Query psy15303
Match_columns 72
No_of_seqs 101 out of 326
Neff 5.7
Searched_HMMs 46136
Date Fri Aug 16 17:37:18 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy15303.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/15303hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3445|consensus 99.9 2.2E-26 4.8E-31 152.8 7.1 63 3-65 17-79 (145)
2 KOG3446|consensus 99.9 7.1E-24 1.5E-28 132.2 1.4 64 4-67 10-73 (97)
3 PF05047 L51_S25_CI-B8: Mitoch 99.6 5E-15 1.1E-19 82.7 5.5 40 26-65 1-40 (52)
4 KOG4079|consensus 98.3 2.6E-07 5.6E-12 62.5 0.7 61 4-64 23-83 (169)
5 PF10780 MRP_L53: 39S ribosoma 96.8 0.0023 5.1E-08 36.0 3.4 48 16-64 1-50 (51)
6 PF13701 DDE_Tnp_1_4: Transpos 69.1 7.3 0.00016 29.9 3.6 35 19-53 193-227 (448)
7 TIGR01159 DRP1 density-regulat 65.6 3.9 8.4E-05 28.2 1.4 25 14-38 14-38 (173)
8 PF02601 Exonuc_VII_L: Exonucl 65.4 11 0.00023 27.1 3.7 39 7-52 12-50 (319)
9 PF13692 Glyco_trans_1_4: Glyc 65.1 8.8 0.00019 23.0 2.8 39 13-51 4-42 (135)
10 KOG0183|consensus 63.5 4.1 9E-05 29.6 1.3 19 18-36 161-179 (249)
11 cd05466 PBP2_LTTR_substrate Th 60.1 17 0.00037 21.4 3.4 27 25-51 10-36 (197)
12 COG4837 Uncharacterized protei 60.0 13 0.00029 23.7 3.0 32 17-51 19-50 (106)
13 cd08418 PBP2_TdcA The C-termin 59.2 15 0.00033 22.3 3.2 29 23-51 8-36 (201)
14 cd08429 PBP2_NhaR The C-termin 58.6 16 0.00035 23.2 3.4 29 24-52 9-37 (204)
15 cd08470 PBP2_CrgA_like_1 The C 57.8 17 0.00037 22.2 3.2 25 26-50 12-36 (197)
16 cd08435 PBP2_GbpR The C-termin 56.3 19 0.00041 21.8 3.3 26 26-51 11-36 (201)
17 cd08481 PBP2_GcdR_like The C-t 54.7 23 0.00051 21.3 3.5 26 27-52 12-37 (194)
18 TIGR02136 ptsS_2 phosphate bin 54.1 15 0.00032 25.9 2.8 26 26-51 46-71 (287)
19 cd08487 PBP2_BlaA The C-termin 52.7 24 0.00052 21.4 3.3 26 26-51 11-36 (189)
20 cd08482 PBP2_TrpI The C-termin 52.6 23 0.00049 21.8 3.2 28 25-52 10-37 (195)
21 cd08440 PBP2_LTTR_like_4 TThe 52.6 22 0.00048 21.3 3.1 26 26-51 11-36 (197)
22 cd08456 PBP2_LysR The C-termin 52.0 22 0.00048 21.5 3.0 27 25-51 10-36 (196)
23 cd08461 PBP2_DntR_like_3 The C 51.9 22 0.00048 21.6 3.1 26 26-51 11-36 (198)
24 PF05762 VWA_CoxE: VWA domain 51.6 33 0.00071 23.6 4.1 40 13-52 60-99 (222)
25 cd08488 PBP2_AmpR The C-termin 51.5 30 0.00065 21.2 3.6 26 27-52 12-37 (191)
26 cd08473 PBP2_CrgA_like_4 The C 51.4 31 0.00067 20.9 3.6 26 26-51 14-39 (202)
27 cd08465 PBP2_ToxR The C-termin 51.1 21 0.00046 22.2 2.9 26 26-51 11-36 (200)
28 cd08452 PBP2_AlsR The C-termin 50.5 21 0.00045 22.0 2.8 27 25-51 10-36 (197)
29 cd08416 PBP2_MdcR The C-termin 50.4 25 0.00055 21.3 3.1 28 25-52 10-37 (199)
30 cd08439 PBP2_LrhA_like The C-t 50.3 30 0.00064 21.1 3.4 27 25-51 10-36 (185)
31 cd08460 PBP2_DntR_like_1 The C 50.1 22 0.00047 22.0 2.8 27 25-51 10-36 (200)
32 cd08477 PBP2_CrgA_like_8 The C 49.3 31 0.00067 20.9 3.4 26 26-51 12-37 (197)
33 cd08412 PBP2_PAO1_like The C-t 48.9 23 0.00049 21.5 2.7 26 26-51 11-36 (198)
34 TIGR00237 xseA exodeoxyribonuc 48.8 28 0.00062 26.6 3.7 30 19-52 136-165 (432)
35 cd08414 PBP2_LTTR_aromatics_li 48.8 27 0.00058 21.0 3.0 26 26-51 11-36 (197)
36 cd08436 PBP2_LTTR_like_3 The C 48.8 24 0.00051 21.2 2.8 27 25-51 10-36 (194)
37 cd08450 PBP2_HcaR The C-termin 48.4 24 0.00051 21.4 2.8 26 26-51 11-36 (196)
38 cd08486 PBP2_CbnR The C-termin 48.4 32 0.00068 21.4 3.4 25 27-51 13-37 (198)
39 PF03466 LysR_substrate: LysR 48.1 21 0.00046 22.0 2.5 27 26-52 17-43 (209)
40 cd08431 PBP2_HupR The C-termin 48.1 25 0.00055 21.4 2.9 25 27-51 12-36 (195)
41 cd08464 PBP2_DntR_like_2 The C 47.9 34 0.00074 20.8 3.4 25 27-51 12-36 (200)
42 cd08444 PBP2_Cbl The C-termina 47.9 29 0.00063 21.5 3.1 26 26-51 11-36 (198)
43 cd08438 PBP2_CidR The C-termin 47.7 24 0.00052 21.3 2.7 25 27-51 12-36 (197)
44 cd08466 PBP2_LeuO The C-termin 47.7 30 0.00064 21.1 3.1 26 26-51 11-36 (200)
45 cd08426 PBP2_LTTR_like_5 The C 47.6 27 0.00059 21.2 3.0 26 26-51 11-36 (199)
46 PRK00286 xseA exodeoxyribonucl 47.5 29 0.00063 26.2 3.6 30 19-52 142-171 (438)
47 cd08420 PBP2_CysL_like C-termi 47.5 31 0.00067 20.7 3.2 26 26-51 11-36 (201)
48 cd02974 AhpF_NTD_N Alkyl hydro 47.4 64 0.0014 19.6 6.3 45 12-61 23-67 (94)
49 cd08448 PBP2_LTTR_aromatics_li 47.3 29 0.00063 20.9 3.0 26 25-50 10-35 (197)
50 cd08476 PBP2_CrgA_like_7 The C 47.2 27 0.00058 21.0 2.9 24 27-50 11-34 (197)
51 cd08434 PBP2_GltC_like The sub 46.7 25 0.00054 21.1 2.6 26 26-51 11-36 (195)
52 cd08483 PBP2_HvrB The C-termin 46.4 31 0.00066 20.9 3.0 25 26-50 11-35 (190)
53 COG1182 AcpD Acyl carrier prot 46.1 30 0.00064 24.5 3.2 52 12-64 5-57 (202)
54 cd08479 PBP2_CrgA_like_9 The C 45.7 37 0.0008 20.6 3.4 27 25-51 11-37 (198)
55 cd08453 PBP2_IlvR The C-termin 45.7 31 0.00067 21.1 3.0 26 26-51 11-36 (200)
56 cd08432 PBP2_GcdR_TrpI_HvrB_Am 45.5 39 0.00085 20.3 3.4 28 25-52 10-37 (194)
57 PRK14003 potassium-transportin 45.4 30 0.00065 24.3 3.1 46 17-62 93-140 (194)
58 PRK13996 potassium-transportin 45.2 19 0.0004 25.4 2.1 44 17-60 91-141 (197)
59 cd08425 PBP2_CynR The C-termin 45.0 32 0.00069 20.9 3.0 27 25-51 11-37 (197)
60 cd08472 PBP2_CrgA_like_3 The C 44.9 43 0.00093 20.3 3.6 25 26-50 12-36 (202)
61 cd08437 PBP2_MleR The substrat 44.5 31 0.00068 21.0 2.9 25 27-51 12-36 (198)
62 cd08478 PBP2_CrgA The C-termin 44.3 27 0.00059 21.3 2.6 26 25-50 13-38 (199)
63 PF04690 YABBY: YABBY protein; 44.0 15 0.00032 25.3 1.5 19 27-45 130-148 (170)
64 cd08445 PBP2_BenM_CatM_CatR Th 43.9 35 0.00076 21.1 3.1 26 26-51 12-37 (203)
65 cd08421 PBP2_LTTR_like_1 The C 43.4 35 0.00076 20.7 3.0 24 28-51 13-36 (198)
66 cd08474 PBP2_CrgA_like_5 The C 43.1 41 0.00088 20.5 3.3 26 26-51 14-39 (202)
67 cd08441 PBP2_MetR The C-termin 42.8 46 0.001 20.3 3.5 24 28-51 13-36 (198)
68 cd08415 PBP2_LysR_opines_like 42.8 17 0.00037 22.0 1.5 26 26-51 11-36 (196)
69 cd08423 PBP2_LTTR_like_6 The C 42.5 37 0.00081 20.4 3.0 25 27-51 12-36 (200)
70 cd08422 PBP2_CrgA_like The C-t 42.1 35 0.00075 20.5 2.8 25 27-51 13-37 (197)
71 PF07315 DUF1462: Protein of u 42.0 48 0.001 20.9 3.4 33 17-52 12-44 (93)
72 PRK13997 potassium-transportin 41.9 23 0.00049 24.9 2.1 45 17-61 87-138 (193)
73 COG1653 UgpB ABC-type sugar tr 41.9 78 0.0017 22.2 4.9 26 27-52 45-70 (433)
74 cd08419 PBP2_CbbR_RubisCO_like 41.5 39 0.00086 20.3 3.0 25 27-51 11-35 (197)
75 cd08480 PBP2_CrgA_like_10 The 41.1 42 0.00091 20.7 3.1 25 26-50 12-36 (198)
76 PLN02870 Probable galacturonos 41.0 23 0.00049 28.5 2.2 26 1-32 1-26 (533)
77 TIGR02200 GlrX_actino Glutared 40.9 29 0.00064 18.7 2.2 23 11-33 1-23 (77)
78 TIGR00681 kdpC K+-transporting 40.9 24 0.00052 24.7 2.1 44 17-60 84-133 (187)
79 cd08449 PBP2_XapR The C-termin 40.6 39 0.00084 20.4 2.9 25 26-50 11-35 (197)
80 cd08471 PBP2_CrgA_like_2 The C 40.5 51 0.0011 20.0 3.4 25 26-50 12-36 (201)
81 cd08447 PBP2_LTTR_aromatics_li 40.4 48 0.001 20.0 3.3 26 26-51 11-36 (198)
82 cd08411 PBP2_OxyR The C-termin 40.1 43 0.00093 20.4 3.0 23 28-50 14-36 (200)
83 PF06244 DUF1014: Protein of u 39.0 25 0.00055 22.9 1.9 20 26-45 80-99 (122)
84 cd08442 PBP2_YofA_SoxR_like Th 38.9 40 0.00087 20.2 2.7 26 27-52 12-37 (193)
85 cd08459 PBP2_DntR_NahR_LinR_li 38.9 65 0.0014 19.6 3.7 27 26-52 11-37 (201)
86 cd08458 PBP2_NocR The C-termin 38.7 39 0.00085 20.7 2.7 26 26-51 11-36 (196)
87 cd08446 PBP2_Chlorocatechol Th 38.6 46 0.001 20.2 3.0 26 26-51 12-37 (198)
88 TIGR00741 yfiA ribosomal subun 38.5 81 0.0018 18.3 4.0 32 12-44 3-34 (95)
89 smart00367 LRR_CC Leucine-rich 38.4 13 0.00027 17.2 0.3 23 7-30 2-24 (26)
90 cd08427 PBP2_LTTR_like_2 The C 38.4 50 0.0011 19.8 3.1 26 26-51 11-36 (195)
91 cd08469 PBP2_PnbR The C-termin 38.3 57 0.0012 20.4 3.5 27 26-52 11-37 (221)
92 PRK13999 potassium-transportin 37.7 30 0.00064 24.5 2.2 45 17-61 97-145 (201)
93 cd08433 PBP2_Nac The C-teminal 37.6 35 0.00076 20.7 2.3 25 27-51 12-36 (198)
94 cd08467 PBP2_SyrM The C-termin 37.2 46 0.00099 20.6 2.8 26 26-51 11-36 (200)
95 cd08475 PBP2_CrgA_like_6 The C 37.0 47 0.001 20.0 2.8 25 26-50 12-36 (199)
96 PRK00315 potassium-transportin 36.8 29 0.00064 24.3 2.0 45 17-61 86-136 (193)
97 cd08485 PBP2_ClcR The C-termin 36.2 37 0.00081 21.0 2.3 26 26-51 12-37 (198)
98 PRK14001 potassium-transportin 36.2 32 0.0007 24.1 2.1 44 17-60 85-135 (189)
99 cd08417 PBP2_Nitroaromatics_li 36.0 54 0.0012 19.9 3.0 26 26-51 11-36 (200)
100 cd08430 PBP2_IlvY The C-termin 36.0 32 0.0007 20.8 2.0 25 27-51 12-36 (199)
101 smart00329 BPI2 BPI/LBP/CETP C 35.8 91 0.002 21.0 4.3 33 29-61 48-80 (202)
102 COG1570 XseA Exonuclease VII, 35.6 57 0.0012 25.7 3.6 30 19-52 142-171 (440)
103 PRK10470 ribosome hibernation 35.3 89 0.0019 18.5 3.8 27 18-44 8-34 (95)
104 KOG1909|consensus 34.8 35 0.00075 26.4 2.3 36 7-48 241-276 (382)
105 PTZ00062 glutaredoxin; Provisi 34.7 1.1E+02 0.0023 21.3 4.6 37 12-52 21-57 (204)
106 cd08462 PBP2_NodD The C-termin 34.6 62 0.0013 19.9 3.1 26 26-51 11-36 (200)
107 cd08484 PBP2_LTTR_beta_lactama 34.1 71 0.0015 19.3 3.3 27 26-52 11-37 (189)
108 cd08468 PBP2_Pa0477 The C-term 33.3 72 0.0016 19.6 3.3 25 27-51 12-36 (202)
109 cd02989 Phd_like_TxnDC9 Phosdu 33.2 97 0.0021 18.9 3.8 34 11-48 25-58 (113)
110 cd08451 PBP2_BudR The C-termin 33.2 43 0.00093 20.2 2.2 23 29-51 15-37 (199)
111 PLN02757 sirohydrochlorine fer 33.0 30 0.00065 22.9 1.5 30 29-58 91-120 (154)
112 PRK14002 potassium-transportin 32.4 36 0.00078 23.8 1.9 45 17-61 81-132 (186)
113 TIGR02036 dsdC D-serine deamin 32.1 74 0.0016 22.1 3.5 28 26-53 107-134 (302)
114 cd08413 PBP2_CysB_like The C-t 31.9 47 0.001 20.5 2.3 26 26-51 11-36 (198)
115 PLN02958 diacylglycerol kinase 31.6 91 0.002 24.2 4.2 44 10-53 112-155 (481)
116 PF02482 Ribosomal_S30AE: Sigm 31.5 97 0.0021 17.9 3.5 32 12-44 2-33 (97)
117 cd00026 BPI2 BPI/LBP/CETP C-te 31.2 1.3E+02 0.0028 20.3 4.5 32 30-61 44-75 (200)
118 PF09457 RBD-FIP: FIP domain ; 31.1 18 0.00039 20.0 0.2 20 25-44 25-44 (48)
119 cd08463 PBP2_DntR_like_4 The C 30.6 74 0.0016 19.9 3.1 25 26-50 11-35 (203)
120 KOG0863|consensus 30.4 24 0.00052 25.9 0.8 25 19-43 161-185 (264)
121 cd03026 AhpF_NTD_C TRX-GRX-lik 30.3 1.2E+02 0.0026 17.9 5.8 37 11-51 15-51 (89)
122 PRK13994 potassium-transportin 30.2 40 0.00086 24.3 1.9 45 17-61 111-166 (222)
123 KOG1777|consensus 30.2 39 0.00085 27.3 2.0 24 48-71 421-444 (625)
124 cd03051 GST_N_GTT2_like GST_N 30.0 93 0.002 16.4 4.1 19 13-31 2-20 (74)
125 PF02638 DUF187: Glycosyl hydr 29.8 77 0.0017 23.1 3.3 29 24-52 203-231 (311)
126 TIGR02196 GlrX_YruB Glutaredox 29.8 61 0.0013 16.9 2.2 21 12-32 2-22 (74)
127 PF13504 LRR_7: Leucine rich r 29.7 23 0.00049 15.1 0.4 11 8-18 2-12 (17)
128 COG0607 PspE Rhodanese-related 29.0 75 0.0016 18.3 2.7 24 10-33 61-84 (110)
129 PF07205 DUF1413: Domain of un 28.4 93 0.002 17.7 3.0 33 18-50 27-59 (70)
130 PF08073 CHDNT: CHDNT (NUC034) 28.2 83 0.0018 17.9 2.6 22 25-46 15-36 (55)
131 cd08457 PBP2_OccR The C-termin 27.9 45 0.00097 20.3 1.6 26 26-51 11-36 (196)
132 cd07945 DRE_TIM_CMS Leptospira 27.8 1.1E+02 0.0024 21.9 3.9 35 13-49 163-197 (280)
133 KOG3239|consensus 27.3 32 0.00069 24.2 0.9 26 12-37 20-45 (193)
134 COG4097 Predicted ferric reduc 27.1 64 0.0014 25.4 2.6 44 10-59 344-388 (438)
135 PF11247 DUF2675: Protein of u 26.9 47 0.001 21.1 1.6 15 24-38 68-82 (98)
136 PRK09375 quinolinate synthetas 26.9 93 0.002 23.3 3.4 33 16-48 223-268 (319)
137 PLN02659 Probable galacturonos 26.9 52 0.0011 26.5 2.2 25 1-31 1-25 (534)
138 cd02066 GRX_family Glutaredoxi 26.5 67 0.0015 16.5 2.0 21 12-32 2-22 (72)
139 PF10262 Rdx: Rdx family; Int 26.5 69 0.0015 18.4 2.2 36 11-50 2-39 (76)
140 PF12876 Cellulase-like: Sugar 26.5 60 0.0013 19.0 1.9 27 23-49 37-63 (88)
141 PRK10696 tRNA 2-thiocytidine b 26.2 64 0.0014 22.6 2.3 25 22-46 206-230 (258)
142 PF10607 CLTH: CTLH/CRA C-term 26.0 48 0.001 20.7 1.5 29 21-49 15-43 (145)
143 PF09822 ABC_transp_aux: ABC-t 25.8 1.9E+02 0.0041 20.0 4.7 39 12-50 29-69 (271)
144 cd06544 GH18_narbonin Narbonin 25.5 57 0.0012 23.2 2.0 20 32-51 59-78 (253)
145 PRK13995 potassium-transportin 25.1 1.1E+02 0.0023 21.8 3.2 44 17-60 95-145 (203)
146 PF07735 FBA_2: F-box associat 25.0 1.2E+02 0.0026 16.6 2.9 36 7-47 32-67 (70)
147 cd02976 NrdH NrdH-redoxin (Nrd 24.8 82 0.0018 16.4 2.2 21 12-32 2-22 (73)
148 PRK11139 DNA-binding transcrip 24.8 86 0.0019 21.5 2.7 25 27-51 106-130 (297)
149 COG1393 ArsC Arsenate reductas 24.4 71 0.0015 20.3 2.1 23 11-33 2-24 (117)
150 PF01547 SBP_bac_1: Bacterial 24.1 67 0.0015 21.3 2.1 23 29-51 9-32 (315)
151 PF13516 LRR_6: Leucine Rich r 24.0 19 0.00041 16.1 -0.5 20 7-28 2-21 (24)
152 TIGR00269 conserved hypothetic 23.9 55 0.0012 20.1 1.5 24 22-45 34-57 (104)
153 cd01388 SOX-TCF_HMG-box SOX-TC 23.7 54 0.0012 18.4 1.3 18 28-45 11-28 (72)
154 PRK10837 putative DNA-binding 23.7 1.1E+02 0.0024 20.6 3.1 26 26-51 100-125 (290)
155 PRK09791 putative DNA-binding 23.7 1.1E+02 0.0024 21.0 3.1 37 10-51 95-131 (302)
156 PRK11151 DNA-binding transcrip 23.3 1.5E+02 0.0032 20.4 3.7 26 26-51 102-127 (305)
157 PRK10324 translation inhibitor 22.7 2E+02 0.0044 17.9 4.1 32 12-44 3-34 (113)
158 cd03027 GRX_DEP Glutaredoxin ( 22.7 1.2E+02 0.0026 16.6 2.7 22 11-32 2-23 (73)
159 PF01624 MutS_I: MutS domain I 22.6 69 0.0015 19.6 1.8 21 31-51 4-24 (113)
160 TIGR02174 CXXU_selWTH selT/sel 22.5 1.6E+02 0.0036 16.7 5.6 38 12-53 1-38 (72)
161 cd00552 RaiA RaiA ("ribosome-a 22.5 1E+02 0.0023 17.7 2.5 27 18-44 7-33 (93)
162 PF13552 DUF4127: Protein of u 22.5 74 0.0016 24.9 2.3 19 32-50 92-110 (497)
163 PRK11716 DNA-binding transcrip 22.4 1.3E+02 0.0029 19.8 3.3 25 27-51 79-103 (269)
164 PRK10974 glycerol-3-phosphate 22.4 1.2E+02 0.0026 22.2 3.3 25 26-50 38-62 (438)
165 PRK09508 leuO leucine transcri 22.3 1.4E+02 0.003 20.8 3.5 26 26-51 123-148 (314)
166 PRK09801 transcriptional activ 22.2 1.5E+02 0.0032 20.8 3.6 28 24-51 105-132 (310)
167 TIGR01616 nitro_assoc nitrogen 22.2 2E+02 0.0043 18.3 3.9 23 11-33 2-24 (126)
168 PF09217 EcoRII-N: Restriction 22.1 50 0.0011 22.6 1.1 40 24-63 33-74 (156)
169 cd03052 GST_N_GDAP1 GST_N fami 22.0 94 0.002 17.3 2.1 20 12-31 1-20 (73)
170 PRK13337 putative lipid kinase 22.0 2.1E+02 0.0045 20.3 4.3 42 10-52 2-43 (304)
171 PRK10341 DNA-binding transcrip 22.0 1.4E+02 0.0031 20.7 3.4 37 10-51 97-133 (312)
172 PF14459 Prok-E2_C: Prokaryoti 21.8 1.3E+02 0.0028 19.8 2.9 22 26-47 38-60 (131)
173 COG2871 NqrF Na+-transporting 21.8 1.7E+02 0.0037 22.6 4.0 37 10-51 305-342 (410)
174 PF02960 K1: K1 glycoprotein; 21.8 35 0.00076 22.5 0.3 43 22-64 30-72 (130)
175 PRK14997 LysR family transcrip 21.8 1.7E+02 0.0037 20.0 3.8 27 26-52 103-129 (301)
176 KOG1454|consensus 21.7 88 0.0019 22.9 2.4 26 33-58 282-307 (326)
177 PRK10026 arsenate reductase; P 21.7 2E+02 0.0044 18.9 3.9 23 11-33 3-25 (141)
178 PRK12681 cysB transcriptional 21.6 1.3E+02 0.0028 21.4 3.2 36 11-51 94-129 (324)
179 cd03045 GST_N_Delta_Epsilon GS 21.6 1.2E+02 0.0025 16.3 2.4 20 12-31 1-20 (74)
180 PF00505 HMG_box: HMG (high mo 21.5 66 0.0014 17.3 1.4 18 28-45 10-27 (69)
181 PRK11914 diacylglycerol kinase 21.4 1.6E+02 0.0034 20.9 3.6 41 8-49 7-47 (306)
182 PRK11074 putative DNA-binding 21.3 1.1E+02 0.0023 21.2 2.7 37 10-51 92-128 (300)
183 COG5575 ORC2 Origin recognitio 21.3 73 0.0016 25.4 2.0 27 25-51 493-519 (535)
184 PF10691 DUF2497: Protein of u 21.0 87 0.0019 18.6 1.9 14 26-39 47-60 (73)
185 PRK03601 transcriptional regul 21.0 1.7E+02 0.0037 20.0 3.6 26 26-51 100-125 (275)
186 cd02987 Phd_like_Phd Phosducin 20.8 1.7E+02 0.0037 19.4 3.5 36 11-50 86-121 (175)
187 PLN02495 oxidoreductase, actin 20.7 1.1E+02 0.0025 23.3 2.9 28 22-50 93-120 (385)
188 TIGR03418 chol_sulf_TF putativ 20.5 1.3E+02 0.0028 20.4 2.9 27 26-52 100-126 (291)
189 PF02886 LBP_BPI_CETP_C: LBP / 20.5 77 0.0017 21.5 1.8 33 29-61 80-112 (238)
190 cd02973 TRX_GRX_like Thioredox 20.2 1.6E+02 0.0034 15.6 5.2 36 11-50 2-37 (67)
191 cd03005 PDI_a_ERp46 PDIa famil 20.1 1.2E+02 0.0027 17.0 2.4 41 11-51 19-59 (102)
192 PRK15421 DNA-binding transcrip 20.1 1.4E+02 0.0031 21.0 3.2 25 27-51 101-125 (317)
193 PRK10086 DNA-binding transcrip 20.1 1.7E+02 0.0036 20.4 3.5 28 25-52 112-139 (311)
194 cd03034 ArsC_ArsC Arsenate Red 20.1 1.8E+02 0.0039 17.8 3.3 22 12-33 1-22 (112)
No 1
>KOG3445|consensus
Probab=99.93 E-value=2.2e-26 Score=152.83 Aligned_cols=63 Identities=30% Similarity=0.518 Sum_probs=61.3
Q ss_pred cccccCceEEEEEecCCCCCCHHHHHHHHhCHHHHHHhCCCCeEEEEEcCCCCCEEEEEecCC
Q psy15303 3 TRFGSKLKELRIHLCQKGGSSSGVRDFLAQHYVPLKQANPKFPILVRECSGVTPVVWARIPTI 65 (72)
Q Consensus 3 ~~f~~qLk~L~~~yC~~~~sS~GvR~Fl~~~l~~~k~~NP~v~i~v~~~~g~~P~l~a~Y~n~ 65 (72)
-+|++||++|+|+||+|||||+|||+||++.|++|+++||+|+|++..++|+||.|+|+|.|+
T Consensus 17 gryv~ql~rit~sfCnwggSSrGmR~Fle~~L~~~a~enP~v~i~v~~rrg~hP~lraeY~NG 79 (145)
T KOG3445|consen 17 GRYVWQLRRITVSFCNWGGSSRGMREFLESELPDLARENPGVVIYVEPRRGQHPLLRAEYLNG 79 (145)
T ss_pred hhhhheeeEEEEEEecCCCccHHHHHHHHHHHHHHHhhCCCeEEEEeccCCCCceEEEEecCC
Confidence 379999999999999999999999999999999999999999999999999999999999994
No 2
>KOG3446|consensus
Probab=99.88 E-value=7.1e-24 Score=132.18 Aligned_cols=64 Identities=59% Similarity=0.992 Sum_probs=60.2
Q ss_pred ccccCceEEEEEecCCCCCCHHHHHHHHhCHHHHHHhCCCCeEEEEEcCCCCCEEEEEecCCcc
Q psy15303 4 RFGSKLKELRIHLCQKGGSSSGVRDFLAQHYVPLKQANPKFPILVRECSGVTPVVWARIPTIGC 67 (72)
Q Consensus 4 ~f~~qLk~L~~~yC~~~~sS~GvR~Fl~~~l~~~k~~NP~v~i~v~~~~g~~P~l~a~Y~n~~~ 67 (72)
.|...||||||+.|+.|+.|+|+|+||+++|+++|+.||++||+||+|.|..|+++|+|+++-+
T Consensus 10 s~~~~lkElRI~lcqkspaSagvR~fvEk~Y~~lKkaNP~lPILIREcSgVqPrl~ARY~~G~E 73 (97)
T KOG3446|consen 10 SFTLKLKELRIHLCQKSPASAGVREFVEKFYVNLKKANPDLPILIRECSGVQPRLWARYGNGVE 73 (97)
T ss_pred ccchhhhhheeeecCCCCcchhHHHHHHHhhhhhhhcCCCCcEeehhhcCCchHHHHHhcCCce
Confidence 4566799999999999999999999999999999999999999999999999999999999433
No 3
>PF05047 L51_S25_CI-B8: Mitochondrial ribosomal protein L51 / S25 / CI-B8 domain ; InterPro: IPR007741 Proteins containing this domain are located in the mitochondrion and include ribosomal protein L51, and S25. This domain is also found in mitochondrial NADH-ubiquinone oxidoreductase B8 subunit (CI-B8) 1.6.5.3 from EC. It is not known whether all members of this family form part of the NADH-ubiquinone oxidoreductase and whether they are also all ribosomal proteins.; PDB: 1S3A_A.
Probab=99.58 E-value=5e-15 Score=82.70 Aligned_cols=40 Identities=33% Similarity=0.403 Sum_probs=32.5
Q ss_pred HHHHHHhCHHHHHHhCCCCeEEEEEcCCCCCEEEEEecCC
Q psy15303 26 VRDFLAQHYVPLKQANPKFPILVRECSGVTPVVWARIPTI 65 (72)
Q Consensus 26 vR~Fl~~~l~~~k~~NP~v~i~v~~~~g~~P~l~a~Y~n~ 65 (72)
||+|++++||+||++||+|+|+|+++++.||.++|+|.|+
T Consensus 1 ~R~F~~~~lp~l~~~NP~v~~~v~~~~~~~P~~~~~y~~G 40 (52)
T PF05047_consen 1 ARDFLKNNLPTLKYHNPQVQFEVRRRRGRHPFLTAEYLNG 40 (52)
T ss_dssp HHHHHHHTHHHHHHHSTT--EEEE---SSS-EEEEEESS-
T ss_pred CHhHHHHhHHHHHHHCCCcEEEEEECCCCCCEEEEEEcCC
Confidence 7999999999999999999999999999999999999994
No 4
>KOG4079|consensus
Probab=98.25 E-value=2.6e-07 Score=62.49 Aligned_cols=61 Identities=18% Similarity=0.317 Sum_probs=57.8
Q ss_pred ccccCceEEEEEecCCCCCCHHHHHHHHhCHHHHHHhCCCCeEEEEEcCCCCCEEEEEecC
Q psy15303 4 RFGSKLKELRIHLCQKGGSSSGVRDFLAQHYVPLKQANPKFPILVRECSGVTPVVWARIPT 64 (72)
Q Consensus 4 ~f~~qLk~L~~~yC~~~~sS~GvR~Fl~~~l~~~k~~NP~v~i~v~~~~g~~P~l~a~Y~n 64 (72)
.|...++-.++.|..+++...|+|+|+--|+|+++.+||.|+++........|++++..+.
T Consensus 23 vlkD~V~vfsvnynt~g~~~~GARdFVfwNipQiQykNP~VQ~~~~knmtpsPF~R~Yldd 83 (169)
T KOG4079|consen 23 VLKDNVNVFSVNYNTNGPEQSGARDFVFWNIPQIQYKNPKVQLVKHKNMTPSPFARAYLDD 83 (169)
T ss_pred EEeccceEEEEeccCCCccccCccceEEecchhhcccCCceEEEeeccCCCChHHHheecC
Confidence 5778899999999999999999999999999999999999999999999999999998877
No 5
>PF10780 MRP_L53: 39S ribosomal protein L53/MRP-L53; InterPro: IPR019716 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. Mitochondrial ribosomal protein L53 (also known as L44) is part of the 39S ribosome [].
Probab=96.76 E-value=0.0023 Score=36.01 Aligned_cols=48 Identities=17% Similarity=0.137 Sum_probs=40.9
Q ss_pred ecCCCCCCHHHHHHHHhC--HHHHHHhCCCCeEEEEEcCCCCCEEEEEecC
Q psy15303 16 LCQKGGSSSGVRDFLAQH--YVPLKQANPKFPILVRECSGVTPVVWARIPT 64 (72)
Q Consensus 16 yC~~~~sS~GvR~Fl~~~--l~~~k~~NP~v~i~v~~~~g~~P~l~a~Y~n 64 (72)
||..++.++.+|+||..- -.....-||+.++..+.. ...|.|...|.+
T Consensus 1 FnPF~~~aksaR~FL~~ip~s~k~~~tni~~~vl~~~~-~~~P~v~V~fkd 50 (51)
T PF10780_consen 1 FNPFSPNAKSARLFLSLIPPSAKARGTNINCEVLPRVS-RSEPSVTVTFKD 50 (51)
T ss_pred CCCCCcccHHHHHHHHhcCCccccccCCCceEEecCCC-CCCCeEEEEecc
Confidence 688999999999999864 445566899999999888 679999999988
No 6
>PF13701 DDE_Tnp_1_4: Transposase DDE domain group 1
Probab=69.09 E-value=7.3 Score=29.93 Aligned_cols=35 Identities=37% Similarity=0.445 Sum_probs=31.4
Q ss_pred CCCCCHHHHHHHHhCHHHHHHhCCCCeEEEEEcCC
Q psy15303 19 KGGSSSGVRDFLAQHYVPLKQANPKFPILVRECSG 53 (72)
Q Consensus 19 ~~~sS~GvR~Fl~~~l~~~k~~NP~v~i~v~~~~g 53 (72)
+..||+|+.+||+.-+..+.+.-|+++|++|-..|
T Consensus 193 n~~sa~g~~~fL~~~l~~lr~~~~~~~ILvR~DSg 227 (448)
T PF13701_consen 193 NVHSAKGAAEFLKRVLRRLRQRWPDTRILVRGDSG 227 (448)
T ss_pred CCChHHHHHHHHHHHHHHHhhhCccceEEEEecCc
Confidence 35689999999999999999999999999998764
No 7
>TIGR01159 DRP1 density-regulated protein DRP1. This protein family shows weak but suggestive similarity to translation initiation factor SUI1 and its prokaryotic homologs.
Probab=65.57 E-value=3.9 Score=28.18 Aligned_cols=25 Identities=16% Similarity=0.279 Sum_probs=22.1
Q ss_pred EEecCCCCCCHHHHHHHHhCHHHHH
Q psy15303 14 IHLCQKGGSSSGVRDFLAQHYVPLK 38 (72)
Q Consensus 14 ~~yC~~~~sS~GvR~Fl~~~l~~~k 38 (72)
.-||+.|++-+-=++||++|.|++-
T Consensus 14 ~EyCEf~~~~~kCk~WL~~n~p~l~ 38 (173)
T TIGR01159 14 PEYCEFSGDLKRCKVWLSENAPDLY 38 (173)
T ss_pred hHHhcCCCCHHHHHHHHHHhChHHH
Confidence 4699999999999999999888654
No 8
>PF02601 Exonuc_VII_L: Exonuclease VII, large subunit; InterPro: IPR020579 Exonuclease VII 3.1.11.6 from EC is composed of two nonidentical subunits; one large subunit and 4 small ones []. Exonuclease VII catalyses exonucleolytic cleavage in either 5'-3' or 3'-5' direction to yield 5'-phosphomononucleotides. The large subunit also contains the OB-fold domains (IPR004365 from INTERPRO) that bind to nucleic acids at the N terminus. This entry represents Exonuclease VII, large subunit, C-terminal. ; GO: 0008855 exodeoxyribonuclease VII activity
Probab=65.42 E-value=11 Score=27.09 Aligned_cols=39 Identities=26% Similarity=0.422 Sum_probs=28.8
Q ss_pred cCceEEEEEecCCCCCCHHHHHHHHhCHHHHHHhCCCCeEEEEEcC
Q psy15303 7 SKLKELRIHLCQKGGSSSGVRDFLAQHYVPLKQANPKFPILVRECS 52 (72)
Q Consensus 7 ~qLk~L~~~yC~~~~sS~GvR~Fl~~~l~~~k~~NP~v~i~v~~~~ 52 (72)
.-.++|=+- +|++++|++||+.. +++.+|.++|.+.+..
T Consensus 12 ~~p~~I~vI---Ts~~gAa~~D~~~~----~~~r~~~~~~~~~p~~ 50 (319)
T PF02601_consen 12 KFPKRIAVI---TSPTGAAIQDFLRT----LKRRNPIVEIILYPAS 50 (319)
T ss_pred CCCCEEEEE---eCCchHHHHHHHHH----HHHhCCCcEEEEEecc
Confidence 334444444 46779999999864 5669999999998764
No 9
>PF13692 Glyco_trans_1_4: Glycosyl transferases group 1; PDB: 3OY2_A 3OY7_B 2Q6V_A 2HY7_A 3CV3_A 3CUY_A.
Probab=65.09 E-value=8.8 Score=23.01 Aligned_cols=39 Identities=13% Similarity=0.267 Sum_probs=27.7
Q ss_pred EEEecCCCCCCHHHHHHHHhCHHHHHHhCCCCeEEEEEc
Q psy15303 13 RIHLCQKGGSSSGVRDFLAQHYVPLKQANPKFPILVREC 51 (72)
Q Consensus 13 ~~~yC~~~~sS~GvR~Fl~~~l~~~k~~NP~v~i~v~~~ 51 (72)
.+-|-......+|+..+++.-+..++++.|++.+.+.-.
T Consensus 4 ~i~~~g~~~~~k~~~~li~~~~~~l~~~~p~~~l~i~G~ 42 (135)
T PF13692_consen 4 YIGYLGRIRPDKGLEELIEAALERLKEKHPDIELIIIGN 42 (135)
T ss_dssp EEE--S-SSGGGTHHHHHH-HHHHHHHHSTTEEEEEECE
T ss_pred cccccccccccccccchhhhHHHHHHHHCcCEEEEEEeC
Confidence 344444444558999999999999999999999888544
No 10
>KOG0183|consensus
Probab=63.51 E-value=4.1 Score=29.55 Aligned_cols=19 Identities=42% Similarity=0.646 Sum_probs=15.9
Q ss_pred CCCCCCHHHHHHHHhCHHH
Q psy15303 18 QKGGSSSGVRDFLAQHYVP 36 (72)
Q Consensus 18 ~~~~sS~GvR~Fl~~~l~~ 36 (72)
-+|-+|+.+|+|++++|.+
T Consensus 161 aiGr~sk~VrEflEK~y~e 179 (249)
T KOG0183|consen 161 AIGRSSKTVREFLEKNYKE 179 (249)
T ss_pred ccccccHHHHHHHHHhccc
Confidence 4677999999999997754
No 11
>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=60.11 E-value=17 Score=21.41 Aligned_cols=27 Identities=15% Similarity=0.130 Sum_probs=22.2
Q ss_pred HHHHHHHhCHHHHHHhCCCCeEEEEEc
Q psy15303 25 GVRDFLAQHYVPLKQANPKFPILVREC 51 (72)
Q Consensus 25 GvR~Fl~~~l~~~k~~NP~v~i~v~~~ 51 (72)
....++...+.+|.+++|++.|.+...
T Consensus 10 ~~~~~l~~~i~~~~~~~p~i~i~~~~~ 36 (197)
T cd05466 10 IAAYLLPPLLAAFRQRYPGVELSLVEG 36 (197)
T ss_pred hHHHHhHHHHHHHHHHCCCCEEEEEEC
Confidence 456678888889999999999998764
No 12
>COG4837 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=59.99 E-value=13 Score=23.75 Aligned_cols=32 Identities=22% Similarity=0.383 Sum_probs=27.5
Q ss_pred cCCCCCCHHHHHHHHhCHHHHHHhCCCCeEEEEEc
Q psy15303 17 CQKGGSSSGVRDFLAQHYVPLKQANPKFPILVREC 51 (72)
Q Consensus 17 C~~~~sS~GvR~Fl~~~l~~~k~~NP~v~i~v~~~ 51 (72)
|=+.|||+-.-+||+ +.+|++.|+.+|..+-.
T Consensus 19 CV~aPtsKdt~eWLe---aalkRKyp~~~F~~~Yi 50 (106)
T COG4837 19 CVNAPTSKDTYEWLE---AALKRKYPNQPFKYTYI 50 (106)
T ss_pred hcCCCcchhHHHHHH---HHHhccCCCCCcEEEEE
Confidence 778999999999998 46899999999987654
No 13
>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=59.15 E-value=15 Score=22.30 Aligned_cols=29 Identities=17% Similarity=0.138 Sum_probs=23.9
Q ss_pred CHHHHHHHHhCHHHHHHhCCCCeEEEEEc
Q psy15303 23 SSGVRDFLAQHYVPLKQANPKFPILVREC 51 (72)
Q Consensus 23 S~GvR~Fl~~~l~~~k~~NP~v~i~v~~~ 51 (72)
......++..-+.+|++++|++.+.+...
T Consensus 8 ~~~~~~~l~~~l~~~~~~~P~i~l~i~~~ 36 (201)
T cd08418 8 SLIAHTLMPAVINRFKEQFPDVQISIYEG 36 (201)
T ss_pred hHHHHhhhHHHHHHHHHHCCCceEEEEeC
Confidence 34567788889999999999999998753
No 14
>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=58.60 E-value=16 Score=23.22 Aligned_cols=29 Identities=10% Similarity=0.122 Sum_probs=24.3
Q ss_pred HHHHHHHHhCHHHHHHhCCCCeEEEEEcC
Q psy15303 24 SGVRDFLAQHYVPLKQANPKFPILVRECS 52 (72)
Q Consensus 24 ~GvR~Fl~~~l~~~k~~NP~v~i~v~~~~ 52 (72)
.-...|+...+.+|.+.+|++++.+....
T Consensus 9 ~~~~~~l~~~l~~f~~~~P~v~l~i~~~~ 37 (204)
T cd08429 9 AVPKSIAYRLLEPAMDLHEPIRLVCREGK 37 (204)
T ss_pred hhhHHHHHHHHHHHHHhCCCcEEEEEeCC
Confidence 34578899999999999999999998743
No 15
>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=57.76 E-value=17 Score=22.18 Aligned_cols=25 Identities=20% Similarity=0.219 Sum_probs=21.8
Q ss_pred HHHHHHhCHHHHHHhCCCCeEEEEE
Q psy15303 26 VRDFLAQHYVPLKQANPKFPILVRE 50 (72)
Q Consensus 26 vR~Fl~~~l~~~k~~NP~v~i~v~~ 50 (72)
...++...+.+|++++|++.+.+..
T Consensus 12 ~~~~l~~~l~~f~~~~P~v~l~i~~ 36 (197)
T cd08470 12 GERFIAPLVNDFMQRYPKLEVDIEL 36 (197)
T ss_pred HHHHHHHHHHHHHHHCCCeEEEEEe
Confidence 4567889999999999999999975
No 16
>cd08435 PBP2_GbpR The C-terminal substrate binding domain of galactose-binding protein regulator contains the type 2 periplasmic binding fold. Galactose-binding protein regulator (GbpR), a member of the LysR family of bacterial transcriptional regulators, regulates the expression of chromosomal virulence gene chvE. The chvE gene is involved in the uptake of specific sugars, in chemotaxis to these sugars, and in the VirA-VirG two-component signal transduction system. In the presence of an inducing sugar such as L-arabinose, D-fucose, or D-galactose, GbpR activates chvE expression, while in the absence of an inducing sugar, GbpR represses expression. The topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a ma
Probab=56.34 E-value=19 Score=21.79 Aligned_cols=26 Identities=19% Similarity=0.241 Sum_probs=22.4
Q ss_pred HHHHHHhCHHHHHHhCCCCeEEEEEc
Q psy15303 26 VRDFLAQHYVPLKQANPKFPILVREC 51 (72)
Q Consensus 26 vR~Fl~~~l~~~k~~NP~v~i~v~~~ 51 (72)
...++...+.+|++.+|++.+.+...
T Consensus 11 ~~~~l~~~l~~~~~~~P~v~i~i~~~ 36 (201)
T cd08435 11 APVLLPPAIARLLARHPRLTVRVVEG 36 (201)
T ss_pred HHHHHHHHHHHHHHHCCCeEEEEEeC
Confidence 45778899999999999999999754
No 17
>cd08481 PBP2_GcdR_like The C-terminal substrate binding domain of LysR-type transcriptional regulators GcdR-like, contains the type 2 periplasmic binding fold. GcdR is involved in the glutaconate/glutarate-specific activation of the Pg promoter driving expression of a glutaryl-CoA dehydrogenase-encoding gene (gcdH). The GcdH protein is essential for the anaerobic catabolism of many aromatic compounds and some alicyclic and dicarboxylic acids. The structural topology of this substrate-binding domain is most similar to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplas
Probab=54.74 E-value=23 Score=21.33 Aligned_cols=26 Identities=8% Similarity=0.153 Sum_probs=21.8
Q ss_pred HHHHHhCHHHHHHhCCCCeEEEEEcC
Q psy15303 27 RDFLAQHYVPLKQANPKFPILVRECS 52 (72)
Q Consensus 27 R~Fl~~~l~~~k~~NP~v~i~v~~~~ 52 (72)
..++...+.+|.+++|++.|.+....
T Consensus 12 ~~~l~~~l~~f~~~~P~i~i~i~~~~ 37 (194)
T cd08481 12 TRWLIPRLPDFLARHPDITVNLVTRD 37 (194)
T ss_pred HHHHHhhhhHHHHHCCCceEEEEecc
Confidence 45778889999999999999998643
No 18
>TIGR02136 ptsS_2 phosphate binding protein. Members of this family are phosphate-binding proteins. Most are found in phosphate ABC-transporter operons, but some are found in phosphate regulatory operons. This model separates members of the current family from the phosphate ABC transporter phosphate binding protein described by TIGRFAMs model TIGR00975.
Probab=54.14 E-value=15 Score=25.92 Aligned_cols=26 Identities=12% Similarity=0.208 Sum_probs=22.6
Q ss_pred HHHHHHhCHHHHHHhCCCCeEEEEEc
Q psy15303 26 VRDFLAQHYVPLKQANPKFPILVREC 51 (72)
Q Consensus 26 vR~Fl~~~l~~~k~~NP~v~i~v~~~ 51 (72)
+-.++..-+.+|++++|++.+.+.+.
T Consensus 46 ~~~~lp~~l~~f~~~~P~i~v~i~~~ 71 (287)
T TIGR02136 46 VAPLAEAAAEEFQKIHPGVSVTVQGA 71 (287)
T ss_pred HHHHHHHHHHHHHhhCCCceEEEccC
Confidence 44688999999999999999999774
No 19
>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=52.70 E-value=24 Score=21.39 Aligned_cols=26 Identities=15% Similarity=0.284 Sum_probs=21.6
Q ss_pred HHHHHHhCHHHHHHhCCCCeEEEEEc
Q psy15303 26 VRDFLAQHYVPLKQANPKFPILVREC 51 (72)
Q Consensus 26 vR~Fl~~~l~~~k~~NP~v~i~v~~~ 51 (72)
...++...+.+|++++|++.+.+...
T Consensus 11 ~~~~l~~~l~~f~~~~P~i~l~i~~~ 36 (189)
T cd08487 11 AVGWLLPRLAEFRQLHPFIELRLRTN 36 (189)
T ss_pred HHHHHhHHHHHHHHHCCCceEEeeec
Confidence 45677778999999999999998764
No 20
>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=52.63 E-value=23 Score=21.75 Aligned_cols=28 Identities=11% Similarity=0.188 Sum_probs=22.9
Q ss_pred HHHHHHHhCHHHHHHhCCCCeEEEEEcC
Q psy15303 25 GVRDFLAQHYVPLKQANPKFPILVRECS 52 (72)
Q Consensus 25 GvR~Fl~~~l~~~k~~NP~v~i~v~~~~ 52 (72)
....++...+.+|.+++|++.+.+....
T Consensus 10 ~~~~~l~~~i~~f~~~~P~v~i~~~~~~ 37 (195)
T cd08482 10 LLMRWLIPRLPAFQAALPDIDLQLSASD 37 (195)
T ss_pred HHHHHHHhhHHHHHHHCCCceEEEEecC
Confidence 3457888889999999999999987543
No 21
>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=52.57 E-value=22 Score=21.27 Aligned_cols=26 Identities=12% Similarity=0.354 Sum_probs=21.8
Q ss_pred HHHHHHhCHHHHHHhCCCCeEEEEEc
Q psy15303 26 VRDFLAQHYVPLKQANPKFPILVREC 51 (72)
Q Consensus 26 vR~Fl~~~l~~~k~~NP~v~i~v~~~ 51 (72)
...++...+..|.+++|++.|.+.+.
T Consensus 11 ~~~~l~~~l~~~~~~~p~v~i~i~~~ 36 (197)
T cd08440 11 AATLLPPVLAAFRRRHPGIRVRLRDV 36 (197)
T ss_pred hhhHHHHHHHHHHHhCCCcEEEEEeC
Confidence 34677888999999999999999764
No 22
>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=51.98 E-value=22 Score=21.54 Aligned_cols=27 Identities=19% Similarity=0.265 Sum_probs=22.4
Q ss_pred HHHHHHHhCHHHHHHhCCCCeEEEEEc
Q psy15303 25 GVRDFLAQHYVPLKQANPKFPILVREC 51 (72)
Q Consensus 25 GvR~Fl~~~l~~~k~~NP~v~i~v~~~ 51 (72)
-...++...+.+|.+++|++.+.+...
T Consensus 10 ~~~~~l~~~l~~~~~~~P~i~~~i~~~ 36 (196)
T cd08456 10 LSQSFLPRAIKAFLQRHPDVTISIHTR 36 (196)
T ss_pred HHHhhHHHHHHHHHHHCCCcEEEEEeC
Confidence 345678899999999999999999764
No 23
>cd08461 PBP2_DntR_like_3 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator similar to DntR, which is involved in the catabolism of dinitrotoluene; contains the type 2 periplasmic binding fold. This CD includes an uncharacterized LysR-type transcriptional regulator similar to DntR, NahR, and LinR, which are involved in the degradation of aromatic compounds. The transcription of the genes encoding enzymes involved in such degradation is regulated and expression of these enzymes is enhanced by inducers, which are either an intermediate in the metabolic pathway or compounds to be degraded. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytra
Probab=51.87 E-value=22 Score=21.65 Aligned_cols=26 Identities=19% Similarity=0.388 Sum_probs=22.4
Q ss_pred HHHHHHhCHHHHHHhCCCCeEEEEEc
Q psy15303 26 VRDFLAQHYVPLKQANPKFPILVREC 51 (72)
Q Consensus 26 vR~Fl~~~l~~~k~~NP~v~i~v~~~ 51 (72)
...++...+.+|++++|++.+.+...
T Consensus 11 ~~~~l~~~l~~f~~~~P~v~i~i~~~ 36 (198)
T cd08461 11 QKAILPPLLAALRQEAPGVRVAIRDL 36 (198)
T ss_pred HHHHhHHHHHHHHHHCCCcEEEEeeC
Confidence 45678899999999999999999764
No 24
>PF05762 VWA_CoxE: VWA domain containing CoxE-like protein; InterPro: IPR008912 This group of proteins contains a VWA type domain and the function of this family is unknown. It is found as part of a CO oxidising (Cox) system operon in several bacteria [].
Probab=51.58 E-value=33 Score=23.58 Aligned_cols=40 Identities=20% Similarity=0.397 Sum_probs=33.8
Q ss_pred EEEecCCCCCCHHHHHHHHhCHHHHHHhCCCCeEEEEEcC
Q psy15303 13 RIHLCQKGGSSSGVRDFLAQHYVPLKQANPKFPILVRECS 52 (72)
Q Consensus 13 ~~~yC~~~~sS~GvR~Fl~~~l~~~k~~NP~v~i~v~~~~ 52 (72)
.+..||.|||=.+.-.|+-.-+-.+....+.+.+.+....
T Consensus 60 lvvl~DvSGSM~~~s~~~l~~~~~l~~~~~~~~~f~F~~~ 99 (222)
T PF05762_consen 60 LVVLCDVSGSMAGYSEFMLAFLYALQRQFRRVRVFVFSTR 99 (222)
T ss_pred EEEEEeCCCChHHHHHHHHHHHHHHHHhCCCEEEEEEeee
Confidence 4567999999999888988888899999999988876543
No 25
>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=51.51 E-value=30 Score=21.20 Aligned_cols=26 Identities=8% Similarity=0.193 Sum_probs=21.8
Q ss_pred HHHHHhCHHHHHHhCCCCeEEEEEcC
Q psy15303 27 RDFLAQHYVPLKQANPKFPILVRECS 52 (72)
Q Consensus 27 R~Fl~~~l~~~k~~NP~v~i~v~~~~ 52 (72)
..++...+.+|.+++|++.+.+....
T Consensus 12 ~~~l~~~l~~f~~~~P~v~i~~~~~~ 37 (191)
T cd08488 12 VGWLLPRLADFQNRHPFIDLRLSTNN 37 (191)
T ss_pred HHHHHhHHHHHHHHCCCcEEEEEecC
Confidence 35777789999999999999998654
No 26
>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=51.41 E-value=31 Score=20.94 Aligned_cols=26 Identities=15% Similarity=0.264 Sum_probs=21.7
Q ss_pred HHHHHHhCHHHHHHhCCCCeEEEEEc
Q psy15303 26 VRDFLAQHYVPLKQANPKFPILVREC 51 (72)
Q Consensus 26 vR~Fl~~~l~~~k~~NP~v~i~v~~~ 51 (72)
...++...+.+|++++|++.+.+...
T Consensus 14 ~~~~l~~~l~~~~~~~P~i~i~~~~~ 39 (202)
T cd08473 14 AQELLAPLLPRFMAAYPQVRLQLEAT 39 (202)
T ss_pred HHHHHHHHHHHHHHHCCCeEEEEEEc
Confidence 34677888999999999999999764
No 27
>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=51.07 E-value=21 Score=22.20 Aligned_cols=26 Identities=19% Similarity=0.267 Sum_probs=22.0
Q ss_pred HHHHHHhCHHHHHHhCCCCeEEEEEc
Q psy15303 26 VRDFLAQHYVPLKQANPKFPILVREC 51 (72)
Q Consensus 26 vR~Fl~~~l~~~k~~NP~v~i~v~~~ 51 (72)
...++..-+..|++++|++++.+...
T Consensus 11 ~~~~l~~~l~~f~~~~P~i~l~i~~~ 36 (200)
T cd08465 11 ARLVLPALMRQLRAEAPGIDLAVSQA 36 (200)
T ss_pred HHHhhhHHHHHHHHHCCCcEEEEecC
Confidence 35778899999999999999988753
No 28
>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=50.49 E-value=21 Score=22.04 Aligned_cols=27 Identities=19% Similarity=0.330 Sum_probs=21.9
Q ss_pred HHHHHHHhCHHHHHHhCCCCeEEEEEc
Q psy15303 25 GVRDFLAQHYVPLKQANPKFPILVREC 51 (72)
Q Consensus 25 GvR~Fl~~~l~~~k~~NP~v~i~v~~~ 51 (72)
-...++...+.+|++++|++.+.+...
T Consensus 10 ~~~~~l~~~l~~~~~~~P~v~i~i~~~ 36 (197)
T cd08452 10 AIYEFLPPIVREYRKKFPSVKVELREL 36 (197)
T ss_pred HHHhHHHHHHHHHHHHCCCcEEEEEec
Confidence 345677889999999999999988653
No 29
>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=50.44 E-value=25 Score=21.33 Aligned_cols=28 Identities=18% Similarity=0.120 Sum_probs=23.1
Q ss_pred HHHHHHHhCHHHHHHhCCCCeEEEEEcC
Q psy15303 25 GVRDFLAQHYVPLKQANPKFPILVRECS 52 (72)
Q Consensus 25 GvR~Fl~~~l~~~k~~NP~v~i~v~~~~ 52 (72)
-...++...+.+|++++|++.+.+....
T Consensus 10 ~~~~~l~~~l~~~~~~~P~i~l~i~~~~ 37 (199)
T cd08416 10 LTVNTVPRIIMGLKLRRPELDIELTLGS 37 (199)
T ss_pred HHHhhhHHHHHHHHHhCCCeEEEEEEcC
Confidence 3466788999999999999999997643
No 30
>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=50.27 E-value=30 Score=21.09 Aligned_cols=27 Identities=15% Similarity=0.044 Sum_probs=22.2
Q ss_pred HHHHHHHhCHHHHHHhCCCCeEEEEEc
Q psy15303 25 GVRDFLAQHYVPLKQANPKFPILVREC 51 (72)
Q Consensus 25 GvR~Fl~~~l~~~k~~NP~v~i~v~~~ 51 (72)
-...++...+.+|++++|++.+.+...
T Consensus 10 ~~~~~l~~~l~~~~~~~P~v~i~~~~~ 36 (185)
T cd08439 10 YADTILPFLLNRFASVYPRLAIEVVCK 36 (185)
T ss_pred HhHHHHHHHHHHHHHHCCCeEEEEEEC
Confidence 345677888999999999999998764
No 31
>cd08460 PBP2_DntR_like_1 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator similar to DntR, which is involved in the catabolism of dinitrotoluene; contains the type 2 periplasmic binding fold. This CD includes an uncharacterized LysR-type transcriptional regulator similar to DntR, NahR, and LinR, which are involved in the degradation of aromatic compounds. The transcription of the genes encoding enzymes involved in such degradation is regulated and expression of these enzymes is enhanced by inducers, which are either an intermediate in the metabolic pathway or compounds to be degraded. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytra
Probab=50.13 E-value=22 Score=21.96 Aligned_cols=27 Identities=11% Similarity=0.006 Sum_probs=23.1
Q ss_pred HHHHHHHhCHHHHHHhCCCCeEEEEEc
Q psy15303 25 GVRDFLAQHYVPLKQANPKFPILVREC 51 (72)
Q Consensus 25 GvR~Fl~~~l~~~k~~NP~v~i~v~~~ 51 (72)
-...|+...+..|++++|++.+.+...
T Consensus 10 ~~~~~l~~~l~~~~~~~P~v~v~l~~~ 36 (200)
T cd08460 10 FVAAFGPALLAAVAAEAPGVRLRFVPE 36 (200)
T ss_pred HHHHHHHHHHHHHHHHCCCCEEEEecC
Confidence 456888999999999999999998653
No 32
>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=49.35 E-value=31 Score=20.89 Aligned_cols=26 Identities=8% Similarity=-0.005 Sum_probs=21.7
Q ss_pred HHHHHHhCHHHHHHhCCCCeEEEEEc
Q psy15303 26 VRDFLAQHYVPLKQANPKFPILVREC 51 (72)
Q Consensus 26 vR~Fl~~~l~~~k~~NP~v~i~v~~~ 51 (72)
...++...+.+|++++|++.+.+...
T Consensus 12 ~~~~l~~~l~~~~~~~P~i~l~i~~~ 37 (197)
T cd08477 12 GSHVLTPALAEYLARYPDVRVDLVLS 37 (197)
T ss_pred HHHHHHHHHHHHHHHCCCcEEEEEec
Confidence 45677888999999999999999753
No 33
>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=48.92 E-value=23 Score=21.48 Aligned_cols=26 Identities=19% Similarity=0.225 Sum_probs=21.7
Q ss_pred HHHHHHhCHHHHHHhCCCCeEEEEEc
Q psy15303 26 VRDFLAQHYVPLKQANPKFPILVREC 51 (72)
Q Consensus 26 vR~Fl~~~l~~~k~~NP~v~i~v~~~ 51 (72)
...++...+.+|++++|++.+.+...
T Consensus 11 ~~~~l~~~l~~~~~~~P~i~l~i~~~ 36 (198)
T cd08412 11 APYYLPGLLRRFREAYPGVEVRVVEG 36 (198)
T ss_pred chhhhHHHHHHHHHHCCCcEEEEEEC
Confidence 34677889999999999999998754
No 34
>TIGR00237 xseA exodeoxyribonuclease VII, large subunit. This family consist of exodeoxyribonuclease VII, large subunit XseA which catalyses exonucleolytic cleavage in either the 5'-3' or 3'-5' direction to yield 5'-phosphomononucleotides. Exonuclease VII consists of one large subunit and four small subunits.
Probab=48.78 E-value=28 Score=26.58 Aligned_cols=30 Identities=17% Similarity=0.368 Sum_probs=24.8
Q ss_pred CCCCCHHHHHHHHhCHHHHHHhCCCCeEEEEEcC
Q psy15303 19 KGGSSSGVRDFLAQHYVPLKQANPKFPILVRECS 52 (72)
Q Consensus 19 ~~~sS~GvR~Fl~~~l~~~k~~NP~v~i~v~~~~ 52 (72)
+|+++++++||+. .+++++|.++|.+.+..
T Consensus 136 ts~~~aa~~D~~~----~~~~r~p~~~~~~~~~~ 165 (432)
T TIGR00237 136 TSQTGAALADILH----ILKRRDPSLKVVIYPTL 165 (432)
T ss_pred eCCccHHHHHHHH----HHHhhCCCceEEEeccc
Confidence 6788999999975 47778899999987754
No 35
>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=48.78 E-value=27 Score=21.04 Aligned_cols=26 Identities=15% Similarity=0.290 Sum_probs=22.1
Q ss_pred HHHHHHhCHHHHHHhCCCCeEEEEEc
Q psy15303 26 VRDFLAQHYVPLKQANPKFPILVREC 51 (72)
Q Consensus 26 vR~Fl~~~l~~~k~~NP~v~i~v~~~ 51 (72)
...++...+.+|++++|++.|.+...
T Consensus 11 ~~~~l~~~l~~~~~~~p~i~i~i~~~ 36 (197)
T cd08414 11 LYGLLPRLLRRFRARYPDVELELREM 36 (197)
T ss_pred HHHHHHHHHHHHHHHCCCcEEEEecC
Confidence 45678899999999999999998753
No 36
>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=48.76 E-value=24 Score=21.24 Aligned_cols=27 Identities=15% Similarity=0.151 Sum_probs=22.3
Q ss_pred HHHHHHHhCHHHHHHhCCCCeEEEEEc
Q psy15303 25 GVRDFLAQHYVPLKQANPKFPILVREC 51 (72)
Q Consensus 25 GvR~Fl~~~l~~~k~~NP~v~i~v~~~ 51 (72)
-...++...+.+|.+++|++.+.+...
T Consensus 10 ~~~~~l~~~l~~~~~~~P~v~i~i~~~ 36 (194)
T cd08436 10 LAAVDLPELLARFHRRHPGVDIRLRQA 36 (194)
T ss_pred HHHHHHHHHHHHHHHHCCCcEEEEecC
Confidence 345677888999999999999998764
No 37
>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=48.41 E-value=24 Score=21.41 Aligned_cols=26 Identities=12% Similarity=0.256 Sum_probs=22.0
Q ss_pred HHHHHHhCHHHHHHhCCCCeEEEEEc
Q psy15303 26 VRDFLAQHYVPLKQANPKFPILVREC 51 (72)
Q Consensus 26 vR~Fl~~~l~~~k~~NP~v~i~v~~~ 51 (72)
...++...+.+|++++|++.+.+.+.
T Consensus 11 ~~~~l~~~l~~~~~~~P~i~l~i~~~ 36 (196)
T cd08450 11 EVQWLPEVLPILREEHPDLDVELSSL 36 (196)
T ss_pred hhhhHHHHHHHHHhhCCCcEEEEEec
Confidence 45777889999999999999998764
No 38
>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=48.36 E-value=32 Score=21.43 Aligned_cols=25 Identities=8% Similarity=0.046 Sum_probs=21.0
Q ss_pred HHHHHhCHHHHHHhCCCCeEEEEEc
Q psy15303 27 RDFLAQHYVPLKQANPKFPILVREC 51 (72)
Q Consensus 27 R~Fl~~~l~~~k~~NP~v~i~v~~~ 51 (72)
..++...+.+|++++|++++.+.+.
T Consensus 13 ~~~l~~~l~~f~~~~P~v~i~i~~~ 37 (198)
T cd08486 13 YRSLPLLLRAFLTSTPTATVSLTHM 37 (198)
T ss_pred HHHHHHHHHHHHHhCCCeEEEEEEC
Confidence 5667788899999999999998764
No 39
>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=48.15 E-value=21 Score=21.96 Aligned_cols=27 Identities=19% Similarity=0.381 Sum_probs=22.9
Q ss_pred HHHHHHhCHHHHHHhCCCCeEEEEEcC
Q psy15303 26 VRDFLAQHYVPLKQANPKFPILVRECS 52 (72)
Q Consensus 26 vR~Fl~~~l~~~k~~NP~v~i~v~~~~ 52 (72)
...++...+.+|.+++|++.|.+.+..
T Consensus 17 ~~~~l~~~l~~~~~~~P~i~i~~~~~~ 43 (209)
T PF03466_consen 17 ASSLLPPLLAEFRERHPNIRIEIREGD 43 (209)
T ss_dssp HHHTHHHHHHHHHHHSTTEEEEEEEES
T ss_pred HHHHHHHHHHHHHHHCCCcEEEEEecc
Confidence 366778899999999999999998754
No 40
>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=48.13 E-value=25 Score=21.40 Aligned_cols=25 Identities=20% Similarity=-0.016 Sum_probs=21.1
Q ss_pred HHHHHhCHHHHHHhCCCCeEEEEEc
Q psy15303 27 RDFLAQHYVPLKQANPKFPILVREC 51 (72)
Q Consensus 27 R~Fl~~~l~~~k~~NP~v~i~v~~~ 51 (72)
..++...+..|.+.+|++.|.+.+.
T Consensus 12 ~~~l~~~l~~~~~~~P~v~i~i~~~ 36 (195)
T cd08431 12 LQPLYPLIAEFYQLNKATRIRLSEE 36 (195)
T ss_pred hHHHHHHHHHHHHHCCCCceEEEEe
Confidence 3567888999999999999999764
No 41
>cd08464 PBP2_DntR_like_2 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator similar to DntR, which is involved in the catabolism of dinitrotoluene; contains the type 2 periplasmic binding fold. This CD includes an uncharacterized LysR-type transcriptional regulator similar to DntR, NahR, and LinR, which are involved in the degradation of aromatic compounds. The transcription of the genes encoding enzymes involved in such degradation is regulated and expression of these enzymes is enhanced by inducers, which are either an intermediate in the metabolic pathway or compounds to be degraded. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytra
Probab=47.92 E-value=34 Score=20.77 Aligned_cols=25 Identities=12% Similarity=0.229 Sum_probs=21.2
Q ss_pred HHHHHhCHHHHHHhCCCCeEEEEEc
Q psy15303 27 RDFLAQHYVPLKQANPKFPILVREC 51 (72)
Q Consensus 27 R~Fl~~~l~~~k~~NP~v~i~v~~~ 51 (72)
..++..-+.+|++++|++.+.+...
T Consensus 12 ~~~l~~~l~~~~~~~P~v~l~i~~~ 36 (200)
T cd08464 12 SWLAPPLLAALRAEAPGVRLVFRQV 36 (200)
T ss_pred HHHHHHHHHHHHHHCCCcEEEEecC
Confidence 3567788999999999999999764
No 42
>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=47.86 E-value=29 Score=21.48 Aligned_cols=26 Identities=15% Similarity=0.190 Sum_probs=20.8
Q ss_pred HHHHHHhCHHHHHHhCCCCeEEEEEc
Q psy15303 26 VRDFLAQHYVPLKQANPKFPILVREC 51 (72)
Q Consensus 26 vR~Fl~~~l~~~k~~NP~v~i~v~~~ 51 (72)
...++...+.+|++++|++.+.+...
T Consensus 11 ~~~~l~~~l~~~~~~~P~v~l~i~~~ 36 (198)
T cd08444 11 ARYALPWVVQAFKEQFPNVHLVLHQG 36 (198)
T ss_pred hhhhhhHHHHHHHHHCCCeEEEEEeC
Confidence 45677888889999999988888754
No 43
>cd08438 PBP2_CidR The C-terminal substrate binding domain of LysR-like transcriptional regulator CidR, contains the type 2 periplasmic binding fold. This CD includes the substrate binding domain of CidR which positively up-regulates the expression of cidABC operon in the presence of acetic acid produced by the metabolism of excess glucose. The CidR affects the control of murein hydrolase activity by enhancing cidABC expression in the presence of acetic acid. Thus, up-regulation of cidABC expression results in increased murein hydrolase activity. This substrate binding domain has significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate
Probab=47.74 E-value=24 Score=21.25 Aligned_cols=25 Identities=16% Similarity=0.238 Sum_probs=21.5
Q ss_pred HHHHHhCHHHHHHhCCCCeEEEEEc
Q psy15303 27 RDFLAQHYVPLKQANPKFPILVREC 51 (72)
Q Consensus 27 R~Fl~~~l~~~k~~NP~v~i~v~~~ 51 (72)
..++...+.+|++++|++.|.+...
T Consensus 12 ~~~l~~~l~~~~~~~p~v~i~i~~~ 36 (197)
T cd08438 12 SLLFAPLLAAFRQRYPNIELELVEY 36 (197)
T ss_pred hhhcHHHHHHHHHHCcCeEEEEEEc
Confidence 4677888999999999999999764
No 44
>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=47.73 E-value=30 Score=21.12 Aligned_cols=26 Identities=19% Similarity=0.160 Sum_probs=22.1
Q ss_pred HHHHHHhCHHHHHHhCCCCeEEEEEc
Q psy15303 26 VRDFLAQHYVPLKQANPKFPILVREC 51 (72)
Q Consensus 26 vR~Fl~~~l~~~k~~NP~v~i~v~~~ 51 (72)
...++..-+.+|.+++|++.+.+...
T Consensus 11 ~~~~l~~~l~~f~~~~P~v~l~~~~~ 36 (200)
T cd08466 11 DLLLLPRLLARLKQLAPNISLRESPS 36 (200)
T ss_pred HHHHHHHHHHHHHHHCCCCEEEEecC
Confidence 34677889999999999999999764
No 45
>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=47.65 E-value=27 Score=21.20 Aligned_cols=26 Identities=15% Similarity=0.193 Sum_probs=21.8
Q ss_pred HHHHHHhCHHHHHHhCCCCeEEEEEc
Q psy15303 26 VRDFLAQHYVPLKQANPKFPILVREC 51 (72)
Q Consensus 26 vR~Fl~~~l~~~k~~NP~v~i~v~~~ 51 (72)
...++...+..|++++|++.+.+...
T Consensus 11 ~~~~l~~~l~~~~~~~P~i~l~i~~~ 36 (199)
T cd08426 11 AAELLPSLIARFRQRYPGVFFTVDVA 36 (199)
T ss_pred HHHHHHHHHHHHHHhCCCeEEEEEeC
Confidence 45677888999999999999999764
No 46
>PRK00286 xseA exodeoxyribonuclease VII large subunit; Reviewed
Probab=47.55 E-value=29 Score=26.15 Aligned_cols=30 Identities=17% Similarity=0.365 Sum_probs=24.4
Q ss_pred CCCCCHHHHHHHHhCHHHHHHhCCCCeEEEEEcC
Q psy15303 19 KGGSSSGVRDFLAQHYVPLKQANPKFPILVRECS 52 (72)
Q Consensus 19 ~~~sS~GvR~Fl~~~l~~~k~~NP~v~i~v~~~~ 52 (72)
+|+++++++||+.. +++++|.+.|.+.+..
T Consensus 142 Ts~~gAa~~D~~~~----~~~r~p~~~~~~~~~~ 171 (438)
T PRK00286 142 TSPTGAAIRDILTV----LRRRFPLVEVIIYPTL 171 (438)
T ss_pred eCCccHHHHHHHHH----HHhcCCCCeEEEecCc
Confidence 57779999999864 5678899999987764
No 47
>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=47.50 E-value=31 Score=20.70 Aligned_cols=26 Identities=8% Similarity=0.124 Sum_probs=22.0
Q ss_pred HHHHHHhCHHHHHHhCCCCeEEEEEc
Q psy15303 26 VRDFLAQHYVPLKQANPKFPILVREC 51 (72)
Q Consensus 26 vR~Fl~~~l~~~k~~NP~v~i~v~~~ 51 (72)
...++..-+.+|++.+|++.+.+.+.
T Consensus 11 ~~~~l~~~l~~~~~~~P~~~l~~~~~ 36 (201)
T cd08420 11 GEYLLPRLLARFRKRYPEVRVSLTIG 36 (201)
T ss_pred hhhhhHHHHHHHHHHCCCceEEEEeC
Confidence 45677888999999999999998764
No 48
>cd02974 AhpF_NTD_N Alkyl hydroperoxide reductase F subunit (AhpF) N-terminal domain (NTD) family, N-terminal TRX-fold subdomain; AhpF is a homodimeric flavoenzyme which catalyzes the NADH-dependent reduction of the peroxiredoxin AhpC, which in turn catalyzes the reduction of hydrogen peroxide and organic hydroperoxides. AhpF contains an NTD forming two contiguous TRX-fold subdomain similar to Pyrococcus furiosus protein disulfide oxidoreductase (PfPDO). It also contains a catalytic core similar to TRX reductase containing FAD and NADH binding domains with an active site disulfide. The proposed mechanism of action of AhpF is similar to a TRX/TRX reductase system. The flow of reducing equivalents goes from NADH - catalytic core of AhpF - NTD of AhpF - AhpC - peroxide substrates. The N-terminal TRX-fold subdomain of AhpF NTD is redox inactive, but is proposed to contain an important residue that aids in the catalytic function of the redox-active CXXC motif contained in the C-terminal TRX-
Probab=47.43 E-value=64 Score=19.65 Aligned_cols=45 Identities=13% Similarity=0.139 Sum_probs=31.9
Q ss_pred EEEEecCCCCCCHHHHHHHHhCHHHHHHhCCCCeEEEEEcCCCCCEEEEE
Q psy15303 12 LRIHLCQKGGSSSGVRDFLAQHYVPLKQANPKFPILVRECSGVTPVVWAR 61 (72)
Q Consensus 12 L~~~yC~~~~sS~GvR~Fl~~~l~~~k~~NP~v~i~v~~~~g~~P~l~a~ 61 (72)
|.+.. +.++.|.=+++|++ +++..+|.+.+.+......-|.+...
T Consensus 23 l~~f~-~~~~~~~e~~~ll~----e~a~lSdkI~~~~~~~~~~~P~~~i~ 67 (94)
T cd02974 23 LVASL-DDSEKSAELLELLE----EIASLSDKITLEEDNDDERKPSFSIN 67 (94)
T ss_pred EEEEe-CCCcchHHHHHHHH----HHHHhCCceEEEEecCCCCCCEEEEe
Confidence 33343 44588888888876 79999999998876644456877764
No 49
>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=47.32 E-value=29 Score=20.87 Aligned_cols=26 Identities=12% Similarity=0.142 Sum_probs=21.7
Q ss_pred HHHHHHHhCHHHHHHhCCCCeEEEEE
Q psy15303 25 GVRDFLAQHYVPLKQANPKFPILVRE 50 (72)
Q Consensus 25 GvR~Fl~~~l~~~k~~NP~v~i~v~~ 50 (72)
-...++...+.+|.+++|++.+.+..
T Consensus 10 ~~~~~l~~~l~~~~~~~P~i~i~i~~ 35 (197)
T cd08448 10 MLYRGLPRILRAFRAEYPGIEVALHE 35 (197)
T ss_pred HHHHHHHHHHHHHHHHCCCCeEEEEe
Confidence 34577888899999999999998875
No 50
>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=47.18 E-value=27 Score=21.03 Aligned_cols=24 Identities=13% Similarity=0.128 Sum_probs=19.9
Q ss_pred HHHHHhCHHHHHHhCCCCeEEEEE
Q psy15303 27 RDFLAQHYVPLKQANPKFPILVRE 50 (72)
Q Consensus 27 R~Fl~~~l~~~k~~NP~v~i~v~~ 50 (72)
..++...+.+|++++|++.+.+..
T Consensus 11 ~~~l~~~l~~~~~~~P~v~i~~~~ 34 (197)
T cd08476 11 GGLLLPVLAAFMQRYPEIELDLDF 34 (197)
T ss_pred HHHHHHHHHHHHHHCCCeEEEEEe
Confidence 356667899999999999999854
No 51
>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=46.68 E-value=25 Score=21.09 Aligned_cols=26 Identities=4% Similarity=0.148 Sum_probs=21.6
Q ss_pred HHHHHHhCHHHHHHhCCCCeEEEEEc
Q psy15303 26 VRDFLAQHYVPLKQANPKFPILVREC 51 (72)
Q Consensus 26 vR~Fl~~~l~~~k~~NP~v~i~v~~~ 51 (72)
...++...+..|.+++|++.+.++..
T Consensus 11 ~~~~l~~~l~~~~~~~P~i~i~i~~~ 36 (195)
T cd08434 11 GTSLVPDLIRAFRKEYPNVTFELHQG 36 (195)
T ss_pred hhhhhHHHHHHHHHhCCCeEEEEecC
Confidence 34677888999999999999998864
No 52
>cd08483 PBP2_HvrB The C-terminal substrate-binding domain of LysR-type transcriptional regulator HvrB, an activator of S-adenosyl-L-homocysteine hydrolase expression, contains the type 2 periplasmic binding fold. The transcriptional regulator HvrB of the LysR family is required for the light-dependent activation of both ahcY, which encoding the enzyme S-adenosyl-L-homocysteine hydrolase (AdoHcyase) that responsible for the reversible hydrolysis of AdoHcy to adenosine and homocysteine, and orf5, a gene of unknown. The topology of this C-terminal domain of HvrB is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transp
Probab=46.40 E-value=31 Score=20.85 Aligned_cols=25 Identities=8% Similarity=0.198 Sum_probs=21.2
Q ss_pred HHHHHHhCHHHHHHhCCCCeEEEEE
Q psy15303 26 VRDFLAQHYVPLKQANPKFPILVRE 50 (72)
Q Consensus 26 vR~Fl~~~l~~~k~~NP~v~i~v~~ 50 (72)
...++...+.+|.+++|++.+.+..
T Consensus 11 ~~~~l~~~l~~~~~~~P~i~l~~~~ 35 (190)
T cd08483 11 ASNWLMPRLGSFWAKHPEIELSLLP 35 (190)
T ss_pred HHhhHHhhHHHHHHHCCCceEEEEe
Confidence 4567778899999999999999874
No 53
>COG1182 AcpD Acyl carrier protein phosphodiesterase [Lipid metabolism]
Probab=46.12 E-value=30 Score=24.51 Aligned_cols=52 Identities=17% Similarity=0.251 Sum_probs=33.8
Q ss_pred EEEEecCCCCCCHHHHHHHHhCHHHHHHhCCCCeEEEEE-cCCCCCEEEEEecC
Q psy15303 12 LRIHLCQKGGSSSGVRDFLAQHYVPLKQANPKFPILVRE-CSGVTPVVWARIPT 64 (72)
Q Consensus 12 L~~~yC~~~~sS~GvR~Fl~~~l~~~k~~NP~v~i~v~~-~~g~~P~l~a~Y~n 64 (72)
|-|.-+..++.|.- |...+.-+.++|++||+.+|..+. ....-|++..+..+
T Consensus 5 L~I~as~~~~~S~S-~~l~~~Fi~~yk~~~P~dev~~~DL~~e~iP~ld~~~~~ 57 (202)
T COG1182 5 LVIKASPLGENSVS-RKLADEFIETYKEKHPNDEVIERDLAAEPIPHLDEELLA 57 (202)
T ss_pred EEEecCCCccccHH-HHHHHHHHHHHHHhCCCCeEEEeecccCCCcccCHHHHh
Confidence 44444444333332 223344556799999999999977 56778888776665
No 54
>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=45.75 E-value=37 Score=20.64 Aligned_cols=27 Identities=11% Similarity=0.127 Sum_probs=22.5
Q ss_pred HHHHHHHhCHHHHHHhCCCCeEEEEEc
Q psy15303 25 GVRDFLAQHYVPLKQANPKFPILVREC 51 (72)
Q Consensus 25 GvR~Fl~~~l~~~k~~NP~v~i~v~~~ 51 (72)
-...++...+.+|++++|++.|.+...
T Consensus 11 ~~~~~l~~~l~~f~~~~P~i~i~~~~~ 37 (198)
T cd08479 11 FGRRHIAPALSDFAKRYPELEVQLELT 37 (198)
T ss_pred HHHHHHHHHHHHHHHHCCCeEEEEEec
Confidence 355778889999999999999998753
No 55
>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=45.69 E-value=31 Score=21.10 Aligned_cols=26 Identities=19% Similarity=0.295 Sum_probs=22.1
Q ss_pred HHHHHHhCHHHHHHhCCCCeEEEEEc
Q psy15303 26 VRDFLAQHYVPLKQANPKFPILVREC 51 (72)
Q Consensus 26 vR~Fl~~~l~~~k~~NP~v~i~v~~~ 51 (72)
...++...+.+|.+++|++.+.+...
T Consensus 11 ~~~~l~~~l~~~~~~~P~i~l~i~~~ 36 (200)
T cd08453 11 DYSVLPELVRRFREAYPDVELQLREA 36 (200)
T ss_pred HhHHHHHHHHHHHHhCCCceEEEEeC
Confidence 34688899999999999999999764
No 56
>cd08432 PBP2_GcdR_TrpI_HvrB_AmpR_like The C-terminal substrate domain of LysR-type GcdR, TrPI, HvR and beta-lactamase regulators, and that of other closely related homologs; contains the type 2 periplasmic binding fold. This CD includes the C-terminal substrate domain of LysR-type transcriptional regulators involved in controlling the expression of glutaryl-CoA dehydrogenase (GcdH), S-adenosyl-L-homocysteine hydrolase, cell division protein FtsW, tryptophan synthase, and beta-lactamase. The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex compris
Probab=45.47 E-value=39 Score=20.31 Aligned_cols=28 Identities=7% Similarity=0.185 Sum_probs=22.6
Q ss_pred HHHHHHHhCHHHHHHhCCCCeEEEEEcC
Q psy15303 25 GVRDFLAQHYVPLKQANPKFPILVRECS 52 (72)
Q Consensus 25 GvR~Fl~~~l~~~k~~NP~v~i~v~~~~ 52 (72)
-...++...+.+|.+++|++.+.+.+..
T Consensus 10 ~~~~~l~~~l~~~~~~~P~v~i~~~~~~ 37 (194)
T cd08432 10 FAARWLIPRLARFQARHPDIDLRLSTSD 37 (194)
T ss_pred HHHHHHHHHhHHHHHHCCCeEEEEEecC
Confidence 3455678889999999999999997643
No 57
>PRK14003 potassium-transporting ATPase subunit C; Provisional
Probab=45.42 E-value=30 Score=24.35 Aligned_cols=46 Identities=13% Similarity=0.152 Sum_probs=37.0
Q ss_pred cCCCCCCHHHHHHHHhCHHHHHHhCCCC--eEEEEEcCCCCCEEEEEe
Q psy15303 17 CQKGGSSSGVRDFLAQHYVPLKQANPKF--PILVRECSGVTPVVWARI 62 (72)
Q Consensus 17 C~~~~sS~GvR~Fl~~~l~~~k~~NP~v--~i~v~~~~g~~P~l~a~Y 62 (72)
++-++++.-+.+-+++....++++||.. +.++....|-+|.|.-++
T Consensus 93 SNl~psnp~l~~~v~~r~~~~~~~~~~pp~DlVTaSgSGLDPhISp~a 140 (194)
T PRK14003 93 SNLAPSNPALIERIKEEANRLQDAGIQPTADLVYTSGSGLDPHISPEA 140 (194)
T ss_pred cCCCCCCHHHHHHHHHHHHHHHHcCCCCChhheecccccCCCCCCHHH
Confidence 4567889999999999999999999654 567777889999876443
No 58
>PRK13996 potassium-transporting ATPase subunit C; Provisional
Probab=45.22 E-value=19 Score=25.43 Aligned_cols=44 Identities=14% Similarity=0.317 Sum_probs=34.5
Q ss_pred cCCCCCCHHHHHHHHhCHHHHHHhCCC-----Ce--EEEEEcCCCCCEEEE
Q psy15303 17 CQKGGSSSGVRDFLAQHYVPLKQANPK-----FP--ILVRECSGVTPVVWA 60 (72)
Q Consensus 17 C~~~~sS~GvR~Fl~~~l~~~k~~NP~-----v~--i~v~~~~g~~P~l~a 60 (72)
++.+++|.-+++-+++....++++||. || .++....|-+|.|.-
T Consensus 91 SNlgpsnp~L~~~v~~r~~~~~~~~~~v~~~~vP~DlvTaSgSGLDPhISp 141 (197)
T PRK13996 91 SNLSPASKEYEALVQERVEKIRANHPEQDEKPIPVDLVTCSGSGLDPHISV 141 (197)
T ss_pred cCCCCCCHHHHHHHHHHHHHHHHhCCCCCCCCCCHHHHhccccCCCCCCCH
Confidence 567889999999999999999999985 44 344556677887653
No 59
>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=45.03 E-value=32 Score=20.91 Aligned_cols=27 Identities=11% Similarity=0.103 Sum_probs=22.7
Q ss_pred HHHHHHHhCHHHHHHhCCCCeEEEEEc
Q psy15303 25 GVRDFLAQHYVPLKQANPKFPILVREC 51 (72)
Q Consensus 25 GvR~Fl~~~l~~~k~~NP~v~i~v~~~ 51 (72)
....++...+.+|++++|++.|.+.+.
T Consensus 11 ~~~~~l~~~l~~~~~~~P~v~i~i~~~ 37 (197)
T cd08425 11 FTAYLIGPLIDRFHARYPGIALSLREM 37 (197)
T ss_pred hhhhhhHHHHHHHHHHCCCcEEEEEEC
Confidence 456677889999999999999999764
No 60
>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=44.86 E-value=43 Score=20.34 Aligned_cols=25 Identities=12% Similarity=0.089 Sum_probs=21.4
Q ss_pred HHHHHHhCHHHHHHhCCCCeEEEEE
Q psy15303 26 VRDFLAQHYVPLKQANPKFPILVRE 50 (72)
Q Consensus 26 vR~Fl~~~l~~~k~~NP~v~i~v~~ 50 (72)
...++...+.+|.+++|++.+.+..
T Consensus 12 ~~~~l~~~l~~~~~~~P~i~v~~~~ 36 (202)
T cd08472 12 ARLLLIPALPDFLARYPDIELDLGV 36 (202)
T ss_pred HHHHHHHHHHHHHHHCCCcEEEEEE
Confidence 4567788999999999999999865
No 61
>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=44.52 E-value=31 Score=21.04 Aligned_cols=25 Identities=12% Similarity=0.018 Sum_probs=21.3
Q ss_pred HHHHHhCHHHHHHhCCCCeEEEEEc
Q psy15303 27 RDFLAQHYVPLKQANPKFPILVREC 51 (72)
Q Consensus 27 R~Fl~~~l~~~k~~NP~v~i~v~~~ 51 (72)
-.++...+.+|.+.+|++.+.+...
T Consensus 12 ~~~l~~~l~~~~~~~P~v~i~~~~~ 36 (198)
T cd08437 12 NYYFPKLAKDLIKTGLMIQIDTYEG 36 (198)
T ss_pred HHHhHHHHHHHHHhCCceEEEEEEc
Confidence 4577889999999999999999753
No 62
>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=44.29 E-value=27 Score=21.35 Aligned_cols=26 Identities=15% Similarity=0.188 Sum_probs=21.8
Q ss_pred HHHHHHHhCHHHHHHhCCCCeEEEEE
Q psy15303 25 GVRDFLAQHYVPLKQANPKFPILVRE 50 (72)
Q Consensus 25 GvR~Fl~~~l~~~k~~NP~v~i~v~~ 50 (72)
-...++...+.+|.+++|++.+.+..
T Consensus 13 ~~~~~l~~~l~~f~~~~P~v~i~~~~ 38 (199)
T cd08478 13 FVLHLLAPLIAKFRERYPDIELELVS 38 (199)
T ss_pred HHHHHHHHHHHHHHHHCCCeEEEEEe
Confidence 34567889999999999999999863
No 63
>PF04690 YABBY: YABBY protein; InterPro: IPR006780 YABBY proteins are a group of plant-specific transcription factors involved in the specification of abaxial polarity in lateral organs such as leaves and floral organs [, ].
Probab=43.98 E-value=15 Score=25.31 Aligned_cols=19 Identities=21% Similarity=0.483 Sum_probs=16.9
Q ss_pred HHHHHhCHHHHHHhCCCCe
Q psy15303 27 RDFLAQHYVPLKQANPKFP 45 (72)
Q Consensus 27 R~Fl~~~l~~~k~~NP~v~ 45 (72)
..||++.+..+|..||++.
T Consensus 130 n~f~k~ei~rik~~~p~is 148 (170)
T PF04690_consen 130 NRFMKEEIQRIKAENPDIS 148 (170)
T ss_pred HHHHHHHHHHHHhcCCCCC
Confidence 4699999999999999975
No 64
>cd08445 PBP2_BenM_CatM_CatR The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in benzoate catabolism; contains the type 2 periplasmic binding fold. This CD includes the C-terminal of LysR-type transcription regulators, BenM, CatM, and CatR, which are involved in the benzoate catabolism. The BenM and CatM are paralogs with overlapping functions. BenM responds synergistically to two effectors, benzoate and cis,cis-muconate, to activate expression of the benABCDE operon which is involved in benzoate catabolism, while CatM responses only to muconate. BenM and CatM share high protein sequence identity and bind to the operator-promoter regions that have similar DNA sequences. In Pseudomonas species, phenolic compounds are converted by different enzymes to central intermediates, such as protocatechuate and catechols. Generally, unsubstituted compounds, such as benzoate, are metabolized by an ortho-cleavage pathway. The catBCA operon encodes three enzymes
Probab=43.87 E-value=35 Score=21.05 Aligned_cols=26 Identities=23% Similarity=0.298 Sum_probs=21.9
Q ss_pred HHHHHHhCHHHHHHhCCCCeEEEEEc
Q psy15303 26 VRDFLAQHYVPLKQANPKFPILVREC 51 (72)
Q Consensus 26 vR~Fl~~~l~~~k~~NP~v~i~v~~~ 51 (72)
...++..-+.+|.+++|++.+.+.+.
T Consensus 12 ~~~~l~~~l~~~~~~~P~i~l~i~~~ 37 (203)
T cd08445 12 LYGLLPELIRRFRQAAPDVEIELIEM 37 (203)
T ss_pred HHhHHHHHHHHHHHHCCCeEEEEEeC
Confidence 35678889999999999999998754
No 65
>cd08421 PBP2_LTTR_like_1 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator, contains the type 2 periplasmic binding fold. LysR-transcriptional regulators comprise the largest family of prokaryotic transcription factor. Homologs of some of LTTRs with similar domain organizations are also found in the archaea and eukaryotic organisms. The LTTRs are composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcriptional repressor undergoes a conformational change upon substrate binding which in turn changes the DNA binding affinity of the repressor. The genes controlled by the LTTRs have diverse functi
Probab=43.42 E-value=35 Score=20.67 Aligned_cols=24 Identities=25% Similarity=0.429 Sum_probs=20.6
Q ss_pred HHHHhCHHHHHHhCCCCeEEEEEc
Q psy15303 28 DFLAQHYVPLKQANPKFPILVREC 51 (72)
Q Consensus 28 ~Fl~~~l~~~k~~NP~v~i~v~~~ 51 (72)
.++..-+.+|.+.+|++++.+...
T Consensus 13 ~~l~~~l~~~~~~~P~i~i~~~~~ 36 (198)
T cd08421 13 EFLPEDLASFLAAHPDVRIDLEER 36 (198)
T ss_pred hhhHHHHHHHHHHCCCceEEEEec
Confidence 467788999999999999998764
No 66
>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=43.06 E-value=41 Score=20.52 Aligned_cols=26 Identities=15% Similarity=0.091 Sum_probs=22.0
Q ss_pred HHHHHHhCHHHHHHhCCCCeEEEEEc
Q psy15303 26 VRDFLAQHYVPLKQANPKFPILVREC 51 (72)
Q Consensus 26 vR~Fl~~~l~~~k~~NP~v~i~v~~~ 51 (72)
...++...+.+|++++|++.+.+...
T Consensus 14 ~~~~l~~~l~~~~~~~P~v~i~~~~~ 39 (202)
T cd08474 14 ARLLLAPLLARFLARYPDIRLELVVD 39 (202)
T ss_pred HHHHHHHHHHHHHHHCCCeEEEEEec
Confidence 35677889999999999999999753
No 67
>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=42.77 E-value=46 Score=20.26 Aligned_cols=24 Identities=13% Similarity=0.207 Sum_probs=20.0
Q ss_pred HHHHhCHHHHHHhCCCCeEEEEEc
Q psy15303 28 DFLAQHYVPLKQANPKFPILVREC 51 (72)
Q Consensus 28 ~Fl~~~l~~~k~~NP~v~i~v~~~ 51 (72)
.++...+.+|.+++|++.+.+...
T Consensus 13 ~~~~~~l~~~~~~~P~i~i~i~~~ 36 (198)
T cd08441 13 DWLMPVLDQFRERWPDVELDLSSG 36 (198)
T ss_pred hhhHHHHHHHHHhCCCeEEEEEeC
Confidence 467778899999999999998764
No 68
>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=42.75 E-value=17 Score=21.98 Aligned_cols=26 Identities=12% Similarity=0.245 Sum_probs=21.2
Q ss_pred HHHHHHhCHHHHHHhCCCCeEEEEEc
Q psy15303 26 VRDFLAQHYVPLKQANPKFPILVREC 51 (72)
Q Consensus 26 vR~Fl~~~l~~~k~~NP~v~i~v~~~ 51 (72)
...++...+.+|++++|++.+.+...
T Consensus 11 ~~~~l~~~l~~~~~~~P~i~l~i~~~ 36 (196)
T cd08415 11 ALSLLPRAIARFRARHPDVRISLHTL 36 (196)
T ss_pred cccccHHHHHHHHHHCCCcEEEEEec
Confidence 34567788899999999999988764
No 69
>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=42.50 E-value=37 Score=20.44 Aligned_cols=25 Identities=20% Similarity=0.420 Sum_probs=21.2
Q ss_pred HHHHHhCHHHHHHhCCCCeEEEEEc
Q psy15303 27 RDFLAQHYVPLKQANPKFPILVREC 51 (72)
Q Consensus 27 R~Fl~~~l~~~k~~NP~v~i~v~~~ 51 (72)
-.++...+.+|++++|++.|.+...
T Consensus 12 ~~~l~~~l~~~~~~~P~i~i~~~~~ 36 (200)
T cd08423 12 AALLPPALAALRARHPGLEVRLREA 36 (200)
T ss_pred HHhhhHHHHHHHHhCCCCeEEEEeC
Confidence 4567888999999999999999764
No 70
>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=42.10 E-value=35 Score=20.47 Aligned_cols=25 Identities=16% Similarity=0.090 Sum_probs=21.2
Q ss_pred HHHHHhCHHHHHHhCCCCeEEEEEc
Q psy15303 27 RDFLAQHYVPLKQANPKFPILVREC 51 (72)
Q Consensus 27 R~Fl~~~l~~~k~~NP~v~i~v~~~ 51 (72)
..++...+.+|++++|++.+.+...
T Consensus 13 ~~~l~~~l~~~~~~~P~v~i~i~~~ 37 (197)
T cd08422 13 RLHLAPLLAEFLARYPDVRLELVLS 37 (197)
T ss_pred HHHHHHHHHHHHHhCCceEEEEecC
Confidence 4567888999999999999999753
No 71
>PF07315 DUF1462: Protein of unknown function (DUF1462); InterPro: IPR009190 There are currently no experimental data for members of this group of bacterial proteins or their homologues. A crystal structure of Q7A6J8 from SWISSPROT revealed a thioredoxin-like fold, its core consisting of three layers alpha/beta/alpha.; PDB: 1XG8_A.
Probab=41.96 E-value=48 Score=20.89 Aligned_cols=33 Identities=24% Similarity=0.376 Sum_probs=24.0
Q ss_pred cCCCCCCHHHHHHHHhCHHHHHHhCCCCeEEEEEcC
Q psy15303 17 CQKGGSSSGVRDFLAQHYVPLKQANPKFPILVRECS 52 (72)
Q Consensus 17 C~~~~sS~GvR~Fl~~~l~~~k~~NP~v~i~v~~~~ 52 (72)
|=+.|||+-.-+||+ +.++++.|+.+|.++-.-
T Consensus 12 CVn~PsSkeTyeWL~---aal~RKyp~~~f~~~YiD 44 (93)
T PF07315_consen 12 CVNAPSSKETYEWLE---AALKRKYPDQPFEFTYID 44 (93)
T ss_dssp GSSS--HHHHHHHHH---HHHHHH-TTS-EEEEEEE
T ss_pred hcCCCCchhHHHHHH---HHHhCcCCCCceEEEEEe
Confidence 778899999999998 467899999999886543
No 72
>PRK13997 potassium-transporting ATPase subunit C; Provisional
Probab=41.92 E-value=23 Score=24.94 Aligned_cols=45 Identities=18% Similarity=0.320 Sum_probs=35.1
Q ss_pred cCCCCCCHHHHHHHHhCHHHHHHhCCC-----Ce--EEEEEcCCCCCEEEEE
Q psy15303 17 CQKGGSSSGVRDFLAQHYVPLKQANPK-----FP--ILVRECSGVTPVVWAR 61 (72)
Q Consensus 17 C~~~~sS~GvR~Fl~~~l~~~k~~NP~-----v~--i~v~~~~g~~P~l~a~ 61 (72)
++-++++.-+++-+++....+++.||. || .++....|-+|.|.-+
T Consensus 87 SNl~psnp~l~~~v~~r~~~~~~~~~~~~~~~vP~DlVTaSgSGLDPhISp~ 138 (193)
T PRK13997 87 NNYAPSNPDLEKRVEKSIEEWKKQNPSVPVTEVPIDLVTNSGSGLDPDISPK 138 (193)
T ss_pred cCCCCCCHHHHHHHHHHHHHHHHhCCCCCCCCCCHHHHhccccCCCCCCCHH
Confidence 567889999999999999999999984 44 3445566778877543
No 73
>COG1653 UgpB ABC-type sugar transport system, periplasmic component [Carbohydrate transport and metabolism]
Probab=41.91 E-value=78 Score=22.17 Aligned_cols=26 Identities=19% Similarity=0.281 Sum_probs=23.3
Q ss_pred HHHHHhCHHHHHHhCCCCeEEEEEcC
Q psy15303 27 RDFLAQHYVPLKQANPKFPILVRECS 52 (72)
Q Consensus 27 R~Fl~~~l~~~k~~NP~v~i~v~~~~ 52 (72)
.++++....+|.++||+|+|.+....
T Consensus 45 ~~~~~~~i~~f~~~~p~ikv~~~~~~ 70 (433)
T COG1653 45 ADALEELIKEFEKENPGIKVKVVNVP 70 (433)
T ss_pred hHHHHHHHHHHHHhCCCeEEEEEecC
Confidence 88899999999999999999887754
No 74
>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=41.52 E-value=39 Score=20.27 Aligned_cols=25 Identities=12% Similarity=0.183 Sum_probs=21.6
Q ss_pred HHHHHhCHHHHHHhCCCCeEEEEEc
Q psy15303 27 RDFLAQHYVPLKQANPKFPILVREC 51 (72)
Q Consensus 27 R~Fl~~~l~~~k~~NP~v~i~v~~~ 51 (72)
..++..-+..|.+++|++.+.+...
T Consensus 11 ~~~l~~~l~~~~~~~P~i~l~i~~~ 35 (197)
T cd08419 11 KYFAPRLLGAFCRRHPGVEVSLRVG 35 (197)
T ss_pred HhHhhHHHHHHHHHCCCceEEEEEC
Confidence 4678889999999999999998763
No 75
>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=41.08 E-value=42 Score=20.65 Aligned_cols=25 Identities=12% Similarity=0.085 Sum_probs=21.2
Q ss_pred HHHHHHhCHHHHHHhCCCCeEEEEE
Q psy15303 26 VRDFLAQHYVPLKQANPKFPILVRE 50 (72)
Q Consensus 26 vR~Fl~~~l~~~k~~NP~v~i~v~~ 50 (72)
...++...+.+|.+++|++.+.+..
T Consensus 12 ~~~~l~~~l~~~~~~~P~i~i~i~~ 36 (198)
T cd08480 12 GTHFLLPLLPAFLARYPEILVDLSL 36 (198)
T ss_pred HhHhhHHHHHHHHHHCCCeEEEEEe
Confidence 3467888999999999999998864
No 76
>PLN02870 Probable galacturonosyltransferase
Probab=40.99 E-value=23 Score=28.53 Aligned_cols=26 Identities=23% Similarity=0.440 Sum_probs=21.9
Q ss_pred CccccccCceEEEEEecCCCCCCHHHHHHHHh
Q psy15303 1 MATRFGSKLKELRIHLCQKGGSSSGVRDFLAQ 32 (72)
Q Consensus 1 ~~~~f~~qLk~L~~~yC~~~~sS~GvR~Fl~~ 32 (72)
|-.+.++.+|.++++ +|.|+||||+=
T Consensus 1 ~~~~~~~~~~~~~~~------~~~~~~~~~~~ 26 (533)
T PLN02870 1 MQLHISPSMRSITIS------SSNGFIDLMKI 26 (533)
T ss_pred CceeecCccceEEEe------cCCcHHHHHHH
Confidence 567889999999997 47999999963
No 77
>TIGR02200 GlrX_actino Glutaredoxin-like protein. This family of glutaredoxin-like proteins is limited to the Actinobacteria and contains the conserved CxxC motif.
Probab=40.93 E-value=29 Score=18.72 Aligned_cols=23 Identities=9% Similarity=-0.015 Sum_probs=19.4
Q ss_pred EEEEEecCCCCCCHHHHHHHHhC
Q psy15303 11 ELRIHLCQKGGSSSGVRDFLAQH 33 (72)
Q Consensus 11 ~L~~~yC~~~~sS~GvR~Fl~~~ 33 (72)
++++.+-.+++.++-+|.|+.+.
T Consensus 1 ~v~ly~~~~C~~C~~~~~~L~~~ 23 (77)
T TIGR02200 1 TITVYGTTWCGYCAQLMRTLDKL 23 (77)
T ss_pred CEEEEECCCChhHHHHHHHHHHc
Confidence 36788889999999999999653
No 78
>TIGR00681 kdpC K+-transporting ATPase, C subunit. This chain has a single predicted transmembrane region near the amino end. It is part of a K+-transport ATPase that contains two other membrane-bound subunits, KdpA and KdpB, and a small subunit KdpF. KdpA is the K+-translocating subunit, KdpB the ATP-hydrolyzing subunit. During assembly of the complex, KdpA and KdpC bind to each other. This interaction is thought to stabilize the complex [PubMed:9858692]. Data indicates that KdpC might connect the KdpA, the K+-transporting subunit, to KdpB, the ATP-hydrolyzing (energy providing) subunit [PubMed:9858692].
Probab=40.91 E-value=24 Score=24.69 Aligned_cols=44 Identities=16% Similarity=0.224 Sum_probs=34.2
Q ss_pred cCCCCCCHHHHHHHHhCHHHHHHhCCC----CeE--EEEEcCCCCCEEEE
Q psy15303 17 CQKGGSSSGVRDFLAQHYVPLKQANPK----FPI--LVRECSGVTPVVWA 60 (72)
Q Consensus 17 C~~~~sS~GvR~Fl~~~l~~~k~~NP~----v~i--~v~~~~g~~P~l~a 60 (72)
++-++|+.-+++-+++....++++||. ||. ++....|-+|.|.-
T Consensus 84 SNl~psnp~l~~~v~~r~~~~~~~~~~~~~~vP~DlvTaSgSGLDPhISp 133 (187)
T TIGR00681 84 SNLAPSNPDLLSRIAARVEAQRLENLDAAVQVPVDLVTSSGSGLDPHISP 133 (187)
T ss_pred cCCCCCCHHHHHHHHHHHHHHHHhCCCCCCCCCHHHHhcccccCCCCCCH
Confidence 567889999999999999999999984 553 34555677887653
No 79
>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=40.65 E-value=39 Score=20.37 Aligned_cols=25 Identities=16% Similarity=0.197 Sum_probs=21.3
Q ss_pred HHHHHHhCHHHHHHhCCCCeEEEEE
Q psy15303 26 VRDFLAQHYVPLKQANPKFPILVRE 50 (72)
Q Consensus 26 vR~Fl~~~l~~~k~~NP~v~i~v~~ 50 (72)
...++..-+.+|++++|++.|.+..
T Consensus 11 ~~~~l~~~l~~~~~~~P~i~i~~~~ 35 (197)
T cd08449 11 LWGGLGPALRRFKRQYPNVTVRFHE 35 (197)
T ss_pred hhhhHHHHHHHHHHHCCCeEEEEEE
Confidence 3467788899999999999999875
No 80
>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=40.48 E-value=51 Score=19.97 Aligned_cols=25 Identities=12% Similarity=0.041 Sum_probs=21.4
Q ss_pred HHHHHHhCHHHHHHhCCCCeEEEEE
Q psy15303 26 VRDFLAQHYVPLKQANPKFPILVRE 50 (72)
Q Consensus 26 vR~Fl~~~l~~~k~~NP~v~i~v~~ 50 (72)
...++...+.+|.+.+|++.+.+..
T Consensus 12 ~~~~l~~~l~~~~~~~P~v~i~i~~ 36 (201)
T cd08471 12 GRLHVLPIITDFLDAYPEVSVRLLL 36 (201)
T ss_pred HHHHHHHHHHHHHHHCCCcEEEEEE
Confidence 4467788999999999999999875
No 81
>cd08447 PBP2_LTTR_aromatics_like_1 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator similar to regulators involved in the catabolism of aromatic compounds, contains type 2 periplasmic binding fold. This CD represents the substrate binding domain of an uncharacterized LysR-type regulator similar to CbnR which is involved in the regulation of chlorocatechol breakdown. The transcription of the genes encoding enzymes involved in such degradation is regulated and expression of these enzymes is enhanced by inducers, which are either an intermediate in the metabolic pathway or compounds to be degraded. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Ve
Probab=40.37 E-value=48 Score=20.04 Aligned_cols=26 Identities=23% Similarity=0.413 Sum_probs=21.6
Q ss_pred HHHHHHhCHHHHHHhCCCCeEEEEEc
Q psy15303 26 VRDFLAQHYVPLKQANPKFPILVREC 51 (72)
Q Consensus 26 vR~Fl~~~l~~~k~~NP~v~i~v~~~ 51 (72)
...++...+.+|.+++|++.+.+.+.
T Consensus 11 ~~~~l~~~l~~~~~~~P~i~v~~~~~ 36 (198)
T cd08447 11 AYSFLPRLLAAARAALPDVDLVLREM 36 (198)
T ss_pred HHHHHHHHHHHHHHHCCCeEEEEEeC
Confidence 45667889999999999999998654
No 82
>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=40.08 E-value=43 Score=20.37 Aligned_cols=23 Identities=35% Similarity=0.534 Sum_probs=19.8
Q ss_pred HHHHhCHHHHHHhCCCCeEEEEE
Q psy15303 28 DFLAQHYVPLKQANPKFPILVRE 50 (72)
Q Consensus 28 ~Fl~~~l~~~k~~NP~v~i~v~~ 50 (72)
.++..-+.+|++++|++.|.+..
T Consensus 14 ~~l~~~l~~~~~~~P~i~i~i~~ 36 (200)
T cd08411 14 YLLPRLLPALRQAYPKLRLYLRE 36 (200)
T ss_pred hhhHHHHHHHHHHCCCcEEEEEe
Confidence 47788899999999999998875
No 83
>PF06244 DUF1014: Protein of unknown function (DUF1014); InterPro: IPR010422 This family consists of several hypothetical eukaryotic proteins of unknown function.
Probab=39.03 E-value=25 Score=22.94 Aligned_cols=20 Identities=25% Similarity=0.428 Sum_probs=17.0
Q ss_pred HHHHHHhCHHHHHHhCCCCe
Q psy15303 26 VRDFLAQHYVPLKQANPKFP 45 (72)
Q Consensus 26 vR~Fl~~~l~~~k~~NP~v~ 45 (72)
-..|-+.+||.+++.||++-
T Consensus 80 y~afeE~~Lp~lK~E~PgLr 99 (122)
T PF06244_consen 80 YKAFEERRLPELKEENPGLR 99 (122)
T ss_pred HHHHHHHHhHHHHhhCCCch
Confidence 45678899999999999874
No 84
>cd08442 PBP2_YofA_SoxR_like The C-terminal substrate binding domain of LysR-type transcriptional regulators, YofA and SoxR, contains the type 2 periplasmic binding fold. YofA is a LysR-like transcriptional regulator of cell growth in Bacillus subtillis. YofA controls cell viability and the formation of constrictions during cell division. YofaA positively regulates expression of the cell division gene ftsW, and thus is essential for cell viability during stationary-phase growth of Bacillus substilis. YofA shows significant homology to SoxR from Arthrobacter sp. TE1826. SoxR is a negative regulator for the sarcosine oxidase gene soxA. Sarcosine oxidase catalyzes the oxidative demethylation of sarcosine, which is involved in the metabolism of creatine and choline. The topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides
Probab=38.92 E-value=40 Score=20.23 Aligned_cols=26 Identities=12% Similarity=0.082 Sum_probs=21.3
Q ss_pred HHHHHhCHHHHHHhCCCCeEEEEEcC
Q psy15303 27 RDFLAQHYVPLKQANPKFPILVRECS 52 (72)
Q Consensus 27 R~Fl~~~l~~~k~~NP~v~i~v~~~~ 52 (72)
..++...+.+|.+++|++.+.+....
T Consensus 12 ~~~l~~~l~~~~~~~P~i~l~i~~~~ 37 (193)
T cd08442 12 AVRLPPLLAAYHARYPKVDLSLSTGT 37 (193)
T ss_pred hhhhHHHHHHHHHHCCCceEEEEeCC
Confidence 35677889999999999999997643
No 85
>cd08459 PBP2_DntR_NahR_LinR_like The C-terminal substrate binding domain of LysR-type transcriptional regulators that are involved in the catabolism of dinitrotoluene, naphthalene and gamma-hexachlorohexane; contains the type 2 periplasmic binding fold. This CD includes LysR-like bacterial transcriptional regulators, DntR, NahR, and LinR, which are involved in the degradation of aromatic compounds. The transcription of the genes encoding enzymes involved in such degradation is regulated and expression of these enzymes is enhanced by inducers, which are either an intermediate in the metabolic pathway or compounds to be degraded. DntR from Burkholderia species controls genes encoding enzymes for oxidative degradation of the nitro-aromatic compound 2,4-dinitrotoluene. The active form of DntR is homotetrameric, consisting of a dimer of dimers. NahR is a salicylate-dependent transcription activator of the nah and sal operons for naphthalene degradation. Salicylic acid is an intermediate o
Probab=38.91 E-value=65 Score=19.62 Aligned_cols=27 Identities=19% Similarity=0.215 Sum_probs=22.1
Q ss_pred HHHHHHhCHHHHHHhCCCCeEEEEEcC
Q psy15303 26 VRDFLAQHYVPLKQANPKFPILVRECS 52 (72)
Q Consensus 26 vR~Fl~~~l~~~k~~NP~v~i~v~~~~ 52 (72)
...++..-+.+|++++|++.+.+....
T Consensus 11 ~~~~l~~~l~~~~~~~P~v~v~i~~~~ 37 (201)
T cd08459 11 EMYFLPRLLAALREVAPGVRIETVRLP 37 (201)
T ss_pred HHHHHHHHHHHHHHHCCCCeEEEEecC
Confidence 345678899999999999999997643
No 86
>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=38.68 E-value=39 Score=20.75 Aligned_cols=26 Identities=8% Similarity=0.220 Sum_probs=21.6
Q ss_pred HHHHHHhCHHHHHHhCCCCeEEEEEc
Q psy15303 26 VRDFLAQHYVPLKQANPKFPILVREC 51 (72)
Q Consensus 26 vR~Fl~~~l~~~k~~NP~v~i~v~~~ 51 (72)
...++..-+.+|++++|++.|.+...
T Consensus 11 ~~~~l~~~l~~f~~~~P~v~i~~~~~ 36 (196)
T cd08458 11 ALSFMSGVIQTFIADRPDVSVYLDTV 36 (196)
T ss_pred hhhhhHHHHHHHHHHCCCcEEEEecc
Confidence 45677888999999999999988764
No 87
>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=38.60 E-value=46 Score=20.19 Aligned_cols=26 Identities=12% Similarity=0.229 Sum_probs=21.2
Q ss_pred HHHHHHhCHHHHHHhCCCCeEEEEEc
Q psy15303 26 VRDFLAQHYVPLKQANPKFPILVREC 51 (72)
Q Consensus 26 vR~Fl~~~l~~~k~~NP~v~i~v~~~ 51 (72)
.-.++..-+.+|++++|++.+.+...
T Consensus 12 ~~~~l~~~i~~~~~~~P~v~l~i~~~ 37 (198)
T cd08446 12 ILDTVPRLLRAFLTARPDVTVSLHNM 37 (198)
T ss_pred HHHHHHHHHHHHHHHCCCeEEEEeeC
Confidence 34567888999999999999998763
No 88
>TIGR00741 yfiA ribosomal subunit interface protein. The member of this family from E. coli is now recognized as a protein at the interace between ribosomal large and small subunits, with about 1/3 as many copies per cell as the number of ribosomes.
Probab=38.50 E-value=81 Score=18.30 Aligned_cols=32 Identities=9% Similarity=0.228 Sum_probs=25.4
Q ss_pred EEEEecCCCCCCHHHHHHHHhCHHHHHHhCCCC
Q psy15303 12 LRIHLCQKGGSSSGVRDFLAQHYVPLKQANPKF 44 (72)
Q Consensus 12 L~~~yC~~~~sS~GvR~Fl~~~l~~~k~~NP~v 44 (72)
+.+.. .+-.-+..+++|+++.+..+.+-.|++
T Consensus 3 i~i~~-~~~~~t~~l~~~i~~k~~kl~k~~~~i 34 (95)
T TIGR00741 3 INITG-KNVEITEALREYVEEKLARLERYFTHI 34 (95)
T ss_pred EEEEE-eccccCHHHHHHHHHHHHHHHHhcCCC
Confidence 44444 666779999999999999998888764
No 89
>smart00367 LRR_CC Leucine-rich repeat - CC (cysteine-containing) subfamily.
Probab=38.44 E-value=13 Score=17.18 Aligned_cols=23 Identities=22% Similarity=0.491 Sum_probs=17.0
Q ss_pred cCceEEEEEecCCCCCCHHHHHHH
Q psy15303 7 SKLKELRIHLCQKGGSSSGVRDFL 30 (72)
Q Consensus 7 ~qLk~L~~~yC~~~~sS~GvR~Fl 30 (72)
++|++|.+.+|.. =+..|++...
T Consensus 2 ~~L~~L~l~~C~~-itD~gl~~l~ 24 (26)
T smart00367 2 PNLRELDLSGCTN-ITDEGLQALA 24 (26)
T ss_pred CCCCEeCCCCCCC-cCHHHHHHHh
Confidence 5799999999973 4566776543
No 90
>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=38.37 E-value=50 Score=19.84 Aligned_cols=26 Identities=12% Similarity=0.336 Sum_probs=21.6
Q ss_pred HHHHHHhCHHHHHHhCCCCeEEEEEc
Q psy15303 26 VRDFLAQHYVPLKQANPKFPILVREC 51 (72)
Q Consensus 26 vR~Fl~~~l~~~k~~NP~v~i~v~~~ 51 (72)
...++...+.+|.+.+|++.+.+...
T Consensus 11 ~~~~l~~~l~~~~~~~P~i~l~~~~~ 36 (195)
T cd08427 11 LTGLLPRALARLRRRHPDLEVHIVPG 36 (195)
T ss_pred HHHHhHHHHHHHHHHCCCceEEEEeC
Confidence 34677889999999999999998753
No 91
>cd08469 PBP2_PnbR The C-terminal substrate binding domain of LysR-type transcriptional regulator PnbR, which is involved in regulating the pnb genes encoding enzymes for 4-nitrobenzoate catabolism, contains the type 2 periplasmic binding fold. PnbR is the regulator of one or both of the two pnb genes that encoding enzymes for 4-nitrobenzoate catabolism. In Pseudomonas putida strain, pnbA encodes a 4-nitrobenzoate reductase, which is responsible for catalyzing the direct reduction of 4-nitrobenzoate to 4-hydroxylaminobenzoate, and pnbB encodes a 4-hydroxylaminobenzoate lyase, which catalyzes the conversion of 4-hydroxylaminobenzoate to 3, 4-dihydroxybenzoic acid and ammonium. The topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft bet
Probab=38.32 E-value=57 Score=20.43 Aligned_cols=27 Identities=15% Similarity=0.222 Sum_probs=22.2
Q ss_pred HHHHHHhCHHHHHHhCCCCeEEEEEcC
Q psy15303 26 VRDFLAQHYVPLKQANPKFPILVRECS 52 (72)
Q Consensus 26 vR~Fl~~~l~~~k~~NP~v~i~v~~~~ 52 (72)
...++...+.+|.+++|++.+.+....
T Consensus 11 ~~~~l~~~l~~f~~~~P~v~l~i~~~~ 37 (221)
T cd08469 11 TAVLLPALVRRLETEAPGIDLRIRPVT 37 (221)
T ss_pred HHHHHHHHHHHHHHHCCCcEEEEeeCC
Confidence 346778889999999999999997643
No 92
>PRK13999 potassium-transporting ATPase subunit C; Provisional
Probab=37.73 E-value=30 Score=24.52 Aligned_cols=45 Identities=24% Similarity=0.406 Sum_probs=34.7
Q ss_pred cCCCCCCHHHHHHHHhCHHHHHHhCC--CCeE--EEEEcCCCCCEEEEE
Q psy15303 17 CQKGGSSSGVRDFLAQHYVPLKQANP--KFPI--LVRECSGVTPVVWAR 61 (72)
Q Consensus 17 C~~~~sS~GvR~Fl~~~l~~~k~~NP--~v~i--~v~~~~g~~P~l~a~ 61 (72)
++-++++.-+.+-+++....++++|| .||. ++....|-+|.|.-+
T Consensus 97 SNlgpsnp~L~~~v~~r~~~~~~~~~~~~vP~DlvTaSgSGLDPhISp~ 145 (201)
T PRK13999 97 SNLGPTSKALADRVKEDVDALKAENPGAPVPVDLVTTSGSGLDPDISPE 145 (201)
T ss_pred cCCCCCCHHHHHHHHHHHHHHHHhCCCCCCCHHHHhcccccCCCCCCHH
Confidence 46678899999999999999999998 5553 345566778877543
No 93
>cd08433 PBP2_Nac The C-teminal substrate binding domain of LysR-like nitrogen assimilation control (NAC) protein, contains the type 2 periplasmic binding fold. The NAC is a LysR-type transcription regulator that activates expression of operons such as hut (histidine utilization) and ure (urea utilization), allowing use of non-preferred (poor) nitrogen sources, and represses expression of operons, such as glutamate dehydrogenase (gdh), allowing assimilation of the preferred nitrogen source. The expression of the nac gene is fully dependent on the nitrogen regulatory system (NTR) and the sigma54-containing RNA polymerase (sigma54-RNAP). In response to nitrogen starvation, NTR system activates the expression of nac, and NAC activates the expression of hut, ure, and put (proline utilization). NAC is not involved in the transcription of Sigma70-RNAP operons such as glnA, which directly respond by the NTR system, but activates the transcription of sigma70-RNAP dependent operons such as hut.
Probab=37.60 E-value=35 Score=20.73 Aligned_cols=25 Identities=8% Similarity=0.108 Sum_probs=20.4
Q ss_pred HHHHHhCHHHHHHhCCCCeEEEEEc
Q psy15303 27 RDFLAQHYVPLKQANPKFPILVREC 51 (72)
Q Consensus 27 R~Fl~~~l~~~k~~NP~v~i~v~~~ 51 (72)
..++...+..|.+++|++.+.+...
T Consensus 12 ~~~l~~~l~~~~~~~P~i~i~~~~~ 36 (198)
T cd08433 12 SVLAVPLLRAVRRRYPGIRLRIVEG 36 (198)
T ss_pred hhcchHHHHHHHHHCCCcEEEEEec
Confidence 3566778889999999999998763
No 94
>cd08467 PBP2_SyrM The C-terminal substrate binding of LysR-type symbiotic regulator SyrM, which activates expression of nodulation gene NodD3, contains the type 2 periplasmic binding fold. Rhizobium is a nitrogen fixing bacteria present in the roots of leguminous plants, which fixes atmospheric nitrogen to the soil. Most Rhizobium species possess multiple nodulation (nod) genes for the development of nodules. For example, Rhizobium meliloti possesses three copies of nodD genes. NodD1 and NodD2 activate nod operons when Rhizobium is exposed to inducers synthesized by the host plant, while NodD3 acts independent of plant inducers and requires the symbiotic regulator SyrM for nod gene expression. SyrM activates the expression of the regulatory nodulation gene nodD3. In turn, NodD3 activates expression of syrM. In addition, SyrM is involved in exopolysaccharide synthesis. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are
Probab=37.19 E-value=46 Score=20.58 Aligned_cols=26 Identities=12% Similarity=0.139 Sum_probs=21.6
Q ss_pred HHHHHHhCHHHHHHhCCCCeEEEEEc
Q psy15303 26 VRDFLAQHYVPLKQANPKFPILVREC 51 (72)
Q Consensus 26 vR~Fl~~~l~~~k~~NP~v~i~v~~~ 51 (72)
...++..-+.+|++++|++.+.+...
T Consensus 11 ~~~~l~~~l~~~~~~~P~i~l~~~~~ 36 (200)
T cd08467 11 EVALLPRLAPRLRERAPGLDLRLCPI 36 (200)
T ss_pred HHHHHHHHHHHHHhhCCCCEEEEecC
Confidence 45677788899999999999998764
No 95
>cd08475 PBP2_CrgA_like_6 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold. This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 6. The LTTRs are acting as both auto-repressors and activators of target promoters, controlling operons involved in a wide variety of cellular processes such as amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to name a few. In contrast to the tetrameric form of other LTTRs, CrgA from Neisseria meningitides assembles into an octameric ring, which can bind up to four 63-bp DNA oligonucleotides. Phylogenetic cluster analysis showed that the CrgA-like regulators form a subclass of the LTTRs that function as octamers. The CrgA is an auto-repressor of its own gene a
Probab=36.96 E-value=47 Score=20.02 Aligned_cols=25 Identities=16% Similarity=0.184 Sum_probs=21.1
Q ss_pred HHHHHHhCHHHHHHhCCCCeEEEEE
Q psy15303 26 VRDFLAQHYVPLKQANPKFPILVRE 50 (72)
Q Consensus 26 vR~Fl~~~l~~~k~~NP~v~i~v~~ 50 (72)
...++...+..|++++|++.+.+..
T Consensus 12 ~~~~l~~~l~~~~~~~P~v~i~i~~ 36 (199)
T cd08475 12 GRLCVAPLLLELARRHPELELELSF 36 (199)
T ss_pred HHhhHHHHHHHHHHHCCCeEEEEEe
Confidence 4467788899999999999999964
No 96
>PRK00315 potassium-transporting ATPase subunit C; Reviewed
Probab=36.85 E-value=29 Score=24.35 Aligned_cols=45 Identities=22% Similarity=0.393 Sum_probs=34.5
Q ss_pred cCCCCCCHHHHHHHHhCHHHHHHhCC----CCe--EEEEEcCCCCCEEEEE
Q psy15303 17 CQKGGSSSGVRDFLAQHYVPLKQANP----KFP--ILVRECSGVTPVVWAR 61 (72)
Q Consensus 17 C~~~~sS~GvR~Fl~~~l~~~k~~NP----~v~--i~v~~~~g~~P~l~a~ 61 (72)
++-++++.-+++-+++....++++|| .|| .++....|-+|.|.-+
T Consensus 86 SNl~psnp~l~~~v~~r~~~~~~~~~~~~~~vP~DlvTaSgSGLDPhIS~~ 136 (193)
T PRK00315 86 SNLAPSNPALDDAIKARVAALRAANPGASSPVPVDLVTASGSGLDPHISPA 136 (193)
T ss_pred cCCCCCCHHHHHHHHHHHHHHHHhCCCCCCCCCHHHHhccccCCCCCCCHH
Confidence 46788899999999999999999998 355 3345566778876543
No 97
>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=36.16 E-value=37 Score=21.02 Aligned_cols=26 Identities=15% Similarity=0.115 Sum_probs=21.2
Q ss_pred HHHHHHhCHHHHHHhCCCCeEEEEEc
Q psy15303 26 VRDFLAQHYVPLKQANPKFPILVREC 51 (72)
Q Consensus 26 vR~Fl~~~l~~~k~~NP~v~i~v~~~ 51 (72)
...++..-+.+|++++|++.+.+.+.
T Consensus 12 ~~~~l~~~l~~~~~~~P~i~l~~~~~ 37 (198)
T cd08485 12 VLHTLPLLLRQLLSVAPSATVSLTQM 37 (198)
T ss_pred hhHHHHHHHHHHHHhCCCcEEEEEEC
Confidence 34577788899999999999998753
No 98
>PRK14001 potassium-transporting ATPase subunit C; Provisional
Probab=36.15 E-value=32 Score=24.08 Aligned_cols=44 Identities=16% Similarity=0.282 Sum_probs=34.4
Q ss_pred cCCCCCCHHHHHHHHhCHHHHHHhCCC-----Ce--EEEEEcCCCCCEEEE
Q psy15303 17 CQKGGSSSGVRDFLAQHYVPLKQANPK-----FP--ILVRECSGVTPVVWA 60 (72)
Q Consensus 17 C~~~~sS~GvR~Fl~~~l~~~k~~NP~-----v~--i~v~~~~g~~P~l~a 60 (72)
++.++++.-+++=+++....++++||. || .++....|-+|.|.-
T Consensus 85 SNl~psnp~l~~~v~~r~~~~~~~~~~~~~~~vP~DlvTaSgSGLDPhIS~ 135 (189)
T PRK14001 85 SNLGPTNEKLLAAVAERVTAYRKENNLPADTLVPVDAVTGSGSGLDPAISV 135 (189)
T ss_pred cCCCCCCHHHHHHHHHHHHHHHHhCCCccCCCCCHHHHhcccccCCCCCCH
Confidence 567889999999999999999999984 44 344556677887753
No 99
>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=36.04 E-value=54 Score=19.85 Aligned_cols=26 Identities=15% Similarity=0.110 Sum_probs=21.5
Q ss_pred HHHHHHhCHHHHHHhCCCCeEEEEEc
Q psy15303 26 VRDFLAQHYVPLKQANPKFPILVREC 51 (72)
Q Consensus 26 vR~Fl~~~l~~~k~~NP~v~i~v~~~ 51 (72)
...++..-+.+|.+++|++.|.+...
T Consensus 11 ~~~~~~~~i~~~~~~~P~i~l~~~~~ 36 (200)
T cd08417 11 EALLLPPLLARLRQEAPGVRLRFVPL 36 (200)
T ss_pred HHHHHHHHHHHHHhhCCCeEEEeccC
Confidence 35677888899999999999998754
No 100
>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=36.02 E-value=32 Score=20.77 Aligned_cols=25 Identities=16% Similarity=0.284 Sum_probs=20.7
Q ss_pred HHHHHhCHHHHHHhCCCCeEEEEEc
Q psy15303 27 RDFLAQHYVPLKQANPKFPILVREC 51 (72)
Q Consensus 27 R~Fl~~~l~~~k~~NP~v~i~v~~~ 51 (72)
..++...+.+|.+.+|++.+.+...
T Consensus 12 ~~~l~~~l~~~~~~~P~v~l~~~~~ 36 (199)
T cd08430 12 YSFLPPILERFRAQHPQVEIKLHTG 36 (199)
T ss_pred eeeccHHHHHHHHHCCCceEEEEeC
Confidence 3567788899999999999998764
No 101
>smart00329 BPI2 BPI/LBP/CETP C-terminal domain. Bactericidal permeability-increasing protein (BPI) / Lipopolysaccharide-binding protein (LBP) / Cholesteryl ester transfer protein (CETP) C-terminal domain
Probab=35.81 E-value=91 Score=21.04 Aligned_cols=33 Identities=9% Similarity=0.039 Sum_probs=27.9
Q ss_pred HHHhCHHHHHHhCCCCeEEEEEcCCCCCEEEEE
Q psy15303 29 FLAQHYVPLKQANPKFPILVRECSGVTPVVWAR 61 (72)
Q Consensus 29 Fl~~~l~~~k~~NP~v~i~v~~~~g~~P~l~a~ 61 (72)
++..-+|+++++.|+-++.+.-.....|.+...
T Consensus 48 ~~~~~iP~l~~~yPn~~~~L~i~~~~~P~v~i~ 80 (202)
T smart00329 48 CFGTLVPEVAEQYPDSTLQLEISVLSPPRVTLQ 80 (202)
T ss_pred HHHHHHHHHHHHCCCCcEEEEEEeCCCCEEEEe
Confidence 777888999999999888887777779998875
No 102
>COG1570 XseA Exonuclease VII, large subunit [DNA replication, recombination, and repair]
Probab=35.64 E-value=57 Score=25.67 Aligned_cols=30 Identities=20% Similarity=0.351 Sum_probs=25.4
Q ss_pred CCCCCHHHHHHHHhCHHHHHHhCCCCeEEEEEcC
Q psy15303 19 KGGSSSGVRDFLAQHYVPLKQANPKFPILVRECS 52 (72)
Q Consensus 19 ~~~sS~GvR~Fl~~~l~~~k~~NP~v~i~v~~~~ 52 (72)
||+++..+||.+. .+++..|.++|++.+..
T Consensus 142 TS~tgAairDIl~----~~~rR~P~~~viv~pt~ 171 (440)
T COG1570 142 TSPTGAALRDILH----TLSRRFPSVEVIVYPTL 171 (440)
T ss_pred cCCchHHHHHHHH----HHHhhCCCCeEEEEecc
Confidence 6888999999986 47889999999998753
No 103
>PRK10470 ribosome hibernation promoting factor HPF; Provisional
Probab=35.27 E-value=89 Score=18.47 Aligned_cols=27 Identities=15% Similarity=0.341 Sum_probs=22.6
Q ss_pred CCCCCCHHHHHHHHhCHHHHHHhCCCC
Q psy15303 18 QKGGSSSGVRDFLAQHYVPLKQANPKF 44 (72)
Q Consensus 18 ~~~~sS~GvR~Fl~~~l~~~k~~NP~v 44 (72)
.+-.-|.++|+|+++.+..+.+-.+++
T Consensus 8 r~i~~t~al~~~v~~kl~kL~r~~~~i 34 (95)
T PRK10470 8 HNVEITEALREFVTAKFAKLEQYFDRI 34 (95)
T ss_pred EeeccCHHHHHHHHHHHHHHHHhcCCC
Confidence 455678999999999999999888765
No 104
>KOG1909|consensus
Probab=34.80 E-value=35 Score=26.44 Aligned_cols=36 Identities=28% Similarity=0.538 Sum_probs=29.3
Q ss_pred cCceEEEEEecCCCCCCHHHHHHHHhCHHHHHHhCCCCeEEE
Q psy15303 7 SKLKELRIHLCQKGGSSSGVRDFLAQHYVPLKQANPKFPILV 48 (72)
Q Consensus 7 ~qLk~L~~~yC~~~~sS~GvR~Fl~~~l~~~k~~NP~v~i~v 48 (72)
++|++|.+.||.-. ++|+-.|++ .+++.||.+++.-
T Consensus 241 ~~L~El~l~dcll~--~~Ga~a~~~----al~~~~p~L~vl~ 276 (382)
T KOG1909|consen 241 PHLRELNLGDCLLE--NEGAIAFVD----ALKESAPSLEVLE 276 (382)
T ss_pred chheeecccccccc--cccHHHHHH----HHhccCCCCceec
Confidence 47999999999875 889988875 5677799888754
No 105
>PTZ00062 glutaredoxin; Provisional
Probab=34.67 E-value=1.1e+02 Score=21.32 Aligned_cols=37 Identities=11% Similarity=0.036 Sum_probs=27.5
Q ss_pred EEEEecCCCCCCHHHHHHHHhCHHHHHHhCCCCeEEEEEcC
Q psy15303 12 LRIHLCQKGGSSSGVRDFLAQHYVPLKQANPKFPILVRECS 52 (72)
Q Consensus 12 L~~~yC~~~~sS~GvR~Fl~~~l~~~k~~NP~v~i~v~~~~ 52 (72)
+-+...+|.+.++-| ..-++++++++|++.|+.-.+.
T Consensus 21 vl~f~a~w~~~C~~m----~~vl~~l~~~~~~~~F~~V~~d 57 (204)
T PTZ00062 21 VLYVKSSKEPEYEQL----MDVCNALVEDFPSLEFYVVNLA 57 (204)
T ss_pred EEEEeCCCCcchHHH----HHHHHHHHHHCCCcEEEEEccc
Confidence 444448888888854 5566788999999998886654
No 106
>cd08462 PBP2_NodD The C-terminal substsrate binding domain of NodD family of LysR-type transcriptional regulators that regulates the expression of nodulation (nod) genes; contains the type 2 periplasmic binding fold. The nodulation (nod) genes in soil bacteria play important roles in the development of nodules. nod genes are involved in synthesis of Nod factors that are required for bacterial entry into root hairs. Thirteen nod genes have been identified and are classified into five transcription units: nodD, nodABCIJ, nodFEL, nodMNT, and nodO. NodD is negatively auto-regulates its own expression of nodD gene, while other nod genes are inducible and positively regulated by NodD in the presence of flavonoids released by plant roots. This substrate-binding domain has significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. T
Probab=34.60 E-value=62 Score=19.91 Aligned_cols=26 Identities=8% Similarity=0.042 Sum_probs=22.0
Q ss_pred HHHHHHhCHHHHHHhCCCCeEEEEEc
Q psy15303 26 VRDFLAQHYVPLKQANPKFPILVREC 51 (72)
Q Consensus 26 vR~Fl~~~l~~~k~~NP~v~i~v~~~ 51 (72)
...++..-+.+|++.+|++.+.+...
T Consensus 11 ~~~~l~~~i~~~~~~~P~i~l~i~~~ 36 (200)
T cd08462 11 ITVLLPPVIERVAREAPGVRFELLPP 36 (200)
T ss_pred HHHHHHHHHHHHHHHCCCCEEEEecC
Confidence 45677888999999999999999763
No 107
>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=34.10 E-value=71 Score=19.31 Aligned_cols=27 Identities=11% Similarity=0.222 Sum_probs=22.3
Q ss_pred HHHHHHhCHHHHHHhCCCCeEEEEEcC
Q psy15303 26 VRDFLAQHYVPLKQANPKFPILVRECS 52 (72)
Q Consensus 26 vR~Fl~~~l~~~k~~NP~v~i~v~~~~ 52 (72)
...++...+.+|.+++|++.+.+....
T Consensus 11 ~~~~l~~~l~~f~~~~P~i~l~~~~~~ 37 (189)
T cd08484 11 AVGWLLPRLAEFRQLHPFIDLRLSTNN 37 (189)
T ss_pred HHHHHHhhhHHHHHHCCCceEEEeccc
Confidence 356777889999999999999997643
No 108
>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=33.30 E-value=72 Score=19.64 Aligned_cols=25 Identities=8% Similarity=0.163 Sum_probs=20.8
Q ss_pred HHHHHhCHHHHHHhCCCCeEEEEEc
Q psy15303 27 RDFLAQHYVPLKQANPKFPILVREC 51 (72)
Q Consensus 27 R~Fl~~~l~~~k~~NP~v~i~v~~~ 51 (72)
..++..-+.+|++++|++.+.+...
T Consensus 12 ~~~l~~~l~~~~~~~P~v~i~~~~~ 36 (202)
T cd08468 12 LAVMPRLMARLEELAPSVRLNLVHA 36 (202)
T ss_pred HHHhHHHHHHHHhhCCCCEEEEEEC
Confidence 4567888899999999999988764
No 109
>cd02989 Phd_like_TxnDC9 Phosducin (Phd)-like family, Thioredoxin (TRX) domain containing protein 9 (TxnDC9) subfamily; composed of predominantly uncharacterized eukaryotic proteins, containing a TRX-like domain without the redox active CXXC motif. The gene name for the human protein is TxnDC9. The two characterized members are described as Phd-like proteins, PLP1 of Saccharomyces cerevisiae and PhLP3 of Dictyostelium discoideum. Gene disruption experiments show that both PLP1 and PhLP3 are non-essential proteins. Unlike Phd and most Phd-like proteins, members of this group do not contain the Phd N-terminal helical domain which is implicated in binding to the G protein betagamma subunit.
Probab=33.18 E-value=97 Score=18.86 Aligned_cols=34 Identities=6% Similarity=-0.139 Sum_probs=24.3
Q ss_pred EEEEEecCCCCCCHHHHHHHHhCHHHHHHhCCCCeEEE
Q psy15303 11 ELRIHLCQKGGSSSGVRDFLAQHYVPLKQANPKFPILV 48 (72)
Q Consensus 11 ~L~~~yC~~~~sS~GvR~Fl~~~l~~~k~~NP~v~i~v 48 (72)
-+...|.+|++.++-+...+ .++++++|++.|.-
T Consensus 25 vvV~f~a~~c~~C~~~~p~l----~~la~~~~~i~f~~ 58 (113)
T cd02989 25 VVCHFYHPEFFRCKIMDKHL----EILAKKHLETKFIK 58 (113)
T ss_pred EEEEEECCCCccHHHHHHHH----HHHHHHcCCCEEEE
Confidence 46677889999998776654 45666778877644
No 110
>cd08451 PBP2_BudR The C-terminal substrate binding domain of LysR-type transcrptional regulator BudR, which is responsible for activation of the expression of the butanediol operon genes; contains the type 2 periplasmic binding fold. This CD represents the substrate binding domain of BudR regulator, which is responsible for induction of the butanediol formation pathway under fermentative growth conditions. Three enzymes are involved in the production of 1 mol of 2,3 butanediol from the condensation of 2 mol of pyruvate with acetolactate and acetoin as intermediates: acetolactate synthetase, acetolactate decarboxylase, and acetoin reductase. In Klebsiella terrigena, BudR regulates the expression of the budABC operon genes, encoding these three enzymes of the butanediol pathway. In many bacterial species, the use of this pathway can prevent intracellular acidification by diverting metabolism from acid production to the formation of neutral compounds (acetoin and butanediol). This substra
Probab=33.16 E-value=43 Score=20.22 Aligned_cols=23 Identities=13% Similarity=0.299 Sum_probs=19.6
Q ss_pred HHHhCHHHHHHhCCCCeEEEEEc
Q psy15303 29 FLAQHYVPLKQANPKFPILVREC 51 (72)
Q Consensus 29 Fl~~~l~~~k~~NP~v~i~v~~~ 51 (72)
++..-+.+|++.+|++.+.+...
T Consensus 15 ~l~~~l~~~~~~~P~i~l~i~~~ 37 (199)
T cd08451 15 LVPGLIRRFREAYPDVELTLEEA 37 (199)
T ss_pred ccHHHHHHHHHHCCCcEEEEecC
Confidence 56778899999999999998754
No 111
>PLN02757 sirohydrochlorine ferrochelatase
Probab=32.98 E-value=30 Score=22.93 Aligned_cols=30 Identities=13% Similarity=0.156 Sum_probs=19.8
Q ss_pred HHHhCHHHHHHhCCCCeEEEEEcCCCCCEE
Q psy15303 29 FLAQHYVPLKQANPKFPILVRECSGVTPVV 58 (72)
Q Consensus 29 Fl~~~l~~~k~~NP~v~i~v~~~~g~~P~l 58 (72)
=|...+.++++++|++.|.+-+.=|.||.+
T Consensus 91 DIp~~v~~~~~~~p~~~i~~~~pLG~~p~l 120 (154)
T PLN02757 91 DIPALTAEAAKEHPGVKYLVTAPIGLHELM 120 (154)
T ss_pred HHHHHHHHHHHHCCCcEEEECCCCCCCHHH
Confidence 344455567777888887777666777643
No 112
>PRK14002 potassium-transporting ATPase subunit C; Provisional
Probab=32.37 E-value=36 Score=23.80 Aligned_cols=45 Identities=18% Similarity=0.262 Sum_probs=34.5
Q ss_pred cCCCCCCHHHHHHHHhCHHHHHHhCCC-----Ce--EEEEEcCCCCCEEEEE
Q psy15303 17 CQKGGSSSGVRDFLAQHYVPLKQANPK-----FP--ILVRECSGVTPVVWAR 61 (72)
Q Consensus 17 C~~~~sS~GvR~Fl~~~l~~~k~~NP~-----v~--i~v~~~~g~~P~l~a~ 61 (72)
++-++++.-+++=+++....++++||+ || .++....|-+|.|.-+
T Consensus 81 SNl~psnp~L~~~v~~r~~~~~~~~~~~~~~~vP~DlvTaSgSGLDPhISp~ 132 (186)
T PRK14002 81 SNKGPSNPEYLAEVQARIDTFLVHHPYLSRKDIPAEMVTASGSGLDPNISPQ 132 (186)
T ss_pred cCCCCCCHHHHHHHHHHHHHHHHhCCCCCCCCCCHHHHhccccCCCCCCCHH
Confidence 567889999999999999999999986 33 3345566778876543
No 113
>TIGR02036 dsdC D-serine deaminase transcriptional activator. This family, part of the LysR family of transcriptional regulators, activates transcription of the gene for D-serine deaminase, dsdA. Trusted members of this family so far are found adjacent to dsdA and only in Gammaproteobacteria, including E. coli, Vibrio cholerae, and Colwellia psychrerythraea.
Probab=32.12 E-value=74 Score=22.10 Aligned_cols=28 Identities=11% Similarity=0.159 Sum_probs=23.3
Q ss_pred HHHHHHhCHHHHHHhCCCCeEEEEEcCC
Q psy15303 26 VRDFLAQHYVPLKQANPKFPILVRECSG 53 (72)
Q Consensus 26 vR~Fl~~~l~~~k~~NP~v~i~v~~~~g 53 (72)
...++...+.+|.+++|++.+.+.....
T Consensus 107 ~~~~l~~~l~~f~~~~P~i~l~l~~~~~ 134 (302)
T TIGR02036 107 AQCWLVPRIGDFTRRYPSISLTVLTGNE 134 (302)
T ss_pred HHHHHHHHHHHHHHHCCCceEEEEeCCc
Confidence 4567888999999999999999987543
No 114
>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=31.87 E-value=47 Score=20.49 Aligned_cols=26 Identities=15% Similarity=0.273 Sum_probs=20.3
Q ss_pred HHHHHHhCHHHHHHhCCCCeEEEEEc
Q psy15303 26 VRDFLAQHYVPLKQANPKFPILVREC 51 (72)
Q Consensus 26 vR~Fl~~~l~~~k~~NP~v~i~v~~~ 51 (72)
...++..-+.+|.+++|++++.+...
T Consensus 11 ~~~~l~~~l~~~~~~~P~i~v~~~~~ 36 (198)
T cd08413 11 ARYVLPPVIAAFRKRYPKVKLSLHQG 36 (198)
T ss_pred hhhhccHHHHHHHHhCCceEEEEEeC
Confidence 35567788889999999998888754
No 115
>PLN02958 diacylglycerol kinase/D-erythro-sphingosine kinase
Probab=31.57 E-value=91 Score=24.23 Aligned_cols=44 Identities=20% Similarity=0.202 Sum_probs=34.9
Q ss_pred eEEEEEecCCCCCCHHHHHHHHhCHHHHHHhCCCCeEEEEEcCC
Q psy15303 10 KELRIHLCQKGGSSSGVRDFLAQHYVPLKQANPKFPILVRECSG 53 (72)
Q Consensus 10 k~L~~~yC~~~~sS~GvR~Fl~~~l~~~k~~NP~v~i~v~~~~g 53 (72)
|++.|-+.+.+|..++.+.|.+.--+.|++++-++.+.+.+..+
T Consensus 112 kr~lvIvNP~SGkg~a~k~~~~~v~~~L~~~gi~~~v~~T~~~g 155 (481)
T PLN02958 112 KRLLVFVNPFGGKKSASKIFFDVVKPLLEDADIQLTIQETKYQL 155 (481)
T ss_pred cEEEEEEcCCCCCcchhHHHHHHHHHHHHHcCCeEEEEeccCcc
Confidence 67889999999999998888777777888888777776655543
No 116
>PF02482 Ribosomal_S30AE: Sigma 54 modulation protein / S30EA ribosomal protein; InterPro: IPR003489 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This family contains the sigma-54 modulation protein family and the S30Ae family of ribosomal proteins which includes the light-repressed protein (lrtA) [].; GO: 0005488 binding, 0044238 primary metabolic process; PDB: 1L4S_A 1VOX_a 1VOV_a 3V2E_Y 3V2C_Y 1N3G_A 1VOS_a 1VOZ_a 1VOQ_a 1IMU_A ....
Probab=31.51 E-value=97 Score=17.89 Aligned_cols=32 Identities=9% Similarity=0.203 Sum_probs=22.7
Q ss_pred EEEEecCCCCCCHHHHHHHHhCHHHHHHhCCCC
Q psy15303 12 LRIHLCQKGGSSSGVRDFLAQHYVPLKQANPKF 44 (72)
Q Consensus 12 L~~~yC~~~~sS~GvR~Fl~~~l~~~k~~NP~v 44 (72)
|.|.+ .+-.-|..+|+++++.+..+.+-.+++
T Consensus 2 i~i~~-~~~~~t~~l~~~i~~kl~kl~~~~~~i 33 (97)
T PF02482_consen 2 IQITG-RNFELTDALREYIEEKLEKLERFFDDI 33 (97)
T ss_dssp EEEEE-CSS---HHHHHHHHHHHHHHHTTSSC-
T ss_pred EEEEE-EcccCCHHHHHHHHHHHHHHHhhcCCC
Confidence 34444 666789999999999999999988755
No 117
>cd00026 BPI2 BPI/LBP/CETP C-terminal domain; Bactericidal permeability-increasing protein (BPI) / Lipopolysaccharide-binding protein (LBP) / Cholesteryl ester transfer protein (CETP) C-terminal domain; binds to and neutralizes lipopolysaccharides from the outer membrane of Gram-negative bacteria.; Apolar pockets on the concave surface bind a molecule of phosphatidylcholine, primarily by interacting with their acyl chains; this suggests that the pockets may also bind the acyl chains of lipopolysaccharide.
Probab=31.19 E-value=1.3e+02 Score=20.30 Aligned_cols=32 Identities=13% Similarity=0.197 Sum_probs=25.3
Q ss_pred HHhCHHHHHHhCCCCeEEEEEcCCCCCEEEEE
Q psy15303 30 LAQHYVPLKQANPKFPILVRECSGVTPVVWAR 61 (72)
Q Consensus 30 l~~~l~~~k~~NP~v~i~v~~~~g~~P~l~a~ 61 (72)
+..-+|+++++.|+-++.+.-.....|.+...
T Consensus 44 ~~~~iP~l~~~yPn~~~~L~i~~~~~P~v~i~ 75 (200)
T cd00026 44 FGIFIPELAKKYPNMPQQLKISVSSPPHLVLS 75 (200)
T ss_pred HHHHHHHHHHHCCCCcEEEEEEeCCCCEEEEe
Confidence 34468999999999888887777778988764
No 118
>PF09457 RBD-FIP: FIP domain ; InterPro: IPR019018 The Rab11 GTPase regulates recycling of internalized plasma membrane receptors and is essential for completion of cytokinesis. A family of Rab11 interacting proteins (FIPs) that conserve a C-terminal Rab-binding domain (RBD) selectively recognise the active form of Rab11. FIPs are diverse in sequence length and composition toward their N-termini, presumably a feature that underpins their specific roles in Rab11-mediated vesicle trafficking. They have been divided into three subfamilies (classe I, II, and III)on the basis of domain architecture. Class I FIPs comprises a subfamily of three proteins (Rip11/pp75/FIP5, Rab-coupling protein (RCP), and FIP2) that possess an N- terminal C2 domain, localize to recycling endosomes, and regulate plasma membrane recycling. The class II subfamily consists of two proteins (FIP3/eferin/arfophilin and FIP4) with tandem EF hands and a proline-rich region. Class II FIPs localize to recycling endosomes, the trans-Golgi network, and have been implicated in the regulation of membrane trafficking during cytokinesis. The class III subfamily consists of a single protein, FIP1, which does not contain obvious homology domains or motifs other than the FIP-RBD [, , , ]. The FIP-RBD domain is also found in Rab6-interacting protein Erc1/Elks. Erc1 is the regulatory subunit of the IKK complex and probably recruits IkappaBalpha/NFKBIA to the complex []. It may be involved in the organisation of the cytomatrix at the nerve terminals active zone (CAZ) which regulates neurotransmitter release. It may also be involved in vesicle trafficking at the CAZ, as well as in Rab-6 regulated endosomes to Golgi transport []. The FIB-RBD domain consists of an N-terminal long alpha-helix, followed by a 90 degrees bend at a conserved proline residue, a 3(10) helix and a C-terminal short beta-strand, adopting an "L" shape. The long alpha-helix forms a parallel coiled-coil homodimer that symmetrically interacts with two Rab11 molecules on both sides, forming a quaternary Rab11-(FIP)2-Rab11 complex. The Rab11-interacting region of FIP-RBD is confined to the C-terminal 24 amino acids, which cover the C-terminal half of the long alpha-helix and the short beta-strand [, , , ]. This entry represents the FIP-RBD domain.; PDB: 2HV8_E 2D7C_D 2K6S_B 2GZD_D 2GZH_B.
Probab=31.05 E-value=18 Score=20.02 Aligned_cols=20 Identities=15% Similarity=0.436 Sum_probs=16.6
Q ss_pred HHHHHHHhCHHHHHHhCCCC
Q psy15303 25 GVRDFLAQHYVPLKQANPKF 44 (72)
Q Consensus 25 GvR~Fl~~~l~~~k~~NP~v 44 (72)
-+++||.+-+..+...+|++
T Consensus 25 eLe~YiD~LL~rVmE~~P~I 44 (48)
T PF09457_consen 25 ELEDYIDNLLVRVMEQTPSI 44 (48)
T ss_dssp HHHHHHHHHHHHHHCC-GGG
T ss_pred HHHHHHHHHHHHHHHhCcch
Confidence 47899999999999999975
No 119
>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=30.63 E-value=74 Score=19.90 Aligned_cols=25 Identities=12% Similarity=0.199 Sum_probs=21.1
Q ss_pred HHHHHHhCHHHHHHhCCCCeEEEEE
Q psy15303 26 VRDFLAQHYVPLKQANPKFPILVRE 50 (72)
Q Consensus 26 vR~Fl~~~l~~~k~~NP~v~i~v~~ 50 (72)
...++..-+.+|++.+|++.+.+.+
T Consensus 11 ~~~~~~~~l~~~~~~~P~~~v~~~~ 35 (203)
T cd08463 11 NALFLPELVARFRREAPGARLEIHP 35 (203)
T ss_pred HHHHhHHHHHHHHHHCCCCEEEEEe
Confidence 3457788999999999999999985
No 120
>KOG0863|consensus
Probab=30.39 E-value=24 Score=25.93 Aligned_cols=25 Identities=20% Similarity=0.489 Sum_probs=21.2
Q ss_pred CCCCCHHHHHHHHhCHHHHHHhCCC
Q psy15303 19 KGGSSSGVRDFLAQHYVPLKQANPK 43 (72)
Q Consensus 19 ~~~sS~GvR~Fl~~~l~~~k~~NP~ 43 (72)
.|--|++.|.||+.++.+|.+.+|+
T Consensus 161 IGsRSQsARTyLEr~~e~f~~~~~e 185 (264)
T KOG0863|consen 161 IGSRSQSARTYLERNLEEFEDSSPE 185 (264)
T ss_pred cccchhhHHHHHHHHHHHHhcCCHH
Confidence 3557999999999999999988765
No 121
>cd03026 AhpF_NTD_C TRX-GRX-like family, Alkyl hydroperoxide reductase F subunit (AhpF) N-terminal domain (NTD) subfamily, C-terminal TRX-fold subdomain; AhpF is a homodimeric flavoenzyme which catalyzes the NADH-dependent reduction of the peroxiredoxin AhpC, which then reduces hydrogen peroxide and organic hydroperoxides. AhpF contains an NTD containing two contiguous TRX-fold subdomains similar to Pyrococcus furiosus protein disulfide oxidoreductase (PfPDO). It also contains a catalytic core similar to TRX reductase containing FAD and NADH binding domains with an active site disulfide. The proposed mechanism of action of AhpF is similar to a TRX/TRX reductase system. The flow of reducing equivalents goes from NADH - catalytic core of AhpF - NTD of AhpF - AhpC - peroxide substrates. The catalytic CXXC motif of the NTD of AhpF is contained in its C-terminal TRX subdomain.
Probab=30.34 E-value=1.2e+02 Score=17.85 Aligned_cols=37 Identities=11% Similarity=0.055 Sum_probs=29.9
Q ss_pred EEEEEecCCCCCCHHHHHHHHhCHHHHHHhCCCCeEEEEEc
Q psy15303 11 ELRIHLCQKGGSSSGVRDFLAQHYVPLKQANPKFPILVREC 51 (72)
Q Consensus 11 ~L~~~yC~~~~sS~GvR~Fl~~~l~~~k~~NP~v~i~v~~~ 51 (72)
+|.+...++.+...-++..+ .++++.+|++.+.+...
T Consensus 15 ~i~~F~~~~C~~C~~~~~~~----~~l~~~~~~i~~~~vd~ 51 (89)
T cd03026 15 NFETYVSLSCHNCPDVVQAL----NLMAVLNPNIEHEMIDG 51 (89)
T ss_pred EEEEEECCCCCCcHHHHHHH----HHHHHHCCCceEEEEEh
Confidence 37778888888888887777 67888999999888664
No 122
>PRK13994 potassium-transporting ATPase subunit C; Provisional
Probab=30.22 E-value=40 Score=24.26 Aligned_cols=45 Identities=13% Similarity=0.310 Sum_probs=33.9
Q ss_pred cCCCCCCHHHHHHHHhCHHHHHHhC--CC-------Ce--EEEEEcCCCCCEEEEE
Q psy15303 17 CQKGGSSSGVRDFLAQHYVPLKQAN--PK-------FP--ILVRECSGVTPVVWAR 61 (72)
Q Consensus 17 C~~~~sS~GvR~Fl~~~l~~~k~~N--P~-------v~--i~v~~~~g~~P~l~a~ 61 (72)
++.++++.-+.+-+++....+++.| |. || .++....|-+|.|.-+
T Consensus 111 SNlgpsnp~L~~~v~~r~~~~~~~~~~p~~~~~~~~VP~DlVTaSGSGLDPhISp~ 166 (222)
T PRK13994 111 TNRSADNEELIQWVKDAKAAVVEDNSVPGYEVKPSDVPADAVTSSGSGLDPDISPA 166 (222)
T ss_pred cCCCCCCHHHHHHHHHHHHHHHHhCCCCccccCCCCCCHHHHhcccccCCCCCCHH
Confidence 5678899999999999999999999 45 33 3344556778876543
No 123
>KOG1777|consensus
Probab=30.16 E-value=39 Score=27.28 Aligned_cols=24 Identities=25% Similarity=0.195 Sum_probs=21.5
Q ss_pred EEEcCCCCCEEEEEecCCcccccc
Q psy15303 48 VRECSGVTPVVWARIPTIGCLGFL 71 (72)
Q Consensus 48 v~~~~g~~P~l~a~Y~n~~~~~~~ 71 (72)
|+.+.|..|+++..-.|.||-|||
T Consensus 421 vqirtGsNP~i~~NkIWggqNGvL 444 (625)
T KOG1777|consen 421 VQIRTGSNPKIRRNKIWGGQNGVL 444 (625)
T ss_pred eEeecCCCCeeeecceecCcccEE
Confidence 566789999999999999999987
No 124
>cd03051 GST_N_GTT2_like GST_N family, Saccharomyces cerevisiae GTT2-like subfamily; composed of predominantly uncharacterized proteins with similarity to the S. cerevisiae GST protein, GTT2. GSTs are cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of glutathione (GSH) with a wide range of endogenous and xenobiotic alkylating agents, including carcinogens, therapeutic drugs, environmental toxins and products of oxidative stress. GSTs also show GSH peroxidase activity and are involved in the synthesis of prostaglandins and leukotrienes. The GST fold contains an N-terminal TRX-fold domain and a C-terminal alpha helical domain, with an active site located in a cleft between the two domains. GTT2, a homodimer, exhibits GST activity with standard substrates. Strains with deleted GTT2 genes are viable but exhibit increased sensitivity to heat shock.
Probab=30.04 E-value=93 Score=16.41 Aligned_cols=19 Identities=26% Similarity=0.282 Sum_probs=15.1
Q ss_pred EEEecCCCCCCHHHHHHHH
Q psy15303 13 RIHLCQKGGSSSGVRDFLA 31 (72)
Q Consensus 13 ~~~yC~~~~sS~GvR~Fl~ 31 (72)
++....+++.|+-+|-++.
T Consensus 2 ~Ly~~~~s~~~~~~~~~L~ 20 (74)
T cd03051 2 KLYDSPTAPNPRRVRIFLA 20 (74)
T ss_pred EEEeCCCCcchHHHHHHHH
Confidence 5666677888999998885
No 125
>PF02638 DUF187: Glycosyl hydrolase like GH101; InterPro: IPR003790 This entry describes proteins of unknown function.
Probab=29.80 E-value=77 Score=23.12 Aligned_cols=29 Identities=14% Similarity=0.343 Sum_probs=24.8
Q ss_pred HHHHHHHHhCHHHHHHhCCCCeEEEEEcC
Q psy15303 24 SGVRDFLAQHYVPLKQANPKFPILVRECS 52 (72)
Q Consensus 24 ~GvR~Fl~~~l~~~k~~NP~v~i~v~~~~ 52 (72)
.-+-+||++-+..+|+.||++.|-+.+..
T Consensus 203 ~~I~~~V~~i~~~ik~~kP~v~~sisp~g 231 (311)
T PF02638_consen 203 DNINNFVKRIYDAIKAIKPWVKFSISPFG 231 (311)
T ss_pred HHHHHHHHHHHHHHHHhCCCCeEEEEeec
Confidence 45778999999999999999999987653
No 126
>TIGR02196 GlrX_YruB Glutaredoxin-like protein, YruB-family. This glutaredoxin-like protein family contains the conserved CxxC motif and includes the Clostridium pasteurianum protein YruB which has been cloned from a rubredoxin operon. Somewhat related to NrdH, it is unknown whether this protein actually interacts with glutathione/glutathione reducatase, or, like NrdH, some other reductant system.
Probab=29.76 E-value=61 Score=16.86 Aligned_cols=21 Identities=5% Similarity=0.180 Sum_probs=18.4
Q ss_pred EEEEecCCCCCCHHHHHHHHh
Q psy15303 12 LRIHLCQKGGSSSGVRDFLAQ 32 (72)
Q Consensus 12 L~~~yC~~~~sS~GvR~Fl~~ 32 (72)
|++.+.++++.++-++.++++
T Consensus 2 i~lf~~~~C~~C~~~~~~l~~ 22 (74)
T TIGR02196 2 VKVYTTPWCPPCKKAKEYLTS 22 (74)
T ss_pred EEEEcCCCChhHHHHHHHHHH
Confidence 678889999999999999864
No 127
>PF13504 LRR_7: Leucine rich repeat; PDB: 3OJA_B 3G06_A 1OOK_G 1QYY_G 1SQ0_B 1P9A_G 1GWB_A 1P8V_A 1M0Z_A 1U0N_D ....
Probab=29.72 E-value=23 Score=15.06 Aligned_cols=11 Identities=18% Similarity=0.317 Sum_probs=7.5
Q ss_pred CceEEEEEecC
Q psy15303 8 KLKELRIHLCQ 18 (72)
Q Consensus 8 qLk~L~~~yC~ 18 (72)
.|+.|.++.|+
T Consensus 2 ~L~~L~l~~n~ 12 (17)
T PF13504_consen 2 NLRTLDLSNNR 12 (17)
T ss_dssp T-SEEEETSS-
T ss_pred ccCEEECCCCC
Confidence 68888888886
No 128
>COG0607 PspE Rhodanese-related sulfurtransferase [Inorganic ion transport and metabolism]
Probab=28.99 E-value=75 Score=18.25 Aligned_cols=24 Identities=17% Similarity=0.224 Sum_probs=19.8
Q ss_pred eEEEEEecCCCCCCHHHHHHHHhC
Q psy15303 10 KELRIHLCQKGGSSSGVRDFLAQH 33 (72)
Q Consensus 10 k~L~~~yC~~~~sS~GvR~Fl~~~ 33 (72)
.+-.+.||..|..|.-+-.++.+.
T Consensus 61 ~~~ivv~C~~G~rS~~aa~~L~~~ 84 (110)
T COG0607 61 DDPIVVYCASGVRSAAAAAALKLA 84 (110)
T ss_pred CCeEEEEeCCCCChHHHHHHHHHc
Confidence 456788999999999999888643
No 129
>PF07205 DUF1413: Domain of unknown function (DUF1413); InterPro: IPR010813 This family consists of several hypothetical bacterial proteins, which seem to be specific to Staphylococcus species. Members of this family are typically around 100 residues in length. The function of this family is unknown.
Probab=28.41 E-value=93 Score=17.68 Aligned_cols=33 Identities=15% Similarity=0.118 Sum_probs=28.5
Q ss_pred CCCCCCHHHHHHHHhCHHHHHHhCCCCeEEEEE
Q psy15303 18 QKGGSSSGVRDFLAQHYVPLKQANPKFPILVRE 50 (72)
Q Consensus 18 ~~~~sS~GvR~Fl~~~l~~~k~~NP~v~i~v~~ 50 (72)
.|..-|.+.|..+.+.+-.+-+++|.++|.+-.
T Consensus 27 ~w~~~s~~~r~~~g~~F~~~V~~~~~~~i~~~~ 59 (70)
T PF07205_consen 27 EWNTLSRAERQSLGRAFLYEVKQGPIVRIKIIG 59 (70)
T ss_pred hhhhCCHHHHHHHHHHHHHHHHhCCCCceEEEe
Confidence 466679999999999999999999999877753
No 130
>PF08073 CHDNT: CHDNT (NUC034) domain; InterPro: IPR012958 The CHD N-terminal domain is found in PHD/RING fingers and chromo domain-associated helicases [].; GO: 0003677 DNA binding, 0005524 ATP binding, 0008270 zinc ion binding, 0016818 hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus
Probab=28.22 E-value=83 Score=17.92 Aligned_cols=22 Identities=32% Similarity=0.449 Sum_probs=16.0
Q ss_pred HHHHHHHhCHHHHHHhCCCCeE
Q psy15303 25 GVRDFLAQHYVPLKQANPKFPI 46 (72)
Q Consensus 25 GvR~Fl~~~l~~~k~~NP~v~i 46 (72)
..+.|=+.-=|.++++||.++.
T Consensus 15 ~yK~Fsq~vRP~l~~~NPk~~~ 36 (55)
T PF08073_consen 15 NYKAFSQHVRPLLAKANPKAPM 36 (55)
T ss_pred HHHHHHHHHHHHHHHHCCCCcH
Confidence 3455666666889999998863
No 131
>cd08457 PBP2_OccR The C-terminal substrate-domain of LysR-type transcriptional regulator, OccR, involved in the catabolism of octopine, contains the type 2 periplasmic binding fold. This CD includes the C-terminal substrate-domain of LysR-type transcriptional regulator OccR, which is involved in the catabolism of octopine. Opines are low molecular weight compounds found in plant crown gall tumors produced by the parasitic bacterium Agrobacterium. There are at least 30 different opines identified so far. Opines are utilized by tumor-colonizing bacteria as a source of carbon, nitrogen, and energy. In Agrobacterium tumefaciens, OccR protein activates the occQ operon of the Ti plasmid in response to octopine. This operon encodes proteins required for the uptake and catabolism of octopine, an arginine derivative. The occ operon also encodes the TraR protein, which is a quorum-sensing transcriptional regulator of the Ti plasmid tra regulon. This substrate-binding domain shows significant h
Probab=27.87 E-value=45 Score=20.34 Aligned_cols=26 Identities=12% Similarity=0.282 Sum_probs=20.5
Q ss_pred HHHHHHhCHHHHHHhCCCCeEEEEEc
Q psy15303 26 VRDFLAQHYVPLKQANPKFPILVREC 51 (72)
Q Consensus 26 vR~Fl~~~l~~~k~~NP~v~i~v~~~ 51 (72)
...++...+.+|.+.+|++.+.++..
T Consensus 11 ~~~~l~~~l~~~~~~~P~i~l~~~~~ 36 (196)
T cd08457 11 ANGFLPRFLAAFLRLRPNLHLSLMGL 36 (196)
T ss_pred hccccHHHHHHHHHHCCCeEEEEEec
Confidence 34566778888999999999988764
No 132
>cd07945 DRE_TIM_CMS Leptospira interrogans citramalate synthase (CMS) and related proteins, N-terminal catalytic TIM barrel domain. Citramalate synthase (CMS) catalyzes the conversion of pyruvate and acetyl-CoA to (R)-citramalate in the first dedicated step of the citramalate pathway. Citramalate is only found in Leptospira interrogans and a few other microorganisms. This family belongs to the DRE-TIM metallolyase superfamily. DRE-TIM metallolyases include 2-isopropylmalate synthase (IPMS), alpha-isopropylmalate synthase (LeuA), 3-hydroxy-3-methylglutaryl-CoA lyase, homocitrate synthase, citramalate synthase, 4-hydroxy-2-oxovalerate aldolase, re-citrate synthase, transcarboxylase 5S, pyruvate carboxylase, AksA, and FrbC. These members all share a conserved triose-phosphate isomerase (TIM) barrel domain consisting of a core beta(8)-alpha(8) motif with the eight parallel beta strands forming an enclosed barrel surrounded by eight alpha helices. The domain has a catalytic center con
Probab=27.78 E-value=1.1e+02 Score=21.94 Aligned_cols=35 Identities=17% Similarity=0.080 Sum_probs=27.7
Q ss_pred EEEecCCCCCCHHHHHHHHhCHHHHHHhCCCCeEEEE
Q psy15303 13 RIHLCQKGGSSSGVRDFLAQHYVPLKQANPKFPILVR 49 (72)
Q Consensus 13 ~~~yC~~~~sS~GvR~Fl~~~l~~~k~~NP~v~i~v~ 49 (72)
+|.+||+.|....-+ +.+.+..+++..|++++.+.
T Consensus 163 ~i~l~DT~G~~~P~~--v~~l~~~l~~~~~~~~i~~H 197 (280)
T cd07945 163 RIMLPDTLGILSPFE--TYTYISDMVKRYPNLHFDFH 197 (280)
T ss_pred EEEecCCCCCCCHHH--HHHHHHHHHhhCCCCeEEEE
Confidence 688999999888776 66777788888898887663
No 133
>KOG3239|consensus
Probab=27.31 E-value=32 Score=24.24 Aligned_cols=26 Identities=19% Similarity=0.391 Sum_probs=21.7
Q ss_pred EEEEecCCCCCCHHHHHHHHhCHHHH
Q psy15303 12 LRIHLCQKGGSSSGVRDFLAQHYVPL 37 (72)
Q Consensus 12 L~~~yC~~~~sS~GvR~Fl~~~l~~~ 37 (72)
|-..||+.+|.-+--|.||..|.|++
T Consensus 20 lP~EYCEf~~~~~kCk~WL~~n~pdl 45 (193)
T KOG3239|consen 20 LPPEYCEFSGDLKKCKEWLEENHPDL 45 (193)
T ss_pred CCHHHHHccccHHHHHHHHHhcChhH
Confidence 34568999999999999999887765
No 134
>COG4097 Predicted ferric reductase [Inorganic ion transport and metabolism]
Probab=27.08 E-value=64 Score=25.41 Aligned_cols=44 Identities=16% Similarity=0.190 Sum_probs=30.4
Q ss_pred eEEEEEecCCCCCCHHHHHHH-HhCHHHHHHhCCCCeEEEEEcCCCCCEEE
Q psy15303 10 KELRIHLCQKGGSSSGVRDFL-AQHYVPLKQANPKFPILVRECSGVTPVVW 59 (72)
Q Consensus 10 k~L~~~yC~~~~sS~GvR~Fl-~~~l~~~k~~NP~v~i~v~~~~g~~P~l~ 59 (72)
+-+.+.||-.+. .+=+ .+.+.+++++||++.+.+ -.++++|++-
T Consensus 344 ~~V~L~Y~~~n~-----e~~~y~~eLr~~~qkl~~~~lHi-iDSs~~g~l~ 388 (438)
T COG4097 344 PPVHLFYCSRNW-----EEALYAEELRALAQKLPNVVLHI-IDSSKDGYLD 388 (438)
T ss_pred CceEEEEEecCC-----chhHHHHHHHHHHhcCCCeEEEE-ecCCCCCccC
Confidence 347889985543 3333 457788999999999999 4444566654
No 135
>PF11247 DUF2675: Protein of unknown function (DUF2675) ; InterPro: IPR022611 Members in this family of proteins include Bacteriophage T7 gene 5.5; they have no known function.
Probab=26.88 E-value=47 Score=21.08 Aligned_cols=15 Identities=13% Similarity=0.366 Sum_probs=13.4
Q ss_pred HHHHHHHHhCHHHHH
Q psy15303 24 SGVRDFLAQHYVPLK 38 (72)
Q Consensus 24 ~GvR~Fl~~~l~~~k 38 (72)
.|+|+||++.+++..
T Consensus 68 ~g~R~~IKe~~~E~s 82 (98)
T PF11247_consen 68 QGIREAIKEMLSEYS 82 (98)
T ss_pred HHHHHHHHHHHHHhc
Confidence 699999999998887
No 136
>PRK09375 quinolinate synthetase; Provisional
Probab=26.87 E-value=93 Score=23.31 Aligned_cols=33 Identities=24% Similarity=0.231 Sum_probs=26.5
Q ss_pred ecCCCCCCHHHHHHHHhC-------------HHHHHHhCCCCeEEE
Q psy15303 16 LCQKGGSSSGVRDFLAQH-------------YVPLKQANPKFPILV 48 (72)
Q Consensus 16 yC~~~~sS~GvR~Fl~~~-------------l~~~k~~NP~v~i~v 48 (72)
.+|..+||.|+-+|+++. .-.++++||+-.|..
T Consensus 223 ~AD~vgSTs~~i~~v~~~~~~~~iigTE~~L~~~l~~~~P~K~fi~ 268 (319)
T PRK09375 223 LADFVGSTSQIIKAAKASPAKKFIVGTEIGIVHRLQKANPDKEFIP 268 (319)
T ss_pred hcCEEecHHHHHHHHHhCCCCeEEEEccHHHHHHHHHHCCCCEEEE
Confidence 478899999999999643 346788899988875
No 137
>PLN02659 Probable galacturonosyltransferase
Probab=26.87 E-value=52 Score=26.53 Aligned_cols=25 Identities=24% Similarity=0.573 Sum_probs=21.7
Q ss_pred CccccccCceEEEEEecCCCCCCHHHHHHHH
Q psy15303 1 MATRFGSKLKELRIHLCQKGGSSSGVRDFLA 31 (72)
Q Consensus 1 ~~~~f~~qLk~L~~~yC~~~~sS~GvR~Fl~ 31 (72)
|-.++++.+|.|+++ +|.|.+||++
T Consensus 1 mq~~~sp~~r~~t~~------~~~~~~~~~~ 25 (534)
T PLN02659 1 MQLHISPSLRHVTVL------PGKGVREFIK 25 (534)
T ss_pred CceeecCccceEEEc------cCccHHHHHH
Confidence 667899999999997 4799999986
No 138
>cd02066 GRX_family Glutaredoxin (GRX) family; composed of GRX, approximately 10 kDa in size, and proteins containing a GRX or GRX-like domain. GRX is a glutathione (GSH) dependent reductase, catalyzing the disulfide reduction of target proteins such as ribonucleotide reductase. It contains a redox active CXXC motif in a TRX fold and uses a similar dithiol mechanism employed by TRXs for intramolecular disulfide bond reduction of protein substrates. Unlike TRX, GRX has preference for mixed GSH disulfide substrates, in which it uses a monothiol mechanism where only the N-terminal cysteine is required. The flow of reducing equivalents in the GRX system goes from NADPH - GSH reductase - GSH - GRX - protein substrates. By altering the redox state of target proteins, GRX is involved in many cellular functions including DNA synthesis, signal transduction and the defense against oxidative stress. Different classes are known including human GRX1 and GRX2, as well as E. coli GRX1 and GRX3, which
Probab=26.54 E-value=67 Score=16.54 Aligned_cols=21 Identities=5% Similarity=0.012 Sum_probs=16.5
Q ss_pred EEEEecCCCCCCHHHHHHHHh
Q psy15303 12 LRIHLCQKGGSSSGVRDFLAQ 32 (72)
Q Consensus 12 L~~~yC~~~~sS~GvR~Fl~~ 32 (72)
+++..-++.+.++.++.++++
T Consensus 2 v~ly~~~~Cp~C~~~~~~L~~ 22 (72)
T cd02066 2 VVVFSKSTCPYCKRAKRLLES 22 (72)
T ss_pred EEEEECCCCHHHHHHHHHHHH
Confidence 566667888889999999864
No 139
>PF10262 Rdx: Rdx family; InterPro: IPR011893 This entry represents the Rdx family of selenoproteins, which includes mammalian selenoproteins SelW, SelV, SelT and SelH, bacterial SelW-like proteins and cysteine-containing proteins of unknown function in all three domains of life. Mammalian Rdx12 and its fish selenoprotein orthologues are also members of this family []. These proteins possess a thioredoxin-like fold and a conserved CXXC or CxxU (U is selenocysteine) motif near the N terminus, suggesting a redox function. Rdx proteins can use catalytic cysteine (or selenocysteine) to form transient mixed disulphides with substrate proteins. Selenium (Se) plays an essential role in cell survival and most of the effects of Se are probably mediated by selenoproteins. Selenoprotein W (SelW) plays an important role in protection of neurons from oxidative stress during neuronal development [], []. Selenoprotein T (SelT) is conserved from plants to humans. SelT is localized to the endoplasmic reticulum through a hydrophobic domain. The protein binds to UDP-glucose:glycoprotein glucosyltransferase (UGTR), the endoplasmic reticulum (ER)-resident protein, which is known to be involved in the quality control of protein folding [, ]. The function of SelT is unknown, although it may have a role in PACAP signaling during PC12 cell differentiation [, ]. Selenoprotein H (SelH) protects neurons against UVB-induced damage by inhibiting apoptotic cell death pathways, by preventing mitochondrial depolarization, and by promoting cell survival pathways [].; GO: 0008430 selenium binding, 0045454 cell redox homeostasis; PDB: 2OJL_B 2FA8_A 2P0G_C 2NPB_A 3DEX_C 2OKA_A 2OBK_G.
Probab=26.51 E-value=69 Score=18.37 Aligned_cols=36 Identities=17% Similarity=0.269 Sum_probs=23.3
Q ss_pred EEEEEecCCCCCCHHHHHHHHhCHHHHHHhCCC--CeEEEEE
Q psy15303 11 ELRIHLCQKGGSSSGVRDFLAQHYVPLKQANPK--FPILVRE 50 (72)
Q Consensus 11 ~L~~~yC~~~~sS~GvR~Fl~~~l~~~k~~NP~--v~i~v~~ 50 (72)
+|+|.||...+-..-.-++- ..+....|+ ..+...+
T Consensus 2 ~V~IeYC~~C~~~~~a~~l~----~~l~~~fp~~~~~v~~~~ 39 (76)
T PF10262_consen 2 KVTIEYCTSCGYRPRALELA----QELLQTFPDRIAEVELSP 39 (76)
T ss_dssp EEEEEEETTTTCHHHHHHHH----HHHHHHSTTTCSEEEEEE
T ss_pred EEEEEECCCCCCHHHHHHHH----HHHHHHCCCcceEEEEEe
Confidence 68999999987555433322 245556677 6666655
No 140
>PF12876 Cellulase-like: Sugar-binding cellulase-like; InterPro: IPR024778 O-Glycosyl hydrolases 3.2.1. from EC are a widespread group of enzymes that hydrolyse the glycosidic bond between two or more carbohydrates, or between a carbohydrate and a non-carbohydrate moiety. A classification system for glycosyl hydrolases, based on sequence similarity, has led to the definition of 85 different families [, ]. This classification is available on the CAZy (CArbohydrate-Active EnZymes) web site. This entry represents a family of putative cellulase enzymes.; PDB: 3GYC_B.
Probab=26.46 E-value=60 Score=19.01 Aligned_cols=27 Identities=11% Similarity=0.361 Sum_probs=20.4
Q ss_pred CHHHHHHHHhCHHHHHHhCCCCeEEEE
Q psy15303 23 SSGVRDFLAQHYVPLKQANPKFPILVR 49 (72)
Q Consensus 23 S~GvR~Fl~~~l~~~k~~NP~v~i~v~ 49 (72)
..-+++++++-...+++.+|+.++.+-
T Consensus 37 ~~~~~~~l~~~~~~iR~~dP~~pvt~g 63 (88)
T PF12876_consen 37 AEAYAEWLKEAFRWIRAVDPSQPVTSG 63 (88)
T ss_dssp SHHHHHHHHHHHHHHHTT-TTS-EE--
T ss_pred HHHHHHHHHHHHHHHHHhCCCCcEEee
Confidence 466889999999999999999998764
No 141
>PRK10696 tRNA 2-thiocytidine biosynthesis protein TtcA; Provisional
Probab=26.19 E-value=64 Score=22.57 Aligned_cols=25 Identities=8% Similarity=-0.013 Sum_probs=20.9
Q ss_pred CCHHHHHHHHhCHHHHHHhCCCCeE
Q psy15303 22 SSSGVRDFLAQHYVPLKQANPKFPI 46 (72)
Q Consensus 22 sS~GvR~Fl~~~l~~~k~~NP~v~i 46 (72)
.....|+.+++-+|.+.+.||++..
T Consensus 206 ~~~~~R~~ir~~l~~L~~~~P~~~~ 230 (258)
T PRK10696 206 QENLQRQVVKEMLRDWEKEYPGRIE 230 (258)
T ss_pred CchhHHHHHHHHHHHHHHHCccHHH
Confidence 4456899999999999999998754
No 142
>PF10607 CLTH: CTLH/CRA C-terminal to LisH motif domain; InterPro: IPR019589 This entry represents the CRA (or CT11-RanBPM) domain, which is a protein-protein interaction domain present in crown eukaryotes (plants, animals, fungi) and which is found in Ran-binding proteins such as Ran-binding protein 9 (RanBP9 or RanBPM) and RanBP10. RanBPM is a scaffolding protein important in regulating cellular function in both the immune system and the nervous system, and may act as an adapter protein to couple membrane receptors to intracellular signaling pathways. This domain is at the C terminus of the proteins and is the binding domain for the CRA motif, which is comprised of approximately 100 amino acids at the C-terminal of RanBPM. It was found to be important for the interaction of RanBPM with fragile X mental retardation protein (FMRP), but its functional significance has yet to be determined [].
Probab=25.97 E-value=48 Score=20.68 Aligned_cols=29 Identities=17% Similarity=0.356 Sum_probs=23.8
Q ss_pred CCCHHHHHHHHhCHHHHHHhCCCCeEEEE
Q psy15303 21 GSSSGVRDFLAQHYVPLKQANPKFPILVR 49 (72)
Q Consensus 21 ~sS~GvR~Fl~~~l~~~k~~NP~v~i~v~ 49 (72)
|.-..+-++++++.|.+.+.|+++.|..+
T Consensus 15 g~i~~Ai~w~~~~~~~l~~~~~~L~f~L~ 43 (145)
T PF10607_consen 15 GDIDPAIEWLNENFPELLKRNSSLEFELR 43 (145)
T ss_pred CCHHHHHHHHHHcCHHHHhcCCchhHHHH
Confidence 44567889999999999999999987653
No 143
>PF09822 ABC_transp_aux: ABC-type uncharacterized transport system; InterPro: IPR019196 This domain is found in various eukaryotic and prokaryotic intra-flagellar transport proteins involved in gliding motility, as well as in several hypothetical proteins.
Probab=25.77 E-value=1.9e+02 Score=20.04 Aligned_cols=39 Identities=10% Similarity=0.123 Sum_probs=29.0
Q ss_pred EEEEecCCCCC-CHHHHHHHHhCHHHHHHhCC-CCeEEEEE
Q psy15303 12 LRIHLCQKGGS-SSGVRDFLAQHYVPLKQANP-KFPILVRE 50 (72)
Q Consensus 12 L~~~yC~~~~s-S~GvR~Fl~~~l~~~k~~NP-~v~i~v~~ 50 (72)
|++.+...-+. -...+.-+++-+.++++.|| ++.+....
T Consensus 29 i~~~~s~~l~~~~~~~~~~v~~lL~~y~~~s~g~i~v~~iD 69 (271)
T PF09822_consen 29 ITVYFSRELPPELSPLRKQVRDLLDEYARYSPGKIKVEFID 69 (271)
T ss_pred EEEEECCCcchhhhHHHHHHHHHHHHHHHhCCCceEEEEEC
Confidence 66666653333 56677778888999999999 98887754
No 144
>cd06544 GH18_narbonin Narbonin is a plant 2S protein from the globulin fraction of narbon bean (Vicia narbonensis L.) cotyledons with unknown function. Narbonin has a glycosyl hydrolase family 18 (GH18) domain without the conserved catalytic residues and with no known enzymatic activity. Narbonin amounts to up to 3% of the total seed globulins of mature seeds and was thought to be a storage protein but was found to degrade too slowly during germination. This family also includes the VfNOD32 nodulin from Vicia faba.
Probab=25.50 E-value=57 Score=23.20 Aligned_cols=20 Identities=10% Similarity=0.273 Sum_probs=16.9
Q ss_pred hCHHHHHHhCCCCeEEEEEc
Q psy15303 32 QHYVPLKQANPKFPILVREC 51 (72)
Q Consensus 32 ~~l~~~k~~NP~v~i~v~~~ 51 (72)
+.+.++|++||++++++.-.
T Consensus 59 ~~~~~lK~~~p~lKvllSiG 78 (253)
T cd06544 59 EAVKSIKAQHPNVKVVISIG 78 (253)
T ss_pred HHHHHHHHhCCCcEEEEEeC
Confidence 46789999999999999653
No 145
>PRK13995 potassium-transporting ATPase subunit C; Provisional
Probab=25.06 E-value=1.1e+02 Score=21.79 Aligned_cols=44 Identities=18% Similarity=0.302 Sum_probs=33.6
Q ss_pred cCCCCCCHHHHHHHHhCHHHHHHhCCC-----CeE--EEEEcCCCCCEEEE
Q psy15303 17 CQKGGSSSGVRDFLAQHYVPLKQANPK-----FPI--LVRECSGVTPVVWA 60 (72)
Q Consensus 17 C~~~~sS~GvR~Fl~~~l~~~k~~NP~-----v~i--~v~~~~g~~P~l~a 60 (72)
++-+++|.-+.+-+++....+++.||. ||+ ++....|-+|.|.-
T Consensus 95 SNlgpsnp~L~~~v~~r~~~~~~~~p~~~~~~vP~DlvTaSgSGLDPhISp 145 (203)
T PRK13995 95 QNYAPTNPELHDRVQKDIDKFLKTNPTVKKEDIPTDLLTASGSGLDPHISP 145 (203)
T ss_pred cCCCCCCHHHHHHHHHHHHHHHHhCCCCCCCCCCHHHHhccccCCCCCCCH
Confidence 466788999999999999999999985 443 33555677887653
No 146
>PF07735 FBA_2: F-box associated; InterPro: IPR012885 This domain is found is found towards the C terminus of proteins that contain an F-box, IPR001810 from INTERPRO, suggesting that they are effectors linked with ubiquitination.
Probab=25.01 E-value=1.2e+02 Score=16.55 Aligned_cols=36 Identities=17% Similarity=0.304 Sum_probs=25.4
Q ss_pred cCceEEEEEecCCCCCCHHHHHHHHhCHHHHHHhCCCCeEE
Q psy15303 7 SKLKELRIHLCQKGGSSSGVRDFLAQHYVPLKQANPKFPIL 47 (72)
Q Consensus 7 ~qLk~L~~~yC~~~~sS~GvR~Fl~~~l~~~k~~NP~v~i~ 47 (72)
-.++.|.+..+. =+++.+..||.+.+.- .||.++..
T Consensus 32 ~nc~~i~l~~~~--~t~~dln~Flk~W~~G---~~~~Le~l 67 (70)
T PF07735_consen 32 MNCKKIELWNSK--FTNEDLNKFLKHWING---SNPRLEYL 67 (70)
T ss_pred cCCCEEEEECCC--CCHHHHHHHHHHHHcC---CCcCCcEE
Confidence 356777776544 4689999999887654 77777643
No 147
>cd02976 NrdH NrdH-redoxin (NrdH) family; NrdH is a small monomeric protein with a conserved redox active CXXC motif within a TRX fold, characterized by a glutaredoxin (GRX)-like sequence and TRX-like activity profile. In vitro, it displays protein disulfide reductase activity that is dependent on TRX reductase, not glutathione (GSH). It is part of the NrdHIEF operon, where NrdEF codes for class Ib ribonucleotide reductase (RNR-Ib), an efficient enzyme at low oxygen levels. Under these conditions when GSH is mostly conjugated to spermidine, NrdH can still function and act as a hydrogen donor for RNR-Ib. It has been suggested that the NrdHEF system may be the oldest RNR reducing system, capable of functioning in a microaerophilic environment, where GSH was not yet available. NrdH from Corynebacterium ammoniagenes can form domain-swapped dimers, although it is unknown if this happens in vivo. Domain-swapped dimerization, which results in the blocking of the TRX reductase binding site, cou
Probab=24.83 E-value=82 Score=16.36 Aligned_cols=21 Identities=10% Similarity=0.140 Sum_probs=17.0
Q ss_pred EEEEecCCCCCCHHHHHHHHh
Q psy15303 12 LRIHLCQKGGSSSGVRDFLAQ 32 (72)
Q Consensus 12 L~~~yC~~~~sS~GvR~Fl~~ 32 (72)
+++....+++.+.-++.++++
T Consensus 2 v~l~~~~~c~~c~~~~~~l~~ 22 (73)
T cd02976 2 VTVYTKPDCPYCKATKRFLDE 22 (73)
T ss_pred EEEEeCCCChhHHHHHHHHHH
Confidence 567778888889999888864
No 148
>PRK11139 DNA-binding transcriptional activator GcvA; Provisional
Probab=24.78 E-value=86 Score=21.50 Aligned_cols=25 Identities=12% Similarity=0.373 Sum_probs=21.8
Q ss_pred HHHHHhCHHHHHHhCCCCeEEEEEc
Q psy15303 27 RDFLAQHYVPLKQANPKFPILVREC 51 (72)
Q Consensus 27 R~Fl~~~l~~~k~~NP~v~i~v~~~ 51 (72)
..++...+.+|.+.+|++.|.+...
T Consensus 106 ~~~l~~~l~~f~~~~p~i~i~l~~~ 130 (297)
T PRK11139 106 IQWLVPRLSSFNEAHPDIDVRLKAV 130 (297)
T ss_pred HHHHHHHHHHHHHHCCCceEEEEeC
Confidence 5788889999999999999999754
No 149
>COG1393 ArsC Arsenate reductase and related proteins, glutaredoxin family [Inorganic ion transport and metabolism]
Probab=24.43 E-value=71 Score=20.25 Aligned_cols=23 Identities=13% Similarity=0.124 Sum_probs=17.9
Q ss_pred EEEEEecCCCCCCHHHHHHHHhC
Q psy15303 11 ELRIHLCQKGGSSSGVRDFLAQH 33 (72)
Q Consensus 11 ~L~~~yC~~~~sS~GvR~Fl~~~ 33 (72)
.++|.....+.+|+-+++|++++
T Consensus 2 ~itiy~~p~C~t~rka~~~L~~~ 24 (117)
T COG1393 2 MITIYGNPNCSTCRKALAWLEEH 24 (117)
T ss_pred eEEEEeCCCChHHHHHHHHHHHc
Confidence 36777888888888888888754
No 150
>PF01547 SBP_bac_1: Bacterial extracellular solute-binding protein; InterPro: IPR006059 Bacterial high affinity transport systems are involved in active transport of solutes across the cytoplasmic membrane. The protein components of these traffic systems include one or two transmembrane protein components, one or two membrane-associated ATP-binding proteins and a high affinity periplasmic solute-binding protein. In Gram-positive bacteria, which are surrounded by a single membrane and therefore have no periplasmic region, the equivalent proteins are bound to the membrane via an N-terminal lipid anchor. These homologue proteins do not play an integral role in the transport process per se, but probably serve as receptors to trigger or initiate translocation of the solute through the membrane by binding to external sites of the integral membrane proteins of the efflux system. In addition at least some solute-binding proteins function in the initiation of sensory transduction pathways. On the basis of sequence similarities, the vast majority of these solute-binding proteins can be grouped into eight family clusters [], which generally correlate with the nature of the solute bound. Family 1 includes the maltose/maltodextrin-binding proteins of Enterobacteriaceae (gene malE) [] and Streptococcus pneumoniae malX; multiple oligosaccharide binding protein of Streptococcus mutans (gene msmE); Escherichia coli glycerol-3-phosphate-binding protein; Serratia marcescens iron-binding protein (gene sfuA) and the homologous proteins (gene fbp) from Haemophilus influenzae and Neisseria; and the E. coli thiamine-binding protein (gene tbpA).; GO: 0005215 transporter activity, 0006810 transport; PDB: 3CFZ_A 2THI_A 3THI_A 4THI_A 1O7T_C 1D9Y_A 1URG_A 1URS_A 1URD_B 3OMB_A ....
Probab=24.14 E-value=67 Score=21.35 Aligned_cols=23 Identities=9% Similarity=0.144 Sum_probs=18.7
Q ss_pred HHHhCH-HHHHHhCCCCeEEEEEc
Q psy15303 29 FLAQHY-VPLKQANPKFPILVREC 51 (72)
Q Consensus 29 Fl~~~l-~~~k~~NP~v~i~v~~~ 51 (72)
.+++.+ .+|.+.||++.|.+...
T Consensus 9 ~~~~~~~~~f~k~~~~i~V~~~~~ 32 (315)
T PF01547_consen 9 ALQELIIEEFEKEHPGIKVEIEFI 32 (315)
T ss_dssp HHHHHHHHHHHHHHTTEEEEEEEE
T ss_pred HHHHHHHHHHHHHCCCcEEEEEEC
Confidence 666666 78999999999998664
No 151
>PF13516 LRR_6: Leucine Rich repeat; PDB: 3RGZ_A 3RJ0_A 3RIZ_A 3RGX_A 1DFJ_I 2BNH_A 3VQ1_A 3VQ2_A 2Z64_A 2OMX_A ....
Probab=24.05 E-value=19 Score=16.09 Aligned_cols=20 Identities=20% Similarity=0.282 Sum_probs=12.2
Q ss_pred cCceEEEEEecCCCCCCHHHHH
Q psy15303 7 SKLKELRIHLCQKGGSSSGVRD 28 (72)
Q Consensus 7 ~qLk~L~~~yC~~~~sS~GvR~ 28 (72)
++|+.|.|+.|+- +..|++.
T Consensus 2 ~~L~~L~l~~n~i--~~~g~~~ 21 (24)
T PF13516_consen 2 PNLETLDLSNNQI--TDEGASA 21 (24)
T ss_dssp TT-SEEE-TSSBE--HHHHHHH
T ss_pred CCCCEEEccCCcC--CHHHHHH
Confidence 4788899888874 3556554
No 152
>TIGR00269 conserved hypothetical protein TIGR00269.
Probab=23.93 E-value=55 Score=20.08 Aligned_cols=24 Identities=25% Similarity=0.290 Sum_probs=20.1
Q ss_pred CCHHHHHHHHhCHHHHHHhCCCCe
Q psy15303 22 SSSGVRDFLAQHYVPLKQANPKFP 45 (72)
Q Consensus 22 sS~GvR~Fl~~~l~~~k~~NP~v~ 45 (72)
+....|..+++.+.++.+.||++.
T Consensus 34 ~~~a~R~~~k~~L~~LE~~~P~~k 57 (104)
T TIGR00269 34 SSLSVRARIRDFLYDLENKKPGVK 57 (104)
T ss_pred CCCCchHHHHHHHHHHHHHCcChH
Confidence 345789999999999999999875
No 153
>cd01388 SOX-TCF_HMG-box SOX-TCF_HMG-box, class I member of the HMG-box superfamily of DNA-binding proteins. These proteins contain a single HMG box, and bind the minor groove of DNA in a highly sequence-specific manner. Members include SRY and its homologs in insects and vertebrates, and transcription factor-like proteins, TCF-1, -3, -4, and LEF-1. They appear to bind the minor groove of the A/T C A A A G/C-motif.
Probab=23.73 E-value=54 Score=18.40 Aligned_cols=18 Identities=22% Similarity=0.119 Sum_probs=14.3
Q ss_pred HHHHhCHHHHHHhCCCCe
Q psy15303 28 DFLAQHYVPLKQANPKFP 45 (72)
Q Consensus 28 ~Fl~~~l~~~k~~NP~v~ 45 (72)
-|+...-++++++||++.
T Consensus 11 ~F~~~~r~~~~~~~p~~~ 28 (72)
T cd01388 11 LFSKRHRRKVLQEYPLKE 28 (72)
T ss_pred HHHHHHHHHHHHHCCCCC
Confidence 356778889999999865
No 154
>PRK10837 putative DNA-binding transcriptional regulator; Provisional
Probab=23.71 E-value=1.1e+02 Score=20.64 Aligned_cols=26 Identities=12% Similarity=0.199 Sum_probs=21.5
Q ss_pred HHHHHHhCHHHHHHhCCCCeEEEEEc
Q psy15303 26 VRDFLAQHYVPLKQANPKFPILVREC 51 (72)
Q Consensus 26 vR~Fl~~~l~~~k~~NP~v~i~v~~~ 51 (72)
...++...+..|++++|++.|.+...
T Consensus 100 ~~~~~~~~l~~~~~~~P~i~i~v~~~ 125 (290)
T PRK10837 100 GNYILPAMIARYRRDYPQLPLELSVG 125 (290)
T ss_pred HhhhhHHHHHHHHHHCCCceEEEEEC
Confidence 34667888899999999999999754
No 155
>PRK09791 putative DNA-binding transcriptional regulator; Provisional
Probab=23.65 E-value=1.1e+02 Score=21.00 Aligned_cols=37 Identities=14% Similarity=0.244 Sum_probs=27.3
Q ss_pred eEEEEEecCCCCCCHHHHHHHHhCHHHHHHhCCCCeEEEEEc
Q psy15303 10 KELRIHLCQKGGSSSGVRDFLAQHYVPLKQANPKFPILVREC 51 (72)
Q Consensus 10 k~L~~~yC~~~~sS~GvR~Fl~~~l~~~k~~NP~v~i~v~~~ 51 (72)
..|+|-..+. -...++...+..|.+++|++.|.++..
T Consensus 95 g~l~I~~~~~-----~~~~~l~~~l~~~~~~~p~i~~~~~~~ 131 (302)
T PRK09791 95 GQINIGMGAS-----IARSLMPAVISRFHQQHPQVKVRIMEG 131 (302)
T ss_pred eEEEEEechH-----HHHhhhHHHHHHHHHHCCCeEEEEEeC
Confidence 4555555332 245677889999999999999999864
No 156
>PRK11151 DNA-binding transcriptional regulator OxyR; Provisional
Probab=23.34 E-value=1.5e+02 Score=20.40 Aligned_cols=26 Identities=23% Similarity=0.252 Sum_probs=22.1
Q ss_pred HHHHHHhCHHHHHHhCCCCeEEEEEc
Q psy15303 26 VRDFLAQHYVPLKQANPKFPILVREC 51 (72)
Q Consensus 26 vR~Fl~~~l~~~k~~NP~v~i~v~~~ 51 (72)
...++..-+.+|.+.+|++.|.+...
T Consensus 102 ~~~~~~~~l~~~~~~~P~v~i~~~~~ 127 (305)
T PRK11151 102 GPYLLPHIIPMLHQTFPKLEMYLHEA 127 (305)
T ss_pred HHHHHHHHHHHHHHHCCCcEEEEEeC
Confidence 45677888899999999999999864
No 157
>PRK10324 translation inhibitor protein RaiA; Provisional
Probab=22.72 E-value=2e+02 Score=17.87 Aligned_cols=32 Identities=13% Similarity=0.255 Sum_probs=25.1
Q ss_pred EEEEecCCCCCCHHHHHHHHhCHHHHHHhCCCC
Q psy15303 12 LRIHLCQKGGSSSGVRDFLAQHYVPLKQANPKF 44 (72)
Q Consensus 12 L~~~yC~~~~sS~GvR~Fl~~~l~~~k~~NP~v 44 (72)
|.|.+ .+-.-|..+|+++++.+..+.+-.|++
T Consensus 3 I~Itg-r~v~~tdalr~~ie~Kl~kL~k~~~~i 34 (113)
T PRK10324 3 MNITS-KQMEITPAIRQHVADRLAKLEKWQTHL 34 (113)
T ss_pred EEEEE-EcCcCCHHHHHHHHHHHHHHHHhcCCC
Confidence 33443 566678999999999999999988765
No 158
>cd03027 GRX_DEP Glutaredoxin (GRX) family, Dishevelled, Egl-10, and Pleckstrin (DEP) subfamily; composed of uncharacterized proteins containing a GRX domain and additional domains DEP and DUF547, both of which have unknown functions. GRX is a glutathione (GSH) dependent reductase containing a redox active CXXC motif in a TRX fold. It has preference for mixed GSH disulfide substrates, in which it uses a monothiol mechanism where only the N-terminal cysteine is required. By altering the redox state of target proteins, GRX is involved in many cellular functions.
Probab=22.69 E-value=1.2e+02 Score=16.56 Aligned_cols=22 Identities=23% Similarity=0.196 Sum_probs=18.3
Q ss_pred EEEEEecCCCCCCHHHHHHHHh
Q psy15303 11 ELRIHLCQKGGSSSGVRDFLAQ 32 (72)
Q Consensus 11 ~L~~~yC~~~~sS~GvR~Fl~~ 32 (72)
++++..-++.+.++-++.++++
T Consensus 2 ~v~ly~~~~C~~C~ka~~~L~~ 23 (73)
T cd03027 2 RVTIYSRLGCEDCTAVRLFLRE 23 (73)
T ss_pred EEEEEecCCChhHHHHHHHHHH
Confidence 5677777888999999999974
No 159
>PF01624 MutS_I: MutS domain I C-terminus.; InterPro: IPR007695 Mismatch repair contributes to the overall fidelity of DNA replication and is essential for combating the adverse effects of damage to the genome. It involves the correction of mismatched base pairs that have been missed by the proofreading element of the DNA polymerase complex. The post-replicative Mismatch Repair System (MMRS) of Escherichia coli involves MutS (Mutator S), MutL and MutH proteins, and acts to correct point mutations or small insertion/deletion loops produced during DNA replication []. MutS and MutL are involved in preventing recombination between partially homologous DNA sequences. The assembly of MMRS is initiated by MutS, which recognises and binds to mispaired nucleotides and allows further action of MutL and MutH to eliminate a portion of newly synthesized DNA strand containing the mispaired base []. MutS can also collaborate with methyltransferases in the repair of O(6)-methylguanine damage, which would otherwise pair with thymine during replication to create an O(6)mG:T mismatch []. MutS exists as a dimer, where the two monomers have different conformations and form a heterodimer at the structural level []. Only one monomer recognises the mismatch specifically and has ADP bound. Non-specific major groove DNA-binding domains from both monomers embrace the DNA in a clamp-like structure. Mismatch binding induces ATP uptake and a conformational change in the MutS protein, resulting in a clamp that translocates on DNA. MutS is a modular protein with a complex structure [], and is composed of: N-terminal mismatch-recognition domain, which is similar in structure to tRNA endonuclease. Connector domain, which is similar in structure to Holliday junction resolvase ruvC. Core domain, which is composed of two separate subdomains that join together to form a helical bundle; from within the core domain, two helices act as levers that extend towards (but do not touch) the DNA. Clamp domain, which is inserted between the two subdomains of the core domain at the top of the lever helices; the clamp domain has a beta-sheet structure. ATPase domain (connected to the core domain), which has a classical Walker A motif. HTH (helix-turn-helix) domain, which is involved in dimer contacts. The MutS family of proteins is named after the Salmonella typhimurium MutS protein involved in mismatch repair. Homologues of MutS have been found in many species including eukaryotes (MSH 1, 2, 3, 4, 5, and 6 proteins), archaea and bacteria, and together these proteins have been grouped into the MutS family. Although many of these proteins have similar activities to the E. coli MutS, there is significant diversity of function among the MutS family members. Human MSH has been implicated in non-polyposis colorectal carcinoma (HNPCC) and is a mismatch binding protein [].This diversity is even seen within species, where many species encode multiple MutS homologues with distinct functions []. Inter-species homologues may have arisen through frequent ancient horizontal gene transfer of MutS (and MutL) from bacteria to archaea and eukaryotes via endosymbiotic ancestors of mitochondria and chloroplasts []. This entry represents the N-terminal domain of proteins in the MutS family of DNA mismatch repair proteins, as well as closely related proteins. The N-terminal domain of MutS is responsible for mismatch recognition and forms a 6-stranded mixed beta-sheet surrounded by three alpha-helices, which is similar to the structure of tRNA endonuclease. Yeast MSH3 [], bacterial proteins involved in DNA mismatch repair, and the predicted protein product of the Rep-3 gene of mouse share extensive sequence similarity. Human MSH has been implicated in non-polyposis colorectal carcinoma (HNPCC) and is a mismatch binding protein.; GO: 0005524 ATP binding, 0030983 mismatched DNA binding, 0006298 mismatch repair; PDB: 1FW6_A 1EWQ_A 1EWR_B 1NNE_B 3THY_B 3THZ_B 3THW_B 3THX_B 2WTU_A 1OH7_A ....
Probab=22.58 E-value=69 Score=19.57 Aligned_cols=21 Identities=29% Similarity=0.379 Sum_probs=17.3
Q ss_pred HhCHHHHHHhCCCCeEEEEEc
Q psy15303 31 AQHYVPLKQANPKFPILVREC 51 (72)
Q Consensus 31 ~~~l~~~k~~NP~v~i~v~~~ 51 (72)
.+.|.++|+++|+.-++++..
T Consensus 4 ~~~y~~lk~k~~d~i~lf~~G 24 (113)
T PF01624_consen 4 EQQYWELKEKYPDTIVLFQVG 24 (113)
T ss_dssp HHHHHHHHCTSTTSEEEEEET
T ss_pred HHHHHHHHhhCCCeEEEEEcC
Confidence 456889999999998888754
No 160
>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=22.51 E-value=1.6e+02 Score=16.74 Aligned_cols=38 Identities=18% Similarity=0.250 Sum_probs=22.9
Q ss_pred EEEEecCCCCCCHHHHHHHHhCHHHHHHhCCCCeEEEEEcCC
Q psy15303 12 LRIHLCQKGGSSSGVRDFLAQHYVPLKQANPKFPILVRECSG 53 (72)
Q Consensus 12 L~~~yC~~~~sS~GvR~Fl~~~l~~~k~~NP~v~i~v~~~~g 53 (72)
++|.||...+-. +--..+. .++....|+.++.+...++
T Consensus 1 V~IeyC~~C~y~-~Ra~~l~---q~L~~~Fp~~~v~~~~~~~ 38 (72)
T TIGR02174 1 VEIEYCGSCGYK-PRAAWLK---QELLEEFPDLEIEGENTPP 38 (72)
T ss_pred CEEEECCCCCCh-HHHHHHH---HHHHHHCCCCeeEEeeecC
Confidence 578999988833 3333332 3556677887666655443
No 161
>cd00552 RaiA RaiA ("ribosome-associated inhibitor A", also known as Protein Y (PY), YfiA, and SpotY, is a stress-response protein that binds the ribosomal subunit interface and arrests translation by interfering with aminoacyl-tRNA binding to the ribosomal A site. RaiA is also thought to counteract miscoding at the A site thus reducing translation errors. The RaiA fold structurally resembles the double-stranded RNA-binding domain (dsRBD).
Probab=22.51 E-value=1e+02 Score=17.70 Aligned_cols=27 Identities=7% Similarity=0.234 Sum_probs=21.9
Q ss_pred CCCCCCHHHHHHHHhCHHHHHHhCCCC
Q psy15303 18 QKGGSSSGVRDFLAQHYVPLKQANPKF 44 (72)
Q Consensus 18 ~~~~sS~GvR~Fl~~~l~~~k~~NP~v 44 (72)
.+-..|..+|+|+++.+..+.+-.+++
T Consensus 7 r~~~~t~al~~~i~~k~~kl~r~~~~i 33 (93)
T cd00552 7 RNIEVTDALREYVEEKLEKLEKYFDRI 33 (93)
T ss_pred EcccCCHHHHHHHHHHHHHHHHhcCCC
Confidence 444568999999999999888887754
No 162
>PF13552 DUF4127: Protein of unknown function (DUF4127)
Probab=22.47 E-value=74 Score=24.93 Aligned_cols=19 Identities=32% Similarity=0.511 Sum_probs=16.7
Q ss_pred hCHHHHHHhCCCCeEEEEE
Q psy15303 32 QHYVPLKQANPKFPILVRE 50 (72)
Q Consensus 32 ~~l~~~k~~NP~v~i~v~~ 50 (72)
+.+-+++++||+++|++..
T Consensus 92 ~~l~~lk~~~p~~~iyaf~ 110 (497)
T PF13552_consen 92 ERLRELKARNPNLPIYAFS 110 (497)
T ss_pred HHHHHHHHHCCCCeEEEEE
Confidence 6788999999999999854
No 163
>PRK11716 DNA-binding transcriptional regulator IlvY; Provisional
Probab=22.44 E-value=1.3e+02 Score=19.76 Aligned_cols=25 Identities=12% Similarity=0.121 Sum_probs=21.1
Q ss_pred HHHHHhCHHHHHHhCCCCeEEEEEc
Q psy15303 27 RDFLAQHYVPLKQANPKFPILVREC 51 (72)
Q Consensus 27 R~Fl~~~l~~~k~~NP~v~i~v~~~ 51 (72)
..++..-+..|.+++|++.+.+...
T Consensus 79 ~~~~~~~l~~~~~~~p~i~l~i~~~ 103 (269)
T PRK11716 79 YSHLPPILDRFRAEHPLVEIKLTTG 103 (269)
T ss_pred HHHHHHHHHHHHHHCCCeEEEEEEC
Confidence 4577888999999999999988753
No 164
>PRK10974 glycerol-3-phosphate transporter periplasmic binding protein; Provisional
Probab=22.40 E-value=1.2e+02 Score=22.24 Aligned_cols=25 Identities=8% Similarity=0.121 Sum_probs=20.5
Q ss_pred HHHHHHhCHHHHHHhCCCCeEEEEE
Q psy15303 26 VRDFLAQHYVPLKQANPKFPILVRE 50 (72)
Q Consensus 26 vR~Fl~~~l~~~k~~NP~v~i~v~~ 50 (72)
-.+.++....+|.++||++.|.+..
T Consensus 38 ~~~~~~~~~~~F~~~~p~i~V~~~~ 62 (438)
T PRK10974 38 LGKEVDSLAQRFNASQPDYKIVPVY 62 (438)
T ss_pred hHHHHHHHHHHHHHhCCCeEEEEee
Confidence 3467888999999999999987753
No 165
>PRK09508 leuO leucine transcriptional activator; Reviewed
Probab=22.26 E-value=1.4e+02 Score=20.76 Aligned_cols=26 Identities=15% Similarity=0.300 Sum_probs=22.7
Q ss_pred HHHHHHhCHHHHHHhCCCCeEEEEEc
Q psy15303 26 VRDFLAQHYVPLKQANPKFPILVREC 51 (72)
Q Consensus 26 vR~Fl~~~l~~~k~~NP~v~i~v~~~ 51 (72)
...++...+.+|++++|++.|.+...
T Consensus 123 ~~~~l~~~l~~f~~~~P~i~l~i~~~ 148 (314)
T PRK09508 123 DIRLTSQIYNRIEQIAPNIHVVFKSS 148 (314)
T ss_pred HHHHHHHHHHHHHHhCCCcEEEEEeC
Confidence 35688899999999999999999875
No 166
>PRK09801 transcriptional activator TtdR; Provisional
Probab=22.19 E-value=1.5e+02 Score=20.82 Aligned_cols=28 Identities=14% Similarity=0.134 Sum_probs=22.9
Q ss_pred HHHHHHHHhCHHHHHHhCCCCeEEEEEc
Q psy15303 24 SGVRDFLAQHYVPLKQANPKFPILVREC 51 (72)
Q Consensus 24 ~GvR~Fl~~~l~~~k~~NP~v~i~v~~~ 51 (72)
.-...|+...+.+|.+++|++.|.+...
T Consensus 105 ~~~~~~l~~~l~~f~~~~P~i~l~i~~~ 132 (310)
T PRK09801 105 GFGRSHIAPAITELMRNYPELQVHFELF 132 (310)
T ss_pred HHHHHHHHHHHHHHHHHCCCeEEEEEec
Confidence 3445688899999999999999998754
No 167
>TIGR01616 nitro_assoc nitrogenase-associated protein. This model describes a small family of uncharacterized proteins found so far in alpha and gamma proteobacteria and in Nostoc sp. PCC 7120, a cyanobacterium. The gene for this protein is associated with nitrogenase genes. This family shows sequence similarity to TIGR00014, a glutaredoxin-dependent arsenate reductase that converts arsentate to arsenite for disposal. This family is one of several included in Pfam model pfam03960.
Probab=22.18 E-value=2e+02 Score=18.33 Aligned_cols=23 Identities=4% Similarity=-0.078 Sum_probs=18.6
Q ss_pred EEEEEecCCCCCCHHHHHHHHhC
Q psy15303 11 ELRIHLCQKGGSSSGVRDFLAQH 33 (72)
Q Consensus 11 ~L~~~yC~~~~sS~GvR~Fl~~~ 33 (72)
.++|..-.+..+|+-+++||+.+
T Consensus 2 ~i~iY~~p~Cst~RKA~~~L~~~ 24 (126)
T TIGR01616 2 TIIFYEKPGCANNARQKAALKAS 24 (126)
T ss_pred eEEEEeCCCCHHHHHHHHHHHHC
Confidence 46777778888999999999754
No 168
>PF09217 EcoRII-N: Restriction endonuclease EcoRII, N-terminal; InterPro: IPR023372 There are four classes of restriction endonucleases: types I, II,III and IV. All types of enzymes recognise specific short DNA sequences and carry out the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. They differ in their recognition sequence, subunit composition, cleavage position, and cofactor requirements [, ], as summarised below: Type I enzymes (3.1.21.3 from EC) cleave at sites remote from recognition site; require both ATP and S-adenosyl-L-methionine to function; multifunctional protein with both restriction and methylase (2.1.1.72 from EC) activities. Type II enzymes (3.1.21.4 from EC) cleave within or at short specific distances from recognition site; most require magnesium; single function (restriction) enzymes independent of methylase. Type III enzymes (3.1.21.5 from EC) cleave at sites a short distance from recognition site; require ATP (but doesn't hydrolyse it); S-adenosyl-L-methionine stimulates reaction but is not required; exists as part of a complex with a modification methylase methylase (2.1.1.72 from EC). Type IV enzymes target methylated DNA. Type II restriction endonucleases (3.1.21.4 from EC) are components of prokaryotic DNA restriction-modification mechanisms that protect the organism against invading foreign DNA. These site-specific deoxyribonucleases catalyse the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. Of the 3000 restriction endonucleases that have been characterised, most are homodimeric or tetrameric enzymes that cleave target DNA at sequence-specific sites close to the recognition site. For homodimeric enzymes, the recognition site is usually a palindromic sequence 4-8 bp in length. Most enzymes require magnesium ions as a cofactor for catalysis. Although they can vary in their mode of recognition, many restriction endonucleases share a similar structural core comprising four beta-strands and one alpha-helix, as well as a similar mechanism of cleavage, suggesting a common ancestral origin []. However, there is still considerable diversity amongst restriction endonucleases [, ]. The target site recognition process triggers large conformational changes of the enzyme and the target DNA, leading to the activation of the catalytic centres. Like other DNA binding proteins, restriction enzymes are capable of non-specific DNA binding as well, which is the prerequisite for efficient target site location by facilitated diffusion. Non-specific binding usually does not involve interactions with the bases but only with the DNA backbone []. This entry represents the N-terminal effector-binding domain of the type II restriction endonuclease EcoRII, which has a DNA recognition fold, allowing for binding to 5'-CCWGG sequences. It assumes a structure composed of an eight-stranded beta-sheet with the strands in the order of b2, b5, b4, b3, b7, b6, b1 and b8. They are mostly antiparallel to each other except that b3 is parallel to b7. Alternatively, it may also be viewed as consisting of two mini beta-sheets of four antiparallel beta-strands, sheet I from beta-strands b2, b5, b4, b3 and sheet II from strands b7, b6, b1, b8, folded into an open mixed beta-barrel with a novel topology. Sheet I has a simple Greek key motif while sheet II does not []. The domain represented by this entry is only found in bacterial proteins.; PDB: 3HQF_A 1NA6_A.
Probab=22.06 E-value=50 Score=22.58 Aligned_cols=40 Identities=15% Similarity=-0.003 Sum_probs=23.3
Q ss_pred HHHHHHHHhCHHHHHHhCCCCeEEEEEcCCCCCEE--EEEec
Q psy15303 24 SGVRDFLAQHYVPLKQANPKFPILVRECSGVTPVV--WARIP 63 (72)
Q Consensus 24 ~GvR~Fl~~~l~~~k~~NP~v~i~v~~~~g~~P~l--~a~Y~ 63 (72)
+...+.+--.++.-+..||++-+.++-..+--+-. ++.|=
T Consensus 33 k~~~~~lFp~~~~~~~~Np~~~~~~~~~s~~~~~~~~r~iYY 74 (156)
T PF09217_consen 33 KSAAELLFPSINHTKEENPDIWLKARWQSHFVTDSQVRFIYY 74 (156)
T ss_dssp HHHHHHH-GGG-SSSSSS-EEEEEEEETTTT---EEEEEEEE
T ss_pred ccHHHHhCCCCCcccccCCceeEEEEECCCCccceeEEEEEE
Confidence 44444454556667889999999999988744434 44443
No 169
>cd03052 GST_N_GDAP1 GST_N family, Ganglioside-induced differentiation-associated protein 1 (GDAP1) subfamily; GDAP1 was originally identified as a highly expressed gene at the differentiated stage of GD3 synthase-transfected cells. More recently, mutations in GDAP1 have been reported to cause both axonal and demyelinating autosomal-recessive Charcot-Marie-Tooth (CMT) type 4A neuropathy. CMT is characterized by slow and progressive weakness and atrophy of muscles. Sequence analysis of GDAP1 shows similarities and differences with GSTs; it appears to contain both N-terminal TRX-fold and C-terminal alpha helical domains of GSTs, however, it also contains additional C-terminal transmembrane domains unlike GSTs. GDAP1 is mainly expressed in neuronal cells and is localized in the mitochondria through its transmembrane domains. It does not exhibit GST activity using standard substrates.
Probab=22.01 E-value=94 Score=17.33 Aligned_cols=20 Identities=30% Similarity=0.157 Sum_probs=16.3
Q ss_pred EEEEecCCCCCCHHHHHHHH
Q psy15303 12 LRIHLCQKGGSSSGVRDFLA 31 (72)
Q Consensus 12 L~~~yC~~~~sS~GvR~Fl~ 31 (72)
++|.++..+++|+-+|-.++
T Consensus 1 ~~ly~~~~s~~s~rv~~~L~ 20 (73)
T cd03052 1 LVLYHWTQSFSSQKVRLVIA 20 (73)
T ss_pred CEEecCCCCccHHHHHHHHH
Confidence 46788888999999998774
No 170
>PRK13337 putative lipid kinase; Reviewed
Probab=21.96 E-value=2.1e+02 Score=20.29 Aligned_cols=42 Identities=17% Similarity=0.094 Sum_probs=28.7
Q ss_pred eEEEEEecCCCCCCHHHHHHHHhCHHHHHHhCCCCeEEEEEcC
Q psy15303 10 KELRIHLCQKGGSSSGVRDFLAQHYVPLKQANPKFPILVRECS 52 (72)
Q Consensus 10 k~L~~~yC~~~~sS~GvR~Fl~~~l~~~k~~NP~v~i~v~~~~ 52 (72)
+++.|-+++.+|+.++.+.+ .+-...+.+.+-++.++..+..
T Consensus 2 ~r~~~I~Np~aG~~~~~~~~-~~~~~~l~~~~~~~~~~~t~~~ 43 (304)
T PRK13337 2 KRARIIYNPTSGRELFKKNL-PDVLQKLEQAGYETSAHATTGP 43 (304)
T ss_pred ceEEEEECCcccchhHHHHH-HHHHHHHHHcCCEEEEEEecCC
Confidence 57889999999998877664 3334456677766665554443
No 171
>PRK10341 DNA-binding transcriptional activator TdcA; Provisional
Probab=21.96 E-value=1.4e+02 Score=20.72 Aligned_cols=37 Identities=14% Similarity=0.113 Sum_probs=26.7
Q ss_pred eEEEEEecCCCCCCHHHHHHHHhCHHHHHHhCCCCeEEEEEc
Q psy15303 10 KELRIHLCQKGGSSSGVRDFLAQHYVPLKQANPKFPILVREC 51 (72)
Q Consensus 10 k~L~~~yC~~~~sS~GvR~Fl~~~l~~~k~~NP~v~i~v~~~ 51 (72)
..|+|-.+.. -...++..-+.+|++.+|++.|.+...
T Consensus 97 ~~l~ig~~~~-----~~~~~l~~~l~~~~~~~p~v~i~~~~~ 133 (312)
T PRK10341 97 VDVSFGFPSL-----IGFTFMSDMINKFKEVFPKAQVSMYEA 133 (312)
T ss_pred eEEEEEechH-----HhHhhHHHHHHHHHHhCCCCEEEEEeC
Confidence 3466654322 234677889999999999999998754
No 172
>PF14459 Prok-E2_C: Prokaryotic E2 family C
Probab=21.83 E-value=1.3e+02 Score=19.84 Aligned_cols=22 Identities=32% Similarity=0.481 Sum_probs=17.7
Q ss_pred HHHHHHhCHHHHHH-hCCCCeEE
Q psy15303 26 VRDFLAQHYVPLKQ-ANPKFPIL 47 (72)
Q Consensus 26 vR~Fl~~~l~~~k~-~NP~v~i~ 47 (72)
.-+|+.+++.++++ -||.+.|-
T Consensus 38 as~~~a~~l~~LA~sINp~I~i~ 60 (131)
T PF14459_consen 38 ASSFQAQNLQSLARSINPRIEIR 60 (131)
T ss_pred hHHHHHHHHHHHHHhcCCCeEEE
Confidence 34688899999988 69998873
No 173
>COG2871 NqrF Na+-transporting NADH:ubiquinone oxidoreductase, subunit NqrF [Energy production and conversion]
Probab=21.79 E-value=1.7e+02 Score=22.60 Aligned_cols=37 Identities=14% Similarity=0.391 Sum_probs=27.9
Q ss_pred eEEEEEecCCCCCCHHHHHHH-HhCHHHHHHhCCCCeEEEEEc
Q psy15303 10 KELRIHLCQKGGSSSGVRDFL-AQHYVPLKQANPKFPILVREC 51 (72)
Q Consensus 10 k~L~~~yC~~~~sS~GvR~Fl-~~~l~~~k~~NP~v~i~v~~~ 51 (72)
|+++|-| ..+..|+-+ ++.|.+++++||+..-.+...
T Consensus 305 Rkis~WY-----GARS~rE~fY~Ed~d~L~ae~pNF~wH~aLS 342 (410)
T COG2871 305 RKISFWY-----GARSLREMFYQEDFDQLQAENPNFHWHLALS 342 (410)
T ss_pred ceeeeee-----ccchHHHhHHHHHHHHHHhhCCCcEEEEEec
Confidence 5677776 244566654 799999999999999877654
No 174
>PF02960 K1: K1 glycoprotein; InterPro: IPR004121 Current genotyping systems for Human herpesvirus 8 (HHV-8) are based on the highly variable gene encoding the K1 glycoprotein []. This entry represents the C-terminal region of the K1 glycoprotein.
Probab=21.77 E-value=35 Score=22.51 Aligned_cols=43 Identities=21% Similarity=0.356 Sum_probs=37.3
Q ss_pred CCHHHHHHHHhCHHHHHHhCCCCeEEEEEcCCCCCEEEEEecC
Q psy15303 22 SSSGVRDFLAQHYVPLKQANPKFPILVRECSGVTPVVWARIPT 64 (72)
Q Consensus 22 sS~GvR~Fl~~~l~~~k~~NP~v~i~v~~~~g~~P~l~a~Y~n 64 (72)
|-.|.|.|=.+.+.++--+..+..+.++|....+|.+...+.-
T Consensus 30 STTGFrTfsTn~lvnIi~aTth~vvvvkEakstn~hi~v~fLv 72 (130)
T PF02960_consen 30 STTGFRTFSTNSLVNIIHATTHDVVVVKEAKSTNPHIQVHFLV 72 (130)
T ss_pred cccceEEEecccccceecccccceEEEEEeecCCceEEeeeeH
Confidence 4468899988888889899999999999999999999888753
No 175
>PRK14997 LysR family transcriptional regulator; Provisional
Probab=21.76 E-value=1.7e+02 Score=19.98 Aligned_cols=27 Identities=4% Similarity=0.144 Sum_probs=22.3
Q ss_pred HHHHHHhCHHHHHHhCCCCeEEEEEcC
Q psy15303 26 VRDFLAQHYVPLKQANPKFPILVRECS 52 (72)
Q Consensus 26 vR~Fl~~~l~~~k~~NP~v~i~v~~~~ 52 (72)
...++...+.+|.+++|++.|.+....
T Consensus 103 ~~~~l~~~l~~~~~~~P~i~i~~~~~~ 129 (301)
T PRK14997 103 LHVHIGPMLAKFMARYPDVSLQLEATN 129 (301)
T ss_pred HHHHHHHHHHHHHHHCCCeEEEEEecC
Confidence 446778899999999999999997644
No 176
>KOG1454|consensus
Probab=21.70 E-value=88 Score=22.90 Aligned_cols=26 Identities=19% Similarity=0.181 Sum_probs=22.3
Q ss_pred CHHHHHHhCCCCeEEEEEcCCCCCEE
Q psy15303 33 HYVPLKQANPKFPILVRECSGVTPVV 58 (72)
Q Consensus 33 ~l~~~k~~NP~v~i~v~~~~g~~P~l 58 (72)
.-..+++++|++++++-+.-|.+|.+
T Consensus 282 ~~~~~~~~~pn~~~~~I~~~gH~~h~ 307 (326)
T KOG1454|consen 282 LAEELKKKLPNAELVEIPGAGHLPHL 307 (326)
T ss_pred HHHHHHhhCCCceEEEeCCCCccccc
Confidence 35678899999999999988888876
No 177
>PRK10026 arsenate reductase; Provisional
Probab=21.65 E-value=2e+02 Score=18.85 Aligned_cols=23 Identities=13% Similarity=0.209 Sum_probs=19.9
Q ss_pred EEEEEecCCCCCCHHHHHHHHhC
Q psy15303 11 ELRIHLCQKGGSSSGVRDFLAQH 33 (72)
Q Consensus 11 ~L~~~yC~~~~sS~GvR~Fl~~~ 33 (72)
.++|..-..+.+|+-+++||+.+
T Consensus 3 ~i~iY~~p~Cst~RKA~~wL~~~ 25 (141)
T PRK10026 3 NITIYHNPACGTSRNTLEMIRNS 25 (141)
T ss_pred EEEEEeCCCCHHHHHHHHHHHHC
Confidence 57888889999999999999765
No 178
>PRK12681 cysB transcriptional regulator CysB; Reviewed
Probab=21.64 E-value=1.3e+02 Score=21.35 Aligned_cols=36 Identities=14% Similarity=0.155 Sum_probs=27.1
Q ss_pred EEEEEecCCCCCCHHHHHHHHhCHHHHHHhCCCCeEEEEEc
Q psy15303 11 ELRIHLCQKGGSSSGVRDFLAQHYVPLKQANPKFPILVREC 51 (72)
Q Consensus 11 ~L~~~yC~~~~sS~GvR~Fl~~~l~~~k~~NP~v~i~v~~~ 51 (72)
.|+|-.+. .-...++...+.+|.+.+|++.|.+...
T Consensus 94 ~l~Ig~~~-----~~~~~~l~~~l~~f~~~~P~i~i~i~~~ 129 (324)
T PRK12681 94 SLYIATTH-----TQARYALPPVIKGFIERYPRVSLHMHQG 129 (324)
T ss_pred eEEEEech-----hHHHHhhHHHHHHHHHHCCCcEEEEEeC
Confidence 46664432 3345688899999999999999998764
No 179
>cd03045 GST_N_Delta_Epsilon GST_N family, Class Delta and Epsilon subfamily; GSTs are cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of glutathione (GSH) with a wide range of endogenous and xenobiotic alkylating agents, including carcinogens, therapeutic drugs, environmental toxins and products of oxidative stress. GSTs also show GSH peroxidase activity and are involved in the synthesis of prostaglandins and leukotrienes. The GST fold contains an N-terminal TRX-fold domain and a C-terminal alpha helical domain, with an active site located in a cleft between the two domains. The class Delta and Epsilon subfamily is made up primarily of insect GSTs, which play major roles in insecticide resistance by facilitating reductive dehydrochlorination of insecticides or conjugating them with GSH to produce water-soluble metabolites that are easily excreted. They are also implicated in protection against cellular damage by oxidative stress.
Probab=21.63 E-value=1.2e+02 Score=16.27 Aligned_cols=20 Identities=5% Similarity=-0.109 Sum_probs=16.9
Q ss_pred EEEEecCCCCCCHHHHHHHH
Q psy15303 12 LRIHLCQKGGSSSGVRDFLA 31 (72)
Q Consensus 12 L~~~yC~~~~sS~GvR~Fl~ 31 (72)
++|.+...++.|+-+|-+++
T Consensus 1 ~~Ly~~~~~~~~~~v~~~l~ 20 (74)
T cd03045 1 IDLYYLPGSPPCRAVLLTAK 20 (74)
T ss_pred CEEEeCCCCCcHHHHHHHHH
Confidence 46788889999999999885
No 180
>PF00505 HMG_box: HMG (high mobility group) box; InterPro: IPR000910 High mobility group (HMG or HMGB) proteins are a family of relatively low molecular weight non-histone components in chromatin. HMG1 (also called HMG-T in fish) and HMG2 are two highly related proteins that bind single-stranded DNA preferentially and unwind double-stranded DNA. Although they have no sequence specificity, they have a high affinity for bent or distorted DNA, and bend linear DNA. HMG1 and HMG2 contain two DNA-binding HMG-box domains (A and B) that show structural and functional differences, and have a long acidic C-terminal domain rich in aspartic and glutamic acid residues. The acidic tail modulates the affinity of the tandem HMG boxes in HMG1 and 2 for a variety of DNA targets. HMG1 and 2 appear to play important architectural roles in the assembly of nucleoprotein complexes in a variety of biological processes, for example V(D)J recombination, the initiation of transcription, and DNA repair []. The profile in this entry describing the HMG-domains is much more general than the signature. In addition to the HMG1 and HMG2 proteins, HMG-domains occur in single or multiple copies in the following protein classes; the SOX family of transcription factors; SRY sex determining region Y protein and related proteins []; LEF1 lymphoid enhancer binding factor 1 []; SSRP recombination signal recognition protein; MTF1 mitochondrial transcription factor 1; UBF1/2 nucleolar transcription factors; Abf2 yeast ARS-binding factor []; and Saccharomyces cerevisiae transcription factors Ixr1, Rox1, Nhp6a, Nhp6b and Spp41.; GO: 0003677 DNA binding; PDB: 1I11_A 1J3C_A 1J3D_A 1WZ6_A 1WGF_A 2D7L_A 1GT0_D 3U2B_C 2CRJ_A 2CS1_A ....
Probab=21.50 E-value=66 Score=17.33 Aligned_cols=18 Identities=28% Similarity=0.451 Sum_probs=14.9
Q ss_pred HHHHhCHHHHHHhCCCCe
Q psy15303 28 DFLAQHYVPLKQANPKFP 45 (72)
Q Consensus 28 ~Fl~~~l~~~k~~NP~v~ 45 (72)
-|.......++..||+..
T Consensus 10 lf~~~~~~~~k~~~p~~~ 27 (69)
T PF00505_consen 10 LFCKEKRAKLKEENPDLS 27 (69)
T ss_dssp HHHHHHHHHHHHHSTTST
T ss_pred HHHHHHHHHHHHHhcccc
Confidence 466788999999999865
No 181
>PRK11914 diacylglycerol kinase; Reviewed
Probab=21.36 E-value=1.6e+02 Score=20.88 Aligned_cols=41 Identities=7% Similarity=0.067 Sum_probs=28.4
Q ss_pred CceEEEEEecCCCCCCHHHHHHHHhCHHHHHHhCCCCeEEEE
Q psy15303 8 KLKELRIHLCQKGGSSSGVRDFLAQHYVPLKQANPKFPILVR 49 (72)
Q Consensus 8 qLk~L~~~yC~~~~sS~GvR~Fl~~~l~~~k~~NP~v~i~v~ 49 (72)
+.+++.|-+++.+|+.++.+.+- +-...+++.+.++.+...
T Consensus 7 ~~~~~~iI~NP~sG~g~~~~~~~-~~~~~l~~~g~~~~~~~t 47 (306)
T PRK11914 7 EIGKVTVLTNPLSGHGAAPHAAE-RAIARLHHRGVDVVEIVG 47 (306)
T ss_pred CCceEEEEECCCCCCCcHHHHHH-HHHHHHHHcCCeEEEEEe
Confidence 45788999999999887776643 334567777766655443
No 182
>PRK11074 putative DNA-binding transcriptional regulator; Provisional
Probab=21.32 E-value=1.1e+02 Score=21.18 Aligned_cols=37 Identities=16% Similarity=0.092 Sum_probs=28.7
Q ss_pred eEEEEEecCCCCCCHHHHHHHHhCHHHHHHhCCCCeEEEEEc
Q psy15303 10 KELRIHLCQKGGSSSGVRDFLAQHYVPLKQANPKFPILVREC 51 (72)
Q Consensus 10 k~L~~~yC~~~~sS~GvR~Fl~~~l~~~k~~NP~v~i~v~~~ 51 (72)
.+|+|-..+.. ...++...+..|++++|++.|.+...
T Consensus 92 g~l~Ig~~~~~-----~~~~l~~~l~~~~~~~p~i~i~i~~~ 128 (300)
T PRK11074 92 GQLSIAVDNIV-----RPDRTRQLIVDFYRHFDDVELIIRQE 128 (300)
T ss_pred ceEEEEEcCcc-----chhHHHHHHHHHHHhCCCceEEEEeh
Confidence 56777764433 35788899999999999999988763
No 183
>COG5575 ORC2 Origin recognition complex, subunit 2 [DNA replication, recombination, and repair]
Probab=21.27 E-value=73 Score=25.38 Aligned_cols=27 Identities=11% Similarity=0.229 Sum_probs=23.1
Q ss_pred HHHHHHHhCHHHHHHhCCCCeEEEEEc
Q psy15303 25 GVRDFLAQHYVPLKQANPKFPILVREC 51 (72)
Q Consensus 25 GvR~Fl~~~l~~~k~~NP~v~i~v~~~ 51 (72)
=+|+|+++++.++++++...+|.-.+.
T Consensus 493 mL~EFidH~l~~i~rn~S~~eI~wvpy 519 (535)
T COG5575 493 MLNEFIDHGLLKIKRNGSEIEICWVPY 519 (535)
T ss_pred HHHHHHhcchhheeccCCccEEEEeec
Confidence 368999999999999999999876553
No 184
>PF10691 DUF2497: Protein of unknown function (DUF2497) ; InterPro: IPR019632 Members of this family belong to the Alphaproteobacteria. The function of the family is not known.
Probab=21.03 E-value=87 Score=18.60 Aligned_cols=14 Identities=14% Similarity=0.430 Sum_probs=9.9
Q ss_pred HHHHHHhCHHHHHH
Q psy15303 26 VRDFLAQHYVPLKQ 39 (72)
Q Consensus 26 vR~Fl~~~l~~~k~ 39 (72)
+++||.+|||.+-+
T Consensus 47 LkeWLD~nLP~lVE 60 (73)
T PF10691_consen 47 LKEWLDENLPGLVE 60 (73)
T ss_pred HHHHHHhccHHHHH
Confidence 46778888887644
No 185
>PRK03601 transcriptional regulator HdfR; Provisional
Probab=20.99 E-value=1.7e+02 Score=19.97 Aligned_cols=26 Identities=15% Similarity=0.032 Sum_probs=22.0
Q ss_pred HHHHHHhCHHHHHHhCCCCeEEEEEc
Q psy15303 26 VRDFLAQHYVPLKQANPKFPILVREC 51 (72)
Q Consensus 26 vR~Fl~~~l~~~k~~NP~v~i~v~~~ 51 (72)
...++...+.+|.+.+|++.|.+...
T Consensus 100 ~~~~l~~~l~~f~~~~P~v~v~~~~~ 125 (275)
T PRK03601 100 WECMLTPWLGRLYQNQEALQFEARIA 125 (275)
T ss_pred HHHHHHHHHHHHHHhCCCcEEEEEEC
Confidence 36777899999999999999988654
No 186
>cd02987 Phd_like_Phd Phosducin (Phd)-like family, Phd subfamily; Phd is a cytosolic regulator of G protein functions. It specifically binds G protein betagamma (Gbg)-subunits with high affinity, resulting in the solubilization of Gbg from the plasma membrane. This impedes the formation of a functional G protein trimer (G protein alphabetagamma), thereby inhibiting G protein-mediated signal transduction. Phd also inhibits the GTPase activity of G protein alpha. Phd can be phosphorylated by protein kinase A and G protein-coupled receptor kinase 2, leading to its inactivation. Phd was originally isolated from the retina, where it is highly expressed and has been implicated to play an important role in light adaptation. It is also found in the pineal gland, liver, spleen, striated muscle and the brain. The C-terminal domain of Phd adopts a thioredoxin fold, but it does not contain a CXXC motif. Phd interacts with G protein beta mostly through the N-terminal helical domain.
Probab=20.78 E-value=1.7e+02 Score=19.42 Aligned_cols=36 Identities=6% Similarity=-0.091 Sum_probs=24.8
Q ss_pred EEEEEecCCCCCCHHHHHHHHhCHHHHHHhCCCCeEEEEE
Q psy15303 11 ELRIHLCQKGGSSSGVRDFLAQHYVPLKQANPKFPILVRE 50 (72)
Q Consensus 11 ~L~~~yC~~~~sS~GvR~Fl~~~l~~~k~~NP~v~i~v~~ 50 (72)
-|...|-+|.+.++-| ...+.++++++|.+.|.--.
T Consensus 86 VVV~Fya~wc~~Ck~m----~~~l~~LA~~~~~vkF~kVd 121 (175)
T cd02987 86 VVVHIYEPGIPGCAAL----NSSLLCLAAEYPAVKFCKIR 121 (175)
T ss_pred EEEEEECCCCchHHHH----HHHHHHHHHHCCCeEEEEEe
Confidence 3445566777888744 44677888899998876533
No 187
>PLN02495 oxidoreductase, acting on the CH-CH group of donors
Probab=20.67 E-value=1.1e+02 Score=23.28 Aligned_cols=28 Identities=21% Similarity=0.322 Sum_probs=23.2
Q ss_pred CCHHHHHHHHhCHHHHHHhCCCCeEEEEE
Q psy15303 22 SSSGVRDFLAQHYVPLKQANPKFPILVRE 50 (72)
Q Consensus 22 sS~GvR~Fl~~~l~~~k~~NP~v~i~v~~ 50 (72)
+.+|+..|++. ++.++++.|++++.+.-
T Consensus 93 s~~g~~~~l~~-i~~~k~~~~~~pvIaSi 120 (385)
T PLN02495 93 SDRPFETMLAE-FKQLKEEYPDRILIASI 120 (385)
T ss_pred cccCHHHHHHH-HHHHHhhCCCCcEEEEc
Confidence 45689999987 78898888998888765
No 188
>TIGR03418 chol_sulf_TF putative choline sulfate-utilization transcription factor. Members of this protein family are transcription factors of the LysR family. Their genes typically are divergently transcribed from choline-sulfatase genes. That enzyme makes choline, a precursor to the osmoprotectant glycine-betaine, available by hydrolysis of choline sulfate.
Probab=20.54 E-value=1.3e+02 Score=20.43 Aligned_cols=27 Identities=15% Similarity=0.210 Sum_probs=22.5
Q ss_pred HHHHHHhCHHHHHHhCCCCeEEEEEcC
Q psy15303 26 VRDFLAQHYVPLKQANPKFPILVRECS 52 (72)
Q Consensus 26 vR~Fl~~~l~~~k~~NP~v~i~v~~~~ 52 (72)
...++...+.+|.+++|++.+.+....
T Consensus 100 ~~~~l~~~l~~~~~~~p~i~i~~~~~~ 126 (291)
T TIGR03418 100 ATYWLMPRLHRFKRAMPDVDVSLVTSQ 126 (291)
T ss_pred HHHHHhhhhHHHHHhCCCceEEEEecC
Confidence 347788889999999999999997643
No 189
>PF02886 LBP_BPI_CETP_C: LBP / BPI / CETP family, C-terminal domain; InterPro: IPR001124 This entry represents the C-terminal domain found in several lipid-binding serum glycoproteins. The N- and C-terminal domains share a similar two-layer alpha/beta structure, but they show little sequence identity. Proteins containing this C-terminal domain include: Bactericidal permeability-increasing protein (BPI) Lipopolysaccharide-binding protein (LBP) Cholesteryl ester transfer protein (CETP) Phospholipid transfer protein (PLTP) Palate, lung and nasal epithelium carcinoma-associated protein (PLUNC) Bactericidal permeability-increasing protein (BPI) is a potent antimicrobial protein of 456 residues that binds to and neutralises lipopolysaccharides from the outer membrane of Gram-negative bacteria []. BPI contains two domains that adopt the same structural fold, even though they have little sequence similarity []. Lipopolysaccharide-binding protein (LBP) is an endotoxin-binding protein that is closely related to, and functions in a co-ordinated manner with BPI to facilitate an integrated host response to invading Gram-negative bacteria []. Cholesteryl ester transfer protein (CETP) is a glycoprotein that facilitates the transfer of lipids (cholesteryl esters and triglycerides) between the different lipoproteins that transport them through plasma, including HDL, LDL, VLDL and chylomicrons. These lipoproteins shield the lipids from water by encapsulating them within a coating of polar lipids and proteins []. Phospholipid transfer protein (PLTP) exchanges phospholipids between lipoproteins and remodels high-density lipoproteins (HDLs) []. Palate, lung and nasal epithelium carcinoma-associated protein (PLUNC) is a potential host defensive protein that is secreted from the submucosal gland to the saliva and nasal lavage fluid. PLUNC aapears to be a secreted product of neutrophil granules that participates in an aspect of the inflammatory response that contributes to host defence []. Short palate, lung and nasal epithelium clone 1 (SPLUNC1) may bind the lipopolysaccharide of Gram-negative nanobacteria, thereby playing an important role in the host defence of nasopharyngeal epithelium [].; GO: 0008289 lipid binding; PDB: 2OBD_A 1EWF_A 1BP1_A.
Probab=20.51 E-value=77 Score=21.55 Aligned_cols=33 Identities=21% Similarity=0.247 Sum_probs=24.1
Q ss_pred HHHhCHHHHHHhCCCCeEEEEEcCCCCCEEEEE
Q psy15303 29 FLAQHYVPLKQANPKFPILVRECSGVTPVVWAR 61 (72)
Q Consensus 29 Fl~~~l~~~k~~NP~v~i~v~~~~g~~P~l~a~ 61 (72)
.+..-+|+++++.|+-++.++-.....|.+...
T Consensus 80 ~~g~~iP~l~~~yPn~~~~l~i~~~~~P~v~~~ 112 (238)
T PF02886_consen 80 CIGDLIPELAKKYPNSPVELKIRSTKPPVVTIS 112 (238)
T ss_dssp CCCTCCCCHHHCSCC-CEEEEEEESS--EEEEE
T ss_pred cHHhhhhhHHhcCCCCeEEEEEEeCCCCEEEEE
Confidence 445688999999999888888877789987754
No 190
>cd02973 TRX_GRX_like Thioredoxin (TRX)-Glutaredoxin (GRX)-like family; composed of archaeal and bacterial proteins that show similarity to both TRX and GRX, including the C-terminal TRX-fold subdomain of Pyrococcus furiosus protein disulfide oxidoreductase (PfPDO). All members contain a redox-active CXXC motif and may function as PDOs. The archaeal proteins Mj0307 and Mt807 show structures more similar to GRX, but activities more similar to TRX. Some members of the family are similar to PfPDO in that they contain a second CXXC motif located in a second TRX-fold subdomain at the N-terminus; the superimposable N- and C-terminal TRX subdomains form a compact structure. PfPDO is postulated to be the archaeal counterpart of bacterial DsbA and eukaryotic protein disulfide isomerase (PDI). The C-terminal CXXC motif of PfPDO is required for its oxidase, reductase and isomerase activities. Also included in the family is the C-terminal TRX-fold subdomain of the N-terminal domain (NTD) of bacteri
Probab=20.17 E-value=1.6e+02 Score=15.56 Aligned_cols=36 Identities=6% Similarity=0.106 Sum_probs=26.8
Q ss_pred EEEEEecCCCCCCHHHHHHHHhCHHHHHHhCCCCeEEEEE
Q psy15303 11 ELRIHLCQKGGSSSGVRDFLAQHYVPLKQANPKFPILVRE 50 (72)
Q Consensus 11 ~L~~~yC~~~~sS~GvR~Fl~~~l~~~k~~NP~v~i~v~~ 50 (72)
++.+.+.++.+-++=++.+++ +++..+|++++....
T Consensus 2 ~v~~f~~~~C~~C~~~~~~l~----~l~~~~~~i~~~~id 37 (67)
T cd02973 2 NIEVFVSPTCPYCPDAVQAAN----RIAALNPNISAEMID 37 (67)
T ss_pred EEEEEECCCCCCcHHHHHHHH----HHHHhCCceEEEEEE
Confidence 577888889999988877764 456678888876654
No 191
>cd03005 PDI_a_ERp46 PDIa family, endoplasmic reticulum protein 46 (ERp46) subfamily; ERp46 is an ER-resident protein containing three redox active TRX domains. Yeast complementation studies show that ERp46 can substitute for protein disulfide isomerase (PDI) function in vivo. It has been detected in many tissues, however, transcript and protein levels do not correlate in all tissues, suggesting regulation at a posttranscriptional level. An identical protein, named endoPDI, has been identified as an endothelial PDI that is highly expressed in the endothelium of tumors and hypoxic lesions. It has a protective effect on cells exposed to hypoxia.
Probab=20.14 E-value=1.2e+02 Score=17.03 Aligned_cols=41 Identities=15% Similarity=0.183 Sum_probs=28.5
Q ss_pred EEEEEecCCCCCCHHHHHHHHhCHHHHHHhCCCCeEEEEEc
Q psy15303 11 ELRIHLCQKGGSSSGVRDFLAQHYVPLKQANPKFPILVREC 51 (72)
Q Consensus 11 ~L~~~yC~~~~sS~GvR~Fl~~~l~~~k~~NP~v~i~v~~~ 51 (72)
-|...|-+|.+.++.+..-+++-..+++..+|.+.+..-.+
T Consensus 19 ~lv~f~a~wC~~C~~~~p~~~~~~~~~~~~~~~~~~~~vd~ 59 (102)
T cd03005 19 HFVKFFAPWCGHCKRLAPTWEQLAKKFNNENPSVKIAKVDC 59 (102)
T ss_pred EEEEEECCCCHHHHHhCHHHHHHHHHHhccCCcEEEEEEEC
Confidence 57778888888888887776666666655556676655433
No 192
>PRK15421 DNA-binding transcriptional regulator MetR; Provisional
Probab=20.13 E-value=1.4e+02 Score=21.00 Aligned_cols=25 Identities=8% Similarity=0.153 Sum_probs=21.8
Q ss_pred HHHHHhCHHHHHHhCCCCeEEEEEc
Q psy15303 27 RDFLAQHYVPLKQANPKFPILVREC 51 (72)
Q Consensus 27 R~Fl~~~l~~~k~~NP~v~i~v~~~ 51 (72)
..++...+.+|++++|++.+.+...
T Consensus 101 ~~~l~~~l~~~~~~~P~i~l~~~~~ 125 (317)
T PRK15421 101 IQWLTPALENFHKNWPQVEMDFKSG 125 (317)
T ss_pred HHHHHHHHHHHHHHCCCceEEEEeC
Confidence 4678889999999999999998764
No 193
>PRK10086 DNA-binding transcriptional regulator DsdC; Provisional
Probab=20.13 E-value=1.7e+02 Score=20.41 Aligned_cols=28 Identities=7% Similarity=0.160 Sum_probs=23.6
Q ss_pred HHHHHHHhCHHHHHHhCCCCeEEEEEcC
Q psy15303 25 GVRDFLAQHYVPLKQANPKFPILVRECS 52 (72)
Q Consensus 25 GvR~Fl~~~l~~~k~~NP~v~i~v~~~~ 52 (72)
-...++...+..|.+++|++.|.+....
T Consensus 112 ~~~~~l~~~l~~f~~~~P~i~i~~~~~~ 139 (311)
T PRK10086 112 IAQCWLVPRLADFTRRYPSISLTILTGN 139 (311)
T ss_pred HHHHHHHHHHHHHHHHCCCeEEEEEeCC
Confidence 4567888899999999999999988644
No 194
>cd03034 ArsC_ArsC Arsenate Reductase (ArsC) family, ArsC subfamily; arsenic reductases similar to that encoded by arsC on the R733 plasmid of Escherichia coli. E. coli ArsC catalyzes the reduction of arsenate [As(V)] to arsenite [As(III)], the first step in the detoxification of arsenic, using reducing equivalents derived from glutathione (GSH) via glutaredoxin (GRX). ArsC contains a single catalytic cysteine, within a thioredoxin fold, that forms a covalent thiolate-As(V) intermediate, which is reduced by GRX through a mixed GSH-arsenate intermediate. This family of predominantly bacterial enzymes is unrelated to two other families of arsenate reductases which show similarity to low-molecular-weight acid phosphatases and phosphotyrosyl phosphatases.
Probab=20.09 E-value=1.8e+02 Score=17.77 Aligned_cols=22 Identities=14% Similarity=0.132 Sum_probs=17.5
Q ss_pred EEEEecCCCCCCHHHHHHHHhC
Q psy15303 12 LRIHLCQKGGSSSGVRDFLAQH 33 (72)
Q Consensus 12 L~~~yC~~~~sS~GvR~Fl~~~ 33 (72)
|+|..-.++.+|+-++.|++.+
T Consensus 1 i~iy~~~~C~t~rkA~~~L~~~ 22 (112)
T cd03034 1 ITIYHNPRCSKSRNALALLEEA 22 (112)
T ss_pred CEEEECCCCHHHHHHHHHHHHC
Confidence 3567778888999999999754
Done!