Query psy15302
Match_columns 68
No_of_seqs 104 out of 332
Neff 6.2
Searched_HMMs 46136
Date Fri Aug 16 17:36:32 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy15302.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/15302hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3445|consensus 100.0 4.2E-30 9.2E-35 165.4 7.3 67 1-67 15-81 (145)
2 KOG3446|consensus 99.9 1.2E-24 2.7E-29 131.3 1.5 61 7-67 13-73 (97)
3 PF05047 L51_S25_CI-B8: Mitoch 99.7 1.1E-16 2.3E-21 87.3 5.2 42 26-67 1-42 (52)
4 KOG4079|consensus 98.5 1.7E-08 3.8E-13 66.0 0.1 61 8-68 27-87 (169)
5 PF10780 MRP_L53: 39S ribosoma 97.5 0.00016 3.6E-09 39.6 3.5 49 16-65 1-51 (51)
6 PF13701 DDE_Tnp_1_4: Transpos 75.1 4.8 0.0001 30.1 3.8 35 19-53 193-227 (448)
7 PF13692 Glyco_trans_1_4: Glyc 74.4 4.7 0.0001 23.7 3.0 39 13-51 4-42 (135)
8 COG4837 Uncharacterized protei 72.7 5.6 0.00012 24.7 3.0 32 17-51 19-50 (106)
9 COG1182 AcpD Acyl carrier prot 71.6 7.2 0.00016 26.8 3.7 53 12-65 5-58 (202)
10 cd08429 PBP2_NhaR The C-termin 70.6 7.8 0.00017 24.2 3.5 29 24-52 9-37 (204)
11 cd08418 PBP2_TdcA The C-termin 70.3 7.6 0.00017 23.2 3.3 29 23-51 8-36 (201)
12 cd08470 PBP2_CrgA_like_1 The C 69.7 8.1 0.00018 23.1 3.3 25 26-50 12-36 (197)
13 cd05466 PBP2_LTTR_substrate Th 69.7 9.4 0.0002 22.1 3.5 27 25-51 10-36 (197)
14 TIGR01159 DRP1 density-regulat 69.6 3 6.5E-05 27.9 1.4 25 14-38 14-38 (173)
15 TIGR02136 ptsS_2 phosphate bin 67.6 6.8 0.00015 27.0 3.0 26 26-51 46-71 (287)
16 PF02601 Exonuc_VII_L: Exonucl 66.6 11 0.00023 26.4 3.8 30 19-52 21-50 (319)
17 cd08465 PBP2_ToxR The C-termin 65.4 8.8 0.00019 23.5 2.9 26 26-51 11-36 (200)
18 cd08488 PBP2_AmpR The C-termin 65.3 13 0.00029 22.3 3.7 26 27-52 12-37 (191)
19 cd08481 PBP2_GcdR_like The C-t 64.7 12 0.00026 22.1 3.4 26 27-52 12-37 (194)
20 cd08456 PBP2_LysR The C-termin 64.7 11 0.00024 22.5 3.2 27 25-51 10-36 (196)
21 cd08460 PBP2_DntR_like_1 The C 64.4 9.8 0.00021 23.1 2.9 27 25-51 10-36 (200)
22 cd08439 PBP2_LrhA_like The C-t 64.4 14 0.00029 22.2 3.6 27 25-51 10-36 (185)
23 cd08435 PBP2_GbpR The C-termin 64.1 12 0.00027 22.2 3.3 26 26-51 11-36 (201)
24 cd08482 PBP2_TrpI The C-termin 63.3 13 0.00028 22.4 3.3 27 25-51 10-36 (195)
25 cd08461 PBP2_DntR_like_3 The C 63.3 11 0.00025 22.5 3.1 26 26-51 11-36 (198)
26 cd08452 PBP2_AlsR The C-termin 63.2 10 0.00023 22.9 2.9 26 26-51 11-36 (197)
27 cd08487 PBP2_BlaA The C-termin 62.7 14 0.00031 22.0 3.4 26 26-51 11-36 (189)
28 cd08440 PBP2_LTTR_like_4 TThe 62.6 12 0.00026 22.0 3.0 25 27-51 12-36 (197)
29 cd08473 PBP2_CrgA_like_4 The C 62.3 17 0.00038 21.6 3.8 26 26-51 14-39 (202)
30 cd08450 PBP2_HcaR The C-termin 62.2 11 0.00024 22.4 2.9 26 26-51 11-36 (196)
31 cd08444 PBP2_Cbl The C-termina 62.2 13 0.00028 22.6 3.2 26 26-51 11-36 (198)
32 PF07315 DUF1462: Protein of u 61.8 16 0.00034 22.4 3.4 32 17-51 12-43 (93)
33 KOG0183|consensus 61.7 4.9 0.00011 28.3 1.3 18 19-36 162-179 (249)
34 cd08448 PBP2_LTTR_aromatics_li 61.6 13 0.00029 21.9 3.2 25 26-50 11-35 (197)
35 cd08416 PBP2_MdcR The C-termin 61.6 15 0.00032 21.9 3.4 27 25-51 10-36 (199)
36 cd08412 PBP2_PAO1_like The C-t 61.4 11 0.00025 22.3 2.8 25 27-51 12-36 (198)
37 cd08477 PBP2_CrgA_like_8 The C 61.1 15 0.00034 21.8 3.4 25 26-50 12-36 (197)
38 cd08431 PBP2_HupR The C-termin 61.1 13 0.00027 22.3 3.0 25 27-51 12-36 (195)
39 cd08436 PBP2_LTTR_like_3 The C 60.8 13 0.00027 22.0 2.9 27 25-51 10-36 (194)
40 cd08426 PBP2_LTTR_like_5 The C 60.8 13 0.00029 22.1 3.1 26 26-51 11-36 (199)
41 cd08478 PBP2_CrgA The C-termin 60.5 11 0.00024 22.6 2.7 25 26-50 14-38 (199)
42 cd08464 PBP2_DntR_like_2 The C 60.3 18 0.00039 21.6 3.6 25 27-51 12-36 (200)
43 cd08486 PBP2_CbnR The C-termin 60.1 13 0.00028 22.7 3.0 25 27-51 13-37 (198)
44 cd08466 PBP2_LeuO The C-termin 59.8 16 0.00034 21.9 3.3 26 26-51 11-36 (200)
45 PF03466 LysR_substrate: LysR 59.7 12 0.00026 22.6 2.7 27 26-52 17-43 (209)
46 cd08432 PBP2_GcdR_TrpI_HvrB_Am 59.5 18 0.0004 21.4 3.5 28 25-52 10-37 (194)
47 cd08414 PBP2_LTTR_aromatics_li 59.4 16 0.00034 21.6 3.2 26 26-51 11-36 (197)
48 PF05762 VWA_CoxE: VWA domain 59.4 22 0.00049 23.8 4.2 40 13-52 60-99 (222)
49 cd08453 PBP2_IlvR The C-termin 58.8 16 0.00034 22.0 3.1 25 27-51 12-36 (200)
50 cd08479 PBP2_CrgA_like_9 The C 58.7 17 0.00037 21.7 3.3 27 25-51 11-37 (198)
51 cd08425 PBP2_CynR The C-termin 58.7 15 0.00033 21.9 3.1 27 25-51 11-37 (197)
52 cd08472 PBP2_CrgA_like_3 The C 58.5 21 0.00046 21.3 3.7 25 26-50 12-36 (202)
53 PF04690 YABBY: YABBY protein; 58.0 7.1 0.00015 26.1 1.6 19 27-45 130-148 (170)
54 cd08437 PBP2_MleR The substrat 58.0 14 0.00031 22.1 2.9 25 27-51 12-36 (198)
55 cd08438 PBP2_CidR The C-termin 57.8 13 0.00028 22.0 2.6 25 27-51 12-36 (197)
56 cd08434 PBP2_GltC_like The sub 57.8 14 0.0003 21.8 2.7 25 27-51 12-36 (195)
57 cd08420 PBP2_CysL_like C-termi 57.8 17 0.00036 21.5 3.1 26 26-51 11-36 (201)
58 PRK14003 potassium-transportin 57.4 16 0.00035 24.9 3.3 45 17-61 93-139 (194)
59 cd08480 PBP2_CrgA_like_10 The 57.2 18 0.00038 21.9 3.2 25 26-50 12-36 (198)
60 cd08415 PBP2_LysR_opines_like 56.6 7.9 0.00017 23.0 1.5 26 26-51 11-36 (196)
61 cd08445 PBP2_BenM_CatM_CatR Th 56.3 19 0.0004 21.8 3.2 25 27-51 13-37 (203)
62 cd08421 PBP2_LTTR_like_1 The C 55.9 17 0.00037 21.6 3.0 24 28-51 13-36 (198)
63 PRK13996 potassium-transportin 55.8 9.8 0.00021 26.1 2.0 44 17-60 91-141 (197)
64 cd08471 PBP2_CrgA_like_2 The C 55.4 24 0.00051 21.1 3.5 25 26-50 12-36 (201)
65 cd08476 PBP2_CrgA_like_7 The C 55.2 15 0.00032 21.8 2.6 24 27-50 11-34 (197)
66 cd08423 PBP2_LTTR_like_6 The C 55.1 19 0.00042 21.3 3.1 25 27-51 12-36 (200)
67 cd08441 PBP2_MetR The C-termin 54.6 25 0.00055 21.0 3.6 24 28-51 13-36 (198)
68 cd08474 PBP2_CrgA_like_5 The C 54.5 25 0.00054 21.1 3.5 26 26-51 14-39 (202)
69 cd08483 PBP2_HvrB The C-termin 54.4 22 0.00047 21.1 3.2 25 26-50 11-35 (190)
70 cd08422 PBP2_CrgA_like The C-t 54.2 16 0.00036 21.5 2.6 24 27-50 13-36 (197)
71 cd08459 PBP2_DntR_NahR_LinR_li 54.2 30 0.00065 20.7 3.8 26 27-52 12-37 (201)
72 cd08411 PBP2_OxyR The C-termin 53.0 22 0.00049 21.2 3.1 24 27-50 13-36 (200)
73 cd08446 PBP2_Chlorocatechol Th 52.9 22 0.00048 21.2 3.1 25 27-51 13-37 (198)
74 cd08419 PBP2_CbbR_RubisCO_like 52.3 23 0.00049 20.9 3.1 25 27-51 11-35 (197)
75 cd08458 PBP2_NocR The C-termin 52.2 20 0.00043 21.7 2.8 26 26-51 11-36 (196)
76 cd08442 PBP2_YofA_SoxR_like Th 52.0 19 0.00041 21.3 2.7 25 27-51 12-36 (193)
77 cd08449 PBP2_XapR The C-termin 51.9 19 0.0004 21.4 2.6 24 27-50 12-35 (197)
78 cd08467 PBP2_SyrM The C-termin 51.9 22 0.00047 21.6 3.0 26 26-51 11-36 (200)
79 PTZ00062 glutaredoxin; Provisi 51.7 45 0.00097 22.6 4.7 37 12-52 21-57 (204)
80 PRK13997 potassium-transportin 51.5 13 0.00028 25.4 2.0 44 17-60 87-137 (193)
81 cd08447 PBP2_LTTR_aromatics_li 50.8 25 0.00054 20.9 3.1 26 26-51 11-36 (198)
82 COG1653 UgpB ABC-type sugar tr 50.3 53 0.0011 22.5 5.0 26 27-52 45-70 (433)
83 cd08485 PBP2_ClcR The C-termin 50.3 18 0.00039 22.0 2.4 26 26-51 12-37 (198)
84 cd08469 PBP2_PnbR The C-termin 50.2 27 0.00058 21.5 3.2 26 27-52 12-37 (221)
85 cd08427 PBP2_LTTR_like_2 The C 50.0 24 0.00052 20.9 2.9 25 27-51 12-36 (195)
86 cd03026 AhpF_NTD_C TRX-GRX-lik 49.8 49 0.0011 19.1 5.4 37 11-51 15-51 (89)
87 TIGR00237 xseA exodeoxyribonuc 49.8 28 0.00061 25.9 3.8 30 19-52 136-165 (432)
88 PRK00286 xseA exodeoxyribonucl 49.4 28 0.00061 25.6 3.7 30 19-52 142-171 (438)
89 cd02989 Phd_like_TxnDC9 Phosdu 49.2 43 0.00093 19.9 4.0 34 11-48 25-58 (113)
90 cd08417 PBP2_Nitroaromatics_li 48.9 28 0.00062 20.7 3.1 26 26-51 11-36 (200)
91 cd08433 PBP2_Nac The C-teminal 48.9 19 0.00042 21.5 2.4 25 27-51 12-36 (198)
92 cd08475 PBP2_CrgA_like_6 The C 48.4 27 0.00058 20.7 3.0 25 26-50 12-36 (199)
93 cd08462 PBP2_NodD The C-termin 48.0 31 0.00068 20.8 3.3 26 26-51 11-36 (200)
94 cd08430 PBP2_IlvY The C-termin 47.7 17 0.00036 21.6 2.0 25 27-51 12-36 (199)
95 PF06244 DUF1014: Protein of u 47.6 17 0.00036 23.1 2.0 20 26-45 80-99 (122)
96 cd08468 PBP2_Pa0477 The C-term 47.5 34 0.00074 20.7 3.4 25 27-51 12-36 (202)
97 PLN02757 sirohydrochlorine fer 47.4 14 0.00031 23.8 1.7 32 27-58 89-120 (154)
98 TIGR00681 kdpC K+-transporting 47.3 11 0.00023 25.7 1.1 44 17-60 84-133 (187)
99 cd08484 PBP2_LTTR_beta_lactama 46.8 36 0.00077 20.2 3.4 26 26-51 11-36 (189)
100 cd08463 PBP2_DntR_like_4 The C 46.6 32 0.00069 21.1 3.2 24 27-50 12-35 (203)
101 cd08451 PBP2_BudR The C-termin 46.3 21 0.00046 21.2 2.3 23 29-51 15-37 (199)
102 smart00329 BPI2 BPI/LBP/CETP C 46.2 55 0.0012 21.5 4.4 33 29-61 48-80 (202)
103 cd08413 PBP2_CysB_like The C-t 45.6 22 0.00048 21.5 2.3 26 26-51 11-36 (198)
104 TIGR02200 GlrX_actino Glutared 45.4 24 0.00052 18.6 2.2 22 11-32 1-22 (77)
105 cd02974 AhpF_NTD_N Alkyl hydro 45.1 65 0.0014 19.1 6.1 40 18-61 28-67 (94)
106 PF09457 RBD-FIP: FIP domain ; 44.5 9 0.00019 20.6 0.3 20 25-44 25-44 (48)
107 PRK13999 potassium-transportin 44.1 16 0.00034 25.2 1.6 44 17-60 97-144 (201)
108 PRK14002 potassium-transportin 43.9 20 0.00043 24.4 2.0 44 17-60 81-131 (186)
109 TIGR02036 dsdC D-serine deamin 43.4 42 0.00091 22.8 3.6 27 26-52 107-133 (302)
110 PLN02958 diacylglycerol kinase 43.3 51 0.0011 24.9 4.3 44 10-53 112-155 (481)
111 PF13516 LRR_6: Leucine Rich r 42.3 6.9 0.00015 17.1 -0.3 21 7-29 2-22 (24)
112 PRK13994 potassium-transportin 41.3 22 0.00048 24.8 2.0 44 17-60 111-165 (222)
113 smart00367 LRR_CC Leucine-rich 40.6 22 0.00047 15.8 1.3 23 7-30 2-24 (26)
114 PRK10470 ribosome hibernation 40.6 72 0.0016 18.4 3.9 32 12-44 3-34 (95)
115 cd08457 PBP2_OccR The C-termin 40.6 22 0.00048 21.3 1.7 26 26-51 11-36 (196)
116 PRK00315 potassium-transportin 40.5 15 0.00033 25.0 1.1 44 17-60 86-135 (193)
117 cd00026 BPI2 BPI/LBP/CETP C-te 40.2 82 0.0018 20.7 4.5 32 30-61 44-75 (200)
118 TIGR00741 yfiA ribosomal subun 40.0 71 0.0015 18.1 4.1 31 12-43 3-33 (95)
119 PF02482 Ribosomal_S30AE: Sigm 38.8 72 0.0016 18.0 3.7 32 12-44 2-33 (97)
120 PF02638 DUF187: Glycosyl hydr 38.7 49 0.0011 23.5 3.5 30 23-52 202-231 (311)
121 COG1570 XseA Exonuclease VII, 38.5 52 0.0011 25.2 3.7 30 19-52 142-171 (440)
122 KOG1909|consensus 38.2 30 0.00066 26.0 2.4 36 7-48 241-276 (382)
123 COG0607 PspE Rhodanese-related 38.0 52 0.0011 18.5 3.0 23 10-32 61-83 (110)
124 PF02114 Phosducin: Phosducin; 37.7 1.1E+02 0.0023 21.6 4.9 50 11-65 149-208 (265)
125 PF11247 DUF2675: Protein of u 37.2 27 0.00058 21.5 1.7 15 24-38 68-82 (98)
126 PF09217 EcoRII-N: Restriction 36.9 31 0.00066 22.9 2.0 43 24-66 33-77 (156)
127 PF07205 DUF1413: Domain of un 36.8 62 0.0013 17.9 3.1 33 18-50 27-59 (70)
128 cd02987 Phd_like_Phd Phosducin 36.7 67 0.0015 20.9 3.6 35 12-50 87-121 (175)
129 TIGR02174 CXXU_selWTH selT/sel 36.6 79 0.0017 17.6 4.3 38 12-53 1-38 (72)
130 PF10262 Rdx: Rdx family; Int 36.4 80 0.0017 17.6 4.9 37 11-51 2-40 (76)
131 TIGR00269 conserved hypothetic 35.3 20 0.00042 21.5 0.9 24 22-45 34-57 (104)
132 PRK10837 putative DNA-binding 35.1 58 0.0013 21.5 3.2 26 26-51 100-125 (290)
133 PF13504 LRR_7: Leucine rich r 35.1 19 0.00041 14.8 0.6 11 8-18 2-12 (17)
134 PF00280 potato_inhibit: Potat 35.0 36 0.00079 19.0 1.9 19 34-52 16-34 (63)
135 PRK10696 tRNA 2-thiocytidine b 34.7 41 0.00088 23.0 2.5 25 22-46 206-230 (258)
136 PRK11139 DNA-binding transcrip 34.6 64 0.0014 21.6 3.4 25 27-51 106-130 (297)
137 PRK11716 DNA-binding transcrip 34.5 67 0.0014 20.8 3.4 25 27-51 79-103 (269)
138 PRK10597 DNA damage-inducible 34.3 1E+02 0.0022 18.2 5.8 43 11-53 2-47 (81)
139 PRK10974 glycerol-3-phosphate 34.3 60 0.0013 23.3 3.4 25 26-50 38-62 (438)
140 PRK13995 potassium-transportin 34.2 65 0.0014 22.2 3.3 44 17-60 95-145 (203)
141 PF08109 Antimicrobial14: Lact 34.1 26 0.00057 16.9 1.0 23 21-43 4-26 (31)
142 COG4097 Predicted ferric reduc 34.1 44 0.00096 25.5 2.7 44 10-59 344-388 (438)
143 PRK11151 DNA-binding transcrip 34.1 72 0.0016 21.5 3.6 27 25-51 101-127 (305)
144 PRK12681 cysB transcriptional 33.6 63 0.0014 22.4 3.3 36 11-51 94-129 (324)
145 PRK09508 leuO leucine transcri 33.6 73 0.0016 21.7 3.6 26 27-52 124-149 (314)
146 PRK09801 transcriptional activ 33.6 76 0.0016 21.7 3.7 28 24-51 105-132 (310)
147 PF07735 FBA_2: F-box associat 33.3 73 0.0016 17.0 3.0 35 8-47 33-67 (70)
148 PF09822 ABC_transp_aux: ABC-t 33.3 1.3E+02 0.0029 20.3 4.8 40 11-50 28-69 (271)
149 PRK14001 potassium-transportin 33.1 70 0.0015 21.8 3.3 44 17-60 85-135 (189)
150 PRK09791 putative DNA-binding 33.0 66 0.0014 21.6 3.2 26 26-51 106-131 (302)
151 TIGR02196 GlrX_YruB Glutaredox 32.8 54 0.0012 16.7 2.3 21 12-32 2-22 (74)
152 cd02957 Phd_like Phosducin (Ph 32.6 1.1E+02 0.0023 17.9 3.9 34 11-48 27-60 (113)
153 PRK11074 putative DNA-binding 32.6 54 0.0012 22.1 2.8 37 10-51 92-128 (300)
154 cd06544 GH18_narbonin Narbonin 32.5 39 0.00084 23.4 2.1 21 32-52 59-79 (253)
155 PRK09375 quinolinate synthetas 32.5 70 0.0015 23.3 3.4 34 16-49 223-269 (319)
156 cd02973 TRX_GRX_like Thioredox 32.3 79 0.0017 16.3 4.7 36 11-50 2-37 (67)
157 PF01547 SBP_bac_1: Bacterial 32.3 44 0.00095 21.8 2.2 23 29-51 9-32 (315)
158 KOG2559|consensus 32.3 55 0.0012 23.8 2.8 36 1-36 1-36 (318)
159 PRK14997 LysR family transcrip 32.1 95 0.002 20.8 3.9 27 26-52 103-129 (301)
160 COG2871 NqrF Na+-transporting 31.9 94 0.002 23.3 4.0 38 9-51 304-342 (410)
161 PRK03601 transcriptional regul 31.9 89 0.0019 20.9 3.7 26 26-51 100-125 (275)
162 cd04864 LigD_Pol_like_1 LigD_P 31.8 39 0.00084 23.6 2.0 45 22-66 156-201 (228)
163 PRK10086 DNA-binding transcrip 31.7 77 0.0017 21.6 3.4 28 25-52 112-139 (311)
164 KOG3170|consensus 31.7 1.2E+02 0.0026 21.4 4.3 33 23-55 122-154 (240)
165 KOG0863|consensus 31.7 23 0.0005 25.2 0.9 24 20-43 162-185 (264)
166 cd01523 RHOD_Lact_B Member of 31.7 67 0.0015 18.1 2.8 20 12-31 63-82 (100)
167 COG0187 GyrB Type IIA topoisom 31.5 70 0.0015 25.7 3.5 39 27-65 186-224 (635)
168 cd07945 DRE_TIM_CMS Leptospira 31.5 99 0.0021 21.7 4.0 34 13-48 163-196 (280)
169 PF12876 Cellulase-like: Sugar 31.2 50 0.0011 18.8 2.1 27 23-49 37-63 (88)
170 PF01903 CbiX: CbiX; InterPro 31.1 14 0.0003 21.4 -0.3 35 24-58 65-99 (105)
171 PRK10341 DNA-binding transcrip 30.8 85 0.0018 21.3 3.5 37 10-51 97-133 (312)
172 PLN02870 Probable galacturonos 30.7 42 0.00092 26.3 2.2 25 1-31 1-25 (533)
173 PF08073 CHDNT: CHDNT (NUC034) 30.6 71 0.0015 17.6 2.5 22 25-46 15-36 (55)
174 PF14363 AAA_assoc: Domain ass 30.3 82 0.0018 18.6 3.0 30 24-53 4-35 (98)
175 cd01388 SOX-TCF_HMG-box SOX-TC 30.2 38 0.00082 18.5 1.4 19 28-46 11-29 (72)
176 PRK13337 putative lipid kinase 29.8 1.3E+02 0.0028 20.8 4.4 42 10-52 2-43 (304)
177 PRK12684 transcriptional regul 28.8 95 0.0021 21.2 3.5 29 23-51 101-129 (313)
178 TIGR02336 1,3-beta-galactosyl- 28.6 58 0.0013 26.5 2.7 27 23-49 184-210 (719)
179 PRK15421 DNA-binding transcrip 28.6 84 0.0018 21.6 3.2 25 27-51 101-125 (317)
180 PF13552 DUF4127: Protein of u 28.5 53 0.0011 25.1 2.3 19 32-50 92-110 (497)
181 PRK11013 DNA-binding transcrip 28.4 97 0.0021 21.0 3.5 26 27-52 106-131 (309)
182 PRK11914 diacylglycerol kinase 28.2 1E+02 0.0023 21.2 3.7 41 8-49 7-47 (306)
183 KOG3239|consensus 28.1 31 0.00067 23.6 1.0 26 12-37 20-45 (193)
184 cd00552 RaiA RaiA ("ribosome-a 28.1 78 0.0017 17.8 2.6 25 20-44 9-33 (93)
185 PF00505 HMG_box: HMG (high mo 27.7 52 0.0011 17.3 1.7 18 28-45 10-27 (69)
186 cd03005 PDI_a_ERp46 PDIa famil 27.7 79 0.0017 17.4 2.6 40 11-50 19-58 (102)
187 TIGR02424 TF_pcaQ pca operon t 27.4 1.1E+02 0.0023 20.5 3.5 28 24-51 102-129 (300)
188 TIGR03418 chol_sulf_TF putativ 27.4 86 0.0019 20.8 3.1 26 27-52 101-126 (291)
189 PF02886 LBP_BPI_CETP_C: LBP / 27.3 48 0.001 22.0 1.8 33 29-61 80-112 (238)
190 TIGR03851 chitin_NgcE carbohyd 27.2 81 0.0018 22.6 3.1 24 27-50 53-76 (450)
191 TIGR00411 redox_disulf_1 small 27.2 1.1E+02 0.0023 16.2 4.3 27 11-37 2-28 (82)
192 cd02066 GRX_family Glutaredoxi 27.1 68 0.0015 16.1 2.1 21 12-32 2-22 (72)
193 TIGR03850 bind_CPR_0540 carboh 26.9 1.2E+02 0.0027 21.4 3.9 25 27-51 47-71 (437)
194 cd02976 NrdH NrdH-redoxin (Nrd 26.9 75 0.0016 16.1 2.2 21 12-32 2-22 (73)
195 PRK11233 nitrogen assimilation 26.6 1.3E+02 0.0028 20.3 3.9 26 26-51 103-128 (305)
196 PLN02495 oxidoreductase, actin 26.5 80 0.0017 23.5 3.0 28 22-50 93-120 (385)
197 PF09508 Lact_bio_phlase: Lact 26.5 59 0.0013 26.4 2.3 28 22-49 180-207 (716)
198 PF00781 DAGK_cat: Diacylglyce 26.3 1.4E+02 0.003 17.8 3.6 38 11-51 1-38 (130)
199 PRK10216 DNA-binding transcrip 26.3 1.1E+02 0.0023 20.9 3.4 26 26-51 108-133 (319)
200 PRK15092 DNA-binding transcrip 25.9 1.3E+02 0.0028 20.8 3.8 27 25-51 109-135 (310)
201 PF01624 MutS_I: MutS domain I 25.9 62 0.0013 19.3 2.0 21 31-51 4-24 (113)
202 PRK10324 translation inhibitor 25.8 1.6E+02 0.0035 17.8 4.2 32 12-44 3-34 (113)
203 cd02975 PfPDO_like_N Pyrococcu 25.7 1.5E+02 0.0033 17.5 4.5 36 11-50 24-60 (113)
204 TIGR01256 modA molybdenum ABC 25.2 93 0.002 19.9 2.8 25 25-50 3-27 (216)
205 PF13905 Thioredoxin_8: Thiore 25.1 62 0.0013 17.8 1.8 38 13-51 6-43 (95)
206 TIGR03339 phn_lysR aminoethylp 25.0 1.1E+02 0.0023 20.0 3.1 24 28-51 97-120 (279)
207 COG1393 ArsC Arsenate reductas 24.7 74 0.0016 19.6 2.2 23 11-33 2-24 (117)
208 PF02669 KdpC: K+-transporting 24.4 63 0.0014 21.9 1.9 44 17-60 85-134 (188)
209 PRK11242 DNA-binding transcrip 24.4 1.1E+02 0.0024 20.2 3.1 26 26-51 102-127 (296)
210 TIGR00550 nadA quinolinate syn 24.3 1.3E+02 0.0028 21.7 3.6 35 15-49 210-257 (310)
211 PF11943 DUF3460: Protein of u 24.2 49 0.0011 18.6 1.2 14 32-45 9-22 (60)
212 PRK13055 putative lipid kinase 24.1 2.4E+02 0.0051 20.0 4.9 40 10-50 3-42 (334)
213 PF08885 GSCFA: GSCFA family; 24.0 1.3E+02 0.0029 21.0 3.5 31 23-53 147-177 (251)
214 PF09345 DUF1987: Domain of un 23.7 1.4E+02 0.003 18.0 3.2 36 11-48 48-83 (99)
215 PRK12682 transcriptional regul 23.7 1.3E+02 0.0028 20.3 3.4 26 26-51 104-129 (309)
216 COG5575 ORC2 Origin recognitio 23.7 62 0.0014 25.0 2.0 35 17-51 484-519 (535)
217 cd08443 PBP2_CysB The C-termin 23.6 54 0.0012 19.8 1.4 25 27-51 12-36 (198)
218 PRK10680 molybdopterin biosynt 23.6 64 0.0014 24.0 2.0 39 19-62 250-289 (411)
219 cd02996 PDI_a_ERp44 PDIa famil 23.4 1.6E+02 0.0034 16.8 3.3 33 11-43 21-53 (108)
220 cd02873 GH18_IDGF The IDGF's ( 23.3 72 0.0016 23.5 2.2 21 32-52 63-83 (413)
221 KOG1454|consensus 23.1 82 0.0018 22.4 2.4 26 33-58 282-307 (326)
222 PRK12680 transcriptional regul 23.1 1.2E+02 0.0027 21.0 3.3 37 10-51 93-129 (327)
223 PF14606 Lipase_GDSL_3: GDSL-l 23.1 1E+02 0.0022 20.6 2.8 31 21-51 71-101 (178)
224 KOG0907|consensus 23.1 1.8E+02 0.0039 17.4 3.9 30 15-48 28-57 (106)
225 CHL00180 rbcR LysR transcripti 23.1 1.3E+02 0.0027 20.4 3.2 25 27-51 107-131 (305)
226 TIGR03521 GldG gliding-associa 22.9 2.1E+02 0.0046 21.9 4.7 39 11-49 51-90 (552)
227 PF10307 DUF2410: Hypothetical 22.8 1.1E+02 0.0025 20.8 3.0 27 6-33 130-156 (197)
228 PHA00684 hypothetical protein 22.8 95 0.0021 20.0 2.4 28 24-52 56-83 (128)
229 cd03409 Chelatase_Class_II Cla 22.7 1.6E+02 0.0034 16.5 3.7 33 25-57 14-46 (101)
230 PF05159 Capsule_synth: Capsul 22.5 1.3E+02 0.0027 20.3 3.2 27 26-52 138-164 (269)
231 PF14421 LmjF365940-deam: A di 22.3 1E+02 0.0023 21.1 2.7 25 31-55 161-185 (193)
232 TIGR03087 stp1 sugar transfera 22.1 1.5E+02 0.0032 20.9 3.5 26 25-50 241-266 (397)
233 cd03027 GRX_DEP Glutaredoxin ( 22.0 1.4E+02 0.003 15.9 2.7 22 11-32 2-23 (73)
234 PF06891 P2_Phage_GpR: P2 phag 21.9 78 0.0017 19.9 1.9 27 24-50 5-31 (135)
235 PRK10632 transcriptional regul 21.8 1.5E+02 0.0032 20.2 3.4 26 26-51 103-128 (309)
236 PRK09986 DNA-binding transcrip 21.8 1.3E+02 0.0028 19.9 3.1 25 27-51 109-133 (294)
237 cd02988 Phd_like_VIAF Phosduci 21.7 2E+02 0.0043 19.0 3.9 35 12-50 106-140 (192)
238 cd03045 GST_N_Delta_Epsilon GS 21.7 1.2E+02 0.0027 15.8 2.5 20 12-31 1-20 (74)
239 PF02944 BESS: BESS motif; In 21.7 67 0.0015 15.7 1.3 18 26-43 4-21 (37)
240 PF00309 Sigma54_AID: Sigma-54 21.6 70 0.0015 16.7 1.4 16 31-46 32-47 (49)
241 PF06121 DUF959: Domain of Unk 21.5 58 0.0013 22.4 1.3 10 24-33 129-138 (202)
242 PHA00440 host protein H-NS-int 21.4 73 0.0016 19.6 1.6 15 24-38 68-82 (98)
243 PF10607 CLTH: CTLH/CRA C-term 21.3 70 0.0015 19.4 1.6 29 21-49 15-43 (145)
244 PF02960 K1: K1 glycoprotein; 21.3 34 0.00074 21.9 0.2 42 22-63 30-71 (130)
245 PF06183 DinI: DinI-like famil 21.2 1.7E+02 0.0036 16.3 3.0 30 24-53 3-33 (65)
246 cd07941 DRE_TIM_LeuA3 Desulfob 21.1 2E+02 0.0042 19.9 3.9 34 13-48 167-200 (273)
247 PRK11062 nhaR transcriptional 21.0 1.3E+02 0.0028 20.3 3.0 25 26-50 104-128 (296)
248 cd03052 GST_N_GDAP1 GST_N fami 20.9 1.1E+02 0.0023 16.6 2.2 20 12-31 1-20 (73)
249 cd04502 SGNH_hydrolase_like_7 20.8 1.9E+02 0.0041 17.6 3.5 28 23-50 69-96 (171)
250 cd03419 GRX_GRXh_1_2_like Glut 20.7 97 0.0021 16.5 2.0 22 12-33 2-23 (82)
251 PRK05972 ligD ATP-dependent DN 20.7 1.2E+02 0.0025 25.2 3.0 41 23-63 742-782 (860)
252 PRK10094 DNA-binding transcrip 20.7 1.3E+02 0.0028 20.5 3.0 38 10-51 92-129 (308)
253 cd02413 40S_S3_KH K homology R 20.5 1.4E+02 0.003 17.2 2.6 31 22-52 48-78 (81)
254 PF01507 PAPS_reduct: Phosphoa 20.5 40 0.00087 20.7 0.3 34 12-50 26-59 (174)
255 cd01836 FeeA_FeeB_like SGNH_hy 20.5 2E+02 0.0043 17.8 3.6 29 22-50 85-113 (191)
256 PRK12683 transcriptional regul 20.3 1.5E+02 0.0033 20.2 3.2 25 27-51 105-129 (309)
257 cd02872 GH18_chitolectin_chito 20.3 84 0.0018 22.2 2.0 19 33-51 60-78 (362)
258 cd06548 GH18_chitinase The GH1 20.2 90 0.0019 21.9 2.1 20 33-52 74-93 (322)
259 PF10691 DUF2497: Protein of u 20.2 99 0.0021 17.8 1.9 14 26-39 47-60 (73)
No 1
>KOG3445|consensus
Probab=99.96 E-value=4.2e-30 Score=165.36 Aligned_cols=67 Identities=28% Similarity=0.480 Sum_probs=64.4
Q ss_pred CcccccCcceEEEEEecCCCCCCHHHHHHHHhCHHHHHHhCCCCeEEEEecCCCCCEEEEEecCCCC
Q psy15302 1 MAARFGSKLKELRIHLCQKGGSSSGVRDFLAQHYVPLKQANPKFPILVRECSGVTPVVWASGKGTHN 67 (68)
Q Consensus 1 Ms~r~v~qlk~l~~~yc~~~~sS~G~R~Fl~~~l~~~~~~NP~v~i~v~~~~~~~P~v~a~Y~nGr~ 67 (68)
|.-||++||++|+|+||+|||||+|||+||++.|++|+++||+|+|++.+++|.||.|+|+|.|||+
T Consensus 15 Glgryv~ql~rit~sfCnwggSSrGmR~Fle~~L~~~a~enP~v~i~v~~rrg~hP~lraeY~NGre 81 (145)
T KOG3445|consen 15 GLGRYVWQLRRITVSFCNWGGSSRGMREFLESELPDLARENPGVVIYVEPRRGQHPLLRAEYLNGRE 81 (145)
T ss_pred chhhhhheeeEEEEEEecCCCccHHHHHHHHHHHHHHHhhCCCeEEEEeccCCCCceEEEEecCCce
Confidence 3458999999999999999999999999999999999999999999999999999999999999986
No 2
>KOG3446|consensus
Probab=99.89 E-value=1.2e-24 Score=131.34 Aligned_cols=61 Identities=59% Similarity=1.014 Sum_probs=59.1
Q ss_pred CcceEEEEEecCCCCCCHHHHHHHHhCHHHHHHhCCCCeEEEEecCCCCCEEEEEecCCCC
Q psy15302 7 SKLKELRIHLCQKGGSSSGVRDFLAQHYVPLKQANPKFPILVRECSGVTPVVWASGKGTHN 67 (68)
Q Consensus 7 ~qlk~l~~~yc~~~~sS~G~R~Fl~~~l~~~~~~NP~v~i~v~~~~~~~P~v~a~Y~nGr~ 67 (68)
+.||||||+.|+.|+.|+|+|+||++.|+++|+.||++||+||+++|..|.++|+|.+|-+
T Consensus 13 ~~lkElRI~lcqkspaSagvR~fvEk~Y~~lKkaNP~lPILIREcSgVqPrl~ARY~~G~E 73 (97)
T KOG3446|consen 13 LKLKELRIHLCQKSPASAGVREFVEKFYVNLKKANPDLPILIRECSGVQPRLWARYGNGVE 73 (97)
T ss_pred hhhhhheeeecCCCCcchhHHHHHHHhhhhhhhcCCCCcEeehhhcCCchHHHHHhcCCce
Confidence 4699999999999999999999999999999999999999999999999999999999964
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=99.67 E-value=1.1e-16 Score=87.27 Aligned_cols=42 Identities=31% Similarity=0.396 Sum_probs=33.0
Q ss_pred HHHHHHhCHHHHHHhCCCCeEEEEecCCCCCEEEEEecCCCC
Q psy15302 26 VRDFLAQHYVPLKQANPKFPILVRECSGVTPVVWASGKGTHN 67 (68)
Q Consensus 26 ~R~Fl~~~l~~~~~~NP~v~i~v~~~~~~~P~v~a~Y~nGr~ 67 (68)
+|+|++++||+||..||+|+|+|+++++.||.|+|+|.||++
T Consensus 1 ~R~F~~~~lp~l~~~NP~v~~~v~~~~~~~P~~~~~y~~G~~ 42 (52)
T PF05047_consen 1 ARDFLKNNLPTLKYHNPQVQFEVRRRRGRHPFLTAEYLNGRE 42 (52)
T ss_dssp HHHHHHHTHHHHHHHSTT--EEEE---SSS-EEEEEESS--E
T ss_pred CHhHHHHhHHHHHHHCCCcEEEEEECCCCCCEEEEEEcCCCE
Confidence 799999999999999999999999999999999999999975
No 4
>KOG4079|consensus
Probab=98.53 E-value=1.7e-08 Score=66.03 Aligned_cols=61 Identities=18% Similarity=0.290 Sum_probs=57.5
Q ss_pred cceEEEEEecCCCCCCHHHHHHHHhCHHHHHHhCCCCeEEEEecCCCCCEEEEEecCCCCC
Q psy15302 8 KLKELRIHLCQKGGSSSGVRDFLAQHYVPLKQANPKFPILVRECSGVTPVVWASGKGTHNF 68 (68)
Q Consensus 8 qlk~l~~~yc~~~~sS~G~R~Fl~~~l~~~~~~NP~v~i~v~~~~~~~P~v~a~Y~nGr~~ 68 (68)
.++-.++.|..+|+...|+|+|+--++|+++.+||.|+++........|++++.+++||+.
T Consensus 27 ~V~vfsvnynt~g~~~~GARdFVfwNipQiQykNP~VQ~~~~knmtpsPF~R~YlddGr~v 87 (169)
T KOG4079|consen 27 NVNVFSVNYNTNGPEQSGARDFVFWNIPQIQYKNPKVQLVKHKNMTPSPFARAYLDDGREV 87 (169)
T ss_pred cceEEEEeccCCCccccCccceEEecchhhcccCCceEEEeeccCCCChHHHheecCcceE
Confidence 4677889999999999999999999999999999999999999999999999999999973
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=97.51 E-value=0.00016 Score=39.59 Aligned_cols=49 Identities=18% Similarity=0.123 Sum_probs=42.3
Q ss_pred ecCCCCCCHHHHHHHHhC--HHHHHHhCCCCeEEEEecCCCCCEEEEEecCC
Q psy15302 16 LCQKGGSSSGVRDFLAQH--YVPLKQANPKFPILVRECSGVTPVVWASGKGT 65 (68)
Q Consensus 16 yc~~~~sS~G~R~Fl~~~--l~~~~~~NP~v~i~v~~~~~~~P~v~a~Y~nG 65 (68)
||..+..++.+|+||..- -+....-||+.++..+.. ...|.|...|.||
T Consensus 1 FnPF~~~aksaR~FL~~ip~s~k~~~tni~~~vl~~~~-~~~P~v~V~fkdg 51 (51)
T PF10780_consen 1 FNPFSPNAKSARLFLSLIPPSAKARGTNINCEVLPRVS-RSEPSVTVTFKDG 51 (51)
T ss_pred CCCCCcccHHHHHHHHhcCCccccccCCCceEEecCCC-CCCCeEEEEeccC
Confidence 688999999999999864 445667899999999888 7799999999998
No 6
>PF13701 DDE_Tnp_1_4: Transposase DDE domain group 1
Probab=75.14 E-value=4.8 Score=30.11 Aligned_cols=35 Identities=37% Similarity=0.445 Sum_probs=31.7
Q ss_pred CCCCCHHHHHHHHhCHHHHHHhCCCCeEEEEecCC
Q psy15302 19 KGGSSSGVRDFLAQHYVPLKQANPKFPILVRECSG 53 (68)
Q Consensus 19 ~~~sS~G~R~Fl~~~l~~~~~~NP~v~i~v~~~~~ 53 (68)
+-.|++|+-+||+.-+..+.+.-|+++|++|-.+|
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 45689999999999999999999999999998764
No 7
>PF13692 Glyco_trans_1_4: Glycosyl transferases group 1; PDB: 3OY2_A 3OY7_B 2Q6V_A 2HY7_A 3CV3_A 3CUY_A.
Probab=74.39 E-value=4.7 Score=23.69 Aligned_cols=39 Identities=13% Similarity=0.267 Sum_probs=27.6
Q ss_pred EEEecCCCCCCHHHHHHHHhCHHHHHHhCCCCeEEEEec
Q psy15302 13 RIHLCQKGGSSSGVRDFLAQHYVPLKQANPKFPILVREC 51 (68)
Q Consensus 13 ~~~yc~~~~sS~G~R~Fl~~~l~~~~~~NP~v~i~v~~~ 51 (68)
.|-|-......+|+..+++.-+..++++.|++.+.+.-.
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 344443333458999999999999999999999998544
No 8
>COG4837 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=72.71 E-value=5.6 Score=24.68 Aligned_cols=32 Identities=22% Similarity=0.383 Sum_probs=27.4
Q ss_pred cCCCCCCHHHHHHHHhCHHHHHHhCCCCeEEEEec
Q psy15302 17 CQKGGSSSGVRDFLAQHYVPLKQANPKFPILVREC 51 (68)
Q Consensus 17 c~~~~sS~G~R~Fl~~~l~~~~~~NP~v~i~v~~~ 51 (68)
|=+.+||+-+-+||+ +.+|++.|..+|..+--
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 46799999999987643
No 9
>COG1182 AcpD Acyl carrier protein phosphodiesterase [Lipid metabolism]
Probab=71.64 E-value=7.2 Score=26.80 Aligned_cols=53 Identities=17% Similarity=0.196 Sum_probs=35.2
Q ss_pred EEEEecCCCCCCHHHHHHHHhCHHHHHHhCCCCeEEEEe-cCCCCCEEEEEecCC
Q psy15302 12 LRIHLCQKGGSSSGVRDFLAQHYVPLKQANPKFPILVRE-CSGVTPVVWASGKGT 65 (68)
Q Consensus 12 l~~~yc~~~~sS~G~R~Fl~~~l~~~~~~NP~v~i~v~~-~~~~~P~v~a~Y~nG 65 (68)
|.|.-+..+..|. -+...+.-+..+|++||+.+|..+. ....-|.|..+..+|
T Consensus 5 L~I~as~~~~~S~-S~~l~~~Fi~~yk~~~P~dev~~~DL~~e~iP~ld~~~~~a 58 (202)
T COG1182 5 LVIKASPLGENSV-SRKLADEFIETYKEKHPNDEVIERDLAAEPIPHLDEELLAA 58 (202)
T ss_pred EEEecCCCccccH-HHHHHHHHHHHHHHhCCCCeEEEeecccCCCcccCHHHHhc
Confidence 4455555533332 2334455566899999999999976 567788887776653
No 10
>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=70.56 E-value=7.8 Score=24.20 Aligned_cols=29 Identities=10% Similarity=0.122 Sum_probs=24.6
Q ss_pred HHHHHHHHhCHHHHHHhCCCCeEEEEecC
Q psy15302 24 SGVRDFLAQHYVPLKQANPKFPILVRECS 52 (68)
Q Consensus 24 ~G~R~Fl~~~l~~~~~~NP~v~i~v~~~~ 52 (68)
.-...|+...+.+|.+.+|++++.+....
T Consensus 9 ~~~~~~l~~~l~~f~~~~P~v~l~i~~~~ 37 (204)
T cd08429 9 AVPKSIAYRLLEPAMDLHEPIRLVCREGK 37 (204)
T ss_pred hhhHHHHHHHHHHHHHhCCCcEEEEEeCC
Confidence 34578999999999999999999998743
No 11
>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=70.28 E-value=7.6 Score=23.19 Aligned_cols=29 Identities=17% Similarity=0.138 Sum_probs=24.1
Q ss_pred CHHHHHHHHhCHHHHHHhCCCCeEEEEec
Q psy15302 23 SSGVRDFLAQHYVPLKQANPKFPILVREC 51 (68)
Q Consensus 23 S~G~R~Fl~~~l~~~~~~NP~v~i~v~~~ 51 (68)
......++...+.+|++++|++.|.+...
T Consensus 8 ~~~~~~~l~~~l~~~~~~~P~i~l~i~~~ 36 (201)
T cd08418 8 SLIAHTLMPAVINRFKEQFPDVQISIYEG 36 (201)
T ss_pred hHHHHhhhHHHHHHHHHHCCCceEEEEeC
Confidence 34567788899999999999999999753
No 12
>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=69.74 E-value=8.1 Score=23.14 Aligned_cols=25 Identities=20% Similarity=0.219 Sum_probs=21.9
Q ss_pred HHHHHHhCHHHHHHhCCCCeEEEEe
Q psy15302 26 VRDFLAQHYVPLKQANPKFPILVRE 50 (68)
Q Consensus 26 ~R~Fl~~~l~~~~~~NP~v~i~v~~ 50 (68)
...++...+.+|++++|++.|.+..
T Consensus 12 ~~~~l~~~l~~f~~~~P~v~l~i~~ 36 (197)
T cd08470 12 GERFIAPLVNDFMQRYPKLEVDIEL 36 (197)
T ss_pred HHHHHHHHHHHHHHHCCCeEEEEEe
Confidence 3567889999999999999999975
No 13
>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=69.66 E-value=9.4 Score=22.09 Aligned_cols=27 Identities=15% Similarity=0.130 Sum_probs=22.6
Q ss_pred HHHHHHHhCHHHHHHhCCCCeEEEEec
Q psy15302 25 GVRDFLAQHYVPLKQANPKFPILVREC 51 (68)
Q Consensus 25 G~R~Fl~~~l~~~~~~NP~v~i~v~~~ 51 (68)
....++...+.+|.+++|++.|.+...
T Consensus 10 ~~~~~l~~~i~~~~~~~p~i~i~~~~~ 36 (197)
T cd05466 10 IAAYLLPPLLAAFRQRYPGVELSLVEG 36 (197)
T ss_pred hHHHHhHHHHHHHHHHCCCCEEEEEEC
Confidence 456678888899999999999998764
No 14
>TIGR01159 DRP1 density-regulated protein DRP1. This protein family shows weak but suggestive similarity to translation initiation factor SUI1 and its prokaryotic homologs.
Probab=69.61 E-value=3 Score=27.91 Aligned_cols=25 Identities=16% Similarity=0.279 Sum_probs=22.0
Q ss_pred EEecCCCCCCHHHHHHHHhCHHHHH
Q psy15302 14 IHLCQKGGSSSGVRDFLAQHYVPLK 38 (68)
Q Consensus 14 ~~yc~~~~sS~G~R~Fl~~~l~~~~ 38 (68)
..||+.|++-+-=++||.++.|++-
T Consensus 14 ~EyCEf~~~~~kCk~WL~~n~p~l~ 38 (173)
T TIGR01159 14 PEYCEFSGDLKRCKVWLSENAPDLY 38 (173)
T ss_pred hHHhcCCCCHHHHHHHHHHhChHHH
Confidence 4699999999999999999888654
No 15
>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=67.60 E-value=6.8 Score=26.97 Aligned_cols=26 Identities=12% Similarity=0.208 Sum_probs=22.8
Q ss_pred HHHHHHhCHHHHHHhCCCCeEEEEec
Q psy15302 26 VRDFLAQHYVPLKQANPKFPILVREC 51 (68)
Q Consensus 26 ~R~Fl~~~l~~~~~~NP~v~i~v~~~ 51 (68)
+-.++..-+.+|++++|++.+.+.+.
T Consensus 46 ~~~~lp~~l~~f~~~~P~i~v~i~~~ 71 (287)
T TIGR02136 46 VAPLAEAAAEEFQKIHPGVSVTVQGA 71 (287)
T ss_pred HHHHHHHHHHHHHhhCCCceEEEccC
Confidence 44689999999999999999999774
No 16
>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=66.61 E-value=11 Score=26.44 Aligned_cols=30 Identities=30% Similarity=0.535 Sum_probs=24.5
Q ss_pred CCCCCHHHHHHHHhCHHHHHHhCCCCeEEEEecC
Q psy15302 19 KGGSSSGVRDFLAQHYVPLKQANPKFPILVRECS 52 (68)
Q Consensus 19 ~~~sS~G~R~Fl~~~l~~~~~~NP~v~i~v~~~~ 52 (68)
+|+++.|++||+.. +++.+|.++|.+.+..
T Consensus 21 Ts~~gAa~~D~~~~----~~~r~~~~~~~~~p~~ 50 (319)
T PF02601_consen 21 TSPTGAAIQDFLRT----LKRRNPIVEIILYPAS 50 (319)
T ss_pred eCCchHHHHHHHHH----HHHhCCCcEEEEEecc
Confidence 46678999999864 5569999999998865
No 17
>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=65.38 E-value=8.8 Score=23.47 Aligned_cols=26 Identities=19% Similarity=0.267 Sum_probs=22.3
Q ss_pred HHHHHHhCHHHHHHhCCCCeEEEEec
Q psy15302 26 VRDFLAQHYVPLKQANPKFPILVREC 51 (68)
Q Consensus 26 ~R~Fl~~~l~~~~~~NP~v~i~v~~~ 51 (68)
...++...+..|.+++|++++.+...
T Consensus 11 ~~~~l~~~l~~f~~~~P~i~l~i~~~ 36 (200)
T cd08465 11 ARLVLPALMRQLRAEAPGIDLAVSQA 36 (200)
T ss_pred HHHhhhHHHHHHHHHCCCcEEEEecC
Confidence 35788899999999999999998753
No 18
>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=65.27 E-value=13 Score=22.31 Aligned_cols=26 Identities=8% Similarity=0.193 Sum_probs=22.0
Q ss_pred HHHHHhCHHHHHHhCCCCeEEEEecC
Q psy15302 27 RDFLAQHYVPLKQANPKFPILVRECS 52 (68)
Q Consensus 27 R~Fl~~~l~~~~~~NP~v~i~v~~~~ 52 (68)
..++...+.+|.+++|++.|.+....
T Consensus 12 ~~~l~~~l~~f~~~~P~v~i~~~~~~ 37 (191)
T cd08488 12 VGWLLPRLADFQNRHPFIDLRLSTNN 37 (191)
T ss_pred HHHHHhHHHHHHHHCCCcEEEEEecC
Confidence 35777789999999999999998654
No 19
>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=64.66 E-value=12 Score=22.14 Aligned_cols=26 Identities=8% Similarity=0.153 Sum_probs=22.0
Q ss_pred HHHHHhCHHHHHHhCCCCeEEEEecC
Q psy15302 27 RDFLAQHYVPLKQANPKFPILVRECS 52 (68)
Q Consensus 27 R~Fl~~~l~~~~~~NP~v~i~v~~~~ 52 (68)
..++...+.+|.+++|++.|.+....
T Consensus 12 ~~~l~~~l~~f~~~~P~i~i~i~~~~ 37 (194)
T cd08481 12 TRWLIPRLPDFLARHPDITVNLVTRD 37 (194)
T ss_pred HHHHHhhhhHHHHHCCCceEEEEecc
Confidence 46778889999999999999998643
No 20
>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=64.66 E-value=11 Score=22.47 Aligned_cols=27 Identities=19% Similarity=0.265 Sum_probs=22.7
Q ss_pred HHHHHHHhCHHHHHHhCCCCeEEEEec
Q psy15302 25 GVRDFLAQHYVPLKQANPKFPILVREC 51 (68)
Q Consensus 25 G~R~Fl~~~l~~~~~~NP~v~i~v~~~ 51 (68)
-...++...+.+|.+++|++.+.+...
T Consensus 10 ~~~~~l~~~l~~~~~~~P~i~~~i~~~ 36 (196)
T cd08456 10 LSQSFLPRAIKAFLQRHPDVTISIHTR 36 (196)
T ss_pred HHHhhHHHHHHHHHHHCCCcEEEEEeC
Confidence 345678899999999999999999764
No 21
>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=64.41 E-value=9.8 Score=23.05 Aligned_cols=27 Identities=11% Similarity=0.006 Sum_probs=23.2
Q ss_pred HHHHHHHhCHHHHHHhCCCCeEEEEec
Q psy15302 25 GVRDFLAQHYVPLKQANPKFPILVREC 51 (68)
Q Consensus 25 G~R~Fl~~~l~~~~~~NP~v~i~v~~~ 51 (68)
-...|+...+..|++++|+++|.+...
T Consensus 10 ~~~~~l~~~l~~~~~~~P~v~v~l~~~ 36 (200)
T cd08460 10 FVAAFGPALLAAVAAEAPGVRLRFVPE 36 (200)
T ss_pred HHHHHHHHHHHHHHHHCCCCEEEEecC
Confidence 457888999999999999999999753
No 22
>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=64.38 E-value=14 Score=22.17 Aligned_cols=27 Identities=15% Similarity=0.044 Sum_probs=22.6
Q ss_pred HHHHHHHhCHHHHHHhCCCCeEEEEec
Q psy15302 25 GVRDFLAQHYVPLKQANPKFPILVREC 51 (68)
Q Consensus 25 G~R~Fl~~~l~~~~~~NP~v~i~v~~~ 51 (68)
-...++...+.+|++++|++.+.+...
T Consensus 10 ~~~~~l~~~l~~~~~~~P~v~i~~~~~ 36 (185)
T cd08439 10 YADTILPFLLNRFASVYPRLAIEVVCK 36 (185)
T ss_pred HhHHHHHHHHHHHHHHCCCeEEEEEEC
Confidence 345677889999999999999999764
No 23
>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=64.09 E-value=12 Score=22.18 Aligned_cols=26 Identities=19% Similarity=0.241 Sum_probs=22.2
Q ss_pred HHHHHHhCHHHHHHhCCCCeEEEEec
Q psy15302 26 VRDFLAQHYVPLKQANPKFPILVREC 51 (68)
Q Consensus 26 ~R~Fl~~~l~~~~~~NP~v~i~v~~~ 51 (68)
...++...+.+|++++|++.|.+...
T Consensus 11 ~~~~l~~~l~~~~~~~P~v~i~i~~~ 36 (201)
T cd08435 11 APVLLPPAIARLLARHPRLTVRVVEG 36 (201)
T ss_pred HHHHHHHHHHHHHHHCCCeEEEEEeC
Confidence 45778899999999999999999753
No 24
>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=63.35 E-value=13 Score=22.43 Aligned_cols=27 Identities=11% Similarity=0.188 Sum_probs=22.7
Q ss_pred HHHHHHHhCHHHHHHhCCCCeEEEEec
Q psy15302 25 GVRDFLAQHYVPLKQANPKFPILVREC 51 (68)
Q Consensus 25 G~R~Fl~~~l~~~~~~NP~v~i~v~~~ 51 (68)
....++...+.+|.+++|++.+.+...
T Consensus 10 ~~~~~l~~~i~~f~~~~P~v~i~~~~~ 36 (195)
T cd08482 10 LLMRWLIPRLPAFQAALPDIDLQLSAS 36 (195)
T ss_pred HHHHHHHhhHHHHHHHCCCceEEEEec
Confidence 345788889999999999999998754
No 25
>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=63.35 E-value=11 Score=22.50 Aligned_cols=26 Identities=19% Similarity=0.388 Sum_probs=22.5
Q ss_pred HHHHHHhCHHHHHHhCCCCeEEEEec
Q psy15302 26 VRDFLAQHYVPLKQANPKFPILVREC 51 (68)
Q Consensus 26 ~R~Fl~~~l~~~~~~NP~v~i~v~~~ 51 (68)
...++...+.+|++++|++.|.+...
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 26
>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=63.16 E-value=10 Score=22.94 Aligned_cols=26 Identities=19% Similarity=0.336 Sum_probs=22.0
Q ss_pred HHHHHHhCHHHHHHhCCCCeEEEEec
Q psy15302 26 VRDFLAQHYVPLKQANPKFPILVREC 51 (68)
Q Consensus 26 ~R~Fl~~~l~~~~~~NP~v~i~v~~~ 51 (68)
...++...+.+|++++|++.|.+...
T Consensus 11 ~~~~l~~~l~~~~~~~P~v~i~i~~~ 36 (197)
T cd08452 11 IYEFLPPIVREYRKKFPSVKVELREL 36 (197)
T ss_pred HHhHHHHHHHHHHHHCCCcEEEEEec
Confidence 45778899999999999999998653
No 27
>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=62.73 E-value=14 Score=21.97 Aligned_cols=26 Identities=15% Similarity=0.284 Sum_probs=21.8
Q ss_pred HHHHHHhCHHHHHHhCCCCeEEEEec
Q psy15302 26 VRDFLAQHYVPLKQANPKFPILVREC 51 (68)
Q Consensus 26 ~R~Fl~~~l~~~~~~NP~v~i~v~~~ 51 (68)
...++...+.+|++++|++.+.+...
T Consensus 11 ~~~~l~~~l~~f~~~~P~i~l~i~~~ 36 (189)
T cd08487 11 AVGWLLPRLAEFRQLHPFIELRLRTN 36 (189)
T ss_pred HHHHHhHHHHHHHHHCCCceEEeeec
Confidence 35677778999999999999999763
No 28
>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=62.62 E-value=12 Score=22.03 Aligned_cols=25 Identities=12% Similarity=0.367 Sum_probs=21.7
Q ss_pred HHHHHhCHHHHHHhCCCCeEEEEec
Q psy15302 27 RDFLAQHYVPLKQANPKFPILVREC 51 (68)
Q Consensus 27 R~Fl~~~l~~~~~~NP~v~i~v~~~ 51 (68)
..++...+..|.+++|++.|.+...
T Consensus 12 ~~~l~~~l~~~~~~~p~v~i~i~~~ 36 (197)
T cd08440 12 ATLLPPVLAAFRRRHPGIRVRLRDV 36 (197)
T ss_pred hhHHHHHHHHHHHhCCCcEEEEEeC
Confidence 4677889999999999999999763
No 29
>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=62.28 E-value=17 Score=21.60 Aligned_cols=26 Identities=15% Similarity=0.264 Sum_probs=21.9
Q ss_pred HHHHHHhCHHHHHHhCCCCeEEEEec
Q psy15302 26 VRDFLAQHYVPLKQANPKFPILVREC 51 (68)
Q Consensus 26 ~R~Fl~~~l~~~~~~NP~v~i~v~~~ 51 (68)
...++...+.+|++++|++.|.+...
T Consensus 14 ~~~~l~~~l~~~~~~~P~i~i~~~~~ 39 (202)
T cd08473 14 AQELLAPLLPRFMAAYPQVRLQLEAT 39 (202)
T ss_pred HHHHHHHHHHHHHHHCCCeEEEEEEc
Confidence 34677889999999999999999764
No 30
>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=62.25 E-value=11 Score=22.43 Aligned_cols=26 Identities=12% Similarity=0.256 Sum_probs=22.3
Q ss_pred HHHHHHhCHHHHHHhCCCCeEEEEec
Q psy15302 26 VRDFLAQHYVPLKQANPKFPILVREC 51 (68)
Q Consensus 26 ~R~Fl~~~l~~~~~~NP~v~i~v~~~ 51 (68)
...++...+.+|.+++|++.+.+...
T Consensus 11 ~~~~l~~~l~~~~~~~P~i~l~i~~~ 36 (196)
T cd08450 11 EVQWLPEVLPILREEHPDLDVELSSL 36 (196)
T ss_pred hhhhHHHHHHHHHhhCCCcEEEEEec
Confidence 35778899999999999999999764
No 31
>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=62.17 E-value=13 Score=22.57 Aligned_cols=26 Identities=15% Similarity=0.190 Sum_probs=21.8
Q ss_pred HHHHHHhCHHHHHHhCCCCeEEEEec
Q psy15302 26 VRDFLAQHYVPLKQANPKFPILVREC 51 (68)
Q Consensus 26 ~R~Fl~~~l~~~~~~NP~v~i~v~~~ 51 (68)
...++...+.+|++.+|++.+.+...
T Consensus 11 ~~~~l~~~l~~~~~~~P~v~l~i~~~ 36 (198)
T cd08444 11 ARYALPWVVQAFKEQFPNVHLVLHQG 36 (198)
T ss_pred hhhhhhHHHHHHHHHCCCeEEEEEeC
Confidence 45678889999999999999998764
No 32
>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=61.84 E-value=16 Score=22.36 Aligned_cols=32 Identities=25% Similarity=0.379 Sum_probs=23.5
Q ss_pred cCCCCCCHHHHHHHHhCHHHHHHhCCCCeEEEEec
Q psy15302 17 CQKGGSSSGVRDFLAQHYVPLKQANPKFPILVREC 51 (68)
Q Consensus 17 c~~~~sS~G~R~Fl~~~l~~~~~~NP~v~i~v~~~ 51 (68)
|=+.+||+-+-+||+- .++++.|+.+|.++-.
T Consensus 12 CVn~PsSkeTyeWL~a---al~RKyp~~~f~~~Yi 43 (93)
T PF07315_consen 12 CVNAPSSKETYEWLEA---ALKRKYPDQPFEFTYI 43 (93)
T ss_dssp GSSS--HHHHHHHHHH---HHHHH-TTS-EEEEEE
T ss_pred hcCCCCchhHHHHHHH---HHhCcCCCCceEEEEE
Confidence 6788999999999984 6789999999988654
No 33
>KOG0183|consensus
Probab=61.67 E-value=4.9 Score=28.31 Aligned_cols=18 Identities=44% Similarity=0.685 Sum_probs=15.3
Q ss_pred CCCCCHHHHHHHHhCHHH
Q psy15302 19 KGGSSSGVRDFLAQHYVP 36 (68)
Q Consensus 19 ~~~sS~G~R~Fl~~~l~~ 36 (68)
+|-+|+-+|+||+++|.+
T Consensus 162 iGr~sk~VrEflEK~y~e 179 (249)
T KOG0183|consen 162 IGRSSKTVREFLEKNYKE 179 (249)
T ss_pred cccccHHHHHHHHHhccc
Confidence 677999999999987654
No 34
>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=61.65 E-value=13 Score=21.94 Aligned_cols=25 Identities=12% Similarity=0.194 Sum_probs=21.8
Q ss_pred HHHHHHhCHHHHHHhCCCCeEEEEe
Q psy15302 26 VRDFLAQHYVPLKQANPKFPILVRE 50 (68)
Q Consensus 26 ~R~Fl~~~l~~~~~~NP~v~i~v~~ 50 (68)
...++...+.+|.+++|++.|.+..
T Consensus 11 ~~~~l~~~l~~~~~~~P~i~i~i~~ 35 (197)
T cd08448 11 LYRGLPRILRAFRAEYPGIEVALHE 35 (197)
T ss_pred HHHHHHHHHHHHHHHCCCCeEEEEe
Confidence 4578889999999999999999875
No 35
>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=61.59 E-value=15 Score=21.93 Aligned_cols=27 Identities=15% Similarity=0.097 Sum_probs=22.8
Q ss_pred HHHHHHHhCHHHHHHhCCCCeEEEEec
Q psy15302 25 GVRDFLAQHYVPLKQANPKFPILVREC 51 (68)
Q Consensus 25 G~R~Fl~~~l~~~~~~NP~v~i~v~~~ 51 (68)
....++...+.+|.+++|+++|.+...
T Consensus 10 ~~~~~l~~~l~~~~~~~P~i~l~i~~~ 36 (199)
T cd08416 10 LTVNTVPRIIMGLKLRRPELDIELTLG 36 (199)
T ss_pred HHHhhhHHHHHHHHHhCCCeEEEEEEc
Confidence 346678899999999999999999764
No 36
>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=61.42 E-value=11 Score=22.34 Aligned_cols=25 Identities=20% Similarity=0.232 Sum_probs=21.6
Q ss_pred HHHHHhCHHHHHHhCCCCeEEEEec
Q psy15302 27 RDFLAQHYVPLKQANPKFPILVREC 51 (68)
Q Consensus 27 R~Fl~~~l~~~~~~NP~v~i~v~~~ 51 (68)
..++...+.+|.+++|++.+.+...
T Consensus 12 ~~~l~~~l~~~~~~~P~i~l~i~~~ 36 (198)
T cd08412 12 PYYLPGLLRRFREAYPGVEVRVVEG 36 (198)
T ss_pred hhhhHHHHHHHHHHCCCcEEEEEEC
Confidence 4677899999999999999999754
No 37
>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=61.08 E-value=15 Score=21.81 Aligned_cols=25 Identities=8% Similarity=-0.007 Sum_probs=21.6
Q ss_pred HHHHHHhCHHHHHHhCCCCeEEEEe
Q psy15302 26 VRDFLAQHYVPLKQANPKFPILVRE 50 (68)
Q Consensus 26 ~R~Fl~~~l~~~~~~NP~v~i~v~~ 50 (68)
...++...+.+|++++|++.|.+..
T Consensus 12 ~~~~l~~~l~~~~~~~P~i~l~i~~ 36 (197)
T cd08477 12 GSHVLTPALAEYLARYPDVRVDLVL 36 (197)
T ss_pred HHHHHHHHHHHHHHHCCCcEEEEEe
Confidence 3567788999999999999999975
No 38
>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=61.06 E-value=13 Score=22.31 Aligned_cols=25 Identities=20% Similarity=-0.016 Sum_probs=21.4
Q ss_pred HHHHHhCHHHHHHhCCCCeEEEEec
Q psy15302 27 RDFLAQHYVPLKQANPKFPILVREC 51 (68)
Q Consensus 27 R~Fl~~~l~~~~~~NP~v~i~v~~~ 51 (68)
..++...+..|.+.+|++.|.+...
T Consensus 12 ~~~l~~~l~~~~~~~P~v~i~i~~~ 36 (195)
T cd08431 12 LQPLYPLIAEFYQLNKATRIRLSEE 36 (195)
T ss_pred hHHHHHHHHHHHHHCCCCceEEEEe
Confidence 4577889999999999999999764
No 39
>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=60.77 E-value=13 Score=22.02 Aligned_cols=27 Identities=15% Similarity=0.151 Sum_probs=22.7
Q ss_pred HHHHHHHhCHHHHHHhCCCCeEEEEec
Q psy15302 25 GVRDFLAQHYVPLKQANPKFPILVREC 51 (68)
Q Consensus 25 G~R~Fl~~~l~~~~~~NP~v~i~v~~~ 51 (68)
-...++...+.+|.+++|++.+.+...
T Consensus 10 ~~~~~l~~~l~~~~~~~P~v~i~i~~~ 36 (194)
T cd08436 10 LAAVDLPELLARFHRRHPGVDIRLRQA 36 (194)
T ss_pred HHHHHHHHHHHHHHHHCCCcEEEEecC
Confidence 345678899999999999999999764
No 40
>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=60.77 E-value=13 Score=22.12 Aligned_cols=26 Identities=15% Similarity=0.193 Sum_probs=22.1
Q ss_pred HHHHHHhCHHHHHHhCCCCeEEEEec
Q psy15302 26 VRDFLAQHYVPLKQANPKFPILVREC 51 (68)
Q Consensus 26 ~R~Fl~~~l~~~~~~NP~v~i~v~~~ 51 (68)
...++...+..|++++|++.+.+...
T Consensus 11 ~~~~l~~~l~~~~~~~P~i~l~i~~~ 36 (199)
T cd08426 11 AAELLPSLIARFRQRYPGVFFTVDVA 36 (199)
T ss_pred HHHHHHHHHHHHHHhCCCeEEEEEeC
Confidence 35677889999999999999999764
No 41
>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=60.52 E-value=11 Score=22.61 Aligned_cols=25 Identities=16% Similarity=0.264 Sum_probs=21.6
Q ss_pred HHHHHHhCHHHHHHhCCCCeEEEEe
Q psy15302 26 VRDFLAQHYVPLKQANPKFPILVRE 50 (68)
Q Consensus 26 ~R~Fl~~~l~~~~~~NP~v~i~v~~ 50 (68)
...++...+.+|.+++|++.|.+..
T Consensus 14 ~~~~l~~~l~~f~~~~P~v~i~~~~ 38 (199)
T cd08478 14 VLHLLAPLIAKFRERYPDIELELVS 38 (199)
T ss_pred HHHHHHHHHHHHHHHCCCeEEEEEe
Confidence 4567889999999999999999863
No 42
>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=60.32 E-value=18 Score=21.59 Aligned_cols=25 Identities=12% Similarity=0.229 Sum_probs=21.6
Q ss_pred HHHHHhCHHHHHHhCCCCeEEEEec
Q psy15302 27 RDFLAQHYVPLKQANPKFPILVREC 51 (68)
Q Consensus 27 R~Fl~~~l~~~~~~NP~v~i~v~~~ 51 (68)
..++...+.+|++++|++.|.+...
T Consensus 12 ~~~l~~~l~~~~~~~P~v~l~i~~~ 36 (200)
T cd08464 12 SWLAPPLLAALRAEAPGVRLVFRQV 36 (200)
T ss_pred HHHHHHHHHHHHHHCCCcEEEEecC
Confidence 4677888999999999999999764
No 43
>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=60.13 E-value=13 Score=22.74 Aligned_cols=25 Identities=8% Similarity=0.046 Sum_probs=21.6
Q ss_pred HHHHHhCHHHHHHhCCCCeEEEEec
Q psy15302 27 RDFLAQHYVPLKQANPKFPILVREC 51 (68)
Q Consensus 27 R~Fl~~~l~~~~~~NP~v~i~v~~~ 51 (68)
..++...+.+|++.+|+++|.+.+.
T Consensus 13 ~~~l~~~l~~f~~~~P~v~i~i~~~ 37 (198)
T cd08486 13 YRSLPLLLRAFLTSTPTATVSLTHM 37 (198)
T ss_pred HHHHHHHHHHHHHhCCCeEEEEEEC
Confidence 5677888999999999999998764
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=59.78 E-value=16 Score=21.89 Aligned_cols=26 Identities=19% Similarity=0.160 Sum_probs=22.3
Q ss_pred HHHHHHhCHHHHHHhCCCCeEEEEec
Q psy15302 26 VRDFLAQHYVPLKQANPKFPILVREC 51 (68)
Q Consensus 26 ~R~Fl~~~l~~~~~~NP~v~i~v~~~ 51 (68)
...++..-+.+|.+++|++.|.+...
T Consensus 11 ~~~~l~~~l~~f~~~~P~v~l~~~~~ 36 (200)
T cd08466 11 DLLLLPRLLARLKQLAPNISLRESPS 36 (200)
T ss_pred HHHHHHHHHHHHHHHCCCCEEEEecC
Confidence 35677889999999999999999764
No 45
>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=59.73 E-value=12 Score=22.62 Aligned_cols=27 Identities=19% Similarity=0.381 Sum_probs=23.2
Q ss_pred HHHHHHhCHHHHHHhCCCCeEEEEecC
Q psy15302 26 VRDFLAQHYVPLKQANPKFPILVRECS 52 (68)
Q Consensus 26 ~R~Fl~~~l~~~~~~NP~v~i~v~~~~ 52 (68)
...++...+.+|.+++|++.|.+....
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 367778999999999999999998754
No 46
>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=59.53 E-value=18 Score=21.35 Aligned_cols=28 Identities=7% Similarity=0.185 Sum_probs=22.8
Q ss_pred HHHHHHHhCHHHHHHhCCCCeEEEEecC
Q psy15302 25 GVRDFLAQHYVPLKQANPKFPILVRECS 52 (68)
Q Consensus 25 G~R~Fl~~~l~~~~~~NP~v~i~v~~~~ 52 (68)
....++...+.+|.+++|++.|.+....
T Consensus 10 ~~~~~l~~~l~~~~~~~P~v~i~~~~~~ 37 (194)
T cd08432 10 FAARWLIPRLARFQARHPDIDLRLSTSD 37 (194)
T ss_pred HHHHHHHHHhHHHHHHCCCeEEEEEecC
Confidence 3455778889999999999999997643
No 47
>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=59.38 E-value=16 Score=21.64 Aligned_cols=26 Identities=15% Similarity=0.290 Sum_probs=22.2
Q ss_pred HHHHHHhCHHHHHHhCCCCeEEEEec
Q psy15302 26 VRDFLAQHYVPLKQANPKFPILVREC 51 (68)
Q Consensus 26 ~R~Fl~~~l~~~~~~NP~v~i~v~~~ 51 (68)
...++...+.+|.+++|++.|.+...
T Consensus 11 ~~~~l~~~l~~~~~~~p~i~i~i~~~ 36 (197)
T cd08414 11 LYGLLPRLLRRFRARYPDVELELREM 36 (197)
T ss_pred HHHHHHHHHHHHHHHCCCcEEEEecC
Confidence 45678899999999999999998753
No 48
>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=59.36 E-value=22 Score=23.77 Aligned_cols=40 Identities=20% Similarity=0.397 Sum_probs=34.0
Q ss_pred EEEecCCCCCCHHHHHHHHhCHHHHHHhCCCCeEEEEecC
Q psy15302 13 RIHLCQKGGSSSGVRDFLAQHYVPLKQANPKFPILVRECS 52 (68)
Q Consensus 13 ~~~yc~~~~sS~G~R~Fl~~~l~~~~~~NP~v~i~v~~~~ 52 (68)
.+..||.|||=.+.-.|+-.-+-.+..+.+.+.+.+....
T Consensus 60 lvvl~DvSGSM~~~s~~~l~~~~~l~~~~~~~~~f~F~~~ 99 (222)
T PF05762_consen 60 LVVLCDVSGSMAGYSEFMLAFLYALQRQFRRVRVFVFSTR 99 (222)
T ss_pred EEEEEeCCCChHHHHHHHHHHHHHHHHhCCCEEEEEEeee
Confidence 4567999999999888888888899999999988886643
No 49
>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=58.78 E-value=16 Score=21.99 Aligned_cols=25 Identities=20% Similarity=0.345 Sum_probs=21.9
Q ss_pred HHHHHhCHHHHHHhCCCCeEEEEec
Q psy15302 27 RDFLAQHYVPLKQANPKFPILVREC 51 (68)
Q Consensus 27 R~Fl~~~l~~~~~~NP~v~i~v~~~ 51 (68)
..++...+.+|.+++|++.+.+...
T Consensus 12 ~~~l~~~l~~~~~~~P~i~l~i~~~ 36 (200)
T cd08453 12 YSVLPELVRRFREAYPDVELQLREA 36 (200)
T ss_pred hHHHHHHHHHHHHhCCCceEEEEeC
Confidence 5688899999999999999999763
No 50
>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=58.72 E-value=17 Score=21.69 Aligned_cols=27 Identities=11% Similarity=0.127 Sum_probs=22.6
Q ss_pred HHHHHHHhCHHHHHHhCCCCeEEEEec
Q psy15302 25 GVRDFLAQHYVPLKQANPKFPILVREC 51 (68)
Q Consensus 25 G~R~Fl~~~l~~~~~~NP~v~i~v~~~ 51 (68)
....++...+.+|++++|++.|.+...
T Consensus 11 ~~~~~l~~~l~~f~~~~P~i~i~~~~~ 37 (198)
T cd08479 11 FGRRHIAPALSDFAKRYPELEVQLELT 37 (198)
T ss_pred HHHHHHHHHHHHHHHHCCCeEEEEEec
Confidence 345778899999999999999998753
No 51
>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=58.70 E-value=15 Score=21.89 Aligned_cols=27 Identities=11% Similarity=0.103 Sum_probs=22.9
Q ss_pred HHHHHHHhCHHHHHHhCCCCeEEEEec
Q psy15302 25 GVRDFLAQHYVPLKQANPKFPILVREC 51 (68)
Q Consensus 25 G~R~Fl~~~l~~~~~~NP~v~i~v~~~ 51 (68)
....++...+.+|.+++|++.|.+...
T Consensus 11 ~~~~~l~~~l~~~~~~~P~v~i~i~~~ 37 (197)
T cd08425 11 FTAYLIGPLIDRFHARYPGIALSLREM 37 (197)
T ss_pred hhhhhhHHHHHHHHHHCCCcEEEEEEC
Confidence 456777899999999999999999764
No 52
>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=58.50 E-value=21 Score=21.29 Aligned_cols=25 Identities=12% Similarity=0.089 Sum_probs=21.6
Q ss_pred HHHHHHhCHHHHHHhCCCCeEEEEe
Q psy15302 26 VRDFLAQHYVPLKQANPKFPILVRE 50 (68)
Q Consensus 26 ~R~Fl~~~l~~~~~~NP~v~i~v~~ 50 (68)
...++...+.+|.+++|++.|.+..
T Consensus 12 ~~~~l~~~l~~~~~~~P~i~v~~~~ 36 (202)
T cd08472 12 ARLLLIPALPDFLARYPDIELDLGV 36 (202)
T ss_pred HHHHHHHHHHHHHHHCCCcEEEEEE
Confidence 4567889999999999999999864
No 53
>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=58.00 E-value=7.1 Score=26.14 Aligned_cols=19 Identities=21% Similarity=0.483 Sum_probs=17.0
Q ss_pred HHHHHhCHHHHHHhCCCCe
Q psy15302 27 RDFLAQHYVPLKQANPKFP 45 (68)
Q Consensus 27 R~Fl~~~l~~~~~~NP~v~ 45 (68)
..||++.+..||+.||++.
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 54
>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=58.00 E-value=14 Score=22.12 Aligned_cols=25 Identities=12% Similarity=0.018 Sum_probs=21.5
Q ss_pred HHHHHhCHHHHHHhCCCCeEEEEec
Q psy15302 27 RDFLAQHYVPLKQANPKFPILVREC 51 (68)
Q Consensus 27 R~Fl~~~l~~~~~~NP~v~i~v~~~ 51 (68)
-.++...+.+|.+.+|++.|.+...
T Consensus 12 ~~~l~~~l~~~~~~~P~v~i~~~~~ 36 (198)
T cd08437 12 NYYFPKLAKDLIKTGLMIQIDTYEG 36 (198)
T ss_pred HHHhHHHHHHHHHhCCceEEEEEEc
Confidence 4677899999999999999999753
No 55
>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=57.81 E-value=13 Score=22.01 Aligned_cols=25 Identities=16% Similarity=0.238 Sum_probs=21.5
Q ss_pred HHHHHhCHHHHHHhCCCCeEEEEec
Q psy15302 27 RDFLAQHYVPLKQANPKFPILVREC 51 (68)
Q Consensus 27 R~Fl~~~l~~~~~~NP~v~i~v~~~ 51 (68)
..++...+.+|++++|++.|.+...
T Consensus 12 ~~~l~~~l~~~~~~~p~v~i~i~~~ 36 (197)
T cd08438 12 SLLFAPLLAAFRQRYPNIELELVEY 36 (197)
T ss_pred hhhcHHHHHHHHHHCcCeEEEEEEc
Confidence 4677889999999999999999764
No 56
>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=57.79 E-value=14 Score=21.76 Aligned_cols=25 Identities=4% Similarity=0.198 Sum_probs=21.6
Q ss_pred HHHHHhCHHHHHHhCCCCeEEEEec
Q psy15302 27 RDFLAQHYVPLKQANPKFPILVREC 51 (68)
Q Consensus 27 R~Fl~~~l~~~~~~NP~v~i~v~~~ 51 (68)
..++...+.+|.+++|++++.+...
T Consensus 12 ~~~l~~~l~~~~~~~P~i~i~i~~~ 36 (195)
T cd08434 12 TSLVPDLIRAFRKEYPNVTFELHQG 36 (195)
T ss_pred hhhhHHHHHHHHHhCCCeEEEEecC
Confidence 4677888999999999999999864
No 57
>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=57.76 E-value=17 Score=21.46 Aligned_cols=26 Identities=8% Similarity=0.124 Sum_probs=22.0
Q ss_pred HHHHHHhCHHHHHHhCCCCeEEEEec
Q psy15302 26 VRDFLAQHYVPLKQANPKFPILVREC 51 (68)
Q Consensus 26 ~R~Fl~~~l~~~~~~NP~v~i~v~~~ 51 (68)
...++...+.+|++.+|++.+.+...
T Consensus 11 ~~~~l~~~l~~~~~~~P~~~l~~~~~ 36 (201)
T cd08420 11 GEYLLPRLLARFRKRYPEVRVSLTIG 36 (201)
T ss_pred hhhhhHHHHHHHHHHCCCceEEEEeC
Confidence 45677889999999999999998764
No 58
>PRK14003 potassium-transporting ATPase subunit C; Provisional
Probab=57.41 E-value=16 Score=24.93 Aligned_cols=45 Identities=13% Similarity=0.160 Sum_probs=36.2
Q ss_pred cCCCCCCHHHHHHHHhCHHHHHHhCCCC--eEEEEecCCCCCEEEEE
Q psy15302 17 CQKGGSSSGVRDFLAQHYVPLKQANPKF--PILVRECSGVTPVVWAS 61 (68)
Q Consensus 17 c~~~~sS~G~R~Fl~~~l~~~~~~NP~v--~i~v~~~~~~~P~v~a~ 61 (68)
++-++++.-+.+-+++....++++||.. ..++...+|-+|.|.-.
T Consensus 93 SNl~psnp~l~~~v~~r~~~~~~~~~~pp~DlVTaSgSGLDPhISp~ 139 (194)
T PRK14003 93 SNLAPSNPALIERIKEEANRLQDAGIQPTADLVYTSGSGLDPHISPE 139 (194)
T ss_pred cCCCCCCHHHHHHHHHHHHHHHHcCCCCChhheecccccCCCCCCHH
Confidence 4567889999999999999999999654 66667778889987543
No 59
>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=57.19 E-value=18 Score=21.90 Aligned_cols=25 Identities=12% Similarity=0.085 Sum_probs=21.4
Q ss_pred HHHHHHhCHHHHHHhCCCCeEEEEe
Q psy15302 26 VRDFLAQHYVPLKQANPKFPILVRE 50 (68)
Q Consensus 26 ~R~Fl~~~l~~~~~~NP~v~i~v~~ 50 (68)
...++...+.+|.+++|++.+.+..
T Consensus 12 ~~~~l~~~l~~~~~~~P~i~i~i~~ 36 (198)
T cd08480 12 GTHFLLPLLPAFLARYPEILVDLSL 36 (198)
T ss_pred HhHhhHHHHHHHHHHCCCeEEEEEe
Confidence 3467889999999999999999864
No 60
>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=56.61 E-value=7.9 Score=23.02 Aligned_cols=26 Identities=12% Similarity=0.245 Sum_probs=21.6
Q ss_pred HHHHHHhCHHHHHHhCCCCeEEEEec
Q psy15302 26 VRDFLAQHYVPLKQANPKFPILVREC 51 (68)
Q Consensus 26 ~R~Fl~~~l~~~~~~NP~v~i~v~~~ 51 (68)
...++...+.+|.+++|++.+.+...
T Consensus 11 ~~~~l~~~l~~~~~~~P~i~l~i~~~ 36 (196)
T cd08415 11 ALSLLPRAIARFRARHPDVRISLHTL 36 (196)
T ss_pred cccccHHHHHHHHHHCCCcEEEEEec
Confidence 34677888999999999999998764
No 61
>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=56.26 E-value=19 Score=21.84 Aligned_cols=25 Identities=24% Similarity=0.285 Sum_probs=21.8
Q ss_pred HHHHHhCHHHHHHhCCCCeEEEEec
Q psy15302 27 RDFLAQHYVPLKQANPKFPILVREC 51 (68)
Q Consensus 27 R~Fl~~~l~~~~~~NP~v~i~v~~~ 51 (68)
..++...+.+|.+.+|++.+.+...
T Consensus 13 ~~~l~~~l~~~~~~~P~i~l~i~~~ 37 (203)
T cd08445 13 YGLLPELIRRFRQAAPDVEIELIEM 37 (203)
T ss_pred HhHHHHHHHHHHHHCCCeEEEEEeC
Confidence 5678899999999999999998754
No 62
>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=55.85 E-value=17 Score=21.61 Aligned_cols=24 Identities=25% Similarity=0.429 Sum_probs=20.8
Q ss_pred HHHHhCHHHHHHhCCCCeEEEEec
Q psy15302 28 DFLAQHYVPLKQANPKFPILVREC 51 (68)
Q Consensus 28 ~Fl~~~l~~~~~~NP~v~i~v~~~ 51 (68)
.++...+.+|.+.+|+++|.+...
T Consensus 13 ~~l~~~l~~~~~~~P~i~i~~~~~ 36 (198)
T cd08421 13 EFLPEDLASFLAAHPDVRIDLEER 36 (198)
T ss_pred hhhHHHHHHHHHHCCCceEEEEec
Confidence 567889999999999999999754
No 63
>PRK13996 potassium-transporting ATPase subunit C; Provisional
Probab=55.82 E-value=9.8 Score=26.06 Aligned_cols=44 Identities=14% Similarity=0.276 Sum_probs=33.9
Q ss_pred cCCCCCCHHHHHHHHhCHHHHHHhCCC-----CeEE--EEecCCCCCEEEE
Q psy15302 17 CQKGGSSSGVRDFLAQHYVPLKQANPK-----FPIL--VRECSGVTPVVWA 60 (68)
Q Consensus 17 c~~~~sS~G~R~Fl~~~l~~~~~~NP~-----v~i~--v~~~~~~~P~v~a 60 (68)
++.+++|.-+++-+++....|++.||. ||.. +...+|-+|.|.-
T Consensus 91 SNlgpsnp~L~~~v~~r~~~~~~~~~~v~~~~vP~DlvTaSgSGLDPhISp 141 (197)
T PRK13996 91 SNLSPASKEYEALVQERVEKIRANHPEQDEKPIPVDLVTCSGSGLDPHISV 141 (197)
T ss_pred cCCCCCCHHHHHHHHHHHHHHHHhCCCCCCCCCCHHHHhccccCCCCCCCH
Confidence 567889999999999999999999995 4433 3445677887653
No 64
>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=55.42 E-value=24 Score=21.06 Aligned_cols=25 Identities=12% Similarity=0.041 Sum_probs=21.6
Q ss_pred HHHHHHhCHHHHHHhCCCCeEEEEe
Q psy15302 26 VRDFLAQHYVPLKQANPKFPILVRE 50 (68)
Q Consensus 26 ~R~Fl~~~l~~~~~~NP~v~i~v~~ 50 (68)
...++...+.+|.+.+|++.|.+..
T Consensus 12 ~~~~l~~~l~~~~~~~P~v~i~i~~ 36 (201)
T cd08471 12 GRLHVLPIITDFLDAYPEVSVRLLL 36 (201)
T ss_pred HHHHHHHHHHHHHHHCCCcEEEEEE
Confidence 3567789999999999999999975
No 65
>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=55.23 E-value=15 Score=21.76 Aligned_cols=24 Identities=13% Similarity=0.128 Sum_probs=20.0
Q ss_pred HHHHHhCHHHHHHhCCCCeEEEEe
Q psy15302 27 RDFLAQHYVPLKQANPKFPILVRE 50 (68)
Q Consensus 27 R~Fl~~~l~~~~~~NP~v~i~v~~ 50 (68)
..++...+.+|++++|++.|.+..
T Consensus 11 ~~~l~~~l~~~~~~~P~v~i~~~~ 34 (197)
T cd08476 11 GGLLLPVLAAFMQRYPEIELDLDF 34 (197)
T ss_pred HHHHHHHHHHHHHHCCCeEEEEEe
Confidence 356667899999999999999854
No 66
>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=55.06 E-value=19 Score=21.28 Aligned_cols=25 Identities=20% Similarity=0.420 Sum_probs=21.5
Q ss_pred HHHHHhCHHHHHHhCCCCeEEEEec
Q psy15302 27 RDFLAQHYVPLKQANPKFPILVREC 51 (68)
Q Consensus 27 R~Fl~~~l~~~~~~NP~v~i~v~~~ 51 (68)
-.++...+.+|.+++|++.|.+...
T Consensus 12 ~~~l~~~l~~~~~~~P~i~i~~~~~ 36 (200)
T cd08423 12 AALLPPALAALRARHPGLEVRLREA 36 (200)
T ss_pred HHhhhHHHHHHHHhCCCCeEEEEeC
Confidence 4577889999999999999999764
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=54.60 E-value=25 Score=21.00 Aligned_cols=24 Identities=13% Similarity=0.207 Sum_probs=20.4
Q ss_pred HHHHhCHHHHHHhCCCCeEEEEec
Q psy15302 28 DFLAQHYVPLKQANPKFPILVREC 51 (68)
Q Consensus 28 ~Fl~~~l~~~~~~NP~v~i~v~~~ 51 (68)
.++...+.+|.+++|++.|.+...
T Consensus 13 ~~~~~~l~~~~~~~P~i~i~i~~~ 36 (198)
T cd08441 13 DWLMPVLDQFRERWPDVELDLSSG 36 (198)
T ss_pred hhhHHHHHHHHHhCCCeEEEEEeC
Confidence 467788899999999999998764
No 68
>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=54.54 E-value=25 Score=21.05 Aligned_cols=26 Identities=15% Similarity=0.091 Sum_probs=22.0
Q ss_pred HHHHHHhCHHHHHHhCCCCeEEEEec
Q psy15302 26 VRDFLAQHYVPLKQANPKFPILVREC 51 (68)
Q Consensus 26 ~R~Fl~~~l~~~~~~NP~v~i~v~~~ 51 (68)
...++...+.+|++++|++.|.+...
T Consensus 14 ~~~~l~~~l~~~~~~~P~v~i~~~~~ 39 (202)
T cd08474 14 ARLLLAPLLARFLARYPDIRLELVVD 39 (202)
T ss_pred HHHHHHHHHHHHHHHCCCeEEEEEec
Confidence 35677889999999999999999753
No 69
>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=54.39 E-value=22 Score=21.07 Aligned_cols=25 Identities=8% Similarity=0.198 Sum_probs=21.3
Q ss_pred HHHHHHhCHHHHHHhCCCCeEEEEe
Q psy15302 26 VRDFLAQHYVPLKQANPKFPILVRE 50 (68)
Q Consensus 26 ~R~Fl~~~l~~~~~~NP~v~i~v~~ 50 (68)
...++...+.+|.+++|++.+.+..
T Consensus 11 ~~~~l~~~l~~~~~~~P~i~l~~~~ 35 (190)
T cd08483 11 ASNWLMPRLGSFWAKHPEIELSLLP 35 (190)
T ss_pred HHhhHHhhHHHHHHHCCCceEEEEe
Confidence 4567788899999999999999974
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=54.20 E-value=16 Score=21.48 Aligned_cols=24 Identities=17% Similarity=0.092 Sum_probs=21.0
Q ss_pred HHHHHhCHHHHHHhCCCCeEEEEe
Q psy15302 27 RDFLAQHYVPLKQANPKFPILVRE 50 (68)
Q Consensus 27 R~Fl~~~l~~~~~~NP~v~i~v~~ 50 (68)
..++...+.+|++++|++.|.+..
T Consensus 13 ~~~l~~~l~~~~~~~P~v~i~i~~ 36 (197)
T cd08422 13 RLHLAPLLAEFLARYPDVRLELVL 36 (197)
T ss_pred HHHHHHHHHHHHHhCCceEEEEec
Confidence 466788999999999999999975
No 71
>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=54.18 E-value=30 Score=20.74 Aligned_cols=26 Identities=19% Similarity=0.248 Sum_probs=22.0
Q ss_pred HHHHHhCHHHHHHhCCCCeEEEEecC
Q psy15302 27 RDFLAQHYVPLKQANPKFPILVRECS 52 (68)
Q Consensus 27 R~Fl~~~l~~~~~~NP~v~i~v~~~~ 52 (68)
..++..-+.+|++++|++.+.+....
T Consensus 12 ~~~l~~~l~~~~~~~P~v~v~i~~~~ 37 (201)
T cd08459 12 MYFLPRLLAALREVAPGVRIETVRLP 37 (201)
T ss_pred HHHHHHHHHHHHHHCCCCeEEEEecC
Confidence 45778899999999999999997643
No 72
>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=52.95 E-value=22 Score=21.21 Aligned_cols=24 Identities=33% Similarity=0.499 Sum_probs=20.6
Q ss_pred HHHHHhCHHHHHHhCCCCeEEEEe
Q psy15302 27 RDFLAQHYVPLKQANPKFPILVRE 50 (68)
Q Consensus 27 R~Fl~~~l~~~~~~NP~v~i~v~~ 50 (68)
..++..-+.+|++++|++.|.+..
T Consensus 13 ~~~l~~~l~~~~~~~P~i~i~i~~ 36 (200)
T cd08411 13 PYLLPRLLPALRQAYPKLRLYLRE 36 (200)
T ss_pred hhhhHHHHHHHHHHCCCcEEEEEe
Confidence 347788899999999999999875
No 73
>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=52.86 E-value=22 Score=21.19 Aligned_cols=25 Identities=12% Similarity=0.196 Sum_probs=21.2
Q ss_pred HHHHHhCHHHHHHhCCCCeEEEEec
Q psy15302 27 RDFLAQHYVPLKQANPKFPILVREC 51 (68)
Q Consensus 27 R~Fl~~~l~~~~~~NP~v~i~v~~~ 51 (68)
-.++...+.+|++++|++.+.+...
T Consensus 13 ~~~l~~~i~~~~~~~P~v~l~i~~~ 37 (198)
T cd08446 13 LDTVPRLLRAFLTARPDVTVSLHNM 37 (198)
T ss_pred HHHHHHHHHHHHHHCCCeEEEEeeC
Confidence 4577888999999999999998763
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=52.33 E-value=23 Score=20.92 Aligned_cols=25 Identities=12% Similarity=0.183 Sum_probs=21.7
Q ss_pred HHHHHhCHHHHHHhCCCCeEEEEec
Q psy15302 27 RDFLAQHYVPLKQANPKFPILVREC 51 (68)
Q Consensus 27 R~Fl~~~l~~~~~~NP~v~i~v~~~ 51 (68)
..++..-+..|.+++|++.+.+...
T Consensus 11 ~~~l~~~l~~~~~~~P~i~l~i~~~ 35 (197)
T cd08419 11 KYFAPRLLGAFCRRHPGVEVSLRVG 35 (197)
T ss_pred HhHhhHHHHHHHHHCCCceEEEEEC
Confidence 4678899999999999999999763
No 75
>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=52.24 E-value=20 Score=21.66 Aligned_cols=26 Identities=8% Similarity=0.220 Sum_probs=22.1
Q ss_pred HHHHHHhCHHHHHHhCCCCeEEEEec
Q psy15302 26 VRDFLAQHYVPLKQANPKFPILVREC 51 (68)
Q Consensus 26 ~R~Fl~~~l~~~~~~NP~v~i~v~~~ 51 (68)
...++...+.+|++++|++.|.+...
T Consensus 11 ~~~~l~~~l~~f~~~~P~v~i~~~~~ 36 (196)
T cd08458 11 ALSFMSGVIQTFIADRPDVSVYLDTV 36 (196)
T ss_pred hhhhhHHHHHHHHHHCCCcEEEEecc
Confidence 45778889999999999999998764
No 76
>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=52.03 E-value=19 Score=21.26 Aligned_cols=25 Identities=12% Similarity=0.065 Sum_probs=21.2
Q ss_pred HHHHHhCHHHHHHhCCCCeEEEEec
Q psy15302 27 RDFLAQHYVPLKQANPKFPILVREC 51 (68)
Q Consensus 27 R~Fl~~~l~~~~~~NP~v~i~v~~~ 51 (68)
..++...+.+|.+++|++.+.+...
T Consensus 12 ~~~l~~~l~~~~~~~P~i~l~i~~~ 36 (193)
T cd08442 12 AVRLPPLLAAYHARYPKVDLSLSTG 36 (193)
T ss_pred hhhhHHHHHHHHHHCCCceEEEEeC
Confidence 3567888999999999999999864
No 77
>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=51.94 E-value=19 Score=21.39 Aligned_cols=24 Identities=17% Similarity=0.180 Sum_probs=20.8
Q ss_pred HHHHHhCHHHHHHhCCCCeEEEEe
Q psy15302 27 RDFLAQHYVPLKQANPKFPILVRE 50 (68)
Q Consensus 27 R~Fl~~~l~~~~~~NP~v~i~v~~ 50 (68)
..++...+.+|.+++|++.|.+..
T Consensus 12 ~~~l~~~l~~~~~~~P~i~i~~~~ 35 (197)
T cd08449 12 WGGLGPALRRFKRQYPNVTVRFHE 35 (197)
T ss_pred hhhHHHHHHHHHHHCCCeEEEEEE
Confidence 467788999999999999999875
No 78
>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=51.89 E-value=22 Score=21.60 Aligned_cols=26 Identities=12% Similarity=0.139 Sum_probs=22.0
Q ss_pred HHHHHHhCHHHHHHhCCCCeEEEEec
Q psy15302 26 VRDFLAQHYVPLKQANPKFPILVREC 51 (68)
Q Consensus 26 ~R~Fl~~~l~~~~~~NP~v~i~v~~~ 51 (68)
...++..-+.+|++++|++.|.+...
T Consensus 11 ~~~~l~~~l~~~~~~~P~i~l~~~~~ 36 (200)
T cd08467 11 EVALLPRLAPRLRERAPGLDLRLCPI 36 (200)
T ss_pred HHHHHHHHHHHHHhhCCCCEEEEecC
Confidence 45677888899999999999999764
No 79
>PTZ00062 glutaredoxin; Provisional
Probab=51.66 E-value=45 Score=22.57 Aligned_cols=37 Identities=14% Similarity=0.055 Sum_probs=27.5
Q ss_pred EEEEecCCCCCCHHHHHHHHhCHHHHHHhCCCCeEEEEecC
Q psy15302 12 LRIHLCQKGGSSSGVRDFLAQHYVPLKQANPKFPILVRECS 52 (68)
Q Consensus 12 l~~~yc~~~~sS~G~R~Fl~~~l~~~~~~NP~v~i~v~~~~ 52 (68)
|-+...+|.+.++- |..-++++++++|++.|....+.
T Consensus 21 vl~f~a~w~~~C~~----m~~vl~~l~~~~~~~~F~~V~~d 57 (204)
T PTZ00062 21 VLYVKSSKEPEYEQ----LMDVCNALVEDFPSLEFYVVNLA 57 (204)
T ss_pred EEEEeCCCCcchHH----HHHHHHHHHHHCCCcEEEEEccc
Confidence 33444788888884 45567789999999999987654
No 80
>PRK13997 potassium-transporting ATPase subunit C; Provisional
Probab=51.51 E-value=13 Score=25.43 Aligned_cols=44 Identities=20% Similarity=0.272 Sum_probs=34.1
Q ss_pred cCCCCCCHHHHHHHHhCHHHHHHhCCC-----CeEE--EEecCCCCCEEEE
Q psy15302 17 CQKGGSSSGVRDFLAQHYVPLKQANPK-----FPIL--VRECSGVTPVVWA 60 (68)
Q Consensus 17 c~~~~sS~G~R~Fl~~~l~~~~~~NP~-----v~i~--v~~~~~~~P~v~a 60 (68)
++-|+++.-+.+-+++....+++.||. ||.. +...+|-+|.|.-
T Consensus 87 SNl~psnp~l~~~v~~r~~~~~~~~~~~~~~~vP~DlVTaSgSGLDPhISp 137 (193)
T PRK13997 87 NNYAPSNPDLEKRVEKSIEEWKKQNPSVPVTEVPIDLVTNSGSGLDPDISP 137 (193)
T ss_pred cCCCCCCHHHHHHHHHHHHHHHHhCCCCCCCCCCHHHHhccccCCCCCCCH
Confidence 567889999999999999999999984 4433 3445677887753
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=50.85 E-value=25 Score=20.88 Aligned_cols=26 Identities=23% Similarity=0.413 Sum_probs=21.9
Q ss_pred HHHHHHhCHHHHHHhCCCCeEEEEec
Q psy15302 26 VRDFLAQHYVPLKQANPKFPILVREC 51 (68)
Q Consensus 26 ~R~Fl~~~l~~~~~~NP~v~i~v~~~ 51 (68)
...++...+.+|.+++|++.+.+...
T Consensus 11 ~~~~l~~~l~~~~~~~P~i~v~~~~~ 36 (198)
T cd08447 11 AYSFLPRLLAAARAALPDVDLVLREM 36 (198)
T ss_pred HHHHHHHHHHHHHHHCCCeEEEEEeC
Confidence 35677899999999999999998653
No 82
>COG1653 UgpB ABC-type sugar transport system, periplasmic component [Carbohydrate transport and metabolism]
Probab=50.35 E-value=53 Score=22.54 Aligned_cols=26 Identities=19% Similarity=0.281 Sum_probs=23.4
Q ss_pred HHHHHhCHHHHHHhCCCCeEEEEecC
Q psy15302 27 RDFLAQHYVPLKQANPKFPILVRECS 52 (68)
Q Consensus 27 R~Fl~~~l~~~~~~NP~v~i~v~~~~ 52 (68)
.++++....+|.++||+|+|.+....
T Consensus 45 ~~~~~~~i~~f~~~~p~ikv~~~~~~ 70 (433)
T COG1653 45 ADALEELIKEFEKENPGIKVKVVNVP 70 (433)
T ss_pred hHHHHHHHHHHHHhCCCeEEEEEecC
Confidence 78899999999999999999987754
No 83
>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=50.33 E-value=18 Score=22.01 Aligned_cols=26 Identities=15% Similarity=0.115 Sum_probs=21.7
Q ss_pred HHHHHHhCHHHHHHhCCCCeEEEEec
Q psy15302 26 VRDFLAQHYVPLKQANPKFPILVREC 51 (68)
Q Consensus 26 ~R~Fl~~~l~~~~~~NP~v~i~v~~~ 51 (68)
...++...+.+|.+++|++.+.+...
T Consensus 12 ~~~~l~~~l~~~~~~~P~i~l~~~~~ 37 (198)
T cd08485 12 VLHTLPLLLRQLLSVAPSATVSLTQM 37 (198)
T ss_pred hhHHHHHHHHHHHHhCCCcEEEEEEC
Confidence 34577888999999999999999763
No 84
>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=50.18 E-value=27 Score=21.49 Aligned_cols=26 Identities=15% Similarity=0.230 Sum_probs=22.1
Q ss_pred HHHHHhCHHHHHHhCCCCeEEEEecC
Q psy15302 27 RDFLAQHYVPLKQANPKFPILVRECS 52 (68)
Q Consensus 27 R~Fl~~~l~~~~~~NP~v~i~v~~~~ 52 (68)
..++...+.+|.+++|++.+.+....
T Consensus 12 ~~~l~~~l~~f~~~~P~v~l~i~~~~ 37 (221)
T cd08469 12 AVLLPALVRRLETEAPGIDLRIRPVT 37 (221)
T ss_pred HHHHHHHHHHHHHHCCCcEEEEeeCC
Confidence 46788899999999999999997643
No 85
>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=49.97 E-value=24 Score=20.86 Aligned_cols=25 Identities=12% Similarity=0.325 Sum_probs=21.5
Q ss_pred HHHHHhCHHHHHHhCCCCeEEEEec
Q psy15302 27 RDFLAQHYVPLKQANPKFPILVREC 51 (68)
Q Consensus 27 R~Fl~~~l~~~~~~NP~v~i~v~~~ 51 (68)
..++...+.+|.+.+|++.+.+...
T Consensus 12 ~~~l~~~l~~~~~~~P~i~l~~~~~ 36 (195)
T cd08427 12 TGLLPRALARLRRRHPDLEVHIVPG 36 (195)
T ss_pred HHHhHHHHHHHHHHCCCceEEEEeC
Confidence 5677889999999999999998753
No 86
>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=49.85 E-value=49 Score=19.06 Aligned_cols=37 Identities=11% Similarity=0.055 Sum_probs=29.8
Q ss_pred EEEEEecCCCCCCHHHHHHHHhCHHHHHHhCCCCeEEEEec
Q psy15302 11 ELRIHLCQKGGSSSGVRDFLAQHYVPLKQANPKFPILVREC 51 (68)
Q Consensus 11 ~l~~~yc~~~~sS~G~R~Fl~~~l~~~~~~NP~v~i~v~~~ 51 (68)
+|.+.+.++.+..+-++.++ .++++.+|.+.+.+...
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 47777878888888887776 67888999999988764
No 87
>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=49.80 E-value=28 Score=25.91 Aligned_cols=30 Identities=17% Similarity=0.368 Sum_probs=24.5
Q ss_pred CCCCCHHHHHHHHhCHHHHHHhCCCCeEEEEecC
Q psy15302 19 KGGSSSGVRDFLAQHYVPLKQANPKFPILVRECS 52 (68)
Q Consensus 19 ~~~sS~G~R~Fl~~~l~~~~~~NP~v~i~v~~~~ 52 (68)
+|+++.+++||+. .+++.+|.++|.+.+..
T Consensus 136 ts~~~aa~~D~~~----~~~~r~p~~~~~~~~~~ 165 (432)
T TIGR00237 136 TSQTGAALADILH----ILKRRDPSLKVVIYPTL 165 (432)
T ss_pred eCCccHHHHHHHH----HHHhhCCCceEEEeccc
Confidence 5778999999975 46778899999988754
No 88
>PRK00286 xseA exodeoxyribonuclease VII large subunit; Reviewed
Probab=49.43 E-value=28 Score=25.55 Aligned_cols=30 Identities=17% Similarity=0.365 Sum_probs=24.1
Q ss_pred CCCCCHHHHHHHHhCHHHHHHhCCCCeEEEEecC
Q psy15302 19 KGGSSSGVRDFLAQHYVPLKQANPKFPILVRECS 52 (68)
Q Consensus 19 ~~~sS~G~R~Fl~~~l~~~~~~NP~v~i~v~~~~ 52 (68)
+|+++.|++||+.. +++.+|.++|.+.+..
T Consensus 142 Ts~~gAa~~D~~~~----~~~r~p~~~~~~~~~~ 171 (438)
T PRK00286 142 TSPTGAAIRDILTV----LRRRFPLVEVIIYPTL 171 (438)
T ss_pred eCCccHHHHHHHHH----HHhcCCCCeEEEecCc
Confidence 56778999999874 5577899999998764
No 89
>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=49.24 E-value=43 Score=19.94 Aligned_cols=34 Identities=6% Similarity=-0.139 Sum_probs=24.3
Q ss_pred EEEEEecCCCCCCHHHHHHHHhCHHHHHHhCCCCeEEE
Q psy15302 11 ELRIHLCQKGGSSSGVRDFLAQHYVPLKQANPKFPILV 48 (68)
Q Consensus 11 ~l~~~yc~~~~sS~G~R~Fl~~~l~~~~~~NP~v~i~v 48 (68)
-|...|.+|.+.++-+...+ .++++++|++.|.-
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 46677889999898776554 45666778877654
No 90
>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=48.92 E-value=28 Score=20.68 Aligned_cols=26 Identities=15% Similarity=0.110 Sum_probs=21.9
Q ss_pred HHHHHHhCHHHHHHhCCCCeEEEEec
Q psy15302 26 VRDFLAQHYVPLKQANPKFPILVREC 51 (68)
Q Consensus 26 ~R~Fl~~~l~~~~~~NP~v~i~v~~~ 51 (68)
...++...+.+|.+++|++.|.+...
T Consensus 11 ~~~~~~~~i~~~~~~~P~i~l~~~~~ 36 (200)
T cd08417 11 EALLLPPLLARLRQEAPGVRLRFVPL 36 (200)
T ss_pred HHHHHHHHHHHHHhhCCCeEEEeccC
Confidence 35677888999999999999999754
No 91
>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=48.86 E-value=19 Score=21.48 Aligned_cols=25 Identities=8% Similarity=0.108 Sum_probs=20.7
Q ss_pred HHHHHhCHHHHHHhCCCCeEEEEec
Q psy15302 27 RDFLAQHYVPLKQANPKFPILVREC 51 (68)
Q Consensus 27 R~Fl~~~l~~~~~~NP~v~i~v~~~ 51 (68)
..++...+..|.+++|++.|.+...
T Consensus 12 ~~~l~~~l~~~~~~~P~i~i~~~~~ 36 (198)
T cd08433 12 SVLAVPLLRAVRRRYPGIRLRIVEG 36 (198)
T ss_pred hhcchHHHHHHHHHCCCcEEEEEec
Confidence 4566788899999999999999763
No 92
>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=48.43 E-value=27 Score=20.70 Aligned_cols=25 Identities=16% Similarity=0.184 Sum_probs=21.3
Q ss_pred HHHHHHhCHHHHHHhCCCCeEEEEe
Q psy15302 26 VRDFLAQHYVPLKQANPKFPILVRE 50 (68)
Q Consensus 26 ~R~Fl~~~l~~~~~~NP~v~i~v~~ 50 (68)
...++...+..|++++|+++|.+..
T Consensus 12 ~~~~l~~~l~~~~~~~P~v~i~i~~ 36 (199)
T cd08475 12 GRLCVAPLLLELARRHPELELELSF 36 (199)
T ss_pred HHhhHHHHHHHHHHHCCCeEEEEEe
Confidence 3567788899999999999999964
No 93
>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=47.96 E-value=31 Score=20.81 Aligned_cols=26 Identities=8% Similarity=0.042 Sum_probs=22.2
Q ss_pred HHHHHHhCHHHHHHhCCCCeEEEEec
Q psy15302 26 VRDFLAQHYVPLKQANPKFPILVREC 51 (68)
Q Consensus 26 ~R~Fl~~~l~~~~~~NP~v~i~v~~~ 51 (68)
...++..-+.+|++.+|++.|.+...
T Consensus 11 ~~~~l~~~i~~~~~~~P~i~l~i~~~ 36 (200)
T cd08462 11 ITVLLPPVIERVAREAPGVRFELLPP 36 (200)
T ss_pred HHHHHHHHHHHHHHHCCCCEEEEecC
Confidence 45778889999999999999999763
No 94
>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=47.69 E-value=17 Score=21.61 Aligned_cols=25 Identities=16% Similarity=0.284 Sum_probs=21.1
Q ss_pred HHHHHhCHHHHHHhCCCCeEEEEec
Q psy15302 27 RDFLAQHYVPLKQANPKFPILVREC 51 (68)
Q Consensus 27 R~Fl~~~l~~~~~~NP~v~i~v~~~ 51 (68)
..++...+.+|.+.+|++.|.+...
T Consensus 12 ~~~l~~~l~~~~~~~P~v~l~~~~~ 36 (199)
T cd08430 12 YSFLPPILERFRAQHPQVEIKLHTG 36 (199)
T ss_pred eeeccHHHHHHHHHCCCceEEEEeC
Confidence 3567788999999999999999764
No 95
>PF06244 DUF1014: Protein of unknown function (DUF1014); InterPro: IPR010422 This family consists of several hypothetical eukaryotic proteins of unknown function.
Probab=47.61 E-value=17 Score=23.12 Aligned_cols=20 Identities=25% Similarity=0.428 Sum_probs=16.9
Q ss_pred HHHHHHhCHHHHHHhCCCCe
Q psy15302 26 VRDFLAQHYVPLKQANPKFP 45 (68)
Q Consensus 26 ~R~Fl~~~l~~~~~~NP~v~ 45 (68)
-..|-+..||.+++.||.+-
T Consensus 80 y~afeE~~Lp~lK~E~PgLr 99 (122)
T PF06244_consen 80 YKAFEERRLPELKEENPGLR 99 (122)
T ss_pred HHHHHHHHhHHHHhhCCCch
Confidence 35678899999999999874
No 96
>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=47.49 E-value=34 Score=20.67 Aligned_cols=25 Identities=8% Similarity=0.163 Sum_probs=21.5
Q ss_pred HHHHHhCHHHHHHhCCCCeEEEEec
Q psy15302 27 RDFLAQHYVPLKQANPKFPILVREC 51 (68)
Q Consensus 27 R~Fl~~~l~~~~~~NP~v~i~v~~~ 51 (68)
..++...+.+|++.+|++.|.+...
T Consensus 12 ~~~l~~~l~~~~~~~P~v~i~~~~~ 36 (202)
T cd08468 12 LAVMPRLMARLEELAPSVRLNLVHA 36 (202)
T ss_pred HHHhHHHHHHHHhhCCCCEEEEEEC
Confidence 5677889999999999999999864
No 97
>PLN02757 sirohydrochlorine ferrochelatase
Probab=47.38 E-value=14 Score=23.81 Aligned_cols=32 Identities=13% Similarity=0.190 Sum_probs=22.9
Q ss_pred HHHHHhCHHHHHHhCCCCeEEEEecCCCCCEE
Q psy15302 27 RDFLAQHYVPLKQANPKFPILVRECSGVTPVV 58 (68)
Q Consensus 27 R~Fl~~~l~~~~~~NP~v~i~v~~~~~~~P~v 58 (68)
++=|...+.++++++|+++|.+-+.-|.||.+
T Consensus 89 ~~DIp~~v~~~~~~~p~~~i~~~~pLG~~p~l 120 (154)
T PLN02757 89 QEDIPALTAEAAKEHPGVKYLVTAPIGLHELM 120 (154)
T ss_pred HhHHHHHHHHHHHHCCCcEEEECCCCCCCHHH
Confidence 44455566677888888888887777777754
No 98
>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=47.25 E-value=11 Score=25.67 Aligned_cols=44 Identities=16% Similarity=0.194 Sum_probs=33.8
Q ss_pred cCCCCCCHHHHHHHHhCHHHHHHhCCC----CeEEE--EecCCCCCEEEE
Q psy15302 17 CQKGGSSSGVRDFLAQHYVPLKQANPK----FPILV--RECSGVTPVVWA 60 (68)
Q Consensus 17 c~~~~sS~G~R~Fl~~~l~~~~~~NP~----v~i~v--~~~~~~~P~v~a 60 (68)
++-++|+.-+.+-+++....|++.||. ||... ...+|-+|.|.-
T Consensus 84 SNl~psnp~l~~~v~~r~~~~~~~~~~~~~~vP~DlvTaSgSGLDPhISp 133 (187)
T TIGR00681 84 SNLAPSNPDLLSRIAARVEAQRLENLDAAVQVPVDLVTSSGSGLDPHISP 133 (187)
T ss_pred cCCCCCCHHHHHHHHHHHHHHHHhCCCCCCCCCHHHHhcccccCCCCCCH
Confidence 567889999999999999999999984 55443 445577887653
No 99
>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=46.85 E-value=36 Score=20.22 Aligned_cols=26 Identities=12% Similarity=0.218 Sum_probs=21.9
Q ss_pred HHHHHHhCHHHHHHhCCCCeEEEEec
Q psy15302 26 VRDFLAQHYVPLKQANPKFPILVREC 51 (68)
Q Consensus 26 ~R~Fl~~~l~~~~~~NP~v~i~v~~~ 51 (68)
...++...+.+|.+++|++.+.+...
T Consensus 11 ~~~~l~~~l~~f~~~~P~i~l~~~~~ 36 (189)
T cd08484 11 AVGWLLPRLAEFRQLHPFIDLRLSTN 36 (189)
T ss_pred HHHHHHhhhHHHHHHCCCceEEEecc
Confidence 35677888999999999999999754
No 100
>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=46.58 E-value=32 Score=21.15 Aligned_cols=24 Identities=13% Similarity=0.238 Sum_probs=21.1
Q ss_pred HHHHHhCHHHHHHhCCCCeEEEEe
Q psy15302 27 RDFLAQHYVPLKQANPKFPILVRE 50 (68)
Q Consensus 27 R~Fl~~~l~~~~~~NP~v~i~v~~ 50 (68)
-.++...+.+|++.+|++.+.+.+
T Consensus 12 ~~~~~~~l~~~~~~~P~~~v~~~~ 35 (203)
T cd08463 12 ALFLPELVARFRREAPGARLEIHP 35 (203)
T ss_pred HHHhHHHHHHHHHHCCCCEEEEEe
Confidence 457788999999999999999985
No 101
>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=46.27 E-value=21 Score=21.15 Aligned_cols=23 Identities=13% Similarity=0.299 Sum_probs=19.9
Q ss_pred HHHhCHHHHHHhCCCCeEEEEec
Q psy15302 29 FLAQHYVPLKQANPKFPILVREC 51 (68)
Q Consensus 29 Fl~~~l~~~~~~NP~v~i~v~~~ 51 (68)
++...+.+|++.+|++.+.+...
T Consensus 15 ~l~~~l~~~~~~~P~i~l~i~~~ 37 (199)
T cd08451 15 LVPGLIRRFREAYPDVELTLEEA 37 (199)
T ss_pred ccHHHHHHHHHHCCCcEEEEecC
Confidence 66788999999999999999754
No 102
>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=46.16 E-value=55 Score=21.55 Aligned_cols=33 Identities=9% Similarity=0.026 Sum_probs=27.7
Q ss_pred HHHhCHHHHHHhCCCCeEEEEecCCCCCEEEEE
Q psy15302 29 FLAQHYVPLKQANPKFPILVRECSGVTPVVWAS 61 (68)
Q Consensus 29 Fl~~~l~~~~~~NP~v~i~v~~~~~~~P~v~a~ 61 (68)
++..-+|++++++|+-++.+.-.....|.+...
T Consensus 48 ~~~~~iP~l~~~yPn~~~~L~i~~~~~P~v~i~ 80 (202)
T smart00329 48 CFGTLVPEVAEQYPDSTLQLEISVLSPPRVTLQ 80 (202)
T ss_pred HHHHHHHHHHHHCCCCcEEEEEEeCCCCEEEEe
Confidence 778889999999999888887777779988764
No 103
>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=45.59 E-value=22 Score=21.54 Aligned_cols=26 Identities=15% Similarity=0.273 Sum_probs=21.3
Q ss_pred HHHHHHhCHHHHHHhCCCCeEEEEec
Q psy15302 26 VRDFLAQHYVPLKQANPKFPILVREC 51 (68)
Q Consensus 26 ~R~Fl~~~l~~~~~~NP~v~i~v~~~ 51 (68)
...++...+.+|.+++|++++.+...
T Consensus 11 ~~~~l~~~l~~~~~~~P~i~v~~~~~ 36 (198)
T cd08413 11 ARYVLPPVIAAFRKRYPKVKLSLHQG 36 (198)
T ss_pred hhhhccHHHHHHHHhCCceEEEEEeC
Confidence 35577888899999999999998764
No 104
>TIGR02200 GlrX_actino Glutaredoxin-like protein. This family of glutaredoxin-like proteins is limited to the Actinobacteria and contains the conserved CxxC motif.
Probab=45.36 E-value=24 Score=18.60 Aligned_cols=22 Identities=9% Similarity=0.013 Sum_probs=18.8
Q ss_pred EEEEEecCCCCCCHHHHHHHHh
Q psy15302 11 ELRIHLCQKGGSSSGVRDFLAQ 32 (68)
Q Consensus 11 ~l~~~yc~~~~sS~G~R~Fl~~ 32 (68)
+|++.+-.|++.++-++.|+..
T Consensus 1 ~v~ly~~~~C~~C~~~~~~L~~ 22 (77)
T TIGR02200 1 TITVYGTTWCGYCAQLMRTLDK 22 (77)
T ss_pred CEEEEECCCChhHHHHHHHHHH
Confidence 3678888999999999999965
No 105
>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=45.15 E-value=65 Score=19.07 Aligned_cols=40 Identities=10% Similarity=0.120 Sum_probs=29.2
Q ss_pred CCCCCCHHHHHHHHhCHHHHHHhCCCCeEEEEecCCCCCEEEEE
Q psy15302 18 QKGGSSSGVRDFLAQHYVPLKQANPKFPILVRECSGVTPVVWAS 61 (68)
Q Consensus 18 ~~~~sS~G~R~Fl~~~l~~~~~~NP~v~i~v~~~~~~~P~v~a~ 61 (68)
+.+..|.=+++|++ +++..+|.+.+.+......-|.+...
T Consensus 28 ~~~~~~~e~~~ll~----e~a~lSdkI~~~~~~~~~~~P~~~i~ 67 (94)
T cd02974 28 DDSEKSAELLELLE----EIASLSDKITLEEDNDDERKPSFSIN 67 (94)
T ss_pred CCCcchHHHHHHHH----HHHHhCCceEEEEecCCCCCCEEEEe
Confidence 44477888888776 78999999999876644456777653
No 106
>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=44.53 E-value=9 Score=20.58 Aligned_cols=20 Identities=15% Similarity=0.436 Sum_probs=16.8
Q ss_pred HHHHHHHhCHHHHHHhCCCC
Q psy15302 25 GVRDFLAQHYVPLKQANPKF 44 (68)
Q Consensus 25 G~R~Fl~~~l~~~~~~NP~v 44 (68)
-+++||.+-|..+...+|++
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 107
>PRK13999 potassium-transporting ATPase subunit C; Provisional
Probab=44.05 E-value=16 Score=25.15 Aligned_cols=44 Identities=25% Similarity=0.382 Sum_probs=34.0
Q ss_pred cCCCCCCHHHHHHHHhCHHHHHHhCC--CCeEEE--EecCCCCCEEEE
Q psy15302 17 CQKGGSSSGVRDFLAQHYVPLKQANP--KFPILV--RECSGVTPVVWA 60 (68)
Q Consensus 17 c~~~~sS~G~R~Fl~~~l~~~~~~NP--~v~i~v--~~~~~~~P~v~a 60 (68)
++-++++.-+.+-+++....|+++|| .||... ...+|-+|.|.-
T Consensus 97 SNlgpsnp~L~~~v~~r~~~~~~~~~~~~vP~DlvTaSgSGLDPhISp 144 (201)
T PRK13999 97 SNLGPTSKALADRVKEDVDALKAENPGAPVPVDLVTTSGSGLDPDISP 144 (201)
T ss_pred cCCCCCCHHHHHHHHHHHHHHHHhCCCCCCCHHHHhcccccCCCCCCH
Confidence 45678899999999999999999998 565443 445677887753
No 108
>PRK14002 potassium-transporting ATPase subunit C; Provisional
Probab=43.95 E-value=20 Score=24.37 Aligned_cols=44 Identities=18% Similarity=0.231 Sum_probs=33.5
Q ss_pred cCCCCCCHHHHHHHHhCHHHHHHhCCC-----CeE--EEEecCCCCCEEEE
Q psy15302 17 CQKGGSSSGVRDFLAQHYVPLKQANPK-----FPI--LVRECSGVTPVVWA 60 (68)
Q Consensus 17 c~~~~sS~G~R~Fl~~~l~~~~~~NP~-----v~i--~v~~~~~~~P~v~a 60 (68)
++-++++.-+.+=+++....|+++||+ ||. ++...+|-+|.|.-
T Consensus 81 SNl~psnp~L~~~v~~r~~~~~~~~~~~~~~~vP~DlvTaSgSGLDPhISp 131 (186)
T PRK14002 81 SNKGPSNPEYLAEVQARIDTFLVHHPYLSRKDIPAEMVTASGSGLDPNISP 131 (186)
T ss_pred cCCCCCCHHHHHHHHHHHHHHHHhCCCCCCCCCCHHHHhccccCCCCCCCH
Confidence 467888999999999999999999986 333 33445677887653
No 109
>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=43.44 E-value=42 Score=22.79 Aligned_cols=27 Identities=11% Similarity=0.175 Sum_probs=23.0
Q ss_pred HHHHHHhCHHHHHHhCCCCeEEEEecC
Q psy15302 26 VRDFLAQHYVPLKQANPKFPILVRECS 52 (68)
Q Consensus 26 ~R~Fl~~~l~~~~~~NP~v~i~v~~~~ 52 (68)
...++...+..|.+++|++.+.+....
T Consensus 107 ~~~~l~~~l~~f~~~~P~i~l~l~~~~ 133 (302)
T TIGR02036 107 AQCWLVPRIGDFTRRYPSISLTVLTGN 133 (302)
T ss_pred HHHHHHHHHHHHHHHCCCceEEEEeCC
Confidence 356788999999999999999997654
No 110
>PLN02958 diacylglycerol kinase/D-erythro-sphingosine kinase
Probab=43.26 E-value=51 Score=24.95 Aligned_cols=44 Identities=20% Similarity=0.202 Sum_probs=34.7
Q ss_pred eEEEEEecCCCCCCHHHHHHHHhCHHHHHHhCCCCeEEEEecCC
Q psy15302 10 KELRIHLCQKGGSSSGVRDFLAQHYVPLKQANPKFPILVRECSG 53 (68)
Q Consensus 10 k~l~~~yc~~~~sS~G~R~Fl~~~l~~~~~~NP~v~i~v~~~~~ 53 (68)
|++.|-+.+.+|..++.+.|...--+.|++..-++.+.+.+..+
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 67889999999998888887777777888888777776655543
No 111
>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=42.26 E-value=6.9 Score=17.11 Aligned_cols=21 Identities=19% Similarity=0.259 Sum_probs=13.3
Q ss_pred CcceEEEEEecCCCCCCHHHHHH
Q psy15302 7 SKLKELRIHLCQKGGSSSGVRDF 29 (68)
Q Consensus 7 ~qlk~l~~~yc~~~~sS~G~R~F 29 (68)
.+|+.|.|++|+-+ ..|++.+
T Consensus 2 ~~L~~L~l~~n~i~--~~g~~~l 22 (24)
T PF13516_consen 2 PNLETLDLSNNQIT--DEGASAL 22 (24)
T ss_dssp TT-SEEE-TSSBEH--HHHHHHH
T ss_pred CCCCEEEccCCcCC--HHHHHHh
Confidence 46889999998853 6666543
No 112
>PRK13994 potassium-transporting ATPase subunit C; Provisional
Probab=41.28 E-value=22 Score=24.80 Aligned_cols=44 Identities=14% Similarity=0.321 Sum_probs=32.9
Q ss_pred cCCCCCCHHHHHHHHhCHHHHHHhC--CC-------CeE--EEEecCCCCCEEEE
Q psy15302 17 CQKGGSSSGVRDFLAQHYVPLKQAN--PK-------FPI--LVRECSGVTPVVWA 60 (68)
Q Consensus 17 c~~~~sS~G~R~Fl~~~l~~~~~~N--P~-------v~i--~v~~~~~~~P~v~a 60 (68)
++.++++.-+.+-+++....|++.| |. ||. ++...+|-+|.|.-
T Consensus 111 SNlgpsnp~L~~~v~~r~~~~~~~~~~p~~~~~~~~VP~DlVTaSGSGLDPhISp 165 (222)
T PRK13994 111 TNRSADNEELIQWVKDAKAAVVEDNSVPGYEVKPSDVPADAVTSSGSGLDPDISP 165 (222)
T ss_pred cCCCCCCHHHHHHHHHHHHHHHHhCCCCccccCCCCCCHHHHhcccccCCCCCCH
Confidence 5678899999999999999999999 45 333 23445677777653
No 113
>smart00367 LRR_CC Leucine-rich repeat - CC (cysteine-containing) subfamily.
Probab=40.57 E-value=22 Score=15.85 Aligned_cols=23 Identities=22% Similarity=0.491 Sum_probs=17.4
Q ss_pred CcceEEEEEecCCCCCCHHHHHHH
Q psy15302 7 SKLKELRIHLCQKGGSSSGVRDFL 30 (68)
Q Consensus 7 ~qlk~l~~~yc~~~~sS~G~R~Fl 30 (68)
++|++|.+.+|..= +..|++...
T Consensus 2 ~~L~~L~l~~C~~i-tD~gl~~l~ 24 (26)
T smart00367 2 PNLRELDLSGCTNI-TDEGLQALA 24 (26)
T ss_pred CCCCEeCCCCCCCc-CHHHHHHHh
Confidence 57999999999843 477777653
No 114
>PRK10470 ribosome hibernation promoting factor HPF; Provisional
Probab=40.57 E-value=72 Score=18.36 Aligned_cols=32 Identities=19% Similarity=0.325 Sum_probs=23.7
Q ss_pred EEEEecCCCCCCHHHHHHHHhCHHHHHHhCCCC
Q psy15302 12 LRIHLCQKGGSSSGVRDFLAQHYVPLKQANPKF 44 (68)
Q Consensus 12 l~~~yc~~~~sS~G~R~Fl~~~l~~~~~~NP~v 44 (68)
+.+.+ .+-.-|.++|+|+++.+..+.+-.+++
T Consensus 3 i~i~~-r~i~~t~al~~~v~~kl~kL~r~~~~i 34 (95)
T PRK10470 3 LNITG-HNVEITEALREFVTAKFAKLEQYFDRI 34 (95)
T ss_pred EEEEE-EeeccCHHHHHHHHHHHHHHHHhcCCC
Confidence 33444 344568999999999888888888754
No 115
>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=40.56 E-value=22 Score=21.31 Aligned_cols=26 Identities=12% Similarity=0.282 Sum_probs=21.2
Q ss_pred HHHHHHhCHHHHHHhCCCCeEEEEec
Q psy15302 26 VRDFLAQHYVPLKQANPKFPILVREC 51 (68)
Q Consensus 26 ~R~Fl~~~l~~~~~~NP~v~i~v~~~ 51 (68)
...++...+.+|.+.+|++.|.+...
T Consensus 11 ~~~~l~~~l~~~~~~~P~i~l~~~~~ 36 (196)
T cd08457 11 ANGFLPRFLAAFLRLRPNLHLSLMGL 36 (196)
T ss_pred hccccHHHHHHHHHHCCCeEEEEEec
Confidence 34567788899999999999998764
No 116
>PRK00315 potassium-transporting ATPase subunit C; Reviewed
Probab=40.51 E-value=15 Score=25.04 Aligned_cols=44 Identities=23% Similarity=0.378 Sum_probs=33.7
Q ss_pred cCCCCCCHHHHHHHHhCHHHHHHhCC----CCeEEE--EecCCCCCEEEE
Q psy15302 17 CQKGGSSSGVRDFLAQHYVPLKQANP----KFPILV--RECSGVTPVVWA 60 (68)
Q Consensus 17 c~~~~sS~G~R~Fl~~~l~~~~~~NP----~v~i~v--~~~~~~~P~v~a 60 (68)
++-++++.-+++-+++....|+++|| .||... ...+|-+|.|.-
T Consensus 86 SNl~psnp~l~~~v~~r~~~~~~~~~~~~~~vP~DlvTaSgSGLDPhIS~ 135 (193)
T PRK00315 86 SNLAPSNPALDDAIKARVAALRAANPGASSPVPVDLVTASGSGLDPHISP 135 (193)
T ss_pred cCCCCCCHHHHHHHHHHHHHHHHhCCCCCCCCCHHHHhccccCCCCCCCH
Confidence 46678899999999999999999998 455443 445677887653
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=40.21 E-value=82 Score=20.74 Aligned_cols=32 Identities=16% Similarity=0.222 Sum_probs=25.1
Q ss_pred HHhCHHHHHHhCCCCeEEEEecCCCCCEEEEE
Q psy15302 30 LAQHYVPLKQANPKFPILVRECSGVTPVVWAS 61 (68)
Q Consensus 30 l~~~l~~~~~~NP~v~i~v~~~~~~~P~v~a~ 61 (68)
+..-+|++++++|+-++.+.-.....|.+...
T Consensus 44 ~~~~iP~l~~~yPn~~~~L~i~~~~~P~v~i~ 75 (200)
T cd00026 44 FGIFIPELAKKYPNMPQQLKISVSSPPHLVLS 75 (200)
T ss_pred HHHHHHHHHHHCCCCcEEEEEEeCCCCEEEEe
Confidence 34478999999999888887776678988754
No 118
>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=40.02 E-value=71 Score=18.08 Aligned_cols=31 Identities=10% Similarity=0.224 Sum_probs=24.4
Q ss_pred EEEEecCCCCCCHHHHHHHHhCHHHHHHhCCC
Q psy15302 12 LRIHLCQKGGSSSGVRDFLAQHYVPLKQANPK 43 (68)
Q Consensus 12 l~~~yc~~~~sS~G~R~Fl~~~l~~~~~~NP~ 43 (68)
|.|.+ .+-.-+.++++|+++.+..+.+-.|+
T Consensus 3 i~i~~-~~~~~t~~l~~~i~~k~~kl~k~~~~ 33 (95)
T TIGR00741 3 INITG-KNVEITEALREYVEEKLARLERYFTH 33 (95)
T ss_pred EEEEE-eccccCHHHHHHHHHHHHHHHHhcCC
Confidence 44555 55556899999999999998888876
No 119
>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=38.76 E-value=72 Score=17.99 Aligned_cols=32 Identities=9% Similarity=0.203 Sum_probs=22.5
Q ss_pred EEEEecCCCCCCHHHHHHHHhCHHHHHHhCCCC
Q psy15302 12 LRIHLCQKGGSSSGVRDFLAQHYVPLKQANPKF 44 (68)
Q Consensus 12 l~~~yc~~~~sS~G~R~Fl~~~l~~~~~~NP~v 44 (68)
|.|.+ .+-.-|..+++|+++.+..|.+-.|++
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 44555 555679999999999999999888754
No 120
>PF02638 DUF187: Glycosyl hydrolase like GH101; InterPro: IPR003790 This entry describes proteins of unknown function.
Probab=38.67 E-value=49 Score=23.49 Aligned_cols=30 Identities=13% Similarity=0.329 Sum_probs=25.5
Q ss_pred CHHHHHHHHhCHHHHHHhCCCCeEEEEecC
Q psy15302 23 SSGVRDFLAQHYVPLKQANPKFPILVRECS 52 (68)
Q Consensus 23 S~G~R~Fl~~~l~~~~~~NP~v~i~v~~~~ 52 (68)
..-+-+||++-+..+|+.+|+|.|-+.+..
T Consensus 202 r~~I~~~V~~i~~~ik~~kP~v~~sisp~g 231 (311)
T PF02638_consen 202 RDNINNFVKRIYDAIKAIKPWVKFSISPFG 231 (311)
T ss_pred HHHHHHHHHHHHHHHHHhCCCCeEEEEeec
Confidence 345778999999999999999999997753
No 121
>COG1570 XseA Exonuclease VII, large subunit [DNA replication, recombination, and repair]
Probab=38.45 E-value=52 Score=25.17 Aligned_cols=30 Identities=20% Similarity=0.351 Sum_probs=25.1
Q ss_pred CCCCCHHHHHHHHhCHHHHHHhCCCCeEEEEecC
Q psy15302 19 KGGSSSGVRDFLAQHYVPLKQANPKFPILVRECS 52 (68)
Q Consensus 19 ~~~sS~G~R~Fl~~~l~~~~~~NP~v~i~v~~~~ 52 (68)
||+++..+||.+. .+++..|.++|+|.+..
T Consensus 142 TS~tgAairDIl~----~~~rR~P~~~viv~pt~ 171 (440)
T COG1570 142 TSPTGAALRDILH----TLSRRFPSVEVIVYPTL 171 (440)
T ss_pred cCCchHHHHHHHH----HHHhhCCCCeEEEEecc
Confidence 6778899999886 47899999999998753
No 122
>KOG1909|consensus
Probab=38.19 E-value=30 Score=25.99 Aligned_cols=36 Identities=28% Similarity=0.538 Sum_probs=29.0
Q ss_pred CcceEEEEEecCCCCCCHHHHHHHHhCHHHHHHhCCCCeEEE
Q psy15302 7 SKLKELRIHLCQKGGSSSGVRDFLAQHYVPLKQANPKFPILV 48 (68)
Q Consensus 7 ~qlk~l~~~yc~~~~sS~G~R~Fl~~~l~~~~~~NP~v~i~v 48 (68)
++|++|.+.||.-. +.|+-.|+. .|++.||.+++.-
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 36999999999974 788888874 5777799888764
No 123
>COG0607 PspE Rhodanese-related sulfurtransferase [Inorganic ion transport and metabolism]
Probab=38.04 E-value=52 Score=18.48 Aligned_cols=23 Identities=17% Similarity=0.245 Sum_probs=19.4
Q ss_pred eEEEEEecCCCCCCHHHHHHHHh
Q psy15302 10 KELRIHLCQKGGSSSGVRDFLAQ 32 (68)
Q Consensus 10 k~l~~~yc~~~~sS~G~R~Fl~~ 32 (68)
.+-.+.||..|..|.-+-.+|..
T Consensus 61 ~~~ivv~C~~G~rS~~aa~~L~~ 83 (110)
T COG0607 61 DDPIVVYCASGVRSAAAAAALKL 83 (110)
T ss_pred CCeEEEEeCCCCChHHHHHHHHH
Confidence 45778999999999998888864
No 124
>PF02114 Phosducin: Phosducin; InterPro: IPR024253 The outer and inner segments of vertebrate rod photoreceptor cells contain phosducin, a soluble phosphoprotein that complexes with the beta/gamma-subunits of the GTP-binding protein, transducin. Light-induced changes in cyclic nucleotide levels modulate the phosphorylation of phosducin by protein kinase A []. The protein is thought to participate in the regulation of visual phototransduction or in the integration of photo-receptor metabolism. Similar proteins have been isolated from the pineal gland and it is believed that the functional role of the protein is the same in both retina and pineal gland []. This entry represents a domain found in members of the phosducin family. This domain has a thioredoxin-like fold [].; PDB: 2DBC_A 1A0R_P 1B9Y_C 1B9X_C 2TRC_P 3EVI_B.
Probab=37.65 E-value=1.1e+02 Score=21.58 Aligned_cols=50 Identities=8% Similarity=-0.039 Sum_probs=31.9
Q ss_pred EEEEEecCCCCCCHHHHHHHHhCHHHHHHhCCCCeEEEEecC----------CCCCEEEEEecCC
Q psy15302 11 ELRIHLCQKGGSSSGVRDFLAQHYVPLKQANPKFPILVRECS----------GVTPVVWASGKGT 65 (68)
Q Consensus 11 ~l~~~yc~~~~sS~G~R~Fl~~~l~~~~~~NP~v~i~v~~~~----------~~~P~v~a~Y~nG 65 (68)
-|+..|-+..+.++ .|.+.|..+|+++|.|.|.--... ..-|.|.+.+ +|
T Consensus 149 VVVHiY~~~~~~C~----~mn~~L~~LA~kyp~vKFvkI~a~~~~~~~~f~~~~LPtllvYk-~G 208 (265)
T PF02114_consen 149 VVVHIYEPGFPRCE----IMNSCLECLARKYPEVKFVKIRASKCPASENFPDKNLPTLLVYK-NG 208 (265)
T ss_dssp EEEEEE-TTSCCHH----HHHHHHHHHHHH-TTSEEEEEEECGCCTTTTS-TTC-SEEEEEE-TT
T ss_pred EEEEEEeCCCchHH----HHHHHHHHHHHhCCceEEEEEehhccCcccCCcccCCCEEEEEE-CC
Confidence 45566666555554 477889999999999999854332 2367776654 55
No 125
>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=37.23 E-value=27 Score=21.54 Aligned_cols=15 Identities=13% Similarity=0.366 Sum_probs=13.5
Q ss_pred HHHHHHHHhCHHHHH
Q psy15302 24 SGVRDFLAQHYVPLK 38 (68)
Q Consensus 24 ~G~R~Fl~~~l~~~~ 38 (68)
+|+|+||++.++++.
T Consensus 68 ~g~R~~IKe~~~E~s 82 (98)
T PF11247_consen 68 QGIREAIKEMLSEYS 82 (98)
T ss_pred HHHHHHHHHHHHHhc
Confidence 699999999999887
No 126
>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=36.87 E-value=31 Score=22.94 Aligned_cols=43 Identities=19% Similarity=0.062 Sum_probs=26.6
Q ss_pred HHHHHHHHhCHHHHHHhCCCCeEEEEecCCC-C-CEEEEEecCCC
Q psy15302 24 SGVRDFLAQHYVPLKQANPKFPILVRECSGV-T-PVVWASGKGTH 66 (68)
Q Consensus 24 ~G~R~Fl~~~l~~~~~~NP~v~i~v~~~~~~-~-P~v~a~Y~nGr 66 (68)
+...+.|--.++.-+..||++.+.++-..+- . -.+++.|=|.|
T Consensus 33 k~~~~~lFp~~~~~~~~Np~~~~~~~~~s~~~~~~~~r~iYYnn~ 77 (156)
T PF09217_consen 33 KSAAELLFPSINHTKEENPDIWLKARWQSHFVTDSQVRFIYYNNR 77 (156)
T ss_dssp HHHHHHH-GGG-SSSSSS-EEEEEEEETTTT---EEEEEEEE-CC
T ss_pred ccHHHHhCCCCCcccccCCceeEEEEECCCCccceeEEEEEEccc
Confidence 3444444455666788999999999998873 3 33677776663
No 127
>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=36.81 E-value=62 Score=17.94 Aligned_cols=33 Identities=15% Similarity=0.118 Sum_probs=28.8
Q ss_pred CCCCCCHHHHHHHHhCHHHHHHhCCCCeEEEEe
Q psy15302 18 QKGGSSSGVRDFLAQHYVPLKQANPKFPILVRE 50 (68)
Q Consensus 18 ~~~~sS~G~R~Fl~~~l~~~~~~NP~v~i~v~~ 50 (68)
+|..-|.|.|..+...+-.+-.++|.+.|.+-.
T Consensus 27 ~w~~~s~~~r~~~g~~F~~~V~~~~~~~i~~~~ 59 (70)
T PF07205_consen 27 EWNTLSRAERQSLGRAFLYEVKQGPIVRIKIIG 59 (70)
T ss_pred hhhhCCHHHHHHHHHHHHHHHHhCCCCceEEEe
Confidence 466689999999999999999999999887754
No 128
>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=36.72 E-value=67 Score=20.85 Aligned_cols=35 Identities=6% Similarity=-0.075 Sum_probs=24.7
Q ss_pred EEEEecCCCCCCHHHHHHHHhCHHHHHHhCCCCeEEEEe
Q psy15302 12 LRIHLCQKGGSSSGVRDFLAQHYVPLKQANPKFPILVRE 50 (68)
Q Consensus 12 l~~~yc~~~~sS~G~R~Fl~~~l~~~~~~NP~v~i~v~~ 50 (68)
|...|-+|.+.++-| ...|.++++++|.+.|.-..
T Consensus 87 VV~Fya~wc~~Ck~m----~~~l~~LA~~~~~vkF~kVd 121 (175)
T cd02987 87 VVHIYEPGIPGCAAL----NSSLLCLAAEYPAVKFCKIR 121 (175)
T ss_pred EEEEECCCCchHHHH----HHHHHHHHHHCCCeEEEEEe
Confidence 445566788877744 45677888999998886543
No 129
>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=36.62 E-value=79 Score=17.61 Aligned_cols=38 Identities=18% Similarity=0.250 Sum_probs=23.3
Q ss_pred EEEEecCCCCCCHHHHHHHHhCHHHHHHhCCCCeEEEEecCC
Q psy15302 12 LRIHLCQKGGSSSGVRDFLAQHYVPLKQANPKFPILVRECSG 53 (68)
Q Consensus 12 l~~~yc~~~~sS~G~R~Fl~~~l~~~~~~NP~v~i~v~~~~~ 53 (68)
|+|.||...+ ..+--..+. .++....|+.++.+...++
T Consensus 1 V~IeyC~~C~-y~~Ra~~l~---q~L~~~Fp~~~v~~~~~~~ 38 (72)
T TIGR02174 1 VEIEYCGSCG-YKPRAAWLK---QELLEEFPDLEIEGENTPP 38 (72)
T ss_pred CEEEECCCCC-ChHHHHHHH---HHHHHHCCCCeeEEeeecC
Confidence 5789999887 333333333 3566677887666655443
No 130
>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=36.36 E-value=80 Score=17.59 Aligned_cols=37 Identities=16% Similarity=0.200 Sum_probs=23.6
Q ss_pred EEEEEecCCCCCCHHHHHHHHhCHHHHHHhCCC--CeEEEEec
Q psy15302 11 ELRIHLCQKGGSSSGVRDFLAQHYVPLKQANPK--FPILVREC 51 (68)
Q Consensus 11 ~l~~~yc~~~~sS~G~R~Fl~~~l~~~~~~NP~--v~i~v~~~ 51 (68)
+|.|.||...+-..-.-+ .-..+....|+ ..|...+.
T Consensus 2 ~V~IeYC~~C~~~~~a~~----l~~~l~~~fp~~~~~v~~~~~ 40 (76)
T PF10262_consen 2 KVTIEYCTSCGYRPRALE----LAQELLQTFPDRIAEVELSPG 40 (76)
T ss_dssp EEEEEEETTTTCHHHHHH----HHHHHHHHSTTTCSEEEEEEE
T ss_pred EEEEEECCCCCCHHHHHH----HHHHHHHHCCCcceEEEEEec
Confidence 689999998874433222 22345666777 67777663
No 131
>TIGR00269 conserved hypothetical protein TIGR00269.
Probab=35.29 E-value=20 Score=21.53 Aligned_cols=24 Identities=25% Similarity=0.290 Sum_probs=20.5
Q ss_pred CCHHHHHHHHhCHHHHHHhCCCCe
Q psy15302 22 SSSGVRDFLAQHYVPLKQANPKFP 45 (68)
Q Consensus 22 sS~G~R~Fl~~~l~~~~~~NP~v~ 45 (68)
+....|..+++.|.++.+.||++.
T Consensus 34 ~~~a~R~~~k~~L~~LE~~~P~~k 57 (104)
T TIGR00269 34 SSLSVRARIRDFLYDLENKKPGVK 57 (104)
T ss_pred CCCCchHHHHHHHHHHHHHCcChH
Confidence 456789999999999999999875
No 132
>PRK10837 putative DNA-binding transcriptional regulator; Provisional
Probab=35.11 E-value=58 Score=21.54 Aligned_cols=26 Identities=12% Similarity=0.199 Sum_probs=21.8
Q ss_pred HHHHHHhCHHHHHHhCCCCeEEEEec
Q psy15302 26 VRDFLAQHYVPLKQANPKFPILVREC 51 (68)
Q Consensus 26 ~R~Fl~~~l~~~~~~NP~v~i~v~~~ 51 (68)
...++...+..|.+++|++.|.+...
T Consensus 100 ~~~~~~~~l~~~~~~~P~i~i~v~~~ 125 (290)
T PRK10837 100 GNYILPAMIARYRRDYPQLPLELSVG 125 (290)
T ss_pred HhhhhHHHHHHHHHHCCCceEEEEEC
Confidence 34667889999999999999999754
No 133
>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=35.10 E-value=19 Score=14.83 Aligned_cols=11 Identities=18% Similarity=0.317 Sum_probs=7.6
Q ss_pred cceEEEEEecC
Q psy15302 8 KLKELRIHLCQ 18 (68)
Q Consensus 8 qlk~l~~~yc~ 18 (68)
.|+.|.++.|+
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 58889888886
No 134
>PF00280 potato_inhibit: Potato inhibitor I family; InterPro: IPR000864 Peptide proteinase inhibitors can be found as single domain proteins or as single or multiple domains within proteins; these are referred to as either simple or compound inhibitors, respectively. In many cases they are synthesised as part of a larger precursor protein, either as a prepropeptide or as an N-terminal domain associated with an inactive peptidase or zymogen. This domain prevents access of the substrate to the active site. Removal of the N-terminal inhibitor domain either by interaction with a second peptidase or by autocatalytic cleavage activates the zymogen. Other inhibitors interact direct with proteinases using a simple noncovalent lock and key mechanism; while yet others use a conformational change-based trapping mechanism that depends on their structural and thermodynamic properties. This family of proteinase inhibitors belong to MEROPS inhibitor family I13, clan IG. They inhibit peptidases of the S1 (IPR001254 from INTERPRO) and S8 (IPR000209 from INTERPRO) families []. Potato inhibitor type I sequences are not solely restricted to potatoes but are found in other plant species for example: barley endosperm chymotrypsin inhibitor [], and pumpkin trypsin inhibitor. Exceptions are found in leech's, e.g.Hirudo medicinalis (Medicinal leech), but not other metazoa []. In general, the proteins have retained a specificity towards chymotrypsin-like and elastase-like proteases []. Structurally these inhibitors are small (60 to 90 residues) and in contrast with other families of protease inhibitors, they lack disulphide bonds. The inhibitor is a wedge-shaped molecule, its pointed edge formed by the protease-binding loop, which contains the scissile bond. The loop binds tightly to the protease active site, subsequent cleavage of the scissile bond causing inhibition of the enzyme []. The inhibitors (designated type I and II) are synthesised in potato tubers, increasing in concentration as the tuber develops. Synthesis of the inhibitors throughout the plant is also induced by leaf damage; this systemic response being triggered by the release of a putative plant hormone []. Examples found in the bacteria and archaea are probable false positives.; GO: 0004867 serine-type endopeptidase inhibitor activity, 0009611 response to wounding; PDB: 1TEC_I 1SBN_I 1ACB_I 1EGP_A 3TEC_I 2SEC_I 1EGL_A 2TEC_I 1SIB_I 1MEE_I ....
Probab=35.04 E-value=36 Score=19.03 Aligned_cols=19 Identities=16% Similarity=0.282 Sum_probs=15.1
Q ss_pred HHHHHHhCCCCeEEEEecC
Q psy15302 34 YVPLKQANPKFPILVRECS 52 (68)
Q Consensus 34 l~~~~~~NP~v~i~v~~~~ 52 (68)
-..|++.||++.+.+-+..
T Consensus 16 ~~~I~~e~P~v~v~vlp~g 34 (63)
T PF00280_consen 16 KAIIERENPDVTVVVLPEG 34 (63)
T ss_dssp HHHHHHHSTTSEEEEEETT
T ss_pred HHHHHHHCCCCeEEEEeCC
Confidence 4568899999999987643
No 135
>PRK10696 tRNA 2-thiocytidine biosynthesis protein TtcA; Provisional
Probab=34.68 E-value=41 Score=22.96 Aligned_cols=25 Identities=8% Similarity=-0.013 Sum_probs=21.0
Q ss_pred CCHHHHHHHHhCHHHHHHhCCCCeE
Q psy15302 22 SSSGVRDFLAQHYVPLKQANPKFPI 46 (68)
Q Consensus 22 sS~G~R~Fl~~~l~~~~~~NP~v~i 46 (68)
.....|+.+++-+|.+.+.||++..
T Consensus 206 ~~~~~R~~ir~~l~~L~~~~P~~~~ 230 (258)
T PRK10696 206 QENLQRQVVKEMLRDWEKEYPGRIE 230 (258)
T ss_pred CchhHHHHHHHHHHHHHHHCccHHH
Confidence 3456899999999999999998754
No 136
>PRK11139 DNA-binding transcriptional activator GcvA; Provisional
Probab=34.62 E-value=64 Score=21.62 Aligned_cols=25 Identities=12% Similarity=0.373 Sum_probs=22.0
Q ss_pred HHHHHhCHHHHHHhCCCCeEEEEec
Q psy15302 27 RDFLAQHYVPLKQANPKFPILVREC 51 (68)
Q Consensus 27 R~Fl~~~l~~~~~~NP~v~i~v~~~ 51 (68)
..++...+.+|.+.+|++.|.+...
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 137
>PRK11716 DNA-binding transcriptional regulator IlvY; Provisional
Probab=34.45 E-value=67 Score=20.76 Aligned_cols=25 Identities=12% Similarity=0.121 Sum_probs=21.5
Q ss_pred HHHHHhCHHHHHHhCCCCeEEEEec
Q psy15302 27 RDFLAQHYVPLKQANPKFPILVREC 51 (68)
Q Consensus 27 R~Fl~~~l~~~~~~NP~v~i~v~~~ 51 (68)
..++..-+..|.+.+|++.+.+...
T Consensus 79 ~~~~~~~l~~~~~~~p~i~l~i~~~ 103 (269)
T PRK11716 79 YSHLPPILDRFRAEHPLVEIKLTTG 103 (269)
T ss_pred HHHHHHHHHHHHHHCCCeEEEEEEC
Confidence 5678889999999999999998753
No 138
>PRK10597 DNA damage-inducible protein I; Provisional
Probab=34.34 E-value=1e+02 Score=18.19 Aligned_cols=43 Identities=19% Similarity=0.254 Sum_probs=34.9
Q ss_pred EEEEEecCCCCCCHHHHHHHH-hCHHHHHHhCCCCe--EEEEecCC
Q psy15302 11 ELRIHLCQKGGSSSGVRDFLA-QHYVPLKQANPKFP--ILVRECSG 53 (68)
Q Consensus 11 ~l~~~yc~~~~sS~G~R~Fl~-~~l~~~~~~NP~v~--i~v~~~~~ 53 (68)
+|.+.|....+-+.|+.+-|+ +..-.+....|++. +.|+....
T Consensus 2 rVEi~~dK~~~lp~ga~~AL~~EL~kRl~~~fPd~~~~v~Vr~~s~ 47 (81)
T PRK10597 2 RIEVTIAKTSPLPAGAIDALAGELSRRIQYAFPDNEGHVSVRYAAA 47 (81)
T ss_pred eEEEEEecCCCCChhHHHHHHHHHHHHHHhhCCCCCccEEEeecCC
Confidence 466777777788899999886 56779999999998 88877664
No 139
>PRK10974 glycerol-3-phosphate transporter periplasmic binding protein; Provisional
Probab=34.28 E-value=60 Score=23.25 Aligned_cols=25 Identities=8% Similarity=0.121 Sum_probs=20.7
Q ss_pred HHHHHHhCHHHHHHhCCCCeEEEEe
Q psy15302 26 VRDFLAQHYVPLKQANPKFPILVRE 50 (68)
Q Consensus 26 ~R~Fl~~~l~~~~~~NP~v~i~v~~ 50 (68)
-.+.++..+.+|.++||+|.|.+..
T Consensus 38 ~~~~~~~~~~~F~~~~p~i~V~~~~ 62 (438)
T PRK10974 38 LGKEVDSLAQRFNASQPDYKIVPVY 62 (438)
T ss_pred hHHHHHHHHHHHHHhCCCeEEEEee
Confidence 3467888999999999999988753
No 140
>PRK13995 potassium-transporting ATPase subunit C; Provisional
Probab=34.18 E-value=65 Score=22.20 Aligned_cols=44 Identities=16% Similarity=0.255 Sum_probs=33.2
Q ss_pred cCCCCCCHHHHHHHHhCHHHHHHhCCC-----CeEEE--EecCCCCCEEEE
Q psy15302 17 CQKGGSSSGVRDFLAQHYVPLKQANPK-----FPILV--RECSGVTPVVWA 60 (68)
Q Consensus 17 c~~~~sS~G~R~Fl~~~l~~~~~~NP~-----v~i~v--~~~~~~~P~v~a 60 (68)
++-+++|.-+.+-+++....|++.||. ||+.. ...+|-+|.|.-
T Consensus 95 SNlgpsnp~L~~~v~~r~~~~~~~~p~~~~~~vP~DlvTaSgSGLDPhISp 145 (203)
T PRK13995 95 QNYAPTNPELHDRVQKDIDKFLKTNPTVKKEDIPTDLLTASGSGLDPHISP 145 (203)
T ss_pred cCCCCCCHHHHHHHHHHHHHHHHhCCCCCCCCCCHHHHhccccCCCCCCCH
Confidence 456788899999999999999999985 44433 445677887643
No 141
>PF08109 Antimicrobial14: Lactocin 705 family; InterPro: IPR012517 This family consists of lactocin 705 which is a bacteriocin produced by Lactobacillus casei CRL 705. Lactocin 705 is a class IIb bacteriocin, whose activity depends upon the complementation of two peptides (705-alpha and 705-beta) of 33 amino acid residues each. Lactocin 705 is active against several Gram-positive bacteria, including food-borne pathogens and is a good candidate to be used for biopreservation of fermented meats [].
Probab=34.13 E-value=26 Score=16.94 Aligned_cols=23 Identities=30% Similarity=0.426 Sum_probs=18.5
Q ss_pred CCCHHHHHHHHhCHHHHHHhCCC
Q psy15302 21 GSSSGVRDFLAQHYVPLKQANPK 43 (68)
Q Consensus 21 ~sS~G~R~Fl~~~l~~~~~~NP~ 43 (68)
|--+|+-+|+...|--+..+|.+
T Consensus 4 gyiqgipdflkgylhgisaankh 26 (31)
T PF08109_consen 4 GYIQGIPDFLKGYLHGISAANKH 26 (31)
T ss_pred ccccccHHHHHHHHhhhhhhccc
Confidence 34578999999999888888765
No 142
>COG4097 Predicted ferric reductase [Inorganic ion transport and metabolism]
Probab=34.08 E-value=44 Score=25.52 Aligned_cols=44 Identities=16% Similarity=0.190 Sum_probs=30.6
Q ss_pred eEEEEEecCCCCCCHHHHHHH-HhCHHHHHHhCCCCeEEEEecCCCCCEEE
Q psy15302 10 KELRIHLCQKGGSSSGVRDFL-AQHYVPLKQANPKFPILVRECSGVTPVVW 59 (68)
Q Consensus 10 k~l~~~yc~~~~sS~G~R~Fl-~~~l~~~~~~NP~v~i~v~~~~~~~P~v~ 59 (68)
+-|.+.||-.+- .+=+ .+.+-+++++||.+.+.+ -.++..|++-
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 347889986542 2333 457888999999999999 4445566654
No 143
>PRK11151 DNA-binding transcriptional regulator OxyR; Provisional
Probab=34.06 E-value=72 Score=21.46 Aligned_cols=27 Identities=22% Similarity=0.202 Sum_probs=22.8
Q ss_pred HHHHHHHhCHHHHHHhCCCCeEEEEec
Q psy15302 25 GVRDFLAQHYVPLKQANPKFPILVREC 51 (68)
Q Consensus 25 G~R~Fl~~~l~~~~~~NP~v~i~v~~~ 51 (68)
....++...+.+|.+.+|++.|.+...
T Consensus 101 ~~~~~~~~~l~~~~~~~P~v~i~~~~~ 127 (305)
T PRK11151 101 VGPYLLPHIIPMLHQTFPKLEMYLHEA 127 (305)
T ss_pred hHHHHHHHHHHHHHHHCCCcEEEEEeC
Confidence 346788889999999999999999864
No 144
>PRK12681 cysB transcriptional regulator CysB; Reviewed
Probab=33.64 E-value=63 Score=22.38 Aligned_cols=36 Identities=14% Similarity=0.155 Sum_probs=27.1
Q ss_pred EEEEEecCCCCCCHHHHHHHHhCHHHHHHhCCCCeEEEEec
Q psy15302 11 ELRIHLCQKGGSSSGVRDFLAQHYVPLKQANPKFPILVREC 51 (68)
Q Consensus 11 ~l~~~yc~~~~sS~G~R~Fl~~~l~~~~~~NP~v~i~v~~~ 51 (68)
.|+|-.+. .-...++...+.+|.+.+|++.|.+...
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 3345688899999999999999999764
No 145
>PRK09508 leuO leucine transcriptional activator; Reviewed
Probab=33.64 E-value=73 Score=21.68 Aligned_cols=26 Identities=15% Similarity=0.310 Sum_probs=22.7
Q ss_pred HHHHHhCHHHHHHhCCCCeEEEEecC
Q psy15302 27 RDFLAQHYVPLKQANPKFPILVRECS 52 (68)
Q Consensus 27 R~Fl~~~l~~~~~~NP~v~i~v~~~~ 52 (68)
..++...+.+|.+++|++.|.+....
T Consensus 124 ~~~l~~~l~~f~~~~P~i~l~i~~~~ 149 (314)
T PRK09508 124 IRLTSQIYNRIEQIAPNIHVVFKSSL 149 (314)
T ss_pred HHHHHHHHHHHHHhCCCcEEEEEeCc
Confidence 56888999999999999999998753
No 146
>PRK09801 transcriptional activator TtdR; Provisional
Probab=33.58 E-value=76 Score=21.74 Aligned_cols=28 Identities=14% Similarity=0.134 Sum_probs=23.0
Q ss_pred HHHHHHHHhCHHHHHHhCCCCeEEEEec
Q psy15302 24 SGVRDFLAQHYVPLKQANPKFPILVREC 51 (68)
Q Consensus 24 ~G~R~Fl~~~l~~~~~~NP~v~i~v~~~ 51 (68)
.-...|+...+.+|.+++|++.|.+...
T Consensus 105 ~~~~~~l~~~l~~f~~~~P~i~l~i~~~ 132 (310)
T PRK09801 105 GFGRSHIAPAITELMRNYPELQVHFELF 132 (310)
T ss_pred HHHHHHHHHHHHHHHHHCCCeEEEEEec
Confidence 3345688899999999999999998754
No 147
>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=33.34 E-value=73 Score=16.99 Aligned_cols=35 Identities=17% Similarity=0.344 Sum_probs=25.5
Q ss_pred cceEEEEEecCCCCCCHHHHHHHHhCHHHHHHhCCCCeEE
Q psy15302 8 KLKELRIHLCQKGGSSSGVRDFLAQHYVPLKQANPKFPIL 47 (68)
Q Consensus 8 qlk~l~~~yc~~~~sS~G~R~Fl~~~l~~~~~~NP~v~i~ 47 (68)
.++.|.|..+.. +++.+..||.+.+.- .||.++..
T Consensus 33 nc~~i~l~~~~~--t~~dln~Flk~W~~G---~~~~Le~l 67 (70)
T PF07735_consen 33 NCKKIELWNSKF--TNEDLNKFLKHWING---SNPRLEYL 67 (70)
T ss_pred CCCEEEEECCCC--CHHHHHHHHHHHHcC---CCcCCcEE
Confidence 467788866655 589999999887654 67776654
No 148
>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=33.26 E-value=1.3e+02 Score=20.32 Aligned_cols=40 Identities=10% Similarity=0.119 Sum_probs=29.4
Q ss_pred EEEEEecCCCCC-CHHHHHHHHhCHHHHHHhCC-CCeEEEEe
Q psy15302 11 ELRIHLCQKGGS-SSGVRDFLAQHYVPLKQANP-KFPILVRE 50 (68)
Q Consensus 11 ~l~~~yc~~~~s-S~G~R~Fl~~~l~~~~~~NP-~v~i~v~~ 50 (68)
+|++.+...-+. -...+.-+++.|.++++.+| ++.+...-
T Consensus 28 ~i~~~~s~~l~~~~~~~~~~v~~lL~~y~~~s~g~i~v~~iD 69 (271)
T PF09822_consen 28 TITVYFSRELPPELSPLRKQVRDLLDEYARYSPGKIKVEFID 69 (271)
T ss_pred EEEEEECCCcchhhhHHHHHHHHHHHHHHHhCCCceEEEEEC
Confidence 466667663332 46677778889999999999 99888743
No 149
>PRK14001 potassium-transporting ATPase subunit C; Provisional
Probab=33.11 E-value=70 Score=21.78 Aligned_cols=44 Identities=16% Similarity=0.268 Sum_probs=33.8
Q ss_pred cCCCCCCHHHHHHHHhCHHHHHHhCCC-----CeEE--EEecCCCCCEEEE
Q psy15302 17 CQKGGSSSGVRDFLAQHYVPLKQANPK-----FPIL--VRECSGVTPVVWA 60 (68)
Q Consensus 17 c~~~~sS~G~R~Fl~~~l~~~~~~NP~-----v~i~--v~~~~~~~P~v~a 60 (68)
++.++++.-+.+-+++....|+++||. ||.. +...+|-+|.|.-
T Consensus 85 SNl~psnp~l~~~v~~r~~~~~~~~~~~~~~~vP~DlvTaSgSGLDPhIS~ 135 (189)
T PRK14001 85 SNLGPTNEKLLAAVAERVTAYRKENNLPADTLVPVDAVTGSGSGLDPAISV 135 (189)
T ss_pred cCCCCCCHHHHHHHHHHHHHHHHhCCCccCCCCCHHHHhcccccCCCCCCH
Confidence 567889999999999999999999984 4433 3445677887653
No 150
>PRK09791 putative DNA-binding transcriptional regulator; Provisional
Probab=32.95 E-value=66 Score=21.62 Aligned_cols=26 Identities=15% Similarity=0.314 Sum_probs=22.3
Q ss_pred HHHHHHhCHHHHHHhCCCCeEEEEec
Q psy15302 26 VRDFLAQHYVPLKQANPKFPILVREC 51 (68)
Q Consensus 26 ~R~Fl~~~l~~~~~~NP~v~i~v~~~ 51 (68)
...++...+..|.+++|++.|.++..
T Consensus 106 ~~~~l~~~l~~~~~~~p~i~~~~~~~ 131 (302)
T PRK09791 106 ARSLMPAVISRFHQQHPQVKVRIMEG 131 (302)
T ss_pred HHhhhHHHHHHHHHHCCCeEEEEEeC
Confidence 45677899999999999999999863
No 151
>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=32.85 E-value=54 Score=16.68 Aligned_cols=21 Identities=5% Similarity=0.180 Sum_probs=18.1
Q ss_pred EEEEecCCCCCCHHHHHHHHh
Q psy15302 12 LRIHLCQKGGSSSGVRDFLAQ 32 (68)
Q Consensus 12 l~~~yc~~~~sS~G~R~Fl~~ 32 (68)
|++.+.++.+.++.++.++++
T Consensus 2 i~lf~~~~C~~C~~~~~~l~~ 22 (74)
T TIGR02196 2 VKVYTTPWCPPCKKAKEYLTS 22 (74)
T ss_pred EEEEcCCCChhHHHHHHHHHH
Confidence 678888999999999998864
No 152
>cd02957 Phd_like Phosducin (Phd)-like family; composed of Phd and Phd-like proteins (PhLP), characterized as cytosolic regulators of G protein functions. Phd and PhLPs specifically bind G protein betagamma (Gbg)-subunits with high affinity, resulting in the solubilization of Gbg from the plasma membrane and impeding G protein-mediated signal transduction by inhibiting the formation of a functional G protein trimer (G protein alphabetagamma). 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-te
Probab=32.59 E-value=1.1e+02 Score=17.88 Aligned_cols=34 Identities=9% Similarity=-0.053 Sum_probs=23.9
Q ss_pred EEEEEecCCCCCCHHHHHHHHhCHHHHHHhCCCCeEEE
Q psy15302 11 ELRIHLCQKGGSSSGVRDFLAQHYVPLKQANPKFPILV 48 (68)
Q Consensus 11 ~l~~~yc~~~~sS~G~R~Fl~~~l~~~~~~NP~v~i~v 48 (68)
-|...|.+|.+.++-+.. .+.+++.++|++.|..
T Consensus 27 vvv~F~a~~c~~C~~l~~----~l~~la~~~~~v~f~~ 60 (113)
T cd02957 27 VVVHFYEPGFPRCKILDS----HLEELAAKYPETKFVK 60 (113)
T ss_pred EEEEEeCCCCCcHHHHHH----HHHHHHHHCCCcEEEE
Confidence 456678889888886554 5556777888876544
No 153
>PRK11074 putative DNA-binding transcriptional regulator; Provisional
Probab=32.56 E-value=54 Score=22.11 Aligned_cols=37 Identities=16% Similarity=0.092 Sum_probs=28.9
Q ss_pred eEEEEEecCCCCCCHHHHHHHHhCHHHHHHhCCCCeEEEEec
Q psy15302 10 KELRIHLCQKGGSSSGVRDFLAQHYVPLKQANPKFPILVREC 51 (68)
Q Consensus 10 k~l~~~yc~~~~sS~G~R~Fl~~~l~~~~~~NP~v~i~v~~~ 51 (68)
..|+|-..+.. ...++...+..|++++|++.|.+...
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 46777764433 36788899999999999999999763
No 154
>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=32.54 E-value=39 Score=23.42 Aligned_cols=21 Identities=10% Similarity=0.267 Sum_probs=17.7
Q ss_pred hCHHHHHHhCCCCeEEEEecC
Q psy15302 32 QHYVPLKQANPKFPILVRECS 52 (68)
Q Consensus 32 ~~l~~~~~~NP~v~i~v~~~~ 52 (68)
+.+.++|++||++++++.-.-
T Consensus 59 ~~~~~lK~~~p~lKvllSiGG 79 (253)
T cd06544 59 EAVKSIKAQHPNVKVVISIGG 79 (253)
T ss_pred HHHHHHHHhCCCcEEEEEeCC
Confidence 568899999999999997644
No 155
>PRK09375 quinolinate synthetase; Provisional
Probab=32.53 E-value=70 Score=23.33 Aligned_cols=34 Identities=24% Similarity=0.218 Sum_probs=27.2
Q ss_pred ecCCCCCCHHHHHHHHhC-------------HHHHHHhCCCCeEEEE
Q psy15302 16 LCQKGGSSSGVRDFLAQH-------------YVPLKQANPKFPILVR 49 (68)
Q Consensus 16 yc~~~~sS~G~R~Fl~~~-------------l~~~~~~NP~v~i~v~ 49 (68)
.+|.-|||.|+-+|++.. +-.+++++|+-+|..-
T Consensus 223 ~AD~vgSTs~~i~~v~~~~~~~~iigTE~~L~~~l~~~~P~K~fi~~ 269 (319)
T PRK09375 223 LADFVGSTSQIIKAAKASPAKKFIVGTEIGIVHRLQKANPDKEFIPA 269 (319)
T ss_pred hcCEEecHHHHHHHHHhCCCCeEEEEccHHHHHHHHHHCCCCEEEEC
Confidence 478889999999999643 4468888999988853
No 156
>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=32.34 E-value=79 Score=16.34 Aligned_cols=36 Identities=6% Similarity=0.106 Sum_probs=26.5
Q ss_pred EEEEEecCCCCCCHHHHHHHHhCHHHHHHhCCCCeEEEEe
Q psy15302 11 ELRIHLCQKGGSSSGVRDFLAQHYVPLKQANPKFPILVRE 50 (68)
Q Consensus 11 ~l~~~yc~~~~sS~G~R~Fl~~~l~~~~~~NP~v~i~v~~ 50 (68)
+|.+.+-+|.+-++=++.+++ +++..+|++++....
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 577888888888888877664 456678888876643
No 157
>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=32.29 E-value=44 Score=21.76 Aligned_cols=23 Identities=9% Similarity=0.144 Sum_probs=19.0
Q ss_pred HHHhCH-HHHHHhCCCCeEEEEec
Q psy15302 29 FLAQHY-VPLKQANPKFPILVREC 51 (68)
Q Consensus 29 Fl~~~l-~~~~~~NP~v~i~v~~~ 51 (68)
+++..+ .+|.+.||.|.|.+...
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 666667 88999999999998664
No 158
>KOG2559|consensus
Probab=32.28 E-value=55 Score=23.76 Aligned_cols=36 Identities=17% Similarity=0.058 Sum_probs=30.2
Q ss_pred CcccccCcceEEEEEecCCCCCCHHHHHHHHhCHHH
Q psy15302 1 MAARFGSKLKELRIHLCQKGGSSSGVRDFLAQHYVP 36 (68)
Q Consensus 1 Ms~r~v~qlk~l~~~yc~~~~sS~G~R~Fl~~~l~~ 36 (68)
|...++|.|.-|--.|=+.|-+|+++|+-|..++-+
T Consensus 1 mg~~~i~kl~Gvl~VYKpsGik~khlr~~i~~~i~k 36 (318)
T KOG2559|consen 1 MGHLDIWKLSGVLCVYKPSGIKSKHLRKLITRKIAK 36 (318)
T ss_pred CCccchhhhcceeEEecCCCccHHHHHHHHHHHHHh
Confidence 677788888888888989999999999999765543
No 159
>PRK14997 LysR family transcriptional regulator; Provisional
Probab=32.10 E-value=95 Score=20.78 Aligned_cols=27 Identities=4% Similarity=0.144 Sum_probs=22.5
Q ss_pred HHHHHHhCHHHHHHhCCCCeEEEEecC
Q psy15302 26 VRDFLAQHYVPLKQANPKFPILVRECS 52 (68)
Q Consensus 26 ~R~Fl~~~l~~~~~~NP~v~i~v~~~~ 52 (68)
...++...+.+|.+++|++.|.+....
T Consensus 103 ~~~~l~~~l~~~~~~~P~i~i~~~~~~ 129 (301)
T PRK14997 103 LHVHIGPMLAKFMARYPDVSLQLEATN 129 (301)
T ss_pred HHHHHHHHHHHHHHHCCCeEEEEEecC
Confidence 346778899999999999999997643
No 160
>COG2871 NqrF Na+-transporting NADH:ubiquinone oxidoreductase, subunit NqrF [Energy production and conversion]
Probab=31.91 E-value=94 Score=23.28 Aligned_cols=38 Identities=13% Similarity=0.363 Sum_probs=29.1
Q ss_pred ceEEEEEecCCCCCCHHHHHHH-HhCHHHHHHhCCCCeEEEEec
Q psy15302 9 LKELRIHLCQKGGSSSGVRDFL-AQHYVPLKQANPKFPILVREC 51 (68)
Q Consensus 9 lk~l~~~yc~~~~sS~G~R~Fl-~~~l~~~~~~NP~v~i~v~~~ 51 (68)
=+||.|-| ..+..|+-+ .+.+.+++++||+..-.+...
T Consensus 304 kRkis~WY-----GARS~rE~fY~Ed~d~L~ae~pNF~wH~aLS 342 (410)
T COG2871 304 KRKISFWY-----GARSLREMFYQEDFDQLQAENPNFHWHLALS 342 (410)
T ss_pred cceeeeee-----ccchHHHhHHHHHHHHHHhhCCCcEEEEEec
Confidence 46788877 355667655 789999999999998887543
No 161
>PRK03601 transcriptional regulator HdfR; Provisional
Probab=31.87 E-value=89 Score=20.86 Aligned_cols=26 Identities=15% Similarity=0.032 Sum_probs=22.2
Q ss_pred HHHHHHhCHHHHHHhCCCCeEEEEec
Q psy15302 26 VRDFLAQHYVPLKQANPKFPILVREC 51 (68)
Q Consensus 26 ~R~Fl~~~l~~~~~~NP~v~i~v~~~ 51 (68)
...++...+.+|.+.+|++.|.+...
T Consensus 100 ~~~~l~~~l~~f~~~~P~v~v~~~~~ 125 (275)
T PRK03601 100 WECMLTPWLGRLYQNQEALQFEARIA 125 (275)
T ss_pred HHHHHHHHHHHHHHhCCCcEEEEEEC
Confidence 36778899999999999999988654
No 162
>cd04864 LigD_Pol_like_1 LigD_Pol_like_1: Polymerase (Pol) domain of mostly bacterial LigD proteins similar to Pseudomonas aeruginosa (Pae) LigD, subgroup 1. The LigD Pol domain belongs to the archaeal/eukaryal primase (AEP) superfamily. In prokaryotes, LigD along with Ku is required for non-homologous end joining (NHEJ)-mediated repair of DNA double-strand breaks (DSB). NHEJ-mediated DNA DSB repair is error-prone. It has been suggested that LigD Pol contributes to NHEJ-mediated DNA DSB repair in vivo, by filling in short 5'-overhangs with ribonucleotides; the filled in termini would then be sealed by the associated LigD ligase domain, resulting in short stretches of RNA incorporated into the genomic DNA. The Pol domains of PaeLigD and Mycobacterium tuberculosis (Mt)LigD are stimulated by manganese, are error-prone, and prefer adding rNTPs to dNTPs in vitro; however PaeLigD and MtLigD belong to other subgroups, proteins in this subgroup await functional characterization.
Probab=31.80 E-value=39 Score=23.58 Aligned_cols=45 Identities=16% Similarity=0.090 Sum_probs=37.9
Q ss_pred CCHHHHHHHHhCHHHHHHhCCCCeEEEEecCCCCCEEEEEec-CCC
Q psy15302 22 SSSGVRDFLAQHYVPLKQANPKFPILVRECSGVTPVVWASGK-GTH 66 (68)
Q Consensus 22 sS~G~R~Fl~~~l~~~~~~NP~v~i~v~~~~~~~P~v~a~Y~-nGr 66 (68)
+..-+|.|.+.--..+.+++|+.-...+....+.-+|...|. |++
T Consensus 156 ~~~~~r~fa~~lA~~l~~~~P~~~t~~~~k~~R~grvfiDylqN~~ 201 (228)
T cd04864 156 DFDDVRAFAAEAADALAKRDPDLLTTEARKAKRGDRVFLDIGRNAY 201 (228)
T ss_pred CHHHHHHHHHHHHHHHHHHCchhhhHHhhHHhCCCcEEEECccCCC
Confidence 357789999999999999999998887777777789999998 665
No 163
>PRK10086 DNA-binding transcriptional regulator DsdC; Provisional
Probab=31.75 E-value=77 Score=21.59 Aligned_cols=28 Identities=7% Similarity=0.160 Sum_probs=23.6
Q ss_pred HHHHHHHhCHHHHHHhCCCCeEEEEecC
Q psy15302 25 GVRDFLAQHYVPLKQANPKFPILVRECS 52 (68)
Q Consensus 25 G~R~Fl~~~l~~~~~~NP~v~i~v~~~~ 52 (68)
-...++...+..|.+.+|++.|.+....
T Consensus 112 ~~~~~l~~~l~~f~~~~P~i~i~~~~~~ 139 (311)
T PRK10086 112 IAQCWLVPRLADFTRRYPSISLTILTGN 139 (311)
T ss_pred HHHHHHHHHHHHHHHHCCCeEEEEEeCC
Confidence 3557888999999999999999998643
No 164
>KOG3170|consensus
Probab=31.69 E-value=1.2e+02 Score=21.41 Aligned_cols=33 Identities=12% Similarity=0.164 Sum_probs=26.8
Q ss_pred CHHHHHHHHhCHHHHHHhCCCCeEEEEecCCCC
Q psy15302 23 SSGVRDFLAQHYVPLKQANPKFPILVRECSGVT 55 (68)
Q Consensus 23 S~G~R~Fl~~~l~~~~~~NP~v~i~v~~~~~~~ 55 (68)
|...=..|...+..++.+.|++.|+--+...+-
T Consensus 122 gvp~c~Ll~~~l~~la~kfp~iKFVki~at~cI 154 (240)
T KOG3170|consen 122 GVPLCALLSHHLQSLACKFPQIKFVKIPATTCI 154 (240)
T ss_pred ccHHHHHHHHHHHHHhhcCCcceEEeccccccc
Confidence 456677889999999999999999987665443
No 165
>KOG0863|consensus
Probab=31.67 E-value=23 Score=25.22 Aligned_cols=24 Identities=21% Similarity=0.538 Sum_probs=20.2
Q ss_pred CCCCHHHHHHHHhCHHHHHHhCCC
Q psy15302 20 GGSSSGVRDFLAQHYVPLKQANPK 43 (68)
Q Consensus 20 ~~sS~G~R~Fl~~~l~~~~~~NP~ 43 (68)
|--|++.|.||+.++.+|-+.+|.
T Consensus 162 GsRSQsARTyLEr~~e~f~~~~~e 185 (264)
T KOG0863|consen 162 GSRSQSARTYLERNLEEFEDSSPE 185 (264)
T ss_pred ccchhhHHHHHHHHHHHHhcCCHH
Confidence 446899999999999999887764
No 166
>cd01523 RHOD_Lact_B Member of the Rhodanese Homology Domain superfamily. This CD includes predicted proteins with rhodanese-like domains found N-terminal of the metallo-beta-lactamase domain.
Probab=31.65 E-value=67 Score=18.08 Aligned_cols=20 Identities=40% Similarity=0.484 Sum_probs=14.3
Q ss_pred EEEEecCCCCCCHHHHHHHH
Q psy15302 12 LRIHLCQKGGSSSGVRDFLA 31 (68)
Q Consensus 12 l~~~yc~~~~sS~G~R~Fl~ 31 (68)
-.+.||..|..|.-+-..|.
T Consensus 63 ~ivv~C~~G~rs~~aa~~L~ 82 (100)
T cd01523 63 EVTVICAKEGSSQFVAELLA 82 (100)
T ss_pred eEEEEcCCCCcHHHHHHHHH
Confidence 35669999988876666654
No 167
>COG0187 GyrB Type IIA topoisomerase (DNA gyrase/topo II, topoisomerase IV), B subunit [DNA replication, recombination, and repair]
Probab=31.50 E-value=70 Score=25.65 Aligned_cols=39 Identities=13% Similarity=-0.016 Sum_probs=30.2
Q ss_pred HHHHHhCHHHHHHhCCCCeEEEEecCCCCCEEEEEecCC
Q psy15302 27 RDFLAQHYVPLKQANPKFPILVRECSGVTPVVWASGKGT 65 (68)
Q Consensus 27 R~Fl~~~l~~~~~~NP~v~i~v~~~~~~~P~v~a~Y~nG 65 (68)
-+.|.+.+-++|-.||.|.|...-.+...+....+|.+|
T Consensus 186 ~~~l~~RlrelA~L~~gl~I~l~d~r~~~~~~~~~y~~G 224 (635)
T COG0187 186 YEILKRRLRELAFLNKGVKITLTDERTGEEKKEFHYEGG 224 (635)
T ss_pred HHHHHHHHHHHhccCCCCEEEEEeccCCcccceeecccH
Confidence 467889999999999999999977665444335777766
No 168
>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=31.46 E-value=99 Score=21.66 Aligned_cols=34 Identities=18% Similarity=0.077 Sum_probs=26.0
Q ss_pred EEEecCCCCCCHHHHHHHHhCHHHHHHhCCCCeEEE
Q psy15302 13 RIHLCQKGGSSSGVRDFLAQHYVPLKQANPKFPILV 48 (68)
Q Consensus 13 ~~~yc~~~~sS~G~R~Fl~~~l~~~~~~NP~v~i~v 48 (68)
+|.+||+.|....-+ +.+.+..+++..|+++|.+
T Consensus 163 ~i~l~DT~G~~~P~~--v~~l~~~l~~~~~~~~i~~ 196 (280)
T cd07945 163 RIMLPDTLGILSPFE--TYTYISDMVKRYPNLHFDF 196 (280)
T ss_pred EEEecCCCCCCCHHH--HHHHHHHHHhhCCCCeEEE
Confidence 588899988776654 5667777888888888765
No 169
>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=31.23 E-value=50 Score=18.85 Aligned_cols=27 Identities=11% Similarity=0.361 Sum_probs=20.4
Q ss_pred CHHHHHHHHhCHHHHHHhCCCCeEEEE
Q psy15302 23 SSGVRDFLAQHYVPLKQANPKFPILVR 49 (68)
Q Consensus 23 S~G~R~Fl~~~l~~~~~~NP~v~i~v~ 49 (68)
..-+++++++-...+++.+|+.+|.+-
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 456889999999999999999998764
No 170
>PF01903 CbiX: CbiX; InterPro: IPR002762 Cobalamin (vitamin B12) is a structurally complex cofactor, consisting of a modified tetrapyrrole with a centrally chelated cobalt. Cobalamin is usually found in one of two biologically active forms: methylcobalamin and adocobalamin. Most prokaryotes, as well as animals, have cobalamin-dependent enzymes, whereas plants and fungi do not appear to use it. In bacteria and archaea, these include methionine synthase, ribonucleotide reductase, glutamate and methylmalonyl-CoA mutases, ethanolamine ammonia lyase, and diol dehydratase []. In mammals, cobalamin is obtained through the diet, and is required for methionine synthase and methylmalonyl-CoA mutase []. There are at least two distinct cobalamin biosynthetic pathways in bacteria []: Aerobic pathway that requires oxygen and in which cobalt is inserted late in the pathway []; found in Pseudomonas denitrificans and Rhodobacter capsulatus. Anaerobic pathway in which cobalt insertion is the first committed step towards cobalamin synthesis []; found in Salmonella typhimurium, Bacillus megaterium, and Propionibacterium freudenreichii subsp. shermanii. Either pathway can be divided into two parts: (1) corrin ring synthesis (differs in aerobic and anaerobic pathways) and (2) adenosylation of corrin ring, attachment of aminopropanol arm, and assembly of the nucleotide loop (common to both pathways) []. There are about 30 enzymes involved in either pathway, where those involved in the aerobic pathway are prefixed Cob and those of the anaerobic pathway Cbi. Several of these enzymes are pathway-specific: CbiD, CbiG, and CbiK are specific to the anaerobic route of S. typhimurium, whereas CobE, CobF, CobG, CobN, CobS, CobT, and CobW are unique to the aerobic pathway of P. denitrificans. This entry represents the CbiX protein, which functions as a cobalt-chelatase in the anaerobic biosynthesis of cobalamin. It catalyses the insertion of cobalt into sirohydrochlorin. The structure of CbiX from Archaeoglobus fulgidus consists of a central mixed beta-sheet flanked by four alpha-helices, although it is about half the size of other Class II tetrapyrrole chelatases []. The CbiX proteins found in archaea appear to be shorter than those found in eubacteria [].; GO: 0016829 lyase activity, 0046872 metal ion binding, 0009236 cobalamin biosynthetic process; PDB: 2XWQ_C 2DJ5_A 1TJN_A 2XWS_A 3LYH_B 2JH3_D.
Probab=31.15 E-value=14 Score=21.43 Aligned_cols=35 Identities=14% Similarity=0.250 Sum_probs=25.2
Q ss_pred HHHHHHHHhCHHHHHHhCCCCeEEEEecCCCCCEE
Q psy15302 24 SGVRDFLAQHYVPLKQANPKFPILVRECSGVTPVV 58 (68)
Q Consensus 24 ~G~R~Fl~~~l~~~~~~NP~v~i~v~~~~~~~P~v 58 (68)
.-++.=|.+.+...+..+|++.|.+-+.-|.||.|
T Consensus 65 ~h~~~DIp~~l~~~~~~~~~~~v~~~~pLG~~p~l 99 (105)
T PF01903_consen 65 YHVKRDIPEALAEARERHPGIEVRVAPPLGPHPLL 99 (105)
T ss_dssp HHHHCHHHHHHCHHHHCSTTEEEEE---GGGSCCH
T ss_pred cchHhHHHHHHHHHHhhCCceEEEECCCCCCCHHH
Confidence 44555566777889999999999998888888864
No 171
>PRK10341 DNA-binding transcriptional activator TdcA; Provisional
Probab=30.84 E-value=85 Score=21.33 Aligned_cols=37 Identities=14% Similarity=0.113 Sum_probs=26.7
Q ss_pred eEEEEEecCCCCCCHHHHHHHHhCHHHHHHhCCCCeEEEEec
Q psy15302 10 KELRIHLCQKGGSSSGVRDFLAQHYVPLKQANPKFPILVREC 51 (68)
Q Consensus 10 k~l~~~yc~~~~sS~G~R~Fl~~~l~~~~~~NP~v~i~v~~~ 51 (68)
..|+|-.++. -...++..-+..|.+.+|+++|.+...
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 3466644322 234678899999999999999999754
No 172
>PLN02870 Probable galacturonosyltransferase
Probab=30.67 E-value=42 Score=26.27 Aligned_cols=25 Identities=24% Similarity=0.484 Sum_probs=20.7
Q ss_pred CcccccCcceEEEEEecCCCCCCHHHHHHHH
Q psy15302 1 MAARFGSKLKELRIHLCQKGGSSSGVRDFLA 31 (68)
Q Consensus 1 Ms~r~v~qlk~l~~~yc~~~~sS~G~R~Fl~ 31 (68)
|-.+-.++++.|+++ +|+|+|+||+
T Consensus 1 ~~~~~~~~~~~~~~~------~~~~~~~~~~ 25 (533)
T PLN02870 1 MQLHISPSMRSITIS------SSNGFIDLMK 25 (533)
T ss_pred CceeecCccceEEEe------cCCcHHHHHH
Confidence 556777889999986 5899999996
No 173
>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=30.57 E-value=71 Score=17.64 Aligned_cols=22 Identities=32% Similarity=0.449 Sum_probs=16.1
Q ss_pred HHHHHHHhCHHHHHHhCCCCeE
Q psy15302 25 GVRDFLAQHYVPLKQANPKFPI 46 (68)
Q Consensus 25 G~R~Fl~~~l~~~~~~NP~v~i 46 (68)
..+.|-..-=|.++++||.++.
T Consensus 15 ~yK~Fsq~vRP~l~~~NPk~~~ 36 (55)
T PF08073_consen 15 NYKAFSQHVRPLLAKANPKAPM 36 (55)
T ss_pred HHHHHHHHHHHHHHHHCCCCcH
Confidence 3455666667899999998863
No 174
>PF14363 AAA_assoc: Domain associated at C-terminal with AAA
Probab=30.30 E-value=82 Score=18.56 Aligned_cols=30 Identities=20% Similarity=0.419 Sum_probs=24.0
Q ss_pred HHHHHHHHhCHHH-HH-HhCCCCeEEEEecCC
Q psy15302 24 SGVRDFLAQHYVP-LK-QANPKFPILVRECSG 53 (68)
Q Consensus 24 ~G~R~Fl~~~l~~-~~-~~NP~v~i~v~~~~~ 53 (68)
..+|+|+.+.+.. |. .-+|.+.|.|.+..|
T Consensus 4 ~~lr~~~~~~~~~~~~~~~s~~~ti~I~E~~g 35 (98)
T PF14363_consen 4 HELRSYLRSLLRRLFSSRFSPYLTIVIPEFDG 35 (98)
T ss_pred HHHHHHHHHHHHHHHhccCCCcEEEEEEeCCC
Confidence 4689999988865 55 788999999988765
No 175
>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=30.15 E-value=38 Score=18.55 Aligned_cols=19 Identities=21% Similarity=0.064 Sum_probs=14.9
Q ss_pred HHHHhCHHHHHHhCCCCeE
Q psy15302 28 DFLAQHYVPLKQANPKFPI 46 (68)
Q Consensus 28 ~Fl~~~l~~~~~~NP~v~i 46 (68)
-|+...-++++++||++.+
T Consensus 11 ~F~~~~r~~~~~~~p~~~~ 29 (72)
T cd01388 11 LFSKRHRRKVLQEYPLKEN 29 (72)
T ss_pred HHHHHHHHHHHHHCCCCCH
Confidence 3567788999999998753
No 176
>PRK13337 putative lipid kinase; Reviewed
Probab=29.79 E-value=1.3e+02 Score=20.83 Aligned_cols=42 Identities=17% Similarity=0.094 Sum_probs=28.7
Q ss_pred eEEEEEecCCCCCCHHHHHHHHhCHHHHHHhCCCCeEEEEecC
Q psy15302 10 KELRIHLCQKGGSSSGVRDFLAQHYVPLKQANPKFPILVRECS 52 (68)
Q Consensus 10 k~l~~~yc~~~~sS~G~R~Fl~~~l~~~~~~NP~v~i~v~~~~ 52 (68)
+++.|-|++.+|+.++.+.+ .+-...+.+.+-++.++..+..
T Consensus 2 ~r~~~I~Np~aG~~~~~~~~-~~~~~~l~~~~~~~~~~~t~~~ 43 (304)
T PRK13337 2 KRARIIYNPTSGRELFKKNL-PDVLQKLEQAGYETSAHATTGP 43 (304)
T ss_pred ceEEEEECCcccchhHHHHH-HHHHHHHHHcCCEEEEEEecCC
Confidence 57889999999987776664 3345567777766666555443
No 177
>PRK12684 transcriptional regulator CysB-like protein; Reviewed
Probab=28.85 E-value=95 Score=21.19 Aligned_cols=29 Identities=17% Similarity=0.190 Sum_probs=23.6
Q ss_pred CHHHHHHHHhCHHHHHHhCCCCeEEEEec
Q psy15302 23 SSGVRDFLAQHYVPLKQANPKFPILVREC 51 (68)
Q Consensus 23 S~G~R~Fl~~~l~~~~~~NP~v~i~v~~~ 51 (68)
......++...+..|.+++|++.+.+...
T Consensus 101 ~~~~~~~l~~~l~~~~~~~p~i~l~~~~~ 129 (313)
T PRK12684 101 HTQARYALPAAIKEFKKRYPKVRLSILQG 129 (313)
T ss_pred hHHHHHHhHHHHHHHHHHCCCceEEEEeC
Confidence 34456778899999999999999999764
No 178
>TIGR02336 1,3-beta-galactosyl-N-acetylhexosamine phosphorylase. Members of this family are found in phylogenetically diverse bacteria, including Clostridium perfringens (in the Firmicutes), Bifidobacterium longum and Propionibacterium acnes (in the Actinobacteria), and Vibrio vulnificus (in the Proteobacteria), most of which occur as mammalian pathogens or commensals. The nominal activity, 1,3-beta-galactosyl-N-acetylhexosamine phosphorylase (EC 2.4.1.211), varies somewhat from instance to instance in relative rates for closely related substrates.
Probab=28.63 E-value=58 Score=26.45 Aligned_cols=27 Identities=7% Similarity=0.176 Sum_probs=23.3
Q ss_pred CHHHHHHHHhCHHHHHHhCCCCeEEEE
Q psy15302 23 SSGVRDFLAQHYVPLKQANPKFPILVR 49 (68)
Q Consensus 23 S~G~R~Fl~~~l~~~~~~NP~v~i~v~ 49 (68)
-.-.|+|+...|.++-+.||++.++-.
T Consensus 184 ~p~t~~~~~~~l~~wl~~~p~~dVvRf 210 (719)
T TIGR02336 184 HPATRKHVFDTFEQWLKDSPQTDVVRF 210 (719)
T ss_pred ChHHHHHHHHHHHHHHHhCCCCcEEEE
Confidence 456899999999999999999988643
No 179
>PRK15421 DNA-binding transcriptional regulator MetR; Provisional
Probab=28.62 E-value=84 Score=21.64 Aligned_cols=25 Identities=8% Similarity=0.153 Sum_probs=21.9
Q ss_pred HHHHHhCHHHHHHhCCCCeEEEEec
Q psy15302 27 RDFLAQHYVPLKQANPKFPILVREC 51 (68)
Q Consensus 27 R~Fl~~~l~~~~~~NP~v~i~v~~~ 51 (68)
..++...+.+|++.+|++.+.+...
T Consensus 101 ~~~l~~~l~~~~~~~P~i~l~~~~~ 125 (317)
T PRK15421 101 IQWLTPALENFHKNWPQVEMDFKSG 125 (317)
T ss_pred HHHHHHHHHHHHHHCCCceEEEEeC
Confidence 4688889999999999999999764
No 180
>PF13552 DUF4127: Protein of unknown function (DUF4127)
Probab=28.49 E-value=53 Score=25.08 Aligned_cols=19 Identities=32% Similarity=0.511 Sum_probs=16.9
Q ss_pred hCHHHHHHhCCCCeEEEEe
Q psy15302 32 QHYVPLKQANPKFPILVRE 50 (68)
Q Consensus 32 ~~l~~~~~~NP~v~i~v~~ 50 (68)
+.+-+|+++||+++|++..
T Consensus 92 ~~l~~lk~~~p~~~iyaf~ 110 (497)
T PF13552_consen 92 ERLRELKARNPNLPIYAFS 110 (497)
T ss_pred HHHHHHHHHCCCCeEEEEE
Confidence 6789999999999999854
No 181
>PRK11013 DNA-binding transcriptional regulator LysR; Provisional
Probab=28.40 E-value=97 Score=21.01 Aligned_cols=26 Identities=12% Similarity=0.201 Sum_probs=22.4
Q ss_pred HHHHHhCHHHHHHhCCCCeEEEEecC
Q psy15302 27 RDFLAQHYVPLKQANPKFPILVRECS 52 (68)
Q Consensus 27 R~Fl~~~l~~~~~~NP~v~i~v~~~~ 52 (68)
..++...+.+|.+.+|++.|.+....
T Consensus 106 ~~~l~~~l~~~~~~~P~v~i~i~~~~ 131 (309)
T PRK11013 106 QSLLPGLCQPFLARYPDVSLNIVPQE 131 (309)
T ss_pred HhhHHHHHHHHHHHCCCCeEEEEeCC
Confidence 45778999999999999999998654
No 182
>PRK11914 diacylglycerol kinase; Reviewed
Probab=28.18 E-value=1e+02 Score=21.22 Aligned_cols=41 Identities=7% Similarity=0.090 Sum_probs=28.3
Q ss_pred cceEEEEEecCCCCCCHHHHHHHHhCHHHHHHhCCCCeEEEE
Q psy15302 8 KLKELRIHLCQKGGSSSGVRDFLAQHYVPLKQANPKFPILVR 49 (68)
Q Consensus 8 qlk~l~~~yc~~~~sS~G~R~Fl~~~l~~~~~~NP~v~i~v~ 49 (68)
+-+++.|-|++.+|+.++.+.+ ++-...+++.+.++.+...
T Consensus 7 ~~~~~~iI~NP~sG~g~~~~~~-~~~~~~l~~~g~~~~~~~t 47 (306)
T PRK11914 7 EIGKVTVLTNPLSGHGAAPHAA-ERAIARLHHRGVDVVEIVG 47 (306)
T ss_pred CCceEEEEECCCCCCCcHHHHH-HHHHHHHHHcCCeEEEEEe
Confidence 3478899999999987766554 3334567777776665444
No 183
>KOG3239|consensus
Probab=28.09 E-value=31 Score=23.56 Aligned_cols=26 Identities=19% Similarity=0.391 Sum_probs=21.6
Q ss_pred EEEEecCCCCCCHHHHHHHHhCHHHH
Q psy15302 12 LRIHLCQKGGSSSGVRDFLAQHYVPL 37 (68)
Q Consensus 12 l~~~yc~~~~sS~G~R~Fl~~~l~~~ 37 (68)
|-..||+.+|.-+--|.||..|.|++
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 184
>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=28.08 E-value=78 Score=17.79 Aligned_cols=25 Identities=8% Similarity=0.222 Sum_probs=20.2
Q ss_pred CCCCHHHHHHHHhCHHHHHHhCCCC
Q psy15302 20 GGSSSGVRDFLAQHYVPLKQANPKF 44 (68)
Q Consensus 20 ~~sS~G~R~Fl~~~l~~~~~~NP~v 44 (68)
=..|..+++|+++.+..+.+-.+++
T Consensus 9 ~~~t~al~~~i~~k~~kl~r~~~~i 33 (93)
T cd00552 9 IEVTDALREYVEEKLEKLEKYFDRI 33 (93)
T ss_pred ccCCHHHHHHHHHHHHHHHHhcCCC
Confidence 3458999999999888888888644
No 185
>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=27.69 E-value=52 Score=17.30 Aligned_cols=18 Identities=28% Similarity=0.451 Sum_probs=15.0
Q ss_pred HHHHhCHHHHHHhCCCCe
Q psy15302 28 DFLAQHYVPLKQANPKFP 45 (68)
Q Consensus 28 ~Fl~~~l~~~~~~NP~v~ 45 (68)
-|..+....+++.||+..
T Consensus 10 lf~~~~~~~~k~~~p~~~ 27 (69)
T PF00505_consen 10 LFCKEKRAKLKEENPDLS 27 (69)
T ss_dssp HHHHHHHHHHHHHSTTST
T ss_pred HHHHHHHHHHHHHhcccc
Confidence 466788999999999875
No 186
>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=27.65 E-value=79 Score=17.43 Aligned_cols=40 Identities=13% Similarity=0.092 Sum_probs=27.8
Q ss_pred EEEEEecCCCCCCHHHHHHHHhCHHHHHHhCCCCeEEEEe
Q psy15302 11 ELRIHLCQKGGSSSGVRDFLAQHYVPLKQANPKFPILVRE 50 (68)
Q Consensus 11 ~l~~~yc~~~~sS~G~R~Fl~~~l~~~~~~NP~v~i~v~~ 50 (68)
-|...|-+|.+.++.+..-+.+...+++..+|.+.+..-.
T Consensus 19 ~lv~f~a~wC~~C~~~~p~~~~~~~~~~~~~~~~~~~~vd 58 (102)
T cd03005 19 HFVKFFAPWCGHCKRLAPTWEQLAKKFNNENPSVKIAKVD 58 (102)
T ss_pred EEEEEECCCCHHHHHhCHHHHHHHHHHhccCCcEEEEEEE
Confidence 5777888888888888776666556665555667666543
No 187
>TIGR02424 TF_pcaQ pca operon transcription factor PcaQ. Members of this family are LysR-family transcription factors associated with operons for catabolism of protocatechuate. Members occur only in Proteobacteria.
Probab=27.40 E-value=1.1e+02 Score=20.49 Aligned_cols=28 Identities=4% Similarity=0.108 Sum_probs=23.5
Q ss_pred HHHHHHHHhCHHHHHHhCCCCeEEEEec
Q psy15302 24 SGVRDFLAQHYVPLKQANPKFPILVREC 51 (68)
Q Consensus 24 ~G~R~Fl~~~l~~~~~~NP~v~i~v~~~ 51 (68)
.-...++...+..|.+++|++.|.+...
T Consensus 102 ~~~~~~~~~~l~~~~~~~P~~~i~~~~~ 129 (300)
T TIGR02424 102 TVAARLMPEVVKRFLARAPRLRVRIMTG 129 (300)
T ss_pred HHHHhhhHHHHHHHHHhCCCcEEEEEeC
Confidence 3456778899999999999999999863
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=27.38 E-value=86 Score=20.81 Aligned_cols=26 Identities=15% Similarity=0.217 Sum_probs=22.2
Q ss_pred HHHHHhCHHHHHHhCCCCeEEEEecC
Q psy15302 27 RDFLAQHYVPLKQANPKFPILVRECS 52 (68)
Q Consensus 27 R~Fl~~~l~~~~~~NP~v~i~v~~~~ 52 (68)
..++...+.+|.+++|++.|.+....
T Consensus 101 ~~~l~~~l~~~~~~~p~i~i~~~~~~ 126 (291)
T TIGR03418 101 TYWLMPRLHRFKRAMPDVDVSLVTSQ 126 (291)
T ss_pred HHHHhhhhHHHHHhCCCceEEEEecC
Confidence 47788889999999999999997643
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=27.25 E-value=48 Score=22.02 Aligned_cols=33 Identities=24% Similarity=0.271 Sum_probs=24.1
Q ss_pred HHHhCHHHHHHhCCCCeEEEEecCCCCCEEEEE
Q psy15302 29 FLAQHYVPLKQANPKFPILVRECSGVTPVVWAS 61 (68)
Q Consensus 29 Fl~~~l~~~~~~NP~v~i~v~~~~~~~P~v~a~ 61 (68)
.+..-+|+++++.|+-++.++-.....|.+...
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 345688999999999888888877789988753
No 190
>TIGR03851 chitin_NgcE carbohydrate ABC transporter, N-acetylglucosamine/diacetylchitobiose-binding protein. Members of this protein family are the substrate-binding protein, a lipid-anchored protein of Gram-positive bacteria in all examples found so far, that include NgcE of the chitin-degrader, Streptomyces olivaceoviridis, and close homologs from other species likely to share the same function. NgcE binds both N-acetylglucosamine and the chitin dimer, N,N'-diacetylchitobiose.
Probab=27.23 E-value=81 Score=22.64 Aligned_cols=24 Identities=17% Similarity=0.170 Sum_probs=20.2
Q ss_pred HHHHHhCHHHHHHhCCCCeEEEEe
Q psy15302 27 RDFLAQHYVPLKQANPKFPILVRE 50 (68)
Q Consensus 27 R~Fl~~~l~~~~~~NP~v~i~v~~ 50 (68)
-++++....+|.++||+|.|.+..
T Consensus 53 ~~~~~~~~~~F~~~~p~i~V~~~~ 76 (450)
T TIGR03851 53 DDYAKDAEPLYKKKYPGATVKVSP 76 (450)
T ss_pred HHHHHHHHHHHHHHCCCcEEEEee
Confidence 357788889999999999998864
No 191
>TIGR00411 redox_disulf_1 small redox-active disulfide protein 1. This protein is homologous to a family of proteins that includes thioredoxins, glutaredoxins, protein-disulfide isomerases, and others, some of which have several such domains. The sequence of this protein at the redox-active disufide site, CPYC, matches glutaredoxins rather than thioredoxins, although its overall sequence seems closer to thioredoxins. It is suggested to be a ribonucleotide-reducing system component distinct from thioredoxin or glutaredoxin.
Probab=27.20 E-value=1.1e+02 Score=16.21 Aligned_cols=27 Identities=0% Similarity=0.049 Sum_probs=21.8
Q ss_pred EEEEEecCCCCCCHHHHHHHHhCHHHH
Q psy15302 11 ELRIHLCQKGGSSSGVRDFLAQHYVPL 37 (68)
Q Consensus 11 ~l~~~yc~~~~sS~G~R~Fl~~~l~~~ 37 (68)
.|.+.+.+|.+.++-+...+++...++
T Consensus 2 ~v~~f~~~~C~~C~~~~~~l~~l~~~~ 28 (82)
T TIGR00411 2 KIELFTSPTCPYCPAAKRVVEEVAKEM 28 (82)
T ss_pred EEEEEECCCCcchHHHHHHHHHHHHHh
Confidence 578889999999999999887655444
No 192
>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=27.12 E-value=68 Score=16.11 Aligned_cols=21 Identities=5% Similarity=0.012 Sum_probs=15.6
Q ss_pred EEEEecCCCCCCHHHHHHHHh
Q psy15302 12 LRIHLCQKGGSSSGVRDFLAQ 32 (68)
Q Consensus 12 l~~~yc~~~~sS~G~R~Fl~~ 32 (68)
|++..-++.+.++.++.+|.+
T Consensus 2 v~ly~~~~Cp~C~~~~~~L~~ 22 (72)
T cd02066 2 VVVFSKSTCPYCKRAKRLLES 22 (72)
T ss_pred EEEEECCCCHHHHHHHHHHHH
Confidence 456666778888888888864
No 193
>TIGR03850 bind_CPR_0540 carbohydrate ABC transporter substrate-binding protein, CPR_0540 family. Members of this protein are the substrate-binding protein of a predicted carbohydrate transporter operon, together with permease subunits of ABC transporter homology families. This substrate-binding protein frequently co-occurs in genomes with a family of disaccharide phosphorylases, TIGR02336, suggesting that the molecule transported will include beta-D-galactopyranosyl-(1-3)-N-acetyl-D-glucosamine and related carbohydrates. Members of this family are sporadically strain by strain, often in species with a human host association, including Propionibacterium acnes and Clostridium perfringens, and Bacillus cereus.
Probab=26.89 E-value=1.2e+02 Score=21.42 Aligned_cols=25 Identities=0% Similarity=0.045 Sum_probs=20.6
Q ss_pred HHHHHhCHHHHHHhCCCCeEEEEec
Q psy15302 27 RDFLAQHYVPLKQANPKFPILVREC 51 (68)
Q Consensus 27 R~Fl~~~l~~~~~~NP~v~i~v~~~ 51 (68)
.+.++..+.+|.++||+|.|.+...
T Consensus 47 ~~~~~~~~~~F~~~~~~i~V~~~~~ 71 (437)
T TIGR03850 47 TKMWEEVVEAFEKSHEGVKVELTVS 71 (437)
T ss_pred HHHHHHHHHHHHHHCCCceEEEEeC
Confidence 3567788889999999999998653
No 194
>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=26.87 E-value=75 Score=16.10 Aligned_cols=21 Identities=10% Similarity=0.140 Sum_probs=16.1
Q ss_pred EEEEecCCCCCCHHHHHHHHh
Q psy15302 12 LRIHLCQKGGSSSGVRDFLAQ 32 (68)
Q Consensus 12 l~~~yc~~~~sS~G~R~Fl~~ 32 (68)
+++.+..+++.+.-++.++.+
T Consensus 2 v~l~~~~~c~~c~~~~~~l~~ 22 (73)
T cd02976 2 VTVYTKPDCPYCKATKRFLDE 22 (73)
T ss_pred EEEEeCCCChhHHHHHHHHHH
Confidence 567777788888888888854
No 195
>PRK11233 nitrogen assimilation transcriptional regulator; Provisional
Probab=26.58 E-value=1.3e+02 Score=20.32 Aligned_cols=26 Identities=8% Similarity=0.143 Sum_probs=22.0
Q ss_pred HHHHHHhCHHHHHHhCCCCeEEEEec
Q psy15302 26 VRDFLAQHYVPLKQANPKFPILVREC 51 (68)
Q Consensus 26 ~R~Fl~~~l~~~~~~NP~v~i~v~~~ 51 (68)
.+.++...+.+|.+.+|++.+.+...
T Consensus 103 ~~~~~~~~l~~~~~~~p~i~l~~~~~ 128 (305)
T PRK11233 103 ASSLTMPLLQAVRAEFPGIVLYLHEN 128 (305)
T ss_pred hHHHHHHHHHHHHHHCCCcEEEEEEC
Confidence 46777888999999999999988754
No 196
>PLN02495 oxidoreductase, acting on the CH-CH group of donors
Probab=26.51 E-value=80 Score=23.47 Aligned_cols=28 Identities=21% Similarity=0.322 Sum_probs=23.3
Q ss_pred CCHHHHHHHHhCHHHHHHhCCCCeEEEEe
Q psy15302 22 SSSGVRDFLAQHYVPLKQANPKFPILVRE 50 (68)
Q Consensus 22 sS~G~R~Fl~~~l~~~~~~NP~v~i~v~~ 50 (68)
|..|+..|++. ++.++++.|++++.+.-
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 78899899998888765
No 197
>PF09508 Lact_bio_phlase: Lacto-N-biose phosphorylase; InterPro: IPR012711 The gene which codes for this protein in gut-bacteria is located in a novel putative operon for galactose metabolism. The protein appears to be a carbohydrate-processing phosphorolytic enzyme (2.4.1.211 from EC), unlike either glycoside hydrolases or glycoside lyase. Intestinal colonisation by Bifidobacteria is important for human health, especially in paediatrics, because colonisation seems to prevent infection by some pathogenic bacteria that cause diarrhoea or other illnesses. The operon seems to be involved in intestinal colonisation by Bifidobacteria mediated by metabolism of mucin sugars. In addition, it may also resolve the question of the nature of the bifidus factor in human milk as the lacto-N-biose structure found in milk oligosaccharides. ; GO: 0016758 transferase activity, transferring hexosyl groups; PDB: 2ZUW_A 2ZUU_C 2ZUT_D 2ZUV_A 2ZUS_B.
Probab=26.49 E-value=59 Score=26.39 Aligned_cols=28 Identities=7% Similarity=0.189 Sum_probs=21.0
Q ss_pred CCHHHHHHHHhCHHHHHHhCCCCeEEEE
Q psy15302 22 SSSGVRDFLAQHYVPLKQANPKFPILVR 49 (68)
Q Consensus 22 sS~G~R~Fl~~~l~~~~~~NP~v~i~v~ 49 (68)
--.-.|+|+.+.|.++-+.||++.++-.
T Consensus 180 r~p~t~~~~~~~L~~wl~~hP~~dVVRF 207 (716)
T PF09508_consen 180 RQPKTREYVLEWLRKWLEEHPDTDVVRF 207 (716)
T ss_dssp TSHHHHHHHHHHHHHHHHT-TT--EEEE
T ss_pred CCHHHHHHHHHHHHHHHHHCCCCcEEEe
Confidence 3457899999999999999999988643
No 198
>PF00781 DAGK_cat: Diacylglycerol kinase catalytic domain; InterPro: IPR001206 The DAG-kinase catalytic domain or DAGKc domain is present in mammalian lipid kinases, such as diacylglycerol (DAG), ceramide and sphingosine kinases, as well as in related bacterial proteins [, ]. Eukaryotic DAG-kinase (2.7.1.107 from EC) catalyses the phosphorylation of DAG to phosphatidic acid, thus modulating the balance between the two signaling lipids. At least ten different isoforms have been identified in mammals, which form 5 groups characterised by different functional domains, such as the calcium-binding EF hand (see PDOC00018 from PROSITEDOC), PH (see PDOC50003 from PROSITEDOC), SAM (see PDOC50105 from PROSITEDOC) , DAG/PE-binding C1 domain (see PDOC00379 from PROSITEDOC) and ankyrin repeats (see PDOC50088 from PROSITEDOC) []. In bacteria, an integral membrane DAG kinase forms a homotrimeric protein that lacks the DAGKc domain (see PDOC00820 from PROSITEDOC). In contrast, the bacterial yegS protein is a soluble cytosolic protein that contains the DAGKc domain in the N-terminal part. YegS is a lipid kinase with two structural domains, wherein the active site is located in the interdomain cleft, C-terminal to the DAGKc domain which forms an alpha/beta fold []. The tertiary structure resembles that of NAD kinases and contains a metal-binding site in the C-terminal region [, ]. This domain is usually associated with an accessory domain (see IPR000756 from INTERPRO).; GO: 0004143 diacylglycerol kinase activity, 0007205 activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway; PDB: 2JGR_A 2BON_A 3T5P_D 3S40_A 2P1R_A 2QV7_A 2QVL_A.
Probab=26.32 E-value=1.4e+02 Score=17.85 Aligned_cols=38 Identities=13% Similarity=0.264 Sum_probs=27.3
Q ss_pred EEEEEecCCCCCCHHHHHHHHhCHHHHHHhCCCCeEEEEec
Q psy15302 11 ELRIHLCQKGGSSSGVRDFLAQHYVPLKQANPKFPILVREC 51 (68)
Q Consensus 11 ~l~~~yc~~~~sS~G~R~Fl~~~l~~~~~~NP~v~i~v~~~ 51 (68)
++-|.+.+.+|+.++. | ++-.+.++.....+.+...+.
T Consensus 1 k~~vi~Np~sG~~~~~--~-~~v~~~l~~~~~~~~~~~t~~ 38 (130)
T PF00781_consen 1 KVLVIINPKSGGGRAK--W-KKVEPALRAAGIDYEVIETES 38 (130)
T ss_dssp SEEEEEETTSTTSHHH--H-HHHHHHHHHTTCEEEEEEESS
T ss_pred CEEEEECCCCCCCchh--H-HHHHHHHHHcCCceEEEEEec
Confidence 4678899999988888 4 666677777776666655443
No 199
>PRK10216 DNA-binding transcriptional regulator YidZ; Provisional
Probab=26.27 E-value=1.1e+02 Score=20.90 Aligned_cols=26 Identities=19% Similarity=0.148 Sum_probs=22.9
Q ss_pred HHHHHHhCHHHHHHhCCCCeEEEEec
Q psy15302 26 VRDFLAQHYVPLKQANPKFPILVREC 51 (68)
Q Consensus 26 ~R~Fl~~~l~~~~~~NP~v~i~v~~~ 51 (68)
.-.++..-+..|++.+|++.|.+...
T Consensus 108 ~~~~~~~~l~~f~~~~P~v~v~i~~~ 133 (319)
T PRK10216 108 MMIMLNALSKRIYQRYPQATIKLRNW 133 (319)
T ss_pred HHHHHHHHHHHHHHHCCCCEEEEEeC
Confidence 45788999999999999999999863
No 200
>PRK15092 DNA-binding transcriptional repressor LrhA; Provisional
Probab=25.90 E-value=1.3e+02 Score=20.76 Aligned_cols=27 Identities=19% Similarity=0.156 Sum_probs=22.9
Q ss_pred HHHHHHHhCHHHHHHhCCCCeEEEEec
Q psy15302 25 GVRDFLAQHYVPLKQANPKFPILVREC 51 (68)
Q Consensus 25 G~R~Fl~~~l~~~~~~NP~v~i~v~~~ 51 (68)
-...++...+.+|.+++|++.|.+...
T Consensus 109 ~~~~~l~~~l~~f~~~~P~i~i~l~~~ 135 (310)
T PRK15092 109 TADTILPFLLNRVSSVYPKLALDVRVK 135 (310)
T ss_pred HHHHHHHHHHHHHHHHCCCcEEEEEEC
Confidence 356788899999999999999988753
No 201
>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=25.88 E-value=62 Score=19.27 Aligned_cols=21 Identities=29% Similarity=0.379 Sum_probs=17.3
Q ss_pred HhCHHHHHHhCCCCeEEEEec
Q psy15302 31 AQHYVPLKQANPKFPILVREC 51 (68)
Q Consensus 31 ~~~l~~~~~~NP~v~i~v~~~ 51 (68)
.+.|.++|+++|+.-+.++..
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 457889999999998888754
No 202
>PRK10324 translation inhibitor protein RaiA; Provisional
Probab=25.76 E-value=1.6e+02 Score=17.82 Aligned_cols=32 Identities=13% Similarity=0.255 Sum_probs=24.4
Q ss_pred EEEEecCCCCCCHHHHHHHHhCHHHHHHhCCCC
Q psy15302 12 LRIHLCQKGGSSSGVRDFLAQHYVPLKQANPKF 44 (68)
Q Consensus 12 l~~~yc~~~~sS~G~R~Fl~~~l~~~~~~NP~v 44 (68)
|.|.+ .+-.-+..+|+++++.+..+.+-.|++
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 44444 444568999999999999998888754
No 203
>cd02975 PfPDO_like_N Pyrococcus furiosus protein disulfide oxidoreductase (PfPDO)-like family, N-terminal TRX-fold subdomain; composed of proteins with similarity to PfPDO, a redox active thermostable protein believed to be the archaeal counterpart of bacterial DsbA and eukaryotic protein disulfide isomerase (PDI), which are both involved in oxidative protein folding. PfPDO contains two redox active CXXC motifs in two contiguous TRX-fold subdomains. The active site in the N-terminal TRX-fold subdomain is required for isomerase but not for reductase activity of PfPDO. The exclusive presence of PfPDO-like proteins in extremophiles may suggest that they have a special role in adaptation to extreme conditions.
Probab=25.73 E-value=1.5e+02 Score=17.46 Aligned_cols=36 Identities=11% Similarity=0.189 Sum_probs=25.5
Q ss_pred EEEEE-ecCCCCCCHHHHHHHHhCHHHHHHhCCCCeEEEEe
Q psy15302 11 ELRIH-LCQKGGSSSGVRDFLAQHYVPLKQANPKFPILVRE 50 (68)
Q Consensus 11 ~l~~~-yc~~~~sS~G~R~Fl~~~l~~~~~~NP~v~i~v~~ 50 (68)
.+.+. +-+|.+.++-++.++++ +++.++.+++....
T Consensus 24 ~vvv~f~a~wC~~C~~~~~~l~~----la~~~~~i~~~~vd 60 (113)
T cd02975 24 DLVVFSSKEGCQYCEVTKQLLEE----LSELSDKLKLEIYD 60 (113)
T ss_pred EEEEEeCCCCCCChHHHHHHHHH----HHHhcCceEEEEEe
Confidence 35555 45788999999988865 45556888777653
No 204
>TIGR01256 modA molybdenum ABC transporter, periplasmic molybdate-binding protein. The model describes the molybdate ABC transporter periplasmic binding protein in bacteria and archae. Several of the periplasmic receptors constitute a diverse class of binding proteins that differ widely in size, sequence and ligand specificity. It has been shown experimentally by radioactive labeling that ModA represent hydrophylioc periplasmic-binding protein in gram-negative organisms and its counterpart in gram-positive organisms is a lipoprotein. The other components of the system include the ModB, an integral membrane protein and ModC the ATP-binding subunit. Invariably almost all of them display a common beta/alpha folding motif and have similar tertiary structures consisting of two globular domains.
Probab=25.19 E-value=93 Score=19.86 Aligned_cols=25 Identities=8% Similarity=0.050 Sum_probs=21.0
Q ss_pred HHHHHHHhCHHHHHHhCCCCeEEEEe
Q psy15302 25 GVRDFLAQHYVPLKQANPKFPILVRE 50 (68)
Q Consensus 25 G~R~Fl~~~l~~~~~~NP~v~i~v~~ 50 (68)
|++.-+..-.+.|.+++| +.|.+..
T Consensus 3 ~l~~~~~~~~~~f~~~~g-i~V~~~~ 27 (216)
T TIGR01256 3 SLTDALKEIAKQFEKRTG-NKVVFSF 27 (216)
T ss_pred chHHHHHHHHHHHHHhhC-CeEEEEe
Confidence 678888899999999998 8887753
No 205
>PF13905 Thioredoxin_8: Thioredoxin-like; PDB: 1FG4_A 1I5G_A 1OC8_B 1O6J_A 1OC9_B 1O81_A 3FKF_A 1O85_A 1O7U_A 1O8W_A ....
Probab=25.12 E-value=62 Score=17.84 Aligned_cols=38 Identities=8% Similarity=-0.044 Sum_probs=21.7
Q ss_pred EEEecCCCCCCHHHHHHHHhCHHHHHHhCCCCeEEEEec
Q psy15302 13 RIHLCQKGGSSSGVRDFLAQHYVPLKQANPKFPILVREC 51 (68)
Q Consensus 13 ~~~yc~~~~sS~G~R~Fl~~~l~~~~~~NP~v~i~v~~~ 51 (68)
...+..|.+.|+....-|.+.+.++++ +.+++|+....
T Consensus 6 l~fwa~~c~~c~~~~~~l~~l~~~~~~-~~~v~~v~Vs~ 43 (95)
T PF13905_consen 6 LYFWASWCPPCKKELPKLKELYKKYKK-KDDVEFVFVSL 43 (95)
T ss_dssp EEEE-TTSHHHHHHHHHHHHHHHHHTT-TTTEEEEEEE-
T ss_pred EEEECCCCHHHHHHHHHHHHHHHHhCC-CCCEEEEEEEe
Confidence 344555666566655555565555555 56888776543
No 206
>TIGR03339 phn_lysR aminoethylphosphonate catabolism associated LysR family transcriptional regulator. This group of sequences represents a number of related clades with numerous examples of members adjacent to operons for the degradation of 2-aminoethylphosphonate (AEP) in Pseudomonas, Ralstonia, Bordetella and Burkholderia species. These are transcriptional regulators of the LysR family which contain a helix-turn-helix (HTH) domain (pfam00126) and a periplasmic substrate-binding protein-like domain (pfam03466).
Probab=24.95 E-value=1.1e+02 Score=19.97 Aligned_cols=24 Identities=17% Similarity=0.235 Sum_probs=20.5
Q ss_pred HHHHhCHHHHHHhCCCCeEEEEec
Q psy15302 28 DFLAQHYVPLKQANPKFPILVREC 51 (68)
Q Consensus 28 ~Fl~~~l~~~~~~NP~v~i~v~~~ 51 (68)
.++...+.+|.+.+|++.+.+...
T Consensus 97 ~~~~~~l~~~~~~~p~v~l~i~~~ 120 (279)
T TIGR03339 97 YYVLDLVARFRQRYPGIEVSVRIG 120 (279)
T ss_pred HHHHHHHHHHHHHCCCcEEEEEEC
Confidence 367788899999999999999764
No 207
>COG1393 ArsC Arsenate reductase and related proteins, glutaredoxin family [Inorganic ion transport and metabolism]
Probab=24.71 E-value=74 Score=19.62 Aligned_cols=23 Identities=13% Similarity=0.124 Sum_probs=17.0
Q ss_pred EEEEEecCCCCCCHHHHHHHHhC
Q psy15302 11 ELRIHLCQKGGSSSGVRDFLAQH 33 (68)
Q Consensus 11 ~l~~~yc~~~~sS~G~R~Fl~~~ 33 (68)
.|+|...+..++|+-+++|++++
T Consensus 2 ~itiy~~p~C~t~rka~~~L~~~ 24 (117)
T COG1393 2 MITIYGNPNCSTCRKALAWLEEH 24 (117)
T ss_pred eEEEEeCCCChHHHHHHHHHHHc
Confidence 36677777777888888888654
No 208
>PF02669 KdpC: K+-transporting ATPase, c chain; InterPro: IPR003820 Kdp, the high affinity ATP-driven K+-transport system of Escherichia coli, is a complex of the membrane-bound subunits KdpA, KdpB, KdpC and the small peptide KdpF. KdpC forms strong interactions with the KdpA subunit, serving to assemble and stabilise the Kdp complex []. It has been suggested that KdpC could be one of the connecting links between the energy providing subunit KdpB and the K+- transporting subunit KdpA []. The K+ transport system actively transports K+ ions via ATP hydrolysis.; GO: 0008556 potassium-transporting ATPase activity, 0006813 potassium ion transport, 0016020 membrane
Probab=24.44 E-value=63 Score=21.94 Aligned_cols=44 Identities=23% Similarity=0.431 Sum_probs=31.5
Q ss_pred cCCCCCCHHHHHHHHhCHHHHHHhCCC----CeE--EEEecCCCCCEEEE
Q psy15302 17 CQKGGSSSGVRDFLAQHYVPLKQANPK----FPI--LVRECSGVTPVVWA 60 (68)
Q Consensus 17 c~~~~sS~G~R~Fl~~~l~~~~~~NP~----v~i--~v~~~~~~~P~v~a 60 (68)
++-|+++.-+++=+++....+++.||. ||. ++...+|-+|.|.-
T Consensus 85 SNl~psn~~l~~~v~~~~~~~~~~~~~~~~~vP~dlvtaSgSGLDP~IS~ 134 (188)
T PF02669_consen 85 SNLGPSNPELRERVEERIAALRKENPVAPSPVPADLVTASGSGLDPHISP 134 (188)
T ss_pred ccCCCCChHHHHHHHHHHHHHHhhcccCCCCCCHHHHhcccccCCCCcCH
Confidence 356777888999999999999999843 222 33445677887754
No 209
>PRK11242 DNA-binding transcriptional regulator CynR; Provisional
Probab=24.40 E-value=1.1e+02 Score=20.24 Aligned_cols=26 Identities=12% Similarity=0.213 Sum_probs=21.7
Q ss_pred HHHHHHhCHHHHHHhCCCCeEEEEec
Q psy15302 26 VRDFLAQHYVPLKQANPKFPILVREC 51 (68)
Q Consensus 26 ~R~Fl~~~l~~~~~~NP~v~i~v~~~ 51 (68)
...++...+..|++++|++.|.+...
T Consensus 102 ~~~~l~~~l~~~~~~~p~~~i~~~~~ 127 (296)
T PRK11242 102 TAYLIGPLIDAFHARYPGITLTIREM 127 (296)
T ss_pred hhhhhHHHHHHHHHHCCCCEEEEEeC
Confidence 35677889999999999999999753
No 210
>TIGR00550 nadA quinolinate synthetase complex, A subunit. This protein, termed NadA, plays a role in the synthesis of pyridine, a precursor to NAD. The quinolinate synthetase complex consists of A protein (this protein) and B protein. B protein converts L-aspartate to iminoaspartate, an unstable reaction product which in the absence of A protein is spontaneously hydrolyzed to form oxaloacetate. The A protein, NadA, converts iminoaspartate to quinolate.
Probab=24.29 E-value=1.3e+02 Score=21.70 Aligned_cols=35 Identities=17% Similarity=0.206 Sum_probs=28.0
Q ss_pred EecCCCCCCHHHHHHHHhC-------------HHHHHHhCCCCeEEEE
Q psy15302 15 HLCQKGGSSSGVRDFLAQH-------------YVPLKQANPKFPILVR 49 (68)
Q Consensus 15 ~yc~~~~sS~G~R~Fl~~~-------------l~~~~~~NP~v~i~v~ 49 (68)
..+|.-|||.++-+|+++. +-.+++++|+-.+..-
T Consensus 210 ~~aD~vgSTs~~i~~v~~~~~~~~ii~TE~~l~~~l~~~~p~k~~i~~ 257 (310)
T TIGR00550 210 DLADFIGSTSQIIRFVLKSPAQKFIIGTEVGLVNRMEAESPDKNTIPL 257 (310)
T ss_pred HhcCEEecHHHHHHHHHhCCCCeEEEEccHHHHHHHHHHCCCCeEEeC
Confidence 4678899999999999765 5578889999866554
No 211
>PF11943 DUF3460: Protein of unknown function (DUF3460); InterPro: IPR021853 This family of proteins are functionally uncharacterised. This protein is found in bacteria. Proteins in this family are about 70 amino acids in length. This protein has a conserved WDK sequence motif.
Probab=24.20 E-value=49 Score=18.61 Aligned_cols=14 Identities=29% Similarity=0.437 Sum_probs=10.8
Q ss_pred hCHHHHHHhCCCCe
Q psy15302 32 QHYVPLKQANPKFP 45 (68)
Q Consensus 32 ~~l~~~~~~NP~v~ 45 (68)
.-+.+++++||+++
T Consensus 9 qFl~~lk~~~Pele 22 (60)
T PF11943_consen 9 QFLNQLKAKHPELE 22 (60)
T ss_pred HHHHHHHHhCCchH
Confidence 34668899999875
No 212
>PRK13055 putative lipid kinase; Reviewed
Probab=24.06 E-value=2.4e+02 Score=19.96 Aligned_cols=40 Identities=18% Similarity=0.126 Sum_probs=27.9
Q ss_pred eEEEEEecCCCCCCHHHHHHHHhCHHHHHHhCCCCeEEEEe
Q psy15302 10 KELRIHLCQKGGSSSGVRDFLAQHYVPLKQANPKFPILVRE 50 (68)
Q Consensus 10 k~l~~~yc~~~~sS~G~R~Fl~~~l~~~~~~NP~v~i~v~~ 50 (68)
+++.|-+++.+|+.++.+. +.+-...+++.+-++.+....
T Consensus 3 ~r~~iI~NP~sG~~~~~~~-~~~i~~~l~~~g~~~~i~~t~ 42 (334)
T PRK13055 3 KRARLIYNPTSGQEIMKKN-VADILDILEQAGYETSAFQTT 42 (334)
T ss_pred ceEEEEECCCCCchhHHHH-HHHHHHHHHHcCCeEEEEEee
Confidence 5788999999998776554 455556677777666665544
No 213
>PF08885 GSCFA: GSCFA family; InterPro: IPR014982 This group of proteins are functionally uncharacterised. They have been named GSCFA after a highly conserved N-terminal motif in the alignment, they are functionally uncharacterised.
Probab=23.99 E-value=1.3e+02 Score=21.00 Aligned_cols=31 Identities=16% Similarity=0.166 Sum_probs=23.8
Q ss_pred CHHHHHHHHhCHHHHHHhCCCCeEEEEecCC
Q psy15302 23 SSGVRDFLAQHYVPLKQANPKFPILVRECSG 53 (68)
Q Consensus 23 S~G~R~Fl~~~l~~~~~~NP~v~i~v~~~~~ 53 (68)
-.-+.+-++.-+..+++-||+++|++.-.+=
T Consensus 147 ~~ei~~~l~~~~~~l~~~nP~~kiilTVSPV 177 (251)
T PF08885_consen 147 VEEILEDLEAIIDLLRSINPDIKIILTVSPV 177 (251)
T ss_pred HHHHHHHHHHHHHHHHhhCCCceEEEEeccc
Confidence 3445566677788899999999999877663
No 214
>PF09345 DUF1987: Domain of unknown function (DUF1987); InterPro: IPR018530 This family of proteins are functionally uncharacterised.
Probab=23.71 E-value=1.4e+02 Score=18.04 Aligned_cols=36 Identities=14% Similarity=0.159 Sum_probs=24.4
Q ss_pred EEEEEecCCCCCCHHHHHHHHhCHHHHHHhCCCCeEEE
Q psy15302 11 ELRIHLCQKGGSSSGVRDFLAQHYVPLKQANPKFPILV 48 (68)
Q Consensus 11 ~l~~~yc~~~~sS~G~R~Fl~~~l~~~~~~NP~v~i~v 48 (68)
.+.|.|=++| ||+.+-+.++ .|.+.+++...|.|.=
T Consensus 48 ~~~L~YfNTS-Ssk~l~~i~~-~Le~~~~~g~~V~v~W 83 (99)
T PF09345_consen 48 NFKLSYFNTS-SSKALMDIFD-LLEDAAQKGGKVTVNW 83 (99)
T ss_pred EEEEEEEecH-hHHHHHHHHH-HHHHHHhcCCcEEEEE
Confidence 3567776665 6777777664 5666677777777654
No 215
>PRK12682 transcriptional regulator CysB-like protein; Reviewed
Probab=23.71 E-value=1.3e+02 Score=20.34 Aligned_cols=26 Identities=15% Similarity=0.286 Sum_probs=21.8
Q ss_pred HHHHHHhCHHHHHHhCCCCeEEEEec
Q psy15302 26 VRDFLAQHYVPLKQANPKFPILVREC 51 (68)
Q Consensus 26 ~R~Fl~~~l~~~~~~NP~v~i~v~~~ 51 (68)
...++...+..|.+++|++.|.+...
T Consensus 104 ~~~~l~~~l~~~~~~~P~i~i~i~~~ 129 (309)
T PRK12682 104 ARYVLPRVVAAFRKRYPKVNLSLHQG 129 (309)
T ss_pred HHHHHHHHHHHHHHhCCCeEEEEecC
Confidence 35677888999999999999998754
No 216
>COG5575 ORC2 Origin recognition complex, subunit 2 [DNA replication, recombination, and repair]
Probab=23.70 E-value=62 Score=24.99 Aligned_cols=35 Identities=11% Similarity=0.201 Sum_probs=26.6
Q ss_pred cCCCCCCHH-HHHHHHhCHHHHHHhCCCCeEEEEec
Q psy15302 17 CQKGGSSSG-VRDFLAQHYVPLKQANPKFPILVREC 51 (68)
Q Consensus 17 c~~~~sS~G-~R~Fl~~~l~~~~~~NP~v~i~v~~~ 51 (68)
|.+-.+=+. +++||.+++.++++++..++|.-.+.
T Consensus 484 ~Sne~~~rSmL~EFidH~l~~i~rn~S~~eI~wvpy 519 (535)
T COG5575 484 LSNETSVRSMLNEFIDHGLLKIKRNGSEIEICWVPY 519 (535)
T ss_pred hcCcHHHHHHHHHHHhcchhheeccCCccEEEEeec
Confidence 333333333 59999999999999999999887654
No 217
>cd08443 PBP2_CysB The C-terminal substrate domain of LysR-type transcriptional regulator CysB 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-binding speci
Probab=23.56 E-value=54 Score=19.81 Aligned_cols=25 Identities=12% Similarity=0.183 Sum_probs=19.7
Q ss_pred HHHHHhCHHHHHHhCCCCeEEEEec
Q psy15302 27 RDFLAQHYVPLKQANPKFPILVREC 51 (68)
Q Consensus 27 R~Fl~~~l~~~~~~NP~v~i~v~~~ 51 (68)
..++...+..|.+.+|++.+.+...
T Consensus 12 ~~~l~~~l~~f~~~~P~~~i~i~~~ 36 (198)
T cd08443 12 RYVLPPVIKGFIERYPRVSLQMHQG 36 (198)
T ss_pred eeECcHHHHHHHHHCCCeEEEEEeC
Confidence 3456778889999999999988753
No 218
>PRK10680 molybdopterin biosynthesis protein MoeA; Provisional
Probab=23.56 E-value=64 Score=23.98 Aligned_cols=39 Identities=21% Similarity=0.319 Sum_probs=27.8
Q ss_pred CCCCCHHHHHHHHhCHHHHHHhCCCCeEE-EEecCCCCCEEEEEe
Q psy15302 19 KGGSSSGVRDFLAQHYVPLKQANPKFPIL-VRECSGVTPVVWASG 62 (68)
Q Consensus 19 ~~~sS~G~R~Fl~~~l~~~~~~NP~v~i~-v~~~~~~~P~v~a~Y 62 (68)
+||+|.|-+||+.+-+.++- .+.|. +..++| .|...|.+
T Consensus 250 tGG~S~G~~D~~~~al~~lG----~~~f~~v~~kPG-kp~~~g~~ 289 (411)
T PRK10680 250 SGGVSVGEADYTKTILEELG----EIAFWKLAIKPG-KPFAFGKL 289 (411)
T ss_pred cCCCCCCCcchHHHHHHhcC----cEEEEEEEEecC-cceEEEEE
Confidence 69999999999988776653 34332 355677 77777766
No 219
>cd02996 PDI_a_ERp44 PDIa family, endoplasmic reticulum protein 44 (ERp44) subfamily; ERp44 is an ER-resident protein, induced during stress, involved in thiol-mediated ER retention. It contains an N-terminal TRX domain, similar to that of PDIa, with a CXFS motif followed by two redox inactive TRX-like domains, homologous to the b and b' domains of PDI. The CXFS motif in the N-terminal domain allows ERp44 to form stable reversible mixed disulfides with its substrates. Through this activity, ERp44 mediates the ER localization of Ero1alpha, a protein that oxidizes protein disulfide isomerases into their active form. ERp44 also prevents the secretion of unassembled cargo protein with unpaired cysteines. It also modulates the activity of inositol 1,4,5-triphosphate type I receptor (IP3R1), an intracellular channel protein that mediates calcium release from the ER to the cytosol.
Probab=23.37 E-value=1.6e+02 Score=16.76 Aligned_cols=33 Identities=12% Similarity=0.041 Sum_probs=25.4
Q ss_pred EEEEEecCCCCCCHHHHHHHHhCHHHHHHhCCC
Q psy15302 11 ELRIHLCQKGGSSSGVRDFLAQHYVPLKQANPK 43 (68)
Q Consensus 11 ~l~~~yc~~~~sS~G~R~Fl~~~l~~~~~~NP~ 43 (68)
-|...|.+|.+.++-+...+++....++...|+
T Consensus 21 vlv~F~a~wC~~C~~~~p~~~~~a~~~~~~~~~ 53 (108)
T cd02996 21 VLVNFYADWCRFSQMLHPIFEEAAAKIKEEFPD 53 (108)
T ss_pred EEEEEECCCCHHHHhhHHHHHHHHHHHhhccCC
Confidence 367778889998998888887777777766665
No 220
>cd02873 GH18_IDGF The IDGF's (imaginal disc growth factors) are a family of growth factors identified in insects that include at least five members, some of which are encoded by genes in a tight cluster. The IDGF's have an eight-stranded alpha/beta barrel fold and are related to the glycosyl hydrolase family 18 (GH18) chitinases, but they have an amino acid substitution known to abolish chitinase catalytic activity. IDGFs may have evolved from chitinases to gain new functions as growth factors, interacting with cell surface glycoproteins involved in growth-promoting processes.
Probab=23.32 E-value=72 Score=23.48 Aligned_cols=21 Identities=19% Similarity=0.352 Sum_probs=17.4
Q ss_pred hCHHHHHHhCCCCeEEEEecC
Q psy15302 32 QHYVPLKQANPKFPILVRECS 52 (68)
Q Consensus 32 ~~l~~~~~~NP~v~i~v~~~~ 52 (68)
+.+..+|++||++.+++.-.-
T Consensus 63 ~~~~~lk~~~p~lKvllSiGG 83 (413)
T cd02873 63 RAITSLKRKYPHLKVLLSVGG 83 (413)
T ss_pred HHHHHHHhhCCCCeEEEeecC
Confidence 356789999999999998754
No 221
>KOG1454|consensus
Probab=23.12 E-value=82 Score=22.45 Aligned_cols=26 Identities=19% Similarity=0.181 Sum_probs=22.4
Q ss_pred CHHHHHHhCCCCeEEEEecCCCCCEE
Q psy15302 33 HYVPLKQANPKFPILVRECSGVTPVV 58 (68)
Q Consensus 33 ~l~~~~~~NP~v~i~v~~~~~~~P~v 58 (68)
.-..+++++|++++++-+.-|.+|.+
T Consensus 282 ~~~~~~~~~pn~~~~~I~~~gH~~h~ 307 (326)
T KOG1454|consen 282 LAEELKKKLPNAELVEIPGAGHLPHL 307 (326)
T ss_pred HHHHHHhhCCCceEEEeCCCCccccc
Confidence 45678899999999999988888876
No 222
>PRK12680 transcriptional regulator CysB-like protein; Reviewed
Probab=23.11 E-value=1.2e+02 Score=21.02 Aligned_cols=37 Identities=19% Similarity=0.307 Sum_probs=27.4
Q ss_pred eEEEEEecCCCCCCHHHHHHHHhCHHHHHHhCCCCeEEEEec
Q psy15302 10 KELRIHLCQKGGSSSGVRDFLAQHYVPLKQANPKFPILVREC 51 (68)
Q Consensus 10 k~l~~~yc~~~~sS~G~R~Fl~~~l~~~~~~NP~v~i~v~~~ 51 (68)
..|+|-..+. -...++...+..|.+.+|++.|.+...
T Consensus 93 g~lrIg~~~~-----~~~~~l~~~l~~f~~~~P~v~i~l~~~ 129 (327)
T PRK12680 93 GQLTLTTTHT-----QARFVLPPAVAQIKQAYPQVSVHLQQA 129 (327)
T ss_pred eEEEEEecch-----hHHHhhHHHHHHHHHHCCCcEEEEEeC
Confidence 3566665443 235677889999999999999998764
No 223
>PF14606 Lipase_GDSL_3: GDSL-like Lipase/Acylhydrolase family; PDB: 3SKV_B.
Probab=23.11 E-value=1e+02 Score=20.56 Aligned_cols=31 Identities=26% Similarity=0.344 Sum_probs=21.8
Q ss_pred CCCHHHHHHHHhCHHHHHHhCCCCeEEEEec
Q psy15302 21 GSSSGVRDFLAQHYVPLKQANPKFPILVREC 51 (68)
Q Consensus 21 ~sS~G~R~Fl~~~l~~~~~~NP~v~i~v~~~ 51 (68)
.+.+-+++=+..-+..+.+++|++||++.+.
T Consensus 71 ~~~~~~~~~~~~fv~~iR~~hP~tPIllv~~ 101 (178)
T PF14606_consen 71 MSPEEFRERLDGFVKTIREAHPDTPILLVSP 101 (178)
T ss_dssp CCTTTHHHHHHHHHHHHHTT-SSS-EEEEE-
T ss_pred CCHHHHHHHHHHHHHHHHHhCCCCCEEEEec
Confidence 4555566666677889999999999999774
No 224
>KOG0907|consensus
Probab=23.11 E-value=1.8e+02 Score=17.43 Aligned_cols=30 Identities=17% Similarity=0.272 Sum_probs=23.3
Q ss_pred EecCCCCCCHHHHHHHHhCHHHHHHhCCCCeEEE
Q psy15302 15 HLCQKGGSSSGVRDFLAQHYVPLKQANPKFPILV 48 (68)
Q Consensus 15 ~yc~~~~sS~G~R~Fl~~~l~~~~~~NP~v~i~v 48 (68)
.|..|.|..+-| .-.+.+|+.++|++.|+-
T Consensus 28 F~a~wCgPCk~i----~P~~~~La~~y~~v~Flk 57 (106)
T KOG0907|consen 28 FYATWCGPCKAI----APKFEKLAEKYPDVVFLK 57 (106)
T ss_pred EECCCCcchhhh----hhHHHHHHHHCCCCEEEE
Confidence 477788888755 456778999999988874
No 225
>CHL00180 rbcR LysR transcriptional regulator; Provisional
Probab=23.09 E-value=1.3e+02 Score=20.37 Aligned_cols=25 Identities=8% Similarity=0.157 Sum_probs=21.4
Q ss_pred HHHHHhCHHHHHHhCCCCeEEEEec
Q psy15302 27 RDFLAQHYVPLKQANPKFPILVREC 51 (68)
Q Consensus 27 R~Fl~~~l~~~~~~NP~v~i~v~~~ 51 (68)
..|+...+.+|.+.+|++.|.+...
T Consensus 107 ~~~~~~~l~~~~~~~P~v~i~~~~~ 131 (305)
T CHL00180 107 TYLMPRLIGLFRQRYPQINVQLQVH 131 (305)
T ss_pred HhHHHHHHHHHHHHCCCceEEEEeC
Confidence 5778889999999999999998653
No 226
>TIGR03521 GldG gliding-associated putative ABC transporter substrate-binding component GldG. Members of this protein family are exclusive to the Bacteroidetes phylum (previously Cytophaga-Flavobacteria-Bacteroides). GldG is a protein linked to a type of rapid surface gliding motility found in certain Bacteroidetes, such as Flavobacterium johnsoniae and Cytophaga hutchinsonii. Knockouts of GldG abolish the gliding phenotype. GldG, along with GldA and GldF are believed to compose an ABC transporter and are observed as an operon. Gliding motility appears closely linked to chitin utilization in the model species Flavobacterium johnsoniae. Bacteroidetes with members of this protein family appear to have all of the genes associated with gliding motility.
Probab=22.91 E-value=2.1e+02 Score=21.94 Aligned_cols=39 Identities=13% Similarity=0.063 Sum_probs=27.8
Q ss_pred EEEEEecCCCCCC-HHHHHHHHhCHHHHHHhCCCCeEEEE
Q psy15302 11 ELRIHLCQKGGSS-SGVRDFLAQHYVPLKQANPKFPILVR 49 (68)
Q Consensus 11 ~l~~~yc~~~~sS-~G~R~Fl~~~l~~~~~~NP~v~i~v~ 49 (68)
+|.+.+.+..+.. +-.+.-+++.|.++++.+|++.+...
T Consensus 51 ~I~~~~s~~~~~~~~~~~~~v~~lL~eY~~~s~~i~~~~i 90 (552)
T TIGR03521 51 SIDIFLDGELPADFRRLQKETRQLLEEFAAYNPNIKFRFV 90 (552)
T ss_pred EEEEEEcCCCchHHHHHHHHHHHHHHHHHHhCCCeEEEEe
Confidence 3666676553322 34567788999999999999887774
No 227
>PF10307 DUF2410: Hypothetical protein (DUF2410); InterPro: IPR018812 This entry represents a family of proteins conserved in fungi whose function is not known. There are two characteristic sequence motifs, GGWW and TGR.
Probab=22.82 E-value=1.1e+02 Score=20.76 Aligned_cols=27 Identities=26% Similarity=0.417 Sum_probs=22.4
Q ss_pred cCcceEEEEEecCCCCCCHHHHHHHHhC
Q psy15302 6 GSKLKELRIHLCQKGGSSSGVRDFLAQH 33 (68)
Q Consensus 6 v~qlk~l~~~yc~~~~sS~G~R~Fl~~~ 33 (68)
..++++|++ |+|-...-+|.|+|+.+.
T Consensus 130 Y~~~~eI~I-YeDR~~hvk~Fr~Ff~~~ 156 (197)
T PF10307_consen 130 YKNAEEIRI-YEDRPKHVKGFRDFFEEL 156 (197)
T ss_pred cCCCCEEEE-EcCCHHHHHHHHHHHHHh
Confidence 457899987 788888899999999753
No 228
>PHA00684 hypothetical protein
Probab=22.78 E-value=95 Score=20.00 Aligned_cols=28 Identities=11% Similarity=0.317 Sum_probs=20.9
Q ss_pred HHHHHHHHhCHHHHHHhCCCCeEEEEecC
Q psy15302 24 SGVRDFLAQHYVPLKQANPKFPILVRECS 52 (68)
Q Consensus 24 ~G~R~Fl~~~l~~~~~~NP~v~i~v~~~~ 52 (68)
.-+|.+|. .+.+++++||+..|.|.+--
T Consensus 56 ~~I~~~V~-~Fi~ya~~hp~~~F~VT~IG 83 (128)
T PHA00684 56 PDIGAAVN-RFIAYATAHPHLNFQVTRVG 83 (128)
T ss_pred HHHHHHHH-HHHHHHHhCCCcEEEeeeec
Confidence 34566664 46689999999999997643
No 229
>cd03409 Chelatase_Class_II Class II Chelatase: a family of ATP-independent monomeric or homodimeric enzymes that catalyze the insertion of metal into protoporphyrin rings. This family includes protoporphyrin IX ferrochelatase (HemH), sirohydrochlorin ferrochelatase (SirB) and the cobaltochelatases, CbiK and CbiX. HemH and SirB are involved in heme and siroheme biosynthesis, respectively, while the cobaltochelatases are associated with cobalamin biosynthesis. Excluded from this family are the ATP-dependent heterotrimeric chelatases (class I) and the multifunctional homodimeric enzymes with dehydrogenase and chelatase activities (class III).
Probab=22.68 E-value=1.6e+02 Score=16.49 Aligned_cols=33 Identities=24% Similarity=0.308 Sum_probs=22.6
Q ss_pred HHHHHHHhCHHHHHHhCCCCeEEEEecCCCCCE
Q psy15302 25 GVRDFLAQHYVPLKQANPKFPILVRECSGVTPV 57 (68)
Q Consensus 25 G~R~Fl~~~l~~~~~~NP~v~i~v~~~~~~~P~ 57 (68)
...+.+......++++.|..++.+--.....|.
T Consensus 14 ~~~~~~~~~~~~l~~~~~~~~v~~a~~~~~~P~ 46 (101)
T cd03409 14 PYKKDIEAQAHNLAESLPDFPYYVGFQSGLGPD 46 (101)
T ss_pred cHHHHHHHHHHHHHHHCCCCCEEEEEECCCCCC
Confidence 667778888888888888777666444433453
No 230
>PF05159 Capsule_synth: Capsule polysaccharide biosynthesis protein; InterPro: IPR007833 This family includes export proteins involved in capsule polysaccharide biosynthesis, such as KpsS P42218 from SWISSPROT and LipB P57038 from SWISSPROT. Capsule polysaccharide modification protein lipB/A is involved in the phospholipid modification of the capsular polysaccharide and is a strong requirement for its translocation to the cell surface. The capsule of Neisseria meningitidis serogroup B and of other meningococcal serogroups and other Gram-negative bacterial pathogens, are anchored in the outer membrane through a 1,2-diacylglycerol moiety. The lipA and lipB genes are located on the 3' end of the ctr operon. lipA and lipB do not encode proteins responsible for diacylglycerophosphatidic acid substitution of the meningococcal capsule polymer, but they are required for proper translocation and surface expression of the lipidated polymer []. KpsS is an unusual sulphate-modified form of the capsular polysaccharide in Rhizobium loti (Mesorhizobium loti). Many plants, including R. loti, enter into symbiotic relationships with bacteria that allow survival in nutrient-limiting environments. KpsS functions as a fucosyl sulphotransferase in vitro. The kpsS gene product shares no significant amino acid similarity with previously identified sulphotransferases []. Sulphated cell surface polysaccharides are required for optimum nodule formation but limit growth rate and nodule colonisation in M. loti [].; GO: 0000271 polysaccharide biosynthetic process, 0015774 polysaccharide transport
Probab=22.54 E-value=1.3e+02 Score=20.31 Aligned_cols=27 Identities=11% Similarity=0.199 Sum_probs=22.0
Q ss_pred HHHHHHhCHHHHHHhCCCCeEEEEecC
Q psy15302 26 VRDFLAQHYVPLKQANPKFPILVRECS 52 (68)
Q Consensus 26 ~R~Fl~~~l~~~~~~NP~v~i~v~~~~ 52 (68)
..+++.+-+.++++.||+..++|++-+
T Consensus 138 ~~~~~~~~l~~~~~~~p~~~lvvK~HP 164 (269)
T PF05159_consen 138 SQADFLDMLESFAKENPDAKLVVKPHP 164 (269)
T ss_pred cHhHHHHHHHHHHHHCCCCEEEEEECc
Confidence 455667788899999999999998844
No 231
>PF14421 LmjF365940-deam: A distinct subfamily of CDD/CDA-like deaminases
Probab=22.33 E-value=1e+02 Score=21.11 Aligned_cols=25 Identities=16% Similarity=0.317 Sum_probs=20.6
Q ss_pred HhCHHHHHHhCCCCeEEEEecCCCC
Q psy15302 31 AQHYVPLKQANPKFPILVRECSGVT 55 (68)
Q Consensus 31 ~~~l~~~~~~NP~v~i~v~~~~~~~ 55 (68)
++.|.++++.||++.++......++
T Consensus 161 ~ewL~KIAe~np~f~v~mFd~t~c~ 185 (193)
T PF14421_consen 161 KEWLRKIAEANPDFRVYMFDDTRCR 185 (193)
T ss_pred HHHHHHHHHhCCCeEEEEecCCCcc
Confidence 4678889999999999998877543
No 232
>TIGR03087 stp1 sugar transferase, PEP-CTERM/EpsH1 system associated. Members of this family include a match to the pfam00534 Glycosyl transferases group 1 domain. Nearly all are found in species that encode the PEP-CTERM/exosortase system predicted to act in protein sorting in a number of Gram-negative bacteria. In particular, these transferases are found proximal to a particular variant of exosortase, EpsH1, which appears to travel with a conserved group of genes summarized by Genome Property GenProp0652. The nature of the sugar transferase reaction catalyzed by members of this clade is unknown and may conceivably be variable with respect to substrate by species, but we hypothesize a conserved substrate.
Probab=22.14 E-value=1.5e+02 Score=20.88 Aligned_cols=26 Identities=12% Similarity=0.198 Sum_probs=20.7
Q ss_pred HHHHHHHhCHHHHHHhCCCCeEEEEe
Q psy15302 25 GVRDFLAQHYVPLKQANPKFPILVRE 50 (68)
Q Consensus 25 G~R~Fl~~~l~~~~~~NP~v~i~v~~ 50 (68)
++..|+..-++.+++.+|++.+.|.-
T Consensus 241 ~l~~~~~~~~~~l~~~~p~~~l~ivG 266 (397)
T TIGR03087 241 AVVWFAERVFPAVRARRPAAEFYIVG 266 (397)
T ss_pred HHHHHHHHHHHHHHHHCCCcEEEEEC
Confidence 44556668889999999999999864
No 233
>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=21.95 E-value=1.4e+02 Score=15.91 Aligned_cols=22 Identities=23% Similarity=0.196 Sum_probs=17.4
Q ss_pred EEEEEecCCCCCCHHHHHHHHh
Q psy15302 11 ELRIHLCQKGGSSSGVRDFLAQ 32 (68)
Q Consensus 11 ~l~~~yc~~~~sS~G~R~Fl~~ 32 (68)
+|+|..-++.+.++-++.+|++
T Consensus 2 ~v~ly~~~~C~~C~ka~~~L~~ 23 (73)
T cd03027 2 RVTIYSRLGCEDCTAVRLFLRE 23 (73)
T ss_pred EEEEEecCCChhHHHHHHHHHH
Confidence 5666666788889999999964
No 234
>PF06891 P2_Phage_GpR: P2 phage tail completion protein R (GpR); InterPro: IPR009678 This family consists of P2 phage tail completion protein R (GpR) and similar sequences from related phage. GpR is thought to be a tail completion protein which is essential for stable head joining []. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=21.87 E-value=78 Score=19.86 Aligned_cols=27 Identities=15% Similarity=0.193 Sum_probs=22.7
Q ss_pred HHHHHHHHhCHHHHHHhCCCCeEEEEe
Q psy15302 24 SGVRDFLAQHYVPLKQANPKFPILVRE 50 (68)
Q Consensus 24 ~G~R~Fl~~~l~~~~~~NP~v~i~v~~ 50 (68)
.-+|+||.+.+|.++.+.-++.+.+..
T Consensus 5 ~sLr~~L~~~lP~~~~~pd~l~~~v~~ 31 (135)
T PF06891_consen 5 QSLRAALTAALPELAANPDRLDSFVDN 31 (135)
T ss_pred HHHHHHHHHhChhhhcChhheEEEEeC
Confidence 468999999999999887788877754
No 235
>PRK10632 transcriptional regulator; Provisional
Probab=21.84 E-value=1.5e+02 Score=20.18 Aligned_cols=26 Identities=12% Similarity=0.162 Sum_probs=22.3
Q ss_pred HHHHHHhCHHHHHHhCCCCeEEEEec
Q psy15302 26 VRDFLAQHYVPLKQANPKFPILVREC 51 (68)
Q Consensus 26 ~R~Fl~~~l~~~~~~NP~v~i~v~~~ 51 (68)
...++...+.+|.+++|++.|.+...
T Consensus 103 ~~~~l~~~l~~~~~~~P~i~i~l~~~ 128 (309)
T PRK10632 103 AQNVLAGLTAKMLKEYPGLSVNLVTG 128 (309)
T ss_pred HHHHHHHHHHHHHHHCCCeEEEEEec
Confidence 34677899999999999999999764
No 236
>PRK09986 DNA-binding transcriptional activator XapR; Provisional
Probab=21.83 E-value=1.3e+02 Score=19.88 Aligned_cols=25 Identities=24% Similarity=0.247 Sum_probs=20.8
Q ss_pred HHHHHhCHHHHHHhCCCCeEEEEec
Q psy15302 27 RDFLAQHYVPLKQANPKFPILVREC 51 (68)
Q Consensus 27 R~Fl~~~l~~~~~~NP~v~i~v~~~ 51 (68)
..++...+.+|.+.+|++.+.+...
T Consensus 109 ~~~l~~~l~~f~~~~p~i~l~i~~~ 133 (294)
T PRK09986 109 WGRLRPAMRHFLKENPNVEWLLREL 133 (294)
T ss_pred HHHHHHHHHHHHHhCCCeEEEEEeC
Confidence 4667788999999999999988644
No 237
>cd02988 Phd_like_VIAF Phosducin (Phd)-like family, Viral inhibitor of apoptosis (IAP)-associated factor (VIAF) subfamily; VIAF is a Phd-like protein that functions in caspase activation during apoptosis. It was identified as an IAP binding protein through a screen of a human B-cell library using a prototype IAP. VIAF lacks a consensus IAP binding motif and while it does not function as an IAP antagonist, it still plays a regulatory role in the complete activation of caspases. VIAF itself is a substrate for IAP-mediated ubiquitination, suggesting that it may be a target of IAPs in the prevention of cell death. The similarity of VIAF to Phd points to a potential role distinct from apoptosis regulation. Phd functions as a cytosolic regulator of G protein by specifically binding to G protein betagamma (Gbg)-subunits. 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=21.74 E-value=2e+02 Score=19.01 Aligned_cols=35 Identities=14% Similarity=-0.056 Sum_probs=24.4
Q ss_pred EEEEecCCCCCCHHHHHHHHhCHHHHHHhCCCCeEEEEe
Q psy15302 12 LRIHLCQKGGSSSGVRDFLAQHYVPLKQANPKFPILVRE 50 (68)
Q Consensus 12 l~~~yc~~~~sS~G~R~Fl~~~l~~~~~~NP~v~i~v~~ 50 (68)
|.-.|-+|.+.++= |...|.++|+++|++.|.--.
T Consensus 106 VV~Fya~wc~~C~~----m~~~l~~LA~k~~~vkFvkI~ 140 (192)
T cd02988 106 VVHLYKDGIPLCRL----LNQHLSELARKFPDTKFVKII 140 (192)
T ss_pred EEEEECCCCchHHH----HHHHHHHHHHHCCCCEEEEEE
Confidence 44455567776664 456777889999999887643
No 238
>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=21.74 E-value=1.2e+02 Score=15.76 Aligned_cols=20 Identities=5% Similarity=-0.109 Sum_probs=16.5
Q ss_pred EEEEecCCCCCCHHHHHHHH
Q psy15302 12 LRIHLCQKGGSSSGVRDFLA 31 (68)
Q Consensus 12 l~~~yc~~~~sS~G~R~Fl~ 31 (68)
++|.+...++.|+-+|-+++
T Consensus 1 ~~Ly~~~~~~~~~~v~~~l~ 20 (74)
T cd03045 1 IDLYYLPGSPPCRAVLLTAK 20 (74)
T ss_pred CEEEeCCCCCcHHHHHHHHH
Confidence 46778888888999998885
No 239
>PF02944 BESS: BESS motif; InterPro: IPR004210 The BESS domain has been named after the three proteins that originally defined the domain: BEAF (Boundary element associated factor 32) [], Suvar(3)7 [] and Stonewall []). The BESS domain is 40 amino acid residues long and is predicted to be composed of three alpha helices, as such it might be related to the myb/SANT HTH domain. The BESS domain directs a variety of protein-protein interactions, including interactions with itself, with Dorsal, and with a TBP-associated factor. It is found in a single copy in Drosophila proteins and is often associated with the MADF domain [, , ]. Proteins known to contain a BESS domain include: Drosophila Boundary element associated factor 32 (BEAF-32). Drosophila Suppressor of variegation protein 3-7 (Su(var)3-7), which could play a role in chromosome condensation. Drosophila Ravus, which is homologous to the C-terminal part of Su(var)3-7 []. Drosophila Stonewall (Stwl), a putative transcription factor required for maintenance of female germline stem cells as well as oocyte differentiation. Drosophila Adf-1, a transcription factor first identified on the basis of its interaction with the alcohol dehydrogenase promoter but that binds the promoters of a diverse group of genes []. Drosophila Dorsal-interacting protein 3 (Dip3). It functions both as an activator to bind DNA in a sequence specific manner and a coactivator to stimulate synergistic activation by Dorsal and Twist []. ; GO: 0003677 DNA binding
Probab=21.67 E-value=67 Score=15.68 Aligned_cols=18 Identities=28% Similarity=0.277 Sum_probs=15.3
Q ss_pred HHHHHHhCHHHHHHhCCC
Q psy15302 26 VRDFLAQHYVPLKQANPK 43 (68)
Q Consensus 26 ~R~Fl~~~l~~~~~~NP~ 43 (68)
...|+.+-+|.+++-+|.
T Consensus 4 d~~Fl~Sl~p~~k~L~~~ 21 (37)
T PF02944_consen 4 DELFLLSLLPHMKRLPPK 21 (37)
T ss_pred HHHHHHHhHHHHHhCCHH
Confidence 467999999999998875
No 240
>PF00309 Sigma54_AID: Sigma-54 factor, Activator interacting domain (AID) ; InterPro: IPR000394 Sigma factors [] are bacterial transcription initiation factors that promote the attachment of the core RNA polymerase to specific initiation sites and are then released. They alter the specificity of promoter recognition. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes: the sigma-54 and sigma-70 families. The sigma-70 family has many different sigma factors (see the relevant entry IPR000943 from INTERPRO). The sigma-54 family consists exclusively of sigma-54 factor [, ] required for the transcription of promoters that have a characteristic -24 and -12 consensus recognition element but which are devoid of the typical -10, -35 sequences recognised by the major sigma factors. The sigma-54 factor is also characterised by its interaction with ATP-dependent positive regulatory proteins that bind to upstream activating sequences. Structurally sigma-54 factors consist of three distinct regions: A relatively well conserved N-terminal glutamine-rich region of about 50 residues that contains a potential leucine zipper motif. A region of variable length which is not well conserved. A well conserved C-terminal region of about 350 residues that contains a second potential leucine zipper, a potential DNA-binding 'helix-turn-helix' motif and a perfectly conserved octapeptide whose function is not known. ; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0003899 DNA-directed RNA polymerase activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent
Probab=21.55 E-value=70 Score=16.70 Aligned_cols=16 Identities=13% Similarity=0.160 Sum_probs=11.3
Q ss_pred HhCHHHHHHhCCCCeE
Q psy15302 31 AQHYVPLKQANPKFPI 46 (68)
Q Consensus 31 ~~~l~~~~~~NP~v~i 46 (68)
.+.+.+.+..||-+++
T Consensus 32 ~~~i~~~~~eNP~Le~ 47 (49)
T PF00309_consen 32 EEYIEEEAEENPFLEV 47 (49)
T ss_pred HHHHHHHHHhCcCccc
Confidence 3455667889998775
No 241
>PF06121 DUF959: Domain of Unknown Function (DUF959) ; InterPro: IPR010363 The function of this collagen XVIII N-terminal domain has not been characterised. It is not expressed in the 'short' isoform of collagen XVIII [].; GO: 0031012 extracellular matrix
Probab=21.46 E-value=58 Score=22.44 Aligned_cols=10 Identities=30% Similarity=0.710 Sum_probs=8.1
Q ss_pred HHHHHHHHhC
Q psy15302 24 SGVRDFLAQH 33 (68)
Q Consensus 24 ~G~R~Fl~~~ 33 (68)
+|||+||+-.
T Consensus 129 qGIRsFVqlW 138 (202)
T PF06121_consen 129 QGIRSFVQLW 138 (202)
T ss_pred HHHHHHHHHh
Confidence 7999999743
No 242
>PHA00440 host protein H-NS-interacting protein
Probab=21.40 E-value=73 Score=19.64 Aligned_cols=15 Identities=13% Similarity=0.233 Sum_probs=12.2
Q ss_pred HHHHHHHHhCHHHHH
Q psy15302 24 SGVRDFLAQHYVPLK 38 (68)
Q Consensus 24 ~G~R~Fl~~~l~~~~ 38 (68)
+|+|++|++.+++..
T Consensus 68 ~giRe~IKe~~~E~~ 82 (98)
T PHA00440 68 QGIREAIKDMHEEST 82 (98)
T ss_pred HHHHHHHHHHhHhhc
Confidence 689999988888754
No 243
>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=21.28 E-value=70 Score=19.41 Aligned_cols=29 Identities=17% Similarity=0.356 Sum_probs=23.6
Q ss_pred CCCHHHHHHHHhCHHHHHHhCCCCeEEEE
Q psy15302 21 GSSSGVRDFLAQHYVPLKQANPKFPILVR 49 (68)
Q Consensus 21 ~sS~G~R~Fl~~~l~~~~~~NP~v~i~v~ 49 (68)
|.-..+-+++.++.|.+.+.|+++.|.++
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 34566788999999999999999987653
No 244
>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=21.26 E-value=34 Score=21.86 Aligned_cols=42 Identities=21% Similarity=0.311 Sum_probs=36.0
Q ss_pred CCHHHHHHHHhCHHHHHHhCCCCeEEEEecCCCCCEEEEEec
Q psy15302 22 SSSGVRDFLAQHYVPLKQANPKFPILVRECSGVTPVVWASGK 63 (68)
Q Consensus 22 sS~G~R~Fl~~~l~~~~~~NP~v~i~v~~~~~~~P~v~a~Y~ 63 (68)
|--|.|.|=.+.+.++--+..+..+.+.|....+|.+...++
T Consensus 30 STTGFrTfsTn~lvnIi~aTth~vvvvkEakstn~hi~v~fL 71 (130)
T PF02960_consen 30 STTGFRTFSTNSLVNIIHATTHDVVVVKEAKSTNPHIQVHFL 71 (130)
T ss_pred cccceEEEecccccceecccccceEEEEEeecCCceEEeeee
Confidence 446888888888888888999999999999999999988764
No 245
>PF06183 DinI: DinI-like family; InterPro: IPR010391 This family of short proteins includes DNA-damage-inducible protein I (DinI) and related proteins. The SOS response, a set of cellular phenomena exhibited by eubacteria, is initiated by various causes that include DNA damage-induced replication arrest, and is positively regulated by the co- protease activity of RecA. Escherichia coli DinI, a LexA-regulated SOS gene product, shuts off the initiation of the SOS response when overexpressed in vivo. Biochemical and genetic studies indicated that DinI physically interacts with RecA to inhibit its co-protease activity []. The structure of DinI is known [].; PDB: 1GHH_A.
Probab=21.18 E-value=1.7e+02 Score=16.33 Aligned_cols=30 Identities=23% Similarity=0.272 Sum_probs=21.6
Q ss_pred HHHHHHHH-hCHHHHHHhCCCCeEEEEecCC
Q psy15302 24 SGVRDFLA-QHYVPLKQANPKFPILVRECSG 53 (68)
Q Consensus 24 ~G~R~Fl~-~~l~~~~~~NP~v~i~v~~~~~ 53 (68)
.|+.+=|+ +....+...+|+..+.|+....
T Consensus 3 ~ga~~AL~~EL~kRl~~~yPd~~v~Vr~~s~ 33 (65)
T PF06183_consen 3 AGALEALESELTKRLHRQYPDAEVRVRPGSA 33 (65)
T ss_dssp TTHHHHHHHHHHHHHHHH-SS-EEEEEEESS
T ss_pred ccHHHHHHHHHHHHHHHHCCCceEeeeeccc
Confidence 46667674 5667899999999999987654
No 246
>cd07941 DRE_TIM_LeuA3 Desulfobacterium autotrophicum LeuA3 and related proteins, N-terminal catalytic TIM barrel domain. Desulfobacterium autotrophicum LeuA3 is sequence-similar to alpha-isopropylmalate synthase (LeuA) but its exact function is unknown. Members of this family have an N-terminal TIM barrel domain that 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 containing a divalent cation-binding site formed by a cluster of in
Probab=21.15 E-value=2e+02 Score=19.87 Aligned_cols=34 Identities=18% Similarity=0.384 Sum_probs=24.4
Q ss_pred EEEecCCCCCCHHHHHHHHhCHHHHHHhCCCCeEEE
Q psy15302 13 RIHLCQKGGSSSGVRDFLAQHYVPLKQANPKFPILV 48 (68)
Q Consensus 13 ~~~yc~~~~sS~G~R~Fl~~~l~~~~~~NP~v~i~v 48 (68)
+|.+||+.|....-+ +.+.+..+++..|+++|.+
T Consensus 167 ~i~l~DT~G~~~P~~--v~~lv~~l~~~~~~~~l~~ 200 (273)
T cd07941 167 WLVLCDTNGGTLPHE--IAEIVKEVRERLPGVPLGI 200 (273)
T ss_pred EEEEecCCCCCCHHH--HHHHHHHHHHhCCCCeeEE
Confidence 577899888655443 5666677888888877766
No 247
>PRK11062 nhaR transcriptional activator NhaR; Provisional
Probab=21.03 E-value=1.3e+02 Score=20.27 Aligned_cols=25 Identities=4% Similarity=0.100 Sum_probs=21.4
Q ss_pred HHHHHHhCHHHHHHhCCCCeEEEEe
Q psy15302 26 VRDFLAQHYVPLKQANPKFPILVRE 50 (68)
Q Consensus 26 ~R~Fl~~~l~~~~~~NP~v~i~v~~ 50 (68)
...|+...+.+|.+.+|++.+.+..
T Consensus 104 ~~~~l~~~l~~f~~~~P~i~l~~~~ 128 (296)
T PRK11062 104 SKRLVSRVLLTAVPEDESIHLRCFE 128 (296)
T ss_pred hHhhHHHHHHHHHhcCCceEEEEEe
Confidence 3567888999999999999999864
No 248
>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=20.95 E-value=1.1e+02 Score=16.60 Aligned_cols=20 Identities=30% Similarity=0.157 Sum_probs=15.9
Q ss_pred EEEEecCCCCCCHHHHHHHH
Q psy15302 12 LRIHLCQKGGSSSGVRDFLA 31 (68)
Q Consensus 12 l~~~yc~~~~sS~G~R~Fl~ 31 (68)
++|.++..+++|.-+|-.+.
T Consensus 1 ~~ly~~~~s~~s~rv~~~L~ 20 (73)
T cd03052 1 LVLYHWTQSFSSQKVRLVIA 20 (73)
T ss_pred CEEecCCCCccHHHHHHHHH
Confidence 36778888888989987774
No 249
>cd04502 SGNH_hydrolase_like_7 Members of the SGNH-hydrolase superfamily, a diverse family of lipases and esterases. The tertiary fold of the enzyme is substantially different from that of the alpha/beta hydrolase family and unique among all known hydrolases; its active site closely resembles the Ser-His-Asp(Glu) triad from other serine hydrolases, but may lack the carboxlic acid.
Probab=20.76 E-value=1.9e+02 Score=17.64 Aligned_cols=28 Identities=14% Similarity=0.148 Sum_probs=20.9
Q ss_pred CHHHHHHHHhCHHHHHHhCCCCeEEEEe
Q psy15302 23 SSGVRDFLAQHYVPLKQANPKFPILVRE 50 (68)
Q Consensus 23 S~G~R~Fl~~~l~~~~~~NP~v~i~v~~ 50 (68)
..-.++-+++-+..+++.+|+++|++-.
T Consensus 69 ~~~~~~~~~~lv~~i~~~~~~~~iil~~ 96 (171)
T cd04502 69 PEEVLRDFRELVNRIRAKLPDTPIAIIS 96 (171)
T ss_pred HHHHHHHHHHHHHHHHHHCCCCcEEEEE
Confidence 3445555677888899999999888754
No 250
>cd03419 GRX_GRXh_1_2_like Glutaredoxin (GRX) family, GRX human class 1 and 2 (h_1_2)-like subfamily; composed of proteins similar to human GRXs, approximately 10 kDa in size, and proteins containing a GRX or GRX-like domain. GRX is a glutathione (GSH) dependent reductase, catalyzing the disulfide reduction of target proteins such as ribonucleotide reductase. It contains a redox active CXXC motif in a TRX fold and uses a similar dithiol mechanism employed by TRXs for intramolecular disulfide bond reduction of protein substrates. Unlike TRX, GRX has preference for mixed GSH disulfide substrates, in which it uses a monothiol mechanism where only the N-terminal cysteine is required. The flow of reducing equivalents in the GRX system goes from NADPH - GSH reductase - GSH - GRX - protein substrates. By altering the redox state of target proteins, GRX is involved in many cellular functions including DNA synthesis, signal transduction and the defense against oxidative stress. Different classes
Probab=20.74 E-value=97 Score=16.49 Aligned_cols=22 Identities=5% Similarity=-0.022 Sum_probs=17.4
Q ss_pred EEEEecCCCCCCHHHHHHHHhC
Q psy15302 12 LRIHLCQKGGSSSGVRDFLAQH 33 (68)
Q Consensus 12 l~~~yc~~~~sS~G~R~Fl~~~ 33 (68)
|++..-++.+.++.+++++.+.
T Consensus 2 v~~y~~~~Cp~C~~~~~~l~~~ 23 (82)
T cd03419 2 VVVFSKSYCPYCKRAKSLLKEL 23 (82)
T ss_pred EEEEEcCCCHHHHHHHHHHHHc
Confidence 5666667888899999999754
No 251
>PRK05972 ligD ATP-dependent DNA ligase; Reviewed
Probab=20.71 E-value=1.2e+02 Score=25.19 Aligned_cols=41 Identities=7% Similarity=-0.041 Sum_probs=35.0
Q ss_pred CHHHHHHHHhCHHHHHHhCCCCeEEEEecCCCCCEEEEEec
Q psy15302 23 SSGVRDFLAQHYVPLKQANPKFPILVRECSGVTPVVWASGK 63 (68)
Q Consensus 23 S~G~R~Fl~~~l~~~~~~NP~v~i~v~~~~~~~P~v~a~Y~ 63 (68)
..-+|.|.+.--..+++++|+.-...+....+.-+|...|.
T Consensus 742 ~~~~~~fa~~ia~~l~~~~P~~~t~~~~k~~R~grifiDyl 782 (860)
T PRK05972 742 WDEVKAFAQAVCQHMARDLPERFLAKMGKKNRVGKIFLDYL 782 (860)
T ss_pred HHHHHHHHHHHHHHHHHHCchhehhhhhHhhCCCcEEEEcc
Confidence 46689999999999999999988877777777788999987
No 252
>PRK10094 DNA-binding transcriptional activator AllS; Provisional
Probab=20.68 E-value=1.3e+02 Score=20.49 Aligned_cols=38 Identities=13% Similarity=0.017 Sum_probs=27.0
Q ss_pred eEEEEEecCCCCCCHHHHHHHHhCHHHHHHhCCCCeEEEEec
Q psy15302 10 KELRIHLCQKGGSSSGVRDFLAQHYVPLKQANPKFPILVREC 51 (68)
Q Consensus 10 k~l~~~yc~~~~sS~G~R~Fl~~~l~~~~~~NP~v~i~v~~~ 51 (68)
..|+|-.+.... ...++.+.+.+|.+++|++.|.+...
T Consensus 92 g~l~Ig~~~~~~----~~~~l~~~l~~~~~~~P~i~l~l~~~ 129 (308)
T PRK10094 92 RQVNIVINNLLY----NPQAVAQLLAWLNERYPFTQFHISRQ 129 (308)
T ss_pred ccEEEEeccccc----CHHHHHHHHHHHHHhCCCcEEEEEee
Confidence 457777654311 13456788999999999999998653
No 253
>cd02413 40S_S3_KH K homology RNA-binding (KH) domain of the eukaryotic 40S small ribosomal subunit protein S3. S3 is part of the head region of the 40S ribosomal subunit and is believed to interact with mRNA as it threads its way from the latch into the channel. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=20.50 E-value=1.4e+02 Score=17.21 Aligned_cols=31 Identities=3% Similarity=0.097 Sum_probs=20.3
Q ss_pred CCHHHHHHHHhCHHHHHHhCCCCeEEEEecC
Q psy15302 22 SSSGVRDFLAQHYVPLKQANPKFPILVRECS 52 (68)
Q Consensus 22 sS~G~R~Fl~~~l~~~~~~NP~v~i~v~~~~ 52 (68)
..+++++.-...-..|.-.||++++++.+-.
T Consensus 48 ~G~~i~~L~~~L~k~~~~~~~~i~v~~~~v~ 78 (81)
T cd02413 48 KGRRIRELTSLVQKRFNFPEGSVELYAEKVA 78 (81)
T ss_pred CchhHHHHHHHHHHHhCCCCCeEEEEEEEcc
Confidence 4566666555544455679999999776543
No 254
>PF01507 PAPS_reduct: Phosphoadenosine phosphosulfate reductase family; InterPro: IPR002500 This domain is found in phosphoadenosine phosphosulphate (PAPS) reductase enzymes or PAPS sulphotransferase. PAPS reductase is part of the adenine nucleotide alpha hydrolases superfamily also including N type ATP PPases and ATP sulphurylases []. The enzyme uses thioredoxin as an electron donor for the reduction of PAPS to phospho-adenosine-phosphate (PAP) [, ]. It is also found in NodP nodulation protein P from Rhizobium meliloti (Sinorhizobium meliloti) which has ATP sulphurylase activity (sulphate adenylate transferase) [].; GO: 0003824 catalytic activity, 0008152 metabolic process; PDB: 2GOY_C 3G5A_C 3G6K_D 3G59_A 3FWK_A 2WSI_A 2OQ2_B 1SUR_A 2O8V_A 1ZUN_A.
Probab=20.47 E-value=40 Score=20.66 Aligned_cols=34 Identities=15% Similarity=0.239 Sum_probs=24.1
Q ss_pred EEEEecCCCCCCHHHHHHHHhCHHHHHHhCCCCeEEEEe
Q psy15302 12 LRIHLCQKGGSSSGVRDFLAQHYVPLKQANPKFPILVRE 50 (68)
Q Consensus 12 l~~~yc~~~~sS~G~R~Fl~~~l~~~~~~NP~v~i~v~~ 50 (68)
+.+.|++++-....+.+|++.....+ +++|.+..
T Consensus 26 ~~vv~~dtg~e~p~t~~~~~~~~~~~-----~~~i~~~~ 59 (174)
T PF01507_consen 26 VPVVFIDTGYEFPETYEFVDELAKRY-----GIPIIVYR 59 (174)
T ss_dssp CEEEEEE-STB-HHHHHHHHHHHHHT-----TCEEEEEE
T ss_pred CcEEEEecCccCHHHHHHHHHHHhhh-----hhhhhhcc
Confidence 46889999999999999998755544 67765543
No 255
>cd01836 FeeA_FeeB_like SGNH_hydrolase subfamily, FeeA, FeeB and similar esterases/lipases. FeeA and FeeB are part of a biosynthetic gene cluster and may participate in the biosynthesis of long-chain N-acyltyrosines by providing saturated and unsaturated fatty acids, which it turn are loaded onto the acyl carrier protein FeeL. SGNH hydrolases are a diverse family of lipases and esterases. The tertiary fold of the enzyme is substantially different from that of the alpha/beta hydrolase family and unique among all known hydrolases; its active site closely resembles the Ser-His-Asp(Glu) triad found in other serine hydrolases.
Probab=20.45 E-value=2e+02 Score=17.81 Aligned_cols=29 Identities=24% Similarity=0.202 Sum_probs=21.5
Q ss_pred CCHHHHHHHHhCHHHHHHhCCCCeEEEEe
Q psy15302 22 SSSGVRDFLAQHYVPLKQANPKFPILVRE 50 (68)
Q Consensus 22 sS~G~R~Fl~~~l~~~~~~NP~v~i~v~~ 50 (68)
+..-.++=+.+-+..+++++|+.+|++..
T Consensus 85 ~~~~~~~~l~~li~~i~~~~~~~~iiv~~ 113 (191)
T cd01836 85 SIARWRKQLAELVDALRAKFPGARVVVTA 113 (191)
T ss_pred CHHHHHHHHHHHHHHHHhhCCCCEEEEEC
Confidence 34455566667788888889999998864
No 256
>PRK12683 transcriptional regulator CysB-like protein; Reviewed
Probab=20.33 E-value=1.5e+02 Score=20.20 Aligned_cols=25 Identities=24% Similarity=0.290 Sum_probs=21.3
Q ss_pred HHHHHhCHHHHHHhCCCCeEEEEec
Q psy15302 27 RDFLAQHYVPLKQANPKFPILVREC 51 (68)
Q Consensus 27 R~Fl~~~l~~~~~~NP~v~i~v~~~ 51 (68)
..++...+..|.+.+|++.|.+...
T Consensus 105 ~~~l~~~i~~f~~~~P~i~l~~~~~ 129 (309)
T PRK12683 105 RYALPKVVRQFKEVFPKVHLALRQG 129 (309)
T ss_pred HHHHHHHHHHHHHHCCCceEEEEeC
Confidence 4677888899999999999999764
No 257
>cd02872 GH18_chitolectin_chitotriosidase This conserved domain family includes a large number of catalytically inactive chitinase-like lectins (chitolectins) including YKL-39, YKL-40 (HCGP39), YM1, oviductin, and AMCase (acidic mammalian chitinase), as well as catalytically active chitotriosidases. The conserved domain is an eight-stranded alpha/beta barrel fold belonging to the family 18 glycosyl hydrolases. The fold has a pronounced active-site cleft at the C-terminal end of the beta-barrel. The chitolectins lack a key active site glutamate (the proton donor required for hydrolytic activity) but retain highly conserved residues involved in oligosaccharide binding. Chitotriosidase is a chitinolytic enzyme expressed in maturing macrophages, which suggests that it plays a part in antimicrobial defense. Chitotriosidase hydrolyzes chitotriose, as well as colloidal chitin to yield chitobiose and is therefore considered an exochitinase. Chitotriosidase occurs in two major forms, the la
Probab=20.30 E-value=84 Score=22.18 Aligned_cols=19 Identities=26% Similarity=0.454 Sum_probs=15.4
Q ss_pred CHHHHHHhCCCCeEEEEec
Q psy15302 33 HYVPLKQANPKFPILVREC 51 (68)
Q Consensus 33 ~l~~~~~~NP~v~i~v~~~ 51 (68)
.+.++|++||++.+++.-.
T Consensus 60 ~~~~lk~~~p~lkvlisiG 78 (362)
T cd02872 60 RFNALKEKNPNLKTLLAIG 78 (362)
T ss_pred HHHHHHhhCCCceEEEEEc
Confidence 4567899999999998654
No 258
>cd06548 GH18_chitinase The GH18 (glycosyl hydrolases, family 18) type II chitinases hydrolyze chitin, an abundant polymer of N-acetylglucosamine and have been identified in bacteria, fungi, insects, plants, viruses, and protozoan parasites. The structure of this domain is an eight-stranded alpha/beta barrel with a pronounced active-site cleft at the C-terminal end of the beta-barrel.
Probab=20.21 E-value=90 Score=21.86 Aligned_cols=20 Identities=35% Similarity=0.448 Sum_probs=16.4
Q ss_pred CHHHHHHhCCCCeEEEEecC
Q psy15302 33 HYVPLKQANPKFPILVRECS 52 (68)
Q Consensus 33 ~l~~~~~~NP~v~i~v~~~~ 52 (68)
.+..+|++||++++++.-.-
T Consensus 74 ~~~~lk~~~p~lkvl~siGG 93 (322)
T cd06548 74 QLRKLKQKNPHLKILLSIGG 93 (322)
T ss_pred HHHHHHHhCCCCEEEEEEeC
Confidence 46789999999999987643
No 259
>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=20.16 E-value=99 Score=17.82 Aligned_cols=14 Identities=14% Similarity=0.430 Sum_probs=9.2
Q ss_pred HHHHHHhCHHHHHH
Q psy15302 26 VRDFLAQHYVPLKQ 39 (68)
Q Consensus 26 ~R~Fl~~~l~~~~~ 39 (68)
+++||.+|||.+-+
T Consensus 47 LkeWLD~nLP~lVE 60 (73)
T PF10691_consen 47 LKEWLDENLPGLVE 60 (73)
T ss_pred HHHHHHhccHHHHH
Confidence 46777777776643
Done!