Query 015881
Match_columns 399
No_of_seqs 187 out of 1042
Neff 6.3
Searched_HMMs 46136
Date Fri Mar 29 01:46:05 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/015881.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/015881hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PRK10422 lipopolysaccharide co 100.0 1.8E-41 3.8E-46 339.5 24.3 249 120-390 3-256 (352)
2 PRK10916 ADP-heptose:LPS hepto 100.0 1.9E-40 4E-45 331.4 26.2 249 123-390 1-255 (348)
3 TIGR02201 heptsyl_trn_III lipo 100.0 1.4E-40 3.1E-45 331.3 23.9 249 124-391 1-255 (344)
4 TIGR02195 heptsyl_trn_II lipop 100.0 6.1E-40 1.3E-44 325.2 25.5 243 124-390 1-245 (334)
5 PRK10964 ADP-heptose:LPS hepto 100.0 2.7E-37 5.9E-42 305.3 21.7 237 123-390 1-247 (322)
6 COG0859 RfaF ADP-heptose:LPS h 100.0 4.3E-37 9.3E-42 306.7 21.5 245 122-391 1-246 (334)
7 TIGR02193 heptsyl_trn_I lipopo 100.0 3.7E-36 8.1E-41 296.1 21.2 239 124-390 1-248 (319)
8 cd03789 GT1_LPS_heptosyltransf 100.0 5.2E-31 1.1E-35 255.1 21.4 191 124-390 1-192 (279)
9 PF01075 Glyco_transf_9: Glyco 99.9 1.1E-21 2.5E-26 185.9 12.2 173 191-390 1-177 (247)
10 PRK10017 colanic acid biosynth 97.8 0.00054 1.2E-08 71.3 14.9 41 123-163 1-44 (426)
11 TIGR03568 NeuC_NnaA UDP-N-acet 97.4 0.0052 1.1E-07 62.5 15.1 235 123-389 1-274 (365)
12 PRK00025 lpxB lipid-A-disaccha 97.2 0.0015 3.3E-08 65.4 8.9 104 122-228 1-113 (380)
13 COG1519 KdtA 3-deoxy-D-manno-o 97.0 0.14 3E-06 53.0 20.8 96 125-228 51-150 (419)
14 PRK05749 3-deoxy-D-manno-octul 96.1 0.74 1.6E-05 47.1 20.1 99 123-229 50-152 (425)
15 cd03807 GT1_WbnK_like This fam 95.1 2 4.3E-05 40.9 17.6 95 124-222 1-101 (365)
16 PF04007 DUF354: Protein of un 93.8 3.5 7.7E-05 41.8 16.6 208 123-361 1-222 (335)
17 PF02684 LpxB: Lipid-A-disacch 93.4 3.8 8.3E-05 42.1 16.2 209 125-371 1-239 (373)
18 PRK01021 lpxB lipid-A-disaccha 93.0 1.3 2.9E-05 48.1 12.7 211 123-370 227-466 (608)
19 PRK12446 undecaprenyldiphospho 91.9 5.9 0.00013 40.0 15.2 104 122-229 1-119 (352)
20 TIGR01133 murG undecaprenyldip 91.7 3.1 6.7E-05 40.8 12.7 101 123-227 1-116 (348)
21 PF13477 Glyco_trans_4_2: Glyc 91.3 4 8.7E-05 34.5 11.5 99 124-228 1-103 (139)
22 COG0763 LpxB Lipid A disacchar 90.8 4.9 0.00011 41.4 13.2 215 122-370 1-242 (381)
23 PRK00726 murG undecaprenyldiph 90.7 2.6 5.6E-05 41.8 11.1 104 122-229 1-119 (357)
24 cd04951 GT1_WbdM_like This fam 90.5 14 0.0003 35.6 15.9 83 124-209 1-86 (360)
25 PF04413 Glycos_transf_N: 3-De 89.7 1.2 2.5E-05 41.3 7.1 97 124-229 22-121 (186)
26 TIGR03088 stp2 sugar transfera 89.1 16 0.00036 36.0 15.4 103 123-229 2-108 (374)
27 cd03786 GT1_UDP-GlcNAc_2-Epime 88.9 7.6 0.00017 38.3 12.8 103 124-228 1-116 (363)
28 PRK13609 diacylglycerol glucos 87.8 16 0.00035 36.5 14.5 37 122-160 4-41 (380)
29 cd03808 GT1_cap1E_like This fa 87.5 5.3 0.00011 37.7 10.3 104 124-230 1-109 (359)
30 TIGR00661 MJ1255 conserved hyp 87.3 5.1 0.00011 39.5 10.4 100 124-228 1-117 (321)
31 PF14595 Thioredoxin_9: Thiore 85.8 1.2 2.7E-05 38.8 4.5 61 122-182 42-107 (129)
32 TIGR03609 S_layer_CsaB polysac 85.5 15 0.00033 35.7 12.6 65 130-211 9-73 (298)
33 cd03785 GT1_MurG MurG is an N- 82.1 24 0.00051 34.5 12.4 102 124-229 1-117 (350)
34 PRK14089 ipid-A-disaccharide s 79.5 55 0.0012 33.3 14.2 106 122-235 1-112 (347)
35 cd03784 GT1_Gtf_like This fami 78.8 8.8 0.00019 38.7 8.3 100 123-227 1-128 (401)
36 PRK10307 putative glycosyl tra 78.2 80 0.0017 31.9 17.4 38 123-162 1-42 (412)
37 TIGR00236 wecB UDP-N-acetylglu 77.8 18 0.00039 36.1 10.1 102 123-227 1-113 (365)
38 COG0707 MurG UDP-N-acetylgluco 76.9 92 0.002 31.8 15.5 107 123-231 1-121 (357)
39 PF13528 Glyco_trans_1_3: Glyc 76.5 23 0.0005 34.3 10.3 103 123-232 1-121 (318)
40 TIGR03492 conserved hypothetic 69.5 20 0.00042 37.0 8.2 96 130-229 4-118 (396)
41 TIGR00521 coaBC_dfp phosphopan 68.4 1.3E+02 0.0028 31.2 13.8 44 122-168 3-46 (390)
42 cd03811 GT1_WabH_like This fam 65.2 1.2E+02 0.0026 28.2 17.4 85 124-211 1-90 (353)
43 COG1819 Glycosyl transferases, 64.6 8.1 0.00018 40.0 4.2 100 122-226 1-118 (406)
44 PRK09922 UDP-D-galactose:(gluc 64.3 46 0.001 33.0 9.5 103 123-228 1-111 (359)
45 cd03812 GT1_CapH_like This fam 64.2 1.4E+02 0.003 28.7 18.3 102 124-230 1-109 (358)
46 PRK12678 transcription termina 63.4 35 0.00076 37.5 8.7 97 122-219 416-518 (672)
47 PRK13982 bifunctional SbtC-lik 62.6 2.2E+02 0.0048 30.4 18.9 44 122-168 70-113 (475)
48 PF02441 Flavoprotein: Flavopr 62.4 8.5 0.00018 33.0 3.3 53 123-178 1-54 (129)
49 cd03801 GT1_YqgM_like This fam 62.2 1.4E+02 0.0029 27.9 15.1 105 124-230 1-114 (374)
50 cd03802 GT1_AviGT4_like This f 62.1 40 0.00087 32.1 8.4 102 123-228 1-111 (335)
51 PF03466 LysR_substrate: LysR 61.5 41 0.00089 29.1 7.7 26 136-161 18-43 (209)
52 COG2327 WcaK Polysaccharide py 60.5 50 0.0011 34.2 9.0 39 123-161 1-42 (385)
53 PRK06849 hypothetical protein; 59.8 44 0.00095 34.0 8.6 84 120-212 2-86 (389)
54 PLN02605 monogalactosyldiacylg 59.8 1.6E+02 0.0034 29.7 12.5 20 193-212 91-110 (382)
55 cd03817 GT1_UGDG_like This fam 59.4 1.6E+02 0.0035 27.8 15.7 38 124-163 1-42 (374)
56 cd03820 GT1_amsD_like This fam 59.4 1E+02 0.0022 28.7 10.5 87 124-212 1-93 (348)
57 cd03799 GT1_amsK_like This is 59.0 1.7E+02 0.0036 27.9 13.5 85 124-210 1-87 (355)
58 cd01133 F1-ATPase_beta F1 ATP 57.3 1.3E+02 0.0028 29.8 10.9 104 111-218 60-177 (274)
59 PRK12767 carbamoyl phosphate s 57.1 58 0.0013 31.9 8.6 77 122-210 1-77 (326)
60 cd03794 GT1_wbuB_like This fam 57.0 1.8E+02 0.0038 27.5 17.3 39 124-164 1-43 (394)
61 PRK12608 transcription termina 56.6 38 0.00083 35.0 7.4 95 122-217 133-233 (380)
62 TIGR00246 tRNA_RlmH_YbeA rRNA 54.4 47 0.001 29.9 6.8 70 298-388 56-127 (153)
63 cd08450 PBP2_HcaR The C-termin 54.0 53 0.0011 28.0 7.0 24 137-160 13-36 (196)
64 cd04962 GT1_like_5 This family 51.7 2.3E+02 0.0051 27.4 15.3 84 123-209 1-91 (371)
65 COG1576 Uncharacterized conser 51.7 48 0.001 30.0 6.3 28 334-361 78-107 (155)
66 TIGR02700 flavo_MJ0208 archaeo 51.6 27 0.00059 33.3 5.1 47 124-170 1-47 (234)
67 cd03798 GT1_wlbH_like This fam 50.4 2.2E+02 0.0047 26.6 16.4 96 133-231 14-124 (377)
68 cd08446 PBP2_Chlorocatechol Th 49.9 76 0.0017 27.1 7.4 30 130-160 8-37 (198)
69 PRK00103 rRNA large subunit me 49.8 59 0.0013 29.4 6.7 74 295-388 54-130 (157)
70 PRK06029 3-octaprenyl-4-hydrox 49.5 30 0.00065 32.1 4.9 46 122-169 1-46 (185)
71 cd08452 PBP2_AlsR The C-termin 47.9 74 0.0016 27.5 7.0 28 132-160 9-36 (197)
72 PRK15490 Vi polysaccharide bio 47.5 2.3E+02 0.005 31.1 11.7 90 136-230 219-309 (578)
73 COG1158 Rho Transcription term 47.1 1.1E+02 0.0024 31.5 8.7 91 122-212 173-269 (422)
74 PF04230 PS_pyruv_trans: Polys 46.5 23 0.00049 32.6 3.7 33 132-164 1-33 (286)
75 PLN02316 synthase/transferase 46.0 90 0.002 36.5 8.9 71 76-163 554-632 (1036)
76 TIGR02174 CXXU_selWTH selT/sel 45.5 33 0.00071 26.7 3.8 50 139-190 15-66 (72)
77 PRK05647 purN phosphoribosylgl 45.2 1.5E+02 0.0032 27.7 8.9 84 122-210 1-88 (200)
78 cd08439 PBP2_LrhA_like The C-t 44.6 1.2E+02 0.0025 25.9 7.7 22 139-160 15-36 (185)
79 PRK12597 F0F1 ATP synthase sub 44.5 2.7E+02 0.0058 29.7 11.6 95 122-218 143-251 (461)
80 cd08465 PBP2_ToxR The C-termin 44.3 59 0.0013 28.3 5.9 28 132-160 9-36 (200)
81 cd08412 PBP2_PAO1_like The C-t 43.4 87 0.0019 26.6 6.7 24 138-161 14-37 (198)
82 cd08449 PBP2_XapR The C-termin 43.4 73 0.0016 27.1 6.2 23 137-159 13-35 (197)
83 COG1105 FruK Fructose-1-phosph 43.3 90 0.0019 31.5 7.4 54 289-356 110-164 (310)
84 cd08431 PBP2_HupR The C-termin 42.9 61 0.0013 27.7 5.6 22 139-160 15-36 (195)
85 cd08468 PBP2_Pa0477 The C-term 42.9 66 0.0014 27.9 6.0 23 138-160 14-36 (202)
86 cd08440 PBP2_LTTR_like_4 TThe 42.5 1.2E+02 0.0025 25.5 7.3 29 131-160 8-36 (197)
87 TIGR03590 PseG pseudaminic aci 42.2 2E+02 0.0043 27.9 9.7 89 122-228 170-264 (279)
88 PF02590 SPOUT_MTase: Predicte 42.1 28 0.0006 31.4 3.3 50 334-388 78-130 (155)
89 PLN02871 UDP-sulfoquinovose:DA 42.0 2.1E+02 0.0045 29.7 10.4 106 122-232 58-176 (465)
90 cd08437 PBP2_MleR The substrat 41.5 78 0.0017 27.1 6.1 23 138-160 14-36 (198)
91 cd08448 PBP2_LTTR_aromatics_li 41.3 98 0.0021 26.1 6.7 23 138-160 14-36 (197)
92 cd08456 PBP2_LysR The C-termin 41.2 1.2E+02 0.0026 25.7 7.3 41 138-179 14-56 (196)
93 cd08411 PBP2_OxyR The C-termin 41.1 1.2E+02 0.0026 25.9 7.2 31 130-161 8-38 (200)
94 cd08436 PBP2_LTTR_like_3 The C 40.7 92 0.002 26.3 6.4 29 131-160 8-36 (194)
95 cd08434 PBP2_GltC_like The sub 40.1 1.2E+02 0.0026 25.5 7.0 31 130-161 7-37 (195)
96 cd08418 PBP2_TdcA The C-termin 40.1 87 0.0019 26.7 6.2 24 138-161 14-37 (201)
97 cd08427 PBP2_LTTR_like_2 The C 40.0 92 0.002 26.4 6.3 41 138-179 14-56 (195)
98 cd08488 PBP2_AmpR The C-termin 39.5 59 0.0013 27.9 5.0 39 139-179 15-53 (191)
99 cd08475 PBP2_CrgA_like_6 The C 39.3 69 0.0015 27.3 5.4 40 139-180 16-55 (199)
100 cd08485 PBP2_ClcR The C-termin 39.2 1.5E+02 0.0032 25.7 7.6 31 129-160 7-37 (198)
101 COG4029 Uncharacterized protei 39.2 98 0.0021 27.1 6.0 53 310-380 6-69 (142)
102 PRK00170 azoreductase; Reviewe 39.0 56 0.0012 29.6 5.0 38 122-159 1-42 (201)
103 cd08444 PBP2_Cbl The C-termina 38.8 1.3E+02 0.0029 25.9 7.2 42 137-179 13-56 (198)
104 cd08486 PBP2_CbnR The C-termin 38.5 91 0.002 27.1 6.1 23 138-160 15-37 (198)
105 cd01635 Glycosyltransferase_GT 38.4 2.1E+02 0.0045 24.9 8.5 64 133-227 13-78 (229)
106 cd08423 PBP2_LTTR_like_6 The C 38.0 1.2E+02 0.0026 25.7 6.7 24 138-161 14-37 (200)
107 cd08466 PBP2_LeuO The C-termin 38.0 1E+02 0.0022 26.3 6.3 41 138-179 14-56 (200)
108 PRK09376 rho transcription ter 37.8 1.3E+02 0.0028 31.6 7.8 91 122-212 169-265 (416)
109 PF03033 Glyco_transf_28: Glyc 37.8 79 0.0017 26.5 5.4 44 125-170 1-44 (139)
110 PRK00326 cell division protein 37.8 1.3E+02 0.0029 26.2 7.0 52 334-390 45-96 (139)
111 PRK13608 diacylglycerol glucos 37.5 4.5E+02 0.0097 26.6 12.4 21 192-212 94-114 (391)
112 cd08422 PBP2_CrgA_like The C-t 37.2 69 0.0015 27.1 5.0 40 139-180 16-55 (197)
113 PRK07313 phosphopantothenoylcy 37.2 63 0.0014 29.7 5.0 44 122-168 1-44 (182)
114 TIGR00215 lpxB lipid-A-disacch 37.0 93 0.002 31.7 6.7 109 122-234 5-122 (385)
115 COG1036 Archaeal flavoproteins 36.9 58 0.0012 30.0 4.4 46 123-169 9-55 (187)
116 cd03818 GT1_ExpC_like This fam 36.2 2.7E+02 0.0059 27.8 9.9 36 124-164 1-36 (396)
117 PF12362 DUF3646: DNA polymera 36.1 29 0.00064 29.9 2.4 21 136-156 94-114 (117)
118 cd03823 GT1_ExpE7_like This fa 35.8 2.9E+02 0.0063 25.9 9.6 38 124-163 1-43 (359)
119 PRK08462 biotin carboxylase; V 35.2 1.3E+02 0.0029 31.1 7.6 84 121-212 3-86 (445)
120 cd08471 PBP2_CrgA_like_2 The C 35.2 85 0.0019 26.8 5.3 41 138-180 15-55 (201)
121 PRK15179 Vi polysaccharide bio 35.0 6.9E+02 0.015 28.0 14.6 39 191-229 389-428 (694)
122 cd08476 PBP2_CrgA_like_7 The C 34.7 78 0.0017 26.8 5.0 40 139-180 14-53 (197)
123 cd08453 PBP2_IlvR The C-termin 34.3 1.4E+02 0.003 25.6 6.6 24 137-160 13-36 (200)
124 cd08419 PBP2_CbbR_RubisCO_like 34.3 1.1E+02 0.0025 25.7 6.0 24 137-160 12-35 (197)
125 PRK03601 transcriptional regul 34.2 1.6E+02 0.0036 27.9 7.6 36 126-161 91-126 (275)
126 COG1182 AcpD Acyl carrier prot 33.9 77 0.0017 30.0 5.0 50 122-177 1-55 (202)
127 PLN02448 UDP-glycosyltransfera 33.8 5.3E+02 0.011 27.0 11.9 51 120-170 8-58 (459)
128 cd08417 PBP2_Nitroaromatics_li 33.7 1E+02 0.0023 26.2 5.6 43 138-181 14-58 (200)
129 TIGR00381 cdhD CO dehydrogenas 33.5 2.8E+02 0.006 28.9 9.3 61 311-380 155-221 (389)
130 cd08415 PBP2_LysR_opines_like 33.4 1E+02 0.0023 26.0 5.6 48 131-180 8-57 (196)
131 cd08429 PBP2_NhaR The C-termin 33.4 1.2E+02 0.0027 26.7 6.2 25 137-161 13-37 (204)
132 cd08426 PBP2_LTTR_like_5 The C 33.4 1.6E+02 0.0035 25.0 6.8 23 138-160 14-36 (199)
133 PRK08591 acetyl-CoA carboxylas 33.2 1.3E+02 0.0029 31.0 7.3 81 122-210 2-82 (451)
134 COG1448 TyrB Aspartate/tyrosin 33.1 3.4E+02 0.0074 28.3 9.8 60 307-375 169-237 (396)
135 cd03806 GT1_ALG11_like This fa 32.9 3.8E+02 0.0083 27.5 10.5 96 135-232 17-136 (419)
136 cd08414 PBP2_LTTR_aromatics_li 32.7 1.5E+02 0.0032 25.0 6.4 23 138-160 14-36 (197)
137 PRK05920 aromatic acid decarbo 32.3 86 0.0019 29.6 5.1 44 122-168 3-46 (204)
138 cd08477 PBP2_CrgA_like_8 The C 32.2 1.7E+02 0.0036 24.8 6.7 41 138-180 15-55 (197)
139 PF00636 Ribonuclease_3: Ribon 32.1 27 0.00059 28.8 1.6 26 129-154 2-27 (114)
140 PF01408 GFO_IDH_MocA: Oxidore 32.1 2.7E+02 0.006 22.5 7.8 84 123-226 1-86 (120)
141 cd08413 PBP2_CysB_like The C-t 32.0 1.7E+02 0.0038 25.1 6.9 41 138-179 14-56 (198)
142 cd08472 PBP2_CrgA_like_3 The C 32.0 1E+02 0.0023 26.2 5.4 40 138-179 15-54 (202)
143 cd03795 GT1_like_4 This family 32.0 4.5E+02 0.0098 24.9 17.1 39 124-164 1-43 (357)
144 PRK06455 riboflavin synthase; 31.3 1E+02 0.0022 27.9 5.2 43 122-165 1-43 (155)
145 TIGR01286 nifK nitrogenase mol 31.2 2.6E+02 0.0055 30.2 9.1 92 123-232 364-464 (515)
146 cd08482 PBP2_TrpI The C-termin 31.2 97 0.0021 26.6 5.1 40 138-179 14-53 (195)
147 TIGR03339 phn_lysR aminoethylp 30.8 2.7E+02 0.0058 25.9 8.3 24 137-160 97-120 (279)
148 KOG0961 Predicted Zn2+-depende 30.5 59 0.0013 36.3 4.0 29 334-362 428-457 (1022)
149 PRK13523 NADPH dehydrogenase N 30.4 2.1E+02 0.0045 28.9 7.9 71 291-373 225-297 (337)
150 PRK02308 uvsE putative UV dama 30.3 1.9E+02 0.004 28.9 7.4 62 302-373 139-204 (303)
151 cd03816 GT1_ALG1_like This fam 29.9 5.9E+02 0.013 25.9 11.3 105 122-229 3-126 (415)
152 PRK09288 purT phosphoribosylgl 29.9 3.9E+02 0.0084 26.9 9.9 75 121-212 11-85 (395)
153 cd08420 PBP2_CysL_like C-termi 29.6 2.6E+02 0.0057 23.4 7.5 25 137-161 13-37 (201)
154 PRK12815 carB carbamoyl phosph 29.2 1E+03 0.022 28.1 16.2 81 121-212 554-640 (1068)
155 cd08487 PBP2_BlaA The C-termin 29.1 1.1E+02 0.0024 25.9 5.0 40 139-180 15-54 (189)
156 cd03822 GT1_ecORF704_like This 28.9 4.2E+02 0.0091 25.0 9.5 81 124-210 1-84 (366)
157 PF12466 GDH_N: Glutamate dehy 28.9 29 0.00063 26.1 1.0 16 139-154 35-50 (60)
158 cd08473 PBP2_CrgA_like_4 The C 28.9 1.2E+02 0.0026 25.7 5.3 39 139-179 18-56 (202)
159 cd08470 PBP2_CrgA_like_1 The C 28.7 1.2E+02 0.0026 25.8 5.2 41 138-180 15-55 (197)
160 TIGR01426 MGT glycosyltransfer 28.5 2.9E+02 0.0063 27.7 8.7 93 130-227 3-116 (392)
161 COG0571 Rnc dsRNA-specific rib 28.0 44 0.00096 32.2 2.4 26 129-154 46-71 (235)
162 COG0381 WecB UDP-N-acetylgluco 27.8 5.3E+02 0.011 26.9 10.2 102 122-232 3-122 (383)
163 PF03808 Glyco_tran_WecB: Glyc 27.7 4.5E+02 0.0098 23.6 9.3 49 336-384 85-136 (172)
164 cd02931 ER_like_FMN Enoate red 27.3 3.7E+02 0.0081 27.6 9.2 74 293-373 252-327 (382)
165 cd03805 GT1_ALG2_like This fam 27.2 5.6E+02 0.012 25.1 10.3 37 123-161 1-39 (392)
166 PLN02496 probable phosphopanto 27.1 1.1E+02 0.0025 28.9 5.0 57 108-168 5-61 (209)
167 PF02590 SPOUT_MTase: Predicte 27.0 4.6E+02 0.01 23.5 11.0 107 123-232 1-125 (155)
168 TIGR00612 ispG_gcpE 1-hydroxy- 26.8 7.1E+02 0.015 25.6 17.0 193 128-367 99-309 (346)
169 cd08479 PBP2_CrgA_like_9 The C 26.7 2.1E+02 0.0045 24.3 6.3 41 137-179 14-54 (198)
170 KOG1198 Zinc-binding oxidoredu 26.7 3.6E+02 0.0078 27.4 8.9 76 123-212 159-235 (347)
171 cd08478 PBP2_CrgA The C-termin 26.0 1.4E+02 0.003 25.5 5.1 40 139-180 18-57 (199)
172 PF13439 Glyco_transf_4: Glyco 25.7 87 0.0019 26.4 3.7 90 137-232 16-109 (177)
173 cd08474 PBP2_CrgA_like_5 The C 25.5 1.4E+02 0.0031 25.4 5.1 41 138-180 17-57 (202)
174 TIGR02699 archaeo_AfpA archaeo 25.4 1.3E+02 0.0028 27.6 4.9 44 124-169 1-45 (174)
175 TIGR01039 atpD ATP synthase, F 25.3 4.2E+02 0.0092 28.2 9.2 104 111-218 134-251 (461)
176 COG3980 spsG Spore coat polysa 25.2 1.7E+02 0.0037 29.4 5.9 74 123-211 1-79 (318)
177 PF03846 SulA: Cell division i 25.1 2.7E+02 0.0058 24.2 6.4 66 138-208 48-116 (119)
178 PRK13267 archaemetzincin-like 25.1 3.2E+02 0.0069 25.2 7.4 76 122-209 1-76 (179)
179 cd02803 OYE_like_FMN_family Ol 24.1 3.9E+02 0.0085 26.2 8.5 73 293-372 228-302 (327)
180 cd04910 ACT_AK-Ectoine_1 ACT d 23.4 50 0.0011 25.9 1.5 19 138-156 52-70 (71)
181 TIGR00242 mraZ protein. Member 23.2 3.5E+02 0.0076 23.7 7.1 52 334-390 41-92 (142)
182 cd08484 PBP2_LTTR_beta_lactama 23.2 1.4E+02 0.003 25.4 4.5 41 138-180 14-54 (189)
183 cd08480 PBP2_CrgA_like_10 The 23.2 1.6E+02 0.0034 25.3 4.9 41 138-180 15-55 (198)
184 PRK12815 carB carbamoyl phosph 23.1 3.5E+02 0.0077 31.8 9.0 81 119-211 4-91 (1068)
185 PRK10595 SOS cell division inh 23.0 5.9E+02 0.013 23.3 8.7 85 119-209 25-113 (164)
186 PRK11716 DNA-binding transcrip 23.0 4.2E+02 0.009 24.4 8.1 51 127-179 71-123 (269)
187 COG1519 KdtA 3-deoxy-D-manno-o 22.4 96 0.0021 32.5 3.8 48 111-159 220-267 (419)
188 cd05466 PBP2_LTTR_substrate Th 22.4 2.9E+02 0.0063 22.6 6.3 24 138-161 14-37 (197)
189 cd08463 PBP2_DntR_like_4 The C 22.1 1.2E+02 0.0027 26.5 4.1 28 131-159 8-35 (203)
190 PRK10086 DNA-binding transcrip 22.1 2.9E+02 0.0064 26.7 7.1 42 137-180 115-156 (311)
191 PF00551 Formyl_trans_N: Formy 21.7 1.7E+02 0.0036 26.5 4.9 93 123-220 1-98 (181)
192 cd08458 PBP2_NocR The C-termin 21.5 1.9E+02 0.0041 24.8 5.1 41 138-179 14-56 (196)
193 PRK12361 hypothetical protein; 21.3 3.8E+02 0.0082 28.8 8.2 30 190-219 163-192 (547)
194 PF03808 Glyco_tran_WecB: Glyc 21.3 1.9E+02 0.0041 26.1 5.1 44 336-379 32-78 (172)
195 PF13614 AAA_31: AAA domain; P 21.1 49 0.0011 28.4 1.2 53 335-387 101-155 (157)
196 cd03825 GT1_wcfI_like This fam 20.8 1.9E+02 0.0042 27.7 5.4 39 123-163 1-41 (365)
197 cd04733 OYE_like_2_FMN Old yel 20.7 5.9E+02 0.013 25.4 9.1 79 291-373 234-314 (338)
198 TIGR00623 sula cell division i 20.7 4.3E+02 0.0094 24.3 7.2 85 119-209 29-117 (168)
199 cd08416 PBP2_MdcR The C-termin 20.6 2.4E+02 0.0052 23.8 5.5 42 138-180 14-57 (199)
200 PF12683 DUF3798: Protein of u 20.6 73 0.0016 31.5 2.3 97 101-233 37-139 (275)
201 cd03819 GT1_WavL_like This fam 20.6 7.4E+02 0.016 23.5 16.6 91 131-227 10-104 (355)
202 PF13579 Glyco_trans_4_4: Glyc 20.6 2.9E+02 0.0064 22.5 5.9 91 139-232 7-104 (160)
203 TIGR01369 CPSaseII_lrg carbamo 20.5 3.5E+02 0.0076 31.8 8.2 82 119-211 3-90 (1050)
204 cd08430 PBP2_IlvY The C-termin 20.4 2.2E+02 0.0047 24.1 5.2 39 140-179 16-56 (199)
205 PRK00005 fmt methionyl-tRNA fo 20.3 3.3E+02 0.0072 27.0 7.1 72 123-210 1-86 (309)
206 cd08441 PBP2_MetR The C-termin 20.3 1.2E+02 0.0025 26.0 3.5 24 138-161 14-37 (198)
207 PRK09280 F0F1 ATP synthase sub 20.1 6.4E+02 0.014 26.9 9.4 104 111-218 135-252 (463)
208 PRK10632 transcriptional regul 20.1 3.3E+02 0.0073 26.3 7.0 54 124-180 93-146 (309)
209 PLN02735 carbamoyl-phosphate s 20.1 3.4E+02 0.0074 32.1 8.0 82 119-211 20-107 (1102)
210 cd08425 PBP2_CynR The C-termin 20.0 3.6E+02 0.0079 22.7 6.6 23 138-160 15-37 (197)
No 1
>PRK10422 lipopolysaccharide core biosynthesis protein; Provisional
Probab=100.00 E-value=1.8e-41 Score=339.48 Aligned_cols=249 Identities=14% Similarity=0.116 Sum_probs=200.2
Q ss_pred CCccEEEEEcCCChhHHHhHHHHHHHHHHHCCCcEEEEEEcCCchHhhhcCCCCCEEEEecCCCC--CCChHHHHHHHHH
Q 015881 120 GDVRRCCCIISGGVYENLLFFPAIQLLKDRYPGVLIDVIASARGKQTFELNKNVRWANVYDLDDD--WPEPAEYTDILGV 197 (399)
Q Consensus 120 ~~v~rILIIr~~~IGDvVLttPalraLK~~yP~A~IdvLv~~~~~~lle~nP~ID~Vi~~d~k~~--~~~~~~~~~l~~~ 197 (399)
.++||||||++++|||+||+||++++||++||+++|||++.+.+++++++||+||+|+.++++.. +..+..+++++++
T Consensus 3 ~~~~~ILii~~~~iGD~vl~~P~l~~Lk~~~P~a~I~~l~~~~~~~l~~~~P~id~vi~~~~~~~~~~~~~~~~~~l~~~ 82 (352)
T PRK10422 3 KPFRRILIIKMRFHGDMLLTTPVISSLKKNYPDAKIDVLLYQDTIPILSENPEINALYGIKNKKAGASEKIKNFFSLIKV 82 (352)
T ss_pred CCCceEEEEEecccCceeeHHHHHHHHHHHCCCCeEEEEeccChHHHhccCCCceEEEEeccccccHHHHHHHHHHHHHH
Confidence 45799999999999999999999999999999999999999999999999999999999997642 1234567889999
Q ss_pred hhhCCCcEEEEcCCCChHHHHHHHHhCCCeEEEecCCCccccccccccceeeccCcCCchhhHHHHHHHHHHHcCCCCCC
Q 015881 198 MKNRYYDMVLSTKLAGLGHAAFLFMTTARDRVSYIYPNVNAAGAGLLLSETFTAESMNLSERGYNMYEQMVDWLGRPFRS 277 (399)
Q Consensus 198 LR~~~YDlvIdl~~~~~rsAll~~LsgA~~RIGy~~~~~~~~~~~~~lt~~v~~~~~~~~~h~v~~yl~LL~~LGi~~~~ 277 (399)
||+++||+|||++++ ++++++++++||+.||||.....+......+|++.++.. . .|.+++|+++++.+|+.
T Consensus 83 lr~~~yD~vidl~~~-~~s~ll~~l~~a~~rig~~~~~~~~~~~~~~~~~~~~~~-~---~h~~~~~~~ll~~lg~~--- 154 (352)
T PRK10422 83 LRANKYDLIVNLTDQ-WMVALLVRLLNARVKISQDYHHRQSAFWRKSFTHLVPLQ-G---GHIVESNLSVLTPLGLS--- 154 (352)
T ss_pred HhhCCCCEEEEcccc-hHHHHHHHHhCCCeEEeeccccccchhHHHHhcccCCCC-C---cchHHhhHhHHhhcCCC---
Confidence 999999999999999 999999999999999999732211111224677766432 2 58899999999999983
Q ss_pred CCCCCCCCceeecCHHHHHHHHHHHHHhCCCCCCeEEEEcCCCCccccccCCCCCCCCCCHHHHHHHHHHhhhCC-CEEE
Q 015881 278 VPRHPVPPLRVSISRRLKEVVAEKYKNAGAEQGKYIVIHGIESDSKASMQSRGDTDSLLPIQVWAEIANGLREFR-PLFV 356 (399)
Q Consensus 278 ~p~~~~p~l~i~is~e~~~~a~~~l~~~gl~~~~~IvIhPgas~~~~~~k~rg~~~KrWP~e~faeLa~~L~~~~-~Vvl 356 (399)
...+.+.+.+.+++.+.++..+...+.. +++|+||||+++.. |+||.|+|++|++.|.+.+ +|++
T Consensus 155 ---~~~~~~~l~~~~~~~~~~~~~~~~~~~~-~~~i~i~pga~~~~----------K~Wp~e~fa~l~~~L~~~~~~vvl 220 (352)
T PRK10422 155 ---SLVKETTMSYRPESWKRMRRQLDHLGVT-QNYVVIQPTARQIF----------KCWDNDKFSAVIDALQARGYEVVL 220 (352)
T ss_pred ---CCCCcceeecCHHHHHHHHHHHHhcCCC-CCeEEEecCCCccc----------cCCCHHHHHHHHHHHHHCCCeEEE
Confidence 2233456777777766666666655543 58999999999864 8999999999999998766 8999
Q ss_pred eCCchh--HHHHHHHHhcCCCCceeecCCccccchh
Q 015881 357 IPHEKE--REGVEDVVGDDASIVFITTPGQVRMSSY 390 (399)
Q Consensus 357 iGgp~E--~e~aeeI~~~~~~~~~i~~~G~ls~~~~ 390 (399)
+||++| ++.+++|.+.+....++++.|+++|...
T Consensus 221 ~ggp~e~e~~~~~~i~~~~~~~~~~~l~g~~sL~el 256 (352)
T PRK10422 221 TSGPDKDDLACVNEIAQGCQTPPVTALAGKTTFPEL 256 (352)
T ss_pred EcCCChHHHHHHHHHHHhcCCCccccccCCCCHHHH
Confidence 999865 4566888876544444778999988754
No 2
>PRK10916 ADP-heptose:LPS heptosyltransferase II; Provisional
Probab=100.00 E-value=1.9e-40 Score=331.40 Aligned_cols=249 Identities=15% Similarity=0.085 Sum_probs=191.6
Q ss_pred cEEEEEcCCChhHHHhHHHHHHHHHHHCCCcEEEEEEcCCchHhhhcCCCCCEEEEecCCCCCCChHHHHHHHHHhhhCC
Q 015881 123 RRCCCIISGGVYENLLFFPAIQLLKDRYPGVLIDVIASARGKQTFELNKNVRWANVYDLDDDWPEPAEYTDILGVMKNRY 202 (399)
Q Consensus 123 ~rILIIr~~~IGDvVLttPalraLK~~yP~A~IdvLv~~~~~~lle~nP~ID~Vi~~d~k~~~~~~~~~~~l~~~LR~~~ 202 (399)
||||||++++|||+||+||++++||++||+|+|||+|.+.+++++++||+||+|+++++++....+..+.+++++||+++
T Consensus 1 mrILii~~~~iGD~il~tP~l~~Lk~~~P~a~I~~l~~~~~~~l~~~~P~vd~vi~~~~~~~~~~~~~~~~l~~~lr~~~ 80 (348)
T PRK10916 1 MKILVIGPSWVGDMMMSQSLYRTLKARYPQAIIDVMAPAWCRPLLSRMPEVNEAIPMPLGHGALEIGERRRLGHSLREKR 80 (348)
T ss_pred CcEEEEccCcccHHHhHHHHHHHHHHHCCCCeEEEEechhhHHHHhcCCccCEEEecccccchhhhHHHHHHHHHHHhcC
Confidence 79999999999999999999999999999999999999999999999999999999997644334556788999999999
Q ss_pred CcEEEEcCCCChHHHHHHHHhCCCeEEEecCCCccccccccccceeeccCcCCchhhHHHHHHHHHHHcCCCCCCCC-CC
Q 015881 203 YDMVLSTKLAGLGHAAFLFMTTARDRVSYIYPNVNAAGAGLLLSETFTAESMNLSERGYNMYEQMVDWLGRPFRSVP-RH 281 (399)
Q Consensus 203 YDlvIdl~~~~~rsAll~~LsgA~~RIGy~~~~~~~~~~~~~lt~~v~~~~~~~~~h~v~~yl~LL~~LGi~~~~~p-~~ 281 (399)
||+|||+|++ ++++++++++|++.|+||. ...+..++++....+.. ...|.+++|++++..+|....... ..
T Consensus 81 yD~vidl~~~-~~s~~l~~~~~~~~rig~~-----~~~~~~~~~~~~~~~~~-~~~h~~~~~~~l~~~~~~~~~~~~~~~ 153 (348)
T PRK10916 81 YDRAYVLPNS-FKSALVPFFAGIPHRTGWR-----GEMRYGLLNDLRVLDKE-AFPLMVERYVALAYDKGVMRTAADLPQ 153 (348)
T ss_pred CCEEEECCCc-HHHHHHHHHcCCCeEeecc-----cCccccccccccccCcc-cCcHHHHHHHHHhcccccccccccCCC
Confidence 9999999999 9999999999999999997 22223344433211211 125889999999876653111000 01
Q ss_pred CCCCceeecCHHHHHHHHHHHHHhCCC-CCCeEEEEcCCCCccccccCCCCCCCCCCHHHHHHHHHHhhhCC-CEEEeCC
Q 015881 282 PVPPLRVSISRRLKEVVAEKYKNAGAE-QGKYIVIHGIESDSKASMQSRGDTDSLLPIQVWAEIANGLREFR-PLFVIPH 359 (399)
Q Consensus 282 ~~p~l~i~is~e~~~~a~~~l~~~gl~-~~~~IvIhPgas~~~~~~k~rg~~~KrWP~e~faeLa~~L~~~~-~VvliGg 359 (399)
....+.+.+++++.+.+ +...++. .+++|+||||++|.. .|+||.|+|++||+.|.+.+ +||++||
T Consensus 154 ~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~i~i~pga~~~~---------~K~Wp~e~~a~l~~~l~~~~~~vvl~Gg 221 (348)
T PRK10916 154 PLLWPQLQVSEGEKSET---CAAFSLSSERPIIGFCPGAEFGP---------AKRWPHYHYAELAQQLIDEGYQVVLFGS 221 (348)
T ss_pred CcCCCccccCHHHHHHH---HHHcCCCCCCCEEEEeCCCCCcc---------ccCCCHHHHHHHHHHHHHCCCeEEEEeC
Confidence 11234556666654433 3333443 568999999998732 48999999999999998665 8999999
Q ss_pred chhHHHHHHHHhcCCCC---ceeecCCccccchh
Q 015881 360 EKEREGVEDVVGDDASI---VFITTPGQVRMSSY 390 (399)
Q Consensus 360 p~E~e~aeeI~~~~~~~---~~i~~~G~ls~~~~ 390 (399)
++|++.+++|.+.++.. .++++.|+++|...
T Consensus 222 ~~e~~~~~~i~~~~~~~~~~~~~~l~g~~sL~el 255 (348)
T PRK10916 222 AKDHEAGNEILAALNTEQQAWCRNLAGETQLEQA 255 (348)
T ss_pred HHhHHHHHHHHHhcccccccceeeccCCCCHHHH
Confidence 99999999998876532 23678899887653
No 3
>TIGR02201 heptsyl_trn_III lipopolysaccharide heptosyltransferase III, putative. This family consists of examples of the putative ADP-heptose:LPS heptosyltransferase III, an enzyme of LPS inner core region biosynthesis. LPS, composed of lipid A, a core region, and O antigen, is found in the outer membrane of Gram-negative bacteria. This enzyme may be less widely distributed than heptosyltransferases I and II.
Probab=100.00 E-value=1.4e-40 Score=331.25 Aligned_cols=249 Identities=16% Similarity=0.131 Sum_probs=201.9
Q ss_pred EEEEEcCCChhHHHhHHHHHHHHHHHCCCcEEEEEEcCCchHhhhcCCCCCEEEEecCCCC---CCChHHHHHHHHHhhh
Q 015881 124 RCCCIISGGVYENLLFFPAIQLLKDRYPGVLIDVIASARGKQTFELNKNVRWANVYDLDDD---WPEPAEYTDILGVMKN 200 (399)
Q Consensus 124 rILIIr~~~IGDvVLttPalraLK~~yP~A~IdvLv~~~~~~lle~nP~ID~Vi~~d~k~~---~~~~~~~~~l~~~LR~ 200 (399)
|||||++++|||+||+||++++||++||+++||||+.+.++++++.+|+||+|+.++++.. +..+..+++++++||+
T Consensus 1 rILii~~~~iGD~vl~tp~l~~Lk~~~P~a~I~~l~~~~~~~l~~~~p~vd~vi~~~~~~~~~~~~~~~~~~~l~~~lr~ 80 (344)
T TIGR02201 1 RILLIKLRHHGDMLLTTPVISSLKKNYPDAKIDVLLYQETIPILSENPDINALYGLDRKKAKAGERKLANQFHLIKVLRA 80 (344)
T ss_pred CEEEEEeccccceeeHHHHHHHHHHHCCCCEEEEEECcChHHHHhcCCCccEEEEeChhhhcchHHHHHHHHHHHHHHHh
Confidence 7999999999999999999999999999999999999999999999999999999986532 2234466788999999
Q ss_pred CCCcEEEEcCCCChHHHHHHHHhCCCeEEEecCCCccccccccccceeeccCcCCchhhHHHHHHHHHHHcCCCCCCCCC
Q 015881 201 RYYDMVLSTKLAGLGHAAFLFMTTARDRVSYIYPNVNAAGAGLLLSETFTAESMNLSERGYNMYEQMVDWLGRPFRSVPR 280 (399)
Q Consensus 201 ~~YDlvIdl~~~~~rsAll~~LsgA~~RIGy~~~~~~~~~~~~~lt~~v~~~~~~~~~h~v~~yl~LL~~LGi~~~~~p~ 280 (399)
++||++||++++ ++++++++++||+.||||...........+++++.+..... ...|.+++|+++++.+|++.
T Consensus 81 ~~yD~vidl~~~-~~s~ll~~l~~a~~riG~~~~~~~~~~~~~~~~~~~~~~~~-~~~h~~~~~l~ll~~lg~~~----- 153 (344)
T TIGR02201 81 NRYDLVVNLTDQ-WMVAILVKLLNARVKIGFDYPKRRSAFWRKSFTALAPLQGG-NTLHTVEQNLSVLTPLGLDS----- 153 (344)
T ss_pred CCCCEEEECCcc-hHHHHHHHhcCCCeEEeecCCCcchhHHHHHhccccCCCCC-CccchHhhhhhHHhhcCCCC-----
Confidence 999999999998 99999999999999999984322111222356665543322 12588999999999999832
Q ss_pred CCCCCceeecCHHHHHHHHHHHHHhCCCCCCeEEEEcCCCCccccccCCCCCCCCCCHHHHHHHHHHhhhCC-CEEEeCC
Q 015881 281 HPVPPLRVSISRRLKEVVAEKYKNAGAEQGKYIVIHGIESDSKASMQSRGDTDSLLPIQVWAEIANGLREFR-PLFVIPH 359 (399)
Q Consensus 281 ~~~p~l~i~is~e~~~~a~~~l~~~gl~~~~~IvIhPgas~~~~~~k~rg~~~KrWP~e~faeLa~~L~~~~-~VvliGg 359 (399)
....+.+.+++++.+.++.++.+.+. .+++|+||||+++.. |+||.|+|++||+.|.+++ +||++||
T Consensus 154 -~~~~~~l~~~~~~~~~~~~~l~~~~~-~~~~i~i~p~a~~~~----------K~Wp~e~~~~l~~~l~~~~~~ivl~g~ 221 (344)
T TIGR02201 154 -LVKQTRMSYPPADWKAMRALLDEAGV-GQNYIVIQPTSRWFF----------KCWDNDRFSALIDALHARGYEVVLTSG 221 (344)
T ss_pred -CCCceeeecCHHHHHHHHHHHHhcCC-CCCEEEEeCCCCccc----------cCCCHHHHHHHHHHHHhCCCeEEEecC
Confidence 22345678888888777777776655 468999999998864 8999999999999998766 8999999
Q ss_pred ch--hHHHHHHHHhcCCCCceeecCCccccchhh
Q 015881 360 EK--EREGVEDVVGDDASIVFITTPGQVRMSSYT 391 (399)
Q Consensus 360 p~--E~e~aeeI~~~~~~~~~i~~~G~ls~~~~~ 391 (399)
++ |++.+++|.+.++...++++.|+++|....
T Consensus 222 p~~~e~~~~~~i~~~~~~~~~~~l~g~~sL~el~ 255 (344)
T TIGR02201 222 PDKDELAMVNEIAQGCQTPRVTSLAGKLTLPQLA 255 (344)
T ss_pred CCHHHHHHHHHHHhhCCCCcccccCCCCCHHHHH
Confidence 76 667889998877654447889999887653
No 4
>TIGR02195 heptsyl_trn_II lipopolysaccharide heptosyltransferase II. This family consists of examples of ADP-heptose:LPS heptosyltransferase II, an enzyme of LPS inner core region biosynthesis. LPS, composed of lipid A, a core region, and O antigen, is found in the outer membrane of Gram-negative bacteria.
Probab=100.00 E-value=6.1e-40 Score=325.21 Aligned_cols=243 Identities=17% Similarity=0.161 Sum_probs=195.3
Q ss_pred EEEEEcCCChhHHHhHHHHHHHHHHHCCCcEEEEEEcCCchHhhhcCCCCCEEEEecCCCCCCChHHHHHHHHHhhhCCC
Q 015881 124 RCCCIISGGVYENLLFFPAIQLLKDRYPGVLIDVIASARGKQTFELNKNVRWANVYDLDDDWPEPAEYTDILGVMKNRYY 203 (399)
Q Consensus 124 rILIIr~~~IGDvVLttPalraLK~~yP~A~IdvLv~~~~~~lle~nP~ID~Vi~~d~k~~~~~~~~~~~l~~~LR~~~Y 203 (399)
|||||++++|||+||+||++++||++||+|+|||++.+.++++++++|+||+|+.++.+.....+..+.+++++||+++|
T Consensus 1 rILii~~~~iGD~i~~~p~l~~Lk~~~P~a~I~~l~~~~~~~l~~~~p~id~v~~~~~~~~~~~~~~~~~~~~~lr~~~y 80 (334)
T TIGR02195 1 KILVIGPSWVGDMVMAQSLYRLLKKRYPQAVIDVLAPAWCRPLLERMPEIRQAIDMPLGHGALELTERRRLGRSLREERY 80 (334)
T ss_pred CEEEEccchhHHHHHHHHHHHHHHHHCCCCEEEEEechhhHHHHhcCchhceeeecCCcccchhhhHHHHHHHHHhhcCC
Confidence 69999999999999999999999999999999999999999999999999999999876443445667889999999999
Q ss_pred cEEEEcCCCChHHHHHHHHhCCCeEEEecCCCccccccccccceeeccCcCCchhhHHHHHHHHHHHcCCCCCCCCCCCC
Q 015881 204 DMVLSTKLAGLGHAAFLFMTTARDRVSYIYPNVNAAGAGLLLSETFTAESMNLSERGYNMYEQMVDWLGRPFRSVPRHPV 283 (399)
Q Consensus 204 DlvIdl~~~~~rsAll~~LsgA~~RIGy~~~~~~~~~~~~~lt~~v~~~~~~~~~h~v~~yl~LL~~LGi~~~~~p~~~~ 283 (399)
|++||++++ ++++++++++|++.|+||. ...+..++++....... ...|.+++|++++..+|... ....
T Consensus 81 D~vi~l~~~-~~s~ll~~~~~~~~riG~~-----~~~~~~~~~~~~~~~~~-~~~h~~~~~~~l~~~~~~~~----~~~~ 149 (334)
T TIGR02195 81 DQAIVLPNS-LKSALIPFFAGIPHRTGWR-----GEMRYGLLNDVRALDKE-RLPLMVERYIALAYDKGQDL----PQPL 149 (334)
T ss_pred CEEEECCCC-HHHHHHHHHcCCCceeeec-----CCCcceecccCcCCCcc-cccHHHHHHHHHhccccCCC----CCCC
Confidence 999999999 9999999999999999998 33333456665432221 12488999999987777521 1112
Q ss_pred CCceeecCHHHHHHHHHHHHHhCCC-CCCeEEEEcCCCCccccccCCCCCCCCCCHHHHHHHHHHhhhCC-CEEEeCCch
Q 015881 284 PPLRVSISRRLKEVVAEKYKNAGAE-QGKYIVIHGIESDSKASMQSRGDTDSLLPIQVWAEIANGLREFR-PLFVIPHEK 361 (399)
Q Consensus 284 p~l~i~is~e~~~~a~~~l~~~gl~-~~~~IvIhPgas~~~~~~k~rg~~~KrWP~e~faeLa~~L~~~~-~VvliGgp~ 361 (399)
..+.+.+++++.+.+ ..+.++. .+++|+||||+++.. .|+||.|+|++|++.|.+.+ +||++|+++
T Consensus 150 ~~p~l~~~~~~~~~~---~~~~~~~~~~~~i~i~pga~~~~---------~K~Wp~e~~~~li~~l~~~~~~ivl~G~~~ 217 (334)
T TIGR02195 150 PRPQLQVSPAEQAAA---LAKFGLDTERPIIAFCPGAEFGP---------AKRWPHEHYAELAKRLIDQGYQVVLFGSAK 217 (334)
T ss_pred CCCcccCCHHHHHHH---HHHcCCCCCCCEEEEcCCCCCCc---------cCCCCHHHHHHHHHHHHHCCCEEEEEEChh
Confidence 345666676654433 3444554 468999999998632 48999999999999998766 899999999
Q ss_pred hHHHHHHHHhcCCCCceeecCCccccchh
Q 015881 362 EREGVEDVVGDDASIVFITTPGQVRMSSY 390 (399)
Q Consensus 362 E~e~aeeI~~~~~~~~~i~~~G~ls~~~~ 390 (399)
|++.+++|.+.++..+ +++.|+++|...
T Consensus 218 e~~~~~~i~~~~~~~~-~~l~g~~sL~el 245 (334)
T TIGR02195 218 DHPAGNEIEALLPGEL-RNLAGETSLDEA 245 (334)
T ss_pred hHHHHHHHHHhCCccc-ccCCCCCCHHHH
Confidence 9999999988877655 678999888754
No 5
>PRK10964 ADP-heptose:LPS heptosyl transferase I; Provisional
Probab=100.00 E-value=2.7e-37 Score=305.31 Aligned_cols=237 Identities=14% Similarity=0.161 Sum_probs=181.7
Q ss_pred cEEEEEcCCChhHHHhHHHHHHHHHHHCCCcEEEEEEcCCchHhhhcCCCCCEEEEecCCCCCCC-------hHHHHHHH
Q 015881 123 RRCCCIISGGVYENLLFFPAIQLLKDRYPGVLIDVIASARGKQTFELNKNVRWANVYDLDDDWPE-------PAEYTDIL 195 (399)
Q Consensus 123 ~rILIIr~~~IGDvVLttPalraLK~~yP~A~IdvLv~~~~~~lle~nP~ID~Vi~~d~k~~~~~-------~~~~~~l~ 195 (399)
||||||++++|||+||++|++++||++||+|+|||+|.+.++++++.||+||+|+.++.+. |.. ...+.+++
T Consensus 1 m~ILii~~~~iGD~v~~~p~~~~lk~~~P~a~I~~l~~~~~~~l~~~~p~vd~vi~~~~~~-~~~~~~~~~~~~~~~~~~ 79 (322)
T PRK10964 1 MRVLIVKTSSMGDVLHTLPALTDAQQAIPGIQFDWVVEEGFAQIPSWHPAVDRVIPVAIRR-WRKAWFSAPIRAERKAFR 79 (322)
T ss_pred CeEEEEeccchHHHHhHHHHHHHHHHhCCCCEEEEEECHHHHHHHhcCCCccEEEeechhH-hhhcccchhHHHHHHHHH
Confidence 7999999999999999999999999999999999999999999999999999999998542 111 12467889
Q ss_pred HHhhhCCCcEEEEcCCCChHHHHHHHHhCCCeEEEecCCCccccccccccceeeccCcCCchhhHHHHHHHHH-HHcCCC
Q 015881 196 GVMKNRYYDMVLSTKLAGLGHAAFLFMTTARDRVSYIYPNVNAAGAGLLLSETFTAESMNLSERGYNMYEQMV-DWLGRP 274 (399)
Q Consensus 196 ~~LR~~~YDlvIdl~~~~~rsAll~~LsgA~~RIGy~~~~~~~~~~~~~lt~~v~~~~~~~~~h~v~~yl~LL-~~LGi~ 274 (399)
++||+++||++||+++. ++++++.++++++.|+||...........+++++.+..... .|.+++|++++ +.+|++
T Consensus 80 ~~lr~~~yD~vidl~~~-~~s~~l~~~~~~~~r~G~~~~~~~~~~~~~~~~~~~~~~~~---~h~~~~~~~l~~~~lg~~ 155 (322)
T PRK10964 80 EALQAEQYDAVIDAQGL-VKSAALVTRLAHGVKHGMDWQSAREPLASLFYNRRHHIAKQ---QHAVERTRELFAKSLGYS 155 (322)
T ss_pred HHHhccCCCEEEEccch-HHHHHHHHHhcCCcEecCCCCcccchHhHhhccCccCCCcc---cCHHHHHHHHHHHHcCCC
Confidence 99999999999999998 88999887777778999973221112234677776654333 68899999987 688873
Q ss_pred CCCCCCCCCCCceeecCHHHHHHHHHHHHHhCCCCCCeEEEEcCCCCccccccCCCCCCCCCCHHHHHHHHHHhhhCC-C
Q 015881 275 FRSVPRHPVPPLRVSISRRLKEVVAEKYKNAGAEQGKYIVIHGIESDSKASMQSRGDTDSLLPIQVWAEIANGLREFR-P 353 (399)
Q Consensus 275 ~~~~p~~~~p~l~i~is~e~~~~a~~~l~~~gl~~~~~IvIhPgas~~~~~~k~rg~~~KrWP~e~faeLa~~L~~~~-~ 353 (399)
. .... .+...++.++.+.....++||+++||+++.. |+||.|+|++|++.|.+++ +
T Consensus 156 ~------~~~~-------~~~~~~~~~~~~~~~~~~~~i~~~~~~s~~~----------k~Wp~e~~a~li~~l~~~~~~ 212 (322)
T PRK10964 156 K------PQTQ-------GDYAIAQHFLTNLPADAGPYLVFLHATTRDD----------KHWPEAHWRELIGLLAPSGLR 212 (322)
T ss_pred c------cCCc-------cchhhhhhhcccccccCCCeEEEEeCCCccc----------ccCCHHHHHHHHHHHHHCCCe
Confidence 1 1111 1112223333333333468998888887753 8999999999999998766 7
Q ss_pred EEEe-CCchhHHHHHHHHhcCCCCceeecCCccccchh
Q 015881 354 LFVI-PHEKEREGVEDVVGDDASIVFITTPGQVRMSSY 390 (399)
Q Consensus 354 Vvli-Ggp~E~e~aeeI~~~~~~~~~i~~~G~ls~~~~ 390 (399)
|+++ |+++|++.+++|.+.++. +...|+++|...
T Consensus 213 ivl~~G~~~e~~~~~~i~~~~~~---~~l~g~~sL~el 247 (322)
T PRK10964 213 IKLPWGAEHEEQRAKRLAEGFPY---VEVLPKLSLEQV 247 (322)
T ss_pred EEEeCCCHHHHHHHHHHHccCCc---ceecCCCCHHHH
Confidence 8886 888999999999887654 335588887654
No 6
>COG0859 RfaF ADP-heptose:LPS heptosyltransferase [Cell envelope biogenesis, outer membrane]
Probab=100.00 E-value=4.3e-37 Score=306.72 Aligned_cols=245 Identities=18% Similarity=0.198 Sum_probs=191.0
Q ss_pred ccEEEEEcCCChhHHHhHHHHHHHHHHHCCCcEEEEEEcCCchHhhhcCCCCCEEEEecCCCCCCChHHHHHHHHHhhhC
Q 015881 122 VRRCCCIISGGVYENLLFFPAIQLLKDRYPGVLIDVIASARGKQTFELNKNVRWANVYDLDDDWPEPAEYTDILGVMKNR 201 (399)
Q Consensus 122 v~rILIIr~~~IGDvVLttPalraLK~~yP~A~IdvLv~~~~~~lle~nP~ID~Vi~~d~k~~~~~~~~~~~l~~~LR~~ 201 (399)
+|||||||+++|||+||++|+++.||++||+|+|||++.++++++++.||+|++|+.++.++.-..++++.++++.||++
T Consensus 1 ~~kIliir~~~iGD~vlt~p~~~~lk~~~P~a~i~~~~~~~~~~i~~~~p~I~~vi~~~~~~~~~~~~~~~~l~~~lr~~ 80 (334)
T COG0859 1 MMKILVIRLSKLGDVVLTLPLLRTLKKAYPNAKIDVLVPKGFAPILKLNPEIDKVIIIDKKKKGLGLKERLALLRTLRKE 80 (334)
T ss_pred CceEEEEeccchhHHHhHHHHHHHHHHHCCCCEEEEEeccchHHHHhcChHhhhhccccccccccchHHHHHHHHHhhcc
Confidence 59999999999999999999999999999999999999999999999999999999876533213578899999999999
Q ss_pred CCcEEEEcCCCChHHHHHHHHhCCCeEEEecCCCccccccccccceeeccCcCCchhhHHHHHHHHHHHcCCCCCCCCCC
Q 015881 202 YYDMVLSTKLAGLGHAAFLFMTTARDRVSYIYPNVNAAGAGLLLSETFTAESMNLSERGYNMYEQMVDWLGRPFRSVPRH 281 (399)
Q Consensus 202 ~YDlvIdl~~~~~rsAll~~LsgA~~RIGy~~~~~~~~~~~~~lt~~v~~~~~~~~~h~v~~yl~LL~~LGi~~~~~p~~ 281 (399)
+||+|||++++ ++++++.++++++.|+||++... +.+++++....-.....+|++++|++++..+|..... .
T Consensus 81 ~yD~vidl~~~-~ksa~l~~~~~~~~r~g~~~~~~----r~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~---~ 152 (334)
T COG0859 81 RYDAVIDLQGL-LKSALLALLLGIPFRIGFDKKSA----RELLLNKFYPRLDKPEGQHVVERYLALLEDLGLYPPP---E 152 (334)
T ss_pred CCCEEEECccc-HHHHHHHHHhCCCcccccccccc----hhHHHHHhhhccCcccchhHHHHHHHHHHHhcCCCCC---C
Confidence 99999999999 99999999999999999994322 2233333222111122379999999999998873211 1
Q ss_pred CCCCceeecCHHHHHHHHHHHHHhCCCCCCeEEEEcCCCCccccccCCCCCCCCCCHHHHHHHHHHhhhCC-CEEEeCCc
Q 015881 282 PVPPLRVSISRRLKEVVAEKYKNAGAEQGKYIVIHGIESDSKASMQSRGDTDSLLPIQVWAEIANGLREFR-PLFVIPHE 360 (399)
Q Consensus 282 ~~p~l~i~is~e~~~~a~~~l~~~gl~~~~~IvIhPgas~~~~~~k~rg~~~KrWP~e~faeLa~~L~~~~-~VvliGgp 360 (399)
....+.+..+..+.... +...+ ++||+|+||++... +|+||.|+|++||+.|.+++ +|+++|++
T Consensus 153 ~~~~~~~~~~~~~~~~~---~~~~~---~~~i~i~pg~s~~~---------~K~wp~e~~~~l~~~l~~~~~~Vvl~g~~ 217 (334)
T COG0859 153 PQLDFPLPRPPIELAKN---LAKFD---RPYIVINPGASRGS---------AKRWPLEHYAELAELLIAKGYQVVLFGGP 217 (334)
T ss_pred CccCcccccCHHHHHHH---HHhcC---CCeEEEeccccccc---------cCCCCHHHHHHHHHHHHHCCCEEEEecCh
Confidence 11112333333332222 22111 58999999955532 59999999999999999988 89999999
Q ss_pred hhHHHHHHHHhcCCCCceeecCCccccchhh
Q 015881 361 KEREGVEDVVGDDASIVFITTPGQVRMSSYT 391 (399)
Q Consensus 361 ~E~e~aeeI~~~~~~~~~i~~~G~ls~~~~~ 391 (399)
+|++.+++|.+.+++.+ . +.|+++|...+
T Consensus 218 ~e~e~~~~i~~~~~~~~-~-l~~k~sL~e~~ 246 (334)
T COG0859 218 DEEERAEEIAKGLPNAV-I-LAGKTSLEELA 246 (334)
T ss_pred HHHHHHHHHHHhcCCcc-c-cCCCCCHHHHH
Confidence 99999999999988755 3 67898887654
No 7
>TIGR02193 heptsyl_trn_I lipopolysaccharide heptosyltransferase I. This family consists of examples of ADP-heptose:LPS heptosyltransferase I, an enzyme of LPS inner core region biosynthesis. LPS, composed of lipid A, a core region, and O antigen, is found in the outer membrane of Gram-negative bacteria.
Probab=100.00 E-value=3.7e-36 Score=296.09 Aligned_cols=239 Identities=15% Similarity=0.157 Sum_probs=181.8
Q ss_pred EEEEEcCCChhHHHhHHHHHHHHHHHCCCcEEEEEEcCCchHhhhcCCCCCEEEEecCCCCCCC------hHHHHHHHHH
Q 015881 124 RCCCIISGGVYENLLFFPAIQLLKDRYPGVLIDVIASARGKQTFELNKNVRWANVYDLDDDWPE------PAEYTDILGV 197 (399)
Q Consensus 124 rILIIr~~~IGDvVLttPalraLK~~yP~A~IdvLv~~~~~~lle~nP~ID~Vi~~d~k~~~~~------~~~~~~l~~~ 197 (399)
||||||+++|||+||++|++++||++||+|+|||++.+.+++++++||+||+|+.++.+...+. ...+..+.+.
T Consensus 1 ~ILiir~~~iGD~vl~~p~l~~Lr~~~P~a~I~~l~~~~~~~~~~~~p~vd~v~~~~~~~~~~~~~~~~~~~~~~~~~~~ 80 (319)
T TIGR02193 1 RILIVKTSSLGDVIHTLPALTDIKRALPDVEIDWVVEEGFADIVRLHPAVDEVIPVALRRWRKTLFSAATWREIKALRAL 80 (319)
T ss_pred CEEEEecccHHHHHHHHHHHHHHHHhCCCCEEEEEEChhHhhhhhcCCCccEEEEechhhhhhccccchhHHHHHHHHHH
Confidence 6999999999999999999999999999999999999999999999999999999986531111 1234556778
Q ss_pred hhhCCCcEEEEcCCCChHHHHHHHHhCCCeEEEecCCCccccccccccceeeccCcCCchhhHHHHHHHHH-HHcCCCCC
Q 015881 198 MKNRYYDMVLSTKLAGLGHAAFLFMTTARDRVSYIYPNVNAAGAGLLLSETFTAESMNLSERGYNMYEQMV-DWLGRPFR 276 (399)
Q Consensus 198 LR~~~YDlvIdl~~~~~rsAll~~LsgA~~RIGy~~~~~~~~~~~~~lt~~v~~~~~~~~~h~v~~yl~LL-~~LGi~~~ 276 (399)
||+++||++||++++ ++++++++++++ .|+||...........+++++.+..+.. .|.+++|++++ +.+|++..
T Consensus 81 lr~~~yD~vi~~~~~-~~s~~l~~~~~~-~r~g~~~~~~~~~~~~~~~~~~~~~~~~---~h~~~~~~~ll~~~lg~~~~ 155 (319)
T TIGR02193 81 LRAERYDAVIDAQGL-IKSALVARMARG-PRHGFDWRSAREPLASLFYNKRVGISYQ---QHAVERNRKLFALALGYPPP 155 (319)
T ss_pred Hhhccchhhhhhhhh-HHHHHHHHhhCC-ceecCCCCccccHHHHHHhcCccCCCcc---cCHHHHHHHHHHHHcCCCCC
Confidence 999999999999999 999999999994 5999974322112234567776554433 68899999987 47888320
Q ss_pred CCCCCCCCCceeecCHHHHHHHHHHHHHhCCCCCCeEEEEcCCCCccccccCCCCCCCCCCHHHHHHHHHHhhhCC-CEE
Q 015881 277 SVPRHPVPPLRVSISRRLKEVVAEKYKNAGAEQGKYIVIHGIESDSKASMQSRGDTDSLLPIQVWAEIANGLREFR-PLF 355 (399)
Q Consensus 277 ~~p~~~~p~l~i~is~e~~~~a~~~l~~~gl~~~~~IvIhPgas~~~~~~k~rg~~~KrWP~e~faeLa~~L~~~~-~Vv 355 (399)
....+.+.++.++. ..++. .. ..+++|++|||+++.. |+||.|+|++|++.|.+++ ++|
T Consensus 156 -----~~~~~~~~~~~~~~---~~~~~-~~-~~~~~i~i~~gas~~~----------K~wp~e~~~~l~~~l~~~~~~~v 215 (319)
T TIGR02193 156 -----IAETIDYGLARRAA---VAFLG-HA-LPAPYAVLLHATSRDD----------KTWPEERWRELARLLLARGLQIV 215 (319)
T ss_pred -----CCCccccCccchhh---hhhhh-cc-CCCCEEEEEeCCCccc----------CCCCHHHHHHHHHHHHHCCCeEE
Confidence 11223444444332 12221 11 2468999999998864 8999999999999998765 777
Q ss_pred Ee-CCchhHHHHHHHHhcCCCCceeecCCccccchh
Q 015881 356 VI-PHEKEREGVEDVVGDDASIVFITTPGQVRMSSY 390 (399)
Q Consensus 356 li-Ggp~E~e~aeeI~~~~~~~~~i~~~G~ls~~~~ 390 (399)
++ |+++|++.+++|.+..++. ++.|+++|.+.
T Consensus 216 l~~g~~~e~~~~~~i~~~~~~~---~l~g~~sL~el 248 (319)
T TIGR02193 216 LPWGNDAEKQRAERIAEALPGA---VVLPKMSLAEV 248 (319)
T ss_pred EeCCCHHHHHHHHHHHhhCCCC---eecCCCCHHHH
Confidence 76 7788999999999877764 34588887764
No 8
>cd03789 GT1_LPS_heptosyltransferase Lipopolysaccharide heptosyltransferase is involved in the biosynthesis of lipooligosaccharide (LOS). Lipopolysaccharide (LPS) is a major component of the outer membrane of gram-negative bacteria. LPS heptosyltransferase transfers heptose molecules from ADP-heptose to 3-deoxy-D-manno-octulosonic acid (KDO), a part of the inner core component of LPS. This family belongs to the GT-B structural superfamily of glycoslytransferases, which have characteristic N- and C-terminal domains each containing a typical Rossmann fold. The two domains have high structural homology despite minimal sequence homology. The large cleft that separates the two domains includes the catalytic center and permits a high degree of flexibility.
Probab=99.97 E-value=5.2e-31 Score=255.13 Aligned_cols=191 Identities=19% Similarity=0.223 Sum_probs=162.5
Q ss_pred EEEEEcCCChhHHHhHHHHHHHHHHHCCCcEEEEEEcCCchHhhhcCCCCCEEEEecCCCCCCChHHHHHHHHHhhhCCC
Q 015881 124 RCCCIISGGVYENLLFFPAIQLLKDRYPGVLIDVIASARGKQTFELNKNVRWANVYDLDDDWPEPAEYTDILGVMKNRYY 203 (399)
Q Consensus 124 rILIIr~~~IGDvVLttPalraLK~~yP~A~IdvLv~~~~~~lle~nP~ID~Vi~~d~k~~~~~~~~~~~l~~~LR~~~Y 203 (399)
|||||+.++|||+|+++|++++||++||+++|||++.+.++++++.+|+||+|+.++.++....+..+++++++||+++|
T Consensus 1 kILii~~~~iGD~i~~~p~l~~Lk~~~P~~~I~~l~~~~~~~l~~~~p~id~v~~~~~~~~~~~~~~~~~~~~~l~~~~~ 80 (279)
T cd03789 1 RILVIRLSWIGDVVLATPLLRALKARYPDARITVLAPPWFAPLLELMPEVDRVIVLPKKHGKLGLGARRRLARALRRRRY 80 (279)
T ss_pred CEEEEecccHHHHHHHHHHHHHHHHHCCCCEEEEEEChhhHHHHhcCCccCEEEEcCCcccccchHHHHHHHHHHhhcCC
Confidence 79999999999999999999999999999999999999999999999999999999875423456788899999999999
Q ss_pred cEEEEcCCCChHHHHHHHHhCCCeEEEecCCCccccccccccceeeccCcCCchhhHHHHHHHHHHHcCCCCCCCCCCCC
Q 015881 204 DMVLSTKLAGLGHAAFLFMTTARDRVSYIYPNVNAAGAGLLLSETFTAESMNLSERGYNMYEQMVDWLGRPFRSVPRHPV 283 (399)
Q Consensus 204 DlvIdl~~~~~rsAll~~LsgA~~RIGy~~~~~~~~~~~~~lt~~v~~~~~~~~~h~v~~yl~LL~~LGi~~~~~p~~~~ 283 (399)
|++|+++.+ .++++++++++++.|+||. ......++++.+
T Consensus 81 D~vi~~~~~-~~~~~~~~~~~~~~~~g~~-----~~~~~~~~~~~~---------------------------------- 120 (279)
T cd03789 81 DLAIDLQGS-LRSALLPFLAGAPRRIGFD-----GERRRGLLTDVV---------------------------------- 120 (279)
T ss_pred CEEEECCCc-cHHHHHHHHhCCCeEEEec-----CCcccccccccc----------------------------------
Confidence 999999999 8999999999999999998 222211211100
Q ss_pred CCceeecCHHHHHHHHHHHHHhCCCCCCeEEEEcCCCCccccccCCCCCCCCCCHHHHHHHHHHhhhCC-CEEEeCCchh
Q 015881 284 PPLRVSISRRLKEVVAEKYKNAGAEQGKYIVIHGIESDSKASMQSRGDTDSLLPIQVWAEIANGLREFR-PLFVIPHEKE 362 (399)
Q Consensus 284 p~l~i~is~e~~~~a~~~l~~~gl~~~~~IvIhPgas~~~~~~k~rg~~~KrWP~e~faeLa~~L~~~~-~VvliGgp~E 362 (399)
+++|++|||+++.. |+||.|+|++|++.|.+++ +|+++|+++|
T Consensus 121 --------------------------~~~i~i~~~~~~~~----------k~w~~~~~~~l~~~l~~~~~~ivl~g~~~e 164 (279)
T cd03789 121 --------------------------KPVVVLPPGASGPA----------KRWPAERFAALADRLLARGARVVLTGGPAE 164 (279)
T ss_pred --------------------------CCEEEECCCCCCcc----------ccCCHHHHHHHHHHHHHCCCEEEEEechhh
Confidence 47999999999875 7899999999999998876 8999999999
Q ss_pred HHHHHHHHhcCCCCceeecCCccccchh
Q 015881 363 REGVEDVVGDDASIVFITTPGQVRMSSY 390 (399)
Q Consensus 363 ~e~aeeI~~~~~~~~~i~~~G~ls~~~~ 390 (399)
++.+++|.+..++..+++..|++++...
T Consensus 165 ~~~~~~i~~~~~~~~~~~~~~~~~l~e~ 192 (279)
T cd03789 165 RELAEEIAAALGGPRVVNLAGKTSLREL 192 (279)
T ss_pred HHHHHHHHHhcCCCccccCcCCCCHHHH
Confidence 9999999887633333667788777654
No 9
>PF01075 Glyco_transf_9: Glycosyltransferase family 9 (heptosyltransferase); InterPro: IPR002201 The biosynthesis of disaccharides, oligosaccharides and polysaccharides involves the action of hundreds of different glycosyltransferases. These enzymes catalyse the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming glycosidic bonds. A classification of glycosyltransferases using nucleotide diphospho-sugar, nucleotide monophospho-sugar and sugar phosphates (2.4.1.- from EC) and related proteins into distinct sequence based families has been described []. This classification is available on the CAZy (CArbohydrate-Active EnZymes) web site. The same three-dimensional fold is expected to occur within each of the families. Because 3-D structures are better conserved than sequences, several of the families defined on the basis of sequence similarities may have similar 3-D structures and therefore form 'clans'. Glycosyltransferase family 9 GT9 from CAZY comprises enzymes with two known activity; lipopolysaccharide N-acetylglucosaminyltransferase (2.4.1.56 from EC), heptosyltransferase (2.4 from EC). Heptosyltransferase I is thought to add L-glycero-D-manno-heptose to the inner 3-deoxy-D-manno-octulosonic acid (Kdo) residue of the lipopolysaccharide core []. Heptosyltransferase II is a glycosyltransferase involved in the synthesis of the inner core region of lipopolysaccharide []. Lipopolysaccharide is a major component of the outer leaflet of the outer membrane in Gram-negative bacteria. It is composed of three domains; lipid A, Core oligosaccharide and the O-antigen. These enzymes transfer heptose to the lipopolysaccharide core [].; GO: 0016757 transferase activity, transferring glycosyl groups, 0008152 metabolic process; PDB: 1PSW_A 2H1F_A 2GT1_A 3TOV_A 2H1H_A.
Probab=99.86 E-value=1.1e-21 Score=185.85 Aligned_cols=173 Identities=18% Similarity=0.279 Sum_probs=118.7
Q ss_pred HHHHHHHhhhCCCcEEEEcCCCChHHHHHHHHhCCCeEEEecCCCccccccccccceeeccCcCCchhhHHHHHHHHHHH
Q 015881 191 YTDILGVMKNRYYDMVLSTKLAGLGHAAFLFMTTARDRVSYIYPNVNAAGAGLLLSETFTAESMNLSERGYNMYEQMVDW 270 (399)
Q Consensus 191 ~~~l~~~LR~~~YDlvIdl~~~~~rsAll~~LsgA~~RIGy~~~~~~~~~~~~~lt~~v~~~~~~~~~h~v~~yl~LL~~ 270 (399)
+++|+++||+++||+|||++++ .++++++++++|+.|+||..... +..+++++.+..... .|.+++|+.++..
T Consensus 1 ~~~l~~~Lr~~~yD~vid~~~~-~~s~~l~~~~~a~~riG~~~~~~---~~~~~~~~~~~~~~~---~~~v~~~~~ll~~ 73 (247)
T PF01075_consen 1 ILALIKKLRKEKYDLVIDLQGS-FRSALLARLSGAKIRIGFGKDDR---GRSLFYNRKVDRPPN---KHMVDRYLSLLSE 73 (247)
T ss_dssp HHHHHHHHCTSB-SEEEE-S-S-HHHHHHTCCCSBSEEEEE-TTTS---GGGGGESEEE-TTSS---SSHHHHHHHHHHH
T ss_pred CHHHHHHHhCCCCCEEEECCCC-ccHHHHHHHHhhccccccCccch---hhhhccccccccccc---chHHHHHHHHHHH
Confidence 3689999999999999999999 99999999999999999983211 224566666655433 5788889988864
Q ss_pred -cCCCCCCCCCCCCCCceeecCHHHHHHHHHHHHHhCCCCCCeEEEEcCCCCccccccCCCCCCCCCCHHHHHHHHHHhh
Q 015881 271 -LGRPFRSVPRHPVPPLRVSISRRLKEVVAEKYKNAGAEQGKYIVIHGIESDSKASMQSRGDTDSLLPIQVWAEIANGLR 349 (399)
Q Consensus 271 -LGi~~~~~p~~~~p~l~i~is~e~~~~a~~~l~~~gl~~~~~IvIhPgas~~~~~~k~rg~~~KrWP~e~faeLa~~L~ 349 (399)
+|++ .....+.+.+++++...+...+. ...+++|+||||+++.. |+||.|+|++|++.|.
T Consensus 74 ~~~~~------~~~~~~~l~~~~~~~~~~~~~~~---~~~~~~i~i~~~a~~~~----------k~wp~e~~~~l~~~l~ 134 (247)
T PF01075_consen 74 LLGIP------YPSTKPELPLSEEEEAAARELLK---SKDKPYIGINPGASWPS----------KRWPAEKWAELIERLK 134 (247)
T ss_dssp HHTS-------SSSSSS----THHHHTTHHTTTT----TTSSEEEEE---SSGG----------GS--HHHHHHHHHHHC
T ss_pred hcCCC------CCCCCcCCcCCHHHHHHHHHhhh---hccCCeEEEeecCCCcc----------ccCCHHHHHHHHHHHH
Confidence 6773 22334567778777766655443 23568999999999964 8899999999999999
Q ss_pred hCC-CEEEeCCchh--HHHHHHHHhcCCCCceeecCCccccchh
Q 015881 350 EFR-PLFVIPHEKE--REGVEDVVGDDASIVFITTPGQVRMSSY 390 (399)
Q Consensus 350 ~~~-~VvliGgp~E--~e~aeeI~~~~~~~~~i~~~G~ls~~~~ 390 (399)
+.+ .|+++|+++| ++.++++.+.+.... +++.|++++.+.
T Consensus 135 ~~~~~vvl~g~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~l~e~ 177 (247)
T PF01075_consen 135 ERGYRVVLLGGPEEQEKEIADQIAAGLQNPV-INLAGKTSLREL 177 (247)
T ss_dssp CCT-EEEE--SSHHHHHHHHHHHHTTHTTTT-EEETTTS-HHHH
T ss_pred hhCceEEEEccchHHHHHHHHHHHHhcccce-EeecCCCCHHHH
Confidence 887 8999999998 677888887765444 778888888763
No 10
>PRK10017 colanic acid biosynthesis protein; Provisional
Probab=97.78 E-value=0.00054 Score=71.30 Aligned_cols=41 Identities=10% Similarity=0.067 Sum_probs=35.9
Q ss_pred cEEEEEc---CCChhHHHhHHHHHHHHHHHCCCcEEEEEEcCCc
Q 015881 123 RRCCCII---SGGVYENLLFFPAIQLLKDRYPGVLIDVIASARG 163 (399)
Q Consensus 123 ~rILIIr---~~~IGDvVLttPalraLK~~yP~A~IdvLv~~~~ 163 (399)
|||+|+- .+..||--+.+.+|.+||+..|+++|+++.....
T Consensus 1 ~~i~i~G~~g~~N~GdeAil~~ii~~l~~~~p~~~i~v~S~~P~ 44 (426)
T PRK10017 1 MKLLILGNHTCGNRGDSAILRGLLDAINILNPHAEVDVMSRYPV 44 (426)
T ss_pred CeEEEEccccCCCccHHHHHHHHHHHHHhhCCCCeEEEEecCcc
Confidence 7899884 4788999999999999999999999999985443
No 11
>TIGR03568 NeuC_NnaA UDP-N-acetyl-D-glucosamine 2-epimerase, UDP-hydrolysing. This family of enzymes catalyzes the combined epimerization and UDP-hydrolysis of UDP-N-acetylglucosamine to N-acetylmannosamine. This is in contrast to the related enzyme WecB (TIGR00236) which retains the UDP moiety. NeuC acts in concert with NeuA and NeuB to synthesize CMP-N5-acetyl-neuraminate.
Probab=97.36 E-value=0.0052 Score=62.50 Aligned_cols=235 Identities=14% Similarity=0.090 Sum_probs=118.2
Q ss_pred cEEEEEcCCChhHHHhHHHHHHHHHHHCCCcEEEEEEcCCc---------hHhhhcCCCCCEEEEecCCC-CCCChH---
Q 015881 123 RRCCCIISGGVYENLLFFPAIQLLKDRYPGVLIDVIASARG---------KQTFELNKNVRWANVYDLDD-DWPEPA--- 189 (399)
Q Consensus 123 ~rILIIr~~~IGDvVLttPalraLK~~yP~A~IdvLv~~~~---------~~lle~nP~ID~Vi~~d~k~-~~~~~~--- 189 (399)
||||+| .+--=|.+..-|++++|++ .++.+..+++.-.. .++.+..=.|+.-+.+.... .-.++.
T Consensus 1 ~ki~~v-~GtRpe~iklapv~~~l~~-~~~~~~~lv~tGqH~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 78 (365)
T TIGR03568 1 KKICVV-TGTRADYGLLRPLLKALQD-DPDLELQLIVTGMHLSPEYGNTVNEIEKDGFDIDEKIEILLDSDSNAGMAKSM 78 (365)
T ss_pred CeEEEE-EecChhHHHHHHHHHHHhc-CCCCcEEEEEeCCCCChhhccHHHHHHHcCCCCCCccccccCCCCCCCHHHHH
Confidence 577765 4555688999999999995 56778777764322 23332210122112221111 101222
Q ss_pred --HHHHHHHHhhhCCCcEEEEcCCC--ChHHHHHHHHhCCCeEEEecCCCccccc-cccccceeeccCcCCchhhHH---
Q 015881 190 --EYTDILGVMKNRYYDMVLSTKLA--GLGHAAFLFMTTARDRVSYIYPNVNAAG-AGLLLSETFTAESMNLSERGY--- 261 (399)
Q Consensus 190 --~~~~l~~~LR~~~YDlvIdl~~~--~~rsAll~~LsgA~~RIGy~~~~~~~~~-~~~~lt~~v~~~~~~~~~h~v--- 261 (399)
....+.+.+++.++|+||..... .+-.++.++..|+|.- +- ..| +++-. . + + ...|.+
T Consensus 79 ~~~~~~~~~~~~~~~Pd~vlv~GD~~~~la~alaA~~~~IPv~--Hv-----eaG~rs~~~---~--e-E-~~r~~i~~l 144 (365)
T TIGR03568 79 GLTIIGFSDAFERLKPDLVVVLGDRFEMLAAAIAAALLNIPIA--HI-----HGGEVTEGA---I--D-E-SIRHAITKL 144 (365)
T ss_pred HHHHHHHHHHHHHhCCCEEEEeCCchHHHHHHHHHHHhCCcEE--EE-----ECCccCCCC---c--h-H-HHHHHHHHH
Confidence 23466777889999999876543 1245777888888843 22 111 11100 0 0 0 001111
Q ss_pred --------HHHHHHHHHcCCCCCCCCCCCCCCce-e-ecCHHHHHHHHHHHHHhCCC-CCCe--EEEEcCCCCccccccC
Q 015881 262 --------NMYEQMVDWLGRPFRSVPRHPVPPLR-V-SISRRLKEVVAEKYKNAGAE-QGKY--IVIHGIESDSKASMQS 328 (399)
Q Consensus 262 --------~~yl~LL~~LGi~~~~~p~~~~p~l~-i-~is~e~~~~a~~~l~~~gl~-~~~~--IvIhPgas~~~~~~k~ 328 (399)
+.+.+-|...|.+...+-....+..+ + ..... .....++++|++ .++| |.+||+++.
T Consensus 145 a~l~f~~t~~~~~~L~~eg~~~~~i~~tG~~~iD~l~~~~~~---~~~~~~~~lgl~~~~~~vlvt~Hp~~~~------- 214 (365)
T TIGR03568 145 SHLHFVATEEYRQRVIQMGEDPDRVFNVGSPGLDNILSLDLL---SKEELEEKLGIDLDKPYALVTFHPVTLE------- 214 (365)
T ss_pred HhhccCCCHHHHHHHHHcCCCCCcEEEECCcHHHHHHhhhcc---CHHHHHHHhCCCCCCCEEEEEeCCCccc-------
Confidence 11222233345532111000011100 0 00000 012345566775 3477 788888652
Q ss_pred CCCCCCCCCHHHHHHHHHHhhhCC-CEEEe---CCchhHHHHHHHHhcCC-CCceeecCCccccch
Q 015881 329 RGDTDSLLPIQVWAEIANGLREFR-PLFVI---PHEKEREGVEDVVGDDA-SIVFITTPGQVRMSS 389 (399)
Q Consensus 329 rg~~~KrWP~e~faeLa~~L~~~~-~Vvli---Ggp~E~e~aeeI~~~~~-~~~~i~~~G~ls~~~ 389 (399)
+.|+.++|.++++.|.+.. .++++ +++.++...+++.+... ... +...|.|+...
T Consensus 215 -----~~~~~~~l~~li~~L~~~~~~~~vi~P~~~p~~~~i~~~i~~~~~~~~~-v~l~~~l~~~~ 274 (365)
T TIGR03568 215 -----KESAEEQIKELLKALDELNKNYIFTYPNADAGSRIINEAIEEYVNEHPN-FRLFKSLGQER 274 (365)
T ss_pred -----ccCchHHHHHHHHHHHHhccCCEEEEeCCCCCchHHHHHHHHHhcCCCC-EEEECCCChHH
Confidence 5699999999999998754 44444 55767666656555322 122 34445555443
No 12
>PRK00025 lpxB lipid-A-disaccharide synthase; Reviewed
Probab=97.17 E-value=0.0015 Score=65.42 Aligned_cols=104 Identities=12% Similarity=-0.066 Sum_probs=65.7
Q ss_pred ccEEEEEcCCChhHHHhHHHHHHHHHHHCCCcEEEEEEcCCchHhhhcCCCCCEEEEecCCCCC---CC----hHHHHHH
Q 015881 122 VRRCCCIISGGVYENLLFFPAIQLLKDRYPGVLIDVIASARGKQTFELNKNVRWANVYDLDDDW---PE----PAEYTDI 194 (399)
Q Consensus 122 v~rILIIr~~~IGDvVLttPalraLK~~yP~A~IdvLv~~~~~~lle~nP~ID~Vi~~d~k~~~---~~----~~~~~~l 194 (399)
+|||+|+.-+--||+..+. ++++||+.+|+++|..++.+....-. .+..-....++-.+-+ +. ...+.++
T Consensus 1 ~~ki~i~~Ggt~G~i~~a~-l~~~L~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~l~~~g~~~~~~~~~~~~~~~~~~ 77 (380)
T PRK00025 1 PLRIAIVAGEVSGDLLGAG-LIRALKARAPNLEFVGVGGPRMQAAG--CESLFDMEELAVMGLVEVLPRLPRLLKIRRRL 77 (380)
T ss_pred CceEEEEecCcCHHHHHHH-HHHHHHhcCCCcEEEEEccHHHHhCC--CccccCHHHhhhccHHHHHHHHHHHHHHHHHH
Confidence 4799999999999999997 99999999999999888765432211 1111011111111100 11 2234566
Q ss_pred HHHhhhCCCcEEEEcCCC--ChHHHHHHHHhCCCeE
Q 015881 195 LGVMKNRYYDMVLSTKLA--GLGHAAFLFMTTARDR 228 (399)
Q Consensus 195 ~~~LR~~~YDlvIdl~~~--~~rsAll~~LsgA~~R 228 (399)
.+.||+.++|+|+..... ..+.+..++..|+|.-
T Consensus 78 ~~~l~~~kPdivi~~~~~~~~~~~a~~a~~~~ip~i 113 (380)
T PRK00025 78 KRRLLAEPPDVFIGIDAPDFNLRLEKKLRKAGIPTI 113 (380)
T ss_pred HHHHHHcCCCEEEEeCCCCCCHHHHHHHHHCCCCEE
Confidence 778999999999976421 1344445666787743
No 13
>COG1519 KdtA 3-deoxy-D-manno-octulosonic-acid transferase [Cell envelope biogenesis, outer membrane]
Probab=96.98 E-value=0.14 Score=52.98 Aligned_cols=96 Identities=17% Similarity=0.152 Sum_probs=66.8
Q ss_pred EEEEcCCChhHHHhHHHHHHHHHHHCCCcEEEEEE-cCCchHhhh-cCCCCCEEEEecCCCCCCChHHHHHHHHHhhhCC
Q 015881 125 CCCIISGGVYENLLFFPAIQLLKDRYPGVLIDVIA-SARGKQTFE-LNKNVRWANVYDLDDDWPEPAEYTDILGVMKNRY 202 (399)
Q Consensus 125 ILIIr~~~IGDvVLttPalraLK~~yP~A~IdvLv-~~~~~~lle-~nP~ID~Vi~~d~k~~~~~~~~~~~l~~~LR~~~ 202 (399)
.+-|.-.++|.++.++|++++|++.||+..|.+-+ .+.+.+.++ ..+....+..++.+.. ...-+-||.-+
T Consensus 51 ~vWiHaaSVGEv~a~~pLv~~l~~~~P~~~ilvTt~T~Tg~e~a~~~~~~~v~h~YlP~D~~-------~~v~rFl~~~~ 123 (419)
T COG1519 51 LVWIHAASVGEVLAALPLVRALRERFPDLRILVTTMTPTGAERAAALFGDSVIHQYLPLDLP-------IAVRRFLRKWR 123 (419)
T ss_pred eEEEEecchhHHHHHHHHHHHHHHhCCCCCEEEEecCccHHHHHHHHcCCCeEEEecCcCch-------HHHHHHHHhcC
Confidence 45589999999999999999999999999998887 666666654 4455333433433221 23445577778
Q ss_pred CcEEEEcCCCChHHHHH--HHHhCCCeE
Q 015881 203 YDMVLSTKLAGLGHAAF--LFMTTARDR 228 (399)
Q Consensus 203 YDlvIdl~~~~~rsAll--~~LsgA~~R 228 (399)
.|++|-+... ..-.++ +...|+|.-
T Consensus 124 P~l~Ii~EtE-lWPnli~e~~~~~~p~~ 150 (419)
T COG1519 124 PKLLIIMETE-LWPNLINELKRRGIPLV 150 (419)
T ss_pred CCEEEEEecc-ccHHHHHHHHHcCCCEE
Confidence 9999999887 444443 335566643
No 14
>PRK05749 3-deoxy-D-manno-octulosonic-acid transferase; Reviewed
Probab=96.15 E-value=0.74 Score=47.14 Aligned_cols=99 Identities=17% Similarity=0.107 Sum_probs=64.2
Q ss_pred cEEEEEcCCChhHHHhHHHHHHHHHHHCCCcEEEEEE-cCCchHhhh-cCCCCCEEEEecCCCCCCChHHHHHHHHHhhh
Q 015881 123 RRCCCIISGGVYENLLFFPAIQLLKDRYPGVLIDVIA-SARGKQTFE-LNKNVRWANVYDLDDDWPEPAEYTDILGVMKN 200 (399)
Q Consensus 123 ~rILIIr~~~IGDvVLttPalraLK~~yP~A~IdvLv-~~~~~~lle-~nP~ID~Vi~~d~k~~~~~~~~~~~l~~~LR~ 200 (399)
.+.+-+.-.++|++..+.|+++.|++++|+.+|-+.+ .+...++++ ..+.-..++.++... + ..+.+.|++
T Consensus 50 ~~~iW~Ha~s~Ge~~~~~~l~~~l~~~~~~~~i~~t~~t~~~~~~~~~~~~~~~~~~~~P~d~----~---~~~~~~l~~ 122 (425)
T PRK05749 50 GPLIWFHAVSVGETRAAIPLIRALRKRYPDLPILVTTMTPTGSERAQALFGDDVEHRYLPYDL----P---GAVRRFLRF 122 (425)
T ss_pred CCeEEEEeCCHHHHHHHHHHHHHHHHhCCCCcEEEeCCCccHHHHHHHhcCCCceEEEecCCc----H---HHHHHHHHh
Confidence 4456689999999999999999999999999886665 344456554 223222344554421 1 244555788
Q ss_pred CCCcEEEEcCCCChHHHHH--HHHhCCCeEE
Q 015881 201 RYYDMVLSTKLAGLGHAAF--LFMTTARDRV 229 (399)
Q Consensus 201 ~~YDlvIdl~~~~~rsAll--~~LsgA~~RI 229 (399)
.++|+++..... ....++ +...|+|..+
T Consensus 123 ~~Pd~v~~~~~~-~~~~~l~~~~~~~ip~vl 152 (425)
T PRK05749 123 WRPKLVIIMETE-LWPNLIAELKRRGIPLVL 152 (425)
T ss_pred hCCCEEEEEecc-hhHHHHHHHHHCCCCEEE
Confidence 889999876554 333333 3455666544
No 15
>cd03807 GT1_WbnK_like This family is most closely related to the GT1 family of glycosyltransferases. WbnK in Shigella dysenteriae has been shown to be involved in the type 7 O-antigen biosynthesis.
Probab=95.11 E-value=2 Score=40.86 Aligned_cols=95 Identities=12% Similarity=0.061 Sum_probs=56.7
Q ss_pred EEEEEcC--CChhHHHhHHHHHHHHHHHCCCcEEEEEEcCCchH---hhhcCCCCCEEEEecCCCCCCChHHHHHHHHHh
Q 015881 124 RCCCIIS--GGVYENLLFFPAIQLLKDRYPGVLIDVIASARGKQ---TFELNKNVRWANVYDLDDDWPEPAEYTDILGVM 198 (399)
Q Consensus 124 rILIIr~--~~IGDvVLttPalraLK~~yP~A~IdvLv~~~~~~---lle~nP~ID~Vi~~d~k~~~~~~~~~~~l~~~L 198 (399)
|||+|-. +.=|.......++++|.+. +.++.+++...... .+.. .+|. ++.+.....+..+..+.++.+.+
T Consensus 1 ~i~~i~~~~~~gG~~~~~~~l~~~l~~~--~~~v~~~~~~~~~~~~~~~~~-~~i~-v~~~~~~~~~~~~~~~~~~~~~~ 76 (365)
T cd03807 1 KVLHVITGLDVGGAERMLVRLLKGLDRD--RFEHVVISLTDRGELGEELEE-AGVP-VYCLGKRPGRPDPGALLRLYKLI 76 (365)
T ss_pred CeEEEEeeccCccHHHHHHHHHHHhhhc--cceEEEEecCcchhhhHHHHh-cCCe-EEEEecccccccHHHHHHHHHHH
Confidence 4555533 3345666777889999665 44666666443332 2222 4554 55555443334556667888889
Q ss_pred hhCCCcEEEEcCCC-ChHHHHHHHH
Q 015881 199 KNRYYDMVLSTKLA-GLGHAAFLFM 222 (399)
Q Consensus 199 R~~~YDlvIdl~~~-~~rsAll~~L 222 (399)
++.++|+++..... .....+..++
T Consensus 77 ~~~~~div~~~~~~~~~~~~~~~~~ 101 (365)
T cd03807 77 RRLRPDVVHTWMYHADLYGGLAARL 101 (365)
T ss_pred HhhCCCEEEeccccccHHHHHHHHh
Confidence 99999999865332 1444455555
No 16
>PF04007 DUF354: Protein of unknown function (DUF354); InterPro: IPR007152 Members of this family are around 350 amino acids in length. They are found in archaea and some bacteria and have no known function.
Probab=93.81 E-value=3.5 Score=41.76 Aligned_cols=208 Identities=15% Similarity=0.132 Sum_probs=112.6
Q ss_pred cEEEEEcCCChhHHHhHHHHHHHHHHHCCCcEEEEEEcCCc--hHhhhcCCCCCEEEEecCCCCC-----CChHHHHHHH
Q 015881 123 RRCCCIISGGVYENLLFFPAIQLLKDRYPGVLIDVIASARG--KQTFELNKNVRWANVYDLDDDW-----PEPAEYTDIL 195 (399)
Q Consensus 123 ~rILIIr~~~IGDvVLttPalraLK~~yP~A~IdvLv~~~~--~~lle~nP~ID~Vi~~d~k~~~-----~~~~~~~~l~ 195 (399)
|||+|=-..- --+-++-++++.|+++ +-+|.+.+.... .++++. -+++.+.+=...... ..+....+++
T Consensus 1 MkIwiDi~~p-~hvhfFk~~I~eL~~~--GheV~it~R~~~~~~~LL~~-yg~~y~~iG~~g~~~~~Kl~~~~~R~~~l~ 76 (335)
T PF04007_consen 1 MKIWIDITHP-AHVHFFKNIIRELEKR--GHEVLITARDKDETEELLDL-YGIDYIVIGKHGDSLYGKLLESIERQYKLL 76 (335)
T ss_pred CeEEEECCCc-hHHHHHHHHHHHHHhC--CCEEEEEEeccchHHHHHHH-cCCCeEEEcCCCCCHHHHHHHHHHHHHHHH
Confidence 5666532221 2667778999999998 557777776543 466775 466666543322211 1233456788
Q ss_pred HHhhhCCCcEEEEcCCCChHHHHHHHHhCCCeEEEecCCCcccc-ccccccceeeccCcCCchhhHHHHHHHHHHHcCCC
Q 015881 196 GVMKNRYYDMVLSTKLAGLGHAAFLFMTTARDRVSYIYPNVNAA-GAGLLLSETFTAESMNLSERGYNMYEQMVDWLGRP 274 (399)
Q Consensus 196 ~~LR~~~YDlvIdl~~~~~rsAll~~LsgA~~RIGy~~~~~~~~-~~~~~lt~~v~~~~~~~~~h~v~~yl~LL~~LGi~ 274 (399)
+.+++.++|++|...+ ...+..+++.|+|..+=++.+-.... .-.+-|.+.+-.+.. +.. .....+|..
T Consensus 77 ~~~~~~~pDv~is~~s--~~a~~va~~lgiP~I~f~D~e~a~~~~~Lt~Pla~~i~~P~~------~~~--~~~~~~G~~ 146 (335)
T PF04007_consen 77 KLIKKFKPDVAISFGS--PEAARVAFGLGIPSIVFNDTEHAIAQNRLTLPLADVIITPEA------IPK--EFLKRFGAK 146 (335)
T ss_pred HHHHhhCCCEEEecCc--HHHHHHHHHhCCCeEEEecCchhhccceeehhcCCeeECCcc------cCH--HHHHhcCCc
Confidence 8899999999996543 56777899999996554442211000 001122332222211 111 122334532
Q ss_pred -----CCCCCCCCCCCceeecCHHHHHHHHHHHHHhCCCCCCeEEEEcCCCCccccccCCCCCCCCCCHHHHHHHHHHhh
Q 015881 275 -----FRSVPRHPVPPLRVSISRRLKEVVAEKYKNAGAEQGKYIVIHGIESDSKASMQSRGDTDSLLPIQVWAEIANGLR 349 (399)
Q Consensus 275 -----~~~~p~~~~p~l~i~is~e~~~~a~~~l~~~gl~~~~~IvIhPgas~~~~~~k~rg~~~KrWP~e~faeLa~~L~ 349 (399)
..++-+...... +..+ ...++++|++..+||++-+.+..+. .=.+...-..++++.|.
T Consensus 147 ~~i~~y~G~~E~ayl~~-F~Pd-------~~vl~~lg~~~~~yIvvR~~~~~A~---------y~~~~~~i~~~ii~~L~ 209 (335)
T PF04007_consen 147 NQIRTYNGYKELAYLHP-FKPD-------PEVLKELGLDDEPYIVVRPEAWKAS---------YDNGKKSILPEIIEELE 209 (335)
T ss_pred CCEEEECCeeeEEeecC-CCCC-------hhHHHHcCCCCCCEEEEEeccccCe---------eecCccchHHHHHHHHH
Confidence 111101000000 1111 3457788888789999998764432 01233344568889998
Q ss_pred hCC-CEEEeCCch
Q 015881 350 EFR-PLFVIPHEK 361 (399)
Q Consensus 350 ~~~-~VvliGgp~ 361 (399)
+.+ .||+++..+
T Consensus 210 ~~~~~vV~ipr~~ 222 (335)
T PF04007_consen 210 KYGRNVVIIPRYE 222 (335)
T ss_pred hhCceEEEecCCc
Confidence 877 466666444
No 17
>PF02684 LpxB: Lipid-A-disaccharide synthetase; InterPro: IPR003835 The biosynthesis of disaccharides, oligosaccharides and polysaccharides involves the action of hundreds of different glycosyltransferases. These enzymes catalyse the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming glycosidic bonds. A classification of glycosyltransferases using nucleotide diphospho-sugar, nucleotide monophospho-sugar and sugar phosphates (2.4.1.- from EC) and related proteins into distinct sequence based families has been described []. This classification is available on the CAZy (CArbohydrate-Active EnZymes) web site. The same three-dimensional fold is expected to occur within each of the families. Because 3-D structures are better conserved than sequences, several of the families defined on the basis of sequence similarities may have similar 3-D structures and therefore form 'clans'. These enzymes belong to the glycosyltransferase family 19 GT19 from CAZY. Lipid-A-disaccharide synthetase 2.4.1.182 from EC is involved with acyl-[acyl-carrier-protein]--UDP-N-acetylglucosamine O-acyltransferase 2.3.1.129 from EC and tetraacyldisaccharide 4'-kinase 2.7.1.130 from EC in the biosynthesis of the phosphorylated glycolipid, lipid A, in the outer membrane of Escherichia coli and other bacteria. These enzymes catalyse the first disaccharide step in the synthesis of lipid-A-disaccharide.; GO: 0008915 lipid-A-disaccharide synthase activity, 0009245 lipid A biosynthetic process
Probab=93.42 E-value=3.8 Score=42.13 Aligned_cols=209 Identities=19% Similarity=0.123 Sum_probs=111.6
Q ss_pred EEEEcCCChhHHHhHHHHHHHHHHHCCCcEEEEEEcCCchHhhhcCCCCCEEEEecCCCCCCC-------hHH----HHH
Q 015881 125 CCCIISGGVYENLLFFPAIQLLKDRYPGVLIDVIASARGKQTFELNKNVRWANVYDLDDDWPE-------PAE----YTD 193 (399)
Q Consensus 125 ILIIr~~~IGDvVLttPalraLK~~yP~A~IdvLv~~~~~~lle~nP~ID~Vi~~d~k~~~~~-------~~~----~~~ 193 (399)
|+|+--..=||. +..-++++||+++|++++.-+..+.-++ -+++-++.++.-. .-+ +.. +.+
T Consensus 1 I~i~AGE~SGD~-~ga~Li~~Lk~~~p~~~~~GvGG~~M~~-----~G~~~l~d~~~ls-vmG~~Evl~~l~~~~~~~~~ 73 (373)
T PF02684_consen 1 IFISAGEASGDL-HGARLIRALKARDPDIEFYGVGGPRMQA-----AGVESLFDMEELS-VMGFVEVLKKLPKLKRLFRK 73 (373)
T ss_pred CEEEeeCccHHH-HHHHHHHHHHhhCCCcEEEEEechHHHh-----CCCceecchHHhh-hccHHHHHHHHHHHHHHHHH
Confidence 566666677886 4556899999999999999999886654 2333333222100 011 111 234
Q ss_pred HHHHhhhCCCcEEE--EcCCCChHHHHHHHHhCCCe-EEEecCCCccccccccccceeeccCcCCchhhHHHHHHHH---
Q 015881 194 ILGVMKNRYYDMVL--STKLAGLGHAAFLFMTTARD-RVSYIYPNVNAAGAGLLLSETFTAESMNLSERGYNMYEQM--- 267 (399)
Q Consensus 194 l~~~LR~~~YDlvI--dl~~~~~rsAll~~LsgA~~-RIGy~~~~~~~~~~~~~lt~~v~~~~~~~~~h~v~~yl~L--- 267 (399)
+.+.+++++.|++| |..+-.++-|-.+.-.|.+. .|=|..|.+=.|+.+ + -+.+.++.+.
T Consensus 74 ~~~~~~~~~pd~vIlID~pgFNlrlak~lk~~~~~~~viyYI~PqvWAWr~~-----R---------~~~i~~~~D~ll~ 139 (373)
T PF02684_consen 74 LVERIKEEKPDVVILIDYPGFNLRLAKKLKKRGIPIKVIYYISPQVWAWRPG-----R---------AKKIKKYVDHLLV 139 (373)
T ss_pred HHHHHHHcCCCEEEEeCCCCccHHHHHHHHHhCCCceEEEEECCceeeeCcc-----H---------HHHHHHHHhheeE
Confidence 55567789999998 44444477777788888774 355654532111110 0 1122222222
Q ss_pred --------HHHcCCCCCCCCCCCCCCceeecCHHHHHHHHHHHHHhCCC-CCCeEEEEcCCCCccccccCCCCCCCCCCH
Q 015881 268 --------VDWLGRPFRSVPRHPVPPLRVSISRRLKEVVAEKYKNAGAE-QGKYIVIHGIESDSKASMQSRGDTDSLLPI 338 (399)
Q Consensus 268 --------L~~LGi~~~~~p~~~~p~l~i~is~e~~~~a~~~l~~~gl~-~~~~IvIhPgas~~~~~~k~rg~~~KrWP~ 338 (399)
.+..|++..-+- .|-++..-........++.+ ++ .+++|++-|||+.+. +.+.+|
T Consensus 140 ifPFE~~~y~~~g~~~~~VG---HPl~d~~~~~~~~~~~~~~~----l~~~~~iIaLLPGSR~~E--------I~rllP- 203 (373)
T PF02684_consen 140 IFPFEPEFYKKHGVPVTYVG---HPLLDEVKPEPDRAEAREKL----LDPDKPIIALLPGSRKSE--------IKRLLP- 203 (373)
T ss_pred CCcccHHHHhccCCCeEEEC---CcchhhhccCCCHHHHHHhc----CCCCCcEEEEeCCCCHHH--------HHHHHH-
Confidence 223344321111 11111110111122222222 33 578999999998764 234566
Q ss_pred HHHHHHHHHhhhCC---CEEEeCCchh-HHHHHHHHh
Q 015881 339 QVWAEIANGLREFR---PLFVIPHEKE-REGVEDVVG 371 (399)
Q Consensus 339 e~faeLa~~L~~~~---~VvliGgp~E-~e~aeeI~~ 371 (399)
-|.+.++.|.++. ++++...+.+ .+..+++..
T Consensus 204 -~~l~aa~~l~~~~p~l~fvvp~a~~~~~~~i~~~~~ 239 (373)
T PF02684_consen 204 -IFLEAAKLLKKQRPDLQFVVPVAPEVHEELIEEILA 239 (373)
T ss_pred -HHHHHHHHHHHhCCCeEEEEecCCHHHHHHHHHHHH
Confidence 7899999998764 4444444443 343555543
No 18
>PRK01021 lpxB lipid-A-disaccharide synthase; Reviewed
Probab=93.04 E-value=1.3 Score=48.15 Aligned_cols=211 Identities=10% Similarity=-0.041 Sum_probs=112.5
Q ss_pred cEEEEEcCCChhHHHhHHHHHHHHHHHCCCcEEEEEEcCCchHhhhcCCCCCEEEEecCCC--C----CCChH----HHH
Q 015881 123 RRCCCIISGGVYENLLFFPAIQLLKDRYPGVLIDVIASARGKQTFELNKNVRWANVYDLDD--D----WPEPA----EYT 192 (399)
Q Consensus 123 ~rILIIr~~~IGDvVLttPalraLK~~yP~A~IdvLv~~~~~~lle~nP~ID~Vi~~d~k~--~----~~~~~----~~~ 192 (399)
.||+|+--..=||+. ..-++++||+++|++++.-+..+.-++. +++-++..+.-. + .+.+. .+.
T Consensus 227 ~kIfI~AGE~SGDlh-gA~Li~aLk~~~P~i~~~GvGG~~M~aa-----G~e~l~d~~eLsVmG~~EVL~~l~~l~~~~~ 300 (608)
T PRK01021 227 TSCFISAGEHSGDTL-GGNLLKEIKALYPDIHCFGVGGPQMRAE-----GFHPLFNMEEFQVSGFWEVLLALFKLWYRYR 300 (608)
T ss_pred CeEEEEeccccHHHH-HHHHHHHHHhcCCCcEEEEEccHHHHhC-----cCcccCChHHhhhhhHHHHHHHHHHHHHHHH
Confidence 589999988889965 5567999999999999999887765532 112121111000 0 01111 223
Q ss_pred HHHHHhhhCCCcEEE--EcCCCChHHHHHHHHhCC-CeEEEecCCCccccccccccceeeccCcCCchhhHHHHHHH---
Q 015881 193 DILGVMKNRYYDMVL--STKLAGLGHAAFLFMTTA-RDRVSYIYPNVNAAGAGLLLSETFTAESMNLSERGYNMYEQ--- 266 (399)
Q Consensus 193 ~l~~~LR~~~YDlvI--dl~~~~~rsAll~~LsgA-~~RIGy~~~~~~~~~~~~~lt~~v~~~~~~~~~h~v~~yl~--- 266 (399)
++.+.+++++.|++| |..+-.++-|-.++-.|. ...|=|..|.+=.+..+ ++ +.+.+|.+
T Consensus 301 ~l~~~i~~~kPD~vIlID~PgFNlrLAK~lkk~Gi~ipviyYVsPqVWAWR~~-----Ri---------kki~k~vD~ll 366 (608)
T PRK01021 301 KLYKTILKTNPRTVICIDFPDFHFLLIKKLRKRGYKGKIVHYVCPSIWAWRPK-----RK---------TILEKYLDLLL 366 (608)
T ss_pred HHHHHHHhcCCCEEEEeCCCCCCHHHHHHHHhcCCCCCEEEEECccceeeCcc-----hH---------HHHHHHhhhhe
Confidence 455668889999998 444433677777777775 12456665543111110 11 11222222
Q ss_pred --------HHHHcCCCCCCCCCCCCCCce-eecCHHHHHHHHHHHHHhCCC-CCCeEEEEcCCCCccccccCCCCCCCCC
Q 015881 267 --------MVDWLGRPFRSVPRHPVPPLR-VSISRRLKEVVAEKYKNAGAE-QGKYIVIHGIESDSKASMQSRGDTDSLL 336 (399)
Q Consensus 267 --------LL~~LGi~~~~~p~~~~p~l~-i~is~e~~~~a~~~l~~~gl~-~~~~IvIhPgas~~~~~~k~rg~~~KrW 336 (399)
+.+.-|++..-+- .|-++ +... .+.. +..++.|++ +++.|++-|||+.+. ..+.+
T Consensus 367 ~IfPFE~~~y~~~gv~v~yVG---HPL~d~i~~~-~~~~---~~r~~lgl~~~~~iIaLLPGSR~~E--------I~rll 431 (608)
T PRK01021 367 LILPFEQNLFKDSPLRTVYLG---HPLVETISSF-SPNL---SWKEQLHLPSDKPIVAAFPGSRRGD--------ILRNL 431 (608)
T ss_pred ecCccCHHHHHhcCCCeEEEC---CcHHhhcccC-CCHH---HHHHHcCCCCCCCEEEEECCCCHHH--------HHHHH
Confidence 1223354322111 11111 1100 1111 224456775 568999999998764 34567
Q ss_pred CHHHHHHHHH--HhhhCCCEEEeCC-chhHHHHHHHH
Q 015881 337 PIQVWAEIAN--GLREFRPLFVIPH-EKEREGVEDVV 370 (399)
Q Consensus 337 P~e~faeLa~--~L~~~~~VvliGg-p~E~e~aeeI~ 370 (399)
| -+.+.|+ .+.++.++++... +.+++..+++.
T Consensus 432 P--v~l~aa~~~~l~~~l~fvvp~a~~~~~~~i~~~~ 466 (608)
T PRK01021 432 T--IQVQAFLASSLASTHQLLVSSANPKYDHLILEVL 466 (608)
T ss_pred H--HHHHHHHHHHhccCeEEEEecCchhhHHHHHHHH
Confidence 7 6778877 5654433444323 33445555544
No 19
>PRK12446 undecaprenyldiphospho-muramoylpentapeptide beta-N-acetylglucosaminyltransferase; Reviewed
Probab=91.86 E-value=5.9 Score=40.03 Aligned_cols=104 Identities=13% Similarity=0.038 Sum_probs=65.7
Q ss_pred ccEEEEEcCCChhHHHhHHHHHHHHHHHCCCcEEEEEEcCCch--HhhhcCCCCCEEEEecCCC-----CCCC-------
Q 015881 122 VRRCCCIISGGVYENLLFFPAIQLLKDRYPGVLIDVIASARGK--QTFELNKNVRWANVYDLDD-----DWPE------- 187 (399)
Q Consensus 122 v~rILIIr~~~IGDvVLttPalraLK~~yP~A~IdvLv~~~~~--~lle~nP~ID~Vi~~d~k~-----~~~~------- 187 (399)
|+||+|.--+-=|=+.=+.-+.++|++ ++.+|.|++....- .++.... ++ .+.++... .++.
T Consensus 1 ~~~i~~~~GGTGGHi~Pala~a~~l~~--~g~~v~~vg~~~~~e~~l~~~~g-~~-~~~~~~~~l~~~~~~~~~~~~~~~ 76 (352)
T PRK12446 1 MKKIVFTGGGSAGHVTPNLAIIPYLKE--DNWDISYIGSHQGIEKTIIEKEN-IP-YYSISSGKLRRYFDLKNIKDPFLV 76 (352)
T ss_pred CCeEEEEcCCcHHHHHHHHHHHHHHHh--CCCEEEEEECCCccccccCcccC-Cc-EEEEeccCcCCCchHHHHHHHHHH
Confidence 467777777777777767777778886 58999999977654 3443322 33 22332211 1111
Q ss_pred hHHHHHHHHHhhhCCCcEEEEcCCC-ChHHHHHHHHhCCCeEE
Q 015881 188 PAEYTDILGVMKNRYYDMVLSTKLA-GLGHAAFLFMTTARDRV 229 (399)
Q Consensus 188 ~~~~~~l~~~LR~~~YDlvIdl~~~-~~rsAll~~LsgA~~RI 229 (399)
+..+++.++.+|+.+.|+||.+-+. +.-..+.+++.|+|..+
T Consensus 77 ~~~~~~~~~i~~~~kPdvvi~~Ggy~s~p~~~aa~~~~~p~~i 119 (352)
T PRK12446 77 MKGVMDAYVRIRKLKPDVIFSKGGFVSVPVVIGGWLNRVPVLL 119 (352)
T ss_pred HHHHHHHHHHHHhcCCCEEEecCchhhHHHHHHHHHcCCCEEE
Confidence 1234455667999999999986543 12247789999999765
No 20
>TIGR01133 murG undecaprenyldiphospho-muramoylpentapeptide beta-N-acetylglucosaminyltransferase. RL J Bacteriol 1993 Mar;175(6):1841-3
Probab=91.71 E-value=3.1 Score=40.76 Aligned_cols=101 Identities=10% Similarity=-0.071 Sum_probs=63.6
Q ss_pred cEEEEEcCCChhHHHhHHHHHHHHHHHCCCcEEEEEEcCCch--HhhhcCCCCCEEEEecCCCCC-CC-----------h
Q 015881 123 RRCCCIISGGVYENLLFFPAIQLLKDRYPGVLIDVIASARGK--QTFELNKNVRWANVYDLDDDW-PE-----------P 188 (399)
Q Consensus 123 ~rILIIr~~~IGDvVLttPalraLK~~yP~A~IdvLv~~~~~--~lle~nP~ID~Vi~~d~k~~~-~~-----------~ 188 (399)
|||+|+--+.-||+-.+..++++|+++ +.++++++.+... .+++. ..+ +++.++..... .. +
T Consensus 1 ~~i~~~~g~~~g~~~~~~~La~~L~~~--g~eV~vv~~~~~~~~~~~~~-~g~-~~~~i~~~~~~~~~~~~~l~~~~~~~ 76 (348)
T TIGR01133 1 KKVVLAAGGTGGHIFPALAVAEELIKR--GVEVLWLGTKRGLEKRLVPK-AGI-EFYFIPVGGLRRKGSFRLIKTPLKLL 76 (348)
T ss_pred CeEEEEeCccHHHHhHHHHHHHHHHhC--CCEEEEEeCCCcchhccccc-CCC-ceEEEeccCcCCCChHHHHHHHHHHH
Confidence 689999888889998778999999987 4689999875432 22221 223 23333321100 01 1
Q ss_pred HHHHHHHHHhhhCCCcEEEEcCCCC-hHHHHHHHHhCCCe
Q 015881 189 AEYTDILGVMKNRYYDMVLSTKLAG-LGHAAFLFMTTARD 227 (399)
Q Consensus 189 ~~~~~l~~~LR~~~YDlvIdl~~~~-~rsAll~~LsgA~~ 227 (399)
..+.++.+.+|+.++|+++...... +...+..++.|.+.
T Consensus 77 ~~~~~l~~~i~~~~pDvVi~~~~~~~~~~~~~~~~~~~p~ 116 (348)
T TIGR01133 77 KAVFQARRILKKFKPDAVIGFGGYVSGPAGLAAKLLGIPL 116 (348)
T ss_pred HHHHHHHHHHHhcCCCEEEEcCCcccHHHHHHHHHcCCCE
Confidence 2234566678999999999875431 33445677778775
No 21
>PF13477 Glyco_trans_4_2: Glycosyl transferase 4-like
Probab=91.34 E-value=4 Score=34.46 Aligned_cols=99 Identities=12% Similarity=0.093 Sum_probs=60.5
Q ss_pred EEEEEcCCChhHHHhHHHHHHHHHHHCCCcEEEEEEcCCchHhhhcCCCCCEEEEecCCC-CCCChHHHHHHHHHhhhCC
Q 015881 124 RCCCIISGGVYENLLFFPAIQLLKDRYPGVLIDVIASARGKQTFELNKNVRWANVYDLDD-DWPEPAEYTDILGVMKNRY 202 (399)
Q Consensus 124 rILIIr~~~IGDvVLttPalraLK~~yP~A~IdvLv~~~~~~lle~nP~ID~Vi~~d~k~-~~~~~~~~~~l~~~LR~~~ 202 (399)
|||+|-... -.+....++.|+++ +.++++++.....+-......| +++.++.+. .......+.++.+.+++.+
T Consensus 1 KIl~i~~~~---~~~~~~~~~~L~~~--g~~V~ii~~~~~~~~~~~~~~i-~~~~~~~~~k~~~~~~~~~~l~k~ik~~~ 74 (139)
T PF13477_consen 1 KILLIGNTP---STFIYNLAKELKKR--GYDVHIITPRNDYEKYEIIEGI-KVIRLPSPRKSPLNYIKYFRLRKIIKKEK 74 (139)
T ss_pred CEEEEecCc---HHHHHHHHHHHHHC--CCEEEEEEcCCCchhhhHhCCe-EEEEecCCCCccHHHHHHHHHHHHhccCC
Confidence 567765544 23567889999998 7799999986554444444444 344444211 1111123457788899999
Q ss_pred CcEEEEcCCC--ChHHHHHHHHhC-CCeE
Q 015881 203 YDMVLSTKLA--GLGHAAFLFMTT-ARDR 228 (399)
Q Consensus 203 YDlvIdl~~~--~~rsAll~~Lsg-A~~R 228 (399)
||++..-... +....++.++.| .+..
T Consensus 75 ~DvIh~h~~~~~~~~~~l~~~~~~~~~~i 103 (139)
T PF13477_consen 75 PDVIHCHTPSPYGLFAMLAKKLLKNKKVI 103 (139)
T ss_pred CCEEEEecCChHHHHHHHHHHHcCCCCEE
Confidence 9999755433 244555667778 4433
No 22
>COG0763 LpxB Lipid A disaccharide synthetase [Cell envelope biogenesis, outer membrane]
Probab=90.83 E-value=4.9 Score=41.35 Aligned_cols=215 Identities=16% Similarity=0.139 Sum_probs=113.2
Q ss_pred ccEEEEEcCCChhHHHhHHHHHHHHHHHCCCcEEEEEEcCCchHh-hhcCCCCCEEEEecC----CCCCCChHHHHHHHH
Q 015881 122 VRRCCCIISGGVYENLLFFPAIQLLKDRYPGVLIDVIASARGKQT-FELNKNVRWANVYDL----DDDWPEPAEYTDILG 196 (399)
Q Consensus 122 v~rILIIr~~~IGDvVLttPalraLK~~yP~A~IdvLv~~~~~~l-le~nP~ID~Vi~~d~----k~~~~~~~~~~~l~~ 196 (399)
++||.|+--..=||++.+- ++++||++||++++.=+..+.-++. ++..=+..++=+.-. +.-.+-++.+.++++
T Consensus 1 ~~ki~i~AGE~SGDllGa~-LikaLk~~~~~~efvGvgG~~m~aeG~~sl~~~~elsvmGf~EVL~~lp~llk~~~~~~~ 79 (381)
T COG0763 1 MLKIALSAGEASGDLLGAG-LIKALKARYPDVEFVGVGGEKMEAEGLESLFDMEELSVMGFVEVLGRLPRLLKIRRELVR 79 (381)
T ss_pred CceEEEEecccchhhHHHH-HHHHHHhhCCCeEEEEeccHHHHhccCccccCHHHHHHhhHHHHHHHHHHHHHHHHHHHH
Confidence 4799999999999987764 7999999999999888876543321 111100011100000 000001122345566
Q ss_pred HhhhCCCcEEEEcCCC--ChHHHHHHHHhC--CCeEEEecCCCccccccccccceeeccCcCCchhhHHHHHHHHH----
Q 015881 197 VMKNRYYDMVLSTKLA--GLGHAAFLFMTT--ARDRVSYIYPNVNAAGAGLLLSETFTAESMNLSERGYNMYEQMV---- 268 (399)
Q Consensus 197 ~LR~~~YDlvIdl~~~--~~rsAll~~Lsg--A~~RIGy~~~~~~~~~~~~~lt~~v~~~~~~~~~h~v~~yl~LL---- 268 (399)
.+...+.|++|-...- ..+-+--++-.| .| .|-|..|++ |++ .. .+ .+.+..|.+.+
T Consensus 80 ~i~~~kpD~~i~IDsPdFnl~vak~lrk~~p~i~-iihYV~PsV---WAW---r~----~R----a~~i~~~~D~lLail 144 (381)
T COG0763 80 YILANKPDVLILIDSPDFNLRVAKKLRKAGPKIK-IIHYVSPSV---WAW---RP----KR----AVKIAKYVDHLLAIL 144 (381)
T ss_pred HHHhcCCCEEEEeCCCCCchHHHHHHHHhCCCCC-eEEEECcce---eee---ch----hh----HHHHHHHhhHeeeec
Confidence 6778999999854433 256666677777 44 567776654 111 00 00 12233333322
Q ss_pred -------HHcCCCCCCCCCCCCCCc--eeecCHHHHHHHHHHHHHhCCC-CCCeEEEEcCCCCccccccCCCCCCCCCCH
Q 015881 269 -------DWLGRPFRSVPRHPVPPL--RVSISRRLKEVVAEKYKNAGAE-QGKYIVIHGIESDSKASMQSRGDTDSLLPI 338 (399)
Q Consensus 269 -------~~LGi~~~~~p~~~~p~l--~i~is~e~~~~a~~~l~~~gl~-~~~~IvIhPgas~~~~~~k~rg~~~KrWP~ 338 (399)
+.+|++...+- .++ ++.+ ..+++.++ ++.+++ +++++++-|||+.+. +.+. .
T Consensus 145 PFE~~~y~k~g~~~~yVG----Hpl~d~i~~-~~~r~~ar---~~l~~~~~~~~lalLPGSR~sE--------I~rl--~ 206 (381)
T COG0763 145 PFEPAFYDKFGLPCTYVG----HPLADEIPL-LPDREAAR---EKLGIDADEKTLALLPGSRRSE--------IRRL--L 206 (381)
T ss_pred CCCHHHHHhcCCCeEEeC----Chhhhhccc-cccHHHHH---HHhCCCCCCCeEEEecCCcHHH--------HHHH--H
Confidence 23344311110 011 1111 11233333 345666 578999999998875 2233 3
Q ss_pred HHHHHHHHHhhhCC---CEEEe-CCchhHHHHHHHH
Q 015881 339 QVWAEIANGLREFR---PLFVI-PHEKEREGVEDVV 370 (399)
Q Consensus 339 e~faeLa~~L~~~~---~Vvli-Ggp~E~e~aeeI~ 370 (399)
+-|.+.++.|.++. .+++- -.+.++...++..
T Consensus 207 ~~f~~a~~~l~~~~~~~~~vlp~~~~~~~~~~~~~~ 242 (381)
T COG0763 207 PPFVQAAQELKARYPDLKFVLPLVNAKYRRIIEEAL 242 (381)
T ss_pred HHHHHHHHHHHhhCCCceEEEecCcHHHHHHHHHHh
Confidence 47899999998653 55543 3444344444443
No 23
>PRK00726 murG undecaprenyldiphospho-muramoylpentapeptide beta-N- acetylglucosaminyltransferase; Provisional
Probab=90.68 E-value=2.6 Score=41.83 Aligned_cols=104 Identities=11% Similarity=-0.046 Sum_probs=66.2
Q ss_pred ccEEEEEcCCChhHHHhHHHHHHHHHHHCCCcEEEEEEcCCc--hHhhhcCCCCCEEEEecCCC--CCC----------C
Q 015881 122 VRRCCCIISGGVYENLLFFPAIQLLKDRYPGVLIDVIASARG--KQTFELNKNVRWANVYDLDD--DWP----------E 187 (399)
Q Consensus 122 v~rILIIr~~~IGDvVLttPalraLK~~yP~A~IdvLv~~~~--~~lle~nP~ID~Vi~~d~k~--~~~----------~ 187 (399)
+|||+|+-.+.=|+.-...-++++|+++ +.++++++.+.. ...++. ..++ ++.++... ... .
T Consensus 1 ~~~i~i~~~g~gG~~~~~~~la~~L~~~--g~ev~vv~~~~~~~~~~~~~-~g~~-~~~~~~~~~~~~~~~~~l~~~~~~ 76 (357)
T PRK00726 1 MKKILLAGGGTGGHVFPALALAEELKKR--GWEVLYLGTARGMEARLVPK-AGIE-FHFIPSGGLRRKGSLANLKAPFKL 76 (357)
T ss_pred CcEEEEEcCcchHhhhHHHHHHHHHHhC--CCEEEEEECCCchhhhcccc-CCCc-EEEEeccCcCCCChHHHHHHHHHH
Confidence 5899999764449998888999999987 779999987663 233332 2332 33333211 000 1
Q ss_pred hHHHHHHHHHhhhCCCcEEEEcCCC-ChHHHHHHHHhCCCeEE
Q 015881 188 PAEYTDILGVMKNRYYDMVLSTKLA-GLGHAAFLFMTTARDRV 229 (399)
Q Consensus 188 ~~~~~~l~~~LR~~~YDlvIdl~~~-~~rsAll~~LsgA~~RI 229 (399)
+..+.++.+.+|+.++|+++..... .+...+..++.+.|.-+
T Consensus 77 ~~~~~~~~~~ik~~~pDvv~~~~~~~~~~~~~~~~~~~~p~v~ 119 (357)
T PRK00726 77 LKGVLQARKILKRFKPDVVVGFGGYVSGPGGLAARLLGIPLVI 119 (357)
T ss_pred HHHHHHHHHHHHhcCCCEEEECCCcchhHHHHHHHHcCCCEEE
Confidence 2334556667888899999988532 24455667777777643
No 24
>cd04951 GT1_WbdM_like This family is most closely related to the GT1 family of glycosyltransferases and is named after WbdM in Escherichia coli. In general glycosyltransferases catalyze the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming glycosidic bonds. The acceptor molecule can be a lipid, a protein, a heterocyclic compound, or another carbohydrate residue. This group of glycosyltransferases is most closely related to the previously defined glycosyltransferase family 1 (GT1). The members of this family may transfer UDP, ADP, GDP, or CMP linked sugars. The diverse enzymatic activities among members of this family reflect a wide range of biological functions. The protein structure available for this family has the GTB topology, one of the two protein topologies observed for nucleotide-sugar-dependent glycosyltransferases. GTB proteins have distinct N- and C- terminal domains each containing a typical Rossmann fold. The two domains have
Probab=90.54 E-value=14 Score=35.62 Aligned_cols=83 Identities=8% Similarity=0.085 Sum_probs=42.7
Q ss_pred EEEEEcCC-Chh-HHHhHHHHHHHHHHHCCCcEEEEEEcCCchHhhhcCCCCCEEEEecCCC-CCCChHHHHHHHHHhhh
Q 015881 124 RCCCIISG-GVY-ENLLFFPAIQLLKDRYPGVLIDVIASARGKQTFELNKNVRWANVYDLDD-DWPEPAEYTDILGVMKN 200 (399)
Q Consensus 124 rILIIr~~-~IG-DvVLttPalraLK~~yP~A~IdvLv~~~~~~lle~nP~ID~Vi~~d~k~-~~~~~~~~~~l~~~LR~ 200 (399)
|||++..+ +.| -...+.-+.+.|+++ +.++++++..... ..+....+..++.+.... .+..+..+..+.+.+++
T Consensus 1 ~il~~~~~~~~gG~~~~~~~l~~~L~~~--g~~v~v~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 77 (360)
T cd04951 1 KILYVITGLGLGGAEKQVVDLADQFVAK--GHQVAIISLTGES-EVKPPIDATIILNLNMSKNPLSFLLALWKLRKILRQ 77 (360)
T ss_pred CeEEEecCCCCCCHHHHHHHHHHhcccC--CceEEEEEEeCCC-CccchhhccceEEecccccchhhHHHHHHHHHHHHh
Confidence 47777553 233 344455778888776 5567777643221 112222222222222211 11223334556677888
Q ss_pred CCCcEEEEc
Q 015881 201 RYYDMVLST 209 (399)
Q Consensus 201 ~~YDlvIdl 209 (399)
.++|++...
T Consensus 78 ~~pdiv~~~ 86 (360)
T cd04951 78 FKPDVVHAH 86 (360)
T ss_pred cCCCEEEEc
Confidence 999988763
No 25
>PF04413 Glycos_transf_N: 3-Deoxy-D-manno-octulosonic-acid transferase (kdotransferase); InterPro: IPR007507 This is a domain found in proteins that transfer activated sugars to a variety of substrates, including glycogen, fructose-6-phosphate and lipopolysaccharides. Proteins bearing this domain transfer UDP, ADP, GDP or CMP linked sugars. This region is flanked at the N terminus by a signal peptide and at the C terminus by a glycosyl transferase group 1 domain (IPR001296 from INTERPRO). The eukaryotic glycogen synthases may be distant members of this bacterial family [].; GO: 0005529 sugar binding, 0016740 transferase activity, 0005975 carbohydrate metabolic process; PDB: 2XCI_A 2XCU_B.
Probab=89.69 E-value=1.2 Score=41.25 Aligned_cols=97 Identities=18% Similarity=0.082 Sum_probs=53.8
Q ss_pred EEEEEcCCChhHHHhHHHHHHHHHHHCCCcEEEEEEc-CCchHhhhcC--CCCCEEEEecCCCCCCChHHHHHHHHHhhh
Q 015881 124 RCCCIISGGVYENLLFFPAIQLLKDRYPGVLIDVIAS-ARGKQTFELN--KNVRWANVYDLDDDWPEPAEYTDILGVMKN 200 (399)
Q Consensus 124 rILIIr~~~IGDvVLttPalraLK~~yP~A~IdvLv~-~~~~~lle~n--P~ID~Vi~~d~k~~~~~~~~~~~l~~~LR~ 200 (399)
+.+-|.-.++|++..+.|+++.|++++|+.+|-+-+. +.+.+.++.. +.|..+ .++.+ .+....++++.+
T Consensus 22 ~~iWiHa~SvGE~~a~~~Li~~l~~~~p~~~illT~~T~tg~~~~~~~~~~~v~~~-~~P~D----~~~~~~rfl~~~-- 94 (186)
T PF04413_consen 22 PLIWIHAASVGEVNAARPLIKRLRKQRPDLRILLTTTTPTGREMARKLLPDRVDVQ-YLPLD----FPWAVRRFLDHW-- 94 (186)
T ss_dssp T-EEEE-SSHHHHHHHHHHHHHHTT---TS-EEEEES-CCHHHHHHGG-GGG-SEE-E---S----SHHHHHHHHHHH--
T ss_pred CcEEEEECCHHHHHHHHHHHHHHHHhCCCCeEEEEecCCchHHHHHHhCCCCeEEE-EeCcc----CHHHHHHHHHHh--
Confidence 6777889999999999999999999999999988885 4445554433 345533 35432 233445555555
Q ss_pred CCCcEEEEcCCCChHHHHHHHHhCCCeEE
Q 015881 201 RYYDMVLSTKLAGLGHAAFLFMTTARDRV 229 (399)
Q Consensus 201 ~~YDlvIdl~~~~~rsAll~~LsgA~~RI 229 (399)
+.|++|-+... +.-.++..+....+.+
T Consensus 95 -~P~~~i~~EtE-lWPnll~~a~~~~ip~ 121 (186)
T PF04413_consen 95 -RPDLLIWVETE-LWPNLLREAKRRGIPV 121 (186)
T ss_dssp ---SEEEEES-----HHHHHH-----S-E
T ss_pred -CCCEEEEEccc-cCHHHHHHHhhcCCCE
Confidence 47999999998 7788877665444333
No 26
>TIGR03088 stp2 sugar transferase, PEP-CTERM/EpsH1 system associated. Members of this family include a match to the pfam00534 Glycosyl transferases group 1 domain. Nearly all are found in species that encode the PEP-CTERM/exosortase system predicted to act in protein sorting in a number of Gram-negative bacteria. In particular, these transferases are found proximal to a particular variant of exosortase, EpsH1, which appears to travel with a conserved group of genes summarized by Genome Property GenProp0652. The nature of the sugar transferase reaction catalyzed by members of this clade is unknown and may conceivably be variable with respect to substrate by species, but we hypothesize a conserved substrate.
Probab=89.06 E-value=16 Score=36.05 Aligned_cols=103 Identities=14% Similarity=0.032 Sum_probs=56.5
Q ss_pred cEEEEEcCC-ChhHH-HhHHHHHHHHHHHCCCcEEEEEEcCCchHhhhcC--CCCCEEEEecCCCCCCChHHHHHHHHHh
Q 015881 123 RRCCCIISG-GVYEN-LLFFPAIQLLKDRYPGVLIDVIASARGKQTFELN--KNVRWANVYDLDDDWPEPAEYTDILGVM 198 (399)
Q Consensus 123 ~rILIIr~~-~IGDv-VLttPalraLK~~yP~A~IdvLv~~~~~~lle~n--P~ID~Vi~~d~k~~~~~~~~~~~l~~~L 198 (399)
.|||.|-.+ ..|-+ -+...+++.|.+. +.++.+++.....++.+.. -+| +++.+..... ..+..+.++.+.+
T Consensus 2 ~~il~ii~~~~~GG~e~~~~~l~~~l~~~--~~~~~v~~~~~~~~~~~~~~~~~i-~~~~~~~~~~-~~~~~~~~l~~~l 77 (374)
T TIGR03088 2 PLIVHVVYRFDVGGLENGLVNLINHLPAD--RYRHAVVALTEVSAFRKRIQRPDV-AFYALHKQPG-KDVAVYPQLYRLL 77 (374)
T ss_pred ceEEEEeCCCCCCcHHHHHHHHHhhcccc--ccceEEEEcCCCChhHHHHHhcCc-eEEEeCCCCC-CChHHHHHHHHHH
Confidence 356655433 34655 5556777777665 3355566533222332211 133 3555554322 3344567788889
Q ss_pred hhCCCcEEEEcCCCChHHHHHHHHhCCCeEE
Q 015881 199 KNRYYDMVLSTKLAGLGHAAFLFMTTARDRV 229 (399)
Q Consensus 199 R~~~YDlvIdl~~~~~rsAll~~LsgA~~RI 229 (399)
++.++|++..-........+++++.+.+.++
T Consensus 78 ~~~~~Divh~~~~~~~~~~~~~~~~~~~~~i 108 (374)
T TIGR03088 78 RQLRPDIVHTRNLAALEAQLPAALAGVPARI 108 (374)
T ss_pred HHhCCCEEEEcchhHHHHHHHHHhcCCCeEE
Confidence 9999999865322212334566777777655
No 27
>cd03786 GT1_UDP-GlcNAc_2-Epimerase Bacterial members of the UDP-N-Acetylglucosamine (GlcNAc) 2-Epimerase family are known to catalyze the reversible interconversion of UDP-GlcNAc and UDP-N-acetylmannosamine (UDP-ManNAc). The enzyme serves to produce an activated form of ManNAc residues (UDP-ManNAc) for use in the biosynthesis of a variety of cell surface polysaccharides; The mammalian enzyme is bifunctional, catalyzing both the inversion of stereochemistry at C-2 and the hydrolysis of the UDP-sugar linkage to generate free ManNAc. It also catalyzes the phosphorylation of ManNAc to generate ManNAc 6-phosphate, a precursor to salic acids. In mammals, sialic acids are found at the termini of oligosaccharides in a large variety of cell surface glycoconjugates and are key mediators of cell-cell recognition events. Mutations in human members of this family have been associated with Sialuria, a rare disease caused by the disorders of sialic acid metabolism. This family belongs to the GT-B st
Probab=88.88 E-value=7.6 Score=38.28 Aligned_cols=103 Identities=17% Similarity=0.175 Sum_probs=57.9
Q ss_pred EEEEEcCCChhHHHhHHHHHHHHHHHCCCcEEEEEEcCC-chH-----hhhc--CCCCCEEEEecCCCC---CCChHHHH
Q 015881 124 RCCCIISGGVYENLLFFPAIQLLKDRYPGVLIDVIASAR-GKQ-----TFEL--NKNVRWANVYDLDDD---WPEPAEYT 192 (399)
Q Consensus 124 rILIIr~~~IGDvVLttPalraLK~~yP~A~IdvLv~~~-~~~-----lle~--nP~ID~Vi~~d~k~~---~~~~~~~~ 192 (399)
||++| ++--=|.+...|++++|++. |+.++.+++.-. ..+ +.+. ....+.-+....... ........
T Consensus 1 ~i~~~-~gtr~~~~~~~pl~~~l~~~-~~~~~~~~~tg~h~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~ 78 (363)
T cd03786 1 KILVV-TGTRPEYIKLAPLIRALKKD-PGFELVLVVTGQHYDMEMGVTFFEILFIIKPDYDLLLGSDSQSLGAQTAGLLI 78 (363)
T ss_pred CEEEE-EecCHHHHHHHHHHHHHhcC-CCCCEEEEEeCCCCChhhhHHHHHhhCCCCCCEEEecCCCCCCHHHHHHHHHH
Confidence 34444 45556788899999999986 899999776532 111 2221 111121111111110 00122345
Q ss_pred HHHHHhhhCCCcEEEEcCCC--ChHHHHHHHHhCCCeE
Q 015881 193 DILGVMKNRYYDMVLSTKLA--GLGHAAFLFMTTARDR 228 (399)
Q Consensus 193 ~l~~~LR~~~YDlvIdl~~~--~~rsAll~~LsgA~~R 228 (399)
++.+.+++.++|+|+..... .+-.++.+++.|+|.-
T Consensus 79 ~l~~~l~~~~pDvV~~~g~~~~~~~~~~aa~~~~iPvv 116 (363)
T cd03786 79 GLEAVLLEEKPDLVLVLGDTNETLAAALAAFKLGIPVA 116 (363)
T ss_pred HHHHHHHHhCCCEEEEeCCchHHHHHHHHHHHcCCCEE
Confidence 67778899999999876322 1224556777888844
No 28
>PRK13609 diacylglycerol glucosyltransferase; Provisional
Probab=87.80 E-value=16 Score=36.54 Aligned_cols=37 Identities=3% Similarity=-0.185 Sum_probs=22.8
Q ss_pred ccEEEEEcCCCh-hHHHhHHHHHHHHHHHCCCcEEEEEEc
Q 015881 122 VRRCCCIISGGV-YENLLFFPAIQLLKDRYPGVLIDVIAS 160 (399)
Q Consensus 122 v~rILIIr~~~I-GDvVLttPalraLK~~yP~A~IdvLv~ 160 (399)
.|||||+-.+.- |=.--+.-+.++|+++.++ +.+++.
T Consensus 4 ~~rili~t~~~G~GH~~~a~al~~~l~~~g~~--~~~~~d 41 (380)
T PRK13609 4 NPKVLILTAHYGNGHVQVAKTLEQTFRQKGIK--DVIVCD 41 (380)
T ss_pred CCeEEEEEcCCCchHHHHHHHHHHHHHhcCCC--cEEEEE
Confidence 589999986663 3344444666777776543 455543
No 29
>cd03808 GT1_cap1E_like This family is most closely related to the GT1 family of glycosyltransferases. cap1E in Streptococcus pneumoniae is required for the synthesis of type 1 capsular polysaccharides.
Probab=87.54 E-value=5.3 Score=37.68 Aligned_cols=104 Identities=12% Similarity=0.069 Sum_probs=64.0
Q ss_pred EEEEEcCCChhHHHhHHHHHHHHHHHCCCcEEEEEEcCCchHhhhcCCCCCEEEEecCCC----CCCChHHHHHHHHHhh
Q 015881 124 RCCCIISGGVYENLLFFPAIQLLKDRYPGVLIDVIASARGKQTFELNKNVRWANVYDLDD----DWPEPAEYTDILGVMK 199 (399)
Q Consensus 124 rILIIr~~~IGDvVLttPalraLK~~yP~A~IdvLv~~~~~~lle~nP~ID~Vi~~d~k~----~~~~~~~~~~l~~~LR 199 (399)
|||+|....-|.......+++.|++. +.++++++......-......++ ++.++... .+.....+..+.+.++
T Consensus 1 kIl~i~~~~~g~~~~~~~l~~~L~~~--g~~v~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 77 (359)
T cd03808 1 KILHIVTVDGGLYSFRLPLIKALRAA--GYEVHVVAPPGDELEELEALGVK-VIPIPLDRRGINPFKDLKALLRLYRLLR 77 (359)
T ss_pred CeeEEEecchhHHHHHHHHHHHHHhc--CCeeEEEecCCCcccccccCCce-EEeccccccccChHhHHHHHHHHHHHHH
Confidence 68999888889999999999999776 77899998765543211222332 33333221 1122334556777888
Q ss_pred hCCCcEEEEcCCCC-hHHHHHHHHhCCCeEEE
Q 015881 200 NRYYDMVLSTKLAG-LGHAAFLFMTTARDRVS 230 (399)
Q Consensus 200 ~~~YDlvIdl~~~~-~rsAll~~LsgA~~RIG 230 (399)
+.++|+++...... .-..+..++.+.+..+-
T Consensus 78 ~~~~dvv~~~~~~~~~~~~~~~~~~~~~~~i~ 109 (359)
T cd03808 78 KERPDIVHTHTPKPGILGRLAARLAGVPKVIY 109 (359)
T ss_pred hcCCCEEEEccccchhHHHHHHHHcCCCCEEE
Confidence 99999998654321 22333344345554443
No 30
>TIGR00661 MJ1255 conserved hypothetical protein. This model represents nearly the full length of MJ1255 from Methanococcus jannaschii and of an unpublished protein from Vibrio cholerae, as well as the C-terminal half of a protein from Methanobacterium thermoautotrophicum. A small region (~50 amino acids) within the domain appears related to a family of sugar transferases.
Probab=87.34 E-value=5.1 Score=39.54 Aligned_cols=100 Identities=12% Similarity=0.016 Sum_probs=65.8
Q ss_pred EEEE-EcCCChhHHHhHHHHHHHHHHHCCCcEEEEEEcCCchHhhhcC--CCCCEE----EEe-cCC-CCCCCh------
Q 015881 124 RCCC-IISGGVYENLLFFPAIQLLKDRYPGVLIDVIASARGKQTFELN--KNVRWA----NVY-DLD-DDWPEP------ 188 (399)
Q Consensus 124 rILI-Ir~~~IGDvVLttPalraLK~~yP~A~IdvLv~~~~~~lle~n--P~ID~V----i~~-d~k-~~~~~~------ 188 (399)
|||+ +.-.++|=+.=..+++++|++ +.+|.+++......+++.. +.+..+ +.. +.+ +.+..+
T Consensus 1 ril~~~~g~G~GH~~r~~ala~~L~~---g~ev~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~l~~~~~~ 77 (321)
T TIGR00661 1 KILYSVCGEGFGHTTRSVAIGEALKN---DYEVSYIASGRSKNYISKYGFKVFETFPGIKLKGEDGKVNIVKTLRNKEYS 77 (321)
T ss_pred CEEEEEeccCccHHHHHHHHHHHHhC---CCeEEEEEcCCHHHhhhhhcCcceeccCCceEeecCCcCcHHHHHHhhccc
Confidence 5666 677788999999999999996 7789999877766665543 111111 111 111 001111
Q ss_pred --HHHHHHHHHhhhCCCcEEEEcCCCChHHHHHHHHhCCCeE
Q 015881 189 --AEYTDILGVMKNRYYDMVLSTKLAGLGHAAFLFMTTARDR 228 (399)
Q Consensus 189 --~~~~~l~~~LR~~~YDlvIdl~~~~~rsAll~~LsgA~~R 228 (399)
..+.+..+.+|+.++|+||.. +. +.+.+.++..|+|.-
T Consensus 78 ~~~~~~~~~~~l~~~~pDlVi~d-~~-~~~~~aA~~~~iP~i 117 (321)
T TIGR00661 78 PKKAIRREINIIREYNPDLIISD-FE-YSTVVAAKLLKIPVI 117 (321)
T ss_pred cHHHHHHHHHHHHhcCCCEEEEC-Cc-hHHHHHHHhcCCCEE
Confidence 123345677888999999987 44 667889999999965
No 31
>PF14595 Thioredoxin_9: Thioredoxin; PDB: 1Z6N_A.
Probab=85.82 E-value=1.2 Score=38.76 Aligned_cols=61 Identities=11% Similarity=0.118 Sum_probs=45.5
Q ss_pred ccEEEEEcCCChhHHHhHHHHHHHHHHHCCCcEEEEEEcCCchHhhhcC-----CCCCEEEEecCC
Q 015881 122 VRRCCCIISGGVYENLLFFPAIQLLKDRYPGVLIDVIASARGKQTFELN-----KNVRWANVYDLD 182 (399)
Q Consensus 122 v~rILIIr~~~IGDvVLttPalraLK~~yP~A~IdvLv~~~~~~lle~n-----P~ID~Vi~~d~k 182 (399)
..+|||+--.|=||.....|++..+.+..|+.++.++......++.+.. ..|=.+|.+|..
T Consensus 42 ~~~ilvi~e~WCgD~~~~vP~l~kiae~~p~i~~~~i~rd~~~el~~~~lt~g~~~IP~~I~~d~~ 107 (129)
T PF14595_consen 42 PYNILVITETWCGDCARNVPVLAKIAEANPNIEVRIILRDENKELMDQYLTNGGRSIPTFIFLDKD 107 (129)
T ss_dssp -EEEEEE--TT-HHHHHHHHHHHHHHHH-TTEEEEEE-HHHHHHHTTTTTT-SS--SSEEEEE-TT
T ss_pred CcEEEEEECCCchhHHHHHHHHHHHHHhCCCCeEEEEEecCChhHHHHHHhCCCeecCEEEEEcCC
Confidence 4699999999999999999999999999999999999988887776643 456677888764
No 32
>TIGR03609 S_layer_CsaB polysaccharide pyruvyl transferase CsaB. The CsaB protein (cell surface anchoring B) of Bacillus anthracis adds a pyruvoyl group to peptidoglycan-associated polysaccharide. This addition is required for proteins with an S-layer homology domain (pfam00395) to bind. Within the larger group of proteins described by Pfam model pfam04230, this model represents a distinct clade that nearly exactly follows the phylogenetic distribution of the S-layer homology domain (pfam00395).
Probab=85.46 E-value=15 Score=35.72 Aligned_cols=65 Identities=20% Similarity=0.242 Sum_probs=40.2
Q ss_pred CCChhHHHhHHHHHHHHHHHCCCcEEEEEEcCCchHhhhcCCCCCEEEEecCCCCCCChHHHHHHHHHhhhCCCcEEEEc
Q 015881 130 SGGVYENLLFFPAIQLLKDRYPGVLIDVIASARGKQTFELNKNVRWANVYDLDDDWPEPAEYTDILGVMKNRYYDMVLST 209 (399)
Q Consensus 130 ~~~IGDvVLttPalraLK~~yP~A~IdvLv~~~~~~lle~nP~ID~Vi~~d~k~~~~~~~~~~~l~~~LR~~~YDlvIdl 209 (399)
.+.+||-++...+++.|+ |+++|.+++.... +.-+.. .|..+ ++. ....+++.++ ++|++|.-
T Consensus 9 ~~N~GDe~~l~~~l~~l~---~~~~~~v~s~~p~-~~~~~~-~v~~~---~r~-------~~~~~~~~l~--~~D~vI~g 71 (298)
T TIGR03609 9 FGNLGDEALLAALLRELP---PGVEPTVLSNDPA-ETAKLY-GVEAV---NRR-------SLLAVLRALR--RADVVIWG 71 (298)
T ss_pred CCCcchHHHHHHHHHhcC---CCCeEEEecCChH-HHHhhc-CceEE---ccC-------CHHHHHHHHH--HCCEEEEC
Confidence 478999999998877774 8999888874322 122222 44433 321 2345566665 47999965
Q ss_pred CC
Q 015881 210 KL 211 (399)
Q Consensus 210 ~~ 211 (399)
-+
T Consensus 72 GG 73 (298)
T TIGR03609 72 GG 73 (298)
T ss_pred Cc
Confidence 44
No 33
>cd03785 GT1_MurG MurG is an N-acetylglucosaminyltransferase, the last enzyme involved in the intracellular phase of peptidoglycan biosynthesis. It transfers N-acetyl-D-glucosamine (GlcNAc) from UDP-GlcNAc to the C4 hydroxyl of a lipid-linked N-acetylmuramoyl pentapeptide (NAM). The resulting disaccharide is then transported across the cell membrane, where it is polymerized into NAG-NAM cell-wall repeat structure. MurG belongs to the GT-B structural superfamily of glycoslytransferases, which have characteristic N- and C-terminal domains, each containing a typical Rossmann fold. The two domains have high structural homology despite minimal sequence homology. The large cleft that separates the two domains includes the catalytic center and permits a high degree of flexibility.
Probab=82.08 E-value=24 Score=34.50 Aligned_cols=102 Identities=10% Similarity=-0.012 Sum_probs=62.5
Q ss_pred EEEEEcCCChhHHHhHHHHHHHHHHHCCCcEEEEEEcCCchH--hhhcCCCCCEEEEecCC----CC-CCC-------hH
Q 015881 124 RCCCIISGGVYENLLFFPAIQLLKDRYPGVLIDVIASARGKQ--TFELNKNVRWANVYDLD----DD-WPE-------PA 189 (399)
Q Consensus 124 rILIIr~~~IGDvVLttPalraLK~~yP~A~IdvLv~~~~~~--lle~nP~ID~Vi~~d~k----~~-~~~-------~~ 189 (399)
||||...+.=|+.--...++++|.++ +-++++++...... .++. ..|+ +..++.. .. +.. +.
T Consensus 1 ~~~~~~~~~gG~~~~~~~la~~l~~~--G~ev~v~~~~~~~~~~~~~~-~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~ 76 (350)
T cd03785 1 RILIAGGGTGGHIFPALALAEELRER--GAEVLFLGTKRGLEARLVPK-AGIP-LHTIPVGGLRRKGSLKKLKAPFKLLK 76 (350)
T ss_pred CEEEEecCchhhhhHHHHHHHHHHhC--CCEEEEEECCCcchhhcccc-cCCc-eEEEEecCcCCCChHHHHHHHHHHHH
Confidence 58888777768888888999999998 56899998765422 1221 1232 3333221 11 111 11
Q ss_pred HHHHHHHHhhhCCCcEEEEcCCC-ChHHHHHHHHhCCCeEE
Q 015881 190 EYTDILGVMKNRYYDMVLSTKLA-GLGHAAFLFMTTARDRV 229 (399)
Q Consensus 190 ~~~~l~~~LR~~~YDlvIdl~~~-~~rsAll~~LsgA~~RI 229 (399)
...++.+.+|+.++|+++..... .+...+.++..|+|.-+
T Consensus 77 ~~~~~~~~i~~~~pDvI~~~~~~~~~~~~~~a~~~~~p~v~ 117 (350)
T cd03785 77 GVLQARKILKKFKPDVVVGFGGYVSGPVGLAAKLLGIPLVI 117 (350)
T ss_pred HHHHHHHHHHhcCCCEEEECCCCcchHHHHHHHHhCCCEEE
Confidence 22345677888999999975432 24445567777877644
No 34
>PRK14089 ipid-A-disaccharide synthase; Provisional
Probab=79.53 E-value=55 Score=33.33 Aligned_cols=106 Identities=12% Similarity=-0.031 Sum_probs=57.2
Q ss_pred ccEEEEEcCCChhHHHhHHHHHHHHHHHCCCcEEEEEEcCCchHhhhcCCCCCEEEEecCCCCCCChHHHHHHHHHhh--
Q 015881 122 VRRCCCIISGGVYENLLFFPAIQLLKDRYPGVLIDVIASARGKQTFELNKNVRWANVYDLDDDWPEPAEYTDILGVMK-- 199 (399)
Q Consensus 122 v~rILIIr~~~IGDvVLttPalraLK~~yP~A~IdvLv~~~~~~lle~nP~ID~Vi~~d~k~~~~~~~~~~~l~~~LR-- 199 (399)
+|||+|+--..=||.. ..-++++||+ ++++.-+..+.- ++..=+++++-+.-.-.-.+.+..+++++++++
T Consensus 1 ~~~i~i~aGE~SGD~~-ga~l~~~l~~---~~~~~G~GG~~m---~~~~~~~~~lsv~G~~evl~~~~~~~~~~~~~~~~ 73 (347)
T PRK14089 1 MMKILVSALEPSANLH-LKELLKNLPK---DYELIGIFDKSL---GNPLYDSREFSIMGFVDVLPKLFFAKKAIKEMVEL 73 (347)
T ss_pred CcEEEEEeccccHHHH-HHHHHHHHhc---CCEEEEEechHH---HHhcCChHHhhhhhHHHHHHHHHHHHHHHHHHHHH
Confidence 5799999988889964 5567999998 888887777655 111111111100000000011122222332222
Q ss_pred hCCCcEEEE--cCCCChHHHHHHHHh--CCCeEEEecCCC
Q 015881 200 NRYYDMVLS--TKLAGLGHAAFLFMT--TARDRVSYIYPN 235 (399)
Q Consensus 200 ~~~YDlvId--l~~~~~rsAll~~Ls--gA~~RIGy~~~~ 235 (399)
.++.|++|- ..+-.++-|-.+.-. |+| .+-|..|.
T Consensus 74 ~~~pd~~i~iD~p~Fnl~lak~~k~~~~~i~-viyyi~Pq 112 (347)
T PRK14089 74 AKQADKVLLMDSSSFNIPLAKKIKKAYPKKE-IIYYILPQ 112 (347)
T ss_pred hcCCCEEEEeCCCCCCHHHHHHHHhcCCCCC-EEEEECcc
Confidence 268999984 444336666666666 466 46676553
No 35
>cd03784 GT1_Gtf_like This family includes the Gtfs, a group of homologous glycosyltransferases involved in the final stages of the biosynthesis of antibiotics vancomycin and related chloroeremomycin. Gtfs transfer sugar moieties from an activated NDP-sugar donor to the oxidatively cross-linked heptapeptide core of vancomycin group antibiotics. The core structure is important for the bioactivity of the antibiotics.
Probab=78.80 E-value=8.8 Score=38.65 Aligned_cols=100 Identities=14% Similarity=0.027 Sum_probs=68.6
Q ss_pred cEEEEEcCCChhHHHhHHHHHHHHHHHCCCcEEEEEEcCCchHhhhcCCCCCEEEEecCCC--------CC-------C-
Q 015881 123 RRCCCIISGGVYENLLFFPAIQLLKDRYPGVLIDVIASARGKQTFELNKNVRWANVYDLDD--------DW-------P- 186 (399)
Q Consensus 123 ~rILIIr~~~IGDvVLttPalraLK~~yP~A~IdvLv~~~~~~lle~nP~ID~Vi~~d~k~--------~~-------~- 186 (399)
||||++-..+.||+-=..++.++|+++ +-+|++++.+..+..++... ++ ++.+.... .. .
T Consensus 1 mrIl~~~~p~~GHv~P~l~la~~L~~r--Gh~V~~~t~~~~~~~v~~~G-~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~ 76 (401)
T cd03784 1 MRVLITTIGSRGDVQPLVALAWALRAA--GHEVRVATPPEFADLVEAAG-LE-FVPVGGDPDELLASPERNAGLLLLGPG 76 (401)
T ss_pred CeEEEEeCCCcchHHHHHHHHHHHHHC--CCeEEEeeCHhHHHHHHHcC-Cc-eeeCCCCHHHHHhhhhhcccccccchH
Confidence 799999999999999999999999987 57999999998888887643 32 33333210 00 0
Q ss_pred ChH------------HHHHHHHHhhhCCCcEEEEcCCCChHHHHHHHHhCCCe
Q 015881 187 EPA------------EYTDILGVMKNRYYDMVLSTKLAGLGHAAFLFMTTARD 227 (399)
Q Consensus 187 ~~~------------~~~~l~~~LR~~~YDlvIdl~~~~~rsAll~~LsgA~~ 227 (399)
... .+..++..++..++|++|.-... .....++...|+|.
T Consensus 77 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~pDlvi~d~~~-~~~~~~A~~~giP~ 128 (401)
T cd03784 77 LLLGALRLLRREAEAMLDDLVAAARDWGPDLVVADPLA-FAGAVAAEALGIPA 128 (401)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHhcccCCCEEEeCcHH-HHHHHHHHHhCCCe
Confidence 000 01123445666899999855444 55566777888873
No 36
>PRK10307 putative glycosyl transferase; Provisional
Probab=78.23 E-value=80 Score=31.85 Aligned_cols=38 Identities=16% Similarity=-0.003 Sum_probs=26.9
Q ss_pred cEEEEEcCCChhH----HHhHHHHHHHHHHHCCCcEEEEEEcCC
Q 015881 123 RRCCCIISGGVYE----NLLFFPAIQLLKDRYPGVLIDVIASAR 162 (399)
Q Consensus 123 ~rILIIr~~~IGD----vVLttPalraLK~~yP~A~IdvLv~~~ 162 (399)
||||||...+.-+ -..+.-+.+.|.++ +.+|+++|.+.
T Consensus 1 mkIlii~~~~~P~~~g~~~~~~~l~~~L~~~--G~~V~vit~~~ 42 (412)
T PRK10307 1 MKILVYGINYAPELTGIGKYTGEMAEWLAAR--GHEVRVITAPP 42 (412)
T ss_pred CeEEEEecCCCCCccchhhhHHHHHHHHHHC--CCeEEEEecCC
Confidence 7899997533222 13556788888886 77999999653
No 37
>TIGR00236 wecB UDP-N-acetylglucosamine 2-epimerase. Epimerase activity was also demonstrated in a bifunctional rat enzyme, for which the N-terminal domain appears to be orthologous. The set of proteins found above the suggested cutoff includes E. coli WecB in one of two deeply branched clusters and the rat UDP-N-acetylglucosamine 2-epimerase domain in the other.
Probab=77.84 E-value=18 Score=36.09 Aligned_cols=102 Identities=19% Similarity=0.149 Sum_probs=62.2
Q ss_pred cEEEEEcCCChhHHHhHHHHHHHHHHHCCCcEEEEEEcCCc----hHhhhcCCCCCEEEEecCCCCCCCh-----HHHHH
Q 015881 123 RRCCCIISGGVYENLLFFPAIQLLKDRYPGVLIDVIASARG----KQTFELNKNVRWANVYDLDDDWPEP-----AEYTD 193 (399)
Q Consensus 123 ~rILIIr~~~IGDvVLttPalraLK~~yP~A~IdvLv~~~~----~~lle~nP~ID~Vi~~d~k~~~~~~-----~~~~~ 193 (399)
|||+|+ .+.--|.+..-|++++|++ .|+.+..+++.-.. .++++.. .|+.-+.+.....-.+. ..+.+
T Consensus 1 ~~i~~~-~gtr~~~~~~~p~~~~l~~-~~~~~~~~~~tg~h~~~~~~~~~~~-~i~~~~~~~~~~~~~~~~~~~~~~~~~ 77 (365)
T TIGR00236 1 LKVSIV-LGTRPEAIKMAPLIRALKK-YPEIDSYVIVTAQHREMLDQVLDLF-HLPPDYDLNIMSPGQTLGEITSNMLEG 77 (365)
T ss_pred CeEEEE-EecCHHHHHHHHHHHHHhh-CCCCCEEEEEeCCCHHHHHHHHHhc-CCCCCeeeecCCCCCCHHHHHHHHHHH
Confidence 577765 4556789999999999995 46777777764332 3455442 22211211111110121 22456
Q ss_pred HHHHhhhCCCcEEEEcCCC--ChHHHHHHHHhCCCe
Q 015881 194 ILGVMKNRYYDMVLSTKLA--GLGHAAFLFMTTARD 227 (399)
Q Consensus 194 l~~~LR~~~YDlvIdl~~~--~~rsAll~~LsgA~~ 227 (399)
+.+.+++.++|+|+..... .+-.++.++..|+|.
T Consensus 78 l~~~l~~~~pDiv~~~gd~~~~la~a~aa~~~~ipv 113 (365)
T TIGR00236 78 LEELLLEEKPDIVLVQGDTTTTLAGALAAFYLQIPV 113 (365)
T ss_pred HHHHHHHcCCCEEEEeCCchHHHHHHHHHHHhCCCE
Confidence 7778999999999877432 134566788888885
No 38
>COG0707 MurG UDP-N-acetylglucosamine:LPS N-acetylglucosamine transferase [Cell envelope biogenesis, outer membrane]
Probab=76.91 E-value=92 Score=31.84 Aligned_cols=107 Identities=8% Similarity=-0.135 Sum_probs=68.3
Q ss_pred cEEEEEcCCChhHHHhHHHHHHHHHHHCCCcEEEEEEcCCchH-hhhcCCCCCEEEEecCCCC-----CC-------ChH
Q 015881 123 RRCCCIISGGVYENLLFFPAIQLLKDRYPGVLIDVIASARGKQ-TFELNKNVRWANVYDLDDD-----WP-------EPA 189 (399)
Q Consensus 123 ~rILIIr~~~IGDvVLttPalraLK~~yP~A~IdvLv~~~~~~-lle~nP~ID~Vi~~d~k~~-----~~-------~~~ 189 (399)
|+|++.--+.=|=+--+.-+.++|+++-.+ ++.|+......+ .+.... -.++..++...- +. -+.
T Consensus 1 ~~ivl~~gGTGGHv~pAlAl~~~l~~~g~~-~v~~~~~~~~~e~~l~~~~-~~~~~~I~~~~~~~~~~~~~~~~~~~~~~ 78 (357)
T COG0707 1 KKIVLTAGGTGGHVFPALALAEELAKRGWE-QVIVLGTGDGLEAFLVKQY-GIEFELIPSGGLRRKGSLKLLKAPFKLLK 78 (357)
T ss_pred CeEEEEeCCCccchhHHHHHHHHHHhhCcc-EEEEecccccceeeecccc-CceEEEEecccccccCcHHHHHHHHHHHH
Confidence 467777777778888888899999999888 999995544433 233222 345555553221 11 112
Q ss_pred HHHHHHHHhhhCCCcEEEEcCCCC-hHHHHHHHHhCCCeEEEe
Q 015881 190 EYTDILGVMKNRYYDMVLSTKLAG-LGHAAFLFMTTARDRVSY 231 (399)
Q Consensus 190 ~~~~l~~~LR~~~YDlvIdl~~~~-~rsAll~~LsgA~~RIGy 231 (399)
.+.+..+.||+.+.|+||.+.+-. .-..+.+++.|+|.-+--
T Consensus 79 ~~~~a~~il~~~kPd~vig~Ggyvs~P~~~Aa~~~~iPv~ihE 121 (357)
T COG0707 79 GVLQARKILKKLKPDVVIGTGGYVSGPVGIAAKLLGIPVIIHE 121 (357)
T ss_pred HHHHHHHHHHHcCCCEEEecCCccccHHHHHHHhCCCCEEEEe
Confidence 233445579999999999988762 334556778888865543
No 39
>PF13528 Glyco_trans_1_3: Glycosyl transferase family 1
Probab=76.50 E-value=23 Score=34.27 Aligned_cols=103 Identities=11% Similarity=0.005 Sum_probs=65.5
Q ss_pred cEEEEEcC-CChhHHHhHHHHHHHHHHHCCCcEEEEEEcCCchHhhhcCCCCCEEEEe---cCCCCCCC-----------
Q 015881 123 RRCCCIIS-GGVYENLLFFPAIQLLKDRYPGVLIDVIASARGKQTFELNKNVRWANVY---DLDDDWPE----------- 187 (399)
Q Consensus 123 ~rILIIr~-~~IGDvVLttPalraLK~~yP~A~IdvLv~~~~~~lle~nP~ID~Vi~~---d~k~~~~~----------- 187 (399)
||||+... .++|=+.-+.+++++|| +.+|++++.......++..=.+.++..+ ..+.....
T Consensus 1 MkIl~~v~~~G~GH~~R~~~la~~Lr----g~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 76 (318)
T PF13528_consen 1 MKILFYVQGHGLGHASRCLALARALR----GHEVTFITSGPAPEFLKPRFPVREIPGLGPIQENGRLDRWKTVRNNIRWL 76 (318)
T ss_pred CEEEEEeCCCCcCHHHHHHHHHHHHc----cCceEEEEcCCcHHHhccccCEEEccCceEeccCCccchHHHHHHHHHhh
Confidence 78888644 59999999999999993 3689999988776777543011111111 01111100
Q ss_pred ---hHHHHHHHHHhhhCCCcEEEEcCCCChHHHHHHHHhCCCeEEEec
Q 015881 188 ---PAEYTDILGVMKNRYYDMVLSTKLAGLGHAAFLFMTTARDRVSYI 232 (399)
Q Consensus 188 ---~~~~~~l~~~LR~~~YDlvIdl~~~~~rsAll~~LsgA~~RIGy~ 232 (399)
.....++++.+++.++|+||+=... -+...+...|+| .|+..
T Consensus 77 ~~~~~~~~~~~~~l~~~~pDlVIsD~~~--~~~~aa~~~giP-~i~i~ 121 (318)
T PF13528_consen 77 ARLARRIRREIRWLREFRPDLVISDFYP--LAALAARRAGIP-VIVIS 121 (318)
T ss_pred HHHHHHHHHHHHHHHhcCCCEEEEcChH--HHHHHHHhcCCC-EEEEE
Confidence 0122345567888999999976543 356778889988 45555
No 40
>TIGR03492 conserved hypothetical protein. This protein family is restricted to the Cyanobacteria, in one or two copies, save for instances in the genus Deinococcus. This protein shows some sequence similarity, especially toward the C-terminus, to lipid-A-disaccharide synthase (TIGR00215 or pfam02684). The function is unknown.
Probab=69.50 E-value=20 Score=36.97 Aligned_cols=96 Identities=10% Similarity=0.068 Sum_probs=63.0
Q ss_pred CCChhHHHhHHHHHHHHHHHCCCcEEE---EEEcCCchHhhhcCCCCCEEEEecCCCCCC--ChH----H--------HH
Q 015881 130 SGGVYENLLFFPAIQLLKDRYPGVLID---VIASARGKQTFELNKNVRWANVYDLDDDWP--EPA----E--------YT 192 (399)
Q Consensus 130 ~~~IGDvVLttPalraLK~~yP~A~Id---vLv~~~~~~lle~nP~ID~Vi~~d~k~~~~--~~~----~--------~~ 192 (399)
.++-|.=+++.-++++|++.+|+++|. |+.....-+ =+.-|.+-....++- +++. ++. . .+
T Consensus 4 snghged~~a~ai~~~l~~~~~~~~v~~~p~vG~~~~~e-~~~ip~~g~~~~~~s-gg~~~~~~~~~~~~~~~gl~~~~~ 81 (396)
T TIGR03492 4 SNGHGEDLIAARIAKALLQLSPDLNLEALPLVGEGRAYQ-NLGIPIIGPTKELPS-GGFSYQSLRGLLRDLRAGLVGLTL 81 (396)
T ss_pred CCCchHHHHHHHHHHHHHhhCCCCCeEEeCcccCCHHHh-hCCCceeCCCCCCCC-CCccCCCHHHHHHHHHhhHHHHHH
Confidence 567788899999999999999999999 888776542 111222222333332 2221 111 1 22
Q ss_pred HHHHHhhhC--CCcEEEEcCCCChHHHHHHHHhCCCeEE
Q 015881 193 DILGVMKNR--YYDMVLSTKLAGLGHAAFLFMTTARDRV 229 (399)
Q Consensus 193 ~l~~~LR~~--~YDlvIdl~~~~~rsAll~~LsgA~~RI 229 (399)
+-++.+|+. +.|+||.+-+- . ..+.+|++|+|.-+
T Consensus 82 ~~~~~~~~~~~~p~~v~~~Gg~-v-~~~aA~~~~~p~~~ 118 (396)
T TIGR03492 82 GQWRALRKWAKKGDLIVAVGDI-V-PLLFAWLSGKPYAF 118 (396)
T ss_pred HHHHHHHHHhhcCCEEEEECcH-H-HHHHHHHcCCCceE
Confidence 233446666 89999998775 4 77789999999666
No 41
>TIGR00521 coaBC_dfp phosphopantothenoylcysteine decarboxylase/phosphopantothenate--cysteine ligase, prokaryotic. This model represents a bifunctional enzyme that catalyzes the second and third steps (cysteine ligation, EC 6.3.2.5, and decarboxylation, EC 4.1.1.36) in the biosynthesis of coenzyme A (CoA) from pantothenate in bacteria. In early descriptions of this flavoprotein, a ts mutation in one region of the protein appeared to cause a defect in DNA metaobolism rather than an increased need for the pantothenate precursor beta-alanine. This protein was then called dfp, for DNA/pantothenate metabolism flavoprotein. The authors responsible for detecting phosphopantothenate--cysteine ligase activity suggest renaming this bifunctional protein coaBC for its role in CoA biosynthesis. This enzyme contains the FMN cofactor, but no FAD or pyruvoyl group. The amino-terminal region contains the phosphopantothenoylcysteine decarboxylase activity.
Probab=68.41 E-value=1.3e+02 Score=31.21 Aligned_cols=44 Identities=16% Similarity=0.242 Sum_probs=37.5
Q ss_pred ccEEEEEcCCChhHHHhHHHHHHHHHHHCCCcEEEEEEcCCchHhhh
Q 015881 122 VRRCCCIISGGVYENLLFFPAIQLLKDRYPGVLIDVIASARGKQTFE 168 (399)
Q Consensus 122 v~rILIIr~~~IGDvVLttPalraLK~~yP~A~IdvLv~~~~~~lle 168 (399)
.+|||+.-.+++|= +-+.-+++.|++. +++|++++.+.+..++.
T Consensus 3 ~k~IllgiTGSiaa-~~~~~ll~~L~~~--g~~V~vv~T~~A~~fv~ 46 (390)
T TIGR00521 3 NKKILLGVTGGIAA-YKTVELVRELVRQ--GAEVKVIMTEAAKKFIT 46 (390)
T ss_pred CCEEEEEEeCHHHH-HHHHHHHHHHHhC--CCEEEEEECHhHHHHHH
Confidence 48999999999987 6688899999875 78999999998887764
No 42
>cd03811 GT1_WabH_like This family is most closely related to the GT1 family of glycosyltransferases. WabH in Klebsiella pneumoniae has been shown to transfer a GlcNAc residue from UDP-GlcNAc onto the acceptor GalUA residue in the cellular outer core.
Probab=65.20 E-value=1.2e+02 Score=28.21 Aligned_cols=85 Identities=13% Similarity=0.089 Sum_probs=47.1
Q ss_pred EEEEEcCCC-hhH-HHhHHHHHHHHHHHCCCcEEEEEEcCCchHhhhcCCCCC---EEEEecCCCCCCChHHHHHHHHHh
Q 015881 124 RCCCIISGG-VYE-NLLFFPAIQLLKDRYPGVLIDVIASARGKQTFELNKNVR---WANVYDLDDDWPEPAEYTDILGVM 198 (399)
Q Consensus 124 rILIIr~~~-IGD-vVLttPalraLK~~yP~A~IdvLv~~~~~~lle~nP~ID---~Vi~~d~k~~~~~~~~~~~l~~~L 198 (399)
|||++-.+. .|. .....-++++|++. +.+|++++............... ....... ...........+.+.+
T Consensus 1 kIl~~~~~~~~gG~~~~~~~l~~~l~~~--g~~v~v~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~ 77 (353)
T cd03811 1 KILFVIPSLGGGGAERVLLNLANGLDKR--GYDVTLVVLRDEGDYLELLPSNVKLIPVRVLKL-KSLRDLLAILRLRRLL 77 (353)
T ss_pred CeEEEeecccCCCcchhHHHHHHHHHhc--CceEEEEEcCCCCccccccccchhhhceeeeec-ccccchhHHHHHHHHH
Confidence 577775554 343 34455788888655 67888888655443222221110 0111111 1112233445677788
Q ss_pred hhCCCcEEEEcCC
Q 015881 199 KNRYYDMVLSTKL 211 (399)
Q Consensus 199 R~~~YDlvIdl~~ 211 (399)
++.++|+++....
T Consensus 78 ~~~~~dii~~~~~ 90 (353)
T cd03811 78 RKEKPDVVISHLT 90 (353)
T ss_pred HhcCCCEEEEcCc
Confidence 8899999998876
No 43
>COG1819 Glycosyl transferases, related to UDP-glucuronosyltransferase [Carbohydrate transport and metabolism / Signal transduction mechanisms]
Probab=64.64 E-value=8.1 Score=40.02 Aligned_cols=100 Identities=11% Similarity=0.052 Sum_probs=68.0
Q ss_pred ccEEEEEcCCChhHHHhHHHHHHHHHHHCCCcEEEEEEcCCchHhhhcCC--CCCEEEEecCC--------CCCCC----
Q 015881 122 VRRCCCIISGGVYENLLFFPAIQLLKDRYPGVLIDVIASARGKQTFELNK--NVRWANVYDLD--------DDWPE---- 187 (399)
Q Consensus 122 v~rILIIr~~~IGDvVLttPalraLK~~yP~A~IdvLv~~~~~~lle~nP--~ID~Vi~~d~k--------~~~~~---- 187 (399)
.||||++-....|++.=+..+.++|+++ +-+|++.+.+.+++.++... ++...+. +.. ..++.
T Consensus 1 ~mkil~~~~~~~Ghv~p~~aL~~eL~~~--gheV~~~~~~~~~~~ve~ag~~f~~~~~~-~~~~~~~~~~~~~~~~~~~~ 77 (406)
T COG1819 1 RMKILFVVCGAYGHVNPCLALGKELRRR--GHEVVFASTGKFKEFVEAAGLAFVAYPIR-DSELATEDGKFAGVKSFRRL 77 (406)
T ss_pred CceEEEEeccccccccchHHHHHHHHhc--CCeEEEEeCHHHHHHHHHhCcceeecccc-CChhhhhhhhhhccchhHHH
Confidence 4899999888899999999999999998 88999999999999999988 4443332 110 00111
Q ss_pred hHHH----HHHHHHhhhCCCcEEEEcCCCChHHHHHHHHhCCC
Q 015881 188 PAEY----TDILGVMKNRYYDMVLSTKLAGLGHAAFLFMTTAR 226 (399)
Q Consensus 188 ~~~~----~~l~~~LR~~~YDlvIdl~~~~~rsAll~~LsgA~ 226 (399)
...+ ..+++.+++...|+++|.... ..+ +++.+.+.+
T Consensus 78 ~~~~~~~~~~~~~~~~e~~~~~~~~~~~~-~~~-~~~~~~~~~ 118 (406)
T COG1819 78 LQQFKKLIRELLELLRELEPDLVVDDARL-SLG-LAARLLGIP 118 (406)
T ss_pred hhhhhhhhHHHHHHHHhcchhhhhcchhh-hhh-hhhhhcccc
Confidence 1111 134445888888988886554 333 444444443
No 44
>PRK09922 UDP-D-galactose:(glucosyl)lipopolysaccharide-1,6-D-galactosyltransferase; Provisional
Probab=64.31 E-value=46 Score=33.03 Aligned_cols=103 Identities=8% Similarity=-0.047 Sum_probs=58.2
Q ss_pred cEEEEEcCC--ChhHH-HhHHHHHHHHHHHCCCcEEEEEEcCCch--HhhhcCCCCCEE--EEecCCCCCCChHHHHHHH
Q 015881 123 RRCCCIISG--GVYEN-LLFFPAIQLLKDRYPGVLIDVIASARGK--QTFELNKNVRWA--NVYDLDDDWPEPAEYTDIL 195 (399)
Q Consensus 123 ~rILIIr~~--~IGDv-VLttPalraLK~~yP~A~IdvLv~~~~~--~lle~nP~ID~V--i~~d~k~~~~~~~~~~~l~ 195 (399)
|||+++... ..|-+ -.+.-++++|.++--+.++.+++..... ..++..+.+..+ +.+.. ...+..+.++.
T Consensus 1 mkI~~~~~~~~~~GG~e~~~~~l~~~L~~~~~g~~v~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~l~ 77 (359)
T PRK09922 1 MKIAFIGEAVSGFGGMETVISNVINTFEESKINCEMFFFCRNDKMDKAWLKEIKYAQSFSNIKLSF---LRRAKHVYNFS 77 (359)
T ss_pred CeeEEecccccCCCchhHHHHHHHHHhhhcCcceeEEEEecCCCCChHHHHhcchhcccccchhhh---hcccHHHHHHH
Confidence 799999664 24555 5556778888887557888888865432 223333221110 11110 01234456778
Q ss_pred HHhhhCCCcEEEEcCCCC-hHHHHHHHHhCCCeE
Q 015881 196 GVMKNRYYDMVLSTKLAG-LGHAAFLFMTTARDR 228 (399)
Q Consensus 196 ~~LR~~~YDlvIdl~~~~-~rsAll~~LsgA~~R 228 (399)
+.+++.++|+++...... +-..++..+.|.+.+
T Consensus 78 ~~l~~~~~Dii~~~~~~~~~~~~~~~~~~~~~~~ 111 (359)
T PRK09922 78 KWLKETQPDIVICIDVISCLYANKARKKSGKQFK 111 (359)
T ss_pred HHHHhcCCCEEEEcCHHHHHHHHHHHHHhCCCCe
Confidence 889999999998764321 112233444566544
No 45
>cd03812 GT1_CapH_like This family is most closely related to the GT1 family of glycosyltransferases. capH in Staphylococcus aureus has been shown to be required for the biosynthesis of the type 1 capsular polysaccharide (CP1).
Probab=64.24 E-value=1.4e+02 Score=28.70 Aligned_cols=102 Identities=9% Similarity=0.029 Sum_probs=53.1
Q ss_pred EEEEEcCC-ChhHH-HhHHHHHHHHHHHCCCcEEEEEEcCCch----HhhhcCCCCCEEEEecCCCCCCChHHHHHHHHH
Q 015881 124 RCCCIISG-GVYEN-LLFFPAIQLLKDRYPGVLIDVIASARGK----QTFELNKNVRWANVYDLDDDWPEPAEYTDILGV 197 (399)
Q Consensus 124 rILIIr~~-~IGDv-VLttPalraLK~~yP~A~IdvLv~~~~~----~lle~nP~ID~Vi~~d~k~~~~~~~~~~~l~~~ 197 (399)
|||++-.+ ..|-+ ....-++++|++. +.++++++..... ..+..+ .+ .++....+.. .....+..+.+.
T Consensus 1 kIl~~~~~~~~GG~~~~~~~l~~~L~~~--~~~v~~i~~~~~~~~~~~~~~~~-~~-~~~~~~~~~~-~~~~~~~~~~~~ 75 (358)
T cd03812 1 KILHIVGTMNRGGIETFIMNYYRNLDRS--KIQFDFLVTSKEEGDYDDEIEKL-GG-KIYYIPARKK-NPLKYFKKLYKL 75 (358)
T ss_pred CEEEEeCCCCCccHHHHHHHHHHhcCcc--ceEEEEEEeCCCCcchHHHHHHc-CC-eEEEecCCCc-cHHHHHHHHHHH
Confidence 57777664 34433 3444667777643 6788888865433 122221 22 2332332221 122233455666
Q ss_pred hhhCCCcEEEEcCCC-ChHHHHHHHHhCCCeEEE
Q 015881 198 MKNRYYDMVLSTKLA-GLGHAAFLFMTTARDRVS 230 (399)
Q Consensus 198 LR~~~YDlvIdl~~~-~~rsAll~~LsgA~~RIG 230 (399)
+++.+||+++..... ..-..++....+.+..+-
T Consensus 76 ~~~~~~Dvv~~~~~~~~~~~~~~~~~~~~~~~v~ 109 (358)
T cd03812 76 IKKNKYDIVHVHGSSASGFILLAAKKAGVKVRIA 109 (358)
T ss_pred HhcCCCCEEEEeCcchhHHHHHHHhhCCCCeEEE
Confidence 788999999875543 122333444556665553
No 46
>PRK12678 transcription termination factor Rho; Provisional
Probab=63.37 E-value=35 Score=37.49 Aligned_cols=97 Identities=9% Similarity=0.023 Sum_probs=68.0
Q ss_pred ccEEEEEcCCChhHHHhHHHHHHHHHHHCCCcE-EEEEEcCCchHhhhcCCCCCEEEEecCCCCCCC-----hHHHHHHH
Q 015881 122 VRRCCCIISGGVYENLLFFPAIQLLKDRYPGVL-IDVIASARGKQTFELNKNVRWANVYDLDDDWPE-----PAEYTDIL 195 (399)
Q Consensus 122 v~rILIIr~~~IGDvVLttPalraLK~~yP~A~-IdvLv~~~~~~lle~nP~ID~Vi~~d~k~~~~~-----~~~~~~l~ 195 (399)
-.|+|||-+..-|=.+|..-+++++...+|++. |.+||..+..+|=+..-.|..-++....+.-.. ..--+.+.
T Consensus 416 GQR~LIvgpp~aGKTtLL~~IAn~i~~n~~~~~~ivvLIgERpeEVtdm~rsVkgeVVasT~D~p~~~~~~~a~~ai~~A 495 (672)
T PRK12678 416 GQRGLIVSPPKAGKTTILQNIANAITTNNPECHLMVVLVDERPEEVTDMQRSVKGEVIASTFDRPPSDHTTVAELAIERA 495 (672)
T ss_pred CCEeEEeCCCCCCHHHHHHHHHHHHhhcCCCeEEEEEEEeCchhhHHHHHHhccceEEEECCCCCHHHHHHHHHHHHHHH
Confidence 479999999999999998888889989999999 466788888888554444422233333222000 01124567
Q ss_pred HHhhhCCCcEEEEcCCCChHHHHH
Q 015881 196 GVMKNRYYDMVLSTKLAGLGHAAF 219 (399)
Q Consensus 196 ~~LR~~~YDlvIdl~~~~~rsAll 219 (399)
+.+|...+|++|.+.+. .+.|-.
T Consensus 496 e~fre~G~dVlillDSl-TR~ArA 518 (672)
T PRK12678 496 KRLVELGKDVVVLLDSI-TRLGRA 518 (672)
T ss_pred HHHHHcCCCEEEEEeCc-hHHHHH
Confidence 78999999999988877 555443
No 47
>PRK13982 bifunctional SbtC-like/phosphopantothenoylcysteine decarboxylase/phosphopantothenate synthase; Provisional
Probab=62.64 E-value=2.2e+02 Score=30.44 Aligned_cols=44 Identities=25% Similarity=0.392 Sum_probs=37.2
Q ss_pred ccEEEEEcCCChhHHHhHHHHHHHHHHHCCCcEEEEEEcCCchHhhh
Q 015881 122 VRRCCCIISGGVYENLLFFPAIQLLKDRYPGVLIDVIASARGKQTFE 168 (399)
Q Consensus 122 v~rILIIr~~~IGDvVLttPalraLK~~yP~A~IdvLv~~~~~~lle 168 (399)
.+|||+.-.++|+=. -+.-+++.|++. +++|.+++.+....++.
T Consensus 70 ~k~IllgVtGsIAay-ka~~lvr~L~k~--G~~V~VvmT~sA~~fv~ 113 (475)
T PRK13982 70 SKRVTLIIGGGIAAY-KALDLIRRLKER--GAHVRCVLTKAAQQFVT 113 (475)
T ss_pred CCEEEEEEccHHHHH-HHHHHHHHHHhC--cCEEEEEECcCHHHHhh
Confidence 589999999999855 778899999876 89999999997776654
No 48
>PF02441 Flavoprotein: Flavoprotein; InterPro: IPR003382 This entry contains a diverse range of flavoprotein enzymes, including epidermin biosynthesis protein, EpiD, which has been shown to be a flavoprotein that binds FMN []. This enzyme catalyzes the removal of two reducing equivalents from the cysteine residue of the C-terminal meso-lanthionine of epidermin to form a --C==C-- double bond. This family also includes the B chain of dipicolinate synthase a small polar molecule that accumulates to high concentrations in bacterial endospores, and is thought to play a role in spore heat resistance, or the maintenance of heat resistance []. Dipicolinate synthase catalyses the formation of dipicolinic acid from dihydroxydipicolinic acid. This family also includes phenylacrylic acid decarboxylase 4.1.1 from EC [].; GO: 0003824 catalytic activity; PDB: 3QJG_L 1G63_G 1G5Q_L 1P3Y_1 1QZU_A 1E20_A 1MVN_A 1MVL_A 3ZQU_A 2EJB_A ....
Probab=62.43 E-value=8.5 Score=33.04 Aligned_cols=53 Identities=13% Similarity=0.063 Sum_probs=43.5
Q ss_pred cEEEEEcCCChhHHHhHHHHHHHHHHHCCCcEEEEEEcCCchHhhhcCC-CCCEEEE
Q 015881 123 RRCCCIISGGVYENLLFFPAIQLLKDRYPGVLIDVIASARGKQTFELNK-NVRWANV 178 (399)
Q Consensus 123 ~rILIIr~~~IGDvVLttPalraLK~~yP~A~IdvLv~~~~~~lle~nP-~ID~Vi~ 178 (399)
|||++.-.++++-.- +..+++.|++. +.+|+++..+.+..++...- ..++|+.
T Consensus 1 k~i~l~vtGs~~~~~-~~~~l~~L~~~--g~~v~vv~S~~A~~~~~~~~~~~~~v~~ 54 (129)
T PF02441_consen 1 KRILLGVTGSIAAYK-APDLLRRLKRA--GWEVRVVLSPSAERFVTPEGLTGEPVYT 54 (129)
T ss_dssp -EEEEEE-SSGGGGG-HHHHHHHHHTT--TSEEEEEESHHHHHHSHHHGHCCSCEEC
T ss_pred CEEEEEEECHHHHHH-HHHHHHHHhhC--CCEEEEEECCcHHHHhhhhccccchhhh
Confidence 799999999987776 99999999999 89999999999998877655 5666664
No 49
>cd03801 GT1_YqgM_like This family is most closely related to the GT1 family of glycosyltransferases and named after YqgM in Bacillus licheniformis about which little is known. Glycosyltransferases catalyze the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming glycosidic bonds. The acceptor molecule can be a lipid, a protein, a heterocyclic compound, or another carbohydrate residue. This group of glycosyltransferases is most closely related to the previously defined glycosyltransferase family 1 (GT1). The members of this family may transfer UDP, ADP, GDP, or CMP linked sugars. The diverse enzymatic activities among members of this family reflect a wide range of biological functions. The protein structure available for this family has the GTB topology, one of the two protein topologies observed for nucleotide-sugar-dependent glycosyltransferases. GTB proteins have distinct N- and C- terminal domains each containing a typical Rossmann fold.
Probab=62.16 E-value=1.4e+02 Score=27.85 Aligned_cols=105 Identities=10% Similarity=-0.094 Sum_probs=56.8
Q ss_pred EEEEEcCCC----hhHHHhHHHHHHHHHHHCCCcEEEEEEcCCchHhhhcCCCCCEEEEe---cCC-CCCCChHHHHHHH
Q 015881 124 RCCCIISGG----VYENLLFFPAIQLLKDRYPGVLIDVIASARGKQTFELNKNVRWANVY---DLD-DDWPEPAEYTDIL 195 (399)
Q Consensus 124 rILIIr~~~----IGDvVLttPalraLK~~yP~A~IdvLv~~~~~~lle~nP~ID~Vi~~---d~k-~~~~~~~~~~~l~ 195 (399)
|||+|.... =|-.....-+++.|++. +.+|++++...........-....+... ... ..+........+.
T Consensus 1 kI~ii~~~~~~~~~G~~~~~~~l~~~L~~~--g~~v~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 78 (374)
T cd03801 1 KILLVTPEYPPSVGGAERHVLELARALAAR--GHEVTVLTPGDGGLPDEEEVGGIVVVRPPPLLRVRRLLLLLLLALRLR 78 (374)
T ss_pred CeeEEecccCCccCcHhHHHHHHHHHHHhc--CceEEEEecCCCCCCceeeecCcceecCCcccccchhHHHHHHHHHHH
Confidence 577776554 35677777889999874 7789888866544332222111111110 000 0001122234566
Q ss_pred HHhhhCCCcEEEEcCCCChHHH-HHHHHhCCCeEEE
Q 015881 196 GVMKNRYYDMVLSTKLAGLGHA-AFLFMTTARDRVS 230 (399)
Q Consensus 196 ~~LR~~~YDlvIdl~~~~~rsA-ll~~LsgA~~RIG 230 (399)
+.++..++|+++.......... .+....+.+..+-
T Consensus 79 ~~~~~~~~Dii~~~~~~~~~~~~~~~~~~~~~~i~~ 114 (374)
T cd03801 79 RLLRRERFDVVHAHDWLALLAAALAARLLGIPLVLT 114 (374)
T ss_pred HHhhhcCCcEEEEechhHHHHHHHHHHhcCCcEEEE
Confidence 6788889999998776622222 3455556554443
No 50
>cd03802 GT1_AviGT4_like This family is most closely related to the GT1 family of glycosyltransferases. aviGT4 in Streptomyces viridochromogenes has been shown to be involved in biosynthesis of oligosaccharide antibiotic avilamycin A. Inactivation of aviGT4 resulted in a mutant that accumulated a novel avilamycin derivative lacking the terminal eurekanate residue.
Probab=62.13 E-value=40 Score=32.15 Aligned_cols=102 Identities=16% Similarity=0.023 Sum_probs=52.6
Q ss_pred cEEEEEcCCC-------hhHH-HhHHHHHHHHHHHCCCcEEEEEEcCCchHhhhcCCCCCEEEEec-CCCCCCChHHHHH
Q 015881 123 RRCCCIISGG-------VYEN-LLFFPAIQLLKDRYPGVLIDVIASARGKQTFELNKNVRWANVYD-LDDDWPEPAEYTD 193 (399)
Q Consensus 123 ~rILIIr~~~-------IGDv-VLttPalraLK~~yP~A~IdvLv~~~~~~lle~nP~ID~Vi~~d-~k~~~~~~~~~~~ 193 (399)
||||+|.... .|-+ ..+.-++++|+++ +.+|++++......-....+........+ ....+........
T Consensus 1 MkI~~i~~~~~~~~~~~~GG~~~~~~~l~~~L~~~--g~~V~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 78 (335)
T cd03802 1 MRIALVAPPREPVPPPAYGGTERVVAALTEGLVAR--GHEVTLFASGDSKTAAPLVPVVPEPLRLDAPGRDRAEAEALAL 78 (335)
T ss_pred CeEEEEcCCcccCCCcccCcHHHHHHHHHHHHHhc--CceEEEEecCCCCcccceeeccCCCcccccchhhHhhHHHHHH
Confidence 7999997653 3333 5566788889887 77899988654321111111111000000 0000111223345
Q ss_pred HHHHhhhCCCcEEEEcCCCChHHHHHHHHhCCCeE
Q 015881 194 ILGVMKNRYYDMVLSTKLAGLGHAAFLFMTTARDR 228 (399)
Q Consensus 194 l~~~LR~~~YDlvIdl~~~~~rsAll~~LsgA~~R 228 (399)
+.+.+++.++|++...... ...++....+.+..
T Consensus 79 ~~~~~~~~~~Divh~~~~~--~~~~~~~~~~~~~v 111 (335)
T cd03802 79 AERALAAGDFDIVHNHSLH--LPLPFARPLPVPVV 111 (335)
T ss_pred HHHHHhcCCCCEEEecCcc--cchhhhcccCCCEE
Confidence 5667888999998754333 12224555555543
No 51
>PF03466 LysR_substrate: LysR substrate binding domain; InterPro: IPR005119 The structure of this domain is known and is similar to the periplasmic binding proteins []. This domain is found in members of the LysR family of prokaryotic transcriptional regulatory proteins IPR000847 from INTERPRO which share sequence similarities over approximately 280 residues including a putative helix-turn-helix DNA-binding motif at their N terminus.; PDB: 3ONM_B 3FZJ_J 3FXR_B 3N6T_A 3FXQ_A 3FXU_A 3N6U_A 2QSX_B 3HO7_B 1IZ1_B ....
Probab=61.46 E-value=41 Score=29.12 Aligned_cols=26 Identities=19% Similarity=0.430 Sum_probs=22.1
Q ss_pred HHhHHHHHHHHHHHCCCcEEEEEEcC
Q 015881 136 NLLFFPAIQLLKDRYPGVLIDVIASA 161 (399)
Q Consensus 136 vVLttPalraLK~~yP~A~IdvLv~~ 161 (399)
..+..+++..++++||+.+|++....
T Consensus 18 ~~~l~~~l~~~~~~~P~i~i~~~~~~ 43 (209)
T PF03466_consen 18 SSLLPPLLAEFRERHPNIRIEIREGD 43 (209)
T ss_dssp HHTHHHHHHHHHHHSTTEEEEEEEES
T ss_pred HHHHHHHHHHHHHHCCCcEEEEEecc
Confidence 66778999999999999999887643
No 52
>COG2327 WcaK Polysaccharide pyruvyl transferase family protein [Cell wall/membrane/envelope biogenesis]
Probab=60.52 E-value=50 Score=34.24 Aligned_cols=39 Identities=10% Similarity=0.197 Sum_probs=33.7
Q ss_pred cEEEEE---cCCChhHHHhHHHHHHHHHHHCCCcEEEEEEcC
Q 015881 123 RRCCCI---ISGGVYENLLFFPAIQLLKDRYPGVLIDVIASA 161 (399)
Q Consensus 123 ~rILII---r~~~IGDvVLttPalraLK~~yP~A~IdvLv~~ 161 (399)
|++++. -.+..||-.+.--++++|++.-|+++|.+++..
T Consensus 1 m~~~L~g~~g~gN~Gdeail~all~~l~~~~~~~~~~~~~~~ 42 (385)
T COG2327 1 MKALLLGYYGFGNIGDEAILKALLDMLRRLNPDAKVLVMGRR 42 (385)
T ss_pred CeeEEEeeecCCCcccHHHHHHHHHHHHhhCcccceeeeecC
Confidence 456665 458899999999999999999999999999863
No 53
>PRK06849 hypothetical protein; Provisional
Probab=59.78 E-value=44 Score=33.96 Aligned_cols=84 Identities=11% Similarity=0.105 Sum_probs=56.4
Q ss_pred CCccEEEEEcCCChhHHHhHHHHHHHHHHHCCCcEEEEEEcCCchHhhhcCCCCCEEEEecCCCCCCChHHHH-HHHHHh
Q 015881 120 GDVRRCCCIISGGVYENLLFFPAIQLLKDRYPGVLIDVIASARGKQTFELNKNVRWANVYDLDDDWPEPAEYT-DILGVM 198 (399)
Q Consensus 120 ~~v~rILIIr~~~IGDvVLttPalraLK~~yP~A~IdvLv~~~~~~lle~nP~ID~Vi~~d~k~~~~~~~~~~-~l~~~L 198 (399)
+..|+|||+-.+. -.+++++++|+++ +.++.++..... .+.....++|+.+.++.... ....+. .++..+
T Consensus 2 ~~~~~VLI~G~~~----~~~l~iar~l~~~--G~~Vi~~d~~~~-~~~~~s~~~d~~~~~p~p~~--d~~~~~~~L~~i~ 72 (389)
T PRK06849 2 NTKKTVLITGARA----PAALELARLFHNA--GHTVILADSLKY-PLSRFSRAVDGFYTIPSPRW--DPDAYIQALLSIV 72 (389)
T ss_pred CCCCEEEEeCCCc----HHHHHHHHHHHHC--CCEEEEEeCCch-HHHHHHHhhhheEEeCCCCC--CHHHHHHHHHHHH
Confidence 3569999995433 2588999999998 888887765432 23345567888887743221 223333 455668
Q ss_pred hhCCCcEEEEcCCC
Q 015881 199 KNRYYDMVLSTKLA 212 (399)
Q Consensus 199 R~~~YDlvIdl~~~ 212 (399)
++++.|++|-+...
T Consensus 73 ~~~~id~vIP~~e~ 86 (389)
T PRK06849 73 QRENIDLLIPTCEE 86 (389)
T ss_pred HHcCCCEEEECChH
Confidence 88899999987654
No 54
>PLN02605 monogalactosyldiacylglycerol synthase
Probab=59.75 E-value=1.6e+02 Score=29.69 Aligned_cols=20 Identities=10% Similarity=0.115 Sum_probs=15.7
Q ss_pred HHHHHhhhCCCcEEEEcCCC
Q 015881 193 DILGVMKNRYYDMVLSTKLA 212 (399)
Q Consensus 193 ~l~~~LR~~~YDlvIdl~~~ 212 (399)
++.+.|++.++|+|+..|..
T Consensus 91 ~l~~~i~~~~pDvIi~thp~ 110 (382)
T PLN02605 91 EVAKGLMKYKPDIIVSVHPL 110 (382)
T ss_pred HHHHHHHhcCcCEEEEeCcC
Confidence 45677888999999997643
No 55
>cd03817 GT1_UGDG_like This family is most closely related to the GT1 family of glycosyltransferases. UDP-glucose-diacylglycerol glucosyltransferase (UGDG; also known as 1,2-diacylglycerol 3-glucosyltransferase) catalyzes the transfer of glucose from UDP-glucose to 1,2-diacylglycerol forming 3-D-glucosyl-1,2-diacylglycerol.
Probab=59.42 E-value=1.6e+02 Score=27.80 Aligned_cols=38 Identities=13% Similarity=-0.034 Sum_probs=25.1
Q ss_pred EEEEEcCCC----hhHHHhHHHHHHHHHHHCCCcEEEEEEcCCc
Q 015881 124 RCCCIISGG----VYENLLFFPAIQLLKDRYPGVLIDVIASARG 163 (399)
Q Consensus 124 rILIIr~~~----IGDvVLttPalraLK~~yP~A~IdvLv~~~~ 163 (399)
|||++-... =|-...+.-++.+|.++ +-++++++....
T Consensus 1 kil~~~~~~~p~~~G~~~~~~~l~~~L~~~--g~~v~v~~~~~~ 42 (374)
T cd03817 1 KIGIFTDTYLPQVNGVATSIRRLAEELEKR--GHEVYVVAPSYP 42 (374)
T ss_pred CeeEeehhccCCCCCeehHHHHHHHHHHHc--CCeEEEEeCCCC
Confidence 577774433 35556666788888877 667888875543
No 56
>cd03820 GT1_amsD_like This family is most closely related to the GT1 family of glycosyltransferases. AmSD in Erwinia amylovora has been shown to be involved in the biosynthesis of amylovoran, the acidic exopolysaccharide acting as a virulence factor. This enzyme may be responsible for the formation of galactose alpha-1,6 linkages in amylovoran.
Probab=59.37 E-value=1e+02 Score=28.65 Aligned_cols=87 Identities=16% Similarity=0.205 Sum_probs=50.6
Q ss_pred EEEEEcCCCh---hHHHhHHHHHHHHHHHCCCcEEEEEEcCCch-HhhhcCCCCCEEEEecCCC--CCCChHHHHHHHHH
Q 015881 124 RCCCIISGGV---YENLLFFPAIQLLKDRYPGVLIDVIASARGK-QTFELNKNVRWANVYDLDD--DWPEPAEYTDILGV 197 (399)
Q Consensus 124 rILIIr~~~I---GDvVLttPalraLK~~yP~A~IdvLv~~~~~-~lle~nP~ID~Vi~~d~k~--~~~~~~~~~~l~~~ 197 (399)
|||++..+.- |......-++++|++. +.+|++++..... ......+.+.......... .+..+.....+.+.
T Consensus 1 kI~i~~~~~~~~gG~~~~~~~l~~~L~~~--g~~v~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 78 (348)
T cd03820 1 KILFVIPSLGNAGGAERVLSNLANALAEK--GHEVTIISLDKGEPPFYELDPKIKVIDLGDKRDSKLLARFKKLRRLRKL 78 (348)
T ss_pred CeEEEeccccCCCChHHHHHHHHHHHHhC--CCeEEEEecCCCCCCccccCCccceeecccccccchhccccchHHHHHh
Confidence 4666654433 4445566788888874 6789998866554 3334444443332211110 01122334566777
Q ss_pred hhhCCCcEEEEcCCC
Q 015881 198 MKNRYYDMVLSTKLA 212 (399)
Q Consensus 198 LR~~~YDlvIdl~~~ 212 (399)
+++.++|+++.....
T Consensus 79 l~~~~~d~i~~~~~~ 93 (348)
T cd03820 79 LKNNKPDVVISFLTS 93 (348)
T ss_pred hcccCCCEEEEcCch
Confidence 888999999988765
No 57
>cd03799 GT1_amsK_like This is a family of GT1 glycosyltransferases found specifically in certain bacteria. amsK in Erwinia amylovora, has been reported to be involved in the biosynthesis of amylovoran, a exopolysaccharide acting as a virulence factor.
Probab=59.01 E-value=1.7e+02 Score=27.94 Aligned_cols=85 Identities=7% Similarity=0.001 Sum_probs=40.9
Q ss_pred EEEEEcCCChh-HHHhHHHHHHHHHHHCCCcEEEEEEcCCchHhhhcCCCCCEEEEecC-CCCCCChHHHHHHHHHhhhC
Q 015881 124 RCCCIISGGVY-ENLLFFPAIQLLKDRYPGVLIDVIASARGKQTFELNKNVRWANVYDL-DDDWPEPAEYTDILGVMKNR 201 (399)
Q Consensus 124 rILIIr~~~IG-DvVLttPalraLK~~yP~A~IdvLv~~~~~~lle~nP~ID~Vi~~d~-k~~~~~~~~~~~l~~~LR~~ 201 (399)
|||++....-+ .-....-.+++|.++ +.+|++++...........-..+....... ...+..+.....+.+.+++.
T Consensus 1 ki~~~~~~~~~~~~~~~~~~~~~L~~~--g~~v~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 78 (355)
T cd03799 1 KIAYLVKEFPRLSETFILREILALEAA--GHEVEIFSLRPPEDTLVHPEDRAELARTRYLARSLALLAQALVLARELRRL 78 (355)
T ss_pred CEEEECCCCCCcchHHHHHHHHHHHhC--CCeEEEEEecCcccccccccccccccchHHHHHHHHHHHHHHHHHHHHHhc
Confidence 57777665544 223334556666665 678888885543322111111111000000 00011122234456667789
Q ss_pred CCcEEEEcC
Q 015881 202 YYDMVLSTK 210 (399)
Q Consensus 202 ~YDlvIdl~ 210 (399)
++|++..-.
T Consensus 79 ~~Dii~~~~ 87 (355)
T cd03799 79 GIDHIHAHF 87 (355)
T ss_pred CCCEEEECC
Confidence 999998643
No 58
>cd01133 F1-ATPase_beta F1 ATP synthase beta subunit, nucleotide-binding domain. The F-ATPase is found in bacterial plasma membranes, mitochondrial inner membranes and in chloroplast thylakoid membranes. It has also been found in the archaea Methanosarcina barkeri. It uses a proton gradient to drive ATP synthesis and hydrolyzes ATP to build the proton gradient. The extrinisic membrane domain, F1, is composed of alpha, beta, gamma, delta and epsilon subunits with a stoichiometry of 3:3:1:1:1. The beta subunit of ATP synthase is catalytic.
Probab=57.31 E-value=1.3e+02 Score=29.77 Aligned_cols=104 Identities=13% Similarity=0.086 Sum_probs=71.0
Q ss_pred cccCcccccCCccEEEEEcCCChhHHHhHHHHHHHHHHHCCCcEEEEEEcCCchHhhh---c---CCCCCEE-EEecCCC
Q 015881 111 IASLPLKIRGDVRRCCCIISGGVYENLLFFPAIQLLKDRYPGVLIDVIASARGKQTFE---L---NKNVRWA-NVYDLDD 183 (399)
Q Consensus 111 ~~~~~~~~~~~v~rILIIr~~~IGDvVLttPalraLK~~yP~A~IdvLv~~~~~~lle---~---nP~ID~V-i~~d~k~ 183 (399)
|+.|..-.+ -.|++|+-..+.|=..|..=+++.+++++.+.-|-.++..+..++-+ . ....++. ++....+
T Consensus 60 ID~l~pig~--GQr~~If~~~G~GKTtLa~~i~~~i~~~~~~~~V~~~iGer~~Ev~e~~~~~~~~~~~~~tvvv~~t~d 137 (274)
T cd01133 60 IDLLAPYAK--GGKIGLFGGAGVGKTVLIMELINNIAKAHGGYSVFAGVGERTREGNDLYHEMKESGVLSKTALVYGQMN 137 (274)
T ss_pred eeccCCccc--CCEEEEecCCCCChhHHHHHHHHHHHhcCCCEEEEEEeccCcHHHHHHHHHHHhcCCcceeEEEEECCC
Confidence 445555555 37999999999999999999999999999998888888888776532 2 2334443 3333332
Q ss_pred CCCChHH------HHHHHHHhhhC-CCcEEEEcCCCChHHHH
Q 015881 184 DWPEPAE------YTDILGVMKNR-YYDMVLSTKLAGLGHAA 218 (399)
Q Consensus 184 ~~~~~~~------~~~l~~~LR~~-~YDlvIdl~~~~~rsAl 218 (399)
. .-..+ -..+...+|.+ .+|+.|-+.+- .|.|-
T Consensus 138 ~-~~~~r~~~~~~a~~~AEyfr~~~g~~Vl~~~Dsl-tr~a~ 177 (274)
T cd01133 138 E-PPGARARVALTGLTMAEYFRDEEGQDVLLFIDNI-FRFTQ 177 (274)
T ss_pred C-CHHHHHHHHHHHHHHHHHHHHhcCCeEEEEEeCh-hHHHH
Confidence 2 11111 13466778887 99999988776 55443
No 59
>PRK12767 carbamoyl phosphate synthase-like protein; Provisional
Probab=57.08 E-value=58 Score=31.88 Aligned_cols=77 Identities=12% Similarity=0.028 Sum_probs=48.1
Q ss_pred ccEEEEEcCCChhHHHhHHHHHHHHHHHCCCcEEEEEEcCCchHhhhcCCCCCEEEEecCCCCCCChHHHHHHHHHhhhC
Q 015881 122 VRRCCCIISGGVYENLLFFPAIQLLKDRYPGVLIDVIASARGKQTFELNKNVRWANVYDLDDDWPEPAEYTDILGVMKNR 201 (399)
Q Consensus 122 v~rILIIr~~~IGDvVLttPalraLK~~yP~A~IdvLv~~~~~~lle~nP~ID~Vi~~d~k~~~~~~~~~~~l~~~LR~~ 201 (399)
||||||.--+.. + +++++|+++..+.+|..+-.....+... ..|+.+..+.... ....-.++..+++.
T Consensus 1 ~~~vLv~g~~~~---~---~~~~~l~~~~~g~~vi~~d~~~~~~~~~---~~d~~~~~p~~~~---~~~~~~l~~~~~~~ 68 (326)
T PRK12767 1 MMNILVTSAGRR---V---QLVKALKKSLLKGRVIGADISELAPALY---FADKFYVVPKVTD---PNYIDRLLDICKKE 68 (326)
T ss_pred CceEEEecCCcc---H---HHHHHHHHhccCCEEEEECCCCcchhhH---hccCcEecCCCCC---hhHHHHHHHHHHHh
Confidence 689999876433 2 7899999998777776664443333322 3455555543211 11223566677888
Q ss_pred CCcEEEEcC
Q 015881 202 YYDMVLSTK 210 (399)
Q Consensus 202 ~YDlvIdl~ 210 (399)
+.|++|-..
T Consensus 69 ~id~ii~~~ 77 (326)
T PRK12767 69 KIDLLIPLI 77 (326)
T ss_pred CCCEEEECC
Confidence 999998754
No 60
>cd03794 GT1_wbuB_like This family is most closely related to the GT1 family of glycosyltransferases. wbuB in E. coli is involved in the biosynthesis of the O26 O-antigen. It has been proposed to function as an N-acetyl-L-fucosamine (L-FucNAc) transferase.
Probab=57.00 E-value=1.8e+02 Score=27.53 Aligned_cols=39 Identities=13% Similarity=-0.038 Sum_probs=29.4
Q ss_pred EEEEEcCCCh----hHHHhHHHHHHHHHHHCCCcEEEEEEcCCch
Q 015881 124 RCCCIISGGV----YENLLFFPAIQLLKDRYPGVLIDVIASARGK 164 (399)
Q Consensus 124 rILIIr~~~I----GDvVLttPalraLK~~yP~A~IdvLv~~~~~ 164 (399)
|||+|....- |....+.-++++|+++ +.+|++++.....
T Consensus 1 kIl~i~~~~~~~~~G~~~~~~~l~~~L~~~--g~~v~~~~~~~~~ 43 (394)
T cd03794 1 KILILSQYFPPELGGGAFRTTELAEELVKR--GHEVTVITGSPNY 43 (394)
T ss_pred CEEEEecccCCccCCcceeHHHHHHHHHhC--CceEEEEecCCCc
Confidence 6788866543 6777778899999987 7899999865443
No 61
>PRK12608 transcription termination factor Rho; Provisional
Probab=56.63 E-value=38 Score=35.03 Aligned_cols=95 Identities=12% Similarity=0.025 Sum_probs=67.5
Q ss_pred ccEEEEEcCCChhHHHhHHHHHHHHHHHCCCcE-EEEEEcCCchHhhhcCCCCCEEEEecCCCC--CCC--hH-HHHHHH
Q 015881 122 VRRCCCIISGGVYENLLFFPAIQLLKDRYPGVL-IDVIASARGKQTFELNKNVRWANVYDLDDD--WPE--PA-EYTDIL 195 (399)
Q Consensus 122 v~rILIIr~~~IGDvVLttPalraLK~~yP~A~-IdvLv~~~~~~lle~nP~ID~Vi~~d~k~~--~~~--~~-~~~~l~ 195 (399)
-.|+||+-..+-|=..+.-=+++.+-+++|++. +.+++..+..++-+..-.|..++.....+. ... .. ....++
T Consensus 133 GQR~LIvG~pGtGKTTLl~~la~~i~~~~~dv~~vv~lIgER~~EV~df~~~i~~~Vvast~de~~~~~~~v~~~~~~~A 212 (380)
T PRK12608 133 GQRGLIVAPPRAGKTVLLQQIAAAVAANHPEVHLMVLLIDERPEEVTDMRRSVKGEVYASTFDRPPDEHIRVAELVLERA 212 (380)
T ss_pred CceEEEECCCCCCHHHHHHHHHHHHHhcCCCceEEEEEecCCCCCHHHHHHHHhhhEEeecCCCCHHHHHHHHHHHHHHH
Confidence 479999999999999999999999999999997 555777777766555544544555433211 011 11 234677
Q ss_pred HHhhhCCCcEEEEcCCCChHHH
Q 015881 196 GVMKNRYYDMVLSTKLAGLGHA 217 (399)
Q Consensus 196 ~~LR~~~YDlvIdl~~~~~rsA 217 (399)
..++++.+|++|.+..- .+.|
T Consensus 213 e~f~~~GkdVVLvlDsl-tr~A 233 (380)
T PRK12608 213 KRLVEQGKDVVILLDSL-TRLA 233 (380)
T ss_pred HHHHHcCCCEEEEEeCc-HHHH
Confidence 78999999999988776 4443
No 62
>TIGR00246 tRNA_RlmH_YbeA rRNA large subunit m3Psi methyltransferase RlmH. This protein, in the SPOUT methyltransferase family, previously designated YbeA in E. coli, was shown to be responsible for a further modification, a methylation, to a pseudouridine base in ribosomal large subunit RNA.
Probab=54.38 E-value=47 Score=29.88 Aligned_cols=70 Identities=4% Similarity=-0.046 Sum_probs=41.5
Q ss_pred HHHHHHHhCCCCCCeEEEEcCCCCccccccCCCCCCCCCCHHHHHHHHHHhhhCC--CEEEeCCchhHHHHHHHHhcCCC
Q 015881 298 VAEKYKNAGAEQGKYIVIHGIESDSKASMQSRGDTDSLLPIQVWAEIANGLREFR--PLFVIPHEKEREGVEDVVGDDAS 375 (399)
Q Consensus 298 a~~~l~~~gl~~~~~IvIhPgas~~~~~~k~rg~~~KrWP~e~faeLa~~L~~~~--~VvliGgp~E~e~aeeI~~~~~~ 375 (399)
++.++.... ....|++.+.. |.+..+.||+.++.....+ -++++||+. ...+++.+.+..
T Consensus 56 ~~~il~~~~--~~~~i~LDe~G--------------k~~sS~~fA~~l~~~~~~g~~i~FvIGGa~--G~~~~v~~~a~~ 117 (153)
T TIGR00246 56 GDRILAAIG--KAHVVTLDIPG--------------KPWTTPQLADTLEKWKTDGRDVTLLIGGPE--GLSPTCKAAAEQ 117 (153)
T ss_pred HHHHHHhCC--CCeEEEEcCCC--------------CcCCHHHHHHHHHHHhccCCeEEEEEcCCC--cCCHHHHHhcCc
Confidence 445565553 34566676542 5699999999999876554 466788885 222344444332
Q ss_pred CceeecCCccccc
Q 015881 376 IVFITTPGQVRMS 388 (399)
Q Consensus 376 ~~~i~~~G~ls~~ 388 (399)
. + +-+++|+.
T Consensus 118 ~--l-SLS~mTfp 127 (153)
T TIGR00246 118 S--W-SLSKLTLP 127 (153)
T ss_pred e--E-EeecCCCc
Confidence 2 2 23455554
No 63
>cd08450 PBP2_HcaR The C-terminal substrate binding domain of LysR-type transcriptional regulator HcaR in involved in 3-phenylpropionic acid catabolism, contains the type2 periplasmic binding fold. HcaR, a member of the LysR family of transcriptional regulators, controls the expression of the hcA1, A2, B, C, and D operon, encoding for the 3-phenylpropionate dioxygenase complex and 3-phenylpropionate-2',3'-dihydrodiol dehydrogenase, that oxidizes 3-phenylpropionate to 3-(2,3-dihydroxyphenyl) propionate. Dioxygenases play an important role in protecting the cell against the toxic effects of dioxygen. The expression of hcaR is negatively auto-regulated, as for other members of the LysR family, and is strongly repressed in the presence of glucose. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, an
Probab=53.99 E-value=53 Score=28.01 Aligned_cols=24 Identities=8% Similarity=0.263 Sum_probs=20.6
Q ss_pred HhHHHHHHHHHHHCCCcEEEEEEc
Q 015881 137 LLFFPAIQLLKDRYPGVLIDVIAS 160 (399)
Q Consensus 137 VLttPalraLK~~yP~A~IdvLv~ 160 (399)
.+..+++..++++||+++|.+...
T Consensus 13 ~~l~~~l~~~~~~~P~i~l~i~~~ 36 (196)
T cd08450 13 QWLPEVLPILREEHPDLDVELSSL 36 (196)
T ss_pred hhHHHHHHHHHhhCCCcEEEEEec
Confidence 455799999999999999998764
No 64
>cd04962 GT1_like_5 This family is most closely related to the GT1 family of glycosyltransferases. Glycosyltransferases catalyze the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming glycosidic bonds. The acceptor molecule can be a lipid, a protein, a heterocyclic compound, or another carbohydrate residue. This group of glycosyltransferases is most closely related to the previously defined glycosyltransferase family 1 (GT1). The members of this family may transfer UDP, ADP, GDP, or CMP linked sugars. The diverse enzymatic activities among members of this family reflect a wide range of biological functions. The protein structure available for this family has the GTB topology, one of the two protein topologies observed for nucleotide-sugar-dependent glycosyltransferases. GTB proteins have distinct N- and C- terminal domains each containing a typical Rossmann fold. The two domains have high structural homology despite minimal sequence homolog
Probab=51.69 E-value=2.3e+02 Score=27.38 Aligned_cols=84 Identities=15% Similarity=0.035 Sum_probs=44.9
Q ss_pred cEEEEEcCCChhH-HHhHHHHHHHHHHHCCCcEEEEEEcCCchHhhhcCCCCCEEEEecCCC------CCCChHHHHHHH
Q 015881 123 RRCCCIISGGVYE-NLLFFPAIQLLKDRYPGVLIDVIASARGKQTFELNKNVRWANVYDLDD------DWPEPAEYTDIL 195 (399)
Q Consensus 123 ~rILIIr~~~IGD-vVLttPalraLK~~yP~A~IdvLv~~~~~~lle~nP~ID~Vi~~d~k~------~~~~~~~~~~l~ 195 (399)
|||+++.....|. -..++-+.+.|.++ +.++++++...........+.+. ++..+... ..........+.
T Consensus 1 mki~~~~~p~~gG~~~~~~~la~~L~~~--G~~v~v~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~l~ 77 (371)
T cd04962 1 MKIGIVCYPTYGGSGVVATELGKALARR--GHEVHFITSSRPFRLDEYSPNIF-FHEVEVPQYPLFQYPPYDLALASKIA 77 (371)
T ss_pred CceeEEEEeCCCCccchHHHHHHHHHhc--CCceEEEecCCCcchhhhccCeE-EEEecccccchhhcchhHHHHHHHHH
Confidence 6888886633333 34556778888887 56788887643221112222221 11111110 001122235667
Q ss_pred HHhhhCCCcEEEEc
Q 015881 196 GVMKNRYYDMVLST 209 (399)
Q Consensus 196 ~~LR~~~YDlvIdl 209 (399)
+.+++.++|++...
T Consensus 78 ~~i~~~~~divh~~ 91 (371)
T cd04962 78 EVAKRYKLDLLHVH 91 (371)
T ss_pred HHHhcCCccEEeec
Confidence 77888999988753
No 65
>COG1576 Uncharacterized conserved protein [Function unknown]
Probab=51.68 E-value=48 Score=30.04 Aligned_cols=28 Identities=21% Similarity=0.254 Sum_probs=23.5
Q ss_pred CCCCHHHHHHHHHHhhhCC--CEEEeCCch
Q 015881 334 SLLPIQVWAEIANGLREFR--PLFVIPHEK 361 (399)
Q Consensus 334 KrWP~e~faeLa~~L~~~~--~VvliGgp~ 361 (399)
|.|..|.||...+.+...+ -++++||+.
T Consensus 78 k~~sSe~fA~~l~~~~~~G~~i~f~IGG~~ 107 (155)
T COG1576 78 KALSSEEFADFLERLRDDGRDISFLIGGAD 107 (155)
T ss_pred CcCChHHHHHHHHHHHhcCCeEEEEEeCcc
Confidence 6799999999999998766 566778876
No 66
>TIGR02700 flavo_MJ0208 archaeoflavoprotein, MJ0208 family. This model describes one of two paralogous families of archaealflavoprotein. The other, described by TIGR02699 and typified by the partially characterized AF1518 of Archaeoglobus fulgidus, is a homodimeric FMN-containing flavoprotein that accepts electrons from ferredoxin and can transfer them to various oxidoreductases. The function of this protein family is unknown.
Probab=51.58 E-value=27 Score=33.29 Aligned_cols=47 Identities=17% Similarity=0.170 Sum_probs=38.8
Q ss_pred EEEEEcCCChhHHHhHHHHHHHHHHHCCCcEEEEEEcCCchHhhhcC
Q 015881 124 RCCCIISGGVYENLLFFPAIQLLKDRYPGVLIDVIASARGKQTFELN 170 (399)
Q Consensus 124 rILIIr~~~IGDvVLttPalraLK~~yP~A~IdvLv~~~~~~lle~n 170 (399)
||++--+++-+=...+..+++.|+++|++++|+++..+.++.++...
T Consensus 1 ~i~~~itGs~~~~~~~~~l~~~L~~~~~g~~V~vv~T~~a~~~i~~~ 47 (234)
T TIGR02700 1 RIGWGITGAGHLLVESFQVMKELKREIEELRVSTFVSRAGEEVVRMY 47 (234)
T ss_pred CeEEEEeCccHhHHHHHHHHHHHHhhcCCCeEEEEEChhHHhHHhhh
Confidence 46666666666667999999999999999999999999888776643
No 67
>cd03798 GT1_wlbH_like This family is most closely related to the GT1 family of glycosyltransferases. wlbH in Bordetella parapertussis has been shown to be required for the biosynthesis of a trisaccharide that, when attached to the B. pertussis lipopolysaccharide (LPS) core (band B), generates band A LPS.
Probab=50.35 E-value=2.2e+02 Score=26.62 Aligned_cols=96 Identities=14% Similarity=-0.048 Sum_probs=48.7
Q ss_pred hhHHHhHHHHHHHHHHHCCCcEEEEEEcCCchHhhhcC-CC-------CCEEEE-e-cCCCCCCChHHHHHHHHHhh--h
Q 015881 133 VYENLLFFPAIQLLKDRYPGVLIDVIASARGKQTFELN-KN-------VRWANV-Y-DLDDDWPEPAEYTDILGVMK--N 200 (399)
Q Consensus 133 IGDvVLttPalraLK~~yP~A~IdvLv~~~~~~lle~n-P~-------ID~Vi~-~-d~k~~~~~~~~~~~l~~~LR--~ 200 (399)
=|-.....-++.+|++. +.++++++......-.... .. ...... . .....+........+.+.++ .
T Consensus 14 ~g~~~~~~~~~~~l~~~--g~~v~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~ 91 (377)
T cd03798 14 GGGGIFVKELARALAKR--GVEVTVLAPGPWGPKLLDLLKGRLVGVERLPVLLPVVPLLKGPLLYLLAARALLKLLKLKR 91 (377)
T ss_pred chHHHHHHHHHHHHHHC--CCceEEEecCCCCCCchhhcccccccccccccCcchhhccccchhHHHHHHHHHHHHhccc
Confidence 56677778889999865 7789999865443221111 00 000000 0 00000111222345566777 8
Q ss_pred CCCcEEEEcCCCChHH---HHHHHHhCCCeEEEe
Q 015881 201 RYYDMVLSTKLAGLGH---AAFLFMTTARDRVSY 231 (399)
Q Consensus 201 ~~YDlvIdl~~~~~rs---All~~LsgA~~RIGy 231 (399)
.++|+++..... ... ..+....+++..+-.
T Consensus 92 ~~~dii~~~~~~-~~~~~~~~~~~~~~~~~i~~~ 124 (377)
T cd03798 92 FRPDLIHAHFAY-PDGFAAALLKRKLGIPLVVTL 124 (377)
T ss_pred CCCCEEEEeccc-hHHHHHHHHHHhcCCCEEEEe
Confidence 999999877544 322 233334444654443
No 68
>cd08446 PBP2_Chlorocatechol The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in the chlorocatechol catabolism, contains the type 2 periplasmic binding fold. This CD includes the substrate binding domain of LysR-type regulators CbnR, ClcR and TfdR, which are involved in the regulation of chlorocatechol breakdown. The chlorocatechol-degradative pathway is often found in bacteria that can use chlorinated aromatic compounds as carbon and energy sources. CbnR is found in the 3-chlorobenzoate degradative bacterium Ralstonia eutropha NH9 and forms a tetramer. CbnR activates the expression of the cbnABCD genes, which are responsible for the degradation of chlorocatechol converted from 3-chlorobenzoate and are transcribed divergently from cbnR. In soil bacterium Pseudomonas putida, the 3-chlorocatechol-degradative pathway is encoded by clcABD operon, which requires the divergently transcribed clcR for activation. TfdR is involved in the activation of tf
Probab=49.88 E-value=76 Score=27.11 Aligned_cols=30 Identities=10% Similarity=0.089 Sum_probs=22.7
Q ss_pred CCChhHHHhHHHHHHHHHHHCCCcEEEEEEc
Q 015881 130 SGGVYENLLFFPAIQLLKDRYPGVLIDVIAS 160 (399)
Q Consensus 130 ~~~IGDvVLttPalraLK~~yP~A~IdvLv~ 160 (399)
...++..+ ..+++..++++||+++|++...
T Consensus 8 ~~~~~~~~-l~~~i~~~~~~~P~v~l~i~~~ 37 (198)
T cd08446 8 FGSAILDT-VPRLLRAFLTARPDVTVSLHNM 37 (198)
T ss_pred chHHHHHH-HHHHHHHHHHHCCCeEEEEeeC
Confidence 34444443 4789999999999999998764
No 69
>PRK00103 rRNA large subunit methyltransferase; Provisional
Probab=49.82 E-value=59 Score=29.37 Aligned_cols=74 Identities=11% Similarity=0.039 Sum_probs=0.0
Q ss_pred HHHHHHHHHHhCCCCCCeEEEEcCCCCccccccCCCCCCCCCCHHHHHHHHHHhhhCC---CEEEeCCchhHHHHHHHHh
Q 015881 295 KEVVAEKYKNAGAEQGKYIVIHGIESDSKASMQSRGDTDSLLPIQVWAEIANGLREFR---PLFVIPHEKEREGVEDVVG 371 (399)
Q Consensus 295 ~~~a~~~l~~~gl~~~~~IvIhPgas~~~~~~k~rg~~~KrWP~e~faeLa~~L~~~~---~VvliGgp~E~e~aeeI~~ 371 (399)
.+.++.+++..... ...|++.+.. |.+..+.||+.++.....+ -++++||+. ...+++.+
T Consensus 54 ~~E~~~il~~l~~~-~~~i~LDe~G--------------k~~sS~~fA~~l~~~~~~g~~~i~F~IGGa~--G~~~~v~~ 116 (157)
T PRK00103 54 AKEGERILAALPKG-ARVIALDERG--------------KQLSSEEFAQELERWRDDGRSDVAFVIGGAD--GLSPAVKK 116 (157)
T ss_pred HHHHHHHHhhCCCC-CEEEEEcCCC--------------CcCCHHHHHHHHHHHHhcCCccEEEEEcCcc--ccCHHHHH
Q ss_pred cCCCCceeecCCccccc
Q 015881 372 DDASIVFITTPGQVRMS 388 (399)
Q Consensus 372 ~~~~~~~i~~~G~ls~~ 388 (399)
.+.... +-|++|+.
T Consensus 117 ~a~~~l---SLS~mTfp 130 (157)
T PRK00103 117 RADQSL---SLSKLTLP 130 (157)
T ss_pred hcCceE---EeccCCCc
No 70
>PRK06029 3-octaprenyl-4-hydroxybenzoate carboxy-lyase; Provisional
Probab=49.53 E-value=30 Score=32.09 Aligned_cols=46 Identities=22% Similarity=0.247 Sum_probs=40.0
Q ss_pred ccEEEEEcCCChhHHHhHHHHHHHHHHHCCCcEEEEEEcCCchHhhhc
Q 015881 122 VRRCCCIISGGVYENLLFFPAIQLLKDRYPGVLIDVIASARGKQTFEL 169 (399)
Q Consensus 122 v~rILIIr~~~IGDvVLttPalraLK~~yP~A~IdvLv~~~~~~lle~ 169 (399)
++|||+.-.++|| .+.+.=+++.|++. .+++|++++.+.+..++..
T Consensus 1 ~k~IllgVTGsia-a~ka~~l~~~L~k~-~g~~V~vv~T~~A~~fv~~ 46 (185)
T PRK06029 1 MKRLIVGISGASG-AIYGVRLLQVLRDV-GEIETHLVISQAARQTLAH 46 (185)
T ss_pred CCEEEEEEECHHH-HHHHHHHHHHHHhh-cCCeEEEEECHHHHHHHHH
Confidence 5799999999999 88888999999875 3789999999999888764
No 71
>cd08452 PBP2_AlsR The C-terminal substrate binding domain of LysR-type trnascriptional regulator AlsR, which regulates acetoin formation under stationary phase growth conditions; contains the type 2 periplasmic binding fold. AlsR is responsible for activating the expression of the acetoin operon (alsSD) in response to inducing signals such as glucose and acetate. Like many other LysR family proteins, AlsR is transcribed divergently from the alsSD operon. The alsS gene encodes acetolactate synthase, an enzyme involved in the production of acetoin in cells of stationary-phase. AlsS catalyzes the conversion of two pyruvate molecules to acetolactate and carbon dioxide. Acetolactate is then converted to acetoin at low pH by acetolactate decarboxylase which encoded by the alsD gene. Acetoin is an important physiological metabolite excreted by many microorganisms grown on glucose or other fermentable carbon sources. This substrate-binding domain shows significant homology to the type 2 perip
Probab=47.92 E-value=74 Score=27.47 Aligned_cols=28 Identities=14% Similarity=0.386 Sum_probs=21.8
Q ss_pred ChhHHHhHHHHHHHHHHHCCCcEEEEEEc
Q 015881 132 GVYENLLFFPAIQLLKDRYPGVLIDVIAS 160 (399)
Q Consensus 132 ~IGDvVLttPalraLK~~yP~A~IdvLv~ 160 (399)
.++..++ .|+++.++++||+++|++...
T Consensus 9 ~~~~~~l-~~~l~~~~~~~P~v~i~i~~~ 36 (197)
T cd08452 9 AAIYEFL-PPIVREYRKKFPSVKVELREL 36 (197)
T ss_pred HHHHhHH-HHHHHHHHHHCCCcEEEEEec
Confidence 3444333 699999999999999999764
No 72
>PRK15490 Vi polysaccharide biosynthesis protein TviE; Provisional
Probab=47.49 E-value=2.3e+02 Score=31.10 Aligned_cols=90 Identities=9% Similarity=-0.085 Sum_probs=51.3
Q ss_pred HHhHHHHHHHHHHHCCCcEEEEEEcCCchHhhhcCCCCCEEEEecCCCCCCChHHHHHHHHHhhhCCCcEEEEcCCCC-h
Q 015881 136 NLLFFPAIQLLKDRYPGVLIDVIASARGKQTFELNKNVRWANVYDLDDDWPEPAEYTDILGVMKNRYYDMVLSTKLAG-L 214 (399)
Q Consensus 136 vVLttPalraLK~~yP~A~IdvLv~~~~~~lle~nP~ID~Vi~~d~k~~~~~~~~~~~l~~~LR~~~YDlvIdl~~~~-~ 214 (399)
.=.+.+.+++ .+-|..+|+.+....+..+--..|.+...+..-++- -...+.++...||+.++|+|-.-+... .
T Consensus 219 ~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~l~~~ir~~rpDIVHt~~~~a~l 293 (578)
T PRK15490 219 QDFFLKEVLE--EQVEVLEIAKITGNLFDDATIESPELRLLLSHLPPV---CKYGIKHLVPHLCERKLDYLSVWQDGACL 293 (578)
T ss_pred cchhHHHHHh--cCCceEEeeccchhhhhhccccchHHHHHHhcCChH---HHHHHHHHHHHHHHcCCCEEEEcCcccHH
Confidence 3345555555 667777777776333322211122222221111100 012456788899999999997665442 4
Q ss_pred HHHHHHHHhCCCeEEE
Q 015881 215 GHAAFLFMTTARDRVS 230 (399)
Q Consensus 215 rsAll~~LsgA~~RIG 230 (399)
..++.++++|.+.++.
T Consensus 294 ~g~laA~lagvpviv~ 309 (578)
T PRK15490 294 MIALAALIAGVPRIQL 309 (578)
T ss_pred HHHHHHHhcCCCEEEE
Confidence 5677899999998775
No 73
>COG1158 Rho Transcription termination factor [Transcription]
Probab=47.10 E-value=1.1e+02 Score=31.48 Aligned_cols=91 Identities=12% Similarity=0.099 Sum_probs=67.4
Q ss_pred ccEEEEEcCCChhHHHhHHHHHHHHHHHCCCcEEEE-EEcCCchHhhhcCCCCC-EEEEecCCCC---CCChHH-HHHHH
Q 015881 122 VRRCCCIISGGVYENLLFFPAIQLLKDRYPGVLIDV-IASARGKQTFELNKNVR-WANVYDLDDD---WPEPAE-YTDIL 195 (399)
Q Consensus 122 v~rILIIr~~~IGDvVLttPalraLK~~yP~A~Idv-Lv~~~~~~lle~nP~ID-~Vi~~d~k~~---~~~~~~-~~~l~ 195 (399)
-.|-|||.+-.-|-++|.--+..++-..+|++++-+ |+.++-.++=++.-.|+ +|+.-..... .-..++ .+.-.
T Consensus 173 GQR~LIVAPPkaGKT~lLq~IA~aIt~N~Pe~~LiVLLIDERPEEVTdmqrsV~geViaSTFDepp~~HvqVAE~viEkA 252 (422)
T COG1158 173 GQRGLIVAPPKAGKTTLLQNIANAITTNHPECELIVLLIDERPEEVTDMQRSVKGEVVASTFDEPPSRHVQVAEMVIEKA 252 (422)
T ss_pred CceeeEecCCCCCchHHHHHHHHHHhcCCCceEEEEEEecCCchHHHHHHHhhcceEEeecCCCcchhhHHHHHHHHHHH
Confidence 479999999999999999999999999999998655 57888888877777776 4554332211 011222 23456
Q ss_pred HHhhhCCCcEEEEcCCC
Q 015881 196 GVMKNRYYDMVLSTKLA 212 (399)
Q Consensus 196 ~~LR~~~YDlvIdl~~~ 212 (399)
++|-..+.|+||-+.+-
T Consensus 253 KRlVE~~kDVVILLDSI 269 (422)
T COG1158 253 KRLVEHGKDVVILLDSI 269 (422)
T ss_pred HHHHHcCCcEEEEehhH
Confidence 67878999999988654
No 74
>PF04230 PS_pyruv_trans: Polysaccharide pyruvyl transferase; InterPro: IPR007345 Pyruvyl-transferases are involved in peptidoglycan-associated polymer biosynthesis. CsaB in Bacillus anthracis is necessary for the non-covalent anchoring of proteins containing an SLH (S-layer homology) domain to peptidoglycan-associated pyruvylated polysaccharides. WcaK and AmsJ are involved in the biosynthesis of colanic acid in Escherichia coli and of amylovoran in Erwinia amylovora [, ].
Probab=46.52 E-value=23 Score=32.56 Aligned_cols=33 Identities=18% Similarity=0.324 Sum_probs=29.0
Q ss_pred ChhHHHhHHHHHHHHHHHCCCcEEEEEEcCCch
Q 015881 132 GVYENLLFFPAIQLLKDRYPGVLIDVIASARGK 164 (399)
Q Consensus 132 ~IGDvVLttPalraLK~~yP~A~IdvLv~~~~~ 164 (399)
.+||.++...+++.|++.+|+++|.++......
T Consensus 1 N~GD~~i~~~~~~~l~~~~~~~~~~~~~~~~~~ 33 (286)
T PF04230_consen 1 NIGDDLILEALLKLLKKHGPDAEIIIFSPDPDE 33 (286)
T ss_pred CchHHHHHHHHHHHHHhcCCceEEEEeCCChHH
Confidence 479999999999999999999999999855443
No 75
>PLN02316 synthase/transferase
Probab=46.04 E-value=90 Score=36.53 Aligned_cols=71 Identities=14% Similarity=0.171 Sum_probs=44.7
Q ss_pred cccccCCCCCCCCCCCCCCCCCCcccccCCCCCcccccCcccccCCccEEEEE--------cCCChhHHHhHHHHHHHHH
Q 015881 76 GSLFADGKQDEDPRPPDDPNNPYGFLKFPMGFNPEIASLPLKIRGDVRRCCCI--------ISGGVYENLLFFPAIQLLK 147 (399)
Q Consensus 76 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~rILII--------r~~~IGDvVLttPalraLK 147 (399)
-=+||+|. |. -.-+|..|. + |...+- ....+...||||.| +.++|||+|-.+| ++|.
T Consensus 554 dfvFs~~~--~g----~~yDn~~~~-d----yh~~v~--g~~~~~~pM~Il~VSsE~~P~aKvGGLgDVV~sLp--~ALa 618 (1036)
T PLN02316 554 DFVFSEKE--EG----GIFDNRNGL-D----YHIPVF--GGIAKEPPMHIVHIAVEMAPIAKVGGLGDVVTSLS--RAVQ 618 (1036)
T ss_pred EEEEecCC--CC----CCcCCCCCc-C----Cccccc--CCCCCCCCcEEEEEEcccCCCCCcCcHHHHHHHHH--HHHH
Confidence 44788882 22 344454442 2 222222 33344557999975 5799999999887 6777
Q ss_pred HHCCCcEEEEEEcCCc
Q 015881 148 DRYPGVLIDVIASARG 163 (399)
Q Consensus 148 ~~yP~A~IdvLv~~~~ 163 (399)
+. +.+|++++....
T Consensus 619 ~~--Gh~V~VitP~Y~ 632 (1036)
T PLN02316 619 DL--NHNVDIILPKYD 632 (1036)
T ss_pred Hc--CCEEEEEecCCc
Confidence 65 668888887654
No 76
>TIGR02174 CXXU_selWTH selT/selW/selH selenoprotein domain. This model represents a domain found in both bacteria and animals, including animal proteins SelT, SelW, and SelH, all of which are selenoproteins. In a CXXC motif near the N-terminus of the domain, selenocysteine may replace the second Cys. Proteins with this domain may include an insert of about 70 amino acids. This model is broader than the current SelW model pfam05169 in Pfam.
Probab=45.51 E-value=33 Score=26.68 Aligned_cols=50 Identities=24% Similarity=0.274 Sum_probs=33.6
Q ss_pred HHHHHHHHHHHCCCcEEEEEEcCCchHhhhcCCCCCEEEEecCCC--CCCChHH
Q 015881 139 FFPAIQLLKDRYPGVLIDVIASARGKQTFELNKNVRWANVYDLDD--DWPEPAE 190 (399)
Q Consensus 139 ttPalraLK~~yP~A~IdvLv~~~~~~lle~nP~ID~Vi~~d~k~--~~~~~~~ 190 (399)
+.=+-++|.++||+..+.....+.....|+-. ||..++|+++. +|....+
T Consensus 15 a~~l~q~L~~~Fp~~~v~~~~~~~~~G~Fev~--~~g~~v~sk~~~~~fp~~~~ 66 (72)
T TIGR02174 15 AAWLKQELLEEFPDLEIEGENTPPTTGAFEVT--VNGQLVWSKLRGGGFPEPEE 66 (72)
T ss_pred HHHHHHHHHHHCCCCeeEEeeecCCCcEEEEE--ECCEEEEEeccCCCCCCHHH
Confidence 34467899999999888877766655555542 36677888753 3455444
No 77
>PRK05647 purN phosphoribosylglycinamide formyltransferase; Reviewed
Probab=45.16 E-value=1.5e+02 Score=27.70 Aligned_cols=84 Identities=14% Similarity=0.145 Sum_probs=50.3
Q ss_pred ccEEEEEcCCChhHHHhHHHHHHHHHHHCCCcEEEEEEcC-CchHh--hhcCCCCCEEEEecCCCCCCChHHH-HHHHHH
Q 015881 122 VRRCCCIISGGVYENLLFFPAIQLLKDRYPGVLIDVIASA-RGKQT--FELNKNVRWANVYDLDDDWPEPAEY-TDILGV 197 (399)
Q Consensus 122 v~rILIIr~~~IGDvVLttPalraLK~~yP~A~IdvLv~~-~~~~l--le~nP~ID~Vi~~d~k~~~~~~~~~-~~l~~~ 197 (399)
||||.|+..+. |. ++-++++++.+..-.+.|.+++.. ....+ +...-+|. ++.++..+ ..+...+ -.++..
T Consensus 1 m~ki~vl~sg~-gs--~~~~ll~~~~~~~~~~~I~~vvs~~~~~~~~~~a~~~gIp-~~~~~~~~-~~~~~~~~~~~~~~ 75 (200)
T PRK05647 1 MKRIVVLASGN-GS--NLQAIIDACAAGQLPAEIVAVISDRPDAYGLERAEAAGIP-TFVLDHKD-FPSREAFDAALVEA 75 (200)
T ss_pred CceEEEEEcCC-Ch--hHHHHHHHHHcCCCCcEEEEEEecCccchHHHHHHHcCCC-EEEECccc-cCchhHhHHHHHHH
Confidence 48888887644 44 345888999888777899887544 22222 23333554 44444322 1111111 246777
Q ss_pred hhhCCCcEEEEcC
Q 015881 198 MKNRYYDMVLSTK 210 (399)
Q Consensus 198 LR~~~YDlvIdl~ 210 (399)
|+..+.|++|...
T Consensus 76 l~~~~~D~iv~~~ 88 (200)
T PRK05647 76 LDAYQPDLVVLAG 88 (200)
T ss_pred HHHhCcCEEEhHH
Confidence 8889999998754
No 78
>cd08439 PBP2_LrhA_like The C-terminal substrate domain of LysR-like regulator LrhA (LysR homologue A) and that of closely related homologs, contains the type 2 periplasmic binding fold. This CD represents the LrhA subfamily of LysR-like bacterial transcriptional regulators, including LrhA, HexA, PecT, and DgdR. LrhA is involved in control of the transcription of flagellar, motility, and chemotaxis genes by regulating the synthesis and concentration of FlhD(2)C(2), the master regulator for the expression of flagellar and chemotaxis genes. The LrhA protein has strong homology to HexA and PecT from plant pathogenic bacteria, in which HexA and PecT act as repressors of motility and of virulence factors, such as exoenzymes required for lytic reactions. DgdR also shares similar characteristics to those of LrhA, HexA and PecT. The topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a vari
Probab=44.58 E-value=1.2e+02 Score=25.90 Aligned_cols=22 Identities=18% Similarity=0.356 Sum_probs=19.4
Q ss_pred HHHHHHHHHHHCCCcEEEEEEc
Q 015881 139 FFPAIQLLKDRYPGVLIDVIAS 160 (399)
Q Consensus 139 ttPalraLK~~yP~A~IdvLv~ 160 (399)
..+++..++++||+++|++...
T Consensus 15 l~~~l~~~~~~~P~v~i~~~~~ 36 (185)
T cd08439 15 LPFLLNRFASVYPRLAIEVVCK 36 (185)
T ss_pred HHHHHHHHHHHCCCeEEEEEEC
Confidence 4589999999999999999874
No 79
>PRK12597 F0F1 ATP synthase subunit beta; Provisional
Probab=44.46 E-value=2.7e+02 Score=29.66 Aligned_cols=95 Identities=14% Similarity=0.131 Sum_probs=67.8
Q ss_pred ccEEEEEcCCChhHHHhHHHHHHHHHHHCCCcEEEEEEcCCchHh---hh---cCCCCCEEE-EecCCCCCCChHH----
Q 015881 122 VRRCCCIISGGVYENLLFFPAIQLLKDRYPGVLIDVIASARGKQT---FE---LNKNVRWAN-VYDLDDDWPEPAE---- 190 (399)
Q Consensus 122 v~rILIIr~~~IGDvVLttPalraLK~~yP~A~IdvLv~~~~~~l---le---~nP~ID~Vi-~~d~k~~~~~~~~---- 190 (399)
-.||+|+-.++.|=.+|..-+++...+++.++-|-.++..+..++ ++ .....++.+ ++...+. ....+
T Consensus 143 GQR~gIfa~~G~GKt~Ll~~~~~~~~~~~~dv~V~~liGER~rEv~ef~~~~~~~~~l~rsvvv~atsd~-~~~~R~~a~ 221 (461)
T PRK12597 143 GGKTGLFGGAGVGKTVLMMELIFNISKQHSGSSVFAGVGERSREGHELYHEMKESGVLDKTVMVYGQMNE-PPGARMRVV 221 (461)
T ss_pred CCEEEeecCCCCChhHHHHHHHHHHHhhCCCEEEEEcCCcchHHHHHHHHHHHhcCCcceeEEEecCCCC-CHHHHHHHH
Confidence 379999999999999999999999998899988888888888765 22 334445444 4433332 11111
Q ss_pred --HHHHHHHhhhC-CCcEEEEcCCCChHHHH
Q 015881 191 --YTDILGVMKNR-YYDMVLSTKLAGLGHAA 218 (399)
Q Consensus 191 --~~~l~~~LR~~-~YDlvIdl~~~~~rsAl 218 (399)
-..+...+|.+ .+|+.+-+.+- .|.|-
T Consensus 222 ~~a~tiAEyfrd~~G~~VLl~~Dsl-TR~A~ 251 (461)
T PRK12597 222 LTGLTIAEYLRDEEKEDVLLFIDNI-FRFVQ 251 (461)
T ss_pred HHHHHHHHHHHHhcCCceEEEeccc-hHHHH
Confidence 13466678987 89999988877 66554
No 80
>cd08465 PBP2_ToxR The C-terminal substrate binding domain of LysR-type transcriptional regulator ToxR regulates the expression of the toxoflavin biosynthesis genes; contains the type 2 periplasmic bindinig fold. In soil bacterium Burkholderia glumae, ToxR regulates the toxABCDE and toxFGHI operons in the presence of toxoflavin as a coinducer. Additionally, the expression of both operons requires a transcriptional activator, ToxJ, whose expression is regulated by the TofI or TofR quorum-sensing system. The biosynthesis of toxoflavin is suggested to be synthesized in a pathway common to the synthesis of riboflavin. The topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After
Probab=44.27 E-value=59 Score=28.31 Aligned_cols=28 Identities=18% Similarity=0.231 Sum_probs=21.6
Q ss_pred ChhHHHhHHHHHHHHHHHCCCcEEEEEEc
Q 015881 132 GVYENLLFFPAIQLLKDRYPGVLIDVIAS 160 (399)
Q Consensus 132 ~IGDvVLttPalraLK~~yP~A~IdvLv~ 160 (399)
.++. .+..++++.++++||+++|++...
T Consensus 9 ~~~~-~~l~~~l~~f~~~~P~i~l~i~~~ 36 (200)
T cd08465 9 YGAR-LVLPALMRQLRAEAPGIDLAVSQA 36 (200)
T ss_pred hhHH-HhhhHHHHHHHHHCCCcEEEEecC
Confidence 3444 344589999999999999998753
No 81
>cd08412 PBP2_PAO1_like The C-terminal substrate-binding domain of putative LysR-type transcriptional regulator PAO1-like, a member of the type 2 periplasmic binding fold protein superfamily. This family includes the C-terminal substrate domain of a putative LysR-type transcriptional regulator from the plant pathogen Pseudomonas aeruginosa PAO1and its closely related homologs. The LysR-type transcriptional regulators (LTTRs) are composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcriptional repressor undergoes a conformational change upon substrate binding which in turn changes the DNA binding affinity of the repressor. The genes controll
Probab=43.37 E-value=87 Score=26.59 Aligned_cols=24 Identities=21% Similarity=0.505 Sum_probs=20.1
Q ss_pred hHHHHHHHHHHHCCCcEEEEEEcC
Q 015881 138 LFFPAIQLLKDRYPGVLIDVIASA 161 (399)
Q Consensus 138 LttPalraLK~~yP~A~IdvLv~~ 161 (399)
+..+++..++++||+++|.+....
T Consensus 14 ~l~~~l~~~~~~~P~i~l~i~~~~ 37 (198)
T cd08412 14 YLPGLLRRFREAYPGVEVRVVEGN 37 (198)
T ss_pred hhHHHHHHHHHHCCCcEEEEEECC
Confidence 356999999999999999997643
No 82
>cd08449 PBP2_XapR The C-terminal substrate binding domain of LysR-type transcriptional regulator XapR involved in xanthosine catabolism, contains the type 2 periplasmic binding fold. In Escherichia coli, XapR is a positive regulator for the expression of xapA gene, encoding xanthosine phosphorylase, and xapB gene, encoding a polypeptide similar to the nucleotide transport protein NupG. As an operon, the expression of both xapA and xapB is fully dependent on the presence of both XapR and the inducer xanthosine. Expression of the xapR is constitutive but not auto-regulated, unlike many other LysR family proteins. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their
Probab=43.36 E-value=73 Score=27.06 Aligned_cols=23 Identities=26% Similarity=0.365 Sum_probs=19.8
Q ss_pred HhHHHHHHHHHHHCCCcEEEEEE
Q 015881 137 LLFFPAIQLLKDRYPGVLIDVIA 159 (399)
Q Consensus 137 VLttPalraLK~~yP~A~IdvLv 159 (399)
.+..++++.++++||+++|.+..
T Consensus 13 ~~l~~~l~~~~~~~P~i~i~~~~ 35 (197)
T cd08449 13 GGLGPALRRFKRQYPNVTVRFHE 35 (197)
T ss_pred hhHHHHHHHHHHHCCCeEEEEEE
Confidence 35679999999999999998865
No 83
>COG1105 FruK Fructose-1-phosphate kinase and related fructose-6-phosphate kinase (PfkB) [Carbohydrate transport and metabolism]
Probab=43.35 E-value=90 Score=31.47 Aligned_cols=54 Identities=22% Similarity=0.225 Sum_probs=35.9
Q ss_pred ecCHHHHHHHHHHHHHhCCCCCCeEEEEcCCCCccccccCCCCCCCCCCHHHHHHHHHHhhhCC-CEEE
Q 015881 289 SISRRLKEVVAEKYKNAGAEQGKYIVIHGIESDSKASMQSRGDTDSLLPIQVWAEIANGLREFR-PLFV 356 (399)
Q Consensus 289 ~is~e~~~~a~~~l~~~gl~~~~~IvIhPgas~~~~~~k~rg~~~KrWP~e~faeLa~~L~~~~-~Vvl 356 (399)
.+++++.+...+.+.+. +....+||++ |+-- +..|.+.|++|++.+++.+ .|++
T Consensus 110 ~is~~~~~~~l~~~~~~-l~~~d~Vvls-GSlP------------~g~~~d~y~~li~~~~~~g~~vil 164 (310)
T COG1105 110 EISEAELEQFLEQLKAL-LESDDIVVLS-GSLP------------PGVPPDAYAELIRILRQQGAKVIL 164 (310)
T ss_pred CCCHHHHHHHHHHHHHh-cccCCEEEEe-CCCC------------CCCCHHHHHHHHHHHHhcCCeEEE
Confidence 46666666555555442 3445677776 4322 2499999999999998877 5544
No 84
>cd08431 PBP2_HupR The C-terminal substrate binding domain of LysR-type transcriptional regulator, HupR, which regulates expression of the heme uptake receptor HupA; contains the type 2 periplasmic binding fold. HupR, a member of the LysR family, activates hupA transcription under low-iron conditions in the presence of hemin. The expression of many iron-uptake genes, such as hupA, is regulated at the transcriptional level by iron and an iron-binding repressor protein called Fur (ferric uptake regulation). Under iron-abundant conditions with heme, the active Fur repressor protein represses transcription of the iron-uptake gene hupA, and prevents transcriptional activation via HupR. Under low-iron conditions with heme, the Fur repressor is inactive and transcription of the hupA is allowed. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, p
Probab=42.93 E-value=61 Score=27.75 Aligned_cols=22 Identities=14% Similarity=0.203 Sum_probs=19.3
Q ss_pred HHHHHHHHHHHCCCcEEEEEEc
Q 015881 139 FFPAIQLLKDRYPGVLIDVIAS 160 (399)
Q Consensus 139 ttPalraLK~~yP~A~IdvLv~ 160 (399)
..+++..++++||+++|++...
T Consensus 15 l~~~l~~~~~~~P~v~i~i~~~ 36 (195)
T cd08431 15 LYPLIAEFYQLNKATRIRLSEE 36 (195)
T ss_pred HHHHHHHHHHHCCCCceEEEEe
Confidence 4599999999999999999764
No 85
>cd08468 PBP2_Pa0477 The C-terminal substrate biniding domain of an uncharacterized LysR-like transcriptional regulator Pa0477 related to DntR, contains the type 2 periplasmic binding fold. LysR-type transcriptional regulator Pa0477 is related to DntR, which controls genes encoding enzymes for oxidative degradation of the nitro-aromatic compound 2,4-dinitrotoluene. The transcription of the genes encoding enzymes involved in such degradation is regulated and expression of these enzymes is enhanced by inducers, which are either an intermediate in the metabolic pathway or compounds to be degraded. The topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their spec
Probab=42.88 E-value=66 Score=27.89 Aligned_cols=23 Identities=13% Similarity=0.299 Sum_probs=20.3
Q ss_pred hHHHHHHHHHHHCCCcEEEEEEc
Q 015881 138 LFFPAIQLLKDRYPGVLIDVIAS 160 (399)
Q Consensus 138 LttPalraLK~~yP~A~IdvLv~ 160 (399)
+..++++.++++||+++|++...
T Consensus 14 ~l~~~l~~~~~~~P~v~i~~~~~ 36 (202)
T cd08468 14 VMPRLMARLEELAPSVRLNLVHA 36 (202)
T ss_pred HhHHHHHHHHhhCCCCEEEEEEC
Confidence 46799999999999999999864
No 86
>cd08440 PBP2_LTTR_like_4 TThe C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator, contains the type 2 periplasmic binding fold. LysR-transcriptional regulators comprise the largest family of prokaryotic transcription factor. Homologs of some of LTTRs with similar domain organizations are also found in the archaea and eukaryotic organisms. The LTTRs are composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcriptional repressor undergoes a conformational change upon substrate binding which in turn changes the DNA binding affinity of the repressor. The genes controlled by the LTTRs have diverse funct
Probab=42.49 E-value=1.2e+02 Score=25.51 Aligned_cols=29 Identities=17% Similarity=0.382 Sum_probs=22.4
Q ss_pred CChhHHHhHHHHHHHHHHHCCCcEEEEEEc
Q 015881 131 GGVYENLLFFPAIQLLKDRYPGVLIDVIAS 160 (399)
Q Consensus 131 ~~IGDvVLttPalraLK~~yP~A~IdvLv~ 160 (399)
..++..+ ..+++..++++||+++|++...
T Consensus 8 ~~~~~~~-l~~~l~~~~~~~p~v~i~i~~~ 36 (197)
T cd08440 8 PSLAATL-LPPVLAAFRRRHPGIRVRLRDV 36 (197)
T ss_pred cchhhhH-HHHHHHHHHHhCCCcEEEEEeC
Confidence 3444444 4699999999999999999864
No 87
>TIGR03590 PseG pseudaminic acid biosynthesis-associated protein PseG. This protein is found in association with enzymes involved in the biosynthesis of pseudaminic acid, a component of polysaccharide in certain Pseudomonas strains as well as a modification of flagellin in Campylobacter and Hellicobacter. The role of this protein is unclear, although it may participate in N-acetylation in conjunction with, or in the absence of PseH (TIGR03585) as it often scores above the trusted cutoff to pfam00583 representing a family of acetyltransferases.
Probab=42.18 E-value=2e+02 Score=27.91 Aligned_cols=89 Identities=12% Similarity=0.106 Sum_probs=54.8
Q ss_pred ccEEEEEcCCChhHHHhHHHHHHHHHHHCCCcEEEEEEcCCc------hHhhhcCCCCCEEEEecCCCCCCChHHHHHHH
Q 015881 122 VRRCCCIISGGVYENLLFFPAIQLLKDRYPGVLIDVIASARG------KQTFELNKNVRWANVYDLDDDWPEPAEYTDIL 195 (399)
Q Consensus 122 v~rILIIr~~~IGDvVLttPalraLK~~yP~A~IdvLv~~~~------~~lle~nP~ID~Vi~~d~k~~~~~~~~~~~l~ 195 (399)
+++|||.--+.=+.. ++..++++|.+..++.+|++++.+.. +...+.+++|. ++.+. -++.
T Consensus 170 ~~~iLi~~GG~d~~~-~~~~~l~~l~~~~~~~~i~vv~G~~~~~~~~l~~~~~~~~~i~-~~~~~-----------~~m~ 236 (279)
T TIGR03590 170 LRRVLVSFGGADPDN-LTLKLLSALAESQINISITLVTGSSNPNLDELKKFAKEYPNII-LFIDV-----------ENMA 236 (279)
T ss_pred cCeEEEEeCCcCCcC-HHHHHHHHHhccccCceEEEEECCCCcCHHHHHHHHHhCCCEE-EEeCH-----------HHHH
Confidence 567877654433333 77889999998778899999997654 23344555543 32221 1344
Q ss_pred HHhhhCCCcEEEEcCCCChHHHHHHHHhCCCeE
Q 015881 196 GVMKNRYYDMVLSTKLAGLGHAAFLFMTTARDR 228 (399)
Q Consensus 196 ~~LR~~~YDlvIdl~~~~~rsAll~~LsgA~~R 228 (399)
..|+. -|++|...+ .+..=+...|.|.-
T Consensus 237 ~lm~~--aDl~Is~~G---~T~~E~~a~g~P~i 264 (279)
T TIGR03590 237 ELMNE--ADLAIGAAG---STSWERCCLGLPSL 264 (279)
T ss_pred HHHHH--CCEEEECCc---hHHHHHHHcCCCEE
Confidence 44543 699999544 35555666777744
No 88
>PF02590 SPOUT_MTase: Predicted SPOUT methyltransferase; InterPro: IPR003742 This family of proteins are predicted to be SPOUT methyltransferases []. ; GO: 0008168 methyltransferase activity, 0006364 rRNA processing, 0005737 cytoplasm; PDB: 1VH0_E 4FAK_A 1TO0_G 1O6D_A 1NS5_B.
Probab=42.07 E-value=28 Score=31.41 Aligned_cols=50 Identities=12% Similarity=0.104 Sum_probs=27.2
Q ss_pred CCCCHHHHHHHHHHhhhCC---CEEEeCCchhHHHHHHHHhcCCCCceeecCCccccc
Q 015881 334 SLLPIQVWAEIANGLREFR---PLFVIPHEKEREGVEDVVGDDASIVFITTPGQVRMS 388 (399)
Q Consensus 334 KrWP~e~faeLa~~L~~~~---~VvliGgp~E~e~aeeI~~~~~~~~~i~~~G~ls~~ 388 (399)
|.|..+.||+.++.+...+ -++++||+.- ..+++.+.+... + .-+++|++
T Consensus 78 k~~sS~~fA~~l~~~~~~g~~~i~F~IGG~~G--~~~~~~~~a~~~--l-SLS~mTfp 130 (155)
T PF02590_consen 78 KQLSSEEFAKKLERWMNQGKSDIVFIIGGADG--LSEEVRKRADEK--L-SLSKMTFP 130 (155)
T ss_dssp EE--HHHHHHHHHHHHHTTS-EEEEEE-BTTB----HHHHHH-SEE--E-ES-SS---
T ss_pred ccCChHHHHHHHHHHHhcCCceEEEEEecCCC--CCHHHHhhcCce--E-EEecCCCc
Confidence 6699999999999987665 4677888863 445556555421 2 33466654
No 89
>PLN02871 UDP-sulfoquinovose:DAG sulfoquinovosyltransferase
Probab=41.98 E-value=2.1e+02 Score=29.66 Aligned_cols=106 Identities=14% Similarity=0.102 Sum_probs=55.7
Q ss_pred ccEEEEEc-CC---ChhH-HHhHHHHHHHHHHHCCCcEEEEEEcCCchHhhhcCCCCCEEEE---ec--CCCCC-CChHH
Q 015881 122 VRRCCCII-SG---GVYE-NLLFFPAIQLLKDRYPGVLIDVIASARGKQTFELNKNVRWANV---YD--LDDDW-PEPAE 190 (399)
Q Consensus 122 v~rILIIr-~~---~IGD-vVLttPalraLK~~yP~A~IdvLv~~~~~~lle~nP~ID~Vi~---~d--~k~~~-~~~~~ 190 (399)
.|||+++- +. .+|- .....-+++.|+++ +.++++++.....+ +....+. ++. +. ..... ..+..
T Consensus 58 ~mrI~~~~~~~~~~~~gG~~~~~~~l~~~L~~~--G~eV~vlt~~~~~~--~~~~g~~-v~~~~~~~~~~~~~~~~~~~~ 132 (465)
T PLN02871 58 PRRIALFVEPSPFSYVSGYKNRFQNFIRYLREM--GDEVLVVTTDEGVP--QEFHGAK-VIGSWSFPCPFYQKVPLSLAL 132 (465)
T ss_pred CceEEEEECCcCCcccccHHHHHHHHHHHHHHC--CCeEEEEecCCCCC--ccccCce-eeccCCcCCccCCCceeeccC
Confidence 48999883 21 2332 24456888999986 77999998654321 1111111 111 10 00000 01111
Q ss_pred HHHHHHHhhhCCCcEEEEcCCCC--hHHHHHHHHhCCCeEEEec
Q 015881 191 YTDILGVMKNRYYDMVLSTKLAG--LGHAAFLFMTTARDRVSYI 232 (399)
Q Consensus 191 ~~~l~~~LR~~~YDlvIdl~~~~--~rsAll~~LsgA~~RIGy~ 232 (399)
..++.+.+++.+||++....... +...+++.+.|+|..+-+.
T Consensus 133 ~~~l~~~i~~~kpDiIh~~~~~~~~~~~~~~ak~~~ip~V~~~h 176 (465)
T PLN02871 133 SPRIISEVARFKPDLIHASSPGIMVFGALFYAKLLCVPLVMSYH 176 (465)
T ss_pred CHHHHHHHHhCCCCEEEECCCchhHHHHHHHHHHhCCCEEEEEe
Confidence 12567788889999987543221 1222345677888766543
No 90
>cd08437 PBP2_MleR The substrate binding domain of LysR-type transcriptional regulator MleR which required for malolactic fermentation, contains type 2 periplasmic binidning fold. MleR, a transcription activator of malolactic fermentation system, is found in gram-positive bacteria and belongs to the lysR family of bacterial transcriptional regulators. The mleR gene is required for the expression and induction of malolactic fermentation. This substrate binding domain has significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase dom
Probab=41.48 E-value=78 Score=27.13 Aligned_cols=23 Identities=17% Similarity=0.008 Sum_probs=19.6
Q ss_pred hHHHHHHHHHHHCCCcEEEEEEc
Q 015881 138 LFFPAIQLLKDRYPGVLIDVIAS 160 (399)
Q Consensus 138 LttPalraLK~~yP~A~IdvLv~ 160 (399)
+..+++..++++||+++|++...
T Consensus 14 ~l~~~l~~~~~~~P~v~i~~~~~ 36 (198)
T cd08437 14 YFPKLAKDLIKTGLMIQIDTYEG 36 (198)
T ss_pred HhHHHHHHHHHhCCceEEEEEEc
Confidence 34589999999999999999764
No 91
>cd08448 PBP2_LTTR_aromatics_like_2 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator similar to regulators involved in the catabolism of aromatic compounds, contains type 2 periplasmic binding fold. This CD represents the substrate binding domain of an uncharacterized LysR-type regulator similar to CbnR which is involved in the regulation of chlorocatechol breakdown. The transcription of the genes encoding enzymes involved in such degradation is regulated and expression of these enzymes is enhanced by inducers, which are either an intermediate in the metabolic pathway or compounds to be degraded. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Ve
Probab=41.32 E-value=98 Score=26.15 Aligned_cols=23 Identities=13% Similarity=0.339 Sum_probs=19.6
Q ss_pred hHHHHHHHHHHHCCCcEEEEEEc
Q 015881 138 LFFPAIQLLKDRYPGVLIDVIAS 160 (399)
Q Consensus 138 LttPalraLK~~yP~A~IdvLv~ 160 (399)
+..+++..++++||+++|++...
T Consensus 14 ~l~~~l~~~~~~~P~i~i~i~~~ 36 (197)
T cd08448 14 GLPRILRAFRAEYPGIEVALHEM 36 (197)
T ss_pred HHHHHHHHHHHHCCCCeEEEEeC
Confidence 34589999999999999999764
No 92
>cd08456 PBP2_LysR The C-terminal substrate binding domain of LysR, transcriptional regulator for lysine biosynthesis, contains the type 2 periplasmic binding fold. LysR, the transcriptional activator of lysA encoding diaminopimelate decarboxylase, catalyses the decarboxylation of diaminopimelate to produce lysine. The LysR-transcriptional regulators comprise the largest family of prokaryotic transcription factor. Homologs of some of LTTRs with similar domain organizations are also found in the archaea and eukaryotic organisms. The LTTRs are composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcriptional repressor undergoes a conformational
Probab=41.18 E-value=1.2e+02 Score=25.71 Aligned_cols=41 Identities=17% Similarity=0.152 Sum_probs=27.5
Q ss_pred hHHHHHHHHHHHCCCcEEEEEEcCCchHhhh--cCCCCCEEEEe
Q 015881 138 LFFPAIQLLKDRYPGVLIDVIASARGKQTFE--LNKNVRWANVY 179 (399)
Q Consensus 138 LttPalraLK~~yP~A~IdvLv~~~~~~lle--~nP~ID~Vi~~ 179 (399)
+..++++.++++||+++|.+...... .+++ .+-.+|=+|.+
T Consensus 14 ~l~~~l~~~~~~~P~i~~~i~~~~~~-~~~~~l~~g~~Dl~i~~ 56 (196)
T cd08456 14 FLPRAIKAFLQRHPDVTISIHTRDSP-TVEQWLSAQQCDLGLVS 56 (196)
T ss_pred hHHHHHHHHHHHCCCcEEEEEeCCHH-HHHHHHHcCCccEEEEe
Confidence 45699999999999999999875422 2222 23455555554
No 93
>cd08411 PBP2_OxyR The C-terminal substrate-binding domain of the LysR-type transcriptional regulator OxyR, a member of the type 2 periplasmic binding fold protein superfamily. OxyR senses hydrogen peroxide and is activated through the formation of an intramolecular disulfide bond. The OxyR activation induces the transcription of genes necessary for the bacterial defense against oxidative stress. The OxyR of LysR-type transcriptional regulator family is composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcriptional repressor undergoes a conformational change upon substrate binding which in turn changes the DNA binding affinity of the repre
Probab=41.07 E-value=1.2e+02 Score=25.94 Aligned_cols=31 Identities=13% Similarity=0.180 Sum_probs=24.0
Q ss_pred CCChhHHHhHHHHHHHHHHHCCCcEEEEEEcC
Q 015881 130 SGGVYENLLFFPAIQLLKDRYPGVLIDVIASA 161 (399)
Q Consensus 130 ~~~IGDvVLttPalraLK~~yP~A~IdvLv~~ 161 (399)
...++.. +..+++..++++||+++|.+....
T Consensus 8 ~~~~~~~-~l~~~l~~~~~~~P~i~i~i~~~~ 38 (200)
T cd08411 8 IPTIAPY-LLPRLLPALRQAYPKLRLYLREDQ 38 (200)
T ss_pred cHHHHhh-hhHHHHHHHHHHCCCcEEEEEeCc
Confidence 3445553 667889999999999999998743
No 94
>cd08436 PBP2_LTTR_like_3 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator, contains the type 2 periplasmic binding fold. LysR-transcriptional regulators comprise the largest family of prokaryotic transcription factor. Homologs of some of LTTRs with similar domain organizations are also found in the archaea and eukaryotic organisms. The LTTRs are composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcriptional repressor undergoes a conformational change upon substrate binding which in turn changes the DNA binding affinity of the repressor. The genes controlled by the LTTRs have diverse functi
Probab=40.68 E-value=92 Score=26.25 Aligned_cols=29 Identities=17% Similarity=0.140 Sum_probs=22.5
Q ss_pred CChhHHHhHHHHHHHHHHHCCCcEEEEEEc
Q 015881 131 GGVYENLLFFPAIQLLKDRYPGVLIDVIAS 160 (399)
Q Consensus 131 ~~IGDvVLttPalraLK~~yP~A~IdvLv~ 160 (399)
..++..+ ..+++..++++||+++|.+...
T Consensus 8 ~~~~~~~-l~~~l~~~~~~~P~v~i~i~~~ 36 (194)
T cd08436 8 TSLAAVD-LPELLARFHRRHPGVDIRLRQA 36 (194)
T ss_pred hHHHHHH-HHHHHHHHHHHCCCcEEEEecC
Confidence 3445444 4789999999999999998764
No 95
>cd08434 PBP2_GltC_like The substrate binding domain of LysR-type transcriptional regulator GltC, which activates gltA expression of glutamate synthase operon, contains type 2 periplasmic binding fold. GltC, a member of the LysR family of bacterial transcriptional factors, activates the expression of gltA gene of glutamate synthase operon and is essential for cell growth in the absence of glutamate. Glutamate synthase is a heterodimeric protein that encoded by gltA and gltB, whose expression is subject to nutritional regulation. GltC also negatively auto-regulates its own expression. This substrate-binding domain has strong homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity,
Probab=40.13 E-value=1.2e+02 Score=25.47 Aligned_cols=31 Identities=16% Similarity=0.284 Sum_probs=23.3
Q ss_pred CCChhHHHhHHHHHHHHHHHCCCcEEEEEEcC
Q 015881 130 SGGVYENLLFFPAIQLLKDRYPGVLIDVIASA 161 (399)
Q Consensus 130 ~~~IGDvVLttPalraLK~~yP~A~IdvLv~~ 161 (399)
...++.. +..++++.++++||+++|++....
T Consensus 7 ~~~~~~~-~l~~~l~~~~~~~P~i~i~i~~~~ 37 (195)
T cd08434 7 LHSLGTS-LVPDLIRAFRKEYPNVTFELHQGS 37 (195)
T ss_pred cchhhhh-hhHHHHHHHHHhCCCeEEEEecCc
Confidence 3344443 456899999999999999988743
No 96
>cd08418 PBP2_TdcA The C-terminal substrate binding domain of LysR-type transcriptional regulator TdcA, which is involved in the degradation of L-serine and L-threonine, contains the type 2 periplasmic binding fold. TdcA, a member of the LysR family, activates the expression of the anaerobically-regulated tdcABCDEFG operon which is involved in the degradation of L-serine and L-threonine to acetate and propionate, respectively. The tdc operon is comprised of one regulatory gene tdcA and six structural genes, tdcB to tdcG. The expression of the tdc operon is affected by several transcription factors including the cAMP receptor protein (CRP), integration host factor (IHF), histone-like protein (HU), and the operon specific regulators TdcA and TcdR. TcdR is divergently transcribed from the operon and encodes a small protein that is required for efficient expression of the Escherichia coli tdc operon. This substrate-binding domain shows significant homology to the type 2 periplasmic binding
Probab=40.13 E-value=87 Score=26.67 Aligned_cols=24 Identities=25% Similarity=0.498 Sum_probs=20.1
Q ss_pred hHHHHHHHHHHHCCCcEEEEEEcC
Q 015881 138 LFFPAIQLLKDRYPGVLIDVIASA 161 (399)
Q Consensus 138 LttPalraLK~~yP~A~IdvLv~~ 161 (399)
+..++++.++++||+++|++.+..
T Consensus 14 ~l~~~l~~~~~~~P~i~l~i~~~~ 37 (201)
T cd08418 14 LMPAVINRFKEQFPDVQISIYEGQ 37 (201)
T ss_pred hhHHHHHHHHHHCCCceEEEEeCc
Confidence 346889999999999999998743
No 97
>cd08427 PBP2_LTTR_like_2 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator, contains the type 2 periplasmic binding fold. LysR-transcriptional regulators comprise the largest family of prokaryotic transcription factor. Homologs of some of LTTRs with similar domain organizations are also found in the archaea and eukaryotic organisms. The LTTRs are composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcriptional repressor undergoes a conformational change upon substrate binding which in turn changes the DNA binding affinity of the repressor. The genes controlled by the LTTRs have diverse functi
Probab=39.97 E-value=92 Score=26.36 Aligned_cols=41 Identities=17% Similarity=0.220 Sum_probs=26.8
Q ss_pred hHHHHHHHHHHHCCCcEEEEEEcCCchHhhh--cCCCCCEEEEe
Q 015881 138 LFFPAIQLLKDRYPGVLIDVIASARGKQTFE--LNKNVRWANVY 179 (399)
Q Consensus 138 LttPalraLK~~yP~A~IdvLv~~~~~~lle--~nP~ID~Vi~~ 179 (399)
+..++++.++++||+++|++.+.... .+.+ .+-.+|=.|.+
T Consensus 14 ~l~~~l~~~~~~~P~i~l~~~~~~~~-~~~~~l~~g~~Dl~i~~ 56 (195)
T cd08427 14 LLPRALARLRRRHPDLEVHIVPGLSA-ELLARVDAGELDAAIVV 56 (195)
T ss_pred HhHHHHHHHHHHCCCceEEEEeCCcH-HHHHHHHCCCCCEEEEc
Confidence 34689999999999999999875322 2221 12345655554
No 98
>cd08488 PBP2_AmpR The C-terminal substrate domain of LysR-type transcriptional regulator AmpR that involved in control of the expression of beta-lactamase gene ampC, contains the type 2 periplasmic binding fold. AmpR acts as a transcriptional activator by binding to a DNA region immediately upstream of the ampC promoter. In the absence of a beta-lactam inducer, AmpR represses the synthesis of beta-lactamase, whereas expression is induced in the presence of a beta-lactam inducer. The AmpD, AmpG, and AmpR proteins are involved in the induction of AmpC-type beta-lactamase (class C) which produced by enterobacterial strains and many other gram-negative bacilli. The activation of ampC by AmpR requires ampG for induction or high-level expression of AmpC. It is probable that the AmpD and AmpG work together to modulate the ability of AmpR to activate ampC expression. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsibl
Probab=39.54 E-value=59 Score=27.95 Aligned_cols=39 Identities=10% Similarity=0.211 Sum_probs=28.1
Q ss_pred HHHHHHHHHHHCCCcEEEEEEcCCchHhhhcCCCCCEEEEe
Q 015881 139 FFPAIQLLKDRYPGVLIDVIASARGKQTFELNKNVRWANVY 179 (399)
Q Consensus 139 ttPalraLK~~yP~A~IdvLv~~~~~~lle~nP~ID~Vi~~ 179 (399)
..|++++++++||+++|.+........+.++ .+|=.+..
T Consensus 15 l~~~l~~f~~~~P~v~i~~~~~~~~~~l~~~--~~D~~i~~ 53 (191)
T cd08488 15 LLPRLADFQNRHPFIDLRLSTNNNRVDIAAE--GLDYAIRF 53 (191)
T ss_pred HHhHHHHHHHHCCCcEEEEEecCCccccCCC--CccEEEEe
Confidence 3589999999999999999875544444432 46655554
No 99
>cd08475 PBP2_CrgA_like_6 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold. This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 6. The LTTRs are acting as both auto-repressors and activators of target promoters, controlling operons involved in a wide variety of cellular processes such as amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to name a few. In contrast to the tetrameric form of other LTTRs, CrgA from Neisseria meningitides assembles into an octameric ring, which can bind up to four 63-bp DNA oligonucleotides. Phylogenetic cluster analysis showed that the CrgA-like regulators form a subclass of the LTTRs that function as octamers. The CrgA is an auto-repressor of its own gene a
Probab=39.28 E-value=69 Score=27.28 Aligned_cols=40 Identities=20% Similarity=0.157 Sum_probs=29.6
Q ss_pred HHHHHHHHHHHCCCcEEEEEEcCCchHhhhcCCCCCEEEEec
Q 015881 139 FFPAIQLLKDRYPGVLIDVIASARGKQTFELNKNVRWANVYD 180 (399)
Q Consensus 139 ttPalraLK~~yP~A~IdvLv~~~~~~lle~nP~ID~Vi~~d 180 (399)
..+++..++++||+++|++.......+.++. .+|=.+.+.
T Consensus 16 l~~~l~~~~~~~P~v~i~i~~~~~~~~~l~~--~~D~~i~~~ 55 (199)
T cd08475 16 VAPLLLELARRHPELELELSFSDRFVDLIEE--GIDLAVRIG 55 (199)
T ss_pred HHHHHHHHHHHCCCeEEEEEeccchhhHhhc--CccEEEEeC
Confidence 4588999999999999999765545555553 378777543
No 100
>cd08485 PBP2_ClcR The C-terminal substrate binding domain of LysR-type transcriptional regulator ClcR involved in the chlorocatechol catabolism, contains type 2 periplasmic binding fold. In soil bacterium Pseudomonas putida, the ortho-pathways of catechol and 3-chlorocatechol are central catabolic pathways that convert aromatic and chloroaromaric compounds to tricarboxylic acid (TCA) cycle intermediates. The 3-chlorocatechol-degradative pathway is encoded by clcABD operon, which requires the divergently transcribed clcR and an intermediate of the pathway, 2-chloromuconate, as an inducer for activation. The topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding th
Probab=39.22 E-value=1.5e+02 Score=25.68 Aligned_cols=31 Identities=13% Similarity=0.078 Sum_probs=23.4
Q ss_pred cCCChhHHHhHHHHHHHHHHHCCCcEEEEEEc
Q 015881 129 ISGGVYENLLFFPAIQLLKDRYPGVLIDVIAS 160 (399)
Q Consensus 129 r~~~IGDvVLttPalraLK~~yP~A~IdvLv~ 160 (399)
-...+++.+ ..++++.+++.||+++|++...
T Consensus 7 ~~~~~~~~~-l~~~l~~~~~~~P~i~l~~~~~ 37 (198)
T cd08485 7 YFGTVVLHT-LPLLLRQLLSVAPSATVSLTQM 37 (198)
T ss_pred EeccchhHH-HHHHHHHHHHhCCCcEEEEEEC
Confidence 344455544 4589999999999999999764
No 101
>COG4029 Uncharacterized protein conserved in archaea [Function unknown]
Probab=39.22 E-value=98 Score=27.13 Aligned_cols=53 Identities=28% Similarity=0.389 Sum_probs=36.9
Q ss_pred CCeEEEEcCCCCccccccCCCCCCCCCCHHHHHHHHHHhhhCC-CEEE--------eCCchh--HHHHHHHHhcCCCCce
Q 015881 310 GKYIVIHGIESDSKASMQSRGDTDSLLPIQVWAEIANGLREFR-PLFV--------IPHEKE--REGVEDVVGDDASIVF 378 (399)
Q Consensus 310 ~~~IvIhPgas~~~~~~k~rg~~~KrWP~e~faeLa~~L~~~~-~Vvl--------iGgp~E--~e~aeeI~~~~~~~~~ 378 (399)
.+||+|.|++.-+. ++|+++|.... +|.+ +-|++| .+++++|.+..++.+|
T Consensus 6 tk~ivlapsa~vsp------------------~elv~~l~~~~~PvtiKeTCfGaii~G~Ed~v~klveriR~~d~~~IF 67 (142)
T COG4029 6 TKYIVLAPSAGVSP------------------KELVQKLLELSPPVTIKETCFGAIIDGPEDEVRKLVERIRELDGNAIF 67 (142)
T ss_pred eEEEEEcCccCcCh------------------HHHHHHHHhcCCCeEeeeeeeeeeecCcHHHHHHHHHHHHHhccCcee
Confidence 58999999886653 46888887754 4432 235554 5788889888887776
Q ss_pred ee
Q 015881 379 IT 380 (399)
Q Consensus 379 i~ 380 (399)
..
T Consensus 68 ~K 69 (142)
T COG4029 68 SK 69 (142)
T ss_pred ec
Confidence 54
No 102
>PRK00170 azoreductase; Reviewed
Probab=39.04 E-value=56 Score=29.64 Aligned_cols=38 Identities=18% Similarity=0.046 Sum_probs=29.0
Q ss_pred ccEEEEEcCCChhH----HHhHHHHHHHHHHHCCCcEEEEEE
Q 015881 122 VRRCCCIISGGVYE----NLLFFPAIQLLKDRYPGVLIDVIA 159 (399)
Q Consensus 122 v~rILIIr~~~IGD----vVLttPalraLK~~yP~A~IdvLv 159 (399)
|||||||.-+--.. ..|+--++..|++++|+.+|+++-
T Consensus 1 Mmkil~i~gSpr~~~s~s~~l~~~~~~~l~~~~~~~~v~~~d 42 (201)
T PRK00170 1 MSKVLVIKSSILGDYSQSMQLGDAFIEAYKEAHPDDEVTVRD 42 (201)
T ss_pred CCeEEEEecCCCCCCcHHHHHHHHHHHHHHHhCCCCeEEEEE
Confidence 58999996655443 345567899999999999988774
No 103
>cd08444 PBP2_Cbl The C-terminal substrate binding domain of LysR-type transcriptional regulator Cbl, which is required for expression of sulfate starvation-inducible (ssi) genes, contains the type 2 periplasmic binding fold. Cbl is a member of the LysR transcriptional regulators that comprise the largest family of prokaryotic transcription factor. Cbl shows high sequence similarity to CysB, the LysR-type transcriptional activator of genes involved in sulfate and thiosulfate transport, sulfate reduction, and cysteine synthesis. In Escherichia coli, the function of Cbl is required for expression of sulfate starvation-inducible (ssi) genes, coupled with the biosynthesis of cysteine from the organic sulfur sources (sulfonates). The ssi genes include the ssuEADCB and tauABCD operons encoding uptake systems for organosulfur compounds, aliphatic sulfonates, and taurine. The genes in these operons encode an ABC-type transport system required for uptake of aliphatic sulfonates and a desulfonati
Probab=38.76 E-value=1.3e+02 Score=25.91 Aligned_cols=42 Identities=12% Similarity=0.136 Sum_probs=28.1
Q ss_pred HhHHHHHHHHHHHCCCcEEEEEEcCCchHhhh--cCCCCCEEEEe
Q 015881 137 LLFFPAIQLLKDRYPGVLIDVIASARGKQTFE--LNKNVRWANVY 179 (399)
Q Consensus 137 VLttPalraLK~~yP~A~IdvLv~~~~~~lle--~nP~ID~Vi~~ 179 (399)
.+..+++..++++||+++|.+.+... .++++ .+-.+|=++.+
T Consensus 13 ~~l~~~l~~~~~~~P~v~l~i~~~~~-~~~~~~l~~g~~Dl~i~~ 56 (198)
T cd08444 13 YALPWVVQAFKEQFPNVHLVLHQGSP-EEIASMLANGQADIGIAT 56 (198)
T ss_pred hhhhHHHHHHHHHCCCeEEEEEeCCH-HHHHHHHHCCCccEEEec
Confidence 34679999999999999999987542 22222 22455655554
No 104
>cd08486 PBP2_CbnR The C-terminal substrate binding domain of LysR-type transcriptional regulator, CbnR, involved in the chlorocatechol catabolism, contains the type 2 periplasmic binding fold. This CD represents the substrate binding domain of LysR-type regulator CbnR which is involved in the regulation of chlorocatechol breakdown. The chlorocatechol-degradative pathway is often found in bacteria that can use chlorinated aromatic compounds as carbon and energy sources. CbnR is found in the 3-chlorobenzoate degradative bacterium Ralstonia eutropha NH9 and forms a tetramer. CbnR activates the expression of the cbnABCD genes, which are responsible for the degradation of chlorocatechol converted from 3-chlorobenzoate and are transcribed divergently from cbnR. The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccha
Probab=38.45 E-value=91 Score=27.12 Aligned_cols=23 Identities=4% Similarity=0.023 Sum_probs=19.6
Q ss_pred hHHHHHHHHHHHCCCcEEEEEEc
Q 015881 138 LFFPAIQLLKDRYPGVLIDVIAS 160 (399)
Q Consensus 138 LttPalraLK~~yP~A~IdvLv~ 160 (399)
+.-+++++++++||+.+|.+...
T Consensus 15 ~l~~~l~~f~~~~P~v~i~i~~~ 37 (198)
T cd08486 15 SLPLLLRAFLTSTPTATVSLTHM 37 (198)
T ss_pred HHHHHHHHHHHhCCCeEEEEEEC
Confidence 44588999999999999998764
No 105
>cd01635 Glycosyltransferase_GTB_type Glycosyltransferases catalyze the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming glycosidic bonds. The acceptor molecule can be a lipid, a protein, a heterocyclic compound, or another carbohydrate residue. The structures of the formed glycoconjugates are extremely diverse, reflecting a wide range of biological functions. The members of this family share a common GTB topology, one of the two protein topologies observed for nucleotide-sugar-dependent glycosyltransferases. GTB proteins have distinct N- and C- terminal domains each containing a typical Rossmann fold. The two domains have high structural homology despite minimal sequence homology. The large cleft that separates the two domains includes the catalytic center and permits a high degree of flexibility.
Probab=38.36 E-value=2.1e+02 Score=24.93 Aligned_cols=64 Identities=16% Similarity=0.034 Sum_probs=41.7
Q ss_pred hhHHHhHHHHHHHHHHHCCCcEEEEEEcCCchHhhhcCCCCCEEEEecCCCCCCChHHHHHHHHHhhhCCCcEEEEcCCC
Q 015881 133 VYENLLFFPAIQLLKDRYPGVLIDVIASARGKQTFELNKNVRWANVYDLDDDWPEPAEYTDILGVMKNRYYDMVLSTKLA 212 (399)
Q Consensus 133 IGDvVLttPalraLK~~yP~A~IdvLv~~~~~~lle~nP~ID~Vi~~d~k~~~~~~~~~~~l~~~LR~~~YDlvIdl~~~ 212 (399)
=|.......+++.|++. +.+++++. . ....+.+.+++.++|+++.....
T Consensus 13 ~G~~~~~~~l~~~L~~~--g~~v~v~~------------------------~-----~~~~~~~~~~~~~~D~i~~~~~~ 61 (229)
T cd01635 13 GGVELVLLDLAKALARR--GHEVEVVA------------------------L-----LLLLLLRILRGFKPDVVHAHGYY 61 (229)
T ss_pred CCchhHHHHHHHHHHHc--CCeEEEEE------------------------e-----chHHHHHHHhhcCCCEEEEcCCC
Confidence 37888888999999886 77888887 0 11234556667899999877665
Q ss_pred ChHHH--HHHHHhCCCe
Q 015881 213 GLGHA--AFLFMTTARD 227 (399)
Q Consensus 213 ~~rsA--ll~~LsgA~~ 227 (399)
..... ...+..+.+.
T Consensus 62 ~~~~~~~~~~~~~~~~~ 78 (229)
T cd01635 62 PAPLALLLAARLLGIPL 78 (229)
T ss_pred cHHHHHHHHHhhCCCCE
Confidence 22222 2344555553
No 106
>cd08423 PBP2_LTTR_like_6 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator, contains the type 2 periplasmic binding fold. LysR-transcriptional regulators comprise the largest family of prokaryotic transcription factor. Homologs of some of LTTRs with similar domain organizations are also found in the archaea and eukaryotic organisms. The LTTRs are composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcriptional repressor undergoes a conformational change upon substrate binding which in turn changes the DNA binding affinity of the repressor. The genes controlled by the LTTRs have diverse functi
Probab=38.02 E-value=1.2e+02 Score=25.71 Aligned_cols=24 Identities=29% Similarity=0.542 Sum_probs=20.6
Q ss_pred hHHHHHHHHHHHCCCcEEEEEEcC
Q 015881 138 LFFPAIQLLKDRYPGVLIDVIASA 161 (399)
Q Consensus 138 LttPalraLK~~yP~A~IdvLv~~ 161 (399)
+..++++.++++||+++|.+....
T Consensus 14 ~l~~~l~~~~~~~P~i~i~~~~~~ 37 (200)
T cd08423 14 LLPPALAALRARHPGLEVRLREAE 37 (200)
T ss_pred hhhHHHHHHHHhCCCCeEEEEeCC
Confidence 356899999999999999998753
No 107
>cd08466 PBP2_LeuO The C-terminal substrate binding domain of LysR-type transcriptional regulator LeuO, an activator of leucine synthesis operon, contains the type 2 periplasmic binding fold. LeuO, a LysR-type transcriptional regulator, was originally identified as an activator of the leucine synthesis operon (leuABCD). Subsequently, LeuO was found to be not a specific regulator of the leu gene but a global regulator of unrelated various genes. LeuO activates bglGFB (utilization of beta-D-glucoside) and represses cadCBA (lysine decarboxylation) and dsrA (encoding a regulatory small RNA for translational control of rpoS and hns). LeuO also regulates the yjjQ-bglJ operon which coding for a LuxR-type transcription factor. In Salmonella enterica serovar Typhi, LeuO is a positive regulator of ompS1 (encoding an outer membrane), ompS2 (encoding a pathogenicity determinant), and assT, while LeuO represses the expression of OmpX and Tpx. Both osmS1 and osmS2 influence virulence in the mouse mo
Probab=37.98 E-value=1e+02 Score=26.34 Aligned_cols=41 Identities=17% Similarity=0.165 Sum_probs=26.9
Q ss_pred hHHHHHHHHHHHCCCcEEEEEEcCCc--hHhhhcCCCCCEEEEe
Q 015881 138 LFFPAIQLLKDRYPGVLIDVIASARG--KQTFELNKNVRWANVY 179 (399)
Q Consensus 138 LttPalraLK~~yP~A~IdvLv~~~~--~~lle~nP~ID~Vi~~ 179 (399)
+..++++.++++||+++|.+...... .+.++ +..+|=.+.+
T Consensus 14 ~l~~~l~~f~~~~P~v~l~~~~~~~~~~~~~l~-~g~~Dl~i~~ 56 (200)
T cd08466 14 LLPRLLARLKQLAPNISLRESPSSEEDLFEDLR-LQEVDLVIDY 56 (200)
T ss_pred HHHHHHHHHHHHCCCCEEEEecCchHhHHHHHH-cCCccEEEec
Confidence 44588999999999999999875322 12222 3455655544
No 108
>PRK09376 rho transcription termination factor Rho; Provisional
Probab=37.82 E-value=1.3e+02 Score=31.60 Aligned_cols=91 Identities=11% Similarity=0.065 Sum_probs=60.4
Q ss_pred ccEEEEEcCCChhHHHhHHHHHHHHHHHCCCcEE-EEEEcCCchHhhhcCCCCCEEEEecCCCCCC-----ChHHHHHHH
Q 015881 122 VRRCCCIISGGVYENLLFFPAIQLLKDRYPGVLI-DVIASARGKQTFELNKNVRWANVYDLDDDWP-----EPAEYTDIL 195 (399)
Q Consensus 122 v~rILIIr~~~IGDvVLttPalraLK~~yP~A~I-dvLv~~~~~~lle~nP~ID~Vi~~d~k~~~~-----~~~~~~~l~ 195 (399)
-.|+||+-+.+.|=+.|.-=+...+.+.++++.+ .+++..+..++.+..-.|..+++...-+.-. ..-......
T Consensus 169 GQR~lIvgppGvGKTTLaK~Ian~I~~nhFDv~~~VvLIgER~~EVtdiqrsIlg~vv~st~d~~~~~~~~~a~~~ie~A 248 (416)
T PRK09376 169 GQRGLIVAPPKAGKTVLLQNIANSITTNHPEVHLIVLLIDERPEEVTDMQRSVKGEVVASTFDEPAERHVQVAEMVIEKA 248 (416)
T ss_pred CceEEEeCCCCCChhHHHHHHHHHHHhhcCCeEEEEEEeCCchhHHHHHHHHhcCcEEEECCCCCHHHHHHHHHHHHHHH
Confidence 4799999999999999999999999998999884 4456665555544443333344444322211 011234566
Q ss_pred HHhhhCCCcEEEEcCCC
Q 015881 196 GVMKNRYYDMVLSTKLA 212 (399)
Q Consensus 196 ~~LR~~~YDlvIdl~~~ 212 (399)
+.+|....|++|-+..-
T Consensus 249 e~~~e~G~dVlL~iDsI 265 (416)
T PRK09376 249 KRLVEHGKDVVILLDSI 265 (416)
T ss_pred HHHHHcCCCEEEEEECh
Confidence 67888889999866544
No 109
>PF03033 Glyco_transf_28: Glycosyltransferase family 28 N-terminal domain; InterPro: IPR004276 The biosynthesis of disaccharides, oligosaccharides and polysaccharides involves the action of hundreds of different glycosyltransferases. These enzymes catalyse the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming glycosidic bonds. A classification of glycosyltransferases using nucleotide diphospho-sugar, nucleotide monophospho-sugar and sugar phosphates (2.4.1.- from EC) and related proteins into distinct sequence based families has been described []. This classification is available on the CAZy (CArbohydrate-Active EnZymes) web site. The same three-dimensional fold is expected to occur within each of the families. Because 3-D structures are better conserved than sequences, several of the families defined on the basis of sequence similarities may have similar 3-D structures and therefore form 'clans'. Glycosyltransferase family 28 GT28 from CAZY comprises enzymes with a number of known activities; 1,2-diacylglycerol 3-beta-galactosyltransferase (2.4.1.46 from EC); 1,2-diacylglycerol 3-beta-glucosyltransferase (2.4.1.157 from EC); beta-N-acetylglucosamine transferase (2.4.1 from EC).; GO: 0016758 transferase activity, transferring hexosyl groups, 0005975 carbohydrate metabolic process, 0030259 lipid glycosylation; PDB: 2IYF_B 2YJN_A 2P6P_A 1PNV_A 3H4T_A 3H4I_A 1PN3_B 3IA7_B 1NLM_B 1F0K_B ....
Probab=37.82 E-value=79 Score=26.47 Aligned_cols=44 Identities=14% Similarity=0.132 Sum_probs=38.6
Q ss_pred EEEEcCCChhHHHhHHHHHHHHHHHCCCcEEEEEEcCCchHhhhcC
Q 015881 125 CCCIISGGVYENLLFFPAIQLLKDRYPGVLIDVIASARGKQTFELN 170 (399)
Q Consensus 125 ILIIr~~~IGDvVLttPalraLK~~yP~A~IdvLv~~~~~~lle~n 170 (399)
|||+-.+.-||+-=.+++.++|+++ +-++.+.+.+...+.++..
T Consensus 1 Ili~~~Gt~Ghv~P~lala~~L~~r--Gh~V~~~~~~~~~~~v~~~ 44 (139)
T PF03033_consen 1 ILIATGGTRGHVYPFLALARALRRR--GHEVRLATPPDFRERVEAA 44 (139)
T ss_dssp EEEEEESSHHHHHHHHHHHHHHHHT--T-EEEEEETGGGHHHHHHT
T ss_pred CEEEEcCChhHHHHHHHHHHHHhcc--CCeEEEeecccceeccccc
Confidence 7899999999999999999999998 6678899999999888653
No 110
>PRK00326 cell division protein MraZ; Reviewed
Probab=37.78 E-value=1.3e+02 Score=26.18 Aligned_cols=52 Identities=15% Similarity=0.374 Sum_probs=33.6
Q ss_pred CCCCHHHHHHHHHHhhhCCCEEEeCCchhHHHHHHHHhcCCCCceeecCCccccchh
Q 015881 334 SLLPIQVWAEIANGLREFRPLFVIPHEKEREGVEDVVGDDASIVFITTPGQVRMSSY 390 (399)
Q Consensus 334 KrWP~e~faeLa~~L~~~~~VvliGgp~E~e~aeeI~~~~~~~~~i~~~G~ls~~~~ 390 (399)
-.||.+.|.++.+.+.... .+.++.+.+...+....-... +...|++++.+-
T Consensus 45 e~~~~~~~~~~~~~i~~l~----~~~~~~~~l~r~~~~~~~~~~-~D~~GRi~iP~~ 96 (139)
T PRK00326 45 LLYPLPEWEKIEEKLAALP----LTNPEARAFQRLLLGGAVEVE-LDKQGRILIPPN 96 (139)
T ss_pred EEcCHHHHHHHHHHHHhCC----CCCHHHHHHHHHHhcCCeEee-eCCCCeEeCCHH
Confidence 3699999999999886543 234444555555555544444 666777776543
No 111
>PRK13608 diacylglycerol glucosyltransferase; Provisional
Probab=37.52 E-value=4.5e+02 Score=26.58 Aligned_cols=21 Identities=14% Similarity=0.248 Sum_probs=17.2
Q ss_pred HHHHHHhhhCCCcEEEEcCCC
Q 015881 192 TDILGVMKNRYYDMVLSTKLA 212 (399)
Q Consensus 192 ~~l~~~LR~~~YDlvIdl~~~ 212 (399)
.++.+.|++.++|++|..+..
T Consensus 94 ~~l~~~l~~~kPDvVi~~~p~ 114 (391)
T PRK13608 94 NKLINLLIKEKPDLILLTFPT 114 (391)
T ss_pred HHHHHHHHHhCcCEEEECCcH
Confidence 467778999999999997654
No 112
>cd08422 PBP2_CrgA_like The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its related homologs, contains the type 2 periplasmic binding domain. This CD includes the substrate binding domain of LysR-type transcriptional regulator (LTTR) CrgA and its related homologs. The LTTRs are acting as both auto-repressors and activators of target promoters, controlling operons involved in a wide variety of cellular processes such as amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to name a few. In contrast to the tetrameric form of other LTTRs, CrgA from Neisseria meningitides assembles into an octameric ring, which can bind up to four 63-bp DNA oligonucleotides. Phylogenetic cluster analysis further showed that the CrgA-like regulators form a subclass of the LTTRs that function as octamers. The CrgA is an auto-repressor of its own
Probab=37.24 E-value=69 Score=27.06 Aligned_cols=40 Identities=23% Similarity=0.282 Sum_probs=30.2
Q ss_pred HHHHHHHHHHHCCCcEEEEEEcCCchHhhhcCCCCCEEEEec
Q 015881 139 FFPAIQLLKDRYPGVLIDVIASARGKQTFELNKNVRWANVYD 180 (399)
Q Consensus 139 ttPalraLK~~yP~A~IdvLv~~~~~~lle~nP~ID~Vi~~d 180 (399)
..+++..++++||+++|++.+......++++ .+|=.+...
T Consensus 16 l~~~l~~~~~~~P~v~i~i~~~~~~~~l~~~--~~D~~i~~~ 55 (197)
T cd08422 16 LAPLLAEFLARYPDVRLELVLSDRLVDLVEE--GFDLAIRIG 55 (197)
T ss_pred HHHHHHHHHHhCCceEEEEecCccccchhhc--CccEEEEeC
Confidence 4588999999999999999875544455443 488777654
No 113
>PRK07313 phosphopantothenoylcysteine decarboxylase; Validated
Probab=37.17 E-value=63 Score=29.73 Aligned_cols=44 Identities=14% Similarity=0.184 Sum_probs=37.3
Q ss_pred ccEEEEEcCCChhHHHhHHHHHHHHHHHCCCcEEEEEEcCCchHhhh
Q 015881 122 VRRCCCIISGGVYENLLFFPAIQLLKDRYPGVLIDVIASARGKQTFE 168 (399)
Q Consensus 122 v~rILIIr~~~IGDvVLttPalraLK~~yP~A~IdvLv~~~~~~lle 168 (399)
+|||++.-.+++|=. .+.-+++.|++. +++|+++..+.++.++.
T Consensus 1 ~k~Ill~vtGsiaa~-~~~~li~~L~~~--g~~V~vv~T~~A~~fi~ 44 (182)
T PRK07313 1 MKNILLAVSGSIAAY-KAADLTSQLTKR--GYQVTVLMTKAATKFIT 44 (182)
T ss_pred CCEEEEEEeChHHHH-HHHHHHHHHHHC--CCEEEEEEChhHHHHcC
Confidence 589999999999865 478899999886 78999999998887755
No 114
>TIGR00215 lpxB lipid-A-disaccharide synthase. Lipid-A precursor biosynthesis producing lipid A disaccharide in a condensation reaction. transcribed as part of an operon including lpxA
Probab=36.96 E-value=93 Score=31.73 Aligned_cols=109 Identities=14% Similarity=0.057 Sum_probs=62.0
Q ss_pred ccEEEEEcCCChhHHHhHHHHHHHHHHHCCCcEEEEEEcCCchHhhhcCCCCCEEEEecCCC---CCCChH----HHHHH
Q 015881 122 VRRCCCIISGGVYENLLFFPAIQLLKDRYPGVLIDVIASARGKQTFELNKNVRWANVYDLDD---DWPEPA----EYTDI 194 (399)
Q Consensus 122 v~rILIIr~~~IGDvVLttPalraLK~~yP~A~IdvLv~~~~~~lle~nP~ID~Vi~~d~k~---~~~~~~----~~~~l 194 (399)
+-||+|+--+-=||+.=+ -++++||++.|++++.-+..+..+. ++.+..-....++-.+ ..+.+. .+...
T Consensus 5 ~~ki~i~aGgtsGhi~pa-al~~~l~~~~~~~~~~g~gg~~m~~--~g~~~~~~~~~l~v~G~~~~l~~~~~~~~~~~~~ 81 (385)
T TIGR00215 5 IPTIALVAGEASGDILGA-GLRQQLKEHYPNARFIGVAGPRMAA--EGCEVLYSMEELSVMGLREVLGRLGRLLKIRKEV 81 (385)
T ss_pred CCeEEEEeCCccHHHHHH-HHHHHHHhcCCCcEEEEEccHHHHh--CcCccccChHHhhhccHHHHHHHHHHHHHHHHHH
Confidence 468888888888999999 9999999988875555444332211 0111100011111100 011111 22344
Q ss_pred HHHhhhCCCcEEEEcCCCC--hHHHHHHHHhCCCeEEEecCC
Q 015881 195 LGVMKNRYYDMVLSTKLAG--LGHAAFLFMTTARDRVSYIYP 234 (399)
Q Consensus 195 ~~~LR~~~YDlvIdl~~~~--~rsAll~~LsgA~~RIGy~~~ 234 (399)
.+.+|+.+.|+||.+.+.+ ++-+..+...|+|. +-|..|
T Consensus 82 ~~~l~~~kPd~vi~~g~~~~~~~~a~aa~~~gip~-v~~i~P 122 (385)
T TIGR00215 82 VQLAKQAKPDLLVGIDAPDFNLTKELKKKDPGIKI-IYYISP 122 (385)
T ss_pred HHHHHhcCCCEEEEeCCCCccHHHHHHHhhCCCCE-EEEeCC
Confidence 5678999999999776533 34455777888885 345434
No 115
>COG1036 Archaeal flavoproteins [Energy production and conversion]
Probab=36.86 E-value=58 Score=29.98 Aligned_cols=46 Identities=24% Similarity=0.250 Sum_probs=38.0
Q ss_pred cEEEEEcCCChhHHHhHH-HHHHHHHHHCCCcEEEEEEcCCchHhhhc
Q 015881 123 RRCCCIISGGVYENLLFF-PAIQLLKDRYPGVLIDVIASARGKQTFEL 169 (399)
Q Consensus 123 ~rILIIr~~~IGDvVLtt-PalraLK~~yP~A~IdvLv~~~~~~lle~ 169 (399)
|||. +...+=||.+.-| -++..||+.||+.+|+++.++.+.++++.
T Consensus 9 ~rIa-WgITGaG~~L~Et~~imk~lk~~~~~~~v~v~lSkageeVvk~ 55 (187)
T COG1036 9 KRIA-WGITGAGHLLPETYQIMKELKKEYGDVEVDVFLSKAGEEVVKM 55 (187)
T ss_pred ceEE-EEEeccccccHHHHHHHHHHHhhcCCceEEEeehhhHHHHHHH
Confidence 4454 5666779988766 89999999999999999999988887764
No 116
>cd03818 GT1_ExpC_like This family is most closely related to the GT1 family of glycosyltransferases. ExpC in Rhizobium meliloti has been shown to be involved in the biosynthesis of galactoglucan (exopolysaccharide II).
Probab=36.24 E-value=2.7e+02 Score=27.83 Aligned_cols=36 Identities=8% Similarity=-0.045 Sum_probs=29.1
Q ss_pred EEEEEcCCChhHHHhHHHHHHHHHHHCCCcEEEEEEcCCch
Q 015881 124 RCCCIISGGVYENLLFFPAIQLLKDRYPGVLIDVIASARGK 164 (399)
Q Consensus 124 rILIIr~~~IGDvVLttPalraLK~~yP~A~IdvLv~~~~~ 164 (399)
|||+|..+.=|..- -+.++|.++ +.+|++++.....
T Consensus 1 ~il~~~~~~p~~~~---~la~~L~~~--G~~v~~~~~~~~~ 36 (396)
T cd03818 1 RILFVHQNFPGQFR---HLAPALAAQ--GHEVVFLTEPNAA 36 (396)
T ss_pred CEEEECCCCchhHH---HHHHHHHHC--CCEEEEEecCCCC
Confidence 69999998888753 378888887 9999999977654
No 117
>PF12362 DUF3646: DNA polymerase III gamma and tau subunits C terminal; InterPro: IPR022107 This domain family is found in bacteria, and is approximately 120 amino acids in length. The family is found in association with PF00004 from PFAM. The proteins in this family are frequently annotated as the gamma and tau subunits of DNA polymerase III, however there is little accompanying literature to back this up.
Probab=36.15 E-value=29 Score=29.86 Aligned_cols=21 Identities=19% Similarity=0.322 Sum_probs=19.6
Q ss_pred HHhHHHHHHHHHHHCCCcEEE
Q 015881 136 NLLFFPAIQLLKDRYPGVLID 156 (399)
Q Consensus 136 vVLttPalraLK~~yP~A~Id 156 (399)
-+...|+++++..+||+|+|.
T Consensus 94 ~a~~~P~V~avL~~FPgA~I~ 114 (117)
T PF12362_consen 94 AARAHPLVKAVLAAFPGAEIV 114 (117)
T ss_pred HHHhCcHHHHHHHHCCCCEEE
Confidence 788899999999999999985
No 118
>cd03823 GT1_ExpE7_like This family is most closely related to the GT1 family of glycosyltransferases. ExpE7 in Sinorhizobium meliloti has been shown to be involved in the biosynthesis of galactoglucans (exopolysaccharide II).
Probab=35.84 E-value=2.9e+02 Score=25.93 Aligned_cols=38 Identities=13% Similarity=0.079 Sum_probs=26.6
Q ss_pred EEEEEcCCC-----hhHHHhHHHHHHHHHHHCCCcEEEEEEcCCc
Q 015881 124 RCCCIISGG-----VYENLLFFPAIQLLKDRYPGVLIDVIASARG 163 (399)
Q Consensus 124 rILIIr~~~-----IGDvVLttPalraLK~~yP~A~IdvLv~~~~ 163 (399)
|||+|-... =|--..+.-++++|+++ +.++++++....
T Consensus 1 kIl~i~~~~~~~~~gG~~~~~~~l~~~L~~~--g~~v~v~~~~~~ 43 (359)
T cd03823 1 RILVVNHLYPPRSVGGAEVVAHDLAEALAKR--GHEVAVLTAGED 43 (359)
T ss_pred CeeEEcccCCcccccchHHHHHHHHHHHHhc--CCceEEEeCCCC
Confidence 688886554 25556677889999876 678888875443
No 119
>PRK08462 biotin carboxylase; Validated
Probab=35.22 E-value=1.3e+02 Score=31.11 Aligned_cols=84 Identities=13% Similarity=0.011 Sum_probs=53.4
Q ss_pred CccEEEEEcCCChhHHHhHHHHHHHHHHHCCCcEEEEEEcCCchHhhhcCCCCCEEEEecCCCCCCChHHHHHHHHHhhh
Q 015881 121 DVRRCCCIISGGVYENLLFFPAIQLLKDRYPGVLIDVIASARGKQTFELNKNVRWANVYDLDDDWPEPAEYTDILGVMKN 200 (399)
Q Consensus 121 ~v~rILIIr~~~IGDvVLttPalraLK~~yP~A~IdvLv~~~~~~lle~nP~ID~Vi~~d~k~~~~~~~~~~~l~~~LR~ 200 (399)
.++||||+..+-+ ..|+++++|+. +.++..+....... .-....-|+.+.......-.+....-.++...++
T Consensus 3 ~~k~ili~~~g~~-----~~~~~~~~~~~--G~~~v~~~~~~d~~-~~~~~~ad~~~~~~~~~~~~~y~~~~~l~~~~~~ 74 (445)
T PRK08462 3 EIKRILIANRGEI-----ALRAIRTIQEM--GKEAIAIYSTADKD-ALYLKYADAKICIGGAKSSESYLNIPAIISAAEI 74 (445)
T ss_pred CCCEEEEECCcHH-----HHHHHHHHHHc--CCCEEEEechhhcC-CchhhhCCEEEEeCCCchhcccCCHHHHHHHHHH
Confidence 4789999988766 67999999998 66666555433221 1122345777777432210111223467788888
Q ss_pred CCCcEEEEcCCC
Q 015881 201 RYYDMVLSTKLA 212 (399)
Q Consensus 201 ~~YDlvIdl~~~ 212 (399)
.+.|+++-..+.
T Consensus 75 ~~~D~i~pg~g~ 86 (445)
T PRK08462 75 FEADAIFPGYGF 86 (445)
T ss_pred cCCCEEEECCCc
Confidence 999999977643
No 120
>cd08471 PBP2_CrgA_like_2 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold. This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 2. The LTTRs are acting as both auto-repressors and activators of target promoters, controlling operons involved in a wide variety of cellular processes such as amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to name a few. In contrast to the tetrameric form of other LTTRs, CrgA from Neisseria meningitides assembles into an octameric ring, which can bind up to four 63-bp DNA oligonucleotides. Phylogenetic cluster analysis showed that the CrgA-like regulators form a subclass of the LTTRs that function as octamers. The CrgA is an auto-repressor of its own gene a
Probab=35.17 E-value=85 Score=26.79 Aligned_cols=41 Identities=24% Similarity=0.287 Sum_probs=30.1
Q ss_pred hHHHHHHHHHHHCCCcEEEEEEcCCchHhhhcCCCCCEEEEec
Q 015881 138 LFFPAIQLLKDRYPGVLIDVIASARGKQTFELNKNVRWANVYD 180 (399)
Q Consensus 138 LttPalraLK~~yP~A~IdvLv~~~~~~lle~nP~ID~Vi~~d 180 (399)
+..+++..++++||+++|++........+++ ..+|=.+.+.
T Consensus 15 ~l~~~l~~~~~~~P~v~i~i~~~~~~~~~~~--~~~Dl~i~~~ 55 (201)
T cd08471 15 HVLPIITDFLDAYPEVSVRLLLLDRVVNLLE--EGVDVAVRIG 55 (201)
T ss_pred HHHHHHHHHHHHCCCcEEEEEEcCccchhhc--ccccEEEEec
Confidence 4558999999999999999987554445443 3677766643
No 121
>PRK15179 Vi polysaccharide biosynthesis protein TviE; Provisional
Probab=34.98 E-value=6.9e+02 Score=28.01 Aligned_cols=39 Identities=15% Similarity=0.041 Sum_probs=27.5
Q ss_pred HHHHHHHhhhCCCcEEEEcCCC-ChHHHHHHHHhCCCeEE
Q 015881 191 YTDILGVMKNRYYDMVLSTKLA-GLGHAAFLFMTTARDRV 229 (399)
Q Consensus 191 ~~~l~~~LR~~~YDlvIdl~~~-~~rsAll~~LsgA~~RI 229 (399)
+.++.+.+|+.+||+|...... .+-+.+.+++.|+|..+
T Consensus 389 ~~~L~~~lk~~kpDIVH~h~~~a~~lg~lAa~~~gvPvIv 428 (694)
T PRK15179 389 TTKLTDVMRSSVPSVVHIWQDGSIFACALAALLAGVPRIV 428 (694)
T ss_pred HHHHHHHHHHcCCcEEEEeCCcHHHHHHHHHHHcCCCEEE
Confidence 4677888999999999864433 13455667778888655
No 122
>cd08476 PBP2_CrgA_like_7 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold. This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 7. The LTTRs are acting as both auto-repressors and activators of target promoters, controlling operons involved in a wide variety of cellular processes such as amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to name a few. In contrast to the tetrameric form of other LTTRs, CrgA from Neisseria meningitides assembles into an octameric ring, which can bind up to four 63-bp DNA oligonucleotides. Phylogenetic cluster analysis showed that the CrgA-like regulators form a subclass of the LTTRs that function as octamers. The CrgA is an auto-repressor of its own gene a
Probab=34.70 E-value=78 Score=26.79 Aligned_cols=40 Identities=18% Similarity=0.250 Sum_probs=29.0
Q ss_pred HHHHHHHHHHHCCCcEEEEEEcCCchHhhhcCCCCCEEEEec
Q 015881 139 FFPAIQLLKDRYPGVLIDVIASARGKQTFELNKNVRWANVYD 180 (399)
Q Consensus 139 ttPalraLK~~yP~A~IdvLv~~~~~~lle~nP~ID~Vi~~d 180 (399)
..|++..++++||+++|.+.......+.+.. .+|=.+...
T Consensus 14 l~~~l~~~~~~~P~v~i~~~~~~~~~~~l~~--~~D~~i~~~ 53 (197)
T cd08476 14 LLPVLAAFMQRYPEIELDLDFSDRLVDVIDE--GFDAVIRTG 53 (197)
T ss_pred HHHHHHHHHHHCCCeEEEEEecCCccccccc--CeeEEEEeC
Confidence 3589999999999999998654444444443 377777654
No 123
>cd08453 PBP2_IlvR The C-terminal substrate binding domain of LysR-type transcriptional regulator, IlvR, involved in the biosynthesis of isoleucine, leucine and valine; contains type 2 periplasmic binding fold. The IlvR is an activator of the upstream and divergently transcribed ilvD gene, which encodes dihydroxy acid dehydratase that participates in isoleucine, leucine, and valine biosynthesis. As in the case of other members of the LysR family, the expression of ilvR gene is repressed in the presence of its own gene product. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport
Probab=34.34 E-value=1.4e+02 Score=25.58 Aligned_cols=24 Identities=13% Similarity=0.358 Sum_probs=20.1
Q ss_pred HhHHHHHHHHHHHCCCcEEEEEEc
Q 015881 137 LLFFPAIQLLKDRYPGVLIDVIAS 160 (399)
Q Consensus 137 VLttPalraLK~~yP~A~IdvLv~ 160 (399)
-+..+++..++++||+.+|++...
T Consensus 13 ~~l~~~l~~~~~~~P~i~l~i~~~ 36 (200)
T cd08453 13 SVLPELVRRFREAYPDVELQLREA 36 (200)
T ss_pred HHHHHHHHHHHHhCCCceEEEEeC
Confidence 355689999999999999998764
No 124
>cd08419 PBP2_CbbR_RubisCO_like The C-terminal substrate binding of LysR-type transcriptional regulator (CbbR) of RubisCO operon, which is involved in the carbon dioxide fixation, contains the type 2 periplasmic binding fold. CbbR, a LysR-type transcriptional regulator, is required to activate expression of RubisCO, one of two unique enzymes in the Calvin-Benson-Bassham (CBB) cycle pathway. All plants, cyanobacteria, and many autotrophic bacteria use the CBB cycle to fix carbon dioxide. Thus, this cycle plays an essential role in assimilating CO2 into organic carbon on earth. The key CBB cycle enzyme is ribulose 1,5-bisphosphate carboxylase/oxygenase (RubisCO), which catalyzes the actual CO2 fixation reaction. The CO2 concentration affects the expression of RubisCO genes. It has also shown that NADPH enhances the DNA-binding ability of the CbbR. RubisCO is composed of eight large (CbbL) and eight small subunits (CbbS). The topology of this substrate-binding domain is most similar to t
Probab=34.30 E-value=1.1e+02 Score=25.71 Aligned_cols=24 Identities=17% Similarity=0.198 Sum_probs=20.4
Q ss_pred HhHHHHHHHHHHHCCCcEEEEEEc
Q 015881 137 LLFFPAIQLLKDRYPGVLIDVIAS 160 (399)
Q Consensus 137 VLttPalraLK~~yP~A~IdvLv~ 160 (399)
.+..+++..++++||+++|.+...
T Consensus 12 ~~l~~~l~~~~~~~P~i~l~i~~~ 35 (197)
T cd08419 12 YFAPRLLGAFCRRHPGVEVSLRVG 35 (197)
T ss_pred hHhhHHHHHHHHHCCCceEEEEEC
Confidence 356788999999999999998764
No 125
>PRK03601 transcriptional regulator HdfR; Provisional
Probab=34.20 E-value=1.6e+02 Score=27.91 Aligned_cols=36 Identities=8% Similarity=0.035 Sum_probs=26.2
Q ss_pred EEEcCCChhHHHhHHHHHHHHHHHCCCcEEEEEEcC
Q 015881 126 CCIISGGVYENLLFFPAIQLLKDRYPGVLIDVIASA 161 (399)
Q Consensus 126 LIIr~~~IGDvVLttPalraLK~~yP~A~IdvLv~~ 161 (399)
+.|-.+......+..+++..++++||+.+|.+.+..
T Consensus 91 l~Ig~~~~~~~~~l~~~l~~f~~~~P~v~v~~~~~~ 126 (275)
T PRK03601 91 LSIGASASLWECMLTPWLGRLYQNQEALQFEARIAQ 126 (275)
T ss_pred EEEeccHHHHHHHHHHHHHHHHHhCCCcEEEEEECC
Confidence 444444444456677899999999999999987754
No 126
>COG1182 AcpD Acyl carrier protein phosphodiesterase [Lipid metabolism]
Probab=33.90 E-value=77 Score=29.96 Aligned_cols=50 Identities=14% Similarity=-0.025 Sum_probs=37.0
Q ss_pred ccEEEEEcCCChhHH----HhHHHHHHHHHHHCCCcEEEEEEcCCchHhhh-cCCCCCEEE
Q 015881 122 VRRCCCIISGGVYEN----LLFFPAIQLLKDRYPGVLIDVIASARGKQTFE-LNKNVRWAN 177 (399)
Q Consensus 122 v~rILIIr~~~IGDv----VLttPalraLK~~yP~A~IdvLv~~~~~~lle-~nP~ID~Vi 177 (399)
|+|||+|..+-.||. .++--.+...|+++|+.+|..+- +.+ ..|++|.-.
T Consensus 1 MskvL~I~as~~~~~S~S~~l~~~Fi~~yk~~~P~dev~~~D------L~~e~iP~ld~~~ 55 (202)
T COG1182 1 MSKVLVIKASPLGENSVSRKLADEFIETYKEKHPNDEVIERD------LAAEPIPHLDEEL 55 (202)
T ss_pred CceEEEEecCCCccccHHHHHHHHHHHHHHHhCCCCeEEEee------cccCCCcccCHHH
Confidence 578999999999886 45557788899999999987763 222 347776543
No 127
>PLN02448 UDP-glycosyltransferase family protein
Probab=33.83 E-value=5.3e+02 Score=27.04 Aligned_cols=51 Identities=14% Similarity=0.095 Sum_probs=44.3
Q ss_pred CCccEEEEEcCCChhHHHhHHHHHHHHHHHCCCcEEEEEEcCCchHhhhcC
Q 015881 120 GDVRRCCCIISGGVYENLLFFPAIQLLKDRYPGVLIDVIASARGKQTFELN 170 (399)
Q Consensus 120 ~~v~rILIIr~~~IGDvVLttPalraLK~~yP~A~IdvLv~~~~~~lle~n 170 (399)
++..+|+++-....|++.=++.+.+.|..+.|+..|++++.+.+...++..
T Consensus 8 ~~~~hVvlvp~pa~GHi~P~l~LA~~L~~~~~G~~VT~~~t~~~~~~i~~~ 58 (459)
T PLN02448 8 TTSCHVVAMPYPGRGHINPMMNLCKLLASRKPDILITFVVTEEWLGLIGSD 58 (459)
T ss_pred CCCcEEEEECCcccccHHHHHHHHHHHHcCCCCcEEEEEeCCchHhHhhcc
Confidence 446799999999999999999999999988889999999999877655553
No 128
>cd08417 PBP2_Nitroaromatics_like The C-terminal substrate binding domain of LysR-type transcriptional regulators that involved in the catabolism of nitroaromatic/naphthalene compounds and that of related regulators; contains the type 2 periplasmic binding fold. This CD includes the C-terminal substrate binding domain of LysR-type transcriptional regulators involved in the catabolism of dinitrotoluene and similar compounds, such as DntR, NahR, and LinR. The transcription of the genes encoding enzymes involved in such degradation is regulated and expression of these enzymes is enhanced by inducers, which are either an intermediate in the metabolic pathway or compounds to be degraded. Also included are related LysR-type regulators clustered together in phylogenetic trees, including NodD, ToxR, LeuO, SyrM, TdcA, and PnbR. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrate
Probab=33.67 E-value=1e+02 Score=26.21 Aligned_cols=43 Identities=21% Similarity=0.206 Sum_probs=28.7
Q ss_pred hHHHHHHHHHHHCCCcEEEEEEcCCchHhhh--cCCCCCEEEEecC
Q 015881 138 LFFPAIQLLKDRYPGVLIDVIASARGKQTFE--LNKNVRWANVYDL 181 (399)
Q Consensus 138 LttPalraLK~~yP~A~IdvLv~~~~~~lle--~nP~ID~Vi~~d~ 181 (399)
+..+++..++++||+++|++.+.... .+.+ .+..+|=+|.+..
T Consensus 14 ~~~~~i~~~~~~~P~i~l~~~~~~~~-~~~~~l~~g~~D~~i~~~~ 58 (200)
T cd08417 14 LLPPLLARLRQEAPGVRLRFVPLDRD-DLEEALESGEIDLAIGVFP 58 (200)
T ss_pred HHHHHHHHHHhhCCCeEEEeccCCHH-HHHHHHHcCCCCEEEeecc
Confidence 35688999999999999999875532 2211 2345676666543
No 129
>TIGR00381 cdhD CO dehydrogenase/acetyl-CoA synthase, delta subunit. This is the small subunit of a heterodimer which catalyzes the reaction CO + H2O + Acceptor = CO2 + Reduced acceptor and is involved in the synthesis of acetyl-CoA from CO2 and H2.
Probab=33.54 E-value=2.8e+02 Score=28.91 Aligned_cols=61 Identities=16% Similarity=0.146 Sum_probs=45.2
Q ss_pred CeEEEEcCCCCccccccCCCCCCCCCCHHHHHHHHHHhhhC-C-CEEEeCC---chhHHHHHHHHhcCCC-Cceee
Q 015881 311 KYIVIHGIESDSKASMQSRGDTDSLLPIQVWAEIANGLREF-R-PLFVIPH---EKEREGVEDVVGDDAS-IVFIT 380 (399)
Q Consensus 311 ~~IvIhPgas~~~~~~k~rg~~~KrWP~e~faeLa~~L~~~-~-~VvliGg---p~E~e~aeeI~~~~~~-~~~i~ 380 (399)
..|+||-.+.++. .+.=+++.|+++++.+.+. . +++|.|+ .+|-+..++..+.+.+ ..+++
T Consensus 155 D~Ialr~~S~DP~---------~~d~~~~e~a~~vk~V~~av~vPLIL~gsg~~~kD~eVLeaaLe~~~G~kpLL~ 221 (389)
T TIGR00381 155 DMVTIHLISTDPK---------LDDKSPSEAAKVLEDVLQAVDVPIVIGGSGNPEKDPLVLEKAAEVAEGERCLLA 221 (389)
T ss_pred CEEEEEecCCCcc---------ccccCHHHHHHHHHHHHHhCCCCEEEeCCCCCcCCHHHHHHHHHHhCCCCcEEE
Confidence 4899997776653 2456899999999999764 3 8888877 6677888887777765 44344
No 130
>cd08415 PBP2_LysR_opines_like The C-terminal substrate-domain of LysR-type transcriptional regulators involved in the catabolism of opines and that of related regulators, contains the type 2 periplasmic binding fold. This CD includes the C-terminal substrate-domain of LysR-type transcriptional regulators, OccR and NocR, involved in the catabolism of opines and that of LysR for lysine biosynthesis which clustered together in phylogenetic trees. Opines, such as octopine and nopaline, are low molecular weight compounds found in plant crown gall tumors that are produced by the parasitic bacterium Agrobacterium. There are at least 30 different opines identified so far. Opines are utilized by tumor-colonizing bacteria as a source of carbon, nitrogen, and energy. NocR and OccR belong to the family of LysR-type transcriptional regulators that positively regulates the catabolism of nopaline and octopine, respectively. Both nopaline and octopalin are arginine derivatives. In Agrobacterium tumefa
Probab=33.45 E-value=1e+02 Score=26.01 Aligned_cols=48 Identities=19% Similarity=0.145 Sum_probs=29.7
Q ss_pred CChhHHHhHHHHHHHHHHHCCCcEEEEEEcCCchHhhh--cCCCCCEEEEec
Q 015881 131 GGVYENLLFFPAIQLLKDRYPGVLIDVIASARGKQTFE--LNKNVRWANVYD 180 (399)
Q Consensus 131 ~~IGDvVLttPalraLK~~yP~A~IdvLv~~~~~~lle--~nP~ID~Vi~~d 180 (399)
..++..+ ..++++.++++||+++|.+...... ++.+ ....+|=+|.+.
T Consensus 8 ~~~~~~~-l~~~l~~~~~~~P~i~l~i~~~~~~-~~~~~l~~~~~Dl~i~~~ 57 (196)
T cd08415 8 PALALSL-LPRAIARFRARHPDVRISLHTLSSS-TVVEAVLSGQADLGLASL 57 (196)
T ss_pred ccccccc-cHHHHHHHHHHCCCcEEEEEecchH-HHHHHHHcCCccEEEEeC
Confidence 3344433 4689999999999999999875322 2222 123566555543
No 131
>cd08429 PBP2_NhaR The C-terminal substrate binding domain of LysR-type transcriptional activator of the nhaA gene, encoding Na+/H+ antiporter, contains the type 2 periplasmic binding fold. NhaR is a positive regulator of the LysR family and is known to be an activator of the nhaA gene encoding a Na(+)/H(+) antiporter. In Escherichia coli, NhaA is the vital antiporter that protects against high sodium stress, and it is essential for growth in high sodium levels, while NhaB becomes essential only if NhaA is not available. The nhaA gene of nhaAR operon is induced by monovalent cations. The nhaR of the operon activates nhaAR, as well as the osmC transcription which is induced at elevated osmolarity. OsmC is transcribed from the two overlapping promoters (osmCp1 and osmP2) and that NhaR is shown to activate only the expression of osmCp1. NhaR also activates the transcription of the pgaABCD operon which is required for production of the biofilm adhesion, poly-beta-1,6-N-acetyl-d-glucosamine
Probab=33.40 E-value=1.2e+02 Score=26.72 Aligned_cols=25 Identities=4% Similarity=-0.029 Sum_probs=21.3
Q ss_pred HhHHHHHHHHHHHCCCcEEEEEEcC
Q 015881 137 LLFFPAIQLLKDRYPGVLIDVIASA 161 (399)
Q Consensus 137 VLttPalraLK~~yP~A~IdvLv~~ 161 (399)
-+..++++.++++||+++|.+.+..
T Consensus 13 ~~l~~~l~~f~~~~P~v~l~i~~~~ 37 (204)
T cd08429 13 SIAYRLLEPAMDLHEPIRLVCREGK 37 (204)
T ss_pred HHHHHHHHHHHHhCCCcEEEEEeCC
Confidence 4556999999999999999998754
No 132
>cd08426 PBP2_LTTR_like_5 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator, contains the type 2 periplasmic binding fold. LysR-transcriptional regulators comprise the largest family of prokaryotic transcription factor. Homologs of some of LTTRs with similar domain organizations are also found in the archaea and eukaryotic organisms. The LTTRs are composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcriptional repressor undergoes a conformational change upon substrate binding which in turn changes the DNA binding affinity of the repressor. The genes controlled by the LTTRs have diverse functi
Probab=33.38 E-value=1.6e+02 Score=24.98 Aligned_cols=23 Identities=35% Similarity=0.616 Sum_probs=19.4
Q ss_pred hHHHHHHHHHHHCCCcEEEEEEc
Q 015881 138 LFFPAIQLLKDRYPGVLIDVIAS 160 (399)
Q Consensus 138 LttPalraLK~~yP~A~IdvLv~ 160 (399)
+..++++.++++||+++|.+...
T Consensus 14 ~l~~~l~~~~~~~P~i~l~i~~~ 36 (199)
T cd08426 14 LLPSLIARFRQRYPGVFFTVDVA 36 (199)
T ss_pred HHHHHHHHHHHhCCCeEEEEEeC
Confidence 35689999999999999988753
No 133
>PRK08591 acetyl-CoA carboxylase biotin carboxylase subunit; Validated
Probab=33.21 E-value=1.3e+02 Score=31.05 Aligned_cols=81 Identities=10% Similarity=-0.005 Sum_probs=48.2
Q ss_pred ccEEEEEcCCChhHHHhHHHHHHHHHHHCCCcEEEEEEcCCchHhhhcCCCCCEEEEecCCCCCCChHHHHHHHHHhhhC
Q 015881 122 VRRCCCIISGGVYENLLFFPAIQLLKDRYPGVLIDVIASARGKQTFELNKNVRWANVYDLDDDWPEPAEYTDILGVMKNR 201 (399)
Q Consensus 122 v~rILIIr~~~IGDvVLttPalraLK~~yP~A~IdvLv~~~~~~lle~nP~ID~Vi~~d~k~~~~~~~~~~~l~~~LR~~ 201 (399)
++||||+-.+-+ ..++++++|+. +.++..+........ ......|+.+.+.....-......-+++...++.
T Consensus 2 ~k~iLi~g~g~~-----a~~i~~aa~~~--G~~vv~~~~~~d~~a-~~~~~ad~~~~~~~~~~~~~y~d~~~l~~~a~~~ 73 (451)
T PRK08591 2 FDKILIANRGEI-----ALRIIRACKEL--GIKTVAVHSTADRDA-LHVQLADEAVCIGPAPSKKSYLNIPAIISAAEIT 73 (451)
T ss_pred cceEEEECCCHH-----HHHHHHHHHHc--CCeEEEEcChhhccC-CCHhHCCEEEEeCCCCcccccCCHHHHHHHHHHh
Confidence 589999966655 58889999998 666666644322211 1113357777653221101112223566777888
Q ss_pred CCcEEEEcC
Q 015881 202 YYDMVLSTK 210 (399)
Q Consensus 202 ~YDlvIdl~ 210 (399)
+.|.++-..
T Consensus 74 ~id~I~p~~ 82 (451)
T PRK08591 74 GADAIHPGY 82 (451)
T ss_pred CCCEEEECC
Confidence 999998654
No 134
>COG1448 TyrB Aspartate/tyrosine/aromatic aminotransferase [Amino acid transport and metabolism]
Probab=33.10 E-value=3.4e+02 Score=28.27 Aligned_cols=60 Identities=20% Similarity=0.319 Sum_probs=41.9
Q ss_pred CCCCCeEEEEcCCCCccccccCCCCCCCCCCHHHHHHHHHHhhhCC--CEEEe-------CCchhHHHHHHHHhcCCC
Q 015881 307 AEQGKYIVIHGIESDSKASMQSRGDTDSLLPIQVWAEIANGLREFR--PLFVI-------PHEKEREGVEDVVGDDAS 375 (399)
Q Consensus 307 l~~~~~IvIhPgas~~~~~~k~rg~~~KrWP~e~faeLa~~L~~~~--~Vvli-------Ggp~E~e~aeeI~~~~~~ 375 (399)
++.+-+|++|+=.-.++ --.-..|.|.+|++.+.+++ +++=+ |..+|+..++.+++..+.
T Consensus 169 a~~~~vvLLH~CcHNPT---------G~D~t~~qW~~l~~~~~~r~lip~~D~AYQGF~~GleeDa~~lR~~a~~~~~ 237 (396)
T COG1448 169 APEGSVVLLHGCCHNPT---------GIDPTEEQWQELADLIKERGLIPFFDIAYQGFADGLEEDAYALRLFAEVGPE 237 (396)
T ss_pred CCCCCEEEEecCCCCCC---------CCCCCHHHHHHHHHHHHHcCCeeeeehhhhhhccchHHHHHHHHHHHHhCCc
Confidence 34567999997666665 24589999999999999887 33311 555666666666666554
No 135
>cd03806 GT1_ALG11_like This family is most closely related to the GT1 family of glycosyltransferases. ALG11 in yeast is involved in adding the final 1,2-linked Man to the Man5GlcNAc2-PP-Dol synthesized on the cytosolic face of the ER. The deletion analysis of ALG11 was shown to block the early steps of core biosynthesis that takes place on the cytoplasmic face of the ER and lead to a defect in the assembly of lipid-linked oligosaccharides.
Probab=32.87 E-value=3.8e+02 Score=27.47 Aligned_cols=96 Identities=15% Similarity=0.171 Sum_probs=49.8
Q ss_pred HHHhHHHHHHHHHHHCCCcEEEEEEcCCch---Hhh---------hcCCCCCEEEEe-c----CCCCCCCh---H----H
Q 015881 135 ENLLFFPAIQLLKDRYPGVLIDVIASARGK---QTF---------ELNKNVRWANVY-D----LDDDWPEP---A----E 190 (399)
Q Consensus 135 DvVLttPalraLK~~yP~A~IdvLv~~~~~---~ll---------e~nP~ID~Vi~~-d----~k~~~~~~---~----~ 190 (399)
|=|| +=++.+|+++.|+.+|++.+..... .++ +....++-+++. - .+..|+.. . .
T Consensus 17 ervl-~~a~~~l~~~~~~~~v~i~t~~~~~~~~~~l~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~r~~~~~~~~~~ 95 (419)
T cd03806 17 ERVL-WCAVRALQKRYPNNIVVIYTGDLDATPEEILEKVESRFNIELDRPRIVFFLLKYRKLVEASTYPRFTLLGQALGS 95 (419)
T ss_pred hHHH-HHHHHHHHHhCCCcEEEEECCCCCCCHHHHHHHHHHhcCeecCCCceEEEEecceeeeccccCCceeeHHHHHHH
Confidence 4444 3457788888999999999865322 222 112233323332 1 11223321 1 1
Q ss_pred HHHHHHHhhhCCCcEEEEcCCCChHHHHHHHHhCCCeEEEec
Q 015881 191 YTDILGVMKNRYYDMVLSTKLAGLGHAAFLFMTTARDRVSYI 232 (399)
Q Consensus 191 ~~~l~~~LR~~~YDlvIdl~~~~~rsAll~~LsgA~~RIGy~ 232 (399)
....++.+.+.++|++|+.++.++..-++.++.++| .|.|.
T Consensus 96 ~~~~~~~~~~~~pDv~i~~~g~~~~~~~~~~~~~~~-~i~y~ 136 (419)
T cd03806 96 MILGLEALLKLVPDIFIDTMGYPFTYPLVRLLGGCP-VGAYV 136 (419)
T ss_pred HHHHHHHHHhcCCCEEEEcCCcccHHHHHHHhcCCe-EEEEe
Confidence 122233344457999999987733333334446664 56676
No 136
>cd08414 PBP2_LTTR_aromatics_like The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in the catabolism of aromatic compounds and that of other related regulators, contains type 2 periplasmic binding fold. This CD includes the C-terminal substrate binding domain of LTTRs involved in degradation of aromatic compounds, such as CbnR, BenM, CatM, ClcR and TfdR, as well as that of other transcriptional regulators clustered together in phylogenetic trees, including XapR, HcaR, MprR, IlvR, BudR, AlsR, LysR, and OccR. The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they ca
Probab=32.66 E-value=1.5e+02 Score=25.01 Aligned_cols=23 Identities=22% Similarity=0.449 Sum_probs=19.9
Q ss_pred hHHHHHHHHHHHCCCcEEEEEEc
Q 015881 138 LFFPAIQLLKDRYPGVLIDVIAS 160 (399)
Q Consensus 138 LttPalraLK~~yP~A~IdvLv~ 160 (399)
+..+++..++++||+++|.+...
T Consensus 14 ~l~~~l~~~~~~~p~i~i~i~~~ 36 (197)
T cd08414 14 LLPRLLRRFRARYPDVELELREM 36 (197)
T ss_pred HHHHHHHHHHHHCCCcEEEEecC
Confidence 45699999999999999998764
No 137
>PRK05920 aromatic acid decarboxylase; Validated
Probab=32.30 E-value=86 Score=29.59 Aligned_cols=44 Identities=11% Similarity=0.178 Sum_probs=39.3
Q ss_pred ccEEEEEcCCChhHHHhHHHHHHHHHHHCCCcEEEEEEcCCchHhhh
Q 015881 122 VRRCCCIISGGVYENLLFFPAIQLLKDRYPGVLIDVIASARGKQTFE 168 (399)
Q Consensus 122 v~rILIIr~~~IGDvVLttPalraLK~~yP~A~IdvLv~~~~~~lle 168 (399)
.|||++--.+++|= +-+.-+++.|++. +++|.+++.+....++.
T Consensus 3 ~krIllgITGsiaa-~ka~~lvr~L~~~--g~~V~vi~T~~A~~fv~ 46 (204)
T PRK05920 3 MKRIVLAITGASGA-IYGVRLLECLLAA--DYEVHLVISKAAQKVLA 46 (204)
T ss_pred CCEEEEEEeCHHHH-HHHHHHHHHHHHC--CCEEEEEEChhHHHHHH
Confidence 58999999999998 6999999999997 89999999998887664
No 138
>cd08477 PBP2_CrgA_like_8 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold. This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 8. The LTTRs are acting as both auto-repressors and activators of target promoters, controlling operons involved in a wide variety of cellular processes such as amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to name a few. In contrast to the tetrameric form of other LTTRs, CrgA from Neisseria meningitides assembles into an octameric ring, which can bind up to four 63-bp DNA oligonucleotides. Phylogenetic cluster analysis showed that the CrgA-like regulators form a subclass of the LTTRs that function as octamers. The CrgA is an auto-repressor of its own gene a
Probab=32.24 E-value=1.7e+02 Score=24.83 Aligned_cols=41 Identities=27% Similarity=0.296 Sum_probs=30.1
Q ss_pred hHHHHHHHHHHHCCCcEEEEEEcCCchHhhhcCCCCCEEEEec
Q 015881 138 LFFPAIQLLKDRYPGVLIDVIASARGKQTFELNKNVRWANVYD 180 (399)
Q Consensus 138 LttPalraLK~~yP~A~IdvLv~~~~~~lle~nP~ID~Vi~~d 180 (399)
+..++++.++++||+++|.+........++++ .+|=++...
T Consensus 15 ~l~~~l~~~~~~~P~i~l~i~~~~~~~~~~~~--~~D~~i~~~ 55 (197)
T cd08477 15 VLTPALAEYLARYPDVRVDLVLSDRLVDLVEE--GFDAAFRIG 55 (197)
T ss_pred HHHHHHHHHHHHCCCcEEEEEecCCcchhhhc--CccEEEECC
Confidence 34589999999999999999875544455543 488777643
No 139
>PF00636 Ribonuclease_3: Ribonuclease III domain; InterPro: IPR000999 Prokaryotic ribonuclease III (3.1.26.3 from EC) (gene rnc) [] is an enzyme that digests double-stranded RNA. It is involved in the processing of ribosomal RNA precursors and of some mRNAs. RNase III is evolutionary related to a number of proteins including []: Saccharomyces cerevisiae (Baker's yeast) protein pac1, a ribonuclease that probably inhibits mating and meiosis by degrading a specific mRNA required for sexual development yeast ribonuclease III (gene RNT1), a dsRNA-specific nuclease that cleaves eukaryotic preribosomal RNA at various sites Caenorhabditis elegans hypothetical protein F26E4.13 Paramecium bursaria Chlorella virus 1 (PBCV-1) 1 protein A464R Synechocystis sp. (strain PCC 6803) hypothetical protein slr0346 yeast hypothetical protein SpAC8A4.08c, a protein with a N-terminal helicase domain and a C-terminal RNase III domain C. elegans hypothetical protein K12H4.8, a protein with the same structure as SpAC8A4.08c ; GO: 0003723 RNA binding, 0004525 ribonuclease III activity, 0006396 RNA processing; PDB: 2GSL_A 2NUE_B 1YYO_A 2NUF_A 1YZ9_A 1JFZ_A 1YYW_C 1RC5_B 1YYK_B 1RC7_A ....
Probab=32.13 E-value=27 Score=28.77 Aligned_cols=26 Identities=15% Similarity=0.163 Sum_probs=22.8
Q ss_pred cCCChhHHHhHHHHHHHHHHHCCCcE
Q 015881 129 ISGGVYENLLFFPAIQLLKDRYPGVL 154 (399)
Q Consensus 129 r~~~IGDvVLttPalraLK~~yP~A~ 154 (399)
|+..|||.||-.=+...|-.+||+..
T Consensus 2 rLefLGDavL~~~v~~~l~~~~p~~~ 27 (114)
T PF00636_consen 2 RLEFLGDAVLKLLVSEYLFEKYPNLN 27 (114)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHTTTSS
T ss_pred cHhHhHHHHHHHHHHHHHHHHCCCCC
Confidence 35679999999999999999999864
No 140
>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=32.12 E-value=2.7e+02 Score=22.50 Aligned_cols=84 Identities=13% Similarity=0.137 Sum_probs=55.0
Q ss_pred cEEEEEcCCChhHHHhHHHHHHHHHHHCCCcEEEEEEcCCchH--hhhcCCCCCEEEEecCCCCCCChHHHHHHHHHhhh
Q 015881 123 RRCCCIISGGVYENLLFFPAIQLLKDRYPGVLIDVIASARGKQ--TFELNKNVRWANVYDLDDDWPEPAEYTDILGVMKN 200 (399)
Q Consensus 123 ~rILIIr~~~IGDvVLttPalraLK~~yP~A~IdvLv~~~~~~--lle~nP~ID~Vi~~d~k~~~~~~~~~~~l~~~LR~ 200 (399)
+||.||=.+.+|-.. +.++++..|+.+|..++.+.... -+...-.+. .|+ + +-..+.+
T Consensus 1 i~v~iiG~G~~g~~~-----~~~~~~~~~~~~v~~v~d~~~~~~~~~~~~~~~~---~~~------~------~~~ll~~ 60 (120)
T PF01408_consen 1 IRVGIIGAGSIGRRH-----LRALLRSSPDFEVVAVCDPDPERAEAFAEKYGIP---VYT------D------LEELLAD 60 (120)
T ss_dssp EEEEEESTSHHHHHH-----HHHHHHTTTTEEEEEEECSSHHHHHHHHHHTTSE---EES------S------HHHHHHH
T ss_pred CEEEEECCcHHHHHH-----HHHHHhcCCCcEEEEEEeCCHHHHHHHHHHhccc---chh------H------HHHHHHh
Confidence 588999888886654 67888888999999999886543 233333444 232 1 1233445
Q ss_pred CCCcEEEEcCCCChHHHHHHHHhCCC
Q 015881 201 RYYDMVLSTKLAGLGHAAFLFMTTAR 226 (399)
Q Consensus 201 ~~YDlvIdl~~~~~rsAll~~LsgA~ 226 (399)
.+.|+|+..........+...+..+.
T Consensus 61 ~~~D~V~I~tp~~~h~~~~~~~l~~g 86 (120)
T PF01408_consen 61 EDVDAVIIATPPSSHAEIAKKALEAG 86 (120)
T ss_dssp TTESEEEEESSGGGHHHHHHHHHHTT
T ss_pred hcCCEEEEecCCcchHHHHHHHHHcC
Confidence 68999998887745555555544443
No 141
>cd08413 PBP2_CysB_like The C-terminal substrate domain of LysR-type transcriptional regulators CysB-like contains type 2 periplasmic binding fold. CysB is a transcriptional activator of genes involved in sulfate and thiosulfate transport, sulfate reduction, and cysteine synthesis. In Escherichia coli, the regulation of transcription in response to sulfur source is attributed to two transcriptional regulators, CysB and Cbl. CysB, in association with Cbl, downregulates the expression of ssuEADCB operon which is required for the utilization of sulfur from aliphatic sulfonates, in the presence of cysteine. Also, Cbl and CysB together directly function as transcriptional activators of tauABCD genes, which are required for utilization of taurine as sulfur source for growth. Like many other members of the LTTR family, CysB is composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-bi
Probab=32.04 E-value=1.7e+02 Score=25.13 Aligned_cols=41 Identities=24% Similarity=0.347 Sum_probs=27.0
Q ss_pred hHHHHHHHHHHHCCCcEEEEEEcCCchHhhh--cCCCCCEEEEe
Q 015881 138 LFFPAIQLLKDRYPGVLIDVIASARGKQTFE--LNKNVRWANVY 179 (399)
Q Consensus 138 LttPalraLK~~yP~A~IdvLv~~~~~~lle--~nP~ID~Vi~~ 179 (399)
+..+++..++++||+++|++..... ..+++ .+-.+|=.+..
T Consensus 14 ~l~~~l~~~~~~~P~i~v~~~~~~~-~~~~~~l~~g~~D~~i~~ 56 (198)
T cd08413 14 VLPPVIAAFRKRYPKVKLSLHQGTP-SQIAEMVLKGEADIAIAT 56 (198)
T ss_pred hccHHHHHHHHhCCceEEEEEeCCH-HHHHHHHHcCCCCEEEEc
Confidence 4568999999999999999987532 22222 13455555543
No 142
>cd08472 PBP2_CrgA_like_3 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold. This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 3. The LTTRs are acting as both auto-repressors and activators of target promoters, controlling operons involved in a wide variety of cellular processes such as amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to name a few. In contrast to the tetrameric form of other LTTRs, CrgA from Neisseria meningitides assembles into an octameric ring, which can bind up to four 63-bp DNA oligonucleotides. Phylogenetic cluster analysis showed that the CrgA-like regulators form a subclass of the LTTRs that function as octamers. The CrgA is an auto-repressor of its own gene a
Probab=32.03 E-value=1e+02 Score=26.25 Aligned_cols=40 Identities=25% Similarity=0.325 Sum_probs=30.0
Q ss_pred hHHHHHHHHHHHCCCcEEEEEEcCCchHhhhcCCCCCEEEEe
Q 015881 138 LFFPAIQLLKDRYPGVLIDVIASARGKQTFELNKNVRWANVY 179 (399)
Q Consensus 138 LttPalraLK~~yP~A~IdvLv~~~~~~lle~nP~ID~Vi~~ 179 (399)
+..+++..++++||+++|.+........+++. .+|=.+..
T Consensus 15 ~l~~~l~~~~~~~P~i~v~~~~~~~~~~~l~~--~~D~~i~~ 54 (202)
T cd08472 15 LLIPALPDFLARYPDIELDLGVSDRPVDLIRE--GVDCVIRV 54 (202)
T ss_pred HHHHHHHHHHHHCCCcEEEEEECCCcchhhcc--cccEEEEc
Confidence 34588999999999999999765555555554 48877764
No 143
>cd03795 GT1_like_4 This family is most closely related to the GT1 family of glycosyltransferases. Glycosyltransferases catalyze the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming glycosidic bonds. The acceptor molecule can be a lipid, a protein, a heterocyclic compound, or another carbohydrate residue. This group of glycosyltransferases is most closely related to the previously defined glycosyltransferase family 1 (GT1). The members of this family may transfer UDP, ADP, GDP, or CMP-linked sugars. The diverse enzymatic activities among members of this family reflect a wide range of biological functions. The protein structure available for this family has the GTB topology, one of the two protein topologies observed for nucleotide-sugar-dependent glycosyltransferases. GTB proteins have distinct N- and C- terminal domains each containing a typical Rossmann fold. The two domains have high structural homology despite minimal sequence homolog
Probab=31.98 E-value=4.5e+02 Score=24.94 Aligned_cols=39 Identities=13% Similarity=0.008 Sum_probs=25.0
Q ss_pred EEEEEcCCCh----hHHHhHHHHHHHHHHHCCCcEEEEEEcCCch
Q 015881 124 RCCCIISGGV----YENLLFFPAIQLLKDRYPGVLIDVIASARGK 164 (399)
Q Consensus 124 rILIIr~~~I----GDvVLttPalraLK~~yP~A~IdvLv~~~~~ 164 (399)
|||+|-.... |-..++.=++++|+++ +.++++++.....
T Consensus 1 kil~i~~~~~p~~gG~~~~~~~l~~~L~~~--g~~v~v~~~~~~~ 43 (357)
T cd03795 1 RVLHVGKFYPPDRGGIEQVIRDLAEGLAAR--GIEVAVLCASPEP 43 (357)
T ss_pred CeeEecCCCCCCCCcHHHHHHHHHHHHHhC--CCceEEEecCCCC
Confidence 5777753322 3444555677888877 7788888865543
No 144
>PRK06455 riboflavin synthase; Provisional
Probab=31.31 E-value=1e+02 Score=27.93 Aligned_cols=43 Identities=14% Similarity=-0.112 Sum_probs=33.1
Q ss_pred ccEEEEEcCCChhHHHhHHHHHHHHHHHCCCcEEEEEEcCCchH
Q 015881 122 VRRCCCIISGGVYENLLFFPAIQLLKDRYPGVLIDVIASARGKQ 165 (399)
Q Consensus 122 v~rILIIr~~~IGDvVLttPalraLK~~yP~A~IdvLv~~~~~~ 165 (399)
+|||.||...|==+ .|..-+++.|++.-+++.|+++.-|...+
T Consensus 1 ~~kigIV~s~fn~~-~L~~gAi~~L~~~g~~~~I~v~~VPGa~E 43 (155)
T PRK06455 1 MMKIGIADTTFARV-DMGSAAIDELRKLDPSAKIIRYTVPGIKD 43 (155)
T ss_pred CcEEEEEEEecchH-HHHHHHHHHHHhcCCCCceEEEECCCHHH
Confidence 47899997766655 56689999999977888888887766543
No 145
>TIGR01286 nifK nitrogenase molybdenum-iron protein beta chain. This model represents the majority of known sequences of the nitrogenase molybdenum-iron protein beta subunit. A distinct clade in a phylogenetic tree contains molybdenum-iron, vanadium-iron, and iron-iron forms of nitrogenase beta subunit and is excluded from this model. Nitrogenase, also called dinitrogenase, is responsible for nitrogen fixation. Note: the trusted cutoff score has recently been lowered to include an additional family in which the beta subunit is shorter by about 50 amino acids at the N-terminus. In species with the shorter form of the beta subunit, the alpha subunit has a novel insert of similar length.
Probab=31.21 E-value=2.6e+02 Score=30.15 Aligned_cols=92 Identities=10% Similarity=0.013 Sum_probs=60.3
Q ss_pred cEEEEEcCCChhHHHhHHHHHHHHHHHCCCcEEEEEEcC-Cc-------hHhhhcCCCCCEEEEecCCCCCCChHHHHHH
Q 015881 123 RRCCCIISGGVYENLLFFPAIQLLKDRYPGVLIDVIASA-RG-------KQTFELNKNVRWANVYDLDDDWPEPAEYTDI 194 (399)
Q Consensus 123 ~rILIIr~~~IGDvVLttPalraLK~~yP~A~IdvLv~~-~~-------~~lle~nP~ID~Vi~~d~k~~~~~~~~~~~l 194 (399)
+|+.|. ||--+..++.+.|.+. ++++..++.. .. +++++..|+..+..++..+ +.+.+
T Consensus 364 KrvaI~-----gdpd~~~~l~~fL~El--Gmepv~v~~~~~~~~~~~~l~~ll~~~~~~~~~~v~~~~-------Dl~~l 429 (515)
T TIGR01286 364 KRFAIY-----GDPDFVMGLVRFVLEL--GCEPVHILCTNGTKRWKAEMKALLAASPYGQNATVWIGK-------DLWHL 429 (515)
T ss_pred ceEEEE-----CCHHHHHHHHHHHHHC--CCEEEEEEeCCCCHHHHHHHHHHHhcCCCCCccEEEeCC-------CHHHH
Confidence 566554 6888999999999874 7776544432 22 2566666765555555432 23566
Q ss_pred HHHhhhCCCcEEEEcCCCChHHHHHHHHhCCC-eEEEec
Q 015881 195 LGVMKNRYYDMVLSTKLAGLGHAAFLFMTTAR-DRVSYI 232 (399)
Q Consensus 195 ~~~LR~~~YDlvIdl~~~~~rsAll~~LsgA~-~RIGy~ 232 (399)
...|++.+.|++|-- .....++.-.|+| .|+||-
T Consensus 430 ~~~l~~~~~DlliG~----s~~k~~a~~~giPlir~gfP 464 (515)
T TIGR01286 430 RSLVFTEPVDFLIGN----SYGKYIQRDTLVPLIRIGFP 464 (515)
T ss_pred HHHHhhcCCCEEEEC----chHHHHHHHcCCCEEEecCC
Confidence 677888899999933 3345566778888 588874
No 146
>cd08482 PBP2_TrpI The C-terminal substrate binding domain of LysR-type transcriptional regulator TrpI, which is involved in control of tryptophan synthesis, contains type 2 periplasmic binding fold. TrpI and indoleglycerol phosphate (InGP), are required to activate transcription of the trpBA, the genes for tryptophan synthase. The trpBA is induced by the InGp substrate, rather than by tryptophan, but the exact mechanism of the activation event is not known. This substrate-binding domain of TrpI shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cy
Probab=31.17 E-value=97 Score=26.56 Aligned_cols=40 Identities=13% Similarity=0.263 Sum_probs=27.9
Q ss_pred hHHHHHHHHHHHCCCcEEEEEEcCCchHhhhcCCCCCEEEEe
Q 015881 138 LFFPAIQLLKDRYPGVLIDVIASARGKQTFELNKNVRWANVY 179 (399)
Q Consensus 138 LttPalraLK~~yP~A~IdvLv~~~~~~lle~nP~ID~Vi~~ 179 (399)
+..+++..++++||+.+|++.......++++ ..+|=.+..
T Consensus 14 ~l~~~i~~f~~~~P~v~i~~~~~~~~~~~~~--~~~Dl~i~~ 53 (195)
T cd08482 14 WLIPRLPAFQAALPDIDLQLSASDGPVDSLR--DGIDAAIRF 53 (195)
T ss_pred HHHhhHHHHHHHCCCceEEEEecCCcccccc--CCcCEEEEc
Confidence 4568999999999999999986543333333 246665553
No 147
>TIGR03339 phn_lysR aminoethylphosphonate catabolism associated LysR family transcriptional regulator. This group of sequences represents a number of related clades with numerous examples of members adjacent to operons for the degradation of 2-aminoethylphosphonate (AEP) in Pseudomonas, Ralstonia, Bordetella and Burkholderia species. These are transcriptional regulators of the LysR family which contain a helix-turn-helix (HTH) domain (pfam00126) and a periplasmic substrate-binding protein-like domain (pfam03466).
Probab=30.85 E-value=2.7e+02 Score=25.93 Aligned_cols=24 Identities=21% Similarity=0.524 Sum_probs=20.8
Q ss_pred HhHHHHHHHHHHHCCCcEEEEEEc
Q 015881 137 LLFFPAIQLLKDRYPGVLIDVIAS 160 (399)
Q Consensus 137 VLttPalraLK~~yP~A~IdvLv~ 160 (399)
.+..|++..+++.||+++|++.+.
T Consensus 97 ~~~~~~l~~~~~~~p~v~l~i~~~ 120 (279)
T TIGR03339 97 YYVLDLVARFRQRYPGIEVSVRIG 120 (279)
T ss_pred HHHHHHHHHHHHHCCCcEEEEEEC
Confidence 466799999999999999998864
No 148
>KOG0961 consensus Predicted Zn2+-dependent endopeptidase, insulinase superfamily [Posttranslational modification, protein turnover, chaperones]
Probab=30.46 E-value=59 Score=36.31 Aligned_cols=29 Identities=21% Similarity=0.234 Sum_probs=23.3
Q ss_pred CCCCHHHHHHHHHHhhhCC-CEEEeCCchh
Q 015881 334 SLLPIQVWAEIANGLREFR-PLFVIPHEKE 362 (399)
Q Consensus 334 KrWP~e~faeLa~~L~~~~-~VvliGgp~E 362 (399)
|.||...|.+|.++.--.. ++.+++-|++
T Consensus 428 ~~w~~kdW~~Llnk~Fven~s~tVia~Ps~ 457 (1022)
T KOG0961|consen 428 KSWPAKDWVQLLNKYFVENPSATVIAVPSE 457 (1022)
T ss_pred hhccHHHHHHHHHHHhccCCCeEEEecCcH
Confidence 5799999999999876544 7888887764
No 149
>PRK13523 NADPH dehydrogenase NamA; Provisional
Probab=30.41 E-value=2.1e+02 Score=28.94 Aligned_cols=71 Identities=11% Similarity=0.008 Sum_probs=44.1
Q ss_pred CHHHHHHHHHHHHHhCCCCCCeEEEEcCCCCccccccCCCCCCCCCCHHHHHHHHHHhhhCC--CEEEeCCchhHHHHHH
Q 015881 291 SRRLKEVVAEKYKNAGAEQGKYIVIHGIESDSKASMQSRGDTDSLLPIQVWAEIANGLREFR--PLFVIPHEKEREGVED 368 (399)
Q Consensus 291 s~e~~~~a~~~l~~~gl~~~~~IvIhPgas~~~~~~k~rg~~~KrWP~e~faeLa~~L~~~~--~VvliGgp~E~e~aee 368 (399)
+.++....-+.+.+.|+ .+|-++.|+.... + ..++...+..+++.+++.. +|+..|+=.+.+.+++
T Consensus 225 ~~~e~~~i~~~l~~~gv---D~i~vs~g~~~~~---~------~~~~~~~~~~~~~~ik~~~~ipVi~~G~i~~~~~a~~ 292 (337)
T PRK13523 225 TVQDYVQYAKWMKEQGV---DLIDVSSGAVVPA---R------IDVYPGYQVPFAEHIREHANIATGAVGLITSGAQAEE 292 (337)
T ss_pred CHHHHHHHHHHHHHcCC---CEEEeCCCCCCCC---C------CCCCccccHHHHHHHHhhcCCcEEEeCCCCCHHHHHH
Confidence 33444444445666665 4888887753321 0 1233444566777777653 7888898888888888
Q ss_pred HHhcC
Q 015881 369 VVGDD 373 (399)
Q Consensus 369 I~~~~ 373 (399)
+++..
T Consensus 293 ~l~~g 297 (337)
T PRK13523 293 ILQNN 297 (337)
T ss_pred HHHcC
Confidence 87753
No 150
>PRK02308 uvsE putative UV damage endonuclease; Provisional
Probab=30.35 E-value=1.9e+02 Score=28.90 Aligned_cols=62 Identities=15% Similarity=0.049 Sum_probs=35.7
Q ss_pred HHHhCCCCCCeEEEEcCCCCccccccCCCCCCCCCCHHHHHHHHHHhhhCC-CEEEe---CCchhHHHHHHHHhcC
Q 015881 302 YKNAGAEQGKYIVIHGIESDSKASMQSRGDTDSLLPIQVWAEIANGLREFR-PLFVI---PHEKEREGVEDVVGDD 373 (399)
Q Consensus 302 l~~~gl~~~~~IvIhPgas~~~~~~k~rg~~~KrWP~e~faeLa~~L~~~~-~Vvli---Ggp~E~e~aeeI~~~~ 373 (399)
+...|+....+||||||+... +|.--.++|++-.+.|.+.. ..+++ ++...-+.+.+|++..
T Consensus 139 ~~~lG~~~~~~vViHpG~~~~----------~ke~al~r~~~~l~~l~~~~~~~L~LEN~~~~~t~~ell~I~e~~ 204 (303)
T PRK02308 139 LDLMGIDDSSKINIHVGGAYG----------DKEKALERFIENIKKLPESIKKRLTLENDDKTYTVEELLYICEKL 204 (303)
T ss_pred HHHCCCCCCCEEEECCCccCC----------CHHHHHHHHHHHHHHhhHHhCCEEEEeeCCCCCCHHHHHHHHHHc
Confidence 344566544599999998653 24446677777777665443 22333 3334444444566644
No 151
>cd03816 GT1_ALG1_like This family is most closely related to the GT1 family of glycosyltransferases. The yeast gene ALG1 has been shown to function as a mannosyltransferase that catalyzes the formation of dolichol pyrophosphate (Dol-PP)-GlcNAc2Man from GDP-Man and Dol-PP-Glc-NAc2, and participates in the formation of the lipid-linked precursor oligosaccharide for N-glycosylation. In humans ALG1 has been associated with the congenital disorders of glycosylation (CDG) designated as subtype CDG-Ik.
Probab=29.89 E-value=5.9e+02 Score=25.93 Aligned_cols=105 Identities=14% Similarity=0.173 Sum_probs=54.4
Q ss_pred ccEEEEEcCCChhHHHhHHHHHHHHHHHCCCcEEEEEEcCCchHhh--hcCCCCCEEEEecCCC-CCCC-hH--------
Q 015881 122 VRRCCCIISGGVYENLLFFPAIQLLKDRYPGVLIDVIASARGKQTF--ELNKNVRWANVYDLDD-DWPE-PA-------- 189 (399)
Q Consensus 122 v~rILIIr~~~IGDvVLttPalraLK~~yP~A~IdvLv~~~~~~ll--e~nP~ID~Vi~~d~k~-~~~~-~~-------- 189 (399)
.+|++++-+..+|=-.-..-....|.++ +-++++++.+...+.. .....|. ++.+..+. .... +.
T Consensus 3 ~~~~~~~~~~~~~~~~R~~~~a~~L~~~--G~~V~ii~~~~~~~~~~~~~~~~v~-~~~~~~~~~~~~~~~~~~~~~~~~ 79 (415)
T cd03816 3 RKRVCVLVLGDIGRSPRMQYHALSLAKH--GWKVDLVGYLETPPHDEILSNPNIT-IHPLPPPPQRLNKLPFLLFAPLKV 79 (415)
T ss_pred ccEEEEEEecccCCCHHHHHHHHHHHhc--CceEEEEEecCCCCCHHHhcCCCEE-EEECCCCccccccchHHHHHHHHH
Confidence 3677777776665444445677888876 6789999876543221 1223443 33333322 1111 11
Q ss_pred --HHHHHHH-HhhhCCCcEEEEcCCCChHH---HH-HHHHhCCCeEE
Q 015881 190 --EYTDILG-VMKNRYYDMVLSTKLAGLGH---AA-FLFMTTARDRV 229 (399)
Q Consensus 190 --~~~~l~~-~LR~~~YDlvIdl~~~~~rs---Al-l~~LsgA~~RI 229 (399)
.++.+++ .++.+++|+++......... ++ +.++.|+|..+
T Consensus 80 ~~~~~~~~~~l~~~~~~Dvi~~~~~~~~~~~~~a~~~~~~~~~~~V~ 126 (415)
T cd03816 80 LWQFFSLLWLLYKLRPADYILIQNPPSIPTLLIAWLYCLLRRTKLII 126 (415)
T ss_pred HHHHHHHHHHHHhcCCCCEEEEeCCCCchHHHHHHHHHHHhCCeEEE
Confidence 1123333 24567899998644332222 22 35556776544
No 152
>PRK09288 purT phosphoribosylglycinamide formyltransferase 2; Validated
Probab=29.89 E-value=3.9e+02 Score=26.88 Aligned_cols=75 Identities=16% Similarity=0.116 Sum_probs=45.7
Q ss_pred CccEEEEEcCCChhHHHhHHHHHHHHHHHCCCcEEEEEEcCCchHhhhcCCCCCEEEEecCCCCCCChHHHHHHHHHhhh
Q 015881 121 DVRRCCCIISGGVYENLLFFPAIQLLKDRYPGVLIDVIASARGKQTFELNKNVRWANVYDLDDDWPEPAEYTDILGVMKN 200 (399)
Q Consensus 121 ~v~rILIIr~~~IGDvVLttPalraLK~~yP~A~IdvLv~~~~~~lle~nP~ID~Vi~~d~k~~~~~~~~~~~l~~~LR~ 200 (399)
..|+||||-.+. +..+++.++++. +.++.++......+-.. ..|+.+..+..+ . -.++..+++
T Consensus 11 ~~~~ilIiG~g~-----~~~~~~~a~~~~--G~~v~~~~~~~~~~~~~---~ad~~~~~~~~d----~---~~l~~~~~~ 73 (395)
T PRK09288 11 SATRVMLLGSGE-----LGKEVAIEAQRL--GVEVIAVDRYANAPAMQ---VAHRSHVIDMLD----G---DALRAVIER 73 (395)
T ss_pred CCCEEEEECCCH-----HHHHHHHHHHHC--CCEEEEEeCCCCCchHH---hhhheEECCCCC----H---HHHHHHHHH
Confidence 357999986654 455677777776 76777666544332222 345555555322 2 234555667
Q ss_pred CCCcEEEEcCCC
Q 015881 201 RYYDMVLSTKLA 212 (399)
Q Consensus 201 ~~YDlvIdl~~~ 212 (399)
.+.|+++.....
T Consensus 74 ~~id~vi~~~e~ 85 (395)
T PRK09288 74 EKPDYIVPEIEA 85 (395)
T ss_pred hCCCEEEEeeCc
Confidence 789999976554
No 153
>cd08420 PBP2_CysL_like C-terminal substrate binding domain of LysR-type transcriptional regulator CysL, which activates the transcription of the cysJI operon encoding sulfite reductase, contains the type 2 periplasmic binding fold. CysL, also known as YwfK, is a regular of sulfur metabolism in Bacillus subtilis. Sulfur is required for the synthesis of proteins and essential cofactors in all living organism. Sulfur can be assimilated either from inorganic sources (sulfate and thiosulfate), or from organic sources (sulfate esters, sulfamates, and sulfonates). CysL activates the transcription of the cysJI operon encoding sulfite reductase, which reduces sulfite to sulfide. Both cysL mutant and cysJI mutant are unable to grow using sulfate or sulfite as the sulfur source. Like other LysR-type regulators, CysL also negatively regulates its own transcription. In Escherichia coli, three LysR-type activators are involved in the regulation of sulfur metabolism: CysB, Cbl and MetR. The topology
Probab=29.56 E-value=2.6e+02 Score=23.36 Aligned_cols=25 Identities=20% Similarity=0.405 Sum_probs=20.5
Q ss_pred HhHHHHHHHHHHHCCCcEEEEEEcC
Q 015881 137 LLFFPAIQLLKDRYPGVLIDVIASA 161 (399)
Q Consensus 137 VLttPalraLK~~yP~A~IdvLv~~ 161 (399)
.+..+++..++++||+++|.+....
T Consensus 13 ~~l~~~l~~~~~~~P~~~l~~~~~~ 37 (201)
T cd08420 13 YLLPRLLARFRKRYPEVRVSLTIGN 37 (201)
T ss_pred hhhHHHHHHHHHHCCCceEEEEeCC
Confidence 3456899999999999999987643
No 154
>PRK12815 carB carbamoyl phosphate synthase large subunit; Reviewed
Probab=29.20 E-value=1e+03 Score=28.11 Aligned_cols=81 Identities=12% Similarity=0.018 Sum_probs=51.1
Q ss_pred CccEEEEEcC--CChhHHH----hHHHHHHHHHHHCCCcEEEEEEcCCchHhhhcCCCCCEEEEecCCCCCCChHHHHHH
Q 015881 121 DVRRCCCIIS--GGVYENL----LFFPAIQLLKDRYPGVLIDVIASARGKQTFELNKNVRWANVYDLDDDWPEPAEYTDI 194 (399)
Q Consensus 121 ~v~rILIIr~--~~IGDvV----LttPalraLK~~yP~A~IdvLv~~~~~~lle~nP~ID~Vi~~d~k~~~~~~~~~~~l 194 (399)
+.+||||+-. ..||-.+ ++..++++||+. +.++.++.... ..+-......|+++. +. ...-.+
T Consensus 554 ~~kkvLIlG~G~~rig~~~efdy~~v~~~~aLk~~--G~~vI~vn~np-etvs~~~~~aD~~y~-ep-------~~~e~v 622 (1068)
T PRK12815 554 EKKKVLILGSGPIRIGQGIEFDYSSVHAAFALKKE--GYETIMINNNP-ETVSTDYDTADRLYF-EP-------LTLEDV 622 (1068)
T ss_pred CCceEEEecccccccccccccchhHHHHHHHHHHc--CCEEEEEeCCc-cccccccccCceEEE-cc-------CCHHHH
Confidence 4689999954 4588777 888999999998 76655554222 111112223455543 21 123456
Q ss_pred HHHhhhCCCcEEEEcCCC
Q 015881 195 LGVMKNRYYDMVLSTKLA 212 (399)
Q Consensus 195 ~~~LR~~~YDlvIdl~~~ 212 (399)
+..+++++.|.||-..+.
T Consensus 623 l~I~~~e~~dgVI~~~g~ 640 (1068)
T PRK12815 623 LNVAEAENIKGVIVQFGG 640 (1068)
T ss_pred HHHHhhcCCCEEEEecCc
Confidence 777888999999975444
No 155
>cd08487 PBP2_BlaA The C-terminal substrate-binding domain of LysR-type trnascriptional regulator BlaA which involved in control of the beta-lactamase gene expression; contains the type 2 periplasmic binding fold. This CD represents the C-terminal substrate binding domain of LysR-type transcriptional regulator, BlaA, that involved in control of the expression of beta-lactamase genes, blaA and blaB. Beta-lactamases are responsible for bacterial resistance to beta-lactam antibiotics such as penicillins. The blaA gene is located just upstream of blaB in the opposite direction and regulates the expression of the blaB. BlaA also negatively auto-regulates the expression of its own gene, blaA. BlaA (a constitutive class A penicllinase) belongs to the LysR family of transcriptional regulators, whereas BlaB (an inducible class C cephalosporinase or AmpC) can be referred to as a penicillin binding protein but it does not act as a beta-lactamase. The topology of this substrate-binding domain is
Probab=29.07 E-value=1.1e+02 Score=25.86 Aligned_cols=40 Identities=8% Similarity=0.134 Sum_probs=28.2
Q ss_pred HHHHHHHHHHHCCCcEEEEEEcCCchHhhhcCCCCCEEEEec
Q 015881 139 FFPAIQLLKDRYPGVLIDVIASARGKQTFELNKNVRWANVYD 180 (399)
Q Consensus 139 ttPalraLK~~yP~A~IdvLv~~~~~~lle~nP~ID~Vi~~d 180 (399)
..++++.++++||+.+|++........++.+ .+|=++.+.
T Consensus 15 l~~~l~~f~~~~P~i~l~i~~~~~~~~~~~~--~~Dl~i~~~ 54 (189)
T cd08487 15 LLPRLAEFRQLHPFIELRLRTNNNVVDLATE--GLDFAIRFG 54 (189)
T ss_pred HhHHHHHHHHHCCCceEEeeecCCccccccC--CcCEEEEec
Confidence 4588999999999999999865443343333 477666654
No 156
>cd03822 GT1_ecORF704_like This family is most closely related to the GT1 family of glycosyltransferases. ORF704 in E. coli has been shown to be involved in the biosynthesis of O-specific mannose homopolysaccharides.
Probab=28.95 E-value=4.2e+02 Score=25.02 Aligned_cols=81 Identities=15% Similarity=0.095 Sum_probs=43.9
Q ss_pred EEEEEcCC---ChhHHHhHHHHHHHHHHHCCCcEEEEEEcCCchHhhhcCCCCCEEEEecCCCCCCChHHHHHHHHHhhh
Q 015881 124 RCCCIISG---GVYENLLFFPAIQLLKDRYPGVLIDVIASARGKQTFELNKNVRWANVYDLDDDWPEPAEYTDILGVMKN 200 (399)
Q Consensus 124 rILIIr~~---~IGDvVLttPalraLK~~yP~A~IdvLv~~~~~~lle~nP~ID~Vi~~d~k~~~~~~~~~~~l~~~LR~ 200 (399)
|||+|... .=|=..++.-+++.|.+...+ +++++...................... .....+..+.+.+++
T Consensus 1 kI~~v~~~~~~~gG~~~~~~~l~~~L~~~g~~--v~v~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~~~~~~~~~~ 74 (366)
T cd03822 1 RIALVSPYPPRKCGIATFTTDLVNALSARGPD--VLVVSVAALYPSLLYGGEQEVVRVIVL----DNPLDYRRAARAIRL 74 (366)
T ss_pred CeEEecCCCCCCCcHHHHHHHHHHHhhhcCCe--EEEEEeecccCcccCCCcccceeeeec----CCchhHHHHHHHHhh
Confidence 57777553 224556667888999988655 444443332222111111011111111 122345667788899
Q ss_pred CCCcEEEEcC
Q 015881 201 RYYDMVLSTK 210 (399)
Q Consensus 201 ~~YDlvIdl~ 210 (399)
.+||+++..+
T Consensus 75 ~~~dii~~~~ 84 (366)
T cd03822 75 SGPDVVVIQH 84 (366)
T ss_pred cCCCEEEEee
Confidence 9999999765
No 157
>PF12466 GDH_N: Glutamate dehydrogenase N terminal; InterPro: IPR024727 Glutamate dehydrogenases (GDHs) are a broadly distributed group of enzymes that catalyse the reversible oxidative deamination of glutamate to ketoglutarate and ammonia []. This entry represents a domain found in the N-terminal region of a bacterial family of putative GDHs.
Probab=28.88 E-value=29 Score=26.05 Aligned_cols=16 Identities=31% Similarity=0.648 Sum_probs=13.4
Q ss_pred HHHHHHHHHHHCCCcE
Q 015881 139 FFPAIQLLKDRYPGVL 154 (399)
Q Consensus 139 ttPalraLK~~yP~A~ 154 (399)
.-|++.+||++||-+.
T Consensus 35 LepVfaALRkryPaa~ 50 (60)
T PF12466_consen 35 LEPVFAALRKRYPAAR 50 (60)
T ss_pred hhHHHHHHHHhCcHHH
Confidence 3499999999999753
No 158
>cd08473 PBP2_CrgA_like_4 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold. This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 4. The LTTRs are acting as both auto-repressors and activators of target promoters, controlling operons involved in a wide variety of cellular processes such as amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to name a few. In contrast to the tetrameric form of other LTTRs, CrgA from Neisseria meningitides assembles into an octameric ring, which can bind up to four 63-bp DNA oligonucleotides. Phylogenetic cluster analysis showed that the CrgA-like regulators form a subclass of the LTTRs that function as octamers. The CrgA is an auto-repressor of its own gene a
Probab=28.87 E-value=1.2e+02 Score=25.74 Aligned_cols=39 Identities=21% Similarity=0.279 Sum_probs=28.9
Q ss_pred HHHHHHHHHHHCCCcEEEEEEcCCchHhhhcCCCCCEEEEe
Q 015881 139 FFPAIQLLKDRYPGVLIDVIASARGKQTFELNKNVRWANVY 179 (399)
Q Consensus 139 ttPalraLK~~yP~A~IdvLv~~~~~~lle~nP~ID~Vi~~ 179 (399)
..+++..++++||+++|++........+++ -.+|=+|.+
T Consensus 18 l~~~l~~~~~~~P~i~i~~~~~~~~~~~~~--~~~D~~i~~ 56 (202)
T cd08473 18 LAPLLPRFMAAYPQVRLQLEATNRRVDLIE--EGIDVALRV 56 (202)
T ss_pred HHHHHHHHHHHCCCeEEEEEEcCCcccccc--cCccEEEEe
Confidence 348899999999999999987554444443 357777754
No 159
>cd08470 PBP2_CrgA_like_1 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding domain. This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 1. The LTTRs are acting as both auto-repressors and activators of target promoters, controlling operons involved in a wide variety of cellular processes such as amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to name a few. In contrast to the tetrameric form of other LTTRs, CrgA from Neisseria meningitides assembles into an octameric ring, which can bind up to four 63-bp DNA oligonucleotides. Phylogenetic cluster analysis showed that the CrgA-like regulators form a subclass of the LTTRs that function as octamers. The CrgA is an auto-repressor of its own gene
Probab=28.73 E-value=1.2e+02 Score=25.77 Aligned_cols=41 Identities=17% Similarity=0.234 Sum_probs=30.0
Q ss_pred hHHHHHHHHHHHCCCcEEEEEEcCCchHhhhcCCCCCEEEEec
Q 015881 138 LFFPAIQLLKDRYPGVLIDVIASARGKQTFELNKNVRWANVYD 180 (399)
Q Consensus 138 LttPalraLK~~yP~A~IdvLv~~~~~~lle~nP~ID~Vi~~d 180 (399)
+..+++..++++||+++|.+........++++ .+|=.+...
T Consensus 15 ~l~~~l~~f~~~~P~v~l~i~~~~~~~~~~~~--~~D~~i~~~ 55 (197)
T cd08470 15 FIAPLVNDFMQRYPKLEVDIELTNRVVDLVSE--GFDLAIRLG 55 (197)
T ss_pred HHHHHHHHHHHHCCCeEEEEEecCCccchhcc--CccEEEEcC
Confidence 34689999999999999999865444444443 588777654
No 160
>TIGR01426 MGT glycosyltransferase, MGT family. This model describes the MGT (macroside glycosyltransferase) subfamily of the UDP-glucuronosyltransferase family. Members include a number of glucosyl transferases for macrolide antibiotic inactivation, but also include transferases of glucose-related sugars for macrolide antibiotic production.
Probab=28.47 E-value=2.9e+02 Score=27.66 Aligned_cols=93 Identities=10% Similarity=-0.045 Sum_probs=62.7
Q ss_pred CCChhHHHhHHHHHHHHHHHCCCcEEEEEEcCCchHhhhcCCCCCEEEEecCCCC--------C-CChHHH---------
Q 015881 130 SGGVYENLLFFPAIQLLKDRYPGVLIDVIASARGKQTFELNKNVRWANVYDLDDD--------W-PEPAEY--------- 191 (399)
Q Consensus 130 ~~~IGDvVLttPalraLK~~yP~A~IdvLv~~~~~~lle~nP~ID~Vi~~d~k~~--------~-~~~~~~--------- 191 (399)
....||+-=++++.++|+++ +-+|.+++.+.+.+.++.... +++.++.... + .++..+
T Consensus 3 ~p~~Ghv~P~l~lA~~L~~~--Gh~V~~~~~~~~~~~v~~~G~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 78 (392)
T TIGR01426 3 IPAHGHVNPTLGVVEELVAR--GHRVTYATTEEFAERVEAAGA--EFVLYGSALPPPDNPPENTEEEPIDIIEKLLDEAE 78 (392)
T ss_pred CCccccccccHHHHHHHHhC--CCeEEEEeCHHHHHHHHHcCC--EEEecCCcCccccccccccCcchHHHHHHHHHHHH
Confidence 46779999999999999998 789999999999988877432 2333332100 0 011111
Q ss_pred ---HHHHHHhhhCCCcEEEEcCCCChHHHHHHHHhCCCe
Q 015881 192 ---TDILGVMKNRYYDMVLSTKLAGLGHAAFLFMTTARD 227 (399)
Q Consensus 192 ---~~l~~~LR~~~YDlvIdl~~~~~rsAll~~LsgA~~ 227 (399)
..+...++..++|+||.-... ....+++...|+|.
T Consensus 79 ~~~~~l~~~~~~~~pDlVi~d~~~-~~~~~~A~~~giP~ 116 (392)
T TIGR01426 79 DVLPQLEEAYKGDRPDLIVYDIAS-WTGRLLARKWDVPV 116 (392)
T ss_pred HHHHHHHHHhcCCCCCEEEECCcc-HHHHHHHHHhCCCE
Confidence 123344566789999876655 55677888899985
No 161
>COG0571 Rnc dsRNA-specific ribonuclease [Transcription]
Probab=28.05 E-value=44 Score=32.25 Aligned_cols=26 Identities=15% Similarity=0.139 Sum_probs=23.7
Q ss_pred cCCChhHHHhHHHHHHHHHHHCCCcE
Q 015881 129 ISGGVYENLLFFPAIQLLKDRYPGVL 154 (399)
Q Consensus 129 r~~~IGDvVLttPalraLK~~yP~A~ 154 (399)
|+-++||.||-.-+.+.|-++||++.
T Consensus 46 RLEFLGDavL~l~vae~Lf~~yP~~~ 71 (235)
T COG0571 46 RLEFLGDAVLGLVVAEYLFKKYPNLP 71 (235)
T ss_pred HHHhhHHHHHHHHHHHHHHHHCCCCC
Confidence 57899999999999999999999854
No 162
>COG0381 WecB UDP-N-acetylglucosamine 2-epimerase [Cell envelope biogenesis, outer membrane]
Probab=27.80 E-value=5.3e+02 Score=26.86 Aligned_cols=102 Identities=18% Similarity=0.226 Sum_probs=60.3
Q ss_pred ccEEEEEcCCChhHHHhHHHHHHHHHHHCCCcEEEEEEcCCch---------HhhhcC-CCCCEEEEecCCCCCCChHH-
Q 015881 122 VRRCCCIISGGVYENLLFFPAIQLLKDRYPGVLIDVIASARGK---------QTFELN-KNVRWANVYDLDDDWPEPAE- 190 (399)
Q Consensus 122 v~rILIIr~~~IGDvVLttPalraLK~~yP~A~IdvLv~~~~~---------~lle~n-P~ID~Vi~~d~k~~~~~~~~- 190 (399)
++|||+| ++--=|.+---|+++++.+. |+.+..+++.-... ++++.. |+.+=-+. +.+ ..+.+
T Consensus 3 ~~Kv~~I-~GTRPE~iKmapli~~~~~~-~~~~~~vi~TGQH~d~em~~~~le~~~i~~pdy~L~i~-~~~---~tl~~~ 76 (383)
T COG0381 3 MLKVLTI-FGTRPEAIKMAPLVKALEKD-PDFELIVIHTGQHRDYEMLDQVLELFGIRKPDYDLNIM-KPG---QTLGEI 76 (383)
T ss_pred ceEEEEE-EecCHHHHHHhHHHHHHHhC-CCCceEEEEecccccHHHHHHHHHHhCCCCCCcchhcc-ccC---CCHHHH
Confidence 5677776 34445888999999999875 66777777655444 233333 44331111 111 12222
Q ss_pred ----HHHHHHHhhhCCCcEEEEc---CCCChHHHHHHHHhCCCeEEEec
Q 015881 191 ----YTDILGVMKNRYYDMVLST---KLAGLGHAAFLFMTTARDRVSYI 232 (399)
Q Consensus 191 ----~~~l~~~LR~~~YDlvIdl---~~~~~rsAll~~LsgA~~RIGy~ 232 (399)
+..+-+.|.+.+.|+|+.. ... +..|+.++...+| ||+.
T Consensus 77 t~~~i~~~~~vl~~~kPD~VlVhGDT~t~-lA~alaa~~~~Ip--V~Hv 122 (383)
T COG0381 77 TGNIIEGLSKVLEEEKPDLVLVHGDTNTT-LAGALAAFYLKIP--VGHV 122 (383)
T ss_pred HHHHHHHHHHHHHhhCCCEEEEeCCcchH-HHHHHHHHHhCCc--eEEE
Confidence 2334455778999998843 333 4446667777766 6776
No 163
>PF03808 Glyco_tran_WecB: Glycosyl transferase WecB/TagA/CpsF family; InterPro: IPR004629 The WecG member of this superfamily, believed to be UDP-N-acetyl-D-mannosaminuronic acid transferase, plays a role in Enterobacterial common antigen (eca) synthesis in Escherichia coli. Another family member, the Bacillus subtilis TagA protein, is involved in the biosynthesis of the cell wall polymer poly(glycerol phosphate). The third family member, CpsF, CMP-N-acetylneuraminic acid synthetase has a role in the capsular polysaccharide biosynthesis pathway.; GO: 0009058 biosynthetic process
Probab=27.66 E-value=4.5e+02 Score=23.57 Aligned_cols=49 Identities=12% Similarity=0.044 Sum_probs=36.8
Q ss_pred CCHHHHHHHHHHhhhCC-CEEEe--CCchhHHHHHHHHhcCCCCceeecCCc
Q 015881 336 LPIQVWAEIANGLREFR-PLFVI--PHEKEREGVEDVVGDDASIVFITTPGQ 384 (399)
Q Consensus 336 WP~e~faeLa~~L~~~~-~Vvli--Ggp~E~e~aeeI~~~~~~~~~i~~~G~ 384 (399)
...+.-.++++.+.+.+ .+|++ |.|+.+..+.+..+..+..+++..-|-
T Consensus 85 f~~~~~~~i~~~I~~~~pdiv~vglG~PkQE~~~~~~~~~l~~~v~i~vG~~ 136 (172)
T PF03808_consen 85 FDEEEEEAIINRINASGPDIVFVGLGAPKQERWIARHRQRLPAGVIIGVGGA 136 (172)
T ss_pred CChhhHHHHHHHHHHcCCCEEEEECCCCHHHHHHHHHHHHCCCCEEEEECch
Confidence 35667889999998877 66665 788888899999888877654554443
No 164
>cd02931 ER_like_FMN Enoate reductase (ER)-like FMN-binding domain. Enoate reductase catalyzes the NADH-dependent reduction of carbon-carbon double bonds of several molecules, including nonactivated 2-enoates, alpha,beta-unsaturated aldehydes, cyclic ketones, and methylketones. ERs are similar to 2,4-dienoyl-CoA reductase from E. coli and to the old yellow enzyme from Saccharomyces cerevisiae.
Probab=27.35 E-value=3.7e+02 Score=27.56 Aligned_cols=74 Identities=11% Similarity=0.094 Sum_probs=44.3
Q ss_pred HHHHHHHHHHHHhCCCCCCeEEEEcCCCCccccccCCCCCCCCCCHHHHHHHHHHhhhCC--CEEEeCCchhHHHHHHHH
Q 015881 293 RLKEVVAEKYKNAGAEQGKYIVIHGIESDSKASMQSRGDTDSLLPIQVWAEIANGLREFR--PLFVIPHEKEREGVEDVV 370 (399)
Q Consensus 293 e~~~~a~~~l~~~gl~~~~~IvIhPgas~~~~~~k~rg~~~KrWP~e~faeLa~~L~~~~--~VvliGgp~E~e~aeeI~ 370 (399)
++...+-+.+.+.|+ .+|-++.|......... ....++...|..+++.+++.. +|+..|+=.+.+.++++.
T Consensus 252 e~~~~~~~~l~~~gv---D~l~vs~g~~~~~~~~~----~~~~~~~~~~~~~~~~ik~~~~~pvi~~G~i~~~~~~~~~l 324 (382)
T cd02931 252 EEGLKAAKILEEAGY---DALDVDAGSYDAWYWNH----PPMYQKKGMYLPYCKALKEVVDVPVIMAGRMEDPELASEAI 324 (382)
T ss_pred HHHHHHHHHHHHhCC---CEEEeCCCCCccccccc----CCccCCcchhHHHHHHHHHHCCCCEEEeCCCCCHHHHHHHH
Confidence 333333345566665 48888866532110000 012345566677777776643 899999999999888888
Q ss_pred hcC
Q 015881 371 GDD 373 (399)
Q Consensus 371 ~~~ 373 (399)
+..
T Consensus 325 ~~g 327 (382)
T cd02931 325 NEG 327 (382)
T ss_pred HcC
Confidence 753
No 165
>cd03805 GT1_ALG2_like This family is most closely related to the GT1 family of glycosyltransferases. ALG2, a 1,3-mannosyltransferase, in yeast catalyzes the mannosylation of Man(2)GlcNAc(2)-dolichol diphosphate and Man(1)GlcNAc(2)-dolichol diphosphate to form Man(3)GlcNAc(2)-dolichol diphosphate. A deficiency of this enzyme causes an abnormal accumulation of Man1GlcNAc2-PP-dolichol and Man2GlcNAc2-PP-dolichol, which is associated with a type of congenital disorders of glycosylation (CDG), designated CDG-Ii, in humans.
Probab=27.16 E-value=5.6e+02 Score=25.07 Aligned_cols=37 Identities=24% Similarity=0.275 Sum_probs=26.2
Q ss_pred cEEEEEcCC-ChhH-HHhHHHHHHHHHHHCCCcEEEEEEcC
Q 015881 123 RRCCCIISG-GVYE-NLLFFPAIQLLKDRYPGVLIDVIASA 161 (399)
Q Consensus 123 ~rILIIr~~-~IGD-vVLttPalraLK~~yP~A~IdvLv~~ 161 (399)
||||++.++ .+|- --+.+=+.++|.++ +.+++++|..
T Consensus 1 mkIl~~~~~~~~gG~e~~~~~la~~L~~~--G~~V~v~~~~ 39 (392)
T cd03805 1 LRVAFIHPDLGIGGAERLVVDAALALQSR--GHEVTIYTSH 39 (392)
T ss_pred CeEEEECCCCCCchHHHHHHHHHHHHHhC--CCeEEEEcCC
Confidence 799999886 3443 23444577888766 6799999864
No 166
>PLN02496 probable phosphopantothenoylcysteine decarboxylase
Probab=27.09 E-value=1.1e+02 Score=28.95 Aligned_cols=57 Identities=12% Similarity=0.141 Sum_probs=41.5
Q ss_pred CcccccCcccccCCccEEEEEcCCChhHHHhHHHHHHHHHHHCCCcEEEEEEcCCchHhhh
Q 015881 108 NPEIASLPLKIRGDVRRCCCIISGGVYENLLFFPAIQLLKDRYPGVLIDVIASARGKQTFE 168 (399)
Q Consensus 108 ~~~~~~~~~~~~~~v~rILIIr~~~IGDvVLttPalraLK~~yP~A~IdvLv~~~~~~lle 168 (399)
.+|.+++...+....+|||+.-.++|.=. =+.-+++.|++ +++|.++..+.+..++.
T Consensus 5 ~~~~~~~~~~~~~~~k~IllgVtGSIAAy-k~~~lvr~L~~---g~~V~VvmT~~A~~FI~ 61 (209)
T PLN02496 5 SPEVDAMEVNTAPRKPRILLAASGSVAAI-KFGNLCHCFSE---WAEVRAVVTKASLHFID 61 (209)
T ss_pred CCCccchhhccCCCCCEEEEEEeCHHHHH-HHHHHHHHhcC---CCeEEEEEChhHhhhcC
Confidence 45667777666556789999999877633 23347788874 68999999988877665
No 167
>PF02590 SPOUT_MTase: Predicted SPOUT methyltransferase; InterPro: IPR003742 This family of proteins are predicted to be SPOUT methyltransferases []. ; GO: 0008168 methyltransferase activity, 0006364 rRNA processing, 0005737 cytoplasm; PDB: 1VH0_E 4FAK_A 1TO0_G 1O6D_A 1NS5_B.
Probab=27.04 E-value=4.6e+02 Score=23.49 Aligned_cols=107 Identities=18% Similarity=0.123 Sum_probs=65.4
Q ss_pred cEEEEEcCCChhHHHhHHHHHHHHHHHCCCcEEEEEEcCCch----------------HhhhcCCCCCEEEEecCCCCCC
Q 015881 123 RRCCCIISGGVYENLLFFPAIQLLKDRYPGVLIDVIASARGK----------------QTFELNKNVRWANVYDLDDDWP 186 (399)
Q Consensus 123 ~rILIIr~~~IGDvVLttPalraLK~~yP~A~IdvLv~~~~~----------------~lle~nP~ID~Vi~~d~k~~~~ 186 (399)
|||-|+..+.+-+--+..-+=.-+|+.-+-+.+.++--+... .+++..+.=+.++.+|.++...
T Consensus 1 Mki~i~~vGk~k~~~~~~~~~eY~kRl~~~~~~e~~e~~~~~~~~~~~~~~~~~~E~~~il~~i~~~~~~i~Ld~~Gk~~ 80 (155)
T PF02590_consen 1 MKIRIIAVGKLKEKFLKELIEEYLKRLSRYAKLEIIELKEEKIAKAQSIEKIKEKEGERILKKIPPNDYVILLDERGKQL 80 (155)
T ss_dssp -EEEEEEESSS-SHHHHHHHHHHHHHHCTTSEEEEEEE------TCHHHHHHHHHHHHHHHCTSHTTSEEEEE-TTSEE-
T ss_pred CEEEEEEEeccCcHHHHHHHHHHHHHcCccCceeEEEeccccccccccHHHHHHHHHHHHHhhccCCCEEEEEcCCCccC
Confidence 788888888888888888888888888888888887644333 4555555567888898765433
Q ss_pred ChHHHHHHHHHhhhCCC-cEEEEcCCC-ChHHHHHHHHhCCCeEEEec
Q 015881 187 EPAEYTDILGVMKNRYY-DMVLSTKLA-GLGHAAFLFMTTARDRVSYI 232 (399)
Q Consensus 187 ~~~~~~~l~~~LR~~~Y-DlvIdl~~~-~~rsAll~~LsgA~~RIGy~ 232 (399)
+-.++-+++..++.... ++++..-+. |+...+. .+|..++.++
T Consensus 81 sS~~fA~~l~~~~~~g~~~i~F~IGG~~G~~~~~~---~~a~~~lSLS 125 (155)
T PF02590_consen 81 SSEEFAKKLERWMNQGKSDIVFIIGGADGLSEEVR---KRADEKLSLS 125 (155)
T ss_dssp -HHHHHHHHHHHHHTTS-EEEEEE-BTTB--HHHH---HH-SEEEES-
T ss_pred ChHHHHHHHHHHHhcCCceEEEEEecCCCCCHHHH---hhcCceEEEe
Confidence 33445566666666665 888877665 3444433 3456677665
No 168
>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=26.78 E-value=7.1e+02 Score=25.56 Aligned_cols=193 Identities=13% Similarity=0.093 Sum_probs=106.0
Q ss_pred EcCCChhHHHhHHHHHHHHHHHCCCcEEEEEEcCCchHhhhcCCCCCEEEEecCCCCCCChHHHHHHHHHhhhCCC-cEE
Q 015881 128 IISGGVYENLLFFPAIQLLKDRYPGVLIDVIASARGKQTFELNKNVRWANVYDLDDDWPEPAEYTDILGVMKNRYY-DMV 206 (399)
Q Consensus 128 Ir~~~IGDvVLttPalraLK~~yP~A~IdvLv~~~~~~lle~nP~ID~Vi~~d~k~~~~~~~~~~~l~~~LR~~~Y-Dlv 206 (399)
|.++.|||---.-+++++.|++-=-.+|-+=..+--+.+++.+-. +.... =...-++.++.|.+..| |++
T Consensus 99 INPGNig~~e~v~~vv~~ak~~~ipIRIGVN~GSL~~~~~~kyg~-------~t~ea--mveSAl~~v~~le~~~F~div 169 (346)
T TIGR00612 99 INPGNIGFRERVRDVVEKARDHGKAMRIGVNHGSLERRLLEKYGD-------ATAEA--MVQSALEEAAILEKLGFRNVV 169 (346)
T ss_pred ECCCCCCCHHHHHHHHHHHHHCCCCEEEecCCCCCcHHHHHHcCC-------CCHHH--HHHHHHHHHHHHHHCCCCcEE
Confidence 899999999999999999999955555555555555677775422 01000 00122344555555554 999
Q ss_pred EEcCCCChHHHHH-----HHHhCCCeEEEecCCCccccccccccceeeccCcCCchhhHHHHHHHHHHHcCCCCCCCCCC
Q 015881 207 LSTKLAGLGHAAF-----LFMTTARDRVSYIYPNVNAAGAGLLLSETFTAESMNLSERGYNMYEQMVDWLGRPFRSVPRH 281 (399)
Q Consensus 207 Idl~~~~~rsAll-----~~LsgA~~RIGy~~~~~~~~~~~~~lt~~v~~~~~~~~~h~v~~yl~LL~~LGi~~~~~p~~ 281 (399)
|++..+.....+- +...--|.-+|.. +.|. ...-++. ..+-.-.-|.+.+|-
T Consensus 170 iS~KsSdv~~~i~ayr~la~~~dyPLHlGVT-----EAG~--~~~G~IK--------Saigig~LL~~GIGD-------- 226 (346)
T TIGR00612 170 LSMKASDVAETVAAYRLLAERSDYPLHLGVT-----EAGM--GVKGIVK--------SSAGIGILLARGIGD-------- 226 (346)
T ss_pred EEEEcCCHHHHHHHHHHHHhhCCCCceeccc-----cCCC--CCCchhH--------HHHHHHHHHhhCCCC--------
Confidence 9999885443332 3223333444443 3332 2222221 111111112233332
Q ss_pred CCCCceeecCH---HHHHHHHHHHHHhCCC-CCCeEEEEcCCCCccccccCCCCCCCCCCHHHHHHHHHH-hhhCC---C
Q 015881 282 PVPPLRVSISR---RLKEVVAEKYKNAGAE-QGKYIVIHGIESDSKASMQSRGDTDSLLPIQVWAEIANG-LREFR---P 353 (399)
Q Consensus 282 ~~p~l~i~is~---e~~~~a~~~l~~~gl~-~~~~IvIhPgas~~~~~~k~rg~~~KrWP~e~faeLa~~-L~~~~---~ 353 (399)
..+++++. +|...+.+.|+.+|+. .+.-|+-||+=+.- .+.....++=++. |.... .
T Consensus 227 ---TIRVSLT~dP~~EV~va~~IL~slglr~~g~~iiSCPtCGR~------------~~dl~~~~~~ve~~l~~~~~~l~ 291 (346)
T TIGR00612 227 ---TIRVSLTDDPTHEVPVAFEILQSLGLRARGVEIVACPSCGRT------------GFDVEKVVRRVQEALFHLKTPLK 291 (346)
T ss_pred ---eEEEECCCCcHHHHHHHHHHHHHcCCCcCCCeEEECCCCCCc------------CCCHHHHHHHHHHHHhcCCCCCE
Confidence 34444443 4556678889999997 45678888876543 3666555544443 43322 4
Q ss_pred EEEeC----CchhHHHHH
Q 015881 354 LFVIP----HEKEREGVE 367 (399)
Q Consensus 354 VvliG----gp~E~e~ae 367 (399)
|-+.| ||+|...|+
T Consensus 292 VAVMGCvVNGPGEak~AD 309 (346)
T TIGR00612 292 VAVMGCVVNGPGEAKHAD 309 (346)
T ss_pred EEEECceecCCchhhccC
Confidence 55554 888876664
No 169
>cd08479 PBP2_CrgA_like_9 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold. This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 9. The LTTRs are acting as both auto-repressors and activators of target promoters, controlling operons involved in a wide variety of cellular processes such as amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to name a few. In contrast to the tetrameric form of other LTTRs, CrgA from Neisseria meningitides assembles into an octameric ring, which can bind up to four 63-bp DNA oligonucleotides. Phylogenetic cluster analysis showed that the CrgA-like regulators form a subclass of the LTTRs that function as octamers. The CrgA is an auto-repressor of its own gene a
Probab=26.71 E-value=2.1e+02 Score=24.33 Aligned_cols=41 Identities=17% Similarity=0.216 Sum_probs=28.4
Q ss_pred HhHHHHHHHHHHHCCCcEEEEEEcCCchHhhhcCCCCCEEEEe
Q 015881 137 LLFFPAIQLLKDRYPGVLIDVIASARGKQTFELNKNVRWANVY 179 (399)
Q Consensus 137 VLttPalraLK~~yP~A~IdvLv~~~~~~lle~nP~ID~Vi~~ 179 (399)
-+..++++.++++||+++|.+.+......+.+ ..+|=.+..
T Consensus 14 ~~l~~~l~~f~~~~P~i~i~~~~~~~~~~l~~--g~~Dl~i~~ 54 (198)
T cd08479 14 RHIAPALSDFAKRYPELEVQLELTDRPVDLVE--EGFDLDIRV 54 (198)
T ss_pred HHHHHHHHHHHHHCCCeEEEEEecCccccccc--cCccEEEEc
Confidence 45568999999999999999987543322222 356666654
No 170
>KOG1198 consensus Zinc-binding oxidoreductase [Energy production and conversion; General function prediction only]
Probab=26.71 E-value=3.6e+02 Score=27.39 Aligned_cols=76 Identities=16% Similarity=0.077 Sum_probs=52.9
Q ss_pred cEEEEEcCC-ChhHHHhHHHHHHHHHHHCCCcEEEEEEcCCchHhhhcCCCCCEEEEecCCCCCCChHHHHHHHHHhhhC
Q 015881 123 RRCCCIISG-GVYENLLFFPAIQLLKDRYPGVLIDVIASARGKQTFELNKNVRWANVYDLDDDWPEPAEYTDILGVMKNR 201 (399)
Q Consensus 123 ~rILIIr~~-~IGDvVLttPalraLK~~yP~A~IdvLv~~~~~~lle~nP~ID~Vi~~d~k~~~~~~~~~~~l~~~LR~~ 201 (399)
++|||+--+ ++| +-+++..|... =+.+...+.....++++..- .|+++.|+. .++...++.....
T Consensus 159 ~~vLv~ggsggVG-----~~aiQlAk~~~-~~~v~t~~s~e~~~l~k~lG-Ad~vvdy~~-------~~~~e~~kk~~~~ 224 (347)
T KOG1198|consen 159 KSVLVLGGSGGVG-----TAAIQLAKHAG-AIKVVTACSKEKLELVKKLG-ADEVVDYKD-------ENVVELIKKYTGK 224 (347)
T ss_pred CeEEEEeCCcHHH-----HHHHHHHHhcC-CcEEEEEcccchHHHHHHcC-CcEeecCCC-------HHHHHHHHhhcCC
Confidence 678888544 676 44577777776 56777777888889888875 578877754 1344444444356
Q ss_pred CCcEEEEcCCC
Q 015881 202 YYDMVLSTKLA 212 (399)
Q Consensus 202 ~YDlvIdl~~~ 212 (399)
.||+|+|+=+.
T Consensus 225 ~~DvVlD~vg~ 235 (347)
T KOG1198|consen 225 GVDVVLDCVGG 235 (347)
T ss_pred CccEEEECCCC
Confidence 89999998776
No 171
>cd08478 PBP2_CrgA The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA, contains the type 2 periplasmic binding domain. This CD represents the substrate binding domain of LysR-type transcriptional regulator (LTTR) CrgA. The LTTRs are acting as both auto-repressors and activators of target promoters, controlling operons involved in a wide variety of cellular processes such as amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to name a few. In contrast to the tetrameric form of other LTTRs, CrgA from Neisseria meningitides assembles into an octameric ring, which can bind up to four 63-bp DNA oligonucleotides. Phylogenetic cluster analysis further showed that the CrgA-like regulators form a subclass of the LTTRs that function as octamers. The CrgA is an auto-repressor of its own gene and activates the expression of the mdaB gene wh
Probab=26.01 E-value=1.4e+02 Score=25.53 Aligned_cols=40 Identities=18% Similarity=0.354 Sum_probs=29.0
Q ss_pred HHHHHHHHHHHCCCcEEEEEEcCCchHhhhcCCCCCEEEEec
Q 015881 139 FFPAIQLLKDRYPGVLIDVIASARGKQTFELNKNVRWANVYD 180 (399)
Q Consensus 139 ttPalraLK~~yP~A~IdvLv~~~~~~lle~nP~ID~Vi~~d 180 (399)
..+++..++++||+++|++........+.+ -.+|=++...
T Consensus 18 l~~~l~~f~~~~P~v~i~~~~~~~~~~l~~--~~~D~~i~~~ 57 (199)
T cd08478 18 LAPLIAKFRERYPDIELELVSNEGIIDLIE--RKTDVAIRIG 57 (199)
T ss_pred HHHHHHHHHHHCCCeEEEEEeccccccchh--ccccEEEEec
Confidence 458999999999999999985444444332 4777777653
No 172
>PF13439 Glyco_transf_4: Glycosyltransferase Family 4; PDB: 2JJM_E 3MBO_C 2GEJ_A 2GEK_A.
Probab=25.65 E-value=87 Score=26.38 Aligned_cols=90 Identities=11% Similarity=-0.057 Sum_probs=44.9
Q ss_pred HhHHHHHHHHHHHCCCcEEEEEEcCCchHhhhcCCCCCEEEEec---CCCCCCChHHHHHHHHHhhhCCCcEEEEcCCCC
Q 015881 137 LLFFPAIQLLKDRYPGVLIDVIASARGKQTFELNKNVRWANVYD---LDDDWPEPAEYTDILGVMKNRYYDMVLSTKLAG 213 (399)
Q Consensus 137 VLttPalraLK~~yP~A~IdvLv~~~~~~lle~nP~ID~Vi~~d---~k~~~~~~~~~~~l~~~LR~~~YDlvIdl~~~~ 213 (399)
..+.=++++|+++ +.++++++.....+.... .+....... .+.....+.....+.+.+++.++|++ ..+...
T Consensus 16 ~~~~~l~~~l~~~--G~~v~v~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~DiV-h~~~~~ 90 (177)
T PF13439_consen 16 RVVLNLARALAKR--GHEVTVVSPGVKDPIEEE--LVKIFVKIPYPIRKRFLRSFFFMRRLRRLIKKEKPDIV-HIHGPP 90 (177)
T ss_dssp HHHHHHHHHHHHT--T-EEEEEESS-TTS-SST--EEEE---TT-SSTSS--HHHHHHHHHHHHHHHHT-SEE-ECCTTH
T ss_pred HHHHHHHHHHHHC--CCEEEEEEcCCCccchhh--ccceeeeeecccccccchhHHHHHHHHHHHHHcCCCeE-Eecccc
Confidence 3444678888886 789999987766555444 111111110 01111123344567778988999998 444431
Q ss_pred -hHHHHHHHHhCCCeEEEec
Q 015881 214 -LGHAAFLFMTTARDRVSYI 232 (399)
Q Consensus 214 -~rsAll~~LsgA~~RIGy~ 232 (399)
...+.+... +.+....+.
T Consensus 91 ~~~~~~~~~~-~~~~v~~~H 109 (177)
T PF13439_consen 91 AFWIALLACR-KVPIVYTIH 109 (177)
T ss_dssp CCCHHHHHHH-CSCEEEEE-
T ss_pred hhHHHHHhcc-CCCEEEEeC
Confidence 233444444 666555554
No 173
>cd08474 PBP2_CrgA_like_5 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold. This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 5. The LTTRs are acting as both auto-repressors and activators of target promoters, controlling operons involved in a wide variety of cellular processes such as amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to name a few. In contrast to the tetrameric form of other LTTRs, CrgA from Neisseria meningitides assembles into an octameric ring, which can bind up to four 63-bp DNA oligonucleotides. Phylogenetic cluster analysis showed that the CrgA-like regulators form a subclass of the LTTRs that function as octamers. The CrgA is an auto-repressor of its own gene a
Probab=25.50 E-value=1.4e+02 Score=25.42 Aligned_cols=41 Identities=12% Similarity=0.236 Sum_probs=29.1
Q ss_pred hHHHHHHHHHHHCCCcEEEEEEcCCchHhhhcCCCCCEEEEec
Q 015881 138 LFFPAIQLLKDRYPGVLIDVIASARGKQTFELNKNVRWANVYD 180 (399)
Q Consensus 138 LttPalraLK~~yP~A~IdvLv~~~~~~lle~nP~ID~Vi~~d 180 (399)
+..++++.++++||+++|.+.+......+.+ ..+|=.+.+.
T Consensus 17 ~l~~~l~~~~~~~P~v~i~~~~~~~~~~l~~--g~~D~~i~~~ 57 (202)
T cd08474 17 LLAPLLARFLARYPDIRLELVVDDGLVDIVA--EGFDAGIRLG 57 (202)
T ss_pred HHHHHHHHHHHHCCCeEEEEEecCCcccccc--cCccEEEEcC
Confidence 3458999999999999999987554434332 3677666543
No 174
>TIGR02699 archaeo_AfpA archaeoflavoprotein AfpA. The prototypical member of this archaeal protein family is AF1518 from Archaeoglobus fulgidus. This homodimer with two non-covalently bound FMN cofactors can receive electrons from ferredoxin, but not from a number of other electron donors such as NADH or rubredoxin. It can then donate electrons to various reductases.
Probab=25.42 E-value=1.3e+02 Score=27.64 Aligned_cols=44 Identities=32% Similarity=0.452 Sum_probs=34.2
Q ss_pred EEEEEcCCChhHHHh-HHHHHHHHHHHCCCcEEEEEEcCCchHhhhc
Q 015881 124 RCCCIISGGVYENLL-FFPAIQLLKDRYPGVLIDVIASARGKQTFEL 169 (399)
Q Consensus 124 rILIIr~~~IGDvVL-ttPalraLK~~yP~A~IdvLv~~~~~~lle~ 169 (399)
||++--.++ |+.+. ...+++.|++++ +++|+++.++.++.+++.
T Consensus 1 ~i~~gitGs-g~~l~e~v~~l~~L~~~~-g~eV~vv~S~~A~~vi~~ 45 (174)
T TIGR02699 1 RIAWGITGS-GDKLPETYSIMKDVKNRY-GDEIDVFLSKAGEQVVKW 45 (174)
T ss_pred CEEEEEEcc-HHHHHHHHHHHHHHHHhc-CCEEEEEECHhHHHHHHH
Confidence 456666666 77766 668899998876 889999999999876553
No 175
>TIGR01039 atpD ATP synthase, F1 beta subunit. The sequences of ATP synthase F1 alpha and beta subunits are related and both contain a nucleotide-binding site for ATP and ADP. They have a common amino terminal domain but vary at the C-terminus. The beta chain has catalytic activity, while the alpha chain is a regulatory subunit. Proton translocating ATP synthase, F1 beta subunit is homologous to proton translocating ATP synthase archaeal/vacuolar(V1), A subunit.
Probab=25.27 E-value=4.2e+02 Score=28.23 Aligned_cols=104 Identities=14% Similarity=0.098 Sum_probs=71.2
Q ss_pred cccCcccccCCccEEEEEcCCChhHHHhHHHHHHHHHHHCCCcEEEEEEcCCchHh---hhcC---CCCCE-EEEecCCC
Q 015881 111 IASLPLKIRGDVRRCCCIISGGVYENLLFFPAIQLLKDRYPGVLIDVIASARGKQT---FELN---KNVRW-ANVYDLDD 183 (399)
Q Consensus 111 ~~~~~~~~~~~v~rILIIr~~~IGDvVLttPalraLK~~yP~A~IdvLv~~~~~~l---le~n---P~ID~-Vi~~d~k~ 183 (399)
|+.|..-.+ -.|++|+-.++.|=..|..-+++...+.++++-|-.++..+..++ ++.. ...++ |+++...+
T Consensus 134 ID~l~pig~--GQr~~If~~~G~GKt~L~~~~~~~~~~~~~~v~V~alIGER~rEv~ef~~~~~~~~~l~rtvvV~atsd 211 (461)
T TIGR01039 134 IDLLAPYAK--GGKIGLFGGAGVGKTVLIQELINNIAKEHGGYSVFAGVGERTREGNDLYHEMKESGVIDKTALVYGQMN 211 (461)
T ss_pred ecccCCccc--CCEEEeecCCCCChHHHHHHHHHHHHhcCCCeEEEEEecCCchHHHHHHHHHHhcCCcceeEEEEECCC
Confidence 344444444 379999999999999999999999998889999999998887764 3322 33333 44554433
Q ss_pred CCCChHH------HHHHHHHhhh-CCCcEEEEcCCCChHHHH
Q 015881 184 DWPEPAE------YTDILGVMKN-RYYDMVLSTKLAGLGHAA 218 (399)
Q Consensus 184 ~~~~~~~------~~~l~~~LR~-~~YDlvIdl~~~~~rsAl 218 (399)
. ....+ -..+...+|. +.+|+.+-+.+- .|.|-
T Consensus 212 ~-p~~~R~~a~~~a~tiAEyfrd~~G~~VLll~Dsl-TR~A~ 251 (461)
T TIGR01039 212 E-PPGARMRVALTGLTMAEYFRDEQGQDVLLFIDNI-FRFTQ 251 (461)
T ss_pred C-CHHHHHHHHHHHHHHHHHHHHhcCCeeEEEecch-hHHHH
Confidence 2 11111 1345667888 789999988877 55544
No 176
>COG3980 spsG Spore coat polysaccharide biosynthesis protein, predicted glycosyltransferase [Cell envelope biogenesis, outer membrane]
Probab=25.18 E-value=1.7e+02 Score=29.36 Aligned_cols=74 Identities=8% Similarity=-0.059 Sum_probs=50.4
Q ss_pred cEEEEEcC----CChhHHHhHHHHHHHHHHHCCCcEEEEEEcCCchHhhhcCCCCCEEEEecCCCCCCChHHHHHHHHHh
Q 015881 123 RRCCCIIS----GGVYENLLFFPAIQLLKDRYPGVLIDVIASARGKQTFELNKNVRWANVYDLDDDWPEPAEYTDILGVM 198 (399)
Q Consensus 123 ~rILIIr~----~~IGDvVLttPalraLK~~yP~A~IdvLv~~~~~~lle~nP~ID~Vi~~d~k~~~~~~~~~~~l~~~L 198 (399)
|||+|+.- .++|-|.-+.-+.++|++.- ..+.+++.+...+++-- +-+++..+.- +.-..|
T Consensus 1 M~V~i~~Dgg~~iGmGHV~R~l~LA~~l~k~~--~~~~fl~k~~~e~~~~~---~~~~f~~~~~----------~~~n~i 65 (318)
T COG3980 1 MKVLIRCDGGLEIGMGHVMRTLTLARELEKRG--FACLFLTKQDIEAIIHK---VYEGFKVLEG----------RGNNLI 65 (318)
T ss_pred CcEEEEecCCcccCcchhhhHHHHHHHHHhcC--ceEEEecccchhhhhhh---hhhhccceee----------eccccc
Confidence 78888854 67999999999999999984 79999998876663322 2333322211 111267
Q ss_pred hhCCCcEEE-EcCC
Q 015881 199 KNRYYDMVL-STKL 211 (399)
Q Consensus 199 R~~~YDlvI-dl~~ 211 (399)
+++++|++| |..+
T Consensus 66 k~~k~d~lI~Dsyg 79 (318)
T COG3980 66 KEEKFDLLIFDSYG 79 (318)
T ss_pred ccccCCEEEEeccC
Confidence 889999987 4433
No 177
>PF03846 SulA: Cell division inhibitor SulA; InterPro: IPR004596 All proteins in this family for which the functions are known are cell division inhibitors. In Escherichia coli, SulA is one of the SOS regulated genes. Accumulation of SulA causes rapid cessation of cell division and the appearance of long, non-septate filaments. In the presence of GTP, SulA binds a polymerisation-competent form of ftsZ in a 1:1 ratio, thus inhibiting ftsZ polymerisation and therefore preventing it from participating in the assembly of the Z ring. This mechanism prevents the premature segregation of damaged DNA to daughter cells during cell division. The expression of SulA is repressed by LexA. The N terminus of SulA may be involved in recognising the cell division apparatus.; GO: 0009432 SOS response, 0051782 negative regulation of cell division, 0009276 Gram-negative-bacterium-type cell wall; PDB: 1OFU_X 1OFT_A.
Probab=25.14 E-value=2.7e+02 Score=24.22 Aligned_cols=66 Identities=14% Similarity=0.204 Sum_probs=43.9
Q ss_pred hHHHHHHHHHHHCCCcEEEEEEcCC--chHhhhc-CCCCCEEEEecCCCCCCChHHHHHHHHHhhhCCCcEEEE
Q 015881 138 LFFPAIQLLKDRYPGVLIDVIASAR--GKQTFEL-NKNVRWANVYDLDDDWPEPAEYTDILGVMKNRYYDMVLS 208 (399)
Q Consensus 138 LttPalraLK~~yP~A~IdvLv~~~--~~~lle~-nP~ID~Vi~~d~k~~~~~~~~~~~l~~~LR~~~YDlvId 208 (399)
+.+|+++.|-++ .--|.|++.+. .+..++. .=.+++|+.+...+. ......+.+.||.++|-+||.
T Consensus 48 lLlPlL~qLsqq--sRWllwi~P~~~ls~~wL~~aGl~~~kvl~l~~~~~---~~tl~amekAL~sGn~s~Vl~ 116 (119)
T PF03846_consen 48 LLLPLLRQLSQQ--SRWLLWIAPPQKLSRQWLQQAGLPLEKVLQLHPRNP---QSTLEAMEKALRSGNYSAVLG 116 (119)
T ss_dssp HHHHHHHHHHSS--SSEEEEES--TTS-HHHHHHTT--CCCEEEE--SST---THHHHHHHHHHHHT-EEEEEE
T ss_pred HHHHHHHHhCcc--ceEEEEECCCcccCHHHHHHcCCChhHeEEeCCCCc---ccHHHHHHHHHHhCCCeEEEE
Confidence 478999999975 56688887654 4555554 357899999977543 345567889999999999984
No 178
>PRK13267 archaemetzincin-like protein; Reviewed
Probab=25.12 E-value=3.2e+02 Score=25.20 Aligned_cols=76 Identities=12% Similarity=0.071 Sum_probs=47.6
Q ss_pred ccEEEEEcCCChhHHHhHHHHHHHHHHHCCCcEEEEEEcCCchHhhhcCCCCCEEEEecCCCCCCChHHHHHHHHHhhhC
Q 015881 122 VRRCCCIISGGVYENLLFFPAIQLLKDRYPGVLIDVIASARGKQTFELNKNVRWANVYDLDDDWPEPAEYTDILGVMKNR 201 (399)
Q Consensus 122 v~rILIIr~~~IGDvVLttPalraLK~~yP~A~IdvLv~~~~~~lle~nP~ID~Vi~~d~k~~~~~~~~~~~l~~~LR~~ 201 (399)
+|+|+||-.+.+.+.++..- -..|++.|++..+.+.... .-+.. .|+.......-..+++.+..++..
T Consensus 1 ~m~i~ivp~g~v~~~~l~~~-~~~l~~~~~~~~v~~~~~~-~~p~~----------a~~~~r~Q~~a~~iL~~l~~~~~~ 68 (179)
T PRK13267 1 MMKILIVPIGYVPASVIREA-SNNLRSVYLDCDVTVDSRQ-SLPIS----------AYDWERGQYRAEKFLPLLSRIGRF 68 (179)
T ss_pred CcEEEEEeCCCCCHHHHHHH-HHHHHHHhccCCeEEecCC-CCCHh----------hcCCCCceecHHHHHHHHHhhCCC
Confidence 47899999999999888764 4489999998887765321 11221 233332223334566666666655
Q ss_pred CCcEEEEc
Q 015881 202 YYDMVLST 209 (399)
Q Consensus 202 ~YDlvIdl 209 (399)
.-|.+|-+
T Consensus 69 ~~~~vl~v 76 (179)
T PRK13267 69 NGDKNIGI 76 (179)
T ss_pred CCceEEEE
Confidence 56666633
No 179
>cd02803 OYE_like_FMN_family Old yellow enzyme (OYE)-like FMN binding domain. OYE was the first flavin-dependent enzyme identified, however its true physiological role remains elusive to this day. Each monomer of OYE contains FMN as a non-covalently bound cofactor, uses NADPH as a reducing agent with oxygens, quinones, and alpha,beta-unsaturated aldehydes and ketones, and can act as electron acceptors in the catalytic reaction. Members of OYE family include trimethylamine dehydrogenase, 2,4-dienoyl-CoA reductase, enoate reductase, pentaerythriol tetranitrate reductase, xenobiotic reductase, and morphinone reductase.
Probab=24.05 E-value=3.9e+02 Score=26.21 Aligned_cols=73 Identities=15% Similarity=0.256 Sum_probs=42.2
Q ss_pred HHHHHHHHHHHHhCCCCCCeEEEEcCCCCccccccCCCCCCCCCCHHHHHHHHHHhhhCC--CEEEeCCchhHHHHHHHH
Q 015881 293 RLKEVVAEKYKNAGAEQGKYIVIHGIESDSKASMQSRGDTDSLLPIQVWAEIANGLREFR--PLFVIPHEKEREGVEDVV 370 (399)
Q Consensus 293 e~~~~a~~~l~~~gl~~~~~IvIhPgas~~~~~~k~rg~~~KrWP~e~faeLa~~L~~~~--~VvliGgp~E~e~aeeI~ 370 (399)
++....-+.+.+.|+ .+|.++.+..... ... ...-.++...+.++++.+++.. +|+..|+-.+.+.+++++
T Consensus 228 ~e~~~la~~l~~~G~---d~i~vs~g~~~~~---~~~-~~~~~~~~~~~~~~~~~ir~~~~iPVi~~Ggi~t~~~a~~~l 300 (327)
T cd02803 228 EEAIEIAKALEEAGV---DALHVSGGSYESP---PPI-IPPPYVPEGYFLELAEKIKKAVKIPVIAVGGIRDPEVAEEIL 300 (327)
T ss_pred HHHHHHHHHHHHcCC---CEEEeCCCCCccc---ccc-cCCCCCCcchhHHHHHHHHHHCCCCEEEeCCCCCHHHHHHHH
Confidence 333333345666665 4888877654322 000 0000134455666777776643 888889888888888887
Q ss_pred hc
Q 015881 371 GD 372 (399)
Q Consensus 371 ~~ 372 (399)
+.
T Consensus 301 ~~ 302 (327)
T cd02803 301 AE 302 (327)
T ss_pred HC
Confidence 75
No 180
>cd04910 ACT_AK-Ectoine_1 ACT domains located C-terminal to the catalytic domain of the aspartokinase of the ectoine (1,4,5,6-tetrahydro-2-methyl pyrimidine-4-carboxylate) biosynthetic pathway. This CD includes the first of two ACT domains located C-terminal to the catalytic domain of the aspartokinase of the ectoine (1,4,5,6-tetrahydro-2-methyl pyrimidine-4-carboxylate) biosynthetic pathway found in Methylomicrobium alcaliphilum, Vibrio cholerae, and various other halotolerant or halophilic bacteria. Bacteria exposed to hyperosmotic stress accumulate organic solutes called 'compatible solutes' of which ectoine, a heterocyclic amino acid, is one. Apart from its osmotic function, ectoine also exhibits a protective effect on proteins, nucleic acids and membranes against a variety of stress factors. de novo synthesis of ectoine starts with the phosphorylation of L-aspartate and shares its first two enzymatic steps with the biosynthesis of amino acids of the aspartate family: aspartokinase
Probab=23.38 E-value=50 Score=25.91 Aligned_cols=19 Identities=21% Similarity=0.316 Sum_probs=15.4
Q ss_pred hHHHHHHHHHHHCCCcEEE
Q 015881 138 LFFPAIQLLKDRYPGVLID 156 (399)
Q Consensus 138 LttPalraLK~~yP~A~Id 156 (399)
..-=++++|+++||+++|+
T Consensus 52 ~~~r~~~~Le~~~p~a~it 70 (71)
T cd04910 52 TIKRLTEDLENRFPNAEIT 70 (71)
T ss_pred HHHHHHHHHHHhCccCccc
Confidence 3345789999999999985
No 181
>TIGR00242 mraZ protein. Members of this family contain two tandem copies of a domain described by pfam02381. This protein often is found with other genes of the dcw (division cell wall) gene cluster, including mraW, ftsI, murE, murF, ftsW, murG, etc.
Probab=23.23 E-value=3.5e+02 Score=23.74 Aligned_cols=52 Identities=21% Similarity=0.383 Sum_probs=34.6
Q ss_pred CCCCHHHHHHHHHHhhhCCCEEEeCCchhHHHHHHHHhcCCCCceeecCCccccchh
Q 015881 334 SLLPIQVWAEIANGLREFRPLFVIPHEKEREGVEDVVGDDASIVFITTPGQVRMSSY 390 (399)
Q Consensus 334 KrWP~e~faeLa~~L~~~~~VvliGgp~E~e~aeeI~~~~~~~~~i~~~G~ls~~~~ 390 (399)
..||.+.|.++.+.+.... ...++-+.+...+.+....+. +...|++.+...
T Consensus 41 ~l~~~~~w~~~~~~~~~~~----~~~~~~r~l~r~l~~~a~~~~-~D~~GRi~iP~~ 92 (142)
T TIGR00242 41 LLYPLQEWEKIEQKLNALP----STQKDTRRLQRLIFGHATECE-MDTAGRVLIANN 92 (142)
T ss_pred EEeCHHHHHHHHHHHHhCC----CCCHHHHHHHHHHhcCCeeee-eCCCCeEeCCHH
Confidence 4699999999999886543 235555566666666655555 666677766543
No 182
>cd08484 PBP2_LTTR_beta_lactamase The C-terminal substrate-domain of LysR-type transcriptional regulators for beta-lactamase genes, contains the type 2 periplasmic binding fold. This CD includes the C-terminal substrate binding domain of LysR-type transcriptional regulators, BlaA and AmpR, that are involved in control of the expression of beta-lactamase genes. Beta-lactamases are responsible for bacterial resistance to beta-lactam antibiotics such as penicillins. BlaA (a constitutive class A penicillinase) belongs to the LysR family of transcriptional regulators, while BlaB (an inducible class C cephalosporinase or AmpC) can be referred to as a penicillin-binding protein, but it does not act as a beta-lactamase. AmpR regulates the expression of beta-lactamases in many enterobacterial strains and many other gram-negative bacilli. In contrast to BlaA, AmpR acts an activator only in the presence of the beta-lactam inducer. In the absence of the inducer, AmpR acts as a repressor. The topol
Probab=23.22 E-value=1.4e+02 Score=25.39 Aligned_cols=41 Identities=7% Similarity=0.145 Sum_probs=29.5
Q ss_pred hHHHHHHHHHHHCCCcEEEEEEcCCchHhhhcCCCCCEEEEec
Q 015881 138 LFFPAIQLLKDRYPGVLIDVIASARGKQTFELNKNVRWANVYD 180 (399)
Q Consensus 138 LttPalraLK~~yP~A~IdvLv~~~~~~lle~nP~ID~Vi~~d 180 (399)
+..+++..++++||+.+|.+........++++ .+|=.+...
T Consensus 14 ~l~~~l~~f~~~~P~i~l~~~~~~~~~~~~~~--~~D~~i~~~ 54 (189)
T cd08484 14 WLLPRLAEFRQLHPFIDLRLSTNNNRVDIAAE--GLDFAIRFG 54 (189)
T ss_pred HHHhhhHHHHHHCCCceEEEecccCccccccC--CccEEEEec
Confidence 34578999999999999999875544444443 477666653
No 183
>cd08480 PBP2_CrgA_like_10 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold. This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 10. The LTTRs are acting as both auto-repressors and activators of target promoters, controlling operons involved in a wide variety of cellular processes such as amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to name a few. In contrast to the tetrameric form of other LTTRs, CrgA from Neisseria meningitides assembles into an octameric ring, which can bind up to four 63-bp DNA oligonucleotides. Phylogenetic cluster analysis showed that the CrgA-like regulators form a subclass of the LTTRs that function as octamers. The CrgA is an auto-repressor of its own gene
Probab=23.18 E-value=1.6e+02 Score=25.34 Aligned_cols=41 Identities=17% Similarity=0.323 Sum_probs=29.1
Q ss_pred hHHHHHHHHHHHCCCcEEEEEEcCCchHhhhcCCCCCEEEEec
Q 015881 138 LFFPAIQLLKDRYPGVLIDVIASARGKQTFELNKNVRWANVYD 180 (399)
Q Consensus 138 LttPalraLK~~yP~A~IdvLv~~~~~~lle~nP~ID~Vi~~d 180 (399)
+..|++..++++||+.+|++........++ ...+|=.+...
T Consensus 15 ~l~~~l~~~~~~~P~i~i~i~~~~~~~~~~--~~~~D~~i~~~ 55 (198)
T cd08480 15 FLLPLLPAFLARYPEILVDLSLTDEVVDLL--AERTDVAIRVG 55 (198)
T ss_pred hhHHHHHHHHHHCCCeEEEEEecCCccccc--cccccEEEEeC
Confidence 446999999999999999997644433433 34677666643
No 184
>PRK12815 carB carbamoyl phosphate synthase large subunit; Reviewed
Probab=23.09 E-value=3.5e+02 Score=31.81 Aligned_cols=81 Identities=15% Similarity=0.063 Sum_probs=52.1
Q ss_pred cCCccEEEEEcCCCh--h-----HHHhHHHHHHHHHHHCCCcEEEEEEcCCchHhhhcCCCCCEEEEecCCCCCCChHHH
Q 015881 119 RGDVRRCCCIISGGV--Y-----ENLLFFPAIQLLKDRYPGVLIDVIASARGKQTFELNKNVRWANVYDLDDDWPEPAEY 191 (399)
Q Consensus 119 ~~~v~rILIIr~~~I--G-----DvVLttPalraLK~~yP~A~IdvLv~~~~~~lle~nP~ID~Vi~~d~k~~~~~~~~~ 191 (399)
+.+++||||+-.+.+ | |. ..+.++++||+. +.++.++-.... .+.......|.++.-+. . .
T Consensus 4 ~~~~~kvlviG~G~~~igq~~E~d~-sg~q~~~aL~e~--G~~vi~v~~np~-~~~~d~~~ad~~y~ep~-----~---~ 71 (1068)
T PRK12815 4 DTDIQKILVIGSGPIVIGQAAEFDY-SGTQACLALKEE--GYQVVLVNPNPA-TIMTDPAPADTVYFEPL-----T---V 71 (1068)
T ss_pred CCCCCEEEEECCCcchhcchhhhhh-HHHHHHHHHHHc--CCEEEEEeCCcc-hhhcCcccCCeeEECCC-----C---H
Confidence 566899999988774 5 44 677899999997 777766654332 23333335566543221 1 1
Q ss_pred HHHHHHhhhCCCcEEEEcCC
Q 015881 192 TDILGVMKNRYYDMVLSTKL 211 (399)
Q Consensus 192 ~~l~~~LR~~~YDlvIdl~~ 211 (399)
-.+.+.+++++.|.++-+-+
T Consensus 72 e~l~~ii~~e~~D~Iip~~g 91 (1068)
T PRK12815 72 EFVKRIIAREKPDALLATLG 91 (1068)
T ss_pred HHHHHHHHHhCcCEEEECCC
Confidence 23455578899999997543
No 185
>PRK10595 SOS cell division inhibitor; Provisional
Probab=22.98 E-value=5.9e+02 Score=23.28 Aligned_cols=85 Identities=11% Similarity=0.057 Sum_probs=56.6
Q ss_pred cCCccEEEEE-cCCChhHHHhHHHHHHHHHHHCCCcEEEEEEcC--CchHhhhcC-CCCCEEEEecCCCCCCChHHHHHH
Q 015881 119 RGDVRRCCCI-ISGGVYENLLFFPAIQLLKDRYPGVLIDVIASA--RGKQTFELN-KNVRWANVYDLDDDWPEPAEYTDI 194 (399)
Q Consensus 119 ~~~v~rILII-r~~~IGDvVLttPalraLK~~yP~A~IdvLv~~--~~~~lle~n-P~ID~Vi~~d~k~~~~~~~~~~~l 194 (399)
.+.+--||.- ..-++|. .|.+|+++.|-.+ +-.|-|+..+ .+++.+... =..++|+.+...+. ....+.+
T Consensus 25 ~g~ltEll~~~~qpg~~e-~LLlP~L~~l~~~--~rwilwI~PP~~p~~~~L~~~Gl~l~rvl~v~~~~~---~d~Lwa~ 98 (164)
T PRK10595 25 AGLISELVYREDQPMMTQ-LLLLPLLQQLGQQ--SRWQLWLTPQQKLSREWLQASGLPLTKVMQLSQLSP---CHTVEAM 98 (164)
T ss_pred CCceEEEeecCCCchHHH-HHHHHHHHHHhcc--CceEEEECCCCCCCHHHHHHcCCCcccEEEEecCCc---HHHHHHH
Confidence 4445555554 3577888 4899999988753 4456666655 355666543 35678888764322 2345677
Q ss_pred HHHhhhCCCcEEEEc
Q 015881 195 LGVMKNRYYDMVLST 209 (399)
Q Consensus 195 ~~~LR~~~YDlvIdl 209 (399)
-+.||...|.+||.=
T Consensus 99 EqaLrsG~~~aVL~W 113 (164)
T PRK10595 99 ERALRTGNYSVVLGW 113 (164)
T ss_pred HHHHhhCCCcEEEEC
Confidence 888999999999974
No 186
>PRK11716 DNA-binding transcriptional regulator IlvY; Provisional
Probab=22.98 E-value=4.2e+02 Score=24.37 Aligned_cols=51 Identities=14% Similarity=0.053 Sum_probs=31.8
Q ss_pred EEcCCChhHHHhHHHHHHHHHHHCCCcEEEEEEcCCchHhhh--cCCCCCEEEEe
Q 015881 127 CIISGGVYENLLFFPAIQLLKDRYPGVLIDVIASARGKQTFE--LNKNVRWANVY 179 (399)
Q Consensus 127 IIr~~~IGDvVLttPalraLK~~yP~A~IdvLv~~~~~~lle--~nP~ID~Vi~~ 179 (399)
|-....++- .+..+++..+.++||+++|++.... ..++++ .+-.+|=+|.+
T Consensus 71 I~~~~~~~~-~~~~~~l~~~~~~~p~i~l~i~~~~-~~~~~~~l~~~~~D~~i~~ 123 (269)
T PRK11716 71 LFCSVTAAY-SHLPPILDRFRAEHPLVEIKLTTGD-AADAVEKVQSGEADLAIAA 123 (269)
T ss_pred EEecchHHH-HHHHHHHHHHHHHCCCeEEEEEECC-HHHHHHHHHCCCccEEEEe
Confidence 334444443 3567899999999999999997653 222222 12456666654
No 187
>COG1519 KdtA 3-deoxy-D-manno-octulosonic-acid transferase [Cell envelope biogenesis, outer membrane]
Probab=22.40 E-value=96 Score=32.52 Aligned_cols=48 Identities=25% Similarity=0.371 Sum_probs=37.9
Q ss_pred cccCcccccCCccEEEEEcCCChhHHHhHHHHHHHHHHHCCCcEEEEEE
Q 015881 111 IASLPLKIRGDVRRCCCIISGGVYENLLFFPAIQLLKDRYPGVLIDVIA 159 (399)
Q Consensus 111 ~~~~~~~~~~~v~rILIIr~~~IGDvVLttPalraLK~~yP~A~IdvLv 159 (399)
.+.+-....+. +++.|.-..+=||-=+..++.++|+++||++.+-|+=
T Consensus 220 ~~~~r~~l~~~-r~v~iaaSTH~GEeei~l~~~~~l~~~~~~~llIlVP 267 (419)
T COG1519 220 LAALRRQLGGH-RPVWVAASTHEGEEEIILDAHQALKKQFPNLLLILVP 267 (419)
T ss_pred HHHHHHhcCCC-CceEEEecCCCchHHHHHHHHHHHHhhCCCceEEEec
Confidence 33444445444 7888888889999999999999999999998776653
No 188
>cd05466 PBP2_LTTR_substrate The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily. This model and hierarchy represent the the substrate-binding domain of the LysR-type transcriptional regulators that form the largest family of prokaryotic transcription factor. Homologs of some of LTTRs with similar domain organizations are also found in the archaea and eukaryotic organisms. The LTTRs are composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcriptional repressor undergoes a conformational change upon substrate binding which in turn changes the DNA bin
Probab=22.37 E-value=2.9e+02 Score=22.61 Aligned_cols=24 Identities=29% Similarity=0.722 Sum_probs=20.3
Q ss_pred hHHHHHHHHHHHCCCcEEEEEEcC
Q 015881 138 LFFPAIQLLKDRYPGVLIDVIASA 161 (399)
Q Consensus 138 LttPalraLK~~yP~A~IdvLv~~ 161 (399)
...++++.+++++|+++|.+....
T Consensus 14 ~l~~~i~~~~~~~p~i~i~~~~~~ 37 (197)
T cd05466 14 LLPPLLAAFRQRYPGVELSLVEGG 37 (197)
T ss_pred HhHHHHHHHHHHCCCCEEEEEECC
Confidence 456889999999999999988754
No 189
>cd08463 PBP2_DntR_like_4 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator similar to DntR, which is involved in the catabolism of dinitrotoluene; contains the type 2 periplasmic binding fold. This CD includes an uncharacterized LysR-type transcriptional regulator similar to DntR, NahR, and LinR, which are involved in the degradation of aromatic compounds. The transcription of the genes encoding enzymes involved in such degradation is regulated and expression of these enzymes is enhanced by inducers, which are either an intermediate in the metabolic pathway or compounds to be degraded. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytra
Probab=22.13 E-value=1.2e+02 Score=26.48 Aligned_cols=28 Identities=11% Similarity=0.253 Sum_probs=22.4
Q ss_pred CChhHHHhHHHHHHHHHHHCCCcEEEEEE
Q 015881 131 GGVYENLLFFPAIQLLKDRYPGVLIDVIA 159 (399)
Q Consensus 131 ~~IGDvVLttPalraLK~~yP~A~IdvLv 159 (399)
..++. .+..+++..++++||+++|++..
T Consensus 8 ~~~~~-~~~~~~l~~~~~~~P~~~v~~~~ 35 (203)
T cd08463 8 DYLNA-LFLPELVARFRREAPGARLEIHP 35 (203)
T ss_pred hhhHH-HHhHHHHHHHHHHCCCCEEEEEe
Confidence 34444 35678999999999999999986
No 190
>PRK10086 DNA-binding transcriptional regulator DsdC; Provisional
Probab=22.09 E-value=2.9e+02 Score=26.69 Aligned_cols=42 Identities=14% Similarity=0.350 Sum_probs=31.5
Q ss_pred HhHHHHHHHHHHHCCCcEEEEEEcCCchHhhhcCCCCCEEEEec
Q 015881 137 LLFFPAIQLLKDRYPGVLIDVIASARGKQTFELNKNVRWANVYD 180 (399)
Q Consensus 137 VLttPalraLK~~yP~A~IdvLv~~~~~~lle~nP~ID~Vi~~d 180 (399)
-+..+++..+++.||+.+|++.+......+. +..+|=++...
T Consensus 115 ~~l~~~l~~f~~~~P~i~i~~~~~~~~~~l~--~~~~Di~i~~~ 156 (311)
T PRK10086 115 CWLVPRLADFTRRYPSISLTILTGNENVNFQ--RAGIDLAIYFD 156 (311)
T ss_pred HHHHHHHHHHHHHCCCeEEEEEeCCcccCCc--cCCccEEEEeC
Confidence 4666899999999999999999866544332 34778777654
No 191
>PF00551 Formyl_trans_N: Formyl transferase; InterPro: IPR002376 A number of formyl transferases belong to this group. Methionyl-tRNA formyltransferase transfers a formyl group onto the amino terminus of the acyl moiety of the methionyl aminoacyl-tRNA. The formyl group appears to play a dual role in the initiator identity of N-formylmethionyl-tRNA by promoting its recognition by IF2 and by impairing its binding to EFTU-GTP. Formyltetrahydrofolate dehydrogenase produces formate from formyl- tetrahydrofolate. This is the N-terminal domain of these enzymes and is found upstream of the C-terminal domain (IPR005793 from INTERPRO). The trifunctional glycinamide ribonucleotide synthetase-aminoimidazole ribonucleotide synthetase-glycinamide ribonucleotide transformylase catalyses the second, third and fifth steps in de novo purine biosynthesis. The glycinamide ribonucleotide transformylase belongs to this group.; GO: 0016742 hydroxymethyl-, formyl- and related transferase activity, 0009058 biosynthetic process; PDB: 3P9X_B 3OBI_A 3R8X_A 3KCQ_C 3RFO_D 3AV3_A 3N0V_D 3LOU_A 3O1L_A 4DS3_A ....
Probab=21.67 E-value=1.7e+02 Score=26.52 Aligned_cols=93 Identities=14% Similarity=0.134 Sum_probs=48.6
Q ss_pred cEEEEEcCCChhHHHhHHHHHHHHHHHCCCcEEEEEEcCCchHh---hhcCCCCCEEEEecCCCCCCChH-HHHHHHHHh
Q 015881 123 RRCCCIISGGVYENLLFFPAIQLLKDRYPGVLIDVIASARGKQT---FELNKNVRWANVYDLDDDWPEPA-EYTDILGVM 198 (399)
Q Consensus 123 ~rILIIr~~~IGDvVLttPalraLK~~yP~A~IdvLv~~~~~~l---le~nP~ID~Vi~~d~k~~~~~~~-~~~~l~~~L 198 (399)
|||+++-.+.- -....++.+|++.-.+++|..++...-+.. ......+-..+ ++... +..-. .--.++..|
T Consensus 1 mrI~~~~Sg~~---~~~~~~l~~l~~~~~~~~iv~Vit~~~~~~~~~~~~~~~~~~~~-~~~~~-~~~~~~~~~~~~~~l 75 (181)
T PF00551_consen 1 MRIVFFGSGSG---SFLKALLEALKARGHNVEIVLVITNPDKPRGRSRAIKNGIPAQV-ADEKN-FQPRSENDEELLELL 75 (181)
T ss_dssp EEEEEEESSSS---HHHHHHHHHHHTTSSEEEEEEEEESSTTTHHHHHHHHTTHHEEE-HHGGG-SSSHHHHHHHHHHHH
T ss_pred CEEEEEEcCCC---HHHHHHHHHHHhCCCCceEEEEeccccccccccccccCCCCEEe-ccccC-CCchHhhhhHHHHHH
Confidence 78888844332 335566889998887788888774433222 11122222222 22211 11111 123578889
Q ss_pred hhCCCcEEEEcCC-CChHHHHHH
Q 015881 199 KNRYYDMVLSTKL-AGLGHAAFL 220 (399)
Q Consensus 199 R~~~YDlvIdl~~-~~~rsAll~ 220 (399)
++.++|++|...- .-....++.
T Consensus 76 ~~~~~Dl~v~~~~~~il~~~~l~ 98 (181)
T PF00551_consen 76 ESLNPDLIVVAGYGRILPKEFLS 98 (181)
T ss_dssp HHTT-SEEEESS-SS---HHHHH
T ss_pred HhhccceeehhhhHHHhhhhhhh
Confidence 9999999998753 313344443
No 192
>cd08458 PBP2_NocR The C-terminal substrate-domain of LysR-type transcriptional regulator, NocR, involved in the catabolism of nopaline, contains the type 2 periplasmic binding fold. This CD includes the C-terminal substrate-domain of LysR-type transcriptional regulator NocR, which is involved in the catabolism of nopaline. Opines are low molecular weight compounds found in plant crown gall tumors produced by the parasitic bacterium Agrobacterium. There are at least 30 different opines identified so far. Opines are utilized by tumor-colonizing bacteria as a source of carbon, nitrogen, and energy. In Agrobacterium tumefaciens, NocR regulates expression of the divergently transcribed nocB and nocR genes of the nopaline catabolism (noc) region. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, an
Probab=21.49 E-value=1.9e+02 Score=24.81 Aligned_cols=41 Identities=15% Similarity=0.120 Sum_probs=28.1
Q ss_pred hHHHHHHHHHHHCCCcEEEEEEcCCchHhhhc--CCCCCEEEEe
Q 015881 138 LFFPAIQLLKDRYPGVLIDVIASARGKQTFEL--NKNVRWANVY 179 (399)
Q Consensus 138 LttPalraLK~~yP~A~IdvLv~~~~~~lle~--nP~ID~Vi~~ 179 (399)
+..++++.++++||+++|++.... ..++.+. +..+|=.+.+
T Consensus 14 ~l~~~l~~f~~~~P~v~i~~~~~~-~~~~~~~l~~g~~Dl~i~~ 56 (196)
T cd08458 14 FMSGVIQTFIADRPDVSVYLDTVP-SQTVLELVSLQHYDLGISI 56 (196)
T ss_pred hhHHHHHHHHHHCCCcEEEEeccC-hHHHHHHHHcCCCCEEEEe
Confidence 456899999999999999997654 2233321 3466665554
No 193
>PRK12361 hypothetical protein; Provisional
Probab=21.32 E-value=3.8e+02 Score=28.77 Aligned_cols=30 Identities=7% Similarity=-0.049 Sum_probs=16.2
Q ss_pred HHHHHHHHhhhCCCcEEEEcCCCChHHHHH
Q 015881 190 EYTDILGVMKNRYYDMVLSTKLAGLGHAAF 219 (399)
Q Consensus 190 ~~~~l~~~LR~~~YDlvIdl~~~~~rsAll 219 (399)
+..+++.+.++++=.+.|.....--||+.+
T Consensus 163 ~a~~~i~~~~~~~~~VlVHC~~G~sRSa~v 192 (547)
T PRK12361 163 QAINWIHRQVRANKSVVVHCALGRGRSVLV 192 (547)
T ss_pred HHHHHHHHHHHCCCeEEEECCCCCCcHHHH
Confidence 334566666666556666554432455543
No 194
>PF03808 Glyco_tran_WecB: Glycosyl transferase WecB/TagA/CpsF family; InterPro: IPR004629 The WecG member of this superfamily, believed to be UDP-N-acetyl-D-mannosaminuronic acid transferase, plays a role in Enterobacterial common antigen (eca) synthesis in Escherichia coli. Another family member, the Bacillus subtilis TagA protein, is involved in the biosynthesis of the cell wall polymer poly(glycerol phosphate). The third family member, CpsF, CMP-N-acetylneuraminic acid synthetase has a role in the capsular polysaccharide biosynthesis pathway.; GO: 0009058 biosynthetic process
Probab=21.28 E-value=1.9e+02 Score=26.08 Aligned_cols=44 Identities=5% Similarity=0.179 Sum_probs=30.5
Q ss_pred CCHHHHHHHHHHhhhCC-CEEEeCCchh--HHHHHHHHhcCCCCcee
Q 015881 336 LPIQVWAEIANGLREFR-PLFVIPHEKE--REGVEDVVGDDASIVFI 379 (399)
Q Consensus 336 WP~e~faeLa~~L~~~~-~VvliGgp~E--~e~aeeI~~~~~~~~~i 379 (399)
=+.+-+.+|.+...+.+ +|+++|+..| ++.++.+.+..+++.++
T Consensus 32 ~g~dl~~~l~~~~~~~~~~ifllG~~~~~~~~~~~~l~~~yP~l~iv 78 (172)
T PF03808_consen 32 TGSDLFPDLLRRAEQRGKRIFLLGGSEEVLEKAAANLRRRYPGLRIV 78 (172)
T ss_pred CHHHHHHHHHHHHHHcCCeEEEEeCCHHHHHHHHHHHHHHCCCeEEE
Confidence 35567777888777665 8888888776 34555677777776643
No 195
>PF13614 AAA_31: AAA domain; PDB: 2VED_B 2PH1_A 3EA0_B 3FKQ_A 3KB1_B 1ION_A 3LA6_H 3BFV_B 3CIO_D.
Probab=21.11 E-value=49 Score=28.42 Aligned_cols=53 Identities=15% Similarity=0.288 Sum_probs=38.9
Q ss_pred CCCHHHHHHHHHHhhhCCCEEEe--CCchhHHHHHHHHhcCCCCceeecCCcccc
Q 015881 335 LLPIQVWAEIANGLREFRPLFVI--PHEKEREGVEDVVGDDASIVFITTPGQVRM 387 (399)
Q Consensus 335 rWP~e~faeLa~~L~~~~~Vvli--Ggp~E~e~aeeI~~~~~~~~~i~~~G~ls~ 387 (399)
.+..+.|.++++.|.+.+.+|++ |..-+......+.+.+..++++..++..++
T Consensus 101 ~~~~~~~~~li~~l~~~yd~IivD~~~~~~~~~~~~~l~~~D~ii~v~~~~~~s~ 155 (157)
T PF13614_consen 101 ELTPEDVEELIDALKEHYDYIIVDLPSSLSNPDTQAVLELADKIILVVRPDVTSI 155 (157)
T ss_dssp HHTSHHHHHHHHHHHHHSSEEEEEEESTTTHTHHHHHHTTHSEEEEEEETTHHHH
T ss_pred hcCHHHHHHHHHHHHHcCCEEEEECcCCccHHHHHHHHHHCCEEEEEECCCcccc
Confidence 47889999999999987655554 555566666668888888776766665544
No 196
>cd03825 GT1_wcfI_like This family is most closely related to the GT1 family of glycosyltransferases. wcfI in Bacteroides fragilis has been shown to be involved in the capsular polysaccharide biosynthesis.
Probab=20.82 E-value=1.9e+02 Score=27.67 Aligned_cols=39 Identities=8% Similarity=0.083 Sum_probs=26.4
Q ss_pred cEEEEEcCCCh--hHHHhHHHHHHHHHHHCCCcEEEEEEcCCc
Q 015881 123 RRCCCIISGGV--YENLLFFPAIQLLKDRYPGVLIDVIASARG 163 (399)
Q Consensus 123 ~rILIIr~~~I--GDvVLttPalraLK~~yP~A~IdvLv~~~~ 163 (399)
||||++..+.. |-...+.=+.++|+++ +.++++++....
T Consensus 1 MkIl~~~~~~~~gG~~~~~~~l~~~l~~~--G~~v~v~~~~~~ 41 (365)
T cd03825 1 MKVLHLNTSDISGGAARAAYRLHRALQAA--GVDSTMLVQEKK 41 (365)
T ss_pred CeEEEEecCCCCCcHHHHHHHHHHHHHhc--CCceeEEEeecc
Confidence 79999976543 3345555678888886 557777775543
No 197
>cd04733 OYE_like_2_FMN Old yellow enzyme (OYE)-related FMN binding domain, group 2. Each monomer of OYE contains FMN as a non-covalently bound cofactor, uses NADPH as a reducing agent with oxygens, quinones, and alpha,beta-unsaturated aldehydes and ketones, and can act as electron acceptors in the catalytic reaction. Other members of OYE family include trimethylamine dehydrogenase, 2,4-dienoyl-CoA reductase, enoate reductase, pentaerythriol tetranitrate reductase, xenobiotic reductase, and morphinone reductase.
Probab=20.71 E-value=5.9e+02 Score=25.41 Aligned_cols=79 Identities=19% Similarity=0.256 Sum_probs=45.2
Q ss_pred CHHHHHHHHHHHHHhCCCCCCeEEEEcCCCCccccccCCCCCCCCCCHHHHHHHHHHhhhCC--CEEEeCCchhHHHHHH
Q 015881 291 SRRLKEVVAEKYKNAGAEQGKYIVIHGIESDSKASMQSRGDTDSLLPIQVWAEIANGLREFR--PLFVIPHEKEREGVED 368 (399)
Q Consensus 291 s~e~~~~a~~~l~~~gl~~~~~IvIhPgas~~~~~~k~rg~~~KrWP~e~faeLa~~L~~~~--~VvliGgp~E~e~aee 368 (399)
+.++....-+.+++.|+ .+|-+|.|......... +......++..+|.++++.+++.. +|+..|+-.+.+.+++
T Consensus 234 ~~eea~~ia~~Le~~Gv---d~iev~~g~~~~~~~~~-~~~~~~~~~~~~~~~~~~~ik~~v~iPVi~~G~i~t~~~a~~ 309 (338)
T cd04733 234 TEEDALEVVEALEEAGV---DLVELSGGTYESPAMAG-AKKESTIAREAYFLEFAEKIRKVTKTPLMVTGGFRTRAAMEQ 309 (338)
T ss_pred CHHHHHHHHHHHHHcCC---CEEEecCCCCCCccccc-cccCCccccchhhHHHHHHHHHHcCCCEEEeCCCCCHHHHHH
Confidence 33443334445666665 37777766432210000 000011134456778888887753 8888898888888888
Q ss_pred HHhcC
Q 015881 369 VVGDD 373 (399)
Q Consensus 369 I~~~~ 373 (399)
+++..
T Consensus 310 ~l~~g 314 (338)
T cd04733 310 ALASG 314 (338)
T ss_pred HHHcC
Confidence 87753
No 198
>TIGR00623 sula cell division inhibitor SulA. All proteins in this family for which the functions are known are cell division inhibitors. In E. coli, SulA is one of the SOS regulated genes.
Probab=20.66 E-value=4.3e+02 Score=24.27 Aligned_cols=85 Identities=9% Similarity=0.063 Sum_probs=55.8
Q ss_pred cCCccEEEEEc-CCChhHHHhHHHHHHHHHHHCCCcEEEEEEcCC--chHhhhcC-CCCCEEEEecCCCCCCChHHHHHH
Q 015881 119 RGDVRRCCCII-SGGVYENLLFFPAIQLLKDRYPGVLIDVIASAR--GKQTFELN-KNVRWANVYDLDDDWPEPAEYTDI 194 (399)
Q Consensus 119 ~~~v~rILIIr-~~~IGDvVLttPalraLK~~yP~A~IdvLv~~~--~~~lle~n-P~ID~Vi~~d~k~~~~~~~~~~~l 194 (399)
++.+--|+.=. .-++|.. |..|+++.|-.. +-.|.|+..|. .++.++.. =.+++|+.+...+. ....+.+
T Consensus 29 ~g~vsEl~~~~~~pg~~el-LLlP~L~~Ls~~--~Rwlv~IaPP~~~~~~~L~~~Gl~l~rvlli~~~~~---~d~lwa~ 102 (168)
T TIGR00623 29 AGLISEVVYREDQPMMAQL-LLLPLLQQLGQQ--SRWQLWLTPQQKLSKEWVQSSGLPLTKVMQISQLSP---CNTVESM 102 (168)
T ss_pred CCcceEEeecCCCchhHHH-HHHHHHHHhccc--CceEEEECCCCccCHHHHHHcCCChhHEEEEecCCc---hhHHHHH
Confidence 34445555543 3677888 899999988752 44577777663 35555543 46678877754322 1234678
Q ss_pred HHHhhhCCCcEEEEc
Q 015881 195 LGVMKNRYYDMVLST 209 (399)
Q Consensus 195 ~~~LR~~~YDlvIdl 209 (399)
-+.||...|..||.=
T Consensus 103 EQaLrSG~c~aVL~W 117 (168)
T TIGR00623 103 IRALRTGNYSVVIGW 117 (168)
T ss_pred HHHHHhCCCcEEEec
Confidence 888999999999975
No 199
>cd08416 PBP2_MdcR The C-terminal substrate-binding domian of LysR-type transcriptional regulator MdcR, which involved in the malonate catabolism contains the type 2 periplasmic binding fold. This family includes the C-terminal substrate binding domain of LysR-type transcriptional regulator (LTTR) MdcR that controls the expression of the malonate decarboxylase (mdc) genes. Like other members of the LTTRs, MdcR is a positive regulatory protein for its target promoter and composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins (PBP2). The PBP2 are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these dom
Probab=20.60 E-value=2.4e+02 Score=23.83 Aligned_cols=42 Identities=17% Similarity=0.066 Sum_probs=27.9
Q ss_pred hHHHHHHHHHHHCCCcEEEEEEcCCchHhhh--cCCCCCEEEEec
Q 015881 138 LFFPAIQLLKDRYPGVLIDVIASARGKQTFE--LNKNVRWANVYD 180 (399)
Q Consensus 138 LttPalraLK~~yP~A~IdvLv~~~~~~lle--~nP~ID~Vi~~d 180 (399)
+..+++..++++||+++|.+...... ++++ .+-.+|=+|.+.
T Consensus 14 ~l~~~l~~~~~~~P~i~l~i~~~~~~-~~~~~l~~~~~Dl~i~~~ 57 (199)
T cd08416 14 TVPRIIMGLKLRRPELDIELTLGSNK-DLLKKLKDGELDAILVAT 57 (199)
T ss_pred hhHHHHHHHHHhCCCeEEEEEEcCcH-HHHHHHhCCCCCEEEEec
Confidence 45689999999999999999875432 2211 223466666543
No 200
>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=20.59 E-value=73 Score=31.51 Aligned_cols=97 Identities=19% Similarity=0.229 Sum_probs=51.3
Q ss_pred cccCCCCCcccccCcccc----cCCccEEEEEcCCChhHHHhHHHHHHHHHHHCCCcEEEEEEcCCchHhhhcCCCCCEE
Q 015881 101 LKFPMGFNPEIASLPLKI----RGDVRRCCCIISGGVYENLLFFPAIQLLKDRYPGVLIDVIASARGKQTFELNKNVRWA 176 (399)
Q Consensus 101 ~~~~~~~~~~~~~~~~~~----~~~v~rILIIr~~~IGDvVLttPalraLK~~yP~A~IdvLv~~~~~~lle~nP~ID~V 176 (399)
.-||.-|+-|..---.++ .+.-||.+||..+--| ++++++.+|+.-||. -+++.....
T Consensus 37 ~tyPdnf~~e~EttIskI~~lAdDp~mKaIVv~q~vpG----t~~af~kIkekRpDI--l~ia~~~~E------------ 98 (275)
T PF12683_consen 37 VTYPDNFMSEQETTISKIVSLADDPDMKAIVVSQAVPG----TAEAFRKIKEKRPDI--LLIAGEPHE------------ 98 (275)
T ss_dssp EE--TTGGGCHHHHHHHHHGGGG-TTEEEEEEE-SS-------HHHHHHHHHH-TTS--EEEESS--S------------
T ss_pred EeCCCcccchHHHHHHHHHHhccCCCccEEEEeCCCcc----hHHHHHHHHhcCCCe--EEEcCCCcC------------
Confidence 357888888743222221 2557999999998888 889999999999993 333332221
Q ss_pred EEecCCCCCCChHHHHHHHHHhhhCCCcEEEEcCCC--ChHHHHHHHHhCCCeEEEecC
Q 015881 177 NVYDLDDDWPEPAEYTDILGVMKNRYYDMVLSTKLA--GLGHAAFLFMTTARDRVSYIY 233 (399)
Q Consensus 177 i~~d~k~~~~~~~~~~~l~~~LR~~~YDlvIdl~~~--~~rsAll~~LsgA~~RIGy~~ 233 (399)
| + .+ | ....|++++...- |......+.-.||+.=|-|..
T Consensus 99 ---D-------p----~~---i-~~~aDi~~~~D~~~~G~~i~~~Ak~mGAktFVh~sf 139 (275)
T PF12683_consen 99 ---D-------P----EV---I-SSAADIVVNPDEISRGYTIVWAAKKMGAKTFVHYSF 139 (275)
T ss_dssp -----------H----HH---H-HHHSSEEEE--HHHHHHHHHHHHHHTT-S-EEEEEE
T ss_pred ---C-------H----HH---H-hhccCeEeccchhhccHHHHHHHHHcCCceEEEEec
Confidence 0 1 11 1 3457999886544 123344566678887777663
No 201
>cd03819 GT1_WavL_like This family is most closely related to the GT1 family of glycosyltransferases. WavL in Vibrio cholerae has been shown to be involved in the biosynthesis of the lipopolysaccharide core.
Probab=20.59 E-value=7.4e+02 Score=23.52 Aligned_cols=91 Identities=15% Similarity=0.060 Sum_probs=48.4
Q ss_pred CChhHHHhHHHHHHHHHHHCCCcEEEEEEcCCc-hHhhhcCCCCCEEEEecCC--CCCCChHHHHHHHHHhhhCCCcEEE
Q 015881 131 GGVYENLLFFPAIQLLKDRYPGVLIDVIASARG-KQTFELNKNVRWANVYDLD--DDWPEPAEYTDILGVMKNRYYDMVL 207 (399)
Q Consensus 131 ~~IGDvVLttPalraLK~~yP~A~IdvLv~~~~-~~lle~nP~ID~Vi~~d~k--~~~~~~~~~~~l~~~LR~~~YDlvI 207 (399)
++++-+++ -+.++|+++ +.++.+++.... ...++. ..++ ++.+... ..+..+..+..+.+.+++.++|+++
T Consensus 10 gG~e~~~~--~l~~~L~~~--g~~v~v~~~~~~~~~~~~~-~~~~-~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~dii~ 83 (355)
T cd03819 10 GGVERGTL--ELARALVER--GHRSLVASAGGRLVAELEA-EGSR-HIKLPFISKNPLRILLNVARLRRLIREEKVDIVH 83 (355)
T ss_pred CcHHHHHH--HHHHHHHHc--CCEEEEEcCCCchHHHHHh-cCCe-EEEccccccchhhhHHHHHHHHHHHHHcCCCEEE
Confidence 44444444 457888876 778888875432 233332 2343 3333321 1122334456677889999999998
Q ss_pred EcCCCC-hHHHHHHHHhCCCe
Q 015881 208 STKLAG-LGHAAFLFMTTARD 227 (399)
Q Consensus 208 dl~~~~-~rsAll~~LsgA~~ 227 (399)
...... +...+.....+++.
T Consensus 84 ~~~~~~~~~~~~~~~~~~~~~ 104 (355)
T cd03819 84 ARSRAPAWSAYLAARRTRPPF 104 (355)
T ss_pred ECCCchhHHHHHHHHhcCCCE
Confidence 754331 22222334445553
No 202
>PF13579 Glyco_trans_4_4: Glycosyl transferase 4-like domain; PDB: 3C4Q_B 3C4V_A 3C48_B 1Z2T_A.
Probab=20.56 E-value=2.9e+02 Score=22.55 Aligned_cols=91 Identities=13% Similarity=-0.007 Sum_probs=39.3
Q ss_pred HHHHHHHHHHHCCCcEEEEEEcCCchHhhh-cCCCCCEEEEecCCCC---CCChHHHHHHHHHh--hhCCCcEEEEcCCC
Q 015881 139 FFPAIQLLKDRYPGVLIDVIASARGKQTFE-LNKNVRWANVYDLDDD---WPEPAEYTDILGVM--KNRYYDMVLSTKLA 212 (399)
Q Consensus 139 ttPalraLK~~yP~A~IdvLv~~~~~~lle-~nP~ID~Vi~~d~k~~---~~~~~~~~~l~~~L--R~~~YDlvIdl~~~ 212 (399)
+.=++++|.++ +.++++++........+ ....+ .++.++.... +..+..+..+.+.+ ++++||++......
T Consensus 7 ~~~l~~~L~~~--G~~V~v~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~Dvv~~~~~~ 83 (160)
T PF13579_consen 7 VRELARALAAR--GHEVTVVTPQPDPEDDEEEEDGV-RVHRLPLPRRPWPLRLLRFLRRLRRLLAARRERPDVVHAHSPT 83 (160)
T ss_dssp HHHHHHHHHHT--T-EEEEEEE---GGG-SEEETTE-EEEEE--S-SSSGGGHCCHHHHHHHHCHHCT---SEEEEEHHH
T ss_pred HHHHHHHHHHC--CCEEEEEecCCCCcccccccCCc-eEEeccCCccchhhhhHHHHHHHHHHHhhhccCCeEEEecccc
Confidence 34467788888 77999998655544321 11222 2333332211 11222344555666 89999999865422
Q ss_pred ChHHHHHHH-HhCCCeEEEec
Q 015881 213 GLGHAAFLF-MTTARDRVSYI 232 (399)
Q Consensus 213 ~~rsAll~~-LsgA~~RIGy~ 232 (399)
....+.++. ..++|..+-..
T Consensus 84 ~~~~~~~~~~~~~~p~v~~~h 104 (160)
T PF13579_consen 84 AGLVAALARRRRGIPLVVTVH 104 (160)
T ss_dssp HHHHHHHHHHHHT--EEEE-S
T ss_pred hhHHHHHHHHccCCcEEEEEC
Confidence 111222333 55677655443
No 203
>TIGR01369 CPSaseII_lrg carbamoyl-phosphate synthase, large subunit. In several thermophilic species (Methanobacterium thermoautotrophicum, Methanococcus jannaschii, Aquifex aeolicus), the large subunit appears split, at different points, into two separate genes.
Probab=20.45 E-value=3.5e+02 Score=31.76 Aligned_cols=82 Identities=18% Similarity=0.169 Sum_probs=52.9
Q ss_pred cCCccEEEEEcCCC--hhHH----HhHHHHHHHHHHHCCCcEEEEEEcCCchHhhhcCCCCCEEEEecCCCCCCChHHHH
Q 015881 119 RGDVRRCCCIISGG--VYEN----LLFFPAIQLLKDRYPGVLIDVIASARGKQTFELNKNVRWANVYDLDDDWPEPAEYT 192 (399)
Q Consensus 119 ~~~v~rILIIr~~~--IGDv----VLttPalraLK~~yP~A~IdvLv~~~~~~lle~nP~ID~Vi~~d~k~~~~~~~~~~ 192 (399)
|.+++|||||-.+. ||.. --.+.++++||+. +.++.++..... .+.......|+++..+. . . -
T Consensus 3 ~~~~~kvlviG~g~~~igq~~e~d~sg~q~~kalke~--G~~vi~v~~np~-~~~~~~~~aD~~y~~p~-~----~---~ 71 (1050)
T TIGR01369 3 RTDIKKILVIGSGPIVIGQAAEFDYSGSQACKALKEE--GYRVILVNSNPA-TIMTDPEMADKVYIEPL-T----P---E 71 (1050)
T ss_pred CCCCcEEEEECCCcchhcchhcccchHHHHHHHHHHc--CCEEEEEecchh-hccCChhcCCEEEECCC-C----H---H
Confidence 46689999998876 6632 3456889999986 777666654332 22233345677766542 1 1 2
Q ss_pred HHHHHhhhCCCcEEEEcCC
Q 015881 193 DILGVMKNRYYDMVLSTKL 211 (399)
Q Consensus 193 ~l~~~LR~~~YDlvIdl~~ 211 (399)
.+.+.+++++.|.++-..+
T Consensus 72 ~v~~ii~~e~~DaIlp~~g 90 (1050)
T TIGR01369 72 AVEKIIEKERPDAILPTFG 90 (1050)
T ss_pred HHHHHHHHhCCCEEEECCC
Confidence 3456677889999997543
No 204
>cd08430 PBP2_IlvY The C-terminal substrate binding of LysR-type transcriptional regulator IlvY, which activates the expression of ilvC gene that encoding acetohydroxy acid isomeroreductase for the biosynthesis of branched amino acids; contains the type 2 periplasmic binding fold. In Escherichia coli, IlvY is required for the regulation of ilvC gene expression that encodes acetohydroxy acid isomeroreductase (AHIR), a key enzyme in the biosynthesis of branched-chain amino acids (isoleucine, valine, and leucine). The ilvGMEDA operon genes encode remaining enzyme activities required for the biosynthesis of these amino acids. Activation of ilvC transcription by IlvY requires the additional binding of a co-inducer molecule (either alpha-acetolactate or alpha-acetohydoxybutyrate, the substrates for AHIR) to a preformed complex of IlvY protein-DNA. Like many other LysR-family members, IlvY negatively auto-regulates the transcription of its own divergently transcribed ilvY gene in an inducer-i
Probab=20.35 E-value=2.2e+02 Score=24.08 Aligned_cols=39 Identities=18% Similarity=0.241 Sum_probs=27.4
Q ss_pred HHHHHHHHHHCCCcEEEEEEcCCchHhhh--cCCCCCEEEEe
Q 015881 140 FPAIQLLKDRYPGVLIDVIASARGKQTFE--LNKNVRWANVY 179 (399)
Q Consensus 140 tPalraLK~~yP~A~IdvLv~~~~~~lle--~nP~ID~Vi~~ 179 (399)
.+++..++++||+++|.+..... .++++ .+..+|=++.+
T Consensus 16 ~~~l~~~~~~~P~v~l~~~~~~~-~~~~~~l~~g~~Dl~i~~ 56 (199)
T cd08430 16 PPILERFRAQHPQVEIKLHTGDP-ADAIDKVLNGEADIAIAA 56 (199)
T ss_pred cHHHHHHHHHCCCceEEEEeCCH-HHHHHHHHCCCCCEEEEe
Confidence 68899999999999999987543 22322 23566766665
No 205
>PRK00005 fmt methionyl-tRNA formyltransferase; Reviewed
Probab=20.31 E-value=3.3e+02 Score=26.96 Aligned_cols=72 Identities=11% Similarity=0.143 Sum_probs=41.8
Q ss_pred cEEEEEcCCChhHHHhHHHHHHHHHHHCCCcEEEEEEc-CCc-------------hHhhhcCCCCCEEEEecCCCCCCCh
Q 015881 123 RRCCCIISGGVYENLLFFPAIQLLKDRYPGVLIDVIAS-ARG-------------KQTFELNKNVRWANVYDLDDDWPEP 188 (399)
Q Consensus 123 ~rILIIr~~~IGDvVLttPalraLK~~yP~A~IdvLv~-~~~-------------~~lle~nP~ID~Vi~~d~k~~~~~~ 188 (399)
|||+++ |..-++.|++++|.+. +.+|..++. +.. ++..+ .-+|. ++..+ + ...
T Consensus 1 mkIvf~-----G~~~~a~~~L~~L~~~--~~~i~~Vvt~~~~~~~r~~~~~~~~v~~~a~-~~~Ip-~~~~~--~-~~~- 67 (309)
T PRK00005 1 MRIVFM-----GTPEFAVPSLKALLES--GHEVVAVVTQPDRPAGRGKKLTPSPVKQLAL-EHGIP-VLQPE--K-LRD- 67 (309)
T ss_pred CEEEEE-----CCCHHHHHHHHHHHHC--CCcEEEEECCCCCCCCCCCCCCCCHHHHHHH-HcCCC-EECcC--C-CCC-
Confidence 577765 6666889999999885 567776663 211 12222 22343 22221 1 111
Q ss_pred HHHHHHHHHhhhCCCcEEEEcC
Q 015881 189 AEYTDILGVMKNRYYDMVLSTK 210 (399)
Q Consensus 189 ~~~~~l~~~LR~~~YDlvIdl~ 210 (399)
-.++..|++.+.|++|...
T Consensus 68 ---~~~~~~l~~~~~Dliv~~~ 86 (309)
T PRK00005 68 ---PEFLAELAALNADVIVVVA 86 (309)
T ss_pred ---HHHHHHHHhcCcCEEEEeh
Confidence 1346678888999998764
No 206
>cd08441 PBP2_MetR The C-terminal substrate binding domain of LysR-type transcriptional regulator metR, which regulates the expression of methionine biosynthetic genes, contains type 2 periplasmic binding fold. MetR, a member of the LysR family, is a positive regulator for the metA, metE, metF, and metH genes. The sulfur-containing amino acid methionine is the universal initiator of protein synthesis in all known organisms and its derivative S-adenosylmethionine (SAM) and autoinducer-2 (AI-2) are involved in various cellular processes. SAM plays a central role as methyl donor in methylation reactions, which are essential for the biosynthesis of phospholipids, proteins, DNA and RNA. The interspecies signaling molecule AI-2 is involved in cell-cell communication process (quorum sensing) and gene regulation in bacteria. Although methionine biosynthetic enzymes and metabolic pathways are well conserved in bacteria, the regulation of methionine biosynthesis involves various regulatory mecha
Probab=20.25 E-value=1.2e+02 Score=25.98 Aligned_cols=24 Identities=21% Similarity=0.610 Sum_probs=20.3
Q ss_pred hHHHHHHHHHHHCCCcEEEEEEcC
Q 015881 138 LFFPAIQLLKDRYPGVLIDVIASA 161 (399)
Q Consensus 138 LttPalraLK~~yP~A~IdvLv~~ 161 (399)
+..|++..++++||+++|.+....
T Consensus 14 ~~~~~l~~~~~~~P~i~i~i~~~~ 37 (198)
T cd08441 14 WLMPVLDQFRERWPDVELDLSSGF 37 (198)
T ss_pred hhHHHHHHHHHhCCCeEEEEEeCC
Confidence 356899999999999999987643
No 207
>PRK09280 F0F1 ATP synthase subunit beta; Validated
Probab=20.10 E-value=6.4e+02 Score=26.90 Aligned_cols=104 Identities=14% Similarity=0.095 Sum_probs=71.7
Q ss_pred cccCcccccCCccEEEEEcCCChhHHHhHHHHHHHHHHHCCCcEEEEEEcCCchHh---hhcCC---CCCE-EEEecCCC
Q 015881 111 IASLPLKIRGDVRRCCCIISGGVYENLLFFPAIQLLKDRYPGVLIDVIASARGKQT---FELNK---NVRW-ANVYDLDD 183 (399)
Q Consensus 111 ~~~~~~~~~~~v~rILIIr~~~IGDvVLttPalraLK~~yP~A~IdvLv~~~~~~l---le~nP---~ID~-Vi~~d~k~ 183 (399)
|..|..-.+ -.||+|+-.++.|=..|..=+++..++.+++.-|-.++..+..++ ++... ..++ |++....+
T Consensus 135 ID~l~pigk--GQR~gIfa~~GvGKt~Ll~~i~~~~~~~~~~v~V~~liGER~rEv~efi~~~~~~~~l~rsvvV~atsd 212 (463)
T PRK09280 135 IDLLAPYAK--GGKIGLFGGAGVGKTVLIQELINNIAKEHGGYSVFAGVGERTREGNDLYHEMKESGVLDKTALVFGQMN 212 (463)
T ss_pred ecccCCccc--CCEEEeecCCCCChhHHHHHHHHHHHhcCCCEEEEEEeccCcHHHHHHHHHHHhcCCcceeEEEEECCC
Confidence 333444444 379999999999999999999999998889999988998888764 44332 2333 44444433
Q ss_pred CCCChHH------HHHHHHHhhh-CCCcEEEEcCCCChHHHH
Q 015881 184 DWPEPAE------YTDILGVMKN-RYYDMVLSTKLAGLGHAA 218 (399)
Q Consensus 184 ~~~~~~~------~~~l~~~LR~-~~YDlvIdl~~~~~rsAl 218 (399)
. .-..+ -..+...+|. +.+|+.|-+.+- .|.|-
T Consensus 213 ~-p~~~r~~a~~~a~tiAEyfrd~~G~~VLll~Dsl-TR~A~ 252 (463)
T PRK09280 213 E-PPGARLRVALTGLTMAEYFRDVEGQDVLLFIDNI-FRFTQ 252 (463)
T ss_pred C-CHHHHHHHHHHHHHHHHHHHHhcCCceEEEecch-HHHHH
Confidence 2 11111 1346677999 999999988877 55544
No 208
>PRK10632 transcriptional regulator; Provisional
Probab=20.09 E-value=3.3e+02 Score=26.25 Aligned_cols=54 Identities=7% Similarity=0.078 Sum_probs=36.1
Q ss_pred EEEEEcCCChhHHHhHHHHHHHHHHHCCCcEEEEEEcCCchHhhhcCCCCCEEEEec
Q 015881 124 RCCCIISGGVYENLLFFPAIQLLKDRYPGVLIDVIASARGKQTFELNKNVRWANVYD 180 (399)
Q Consensus 124 rILIIr~~~IGDvVLttPalraLK~~yP~A~IdvLv~~~~~~lle~nP~ID~Vi~~d 180 (399)
+|-|-....++. -+..++++.+.+.||+++|++........+.+ ..+|=+|...
T Consensus 93 ~l~I~~~~~~~~-~~l~~~l~~~~~~~P~i~i~l~~~~~~~~l~~--~~~Dl~i~~~ 146 (309)
T PRK10632 93 TLRIGCSSTMAQ-NVLAGLTAKMLKEYPGLSVNLVTGIPAPDLIA--DGLDVVIRVG 146 (309)
T ss_pred EEEEeccHHHHH-HHHHHHHHHHHHHCCCeEEEEEecCcccCccc--CCeeEEEEec
Confidence 333333444444 44568999999999999999988655444444 3577777654
No 209
>PLN02735 carbamoyl-phosphate synthase
Probab=20.05 E-value=3.4e+02 Score=32.13 Aligned_cols=82 Identities=18% Similarity=0.172 Sum_probs=51.6
Q ss_pred cCCccEEEEEcCCC--hhHH----HhHHHHHHHHHHHCCCcEEEEEEcCCchHhhhcCCCCCEEEEecCCCCCCChHHHH
Q 015881 119 RGDVRRCCCIISGG--VYEN----LLFFPAIQLLKDRYPGVLIDVIASARGKQTFELNKNVRWANVYDLDDDWPEPAEYT 192 (399)
Q Consensus 119 ~~~v~rILIIr~~~--IGDv----VLttPalraLK~~yP~A~IdvLv~~~~~~lle~nP~ID~Vi~~d~k~~~~~~~~~~ 192 (399)
|.+++||||+-.+. ||-. .-.+.++++||+. +.++..+-... ..+.......|+++..+. . . +
T Consensus 20 ~~~~kkVLiiGsG~~~igqa~e~d~SG~q~~kaLke~--G~~Vi~vd~np-~t~~~~~~~aD~~yi~p~-~----~-e-- 88 (1102)
T PLN02735 20 RTDLKKIMILGAGPIVIGQACEFDYSGTQACKALKEE--GYEVVLINSNP-ATIMTDPETADRTYIAPM-T----P-E-- 88 (1102)
T ss_pred ccCCCEEEEECCCccccccceeecchHHHHHHHHHHc--CCEEEEEeCCc-ccccCChhhCcEEEeCCC-C----H-H--
Confidence 55689999998887 4522 4467899999988 66765554322 222223334677765332 1 1 1
Q ss_pred HHHHHhhhCCCcEEEEcCC
Q 015881 193 DILGVMKNRYYDMVLSTKL 211 (399)
Q Consensus 193 ~l~~~LR~~~YDlvIdl~~ 211 (399)
.+.+.+++++.|.++-.-+
T Consensus 89 ~v~~ii~~e~~D~Iip~~g 107 (1102)
T PLN02735 89 LVEQVIAKERPDALLPTMG 107 (1102)
T ss_pred HHHHHHHHhCCCEEEECCC
Confidence 2445578899999997643
No 210
>cd08425 PBP2_CynR The C-terminal substrate-binding domain of the LysR-type transcriptional regulator CynR, contains the type 2 periplasmic binding fold. CynR is a LysR-like transcriptional regulator of the cyn operon, which encodes genes that allow cyanate to be used as a sole source of nitrogen. The operon includes three genes in the following order: cynT (cyanate permease), cynS (cyanase), and cynX (a protein of unknown function). CynR negatively regulates its own expression independently of cyanate. CynR binds to DNA and induces bending of DNA in the presence or absence of cyanate, but the amount of bending is decreased by cyanate. The CynR of LysR-type transcriptional regulator family is composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding
Probab=20.01 E-value=3.6e+02 Score=22.72 Aligned_cols=23 Identities=30% Similarity=0.596 Sum_probs=20.0
Q ss_pred hHHHHHHHHHHHCCCcEEEEEEc
Q 015881 138 LFFPAIQLLKDRYPGVLIDVIAS 160 (399)
Q Consensus 138 LttPalraLK~~yP~A~IdvLv~ 160 (399)
+..++++.++++||+++|.+...
T Consensus 15 ~l~~~l~~~~~~~P~v~i~i~~~ 37 (197)
T cd08425 15 LIGPLIDRFHARYPGIALSLREM 37 (197)
T ss_pred hhHHHHHHHHHHCCCcEEEEEEC
Confidence 34699999999999999999874
Done!