Query 024560
Match_columns 266
No_of_seqs 157 out of 1081
Neff 6.3
Searched_HMMs 46136
Date Fri Mar 29 05:33:31 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/024560.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/024560hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PLN02235 ATP citrate (pro-S)-l 100.0 2.5E-72 5.5E-77 534.8 27.3 262 1-262 158-419 (423)
2 COG0045 SucC Succinyl-CoA synt 100.0 1.2E-66 2.5E-71 486.3 25.0 227 4-264 156-386 (387)
3 PLN00124 succinyl-CoA ligase [ 100.0 7.1E-63 1.5E-67 473.4 25.4 228 2-263 191-421 (422)
4 PRK14046 malate--CoA ligase su 100.0 9.4E-58 2E-62 435.5 26.0 230 2-265 156-388 (392)
5 KOG1447 GTP-specific succinyl- 100.0 4.2E-56 9.1E-61 398.6 18.2 227 1-261 181-410 (412)
6 TIGR01016 sucCoAbeta succinyl- 100.0 1.2E-50 2.5E-55 385.5 23.7 217 12-262 168-385 (386)
7 KOG2799 Succinyl-CoA synthetas 100.0 1.7E-49 3.7E-54 366.1 10.3 225 2-260 185-413 (434)
8 PRK00696 sucC succinyl-CoA syn 100.0 1.6E-44 3.5E-49 343.6 25.5 229 2-264 156-387 (388)
9 PF00549 Ligase_CoA: CoA-ligas 99.8 1.3E-19 2.8E-24 152.7 9.2 123 118-260 1-152 (153)
10 KOG1254 ATP-citrate lyase [Ene 99.7 3.8E-19 8.2E-24 170.3 -1.9 254 3-257 196-488 (600)
11 TIGR02717 AcCoA-syn-alpha acet 99.7 3E-15 6.5E-20 145.6 16.4 129 111-263 294-445 (447)
12 COG1042 Acyl-CoA synthetase (N 99.2 1.2E-10 2.6E-15 116.9 13.2 128 112-263 299-449 (598)
13 PLN02522 ATP citrate (pro-S)-l 97.6 0.0012 2.5E-08 67.1 13.6 125 112-260 167-312 (608)
14 PRK06091 membrane protein FdrA 97.5 0.00087 1.9E-08 67.1 11.8 120 111-263 192-317 (555)
15 PF13607 Succ_CoA_lig: Succiny 97.4 0.0021 4.5E-08 53.4 11.1 120 113-257 2-134 (138)
16 PTZ00187 succinyl-CoA syntheta 97.4 0.0038 8.1E-08 58.8 13.2 128 111-262 168-313 (317)
17 COG0074 SucD Succinyl-CoA synt 97.4 0.0025 5.4E-08 58.8 11.4 137 103-263 134-290 (293)
18 TIGR02717 AcCoA-syn-alpha acet 97.1 0.0095 2.1E-07 58.4 13.7 126 112-262 150-288 (447)
19 PLN00125 Succinyl-CoA ligase [ 96.9 0.023 4.9E-07 53.2 12.8 125 111-260 149-292 (300)
20 TIGR01019 sucCoAalpha succinyl 96.8 0.025 5.4E-07 52.5 13.0 126 111-260 142-284 (286)
21 PRK05678 succinyl-CoA syntheta 96.7 0.015 3.2E-07 54.2 10.7 127 112-262 145-288 (291)
22 PF13549 ATP-grasp_5: ATP-gras 96.2 0.0082 1.8E-07 53.7 5.5 54 7-61 164-222 (222)
23 KOG1255 Succinyl-CoA synthetas 94.4 0.091 2E-06 47.9 5.8 108 107-230 171-280 (329)
24 TIGR00640 acid_CoA_mut_C methy 94.2 0.92 2E-05 37.3 11.0 95 144-262 33-127 (132)
25 PRK02261 methylaspartate mutas 93.4 1.5 3.3E-05 36.2 10.9 111 123-263 19-135 (137)
26 cd02071 MM_CoA_mut_B12_BD meth 91.4 2.9 6.3E-05 33.4 10.0 102 128-258 19-120 (122)
27 PF02601 Exonuc_VII_L: Exonucl 90.7 4.8 0.0001 37.4 12.1 125 111-262 13-145 (319)
28 COG0616 SppA Periplasmic serin 89.2 1.6 3.5E-05 40.9 7.7 59 150-223 79-139 (317)
29 PRK06091 membrane protein FdrA 88.7 5.3 0.00012 40.5 11.3 81 170-263 407-494 (555)
30 cd07014 S49_SppA Signal peptid 87.8 3.8 8.2E-05 34.7 8.5 73 146-232 17-91 (177)
31 PRK10949 protease 4; Provision 86.9 2.4 5.1E-05 43.6 7.8 61 149-224 345-408 (618)
32 cd07019 S49_SppA_1 Signal pept 86.0 6.4 0.00014 34.5 9.2 72 149-232 19-90 (211)
33 cd02072 Glm_B12_BD B12 binding 85.7 12 0.00026 30.7 10.0 91 143-257 29-125 (128)
34 cd07018 S49_SppA_67K_type Sign 85.3 3.9 8.5E-05 36.1 7.5 58 150-221 28-87 (222)
35 TIGR00705 SppA_67K signal pept 83.4 4.1 9E-05 41.5 7.6 63 151-227 329-393 (584)
36 TIGR00237 xseA exodeoxyribonuc 81.8 15 0.00033 36.0 10.6 122 111-260 128-255 (432)
37 cd07023 S49_Sppa_N_C Signal pe 80.6 17 0.00038 31.5 9.7 69 150-232 16-86 (208)
38 TIGR00706 SppA_dom signal pept 80.5 9.9 0.00021 33.2 8.1 66 152-232 14-81 (207)
39 cd00394 Clp_protease_like Case 80.1 12 0.00026 30.8 8.1 64 152-232 12-77 (161)
40 cd00952 CHBPH_aldolase Trans-o 79.1 35 0.00076 31.7 11.7 103 149-265 24-133 (309)
41 PF00885 DMRL_synthase: 6,7-di 77.3 21 0.00047 29.7 8.8 113 126-263 23-139 (144)
42 cd02067 B12-binding B12 bindin 76.6 34 0.00073 26.7 9.6 99 128-258 19-117 (119)
43 PRK12419 riboflavin synthase s 76.2 48 0.001 28.3 13.6 116 124-263 28-149 (158)
44 PRK04147 N-acetylneuraminate l 76.2 48 0.001 30.4 11.7 109 143-264 13-128 (293)
45 TIGR01501 MthylAspMutase methy 75.9 44 0.00094 27.6 10.7 94 143-260 31-130 (134)
46 cd00578 L-fuc_L-ara-isomerases 75.3 85 0.0018 30.6 14.2 112 114-246 2-134 (452)
47 COG0329 DapA Dihydrodipicolina 75.3 51 0.0011 30.6 11.6 105 148-265 19-129 (299)
48 COG0075 Serine-pyruvate aminot 74.3 29 0.00064 33.7 10.0 82 107-205 75-161 (383)
49 cd07022 S49_Sppa_36K_type Sign 74.2 29 0.00064 30.3 9.3 66 150-230 24-91 (214)
50 PF13433 Peripla_BP_5: Peripla 72.8 9.7 0.00021 36.7 6.3 68 124-205 23-92 (363)
51 TIGR00683 nanA N-acetylneurami 70.3 81 0.0017 29.0 11.6 108 143-264 10-125 (290)
52 PRK00286 xseA exodeoxyribonucl 70.0 35 0.00077 33.2 9.6 121 111-260 134-260 (438)
53 cd07021 Clp_protease_NfeD_like 69.0 23 0.00051 30.4 7.3 60 155-232 17-78 (178)
54 COG0673 MviM Predicted dehydro 68.9 60 0.0013 29.6 10.5 122 114-262 5-140 (342)
55 TIGR02313 HpaI-NOT-DapA 2,4-di 68.4 92 0.002 28.7 11.6 109 143-264 10-124 (294)
56 COG2185 Sbm Methylmalonyl-CoA 68.1 72 0.0016 26.8 11.2 94 146-263 45-138 (143)
57 PRK00061 ribH 6,7-dimethyl-8-r 64.7 86 0.0019 26.5 13.7 126 113-263 13-148 (154)
58 PLN02417 dihydrodipicolinate s 63.5 1.2E+02 0.0026 27.7 11.6 108 143-263 11-124 (280)
59 TIGR03249 KdgD 5-dehydro-4-deo 60.8 1.4E+02 0.003 27.5 12.6 107 143-264 15-128 (296)
60 cd00408 DHDPS-like Dihydrodipi 60.8 1.3E+02 0.0028 27.1 11.8 107 144-264 8-121 (281)
61 COG1090 Predicted nucleoside-d 60.6 23 0.0005 33.1 5.9 132 113-260 158-295 (297)
62 cd07016 S14_ClpP_1 Caseinolyti 59.9 39 0.00085 27.8 6.9 64 151-232 15-78 (160)
63 cd07020 Clp_protease_NfeD_1 No 58.4 49 0.0011 28.3 7.3 62 153-232 15-81 (187)
64 cd06288 PBP1_sucrose_transcrip 58.3 1.2E+02 0.0026 26.0 11.7 119 113-262 117-244 (269)
65 PF00701 DHDPS: Dihydrodipicol 57.9 1.5E+02 0.0032 26.9 12.7 110 143-264 11-125 (289)
66 cd06319 PBP1_ABC_sugar_binding 57.5 1.3E+02 0.0027 26.0 12.2 122 112-262 125-252 (277)
67 cd06289 PBP1_MalI_like Ligand- 57.0 1.2E+02 0.0027 25.8 11.3 79 112-205 117-201 (268)
68 PRK03170 dihydrodipicolinate s 56.3 1.6E+02 0.0034 26.8 12.3 109 143-264 11-125 (292)
69 TIGR00705 SppA_67K signal pept 55.9 50 0.0011 33.7 8.0 55 152-221 77-135 (584)
70 cd07110 ALDH_F10_BADH Arabidop 55.8 1.4E+02 0.0031 29.0 11.0 23 19-41 41-63 (456)
71 PRK11579 putative oxidoreducta 55.7 65 0.0014 30.0 8.3 56 170-242 62-118 (346)
72 PF01408 GFO_IDH_MocA: Oxidore 55.2 91 0.002 23.7 10.5 103 114-242 2-116 (120)
73 cd00950 DHDPS Dihydrodipicolin 54.9 1.6E+02 0.0035 26.5 12.1 109 143-264 10-124 (284)
74 COG0054 RibH Riboflavin syntha 54.6 1.3E+02 0.0029 25.5 12.0 126 112-264 12-149 (152)
75 cd06270 PBP1_GalS_like Ligand 54.1 1E+02 0.0023 26.5 8.9 79 112-205 116-200 (268)
76 COG5012 Predicted cobalamin bi 53.6 1.2E+02 0.0027 27.4 9.1 93 142-262 133-225 (227)
77 TIGR01101 V_ATP_synt_F vacuola 53.0 87 0.0019 25.2 7.4 60 142-221 34-93 (115)
78 cd07013 S14_ClpP Caseinolytic 52.5 39 0.00085 28.3 5.7 59 152-227 13-73 (162)
79 PRK10727 DNA-binding transcrip 52.3 91 0.002 28.4 8.6 78 113-205 177-260 (343)
80 cd07143 ALDH_AldA_AN0554 Asper 52.2 1.8E+02 0.004 28.6 11.2 20 22-41 71-90 (481)
81 TIGR00674 dapA dihydrodipicoli 52.2 1.8E+02 0.004 26.3 11.7 109 143-264 8-122 (285)
82 PRK01368 murD UDP-N-acetylmura 51.5 1.3E+02 0.0027 29.6 9.8 88 144-264 322-409 (454)
83 PLN02766 coniferyl-aldehyde de 51.5 1.9E+02 0.004 28.8 11.1 21 20-40 83-103 (501)
84 PRK03620 5-dehydro-4-deoxygluc 50.9 2E+02 0.0044 26.5 12.5 108 143-264 17-130 (303)
85 PRK10949 protease 4; Provision 50.8 48 0.001 34.2 7.0 51 153-218 97-151 (618)
86 cd07088 ALDH_LactADH-AldA Esch 50.1 2E+02 0.0043 28.0 11.0 19 241-260 248-266 (468)
87 TIGR03216 OH_muco_semi_DH 2-hy 49.6 2E+02 0.0043 28.3 10.9 24 20-43 60-83 (481)
88 cd07015 Clp_protease_NfeD Nodu 49.6 61 0.0013 27.8 6.4 44 172-228 29-77 (172)
89 cd07113 ALDH_PADH_NahF Escheri 49.0 2E+02 0.0044 28.2 10.9 32 19-52 60-91 (477)
90 cd07131 ALDH_AldH-CAJ73105 Unc 48.8 1.9E+02 0.0042 28.2 10.7 20 22-41 62-81 (478)
91 TIGR00877 purD phosphoribosyla 48.7 1.4E+02 0.0031 28.5 9.6 21 114-135 2-22 (423)
92 cd07093 ALDH_F8_HMSADH Human a 47.3 2.1E+02 0.0046 27.7 10.6 21 20-40 42-62 (455)
93 cd07097 ALDH_KGSADH-YcbD Bacil 46.9 2.3E+02 0.0049 27.8 10.8 16 21-36 61-76 (473)
94 COG2185 Sbm Methylmalonyl-CoA 46.7 40 0.00086 28.3 4.7 46 215-260 15-61 (143)
95 cd07144 ALDH_ALD2-YMR170C Sacc 46.7 2.2E+02 0.0047 28.0 10.7 22 20-41 69-90 (484)
96 PLN02467 betaine aldehyde dehy 46.7 2.4E+02 0.0051 28.1 11.0 20 21-40 74-93 (503)
97 TIGR01804 BADH glycine betaine 46.5 2.4E+02 0.0053 27.5 11.0 22 20-41 58-79 (467)
98 cd06298 PBP1_CcpA_like Ligand- 46.1 1.9E+02 0.0041 24.7 11.5 78 112-205 116-200 (268)
99 cd07109 ALDH_AAS00426 Uncharac 45.3 2.6E+02 0.0056 27.1 10.9 22 110-131 116-137 (454)
100 cd02070 corrinoid_protein_B12- 44.8 2E+02 0.0044 24.7 9.8 102 123-258 98-199 (201)
101 PLN02404 6,7-dimethyl-8-ribity 44.4 1.9E+02 0.0041 24.2 12.5 94 124-230 25-122 (141)
102 cd06300 PBP1_ABC_sugar_binding 43.6 1.7E+02 0.0037 25.2 8.7 89 112-222 125-219 (272)
103 TIGR02299 HpaE 5-carboxymethyl 43.4 2.5E+02 0.0055 27.5 10.6 20 22-41 63-82 (488)
104 cd02810 DHOD_DHPD_FMN Dihydroo 43.4 2.4E+02 0.0053 25.4 9.8 79 146-241 104-191 (289)
105 PRK00366 ispG 4-hydroxy-3-meth 42.8 1.1E+02 0.0024 29.6 7.5 69 170-263 99-167 (360)
106 PLN02466 aldehyde dehydrogenas 42.7 2.8E+02 0.006 28.0 10.9 18 242-260 312-329 (538)
107 cd07138 ALDH_CddD_SSP0762 Rhod 42.6 2.9E+02 0.0064 26.9 10.9 23 20-42 59-81 (466)
108 cd06283 PBP1_RegR_EndR_KdgR_li 42.5 2.1E+02 0.0046 24.3 11.3 117 113-262 117-244 (267)
109 cd06311 PBP1_ABC_sugar_binding 41.9 1.5E+02 0.0033 25.7 8.0 65 149-232 165-229 (274)
110 cd07115 ALDH_HMSADH_HapE Pseud 41.6 3E+02 0.0064 26.7 10.7 22 20-41 42-63 (453)
111 cd07119 ALDH_BADH-GbsA Bacillu 41.3 3.3E+02 0.0071 26.7 11.0 20 22-41 62-81 (482)
112 cd06344 PBP1_ABC_ligand_bindin 41.1 1.5E+02 0.0033 26.8 8.2 94 125-232 22-126 (332)
113 PRK11905 bifunctional proline 40.9 3E+02 0.0065 30.9 11.6 72 128-223 722-793 (1208)
114 cd07091 ALDH_F1-2_Ald2-like AL 40.8 3.5E+02 0.0076 26.4 11.1 23 19-41 65-87 (476)
115 KOG3019 Predicted nucleoside-d 40.6 52 0.0011 30.3 4.8 127 114-259 178-314 (315)
116 PRK13789 phosphoribosylamine-- 40.4 1.7E+02 0.0037 28.5 8.8 118 114-258 6-139 (426)
117 PRK11904 bifunctional proline 40.3 2.8E+02 0.0061 30.6 11.1 46 161-223 756-801 (1038)
118 COG3693 XynA Beta-1,4-xylanase 40.3 1.9E+02 0.0041 27.8 8.6 95 145-245 162-256 (345)
119 cd00951 KDGDH 5-dehydro-4-deox 40.2 2.9E+02 0.0063 25.2 11.7 106 144-264 11-123 (289)
120 PRK11809 putA trifunctional tr 40.0 3E+02 0.0066 31.2 11.4 75 128-223 814-888 (1318)
121 PF00532 Peripla_BP_1: Peripla 40.0 1.1E+02 0.0023 27.7 6.9 77 113-205 119-203 (279)
122 PF15609 PRTase_2: Phosphoribo 39.7 83 0.0018 27.7 5.8 116 112-244 52-183 (191)
123 PRK01438 murD UDP-N-acetylmura 39.6 2.5E+02 0.0054 27.3 9.9 94 144-263 347-442 (480)
124 cd07145 ALDH_LactADH_F420-Bios 38.9 3.3E+02 0.0072 26.4 10.6 21 20-40 44-64 (456)
125 cd07089 ALDH_CddD-AldA-like Rh 38.8 3.8E+02 0.0082 26.1 11.0 22 20-41 43-64 (459)
126 cd07103 ALDH_F5_SSADH_GabD Mit 38.7 3.7E+02 0.008 25.9 10.8 15 22-36 44-58 (451)
127 PRK04690 murD UDP-N-acetylmura 38.6 2.6E+02 0.0057 27.4 9.9 93 144-260 325-417 (468)
128 PF03709 OKR_DC_1_N: Orn/Lys/A 38.4 1.1E+02 0.0024 24.0 6.0 87 156-264 26-114 (115)
129 cd06302 PBP1_LsrB_Quorum_Sensi 38.4 2.9E+02 0.0062 24.6 10.7 123 113-263 124-253 (298)
130 COG0769 MurE UDP-N-acetylmuram 38.3 1.2E+02 0.0026 30.2 7.4 103 143-264 335-438 (475)
131 PRK00208 thiG thiazole synthas 38.3 54 0.0012 30.1 4.5 80 103-203 142-226 (250)
132 cd07142 ALDH_F2BC Arabidosis a 38.3 3.4E+02 0.0073 26.6 10.6 23 20-42 66-88 (476)
133 COG0299 PurN Folate-dependent 38.2 2E+02 0.0044 25.5 8.0 67 177-259 4-75 (200)
134 cd07083 ALDH_P5CDH ALDH subfam 38.2 3.2E+02 0.0069 27.1 10.4 22 20-41 78-99 (500)
135 PLN02419 methylmalonate-semial 37.9 3.5E+02 0.0076 27.9 10.9 19 22-40 176-194 (604)
136 PF13407 Peripla_BP_4: Peripla 37.6 2.6E+02 0.0057 23.9 9.5 119 113-262 123-249 (257)
137 cd01575 PBP1_GntR Ligand-bindi 37.6 2.6E+02 0.0056 23.8 10.1 120 112-263 116-244 (268)
138 PRK11241 gabD succinate-semial 37.1 4E+02 0.0087 26.3 10.9 19 22-40 73-91 (482)
139 TIGR00640 acid_CoA_mut_C methy 37.0 1.3E+02 0.0027 24.6 6.2 43 218-260 9-51 (132)
140 cd04728 ThiG Thiazole synthase 37.0 61 0.0013 29.7 4.7 80 103-203 142-226 (248)
141 KOG0237 Glycinamide ribonucleo 36.9 1.5E+02 0.0032 30.9 7.7 29 231-259 112-140 (788)
142 PRK02228 V-type ATP synthase s 36.9 2E+02 0.0043 22.2 8.2 54 152-223 28-81 (100)
143 PRK13252 betaine aldehyde dehy 36.8 3.9E+02 0.0084 26.3 10.8 20 22-41 69-88 (488)
144 PRK09526 lacI lac repressor; R 36.7 3.2E+02 0.0069 24.6 10.9 76 113-205 182-263 (342)
145 cd07017 S14_ClpP_2 Caseinolyti 36.6 1.9E+02 0.0041 24.2 7.5 75 144-232 11-87 (171)
146 TIGR02990 ectoine_eutA ectoine 36.4 1.3E+02 0.0028 27.1 6.7 65 150-242 164-228 (239)
147 TIGR02370 pyl_corrinoid methyl 36.4 2.1E+02 0.0045 24.8 7.8 78 123-224 100-177 (197)
148 PTZ00323 NAD+ synthase; Provis 36.3 2.9E+02 0.0062 25.8 9.2 62 171-245 44-111 (294)
149 cd07151 ALDH_HBenzADH NADP+-de 36.2 4.2E+02 0.0091 25.8 11.0 22 20-41 55-76 (465)
150 COG1012 PutA NAD-dependent ald 36.1 4.1E+02 0.0088 26.4 10.8 32 212-261 236-267 (472)
151 TIGR01780 SSADH succinate-semi 35.9 4.2E+02 0.009 25.7 10.7 19 21-39 43-61 (448)
152 PRK14194 bifunctional 5,10-met 35.7 3.8E+02 0.0082 25.2 10.3 98 145-257 68-202 (301)
153 cd07141 ALDH_F1AB_F2_RALDH1 NA 35.5 4.4E+02 0.0095 25.9 11.2 22 20-41 70-91 (481)
154 cd07125 ALDH_PutA-P5CDH Delta( 35.2 3.9E+02 0.0084 26.6 10.6 20 22-41 94-113 (518)
155 PF01990 ATP-synt_F: ATP synth 35.2 1.3E+02 0.0027 22.8 5.6 54 152-223 26-79 (95)
156 TIGR01238 D1pyr5carbox3 delta- 34.7 4.7E+02 0.01 26.0 11.0 11 213-223 267-277 (500)
157 PRK00885 phosphoribosylamine-- 34.7 3.9E+02 0.0085 25.5 10.2 27 226-256 105-131 (420)
158 cd07090 ALDH_F9_TMBADH NAD+-de 34.6 3.4E+02 0.0073 26.4 9.9 23 20-42 42-64 (457)
159 cd06327 PBP1_SBP_like_1 Peripl 34.5 1.8E+02 0.0039 26.3 7.6 66 125-204 24-89 (334)
160 PRK11778 putative inner membra 33.9 95 0.0021 29.6 5.7 41 174-224 124-166 (330)
161 cd00953 KDG_aldolase KDG (2-ke 33.8 3.7E+02 0.0079 24.4 11.9 103 144-263 11-120 (279)
162 cd06312 PBP1_ABC_sugar_binding 33.7 3.1E+02 0.0066 23.7 8.7 65 149-232 163-227 (271)
163 PF09673 TrbC_Ftype: Type-F co 33.7 64 0.0014 25.6 3.9 45 1-48 8-65 (113)
164 PRK10090 aldehyde dehydrogenas 33.6 4.5E+02 0.0097 25.4 10.6 72 125-223 114-185 (409)
165 PF12683 DUF3798: Protein of u 33.6 47 0.001 30.8 3.4 10 170-179 60-69 (275)
166 COG3958 Transketolase, C-termi 33.5 1.6E+02 0.0035 27.8 6.9 114 106-261 186-311 (312)
167 PRK04308 murD UDP-N-acetylmura 33.1 3.5E+02 0.0076 26.0 9.7 90 144-263 322-411 (445)
168 PRK03369 murD UDP-N-acetylmura 33.0 3.8E+02 0.0083 26.4 10.0 95 144-264 330-453 (488)
169 TIGR00114 lumazine-synth 6,7-d 32.9 2.8E+02 0.0062 22.9 12.9 114 125-263 19-136 (138)
170 TIGR00612 ispG_gcpE 1-hydroxy- 32.7 1.4E+02 0.003 28.7 6.5 75 156-262 83-157 (346)
171 TIGR03175 AllD ureidoglycolate 32.5 57 0.0012 31.2 4.0 66 181-259 270-336 (349)
172 cd06340 PBP1_ABC_ligand_bindin 32.3 3.9E+02 0.0085 24.4 10.3 94 125-231 23-130 (347)
173 cd01304 FMDH_A Formylmethanofu 32.3 4.5E+02 0.0098 26.9 10.4 98 152-264 156-293 (541)
174 COG3660 Predicted nucleoside-d 32.3 2.6E+02 0.0056 26.4 7.9 89 116-223 73-172 (329)
175 cd07085 ALDH_F6_MMSDH Methylma 32.2 4.9E+02 0.011 25.4 10.7 21 21-41 62-82 (478)
176 TIGR00736 nifR3_rel_arch TIM-b 32.1 2.2E+02 0.0047 25.6 7.4 22 152-179 78-99 (231)
177 cd06287 PBP1_LacI_like_8 Ligan 32.0 2.2E+02 0.0048 25.0 7.5 77 113-205 119-201 (269)
178 PRK13602 putative ribosomal pr 31.9 1.7E+02 0.0037 21.8 5.7 38 213-253 27-64 (82)
179 cd07150 ALDH_VaniDH_like Pseud 31.8 4.8E+02 0.01 25.2 10.8 23 20-42 44-66 (451)
180 cd06273 PBP1_GntR_like_1 This 31.3 3.3E+02 0.0072 23.2 9.7 120 112-263 116-245 (268)
181 COG1609 PurR Transcriptional r 31.3 4.3E+02 0.0094 24.5 11.3 77 113-205 176-260 (333)
182 cd00954 NAL N-Acetylneuraminic 31.2 4E+02 0.0088 24.2 12.5 109 143-264 10-125 (288)
183 KOG3432 Vacuolar H+-ATPase V1 31.1 1.3E+02 0.0029 24.3 5.2 35 142-180 36-70 (121)
184 TIGR01037 pyrD_sub1_fam dihydr 30.9 4.1E+02 0.0089 24.1 9.3 80 146-241 96-184 (300)
185 cd06317 PBP1_ABC_sugar_binding 30.7 3.4E+02 0.0074 23.2 9.6 121 112-262 125-254 (275)
186 PRK14188 bifunctional 5,10-met 30.7 4.1E+02 0.009 24.8 9.3 103 145-257 67-201 (296)
187 PLN02278 succinic semialdehyde 30.3 5.3E+02 0.011 25.5 10.6 15 22-36 87-101 (498)
188 cd06356 PBP1_Amide_Urea_BP_lik 30.1 4.2E+02 0.0092 24.0 12.7 95 125-232 23-125 (334)
189 cd06359 PBP1_Nba_like Type I p 30.0 2.3E+02 0.005 25.6 7.5 47 126-177 24-70 (333)
190 COG0436 Aspartate/tyrosine/aro 30.0 2.8E+02 0.0061 26.6 8.4 78 114-205 90-196 (393)
191 COG0541 Ffh Signal recognition 30.0 4.1E+02 0.0089 26.5 9.4 64 195-265 118-181 (451)
192 cd06297 PBP1_LacI_like_12 Liga 30.0 2.2E+02 0.0047 24.7 7.1 79 112-205 113-203 (269)
193 PF13844 Glyco_transf_41: Glyc 29.4 2.2E+02 0.0048 28.4 7.6 46 211-263 383-429 (468)
194 TIGR03240 arg_catab_astD succi 29.4 5.6E+02 0.012 25.2 10.9 23 20-42 58-80 (484)
195 cd07123 ALDH_F4-17_P5CDH Delta 29.3 4.8E+02 0.01 26.1 10.1 10 214-223 280-289 (522)
196 cd06348 PBP1_ABC_ligand_bindin 29.2 2.2E+02 0.0047 25.9 7.2 62 111-176 8-71 (344)
197 cd07140 ALDH_F1L_FTFDH 10-form 29.2 5.7E+02 0.012 25.3 11.4 22 20-41 68-89 (486)
198 cd07148 ALDH_RL0313 Uncharacte 28.8 4.9E+02 0.011 25.3 9.9 19 22-40 47-65 (455)
199 cd06331 PBP1_AmiC_like Type I 28.7 2.7E+02 0.0059 25.1 7.7 65 125-204 23-90 (333)
200 cd01169 HMPP_kinase 4-amino-5- 28.7 2E+02 0.0044 24.8 6.6 43 151-204 51-93 (242)
201 cd06285 PBP1_LacI_like_7 Ligan 28.6 3.7E+02 0.0081 22.9 9.8 44 149-205 155-198 (265)
202 cd06286 PBP1_CcpB_like Ligand- 28.6 2.5E+02 0.0053 24.0 7.1 120 112-262 114-239 (260)
203 PF14639 YqgF: Holliday-juncti 28.4 38 0.00082 28.4 1.8 77 171-264 62-138 (150)
204 cd06335 PBP1_ABC_ligand_bindin 28.3 2.2E+02 0.0048 26.0 7.1 67 125-204 23-90 (347)
205 cd07105 ALDH_SaliADH Salicylal 28.2 5.5E+02 0.012 24.7 11.4 22 20-41 23-44 (432)
206 PRK15025 ureidoglycolate dehyd 28.1 74 0.0016 30.5 3.9 52 181-242 270-323 (349)
207 PRK15395 methyl-galactoside AB 27.8 4.7E+02 0.01 23.8 11.2 86 149-262 203-291 (330)
208 TIGR00250 RNAse_H_YqgF RNAse H 27.8 3.3E+02 0.0071 22.0 8.3 84 141-241 21-108 (130)
209 cd06352 PBP1_NPR_GC_like Ligan 27.7 2.6E+02 0.0056 25.9 7.5 66 111-186 8-78 (389)
210 TIGR01362 KDO8P_synth 3-deoxy- 27.7 3.2E+02 0.0069 25.2 7.7 25 219-243 53-77 (258)
211 PF12327 FtsZ_C: FtsZ family, 27.7 96 0.0021 23.8 3.8 48 153-204 13-64 (95)
212 cd07118 ALDH_SNDH Gluconobacte 27.6 5.8E+02 0.013 24.8 10.5 31 19-52 43-74 (454)
213 PRK05198 2-dehydro-3-deoxyphos 27.6 3.3E+02 0.0071 25.2 7.8 25 219-243 61-85 (264)
214 cd07114 ALDH_DhaS Uncharacteri 27.3 5.8E+02 0.013 24.7 10.9 30 20-52 44-74 (457)
215 TIGR03407 urea_ABC_UrtA urea A 27.2 5E+02 0.011 23.9 12.7 104 125-241 24-135 (359)
216 PF00171 Aldedh: Aldehyde dehy 26.8 3.6E+02 0.0079 26.2 8.6 20 241-261 241-260 (462)
217 PRK09195 gatY tagatose-bisphos 26.6 3E+02 0.0065 25.6 7.5 21 212-232 74-95 (284)
218 PLN02898 HMP-P kinase/thiamin- 26.5 3.1E+02 0.0067 27.1 8.2 74 120-204 20-103 (502)
219 TIGR01236 D1pyr5carbox1 delta- 26.3 5.7E+02 0.012 25.7 10.1 19 241-260 290-308 (533)
220 PRK00141 murD UDP-N-acetylmura 26.3 5.7E+02 0.012 25.0 9.9 90 150-263 342-432 (473)
221 KOG2862 Alanine-glyoxylate ami 26.2 3.9E+02 0.0084 25.8 8.1 109 8-180 39-150 (385)
222 PRK01390 murD UDP-N-acetylmura 26.2 4.3E+02 0.0093 25.5 9.0 86 144-262 334-419 (460)
223 PRK10206 putative oxidoreducta 26.1 3.5E+02 0.0077 25.3 8.1 56 170-242 62-118 (344)
224 PRK09457 astD succinylglutamic 26.0 6.4E+02 0.014 24.8 11.1 22 20-41 60-81 (487)
225 cd07111 ALDH_F16 Aldehyde dehy 25.7 6.5E+02 0.014 24.8 10.4 15 22-36 84-98 (480)
226 PRK02628 nadE NAD synthetase; 25.7 5.1E+02 0.011 27.0 9.8 85 163-260 352-438 (679)
227 PF10440 WIYLD: Ubiquitin-bind 25.5 62 0.0013 23.6 2.2 26 12-41 22-47 (65)
228 cd05569 PTS_IIB_fructose PTS_I 25.2 3E+02 0.0066 20.9 6.3 71 179-264 6-93 (96)
229 PRK07511 enoyl-CoA hydratase; 25.1 4.1E+02 0.0089 23.6 8.1 75 158-232 33-118 (260)
230 PF00448 SRP54: SRP54-type pro 25.1 4.5E+02 0.0097 22.6 8.4 78 175-263 3-80 (196)
231 COG0124 HisS Histidyl-tRNA syn 25.1 6.7E+02 0.014 24.8 10.0 94 93-204 265-361 (429)
232 PRK00414 gmhA phosphoheptose i 25.1 4.4E+02 0.0095 22.6 10.6 17 110-126 42-58 (192)
233 PRK10401 DNA-binding transcrip 25.0 2.8E+02 0.006 25.2 7.1 78 113-205 177-260 (346)
234 cd06296 PBP1_CatR_like Ligand- 25.0 2.8E+02 0.006 23.7 6.8 79 112-205 117-201 (270)
235 PF13458 Peripla_BP_6: Peripla 25.0 3.1E+02 0.0068 24.5 7.3 101 126-239 26-134 (343)
236 cd06281 PBP1_LacI_like_5 Ligan 25.0 4.4E+02 0.0096 22.6 9.0 119 112-263 116-243 (269)
237 PF02782 FGGY_C: FGGY family o 24.9 3.7E+02 0.008 22.3 7.4 85 170-259 104-192 (198)
238 COG2055 Malate/L-lactate dehyd 24.9 1.6E+02 0.0034 28.4 5.4 22 217-242 307-328 (349)
239 PRK05286 dihydroorotate dehydr 24.8 5.5E+02 0.012 24.1 9.2 63 152-221 155-220 (344)
240 KOG2270 Serine/threonine prote 24.8 82 0.0018 31.3 3.5 47 17-64 269-315 (520)
241 cd06294 PBP1_ycjW_transcriptio 24.6 3.6E+02 0.0079 22.9 7.5 78 113-205 123-206 (270)
242 PRK15408 autoinducer 2-binding 24.6 5.7E+02 0.012 23.7 9.4 63 150-232 190-252 (336)
243 PLN02331 phosphoribosylglycina 24.5 2.7E+02 0.0058 24.5 6.6 44 194-246 13-56 (207)
244 cd07095 ALDH_SGSD_AstD N-succi 24.4 6.5E+02 0.014 24.3 10.3 21 20-40 23-43 (431)
245 PF00378 ECH: Enoyl-CoA hydrat 24.3 4E+02 0.0088 23.2 7.8 75 158-232 28-110 (245)
246 PRK09847 gamma-glutamyl-gamma- 24.3 7E+02 0.015 24.7 11.1 22 110-131 156-177 (494)
247 PRK00421 murC UDP-N-acetylmura 24.3 6.6E+02 0.014 24.3 11.6 92 152-263 333-432 (461)
248 PRK14987 gluconate operon tran 24.2 4.9E+02 0.011 23.3 8.5 77 113-205 181-262 (331)
249 COG1509 KamA Lysine 2,3-aminom 23.8 5.6E+02 0.012 24.9 8.9 127 112-263 110-246 (369)
250 TIGR03250 PhnAcAld_DH putative 23.7 7E+02 0.015 24.4 10.1 19 22-40 61-79 (472)
251 cd06347 PBP1_ABC_ligand_bindin 23.7 3.9E+02 0.0084 23.7 7.7 48 125-176 23-71 (334)
252 PRK12738 kbaY tagatose-bisphos 23.7 3.8E+02 0.0083 24.9 7.7 10 195-204 32-41 (286)
253 cd07107 ALDH_PhdK-like Nocardi 23.7 3.3E+02 0.0072 26.5 7.7 19 111-129 116-134 (456)
254 cd04738 DHOD_2_like Dihydrooro 23.7 5.6E+02 0.012 23.8 9.0 85 145-241 133-231 (327)
255 PRK06683 hypothetical protein; 23.6 2.8E+02 0.0062 20.7 5.7 36 215-253 29-64 (82)
256 cd07041 STAS_RsbR_RsbS_like Su 23.6 3.2E+02 0.0069 20.5 7.9 70 171-254 39-108 (109)
257 PRK06801 hypothetical protein; 23.6 4E+02 0.0086 24.7 7.8 10 195-204 32-41 (286)
258 PF12357 PLD_C: Phospholipase 23.6 1.7E+02 0.0038 21.8 4.3 48 16-63 12-64 (74)
259 PRK11468 dihydroxyacetone kina 23.3 1.6E+02 0.0035 28.4 5.2 59 112-191 43-117 (356)
260 cd06366 PBP1_GABAb_receptor Li 23.3 5.2E+02 0.011 23.4 8.6 66 125-203 21-88 (350)
261 cd02069 methionine_synthase_B1 23.3 5.1E+02 0.011 22.7 10.0 105 123-260 104-211 (213)
262 cd01541 PBP1_AraR Ligand-bindi 23.2 2.2E+02 0.0047 24.6 5.8 39 154-205 168-206 (273)
263 TIGR01501 MthylAspMutase methy 23.1 2.9E+02 0.0064 22.7 6.1 47 215-261 4-51 (134)
264 smart00256 FBOX A Receptor for 23.1 1.8E+02 0.0039 17.4 3.9 33 1-33 1-33 (41)
265 PRK12616 pyridoxal kinase; Rev 23.0 2.6E+02 0.0057 25.1 6.4 44 150-204 56-99 (270)
266 PTZ00106 60S ribosomal protein 23.0 2.6E+02 0.0056 22.1 5.6 32 214-245 42-73 (108)
267 COG0399 WecE Predicted pyridox 23.0 2.6E+02 0.0057 27.0 6.7 36 143-187 99-138 (374)
268 cd04741 DHOD_1A_like Dihydroor 22.9 5.9E+02 0.013 23.3 9.6 61 145-221 96-166 (294)
269 KOG3040 Predicted sugar phosph 22.9 1.5E+02 0.0032 27.0 4.5 78 171-257 5-82 (262)
270 PRK09426 methylmalonyl-CoA mut 22.9 9.1E+02 0.02 25.5 11.0 104 129-262 603-707 (714)
271 PRK11041 DNA-binding transcrip 22.7 5.3E+02 0.011 22.6 10.7 79 112-205 152-236 (309)
272 COG2759 MIS1 Formyltetrahydrof 22.7 1.9E+02 0.0041 29.2 5.6 33 210-243 367-402 (554)
273 COG3473 Maleate cis-trans isom 22.7 4.8E+02 0.01 23.7 7.6 69 145-242 158-226 (238)
274 cd07120 ALDH_PsfA-ACA09737 Pse 22.6 7.2E+02 0.016 24.2 11.0 20 21-40 44-63 (455)
275 KOG3405 RNA polymerase subunit 22.6 1.7E+02 0.0036 24.2 4.4 30 176-219 88-117 (136)
276 PRK14483 DhaKLM operon coactiv 22.4 1.6E+02 0.0034 28.2 4.9 59 112-191 42-116 (329)
277 cd07112 ALDH_GABALDH-PuuC Esch 22.4 7.3E+02 0.016 24.2 10.9 19 19-37 48-66 (462)
278 PF01171 ATP_bind_3: PP-loop f 22.3 4.6E+02 0.01 21.8 11.0 99 147-260 6-115 (182)
279 COG3077 RelB DNA-damage-induci 22.2 1.2E+02 0.0026 23.4 3.4 33 217-262 9-41 (88)
280 PF00763 THF_DHG_CYH: Tetrahyd 22.2 1.7E+02 0.0038 23.1 4.5 66 114-184 31-101 (117)
281 TIGR01036 pyrD_sub2 dihydrooro 22.2 6.6E+02 0.014 23.6 10.0 80 152-241 152-239 (335)
282 TIGR01082 murC UDP-N-acetylmur 22.1 7.2E+02 0.016 24.0 11.3 91 151-263 326-427 (448)
283 cd06291 PBP1_Qymf_like Ligand 22.1 5E+02 0.011 22.1 12.2 78 112-205 112-196 (265)
284 TIGR01506 ribC_arch riboflavin 22.0 4.9E+02 0.011 22.0 12.2 109 127-263 17-128 (151)
285 COG0151 PurD Phosphoribosylami 22.0 1E+02 0.0023 30.4 3.7 54 195-260 77-136 (428)
286 PRK02705 murD UDP-N-acetylmura 21.7 7.2E+02 0.016 23.8 10.3 89 145-263 329-419 (459)
287 PRK11303 DNA-binding transcrip 21.7 5.8E+02 0.012 22.7 10.9 77 112-205 179-261 (328)
288 PRK10014 DNA-binding transcrip 21.7 5.9E+02 0.013 22.8 9.6 78 113-205 183-266 (342)
289 KOG0781 Signal recognition par 21.7 6.9E+02 0.015 25.5 9.3 85 170-262 464-554 (587)
290 cd07108 ALDH_MGR_2402 Magnetos 21.6 4.2E+02 0.0091 25.7 7.9 22 20-41 42-63 (457)
291 PRK12553 ATP-dependent Clp pro 21.5 4.3E+02 0.0092 23.1 7.2 75 145-232 38-113 (207)
292 cd07130 ALDH_F7_AASADH NAD+-de 21.5 4.8E+02 0.01 25.6 8.4 20 20-39 57-76 (474)
293 TIGR01722 MMSDH methylmalonic 21.5 7.7E+02 0.017 24.1 11.2 19 108-126 133-151 (477)
294 TIGR01481 ccpA catabolite cont 21.4 4E+02 0.0086 23.8 7.3 76 113-205 177-259 (329)
295 TIGR03374 ABALDH 1-pyrroline d 21.3 4.6E+02 0.0099 25.8 8.2 22 20-41 61-82 (472)
296 COG1433 Uncharacterized conser 21.2 2.4E+02 0.0052 22.9 5.1 28 227-259 78-105 (121)
297 COG1181 DdlA D-alanine-D-alani 21.2 1.2E+02 0.0026 28.5 3.9 36 11-46 237-286 (317)
298 cd06558 crotonase-like Crotona 21.0 4.8E+02 0.01 21.5 7.3 75 154-232 29-113 (195)
299 cd01822 Lysophospholipase_L1_l 21.0 4.4E+02 0.0095 21.0 6.9 29 151-180 81-109 (177)
300 cd06301 PBP1_rhizopine_binding 20.9 5.3E+02 0.012 22.0 9.7 76 113-205 124-206 (272)
301 PRK03137 1-pyrroline-5-carboxy 20.9 8.3E+02 0.018 24.2 10.4 14 110-123 170-183 (514)
302 COG3148 Uncharacterized conser 20.9 3.7E+02 0.0079 24.3 6.5 58 170-242 100-157 (231)
303 PF00574 CLP_protease: Clp pro 20.9 3.2E+02 0.007 22.8 6.2 77 143-232 17-94 (182)
304 PRK14022 UDP-N-acetylmuramoyla 20.8 7.9E+02 0.017 24.0 10.7 98 149-263 346-443 (481)
305 cd07152 ALDH_BenzADH NAD-depen 20.8 7.6E+02 0.016 23.8 11.3 21 21-41 37-57 (443)
306 KOG4826 C-8,7 sterol isomerase 20.8 52 0.0011 29.5 1.3 41 21-61 89-130 (229)
307 cd06358 PBP1_NHase Type I peri 20.8 6.2E+02 0.014 22.7 9.4 100 125-240 23-132 (333)
308 TIGR01858 tag_bisphos_ald clas 20.7 5E+02 0.011 24.1 7.8 21 212-232 72-93 (282)
309 cd07104 ALDH_BenzADH-like ALDH 20.7 7.4E+02 0.016 23.6 11.1 22 20-41 23-44 (431)
310 PRK11235 bifunctional antitoxi 20.7 1.6E+02 0.0034 22.3 3.7 33 217-262 6-38 (80)
311 TIGR01234 L-ribulokinase L-rib 20.7 4.9E+02 0.011 25.9 8.3 74 170-246 391-468 (536)
312 PRK06806 fructose-bisphosphate 20.7 4.8E+02 0.01 24.1 7.7 21 212-232 74-95 (281)
313 PF02887 PK_C: Pyruvate kinase 20.6 2.5E+02 0.0055 21.8 5.1 72 170-264 14-86 (117)
314 PRK07565 dihydroorotate dehydr 20.6 6.9E+02 0.015 23.2 9.5 81 145-241 106-192 (334)
315 PF08353 DUF1727: Domain of un 20.4 4.4E+02 0.0096 20.9 6.7 85 153-261 5-97 (113)
316 TIGR02362 dhaK1b probable dihy 20.3 1.8E+02 0.0039 27.7 4.8 59 112-191 40-114 (326)
317 cd06274 PBP1_FruR Ligand bindi 20.3 5.4E+02 0.012 21.9 10.6 119 112-262 116-244 (264)
318 PRK00109 Holliday junction res 20.2 4.8E+02 0.01 21.3 8.3 67 158-241 44-114 (138)
No 1
>PLN02235 ATP citrate (pro-S)-lyase
Probab=100.00 E-value=2.5e-72 Score=534.76 Aligned_cols=262 Identities=92% Similarity=1.436 Sum_probs=244.9
Q ss_pred CCHhhHHHHHcCCChhHHHHHHHHHHHHHHHHHhCCceeeEeecceecCCceEEeeccccccCcccccCccccccccCCC
Q 024560 1 MTLDACAPLIATLPLEFRGKIGDFIMGVFAVFQDLDFSFIEMNPFTLVNGEPYPLDMRGELDDTAAFKNFKKWANIEFPL 80 (266)
Q Consensus 1 ~~~~~~~~l~~gl~~~~~~~~~~ii~~Ly~~f~~~D~~l~EINPLvv~~g~~~alD~k~~iDd~A~~R~~~~~~~~~~~~ 80 (266)
+++.+++.++.+++.+..+++.+++.+||++|.++||+|+|||||++.||+++|||+|++|||||+|||++.|..++||.
T Consensus 158 l~~~~~~~~~~~l~~~~~~~~~~~l~~Ly~~F~~~D~tllEINPLv~~dg~~~alDaK~~~DDnA~fR~~~~~~~~~f~~ 237 (423)
T PLN02235 158 LTSEICAPLIATLPLEIRGKIEEFIKGVFAVFQDLDFTFLEMNPFTLVDGEPYPLDMRGELDDTAAFKNFKKWGNIEFPL 237 (423)
T ss_pred CCHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHcCCeEEEecceEeeCCCEEEEEeEEcccCCCcccCHhHhhhhcccc
Confidence 36788899999999889999999999999999999999999999999889999999999999999999999899999999
Q ss_pred CCCCCCChhhhhhcccccccccccCceEecCCCcEEEEecCchHHHHHHHHHHhcCCCCCCCceeeccCCCCHHHHHHHH
Q 024560 81 PFGRVLSSTESFIHSLDEKTSASLKFTVLNPKGRIWTMVAGGGASVIYADTVGDLGYASELGNYAEYSGAPNEEEVLQYA 160 (266)
Q Consensus 81 ~~~~~~~~~E~~a~~~d~~~~~~~~l~~v~l~G~Igii~NGaGlam~t~D~l~~~g~gg~pAN~lDlgG~a~~~~~~~al 160 (266)
+|+|+.+|+|.++.++|++++.++.+++|+|+||||||+||||++|+|||+++.+|++|+||||+|+||+|+.+++++++
T Consensus 238 ~fgr~~~~~E~~~~~~d~a~~~~l~y~~v~ldG~Ig~mvnGAGlamaTmD~I~~~G~~g~pANFlDvGG~a~~e~v~~a~ 317 (423)
T PLN02235 238 PFGRVMSPTESFIHGLDEKTSASLKFTVLNPKGRIWTMVAGGGASVIYADTVGDLGYASELGNYAEYSGAPNEEEVLQYA 317 (423)
T ss_pred cccCCCCHHHHhhccchhhhccCCceEEeCCCCeEEEEecCcHHHHHHHHHHHHcCCCCCCceeeecCCCCCHHHHHHHH
Confidence 99999999999999999888888666669999999999999999999999999995349999999999999999999999
Q ss_pred HHHHhhhccCCCCCeEEEEecccccchhHhhhhHHHHHHHHHHhhhhhhcccceEEEEeCCCCHHHHHHHHHhhhhhcCC
Q 024560 161 RVVIDCATADPDGRKRALLIGGGIANFTDVATTFNGIIRALREKESKLKAARMHIFVRRGGPNYQTGLAKMRALGEELGI 240 (266)
Q Consensus 161 ~~ll~~~~~d~~v~~vlvni~ggi~~~~~vA~~~~gii~al~~~~~~~~~~~~pvvvrl~G~~~~~~~~~L~~~~~~~Gi 240 (266)
+++|+++++||++|+|||||||||+|||+||+||+||++|++++..++++.++||||||+|||+++|+++|++.++++|+
T Consensus 318 ~iil~~~~~~~~vk~ilvnIfGGI~rcd~VA~tf~GIi~A~~e~~~kl~~~~vpivVRl~GtN~eeG~~il~e~~~~~gl 397 (423)
T PLN02235 318 RVVIDCATANPDGRKRALLIGGGIANFTDVAATFNGIIRALREKESKLKAARMHIFVRRGGPNYQKGLAKMRALGEEIGV 397 (423)
T ss_pred HHHHhhhhcCCCCcEEEEEEecccccchhhhhhhhHHHHHHHHhhhccccCCccEEEECCCCCHHHHHHHHHHhHHhcCC
Confidence 99998888899999999999999999999999999999999998644445689999999999999999999988888899
Q ss_pred ceeecCCCCCHHHHHHHHHHHh
Q 024560 241 PLEVYGPEATMTGICKQAIDCI 262 (266)
Q Consensus 241 p~~~~~~~~~~~eAv~~av~~~ 262 (266)
|+++|++.+||++||+++|+..
T Consensus 398 ~i~~~~~~~~m~~a~~~av~~~ 419 (423)
T PLN02235 398 PIEVYGPEATMTGICKQAIDYI 419 (423)
T ss_pred cEEEeCCCCCHHHHHHHHHhhh
Confidence 9999999999999999999754
No 2
>COG0045 SucC Succinyl-CoA synthetase, beta subunit [Energy production and conversion]
Probab=100.00 E-value=1.2e-66 Score=486.26 Aligned_cols=227 Identities=23% Similarity=0.354 Sum_probs=208.5
Q ss_pred hhHHHHH--cCCChhHHHHHHHHHHHHHHHHHhCCceeeEeeccee-c-CCceEEeeccccccCcccccCccccccccCC
Q 024560 4 DACAPLI--ATLPLEFRGKIGDFIMGVFAVFQDLDFSFIEMNPFTL-V-NGEPYPLDMRGELDDTAAFKNFKKWANIEFP 79 (266)
Q Consensus 4 ~~~~~l~--~gl~~~~~~~~~~ii~~Ly~~f~~~D~~l~EINPLvv-~-~g~~~alD~k~~iDd~A~~R~~~~~~~~~~~ 79 (266)
-+.+.++ .||++++++++++++.+||++|.++|++|+|||||++ . +|+++|||+|++|||||+||||++ .++.
T Consensus 156 ~~aR~la~~lgl~~~~~~~~~~ii~~Ly~~f~~~Da~lvEINPLvvt~~~g~v~aLDaKi~~DdnAlfRHp~~---~~~~ 232 (387)
T COG0045 156 YQARELAFKLGLEGELVKQVADIIKKLYKLFVEKDATLVEINPLVVTPDGGDVLALDAKITLDDNALFRHPDL---AELR 232 (387)
T ss_pred HHHHHHHHHcCCCHHHHHHHHHHHHHHHHHHHHcCCcEEEeeccEEeCCCCcEEEEeeeeeccCcccccCcch---hhhh
Confidence 3444444 4888999999999999999999999999999999999 6 559999999999999999999985 1222
Q ss_pred CCCCCCCChhhhhhcccccccccccCceEecCCCcEEEEecCchHHHHHHHHHHhcCCCCCCCceeeccCCCCHHHHHHH
Q 024560 80 LPFGRVLSSTESFIHSLDEKTSASLKFTVLNPKGRIWTMVAGGGASVIYADTVGDLGYASELGNYAEYSGAPNEEEVLQY 159 (266)
Q Consensus 80 ~~~~~~~~~~E~~a~~~d~~~~~~~~l~~v~l~G~Igii~NGaGlam~t~D~l~~~g~gg~pAN~lDlgG~a~~~~~~~a 159 (266)
+..+++|.|.+++ .++|+||.|+||||||+||+||+|+|||+++.+ ||+||||||+||+|+.+++++|
T Consensus 233 --d~~~ed~~e~~a~--------~~~l~yV~LdG~IG~ivNGAGLaMaTmDii~~~--Gg~PANFLDvGGgA~~e~v~~a 300 (387)
T COG0045 233 --DESEEDPREAEAS--------GYGLNYVELDGNIGCIVNGAGLAMATMDIVKLY--GGKPANFLDVGGGATAERVKEA 300 (387)
T ss_pred --cccccChhHHHhh--------hCCCceEEecCcEEEEecChhHHHHHHHHHHHc--CCCCcceeecCCCCCHHHHHHH
Confidence 4478899999988 899999999999999999999999999999999 8999999999999999999999
Q ss_pred HHHHHhhhccCCCCCeEEEEecccccchhHhhhhHHHHHHHHHHhhhhhhcccceEEEEeCCCCHHHHHHHHHhhhhhcC
Q 024560 160 ARVVIDCATADPDGRKRALLIGGGIANFTDVATTFNGIIRALREKESKLKAARMHIFVRRGGPNYQTGLAKMRALGEELG 239 (266)
Q Consensus 160 l~~ll~~~~~d~~v~~vlvni~ggi~~~~~vA~~~~gii~al~~~~~~~~~~~~pvvvrl~G~~~~~~~~~L~~~~~~~G 239 (266)
++++++ ||++|+|||||||||++||.|| +||++|+++.. .++|+||||.|||+++||++|+ ++|
T Consensus 301 ~~~il~----d~~vk~IfVNIfGGI~rcD~vA---~GIi~Al~e~~-----~~vPlVVRL~GtN~e~Gk~iL~----esg 364 (387)
T COG0045 301 FKLILS----DPNVKAIFVNIFGGITRCDEVA---EGIIAALKEVG-----VNVPLVVRLEGTNVEEGKRILA----ESG 364 (387)
T ss_pred HHHHhc----CCCccEEEEEEccCcCccHHHH---HHHHHHHHhcC-----CCCCEEEEcCCCCHHHHHHHHH----HcC
Confidence 999999 9999999999999999999999 99999999984 6899999999999999999999 669
Q ss_pred CceeecCCCCCHHHHHHHHHHHhhh
Q 024560 240 IPLEVYGPEATMTGICKQAIDCIMS 264 (266)
Q Consensus 240 ip~~~~~~~~~~~eAv~~av~~~~~ 264 (266)
+++++| ++|++|+++++++++.
T Consensus 365 ~~i~~~---~~l~~aa~k~v~~~~~ 386 (387)
T COG0045 365 LNIIAA---DDLDEAAEKAVELAKG 386 (387)
T ss_pred CceEec---ccHHHHHHHHHHHhhc
Confidence 887754 5999999999999875
No 3
>PLN00124 succinyl-CoA ligase [GDP-forming] subunit beta; Provisional
Probab=100.00 E-value=7.1e-63 Score=473.39 Aligned_cols=228 Identities=21% Similarity=0.329 Sum_probs=209.9
Q ss_pred CHhhHHHHHcCCC--hhHHHHHHHHHHHHHHHHHhCCceeeEeeccee-cCCceEEeeccccccCcccccCccccccccC
Q 024560 2 TLDACAPLIATLP--LEFRGKIGDFIMGVFAVFQDLDFSFIEMNPFTL-VNGEPYPLDMRGELDDTAAFKNFKKWANIEF 78 (266)
Q Consensus 2 ~~~~~~~l~~gl~--~~~~~~~~~ii~~Ly~~f~~~D~~l~EINPLvv-~~g~~~alD~k~~iDd~A~~R~~~~~~~~~~ 78 (266)
++.++++++.++. +...+++.+++.+||++|.++|++++|||||++ ++|+++|+|+|+++||||+||||++|. +
T Consensus 191 ~~~~a~~~~~~L~~~~~~~~~l~~ii~~L~~lf~~~d~~~lEINPL~vt~~G~~valDAKi~~DdnA~~R~~~~~~---~ 267 (422)
T PLN00124 191 TDEDAAKVVDGLAPKVADRNDAIEQVKKLYKLFCKCDCTMVEINPLAETADGQLVAADAKLNFDDNAAFRQKEIFA---L 267 (422)
T ss_pred CHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHHHhCCCeEEEeeceEEccCCCEEEEEEEECcCCchhhcChhhhh---c
Confidence 5677888888774 668899999999999999999999999999999 999999999999999999999999863 2
Q ss_pred CCCCCCCCChhhhhhcccccccccccCceEecCCCcEEEEecCchHHHHHHHHHHhcCCCCCCCceeeccCCCCHHHHHH
Q 024560 79 PLPFGRVLSSTESFIHSLDEKTSASLKFTVLNPKGRIWTMVAGGGASVIYADTVGDLGYASELGNYAEYSGAPNEEEVLQ 158 (266)
Q Consensus 79 ~~~~~~~~~~~E~~a~~~d~~~~~~~~l~~v~l~G~Igii~NGaGlam~t~D~l~~~g~gg~pAN~lDlgG~a~~~~~~~ 158 (266)
. +.++.+|+|.+++ .++++||+|+||||||+||||++|+|||+|..+ ||+||||+|+||+|+.+++++
T Consensus 268 ~--~~~~~~~~E~~a~--------~~~l~yv~ldG~Ig~~vnGaGlamaTmD~i~~~--Gg~pANFlD~GG~a~~~~v~~ 335 (422)
T PLN00124 268 R--DTSQEDPREVAAA--------KADLNYIGLDGEIGCMVNGAGLAMATMDIIKLH--GGSPANFLDVGGNASEQQVVE 335 (422)
T ss_pred c--CcccCChhHHHHh--------hCCCceECCCCcEEEEecCchHHHHHHHHHHHc--CCCcceeeecCCCCCHHHHHH
Confidence 2 3356788898877 889999999999999999999999999999999 899999999999999999999
Q ss_pred HHHHHHhhhccCCCCCeEEEEecccccchhHhhhhHHHHHHHHHHhhhhhhcccceEEEEeCCCCHHHHHHHHHhhhhhc
Q 024560 159 YARVVIDCATADPDGRKRALLIGGGIANFTDVATTFNGIIRALREKESKLKAARMHIFVRRGGPNYQTGLAKMRALGEEL 238 (266)
Q Consensus 159 al~~ll~~~~~d~~v~~vlvni~ggi~~~~~vA~~~~gii~al~~~~~~~~~~~~pvvvrl~G~~~~~~~~~L~~~~~~~ 238 (266)
+++++++ ||++|+|||||||||++||.|| +||++|+++.. .++||||||.|||+++|+++|+ ++
T Consensus 336 a~~ii~~----d~~vk~iliNIfGGI~~cd~iA---~gii~a~~~~~-----~~~pivvRl~Gtn~~~g~~~l~----~~ 399 (422)
T PLN00124 336 AFKILTS----DDKVKAILVNIFGGIMKCDVIA---SGIVNAAKQVG-----LKVPLVVRLEGTNVDQGKRILK----ES 399 (422)
T ss_pred HHHHHhc----CCCCcEEEEEecCCccchHHHH---HHHHHHHHhcC-----CCCcEEEEcCCCCHHHHHHHHH----hC
Confidence 9999999 9999999999999999999999 99999999874 6899999999999999999999 66
Q ss_pred CCceeecCCCCCHHHHHHHHHHHhh
Q 024560 239 GIPLEVYGPEATMTGICKQAIDCIM 263 (266)
Q Consensus 239 Gip~~~~~~~~~~~eAv~~av~~~~ 263 (266)
|+++++++ +|+|||+++|+++.
T Consensus 400 ~~~~~~~~---~l~~A~~~~v~~~~ 421 (422)
T PLN00124 400 GMTLITAE---DLDDAAEKAVKALA 421 (422)
T ss_pred CCCeEEcC---CHHHHHHHHHHHhc
Confidence 99888654 99999999999864
No 4
>PRK14046 malate--CoA ligase subunit beta; Provisional
Probab=100.00 E-value=9.4e-58 Score=435.54 Aligned_cols=230 Identities=23% Similarity=0.325 Sum_probs=209.6
Q ss_pred CHhhHHHHHc--CCChhHHHHHHHHHHHHHHHHHhCCceeeEeeccee-cCCceEEeeccccccCcccccCccccccccC
Q 024560 2 TLDACAPLIA--TLPLEFRGKIGDFIMGVFAVFQDLDFSFIEMNPFTL-VNGEPYPLDMRGELDDTAAFKNFKKWANIEF 78 (266)
Q Consensus 2 ~~~~~~~l~~--gl~~~~~~~~~~ii~~Ly~~f~~~D~~l~EINPLvv-~~g~~~alD~k~~iDd~A~~R~~~~~~~~~~ 78 (266)
++.+++.++. |++++..+++.+|+.+||++|.++||+|+|||||++ .||+++|||+|++|||||+||||++|. +.
T Consensus 156 ~~~~~~~~~~~lg~~~~~~~~~~~~~~~l~~~f~~~d~~l~EINPl~~~~~g~~~alD~k~~~Ddna~~r~~~~~~-~~- 233 (392)
T PRK14046 156 QQFQAREIAFGLGLDIKQVSRAVKTIMGCYRAFRDLDATMLEINPLVVTKDDRVLALDAKMSFDDNALFRRPNIAE-MR- 233 (392)
T ss_pred CHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHHHhcCcEEEEEEcceEcCCCcEEEEeeeECccCCchhcChhHHh-hc-
Confidence 4555666655 668899999999999999999999999999999999 999999999999999999999999652 33
Q ss_pred CCCCCCCCChhhhhhcccccccccccCceEecCCCcEEEEecCchHHHHHHHHHHhcCCCCCCCceeeccCCCCHHHHHH
Q 024560 79 PLPFGRVLSSTESFIHSLDEKTSASLKFTVLNPKGRIWTMVAGGGASVIYADTVGDLGYASELGNYAEYSGAPNEEEVLQ 158 (266)
Q Consensus 79 ~~~~~~~~~~~E~~a~~~d~~~~~~~~l~~v~l~G~Igii~NGaGlam~t~D~l~~~g~gg~pAN~lDlgG~a~~~~~~~ 158 (266)
+..+.+|+|.+++ .++++||+|+||||||+||+|++|+|||+|..+ ||+|+||+|+||++++++|.+
T Consensus 234 ---~~~~~~~~e~~a~--------~~~l~yv~l~G~ig~i~nGaGl~m~t~D~i~~~--gg~paNPlDlgg~a~~e~~~~ 300 (392)
T PRK14046 234 ---DPSQEDPREAQAA--------EHGLSYVGLDGDIGCIVNGAGLAMATMDMIKLA--GGEPANFLDVGGGASPERVAK 300 (392)
T ss_pred ---CcccCChhHHHHH--------HcCCceEccCCcEEEEeCCccHHHHHHHHHHhc--CCCCcCCEEecCCCCHHHHHH
Confidence 3356789999988 899999999999999999999999999999999 799999999999999999999
Q ss_pred HHHHHHhhhccCCCCCeEEEEecccccchhHhhhhHHHHHHHHHHhhhhhhcccceEEEEeCCCCHHHHHHHHHhhhhhc
Q 024560 159 YARVVIDCATADPDGRKRALLIGGGIANFTDVATTFNGIIRALREKESKLKAARMHIFVRRGGPNYQTGLAKMRALGEEL 238 (266)
Q Consensus 159 al~~ll~~~~~d~~v~~vlvni~ggi~~~~~vA~~~~gii~al~~~~~~~~~~~~pvvvrl~G~~~~~~~~~L~~~~~~~ 238 (266)
+++++++ ||++++||+|++||+++|+.+| ++|+++.++.. .++||++|+.|++.++++++|+ ++
T Consensus 301 aL~~ll~----Dp~VdaVlv~i~ggi~~~~~vA---~~Ii~a~~~~~-----~~kPvvv~l~G~~~e~~~~iL~----~~ 364 (392)
T PRK14046 301 AFRLVLS----DRNVKAILVNIFAGINRCDWVA---EGVVQAAREVG-----IDVPLVVRLAGTNVEEGRKILA----ES 364 (392)
T ss_pred HHHHHHc----CCCCCEEEEEcCCCCCCHHHHH---HHHHHHHHhcC-----CCCcEEEEcCCCCHHHHHHHHH----Hc
Confidence 9999999 9999999999999999999999 99999988742 4689999999999999999999 67
Q ss_pred CCceeecCCCCCHHHHHHHHHHHhhhc
Q 024560 239 GIPLEVYGPEATMTGICKQAIDCIMSA 265 (266)
Q Consensus 239 Gip~~~~~~~~~~~eAv~~av~~~~~~ 265 (266)
|+|++. +++|++||+++|++++++
T Consensus 365 Gipvf~---~~~~~~a~~~~v~~~~~~ 388 (392)
T PRK14046 365 GLPIIT---ADTLAEAAEKAVEAWKGA 388 (392)
T ss_pred CCCeee---cCCHHHHHHHHHHHHhhh
Confidence 999975 559999999999999765
No 5
>KOG1447 consensus GTP-specific succinyl-CoA synthetase, beta subunit [Energy production and conversion]
Probab=100.00 E-value=4.2e-56 Score=398.58 Aligned_cols=227 Identities=22% Similarity=0.350 Sum_probs=210.3
Q ss_pred CCHhhHHHHHcCC--ChhHHHHHHHHHHHHHHHHHhCCceeeEeeccee-cCCceEEeeccccccCcccccCcccccccc
Q 024560 1 MTLDACAPLIATL--PLEFRGKIGDFIMGVFAVFQDLDFSFIEMNPFTL-VNGEPYPLDMRGELDDTAAFKNFKKWANIE 77 (266)
Q Consensus 1 ~~~~~~~~l~~gl--~~~~~~~~~~ii~~Ly~~f~~~D~~l~EINPLvv-~~g~~~alD~k~~iDd~A~~R~~~~~~~~~ 77 (266)
|++.++-++.+.| .+++..+.++-|++||.+|..-|++.+|||||+. ++|+++|.|+|++|||||.|||+|+|
T Consensus 181 i~esq~l~~Ak~L~F~G~l~~~aA~eI~kLY~LF~avDAtQvEiNPl~ET~~G~V~cvDAK~NFDDnA~fRQKdIF---- 256 (412)
T KOG1447|consen 181 IKESQALRMAKNLGFVGPLKSQAADEITKLYNLFLAVDATQVEINPLGETPEGQVVCVDAKINFDDNAEFRQKDIF---- 256 (412)
T ss_pred CchHHHHHHHHhccccCcHHHHHHHHHHHHHHHHhhhcceEEEecccccCCCceEEEEeeeccCCchHhhhhccee----
Confidence 4666777777755 4889999999999999999999999999999999 99999999999999999999999984
Q ss_pred CCCCCCCCCChhhhhhcccccccccccCceEecCCCcEEEEecCchHHHHHHHHHHhcCCCCCCCceeeccCCCCHHHHH
Q 024560 78 FPLPFGRVLSSTESFIHSLDEKTSASLKFTVLNPKGRIWTMVAGGGASVIYADTVGDLGYASELGNYAEYSGAPNEEEVL 157 (266)
Q Consensus 78 ~~~~~~~~~~~~E~~a~~~d~~~~~~~~l~~v~l~G~Igii~NGaGlam~t~D~l~~~g~gg~pAN~lDlgG~a~~~~~~ 157 (266)
..++..+.+|+|.+|. ++.++|+-++|||+|++||+||+|+|||++... ||+||||+|+||+...++++
T Consensus 257 -amd~~eE~dPrEveAa--------kynLnYigmDGNIaClVNGAGLAMATmDiIkLn--GGePANFLDvGGgV~EdqV~ 325 (412)
T KOG1447|consen 257 -AMDDKEENDPREVEAA--------KYNLNYIGMDGNIACLVNGAGLAMATMDIIKLN--GGEPANFLDVGGGVKEDQVY 325 (412)
T ss_pred -ecccccccCchhhhhh--------hcCcceeeccCceEEEEccchhhhheeeeEEec--CCCCcceeeccCcccHHHHH
Confidence 3334567799999988 999999999999999999999999999999999 89999999999999999999
Q ss_pred HHHHHHHhhhccCCCCCeEEEEecccccchhHhhhhHHHHHHHHHHhhhhhhcccceEEEEeCCCCHHHHHHHHHhhhhh
Q 024560 158 QYARVVIDCATADPDGRKRALLIGGGIANFTDVATTFNGIIRALREKESKLKAARMHIFVRRGGPNYQTGLAKMRALGEE 237 (266)
Q Consensus 158 ~al~~ll~~~~~d~~v~~vlvni~ggi~~~~~vA~~~~gii~al~~~~~~~~~~~~pvvvrl~G~~~~~~~~~L~~~~~~ 237 (266)
+|++++.+ ||.|++|||||||||.+|..|| .||+.|.++.. .++|+||||.|||.++++++|+ +
T Consensus 326 ~Af~ilTa----DPkVk~iLvNiFGGIVNCAtIA---NGiv~A~~kl~-----LnVPlVVRLEGTNV~~A~~Ilk----~ 389 (412)
T KOG1447|consen 326 QAFKILTA----DPKVKAILVNIFGGIVNCATIA---NGIVKACRKLE-----LNVPLVVRLEGTNVQEAQKILK----K 389 (412)
T ss_pred HHhhhhcc----CCceeEEEEehhcceehhHhHh---hHHHHHHHhhc-----CCCcEEEEEcCCCHHHHHHHHH----h
Confidence 99999988 9999999999999999999999 99999999984 7899999999999999999999 6
Q ss_pred cCCceeecCCCCCHHHHHHHHHHH
Q 024560 238 LGIPLEVYGPEATMTGICKQAIDC 261 (266)
Q Consensus 238 ~Gip~~~~~~~~~~~eAv~~av~~ 261 (266)
+|+|+. +..++++|+.+||..
T Consensus 390 SGLpI~---tA~dLddAA~KAVas 410 (412)
T KOG1447|consen 390 SGLPIT---TAIDLDDAAKKAVAS 410 (412)
T ss_pred cCCcee---eccchHHHHHHHhhc
Confidence 699987 466999999999864
No 6
>TIGR01016 sucCoAbeta succinyl-CoA synthetase, beta subunit. This family contains a split seen both in a maximum parsimony tree (which ignores gaps) and in the gap pattern near position 85 of the seed alignment. Eukaryotic and most bacterial sequences are longer and contain a region similar to TXQTXXXG. Sequences from Deinococcus radiodurans, Mycobacterium tuberculosis, Streptomyces coelicolor, and the Archaea are 6 amino acids shorter in that region and contain a motif resembling [KR]G
Probab=100.00 E-value=1.2e-50 Score=385.48 Aligned_cols=217 Identities=24% Similarity=0.370 Sum_probs=196.7
Q ss_pred CCChhHHHHHHHHHHHHHHHHHhCCceeeEeeccee-cCCceEEeeccccccCcccccCccccccccCCCCCCCCCChhh
Q 024560 12 TLPLEFRGKIGDFIMGVFAVFQDLDFSFIEMNPFTL-VNGEPYPLDMRGELDDTAAFKNFKKWANIEFPLPFGRVLSSTE 90 (266)
Q Consensus 12 gl~~~~~~~~~~ii~~Ly~~f~~~D~~l~EINPLvv-~~g~~~alD~k~~iDd~A~~R~~~~~~~~~~~~~~~~~~~~~E 90 (266)
++++...+++.+++.+||++|.++|++++|||||++ .+|+++|+|+|++|||||+|||+++ .. +. +.++.++.|
T Consensus 168 ~~~~~~~~~l~~~l~~l~~~~~~~~~~~lEINPl~v~~~g~~~a~Daki~~dd~a~~r~~~~-~~--~~--~~~~~~~~e 242 (386)
T TIGR01016 168 GLEGELVKQVADIIKKLYQIFLEYDASLVEINPLVITKDGNLIALDAKLTIDDNALFRHPDL-EE--MR--DYSQEDPRE 242 (386)
T ss_pred CCCHHHHHHHHHHHHHHHHHHHhCCceEEEeeeeEEcCCCCEEEEeeeEeeccchhhhcHHH-HH--hh--cCCcCChhh
Confidence 567888999999999999999999999999999999 8999999999999999999999984 22 22 335678888
Q ss_pred hhhcccccccccccCceEecCCCcEEEEecCchHHHHHHHHHHhcCCCCCCCceeeccCCCCHHHHHHHHHHHHhhhccC
Q 024560 91 SFIHSLDEKTSASLKFTVLNPKGRIWTMVAGGGASVIYADTVGDLGYASELGNYAEYSGAPNEEEVLQYARVVIDCATAD 170 (266)
Q Consensus 91 ~~a~~~d~~~~~~~~l~~v~l~G~Igii~NGaGlam~t~D~l~~~g~gg~pAN~lDlgG~a~~~~~~~al~~ll~~~~~d 170 (266)
.+++ +.+++||+|+||||||+||||++|+|||++..+ |++|+||+|+||+++++.++++++++++ |
T Consensus 243 ~~~~--------~~~l~~v~l~G~i~~i~nG~Gl~~~t~D~~~~~--g~~~aNplDlgg~a~~~~~~~al~~l~~----d 308 (386)
T TIGR01016 243 VLAK--------QWGLNYVALDGNIGCMVNGAGLAMATMDIIKLY--GGEPANFLDVGGGASAERVREALKLVLS----D 308 (386)
T ss_pred hHHH--------HcCCcEEccCCcEEEEECCccHHHHHHHHHHHc--CCCCCCcEEecCCCCHHHHHHHHHHHHc----C
Confidence 8877 889999999999999999999999999999999 7999999999999999999999999999 9
Q ss_pred CCCCeEEEEecccccchhHhhhhHHHHHHHHHHhhhhhhcccceEEEEeCCCCHHHHHHHHHhhhhhcCCceeecCCCCC
Q 024560 171 PDGRKRALLIGGGIANFTDVATTFNGIIRALREKESKLKAARMHIFVRRGGPNYQTGLAKMRALGEELGIPLEVYGPEAT 250 (266)
Q Consensus 171 ~~v~~vlvni~ggi~~~~~vA~~~~gii~al~~~~~~~~~~~~pvvvrl~G~~~~~~~~~L~~~~~~~Gip~~~~~~~~~ 250 (266)
|++++||+|++||+++|+.+| ++|++++++.. +++||++|+.|++.++++++|+ ++|+|+.+ |++
T Consensus 309 p~vd~ilv~i~gg~~~~~~va---~~i~~a~~~~~-----~~kPvvv~~~g~~~~~~~~~L~----~~G~~ip~---~~~ 373 (386)
T TIGR01016 309 KSVKVVFINIFGGITRCDLVA---KGLVEALKEVG-----VNVPVVVRLEGTNVEEGKKILA----ESGLNIIF---ATS 373 (386)
T ss_pred CCCCEEEEECCCCCCCHHHHH---HHHHHHHHhcC-----CCCcEEEEeCCccHHHHHHHHH----HcCCCccc---cCC
Confidence 999999999999999999999 99999998762 4589999999999999999999 66933332 669
Q ss_pred HHHHHHHHHHHh
Q 024560 251 MTGICKQAIDCI 262 (266)
Q Consensus 251 ~~eAv~~av~~~ 262 (266)
|++||+++|+++
T Consensus 374 ~~~Av~~~~~~~ 385 (386)
T TIGR01016 374 MEEAAEKAVEAA 385 (386)
T ss_pred HHHHHHHHHHhh
Confidence 999999999876
No 7
>KOG2799 consensus Succinyl-CoA synthetase, beta subunit [Energy production and conversion]
Probab=100.00 E-value=1.7e-49 Score=366.08 Aligned_cols=225 Identities=20% Similarity=0.240 Sum_probs=205.3
Q ss_pred CHhhHHHHHc--CCChhHHHHHHHHHHHHHHHHHhCCceeeEeeccee-cCC-ceEEeeccccccCcccccCcccccccc
Q 024560 2 TLDACAPLIA--TLPLEFRGKIGDFIMGVFAVFQDLDFSFIEMNPFTL-VNG-EPYPLDMRGELDDTAAFKNFKKWANIE 77 (266)
Q Consensus 2 ~~~~~~~l~~--gl~~~~~~~~~~ii~~Ly~~f~~~D~~l~EINPLvv-~~g-~~~alD~k~~iDd~A~~R~~~~~~~~~ 77 (266)
++++...+.. |+++.-+++..+.+.+||++|.+.|++.+|||||+. +++ .++|.|+|+++||||.|||..+ +.
T Consensus 185 s~~~a~~v~~~lgfs~~~~~~a~~~~~kly~vf~~~dat~veinpl~e~t~d~~v~c~dak~~fd~na~fRq~~i---F~ 261 (434)
T KOG2799|consen 185 SPEIACLVADKLGFSPDGIRKAAKAVPKLYKVFHKSDATQVEINPLAEITSDHKVTCMDAKLNFDDNAAFRQKKI---FL 261 (434)
T ss_pred CHHHHHHHHhhcCCCcccHHHHHHHHHHHHHHHhhccceeEEecchhhcccCceeeechhhhcccccHHHHhhhh---hh
Confidence 5666666665 556888999999999999999999999999999999 655 9999999999999999999964 23
Q ss_pred CCCCCCCCCChhhhhhcccccccccccCceEecCCCcEEEEecCchHHHHHHHHHHhcCCCCCCCceeeccCCCCHHHHH
Q 024560 78 FPLPFGRVLSSTESFIHSLDEKTSASLKFTVLNPKGRIWTMVAGGGASVIYADTVGDLGYASELGNYAEYSGAPNEEEVL 157 (266)
Q Consensus 78 ~~~~~~~~~~~~E~~a~~~d~~~~~~~~l~~v~l~G~Igii~NGaGlam~t~D~l~~~g~gg~pAN~lDlgG~a~~~~~~ 157 (266)
+. +..+++|+|..+. ++++||+.++|+|||++||+|++|+|||+++.+ ||.||||+|+||+|+.|++.
T Consensus 262 ~r--d~~QEd~re~~aa--------k~~ln~igldG~igC~vngaglamaTmdiiklh--gg~panfldVGg~Atve~v~ 329 (434)
T KOG2799|consen 262 LR--DLSQEDPREVTAA--------KVDLNYIGLDGNIGCLVNGAGLAMATMDIIKLH--GGTPANFLDVGGGATVEQVR 329 (434)
T ss_pred cc--chhhcCchhhhHH--------HhccceeccCCccceeeccchhhhhheeeeeec--CCCCcceeeeCCCCcHHHHH
Confidence 33 5688999999877 899999999999999999999999999999999 89999999999999999999
Q ss_pred HHHHHHHhhhccCCCCCeEEEEecccccchhHhhhhHHHHHHHHHHhhhhhhcccceEEEEeCCCCHHHHHHHHHhhhhh
Q 024560 158 QYARVVIDCATADPDGRKRALLIGGGIANFTDVATTFNGIIRALREKESKLKAARMHIFVRRGGPNYQTGLAKMRALGEE 237 (266)
Q Consensus 158 ~al~~ll~~~~~d~~v~~vlvni~ggi~~~~~vA~~~~gii~al~~~~~~~~~~~~pvvvrl~G~~~~~~~~~L~~~~~~ 237 (266)
++|+++.+ ||++.+||+||||||++||.+| .|++.+.|++. .++||++|+.|++.++|+.++. +
T Consensus 330 eaf~lits----d~kv~ailvnifGgi~rCDvia---~Giv~aar~l~-----~~ipiv~rlqgt~v~~ak~~i~----~ 393 (434)
T KOG2799|consen 330 EAFSLITS----DKKVMAILVNIFGGIMRCDVIA---FGIVLAARELE-----LNIPIVVRLQGTRVEAAKPIIN----T 393 (434)
T ss_pred HHHHHHhc----ChhHHHHHHHHhcCeeecccee---cchhhhhhhhh-----cCCCEEEEecCCchhhhhhhHh----h
Confidence 99999998 9999999999999999999999 99999999984 7899999999999999999999 6
Q ss_pred cCCceeecCCCCCHHHHHHHHHH
Q 024560 238 LGIPLEVYGPEATMTGICKQAID 260 (266)
Q Consensus 238 ~Gip~~~~~~~~~~~eAv~~av~ 260 (266)
+|+.++. ++++++|++++|.
T Consensus 394 sgmri~~---~deldeaa~~~v~ 413 (434)
T KOG2799|consen 394 SGMRIRS---FDELDEAAKKAVG 413 (434)
T ss_pred cCceEEe---chhhhHHhhhhcc
Confidence 6998875 5599999999643
No 8
>PRK00696 sucC succinyl-CoA synthetase subunit beta; Provisional
Probab=100.00 E-value=1.6e-44 Score=343.59 Aligned_cols=229 Identities=23% Similarity=0.365 Sum_probs=201.6
Q ss_pred CHhhHHHHHcC--CChhHHHHHHHHHHHHHHHHHhCCceeeEeeccee-cCCceEEeeccccccCcccccCccccccccC
Q 024560 2 TLDACAPLIAT--LPLEFRGKIGDFIMGVFAVFQDLDFSFIEMNPFTL-VNGEPYPLDMRGELDDTAAFKNFKKWANIEF 78 (266)
Q Consensus 2 ~~~~~~~l~~g--l~~~~~~~~~~ii~~Ly~~f~~~D~~l~EINPLvv-~~g~~~alD~k~~iDd~A~~R~~~~~~~~~~ 78 (266)
+++++..++.. +++...+++.+++.+||++|.++|++++|||||++ ++|+++|+|+|+.+||||.|||++ |.++..
T Consensus 156 ~~~~a~~~~~~~~~~~~~~~~l~~~l~~l~~l~~~~~~~~leiNPl~v~~~g~~~a~Dak~~ld~~a~~r~~~-~~~~~~ 234 (388)
T PRK00696 156 QPFQAREIAFKLGLPGEQVKQFAKILMGLYKAFVEKDASLVEINPLVVTKDGDLIALDAKINFDDNALFRHPD-LAELRD 234 (388)
T ss_pred CHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHHHhCCccEEEEeceEECCCCcEEEEeeEEeecCCccccCHh-HHhhcC
Confidence 34566666665 67888999999999999999999999999999999 889999999999999999999998 644433
Q ss_pred CCCCCCCCChhhhhhcccccccccccCceEecCCCcEEEEecCchHHHHHHHHHHhcCCCCCCCceeeccCCCCHHHHHH
Q 024560 79 PLPFGRVLSSTESFIHSLDEKTSASLKFTVLNPKGRIWTMVAGGGASVIYADTVGDLGYASELGNYAEYSGAPNEEEVLQ 158 (266)
Q Consensus 79 ~~~~~~~~~~~E~~a~~~d~~~~~~~~l~~v~l~G~Igii~NGaGlam~t~D~l~~~g~gg~pAN~lDlgG~a~~~~~~~ 158 (266)
. .+.++.|.+++ ..+++||+++||||||+||||++|+|+|++..+ |++|+||+|++|+++++.|++
T Consensus 235 ~----~~~~~~e~~~~--------~~~~~~v~l~~~i~ii~ng~G~~~~~~D~l~~~--g~~~~NPvDl~g~~~~e~~~~ 300 (388)
T PRK00696 235 L----SEEDPLEAEAS--------KYGLNYVKLDGNIGCMVNGAGLAMATMDIIKLY--GGEPANFLDVGGGATAERVAE 300 (388)
T ss_pred C----CcCChhhhHHH--------hcCCcEEecCCcEEEEECCchHHHHHHHHHHHc--CCCcCCeEEecCCCCHHHHHH
Confidence 2 33567777766 788999999999999999999999999999999 799999999999999999999
Q ss_pred HHHHHHhhhccCCCCCeEEEEecccccchhHhhhhHHHHHHHHHHhhhhhhcccceEEEEeCCCCHHHHHHHHHhhhhhc
Q 024560 159 YARVVIDCATADPDGRKRALLIGGGIANFTDVATTFNGIIRALREKESKLKAARMHIFVRRGGPNYQTGLAKMRALGEEL 238 (266)
Q Consensus 159 al~~ll~~~~~d~~v~~vlvni~ggi~~~~~vA~~~~gii~al~~~~~~~~~~~~pvvvrl~G~~~~~~~~~L~~~~~~~ 238 (266)
+++++++ ||++++|++|++|++++|+.+| ++|+++.++.. .++||++|+.|++.++++++|+ ++
T Consensus 301 aL~~l~~----d~~vd~vlv~~~~~~~~~~~va---~~i~~~~~~~~-----~~kPvv~~~~g~~~~~~~~~L~----~~ 364 (388)
T PRK00696 301 AFKIILS----DPNVKAILVNIFGGITRCDVIA---EGIIAAVKEVG-----VTVPLVVRLEGTNVELGKKILA----ES 364 (388)
T ss_pred HHHHHhc----CCCCCEEEEEeCCCCCCHHHHH---HHHHHHHHhcC-----CCCcEEEEeCCCCHHHHHHHHH----HC
Confidence 9999999 9999999999999999999999 99999887631 4689999999999999999999 67
Q ss_pred CCceeecCCCCCHHHHHHHHHHHhhh
Q 024560 239 GIPLEVYGPEATMTGICKQAIDCIMS 264 (266)
Q Consensus 239 Gip~~~~~~~~~~~eAv~~av~~~~~ 264 (266)
|||+.+ |.+|++|++++.++++.
T Consensus 365 Gi~ip~---f~~pe~A~~al~~~~~~ 387 (388)
T PRK00696 365 GLNIIA---ADTLDDAAQKAVEAAKG 387 (388)
T ss_pred CCCcee---cCCHHHHHHHHHHHhcc
Confidence 966544 55999999999998753
No 9
>PF00549 Ligase_CoA: CoA-ligase; InterPro: IPR005811 This entry represents a domain found in both the alpha and beta chains of succinyl-CoA synthase (6.2.1.4 from EC (GDP-forming) and 6.2.1.5 from EC (ADP-forming)) [, ]. This domain can also be found in ATP citrate synthase (2.3.3.8 from EC) and malate-CoA ligase (6.2.1.9 from EC). Some members of the domain utilise ATP others use GTP.; GO: 0003824 catalytic activity, 0008152 metabolic process; PDB: 3DMY_B 3MWE_B 3PFF_A 3MWD_B 2YV1_A 1EUC_A 2FP4_A 1EUD_A 2FPI_A 2FPG_A ....
Probab=99.80 E-value=1.3e-19 Score=152.71 Aligned_cols=123 Identities=20% Similarity=0.304 Sum_probs=109.0
Q ss_pred EecCchHHHHHHHHHHhc--------------CCCCCCCceeeccCCCC----------HHHHHHHHHHHHhhhccCCCC
Q 024560 118 MVAGGGASVIYADTVGDL--------------GYASELGNYAEYSGAPN----------EEEVLQYARVVIDCATADPDG 173 (266)
Q Consensus 118 i~NGaGlam~t~D~l~~~--------------g~gg~pAN~lDlgG~a~----------~~~~~~al~~ll~~~~~d~~v 173 (266)
|.|||||+|-|+|++..+ | +.++||+|+||++. ++...++++.+++ ||++
T Consensus 1 l~~GgtL~~Ea~~~i~~~~~~~~sn~~~~~~~g--~~~~~~lDlGgd~~t~GrphPmid~~~~~~~l~~~~~----Dp~v 74 (153)
T PF00549_consen 1 LYNGGTLAMEAMDLISDALGDVYSNFKLANPLG--GGPANFLDLGGDAFTQGRPHPMIDPSTRNEALEIEAA----DPEV 74 (153)
T ss_dssp EESSHHHHHHHHHHHHHTTT------GCCEEET--CTEEEEEECTSSSSHTTS--TTT-SSHHHHHHHHHHT----STTE
T ss_pred CcCcHHHHHHHHHHHHHhhccccccccccccCC--CCceeEEEeCCCcccccCcCCCcCHHHHHHHHHHHhc----CCCc
Confidence 689999999999999998 5 77999999999999 8999999999999 9999
Q ss_pred CeEEEEecccccchhHhhhhHHHHHHHHHHhhhhhhcccceEEEEeCCCCHH-----HHHHHHHhhhhhcCCceeecCCC
Q 024560 174 RKRALLIGGGIANFTDVATTFNGIIRALREKESKLKAARMHIFVRRGGPNYQ-----TGLAKMRALGEELGIPLEVYGPE 248 (266)
Q Consensus 174 ~~vlvni~ggi~~~~~vA~~~~gii~al~~~~~~~~~~~~pvvvrl~G~~~~-----~~~~~L~~~~~~~Gip~~~~~~~ 248 (266)
++||+|+++|+.+|+++| .++++++++... +..++|||+|+.||+++ +.+++|+ ++|+.+ +
T Consensus 75 ~vIlvd~~~G~g~~~~~A---~~l~~a~~~~~~--~~~~~pvVa~v~GT~~dpq~~~~~~~~L~----~~G~~v-----~ 140 (153)
T PF00549_consen 75 KVILVDIVGGIGSCEDPA---AGLIPAIKEAKA--EGRKKPVVARVCGTNADPQGRMGQAGALE----DAGVIV-----A 140 (153)
T ss_dssp SEEEEEEESSSSSHHHHH---HHHHHHHSHCTH--TTT-SEEEEEEESTTCHTTSCHHHHHHHH----CTTCSC-----H
T ss_pred cEEEEEeccccCchHHHH---HHHHHHHHhccc--cCCCCcEEEEeeeecCCCCCcHHHHHHHH----hCCCcc-----c
Confidence 999999999999999999 999999988641 12579999999999999 9999999 679987 5
Q ss_pred CCHHHHHHHHHH
Q 024560 249 ATMTGICKQAID 260 (266)
Q Consensus 249 ~~~~eAv~~av~ 260 (266)
.+..+|++.|..
T Consensus 141 ~s~~~A~~~A~a 152 (153)
T PF00549_consen 141 ESNAQAARAAGA 152 (153)
T ss_dssp HHHHHHHHHHTH
T ss_pred ccHHHHHHHcCC
Confidence 588888877643
No 10
>KOG1254 consensus ATP-citrate lyase [Energy production and conversion]
Probab=99.72 E-value=3.8e-19 Score=170.34 Aligned_cols=254 Identities=39% Similarity=0.541 Sum_probs=224.1
Q ss_pred HhhHHHHHcCCChhHHHHHHHHHHHHHHHHHhCCceeeEee-------ccee-cCCc---eEEeeccccccCcccccCcc
Q 024560 3 LDACAPLIATLPLEFRGKIGDFIMGVFAVFQDLDFSFIEMN-------PFTL-VNGE---PYPLDMRGELDDTAAFKNFK 71 (266)
Q Consensus 3 ~~~~~~l~~gl~~~~~~~~~~ii~~Ly~~f~~~D~~l~EIN-------PLvv-~~g~---~~alD~k~~iDd~A~~R~~~ 71 (266)
+...+.|+.+++-.......++|..||.+|.+.|++++|+| |||. .-|. +.-+|.....|+.+.|.+-+
T Consensus 196 ~~pgSTl~dhi~r~q~~~~vk~Iv~Lgevgg~~ey~~~e~~k~g~~tkPlVaw~~gtcA~~F~~evqfghagtaa~~~~e 275 (600)
T KOG1254|consen 196 RYPGSTLIDHIPREQHDPLVKFIVVLGEVGGDEEYTFLEANKEGKITKPLVAWCIGTCADMFPLEVQFGHAGTAAFKNGE 275 (600)
T ss_pred CccCchHhhhhhhhhccChhheEEeehhhcccceeehhhhhhcCCccCCEEEEecCccccccchhhhccccchhhhcchh
Confidence 45678899999988899999999999999999999999999 9999 6564 78899999999999999999
Q ss_pred ccc--------------------------cccCCCCCCCCCChhhhhhcccccccccccCceEecCCCcEEEEecCc-hH
Q 024560 72 KWA--------------------------NIEFPLPFGRVLSSTESFIHSLDEKTSASLKFTVLNPKGRIWTMVAGG-GA 124 (266)
Q Consensus 72 ~~~--------------------------~~~~~~~~~~~~~~~E~~a~~~d~~~~~~~~l~~v~l~G~Igii~NGa-Gl 124 (266)
.|+ .++++-++++..+..|.....+|++++++.+++.++..|+||++..|+ |.
T Consensus 276 ka~akn~al~~ag~~vpesf~~l~~~i~~~~e~lv~~Grvvp~~Ev~pp~lp~d~saalklgllr~p~~i~t~Ia~~rGa 355 (600)
T KOG1254|consen 276 KAAAKNQALRDAGATVPESFDALGADIQETYEFLVPFGRVVPKTEVPPPGLPEDTSAALKLGLLRKPGRIWTSIAGGRGA 355 (600)
T ss_pred hhhhcchhhhhccccCccchhhhhhhhccchhcccccceecCcccCCCCCCChhhhhHhhhccccCCceEEEEecCCCCc
Confidence 998 788888899999999999999999999999999999999999888777 99
Q ss_pred HHHHHHHHHhcCCCCCCCceeeccCCCCHHHHHHHHHHHHhhhc-cCCCCCeEEEEecccccchhHhhhhHHHHHHHHHH
Q 024560 125 SVIYADTVGDLGYASELGNYAEYSGAPNEEEVLQYARVVIDCAT-ADPDGRKRALLIGGGIANFTDVATTFNGIIRALRE 203 (266)
Q Consensus 125 am~t~D~l~~~g~gg~pAN~lDlgG~a~~~~~~~al~~ll~~~~-~d~~v~~vlvni~ggi~~~~~vA~~~~gii~al~~ 203 (266)
.+.+.|+....|+--+.+|+-.+++-+...++.+..+..+++++ -.|+-+....-+.|+|+++...+++|.+|+.+|.+
T Consensus 356 eviYA~~p~~~~~a~elG~gg~~Sllw~~~~lp~Ya~kfie~~~m~~aDhgp~Vsga~ntI~~~ra~kdl~sslv~gLlt 435 (600)
T KOG1254|consen 356 EVIYADVPISLGYASELGNGGVYSLLWFQRRLPQYARKFIEICTMLTADHGPAVSGAGNTIANFRAGKDLFSSLVRGLLT 435 (600)
T ss_pred eeeecCchhhhhhHhhccccceEccccccccchHHHHHHHHHHhhccCCCCceeEeccCceEEeccHHHHHHHHHHHHhh
Confidence 99999999988666678999999999999999888888888876 35665555666789999999999999999999998
Q ss_pred hhhhhhcccceEEEEeCCCCHHHHHHHHHhhhhhcCCceeecCCCCCHHHHHHH
Q 024560 204 KESKLKAARMHIFVRRGGPNYQTGLAKMRALGEELGIPLEVYGPEATMTGICKQ 257 (266)
Q Consensus 204 ~~~~~~~~~~pvvvrl~G~~~~~~~~~L~~~~~~~Gip~~~~~~~~~~~eAv~~ 257 (266)
...++.. .+-+.+|+.|++.++++.-++...+..+.|.++||..-++......
T Consensus 436 igdRfgg-ald~aaR~f~~ayd~GL~~m~fv~~~~k~~~~V~Gighriksi~n~ 488 (600)
T KOG1254|consen 436 IGDRFGG-ALDIAARRFGPAYDKGLAPMRFVGKMRKVPIEVYGIGHRIKSINNP 488 (600)
T ss_pred hhhhhcc-hhhHHHHhcChhhhccCchHHHhhhhhCCCceecCCcceeeccCCc
Confidence 8765543 5667899999999999999998888889999999988777665443
No 11
>TIGR02717 AcCoA-syn-alpha acetyl coenzyme A synthetase (ADP forming), alpha domain. Although technically reversible, it is believed that this group of ADP-dependent acetyl-CoA synthetases (ACS) act in the direction of acetate and ATP production in the organisms in which it has been characterized. In most species this protein exists as a fused alpha-beta domain polypeptide. In Pyrococcus and related species, however the domains exist as separate polypeptides. This model 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. In reference, one of these (along with its beta-domain partner) was characterized as ACS-II showing specificity for phenylacetyl-CoA. This model has been constructed to exclude these non-ACS-I paralogs. This may result in new, authentic ACS-I sequences falling below the trusted cutoff.
Probab=99.65 E-value=3e-15 Score=145.56 Aligned_cols=129 Identities=19% Similarity=0.242 Sum_probs=111.5
Q ss_pred CCCcEEEEecCchHHHHHHHHHHhcCCCCCC---------------------CceeeccCCCCHHHHHHHHHHHHhhhcc
Q 024560 111 PKGRIWTMVAGGGASVIYADTVGDLGYASEL---------------------GNYAEYSGAPNEEEVLQYARVVIDCATA 169 (266)
Q Consensus 111 l~G~Igii~NGaGlam~t~D~l~~~g~gg~p---------------------AN~lDlgG~a~~~~~~~al~~ll~~~~~ 169 (266)
.+.||++|+||||+++++.|.+... |.++ .||+|+++..+++.|.++++++++
T Consensus 294 ~g~rvaivs~sGG~g~l~aD~~~~~--Gl~lp~ls~~t~~~L~~~lp~~~~~~NPlDl~~~~~~~~~~~al~~l~~---- 367 (447)
T TIGR02717 294 KGNRVAIITNAGGPGVIATDACEEN--GLELAELSEATKNKLRNILPPEASIKNPVDVLGDATPERYAKALKTVAE---- 367 (447)
T ss_pred CCCeEEEEECCchHHHHHHHHHHHc--CCCcCCCCHHHHHHHHHhCccccccCCCEecCCCCCHHHHHHHHHHHHc----
Confidence 3778999999999999999999998 6774 399999999999999999999999
Q ss_pred CCCCCeEEEEe-cccccchhHhhhhHHHHHHHHHHhhhhhhcccceEEE-EeCCCCHHHHHHHHHhhhhhcCCceeecCC
Q 024560 170 DPDGRKRALLI-GGGIANFTDVATTFNGIIRALREKESKLKAARMHIFV-RRGGPNYQTGLAKMRALGEELGIPLEVYGP 247 (266)
Q Consensus 170 d~~v~~vlvni-~ggi~~~~~vA~~~~gii~al~~~~~~~~~~~~pvvv-rl~G~~~~~~~~~L~~~~~~~Gip~~~~~~ 247 (266)
||++++|++++ +++..+++.++ ++++++.++. ..+||++ |.||...++.++.|+ ++|||+
T Consensus 368 dp~vd~Vlv~~~~~~~~~~~~~a---~~l~~~~~~~------~~KPvv~~~~gg~~~~~~~~~L~----~~Gip~----- 429 (447)
T TIGR02717 368 DENVDGVVVVLTPTAMTDPEEVA---KGIIEGAKKS------NEKPVVAGFMGGKSVDPAKRILE----ENGIPN----- 429 (447)
T ss_pred CCCCCEEEEEccCCccCCHHHHH---HHHHHHHHhc------CCCcEEEEecCCccHHHHHHHHH----hCCCCc-----
Confidence 99999999885 67788888888 9999887664 1578876 767788899999999 679998
Q ss_pred CCCHHHHHHHHHHHhh
Q 024560 248 EATMTGICKQAIDCIM 263 (266)
Q Consensus 248 ~~~~~eAv~~av~~~~ 263 (266)
|.++++|++.+..+.+
T Consensus 430 f~~p~~A~~al~~~~~ 445 (447)
T TIGR02717 430 YTFPERAVKALSALYR 445 (447)
T ss_pred cCCHHHHHHHHHHHHh
Confidence 7799999998876654
No 12
>COG1042 Acyl-CoA synthetase (NDP forming) [Energy production and conversion]
Probab=99.22 E-value=1.2e-10 Score=116.86 Aligned_cols=128 Identities=20% Similarity=0.277 Sum_probs=110.3
Q ss_pred CCcEEEEecCchHHHHHHHHHHhcCCCCC---------------------CCceeeccCCCCHHHHHHHHHHHHhhhccC
Q 024560 112 KGRIWTMVAGGGASVIYADTVGDLGYASE---------------------LGNYAEYSGAPNEEEVLQYARVVIDCATAD 170 (266)
Q Consensus 112 ~G~Igii~NGaGlam~t~D~l~~~g~gg~---------------------pAN~lDlgG~a~~~~~~~al~~ll~~~~~d 170 (266)
+.|+++++||||.+.++.|.+... |.+ ..||+|+.|+++.++|.++++.+++ +
T Consensus 299 g~~~~ivtn~Gg~gvla~D~l~~~--g~~l~~~~~~~~~~l~~~Lp~~~~~~NPvD~~~~a~~e~y~~~~~~~~~----~ 372 (598)
T COG1042 299 GDRVAIITNGGGPGVLAADALEER--GLKLAELSEETIEKLRSRLPPHASVKNPVDLTGDADAERYKKTLEILLR----D 372 (598)
T ss_pred CcceeEEecCCCccccchhHHHHc--CCCcCCCCHHHHHHHHhhcCccccccCCeeeecCCcHHHHHHHHHHHHh----c
Confidence 678999999999999999999999 566 1599999999999999999999999 9
Q ss_pred CCCCeEEEE-ecccccchhHhhhhHHHHHHHHHHhhhhhhcccceEE-EEeCCCCHHHHHHHHHhhhhhcCCceeecCCC
Q 024560 171 PDGRKRALL-IGGGIANFTDVATTFNGIIRALREKESKLKAARMHIF-VRRGGPNYQTGLAKMRALGEELGIPLEVYGPE 248 (266)
Q Consensus 171 ~~v~~vlvn-i~ggi~~~~~vA~~~~gii~al~~~~~~~~~~~~pvv-vrl~G~~~~~~~~~L~~~~~~~Gip~~~~~~~ 248 (266)
++++++++. +++..+...++| +.++.+..+. .++|++ .++||.+.+.++++|+ +.|||+ |
T Consensus 373 ~~~~~llvi~~~~~~~~~~~~a---~~~~~~~~~~------~~k~~v~~~~gg~~~~~~~~~l~----~~gip~-----~ 434 (598)
T COG1042 373 ENVDALLVIVLPPASADPEETA---EAIIRATAKK------RGKPVVVSSMGGESSEKARRLLE----EAGIPT-----Y 434 (598)
T ss_pred cCCceEEEEecCCCCCCchhhh---HHHHHhhhhh------CCCceEEEecCCcchHHHHHHhh----hcCCCC-----c
Confidence 999999999 588877777888 8898872222 457755 5999999999999999 779998 6
Q ss_pred CCHHHHHHHHHHHhh
Q 024560 249 ATMTGICKQAIDCIM 263 (266)
Q Consensus 249 ~~~~eAv~~av~~~~ 263 (266)
.+++.+++....+++
T Consensus 435 ~~pe~a~~a~~~l~~ 449 (598)
T COG1042 435 PTPERAVKALSALAR 449 (598)
T ss_pred cCchHHHHHHHHHHH
Confidence 799999998877764
No 13
>PLN02522 ATP citrate (pro-S)-lyase
Probab=97.59 E-value=0.0012 Score=67.07 Aligned_cols=125 Identities=10% Similarity=0.073 Sum_probs=88.5
Q ss_pred CCcEEEEecCchHHHHHHHHHHhcCCCCCCCceeeccCCCC-HHHHHHHHHHHHhhhccCCCCCeEEEEe-cccccchhH
Q 024560 112 KGRIWTMVAGGGASVIYADTVGDLGYASELGNYAEYSGAPN-EEEVLQYARVVIDCATADPDGRKRALLI-GGGIANFTD 189 (266)
Q Consensus 112 ~G~Igii~NGaGlam~t~D~l~~~g~gg~pAN~lDlgG~a~-~~~~~~al~~ll~~~~~d~~v~~vlvni-~ggi~~~~~ 189 (266)
.|+||+++-.|+++...++.+...| --..-++-+||++. ...+.+.++.+.+ ||++++|++.. .|+. +.
T Consensus 167 pG~VgiVSqSGtL~~ei~~~~~~~G--lG~S~~VsiGnd~~~g~~~~D~L~~~~~----Dp~Tk~IvlygEiGg~-~e-- 237 (608)
T PLN02522 167 PGSVGFVSKSGGMSNEMYNVIARVT--DGIYEGIAIGGDVFPGSTLSDHVLRFNN----IPQIKMIVVLGELGGR-DE-- 237 (608)
T ss_pred CCcEEEEeccHHHHHHHHHHHHHcC--CCeEEEEEeCCCCCCCCCHHHHHHHHhc----CCCCCEEEEEEecCch-hH--
Confidence 7999999999999999999999985 33466788899886 2457788777777 99999999885 3553 22
Q ss_pred hhhhHHHHHHHHHHhhhhhhcccceEEEEeCCCCHH----HHH---------------HHHHhhhhhcCCceeecCCCCC
Q 024560 190 VATTFNGIIRALREKESKLKAARMHIFVRRGGPNYQ----TGL---------------AKMRALGEELGIPLEVYGPEAT 250 (266)
Q Consensus 190 vA~~~~gii~al~~~~~~~~~~~~pvvvrl~G~~~~----~~~---------------~~L~~~~~~~Gip~~~~~~~~~ 250 (266)
+.+++++++.. .++|||++..|..+. .++ +...+..+++|+.+ .++
T Consensus 238 -----~~f~ea~~~a~-----~~KPVVa~kaGrsa~~~~~~aa~gHtGAiag~~~~ta~~k~aAlr~aGv~v-----v~s 302 (608)
T PLN02522 238 -----YSLVEALKQGK-----VSKPVVAWVSGTCARLFKSEVQFGHAGAKSGGDMESAQAKNKALKDAGAIV-----PTS 302 (608)
T ss_pred -----HHHHHHHHHhc-----CCCCEEEEeccCCCccCccccccccccccccCCCccHHHHHHHHHHCCCeE-----eCC
Confidence 44556666642 469999998888762 000 22333334789976 457
Q ss_pred HHHHHHHHHH
Q 024560 251 MTGICKQAID 260 (266)
Q Consensus 251 ~~eAv~~av~ 260 (266)
++|....+.+
T Consensus 303 ~~El~~~~~~ 312 (608)
T PLN02522 303 FEALEAAIKE 312 (608)
T ss_pred HHHHHHHHHH
Confidence 7776655544
No 14
>PRK06091 membrane protein FdrA; Validated
Probab=97.55 E-value=0.00087 Score=67.07 Aligned_cols=120 Identities=15% Similarity=0.105 Sum_probs=89.6
Q ss_pred CCCcEEEEecCchHHHHHHHHHHhcCCCCCCCceeeccCC-----CCHHHHHHHHHHHHhhhccCCCCCeEEEEe-cccc
Q 024560 111 PKGRIWTMVAGGGASVIYADTVGDLGYASELGNYAEYSGA-----PNEEEVLQYARVVIDCATADPDGRKRALLI-GGGI 184 (266)
Q Consensus 111 l~G~Igii~NGaGlam~t~D~l~~~g~gg~pAN~lDlgG~-----a~~~~~~~al~~ll~~~~~d~~v~~vlvni-~ggi 184 (266)
..|+||+++-.|+++...++.+...| .-...++-+|+. +..-.+..+++.+.+ ||++++|++.+ |
T Consensus 192 ~~G~IgiVSQSGtl~~~v~~~a~~~G--iG~S~~Vs~Gn~Dls~~~ggi~~~D~L~~L~~----DP~TkvIvly~kp--- 262 (555)
T PRK06091 192 PEGNIGVIGASGTGIQELCSQIALAG--EGITHAIGLGGRDLSAEVGGISALTALEMLSA----DEKSEVIAFVSKP--- 262 (555)
T ss_pred CCCCEEEEeCcHHHHHHHHHHHHHcC--CCeEEEEECCCCccccccCCCCHHHHHHHHhh----CCCCcEEEEEEec---
Confidence 48999999999999999999999994 556777888877 212347788888888 99999999886 5
Q ss_pred cchhHhhhhHHHHHHHHHHhhhhhhcccceEEEEeCCCCHHHHHHHHHhhhhhcCCceeecCCCCCHHHHHHHHHHHhh
Q 024560 185 ANFTDVATTFNGIIRALREKESKLKAARMHIFVRRGGPNYQTGLAKMRALGEELGIPLEVYGPEATMTGICKQAIDCIM 263 (266)
Q Consensus 185 ~~~~~vA~~~~gii~al~~~~~~~~~~~~pvvvrl~G~~~~~~~~~L~~~~~~~Gip~~~~~~~~~~~eAv~~av~~~~ 263 (266)
+.+.+. +.++++++.. .+|||+...|.+..-+ + +.|+-. .+|++|++..++.++.
T Consensus 263 -paE~v~---~~fl~aar~~-------~KPVVvlk~Grs~~g~----~----q~GVi~-----a~tleEl~~~A~~la~ 317 (555)
T PRK06091 263 -PAEAVR---LKIINAMKAT-------GKPVVALFLGYTPAVA----R----DENVWF-----ASTLDEAARLACLLSR 317 (555)
T ss_pred -CchHHH---HHHHHHHhhC-------CCCEEEEEecCCchhh----h----cCCeEE-----eCCHHHHHHHHHHHhc
Confidence 236666 6666666643 6999986666554322 4 568733 5699999999988763
No 15
>PF13607 Succ_CoA_lig: Succinyl-CoA ligase like flavodoxin domain; PDB: 2CSU_A.
Probab=97.45 E-value=0.0021 Score=53.44 Aligned_cols=120 Identities=17% Similarity=0.206 Sum_probs=70.6
Q ss_pred CcEEEEecCchHHHHHHHHHHhcCCCCCCCceeeccCCCCHHHHHHHHHHHHhhhccCCCCCeEEEEecccccchhHhhh
Q 024560 113 GRIWTMVAGGGASVIYADTVGDLGYASELGNYAEYSGAPNEEEVLQYARVVIDCATADPDGRKRALLIGGGIANFTDVAT 192 (266)
Q Consensus 113 G~Igii~NGaGlam~t~D~l~~~g~gg~pAN~lDlgG~a~~~~~~~al~~ll~~~~~d~~v~~vlvni~ggi~~~~~vA~ 192 (266)
|+|++++..|+++...++.+...| --..-++-+|..++- .+.+.++.+.+ ||++++|++-+= ++-+.
T Consensus 2 G~valisQSG~~~~~~~~~~~~~g--~g~s~~vs~Gn~~dv-~~~d~l~~~~~----D~~t~~I~ly~E-~~~d~----- 68 (138)
T PF13607_consen 2 GGVALISQSGALGTAILDWAQDRG--IGFSYVVSVGNEADV-DFADLLEYLAE----DPDTRVIVLYLE-GIGDG----- 68 (138)
T ss_dssp -SEEEEES-HHHHHHHHHHHHHTT---EESEEEE-TT-SSS--HHHHHHHHCT-----SS--EEEEEES---S-H-----
T ss_pred CCEEEEECCHHHHHHHHHHHHHcC--CCeeEEEEeCccccC-CHHHHHHHHhc----CCCCCEEEEEcc-CCCCH-----
Confidence 899999999999999999999983 445666777777765 47788777777 999999888763 23332
Q ss_pred hHHHHHHHHHHhhhhhhcccceEEEEeCCCCHHH-------------HHHHHHhhhhhcCCceeecCCCCCHHHHHHH
Q 024560 193 TFNGIIRALREKESKLKAARMHIFVRRGGPNYQT-------------GLAKMRALGEELGIPLEVYGPEATMTGICKQ 257 (266)
Q Consensus 193 ~~~gii~al~~~~~~~~~~~~pvvvrl~G~~~~~-------------~~~~L~~~~~~~Gip~~~~~~~~~~~eAv~~ 257 (266)
+.+++++++.. .++|||+...|.+..- ..+.+...++++|+-. .++++|.+..
T Consensus 69 --~~f~~~~~~a~-----~~KPVv~lk~Grt~~g~~aa~sHTgslag~~~~~~a~~~~aGv~~-----v~~~~el~~~ 134 (138)
T PF13607_consen 69 --RRFLEAARRAA-----RRKPVVVLKAGRTEAGARAAASHTGSLAGDDAVYDAALRQAGVVR-----VDDLDELLDA 134 (138)
T ss_dssp --HHHHHHHHHHC-----CCS-EEEEE---------------------HHHHHHHHHHCTEEE-----ESSHHHHHHH
T ss_pred --HHHHHHHHHHh-----cCCCEEEEeCCCchhhhhhhhccCCcccCcHHHHHHHHHHcCceE-----ECCHHHHHHH
Confidence 66677777764 3499998666642221 1133333344778743 3477776554
No 16
>PTZ00187 succinyl-CoA synthetase alpha subunit; Provisional
Probab=97.38 E-value=0.0038 Score=58.76 Aligned_cols=128 Identities=16% Similarity=0.228 Sum_probs=88.6
Q ss_pred CCCcEEEEecCchHHHHHHHHHHhcCCCCCCCceeeccCCC-CHHHHHHHHHHHHhhhccCCCCCeEEEEe-cccccchh
Q 024560 111 PKGRIWTMVAGGGASVIYADTVGDLGYASELGNYAEYSGAP-NEEEVLQYARVVIDCATADPDGRKRALLI-GGGIANFT 188 (266)
Q Consensus 111 l~G~Igii~NGaGlam~t~D~l~~~g~gg~pAN~lDlgG~a-~~~~~~~al~~ll~~~~~d~~v~~vlvni-~ggi~~~~ 188 (266)
..|+||+++-.|+++...++.+...| --...++-+|+++ ..-.+.+.++.+.+ ||+.++|++.. .||.. +
T Consensus 168 ~~G~VgiVSqSGtl~~ei~~~~~~~G--lG~S~~VsiGnd~~~g~~~~D~L~~~~~----Dp~T~~Ivl~~E~gG~~--e 239 (317)
T PTZ00187 168 KKGKIGIVSRSGTLTYEAVAQTTAVG--LGQSTCVGIGGDPFNGTNFIDCLKLFLN----DPETEGIILIGEIGGTA--E 239 (317)
T ss_pred CCCCEEEEeCCHHHHHHHHHHHHHcC--CCEEEEEEeCCCCCCCCCHHHHHHHHhh----CCCccEEEEEEecCCch--h
Confidence 37999999999999999999999994 4457788899997 23458889888888 99999999885 44322 1
Q ss_pred HhhhhHHHHHHHHHHhhhhhhcccceEEEEeCCCCHHHHHH----------------HHHhhhhhcCCceeecCCCCCHH
Q 024560 189 DVATTFNGIIRALREKESKLKAARMHIFVRRGGPNYQTGLA----------------KMRALGEELGIPLEVYGPEATMT 252 (266)
Q Consensus 189 ~vA~~~~gii~al~~~~~~~~~~~~pvvvrl~G~~~~~~~~----------------~L~~~~~~~Gip~~~~~~~~~~~ 252 (266)
+-+ ...++ .. ..++|||+...|.++..+++ ...+..+++|+.+ .++++
T Consensus 240 ~~a---a~fi~---~~-----~~~KPVVa~~aGrsap~G~r~gHaGAi~~~~~G~~~~k~aal~qaGv~v-----~~~~~ 303 (317)
T PTZ00187 240 EEA---AEWIK---NN-----PIKKPVVSFIAGITAPPGRRMGHAGAIISGGKGTAPGKIEALEAAGVRV-----VKSPA 303 (317)
T ss_pred HHH---HHHHH---hh-----cCCCcEEEEEecCCCCCCCcccchhhhhccCCCCHHHHHHHHHHCCCeE-----eCCHH
Confidence 112 22333 22 14699999888877532222 1123334789976 56888
Q ss_pred HHHHHHHHHh
Q 024560 253 GICKQAIDCI 262 (266)
Q Consensus 253 eAv~~av~~~ 262 (266)
|..+...+..
T Consensus 304 el~~~~~~~~ 313 (317)
T PTZ00187 304 QLGKTMLEVM 313 (317)
T ss_pred HHHHHHHHHH
Confidence 8777665543
No 17
>COG0074 SucD Succinyl-CoA synthetase, alpha subunit [Energy production and conversion]
Probab=97.36 E-value=0.0025 Score=58.83 Aligned_cols=137 Identities=13% Similarity=0.173 Sum_probs=95.2
Q ss_pred ccCc--eEecCCCcEEEEecCchHHHHHHHHHHhcCCCCCCCceeeccCCC-CHHHHHHHHHHHHhhhccCCCCCeEEEE
Q 024560 103 SLKF--TVLNPKGRIWTMVAGGGASVIYADTVGDLGYASELGNYAEYSGAP-NEEEVLQYARVVIDCATADPDGRKRALL 179 (266)
Q Consensus 103 ~~~l--~~v~l~G~Igii~NGaGlam~t~D~l~~~g~gg~pAN~lDlgG~a-~~~~~~~al~~ll~~~~~d~~v~~vlvn 179 (266)
+.++ .++...|+||+++-.|.|+-=+.-.+...| -| -.-.+=+||++ ....+..+++.+.+ ||+.++|+++
T Consensus 134 kiGimp~~i~~~G~IGiVSrSGTLTyE~~~qlt~~G-~G-qS~~IGiGGDpi~Gt~fid~L~~fe~----Dp~T~~ivmi 207 (293)
T COG0074 134 KIGIMPGNIYKPGNIGIVSRSGTLTYEAVSQLTEAG-LG-QSTAIGIGGDPIPGTSFIDALEMFEA----DPETEAIVMI 207 (293)
T ss_pred eeeechhhhccCCceEEEecCcchHHHHHHHHHhcC-Cc-eEEEEEeCCCCcCCccHHHHHHHHhc----CccccEEEEE
Confidence 3455 566679999999999999999999999986 23 34446778886 34568888888888 9999999888
Q ss_pred -ecccccchhHhhhhHHHHHHHHHHhhhhhhcccceEEEEeCCCCHHHHHHHHH----------------hhhhhcCCce
Q 024560 180 -IGGGIANFTDVATTFNGIIRALREKESKLKAARMHIFVRRGGPNYQTGLAKMR----------------ALGEELGIPL 242 (266)
Q Consensus 180 -i~ggi~~~~~vA~~~~gii~al~~~~~~~~~~~~pvvvrl~G~~~~~~~~~L~----------------~~~~~~Gip~ 242 (266)
=.|| +.++.| +++++++. .++|||.++.|..+.+++++=. +..+++|+++
T Consensus 208 GEiGG--~aEe~A------A~~i~~~~-----~~KPVVa~iaG~tap~gkrmGhaGaiv~~~~gta~~Ki~al~~aGv~v 274 (293)
T COG0074 208 GEIGG--PAEEEA------AEYIKANA-----TRKPVVAYIAGRTAPEGKRMGHAGAIVSGGKGTAESKIAALEAAGVKV 274 (293)
T ss_pred ecCCC--cHHHHH------HHHHHHhc-----cCCCEEEEEeccCCCccchhhhhhhhhcCCCccHHHHHHHHHHcCCee
Confidence 2555 345555 34445421 3599999998887766554322 1223678876
Q ss_pred eecCCCCCHHHHHHHHHHHhh
Q 024560 243 EVYGPEATMTGICKQAIDCIM 263 (266)
Q Consensus 243 ~~~~~~~~~~eAv~~av~~~~ 263 (266)
.++|.+..+...+..+
T Consensus 275 -----~etp~~l~~~l~~vl~ 290 (293)
T COG0074 275 -----AETPAELGELLLEVLK 290 (293)
T ss_pred -----cCCHHHHHHHHHHHhh
Confidence 5588877776665543
No 18
>TIGR02717 AcCoA-syn-alpha acetyl coenzyme A synthetase (ADP forming), alpha domain. Although technically reversible, it is believed that this group of ADP-dependent acetyl-CoA synthetases (ACS) act in the direction of acetate and ATP production in the organisms in which it has been characterized. In most species this protein exists as a fused alpha-beta domain polypeptide. In Pyrococcus and related species, however the domains exist as separate polypeptides. This model 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. In reference, one of these (along with its beta-domain partner) was characterized as ACS-II showing specificity for phenylacetyl-CoA. This model has been constructed to exclude these non-ACS-I paralogs. This may result in new, authentic ACS-I sequences falling below the trusted cutoff.
Probab=97.14 E-value=0.0095 Score=58.36 Aligned_cols=126 Identities=16% Similarity=0.170 Sum_probs=90.9
Q ss_pred CCcEEEEecCchHHHHHHHHHHhcCCCCCCCceeeccCCCCHHHHHHHHHHHHhhhccCCCCCeEEEEecccccchhHhh
Q 024560 112 KGRIWTMVAGGGASVIYADTVGDLGYASELGNYAEYSGAPNEEEVLQYARVVIDCATADPDGRKRALLIGGGIANFTDVA 191 (266)
Q Consensus 112 ~G~Igii~NGaGlam~t~D~l~~~g~gg~pAN~lDlgG~a~~~~~~~al~~ll~~~~~d~~v~~vlvni~ggi~~~~~vA 191 (266)
.|+|++++-.|+++...+|..... |-...-++-+|+.++- .+.+.++.+.+ ||++++|++-+=| +.+.
T Consensus 150 ~G~valvsqSG~~~~~~~~~~~~~--g~g~s~~vs~Gn~~d~-~~~d~l~~l~~----D~~t~~I~ly~E~-~~~~---- 217 (447)
T TIGR02717 150 KGGIAFISQSGALLTALLDWAEKN--GVGFSYFVSLGNKADI-DESDLLEYLAD----DPDTKVILLYLEG-IKDG---- 217 (447)
T ss_pred CCCEEEEechHHHHHHHHHHHHhc--CCCcceEEECCchhhC-CHHHHHHHHhh----CCCCCEEEEEecC-CCCH----
Confidence 689999999999999999999998 4556788888888763 57788888888 9999999887643 3332
Q ss_pred hhHHHHHHHHHHhhhhhhcccceEEEEeCCCCHHHHH-------------HHHHhhhhhcCCceeecCCCCCHHHHHHHH
Q 024560 192 TTFNGIIRALREKESKLKAARMHIFVRRGGPNYQTGL-------------AKMRALGEELGIPLEVYGPEATMTGICKQA 258 (266)
Q Consensus 192 ~~~~gii~al~~~~~~~~~~~~pvvvrl~G~~~~~~~-------------~~L~~~~~~~Gip~~~~~~~~~~~eAv~~a 258 (266)
+.++++++... .++|||+...|.+..-.+ +.+....+++|+.. .++++|....+
T Consensus 218 ---~~f~~aa~~a~-----~~KPVv~~k~Grs~~g~~aa~sHtgalag~~~~~~a~~~~~Gv~~-----~~~~~el~~~~ 284 (447)
T TIGR02717 218 ---RKFLKTAREIS-----KKKPIVVLKSGTSEAGAKAASSHTGALAGSDEAYDAAFKQAGVIR-----ADSIEELFDLA 284 (447)
T ss_pred ---HHHHHHHHHHc-----CCCCEEEEecCCChhhhhhhhhccccccChHHHHHHHHHHCCeEE-----eCCHHHHHHHH
Confidence 55666766653 379999977777653222 23344445789865 45888877665
Q ss_pred HHHh
Q 024560 259 IDCI 262 (266)
Q Consensus 259 v~~~ 262 (266)
.-++
T Consensus 285 ~~l~ 288 (447)
T TIGR02717 285 RLLS 288 (447)
T ss_pred HHHh
Confidence 5444
No 19
>PLN00125 Succinyl-CoA ligase [GDP-forming] subunit alpha
Probab=96.85 E-value=0.023 Score=53.17 Aligned_cols=125 Identities=15% Similarity=0.135 Sum_probs=84.2
Q ss_pred CCCcEEEEecCchHHHHHHHHHHhcCCCCCCCceeeccCC--CCHHHHHHHHHHHHhhhccCCCCCeEEEEe-cccccch
Q 024560 111 PKGRIWTMVAGGGASVIYADTVGDLGYASELGNYAEYSGA--PNEEEVLQYARVVIDCATADPDGRKRALLI-GGGIANF 187 (266)
Q Consensus 111 l~G~Igii~NGaGlam~t~D~l~~~g~gg~pAN~lDlgG~--a~~~~~~~al~~ll~~~~~d~~v~~vlvni-~ggi~~~ 187 (266)
..|+|++++-.|+++...++.+...| --..-++-+|+. ++- .+.+.++.+.+ ||++++|++-+ .||..-.
T Consensus 149 ~~G~ValiSQSG~l~~~l~~~~~~~g--iG~S~~VS~Gn~~~adv-~~~d~L~yl~~----Dp~T~~I~ly~E~~G~~~~ 221 (300)
T PLN00125 149 KPGRIGIVSRSGTLTYEAVFQTTAVG--LGQSTCVGIGGDPFNGT-NFVDCLEKFVK----DPQTEGIILIGEIGGTAEE 221 (300)
T ss_pred CCCcEEEEeCCccHHHHHHHHHHHcC--CCeEEEEEeCCCCCCCC-CHHHHHHHHhh----CCCCcEEEEEeccCCchHH
Confidence 37999999999999999999999984 445777888888 664 47788887877 99999999887 3343211
Q ss_pred hHhhhhHHHHHHHHHHhhhhhhcccceEEEEeCCCCHHHHH----------------HHHHhhhhhcCCceeecCCCCCH
Q 024560 188 TDVATTFNGIIRALREKESKLKAARMHIFVRRGGPNYQTGL----------------AKMRALGEELGIPLEVYGPEATM 251 (266)
Q Consensus 188 ~~vA~~~~gii~al~~~~~~~~~~~~pvvvrl~G~~~~~~~----------------~~L~~~~~~~Gip~~~~~~~~~~ 251 (266)
-+ +.++++.+ .++|||++-.|.+...++ +.+....+++|+.. .+++
T Consensus 222 --d~---~~f~~aa~--------~~KPVV~lk~Grs~~~g~~~sHTGala~~~~G~~~~~~a~~rq~Gvi~-----v~~~ 283 (300)
T PLN00125 222 --DA---AAFIKESG--------TEKPVVAFIAGLTAPPGRRMGHAGAIVSGGKGTAQDKIKALREAGVTV-----VESP 283 (300)
T ss_pred --HH---HHHHHHhc--------CCCCEEEEEecCCCCCCCCccchhhhhcCCCCCHHHHHHHHHHCCCeE-----eCCH
Confidence 11 33444322 369999877776641111 23344444789865 4577
Q ss_pred HHHHHHHHH
Q 024560 252 TGICKQAID 260 (266)
Q Consensus 252 ~eAv~~av~ 260 (266)
+|.....-+
T Consensus 284 ~el~~~~~~ 292 (300)
T PLN00125 284 AKIGVAMLE 292 (300)
T ss_pred HHHHHHHHH
Confidence 776554433
No 20
>TIGR01019 sucCoAalpha succinyl-CoA synthetase, alpha subunit. ATP citrate lyases appear to form an outgroup.
Probab=96.84 E-value=0.025 Score=52.49 Aligned_cols=126 Identities=11% Similarity=0.110 Sum_probs=81.8
Q ss_pred CCCcEEEEecCchHHHHHHHHHHhcCCCCCCCceeeccCCCC-HHHHHHHHHHHHhhhccCCCCCeEEEEecccccchhH
Q 024560 111 PKGRIWTMVAGGGASVIYADTVGDLGYASELGNYAEYSGAPN-EEEVLQYARVVIDCATADPDGRKRALLIGGGIANFTD 189 (266)
Q Consensus 111 l~G~Igii~NGaGlam~t~D~l~~~g~gg~pAN~lDlgG~a~-~~~~~~al~~ll~~~~~d~~v~~vlvni~ggi~~~~~ 189 (266)
..|+|++++-.|+++...+|.....| --..-++-+|..+. .-.+.+.++.+.+ ||++++|++-+=+......+
T Consensus 142 ~~G~ValiSQSG~l~~~~~~~a~~~g--iG~S~~Vs~Gn~a~~dv~~~D~l~~l~~----Dp~T~~I~lylE~~~~~~~~ 215 (286)
T TIGR01019 142 KPGNVGIVSRSGTLTYEAVHQLTKAG--FGQSTCVGIGGDPVNGTSFIDVLEAFEK----DPETEAIVMIGEIGGSAEEE 215 (286)
T ss_pred CCCcEEEEeccHHHHHHHHHHHHHcC--CCeEEEEEeCCCcCCCCCHHHHHHHHhh----CCCCcEEEEEEecCCchHHH
Confidence 36999999999999999999999984 44567888888854 1247788887877 99999999886322111112
Q ss_pred hhhhHHHHHHHHHHhhhhhhcccceEEEEeCCCCHHHH----------------HHHHHhhhhhcCCceeecCCCCCHHH
Q 024560 190 VATTFNGIIRALREKESKLKAARMHIFVRRGGPNYQTG----------------LAKMRALGEELGIPLEVYGPEATMTG 253 (266)
Q Consensus 190 vA~~~~gii~al~~~~~~~~~~~~pvvvrl~G~~~~~~----------------~~~L~~~~~~~Gip~~~~~~~~~~~e 253 (266)
.+ +.++.. .++|||++-.|..+..+ .+.+....+++|+.. .++++|
T Consensus 216 ~~-------~~~~~~------~~KPVV~lk~Grs~~~g~~~sHTGala~~~~g~~~~~~aa~rqaGvi~-----v~~~~e 277 (286)
T TIGR01019 216 AA-------DFIKQN------MSKPVVGFIAGATAPPGKRMGHAGAIISGGKGTAESKIEALEAAGVTV-----VKSPSD 277 (286)
T ss_pred HH-------HHHHhc------CCCCEEEEEecCCCCccccccchhhhhcCCCCCHHHHHHHHHHCCCeE-----eCCHHH
Confidence 11 111111 46999986666654111 122333344778854 457877
Q ss_pred HHHHHHH
Q 024560 254 ICKQAID 260 (266)
Q Consensus 254 Av~~av~ 260 (266)
......+
T Consensus 278 l~d~l~~ 284 (286)
T TIGR01019 278 IGELLAE 284 (286)
T ss_pred HHHHHHH
Confidence 6665543
No 21
>PRK05678 succinyl-CoA synthetase subunit alpha; Validated
Probab=96.75 E-value=0.015 Score=54.16 Aligned_cols=127 Identities=15% Similarity=0.187 Sum_probs=83.3
Q ss_pred CCcEEEEecCchHHHHHHHHHHhcCCCCCCCceeeccCCCCH-HHHHHHHHHHHhhhccCCCCCeEEEEecccccchhHh
Q 024560 112 KGRIWTMVAGGGASVIYADTVGDLGYASELGNYAEYSGAPNE-EEVLQYARVVIDCATADPDGRKRALLIGGGIANFTDV 190 (266)
Q Consensus 112 ~G~Igii~NGaGlam~t~D~l~~~g~gg~pAN~lDlgG~a~~-~~~~~al~~ll~~~~~d~~v~~vlvni~ggi~~~~~v 190 (266)
.|+|++++-.|+++...+|.....| --...++-+|..+.. -...+.++.+.+ ||++++|++-+=+......+.
T Consensus 145 ~G~valiSQSGal~~~~~~~~~~~g--iG~s~~Vs~Gn~~~~dv~~~D~l~~l~~----Dp~T~~I~lylE~~~~~~~~a 218 (291)
T PRK05678 145 KGRVGVVSRSGTLTYEAVAQLTDLG--FGQSTCVGIGGDPINGTNFIDVLEAFEE----DPETEAIVMIGEIGGSAEEEA 218 (291)
T ss_pred CCCEEEEeccHHHHHHHHHHHHHcC--CCeEEEEEeCCCcCCCCCHHHHHHHHhh----CCCCcEEEEEEecCCcHHHHH
Confidence 6999999999999999999999984 446788888887431 246777777777 999999998763221111122
Q ss_pred hhhHHHHHHHHHHhhhhhhcccceEEEEeCCCCHHHHH----------------HHHHhhhhhcCCceeecCCCCCHHHH
Q 024560 191 ATTFNGIIRALREKESKLKAARMHIFVRRGGPNYQTGL----------------AKMRALGEELGIPLEVYGPEATMTGI 254 (266)
Q Consensus 191 A~~~~gii~al~~~~~~~~~~~~pvvvrl~G~~~~~~~----------------~~L~~~~~~~Gip~~~~~~~~~~~eA 254 (266)
+ + .++.. .++|||+.-.|..+..++ +++...++++|+.. .++++|.
T Consensus 219 ~---~----~~~~~------~~KPVV~lk~Grs~~~g~~~sHTGala~~~~g~~~~~~a~~~q~Gvi~-----v~~~~el 280 (291)
T PRK05678 219 A---E----YIKAN------VTKPVVGYIAGVTAPPGKRMGHAGAIISGGKGTAEEKKEALEAAGVKV-----ARTPSEI 280 (291)
T ss_pred H---H----HHHHc------CCCCEEEEEecCCCCCCCcccchhhhccCCCCCHHHHHHHHHHCCCeE-----CCCHHHH
Confidence 2 1 11111 369999866666551211 22334444779865 5688887
Q ss_pred HHHHHHHh
Q 024560 255 CKQAIDCI 262 (266)
Q Consensus 255 v~~av~~~ 262 (266)
...+.++-
T Consensus 281 ~~~~~~~~ 288 (291)
T PRK05678 281 GELLKEVL 288 (291)
T ss_pred HHHHHHHH
Confidence 77665553
No 22
>PF13549 ATP-grasp_5: ATP-grasp domain; PDB: 1WR2_A.
Probab=96.24 E-value=0.0082 Score=53.71 Aligned_cols=54 Identities=19% Similarity=0.338 Sum_probs=38.5
Q ss_pred HHHHcCCC---hhHHHHHHHHHHHHHHHHHh-CCceeeEeeccee-cCCceEEeeccccc
Q 024560 7 APLIATLP---LEFRGKIGDFIMGVFAVFQD-LDFSFIEMNPFTL-VNGEPYPLDMRGEL 61 (266)
Q Consensus 7 ~~l~~gl~---~~~~~~~~~ii~~Ly~~f~~-~D~~l~EINPLvv-~~g~~~alD~k~~i 61 (266)
.+++.|.. +-..+.+.+.+.++-++..+ -+..-+|||||.+ .+| ++|+|++|.+
T Consensus 164 ~~lL~G~RG~p~~d~~al~~~l~~ls~l~~~~p~I~eldiNPl~v~~~g-~~avDa~i~l 222 (222)
T PF13549_consen 164 YPLLRGYRGRPPADLDALADLLVRLSQLAADLPEIAELDINPLIVTPDG-AVAVDARIRL 222 (222)
T ss_dssp HHHHH-------B-HHHHHHHHHHHHHHHHHTTTEEEEEEEEEEE-BS--EEE--EEEEE
T ss_pred HHhhcccCCCCCcCHHHHHHHHHHHHHHHHhCCCEEEEEeeceEEcCCc-eEEEEEEEEC
Confidence 34555543 34688999999999999988 5688999999999 655 9999999864
No 23
>KOG1255 consensus Succinyl-CoA synthetase, alpha subunit [Energy production and conversion]
Probab=94.40 E-value=0.091 Score=47.88 Aligned_cols=108 Identities=18% Similarity=0.223 Sum_probs=67.7
Q ss_pred eEecCCCcEEEEecCchHHHHHHHHHHhcCCCCCCCceeeccCCC-CHHHHHHHHHHHHhhhccCCCCCeEEEE-ecccc
Q 024560 107 TVLNPKGRIWTMVAGGGASVIYADTVGDLGYASELGNYAEYSGAP-NEEEVLQYARVVIDCATADPDGRKRALL-IGGGI 184 (266)
Q Consensus 107 ~~v~l~G~Igii~NGaGlam~t~D~l~~~g~gg~pAN~lDlgG~a-~~~~~~~al~~ll~~~~~d~~v~~vlvn-i~ggi 184 (266)
.++.-.|.|||++-.|=|..=++---..-| ---.-++-+||+| +...+..++++.|+ ||+.++|+++ =.||-
T Consensus 171 g~Ihk~G~IGIVSRSGTLTYEaVhQTT~vg--lGQslcvGiGGDpFnGT~FID~L~vFl~----D~~t~GIiliGEIGG~ 244 (329)
T KOG1255|consen 171 GHIHKRGKIGIVSRSGTLTYEAVHQTTQVG--LGQSLCVGIGGDPFNGTNFIDCLEVFLE----DPETEGIILIGEIGGS 244 (329)
T ss_pred cccccCCeeEEEecCCceeehhhhhhcccc--ccceeEEeecCCCCCCccHHHHHHHHhc----CcccceEEEEeccCCh
Confidence 345567999999987755433322222221 1123456677777 45668899999998 9999999888 24553
Q ss_pred cchhHhhhhHHHHHHHHHHhhhhhhcccceEEEEeCCCCHHHHHHH
Q 024560 185 ANFTDVATTFNGIIRALREKESKLKAARMHIFVRRGGPNYQTGLAK 230 (266)
Q Consensus 185 ~~~~~vA~~~~gii~al~~~~~~~~~~~~pvvvrl~G~~~~~~~~~ 230 (266)
.++-| ++.++++... ...+|||-.+.|..+-.+|++
T Consensus 245 --AEe~A------A~flk~~nSg--~~~kPVvsFIAG~tAppGrRM 280 (329)
T KOG1255|consen 245 --AEEEA------AEFLKEYNSG--STAKPVVSFIAGVTAPPGRRM 280 (329)
T ss_pred --hhHHH------HHHHHHhccC--CCCCceeEEeecccCCCcccc
Confidence 23323 4566665321 256899988777666555543
No 24
>TIGR00640 acid_CoA_mut_C methylmalonyl-CoA mutase C-terminal domain. Methylmalonyl-CoA mutase (EC 5.4.99.2) catalyzes a reversible isomerization between L-methylmalonyl-CoA and succinyl-CoA. The enzyme uses an adenosylcobalamin cofactor. It may be a homodimer, as in mitochondrion, or a heterodimer with partially homologous beta chain that does not bind the adenosylcobalamin cofactor, as in Propionibacterium freudenreichii. The most similar archaeal sequences are separate chains, such as AF2215 and AF2219 of Archaeoglobus fulgidus, that correspond roughly to the first 500 and last 130 residues, respectively of known methylmalonyl-CoA mutases. This model describes the C-terminal domain subfamily. In a neighbor-joining tree (methylaspartate mutase S chain as the outgroup), AF2219 branches with a coenzyme B12-dependent enzyme known not to be 5.4.99.2.
Probab=94.23 E-value=0.92 Score=37.25 Aligned_cols=95 Identities=13% Similarity=0.205 Sum_probs=62.4
Q ss_pred eeeccCCCCHHHHHHHHHHHHhhhccCCCCCeEEEEecccccchhHhhhhHHHHHHHHHHhhhhhhcccceEEEEeCCCC
Q 024560 144 YAEYSGAPNEEEVLQYARVVIDCATADPDGRKRALLIGGGIANFTDVATTFNGIIRALREKESKLKAARMHIFVRRGGPN 223 (266)
Q Consensus 144 ~lDlgG~a~~~~~~~al~~ll~~~~~d~~v~~vlvni~ggi~~~~~vA~~~~gii~al~~~~~~~~~~~~pvvvrl~G~~ 223 (266)
-+|+|++.+++.+.++. .+ .+.++|.+. +-.+..-+.. ..+++.+++... ...+|++ ||..
T Consensus 33 Vi~lg~~~s~e~~v~aa---~e-----~~adii~iS--sl~~~~~~~~---~~~~~~L~~~g~----~~i~viv--GG~~ 93 (132)
T TIGR00640 33 VDVGPLFQTPEEIARQA---VE-----ADVHVVGVS--SLAGGHLTLV---PALRKELDKLGR----PDILVVV--GGVI 93 (132)
T ss_pred EEECCCCCCHHHHHHHH---HH-----cCCCEEEEc--CchhhhHHHH---HHHHHHHHhcCC----CCCEEEE--eCCC
Confidence 36899999999776663 33 455655553 2223333334 888888887631 2344444 8766
Q ss_pred HHHHHHHHHhhhhhcCCceeecCCCCCHHHHHHHHHHHh
Q 024560 224 YQTGLAKMRALGEELGIPLEVYGPEATMTGICKQAIDCI 262 (266)
Q Consensus 224 ~~~~~~~L~~~~~~~Gip~~~~~~~~~~~eAv~~av~~~ 262 (266)
..+-.+.|. ++|+.- +|.+-+++.+.+....+..
T Consensus 94 ~~~~~~~l~----~~Gvd~-~~~~gt~~~~i~~~l~~~~ 127 (132)
T TIGR00640 94 PPQDFDELK----EMGVAE-IFGPGTPIPESAIFLLKKL 127 (132)
T ss_pred ChHhHHHHH----HCCCCE-EECCCCCHHHHHHHHHHHH
Confidence 666667788 679963 5667889999999887754
No 25
>PRK02261 methylaspartate mutase subunit S; Provisional
Probab=93.36 E-value=1.5 Score=36.19 Aligned_cols=111 Identities=14% Similarity=0.148 Sum_probs=71.9
Q ss_pred hHHHHHHHHHHhcCCCCCCCceeeccCCCCHHHHHHHHHHHHhhhccCCCCCeEEEEecccccchhHhhhhHHHHHHHHH
Q 024560 123 GASVIYADTVGDLGYASELGNYAEYSGAPNEEEVLQYARVVIDCATADPDGRKRALLIGGGIANFTDVATTFNGIIRALR 202 (266)
Q Consensus 123 Glam~t~D~l~~~g~gg~pAN~lDlgG~a~~~~~~~al~~ll~~~~~d~~v~~vlvni~ggi~~~~~vA~~~~gii~al~ 202 (266)
|+-|+ .-++... |- .-+++|-+.+++.+.++ .. ..+++.|.+....+ .....+ +.+++.++
T Consensus 19 G~~iv-~~~lr~~--G~---eVi~LG~~vp~e~i~~~----a~----~~~~d~V~lS~~~~--~~~~~~---~~~~~~L~ 79 (137)
T PRK02261 19 GNKIL-DRALTEA--GF---EVINLGVMTSQEEFIDA----AI----ETDADAILVSSLYG--HGEIDC---RGLREKCI 79 (137)
T ss_pred HHHHH-HHHHHHC--CC---EEEECCCCCCHHHHHHH----HH----HcCCCEEEEcCccc--cCHHHH---HHHHHHHH
Confidence 44433 3455555 33 45889999999988777 33 34666777764332 333444 77777777
Q ss_pred HhhhhhhcccceEEEEeCCCC------HHHHHHHHHhhhhhcCCceeecCCCCCHHHHHHHHHHHhh
Q 024560 203 EKESKLKAARMHIFVRRGGPN------YQTGLAKMRALGEELGIPLEVYGPEATMTGICKQAIDCIM 263 (266)
Q Consensus 203 ~~~~~~~~~~~pvvvrl~G~~------~~~~~~~L~~~~~~~Gip~~~~~~~~~~~eAv~~av~~~~ 263 (266)
+... .+ +.++.||.- .++-++.|+ +.|+. .+|++-+++++++....+.++
T Consensus 80 ~~~~----~~--~~i~vGG~~~~~~~~~~~~~~~l~----~~G~~-~vf~~~~~~~~i~~~l~~~~~ 135 (137)
T PRK02261 80 EAGL----GD--ILLYVGGNLVVGKHDFEEVEKKFK----EMGFD-RVFPPGTDPEEAIDDLKKDLN 135 (137)
T ss_pred hcCC----CC--CeEEEECCCCCCccChHHHHHHHH----HcCCC-EEECcCCCHHHHHHHHHHHhc
Confidence 6531 23 456777764 566677788 66974 467778899999998877654
No 26
>cd02071 MM_CoA_mut_B12_BD methylmalonyl CoA mutase B12 binding domain. This domain binds to B12 (adenosylcobamide), which initiates the conversion of succinyl CoA and methylmalonyl CoA by forming an adenosyl radical, which then undergoes a rearrangement exchanging a hydrogen atom with a group attached to a neighboring carbon atom. This family is present in both mammals and bacteria. Bacterial members are heterodimers and involved in the fermentation of pyruvate to propionate. Mammalian members are homodimers and responsible for the conversion of odd-chain fatty acids and branched-chain amino acids via propionyl CoA to succinyl CoA for further degradation.
Probab=91.43 E-value=2.9 Score=33.39 Aligned_cols=102 Identities=21% Similarity=0.229 Sum_probs=64.0
Q ss_pred HHHHHHhcCCCCCCCceeeccCCCCHHHHHHHHHHHHhhhccCCCCCeEEEEecccccchhHhhhhHHHHHHHHHHhhhh
Q 024560 128 YADTVGDLGYASELGNYAEYSGAPNEEEVLQYARVVIDCATADPDGRKRALLIGGGIANFTDVATTFNGIIRALREKESK 207 (266)
Q Consensus 128 t~D~l~~~g~gg~pAN~lDlgG~a~~~~~~~al~~ll~~~~~d~~v~~vlvni~ggi~~~~~vA~~~~gii~al~~~~~~ 207 (266)
...++... | -.-+++|.+.+++.+.++.+ ..+.+.|.+- +......+.+ +.+++.+++..
T Consensus 19 ~~~~l~~~---G--~~vi~lG~~vp~e~~~~~a~--------~~~~d~V~iS--~~~~~~~~~~---~~~~~~L~~~~-- 78 (122)
T cd02071 19 IARALRDA---G--FEVIYTGLRQTPEEIVEAAI--------QEDVDVIGLS--SLSGGHMTLF---PEVIELLRELG-- 78 (122)
T ss_pred HHHHHHHC---C--CEEEECCCCCCHHHHHHHHH--------HcCCCEEEEc--ccchhhHHHH---HHHHHHHHhcC--
Confidence 34556555 2 34568899999887766632 2344555543 3333444444 77777777652
Q ss_pred hhcccceEEEEeCCCCHHHHHHHHHhhhhhcCCceeecCCCCCHHHHHHHH
Q 024560 208 LKAARMHIFVRRGGPNYQTGLAKMRALGEELGIPLEVYGPEATMTGICKQA 258 (266)
Q Consensus 208 ~~~~~~pvvvrl~G~~~~~~~~~L~~~~~~~Gip~~~~~~~~~~~eAv~~a 258 (266)
.+ .+.++.||....+-.+.|. ++|+.- +|++-+++++++...
T Consensus 79 ---~~-~i~i~~GG~~~~~~~~~~~----~~G~d~-~~~~~~~~~~~~~~~ 120 (122)
T cd02071 79 ---AG-DILVVGGGIIPPEDYELLK----EMGVAE-IFGPGTSIEEIIDKI 120 (122)
T ss_pred ---CC-CCEEEEECCCCHHHHHHHH----HCCCCE-EECCCCCHHHHHHHH
Confidence 22 3567889887777777788 679874 455578888887653
No 27
>PF02601 Exonuc_VII_L: Exonuclease VII, large subunit; InterPro: IPR020579 Exonuclease VII 3.1.11.6 from EC is composed of two nonidentical subunits; one large subunit and 4 small ones []. Exonuclease VII catalyses exonucleolytic cleavage in either 5'-3' or 3'-5' direction to yield 5'-phosphomononucleotides. The large subunit also contains the OB-fold domains (IPR004365 from INTERPRO) that bind to nucleic acids at the N terminus. This entry represents Exonuclease VII, large subunit, C-terminal. ; GO: 0008855 exodeoxyribonuclease VII activity
Probab=90.70 E-value=4.8 Score=37.38 Aligned_cols=125 Identities=15% Similarity=0.074 Sum_probs=74.6
Q ss_pred CCCcEEEEecCchHHHHHHHHHHhcCCCCCC-Ccee----eccCCCCHHHHHHHHHHHHhhhccCC---CCCeEEEEecc
Q 024560 111 PKGRIWTMVAGGGASVIYADTVGDLGYASEL-GNYA----EYSGAPNEEEVLQYARVVIDCATADP---DGRKRALLIGG 182 (266)
Q Consensus 111 l~G~Igii~NGaGlam~t~D~l~~~g~gg~p-AN~l----DlgG~a~~~~~~~al~~ll~~~~~d~---~v~~vlvni~g 182 (266)
.--+||+|+.-.|.++ -|.+.... ---| .++. =+-|.-.++.+.+|++.+-+ .+ .+|+|+|.=.|
T Consensus 13 ~p~~I~vITs~~gAa~--~D~~~~~~-~r~~~~~~~~~p~~vQG~~A~~~I~~al~~~~~----~~~~~~~Dviii~RGG 85 (319)
T PF02601_consen 13 FPKRIAVITSPTGAAI--QDFLRTLK-RRNPIVEIILYPASVQGEGAAASIVSALRKANE----MGQADDFDVIIIIRGG 85 (319)
T ss_pred CCCEEEEEeCCchHHH--HHHHHHHH-HhCCCcEEEEEeccccccchHHHHHHHHHHHHh----ccccccccEEEEecCC
Confidence 3568999999998887 68887662 1123 3322 34477778889999998865 43 57866665444
Q ss_pred cccchhHhhhhHHHHHHHHHHhhhhhhcccceEEEEeCCCCHHHHHHHHHhhhhhcCCceeecCCCCCHHHHHHHHHHHh
Q 024560 183 GIANFTDVATTFNGIIRALREKESKLKAARMHIFVRRGGPNYQTGLAKMRALGEELGIPLEVYGPEATMTGICKQAIDCI 262 (266)
Q Consensus 183 gi~~~~~vA~~~~gii~al~~~~~~~~~~~~pvvvrl~G~~~~~~~~~L~~~~~~~Gip~~~~~~~~~~~eAv~~av~~~ 262 (266)
| +-.|--+=+=+.|++|+-+ .++||+.=.|=..-..--....+ . .+.||+.|++.++...
T Consensus 86 G-s~eDL~~FN~e~varai~~-------~~~PvisaIGHe~D~ti~D~vAd------~------ra~TPtaaAe~~~~~~ 145 (319)
T PF02601_consen 86 G-SIEDLWAFNDEEVARAIAA-------SPIPVISAIGHETDFTIADFVAD------L------RAPTPTAAAELIVPDR 145 (319)
T ss_pred C-ChHHhcccChHHHHHHHHh-------CCCCEEEecCCCCCchHHHHHHH------h------hCCCHHHHHHHHhhhH
Confidence 4 2111111011344444443 36999987776543333333331 1 3669999999887643
No 28
>COG0616 SppA Periplasmic serine proteases (ClpP class) [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]
Probab=89.19 E-value=1.6 Score=40.94 Aligned_cols=59 Identities=24% Similarity=0.305 Sum_probs=42.9
Q ss_pred CCCHHHHHHHHHHHHhhhccCCCCCeEEEEe--cccccchhHhhhhHHHHHHHHHHhhhhhhcccceEEEEeCCCC
Q 024560 150 APNEEEVLQYARVVIDCATADPDGRKRALLI--GGGIANFTDVATTFNGIIRALREKESKLKAARMHIFVRRGGPN 223 (266)
Q Consensus 150 ~a~~~~~~~al~~ll~~~~~d~~v~~vlvni--~ggi~~~~~vA~~~~gii~al~~~~~~~~~~~~pvvvrl~G~~ 223 (266)
..+.+.+.+.++.+.. ||++|+|++.+ |||.+-.. +-|.++++++.. .+ ||+|.+++--
T Consensus 79 ~~~~~~~~~~l~~~~~----~~~vk~vvL~inSPGG~v~as------~~i~~~l~~l~~----~~-PV~v~v~~~A 139 (317)
T COG0616 79 FIGGDDIEEILRAARA----DPSVKAVVLRINSPGGSVVAS------ELIARALKRLRA----KK-PVVVSVGGYA 139 (317)
T ss_pred cccHHHHHHHHHHHhc----CCCCceEEEEEECcCCchhHH------HHHHHHHHHHhh----cC-CEEEEECCee
Confidence 4567888889888888 99999999884 88865433 445566676642 23 8998888753
No 29
>PRK06091 membrane protein FdrA; Validated
Probab=88.70 E-value=5.3 Score=40.49 Aligned_cols=81 Identities=17% Similarity=0.170 Sum_probs=54.7
Q ss_pred CCCCCeEEEEe-cccccchhHhhhhHHHHHHHHHHhhhh-hhcccceEEEEeCCCC-----HHHHHHHHHhhhhhcCCce
Q 024560 170 DPDGRKRALLI-GGGIANFTDVATTFNGIIRALREKESK-LKAARMHIFVRRGGPN-----YQTGLAKMRALGEELGIPL 242 (266)
Q Consensus 170 d~~v~~vlvni-~ggi~~~~~vA~~~~gii~al~~~~~~-~~~~~~pvvvrl~G~~-----~~~~~~~L~~~~~~~Gip~ 242 (266)
||.+.+||+-+ .|-.+.. +-| ..++.++++.... ..++++++|+-+.||. .++.++.|. ++|+-+
T Consensus 407 dp~~~VillD~vlGyGah~-dpa---~~l~~ai~~~~~~~~~~r~l~~v~~v~GT~~DpQ~~~~q~~~L~----~aGv~v 478 (555)
T PRK06091 407 KPQVRVLLLDVVIGFGATA-DPA---GSLVSAIQKACAARADGQPLYAIATVTGTERDPQCRSQQIATLE----DAGIAV 478 (555)
T ss_pred CCcceEEEEEeeeccCCCC-ChH---HHHHHHHHHHHhhhhcCCceEEEEEEeCCCCCCcCHHHHHHHHH----hCCeEE
Confidence 89999999985 3433333 334 4555555543211 1124577777888884 557888898 779855
Q ss_pred eecCCCCCHHHHHHHHHHHhh
Q 024560 243 EVYGPEATMTGICKQAIDCIM 263 (266)
Q Consensus 243 ~~~~~~~~~~eAv~~av~~~~ 263 (266)
+++-.+|++.|.++++
T Consensus 479 -----~~sn~~a~~~a~~~~~ 494 (555)
T PRK06091 479 -----VDSLPEATLLAAALIR 494 (555)
T ss_pred -----EcCcHHHHHHHHHHhh
Confidence 5699999999999875
No 30
>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=87.83 E-value=3.8 Score=34.72 Aligned_cols=73 Identities=21% Similarity=0.189 Sum_probs=48.7
Q ss_pred eccCCCCHHHHHHHHHHHHhhhccCCCCCeEEEEe--cccccchhHhhhhHHHHHHHHHHhhhhhhcccceEEEEeCCCC
Q 024560 146 EYSGAPNEEEVLQYARVVIDCATADPDGRKRALLI--GGGIANFTDVATTFNGIIRALREKESKLKAARMHIFVRRGGPN 223 (266)
Q Consensus 146 DlgG~a~~~~~~~al~~ll~~~~~d~~v~~vlvni--~ggi~~~~~vA~~~~gii~al~~~~~~~~~~~~pvvvrl~G~~ 223 (266)
+..|..+.+.+.++++-+.+ ||++++|++.+ +||- ... . +-+.++++... ..++||++...|.-
T Consensus 17 ~~~~~~~~~~l~~~l~~a~~----d~~v~~vvl~~~~~gg~--~~~-~---~~~~~~i~~~~----~~~kpVia~v~G~a 82 (177)
T cd07014 17 DTQGNVSGDTTAAQIRDARL----DPKVKAIVLRVNSPGGS--VTA-S---EVIRAELAAAR----AAGKPVVASGGGNA 82 (177)
T ss_pred CCCCCcCHHHHHHHHHHHhc----CCCceEEEEEeeCCCcC--HHH-H---HHHHHHHHHHH----hCCCCEEEEECCch
Confidence 44556778889999888887 99999999986 3331 111 1 33344444443 24799999999877
Q ss_pred HHHHHHHHH
Q 024560 224 YQTGLAKMR 232 (266)
Q Consensus 224 ~~~~~~~L~ 232 (266)
...|-.+..
T Consensus 83 ~g~g~~la~ 91 (177)
T cd07014 83 ASGGYWIST 91 (177)
T ss_pred hHHHHHHHH
Confidence 666655554
No 31
>PRK10949 protease 4; Provisional
Probab=86.85 E-value=2.4 Score=43.59 Aligned_cols=61 Identities=23% Similarity=0.197 Sum_probs=41.4
Q ss_pred CCCCHHHHHHHHHHHHhhhccCCCCCeEEEEe--cccc-cchhHhhhhHHHHHHHHHHhhhhhhcccceEEEEeCCCCH
Q 024560 149 GAPNEEEVLQYARVVIDCATADPDGRKRALLI--GGGI-ANFTDVATTFNGIIRALREKESKLKAARMHIFVRRGGPNY 224 (266)
Q Consensus 149 G~a~~~~~~~al~~ll~~~~~d~~v~~vlvni--~ggi-~~~~~vA~~~~gii~al~~~~~~~~~~~~pvvvrl~G~~~ 224 (266)
|....+.+.+.++-+.+ ||+||+|++-| |||- ..+++ |.++++..+ ..++|||+.+++.-+
T Consensus 345 g~~~~~~~~~~l~~a~~----D~~vkaVvLrInSpGGs~~ase~-------i~~~i~~~r----~~gKPVvas~~~~aA 408 (618)
T PRK10949 345 GNVGGDTTAAQIRDARL----DPKVKAIVLRVNSPGGSVTASEV-------IRAELAAAR----AAGKPVVVSMGGMAA 408 (618)
T ss_pred CCcCHHHHHHHHHHHHh----CCCCcEEEEEecCCCCcHHHHHH-------HHHHHHHHH----hcCCcEEEEECCCCc
Confidence 44566788888887777 99999999886 6653 33333 444444442 136899999987643
No 32
>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=86.00 E-value=6.4 Score=34.46 Aligned_cols=72 Identities=19% Similarity=0.135 Sum_probs=45.9
Q ss_pred CCCCHHHHHHHHHHHHhhhccCCCCCeEEEEecccccchhHhhhhHHHHHHHHHHhhhhhhcccceEEEEeCCCCHHHHH
Q 024560 149 GAPNEEEVLQYARVVIDCATADPDGRKRALLIGGGIANFTDVATTFNGIIRALREKESKLKAARMHIFVRRGGPNYQTGL 228 (266)
Q Consensus 149 G~a~~~~~~~al~~ll~~~~~d~~v~~vlvni~ggi~~~~~vA~~~~gii~al~~~~~~~~~~~~pvvvrl~G~~~~~~~ 228 (266)
|....+.+.++++-+.+ ||++++|++.+++...+.... +.+.++++... ..++||++...|.....+-
T Consensus 19 ~~~~~~~l~~~l~~a~~----d~~v~~ivL~~~s~Gg~~~~~----~~~~~~l~~~~----~~~kpVia~v~g~a~s~gy 86 (211)
T cd07019 19 GNVGGDTTAAQIRDARL----DPKVKAIVLRVNSPGGSVTAS----EVIRAELAAAR----AAGKPVVVSAGGAAASGGY 86 (211)
T ss_pred CccCHHHHHHHHHHHhh----CCCceEEEEEEcCCCcCHHHH----HHHHHHHHHHH----hCCCCEEEEECCeehhHHH
Confidence 45567888999888887 999999999864332222221 23334444432 2479999999887655554
Q ss_pred HHHH
Q 024560 229 AKMR 232 (266)
Q Consensus 229 ~~L~ 232 (266)
.+..
T Consensus 87 ~la~ 90 (211)
T cd07019 87 WIST 90 (211)
T ss_pred HHHH
Confidence 4433
No 33
>cd02072 Glm_B12_BD B12 binding domain of glutamate mutase (Glm). Glutamate mutase catalysis the conversion of (S)-glutamate with (2S,3S)-3-methylaspartate. The rearrangement reaction is initiated by the extraction of a hydrogen from the protein-bound substrate by a 5'-desoxyadenosyl radical, which is generated by the homolytic cleavage of the organometallic bond of the cofactor B12. Glm is a heterotetrameric molecule consisting of two alpha and two epsilon polypeptide chains.
Probab=85.68 E-value=12 Score=30.73 Aligned_cols=91 Identities=16% Similarity=0.187 Sum_probs=58.0
Q ss_pred ceeeccCCCCHHHHHHHHHHHHhhhccCCCCCeEEEEecccccchhHhhhhHHHHHHHHHHhhhhhhcccceEEEEeCCC
Q 024560 143 NYAEYSGAPNEEEVLQYARVVIDCATADPDGRKRALLIGGGIANFTDVATTFNGIIRALREKESKLKAARMHIFVRRGGP 222 (266)
Q Consensus 143 N~lDlgG~a~~~~~~~al~~ll~~~~~d~~v~~vlvni~ggi~~~~~vA~~~~gii~al~~~~~~~~~~~~pvvvrl~G~ 222 (266)
.-+|+|-+-+++.+.++. . ..+.++|.+...-+ ..... ++.+++.+++..- ...| +..||.
T Consensus 29 eVidLG~~v~~e~~v~aa---~-----~~~adiVglS~L~t--~~~~~---~~~~~~~l~~~gl----~~v~--vivGG~ 89 (128)
T cd02072 29 NVVNLGVLSPQEEFIDAA---I-----ETDADAILVSSLYG--HGEID---CKGLREKCDEAGL----KDIL--LYVGGN 89 (128)
T ss_pred EEEECCCCCCHHHHHHHH---H-----HcCCCEEEEecccc--CCHHH---HHHHHHHHHHCCC----CCCe--EEEECC
Confidence 468999999999887772 2 34667777763222 12222 3777787877531 2334 455665
Q ss_pred C------HHHHHHHHHhhhhhcCCceeecCCCCCHHHHHHH
Q 024560 223 N------YQTGLAKMRALGEELGIPLEVYGPEATMTGICKQ 257 (266)
Q Consensus 223 ~------~~~~~~~L~~~~~~~Gip~~~~~~~~~~~eAv~~ 257 (266)
- .++-++.|+ ++|+. .+|++-+++++++..
T Consensus 90 ~~i~~~d~~~~~~~L~----~~Gv~-~vf~pgt~~~~i~~~ 125 (128)
T cd02072 90 LVVGKQDFEDVEKRFK----EMGFD-RVFAPGTPPEEAIAD 125 (128)
T ss_pred CCCChhhhHHHHHHHH----HcCCC-EEECcCCCHHHHHHH
Confidence 2 244556788 67995 578888899988764
No 34
>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=85.26 E-value=3.9 Score=36.11 Aligned_cols=58 Identities=12% Similarity=0.137 Sum_probs=38.0
Q ss_pred CCCHHHHHHHHHHHHhhhccCCCCCeEEEEe--cccccchhHhhhhHHHHHHHHHHhhhhhhcccceEEEEeCC
Q 024560 150 APNEEEVLQYARVVIDCATADPDGRKRALLI--GGGIANFTDVATTFNGIIRALREKESKLKAARMHIFVRRGG 221 (266)
Q Consensus 150 ~a~~~~~~~al~~ll~~~~~d~~v~~vlvni--~ggi~~~~~vA~~~~gii~al~~~~~~~~~~~~pvvvrl~G 221 (266)
..+.+.+.++++-+.+ ||++++|++.+ +|| .... . +.|.++++...+ .++||++...+
T Consensus 28 ~~~~~~l~~~l~~a~~----d~~ik~vvL~~~s~gg--~~~~-~---~el~~~i~~~~~----~~kpVia~~~~ 87 (222)
T cd07018 28 ELSLRDLLEALEKAAE----DDRIKGIVLDLDGLSG--GLAK-L---EELRQALERFRA----SGKPVIAYADG 87 (222)
T ss_pred CccHHHHHHHHHHHhc----CCCeEEEEEECCCCCC--CHHH-H---HHHHHHHHHHHH----hCCeEEEEeCC
Confidence 4556677777666666 99999999996 444 1111 1 455566665532 36899987765
No 35
>TIGR00705 SppA_67K signal peptide peptidase SppA, 67K type. 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.
Probab=83.37 E-value=4.1 Score=41.49 Aligned_cols=63 Identities=25% Similarity=0.279 Sum_probs=41.9
Q ss_pred CCHHHHHHHHHHHHhhhccCCCCCeEEEEe--cccccchhHhhhhHHHHHHHHHHhhhhhhcccceEEEEeCCCCHHHH
Q 024560 151 PNEEEVLQYARVVIDCATADPDGRKRALLI--GGGIANFTDVATTFNGIIRALREKESKLKAARMHIFVRRGGPNYQTG 227 (266)
Q Consensus 151 a~~~~~~~al~~ll~~~~~d~~v~~vlvni--~ggi~~~~~vA~~~~gii~al~~~~~~~~~~~~pvvvrl~G~~~~~~ 227 (266)
...+.+.+.++-+.+ ||+||+|++-+ |||-+.+. +.|.++++.++. .++|||+.++|.-...|
T Consensus 329 ~~~~~~~~~l~~a~~----D~~VkaIVLrinSpGGs~~as------e~i~~~i~~~~~----~gKPVva~~~g~aaSgg 393 (584)
T TIGR00705 329 TGGDTVAALLRVARS----DPDIKAVVLRINSPGGSVFAS------EIIRRELARAQA----RGKPVIVSMGAMAASGG 393 (584)
T ss_pred cCHHHHHHHHHHHhh----CCCceEEEEEecCCCCCHHHH------HHHHHHHHHHHh----CCCcEEEEECCccccHH
Confidence 345677788777777 99999999986 77744332 334444444431 35999999988654444
No 36
>TIGR00237 xseA exodeoxyribonuclease VII, large subunit. This family consist of exodeoxyribonuclease VII, large subunit XseA which catalyses exonucleolytic cleavage in either the 5'-3' or 3'-5' direction to yield 5'-phosphomononucleotides. Exonuclease VII consists of one large subunit and four small subunits.
Probab=81.76 E-value=15 Score=35.96 Aligned_cols=122 Identities=13% Similarity=0.056 Sum_probs=73.1
Q ss_pred CCCcEEEEecCchHHHHHHHHHHhcCCCCC-CC-cee----eccCCCCHHHHHHHHHHHHhhhccCCCCCeEEEEecccc
Q 024560 111 PKGRIWTMVAGGGASVIYADTVGDLGYASE-LG-NYA----EYSGAPNEEEVLQYARVVIDCATADPDGRKRALLIGGGI 184 (266)
Q Consensus 111 l~G~Igii~NGaGlam~t~D~l~~~g~gg~-pA-N~l----DlgG~a~~~~~~~al~~ll~~~~~d~~v~~vlvni~ggi 184 (266)
+--+||+||.-.|.+. -|.+.... -+ |. ++. -+-|.-.+..+.+|++.+-. .+++|+|+|.=.||
T Consensus 128 ~p~~i~vits~~~aa~--~D~~~~~~--~r~p~~~~~~~~~~vQG~~a~~~i~~al~~~~~----~~~~dviii~RGGG- 198 (432)
T TIGR00237 128 FPKRVGVITSQTGAAL--ADILHILK--RRDPSLKVVIYPTLVQGEGAVQSIVESIELANT----KNECDVLIVGRGGG- 198 (432)
T ss_pred CCCEEEEEeCCccHHH--HHHHHHHH--hhCCCceEEEecccccCccHHHHHHHHHHHhhc----CCCCCEEEEecCCC-
Confidence 4689999999998877 68887762 22 42 332 34477778889999887755 55677666654444
Q ss_pred cchhHhhhhHHHHHHHHHHhhhhhhcccceEEEEeCCCCHHHHHHHHHhhhhhcCCceeecCCCCCHHHHHHHHHH
Q 024560 185 ANFTDVATTFNGIIRALREKESKLKAARMHIFVRRGGPNYQTGLAKMRALGEELGIPLEVYGPEATMTGICKQAID 260 (266)
Q Consensus 185 ~~~~~vA~~~~gii~al~~~~~~~~~~~~pvvvrl~G~~~~~~~~~L~~~~~~~Gip~~~~~~~~~~~eAv~~av~ 260 (266)
+-.|--+=+=+.+++++-. .++|||.=.|=.....--..-. .. .+.||+.|++.++.
T Consensus 199 s~eDL~~Fn~e~~~rai~~-------~~~Pvis~iGHe~D~ti~D~vA------d~------ra~TPtaaae~~~p 255 (432)
T TIGR00237 199 SLEDLWSFNDEKVARAIFL-------SKIPIISAVGHETDFTISDFVA------DL------RAPTPSAAAEIVSP 255 (432)
T ss_pred CHHHhhhcCcHHHHHHHHc-------CCCCEEEecCcCCCccHHHHhh------hc------cCCCcHHHHHHhCc
Confidence 2222211111445555433 4799998766533222222222 11 35699999987753
No 37
>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=80.61 E-value=17 Score=31.47 Aligned_cols=69 Identities=17% Similarity=0.206 Sum_probs=44.4
Q ss_pred CCCHHHHHHHHHHHHhhhccCCCCCeEEEEe--cccccchhHhhhhHHHHHHHHHHhhhhhhcccceEEEEeCCCCHHHH
Q 024560 150 APNEEEVLQYARVVIDCATADPDGRKRALLI--GGGIANFTDVATTFNGIIRALREKESKLKAARMHIFVRRGGPNYQTG 227 (266)
Q Consensus 150 ~a~~~~~~~al~~ll~~~~~d~~v~~vlvni--~ggi~~~~~vA~~~~gii~al~~~~~~~~~~~~pvvvrl~G~~~~~~ 227 (266)
......+.++++.+.+ ||++++|++.+ +||-... + +.+.++++... ..++||++...|.....+
T Consensus 16 ~~~~~~l~~~l~~a~~----d~~i~~ivl~~~s~Gg~~~~---~---~~i~~~i~~~~----~~~kpvia~v~g~~~s~g 81 (208)
T cd07023 16 GIGADSLIEQLRKARE----DDSVKAVVLRINSPGGSVVA---S---EEIYREIRRLR----KAKKPVVASMGDVAASGG 81 (208)
T ss_pred CCCHHHHHHHHHHHHh----CCCCcEEEEEEECCCCCHHH---H---HHHHHHHHHHH----hcCCcEEEEECCcchhHH
Confidence 4566778888777776 99999999986 4442111 1 44455555543 247899998888765555
Q ss_pred HHHHH
Q 024560 228 LAKMR 232 (266)
Q Consensus 228 ~~~L~ 232 (266)
-.+..
T Consensus 82 ~~lA~ 86 (208)
T cd07023 82 YYIAA 86 (208)
T ss_pred HHHHh
Confidence 44433
No 38
>TIGR00706 SppA_dom signal peptide peptidase SppA, 36K type. The member of this family from Bacillus subtilis was shown to have properties consistent with a role in degrading signal peptides after cleavage from precursor proteins, although it was not demonstrated conclusively.
Probab=80.54 E-value=9.9 Score=33.17 Aligned_cols=66 Identities=20% Similarity=0.212 Sum_probs=44.3
Q ss_pred CHHHHHHHHHHHHhhhccCCCCCeEEEEe--cccccchhHhhhhHHHHHHHHHHhhhhhhcccceEEEEeCCCCHHHHHH
Q 024560 152 NEEEVLQYARVVIDCATADPDGRKRALLI--GGGIANFTDVATTFNGIIRALREKESKLKAARMHIFVRRGGPNYQTGLA 229 (266)
Q Consensus 152 ~~~~~~~al~~ll~~~~~d~~v~~vlvni--~ggi~~~~~vA~~~~gii~al~~~~~~~~~~~~pvvvrl~G~~~~~~~~ 229 (266)
+.+.+.++++-+.+ |+++++|++.+ +||-.. ..+.+.+++++.+ .++||+++..|.....+-.
T Consensus 14 s~~~l~~~l~~a~~----d~~i~~vvl~~~s~Gg~~~------~~~~l~~~i~~~~-----~~kpvia~v~g~a~s~g~~ 78 (207)
T TIGR00706 14 SPEDFDKKIKRIKD----DKSIKALLLRINSPGGTVV------ASEEIYEKLKKLK-----AKKPVVASMGGVAASGGYY 78 (207)
T ss_pred CHHHHHHHHHHHhh----CCCccEEEEEecCCCCCHH------HHHHHHHHHHHhc-----CCCCEEEEECCccchHHHH
Confidence 56778888887777 99999999876 444221 1255666666652 3589999998876555544
Q ss_pred HHH
Q 024560 230 KMR 232 (266)
Q Consensus 230 ~L~ 232 (266)
+..
T Consensus 79 la~ 81 (207)
T TIGR00706 79 IAM 81 (207)
T ss_pred HHh
Confidence 433
No 39
>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=80.10 E-value=12 Score=30.82 Aligned_cols=64 Identities=20% Similarity=0.250 Sum_probs=40.6
Q ss_pred CHHHHHHHHHHHHhhhccCCCCCeEEEEe--cccccchhHhhhhHHHHHHHHHHhhhhhhcccceEEEEeCCCCHHHHHH
Q 024560 152 NEEEVLQYARVVIDCATADPDGRKRALLI--GGGIANFTDVATTFNGIIRALREKESKLKAARMHIFVRRGGPNYQTGLA 229 (266)
Q Consensus 152 ~~~~~~~al~~ll~~~~~d~~v~~vlvni--~ggi~~~~~vA~~~~gii~al~~~~~~~~~~~~pvvvrl~G~~~~~~~~ 229 (266)
+.+.+.++++-+-. |+++++|++.+ +||-. .- +..|.+++++. ++||+++..|.-...+--
T Consensus 12 ~~~~l~~~l~~a~~----d~~~~~ivl~~~s~Gg~~---~~---~~~i~~~l~~~-------~kpvva~~~g~~~s~g~~ 74 (161)
T cd00394 12 SADQLAAQIRFAEA----DNSVKAIVLEVNTPGGRV---DA---GMNIVDALQAS-------RKPVIAYVGGQAASAGYY 74 (161)
T ss_pred hHHHHHHHHHHHHh----CCCCceEEEEEECCCcCH---HH---HHHHHHHHHHh-------CCCEEEEECChhHHHHHH
Confidence 34455555555544 89999998875 56522 11 25667777665 489999998876655544
Q ss_pred HHH
Q 024560 230 KMR 232 (266)
Q Consensus 230 ~L~ 232 (266)
+..
T Consensus 75 la~ 77 (161)
T cd00394 75 IAT 77 (161)
T ss_pred HHh
Confidence 433
No 40
>cd00952 CHBPH_aldolase Trans-o-hydroxybenzylidenepyruvate hydratase-aldolase (HBPHA) and trans-2'-carboxybenzalpyruvate hydratase-aldolase (CBPHA). HBPHA catalyzes HBP to salicyaldehyde and pyruvate. This reaction is part of the degradative pathways for naphthalene and naphthalenesulfonates by bacteria. CBPHA is homologous to HBPHA and catalyzes the cleavage of CBP to 2-carboxylbenzaldehyde and pyruvate during the degradation of phenanthrene. They are member of the DHDPS family of Schiff-base-dependent class I aldolases.
Probab=79.06 E-value=35 Score=31.73 Aligned_cols=103 Identities=17% Similarity=0.134 Sum_probs=67.0
Q ss_pred CCCCHHHHHHHHHHHHhhhccCCCCCeEEEE-ecccccchhHhhhhHHHHHHHHHHhhhhhhcccceEEEEeCCCCHHHH
Q 024560 149 GAPNEEEVLQYARVVIDCATADPDGRKRALL-IGGGIANFTDVATTFNGIIRALREKESKLKAARMHIFVRRGGPNYQTG 227 (266)
Q Consensus 149 G~a~~~~~~~al~~ll~~~~~d~~v~~vlvn-i~ggi~~~~~vA~~~~gii~al~~~~~~~~~~~~pvvvrl~G~~~~~~ 227 (266)
|..+.+.+.+-++.+++ .++++++++ ..|-...-+. +--+.++++..+.. ..++||++-.+.++.+++
T Consensus 24 g~iD~~~l~~lv~~li~-----~Gv~Gi~v~GstGE~~~Lt~--eEr~~v~~~~~~~~----~grvpvi~Gv~~~~t~~a 92 (309)
T cd00952 24 DTVDLDETARLVERLIA-----AGVDGILTMGTFGECATLTW--EEKQAFVATVVETV----AGRVPVFVGATTLNTRDT 92 (309)
T ss_pred CCcCHHHHHHHHHHHHH-----cCCCEEEECcccccchhCCH--HHHHHHHHHHHHHh----CCCCCEEEEeccCCHHHH
Confidence 67888999999888885 799999998 4333222211 11244555554443 246999999999999999
Q ss_pred HHHHHhhhhhcCCc------eeecCCCCCHHHHHHHHHHHhhhc
Q 024560 228 LAKMRALGEELGIP------LEVYGPEATMTGICKQAIDCIMSA 265 (266)
Q Consensus 228 ~~~L~~~~~~~Gip------~~~~~~~~~~~eAv~~av~~~~~~ 265 (266)
.+..+.+ ++.|.. -++| -.+.++.++.+-+++.+.
T Consensus 93 i~~a~~A-~~~Gad~vlv~~P~y~--~~~~~~l~~yf~~va~a~ 133 (309)
T cd00952 93 IARTRAL-LDLGADGTMLGRPMWL--PLDVDTAVQFYRDVAEAV 133 (309)
T ss_pred HHHHHHH-HHhCCCEEEECCCcCC--CCCHHHHHHHHHHHHHhC
Confidence 8887743 345632 1222 235688888887777643
No 41
>PF00885 DMRL_synthase: 6,7-dimethyl-8-ribityllumazine synthase; InterPro: IPR002180 6,7-dimethyl-8-ribityllumazine synthase (riboflavin synthase) catalyses the biosynthesis of riboflavin according to the reaction: 2 6,7-dimethyl-8-(1-D-ribityl)lumazine = riboflavin + 4-(1-D-ribitylamino)-5-amino-2,6-dihydroxypyrimidine. The biosynthesis of one riboflavin molecule requires one molecule of GTP and two molecules of ribulose 5-phosphate as substrates. The final step in the biosynthesis of the vitamin involves the dismutation of 6,7-dimethyl-8-ribityllumazine catalyzed by riboflavin synthase. The second product, 5-amino-6-ribitylamino-2,4(1H,3H)-pyrimidinedione, is recycled in the biosynthetic pathway by 6,7-dimethyl-8-ribityllumazine synthase []. N-[2,4-dioxo-6-d-ribitylamino-1,2,3,4-tetrahydropyrimidin-5-yl]oxalamic acid derivatives inhibit riboflavin synthase []. This family includes the beta chain of 6,7-dimethyl-8-ribityllumazine synthase 2.5.1.9 from EC. The family also includes a subfamily of distant archaebacterial proteins that may also have the same function for example O28856 from SWISSPROT.; GO: 0009231 riboflavin biosynthetic process, 0009349 riboflavin synthase complex; PDB: 2O6H_D 1C41_C 2OBX_H 1VSX_H 1VSW_3 3JV8_C 3MK3_r 3NQ4_G 2A58_A 2A57_D ....
Probab=77.28 E-value=21 Score=29.72 Aligned_cols=113 Identities=14% Similarity=0.079 Sum_probs=73.5
Q ss_pred HHHHHHHHhcCCCCCCCceeeccCCCCHHHHHHHHHHHHhhhccCCCCCeEEEE---ecccccchhHhhhhHHHHHHHHH
Q 024560 126 VIYADTVGDLGYASELGNYAEYSGAPNEEEVLQYARVVIDCATADPDGRKRALL---IGGGIANFTDVATTFNGIIRALR 202 (266)
Q Consensus 126 m~t~D~l~~~g~gg~pAN~lDlgG~a~~~~~~~al~~ll~~~~~d~~v~~vlvn---i~ggi~~~~~vA~~~~gii~al~ 202 (266)
--+.+.|..+ |.++.|.- +---|-+-.+.-+++.+++ ..+.++|++. |-|....++-|+ +++.+.+-
T Consensus 23 ~~a~~~l~~~--g~~~~~i~-~~~VPGa~ElP~a~~~l~~----~~~~Davi~lG~VI~G~T~H~~~v~---~~v~~gl~ 92 (144)
T PF00885_consen 23 EGALEELKRH--GVAEENIE-VIRVPGAFELPLAAKRLAE----SGRYDAVIALGCVIRGETDHFEYVA---NAVSRGLM 92 (144)
T ss_dssp HHHHHHHHHT--TTTGGCEE-EEEESSGGGHHHHHHHHHH----CSTESEEEEEEEEE--SSTHHHHHH---HHHHHHHH
T ss_pred HHHHHHHHHc--CCCccceE-EEEcCCHHHHHHHHHHHhc----ccCccEEEEeccccCCCchHHHHHH---HHHHHHHH
Confidence 3467888887 55444432 2222223346677777777 6789999887 467888888888 88888877
Q ss_pred HhhhhhhcccceEEE-EeCCCCHHHHHHHHHhhhhhcCCceeecCCCCCHHHHHHHHHHHhh
Q 024560 203 EKESKLKAARMHIFV-RRGGPNYQTGLAKMRALGEELGIPLEVYGPEATMTGICKQAIDCIM 263 (266)
Q Consensus 203 ~~~~~~~~~~~pvvv-rl~G~~~~~~~~~L~~~~~~~Gip~~~~~~~~~~~eAv~~av~~~~ 263 (266)
+..- ..++||.. -+.-.+.+++++... +.. ..-=.||++.++++++
T Consensus 93 ~lsl---~~~~PV~~gvlt~~~~eqa~~R~~------~~~------~nkG~eaA~aal~m~~ 139 (144)
T PF00885_consen 93 DLSL---EYGIPVIFGVLTPDTEEQALERAG------GKA------GNKGREAAEAALEMAK 139 (144)
T ss_dssp HHHH---HHTSEEEEEEEEESSHHHHHHHCE------ETT------EEHHHHHHHHHHHHHH
T ss_pred HHhc---cCCccEEEEecCCCCHHHHHHHhc------chh------hhhHHHHHHHHHHHHH
Confidence 6642 25799885 677788888876655 211 1245678888888764
No 42
>cd02067 B12-binding B12 binding domain (B12-BD). This domain binds different cobalamid derivates, like B12 (adenosylcobamide) or methylcobalamin or methyl-Co(III) 5-hydroxybenzimidazolylcobamide, it is found in several enzymes, such as glutamate mutase, methionine synthase and methylmalonyl-CoA mutase. Cobalamin undergoes a conformational change on binding the protein; the dimethylbenzimidazole group, which is coordinated to the cobalt in the free cofactor, moves away from the corrin and is replaced by a histidine contributed by the protein. The sequence Asp-X-His-X-X-Gly, which contains this histidine ligand, is conserved in many cobalamin-binding proteins.
Probab=76.62 E-value=34 Score=26.66 Aligned_cols=99 Identities=18% Similarity=0.193 Sum_probs=56.8
Q ss_pred HHHHHHhcCCCCCCCceeeccCCCCHHHHHHHHHHHHhhhccCCCCCeEEEEecccccchhHhhhhHHHHHHHHHHhhhh
Q 024560 128 YADTVGDLGYASELGNYAEYSGAPNEEEVLQYARVVIDCATADPDGRKRALLIGGGIANFTDVATTFNGIIRALREKESK 207 (266)
Q Consensus 128 t~D~l~~~g~gg~pAN~lDlgG~a~~~~~~~al~~ll~~~~~d~~v~~vlvni~ggi~~~~~vA~~~~gii~al~~~~~~ 207 (266)
..+++... |-+ -+++|.+.+++.+.++ +.+ .+.+.|.+. ...+.....+ ..+++.+++..
T Consensus 19 ~~~~l~~~--G~~---V~~lg~~~~~~~l~~~---~~~-----~~pdvV~iS--~~~~~~~~~~---~~~i~~l~~~~-- 78 (119)
T cd02067 19 VARALRDA--GFE---VIDLGVDVPPEEIVEA---AKE-----EDADAIGLS--GLLTTHMTLM---KEVIEELKEAG-- 78 (119)
T ss_pred HHHHHHHC--CCE---EEECCCCCCHHHHHHH---HHH-----cCCCEEEEe--ccccccHHHH---HHHHHHHHHcC--
Confidence 34566665 333 3788888888876666 232 344445543 2223333444 77777777652
Q ss_pred hhcccceEEEEeCCCCHHHHHHHHHhhhhhcCCceeecCCCCCHHHHHHHH
Q 024560 208 LKAARMHIFVRRGGPNYQTGLAKMRALGEELGIPLEVYGPEATMTGICKQA 258 (266)
Q Consensus 208 ~~~~~~pvvvrl~G~~~~~~~~~L~~~~~~~Gip~~~~~~~~~~~eAv~~a 258 (266)
. --+.+.+||....+--+.+. +.|.... +.+-+++++..
T Consensus 79 ---~-~~~~i~vGG~~~~~~~~~~~----~~G~D~~----~~~~~~~~~~~ 117 (119)
T cd02067 79 ---L-DDIPVLVGGAIVTRDFKFLK----EIGVDAY----FGPATEAVEVL 117 (119)
T ss_pred ---C-CCCeEEEECCCCChhHHHHH----HcCCeEE----ECCHHHHHHHH
Confidence 2 12557778876665445677 6688653 33666666543
No 43
>PRK12419 riboflavin synthase subunit beta; Provisional
Probab=76.19 E-value=48 Score=28.26 Aligned_cols=116 Identities=11% Similarity=0.108 Sum_probs=76.4
Q ss_pred HHHHHHHHHHhcCCCCCCCceeeccCCCCHHHHHHHHHHHHhhhccCCCCCeEEEE---ecccccchhHhhhhHHHHHHH
Q 024560 124 ASVIYADTVGDLGYASELGNYAEYSGAPNEEEVLQYARVVIDCATADPDGRKRALL---IGGGIANFTDVATTFNGIIRA 200 (266)
Q Consensus 124 lam~t~D~l~~~g~gg~pAN~lDlgG~a~~~~~~~al~~ll~~~~~d~~v~~vlvn---i~ggi~~~~~vA~~~~gii~a 200 (266)
|---+.|.|..+ |.+..|. ++---|-+-.+.-+.+.+++ ..+.++|+.. |=|....++-|+ +++.+.
T Consensus 28 Ll~gA~~~l~~~--G~~~~~i-~v~~VPGA~EiP~~a~~l~~----~~~yDaiIaLG~VIrGeT~H~e~V~---~~v~~g 97 (158)
T PRK12419 28 ARKGFVAEIAAR--GGAASQV-DIFDVPGAFEIPLHAQTLAK----TGRYAAIVAAALVVDGGIYRHEFVA---QAVIDG 97 (158)
T ss_pred HHHHHHHHHHHc--CCCccce-EEEECCcHHHHHHHHHHHHh----cCCCCEEEEEEEEEcCCCchhHHHH---HHHHHH
Confidence 444467888888 5655654 44444444456666666665 6779999887 467788888888 888888
Q ss_pred HHHhhhhhhcccceEEE-EeCCCCHHHHH--HHHHhhhhhcCCceeecCCCCCHHHHHHHHHHHhh
Q 024560 201 LREKESKLKAARMHIFV-RRGGPNYQTGL--AKMRALGEELGIPLEVYGPEATMTGICKQAIDCIM 263 (266)
Q Consensus 201 l~~~~~~~~~~~~pvvv-rl~G~~~~~~~--~~L~~~~~~~Gip~~~~~~~~~~~eAv~~av~~~~ 263 (266)
+.+..- ...+||.. -|.-.+.+++. +-+. .+|.. .-=.||+..+++++.
T Consensus 98 l~~vsl---~~~~PV~fGVLT~~~~eqA~~rqa~~----Ra~~~-------nKG~eaA~aalem~~ 149 (158)
T PRK12419 98 LMRVQL---DTEVPVFSVVLTPHHFHESEEHHDFF----RAHFV-------VKGAEAAHACADTLL 149 (158)
T ss_pred HHHHHh---ccCCCEEEEecCCCcHHHHHHHHHHh----hcCcc-------ccHHHHHHHHHHHHH
Confidence 777642 25799885 67777777543 3444 23432 245678888887763
No 44
>PRK04147 N-acetylneuraminate lyase; Provisional
Probab=76.17 E-value=48 Score=30.37 Aligned_cols=109 Identities=17% Similarity=0.202 Sum_probs=68.1
Q ss_pred ceeeccCCCCHHHHHHHHHHHHhhhccCCCCCeEEEEecccccchhHhhhhHHHHHHHHHHhhhhhhcccceEEEEeCCC
Q 024560 143 NYAEYSGAPNEEEVLQYARVVIDCATADPDGRKRALLIGGGIANFTDVATTFNGIIRALREKESKLKAARMHIFVRRGGP 222 (266)
Q Consensus 143 N~lDlgG~a~~~~~~~al~~ll~~~~~d~~v~~vlvni~ggi~~~~~vA~~~~gii~al~~~~~~~~~~~~pvvvrl~G~ 222 (266)
-|+|=-|..+.+.+.+-++.+++ ..++++++++-..|-..+-... --..+++...+.. ..++||++-.+.+
T Consensus 13 TPf~~dg~iD~~~~~~li~~l~~----~~Gv~gi~v~GstGE~~~Ls~e-Er~~~~~~~~~~~----~~~~~viagvg~~ 83 (293)
T PRK04147 13 TPFDEDGQIDEQGLRRLVRFNIE----KQGIDGLYVGGSTGEAFLLSTE-EKKQVLEIVAEEA----KGKVKLIAQVGSV 83 (293)
T ss_pred CcCCCCCCcCHHHHHHHHHHHHh----cCCCCEEEECCCccccccCCHH-HHHHHHHHHHHHh----CCCCCEEecCCCC
Confidence 45666788899999998888874 3789999988322221111111 1134555444432 1368999988888
Q ss_pred CHHHHHHHHHhhhhhcCC-------ceeecCCCCCHHHHHHHHHHHhhh
Q 024560 223 NYQTGLAKMRALGEELGI-------PLEVYGPEATMTGICKQAIDCIMS 264 (266)
Q Consensus 223 ~~~~~~~~L~~~~~~~Gi-------p~~~~~~~~~~~eAv~~av~~~~~ 264 (266)
+.+++.+..+. +++.|. |.+ + ..+.++.++.+-+++.+
T Consensus 84 ~t~~ai~~a~~-a~~~Gad~v~v~~P~y-~--~~~~~~l~~~f~~va~a 128 (293)
T PRK04147 84 NTAEAQELAKY-ATELGYDAISAVTPFY-Y--PFSFEEICDYYREIIDS 128 (293)
T ss_pred CHHHHHHHHHH-HHHcCCCEEEEeCCcC-C--CCCHHHHHHHHHHHHHh
Confidence 88888777664 235565 432 2 23567777777777654
No 45
>TIGR01501 MthylAspMutase methylaspartate mutase, S subunit. This model represents the S (sigma) subunit of methylaspartate mutase (glutamate mutase), a cobalamin-dependent enzyme that catalyzes the first step in a pathway of glutamate fermentation.
Probab=75.95 E-value=44 Score=27.62 Aligned_cols=94 Identities=15% Similarity=0.132 Sum_probs=57.9
Q ss_pred ceeeccCCCCHHHHHHHHHHHHhhhccCCCCCeEEEEecccccchhHhhhhHHHHHHHHHHhhhhhhcccceEEEEeCCC
Q 024560 143 NYAEYSGAPNEEEVLQYARVVIDCATADPDGRKRALLIGGGIANFTDVATTFNGIIRALREKESKLKAARMHIFVRRGGP 222 (266)
Q Consensus 143 N~lDlgG~a~~~~~~~al~~ll~~~~~d~~v~~vlvni~ggi~~~~~vA~~~~gii~al~~~~~~~~~~~~pvvvrl~G~ 222 (266)
.-+|+|-+-+++++.++. . ..++++|.+...-+ ..... ++.+++.+++..- ..++ +-.||.
T Consensus 31 eVi~LG~~v~~e~~v~aa---~-----~~~adiVglS~l~~--~~~~~---~~~~~~~l~~~gl----~~~~--vivGG~ 91 (134)
T TIGR01501 31 NVVNLGVLSPQEEFIKAA---I-----ETKADAILVSSLYG--HGEID---CKGLRQKCDEAGL----EGIL--LYVGGN 91 (134)
T ss_pred EEEECCCCCCHHHHHHHH---H-----HcCCCEEEEecccc--cCHHH---HHHHHHHHHHCCC----CCCE--EEecCC
Confidence 468999999999887772 2 34677777764322 12222 3677777877531 2333 345664
Q ss_pred C----HHH--HHHHHHhhhhhcCCceeecCCCCCHHHHHHHHHH
Q 024560 223 N----YQT--GLAKMRALGEELGIPLEVYGPEATMTGICKQAID 260 (266)
Q Consensus 223 ~----~~~--~~~~L~~~~~~~Gip~~~~~~~~~~~eAv~~av~ 260 (266)
- .+. -++.|+ ++|+. .+|++-+++++++.....
T Consensus 92 ~vi~~~d~~~~~~~l~----~~Gv~-~vF~pgt~~~~iv~~l~~ 130 (134)
T TIGR01501 92 LVVGKQDFPDVEKRFK----EMGFD-RVFAPGTPPEVVIADLKK 130 (134)
T ss_pred cCcChhhhHHHHHHHH----HcCCC-EEECcCCCHHHHHHHHHH
Confidence 1 111 244577 67975 478888899888876544
No 46
>cd00578 L-fuc_L-ara-isomerases L-fucose isomerase (FucIase) and L-arabinose isomerase (AI) family; composed of FucIase, AI and similar proteins. FucIase converts L-fucose, an aldohexose, to its ketose form, which prepares it for aldol cleavage (similar to the isomerization of glucose in glycolysis). L-fucose (or 6-deoxy-L-galactose) is found in various oligo- and polysaccharides in mammals, bacteria and plants. AI catalyzes the isomerization of L-arabinose to L-ribulose, the first reaction in its conversion to D-xylulose-5-phosphate, an intermediate in the pentose phosphate pathway, which allows L-arabinose to be used as a carbon source. AI can also convert D-galactose to D-tagatose at elevated temperatures in the presence of divalent metal ions. D-tagatose, rarely found in nature, is of commercial interest as a low-calorie sugar substitute.
Probab=75.28 E-value=85 Score=30.62 Aligned_cols=112 Identities=19% Similarity=0.150 Sum_probs=60.3
Q ss_pred cEEEEecCchH--------HHHHHHHHHhcCCCCCCCceeeccCCC-CHHHHHHHHHHHHhhhccCCCCCeEEEEecccc
Q 024560 114 RIWTMVAGGGA--------SVIYADTVGDLGYASELGNYAEYSGAP-NEEEVLQYARVVIDCATADPDGRKRALLIGGGI 184 (266)
Q Consensus 114 ~Igii~NGaGl--------am~t~D~l~~~g~gg~pAN~lDlgG~a-~~~~~~~al~~ll~~~~~d~~v~~vlvni~ggi 184 (266)
+||+++.+-++ ..-....+...= ...+...++.+--. +++...++.+..-. + +++++++.+....
T Consensus 2 ~ig~v~~~~~~~~~~~~~~~~~~~~~~~~~l-~~~~~~vv~~~~~~~~~~~~~~~~~~~~~----~-~~d~ii~~~~tf~ 75 (452)
T cd00578 2 KIGFVTGSQHLYGEELLEQVEEYAREVADLL-NELPVEVVDKPEVTGTPDEARKAAEEFNE----A-NCDGLIVWMHTFG 75 (452)
T ss_pred EEEEEEecccccChhHHHHHHHHHHHHHHHH-hcCCceEEecCcccCCHHHHHHHHHHHhh----c-CCcEEEEcccccc
Confidence 46777777772 222222222220 12245666655444 77777787766654 5 8999988864432
Q ss_pred cchhHhhhhHHHHHHHHHHhhhhhhcccceEEEEeCCC-----------CHHHHHHHHHhhhhhcCCcee-ecC
Q 024560 185 ANFTDVATTFNGIIRALREKESKLKAARMHIFVRRGGP-----------NYQTGLAKMRALGEELGIPLE-VYG 246 (266)
Q Consensus 185 ~~~~~vA~~~~gii~al~~~~~~~~~~~~pvvvrl~G~-----------~~~~~~~~L~~~~~~~Gip~~-~~~ 246 (266)
. . ..++.+++.. ++||++|=-.. +..-|...+.....+.|+|.. ++|
T Consensus 76 ~-~-------~~~~~~~~~~-------~~Pvll~a~~~~~~~~~~~~~~~s~~g~~~~~~~l~r~gi~~~~v~g 134 (452)
T cd00578 76 P-A-------KMWIAGLSEL-------RKPVLLLATQFNREIPDFMNLNQSACGLREFGNILARLGIPFKVVYG 134 (452)
T ss_pred c-H-------HHHHHHHHhc-------CCCEEEEeCCCCCCCCchhhhhcchhhhHHHHHHHHHcCCceeEEEC
Confidence 2 1 3344555443 68988765443 232233333333337799954 555
No 47
>COG0329 DapA Dihydrodipicolinate synthase/N-acetylneuraminate lyase [Amino acid transport and metabolism / Cell envelope biogenesis, outer membrane]
Probab=75.26 E-value=51 Score=30.61 Aligned_cols=105 Identities=14% Similarity=0.197 Sum_probs=69.3
Q ss_pred cCCCCHHHHHHHHHHHHhhhccCCCCCeEEEEecccccchhHhhhhHHHHHHHHHHhhhhhhcccceEEEEeCCCCHHHH
Q 024560 148 SGAPNEEEVLQYARVVIDCATADPDGRKRALLIGGGIANFTDVATTFNGIIRALREKESKLKAARMHIFVRRGGPNYQTG 227 (266)
Q Consensus 148 gG~a~~~~~~~al~~ll~~~~~d~~v~~vlvni~ggi~~~~~vA~~~~gii~al~~~~~~~~~~~~pvvvrl~G~~~~~~ 227 (266)
-|..+.+.+.+.++.+++ .++++++++=.+|-...-...+. ..+++...+.. ..++||++-.|+++-+++
T Consensus 19 dg~vD~~a~~~lv~~li~-----~Gv~gi~~~GttGE~~~Ls~eEr-~~v~~~~v~~~----~grvpviaG~g~~~t~ea 88 (299)
T COG0329 19 DGSVDEEALRRLVEFLIA-----AGVDGLVVLGTTGESPTLTLEER-KEVLEAVVEAV----GGRVPVIAGVGSNSTAEA 88 (299)
T ss_pred CCCcCHHHHHHHHHHHHH-----cCCCEEEECCCCccchhcCHHHH-HHHHHHHHHHH----CCCCcEEEecCCCcHHHH
Confidence 366899999999999886 57999999955554333333322 33445555443 246999999999999999
Q ss_pred HHHHHhhhhhcCC------ceeecCCCCCHHHHHHHHHHHhhhc
Q 024560 228 LAKMRALGEELGI------PLEVYGPEATMTGICKQAIDCIMSA 265 (266)
Q Consensus 228 ~~~L~~~~~~~Gi------p~~~~~~~~~~~eAv~~av~~~~~~ 265 (266)
.++-+. +++.|+ |-+++ -.+.++..+.+-.++.++
T Consensus 89 i~lak~-a~~~Gad~il~v~PyY~--k~~~~gl~~hf~~ia~a~ 129 (299)
T COG0329 89 IELAKH-AEKLGADGILVVPPYYN--KPSQEGLYAHFKAIAEAV 129 (299)
T ss_pred HHHHHH-HHhcCCCEEEEeCCCCc--CCChHHHHHHHHHHHHhc
Confidence 888774 345563 22222 235667777777666543
No 48
>COG0075 Serine-pyruvate aminotransferase/archaeal aspartate aminotransferase [Amino acid transport and metabolism]
Probab=74.34 E-value=29 Score=33.66 Aligned_cols=82 Identities=23% Similarity=0.347 Sum_probs=59.9
Q ss_pred eEecCCCcEEEEecCchHHHHHHHHHHhcCCCCCCCceee--ccCCCCHHHHHHHHHHHHhhhccCCCCCeEEEEe---c
Q 024560 107 TVLNPKGRIWTMVAGGGASVIYADTVGDLGYASELGNYAE--YSGAPNEEEVLQYARVVIDCATADPDGRKRALLI---G 181 (266)
Q Consensus 107 ~~v~l~G~Igii~NGaGlam~t~D~l~~~g~gg~pAN~lD--lgG~a~~~~~~~al~~ll~~~~~d~~v~~vlvni---~ 181 (266)
+++++++++-++.||. .+=--.|++..+ |.+. -.++ -|-..+++.+.++++ + +|+++.|.+.+ .
T Consensus 75 sl~~pgdkVLv~~nG~-FG~R~~~ia~~~--g~~v-~~~~~~wg~~v~p~~v~~~L~---~----~~~~~~V~~vH~ETS 143 (383)
T COG0075 75 SLVEPGDKVLVVVNGK-FGERFAEIAERY--GAEV-VVLEVEWGEAVDPEEVEEALD---K----DPDIKAVAVVHNETS 143 (383)
T ss_pred hccCCCCeEEEEeCCh-HHHHHHHHHHHh--CCce-EEEeCCCCCCCCHHHHHHHHh---c----CCCccEEEEEeccCc
Confidence 4677899999999998 455557899888 4543 2333 346678888888855 4 89999999885 5
Q ss_pred ccccchhHhhhhHHHHHHHHHHhh
Q 024560 182 GGIANFTDVATTFNGIIRALREKE 205 (266)
Q Consensus 182 ggi~~~~~vA~~~~gii~al~~~~ 205 (266)
+|+.+.- ++|.++++++.
T Consensus 144 TGvlnpl------~~I~~~~k~~g 161 (383)
T COG0075 144 TGVLNPL------KEIAKAAKEHG 161 (383)
T ss_pred ccccCcH------HHHHHHHHHcC
Confidence 6766532 67788888774
No 49
>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=74.19 E-value=29 Score=30.29 Aligned_cols=66 Identities=23% Similarity=0.181 Sum_probs=43.0
Q ss_pred CCCHHHHHHHHHHHHhhhccCCCCCeEEEEe--cccccchhHhhhhHHHHHHHHHHhhhhhhcccceEEEEeCCCCHHHH
Q 024560 150 APNEEEVLQYARVVIDCATADPDGRKRALLI--GGGIANFTDVATTFNGIIRALREKESKLKAARMHIFVRRGGPNYQTG 227 (266)
Q Consensus 150 ~a~~~~~~~al~~ll~~~~~d~~v~~vlvni--~ggi~~~~~vA~~~~gii~al~~~~~~~~~~~~pvvvrl~G~~~~~~ 227 (266)
......+.++++-+.+ ||++++|++.+ +||- .. -. +.+.++++..+ . ++||++...|.-...|
T Consensus 24 ~~~~~~l~~~l~~a~~----d~~i~~Vvl~~~s~gg~--~~-~~---~~l~~~l~~~~----~-~KpViA~v~g~a~s~g 88 (214)
T cd07022 24 LTSYEGIAAAIRAALA----DPDVRAIVLDIDSPGGE--VA-GV---FELADAIRAAR----A-GKPIVAFVNGLAASAA 88 (214)
T ss_pred cccHHHHHHHHHHHhh----CCCCcEEEEEEeCCCCc--HH-HH---HHHHHHHHHHh----c-CCCEEEEECCchhhHH
Confidence 3456778888777777 99999999975 4431 11 11 44556666553 2 5899998888654444
Q ss_pred HHH
Q 024560 228 LAK 230 (266)
Q Consensus 228 ~~~ 230 (266)
-.+
T Consensus 89 y~l 91 (214)
T cd07022 89 YWI 91 (214)
T ss_pred HHH
Confidence 433
No 50
>PF13433 Peripla_BP_5: Periplasmic binding protein domain; PDB: 1QNL_A 1QO0_A 1PEA_A.
Probab=72.85 E-value=9.7 Score=36.69 Aligned_cols=68 Identities=10% Similarity=0.165 Sum_probs=46.1
Q ss_pred HHHHHHHHHHhcCCC--CCCCceeeccCCCCHHHHHHHHHHHHhhhccCCCCCeEEEEecccccchhHhhhhHHHHHHHH
Q 024560 124 ASVIYADTVGDLGYA--SELGNYAEYSGAPNEEEVLQYARVVIDCATADPDGRKRALLIGGGIANFTDVATTFNGIIRAL 201 (266)
Q Consensus 124 lam~t~D~l~~~g~g--g~pAN~lDlgG~a~~~~~~~al~~ll~~~~~d~~v~~vlvni~ggi~~~~~vA~~~~gii~al 201 (266)
.+++++|-|+..| | |++-.++-.-+..++..|.+..+-++. +.+|++|| |+.|+..- ++|...+
T Consensus 23 ~~~lAI~eINa~G-GvlG~~le~v~~Dp~Sd~~~ya~~A~~Li~----~d~V~~if----Gc~TSasR-----KaVlPvv 88 (363)
T PF13433_consen 23 GALLAIEEINAAG-GVLGRQLEPVIYDPASDPSTYAEKAEKLIR----EDGVRAIF----GCYTSASR-----KAVLPVV 88 (363)
T ss_dssp HHHHHHHHHHCTT-TBTTB--EEEEE--TT-HHHHHHHHHHHHH----HS---EEE----E--SHHHH-----HHHHHHH
T ss_pred HHHHHHHHHHhcC-CcCCeEEEEEEECCCCCHHHHHHHHHHHHH----hCCccEEE----ecchhhhH-----HHHHHHH
Confidence 4688999999996 5 688888888899999999999888877 67776555 88887765 7777777
Q ss_pred HHhh
Q 024560 202 REKE 205 (266)
Q Consensus 202 ~~~~ 205 (266)
+++.
T Consensus 89 E~~~ 92 (363)
T PF13433_consen 89 ERHN 92 (363)
T ss_dssp HHCT
T ss_pred HhcC
Confidence 7654
No 51
>TIGR00683 nanA N-acetylneuraminate lyase. N-acetylneuraminate lyase is also known as N-acetylneuraminic acid aldolase, sialic acid aldolase, or sialate lyase. It is an intracellular enzyme. The structure of this homotetrameric enzyme related to dihydrodipicolinate synthase is known. In Clostridium tertium, the enzyme appears to be in an operon with a secreted sialidase that releases sialic acid from host sialoglycoconjugates. In several E. coli strains, however, this enzyme is responsible for N-acetyl-D-neuraminic acid synthesis for capsule production by condensing N-acetyl-D-mannosamine and pyruvate.
Probab=70.32 E-value=81 Score=28.99 Aligned_cols=108 Identities=17% Similarity=0.108 Sum_probs=69.6
Q ss_pred ceeeccCCCCHHHHHHHHHHHHhhhccCCC-CCeEEEE-ecccccchhHhhhhHHHHHHHHHHhhhhhhcccceEEEEeC
Q 024560 143 NYAEYSGAPNEEEVLQYARVVIDCATADPD-GRKRALL-IGGGIANFTDVATTFNGIIRALREKESKLKAARMHIFVRRG 220 (266)
Q Consensus 143 N~lDlgG~a~~~~~~~al~~ll~~~~~d~~-v~~vlvn-i~ggi~~~~~vA~~~~gii~al~~~~~~~~~~~~pvvvrl~ 220 (266)
-|+|=-|..+.+.+.+-++.+++ .+ +++++++ ..|-...- ... --+.+++...+.. ..++||++-.+
T Consensus 10 TPf~~dg~iD~~~~~~~i~~~i~-----~G~v~gi~~~GstGE~~~L-t~e-Er~~~~~~~~~~~----~~~~pvi~gv~ 78 (290)
T TIGR00683 10 VSFNEDGTINEKGLRQIIRHNID-----KMKVDGLYVGGSTGENFML-STE-EKKEIFRIAKDEA----KDQIALIAQVG 78 (290)
T ss_pred cCCCCCCCcCHHHHHHHHHHHHh-----CCCcCEEEECCcccccccC-CHH-HHHHHHHHHHHHh----CCCCcEEEecC
Confidence 45566678899999999998885 56 9999998 32221111 111 1144555544443 24689999999
Q ss_pred CCCHHHHHHHHHhhhhhcCC------ceeecCCCCCHHHHHHHHHHHhhh
Q 024560 221 GPNYQTGLAKMRALGEELGI------PLEVYGPEATMTGICKQAIDCIMS 264 (266)
Q Consensus 221 G~~~~~~~~~L~~~~~~~Gi------p~~~~~~~~~~~eAv~~av~~~~~ 264 (266)
..+.+++.+..+. ++++|. |-+++ ..+.++.+..+-+++.+
T Consensus 79 ~~~t~~~i~la~~-a~~~Gad~v~v~~P~y~--~~~~~~i~~yf~~v~~~ 125 (290)
T TIGR00683 79 SVNLKEAVELGKY-ATELGYDCLSAVTPFYY--KFSFPEIKHYYDTIIAE 125 (290)
T ss_pred CCCHHHHHHHHHH-HHHhCCCEEEEeCCcCC--CCCHHHHHHHHHHHHhh
Confidence 9898888877774 345664 22222 34678888888887654
No 52
>PRK00286 xseA exodeoxyribonuclease VII large subunit; Reviewed
Probab=69.99 E-value=35 Score=33.16 Aligned_cols=121 Identities=16% Similarity=0.079 Sum_probs=69.9
Q ss_pred CCCcEEEEecCchHHHHHHHHHHhcCCCCC-CC-cee----eccCCCCHHHHHHHHHHHHhhhccCCCCCeEEEEecccc
Q 024560 111 PKGRIWTMVAGGGASVIYADTVGDLGYASE-LG-NYA----EYSGAPNEEEVLQYARVVIDCATADPDGRKRALLIGGGI 184 (266)
Q Consensus 111 l~G~Igii~NGaGlam~t~D~l~~~g~gg~-pA-N~l----DlgG~a~~~~~~~al~~ll~~~~~d~~v~~vlvni~ggi 184 (266)
.--+||+||.-.|.++ -|.+.... -+ |. ++. =+-|.-.+..+.+|++.+-. .+.|+|+|.=.||
T Consensus 134 ~p~~I~viTs~~gAa~--~D~~~~~~--~r~p~~~~~~~~~~vQG~~A~~~i~~al~~~~~-----~~~Dviii~RGGG- 203 (438)
T PRK00286 134 FPKRIGVITSPTGAAI--RDILTVLR--RRFPLVEVIIYPTLVQGEGAAASIVAAIERANA-----RGEDVLIVARGGG- 203 (438)
T ss_pred CCCEEEEEeCCccHHH--HHHHHHHH--hcCCCCeEEEecCcCcCccHHHHHHHHHHHhcC-----CCCCEEEEecCCC-
Confidence 4689999999999886 68887762 22 42 222 33477677889999887643 2367665554444
Q ss_pred cchhHhhhhHHHHHHHHHHhhhhhhcccceEEEEeCCCCHHHHHHHHHhhhhhcCCceeecCCCCCHHHHHHHHHH
Q 024560 185 ANFTDVATTFNGIIRALREKESKLKAARMHIFVRRGGPNYQTGLAKMRALGEELGIPLEVYGPEATMTGICKQAID 260 (266)
Q Consensus 185 ~~~~~vA~~~~gii~al~~~~~~~~~~~~pvvvrl~G~~~~~~~~~L~~~~~~~Gip~~~~~~~~~~~eAv~~av~ 260 (266)
+--|--+=+=+.|++|+-+ .++|||.=.|=.....--..-. .. .+.||+.|++.++.
T Consensus 204 S~eDL~~Fn~e~v~~ai~~-------~~~Pvis~IGHE~D~tl~D~vA------d~------ra~TPtaaae~~~~ 260 (438)
T PRK00286 204 SLEDLWAFNDEAVARAIAA-------SRIPVISAVGHETDFTIADFVA------DL------RAPTPTAAAELAVP 260 (438)
T ss_pred CHHHhhccCcHHHHHHHHc-------CCCCEEEeccCCCCccHHHHhh------hc------cCCChHHHHHHhCc
Confidence 3111111011444454443 3699998666533222212222 11 36699999987754
No 53
>cd07021 Clp_protease_NfeD_like Nodulation formation efficiency D (NfeD) is a membrane-bound ClpP-class protease. Nodulation formation efficiency D (NfeD; stomatin operon partner protein, STOPP; DUF107) is a member of membrane-anchored ClpP-class proteases. Currently, more than 300 NfeD homologs have been identified - all of which are bacterial or archaeal in origin. Majority of these genomes have been shown to possess operons containing a homologous NfeD/stomatin gene pair, causing NfeD to be previously named STOPP (stomatin operon partner protein). NfeD homologs can be divided into two groups: long and short forms. Long-form homologs have a putative ClpP-class serine protease domain while the short form homologs do not. Downstream from the ClpP-class domain is the so-called NfeD or DUF107 domain. N-terminal region of the NfeD homolog PH1510 (1510-N or PH1510-N) from Pyrococcus horikoshii has been shown to possess serine protease activity and has a Ser-Lys catalytic dyad, preferentiall
Probab=69.02 E-value=23 Score=30.40 Aligned_cols=60 Identities=10% Similarity=0.012 Sum_probs=38.2
Q ss_pred HHHHHHHHHHhhhccCCCCCeEEEE--ecccccchhHhhhhHHHHHHHHHHhhhhhhcccceEEEEeCCCCHHHHHHHHH
Q 024560 155 EVLQYARVVIDCATADPDGRKRALL--IGGGIANFTDVATTFNGIIRALREKESKLKAARMHIFVRRGGPNYQTGLAKMR 232 (266)
Q Consensus 155 ~~~~al~~ll~~~~~d~~v~~vlvn--i~ggi~~~~~vA~~~~gii~al~~~~~~~~~~~~pvvvrl~G~~~~~~~~~L~ 232 (266)
.+.++++-..+ ++ .+.|++. .|||...+. +.|.+.++.. ++|++++..|.-.-.|--+.-
T Consensus 17 ~l~~~l~~a~~----~~-~~~ivl~inspGG~v~~~------~~I~~~l~~~-------~~pvva~V~g~AaSaG~~ia~ 78 (178)
T cd07021 17 FVERALKEAKE----EG-ADAVVLDIDTPGGRVDSA------LEIVDLILNS-------PIPTIAYVNDRAASAGALIAL 78 (178)
T ss_pred HHHHHHHHHHh----CC-CCeEEEEEECcCCCHHHH------HHHHHHHHhC-------CCCEEEEECCchHHHHHHHHH
Confidence 35555555544 55 6666555 588876443 6777777754 589999998876655544443
No 54
>COG0673 MviM Predicted dehydrogenases and related proteins [General function prediction only]
Probab=68.94 E-value=60 Score=29.58 Aligned_cols=122 Identities=15% Similarity=0.105 Sum_probs=64.9
Q ss_pred cEEEEecCchHHHHHHHHHHhcCCCCCCCceeecc-CCCCHHHHH------------HHHHHHHhhhccCCCCCeEEEEe
Q 024560 114 RIWTMVAGGGASVIYADTVGDLGYASELGNYAEYS-GAPNEEEVL------------QYARVVIDCATADPDGRKRALLI 180 (266)
Q Consensus 114 ~Igii~NGaGlam~t~D~l~~~g~gg~pAN~lDlg-G~a~~~~~~------------~al~~ll~~~~~d~~v~~vlvni 180 (266)
+||+|+-|+-..-.-+-.+... ++. +.-++ -+.++++.. .-++-+|+ +|++++|.|-.
T Consensus 5 rvgiiG~G~~~~~~~~~~~~~~--~~~---~~~vav~d~~~~~a~~~a~~~~~~~~~~~~~~ll~----~~~iD~V~Iat 75 (342)
T COG0673 5 RVGIIGAGGIAGKAHLPALAAL--GGG---LELVAVVDRDPERAEAFAEEFGIAKAYTDLEELLA----DPDIDAVYIAT 75 (342)
T ss_pred EEEEEcccHHHHHHhHHHHHhC--CCc---eEEEEEecCCHHHHHHHHHHcCCCcccCCHHHHhc----CCCCCEEEEcC
Confidence 6889988754444455666665 221 11111 234444422 22333455 89999998887
Q ss_pred cccccchhHhhhhHHHHHHHHHHhhhhhhcccceEEE-EeCCCCHHHHHHHHHhhhhhcCCceeecCCCCCHHHHHHHHH
Q 024560 181 GGGIANFTDVATTFNGIIRALREKESKLKAARMHIFV-RRGGPNYQTGLAKMRALGEELGIPLEVYGPEATMTGICKQAI 259 (266)
Q Consensus 181 ~ggi~~~~~vA~~~~gii~al~~~~~~~~~~~~pvvv-rl~G~~~~~~~~~L~~~~~~~Gip~~~~~~~~~~~eAv~~av 259 (266)
|... +++-+.+|++ ..++|++ .=-..+.++++++.+. ++++|+.+.+.- -.-...+++++.
T Consensus 76 p~~~--------H~e~~~~AL~--------aGkhVl~EKPla~t~~ea~~l~~~-a~~~~~~l~v~~-~~Rf~p~~~~~k 137 (342)
T COG0673 76 PNAL--------HAELALAALE--------AGKHVLCEKPLALTLEEAEELVEL-ARKAGVKLMVGF-NRRFDPAVQALK 137 (342)
T ss_pred CChh--------hHHHHHHHHh--------cCCEEEEcCCCCCCHHHHHHHHHH-HHHcCCceeeeh-hhhcCHHHHHHH
Confidence 6542 2233344544 2466777 5556688888877764 445576643211 112234555555
Q ss_pred HHh
Q 024560 260 DCI 262 (266)
Q Consensus 260 ~~~ 262 (266)
++.
T Consensus 138 ~li 140 (342)
T COG0673 138 ELI 140 (342)
T ss_pred HHH
Confidence 544
No 55
>TIGR02313 HpaI-NOT-DapA 2,4-dihydroxyhept-2-ene-1,7-dioic acid aldolase. This model represents a subset of the DapA (dihydrodipicolinate synthase) family which has apparently evolved a separate function. The product of DapA, dihydrodipicolinate, results from the non-enzymatic cyclization and dehydration of 6-amino-2,4-dihydroxyhept-2-ene-1,7-dioic acid, which is different from the substrate of this reaction only in the presence of the amino group. In the absence of this amino group, and running the reaction in the opposite direction, the reaction corresponds to the HpaI aldolase component of the 4-hydroxyphenylacetic acid catabolism pathway (see TIGR02311). At present, this variant of DapA is found only in Oceanobacillus iheyensis HTE831 and Thermus thermophilus HB27. In both of these cases, one or more other DapA genes can be found and the one identified by this model is part of an operon for 4-hydroxyphenylacetic acid catabolism.
Probab=68.39 E-value=92 Score=28.69 Aligned_cols=109 Identities=13% Similarity=0.078 Sum_probs=69.0
Q ss_pred ceeeccCCCCHHHHHHHHHHHHhhhccCCCCCeEEEEecccccchhHhhhhHHHHHHHHHHhhhhhhcccceEEEEeCCC
Q 024560 143 NYAEYSGAPNEEEVLQYARVVIDCATADPDGRKRALLIGGGIANFTDVATTFNGIIRALREKESKLKAARMHIFVRRGGP 222 (266)
Q Consensus 143 N~lDlgG~a~~~~~~~al~~ll~~~~~d~~v~~vlvni~ggi~~~~~vA~~~~gii~al~~~~~~~~~~~~pvvvrl~G~ 222 (266)
-|+|=.|..+.+.+.+-++.+++ .++++++++=..|-...-...+- .-+++...+.. ..++||++-.+.+
T Consensus 10 TPf~~dg~iD~~~l~~lv~~~~~-----~Gv~gi~v~GstGE~~~Ls~~Er-~~l~~~~~~~~----~g~~pvi~gv~~~ 79 (294)
T TIGR02313 10 TPFKRNGDIDEEALRELIEFQIE-----GGSHAISVGGTSGEPGSLTLEER-KQAIENAIDQI----AGRIPFAPGTGAL 79 (294)
T ss_pred CCcCCCCCcCHHHHHHHHHHHHH-----cCCCEEEECccCcccccCCHHHH-HHHHHHHHHHh----CCCCcEEEECCcc
Confidence 46667788999999999999885 68999999833332222111111 23344333322 2468999999999
Q ss_pred CHHHHHHHHHhhhhhcCCc------eeecCCCCCHHHHHHHHHHHhhh
Q 024560 223 NYQTGLAKMRALGEELGIP------LEVYGPEATMTGICKQAIDCIMS 264 (266)
Q Consensus 223 ~~~~~~~~L~~~~~~~Gip------~~~~~~~~~~~eAv~~av~~~~~ 264 (266)
+.+++.+.-+.. ++.|.. -+.| ..+.++.++.+-.++.+
T Consensus 80 ~t~~ai~~a~~A-~~~Gad~v~v~pP~y~--~~~~~~l~~~f~~ia~a 124 (294)
T TIGR02313 80 NHDETLELTKFA-EEAGADAAMVIVPYYN--KPNQEALYDHFAEVADA 124 (294)
T ss_pred hHHHHHHHHHHH-HHcCCCEEEEcCccCC--CCCHHHHHHHHHHHHHh
Confidence 988887777753 455642 1222 23567788888777654
No 56
>COG2185 Sbm Methylmalonyl-CoA mutase, C-terminal domain/subunit (cobalamin-binding) [Lipid metabolism]
Probab=68.07 E-value=72 Score=26.79 Aligned_cols=94 Identities=18% Similarity=0.279 Sum_probs=63.2
Q ss_pred eccCCCCHHHHHHHHHHHHhhhccCCCCCeEEEEecccccchhHhhhhHHHHHHHHHHhhhhhhcccceEEEEeCCCCHH
Q 024560 146 EYSGAPNEEEVLQYARVVIDCATADPDGRKRALLIGGGIANFTDVATTFNGIIRALREKESKLKAARMHIFVRRGGPNYQ 225 (266)
Q Consensus 146 DlgG~a~~~~~~~al~~ll~~~~~d~~v~~vlvni~ggi~~~~~vA~~~~gii~al~~~~~~~~~~~~pvvvrl~G~~~~ 225 (266)
..|...+++.+.++ .++ .++++|.|-+..|- -.+.. ..+++++++... -.+.+-.||.-..
T Consensus 45 ~~g~~~tp~e~v~a---A~~-----~dv~vIgvSsl~g~--h~~l~---~~lve~lre~G~------~~i~v~~GGvip~ 105 (143)
T COG2185 45 NLGLFQTPEEAVRA---AVE-----EDVDVIGVSSLDGG--HLTLV---PGLVEALREAGV------EDILVVVGGVIPP 105 (143)
T ss_pred ecCCcCCHHHHHHH---HHh-----cCCCEEEEEeccch--HHHHH---HHHHHHHHHhCC------cceEEeecCccCc
Confidence 35556677655444 343 57777887753321 22333 899999999752 2344677888777
Q ss_pred HHHHHHHhhhhhcCCceeecCCCCCHHHHHHHHHHHhh
Q 024560 226 TGLAKMRALGEELGIPLEVYGPEATMTGICKQAIDCIM 263 (266)
Q Consensus 226 ~~~~~L~~~~~~~Gip~~~~~~~~~~~eAv~~av~~~~ 263 (266)
+-.+.|+ +.|+. .+|++-+++.+++...+....
T Consensus 106 ~d~~~l~----~~G~~-~if~pgt~~~~~~~~v~~~l~ 138 (143)
T COG2185 106 GDYQELK----EMGVD-RIFGPGTPIEEALSDLLTRLG 138 (143)
T ss_pred hhHHHHH----HhCcc-eeeCCCCCHHHHHHHHHHHHH
Confidence 7788888 66875 467788899999888776543
No 57
>PRK00061 ribH 6,7-dimethyl-8-ribityllumazine synthase; Provisional
Probab=64.70 E-value=86 Score=26.48 Aligned_cols=126 Identities=13% Similarity=0.025 Sum_probs=83.4
Q ss_pred CcEEEEecCc------hHHHHHHHHHHhcCCCCCCCceeeccCCCCHHHHHHHHHHHHhhhccCCCCCeEEEE-e--ccc
Q 024560 113 GRIWTMVAGG------GASVIYADTVGDLGYASELGNYAEYSGAPNEEEVLQYARVVIDCATADPDGRKRALL-I--GGG 183 (266)
Q Consensus 113 G~Igii~NGa------Glam~t~D~l~~~g~gg~pAN~lDlgG~a~~~~~~~al~~ll~~~~~d~~v~~vlvn-i--~gg 183 (266)
-||+|+..=- .+---+.+.|..+ |....|.--+ --|-.-.+.-+++.+++ ..+.++++.. . =|.
T Consensus 13 ~riaIV~s~~n~~i~~~l~~ga~~~l~~~--gv~~~~i~v~-~VPGa~EiP~a~~~l~~----~~~~DavIalG~VIrG~ 85 (154)
T PRK00061 13 LRIGIVVARFNDFITDALLEGALDALKRH--GVSEENIDVV-RVPGAFEIPLAAKKLAE----SGKYDAVIALGAVIRGE 85 (154)
T ss_pred CEEEEEEecCcHHHHHHHHHHHHHHHHHc--CCCccceEEE-ECCCHHHHHHHHHHHHH----cCCCCEEEEEeeEEcCC
Confidence 3677765322 3445567888888 5555554332 34445567777777776 6678998887 3 488
Q ss_pred ccchhHhhhhHHHHHHHHHHhhhhhhcccceEEE-EeCCCCHHHHHHHHHhhhhhcCCceeecCCCCCHHHHHHHHHHHh
Q 024560 184 IANFTDVATTFNGIIRALREKESKLKAARMHIFV-RRGGPNYQTGLAKMRALGEELGIPLEVYGPEATMTGICKQAIDCI 262 (266)
Q Consensus 184 i~~~~~vA~~~~gii~al~~~~~~~~~~~~pvvv-rl~G~~~~~~~~~L~~~~~~~Gip~~~~~~~~~~~eAv~~av~~~ 262 (266)
...++-|+ +++.+.+.+..- ...+||.. -+...|.+++.+.-. +- . ..-=.||++.+++++
T Consensus 86 T~H~e~V~---~~v~~gl~~v~l---~~~~PV~~GVLt~~~~eQa~~R~~------~~-~-----~nkG~eaa~aal~m~ 147 (154)
T PRK00061 86 TPHFDYVA---NEVAKGLADVSL---ETGVPVGFGVLTTDTIEQAIERAG------TK-A-----GNKGAEAALAALEMA 147 (154)
T ss_pred CchHHHHH---HHHHHHHHHHHh---ccCCCEEEEecCCCCHHHHHHHhC------cc-c-----cccHHHHHHHHHHHH
Confidence 88888888 888888777642 25799886 788888888876554 11 1 224567888888876
Q ss_pred h
Q 024560 263 M 263 (266)
Q Consensus 263 ~ 263 (266)
.
T Consensus 148 ~ 148 (154)
T PRK00061 148 N 148 (154)
T ss_pred H
Confidence 4
No 58
>PLN02417 dihydrodipicolinate synthase
Probab=63.52 E-value=1.2e+02 Score=27.68 Aligned_cols=108 Identities=8% Similarity=-0.014 Sum_probs=69.3
Q ss_pred ceeeccCCCCHHHHHHHHHHHHhhhccCCCCCeEEEEecccccchhHhhhhHHHHHHHHHHhhhhhhcccceEEEEeCCC
Q 024560 143 NYAEYSGAPNEEEVLQYARVVIDCATADPDGRKRALLIGGGIANFTDVATTFNGIIRALREKESKLKAARMHIFVRRGGP 222 (266)
Q Consensus 143 N~lDlgG~a~~~~~~~al~~ll~~~~~d~~v~~vlvni~ggi~~~~~vA~~~~gii~al~~~~~~~~~~~~pvvvrl~G~ 222 (266)
-|+|=-|..+.+.+.+-++.+++ .++++++++=..|-...-...+ -+-+++...+.. ..++||++-.+.+
T Consensus 11 TPf~~~g~iD~~~~~~~i~~l~~-----~Gv~Gi~~~GstGE~~~ls~~E-r~~~~~~~~~~~----~~~~pvi~gv~~~ 80 (280)
T PLN02417 11 TPYLPDGRFDLEAYDSLVNMQIE-----NGAEGLIVGGTTGEGQLMSWDE-HIMLIGHTVNCF----GGKIKVIGNTGSN 80 (280)
T ss_pred CCcCCCCCcCHHHHHHHHHHHHH-----cCCCEEEECccCcchhhCCHHH-HHHHHHHHHHHh----CCCCcEEEECCCc
Confidence 45666788999999999999885 6999999983323221111111 133444433332 2468999999999
Q ss_pred CHHHHHHHHHhhhhhcCCc------eeecCCCCCHHHHHHHHHHHhh
Q 024560 223 NYQTGLAKMRALGEELGIP------LEVYGPEATMTGICKQAIDCIM 263 (266)
Q Consensus 223 ~~~~~~~~L~~~~~~~Gip------~~~~~~~~~~~eAv~~av~~~~ 263 (266)
+..++.+..+.. +++|.. -+++ ..+.++.++.+-.++.
T Consensus 81 ~t~~~i~~a~~a-~~~Gadav~~~~P~y~--~~~~~~i~~~f~~va~ 124 (280)
T PLN02417 81 STREAIHATEQG-FAVGMHAALHINPYYG--KTSQEGLIKHFETVLD 124 (280)
T ss_pred cHHHHHHHHHHH-HHcCCCEEEEcCCccC--CCCHHHHHHHHHHHHh
Confidence 999998887743 455642 1222 2356778887777665
No 59
>TIGR03249 KdgD 5-dehydro-4-deoxyglucarate dehydratase. 5-dehydro-4-deoxyglucarate dehydratase not only catalyzes the dehydration of the substrate (diol to ketone + water), but causes the decarboxylation of the intermediate product to yield 2-oxoglutarate semialdehyde (2,5-dioxopentanoate). The gene for the enzyme is usually observed in the vicinity of transporters and dehydratases handling D-galactarate and D-gluconate as well as aldehyde dehydrogenases which convert the product to alpha-ketoglutarate.
Probab=60.85 E-value=1.4e+02 Score=27.46 Aligned_cols=107 Identities=12% Similarity=0.137 Sum_probs=63.8
Q ss_pred ceeeccCCCCHHHHHHHHHHHHhhhccCCCCCeEEEE-ecccccchhHhhhhHHHHHHHHHHhhhhhhcccceEEEEeCC
Q 024560 143 NYAEYSGAPNEEEVLQYARVVIDCATADPDGRKRALL-IGGGIANFTDVATTFNGIIRALREKESKLKAARMHIFVRRGG 221 (266)
Q Consensus 143 N~lDlgG~a~~~~~~~al~~ll~~~~~d~~v~~vlvn-i~ggi~~~~~vA~~~~gii~al~~~~~~~~~~~~pvvvrl~G 221 (266)
-|+|=-|..+.+.+.+-++.+++ .++++++++ ..|-....+. . --+.+++...+.. ..++||++-.+.
T Consensus 15 TPf~~dg~iD~~~l~~li~~l~~-----~Gv~gi~v~GstGE~~~Lt~-e-Er~~v~~~~~~~~----~g~~pvi~gv~~ 83 (296)
T TIGR03249 15 TPFDADGSFDEAAYRENIEWLLG-----YGLEALFAAGGTGEFFSLTP-A-EYEQVVEIAVSTA----KGKVPVYTGVGG 83 (296)
T ss_pred CCcCCCCCcCHHHHHHHHHHHHh-----cCCCEEEECCCCcCcccCCH-H-HHHHHHHHHHHHh----CCCCcEEEecCc
Confidence 45556678888888888888875 689999988 3332222211 1 1144555444432 246888887775
Q ss_pred CCHHHHHHHHHhhhhhcCCc------eeecCCCCCHHHHHHHHHHHhhh
Q 024560 222 PNYQTGLAKMRALGEELGIP------LEVYGPEATMTGICKQAIDCIMS 264 (266)
Q Consensus 222 ~~~~~~~~~L~~~~~~~Gip------~~~~~~~~~~~eAv~~av~~~~~ 264 (266)
+.+++.+..+. ++++|.. -+++ -.+.++.++.+-.++.+
T Consensus 84 -~t~~ai~~a~~-a~~~Gadav~~~pP~y~--~~s~~~i~~~f~~v~~a 128 (296)
T TIGR03249 84 -NTSDAIEIARL-AEKAGADGYLLLPPYLI--NGEQEGLYAHVEAVCES 128 (296)
T ss_pred -cHHHHHHHHHH-HHHhCCCEEEECCCCCC--CCCHHHHHHHHHHHHhc
Confidence 67888777664 3445643 1222 12557777777666653
No 60
>cd00408 DHDPS-like Dihydrodipicolinate synthase family. A member of the class I aldolases, which use an active-site lysine which stablilzes a reaction intermediate via Schiff base formation, and have TIM beta/alpha barrel fold. The dihydrodipicolinate synthase family comprises several pyruvate-dependent class I aldolases that use the same catalytic step to catalyze different reactions in different pathways and includes such proteins as N-acetylneuraminate lyase, MosA protein, 5-keto-4-deoxy-glucarate dehydratase, trans-o-hydroxybenzylidenepyruvate hydratase-aldolase, trans-2'-carboxybenzalpyruvate hydratase-aldolase, and 2-keto-3-deoxy- gluconate aldolase. The family is also referred to as the N-acetylneuraminate lyase (NAL) family.
Probab=60.78 E-value=1.3e+02 Score=27.10 Aligned_cols=107 Identities=16% Similarity=0.143 Sum_probs=68.8
Q ss_pred eeeccCCCCHHHHHHHHHHHHhhhccCCCCCeEEEEe-cccccchhHhhhhHHHHHHHHHHhhhhhhcccceEEEEeCCC
Q 024560 144 YAEYSGAPNEEEVLQYARVVIDCATADPDGRKRALLI-GGGIANFTDVATTFNGIIRALREKESKLKAARMHIFVRRGGP 222 (266)
Q Consensus 144 ~lDlgG~a~~~~~~~al~~ll~~~~~d~~v~~vlvni-~ggi~~~~~vA~~~~gii~al~~~~~~~~~~~~pvvvrl~G~ 222 (266)
|++=.|..+.+.+.+-++.+++ .++++++++= .|-....+ ..+ -+.+++...+.. ..+.||++-.+++
T Consensus 8 Pf~~dg~iD~~~~~~~i~~l~~-----~Gv~gi~~~GstGE~~~ls-~~E-r~~l~~~~~~~~----~~~~~vi~gv~~~ 76 (281)
T cd00408 8 PFTADGEVDLDALRRLVEFLIE-----AGVDGLVVLGTTGEAPTLT-DEE-RKEVIEAVVEAV----AGRVPVIAGVGAN 76 (281)
T ss_pred CcCCCCCcCHHHHHHHHHHHHH-----cCCCEEEECCCCcccccCC-HHH-HHHHHHHHHHHh----CCCCeEEEecCCc
Confidence 4455678899999999999986 5999999983 33222211 111 144555555443 2468999999999
Q ss_pred CHHHHHHHHHhhhhhcCCce------eecCCCCCHHHHHHHHHHHhhh
Q 024560 223 NYQTGLAKMRALGEELGIPL------EVYGPEATMTGICKQAIDCIMS 264 (266)
Q Consensus 223 ~~~~~~~~L~~~~~~~Gip~------~~~~~~~~~~eAv~~av~~~~~ 264 (266)
+.+++.+..+.. +++|... +++ ..+.++.++.+-.++.+
T Consensus 77 ~~~~~i~~a~~a-~~~Gad~v~v~pP~y~--~~~~~~~~~~~~~ia~~ 121 (281)
T cd00408 77 STREAIELARHA-EEAGADGVLVVPPYYN--KPSQEGIVAHFKAVADA 121 (281)
T ss_pred cHHHHHHHHHHH-HHcCCCEEEECCCcCC--CCCHHHHHHHHHHHHhc
Confidence 988888877643 3456431 111 23668888887777654
No 61
>COG1090 Predicted nucleoside-diphosphate sugar epimerase [General function prediction only]
Probab=60.64 E-value=23 Score=33.12 Aligned_cols=132 Identities=14% Similarity=0.121 Sum_probs=81.5
Q ss_pred CcEEEEecCchHHHHHHHHHHhcCCCCCCCceeeccCCCCHHHHHHHHHHHHhhhccCCCCCeEEEEe-cccccchhHhh
Q 024560 113 GRIWTMVAGGGASVIYADTVGDLGYASELGNYAEYSGAPNEEEVLQYARVVIDCATADPDGRKRALLI-GGGIANFTDVA 191 (266)
Q Consensus 113 G~Igii~NGaGlam~t~D~l~~~g~gg~pAN~lDlgG~a~~~~~~~al~~ll~~~~~d~~v~~vlvni-~ggi~~~~~vA 191 (266)
-|+|++-.+.|-++..|=-+...|.||+.++=--.=-=..-+.+.+++..+++ ++++.+.+=.. |.. ++..+.+
T Consensus 158 lRtGvVLs~~GGaL~~m~~~fk~glGG~~GsGrQ~~SWIhieD~v~~I~fll~----~~~lsGp~N~taP~P-V~~~~F~ 232 (297)
T COG1090 158 LRTGVVLSPDGGALGKMLPLFKLGLGGKLGSGRQWFSWIHIEDLVNAILFLLE----NEQLSGPFNLTAPNP-VRNKEFA 232 (297)
T ss_pred EEEEEEecCCCcchhhhcchhhhccCCccCCCCceeeeeeHHHHHHHHHHHHh----CcCCCCcccccCCCc-CcHHHHH
Confidence 47888888777788888888888878886520000001246788999999998 88888876333 433 4455666
Q ss_pred hhHHHHHHHHHHhhhhhhcccceEE-EE--eCCCC--HHHHHHHHHhhhhhcCCceeecCCCCCHHHHHHHHHH
Q 024560 192 TTFNGIIRALREKESKLKAARMHIF-VR--RGGPN--YQTGLAKMRALGEELGIPLEVYGPEATMTGICKQAID 260 (266)
Q Consensus 192 ~~~~gii~al~~~~~~~~~~~~pvv-vr--l~G~~--~~~~~~~L~~~~~~~Gip~~~~~~~~~~~eAv~~av~ 260 (266)
+++.+++++-. ..++|=+ +| ||... .-.+++.+-+...++|.... |.++++|....+.
T Consensus 233 ---~al~r~l~RP~----~~~vP~~~~rl~LGe~a~~lL~gQrvlP~kl~~aGF~F~----y~dl~~AL~~il~ 295 (297)
T COG1090 233 ---HALGRALHRPA----ILPVPSFALRLLLGEMADLLLGGQRVLPKKLEAAGFQFQ----YPDLEEALADILK 295 (297)
T ss_pred ---HHHHHHhCCCc----cccCcHHHHHHHhhhhHHHHhccchhhHHHHHHCCCeee----cCCHHHHHHHHHh
Confidence 66666654210 1344422 22 23211 11345555555557898763 8899999987664
No 62
>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=59.94 E-value=39 Score=27.83 Aligned_cols=64 Identities=16% Similarity=0.078 Sum_probs=42.0
Q ss_pred CCHHHHHHHHHHHHhhhccCCCCCeEEEEecccccchhHhhhhHHHHHHHHHHhhhhhhcccceEEEEeCCCCHHHHHHH
Q 024560 151 PNEEEVLQYARVVIDCATADPDGRKRALLIGGGIANFTDVATTFNGIIRALREKESKLKAARMHIFVRRGGPNYQTGLAK 230 (266)
Q Consensus 151 a~~~~~~~al~~ll~~~~~d~~v~~vlvni~ggi~~~~~vA~~~~gii~al~~~~~~~~~~~~pvvvrl~G~~~~~~~~~ 230 (266)
.+++.+.+.++-+-+ + +.=.+.||.|||-..+ + ..|.+.++.. ++|+++...|.-...|--+
T Consensus 15 ~~~~~~~~~l~~~~~----~-~~i~l~inspGG~~~~---~---~~i~~~i~~~-------~~pvi~~v~g~a~s~g~~i 76 (160)
T cd07016 15 VTAKEFKDALDALGD----D-SDITVRINSPGGDVFA---G---LAIYNALKRH-------KGKVTVKIDGLAASAASVI 76 (160)
T ss_pred cCHHHHHHHHHhccC----C-CCEEEEEECCCCCHHH---H---HHHHHHHHhc-------CCCEEEEEcchHHhHHHHH
Confidence 567777777665433 4 2224667789986432 2 6777777664 5889998888766666555
Q ss_pred HH
Q 024560 231 MR 232 (266)
Q Consensus 231 L~ 232 (266)
+-
T Consensus 77 a~ 78 (160)
T cd07016 77 AM 78 (160)
T ss_pred Hh
Confidence 55
No 63
>cd07020 Clp_protease_NfeD_1 Nodulation formation efficiency D (NfeD) is a membrane-bound ClpP-class protease. Nodulation formation efficiency D (NfeD; stomatin operon partner protein, STOPP; DUF107) is a member of membrane-anchored ClpP-class proteases. Currently, more than 300 NfeD homologs have been identified - all of which are bacterial or archaeal in origin. Majority of these genomes have been shown to possess operons containing a homologous NfeD/stomatin gene pair, causing NfeD to be previously named STOPP (stomatin operon partner protein). NfeD homologs can be divided into two groups: long and short forms. Long-form homologs have a putative ClpP-class serine protease domain while the short form homologs do not. Downstream from the ClpP-class domain is the so-called NfeD or DUF107 domain. N-terminal region of the NfeD homolog PH1510 (1510-N or PH1510-N) from Pyrococcus horikoshii has been shown to possess serine protease activity and has a Ser-Lys catalytic dyad, preferentially c
Probab=58.42 E-value=49 Score=28.30 Aligned_cols=62 Identities=11% Similarity=0.087 Sum_probs=36.8
Q ss_pred HHHHHHHHHHHHhhhccCCCCCeEEEE--ecccccchhHhhhhHHHHHHHHHHhhhhhhcccceEEEEeC---CCCHHHH
Q 024560 153 EEEVLQYARVVIDCATADPDGRKRALL--IGGGIANFTDVATTFNGIIRALREKESKLKAARMHIFVRRG---GPNYQTG 227 (266)
Q Consensus 153 ~~~~~~al~~ll~~~~~d~~v~~vlvn--i~ggi~~~~~vA~~~~gii~al~~~~~~~~~~~~pvvvrl~---G~~~~~~ 227 (266)
.+.+.++++.+-+ ++ ++.|++- .|||-.... ..+.++++. .++|+++... |.-...|
T Consensus 15 ~~~l~~~l~~a~~----~~-~~~vvl~InSpGG~v~~~------~~i~~~l~~-------~~kPvia~v~~~~G~AasgG 76 (187)
T cd07020 15 ADYLERAIDQAEE----GG-ADALIIELDTPGGLLDST------REIVQAILA-------SPVPVVVYVYPSGARAASAG 76 (187)
T ss_pred HHHHHHHHHHHHh----CC-CCEEEEEEECCCCCHHHH------HHHHHHHHh-------CCCCEEEEEecCCCCchhHH
Confidence 4456666665554 54 6765554 588853221 455555543 3689998875 7666555
Q ss_pred HHHHH
Q 024560 228 LAKMR 232 (266)
Q Consensus 228 ~~~L~ 232 (266)
--+.-
T Consensus 77 ~~ial 81 (187)
T cd07020 77 TYILL 81 (187)
T ss_pred HHHHH
Confidence 55444
No 64
>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=58.30 E-value=1.2e+02 Score=26.00 Aligned_cols=119 Identities=13% Similarity=0.072 Sum_probs=63.2
Q ss_pred CcEEEEecCchHHH------HHHHHHHhcCCCCCCCceeeccCCCCHHHHHHHHHHHHhhhccCCCCCeEEEEecccccc
Q 024560 113 GRIWTMVAGGGASV------IYADTVGDLGYASELGNYAEYSGAPNEEEVLQYARVVIDCATADPDGRKRALLIGGGIAN 186 (266)
Q Consensus 113 G~Igii~NGaGlam------~t~D~l~~~g~gg~pAN~lDlgG~a~~~~~~~al~~ll~~~~~d~~v~~vlvni~ggi~~ 186 (266)
++|+++.+..+... -..+.+..+ |.+..-+.-+.++.+.+..+++++-+++ +.|++++|+..
T Consensus 117 ~~i~~l~~~~~~~~~~~R~~gf~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~l~---~~~~~~ai~~~------- 184 (269)
T cd06288 117 RRIAFINGEPWMLAAKDRLKGYRQALAEA--GIPFDPDLVVHGDWSADDGYEAAAALLD---LDDRPTAIFCG------- 184 (269)
T ss_pred ceEEEEeCCccchhHHHHHHHHHHHHHHc--CCCCCHHHeEeCCCChHHHHHHHHHHHh---CCCCCCEEEEe-------
Confidence 57888875544221 123445554 3332211122333444445555555554 25778888753
Q ss_pred hhHhhhhHHHHHHHHHHhhhhhhcccce--E-EEEeCCCCHHHHHHHHHhhhhhcCCceeecCCCCCHHHHHHHHHHHh
Q 024560 187 FTDVATTFNGIIRALREKESKLKAARMH--I-FVRRGGPNYQTGLAKMRALGEELGIPLEVYGPEATMTGICKQAIDCI 262 (266)
Q Consensus 187 ~~~vA~~~~gii~al~~~~~~~~~~~~p--v-vvrl~G~~~~~~~~~L~~~~~~~Gip~~~~~~~~~~~eAv~~av~~~ 262 (266)
++..| .++++++++.+ .++| + |+-.++. ..+++.+. -++.+. ..++++..+.+++++
T Consensus 185 ~d~~a---~~~~~~l~~~g-----~~vp~di~v~g~d~~--~~~~~~~~-----~~~~ti----~~~~~~~g~~a~~~l 244 (269)
T cd06288 185 NDRMA---MGAYQALLERG-----LRIPQDVSVVGFDNQ--EIIAEHLR-----PPLTTV----ALPHYEMGRWAVELL 244 (269)
T ss_pred CcHHH---HHHHHHHHHcC-----CCCcccceEEeeCCc--hhhhhccC-----CCceeE----ecCHHHHHHHHHHHH
Confidence 56777 89999999874 2233 2 2344443 44544544 155442 346677777776654
No 65
>PF00701 DHDPS: Dihydrodipicolinate synthetase family; InterPro: IPR002220 Dihydropicolinate synthase (DHDPS) is the key enzyme in lysine biosynthesis via the diaminopimelate pathway of prokaryotes, some phycomycetes and higher plants. The enzyme catalyses the condensation of L-aspartate-beta- semialdehyde and pyruvate to dihydropicolinic acid via a ping-pong mechanism in which pyruvate binds to the enzyme by forming a Schiff-base with a lysine residue []. Three other proteins are structurally related to DHDPS and probably also act via a similar catalytic mechanism. These are Escherichia coli N-acetylneuraminate lyase (4.1.3.3 from EC) (gene nanA), which catalyzes the condensation of N-acetyl-D-mannosamine and pyruvate to form N-acetylneuraminate; Rhizobium meliloti (Sinorhizobium meliloti) protein mosA [], which is involved in the biosynthesis of the rhizopine 3-o-methyl-scyllo-inosamine; and E. coli hypothetical protein yjhH. The sequences of DHDPS from different sources are well-conserved. The structure takes the form of a homotetramer, in which 2 monomers are related by an approximate 2-fold symmetry []. Each monomer comprises 2 domains: an 8-fold alpha-/beta-barrel, and a C-terminal alpha-helical domain. The fold resembles that of N-acetylneuraminate lyase. The active site lysine is located in the barrel domain, and has access via 2 channels on the C-terminal side of the barrel.; GO: 0016829 lyase activity, 0008152 metabolic process; PDB: 3B4U_B 3S8H_A 3QZE_B 1XXX_F 3L21_F 3IRD_A 3A5F_B 3G0S_B 3DAQ_C 3UQN_A ....
Probab=57.94 E-value=1.5e+02 Score=26.93 Aligned_cols=110 Identities=11% Similarity=0.086 Sum_probs=70.0
Q ss_pred ceeeccCCCCHHHHHHHHHHHHhhhccCCCCCeEEEEecccccchhHhhhhHHHHHHHHHHhhhhhhcccceEEEEeCCC
Q 024560 143 NYAEYSGAPNEEEVLQYARVVIDCATADPDGRKRALLIGGGIANFTDVATTFNGIIRALREKESKLKAARMHIFVRRGGP 222 (266)
Q Consensus 143 N~lDlgG~a~~~~~~~al~~ll~~~~~d~~v~~vlvni~ggi~~~~~vA~~~~gii~al~~~~~~~~~~~~pvvvrl~G~ 222 (266)
-|++=.|..+.+.+.+-++.+++ .++++++++-.+|-..+-...+ -+-+++...+.. +.++||++-.++.
T Consensus 11 TPf~~dg~id~~~~~~~i~~l~~-----~Gv~gl~~~GstGE~~~Lt~~E-r~~l~~~~~~~~----~~~~~vi~gv~~~ 80 (289)
T PF00701_consen 11 TPFNADGSIDEDALKRLIDFLIE-----AGVDGLVVLGSTGEFYSLTDEE-RKELLEIVVEAA----AGRVPVIAGVGAN 80 (289)
T ss_dssp --BETTSSB-HHHHHHHHHHHHH-----TTSSEEEESSTTTTGGGS-HHH-HHHHHHHHHHHH----TTSSEEEEEEESS
T ss_pred CCCCCCcCcCHHHHHHHHHHHHH-----cCCCEEEECCCCcccccCCHHH-HHHHHHHHHHHc----cCceEEEecCcch
Confidence 35566788899999999999886 5899999884333222211111 134555544443 2469999999999
Q ss_pred CHHHHHHHHHhhhhhcCCcee-----ecCCCCCHHHHHHHHHHHhhh
Q 024560 223 NYQTGLAKMRALGEELGIPLE-----VYGPEATMTGICKQAIDCIMS 264 (266)
Q Consensus 223 ~~~~~~~~L~~~~~~~Gip~~-----~~~~~~~~~eAv~~av~~~~~ 264 (266)
+.+++.+..+.+ +++|.... .|. ..+.++.++.+-.++..
T Consensus 81 st~~~i~~a~~a-~~~Gad~v~v~~P~~~-~~s~~~l~~y~~~ia~~ 125 (289)
T PF00701_consen 81 STEEAIELARHA-QDAGADAVLVIPPYYF-KPSQEELIDYFRAIADA 125 (289)
T ss_dssp SHHHHHHHHHHH-HHTT-SEEEEEESTSS-SCCHHHHHHHHHHHHHH
T ss_pred hHHHHHHHHHHH-hhcCceEEEEeccccc-cchhhHHHHHHHHHHhh
Confidence 999999988853 45664321 121 35888888888877743
No 66
>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=57.49 E-value=1.3e+02 Score=26.03 Aligned_cols=122 Identities=10% Similarity=0.071 Sum_probs=63.4
Q ss_pred CCcEEEEecCchH------HHHHHHHHHhcCCCCCCCceeeccCCCCHHHHHHHHHHHHhhhccCCCCCeEEEEeccccc
Q 024560 112 KGRIWTMVAGGGA------SVIYADTVGDLGYASELGNYAEYSGAPNEEEVLQYARVVIDCATADPDGRKRALLIGGGIA 185 (266)
Q Consensus 112 ~G~Igii~NGaGl------am~t~D~l~~~g~gg~pAN~lDlgG~a~~~~~~~al~~ll~~~~~d~~v~~vlvni~ggi~ 185 (266)
.++|++++...+. .....+.+..+ |- +-..+...++.+.+.-+++++-+++ +.|+.++++..
T Consensus 125 ~~~i~~i~~~~~~~~~~~r~~gf~~~l~~~--~~-~~~~~~~~~~~~~~~~~~~~~~~l~---~~~~~~ai~~~------ 192 (277)
T cd06319 125 DGKVGMVAIPQKRKNGQKRTKGFKEAMKEA--GC-DLAGIRQQKDFSYQETFDYTNDLLT---ANPDIRAIWLQ------ 192 (277)
T ss_pred CCcEEEEeccCCCccHHHHHHHHHHHHHhc--CC-ceEeeccCCCCCHHHHHHHHHHHHH---hCCCCCEEEEC------
Confidence 3688888642221 12235666665 22 2222333455565655566555554 26777777643
Q ss_pred chhHhhhhHHHHHHHHHHhhhhhhcccceEEEEeCCCCHHHHHHHHHhhhhhcCCceeecCCCCCHHHHHHHHHHHh
Q 024560 186 NFTDVATTFNGIIRALREKESKLKAARMHIFVRRGGPNYQTGLAKMRALGEELGIPLEVYGPEATMTGICKQAIDCI 262 (266)
Q Consensus 186 ~~~~vA~~~~gii~al~~~~~~~~~~~~pvvvrl~G~~~~~~~~~L~~~~~~~Gip~~~~~~~~~~~eAv~~av~~~ 262 (266)
++.+| .|+++++++.+. ..++. |+-.++ ...+.+.+.+ --+...+ ..++.+..+.++++.
T Consensus 193 -~d~~a---~g~~~al~~~g~---~~di~-vvg~d~--~~~~~~~~~~----~~~~~tv---~~~~~~~g~~a~~~l 252 (277)
T cd06319 193 -GSDRY---QGALDAIATAGK---TGKVL-LICFDA--EPEFIELLKS----GALVGAG---MQQPFLMGERAVETV 252 (277)
T ss_pred -CCccc---hHHHHHHHHcCC---CCCEE-EEEcCC--CHHHHHHhhc----CceEEEE---ecCHHHHHHHHHHHH
Confidence 45667 899999998742 11223 333343 3556666652 1122111 235666666665543
No 67
>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=56.95 E-value=1.2e+02 Score=25.80 Aligned_cols=79 Identities=16% Similarity=0.146 Sum_probs=43.4
Q ss_pred CCcEEEEecCchHH------HHHHHHHHhcCCCCCCCceeeccCCCCHHHHHHHHHHHHhhhccCCCCCeEEEEeccccc
Q 024560 112 KGRIWTMVAGGGAS------VIYADTVGDLGYASELGNYAEYSGAPNEEEVLQYARVVIDCATADPDGRKRALLIGGGIA 185 (266)
Q Consensus 112 ~G~Igii~NGaGla------m~t~D~l~~~g~gg~pAN~lDlgG~a~~~~~~~al~~ll~~~~~d~~v~~vlvni~ggi~ 185 (266)
.++|+++.+-.+.. -...+.+..+ |.+.....-+.++.+.+..+++++-+|. ++|++++|+..
T Consensus 117 ~~~i~~l~~~~~~~~~~~r~~gf~~~l~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~l~---~~~~~~~i~~~------ 185 (268)
T cd06289 117 HRRIAFIGGLEDSSTRRERLAGYRAALAEA--GLPFDSELVVEGPPSRQGGAEAVAQLLD---LPPRPTAIVCF------ 185 (268)
T ss_pred CCCEEEecCCccccchHHHHHHHHHHHHHc--CCCCCchhEEecCcchhhHHHHHHHHHc---CCCCCCEEEEc------
Confidence 35788875433211 2223455555 3222111112334445556666666664 25788887743
Q ss_pred chhHhhhhHHHHHHHHHHhh
Q 024560 186 NFTDVATTFNGIIRALREKE 205 (266)
Q Consensus 186 ~~~~vA~~~~gii~al~~~~ 205 (266)
++..| .|+++++++.+
T Consensus 186 -~~~~a---~~~~~al~~~g 201 (268)
T cd06289 186 -NDLVA---FGAMSGLRRAG 201 (268)
T ss_pred -CcHHH---HHHHHHHHHcC
Confidence 45566 89999999874
No 68
>PRK03170 dihydrodipicolinate synthase; Provisional
Probab=56.25 E-value=1.6e+02 Score=26.80 Aligned_cols=109 Identities=12% Similarity=0.087 Sum_probs=68.4
Q ss_pred ceeeccCCCCHHHHHHHHHHHHhhhccCCCCCeEEEEecccccchhHhhhhHHHHHHHHHHhhhhhhcccceEEEEeCCC
Q 024560 143 NYAEYSGAPNEEEVLQYARVVIDCATADPDGRKRALLIGGGIANFTDVATTFNGIIRALREKESKLKAARMHIFVRRGGP 222 (266)
Q Consensus 143 N~lDlgG~a~~~~~~~al~~ll~~~~~d~~v~~vlvni~ggi~~~~~vA~~~~gii~al~~~~~~~~~~~~pvvvrl~G~ 222 (266)
-|+|=.|..+.+.+.+-++.+++ .++++++++-..|-...-...+ -.-+++...+.. ..++||++-.++.
T Consensus 11 TPf~~dg~iD~~~l~~~i~~l~~-----~Gv~gi~~~Gs~GE~~~ls~~E-r~~~~~~~~~~~----~~~~~vi~gv~~~ 80 (292)
T PRK03170 11 TPFKEDGSVDFAALRKLVDYLIA-----NGTDGLVVVGTTGESPTLTHEE-HEELIRAVVEAV----NGRVPVIAGTGSN 80 (292)
T ss_pred CCcCCCCCcCHHHHHHHHHHHHH-----cCCCEEEECCcCCccccCCHHH-HHHHHHHHHHHh----CCCCcEEeecCCc
Confidence 45566788899999999888885 7899999983332221111111 133445444432 2368999999998
Q ss_pred CHHHHHHHHHhhhhhcCCce------eecCCCCCHHHHHHHHHHHhhh
Q 024560 223 NYQTGLAKMRALGEELGIPL------EVYGPEATMTGICKQAIDCIMS 264 (266)
Q Consensus 223 ~~~~~~~~L~~~~~~~Gip~------~~~~~~~~~~eAv~~av~~~~~ 264 (266)
+.+++.+..+.+ +++|... ++| ..+.++.++.+-.++.+
T Consensus 81 ~~~~~i~~a~~a-~~~G~d~v~~~pP~~~--~~~~~~i~~~~~~ia~~ 125 (292)
T PRK03170 81 STAEAIELTKFA-EKAGADGALVVTPYYN--KPTQEGLYQHFKAIAEA 125 (292)
T ss_pred hHHHHHHHHHHH-HHcCCCEEEECCCcCC--CCCHHHHHHHHHHHHhc
Confidence 888888877743 4566431 222 22567777777776654
No 69
>TIGR00705 SppA_67K signal peptide peptidase SppA, 67K type. 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.
Probab=55.86 E-value=50 Score=33.74 Aligned_cols=55 Identities=15% Similarity=0.088 Sum_probs=36.0
Q ss_pred CHHHHHHHHHHHHhhhccCCCCCeEEEEe--ccc--ccchhHhhhhHHHHHHHHHHhhhhhhcccceEEEEeCC
Q 024560 152 NEEEVLQYARVVIDCATADPDGRKRALLI--GGG--IANFTDVATTFNGIIRALREKESKLKAARMHIFVRRGG 221 (266)
Q Consensus 152 ~~~~~~~al~~ll~~~~~d~~v~~vlvni--~gg--i~~~~~vA~~~~gii~al~~~~~~~~~~~~pvvvrl~G 221 (266)
+...+.++++-..+ ||+|++|++.+ ++| .+.. +-|.+++++++. ..+||++....
T Consensus 77 ~l~~i~~~i~~A~~----D~~IkgIvL~i~~~~g~~~~~~-------~ei~~ai~~fk~----sgKpVvA~~~~ 135 (584)
T TIGR00705 77 SLFDIVNAIRQAAD----DRRIEGLVFDLSNFSGWDSPHL-------VEIGSALSEFKD----SGKPVYAYGTN 135 (584)
T ss_pred CHHHHHHHHHHHhc----CCCceEEEEEccCCCCCCHHHH-------HHHHHHHHHHHh----cCCeEEEEEcc
Confidence 55677788777776 99999999996 333 2333 344555565542 46899986443
No 70
>cd07110 ALDH_F10_BADH Arabidopsis betaine aldehyde dehydrogenase 1 and 2, ALDH family 10A8 and 10A9-like. Present in this CD are the Arabidopsis betaine aldehyde dehydrogenase (BADH) 1 (chloroplast) and 2 (mitochondria), also known as, aldehyde dehydrogenase family 10 member A8 and aldehyde dehydrogenase family 10 member A9, respectively, and are putative dehydration- and salt-inducible BADHs (EC 1.2.1.8) that catalyze the oxidation of betaine aldehyde to the compatible solute glycine betaine.
Probab=55.82 E-value=1.4e+02 Score=28.98 Aligned_cols=23 Identities=4% Similarity=0.109 Sum_probs=14.8
Q ss_pred HHHHHHHHHHHHHHHhCCceeeE
Q 024560 19 GKIGDFIMGVFAVFQDLDFSFIE 41 (266)
Q Consensus 19 ~~~~~ii~~Ly~~f~~~D~~l~E 41 (266)
++-.+++.++.+++.++--.|++
T Consensus 41 ~~R~~~L~~~a~~l~~~~~~la~ 63 (456)
T cd07110 41 AERAKYLRAIAEGVRERREELAE 63 (456)
T ss_pred HHHHHHHHHHHHHHHHhHHHHHH
Confidence 34466777777777766555554
No 71
>PRK11579 putative oxidoreductase; Provisional
Probab=55.72 E-value=65 Score=30.00 Aligned_cols=56 Identities=18% Similarity=0.088 Sum_probs=35.5
Q ss_pred CCCCCeEEEEecccccchhHhhhhHHHHHHHHHHhhhhhhcccceEEE-EeCCCCHHHHHHHHHhhhhhcCCce
Q 024560 170 DPDGRKRALLIGGGIANFTDVATTFNGIIRALREKESKLKAARMHIFV-RRGGPNYQTGLAKMRALGEELGIPL 242 (266)
Q Consensus 170 d~~v~~vlvni~ggi~~~~~vA~~~~gii~al~~~~~~~~~~~~pvvv-rl~G~~~~~~~~~L~~~~~~~Gip~ 242 (266)
++++++|+|-.|.. .+++-++++++. .++|++ .=-..+.++++++++. +++.|+.+
T Consensus 62 ~~~vD~V~I~tp~~--------~H~~~~~~al~a--------GkhVl~EKPla~t~~ea~~l~~~-a~~~g~~l 118 (346)
T PRK11579 62 DPNIDLIVIPTPND--------THFPLAKAALEA--------GKHVVVDKPFTVTLSQARELDAL-AKSAGRVL 118 (346)
T ss_pred CCCCCEEEEcCCcH--------HHHHHHHHHHHC--------CCeEEEeCCCCCCHHHHHHHHHH-HHHhCCEE
Confidence 89999998765532 122545555542 466776 4455578888887763 44568765
No 72
>PF01408 GFO_IDH_MocA: Oxidoreductase family, NAD-binding Rossmann fold; InterPro: IPR000683 This group of enzymes utilise NADP or NAD, and is known as the GFO/IDH/MOCA family in UniProtKB/Swiss-Prot. GFO is a glucose--fructose oxidoreductase, which converts D-glucose and D-fructose into D-gluconolactone and D-glucitol in the sorbitol-gluconate pathway. MOCA is a rhizopine catabolism protein which may catalyse the NADH-dependent dehydrogenase reaction involved in rhizopine catabolism. Other proteins belonging to this family include Gal80, a negative regulator for the expression of lactose and galactose metabolic genes; and several hypothetical proteins from yeast, Escherichia coli and Bacillus subtilis. The oxidoreductase, N-terminal domain is almost always associated with the oxidoreductase, C-terminal domain (see IPR004104 from INTERPRO).; GO: 0016491 oxidoreductase activity; PDB: 1LC0_A 1LC3_A 1GCU_A 3IP3_E 3CEA_C 3EVN_A 3NTQ_A 3NTR_B 3NT5_A 3MZ0_A ....
Probab=55.18 E-value=91 Score=23.70 Aligned_cols=103 Identities=16% Similarity=0.098 Sum_probs=58.5
Q ss_pred cEEEEecCchHHHHHHHHHHhcCCCCCCCceeeccCCCCHHHHHHH-----------HHHHHhhhccCCCCCeEEEEecc
Q 024560 114 RIWTMVAGGGASVIYADTVGDLGYASELGNYAEYSGAPNEEEVLQY-----------ARVVIDCATADPDGRKRALLIGG 182 (266)
Q Consensus 114 ~Igii~NGaGlam~t~D~l~~~g~gg~pAN~lDlgG~a~~~~~~~a-----------l~~ll~~~~~d~~v~~vlvni~g 182 (266)
|||+|+-|.- +-..+..+....-+.+. .--=+.++++..++ ++-+++ ++++++|+|-.+.
T Consensus 2 ~v~iiG~G~~-g~~~~~~~~~~~~~~~v----~~v~d~~~~~~~~~~~~~~~~~~~~~~~ll~----~~~~D~V~I~tp~ 72 (120)
T PF01408_consen 2 RVGIIGAGSI-GRRHLRALLRSSPDFEV----VAVCDPDPERAEAFAEKYGIPVYTDLEELLA----DEDVDAVIIATPP 72 (120)
T ss_dssp EEEEESTSHH-HHHHHHHHHHTTTTEEE----EEEECSSHHHHHHHHHHTTSEEESSHHHHHH----HTTESEEEEESSG
T ss_pred EEEEECCcHH-HHHHHHHHHhcCCCcEE----EEEEeCCHHHHHHHHHHhcccchhHHHHHHH----hhcCCEEEEecCC
Confidence 5788877654 44455555554101111 11123445554443 333555 7899999888654
Q ss_pred cccchhHhhhhHHHHHHHHHHhhhhhhcccceEEE-EeCCCCHHHHHHHHHhhhhhcCCce
Q 024560 183 GIANFTDVATTFNGIIRALREKESKLKAARMHIFV-RRGGPNYQTGLAKMRALGEELGIPL 242 (266)
Q Consensus 183 gi~~~~~vA~~~~gii~al~~~~~~~~~~~~pvvv-rl~G~~~~~~~~~L~~~~~~~Gip~ 242 (266)
.. +++-+.++++ ..++|++ +=-..+.++++++++. +++.|..+
T Consensus 73 ~~--------h~~~~~~~l~--------~g~~v~~EKP~~~~~~~~~~l~~~-a~~~~~~~ 116 (120)
T PF01408_consen 73 SS--------HAEIAKKALE--------AGKHVLVEKPLALTLEEAEELVEA-AKEKGVKV 116 (120)
T ss_dssp GG--------HHHHHHHHHH--------TTSEEEEESSSSSSHHHHHHHHHH-HHHHTSCE
T ss_pred cc--------hHHHHHHHHH--------cCCEEEEEcCCcCCHHHHHHHHHH-HHHhCCEE
Confidence 21 1233344443 3468888 7777789999888874 34557654
No 73
>cd00950 DHDPS Dihydrodipicolinate synthase (DHDPS) is a key enzyme in lysine biosynthesis. It catalyzes the aldol condensation of L-aspartate-beta- semialdehyde and pyruvate to dihydropicolinic acid via a Schiff base formation between pyruvate and a lysine residue. The functional enzyme is a homotetramer consisting of a dimer of dimers. DHDPS is member of dihydrodipicolinate synthase family that comprises several pyruvate-dependent class I aldolases that use the same catalytic step to catalyze different reactions in different pathways.
Probab=54.89 E-value=1.6e+02 Score=26.52 Aligned_cols=109 Identities=11% Similarity=0.084 Sum_probs=68.3
Q ss_pred ceeeccCCCCHHHHHHHHHHHHhhhccCCCCCeEEEEecccccchhHhhhhHHHHHHHHHHhhhhhhcccceEEEEeCCC
Q 024560 143 NYAEYSGAPNEEEVLQYARVVIDCATADPDGRKRALLIGGGIANFTDVATTFNGIIRALREKESKLKAARMHIFVRRGGP 222 (266)
Q Consensus 143 N~lDlgG~a~~~~~~~al~~ll~~~~~d~~v~~vlvni~ggi~~~~~vA~~~~gii~al~~~~~~~~~~~~pvvvrl~G~ 222 (266)
-|++=.|..+.+.+.+-++.+++ .++++++++-..|-...-...+ -+-+++...+.. ..++||++-.+++
T Consensus 10 TPf~~dg~iD~~~~~~~i~~l~~-----~Gv~gl~v~GstGE~~~lt~~E-r~~l~~~~~~~~----~~~~~vi~gv~~~ 79 (284)
T cd00950 10 TPFKDDGSVDFDALERLIEFQIE-----NGTDGLVVCGTTGESPTLSDEE-HEAVIEAVVEAV----NGRVPVIAGTGSN 79 (284)
T ss_pred CCcCCCCCcCHHHHHHHHHHHHH-----cCCCEEEECCCCcchhhCCHHH-HHHHHHHHHHHh----CCCCcEEeccCCc
Confidence 34555678889999999888885 7899999983322222211111 244555555543 2468999999999
Q ss_pred CHHHHHHHHHhhhhhcCCce------eecCCCCCHHHHHHHHHHHhhh
Q 024560 223 NYQTGLAKMRALGEELGIPL------EVYGPEATMTGICKQAIDCIMS 264 (266)
Q Consensus 223 ~~~~~~~~L~~~~~~~Gip~------~~~~~~~~~~eAv~~av~~~~~ 264 (266)
+.+++.+..+.. +++|... ++|. .+.++.++.+-.++..
T Consensus 80 ~~~~~~~~a~~a-~~~G~d~v~~~~P~~~~--~~~~~l~~~~~~ia~~ 124 (284)
T cd00950 80 NTAEAIELTKRA-EKAGADAALVVTPYYNK--PSQEGLYAHFKAIAEA 124 (284)
T ss_pred cHHHHHHHHHHH-HHcCCCEEEEcccccCC--CCHHHHHHHHHHHHhc
Confidence 999988887753 4567541 2221 2556777776666553
No 74
>COG0054 RibH Riboflavin synthase beta-chain [Coenzyme metabolism]
Probab=54.59 E-value=1.3e+02 Score=25.46 Aligned_cols=126 Identities=17% Similarity=0.105 Sum_probs=76.9
Q ss_pred CCcEEEEecCc------hHHHHHHHHHHhcCCCCCCCc--eeeccCCCCHHHHHHHHHHHHhhhccCCCCCeEEEE---e
Q 024560 112 KGRIWTMVAGG------GASVIYADTVGDLGYASELGN--YAEYSGAPNEEEVLQYARVVIDCATADPDGRKRALL---I 180 (266)
Q Consensus 112 ~G~Igii~NGa------Glam~t~D~l~~~g~gg~pAN--~lDlgG~a~~~~~~~al~~ll~~~~~d~~v~~vlvn---i 180 (266)
+-||+|+..=- -+--.+.|.+..+ |++..| -+.+.|.-. +.-+.+-+++ ..+.++|+.. |
T Consensus 12 ~~riaIV~arfn~~I~d~ll~gA~~~l~~~--G~~~~~i~vv~VPGa~E---iPl~a~~La~----~~~yDAvv~lG~VI 82 (152)
T COG0054 12 GLRIAIVVARFNDDITDALLEGAVDALKRH--GADVDNIDVVRVPGAFE---IPLAAKKLAR----TGKYDAVVALGAVI 82 (152)
T ss_pred CceEEEEEeehhHHHHHHHHHHHHHHHHHc--CCCcccceEEEeCCcch---hHHHHHHHHh----cCCcceEEEEeeEE
Confidence 44666664321 1333467888887 677663 345555433 3344455555 5678988876 5
Q ss_pred cccccchhHhhhhHHHHHHHHHHhhhhhhcccceEEE-EeCCCCHHHHHHHHHhhhhhcCCceeecCCCCCHHHHHHHHH
Q 024560 181 GGGIANFTDVATTFNGIIRALREKESKLKAARMHIFV-RRGGPNYQTGLAKMRALGEELGIPLEVYGPEATMTGICKQAI 259 (266)
Q Consensus 181 ~ggi~~~~~vA~~~~gii~al~~~~~~~~~~~~pvvv-rl~G~~~~~~~~~L~~~~~~~Gip~~~~~~~~~~~eAv~~av 259 (266)
=|+...++-|+ ..+.+.+-+..- ...+||.. -|+-.+.+++.+.= |+.- -..=.+|+..|+
T Consensus 83 rG~T~Hfd~Va---~~~~~gl~~vsl---~~~~PV~~GVLt~~~~eqA~~ra-------g~~~-----gnkG~~Aa~aAl 144 (152)
T COG0054 83 RGETYHFDYVA---NEVARGLMDVSL---ETGVPVTFGVLTTDNIEQAIERA-------GTKA-----GNKGAEAAEAAL 144 (152)
T ss_pred eCCCccHHHHH---HHHHHHHHHHHH---hhCCCeEeeecCCCcHHHHHHHh-------Cccc-----cccHHHHHHHHH
Confidence 68888888888 666666555432 25799997 55554777765433 4432 124567888888
Q ss_pred HHhhh
Q 024560 260 DCIMS 264 (266)
Q Consensus 260 ~~~~~ 264 (266)
+++.-
T Consensus 145 em~~l 149 (152)
T COG0054 145 EMANL 149 (152)
T ss_pred HHHHH
Confidence 88753
No 75
>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=54.10 E-value=1e+02 Score=26.53 Aligned_cols=79 Identities=18% Similarity=0.107 Sum_probs=45.6
Q ss_pred CCcEEEEecCchHHH------HHHHHHHhcCCCCCCCceeeccCCCCHHHHHHHHHHHHhhhccCCCCCeEEEEeccccc
Q 024560 112 KGRIWTMVAGGGASV------IYADTVGDLGYASELGNYAEYSGAPNEEEVLQYARVVIDCATADPDGRKRALLIGGGIA 185 (266)
Q Consensus 112 ~G~Igii~NGaGlam------~t~D~l~~~g~gg~pAN~lDlgG~a~~~~~~~al~~ll~~~~~d~~v~~vlvni~ggi~ 185 (266)
.++|+++....+... ...+.+..+ |.+.-....+.++.+.+..+++++-+++ .+|++++|+..
T Consensus 116 ~~~i~~i~~~~~~~~~~~R~~gf~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~l~---~~~~~~ai~~~------ 184 (268)
T cd06270 116 HRKIACITGPLTKEDARLRLQGYRDALAEA--GIALDESLIIEGDFTEEGGYAAMQELLA---RGAPFTAVFCA------ 184 (268)
T ss_pred CceEEEEeCCcccccHHHHHHHHHHHHHHc--CCCCCcceEEECCCCHHHHHHHHHHHHh---CCCCCCEEEEc------
Confidence 356888754322211 123455555 3333222334455566666666666664 26778888743
Q ss_pred chhHhhhhHHHHHHHHHHhh
Q 024560 186 NFTDVATTFNGIIRALREKE 205 (266)
Q Consensus 186 ~~~~vA~~~~gii~al~~~~ 205 (266)
++.+| .|+++++++.+
T Consensus 185 -~d~~a---~g~~~~l~~~g 200 (268)
T cd06270 185 -NDEMA---AGAISALREHG 200 (268)
T ss_pred -CcHHH---HHHHHHHHHcC
Confidence 45677 99999999874
No 76
>COG5012 Predicted cobalamin binding protein [General function prediction only]
Probab=53.58 E-value=1.2e+02 Score=27.37 Aligned_cols=93 Identities=17% Similarity=0.245 Sum_probs=59.2
Q ss_pred CceeeccCCCCHHHHHHHHHHHHhhhccCCCCCeEEEEecccccchhHhhhhHHHHHHHHHHhhhhhhcccceEEEEeCC
Q 024560 142 GNYAEYSGAPNEEEVLQYARVVIDCATADPDGRKRALLIGGGIANFTDVATTFNGIIRALREKESKLKAARMHIFVRRGG 221 (266)
Q Consensus 142 AN~lDlgG~a~~~~~~~al~~ll~~~~~d~~v~~vlvni~ggi~~~~~vA~~~~gii~al~~~~~~~~~~~~pvvvrl~G 221 (266)
-+-+|+|-+.|.+.+.++.+=. .|. +| ..+.....+... ++-|++.|++.+ .+-|+.+-.||
T Consensus 133 fevidLG~dvP~e~fve~a~e~------k~d----~v-~~SalMTttm~~--~~~viE~L~eeG-----iRd~v~v~vGG 194 (227)
T COG5012 133 FEVIDLGRDVPVEEFVEKAKEL------KPD----LV-SMSALMTTTMIG--MKDVIELLKEEG-----IRDKVIVMVGG 194 (227)
T ss_pred cEEEecCCCCCHHHHHHHHHHc------CCc----EE-echHHHHHHHHH--HHHHHHHHHHcC-----CccCeEEeecC
Confidence 4779999999999988874432 232 22 233333333322 677888888764 67788888898
Q ss_pred CCHHHHHHHHHhhhhhcCCceeecCCCCCHHHHHHHHHHHh
Q 024560 222 PNYQTGLAKMRALGEELGIPLEVYGPEATMTGICKQAIDCI 262 (266)
Q Consensus 222 ~~~~~~~~~L~~~~~~~Gip~~~~~~~~~~~eAv~~av~~~ 262 (266)
....+.+ +++-|-..+ ..+..+||+.+-++.
T Consensus 195 Apvtq~~------a~~iGAD~~----~~dAs~Av~~ak~~l 225 (227)
T COG5012 195 APVTQDW------ADKIGADAY----AEDASDAVKKAKAIL 225 (227)
T ss_pred ccccHHH------HHHhCCCcc----CcCHHHHHHHHHHHh
Confidence 7433321 124466654 568899998887654
No 77
>TIGR01101 V_ATP_synt_F vacuolar ATP synthase F subunit. This model describes the vacuolar ATP synthase F subunit (14 kDa subunit) in eukaryotes. In some archaeal species this protein subunit is referred as G subunit
Probab=52.96 E-value=87 Score=25.24 Aligned_cols=60 Identities=10% Similarity=0.035 Sum_probs=43.7
Q ss_pred CceeeccCCCCHHHHHHHHHHHHhhhccCCCCCeEEEEecccccchhHhhhhHHHHHHHHHHhhhhhhcccceEEEEeCC
Q 024560 142 GNYAEYSGAPNEEEVLQYARVVIDCATADPDGRKRALLIGGGIANFTDVATTFNGIIRALREKESKLKAARMHIFVRRGG 221 (266)
Q Consensus 142 AN~lDlgG~a~~~~~~~al~~ll~~~~~d~~v~~vlvni~ggi~~~~~vA~~~~gii~al~~~~~~~~~~~~pvvvrl~G 221 (266)
-||+-+....+.+.+.++++-++. ++++-.|+|+ +.+| +-+-+.++++. ..+|.++=+.+
T Consensus 34 ~nf~~v~~~t~~eei~~~~~~~l~----~~digIIlIt--------e~~a---~~i~~~I~~~~-----~~~PaIieIP~ 93 (115)
T TIGR01101 34 PNFLVVDKNTTVSEIEDCFNRFLK----RDDIAIILIN--------QHIA---EMIRHAVDAHT-----RSIPAVLEIPS 93 (115)
T ss_pred cceeeecCCCCHHHHHHHHHHHhh----cCCeEEEEEc--------HHHH---HHhHHHHHhcC-----CcCCEEEEECC
Confidence 589988888889999999998887 8888766664 4455 44444454442 35898887776
No 78
>cd07013 S14_ClpP 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. 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. Additionally, they are 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 are required for effective levels of proteas
Probab=52.51 E-value=39 Score=28.33 Aligned_cols=59 Identities=10% Similarity=0.019 Sum_probs=34.9
Q ss_pred CHHHHHHHHHHHHhhhccCCCCCeEEEE--ecccccchhHhhhhHHHHHHHHHHhhhhhhcccceEEEEeCCCCHHHH
Q 024560 152 NEEEVLQYARVVIDCATADPDGRKRALL--IGGGIANFTDVATTFNGIIRALREKESKLKAARMHIFVRRGGPNYQTG 227 (266)
Q Consensus 152 ~~~~~~~al~~ll~~~~~d~~v~~vlvn--i~ggi~~~~~vA~~~~gii~al~~~~~~~~~~~~pvvvrl~G~~~~~~ 227 (266)
..+.+.+.+..+-+ +++.+.|.+. .|||-... + .+|.++++.. +.||++...|--.-.|
T Consensus 13 ~~~~~~~~L~~l~~----~~~~~~i~l~InSpGG~v~~---~---~~i~~~i~~~-------~~~v~~~~~g~aaS~~ 73 (162)
T cd07013 13 SANQFAAQLLFLGA----VNPEKDIYLYINSPGGDVFA---G---MAIYDTIKFI-------KADVVTIIDGLAASMG 73 (162)
T ss_pred HHHHHHHHHHHHhc----CCCCCCEEEEEECCCCcHHH---H---HHHHHHHHhc-------CCCceEEEEeehhhHH
Confidence 34555555555444 6666665555 58885422 2 6788888875 3567766666554444
No 79
>PRK10727 DNA-binding transcriptional regulator GalR; Provisional
Probab=52.33 E-value=91 Score=28.40 Aligned_cols=78 Identities=17% Similarity=0.121 Sum_probs=46.0
Q ss_pred CcEEEEecCchHH------HHHHHHHHhcCCCCCCCceeeccCCCCHHHHHHHHHHHHhhhccCCCCCeEEEEecccccc
Q 024560 113 GRIWTMVAGGGAS------VIYADTVGDLGYASELGNYAEYSGAPNEEEVLQYARVVIDCATADPDGRKRALLIGGGIAN 186 (266)
Q Consensus 113 G~Igii~NGaGla------m~t~D~l~~~g~gg~pAN~lDlgG~a~~~~~~~al~~ll~~~~~d~~v~~vlvni~ggi~~ 186 (266)
++|++++...+.. --..+.+..+ |..+...+-.-++.+.+.-+++++-+|+ ..+.+++||. .
T Consensus 177 ~~I~~i~~~~~~~~~~~R~~Gf~~al~~~--gi~~~~~~~~~~~~~~~~~~~~~~~~l~---~~~~~~ai~~-------~ 244 (343)
T PRK10727 177 TRIGYLCSNHSISDAEDRLQGYYDALAES--GIPANDRLVTFGEPDESGGEQAMTELLG---RGRNFTAVAC-------Y 244 (343)
T ss_pred ccEEEEeCCccccchHHHHHHHHHHHHHC--CCCCChhhEEeCCCChhHHHHHHHHHHh---CCCCCCEEEE-------c
Confidence 6799885433211 1234666666 4433221222355555555566666654 2456777763 3
Q ss_pred hhHhhhhHHHHHHHHHHhh
Q 024560 187 FTDVATTFNGIIRALREKE 205 (266)
Q Consensus 187 ~~~vA~~~~gii~al~~~~ 205 (266)
+|.+| -|+++++++.+
T Consensus 245 nD~~A---~g~~~al~~~G 260 (343)
T PRK10727 245 NDSMA---AGAMGVLNDNG 260 (343)
T ss_pred CcHHH---HHHHHHHHHcC
Confidence 77888 99999999874
No 80
>cd07143 ALDH_AldA_AN0554 Aspergillus nidulans aldehyde dehydrogenase, AldA (AN0554)-like. NAD(P)+-dependent aldehyde dehydrogenase (AldA) of Aspergillus nidulans (locus AN0554), and other similar sequences, are present in this CD.
Probab=52.19 E-value=1.8e+02 Score=28.63 Aligned_cols=20 Identities=5% Similarity=-0.034 Sum_probs=9.6
Q ss_pred HHHHHHHHHHHHhCCceeeE
Q 024560 22 GDFIMGVFAVFQDLDFSFIE 41 (266)
Q Consensus 22 ~~ii~~Ly~~f~~~D~~l~E 41 (266)
.+++.++.++..++--.|++
T Consensus 71 ~~~L~~~a~~l~~~~~~l~~ 90 (481)
T cd07143 71 GRCLSKLADLMERNLDYLAS 90 (481)
T ss_pred HHHHHHHHHHHHHhHHHHHH
Confidence 34555555555554433333
No 81
>TIGR00674 dapA dihydrodipicolinate synthase. Dihydrodipicolinate synthase is a homotetrameric enzyme of lysine biosynthesis. E. coli has several paralogs closely related to dihydrodipicoline synthase (DapA), as well as the more distant N-acetylneuraminate lyase. In Pyrococcus horikoshii, the bidirectional best hit with E. coli is to an uncharacterized paralog of DapA, not DapA itself, and it is omitted from the seed. The putative members from the Chlamydias (pathogens with a parasitic metabolism) are easily the most divergent members of the multiple alignment.
Probab=52.18 E-value=1.8e+02 Score=26.34 Aligned_cols=109 Identities=9% Similarity=0.075 Sum_probs=67.8
Q ss_pred ceeeccCCCCHHHHHHHHHHHHhhhccCCCCCeEEEEecccccchhHhhhhHHHHHHHHHHhhhhhhcccceEEEEeCCC
Q 024560 143 NYAEYSGAPNEEEVLQYARVVIDCATADPDGRKRALLIGGGIANFTDVATTFNGIIRALREKESKLKAARMHIFVRRGGP 222 (266)
Q Consensus 143 N~lDlgG~a~~~~~~~al~~ll~~~~~d~~v~~vlvni~ggi~~~~~vA~~~~gii~al~~~~~~~~~~~~pvvvrl~G~ 222 (266)
-|+|=-|..+.+.+.+-++.+++ .++++++++-..|-...-...+ -+.+++...+.. ..++||++-.+.+
T Consensus 8 TPf~~~g~iD~~~~~~~i~~l~~-----~Gv~Gi~~~GstGE~~~Ls~~E-r~~~~~~~~~~~----~~~~~vi~gv~~~ 77 (285)
T TIGR00674 8 TPFKEDGSVDFAALEKLIDFQIE-----NGTDAIVVVGTTGESPTLSHEE-HKKVIEFVVDLV----NGRVPVIAGTGSN 77 (285)
T ss_pred CCcCCCCCcCHHHHHHHHHHHHH-----cCCCEEEECccCcccccCCHHH-HHHHHHHHHHHh----CCCCeEEEeCCCc
Confidence 34555688899999999888875 7999999983333222222221 134444444432 2468999999988
Q ss_pred CHHHHHHHHHhhhhhcCCc------eeecCCCCCHHHHHHHHHHHhhh
Q 024560 223 NYQTGLAKMRALGEELGIP------LEVYGPEATMTGICKQAIDCIMS 264 (266)
Q Consensus 223 ~~~~~~~~L~~~~~~~Gip------~~~~~~~~~~~eAv~~av~~~~~ 264 (266)
+.+++.+..+.. ++.|.. -++| ..+.++.++.+-.++.+
T Consensus 78 s~~~~i~~a~~a-~~~Gad~v~v~pP~y~--~~~~~~i~~~~~~i~~~ 122 (285)
T TIGR00674 78 ATEEAISLTKFA-EDVGADGFLVVTPYYN--KPTQEGLYQHFKAIAEE 122 (285)
T ss_pred cHHHHHHHHHHH-HHcCCCEEEEcCCcCC--CCCHHHHHHHHHHHHhc
Confidence 888888777743 345632 2222 22567777777776654
No 82
>PRK01368 murD UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional
Probab=51.50 E-value=1.3e+02 Score=29.62 Aligned_cols=88 Identities=13% Similarity=0.119 Sum_probs=50.2
Q ss_pred eeeccCCCCHHHHHHHHHHHHhhhccCCCCCeEEEEecccccchhHhhhhHHHHHHHHHHhhhhhhcccceEEEEeCCCC
Q 024560 144 YAEYSGAPNEEEVLQYARVVIDCATADPDGRKRALLIGGGIANFTDVATTFNGIIRALREKESKLKAARMHIFVRRGGPN 223 (266)
Q Consensus 144 ~lDlgG~a~~~~~~~al~~ll~~~~~d~~v~~vlvni~ggi~~~~~vA~~~~gii~al~~~~~~~~~~~~pvvvrl~G~~ 223 (266)
|+|=++..+++.+..+++.+ ++ ++.|+||....... +-++..++. + ..+.+-|..
T Consensus 322 ~i~DS~atN~~a~~~al~~~------~~-----i~lI~Gg~dk~~~~----~~L~~~~~~---------v-~~v~~~g~~ 376 (454)
T PRK01368 322 FYNDSKATNAISAVQSIKAL------DN-----IYWLAGGIPKEGGI----EEIKPYFSK---------I-KKAYFYGQA 376 (454)
T ss_pred EEECCCCCCHHHHHHHHHhc------CC-----eEEEecccCCCCCH----HHHHHHHHh---------h-cEEEEECcC
Confidence 55445667788777775554 22 34567887433222 333333321 1 223445666
Q ss_pred HHHHHHHHHhhhhhcCCceeecCCCCCHHHHHHHHHHHhhh
Q 024560 224 YQTGLAKMRALGEELGIPLEVYGPEATMTGICKQAIDCIMS 264 (266)
Q Consensus 224 ~~~~~~~L~~~~~~~Gip~~~~~~~~~~~eAv~~av~~~~~ 264 (266)
.++-.+.+. .. .|+.. +.+|++|++.+.++++.
T Consensus 377 ~~~l~~~~~----~~-~~~~~---~~~l~~Av~~a~~~a~~ 409 (454)
T PRK01368 377 KEIFANTAK----NI-VDFVI---CDNLEQAFDLAYKDAVG 409 (454)
T ss_pred HHHHHHHhh----cC-CCEEE---cCCHHHHHHHHHHHhcC
Confidence 666666665 21 45554 45899999999887754
No 83
>PLN02766 coniferyl-aldehyde dehydrogenase
Probab=51.47 E-value=1.9e+02 Score=28.82 Aligned_cols=21 Identities=10% Similarity=0.134 Sum_probs=11.9
Q ss_pred HHHHHHHHHHHHHHhCCceee
Q 024560 20 KIGDFIMGVFAVFQDLDFSFI 40 (266)
Q Consensus 20 ~~~~ii~~Ly~~f~~~D~~l~ 40 (266)
+=.+++.++.+++.++--.|.
T Consensus 83 ~R~~~L~~~a~~l~~~~~ela 103 (501)
T PLN02766 83 ERGRIMMKFADLIEEHIEELA 103 (501)
T ss_pred HHHHHHHHHHHHHHHhHHHHH
Confidence 445566666666666544333
No 84
>PRK03620 5-dehydro-4-deoxyglucarate dehydratase; Provisional
Probab=50.90 E-value=2e+02 Score=26.46 Aligned_cols=108 Identities=17% Similarity=0.129 Sum_probs=65.5
Q ss_pred ceeeccCCCCHHHHHHHHHHHHhhhccCCCCCeEEEEecccccchhHhhhhHHHHHHHHHHhhhhhhcccceEEEEeCCC
Q 024560 143 NYAEYSGAPNEEEVLQYARVVIDCATADPDGRKRALLIGGGIANFTDVATTFNGIIRALREKESKLKAARMHIFVRRGGP 222 (266)
Q Consensus 143 N~lDlgG~a~~~~~~~al~~ll~~~~~d~~v~~vlvni~ggi~~~~~vA~~~~gii~al~~~~~~~~~~~~pvvvrl~G~ 222 (266)
-|+|=-|..+.+.+.+-++.+++ .++++++++=..|-...-...+ -+-+++...+.. ..++||++-.++
T Consensus 17 TPf~~dg~iD~~~l~~li~~l~~-----~Gv~Gi~~~GstGE~~~Lt~eE-r~~~~~~~~~~~----~~~~pvi~gv~~- 85 (303)
T PRK03620 17 TPFDADGSFDEAAYREHLEWLAP-----YGAAALFAAGGTGEFFSLTPDE-YSQVVRAAVETT----AGRVPVIAGAGG- 85 (303)
T ss_pred CCCCCCCCcCHHHHHHHHHHHHH-----cCCCEEEECcCCcCcccCCHHH-HHHHHHHHHHHh----CCCCcEEEecCC-
Confidence 45566688899999999888885 6899999983222211111111 133444443332 246899987775
Q ss_pred CHHHHHHHHHhhhhhcCCc------eeecCCCCCHHHHHHHHHHHhhh
Q 024560 223 NYQTGLAKMRALGEELGIP------LEVYGPEATMTGICKQAIDCIMS 264 (266)
Q Consensus 223 ~~~~~~~~L~~~~~~~Gip------~~~~~~~~~~~eAv~~av~~~~~ 264 (266)
+..++.+..+.+ +++|.. -+++ ..+.++.++.+..++.+
T Consensus 86 ~t~~~i~~~~~a-~~~Gadav~~~pP~y~--~~~~~~i~~~f~~va~~ 130 (303)
T PRK03620 86 GTAQAIEYAQAA-ERAGADGILLLPPYLT--EAPQEGLAAHVEAVCKS 130 (303)
T ss_pred CHHHHHHHHHHH-HHhCCCEEEECCCCCC--CCCHHHHHHHHHHHHHh
Confidence 788888877743 445642 1222 23667777777777654
No 85
>PRK10949 protease 4; Provisional
Probab=50.83 E-value=48 Score=34.22 Aligned_cols=51 Identities=18% Similarity=0.192 Sum_probs=32.8
Q ss_pred HHHHHHHHHHHHhhhccCCCCCeEEEEe--cccc--cchhHhhhhHHHHHHHHHHhhhhhhcccceEEEE
Q 024560 153 EEEVLQYARVVIDCATADPDGRKRALLI--GGGI--ANFTDVATTFNGIIRALREKESKLKAARMHIFVR 218 (266)
Q Consensus 153 ~~~~~~al~~ll~~~~~d~~v~~vlvni--~ggi--~~~~~vA~~~~gii~al~~~~~~~~~~~~pvvvr 218 (266)
-..+.++++-..+ ||+|++|++.+ +||. +..+++. +++++++. ..+||+++
T Consensus 97 l~div~~i~~Aa~----D~rIkgivL~i~s~gG~~~a~~~eI~-------~ai~~fk~----sGKpVvA~ 151 (618)
T PRK10949 97 LFDIVNTIRQAKD----DRNITGIVLDLKNFAGADQPSMQYIG-------KALREFRD----SGKPVYAV 151 (618)
T ss_pred HHHHHHHHHHHhc----CCCceEEEEEeCCCCCccHHHHHHHH-------HHHHHHHH----hCCeEEEE
Confidence 3457777666666 99999999996 5442 3344444 45555532 35888885
No 86
>cd07088 ALDH_LactADH-AldA Escherichia coli lactaldehyde dehydrogenase AldA-like. Lactaldehyde dehydrogenase from Escherichia coli (AldA, LactADH, EC=1.2.1.22), an NAD(+)-dependent enzyme involved in the metabolism of L-fucose and L-rhamnose, and other similar sequences are present in this CD.
Probab=50.06 E-value=2e+02 Score=28.02 Aligned_cols=19 Identities=26% Similarity=0.326 Sum_probs=10.6
Q ss_pred ceeecCCCCCHHHHHHHHHH
Q 024560 241 PLEVYGPEATMTGICKQAID 260 (266)
Q Consensus 241 p~~~~~~~~~~~eAv~~av~ 260 (266)
|+.++. ..+++.|++..+.
T Consensus 248 ~~iV~~-dadl~~aa~~iv~ 266 (468)
T cd07088 248 PAIVMK-DADLDLAVKAIVD 266 (468)
T ss_pred eEEECC-CCCHHHHHHHHHH
Confidence 334444 4566666666654
No 87
>TIGR03216 OH_muco_semi_DH 2-hydroxymuconic semialdehyde dehydrogenase. Members of this protein family are 2-hydroxymuconic semialdehyde dehydrogenase. Many aromatic compounds are catabolized by way of the catechol, via the meta-cleavage pathway, to pyruvate and acetyl-CoA. This enzyme performs the second of seven steps in that pathway for catechol degradation.
Probab=49.57 E-value=2e+02 Score=28.32 Aligned_cols=24 Identities=13% Similarity=0.137 Sum_probs=15.4
Q ss_pred HHHHHHHHHHHHHHhCCceeeEee
Q 024560 20 KIGDFIMGVFAVFQDLDFSFIEMN 43 (266)
Q Consensus 20 ~~~~ii~~Ly~~f~~~D~~l~EIN 43 (266)
+=.+++.++.+++.+.--.|++++
T Consensus 60 ~R~~~L~~~a~~l~~~~~ela~~~ 83 (481)
T TIGR03216 60 ERADLLYAVADEIERRFDDFLAAE 83 (481)
T ss_pred HHHHHHHHHHHHHHHhHHHHHHHH
Confidence 445677777777777765555543
No 88
>cd07015 Clp_protease_NfeD Nodulation formation efficiency D (NfeD) is a membrane-bound ClpP-class protease. Nodulation formation efficiency D (NfeD; stomatin operon partner protein, STOPP; DUF107) is a member of membrane-anchored ClpP-class proteases. Currently, more than 300 NfeD homologs have been identified - all of which are bacterial or archaeal in origin. Majority of these genomes have been shown to possess operons containing a homologous NfeD/stomatin gene pair, causing NfeD to be previously named STOPP (stomatin operon partner protein). NfeD homologs can be divided into two groups: long and short forms. Long-form homologs have a putative ClpP-class serine protease domain while the short form homologs do not. Downstream from the ClpP-class domain is the so-called NfeD or DUF107 domain. N-terminal region of the NfeD homolog PH1510 (1510-N or PH1510-N) from Pyrococcus horikoshii has been shown to possess serine protease activity and has a Ser-Lys catalytic dyad, preferentially cle
Probab=49.56 E-value=61 Score=27.83 Aligned_cols=44 Identities=14% Similarity=0.258 Sum_probs=27.7
Q ss_pred CCCeEE--EEecccccchhHhhhhHHHHHHHHHHhhhhhhcccceEEEEeC---CCCHHHHH
Q 024560 172 DGRKRA--LLIGGGIANFTDVATTFNGIIRALREKESKLKAARMHIFVRRG---GPNYQTGL 228 (266)
Q Consensus 172 ~v~~vl--vni~ggi~~~~~vA~~~~gii~al~~~~~~~~~~~~pvvvrl~---G~~~~~~~ 228 (266)
+.+.|+ ||.|||...+. ..|.++++.. ++||+++.. |--.-.|-
T Consensus 29 ~~~~i~l~inSPGG~v~~~------~~I~~~i~~~-------~~pvv~~v~p~g~~AaSag~ 77 (172)
T cd07015 29 NAEAIIIELDTPGGRADAA------GNIVQRIQQS-------KIPVIIYVYPPGASAASAGT 77 (172)
T ss_pred CCCeEEEEEECCCCCHHHH------HHHHHHHHhc-------CcCEEEEEecCCCeehhHHH
Confidence 456554 44699976543 6777777653 588887775 54444443
No 89
>cd07113 ALDH_PADH_NahF Escherichia coli NAD+-dependent phenylacetaldehyde dehydrogenase PadA-like. NAD+-dependent, homodimeric, phenylacetaldehyde dehydrogenase (PADH, EC=1.2.1.39) PadA of Escherichia coli involved in the catabolism of 2-phenylethylamine, and other related sequences, are present in this CD. Also included is the Pseudomonas fluorescens ST StyD PADH involved in styrene catabolism, the Sphingomonas sp. LB126 FldD protein involved in fluorene degradation, and the Novosphingobium aromaticivorans NahF salicylaldehyde dehydrogenase involved in the NAD+-dependent conversion of salicylaldehyde to salicylate.
Probab=49.00 E-value=2e+02 Score=28.19 Aligned_cols=32 Identities=13% Similarity=0.290 Sum_probs=19.3
Q ss_pred HHHHHHHHHHHHHHHhCCceeeEeecceecCCce
Q 024560 19 GKIGDFIMGVFAVFQDLDFSFIEMNPFTLVNGEP 52 (266)
Q Consensus 19 ~~~~~ii~~Ly~~f~~~D~~l~EINPLvv~~g~~ 52 (266)
++-.+++.++.+++.++--.|+++ +..+.|+.
T Consensus 60 ~~R~~~L~~~a~~l~~~~~ela~~--~~~e~Gk~ 91 (477)
T cd07113 60 AERGRILLRLADLIEQHGEELAQL--ETLCSGKS 91 (477)
T ss_pred HHHHHHHHHHHHHHHHCHHHHHHH--HHHhcCCC
Confidence 344667777777777776666654 22255654
No 90
>cd07131 ALDH_AldH-CAJ73105 Uncharacterized Candidatus kuenenia aldehyde dehydrogenase AldH (CAJ73105)-like. Uncharacterized aldehyde dehydrogenase of Candidatus kuenenia AldH (locus CAJ73105) and similar sequences with similarity to alpha-aminoadipic semialdehyde dehydrogenase (AASADH, human ALDH7A1, EC=1.2.1.31), Arabidopsis ALDH7B4, and Streptomyces clavuligerus delta-1-piperideine-6-carboxylate dehydrogenase (P6CDH) are included in this CD.
Probab=48.84 E-value=1.9e+02 Score=28.25 Aligned_cols=20 Identities=0% Similarity=0.193 Sum_probs=11.6
Q ss_pred HHHHHHHHHHHHhCCceeeE
Q 024560 22 GDFIMGVFAVFQDLDFSFIE 41 (266)
Q Consensus 22 ~~ii~~Ly~~f~~~D~~l~E 41 (266)
.+++.++.+++.+.--.+++
T Consensus 62 ~~~l~~~a~~l~~~~~ela~ 81 (478)
T cd07131 62 AEYLFRAAELLKKRKEELAR 81 (478)
T ss_pred HHHHHHHHHHHHHHHHHHHH
Confidence 45566666666655544554
No 91
>TIGR00877 purD phosphoribosylamine--glycine ligase. This enzyme appears as a monofunctional protein in prokaryotes but as part of a larger, multidomain protein in eukaryotes.
Probab=48.66 E-value=1.4e+02 Score=28.48 Aligned_cols=21 Identities=14% Similarity=0.276 Sum_probs=13.9
Q ss_pred cEEEEecCchHHHHHHHHHHhc
Q 024560 114 RIWTMVAGGGASVIYADTVGDL 135 (266)
Q Consensus 114 ~Igii~NGaGlam~t~D~l~~~ 135 (266)
+|+|+++|+..-|+ ...+...
T Consensus 2 kiliiG~G~~~~~l-~~~~~~~ 22 (423)
T TIGR00877 2 KVLVIGNGGREHAL-AWKLAQS 22 (423)
T ss_pred EEEEECCChHHHHH-HHHHHhC
Confidence 58899888875554 4555554
No 92
>cd07093 ALDH_F8_HMSADH Human aldehyde dehydrogenase family 8 member A1-like. In humans, the aldehyde dehydrogenase family 8 member A1 (ALDH8A1) protein functions to convert 9-cis-retinal to 9-cis-retinoic acid and has a preference for NAD+. Also included in this CD is the 2-hydroxymuconic semialdehyde dehydrogenase (HMSADH) which catalyzes the conversion of 2-hydroxymuconic semialdehyde to 4-oxalocrotonate, a step in the meta cleavage pathway of aromatic hydrocarbons in bacteria. Such HMSADHs seen here are: XylG of the TOL plasmid pWW0 of Pseudomonas putida, TomC of Burkholderia cepacia G4, and AphC of Comamonas testosterone.
Probab=47.27 E-value=2.1e+02 Score=27.69 Aligned_cols=21 Identities=5% Similarity=-0.001 Sum_probs=13.1
Q ss_pred HHHHHHHHHHHHHHhCCceee
Q 024560 20 KIGDFIMGVFAVFQDLDFSFI 40 (266)
Q Consensus 20 ~~~~ii~~Ly~~f~~~D~~l~ 40 (266)
+-.+++.++.+++.+.--.|+
T Consensus 42 ~R~~~L~~~a~~l~~~~~ela 62 (455)
T cd07093 42 ERARILHKVADLIEARADELA 62 (455)
T ss_pred HHHHHHHHHHHHHHHHHHHHH
Confidence 445667777777776654444
No 93
>cd07097 ALDH_KGSADH-YcbD Bacillus subtilis NADP+-dependent alpha-ketoglutaric semialdehyde dehydrogenase ycbD-like. Kinetic studies of the Bacillus subtilis ALDH-like ycbD protein, which is involved in d-glucarate/d-galactarate utilization, reveal that it is a NADP+-dependent, alpha-ketoglutaric semialdehyde dehydrogenase (KGSADH). KGSADHs (EC 1.2.1.26) catalyze the NAD(P)+-dependent conversion of KGSA to alpha-ketoglutarate. Interestingly, the NADP+-dependent, tetrameric, 2,5-dioxopentanoate dehydrogenase (EC=1.2.1.26), an enzyme involved in the catabolic pathway for D-arabinose in Sulfolobus solfataricus, also clusters in this group. This CD shows a distant phylogenetic relationship to the Azospirillum brasilense KGSADH-II (-III) group.
Probab=46.91 E-value=2.3e+02 Score=27.80 Aligned_cols=16 Identities=6% Similarity=-0.062 Sum_probs=8.9
Q ss_pred HHHHHHHHHHHHHhCC
Q 024560 21 IGDFIMGVFAVFQDLD 36 (266)
Q Consensus 21 ~~~ii~~Ly~~f~~~D 36 (266)
=.+++.++.+++.++-
T Consensus 61 R~~~L~~~a~~l~~~~ 76 (473)
T cd07097 61 RADILDKAGDELEARK 76 (473)
T ss_pred HHHHHHHHHHHHHHhH
Confidence 3455666666665543
No 94
>COG2185 Sbm Methylmalonyl-CoA mutase, C-terminal domain/subunit (cobalamin-binding) [Lipid metabolism]
Probab=46.73 E-value=40 Score=28.35 Aligned_cols=46 Identities=15% Similarity=0.170 Sum_probs=32.7
Q ss_pred EEE-EeCCCCHHHHHHHHHhhhhhcCCceeecCCCCCHHHHHHHHHH
Q 024560 215 IFV-RRGGPNYQTGLAKMRALGEELGIPLEVYGPEATMTGICKQAID 260 (266)
Q Consensus 215 vvv-rl~G~~~~~~~~~L~~~~~~~Gip~~~~~~~~~~~eAv~~av~ 260 (266)
|++ .+|=..=+.+-+.+.....+.|+.+..-+.+.|++|+|++|++
T Consensus 15 vlvak~GlDgHd~gakvia~~l~d~GfeVi~~g~~~tp~e~v~aA~~ 61 (143)
T COG2185 15 VLVAKLGLDGHDRGAKVIARALADAGFEVINLGLFQTPEEAVRAAVE 61 (143)
T ss_pred EEEeccCccccccchHHHHHHHHhCCceEEecCCcCCHHHHHHHHHh
Confidence 443 6664444455555555555789998888889999999999976
No 95
>cd07144 ALDH_ALD2-YMR170C Saccharomyces cerevisiae aldehyde dehydrogenase 2 (YMR170c)-like. NAD(P)+-dependent Saccharomyces cerevisiae aldehyde dehydrogenase 2 (YMR170c, ALD5, EC=1.2.1.5) and other similar sequences, are present in this CD.
Probab=46.69 E-value=2.2e+02 Score=28.03 Aligned_cols=22 Identities=5% Similarity=0.054 Sum_probs=13.6
Q ss_pred HHHHHHHHHHHHHHhCCceeeE
Q 024560 20 KIGDFIMGVFAVFQDLDFSFIE 41 (266)
Q Consensus 20 ~~~~ii~~Ly~~f~~~D~~l~E 41 (266)
+=.+++.++.+++.+.--.+++
T Consensus 69 ~R~~iL~~~a~~l~~~~~~l~~ 90 (484)
T cd07144 69 ERGELLDKLADLVEKNRDLLAA 90 (484)
T ss_pred HHHHHHHHHHHHHHHhHHHHHH
Confidence 3456677777777766544544
No 96
>PLN02467 betaine aldehyde dehydrogenase
Probab=46.68 E-value=2.4e+02 Score=28.12 Aligned_cols=20 Identities=5% Similarity=0.125 Sum_probs=12.3
Q ss_pred HHHHHHHHHHHHHhCCceee
Q 024560 21 IGDFIMGVFAVFQDLDFSFI 40 (266)
Q Consensus 21 ~~~ii~~Ly~~f~~~D~~l~ 40 (266)
=.+++.++.+++.++--.|+
T Consensus 74 R~~~L~~~a~~l~~~~~ela 93 (503)
T PLN02467 74 RAKYLRAIAAKITERKSELA 93 (503)
T ss_pred HHHHHHHHHHHHHHhHHHHH
Confidence 35567777777776654444
No 97
>TIGR01804 BADH glycine betaine aldehyde dehydrogenase. Betaine aldehyde dehydrogenase is a member of the aldehyde dehydrogenase family (pfam00171).
Probab=46.46 E-value=2.4e+02 Score=27.48 Aligned_cols=22 Identities=5% Similarity=0.194 Sum_probs=12.1
Q ss_pred HHHHHHHHHHHHHHhCCceeeE
Q 024560 20 KIGDFIMGVFAVFQDLDFSFIE 41 (266)
Q Consensus 20 ~~~~ii~~Ly~~f~~~D~~l~E 41 (266)
+=.+++.++.+++.++--.|++
T Consensus 58 ~R~~~L~~~a~~l~~~~~~la~ 79 (467)
T TIGR01804 58 ERGRILRRIAELIRERNEELAK 79 (467)
T ss_pred HHHHHHHHHHHHHHHhHHHHHH
Confidence 3355666666666655444443
No 98
>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=46.13 E-value=1.9e+02 Score=24.71 Aligned_cols=78 Identities=13% Similarity=0.141 Sum_probs=43.3
Q ss_pred CCcEEEEecCch-HH------HHHHHHHHhcCCCCCCCceeeccCCCCHHHHHHHHHHHHhhhccCCCCCeEEEEecccc
Q 024560 112 KGRIWTMVAGGG-AS------VIYADTVGDLGYASELGNYAEYSGAPNEEEVLQYARVVIDCATADPDGRKRALLIGGGI 184 (266)
Q Consensus 112 ~G~Igii~NGaG-la------m~t~D~l~~~g~gg~pAN~lDlgG~a~~~~~~~al~~ll~~~~~d~~v~~vlvni~ggi 184 (266)
.++|++++...+ .. --..+.+..+ |.+..-..-+.++.+.+..+++++-+++ +.| ++++++.
T Consensus 116 ~~~i~~l~~~~~~~~~~~~r~~gf~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~l~---~~~-~~ai~~~----- 184 (268)
T cd06298 116 HKKIAFISGPLEDSINGDERLAGYKEALSEA--NIEFDESLIFEGDYTYESGYELAEELLE---DGK-PTAAFVT----- 184 (268)
T ss_pred CceEEEEeCCcccccchhHHHHHHHHHHHHc--CCCCCHHHeEeCCCChhHHHHHHHHHhc---CCC-CCEEEEc-----
Confidence 367888864333 11 1224566665 3432211112233345555666666654 244 8888853
Q ss_pred cchhHhhhhHHHHHHHHHHhh
Q 024560 185 ANFTDVATTFNGIIRALREKE 205 (266)
Q Consensus 185 ~~~~~vA~~~~gii~al~~~~ 205 (266)
++..| .++++++++.+
T Consensus 185 --~d~~a---~~~~~~l~~~g 200 (268)
T cd06298 185 --DDELA---IGILNAAQDAG 200 (268)
T ss_pred --CcHHH---HHHHHHHHHcC
Confidence 55667 89999999874
No 99
>cd07109 ALDH_AAS00426 Uncharacterized Saccharopolyspora spinosa aldehyde dehydrogenase (AAS00426)-like. Uncharacterized aldehyde dehydrogenase of Saccharopolyspora spinosa (AAS00426) and other similar sequences, are present in this CD.
Probab=45.27 E-value=2.6e+02 Score=27.13 Aligned_cols=22 Identities=14% Similarity=0.117 Sum_probs=12.6
Q ss_pred cCCCcEEEEecCchHHHHHHHH
Q 024560 110 NPKGRIWTMVAGGGASVIYADT 131 (266)
Q Consensus 110 ~l~G~Igii~NGaGlam~t~D~ 131 (266)
.+-|-|++|+--.-+...++-.
T Consensus 116 ~P~GVv~~I~P~N~P~~~~~~~ 137 (454)
T cd07109 116 EPHGVTGHIIPWNYPLQITGRS 137 (454)
T ss_pred eeeeEEEEECCCchHHHHHHHH
Confidence 3557777777655554444433
No 100
>cd02070 corrinoid_protein_B12-BD B12 binding domain of corrinoid proteins. A family of small methanogenic corrinoid proteins that bind methyl-Co(III) 5-hydroxybenzimidazolylcobamide as a cofactor. They play a role on the methanogenesis from trimethylamine, dimethylamine or monomethylamine, which is initiated by a series of corrinoid-dependent methyltransferases.
Probab=44.84 E-value=2e+02 Score=24.71 Aligned_cols=102 Identities=17% Similarity=0.130 Sum_probs=57.5
Q ss_pred hHHHHHHHHHHhcCCCCCCCceeeccCCCCHHHHHHHHHHHHhhhccCCCCCeEEEEecccccchhHhhhhHHHHHHHHH
Q 024560 123 GASVIYADTVGDLGYASELGNYAEYSGAPNEEEVLQYARVVIDCATADPDGRKRALLIGGGIANFTDVATTFNGIIRALR 202 (266)
Q Consensus 123 Glam~t~D~l~~~g~gg~pAN~lDlgG~a~~~~~~~al~~ll~~~~~d~~v~~vlvni~ggi~~~~~vA~~~~gii~al~ 202 (266)
|+-|+ .+++... |-+ -+|+|-+.+++.+.+++ . ..+.+.|.+-. ..+..-... +.+++.++
T Consensus 98 G~~~v-~~~l~~~--G~~---vi~lG~~~p~~~l~~~~----~----~~~~d~v~lS~--~~~~~~~~~---~~~i~~lr 158 (201)
T cd02070 98 GKNLV-ATMLEAN--GFE---VIDLGRDVPPEEFVEAV----K----EHKPDILGLSA--LMTTTMGGM---KEVIEALK 158 (201)
T ss_pred HHHHH-HHHHHHC--CCE---EEECCCCCCHHHHHHHH----H----HcCCCEEEEec--cccccHHHH---HHHHHHHH
Confidence 55554 5777777 333 38899999999888773 2 33445555442 122222333 67777777
Q ss_pred HhhhhhhcccceEEEEeCCCCHHHHHHHHHhhhhhcCCceeecCCCCCHHHHHHHH
Q 024560 203 EKESKLKAARMHIFVRRGGPNYQTGLAKMRALGEELGIPLEVYGPEATMTGICKQA 258 (266)
Q Consensus 203 ~~~~~~~~~~~pvvvrl~G~~~~~~~~~L~~~~~~~Gip~~~~~~~~~~~eAv~~a 258 (266)
+.. .+..+-++.||.-..+ +.-. +.|-..+ ..+..+|++.+
T Consensus 159 ~~~-----~~~~~~i~vGG~~~~~--~~~~----~~GaD~~----~~da~~av~~~ 199 (201)
T cd02070 159 EAG-----LRDKVKVMVGGAPVNQ--EFAD----EIGADGY----AEDAAEAVAIA 199 (201)
T ss_pred HCC-----CCcCCeEEEECCcCCH--HHHH----HcCCcEE----ECCHHHHHHHH
Confidence 753 2123445667764432 2223 4576553 45777777654
No 101
>PLN02404 6,7-dimethyl-8-ribityllumazine synthase
Probab=44.45 E-value=1.9e+02 Score=24.18 Aligned_cols=94 Identities=12% Similarity=0.041 Sum_probs=62.1
Q ss_pred HHHHHHHHHHhcCCCCCCCceeeccCCCCHHHHHHHHHHHHhhhccCCCCCeEEEE---ecccccchhHhhhhHHHHHHH
Q 024560 124 ASVIYADTVGDLGYASELGNYAEYSGAPNEEEVLQYARVVIDCATADPDGRKRALL---IGGGIANFTDVATTFNGIIRA 200 (266)
Q Consensus 124 lam~t~D~l~~~g~gg~pAN~lDlgG~a~~~~~~~al~~ll~~~~~d~~v~~vlvn---i~ggi~~~~~vA~~~~gii~a 200 (266)
|---+.+.|..+ |.++.|.- +=--|-+-.+.-+.+.+++ ..+.++++.. |=|....++-|+ +++.+.
T Consensus 25 Ll~ga~~~l~~~--gv~~~~i~-v~~VPGa~EiP~a~~~l~~----s~~~DavIaLG~VIrGeT~H~e~V~---~~v~~g 94 (141)
T PLN02404 25 LLEGALETFKRY--SVKEENID-VVWVPGSFEIPVVAQRLAK----SGKYDAILCIGAVIRGDTTHYDAVA---NSAASG 94 (141)
T ss_pred HHHHHHHHHHHc--CCCccceE-EEEcCcHHHHHHHHHHHHh----cCCCCEEEEEEEEEeCCCchhHHHH---HHHHHH
Confidence 444567888888 56555422 2222333445566666665 6679999887 457788888888 888888
Q ss_pred HHHhhhhhhcccceEEE-EeCCCCHHHHHHH
Q 024560 201 LREKESKLKAARMHIFV-RRGGPNYQTGLAK 230 (266)
Q Consensus 201 l~~~~~~~~~~~~pvvv-rl~G~~~~~~~~~ 230 (266)
+.+..- ...+||.. -|.-.|.+++.+.
T Consensus 95 l~~vsl---~~~~PV~~GVLt~~~~eQA~~R 122 (141)
T PLN02404 95 VLSAGL---NSGVPCIFGVLTCDDMEQALNR 122 (141)
T ss_pred HHHHHh---ccCCCEEEEEcCCCCHHHHHHH
Confidence 877643 35799886 7777777776543
No 102
>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=43.64 E-value=1.7e+02 Score=25.21 Aligned_cols=89 Identities=12% Similarity=0.072 Sum_probs=48.9
Q ss_pred CCcEEEEecCchH------HHHHHHHHHhcCCCCCCCceeeccCCCCHHHHHHHHHHHHhhhccCCCCCeEEEEeccccc
Q 024560 112 KGRIWTMVAGGGA------SVIYADTVGDLGYASELGNYAEYSGAPNEEEVLQYARVVIDCATADPDGRKRALLIGGGIA 185 (266)
Q Consensus 112 ~G~Igii~NGaGl------am~t~D~l~~~g~gg~pAN~lDlgG~a~~~~~~~al~~ll~~~~~d~~v~~vlvni~ggi~ 185 (266)
.++|+++..-.+. .-...+.+..+| +.++- . ..-++.+.+..+++++-+++ ++|++++++..
T Consensus 125 ~~~i~~i~~~~~~~~~~~R~~g~~~a~~~~~-~~~~~-~-~~~~~~~~~~~~~~~~~~l~---~~~~~~~i~~~------ 192 (272)
T cd06300 125 KGNVLVVRGLAGHPVDEDRYAGAKEVLKEYP-GIKIV-G-EVYGDWDQAVAQKAVADFLA---SNPDVDGIWTQ------ 192 (272)
T ss_pred CceEEEEECCCCCcchHHHHHHHHHHHHHCC-CcEEE-e-ecCCCCCHHHHHHHHHHHHH---hCCCcCEEEec------
Confidence 3568888521111 122345555551 12221 1 23345555555666555554 36778877754
Q ss_pred chhHhhhhHHHHHHHHHHhhhhhhcccceEEEEeCCC
Q 024560 186 NFTDVATTFNGIIRALREKESKLKAARMHIFVRRGGP 222 (266)
Q Consensus 186 ~~~~vA~~~~gii~al~~~~~~~~~~~~pvvvrl~G~ 222 (266)
++. | .|+++++++.+ .+.|.++-.+++
T Consensus 193 -~d~-A---~g~~~al~~~g-----~~~p~v~g~d~~ 219 (272)
T cd06300 193 -GGD-A---VGAVQAFEQAG-----RDIPPVTGEDEN 219 (272)
T ss_pred -CCC-c---HHHHHHHHHcC-----CCCcEEEeeCCc
Confidence 445 6 89999999874 456766655543
No 103
>TIGR02299 HpaE 5-carboxymethyl-2-hydroxymuconate semialdehyde dehydrogenase. This model represents the dehydrogenase responsible for the conversion of 5-carboxymethyl-2-hydroxymuconate semialdehyde to 5-carboxymethyl-2-hydroxymuconate (a tricarboxylic acid). This is the step in the degradation of 4-hydroxyphenylacetic acid via homoprotocatechuate following the oxidative opening of the aromatic ring.
Probab=43.44 E-value=2.5e+02 Score=27.55 Aligned_cols=20 Identities=0% Similarity=0.032 Sum_probs=12.1
Q ss_pred HHHHHHHHHHHHhCCceeeE
Q 024560 22 GDFIMGVFAVFQDLDFSFIE 41 (266)
Q Consensus 22 ~~ii~~Ly~~f~~~D~~l~E 41 (266)
.+++.++.+++.++--.+++
T Consensus 63 ~~iL~~~a~~l~~~~~~l~~ 82 (488)
T TIGR02299 63 KRYLHKIADLIEQHADEIAV 82 (488)
T ss_pred HHHHHHHHHHHHHhHHHHHH
Confidence 46666666666666544444
No 104
>cd02810 DHOD_DHPD_FMN Dihydroorotate dehydrogenase (DHOD) and Dihydropyrimidine dehydrogenase (DHPD) FMN-binding domain. DHOD catalyzes the oxidation of (S)-dihydroorotate to orotate. This is the fourth step and the only redox reaction in the de novo biosynthesis of UMP, the precursor of all pyrimidine nucleotides. DHOD requires FMN as co-factor. DHOD divides into class 1 and class 2 based on their amino acid sequences and cellular location. Members of class 1 are cytosolic enzymes and multimers while class 2 enzymes are membrane associated and monomeric. The class 1 enzymes can be further divided into subtypes 1A and 1B which are homodimers and heterotetrameric proteins, respectively. DHPD catalyzes the first step in pyrimidine degradation: the NADPH-dependent reduction of uracil and thymine to the corresponding 5,6-dihydropyrimidines. DHPD contains two FAD, two FMN and eight [4Fe-4S] clusters, arranged in two electron transfer chains that pass its homodimeric interface twice. Two of
Probab=43.38 E-value=2.4e+02 Score=25.37 Aligned_cols=79 Identities=11% Similarity=0.167 Sum_probs=46.3
Q ss_pred eccCCCCHHHHHHHHHHHHhhhccCCCCCeEEEEe--ccccc------chhHhhhhHHHHHHHHHHhhhhhhcccceEEE
Q 024560 146 EYSGAPNEEEVLQYARVVIDCATADPDGRKRALLI--GGGIA------NFTDVATTFNGIIRALREKESKLKAARMHIFV 217 (266)
Q Consensus 146 DlgG~a~~~~~~~al~~ll~~~~~d~~v~~vlvni--~ggi~------~~~~vA~~~~gii~al~~~~~~~~~~~~pvvv 217 (266)
.++|. +++.+.++.+.+.+ .+.++|=+|+ |.... +.+ .. .-+++++++. .++||.+
T Consensus 104 si~g~-~~~~~~~~a~~~~~-----~G~d~ielN~~cP~~~~~~~~~~~~~-~~---~eiv~~vr~~------~~~pv~v 167 (289)
T cd02810 104 SVGGS-SKEDYVELARKIER-----AGAKALELNLSCPNVGGGRQLGQDPE-AV---ANLLKAVKAA------VDIPLLV 167 (289)
T ss_pred EeccC-CHHHHHHHHHHHHH-----hCCCEEEEEcCCCCCCCCcccccCHH-HH---HHHHHHHHHc------cCCCEEE
Confidence 35554 67889999888865 4788999995 32211 111 12 3455666554 3689999
Q ss_pred EeCCCCH-HHHHHHHHhhhhhcCCc
Q 024560 218 RRGGPNY-QTGLAKMRALGEELGIP 241 (266)
Q Consensus 218 rl~G~~~-~~~~~~L~~~~~~~Gip 241 (266)
++++... ++..++.+ .++++|+.
T Consensus 168 Kl~~~~~~~~~~~~a~-~l~~~Gad 191 (289)
T cd02810 168 KLSPYFDLEDIVELAK-AAERAGAD 191 (289)
T ss_pred EeCCCCCHHHHHHHHH-HHHHcCCC
Confidence 9887543 23433333 22356765
No 105
>PRK00366 ispG 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase; Reviewed
Probab=42.80 E-value=1.1e+02 Score=29.57 Aligned_cols=69 Identities=12% Similarity=0.160 Sum_probs=44.3
Q ss_pred CCCCCeEEEEecccccchhHhhhhHHHHHHHHHHhhhhhhcccceEEEEeCCCCHHHHHHHHHhhhhhcCCceeecCCCC
Q 024560 170 DPDGRKRALLIGGGIANFTDVATTFNGIIRALREKESKLKAARMHIFVRRGGPNYQTGLAKMRALGEELGIPLEVYGPEA 249 (266)
Q Consensus 170 d~~v~~vlvni~ggi~~~~~vA~~~~gii~al~~~~~~~~~~~~pvvvrl~G~~~~~~~~~L~~~~~~~Gip~~~~~~~~ 249 (266)
+..++.+=|| ||.|-+.++ .++.|+++.+++ ++| +|.|-+.-.-.+++++ +.|- .
T Consensus 99 ~~G~~~iRIN-PGNig~~~~---~v~~vv~~ak~~-------~ip--IRIGvN~GSL~~~~~~----~yg~--------~ 153 (360)
T PRK00366 99 EAGADALRIN-PGNIGKRDE---RVREVVEAAKDY-------GIP--IRIGVNAGSLEKDLLE----KYGE--------P 153 (360)
T ss_pred HhCCCEEEEC-CCCCCchHH---HHHHHHHHHHHC-------CCC--EEEecCCccChHHHHH----HcCC--------C
Confidence 3468888788 888866343 237888888876 333 5777766555677777 3342 3
Q ss_pred CHHHHHHHHHHHhh
Q 024560 250 TMTGICKQAIDCIM 263 (266)
Q Consensus 250 ~~~eAv~~av~~~~ 263 (266)
+++.-|+.|++.++
T Consensus 154 t~eamveSAl~~~~ 167 (360)
T PRK00366 154 TPEALVESALRHAK 167 (360)
T ss_pred CHHHHHHHHHHHHH
Confidence 56666666666553
No 106
>PLN02466 aldehyde dehydrogenase family 2 member
Probab=42.70 E-value=2.8e+02 Score=27.99 Aligned_cols=18 Identities=17% Similarity=0.030 Sum_probs=9.2
Q ss_pred eeecCCCCCHHHHHHHHHH
Q 024560 242 LEVYGPEATMTGICKQAID 260 (266)
Q Consensus 242 ~~~~~~~~~~~eAv~~av~ 260 (266)
+.++. ..+++.|++.++.
T Consensus 312 ~iV~~-dADl~~Aa~~i~~ 329 (538)
T PLN02466 312 FIVCE-DADVDKAVELAHF 329 (538)
T ss_pred EEEcC-CCCHHHHHHHHHH
Confidence 34443 4466666665543
No 107
>cd07138 ALDH_CddD_SSP0762 Rhodococcus ruber 6-oxolauric acid dehydrogenase-like. The 6-oxolauric acid dehydrogenase (CddD) from Rhodococcus ruber SC1 which converts 6-oxolauric acid to dodecanedioic acid, and the aldehyde dehydrogenase (locus SSP0762) from Staphylococcus saprophyticus subsp. saprophyticus ATCC 15305 and other similar sequences, are included in this CD.
Probab=42.59 E-value=2.9e+02 Score=26.88 Aligned_cols=23 Identities=0% Similarity=0.055 Sum_probs=14.6
Q ss_pred HHHHHHHHHHHHHHhCCceeeEe
Q 024560 20 KIGDFIMGVFAVFQDLDFSFIEM 42 (266)
Q Consensus 20 ~~~~ii~~Ly~~f~~~D~~l~EI 42 (266)
+-.+++.++.+++.++--.++++
T Consensus 59 ~R~~~L~~~a~~l~~~~~~la~~ 81 (466)
T cd07138 59 ERAALLERIAEAYEARADELAQA 81 (466)
T ss_pred HHHHHHHHHHHHHHHhHHHHHHH
Confidence 44567777777777665555554
No 108
>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=42.52 E-value=2.1e+02 Score=24.29 Aligned_cols=117 Identities=12% Similarity=0.113 Sum_probs=62.4
Q ss_pred CcEEEEecCch-HH------HHHHHHHHhcCCCCCC-CceeeccCCCCHHHHHHHHHHHHhhhccCCCCCeEEEEecccc
Q 024560 113 GRIWTMVAGGG-AS------VIYADTVGDLGYASEL-GNYAEYSGAPNEEEVLQYARVVIDCATADPDGRKRALLIGGGI 184 (266)
Q Consensus 113 G~Igii~NGaG-la------m~t~D~l~~~g~gg~p-AN~lDlgG~a~~~~~~~al~~ll~~~~~d~~v~~vlvni~ggi 184 (266)
.+|++++...+ .. ....+.+..+ |..+ ...+... +.+.+..+++++-+++ +.|.+++|+..
T Consensus 117 ~~i~~l~~~~~~~~~~~~r~~g~~~~~~~~--~~~~~~~~~~~~-~~~~~~~~~~~~~~l~---~~~~~~ai~~~----- 185 (267)
T cd06283 117 ERILFVTEPLDEISPRMERYEGFKEALAEH--GIGVNEELIEID-DEDADELDERLRQLLN---KPKKKTAIFAA----- 185 (267)
T ss_pred CcEEEEecCccccccHHHHHHHHHHHHHHc--CCCCCcceeEec-ccchHHHHHHHHHHHc---CCCCCCEEEEc-----
Confidence 57888864433 11 2235566666 3322 2223332 2334555666666654 25667888754
Q ss_pred cchhHhhhhHHHHHHHHHHhhhhhhcccce---EEEEeCCCCHHHHHHHHHhhhhhcCCceeecCCCCCHHHHHHHHHHH
Q 024560 185 ANFTDVATTFNGIIRALREKESKLKAARMH---IFVRRGGPNYQTGLAKMRALGEELGIPLEVYGPEATMTGICKQAIDC 261 (266)
Q Consensus 185 ~~~~~vA~~~~gii~al~~~~~~~~~~~~p---vvvrl~G~~~~~~~~~L~~~~~~~Gip~~~~~~~~~~~eAv~~av~~ 261 (266)
++.+| .|+++++++++ .++| .|+-.+++.. + +.+. -++.+ ...++.+....++++
T Consensus 186 --~d~~a---~g~~~~l~~~g-----~~vp~di~v~g~d~~~~--~-~~~~-----~~l~t----v~~~~~~~g~~a~~~ 243 (267)
T cd06283 186 --NGLIL---LEVLKALKELG-----IRIPEDVGLIGFDDTEW--A-ELIG-----PGITT----IAQPTYEMGKTAAEL 243 (267)
T ss_pred --CcHHH---HHHHHHHHHcC-----CCCccceEEEEeCCccH--h-hhcC-----CcceE----ecCCHHHHHHHHHHH
Confidence 56777 99999999874 2222 2345555432 2 2222 13433 134777777777664
Q ss_pred h
Q 024560 262 I 262 (266)
Q Consensus 262 ~ 262 (266)
+
T Consensus 244 l 244 (267)
T cd06283 244 L 244 (267)
T ss_pred H
Confidence 4
No 109
>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=41.89 E-value=1.5e+02 Score=25.68 Aligned_cols=65 Identities=12% Similarity=0.162 Sum_probs=37.4
Q ss_pred CCCCHHHHHHHHHHHHhhhccCCCCCeEEEEecccccchhHhhhhHHHHHHHHHHhhhhhhcccceEEEEeCCCCHHHHH
Q 024560 149 GAPNEEEVLQYARVVIDCATADPDGRKRALLIGGGIANFTDVATTFNGIIRALREKESKLKAARMHIFVRRGGPNYQTGL 228 (266)
Q Consensus 149 G~a~~~~~~~al~~ll~~~~~d~~v~~vlvni~ggi~~~~~vA~~~~gii~al~~~~~~~~~~~~pvvvrl~G~~~~~~~ 228 (266)
++.+.+..++.++-+|+ ++|++++|+.. .+..| .|+++++++.+. ..+++++ |+....++.
T Consensus 165 ~~~~~~~~~~~~~~~l~---~~~~~~ai~~~-------~d~~a---~g~~~al~~~g~---~~~~~iv---g~d~~~~~~ 225 (274)
T cd06311 165 ANWNRDDAFSVMQDLLT---KFPKIDAVWAH-------DDDMA---VGVLAAIKQAGR---TDIKFVV---GGAGSKDMI 225 (274)
T ss_pred CCCcHHHHHHHHHHHHH---hCCCcCEEEEC-------CCcHH---HHHHHHHHHcCC---CCCceEE---EeCCCHHHH
Confidence 33444555555555553 36788887753 45667 899999998742 1123332 223335566
Q ss_pred HHHH
Q 024560 229 AKMR 232 (266)
Q Consensus 229 ~~L~ 232 (266)
+.++
T Consensus 226 ~~i~ 229 (274)
T cd06311 226 KMIM 229 (274)
T ss_pred HHHH
Confidence 7777
No 110
>cd07115 ALDH_HMSADH_HapE Pseudomonas fluorescens 4-hydroxymuconic semialdehyde dehydrogenase-like. 4-hydroxymuconic semialdehyde dehydrogenase (HapE, EC=1.2.1.61) of Pseudomonas fluorescens ACB involved in 4-hydroxyacetophenone degradation, and putative hydroxycaproate semialdehyde dehydrogenase (ChnE) of Brachymonas petroleovorans involved in cyclohexane metabolism, and other similar sequences, are present in this CD.
Probab=41.61 E-value=3e+02 Score=26.72 Aligned_cols=22 Identities=5% Similarity=0.022 Sum_probs=13.1
Q ss_pred HHHHHHHHHHHHHHhCCceeeE
Q 024560 20 KIGDFIMGVFAVFQDLDFSFIE 41 (266)
Q Consensus 20 ~~~~ii~~Ly~~f~~~D~~l~E 41 (266)
+=.+++.++.+++.++--.+++
T Consensus 42 ~R~~~l~~~a~~l~~~~~~la~ 63 (453)
T cd07115 42 ERGRILWRLAELILANADELAR 63 (453)
T ss_pred HHHHHHHHHHHHHHHhHHHHHH
Confidence 3356677777777665444443
No 111
>cd07119 ALDH_BADH-GbsA Bacillus subtilis NAD+-dependent betaine aldehyde dehydrogenase-like. Included in this CD is the NAD+-dependent, betaine aldehyde dehydrogenase (BADH, GbsA, EC=1.2.1.8) of Bacillus subtilis involved in the synthesis of the osmoprotectant glycine betaine from choline or glycine betaine aldehyde.
Probab=41.31 E-value=3.3e+02 Score=26.68 Aligned_cols=20 Identities=0% Similarity=0.056 Sum_probs=12.1
Q ss_pred HHHHHHHHHHHHhCCceeeE
Q 024560 22 GDFIMGVFAVFQDLDFSFIE 41 (266)
Q Consensus 22 ~~ii~~Ly~~f~~~D~~l~E 41 (266)
.+++.++.+++.+.--.|++
T Consensus 62 ~~~L~~~a~~l~~~~~~la~ 81 (482)
T cd07119 62 AALLFRIADKIREDAEELAR 81 (482)
T ss_pred HHHHHHHHHHHHHhHHHHHH
Confidence 36677777777666444443
No 112
>cd06344 PBP1_ABC_ligand_binding_like_9 Type I periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type active transport systems that are predicted to be involved in uptake of amino acids, peptides, or inorganic ions. This subgroup includes the type I periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type active transport systems that are predicted to be involved in uptake of amino acids, peptides, or inorganic ions. Members of this group are sequence-similar to members of the family of ABC-type hydrophobic amino acid transporters, such as leucine/isoleucine/valine binding protein (LIVBP); however their ligand specificity has not been determined experimentally.
Probab=41.07 E-value=1.5e+02 Score=26.83 Aligned_cols=94 Identities=13% Similarity=0.050 Sum_probs=50.4
Q ss_pred HHHHHHHHHhcC-CCCCCCceeeccCCCCHHHHHHHHHHHHhhhccCCCCCeEEEEecccccchhHhhhhHHHHHHHHHH
Q 024560 125 SVIYADTVGDLG-YASELGNYAEYSGAPNEEEVLQYARVVIDCATADPDGRKRALLIGGGIANFTDVATTFNGIIRALRE 203 (266)
Q Consensus 125 am~t~D~l~~~g-~gg~pAN~lDlgG~a~~~~~~~al~~ll~~~~~d~~v~~vlvni~ggi~~~~~vA~~~~gii~al~~ 203 (266)
+.+++|.++..| ..|++-.++-.--..++++..++.+-+++ +++|.+|+ |+.++... .++...+++
T Consensus 22 ~~lA~~~iNa~ggi~G~~ielv~~D~~~~p~~a~~~a~~li~----~~~v~aii----G~~~s~~~-----~a~~~~~~~ 88 (332)
T cd06344 22 VAQAQTEINLQGGINGKLLKVVIANDGNDPEIAKKVADELVK----DPEILGVV----GHYSSDAT-----LAALDIYQK 88 (332)
T ss_pred HHHHHHHHHhcCCCCCCeEEEEEECCCCChHHHHHHHHHHhc----ccCceEEE----cCCCcHHH-----HHHHHHHhh
Confidence 346789999873 12333333322233355666677666666 66654443 66544433 344555554
Q ss_pred hhhh----------hhcccceEEEEeCCCCHHHHHHHHH
Q 024560 204 KESK----------LKAARMHIFVRRGGPNYQTGLAKMR 232 (266)
Q Consensus 204 ~~~~----------~~~~~~pvvvrl~G~~~~~~~~~L~ 232 (266)
.+-+ +. ...|.+.|...+....++.+.+
T Consensus 89 ~~ip~i~~~a~~~~lt-~~~~~~fr~~~~~~~~~~~~~~ 126 (332)
T cd06344 89 AKLVLISPTSTSVKLS-NPGPYFFRTVPSNAVAARALAK 126 (332)
T ss_pred cCceEEccCcCchhhc-CCCCcEEEeCCCcHHHHHHHHH
Confidence 3311 00 1345677888877777765544
No 113
>PRK11905 bifunctional proline dehydrogenase/pyrroline-5-carboxylate dehydrogenase; Reviewed
Probab=40.87 E-value=3e+02 Score=30.88 Aligned_cols=72 Identities=17% Similarity=0.177 Sum_probs=38.8
Q ss_pred HHHHHHhcCCCCCCCceeeccCCCCHHHHHHHHHHHHhhhccCCCCCeEEEEecccccchhHhhhhHHHHHHHHHHhhhh
Q 024560 128 YADTVGDLGYASELGNYAEYSGAPNEEEVLQYARVVIDCATADPDGRKRALLIGGGIANFTDVATTFNGIIRALREKESK 207 (266)
Q Consensus 128 t~D~l~~~g~gg~pAN~lDlgG~a~~~~~~~al~~ll~~~~~d~~v~~vlvni~ggi~~~~~vA~~~~gii~al~~~~~~ 207 (266)
.+.++..+ |=|.+-+.+--+...+ ..+.+++ ||++++|. |+| ++.++ +.|.+.+.+..
T Consensus 722 l~~ll~eA---GlP~gvl~lV~G~g~~----vg~~Lv~----~p~v~~V~---FTG---St~vg---~~I~~~~A~~~-- 779 (1208)
T PRK11905 722 AVRLLHEA---GVPKDALQLLPGDGRT----VGAALVA----DPRIAGVM---FTG---STEVA---RLIQRTLAKRS-- 779 (1208)
T ss_pred HHHHHHHc---CCCcccEEEeeCCchH----HHHHHHc----CCCcCEEE---EeC---CHHHH---HHHHHHHHhhc--
Confidence 35666665 3355444332222221 2344556 88888665 444 44555 66666554431
Q ss_pred hhcccceEEEEeCCCC
Q 024560 208 LKAARMHIFVRRGGPN 223 (266)
Q Consensus 208 ~~~~~~pvvvrl~G~~ 223 (266)
+..+|++.=+||.|
T Consensus 780 --~~~~pli~ElGGkN 793 (1208)
T PRK11905 780 --GPPVPLIAETGGQN 793 (1208)
T ss_pred --CCCCeEEEecCCcC
Confidence 13478888888865
No 114
>cd07091 ALDH_F1-2_Ald2-like ALDH subfamily: ALDH families 1and 2, including 10-formyltetrahydrofolate dehydrogenase, NAD+-dependent retinal dehydrogenase 1 and related proteins. ALDH subfamily which includes the NAD+-dependent retinal dehydrogenase 1 (RALDH 1, ALDH1, EC=1.2.1.36), also known as aldehyde dehydrogenase family 1 member A1 (ALDH1A1), in humans, a homotetrameric, cytosolic enzyme that catalyzes the oxidation of retinaldehyde to retinoic acid. Human ALDH1B1 and ALDH2 are also in this cluster; both are mitochrondrial homotetramers which play important roles in acetaldehyde oxidation; ALDH1B1 in response to UV light exposure and ALDH2 during ethanol metabolism. 10-formyltetrahydrofolate dehydrogenase (FTHFDH, EC=1.5.1.6), also known as aldehyde dehydrogenase family 1 member L1 (ALDH1L1), in humans, a multi-domain homotetramer with an N-terminal formyl transferase domain and a C-terminal ALDH domain. FTHFDH catalyzes an NADP+-dependent dehydrogenase reaction resulting in the co
Probab=40.76 E-value=3.5e+02 Score=26.43 Aligned_cols=23 Identities=4% Similarity=0.026 Sum_probs=14.4
Q ss_pred HHHHHHHHHHHHHHHhCCceeeE
Q 024560 19 GKIGDFIMGVFAVFQDLDFSFIE 41 (266)
Q Consensus 19 ~~~~~ii~~Ly~~f~~~D~~l~E 41 (266)
++=.+++.++.+++.+.--.+++
T Consensus 65 ~~R~~~L~~~a~~l~~~~~~la~ 87 (476)
T cd07091 65 RERGRLLNKLADLIERDRDELAA 87 (476)
T ss_pred HHHHHHHHHHHHHHHHhHHHHHH
Confidence 34456777777777766554544
No 115
>KOG3019 consensus Predicted nucleoside-diphosphate sugar epimerase [Nucleotide transport and metabolism]
Probab=40.55 E-value=52 Score=30.32 Aligned_cols=127 Identities=12% Similarity=0.141 Sum_probs=65.8
Q ss_pred cEEEEecCchHHHHHHHHHHhcCCCCCCCc----eeeccCCCCHHHHHHHHHHHHhhhccCCCCCeEEEEecccccchhH
Q 024560 114 RIWTMVAGGGASVIYADTVGDLGYASELGN----YAEYSGAPNEEEVLQYARVVIDCATADPDGRKRALLIGGGIANFTD 189 (266)
Q Consensus 114 ~Igii~NGaGlam~t~D~l~~~g~gg~pAN----~lDlgG~a~~~~~~~al~~ll~~~~~d~~v~~vlvni~ggi~~~~~ 189 (266)
|+|++..=+|-+|..|=+--..|.||-.+| |-.+ .-..+...+.-.|+ +|.+++|+=-+--.+++..+
T Consensus 178 R~GvVlG~gGGa~~~M~lpF~~g~GGPlGsG~Q~fpWI----Hv~DL~~li~~ale----~~~v~GViNgvAP~~~~n~E 249 (315)
T KOG3019|consen 178 RIGVVLGKGGGALAMMILPFQMGAGGPLGSGQQWFPWI----HVDDLVNLIYEALE----NPSVKGVINGVAPNPVRNGE 249 (315)
T ss_pred EEeEEEecCCcchhhhhhhhhhccCCcCCCCCeeeeee----ehHHHHHHHHHHHh----cCCCCceecccCCCccchHH
Confidence 466655444445555555555665665442 1122 12234444444466 89999986335444566667
Q ss_pred hhhhHHHHHHHHHHhhhhhhcccce--EE-EEeC---CCCHHHHHHHHHhhhhhcCCceeecCCCCCHHHHHHHHH
Q 024560 190 VATTFNGIIRALREKESKLKAARMH--IF-VRRG---GPNYQTGLAKMRALGEELGIPLEVYGPEATMTGICKQAI 259 (266)
Q Consensus 190 vA~~~~gii~al~~~~~~~~~~~~p--vv-vrl~---G~~~~~~~~~L~~~~~~~Gip~~~~~~~~~~~eAv~~av 259 (266)
.+ +.+-.++..-. =.++| +| .-+| -+-.-+|.|.+-..+.++|..+ .|....+|++..+
T Consensus 250 f~---q~lg~aL~Rp~----~~pvP~fvvqA~fG~erA~~vLeGqKV~Pqral~~Gf~f----~yp~vk~Al~~i~ 314 (315)
T KOG3019|consen 250 FC---QQLGSALSRPS----WLPVPDFVVQALFGPERATVVLEGQKVLPQRALELGFEF----KYPYVKDALRAIM 314 (315)
T ss_pred HH---HHHHHHhCCCc----ccCCcHHHHHHHhCccceeEEeeCCcccchhHhhcCcee----echHHHHHHHHHh
Confidence 77 77777764311 01222 11 0111 1122345556655555678765 3668888887654
No 116
>PRK13789 phosphoribosylamine--glycine ligase; Provisional
Probab=40.44 E-value=1.7e+02 Score=28.50 Aligned_cols=118 Identities=15% Similarity=0.081 Sum_probs=59.3
Q ss_pred cEEEEecCchHHHHHHHHHHhcCCCCC----CCce--eeccC----CCCHHHHHHHHHHHHhhhccCCCCCeEEEEeccc
Q 024560 114 RIWTMVAGGGASVIYADTVGDLGYASE----LGNY--AEYSG----APNEEEVLQYARVVIDCATADPDGRKRALLIGGG 183 (266)
Q Consensus 114 ~Igii~NGaGlam~t~D~l~~~g~gg~----pAN~--lDlgG----~a~~~~~~~al~~ll~~~~~d~~v~~vlvni~gg 183 (266)
+|-++++|+.---+++-+ ...+..-+ |.|. ...+. ..+.......++++- ..+++.|++ |.
T Consensus 6 kvLviG~g~rehal~~~~-~~~~~~~~~~~~pgn~g~~~~~~~~~~~~~~~d~~~l~~~a~-----~~~iD~Vv~---g~ 76 (426)
T PRK13789 6 KVLLIGSGGRESAIAFAL-RKSNLLSELKVFPGNGGFPDDELLPADSFSILDKSSVQSFLK-----SNPFDLIVV---GP 76 (426)
T ss_pred EEEEECCCHHHHHHHHHH-HhCCCCCEEEEECCchHHhccccccccCcCcCCHHHHHHHHH-----HcCCCEEEE---CC
Confidence 677787777655555444 44421111 4554 11110 011222333344433 356776663 32
Q ss_pred ccchhHhhhhHHHHHHHHHHhhhhhhcccceEE------EEeCCCCHHHHHHHHHhhhhhcCCceeecCCCCCHHHHHHH
Q 024560 184 IANFTDVATTFNGIIRALREKESKLKAARMHIF------VRRGGPNYQTGLAKMRALGEELGIPLEVYGPEATMTGICKQ 257 (266)
Q Consensus 184 i~~~~~vA~~~~gii~al~~~~~~~~~~~~pvv------vrl~G~~~~~~~~~L~~~~~~~Gip~~~~~~~~~~~eAv~~ 257 (266)
.+-.. +++++.+++. .+|++ .++.+ +-...++.|. ++|||+-.|..+++.+++.+.
T Consensus 77 ---E~~l~---~glad~~~~~-------Gip~~Gp~~~aa~le~-dK~~~K~~l~----~~gIpt~~~~~~~~~~ea~~~ 138 (426)
T PRK13789 77 ---EDPLV---AGFADWAAEL-------GIPCFGPDSYCAQVEG-SKHFAKSLMK----EAKIPTASYKTFTEYSSSLSY 138 (426)
T ss_pred ---chHHH---HHHHHHHHHc-------CCCcCCCHHHHHHHHc-CHHHHHHHHH----HcCCCCCCeEeeCCHHHHHHH
Confidence 12222 6777777665 35543 12222 2344555666 779997655567788887554
Q ss_pred H
Q 024560 258 A 258 (266)
Q Consensus 258 a 258 (266)
+
T Consensus 139 ~ 139 (426)
T PRK13789 139 L 139 (426)
T ss_pred H
Confidence 3
No 117
>PRK11904 bifunctional proline dehydrogenase/pyrroline-5-carboxylate dehydrogenase; Reviewed
Probab=40.34 E-value=2.8e+02 Score=30.56 Aligned_cols=46 Identities=26% Similarity=0.310 Sum_probs=26.9
Q ss_pred HHHHhhhccCCCCCeEEEEecccccchhHhhhhHHHHHHHHHHhhhhhhcccceEEEEeCCCC
Q 024560 161 RVVIDCATADPDGRKRALLIGGGIANFTDVATTFNGIIRALREKESKLKAARMHIFVRRGGPN 223 (266)
Q Consensus 161 ~~ll~~~~~d~~v~~vlvni~ggi~~~~~vA~~~~gii~al~~~~~~~~~~~~pvvvrl~G~~ 223 (266)
+.+++ +|++++|. |+| ++.++ +.|.+.+-+.. +..+|++.=+||.|
T Consensus 756 ~~Lv~----~p~v~~V~---FTG---S~~~g---~~I~~~~A~~~----g~~~pvi~ElGGkN 801 (1038)
T PRK11904 756 AALTA----DPRIAGVA---FTG---STETA---RIINRTLAARD----GPIVPLIAETGGQN 801 (1038)
T ss_pred HHHhc----CCCcCeEE---EEC---CHHHH---HHHHHHHhhcc----CCCceEEEEcCCcC
Confidence 44555 78887655 444 34455 66665544331 13468778888865
No 118
>COG3693 XynA Beta-1,4-xylanase [Carbohydrate transport and metabolism]
Probab=40.28 E-value=1.9e+02 Score=27.76 Aligned_cols=95 Identities=19% Similarity=0.267 Sum_probs=58.5
Q ss_pred eeccCCCCHHHHHHHHHHHHhhhccCCCCCeEEEEecccccchhHhhhhHHHHHHHHHHhhhhhhcccceEEEEeCCCCH
Q 024560 145 AEYSGAPNEEEVLQYARVVIDCATADPDGRKRALLIGGGIANFTDVATTFNGIIRALREKESKLKAARMHIFVRRGGPNY 224 (266)
Q Consensus 145 lDlgG~a~~~~~~~al~~ll~~~~~d~~v~~vlvni~ggi~~~~~vA~~~~gii~al~~~~~~~~~~~~pvvvrl~G~~~ 224 (266)
..+-+..-++-+..++++.-+ .||+-+ .++|=++ ++....=...+.-+|+.|++.+-+..+..+.-=..++++..
T Consensus 162 ~w~~~~~gpd~I~~aF~~Are---adP~Ak-L~~NDY~-ie~~~~kr~~~~nlI~~LkekG~pIDgiG~QsH~~~~~~~~ 236 (345)
T COG3693 162 AWYDGGTGPDYIKLAFHIARE---ADPDAK-LVINDYS-IEGNPAKRNYVLNLIEELKEKGAPIDGIGIQSHFSGDGPSI 236 (345)
T ss_pred hhhccCCccHHHHHHHHHHHh---hCCCce-EEeeccc-ccCChHHHHHHHHHHHHHHHCCCCccceeeeeeecCCCCCH
Confidence 334444456788888888765 266532 5556454 44444433345667777777642211122222368999999
Q ss_pred HHHHHHHHhhhhhcCCceeec
Q 024560 225 QTGLAKMRALGEELGIPLEVY 245 (266)
Q Consensus 225 ~~~~~~L~~~~~~~Gip~~~~ 245 (266)
+..+..|.+..+. |+|+++.
T Consensus 237 ~~~~~a~~~~~k~-Gl~i~VT 256 (345)
T COG3693 237 EKMRAALLKFSKL-GLPIYVT 256 (345)
T ss_pred HHHHHHHHHHhhc-CCCceEE
Confidence 9999999876666 9998764
No 119
>cd00951 KDGDH 5-dehydro-4-deoxyglucarate dehydratase, also called 5-keto-4-deoxy-glucarate dehydratase (KDGDH), which is member of dihydrodipicolinate synthase (DHDPS) family that comprises several pyruvate-dependent class I aldolases. The enzyme is involved in glucarate metabolism, and its mechanism presumbly involves a Schiff-base intermediate similar to members of DHDPS family. While in the case of Pseudomonas sp. 5-dehydro-4-deoxy-D-glucarate is degraded by KDGDH to 2,5-dioxopentanoate, in certain species of Enterobacteriaceae it is degraded instead to pyruvate and glycerate.
Probab=40.22 E-value=2.9e+02 Score=25.19 Aligned_cols=106 Identities=18% Similarity=0.175 Sum_probs=61.7
Q ss_pred eeeccCCCCHHHHHHHHHHHHhhhccCCCCCeEEEE-ecccccchhHhhhhHHHHHHHHHHhhhhhhcccceEEEEeCCC
Q 024560 144 YAEYSGAPNEEEVLQYARVVIDCATADPDGRKRALL-IGGGIANFTDVATTFNGIIRALREKESKLKAARMHIFVRRGGP 222 (266)
Q Consensus 144 ~lDlgG~a~~~~~~~al~~ll~~~~~d~~v~~vlvn-i~ggi~~~~~vA~~~~gii~al~~~~~~~~~~~~pvvvrl~G~ 222 (266)
|+|=-|..+.+.+.+-++.+++ .++++++++ ..|-...-+. .+ -+.+++...+.. ..++||++-.+.
T Consensus 11 Pf~~dg~iD~~~l~~l~~~l~~-----~Gv~gi~v~GstGE~~~Ls~-eE-r~~l~~~~~~~~----~~~~pvi~gv~~- 78 (289)
T cd00951 11 HFDADGSFDEDAYRAHVEWLLS-----YGAAALFAAGGTGEFFSLTP-DE-YAQVVRAAVEET----AGRVPVLAGAGY- 78 (289)
T ss_pred CCCCCCCcCHHHHHHHHHHHHH-----cCCCEEEECcCCcCcccCCH-HH-HHHHHHHHHHHh----CCCCCEEEecCC-
Confidence 4455577888888888888875 689999988 3322211111 10 133444433332 136888987765
Q ss_pred CHHHHHHHHHhhhhhcCCc------eeecCCCCCHHHHHHHHHHHhhh
Q 024560 223 NYQTGLAKMRALGEELGIP------LEVYGPEATMTGICKQAIDCIMS 264 (266)
Q Consensus 223 ~~~~~~~~L~~~~~~~Gip------~~~~~~~~~~~eAv~~av~~~~~ 264 (266)
+..++.+..+. ++++|.. -+++ ..+.++.++.+-.++.+
T Consensus 79 ~t~~~i~~a~~-a~~~Gad~v~~~pP~y~--~~~~~~i~~~f~~v~~~ 123 (289)
T cd00951 79 GTATAIAYAQA-AEKAGADGILLLPPYLT--EAPQEGLYAHVEAVCKS 123 (289)
T ss_pred CHHHHHHHHHH-HHHhCCCEEEECCCCCC--CCCHHHHHHHHHHHHhc
Confidence 77777776653 3455643 2222 23566677777666653
No 120
>PRK11809 putA trifunctional transcriptional regulator/proline dehydrogenase/pyrroline-5-carboxylate dehydrogenase; Reviewed
Probab=40.00 E-value=3e+02 Score=31.21 Aligned_cols=75 Identities=17% Similarity=0.174 Sum_probs=40.8
Q ss_pred HHHHHHhcCCCCCCCceeeccCCCCHHHHHHHHHHHHhhhccCCCCCeEEEEecccccchhHhhhhHHHHHHHHHHhhhh
Q 024560 128 YADTVGDLGYASELGNYAEYSGAPNEEEVLQYARVVIDCATADPDGRKRALLIGGGIANFTDVATTFNGIIRALREKESK 207 (266)
Q Consensus 128 t~D~l~~~g~gg~pAN~lDlgG~a~~~~~~~al~~ll~~~~~d~~v~~vlvni~ggi~~~~~vA~~~~gii~al~~~~~~ 207 (266)
.+.++.++ |=|.+-+.+--+.. +.+ -+.+.+ ||+|++|. |.| +++++ +.|.+.+.+...+
T Consensus 814 lv~ll~eA---GlP~gvlqlv~G~g-~~v---g~~Lv~----~p~V~~V~---FTG---St~tg---~~I~~~aA~~l~~ 873 (1318)
T PRK11809 814 AVRILLEA---GVPAGVVQLLPGRG-ETV---GAALVA----DARVRGVM---FTG---STEVA---RLLQRNLAGRLDP 873 (1318)
T ss_pred HHHHHHHh---CcCcCeEEEeeCCc-HHH---HHHHhc----CCCcCEEE---EeC---CHHHH---HHHHHHHhhhccc
Confidence 35556555 34655554443322 222 334455 89888665 444 45566 7776665443110
Q ss_pred hhcccceEEEEeCCCC
Q 024560 208 LKAARMHIFVRRGGPN 223 (266)
Q Consensus 208 ~~~~~~pvvvrl~G~~ 223 (266)
....+|++.=+||.|
T Consensus 874 -~g~~~pliaElGGkN 888 (1318)
T PRK11809 874 -QGRPIPLIAETGGQN 888 (1318)
T ss_pred -ccCceeEEEecCCcc
Confidence 123578888999966
No 121
>PF00532 Peripla_BP_1: Periplasmic binding proteins and sugar binding domain of LacI family; InterPro: IPR001761 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 (lacI) [, ].; PDB: 1BAP_A 7ABP_A 6ABP_A 1ABF_A 5ABP_A 2WRZ_B 9ABP_A 1APB_A 1ABE_A 8ABP_A ....
Probab=39.95 E-value=1.1e+02 Score=27.66 Aligned_cols=77 Identities=25% Similarity=0.207 Sum_probs=50.3
Q ss_pred Cc-EEEEecCchHH----H--HHHHHHHhcCCCCCCCcee-eccCCCCHHHHHHHHHHHHhhhccCCCCCeEEEEecccc
Q 024560 113 GR-IWTMVAGGGAS----V--IYADTVGDLGYASELGNYA-EYSGAPNEEEVLQYARVVIDCATADPDGRKRALLIGGGI 184 (266)
Q Consensus 113 G~-Igii~NGaGla----m--~t~D~l~~~g~gg~pAN~l-DlgG~a~~~~~~~al~~ll~~~~~d~~v~~vlvni~ggi 184 (266)
-+ |++++.-.... - -+.+++..+ |- |-+.. -.-|+.+.+.-+++++-+|+ .+|.+++|+.
T Consensus 119 ~~~I~~i~~~~~~~~~~~R~~Gy~~Al~~~--Gl-~~~~~~i~~~~~~~~~g~~~~~~ll~---~~p~idai~~------ 186 (279)
T PF00532_consen 119 RRPIAFIGGPEDSSTSRERLQGYRDALKEA--GL-PIDEEWIFEGDFDYESGYEAARELLE---SHPDIDAIFC------ 186 (279)
T ss_dssp CSTEEEEEESTTTHHHHHHHHHHHHHHHHT--TS-CEEEEEEEESSSSHHHHHHHHHHHHH---TSTT-SEEEE------
T ss_pred CCeEEEEecCcchHHHHHHHHHHHHHHHHc--CC-CCCcccccccCCCHHHHHHHHHHHHh---hCCCCEEEEE------
Confidence 56 88886543322 1 246778887 34 43333 23466677777777777766 2678888873
Q ss_pred cchhHhhhhHHHHHHHHHHhh
Q 024560 185 ANFTDVATTFNGIIRALREKE 205 (266)
Q Consensus 185 ~~~~~vA~~~~gii~al~~~~ 205 (266)
.++.+| .|+++++++.+
T Consensus 187 -~nd~~A---~ga~~~l~~~g 203 (279)
T PF00532_consen 187 -ANDMMA---IGAIRALRERG 203 (279)
T ss_dssp -SSHHHH---HHHHHHHHHTT
T ss_pred -eCHHHH---HHHHHHHHHcC
Confidence 478888 99999999975
No 122
>PF15609 PRTase_2: Phosphoribosyl transferase
Probab=39.68 E-value=83 Score=27.72 Aligned_cols=116 Identities=22% Similarity=0.264 Sum_probs=60.8
Q ss_pred CCcEEEEe---cCchHHHHHHHHHHhcC-C--------CC-CC-CceeeccCCCCHHHHHHHHHHHHhhhccCCCCCeEE
Q 024560 112 KGRIWTMV---AGGGASVIYADTVGDLG-Y--------AS-EL-GNYAEYSGAPNEEEVLQYARVVIDCATADPDGRKRA 177 (266)
Q Consensus 112 ~G~Igii~---NGaGlam~t~D~l~~~g-~--------gg-~p-AN~lDlgG~a~~~~~~~al~~ll~~~~~d~~v~~vl 177 (266)
.|.+-+|+ -.-|++-...|.+.... | .| .+ ..|-+=---|+...++..-.-.+. +.. ..||
T Consensus 52 ~~~~lvIGfAETATgLG~~V~~~~~~~~~ylhTTR~~v~~~~~~~~F~E~HSHAt~h~ly~~~~~~l~----~~~-~lVL 126 (191)
T PF15609_consen 52 PGPVLVIGFAETATGLGHGVFDALGAACLYLHTTREPVPGVPPLLEFEEEHSHATDHLLYPPDPDLLR----NAR-TLVL 126 (191)
T ss_pred CCCeEEEEEhHHHHHHHHHHHHHhhhccceeeeccccCCCCccceeeeccccccccceecCCChHHhc----CCC-CEEE
Confidence 55554443 34567777788886542 1 01 11 233332333444444433323333 333 5677
Q ss_pred EE--ecccccchhHhhhhHHHHHHHHHHhhhhhhcccceEEEEeCCCCHHHHHHHHHhhhhhcCCceee
Q 024560 178 LL--IGGGIANFTDVATTFNGIIRALREKESKLKAARMHIFVRRGGPNYQTGLAKMRALGEELGIPLEV 244 (266)
Q Consensus 178 vn--i~ggi~~~~~vA~~~~gii~al~~~~~~~~~~~~pvvvrl~G~~~~~~~~~L~~~~~~~Gip~~~ 244 (266)
|- |.+| .|+-.+|+++++.. +.+..+++-+-.-..++.++.+.+..++.|+|+.+
T Consensus 127 VDDEiSTG--------~T~lnli~al~~~~----p~~~yvvasL~d~~~~~~~~~~~~~~~~lgi~i~~ 183 (191)
T PF15609_consen 127 VDDEISTG--------NTFLNLIRALHAKY----PRKRYVVASLLDWRSEEDRARFEALAEELGIPIDV 183 (191)
T ss_pred EecCccch--------HHHHHHHHHHHHhC----CCceEEEEEEeeCCCHHHHHHHHHHHHHcCCcEEE
Confidence 77 6555 44577888888763 23344444333333344565566555688999864
No 123
>PRK01438 murD UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional
Probab=39.58 E-value=2.5e+02 Score=27.30 Aligned_cols=94 Identities=15% Similarity=0.183 Sum_probs=52.0
Q ss_pred eeeccCCCCHHHHHHHHHHHHhhhccCCCCCeEEEEecccccchhHhhhhHHHHHHHHHHhhhhhhcccceEEEEeCCCC
Q 024560 144 YAEYSGAPNEEEVLQYARVVIDCATADPDGRKRALLIGGGIANFTDVATTFNGIIRALREKESKLKAARMHIFVRRGGPN 223 (266)
Q Consensus 144 ~lDlgG~a~~~~~~~al~~ll~~~~~d~~v~~vlvni~ggi~~~~~vA~~~~gii~al~~~~~~~~~~~~pvvvrl~G~~ 223 (266)
++|=.++.+|+.+..+++.+ + + ++.++||+.+-.++. .+++.+.+.. ..|++ . |..
T Consensus 347 iiDDs~ahNp~a~~aaL~~l-------~--~--i~~I~gG~~~~kd~~----~~~~~l~~~~-------~~vi~-~-g~~ 402 (480)
T PRK01438 347 WVDDSKATNPHAAAASLAAY-------P--S--VVWIAGGLAKGADFD----DLVRRAAGRL-------RGVVL-I-GAD 402 (480)
T ss_pred EEecCccCCHHHHHHHHHhC-------C--C--EEEEEecccCCCCHH----HHHHHHHhhc-------eEEEE-E-CCC
Confidence 46644777888888875544 1 2 234567777655544 4666554431 11222 2 444
Q ss_pred HHHHHHHHHhhhhhcCCceeecC--CCCCHHHHHHHHHHHhh
Q 024560 224 YQTGLAKMRALGEELGIPLEVYG--PEATMTGICKQAIDCIM 263 (266)
Q Consensus 224 ~~~~~~~L~~~~~~~Gip~~~~~--~~~~~~eAv~~av~~~~ 263 (266)
.+.-.+.|++. -.++++..+. .++++++|++.+.+.+.
T Consensus 403 ~~~~~~~l~~~--~~~~~~~~~~~~~~~~~~~A~~~a~~~~~ 442 (480)
T PRK01438 403 RAEIAEALARH--APDVPVVEVDRTDTGAMDEAVAAAAKLAR 442 (480)
T ss_pred HHHHHHHHHhc--CCCCCEEEecCCCcCCHHHHHHHHHHhCC
Confidence 44444555532 1244555443 23489999999887654
No 124
>cd07145 ALDH_LactADH_F420-Bios Methanocaldococcus jannaschii NAD+-dependent lactaldehyde dehydrogenase-like. NAD+-dependent, lactaldehyde dehydrogenase (EC=1.2.1.22) involved the biosynthesis of coenzyme F(420) in Methanocaldococcus jannaschii through the oxidation of lactaldehyde to lactate and generation of NAPH, and similar sequences are included in this CD.
Probab=38.88 E-value=3.3e+02 Score=26.41 Aligned_cols=21 Identities=14% Similarity=0.088 Sum_probs=12.9
Q ss_pred HHHHHHHHHHHHHHhCCceee
Q 024560 20 KIGDFIMGVFAVFQDLDFSFI 40 (266)
Q Consensus 20 ~~~~ii~~Ly~~f~~~D~~l~ 40 (266)
+-.+++.++.+++.++--.|.
T Consensus 44 ~R~~~L~~~a~~l~~~~~ela 64 (456)
T cd07145 44 KRYKILMKVAELIERRKEELA 64 (456)
T ss_pred HHHHHHHHHHHHHHHhHHHHH
Confidence 345667777777776654444
No 125
>cd07089 ALDH_CddD-AldA-like Rhodococcus ruber 6-oxolauric acid dehydrogenase-like and related proteins. The 6-oxolauric acid dehydrogenase (CddD) from Rhodococcus ruber SC1 which converts 6-oxolauric acid to dodecanedioic acid; and the aldehyde dehydrogenase (locus SSP0762) from Staphylococcus saprophyticus subsp. saprophyticus ATCC 15305 and also, the Mycobacterium tuberculosis H37Rv ALDH AldA (locus Rv0768) sequence; and other similar sequences, are included in this CD.
Probab=38.83 E-value=3.8e+02 Score=26.14 Aligned_cols=22 Identities=0% Similarity=-0.032 Sum_probs=13.3
Q ss_pred HHHHHHHHHHHHHHhCCceeeE
Q 024560 20 KIGDFIMGVFAVFQDLDFSFIE 41 (266)
Q Consensus 20 ~~~~ii~~Ly~~f~~~D~~l~E 41 (266)
+=.+++.++.+++.++--.+.+
T Consensus 43 ~R~~~L~~~a~~l~~~~~~la~ 64 (459)
T cd07089 43 ERARCLRQLHEALEARKEELRA 64 (459)
T ss_pred HHHHHHHHHHHHHHHhHHHHHH
Confidence 3356677777777766544443
No 126
>cd07103 ALDH_F5_SSADH_GabD Mitochondrial succinate-semialdehyde dehydrogenase and ALDH family members 5A1 and 5F1-like. Succinate-semialdehyde dehydrogenase, mitochondrial (SSADH, GabD, EC=1.2.1.24) catalyzes the NAD+-dependent oxidation of succinate semialdehyde (SSA) to succinate. This group includes the human aldehyde dehydrogenase family 5 member A1 (ALDH5A1) which is a mitochondrial homotetramer that converts SSA to succinate in the last step of 4-aminobutyric acid (GABA) catabolism. This CD also includes the Arabidopsis SSADH gene product ALDH5F1. Mutations in this gene result in the accumulation of H2O2, suggesting a role in plant defense against the environmental stress of elevated reactive oxygen species.
Probab=38.67 E-value=3.7e+02 Score=25.92 Aligned_cols=15 Identities=0% Similarity=0.016 Sum_probs=8.0
Q ss_pred HHHHHHHHHHHHhCC
Q 024560 22 GDFIMGVFAVFQDLD 36 (266)
Q Consensus 22 ~~ii~~Ly~~f~~~D 36 (266)
.+++.++.+++.+.-
T Consensus 44 ~~~L~~~a~~l~~~~ 58 (451)
T cd07103 44 AAILRRWADLIRERA 58 (451)
T ss_pred HHHHHHHHHHHHHHH
Confidence 445555555555543
No 127
>PRK04690 murD UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional
Probab=38.58 E-value=2.6e+02 Score=27.39 Aligned_cols=93 Identities=17% Similarity=0.099 Sum_probs=49.0
Q ss_pred eeeccCCCCHHHHHHHHHHHHhhhccCCCCCeEEEEecccccchhHhhhhHHHHHHHHHHhhhhhhcccceEEEEeCCCC
Q 024560 144 YAEYSGAPNEEEVLQYARVVIDCATADPDGRKRALLIGGGIANFTDVATTFNGIIRALREKESKLKAARMHIFVRRGGPN 223 (266)
Q Consensus 144 ~lDlgG~a~~~~~~~al~~ll~~~~~d~~v~~vlvni~ggi~~~~~vA~~~~gii~al~~~~~~~~~~~~pvvvrl~G~~ 223 (266)
++|=....+++.+..+++.+ . +. -++.++||..+-.++ +.+++.+.+. . ...++ +-|.+
T Consensus 325 iidDs~ahNp~a~~~al~~~-~----~~----~i~~i~Gg~~k~kd~----~~l~~~l~~~------~-~~~v~-~~g~~ 383 (468)
T PRK04690 325 YVNDSISTTPHASLAALDCF-A----GR----RVALLVGGHDRGLDW----TDFAAHMAQR------A-PLEIV-TMGAN 383 (468)
T ss_pred EEEeCCCCCHHHHHHHHHhc-c----CC----cEEEEEcCCCCCCCH----HHHHHHHHhc------c-CeEEE-EeCCC
Confidence 45544566777777765432 1 21 234467876544332 4566665432 0 11222 23444
Q ss_pred HHHHHHHHHhhhhhcCCceeecCCCCCHHHHHHHHHH
Q 024560 224 YQTGLAKMRALGEELGIPLEVYGPEATMTGICKQAID 260 (266)
Q Consensus 224 ~~~~~~~L~~~~~~~Gip~~~~~~~~~~~eAv~~av~ 260 (266)
.+.+.+.|.+...+.+.++.. +.++++|++.+.+
T Consensus 384 ~~r~~~~l~~~~~~~~~~~~~---~~~~~~Av~~A~~ 417 (468)
T PRK04690 384 GPRIHALLAPLAAAGRFGLHA---ADDLAHAVRLART 417 (468)
T ss_pred HHHHHHHHHhcccccCCceEE---cCCHHHHHHHHHH
Confidence 455555565322122445543 4599999999987
No 128
>PF03709 OKR_DC_1_N: Orn/Lys/Arg decarboxylase, N-terminal domain; InterPro: IPR005308 This domain has a flavodoxin-like fold, and is termed the "wing" domain because of its position in the overall 3D structure. Ornithine decarboxylase from Lactobacillus 30a (L30a OrnDC, P43099 from SWISSPROT) is representative of the large, pyridoxal-5'-phosphate-dependent decarboxylases that act on lysine, arginine or ornithine. The crystal structure of the L30a OrnDC has been solved to 3.0 A resolution. Six dimers related by C6 symmetry compose the enzymatically active dodecamer (approximately 106 Da). Each monomer of L30a OrnDC can be described in terms of five sequential folding domains. The amino-terminal domain, residues 1 to 107, consists of a five-stranded beta-sheet termed the "wing" domain. Two wing domains of each dimer project inward towards the centre of the dodecamer and contribute to dodecamer stabilisation [].; GO: 0016831 carboxy-lyase activity; PDB: 3Q16_C 3N75_A 1C4K_A 1ORD_A 2VYC_D.
Probab=38.41 E-value=1.1e+02 Score=24.03 Aligned_cols=87 Identities=10% Similarity=0.030 Sum_probs=54.7
Q ss_pred HHHHHHHHHhhhccCCCCCeEEEEecccccchhHhhhhHHHHHHHHHHhhhhhhcccceEEEEeCCC-CHHHHHHHHHhh
Q 024560 156 VLQYARVVIDCATADPDGRKRALLIGGGIANFTDVATTFNGIIRALREKESKLKAARMHIFVRRGGP-NYQTGLAKMRAL 234 (266)
Q Consensus 156 ~~~al~~ll~~~~~d~~v~~vlvni~ggi~~~~~vA~~~~gii~al~~~~~~~~~~~~pvvvrl~G~-~~~~~~~~L~~~ 234 (266)
+..++.++-+ ++++.+|++..= ....+.+ .++++.+++.+ .++||++-..-. ...--.+.|.
T Consensus 26 ~dd~~~~i~~----~~~i~avvi~~d---~~~~~~~---~~ll~~i~~~~-----~~iPVFl~~~~~~~~~l~~~~l~-- 88 (115)
T PF03709_consen 26 TDDALAIIES----FTDIAAVVISWD---GEEEDEA---QELLDKIRERN-----FGIPVFLLAERDTTEDLPAEVLG-- 88 (115)
T ss_dssp HHHHHHHHHC----TTTEEEEEEECH---HHHHHHH---HHHHHHHHHHS-----TT-EEEEEESCCHHHCCCHHHHC--
T ss_pred hHHHHHHHHh----CCCeeEEEEEcc---cccchhH---HHHHHHHHHhC-----CCCCEEEEecCCCcccCCHHHHh--
Confidence 4466666766 899999998753 2233555 88999888874 679999744422 1122245555
Q ss_pred hhhcCCc-eeecCCCCCHHHHHHHHHHHhhh
Q 024560 235 GEELGIP-LEVYGPEATMTGICKQAIDCIMS 264 (266)
Q Consensus 235 ~~~~Gip-~~~~~~~~~~~eAv~~av~~~~~ 264 (266)
.+. +.+. ..+|++-.+++....+.+
T Consensus 89 ----~v~~~i~l-~~~t~~fia~rI~~Aa~~ 114 (115)
T PF03709_consen 89 ----EVDGFIWL-FEDTAEFIARRIEAAARR 114 (115)
T ss_dssp ----CESEEEET-TTTTHHHHHHHHHHHHHH
T ss_pred ----hccEEEEe-cCCCHHHHHHHHHHHHHh
Confidence 222 2344 378999988888777653
No 129
>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=38.36 E-value=2.9e+02 Score=24.58 Aligned_cols=123 Identities=12% Similarity=-0.011 Sum_probs=64.2
Q ss_pred CcEEEEecCchHH------HHHHHHHHhcCCCCCCCceeec-cCCCCHHHHHHHHHHHHhhhccCCCCCeEEEEeccccc
Q 024560 113 GRIWTMVAGGGAS------VIYADTVGDLGYASELGNYAEY-SGAPNEEEVLQYARVVIDCATADPDGRKRALLIGGGIA 185 (266)
Q Consensus 113 G~Igii~NGaGla------m~t~D~l~~~g~gg~pAN~lDl-gG~a~~~~~~~al~~ll~~~~~d~~v~~vlvni~ggi~ 185 (266)
++|++++...... ....+.+..+ |..+-+.+.+ -++.+.+.-+++++-+|+ ++|++++++..
T Consensus 124 ~~I~~l~g~~~~~~~~~R~~Gf~~~l~~~--g~~~~~~~~~~~~~~~~~~~~~~~~~~l~---~~~~~~ai~~~------ 192 (298)
T cd06302 124 GEYAIFVGSLTATNQNAWIDAAKAYQKEK--YYPMLELVDRQYGDDDADKSYQTAQELLK---AYPDLKGIIGP------ 192 (298)
T ss_pred CEEEEEeCCCCCcchHHHHHHHHHHHhhc--CCCCeEEeCcccCCCCHHHHHHHHHHHHH---hCCCceEEEEC------
Confidence 5888886433211 1224555565 3222233222 344455555555555553 26777777742
Q ss_pred chhHhhhhHHHHHHHHHHhhhhhhcccceEEEEeCCCCHHHHHHHHHhhhhhcCCceeecCCCCCHHHHHHHHHHHhh
Q 024560 186 NFTDVATTFNGIIRALREKESKLKAARMHIFVRRGGPNYQTGLAKMRALGEELGIPLEVYGPEATMTGICKQAIDCIM 263 (266)
Q Consensus 186 ~~~~vA~~~~gii~al~~~~~~~~~~~~pvvvrl~G~~~~~~~~~L~~~~~~~Gip~~~~~~~~~~~eAv~~av~~~~ 263 (266)
++..| .++++++++.+.. .++.| +-. .+.....+.+. .-.+...+ ..++.+..+.+++++.
T Consensus 193 -~D~~A---~g~~~al~~~g~~---~dv~v-vG~--D~~~~~~~~~~----~g~i~~tv---~~~~~~~g~~a~~~l~ 253 (298)
T cd06302 193 -TSVGI---PGAARAVEEAGLK---GKVAV-TGL--GLPNQMAPYVK----SGAVKEFA---LWNPADLGYAAVYVAK 253 (298)
T ss_pred -CCcch---hHHHHHHHhcCCC---CCEEE-EEe--CCCHHHHHHHh----CCeeEEEE---ecCHHHHHHHHHHHHH
Confidence 46677 9999999987521 12222 323 33445566666 21243322 2367777777766653
No 130
>COG0769 MurE UDP-N-acetylmuramyl tripeptide synthase [Cell envelope biogenesis, outer membrane]
Probab=38.28 E-value=1.2e+02 Score=30.19 Aligned_cols=103 Identities=17% Similarity=0.164 Sum_probs=62.7
Q ss_pred ceeeccCCCCHHHHHHHHHHHHhhhccCCCCCeEEEEecccccchhHhhhhHHHHHHHHHHhhhhhhcccceEEEEeCCC
Q 024560 143 NYAEYSGAPNEEEVLQYARVVIDCATADPDGRKRALLIGGGIANFTDVATTFNGIIRALREKESKLKAARMHIFVRRGGP 222 (266)
Q Consensus 143 N~lDlgG~a~~~~~~~al~~ll~~~~~d~~v~~vlvni~ggi~~~~~vA~~~~gii~al~~~~~~~~~~~~pvvvrl~G~ 222 (266)
-++|+-- +|+.+.++++.+-. ..+.+.++|| |...+-|..- +-++..+.+.. .+ -+++--.++
T Consensus 335 v~VDyAH--nPd~le~~L~~~~~----~~~g~li~Vf--G~gGDrD~~k---r~~mg~ia~~~-----ad-~vivt~dnp 397 (475)
T COG0769 335 VIVDYAH--NPDGLEKALRAVRL----HAAGRLIVVF--GCGGDRDKSK---RPDMGAIAEQL-----AD-IVIVTSDNP 397 (475)
T ss_pred EEEEecc--ChHHHHHHHHHHHh----hcCCcEEEEE--CccCCCCccc---ccchHHHHHhc-----CC-cEEEcCCCC
Confidence 3455555 45678899888863 3445544444 4444445544 55555444331 12 244567788
Q ss_pred CHHHHHHHHHhhhhhcCCceee-cCCCCCHHHHHHHHHHHhhh
Q 024560 223 NYQTGLAKMRALGEELGIPLEV-YGPEATMTGICKQAIDCIMS 264 (266)
Q Consensus 223 ~~~~~~~~L~~~~~~~Gip~~~-~~~~~~~~eAv~~av~~~~~ 264 (266)
+.++-..++++. ..|++... |....+-.+|++++++.++.
T Consensus 398 R~edp~~i~~~i--~~g~~~~~~~~~~~dr~~AI~~ai~~a~~ 438 (475)
T COG0769 398 RSEDPAVILADI--LAGIEAPEKYEIIEDREEAIRKALDLAKE 438 (475)
T ss_pred CCcCHHHHHHHH--HhccCCccceecchhHHHHHHHHHHhhcc
Confidence 888888899877 44655210 22245889999999999873
No 131
>PRK00208 thiG thiazole synthase; Reviewed
Probab=38.26 E-value=54 Score=30.07 Aligned_cols=80 Identities=14% Similarity=0.055 Sum_probs=48.2
Q ss_pred ccCceEecCCCc-EEEEecCchHHHHHHHHHHhcCCCCCCCceeeccCCC-CHHHHHHHHHHHHhhhccCCCCCeEEEEe
Q 024560 103 SLKFTVLNPKGR-IWTMVAGGGASVIYADTVGDLGYASELGNYAEYSGAP-NEEEVLQYARVVIDCATADPDGRKRALLI 180 (266)
Q Consensus 103 ~~~l~~v~l~G~-Igii~NGaGlam~t~D~l~~~g~gg~pAN~lDlgG~a-~~~~~~~al~~ll~~~~~d~~v~~vlvni 180 (266)
..|-.+|-+-|. || .|.| +...|.+... --.+..++-.+|+. +++.++++++ -+.++|+||
T Consensus 142 ~~G~~~vmPlg~pIG---sg~g--i~~~~~i~~i--~e~~~vpVIveaGI~tpeda~~Ame---------lGAdgVlV~- 204 (250)
T PRK00208 142 EAGCAAVMPLGAPIG---SGLG--LLNPYNLRII--IEQADVPVIVDAGIGTPSDAAQAME---------LGADAVLLN- 204 (250)
T ss_pred HcCCCEeCCCCcCCC---CCCC--CCCHHHHHHH--HHhcCCeEEEeCCCCCHHHHHHHHH---------cCCCEEEEC-
Confidence 445566654333 44 3344 4446666555 23344566665554 6788888844 356789988
Q ss_pred cccccc---hhHhhhhHHHHHHHHHH
Q 024560 181 GGGIAN---FTDVATTFNGIIRALRE 203 (266)
Q Consensus 181 ~ggi~~---~~~vA~~~~gii~al~~ 203 (266)
++|++ ...+| +++..+++.
T Consensus 205 -SAItka~dP~~ma---~af~~Av~a 226 (250)
T PRK00208 205 -TAIAVAGDPVAMA---RAFKLAVEA 226 (250)
T ss_pred -hHhhCCCCHHHHH---HHHHHHHHH
Confidence 66777 77777 777777654
No 132
>cd07142 ALDH_F2BC Arabidosis aldehyde dehydrogenase family 2 B4, B7, C4-like. Included in this CD is the Arabidosis aldehyde dehydrogenase family 2 members B4 and B7 (EC=1.2.1.3), which are mitochondrial homotetramers that oxidize acetaldehyde and glycolaldehyde, but not L-lactaldehyde. Also in this group, is the Arabidosis cytosolic, homotetramer ALDH2C4 (EC=1.2.1.3), an enzyme involved in the oxidation of sinapalehyde and coniferaldehyde.
Probab=38.25 E-value=3.4e+02 Score=26.64 Aligned_cols=23 Identities=0% Similarity=0.082 Sum_probs=14.7
Q ss_pred HHHHHHHHHHHHHHhCCceeeEe
Q 024560 20 KIGDFIMGVFAVFQDLDFSFIEM 42 (266)
Q Consensus 20 ~~~~ii~~Ly~~f~~~D~~l~EI 42 (266)
+=.+++.++.+++.+.--.|+++
T Consensus 66 ~R~~~L~~~a~~l~~~~~~la~~ 88 (476)
T cd07142 66 ERSRILLRFADLLEKHADELAAL 88 (476)
T ss_pred HHHHHHHHHHHHHHHhHHHHHHH
Confidence 33567777777777766655553
No 133
>COG0299 PurN Folate-dependent phosphoribosylglycinamide formyltransferase PurN [Nucleotide transport and metabolism]
Probab=38.24 E-value=2e+02 Score=25.49 Aligned_cols=67 Identities=21% Similarity=0.260 Sum_probs=38.5
Q ss_pred EEEecccccchhHhhhhHHHHHHHHHHhhhhhhcccceEEEEeCCCCHHHHHHHHHhhhhhcCCceeecCCCCC-----H
Q 024560 177 ALLIGGGIANFTDVATTFNGIIRALREKESKLKAARMHIFVRRGGPNYQTGLAKMRALGEELGIPLEVYGPEAT-----M 251 (266)
Q Consensus 177 lvni~ggi~~~~~vA~~~~gii~al~~~~~~~~~~~~pvvvrl~G~~~~~~~~~L~~~~~~~Gip~~~~~~~~~-----~ 251 (266)
.|.+.|..+| +|+|+++++... .+.-|..-+.......+++.-+ ++|||+.++..-+. +
T Consensus 4 ~VlaSG~GSN-------lqaiida~~~~~-----~~a~i~~Visd~~~A~~lerA~----~~gIpt~~~~~k~~~~r~~~ 67 (200)
T COG0299 4 AVLASGNGSN-------LQAIIDAIKGGK-----LDAEIVAVISDKADAYALERAA----KAGIPTVVLDRKEFPSREAF 67 (200)
T ss_pred EEEEeCCccc-------HHHHHHHHhcCC-----CCcEEEEEEeCCCCCHHHHHHH----HcCCCEEEeccccCCCHHHH
Confidence 3444455544 488888877421 2333555555554566666666 77999877654433 4
Q ss_pred HHHHHHHH
Q 024560 252 TGICKQAI 259 (266)
Q Consensus 252 ~eAv~~av 259 (266)
++++-..+
T Consensus 68 d~~l~~~l 75 (200)
T COG0299 68 DRALVEAL 75 (200)
T ss_pred HHHHHHHH
Confidence 44444443
No 134
>cd07083 ALDH_P5CDH ALDH subfamily NAD+-dependent delta(1)-pyrroline-5-carboxylate dehydrogenase-like. ALDH subfamily of the NAD+-dependent, delta(1)-pyrroline-5-carboxylate dehydrogenases (P5CDH, EC=1.5.1.12). The proline catabolic enzymes, proline dehydrogenase and P5CDH catalyze the two-step oxidation of proline to glutamate. P5CDH catalyzes the oxidation of glutamate semialdehyde, utilizing NAD+ as the electron acceptor. In some bacteria, the two enzymes are fused into the bifunctional flavoenzyme, proline utilization A (PutA). These enzymes play important roles in cellular redox control, superoxide generation, and apoptosis. In certain prokaryotes such as Escherichia coli, PutA is also a transcriptional repressor of the proline utilization genes. Monofunctional enzyme sequences such as those seen in the Bacillus RocA P5CDH are also present in this subfamily as well as the human ALDH4A1 P5CDH and the Drosophila Aldh17 P5CDH.
Probab=38.19 E-value=3.2e+02 Score=27.06 Aligned_cols=22 Identities=5% Similarity=0.120 Sum_probs=13.2
Q ss_pred HHHHHHHHHHHHHHhCCceeeE
Q 024560 20 KIGDFIMGVFAVFQDLDFSFIE 41 (266)
Q Consensus 20 ~~~~ii~~Ly~~f~~~D~~l~E 41 (266)
+-.+++.++.+++.++--.+++
T Consensus 78 ~R~~~L~~~a~~l~~~~~ela~ 99 (500)
T cd07083 78 DRARLLLKAADLLRRRRRELIA 99 (500)
T ss_pred HHHHHHHHHHHHHHhCHHHHHH
Confidence 3456677777777766544443
No 135
>PLN02419 methylmalonate-semialdehyde dehydrogenase [acylating]
Probab=37.87 E-value=3.5e+02 Score=27.89 Aligned_cols=19 Identities=0% Similarity=-0.066 Sum_probs=10.1
Q ss_pred HHHHHHHHHHHHhCCceee
Q 024560 22 GDFIMGVFAVFQDLDFSFI 40 (266)
Q Consensus 22 ~~ii~~Ly~~f~~~D~~l~ 40 (266)
.+++.++.+++.++--.|.
T Consensus 176 ~~iL~k~a~~L~~~~~ela 194 (604)
T PLN02419 176 QRVMLKFQELIRKNMDKLA 194 (604)
T ss_pred HHHHHHHHHHHHHhHHHHH
Confidence 3456666666655544333
No 136
>PF13407 Peripla_BP_4: Periplasmic binding protein domain; PDB: 3BRS_B 3GBP_A 3GA5_A 1GCG_A 1GCA_A 3H75_A 3D02_A 3L49_B 3EJW_B 3T95_A ....
Probab=37.58 E-value=2.6e+02 Score=23.87 Aligned_cols=119 Identities=16% Similarity=0.148 Sum_probs=65.8
Q ss_pred CcEEEEecCchHHHHH------HHHHHhcCCCCCCCceee--ccCCCCHHHHHHHHHHHHhhhccCCCCCeEEEEecccc
Q 024560 113 GRIWTMVAGGGASVIY------ADTVGDLGYASELGNYAE--YSGAPNEEEVLQYARVVIDCATADPDGRKRALLIGGGI 184 (266)
Q Consensus 113 G~Igii~NGaGlam~t------~D~l~~~g~gg~pAN~lD--lgG~a~~~~~~~al~~ll~~~~~d~~v~~vlvni~ggi 184 (266)
++|++++...+..... .+.+..+ + . -+.+. ...+.+++...+.++-+|. ++| +++|+.
T Consensus 123 ~~v~~~~~~~~~~~~~~r~~g~~~~l~~~--~-~-~~~~~~~~~~~~~~~~a~~~~~~~l~---~~~-~~~i~~------ 188 (257)
T PF13407_consen 123 GKVLILSGSPGNPNTQERLEGFRDALKEY--P-G-VEIVDEYEYTDWDPEDARQAIENLLQ---ANP-VDAIIA------ 188 (257)
T ss_dssp EEEEEEESSTTSHHHHHHHHHHHHHHHHC--T-T-EEEEEEEEECTTSHHHHHHHHHHHHH---HTT-EEEEEE------
T ss_pred ceEEeccCCCCchHHHHHHHHHHHHHhhc--c-e-eeeeeeeeccCCCHHHHHHHHHHhhh---cCC-ceEEEe------
Confidence 7888887666644321 2333332 1 1 11121 2345677777777666665 355 655543
Q ss_pred cchhHhhhhHHHHHHHHHHhhhhhhcccceEEEEeCCCCHHHHHHHHHhhhhhcCCceeecCCCCCHHHHHHHHHHHh
Q 024560 185 ANFTDVATTFNGIIRALREKESKLKAARMHIFVRRGGPNYQTGLAKMRALGEELGIPLEVYGPEATMTGICKQAIDCI 262 (266)
Q Consensus 185 ~~~~~vA~~~~gii~al~~~~~~~~~~~~pvvvrl~G~~~~~~~~~L~~~~~~~Gip~~~~~~~~~~~eAv~~av~~~ 262 (266)
.++..+ .|+++++++.+. .+.+.++=.++ ..+..+.++ +-.+...+. .++.+....+++++
T Consensus 189 -~~~~~~---~g~~~al~~~g~----~~~~~v~g~d~--~~~~~~~i~----~g~~~a~v~---~~~~~~g~~av~~l 249 (257)
T PF13407_consen 189 -CNDGMA---LGAAQALQQAGR----AGKVIVVGFDG--SPEALEAIK----DGNITATVG---QDPYQQGYKAVEAL 249 (257)
T ss_dssp -SSHHHH---HHHHHHHHHTTC----TTTSEEEEEEC--HHHHHHHHH----TTSSSEEEE---E-HHHHHHHHHHHH
T ss_pred -CCChHH---HHHHHHHHHcCC----cccceeecCCC--CHHHHHHHH----CCCCeEEEe---CCHHHHHHHHHHHH
Confidence 255666 899999999753 23444554444 456667777 334543332 37777666666654
No 137
>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=37.57 E-value=2.6e+02 Score=23.79 Aligned_cols=120 Identities=10% Similarity=-0.000 Sum_probs=64.0
Q ss_pred CCcEEEEecCchHHH------HHHHHHHhcCCCCCCCceeeccCCCCHHHHHHHHHHHHhhhccCCCCCeEEEEeccccc
Q 024560 112 KGRIWTMVAGGGASV------IYADTVGDLGYASELGNYAEYSGAPNEEEVLQYARVVIDCATADPDGRKRALLIGGGIA 185 (266)
Q Consensus 112 ~G~Igii~NGaGlam------~t~D~l~~~g~gg~pAN~lDlgG~a~~~~~~~al~~ll~~~~~d~~v~~vlvni~ggi~ 185 (266)
.++|++++....... -..+.+..+ |..+-.+....++.+.+..+++++-+++ ++|++++++..
T Consensus 116 ~~~i~~i~~~~~~~~~~~r~~gf~~~l~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~l~---~~~~~~ai~~~------ 184 (268)
T cd01575 116 YRRIGFLGARMDDTRAQQRLEGFRAALRAA--GLDPPLVVTTPEPSSFALGRELLAELLA---RWPDLDAVFCS------ 184 (268)
T ss_pred CCcEEEecCCCCcccHHHHHHHHHHHHHHc--CCCCCceeEeccCCCHHHHHHHHHHHHh---CCCCCCEEEEC------
Confidence 356888864433111 122344455 3333333333444555666666666664 36788888753
Q ss_pred chhHhhhhHHHHHHHHHHhhhhhhcccce--E-EEEeCCCCHHHHHHHHHhhhhhcCCceeecCCCCCHHHHHHHHHHHh
Q 024560 186 NFTDVATTFNGIIRALREKESKLKAARMH--I-FVRRGGPNYQTGLAKMRALGEELGIPLEVYGPEATMTGICKQAIDCI 262 (266)
Q Consensus 186 ~~~~vA~~~~gii~al~~~~~~~~~~~~p--v-vvrl~G~~~~~~~~~L~~~~~~~Gip~~~~~~~~~~~eAv~~av~~~ 262 (266)
++.+| .++++++++.+ .++| + |+-.++... .. .+. -++.+ ...++++..+.++++.
T Consensus 185 -~d~~a---~~~~~~l~~~g-----~~~p~di~vig~d~~~~--~~-~~~-----~~itt----i~~~~~~~g~~a~~~l 243 (268)
T cd01575 185 -NDDLA---LGALFECQRRG-----ISVPEDIAIAGFGDLEI--AA-ALP-----PALTT----VRTPRREIGRRAAELL 243 (268)
T ss_pred -CcHHH---HHHHHHHHHhC-----CCCCcceEEEecCCchh--hh-ccC-----CCcee----eeCCHHHHHHHHHHHH
Confidence 45667 89999998874 2233 3 345555432 21 111 13332 1347777777777665
Q ss_pred h
Q 024560 263 M 263 (266)
Q Consensus 263 ~ 263 (266)
.
T Consensus 244 ~ 244 (268)
T cd01575 244 L 244 (268)
T ss_pred H
Confidence 3
No 138
>PRK11241 gabD succinate-semialdehyde dehydrogenase I; Provisional
Probab=37.07 E-value=4e+02 Score=26.33 Aligned_cols=19 Identities=5% Similarity=0.163 Sum_probs=9.8
Q ss_pred HHHHHHHHHHHHhCCceee
Q 024560 22 GDFIMGVFAVFQDLDFSFI 40 (266)
Q Consensus 22 ~~ii~~Ly~~f~~~D~~l~ 40 (266)
.+++.++.+++.++--.|+
T Consensus 73 ~~~L~~~a~~l~~~~~ela 91 (482)
T PRK11241 73 ANILRRWFNLMMEHQDDLA 91 (482)
T ss_pred HHHHHHHHHHHHHhHHHHH
Confidence 4455566666555543333
No 139
>TIGR00640 acid_CoA_mut_C methylmalonyl-CoA mutase C-terminal domain. Methylmalonyl-CoA mutase (EC 5.4.99.2) catalyzes a reversible isomerization between L-methylmalonyl-CoA and succinyl-CoA. The enzyme uses an adenosylcobalamin cofactor. It may be a homodimer, as in mitochondrion, or a heterodimer with partially homologous beta chain that does not bind the adenosylcobalamin cofactor, as in Propionibacterium freudenreichii. The most similar archaeal sequences are separate chains, such as AF2215 and AF2219 of Archaeoglobus fulgidus, that correspond roughly to the first 500 and last 130 residues, respectively of known methylmalonyl-CoA mutases. This model describes the C-terminal domain subfamily. In a neighbor-joining tree (methylaspartate mutase S chain as the outgroup), AF2219 branches with a coenzyme B12-dependent enzyme known not to be 5.4.99.2.
Probab=37.01 E-value=1.3e+02 Score=24.57 Aligned_cols=43 Identities=21% Similarity=0.251 Sum_probs=19.7
Q ss_pred EeCCCCHHHHHHHHHhhhhhcCCceeecCCCCCHHHHHHHHHH
Q 024560 218 RRGGPNYQTGLAKMRALGEELGIPLEVYGPEATMTGICKQAID 260 (266)
Q Consensus 218 rl~G~~~~~~~~~L~~~~~~~Gip~~~~~~~~~~~eAv~~av~ 260 (266)
-++|..-+.+..+.....+.+|+.+.--+.+.++++.|+++++
T Consensus 9 ~~g~D~Hd~g~~iv~~~l~~~GfeVi~lg~~~s~e~~v~aa~e 51 (132)
T TIGR00640 9 KMGQDGHDRGAKVIATAYADLGFDVDVGPLFQTPEEIARQAVE 51 (132)
T ss_pred eeCCCccHHHHHHHHHHHHhCCcEEEECCCCCCHHHHHHHHHH
Confidence 4444444444444444444445544444444455555554443
No 140
>cd04728 ThiG Thiazole synthase (ThiG) is the tetrameric enzyme that is involved in the formation of the thiazole moiety of thiamin pyrophosphate, an essential ubiquitous cofactor that plays an important role in carbohydrate and amino acid metabolism. ThiG catalyzes the formation of thiazole from 1-deoxy-D-xylulose 5-phosphate (DXP) and dehydroglycine, with the help of the sulfur carrier protein ThiS that carries the sulfur needed for thiazole assembly on its carboxy terminus (ThiS-COSH).
Probab=36.96 E-value=61 Score=29.69 Aligned_cols=80 Identities=13% Similarity=0.054 Sum_probs=48.9
Q ss_pred ccCceEecCCCc-EEEEecCchHHHHHHHHHHhcCCCCCCCceeeccCCC-CHHHHHHHHHHHHhhhccCCCCCeEEEEe
Q 024560 103 SLKFTVLNPKGR-IWTMVAGGGASVIYADTVGDLGYASELGNYAEYSGAP-NEEEVLQYARVVIDCATADPDGRKRALLI 180 (266)
Q Consensus 103 ~~~l~~v~l~G~-Igii~NGaGlam~t~D~l~~~g~gg~pAN~lDlgG~a-~~~~~~~al~~ll~~~~~d~~v~~vlvni 180 (266)
..|-.+|-+-|. || .|. ++...|.|... -..+..|+-.+|+. +++.++++++ -+.++|++|
T Consensus 142 ~~G~~~vmPlg~pIG---sg~--Gi~~~~~I~~I--~e~~~vpVI~egGI~tpeda~~Ame---------lGAdgVlV~- 204 (248)
T cd04728 142 DAGCAAVMPLGSPIG---SGQ--GLLNPYNLRII--IERADVPVIVDAGIGTPSDAAQAME---------LGADAVLLN- 204 (248)
T ss_pred HcCCCEeCCCCcCCC---CCC--CCCCHHHHHHH--HHhCCCcEEEeCCCCCHHHHHHHHH---------cCCCEEEEC-
Confidence 345566654333 44 334 44456766654 23345567666654 6788888854 356688988
Q ss_pred cccccc---hhHhhhhHHHHHHHHHH
Q 024560 181 GGGIAN---FTDVATTFNGIIRALRE 203 (266)
Q Consensus 181 ~ggi~~---~~~vA~~~~gii~al~~ 203 (266)
++|++ ...++ +++..+++.
T Consensus 205 -SAIt~a~dP~~ma---~af~~Av~a 226 (248)
T cd04728 205 -TAIAKAKDPVAMA---RAFKLAVEA 226 (248)
T ss_pred -hHhcCCCCHHHHH---HHHHHHHHH
Confidence 67777 66677 777777654
No 141
>KOG0237 consensus Glycinamide ribonucleotide synthetase (GARS)/Aminoimidazole ribonucleotide synthetase (AIRS) [Nucleotide transport and metabolism]
Probab=36.89 E-value=1.5e+02 Score=30.86 Aligned_cols=29 Identities=10% Similarity=-0.011 Sum_probs=21.2
Q ss_pred HHhhhhhcCCceeecCCCCCHHHHHHHHH
Q 024560 231 MRALGEELGIPLEVYGPEATMTGICKQAI 259 (266)
Q Consensus 231 L~~~~~~~Gip~~~~~~~~~~~eAv~~av 259 (266)
-+++..+.|||+-.|.+|+++++|-.-..
T Consensus 112 sK~fm~r~~IPTA~y~~ft~~e~a~sfi~ 140 (788)
T KOG0237|consen 112 SKDFMHRHNIPTAKYKTFTDPEEAKSFIQ 140 (788)
T ss_pred HHHHHHhcCCCcceeeeeCCHHHHHHHHH
Confidence 33455578999999999999977765443
No 142
>PRK02228 V-type ATP synthase subunit F; Provisional
Probab=36.86 E-value=2e+02 Score=22.25 Aligned_cols=54 Identities=20% Similarity=0.220 Sum_probs=35.6
Q ss_pred CHHHHHHHHHHHHhhhccCCCCCeEEEEecccccchhHhhhhHHHHHHHHHHhhhhhhcccceEEEEeCCCC
Q 024560 152 NEEEVLQYARVVIDCATADPDGRKRALLIGGGIANFTDVATTFNGIIRALREKESKLKAARMHIFVRRGGPN 223 (266)
Q Consensus 152 ~~~~~~~al~~ll~~~~~d~~v~~vlvni~ggi~~~~~vA~~~~gii~al~~~~~~~~~~~~pvvvrl~G~~ 223 (266)
+++...++++-++. ++++..|+|+ +.++ +-+-+.+++... ....|+++-+.|.+
T Consensus 28 ~~ee~~~~l~~l~~----~~d~gII~It--------e~~~---~~i~e~i~~~~~---~~~~P~ii~IP~~~ 81 (100)
T PRK02228 28 DDEKLDEAVEEVLE----DDDVGILVMH--------DDDL---EKLPRRLRRTLE---ESVEPTVVTLGGGG 81 (100)
T ss_pred CHHHHHHHHHHHhh----CCCEEEEEEe--------hhHh---HhhHHHHHHHHh---cCCCCEEEEECCCc
Confidence 45778888888776 8888877776 2333 445455554221 25699999888744
No 143
>PRK13252 betaine aldehyde dehydrogenase; Provisional
Probab=36.78 E-value=3.9e+02 Score=26.28 Aligned_cols=20 Identities=0% Similarity=0.124 Sum_probs=10.8
Q ss_pred HHHHHHHHHHHHhCCceeeE
Q 024560 22 GDFIMGVFAVFQDLDFSFIE 41 (266)
Q Consensus 22 ~~ii~~Ly~~f~~~D~~l~E 41 (266)
.+++.++.+++.++--.+++
T Consensus 69 ~~~L~~~a~~l~~~~~ela~ 88 (488)
T PRK13252 69 SRILRRAVDILRERNDELAA 88 (488)
T ss_pred HHHHHHHHHHHHHhHHHHHH
Confidence 45566666666655444443
No 144
>PRK09526 lacI lac repressor; Reviewed
Probab=36.73 E-value=3.2e+02 Score=24.61 Aligned_cols=76 Identities=16% Similarity=0.113 Sum_probs=42.6
Q ss_pred CcEEEEecCchHH------HHHHHHHHhcCCCCCCCceeeccCCCCHHHHHHHHHHHHhhhccCCCCCeEEEEecccccc
Q 024560 113 GRIWTMVAGGGAS------VIYADTVGDLGYASELGNYAEYSGAPNEEEVLQYARVVIDCATADPDGRKRALLIGGGIAN 186 (266)
Q Consensus 113 G~Igii~NGaGla------m~t~D~l~~~g~gg~pAN~lDlgG~a~~~~~~~al~~ll~~~~~d~~v~~vlvni~ggi~~ 186 (266)
++|+++++..+.. .-..+.+..+ |-++.. . +.++-+.+.-+++++-++. ..+.+++|+. .
T Consensus 182 ~~I~~l~g~~~~~~~~~R~~Gf~~al~~~--gi~~~~-~-~~~~~~~~~~~~~~~~~l~---~~~~~~ai~~-------~ 247 (342)
T PRK09526 182 QRIALLAGPESSVSARLRLAGWLEYLTDY--QLQPIA-V-REGDWSAMSGYQQTLQMLR---EGPVPSAILV-------A 247 (342)
T ss_pred CeEEEEeCCCccccHHHHHHHHHHHHHHc--CCCcce-E-EeCCCchHHHHHHHHHHhc---CCCCCcEEEE-------c
Confidence 5788886433221 1234566665 343321 2 2244444444444444443 2566777774 3
Q ss_pred hhHhhhhHHHHHHHHHHhh
Q 024560 187 FTDVATTFNGIIRALREKE 205 (266)
Q Consensus 187 ~~~vA~~~~gii~al~~~~ 205 (266)
++.+| .|+++++++++
T Consensus 248 ~d~~A---~g~~~al~~~g 263 (342)
T PRK09526 248 NDQMA---LGVLRALHESG 263 (342)
T ss_pred CcHHH---HHHHHHHHHcC
Confidence 67788 99999999874
No 145
>cd07017 S14_ClpP_2 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. 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 are required for effective levels of protease activ
Probab=36.62 E-value=1.9e+02 Score=24.24 Aligned_cols=75 Identities=9% Similarity=0.008 Sum_probs=41.7
Q ss_pred eeeccCCCCHHHHHHHHHHHHhhhccCCCCC--eEEEEecccccchhHhhhhHHHHHHHHHHhhhhhhcccceEEEEeCC
Q 024560 144 YAEYSGAPNEEEVLQYARVVIDCATADPDGR--KRALLIGGGIANFTDVATTFNGIIRALREKESKLKAARMHIFVRRGG 221 (266)
Q Consensus 144 ~lDlgG~a~~~~~~~al~~ll~~~~~d~~v~--~vlvni~ggi~~~~~vA~~~~gii~al~~~~~~~~~~~~pvvvrl~G 221 (266)
-+-++|..+++........++..-. ++..+ .+.||.|||-. .-+ .+|.+.++.+ +.|+++...|
T Consensus 11 ~i~i~g~I~~~~~~~i~~~l~~~~~-~~~~~~i~l~inSpGG~v---~~~---~~i~~~l~~~-------~~~v~t~~~g 76 (171)
T cd07017 11 IIFLGGPIDDEVANLIIAQLLYLES-EDPKKPIYLYINSPGGSV---TAG---LAIYDTMQYI-------KPPVSTICLG 76 (171)
T ss_pred EEEEcCEEcHHHHHHHHHHHHHHHc-cCCCCceEEEEECCCCCH---HHH---HHHHHHHHhc-------CCCEEEEEEe
Confidence 4556677777666555555543222 33333 45556799843 223 6778887765 4667765556
Q ss_pred CCHHHHHHHHH
Q 024560 222 PNYQTGLAKMR 232 (266)
Q Consensus 222 ~~~~~~~~~L~ 232 (266)
.-.-.|-=++.
T Consensus 77 ~aaS~~~~i~~ 87 (171)
T cd07017 77 LAASMGALLLA 87 (171)
T ss_pred EehhHHHHHHH
Confidence 55555544444
No 146
>TIGR02990 ectoine_eutA ectoine utilization protein EutA. Members of this protein family are EutA, a predicted arylmalonate decarboxylase found in a conserved ectoine utilization operon of species that include Sinorhizobium meliloti 1021 (where it is known to be induced by ectoine), Mesorhizobium loti and Silicibacter pomeroyi. It is missing from two other species with the other ectoine transport and utilization genes: Pseudomonas putida and Agrobacterium tumefaciens.
Probab=36.41 E-value=1.3e+02 Score=27.14 Aligned_cols=65 Identities=15% Similarity=0.107 Sum_probs=42.0
Q ss_pred CCCHHHHHHHHHHHHhhhccCCCCCeEEEEecccccchhHhhhhHHHHHHHHHHhhhhhhcccceEEEEeCCCCHHHHHH
Q 024560 150 APNEEEVLQYARVVIDCATADPDGRKRALLIGGGIANFTDVATTFNGIIRALREKESKLKAARMHIFVRRGGPNYQTGLA 229 (266)
Q Consensus 150 ~a~~~~~~~al~~ll~~~~~d~~v~~vlvni~ggi~~~~~vA~~~~gii~al~~~~~~~~~~~~pvvvrl~G~~~~~~~~ 229 (266)
..+++.++++++-+ . +|+.++||+- .++.- + -.+++.+++. ..+||+. .|..-.+.
T Consensus 164 ~i~p~~i~~~~~~~-~----~~~aDAifis-CTnLr-t-------~~vi~~lE~~------lGkPVls----SNqat~W~ 219 (239)
T TIGR02990 164 RISPDCIVEAALAA-F----DPDADALFLS-CTALR-A-------ATCAQRIEQA------IGKPVVT----SNQATAWR 219 (239)
T ss_pred ecCHHHHHHHHHHh-c----CCCCCEEEEe-CCCch-h-------HHHHHHHHHH------HCCCEEE----HHHHHHHH
Confidence 35778888877666 3 6889999876 22221 1 2344445443 4789886 57778889
Q ss_pred HHHhhhhhcCCce
Q 024560 230 KMRALGEELGIPL 242 (266)
Q Consensus 230 ~L~~~~~~~Gip~ 242 (266)
.|+ .+|++.
T Consensus 220 ~Lr----~~G~~~ 228 (239)
T TIGR02990 220 CLR----LCGDPD 228 (239)
T ss_pred HHH----HcCCCC
Confidence 998 567764
No 147
>TIGR02370 pyl_corrinoid methyltransferase cognate corrinoid proteins, Methanosarcina family. This model describes a subfamily of the B12 binding domain (pfam02607, pfam02310) proteins. Members of the seed alignment include corrinoid proteins specific to four different, mutally non-homologous enzymes of the genus Methanosarcina. Three of the four cognate enzymes (trimethylamine, dimethylamine, and monomethylamine methyltransferases) all have the unusual, ribosomally incorporated amino acid pyrrolysine at the active site. All act in systems in which a methyl group is transferred to the corrinoid protein to create methylcobalamin, from which the methyl group is later transferred elsewhere.
Probab=36.40 E-value=2.1e+02 Score=24.75 Aligned_cols=78 Identities=12% Similarity=0.026 Sum_probs=46.4
Q ss_pred hHHHHHHHHHHhcCCCCCCCceeeccCCCCHHHHHHHHHHHHhhhccCCCCCeEEEEecccccchhHhhhhHHHHHHHHH
Q 024560 123 GASVIYADTVGDLGYASELGNYAEYSGAPNEEEVLQYARVVIDCATADPDGRKRALLIGGGIANFTDVATTFNGIIRALR 202 (266)
Q Consensus 123 Glam~t~D~l~~~g~gg~pAN~lDlgG~a~~~~~~~al~~ll~~~~~d~~v~~vlvni~ggi~~~~~vA~~~~gii~al~ 202 (266)
|+-| ..+++...| -.-+++|-+.+++.+.+++ . ..+.+.|.+... .+..-.- ++-+++.++
T Consensus 100 G~~~-v~~~l~~~G-----~~vi~LG~~vp~e~~v~~~----~----~~~pd~v~lS~~--~~~~~~~---~~~~i~~l~ 160 (197)
T TIGR02370 100 GKNI-VVTMLRANG-----FDVIDLGRDVPIDTVVEKV----K----KEKPLMLTGSAL--MTTTMYG---QKDINDKLK 160 (197)
T ss_pred HHHH-HHHHHHhCC-----cEEEECCCCCCHHHHHHHH----H----HcCCCEEEEccc--cccCHHH---HHHHHHHHH
Confidence 5544 456777763 4668899999999888883 3 345555665532 1222222 266777777
Q ss_pred HhhhhhhcccceEEEEeCCCCH
Q 024560 203 EKESKLKAARMHIFVRRGGPNY 224 (266)
Q Consensus 203 ~~~~~~~~~~~pvvvrl~G~~~ 224 (266)
+.. .+..+-++.||.-.
T Consensus 161 ~~~-----~~~~v~i~vGG~~~ 177 (197)
T TIGR02370 161 EEG-----YRDSVKFMVGGAPV 177 (197)
T ss_pred HcC-----CCCCCEEEEEChhc
Confidence 652 22225567788654
No 148
>PTZ00323 NAD+ synthase; Provisional
Probab=36.30 E-value=2.9e+02 Score=25.80 Aligned_cols=62 Identities=15% Similarity=0.074 Sum_probs=32.2
Q ss_pred CCCCeEEEEecccccchhHhhhhHHHHHHHHHHhhhhhhccc-ceEE-EEeCCCCH----HHHHHHHHhhhhhcCCceee
Q 024560 171 PDGRKRALLIGGGIANFTDVATTFNGIIRALREKESKLKAAR-MHIF-VRRGGPNY----QTGLAKMRALGEELGIPLEV 244 (266)
Q Consensus 171 ~~v~~vlvni~ggi~~~~~vA~~~~gii~al~~~~~~~~~~~-~pvv-vrl~G~~~----~~~~~~L~~~~~~~Gip~~~ 244 (266)
-+.+.++|.+-||+ ++..+| .-..+++.+.. .+ .-++ +.+...+. +.+++.++ ..|++.+.
T Consensus 44 ~g~~~vVVglSGGV-DSav~a---aLa~~alg~~~-----~~~~~~~~v~~P~~ss~~~~~~A~~la~----~lGi~~~~ 110 (294)
T PTZ00323 44 CGLKGCVTSVSGGI-DSAVVL---ALCARAMRMPN-----SPIQKNVGLCQPIHSSAWALNRGRENIQ----ACGATEVT 110 (294)
T ss_pred cCCCcEEEECCCCH-HHHHHH---HHHHHHhcccc-----CCceEEEEEECCCCCCHHHHHHHHHHHH----HhCCcEEE
Confidence 45677777776666 555555 33444444311 11 1122 35553222 44555555 77999765
Q ss_pred c
Q 024560 245 Y 245 (266)
Q Consensus 245 ~ 245 (266)
.
T Consensus 111 i 111 (294)
T PTZ00323 111 V 111 (294)
T ss_pred E
Confidence 4
No 149
>cd07151 ALDH_HBenzADH NADP+-dependent p-hydroxybenzaldehyde dehydrogenase-like. NADP+-dependent, p-hydroxybenzaldehyde dehydrogenase (PchA, HBenzADH) which catalyzes oxidation of p-hydroxybenzaldehyde to p-hydroxybenzoic acid and other related sequences are included in this CD.
Probab=36.20 E-value=4.2e+02 Score=25.84 Aligned_cols=22 Identities=5% Similarity=0.164 Sum_probs=12.8
Q ss_pred HHHHHHHHHHHHHHhCCceeeE
Q 024560 20 KIGDFIMGVFAVFQDLDFSFIE 41 (266)
Q Consensus 20 ~~~~ii~~Ly~~f~~~D~~l~E 41 (266)
+=.+++.++.+++.++--.+++
T Consensus 55 ~R~~~L~~~a~~l~~~~~ela~ 76 (465)
T cd07151 55 ERAEILEKAAQILEERRDEIVE 76 (465)
T ss_pred HHHHHHHHHHHHHHHhHHHHHH
Confidence 3356666677766665544444
No 150
>COG1012 PutA NAD-dependent aldehyde dehydrogenases [Energy production and conversion]
Probab=36.15 E-value=4.1e+02 Score=26.37 Aligned_cols=32 Identities=16% Similarity=0.180 Sum_probs=20.9
Q ss_pred cceEEEEeCCCCHHHHHHHHHhhhhhcCCceeecCCCCCHHHHHHHHHHH
Q 024560 212 RMHIFVRRGGPNYQTGLAKMRALGEELGIPLEVYGPEATMTGICKQAIDC 261 (266)
Q Consensus 212 ~~pvvvrl~G~~~~~~~~~L~~~~~~~Gip~~~~~~~~~~~eAv~~av~~ 261 (266)
-+|+..=|||.+ |..++... +++.||..++.-
T Consensus 236 ~k~~~lELGGk~-----------------p~IV~~dA-dl~~Av~~~~~g 267 (472)
T COG1012 236 LKPVTLELGGKS-----------------PAIVLEDA-DLDAAVDAAVFG 267 (472)
T ss_pred CCcEEEECCCCC-----------------CeEECCCC-CHHHHHHHHHHH
Confidence 466777777744 56667634 777777776653
No 151
>TIGR01780 SSADH succinate-semialdehyde dehydrogenase. SSADH enzyme belongs to the aldehyde dehydrogenase family (pfam00171), sharing a common evolutionary origin and enzymatic mechanism with lactaldehyde dehydrogenase. Like in lactaldehyde dehydrogenase and succinate semialdehyde dehydrogenase, the mammalian catalytic glutamic acid and cysteine residues are conserved in all the enzymes of this family (PS00687, PS00070).
Probab=35.90 E-value=4.2e+02 Score=25.72 Aligned_cols=19 Identities=0% Similarity=0.060 Sum_probs=11.0
Q ss_pred HHHHHHHHHHHHHhCCcee
Q 024560 21 IGDFIMGVFAVFQDLDFSF 39 (266)
Q Consensus 21 ~~~ii~~Ly~~f~~~D~~l 39 (266)
-.+++.++.+++.++--.+
T Consensus 43 R~~~L~~~a~~l~~~~~~l 61 (448)
T TIGR01780 43 RSSLLRKWYNLMMENKDDL 61 (448)
T ss_pred HHHHHHHHHHHHHHhHHHH
Confidence 3556666666666654433
No 152
>PRK14194 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional
Probab=35.70 E-value=3.8e+02 Score=25.19 Aligned_cols=98 Identities=16% Similarity=0.190 Sum_probs=58.6
Q ss_pred eeccCCCCHHHHHHHHHHHHhhhccCCCCCeEEEEe--ccccc---------------------------------chhH
Q 024560 145 AEYSGAPNEEEVLQYARVVIDCATADPDGRKRALLI--GGGIA---------------------------------NFTD 189 (266)
Q Consensus 145 lDlgG~a~~~~~~~al~~ll~~~~~d~~v~~vlvni--~ggi~---------------------------------~~~~ 189 (266)
..+..+.+.+.+.+.++-+-+ ||+|++|+|-. |.++. +|+
T Consensus 68 ~~l~~~~t~~~l~~~I~~lN~----D~~V~GIlvqlPLP~~i~~~~i~~~I~p~KDVDGl~~~N~g~l~~~~~~~~PcT- 142 (301)
T PRK14194 68 HRLPADTSQARLLALIAELNA----DPSVNGILLQLPLPAHIDEARVLQAINPLKDVDGFHSENVGGLSQGRDVLTPCT- 142 (301)
T ss_pred EECCCCCCHHHHHHHHHHHcC----CCCCCeEEEeCCCCCCCCHHHHHhccCchhccCccChhhhhHHhcCCCCCCCCc-
Confidence 466777788877777666555 99999999885 34432 333
Q ss_pred hhhhHHHHHHHHHHhhhhhhcccceEE-EEeCCCCHHHHHHHHHhhhhhcCCceeecC-CCCCHHHHHHH
Q 024560 190 VATTFNGIIRALREKESKLKAARMHIF-VRRGGPNYQTGLAKMRALGEELGIPLEVYG-PEATMTGICKQ 257 (266)
Q Consensus 190 vA~~~~gii~al~~~~~~~~~~~~pvv-vrl~G~~~~~~~~~L~~~~~~~Gip~~~~~-~~~~~~eAv~~ 257 (266)
..|+++-++.+.-.. ..+.|+ +-++|.--..--.+|. +.|.++.++. ...++.++++.
T Consensus 143 ----p~aii~lL~~~~i~l--~Gk~V~vIG~s~ivG~PmA~~L~----~~gatVtv~~~~t~~l~e~~~~ 202 (301)
T PRK14194 143 ----PSGCLRLLEDTCGDL--TGKHAVVIGRSNIVGKPMAALLL----QAHCSVTVVHSRSTDAKALCRQ 202 (301)
T ss_pred ----HHHHHHHHHHhCCCC--CCCEEEEECCCCccHHHHHHHHH----HCCCEEEEECCCCCCHHHHHhc
Confidence 378888877663211 234444 3555544444444555 4588877663 23356666554
No 153
>cd07141 ALDH_F1AB_F2_RALDH1 NAD+-dependent retinal dehydrogenase 1, ALDH families 1A, 1B, and 2-like. NAD+-dependent retinal dehydrogenase 1 (RALDH 1, ALDH1, EC=1.2.1.36) also known as aldehyde dehydrogenase family 1 member A1 (ALDH1A1) in humans, is a homotetrameric, cytosolic enzyme that catalyzes the oxidation of retinaldehyde to retinoic acid. Human ALDH1B1 and ALDH2 are also in this cluster; both are mitochrondrial homotetramers which play important roles in acetaldehyde oxidation; ALDH1B1 in response to UV light exposure and ALDH2 during ethanol metabolism.
Probab=35.52 E-value=4.4e+02 Score=25.87 Aligned_cols=22 Identities=5% Similarity=0.046 Sum_probs=13.1
Q ss_pred HHHHHHHHHHHHHHhCCceeeE
Q 024560 20 KIGDFIMGVFAVFQDLDFSFIE 41 (266)
Q Consensus 20 ~~~~ii~~Ly~~f~~~D~~l~E 41 (266)
+=.+++.++.+++.++--.|++
T Consensus 70 ~R~~~L~~~a~~l~~~~~~la~ 91 (481)
T cd07141 70 ERGRLLNKLADLIERDRAYLAS 91 (481)
T ss_pred HHHHHHHHHHHHHHHhHHHHHH
Confidence 4456667777777666444444
No 154
>cd07125 ALDH_PutA-P5CDH Delta(1)-pyrroline-5-carboxylate dehydrogenase, PutA. The proline catabolic enzymes of the aldehyde dehydrogenase (ALDH) protein superfamily, proline dehydrogenase and Delta(1)-pyrroline-5-carboxylate dehydrogenase (P5CDH, (EC=1.5.1.12 )), catalyze the two-step oxidation of proline to glutamate; P5CDH catalyzes the oxidation of glutamate semialdehyde, utilizing NAD+ as the electron acceptor. In some bacteria, the two enzymes are fused into the bifunctional flavoenzyme, proline utilization A (PutA) These enzymes play important roles in cellular redox control, superoxide generation, and apoptosis. In certain prokaryotes such as Escherichia coli, PutA is also a transcriptional repressor of the proline utilization genes.
Probab=35.22 E-value=3.9e+02 Score=26.62 Aligned_cols=20 Identities=5% Similarity=0.074 Sum_probs=11.0
Q ss_pred HHHHHHHHHHHHhCCceeeE
Q 024560 22 GDFIMGVFAVFQDLDFSFIE 41 (266)
Q Consensus 22 ~~ii~~Ly~~f~~~D~~l~E 41 (266)
.+++.++.+++.++--.+++
T Consensus 94 ~~~L~~~a~~l~~~~~~la~ 113 (518)
T cd07125 94 AEILEKAADLLEANRGELIA 113 (518)
T ss_pred HHHHHHHHHHHHHhHHHHHH
Confidence 45566666666655444443
No 155
>PF01990 ATP-synt_F: ATP synthase (F/14-kDa) subunit; InterPro: IPR008218 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 (e.g., F-, V- and A-ATPases, which contain rotary motors) and in the type of ions they transport [, ]. The different types include: F-ATPases (F1F0-ATPases), which are found in mitochondria, chloroplasts and bacterial plasma membranes where they are the prime producers of ATP, using the proton gradient generated by oxidative phosphorylation (mitochondria) or photosynthesis (chloroplasts). V-ATPases (V1V0-ATPases), which are primarily found in eukaryotic vacuoles and catalyse ATP hydrolysis to transport solutes and lower pH in organelles. A-ATPases (A1A0-ATPases), which are found in Archaea and function like F-ATPases (though with respect to their structure and some inhibitor responses, A-ATPases are more closely related to the V-ATPases). P-ATPases (E1E2-ATPases), which are found in bacteria and in eukaryotic plasma membranes and organelles, and function to transport a variety of different ions across membranes. E-ATPases, which are cell-surface enzymes that hydrolyse a range of NTPs, including extracellular ATP. The V-ATPases (or V1V0-ATPase) and A-ATPases (or A1A0-ATPase) are each composed of two linked complexes: the V1 or A1 complex contains the catalytic core that hydrolyses/synthesizes ATP, and the V0 or A0 complex that forms the membrane-spanning pore. The V- and A-ATPases both contain rotary motors, one that drives proton translocation across the membrane and one that drives ATP synthesis/hydrolysis [, , ]. The V- and A-ATPases more closely resemble one another in subunit structure than they do the F-ATPases, although the function of A-ATPases is closer to that of F-ATPases. This entry represents subunit F found in the V1 complex of V-ATPases (both eukaryotic and bacterial), as well as in the A1 complex of A-ATPases. Subunit F is a 16 kDa protein that is required for the assembly and activity of V-ATPase, and has a potential role in the differential targeting and regulation of the enzyme for specific organelles. This subunit is not necessary for the rotation of the ATPase V1 rotor, but it does promote catalysis []. More information about this protein can be found at Protein of the Month: ATP Synthases [].; GO: 0046933 hydrogen ion transporting ATP synthase activity, rotational mechanism, 0046961 proton-transporting ATPase activity, rotational mechanism, 0015991 ATP hydrolysis coupled proton transport, 0033178 proton-transporting two-sector ATPase complex, catalytic domain; PDB: 2D00_E 3A5C_P 3J0J_H 3A5D_H 2OV6_A 2QAI_B 3AON_B 2I4R_A.
Probab=35.20 E-value=1.3e+02 Score=22.80 Aligned_cols=54 Identities=19% Similarity=0.211 Sum_probs=36.8
Q ss_pred CHHHHHHHHHHHHhhhccCCCCCeEEEEecccccchhHhhhhHHHHHHHHHHhhhhhhcccceEEEEeCCCC
Q 024560 152 NEEEVLQYARVVIDCATADPDGRKRALLIGGGIANFTDVATTFNGIIRALREKESKLKAARMHIFVRRGGPN 223 (266)
Q Consensus 152 ~~~~~~~al~~ll~~~~~d~~v~~vlvni~ggi~~~~~vA~~~~gii~al~~~~~~~~~~~~pvvvrl~G~~ 223 (266)
+++...++++-+++ ++++..|++. +.++ +.+-+.+++... ....|+|+-+.+.+
T Consensus 26 ~~ee~~~~l~~l~~----~~~~gIIii~--------e~~~---~~~~~~l~~~~~---~~~~P~iv~IP~~~ 79 (95)
T PF01990_consen 26 DPEEAEEALKELLK----DEDVGIIIIT--------EDLA---EKIRDELDEYRE---ESSLPLIVEIPSKE 79 (95)
T ss_dssp SHHHHHHHHHHHHH----HTTEEEEEEE--------HHHH---TTHHHHHHHHHH---TSSSSEEEEESTTC
T ss_pred CHHHHHHHHHHHhc----CCCccEEEee--------HHHH---HHHHHHHHHHHh---ccCCceEEEcCCCC
Confidence 78899999999987 7888666653 4555 555555555422 24689998776654
No 156
>TIGR01238 D1pyr5carbox3 delta-1-pyrroline-5-carboxylate dehydrogenase (PutA C-terminal domain). This model represents one of several related branches of delta-1-pyrroline-5-carboxylate dehydrogenase. Members of this branch are the C-terminal domain of the PutA bifunctional proline dehydrogenase / delta-1-pyrroline-5-carboxylate dehydrogenase.
Probab=34.69 E-value=4.7e+02 Score=26.04 Aligned_cols=11 Identities=27% Similarity=0.649 Sum_probs=7.1
Q ss_pred ceEEEEeCCCC
Q 024560 213 MHIFVRRGGPN 223 (266)
Q Consensus 213 ~pvvvrl~G~~ 223 (266)
+|++.-+||.|
T Consensus 267 ~~v~lElGGkn 277 (500)
T TIGR01238 267 VPLIAETGGQN 277 (500)
T ss_pred ceEEEecCCcC
Confidence 56666777744
No 157
>PRK00885 phosphoribosylamine--glycine ligase; Provisional
Probab=34.68 E-value=3.9e+02 Score=25.51 Aligned_cols=27 Identities=19% Similarity=0.165 Sum_probs=16.6
Q ss_pred HHHHHHHhhhhhcCCceeecCCCCCHHHHHH
Q 024560 226 TGLAKMRALGEELGIPLEVYGPEATMTGICK 256 (266)
Q Consensus 226 ~~~~~L~~~~~~~Gip~~~~~~~~~~~eAv~ 256 (266)
..++.|+ ++|||+-.|..+.+++++.+
T Consensus 105 ~~k~~l~----~~gip~p~~~~~~~~~~~~~ 131 (420)
T PRK00885 105 FAKDFMA----RYGIPTAAYETFTDAEEALA 131 (420)
T ss_pred HHHHHHH----HcCCCCCCeEEeCCHHHHHH
Confidence 3455566 77998754444567776644
No 158
>cd07090 ALDH_F9_TMBADH NAD+-dependent 4-trimethylaminobutyraldehyde dehydrogenase, ALDH family 9A1. NAD+-dependent, 4-trimethylaminobutyraldehyde dehydrogenase (TMABADH, EC=1.2.1.47), also known as aldehyde dehydrogenase family 9 member A1 (ALDH9A1) in humans, is a cytosolic tetramer which catalyzes the oxidation of gamma-aminobutyraldehyde involved in 4-aminobutyric acid (GABA) biosynthesis and also oxidizes betaine aldehyde (gamma-trimethylaminobutyraldehyde) which is involved in carnitine biosynthesis.
Probab=34.64 E-value=3.4e+02 Score=26.36 Aligned_cols=23 Identities=4% Similarity=0.157 Sum_probs=14.7
Q ss_pred HHHHHHHHHHHHHHhCCceeeEe
Q 024560 20 KIGDFIMGVFAVFQDLDFSFIEM 42 (266)
Q Consensus 20 ~~~~ii~~Ly~~f~~~D~~l~EI 42 (266)
+=.+++.++.+++.+.--.|+++
T Consensus 42 ~R~~~L~~~a~~l~~~~~~la~~ 64 (457)
T cd07090 42 ERGRILRKAADLLRERNDEIARL 64 (457)
T ss_pred HHHHHHHHHHHHHHHhHHHHHHH
Confidence 44667777777777765555553
No 159
>cd06327 PBP1_SBP_like_1 Periplasmic solute-binding domain of active transport proteins that belong to the type I periplasmic binding fold protein family. Periplasmic solute-binding domain of active transport proteins that belong to the type I periplasmic binding fold protein family. Solute binding proteins are the primary specific receptors that initiate uptake of a broad range of solutes, including amino acids, peptides and inorganic ions. The members are predicted to have a similar function to an active transport system for short chain amides and urea by sequence comparison and phylogenetic analysis. Moreover, this binding domain has high sequence identity to the family of hydrophobic amino acid transporters (HAAT), and thus may also be involved in transport of amino acids.
Probab=34.50 E-value=1.8e+02 Score=26.30 Aligned_cols=66 Identities=18% Similarity=0.104 Sum_probs=34.3
Q ss_pred HHHHHHHHHhcCCCCCCCceeeccCCCCHHHHHHHHHHHHhhhccCCCCCeEEEEecccccchhHhhhhHHHHHHHHHHh
Q 024560 125 SVIYADTVGDLGYASELGNYAEYSGAPNEEEVLQYARVVIDCATADPDGRKRALLIGGGIANFTDVATTFNGIIRALREK 204 (266)
Q Consensus 125 am~t~D~l~~~g~gg~pAN~lDlgG~a~~~~~~~al~~ll~~~~~d~~v~~vlvni~ggi~~~~~vA~~~~gii~al~~~ 204 (266)
..+++|.++ .|..|++-.++-.--..++.+..++.+-+++ +.+|.+|+ |..++.. + .++...+++.
T Consensus 24 ~~la~~~iN-ggi~G~~v~l~~~D~~~~p~~a~~~~~~l~~----~~~V~avi----G~~~s~~--~---~a~~~~~~~~ 89 (334)
T cd06327 24 AELAVEDFG-GGVLGRPIELVVADHQNKADVAAAKAREWID----RDGVDMIV----GGPNSAV--A---LAVQEVAREK 89 (334)
T ss_pred HHHHHHHhc-CCccCeEEEEEEecCCCCchHHHHHHHHHHh----hcCceEEE----CCccHHH--H---HHHHHHHHHh
Confidence 455678887 5555666444433333344555566666665 55665444 5543332 3 4444555443
No 160
>PRK11778 putative inner membrane peptidase; Provisional
Probab=33.94 E-value=95 Score=29.57 Aligned_cols=41 Identities=20% Similarity=0.190 Sum_probs=23.6
Q ss_pred CeEEEE--ecccccchhHhhhhHHHHHHHHHHhhhhhhcccceEEEEeCCCCH
Q 024560 174 RKRALL--IGGGIANFTDVATTFNGIIRALREKESKLKAARMHIFVRRGGPNY 224 (266)
Q Consensus 174 ~~vlvn--i~ggi~~~~~vA~~~~gii~al~~~~~~~~~~~~pvvvrl~G~~~ 224 (266)
++|++. .|||.+..-..| ...+..+++ .++||++.+++.-.
T Consensus 124 ~aVvLridSpGG~v~~s~~a---~~~l~~lr~-------~~kpVva~v~~~AA 166 (330)
T PRK11778 124 DEVLLRLESPGGVVHGYGLA---ASQLQRLRD-------AGIPLTVAVDKVAA 166 (330)
T ss_pred CeEEEEEeCCCCchhHHHHH---HHHHHHHHh-------cCCCEEEEECCchh
Confidence 566666 488876543333 222333333 35899988877543
No 161
>cd00953 KDG_aldolase KDG (2-keto-3-deoxygluconate) aldolases found in archaea. This subfamily of enzymes is adapted for high thermostability and shows specificity for non-phosphorylated substrates. The enzyme catalyses the reversible aldol cleavage of 2-keto-3-dexoygluconate to pyruvate and glyceraldehyde, the third step of a modified non-phosphorylated Entner-Doudoroff pathway of glucose oxidation. KDG aldolase shows no significant sequence similarity to microbial 2-keto-3-deoxyphosphogluconate (KDPG) aldolases, and the enzyme shows no activity with glyceraldehyde 3-phosphate as substrate. The enzyme is a tetramer and a member of the DHDPS family of Schiff-base-dependent class I aldolases.
Probab=33.84 E-value=3.7e+02 Score=24.45 Aligned_cols=103 Identities=12% Similarity=0.031 Sum_probs=62.8
Q ss_pred eeeccCCCCHHHHHHHHHHHHhhhccCCCCCeEEEE-ecccccchhHhhhhHHHHHHHHHHhhhhhhcccceEEEEeCCC
Q 024560 144 YAEYSGAPNEEEVLQYARVVIDCATADPDGRKRALL-IGGGIANFTDVATTFNGIIRALREKESKLKAARMHIFVRRGGP 222 (266)
Q Consensus 144 ~lDlgG~a~~~~~~~al~~ll~~~~~d~~v~~vlvn-i~ggi~~~~~vA~~~~gii~al~~~~~~~~~~~~pvvvrl~G~ 222 (266)
|++= |..+.+.+.+-++.+++ .++++++++ ..|-...-+. . --+.+++...+.. + +|++-.|.+
T Consensus 11 Pf~~-g~iD~~~~~~li~~l~~-----~Gv~Gl~~~GstGE~~~Lt~-e-Er~~l~~~~~~~~------~-~vi~gvg~~ 75 (279)
T cd00953 11 PFTG-NKIDKEKFKKHCENLIS-----KGIDYVFVAGTTGLGPSLSF-Q-EKLELLKAYSDIT------D-KVIFQVGSL 75 (279)
T ss_pred CcCC-CCcCHHHHHHHHHHHHH-----cCCcEEEEcccCCCcccCCH-H-HHHHHHHHHHHHc------C-CEEEEeCcC
Confidence 3443 78999999999888885 799999998 4343322221 1 1144555544432 1 377788888
Q ss_pred CHHHHHHHHHhhhhhcCCc------eeecCCCCCHHHHHHHHHHHhh
Q 024560 223 NYQTGLAKMRALGEELGIP------LEVYGPEATMTGICKQAIDCIM 263 (266)
Q Consensus 223 ~~~~~~~~L~~~~~~~Gip------~~~~~~~~~~~eAv~~av~~~~ 263 (266)
+.+++.+..+.. +++|.. -++|. ..+.++.++.+..++.
T Consensus 76 ~~~~ai~~a~~a-~~~Gad~v~v~~P~y~~-~~~~~~i~~yf~~v~~ 120 (279)
T cd00953 76 NLEESIELARAA-KSFGIYAIASLPPYYFP-GIPEEWLIKYFTDISS 120 (279)
T ss_pred CHHHHHHHHHHH-HHcCCCEEEEeCCcCCC-CCCHHHHHHHHHHHHh
Confidence 888888887753 455632 12221 1245666677766553
No 162
>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=33.75 E-value=3.1e+02 Score=23.71 Aligned_cols=65 Identities=17% Similarity=0.145 Sum_probs=38.8
Q ss_pred CCCCHHHHHHHHHHHHhhhccCCCCCeEEEEecccccchhHhhhhHHHHHHHHHHhhhhhhcccceEEEEeCCCCHHHHH
Q 024560 149 GAPNEEEVLQYARVVIDCATADPDGRKRALLIGGGIANFTDVATTFNGIIRALREKESKLKAARMHIFVRRGGPNYQTGL 228 (266)
Q Consensus 149 G~a~~~~~~~al~~ll~~~~~d~~v~~vlvni~ggi~~~~~vA~~~~gii~al~~~~~~~~~~~~pvvvrl~G~~~~~~~ 228 (266)
++-+.+..+++++-++. ..|++++|+.. ++..| .|+++++++++.. .++. |+-.+++ ....
T Consensus 163 ~~~~~~~~~~~~~~~l~---~~~~~~aI~~~-------~d~~a---~g~~~al~~~g~~---~di~-vvg~d~~--~~~~ 223 (271)
T cd06312 163 TGADPTEVASRIAAYLR---ANPDVDAVLTL-------GAPSA---APAAKALKQAGLK---GKVK-LGGFDLS--PATL 223 (271)
T ss_pred cCCCHHHHHHHHHHHHH---hCCCccEEEEe-------CCccc---hHHHHHHHhcCCC---CCeE-EEEecCC--HHHH
Confidence 34455666677666664 25778887765 55667 9999999987521 1333 3344443 4445
Q ss_pred HHHH
Q 024560 229 AKMR 232 (266)
Q Consensus 229 ~~L~ 232 (266)
+.+.
T Consensus 224 ~~l~ 227 (271)
T cd06312 224 QAIK 227 (271)
T ss_pred HHHh
Confidence 5554
No 163
>PF09673 TrbC_Ftype: Type-F conjugative transfer system pilin assembly protein; InterPro: IPR019106 This entry represents TrbC, a protein that is an essential component of the F-type conjugative pilus assembly system (aka type 4 secretion system) for the transfer of plasmid DNA [, ]. The N-terminal portion of these proteins is heterogeneous.
Probab=33.72 E-value=64 Score=25.57 Aligned_cols=45 Identities=11% Similarity=0.109 Sum_probs=33.0
Q ss_pred CCHhhHHHHHc------------CCChhHHHHHHHHHHHHHHHHHhCCce-eeEeecceec
Q 024560 1 MTLDACAPLIA------------TLPLEFRGKIGDFIMGVFAVFQDLDFS-FIEMNPFTLV 48 (266)
Q Consensus 1 ~~~~~~~~l~~------------gl~~~~~~~~~~ii~~Ly~~f~~~D~~-l~EINPLvv~ 48 (266)
||++.+.++++ |+.+. .+.+.+.++-++..+.+-. -++|||....
T Consensus 8 MP~~~L~~l~~~a~~~~~~~V~RG~~~g---~~~~t~~~~~~l~~~~~~~~~v~IdP~~F~ 65 (113)
T PF09673_consen 8 MPDASLRNLLKQAERAGVVVVFRGFPDG---SFKPTAKAIQELLRKDDPCPGVQIDPRLFR 65 (113)
T ss_pred CCHHHHHHHHHHHHhCCcEEEEECCCCC---CHHHHHHHHHHHhhccCCCcceeEChhHHh
Confidence 67777777765 67665 6777777777787777643 7899998873
No 164
>PRK10090 aldehyde dehydrogenase A; Provisional
Probab=33.64 E-value=4.5e+02 Score=25.40 Aligned_cols=72 Identities=14% Similarity=0.185 Sum_probs=36.2
Q ss_pred HHHHHHHHHhcCCCCCCCceeeccCCCCHHHHHHHHHHHHhhhccCCCCCeEEEEecccccchhHhhhhHHHHHHHHHHh
Q 024560 125 SVIYADTVGDLGYASELGNYAEYSGAPNEEEVLQYARVVIDCATADPDGRKRALLIGGGIANFTDVATTFNGIIRALREK 204 (266)
Q Consensus 125 am~t~D~l~~~g~gg~pAN~lDlgG~a~~~~~~~al~~ll~~~~~d~~v~~vlvni~ggi~~~~~vA~~~~gii~al~~~ 204 (266)
+....+++..+ |=|.+.+.+--+...+ + .+.+++ +|.++.|. |.| +..+. +-|.+...++
T Consensus 114 ~~~l~~~~~~a---glP~gv~~~v~g~~~~-~---~~~l~~----~~~v~~V~---ftG---s~~~g---~~v~~~aa~~ 173 (409)
T PRK10090 114 AIAFAKIVDEI---GLPKGVFNLVLGRGET-V---GQELAG----NPKVAMVS---MTG---SVSAG---EKIMAAAAKN 173 (409)
T ss_pred HHHHHHHHHHc---CCCcccEEEEeCCChh-H---HHHHhc----CCCcCEEE---EEC---CHHHH---HHHHHHHHhc
Confidence 34446777766 4566555554332222 2 234455 78887554 333 23333 5555443332
Q ss_pred hhhhhcccceEEEEeCCCC
Q 024560 205 ESKLKAARMHIFVRRGGPN 223 (266)
Q Consensus 205 ~~~~~~~~~pvvvrl~G~~ 223 (266)
-+|++.-+||.|
T Consensus 174 -------~~~~~lElgGk~ 185 (409)
T PRK10090 174 -------ITKVCLELGGKA 185 (409)
T ss_pred -------CCeEEEECCCCC
Confidence 345666666644
No 165
>PF12683 DUF3798: Protein of unknown function (DUF3798); InterPro: IPR024258 This entry represents functionally uncharacterised proteins that are found in bacteria. They are typically between 247 and 417 amino acids in length. Most of the proteins in this entry have an N-terminal lipoprotein attachment site. These proteins have distant similarity to periplasmic ligand binding families suggesting that this family has a similar role.; PDB: 3QI7_A.
Probab=33.57 E-value=47 Score=30.83 Aligned_cols=10 Identities=30% Similarity=0.441 Sum_probs=8.7
Q ss_pred CCCCCeEEEE
Q 024560 170 DPDGRKRALL 179 (266)
Q Consensus 170 d~~v~~vlvn 179 (266)
||++|+|+||
T Consensus 60 Dp~mKaIVv~ 69 (275)
T PF12683_consen 60 DPDMKAIVVS 69 (275)
T ss_dssp -TTEEEEEEE
T ss_pred CCCccEEEEe
Confidence 9999999999
No 166
>COG3958 Transketolase, C-terminal subunit [Carbohydrate transport and metabolism]
Probab=33.46 E-value=1.6e+02 Score=27.80 Aligned_cols=114 Identities=16% Similarity=0.207 Sum_probs=61.7
Q ss_pred ceEecCCCcEEEEecCc--hHHHHHHHHHHhcCCCCCCC--ceeeccCCCCHHHHHHHHHHHHhhhccCCCCCeEEE---
Q 024560 106 FTVLNPKGRIWTMVAGG--GASVIYADTVGDLGYASELG--NYAEYSGAPNEEEVLQYARVVIDCATADPDGRKRAL--- 178 (266)
Q Consensus 106 l~~v~l~G~Igii~NGa--Glam~t~D~l~~~g~gg~pA--N~lDlgG~a~~~~~~~al~~ll~~~~~d~~v~~vlv--- 178 (266)
-+.++.+.+|.+|+||- .-++-+.+.|...| -+.+ |..-+-. .+.+.+.++ .+ .+ +-|+.
T Consensus 186 a~vLrdG~D~tiiA~G~mv~~al~AA~~L~~~G--Isa~Vi~m~tIKP-iD~~~i~~~----A~----~t--~~IvT~Ee 252 (312)
T COG3958 186 ANVLRDGSDLTIIATGVMVAEALEAAEILKKEG--ISAAVINMFTIKP-IDEQAILKA----AR----ET--GRIVTAEE 252 (312)
T ss_pred eeEeecCCceEEEecCcchHHHHHHHHHHHhcC--CCEEEEecCccCC-CCHHHHHHH----Hh----hc--CcEEEEec
Confidence 44555667799999996 44566677777773 3321 2221111 122333333 22 12 22222
Q ss_pred -EecccccchhHhhhhHHHHHHHHHHhhhhhhcccceEEEEeCCCC----HHHHHHHHHhhhhhcCCceeecCCCCCHHH
Q 024560 179 -LIGGGIANFTDVATTFNGIIRALREKESKLKAARMHIFVRRGGPN----YQTGLAKMRALGEELGIPLEVYGPEATMTG 253 (266)
Q Consensus 179 -ni~ggi~~~~~vA~~~~gii~al~~~~~~~~~~~~pvvvrl~G~~----~~~~~~~L~~~~~~~Gip~~~~~~~~~~~e 253 (266)
+|+||+- .+|.+.+.+.. + +-+.|+|-+. .....++|+ ..|+ +++.
T Consensus 253 Hsi~GGlG---------saVAEvlse~~------p-~~~~riGvp~~fg~sg~~~~Ll~----~ygl---------~~~~ 303 (312)
T COG3958 253 HSIIGGLG---------SAVAEVLSENG------P-TPMRRIGVPDTFGRSGKADELLD----YYGL---------DPES 303 (312)
T ss_pred ceeecchh---------HHHHHHHHhcC------C-cceEEecCCchhccccchHHHHH----HhCC---------CHHH
Confidence 3688874 55566666552 2 3345776632 223466666 4476 7788
Q ss_pred HHHHHHHH
Q 024560 254 ICKQAIDC 261 (266)
Q Consensus 254 Av~~av~~ 261 (266)
.++++.++
T Consensus 304 I~~~v~~~ 311 (312)
T COG3958 304 IAARVLEL 311 (312)
T ss_pred HHHHHHhh
Confidence 88888765
No 167
>PRK04308 murD UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional
Probab=33.13 E-value=3.5e+02 Score=26.00 Aligned_cols=90 Identities=19% Similarity=0.154 Sum_probs=47.1
Q ss_pred eeeccCCCCHHHHHHHHHHHHhhhccCCCCCeEEEEecccccchhHhhhhHHHHHHHHHHhhhhhhcccceEEEEeCCCC
Q 024560 144 YAEYSGAPNEEEVLQYARVVIDCATADPDGRKRALLIGGGIANFTDVATTFNGIIRALREKESKLKAARMHIFVRRGGPN 223 (266)
Q Consensus 144 ~lDlgG~a~~~~~~~al~~ll~~~~~d~~v~~vlvni~ggi~~~~~vA~~~~gii~al~~~~~~~~~~~~pvvvrl~G~~ 223 (266)
++|-.-+.+++.+..+++.+ . .+ ++.|+||+....+.. .+.+.+.+. .+ .|+ +-|..
T Consensus 322 ~iDDs~~~n~~s~~~al~~~-~----~~-----~i~IlGg~~~~~~~~----~~~~~l~~~------~~--~vi-l~G~~ 378 (445)
T PRK04308 322 FIDDSKGTNVGATAAAIAGL-Q----NP-----LFVILGGMGKGQDFT----PLRDALAGK------AK--GVF-LIGVD 378 (445)
T ss_pred EEEcCCCCCHHHHHHHHHhC-C----CC-----EEEEeCCCCCCCCHH----HHHHHHHHh------Cc--EEE-EECCC
Confidence 34333346677777775554 1 22 344668775554433 344444332 11 222 23444
Q ss_pred HHHHHHHHHhhhhhcCCceeecCCCCCHHHHHHHHHHHhh
Q 024560 224 YQTGLAKMRALGEELGIPLEVYGPEATMTGICKQAIDCIM 263 (266)
Q Consensus 224 ~~~~~~~L~~~~~~~Gip~~~~~~~~~~~eAv~~av~~~~ 263 (266)
.+.-.+.+. +.+.++.+ +.++++|++.+.+.++
T Consensus 379 ~~~l~~~l~----~~~~~~~~---~~~~e~a~~~~~~~~~ 411 (445)
T PRK04308 379 APQIRRDLD----GCGLNLTD---CATLEEAVQRAYAQAE 411 (445)
T ss_pred HHHHHHHHH----hcCCCeEe---cCCHHHHHHHHHHhCC
Confidence 444444554 33555543 4599999998887654
No 168
>PRK03369 murD UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional
Probab=32.97 E-value=3.8e+02 Score=26.42 Aligned_cols=95 Identities=16% Similarity=0.196 Sum_probs=54.1
Q ss_pred eeeccCCCCHHHHHHHHHHHHhhhccCCCCCeEEEEecccccchhHhhhhHHHHHHHHHHhhhhhhcccceEEEEeCCCC
Q 024560 144 YAEYSGAPNEEEVLQYARVVIDCATADPDGRKRALLIGGGIANFTDVATTFNGIIRALREKESKLKAARMHIFVRRGGPN 223 (266)
Q Consensus 144 ~lDlgG~a~~~~~~~al~~ll~~~~~d~~v~~vlvni~ggi~~~~~vA~~~~gii~al~~~~~~~~~~~~pvvvrl~G~~ 223 (266)
|+|=.++.+++.+..+++.. + + ++.|+||..+..+.. .+++.+++.. +-+++ +|. +
T Consensus 330 iIDDS~AhNp~s~~aal~~~-------~--~--iilI~GG~~k~~d~~----~l~~~l~~~~-------~~vi~-iG~-~ 385 (488)
T PRK03369 330 YVDDSKATNPHAARASILAY-------P--R--VVWIAGGLLKGASVD----ALVAEMASRL-------VGAVL-IGR-D 385 (488)
T ss_pred EEECCCCCCHHHHHHHHHhC-------C--C--eEEEecCcCCCCCHH----HHHHHHhhhe-------eEEEE-EcC-C
Confidence 45544677888888886522 2 2 355789988765544 5666665431 22333 544 4
Q ss_pred HHHHHHHHHhhhhhcCCceeecCC-----------------------------CCCHHHHHHHHHHHhhh
Q 024560 224 YQTGLAKMRALGEELGIPLEVYGP-----------------------------EATMTGICKQAIDCIMS 264 (266)
Q Consensus 224 ~~~~~~~L~~~~~~~Gip~~~~~~-----------------------------~~~~~eAv~~av~~~~~ 264 (266)
...-.+.|.+. ..++|+..+.. +++|++||+.|.++++.
T Consensus 386 ~~~i~~~l~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~av~~a~~~a~~ 453 (488)
T PRK03369 386 RAVVAEALSRH--APDVPVVQVVTGEDAGMPATPEVPVACVTDVADDDGETLGDAVMAAAVAAARRLARP 453 (488)
T ss_pred HHHHHHHHHhc--CCCCCEEEeccccccccccccccccccccccccccccccchhhHHHHHHHHHHhCCC
Confidence 44445555421 02456543310 01699999999987753
No 169
>TIGR00114 lumazine-synth 6,7-dimethyl-8-ribityllumazine synthase. Archaeal members of this family are considered putative, although included in the seed and scoring above the trusted cutoff.
Probab=32.91 E-value=2.8e+02 Score=22.91 Aligned_cols=114 Identities=13% Similarity=0.099 Sum_probs=72.2
Q ss_pred HHHHHHHHHhcCCCCCCCceeeccCCCCHHHHHHHHHHHHhhhccCCCCCeEEEE---ecccccchhHhhhhHHHHHHHH
Q 024560 125 SVIYADTVGDLGYASELGNYAEYSGAPNEEEVLQYARVVIDCATADPDGRKRALL---IGGGIANFTDVATTFNGIIRAL 201 (266)
Q Consensus 125 am~t~D~l~~~g~gg~pAN~lDlgG~a~~~~~~~al~~ll~~~~~d~~v~~vlvn---i~ggi~~~~~vA~~~~gii~al 201 (266)
---+.+.|..+ |-..-| +++---|-.-.+.-+.+.+++ ..+.++++.. |=|....++-|+ +++.+.+
T Consensus 19 ~~ga~~~l~~~--g~~~~~-i~v~~VPGa~EiP~a~~~l~~----~~~~DavI~LG~VIrG~T~H~e~v~---~~v~~gl 88 (138)
T TIGR00114 19 LKGAIDALKRL--GAEVDN-IDVIWVPGAFELPLAVKKLAE----TGKYDAVIALGCVIRGGTPHFEYVA---DEAAKGI 88 (138)
T ss_pred HHHHHHHHHHc--CCCccc-eEEEECCcHHHHHHHHHHHHh----cCCCCEEEEEeeEEeCCCchhHHHH---HHHHHHH
Confidence 33467788887 444443 222222333345566666665 5679998887 348888888888 8888888
Q ss_pred HHhhhhhhcccceEEE-EeCCCCHHHHHHHHHhhhhhcCCceeecCCCCCHHHHHHHHHHHhh
Q 024560 202 REKESKLKAARMHIFV-RRGGPNYQTGLAKMRALGEELGIPLEVYGPEATMTGICKQAIDCIM 263 (266)
Q Consensus 202 ~~~~~~~~~~~~pvvv-rl~G~~~~~~~~~L~~~~~~~Gip~~~~~~~~~~~eAv~~av~~~~ 263 (266)
.+..- ..++||.. -|.-.+.+++...- |... ..-=.||+..++++++
T Consensus 89 ~~~sl---~~~~PV~~GvLt~~~~eQa~~R~-------~~~~-----~nkG~eaA~aal~m~~ 136 (138)
T TIGR00114 89 ADLAL---DYDKPVIFGILTTGTIEQAIERA-------GDKA-----GNKGVEAAVAALEMAK 136 (138)
T ss_pred HHHHh---hhCCCEEEEecCCCCHHHHHHHc-------cccc-----cccHHHHHHHHHHHHh
Confidence 77643 25799986 67777777665433 3111 1255678888887765
No 170
>TIGR00612 ispG_gcpE 1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate synthase. Chlamydial members of the family have a long insert. The family is largely restricted to Bacteria, where it is widely but not universally distributed. No homology can be detected between the GcpE family and other proteins.
Probab=32.71 E-value=1.4e+02 Score=28.67 Aligned_cols=75 Identities=13% Similarity=0.085 Sum_probs=47.1
Q ss_pred HHHHHHHHHhhhccCCCCCeEEEEecccccchhHhhhhHHHHHHHHHHhhhhhhcccceEEEEeCCCCHHHHHHHHHhhh
Q 024560 156 VLQYARVVIDCATADPDGRKRALLIGGGIANFTDVATTFNGIIRALREKESKLKAARMHIFVRRGGPNYQTGLAKMRALG 235 (266)
Q Consensus 156 ~~~al~~ll~~~~~d~~v~~vlvni~ggi~~~~~vA~~~~gii~al~~~~~~~~~~~~pvvvrl~G~~~~~~~~~L~~~~ 235 (266)
|..|+..+ ...++.+=|| ||.|.+-+. ++.|+++.+++ ++| +|.|-+.-.-.++++.
T Consensus 83 ~~lAl~a~------~~g~dkiRIN-PGNig~~e~----v~~vv~~ak~~-------~ip--IRIGVN~GSL~~~~~~--- 139 (346)
T TIGR00612 83 YRLAALAM------AKGVAKVRIN-PGNIGFRER----VRDVVEKARDH-------GKA--MRIGVNHGSLERRLLE--- 139 (346)
T ss_pred cHHHHHHH------HhccCeEEEC-CCCCCCHHH----HHHHHHHHHHC-------CCC--EEEecCCCCCcHHHHH---
Confidence 55565555 3467788888 888876544 35788888775 344 5777665555567777
Q ss_pred hhcCCceeecCCCCCHHHHHHHHHHHh
Q 024560 236 EELGIPLEVYGPEATMTGICKQAIDCI 262 (266)
Q Consensus 236 ~~~Gip~~~~~~~~~~~eAv~~av~~~ 262 (266)
+.|-| +++.-|+.|++.+
T Consensus 140 -kyg~~--------t~eamveSAl~~v 157 (346)
T TIGR00612 140 -KYGDA--------TAEAMVQSALEEA 157 (346)
T ss_pred -HcCCC--------CHHHHHHHHHHHH
Confidence 33532 5566666666554
No 171
>TIGR03175 AllD ureidoglycolate dehydrogenase. This enzyme converts ureidoglycolate to oxalureate in the non-urea-forming catabolism of allantoin (GenProp0687). The pathway has been characterized in E. coli and is observed in the genomes of Entercoccus faecalis and Bacillus licheniformis.
Probab=32.50 E-value=57 Score=31.23 Aligned_cols=66 Identities=11% Similarity=0.054 Sum_probs=35.4
Q ss_pred cccccchhHhhhhHHHHHHHHHHhhhhhhcccceEE-EEeCCCCHHHHHHHHHhhhhhcCCceeecCCCCCHHHHHHHHH
Q 024560 181 GGGIANFTDVATTFNGIIRALREKESKLKAARMHIF-VRRGGPNYQTGLAKMRALGEELGIPLEVYGPEATMTGICKQAI 259 (266)
Q Consensus 181 ~ggi~~~~~vA~~~~gii~al~~~~~~~~~~~~pvv-vrl~G~~~~~~~~~L~~~~~~~Gip~~~~~~~~~~~eAv~~av 259 (266)
|.-..+.++..+.+..+++.++..++ .-+.= ||+.|..+.+.++.-. +.|||+ .....++..+.+|
T Consensus 270 P~~F~~~~~f~~~~~~~~~~~r~~~~-----a~g~~~V~~PGe~e~~~~~~~~----~~GI~l----~~~~~~~L~~la~ 336 (349)
T TIGR03175 270 PAFFTDCELFKKHISQMMQELNSVPP-----AEGFKQVYYPGEDGDLKQKKAD----MEGIEI----VDDIYQYLVSDAV 336 (349)
T ss_pred hHHcCCHHHHHHHHHHHHHHHhcCCC-----CCCCCceECCCcHHHHHHHHHH----ccCCcc----CHHHHHHHHHHHH
Confidence 55554555555334566666665421 11111 6889976666554444 459998 2444454444444
No 172
>cd06340 PBP1_ABC_ligand_binding_like_6 Type I periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type active transport systems that are predicted to be involved in transport of amino acids, peptides, or inorganic ions. This subgroup includes the type I periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type active transport systems that are predicted to be involved in transport of amino acids, peptides, or inorganic ions. This subgroup has high sequence similarity to members of the family of hydrophobic amino acid transporters (HAAT), such as leucine-isoleucine-valine-binding protein (LIVBP); however their ligand specificity has not been determined experimentally.
Probab=32.34 E-value=3.9e+02 Score=24.35 Aligned_cols=94 Identities=6% Similarity=-0.073 Sum_probs=46.6
Q ss_pred HHHHHHHHHhcCC----CCCCCceeeccCCCCHHHHHHHHHHHHhhhccCCCCCeEEEEecccccchhHhhhhHHHHHHH
Q 024560 125 SVIYADTVGDLGY----ASELGNYAEYSGAPNEEEVLQYARVVIDCATADPDGRKRALLIGGGIANFTDVATTFNGIIRA 200 (266)
Q Consensus 125 am~t~D~l~~~g~----gg~pAN~lDlgG~a~~~~~~~al~~ll~~~~~d~~v~~vlvni~ggi~~~~~vA~~~~gii~a 200 (266)
..+++|.++..|. .|++=.++..-...+++...++++-+++ +.++.+|+ |+..+.. + .++...
T Consensus 23 ~~lA~~~iN~~GGi~~i~G~~v~lv~~D~~~~~~~a~~~~~~li~----~~~v~aii----G~~~s~~--~---~a~~~~ 89 (347)
T cd06340 23 AELAVEEINAAGGIKSLGGAKLELVFGDSQGNPDIGATEAERLIT----EEGVVALV----GAYQSAV--T---LAASQV 89 (347)
T ss_pred HHHHHHHHHhcCCccCCCCceEEEEEecCCCCHHHHHHHHHHHhc----cCCceEEe----cccchHh--H---HHHHHH
Confidence 4567899998851 2344333322333355666666666665 55665444 5544332 2 344444
Q ss_pred HHHhhhh----------hhcccceEEEEeCCCCHHHHHHHH
Q 024560 201 LREKESK----------LKAARMHIFVRRGGPNYQTGLAKM 231 (266)
Q Consensus 201 l~~~~~~----------~~~~~~pvvvrl~G~~~~~~~~~L 231 (266)
+++.+-+ +.+...|.+.|+..+....++.+.
T Consensus 90 ~~~~~ip~i~~~~~~~~l~~~~~~~~fr~~p~~~~~~~~~~ 130 (347)
T cd06340 90 AERYGVPFVVDGAVSDSITERGFKYTFRITPHDGMFTRDMF 130 (347)
T ss_pred HHHhCCCEEeccccchHHhhcCCceEEecCCChHHHHHHHH
Confidence 4433200 111223555677666555555443
No 173
>cd01304 FMDH_A Formylmethanofuran dehydrogenase (FMDH) subunit A; Methanogenic bacteria and archea derive the energy for autotrophic growth from methanogenesis, the reduction of CO2 with molecular hydrogen as the electron donor. FMDH catalyzes the first step in methanogenesis, the formyl-methanofuran synthesis. In this step, CO2 is bound to methanofuran and subsequently reduced to the formyl state with electrons derived from hydrogen.
Probab=32.33 E-value=4.5e+02 Score=26.86 Aligned_cols=98 Identities=22% Similarity=0.352 Sum_probs=58.9
Q ss_pred CHHHHHHHHHHHHhhhccCCCCCeEEEEecccccc--------------------hhHhhhhHHHHHHHHHHhhhhhhcc
Q 024560 152 NEEEVLQYARVVIDCATADPDGRKRALLIGGGIAN--------------------FTDVATTFNGIIRALREKESKLKAA 211 (266)
Q Consensus 152 ~~~~~~~al~~ll~~~~~d~~v~~vlvni~ggi~~--------------------~~~vA~~~~gii~al~~~~~~~~~~ 211 (266)
+.++....+..+|+. .+..-..+|| |||+.. +-+|. ++++++.++.+ .
T Consensus 156 ~~~~~~~~vaw~l~~---tk~~giK~vn-pgG~~a~~~~~~~~~~d~~~~~~~vtp~~ii---~~l~~~~~~lg-----~ 223 (541)
T cd01304 156 DMEKLAAYVAWTLKA---SKGYGIKVVN-PGGTEAWGWGQNVLSLDDPVPYFDITPREIL---KGLAEANEELG-----L 223 (541)
T ss_pred CHHHHHHHHHHHHHh---ccceEEEEEC-CCchhhhccCCccccccCCCCCCCCCHHHHH---HHHHHHHHhcC-----C
Confidence 567777777777761 3455566777 555221 23444 66666666653 4
Q ss_pred cceEEEE---eCCC-CHHHHHHHHHhhhhhcCCc--------------eeecCCCC--CHHHHHHHHHHHhhh
Q 024560 212 RMHIFVR---RGGP-NYQTGLAKMRALGEELGIP--------------LEVYGPEA--TMTGICKQAIDCIMS 264 (266)
Q Consensus 212 ~~pvvvr---l~G~-~~~~~~~~L~~~~~~~Gip--------------~~~~~~~~--~~~eAv~~av~~~~~ 264 (266)
+.||=++ ||.+ |.+..++.++-. + |++ .|.|+... +++.+++...+..++
T Consensus 224 ph~iH~h~nnlg~pgn~~~t~~t~~~~-~--~~~~~~~~~~~h~tH~qfhsyg~~~~~~~~s~a~~i~~~~n~ 293 (541)
T cd01304 224 PHSIHVHCNNLGVPGNYETTLETMKAA-E--GVKPDPRRQVLHLTHVQFHSYGGTSWRDFESGAERIADYVNA 293 (541)
T ss_pred ceEEEEccccCCCCCcHHHHHHHHHHh-h--cCCCccccceeEeeeeeEEeeccCCcccHhHHHHHHHHHHHc
Confidence 4566677 8776 677666666621 1 443 24677554 788887777666543
No 174
>COG3660 Predicted nucleoside-diphosphate-sugar epimerase [Cell envelope biogenesis, outer membrane]
Probab=32.33 E-value=2.6e+02 Score=26.38 Aligned_cols=89 Identities=21% Similarity=0.141 Sum_probs=52.0
Q ss_pred EEEecCchHHHHHHHHHHhcCCCCC----------CCceeeccCCCCHHHHHHHHHHHHhhhccCCCCCeEEEEeccccc
Q 024560 116 WTMVAGGGASVIYADTVGDLGYASE----------LGNYAEYSGAPNEEEVLQYARVVIDCATADPDGRKRALLIGGGIA 185 (266)
Q Consensus 116 gii~NGaGlam~t~D~l~~~g~gg~----------pAN~lDlgG~a~~~~~~~al~~ll~~~~~d~~v~~vlvni~ggi~ 185 (266)
-+|+.|.-.+.++.++=+.+ ||- |.|-.|+-=-+.-+.+.. ++ +..-. | +-|.|.+-
T Consensus 73 l~I~aGrrta~l~~~lkk~~--~~~~vVqI~~Prlp~~~fDlvivp~HD~~~~-----~s----~~~~N-i-lpi~Gs~h 139 (329)
T COG3660 73 LIITAGRRTAPLAFYLKKKF--GGIKVVQIQDPRLPYNHFDLVIVPYHDWREE-----LS----DQGPN-I-LPINGSPH 139 (329)
T ss_pred eEEecccchhHHHHHHHHhc--CCceEEEeeCCCCCcccceEEeccchhhhhh-----hh----ccCCc-e-eeccCCCC
Confidence 46788888999999998887 452 578888877776665544 22 22111 1 22446665
Q ss_pred chhHhhhhHHHHHHHHHHhhhhhhcccceEE-EEeCCCC
Q 024560 186 NFTDVATTFNGIIRALREKESKLKAARMHIF-VRRGGPN 223 (266)
Q Consensus 186 ~~~~vA~~~~gii~al~~~~~~~~~~~~pvv-vrl~G~~ 223 (266)
+-+.+- ..+.++..++..+..+|.| |-.||+|
T Consensus 140 ~Vt~~~------lAa~~e~~~~~~p~~rq~vAVlVGg~n 172 (329)
T COG3660 140 NVTSQR------LAALREAFKHLLPLPRQRVAVLVGGNN 172 (329)
T ss_pred cccHHH------hhhhHHHHHhhCCCCCceEEEEecCCC
Confidence 555433 2233333332223566767 5778876
No 175
>cd07085 ALDH_F6_MMSDH Methylmalonate semialdehyde dehydrogenase and ALDH family members 6A1 and 6B2. Methylmalonate semialdehyde dehydrogenase (MMSDH, EC=1.2.1.27) [acylating] from Bacillus subtilis is involved in valine metabolism and catalyses the NAD+- and CoA-dependent oxidation of methylmalonate semialdehyde into propionyl-CoA. Mitochondrial human MMSDH ALDH6A1 and Arabidopsis MMSDH ALDH6B2 are also present in this CD.
Probab=32.15 E-value=4.9e+02 Score=25.45 Aligned_cols=21 Identities=0% Similarity=-0.064 Sum_probs=11.0
Q ss_pred HHHHHHHHHHHHHhCCceeeE
Q 024560 21 IGDFIMGVFAVFQDLDFSFIE 41 (266)
Q Consensus 21 ~~~ii~~Ly~~f~~~D~~l~E 41 (266)
=.+++.++.+++.++--.|++
T Consensus 62 R~~~L~~~a~~l~~~~~el~~ 82 (478)
T cd07085 62 RQQVMFKFRQLLEENLDELAR 82 (478)
T ss_pred HHHHHHHHHHHHHHHHHHHHH
Confidence 345566666666555433433
No 176
>TIGR00736 nifR3_rel_arch TIM-barrel protein, putative. Members of this family show a distant relationship by PSI-BLAST to alpha/beta (TIM) barrel enzymes such as dihydroorotate dehydrogenase and glycolate oxidase. At least two closely related but well-separable families among the bacteria, the nifR3/yhdG family and the yjbN family, share a more distant relationship to this family of shorter, exclusively archaeal proteins.
Probab=32.12 E-value=2.2e+02 Score=25.65 Aligned_cols=22 Identities=9% Similarity=0.015 Sum_probs=14.0
Q ss_pred CHHHHHHHHHHHHhhhccCCCCCeEEEE
Q 024560 152 NEEEVLQYARVVIDCATADPDGRKRALL 179 (266)
Q Consensus 152 ~~~~~~~al~~ll~~~~~d~~v~~vlvn 179 (266)
+++.+.++.+.+. +..++|=||
T Consensus 78 ~~ee~~~~a~~v~------~~~d~IdiN 99 (231)
T TIGR00736 78 DLEEAYDVLLTIA------EHADIIEIN 99 (231)
T ss_pred CHHHHHHHHHHHh------cCCCEEEEE
Confidence 5566777766662 356677777
No 177
>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=32.00 E-value=2.2e+02 Score=25.03 Aligned_cols=77 Identities=17% Similarity=0.125 Sum_probs=43.9
Q ss_pred CcEEEEecCchHH------HHHHHHHHhcCCCCCCCceeeccCCCCHHHHHHHHHHHHhhhccCCCCCeEEEEecccccc
Q 024560 113 GRIWTMVAGGGAS------VIYADTVGDLGYASELGNYAEYSGAPNEEEVLQYARVVIDCATADPDGRKRALLIGGGIAN 186 (266)
Q Consensus 113 G~Igii~NGaGla------m~t~D~l~~~g~gg~pAN~lDlgG~a~~~~~~~al~~ll~~~~~d~~v~~vlvni~ggi~~ 186 (266)
.+|++++...... -...+++..+ |..+ ....+.+..+.+.-+++++-+++ +.|.+++|+..
T Consensus 119 ~~I~~i~~~~~~~~~~~R~~gf~~a~~~~--g~~~-~~~~~~~~~~~~~~~~~~~~~l~---~~~~~~ai~~~------- 185 (269)
T cd06287 119 RQIALIVGSARRNSYLEAEAAYRAFAAEH--GMPP-VVLRVDEAGGEEAGYAACAQLLA---QHPDLDALCVP------- 185 (269)
T ss_pred CcEEEEeCCcccccHHHHHHHHHHHHHHc--CCCc-ceeEecCCCChHHHHHHHHHHHh---CCCCCCEEEEc-------
Confidence 4788886332211 1134455555 3333 23333444444444555555554 24567887743
Q ss_pred hhHhhhhHHHHHHHHHHhh
Q 024560 187 FTDVATTFNGIIRALREKE 205 (266)
Q Consensus 187 ~~~vA~~~~gii~al~~~~ 205 (266)
++.+| .|+++++++.+
T Consensus 186 ~d~~A---~gvl~al~~~g 201 (269)
T cd06287 186 VDAFA---VGAVRAATELG 201 (269)
T ss_pred CcHHH---HHHHHHHHHcC
Confidence 77888 99999999874
No 178
>PRK13602 putative ribosomal protein L7Ae-like; Provisional
Probab=31.90 E-value=1.7e+02 Score=21.82 Aligned_cols=38 Identities=21% Similarity=0.140 Sum_probs=28.4
Q ss_pred ceEEEEeCCCCHHHHHHHHHhhhhhcCCceeecCCCCCHHH
Q 024560 213 MHIFVRRGGPNYQTGLAKMRALGEELGIPLEVYGPEATMTG 253 (266)
Q Consensus 213 ~pvvvrl~G~~~~~~~~~L~~~~~~~Gip~~~~~~~~~~~e 253 (266)
..-+|-+..+-.+.-++.+.+.+++.++|++.|+ |.+|
T Consensus 27 kaklViiA~D~~~~~~~~i~~~c~~~~Vp~~~~~---s~~e 64 (82)
T PRK13602 27 SVKEVVVAEDADPRLTEKVEALANEKGVPVSKVD---SMKK 64 (82)
T ss_pred CeeEEEEECCCCHHHHHHHHHHHHHcCCCEEEEC---CHHH
Confidence 3345566777667788889888889999998765 6655
No 179
>cd07150 ALDH_VaniDH_like Pseudomonas putida vanillin dehydrogenase-like. Vanillin dehydrogenase (Vdh, VaniDH) involved in the metabolism of ferulic acid and other related sequences are included in this CD. The E. coli vanillin dehydrogenase (LigV) preferred NAD+ to NADP+ and exhibited a broad substrate preference, including vanillin, benzaldehyde, protocatechualdehyde, m-anisaldehyde, and p-hydroxybenzaldehyde.
Probab=31.84 E-value=4.8e+02 Score=25.18 Aligned_cols=23 Identities=4% Similarity=0.177 Sum_probs=13.5
Q ss_pred HHHHHHHHHHHHHHhCCceeeEe
Q 024560 20 KIGDFIMGVFAVFQDLDFSFIEM 42 (266)
Q Consensus 20 ~~~~ii~~Ly~~f~~~D~~l~EI 42 (266)
+-.+++.++.+++.++--.+.++
T Consensus 44 ~R~~~L~~~a~~l~~~~~ela~~ 66 (451)
T cd07150 44 ERERILLKAAEIMERRADDLIDL 66 (451)
T ss_pred HHHHHHHHHHHHHHHhHHHHHHH
Confidence 33566667777776665444443
No 180
>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=31.28 E-value=3.3e+02 Score=23.20 Aligned_cols=120 Identities=10% Similarity=0.049 Sum_probs=60.9
Q ss_pred CCcEEEEecCch---HH----HHHHHHHHhcCCCCCCCceeeccCCCCHHHHHHHHHHHHhhhccCCCCCeEEEEecccc
Q 024560 112 KGRIWTMVAGGG---AS----VIYADTVGDLGYASELGNYAEYSGAPNEEEVLQYARVVIDCATADPDGRKRALLIGGGI 184 (266)
Q Consensus 112 ~G~Igii~NGaG---la----m~t~D~l~~~g~gg~pAN~lDlgG~a~~~~~~~al~~ll~~~~~d~~v~~vlvni~ggi 184 (266)
.++|++++.... .+ --..+.+..+ |...-+..-+.++.+.+...+.++-+++ +.+..++|+..
T Consensus 116 ~~~i~~i~~~~~~~~~~~~r~~gf~~~l~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~l~---~~~~~~ai~~~----- 185 (268)
T cd06273 116 HRRIAMIFGPTQGNDRARARRAGVRAALAEA--GLELPELWQVEAPYSIADGRAALRQLLE---QPPRPTAVICG----- 185 (268)
T ss_pred CCeEEEEeccccCCccHHHHHHHHHHHHHHc--CCCCCHHHeeeCCCcHHHHHHHHHHHHc---CCCCCCEEEEc-----
Confidence 357898863221 11 1123455555 3332221122334444444555554443 25677877752
Q ss_pred cchhHhhhhHHHHHHHHHHhhhhhhcccce--E-EEEeCCCCHHHHHHHHHhhhhhcCCceeecCCCCCHHHHHHHHHHH
Q 024560 185 ANFTDVATTFNGIIRALREKESKLKAARMH--I-FVRRGGPNYQTGLAKMRALGEELGIPLEVYGPEATMTGICKQAIDC 261 (266)
Q Consensus 185 ~~~~~vA~~~~gii~al~~~~~~~~~~~~p--v-vvrl~G~~~~~~~~~L~~~~~~~Gip~~~~~~~~~~~eAv~~av~~ 261 (266)
++..| .++++++++.+ .++| | |+-.++ ...+.. +. -++.+ ...++++.++.++++
T Consensus 186 --~~~~a---~~~~~~l~~~g-----~~~p~~i~vig~d~--~~~~~~-~~-----~~l~~----i~~~~~~~g~~a~~~ 243 (268)
T cd06273 186 --NDVLA---LGALYEARRLG-----LSVPEDLSIVGFDD--IDGSAE-LE-----PALTT----VRVPAREIGRIAAEA 243 (268)
T ss_pred --ChHHH---HHHHHHHHHcC-----CCCCCceEEEecCC--hhHHhh-cC-----CCcee----eeCCHHHHHHHHHHH
Confidence 56667 89999998874 2333 2 233333 233322 22 14433 144788888888876
Q ss_pred hh
Q 024560 262 IM 263 (266)
Q Consensus 262 ~~ 263 (266)
+.
T Consensus 244 l~ 245 (268)
T cd06273 244 LL 245 (268)
T ss_pred HH
Confidence 53
No 181
>COG1609 PurR Transcriptional regulators [Transcription]
Probab=31.26 E-value=4.3e+02 Score=24.50 Aligned_cols=77 Identities=18% Similarity=0.095 Sum_probs=49.4
Q ss_pred CcEEEEecCc-hHH-----HHHHHHHHhcCCCCCC-CceeeccCCCCHHHHHHHHHHHHhhhccCCC-CCeEEEEecccc
Q 024560 113 GRIWTMVAGG-GAS-----VIYADTVGDLGYASEL-GNYAEYSGAPNEEEVLQYARVVIDCATADPD-GRKRALLIGGGI 184 (266)
Q Consensus 113 G~Igii~NGa-Gla-----m~t~D~l~~~g~gg~p-AN~lDlgG~a~~~~~~~al~~ll~~~~~d~~-v~~vlvni~ggi 184 (266)
.+|++++.+. ..+ --..+.+..+ |..+ ..++- -|+.+.+..+++++-++.. .+. .++||..
T Consensus 176 ~~i~~i~~~~~~~~~~~R~~Gf~~al~~~--~~~~~~~~i~-~~~~~~~~g~~~~~~ll~~---~~~~ptAif~~----- 244 (333)
T COG1609 176 RRIAFIGGPLDSSASRERLEGYRAALREA--GLPINPEWIV-EGDFSEESGYEAAERLLAR---GEPRPTAIFCA----- 244 (333)
T ss_pred ceEEEEeCCCccccHhHHHHHHHHHHHHC--CCCCCcceEE-ecCCChHHHHHHHHHHHhc---CCCCCcEEEEc-----
Confidence 4589987773 222 2345777777 4554 34443 3444666677776666651 333 7888853
Q ss_pred cchhHhhhhHHHHHHHHHHhh
Q 024560 185 ANFTDVATTFNGIIRALREKE 205 (266)
Q Consensus 185 ~~~~~vA~~~~gii~al~~~~ 205 (266)
+|.+| -|+++++++.+
T Consensus 245 --nD~~A---lg~l~~~~~~g 260 (333)
T COG1609 245 --NDLMA---LGALRALRELG 260 (333)
T ss_pred --CcHHH---HHHHHHHHHcC
Confidence 78899 99999999874
No 182
>cd00954 NAL N-Acetylneuraminic acid aldolase, also called N-acetylneuraminate lyase (NAL), which catalyses the reversible aldol reaction of N-acetyl-D-mannosamine and pyruvate to give N-acetyl-D-neuraminic acid (D-sialic acid). It has a widespread application as biocatalyst for the synthesis of sialic acid and its derivatives. This enzyme has been shown to be quite specific for pyruvate as the donor, but flexible to a variety of D- and, to some extent, L-hexoses and pentoses as acceptor substrates. NAL is member of dihydrodipicolinate synthase family that comprises several pyruvate-dependent class I aldolases.
Probab=31.24 E-value=4e+02 Score=24.17 Aligned_cols=109 Identities=16% Similarity=0.134 Sum_probs=67.8
Q ss_pred ceeeccCCCCHHHHHHHHHHHHhhhccCC-CCCeEEEEecccccchhHhhhhHHHHHHHHHHhhhhhhcccceEEEEeCC
Q 024560 143 NYAEYSGAPNEEEVLQYARVVIDCATADP-DGRKRALLIGGGIANFTDVATTFNGIIRALREKESKLKAARMHIFVRRGG 221 (266)
Q Consensus 143 N~lDlgG~a~~~~~~~al~~ll~~~~~d~-~v~~vlvni~ggi~~~~~vA~~~~gii~al~~~~~~~~~~~~pvvvrl~G 221 (266)
-|++=-|..+.+.+.+-++.+++ . ++++++++-..|-...-...+ -+-++++..+.. ..++||++-.+.
T Consensus 10 TPf~~dg~iD~~~~~~~i~~l~~-----~~Gv~gi~~~GstGE~~~Lt~~E-r~~~~~~~~~~~----~~~~~viagv~~ 79 (288)
T cd00954 10 TPFDENGEINEDVLRAIVDYLIE-----KQGVDGLYVNGSTGEGFLLSVEE-RKQIAEIVAEAA----KGKVTLIAHVGS 79 (288)
T ss_pred CCCCCCCCCCHHHHHHHHHHHHh-----cCCCCEEEECcCCcCcccCCHHH-HHHHHHHHHHHh----CCCCeEEeccCC
Confidence 45555678899999999888885 5 899999984333222222221 133444444432 136899998888
Q ss_pred CCHHHHHHHHHhhhhhcCCce------eecCCCCCHHHHHHHHHHHhhh
Q 024560 222 PNYQTGLAKMRALGEELGIPL------EVYGPEATMTGICKQAIDCIMS 264 (266)
Q Consensus 222 ~~~~~~~~~L~~~~~~~Gip~------~~~~~~~~~~eAv~~av~~~~~ 264 (266)
++.+++.+..+. ++++|... +++ -.+.++.++.+-.++.+
T Consensus 80 ~~~~~ai~~a~~-a~~~Gad~v~~~~P~y~--~~~~~~i~~~~~~v~~a 125 (288)
T cd00954 80 LNLKESQELAKH-AEELGYDAISAITPFYY--KFSFEEIKDYYREIIAA 125 (288)
T ss_pred CCHHHHHHHHHH-HHHcCCCEEEEeCCCCC--CCCHHHHHHHHHHHHHh
Confidence 888888777664 24556332 222 13667788877777654
No 183
>KOG3432 consensus Vacuolar H+-ATPase V1 sector, subunit F [Energy production and conversion]
Probab=31.07 E-value=1.3e+02 Score=24.26 Aligned_cols=35 Identities=11% Similarity=-0.017 Sum_probs=30.3
Q ss_pred CceeeccCCCCHHHHHHHHHHHHhhhccCCCCCeEEEEe
Q 024560 142 GNYAEYSGAPNEEEVLQYARVVIDCATADPDGRKRALLI 180 (266)
Q Consensus 142 AN~lDlgG~a~~~~~~~al~~ll~~~~~d~~v~~vlvni 180 (266)
-||+-+--..+.+.+.++++-.++ -+++..||||.
T Consensus 36 ~Nf~vv~~~Tt~~eiedaF~~f~~----RdDIaIiLInq 70 (121)
T KOG3432|consen 36 PNFLVVDSKTTVEEIEDAFKSFTA----RDDIAIILINQ 70 (121)
T ss_pred CCEEEEeccCCHHHHHHHHHhhcc----ccCeEEEEEhH
Confidence 699999999999999999888877 67888888773
No 184
>TIGR01037 pyrD_sub1_fam dihydroorotate dehydrogenase (subfamily 1) family protein. This family includes subfamily 1 dihydroorotate dehydrogenases while excluding the closely related subfamily 2 (TIGR01036). This family also includes a number of uncharacterized proteins and a domain of dihydropyrimidine dehydrogenase. The uncharacterized proteins might all be dihydroorotate dehydrogenase.
Probab=30.93 E-value=4.1e+02 Score=24.14 Aligned_cols=80 Identities=15% Similarity=0.185 Sum_probs=45.5
Q ss_pred eccCCCCHHHHHHHHHHHHhhhccC-CCCCeEEEEeccccc--------chhHhhhhHHHHHHHHHHhhhhhhcccceEE
Q 024560 146 EYSGAPNEEEVLQYARVVIDCATAD-PDGRKRALLIGGGIA--------NFTDVATTFNGIIRALREKESKLKAARMHIF 216 (266)
Q Consensus 146 DlgG~a~~~~~~~al~~ll~~~~~d-~~v~~vlvni~ggi~--------~~~~vA~~~~gii~al~~~~~~~~~~~~pvv 216 (266)
.+.| .+++.+.++.+.+-+ - +..+++-+|+..-.. ...+.. .-|++++++. .++||.
T Consensus 96 qi~g-~~~~~~~~~a~~~~~----~~~~~d~ielN~~cP~~~~~g~~l~~~~~~~---~eiv~~vr~~------~~~pv~ 161 (300)
T TIGR01037 96 SVYG-SSVEEFAEVAEKLEK----APPYVDAYELNLSCPHVKGGGIAIGQDPELS---ADVVKAVKDK------TDVPVF 161 (300)
T ss_pred Eeec-CCHHHHHHHHHHHHh----ccCccCEEEEECCCCCCCCCccccccCHHHH---HHHHHHHHHh------cCCCEE
Confidence 4444 457788888888754 3 458999999421111 111222 4566666654 368999
Q ss_pred EEeCCCCHHHHHHHHHhhhhhcCCc
Q 024560 217 VRRGGPNYQTGLAKMRALGEELGIP 241 (266)
Q Consensus 217 vrl~G~~~~~~~~~L~~~~~~~Gip 241 (266)
+++..+ .++..++.+ .++++|+.
T Consensus 162 vKi~~~-~~~~~~~a~-~l~~~G~d 184 (300)
T TIGR01037 162 AKLSPN-VTDITEIAK-AAEEAGAD 184 (300)
T ss_pred EECCCC-hhhHHHHHH-HHHHcCCC
Confidence 999854 333333332 12256765
No 185
>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=30.73 E-value=3.4e+02 Score=23.17 Aligned_cols=121 Identities=16% Similarity=0.160 Sum_probs=61.6
Q ss_pred CCcEEEEec--CchHHH----HHHHHHHhcCCCCCCCceeec-cCCCCHHHHHHHHHHHHhhhccC-CCCCeEEEEeccc
Q 024560 112 KGRIWTMVA--GGGASV----IYADTVGDLGYASELGNYAEY-SGAPNEEEVLQYARVVIDCATAD-PDGRKRALLIGGG 183 (266)
Q Consensus 112 ~G~Igii~N--GaGlam----~t~D~l~~~g~gg~pAN~lDl-gG~a~~~~~~~al~~ll~~~~~d-~~v~~vlvni~gg 183 (266)
.++|++++. .-+.+. ...+.+..+| -.-+..+. .++-+.+.-++.++-+|+ ++ |++++|++.
T Consensus 125 ~~~i~~l~~~~~~~~~~~r~~g~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~~l~---~~~~~~~ai~~~---- 194 (275)
T cd06317 125 KGQIVVIAGQPGNGTAIERQKGFEDELAEVC---PGVEVLDTQPADWDREKAQVAMEALIT---KFGDDIDGVYAG---- 194 (275)
T ss_pred CceEEEEecCCCCchHHHHHHHHHHHHHhhC---CCCEEEeccCCCCCHHHHHHHHHHHHH---hCCCCccEEEEC----
Confidence 368988853 222222 2335555552 11222222 233344444555555554 24 778888853
Q ss_pred ccchhHhhhhHHHHHHHHHHhhhhhhcccceEEEEeCCCCHHHHHHHHHhhhhhcCCc-eeecCCCCCHHHHHHHHHHHh
Q 024560 184 IANFTDVATTFNGIIRALREKESKLKAARMHIFVRRGGPNYQTGLAKMRALGEELGIP-LEVYGPEATMTGICKQAIDCI 262 (266)
Q Consensus 184 i~~~~~vA~~~~gii~al~~~~~~~~~~~~pvvvrl~G~~~~~~~~~L~~~~~~~Gip-~~~~~~~~~~~eAv~~av~~~ 262 (266)
.+..| .++++++++.+.. .++.|+ -.++ ...+...+.+ |.+ ..+ .-++.+..+.++++.
T Consensus 195 ---~d~~a---~g~~~~l~~~g~~---~dv~v~-g~d~--~~~~~~~i~~-----~~~~ttv---~~~~~~~g~~a~~~l 254 (275)
T cd06317 195 ---DDNMA---RGALNAAKEAGLA---GGIVIV-GANN--FAVGYEAIRA-----GKYYGTI---YQSPVDDGEAALQTA 254 (275)
T ss_pred ---CCcHH---HHHHHHHHhcCCc---CCcEEE-EeCC--CHHHHHHHHc-----CCceEEE---ecCHHHHHHHHHHHH
Confidence 56677 9999999987521 234444 3333 3445555542 322 122 236666666666654
No 186
>PRK14188 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional
Probab=30.67 E-value=4.1e+02 Score=24.79 Aligned_cols=103 Identities=13% Similarity=0.140 Sum_probs=56.5
Q ss_pred eeccCCCCHHHHHHHHHHHHhhhccCCCCCeEEEEe--cccccchhH----------------------------hhhhH
Q 024560 145 AEYSGAPNEEEVLQYARVVIDCATADPDGRKRALLI--GGGIANFTD----------------------------VATTF 194 (266)
Q Consensus 145 lDlgG~a~~~~~~~al~~ll~~~~~d~~v~~vlvni--~ggi~~~~~----------------------------vA~~~ 194 (266)
..+..+.+.+.+.+.++-+-+ |++|++|+|-. |.++....- +--|.
T Consensus 67 ~~l~~~~~~~el~~~i~~lN~----d~~V~GIlvq~Plp~~~~~~~i~~~I~p~KDVDGl~~~n~g~l~~~~~~~~PcTp 142 (296)
T PRK14188 67 HKLPADTSQAELLALIARLNA----DPAIHGILVQLPLPKHLDSEAVIQAIDPEKDVDGLHVVNAGRLATGETALVPCTP 142 (296)
T ss_pred EECCCCCCHHHHHHHHHHHhC----CCCCcEEEEeCCCCCCCCHHHHHhccCcccccccCChhhHHHHhCCCCCCcCCCH
Confidence 356677888877777555555 99999999884 455421100 01123
Q ss_pred HHHHHHHHHhhhhhhcccceEEE-EeCCCCHHHHHHHHHhhhhhcCCceeecC-CCCCHHHHHHH
Q 024560 195 NGIIRALREKESKLKAARMHIFV-RRGGPNYQTGLAKMRALGEELGIPLEVYG-PEATMTGICKQ 257 (266)
Q Consensus 195 ~gii~al~~~~~~~~~~~~pvvv-rl~G~~~~~~~~~L~~~~~~~Gip~~~~~-~~~~~~eAv~~ 257 (266)
+||++-++.+.-.. ..+.|++ -+.+..-..--..|. +.|.++.++. .-.++.++++.
T Consensus 143 ~ai~~ll~~~~i~~--~Gk~V~viGrs~~mG~PmA~~L~----~~g~tVtv~~~rT~~l~e~~~~ 201 (296)
T PRK14188 143 LGCMMLLRRVHGDL--SGLNAVVIGRSNLVGKPMAQLLL----AANATVTIAHSRTRDLPAVCRR 201 (296)
T ss_pred HHHHHHHHHhCCCC--CCCEEEEEcCCcchHHHHHHHHH----hCCCEEEEECCCCCCHHHHHhc
Confidence 88888887753111 2345554 223333333333444 3588887663 22356655543
No 187
>PLN02278 succinic semialdehyde dehydrogenase
Probab=30.30 E-value=5.3e+02 Score=25.54 Aligned_cols=15 Identities=0% Similarity=0.054 Sum_probs=8.3
Q ss_pred HHHHHHHHHHHHhCC
Q 024560 22 GDFIMGVFAVFQDLD 36 (266)
Q Consensus 22 ~~ii~~Ly~~f~~~D 36 (266)
.+++.++.+++.++-
T Consensus 87 ~~~L~~~a~~l~~~~ 101 (498)
T PLN02278 87 SKILRRWYDLIIANK 101 (498)
T ss_pred HHHHHHHHHHHHHhH
Confidence 455566666665543
No 188
>cd06356 PBP1_Amide_Urea_BP_like Periplasmic component (FmdD) of an active transport system for short-chain amides and urea (FmdDEF). This group includes the type I periplasmic-binding proteins that are predicted to have a function similar to that of an active transport system for short chain amides and/or urea in bacteria and Archaea, by sequence comparison and phylogenetic analysis.
Probab=30.12 E-value=4.2e+02 Score=24.03 Aligned_cols=95 Identities=14% Similarity=0.085 Sum_probs=49.9
Q ss_pred HHHHHHHHHhcC-CCCCCCceeeccCCCCHHHHHHHHHHHHhhhccCCCCCeEEEEecccccchhHhhhhHHHHHHHHHH
Q 024560 125 SVIYADTVGDLG-YASELGNYAEYSGAPNEEEVLQYARVVIDCATADPDGRKRALLIGGGIANFTDVATTFNGIIRALRE 203 (266)
Q Consensus 125 am~t~D~l~~~g-~gg~pAN~lDlgG~a~~~~~~~al~~ll~~~~~d~~v~~vlvni~ggi~~~~~vA~~~~gii~al~~ 203 (266)
..+++|.++..| ..|+|-.++-.--.-+++.-.++.+-+++ +.+|.+|+ |+..+. ++ .++...+++
T Consensus 23 ~~la~~~iNa~gGi~Gr~v~lv~~D~~~~p~~a~~~~~~Li~----~~~V~aii----G~~~s~--~~---~a~~~~~~~ 89 (334)
T cd06356 23 TQLAVDEINASGGILGREVELVDYDTQSDNERYQQYAQRLAL----QDKVDVVW----GGISSA--SR---EAIRPIMDR 89 (334)
T ss_pred HHHHHHHHHhcCCCCCceEEEEEECCCCCHHHHHHHHHHHHH----hCCCCEEE----eCcchH--HH---HHHHHHHHh
Confidence 345788888764 23566555533333455666666666665 56776555 554433 22 444554544
Q ss_pred hhhhhh-------cccceEEEEeCCCCHHHHHHHHH
Q 024560 204 KESKLK-------AARMHIFVRRGGPNYQTGLAKMR 232 (266)
Q Consensus 204 ~~~~~~-------~~~~pvvvrl~G~~~~~~~~~L~ 232 (266)
.+-+.- ....|.+.|++.+....++.+.+
T Consensus 90 ~~vp~i~~~~~~~~~~~~~~F~~~~~~~~~~~~~~~ 125 (334)
T cd06356 90 TKQLYFYTTQYEGGVCDRNTFCTGATPAQQFSTLVP 125 (334)
T ss_pred cCceEEeCCCccCCcccCCEEEeCCCcHHHHHHHHH
Confidence 421100 01124555777776665554443
No 189
>cd06359 PBP1_Nba_like Type I periplasmic binding component of active transport systems that are predicted to be involved in 2-nitrobenzoic acid degradation pathway. This group includes the type I periplasmic binding component of active transport systems that are predicted to be involved in 2-nitrobenzoic acid degradation pathway; their substrate specificities are not well characterized.
Probab=30.03 E-value=2.3e+02 Score=25.60 Aligned_cols=47 Identities=9% Similarity=-0.098 Sum_probs=25.5
Q ss_pred HHHHHHHHhcCCCCCCCceeeccCCCCHHHHHHHHHHHHhhhccCCCCCeEE
Q 024560 126 VIYADTVGDLGYASELGNYAEYSGAPNEEEVLQYARVVIDCATADPDGRKRA 177 (266)
Q Consensus 126 m~t~D~l~~~g~gg~pAN~lDlgG~a~~~~~~~al~~ll~~~~~d~~v~~vl 177 (266)
.+++|.++ .|.+|++-.++-.--..++++..++.+-+++ +++|.+|+
T Consensus 24 ~lAv~~in-ggi~G~~i~l~~~D~~~~p~~a~~~~~~lv~----~~~v~~vi 70 (333)
T cd06359 24 QLALKQLG-GKLGGLPVEVVVEDDGLKPDVAKQAAERLIK----RDKVDFVT 70 (333)
T ss_pred HHHHHHhC-CccCCEEEEEEecCCCCChHHHHHHHHHHHh----hcCCcEEE
Confidence 34556654 3345666444433333345666666666666 66776554
No 190
>COG0436 Aspartate/tyrosine/aromatic aminotransferase [Amino acid transport and metabolism]
Probab=29.97 E-value=2.8e+02 Score=26.61 Aligned_cols=78 Identities=17% Similarity=0.135 Sum_probs=48.3
Q ss_pred cEEEEecCchHHHH-HHHHHHhcCCCCC-----C-------------C--ceee-----ccCCCCHHHHHHHHHHHHhhh
Q 024560 114 RIWTMVAGGGASVI-YADTVGDLGYASE-----L-------------G--NYAE-----YSGAPNEEEVLQYARVVIDCA 167 (266)
Q Consensus 114 ~Igii~NGaGlam~-t~D~l~~~g~gg~-----p-------------A--N~lD-----lgG~a~~~~~~~al~~ll~~~ 167 (266)
+=-++++|+--++. ++.++... |-+ | + .++. -+-.++.+.+.++ ++
T Consensus 90 ~eiivt~Ga~~al~~~~~a~~~p--GDeVlip~P~Y~~y~~~~~~~gg~~v~v~l~~~~~~f~~d~~~l~~~----i~-- 161 (393)
T COG0436 90 EEIIVTAGAKEALFLAFLALLNP--GDEVLIPDPGYPSYEAAVKLAGGKPVPVPLDEEENGFKPDLEDLEAA----IT-- 161 (393)
T ss_pred CeEEEeCCHHHHHHHHHHHhcCC--CCEEEEeCCCCcCHHHHHHhcCCEEEEEeCCcCccCCcCCHHHHHhh----cC--
Confidence 43566777766655 67777775 332 2 1 2222 2445666666665 53
Q ss_pred ccCCCCCeEEEEe---cccccchhHhhhhHHHHHHHHHHhh
Q 024560 168 TADPDGRKRALLI---GGGIANFTDVATTFNGIIRALREKE 205 (266)
Q Consensus 168 ~~d~~v~~vlvni---~ggi~~~~~vA~~~~gii~al~~~~ 205 (266)
+++|+++||. |+|.+=+.+-- +.|++.++++.
T Consensus 162 ---~ktk~i~ln~P~NPTGav~~~~~l---~~i~~~a~~~~ 196 (393)
T COG0436 162 ---PKTKAIILNSPNNPTGAVYSKEEL---KAIVELAREHD 196 (393)
T ss_pred ---ccceEEEEeCCCCCcCcCCCHHHH---HHHHHHHHHcC
Confidence 5899999996 55555555444 88999888764
No 191
>COG0541 Ffh Signal recognition particle GTPase [Intracellular trafficking and secretion]
Probab=29.97 E-value=4.1e+02 Score=26.51 Aligned_cols=64 Identities=19% Similarity=0.352 Sum_probs=41.7
Q ss_pred HHHHHHHHHhhhhhhcccceEEEEeCCCCHHHHHHHHHhhhhhcCCceeecCCCCCHHHHHHHHHHHhhhc
Q 024560 195 NGIIRALREKESKLKAARMHIFVRRGGPNYQTGLAKMRALGEELGIPLEVYGPEATMTGICKQAIDCIMSA 265 (266)
Q Consensus 195 ~gii~al~~~~~~~~~~~~pvvvrl~G~~~~~~~~~L~~~~~~~Gip~~~~~~~~~~~eAv~~av~~~~~~ 265 (266)
--++.++++. ..+|.+|- ..+---+|.+-|+..+++.|+|++--++..+|-+.++.+++.++..
T Consensus 118 ~KLA~~lkk~------~~kvllVa-aD~~RpAA~eQL~~La~q~~v~~f~~~~~~~Pv~Iak~al~~ak~~ 181 (451)
T COG0541 118 GKLAKYLKKK------GKKVLLVA-ADTYRPAAIEQLKQLAEQVGVPFFGSGTEKDPVEIAKAALEKAKEE 181 (451)
T ss_pred HHHHHHHHHc------CCceEEEe-cccCChHHHHHHHHHHHHcCCceecCCCCCCHHHHHHHHHHHHHHc
Confidence 3466777774 24555542 2222234555566666688999875556678999999999988753
No 192
>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=29.97 E-value=2.2e+02 Score=24.75 Aligned_cols=79 Identities=13% Similarity=0.047 Sum_probs=44.6
Q ss_pred CCcEEEEecCchHHH-----HH-------HHHHHhcCCCCCCCceeeccCCCCHHHHHHHHHHHHhhhccCCCCCeEEEE
Q 024560 112 KGRIWTMVAGGGASV-----IY-------ADTVGDLGYASELGNYAEYSGAPNEEEVLQYARVVIDCATADPDGRKRALL 179 (266)
Q Consensus 112 ~G~Igii~NGaGlam-----~t-------~D~l~~~g~gg~pAN~lDlgG~a~~~~~~~al~~ll~~~~~d~~v~~vlvn 179 (266)
.++|++++...+..- .. .+.+..+ |-+......+.++.+.+..+++++-+++ +.+.+++|+..
T Consensus 113 ~~~i~~i~~~~~~~~~~~~~~~~~R~~gf~~~~~~~--g~~~~~~~~~~~~~~~~~~~~~~~~~l~---~~~~~~ai~~~ 187 (269)
T cd06297 113 PGRIGAITVEEEPDRAFRRTVFAERRAGFQQALKDA--GRPFSPDLLAITDHSEEGGRLAMRHLLE---KASPPLAVFAS 187 (269)
T ss_pred CCceEEEeCccccccccccccHHHHHHHHHHHHHHc--CCCCChhhEEeCCCChhhHHHHHHHHHc---CCCCCcEEEEc
Confidence 578998864332210 12 3344555 3332111223344445555566655554 25667887754
Q ss_pred ecccccchhHhhhhHHHHHHHHHHhh
Q 024560 180 IGGGIANFTDVATTFNGIIRALREKE 205 (266)
Q Consensus 180 i~ggi~~~~~vA~~~~gii~al~~~~ 205 (266)
++.+| -|+++++++.+
T Consensus 188 -------~d~~a---~g~~~~l~~~g 203 (269)
T cd06297 188 -------ADQQA---LGALQEAVELG 203 (269)
T ss_pred -------CcHHH---HHHHHHHHHcC
Confidence 67788 99999999874
No 193
>PF13844 Glyco_transf_41: Glycosyl transferase family 41; PDB: 3PE4_C 3PE3_D 3TAX_C 2XGO_A 2JLB_B 2XGM_A 2VSY_B 2XGS_B 2VSN_A.
Probab=29.42 E-value=2.2e+02 Score=28.44 Aligned_cols=46 Identities=15% Similarity=0.232 Sum_probs=29.2
Q ss_pred ccceEEEEeCCCC-HHHHHHHHHhhhhhcCCceeecCCCCCHHHHHHHHHHHhh
Q 024560 211 ARMHIFVRRGGPN-YQTGLAKMRALGEELGIPLEVYGPEATMTGICKQAIDCIM 263 (266)
Q Consensus 211 ~~~pvvvrl~G~~-~~~~~~~L~~~~~~~Gip~~~~~~~~~~~eAv~~av~~~~ 263 (266)
..+|+|++.|.+- ..-+-.+|+ .+|+|=-+ ..+.++=|+.|++++.
T Consensus 383 mGVPvVTl~G~~~~sR~~aSiL~----~lGl~ElI---A~s~~eYv~~Av~La~ 429 (468)
T PF13844_consen 383 MGVPVVTLPGETMASRVGASILR----ALGLPELI---ADSEEEYVEIAVRLAT 429 (468)
T ss_dssp HT--EEB---SSGGGSHHHHHHH----HHT-GGGB----SSHHHHHHHHHHHHH
T ss_pred cCCCEEeccCCCchhHHHHHHHH----HcCCchhc---CCCHHHHHHHHHHHhC
Confidence 3699998777663 336677888 67998433 5699999999999875
No 194
>TIGR03240 arg_catab_astD succinylglutamic semialdehyde dehydrogenase. Members of this protein family are succinylglutamic semialdehyde dehydrogenase (EC 1.2.1.71), the fourth enzyme in the arginine succinyltransferase (AST) pathway for arginine catabolism.
Probab=29.35 E-value=5.6e+02 Score=25.19 Aligned_cols=23 Identities=4% Similarity=0.036 Sum_probs=14.7
Q ss_pred HHHHHHHHHHHHHHhCCceeeEe
Q 024560 20 KIGDFIMGVFAVFQDLDFSFIEM 42 (266)
Q Consensus 20 ~~~~ii~~Ly~~f~~~D~~l~EI 42 (266)
+=.+++.++.+++.++--.++++
T Consensus 58 ~R~~~L~~~a~~l~~~~~ela~~ 80 (484)
T TIGR03240 58 ERIAVVQRFAALLEERKEALARV 80 (484)
T ss_pred HHHHHHHHHHHHHHHhHHHHHHH
Confidence 44567777777777766555553
No 195
>cd07123 ALDH_F4-17_P5CDH Delta(1)-pyrroline-5-carboxylate dehydrogenase, ALDH families 4 and 17. Delta(1)-pyrroline-5-carboxylate dehydrogenase (EC=1.5.1.12 ), families 4 and 17: a proline catabolic enzyme of the aldehyde dehydrogenase (ALDH) protein superfamily. Delta(1)-pyrroline-5-carboxylate dehydrogenase (P5CDH), also known as ALDH4A1 in humans, is a mitochondrial homodimer involved in proline degradation and catalyzes the NAD + -dependent conversion of P5C to glutamate. This is a necessary step in the pathway interconnecting the urea and tricarboxylic acid cycles. The preferred substrate is glutamic gamma-semialdehyde, other substrates include succinic, glutaric and adipic semialdehydes. Also included in this CD is the Aldh17 Drosophila melanogaster (Q9VUC0) P5CDH and similar sequences.
Probab=29.35 E-value=4.8e+02 Score=26.06 Aligned_cols=10 Identities=40% Similarity=0.601 Sum_probs=6.6
Q ss_pred eEEEEeCCCC
Q 024560 214 HIFVRRGGPN 223 (266)
Q Consensus 214 pvvvrl~G~~ 223 (266)
|++.-+||.|
T Consensus 280 ~v~lElGGkn 289 (522)
T cd07123 280 RIVGETGGKN 289 (522)
T ss_pred CEEEECCCCC
Confidence 5666777754
No 196
>cd06348 PBP1_ABC_ligand_binding_like_13 Type I periplasmic ligand-binding domain of uncharacterized ABC (Atpase Binding Cassette)-type active transport systems that are predicted to be involved in uptake of amino acids, peptides, or inorganic ions. This subgroup includes the type I periplasmic ligand-binding domain of uncharacterized ABC (Atpase Binding Cassette)-type active transport systems that are predicted to be involved in uptake of amino acids, peptides, or inorganic ions. This subgroup has high sequence similarity to members of the family of hydrophobic amino acid transporters (HAAT), such as leucine/isoleucine/valine binding protein (LIVBP); however its ligand specificity has not been determined experimentally.
Probab=29.19 E-value=2.2e+02 Score=25.85 Aligned_cols=62 Identities=10% Similarity=0.001 Sum_probs=32.1
Q ss_pred CCCcEEEEecCc-hHHHHHHHHHHhcC-CCCCCCceeeccCCCCHHHHHHHHHHHHhhhccCCCCCeE
Q 024560 111 PKGRIWTMVAGG-GASVIYADTVGDLG-YASELGNYAEYSGAPNEEEVLQYARVVIDCATADPDGRKR 176 (266)
Q Consensus 111 l~G~Igii~NGa-Glam~t~D~l~~~g-~gg~pAN~lDlgG~a~~~~~~~al~~ll~~~~~d~~v~~v 176 (266)
+.|..+..+... -.+.+++|.++..| ..|++-.++-.--..++.+..++++-+++ +.++.+|
T Consensus 8 lsG~~a~~g~~~~~g~~~a~~~iNa~ggi~G~~v~lv~~D~~~~p~~a~~~~~~li~----~~~v~~i 71 (344)
T cd06348 8 LTGNAALYGQEQLAGLKLAEDRFNQAGGVNGRPIKLVIEDSGGDEAEAINAFQTLIN----KDRVLAI 71 (344)
T ss_pred ccCchhhcCHhHHHHHHHHHHHHhhcCCcCCcEEEEEEecCCCChHHHHHHHHHHhh----hcCceEE
Confidence 345544443322 23466889999874 12444333322223345666677776766 5565433
No 197
>cd07140 ALDH_F1L_FTFDH 10-formyltetrahydrofolate dehydrogenase, ALDH family 1L. 10-formyltetrahydrofolate dehydrogenase (FTHFDH, EC=1.5.1.6), also known as aldehyde dehydrogenase family 1 member L1 (ALDH1L1) in humans, is a multi-domain homotetramer with an N-terminal formyl transferase domain and a C-terminal ALDH domain. FTHFDH catalyzes an NADP+-dependent dehydrogenase reaction resulting in the conversion of 10-formyltetrahydrofolate to tetrahydrofolate and CO2. The ALDH domain is also capable of the oxidation of short chain aldehydes to their corresponding acids.
Probab=29.18 E-value=5.7e+02 Score=25.25 Aligned_cols=22 Identities=5% Similarity=0.170 Sum_probs=12.5
Q ss_pred HHHHHHHHHHHHHHhCCceeeE
Q 024560 20 KIGDFIMGVFAVFQDLDFSFIE 41 (266)
Q Consensus 20 ~~~~ii~~Ly~~f~~~D~~l~E 41 (266)
+=.+++.++.+++.+.--.|++
T Consensus 68 ~R~~~L~~~a~~l~~~~~ela~ 89 (486)
T cd07140 68 DRGRLMYRLADLMEEHQEELAT 89 (486)
T ss_pred HHHHHHHHHHHHHHHhHHHHHH
Confidence 3346666666666665544444
No 198
>cd07148 ALDH_RL0313 Uncharacterized ALDH ( RL0313) with similarity to Tortula ruralis aldehyde dehydrogenase ALDH21A1. Uncharacterized aldehyde dehydrogenase (locus RL0313) with sequence similarity to the moss Tortula ruralis aldehyde dehydrogenase ALDH21A1 (RNP123) believed to play an important role in the detoxification of aldehydes generated in response to desiccation- and salinity-stress, and similar sequences are included in this CD.
Probab=28.81 E-value=4.9e+02 Score=25.32 Aligned_cols=19 Identities=0% Similarity=-0.043 Sum_probs=12.6
Q ss_pred HHHHHHHHHHHHhCCceee
Q 024560 22 GDFIMGVFAVFQDLDFSFI 40 (266)
Q Consensus 22 ~~ii~~Ly~~f~~~D~~l~ 40 (266)
.+++.++.+++.++--.|+
T Consensus 47 ~~~L~~~a~~l~~~~~ela 65 (455)
T cd07148 47 IAILERLADLMEERADELA 65 (455)
T ss_pred HHHHHHHHHHHHHHHHHHH
Confidence 4677777777776655444
No 199
>cd06331 PBP1_AmiC_like Type I periplasmic components of amide-binding protein (AmiC) and the active transport system for short-chain and urea (FmdDEF). This group includes the type I periplasmic components of amide-binding protein (AmiC) and the active transport system for short-chain and urea (FmdDEF), found in bacteria and Archaea. AmiC controls expression of the amidase operon by a ligand-triggered conformational switch. In the absence of ligand or presence of butyramide (repressor), AmiC (the ligand sensor and negative regulator) adopts an open conformation and inhibits the transcription antitermination function of AmiR by direct protein-protein interaction. In the presence of inducing ligands such as acetamide, AmiC adopts a closed conformation which disrupts a silencing AmiC-AmiR complex and the expression of amidase and other genes of the operon is induced. FmdDEF is predicted to be an ATP-dependent transporter and closely resembles the periplasmic binding protein and the two t
Probab=28.74 E-value=2.7e+02 Score=25.08 Aligned_cols=65 Identities=9% Similarity=0.098 Sum_probs=37.1
Q ss_pred HHHHHHHHHhcC-CCCCCC--ceeeccCCCCHHHHHHHHHHHHhhhccCCCCCeEEEEecccccchhHhhhhHHHHHHHH
Q 024560 125 SVIYADTVGDLG-YASELG--NYAEYSGAPNEEEVLQYARVVIDCATADPDGRKRALLIGGGIANFTDVATTFNGIIRAL 201 (266)
Q Consensus 125 am~t~D~l~~~g-~gg~pA--N~lDlgG~a~~~~~~~al~~ll~~~~~d~~v~~vlvni~ggi~~~~~vA~~~~gii~al 201 (266)
..+++|.++..| ..|++- -+.|.++ +++.-.++++-+++ +.+|.+|+ |+.++.. + .++...+
T Consensus 23 ~~~a~~~iN~~gGi~G~~i~l~~~D~~~--~p~~a~~~a~~Li~----~~~V~aii----G~~~s~~--~---~a~~~~~ 87 (333)
T cd06331 23 ALLAIEEINAAGGILGRPLELVVEDPAS--DPAFAAKAARRLIR----DDKVDAVF----GCYTSAS--R---KAVLPVV 87 (333)
T ss_pred HHHHHHHHHhcCCCCCeEEEEEEECCCC--CHHHHHHHHHHHHh----ccCCcEEE----ecccHHH--H---HHHHHHH
Confidence 345788998884 123443 3445565 45666677777766 66776555 5544332 3 4555655
Q ss_pred HHh
Q 024560 202 REK 204 (266)
Q Consensus 202 ~~~ 204 (266)
++.
T Consensus 88 ~~~ 90 (333)
T cd06331 88 ERG 90 (333)
T ss_pred Hhc
Confidence 554
No 200
>cd01169 HMPP_kinase 4-amino-5-hydroxymethyl-2-methyl-pyrimidine phosphate kinase (HMPP-kinase) catalyzes two consecutive phosphorylation steps in the thiamine phosphate biosynthesis pathway, leading to the synthesis of vitamin B1. The first step is the phosphorylation of the hydroxyl group of HMP to form 4-amino-5-hydroxymethyl-2-methyl-pyrimidine phosphate (HMP-P) and then the phophorylation of HMP-P to form 4-amino-5-hydroxymethyl-2-methyl-pyrimidine pyrophosphate (HMP-PP), which is the substrate for the thiamine synthase coupling reaction.
Probab=28.71 E-value=2e+02 Score=24.79 Aligned_cols=43 Identities=16% Similarity=0.208 Sum_probs=30.7
Q ss_pred CCHHHHHHHHHHHHhhhccCCCCCeEEEEecccccchhHhhhhHHHHHHHHHHh
Q 024560 151 PNEEEVLQYARVVIDCATADPDGRKRALLIGGGIANFTDVATTFNGIIRALREK 204 (266)
Q Consensus 151 a~~~~~~~al~~ll~~~~~d~~v~~vlvni~ggi~~~~~vA~~~~gii~al~~~ 204 (266)
.+++.+.+.++.+++ +-++++|.+ |...+.++. +.+.+.+++.
T Consensus 51 ~~~~~~~~~l~~~~~----~~~~~~i~~----G~l~~~~~~---~~i~~~~~~~ 93 (242)
T cd01169 51 VPPEFVAAQLDAVLE----DIPVDAIKI----GMLGSAEII---EAVAEALKDY 93 (242)
T ss_pred CCHHHHHHHHHHHHh----CCCCCEEEE----CCCCCHHHH---HHHHHHHHhC
Confidence 467889999999888 777888876 333445555 6777777664
No 201
>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=28.61 E-value=3.7e+02 Score=22.94 Aligned_cols=44 Identities=16% Similarity=0.073 Sum_probs=28.5
Q ss_pred CCCCHHHHHHHHHHHHhhhccCCCCCeEEEEecccccchhHhhhhHHHHHHHHHHhh
Q 024560 149 GAPNEEEVLQYARVVIDCATADPDGRKRALLIGGGIANFTDVATTFNGIIRALREKE 205 (266)
Q Consensus 149 G~a~~~~~~~al~~ll~~~~~d~~v~~vlvni~ggi~~~~~vA~~~~gii~al~~~~ 205 (266)
++.+.+..+++++-+++ +.|.+++|+.. .+.+| .|+++++++++
T Consensus 155 ~~~~~~~~~~~~~~~l~---~~~~~~ai~~~-------~d~~a---~g~~~~l~~~g 198 (265)
T cd06285 155 SGFDIEGGEAAAEKLLR---SDSPPTAIFAV-------NDFAA---IGVMGAARDRG 198 (265)
T ss_pred CCCCHHHHHHHHHHHHc---CCCCCCEEEEc-------CcHHH---HHHHHHHHHcC
Confidence 44455555555555553 25667777743 55677 89999999874
No 202
>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=28.57 E-value=2.5e+02 Score=23.97 Aligned_cols=120 Identities=12% Similarity=0.129 Sum_probs=60.6
Q ss_pred CCcEEEEecCchHHH------HHHHHHHhcCCCCCCCceeeccCCCCHHHHHHHHHHHHhhhccCCCCCeEEEEeccccc
Q 024560 112 KGRIWTMVAGGGASV------IYADTVGDLGYASELGNYAEYSGAPNEEEVLQYARVVIDCATADPDGRKRALLIGGGIA 185 (266)
Q Consensus 112 ~G~Igii~NGaGlam------~t~D~l~~~g~gg~pAN~lDlgG~a~~~~~~~al~~ll~~~~~d~~v~~vlvni~ggi~ 185 (266)
.++|++++.-.+... -..+.+..+ |.++.+..-+.+..+.+.-.++++-++. ..|+.+++++.
T Consensus 114 ~~~i~~i~~~~~~~~~~~R~~Gf~~~l~~~--~~~~~~~~i~~~~~~~~~~~~~~~~~l~---~~~~~~ai~~~------ 182 (260)
T cd06286 114 YRKIAYCIGRKKSLNSQSRKKAYKDALEEY--GLTPDEEWIFEGCFTIEDGERIGHQLLK---MKDRPDAIFTG------ 182 (260)
T ss_pred CceEEEEcCCcccchhHHHHHHHHHHHHHc--CCCCChHheEeCCCCHHHHHHHHHHHHc---CCCCCCEEEEc------
Confidence 357888853322111 122344455 3333222222334444555566666664 24678877744
Q ss_pred chhHhhhhHHHHHHHHHHhhhhhhcccceEEEEeCCCCHHHHHHHHHhhhhhcCCceeecCCCCCHHHHHHHHHHHh
Q 024560 186 NFTDVATTFNGIIRALREKESKLKAARMHIFVRRGGPNYQTGLAKMRALGEELGIPLEVYGPEATMTGICKQAIDCI 262 (266)
Q Consensus 186 ~~~~vA~~~~gii~al~~~~~~~~~~~~pvvvrl~G~~~~~~~~~L~~~~~~~Gip~~~~~~~~~~~eAv~~av~~~ 262 (266)
++.+| .++.+++++.+.+. +.++ -|+-..++... . ...+.+ ...++.+..+.+++++
T Consensus 183 -~d~~a---~~~~~~l~~~g~~i-p~di-~v~g~d~~~~~------~----~~~~tt----v~~~~~~~g~~a~~~l 239 (260)
T cd06286 183 -SDEVA---AGIITEAKKQGIRV-PEDL-AIIGFDNQPIS------E----LLGITT----IDQPVKELGEKAFELL 239 (260)
T ss_pred -chHHH---HHHHHHHHHcCCCC-Ccce-EEEeecCcccc------c----CCCCcc----cCCCHHHHHHHHHHHH
Confidence 56777 99999999875210 0112 33445554322 1 112222 1347777777777655
No 203
>PF14639 YqgF: Holliday-junction resolvase-like of SPT6 ; PDB: 3PSI_A 3PSF_A.
Probab=28.38 E-value=38 Score=28.41 Aligned_cols=77 Identities=8% Similarity=-0.029 Sum_probs=32.6
Q ss_pred CCCCeEEEEecccccchhHhhhhHHHHHHHHHHhhhhhhcccceEEEEeCCCCHHHHHHHHHhhhhhcCCceeecCCCCC
Q 024560 171 PDGRKRALLIGGGIANFTDVATTFNGIIRALREKESKLKAARMHIFVRRGGPNYQTGLAKMRALGEELGIPLEVYGPEAT 250 (266)
Q Consensus 171 ~~v~~vlvni~ggi~~~~~vA~~~~gii~al~~~~~~~~~~~~pvvvrl~G~~~~~~~~~L~~~~~~~Gip~~~~~~~~~ 250 (266)
.++++|.|+ |.-+.+..+. +-|-+.+++.....+..++||++ . .++.-++...+ ..... -|.+
T Consensus 62 ~kP~vI~v~--g~~~~s~~l~---~~v~~~v~~~~~~~~~~~i~V~~-v----~~~~A~lY~~S----~rA~~---EFP~ 124 (150)
T PF14639_consen 62 HKPDVIAVG--GNSRESRKLY---DDVRDIVEELDEDEQMPPIPVVI-V----DDEVARLYSNS----KRAAE---EFPD 124 (150)
T ss_dssp H--SEEEE----SSTHHHHHH---HHHHHHHHHTTB-TTS-B--EEE--------TTHHHHHTS----HHHHH---HSTT
T ss_pred cCCeEEEEc--CCChhHHHHH---HHHHHHHHHhhhcccCCCceEEE-E----CcHHHHHHhcC----HHHHH---HCCC
Confidence 466677775 3334555555 55555555542111113466543 1 23334455532 11111 1446
Q ss_pred HHHHHHHHHHHhhh
Q 024560 251 MTGICKQAIDCIMS 264 (266)
Q Consensus 251 ~~eAv~~av~~~~~ 264 (266)
....++.|+++|+-
T Consensus 125 ~p~~~R~AIslAR~ 138 (150)
T PF14639_consen 125 YPPLLRYAISLARY 138 (150)
T ss_dssp --HHHHHHHHHHHH
T ss_pred CCHHHHHHHHHHHH
Confidence 77889999998863
No 204
>cd06335 PBP1_ABC_ligand_binding_like_2 Type I periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type active transport systems that are predicted to be involved in transport of amino acids, peptides, or inorganic ions. This subgroup includes the type I periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type active transport systems that are predicted to be involved in transport of amino acids, peptides, or inorganic ions. Members of this group are sequence-similar to members of the family of ABC-type hydrophobic amino acid transporters, such as leucine-isoleucine-valine-binding protein (LIVBP); however their ligand specificity has not been determined experimentally.
Probab=28.32 E-value=2.2e+02 Score=26.05 Aligned_cols=67 Identities=16% Similarity=0.132 Sum_probs=35.7
Q ss_pred HHHHHHHHHhcC-CCCCCCceeeccCCCCHHHHHHHHHHHHhhhccCCCCCeEEEEecccccchhHhhhhHHHHHHHHHH
Q 024560 125 SVIYADTVGDLG-YASELGNYAEYSGAPNEEEVLQYARVVIDCATADPDGRKRALLIGGGIANFTDVATTFNGIIRALRE 203 (266)
Q Consensus 125 am~t~D~l~~~g-~gg~pAN~lDlgG~a~~~~~~~al~~ll~~~~~d~~v~~vlvni~ggi~~~~~vA~~~~gii~al~~ 203 (266)
..++++.++..| ..|++-.++..--..++++-.++.+-+++ +.+|.+|+ |+..+.. + .++...+++
T Consensus 23 ~~la~~~iN~~gGi~G~~i~lv~~D~~~~p~~a~~~a~~Li~----~~~V~aii----G~~~s~~--~---~a~~~~~~~ 89 (347)
T cd06335 23 ARLAIDEINAAGGVLGRKLELVERDDRGNPARGLQNAQELAA----DEKVVAVL----GGLHTPV--A---LANLEFIQQ 89 (347)
T ss_pred HHHHHHHHHhcCCcCCeEEEEEeccCCCCcHHHHHHHHHHhc----cCCeEEEE----cCCCCHH--H---HhhhHHHHh
Confidence 345788888884 23566555533333445555566666665 55653333 5543332 2 445555554
Q ss_pred h
Q 024560 204 K 204 (266)
Q Consensus 204 ~ 204 (266)
.
T Consensus 90 ~ 90 (347)
T cd06335 90 N 90 (347)
T ss_pred c
Confidence 4
No 205
>cd07105 ALDH_SaliADH Salicylaldehyde dehydrogenase, DoxF-like. Salicylaldehyde dehydrogenase (DoxF, SaliADH, EC=1.2.1.65) involved in the upper naphthalene catabolic pathway of Pseudomonas strain C18 and other similar sequences are present in this CD.
Probab=28.23 E-value=5.5e+02 Score=24.72 Aligned_cols=22 Identities=18% Similarity=0.294 Sum_probs=12.5
Q ss_pred HHHHHHHHHHHHHHhCCceeeE
Q 024560 20 KIGDFIMGVFAVFQDLDFSFIE 41 (266)
Q Consensus 20 ~~~~ii~~Ly~~f~~~D~~l~E 41 (266)
+=.+++.++.+++.+.--.+++
T Consensus 23 ~R~~~L~~~a~~l~~~~~~la~ 44 (432)
T cd07105 23 ERRDILLKAADLLESRRDEFIE 44 (432)
T ss_pred HHHHHHHHHHHHHHhCHHHHHH
Confidence 3345566666666665544554
No 206
>PRK15025 ureidoglycolate dehydrogenase; Provisional
Probab=28.09 E-value=74 Score=30.49 Aligned_cols=52 Identities=15% Similarity=0.071 Sum_probs=28.0
Q ss_pred cccccchhHhhhhHHHHHHHHHHhhhhhhcccceEE--EEeCCCCHHHHHHHHHhhhhhcCCce
Q 024560 181 GGGIANFTDVATTFNGIIRALREKESKLKAARMHIF--VRRGGPNYQTGLAKMRALGEELGIPL 242 (266)
Q Consensus 181 ~ggi~~~~~vA~~~~gii~al~~~~~~~~~~~~pvv--vrl~G~~~~~~~~~L~~~~~~~Gip~ 242 (266)
|....+.++.......+++.++... +.+=. ||+.|..+.+.++.-. +.|||+
T Consensus 270 p~~F~~~~~f~~~~~~~~~~l~~~~------~a~g~~~V~~PGe~e~~~~~~~~----~~GI~v 323 (349)
T PRK15025 270 PAFFSSSELFRQHISQTMRELNAIT------PAPGFNQVYYPGQDQDIKQKKAA----VEGIEI 323 (349)
T ss_pred hHHcCCHHHHHHHHHHHHHHHHcCC------CCCCCCceECCCcHHHHHHHHHH----ccCccc
Confidence 4444444444433356666666542 11111 5888876665554443 459988
No 207
>PRK15395 methyl-galactoside ABC transporter galactose-binding periplasmic protein MglB; Provisional
Probab=27.82 E-value=4.7e+02 Score=23.85 Aligned_cols=86 Identities=12% Similarity=0.068 Sum_probs=49.0
Q ss_pred CCCCHHHHHHHHHHHHhhhccC--CCCCeEEEEecccccchhHhhhhHHHHHHHHHHhhhhhhcc-cceEEEEeCCCCHH
Q 024560 149 GAPNEEEVLQYARVVIDCATAD--PDGRKRALLIGGGIANFTDVATTFNGIIRALREKESKLKAA-RMHIFVRRGGPNYQ 225 (266)
Q Consensus 149 G~a~~~~~~~al~~ll~~~~~d--~~v~~vlvni~ggi~~~~~vA~~~~gii~al~~~~~~~~~~-~~pvvvrl~G~~~~ 225 (266)
+..+.+.-+++++-+++ ++ |++++|+. .++.+| .|+++++++.+ . ++| |+-. .+..
T Consensus 203 ~~~~~~~a~~~~~~~l~---~~~~~~~~ai~~-------~~d~~A---~gvl~al~~~G-----l~~vp-Vvg~--D~~~ 261 (330)
T PRK15395 203 AMWDTAQAKDKMDAWLS---GPNANKIEVVIA-------NNDAMA---MGAVEALKAHN-----KSSIP-VFGV--DALP 261 (330)
T ss_pred CCcCHHHHHHHHHHHHh---hCcCCCeeEEEE-------CCchHH---HHHHHHHHhcC-----CCCCe-EEee--CCCH
Confidence 44455555566655554 12 45676663 366777 99999999874 4 677 3333 3446
Q ss_pred HHHHHHHhhhhhcCCceeecCCCCCHHHHHHHHHHHh
Q 024560 226 TGLAKMRALGEELGIPLEVYGPEATMTGICKQAIDCI 262 (266)
Q Consensus 226 ~~~~~L~~~~~~~Gip~~~~~~~~~~~eAv~~av~~~ 262 (266)
.++..+.+ |.....+ ..++.+..+.++++.
T Consensus 262 ~~~~~~~~-----g~~~ttv--~~~~~~~G~~a~~~l 291 (330)
T PRK15395 262 EALALVKS-----GAMAGTV--LNDANNQAKATFDLA 291 (330)
T ss_pred HHHHHHHh-----CCceEEE--ecCHHHHHHHHHHHH
Confidence 66666651 3221111 336676666666554
No 208
>TIGR00250 RNAse_H_YqgF RNAse H-fold protein YqgF. This protein family, which exhibits an RNAse H fold in crystal structure, has been proposed as a putative Holliday junction resolvase, an alternate to RuvC.
Probab=27.76 E-value=3.3e+02 Score=22.02 Aligned_cols=84 Identities=10% Similarity=-0.028 Sum_probs=45.5
Q ss_pred CCceeeccCCCCHHHHHHHHHHHHhhhccCCCCCeEEEEec----ccccchhHhhhhHHHHHHHHHHhhhhhhcccceEE
Q 024560 141 LGNYAEYSGAPNEEEVLQYARVVIDCATADPDGRKRALLIG----GGIANFTDVATTFNGIIRALREKESKLKAARMHIF 216 (266)
Q Consensus 141 pAN~lDlgG~a~~~~~~~al~~ll~~~~~d~~v~~vlvni~----ggi~~~~~vA~~~~gii~al~~~~~~~~~~~~pvv 216 (266)
.++|+..--..+.....+.++-+++ ..+++.++|=.| |.....+..+ +..++-+++. .++||.
T Consensus 21 ~a~pl~~i~~~~~~~~~~~l~~~i~----~~~~~~iVvGlP~~~dG~~~~~a~~v---~~f~~~L~~~------~~~~v~ 87 (130)
T TIGR00250 21 TAQGIPTIKAQDGEPDWSRIEELLK----EWTPDKIVVGLPLNMDGTEGPLTERA---QKFANRLEGR------FGVPVV 87 (130)
T ss_pred EEeceEEEEecCCcHHHHHHHHHHH----HcCCCEEEEeccCCCCcCcCHHHHHH---HHHHHHHHHH------hCCCEE
Confidence 3444444333222334455555565 677887777654 3333223333 4444444432 368887
Q ss_pred EEeCCCCHHHHHHHHHhhhhhcCCc
Q 024560 217 VRRGGPNYQTGLAKMRALGEELGIP 241 (266)
Q Consensus 217 vrl~G~~~~~~~~~L~~~~~~~Gip 241 (266)
.|=.--...+|++.|. +.|++
T Consensus 88 ~~DEr~TT~~A~~~l~----~~g~~ 108 (130)
T TIGR00250 88 LWDERLSTVEAESGLF----ARGGF 108 (130)
T ss_pred EEcCCcCHHHHHHHHH----HcCCC
Confidence 6555556688888888 44654
No 209
>cd06352 PBP1_NPR_GC_like Ligand-binding domain of membrane guanylyl-cyclase receptors. Ligand-binding domain of membrane guanylyl-cyclase receptors. Membrane guanylyl cyclases (GC) have a single membrane-spanning region and are activated by endogenous and exogenous peptides. This family can be divided into three major subfamilies: the natriuretic peptide receptors (NPRs), sensory organ-specific membrane GCs, and the enterotoxin/guanylin receptors. The binding of peptide ligands to the receptor results in the activation of the cytosolic catalytic domain. Three types of NPRs have been cloned from mammalian tissues: NPR-A/GC-A, NPR-B/ GC-B, and NPR-C. In addition, two of the GCs, GC-D and GC-G, appear to be pseudogenes in humans. Atrial natriuretic peptide (ANP) and brain natriuretic peptide (BNP) are produced in the heart, and both bind to the NPR-A. NPR-C, also termed the clearance receptor, binds each of the natriuretic peptides and can alter circulating levels of these peptides. The l
Probab=27.74 E-value=2.6e+02 Score=25.86 Aligned_cols=66 Identities=8% Similarity=-0.111 Sum_probs=32.4
Q ss_pred CCCcEEEEecCchH-HHHHHHHHHhcC--CCCCCCcee--eccCCCCHHHHHHHHHHHHhhhccCCCCCeEEEEeccccc
Q 024560 111 PKGRIWTMVAGGGA-SVIYADTVGDLG--YASELGNYA--EYSGAPNEEEVLQYARVVIDCATADPDGRKRALLIGGGIA 185 (266)
Q Consensus 111 l~G~Igii~NGaGl-am~t~D~l~~~g--~gg~pAN~l--DlgG~a~~~~~~~al~~ll~~~~~d~~v~~vlvni~ggi~ 185 (266)
+.|..+........ ..+++|.|+..| .+|.+-.++ |..+++. .....+.+++ . ++++.+|+ |+..
T Consensus 8 ~sG~~~~~g~~~~~a~~lAve~iN~~g~~i~g~~l~~~~~D~~~~~~-~a~~~a~~l~-~----~~~v~aii----G~~~ 77 (389)
T cd06352 8 WNTDYPFSLARVGPAIQLAVERVNADPNLLPGYDFTFVYLDTECSES-VALLAAVDLY-W----EHNVDAFI----GPGC 77 (389)
T ss_pred CCCCCCchhhcchHHHHHHHHHHhcCCCCCCCceEEEEEecCCCchh-hhHHHHHHHH-h----hcCCcEEE----CCCC
Confidence 34444444333333 346899999985 123343333 4444332 2344444443 3 46766544 6654
Q ss_pred c
Q 024560 186 N 186 (266)
Q Consensus 186 ~ 186 (266)
+
T Consensus 78 s 78 (389)
T cd06352 78 P 78 (389)
T ss_pred h
Confidence 4
No 210
>TIGR01362 KDO8P_synth 3-deoxy-8-phosphooctulonate synthase. In Gram-negative bacteria, this is the first step in the biosynthesis of 3-deoxy-D-manno-octulosonate, part of the oligosaccharide core of lipopolysaccharide.
Probab=27.72 E-value=3.2e+02 Score=25.24 Aligned_cols=25 Identities=32% Similarity=0.683 Sum_probs=21.7
Q ss_pred eCCCCHHHHHHHHHhhhhhcCCcee
Q 024560 219 RGGPNYQTGLAKMRALGEELGIPLE 243 (266)
Q Consensus 219 l~G~~~~~~~~~L~~~~~~~Gip~~ 243 (266)
..|...++|+++|++..++.|+|+.
T Consensus 53 FqG~G~eeGL~iL~~vk~~~glpvv 77 (258)
T TIGR01362 53 FRGPGLEEGLKILQKVKEEFGVPIL 77 (258)
T ss_pred CCCCCHHHHHHHHHHHHHHhCCceE
Confidence 5677779999999999999999973
No 211
>PF12327 FtsZ_C: FtsZ family, C-terminal domain; InterPro: IPR024757 The FtsZ family of proteins are involved in polymer formation. FtsZ is the polymer-forming protein of bacterial cell division. It is part of a ring in the middle of the dividing cell that is required for constriction of cell membrane and cell envelope to yield two daughter cells. FtsZ is a GTPase, like tubulin []. FtsZ can polymerise into tubes, sheets, and rings in vitro and is ubiquitous in eubacteria and archaea []. This entry represents a domain of FtsZ. In most FtsZ proteins is found in the C terminus, except in some alphaproteobacteria proteins where there is an extension C-terminal domain TIGR03483 from TIGRFAMs.; PDB: 2RHO_B 2RHJ_A 2VXY_A 2RHL_B 2RHH_A 2VAM_A 1W5F_B 2R75_1 2R6R_1 1RQ7_A ....
Probab=27.66 E-value=96 Score=23.76 Aligned_cols=48 Identities=21% Similarity=0.328 Sum_probs=26.6
Q ss_pred HHHHHHHHHHHHhhhccC---CCCCeEEEEecccc-cchhHhhhhHHHHHHHHHHh
Q 024560 153 EEEVLQYARVVIDCATAD---PDGRKRALLIGGGI-ANFTDVATTFNGIIRALREK 204 (266)
Q Consensus 153 ~~~~~~al~~ll~~~~~d---~~v~~vlvni~ggi-~~~~~vA~~~~gii~al~~~ 204 (266)
..+..+|++-.++..+-+ .+-+++|||+.||- .+-.++ +-+++.++++
T Consensus 13 ~~r~~~Av~~Al~spLl~~~i~~A~~vLvni~~~~d~~l~ev----~~~~~~i~~~ 64 (95)
T PF12327_consen 13 ENRAEEAVEQALNSPLLDVDIKGAKGVLVNITGGPDLSLSEV----NEAMEIIREK 64 (95)
T ss_dssp TTHHHHHHHHHHTSTTSTS-GGG-SEEEEEEEE-TTS-HHHH----HHHHHHHHHH
T ss_pred ccHHHHHHHHHHhCccccCChHHhceEEEEEEcCCCCCHHHH----HHHHHHHHHH
Confidence 456777777777621111 14679999987764 333343 4455666665
No 212
>cd07118 ALDH_SNDH Gluconobacter oxydans L-sorbosone dehydrogenase-like. Included in this CD is the L-sorbosone dehydrogenase (SNDH) from Gluconobacter oxydans UV10. In G. oxydans, D-sorbitol is converted to 2-keto-L-gulonate (a precursor of L-ascorbic acid) in sequential oxidation steps catalyzed by a FAD-dependent, L-sorbose dehydrogenase and an NAD(P)+-dependent, L-sorbosone dehydrogenase.
Probab=27.57 E-value=5.8e+02 Score=24.80 Aligned_cols=31 Identities=10% Similarity=0.160 Sum_probs=18.1
Q ss_pred HHHHHHHHHHHHHHHhCCceeeEeeccee-cCCce
Q 024560 19 GKIGDFIMGVFAVFQDLDFSFIEMNPFTL-VNGEP 52 (266)
Q Consensus 19 ~~~~~ii~~Ly~~f~~~D~~l~EINPLvv-~~g~~ 52 (266)
++-.+++.++.+++.++--.|++ +.. +.|+.
T Consensus 43 ~~R~~~l~~~a~~l~~~~~~la~---~~~~e~Gk~ 74 (454)
T cd07118 43 AERAAVLLKVADLIRARRERLAL---IETLESGKP 74 (454)
T ss_pred HHHHHHHHHHHHHHHHhHHHHHH---HHHHHcCCC
Confidence 45566777777777776543333 333 45554
No 213
>PRK05198 2-dehydro-3-deoxyphosphooctonate aldolase; Provisional
Probab=27.56 E-value=3.3e+02 Score=25.23 Aligned_cols=25 Identities=28% Similarity=0.626 Sum_probs=21.8
Q ss_pred eCCCCHHHHHHHHHhhhhhcCCcee
Q 024560 219 RGGPNYQTGLAKMRALGEELGIPLE 243 (266)
Q Consensus 219 l~G~~~~~~~~~L~~~~~~~Gip~~ 243 (266)
..|...++|+++|++..++.|+|+.
T Consensus 61 FqG~G~eeGL~~L~~vk~~~Glpvv 85 (264)
T PRK05198 61 FRGPGLEEGLKILQEVKETFGVPVL 85 (264)
T ss_pred CCCCChHHHHHHHHHHHHHHCCceE
Confidence 5677789999999999999999973
No 214
>cd07114 ALDH_DhaS Uncharacterized Candidatus pelagibacter aldehyde dehydrogenase, DhaS-like. Uncharacterized aldehyde dehydrogenase from Candidatus pelagibacter (DhaS) and other related sequences are present in this CD.
Probab=27.25 E-value=5.8e+02 Score=24.71 Aligned_cols=30 Identities=13% Similarity=0.191 Sum_probs=16.4
Q ss_pred HHHHHHHHHHHHHHhCCceeeEeeccee-cCCce
Q 024560 20 KIGDFIMGVFAVFQDLDFSFIEMNPFTL-VNGEP 52 (266)
Q Consensus 20 ~~~~ii~~Ly~~f~~~D~~l~EINPLvv-~~g~~ 52 (266)
+=.+++.++.+++.++--.|+++ .. ..|+.
T Consensus 44 ~R~~~L~~~a~~l~~~~~~l~~~---~~~e~Gk~ 74 (457)
T cd07114 44 ERGKLLRRLADLIEANAEELAEL---ETRDNGKL 74 (457)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHH---HHHhcCCC
Confidence 33566667777776654444443 23 55654
No 215
>TIGR03407 urea_ABC_UrtA urea ABC transporter, urea binding protein. Members of this protein family are ABC transporter substrate-binding proteins associated with urea transport and metabolism. This protein is found in a conserved five-gene transport operon typically found adjacent to urease genes. It was shown in Cyanobacteria that disruption leads to the loss of high-affinity urea transport activity. Members of this protein family tend to have the twin-arginine signal for Sec-independent transport across the plasma membrane.
Probab=27.20 E-value=5e+02 Score=23.92 Aligned_cols=104 Identities=13% Similarity=0.078 Sum_probs=52.8
Q ss_pred HHHHHHHHHhcC-CCCCCCceeeccCCCCHHHHHHHHHHHHhhhccCCCCCeEEEEecccccchhHhhhhHHHHHHHHHH
Q 024560 125 SVIYADTVGDLG-YASELGNYAEYSGAPNEEEVLQYARVVIDCATADPDGRKRALLIGGGIANFTDVATTFNGIIRALRE 203 (266)
Q Consensus 125 am~t~D~l~~~g-~gg~pAN~lDlgG~a~~~~~~~al~~ll~~~~~d~~v~~vlvni~ggi~~~~~vA~~~~gii~al~~ 203 (266)
+.++.|.++..| ..|+|-..+-.--..++++-..+.+-+++ +.+|.+|+ |+..+.. + .+++..+.+
T Consensus 24 ~~lav~~iN~~GGi~G~~i~l~~~Dd~~~p~~a~~~a~~Lv~----~~~V~~ii----G~~~S~~--~---~a~~~~~~~ 90 (359)
T TIGR03407 24 ELMAIEEINASGGVLGKKIEPVVEDGASDWPTFAEKARKLIT----QDKVAAVF----GCWTSAS--R---KAVLPVFEE 90 (359)
T ss_pred HHHHHHHHHhcCCCCCcEEEEEEeCCCCCHHHHHHHHHHHHh----hCCCcEEE----cCCcHHH--H---HHHHHHHhc
Confidence 455788998884 12555444433333456666666666665 56665554 6554443 2 344554444
Q ss_pred hhhhhh-------cccceEEEEeCCCCHHHHHHHHHhhhhhcCCc
Q 024560 204 KESKLK-------AARMHIFVRRGGPNYQTGLAKMRALGEELGIP 241 (266)
Q Consensus 204 ~~~~~~-------~~~~pvvvrl~G~~~~~~~~~L~~~~~~~Gip 241 (266)
.+..+. ....|.+.|.+.+....+..+++-..++.|+.
T Consensus 91 ~~~~~i~~~~~~~~~~~~~~F~~~~~~~~~~~~~~~~~~~~~g~k 135 (359)
T TIGR03407 91 NNGLLFYPVQYEGEECSPNIFYTGAAPNQQIIPAVDYLLSKKGAK 135 (359)
T ss_pred cCCceEeCCcccCcccCCCEEEcCCChHHHHHHHHHHHHhccCCc
Confidence 321000 01234455777776666555544332334643
No 216
>PF00171 Aldedh: Aldehyde dehydrogenase family; InterPro: IPR015590 Aldehyde dehydrogenases (1.2.1.3 from EC and 1.2.1.5 from EC) are enzymes that oxidize a wide variety of aliphatic and aromatic aldehydes using NADP as a cofactor. In mammals at least four different forms of the enzyme are known []: class-1 (or Ald C) a tetrameric cytosolic enzyme, class-2 (or Ald M) a tetrameric mitochondrial enzyme, class- 3 (or Ald D) a dimeric cytosolic enzyme, and class IV a microsomal enzyme. Aldehyde dehydrogenases have also been sequenced from fungal and bacterial species. A number of enzymes are known to be evolutionary related to aldehyde dehydrogenases. A glutamic acid and a cysteine residue have been implicated in the catalytic activity of mammalian aldehyde dehydrogenase. These residues are conserved in all the enzymes of this entry. Some of the proteins in this entry are allergens. Allergies are hypersensitivity reactions of the immune system to specific substances called allergens (such as pollen, stings, drugs, or food) that, in most people, result in no symptoms. A nomenclature system has been established for antigens (allergens) that cause IgE-mediated atopic allergies in humans [WHO/IUIS Allergen Nomenclature Subcommittee King T.P., Hoffmann D., Loewenstein H., Marsh D.G., Platts-Mills T.A.E., Thomas W. Bull. World Health Organ. 72:797-806(1994)]. This nomenclature system is defined by a designation that is composed of the first three letters of the genus; a space; the first letter of the species name; a space and an arabic number. In the event that two species names have identical designations, they are discriminated from one another by adding one or more letters (as necessary) to each species designation. The allergens in this family include allergens with the following designations: Alt a 10 and Cla h 3.; GO: 0016491 oxidoreductase activity, 0008152 metabolic process, 0055114 oxidation-reduction process; PDB: 3R31_A 3HAZ_A 1UXQ_A 1UXP_A 1UXR_A 1UXU_A 1UXN_A 1KY8_A 1UXT_A 1UXV_A ....
Probab=26.85 E-value=3.6e+02 Score=26.18 Aligned_cols=20 Identities=15% Similarity=0.222 Sum_probs=10.2
Q ss_pred ceeecCCCCCHHHHHHHHHHH
Q 024560 241 PLEVYGPEATMTGICKQAIDC 261 (266)
Q Consensus 241 p~~~~~~~~~~~eAv~~av~~ 261 (266)
|+.++. ..+++.|++..+.-
T Consensus 241 p~iV~~-daDld~aa~~iv~~ 260 (462)
T PF00171_consen 241 PVIVDP-DADLDKAAEAIVRG 260 (462)
T ss_dssp EEEE-T-TSHHHHHHHHHHHH
T ss_pred eeeEec-ccccccccccccch
Confidence 334444 44666666666553
No 217
>PRK09195 gatY tagatose-bisphosphate aldolase; Reviewed
Probab=26.56 E-value=3e+02 Score=25.57 Aligned_cols=21 Identities=10% Similarity=0.097 Sum_probs=9.4
Q ss_pred cceEEEEe-CCCCHHHHHHHHH
Q 024560 212 RMHIFVRR-GGPNYQTGLAKMR 232 (266)
Q Consensus 212 ~~pvvvrl-~G~~~~~~~~~L~ 232 (266)
++||.+-| -|.+.+..++.++
T Consensus 74 ~VPV~lHLDHg~~~e~i~~Ai~ 95 (284)
T PRK09195 74 HHPLALHLDHHEKFDDIAQKVR 95 (284)
T ss_pred CCCEEEECCCCCCHHHHHHHHH
Confidence 45555522 2334444444444
No 218
>PLN02898 HMP-P kinase/thiamin-monophosphate pyrophosphorylase
Probab=26.46 E-value=3.1e+02 Score=27.15 Aligned_cols=74 Identities=19% Similarity=0.179 Sum_probs=46.7
Q ss_pred cCchHHHHH-HHHHHhcCCCCCC-------CceeeccC--CCCHHHHHHHHHHHHhhhccCCCCCeEEEEecccccchhH
Q 024560 120 AGGGASVIY-ADTVGDLGYASEL-------GNYAEYSG--APNEEEVLQYARVVIDCATADPDGRKRALLIGGGIANFTD 189 (266)
Q Consensus 120 NGaGlam~t-~D~l~~~g~gg~p-------AN~lDlgG--~a~~~~~~~al~~ll~~~~~d~~v~~vlvni~ggi~~~~~ 189 (266)
..||.++.+ .=.+...|+.+-+ .|...+.+ ..+++-+.+.++.+++ |-.+++|.+ |-+ .+.+
T Consensus 20 ~~gGAGi~aDl~t~~a~G~~~~~v~Talt~q~t~~v~~~~~~~~~~~~~ql~~~~~----d~~~~aik~---G~l-~~~~ 91 (502)
T PLN02898 20 SGAGAGIQADIKACAARGVYCTTAITAVTAQNTVGVQGVHAVPLDFVAEQLKSVLS----DMPVDVVKT---GML-PSAE 91 (502)
T ss_pred CCcHHHHHHHHHHHHHcCCEecceeeEEEEEcCCccceeeeCCHHHHHHHHHHHHh----CCCCCEEEE---CCc-CCHH
Confidence 345566655 6667777433332 25444444 5677888899999987 778887774 333 3355
Q ss_pred hhhhHHHHHHHHHHh
Q 024560 190 VATTFNGIIRALREK 204 (266)
Q Consensus 190 vA~~~~gii~al~~~ 204 (266)
++ +.|++.+++.
T Consensus 92 ~i---~~i~~~l~~~ 103 (502)
T PLN02898 92 IV---KVLCQALKEF 103 (502)
T ss_pred HH---HHHHHHHHhC
Confidence 55 7788877765
No 219
>TIGR01236 D1pyr5carbox1 delta-1-pyrroline-5-carboxylate dehydrogenase, group 1. This model represents one of two related branches of delta-1-pyrroline-5-carboxylate dehydrogenase. The two branches are not as closely related to each other as some aldehyde dehydrogenases are to this branch, and separate models are built for this reason. The enzyme is the second of two in the degradation of proline to glutamate.
Probab=26.35 E-value=5.7e+02 Score=25.66 Aligned_cols=19 Identities=16% Similarity=-0.013 Sum_probs=9.9
Q ss_pred ceeecCCCCCHHHHHHHHHH
Q 024560 241 PLEVYGPEATMTGICKQAID 260 (266)
Q Consensus 241 p~~~~~~~~~~~eAv~~av~ 260 (266)
|+.++. ..+++.|++.++.
T Consensus 290 p~IV~~-dADl~~Aa~~i~~ 308 (533)
T TIGR01236 290 FHVVHP-SADIDHAVTATIR 308 (533)
T ss_pred eEEECC-CCCHHHHHHHHHH
Confidence 334444 4466666665554
No 220
>PRK00141 murD UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional
Probab=26.31 E-value=5.7e+02 Score=25.02 Aligned_cols=90 Identities=16% Similarity=0.168 Sum_probs=45.7
Q ss_pred CCCHHHHHHHHHHHHhhhccCCCCCeEEEEecccccchhHhhhhHHHHHHHHHHhhhhhhcccceEEEEeCCCCHHHHHH
Q 024560 150 APNEEEVLQYARVVIDCATADPDGRKRALLIGGGIANFTDVATTFNGIIRALREKESKLKAARMHIFVRRGGPNYQTGLA 229 (266)
Q Consensus 150 ~a~~~~~~~al~~ll~~~~~d~~v~~vlvni~ggi~~~~~vA~~~~gii~al~~~~~~~~~~~~pvvvrl~G~~~~~~~~ 229 (266)
+.+|+.+..+++.+ .+ ++.++||..+-.++ +.++..+.+.. . -+++ ++.+.. .-.+
T Consensus 342 ahNp~s~~~~l~~l------~~-----~~~i~gG~~kdkd~----~~~~~~l~~~~------~-~~~~-~~~~r~-~~~~ 397 (473)
T PRK00141 342 ATNPHAADAALAGH------ES-----VVWVAGGQLKGADI----DDLIRTHAPRI------K-AAVV-LGVDRA-EIVA 397 (473)
T ss_pred CCCHHHHHHHHHhc------CC-----EEEEecCccCCCCh----HHHHHHHHhhc------c-EEEE-ECCCHH-HHHH
Confidence 67888888886664 11 24458888665443 45666554431 1 1333 454433 2233
Q ss_pred HHHhhhhhcCCceeec-CCCCCHHHHHHHHHHHhh
Q 024560 230 KMRALGEELGIPLEVY-GPEATMTGICKQAIDCIM 263 (266)
Q Consensus 230 ~L~~~~~~~Gip~~~~-~~~~~~~eAv~~av~~~~ 263 (266)
-|.+.....++....+ +.++++++|++.+.+++.
T Consensus 398 ~l~~~~~~~~~~~~~~~~~~~~l~~Av~~a~~~a~ 432 (473)
T PRK00141 398 ALAEHAPDAPVTVTDSTDPEEAMEEAVSAAVSLAE 432 (473)
T ss_pred HHHhcCCCCcEEEecCcccccCHHHHHHHHHHhCC
Confidence 3332111122222111 112367999999988764
No 221
>KOG2862 consensus Alanine-glyoxylate aminotransferase AGT1 [General function prediction only]
Probab=26.19 E-value=3.9e+02 Score=25.80 Aligned_cols=109 Identities=17% Similarity=0.271 Sum_probs=79.8
Q ss_pred HHHcCCChhHHHHHHHHHHHHHHHHHhCCceeeEeeccee-cCCceEEeeccccccCcccccCccccccccCCCCCCCCC
Q 024560 8 PLIATLPLEFRGKIGDFIMGVFAVFQDLDFSFIEMNPFTL-VNGEPYPLDMRGELDDTAAFKNFKKWANIEFPLPFGRVL 86 (266)
Q Consensus 8 ~l~~gl~~~~~~~~~~ii~~Ly~~f~~~D~~l~EINPLvv-~~g~~~alD~k~~iDd~A~~R~~~~~~~~~~~~~~~~~~ 86 (266)
+.+-...++....+.++++.+-.+|..... -|+++ ..| |.- |.
T Consensus 39 ~~lgh~sPe~~qIm~~v~egikyVFkT~n~-----~tf~isgsG------------------h~g-~E------------ 82 (385)
T KOG2862|consen 39 PSLGHMSPEFVQIMDEVLEGIKYVFKTANA-----QTFVISGSG------------------HSG-WE------------ 82 (385)
T ss_pred CccccCCHHHHHHHHHHHHHHHHHhccCCC-----ceEEEecCC------------------cch-HH------------
Confidence 445566788888888888888888886544 46677 555 333 31
Q ss_pred ChhhhhhcccccccccccCceEecCCCcEEEEecCchHHHHHHHHHHhcCCCCC--CCceeeccCCCCHHHHHHHHHHHH
Q 024560 87 SSTESFIHSLDEKTSASLKFTVLNPKGRIWTMVAGGGASVIYADTVGDLGYASE--LGNYAEYSGAPNEEEVLQYARVVI 164 (266)
Q Consensus 87 ~~~E~~a~~~d~~~~~~~~l~~v~l~G~Igii~NGaGlam~t~D~l~~~g~gg~--pAN~lDlgG~a~~~~~~~al~~ll 164 (266)
. .=.|.++++.++-+..+|- -+--+.|....+ |-+ +- ..|.|+..+-+.+.++ |
T Consensus 83 ----~------------al~N~lePgd~vLv~~~G~-wg~ra~D~~~r~--ga~V~~v-~~~~G~~~~le~i~~~----l 138 (385)
T KOG2862|consen 83 ----A------------ALVNLLEPGDNVLVVSTGT-WGQRAADCARRY--GAEVDVV-EADIGQAVPLEEITEK----L 138 (385)
T ss_pred ----H------------HHHhhcCCCCeEEEEEech-HHHHHHHHHHhh--CceeeEE-ecCcccCccHHHHHHH----H
Confidence 1 1145677888898888887 788889999999 454 23 6789999999998888 6
Q ss_pred hhhccCCCCCeEEEEe
Q 024560 165 DCATADPDGRKRALLI 180 (266)
Q Consensus 165 ~~~~~d~~v~~vlvni 180 (266)
+ +-..+++||-+
T Consensus 139 s----qh~p~~vfv~h 150 (385)
T KOG2862|consen 139 S----QHKPKAVFVTH 150 (385)
T ss_pred H----hcCCceEEEEe
Confidence 6 56778888875
No 222
>PRK01390 murD UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional
Probab=26.19 E-value=4.3e+02 Score=25.53 Aligned_cols=86 Identities=17% Similarity=0.155 Sum_probs=47.1
Q ss_pred eeeccCCCCHHHHHHHHHHHHhhhccCCCCCeEEEEecccccchhHhhhhHHHHHHHHHHhhhhhhcccceEEEEeCCCC
Q 024560 144 YAEYSGAPNEEEVLQYARVVIDCATADPDGRKRALLIGGGIANFTDVATTFNGIIRALREKESKLKAARMHIFVRRGGPN 223 (266)
Q Consensus 144 ~lDlgG~a~~~~~~~al~~ll~~~~~d~~v~~vlvni~ggi~~~~~vA~~~~gii~al~~~~~~~~~~~~pvvvrl~G~~ 223 (266)
++|=.++.+++.+.++++.+ . + ++.|+|+...- ... +.+...+. .+..+ .+-|.+
T Consensus 334 vIdDs~ahNp~s~~~aL~~~------~---~--i~~I~G~~d~~-~~~---~~L~~~~~---------~v~~v-~~~g~~ 388 (460)
T PRK01390 334 FVNDSKATNADAAAKALSSF------D---R--IYWIAGGKPKE-GGI---ESLAPFFP---------RIAKA-YLIGEA 388 (460)
T ss_pred EEEcCCCCCHHHHHHHHHhC------C---C--eEEEecCccCC-CCH---HHHHHHHH---------hhCEE-EEECCC
Confidence 45334668888888876632 1 2 23356764322 222 33333221 11122 223667
Q ss_pred HHHHHHHHHhhhhhcCCceeecCCCCCHHHHHHHHHHHh
Q 024560 224 YQTGLAKMRALGEELGIPLEVYGPEATMTGICKQAIDCI 262 (266)
Q Consensus 224 ~~~~~~~L~~~~~~~Gip~~~~~~~~~~~eAv~~av~~~ 262 (266)
.++-++.+. .. +++.. +.++++|++.+.+.+
T Consensus 389 ~~~l~~~~~----~~-~~~~~---~~~l~~Av~~a~~~a 419 (460)
T PRK01390 389 AEAFAATLG----GA-VPFEI---CGTLERAVAAAAADA 419 (460)
T ss_pred HHHHHHHHh----cC-CCEEE---eCCHHHHHHHHHHhh
Confidence 777667776 32 45554 459999999998876
No 223
>PRK10206 putative oxidoreductase; Provisional
Probab=26.11 E-value=3.5e+02 Score=25.25 Aligned_cols=56 Identities=18% Similarity=0.256 Sum_probs=32.2
Q ss_pred CCCCCeEEEEecccccchhHhhhhHHHHHHHHHHhhhhhhcccceEEE-EeCCCCHHHHHHHHHhhhhhcCCce
Q 024560 170 DPDGRKRALLIGGGIANFTDVATTFNGIIRALREKESKLKAARMHIFV-RRGGPNYQTGLAKMRALGEELGIPL 242 (266)
Q Consensus 170 d~~v~~vlvni~ggi~~~~~vA~~~~gii~al~~~~~~~~~~~~pvvv-rl~G~~~~~~~~~L~~~~~~~Gip~ 242 (266)
++++++|+|-.|.. .+++-+.++++. .++|++ .=-..+.++++++++. ++++|+.+
T Consensus 62 ~~~iD~V~I~tp~~--------~H~~~~~~al~a--------GkhVl~EKPla~~~~ea~~l~~~-a~~~~~~l 118 (344)
T PRK10206 62 DPDVKLVVVCTHAD--------SHFEYAKRALEA--------GKNVLVEKPFTPTLAEAKELFAL-AKSKGLTV 118 (344)
T ss_pred CCCCCEEEEeCCch--------HHHHHHHHHHHc--------CCcEEEecCCcCCHHHHHHHHHH-HHHhCCEE
Confidence 78888888765532 122444444432 355665 4444567777777663 34557664
No 224
>PRK09457 astD succinylglutamic semialdehyde dehydrogenase; Reviewed
Probab=25.98 E-value=6.4e+02 Score=24.80 Aligned_cols=22 Identities=9% Similarity=0.087 Sum_probs=12.9
Q ss_pred HHHHHHHHHHHHHHhCCceeeE
Q 024560 20 KIGDFIMGVFAVFQDLDFSFIE 41 (266)
Q Consensus 20 ~~~~ii~~Ly~~f~~~D~~l~E 41 (266)
+=.+++.++.+++.++--.+++
T Consensus 60 ~R~~~L~~~a~~l~~~~~ela~ 81 (487)
T PRK09457 60 ERQAIVERFAALLEENKEELAE 81 (487)
T ss_pred HHHHHHHHHHHHHHhHHHHHHH
Confidence 3456666677766666544444
No 225
>cd07111 ALDH_F16 Aldehyde dehydrogenase family 16A1-like. Uncharacterized aldehyde dehydrogenase family 16 member A1 (ALDH16A1) and other related sequences are present in this CD. The active site cysteine and glutamate residues are not conserved in the human ALDH16A1 protein sequence.
Probab=25.72 E-value=6.5e+02 Score=24.79 Aligned_cols=15 Identities=7% Similarity=0.071 Sum_probs=7.9
Q ss_pred HHHHHHHHHHHHhCC
Q 024560 22 GDFIMGVFAVFQDLD 36 (266)
Q Consensus 22 ~~ii~~Ly~~f~~~D 36 (266)
.+++.++.+++.+.-
T Consensus 84 ~~~L~~~a~~l~~~~ 98 (480)
T cd07111 84 ARHLYRIARHIQKHQ 98 (480)
T ss_pred HHHHHHHHHHHHHhH
Confidence 455555555555543
No 226
>PRK02628 nadE NAD synthetase; Reviewed
Probab=25.67 E-value=5.1e+02 Score=26.96 Aligned_cols=85 Identities=16% Similarity=0.132 Sum_probs=49.5
Q ss_pred HHhhhccCCCCCeEEEEecccccchhHhhhhHHHHHHHHHHhhhhhhcccceEE-EEeCCC-CHHHHHHHHHhhhhhcCC
Q 024560 163 VIDCATADPDGRKRALLIGGGIANFTDVATTFNGIIRALREKESKLKAARMHIF-VRRGGP-NYQTGLAKMRALGEELGI 240 (266)
Q Consensus 163 ll~~~~~d~~v~~vlvni~ggi~~~~~vA~~~~gii~al~~~~~~~~~~~~pvv-vrl~G~-~~~~~~~~L~~~~~~~Gi 240 (266)
+.+++.+ -+.+.++|-+-||+-++ .++ --.+++++..+. .+..|+ +.|.|. +.+..++..++.++..|+
T Consensus 352 l~~~~~~-~~~~~vvvglSGGiDSa-l~l---~l~~~a~~~lg~----~~~~v~~v~mp~~~ss~~s~~~a~~la~~LGi 422 (679)
T PRK02628 352 LAQRLRA-TGLKKVVIGISGGLDST-HAL---LVAAKAMDRLGL----PRKNILAYTMPGFATTDRTKNNAVALMKALGV 422 (679)
T ss_pred HHHHHHH-cCCCeEEEECCCCHHHH-HHH---HHHHHHHHhhCC----CcceEEEEECCCCCCCHHHHHHHHHHHHHhCC
Confidence 3344443 34788888898887655 333 334455443320 123344 577664 334555666666668899
Q ss_pred ceeecCCCCCHHHHHHHHHH
Q 024560 241 PLEVYGPEATMTGICKQAID 260 (266)
Q Consensus 241 p~~~~~~~~~~~eAv~~av~ 260 (266)
+.+.. ++++++.....
T Consensus 423 ~~~~i----~I~~~~~~~~~ 438 (679)
T PRK02628 423 TAREI----DIRPAALQMLK 438 (679)
T ss_pred eEEEE----EcHHHHHHHHH
Confidence 98754 56777766544
No 227
>PF10440 WIYLD: Ubiquitin-binding WIYLD domain; InterPro: IPR018848 This entry represents a presumed domain which has been predicted to contain three alpha helices. It was named the WIYLD domain based on the pattern of the ost conserved residues []. This domain appears to be specific to plant SET-domain proteins. ; GO: 0018024 histone-lysine N-methyltransferase activity
Probab=25.51 E-value=62 Score=23.60 Aligned_cols=26 Identities=8% Similarity=0.355 Sum_probs=19.7
Q ss_pred CCChhHHHHHHHHHHHHHHHHHhCCceeeE
Q 024560 12 TLPLEFRGKIGDFIMGVFAVFQDLDFSFIE 41 (266)
Q Consensus 12 gl~~~~~~~~~~ii~~Ly~~f~~~D~~l~E 41 (266)
|++.+ ++...+.+|+++|. ++-.++|
T Consensus 22 G~~~~---~v~~vl~~LL~lY~-~nW~lIE 47 (65)
T PF10440_consen 22 GFSKK---QVRPVLKNLLKLYD-GNWELIE 47 (65)
T ss_pred CCCHH---HHHHHHHHHHHHHc-CCchhhh
Confidence 66644 78888999999995 5577776
No 228
>cd05569 PTS_IIB_fructose PTS_IIB_fructose: subunit IIB of enzyme II (EII) of the fructose-specific phosphoenolpyruvate:carbohydrate phosphotransferase system (PTS). In this system, EII (also referred to as FruAB) is a fructose-specific permease made up of two proteins (FruA and FruB) each containing 3 domains. The FruA protein contains two tandem nonidentical IIB domains and a C-terminal IIC transmembrane domain. Both IIB domains of FruA are included in this alignment. The FruB protein (also referred to as diphosphoryl transfer protein) contains a IIA domain, a domain of unknown function, and an Hpr-like domain called FPr (fructose-inducible HPr). This familiy also includes the IIB domains of several fructose-like PTS permeases including the Frv permease encoded by the frvABXR operon, the Frw permease encoded by the frwACBD operon, the Frx permease encoded by the hrsA gene, and the Fry permease encoded by the fryABC (ypdDGH) operon. FruAB takes up exogenous fructose, releasing the 1-p
Probab=25.22 E-value=3e+02 Score=20.86 Aligned_cols=71 Identities=17% Similarity=0.144 Sum_probs=40.7
Q ss_pred EecccccchhHhhhhHHHHHHHHHHhhhhhh-----------------cccceEEEEeCCCCHHHHHHHHHhhhhhcCCc
Q 024560 179 LIGGGIANFTDVATTFNGIIRALREKESKLK-----------------AARMHIFVRRGGPNYQTGLAKMRALGEELGIP 241 (266)
Q Consensus 179 ni~ggi~~~~~vA~~~~gii~al~~~~~~~~-----------------~~~~pvvvrl~G~~~~~~~~~L~~~~~~~Gip 241 (266)
..+.|++.+..++ +.+-+++++.+-... -..--+|+..+....+. ..|. |.|
T Consensus 6 ac~~G~a~s~laa---~~L~~aa~~~g~~~~ve~~~~~g~~~~l~~~~i~~Ad~vi~~~~~~~~~--~rf~------gk~ 74 (96)
T cd05569 6 ACPTGIAHTYMAA---EALEKAAKKLGWEIKVETQGSLGIENELTAEDIAEADAVILAADVPVDD--ERFA------GKR 74 (96)
T ss_pred ECCCchhHHHHHH---HHHHHHHHHCCCeEEEEEecCcCccCcCCHHHHhhCCEEEEecCCCCch--hhhC------CCe
Confidence 3578888888777 888787776541000 00111333444433333 4555 777
Q ss_pred eeecCCCCCHHHHHHHHHHHhhh
Q 024560 242 LEVYGPEATMTGICKQAIDCIMS 264 (266)
Q Consensus 242 ~~~~~~~~~~~eAv~~av~~~~~ 264 (266)
++ ..+++++++..-....+
T Consensus 75 v~----~~~~~~~l~~~~~vl~~ 93 (96)
T cd05569 75 VY----EVSVAEAIKDAEAVIER 93 (96)
T ss_pred EE----EecHHHHHHHHHHHHHH
Confidence 75 45888888877665544
No 229
>PRK07511 enoyl-CoA hydratase; Provisional
Probab=25.08 E-value=4.1e+02 Score=23.59 Aligned_cols=75 Identities=15% Similarity=0.078 Sum_probs=39.1
Q ss_pred HHHHHHHhhhccCCCCCeEEEEe----cccccchhHhhh-------hHHHHHHHHHHhhhhhhcccceEEEEeCCCCHHH
Q 024560 158 QYARVVIDCATADPDGRKRALLI----GGGIANFTDVAT-------TFNGIIRALREKESKLKAARMHIFVRRGGPNYQT 226 (266)
Q Consensus 158 ~al~~ll~~~~~d~~v~~vlvni----~ggi~~~~~vA~-------~~~gii~al~~~~~~~~~~~~pvvvrl~G~~~~~ 226 (266)
+.+.-.++.+..||++++|++-- |....+..++.. ........+++.-+.+...++|+|..+.|.-..-
T Consensus 33 ~~l~~~l~~~~~d~~vr~vVl~g~g~~F~~G~Dl~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~kpvIAav~G~a~Gg 112 (260)
T PRK07511 33 AAGIEALNTAERDPSIRAVVLTGAGGFFCAGGNLNRLLENRAKPPSVQAASIDGLHDWIRAIRAFPKPVIAAVEGAAAGA 112 (260)
T ss_pred HHHHHHHHHhccCCCeEEEEEECCCCCcccCcCHHHHhhcccccchhHHHHHHHHHHHHHHHHcCCCCEEEEECCeeehH
Confidence 33444444455599999888852 222233332221 0011122222221112235799999999988887
Q ss_pred HHHHHH
Q 024560 227 GLAKMR 232 (266)
Q Consensus 227 ~~~~L~ 232 (266)
|..+.-
T Consensus 113 G~~lal 118 (260)
T PRK07511 113 GFSLAL 118 (260)
T ss_pred HHHHHH
Confidence 777665
No 230
>PF00448 SRP54: SRP54-type protein, GTPase domain; InterPro: IPR000897 The signal recognition particle (SRP) is a multimeric protein, which along with its conjugate receptor (SR), is involved in targeting secretory proteins to the rough endoplasmic reticulum (RER) membrane in eukaryotes, or to the plasma membrane in prokaryotes [, ]. SRP recognises the signal sequence of the nascent polypeptide on the ribosome, retards its elongation, and docks the SRP-ribosome-polypeptide complex to the RER membrane via the SR receptor. Eukaryotic SRP consists of six polypeptides (SRP9, SRP14, SRP19, SRP54, SRP68 and SRP72) and a single 300 nucleotide 7S RNA molecule. The RNA component catalyses the interaction of SRP with its SR receptor []. In higher eukaryotes, the SRP complex consists of the Alu domain and the S domain linked by the SRP RNA. The Alu domain consists of a heterodimer of SRP9 and SRP14 bound to the 5' and 3' terminal sequences of SRP RNA. This domain is necessary for retarding the elongation of the nascent polypeptide chain, which gives SRP time to dock the ribosome-polypeptide complex to the RER membrane. In archaea, the SRP complex contains 7S RNA like its eukaryotic counterpart, yet only includes two of the six protein subunits found in the eukarytic complex: SRP19 and SRP54 []. This entry represents the GTPase domain of the 54 kDa SRP54 component, a GTP-binding protein that interacts with the signal sequence when it emerges from the ribosome. SRP54 of the signal recognition particle has a three-domain structure: an N-terminal helical bundle domain, a GTPase domain, and the M-domain that binds the 7s RNA and also binds the signal sequence. The extreme C-terminal region is glycine-rich and lower in complexity and poorly conserved between species. The GTPase domain is evolutionary related to P-loop NTPase domains found in a variety of other proteins []. These proteins include Escherichia coli and Bacillus subtilis ffh protein (P48), which seems to be the prokaryotic counterpart of SRP54; signal recognition particle receptor alpha subunit (docking protein), an integral membrane GTP-binding protein which ensures, in conjunction with SRP, the correct targeting of nascent secretory proteins to the endoplasmic reticulum membrane; bacterial FtsY protein, which is believed to play a similar role to that of the docking protein in eukaryotes; the pilA protein from Neisseria gonorrhoeae, the homologue of ftsY; and bacterial flagellar biosynthesis protein flhF.; GO: 0005525 GTP binding, 0006614 SRP-dependent cotranslational protein targeting to membrane; PDB: 2OG2_A 3B9Q_A 3DM9_B 3DMD_B 3E70_C 3DM5_B 2XXA_C 2J28_9 1ZU5_B 1ZU4_A ....
Probab=25.07 E-value=4.5e+02 Score=22.64 Aligned_cols=78 Identities=19% Similarity=0.294 Sum_probs=45.2
Q ss_pred eEEEEecccccchhHhhhhHHHHHHHHHHhhhhhhcccceEEEEeCCCCHHHHHHHHHhhhhhcCCceeecCCCCCHHHH
Q 024560 175 KRALLIGGGIANFTDVATTFNGIIRALREKESKLKAARMHIFVRRGGPNYQTGLAKMRALGEELGIPLEVYGPEATMTGI 254 (266)
Q Consensus 175 ~vlvni~ggi~~~~~vA~~~~gii~al~~~~~~~~~~~~pvvvrl~G~~~~~~~~~L~~~~~~~Gip~~~~~~~~~~~eA 254 (266)
++++.=|.|.-..+.+| + ++..++..+ .++-++. . .+.-..|.+-|+.+++..|+|++......++.+.
T Consensus 3 vi~lvGptGvGKTTt~a---K-LAa~~~~~~-----~~v~lis-~-D~~R~ga~eQL~~~a~~l~vp~~~~~~~~~~~~~ 71 (196)
T PF00448_consen 3 VIALVGPTGVGKTTTIA---K-LAARLKLKG-----KKVALIS-A-DTYRIGAVEQLKTYAEILGVPFYVARTESDPAEI 71 (196)
T ss_dssp EEEEEESTTSSHHHHHH---H-HHHHHHHTT-------EEEEE-E-STSSTHHHHHHHHHHHHHTEEEEESSTTSCHHHH
T ss_pred EEEEECCCCCchHhHHH---H-HHHHHhhcc-----ccceeec-C-CCCCccHHHHHHHHHHHhccccchhhcchhhHHH
Confidence 34444478888888887 4 333333321 2333442 2 2222345666666667889998765545567777
Q ss_pred HHHHHHHhh
Q 024560 255 CKQAIDCIM 263 (266)
Q Consensus 255 v~~av~~~~ 263 (266)
++.+++..+
T Consensus 72 ~~~~l~~~~ 80 (196)
T PF00448_consen 72 AREALEKFR 80 (196)
T ss_dssp HHHHHHHHH
T ss_pred HHHHHHHHh
Confidence 777776543
No 231
>COG0124 HisS Histidyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]
Probab=25.05 E-value=6.7e+02 Score=24.79 Aligned_cols=94 Identities=16% Similarity=0.050 Sum_probs=51.0
Q ss_pred hcccccccccccCceEecCCCcEEEEecCchHHHHHHH-HHHhcCCCCCC--CceeeccCCCCHHHHHHHHHHHHhhhcc
Q 024560 93 IHSLDEKTSASLKFTVLNPKGRIWTMVAGGGASVIYAD-TVGDLGYASEL--GNYAEYSGAPNEEEVLQYARVVIDCATA 169 (266)
Q Consensus 93 a~~~d~~~~~~~~l~~v~l~G~Igii~NGaGlam~t~D-~l~~~g~gg~p--AN~lDlgG~a~~~~~~~al~~ll~~~~~ 169 (266)
+.-||+++|--..+.+.. .|..+.||.|| -.| ++... ||+| | +|-..--+++..+++..-.. ..
T Consensus 265 vRGLDYYtg~VFE~~~~~-~~~~~sI~gGG-----RYD~Lv~~~--gG~~~pa----vGFaiGveRl~~~l~~~~~~-~~ 331 (429)
T COG0124 265 VRGLDYYTGTVFEAVTDG-LGAQGSVCGGG-----RYDGLVEEF--GGKPTPA----VGFAIGVERLILALEEEGKE-DP 331 (429)
T ss_pred ecchhhccceEEEEEEcC-CccccceecCc-----cchHHHHHh--CCCCCCc----eeEehHHHHHHHHHHHcCCC-CC
Confidence 447888888765554433 45588888887 467 66666 6764 4 34444456666665544210 00
Q ss_pred CCCCCeEEEEecccccchhHhhhhHHHHHHHHHHh
Q 024560 170 DPDGRKRALLIGGGIANFTDVATTFNGIIRALREK 204 (266)
Q Consensus 170 d~~v~~vlvni~ggi~~~~~vA~~~~gii~al~~~ 204 (266)
.+...-|+|..+|..+ ..-| --+++.+|+.
T Consensus 332 ~~~~~~v~v~~~~~~~--~~~a---~~la~~LR~~ 361 (429)
T COG0124 332 VETRVDVYVVPLGEDA--EPEA---LKLAQKLRAA 361 (429)
T ss_pred cCCCCCEEEEEcCchh--HHHH---HHHHHHHHHc
Confidence 1223335555555544 2333 4556666654
No 232
>PRK00414 gmhA phosphoheptose isomerase; Reviewed
Probab=25.05 E-value=4.4e+02 Score=22.56 Aligned_cols=17 Identities=18% Similarity=0.368 Sum_probs=13.5
Q ss_pred cCCCcEEEEecCchHHH
Q 024560 110 NPKGRIWTMVAGGGASV 126 (266)
Q Consensus 110 ~l~G~Igii~NGaGlam 126 (266)
..+++|-+.++|+...+
T Consensus 42 ~~~~rI~i~G~G~S~~~ 58 (192)
T PRK00414 42 KAGGKVLSCGNGGSHCD 58 (192)
T ss_pred HCCCEEEEEeCcHHHHH
Confidence 35799999999997664
No 233
>PRK10401 DNA-binding transcriptional regulator GalS; Provisional
Probab=25.03 E-value=2.8e+02 Score=25.19 Aligned_cols=78 Identities=12% Similarity=0.057 Sum_probs=44.5
Q ss_pred CcEEEEecCchHH------HHHHHHHHhcCCCCCCCceeeccCCCCHHHHHHHHHHHHhhhccCCCCCeEEEEecccccc
Q 024560 113 GRIWTMVAGGGAS------VIYADTVGDLGYASELGNYAEYSGAPNEEEVLQYARVVIDCATADPDGRKRALLIGGGIAN 186 (266)
Q Consensus 113 G~Igii~NGaGla------m~t~D~l~~~g~gg~pAN~lDlgG~a~~~~~~~al~~ll~~~~~d~~v~~vlvni~ggi~~ 186 (266)
.+|++++...... --..+.+..+ |-.+....-..++.+.+.-+++++-+++ +.+.+++||. .
T Consensus 177 ~~I~~i~~~~~~~~~~~R~~Gf~~al~~~--gi~~~~~~~~~~~~~~~~~~~~~~~~l~---~~~~~~ai~~-------~ 244 (346)
T PRK10401 177 QRIGYLSSSHGIEDDAMRRAGWMSALKEQ--GIIPPESWIGTGTPDMQGGEAAMVELLG---RNLQLTAVFA-------Y 244 (346)
T ss_pred CeEEEEeCCCcCcchHHHHHHHHHHHHHc--CCCCChhheecCCCChHHHHHHHHHHHc---CCCCCcEEEE-------C
Confidence 5788885433211 1234666666 3333221223355555555555555554 2456777774 2
Q ss_pred hhHhhhhHHHHHHHHHHhh
Q 024560 187 FTDVATTFNGIIRALREKE 205 (266)
Q Consensus 187 ~~~vA~~~~gii~al~~~~ 205 (266)
++.+| -|+++++++++
T Consensus 245 nd~~A---~g~~~al~~~G 260 (346)
T PRK10401 245 NDNMA---AGALTALKDNG 260 (346)
T ss_pred CcHHH---HHHHHHHHHcC
Confidence 67788 99999999874
No 234
>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=25.00 E-value=2.8e+02 Score=23.74 Aligned_cols=79 Identities=14% Similarity=0.030 Sum_probs=43.1
Q ss_pred CCcEEEEecCchHHH------HHHHHHHhcCCCCCCCceeeccCCCCHHHHHHHHHHHHhhhccCCCCCeEEEEeccccc
Q 024560 112 KGRIWTMVAGGGASV------IYADTVGDLGYASELGNYAEYSGAPNEEEVLQYARVVIDCATADPDGRKRALLIGGGIA 185 (266)
Q Consensus 112 ~G~Igii~NGaGlam------~t~D~l~~~g~gg~pAN~lDlgG~a~~~~~~~al~~ll~~~~~d~~v~~vlvni~ggi~ 185 (266)
.++|++++...+... ...+.+..+ +.+.-....+.++.+.+..++.++-+++ +.|.+++++..
T Consensus 117 ~~~i~~i~~~~~~~~~~~r~~gf~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~l~---~~~~~~ai~~~------ 185 (270)
T cd06296 117 HRRIGFITGPPDLLCSRARLDGYRAALAEA--GIPVDPALVREGDFSTESGFRAAAELLA---LPERPTAIFAG------ 185 (270)
T ss_pred CCcEEEEcCCCcchhHHHHHHHHHHHHHHc--CCCCChHHheeCCCCHHHHHHHHHHHHh---CCCCCcEEEEc------
Confidence 357888764433211 123444444 3332221222345555555555555554 24677777643
Q ss_pred chhHhhhhHHHHHHHHHHhh
Q 024560 186 NFTDVATTFNGIIRALREKE 205 (266)
Q Consensus 186 ~~~~vA~~~~gii~al~~~~ 205 (266)
++..| .|+++++++.+
T Consensus 186 -~d~~a---~~~~~~l~~~g 201 (270)
T cd06296 186 -NDLMA---LGVYEAARERG 201 (270)
T ss_pred -CcHHH---HHHHHHHHHhC
Confidence 56677 89999999875
No 235
>PF13458 Peripla_BP_6: Periplasmic binding protein; PDB: 4EVS_A 4EY3_A 4EYG_B 4EYK_A 3H5L_B 3TD9_A 3EAF_A 1Z18_A 1Z17_A 2LIV_A ....
Probab=24.99 E-value=3.1e+02 Score=24.46 Aligned_cols=101 Identities=18% Similarity=0.188 Sum_probs=56.4
Q ss_pred HHHHHHHHhcC-CCCCCCceeeccCCCCHHHHHHHHHHHHhhhccCCCCCeEEEEecccccchhHhhhhHHHHHHHHHHh
Q 024560 126 VIYADTVGDLG-YASELGNYAEYSGAPNEEEVLQYARVVIDCATADPDGRKRALLIGGGIANFTDVATTFNGIIRALREK 204 (266)
Q Consensus 126 m~t~D~l~~~g-~gg~pAN~lDlgG~a~~~~~~~al~~ll~~~~~d~~v~~vlvni~ggi~~~~~vA~~~~gii~al~~~ 204 (266)
.++++.++..| ++|++=.++.+-...++++..++++-+++ +.++.+|+ |+.. ...+ .++.+.+++.
T Consensus 26 ~~a~~~~N~~ggi~G~~i~l~~~D~~~~~~~a~~~~~~l~~----~~~v~~vv----g~~~--s~~~---~~~~~~~~~~ 92 (343)
T PF13458_consen 26 ELAVDEINAAGGINGRKIELVVYDDGGDPAQAVQAARKLID----DDGVDAVV----GPLS--SAQA---EAVAPIAEEA 92 (343)
T ss_dssp HHHHHHHHHTTEETTEEEEEEEEE-TT-HHHHHHHHHHHHH----TSTESEEE----ESSS--HHHH---HHHHHHHHHH
T ss_pred HHHHHHHHHhCCcCCccceeeeccCCCChHHHHHHHHHhhh----hcCcEEEE----ecCC--cHHH---HHHHHHHHhc
Confidence 35678888773 23666666655556677888888888887 77776555 4332 2333 6667777664
Q ss_pred hhh-------hhcccceEEEEeCCCCHHHHHHHHHhhhhhcC
Q 024560 205 ESK-------LKAARMHIFVRRGGPNYQTGLAKMRALGEELG 239 (266)
Q Consensus 205 ~~~-------~~~~~~pvvvrl~G~~~~~~~~~L~~~~~~~G 239 (266)
+-+ ......|.+.|+..+...++..+++...+..|
T Consensus 93 ~ip~i~~~~~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~~g 134 (343)
T PF13458_consen 93 GIPYISPSASSPSPDSPNVFRLSPSDSQQAAALAEYLAKKLG 134 (343)
T ss_dssp T-EEEESSGGGGTTTHTTEEESS--HHHHHHHHHHHHHHTTT
T ss_pred CcEEEEeeccCCCCCCCcEEEEeccccHHHHHHHHHHHHHcC
Confidence 311 00123445556666666666666664444444
No 236
>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=24.96 E-value=4.4e+02 Score=22.58 Aligned_cols=119 Identities=16% Similarity=0.163 Sum_probs=60.9
Q ss_pred CCcEEEEecCchH--H----HHHHHHHHhcCCCCCCCceeeccCCCCHHHHHHHHHHHHhhhccCCCCCeEEEEeccccc
Q 024560 112 KGRIWTMVAGGGA--S----VIYADTVGDLGYASELGNYAEYSGAPNEEEVLQYARVVIDCATADPDGRKRALLIGGGIA 185 (266)
Q Consensus 112 ~G~Igii~NGaGl--a----m~t~D~l~~~g~gg~pAN~lDlgG~a~~~~~~~al~~ll~~~~~d~~v~~vlvni~ggi~ 185 (266)
.++|++++...+. . .-..+.+..+ |-++.+......+. .+..+++++-+++ +.+.+++++.
T Consensus 116 ~~~i~~l~~~~~~~~~~~R~~Gf~~~~~~~--~~~~~~~~~~~~~~-~~~~~~~~~~~l~---~~~~~~ai~~------- 182 (269)
T cd06281 116 HRRIALVGGGSNTRPGRERLEGYKAAFAAA--GLPPDPALVRLSTP-AASGFDATRALLA---LPDRPTAIIA------- 182 (269)
T ss_pred CcEEEEecCccccccHHHHHHHHHHHHHHc--CCCCCHHHeecCcH-HHHHHHHHHHHHc---CCCCCcEEEE-------
Confidence 3568877643321 1 1223555665 33332222222222 3444444444443 3567888764
Q ss_pred chhHhhhhHHHHHHHHHHhhhhhhcccce--E-EEEeCCCCHHHHHHHHHhhhhhcCCceeecCCCCCHHHHHHHHHHHh
Q 024560 186 NFTDVATTFNGIIRALREKESKLKAARMH--I-FVRRGGPNYQTGLAKMRALGEELGIPLEVYGPEATMTGICKQAIDCI 262 (266)
Q Consensus 186 ~~~~vA~~~~gii~al~~~~~~~~~~~~p--v-vvrl~G~~~~~~~~~L~~~~~~~Gip~~~~~~~~~~~eAv~~av~~~ 262 (266)
.++.+| .|+++++++.+ .++| + ++-.+++. .. +.+. -.+.+. ..++.+..++++++.
T Consensus 183 ~~d~~a---~g~~~~l~~~g-----~~ip~dv~iig~d~~~--~~-~~~~-----~~l~ti----~~~~~~~g~~a~~~l 242 (269)
T cd06281 183 GGTQVL---VGVLRALREAG-----LRIPRDLSVISIGDSD--LA-ELMD-----PPITAL----RRDREAVGRTAAELM 242 (269)
T ss_pred cCcHHH---HHHHHHHHHcC-----CCCCcceeEEEecCch--HH-HhcC-----CceeEE----ecCHHHHHHHHHHHH
Confidence 266777 89999999874 2222 2 33444432 22 2232 133322 347888888888765
Q ss_pred h
Q 024560 263 M 263 (266)
Q Consensus 263 ~ 263 (266)
.
T Consensus 243 ~ 243 (269)
T cd06281 243 L 243 (269)
T ss_pred H
Confidence 3
No 237
>PF02782 FGGY_C: FGGY family of carbohydrate kinases, C-terminal domain; InterPro: IPR018485 It has been shown [] that four different type of carbohydrate kinases seem to be evolutionary related. These enzymes include L-fucolokinase (2.7.1.51 from EC) (gene fucK); gluconokinase (2.7.1.12 from EC) (gene gntK); glycerol kinase (2.7.1.30 from EC) (gene glpK); xylulokinase (2.7.1.17 from EC) (gene xylB); and L-xylulose kinase (2.7.1.53 from EC) (gene lyxK). These enzymes are proteins of from 480 to 520 amino acid residues. This entry represents the C-terminal domain of these proteins. It adopts a ribonuclease H-like fold and is structurally related to the N-terminal domain [, ].; GO: 0016773 phosphotransferase activity, alcohol group as acceptor, 0005975 carbohydrate metabolic process; PDB: 4E1J_B 2W40_C 2W41_A 2UYT_A 2CGK_B 2CGL_A 2CGJ_A 3GBT_A 3LL3_B 3HZ6_A ....
Probab=24.94 E-value=3.7e+02 Score=22.25 Aligned_cols=85 Identities=20% Similarity=0.220 Sum_probs=44.8
Q ss_pred CCCCCeEEEEecccccchhHhhhhHHHHHHHHHHhhhhhhc----ccceEEEEeCCCCHHHHHHHHHhhhhhcCCceeec
Q 024560 170 DPDGRKRALLIGGGIANFTDVATTFNGIIRALREKESKLKA----ARMHIFVRRGGPNYQTGLAKMRALGEELGIPLEVY 245 (266)
Q Consensus 170 d~~v~~vlvni~ggi~~~~~vA~~~~gii~al~~~~~~~~~----~~~pvvvrl~G~~~~~~~~~L~~~~~~~Gip~~~~ 245 (266)
+|+.++.|+++....++.+.+....+|++-.++..-+.+.+ ...+|++==|+.+...-.+++.+ -.|.|++..
T Consensus 104 ~~~~~g~~~gl~~~~~~~~~~rAv~Egia~~~~~~~~~l~~~~~~~~~~i~~~GG~~~n~~~~q~~Ad---vl~~~V~~~ 180 (198)
T PF02782_consen 104 DPDARGSFIGLSSDTTRADLARAVLEGIAFSLRQILEELEELTGIPIRRIRVSGGGAKNPLWMQILAD---VLGRPVVRP 180 (198)
T ss_dssp BTTHCEEEEEEETTTSHHHHHHHHHHHHHHHHHHHHHHHHHHHTSCESEEEEESGGGGSHHHHHHHHH---HHTSEEEEE
T ss_pred ccccccccccCCcccCHHHHHHHHHHhHHHHHHHhhhhccccccccceeeEeccccccChHHHHHHHH---HhCCceEeC
Confidence 56777888887555555554444455555555543322211 12334443334444555677775 468998765
Q ss_pred CCCCCHHHHHHHHH
Q 024560 246 GPEATMTGICKQAI 259 (266)
Q Consensus 246 ~~~~~~~eAv~~av 259 (266)
+ ..-..|...|+
T Consensus 181 ~--~~e~~a~GaA~ 192 (198)
T PF02782_consen 181 E--VEEASALGAAL 192 (198)
T ss_dssp S--SSTHHHHHHHH
T ss_pred C--CCchHHHHHHH
Confidence 4 12333444444
No 238
>COG2055 Malate/L-lactate dehydrogenases [Energy production and conversion]
Probab=24.89 E-value=1.6e+02 Score=28.42 Aligned_cols=22 Identities=32% Similarity=0.406 Sum_probs=16.9
Q ss_pred EEeCCCCHHHHHHHHHhhhhhcCCce
Q 024560 217 VRRGGPNYQTGLAKMRALGEELGIPL 242 (266)
Q Consensus 217 vrl~G~~~~~~~~~L~~~~~~~Gip~ 242 (266)
||+.|......++.=. +.|||+
T Consensus 307 V~lPG~~~~~~~~~~~----~~GI~i 328 (349)
T COG2055 307 VRLPGEREFAAREKRQ----KEGIPI 328 (349)
T ss_pred eecCCcHHHHHHHHHH----hcCCcc
Confidence 7999987777766555 569998
No 239
>PRK05286 dihydroorotate dehydrogenase 2; Reviewed
Probab=24.76 E-value=5.5e+02 Score=24.14 Aligned_cols=63 Identities=13% Similarity=0.172 Sum_probs=33.5
Q ss_pred CHHHHHHHHHHHHhhhccCCCCCeEEEEeccccc---chhHhhhhHHHHHHHHHHhhhhhhcccceEEEEeCC
Q 024560 152 NEEEVLQYARVVIDCATADPDGRKRALLIGGGIA---NFTDVATTFNGIIRALREKESKLKAARMHIFVRRGG 221 (266)
Q Consensus 152 ~~~~~~~al~~ll~~~~~d~~v~~vlvni~ggi~---~~~~vA~~~~gii~al~~~~~~~~~~~~pvvvrl~G 221 (266)
..+.|.+.++.+- +..+++-+|+..--+ +..+.-....-|++++++..... ..++||++++.-
T Consensus 155 ~~~d~~~~~~~~~------~~ad~lelN~scP~~~g~~~~~~~~~~~eiv~aVr~~~~~~-~~~~PV~vKlsp 220 (344)
T PRK05286 155 AVDDYLICLEKLY------PYADYFTVNISSPNTPGLRDLQYGEALDELLAALKEAQAEL-HGYVPLLVKIAP 220 (344)
T ss_pred CHHHHHHHHHHHH------hhCCEEEEEccCCCCCCcccccCHHHHHHHHHHHHHHHhcc-ccCCceEEEeCC
Confidence 4567777777652 358899999621111 11111111245556665542100 013899998884
No 240
>KOG2270 consensus Serine/threonine protein kinase involved in cell cycle control [Signal transduction mechanisms; Cell cycle control, cell division, chromosome partitioning]
Probab=24.76 E-value=82 Score=31.26 Aligned_cols=47 Identities=11% Similarity=0.213 Sum_probs=39.7
Q ss_pred HHHHHHHHHHHHHHHHHhCCceeeEeecceecCCceEEeeccccccCc
Q 024560 17 FRGKIGDFIMGVFAVFQDLDFSFIEMNPFTLVNGEPYPLDMRGELDDT 64 (266)
Q Consensus 17 ~~~~~~~ii~~Ly~~f~~~D~~l~EINPLvv~~g~~~alD~k~~iDd~ 64 (266)
.-.++..++..||+...--.+.|-|-|-|. .+|+||.+|-.=+++-+
T Consensus 269 ~Y~~~v~~MR~lY~~c~LVHADLSEfN~Ly-hdG~lyiIDVSQSVE~D 315 (520)
T KOG2270|consen 269 LYQQCVRIMRRLYQKCRLVHADLSEFNLLY-HDGKLYIIDVSQSVEHD 315 (520)
T ss_pred HHHHHHHHHHHHHHHhceeccchhhhhheE-ECCEEEEEEccccccCC
Confidence 455788888899999888999999999887 78999999988777654
No 241
>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=24.64 E-value=3.6e+02 Score=22.92 Aligned_cols=78 Identities=17% Similarity=0.060 Sum_probs=42.9
Q ss_pred CcEEEEecCchHHH------HHHHHHHhcCCCCCCCceeeccCCCCHHHHHHHHHHHHhhhccCCCCCeEEEEecccccc
Q 024560 113 GRIWTMVAGGGASV------IYADTVGDLGYASELGNYAEYSGAPNEEEVLQYARVVIDCATADPDGRKRALLIGGGIAN 186 (266)
Q Consensus 113 G~Igii~NGaGlam------~t~D~l~~~g~gg~pAN~lDlgG~a~~~~~~~al~~ll~~~~~d~~v~~vlvni~ggi~~ 186 (266)
++|++++.-.+... ...|.+..+ |-.+.+..-..++.+.+..+++++-++. +.+++++|+..
T Consensus 123 ~~i~~i~~~~~~~~~~~r~~gf~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~l~---~~~~~~ai~~~------- 190 (270)
T cd06294 123 KKIAFVGGDLDLEVTQDRLQGYKQALEDH--GIPDRNEVIISLDFSEEGGYKALKKLLE---QHPRPTAIVAT------- 190 (270)
T ss_pred ccEEEecCCcccHHHHHHHHHHHHHHHHc--CCCCCcceEEecCCchHHHHHHHHHHHh---CCCCCCEEEEC-------
Confidence 67998863333211 123555555 2222222223344444555555555443 35678877742
Q ss_pred hhHhhhhHHHHHHHHHHhh
Q 024560 187 FTDVATTFNGIIRALREKE 205 (266)
Q Consensus 187 ~~~vA~~~~gii~al~~~~ 205 (266)
++..| .++++++++.+
T Consensus 191 ~d~~a---~g~~~al~~~g 206 (270)
T cd06294 191 DDLLA---LGVLKVLNELG 206 (270)
T ss_pred ChHHH---HHHHHHHHHcC
Confidence 45677 89999999874
No 242
>PRK15408 autoinducer 2-binding protein lsrB; Provisional
Probab=24.63 E-value=5.7e+02 Score=23.72 Aligned_cols=63 Identities=13% Similarity=0.063 Sum_probs=35.5
Q ss_pred CCCHHHHHHHHHHHHhhhccCCCCCeEEEEecccccchhHhhhhHHHHHHHHHHhhhhhhcccceEEEEeCCCCHHHHHH
Q 024560 150 APNEEEVLQYARVVIDCATADPDGRKRALLIGGGIANFTDVATTFNGIIRALREKESKLKAARMHIFVRRGGPNYQTGLA 229 (266)
Q Consensus 150 ~a~~~~~~~al~~ll~~~~~d~~v~~vlvni~ggi~~~~~vA~~~~gii~al~~~~~~~~~~~~pvvvrl~G~~~~~~~~ 229 (266)
+-+.++-++.++-+|+ ++|++++|+.. + +..+ .|+++|+++.+. .++ .|+-.. ...+.++
T Consensus 190 ~~d~~~a~~~~~~lL~---~~pdi~aI~~~--~-----~~~~---~Ga~~Al~~~g~----~~v-~VvG~D--~~~~~~~ 249 (336)
T PRK15408 190 YNDATKSLQTAEGILK---AYPDLDAIIAP--D-----ANAL---PAAAQAAENLKR----DKV-AIVGFS--TPNVMRP 249 (336)
T ss_pred CCcHHHHHHHHHHHHH---HCCCCcEEEEC--C-----CccH---HHHHHHHHhCCC----CCE-EEEEeC--CcHHHHH
Confidence 3445554445444443 38999988843 1 1222 678888888642 222 234444 3456777
Q ss_pred HHH
Q 024560 230 KMR 232 (266)
Q Consensus 230 ~L~ 232 (266)
.++
T Consensus 250 ~i~ 252 (336)
T PRK15408 250 YVK 252 (336)
T ss_pred HHh
Confidence 777
No 243
>PLN02331 phosphoribosylglycinamide formyltransferase
Probab=24.48 E-value=2.7e+02 Score=24.52 Aligned_cols=44 Identities=27% Similarity=0.266 Sum_probs=25.1
Q ss_pred HHHHHHHHHHhhhhhhcccceEEEEeCCCCHHHHHHHHHhhhhhcCCceeecC
Q 024560 194 FNGIIRALREKESKLKAARMHIFVRRGGPNYQTGLAKMRALGEELGIPLEVYG 246 (266)
Q Consensus 194 ~~gii~al~~~~~~~~~~~~pvvvrl~G~~~~~~~~~L~~~~~~~Gip~~~~~ 246 (266)
+++|++++++.. .+.-|++-+.-.....+++... +.|||++.+.
T Consensus 13 ~~al~~~~~~~~-----l~~~i~~visn~~~~~~~~~A~----~~gIp~~~~~ 56 (207)
T PLN02331 13 FRAIHDACLDGR-----VNGDVVVVVTNKPGCGGAEYAR----ENGIPVLVYP 56 (207)
T ss_pred HHHHHHHHHcCC-----CCeEEEEEEEeCCCChHHHHHH----HhCCCEEEec
Confidence 478888877642 2223333333333344555555 6799987765
No 244
>cd07095 ALDH_SGSD_AstD N-succinylglutamate 5-semialdehyde dehydrogenase, AstD-like. N-succinylglutamate 5-semialdehyde dehydrogenase or succinylglutamic semialdehyde dehydrogenase (SGSD, E. coli AstD, EC=1.2.1.71) involved in L-arginine degradation via the arginine succinyltransferase (AST) pathway and catalyzes the NAD+-dependent reduction of succinylglutamate semialdehyde into succinylglutamate.
Probab=24.45 E-value=6.5e+02 Score=24.32 Aligned_cols=21 Identities=0% Similarity=-0.031 Sum_probs=11.7
Q ss_pred HHHHHHHHHHHHHHhCCceee
Q 024560 20 KIGDFIMGVFAVFQDLDFSFI 40 (266)
Q Consensus 20 ~~~~ii~~Ly~~f~~~D~~l~ 40 (266)
+-.+++.++.+++.++--.|.
T Consensus 23 ~R~~~L~~~a~~l~~~~~~la 43 (431)
T cd07095 23 ERAAILRRFAELLKANKEELA 43 (431)
T ss_pred HHHHHHHHHHHHHHhHHHHHH
Confidence 345666666666666544333
No 245
>PF00378 ECH: Enoyl-CoA hydratase/isomerase family; InterPro: IPR001753 The crotonase superfamily is comprised of mechanistically diverse proteins that share a conserved trimeric quaternary structure (sometimes a hexamer consisting of a dimer of trimers), the core of which consists of 4 turns of a (beta/beta/alpha)n superhelix. Some enzymes in the superfamily have been shown to display dehalogenase, hydratase, and isomerase activities, while others have been implicated in carbon-carbon bond formation and cleavage as well as the hydrolysis of thioesters []. However, these different enzymes share the need to stabilise an enolate anion intermediate derived from an acyl-CoA substrate. This is accomplished by two structurally conserved peptidic NH groups that provide hydrogen bonds to the carbonyl moieties of the acyl-CoA substrates and form an "oxyanion hole". The CoA thioester derivatives bind in a characteristic hooked shape and a conserved tunnel binds the pantetheine group of CoA, which links the 3'-phosphate ADP binding site to the site of reaction []. Enzymes in the crotonase superfamily include: Enoyl-CoA hydratase (crotonase; 4.2.1.17 from EC), which catalyses the hydratation of 2-trans-enoyl-CoA into 3-hydroxyacyl-CoA []. 3-2trans-enoyl-CoA isomerase (or dodecenoyl-CoA isomerise; 5.3.3.8 from EC), which shifts the 3-double bond of the intermediates of unsaturated fatty acid oxidation to the 2-trans position []. 3-hydroxbutyryl-CoA dehydratase (crotonase; 4.2.1.55 from EC), a bacterial enzyme involved in the butyrate/butanol-producing pathway. 4-Chlorobenzoyl-CoA dehalogenase (3.8.1.6 from EC), a Pseudomonas enzyme which catalyses the conversion of 4-chlorobenzoate-CoA to 4-hydroxybenzoate-CoA []. Dienoyl-CoA isomerise, which catalyses the isomerisation of 3-trans,5-cis-dienoyl-CoA to 2-trans,4-trans-dienoyl-CoA []. Naphthoate synthase (MenB, or DHNA synthetase; 4.1.3.36 from EC), a bacterial enzyme involved in the biosynthesis of menaquinone (vitamin K2) []. Carnitine racemase (gene caiD), which catalyses the reversible conversion of crotonobetaine to L-carnitine in Escherichia coli []. Methylmalonyl CoA decarboxylase (MMCD; 4.1.1.41 from EC), which has a hexameric structure (dimer of trimers) []. Carboxymethylproline synthase (CarB), which is involved in carbapenem biosynthesis []. 6-oxo camphor hydrolase, which catalyses the desymmetrisation of bicyclic beta-diketones to optically active keto acids []. The alpha subunit of fatty oxidation complex, a multi-enzyme complex that catalyses the last three reactions in the fatty acid beta-oxidation cycle []. AUH protein, a bifunctional RNA-binding homologue of enoyl-CoA hydratase []. This entry represents the core domain found in crotonase superfamily members.; GO: 0003824 catalytic activity, 0008152 metabolic process; PDB: 2VRE_B 3RSI_A 1HZD_F 2ZQR_E 2ZQQ_D 3R9S_C 1O8U_E 1SZO_C 3MOY_A 2UZF_A ....
Probab=24.35 E-value=4e+02 Score=23.24 Aligned_cols=75 Identities=17% Similarity=0.129 Sum_probs=38.3
Q ss_pred HHHHHHHhhhccCCCCCeEEEE----ecccccchhHhhhh----HHHHHHHHHHhhhhhhcccceEEEEeCCCCHHHHHH
Q 024560 158 QYARVVIDCATADPDGRKRALL----IGGGIANFTDVATT----FNGIIRALREKESKLKAARMHIFVRRGGPNYQTGLA 229 (266)
Q Consensus 158 ~al~~ll~~~~~d~~v~~vlvn----i~ggi~~~~~vA~~----~~gii~al~~~~~~~~~~~~pvvvrl~G~~~~~~~~ 229 (266)
+.+.-.++.+..|+++++|++- .|....+..++... .+.+.+.+++.-......++|+|.-+.|.-..-|-.
T Consensus 28 ~~l~~~l~~~~~d~~v~vvv~~~~~~~F~~G~Dl~~~~~~~~~~~~~~~~~~~~l~~~l~~~~kp~Iaav~G~a~GgG~~ 107 (245)
T PF00378_consen 28 DELEEALDEAEADPDVKVVVISGGGKAFCAGADLKEFLNSDEEEAREFFRRFQELLSRLANFPKPTIAAVNGHAVGGGFE 107 (245)
T ss_dssp HHHHHHHHHHHHSTTESEEEEEESTSESBESB-HHHHHHHHHHHHHHHHHHHHHHHHHHHHSSSEEEEEESSEEETHHHH
T ss_pred HHHHHHHHHHHhcCCccEEEEeecccccccccchhhhhccccccccccchhhccccccchhhhhheeecccccccccccc
Confidence 3334444444459999966665 23323333333211 111222222222222236799999998987777776
Q ss_pred HHH
Q 024560 230 KMR 232 (266)
Q Consensus 230 ~L~ 232 (266)
+.-
T Consensus 108 lal 110 (245)
T PF00378_consen 108 LAL 110 (245)
T ss_dssp HHH
T ss_pred ccc
Confidence 655
No 246
>PRK09847 gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase; Provisional
Probab=24.29 E-value=7e+02 Score=24.65 Aligned_cols=22 Identities=18% Similarity=0.095 Sum_probs=12.1
Q ss_pred cCCCcEEEEecCchHHHHHHHH
Q 024560 110 NPKGRIWTMVAGGGASVIYADT 131 (266)
Q Consensus 110 ~l~G~Igii~NGaGlam~t~D~ 131 (266)
++-|=+++|+----+.++++-.
T Consensus 156 ~P~GVv~~I~PwN~P~~~~~~~ 177 (494)
T PRK09847 156 EPVGVIAAIVPWNFPLLLTCWK 177 (494)
T ss_pred cceeEEEEECCCccHHHHHHHH
Confidence 3556677776555555544433
No 247
>PRK00421 murC UDP-N-acetylmuramate--L-alanine ligase; Provisional
Probab=24.27 E-value=6.6e+02 Score=24.32 Aligned_cols=92 Identities=14% Similarity=0.131 Sum_probs=48.6
Q ss_pred CHHHHHHHHHHHHhhhccCCCCCeEEEEecccccchhHhhhhHHHHHHHHHHhhhhhhcccceEEEEe--------CCCC
Q 024560 152 NEEEVLQYARVVIDCATADPDGRKRALLIGGGIANFTDVATTFNGIIRALREKESKLKAARMHIFVRR--------GGPN 223 (266)
Q Consensus 152 ~~~~~~~al~~ll~~~~~d~~v~~vlvni~ggi~~~~~vA~~~~gii~al~~~~~~~~~~~~pvvvrl--------~G~~ 223 (266)
+++.+..+++.+-+. .++-+.++|.-|.|..+-.+.. ..+.+.+ +. .+.-+++.. .|.+
T Consensus 333 np~~~~a~~~al~~~---~~~~~i~~v~gp~~~~r~kd~~---~~~~~~l-~~------~d~vi~~~~~~~~e~~~~~~~ 399 (461)
T PRK00421 333 HPTEIKATLKAARQG---YPDKRIVAVFQPHRYSRTRDLL---DEFAEAL-SD------ADEVILLDIYAAGEEPIGGVD 399 (461)
T ss_pred CHHHHHHHHHHHHhh---CCCCeEEEEECCCCCccHHHHH---HHHHHHH-HH------CCEEEEcCccCCCCCCCCCCC
Confidence 677777777776541 1222333332234666666655 5566655 22 122222222 2334
Q ss_pred HHHHHHHHHhhhhhcCCceeecCCCCCHHHHHHHHHHHhh
Q 024560 224 YQTGLAKMRALGEELGIPLEVYGPEATMTGICKQAIDCIM 263 (266)
Q Consensus 224 ~~~~~~~L~~~~~~~Gip~~~~~~~~~~~eAv~~av~~~~ 263 (266)
.++-.+.++ +.+.++.++ .++++|++.+.+.++
T Consensus 400 ~~~l~~~~~----~~~~~~~~~---~~~~~a~~~a~~~a~ 432 (461)
T PRK00421 400 SEDLARKIK----RGHRDPIFV---PDLEDLAELLAEVLK 432 (461)
T ss_pred HHHHHHHHh----ccCCceEEe---CCHHHHHHHHHHhcC
Confidence 444444444 334555544 499999999988764
No 248
>PRK14987 gluconate operon transcriptional regulator; Provisional
Probab=24.23 E-value=4.9e+02 Score=23.33 Aligned_cols=77 Identities=12% Similarity=-0.065 Sum_probs=41.3
Q ss_pred CcEEEEecCchHH-----HHHHHHHHhcCCCCCCCceeeccCCCCHHHHHHHHHHHHhhhccCCCCCeEEEEecccccch
Q 024560 113 GRIWTMVAGGGAS-----VIYADTVGDLGYASELGNYAEYSGAPNEEEVLQYARVVIDCATADPDGRKRALLIGGGIANF 187 (266)
Q Consensus 113 G~Igii~NGaGla-----m~t~D~l~~~g~gg~pAN~lDlgG~a~~~~~~~al~~ll~~~~~d~~v~~vlvni~ggi~~~ 187 (266)
.+|++++.-.... .-..+.+..+ |..+...+ +.+..+.+.-+++++-+++ ..|++++||. .+
T Consensus 181 ~~I~~i~~~~~~~~~~R~~Gf~~al~~~--g~~~~~~~-~~~~~~~~~~~~~~~~~l~---~~~~~~ai~~-------~n 247 (331)
T PRK14987 181 RHIAYLGARLDERTIIKQKGYEQAMLDA--GLVPYSVM-VEQSSSYSSGIELIRQARR---EYPQLDGVFC-------TN 247 (331)
T ss_pred ceEEEEcCCCcccHHHHHHHHHHHHHHc--CCCcccee-ecCCCChhhHHHHHHHHHh---cCCCCCEEEE-------CC
Confidence 5688884211111 2234566666 33222122 2233344444455554543 2466778774 36
Q ss_pred hHhhhhHHHHHHHHHHhh
Q 024560 188 TDVATTFNGIIRALREKE 205 (266)
Q Consensus 188 ~~vA~~~~gii~al~~~~ 205 (266)
|.+| -|+++++++.+
T Consensus 248 D~~A---~g~~~al~~~g 262 (331)
T PRK14987 248 DDLA---VGAAFECQRLG 262 (331)
T ss_pred cHHH---HHHHHHHHHcC
Confidence 7888 99999999874
No 249
>COG1509 KamA Lysine 2,3-aminomutase [Amino acid transport and metabolism]
Probab=23.80 E-value=5.6e+02 Score=24.92 Aligned_cols=127 Identities=15% Similarity=0.077 Sum_probs=64.9
Q ss_pred CCcEEEEecCchHHHHHHHHHHhcCCCCCCCceeeccCCCCHHHHHHHHHHHHhhhccCCCCCeEEEEeccc--ccchhH
Q 024560 112 KGRIWTMVAGGGASVIYADTVGDLGYASELGNYAEYSGAPNEEEVLQYARVVIDCATADPDGRKRALLIGGG--IANFTD 189 (266)
Q Consensus 112 ~G~Igii~NGaGlam~t~D~l~~~g~gg~pAN~lDlgG~a~~~~~~~al~~ll~~~~~d~~v~~vlvni~gg--i~~~~~ 189 (266)
..|+-+++.|....- +.-+.. -.-+.| -+.+-+.+++.++++.+-+ +|.+.=|++- || ..=++.
T Consensus 110 ~drvLll~t~~C~vy---CRyCfR--r~~~~~---~~~~~~~~~~~~al~YIa~----hPeI~eVllS--GGDPL~ls~~ 175 (369)
T COG1509 110 PDRVLLLVTGVCAVY---CRYCFR--RRFVGQ---DNQGFNKEEWDKALDYIAA----HPEIREVLLS--GGDPLSLSDK 175 (369)
T ss_pred CCeEEEEecCcccce---eeeccc--cccccc---ccccCCHHHHHHHHHHHHc----CchhheEEec--CCCccccCHH
Confidence 577878877775432 222222 111332 2222477888888777776 8988766653 33 222332
Q ss_pred hhhhHHHHHHHHHHhhhh---hhcccceEEE--EeCCCCHHHHHHHHHhhhhhcCCceeecCCCCCHH---HHHHHHHHH
Q 024560 190 VATTFNGIIRALREKESK---LKAARMHIFV--RRGGPNYQTGLAKMRALGEELGIPLEVYGPEATMT---GICKQAIDC 261 (266)
Q Consensus 190 vA~~~~gii~al~~~~~~---~~~~~~pvvv--rl~G~~~~~~~~~L~~~~~~~Gip~~~~~~~~~~~---eAv~~av~~ 261 (266)
-- +-|++.+++.+.- ....+.|||. |+. ++-.++|. +.+.++.+.--+.|+- ..++.|++.
T Consensus 176 ~L---~~ll~~L~~IpHv~iiRi~TR~pvv~P~RIt----~~L~~~l~----~~~~~v~~~tH~NHp~Eit~e~~~A~~~ 244 (369)
T COG1509 176 KL---EWLLKRLRAIPHVKIIRIGTRLPVVLPQRIT----DELCEILG----KSRKPVWLVTHFNHPNEITPEAREACAK 244 (369)
T ss_pred HH---HHHHHHHhcCCceeEEEeecccceechhhcc----HHHHHHHh----ccCceEEEEcccCChhhcCHHHHHHHHH
Confidence 22 5566666654310 1124566665 554 45556666 4355543322233443 355555555
Q ss_pred hh
Q 024560 262 IM 263 (266)
Q Consensus 262 ~~ 263 (266)
..
T Consensus 245 L~ 246 (369)
T COG1509 245 LR 246 (369)
T ss_pred HH
Confidence 43
No 250
>TIGR03250 PhnAcAld_DH putative phosphonoacetaldehyde dehydrogenase. It seems reasonably certain then, that this enzyme catalyzes the NAD-dependent oxidation of phosphonoacetaldehyde to phosphonoacetate, bridging the metabolic gap between PhnW and PhnA. We propose the name phosphonoacetaldehyde dehydrogenase and the gene symbol PhnY for this enzyme.
Probab=23.74 E-value=7e+02 Score=24.43 Aligned_cols=19 Identities=5% Similarity=-0.046 Sum_probs=12.1
Q ss_pred HHHHHHHHHHHHhCCceee
Q 024560 22 GDFIMGVFAVFQDLDFSFI 40 (266)
Q Consensus 22 ~~ii~~Ly~~f~~~D~~l~ 40 (266)
.+++.++.+++.++--.|+
T Consensus 61 ~~~l~~~a~~l~~~~~ela 79 (472)
T TIGR03250 61 SAILDRAAALLAARKEEIS 79 (472)
T ss_pred HHHHHHHHHHHHHhHHHHH
Confidence 4677777777776654443
No 251
>cd06347 PBP1_ABC_ligand_binding_like_12 Type I periplasmic ligand-binding domain of uncharacterized ABC (Atpase Binding Cassette)-type active transport systems that are predicted to be involved in uptake of amino acids, peptides, or inorganic ions. This subgroup includes the type I periplasmic ligand-binding domain of uncharacterized ABC (Atpase Binding Cassette)-type active transport systems that are predicted to be involved in uptake of amino acids, peptides, or inorganic ions. This subgroup has high sequence similarity to members of the family of hydrophobic amino acid transporters (HAAT), such as leucine/isoleucine/valine binding protein (LIVBP); however its ligand specificity has not been determined experimentally.
Probab=23.71 E-value=3.9e+02 Score=23.71 Aligned_cols=48 Identities=13% Similarity=0.075 Sum_probs=26.1
Q ss_pred HHHHHHHHHhcC-CCCCCCceeeccCCCCHHHHHHHHHHHHhhhccCCCCCeE
Q 024560 125 SVIYADTVGDLG-YASELGNYAEYSGAPNEEEVLQYARVVIDCATADPDGRKR 176 (266)
Q Consensus 125 am~t~D~l~~~g-~gg~pAN~lDlgG~a~~~~~~~al~~ll~~~~~d~~v~~v 176 (266)
..+++|.++..| ..|.+-.++..--.-++.+..++++-+++ ++++++|
T Consensus 23 ~~~a~~~iN~~ggi~g~~l~~~~~D~~~~~~~~~~~~~~li~----~~~v~ai 71 (334)
T cd06347 23 AKLAVKEINAAGGVLGKKIELVVEDNKSDKEEAANAATRLID----QDKVVAI 71 (334)
T ss_pred HHHHHHHHHhcCCCCCeeEEEEEecCCCChHHHHHHHHHHhc----ccCeEEE
Confidence 445789998873 12333344333333345556666666665 5566554
No 252
>PRK12738 kbaY tagatose-bisphosphate aldolase; Reviewed
Probab=23.66 E-value=3.8e+02 Score=24.92 Aligned_cols=10 Identities=20% Similarity=0.301 Sum_probs=6.4
Q ss_pred HHHHHHHHHh
Q 024560 195 NGIIRALREK 204 (266)
Q Consensus 195 ~gii~al~~~ 204 (266)
+++++|.++.
T Consensus 32 ~avi~AAee~ 41 (286)
T PRK12738 32 QAILEVCSEM 41 (286)
T ss_pred HHHHHHHHHH
Confidence 6666666654
No 253
>cd07107 ALDH_PhdK-like Nocardioides 2-carboxybenzaldehyde dehydrogenase, PhdK-like. Nocardioides sp. strain KP72-carboxybenzaldehyde dehydrogenase (PhdK), an enzyme involved in phenanthrene degradation, and other similar sequences, are present in this CD.
Probab=23.66 E-value=3.3e+02 Score=26.45 Aligned_cols=19 Identities=26% Similarity=0.221 Sum_probs=11.2
Q ss_pred CCCcEEEEecCchHHHHHH
Q 024560 111 PKGRIWTMVAGGGASVIYA 129 (266)
Q Consensus 111 l~G~Igii~NGaGlam~t~ 129 (266)
+-|-+++|+-=--+.++.+
T Consensus 116 P~GVv~~I~p~N~P~~~~~ 134 (456)
T cd07107 116 PYGVVARIVAFNHPLMFAA 134 (456)
T ss_pred cceEEEEECCcccHHHHHH
Confidence 6677887765544444433
No 254
>cd04738 DHOD_2_like Dihydroorotate dehydrogenase (DHOD) class 2. DHOD catalyzes the oxidation of (S)-dihydroorotate to orotate. This is the fourth step and the only redox reaction in the de novo biosynthesis of UMP, the precursor of all pyrimidine nucleotides. DHOD requires FMN as co-factor. DHOD divides into class 1 and class 2 based on their amino acid sequences, their cellular location and their natural electron acceptor used to reoxidize the flavin group. Members of class 1 are cytosolic enzymes and multimers, while class 2 enzymes are membrane associated, monomeric and use respiratory quinones as their physiological electron acceptors.
Probab=23.66 E-value=5.6e+02 Score=23.82 Aligned_cols=85 Identities=12% Similarity=0.133 Sum_probs=42.5
Q ss_pred eeccCCCC------HHHHHHHHHHHHhhhccCCCCCeEEEEe--ccc-----ccchhHhhhhHHHHHHHHHHhhhhhhcc
Q 024560 145 AEYSGAPN------EEEVLQYARVVIDCATADPDGRKRALLI--GGG-----IANFTDVATTFNGIIRALREKESKLKAA 211 (266)
Q Consensus 145 lDlgG~a~------~~~~~~al~~ll~~~~~d~~v~~vlvni--~gg-----i~~~~~vA~~~~gii~al~~~~~~~~~~ 211 (266)
+.++|+.. .+.+.+.++.+- +..+++-+|+ |.. ..+.+.+ .-|++++++..... ..
T Consensus 133 vsi~g~~~~~~~~~~~d~~~~~~~~~------~~ad~ielN~scP~~~g~~~~~~~~~~----~~iv~av~~~~~~~-~~ 201 (327)
T cd04738 133 VNIGKNKDTPLEDAVEDYVIGVRKLG------PYADYLVVNVSSPNTPGLRDLQGKEAL----RELLTAVKEERNKL-GK 201 (327)
T ss_pred EEEeCCCCCcccccHHHHHHHHHHHH------hhCCEEEEECCCCCCCccccccCHHHH----HHHHHHHHHHHhhc-cc
Confidence 55666542 456777666653 3478999995 211 0111222 44555555542100 12
Q ss_pred cceEEEEeCCCCH-HHHHHHHHhhhhhcCCc
Q 024560 212 RMHIFVRRGGPNY-QTGLAKMRALGEELGIP 241 (266)
Q Consensus 212 ~~pvvvrl~G~~~-~~~~~~L~~~~~~~Gip 241 (266)
++||++++.-... ++..++.+ .++++|+.
T Consensus 202 ~~Pv~vKl~~~~~~~~~~~ia~-~l~~aGad 231 (327)
T cd04738 202 KVPLLVKIAPDLSDEELEDIAD-VALEHGVD 231 (327)
T ss_pred CCCeEEEeCCCCCHHHHHHHHH-HHHHcCCc
Confidence 4899998874321 23333222 23366765
No 255
>PRK06683 hypothetical protein; Provisional
Probab=23.64 E-value=2.8e+02 Score=20.68 Aligned_cols=36 Identities=8% Similarity=-0.107 Sum_probs=26.6
Q ss_pred EEEEeCCCCHHHHHHHHHhhhhhcCCceeecCCCCCHHH
Q 024560 215 IFVRRGGPNYQTGLAKMRALGEELGIPLEVYGPEATMTG 253 (266)
Q Consensus 215 vvvrl~G~~~~~~~~~L~~~~~~~Gip~~~~~~~~~~~e 253 (266)
-+|-+..+-.+.-++-+.+.++..+||++.|. |++|
T Consensus 29 klViiA~Da~~~~~~~i~~~~~~~~Vpv~~~~---t~~e 64 (82)
T PRK06683 29 KEVVIAEDADMRLTHVIIRTALQHNIPITKVE---SVRK 64 (82)
T ss_pred eEEEEECCCCHHHHHHHHHHHHhcCCCEEEEC---CHHH
Confidence 34556666667788888888888999998665 7665
No 256
>cd07041 STAS_RsbR_RsbS_like Sulphate Transporter and Anti-Sigma factor antagonist domain of the "stressosome" complex proteins RsbS and RsbR, regulators of the bacterial stress activated alternative sigma factor sigma-B by phosphorylation. The STAS (Sulphate Transporter and Anti-Sigma factor antagonist) domain of proteins related to RsbS and RsbR which are part of the "stressosome" complex that plays an important role in the regulation of the bacterial stress activated alternative sigma factor sigma-B. During stress conditions RsbS and RsbR are phosphorylated which leads to the release of RsbT, an activator of of the RsbU phosphatase, which in turn activates RsbV which leads to the release and activation of sigma factor B. RsbS is a single domain protein (STAS domain), while RsbR-like proteins have a well-conserved C-terminal STATS domain and a variable N-terminal domain. The STAS domain is also found in the C- terminal region of sulphate transporters and anti-anti-sigma factors.
Probab=23.59 E-value=3.2e+02 Score=20.46 Aligned_cols=70 Identities=17% Similarity=0.095 Sum_probs=37.6
Q ss_pred CCCCeEEEEecccccchhHhhhhHHHHHHHHHHhhhhhhcccceEEEEeCCCCHHHHHHHHHhhhhhcCCceeecCCCCC
Q 024560 171 PDGRKRALLIGGGIANFTDVATTFNGIIRALREKESKLKAARMHIFVRRGGPNYQTGLAKMRALGEELGIPLEVYGPEAT 250 (266)
Q Consensus 171 ~~v~~vlvni~ggi~~~~~vA~~~~gii~al~~~~~~~~~~~~pvvvrl~G~~~~~~~~~L~~~~~~~Gip~~~~~~~~~ 250 (266)
.+.+.++++ ++++.-.|..+ ...+.+..++... ... -+++.|.+ ..-++.|. .+|+....+..+.|
T Consensus 39 ~~~~~vvlD-ls~v~~iDssg--~~~l~~~~~~~~~----~g~--~l~l~g~~-~~v~~~l~----~~gl~~~~~~~~~t 104 (109)
T cd07041 39 RRARGVIID-LTGVPVIDSAV--ARHLLRLARALRL----LGA--RTILTGIR-PEVAQTLV----ELGIDLSGIRTAAT 104 (109)
T ss_pred cCCCEEEEE-CCCCchhcHHH--HHHHHHHHHHHHH----cCC--eEEEEeCC-HHHHHHHH----HhCCChhhceeecc
Confidence 455666666 56666666544 3555555555432 232 33444544 45567787 45774312223558
Q ss_pred HHHH
Q 024560 251 MTGI 254 (266)
Q Consensus 251 ~~eA 254 (266)
.++|
T Consensus 105 ~~~A 108 (109)
T cd07041 105 LQQA 108 (109)
T ss_pred HHHh
Confidence 8776
No 257
>PRK06801 hypothetical protein; Provisional
Probab=23.59 E-value=4e+02 Score=24.73 Aligned_cols=10 Identities=10% Similarity=0.361 Sum_probs=5.9
Q ss_pred HHHHHHHHHh
Q 024560 195 NGIIRALREK 204 (266)
Q Consensus 195 ~gii~al~~~ 204 (266)
+++++|.++.
T Consensus 32 ~avi~AAe~~ 41 (286)
T PRK06801 32 RALFAAAKQE 41 (286)
T ss_pred HHHHHHHHHH
Confidence 6666665554
No 258
>PF12357 PLD_C: Phospholipase D C terminal ; InterPro: IPR024632 Phospholipase D (PLD) catalyses the hydrolysis of the phosphodiester bond of glycerophospholipids to generate phosphatidic acid and a free head group. Phospholipase D activities have been detected in simple to complex organisms from viruses and bacteria to yeast, plants, and mammals []. In higher organisms, PLD specifically catalyzes the hydrolysis of phosphatidylcholine (PC) to phosphatidic acid (PA) and choline and is activated in response to stimulators of vesicle transport, endocytosis, exocytosis, cell migration, and mitosis. This entry represents the C-terminal domain of eukaryotic phospholipase D. The domain is approximately 70 amino acids in length and contains a conserved FPD sequence motif.
Probab=23.58 E-value=1.7e+02 Score=21.82 Aligned_cols=48 Identities=13% Similarity=0.180 Sum_probs=36.2
Q ss_pred hHHHHHHHHHHHHHHHHHhCCceeeEe----eccee-cCCceEEeeccccccC
Q 024560 16 EFRGKIGDFIMGVFAVFQDLDFSFIEM----NPFTL-VNGEPYPLDMRGELDD 63 (266)
Q Consensus 16 ~~~~~~~~ii~~Ly~~f~~~D~~l~EI----NPLvv-~~g~~~alD~k~~iDd 63 (266)
+-++++.+|..+.|+.|...+.+-+.= =|+.| .||+|-.|.+.-.|=|
T Consensus 12 eCVr~Vn~iae~nW~~y~~ee~~dl~GHLl~YPv~V~~dG~V~~LpG~e~FPD 64 (74)
T PF12357_consen 12 ECVRRVNEIAEENWKQYASEEVTDLPGHLLKYPVQVDRDGKVTPLPGCEFFPD 64 (74)
T ss_pred HHHHHHHHHHHHHHHHhhccccccCCCccccCCeEEcCCCCEeeCCCCCcCCC
Confidence 568899999999999999998732221 37788 7898888776655544
No 259
>PRK11468 dihydroxyacetone kinase subunit DhaK; Provisional
Probab=23.30 E-value=1.6e+02 Score=28.44 Aligned_cols=59 Identities=20% Similarity=0.305 Sum_probs=40.2
Q ss_pred CCcEEEEecCchHHHHHHHHHHhcCCCCCCC-------------ceeeccCCCCHHHHHHHHHHHHhhhccCCCCCeEEE
Q 024560 112 KGRIWTMVAGGGASVIYADTVGDLGYASELG-------------NYAEYSGAPNEEEVLQYARVVIDCATADPDGRKRAL 178 (266)
Q Consensus 112 ~G~Igii~NGaGlam~t~D~l~~~g~gg~pA-------------N~lDlgG~a~~~~~~~al~~ll~~~~~d~~v~~vlv 178 (266)
.+++++|+.||. |.+|+ .+=++=-.|+++++.++++.+-. . ++||+
T Consensus 43 ~~kValIsGGGS--------------GHEPah~GyVG~GmLdAAv~G~VFaSPs~~qI~~ai~av~~----~---~GvLl 101 (356)
T PRK11468 43 AGKVALLSGGGS--------------GHEPMHCGFVGQGMLDGACPGEIFTSPTPDQMFECAMQVDG----G---EGVLL 101 (356)
T ss_pred CCcEEEEecCCc--------------cccccccceecCCcccceeeccccCCCCHHHHHHHHHhhcC----C---CCEEE
Confidence 478999988873 56663 44456678999999999888743 3 45555
Q ss_pred E---ecccccchhHhh
Q 024560 179 L---IGGGIANFTDVA 191 (266)
Q Consensus 179 n---i~ggi~~~~~vA 191 (266)
+ ..|=..++..-+
T Consensus 102 ivkNYtGDvlNF~mAa 117 (356)
T PRK11468 102 IIKNYTGDVLNFETAT 117 (356)
T ss_pred EecccHHhhccHHHHH
Confidence 4 356666665544
No 260
>cd06366 PBP1_GABAb_receptor Ligand-binding domain of GABAb receptors, which are metabotropic transmembrane receptors for gamma-aminobutyric acid (GABA). Ligand-binding domain of GABAb receptors, which are metabotropic transmembrane receptors for gamma-aminobutyric acid (GABA). GABA is the major inhibitory neurotransmitter in the mammalian CNS and, like glutamate and other transmitters, acts via both ligand gated ion channels (GABAa receptors) and G-protein coupled receptors (GABAb). GABAa receptors are members of the ionotropic receptor superfamily which includes alpha-adrenergic and glycine receptors. The GABAb receptor is a member of a receptor superfamily which includes the mGlu receptors. The GABAb receptor is coupled to G alpha_i proteins, and activation causes a decrease in calcium, an increase in potassium membrane conductance, and inhibition of cAMP formation. The response is thus inhibitory and leads to hyperpolarization and decreased neurotransmitter release, for example.
Probab=23.29 E-value=5.2e+02 Score=23.36 Aligned_cols=66 Identities=9% Similarity=-0.075 Sum_probs=32.6
Q ss_pred HHHHHHHHHhcCC--CCCCCceeeccCCCCHHHHHHHHHHHHhhhccCCCCCeEEEEecccccchhHhhhhHHHHHHHHH
Q 024560 125 SVIYADTVGDLGY--ASELGNYAEYSGAPNEEEVLQYARVVIDCATADPDGRKRALLIGGGIANFTDVATTFNGIIRALR 202 (266)
Q Consensus 125 am~t~D~l~~~g~--gg~pAN~lDlgG~a~~~~~~~al~~ll~~~~~d~~v~~vlvni~ggi~~~~~vA~~~~gii~al~ 202 (266)
..+++|.++..|. +|.+-.+.-.-...++.+-.++++-+++ ++++.+++ |+. |..++ .++...++
T Consensus 21 ~~lAv~~iN~~gg~~~g~~i~~~~~D~~~~~~~a~~~a~~l~~----~~~v~~vi----G~~--~s~~~---~a~~~~~~ 87 (350)
T cd06366 21 IEMALEDVNADNSILPGYRLVLHVRDSKCDPVQAASAALDLLE----NKPVVAII----GPQ--CSSVA---EFVAEVAN 87 (350)
T ss_pred HHHHHHHHhcCCCcCCCcEEEEEecCCCCCHHHHHHHHHHHhc----cCCceEEE----CCC--cHHHH---HHHHHHhh
Confidence 4467899998841 1233333322233344555555544554 45654443 554 33344 45555544
Q ss_pred H
Q 024560 203 E 203 (266)
Q Consensus 203 ~ 203 (266)
+
T Consensus 88 ~ 88 (350)
T cd06366 88 E 88 (350)
T ss_pred c
Confidence 4
No 261
>cd02069 methionine_synthase_B12_BD B12 binding domain of methionine synthase. This domain binds methylcobalamin, which it uses as an intermediate methyl carrier from methyltetrahydrofolate (CH3H4folate) to homocysteine (Hcy).
Probab=23.29 E-value=5.1e+02 Score=22.71 Aligned_cols=105 Identities=13% Similarity=0.059 Sum_probs=58.4
Q ss_pred hHHHHHHHHHHhcCCCCCCCceeeccCCCCHHHHHHHHHHHHhhhccCCCCCeEEEEecccccchhHhhhhHHHHHHHHH
Q 024560 123 GASVIYADTVGDLGYASELGNYAEYSGAPNEEEVLQYARVVIDCATADPDGRKRALLIGGGIANFTDVATTFNGIIRALR 202 (266)
Q Consensus 123 Glam~t~D~l~~~g~gg~pAN~lDlgG~a~~~~~~~al~~ll~~~~~d~~v~~vlvni~ggi~~~~~vA~~~~gii~al~ 202 (266)
|+-| ...++...| -.-+|+|-+.+++.+.++. . ..+.+.|.+-.. .+..-.- ++.+++.++
T Consensus 104 G~~i-v~~~l~~~G-----~~Vi~LG~~vp~e~~v~~~----~----~~~~~~V~lS~~--~~~~~~~---~~~~i~~L~ 164 (213)
T cd02069 104 GKNL-VGVILSNNG-----YEVIDLGVMVPIEKILEAA----K----EHKADIIGLSGL--LVPSLDE---MVEVAEEMN 164 (213)
T ss_pred HHHH-HHHHHHhCC-----CEEEECCCCCCHHHHHHHH----H----HcCCCEEEEccc--hhccHHH---HHHHHHHHH
Confidence 4433 457777773 3568999999999888873 3 345555555422 2222222 377777777
Q ss_pred HhhhhhhcccceEEEEeCCC--CHHHHHHH-HHhhhhhcCCceeecCCCCCHHHHHHHHHH
Q 024560 203 EKESKLKAARMHIFVRRGGP--NYQTGLAK-MRALGEELGIPLEVYGPEATMTGICKQAID 260 (266)
Q Consensus 203 ~~~~~~~~~~~pvvvrl~G~--~~~~~~~~-L~~~~~~~Gip~~~~~~~~~~~eAv~~av~ 260 (266)
+.. .+ +-+++||. +.+-+.+. +. +..|-..+ ..+..+||+.+-+
T Consensus 165 ~~~-----~~--~~i~vGG~~~~~~~~~~~~~~---~~~gad~y----~~da~~~v~~~~~ 211 (213)
T cd02069 165 RRG-----IK--IPLLIGGAATSRKHTAVKIAP---EYDGPVVY----VKDASRALGVANK 211 (213)
T ss_pred hcC-----CC--CeEEEEChhcCHHHHhhhhcc---ccCCCceE----ecCHHHHHHHHHH
Confidence 652 33 44566664 44444332 11 12354433 4577777776544
No 262
>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=23.17 E-value=2.2e+02 Score=24.60 Aligned_cols=39 Identities=13% Similarity=0.178 Sum_probs=26.1
Q ss_pred HHHHHHHHHHHhhhccCCCCCeEEEEecccccchhHhhhhHHHHHHHHHHhh
Q 024560 154 EEVLQYARVVIDCATADPDGRKRALLIGGGIANFTDVATTFNGIIRALREKE 205 (266)
Q Consensus 154 ~~~~~al~~ll~~~~~d~~v~~vlvni~ggi~~~~~vA~~~~gii~al~~~~ 205 (266)
+..++.++-+++ ++|.+++|+.. ++.+| .|+++++++.+
T Consensus 168 ~~~~~~~~~~l~---~~~~~~av~~~-------~d~~a---~g~~~al~~~g 206 (273)
T cd01541 168 EKLFEKIKEILK---RPERPTAIVCY-------NDEIA---LRVIDLLKELG 206 (273)
T ss_pred hHHHHHHHHHHc---CCCCCCEEEEc-------CcHHH---HHHHHHHHHcC
Confidence 334444444443 35778888753 67788 99999999874
No 263
>TIGR01501 MthylAspMutase methylaspartate mutase, S subunit. This model represents the S (sigma) subunit of methylaspartate mutase (glutamate mutase), a cobalamin-dependent enzyme that catalyzes the first step in a pathway of glutamate fermentation.
Probab=23.12 E-value=2.9e+02 Score=22.68 Aligned_cols=47 Identities=17% Similarity=0.121 Sum_probs=35.4
Q ss_pred EEE-EeCCCCHHHHHHHHHhhhhhcCCceeecCCCCCHHHHHHHHHHH
Q 024560 215 IFV-RRGGPNYQTGLAKMRALGEELGIPLEVYGPEATMTGICKQAIDC 261 (266)
Q Consensus 215 vvv-rl~G~~~~~~~~~L~~~~~~~Gip~~~~~~~~~~~eAv~~av~~ 261 (266)
|++ -.+|.-=+-|+.++....+++|..+.-.|...++++.++.+.+.
T Consensus 4 vvigtv~~D~HdiGk~iv~~~l~~~GfeVi~LG~~v~~e~~v~aa~~~ 51 (134)
T TIGR01501 4 IVLGVIGSDCHAVGNKILDHAFTNAGFNVVNLGVLSPQEEFIKAAIET 51 (134)
T ss_pred EEEEEecCChhhHhHHHHHHHHHHCCCEEEECCCCCCHHHHHHHHHHc
Confidence 443 67777667777777776678888888788888888888888763
No 264
>smart00256 FBOX A Receptor for Ubiquitination Targets.
Probab=23.07 E-value=1.8e+02 Score=17.38 Aligned_cols=33 Identities=6% Similarity=0.049 Sum_probs=24.0
Q ss_pred CCHhhHHHHHcCCChhHHHHHHHHHHHHHHHHH
Q 024560 1 MTLDACAPLIATLPLEFRGKIGDFIMGVFAVFQ 33 (266)
Q Consensus 1 ~~~~~~~~l~~gl~~~~~~~~~~ii~~Ly~~f~ 33 (266)
||+|++..++..++....-.++..=.+++++..
T Consensus 1 lP~~ll~~I~~~l~~~d~~~~~~vc~~~~~~~~ 33 (41)
T smart00256 1 LPDEILEEILSKLPPKDLLRLRKVSRRWRSLID 33 (41)
T ss_pred CCHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhc
Confidence 689999999999998766666655555555443
No 265
>PRK12616 pyridoxal kinase; Reviewed
Probab=23.05 E-value=2.6e+02 Score=25.09 Aligned_cols=44 Identities=11% Similarity=0.157 Sum_probs=33.7
Q ss_pred CCCHHHHHHHHHHHHhhhccCCCCCeEEEEecccccchhHhhhhHHHHHHHHHHh
Q 024560 150 APNEEEVLQYARVVIDCATADPDGRKRALLIGGGIANFTDVATTFNGIIRALREK 204 (266)
Q Consensus 150 ~a~~~~~~~al~~ll~~~~~d~~v~~vlvni~ggi~~~~~vA~~~~gii~al~~~ 204 (266)
..+++-+.+.++.+++ |-.+++|.+ |...+.+++ +.+.+.++++
T Consensus 56 ~~~~~~i~~ql~~l~~----d~~~~aiki----G~l~s~~~i---~~i~~~l~~~ 99 (270)
T PRK12616 56 PIDTDTIRAQLSTIVD----GIGVDAMKT----GMLPTVDII---ELAADTIKEK 99 (270)
T ss_pred ECCHHHHHHHHHHHHc----CCCCCEEEE----CCCCCHHHH---HHHHHHHHhc
Confidence 4578899999999998 888888885 334455666 7888888776
No 266
>PTZ00106 60S ribosomal protein L30; Provisional
Probab=23.02 E-value=2.6e+02 Score=22.09 Aligned_cols=32 Identities=6% Similarity=-0.101 Sum_probs=22.4
Q ss_pred eEEEEeCCCCHHHHHHHHHhhhhhcCCceeec
Q 024560 214 HIFVRRGGPNYQTGLAKMRALGEELGIPLEVY 245 (266)
Q Consensus 214 pvvvrl~G~~~~~~~~~L~~~~~~~Gip~~~~ 245 (266)
.-+|-+..+-.+.-++-+...++..++|++.|
T Consensus 42 aklViiA~D~~~~~kkki~~~~~~~~Vpv~~~ 73 (108)
T PTZ00106 42 AKLVIISNNCPPIRRSEIEYYAMLSKTGVHHY 73 (108)
T ss_pred eeEEEEeCCCCHHHHHHHHHHHhhcCCCEEEe
Confidence 34455666666777777877777889998754
No 267
>COG0399 WecE Predicted pyridoxal phosphate-dependent enzyme apparently involved in regulation of cell wall biogenesis [Cell envelope biogenesis, outer membrane]
Probab=22.96 E-value=2.6e+02 Score=27.04 Aligned_cols=36 Identities=8% Similarity=0.114 Sum_probs=24.5
Q ss_pred ceeecc---CCCCHHHHHHHHHHHHhhhccCCCCCeEEEEe-cccccch
Q 024560 143 NYAEYS---GAPNEEEVLQYARVVIDCATADPDGRKRALLI-GGGIANF 187 (266)
Q Consensus 143 N~lDlg---G~a~~~~~~~al~~ll~~~~~d~~v~~vlvni-~ggi~~~ 187 (266)
=|+|+- .+-+++.+.++ +. |+.|+|+..+ +|-..+-
T Consensus 99 VFvDid~~T~nid~~~ie~a----It-----~~tKAIipVhl~G~~~dm 138 (374)
T COG0399 99 VFVDIDPDTLNIDPDLIEAA----IT-----PRTKAIIPVHLAGQPCDM 138 (374)
T ss_pred EEEecCCcccCCCHHHHHHH----cc-----cCCeEEEEehhccCCCCH
Confidence 366776 55688887777 54 5689999986 5554433
No 268
>cd04741 DHOD_1A_like Dihydroorotate dehydrogenase (DHOD) class 1A FMN-binding domain. DHOD catalyzes the oxidation of (S)-dihydroorotate to orotate. This is the fourth step and the only redox reaction in the de novo biosynthesis of UMP, the precursor of all pyrimidine nucleotides. DHOD requires FMN as co-factor. DHOD divides into class 1 and class 2 based on their amino acid sequences and cellular location. Members of class 1 are cytosolic enzymes and multimers while class 2 enzymes are membrane associated and monomeric. The class 1 enzymes can be further divided into subtypes 1A and 1B which are homodimers and heterotetrameric proteins, respectively.
Probab=22.92 E-value=5.9e+02 Score=23.31 Aligned_cols=61 Identities=11% Similarity=0.101 Sum_probs=37.8
Q ss_pred eeccCCCCHHHHHHHHHHHHhhhccCC--CCCeEEEEe--ccc-----cc-chhHhhhhHHHHHHHHHHhhhhhhcccce
Q 024560 145 AEYSGAPNEEEVLQYARVVIDCATADP--DGRKRALLI--GGG-----IA-NFTDVATTFNGIIRALREKESKLKAARMH 214 (266)
Q Consensus 145 lDlgG~a~~~~~~~al~~ll~~~~~d~--~v~~vlvni--~gg-----i~-~~~~vA~~~~gii~al~~~~~~~~~~~~p 214 (266)
+.+.|. ++.+.+.++.+.+ .. ..+++=+|+ |.. .. +.+.+ .-|++++++. .++|
T Consensus 96 vsi~g~--~~~~~~~~~~~~~----~~~~~ad~ielN~sCPn~~~~~~~~~~~~~~----~~i~~~v~~~------~~iP 159 (294)
T cd04741 96 ISVTGS--AEDIAAMYKKIAA----HQKQFPLAMELNLSCPNVPGKPPPAYDFDAT----LEYLTAVKAA------YSIP 159 (294)
T ss_pred EECCCC--HHHHHHHHHHHHh----hccccccEEEEECCCCCCCCcccccCCHHHH----HHHHHHHHHh------cCCC
Confidence 345666 6788888777754 33 688999995 321 11 22322 3466666654 4699
Q ss_pred EEEEeCC
Q 024560 215 IFVRRGG 221 (266)
Q Consensus 215 vvvrl~G 221 (266)
|++.+.-
T Consensus 160 v~vKl~p 166 (294)
T cd04741 160 VGVKTPP 166 (294)
T ss_pred EEEEeCC
Confidence 9997764
No 269
>KOG3040 consensus Predicted sugar phosphatase (HAD superfamily) [General function prediction only]
Probab=22.92 E-value=1.5e+02 Score=26.95 Aligned_cols=78 Identities=12% Similarity=0.077 Sum_probs=44.8
Q ss_pred CCCCeEEEEecccccchhHhhhhHHHHHHHHHHhhhhhhcccceEEEEeCCCCHHHHHHHHHhhhhhcCCceeecCCCCC
Q 024560 171 PDGRKRALLIGGGIANFTDVATTFNGIIRALREKESKLKAARMHIFVRRGGPNYQTGLAKMRALGEELGIPLEVYGPEAT 250 (266)
Q Consensus 171 ~~v~~vlvni~ggi~~~~~vA~~~~gii~al~~~~~~~~~~~~pvvvrl~G~~~~~~~~~L~~~~~~~Gip~~~~~~~~~ 250 (266)
..++++|+.+.|-+-..+.-. -+-++|++...+ --+.||.--+.-.++++.|.+.....|+.+.--+.+++
T Consensus 5 ~~v~gvLlDlSGtLh~e~~av---pga~eAl~rLr~------~~~kVkFvTNttk~Sk~~l~~rL~rlgf~v~eeei~ts 75 (262)
T KOG3040|consen 5 RAVKGVLLDLSGTLHIEDAAV---PGAVEALKRLRD------QHVKVKFVTNTTKESKRNLHERLQRLGFDVSEEEIFTS 75 (262)
T ss_pred cccceEEEeccceEecccccC---CCHHHHHHHHHh------cCceEEEEecCcchhHHHHHHHHHHhCCCccHHHhcCc
Confidence 468889988877665555422 455667666542 11445554455566666666555567888743333445
Q ss_pred HHHHHHH
Q 024560 251 MTGICKQ 257 (266)
Q Consensus 251 ~~eAv~~ 257 (266)
...|++.
T Consensus 76 l~aa~~~ 82 (262)
T KOG3040|consen 76 LPAARQY 82 (262)
T ss_pred cHHHHHH
Confidence 5544443
No 270
>PRK09426 methylmalonyl-CoA mutase; Reviewed
Probab=22.87 E-value=9.1e+02 Score=25.51 Aligned_cols=104 Identities=17% Similarity=0.205 Sum_probs=58.2
Q ss_pred HHHHHhcCCCCCCCceeeccC-CCCHHHHHHHHHHHHhhhccCCCCCeEEEEecccccchhHhhhhHHHHHHHHHHhhhh
Q 024560 129 ADTVGDLGYASELGNYAEYSG-APNEEEVLQYARVVIDCATADPDGRKRALLIGGGIANFTDVATTFNGIIRALREKESK 207 (266)
Q Consensus 129 ~D~l~~~g~gg~pAN~lDlgG-~a~~~~~~~al~~ll~~~~~d~~v~~vlvni~ggi~~~~~vA~~~~gii~al~~~~~~ 207 (266)
..++... |-+ +++++ ..+++.+.+++ .+ .+.++|.|- +-....-+.+ ..+++++++.+.
T Consensus 603 ~~~l~~~--Gfe----V~~~~~~~s~e~~v~aa---~~-----~~a~ivvlc--s~d~~~~e~~---~~l~~~Lk~~G~- 662 (714)
T PRK09426 603 ATAFADL--GFD----VDIGPLFQTPEEAARQA---VE-----NDVHVVGVS--SLAAGHKTLV---PALIEALKKLGR- 662 (714)
T ss_pred HHHHHhC--Cee----EecCCCCCCHHHHHHHH---HH-----cCCCEEEEe--ccchhhHHHH---HHHHHHHHhcCC-
Confidence 4555554 333 24553 56777666663 33 355545443 3333333344 888888888631
Q ss_pred hhcccceEEEEeCCCCHHHHHHHHHhhhhhcCCceeecCCCCCHHHHHHHHHHHh
Q 024560 208 LKAARMHIFVRRGGPNYQTGLAKMRALGEELGIPLEVYGPEATMTGICKQAIDCI 262 (266)
Q Consensus 208 ~~~~~~pvvvrl~G~~~~~~~~~L~~~~~~~Gip~~~~~~~~~~~eAv~~av~~~ 262 (266)
.+ +.+-+||.-..+-.+.++ ++|+.-+++ +-++..+.++...+..
T Consensus 663 ---~~--v~vl~GG~~~~~~~~~l~----~aGvD~~i~-~g~d~~~~L~~l~~~l 707 (714)
T PRK09426 663 ---ED--IMVVVGGVIPPQDYDFLY----EAGVAAIFG-PGTVIADAAIDLLELL 707 (714)
T ss_pred ---CC--cEEEEeCCCChhhHHHHH----hCCCCEEEC-CCCCHHHHHHHHHHHH
Confidence 12 333467652222236677 679986544 4678888888776654
No 271
>PRK11041 DNA-binding transcriptional regulator CytR; Provisional
Probab=22.73 E-value=5.3e+02 Score=22.64 Aligned_cols=79 Identities=10% Similarity=-0.023 Sum_probs=43.1
Q ss_pred CCcEEEEecCchHH------HHHHHHHHhcCCCCCCCceeeccCCCCHHHHHHHHHHHHhhhccCCCCCeEEEEeccccc
Q 024560 112 KGRIWTMVAGGGAS------VIYADTVGDLGYASELGNYAEYSGAPNEEEVLQYARVVIDCATADPDGRKRALLIGGGIA 185 (266)
Q Consensus 112 ~G~Igii~NGaGla------m~t~D~l~~~g~gg~pAN~lDlgG~a~~~~~~~al~~ll~~~~~d~~v~~vlvni~ggi~ 185 (266)
.++|++++.-.+.. .-..+.+..+ |-+.-....+.++.+.+..++.++-+++ ..+..++++..
T Consensus 152 ~~~I~~l~~~~~~~~~~~R~~Gf~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~l~---~~~~~~ai~~~------ 220 (309)
T PRK11041 152 HKRIACIAGPEEMPLCHYRLQGYVQALRRC--GITVDPQYIARGDFTFEAGAKALKQLLD---LPQPPTAVFCH------ 220 (309)
T ss_pred CceEEEEeCCccccchHHHHHHHHHHHHHc--CCCCCHHHeEeCCCCHHHHHHHHHHHHc---CCCCCCEEEEc------
Confidence 37899886332221 1113455554 2221111122344455555566555554 24557777743
Q ss_pred chhHhhhhHHHHHHHHHHhh
Q 024560 186 NFTDVATTFNGIIRALREKE 205 (266)
Q Consensus 186 ~~~~vA~~~~gii~al~~~~ 205 (266)
++.+| .|+++++++.+
T Consensus 221 -~d~~a---~gv~~al~~~g 236 (309)
T PRK11041 221 -SDVMA---LGALSQAKRMG 236 (309)
T ss_pred -CcHHH---HHHHHHHHHcC
Confidence 66777 89999999874
No 272
>COG2759 MIS1 Formyltetrahydrofolate synthetase [Nucleotide transport and metabolism]
Probab=22.70 E-value=1.9e+02 Score=29.16 Aligned_cols=33 Identities=18% Similarity=0.292 Sum_probs=24.2
Q ss_pred cccceEEE---EeCCCCHHHHHHHHHhhhhhcCCcee
Q 024560 210 AARMHIFV---RRGGPNYQTGLAKMRALGEELGIPLE 243 (266)
Q Consensus 210 ~~~~pvvv---rl~G~~~~~~~~~L~~~~~~~Gip~~ 243 (266)
+..+|+|| |.- +..++-.+.+++.++++|+++.
T Consensus 367 kfgvp~VVAIN~F~-tDt~~Ei~~i~~~~~~~gv~~~ 402 (554)
T COG2759 367 KFGVPVVVAINKFP-TDTEAEIAAIEKLCEEHGVEVA 402 (554)
T ss_pred HcCCCeEEEeccCC-CCCHHHHHHHHHHHHHcCCcee
Confidence 35788875 555 5556667788888889998863
No 273
>COG3473 Maleate cis-trans isomerase [Secondary metabolites biosynthesis, transport, and catabolism]
Probab=22.66 E-value=4.8e+02 Score=23.67 Aligned_cols=69 Identities=23% Similarity=0.296 Sum_probs=44.3
Q ss_pred eeccCCCCHHHHHHHHHHHHhhhccCCCCCeEEEEecccccchhHhhhhHHHHHHHHHHhhhhhhcccceEEEEeCCCCH
Q 024560 145 AEYSGAPNEEEVLQYARVVIDCATADPDGRKRALLIGGGIANFTDVATTFNGIIRALREKESKLKAARMHIFVRRGGPNY 224 (266)
Q Consensus 145 lDlgG~a~~~~~~~al~~ll~~~~~d~~v~~vlvni~ggi~~~~~vA~~~~gii~al~~~~~~~~~~~~pvvvrl~G~~~ 224 (266)
+++| .-+|..+++..+-+. .|+.|++|+- |+.+- ||+ +++.+++- ..+|||. .|.
T Consensus 158 ~eig-r~~P~~~y~lAk~~~-----~~~~DaiFiS-------CTnlR-t~e-ii~~lE~~------~G~PVvs----SN~ 212 (238)
T COG3473 158 LEIG-RQEPWAVYRLAKEVF-----TPDADAIFIS-------CTNLR-TFE-IIEKLERD------TGVPVVS----SNQ 212 (238)
T ss_pred chhc-ccChHHHHHHHHHhc-----CCCCCeEEEE-------eeccc-cHH-HHHHHHHH------hCCceee----ccH
Confidence 3444 445666777666665 5999999986 33322 223 45555543 5799996 578
Q ss_pred HHHHHHHHhhhhhcCCce
Q 024560 225 QTGLAKMRALGEELGIPL 242 (266)
Q Consensus 225 ~~~~~~L~~~~~~~Gip~ 242 (266)
...+..|+ ..|+..
T Consensus 213 AT~W~~Lr----~~g~~~ 226 (238)
T COG3473 213 ATLWMALR----LIGLRE 226 (238)
T ss_pred HHHHHHHH----HcCCcc
Confidence 88889998 446543
No 274
>cd07120 ALDH_PsfA-ACA09737 Pseudomonas putida aldehyde dehydrogenase PsfA (ACA09737)-like. Included in this CD is the aldehyde dehydrogenase (PsfA, locus ACA09737) of Pseudomonas putida involved in furoic acid metabolism. Transcription of psfA was induced in response to 2-furoic acid, furfuryl alcohol, and furfural.
Probab=22.64 E-value=7.2e+02 Score=24.22 Aligned_cols=20 Identities=5% Similarity=0.072 Sum_probs=11.3
Q ss_pred HHHHHHHHHHHHHhCCceee
Q 024560 21 IGDFIMGVFAVFQDLDFSFI 40 (266)
Q Consensus 21 ~~~ii~~Ly~~f~~~D~~l~ 40 (266)
=.+++.++.+++.++--.|.
T Consensus 44 R~~~L~~~a~~l~~~~~~l~ 63 (455)
T cd07120 44 RARVLLELADAFEANAERLA 63 (455)
T ss_pred HHHHHHHHHHHHHHHHHHHH
Confidence 35566666666666544333
No 275
>KOG3405 consensus RNA polymerase subunit K [Transcription]
Probab=22.55 E-value=1.7e+02 Score=24.18 Aligned_cols=30 Identities=17% Similarity=0.307 Sum_probs=21.2
Q ss_pred EEEEecccccchhHhhhhHHHHHHHHHHhhhhhhcccceEEEEe
Q 024560 176 RALLIGGGIANFTDVATTFNGIIRALREKESKLKAARMHIFVRR 219 (266)
Q Consensus 176 vlvni~ggi~~~~~vA~~~~gii~al~~~~~~~~~~~~pvvvrl 219 (266)
|+|- .+|-++.-+|| .+++.+ .++|+++|+
T Consensus 88 vmVe-LegETdPL~IA---------mkEL~q----kKIP~iIRR 117 (136)
T KOG3405|consen 88 VMVE-LEGETDPLEIA---------MKELKQ----KKIPFIIRR 117 (136)
T ss_pred eEEe-cCCCCCHHHHH---------HHHHhh----ccCceEEee
Confidence 4554 47788898888 455542 579999975
No 276
>PRK14483 DhaKLM operon coactivator DhaQ; Provisional
Probab=22.41 E-value=1.6e+02 Score=28.17 Aligned_cols=59 Identities=17% Similarity=0.277 Sum_probs=40.0
Q ss_pred CCcEEEEecCchHHHHHHHHHHhcCCCCCCC-------------ceeeccCCCCHHHHHHHHHHHHhhhccCCCCCeEEE
Q 024560 112 KGRIWTMVAGGGASVIYADTVGDLGYASELG-------------NYAEYSGAPNEEEVLQYARVVIDCATADPDGRKRAL 178 (266)
Q Consensus 112 ~G~Igii~NGaGlam~t~D~l~~~g~gg~pA-------------N~lDlgG~a~~~~~~~al~~ll~~~~~d~~v~~vlv 178 (266)
.+++++|+.||. |.+|+ -+=++=-.|+++++.++++.+-. . +++|+
T Consensus 42 ~~kV~lIsGGGS--------------GHEPah~GyVG~GmLdAav~G~VFaSPs~~qI~~ai~av~~----~---~GvL~ 100 (329)
T PRK14483 42 DQLVPIISGGGS--------------GHEPAHIGYVGKGMLTAAVNGSIFTPPTAEQILAATRLVPK----G---KGVFF 100 (329)
T ss_pred CCcEEEEecCCc--------------cccccccccccCCccceeEeccccCCCCHHHHHHHHHhhcC----C---CCEEE
Confidence 478999988873 56663 44455578999999999888743 3 45555
Q ss_pred E---ecccccchhHhh
Q 024560 179 L---IGGGIANFTDVA 191 (266)
Q Consensus 179 n---i~ggi~~~~~vA 191 (266)
+ ..|=+.+++..+
T Consensus 101 ivkNYtGDvlnF~mA~ 116 (329)
T PRK14483 101 IIKNFEADVAEFSAAI 116 (329)
T ss_pred EecccHHHhhhHHHHH
Confidence 5 356566665444
No 277
>cd07112 ALDH_GABALDH-PuuC Escherichia coli NADP+-dependent gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase PuuC-like. NADP+-dependent, gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase (GABALDH) PuuC of Escherichia coli which catalyzes the conversion of putrescine to 4-aminobutanoate and other similar sequences are present in this CD.
Probab=22.36 E-value=7.3e+02 Score=24.15 Aligned_cols=19 Identities=0% Similarity=-0.010 Sum_probs=11.5
Q ss_pred HHHHHHHHHHHHHHHhCCc
Q 024560 19 GKIGDFIMGVFAVFQDLDF 37 (266)
Q Consensus 19 ~~~~~ii~~Ly~~f~~~D~ 37 (266)
++-.+++.++.+++.++--
T Consensus 48 ~~R~~~L~~~a~~l~~~~~ 66 (462)
T cd07112 48 AERKAVLLRLADLIEAHRD 66 (462)
T ss_pred HHHHHHHHHHHHHHHHhHH
Confidence 3445666777777766543
No 278
>PF01171 ATP_bind_3: PP-loop family; InterPro: IPR011063 This entry represents the PP-loop motif superfamily [,]. The PP-loop motif appears to be a modified version of the P-loop of nucleotide binding domain that is involved in phosphate binding []. Named PP-motif, since it appears to be a part of a previously uncharacterised ATP pyrophophatase domain. ATP sulfurylases, Escherichia coli NtrL, and Bacillus subtilis OutB consist of this domain alone. In other proteins, the pyrophosphatase domain is associated with amidotransferase domains (type I or type II), a putative citrulline-aspartate ligase domain or a nitrilase/amidase domain.; PDB: 3A2K_A 2E89_B 2E21_D 1WY5_B 1NI5_A.
Probab=22.31 E-value=4.6e+02 Score=21.83 Aligned_cols=99 Identities=11% Similarity=0.069 Sum_probs=48.8
Q ss_pred ccCCCCHHHHHHHHHHHHhhhccCCCCCeEEEEecccccchhHhhhhHHHHHHHHHHhhhhhhcccceEEE-EeC-----
Q 024560 147 YSGAPNEEEVLQYARVVIDCATADPDGRKRALLIGGGIANFTDVATTFNGIIRALREKESKLKAARMHIFV-RRG----- 220 (266)
Q Consensus 147 lgG~a~~~~~~~al~~ll~~~~~d~~v~~vlvni~ggi~~~~~vA~~~~gii~al~~~~~~~~~~~~pvvv-rl~----- 220 (266)
++|+.+.-.+...+.-+.... ..++.++.||+.-. ..+..-+ +-+.+.++++ .+|+.+ ++.
T Consensus 6 ~SGG~DS~~Ll~~l~~~~~~~--~~~~~~~~vdh~~~-~~s~~~~---~~v~~~~~~~-------~i~~~~~~~~~~~~~ 72 (182)
T PF01171_consen 6 VSGGKDSMALLHLLKELRRRN--GIKLIAVHVDHGLR-EESDEEA---EFVEEICEQL-------GIPLYIVRIDEDRKK 72 (182)
T ss_dssp --SSHHHHHHHHHHHHHHTTT--TTEEEEEEEE-STS-CCHHHHH---HHHHHHHHHT-------T-EEEEEE--CHCCT
T ss_pred EcCCHHHHHHHHHHHHHHHhc--CCCeEEEEEecCCC-cccchhH---HHHHHHHHhc-------CCceEEEEeeeeecc
Confidence 566666665555554443310 12455666665322 2333333 4444444443 466553 322
Q ss_pred C-CCHHHHH----HHHHhhhhhcCCceeecCCCCCHHHHHHHHHH
Q 024560 221 G-PNYQTGL----AKMRALGEELGIPLEVYGPEATMTGICKQAID 260 (266)
Q Consensus 221 G-~~~~~~~----~~L~~~~~~~Gip~~~~~~~~~~~eAv~~av~ 260 (266)
+ +-+..+| +.|.+.+.+.|.+..+.| -+.+|.++-++-
T Consensus 73 ~~~~e~~aR~~Ry~~l~~~a~~~g~~~i~~G--Hh~dD~~ET~l~ 115 (182)
T PF01171_consen 73 GSNIEECARELRYQFLREIAKEEGCNKIALG--HHLDDQAETFLM 115 (182)
T ss_dssp TSTCHHHHHHHHHHHHHHHHHTTT-CEEE-----BHHHHHHHHHH
T ss_pred cCCHHHHHHHHHHHHHHHhhhcccccceeec--CcCCccHHHHHH
Confidence 2 3344555 566777778898877766 588888887643
No 279
>COG3077 RelB DNA-damage-inducible protein J [DNA replication, recombination, and repair]
Probab=22.23 E-value=1.2e+02 Score=23.40 Aligned_cols=33 Identities=15% Similarity=0.259 Sum_probs=22.1
Q ss_pred EEeCCCCHHHHHHHHHhhhhhcCCceeecCCCCCHHHHHHHHHHHh
Q 024560 217 VRRGGPNYQTGLAKMRALGEELGIPLEVYGPEATMTGICKQAIDCI 262 (266)
Q Consensus 217 vrl~G~~~~~~~~~L~~~~~~~Gip~~~~~~~~~~~eAv~~av~~~ 262 (266)
+|+...--+++-.+|. +.|+ |+++|++.++..+
T Consensus 9 ~RiD~~vK~eA~~Vl~----~mGl---------t~S~airm~L~~v 41 (88)
T COG3077 9 ARIDDEVKEEATAVLE----EMGL---------TISDAIRMFLTKV 41 (88)
T ss_pred heecHHHHHHHHHHHH----HhCC---------CHHHHHHHHHHHH
Confidence 3666666667777777 4576 6777777777654
No 280
>PF00763 THF_DHG_CYH: Tetrahydrofolate dehydrogenase/cyclohydrolase, catalytic domain; InterPro: IPR020630 Enzymes that participate in the transfer of one-carbon units require the coenzyme tetrahydrofolate (THF). Various reactions generate one-carbon derivatives of THF, which can be interconverted between different oxidation states by methylene-THF dehydrogenase (1.5.1.5 from EC), methenyl-THF cyclohydrolase (3.5.4.9 from EC) and formyl-THF synthetase (6.3.4.3 from EC) [, ]. The dehydrogenase and cyclohydrolase activities are expressed by a variety of multifunctional enzymes, including the tri-functional eukaryotic C1-tetrahydrofolate synthase []; a bifunctional eukaryotic mitochondrial protein; and the bifunctional Escherichia coli folD protein [, ]. Methylene-tetrahydrofolate dehydrogenase and methenyltetrahydrofolate cyclo-hydrolase share an overlapping active site [], and as such are usually located together in proteins, acting in tandem on the carbon-nitrogen bonds of substrates other than peptide bonds. This entry represents the N-terminal catalytic domain of these enzymes. ; GO: 0003824 catalytic activity, 0004488 methylenetetrahydrofolate dehydrogenase (NADP+) activity, 0009396 folic acid-containing compound biosynthetic process, 0055114 oxidation-reduction process; PDB: 2C2X_B 2C2Y_A 1EDZ_A 1EE9_A 4A26_B 3NGL_C 3NGX_A 1B0A_A 1DIA_A 1A4I_B ....
Probab=22.19 E-value=1.7e+02 Score=23.11 Aligned_cols=66 Identities=18% Similarity=0.196 Sum_probs=39.5
Q ss_pred cEEEEecCc-hHHHHHHHHHHhcCC--CCCCCceeeccCCCCHHHHHHHHHHHHhhhccCCCCCeEEEEe--cccc
Q 024560 114 RIWTMVAGG-GASVIYADTVGDLGY--ASELGNYAEYSGAPNEEEVLQYARVVIDCATADPDGRKRALLI--GGGI 184 (266)
Q Consensus 114 ~Igii~NGa-Glam~t~D~l~~~g~--gg~pAN~lDlgG~a~~~~~~~al~~ll~~~~~d~~v~~vlvni--~ggi 184 (266)
.++++--|- -.+.+|........- |. ..--..+..+.+.+.+.+.++-+-+ ||+|.||+|-. |.++
T Consensus 31 ~Laii~vg~d~~S~~Y~~~k~k~~~~~Gi-~~~~~~l~~~~~~~el~~~i~~lN~----D~~V~GIlvq~PLP~~i 101 (117)
T PF00763_consen 31 KLAIILVGDDPASISYVRSKQKAAEKLGI-EFELIELPEDISEEELLELIEKLNE----DPSVHGILVQLPLPKHI 101 (117)
T ss_dssp EEEEEEES--HHHHHHHHHHHHHHHHHT--EEEEEEE-TTSSHHHHHHHHHHHHH-----TT-SEEEEESSSSTTS
T ss_pred EEEEEecCCChhHHHHHHHHHHHHHHcCC-ceEEEECCCCcCHHHHHHHHHHHhC----CCCCCEEEEcCCCCCCc
Confidence 355555553 345666655543300 12 2334567788999999999888877 99999999994 5554
No 281
>TIGR01036 pyrD_sub2 dihydroorotate dehydrogenase, subfamily 2. The subfamilies 1 and 2 share extensive homology, particularly toward the C-terminus. This subfamily has a longer N-terminal region.
Probab=22.18 E-value=6.6e+02 Score=23.62 Aligned_cols=80 Identities=15% Similarity=0.227 Sum_probs=40.4
Q ss_pred CHHHHHHHHHHHHhhhccCCCCCeEEEEe--ccc-----ccchhHhhhhHHHHHHHHHHhhhhh-hcccceEEEEeCCCC
Q 024560 152 NEEEVLQYARVVIDCATADPDGRKRALLI--GGG-----IANFTDVATTFNGIIRALREKESKL-KAARMHIFVRRGGPN 223 (266)
Q Consensus 152 ~~~~~~~al~~ll~~~~~d~~v~~vlvni--~gg-----i~~~~~vA~~~~gii~al~~~~~~~-~~~~~pvvvrl~G~~ 223 (266)
..+.|.+.++.+- +..+++=+|+ |.. ....+.+ .-+++++++..+.+ +..++||++.|.-.-
T Consensus 152 ~~~dy~~~~~~~~------~~ad~iElNlScPn~~~~~~~~~~~~~----~~i~~~V~~~~~~~~~~~~~Pv~vKLsP~~ 221 (335)
T TIGR01036 152 AKEDYAACLRKLG------PLADYLVVNVSSPNTPGLRDLQYKAEL----RDLLTAVKQEQDGLRRVHRVPVLVKIAPDL 221 (335)
T ss_pred CHHHHHHHHHHHh------hhCCEEEEEccCCCCCCcccccCHHHH----HHHHHHHHHHHHhhhhccCCceEEEeCCCC
Confidence 4677888777663 3478999995 321 1122222 33444444332100 012499999999764
Q ss_pred HHHHHHHHHhhhhhcCCc
Q 024560 224 YQTGLAKMRALGEELGIP 241 (266)
Q Consensus 224 ~~~~~~~L~~~~~~~Gip 241 (266)
..+...-+.+.+.++|+.
T Consensus 222 ~~~~i~~ia~~~~~~Gad 239 (335)
T TIGR01036 222 TESDLEDIADSLVELGID 239 (335)
T ss_pred CHHHHHHHHHHHHHhCCc
Confidence 322222222223355654
No 282
>TIGR01082 murC UDP-N-acetylmuramate--alanine ligase. UDP-N-acetylmuramate:L-alanyl-gamma-D-glutamyl-meso-diaminopimelate ligase (murein tripeptide ligase) is described by TIGR01081.
Probab=22.10 E-value=7.2e+02 Score=23.96 Aligned_cols=91 Identities=13% Similarity=0.165 Sum_probs=49.8
Q ss_pred CCHHHHHHHHHHHHhhhccCCCCCeEEEEecc--cccchhHhhhhHHHHHHHHHHhhhhhhcccceEEEEe--------C
Q 024560 151 PNEEEVLQYARVVIDCATADPDGRKRALLIGG--GIANFTDVATTFNGIIRALREKESKLKAARMHIFVRR--------G 220 (266)
Q Consensus 151 a~~~~~~~al~~ll~~~~~d~~v~~vlvni~g--gi~~~~~vA~~~~gii~al~~~~~~~~~~~~pvvvrl--------~ 220 (266)
..++.+..+++.+-+. .++-+ ++.++| +..+..+.. +.+.+.++.. +.-+++-. .
T Consensus 326 hn~~~~~a~~~al~~~---~~~~~--ii~i~g~~~~~r~k~~~---~~~~~~l~~~-------d~v~l~~~~~~~~~~~~ 390 (448)
T TIGR01082 326 HHPTEIKATLKAARQG---YPDKR--IVVVFQPHRYSRTRDLF---DDFAKVLSDA-------DELILLDIYAAGEEPIN 390 (448)
T ss_pred CCHHHHHHHHHHHHHh---cCCCe--EEEEECCCCCccHHHHH---HHHHHHHHhC-------CEEEEecccCCCCCCCC
Confidence 3677888888777552 12222 233455 466655544 5666666532 22222322 2
Q ss_pred CCCHHHHHHHHHhhhhhcC-CceeecCCCCCHHHHHHHHHHHhh
Q 024560 221 GPNYQTGLAKMRALGEELG-IPLEVYGPEATMTGICKQAIDCIM 263 (266)
Q Consensus 221 G~~~~~~~~~L~~~~~~~G-ip~~~~~~~~~~~eAv~~av~~~~ 263 (266)
|...++-.+.+. +.+ .+... +.++++|++.+.+.++
T Consensus 391 g~~~~~i~~~~~----~~~~~~~~~---~~~~~~a~~~a~~~a~ 427 (448)
T TIGR01082 391 GIDGKSLARKIT----QLGKIEPYF---VPDLAELVEFLAAVLQ 427 (448)
T ss_pred CCCHHHHHHHHh----hcCCCceEE---eCCHHHHHHHHHHhcC
Confidence 444444444454 334 55554 3489999999987664
No 283
>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=22.06 E-value=5e+02 Score=22.09 Aligned_cols=78 Identities=10% Similarity=0.036 Sum_probs=43.4
Q ss_pred CCcEEEEecCch--HH-----HHHHHHHHhcCCCCCCCceeeccCCCCHHHHHHHHHHHHhhhccCCCCCeEEEEecccc
Q 024560 112 KGRIWTMVAGGG--AS-----VIYADTVGDLGYASELGNYAEYSGAPNEEEVLQYARVVIDCATADPDGRKRALLIGGGI 184 (266)
Q Consensus 112 ~G~Igii~NGaG--la-----m~t~D~l~~~g~gg~pAN~lDlgG~a~~~~~~~al~~ll~~~~~d~~v~~vlvni~ggi 184 (266)
.++|+++.+... .. -...+.+..+ |-++ +..+...+.+.+..+++++-+|. ++|.+++++.+
T Consensus 112 ~~~i~~i~~~~~~~~~~~~r~~gf~~~l~~~--~~~~-~~~~~~~~~~~~~~~~~~~~~l~---~~~~~~ai~~~----- 180 (265)
T cd06291 112 CKHIAHIGGPNNTVSPTNLRYEGFLDVLKEN--GLEV-RIIEIQENFDDAEKKEEIKELLE---EYPDIDGIFAS----- 180 (265)
T ss_pred CcEEEEEccCcccccchHHHHHHHHHHHHHc--CCCC-ChheeeccccchHHHHHHHHHHh---CCCCCCEEEEC-----
Confidence 357888875443 11 2235666666 3332 23344333333333444444443 36777887753
Q ss_pred cchhHhhhhHHHHHHHHHHhh
Q 024560 185 ANFTDVATTFNGIIRALREKE 205 (266)
Q Consensus 185 ~~~~~vA~~~~gii~al~~~~ 205 (266)
++..| .++++++++.+
T Consensus 181 --~d~~a---~~~~~al~~~g 196 (265)
T cd06291 181 --NDLTA---ILVLKEAQQRG 196 (265)
T ss_pred --ChHHH---HHHHHHHHHcC
Confidence 45667 89999999874
No 284
>TIGR01506 ribC_arch riboflavin synthase. This archaeal protein catalyzes the same reaction, the final step in riboflavin biosynthesis, as bacterial riboflavin biosynthesis alpha chain. However, it is more similar in sequence to 6,7-dimethyl-8-ribityllumazine synthase, which catalyzes the previous reaction and which (in bacteria) is called the riboflavin synthase beta chain.
Probab=22.04 E-value=4.9e+02 Score=22.02 Aligned_cols=109 Identities=7% Similarity=0.006 Sum_probs=67.8
Q ss_pred HHHHHHHhcCCCCCCCceeeccCCCCHHHHHHHHHHHHhhhccCCCCCeEEEE---ecccccchhHhhhhHHHHHHHHHH
Q 024560 127 IYADTVGDLGYASELGNYAEYSGAPNEEEVLQYARVVIDCATADPDGRKRALL---IGGGIANFTDVATTFNGIIRALRE 203 (266)
Q Consensus 127 ~t~D~l~~~g~gg~pAN~lDlgG~a~~~~~~~al~~ll~~~~~d~~v~~vlvn---i~ggi~~~~~vA~~~~gii~al~~ 203 (266)
-+.|.|..+| ...+ +++---|-.-.+.-+.+.+++ ..+.++|+.. |-|....++-| +..+||.+.--+
T Consensus 17 gA~~~L~~~g---~g~~-i~v~~VPGa~EiP~aak~l~~----~~~~DaVIaLG~VIrGeT~Hfd~V-~vs~GL~~lsl~ 87 (151)
T TIGR01506 17 AAIDELRKHT---AGIK-IIRRTVPGIKDLPVAAKKLLE----EEGCEMVITLGWVGPEEKDKLSYH-EASTGLIQVQLM 87 (151)
T ss_pred HHHHHHHhcC---CCCe-EEEEECCcHhHHHHHHHHHHh----cCCCCEEEEeceEEcCCCCcEeHH-HHHHHHHHHHhh
Confidence 3678888762 2233 444444445556667666665 5679998877 46666666665 455777765333
Q ss_pred hhhhhhcccceEEEEeCCCCHHHHHHHHHhhhhhcCCceeecCCCCCHHHHHHHHHHHhh
Q 024560 204 KESKLKAARMHIFVRRGGPNYQTGLAKMRALGEELGIPLEVYGPEATMTGICKQAIDCIM 263 (266)
Q Consensus 204 ~~~~~~~~~~pvvvrl~G~~~~~~~~~L~~~~~~~Gip~~~~~~~~~~~eAv~~av~~~~ 263 (266)
.++||.--+--.|++++.+.+. +. . ..-=.|++..+++++.
T Consensus 88 -------~~~PVi~VlT~e~eeQA~~Rag------~~-~-----~nkG~eaA~aaleMi~ 128 (151)
T TIGR01506 88 -------TNKHVIDVTVHEDEAEDPEELK------VL-A-----DNRAREHAQNLIMLLF 128 (151)
T ss_pred -------hCCCEEEEEeeCCHHHHHHHhc------cc-c-----cChHHHHHHHHHHHHH
Confidence 4688776666777787766665 21 1 2355677777777763
No 285
>COG0151 PurD Phosphoribosylamine-glycine ligase [Nucleotide transport and metabolism]
Probab=22.04 E-value=1e+02 Score=30.38 Aligned_cols=54 Identities=20% Similarity=0.273 Sum_probs=38.6
Q ss_pred HHHHHHHHHhhhhhhcccceEE------EEeCCCCHHHHHHHHHhhhhhcCCceeecCCCCCHHHHHHHHHH
Q 024560 195 NGIIRALREKESKLKAARMHIF------VRRGGPNYQTGLAKMRALGEELGIPLEVYGPEATMTGICKQAID 260 (266)
Q Consensus 195 ~gii~al~~~~~~~~~~~~pvv------vrl~G~~~~~~~~~L~~~~~~~Gip~~~~~~~~~~~eAv~~av~ 260 (266)
.||++.+++. .+|++ .|+.| +-.-+|+.+. +.|||+-.|.+|+++++|-...-+
T Consensus 77 ~GvvD~l~~~-------Gi~vFGPsk~AA~lE~-SK~faK~fm~----k~~IPta~y~~f~~~e~a~ayi~~ 136 (428)
T COG0151 77 AGVVDALRAA-------GIPVFGPTKAAAQLEG-SKAFAKDFMK----KYGIPTAEYEVFTDPEEAKAYIDE 136 (428)
T ss_pred hhhHHHHHHC-------CCceeCcCHHHHHHHh-hHHHHHHHHH----HcCCCcccccccCCHHHHHHHHHH
Confidence 8999999885 46666 14444 2244566666 779998888889999988776544
No 286
>PRK02705 murD UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional
Probab=21.73 E-value=7.2e+02 Score=23.84 Aligned_cols=89 Identities=20% Similarity=0.218 Sum_probs=46.9
Q ss_pred eeccCCCCHHHHHHHHHHHHhhhccCCCCCeEEEEecccccchhHhhhhHHHHHHHHHHhhhhhhcccceEEEEeCCCCH
Q 024560 145 AEYSGAPNEEEVLQYARVVIDCATADPDGRKRALLIGGGIANFTDVATTFNGIIRALREKESKLKAARMHIFVRRGGPNY 224 (266)
Q Consensus 145 lDlgG~a~~~~~~~al~~ll~~~~~d~~v~~vlvni~ggi~~~~~vA~~~~gii~al~~~~~~~~~~~~pvvvrl~G~~~ 224 (266)
+|=+++.+++.+..+++.+ . . + .+.|+||+....+.. .+.+.+.+. ..-++.. |...
T Consensus 329 i~Ds~a~N~~s~~~al~~l-~----~---~--~i~IlGg~~~~~d~~----~~~~~l~~~--------~~~vi~~-g~~~ 385 (459)
T PRK02705 329 INDSKATNYDAAEVGLKAV-P----G---P--VILIAGGEAKQGDDS----AWLKQIKAK--------AAAVLLF-GEAA 385 (459)
T ss_pred EEeCCCCCHHHHHHHHHhC-C----C---C--eEEEecCccCCCCHH----HHHHHHHhh--------eeEEEEE-CCCH
Confidence 4334567788888776554 1 2 2 234567765444433 333333321 2223333 4454
Q ss_pred HHHHHHHHhhhhhcCCc--eeecCCCCCHHHHHHHHHHHhh
Q 024560 225 QTGLAKMRALGEELGIP--LEVYGPEATMTGICKQAIDCIM 263 (266)
Q Consensus 225 ~~~~~~L~~~~~~~Gip--~~~~~~~~~~~eAv~~av~~~~ 263 (266)
+.-.+.|. ..+.+ ++. +.++++|++.+.++++
T Consensus 386 ~~l~~~l~----~~~~~~~~~~---~~~~~eA~~~a~~~a~ 419 (459)
T PRK02705 386 PTLAQRLQ----ESGYTGEYEI---VETLDEAVPRAFELAK 419 (459)
T ss_pred HHHHHHHH----hcCCCcceEE---cCCHHHHHHHHHHHhC
Confidence 44445555 33433 443 4599999999887764
No 287
>PRK11303 DNA-binding transcriptional regulator FruR; Provisional
Probab=21.73 E-value=5.8e+02 Score=22.72 Aligned_cols=77 Identities=17% Similarity=0.145 Sum_probs=44.7
Q ss_pred CCcEEEEecCchHH------HHHHHHHHhcCCCCCCCceeeccCCCCHHHHHHHHHHHHhhhccCCCCCeEEEEeccccc
Q 024560 112 KGRIWTMVAGGGAS------VIYADTVGDLGYASELGNYAEYSGAPNEEEVLQYARVVIDCATADPDGRKRALLIGGGIA 185 (266)
Q Consensus 112 ~G~Igii~NGaGla------m~t~D~l~~~g~gg~pAN~lDlgG~a~~~~~~~al~~ll~~~~~d~~v~~vlvni~ggi~ 185 (266)
..+|++++.-.... -...+.+..+ |..+ .++ ..++.+.+.-+++++-+|+ ..+..++||..
T Consensus 179 ~r~I~~i~~~~~~~~~~~R~~Gf~~al~~~--g~~~-~~~-~~~~~~~~~~~~~~~~~l~---~~~~~~ai~~~------ 245 (328)
T PRK11303 179 AESILLLGALPELSVSFEREQGFRQALKDD--PREV-HYL-YANSFEREAGAQLFEKWLE---THPMPDALFTT------ 245 (328)
T ss_pred CCeEEEEeCccccccHHHHHHHHHHHHHHc--CCCc-eEE-EeCCCChHHHHHHHHHHHc---CCCCCCEEEEc------
Confidence 36688886432211 2235667776 3432 222 2344444545555555554 24667887753
Q ss_pred chhHhhhhHHHHHHHHHHhh
Q 024560 186 NFTDVATTFNGIIRALREKE 205 (266)
Q Consensus 186 ~~~~vA~~~~gii~al~~~~ 205 (266)
++.+| .|+++++++.+
T Consensus 246 -~d~~A---~g~~~al~~~g 261 (328)
T PRK11303 246 -SYTLL---QGVLDVLLERP 261 (328)
T ss_pred -CcHHH---HHHHHHHHHcC
Confidence 67788 99999998874
No 288
>PRK10014 DNA-binding transcriptional repressor MalI; Provisional
Probab=21.72 E-value=5.9e+02 Score=22.82 Aligned_cols=78 Identities=10% Similarity=0.023 Sum_probs=43.7
Q ss_pred CcEEEEecCchH-H-----HHHHHHHHhcCCCCCCCceeeccCCCCHHHHHHHHHHHHhhhccCCCCCeEEEEecccccc
Q 024560 113 GRIWTMVAGGGA-S-----VIYADTVGDLGYASELGNYAEYSGAPNEEEVLQYARVVIDCATADPDGRKRALLIGGGIAN 186 (266)
Q Consensus 113 G~Igii~NGaGl-a-----m~t~D~l~~~g~gg~pAN~lDlgG~a~~~~~~~al~~ll~~~~~d~~v~~vlvni~ggi~~ 186 (266)
++|+++++-... . .-..+.+..+ |-.+-....+.++.+.+..+++++-+|+ .+|.+++|+. .
T Consensus 183 ~~I~~i~g~~~~~~~~~R~~Gf~~al~~~--g~~~~~~~~~~~~~~~~~~~~~~~~~l~---~~~~~~ai~~-------~ 250 (342)
T PRK10014 183 QRIAWLGGQSSSLTRAERVGGYCATLLKF--GLPFHSEWVLECTSSQKQAAEAITALLR---HNPTISAVVC-------Y 250 (342)
T ss_pred CEEEEEcCCcccccHHHHHHHHHHHHHHc--CCCCCcceEecCCCChHHHHHHHHHHHc---CCCCCCEEEE-------C
Confidence 578888532211 1 1235666666 3332211122233344555566555554 2567787773 3
Q ss_pred hhHhhhhHHHHHHHHHHhh
Q 024560 187 FTDVATTFNGIIRALREKE 205 (266)
Q Consensus 187 ~~~vA~~~~gii~al~~~~ 205 (266)
+|.+| -|+++++++.+
T Consensus 251 nd~~A---~g~~~~l~~~g 266 (342)
T PRK10014 251 NETIA---MGAWFGLLRAG 266 (342)
T ss_pred CcHHH---HHHHHHHHHcC
Confidence 77888 99999998874
No 289
>KOG0781 consensus Signal recognition particle receptor, alpha subunit [Intracellular trafficking, secretion, and vesicular transport]
Probab=21.67 E-value=6.9e+02 Score=25.54 Aligned_cols=85 Identities=12% Similarity=0.096 Sum_probs=51.4
Q ss_pred CCCCCeEEEEecccccchhHhhhhHHHHHHHHHHhhhhhhcccceEEE--EeCCCCHHHHHHHHHhhhhhcC----Ccee
Q 024560 170 DPDGRKRALLIGGGIANFTDVATTFNGIIRALREKESKLKAARMHIFV--RRGGPNYQTGLAKMRALGEELG----IPLE 243 (266)
Q Consensus 170 d~~v~~vlvni~ggi~~~~~vA~~~~gii~al~~~~~~~~~~~~pvvv--rl~G~~~~~~~~~L~~~~~~~G----ip~~ 243 (266)
+.+-++|||..-|-+-+....- ..+...++-. ++++-++| -|-|+..-.-.+.|++...... |.-.
T Consensus 464 ~~gfDVvLiDTAGR~~~~~~lm---~~l~k~~~~~-----~pd~i~~vgealvg~dsv~q~~~fn~al~~~~~~r~id~~ 535 (587)
T KOG0781|consen 464 NQGFDVVLIDTAGRMHNNAPLM---TSLAKLIKVN-----KPDLILFVGEALVGNDSVDQLKKFNRALADHSTPRLIDGI 535 (587)
T ss_pred hcCCCEEEEeccccccCChhHH---HHHHHHHhcC-----CCceEEEehhhhhCcHHHHHHHHHHHHHhcCCCccccceE
Confidence 6789999999888876664333 3333332222 13344445 5667766666666665433332 3333
Q ss_pred ecCCCCCHHHHHHHHHHHh
Q 024560 244 VYGPEATMTGICKQAIDCI 262 (266)
Q Consensus 244 ~~~~~~~~~eAv~~av~~~ 262 (266)
+...++|.++-|..+|.++
T Consensus 536 ~ltk~dtv~d~vg~~~~m~ 554 (587)
T KOG0781|consen 536 LLTKFDTVDDKVGAAVSMV 554 (587)
T ss_pred EEEeccchhhHHHHHhhhe
Confidence 3334779999999999875
No 290
>cd07108 ALDH_MGR_2402 Magnetospirillum NAD(P)+-dependent aldehyde dehydrogenase MSR-1-like. NAD(P)+-dependent aldehyde dehydrogenase of Magnetospirillum gryphiswaldense MSR-1 (MGR_2402) , and other similar sequences, are present in this CD.
Probab=21.61 E-value=4.2e+02 Score=25.69 Aligned_cols=22 Identities=5% Similarity=0.141 Sum_probs=12.8
Q ss_pred HHHHHHHHHHHHHHhCCceeeE
Q 024560 20 KIGDFIMGVFAVFQDLDFSFIE 41 (266)
Q Consensus 20 ~~~~ii~~Ly~~f~~~D~~l~E 41 (266)
+=.+++.++.+++.+.--.+++
T Consensus 42 ~R~~~L~~~a~~l~~~~~ela~ 63 (457)
T cd07108 42 ERGKLLARIADALEARSEELAR 63 (457)
T ss_pred HHHHHHHHHHHHHHHhHHHHHH
Confidence 3355666677766665544444
No 291
>PRK12553 ATP-dependent Clp protease proteolytic subunit; Reviewed
Probab=21.52 E-value=4.3e+02 Score=23.08 Aligned_cols=75 Identities=12% Similarity=0.123 Sum_probs=40.3
Q ss_pred eeccCCCCHHHHHHHHHHHHhhhccCC-CCCeEEEEecccccchhHhhhhHHHHHHHHHHhhhhhhcccceEEEEeCCCC
Q 024560 145 AEYSGAPNEEEVLQYARVVIDCATADP-DGRKRALLIGGGIANFTDVATTFNGIIRALREKESKLKAARMHIFVRRGGPN 223 (266)
Q Consensus 145 lDlgG~a~~~~~~~al~~ll~~~~~d~-~v~~vlvni~ggi~~~~~vA~~~~gii~al~~~~~~~~~~~~pvvvrl~G~~ 223 (266)
+-++|..+++...+..+.++..-..++ +.=.+.||.|||-. ..+ .+|.++++.+ +.|+++...|--
T Consensus 38 I~l~g~I~~~~~~~i~~~L~~l~~~~~~~~I~l~INSpGG~v---~~g---~~I~d~i~~~-------~~~v~t~~~G~a 104 (207)
T PRK12553 38 IFLGGQVDDASANDVMAQLLVLESIDPDRDITLYINSPGGSV---TAG---DAIYDTIQFI-------RPDVQTVCTGQA 104 (207)
T ss_pred EEEcceECHHHHHHHHHHHHHHHhCCCCCCEEEEEeCCCCcH---HHH---HHHHHHHHhc-------CCCcEEEEEeeh
Confidence 445566666655555555543211221 22245666799854 223 7788888876 356776555644
Q ss_pred HHHHHHHHH
Q 024560 224 YQTGLAKMR 232 (266)
Q Consensus 224 ~~~~~~~L~ 232 (266)
...|-=++-
T Consensus 105 aSaa~lI~~ 113 (207)
T PRK12553 105 ASAGAVLLA 113 (207)
T ss_pred hhHHHHHHH
Confidence 444433443
No 292
>cd07130 ALDH_F7_AASADH NAD+-dependent alpha-aminoadipic semialdehyde dehydrogenase, ALDH family members 7A1 and 7B. Alpha-aminoadipic semialdehyde dehydrogenase (AASADH, EC=1.2.1.31), also known as ALDH7A1, Antiquitin-1, ALDH7B, or delta-1-piperideine-6-carboxylate dehydrogenase (P6CDH), is a NAD+-dependent ALDH. Human ALDH7A1 is involved in the pipecolic acid pathway of lysine catabolism, catalyzing the oxidation of alpha-aminoadipic semialdehyde to alpha-aminoadipate. Arabidopsis thaliana ALDH7B4 appears to be an osmotic-stress-inducible ALDH gene encoding a turgor-responsive or stress-inducible ALDH. The Streptomyces clavuligerus P6CDH appears to be involved in cephamycin biosynthesis, catalyzing the second stage of the two-step conversion of lysine to alpha-aminoadipic acid. The ALDH7A1 enzyme and others in this group have been observed as tetramers, yet the bacterial P6CDH enzyme has been reported as a monomer.
Probab=21.49 E-value=4.8e+02 Score=25.57 Aligned_cols=20 Identities=10% Similarity=0.182 Sum_probs=11.8
Q ss_pred HHHHHHHHHHHHHHhCCcee
Q 024560 20 KIGDFIMGVFAVFQDLDFSF 39 (266)
Q Consensus 20 ~~~~ii~~Ly~~f~~~D~~l 39 (266)
+=.+++.++.+++.++--.+
T Consensus 57 ~R~~~L~~~a~~l~~~~~~l 76 (474)
T cd07130 57 KRGEIVRQIGDALRKKKEAL 76 (474)
T ss_pred HHHHHHHHHHHHHHHHHHHH
Confidence 33566667777776664433
No 293
>TIGR01722 MMSDH methylmalonic acid semialdehyde dehydrogenase. In Bacillus, a highly homologous protein to methylmalonic acid semialdehyde dehydrogenase, groups out from the main MMSDH clade with Listeria and Sulfolobus. This Bacillus protein has been suggested to be located in an iol operon and/or involved in myo-inositol catabolism, converting malonic semialdehyde to acetyl CoA ad CO2. The preceeding enzymes responsible for valine catabolism are present in Bacillus, Listeria, and Sulfolobus.
Probab=21.46 E-value=7.7e+02 Score=24.10 Aligned_cols=19 Identities=11% Similarity=0.032 Sum_probs=11.6
Q ss_pred EecCCCcEEEEecCchHHH
Q 024560 108 VLNPKGRIWTMVAGGGASV 126 (266)
Q Consensus 108 ~v~l~G~Igii~NGaGlam 126 (266)
+-.+-|-|++|+--.-+..
T Consensus 133 ~~~P~Gvv~~I~p~N~P~~ 151 (477)
T TIGR01722 133 IRQPLGVCAGITPFNFPAM 151 (477)
T ss_pred EEcccceEEEEccCChHHH
Confidence 3456788888884443433
No 294
>TIGR01481 ccpA catabolite control protein A. Catabolite control protein A is a LacI family global transcriptional regulator found in Gram-positive bacteria. CcpA is involved in repressing carbohydrate utilization genes [ex: alpha-amylase (amyE), acetyl-coenzyme A synthase (acsA)] and in activating genes involved in transporting excess carbon from the cell [ex: acetate kinase (ackA), alpha-acetolactate synthase (alsS)]. Additionally, disruption of CcpA in Bacillus megaterium, Staphylococcus xylosus, Lactobacillus casei and Lactocacillus pentosus also decreases growth rate, which suggests CcpA is involved in the regulation of other metabolic pathways.
Probab=21.43 E-value=4e+02 Score=23.79 Aligned_cols=76 Identities=12% Similarity=0.026 Sum_probs=42.2
Q ss_pred CcEEEEecCchHH-------HHHHHHHHhcCCCCCCCceeeccCCCCHHHHHHHHHHHHhhhccCCCCCeEEEEeccccc
Q 024560 113 GRIWTMVAGGGAS-------VIYADTVGDLGYASELGNYAEYSGAPNEEEVLQYARVVIDCATADPDGRKRALLIGGGIA 185 (266)
Q Consensus 113 G~Igii~NGaGla-------m~t~D~l~~~g~gg~pAN~lDlgG~a~~~~~~~al~~ll~~~~~d~~v~~vlvni~ggi~ 185 (266)
.+|++++...... ....+.+..+ |-++....-..++.+.+.-+++++-+++ . ..++||..
T Consensus 177 ~~I~~i~g~~~~~~~~~~R~~Gf~~~l~~~--g~~~~~~~~~~~~~~~~~~~~~~~~ll~----~-~p~ai~~~------ 243 (329)
T TIGR01481 177 KSIAFVGGPLSDSINGEDRLEGYKEALNKA--GIQFGEDLVCEGKYSYDAGYKAFAELKG----S-LPTAVFVA------ 243 (329)
T ss_pred CeEEEEecCcccccchHHHHHHHHHHHHHc--CCCCCcceEEecCCChHHHHHHHHHHhC----C-CCCEEEEc------
Confidence 5788885322111 1234556666 3433211122344455555566666554 2 34677743
Q ss_pred chhHhhhhHHHHHHHHHHhh
Q 024560 186 NFTDVATTFNGIIRALREKE 205 (266)
Q Consensus 186 ~~~~vA~~~~gii~al~~~~ 205 (266)
++.+| .|+++++++.+
T Consensus 244 -~d~~A---~g~~~al~~~g 259 (329)
T TIGR01481 244 -SDEMA---AGILNAAMDAG 259 (329)
T ss_pred -CcHHH---HHHHHHHHHcC
Confidence 67788 99999999874
No 295
>TIGR03374 ABALDH 1-pyrroline dehydrogenase. Members of this protein family are 1-pyrroline dehydrogenase (1.5.1.35), also called gamma-aminobutyraldehyde dehydrogenase. This enzyme can follow putrescine transaminase (EC 2.6.1.82) for a two-step conversion of putrescine to gamma-aminobutyric acid (GABA). The member from Escherichia coli is characterized as a homotetramer that binds one NADH per momomer. This enzyme belongs to the medium-chain aldehyde dehydrogenases, and is quite similar in sequence to the betaine aldehyde dehydrogenase (EC 1.2.1.8) family.
Probab=21.28 E-value=4.6e+02 Score=25.80 Aligned_cols=22 Identities=14% Similarity=0.229 Sum_probs=12.9
Q ss_pred HHHHHHHHHHHHHHhCCceeeE
Q 024560 20 KIGDFIMGVFAVFQDLDFSFIE 41 (266)
Q Consensus 20 ~~~~ii~~Ly~~f~~~D~~l~E 41 (266)
+=.+++.++.+++.++--.|++
T Consensus 61 ~R~~~L~~~a~~l~~~~~ela~ 82 (472)
T TIGR03374 61 ARAECLLKLADVIEENAQVFAE 82 (472)
T ss_pred HHHHHHHHHHHHHHHhHHHHHH
Confidence 3356667777777666544443
No 296
>COG1433 Uncharacterized conserved protein [Function unknown]
Probab=21.24 E-value=2.4e+02 Score=22.91 Aligned_cols=28 Identities=18% Similarity=0.208 Sum_probs=16.1
Q ss_pred HHHHHHhhhhhcCCceeecCCCCCHHHHHHHHH
Q 024560 227 GLAKMRALGEELGIPLEVYGPEATMTGICKQAI 259 (266)
Q Consensus 227 ~~~~L~~~~~~~Gip~~~~~~~~~~~eAv~~av 259 (266)
+...|+ ++||.++... ..+.+|+++++.
T Consensus 78 a~~~l~----~~GIkv~~~~-~~~V~e~i~~~~ 105 (121)
T COG1433 78 AYNALK----AAGIKVYVAP-GGTVEEAIKAFL 105 (121)
T ss_pred HHHHHH----HcCcEEEecC-CCCHHHHHHHHh
Confidence 445555 4566665554 356666666554
No 297
>COG1181 DdlA D-alanine-D-alanine ligase and related ATP-grasp enzymes [Cell envelope biogenesis, outer membrane]
Probab=21.18 E-value=1.2e+02 Score=28.52 Aligned_cols=36 Identities=19% Similarity=0.366 Sum_probs=29.5
Q ss_pred cCCChhHHHHHHHHHHHHHHHHH--------------hCCceeeEeecce
Q 024560 11 ATLPLEFRGKIGDFIMGVFAVFQ--------------DLDFSFIEMNPFT 46 (266)
Q Consensus 11 ~gl~~~~~~~~~~ii~~Ly~~f~--------------~~D~~l~EINPLv 46 (266)
.+++++..+++.++..+.|+... +.+.-++||||.-
T Consensus 237 a~lt~~~~~~i~~lA~~a~~alg~~g~~rvDf~~~~~~g~~~l~EvNt~P 286 (317)
T COG1181 237 AGLTDEIHEEIKELALRAYKALGCLGLARVDFFVDDDEGEFVLLEVNTNP 286 (317)
T ss_pred CCCCHHHHHHHHHHHHHHHHhcCCCceEEEEEEEECCCCCEEEEEEeCCC
Confidence 35888999999999999999987 4567788888863
No 298
>cd06558 crotonase-like Crotonase/Enoyl-Coenzyme A (CoA) hydratase superfamily. This superfamily contains a diverse set of enzymes including enoyl-CoA hydratase, napthoate synthase, methylmalonyl-CoA decarboxylase, 3-hydoxybutyryl-CoA dehydratase, and dienoyl-CoA isomerase. Many of these play important roles in fatty acid metabolism. In addition to a conserved structural core and the formation of trimers (or dimers of trimers), a common feature in this superfamily is the stabilization of an enolate anion intermediate derived from an acyl-CoA substrate. This is accomplished by two conserved backbone NH groups in active sites that form an oxyanion hole.
Probab=21.04 E-value=4.8e+02 Score=21.54 Aligned_cols=75 Identities=21% Similarity=0.176 Sum_probs=38.4
Q ss_pred HHHHHHHHHHHhhhccCCCCCeEEEEec----ccccchhHhhhh------HHHHHHHHHHhhhhhhcccceEEEEeCCCC
Q 024560 154 EEVLQYARVVIDCATADPDGRKRALLIG----GGIANFTDVATT------FNGIIRALREKESKLKAARMHIFVRRGGPN 223 (266)
Q Consensus 154 ~~~~~al~~ll~~~~~d~~v~~vlvni~----ggi~~~~~vA~~------~~gii~al~~~~~~~~~~~~pvvvrl~G~~ 223 (266)
+.+.++++.+-. |+.+++|++.-. +...+..++... .....+..++.-+.....++|++.-+.|.-
T Consensus 29 ~~l~~~l~~~~~----d~~~~~vvl~~~~~~Fs~G~dl~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~p~Ia~v~G~a 104 (195)
T cd06558 29 DELAAALDEAEA----DPDVRVVVLTGAGKAFCAGADLKELAALSDAGEEARAFIRELQELLRALLRLPKPVIAAVNGAA 104 (195)
T ss_pred HHHHHHHHHHHh----CCCceEEEEECCCCceEeCcCHHHHhcccccchhHHHHHHHHHHHHHHHHcCCCCEEEEECCee
Confidence 334455554444 899998888632 112222221100 012222222222212235799998888887
Q ss_pred HHHHHHHHH
Q 024560 224 YQTGLAKMR 232 (266)
Q Consensus 224 ~~~~~~~L~ 232 (266)
...|..+.-
T Consensus 105 ~g~G~~la~ 113 (195)
T cd06558 105 LGGGLELAL 113 (195)
T ss_pred ecHHHHHHH
Confidence 777766665
No 299
>cd01822 Lysophospholipase_L1_like Lysophospholipase L1-like subgroup of SGNH-hydrolases. The best characterized member in this family is TesA, an E. coli periplasmic protein with thioesterase, esterase, arylesterase, protease and lysophospholipase activity.
Probab=20.96 E-value=4.4e+02 Score=21.04 Aligned_cols=29 Identities=14% Similarity=0.064 Sum_probs=18.8
Q ss_pred CCHHHHHHHHHHHHhhhccCCCCCeEEEEe
Q 024560 151 PNEEEVLQYARVVIDCATADPDGRKRALLI 180 (266)
Q Consensus 151 a~~~~~~~al~~ll~~~~~d~~v~~vlvni 180 (266)
.+++.+.+.++-+++.+.+. +.+.+++..
T Consensus 81 ~~~~~~~~~l~~li~~~~~~-~~~vil~~~ 109 (177)
T cd01822 81 IPPDQTRANLRQMIETAQAR-GAPVLLVGM 109 (177)
T ss_pred CCHHHHHHHHHHHHHHHHHC-CCeEEEEec
Confidence 45677777777777665543 666666654
No 300
>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=20.92 E-value=5.3e+02 Score=22.01 Aligned_cols=76 Identities=14% Similarity=0.155 Sum_probs=43.3
Q ss_pred CcEEEEecCchHH------HHHHHHHHhcCCCCCCCceee-ccCCCCHHHHHHHHHHHHhhhccCCCCCeEEEEeccccc
Q 024560 113 GRIWTMVAGGGAS------VIYADTVGDLGYASELGNYAE-YSGAPNEEEVLQYARVVIDCATADPDGRKRALLIGGGIA 185 (266)
Q Consensus 113 G~Igii~NGaGla------m~t~D~l~~~g~gg~pAN~lD-lgG~a~~~~~~~al~~ll~~~~~d~~v~~vlvni~ggi~ 185 (266)
++|++++..-+.. -...+.+..+ | .. .... ..++.+.+..+++++-+|+ +.+++++|+.
T Consensus 124 ~~i~~i~~~~~~~~~~~R~~gf~~~l~~~--~-~~-~~~~~~~~~~~~~~~~~~~~~~l~---~~~~~~ai~~------- 189 (272)
T cd06301 124 GNVAILMGPLGQSAQIDRTKGVEEVLAKY--P-DI-KVVEEQTANWSRAEAMDLMENWLS---SGGKIDAVVA------- 189 (272)
T ss_pred ccEEEEECCCCCccHHHHHHHHHHHHHHC--C-Cc-EEEecCCCCccHHHHHHHHHHHHH---hCCCCCEEEE-------
Confidence 4788886433221 2234555555 3 11 1222 2344455555566665554 2567887764
Q ss_pred chhHhhhhHHHHHHHHHHhh
Q 024560 186 NFTDVATTFNGIIRALREKE 205 (266)
Q Consensus 186 ~~~~vA~~~~gii~al~~~~ 205 (266)
..+.+| .|+++++++.+
T Consensus 190 ~~d~~a---~~~~~~l~~~g 206 (272)
T cd06301 190 NNDEMA---LGAIMALKAAG 206 (272)
T ss_pred CCCchH---HHHHHHHHHcC
Confidence 356777 99999999875
No 301
>PRK03137 1-pyrroline-5-carboxylate dehydrogenase; Provisional
Probab=20.91 E-value=8.3e+02 Score=24.25 Aligned_cols=14 Identities=14% Similarity=-0.159 Sum_probs=7.9
Q ss_pred cCCCcEEEEecCch
Q 024560 110 NPKGRIWTMVAGGG 123 (266)
Q Consensus 110 ~l~G~Igii~NGaG 123 (266)
.+-|-+++|+-=--
T Consensus 170 ~P~GVv~~I~PwN~ 183 (514)
T PRK03137 170 IPLGVGVVISPWNF 183 (514)
T ss_pred ecCcEEEEECCCcc
Confidence 35566677655443
No 302
>COG3148 Uncharacterized conserved protein [Function unknown]
Probab=20.88 E-value=3.7e+02 Score=24.31 Aligned_cols=58 Identities=12% Similarity=0.260 Sum_probs=37.9
Q ss_pred CCCCCeEEEEecccccchhHhhhhHHHHHHHHHHhhhhhhcccceEEEEeCCCCHHHHHHHHHhhhhhcCCce
Q 024560 170 DPDGRKRALLIGGGIANFTDVATTFNGIIRALREKESKLKAARMHIFVRRGGPNYQTGLAKMRALGEELGIPL 242 (266)
Q Consensus 170 d~~v~~vlvni~ggi~~~~~vA~~~~gii~al~~~~~~~~~~~~pvvvrl~G~~~~~~~~~L~~~~~~~Gip~ 242 (266)
+|+.+-++|. |+ +-| +..-+.+..... .+.|++|-+.|| ..+|||+++.+---+++|.
T Consensus 100 ~P~~~p~lvf-P~------e~a---~e~t~v~~~~p~----~k~plfIllDgT-W~eArKMfrksPyLa~lP~ 157 (231)
T COG3148 100 NPDYQPYLVF-PA------EYA---EELTEVISTAPA----EKPPLFILLDGT-WREARKMFRKSPYLADLPV 157 (231)
T ss_pred CCCCceEEEc-ch------HHH---HHHHHHhhcccc----cCCceEEEecCc-cHHHHHHHhcCchhccCCc
Confidence 8999988765 43 223 444444444421 246799999997 5899999995433356775
No 303
>PF00574 CLP_protease: Clp protease; InterPro: IPR001907 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: 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-, N-, 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. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; 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. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. 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) [, ]. This group of serine peptidases belong to the MEROPS peptidase family S14 (ClpP endopeptidase family, clan SK). ClpP is an ATP-dependent protease that cleaves a number of proteins, such as casein and albumin []. It exists as a heterodimer of ATP-binding regulatory A and catalytic P subunits, both of which are required for effective levels of protease activity in the presence of ATP [], although the P subunit alone does possess some catalytic activity. This family of sequences represent the P subunit. Proteases highly similar to ClpP have been found to be encoded in the genome of bacteria, metazoa, some viruses and in the chloroplast of plants. A number of the proteins in this family are classified as non-peptidase homologues as they have been found experimentally to be without peptidase activity, or lack amino acid residues that are believed to be essential for catalytic activity. ; GO: 0004252 serine-type endopeptidase activity, 0006508 proteolysis; PDB: 2ZL3_L 2ZL0_F 2ZL2_M 2ZL4_C 1TG6_D 2F6I_D 3V5I_b 3V5E_M 3QWD_D 2DEO_A ....
Probab=20.86 E-value=3.2e+02 Score=22.79 Aligned_cols=77 Identities=13% Similarity=0.063 Sum_probs=47.0
Q ss_pred ceeeccCCCCHHHHHHHHHHHHhhhccCCCC-CeEEEEecccccchhHhhhhHHHHHHHHHHhhhhhhcccceEEEEeCC
Q 024560 143 NYAEYSGAPNEEEVLQYARVVIDCATADPDG-RKRALLIGGGIANFTDVATTFNGIIRALREKESKLKAARMHIFVRRGG 221 (266)
Q Consensus 143 N~lDlgG~a~~~~~~~al~~ll~~~~~d~~v-~~vlvni~ggi~~~~~vA~~~~gii~al~~~~~~~~~~~~pvvvrl~G 221 (266)
+.+-+.|..+.+........++.+-..++.- =-+++|.|||-... + -+|.++++.. +.||.+...|
T Consensus 17 r~i~l~g~I~~~~~~~~~~~L~~l~~~~~~~~i~i~INSpGG~v~~---g---~~i~~~i~~~-------~~~v~t~~~G 83 (182)
T PF00574_consen 17 RIIFLNGPIDEESANRLISQLLYLENEDKNKPINIYINSPGGDVDA---G---LAIYDAIRSS-------KAPVTTVVLG 83 (182)
T ss_dssp TEEEEESSBSHHHHHHHHHHHHHHHHHTSSSEEEEEEEECEBCHHH---H---HHHHHHHHHS-------SSEEEEEEEE
T ss_pred eEEEECCccCHHHHHHHHHHHHHHhccCCCceEEEEEcCCCCccHH---H---HHHHHHHHhc-------CCCeEEEEeC
Confidence 4566778888888777777664321223321 14566789986422 2 7788888775 5777776666
Q ss_pred CCHHHHHHHHH
Q 024560 222 PNYQTGLAKMR 232 (266)
Q Consensus 222 ~~~~~~~~~L~ 232 (266)
-..-.|-=++.
T Consensus 84 ~aaSaa~~i~~ 94 (182)
T PF00574_consen 84 LAASAATLIFL 94 (182)
T ss_dssp EEETHHHHHHH
T ss_pred ccccceehhhh
Confidence 55555544444
No 304
>PRK14022 UDP-N-acetylmuramoylalanyl-D-glutamate--L-lysine ligase; Provisional
Probab=20.85 E-value=7.9e+02 Score=23.98 Aligned_cols=98 Identities=14% Similarity=0.177 Sum_probs=45.6
Q ss_pred CCCCHHHHHHHHHHHHhhhccCCCCCeEEEEecccccchhHhhhhHHHHHHHHHHhhhhhhcccceEEEEeCCCCHHHHH
Q 024560 149 GAPNEEEVLQYARVVIDCATADPDGRKRALLIGGGIANFTDVATTFNGIIRALREKESKLKAARMHIFVRRGGPNYQTGL 228 (266)
Q Consensus 149 G~a~~~~~~~al~~ll~~~~~d~~v~~vlvni~ggi~~~~~vA~~~~gii~al~~~~~~~~~~~~pvvvrl~G~~~~~~~ 228 (266)
++.+|+.+..+++.+-. -+.-+.++ ++|.+..-+.-.+ .-+.+.+.+.. ..-+++.-..+..+...
T Consensus 346 yahNP~s~~aal~~l~~----~~~~r~i~--V~G~~~e~g~~~~--~~~~~~~~~~~------~~~vi~~~~~~r~e~~~ 411 (481)
T PRK14022 346 YAHNGDSLNKLIDVVEE----HQKGKLIL--LLGAAGNKGESRR--PDFGRVANRHP------YLQVILTADDPNNEDPK 411 (481)
T ss_pred CCCCHHHHHHHHHHHhh----hCCCCEEE--EECCCCCCCcchh--HHHHHHHHhcC------CceEEEccCCCCCCCHH
Confidence 57899999999888844 22223333 4553322111110 22333333321 11133321111112223
Q ss_pred HHHHhhhhhcCCceeecCCCCCHHHHHHHHHHHhh
Q 024560 229 AKMRALGEELGIPLEVYGPEATMTGICKQAIDCIM 263 (266)
Q Consensus 229 ~~L~~~~~~~Gip~~~~~~~~~~~eAv~~av~~~~ 263 (266)
++.++..+..+.++.+ +.+.++|++.+++.++
T Consensus 412 ~i~~~i~~~~~~~~~~---~~d~~~Ai~~a~~~a~ 443 (481)
T PRK14022 412 MITQEIASHITHPVEI---IDDRAEAIKHAMSITE 443 (481)
T ss_pred HHHHHHHhcCCCCeEE---ECCHHHHHHHHHHhcC
Confidence 3333221111223444 3499999999988765
No 305
>cd07152 ALDH_BenzADH NAD-dependent benzaldehyde dehydrogenase II-like. NAD-dependent, benzaldehyde dehydrogenase II (XylC, BenzADH, EC=1.2.1.28) is involved in the oxidation of benzyl alcohol to benzoate. In Acinetobacter calcoaceticus, this process is carried out by the chromosomally encoded, benzyl alcohol dehydrogenase (xylB) and benzaldehyde dehydrogenase II (xylC) enzymes; whereas in Pseudomonas putida they are encoded by TOL plasmids.
Probab=20.79 E-value=7.6e+02 Score=23.77 Aligned_cols=21 Identities=0% Similarity=0.004 Sum_probs=10.7
Q ss_pred HHHHHHHHHHHHHhCCceeeE
Q 024560 21 IGDFIMGVFAVFQDLDFSFIE 41 (266)
Q Consensus 21 ~~~ii~~Ly~~f~~~D~~l~E 41 (266)
-.+++.++.+++.++--.+++
T Consensus 37 R~~~L~~~a~~l~~~~~ela~ 57 (443)
T cd07152 37 RAAVLRRAADLLEEHADEIAD 57 (443)
T ss_pred HHHHHHHHHHHHHHhHHHHHH
Confidence 345555665555554433443
No 306
>KOG4826 consensus C-8,7 sterol isomerase [Lipid transport and metabolism]
Probab=20.78 E-value=52 Score=29.50 Aligned_cols=41 Identities=12% Similarity=0.178 Sum_probs=37.9
Q ss_pred HHHHHHHHHHHHHhCCceeeEeeccee-cCCceEEeeccccc
Q 024560 21 IGDFIMGVFAVFQDLDFSFIEMNPFTL-VNGEPYPLDMRGEL 61 (266)
Q Consensus 21 ~~~ii~~Ly~~f~~~D~~l~EINPLvv-~~g~~~alD~k~~i 61 (266)
.+.++..+|+.|-.-|...+--||.++ ..|..+++++-.++
T Consensus 89 ~s~~L~~~WKeYsk~D~RYv~~d~~vvc~eg~t~~l~g~Lsl 130 (229)
T KOG4826|consen 89 SSALLAQLWKEYSKGDSRYVLTDDVVVCVEGITALLEGPLSL 130 (229)
T ss_pred HHHHHHHHHHHhcccceeEeccCCcEEeeeeehhhhhccHHH
Confidence 678899999999999999999999999 89999999998765
No 307
>cd06358 PBP1_NHase Type I periplasmic-binding protein of the nitrile hydratase (NHase) system that selectively converts nitriles to corresponding amides. This group includes the type I periplasmic-binding protein of the nitrile hydratase (NHase) system that selectively converts nitriles to corresponding amides, which are subsequently converted by amidases to yield free carboxylic acids and ammonia. NHases from bacteria and fungi have been purified and characterized. In Rhodococcus sp., the nitrile hydratase operon consists of six genes encoding NHase regulator 2, NHase regulator 1, amidase, NHase alpha subunit, NHase beta subunit, and NHase activator. The operon produces a constitutive hydratase that has a broad substrate spectrum: aliphatic and aromatic nitriles, mononitriles and dinitriles, hydroxynitriles and amino-nitriles, and a constitutive amidase of equally low substrate specificity. NHases are metalloenzymes containing either cobalt or iron, and therefore can be classified int
Probab=20.76 E-value=6.2e+02 Score=22.75 Aligned_cols=100 Identities=13% Similarity=0.067 Sum_probs=51.1
Q ss_pred HHHHHHHHHhcCC-CCCCCce--eeccCCCCHHHHHHHHHHHHhhhccCCCCCeEEEEecccccchhHhhhhHHHHHHHH
Q 024560 125 SVIYADTVGDLGY-ASELGNY--AEYSGAPNEEEVLQYARVVIDCATADPDGRKRALLIGGGIANFTDVATTFNGIIRAL 201 (266)
Q Consensus 125 am~t~D~l~~~g~-gg~pAN~--lDlgG~a~~~~~~~al~~ll~~~~~d~~v~~vlvni~ggi~~~~~vA~~~~gii~al 201 (266)
..+++|.++..|. .|++-.+ .|-+++ +.+-..+.+-+++ +++|.+|+ |+.+ ..++ .++...+
T Consensus 23 ~~la~~~iN~~gGi~G~~i~l~~~D~~~~--p~~a~~~a~~Li~----~~~v~avi----G~~~--s~~a---~a~~~~~ 87 (333)
T cd06358 23 AELAVEEINAAGGILGREVELVIVDDGSP--PAEAAAAAARLVD----EGGVDAII----GWHT--SAVR---NAVAPVV 87 (333)
T ss_pred HHHHHHHHHhcCCcCCcEEEEEEECCCCC--hHHHHHHHHHHHH----hCCCcEEE----ecCc--HHHH---HHHHHHH
Confidence 4578899998841 2444333 344554 4555566666666 66776555 5543 3334 4444444
Q ss_pred HHhhhh-h-----h-cccceEEEEeCCCCHHHHHHHHHhhhhhcCC
Q 024560 202 REKESK-L-----K-AARMHIFVRRGGPNYQTGLAKMRALGEELGI 240 (266)
Q Consensus 202 ~~~~~~-~-----~-~~~~pvvvrl~G~~~~~~~~~L~~~~~~~Gi 240 (266)
. .+-+ . . ....|.+.|.+.+....++..+.-..+..|+
T Consensus 88 ~-~~vp~i~~~~~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~~g~ 132 (333)
T cd06358 88 A-GRVPYVYTSLYEGGECNPGVFLTGETPEQQLAPAIPWLAEEKGA 132 (333)
T ss_pred h-cCceEEeCCCcCCCCCCCCEEEcCCCcHHHHHHHHHHHHHhcCC
Confidence 3 2100 0 0 0123455567666666665555433233454
No 308
>TIGR01858 tag_bisphos_ald class II aldolase, tagatose bisphosphate family. This model describes tagatose-1,6-bisphosphate aldolases, and perhaps other closely related class II aldolases. This tetrameric, Zn2+-dependent enzyme is related to the class II fructose bisphosphate aldolase; fructose 1,6-bisphosphate and tagatose 1,6 bisphosphate differ only in chirality at C4.
Probab=20.74 E-value=5e+02 Score=24.09 Aligned_cols=21 Identities=10% Similarity=0.045 Sum_probs=10.7
Q ss_pred cceEEEEeC-CCCHHHHHHHHH
Q 024560 212 RMHIFVRRG-GPNYQTGLAKMR 232 (266)
Q Consensus 212 ~~pvvvrl~-G~~~~~~~~~L~ 232 (266)
++||.+-|. |.+.+..++.++
T Consensus 72 ~VPValHLDHg~~~e~i~~ai~ 93 (282)
T TIGR01858 72 NMPLALHLDHHESLDDIRQKVH 93 (282)
T ss_pred CCCEEEECCCCCCHHHHHHHHH
Confidence 455555443 445555555554
No 309
>cd07104 ALDH_BenzADH-like ALDH subfamily: NAD(P)+-dependent benzaldehyde dehydrogenase II, vanillin dehydrogenase, p-hydroxybenzaldehyde dehydrogenase and related proteins. ALDH subfamily which includes the NAD(P)+-dependent, benzaldehyde dehydrogenase II (XylC, BenzADH, EC=1.2.1.28) involved in the oxidation of benzyl alcohol to benzoate; p-hydroxybenzaldehyde dehydrogenase (PchA, HBenzADH) which catalyzes the oxidation of p-hydroxybenzaldehyde to p-hydroxybenzoic acid; vanillin dehydrogenase (Vdh, VaniDH) involved in the metabolism of ferulic acid as seen in Pseudomonas putida KT2440; and other related sequences.
Probab=20.67 E-value=7.4e+02 Score=23.59 Aligned_cols=22 Identities=0% Similarity=0.054 Sum_probs=11.1
Q ss_pred HHHHHHHHHHHHHHhCCceeeE
Q 024560 20 KIGDFIMGVFAVFQDLDFSFIE 41 (266)
Q Consensus 20 ~~~~ii~~Ly~~f~~~D~~l~E 41 (266)
+-.+++.++.+++.++--.+++
T Consensus 23 ~R~~~L~~~a~~l~~~~~ela~ 44 (431)
T cd07104 23 ERAAILRKAAEILEERRDEIAD 44 (431)
T ss_pred HHHHHHHHHHHHHHHhHHHHHH
Confidence 3345555666655554444444
No 310
>PRK11235 bifunctional antitoxin/transcriptional repressor RelB; Provisional
Probab=20.67 E-value=1.6e+02 Score=22.26 Aligned_cols=33 Identities=18% Similarity=0.247 Sum_probs=20.3
Q ss_pred EEeCCCCHHHHHHHHHhhhhhcCCceeecCCCCCHHHHHHHHHHHh
Q 024560 217 VRRGGPNYQTGLAKMRALGEELGIPLEVYGPEATMTGICKQAIDCI 262 (266)
Q Consensus 217 vrl~G~~~~~~~~~L~~~~~~~Gip~~~~~~~~~~~eAv~~av~~~ 262 (266)
+|+...--+++.++|+ +.|+ ++++|++++++-+
T Consensus 6 vRiD~~lK~~A~~vl~----~lGl---------s~S~Ai~~fl~qi 38 (80)
T PRK11235 6 VRVDDELKARAYAVLE----KLGV---------TPSEALRLLLQYV 38 (80)
T ss_pred EEeCHHHHHHHHHHHH----HhCC---------CHHHHHHHHHHHH
Confidence 4555555566666666 4465 6666777666543
No 311
>TIGR01234 L-ribulokinase L-ribulokinase. This enzyme catalyzes the second step in arabinose catabolism. The most closely related protein subfamily outside the scope of this model includes ribitol kinase from E. coli.
Probab=20.66 E-value=4.9e+02 Score=25.89 Aligned_cols=74 Identities=8% Similarity=-0.029 Sum_probs=37.1
Q ss_pred CCCCCeEEEEecccccchhHhhhhHHHHHHHHHHhhhhhhcccce--EEEEeCC--CCHHHHHHHHHhhhhhcCCceeec
Q 024560 170 DPDGRKRALLIGGGIANFTDVATTFNGIIRALREKESKLKAARMH--IFVRRGG--PNYQTGLAKMRALGEELGIPLEVY 245 (266)
Q Consensus 170 d~~v~~vlvni~ggi~~~~~vA~~~~gii~al~~~~~~~~~~~~p--vvvrl~G--~~~~~~~~~L~~~~~~~Gip~~~~ 245 (266)
||+.++.|+++.-..++.+.+-+.++||+-.++..-..+.....+ -+.-.|| .+.+.=++++.+ -.|+|+++.
T Consensus 391 d~~arG~~~Gl~~~~~~~~~~RAvlEgia~~~~~~l~~l~~~g~~~~~i~~~GGg~a~s~~w~Qi~Ad---v~g~pV~~~ 467 (536)
T TIGR01234 391 DQRLKGVITGLTLATDAPLLYRALIEATAFGTRMIMETFTDSGVPVEELMAAGGIARKNPVIMQIYAD---VTNRPLQIV 467 (536)
T ss_pred CCcceEEEECCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcceEEEeCCccccCHHHHHHHHH---hhCCeeEec
Confidence 445566666644333444433333455544444433222211222 2333444 366666788886 479999754
Q ss_pred C
Q 024560 246 G 246 (266)
Q Consensus 246 ~ 246 (266)
.
T Consensus 468 ~ 468 (536)
T TIGR01234 468 A 468 (536)
T ss_pred c
Confidence 4
No 312
>PRK06806 fructose-bisphosphate aldolase; Provisional
Probab=20.66 E-value=4.8e+02 Score=24.06 Aligned_cols=21 Identities=10% Similarity=0.180 Sum_probs=9.9
Q ss_pred cceEEEEe-CCCCHHHHHHHHH
Q 024560 212 RMHIFVRR-GGPNYQTGLAKMR 232 (266)
Q Consensus 212 ~~pvvvrl-~G~~~~~~~~~L~ 232 (266)
++||.+-| -|.+.+..++.++
T Consensus 74 ~vpv~lHlDH~~~~e~i~~Al~ 95 (281)
T PRK06806 74 KVPVAVHFDHGMTFEKIKEALE 95 (281)
T ss_pred CCCEEEECCCCCCHHHHHHHHH
Confidence 45555522 2444454555444
No 313
>PF02887 PK_C: Pyruvate kinase, alpha/beta domain; InterPro: IPR015795 Pyruvate kinase (2.7.1.40 from EC) (PK) catalyses the final step in glycolysis [], the conversion of phosphoenolpyruvate to pyruvate with concomitant phosphorylation of ADP to ATP: ADP + phosphoenolpyruvate = ATP + pyruvate The enzyme, which is found in all living organisms, requires both magnesium and potassium ions for its activity. In vertebrates, there are four tissue-specific isozymes: L (liver), R (red cells), M1 (muscle, heart and brain), and M2 (early foetal tissue). In plants, PK exists as cytoplasmic and plastid isozymes, while most bacteria and lower eukaryotes have one form, except in certain bacteria, such as Escherichia coli, that have two isozymes. All isozymes appear to be tetramers of identical subunits of ~500 residues. PK helps control the rate of glycolysis, along with phosphofructokinase (IPR000023 from INTERPRO) and hexokinase (IPR001312 from INTERPRO). PK possesses allosteric sites for numerous effectors, yet the isozymes respond differently, in keeping with their different tissue distributions []. The activity of L-type (liver) PK is increased by fructose-1,6-bisphosphate (F1,6BP) and lowered by ATP and alanine (gluconeogenic precursor), therefore when glucose levels are high, glycolysis is promoted, and when levels are low, gluconeogenesis is promoted. L-type PK is also hormonally regulated, being activated by insulin and inhibited by glucagon, which covalently modifies the PK enzyme. M1-type (muscle, brain) PK is inhibited by ATP, but F1,6BP and alanine have no effect, which correlates with the function of muscle and brain, as opposed to the liver. The structure of several pyruvate kinases from various organisms have been determined [, ]. The protein comprises three-four domains: a small N-terminal helical domain (absent in bacterial PK), a beta/alpha-barrel domain, a beta-barrel domain (inserted within the beta/alpha-barrel domain), and a 3-layer alpha/beta/alpha sandwich domain. This entry represents the 3-layer alpha/beta/alpha sandwich domain. This domain has a similar topology to the archaeal hypothetical protein, MTH1675 from Methanobacterium thermoautotrophicum.; PDB: 3QTG_B 1VP8_A 1T57_C 3N25_A 1AQF_C 2G50_B 1F3X_G 1A5U_F 1A49_E 1F3W_C ....
Probab=20.59 E-value=2.5e+02 Score=21.77 Aligned_cols=72 Identities=10% Similarity=0.060 Sum_probs=40.5
Q ss_pred CCCCCeEEEEecccccchhHhhhhHHHHHHHHHHhhhhhhcccceEEEEeCCCCHHHHHHHHHhhhhhcCCceeecCCCC
Q 024560 170 DPDGRKRALLIGGGIANFTDVATTFNGIIRALREKESKLKAARMHIFVRRGGPNYQTGLAKMRALGEELGIPLEVYGPEA 249 (266)
Q Consensus 170 d~~v~~vlvni~ggi~~~~~vA~~~~gii~al~~~~~~~~~~~~pvvvrl~G~~~~~~~~~L~~~~~~~Gip~~~~~~~~ 249 (266)
+-+.|+|++..-+| ..| +-+ .++. ++.||++--.- ...+|++-- --|+--..+....
T Consensus 14 ~~~ak~Ivv~T~sG-----~ta---~~i----sk~R-----P~~pIiavt~~--~~~~r~l~l----~~GV~p~~~~~~~ 70 (117)
T PF02887_consen 14 DLNAKAIVVFTESG-----RTA---RLI----SKYR-----PKVPIIAVTPN--ESVARQLSL----YWGVYPVLIEEFD 70 (117)
T ss_dssp HHTESEEEEE-SSS-----HHH---HHH----HHT------TSSEEEEEESS--HHHHHHGGG----STTEEEEECSSHS
T ss_pred hcCCCEEEEECCCc-----hHH---HHH----HhhC-----CCCeEEEEcCc--HHHHhhhhc----ccceEEEEecccc
Confidence 45677777775444 223 333 3332 56888875444 333433332 3477443444455
Q ss_pred -CHHHHHHHHHHHhhh
Q 024560 250 -TMTGICKQAIDCIMS 264 (266)
Q Consensus 250 -~~~eAv~~av~~~~~ 264 (266)
++++.+..+++.+++
T Consensus 71 ~~~~~~~~~a~~~~~~ 86 (117)
T PF02887_consen 71 KDTEELIAEALEYAKE 86 (117)
T ss_dssp HSHHHHHHHHHHHHHH
T ss_pred ccHHHHHHHHHHHHHH
Confidence 789999999888754
No 314
>PRK07565 dihydroorotate dehydrogenase 2; Reviewed
Probab=20.56 E-value=6.9e+02 Score=23.22 Aligned_cols=81 Identities=16% Similarity=0.174 Sum_probs=43.4
Q ss_pred eeccCCCCHHHHHHHHHHHHhhhccCCCCCeEEEEecc--cccc--hhHhhhhHHHHHHHHHHhhhhhhcccceEEEEeC
Q 024560 145 AEYSGAPNEEEVLQYARVVIDCATADPDGRKRALLIGG--GIAN--FTDVATTFNGIIRALREKESKLKAARMHIFVRRG 220 (266)
Q Consensus 145 lDlgG~a~~~~~~~al~~ll~~~~~d~~v~~vlvni~g--gi~~--~~~vA~~~~gii~al~~~~~~~~~~~~pvvvrl~ 220 (266)
+.++| .+.+.+.++.+.+- +.+.+++-+|+.. +-.. ..+.-.....+++++++. .++||++.+.
T Consensus 106 ~sI~g-~~~~e~~~~a~~~~-----~agad~ielN~scpp~~~~~~g~~~~~~~~eil~~v~~~------~~iPV~vKl~ 173 (334)
T PRK07565 106 ASLNG-SSAGGWVDYARQIE-----QAGADALELNIYYLPTDPDISGAEVEQRYLDILRAVKSA------VSIPVAVKLS 173 (334)
T ss_pred EEecc-CCHHHHHHHHHHHH-----HcCCCEEEEeCCCCCCCCCCccccHHHHHHHHHHHHHhc------cCCcEEEEeC
Confidence 44555 45566777777654 3568999999521 1100 111110113344444443 4699999987
Q ss_pred CCC--HHHHHHHHHhhhhhcCCc
Q 024560 221 GPN--YQTGLAKMRALGEELGIP 241 (266)
Q Consensus 221 G~~--~~~~~~~L~~~~~~~Gip 241 (266)
+.- ..+..+.+. ++|+.
T Consensus 174 p~~~~~~~~a~~l~----~~G~d 192 (334)
T PRK07565 174 PYFSNLANMAKRLD----AAGAD 192 (334)
T ss_pred CCchhHHHHHHHHH----HcCCC
Confidence 742 344445555 55665
No 315
>PF08353 DUF1727: Domain of unknown function (DUF1727); InterPro: IPR013564 This domain of unknown function is found at the C terminus of bacterial proteins which include UDP-N-acetylmuramyl tripeptide synthase and the related Mur ligase.
Probab=20.36 E-value=4.4e+02 Score=20.90 Aligned_cols=85 Identities=13% Similarity=0.227 Sum_probs=49.5
Q ss_pred HHHHHHHHHHHHhhhccCCCCCeEEEEecccccchhHhh---h-hHHHHHHHHHHhhhhhhccc-ceEEEEeCCCCHHHH
Q 024560 153 EEEVLQYARVVIDCATADPDGRKRALLIGGGIANFTDVA---T-TFNGIIRALREKESKLKAAR-MHIFVRRGGPNYQTG 227 (266)
Q Consensus 153 ~~~~~~al~~ll~~~~~d~~v~~vlvni~ggi~~~~~vA---~-~~~gii~al~~~~~~~~~~~-~pvvvrl~G~~~~~~ 227 (266)
|.-+.++++++.+ +++-+.+++.+=...++..++. + .|+-+ .+ .+ .++++ +|++..+-
T Consensus 5 P~G~n~~l~~i~~----~~~~~~~~~~lNd~~aDG~DvSWiWDvdFE~L----~~-------~~i~~viv--~G~Ra~Dm 67 (113)
T PF08353_consen 5 PAGFNEVLDMIAS----DPGPKSVLIALNDNYADGRDVSWIWDVDFEKL----AD-------PNIKQVIV--SGTRAEDM 67 (113)
T ss_pred cHHHHHHHHHHHh----CCCCceEEEEecCCCCCCccceEEeecCHHHH----hc-------CCCCEEEE--EeeeHHHH
Confidence 4456788888877 7777777766543333333322 0 03322 11 22 33444 77776666
Q ss_pred HHHHHhhhhhcCCc---eeecCCCCCHHHHHHHHHHH
Q 024560 228 LAKMRALGEELGIP---LEVYGPEATMTGICKQAIDC 261 (266)
Q Consensus 228 ~~~L~~~~~~~Gip---~~~~~~~~~~~eAv~~av~~ 261 (266)
.-.|+ =+|++ +.+ ..++++|++.++..
T Consensus 68 alRLk----yAGv~~~~i~v---~~d~~~a~~~~~~~ 97 (113)
T PF08353_consen 68 ALRLK----YAGVDEEKIIV---EEDLEEALDAFLIK 97 (113)
T ss_pred HhHee----ecCcchHHeEe---cCCHHHHHHHHHHh
Confidence 55555 46998 544 56999999986543
No 316
>TIGR02362 dhaK1b probable dihydroxyacetone kinase DhaK1b subunit. Two types of dihydroxyacetone kinase (glycerone kinase) are described. In yeast and a few bacteria, e.g. Citrobacter freundii, the enzyme is a single chain that uses ATP as phosphoryl donor and is designated EC 2.7.1.29. By contract, E. coli and many other bacterial species have a multisubunit form with a phosphoprotein donor related to PTS transport proteins. This family represents a protein, unique to the Firmicutes (low GC Gram-positives), that appears to be a divergent second copy of the K subunit of that complex; its gene is always found in operons with the other three proteins of the complex.
Probab=20.31 E-value=1.8e+02 Score=27.73 Aligned_cols=59 Identities=17% Similarity=0.287 Sum_probs=39.6
Q ss_pred CCcEEEEecCchHHHHHHHHHHhcCCCCCCC-------------ceeeccCCCCHHHHHHHHHHHHhhhccCCCCCeEEE
Q 024560 112 KGRIWTMVAGGGASVIYADTVGDLGYASELG-------------NYAEYSGAPNEEEVLQYARVVIDCATADPDGRKRAL 178 (266)
Q Consensus 112 ~G~Igii~NGaGlam~t~D~l~~~g~gg~pA-------------N~lDlgG~a~~~~~~~al~~ll~~~~~d~~v~~vlv 178 (266)
.+++++|+.||. |.+|+ -+=|+=-.|+++++.++++.+-. . +++|+
T Consensus 40 ~~kValIsGGGS--------------GHEPah~GfVG~GmLdAav~G~VFaSPs~~~I~~ai~av~~----~---~GvL~ 98 (326)
T TIGR02362 40 DQQIPIISGGGS--------------GHEPAHWGYVGEGMLSAAIMGDVFVPPTAQDILEAIRQVDR----G---KGVFV 98 (326)
T ss_pred CCcEEEEecCCc--------------cccccccccccCCccceeEeccccCCCCHHHHHHHHHhhcC----C---CCEEE
Confidence 478999988873 56763 44455678999999999888743 3 45555
Q ss_pred Ee---cccccchhHhh
Q 024560 179 LI---GGGIANFTDVA 191 (266)
Q Consensus 179 ni---~ggi~~~~~vA 191 (266)
++ .|=..++..-+
T Consensus 99 ivkNYtGD~lNF~mA~ 114 (326)
T TIGR02362 99 IIKNFEADLSEFSQAI 114 (326)
T ss_pred EeccCHHHHhhHHHHH
Confidence 53 45566665443
No 317
>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=20.29 E-value=5.4e+02 Score=21.88 Aligned_cols=119 Identities=11% Similarity=-0.001 Sum_probs=59.7
Q ss_pred CCcEEEEecCchHHH------HHHHHHHhcCCCCCCCceeeccCCCCHHHHHHHHHHHHhhhccC-CCCCeEEEEecccc
Q 024560 112 KGRIWTMVAGGGASV------IYADTVGDLGYASELGNYAEYSGAPNEEEVLQYARVVIDCATAD-PDGRKRALLIGGGI 184 (266)
Q Consensus 112 ~G~Igii~NGaGlam------~t~D~l~~~g~gg~pAN~lDlgG~a~~~~~~~al~~ll~~~~~d-~~v~~vlvni~ggi 184 (266)
.++|+++++-.+... ...+.+..+ |.......-..++.+.+.-+++++-+++ ++ |..++|+..
T Consensus 116 ~~~i~~i~~~~~~~~~~~R~~gf~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~l~---~~~~~~~ai~~~----- 185 (264)
T cd06274 116 PEEVLFLGGLPELSPSRERLAGFRQALADA--GLPVQPDWIYAEGYSPESGYQLMAELLA---RLGRLPRALFTT----- 185 (264)
T ss_pred CCcEEEEeCCCcccchHHHHHHHHHHHHHc--CCCCCcceeecCCCChHHHHHHHHHHHc---cCCCCCcEEEEc-----
Confidence 367888855433211 123445555 2221111122233444444444444443 34 667877743
Q ss_pred cchhHhhhhHHHHHHHHHHhhhhhhcccce---EEEEeCCCCHHHHHHHHHhhhhhcCCceeecCCCCCHHHHHHHHHHH
Q 024560 185 ANFTDVATTFNGIIRALREKESKLKAARMH---IFVRRGGPNYQTGLAKMRALGEELGIPLEVYGPEATMTGICKQAIDC 261 (266)
Q Consensus 185 ~~~~~vA~~~~gii~al~~~~~~~~~~~~p---vvvrl~G~~~~~~~~~L~~~~~~~Gip~~~~~~~~~~~eAv~~av~~ 261 (266)
++.+| .|+++++++++ .++| .|+=.++.. -.+.+.. ++.+. .-++.+..+.++++
T Consensus 186 --~d~~A---~g~~~al~~~g-----~~ip~dv~v~g~d~~~---~~~~~~~-----~ltti----~~~~~~~g~~a~~~ 243 (264)
T cd06274 186 --SYTLL---EGVLRFLRERP-----GLAPSDLRIATFDDHP---LLDFLPF-----PVHSV----PQDHEALAEAAFEL 243 (264)
T ss_pred --ChHHH---HHHHHHHHHcC-----CCCCcceEEEEeCCHH---HHHhcCC-----CceEE----eCCHHHHHHHHHHH
Confidence 56777 99999999874 2222 233444422 2333331 34332 34777777777775
Q ss_pred h
Q 024560 262 I 262 (266)
Q Consensus 262 ~ 262 (266)
.
T Consensus 244 l 244 (264)
T cd06274 244 A 244 (264)
T ss_pred H
Confidence 4
No 318
>PRK00109 Holliday junction resolvase-like protein; Reviewed
Probab=20.19 E-value=4.8e+02 Score=21.25 Aligned_cols=67 Identities=9% Similarity=0.053 Sum_probs=39.2
Q ss_pred HHHHHHHhhhccCCCCCeEEEEec---ccc-cchhHhhhhHHHHHHHHHHhhhhhhcccceEEEEeCCCCHHHHHHHHHh
Q 024560 158 QYARVVIDCATADPDGRKRALLIG---GGI-ANFTDVATTFNGIIRALREKESKLKAARMHIFVRRGGPNYQTGLAKMRA 233 (266)
Q Consensus 158 ~al~~ll~~~~~d~~v~~vlvni~---ggi-~~~~~vA~~~~gii~al~~~~~~~~~~~~pvvvrl~G~~~~~~~~~L~~ 233 (266)
+.+.-+++ ..+++.++|=.| .|- ..-...+ +-+++-+++. .++||+.|=.--...+|+++|.
T Consensus 44 ~~l~~~i~----~~~i~~iVvGlP~~~~G~~~~~~~~v---~~f~~~L~~~------~~~~v~~~DEr~TT~~A~~~l~- 109 (138)
T PRK00109 44 DRLEKLIK----EWQPDGLVVGLPLNMDGTEGPRTERA---RKFANRLEGR------FGLPVVLVDERLSTVEAERALA- 109 (138)
T ss_pred HHHHHHHH----HhCCCEEEEeccCCCCCCcCHHHHHH---HHHHHHHHHH------hCCCEEEEcCCcCHHHHHHHHH-
Confidence 44444455 577888777665 222 2222222 4445545443 3688887666667789999998
Q ss_pred hhhhcCCc
Q 024560 234 LGEELGIP 241 (266)
Q Consensus 234 ~~~~~Gip 241 (266)
+.|.+
T Consensus 110 ---~~~~~ 114 (138)
T PRK00109 110 ---DVGSR 114 (138)
T ss_pred ---HcCCC
Confidence 44654
Done!