSDSSVKGILINIFGGIMRCDVLVKG 341 (398)
Q Consensus 274 nGaGlamatmD~i~~~Gg~pANFlD~gG~a~~e~~~~a~~~il~~~~vk~iliNifGGI~~cd~vA~g 341 (398)
|.|.=|+-.| |+.=++..=..|..=|+=|-.+|=.|
T Consensus 316 --------------------ATFG~YSPiA------------La~Y~Id~pVMNLGlGVERlAMIlyg 351 (558)
T TIGR00470 316 --------------------ATFGVYSPIA------------LAKYDIDVPVMNLGLGVERLAMILYG 351 (558)
T ss_pred --------------------EECCCCHHHH------------HHHCCCCCCEEECCCHHHHHHHHHHC
T ss_conf --------------------7434310467------------74168496522256318767877814
No 181
>cd01391 Periplasmic_Binding_Protein_Type_1 Type 1 periplasmic binding fold superfamily. Type 1 periplasmic binding fold superfamily. This model and hierarchy represent the ligand binding domains of the LacI family of transcriptional regulators, periplasmic binding proteins of the ABC-type transport systems, the family C G-protein couples receptors (GPCRs), membrane bound guanylyl cyclases including the family of natriuretic peptide receptors (NPRs), and the N-terminal leucine/isoleucine/valine- binding protein (LIVBP)-like domains of the ionotropic glutamate receptors (iGluRs). In LacI-like transcriptional regulator and the bacterial periplasmic binding proteins the ligands are monosaccharides including lactose, ribose, fructose, xylose, arabinose, galactose/glucose, and other sugars, with a few exceptions. Periplasmic sugar binding proteins are one of the components of ABC transporters and are involved in the active transport of water-soluble ligands. The LacI family of proteins con
Probab=70.42 E-value=8.1 Score=18.50 Aligned_cols=72 Identities=17% Similarity=0.259 Sum_probs=40.6
Q ss_pred HHHHHCCCCCCEEEECCCCCCH-HHHHHHHHHHHCCCCCCEEEEECCCCHHHHHHHHHHHHHHHHHCCCCCC---EEEEC
Q ss_conf 9999658996248842788898-9999999998619986589996358613289999999999997299987---99974
Q gi|254781049|r 284 DIIKLYGGAPANFLDVGGGADQ-DKVAAAFKIITSDSSVKGILINIFGGIMRCDVLVKGILSAVKEVKINIP---LVMRL 359 (398)
Q Consensus 284 D~i~~~Gg~pANFlD~gG~a~~-e~~~~a~~~il~~~~vk~iliNifGGI~~cd~vA~gii~a~~~~~~~~p---ivvRl 359 (398)
+.++.+|.+....... ..+. +....+.+++.+.+++++|+ ..+|.+|.|+++++++.+++ | -|+=.
T Consensus 147 ~~~~~~g~~~~~~~~~--~~~~~~~~~~~~~~l~~~~~~~ai~-------~~~d~~a~g~~~a~~~~G~~-p~d~~iig~ 216 (269)
T cd01391 147 AALKKAGIEVVAIEYG--DLDTEKGFQALLQLLKAAPKPDAIF-------ACNDEMAAGALKAAREAGLT-PGDISIIGF 216 (269)
T ss_pred HHHHHCCCCEEEEEEE--CCCCCHHHHHHHHHHHHCCCCEEEE-------ECCHHHHHHHHHHHHHCCCC-CCCEEEEEE
T ss_conf 9999869986799971--3432148999999986189973999-------88889999999999986989-476599817
Q ss_pred CCCCHH
Q ss_conf 898589
Q gi|254781049|r 360 EGANVD 365 (398)
Q Consensus 360 ~Gtn~~ 365 (398)
.++...
T Consensus 217 d~~~~~ 222 (269)
T cd01391 217 DGSPAA 222 (269)
T ss_pred CCCHHH
T ss_conf 898899
No 182
>PRK10949 protease 4; Provisional
Probab=69.87 E-value=8.3 Score=18.42 Aligned_cols=247 Identities=19% Similarity=0.275 Sum_probs=114.1
Q ss_pred CHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCEEECCCCCCCEEEEEEEEEECCCCCEEEEEECCCCCCHHHHHHHCH---
Q ss_conf 99999999998618765442122222443301103455565058999998347780489984478840245557483---
Q gi|254781049|r 75 SLKSVISDIREILGSTLITKQTGPTGSRVNCVYVEDGADILRELYLSLLVDRTSGMVAFIASTQGGMDIEEVAKDYP--- 151 (398)
Q Consensus 75 s~~ea~~~a~~ilg~~l~t~qt~~~G~~v~~vLVEe~v~~~~E~ylgi~~Dr~~~~~vii~S~~GGvdIE~va~~~p--- 151 (398)
+.+|++++..+. + ..|++|-. .-+. -....|||+-.-|. +.| .+.|+|++.-.+...+
T Consensus 130 ~l~eI~~AL~~F-------K---~SGK~ViA--y~d~-ysq~~YyLAS~AD~-----I~L-~P~G~v~l~Gl~~~~~y~K 190 (618)
T PRK10949 130 SMQYIGKALREF-------R---DSGKPVYA--VGDN-YSQGQYYLASFANK-----IWL-SPQGVVDLHGFATNGLYYK 190 (618)
T ss_pred HHHHHHHHHHHH-------H---HHCCEEEE--EECC-CCCCCEEEEEECCE-----EEE-CCCCEEEEECCCHHHHHHH
T ss_conf 999999999999-------9---81993999--9667-78530102110777-----898-8996687866301177899
Q ss_pred HHHEEEECCCCC-CCCHH--HHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHC-----CCCCCCCCEEEE--------C-
Q ss_conf 122033214445-78957--888788751988899885999999998999955-----975102326799--------0-
Q gi|254781049|r 152 QKIFKLLIDPLI-GVTSE--DVASLCDMLELQGQARIDGGDLFPNLYKAFCDK-----DMSLLEINPLII--------M- 214 (398)
Q Consensus 152 ~~I~~~~id~~~-gl~~~--~~~~l~~~lg~~~~~~~~~~~ii~~L~~~f~e~-----Da~liEINPLvv--------t- 214 (398)
+.+-+..|.+.. ..-.| ....+.. -.++.+..++...++..||+-|.+. ..+.-+++|..- .
T Consensus 191 ~lLdKlgI~~~vfrvG~YKSAvEpf~r-~~MS~e~re~~~~~l~~lw~~~~~~Ia~~R~l~~~~l~~~~~~~~~~l~~~~ 269 (618)
T PRK10949 191 SLLDKLKVSTHVFRVGTYKSAVEPFIR-DDMSPAAREADSRWIGELWQNYLNTVAANRQITPQQLFPGAQGILEGLTKVG 269 (618)
T ss_pred HHHHHCCCEEEEEEECCCCCCCCCCCC-CCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHC
T ss_conf 999974982899981375674651114-4599999999999999999999999998659997897777999999998708
Q ss_pred CCCCEEEEEEEEEECCCHHHHHHHHHHHHCCCCCCHHHHHHHHCCCCEEEC-----------CCCEEEEECCCHHHHHHH
Q ss_conf 599679940013215735564102786310001562224577539864422-----------881799955503689999
Q gi|254781049|r 215 KNGRLRVLDSKISFDDNALYRHLDIQELRDVSEEDSREIEAKQHNLSYIAL-----------DGNIGCMVNGAGLAMATM 283 (398)
Q Consensus 215 ~dg~vvAlDAKi~iDDnA~fR~~~~~~~~d~~~~~~~E~~A~~~~l~yv~L-----------dG~Ig~~vnGaGlamatm 283 (398)
.+..-.|++.++ +| .-.+|..-...+.+....+.. +.++++|.+ ...|+++..=+...
T Consensus 270 g~~a~~Al~~gL-VD-~l~~~~e~~~~l~~~~g~~~~-----~~~~~~is~~~y~~~~~~~~~~~IAVI~a~G~Iv---- 338 (618)
T PRK10949 270 GDTAKYALDNKL-VD-ALASSAEIEKALTKAFGWSKT-----DKNYRAISIYDYALKTPADTGGQIAVIFANGAIM---- 338 (618)
T ss_pred CCHHHHHHHCCC-CC-CCCCHHHHHHHHHHHHCCCCC-----CCCCCEECHHHHCCCCCCCCCCEEEEEEEEEEEE----
T ss_conf 840999987699-85-467688999999998488743-----5675443287723236887798389999687685----
Q ss_pred HHHHHCCCCCCEEEECCCCCCHHHHHHHHHHHHCCCCCCEEE--EECCCCHHH-HHHHHHHHHHHHHHCCCCCCEEEECC
Q ss_conf 999965899624884278889899999999986199865899--963586132-89999999999997299987999748
Q gi|254781049|r 284 DIIKLYGGAPANFLDVGGGADQDKVAAAFKIITSDSSVKGIL--INIFGGIMR-CDVLVKGILSAVKEVKINIPLVMRLE 360 (398)
Q Consensus 284 D~i~~~Gg~pANFlD~gG~a~~e~~~~a~~~il~~~~vk~il--iNifGGI~~-cd~vA~gii~a~~~~~~~~pivvRl~ 360 (398)
-|-.+ .|....+.+.+.++-.-.|++||+|. ||=-||=+- .|.|-+-|.. ++ +.++||||-|.
T Consensus 339 -----~G~~~------~g~ig~dt~~~~lr~a~~D~~VKAvVLRVnSPGGSa~ASE~I~~el~~-lk--~~gKPVVvSMG 404 (618)
T PRK10949 339 -----DGEET------PGNVGGDTTAAQIRDARLDPKVKAIVLRVNSPGGSVTASEVIRAELAA-AR--AAGKPVVVSMG 404 (618)
T ss_pred -----CCCCC------CCCCCHHHHHHHHHHHHCCCCCEEEEEEEECCCCCHHHHHHHHHHHHH-HH--HCCCCEEEEEC
T ss_conf -----48887------886655899999999730867228999985899866789999999999-98--44997999970
Q ss_pred CCCHHH
Q ss_conf 985899
Q gi|254781049|r 361 GANVDI 366 (398)
Q Consensus 361 Gtn~~~ 366 (398)
+.-+.-
T Consensus 405 ~vAASG 410 (618)
T PRK10949 405 GMAASG 410 (618)
T ss_pred CCCCCC
T ss_conf 101566
No 183
>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=68.02 E-value=9 Score=18.17 Aligned_cols=83 Identities=18% Similarity=0.304 Sum_probs=50.3
Q ss_pred CHHHHHHHHHHHH-CCCCCCEEEEECCCCHHHHHHHHHHHHHHHHHCCCCCCEEEECCCCCHHHHHHHHHHCCCCEEEEC
Q ss_conf 9899999999986-199865899963586132899999999999972999879997489858999999997699589949
Q gi|254781049|r 304 DQDKVAAAFKIIT-SDSSVKGILINIFGGIMRCDVLVKGILSAVKEVKINIPLVMRLEGANVDIGNRLIAESGLNVITAI 382 (398)
Q Consensus 304 ~~e~~~~a~~~il-~~~~vk~iliNifGGI~~cd~vA~gii~a~~~~~~~~pivvRl~Gtn~~~g~~il~~~g~~~~~~~ 382 (398)
+.+.-++++.-++ +.+.+.+|| +..|.+|.|+++++++.++++|==+.+-|-+-..--+++ ...+.- ...
T Consensus 155 ~~~~~~~~~~~~l~~~~~~~ai~-------~~nD~~A~g~l~~l~~~g~~vP~disviGfDd~~~a~~~-~P~LTT-v~~ 225 (263)
T cd06280 155 TAEAAEAALAAWLAAPERPEALV-------ASNGLLLLGALRAVRAAGLRIPQDLALAGFDNDPWTELV-GPGITV-IEQ 225 (263)
T ss_pred CHHHHHHHHHHHHHCCCCCCEEE-------ECCHHHHHHHHHHHHHHCCCCCCCCEEEEECCHHHHHCC-CCCCEE-EEE
T ss_conf 76789999999982799997899-------678899999999999848999998789997785888617-999779-980
Q ss_pred CHHHHHHHHHHHH
Q ss_conf 9899999999985
Q gi|254781049|r 383 DLDDAAQKIVHAV 395 (398)
Q Consensus 383 ~~~~A~~~~v~~~ 395 (398)
+.++..+.|+++.
T Consensus 226 ~~~~~g~~A~~~L 238 (263)
T cd06280 226 PVEEIGRAAMSLL 238 (263)
T ss_pred CHHHHHHHHHHHH
T ss_conf 9999999999999
No 184
>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=66.51 E-value=9.7 Score=17.98 Aligned_cols=79 Identities=10% Similarity=0.119 Sum_probs=47.9
Q ss_pred HHHHHHHHHHHHCCCCCCEEEEECCCCHHHHHHHHHHHHHHHHHCCCCCCEEEECCCCCHHHHHHHHHHCCCCEE-EECC
Q ss_conf 899999999986199865899963586132899999999999972999879997489858999999997699589-9499
Q gi|254781049|r 305 QDKVAAAFKIITSDSSVKGILINIFGGIMRCDVLVKGILSAVKEVKINIPLVMRLEGANVDIGNRLIAESGLNVI-TAID 383 (398)
Q Consensus 305 ~e~~~~a~~~il~~~~vk~iliNifGGI~~cd~vA~gii~a~~~~~~~~pivvRl~Gtn~~~g~~il~~~g~~~~-~~~~ 383 (398)
.+...+.++.+ ++...+|| +..|.+|.|+++++++.++++|==+.+-|-+-.. +.+-..-++. ...+
T Consensus 164 ~~~~~~~~~~~--~~~ptAi~-------~~nD~~A~g~~~~l~~~g~~vP~Disivgfdd~~---~~~~~~P~LTtv~~~ 231 (268)
T cd06277 164 EEDIGKFIDEL--KPLPTAFF-------CSNDGVAFLLIKVLKEMGIRVPEDVSVIGFDDIE---YATIFTPPLTTVRVD 231 (268)
T ss_pred HHHHHHHHHHC--CCCCCEEE-------ECCHHHHHHHHHHHHHCCCCCCCCCEEEEECCHH---HHHHCCCCEEEEEEC
T ss_conf 99999999847--88998799-------6885999999999998599999862899978878---998448980899929
Q ss_pred HHHHHHHHHHHH
Q ss_conf 899999999985
Q gi|254781049|r 384 LDDAAQKIVHAV 395 (398)
Q Consensus 384 ~~~A~~~~v~~~ 395 (398)
..+..+.|+++.
T Consensus 232 ~~~~G~~A~~~L 243 (268)
T cd06277 232 KEEMGKLAVKRL 243 (268)
T ss_pred HHHHHHHHHHHH
T ss_conf 999999999999
No 185
>pfam08886 GshA Glutamate-cysteine ligase. This is a rare family of glutamate--cysteine ligases, demonstrated first in Thiobacillus ferrooxidans and present in a few other Proteobacteria. It is the first of two enzymes for glutathione biosynthesis. It is also called gamma-glutamylcysteine synthetase.
Probab=64.92 E-value=10 Score=17.78 Aligned_cols=29 Identities=14% Similarity=0.142 Sum_probs=12.8
Q ss_pred CEEEEEEEEEECCCCCEEEEEECCCC-CCHH
Q ss_conf 50589999983477804899844788-4024
Q gi|254781049|r 115 LRELYLSLLVDRTSGMVAFIASTQGG-MDIE 144 (398)
Q Consensus 115 ~~E~ylgi~~Dr~~~~~vii~S~~GG-vdIE 144 (398)
+-+..+|-. ||+...|..+-+..|. +.+|
T Consensus 108 G~~VrvGs~-~pei~~~~~~~~~~g~~l~le 137 (404)
T pfam08886 108 GLNVRIGSL-DPEITEPTTLELPNGDTLTLE 137 (404)
T ss_pred CCEEEEECC-CCCCCCCEEEECCCCCEEEEE
T ss_conf 966996078-701268656755899756788
No 186
>KOG3432 consensus
Probab=64.79 E-value=10 Score=17.77 Aligned_cols=64 Identities=25% Similarity=0.384 Sum_probs=52.5
Q ss_pred CCCEEEECCCCCCHHHHHHHHHHHHCCCCCCEEEEECCCCHHHHHHHHHHHHHHHHHCCCCCCEEEECCCCC
Q ss_conf 962488427888989999999998619986589996358613289999999999997299987999748985
Q gi|254781049|r 292 APANFLDVGGGADQDKVAAAFKIITSDSSVKGILINIFGGIMRCDVLVKGILSAVKEVKINIPLVMRLEGAN 363 (398)
Q Consensus 292 ~pANFlD~gG~a~~e~~~~a~~~il~~~~vk~iliNifGGI~~cd~vA~gii~a~~~~~~~~pivvRl~Gtn 363 (398)
.--||+=+--..|.+.+..+|+-.++.+.+-.|||| +.+|+-|-..+......+|-|.-+.--+
T Consensus 34 r~~Nf~vv~~~Tt~~eiedaF~~f~~RdDIaIiLIn--------q~~Ae~iR~~vD~h~~~vPAvLeIpSKd 97 (121)
T KOG3432 34 REPNFLVVDSKTTVEEIEDAFKSFTARDDIAIILIN--------QFIAEMIRDRVDAHTQAVPAVLEIPSKD 97 (121)
T ss_pred CCCCEEEEECCCCHHHHHHHHHHHCCCCCEEEEEEH--------HHHHHHHHHHHHHCCCCCCEEEEECCCC
T ss_conf 898889995568989999999863345675898773--------8899999999874034677368825878
No 187
>PRK01390 murD UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional
Probab=64.58 E-value=11 Score=17.74 Aligned_cols=87 Identities=13% Similarity=0.110 Sum_probs=54.9
Q ss_pred EEECCCCCCHHHHHHHHHHHHCCCCCCEEEEECCCCHHHHHHHHHHHHHHHHHCCCCCCEEEECCCCCHHHHHHHHHHCC
Q ss_conf 88427888989999999998619986589996358613289999999999997299987999748985899999999769
Q gi|254781049|r 296 FLDVGGGADQDKVAAAFKIITSDSSVKGILINIFGGIMRCDVLVKGILSAVKEVKINIPLVMRLEGANVDIGNRLIAESG 375 (398)
Q Consensus 296 FlD~gG~a~~e~~~~a~~~il~~~~vk~iliNifGGI~~cd~vA~gii~a~~~~~~~~pivvRl~Gtn~~~g~~il~~~g 375 (398)
|.|=+=+++.+.+..|++-. ++ .+| |.||..+-.+... +...++ ++.-++- -|-..++=.+.|++.
T Consensus 332 ~iNDSKaTN~~at~~Al~s~---~~--i~l--I~GG~~K~~d~~~-l~~~~~----~v~~~~l-iG~~~~~~~~~l~~~- 397 (457)
T PRK01390 332 FVNDSKATNADAAAPALSSF---PN--IYW--IAGGKPKAGGIES-LAPFFP----RIAKAYL-IGEAAEEFAATLGGA- 397 (457)
T ss_pred EECCCCCCCHHHHHHHHHCC---CC--EEE--EECCCCCCCCHHH-HHHHHH----CCCEEEE-ECCCHHHHHHHHHCC-
T ss_conf 85377678989999999737---88--599--9450478889799-999874----3359999-898889999987367-
Q ss_pred CCEEEECCHHHHHHHHHHHHH
Q ss_conf 958994998999999999850
Q gi|254781049|r 376 LNVITAIDLDDAAQKIVHAVK 396 (398)
Q Consensus 376 ~~~~~~~~~~~A~~~~v~~~k 396 (398)
.++..+.+|++|++.|+..++
T Consensus 398 ~~~~~~~~l~~av~~a~~~a~ 418 (457)
T PRK01390 398 VPYEISGTLEAAVAAAARDAA 418 (457)
T ss_pred CCEEECCCHHHHHHHHHHHHH
T ss_conf 987985989999999999998
No 188
>PRK09526 lacI lac repressor; Reviewed
Probab=63.74 E-value=11 Score=17.64 Aligned_cols=101 Identities=12% Similarity=0.100 Sum_probs=63.3
Q ss_pred HHHHHHHHHCCCCCCEEEECCCCCCHHHHHHHHHHHH-CCCCCCEEEEECCCCHHHHHHHHHHHHHHHHHCCCCCC---E
Q ss_conf 9999999965899624884278889899999999986-19986589996358613289999999999997299987---9
Q gi|254781049|r 280 MATMDIIKLYGGAPANFLDVGGGADQDKVAAAFKIIT-SDSSVKGILINIFGGIMRCDVLVKGILSAVKEVKINIP---L 355 (398)
Q Consensus 280 matmD~i~~~Gg~pANFlD~gG~a~~e~~~~a~~~il-~~~~vk~iliNifGGI~~cd~vA~gii~a~~~~~~~~p---i 355 (398)
....+.++.+|..|-.-+ -+..+.+.-+++++-++ ..++..+|| ...|.+|-|+++++++.++++| -
T Consensus 201 ~Gf~~~~~~~~l~~~~~~--~~~~~~~~~~~~~~~~l~~~~~ptai~-------~~~D~~A~g~i~~l~~~g~~vP~Dis 271 (342)
T PRK09526 201 AGWLEYLTRNQLSPIAVR--EGDWSAMSGYQQTLQMLNEGPVFTAVL-------VANDQMALGVLRALHESGLRVPGDIS 271 (342)
T ss_pred HHHHHHHHHCCCCCCEEE--ECCCCHHHHHHHHHHHHHCCCCCCEEE-------ECCHHHHHHHHHHHHHHCCCCCCCEE
T ss_conf 999999997798961699--568987899999999983699997587-------56779999999999980999999749
Q ss_pred EEECCCCCHHHHHHHHHHCCCCEE-EECCHHHHHHHHHHHH
Q ss_conf 997489858999999997699589-9499899999999985
Q gi|254781049|r 356 VMRLEGANVDIGNRLIAESGLNVI-TAIDLDDAAQKIVHAV 395 (398)
Q Consensus 356 vvRl~Gtn~~~g~~il~~~g~~~~-~~~~~~~A~~~~v~~~ 395 (398)
|+=..++. +.+-..-++. ...+.++.++.|+++.
T Consensus 272 IigfDd~~------~~~~~~P~LTtv~~p~~~ig~~A~~~L 306 (342)
T PRK09526 272 VIGYDDTE------DSSYFIPPLTTIKQDFRLLGKEAVDRL 306 (342)
T ss_pred EEEECCCH------HHHHCCCCEEEEEECHHHHHHHHHHHH
T ss_conf 99989808------998248980899819999999999999
No 189
>TIGR01019 sucCoAalpha succinyl-CoA synthetase, alpha subunit; InterPro: IPR005810 There are four different enzymes that share a similar catalytic mechanism which involves the phosphorylation by ATP (or GTP) of a specific histidine residue in the active site. These enzymes are: ATP citrate-lyase (4.1.3.8 from EC) , the primary enzyme responsible for the synthesis of cytosolic acetyl-CoA in many tissues, catalyzes the formation of acetyl-CoA and oxaloacetate from citrate and CoA with the concomitant hydrolysis of ATP to ADP and phosphate. ATP-citrate lyase is a tetramer of identical subunits; Succinyl-CoA ligase (GDP-forming) (6.2.1.4 from EC) is a mitochondrial enzyme that catalyzes the substrate level phosphorylation step of the tricarboxylic acid cycle: the formation of succinyl-CoA from succinate with a concomitant hydrolysis of GTP to GDP and phosphate. This enzyme is a dimer composed of an alpha and a beta subunits; Succinyl-CoA ligase (ADP-forming) (6.2.1.5 from EC) is a bacterial enzyme that during aerobic metabolism functions in the citric acid cycle, coupling the hydrolysis of succinyl-CoA to the synthesis of ATP. It can also function in the other direction for anabolic purposes. This enzyme is a tetramer composed of two alpha and two beta subunits; and Malate-CoA ligase (6.2.1.9 from EC) (malyl-CoA synthetase) , is a bacterial enzyme that forms malyl-CoA from malate and CoA with the concomitant hydrolysis of ATP to ADP and phosphate. Malate-CoA ligase is composed of two different subunits. This entry corresponds to two regions, a glycine-rich conserved region, located in the second half of ATP citrate lyase and in the alpha subunits of succinyl-CoA ligases and malate-CoA ligase; and the active site phosphorylated histidine residue, which is located some 50 residues to the C-terminal of the first region. ; GO: 0003824 catalytic activity, 0008152 metabolic process.
Probab=62.33 E-value=12 Score=17.48 Aligned_cols=104 Identities=16% Similarity=0.312 Sum_probs=76.8
Q ss_pred CEEECCCCEEEEECCCHHHHHHHHHHHHCCCCCCEEEECCCCC-CHHHHHHHHHHHHCCCCCCEEEEECCCCHH-HHHHH
Q ss_conf 6442288179995550368999999996589962488427888-989999999998619986589996358613-28999
Q gi|254781049|r 261 SYIALDGNIGCMVNGAGLAMATMDIIKLYGGAPANFLDVGGGA-DQDKVAAAFKIITSDSSVKGILINIFGGIM-RCDVL 338 (398)
Q Consensus 261 ~yv~LdG~Ig~~vnGaGlamatmD~i~~~Gg~pANFlD~gG~a-~~e~~~~a~~~il~~~~vk~iliNifGGI~-~cd~v 338 (398)
.|+...|++|++...+-|+.-.+-.+...|.-.....-+||.+ +.......++....||..+.+++ .|-|- ..+.-
T Consensus 140 ~~~~~~g~~g~~~~~g~l~~~~~~~~~~~g~g~~~~~g~ggdp~~g~~~~~~~~~~~~d~~~~~~~~--~g~~gg~~~~~ 217 (288)
T TIGR01019 140 GHIHKPGNVGLVSRSGTLTYEAVWQLTEAGFGQSTCVGIGGDPVNGTSFVDVLELFEEDPETEAVVL--IGEIGGSAEEE 217 (288)
T ss_pred CEEECCCCCEEEECCCCHHHHHHHHHHHHCCCCCEEEECCCCCCCCCHHHHHHHHHHCCCCCEEEEE--EECCCCCHHHH
T ss_conf 0010356400442354125777887764126620144136654455227888987514766505888--62147850367
Q ss_pred HHHHHHHHHHCCCCCCEEEECCCCCHHHHHHH
Q ss_conf 99999999972999879997489858999999
Q gi|254781049|r 339 VKGILSAVKEVKINIPLVMRLEGANVDIGNRL 370 (398)
Q Consensus 339 A~gii~a~~~~~~~~pivvRl~Gtn~~~g~~i 370 (398)
|.-.++ ...+.|++--+.|...-.|+++
T Consensus 218 ~~~~~~----~~~~~p~~~~~~g~~~p~g~~~ 245 (288)
T TIGR01019 218 AADFIK----ENLSKPVVGFIAGLTAPPGKRL 245 (288)
T ss_pred HHHHHH----HHCCCCHHHHHCCCCCCCCCCC
T ss_conf 899987----5214421111102346754323
No 190
>PTZ00294 glycerol kinase; Provisional
Probab=61.68 E-value=12 Score=17.40 Aligned_cols=92 Identities=13% Similarity=0.173 Sum_probs=57.5
Q ss_pred CEEEECCCCCCHHHHHHHH------------HHHHCCC--CCCEEEEECCCCHHHHHHHHHHHHHHHHHCCCCCCEEEEC
Q ss_conf 2488427888989999999------------9986199--8658999635861328999999999999729998799974
Q gi|254781049|r 294 ANFLDVGGGADQDKVAAAF------------KIITSDS--SVKGILINIFGGIMRCDVLVKGILSAVKEVKINIPLVMRL 359 (398)
Q Consensus 294 ANFlD~gG~a~~e~~~~a~------------~~il~~~--~vk~iliNifGGI~~cd~vA~gii~a~~~~~~~~pivvRl 359 (398)
+.|+-++-..+...+++|+ +.+..+. +++.|. +.||.++-+..-+=+.+.+ ++||.+--
T Consensus 373 g~~~Gl~~~~~~~~i~RAvlEgia~~~r~~~e~l~~~~G~~~~~I~--~~GG~a~s~lw~Qi~ADv~-----g~pV~~~~ 445 (510)
T PTZ00294 373 GTIVGMTYKTTRAHIIRAALEAIALQLNDVVLAMKRDSGIELNSLR--VDGGLTKNKLLMQIQADIL-----GVKLEVPE 445 (510)
T ss_pred CCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCEEE--EECCCHHCHHHHHHHHHHH-----CCEEEECC
T ss_conf 2224888889999999999998999999999999986099978799--9778323899999999965-----98479468
Q ss_pred CCCCHHHHHHHHHHCCCCEEEECCHHHHHHHHHHH
Q ss_conf 89858999999997699589949989999999998
Q gi|254781049|r 360 EGANVDIGNRLIAESGLNVITAIDLDDAAQKIVHA 394 (398)
Q Consensus 360 ~Gtn~~~g~~il~~~g~~~~~~~~~~~A~~~~v~~ 394 (398)
.....-.|-.|+.-.+..++ .|++||+++.+..
T Consensus 446 ~~e~~alGaAilAavg~G~~--~s~~eA~~~~~~~ 478 (510)
T PTZ00294 446 MHETTALGAALCAGLAAGVW--TSLEEVKALSRRE 478 (510)
T ss_pred CCCHHHHHHHHHHHHHHCCC--CCHHHHHHHCCCC
T ss_conf 88708999999999981989--9999999747778
No 191
>pfam10281 Ish1 Putative stress-responsive nuclear envelope protein. This family of proteins found in fungi is a putative stress-responsive nuclear envelope protein Ish1.
Probab=61.64 E-value=10 Score=17.79 Aligned_cols=32 Identities=13% Similarity=0.185 Sum_probs=25.3
Q ss_pred CHHHHHHHHHHCCCCCCCCEEECCHHHHHHHHHH
Q ss_conf 5799999999868988881574799999999987
Q gi|254781049|r 4 HEYQAKALLRKYNVPVAKGVVISSVHAAESAIKT 37 (398)
Q Consensus 4 ~EyqaK~lL~~~GIpvp~g~~a~s~~ea~~~a~~ 37 (398)
.+-|-|+.|.+||||+|+..- +-++..+.+.+
T Consensus 5 s~~~Lk~wL~~~gi~~~~~~~--~rd~Ll~~a~~ 36 (38)
T pfam10281 5 SDSDLKEWLDSHGIPVPQKAA--TRDELLALARK 36 (38)
T ss_pred CHHHHHHHHHHCCCCCCCCHH--HHHHHHHHHHH
T ss_conf 488999999984997897136--89999999986
No 192
>TIGR00417 speE spermidine synthase; InterPro: IPR001045 Synonym(s): Spermidine aminopropyltransferase A group of polyamine biosynthetic enzymes involved in the fifth (last) step in the biosynthesis of spermidine from arginine and methionine which includes; spermidine synthase (), spermine synthase () and putrescine N-methyltransferase () . The Thermotoga maritima spermidine synthase monomer consists of two domains: an N-terminal domain composed of six beta-strands, and a Rossmann-like C- terminal domain . The larger C-terminal catalytic core domain consists of a seven-stranded beta-sheet flanked by nine alpha helices. This domain resembles a topology observed in a number of nucleotide and dinucleotide-binding enzymes, and in S-adenosyl-L-methionine (AdoMet)- dependent methyltransferase (MTases) . ; GO: 0003824 catalytic activity.
Probab=61.33 E-value=4.8 Score=19.99 Aligned_cols=51 Identities=20% Similarity=0.160 Sum_probs=39.0
Q ss_pred EEECCCCCCCEEEEEEEEEECCCCCEEEEEECCCCCCHHHHHHHCHHHHEEEECCC
Q ss_conf 11034555650589999983477804899844788402455574831220332144
Q gi|254781049|r 106 VYVEDGADILRELYLSLLVDRTSGMVAFIASTQGGMDIEEVAKDYPQKIFKLLIDP 161 (398)
Q Consensus 106 vLVEe~v~~~~E~ylgi~~Dr~~~~~vii~S~~GGvdIE~va~~~p~~I~~~~id~ 161 (398)
+.=.||+.| +.+.--++-++++++|++-|||-=|-+-.++-+.+.-+.||-
T Consensus 59 F~YhEMi~H-----vpL~~H~NPk~VLvIGGGDGG~lREV~KH~sVE~~~lVdID~ 109 (284)
T TIGR00417 59 FIYHEMIAH-----VPLFAHPNPKKVLVIGGGDGGVLREVVKHKSVEKATLVDIDE 109 (284)
T ss_pred HHHHHHHHH-----HHHHCCCCCCEEEEEECCCCCEEEEEEECCCCCEEEEEECCH
T ss_conf 356789987-----565368988547899638884687887559816799997274
No 193
>PRK00683 murD UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional
Probab=60.48 E-value=12 Score=17.27 Aligned_cols=103 Identities=14% Similarity=0.250 Sum_probs=61.3
Q ss_pred HHHHHHCCCCCC-----------EEEECCCCCCHHHHHHHHHHHHCCCCCCEEEEECCCCHHHHHHHHHHHHHHHHHCCC
Q ss_conf 999996589962-----------488427888989999999998619986589996358613289999999999997299
Q gi|254781049|r 283 MDIIKLYGGAPA-----------NFLDVGGGADQDKVAAAFKIITSDSSVKGILINIFGGIMRCDVLVKGILSAVKEVKI 351 (398)
Q Consensus 283 mD~i~~~Gg~pA-----------NFlD~gG~a~~e~~~~a~~~il~~~~vk~iliNifGGI~~cd~vA~gii~a~~~~~~ 351 (398)
.+.++.|.|-|- .|.|=+=+++.+.+..|++-.- . +.|| |.||..+-.+... +...+++
T Consensus 268 ~~al~~F~glpHR~E~v~~~~Gv~fiNDSKaTN~~a~~~AL~s~~--~--~iil--I~GG~~K~~d~~~-L~~~~~~--- 337 (418)
T PRK00683 268 LEAVATFEKPPHRMEYLGEKDGVHYINDSKATTVSAVEKALLAVG--K--DVIV--ILGGRNKGGDFPS-LLPVLRQ--- 337 (418)
T ss_pred HHHHHHCCCCCCCEEEEEEECCCEEECCCCCCCHHHHHHHHHHCC--C--CCEE--EECCCCCCCCHHH-HHHHHHH---
T ss_conf 999973488411136888817823763776789899999998567--8--8589--9757876678699-9999863---
Q ss_pred CCCEEEECCCCCHHHHHHHHHHCCCCEEEECCHHHHHHHHHHHHHC
Q ss_conf 9879997489858999999997699589949989999999998506
Q gi|254781049|r 352 NIPLVMRLEGANVDIGNRLIAESGLNVITAIDLDDAAQKIVHAVKG 397 (398)
Q Consensus 352 ~~pivvRl~Gtn~~~g~~il~~~g~~~~~~~~~~~A~~~~v~~~k~ 397 (398)
++.-++=+ |...++=.+.+++ .+++..+.+|++|+..|.++++.
T Consensus 338 ~vk~v~~~-G~~~~~i~~~l~~-~~~~~~~~~l~eAv~~a~~~a~~ 381 (418)
T PRK00683 338 TAKHVVAM-GECRQEIAQALSE-KFPLTVVKDLQEAVSCAQEIAQP 381 (418)
T ss_pred CCCEEEEE-CCCHHHHHHHHHC-CCCEEECCCHHHHHHHHHHHCCC
T ss_conf 18499996-8899999998756-99879859899999999984789
No 194
>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=60.41 E-value=12 Score=17.26 Aligned_cols=101 Identities=17% Similarity=0.183 Sum_probs=58.6
Q ss_pred HHHHHHCCCCCCEEEECCCCCCHHHHHHHHHHHH-CCCCCCEEEEECCCCHHHHHHHHHHHHHHHH-HCCCCCCEEEECC
Q ss_conf 9999965899624884278889899999999986-1998658999635861328999999999999-7299987999748
Q gi|254781049|r 283 MDIIKLYGGAPANFLDVGGGADQDKVAAAFKIIT-SDSSVKGILINIFGGIMRCDVLVKGILSAVK-EVKINIPLVMRLE 360 (398)
Q Consensus 283 mD~i~~~Gg~pANFlD~gG~a~~e~~~~a~~~il-~~~~vk~iliNifGGI~~cd~vA~gii~a~~-~~~~~~pivvRl~ 360 (398)
.+.+..+|.++.. .+-+..+.+.-+++++-++ ..+.+.+|| +..|.+|-|++++++ +.+.++|==+.+-
T Consensus 138 ~~al~~~gl~~~~--~~~~~~~~~~g~~~~~~ll~~~~~ptAi~-------~~nD~~A~g~l~~l~~~~g~~vP~disvv 208 (266)
T cd06278 138 RDALAAAGVPVVV--EEAGDYSYEGGYEAARRLLASRPRPDAIF-------CANDLLAIGVMDAARQEGGLRVPEDVSVI 208 (266)
T ss_pred HHHHHHCCCCCEE--EECCCCCHHHHHHHHHHHHHCCCCCCCCE-------ECCHHHHHHHHHHHHHHCCCCCCCCEEEE
T ss_conf 9999986999438--98189998999999999984599988625-------07789999999999973588888866999
Q ss_pred CCCHHHHHHHHHHCCCCEE-EECCHHHHHHHHHHHH
Q ss_conf 9858999999997699589-9499899999999985
Q gi|254781049|r 361 GANVDIGNRLIAESGLNVI-TAIDLDDAAQKIVHAV 395 (398)
Q Consensus 361 Gtn~~~g~~il~~~g~~~~-~~~~~~~A~~~~v~~~ 395 (398)
|-+-. .+-+-..-++. ...+..+..++|+++.
T Consensus 209 gfD~~---~~~~~~~p~LTtv~~~~~~~g~~A~~~L 241 (266)
T cd06278 209 GFDDI---PMAAWPSYQLTTVRQPVDRMAEEAVDLL 241 (266)
T ss_pred EECCH---HHHHCCCCCEEEEECCHHHHHHHHHHHH
T ss_conf 87880---8985449984899839999999999999
No 195
>KOG1663 consensus
Probab=58.41 E-value=7.8 Score=18.58 Aligned_cols=28 Identities=29% Similarity=0.264 Sum_probs=24.9
Q ss_pred HHHHHHHHCCCCCCEEEEECCCCHHHHH
Q ss_conf 9999998619986589996358613289
Q gi|254781049|r 309 AAAFKIITSDSSVKGILINIFGGIMRCD 336 (398)
Q Consensus 309 ~~a~~~il~~~~vk~iliNifGGI~~cd 336 (398)
.+..+.|..||+|..-+++|+.|++.|-
T Consensus 208 ~~~n~~l~~D~rV~~s~~~igdG~~i~~ 235 (237)
T KOG1663 208 LNLNKKLARDPRVYISLLPIGDGITICR 235 (237)
T ss_pred HHHHHHHCCCCCEEEEEEECCCCEEEEC
T ss_conf 5366675048603567630368505630
No 196
>cd01820 PAF_acetylesterase_like PAF_acetylhydrolase (PAF-AH)_like subfamily of SGNH-hydrolases. Platelet-activating factor (PAF) and PAF-AH are key players in inflammation and in atherosclerosis. PAF-AH is a calcium independent phospholipase A2 which exhibits strong substrate specificity towards PAF, hydrolyzing an acetyl ester at the sn-2 position. PAF-AH also degrades a family of oxidized PAF-like phospholipids with short sn-2 residues. In addition, PAF and PAF-AH are associated with neural migration and mammalian reproduction.
Probab=57.18 E-value=14 Score=16.90 Aligned_cols=19 Identities=16% Similarity=0.513 Sum_probs=14.5
Q ss_pred CCCCCCCCCEEEECCCCCE
Q ss_conf 5975102326799059967
Q gi|254781049|r 201 KDMSLLEINPLIIMKNGRL 219 (398)
Q Consensus 201 ~Da~liEINPLvvt~dg~v 219 (398)
.+.+.+++++..+.++|++
T Consensus 165 ~~v~yiD~~~~fl~~dG~l 183 (214)
T cd01820 165 PNVTFLDIDKGFVQSDGTI 183 (214)
T ss_pred CCEEEEECCHHHCCCCCCC
T ss_conf 8858972742311999992
No 197
>PRK12412 pyridoxal kinase; Reviewed
Probab=57.08 E-value=14 Score=16.89 Aligned_cols=17 Identities=24% Similarity=0.264 Sum_probs=8.9
Q ss_pred CCCHHHHHHHHHHHHCC
Q ss_conf 55036899999999658
Q gi|254781049|r 274 NGAGLAMATMDIIKLYG 290 (398)
Q Consensus 274 nGaGlamatmD~i~~~G 290 (398)
.|.|=+.++.=+-...-
T Consensus 209 HGTGCtlSSAIAa~LA~ 225 (268)
T PRK12412 209 HGAGCTYSAAITAELAK 225 (268)
T ss_pred CCHHHHHHHHHHHHHHC
T ss_conf 30889999999999987
No 198
>TIGR01320 mal_quin_oxido malate:quinone-oxidoreductase; InterPro: IPR006231 The membrane-associated enzyme, malate:quinone-oxidoreductase, is an alternative to the better-known NAD-dependent malate dehydrogenase as part of the TCA cycle. The reduction of a quinone rather than NAD+ makes the reaction essentially irreversible in the direction of malate oxidation to oxaloacetate. Both forms of malate dehydrogenase are active in E. coli; disruption of this form causes less phenotypic change. In some bacteria, this form is the only or the more important malate dehydrogenase . ; GO: 0008924 malate dehydrogenase (acceptor) activity, 0006099 tricarboxylic acid cycle.
Probab=56.51 E-value=14 Score=16.83 Aligned_cols=21 Identities=19% Similarity=0.216 Sum_probs=9.7
Q ss_pred CEEEE-ECCHHHHHHHHHHHCC
Q ss_conf 70799-5899999999998618
Q gi|254781049|r 68 GGVRV-ESSLKSVISDIREILG 88 (398)
Q Consensus 68 GGV~l-~~s~~ea~~~a~~ilg 88 (398)
+|--+ |.|++=+++...+.-|
T Consensus 263 SG~fLR~~Npe~~~qH~AKVYG 284 (487)
T TIGR01320 263 SGLFLRCSNPELVEQHRAKVYG 284 (487)
T ss_pred CCEECCCCCHHHHHHHCCCCCC
T ss_conf 5500017887999850562157
No 199
>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=52.54 E-value=17 Score=16.42 Aligned_cols=82 Identities=16% Similarity=0.254 Sum_probs=53.5
Q ss_pred CHHHHHHHHH-HHHCCCCCCEEEEECCCCHHHHHHHHHHHHHHHHHCCCCCCEEEECCCCCHHHHHHHHHHCCCCEEE-E
Q ss_conf 9899999999-9861998658999635861328999999999999729998799974898589999999976995899-4
Q gi|254781049|r 304 DQDKVAAAFK-IITSDSSVKGILINIFGGIMRCDVLVKGILSAVKEVKINIPLVMRLEGANVDIGNRLIAESGLNVIT-A 381 (398)
Q Consensus 304 ~~e~~~~a~~-~il~~~~vk~iliNifGGI~~cd~vA~gii~a~~~~~~~~pivvRl~Gtn~~~g~~il~~~g~~~~~-~ 381 (398)
+.+..++.++ ++-..+++.+|| +.-|.+|.|+++++++.+.++|==+.+-|-+-. .+.+-..-++.+ .
T Consensus 166 ~~~~~~~~~~~ll~~~~~~~av~-------~~~D~~A~g~~~~l~~~g~~vP~dvsIigfd~~---~~~~~~~P~LTti~ 235 (273)
T cd01541 166 KEEKLFEKIKEILKRPERPTAIV-------CYNDEIALRVIDLLKELGLKIPEDISVVGFDDS---YLSVASEVKLTTVT 235 (273)
T ss_pred HHHHHHHHHHHHHHCCCCCCEEE-------ECCHHHHHHHHHHHHHCCCCCCCCEEEEECCCH---HHHHHCCCCEEEEE
T ss_conf 68999999999983699995698-------488899988998653148888877247612877---88974389829999
Q ss_pred CCHHHHHHHHHHHH
Q ss_conf 99899999999985
Q gi|254781049|r 382 IDLDDAAQKIVHAV 395 (398)
Q Consensus 382 ~~~~~A~~~~v~~~ 395 (398)
.+.++..+.|+++.
T Consensus 236 ~~~~~~g~~A~~~L 249 (273)
T cd01541 236 HPKEQMGEDAAKMI 249 (273)
T ss_pred ECHHHHHHHHHHHH
T ss_conf 39999999999999
No 200
>TIGR02584 cas_NE0113 CRISPR-associated protein, NE0113 family; InterPro: IPR013413 Members of this minor CRISPR-associated (Cas) protein family are encoded in cas gene clusters in Vibrio vulnificus YJ016, Nitrosomonas europaea ATCC 19718, Mannheimia succiniciproducens MBEL55E, and Verrucomicrobium spinosum..
Probab=52.51 E-value=14 Score=17.03 Aligned_cols=67 Identities=19% Similarity=0.302 Sum_probs=39.5
Q ss_pred CCCCCCCCCEEEEECCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCEEECCCCCCCEEEEEEEEEECCCCCEEEEEECCC
Q ss_conf 56777777707995899999999998618765442122222443301103455565058999998347780489984478
Q gi|254781049|r 60 KELPADSKGGVRVESSLKSVISDIREILGSTLITKQTGPTGSRVNCVYVEDGADILRELYLSLLVDRTSGMVAFIASTQG 139 (398)
Q Consensus 60 ~~~hk~~~GGV~l~~s~~ea~~~a~~ilg~~l~t~qt~~~G~~v~~vLVEe~v~~~~E~ylgi~~Dr~~~~~vii~S~~G 139 (398)
...|-|-.||= +|---..-.|=+||+++ . =++..|||.|-.+..++|| + |...++.+..-+.-
T Consensus 134 ~~lh~SlAGGR---KTMGfyLG~Al~Lfar~--------~-D~l~HVLV~eeFE~~r~Fy----Y-P~~~~~~l~~~~~d 196 (224)
T TIGR02584 134 AVLHASLAGGR---KTMGFYLGYALSLFARE--------Q-DRLSHVLVSEEFENLREFY----Y-PPRKSKILVIKTRD 196 (224)
T ss_pred CEEEEEECCCH---HHHHHHHHHHHHHHCCC--------C-CEEEEEEECCCCCCCCCCC----C-CCCCCCEEEEECCC
T ss_conf 38998606872---57889999999973688--------8-7068886357778855874----8-44787267860888
Q ss_pred CCCH
Q ss_conf 8402
Q gi|254781049|r 140 GMDI 143 (398)
Q Consensus 140 GvdI 143 (398)
|-.+
T Consensus 197 G~~~ 200 (224)
T TIGR02584 197 GENL 200 (224)
T ss_pred CCCC
T ss_conf 9756
No 201
>TIGR02049 gshA_ferroox glutamate--cysteine ligase; InterPro: IPR011718 This entry represents a rare family of glutamate--cysteine ligases, demonstrated first in Thiobacillus ferrooxidans and present in a few other Proteobacteria . It is the first of two enzymes for glutathione biosynthesis. It is also called gamma-glutamylcysteine synthetase..
Probab=52.06 E-value=17 Score=16.37 Aligned_cols=75 Identities=23% Similarity=0.301 Sum_probs=42.1
Q ss_pred CCEEECCHHHHHHHHHH------C-CCCEEEEECCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHHHHHHHCCCCCCC
Q ss_conf 81574799999999987------2-9986999712136876565655677777770799589999999999861876544
Q gi|254781049|r 21 KGVVISSVHAAESAIKT------L-PGPLYVVKSQIHAGGRGKGRFKELPADSKGGVRVESSLKSVISDIREILGSTLIT 93 (398)
Q Consensus 21 ~g~~a~s~~ea~~~a~~------i-g~p~~VvKaQV~aGgRGKa~~~~~hk~~~GGV~l~~s~~ea~~~a~~ilg~~l~t 93 (398)
++.+|+..|..-+...+ | ..|=++|||. +|-=| =||..+.|.+|++.-=++ =.+
T Consensus 237 ~~~la~~Vd~vL~~~~~kY~eYgI~~~Pyv~vKAd--aGTYG------------MGimTa~sgeE~l~LNrK-----~R~ 297 (436)
T TIGR02049 237 EDALATAVDQVLSKVQKKYEEYGIHEKPYVIVKAD--AGTYG------------MGIMTAKSGEEVLGLNRK-----ERN 297 (436)
T ss_pred HHHHHHHHHHHHHHHHHHHHHCCCCCCCEEEEEEC--CCCCC------------CCEEEEECHHHHHCCCCC-----CCC
T ss_conf 36899999999999999887558756875899707--88745------------505884263785425300-----013
Q ss_pred CC-CCCCCCCCCCEEECCCCCC
Q ss_conf 21-2222244330110345556
Q gi|254781049|r 94 KQ-TGPTGSRVNCVYVEDGADI 114 (398)
Q Consensus 94 ~q-t~~~G~~v~~vLVEe~v~~ 114 (398)
+. .-.+|..|+.|+|+|.|.-
T Consensus 298 kM~k~KEGl~vs~ViiQEGV~T 319 (436)
T TIGR02049 298 KMAKVKEGLEVSEVIIQEGVYT 319 (436)
T ss_pred CCCEEECCCCCCCEEEECCCCH
T ss_conf 4431125701055678478440
No 202
>PRK04531 acetylglutamate kinase; Provisional
Probab=51.48 E-value=17 Score=16.31 Aligned_cols=60 Identities=15% Similarity=0.133 Sum_probs=29.5
Q ss_pred HHHHHHHHHHHHHHHHCCCCCCEEEECCCCCHHHHHHH------HHHCCCCEEEE--CCHHHHHHHHHHHH
Q ss_conf 32899999999999972999879997489858999999------99769958994--99899999999985
Q gi|254781049|r 333 MRCDVLVKGILSAVKEVKINIPLVMRLEGANVDIGNRL------IAESGLNVITA--IDLDDAAQKIVHAV 395 (398)
Q Consensus 333 ~~cd~vA~gii~a~~~~~~~~pivvRl~Gtn~~~g~~i------l~~~g~~~~~~--~~~~~A~~~~v~~~ 395 (398)
.+-+-++..|=+++++--++ ++=|-.-+|.--.+-. ++..+-.++.+ +|+++ +.+.|+.+
T Consensus 345 a~g~gv~d~vw~~~~~d~~~--L~Wrsr~~n~~n~wyf~~~dG~~~~~~w~~FW~Gi~d~~~-~~~~i~~a 412 (421)
T PRK04531 345 ARGEGLGRDVWDVMREETPQ--LFWRSRHNNTINKWYMAESDGCYKQENWKVFWYGVQEFEQ-IPHIVAHL 412 (421)
T ss_pred HHHCCHHHHHHHHHHHHCCC--EEEECCCCCCCCCHHHHCCEEEEECCCEEEEEECCCCHHH-HHHHHHHH
T ss_conf 24307699999999855885--1897489997340001035026964985999935787899-99999999
No 203
>TIGR01087 murD UDP-N-acetylmuramoylalanine--D-glutamate ligase; InterPro: IPR005762 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-acetylmuramoylalanine-D-glutamate ligase (MurD). MurD catalyses the addition of d-glutamate to the nucleotide precursor UDP-N-acetylmuramoyl-l-alanine. ; GO: 0005524 ATP binding, 0008764 UDP-N-acetylmuramoylalanine-D-glutamate ligase activity, 0008360 regulation of cell shape, 0009252 peptidoglycan biosynthetic process, 0009273 peptidoglycan-based cell wall biogenesis, 0051301 cell division, 0005737 cytoplasm.
Probab=50.64 E-value=18 Score=16.23 Aligned_cols=109 Identities=22% Similarity=0.271 Sum_probs=72.9
Q ss_pred HHHHHHHHHHCCCCC---CEEEECCC--------CCCHHHHHHHHHHHHCCCCCCEEEEECCCCHHH-HHHHHHHHHHHH
Q ss_conf 899999999658996---24884278--------889899999999986199865899963586132-899999999999
Q gi|254781049|r 279 AMATMDIIKLYGGAP---ANFLDVGG--------GADQDKVAAAFKIITSDSSVKGILINIFGGIMR-CDVLVKGILSAV 346 (398)
Q Consensus 279 amatmD~i~~~Gg~p---ANFlD~gG--------~a~~e~~~~a~~~il~~~~vk~iliNifGGI~~-cd~vA~gii~a~ 346 (398)
.-+..++|+.|-|-| =-+.+..| .++.+-+..|++-+ .+|+ |++| |-||.-+ +|--+. ..++
T Consensus 317 ~~~~~~~l~~F~~~~HRlE~~~~~~G~~f~NDSKATn~~At~~AL~~~-~~~~-~~~L--I~GG~~KG~df~~L--~~~~ 390 (476)
T TIGR01087 317 LEAILEALRSFKGLPHRLEYVGQKNGVHFINDSKATNVHATLAALSAL-KNPK-RVIL--IVGGDDKGADFSPL--APAL 390 (476)
T ss_pred HHHHHHHHHHCCCCCCCEEEEEECCCEEEEECCCCCCHHHHHHHHHHC-CCCC-EEEE--EEECCCCCCCHHHH--HHHH
T ss_conf 689999998457987626887772854798256212189999999847-9997-1899--96034689984899--9984
Q ss_pred HHCCCCCCEEEECCCCCHHHHHHHHHHCCCCE-E----EECCHHHHHHHHHHHHHC
Q ss_conf 97299987999748985899999999769958-9----949989999999998506
Q gi|254781049|r 347 KEVKINIPLVMRLEGANVDIGNRLIAESGLNV-I----TAIDLDDAAQKIVHAVKG 397 (398)
Q Consensus 347 ~~~~~~~pivvRl~Gtn~~~g~~il~~~g~~~-~----~~~~~~~A~~~~v~~~k~ 397 (398)
+ +..+-+=+-|--.++=.+.+++.+..+ . .+++|++|++.+.+.++.
T Consensus 391 ~----~~~~~~~~~G~~~~~~~~~l~~~~~~~~~~~~~~~~~l~~Av~~a~~~~~~ 442 (476)
T TIGR01087 391 K----KKVKAVLAIGEDAAKIAKLLKEIGLVVKYGEETLVESLEEAVQAAREVAKE 442 (476)
T ss_pred C----CCEEEEEEECCCHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHCC
T ss_conf 3----650799985354789999863427643546530577899999999997127
No 204
>TIGR00326 eubact_ribD riboflavin biosynthesis protein RibD; InterPro: IPR004794 This entry describes the riboflavin biosynthesis protein (ribD) as found in Escherichia coli. The N-terminal domain includes the conserved zinc-binding site region that is shared by proteins such as cytosine deaminase, mammalian apolipoprotein B mRNA editing protein, blasticidin-S deaminase, and Bacillus subtilis competence protein comEB. The C-terminal domain is homologous to the full length of yeast HTP reductase, a protein required for riboflavin biosynthesis. A number of archaeal proteins that may be related to the riboflavin biosynthesis protein contain only the C-terminal domain.; GO: 0008703 5-amino-6-(5-phosphoribosylamino)uracil reductase activity, 0008835 diaminohydroxyphosphoribosylaminopyrimidine deaminase activity, 0009231 riboflavin biosynthetic process.
Probab=50.47 E-value=18 Score=16.21 Aligned_cols=37 Identities=8% Similarity=0.273 Sum_probs=23.1
Q ss_pred HHHHHHHHHCCCCCCEEEEECCCCHHHHHHHHHHHHHHH
Q ss_conf 999999986199865899963586132899999999999
Q gi|254781049|r 308 VAAAFKIITSDSSVKGILINIFGGIMRCDVLVKGILSAV 346 (398)
Q Consensus 308 ~~~a~~~il~~~~vk~iliNifGGI~~cd~vA~gii~a~ 346 (398)
..+.++. |.+.+++.|++= .|+...-..+.+|.++-+
T Consensus 305 ~~~~~~~-L~~r~~~~v~vE-gG~~l~~~f~~~G~~d~l 341 (393)
T TIGR00326 305 IEEVMEQ-LGKRGINSVLVE-GGPNLLGSFIDEGLVDEL 341 (393)
T ss_pred HHHHHHH-HHHCCCCEEEEE-CHHHHHHHHHHCCCHHHH
T ss_conf 8999999-874475489872-158999999745843003
No 205
>PRK09585 anmK anhydro-N-acetylmuramic acid kinase; Reviewed
Probab=50.40 E-value=9.9 Score=17.91 Aligned_cols=119 Identities=20% Similarity=0.132 Sum_probs=57.6
Q ss_pred EEECCCHHHHHHHHHH-HHCCCCCCEEEECCC------CCCHHHHHHHHHHH-HCCCCCCEEEEECCC------------
Q ss_conf 9955503689999999-965899624884278------88989999999998-619986589996358------------
Q gi|254781049|r 271 CMVNGAGLAMATMDII-KLYGGAPANFLDVGG------GADQDKVAAAFKII-TSDSSVKGILINIFG------------ 330 (398)
Q Consensus 271 ~~vnGaGlamatmD~i-~~~Gg~pANFlD~gG------~a~~e~~~~a~~~i-l~~~~vk~iliNifG------------ 330 (398)
+++.--|-+.+-||.. ..+.+++ | |-.| ..+.+-+.+.+..- ++.+-.|..=-+.|+
T Consensus 181 ~~afD~GPgN~liD~~~~~~~~~~--y-D~~G~~A~~G~v~~~ll~~ll~~~yf~~~~PKS~gre~F~~~~l~~~~~~~~ 257 (366)
T PRK09585 181 VIGFDTGPGNALIDAWVQRHTGGP--Y-DKDGAWAASGKVDEALLERLLAHPYFALPPPKSTGRELFNLAWLERLLAAFP 257 (366)
T ss_pred EEEECCCCCHHHHHHHHHHHCCCC--C-CCCCHHHHCCCCCHHHHHHHHHHHHHCCCCCCCCCHHHCCHHHHHHHHHHHC
T ss_conf 577568852689999999851999--6-8998578289819999999851475158999887957669899998887641
Q ss_pred CHHHHH-------HHHHHHHHHHHHCCCC-CCEEEECCCCCHHHHHHHHHHC--CCCEEEEC------CHHHHHHHHH
Q ss_conf 613289-------9999999999972999-8799974898589999999976--99589949------9899999999
Q gi|254781049|r 331 GIMRCD-------VLVKGILSAVKEVKIN-IPLVMRLEGANVDIGNRLIAES--GLNVITAI------DLDDAAQKIV 392 (398)
Q Consensus 331 GI~~cd-------~vA~gii~a~~~~~~~-~pivvRl~Gtn~~~g~~il~~~--g~~~~~~~------~~~~A~~~~v 392 (398)
+....| ..|+.|.++++....+ .-|+|-=.|..-.-=.+.|++. +.++.+.+ |+-||.--|.
T Consensus 258 ~ls~~D~laTlt~~ta~sI~~~~~~~~~~~~~i~v~GGG~~N~~L~~~l~~~l~~~~v~~~d~~gi~~d~~EA~~FA~ 335 (366)
T PRK09585 258 GLSPEDVQATLTELTAASIARAVLLLPPGPRELLVCGGGARNPTLMERLAALLPGARVATTDALGIDPDAVEALAFAW 335 (366)
T ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCEEEEECCCCCCHHHHHHHHHHCCCCEEECHHHHCCCHHHHHHHHHHH
T ss_conf 598778999999999999999998647996689997887557999999997689987844898099904999999999
No 206
>pfam07364 DUF1485 Protein of unknown function (DUF1485). This family consists of several hypothetical bacterial proteins of around 300 residues in length. Members of this family all appear to be in the Phylum Proteobacteria. The function of this family is unknown.
Probab=49.92 E-value=18 Score=16.15 Aligned_cols=75 Identities=13% Similarity=0.194 Sum_probs=33.0
Q ss_pred CCCHHHHHHHHHHHHCCCCCCEEEEECCCCHHHHHHHHHHHHHHHHHCCCCCCEEEECCCCCHHHHHHHHHH--------
Q ss_conf 889899999999986199865899963586132899999999999972999879997489858999999997--------
Q gi|254781049|r 302 GADQDKVAAAFKIITSDSSVKGILINIFGGIMRCDVLVKGILSAVKEVKINIPLVMRLEGANVDIGNRLIAE-------- 373 (398)
Q Consensus 302 ~a~~e~~~~a~~~il~~~~vk~iliNifGGI~~cd~vA~gii~a~~~~~~~~pivvRl~Gtn~~~g~~il~~-------- 373 (398)
+|-.+-+..+-++ -++|+ ++-+++|+|..-.|. .+.+.+ ++|-=. .+.+.+.++.++
T Consensus 208 ~Pm~~l~~~~~~~-e~~~~--vl~~sv~~Gfp~aDv---------~~~G~s--vvv~td-~d~~~a~~~a~~la~~~w~~ 272 (292)
T pfam07364 208 EPMRGLVDRLREL-EARGG--VLSASFFHGFPWADV---------PEMGPS--VLVYTD-GDPAAAEAAADELAAELWAR 272 (292)
T ss_pred CCHHHHHHHHHHH-HHCCC--EEEEEEECCCCCCCC---------CCCCCE--EEEECC-CCHHHHHHHHHHHHHHHHHH
T ss_conf 8679999999999-71799--079988578555457---------777757--999908-98999999999999999975
Q ss_pred -CCCCEEEECCHHHHHHHHH
Q ss_conf -6995899499899999999
Q gi|254781049|r 374 -SGLNVITAIDLDDAAQKIV 392 (398)
Q Consensus 374 -~g~~~~~~~~~~~A~~~~v 392 (398)
..+.. ...++++|+.+|.
T Consensus 273 R~~f~~-~~~~~~eAl~~A~ 291 (292)
T pfam07364 273 RDDFVF-PFLPLDEAVDRAL 291 (292)
T ss_pred HHHHCC-CCCCHHHHHHHHH
T ss_conf 550077-9999899999975
No 207
>COG0821 gcpE 1-hydroxy-2-methyl-2-(e)-butenyl 4-diphosphate synthase [Lipid metabolism]
Probab=49.68 E-value=18 Score=16.13 Aligned_cols=10 Identities=60% Similarity=1.335 Sum_probs=5.3
Q ss_pred EEEEECCCHH
Q ss_conf 7999555036
Q gi|254781049|r 269 IGCMVNGAGL 278 (398)
Q Consensus 269 Ig~~vnGaGl 278 (398)
+||+|||-|=
T Consensus 297 MGCVVNGPGE 306 (361)
T COG0821 297 MGCVVNGPGE 306 (361)
T ss_pred EEEEECCCCC
T ss_conf 9757407850
No 208
>COG0069 GltB Glutamate synthase domain 2 [Amino acid transport and metabolism]
Probab=48.97 E-value=4.2 Score=20.34 Aligned_cols=117 Identities=19% Similarity=0.147 Sum_probs=70.9
Q ss_pred CCCHHHHHHHHHHHHCCCCCCHHHHHHHHCCCCEEECCCCEEEEECCCHHHHHHHHHHHHCC------CCCCEEEECCCC
Q ss_conf 57355641027863100015622245775398644228817999555036899999999658------996248842788
Q gi|254781049|r 229 DDNALYRHLDIQELRDVSEEDSREIEAKQHNLSYIALDGNIGCMVNGAGLAMATMDIIKLYG------GAPANFLDVGGG 302 (398)
Q Consensus 229 DDnA~fR~~~~~~~~d~~~~~~~E~~A~~~~l~yv~LdG~Ig~~vnGaGlamatmD~i~~~G------g~pANFlD~gG~ 302 (398)
|-.+-+||.|+....|..|.-..=.++.....-+|||--..+.=.-.+|.+=|.-|.|.--| ..|-.|.|.-|-
T Consensus 274 ~~ISP~pHHDiysieDLaqlI~dLk~~~~~~~I~VKlva~~~v~~iaagvakA~AD~I~IdG~~GGTGAsP~~~~~~~Gi 353 (485)
T COG0069 274 GLISPPPHHDIYSIEDLAQLIKDLKEANPWAKISVKLVAEHGVGTIAAGVAKAGADVITIDGADGGTGASPLTSIDHAGI 353 (485)
T ss_pred CCCCCCCCCCCCCHHHHHHHHHHHHHCCCCCEEEEEEECCCCHHHHHHHHHHCCCCEEEECCCCCCCCCCCHHHHHCCCC
T ss_conf 77589974665698899999999996188970699992565567787666404698899758998678785657636870
Q ss_pred CCHHHHHHHHHHHHCCCCCCEEEEECCCCHHHHHHHHHHHHHH
Q ss_conf 8989999999998619986589996358613289999999999
Q gi|254781049|r 303 ADQDKVAAAFKIITSDSSVKGILINIFGGIMRCDVLVKGILSA 345 (398)
Q Consensus 303 a~~e~~~~a~~~il~~~~vk~iliNifGGI~~cd~vA~gii~a 345 (398)
|...-+.++-..+..+--=..+.|-+=||+..-++||.++.--
T Consensus 354 P~e~glae~~q~L~~~glRd~v~l~~~Ggl~Tg~DVaka~aLG 396 (485)
T COG0069 354 PWELGLAETHQTLVLNGLRDKVKLIADGGLRTGADVAKAAALG 396 (485)
T ss_pred HHHHHHHHHHHHHHHCCCCCEEEEEECCCCCCHHHHHHHHHHC
T ss_conf 7998899999999975986416999428706789999999708
No 209
>COG0769 MurE UDP-N-acetylmuramyl tripeptide synthase [Cell envelope biogenesis, outer membrane]
Probab=48.54 E-value=19 Score=16.01 Aligned_cols=100 Identities=15% Similarity=0.158 Sum_probs=62.0
Q ss_pred CCEEEECCCCCCHHHHHHHHHHHHCCCCCCEEEEECCCCHHHHHHHHHHHHHHHHHCCCCCCEEEECCCCCHHHHHHHHH
Q ss_conf 62488427888989999999998619986589996358613289999999999997299987999748985899999999
Q gi|254781049|r 293 PANFLDVGGGADQDKVAAAFKIITSDSSVKGILINIFGGIMRCDVLVKGILSAVKEVKINIPLVMRLEGANVDIGNRLIA 372 (398)
Q Consensus 293 pANFlD~gG~a~~e~~~~a~~~il~~~~vk~iliNifGGI~~cd~vA~gii~a~~~~~~~~pivvRl~Gtn~~~g~~il~ 372 (398)
|--+.|+.- |++-+.++++.+-...+-+.++||=+|| -| |.-=.-+..+..+...+ -++|-=.+++.|.-..|++
T Consensus 333 ~~v~VDyAH--nPd~le~~L~~~~~~~~g~li~VfG~gG-Dr-D~~kr~~mg~ia~~~ad-~vivt~dnpR~edp~~i~~ 407 (475)
T COG0769 333 KLVIVDYAH--NPDGLEKALRAVRLHAAGRLIVVFGCGG-DR-DKSKRPDMGAIAEQLAD-IVIVTSDNPRSEDPAVILA 407 (475)
T ss_pred CEEEEEECC--CHHHHHHHHHHHHHHCCCCEEEEECCCC-CC-CCCCCHHHHHHHHHCCC-CEEECCCCCCCCCHHHHHH
T ss_conf 769999534--8699999999987534984899977668-87-53430315999985599-3699189988768899999
Q ss_pred HCCCC------EEEECCHHHHHHHHHHHHHC
Q ss_conf 76995------89949989999999998506
Q gi|254781049|r 373 ESGLN------VITAIDLDDAAQKIVHAVKG 397 (398)
Q Consensus 373 ~~g~~------~~~~~~~~~A~~~~v~~~k~ 397 (398)
+.... +....|-.+|.+++++.++.
T Consensus 408 ~i~~g~~~~~~~~~~~dr~~AI~~ai~~a~~ 438 (475)
T COG0769 408 DILAGIEAPEKYEIIEDREEAIRKALDLAKE 438 (475)
T ss_pred HHHHCCCCCCCEEECHHHHHHHHHHHHHHCC
T ss_conf 9983647664143011099999999986324
No 210
>TIGR00017 cmk cytidylate kinase; InterPro: IPR003136 This family consists of cytidylate kinase (2.7.4.14 from EC), which catalyzes the phosphorylation of cytidine 5-monophosphate (dCMP) to cytidine 5 -diphosphate (dCDP) in the presence of ATP or GTP. UMP and dCMP can also act as acceptors .; GO: 0004127 cytidylate kinase activity, 0005524 ATP binding, 0006139 nucleobase nucleoside nucleotide and nucleic acid metabolic process.
Probab=48.52 E-value=19 Score=16.01 Aligned_cols=76 Identities=17% Similarity=0.236 Sum_probs=39.3
Q ss_pred CCCCHHHHHHHCHHHHEEEECCCCCCCCHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHC--CCCCC---CCCEEEE
Q ss_conf 884024555748312203321444578957888788751988899885999999998999955--97510---2326799
Q gi|254781049|r 139 GGMDIEEVAKDYPQKIFKLLIDPLIGVTSEDVASLCDMLELQGQARIDGGDLFPNLYKAFCDK--DMSLL---EINPLII 213 (398)
Q Consensus 139 GGvdIE~va~~~p~~I~~~~id~~~gl~~~~~~~l~~~lg~~~~~~~~~~~ii~~L~~~f~e~--Da~li---EINPLvv 213 (398)
-|.||++ .|.+..|+- ++..++.. ..+-+.+.+..|-|.+. +-..+ +|-- +|
T Consensus 83 nG~DV~~-------~I~t~~v~~-------~aS~~A~~--------~~vR~~~~~~Qq~~~~~sd~g~v~dGRDiGT-vV 139 (223)
T TIGR00017 83 NGEDVSE-------AIRTQEVAN-------LASKVAAF--------PKVREILLKRQQKLAKNSDDGIVADGRDIGT-VV 139 (223)
T ss_pred CCCCHHH-------HCCCHHHHH-------HHHHHHCC--------HHHHHHHHHHHHHHHHHCCCCEEEECCCCCC-EE
T ss_conf 0777132-------206835899-------99987237--------7799999999999875158975884552374-46
Q ss_pred CCCCC--EEEEEEEEEECCCHHHHHHHHH
Q ss_conf 05996--7994001321573556410278
Q gi|254781049|r 214 MKNGR--LRVLDSKISFDDNALYRHLDIQ 240 (398)
Q Consensus 214 t~dg~--vvAlDAKi~iDDnA~fR~~~~~ 240 (398)
.||-+ ++ |||++.+ .|.=|-+++.
T Consensus 140 fPnA~~KiF-LdAsve~--RA~RR~~~~~ 165 (223)
T TIGR00017 140 FPNAELKIF-LDASVEE--RAKRRYKDLQ 165 (223)
T ss_pred CCCCCCCEE-ECCCHHH--HHHHHHHHHH
T ss_conf 788751324-3178789--9887699988
No 211
>PRK12483 threonine dehydratase; Reviewed
Probab=48.21 E-value=19 Score=15.98 Aligned_cols=13 Identities=8% Similarity=0.250 Sum_probs=6.9
Q ss_pred CCHHHHHHHHHHH
Q ss_conf 8999999999986
Q gi|254781049|r 74 SSLKSVISDIREI 86 (398)
Q Consensus 74 ~s~~ea~~~a~~i 86 (398)
.+.+++.+.+.++
T Consensus 139 ~~~dea~~~A~~l 151 (521)
T PRK12483 139 ESFPDALAHALKL 151 (521)
T ss_pred CCHHHHHHHHHHH
T ss_conf 9869999999999
No 212
>pfam11379 DUF3182 Protein of unknown function (DUF3182). This family of proteins with unknown function appears to be restricted to Proteobacteria.
Probab=46.47 E-value=21 Score=15.81 Aligned_cols=54 Identities=26% Similarity=0.417 Sum_probs=41.1
Q ss_pred CCCCCEEECCHHHHHHHHHHC--CCCEEEEECCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHHHHHHH
Q ss_conf 888815747999999999872--998699971213687656565567777777079958999999999986
Q gi|254781049|r 18 PVAKGVVISSVHAAESAIKTL--PGPLYVVKSQIHAGGRGKGRFKELPADSKGGVRVESSLKSVISDIREI 86 (398)
Q Consensus 18 pvp~g~~a~s~~ea~~~a~~i--g~p~~VvKaQV~aGgRGKa~~~~~hk~~~GGV~l~~s~~ea~~~a~~i 86 (398)
-|.+|.-+.|.++|..++..+ ++|+ =+|.---.||||.. ++.+.+++..+-..+
T Consensus 113 ~vLpG~tvFs~~DAr~Aa~~Ll~~G~V-RlK~~~a~gG~GQ~--------------vv~d~~~Le~~L~a~ 168 (355)
T pfam11379 113 AVLPGYTVFSLEDARDAAARLLKGGPV-RLKPPRACGGRGQQ--------------VVADADALDAALAAL 168 (355)
T ss_pred HCCCCCCCCCHHHHHHHHHHHHCCCCE-EECCCCCCCCCCCE--------------EECCHHHHHHHHHCC
T ss_conf 103873222678899999998537972-55056223788855--------------743899999998727
No 213
>pfam03702 UPF0075 Uncharacterized protein family (UPF0075). The proteins is this family are about 370 amino acids long and have no known function.
Probab=46.12 E-value=11 Score=17.74 Aligned_cols=119 Identities=19% Similarity=0.140 Sum_probs=63.7
Q ss_pred EEECCCHHHHHHHHH-HHHCCCCCCEEEECCC------CCCHHHHHHHHHH-HHCCCCCCEEEEECCC----------CH
Q ss_conf 995550368999999-9965899624884278------8898999999999-8619986589996358----------61
Q gi|254781049|r 271 CMVNGAGLAMATMDI-IKLYGGAPANFLDVGG------GADQDKVAAAFKI-ITSDSSVKGILINIFG----------GI 332 (398)
Q Consensus 271 ~~vnGaGlamatmD~-i~~~Gg~pANFlD~gG------~a~~e~~~~a~~~-il~~~~vk~iliNifG----------GI 332 (398)
+++.--|-++.-||. +..+.++| | |-.| ..+.+-+.+.+.- -++.+-.|..=.+.|+ +.
T Consensus 180 i~afD~GPgN~liD~~~~~~~~~~--y-D~~G~~A~~G~v~~~ll~~ll~~~~f~~~~PKS~gre~F~~~~~~~~~~~~~ 256 (363)
T pfam03702 180 VLGFDTGPGNALMDAWIQKHRGEP--F-DKNGAWAASGKVNHALLARLLADPYFALPAPKSTGRELFNLPWLEKKLAKFP 256 (363)
T ss_pred EEEECCCCHHHHHHHHHHHCCCCC--C-CCCHHHHHCCCCCHHHHHHHHHHHHHCCCCCCCCCHHHCCHHHHHHHHCCCC
T ss_conf 366278824789999999713668--2-8681788389858999999974565326899877646459588766532589
Q ss_pred -------HHHHHHHHHHHHHHHHCCCCC-CEEEECCCCCHHHHHHHHHHC--CCCEEEEC------CHHHHHHHHH
Q ss_conf -------328999999999999729998-799974898589999999976--99589949------9899999999
Q gi|254781049|r 333 -------MRCDVLVKGILSAVKEVKINI-PLVMRLEGANVDIGNRLIAES--GLNVITAI------DLDDAAQKIV 392 (398)
Q Consensus 333 -------~~cd~vA~gii~a~~~~~~~~-pivvRl~Gtn~~~g~~il~~~--g~~~~~~~------~~~~A~~~~v 392 (398)
|=+...|+.|.++++....+. .|+|-=.|..-.-=.+.|++. +.++.+.+ ++-||..-|.
T Consensus 257 ~~~D~~aTlt~~ta~sIa~~i~~~~~~~~~iiv~GGG~~N~~L~~~l~~~l~~~~v~~~d~~g~~~~~~EA~~FA~ 332 (363)
T pfam03702 257 VPEDVQATLVELTAVTIVDALLQAGPDCERLLVCGGGARNPLLMARLAELLPNVDVASTDELGLDPDYMEAMAFAW 332 (363)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHCCCCCCEEEEECCCCCCHHHHHHHHHHCCCCEEECHHHCCCCHHHHHHHHHHH
T ss_conf 8778999999999999999999628997589997887568899999997779998842888399822899999999
No 214
>PRK03562 glutathione-regulated potassium-efflux system protein KefC; Provisional
Probab=45.48 E-value=21 Score=15.71 Aligned_cols=111 Identities=12% Similarity=0.148 Sum_probs=67.0
Q ss_pred HCCCCEEECCCCEEEEECCCHHHHHHHHHHHHCCCCCCEEEECCCCCCHHHHHHHHHHHHCCCCCCEEEEECCCCHHHHH
Q ss_conf 53986442288179995550368999999996589962488427888989999999998619986589996358613289
Q gi|254781049|r 257 QHNLSYIALDGNIGCMVNGAGLAMATMDIIKLYGGAPANFLDVGGGADQDKVAAAFKIITSDSSVKGILINIFGGIMRCD 336 (398)
Q Consensus 257 ~~~l~yv~LdG~Ig~~vnGaGlamatmD~i~~~Gg~pANFlD~gG~a~~e~~~~a~~~il~~~~vk~iliNifGGI~~cd 336 (398)
+.|.+|+-+|=| -.+.+..+.+|. |.-| |.++...+-++..+ .+.|.+.|-| .-.
T Consensus 420 ~~gi~~vviD~d-----------~~~V~~~r~~G~-~v~y----GDat~~~vL~~AGi----~~Ar~vViai-----dd~ 474 (615)
T PRK03562 420 SSGVKMVVLDHD-----------PDHIETLRKFGM-KVFY----GDATRMDLLESAGA----AKAEVLINAI-----DDP 474 (615)
T ss_pred HCCCCEEEEECC-----------HHHHHHHHHCCC-EEEE----ECCCCHHHHHHCCC----CCCCEEEEEE-----CCH
T ss_conf 789987999799-----------999999996799-0897----68999999986791----4068899994-----989
Q ss_pred HHHHHHHHHHHHCCCCCCEEEECCCCCHHHHHHHHHHCCCCEEEECCHHHHHHHHHHHH
Q ss_conf 99999999999729998799974898589999999976995899499899999999985
Q gi|254781049|r 337 VLVKGILSAVKEVKINIPLVMRLEGANVDIGNRLIAESGLNVITAIDLDDAAQKIVHAV 395 (398)
Q Consensus 337 ~vA~gii~a~~~~~~~~pivvRl~Gtn~~~g~~il~~~g~~~~~~~~~~~A~~~~v~~~ 395 (398)
.-+.-|++.++++.|++||++|-..-.. ..-|.+.|.+...-++++.+.+...+..
T Consensus 475 ~~~~~iv~~~r~~~P~l~IiaRard~~~---~~~L~~~Ga~~vv~Et~essL~l~~~~L 530 (615)
T PRK03562 475 QTNLQLTELVKEHFPHLQIIARARDVDH---YIRLRQAGVEKPERETFEGALKSGRLAL 530 (615)
T ss_pred HHHHHHHHHHHHHCCCCEEEEEECCHHH---HHHHHHCCCCEEECCHHHHHHHHHHHHH
T ss_conf 9999999999975899869998397788---9999978999896665899999999999
No 215
>PRK04169 geranylgeranylglyceryl phosphate synthase-like protein; Reviewed
Probab=45.19 E-value=22 Score=15.68 Aligned_cols=50 Identities=32% Similarity=0.474 Sum_probs=31.2
Q ss_pred CCCCCEEEECCCCCCHH---HHHHHHHHHHCCCCCCEEEEECCCCHHHHHHHHHHHHHH
Q ss_conf 89962488427888989---999999998619986589996358613289999999999
Q gi|254781049|r 290 GGAPANFLDVGGGADQD---KVAAAFKIITSDSSVKGILINIFGGIMRCDVLVKGILSA 345 (398)
Q Consensus 290 Gg~pANFlD~gG~a~~e---~~~~a~~~il~~~~vk~iliNifGGI~~cd~vA~gii~a 345 (398)
=|.|.=|||+||++..- .+.++.+-.+++ ..|+ +.|||.+-+. |+-+.+|
T Consensus 154 ~g~~~iYLE~gsga~~pv~~e~V~~v~~~l~~----~~Li-vGGGIrs~e~-a~~~~~a 206 (229)
T PRK04169 154 LGMPIVYLEYGGGAGDPVPPEMVKAVKKALTD----TPLI-VGGGIRSPEQ-AREMAKA 206 (229)
T ss_pred HCCCEEEEECCCCCCCCCCHHHHHHHHHHCCC----CCEE-EECCCCCHHH-HHHHHHC
T ss_conf 39808999658888997899999999973789----8789-9289699999-9999976
No 216
>pfam01990 ATP-synt_F ATP synthase (F/14-kDa) subunit. This family includes 14-kDa subunit from vATPases, which is in the peripheral catalytic part of the complex. The family also includes archaebacterial ATP synthase subunit F.
Probab=45.07 E-value=22 Score=15.67 Aligned_cols=52 Identities=13% Similarity=0.307 Sum_probs=38.5
Q ss_pred CCHHHHHHHHHHHHCCCCCCEEEEECCCCHHHHHHHHHHHHHHHHHCCCCCCEEEECCCC
Q ss_conf 898999999999861998658999635861328999999999999729998799974898
Q gi|254781049|r 303 ADQDKVAAAFKIITSDSSVKGILINIFGGIMRCDVLVKGILSAVKEVKINIPLVMRLEGA 362 (398)
Q Consensus 303 a~~e~~~~a~~~il~~~~vk~iliNifGGI~~cd~vA~gii~a~~~~~~~~pivvRl~Gt 362 (398)
.+.+...++|+-+++++++-.|+| |+.+|+-|-+.+.+.+...|+++.+-+.
T Consensus 24 ~~~~e~~~~l~~l~~~~d~gII~i--------te~~a~~i~~~i~~~~~~~P~Ii~IP~~ 75 (92)
T pfam01990 24 VSPEEAEEAFEKLLEREDIGIILI--------TEDIAEEIRETIDRYESVLPAILEIPSK 75 (92)
T ss_pred CCHHHHHHHHHHHHCCCCEEEEEE--------CHHHHHHHHHHHHHHCCCCCEEEEECCC
T ss_conf 998999999999854898599997--------4899998899999847688879996899
No 217
>COG2115 XylA Xylose isomerase [Carbohydrate transport and metabolism]
Probab=44.66 E-value=14 Score=17.02 Aligned_cols=128 Identities=23% Similarity=0.382 Sum_probs=73.8
Q ss_pred HCCC-CEEECC--CCEEEEEC-CCHHHHHHHHHHHHCCCCCCEEEECCCCCCH--------HHHHHHHHHHHC-------
Q ss_conf 5398-644228--81799955-5036899999999658996248842788898--------999999999861-------
Q gi|254781049|r 257 QHNL-SYIALD--GNIGCMVN-GAGLAMATMDIIKLYGGAPANFLDVGGGADQ--------DKVAAAFKIITS------- 317 (398)
Q Consensus 257 ~~~l-~yv~Ld--G~Ig~~vn-GaGlamatmD~i~~~Gg~pANFlD~gG~a~~--------e~~~~a~~~il~------- 317 (398)
++|| ++++++ -|-++++. -=---+++.-+...+|---||=.|+-=|.+. |......+++..
T Consensus 257 ~~gLek~~K~NiEanHA~LaGHsFeHEl~~A~~lg~fGSiDaNrgd~~lGWDTDqFPn~v~e~tLamyeiL~~GGf~~GG 336 (438)
T COG2115 257 QFGLEKEFKLNIEANHATLAGHSFEHELATARALGIFGSIDANRGDYQLGWDTDQFPNNVEENTLAMYEILKAGGFTTGG 336 (438)
T ss_pred HCCCHHHEEEECCCCCEECCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHCCCCCCCC
T ss_conf 80846553641204830011541798999998862004403688883347752326653388899999999808867787
Q ss_pred ---CCCCCE------EEEECCCCHHHHHHHHHHHHHHHHHC---CCCCCEEEECCCCCHHHHHHHHHHCCCCEEEECCHH
Q ss_conf ---998658------99963586132899999999999972---999879997489858999999997699589949989
Q gi|254781049|r 318 ---DSSVKG------ILINIFGGIMRCDVLVKGILSAVKEV---KINIPLVMRLEGANVDIGNRLIAESGLNVITAIDLD 385 (398)
Q Consensus 318 ---~~~vk~------iliNifGGI~~cd~vA~gii~a~~~~---~~~~pivvRl~Gtn~~~g~~il~~~g~~~~~~~~~~ 385 (398)
|.+|+- =| ++|.|.-.|..|.|+-.|.+-. -.+.||--|-.|-|++.|++|++.. .+++
T Consensus 337 ~NFDAKvRRqS~d~~DL--~~gHI~gMD~~A~gLK~AakmieD~~l~~~i~eRY~~~~s~~gq~il~G~-------~~le 407 (438)
T COG2115 337 LNFDAKVRRQSFDPYDL--FYGHIGGMDTFARGLKIAAKMIEDGVLSKPIAERYAGWNSELGQQILNGK-------TSLE 407 (438)
T ss_pred CCCCHHHHHCCCCHHHH--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHCCC-------CCHH
T ss_conf 56115666335877887--88755218899999999999875215668999886003428779998276-------7799
Q ss_pred HHHHHHHH
Q ss_conf 99999999
Q gi|254781049|r 386 DAAQKIVH 393 (398)
Q Consensus 386 ~A~~~~v~ 393 (398)
+-++.+.+
T Consensus 408 ~la~~~~~ 415 (438)
T COG2115 408 ELAAYALE 415 (438)
T ss_pred HHHHHHHH
T ss_conf 99999985
No 218
>PRK09224 threonine dehydratase; Reviewed
Probab=44.54 E-value=22 Score=15.62 Aligned_cols=18 Identities=17% Similarity=0.222 Sum_probs=10.7
Q ss_pred EEEE-CCHHHHHHHHHHHC
Q ss_conf 7995-89999999999861
Q gi|254781049|r 70 VRVE-SSLKSVISDIREIL 87 (398)
Q Consensus 70 V~l~-~s~~ea~~~a~~il 87 (398)
|.+. .+.+++.+.|.++-
T Consensus 117 Vvl~G~~~dea~~~A~~la 135 (504)
T PRK09224 117 VVLHGDSFDEAYAHAIELA 135 (504)
T ss_pred EEEECCCHHHHHHHHHHHH
T ss_conf 9995999899999999999
No 219
>cd00616 AHBA_syn 3-amino-5-hydroxybenzoic acid synthase family (AHBA_syn). AHBA_syn family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). The members of this CD are involved in various biosynthetic pathways for secondary metabolites. Some well studied proteins in this CD are AHBA_synthase, protein product of pleiotropic regulatory gene degT, Arnb aminotransferase and pilin glycosylation protein. The prototype of this family, the AHBA_synthase, is a dimeric PLP dependent enzyme. AHBA_syn is the terminal enzyme of 3-amino-5-hydroxybenzoic acid (AHBA) formation which is involved in the biosynthesis of ansamycin antibiotics, including rifamycin B. Some members of this CD are involved in 4-amino-6-deoxy-monosaccharide D-perosamine synthesis. Perosamine is an important element in the glycosylation of several cell products, such as antibiotics and lipopolysaccharides of gram-positive and gram-negative bacteria. The pilin glycosylation protein
Probab=43.87 E-value=23 Score=15.55 Aligned_cols=14 Identities=29% Similarity=0.439 Sum_probs=8.4
Q ss_pred HHHHHHHHHHCCCC
Q ss_conf 99999999972999
Q gi|254781049|r 339 VKGILSAVKEVKIN 352 (398)
Q Consensus 339 A~gii~a~~~~~~~ 352 (398)
-+.+++.+++.++.
T Consensus 282 R~~l~~~L~~~gI~ 295 (352)
T cd00616 282 RDELIEALKEAGIE 295 (352)
T ss_pred HHHHHHHHHHCCCC
T ss_conf 99999999987998
No 220
>pfam00462 Glutaredoxin Glutaredoxin.
Probab=43.66 E-value=23 Score=15.53 Aligned_cols=43 Identities=23% Similarity=0.169 Sum_probs=23.5
Q ss_pred HHHHHHHHHCCCCCCCCEEECCHHHHHHHHHHC-CCCEEEEECCCCCC
Q ss_conf 999999998689888815747999999999872-99869997121368
Q gi|254781049|r 6 YQAKALLRKYNVPVAKGVVISSVHAAESAIKTL-PGPLYVVKSQIHAG 52 (398)
Q Consensus 6 yqaK~lL~~~GIpvp~g~~a~s~~ea~~~a~~i-g~p~~VvKaQV~aG 52 (398)
..+|++|+++|++.-.--+-.++ ++.....+. |.+- | +||-.+
T Consensus 13 ~~ak~~L~~~~i~y~~~~v~~~~-~~~~~l~~~~g~~t-v--PqI~i~ 56 (60)
T pfam00462 13 KRAKRLLKSLGVKFEEIDVDEDP-EIREELKELSGWRT-V--PQVFID 56 (60)
T ss_pred HHHHHHHHHCCCCCEEEECCCCH-HHHHHHHHHHCCCC-C--CEEEEC
T ss_conf 99999999809975332158999-99999999829998-1--979889
No 221
>PRK09084 aspartate kinase III; Validated
Probab=43.44 E-value=23 Score=15.51 Aligned_cols=20 Identities=10% Similarity=0.361 Sum_probs=10.8
Q ss_pred CCC-CHHHHHHHHHHHHHHHH
Q ss_conf 358-61328999999999999
Q gi|254781049|r 328 IFG-GIMRCDVLVKGILSAVK 347 (398)
Q Consensus 328 ifG-GI~~cd~vA~gii~a~~ 347 (398)
+-| |+...--+|--+..++.
T Consensus 389 vVG~gm~~~~gva~r~f~aL~ 409 (447)
T PRK09084 389 LIGNNLSKACGVAKRVFGVLE 409 (447)
T ss_pred EECCCCCCCHHHHHHHHHHHH
T ss_conf 989672328549999999853
No 222
>PRK03659 glutathione-regulated potassium-efflux system protein KefB; Provisional
Probab=43.02 E-value=23 Score=15.47 Aligned_cols=112 Identities=12% Similarity=0.198 Sum_probs=71.6
Q ss_pred HHCCCCEEECCCCEEEEECCCHHHHHHHHHHHHCCCCCCEEEECCCCCCHHHHHHHHHHHHCCCCCCEEEEECCCCHHHH
Q ss_conf 75398644228817999555036899999999658996248842788898999999999861998658999635861328
Q gi|254781049|r 256 KQHNLSYIALDGNIGCMVNGAGLAMATMDIIKLYGGAPANFLDVGGGADQDKVAAAFKIITSDSSVKGILINIFGGIMRC 335 (398)
Q Consensus 256 ~~~~l~yv~LdG~Ig~~vnGaGlamatmD~i~~~Gg~pANFlD~gG~a~~e~~~~a~~~il~~~~vk~iliNifGGI~~c 335 (398)
++.|.+|+-+|=| ..+.+..+.+| .|.=| |.++...+-++..+ .+.|.+.|-+ .-
T Consensus 420 ~~~gi~~vviD~d-----------~~~V~~~r~~G-~~v~y----GDat~~~vL~~AGi----~~A~~vViai-----~d 474 (602)
T PRK03659 420 MANKMRITVLERD-----------ISAVNLMRKYG-YKVYY----GDATQLELLRAAGA----EKAEAIVITC-----NE 474 (602)
T ss_pred HHCCCCEEEEECC-----------HHHHHHHHHCC-CEEEE----ECCCCHHHHHHCCC----CCCCEEEEEE-----CC
T ss_conf 9789998999786-----------79999999789-90897----58999999986790----4058899982-----98
Q ss_pred HHHHHHHHHHHHHCCCCCCEEEECCCCCHHHHHHHHHHCCCCEEEECCHHHHHHHHHHHH
Q ss_conf 999999999999729998799974898589999999976995899499899999999985
Q gi|254781049|r 336 DVLVKGILSAVKEVKINIPLVMRLEGANVDIGNRLIAESGLNVITAIDLDDAAQKIVHAV 395 (398)
Q Consensus 336 d~vA~gii~a~~~~~~~~pivvRl~Gtn~~~g~~il~~~g~~~~~~~~~~~A~~~~v~~~ 395 (398)
..-+.-|++..+++.|++||++|-.--.. ..-|.+.|.+...-++++.+.+..-+..
T Consensus 475 ~~~~~~iv~~~r~~~P~l~I~aRar~~~~---~~~L~~~Ga~~vv~Et~essL~l~~~~L 531 (602)
T PRK03659 475 PEDTMKLVELCQQHFPHLHILARARGRVE---AHELLQAGVTQFSRETFSSALELGRKTL 531 (602)
T ss_pred HHHHHHHHHHHHHHCCCCEEEEEECCHHH---HHHHHHCCCCEEECCHHHHHHHHHHHHH
T ss_conf 99999999999987869969998697899---9999978999786627899999999999
No 223
>PRK10638 glutaredoxin 3; Provisional
Probab=42.99 E-value=23 Score=15.46 Aligned_cols=46 Identities=26% Similarity=0.198 Sum_probs=30.4
Q ss_pred HHHHHHHHHCCCCCCCCEEECCHHHHHHHHHHCCCCEEEEECCCCCCCC
Q ss_conf 9999999986898888157479999999998729986999712136876
Q gi|254781049|r 6 YQAKALLRKYNVPVAKGVVISSVHAAESAIKTLPGPLYVVKSQIHAGGR 54 (398)
Q Consensus 6 yqaK~lL~~~GIpvp~g~~a~s~~ea~~~a~~ig~p~~VvKaQV~aGgR 54 (398)
..||++|+..||+...-.+-..++......+.-|..- | +||-.+|.
T Consensus 16 ~~Ak~lL~~~gi~y~ei~v~~~~~~~~~l~~~tg~~T-V--PqIfI~g~ 61 (83)
T PRK10638 16 HRAKALLNSKGVSFQEIPIDGDAAKREEMIKRSGRTT-V--PQIFIDAQ 61 (83)
T ss_pred HHHHHHHHHCCCCCEEEECCCCHHHHHHHHHHCCCCC-C--CEEEECCE
T ss_conf 9999999975998769986799999999997369996-1--96999999
No 224
>TIGR03628 arch_S11P archaeal ribosomal protein S11P. This model describes exclusively the archaeal ribosomal protein S11P. It excludes homologous ribosomal proteins S14 from eukaryotes and S11 from bacteria.
Probab=42.61 E-value=24 Score=15.43 Aligned_cols=47 Identities=21% Similarity=0.248 Sum_probs=35.9
Q ss_pred HHHHHHHHHHHHCCCC-CCEEEEC--------CCCCHHHHHHHHHHCCCCEEEECC
Q ss_conf 9999999999972999-8799974--------898589999999976995899499
Q gi|254781049|r 337 VLVKGILSAVKEVKIN-IPLVMRL--------EGANVDIGNRLIAESGLNVITAID 383 (398)
Q Consensus 337 ~vA~gii~a~~~~~~~-~pivvRl--------~Gtn~~~g~~il~~~g~~~~~~~~ 383 (398)
..|+-+.+.+++++++ +.|.+|= .|+-.|-+.|-|..+|+++....|
T Consensus 50 ~aae~~a~~~~~~Gi~~v~V~ikG~G~n~~~~pGpGresAiral~~~Gl~I~~I~D 105 (114)
T TIGR03628 50 QAAGRAAEKAKERGITGLHIKVRAPGGNGQKSPGPGAQAAIRALARAGLRIGRIED 105 (114)
T ss_pred HHHHHHHHHHHHCCCCEEEEEEEECCCCCCCCCCCCHHHHHHHHHHCCCEEEEEEE
T ss_conf 99999999999869849999999478787778986289999999868979999898
No 225
>cd07016 S14_ClpP_1 Caseinolytic protease (ClpP) is an ATP-dependent, highly conserved serine protease. Clp protease (caseinolytic protease; ClpP; Peptidase S14) is a highly conserved serine protease present throughout in bacteria and eukaryota, but seems to be absent in archaea, mollicutes and some fungi. This subfamily only contains bacterial sequences. Clp proteases are involved in a number of cellular processes such as degradation of misfolded proteins, regulation of short-lived proteins and housekeeping removal of dysfunctional proteins. They are also implicated in the control of cell growth, targeting DNA-binding protein from starved cells. ClpP has also been linked to the tight regulation of virulence genes in the pathogens Listeria monocytogenes and Salmonella typhimurium. This enzyme belong to the family of ATP-dependent proteases; the functional Clp protease is comprised of two components: a proteolytic component and one of several regulatory ATPase components, both of which a
Probab=42.52 E-value=24 Score=15.42 Aligned_cols=14 Identities=14% Similarity=0.223 Sum_probs=6.5
Q ss_pred CCHHHHHHHHHHCC
Q ss_conf 79999999998729
Q gi|254781049|r 26 SSVHAAESAIKTLP 39 (398)
Q Consensus 26 ~s~~ea~~~a~~ig 39 (398)
.++++.....+.++
T Consensus 15 ~~~~~~~~~L~~~~ 28 (160)
T cd07016 15 VTAKEFKDALDALG 28 (160)
T ss_pred CCHHHHHHHHHHCC
T ss_conf 39999999998279
No 226
>cd02066 GRX_family Glutaredoxin (GRX) family; composed of GRX, approximately 10 kDa in size, and proteins containing a GRX or GRX-like domain. GRX is a glutathione (GSH) dependent reductase, catalyzing the disulfide reduction of target proteins such as ribonucleotide reductase. It contains a redox active CXXC motif in a TRX fold and uses a similar dithiol mechanism employed by TRXs for intramolecular disulfide bond reduction of protein substrates. Unlike TRX, GRX has preference for mixed GSH disulfide substrates, in which it uses a monothiol mechanism where only the N-terminal cysteine is required. The flow of reducing equivalents in the GRX system goes from NADPH - GSH reductase - GSH - GRX - protein substrates. By altering the redox state of target proteins, GRX is involved in many cellular functions including DNA synthesis, signal transduction and the defense against oxidative stress. Different classes are known including human GRX1 and GRX2, as well as E. coli GRX1 and GRX3, which
Probab=42.36 E-value=24 Score=15.40 Aligned_cols=45 Identities=22% Similarity=0.204 Sum_probs=24.8
Q ss_pred HHHHHHHHHCCCCCCCCEEECCHHHHHHHHHHCCCCEEEEECCCCCCC
Q ss_conf 999999998689888815747999999999872998699971213687
Q gi|254781049|r 6 YQAKALLRKYNVPVAKGVVISSVHAAESAIKTLPGPLYVVKSQIHAGG 53 (398)
Q Consensus 6 yqaK~lL~~~GIpvp~g~~a~s~~ea~~~a~~ig~p~~VvKaQV~aGg 53 (398)
-.+|++|++.||+.-.--+..+++......+..|.+. | +||-.||
T Consensus 14 ~~ak~~L~~~~i~y~e~di~~~~~~~~~l~~~~g~~t-v--PqIfi~g 58 (72)
T cd02066 14 KRAKRLLESLGIEFEEIDILEDGELREELKELSGWPT-V--PQIFING 58 (72)
T ss_pred HHHHHHHHHCCCCCEEEEECCCHHHHHHHHHHHCCCC-C--CEEEECC
T ss_conf 9999999956997789980598889999999849988-9--9599999
No 227
>PRK03806 murD UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional
Probab=42.33 E-value=24 Score=15.40 Aligned_cols=91 Identities=12% Similarity=0.096 Sum_probs=51.2
Q ss_pred EEEECCCCCCHHHHHHHHHHHHCCCCCCEEEEECCCCHHHHHHHHHHHHHHHHHCCCCCCEEEECCCCCHHHHHHHHHHC
Q ss_conf 48842788898999999999861998658999635861328999999999999729998799974898589999999976
Q gi|254781049|r 295 NFLDVGGGADQDKVAAAFKIITSDSSVKGILINIFGGIMRCDVLVKGILSAVKEVKINIPLVMRLEGANVDIGNRLIAES 374 (398)
Q Consensus 295 NFlD~gG~a~~e~~~~a~~~il~~~~vk~iliNifGGI~~cd~vA~gii~a~~~~~~~~pivvRl~Gtn~~~g~~il~~~ 374 (398)
.|.|=+=+++.+.+..|++-+-.+. +.+| |.||..+-.+..+ +.+.+++. + +.+=+-|.+.+.=.++..+.
T Consensus 314 ~fiNDSKaTN~~a~~~Al~s~~~~~--~i~l--I~GG~~K~~d~~~-l~~~~~~~---~-~~~~~~G~~~~~~~~~~~~~ 384 (438)
T PRK03806 314 RWINDSKATNVGSTEAALNGLHVDG--TLHL--LLGGDGKSADFSP-LARYLNGD---N-IRLYCFGRDGAQLAALRPEV 384 (438)
T ss_pred EEEECCCCCCHHHHHHHHHHCCCCC--CEEE--EECCCCCCCCHHH-HHHHHHCC---C-EEEEEECCCHHHHHHHCCCC
T ss_conf 9998972158999999998262039--7799--9547755578799-99986126---5-69999777889999641220
Q ss_pred CCCEEEECCHHHHHHHHHHHHHC
Q ss_conf 99589949989999999998506
Q gi|254781049|r 375 GLNVITAIDLDDAAQKIVHAVKG 397 (398)
Q Consensus 375 g~~~~~~~~~~~A~~~~v~~~k~ 397 (398)
...+++|++|++.|.+.++.
T Consensus 385 ---~~~~~~l~~Av~~a~~~a~~ 404 (438)
T PRK03806 385 ---AQLTETMEQAMRLLAPRVQP 404 (438)
T ss_pred ---CHHHHHHHHHHHHHHHHCCC
T ss_conf ---41540099999999986689
No 228
>COG0771 MurD UDP-N-acetylmuramoylalanine-D-glutamate ligase [Cell envelope biogenesis, outer membrane]
Probab=42.16 E-value=24 Score=15.38 Aligned_cols=106 Identities=17% Similarity=0.187 Sum_probs=66.9
Q ss_pred HHHHHHHHCCCCC---CEEEECC--------CCCCHHHHHHHHHHHHCCCCCCEEEEECCCCHHHHHHHHHHHHHHHHHC
Q ss_conf 9999999658996---2488427--------8889899999999986199865899963586132899999999999972
Q gi|254781049|r 281 ATMDIIKLYGGAP---ANFLDVG--------GGADQDKVAAAFKIITSDSSVKGILINIFGGIMRCDVLVKGILSAVKEV 349 (398)
Q Consensus 281 atmD~i~~~Gg~p---ANFlD~g--------G~a~~e~~~~a~~~il~~~~vk~iliNifGGI~~cd~vA~gii~a~~~~ 349 (398)
+..+.++.|.|-| =-+.+.+ =.++...+..|++-. + -+++| |.||.-+--+ -..+...++
T Consensus 297 ~i~~~L~~F~gl~HR~e~v~~~~gv~f~NDSKATN~~At~~AL~~~---~-~~v~l--I~GG~~Kg~d-f~~L~~~~~-- 367 (448)
T COG0771 297 AILEALSSFTGLPHRLEFVGEKDGVLFINDSKATNVDATLAALSGF---D-GPVIL--IAGGDDKGAD-FSPLAEILA-- 367 (448)
T ss_pred HHHHHHHHCCCCCCCEEEEEECCCEEEECCCCCCCHHHHHHHHHCC---C-CCEEE--EECCCCCCCC-HHHHHHHHH--
T ss_conf 9999997389998622798861988996078788888999999718---9-97799--9777788888-168899774--
Q ss_pred CCCCCEEEECCCCCHHHHHHHHHHCCCCEEEECCHHHHHHHHHHHHHC
Q ss_conf 999879997489858999999997699589949989999999998506
Q gi|254781049|r 350 KINIPLVMRLEGANVDIGNRLIAESGLNVITAIDLDDAAQKIVHAVKG 397 (398)
Q Consensus 350 ~~~~pivvRl~Gtn~~~g~~il~~~g~~~~~~~~~~~A~~~~v~~~k~ 397 (398)
+.+..+-+-|-..+.=.+.|++.+.+++.+++|++|++.+-+.++.
T Consensus 368 --~~~~~~~~~G~~~~~i~~~l~~~~~~~~~~~~le~Av~~a~~~a~~ 413 (448)
T COG0771 368 --KVIKKLVLIGEDAEKIAAALKEAGPSLVICETLEEAVQLARELAQP 413 (448)
T ss_pred --HCCEEEEEECCCHHHHHHHHHHCCCCEEECCCHHHHHHHHHHHHCC
T ss_conf --1555999947888999999875278536147699999999987258
No 229
>KOG2519 consensus
Probab=42.13 E-value=22 Score=15.59 Aligned_cols=27 Identities=15% Similarity=0.210 Sum_probs=17.1
Q ss_pred CEEEECCCCCCHHHHHHHHHHHHCCCC
Q ss_conf 248842788898999999999861998
Q gi|254781049|r 294 ANFLDVGGGADQDKVAAAFKIITSDSS 320 (398)
Q Consensus 294 ANFlD~gG~a~~e~~~~a~~~il~~~~ 320 (398)
-||++.==+.+.+++..+++-+.+..+
T Consensus 305 i~fl~~~~~f~~~rv~~~~~kl~~~~~ 331 (449)
T KOG2519 305 IQFLVGEKQFNEERVRKGIRKLKSSLK 331 (449)
T ss_pred HHHHHHHHCCCHHHHHHHHHHHHHHHC
T ss_conf 999976642597887500677765521
No 230
>PRK06253 O-phosphoseryl-tRNA synthetase; Reviewed
Probab=41.84 E-value=24 Score=15.35 Aligned_cols=17 Identities=12% Similarity=0.114 Sum_probs=11.4
Q ss_pred HHHHHHHHHHHHHHHCC
Q ss_conf 28999999999999729
Q gi|254781049|r 334 RCDVLVKGILSAVKEVK 350 (398)
Q Consensus 334 ~cd~vA~gii~a~~~~~ 350 (398)
-...+|++|+..+...+
T Consensus 368 eg~~~a~~ii~~~~~~~ 384 (527)
T PRK06253 368 EGKDLAREIVETCVKHA 384 (527)
T ss_pred HHHHHHHHHHHHHHHHC
T ss_conf 89999999999999818
No 231
>cd03419 GRX_GRXh_1_2_like Glutaredoxin (GRX) family, GRX human class 1 and 2 (h_1_2)-like subfamily; composed of proteins similar to human GRXs, approximately 10 kDa in size, and proteins containing a GRX or GRX-like domain. GRX is a glutathione (GSH) dependent reductase, catalyzing the disulfide reduction of target proteins such as ribonucleotide reductase. It contains a redox active CXXC motif in a TRX fold and uses a similar dithiol mechanism employed by TRXs for intramolecular disulfide bond reduction of protein substrates. Unlike TRX, GRX has preference for mixed GSH disulfide substrates, in which it uses a monothiol mechanism where only the N-terminal cysteine is required. The flow of reducing equivalents in the GRX system goes from NADPH - GSH reductase - GSH - GRX - protein substrates. By altering the redox state of target proteins, GRX is involved in many cellular functions including DNA synthesis, signal transduction and the defense against oxidative stress. Different classes
Probab=41.50 E-value=23 Score=15.55 Aligned_cols=47 Identities=23% Similarity=0.308 Sum_probs=25.0
Q ss_pred HHHHHHHHHCCCCCCCCEEECCH--HHHHHHHHHCCCCEEEEECCCCCCCC
Q ss_conf 99999999868988881574799--99999998729986999712136876
Q gi|254781049|r 6 YQAKALLRKYNVPVAKGVVISSV--HAAESAIKTLPGPLYVVKSQIHAGGR 54 (398)
Q Consensus 6 yqaK~lL~~~GIpvp~g~~a~s~--~ea~~~a~~ig~p~~VvKaQV~aGgR 54 (398)
-.||++|.++||+-..-.+-..+ .+......++++...| +||..+|+
T Consensus 14 ~~ak~lL~~~~i~~~~~~~d~~~~~~~~~~~l~~~~g~~Tv--PqIfi~g~ 62 (82)
T cd03419 14 KRAKSLLKELGVKPAVVELDQHEDGSEIQDYLQELTGQRTV--PNVFIGGK 62 (82)
T ss_pred HHHHHHHHHCCCCEEEEECCCCCCHHHHHHHHHHHCCCCCC--CEEEECCE
T ss_conf 99999999849980699646564399999999984399988--86999998
No 232
>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=41.08 E-value=13 Score=17.17 Aligned_cols=52 Identities=27% Similarity=0.307 Sum_probs=35.8
Q ss_pred CHHHHHH-HHHHHHCCCCCCEEEECCCCCCHHHHHHHHHHHHCCCCCCEEEEEC
Q ss_conf 0368999-9999965899624884278889899999999986199865899963
Q gi|254781049|r 276 AGLAMAT-MDIIKLYGGAPANFLDVGGGADQDKVAAAFKIITSDSSVKGILINI 328 (398)
Q Consensus 276 aGlamat-mD~i~~~Gg~pANFlD~gG~a~~e~~~~a~~~il~~~~vk~iliNi 328 (398)
|..+.|| .-.+-.-|.--|-.||+---|-.+.++-||+||-+ -.++...++|
T Consensus 479 aaisiatefGallldGlGeavvldlPnlPlqdvlkia~eiL~~-~G~R~~~v~~ 531 (633)
T TIGR00612 479 AAISIATEFGALLLDGLGEAVVLDLPNLPLQDVLKIAYEILQS-LGLRKRGVEI 531 (633)
T ss_pred HHHHHHHHHHHHHHHCCCCEEEEECCCCCHHHHHHHHHHHHHH-CCCCCCCCEE
T ss_conf 4434566666787630453356416787777899999999996-4877567378
No 233
>PRK10014 DNA-binding transcriptional repressor MalI; Provisional
Probab=41.07 E-value=25 Score=15.27 Aligned_cols=106 Identities=6% Similarity=-0.001 Sum_probs=63.9
Q ss_pred HHHHHHHHHCCCCCCEEEECCCCCCHHHHHHHHHHHH-CCCCCCEEEEECCCCHHHHHHHHHHHHHHHHHCCCCCCEE--
Q ss_conf 9999999965899624884278889899999999986-1998658999635861328999999999999729998799--
Q gi|254781049|r 280 MATMDIIKLYGGAPANFLDVGGGADQDKVAAAFKIIT-SDSSVKGILINIFGGIMRCDVLVKGILSAVKEVKINIPLV-- 356 (398)
Q Consensus 280 matmD~i~~~Gg~pANFlD~gG~a~~e~~~~a~~~il-~~~~vk~iliNifGGI~~cd~vA~gii~a~~~~~~~~piv-- 356 (398)
....+.++.+|.+...-.=+.+..+.+..++++.-++ .+|.+.++|. -.|.+|-|.+.++.+.+..+|--
T Consensus 202 ~gf~~al~~~~l~~~~~~i~~~~~~~~~~~~~~~~ll~~~~~~tAi~c-------~~D~~A~g~~~~l~~~g~~v~~d~~ 274 (342)
T PRK10014 202 GGYCATLLKFGLPFHSEWVLECTSSQKQAAEAITALLRHNPTISAVVC-------YNETIAMGAWFGLLRAGRQSGESGV 274 (342)
T ss_pred HHHHHHHHHCCCCCCCCEEEECCCCHHHHHHHHHHHHHCCCCCCEEEE-------ECHHHHHHHHHHHHHHCHHCCCCCC
T ss_conf 999999997699988334896689789999999999836999718999-------6789999999999995822175533
Q ss_pred -------EECCCCCHHHHHHHHHHCCCCEE-EECCHHHHHHHHHHHH
Q ss_conf -------97489858999999997699589-9499899999999985
Q gi|254781049|r 357 -------MRLEGANVDIGNRLIAESGLNVI-TAIDLDDAAQKIVHAV 395 (398)
Q Consensus 357 -------vRl~Gtn~~~g~~il~~~g~~~~-~~~~~~~A~~~~v~~~ 395 (398)
+.+-|-+--. +.....-++. ...+.++-.++|++..
T Consensus 275 ~~~ip~~vsIigfdd~~---~~~~~~P~LTtv~~~~~~ig~~a~~~L 318 (342)
T PRK10014 275 DRYFEQQVALAAFTDVP---EAELDDPPLTWASTPAREIGRTLADRM 318 (342)
T ss_pred CCCCCCCEEEEEECCHH---HHHCCCCCCEEEECCHHHHHHHHHHHH
T ss_conf 34789858999988848---886258985699839999999999999
No 234
>cd03027 GRX_DEP Glutaredoxin (GRX) family, Dishevelled, Egl-10, and Pleckstrin (DEP) subfamily; composed of uncharacterized proteins containing a GRX domain and additional domains DEP and DUF547, both of which have unknown functions. GRX is a glutathione (GSH) dependent reductase containing a redox active CXXC motif in a TRX fold. It has preference for mixed GSH disulfide substrates, in which it uses a monothiol mechanism where only the N-terminal cysteine is required. By altering the redox state of target proteins, GRX is involved in many cellular functions.
Probab=40.70 E-value=25 Score=15.23 Aligned_cols=46 Identities=13% Similarity=0.091 Sum_probs=29.5
Q ss_pred HHHHHHHHHCCCCCCCCEEECCHHHHHHHHHHCCCCEEEEECCCCCCCC
Q ss_conf 9999999986898888157479999999998729986999712136876
Q gi|254781049|r 6 YQAKALLRKYNVPVAKGVVISSVHAAESAIKTLPGPLYVVKSQIHAGGR 54 (398)
Q Consensus 6 yqaK~lL~~~GIpvp~g~~a~s~~ea~~~a~~ig~p~~VvKaQV~aGgR 54 (398)
..||+||.+.|||.-.-.+-..++......+.-|... | +||-.++.
T Consensus 15 ~~AK~lL~~kgi~y~ei~l~~~~~~~~~l~~~tg~~T-V--PQIFi~~~ 60 (73)
T cd03027 15 TAVRLFLREKGLPYVEINIDIFPERKAELEERTGSSV-V--PQIFFNEK 60 (73)
T ss_pred HHHHHHHHHCCCCEEEEECCCCHHHHHHHHHHHCCCC-C--CEEEECCE
T ss_conf 9999999987996499988899899999999719997-5--97999999
No 235
>PRK06382 threonine dehydratase; Provisional
Probab=39.92 E-value=26 Score=15.16 Aligned_cols=25 Identities=16% Similarity=0.202 Sum_probs=16.9
Q ss_pred CCCEEEEECCCHHHHHHHHHHHHCC
Q ss_conf 8817999555036899999999658
Q gi|254781049|r 266 DGNIGCMVNGAGLAMATMDIIKLYG 290 (398)
Q Consensus 266 dG~Ig~~vnGaGlamatmD~i~~~G 290 (398)
+.+|+|+..|+-.-+.++.-|...|
T Consensus 293 gk~Vv~vlsGGNiD~~~l~~ii~r~ 317 (400)
T PRK06382 293 GKKVAIVVSGGNINPLLMSKIIYKE 317 (400)
T ss_pred CCEEEEEECCCCCCHHHHHHHHHHH
T ss_conf 9849999637887978999999998
No 236
>PRK10936 periplasmic sensory protein associated with the TorRS two-component regulatory system; Provisional
Probab=39.85 E-value=26 Score=15.15 Aligned_cols=117 Identities=15% Similarity=0.215 Sum_probs=71.0
Q ss_pred CEEEEEC--CCHHHHHH----HHHHHHCCCCCCEEEECCCC-CCHHHHHHHHHHHH-CCCCCCEEEEECCCCHHHHHHHH
Q ss_conf 1799955--50368999----99999658996248842788-89899999999986-19986589996358613289999
Q gi|254781049|r 268 NIGCMVN--GAGLAMAT----MDIIKLYGGAPANFLDVGGG-ADQDKVAAAFKIIT-SDSSVKGILINIFGGIMRCDVLV 339 (398)
Q Consensus 268 ~Ig~~vn--GaGlamat----mD~i~~~Gg~pANFlD~gG~-a~~e~~~~a~~~il-~~~~vk~iliNifGGI~~cd~vA 339 (398)
+|+++-. |+|-+..- .|.++ +.+-...+.--+ .+.+.-.+.++-+| ++|++++|| | ++..|
T Consensus 171 ~Va~l~G~~~~~~~~~r~~GF~~al~---~~~ikIv~~q~ad~~r~~a~~~~e~iL~~~pdid~I~----g----~~~~a 239 (340)
T PRK10936 171 NVALLPGPEGAGGSKAVEQGFRAAIK---GSDVRIVDIAHGDNDKELQRNLLQELLERHPEIDYIA----G----SAVAA 239 (340)
T ss_pred EEEEECCCCCCCHHHHHHHHHHHHHC---CCCCEEEEEECCCCCHHHHHHHHHHHHHHCCCCCEEE----E----CCHHH
T ss_conf 99995287665147689887999970---7996799884377749999999999998499967998----0----75669
Q ss_pred HHHHHHHHHCCCC-CCEEEECCCCCHHHHHHHHHHCCCCEEEECCHHH----HHHHHHHHHHC
Q ss_conf 9999999972999-8799974898589999999976995899499899----99999998506
Q gi|254781049|r 340 KGILSAVKEVKIN-IPLVMRLEGANVDIGNRLIAESGLNVITAIDLDD----AAQKIVHAVKG 397 (398)
Q Consensus 340 ~gii~a~~~~~~~-~pivvRl~Gtn~~~g~~il~~~g~~~~~~~~~~~----A~~~~v~~~k~ 397 (398)
++-+.++++.+.. ...+|-.-++.. ..+-|++-.+.....++.-. |++.+|.+.+|
T Consensus 240 ~~Ai~al~~~g~~~~v~ivg~D~s~~--~~~~Ik~G~i~atv~Q~p~~~G~~AV~~av~~l~G 300 (340)
T PRK10936 240 EAAIGELRGRNLTDPVKLVSFYLSHQ--VYRGLKRGKVLAAPSDQMVLQGRLAIDQAVRQLEG 300 (340)
T ss_pred HHHHHHHHHCCCCCCEEEEEECCCHH--HHHHHHCCCEEEEECCCHHHHHHHHHHHHHHHHCC
T ss_conf 99999999608888749999269999--99999849779995378899999999999999779
No 237
>cd01844 SGNH_hydrolase_like_6 SGNH_hydrolase subfamily. SGNH hydrolases are a diverse family of lipases and esterases. The tertiary fold of the enzyme is substantially different from that of the alpha/beta hydrolase family and unique among all known hydrolases; its active site closely resembles the Ser-His-Asp(Glu) triad found in other serine hydrolases.
Probab=39.79 E-value=26 Score=15.14 Aligned_cols=28 Identities=18% Similarity=0.224 Sum_probs=13.9
Q ss_pred CCCCCCCCEEECCHHHH--HHHHHHCCCCE
Q ss_conf 68988881574799999--99998729986
Q gi|254781049|r 15 YNVPVAKGVVISSVHAA--ESAIKTLPGPL 42 (398)
Q Consensus 15 ~GIpvp~g~~a~s~~ea--~~~a~~ig~p~ 42 (398)
||=.+..|.-++.|..+ .-++..+|+++
T Consensus 5 yG~SITqG~~AsrP~~a~~~~l~r~lg~~v 34 (177)
T cd01844 5 YGTSISQGACASRPGMAWTAILARRLGLEV 34 (177)
T ss_pred EECHHHCCCCCCCCCCCHHHHHHHHCCCCE
T ss_conf 828376488889864416999998549977
No 238
>cd03418 GRX_GRXb_1_3_like Glutaredoxin (GRX) family, GRX bacterial class 1 and 3 (b_1_3)-like subfamily; composed of bacterial GRXs, approximately 10 kDa in size, and proteins containing a GRX or GRX-like domain. GRX is a glutathione (GSH) dependent reductase, catalyzing the disulfide reduction of target proteins such as ribonucleotide reductase. It contains a redox active CXXC motif in a TRX fold and uses a similar dithiol mechanism employed by TRXs for intramolecular disulfide bond reduction of protein substrates. Unlike TRX, GRX has preference for mixed GSH disulfide substrates, in which it uses a monothiol mechanism where only the N-terminal cysteine is required. The flow of reducing equivalents in the GRX system goes from NADPH - GSH reductase - GSH - GRX - protein substrates. By altering the redox state of target proteins, GRX is involved in many cellular functions including DNA synthesis, signal transduction and the defense against oxidative stress. Different classes are known i
Probab=39.55 E-value=26 Score=15.12 Aligned_cols=34 Identities=29% Similarity=0.131 Sum_probs=22.9
Q ss_pred HHHHHHHHHCCCCCCCCEEECCHHHHHHHHHHCC
Q ss_conf 9999999986898888157479999999998729
Q gi|254781049|r 6 YQAKALLRKYNVPVAKGVVISSVHAAESAIKTLP 39 (398)
Q Consensus 6 yqaK~lL~~~GIpvp~g~~a~s~~ea~~~a~~ig 39 (398)
..||++|+++||+...--+-.+++......+..+
T Consensus 14 ~~aK~lL~~~~i~y~ei~v~~~~~~~~~~~~~~~ 47 (75)
T cd03418 14 VRAKALLDKKGVDYEEIDVDGDPALREEMINRSG 47 (75)
T ss_pred HHHHHHHHHHCCCCEEEECCCCHHHHHHHHHHCC
T ss_conf 9999999981998689862799999999999808
No 239
>pfam03411 Peptidase_M74 Penicillin-insensitive murein endopeptidase.
Probab=39.41 E-value=26 Score=15.11 Aligned_cols=52 Identities=19% Similarity=0.277 Sum_probs=26.6
Q ss_pred HHHHHHHHHHHCCCCCCEEEEECCCCHH--HHHHHHHHHHHHHHHCC----CCCCEEEECC
Q ss_conf 9999999998619986589996358613--28999999999999729----9987999748
Q gi|254781049|r 306 DKVAAAFKIITSDSSVKGILINIFGGIM--RCDVLVKGILSAVKEVK----INIPLVMRLE 360 (398)
Q Consensus 306 e~~~~a~~~il~~~~vk~iliNifGGI~--~cd~vA~gii~a~~~~~----~~~pivvRl~ 360 (398)
..-.+.+++-.+||+|.-|||| -+|- -|+. |.|=-.-+..+. -.--+-|||.
T Consensus 124 ~~h~~lik~AA~dp~V~RIFVn--p~IK~~lC~~-~~~DR~WL~KvRPw~GH~~HfHVRL~ 181 (240)
T pfam03411 124 PEIFSLIKLAAQDPDVTRIFVN--PAIKQQLCLT-AGTDRDWLRKVRPWFGHRAHFHVRLT 181 (240)
T ss_pred HHHHHHHHHHHCCCCEEEEEEC--HHHHHHHHHC-CCCCHHHHHHCCCCCCCCCEEEEEEC
T ss_conf 8999999998358771488658--9999999865-16657789742853466542478720
No 240
>TIGR00273 TIGR00273 iron-sulfur cluster binding protein; InterPro: IPR004452 Members of this family have a perfect 4Fe-4S binding motif C-x(2)-C-x(2)-C-x(3)-CP followed by either a perfect or imperfect (the first Cys replaced by Ser) second copy. Members probably bind two 4fe-4S iron-sulphur clusters..
Probab=39.38 E-value=26 Score=15.10 Aligned_cols=122 Identities=16% Similarity=0.219 Sum_probs=59.0
Q ss_pred EEEECCHHHHHHHHHHHCCCC---CCCCC--CCCCCCCCCCEEECCCCCCCE----EEEEEEE-EECCCCCEEEEEECCC
Q ss_conf 799589999999999861876---54421--222224433011034555650----5899999-8347780489984478
Q gi|254781049|r 70 VRVESSLKSVISDIREILGST---LITKQ--TGPTGSRVNCVYVEDGADILR----ELYLSLL-VDRTSGMVAFIASTQG 139 (398)
Q Consensus 70 V~l~~s~~ea~~~a~~ilg~~---l~t~q--t~~~G~~v~~vLVEe~v~~~~----E~ylgi~-~Dr~~~~~vii~S~~G 139 (398)
|..++|.|||.+.+.++.+.+ .+.+| .-..-.-++.+|=++.+.... ||+|=+. .|+ |+=|.-
T Consensus 67 vYyA~~~eeA~~ii~~v~~~KN~k~vvK~KSMvsEEI~Ln~~L~~~G~~v~ETDLGElI~Q~~d~d~----P~H~Vv--- 139 (450)
T TIGR00273 67 VYYAKTAEEARKIILKVAQEKNGKKVVKSKSMVSEEIGLNEVLEKKGIEVVETDLGELILQLDDNDP----PSHIVV--- 139 (450)
T ss_pred EEEECCHHHHHHHHHHHHHHHCCCEEECCCCCCEEECCHHHHHHHCCCEEEEECCCEEEEEEECCCC----CEEEEE---
T ss_conf 9872787899999999886413344211346400032214888765977998004307887745888----427885---
Q ss_pred CCCHHHHHHHCHHHHEEEECCCCCCCCHHHHHHHHH-HCCCCH-HHHHHHHHHHHHHHH-HHHHCCCCCCCCCEEEECCC
Q ss_conf 840245557483122033214445789578887887-519888-998859999999989-99955975102326799059
Q gi|254781049|r 140 GMDIEEVAKDYPQKIFKLLIDPLIGVTSEDVASLCD-MLELQG-QARIDGGDLFPNLYK-AFCDKDMSLLEINPLIIMKN 216 (398)
Q Consensus 140 GvdIE~va~~~p~~I~~~~id~~~gl~~~~~~~l~~-~lg~~~-~~~~~~~~ii~~L~~-~f~e~Da~liEINPLvvt~d 216 (398)
|..--...|+++++. +||..+ +..+.+...+.+..| =|.+.|.=.-=.| +++-..
T Consensus 140 ---------------------PAlHk~~~qig~il~Erl~~~~~E~pE~L~~~~R~~~R~~Fl~a~~GisGcN-fa~A~t 197 (450)
T TIGR00273 140 ---------------------PALHKNRKQIGEILKERLGYEGEEEPEKLALIARKFMRKKFLSADIGISGCN-FAIAET 197 (450)
T ss_pred ---------------------CCCCCCHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHCCCCCEEECC-EEEECC
T ss_conf ---------------------5722786898889987458998888789999999986266511345300002-046557
Q ss_pred CCEE
Q ss_conf 9679
Q gi|254781049|r 217 GRLR 220 (398)
Q Consensus 217 g~vv 220 (398)
|++.
T Consensus 198 G~i~ 201 (450)
T TIGR00273 198 GSIF 201 (450)
T ss_pred CEEE
T ss_conf 5189
No 241
>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=38.76 E-value=27 Score=15.04 Aligned_cols=84 Identities=6% Similarity=0.070 Sum_probs=57.3
Q ss_pred CCCCHHHHHHHHH-HHHCCCCCCEEEEECCCCHHHHHHHHHHHHHHHHHCCCC-CCEEEECCCCCHHHHHHHHHHCCCCE
Q ss_conf 8889899999999-986199865899963586132899999999999972999-87999748985899999999769958
Q gi|254781049|r 301 GGADQDKVAAAFK-IITSDSSVKGILINIFGGIMRCDVLVKGILSAVKEVKIN-IPLVMRLEGANVDIGNRLIAESGLNV 378 (398)
Q Consensus 301 G~a~~e~~~~a~~-~il~~~~vk~iliNifGGI~~cd~vA~gii~a~~~~~~~-~pivvRl~Gtn~~~g~~il~~~g~~~ 378 (398)
|..+.+..++.++ ++.++|++++|+ | ++..+.|.++++++.+.. ...++=..++ .+..+.+++-.+..
T Consensus 164 ~~~~~~~a~~~~~~~L~~~pdi~~i~----~----~~~~a~~a~~a~~~~g~~~~v~vvg~d~~--~~~~~~i~~G~i~a 233 (268)
T cd06306 164 GDTGKEVQRKLVEEALEAHPDIDYIV----G----SAVAAEAAVGILRQRGLTDQIKIVSTYLS--HAVYRGLKRGKILA 233 (268)
T ss_pred CCCCHHHHHHHHHHHHHHCCCCCEEE----E----CCHHHHHHHHHHHHCCCCCCEEEEEECCC--HHHHHHHHCCCEEE
T ss_conf 78749999999999986299988999----5----74679999999986077997599993699--89999998598379
Q ss_pred EEECCHHHHHHHHHHH
Q ss_conf 9949989999999998
Q gi|254781049|r 379 ITAIDLDDAAQKIVHA 394 (398)
Q Consensus 379 ~~~~~~~~A~~~~v~~ 394 (398)
....+....-..+|+.
T Consensus 234 tv~Q~p~~~G~~av~~ 249 (268)
T cd06306 234 APTDSMVLQGRLAIDQ 249 (268)
T ss_pred EEECCHHHHHHHHHHH
T ss_conf 9956999999999999
No 242
>KOG3857 consensus
Probab=38.39 E-value=13 Score=17.05 Aligned_cols=37 Identities=22% Similarity=0.074 Sum_probs=24.0
Q ss_pred HHHHHHHHCCCCCCCC------EEECCHHHHHHHHHHCCCCEE
Q ss_conf 9999999868988881------574799999999987299869
Q gi|254781049|r 7 QAKALLRKYNVPVAKG------VVISSVHAAESAIKTLPGPLY 43 (398)
Q Consensus 7 qaK~lL~~~GIpvp~g------~~a~s~~ea~~~a~~ig~p~~ 43 (398)
-+++.|.+-||++--+ --+.|..++.+.+++=.+..+
T Consensus 89 ~a~~~L~~~~I~~~vyD~v~~ePtv~s~~~alefak~~~fDs~ 131 (465)
T KOG3857 89 VAQDSLEENGINVEVYDKVQPEPTVGSVTAALEFAKKKNFDSF 131 (465)
T ss_pred HHHHHHHHCCCCEEEECCCCCCCCHHHHHHHHHHHHHCCCCEE
T ss_conf 9999999759816972476479862349999999873366558
No 243
>PRK01077 cobyrinic acid a,c-diamide synthase; Validated
Probab=38.30 E-value=27 Score=14.99 Aligned_cols=15 Identities=27% Similarity=0.184 Sum_probs=8.8
Q ss_pred HHHHHCCCCCCCCEE
Q ss_conf 999986898888157
Q gi|254781049|r 10 ALLRKYNVPVAKGVV 24 (398)
Q Consensus 10 ~lL~~~GIpvp~g~~ 24 (398)
++|++-|+.|.++.+
T Consensus 26 r~l~~rG~~VapFK~ 40 (451)
T PRK01077 26 RALRRRGLRVQPFKV 40 (451)
T ss_pred HHHHHCCCCCCCCCC
T ss_conf 999968794575357
No 244
>PRK09607 rps11p 30S ribosomal protein S11P; Reviewed
Probab=38.25 E-value=28 Score=14.99 Aligned_cols=49 Identities=18% Similarity=0.207 Sum_probs=34.5
Q ss_pred HHHHHHHHHHHHHCCCC-CCEEEECC--------CCCHHHHHHHHHHCCCCEEEECCH
Q ss_conf 99999999999972999-87999748--------985899999999769958994998
Q gi|254781049|r 336 DVLVKGILSAVKEVKIN-IPLVMRLE--------GANVDIGNRLIAESGLNVITAIDL 384 (398)
Q Consensus 336 d~vA~gii~a~~~~~~~-~pivvRl~--------Gtn~~~g~~il~~~g~~~~~~~~~ 384 (398)
-..|+-+.+.+++++++ +.|.||=. |+..|-+.+-|..+|+++....|.
T Consensus 53 q~aae~~~~~a~~~Gi~~v~V~vkG~G~~~~k~pGpGr~~air~l~~~Gl~I~~I~Dv 110 (129)
T PRK09607 53 MQAAFRAAELAKDKGITGVHIKVRAPGGNGSKTPGPGAQAAIRALARAGLRIGRIEDV 110 (129)
T ss_pred HHHHHHHHHHHHHCCCCEEEEEEEECCCCCCCCCCCCHHHHHHHHHHCCCEEEEEEEE
T ss_conf 9999999999997698589999983787776788842899999998689789898870
No 245
>cd00394 Clp_protease_like Caseinolytic protease (ClpP) is an ATP-dependent protease. Clp protease (caseinolytic protease; ClpP; endopeptidase Clp; Peptidase S14; ATP-dependent protease, ClpAP)-like enzymes are highly conserved serine proteases and belong to the ClpP/Crotonase superfamily. Included in this family are Clp proteases that are involved in a number of cellular processes such as degradation of misfolded proteins, regulation of short-lived proteins and housekeeping removal of dysfunctional proteins. They are also implicated in the control of cell growth, targeting DNA-binding protein from starved cells. The functional Clp protease is comprised of two components: a proteolytic component and one of several regulatory ATPase components, both of which are required for effective levels of protease activity in the presence of ATP. Active site consists of the triad Ser, His and Asp, preferring hydrophobic or non-polar residues at P1 or P1' positions. The protease exists as a tetradec
Probab=38.08 E-value=28 Score=14.97 Aligned_cols=11 Identities=9% Similarity=0.184 Sum_probs=4.3
Q ss_pred HHHHHHHHHHH
Q ss_conf 99999989999
Q gi|254781049|r 189 DLFPNLYKAFC 199 (398)
Q Consensus 189 ~ii~~L~~~f~ 199 (398)
+.+.++++.|.
T Consensus 113 ~~~~~~~~~~~ 123 (161)
T cd00394 113 RIILYFIARFI 123 (161)
T ss_pred HHHHHHHHHHH
T ss_conf 99999999999
No 246
>PRK04663 murD UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional
Probab=37.77 E-value=28 Score=14.94 Aligned_cols=90 Identities=14% Similarity=0.175 Sum_probs=52.8
Q ss_pred EEEECCCCCCHHHHHHHHHHHHCCCCCCEEEEECCCCHHHHHHHHHHHHHHHHHCCCCCCEEEECCCCCHHHHHHHHHHC
Q ss_conf 48842788898999999999861998658999635861328999999999999729998799974898589999999976
Q gi|254781049|r 295 NFLDVGGGADQDKVAAAFKIITSDSSVKGILINIFGGIMRCDVLVKGILSAVKEVKINIPLVMRLEGANVDIGNRLIAES 374 (398)
Q Consensus 295 NFlD~gG~a~~e~~~~a~~~il~~~~vk~iliNifGGI~~cd~vA~gii~a~~~~~~~~pivvRl~Gtn~~~g~~il~~~ 374 (398)
.|-|=+=+++.+.+..|++-+- .|+ +.+| |.||..+-.+..+ +.+.+++. ..-+-+-|.+.++ +...
T Consensus 315 ~~iNDSKaTN~~a~~~Al~~~~-~~~-~i~l--I~GG~~Kg~d~~~-l~~~~~~~----~~~~~~~G~~~~~---~~~~- 381 (438)
T PRK04663 315 KWVNDSKATNVASTLAALSGLN-LEG-KLYL--LVGGVGKGADFSE-LKPVLATL----NLQLCCFGEDGDQ---FMPL- 381 (438)
T ss_pred EEECCCCCCCHHHHHHHHHHCC-CCC-CEEE--EECCCCCCCCHHH-HHHHHHHC----CEEEEEECCCHHH---HHHH-
T ss_conf 9974787788789999998367-778-4799--9657666668799-99998523----7699998888999---9743-
Q ss_pred CCCEEEECCHHHHHHHHHHHHHC
Q ss_conf 99589949989999999998506
Q gi|254781049|r 375 GLNVITAIDLDDAAQKIVHAVKG 397 (398)
Q Consensus 375 g~~~~~~~~~~~A~~~~v~~~k~ 397 (398)
.-+...+++|++|++.|-+.++.
T Consensus 382 ~~~~~~~~~l~~Av~~a~~~a~~ 404 (438)
T PRK04663 382 HPSARRFETMEDAIESISPQLKS 404 (438)
T ss_pred CCCCEECCCHHHHHHHHHHHCCC
T ss_conf 24534406799999999986779
No 247
>PRK08190 bifunctional enoyl-CoA hydratase/phosphate acetyltransferase; Validated
Probab=37.69 E-value=18 Score=16.23 Aligned_cols=72 Identities=19% Similarity=0.231 Sum_probs=32.8
Q ss_pred EECCCCHHHHHHHHHHHHHHHHHCCCCCCEEEECCC----------CCHHHHHHHHHHCC-CC-EEE--ECCHHHHHHHH
Q ss_conf 963586132899999999999972999879997489----------85899999999769-95-899--49989999999
Q gi|254781049|r 326 INIFGGIMRCDVLVKGILSAVKEVKINIPLVMRLEG----------ANVDIGNRLIAESG-LN-VIT--AIDLDDAAQKI 391 (398)
Q Consensus 326 iNifGGI~~cd~vA~gii~a~~~~~~~~pivvRl~G----------tn~~~g~~il~~~g-~~-~~~--~~~~~~A~~~~ 391 (398)
+||+=..-.--++-+--|+..+.+++..|=|.=|+- |-....+..+.+.| ++ .+. --.||.|+.+-
T Consensus 303 ini~P~l~~K~~Ii~Nai~~a~~lG~~~PKVAiLsAvE~vnp~mpsTlDAa~L~kma~rGqi~g~ivdGPLa~DnAis~e 382 (465)
T PRK08190 303 INIAPTLEQKRDIVQNAIDLAHALGVEEPKVAILSAVETVNPKIPSTLDAAALCKMADRGQITGGIVDGPLAFDNAISAE 382 (465)
T ss_pred EEECCCHHHHHHHHHHHHHHHHHHCCCCCEEEEEEEEEECCCCCCCHHHHHHHHHHHHCCCCCCCEEECCCHHHHHCCHH
T ss_conf 33488989999999999999998199998299996001448889645889999999974896884887784277537998
Q ss_pred HHHHHC
Q ss_conf 998506
Q gi|254781049|r 392 VHAVKG 397 (398)
Q Consensus 392 v~~~k~ 397 (398)
-...||
T Consensus 383 AA~~Kg 388 (465)
T PRK08190 383 AAKTKG 388 (465)
T ss_pred HHHHCC
T ss_conf 996469
No 248
>PRK06464 phosphoenolpyruvate synthase; Validated
Probab=37.57 E-value=16 Score=16.47 Aligned_cols=55 Identities=13% Similarity=0.111 Sum_probs=29.1
Q ss_pred CCHHHHHHHHHHH----CCCCCCCCCCCCCCC----CCCCEEECCCCCCCE-EEEEEEEEECCCC
Q ss_conf 8999999999986----187654421222224----433011034555650-5899999834778
Q gi|254781049|r 74 SSLKSVISDIREI----LGSTLITKQTGPTGS----RVNCVYVEDGADILR-ELYLSLLVDRTSG 129 (398)
Q Consensus 74 ~s~~ea~~~a~~i----lg~~l~t~qt~~~G~----~v~~vLVEe~v~~~~-E~ylgi~~Dr~~~ 129 (398)
...+++..+.+.. ++.+-++.... .|. .-..|.|++||.... --=+.+++||.++
T Consensus 148 ~g~e~L~~Aik~v~aS~~s~RAi~YR~~-~gi~~~~~~~AV~VQ~MV~~d~~asGV~FTrdP~tG 211 (794)
T PRK06464 148 RGIDDVLDAVKHCFASLFTDRAISYRVH-QGFDHFKVALSAGVQKMVRSDLAASGVMFTLDTESG 211 (794)
T ss_pred CCHHHHHHHHHHHHHHHCCHHHHHHHHH-CCCCHHHHCCEEEEEEEECCCCCCCEEEEEECCCCC
T ss_conf 8999999999999986026899999998-499826637068999863266645425784067789
No 249
>PRK08198 threonine dehydratase; Provisional
Probab=37.46 E-value=28 Score=14.91 Aligned_cols=25 Identities=8% Similarity=0.234 Sum_probs=14.5
Q ss_pred CCCEEEEECCCHHHHHHHHHHHHCC
Q ss_conf 8817999555036899999999658
Q gi|254781049|r 266 DGNIGCMVNGAGLAMATMDIIKLYG 290 (398)
Q Consensus 266 dG~Ig~~vnGaGlamatmD~i~~~G 290 (398)
+.+|+|+..|+-.-+.++.-|...|
T Consensus 298 gk~Vv~ilsGGNiD~~~l~~i~er~ 322 (406)
T PRK08198 298 GKKVVAVLSGGNIDVLLLSRVIERG 322 (406)
T ss_pred CCEEEEEECCCCCCHHHHHHHHHHH
T ss_conf 9849999725787989999999998
No 250
>COG4789 EscV Type III secretory pathway, component EscV [Intracellular trafficking and secretion]
Probab=36.75 E-value=15 Score=16.71 Aligned_cols=14 Identities=14% Similarity=0.332 Sum_probs=8.0
Q ss_pred CCHHHHHHHHHHCC
Q ss_conf 65799999999868
Q gi|254781049|r 3 IHEYQAKALLRKYN 16 (398)
Q Consensus 3 L~EyqaK~lL~~~G 16 (398)
|.|++|-++...||
T Consensus 90 LL~adAG~II~sFG 103 (689)
T COG4789 90 LLEADAGEIIYSFG 103 (689)
T ss_pred HHHCCCCHHHHHHC
T ss_conf 87523251888727
No 251
>COG1646 Predicted phosphate-binding enzymes, TIM-barrel fold [General function prediction only]
Probab=36.36 E-value=29 Score=14.80 Aligned_cols=51 Identities=27% Similarity=0.413 Sum_probs=34.0
Q ss_pred CCCCEEEECCCCCCHHHHHHHHHHHHCCCCCCEEEEECCCCHHHHHHHHHHHHHHHH
Q ss_conf 996248842788898999999999861998658999635861328999999999999
Q gi|254781049|r 291 GAPANFLDVGGGADQDKVAAAFKIITSDSSVKGILINIFGGIMRCDVLVKGILSAVK 347 (398)
Q Consensus 291 g~pANFlD~gG~a~~e~~~~a~~~il~~~~vk~iliNifGGI~~cd~vA~gii~a~~ 347 (398)
|-|.-||++||++..-.-.+..+.++++- .| |+||-.|.-+.|.-+..|.-
T Consensus 164 g~~~~YlEagsga~~Pv~~e~v~~v~~~~----~L--ivGGGIrs~E~A~~~a~agA 214 (240)
T COG1646 164 GMPVVYLEAGSGAGDPVPVEMVSRVLSDT----PL--IVGGGIRSPEQAREMAEAGA 214 (240)
T ss_pred CCEEEEEEECCCCCCCCCHHHHHHHHCCC----EE--EECCCCCCHHHHHHHHHCCC
T ss_conf 98589998068889986889999861455----08--98588498999999997179
No 252
>pfam08981 consensus
Probab=36.23 E-value=30 Score=14.78 Aligned_cols=17 Identities=29% Similarity=0.100 Sum_probs=7.4
Q ss_pred HHHHHHHHHCCCCEEEE
Q ss_conf 99999998729986999
Q gi|254781049|r 29 HAAESAIKTLPGPLYVV 45 (398)
Q Consensus 29 ~ea~~~a~~ig~p~~Vv 45 (398)
+-|.+-++++|-..+||
T Consensus 15 ~~a~~ra~e~gI~~iVv 31 (181)
T pfam08981 15 ELAAERAKELGIKHIVV 31 (181)
T ss_pred HHHHHHHHHCCCCEEEE
T ss_conf 99999999769976999
No 253
>PRK08526 threonine dehydratase; Provisional
Probab=35.76 E-value=30 Score=14.74 Aligned_cols=24 Identities=21% Similarity=0.538 Sum_probs=16.6
Q ss_pred CCEEEEECCCHHHHHHHHHHHHCC
Q ss_conf 817999555036899999999658
Q gi|254781049|r 267 GNIGCMVNGAGLAMATMDIIKLYG 290 (398)
Q Consensus 267 G~Ig~~vnGaGlamatmD~i~~~G 290 (398)
.+|+|+..|+-.-+.++.-|...|
T Consensus 296 k~Vv~ilsGGNiD~~~l~~ii~r~ 319 (403)
T PRK08526 296 AKIGVVLSGGNIDVQMLNVIIEKG 319 (403)
T ss_pred CEEEEEECCCCCCHHHHHHHHHHH
T ss_conf 979999715888988999999998
No 254
>COG1058 CinA Predicted nucleotide-utilizing enzyme related to molybdopterin-biosynthesis enzyme MoeA [General function prediction only]
Probab=35.62 E-value=30 Score=14.72 Aligned_cols=63 Identities=16% Similarity=0.127 Sum_probs=33.8
Q ss_pred HHHHHCCCCCCCCEEE-CCHHHHHHHHHHC--CCCEEEEECCCCCCCCCCCCCCCCCCC--CCCEEEEECCHH
Q ss_conf 9999868988881574-7999999999872--998699971213687656565567777--777079958999
Q gi|254781049|r 10 ALLRKYNVPVAKGVVI-SSVHAAESAIKTL--PGPLYVVKSQIHAGGRGKGRFKELPAD--SKGGVRVESSLK 77 (398)
Q Consensus 10 ~lL~~~GIpvp~g~~a-~s~~ea~~~a~~i--g~p~~VvKaQV~aGgRGKa~~~~~hk~--~~GGV~l~~s~~ 77 (398)
+.|..+|+++-+..++ +++++...+.... .+. +| |.+||=|--+.|++.-. ..=|+.++.+++
T Consensus 28 ~~L~~~G~~v~~~~~VgD~~~~I~~~l~~a~~r~D-~v----I~tGGLGPT~DDiT~e~vAka~g~~lv~~~~ 95 (255)
T COG1058 28 DELTELGVDLARITTVGDNPDRIVEALREASERAD-VV----ITTGGLGPTHDDLTAEAVAKALGRPLVLDEE 95 (255)
T ss_pred HHHHHCCCEEEEEEECCCCHHHHHHHHHHHHHCCC-EE----EECCCCCCCCCHHHHHHHHHHHCCCCCCCHH
T ss_conf 99996496189999639999999999999971899-89----9879858996276899999982998566999
No 255
>pfam02195 ParBc ParB-like nuclease domain.
Probab=35.44 E-value=30 Score=14.70 Aligned_cols=55 Identities=20% Similarity=0.374 Sum_probs=22.4
Q ss_pred HHHHHHHCCCCCCEEEEC---------CCCCHHHHHHHHHHCCCCEEEECCHHHHHHHHHHHHHC
Q ss_conf 999999729998799974---------89858999999997699589949989999999998506
Q gi|254781049|r 342 ILSAVKEVKINIPLVMRL---------EGANVDIGNRLIAESGLNVITAIDLDDAAQKIVHAVKG 397 (398)
Q Consensus 342 ii~a~~~~~~~~pivvRl---------~Gtn~~~g~~il~~~g~~~~~~~~~~~A~~~~v~~~k~ 397 (398)
+...+++.+...|++||- .|..--.+.+.+....+++.. .++++.-.++..++++
T Consensus 26 L~~SI~~~G~~~PiiV~~~~~~~y~ii~G~~R~~A~~~lg~~~ip~~v-~d~~~~ea~~~~l~eN 89 (90)
T pfam02195 26 LIASIKEHGLLQPIIVRKTPGGRYEIIDGHRRLRAAKLLGLKEVPVIV-LELDDEEAIALSLEEN 89 (90)
T ss_pred HHHHHHHHCCCCCEEEEECCCCCEEEEEEEEHHHHHHHCCCCEEEEEE-EECCHHHHHHHHHHCC
T ss_conf 999999859647879997488978995686199999986998610999-9899899999998745
No 256
>PRK03995 hypothetical protein; Provisional
Probab=34.77 E-value=31 Score=14.63 Aligned_cols=40 Identities=20% Similarity=0.213 Sum_probs=21.2
Q ss_pred HHHHHHHHHCCCCCC-EEEECC---CCCHHHHHHHHHHCCCCEE
Q ss_conf 999999997299987-999748---9858999999997699589
Q gi|254781049|r 340 KGILSAVKEVKINIP-LVMRLE---GANVDIGNRLIAESGLNVI 379 (398)
Q Consensus 340 ~gii~a~~~~~~~~p-ivvRl~---Gtn~~~g~~il~~~g~~~~ 379 (398)
+-+.+++.+.....+ +++-.. |..-+.-.++|++.|+++.
T Consensus 219 e~~~~~~~~~~~~~~~a~iD~K~~kg~~R~~i~~~l~~~gi~v~ 262 (264)
T PRK03995 219 EVILRAIIKHTEPVDAAYIDRKGLKSEDRREIEEFLDELGLEVI 262 (264)
T ss_pred HHHHHHHHHHCCCCCEEEEECCCCCHHHHHHHHHHHHHCCCEEE
T ss_conf 99999999731689889995577987899999999998699461
No 257
>PRK04690 murD UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional
Probab=34.43 E-value=32 Score=14.60 Aligned_cols=91 Identities=20% Similarity=0.164 Sum_probs=54.5
Q ss_pred EEEECCCCCCHHHHHHHHHHHHCCCCCCEEEEECCCCHHHHHHHHHHHHHHHHHCCCCCCEEEECCCCCHHHHHHHHH--
Q ss_conf 488427888989999999998619986589996358613289999999999997299987999748985899999999--
Q gi|254781049|r 295 NFLDVGGGADQDKVAAAFKIITSDSSVKGILINIFGGIMRCDVLVKGILSAVKEVKINIPLVMRLEGANVDIGNRLIA-- 372 (398)
Q Consensus 295 NFlD~gG~a~~e~~~~a~~~il~~~~vk~iliNifGGI~~cd~vA~gii~a~~~~~~~~pivvRl~Gtn~~~g~~il~-- 372 (398)
.|.+=+=+++.+.+..|++-. .++ +.+| |.||..+-.+... +...+ ..++++.+=+-|-+.++=.+.++
T Consensus 324 ~fiNDSKATN~~a~~~AL~~f-~~~--~iil--I~GG~~Kg~d~~~-l~~~~---~~~~~~~vi~~G~~~~~i~~~~~~~ 394 (468)
T PRK04690 324 TYVNDSISTTPHASLAALDCF-AGR--RVAL--LVGGHDRGLDWTD-FAAHM---AQQAPLEIVTMGANGPRIHALLAPL 394 (468)
T ss_pred EEECCCCCCCHHHHHHHHHHC-CCC--CEEE--EECCCCCCCCHHH-HHHHH---HHCCCEEEEEECCCHHHHHHHHHHC
T ss_conf 997378778989999999727-668--5799--9736766778799-99998---6337689999747889999997523
Q ss_pred --HCCCCEEEECCHHHHHHHHHHH
Q ss_conf --7699589949989999999998
Q gi|254781049|r 373 --ESGLNVITAIDLDDAAQKIVHA 394 (398)
Q Consensus 373 --~~g~~~~~~~~~~~A~~~~v~~ 394 (398)
...++++.+++|++|++.+.+.
T Consensus 395 ~~~~~~~~~~~~~l~~Av~~a~~~ 418 (468)
T PRK04690 395 ADAGRFGLHAADDLPHAMALARTA 418 (468)
T ss_pred CCCCCEEEEECCCHHHHHHHHHHH
T ss_conf 445631025406799999999996
No 258
>PTZ00317 malic enzyme; Provisional
Probab=34.11 E-value=32 Score=14.57 Aligned_cols=22 Identities=14% Similarity=0.300 Sum_probs=10.7
Q ss_pred HHHHHHHHHCCCCCCEEEECCCC
Q ss_conf 99999999729998799974898
Q gi|254781049|r 340 KGILSAVKEVKINIPLVMRLEGA 362 (398)
Q Consensus 340 ~gii~a~~~~~~~~pivvRl~Gt 362 (398)
+-+++++... ...|||.-|+-+
T Consensus 396 eevv~~Ma~~-~erPIIFaLSNP 417 (570)
T PTZ00317 396 EEIVKFMASN-CERPIIFPLSNP 417 (570)
T ss_pred HHHHHHHHHC-CCCCEEEECCCC
T ss_conf 9999999855-998879977898
No 259
>PRK05878 pyruvate phosphate dikinase; Provisional
Probab=33.84 E-value=22 Score=15.69 Aligned_cols=32 Identities=9% Similarity=-0.146 Sum_probs=20.7
Q ss_pred CCEEECCCCCCCE----EEEEEEEEECCCCCEEEEE
Q ss_conf 3011034555650----5899999834778048998
Q gi|254781049|r 104 NCVYVEDGADILR----ELYLSLLVDRTSGMVAFIA 135 (398)
Q Consensus 104 ~~vLVEe~v~~~~----E~ylgi~~Dr~~~~~vii~ 135 (398)
..|-|+.||-..+ --=+.+++||.+|.+-+++
T Consensus 192 ~AV~VQ~MVfgn~~d~sgsGV~FTrdP~TG~~~~~g 227 (529)
T PRK05878 192 TAVVVQAMVFGNLDANSGAGVLFSRNPITGANEPFG 227 (529)
T ss_pred CEEEEEEEEECCCCCCCCCEEEEEECCCCCCCEEEE
T ss_conf 316899835527899876137897068889960799
No 260
>cd03364 TOPRIM_DnaG_primases TOPRIM_DnaG_primases: The topoisomerase-primase (TORPIM) nucleotidyl transferase/hydrolase domain found in the active site regions of proteins similar to Escherichia coli DnaG. Primases synthesize RNA primers for the initiation of DNA replication. DnaG type primases are often closely associated with DNA helicases in primosome assemblies. The TOPRIM domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD). This glutamate and two aspartates, cluster together to form a highly acid surface patch. The conserved glutamate may act as a general base in nucleotide polymerization by primases. The DXD motif may co-ordinate Mg2+, a cofactor required for full catalytic function. E. coli DnaG is a single subunit enzyme.
Probab=33.74 E-value=32 Score=14.53 Aligned_cols=54 Identities=24% Similarity=0.260 Sum_probs=31.4
Q ss_pred HHHHHHHHHCCCCCCEEEECCCCCHH-HHHHHHHHCCCCEEEECCHHHHHHHHHH
Q ss_conf 99999999729998799974898589-9999999769958994998999999999
Q gi|254781049|r 340 KGILSAVKEVKINIPLVMRLEGANVD-IGNRLIAESGLNVITAIDLDDAAQKIVH 393 (398)
Q Consensus 340 ~gii~a~~~~~~~~pivvRl~Gtn~~-~g~~il~~~g~~~~~~~~~~~A~~~~v~ 393 (398)
||..+++.-....++-+|-+.||+-. +-.++|++..-+++.+-|-|+|-++|..
T Consensus 7 EG~~D~i~~~~~G~~n~VA~~Gt~~t~~q~~~L~~~~~~vil~~D~D~AG~~Aa~ 61 (79)
T cd03364 7 EGYMDVIALHQAGIKNVVASLGTALTEEQAELLKRLAKEVILAFDGDEAGQKAAL 61 (79)
T ss_pred ECHHHHHHHHHCCCCCEEECCCCCCCHHHHHHHHCCCCCEEEEECCCHHHHHHHH
T ss_conf 6779999999859962562566547199999772315867999789889999999
No 261
>PRK08928 consensus
Probab=33.73 E-value=32 Score=14.53 Aligned_cols=25 Identities=16% Similarity=0.167 Sum_probs=16.2
Q ss_pred CHHHHHHHHHHHHCCCCCCEEEEEC
Q ss_conf 9899999999986199865899963
Q gi|254781049|r 304 DQDKVAAAFKIITSDSSVKGILINI 328 (398)
Q Consensus 304 ~~e~~~~a~~~il~~~~vk~iliNi 328 (398)
..+.....++-++.|++++.|.=|+
T Consensus 358 ~~~~~~~~l~~lLed~~i~KIghNl 382 (861)
T PRK08928 358 ITDAFSDIIFNLLTDKSILKITYDL 382 (861)
T ss_pred CHHHHHHHHHHHHCCCCCCEEECCH
T ss_conf 2478999999984399975445457
No 262
>pfam00411 Ribosomal_S11 Ribosomal protein S11.
Probab=33.59 E-value=33 Score=14.51 Aligned_cols=49 Identities=20% Similarity=0.252 Sum_probs=36.3
Q ss_pred HHHHHHHHHHHHHHCCCC-CCEEEECCCCCHHHHHHHHHHCCCCEEEECC
Q ss_conf 899999999999972999-8799974898589999999976995899499
Q gi|254781049|r 335 CDVLVKGILSAVKEVKIN-IPLVMRLEGANVDIGNRLIAESGLNVITAID 383 (398)
Q Consensus 335 cd~vA~gii~a~~~~~~~-~pivvRl~Gtn~~~g~~il~~~g~~~~~~~~ 383 (398)
...+|+-+.+.+++++++ +.|++|=-|+..+-..+-|..+|+++....|
T Consensus 45 a~~aa~~~~~~~~~~gi~~v~v~ikG~G~Gr~~air~l~~~gl~I~~I~D 94 (109)
T pfam00411 45 AQTAAENAAKIAKEQGIKALEVKIKGPGPGRESALRALARSGLRIGRIRD 94 (109)
T ss_pred HHHHHHHHHHHHHHHCCCEEEEEEECCCCCHHHHHHHHHHCCCEEEEEEE
T ss_conf 99999999999998198599999988998789999999877998999998
No 263
>TIGR03632 bact_S11 30S ribosomal protein S11. This model describes the bacterial 30S ribosomal protein S11. Cutoffs are set such that the model excludes archaeal and eukaryotic ribosomal proteins, but many chloroplast and mitochondrial equivalents of S11 are detected.
Probab=33.41 E-value=33 Score=14.49 Aligned_cols=49 Identities=18% Similarity=0.298 Sum_probs=35.4
Q ss_pred HHHHHHHHHHHHHHCCCC-CCEEEECCCCCHHHHHHHHHHCCCCEEEECC
Q ss_conf 899999999999972999-8799974898589999999976995899499
Q gi|254781049|r 335 CDVLVKGILSAVKEVKIN-IPLVMRLEGANVDIGNRLIAESGLNVITAID 383 (398)
Q Consensus 335 cd~vA~gii~a~~~~~~~-~pivvRl~Gtn~~~g~~il~~~g~~~~~~~~ 383 (398)
...+|+-+.+.+++++++ +-|++|=-|+..+-..+-|..+|+.+....|
T Consensus 45 a~~aa~~~~~~~~~~gi~~v~V~ikG~G~Gr~~air~l~~~glkI~~I~D 94 (108)
T TIGR03632 45 AQLAAEDAAKKAKEFGMKTVDVYVKGPGAGRESAIRALQAAGLEVTSIKD 94 (108)
T ss_pred HHHHHHHHHHHHHHCCCEEEEEEEECCCCCHHHHHHHHHHCCCEEEEEEE
T ss_conf 99999999999997096199999968997479999999988988999998
No 264
>COG1879 RbsB ABC-type sugar transport system, periplasmic component [Carbohydrate transport and metabolism]
Probab=33.37 E-value=33 Score=14.49 Aligned_cols=120 Identities=17% Similarity=0.207 Sum_probs=74.9
Q ss_pred CCEEEEECCCHHH------HHHHHHHHHCCCCCCEEEECCCCCCHHHHHHHHH-HHHCCCCCCEEEEECCCCHHHHHHHH
Q ss_conf 8179995550368------9999999965899624884278889899999999-98619986589996358613289999
Q gi|254781049|r 267 GNIGCMVNGAGLA------MATMDIIKLYGGAPANFLDVGGGADQDKVAAAFK-IITSDSSVKGILINIFGGIMRCDVLV 339 (398)
Q Consensus 267 G~Ig~~vnGaGla------matmD~i~~~Gg~pANFlD~gG~a~~e~~~~a~~-~il~~~~vk~iliNifGGI~~cd~vA 339 (398)
|++.++..-.|.. ....+.+..+++..---....+..+.++.++..+ ++.++|++++|+- .-|.+|
T Consensus 159 g~v~~~~g~~~~~~~~~R~~G~~~~l~~~~~~~~v~~~~~~~~~~~~a~~~~~~~L~~~pdi~~i~~-------~~d~~a 231 (322)
T COG1879 159 GKVVVLVGSPGNSSAEERVKGFRDALKEHPPDIEVVDVQTGDWDRDKALEVMEDLLAANPDIDGIYA-------ANDGMA 231 (322)
T ss_pred CCEEEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEEEECCCCCCHHHHHHHHHHHHHHCCCCEEEEE-------CCCCHH
T ss_conf 8489997888995199999999999975599559975436887688999999999975899449998-------997069
Q ss_pred HHHHHHHHHCCCCC-CEEEECCCCCHHHHHHHHHHCCCCEEEECCHHHHHHHHHHHH
Q ss_conf 99999999729998-799974898589999999976995899499899999999985
Q gi|254781049|r 340 KGILSAVKEVKINI-PLVMRLEGANVDIGNRLIAESGLNVITAIDLDDAAQKIVHAV 395 (398)
Q Consensus 340 ~gii~a~~~~~~~~-pivvRl~Gtn~~~g~~il~~~g~~~~~~~~~~~A~~~~v~~~ 395 (398)
.|.++|+++.+..- ..|+=..|+. +.++.+++-.+......+.......+++++
T Consensus 232 ~ga~~a~~~ag~~~~v~v~g~D~~~--~~~~~i~~G~~~~~v~q~p~~~g~~~~~~~ 286 (322)
T COG1879 232 LGAIQALKAAGRKGDVVVVGFDGTP--DALKALKDGKLDATVLQDPAAQGAAAVELA 286 (322)
T ss_pred HHHHHHHHHCCCCCCEEEEEECCCH--HHHHHHHCCCEEEEECCCHHHHHHHHHHHH
T ss_conf 9999999976998806999947979--999999669736996379888899999999
No 265
>PRK00536 speE spermidine synthase; Provisional
Probab=33.22 E-value=27 Score=15.00 Aligned_cols=39 Identities=5% Similarity=-0.072 Sum_probs=25.2
Q ss_pred EEEEEECCCCCEEEEEECCCCCCHHHHHHHCHHHHEEEECC
Q ss_conf 99998347780489984478840245557483122033214
Q gi|254781049|r 120 LSLLVDRTSGMVAFIASTQGGMDIEEVAKDYPQKIFKLLID 160 (398)
Q Consensus 120 lgi~~Dr~~~~~vii~S~~GGvdIE~va~~~p~~I~~~~id 160 (398)
+.+..-|+-.++++++++-||+-=|-+.. |..+.-+.||
T Consensus 65 vpl~~Hp~Pk~VLIIGGGDGG~~REvlKH--~~~v~~VEID 103 (262)
T PRK00536 65 MGGCTKKELKEVLIVDGFDLELAHQLFKY--DTHVDFVQAD 103 (262)
T ss_pred HHHHCCCCCCEEEEECCCCHHHHHHHHCC--CCEEEEEEEC
T ss_conf 02321899787999868755999998728--9766999967
No 266
>CHL00041 rps11 ribosomal protein S11
Probab=32.30 E-value=34 Score=14.37 Aligned_cols=49 Identities=18% Similarity=0.278 Sum_probs=33.7
Q ss_pred HHHHHHHHHHHHHHCCCC-CCEEEECCCCCHHHHHHHHHHCCCCEEEECC
Q ss_conf 899999999999972999-8799974898589999999976995899499
Q gi|254781049|r 335 CDVLVKGILSAVKEVKIN-IPLVMRLEGANVDIGNRLIAESGLNVITAID 383 (398)
Q Consensus 335 cd~vA~gii~a~~~~~~~-~pivvRl~Gtn~~~g~~il~~~g~~~~~~~~ 383 (398)
+..+|+-+.+..++++++ +-|++|=-|...+-..+-|+.+|+++....|
T Consensus 58 a~~aa~~~~~~a~~~Gi~~v~v~vkG~G~GR~~aik~l~~~glkI~~I~D 107 (116)
T CHL00041 58 AQTAAENAIRTVIDQGMKRAEVMIKGPGLGRDTALRAIRRSGLKLSSIRD 107 (116)
T ss_pred HHHHHHHHHHHHHHCCCEEEEEEEECCCCCHHHHHHHHHHCCCEEEEEEE
T ss_conf 99999999999997398499999978884589999999878988999998
No 267
>COG0281 SfcA Malic enzyme [Energy production and conversion]
Probab=32.22 E-value=34 Score=14.37 Aligned_cols=28 Identities=32% Similarity=0.444 Sum_probs=11.1
Q ss_pred EEEEECCCHHH-HHHHHHHHHCCCCCCEE
Q ss_conf 79995550368-99999999658996248
Q gi|254781049|r 269 IGCMVNGAGLA-MATMDIIKLYGGAPANF 296 (398)
Q Consensus 269 Ig~~vnGaGla-matmD~i~~~Gg~pANF 296 (398)
+=+++||||.| .+.++++..+|-++.|+
T Consensus 200 ~kiv~~GAGAAgiaia~~l~~~g~~~~~i 228 (432)
T COG0281 200 QKIVINGAGAAGIAIADLLVAAGVKEENI 228 (432)
T ss_pred EEEEEECCCHHHHHHHHHHHHHCCCCCCE
T ss_conf 38999677588999999999828984458
No 268
>TIGR02903 spore_lon_C ATP-dependent protease, Lon family; InterPro: IPR014252 This entry shows some relation to the widely distributed ATP-dependent protease La, also called Lon or LonA (IPR004815 from INTERPRO), but is more closely related to LonB (IPR014251 from INTERPRO), a LonA paralog found only in endospore-forming bacteria. Proteins in this entry are unassigned peptidases belonging to the MEROPS peptidase family S16 (lon protease family, clan SJ). They are restricted to a subset of endospore-forming species, and probably participate in the program of endospore formation. We propose the designation LonC..
Probab=31.72 E-value=3.3 Score=21.10 Aligned_cols=58 Identities=28% Similarity=0.405 Sum_probs=39.8
Q ss_pred CEEEECCCCCCHHHHHHHHHHHH--CCCCCC--EEEEECCCCHH----H-HHHHHHHHHHHHHHCCC
Q ss_conf 24884278889899999999986--199865--89996358613----2-89999999999997299
Q gi|254781049|r 294 ANFLDVGGGADQDKVAAAFKIIT--SDSSVK--GILINIFGGIM----R-CDVLVKGILSAVKEVKI 351 (398)
Q Consensus 294 ANFlD~gG~a~~e~~~~a~~~il--~~~~vk--~iliNifGGI~----~-cd~vA~gii~a~~~~~~ 351 (398)
--|=|.-|+=+.+.+-+|+..|= .+..++ =|-||+-||-- + -.-+--.|+.|+.+..+
T Consensus 480 ~RfNdTAGSMaKDSvFNAasviRk~T~~D~~~yD~HVNViGGG~IDGPSAG~Ai~~~~~SA~~~~p~ 546 (616)
T TIGR02903 480 VRFNDTAGSMAKDSVFNAASVIRKITGKDLKDYDIHVNVIGGGRIDGPSAGAAITLCIISAILDKPI 546 (616)
T ss_pred EEEECCCCCCHHHHHHHHHHHHHHHCCCCCCCCCEEEEEECCCCCCCCCHHHHHHHHHHHHHCCCCC
T ss_conf 8861565530357789889998653046834165178885277017532579999999998708983
No 269
>PRK11660 putative sulfate transporter YchM; Provisional
Probab=31.67 E-value=35 Score=14.31 Aligned_cols=84 Identities=10% Similarity=0.133 Sum_probs=56.8
Q ss_pred CHHHHHHHHHHHHCCCCCCEEEEECCCCHHHHHHHH-HHHHHHHHHCCCCCCEEEECCCCCHHHHHHHHHHCCCC-----
Q ss_conf 989999999998619986589996358613289999-99999999729998799974898589999999976995-----
Q gi|254781049|r 304 DQDKVAAAFKIITSDSSVKGILINIFGGIMRCDVLV-KGILSAVKEVKINIPLVMRLEGANVDIGNRLIAESGLN----- 377 (398)
Q Consensus 304 ~~e~~~~a~~~il~~~~vk~iliNifGGI~~cd~vA-~gii~a~~~~~~~~pivvRl~Gtn~~~g~~il~~~g~~----- 377 (398)
+.+++.+.++- ..+++|.+.+ -+.+++..|.-| +.+-+-.++.+- -+.+.+.+-+.+. ++.|+.+|+-
T Consensus 476 na~~~~~~l~~--~~~~~~~vVl-d~~~v~~iD~Tg~~~L~~l~~~l~~--gi~l~~a~~~~~v-~~~l~r~gl~~~ig~ 549 (567)
T PRK11660 476 AAERLFTELES--RTEGKRIVVL-KWDAVPVLDAGGLDAFQRFVERLPE--GCELRICNLQFQP-LRTLARAGIQPIPGR 549 (567)
T ss_pred HHHHHHHHHHH--HCCCCCEEEE-ECCCCCCCCHHHHHHHHHHHHHHHC--CCEEEEECCCHHH-HHHHHHCCCHHHCCC
T ss_conf 39999999986--2689988999-7489996168999999999999977--9989996698689-999998799312596
Q ss_pred EEEECCHHHHHHHHHH
Q ss_conf 8994998999999999
Q gi|254781049|r 378 VITAIDLDDAAQKIVH 393 (398)
Q Consensus 378 ~~~~~~~~~A~~~~v~ 393 (398)
-+.+.+.+||++.+++
T Consensus 550 ~~~f~t~~~Av~~~~~ 565 (567)
T PRK11660 550 LAFYPTLREALADLLS 565 (567)
T ss_pred CCEECCHHHHHHHHHH
T ss_conf 5426989999999984
No 270
>PRK07334 threonine dehydratase; Provisional
Probab=31.64 E-value=35 Score=14.30 Aligned_cols=23 Identities=17% Similarity=0.401 Sum_probs=13.4
Q ss_pred CEEEEECCCHHHHHHHHHHHHCC
Q ss_conf 17999555036899999999658
Q gi|254781049|r 268 NIGCMVNGAGLAMATMDIIKLYG 290 (398)
Q Consensus 268 ~Ig~~vnGaGlamatmD~i~~~G 290 (398)
+|+|+..|+-.-+.++.-|...|
T Consensus 294 ~Vv~vlsGGNiD~~~l~~ii~r~ 316 (399)
T PRK07334 294 KVGLVLCGGNIDTRLLANVLLRG 316 (399)
T ss_pred EEEEEECCCCCCHHHHHHHHHHH
T ss_conf 19999686886988999999998
No 271
>PRK09492 treR trehalose repressor; Provisional
Probab=31.52 E-value=35 Score=14.29 Aligned_cols=98 Identities=13% Similarity=0.140 Sum_probs=62.2
Q ss_pred HHHHHHHHCCCCCCEEEECCCCCCHHHHHHHHHHHHCCCCCCEEEEECCCCHHHHHHHHHHHHHHHHHCCCCCCE-EEEC
Q ss_conf 999999965899624884278889899999999986199865899963586132899999999999972999879-9974
Q gi|254781049|r 281 ATMDIIKLYGGAPANFLDVGGGADQDKVAAAFKIITSDSSVKGILINIFGGIMRCDVLVKGILSAVKEVKINIPL-VMRL 359 (398)
Q Consensus 281 atmD~i~~~Gg~pANFlD~gG~a~~e~~~~a~~~il~~~~vk~iliNifGGI~~cd~vA~gii~a~~~~~~~~pi-vvRl 359 (398)
...+..+.+|..|.-+. +..+.+.-++..+-+++ +++.+||. -.|.+|-|+++++++.+++ ++ |+=+
T Consensus 197 g~~~~~~~~~l~~~~~~---~~~~~~~~~~~~~~~l~-~~~~ai~~-------~~D~~A~g~~~~l~~~gi~-disi~g~ 264 (315)
T PRK09492 197 AYLAFCKQHKLHPVAAL---GGLSMKSGYELVAKVLT-PETTALVC-------ATDTLALGASKYLQEQGRE-TLQVAGV 264 (315)
T ss_pred HHHHHHHHCCCCCEEEE---CCCCHHHHHHHHHHHHC-CCCCEEEE-------ECHHHHHHHHHHHHHCCCC-CEEEEEE
T ss_conf 99999997799960665---68887889999999606-79985999-------5679999999999971999-8589998
Q ss_pred CCCCHHHHHHHHHHCCCCEEEECCHHHHHHHHHHHH
Q ss_conf 898589999999976995899499899999999985
Q gi|254781049|r 360 EGANVDIGNRLIAESGLNVITAIDLDDAAQKIVHAV 395 (398)
Q Consensus 360 ~Gtn~~~g~~il~~~g~~~~~~~~~~~A~~~~v~~~ 395 (398)
.++. .. +++ ...+.- ...+.++..++|+++.
T Consensus 265 d~~~--~~-~~~-~P~LTT-i~~~~~~~g~~A~~~L 295 (315)
T PRK09492 265 GNTP--LL-KFL-FPNIVS-VDPGYAEAGRQAACQL 295 (315)
T ss_pred CCHH--HH-HHC-CCCCEE-EEECHHHHHHHHHHHH
T ss_conf 8818--89-845-899749-9859999999999999
No 272
>pfam09840 DUF2067 Uncharacterized protein conserved in archaea (DUF2067). This domain, found in various archaeal proteins, has no known function.
Probab=31.51 E-value=35 Score=14.29 Aligned_cols=20 Identities=5% Similarity=-0.017 Sum_probs=12.3
Q ss_pred HHHHHHHHHHHHHHHHHHCC
Q ss_conf 98859999999989999559
Q gi|254781049|r 183 ARIDGGDLFPNLYKAFCDKD 202 (398)
Q Consensus 183 ~~~~~~~ii~~L~~~f~e~D 202 (398)
.++.+.+++.+|+.++.+..
T Consensus 114 p~eev~e~~~~L~eiy~ei~ 133 (190)
T pfam09840 114 PLEEVVEVARELSEIYKELR 133 (190)
T ss_pred CHHHHHHHHHHHHHHHHHHH
T ss_conf 79999999999999999985
No 273
>PRK13529 malate dehydrogenase; Provisional
Probab=31.32 E-value=35 Score=14.27 Aligned_cols=14 Identities=7% Similarity=0.000 Sum_probs=5.7
Q ss_pred ECCHHHHHHHHHHH
Q ss_conf 58999999999986
Q gi|254781049|r 73 ESSLKSVISDIREI 86 (398)
Q Consensus 73 ~~s~~ea~~~a~~i 86 (398)
..+...+.+..++|
T Consensus 129 ~~d~g~i~~il~nw 142 (563)
T PRK13529 129 YPDRDRIDDILRNA 142 (563)
T ss_pred CCCHHHHHHHHHHC
T ss_conf 26666899999708
No 274
>pfam01341 Glyco_hydro_6 Glycosyl hydrolases family 6.
Probab=31.04 E-value=36 Score=14.24 Aligned_cols=67 Identities=19% Similarity=0.207 Sum_probs=47.9
Q ss_pred CCCEEEECCCC--------CCHHHHHHHHHHHHCCCCCCEEEEECCCCHHHHHHHH--HHHHHHHHHCCCCCCEEEE
Q ss_conf 96248842788--------8989999999998619986589996358613289999--9999999972999879997
Q gi|254781049|r 292 APANFLDVGGG--------ADQDKVAAAFKIITSDSSVKGILINIFGGIMRCDVLV--KGILSAVKEVKINIPLVMR 358 (398)
Q Consensus 292 ~pANFlD~gG~--------a~~e~~~~a~~~il~~~~vk~iliNifGGI~~cd~vA--~gii~a~~~~~~~~pivvR 358 (398)
....|||.|.+ ++.+.+.+.++-.-.-.+++++..|+-.=-.-+|+++ +.+..++...+.....||-
T Consensus 154 nv~vYlDaGh~~Wlgw~~n~~a~~~a~~l~~ag~~~~~rGfatNvSNy~~t~~e~~y~~~l~~~l~~~G~~~~fVID 230 (295)
T pfam01341 154 NVAVYLDAGHSGWLGWDANPAAQLFAERLKNAGSGASARGFATNVSNYNPTADEKAYAEALSPALGAAGFGAHFVID 230 (295)
T ss_pred CEEEEEECCCCCCCCCCCCCCHHHHHHHHHHCCCCCEEEEEEEECCCCCCCHHHHHHHHHHHHHHHCCCCCCCEEEE
T ss_conf 84899968773224887653899999999965885402478850456777178999999999998505898886886
No 275
>COG0646 MetH Methionine synthase I (cobalamin-dependent), methyltransferase domain [Amino acid transport and metabolism]
Probab=30.96 E-value=36 Score=14.23 Aligned_cols=159 Identities=17% Similarity=0.298 Sum_probs=92.8
Q ss_pred HHHHHHHHHHHHHHHHHHCCCCCCCCCEEEECCCCCEEEEEEEEEECCCHHHHHHHHHHHHCCCCCCHHHHHHHHCC---
Q ss_conf 98859999999989999559751023267990599679940013215735564102786310001562224577539---
Q gi|254781049|r 183 ARIDGGDLFPNLYKAFCDKDMSLLEINPLIIMKNGRLRVLDSKISFDDNALYRHLDIQELRDVSEEDSREIEAKQHN--- 259 (398)
Q Consensus 183 ~~~~~~~ii~~L~~~f~e~Da~liEINPLvvt~dg~vvAlDAKi~iDDnA~fR~~~~~~~~d~~~~~~~E~~A~~~~--- 259 (398)
....--+.|.++-+.|.+-.|..+|-|-+--| -+++ ++-.+.|....-+.+-.++ .++ -|.+.+
T Consensus 47 LnlT~Pd~I~~IH~aY~eAGADiIeTNTFgat----~i~l-ady~led~v~~in~~aa~i-------AR~-aA~~~~~~k 113 (311)
T COG0646 47 LNLTKPDVIEAIHRAYIEAGADIIETNTFGAT----TIKL-ADYGLEDKVYEINQKAARI-------ARR-AADEAGDPK 113 (311)
T ss_pred HHCCCCHHHHHHHHHHHHCCCCEEEECCCCCC----HHHH-HHHCHHHHHHHHHHHHHHH-------HHH-HHHHCCCCC
T ss_conf 75479499999999999646767873477865----3657-5507388999999999999-------999-986447887
Q ss_pred CCEEECCCCEEEEECCCHHHHHHHHHHHHCCCCCCE-EEECCC--CCCHHHHHHHHHH---HHCCCCCCEEEEECCCCHH
Q ss_conf 864422881799955503689999999965899624-884278--8898999999999---8619986589996358613
Q gi|254781049|r 260 LSYIALDGNIGCMVNGAGLAMATMDIIKLYGGAPAN-FLDVGG--GADQDKVAAAFKI---ITSDSSVKGILINIFGGIM 333 (398)
Q Consensus 260 l~yv~LdG~Ig~~vnGaGlamatmD~i~~~Gg~pAN-FlD~gG--~a~~e~~~~a~~~---il~~~~vk~iliNifGGI~ 333 (398)
=.||- |.|| |-| ++.+.| ..+-+.++.+++- .|-+-.+..+||--+=-+-
T Consensus 114 ~rfVa--GsiG----------------------Pt~k~~~~~~~~~v~fd~l~~ay~eq~~~Li~gG~D~iLiET~~D~l 169 (311)
T COG0646 114 PRFVA--GSIG----------------------PTNKTLSISPDFAVTFDELVEAYREQVEGLIDGGADLILIETIFDTL 169 (311)
T ss_pred CEEEE--EECC----------------------CCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHCCCCEEEEEHHCCHH
T ss_conf 53898--7326----------------------86776776876663599999999999999983787589975221689
Q ss_pred HHHHHHHHHHHHHHHCCCCCCEEEE---------CCCCCHHHHHHHHHHCCCCE
Q ss_conf 2899999999999972999879997---------48985899999999769958
Q gi|254781049|r 334 RCDVLVKGILSAVKEVKINIPLVMR---------LEGANVDIGNRLIAESGLNV 378 (398)
Q Consensus 334 ~cd~vA~gii~a~~~~~~~~pivvR---------l~Gtn~~~g~~il~~~g~~~ 378 (398)
++.....++-+..++.+..+|+++. |.|..-+..+.-|+..+...
T Consensus 170 ~~KaA~~a~~~~~~~~~~~LPv~~s~Ti~~sG~tl~Gq~~~a~~~~l~~~~~~~ 223 (311)
T COG0646 170 NAKAAVFAAREVFEELGVRLPVMISGTITDSGRTLSGQTIEAFLNSLEHLGPDA 223 (311)
T ss_pred HHHHHHHHHHHHHHHCCCCCCEEEEEEEECCCEECCCCCHHHHHHHHHCCCCCE
T ss_conf 899999999999873277654799999803761237986899999866359747
No 276
>TIGR00962 atpA ATP synthase F1, alpha subunit; InterPro: IPR005294 ATPases (or ATP synthases) are membrane-bound enzyme complexes/ion transporters that combine ATP synthesis and/or hydrolysis with the transport of protons across a membrane. ATPases can harness the energy from a proton gradient, using the flux of ions across the membrane via the ATPase proton channel to drive the synthesis of ATP. Some ATPases work in reverse, using the energy from the hydrolysis of ATP to create a proton gradient. There are different types of ATPases, which can differ in function (ATP synthesis and/or hydrolysis), structure (F-, V- and A-ATPases contain rotary motors) and in the type of ions they transport , . F-ATPases (F1F0-ATPases) in mitochondria, chloroplasts and bacterial plasma membranes are the prime producers of ATP, using the proton gradient generated by oxidative phosphorylation (mitochondria) or photosynthesis (chloroplasts). V-ATPases (V1V0-ATPases) are primarily found in eukaryotic vacuoles, catalysing ATP hydrolysis to transport solutes and lower pH in organelles. A-ATPases (A1A0-ATPases) are found in Archaea and function like F-ATPases. P-ATPases (E1E2-ATPases) are found in bacteria and in eukaryotic plasma membranes and organelles, and function to transport a variety of different ions across membranes. E-ATPases are cell-surface enzymes that hydrolyse a range of NTPs, including extracellular ATP. F-ATPases (also known as F1F0-ATPase, or H(+)-transporting two-sector ATPase) (3.6.3.14 from EC) are composed of two linked complexes: the F1 ATPase complex is the catalytic core and is composed of 5 subunits (alpha, beta, gamma, delta, epsilon), while the F0 ATPase complex is the membrane-embedded proton channel that is composed of at least 3 subunits (A-C), nine in mitochondria (A-G, F6, F8). Both the F1 and F0 complexes are rotary motors that are coupled back-to-back. In the F1 complex, the central gamma subunit forms the rotor inside the cylinder made of the alpha(3)beta(3) subunits, while in the F0 complex, the ring-shaped C subunits forms the rotor. The two rotors rotate in opposite directions, but the F0 rotor is usually stronger, using the force from the proton gradient to push the F1 rotor in reverse in order to drive ATP synthesis . These ATPases can also work in reverse to hydrolyse ATP to create a proton gradient. This entry represents the alpha subunit found in the F1 complex of F-ATPases. In F-ATPases, there are three copies each of the alpha and beta subunits that form the catalytic core of the F1 complex, while the remaining F1 subunits (gamma, delta, epsilon) form part of the stalks. There is a substrate-binding site on each of the alpha and beta subunits, those on the beta subunits being catalytic, while those on the alpha subunits are regulatory. The alpha-subunit contains a highly conserved adenine-specific non-catalytic nucleotide-binding domain, with a conserved amino acid sequence of Gly-X-X-X-X-Gly-Lys. The alpha and beta subunits form a cylinder that is attached to the central stalk. The alpha/beta subunits undergo a sequence of conformational changes leading to the formation of ATP from ADP, which are induced by the rotation of the gamma subunit, itself is driven by the movement of protons through the F0 complex C subunit . More information about this protein can be found at Protein of the Month: ATP Synthases .; GO: 0016820 hydrolase activity acting on acid anhydrides catalyzing transmembrane movement of substances, 0015986 ATP synthesis coupled proton transport, 0016469 proton-transporting two-sector ATPase complex.
Probab=30.90 E-value=22 Score=15.64 Aligned_cols=49 Identities=22% Similarity=0.315 Sum_probs=29.7
Q ss_pred CHHHHHHHHHHHCCCCCCCC--CCCCCCCCCCCEEECCCCCCCE---EEEEEEEEECCCCCEEE
Q ss_conf 99999999998618765442--1222224433011034555650---58999998347780489
Q gi|254781049|r 75 SLKSVISDIREILGSTLITK--QTGPTGSRVNCVYVEDGADILR---ELYLSLLVDRTSGMVAF 133 (398)
Q Consensus 75 s~~ea~~~a~~ilg~~l~t~--qt~~~G~~v~~vLVEe~v~~~~---E~ylgi~~Dr~~~~~vi 133 (398)
....+...|--++.++-+.. |||-+ =|-.|+||+| ||++| ||++|+-.+
T Consensus 124 ~~~~~E~~APGv~~RkSV~ePlQTGIk-------AIDAliPIGRGQRELIIG---DRqTGKTav 177 (520)
T TIGR00962 124 EFRPIEKIAPGVIERKSVHEPLQTGIK-------AIDALIPIGRGQRELIIG---DRQTGKTAV 177 (520)
T ss_pred CCCCCCCCCCCEEECCCCCCCCHHHHH-------HHHCCCCCCCCCEEEEEC---CCCCCCCHH
T ss_conf 634321458855214667873000055-------764146898762223423---266673056
No 277
>COG0272 Lig NAD-dependent DNA ligase (contains BRCT domain type II) [DNA replication, recombination, and repair]
Probab=30.24 E-value=37 Score=14.15 Aligned_cols=35 Identities=11% Similarity=0.181 Sum_probs=28.7
Q ss_pred CHHHHHHHHHHCCCCCCC-CEEECCHHHHHHHHHHC
Q ss_conf 579999999986898888-15747999999999872
Q gi|254781049|r 4 HEYQAKALLRKYNVPVAK-GVVISSVHAAESAIKTL 38 (398)
Q Consensus 4 ~EyqaK~lL~~~GIpvp~-g~~a~s~~ea~~~a~~i 38 (398)
+.||.-+.|++.|+||.+ ..+|.+.+|..+..+.+
T Consensus 237 t~~e~l~~L~~~GF~v~~~~~~~~~~~ev~~~~~~~ 272 (667)
T COG0272 237 TQSERLAFLKAWGFPVNPYTRLCKNADEVLAFYEEW 272 (667)
T ss_pred CHHHHHHHHHHCCCCCCCHHHHCCCHHHHHHHHHHH
T ss_conf 799999999975999880766608999999999999
No 278
>COG2759 MIS1 Formyltetrahydrofolate synthetase [Nucleotide transport and metabolism]
Probab=30.16 E-value=37 Score=14.14 Aligned_cols=14 Identities=43% Similarity=0.821 Sum_probs=7.3
Q ss_pred HHHHHHHHHCCCCC
Q ss_conf 99999999658996
Q gi|254781049|r 280 MATMDIIKLYGGAP 293 (398)
Q Consensus 280 matmD~i~~~Gg~p 293 (398)
.||.-.++.+||-|
T Consensus 326 VATvRALK~hGG~~ 339 (554)
T COG2759 326 VATVRALKMHGGVP 339 (554)
T ss_pred EEEHHHHHHCCCCC
T ss_conf 61368998728988
No 279
>TIGR01418 PEP_synth phosphoenolpyruvate synthase; InterPro: IPR006319 This family represents phosphoenolpyruvate synthase; also called pyruvate,water dikinase and PEP synthase. The member from Methanococcus jannaschii contains a large intein. This enzyme generates phosphoenolpyruvate (PEP) from pyruvate, hydrolyzing ATP to AMP and releasing inorganic phosphate in the process. The enzyme shows extensive homology to other enzymes that use PEP as substrate or product. This enzyme may provide PEP for gluconeogenesis, for PTS-type carbohydrate transport systems, or for other processes. ; GO: 0008986 pyruvate water dikinase activity, 0006094 gluconeogenesis.
Probab=29.77 E-value=17 Score=16.35 Aligned_cols=95 Identities=21% Similarity=0.233 Sum_probs=47.9
Q ss_pred CCHHHHHHHHHHHHCCCCCCEEEECCCCCCHHHHHHHHHHHHCCCCCCEEEEE----------CCCCH----HH-HHHHH
Q ss_conf 50368999999996589962488427888989999999998619986589996----------35861----32-89999
Q gi|254781049|r 275 GAGLAMATMDIIKLYGGAPANFLDVGGGADQDKVAAAFKIITSDSSVKGILIN----------IFGGI----MR-CDVLV 339 (398)
Q Consensus 275 GaGlamatmD~i~~~Gg~pANFlD~gG~a~~e~~~~a~~~il~~~~vk~iliN----------ifGGI----~~-cd~vA 339 (398)
|=||+=.=+=+...-+-.|=-|+|+---.+.+ =.+--+++-..--|+.-||- ++-|- .. -|.+|
T Consensus 564 GVGLaR~EfII~~~i~~HP~aLi~~~d~~~~~-K~EI~el~dekGfvqfkliyhyanGrlanKL~aGY~~~~~~fv~kLa 642 (877)
T TIGR01418 564 GVGLARIEFIILNWIKIHPLALIDDDDLKEVE-KAEIEELMDEKGFVQFKLIYHYANGRLANKLAAGYANPRDFFVDKLA 642 (877)
T ss_pred CCHHHHHHHHHHHHHHHHHHHHCCCCCCCHHH-HHHHHHHHCCCCEEEEEEEEEECCCHHHHHHHCCCCCCHHHHHHHHH
T ss_conf 62278899999857765468745776877588-89998632057605667765420432667765045881257889999
Q ss_pred HHHHHHHHHCCCCCCEEEECCCCCHHHHHHHH
Q ss_conf 99999999729998799974898589999999
Q gi|254781049|r 340 KGILSAVKEVKINIPLVMRLEGANVDIGNRLI 371 (398)
Q Consensus 340 ~gii~a~~~~~~~~pivvRl~Gtn~~~g~~il 371 (398)
+||..-.... ...||+||++=--..|=++|+
T Consensus 643 eGia~vA~AF-YPkPV~VR~SDFKsNEY~~L~ 673 (877)
T TIGR01418 643 EGIAKVAAAF-YPKPVIVRTSDFKSNEYRNLI 673 (877)
T ss_pred HHHHHHHHHH-CCCCCEEEECCCCCHHHHHHC
T ss_conf 9999998753-889718981369836998716
No 280
>pfam01949 DUF99 Protein of unknown function DUF99. The function of this archaebacterial protein family is unknown.
Probab=29.00 E-value=39 Score=14.01 Aligned_cols=20 Identities=20% Similarity=0.458 Sum_probs=9.0
Q ss_pred CEEEECCCCCHHHHHHHHHH
Q ss_conf 79997489858999999997
Q gi|254781049|r 354 PLVMRLEGANVDIGNRLIAE 373 (398)
Q Consensus 354 pivvRl~Gtn~~~g~~il~~ 373 (398)
|+++|..|-+.+++.++++.
T Consensus 139 ~iyvq~~Gi~~~~A~~ii~~ 158 (185)
T pfam01949 139 PVYIQAAGIDPEEAKELIER 158 (185)
T ss_pred CEEEEECCCCHHHHHHHHHH
T ss_conf 69999869999999999999
No 281
>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=28.88 E-value=39 Score=14.00 Aligned_cols=14 Identities=14% Similarity=0.048 Sum_probs=8.1
Q ss_pred ECCHHHHHHHHHHH
Q ss_conf 58999999999986
Q gi|254781049|r 73 ESSLKSVISDIREI 86 (398)
Q Consensus 73 ~~s~~ea~~~a~~i 86 (398)
.+++.++.+-++++
T Consensus 422 ~~d~~~a~~la~~l 435 (705)
T TIGR00644 422 TDDPKQARELAEEL 435 (705)
T ss_pred HHHHHHHHHHHHHH
T ss_conf 30389999999999
No 282
>COG2379 GckA Putative glycerate kinase [Carbohydrate transport and metabolism]
Probab=28.85 E-value=17 Score=16.40 Aligned_cols=54 Identities=22% Similarity=0.290 Sum_probs=25.9
Q ss_pred CCEEEEEECCCCCCHHHHHHHCHHHHEEEECCCCCCCCHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHH
Q ss_conf 804899844788402455574831220332144457895788878875198889988599999999899
Q gi|254781049|r 129 GMVAFIASTQGGMDIEEVAKDYPQKIFKLLIDPLIGVTSEDVASLCDMLELQGQARIDGGDLFPNLYKA 197 (398)
Q Consensus 129 ~~~vii~S~~GGvdIE~va~~~p~~I~~~~id~~~gl~~~~~~~l~~~lg~~~~~~~~~~~ii~~L~~~ 197 (398)
...+++.|+ ||- .+. + -|..|++-.+...+-+.|=-+|..+..+..+=+.|+++
T Consensus 113 D~Vi~LISG-GGS-----------aL~--e-~P~eGitL~d~~avn~~LL~sGA~I~emNtVRkhLS~V 166 (422)
T COG2379 113 DLVIVLISG-GGS-----------ALL--E-LPAEGITLEDLIAVNRALLKSGAPISEMNTVRKHLSRV 166 (422)
T ss_pred CEEEEEEEC-CCH-----------HHC--C-CCCCCCCHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHC
T ss_conf 679999817-831-----------400--3-89667878999999999997599869999999988561
No 283
>TIGR01746 Thioester-redct thioester reductase domain; InterPro: IPR010080 This domain includes the C-terminal domain from the fungal alpha aminoadipate reductase enzyme (also known as aminoadipate semialdehyde dehydrogenase) which is involved in the biosynthesis of lysine , as well as the reductase-containing component of the myxochelin biosynthetic gene cluster, MxcG . The mechanism of reduction involves activation of the substrate by adenylation and transfer to a covalently-linked pantetheine cofactor as a thioester. This thioester is then reduced to give an aldehyde (thus releasing the product) and a regenerated pantetheine thiol ; in myxochelin biosynthesis this aldehyde is further reduced to an alcohol or converted to an amine by an aminotransferase. This is a fundamentally different reaction than beta-ketoreductase domains of polyketide synthases which act at a carbonyl two carbons removed from the thioester and forms an alcohol as a product. The majority of bacterial sequences containing this domain are non-ribosomal peptide synthetases in which this domain is similarly located proximal to a thiolation domain (IPR006163 from INTERPRO). In some cases this domain is found at the end of a polyketide synthetase enzyme, but is unlike ketoreductase domains which are found before the thiolase domains. Exceptions to this observed relationship with the thiolase domain include three proteins which consist of stand-alone reductase domains (from Mycobacterium leprae, Anabaena and from Streptomyces coelicolor) and one protein (from Nostoc) which contains N-terminal homology with a small group of hypothetical proteins but no evidence of a thiolation domain next to the putative reductase domain.; GO: 0004043 L-aminoadipate-semialdehyde dehydrogenase activity.
Probab=28.81 E-value=39 Score=13.99 Aligned_cols=62 Identities=13% Similarity=0.210 Sum_probs=29.4
Q ss_pred HHHHHHHHHHHHHHHHHCCCCC---CEEEECCC-----CCHHHHHHHHHH-CCCCEEEECCHHHHHHHHHH
Q ss_conf 1328999999999999729998---79997489-----858999999997-69958994998999999999
Q gi|254781049|r 332 IMRCDVLVKGILSAVKEVKINI---PLVMRLEG-----ANVDIGNRLIAE-SGLNVITAIDLDDAAQKIVH 393 (398)
Q Consensus 332 I~~cd~vA~gii~a~~~~~~~~---pivvRl~G-----tn~~~g~~il~~-~g~~~~~~~~~~~A~~~~v~ 393 (398)
.+.-|.+|+.|..-......+. -.+.-+.+ =..++=...+++ .|.++....+++|.-++.=+
T Consensus 257 ~~pVd~~a~ai~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~f~~~~~~~~G~~~~~~~~~~eW~~~l~~ 327 (405)
T TIGR01746 257 LTPVDYVARAIVALSSQPAAEAQAGGAVFHLVNPEPEPVSLDEFLEWLKRSAGYELKLLVSFDEWLQRLED 327 (405)
T ss_pred CCCHHHHHHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCCHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHH
T ss_conf 31099999999999987646432772178722899856578999999988618865342898999999986
No 284
>PRK02255 putrescine carbamoyltransferase; Provisional
Probab=28.77 E-value=39 Score=13.99 Aligned_cols=15 Identities=27% Similarity=0.301 Sum_probs=7.6
Q ss_pred HHHHHHHCCCCEEEE
Q ss_conf 999998729986999
Q gi|254781049|r 31 AESAIKTLPGPLYVV 45 (398)
Q Consensus 31 a~~~a~~ig~p~~Vv 45 (398)
-..++.++|+.+..+
T Consensus 61 FE~A~~~LGg~~i~l 75 (341)
T PRK02255 61 FETAMTQLGGHAQYL 75 (341)
T ss_pred HHHHHHHCCCCEEEC
T ss_conf 999999859979982
No 285
>COG0616 SppA Periplasmic serine proteases (ClpP class) [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]
Probab=28.75 E-value=39 Score=13.99 Aligned_cols=24 Identities=25% Similarity=0.252 Sum_probs=15.4
Q ss_pred CCCHHHHHHHHHHHHHHHHHHHHC
Q ss_conf 988899885999999998999955
Q gi|254781049|r 178 ELQGQARIDGGDLFPNLYKAFCDK 201 (398)
Q Consensus 178 g~~~~~~~~~~~ii~~L~~~f~e~ 201 (398)
.+..+....+...+...|+.|.+.
T Consensus 201 ~~t~e~~~~~q~~~~e~y~~F~~~ 224 (317)
T COG0616 201 PLTEEEREILQKEIDETYDEFVDK 224 (317)
T ss_pred CCCHHHHHHHHHHHHHHHHHHHHH
T ss_conf 369899999999999999999999
No 286
>TIGR01828 pyru_phos_dikin pyruvate, phosphate dikinase; InterPro: IPR010121 Pyruvate phosphate dikinase (PPDK, or pyruvate orthophosphate dikinase) is found in plants, bacteria and archaea. The amino acid sequence identity between bacterial and plant enzymes is high, and they are similar in sequence to other PEP-utilizing enzymes. PPDK catalyses the reversible conversion of ATP and pyruvate to AMP and PEP (phosphoenolpyruvate). In bacteria such as Clostridium symbiosum, PPDK uses Mg2+ and NH4+ ions as cofactors . The enzyme has three domains: the N- and C-terminal domains each have an active site centre that catalyses a different step in the reaction, and the middle domain has a carrier histidine residue that moves between the two active centres. In plants, PPDK is localised predominantly in chloroplast stroma where it catalyses the rate-limiting step in the C4 photosynthetic pathway, namely the synthesis of PEP, which acts as the primary CO2 acceptor in C4 photosynthesis . PPDK activity in C4 plants is strictly regulated by light, its activity decreasing in darkness. This response is regulated by phosphorylation and dephosphorylation of the enzyme using ADP; such regulation is not seen in the bacterial form of the enzyme. PPDK is also found in C3 plants, but it is not known to have a photosynthetic role .; GO: 0050242 pyruvate phosphate dikinase activity.
Probab=28.73 E-value=27 Score=15.07 Aligned_cols=46 Identities=26% Similarity=0.302 Sum_probs=29.2
Q ss_pred CEEECCCCEEEEECCCHHHHHHHHHHHHCCCCCCEEEECCCCCCHHHHHHHHHHHHC
Q ss_conf 644228817999555036899999999658996248842788898999999999861
Q gi|254781049|r 261 SYIALDGNIGCMVNGAGLAMATMDIIKLYGGAPANFLDVGGGADQDKVAAAFKIITS 317 (398)
Q Consensus 261 ~yv~LdG~Ig~~vnGaGlamatmD~i~~~Gg~pANFlD~gG~a~~e~~~~a~~~il~ 317 (398)
.||.+||.-|++-+|.=.. -+|.+=-|+-|.|..+.+.+|.+.||+
T Consensus 519 D~isiDGsTG~iYlGe~~~-----------~~p~~~~~f~G~Paedelvravd~im~ 564 (920)
T TIGR01828 519 DIISIDGSTGEIYLGEVPL-----------IEPEVSGDFEGEPAEDELVRAVDTIMS 564 (920)
T ss_pred EEEEEECCCCCEECCCCCC-----------CCCCCCCCCCCCCCHHHHHHHHHHHHH
T ss_conf 3799708606235375442-----------166778766787505789999999999
No 287
>PRK05309 30S ribosomal protein S11; Validated
Probab=28.52 E-value=39 Score=13.96 Aligned_cols=48 Identities=19% Similarity=0.298 Sum_probs=25.0
Q ss_pred HHHHHHHHHHHHHCCCC-CCEEEECCCCCHHHHHHHHHHCCCCEEEECC
Q ss_conf 99999999999972999-8799974898589999999976995899499
Q gi|254781049|r 336 DVLVKGILSAVKEVKIN-IPLVMRLEGANVDIGNRLIAESGLNVITAID 383 (398)
Q Consensus 336 d~vA~gii~a~~~~~~~-~pivvRl~Gtn~~~g~~il~~~g~~~~~~~~ 383 (398)
...|+-+.+-+++++++ +-|.+|=-|+..+-+.+-|..+|+.+....|
T Consensus 62 ~~aa~~~~~~~~~~Gi~~v~V~ikG~G~GR~~air~L~~~gikI~~I~D 110 (126)
T PRK05309 62 QVAAEDAAKKAKEHGMKTVEVFVKGPGSGRESAIRALQAAGLEVTSIKD 110 (126)
T ss_pred HHHHHHHHHHHHHCCCEEEEEEEECCCCCHHHHHHHHHHCCCEEEEEEE
T ss_conf 9999999999997297199999977883389999999878988999998
No 288
>COG1405 SUA7 Transcription initiation factor TFIIIB, Brf1 subunit/Transcription initiation factor TFIIB [Transcription]
Probab=28.42 E-value=25 Score=15.29 Aligned_cols=17 Identities=18% Similarity=0.260 Sum_probs=7.5
Q ss_pred HHHHHHHCCCCHHHHHH
Q ss_conf 88788751988899885
Q gi|254781049|r 170 VASLCDMLELQGQARID 186 (398)
Q Consensus 170 ~~~l~~~lg~~~~~~~~ 186 (398)
+..++..|+++....+.
T Consensus 104 l~~~~~~l~LP~~v~e~ 120 (285)
T COG1405 104 LERIASALGLPESVRET 120 (285)
T ss_pred HHHHHHHHCCCCHHHHH
T ss_conf 99999871898037999
No 289
>pfam02571 CbiJ Precorrin-6x reductase CbiJ/CobK. This family consists of Precorrin-6x reductase EC:1.3.1.54. This enzyme catalyses the reaction: precorrin-6Y + NADP(+) <= precorrin-6X + NADPH. CbiJ and CobK both catalyse the reduction of macocycle in the colbalmin biosynthesis pathway.
Probab=28.39 E-value=40 Score=13.95 Aligned_cols=62 Identities=13% Similarity=0.209 Sum_probs=38.5
Q ss_pred HCCCCCCEEEECCCCCCHHHHHHHHHHHHCCCCCCEEEEECCCCHHHHHHHHHHHHHHHHHCCCCCCEEEEC
Q ss_conf 658996248842788898999999999861998658999635861328999999999999729998799974
Q gi|254781049|r 288 LYGGAPANFLDVGGGADQDKVAAAFKIITSDSSVKGILINIFGGIMRCDVLVKGILSAVKEVKINIPLVMRL 359 (398)
Q Consensus 288 ~~Gg~pANFlD~gG~a~~e~~~~a~~~il~~~~vk~iliNifGGI~~cd~vA~gii~a~~~~~~~~pivvRl 359 (398)
..|..+.|+.-.-|--+.|.=. -++..-++.+++--==||- -.. .=++|.+++++.+ |++++
T Consensus 162 ~~g~~~~~iIa~~gPfs~e~n~----al~~~~~i~~lVtK~SG~~-g~~----~Ki~AA~~lgi~v-ivI~R 223 (246)
T pfam02571 162 ALGFPNAEIIAARGPFSLELER----ALLRRHGIDVLVTKNSGGA-GTY----AKLAAARELGLPV-IMIKR 223 (246)
T ss_pred CCCCCHHCEEEECCCCCHHHHH----HHHHHCCCCEEEEECCCCH-HHH----HHHHHHHHCCCEE-EEEEC
T ss_conf 4799800189904999989999----9999709999999288865-069----9999999849929-99958
No 290
>pfam04223 CitF Citrate lyase, alpha subunit (CitF). In citrate-utilising prokaryotes, citrate lyase EC:4.1.3.6 cleaves intracellular citrate into acetate and oxaloacetate, and is organized as a functional complex consisting of alpha, beta, and gamma subunits. The gamma subunit serves as an acyl carrier protein (ACP), and has a 2'-(5''-phosphoribosyl)-3'-dephospho-CoA prosthetic group. The citrate lyase is active only if this prosthetic group is acetylated; this acetylation is catalysed by an acetate:SH-citrate lyase ligase. The alpha subunit substitutes citryl for the acetyl group to form citryl-S-ACP. The beta subunit completes the reaction by cleaving the citryl to yield oxaloacetate and (regenerated) acetyl-S-ACP. This family represents the alpha subunit EC:2.8.3.10.
Probab=28.06 E-value=40 Score=13.91 Aligned_cols=66 Identities=20% Similarity=0.278 Sum_probs=48.0
Q ss_pred HHHHHHHCCC-CCCEEEECCCCCCHHHHHHHHHHHHCCCCCCEEEEECCCCHHH--HHHHHHHHHHHHHHC
Q ss_conf 9999996589-9624884278889899999999986199865899963586132--899999999999972
Q gi|254781049|r 282 TMDIIKLYGG-APANFLDVGGGADQDKVAAAFKIITSDSSVKGILINIFGGIMR--CDVLVKGILSAVKEV 349 (398)
Q Consensus 282 tmD~i~~~Gg-~pANFlD~gG~a~~e~~~~a~~~il~~~~vk~iliNifGGI~~--cd~vA~gii~a~~~~ 349 (398)
..+.|...|. +..=-+-.|-|-.+-.+.+.++-.+...++|+=|. .||||. ||..-+|+++++-+.
T Consensus 216 aa~vI~~sg~~kdGFSfQTGaGGaSLAv~~~l~~~M~~~~Ik~sFa--~GGIT~~~vdmleeGL~~~l~Dv 284 (466)
T pfam04223 216 AADVIVNSPYFKEGFSFQTGTGGASLAVTRFLREKMIRENIKASFA--LGGITATMVDLLEEGLVDKLLDV 284 (466)
T ss_pred HHHHHHHCCCCCCCEEEECCCCHHHHHHHHHHHHHHHHCCCEEEEE--CCCCHHHHHHHHHHHHHHHHHCC
T ss_conf 9999985776537636665888699999999999999759769988--77740999999871334634113
No 291
>PRK09466 metL bifunctional aspartate kinase II/homoserine dehydrogenase II; Provisional
Probab=27.56 E-value=41 Score=13.85 Aligned_cols=23 Identities=17% Similarity=0.205 Sum_probs=10.5
Q ss_pred CCEEEECCCC-------CCHHHHHHHHHHH
Q ss_conf 6248842788-------8989999999998
Q gi|254781049|r 293 PANFLDVGGG-------ADQDKVAAAFKII 315 (398)
Q Consensus 293 pANFlD~gG~-------a~~e~~~~a~~~i 315 (398)
.-|..-+|-+ -....+.+|++.+
T Consensus 419 nI~iiaqg~SEinIS~VI~~~d~~kAv~aL 448 (810)
T PRK09466 419 PVEFLWQSEDGLSLVAVLRQGPTESLIQGL 448 (810)
T ss_pred CCEEEEECCCCCEEEEEECHHHHHHHHHHH
T ss_conf 940899817885699997476699999999
No 292
>TIGR01091 upp uracil phosphoribosyltransferase; InterPro: IPR005765 The enzyme uracil phosphoribosyltransferase (UPRT, 2.4.2.9 from EC) catalyzes conversion of uracil to uridine 5'-monophosphate utilizing 5'-phosphoribosyl--1-pyrophosphate (PRPP). UMP + diphosphate = uracil + 5-phospho-alpha-D-ribose 1-diphosphate ; GO: 0004845 uracil phosphoribosyltransferase activity, 0006223 uracil salvage.
Probab=27.25 E-value=41 Score=13.82 Aligned_cols=33 Identities=24% Similarity=0.382 Sum_probs=18.2
Q ss_pred CCEEECC----CCEEE----EECCCHHHHHHHHHHHHCCCC
Q ss_conf 8644228----81799----955503689999999965899
Q gi|254781049|r 260 LSYIALD----GNIGC----MVNGAGLAMATMDIIKLYGGA 292 (398)
Q Consensus 260 l~yv~Ld----G~Ig~----~vnGaGlamatmD~i~~~Gg~ 292 (398)
.-|.||- ++.-+ |-.=+|..++|.|.++.+|-+
T Consensus 117 ~Yy~KLP~~~~~~~v~v~DPMLATGgt~~~a~~~lk~~g~~ 157 (213)
T TIGR01091 117 VYYSKLPEDIDERTVIVLDPMLATGGTMIAALDLLKKRGAK 157 (213)
T ss_pred ECCCCCCCCCCCCEEEEECCCCCCCHHHHHHHHHHHHCCCC
T ss_conf 32200543468886999728734305899999999853999
No 293
>cd03028 GRX_PICOT_like Glutaredoxin (GRX) family, PKC-interacting cousin of TRX (PICOT)-like subfamily; composed of PICOT and GRX-PICOT-like proteins. The non-PICOT members of this family contain only the GRX-like domain, whereas PICOT contains an N-terminal TRX-like domain followed by one to three GRX-like domains. It is interesting to note that PICOT from plants contain three repeats of the GRX-like domain, metazoan proteins (except for insect) have two repeats, while fungal sequences contain only one copy of the domain. PICOT is a protein that interacts with protein kinase C (PKC) theta, a calcium independent PKC isoform selectively expressed in skeletal muscle and T lymphocytes. PICOT inhibits the activation of c-Jun N-terminal kinase and the transcription factors, AP-1 and NF-kB, induced by PKC theta or T-cell activating stimuli. Both GRX and TRX domains of PICOT are required for its activity. Characterized non-PICOT members of this family include CXIP1, a CAX-interacting protein
Probab=27.12 E-value=42 Score=13.80 Aligned_cols=45 Identities=13% Similarity=0.200 Sum_probs=23.2
Q ss_pred HHHHHHHHHCCCCCCCCEEECCHHHHHHHHHHC-CCCEEEEECCCCCCCC
Q ss_conf 999999998689888815747999999999872-9986999712136876
Q gi|254781049|r 6 YQAKALLRKYNVPVAKGVVISSVHAAESAIKTL-PGPLYVVKSQIHAGGR 54 (398)
Q Consensus 6 yqaK~lL~~~GIpvp~g~~a~s~~ea~~~a~~i-g~p~~VvKaQV~aGgR 54 (398)
..||+||.++|++.-..-+-.++ +......++ +.|- | +||-.+|.
T Consensus 27 ~~a~~lL~~~~v~~~~~dv~~d~-~~r~~l~~~s~~~T-v--Pqifi~g~ 72 (90)
T cd03028 27 RKVVQILNQLGVDFGTFDILEDE-EVRQGLKEYSNWPT-F--PQLYVNGE 72 (90)
T ss_pred HHHHHHHHHHCCCCEECCHHCCH-HHHHHHHHHCCCCC-C--CCEEECCE
T ss_conf 99999999968997413300589-99999999716898-8--83779998
No 294
>PRK09429 mepA penicillin-insensitive murein endopeptidase; Reviewed
Probab=26.94 E-value=42 Score=13.78 Aligned_cols=54 Identities=24% Similarity=0.346 Sum_probs=31.1
Q ss_pred HHHHHHHHHHHHCCCCCCEEEEECCCCHH--HHHHHHHHHHHHHHHCC----CCCCEEEECCC
Q ss_conf 89999999998619986589996358613--28999999999999729----99879997489
Q gi|254781049|r 305 QDKVAAAFKIITSDSSVKGILINIFGGIM--RCDVLVKGILSAVKEVK----INIPLVMRLEG 361 (398)
Q Consensus 305 ~e~~~~a~~~il~~~~vk~iliNifGGI~--~cd~vA~gii~a~~~~~----~~~pivvRl~G 361 (398)
..+-.+.+++-.+||+|.-|||| -+|- -|++ |.|=-.-+..+. -+--+-|||.=
T Consensus 153 t~~h~~li~~AA~dp~V~RIFVn--p~IK~~lC~~-~~~DR~WL~KvRPw~GH~~HfHVRL~C 212 (270)
T PRK09429 153 TPQHASLIKLAAQDPRVTRIFVN--PAIKKQLCRT-AGGDRSWLRKVRPWWGHDYHFHVRLRC 212 (270)
T ss_pred CHHHHHHHHHHHCCCCEEEEEEC--HHHHHHHHHH-CCCCHHHHHCCCCCCCCCCEEEEEEEC
T ss_conf 68999999998448652477646--8988999870-024177886568535766414788527
No 295
>cd04258 AAK_AKiii-LysC-EC AAK_AKiii-LysC-EC: Amino Acid Kinase Superfamily (AAK), AKiii-LysC-EC: this CD includes the N-terminal catalytic aspartokinase (AK) domain of the lysine-sensitive aspartokinase isoenzyme AKIII. AKIII is a monofunctional class enzyme (LysC) found in some bacteria such as E. coli. Aspartokinase is the first enzyme in the aspartate metabolic pathway and catalyzes the conversion of aspartate and ATP to aspartylphosphate and ADP. In E. coli, LysC is reported to be a homodimer of 50 kD subunits.
Probab=26.74 E-value=42 Score=13.76 Aligned_cols=41 Identities=17% Similarity=0.035 Sum_probs=25.5
Q ss_pred EEECCCCEEEEECCCHHHHHHHHHHHHCCCCCCEEEECCCC
Q ss_conf 44228817999555036899999999658996248842788
Q gi|254781049|r 262 YIALDGNIGCMVNGAGLAMATMDIIKLYGGAPANFLDVGGG 302 (398)
Q Consensus 262 yv~LdG~Ig~~vnGaGlamatmD~i~~~Gg~pANFlD~gG~ 302 (398)
-..-+|.+-++.-|+-=--||+=.....--+.-++-|+-|=
T Consensus 188 g~~~~G~~ttLGRGGSDyTA~~la~~l~A~~v~iwtDV~Gi 228 (292)
T cd04258 188 GSTEKGRTTTLGRGGSDYSAALLAEALHAEELQIWTDVAGI 228 (292)
T ss_pred EECCCCCEEECCCCCCHHHHHHHHHHCCCCEEEEEECCCCC
T ss_conf 43799977753789616899999997699889999678878
No 296
>PRK12861 malic enzyme; Reviewed
Probab=26.51 E-value=43 Score=13.73 Aligned_cols=38 Identities=18% Similarity=0.274 Sum_probs=14.4
Q ss_pred HHHHHHHHHHCCCCC-CEEEECC-----CCCCHHHHHHHHHHHH
Q ss_conf 899999999658996-2488427-----8889899999999986
Q gi|254781049|r 279 AMATMDIIKLYGGAP-ANFLDVG-----GGADQDKVAAAFKIIT 316 (398)
Q Consensus 279 amatmD~i~~~Gg~p-ANFlD~g-----G~a~~e~~~~a~~~il 316 (398)
|..|-+.++.+|-+| .-||-++ -+++.++|.+|.+++-
T Consensus 617 Ai~aA~~ar~fGiePRVAmLSfSnFGS~~~~~~~KVreAveil~ 660 (762)
T PRK12861 617 TIAAARQMEWLNLTPKVALLSRSNFGSGSAASGVKMRRALEIVR 660 (762)
T ss_pred HHHHHHHHHHCCCCCCEEEEECCCCCCCCCCCHHHHHHHHHHHH
T ss_conf 99999999983999738998057899999971579999999999
No 297
>TIGR00575 dnlj DNA ligase, NAD-dependent; InterPro: IPR001679 DNA ligase (polydeoxyribonucleotide synthase) is the enzyme that joins two DNA fragments by catalyzing the formation of an internucleotide ester bond between phosphate and deoxyribose. It is active during DNA replication, DNA repair and DNA recombination. There are two forms of DNA ligase: one requires ATP (6.5.1.1 from EC), the other NAD (6.5.1.2 from EC). This family is predominantly composed of NAD-dependent bacterial DNA ligases. They are proteins of about 75 to 85 Kd whose sequence is well conserved , . They also show similarity to yicF, an Escherichia coli hypothetical protein of 63 Kd.; GO: 0003911 DNA ligase (NAD+) activity, 0006260 DNA replication, 0006281 DNA repair.
Probab=25.94 E-value=44 Score=13.66 Aligned_cols=36 Identities=22% Similarity=0.350 Sum_probs=29.9
Q ss_pred CCHHHHHHHHHHCCCC-CCCCE-EEC--CHHHHHHHHHHC
Q ss_conf 6579999999986898-88815-747--999999999872
Q gi|254781049|r 3 IHEYQAKALLRKYNVP-VAKGV-VIS--SVHAAESAIKTL 38 (398)
Q Consensus 3 L~EyqaK~lL~~~GIp-vp~g~-~a~--s~~ea~~~a~~i 38 (398)
-+.||+-++|++.|+| |-+.. .|. +.+|..+..+++
T Consensus 240 ~t~~~~L~~L~~~GF~TV~~~~~~~~ln~~~eV~~~~~~~ 279 (706)
T TIGR00575 240 RTQYEALAWLKKLGFPTVNPHIRLCKLNSIEEVLEYYEEI 279 (706)
T ss_pred CCHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHHH
T ss_conf 7789999999863884201257763038988999999999
No 298
>TIGR00416 sms DNA repair protein RadA; InterPro: IPR004504 RadA/Sms is a highly conserved eubacterial protein that shares sequence similarity with both RecA strand transferase and lon protease. The RadA/Sms family are probable ATP-dependent proteases involved in both DNA repair and degradation of proteins, peptides, glycopeptides. They are classified in as non-peptidase homologues and unassigned peptidases in MEROPS peptidase family S16 (lon protease family, clan SJ). RadA/Sms is involved in recombination and recombinational repair, most likely involving the stabilisation or processing of branched DNA molecules or blocked replication forks because of its genetic redundancy with RecG and RuvABC .; GO: 0003684 damaged DNA binding, 0005524 ATP binding, 0006281 DNA repair.
Probab=25.81 E-value=44 Score=13.65 Aligned_cols=163 Identities=17% Similarity=0.353 Sum_probs=78.0
Q ss_pred HHHHHHHHHHHHHHHHHHCCCCCCCCCEEEECCCCCE-------EEEEEEEEECCCHHHHHHHHHHHHCCCCCCHHHH--
Q ss_conf 9885999999998999955975102326799059967-------9940013215735564102786310001562224--
Q gi|254781049|r 183 ARIDGGDLFPNLYKAFCDKDMSLLEINPLIIMKNGRL-------RVLDSKISFDDNALYRHLDIQELRDVSEEDSREI-- 253 (398)
Q Consensus 183 ~~~~~~~ii~~L~~~f~e~Da~liEINPLvvt~dg~v-------vAlDAKi~iDDnA~fR~~~~~~~~d~~~~~~~E~-- 253 (398)
-..|+-++-.-|-|+-...+..++=|= =||+||.+ .++|+.+-||-++.-+|.=|-..+. +--...|+
T Consensus 219 SVsQVRE~t~~Lmr~AKt~~iaifiVG--HVTKeGsiAGPkvLEH~vD~vLyfeGd~~~~~R~LRS~KN-RFGat~E~G~ 295 (481)
T TIGR00416 219 SVSQVRECTAELMRLAKTRGIAIFIVG--HVTKEGSIAGPKVLEHMVDTVLYFEGDRDSRFRILRSVKN-RFGATNEIGI 295 (481)
T ss_pred CHHHHHHHHHHHHHHHHHCCCCEEEEE--EECCCCCCCCCHHHHHHHHHHEECCCCCCCCCCHHHCCCC-CCCCCCCCCC
T ss_conf 423888999999876521686579970--0435675434046663433110115887534440100015-6787342101
Q ss_pred -HHHHCCCCEEE-------------CCCC-EEEEECCCHHHHHHHHHHHHCC--CCC---CEEEECCCCCCHHHHHHHHH
Q ss_conf -57753986442-------------2881-7999555036899999999658--996---24884278889899999999
Q gi|254781049|r 254 -EAKQHNLSYIA-------------LDGN-IGCMVNGAGLAMATMDIIKLYG--GAP---ANFLDVGGGADQDKVAAAFK 313 (398)
Q Consensus 254 -~A~~~~l~yv~-------------LdG~-Ig~~vnGaGlamatmD~i~~~G--g~p---ANFlD~gG~a~~e~~~~a~~ 313 (398)
+.++.||.=|+ ..|. |-+..-|.=-=+.=+-++..+- ++| ||=+ +.-|+.--+=
T Consensus 296 FeM~e~GL~ev~nPS~iFL~~~~e~~~GSsitv~~EGtRPLlvEiQALVs~~s~anPrR~A~G~------d~NRL~~LlA 369 (481)
T TIGR00416 296 FEMTEQGLREVLNPSAIFLSRREEVMSGSSITVALEGTRPLLVEIQALVSPTSFANPRRVATGL------DQNRLALLLA 369 (481)
T ss_pred CCCCHHHHHHHHHHHHHHCCCCCCCCCCCCEEEEECCCHHHHHHHHHHCCCCCCCCCCCEECCH------HHHHHHHHHH
T ss_conf 0000233564531456641576456667301234237348888887522614368863100442------2568999999
Q ss_pred HH-------HCCCCCCEEEEECCCCH----HHHHH-HHHHHHHHHHHCCCCCCEEE
Q ss_conf 98-------61998658999635861----32899-99999999997299987999
Q gi|254781049|r 314 II-------TSDSSVKGILINIFGGI----MRCDV-LVKGILSAVKEVKINIPLVM 357 (398)
Q Consensus 314 ~i-------l~~~~vk~iliNifGGI----~~cd~-vA~gii~a~~~~~~~~pivv 357 (398)
++ |++.. +|||+-||+ +.||. ++-.|+-.+++..++-..++
T Consensus 370 vLek~~Gl~l~~~D---vf~~V~GGvkv~Epa~DLA~~~a~~SSFrdr~~~~~~~~ 422 (481)
T TIGR00416 370 VLEKRLGLPLADQD---VFLNVAGGVKVSEPAVDLALLIALVSSFRDRPLDPDLVI 422 (481)
T ss_pred HHHHHCCCCHHHCC---EEEEEECCEEECCHHHHHHHHHHHHHHHCCCCCCCCEEE
T ss_conf 98764066111173---479862350541057889999999987517887856388
No 299
>PRK09902 hypothetical protein; Provisional
Probab=25.72 E-value=40 Score=13.91 Aligned_cols=17 Identities=6% Similarity=-0.087 Sum_probs=5.8
Q ss_pred HHHHHHHHHHHHHHCCC
Q ss_conf 99999999899995597
Q gi|254781049|r 187 GGDLFPNLYKAFCDKDM 203 (398)
Q Consensus 187 ~~~ii~~L~~~f~e~Da 203 (398)
++.++.+|-..=....|
T Consensus 137 ~a~~l~rlH~~~~qHgc 153 (216)
T PRK09902 137 VALAFKKMHSVNRQHGC 153 (216)
T ss_pred HHHHHHHHHHCCCCCCC
T ss_conf 99999999867833467
No 300
>pfam00730 HhH-GPD HhH-GPD superfamily base excision DNA repair protein. This family contains a diverse range of structurally related DNA repair proteins. The superfamily is called the HhH-GPD family after its hallmark Helix-hairpin-helix and Gly/Pro rich loop followed by a conserved aspartate. This includes endonuclease III, EC:4.2.99.18 and MutY an A/G-specific adenine glycosylase, both have a C terminal 4Fe-4S cluster. The family also includes 8-oxoguanine DNA glycosylases. The methyl-CPG binding protein MBD4 also contains a related domain that is a thymine DNA glycosylase. The family also includes DNA-3-methyladenine glycosylase II EC:3.2.2.21 and other members of the AlkA family.
Probab=25.71 E-value=42 Score=13.75 Aligned_cols=35 Identities=20% Similarity=0.243 Sum_probs=24.9
Q ss_pred HHHHHHHCCCCCCCCEEECCHHHHHHHHHHCCCCE
Q ss_conf 99999986898888157479999999998729986
Q gi|254781049|r 8 AKALLRKYNVPVAKGVVISSVHAAESAIKTLPGPL 42 (398)
Q Consensus 8 aK~lL~~~GIpvp~g~~a~s~~ea~~~a~~ig~p~ 42 (398)
.++|++.||-|.|+.....++++..++.+.+|++.
T Consensus 18 ~~rl~~~~~~pt~~~l~~~~~~~l~~~i~~~G~~~ 52 (144)
T pfam00730 18 TKRLFERYGFPTPEDLAEADEEELRELIKGLGFYR 52 (144)
T ss_pred HHHHHHHHCCCCHHHHHCCCHHHHHHHHHCCCCHH
T ss_conf 99999982898999998599999999987089769
No 301
>pfam06714 Gp5_OB Gp5 N-terminal OB domain. This domain is found at the N terminus of the Gp5 baseplate protein of bacteriophage T4. This domain binds to the Gp27 protein. This domain has the common OB fold.
Probab=24.64 E-value=46 Score=13.51 Aligned_cols=28 Identities=11% Similarity=0.124 Sum_probs=23.0
Q ss_pred EEEEEEEEECCCCCEEEEEECCCCCCHHH
Q ss_conf 58999998347780489984478840245
Q gi|254781049|r 117 ELYLSLLVDRTSGMVAFIASTQGGMDIEE 145 (398)
Q Consensus 117 E~ylgi~~Dr~~~~~vii~S~~GGvdIE~ 145 (398)
-+.+|+.+|.....|++|+| .+|+-.|.
T Consensus 48 swV~GFF~D~~~Q~PvImGt-lpG~P~e~ 75 (144)
T pfam06714 48 THVYGFFLDKWYQNGVILGT-YPGIYKEK 75 (144)
T ss_pred CEEEEEEECCCCCCCEEEEC-CCCCCCCC
T ss_conf 88999887821367768860-79975667
No 302
>TIGR02181 GRX_bact glutaredoxin 3; InterPro: IPR011900 Glutaredoxins , , , also known as thioltransferases (disulphide reductases, are small proteins of approximately one hundred amino-acid residues which utilise glutathione and NADPH as cofactors. Oxidized glutathione is regenerated by glutathione reductase. Together these components compose the glutathione system . Glutaredoxin functions as an electron carrier in the glutathione-dependent synthesis of deoxyribonucleotides by the enzyme ribonucleotide reductase. Like thioredoxin, which functions in a similar way, glutaredoxin possesses an active centre disulphide bond . It exists in either a reduced or an oxidized form where the two cysteine residues are linked in an intramolecular disulphide bond. Glutaredoxin has been sequenced in a variety of species. On the basis of extensive sequence similarity, it has been proposed that Vaccinia virus protein O2L is most probably a glutaredoxin. Finally, it must be noted that Bacteriophage T4 thioredoxin seems also to be evolutionary related. In position 5 of the pattern T4 thioredoxin has Val instead of Pro. This family of glutaredoxins includes the E. coli protein GrxC (Grx3) which appears to have a secondary role in reducing ribonucleotide reductase (in the absence of GrxA) possibly indicating a role in the reduction of other protein disulphides .; GO: 0006118 electron transport, 0045454 cell redox homeostasis.
Probab=24.46 E-value=47 Score=13.48 Aligned_cols=44 Identities=27% Similarity=0.240 Sum_probs=31.2
Q ss_pred HHHHHHHHCCC-CCCCCEEECCH-HHHHHHHHHCCCCEEEEECCCCCC
Q ss_conf 99999998689-88881574799-999999987299869997121368
Q gi|254781049|r 7 QAKALLRKYNV-PVAKGVVISSV-HAAESAIKTLPGPLYVVKSQIHAG 52 (398)
Q Consensus 7 qaK~lL~~~GI-pvp~g~~a~s~-~ea~~~a~~ig~p~~VvKaQV~aG 52 (398)
.||.||++-|| ..-+-.+-.++ ..-.+-.+.=++-.-| +||=.|
T Consensus 14 rAK~LL~~kGv~~~~Ei~vd~dpD~~r~eM~~Rs~Gr~TV--PQIFIg 59 (82)
T TIGR02181 14 RAKALLESKGVGTFTEIRVDGDPDALRDEMMQRSGGRRTV--PQIFIG 59 (82)
T ss_pred HHHHHHHHCCCCCCEEEECCCCCCHHHHHHHHHHCCCCCC--CEEEEC
T ss_conf 8899998569886303445798106889999982899404--337629
No 303
>PRK00766 hypothetical protein; Provisional
Probab=24.36 E-value=47 Score=13.47 Aligned_cols=21 Identities=14% Similarity=0.275 Sum_probs=10.4
Q ss_pred CEEEECCCCCHHHHHHHHHHC
Q ss_conf 799974898589999999976
Q gi|254781049|r 354 PLVMRLEGANVDIGNRLIAES 374 (398)
Q Consensus 354 pivvRl~Gtn~~~g~~il~~~ 374 (398)
++++|..|-+.+++.++++..
T Consensus 146 ~iyvq~~Gi~~~~A~~ii~~~ 166 (194)
T PRK00766 146 NLYIQAAGIEPETAAEVIRVT 166 (194)
T ss_pred CEEEEECCCCHHHHHHHHHHH
T ss_conf 279998599999999999997
No 304
>cd05147 RIO1_euk RIO kinase family; eukaryotic RIO1, catalytic domain. The RIO kinase catalytic domain family is part of a larger superfamily, that includes the catalytic domains of other kinases such as the typical serine/threonine/tyrosine protein kinases (PKs), aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase (PI3K). RIO kinases are atypical protein serine kinases containing a kinase catalytic signature, but otherwise show very little sequence similarity to typical PKs. Serine kinases catalyze the transfer of the gamma-phosphoryl group from ATP to serine residues in protein substrates. The RIO catalytic domain is truncated compared to the catalytic domains of typical PKs, with deletions of the loops responsible for substrate binding. RIO1 is present in archaea, bacteria and eukaryotes. This subfamily is composed of RIO1 proteins from eukaryotes. RIO1 is essential for survival and is required for 18S rRNA processing, proper cell cycle progression and c
Probab=24.14 E-value=47 Score=13.45 Aligned_cols=36 Identities=22% Similarity=0.264 Sum_probs=19.6
Q ss_pred HHHHHHHHHHHHHHC---CCCCCCCCEEEECCCCCEEEEEE
Q ss_conf 999999998999955---97510232679905996799400
Q gi|254781049|r 187 GGDLFPNLYKAFCDK---DMSLLEINPLIIMKNGRLRVLDS 224 (398)
Q Consensus 187 ~~~ii~~L~~~f~e~---Da~liEINPLvvt~dg~vvAlDA 224 (398)
+.+++..+.++|.+. ..+|=|-|=|+ .+++++..|-
T Consensus 123 ~~~il~~~~~ly~~~~lVHGDLSEyNIl~--~~~~~~iID~ 161 (190)
T cd05147 123 YLQVIQIMRILYQDCRLVHADLSEYNLLY--HDGKLYIIDV 161 (190)
T ss_pred HHHHHHHHHHHHHHCCCEECCCCHHHEEE--CCCCEEEEEC
T ss_conf 99999999999997493224531542052--4899899966
No 305
>TIGR00593 pola DNA polymerase I; InterPro: IPR002298 DNA carries the biological information that instructs cells how to exist in an ordered fashion. Accurate replication is thus one of the most important events in the cell life cycle. This function is mediated by DNA-directed DNA polymerases, which add nucleotide triphosphate (dNTP) residues to the 5'-end of the growing DNA chain, using a complementary DNA as template. Small RNA molecules are generally used as primers for chain elongation, although terminal proteins may also be used. DNA-dependent DNA polymerases have been grouped into families, denoted A, B and X, on the basis of sequence similarities , . Members of family A, which includes bacterial and bacteriophage polymerases, share significant similarity to Escherichia coli polymerase I; hence family A is also known as the pol I family. The bacterial polymerases also contain an exonuclease activity, which is coded for in the N-terminal portion. Three motifs, A, B and C , are seen to be conserved across all DNA polymerases, with motifs A and C also seen in RNA polymerases. They are centred on invariant residues, and their structural significance was implied from the Klenow (E. coli) structure. Motif A contains a strictly-conserved aspartate at the junction of a beta-strand and an alpha-helix; motif B contains an alpha-helix with positive charges; and motif C has a doublet of negative charges, located in a beta-turn-beta secondary structure .; GO: 0003677 DNA binding, 0003887 DNA-directed DNA polymerase activity, 0006260 DNA replication.
Probab=23.52 E-value=48 Score=13.37 Aligned_cols=39 Identities=15% Similarity=0.243 Sum_probs=20.3
Q ss_pred HHHHHHHCCCCCCC--CEEECCH-HHHHHHHHHCCCCEEEEE
Q ss_conf 99999986898888--1574799-999999987299869997
Q gi|254781049|r 8 AKALLRKYNVPVAK--GVVISSV-HAAESAIKTLPGPLYVVK 46 (398)
Q Consensus 8 aK~lL~~~GIpvp~--g~~a~s~-~ea~~~a~~ig~p~~VvK 46 (398)
.|++|.++|||+-+ |+=|++. --..+.+..-||.+.+|-
T Consensus 92 i~e~l~algi~~~e~~GYEADD~IaTLA~~a~~~G~~V~I~s 133 (1005)
T TIGR00593 92 IKELLEALGIPILEVEGYEADDVIATLAKQAEKEGYEVRIIS 133 (1005)
T ss_pred HHHHHHHCCCEEEECCCCCHHHHHHHHHHHHHHCCCEEEEEE
T ss_conf 999999719818822887101289998887754685489983
No 306
>pfam04414 tRNA_deacylase D-aminoacyl-tRNA deacylase. Several aminoacyl-tRNA synthetases have the ability to transfer the D-isomer of their amino acid onto their cognate tRNA. D-aminoacyl-tRNA deacylases hydrolyse the ester bond between the polynucleotide and the D-amino acid, thereby preventing the accumulation of such mis-acylated and metabolically inactive tRNA molecules.
Probab=22.94 E-value=50 Score=13.30 Aligned_cols=38 Identities=18% Similarity=0.229 Sum_probs=16.8
Q ss_pred HHHHHHHHCCCCCCEEEECCCCC---HHHHHHHHHHCCCCEE
Q ss_conf 99999997299987999748985---8999999997699589
Q gi|254781049|r 341 GILSAVKEVKINIPLVMRLEGAN---VDIGNRLIAESGLNVI 379 (398)
Q Consensus 341 gii~a~~~~~~~~pivvRl~Gtn---~~~g~~il~~~g~~~~ 379 (398)
-|.+|++...... +++-..|.+ -+.-.++|++.|+++.
T Consensus 172 ~l~~a~~~s~~~~-a~iD~Ks~kg~~r~~i~~~l~~~gi~v~ 212 (214)
T pfam04414 172 VIRQAIEKSGADA-AIIDRKSLKSEDRSRITEFLEELGLEVI 212 (214)
T ss_pred HHHHHHHHCCCCE-EEEECCCCCHHHHHHHHHHHHHCCCCEE
T ss_conf 9999998389968-9997577977899999999998699210
No 307
>TIGR02665 molyb_mobA molybdopterin-guanine dinucleotide biosynthesis protein A; InterPro: IPR013482 In many molybdopterin-containing enzymes, including nitrate reductase and dimethylsulphoxide reductase, the cofactor is molybdopterin-guanine dinucleotide. This entry describes proteobacterial MobA (molybdopterin-guanine dinucleotide biosynthesis protein A). MobA synthesises molybdopterin-guanine dinucleotide from molybdopterin and GTP. ; GO: 0003824 catalytic activity, 0006777 Mo-molybdopterin cofactor biosynthetic process.
Probab=22.85 E-value=45 Score=13.61 Aligned_cols=120 Identities=21% Similarity=0.278 Sum_probs=62.6
Q ss_pred CCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCEEECCCCCCCE--EEEE--EEE
Q ss_conf 213687656565567777777079958999999999986187654421222224433011034555650--5899--999
Q gi|254781049|r 48 QIHAGGRGKGRFKELPADSKGGVRVESSLKSVISDIREILGSTLITKQTGPTGSRVNCVYVEDGADILR--ELYL--SLL 123 (398)
Q Consensus 48 QV~aGgRGKa~~~~~hk~~~GGV~l~~s~~ea~~~a~~ilg~~l~t~qt~~~G~~v~~vLVEe~v~~~~--E~yl--gi~ 123 (398)
=|||||||- =|...|+|.|-+.. .-+.+..-+.+ ++| |..|+|.-=-+.++ .+.+ -++
T Consensus 4 viLAGG~ar----RMGG~DKGL~~L~g--~PL~~hv~~rL-----~PQ-------v~~~~IsANRn~~~Y~~~g~Gl~V~ 65 (202)
T TIGR02665 4 VILAGGRAR----RMGGRDKGLVELGG--KPLIEHVLARL-----RPQ-------VSDLAISANRNPERYAQAGFGLPVV 65 (202)
T ss_pred EEECCCCCC----CCCCCCCCCEECCC--CCHHHHHHHHH-----CCC-------HHHHHHHCCCCHHHHHHHCCCCEEC
T ss_conf 676587400----26888866101286--52899999984-----350-------7666741388977898860897312
Q ss_pred EEC---CCCCEEEEEECCCCCCHHHHHH---HCHHHHEEEECC-CCCCCCHHHHHHHHHHCCCCHHHHHHHHHHHHHHHH
Q ss_conf 834---7780489984478840245557---483122033214-445789578887887519888998859999999989
Q gi|254781049|r 124 VDR---TSGMVAFIASTQGGMDIEEVAK---DYPQKIFKLLID-PLIGVTSEDVASLCDMLELQGQARIDGGDLFPNLYK 196 (398)
Q Consensus 124 ~Dr---~~~~~vii~S~~GGvdIE~va~---~~p~~I~~~~id-~~~gl~~~~~~~l~~~lg~~~~~~~~~~~ii~~L~~ 196 (398)
-|. ..+.+ .+..||.-=-.+- ..-+-+...|-| |+ ++ .+++.+|+.
T Consensus 66 ~D~~DA~~~F~----GPLAGilagL~~a~~~~~~~~vl~~PCD~P~----------------lP-------~dLv~RL~~ 118 (202)
T TIGR02665 66 PDDVDALADFP----GPLAGILAGLRWAVAGTGTDWVLTVPCDTPF----------------LP-------EDLVARLAA 118 (202)
T ss_pred CCCCCCCCCCC----CCHHHHHHHHHHHHHCCCCCEEEEECCCCCC----------------CC-------HHHHHHHHH
T ss_conf 78534357888----8768999999999844699828882288899----------------88-------789999999
Q ss_pred HHHHCCCCCCCCCEEEE--CCCCC
Q ss_conf 99955975102326799--05996
Q gi|254781049|r 197 AFCDKDMSLLEINPLII--MKNGR 218 (398)
Q Consensus 197 ~f~e~Da~liEINPLvv--t~dg~ 218 (398)
.....+ +++++ -.||.
T Consensus 119 a~~~~~------a~iavATA~~G~ 136 (202)
T TIGR02665 119 ALEAQD------ADIAVATAHDGG 136 (202)
T ss_pred HHHCCC------CCEEEEECCCCC
T ss_conf 975289------978998704488
No 308
>TIGR02291 rimK_rel_E_lig alpha-L-glutamate ligase homolog; InterPro: IPR011758 Members of this protein family contain a region of homology to the RimK family of alpha-L-glutamate ligases (IPR004666 from INTERPRO), various members of which modify the Glu-Glu C-terminus of ribosomal protein S6, or tetrahydromethanopterin, or a form of coenzyme F420 derivative. Members of this family are found so far in various Vibrio and Pseudomonas species and some other gamma and beta Proteobacteria. The function is unknown..
Probab=22.78 E-value=50 Score=13.28 Aligned_cols=99 Identities=18% Similarity=0.145 Sum_probs=59.6
Q ss_pred HHHHHHHHCCCCCCCCE-EECCHHHHHHHHHHC-CCCEEEEECCCCCCCCCCCCCCCCCCCC-----CCEEEEECCHHHH
Q ss_conf 99999998689888815-747999999999872-9986999712136876565655677777-----7707995899999
Q gi|254781049|r 7 QAKALLRKYNVPVAKGV-VISSVHAAESAIKTL-PGPLYVVKSQIHAGGRGKGRFKELPADS-----KGGVRVESSLKSV 79 (398)
Q Consensus 7 qaK~lL~~~GIpvp~g~-~a~s~~ea~~~a~~i-g~p~~VvKaQV~aGgRGKa~~~~~hk~~-----~GGV~l~~s~~ea 79 (398)
..|.+=.+.||.||.=. ++++-.|....-+=+ +.|-+|+|+--=|||.|-. .++.+-+ .-|- .-|.+|+
T Consensus 40 ~TK~~A~AaGi~VPelyGVI~~q~ev~~~~~ivkdh~dFVIKPAqGsGG~GIl--Vit~r~~~ryr~~sG~--~i~~eei 115 (320)
T TIGR02291 40 KTKILAIAAGIAVPELYGVIEIQKEVKSLDDIVKDHEDFVIKPAQGSGGDGIL--VITDRLDERYRKSSGA--LISKEEI 115 (320)
T ss_pred HHHHHHHHCCCCCCHHCCCCCCHHHHHHHHHHHCCCCCCEEECCCCCCCCEEE--EECCCCCCCEECCCCC--CCCHHHH
T ss_conf 78899873367110130100234665434666278898367266067987279--9703668840354101--0154567
Q ss_pred HHHHHHHCCCCCCCCCCCCCCCCCCCEEECCCCCCC
Q ss_conf 999998618765442122222443301103455565
Q gi|254781049|r 80 ISDIREILGSTLITKQTGPTGSRVNCVYVEDGADIL 115 (398)
Q Consensus 80 ~~~a~~ilg~~l~t~qt~~~G~~v~~vLVEe~v~~~ 115 (398)
+....++|.=- -.--|++ ..=|||-.+..+
T Consensus 116 E~hvSniL~GL-----ySLGG~~-D~AliEyrvkfD 145 (320)
T TIGR02291 116 ERHVSNILAGL-----YSLGGKR-DRALIEYRVKFD 145 (320)
T ss_pred HHHHHHHHHHH-----HHCCCCC-CEEEEEEECCCC
T ss_conf 78888888777-----6507997-736885320105
No 309
>pfam01163 RIO1 RIO1 family. This is a family of atypical serine kinases which are found in archaea, bacteria and eukaryotes. Activity of Rio1 is vital in Saccharomyces cerevisiae for the processing of ribosomal RNA, as well as for proper cell cycle progression and chromosome maintenance. The structure of RIO1 has been determined.
Probab=22.73 E-value=50 Score=13.27 Aligned_cols=38 Identities=13% Similarity=0.227 Sum_probs=21.2
Q ss_pred HHHHHHHHHHHHHHHHC---CCCCCCCCEEEECCCCCEEEEEE
Q ss_conf 85999999998999955---97510232679905996799400
Q gi|254781049|r 185 IDGGDLFPNLYKAFCDK---DMSLLEINPLIIMKNGRLRVLDS 224 (398)
Q Consensus 185 ~~~~~ii~~L~~~f~e~---Da~liEINPLvvt~dg~vvAlDA 224 (398)
.-+.+++..+.++|... .+.|=|-|=|+ .+++++..|-
T Consensus 107 ~~~~~ii~~~~~~y~~~glVHgDLSEyNIL~--~~~~~~iID~ 147 (186)
T pfam01163 107 EIYDEIIREMRRLYQEAGLVHGDLSEYNVLV--DDDKPVIIDV 147 (186)
T ss_pred HHHHHHHHHHHHHHHHCCCEECCCHHHHEEE--ECCCEEEEEC
T ss_conf 9999999999999996693213620655064--3896799956
No 310
>PRK06740 histidinol-phosphatase; Validated
Probab=22.35 E-value=51 Score=13.22 Aligned_cols=89 Identities=15% Similarity=0.209 Sum_probs=55.1
Q ss_pred HHHHHHHHHHCCCCCCEEEECCCCCCHHHHHHHHHHHHCCCCCCEEEEECCCCHHH--HHHH--HHHHHHHHHHCCCCCC
Q ss_conf 89999999965899624884278889899999999986199865899963586132--8999--9999999997299987
Q gi|254781049|r 279 AMATMDIIKLYGGAPANFLDVGGGADQDKVAAAFKIITSDSSVKGILINIFGGIMR--CDVL--VKGILSAVKEVKINIP 354 (398)
Q Consensus 279 amatmD~i~~~Gg~pANFlD~gG~a~~e~~~~a~~~il~~~~vk~iliNifGGI~~--cd~v--A~gii~a~~~~~~~~p 354 (398)
.++-+|+||.+|.+|- ...-.+-..++++.+ .+.+ -+|=|| -|.--| |-++ ..-+.+.+.+ .++|
T Consensus 218 IiGHlDlIK~Fg~rp~------~~~~~~~~e~~a~ai-k~~~-~avEIN-AGLg~RkPV~EiYPs~~~Le~~~~--~gIP 286 (338)
T PRK06740 218 IIAHLDNIKVFNYRLD------ENEQLSYYKEIARAL-VETN-TATEIN-AGLYYRYPVREMCPSPLYLQVLAK--HGVP 286 (338)
T ss_pred EECCHHHHHHCCCCCC------CHHHHHHHHHHHHHH-HHCC-CEEEEE-CCCCCCCCCCCCCCCHHHHHHHHH--CCCC
T ss_conf 6236216766188899------125899999999999-9749-379982-675346874456887999999997--6998
Q ss_pred EEEEC-------CCCCHHHHHHHHHHCCCCE
Q ss_conf 99974-------8985899999999769958
Q gi|254781049|r 355 LVMRL-------EGANVDIGNRLIAESGLNV 378 (398)
Q Consensus 355 ivvRl-------~Gtn~~~g~~il~~~g~~~ 378 (398)
|++-- -|...+++.+++++.|+.-
T Consensus 287 ItlgSDAH~Pe~VG~~~~ea~~llk~~Gyte 317 (338)
T PRK06740 287 ITLSSDAHYPNDLGKYVEENVKTLRNHGISH 317 (338)
T ss_pred EEEECCCCCHHHHCCCHHHHHHHHHHCCCCE
T ss_conf 7851688996785665999999999749825
No 311
>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=22.27 E-value=51 Score=13.21 Aligned_cols=84 Identities=12% Similarity=-0.001 Sum_probs=53.9
Q ss_pred CCHHHHHH-HHHHHHCCCCCCEEEEECCCCHHHHHHHHHHHHHHHHHCCC-CCCEEEECCCCCHHHHHHHHHHCCCCEEE
Q ss_conf 89899999-99998619986589996358613289999999999997299-98799974898589999999976995899
Q gi|254781049|r 303 ADQDKVAA-AFKIITSDSSVKGILINIFGGIMRCDVLVKGILSAVKEVKI-NIPLVMRLEGANVDIGNRLIAESGLNVIT 380 (398)
Q Consensus 303 a~~e~~~~-a~~~il~~~~vk~iliNifGGI~~cd~vA~gii~a~~~~~~-~~pivvRl~Gtn~~~g~~il~~~g~~~~~ 380 (398)
.+.+..+. .-.++.++|++++|+- ..|..+.|.++|+++.+. ..-.|+=..|+. ++.+.+++--+....
T Consensus 161 ~~~~~a~~~~~~~L~~~pdi~~i~~-------~~~~~a~ga~~Al~~~g~~~~i~vvg~D~~~--~~~~~i~~G~i~~tv 231 (271)
T cd06314 161 EDFAKAKSNAEDALNAHPDLKCMFG-------LYAYNGPAIAEAVKAAGKLGKVKIVGFDEDP--DTLQGVKEGTIQGTV 231 (271)
T ss_pred CCHHHHHHHHHHHHHHCCCCCEEEE-------ECCCCHHHHHHHHHHHCCCCCCEEEEECCCH--HHHHHHHCCCCEEEE
T ss_conf 6388999999999975899878998-------0885169999999984758996799878989--999999829985998
Q ss_pred ECCHHHHHHHHHHHH
Q ss_conf 499899999999985
Q gi|254781049|r 381 AIDLDDAAQKIVHAV 395 (398)
Q Consensus 381 ~~~~~~A~~~~v~~~ 395 (398)
..+..+--..+|+.+
T Consensus 232 ~Q~p~~~G~~av~~~ 246 (271)
T cd06314 232 VQRPYQMGYLSVTVL 246 (271)
T ss_pred ECCHHHHHHHHHHHH
T ss_conf 389999999999999
No 312
>TIGR03470 HpnH hopanoid biosynthesis associated radical SAM protein HpnH. The sequences represented by this model are members of the radical SAM superfamily of enzymes (pfam04055). These enzymes utilize an iron-sulfur redox cluster and S-adenosylmethionine to carry out diverse radical mediated reactions. The members of this clade are frequently found in the same locus as squalene-hopene cyclase (SHC, TIGR01507) and other genes associated with the biosynthesis of hopanoid natural products. The linkage between SHC and this radical SAM enzyme is strong; one is nearly always observed in the same genome where the other is found. A hopanoid biosynthesis locus was described in Zymomonas mobilis consisting of the genes HpnA-E and SHC (HpnF). Continuing past SHC are found a phosphorylase enzyme (ZMO0873, i.e. HpnG, TIGR03468) and this radical SAM enzyme (ZMO0874) which we name here HpnH. Granted, in Z. mobilis, HpnH is in a convergent orientation with respect to HpnA-G, but one gene beyond HpnH
Probab=22.23 E-value=51 Score=13.20 Aligned_cols=71 Identities=20% Similarity=0.231 Sum_probs=41.9
Q ss_pred CCHHHHHHHHHHCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCEEEE-ECCHHHHHHHHHHHCCCCCCCCCCCCCCCCCC
Q ss_conf 79999999998729986999712136876565655677777770799-58999999999986187654421222224433
Q gi|254781049|r 26 SSVHAAESAIKTLPGPLYVVKSQIHAGGRGKGRFKELPADSKGGVRV-ESSLKSVISDIREILGSTLITKQTGPTGSRVN 104 (398)
Q Consensus 26 ~s~~ea~~~a~~ig~p~~VvKaQV~aGgRGKa~~~~~hk~~~GGV~l-~~s~~ea~~~a~~ilg~~l~t~qt~~~G~~v~ 104 (398)
-|++|...++++.|.|+ |. .+ ||==+ -.+..|..+.+.+. ++.+ +-.| +
T Consensus 59 Ls~ee~~~~~~e~Gap~-V~----it----------------GGEPLLr~dl~eIv~~a~~~-g~~v-~l~T-------N 108 (318)
T TIGR03470 59 LSVEECLRAVDECGAPV-VS----IP----------------GGEPLLHPEIDEIVRGLVAR-KKFV-YLCT-------N 108 (318)
T ss_pred CCHHHHHHHHHHCCCCE-EE----EC----------------CCCCCCCCCHHHHHHHHHHC-CCEE-EEEC-------C
T ss_conf 89999999999849978-99----51----------------88745564799999999975-9979-9977-------5
Q ss_pred CEEECCCCCC---CEEEEEEEEEEC
Q ss_conf 0110345556---505899999834
Q gi|254781049|r 105 CVYVEDGADI---LRELYLSLLVDR 126 (398)
Q Consensus 105 ~vLVEe~v~~---~~E~ylgi~~Dr 126 (398)
+.|+++.++- ..=+|++|.+|.
T Consensus 109 G~Ll~k~i~~~~~~~~~~~~VsLDG 133 (318)
T TIGR03470 109 ALLLEKKLDKFEPSPYLTFSVHLDG 133 (318)
T ss_pred HHHHHHHHHHHHHCCCCEEEEECCC
T ss_conf 5200999999851888369998017
No 313
>PRK00286 xseA exodeoxyribonuclease VII large subunit; Reviewed
Probab=22.15 E-value=51 Score=13.19 Aligned_cols=90 Identities=19% Similarity=0.352 Sum_probs=58.1
Q ss_pred CCCCEEEEECCCHHHHHHHHHHHHCCCC-C-CEEEE----CCCCCCHHHHHHHHHHHHCCCCCCEEEEECCCCHHHHHHH
Q ss_conf 2881799955503689999999965899-6-24884----2788898999999999861998658999635861328999
Q gi|254781049|r 265 LDGNIGCMVNGAGLAMATMDIIKLYGGA-P-ANFLD----VGGGADQDKVAAAFKIITSDSSVKGILINIFGGIMRCDVL 338 (398)
Q Consensus 265 LdG~Ig~~vnGaGlamatmD~i~~~Gg~-p-ANFlD----~gG~a~~e~~~~a~~~il~~~~vk~iliNifGGI~~cd~v 338 (398)
+-=+||++..-.|.+.. |+++-..-+ | .+|.= +=|.-.+..+.+|++.+-.++.+.+|.| +=||--.-|..
T Consensus 134 ~P~~IgvITS~tgAa~~--Di~~~~~~R~p~~~i~l~p~~VQG~~A~~~I~~ai~~~~~~~~~DvIIi-~RGGGS~eDL~ 210 (443)
T PRK00286 134 FPKRIGVITSPTGAAIR--DILTVLSRRFPSVEVIIYPTLVQGEGAAASIVEAIERANARGEVDVLIV-ARGGGSLEDLW 210 (443)
T ss_pred CCCEEEEEECCCHHHHH--HHHHHHHCCCCCEEEEEEECCCCHHHHHHHHHHHHHHHHHHCCCCEEEE-ECCCCCHHHHH
T ss_conf 85579998368438999--9999985049965999981456265479999999999852248888999-36878888976
Q ss_pred H---HHHHHHHHHCCCCCCEEEEC
Q ss_conf 9---99999999729998799974
Q gi|254781049|r 339 V---KGILSAVKEVKINIPLVMRL 359 (398)
Q Consensus 339 A---~gii~a~~~~~~~~pivvRl 359 (398)
+ |.+++|+-+ .++|||.=.
T Consensus 211 ~FNdE~varaI~~--s~iPVISaI 232 (443)
T PRK00286 211 AFNDEAVARAIAA--SKIPVISAV 232 (443)
T ss_pred HCCCHHHHHHHHH--CCCCEEECC
T ss_conf 5187999999984--899789514
No 314
>COG1486 CelF Alpha-galactosidases/6-phospho-beta-glucosidases, family 4 of glycosyl hydrolases [Carbohydrate transport and metabolism]
Probab=21.79 E-value=52 Score=13.15 Aligned_cols=39 Identities=28% Similarity=0.419 Sum_probs=24.2
Q ss_pred HHHHHHHHCCCCCCCCEEECCHHHHHHHHHHCCCCEEEEECCCCCCC
Q ss_conf 99999998689888815747999999999872998699971213687
Q gi|254781049|r 7 QAKALLRKYNVPVAKGVVISSVHAAESAIKTLPGPLYVVKSQIHAGG 53 (398)
Q Consensus 7 qaK~lL~~~GIpvp~g~~a~s~~ea~~~a~~ig~p~~VvKaQV~aGg 53 (398)
-+|.++++.|.| -+-...++.++|..- .. +|+ .|+..||
T Consensus 51 ~~~~~v~~~g~~-~kv~~ttd~~eAl~g-----Ad-fVi-~~~rvG~ 89 (442)
T COG1486 51 LAKKLVEEAGAP-VKVEATTDRREALEG-----AD-FVI-TQIRVGG 89 (442)
T ss_pred HHHHHHHHHCCC-EEEEEECCHHHHHCC-----CC-EEE-EEEEECC
T ss_conf 999999963998-589994589998447-----98-899-9875068
No 315
>pfam11094 UL11 Membrane-associated tegument protein. The UL11 gene product of herpes simplex virus is a membrane-associated tegument protein that is incorporated into the HSV virion and functions in viral envelopment. UL11 is acylated which is crucial for lipid raft association.
Probab=21.63 E-value=53 Score=13.13 Aligned_cols=16 Identities=25% Similarity=0.509 Sum_probs=12.6
Q ss_pred CEEEECCCCCEEEEEEE
Q ss_conf 26799059967994001
Q gi|254781049|r 209 NPLIIMKNGRLRVLDSK 225 (398)
Q Consensus 209 NPLvvt~dg~vvAlDAK 225 (398)
|- ++|.+|++++|||-
T Consensus 16 N~-LvT~~GevvsL~a~ 31 (39)
T pfam11094 16 NV-LVTSSGEVVSLDAD 31 (39)
T ss_pred CE-EECCCCCEEEECHH
T ss_conf 88-98058868987234
No 316
>TIGR02392 rpoH_proteo alternative sigma factor RpoH; InterPro: IPR012759 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme . RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognized by the major sigma factors , . This entry represents the proteobacterial clade of sigma factors called RpoH. This protein may be called sigma-32, sigma factor H, heat shock sigma factor, and alternative sigma factor RpoH. Note that in some species the single locus rpoH may be replaced by two or more differentially regulated stress response sigma factors.; GO: 0003677 DNA binding, 0003700 transcription factor activity, 0008270 zinc ion binding, 0016987 sigma factor activity, 0006352 transcription initiation, 0006355 regulation of transcription DNA-dependent, 0009408 response to heat.
Probab=21.46 E-value=17 Score=16.40 Aligned_cols=22 Identities=14% Similarity=0.200 Sum_probs=12.9
Q ss_pred CCCCHHHHHHHHHHCCCCHHHH
Q ss_conf 5789578887887519888998
Q gi|254781049|r 163 IGVTSEDVASLCDMLELQGQAR 184 (398)
Q Consensus 163 ~gl~~~~~~~l~~~lg~~~~~~ 184 (398)
..+++.++..+|..||++....
T Consensus 139 gw~~~~e~~~~A~~L~V~~~eV 160 (279)
T TIGR02392 139 GWLNPEEVEAIAEELGVSEEEV 160 (279)
T ss_pred CCCCHHHHHHHHHHCCCCHHHH
T ss_conf 7989899999997638988899
No 317
>cd08025 RNR_PFL_like_DUF711 Uncharacterized proteins with similarity to Ribonucleotide reductase and Pyruvate formate lyase. This subfamily contains Streptococcus pneumoniae Sp0239 and similar uncharacterized proteins. Sp0239 is structurally similar to ribonucleotide reductase (RNR) and pyruvate formate lyase (PFL), which are believed to have diverged from a common ancestor. RNR and PFL possess a ten-stranded alpha-beta barrel domain that hosts the active site, and are radical enzymes. RNRs are found in all organisms and provide the only mechanism by which nucleotides are converted to deoxynucleotides. PFL is an essential enzyme in anaerobic bacteria that catalyzes the conversion of pyruvate and CoA to acteylCoA and formate.
Probab=21.35 E-value=53 Score=13.09 Aligned_cols=23 Identities=9% Similarity=0.177 Sum_probs=17.6
Q ss_pred HHHHHHHHCCCCCCCCEEECCHH
Q ss_conf 99999998689888815747999
Q gi|254781049|r 7 QAKALLRKYNVPVAKGVVISSVH 29 (398)
Q Consensus 7 qaK~lL~~~GIpvp~g~~a~s~~ 29 (398)
.++++.++|||||-.-++..||=
T Consensus 55 ~~~~i~~~~GipIvnkRisvtPi 77 (400)
T cd08025 55 TVEEVSSELGVPIVNKRISVTPI 77 (400)
T ss_pred HHHHHHHHHCCCEEEEEEEECHH
T ss_conf 99999998599447657750439
No 318
>PRK01368 murD UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional
Probab=21.34 E-value=53 Score=13.09 Aligned_cols=89 Identities=12% Similarity=0.146 Sum_probs=53.5
Q ss_pred EEEECCCCCCHHHHHHHHHHHHCCCCCCEEEEECCCCHHHHHHHHHHHHHHHHHCCCCCCEEEECCCCCHHHHHHHHHHC
Q ss_conf 48842788898999999999861998658999635861328999999999999729998799974898589999999976
Q gi|254781049|r 295 NFLDVGGGADQDKVAAAFKIITSDSSVKGILINIFGGIMRCDVLVKGILSAVKEVKINIPLVMRLEGANVDIGNRLIAES 374 (398)
Q Consensus 295 NFlD~gG~a~~e~~~~a~~~il~~~~vk~iliNifGGI~~cd~vA~gii~a~~~~~~~~pivvRl~Gtn~~~g~~il~~~ 374 (398)
.|-|=+=+++.+.+..|++-. ++ .+| |.||..+-....+ +...+++ +.-++ +-|...+.=.+.++.
T Consensus 321 ~~iNDSKaTN~~a~~~Al~~~---~~--i~l--I~GG~~K~~d~~~-l~~~~~~----v~~~~-l~G~~~~~~~~~~~~- 386 (450)
T PRK01368 321 SFYNDSKATNAISAVQSIKAL---DN--IYW--LAGGIPKEGGIEE-IKPYFSK----IKKAY-FYGQAKEMFANTAKN- 386 (450)
T ss_pred EEECCCCCCCHHHHHHHHHCC---CC--EEE--EEECCCCCCCHHH-HHHHHHC----CCEEE-EECCCHHHHHHHCCC-
T ss_conf 997178878999999998568---97--399--9941577788799-9988743----87999-989789999986058-
Q ss_pred CCCEEEECCHHHHHHHHHHHHHC
Q ss_conf 99589949989999999998506
Q gi|254781049|r 375 GLNVITAIDLDDAAQKIVHAVKG 397 (398)
Q Consensus 375 g~~~~~~~~~~~A~~~~v~~~k~ 397 (398)
..++..+++|++|+..|+..++.
T Consensus 387 ~~~~~~~~~l~~av~~a~~~a~~ 409 (450)
T PRK01368 387 IVDFVICDNLEQAFDLAYKDAVG 409 (450)
T ss_pred CCCEEECCCHHHHHHHHHHHHHC
T ss_conf 98769649999999999999755
No 319
>PRK09271 flavodoxin; Provisional
Probab=21.00 E-value=54 Score=13.04 Aligned_cols=13 Identities=15% Similarity=0.038 Sum_probs=7.4
Q ss_pred CHHHHHHHHHHHC
Q ss_conf 9999999999861
Q gi|254781049|r 75 SLKSVISDIREIL 87 (398)
Q Consensus 75 s~~ea~~~a~~il 87 (398)
|.+++.+...+-|
T Consensus 13 NTE~vA~~I~~~l 25 (160)
T PRK09271 13 NTREVARMIAARC 25 (160)
T ss_pred CHHHHHHHHHHHH
T ss_conf 6899999999999
No 320
>PRK03992 proteasome-activating nucleotidase; Provisional
Probab=20.99 E-value=54 Score=13.04 Aligned_cols=49 Identities=18% Similarity=0.218 Sum_probs=29.5
Q ss_pred CEEEEEECCCCCCHH--------HHHHHCHHHHEEEECCCCCCCC---------HHHHHHHHHHCC
Q ss_conf 048998447884024--------5557483122033214445789---------578887887519
Q gi|254781049|r 130 MVAFIASTQGGMDIE--------EVAKDYPQKIFKLLIDPLIGVT---------SEDVASLCDMLE 178 (398)
Q Consensus 130 ~~vii~S~~GGvdIE--------~va~~~p~~I~~~~id~~~gl~---------~~~~~~l~~~lg 178 (398)
.|-+-++.-||.+-. +..-++|+...+..+.|-.|+- ...++.++...+
T Consensus 126 ~P~v~~~dIGGl~~~k~el~E~velPl~~pe~f~~~Gi~pPkGvLLyGPPGtGKTllAkAvA~e~~ 191 (390)
T PRK03992 126 SPDVTYEDIGGLDEQIREVREAVELPLKNPELFEEVGIEPPKGVLLYGPPGTGKTLLAKAVAHETN 191 (390)
T ss_pred CCCCCHHHHCCHHHHHHHHHHHHHHHHHCHHHHHHCCCCCCCEEEEECCCCCCHHHHHHHHHHHHC
T ss_conf 999984661498999999999999986598999976999997278689899978999999998748
No 321
>PRK07679 pyrroline-5-carboxylate reductase; Reviewed
Probab=20.71 E-value=28 Score=14.94 Aligned_cols=38 Identities=16% Similarity=0.158 Sum_probs=25.4
Q ss_pred CCCCCHHHHHHHHHHCCCCEEEECCHHHHHHHHHHHHHC
Q ss_conf 489858999999997699589949989999999998506
Q gi|254781049|r 359 LEGANVDIGNRLIAESGLNVITAIDLDDAAQKIVHAVKG 397 (398)
Q Consensus 359 l~Gtn~~~g~~il~~~g~~~~~~~~~~~A~~~~v~~~k~ 397 (398)
=.||. ++|.+.|++.+++-...+.++.|.+|+-|++|.
T Consensus 234 pgGtT-~~gl~~Le~~~~~~~i~~Av~aA~~Rs~el~k~ 271 (279)
T PRK07679 234 PGGTT-EAGIEVLQEHKFQQALISCITQATQRSHNLGKT 271 (279)
T ss_pred CCHHH-HHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 94659-999999998881999999999999999999999
No 322
>cd05119 RIO RIO kinase family, catalytic domain. The RIO kinase catalytic domain family is part of a larger superfamily, that includes the catalytic domains of other kinases such as the typical serine/threonine/tyrosine protein kinases (PKs), aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase (PI3K). RIO kinases are atypical protein serine kinases present in archaea, bacteria and eukaryotes. Serine kinases catalyze the transfer of the gamma-phosphoryl group from ATP to serine residues in protein substrates. RIO kinases contain a kinase catalytic signature, but otherwise show very little sequence similarity to typical PKs. The RIO catalytic domain is truncated compared to the catalytic domains of typical PKs, with deletions of the loops responsible for substrate binding. Most organisms contain at least two RIO kinases, RIO1 and RIO2. A third protein, RIO3, is present in multicellular eukaryotes. In yeast, RIO1 and RIO2 are essential for survival. They funct
Probab=20.43 E-value=56 Score=12.97 Aligned_cols=37 Identities=19% Similarity=0.344 Sum_probs=19.3
Q ss_pred HHHHHHHHHHHHHHC---CCCCCCCCEEEECCCCCEEEEEEE
Q ss_conf 999999998999955---975102326799059967994001
Q gi|254781049|r 187 GGDLFPNLYKAFCDK---DMSLLEINPLIIMKNGRLRVLDSK 225 (398)
Q Consensus 187 ~~~ii~~L~~~f~e~---Da~liEINPLvvt~dg~vvAlDAK 225 (398)
+.+++..+.+++.+. .++|=|-|=|+ .+++++..|-=
T Consensus 120 ~~~il~~~~~~~~~~glVHgDLSeyNilv--~~~~~~iID~p 159 (187)
T cd05119 120 YDQILELMRKLYREAGLVHGDLSEYNILV--DDGKVYIIDVP 159 (187)
T ss_pred HHHHHHHHHHHHHHCCCCCCCCCHHHEEE--ECCEEEEEECC
T ss_conf 99999999999997493103655554589--89908999557
No 323
>cd02812 PcrB_like PcrB_like proteins. One member of this family, a protein from Archaeoglobus fulgidus, has been characterized as a (S)-3-O-geranylgeranylglyceryl phosphate synthase (AfGGGPS). AfGGGPS catalyzes the formation of an ether linkage between sn-glycerol-1-phosphate (G1P) and geranylgeranyl diphosphate (GGPP), the committed step in archaeal lipid biosynthesis. Therefore, it has been proposed that PcrB-like proteins are either prenyltransferases or are involved in lipoteichoic acid biosynthesis although the exact function is still unknown.
Probab=20.37 E-value=56 Score=12.96 Aligned_cols=60 Identities=28% Similarity=0.337 Sum_probs=35.8
Q ss_pred HHHHHHHHHHCCCCCCEEEECCCCCCHHHHHHHHHHHHCCCCCCEEEEECCCCHHHHHHHHHHHHHH
Q ss_conf 8999999996589962488427888989999999998619986589996358613289999999999
Q gi|254781049|r 279 AMATMDIIKLYGGAPANFLDVGGGADQDKVAAAFKIITSDSSVKGILINIFGGIMRCDVLVKGILSA 345 (398)
Q Consensus 279 amatmD~i~~~Gg~pANFlD~gG~a~~e~~~~a~~~il~~~~vk~iliNifGGI~~cd~vA~gii~a 345 (398)
+.+|.=+-.++| -|-=|||.+|.+-...+.++.+-.+++ ..|+ +.|||-+-+ -|+-+.+|
T Consensus 137 ~~ayAlaae~lg-~~~iYLEgSGa~v~~e~V~~vk~~l~~----~~Li-vGGGIrs~e-~a~~~~~A 196 (219)
T cd02812 137 AAAYALAAEYLG-MPIVYLEYSGAYGPPEVVRAVKKVLGD----TPLI-VGGGIRSGE-QAKEMAEA 196 (219)
T ss_pred HHHHHHHHHHHC-CCEEEEECCCCCCCHHHHHHHHHHCCC----CEEE-EECCCCCHH-HHHHHHHC
T ss_conf 999999999829-938999568997999999999984679----7099-928979999-99999986
No 324
>PRK11706 TDP-4-oxo-6-deoxy-D-glucose transaminase; Provisional
Probab=20.30 E-value=56 Score=12.95 Aligned_cols=14 Identities=21% Similarity=0.321 Sum_probs=8.9
Q ss_pred HHHHHHHHHCCCCC
Q ss_conf 99999999729998
Q gi|254781049|r 340 KGILSAVKEVKINI 353 (398)
Q Consensus 340 ~gii~a~~~~~~~~ 353 (398)
..+++.+++.++..
T Consensus 303 d~l~~~L~~~gI~t 316 (375)
T PRK11706 303 SALINFLKEAGIMA 316 (375)
T ss_pred HHHHHHHHHCCCCE
T ss_conf 99999999879983
No 325
>TIGR01063 gyrA DNA gyrase, A subunit; InterPro: IPR005743 DNA topoisomerases regulate the number of topological links between two DNA strands (i.e. change the number of superhelical turns) by catalysing transient single- or double-strand breaks, crossing the strands through one another, then resealing the breaks. These enzymes have several functions: to remove DNA supercoils during transcription and DNA replication; for strand breakage during recombination; for chromosome condensation; and to disentangle intertwined DNA during mitosis , . DNA topoisomerases are divided into two classes: type I enzymes (5.99.1.2 from EC; topoisomerases I, III and V) break single-strand DNA, and type II enzymes (5.99.1.3 from EC; topoisomerases II, IV and VI) break double-strand DNA . Type II topoisomerases are ATP-dependent enzymes, and can be subdivided according to their structure and reaction mechanisms: type IIA (topoisomerase II or gyrase, and topoisomerase IV) and type IIB (topoisomerase VI). These enzymes are responsible for relaxing supercoiled DNA as well as for introducing both negative and positive supercoils . Topoisomerase II (called gyrase in bacteria) primarily introduces negative supercoils into DNA. In bacteria, topoisomerase II consists of two polypeptide subunits, gyrA and gyrB, which form a heterotetramer: (BA)2. In most eukaryotes, topoisomerase II consists of a single polypeptide, where the N- and C-terminal regions correspond to gyrB and gyrA, respectively. This entry represents the A subunit (gyrA) as found predominantly in bacteria, but does not include the topoisomerase II enzymes composed of a single polypeptide, as are found in most eukaryotes. GyrA has two functional domains: an N-terminal that forms the covalent DNA-protein bridge that is responsible for the breaking- and rejoining function, and a C-terminal that can bind DNA non-specifically . More information about this protein can be found at Protein of the Month: DNA Topoisomerase .; GO: 0003677 DNA binding, 0003918 DNA topoisomerase (ATP-hydrolyzing) activity, 0005524 ATP binding, 0006265 DNA topological change, 0006268 DNA unwinding during replication, 0005694 chromosome.
Probab=20.04 E-value=57 Score=12.91 Aligned_cols=37 Identities=22% Similarity=0.407 Sum_probs=19.3
Q ss_pred CCCCCCEEECCCCCCCEEEEEEEEEECCCCCEEEEEECCCCC
Q ss_conf 244330110345556505899999834778048998447884
Q gi|254781049|r 100 GSRVNCVYVEDGADILRELYLSLLVDRTSGMVAFIASTQGGM 141 (398)
Q Consensus 100 G~~v~~vLVEe~v~~~~E~ylgi~~Dr~~~~~vii~S~~GGv 141 (398)
|+-++++-..+.-|+-..+|++-|.| .+++||..|=+
T Consensus 550 GkG~~g~~~~~G~D~i~~~lvasTHD-----~~Lfftn~G~v 586 (864)
T TIGR01063 550 GKGVSGADLKDGDDFIEQLLVASTHD-----YLLFFTNRGKV 586 (864)
T ss_pred CCCCCCCCCCCCCCEEEEEEEEECCC-----EEEEEECCCCE
T ss_conf 64643253123685056778830776-----07888188826
Done!