Query 041692
Match_columns 73
No_of_seqs 104 out of 313
Neff 5.3
Searched_HMMs 46136
Date Fri Mar 29 09:41:49 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/041692.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/041692hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3445 Mitochondrial/chloropl 99.9 6.3E-26 1.4E-30 152.8 7.0 62 10-73 15-76 (145)
2 KOG3446 NADH:ubiquinone oxidor 99.9 1.1E-24 2.4E-29 137.9 1.8 65 9-73 4-68 (97)
3 PF05047 L51_S25_CI-B8: Mitoch 99.4 2.5E-13 5.4E-18 76.6 4.7 37 37-73 1-37 (52)
4 PF10780 MRP_L53: 39S ribosoma 95.5 0.018 3.8E-07 32.9 2.9 46 27-73 1-48 (51)
5 KOG4079 Putative mitochondrial 91.4 0.049 1.1E-06 37.6 -0.3 56 16-71 24-79 (169)
6 KOG0183 20S proteasome, regula 73.3 1.8 3.9E-05 31.8 1.1 21 27-47 158-179 (249)
7 cd05466 PBP2_LTTR_substrate Th 65.2 14 0.00031 21.9 3.8 28 36-63 10-37 (197)
8 PF05762 VWA_CoxE: VWA domain 64.5 14 0.00031 25.6 4.1 36 24-59 60-95 (222)
9 PF13692 Glyco_trans_1_4: Glyc 64.1 14 0.00029 22.3 3.6 37 25-61 5-41 (135)
10 cd08418 PBP2_TdcA The C-termin 64.0 13 0.00029 22.8 3.5 28 35-62 9-36 (201)
11 PF13701 DDE_Tnp_1_4: Transpos 62.9 21 0.00045 27.8 5.1 42 23-64 185-227 (448)
12 cd08429 PBP2_NhaR The C-termin 62.0 16 0.00034 23.5 3.7 28 36-63 10-37 (204)
13 cd08470 PBP2_CrgA_like_1 The C 61.6 16 0.00034 22.5 3.6 25 37-61 12-36 (197)
14 TIGR02136 ptsS_2 phosphate bin 60.6 11 0.00025 26.8 3.1 26 37-62 46-71 (287)
15 cd08435 PBP2_GbpR The C-termin 60.6 17 0.00038 22.1 3.6 26 37-62 11-36 (201)
16 cd08440 PBP2_LTTR_like_4 TThe 56.7 19 0.00042 21.7 3.3 26 37-62 11-36 (197)
17 TIGR01159 DRP1 density-regulat 55.9 6.8 0.00015 27.3 1.3 25 25-49 14-38 (173)
18 cd08461 PBP2_DntR_like_3 The C 55.6 21 0.00046 21.9 3.4 26 37-62 11-36 (198)
19 cd08450 PBP2_HcaR The C-termin 55.4 19 0.00041 22.0 3.1 26 37-62 11-36 (196)
20 cd08465 PBP2_ToxR The C-termin 55.3 19 0.00042 22.6 3.3 26 37-62 11-36 (200)
21 cd08456 PBP2_LysR The C-termin 55.2 24 0.00051 21.6 3.6 26 37-62 11-36 (196)
22 cd08481 PBP2_GcdR_like The C-t 55.0 23 0.0005 21.5 3.5 26 38-63 12-37 (194)
23 cd08452 PBP2_AlsR The C-termin 54.8 21 0.00045 22.2 3.3 26 37-62 11-36 (197)
24 cd08416 PBP2_MdcR The C-termin 54.5 24 0.00051 21.6 3.5 27 37-63 11-37 (199)
25 PF03466 LysR_substrate: LysR 53.9 20 0.00042 22.3 3.1 27 37-63 17-43 (209)
26 cd08439 PBP2_LrhA_like The C-t 53.6 29 0.00063 21.3 3.8 26 37-62 11-36 (185)
27 cd08464 PBP2_DntR_like_2 The C 53.4 27 0.00057 21.4 3.6 26 38-63 12-37 (200)
28 cd08426 PBP2_LTTR_like_5 The C 53.2 25 0.00054 21.5 3.5 26 37-62 11-36 (199)
29 COG4837 Uncharacterized protei 53.1 21 0.00045 23.3 3.1 33 28-63 19-51 (106)
30 cd08436 PBP2_LTTR_like_3 The C 52.9 22 0.00048 21.5 3.2 27 36-62 10-36 (194)
31 cd08438 PBP2_CidR The C-termin 52.9 19 0.00041 21.9 2.8 25 38-62 12-36 (197)
32 cd08414 PBP2_LTTR_aromatics_li 52.8 26 0.00056 21.3 3.4 26 37-62 11-36 (197)
33 cd08488 PBP2_AmpR The C-termin 52.3 31 0.00066 21.3 3.8 26 38-63 12-37 (191)
34 cd08477 PBP2_CrgA_like_8 The C 52.3 29 0.00062 21.2 3.6 25 37-61 12-36 (197)
35 cd08448 PBP2_LTTR_aromatics_li 52.1 29 0.00063 21.0 3.6 26 37-62 11-36 (197)
36 cd08486 PBP2_CbnR The C-termin 52.0 23 0.0005 22.2 3.2 25 38-62 13-37 (198)
37 cd08412 PBP2_PAO1_like The C-t 51.8 23 0.0005 21.6 3.1 25 38-62 12-36 (198)
38 cd08444 PBP2_Cbl The C-termina 51.4 28 0.0006 21.7 3.5 26 37-62 11-36 (198)
39 cd08460 PBP2_DntR_like_1 The C 51.3 24 0.00052 21.9 3.2 27 36-62 10-36 (200)
40 PF02601 Exonuc_VII_L: Exonucl 51.3 23 0.00051 25.6 3.5 42 15-63 9-50 (319)
41 COG1653 UgpB ABC-type sugar tr 51.2 50 0.0011 23.3 5.1 39 22-63 32-70 (433)
42 cd08466 PBP2_LeuO The C-termin 51.1 29 0.00064 21.3 3.5 25 38-62 12-36 (200)
43 cd08437 PBP2_MleR The substrat 50.9 26 0.00056 21.6 3.3 25 38-62 12-36 (198)
44 PRK13996 potassium-transportin 50.3 18 0.00039 25.8 2.7 43 28-70 91-140 (197)
45 cd08431 PBP2_HupR The C-termin 50.3 27 0.00059 21.4 3.3 25 38-62 12-36 (195)
46 cd08434 PBP2_GltC_like The sub 50.0 24 0.00053 21.3 3.0 25 38-62 12-36 (195)
47 cd08423 PBP2_LTTR_like_6 The C 49.9 29 0.00063 21.1 3.3 25 38-62 12-36 (200)
48 cd08479 PBP2_CrgA_like_9 The C 49.8 32 0.00069 21.1 3.5 27 36-62 11-37 (198)
49 cd08420 PBP2_CysL_like C-termi 49.6 32 0.0007 20.7 3.5 27 37-63 11-37 (201)
50 cd08482 PBP2_TrpI The C-termin 49.1 35 0.00076 21.0 3.7 26 37-62 11-36 (195)
51 cd08453 PBP2_IlvR The C-termin 49.1 29 0.00063 21.4 3.3 25 38-62 12-36 (200)
52 cd08425 PBP2_CynR The C-termin 49.0 30 0.00065 21.2 3.3 27 36-62 11-37 (197)
53 cd08472 PBP2_CrgA_like_3 The C 48.8 41 0.00089 20.6 3.9 25 37-61 12-36 (202)
54 cd08445 PBP2_BenM_CatM_CatR Th 48.1 33 0.00071 21.3 3.4 25 38-62 13-37 (203)
55 cd08421 PBP2_LTTR_like_1 The C 47.9 32 0.0007 21.0 3.4 24 39-62 13-36 (198)
56 cd08487 PBP2_BlaA The C-termin 47.9 34 0.00073 20.9 3.4 26 37-62 11-36 (189)
57 PRK14003 potassium-transportin 47.7 33 0.0007 24.5 3.7 43 28-70 93-137 (194)
58 cd08432 PBP2_GcdR_TrpI_HvrB_Am 47.1 38 0.00083 20.5 3.6 28 36-63 10-37 (194)
59 cd08415 PBP2_LysR_opines_like 47.1 16 0.00034 22.3 1.8 26 37-62 11-36 (196)
60 cd08473 PBP2_CrgA_like_4 The C 47.1 41 0.00088 20.5 3.7 25 38-62 15-39 (202)
61 cd08476 PBP2_CrgA_like_7 The C 46.5 27 0.00059 21.1 2.8 24 38-61 11-34 (197)
62 cd08422 PBP2_CrgA_like The C-t 46.5 28 0.00061 21.0 2.9 25 38-62 13-37 (197)
63 cd08474 PBP2_CrgA_like_5 The C 46.5 40 0.00087 20.7 3.6 26 37-62 14-39 (202)
64 PRK13997 potassium-transportin 46.4 23 0.0005 25.2 2.7 43 28-70 87-136 (193)
65 cd08449 PBP2_XapR The C-termin 46.4 34 0.00073 20.8 3.2 25 38-62 12-36 (197)
66 cd08427 PBP2_LTTR_like_2 The C 46.3 33 0.00071 20.8 3.2 25 38-62 12-36 (195)
67 cd08478 PBP2_CrgA The C-termin 46.1 29 0.00063 21.3 3.0 25 37-61 14-38 (199)
68 cd08441 PBP2_MetR The C-termin 46.0 47 0.001 20.4 3.9 24 39-62 13-36 (198)
69 TIGR00681 kdpC K+-transporting 45.8 24 0.00051 25.0 2.7 43 28-70 84-132 (187)
70 cd08419 PBP2_CbbR_RubisCO_like 45.4 37 0.00081 20.5 3.3 25 38-62 11-35 (197)
71 cd08458 PBP2_NocR The C-termin 45.1 32 0.0007 21.3 3.1 27 37-63 11-37 (196)
72 cd08442 PBP2_YofA_SoxR_like Th 44.7 34 0.00075 20.7 3.1 26 38-63 12-37 (193)
73 cd08447 PBP2_LTTR_aromatics_li 44.3 46 0.00099 20.3 3.6 26 37-62 11-36 (198)
74 PRK00286 xseA exodeoxyribonucl 43.7 36 0.00079 25.9 3.6 37 20-63 135-171 (438)
75 TIGR00237 xseA exodeoxyribonuc 43.7 37 0.00081 26.2 3.7 37 20-63 129-165 (432)
76 cd08471 PBP2_CrgA_like_2 The C 43.6 51 0.0011 20.1 3.8 25 37-61 12-36 (201)
77 cd08446 PBP2_Chlorocatechol Th 43.6 42 0.0009 20.5 3.4 25 38-62 13-37 (198)
78 cd08483 PBP2_HvrB The C-termin 43.4 41 0.00089 20.4 3.3 25 37-61 11-35 (190)
79 cd08411 PBP2_OxyR The C-termin 43.4 42 0.00091 20.6 3.4 24 39-62 14-37 (200)
80 cd08459 PBP2_DntR_NahR_LinR_li 43.4 52 0.0011 20.2 3.8 26 38-63 12-37 (201)
81 TIGR02174 CXXU_selWTH selT/sel 42.9 68 0.0015 18.6 4.7 38 23-64 1-38 (72)
82 PRK00315 potassium-transportin 42.4 28 0.00061 24.8 2.7 43 28-70 86-134 (193)
83 cd08469 PBP2_PnbR The C-termin 42.2 46 0.001 21.0 3.5 26 38-63 12-37 (221)
84 PRK13999 potassium-transportin 42.2 30 0.00064 24.8 2.8 43 28-70 97-143 (201)
85 cd08485 PBP2_ClcR The C-termin 41.9 46 0.001 20.7 3.4 26 37-62 12-37 (198)
86 cd02989 Phd_like_TxnDC9 Phosdu 41.5 72 0.0016 19.7 4.2 33 23-59 26-58 (113)
87 cd08433 PBP2_Nac The C-teminal 41.5 32 0.0007 21.1 2.6 25 38-62 12-36 (198)
88 PF06244 DUF1014: Protein of u 41.5 22 0.00048 23.5 1.9 20 37-56 80-99 (122)
89 cd08480 PBP2_CrgA_like_10 The 41.2 46 0.001 20.6 3.3 25 37-61 12-36 (198)
90 cd08467 PBP2_SyrM The C-termin 41.0 44 0.00096 20.8 3.2 27 37-63 11-37 (200)
91 cd08475 PBP2_CrgA_like_6 The C 40.8 46 0.00099 20.2 3.2 25 37-61 12-36 (199)
92 PRK14001 potassium-transportin 40.3 33 0.00071 24.3 2.8 43 28-70 85-134 (189)
93 cd08417 PBP2_Nitroaromatics_li 40.0 51 0.0011 20.1 3.4 25 38-62 12-36 (200)
94 PTZ00062 glutaredoxin; Provisi 39.9 83 0.0018 22.1 4.7 37 23-63 20-57 (204)
95 COG2871 NqrF Na+-transporting 39.8 58 0.0013 25.4 4.2 37 21-62 305-342 (410)
96 KOG0863 20S proteasome, regula 39.8 18 0.0004 26.9 1.5 24 31-54 162-185 (264)
97 cd08430 PBP2_IlvY The C-termin 39.8 29 0.00063 21.1 2.2 25 38-62 12-36 (199)
98 PLN02757 sirohydrochlorine fer 39.6 26 0.00056 23.5 2.1 31 39-69 90-120 (154)
99 PF04690 YABBY: YABBY protein; 39.3 24 0.00051 24.7 1.9 19 38-56 130-148 (170)
100 cd08462 PBP2_NodD The C-termin 39.2 60 0.0013 20.1 3.7 26 37-62 11-36 (200)
101 cd03026 AhpF_NTD_C TRX-GRX-lik 38.7 87 0.0019 18.7 5.4 36 23-62 16-51 (89)
102 cd08451 PBP2_BudR The C-termin 38.3 37 0.0008 20.7 2.5 23 40-62 15-37 (199)
103 PF01624 MutS_I: MutS domain I 38.2 33 0.00072 21.3 2.3 21 42-62 4-24 (113)
104 cd08468 PBP2_Pa0477 The C-term 37.7 65 0.0014 20.0 3.6 26 38-63 12-37 (202)
105 TIGR00741 yfiA ribosomal subun 37.7 87 0.0019 18.4 4.4 32 23-55 3-34 (95)
106 PRK14002 potassium-transportin 37.7 34 0.00074 24.2 2.5 43 28-70 81-130 (186)
107 PF02638 DUF187: Glycosyl hydr 36.7 59 0.0013 24.0 3.7 30 34-63 202-231 (311)
108 PLN02958 diacylglycerol kinase 36.3 81 0.0018 24.8 4.6 44 21-64 112-155 (481)
109 PF13516 LRR_6: Leucine Rich r 35.8 10 0.00022 17.3 -0.3 20 18-39 2-21 (24)
110 PRK10974 glycerol-3-phosphate 35.7 62 0.0013 24.0 3.7 36 22-61 27-62 (438)
111 smart00367 LRR_CC Leucine-rich 35.4 28 0.00062 16.1 1.3 23 18-41 2-24 (26)
112 cd03076 GST_N_Pi GST_N family, 35.4 83 0.0018 17.5 3.6 37 23-59 2-54 (73)
113 PF01547 SBP_bac_1: Bacterial 35.4 44 0.00096 22.4 2.7 23 40-62 9-32 (315)
114 cd08463 PBP2_DntR_like_4 The C 35.1 67 0.0015 20.3 3.4 24 38-61 12-35 (203)
115 PF02482 Ribosomal_S30AE: Sigm 35.0 96 0.0021 18.1 4.0 27 29-55 7-33 (97)
116 cd02974 AhpF_NTD_N Alkyl hydro 34.7 1.1E+02 0.0024 18.8 5.9 55 12-70 10-65 (94)
117 KOG1909 Ran GTPase-activating 34.5 49 0.0011 26.0 3.1 44 9-59 232-276 (382)
118 COG0607 PspE Rhodanese-related 34.5 61 0.0013 18.8 3.0 23 21-43 61-83 (110)
119 PRK13994 potassium-transportin 34.4 40 0.00086 24.6 2.5 43 28-70 111-164 (222)
120 TIGR02200 GlrX_actino Glutared 34.4 46 0.001 18.1 2.3 21 23-43 2-22 (77)
121 cd08484 PBP2_LTTR_beta_lactama 33.8 71 0.0015 19.4 3.3 26 37-62 11-36 (189)
122 PRK13995 potassium-transportin 33.2 48 0.001 23.8 2.7 43 28-70 95-144 (203)
123 PF07205 DUF1413: Domain of un 32.8 86 0.0019 18.0 3.4 34 29-62 27-60 (70)
124 PF10262 Rdx: Rdx family; Int 32.6 56 0.0012 19.0 2.6 37 22-62 2-40 (76)
125 cd08413 PBP2_CysB_like The C-t 32.3 52 0.0011 20.5 2.5 25 38-62 12-36 (198)
126 TIGR00269 conserved hypothetic 32.2 43 0.00093 20.8 2.1 27 28-56 31-57 (104)
127 TIGR02036 dsdC D-serine deamin 32.2 86 0.0019 22.0 3.9 38 21-63 96-133 (302)
128 PF07315 DUF1462: Protein of u 32.1 97 0.0021 19.8 3.7 37 28-67 12-48 (93)
129 KOG1454 Predicted hydrolase/ac 32.0 46 0.001 24.6 2.5 26 44-69 282-307 (326)
130 TIGR03850 bind_CPR_0540 carboh 32.0 1.3E+02 0.0028 22.0 4.9 25 38-62 47-71 (437)
131 PRK10680 molybdopterin biosynt 31.8 33 0.00071 26.5 1.8 38 30-72 250-288 (411)
132 PF12876 Cellulase-like: Sugar 31.5 57 0.0012 19.3 2.5 26 35-60 38-63 (88)
133 COG1570 XseA Exonuclease VII, 31.5 73 0.0016 25.4 3.7 30 30-63 142-171 (440)
134 cd03005 PDI_a_ERp46 PDIa famil 31.3 59 0.0013 18.6 2.5 41 22-62 19-59 (102)
135 PF13552 DUF4127: Protein of u 31.1 43 0.00094 26.5 2.4 18 43-60 92-109 (497)
136 cd08457 PBP2_OccR The C-termin 31.0 43 0.00093 20.6 2.0 26 37-62 11-36 (196)
137 PRK10696 tRNA 2-thiocytidine b 30.3 55 0.0012 23.1 2.6 25 33-57 206-230 (258)
138 PRK10597 DNA damage-inducible 29.5 1.4E+02 0.0031 18.3 5.8 43 22-64 2-47 (81)
139 cd07945 DRE_TIM_CMS Leptospira 29.4 1.4E+02 0.0031 21.7 4.7 35 24-60 163-197 (280)
140 PF05159 Capsule_synth: Capsul 28.9 88 0.0019 21.8 3.4 27 37-63 138-164 (269)
141 PRK09375 quinolinate synthetas 28.4 83 0.0018 23.9 3.4 34 27-60 223-269 (319)
142 PRK14690 molybdopterin biosynt 28.3 34 0.00074 26.5 1.3 39 30-72 266-304 (419)
143 cd03051 GST_N_GTT2_like GST_N 28.1 1E+02 0.0023 16.4 3.9 19 24-42 2-20 (74)
144 cd01388 SOX-TCF_HMG-box SOX-TC 28.0 51 0.0011 18.7 1.8 18 40-57 12-29 (72)
145 PRK10470 ribosome hibernation 28.0 87 0.0019 18.7 2.9 25 31-55 10-34 (95)
146 PRK09508 leuO leucine transcri 27.9 1.1E+02 0.0024 21.5 3.8 26 38-63 124-149 (314)
147 KOG1806 DEAD box containing he 27.9 52 0.0011 29.5 2.5 50 24-73 494-556 (1320)
148 PRK10837 putative DNA-binding 27.8 98 0.0021 21.1 3.5 25 38-62 101-125 (290)
149 smart00579 FBD domain in FBox 27.5 97 0.0021 17.3 2.9 40 17-59 32-71 (72)
150 PRK13337 putative lipid kinase 27.4 1.7E+02 0.0037 21.0 4.8 43 21-64 2-44 (304)
151 PF01507 PAPS_reduct: Phosphoa 27.2 1E+02 0.0022 19.4 3.3 38 19-61 22-59 (174)
152 cd01523 RHOD_Lact_B Member of 27.0 86 0.0019 18.3 2.7 20 23-42 63-82 (100)
153 COG4097 Predicted ferric reduc 26.9 73 0.0016 25.4 2.9 43 21-69 344-387 (438)
154 cd02987 Phd_like_Phd Phosducin 26.6 1.3E+02 0.0029 20.2 3.9 34 24-61 88-121 (175)
155 cd00552 RaiA RaiA ("ribosome-a 26.5 97 0.0021 18.0 2.9 25 31-55 9-33 (93)
156 PF13504 LRR_7: Leucine rich r 26.4 33 0.00072 14.8 0.6 11 19-29 2-12 (17)
157 TIGR02196 GlrX_YruB Glutaredox 26.4 84 0.0018 16.5 2.4 21 23-43 2-22 (74)
158 PF00309 Sigma54_AID: Sigma-54 26.3 59 0.0013 17.8 1.8 15 43-57 33-47 (49)
159 COG0279 GmhA Phosphoheptose is 26.2 97 0.0021 21.9 3.2 36 24-59 43-78 (176)
160 PF00505 HMG_box: HMG (high mo 26.1 66 0.0014 17.5 2.0 18 39-56 10-27 (69)
161 PF11943 DUF3460: Protein of u 26.1 50 0.0011 19.4 1.5 15 42-56 8-22 (60)
162 PRK11914 diacylglycerol kinase 25.9 1.3E+02 0.0029 21.4 4.0 42 19-61 7-48 (306)
163 TIGR03851 chitin_NgcE carbohyd 25.9 95 0.0021 23.0 3.3 25 38-62 53-77 (450)
164 TIGR03341 YhgI_GntY IscR-regul 25.7 59 0.0013 22.6 2.1 38 28-68 148-189 (190)
165 PHA00684 hypothetical protein 25.4 85 0.0018 21.1 2.7 28 36-64 57-84 (128)
166 PRK11716 DNA-binding transcrip 25.1 1.3E+02 0.0028 20.0 3.6 25 38-62 79-103 (269)
167 PRK14491 putative bifunctional 25.1 53 0.0011 26.6 1.9 37 30-71 440-477 (597)
168 PRK12681 cysB transcriptional 25.0 1.2E+02 0.0025 21.8 3.6 37 21-62 93-129 (324)
169 PF10607 CLTH: CTLH/CRA C-term 25.0 51 0.0011 20.8 1.5 29 32-60 15-43 (145)
170 PF09457 RBD-FIP: FIP domain ; 24.9 44 0.00095 18.7 1.1 20 36-55 25-44 (48)
171 PF09822 ABC_transp_aux: ABC-t 24.8 2.4E+02 0.0052 19.7 5.1 39 23-61 29-69 (271)
172 PRK13055 putative lipid kinase 24.2 2.5E+02 0.0053 20.6 5.2 40 21-61 3-42 (334)
173 PRK11151 DNA-binding transcrip 24.1 1.5E+02 0.0032 20.6 3.8 26 37-62 102-127 (305)
174 COG0694 Thioredoxin-like prote 24.0 75 0.0016 20.0 2.1 24 27-50 52-76 (93)
175 PF13890 Rab3-GTPase_cat: Rab3 24.0 63 0.0014 22.4 1.9 19 39-57 71-89 (164)
176 PF14363 AAA_assoc: Domain ass 23.9 1.3E+02 0.0029 18.3 3.3 29 36-64 5-35 (98)
177 PRK09791 putative DNA-binding 23.7 1.3E+02 0.0028 20.9 3.5 39 19-62 93-131 (302)
178 KOG4131 Ngg1-interacting facto 23.6 1.5E+02 0.0033 22.3 3.9 56 9-68 214-269 (272)
179 PRK09801 transcriptional activ 23.6 1.5E+02 0.0033 20.9 3.9 28 35-62 105-132 (310)
180 cd06544 GH18_narbonin Narbonin 23.5 76 0.0016 22.8 2.3 20 43-62 59-78 (253)
181 PF01903 CbiX: CbiX; InterPro 23.4 29 0.00062 20.8 0.1 35 35-69 65-99 (105)
182 PRK11074 putative DNA-binding 23.4 1.1E+02 0.0023 21.4 3.0 39 19-62 90-128 (300)
183 cd02973 TRX_GRX_like Thioredox 23.4 1.3E+02 0.0029 16.0 4.9 36 22-61 2-37 (67)
184 COG1393 ArsC Arsenate reductas 23.3 78 0.0017 20.3 2.2 23 22-44 2-24 (117)
185 smart00329 BPI2 BPI/LBP/CETP C 23.2 2.3E+02 0.0051 19.2 4.7 32 40-71 48-79 (202)
186 PRK03601 transcriptional regul 23.0 1.7E+02 0.0037 20.2 4.0 27 37-63 100-126 (275)
187 PRK15421 DNA-binding transcrip 22.9 1.4E+02 0.0031 21.2 3.6 25 38-62 101-125 (317)
188 PRK10086 DNA-binding transcrip 22.8 1.6E+02 0.0034 20.7 3.8 28 36-63 112-139 (311)
189 cd02976 NrdH NrdH-redoxin (Nrd 22.7 1E+02 0.0022 16.1 2.3 21 23-43 2-22 (73)
190 PRK10341 DNA-binding transcrip 22.7 1.6E+02 0.0034 20.7 3.8 38 21-63 97-134 (312)
191 PRK14997 LysR family transcrip 22.5 1.6E+02 0.0034 20.4 3.7 38 21-63 92-129 (301)
192 TIGR00550 nadA quinolinate syn 22.5 1.3E+02 0.0029 22.4 3.6 35 26-60 210-257 (310)
193 PRK11139 DNA-binding transcrip 22.4 1.3E+02 0.0029 20.7 3.4 25 38-62 106-130 (297)
194 PF05725 FNIP: FNIP Repeat; I 22.2 60 0.0013 16.9 1.2 16 13-28 29-44 (44)
195 PF02669 KdpC: K+-transporting 22.1 90 0.0019 22.1 2.4 43 28-70 85-133 (188)
196 KOG0026 Anthranilate synthase, 22.0 72 0.0016 23.0 1.9 23 44-68 55-77 (223)
197 PRK11233 nitrogen assimilation 21.9 1.9E+02 0.0042 20.1 4.1 27 37-63 103-129 (305)
198 PF13589 HATPase_c_3: Histidin 21.9 2.2E+02 0.0048 18.0 5.2 35 34-71 4-38 (137)
199 PF08885 GSCFA: GSCFA family; 21.9 1.6E+02 0.0035 21.4 3.8 30 35-64 148-177 (251)
200 TIGR00411 redox_disulf_1 small 21.7 1.5E+02 0.0033 16.1 4.6 27 22-48 2-28 (82)
201 cd03409 Chelatase_Class_II Cla 21.7 1.8E+02 0.0039 16.8 4.1 33 36-68 14-46 (101)
202 PF11247 DUF2675: Protein of u 21.6 77 0.0017 20.4 1.8 15 35-49 68-82 (98)
203 PRK15317 alkyl hydroperoxide r 21.3 1.7E+02 0.0038 22.6 4.1 38 22-63 119-156 (517)
204 cd01844 SGNH_hydrolase_like_6 21.2 2.4E+02 0.0051 18.1 4.9 40 22-61 59-100 (177)
205 cd02957 Phd_like Phosducin (Ph 21.2 2E+02 0.0044 17.3 4.2 33 23-59 28-60 (113)
206 PF09345 DUF1987: Domain of un 20.9 1.7E+02 0.0036 18.4 3.3 34 23-58 49-82 (99)
207 PF02960 K1: K1 glycoprotein; 20.9 29 0.00062 23.3 -0.3 41 33-73 30-70 (130)
208 KOG3170 Conserved phosducin-li 20.8 3.3E+02 0.0072 20.1 5.1 47 7-62 104-150 (240)
209 PF03562 MltA: MltA specific i 20.6 1.2E+02 0.0025 20.8 2.7 28 30-57 126-156 (158)
210 cd07941 DRE_TIM_LeuA3 Desulfob 20.5 2.5E+02 0.0055 20.0 4.6 35 24-60 167-201 (273)
211 PRK11013 DNA-binding transcrip 20.5 1.8E+02 0.0039 20.3 3.7 38 21-63 94-131 (309)
212 COG0007 CysG Uroporphyrinogen- 20.5 1.4E+02 0.0031 21.9 3.3 33 36-72 65-97 (244)
213 PRK12684 transcriptional regul 20.4 1.8E+02 0.004 20.5 3.8 38 21-63 93-130 (313)
214 PF01076 Mob_Pre: Plasmid reco 20.3 2.7E+02 0.0059 19.0 4.5 51 21-71 81-136 (196)
215 PF14606 Lipase_GDSL_3: GDSL-l 20.2 1.5E+02 0.0032 20.7 3.1 32 32-63 71-102 (178)
216 PF00781 DAGK_cat: Diacylglyce 20.2 2.3E+02 0.005 17.5 3.9 38 22-62 1-38 (130)
217 cd02066 GRX_family Glutaredoxi 20.0 1.2E+02 0.0025 15.7 2.2 21 23-43 2-22 (72)
No 1
>KOG3445 consensus Mitochondrial/chloroplast ribosomal protein 36a [Translation, ribosomal structure and biogenesis]
Probab=99.93 E-value=6.3e-26 Score=152.82 Aligned_cols=62 Identities=26% Similarity=0.392 Sum_probs=59.5
Q ss_pred hHhhhccccccceEEEEeCCCCCCCHHHHHHHHHcHHHHHHhCCCCeEEEEEcCCCCCEEEEeC
Q 041692 10 MAWRGQLSRSMKELRILLCQTSPSSSSTRSFVERNYKELKTLNPKLPILIRECSGIEPQLWARY 73 (73)
Q Consensus 10 Ms~rg~~~~qLk~l~~~yC~~~~SS~G~R~Fl~~~l~~fk~~NP~v~i~v~~~~g~~P~l~a~Y 73 (73)
|..|++| ||++|+|+||+|||||+|||+||++.|++|+++||+|+|+|.+++|.||.|+|+|
T Consensus 15 Glgryv~--ql~rit~sfCnwggSSrGmR~Fle~~L~~~a~enP~v~i~v~~rrg~hP~lraeY 76 (145)
T KOG3445|consen 15 GLGRYVW--QLRRITVSFCNWGGSSRGMREFLESELPDLARENPGVVIYVEPRRGQHPLLRAEY 76 (145)
T ss_pred chhhhhh--eeeEEEEEEecCCCccHHHHHHHHHHHHHHHhhCCCeEEEEeccCCCCceEEEEe
Confidence 5567777 9999999999999999999999999999999999999999999999999999998
No 2
>KOG3446 consensus NADH:ubiquinone oxidoreductase NDUFA2/B8 subunit [Energy production and conversion]
Probab=99.89 E-value=1.1e-24 Score=137.89 Aligned_cols=65 Identities=55% Similarity=1.015 Sum_probs=63.2
Q ss_pred HhHhhhccccccceEEEEeCCCCCCCHHHHHHHHHcHHHHHHhCCCCeEEEEEcCCCCCEEEEeC
Q 041692 9 EMAWRGQLSRSMKELRILLCQTSPSSSSTRSFVERNYKELKTLNPKLPILIRECSGIEPQLWARY 73 (73)
Q Consensus 9 ~Ms~rg~~~~qLk~l~~~yC~~~~SS~G~R~Fl~~~l~~fk~~NP~v~i~v~~~~g~~P~l~a~Y 73 (73)
.|||++.+.+.|||||++.|+.|+.|+|+|+||+++|+++|+.||++||+|+|++|..|+++|+|
T Consensus 4 a~sr~~s~~~~lkElRI~lcqkspaSagvR~fvEk~Y~~lKkaNP~lPILIREcSgVqPrl~ARY 68 (97)
T KOG3446|consen 4 ALSRLASFTLKLKELRIHLCQKSPASAGVREFVEKFYVNLKKANPDLPILIRECSGVQPRLWARY 68 (97)
T ss_pred hhhcccccchhhhhheeeecCCCCcchhHHHHHHHhhhhhhhcCCCCcEeehhhcCCchHHHHHh
Confidence 47899999999999999999999999999999999999999999999999999999999999998
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=99.43 E-value=2.5e-13 Score=76.57 Aligned_cols=37 Identities=35% Similarity=0.557 Sum_probs=30.2
Q ss_pred HHHHHHHcHHHHHHhCCCCeEEEEEcCCCCCEEEEeC
Q 041692 37 TRSFVERNYKELKTLNPKLPILIRECSGIEPQLWARY 73 (73)
Q Consensus 37 ~R~Fl~~~l~~fk~~NP~v~i~v~~~~g~~P~l~a~Y 73 (73)
||+||+++|++||..||+|+|+|++++|.||.|.|+|
T Consensus 1 ~R~F~~~~lp~l~~~NP~v~~~v~~~~~~~P~~~~~y 37 (52)
T PF05047_consen 1 ARDFLKNNLPTLKYHNPQVQFEVRRRRGRHPFLTAEY 37 (52)
T ss_dssp HHHHHHHTHHHHHHHSTT--EEEE---SSS-EEEEEE
T ss_pred CHhHHHHhHHHHHHHCCCcEEEEEECCCCCCEEEEEE
Confidence 7999999999999999999999999999999999997
No 4
>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=95.51 E-value=0.018 Score=32.86 Aligned_cols=46 Identities=22% Similarity=0.265 Sum_probs=38.1
Q ss_pred eCCCCCCCHHHHHHHHHc--HHHHHHhCCCCeEEEEEcCCCCCEEEEeC
Q 041692 27 LCQTSPSSSSTRSFVERN--YKELKTLNPKLPILIRECSGIEPQLWARY 73 (73)
Q Consensus 27 yC~~~~SS~G~R~Fl~~~--l~~fk~~NP~v~i~v~~~~g~~P~l~a~Y 73 (73)
||+.++.++.+|+||..- -.....-||++.+..+.. ...|.|...|
T Consensus 1 FnPF~~~aksaR~FL~~ip~s~k~~~tni~~~vl~~~~-~~~P~v~V~f 48 (51)
T PF10780_consen 1 FNPFSPNAKSARLFLSLIPPSAKARGTNINCEVLPRVS-RSEPSVTVTF 48 (51)
T ss_pred CCCCCcccHHHHHHHHhcCCccccccCCCceEEecCCC-CCCCeEEEEe
Confidence 789999999999999764 445666899999999888 6699988765
No 5
>KOG4079 consensus Putative mitochondrial ribosomal protein mRpS25 [Translation, ribosomal structure and biogenesis]
Probab=91.38 E-value=0.049 Score=37.64 Aligned_cols=56 Identities=21% Similarity=0.302 Sum_probs=46.2
Q ss_pred cccccceEEEEeCCCCCCCHHHHHHHHHcHHHHHHhCCCCeEEEEEcCCCCCEEEE
Q 041692 16 LSRSMKELRILLCQTSPSSSSTRSFVERNYKELKTLNPKLPILIRECSGIEPQLWA 71 (73)
Q Consensus 16 ~~~qLk~l~~~yC~~~~SS~G~R~Fl~~~l~~fk~~NP~v~i~v~~~~g~~P~l~a 71 (73)
|--.++-.++.|-..|+.-.|+|+|+-=|++.++-.||.|.++.-..--..|.+++
T Consensus 24 lkD~V~vfsvnynt~g~~~~GARdFVfwNipQiQykNP~VQ~~~~knmtpsPF~R~ 79 (169)
T KOG4079|consen 24 LKDNVNVFSVNYNTNGPEQSGARDFVFWNIPQIQYKNPKVQLVKHKNMTPSPFARA 79 (169)
T ss_pred EeccceEEEEeccCCCccccCccceEEecchhhcccCCceEEEeeccCCCChHHHh
Confidence 33456667889999999999999999999999999999999988766655666554
No 6
>KOG0183 consensus 20S proteasome, regulatory subunit alpha type PSMA7/PRE6 [Posttranslational modification, protein turnover, chaperones]
Probab=73.29 E-value=1.8 Score=31.80 Aligned_cols=21 Identities=43% Similarity=0.673 Sum_probs=17.0
Q ss_pred eCC-CCCCCHHHHHHHHHcHHH
Q 041692 27 LCQ-TSPSSSSTRSFVERNYKE 47 (73)
Q Consensus 27 yC~-~~~SS~G~R~Fl~~~l~~ 47 (73)
.|+ +|-+|+.+|+||+++|.+
T Consensus 158 ka~aiGr~sk~VrEflEK~y~e 179 (249)
T KOG0183|consen 158 KANAIGRSSKTVREFLEKNYKE 179 (249)
T ss_pred hccccccccHHHHHHHHHhccc
Confidence 344 677999999999998764
No 7
>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=65.23 E-value=14 Score=21.86 Aligned_cols=28 Identities=7% Similarity=0.094 Sum_probs=22.8
Q ss_pred HHHHHHHHcHHHHHHhCCCCeEEEEEcC
Q 041692 36 STRSFVERNYKELKTLNPKLPILIRECS 63 (73)
Q Consensus 36 G~R~Fl~~~l~~fk~~NP~v~i~v~~~~ 63 (73)
....++...+..|.+++|++.|.+....
T Consensus 10 ~~~~~l~~~i~~~~~~~p~i~i~~~~~~ 37 (197)
T cd05466 10 IAAYLLPPLLAAFRQRYPGVELSLVEGG 37 (197)
T ss_pred hHHHHhHHHHHHHHHHCCCCEEEEEECC
Confidence 4566788888999999999999987653
No 8
>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=64.45 E-value=14 Score=25.63 Aligned_cols=36 Identities=17% Similarity=0.294 Sum_probs=30.6
Q ss_pred EEEeCCCCCCCHHHHHHHHHcHHHHHHhCCCCeEEE
Q 041692 24 RILLCQTSPSSSSTRSFVERNYKELKTLNPKLPILI 59 (73)
Q Consensus 24 ~~~yC~~~~SS~G~R~Fl~~~l~~fk~~NP~v~i~v 59 (73)
.+..||.|||=.|.-.|+-..+..+.+..+.+.+.+
T Consensus 60 lvvl~DvSGSM~~~s~~~l~~~~~l~~~~~~~~~f~ 95 (222)
T PF05762_consen 60 LVVLCDVSGSMAGYSEFMLAFLYALQRQFRRVRVFV 95 (222)
T ss_pred EEEEEeCCCChHHHHHHHHHHHHHHHHhCCCEEEEE
Confidence 467899999999988888888889999999777654
No 9
>PF13692 Glyco_trans_1_4: Glycosyl transferases group 1; PDB: 3OY2_A 3OY7_B 2Q6V_A 2HY7_A 3CV3_A 3CUY_A.
Probab=64.08 E-value=14 Score=22.35 Aligned_cols=37 Identities=16% Similarity=0.248 Sum_probs=26.1
Q ss_pred EEeCCCCCCCHHHHHHHHHcHHHHHHhCCCCeEEEEE
Q 041692 25 ILLCQTSPSSSSTRSFVERNYKELKTLNPKLPILIRE 61 (73)
Q Consensus 25 ~~yC~~~~SS~G~R~Fl~~~l~~fk~~NP~v~i~v~~ 61 (73)
|.|-......+|+..+++.-+..++++.|++.+.+--
T Consensus 5 i~~~g~~~~~k~~~~li~~~~~~l~~~~p~~~l~i~G 41 (135)
T PF13692_consen 5 IGYLGRIRPDKGLEELIEAALERLKEKHPDIELIIIG 41 (135)
T ss_dssp EE--S-SSGGGTHHHHHH-HHHHHHHHSTTEEEEEEC
T ss_pred ccccccccccccccchhhhHHHHHHHHCcCEEEEEEe
Confidence 3344333445899999999999999999999988843
No 10
>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=64.05 E-value=13 Score=22.75 Aligned_cols=28 Identities=18% Similarity=0.185 Sum_probs=23.5
Q ss_pred HHHHHHHHHcHHHHHHhCCCCeEEEEEc
Q 041692 35 SSTRSFVERNYKELKTLNPKLPILIREC 62 (73)
Q Consensus 35 ~G~R~Fl~~~l~~fk~~NP~v~i~v~~~ 62 (73)
.....++...+.+|++.+|++.|.+...
T Consensus 9 ~~~~~~l~~~l~~~~~~~P~i~l~i~~~ 36 (201)
T cd08418 9 LIAHTLMPAVINRFKEQFPDVQISIYEG 36 (201)
T ss_pred HHHHhhhHHHHHHHHHHCCCceEEEEeC
Confidence 3467788889999999999999998764
No 11
>PF13701 DDE_Tnp_1_4: Transposase DDE domain group 1
Probab=62.91 E-value=21 Score=27.77 Aligned_cols=42 Identities=29% Similarity=0.373 Sum_probs=34.7
Q ss_pred EEEEeCC-CCCCCHHHHHHHHHcHHHHHHhCCCCeEEEEEcCC
Q 041692 23 LRILLCQ-TSPSSSSTRSFVERNYKELKTLNPKLPILIRECSG 64 (73)
Q Consensus 23 l~~~yC~-~~~SS~G~R~Fl~~~l~~fk~~NP~v~i~v~~~~g 64 (73)
|...+.+ +..|++|+-+||+.-+..+.+.-|.++|+||--+|
T Consensus 185 l~a~LRpGn~~sa~g~~~fL~~~l~~lr~~~~~~~ILvR~DSg 227 (448)
T PF13701_consen 185 LAAELRPGNVHSAKGAAEFLKRVLRRLRQRWPDTRILVRGDSG 227 (448)
T ss_pred EEEEccCCCCChHHHHHHHHHHHHHHHhhhCccceEEEEecCc
Confidence 3344544 55689999999999999999999999999998765
No 12
>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=62.01 E-value=16 Score=23.52 Aligned_cols=28 Identities=18% Similarity=0.217 Sum_probs=24.0
Q ss_pred HHHHHHHHcHHHHHHhCCCCeEEEEEcC
Q 041692 36 STRSFVERNYKELKTLNPKLPILIRECS 63 (73)
Q Consensus 36 G~R~Fl~~~l~~fk~~NP~v~i~v~~~~ 63 (73)
....|+-..+.+|.+.+|++.|.+....
T Consensus 10 ~~~~~l~~~l~~f~~~~P~v~l~i~~~~ 37 (204)
T cd08429 10 VPKSIAYRLLEPAMDLHEPIRLVCREGK 37 (204)
T ss_pred hhHHHHHHHHHHHHHhCCCcEEEEEeCC
Confidence 4578899999999999999999998753
No 13
>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=61.59 E-value=16 Score=22.47 Aligned_cols=25 Identities=20% Similarity=0.264 Sum_probs=21.7
Q ss_pred HHHHHHHcHHHHHHhCCCCeEEEEE
Q 041692 37 TRSFVERNYKELKTLNPKLPILIRE 61 (73)
Q Consensus 37 ~R~Fl~~~l~~fk~~NP~v~i~v~~ 61 (73)
...|+...+.+|++.+|++.|.+..
T Consensus 12 ~~~~l~~~l~~f~~~~P~v~l~i~~ 36 (197)
T cd08470 12 GERFIAPLVNDFMQRYPKLEVDIEL 36 (197)
T ss_pred HHHHHHHHHHHHHHHCCCeEEEEEe
Confidence 3567889999999999999999875
No 14
>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=60.65 E-value=11 Score=26.79 Aligned_cols=26 Identities=12% Similarity=0.381 Sum_probs=22.7
Q ss_pred HHHHHHHcHHHHHHhCCCCeEEEEEc
Q 041692 37 TRSFVERNYKELKTLNPKLPILIREC 62 (73)
Q Consensus 37 ~R~Fl~~~l~~fk~~NP~v~i~v~~~ 62 (73)
+-.++..-+.+|++.+|++.|.+.+.
T Consensus 46 ~~~~lp~~l~~f~~~~P~i~v~i~~~ 71 (287)
T TIGR02136 46 VAPLAEAAAEEFQKIHPGVSVTVQGA 71 (287)
T ss_pred HHHHHHHHHHHHHhhCCCceEEEccC
Confidence 44688999999999999999999875
No 15
>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=60.63 E-value=17 Score=22.12 Aligned_cols=26 Identities=15% Similarity=0.253 Sum_probs=22.5
Q ss_pred HHHHHHHcHHHHHHhCCCCeEEEEEc
Q 041692 37 TRSFVERNYKELKTLNPKLPILIREC 62 (73)
Q Consensus 37 ~R~Fl~~~l~~fk~~NP~v~i~v~~~ 62 (73)
...++...+.+|.+++|++.|.+...
T Consensus 11 ~~~~l~~~l~~~~~~~P~v~i~i~~~ 36 (201)
T cd08435 11 APVLLPPAIARLLARHPRLTVRVVEG 36 (201)
T ss_pred HHHHHHHHHHHHHHHCCCeEEEEEeC
Confidence 45778899999999999999999764
No 16
>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=56.69 E-value=19 Score=21.68 Aligned_cols=26 Identities=8% Similarity=0.313 Sum_probs=22.1
Q ss_pred HHHHHHHcHHHHHHhCCCCeEEEEEc
Q 041692 37 TRSFVERNYKELKTLNPKLPILIREC 62 (73)
Q Consensus 37 ~R~Fl~~~l~~fk~~NP~v~i~v~~~ 62 (73)
...++...+..|.+++|++.|.+...
T Consensus 11 ~~~~l~~~l~~~~~~~p~v~i~i~~~ 36 (197)
T cd08440 11 AATLLPPVLAAFRRRHPGIRVRLRDV 36 (197)
T ss_pred hhhHHHHHHHHHHHhCCCcEEEEEeC
Confidence 34677889999999999999999864
No 17
>TIGR01159 DRP1 density-regulated protein DRP1. This protein family shows weak but suggestive similarity to translation initiation factor SUI1 and its prokaryotic homologs.
Probab=55.87 E-value=6.8 Score=27.32 Aligned_cols=25 Identities=16% Similarity=0.232 Sum_probs=21.0
Q ss_pred EEeCCCCCCCHHHHHHHHHcHHHHH
Q 041692 25 ILLCQTSPSSSSTRSFVERNYKELK 49 (73)
Q Consensus 25 ~~yC~~~~SS~G~R~Fl~~~l~~fk 49 (73)
.-||+.|++-.-=+.||..|+|++-
T Consensus 14 ~EyCEf~~~~~kCk~WL~~n~p~l~ 38 (173)
T TIGR01159 14 PEYCEFSGDLKRCKVWLSENAPDLY 38 (173)
T ss_pred hHHhcCCCCHHHHHHHHHHhChHHH
Confidence 4589999999999999988777554
No 18
>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=55.56 E-value=21 Score=21.88 Aligned_cols=26 Identities=15% Similarity=0.317 Sum_probs=22.5
Q ss_pred HHHHHHHcHHHHHHhCCCCeEEEEEc
Q 041692 37 TRSFVERNYKELKTLNPKLPILIREC 62 (73)
Q Consensus 37 ~R~Fl~~~l~~fk~~NP~v~i~v~~~ 62 (73)
...++...+.+|++++|++.|.+...
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 19
>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=55.45 E-value=19 Score=22.02 Aligned_cols=26 Identities=12% Similarity=0.206 Sum_probs=22.3
Q ss_pred HHHHHHHcHHHHHHhCCCCeEEEEEc
Q 041692 37 TRSFVERNYKELKTLNPKLPILIREC 62 (73)
Q Consensus 37 ~R~Fl~~~l~~fk~~NP~v~i~v~~~ 62 (73)
...++...+.+|.+.+|++.|.+.+.
T Consensus 11 ~~~~l~~~l~~~~~~~P~i~l~i~~~ 36 (196)
T cd08450 11 EVQWLPEVLPILREEHPDLDVELSSL 36 (196)
T ss_pred hhhhHHHHHHHHHhhCCCcEEEEEec
Confidence 35777889999999999999999864
No 20
>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=55.34 E-value=19 Score=22.56 Aligned_cols=26 Identities=12% Similarity=0.318 Sum_probs=22.1
Q ss_pred HHHHHHHcHHHHHHhCCCCeEEEEEc
Q 041692 37 TRSFVERNYKELKTLNPKLPILIREC 62 (73)
Q Consensus 37 ~R~Fl~~~l~~fk~~NP~v~i~v~~~ 62 (73)
...++...+..|.+.+|++.|.+...
T Consensus 11 ~~~~l~~~l~~f~~~~P~i~l~i~~~ 36 (200)
T cd08465 11 ARLVLPALMRQLRAEAPGIDLAVSQA 36 (200)
T ss_pred HHHhhhHHHHHHHHHCCCcEEEEecC
Confidence 35778899999999999999998763
No 21
>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=55.17 E-value=24 Score=21.57 Aligned_cols=26 Identities=27% Similarity=0.430 Sum_probs=22.0
Q ss_pred HHHHHHHcHHHHHHhCCCCeEEEEEc
Q 041692 37 TRSFVERNYKELKTLNPKLPILIREC 62 (73)
Q Consensus 37 ~R~Fl~~~l~~fk~~NP~v~i~v~~~ 62 (73)
...++...+.+|.+.+|++.|.+...
T Consensus 11 ~~~~l~~~l~~~~~~~P~i~~~i~~~ 36 (196)
T cd08456 11 SQSFLPRAIKAFLQRHPDVTISIHTR 36 (196)
T ss_pred HHhhHHHHHHHHHHHCCCcEEEEEeC
Confidence 45677889999999999999999764
No 22
>cd08481 PBP2_GcdR_like The C-terminal substrate binding domain of LysR-type transcriptional regulators GcdR-like, contains the type 2 periplasmic binding fold. GcdR is involved in the glutaconate/glutarate-specific activation of the Pg promoter driving expression of a glutaryl-CoA dehydrogenase-encoding gene (gcdH). The GcdH protein is essential for the anaerobic catabolism of many aromatic compounds and some alicyclic and dicarboxylic acids. The structural topology of this substrate-binding domain is most similar to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplas
Probab=54.98 E-value=23 Score=21.48 Aligned_cols=26 Identities=4% Similarity=0.174 Sum_probs=21.8
Q ss_pred HHHHHHcHHHHHHhCCCCeEEEEEcC
Q 041692 38 RSFVERNYKELKTLNPKLPILIRECS 63 (73)
Q Consensus 38 R~Fl~~~l~~fk~~NP~v~i~v~~~~ 63 (73)
..++...+.+|.+.+|++.|.+....
T Consensus 12 ~~~l~~~l~~f~~~~P~i~i~i~~~~ 37 (194)
T cd08481 12 TRWLIPRLPDFLARHPDITVNLVTRD 37 (194)
T ss_pred HHHHHhhhhHHHHHCCCceEEEEecc
Confidence 45777889999999999999998643
No 23
>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=54.79 E-value=21 Score=22.23 Aligned_cols=26 Identities=19% Similarity=0.309 Sum_probs=21.8
Q ss_pred HHHHHHHcHHHHHHhCCCCeEEEEEc
Q 041692 37 TRSFVERNYKELKTLNPKLPILIREC 62 (73)
Q Consensus 37 ~R~Fl~~~l~~fk~~NP~v~i~v~~~ 62 (73)
...++...+.+|++++|++.|.+...
T Consensus 11 ~~~~l~~~l~~~~~~~P~v~i~i~~~ 36 (197)
T cd08452 11 IYEFLPPIVREYRKKFPSVKVELREL 36 (197)
T ss_pred HHhHHHHHHHHHHHHCCCcEEEEEec
Confidence 35677889999999999999998764
No 24
>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=54.53 E-value=24 Score=21.62 Aligned_cols=27 Identities=33% Similarity=0.229 Sum_probs=22.9
Q ss_pred HHHHHHHcHHHHHHhCCCCeEEEEEcC
Q 041692 37 TRSFVERNYKELKTLNPKLPILIRECS 63 (73)
Q Consensus 37 ~R~Fl~~~l~~fk~~NP~v~i~v~~~~ 63 (73)
...++...+.+|.+.+|++.|.+....
T Consensus 11 ~~~~l~~~l~~~~~~~P~i~l~i~~~~ 37 (199)
T cd08416 11 TVNTVPRIIMGLKLRRPELDIELTLGS 37 (199)
T ss_pred HHhhhHHHHHHHHHhCCCeEEEEEEcC
Confidence 456788999999999999999998653
No 25
>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=53.93 E-value=20 Score=22.27 Aligned_cols=27 Identities=26% Similarity=0.385 Sum_probs=23.1
Q ss_pred HHHHHHHcHHHHHHhCCCCeEEEEEcC
Q 041692 37 TRSFVERNYKELKTLNPKLPILIRECS 63 (73)
Q Consensus 37 ~R~Fl~~~l~~fk~~NP~v~i~v~~~~ 63 (73)
...++...+..|.+.+|++.|.+.+..
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 366778999999999999999998764
No 26
>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=53.59 E-value=29 Score=21.29 Aligned_cols=26 Identities=12% Similarity=0.177 Sum_probs=22.1
Q ss_pred HHHHHHHcHHHHHHhCCCCeEEEEEc
Q 041692 37 TRSFVERNYKELKTLNPKLPILIREC 62 (73)
Q Consensus 37 ~R~Fl~~~l~~fk~~NP~v~i~v~~~ 62 (73)
...++...+..|.+++|++.|.+...
T Consensus 11 ~~~~l~~~l~~~~~~~P~v~i~~~~~ 36 (185)
T cd08439 11 ADTILPFLLNRFASVYPRLAIEVVCK 36 (185)
T ss_pred hHHHHHHHHHHHHHHCCCeEEEEEEC
Confidence 45677888999999999999999764
No 27
>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=53.42 E-value=27 Score=21.41 Aligned_cols=26 Identities=12% Similarity=0.231 Sum_probs=21.8
Q ss_pred HHHHHHcHHHHHHhCCCCeEEEEEcC
Q 041692 38 RSFVERNYKELKTLNPKLPILIRECS 63 (73)
Q Consensus 38 R~Fl~~~l~~fk~~NP~v~i~v~~~~ 63 (73)
..++...+.+|.+.+|++.|.+....
T Consensus 12 ~~~l~~~l~~~~~~~P~v~l~i~~~~ 37 (200)
T cd08464 12 SWLAPPLLAALRAEAPGVRLVFRQVD 37 (200)
T ss_pred HHHHHHHHHHHHHHCCCcEEEEecCC
Confidence 35678889999999999999998653
No 28
>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=53.24 E-value=25 Score=21.50 Aligned_cols=26 Identities=4% Similarity=0.083 Sum_probs=21.9
Q ss_pred HHHHHHHcHHHHHHhCCCCeEEEEEc
Q 041692 37 TRSFVERNYKELKTLNPKLPILIREC 62 (73)
Q Consensus 37 ~R~Fl~~~l~~fk~~NP~v~i~v~~~ 62 (73)
...++...+..|.+.+|++.|.+...
T Consensus 11 ~~~~l~~~l~~~~~~~P~i~l~i~~~ 36 (199)
T cd08426 11 AAELLPSLIARFRQRYPGVFFTVDVA 36 (199)
T ss_pred HHHHHHHHHHHHHHhCCCeEEEEEeC
Confidence 35677889999999999999999764
No 29
>COG4837 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=53.11 E-value=21 Score=23.26 Aligned_cols=33 Identities=27% Similarity=0.460 Sum_probs=27.8
Q ss_pred CCCCCCCHHHHHHHHHcHHHHHHhCCCCeEEEEEcC
Q 041692 28 CQTSPSSSSTRSFVERNYKELKTLNPKLPILIRECS 63 (73)
Q Consensus 28 C~~~~SS~G~R~Fl~~~l~~fk~~NP~v~i~v~~~~ 63 (73)
|=..+||+-+-+||+- .+|+..|+.+|.++---
T Consensus 19 CV~aPtsKdt~eWLea---alkRKyp~~~F~~~YiD 51 (106)
T COG4837 19 CVNAPTSKDTYEWLEA---ALKRKYPNQPFKYTYID 51 (106)
T ss_pred hcCCCcchhHHHHHHH---HHhccCCCCCcEEEEEE
Confidence 7788999999999984 57899999999887544
No 30
>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=52.93 E-value=22 Score=21.50 Aligned_cols=27 Identities=11% Similarity=0.145 Sum_probs=22.6
Q ss_pred HHHHHHHHcHHHHHHhCCCCeEEEEEc
Q 041692 36 STRSFVERNYKELKTLNPKLPILIREC 62 (73)
Q Consensus 36 G~R~Fl~~~l~~fk~~NP~v~i~v~~~ 62 (73)
-...++...+..|.+++|++.|.+...
T Consensus 10 ~~~~~l~~~l~~~~~~~P~v~i~i~~~ 36 (194)
T cd08436 10 LAAVDLPELLARFHRRHPGVDIRLRQA 36 (194)
T ss_pred HHHHHHHHHHHHHHHHCCCcEEEEecC
Confidence 345678889999999999999998764
No 31
>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=52.85 E-value=19 Score=21.86 Aligned_cols=25 Identities=8% Similarity=0.151 Sum_probs=21.7
Q ss_pred HHHHHHcHHHHHHhCCCCeEEEEEc
Q 041692 38 RSFVERNYKELKTLNPKLPILIREC 62 (73)
Q Consensus 38 R~Fl~~~l~~fk~~NP~v~i~v~~~ 62 (73)
..++...+.+|.+++|++.|.+...
T Consensus 12 ~~~l~~~l~~~~~~~p~v~i~i~~~ 36 (197)
T cd08438 12 SLLFAPLLAAFRQRYPNIELELVEY 36 (197)
T ss_pred hhhcHHHHHHHHHHCcCeEEEEEEc
Confidence 4677889999999999999999864
No 32
>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=52.80 E-value=26 Score=21.27 Aligned_cols=26 Identities=15% Similarity=0.344 Sum_probs=22.2
Q ss_pred HHHHHHHcHHHHHHhCCCCeEEEEEc
Q 041692 37 TRSFVERNYKELKTLNPKLPILIREC 62 (73)
Q Consensus 37 ~R~Fl~~~l~~fk~~NP~v~i~v~~~ 62 (73)
...++...+.+|.+++|++.|.+...
T Consensus 11 ~~~~l~~~l~~~~~~~p~i~i~i~~~ 36 (197)
T cd08414 11 LYGLLPRLLRRFRARYPDVELELREM 36 (197)
T ss_pred HHHHHHHHHHHHHHHCCCcEEEEecC
Confidence 45678899999999999999998754
No 33
>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=52.33 E-value=31 Score=21.32 Aligned_cols=26 Identities=4% Similarity=0.185 Sum_probs=21.7
Q ss_pred HHHHHHcHHHHHHhCCCCeEEEEEcC
Q 041692 38 RSFVERNYKELKTLNPKLPILIRECS 63 (73)
Q Consensus 38 R~Fl~~~l~~fk~~NP~v~i~v~~~~ 63 (73)
..|+-..+.+|.+++|++.|.+....
T Consensus 12 ~~~l~~~l~~f~~~~P~v~i~~~~~~ 37 (191)
T cd08488 12 VGWLLPRLADFQNRHPFIDLRLSTNN 37 (191)
T ss_pred HHHHHhHHHHHHHHCCCcEEEEEecC
Confidence 35777789999999999999998654
No 34
>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=52.33 E-value=29 Score=21.19 Aligned_cols=25 Identities=8% Similarity=0.046 Sum_probs=21.4
Q ss_pred HHHHHHHcHHHHHHhCCCCeEEEEE
Q 041692 37 TRSFVERNYKELKTLNPKLPILIRE 61 (73)
Q Consensus 37 ~R~Fl~~~l~~fk~~NP~v~i~v~~ 61 (73)
...++...+..|++++|++.|.+..
T Consensus 12 ~~~~l~~~l~~~~~~~P~i~l~i~~ 36 (197)
T cd08477 12 GSHVLTPALAEYLARYPDVRVDLVL 36 (197)
T ss_pred HHHHHHHHHHHHHHHCCCcEEEEEe
Confidence 3567788899999999999999975
No 35
>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=52.14 E-value=29 Score=21.01 Aligned_cols=26 Identities=12% Similarity=0.198 Sum_probs=22.2
Q ss_pred HHHHHHHcHHHHHHhCCCCeEEEEEc
Q 041692 37 TRSFVERNYKELKTLNPKLPILIREC 62 (73)
Q Consensus 37 ~R~Fl~~~l~~fk~~NP~v~i~v~~~ 62 (73)
...++...+..|.+++|++.|.+...
T Consensus 11 ~~~~l~~~l~~~~~~~P~i~i~i~~~ 36 (197)
T cd08448 11 LYRGLPRILRAFRAEYPGIEVALHEM 36 (197)
T ss_pred HHHHHHHHHHHHHHHCCCCeEEEEeC
Confidence 45778899999999999999998753
No 36
>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=51.98 E-value=23 Score=22.25 Aligned_cols=25 Identities=8% Similarity=0.062 Sum_probs=20.7
Q ss_pred HHHHHHcHHHHHHhCCCCeEEEEEc
Q 041692 38 RSFVERNYKELKTLNPKLPILIREC 62 (73)
Q Consensus 38 R~Fl~~~l~~fk~~NP~v~i~v~~~ 62 (73)
..++-..+.+|++++|++.|.+.+.
T Consensus 13 ~~~l~~~l~~f~~~~P~v~i~i~~~ 37 (198)
T cd08486 13 YRSLPLLLRAFLTSTPTATVSLTHM 37 (198)
T ss_pred HHHHHHHHHHHHHhCCCeEEEEEEC
Confidence 5667788899999999999988764
No 37
>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=51.81 E-value=23 Score=21.56 Aligned_cols=25 Identities=8% Similarity=0.216 Sum_probs=21.6
Q ss_pred HHHHHHcHHHHHHhCCCCeEEEEEc
Q 041692 38 RSFVERNYKELKTLNPKLPILIREC 62 (73)
Q Consensus 38 R~Fl~~~l~~fk~~NP~v~i~v~~~ 62 (73)
..++...+.+|.+++|++.|.+...
T Consensus 12 ~~~l~~~l~~~~~~~P~i~l~i~~~ 36 (198)
T cd08412 12 PYYLPGLLRRFREAYPGVEVRVVEG 36 (198)
T ss_pred hhhhHHHHHHHHHHCCCcEEEEEEC
Confidence 4677899999999999999998764
No 38
>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=51.37 E-value=28 Score=21.72 Aligned_cols=26 Identities=12% Similarity=0.210 Sum_probs=21.3
Q ss_pred HHHHHHHcHHHHHHhCCCCeEEEEEc
Q 041692 37 TRSFVERNYKELKTLNPKLPILIREC 62 (73)
Q Consensus 37 ~R~Fl~~~l~~fk~~NP~v~i~v~~~ 62 (73)
...++...+.+|.+.+|++.|.+...
T Consensus 11 ~~~~l~~~l~~~~~~~P~v~l~i~~~ 36 (198)
T cd08444 11 ARYALPWVVQAFKEQFPNVHLVLHQG 36 (198)
T ss_pred hhhhhhHHHHHHHHHCCCeEEEEEeC
Confidence 45677888999999999999888764
No 39
>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=51.30 E-value=24 Score=21.90 Aligned_cols=27 Identities=7% Similarity=-0.006 Sum_probs=23.0
Q ss_pred HHHHHHHHcHHHHHHhCCCCeEEEEEc
Q 041692 36 STRSFVERNYKELKTLNPKLPILIREC 62 (73)
Q Consensus 36 G~R~Fl~~~l~~fk~~NP~v~i~v~~~ 62 (73)
-...|+...+..|.+.+|++.|.+...
T Consensus 10 ~~~~~l~~~l~~~~~~~P~v~v~l~~~ 36 (200)
T cd08460 10 FVAAFGPALLAAVAAEAPGVRLRFVPE 36 (200)
T ss_pred HHHHHHHHHHHHHHHHCCCCEEEEecC
Confidence 356788899999999999999998753
No 40
>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=51.28 E-value=23 Score=25.62 Aligned_cols=42 Identities=29% Similarity=0.521 Sum_probs=30.7
Q ss_pred ccccccceEEEEeCCCCCCCHHHHHHHHHcHHHHHHhCCCCeEEEEEcC
Q 041692 15 QLSRSMKELRILLCQTSPSSSSTRSFVERNYKELKTLNPKLPILIRECS 63 (73)
Q Consensus 15 ~~~~qLk~l~~~yC~~~~SS~G~R~Fl~~~l~~fk~~NP~v~i~v~~~~ 63 (73)
.++...++|=+. +|++++|++||+.. +++.+|.+.|.+-+..
T Consensus 9 ~lP~~p~~I~vI---Ts~~gAa~~D~~~~----~~~r~~~~~~~~~p~~ 50 (319)
T PF02601_consen 9 PLPKFPKRIAVI---TSPTGAAIQDFLRT----LKRRNPIVEIILYPAS 50 (319)
T ss_pred CCCCCCCEEEEE---eCCchHHHHHHHHH----HHHhCCCcEEEEEecc
Confidence 345556666666 45668999999864 4559999999987764
No 41
>COG1653 UgpB ABC-type sugar transport system, periplasmic component [Carbohydrate transport and metabolism]
Probab=51.23 E-value=50 Score=23.32 Aligned_cols=39 Identities=15% Similarity=0.198 Sum_probs=29.5
Q ss_pred eEEEEeCCCCCCCHHHHHHHHHcHHHHHHhCCCCeEEEEEcC
Q 041692 22 ELRILLCQTSPSSSSTRSFVERNYKELKTLNPKLPILIRECS 63 (73)
Q Consensus 22 ~l~~~yC~~~~SS~G~R~Fl~~~l~~fk~~NP~v~i~v~~~~ 63 (73)
+|++..--.++.. .++++....+|.++||+|.|.+...+
T Consensus 32 ~i~~~~~~~~~~~---~~~~~~~i~~f~~~~p~ikv~~~~~~ 70 (433)
T COG1653 32 TITFWHSWTGGEE---ADALEELIKEFEKENPGIKVKVVNVP 70 (433)
T ss_pred eEEEEEEecCCCc---hHHHHHHHHHHHHhCCCeEEEEEecC
Confidence 5555554444333 78889999999999999999888765
No 42
>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=51.08 E-value=29 Score=21.28 Aligned_cols=25 Identities=20% Similarity=0.275 Sum_probs=21.8
Q ss_pred HHHHHHcHHHHHHhCCCCeEEEEEc
Q 041692 38 RSFVERNYKELKTLNPKLPILIREC 62 (73)
Q Consensus 38 R~Fl~~~l~~fk~~NP~v~i~v~~~ 62 (73)
..++..-+.+|.+++|++.|.+...
T Consensus 12 ~~~l~~~l~~f~~~~P~v~l~~~~~ 36 (200)
T cd08466 12 LLLLPRLLARLKQLAPNISLRESPS 36 (200)
T ss_pred HHHHHHHHHHHHHHCCCCEEEEecC
Confidence 4677889999999999999999864
No 43
>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=50.87 E-value=26 Score=21.57 Aligned_cols=25 Identities=16% Similarity=0.078 Sum_probs=21.5
Q ss_pred HHHHHHcHHHHHHhCCCCeEEEEEc
Q 041692 38 RSFVERNYKELKTLNPKLPILIREC 62 (73)
Q Consensus 38 R~Fl~~~l~~fk~~NP~v~i~v~~~ 62 (73)
-.|+...+.+|.+.+|++.|.+...
T Consensus 12 ~~~l~~~l~~~~~~~P~v~i~~~~~ 36 (198)
T cd08437 12 NYYFPKLAKDLIKTGLMIQIDTYEG 36 (198)
T ss_pred HHHhHHHHHHHHHhCCceEEEEEEc
Confidence 4577889999999999999999764
No 44
>PRK13996 potassium-transporting ATPase subunit C; Provisional
Probab=50.27 E-value=18 Score=25.81 Aligned_cols=43 Identities=21% Similarity=0.528 Sum_probs=33.8
Q ss_pred CCCCCCCHHHHHHHHHcHHHHHHhCCC-----CeE--EEEEcCCCCCEEE
Q 041692 28 CQTSPSSSSTRSFVERNYKELKTLNPK-----LPI--LIRECSGIEPQLW 70 (73)
Q Consensus 28 C~~~~SS~G~R~Fl~~~l~~fk~~NP~-----v~i--~v~~~~g~~P~l~ 70 (73)
++.++++.-+.+-++.....|.+.||. ||+ .+.-.+|-+|+|.
T Consensus 91 SNlgpsnp~L~~~v~~r~~~~~~~~~~v~~~~vP~DlvTaSgSGLDPhIS 140 (197)
T PRK13996 91 SNLSPASKEYEALVQERVEKIRANHPEQDEKPIPVDLVTCSGSGLDPHIS 140 (197)
T ss_pred cCCCCCCHHHHHHHHHHHHHHHHhCCCCCCCCCCHHHHhccccCCCCCCC
Confidence 567889999999999999999999995 443 3445567788764
No 45
>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=50.26 E-value=27 Score=21.40 Aligned_cols=25 Identities=20% Similarity=0.021 Sum_probs=21.5
Q ss_pred HHHHHHcHHHHHHhCCCCeEEEEEc
Q 041692 38 RSFVERNYKELKTLNPKLPILIREC 62 (73)
Q Consensus 38 R~Fl~~~l~~fk~~NP~v~i~v~~~ 62 (73)
..++...+..|.+.+|++.|.+.+.
T Consensus 12 ~~~l~~~l~~~~~~~P~v~i~i~~~ 36 (195)
T cd08431 12 LQPLYPLIAEFYQLNKATRIRLSEE 36 (195)
T ss_pred hHHHHHHHHHHHHHCCCCceEEEEe
Confidence 4567888999999999999999764
No 46
>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=50.01 E-value=24 Score=21.25 Aligned_cols=25 Identities=12% Similarity=0.239 Sum_probs=21.5
Q ss_pred HHHHHHcHHHHHHhCCCCeEEEEEc
Q 041692 38 RSFVERNYKELKTLNPKLPILIREC 62 (73)
Q Consensus 38 R~Fl~~~l~~fk~~NP~v~i~v~~~ 62 (73)
..++...+..|.+++|++.|.+...
T Consensus 12 ~~~l~~~l~~~~~~~P~i~i~i~~~ 36 (195)
T cd08434 12 TSLVPDLIRAFRKEYPNVTFELHQG 36 (195)
T ss_pred hhhhHHHHHHHHHhCCCeEEEEecC
Confidence 4677889999999999999998864
No 47
>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=49.91 E-value=29 Score=21.09 Aligned_cols=25 Identities=20% Similarity=0.414 Sum_probs=21.5
Q ss_pred HHHHHHcHHHHHHhCCCCeEEEEEc
Q 041692 38 RSFVERNYKELKTLNPKLPILIREC 62 (73)
Q Consensus 38 R~Fl~~~l~~fk~~NP~v~i~v~~~ 62 (73)
-.|+...+..|.+.+|++.|.+...
T Consensus 12 ~~~l~~~l~~~~~~~P~i~i~~~~~ 36 (200)
T cd08423 12 AALLPPALAALRARHPGLEVRLREA 36 (200)
T ss_pred HHhhhHHHHHHHHhCCCCeEEEEeC
Confidence 4567889999999999999999764
No 48
>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=49.80 E-value=32 Score=21.08 Aligned_cols=27 Identities=11% Similarity=0.212 Sum_probs=22.5
Q ss_pred HHHHHHHHcHHHHHHhCCCCeEEEEEc
Q 041692 36 STRSFVERNYKELKTLNPKLPILIREC 62 (73)
Q Consensus 36 G~R~Fl~~~l~~fk~~NP~v~i~v~~~ 62 (73)
....++-..+.+|.+++|++.|.+...
T Consensus 11 ~~~~~l~~~l~~f~~~~P~i~i~~~~~ 37 (198)
T cd08479 11 FGRRHIAPALSDFAKRYPELEVQLELT 37 (198)
T ss_pred HHHHHHHHHHHHHHHHCCCeEEEEEec
Confidence 345778899999999999999998753
No 49
>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=49.65 E-value=32 Score=20.74 Aligned_cols=27 Identities=7% Similarity=0.164 Sum_probs=22.5
Q ss_pred HHHHHHHcHHHHHHhCCCCeEEEEEcC
Q 041692 37 TRSFVERNYKELKTLNPKLPILIRECS 63 (73)
Q Consensus 37 ~R~Fl~~~l~~fk~~NP~v~i~v~~~~ 63 (73)
...++..-+..|.+.+|++.|.+.+..
T Consensus 11 ~~~~l~~~l~~~~~~~P~~~l~~~~~~ 37 (201)
T cd08420 11 GEYLLPRLLARFRKRYPEVRVSLTIGN 37 (201)
T ss_pred hhhhhHHHHHHHHHHCCCceEEEEeCC
Confidence 456778899999999999999988643
No 50
>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=49.11 E-value=35 Score=21.03 Aligned_cols=26 Identities=4% Similarity=0.160 Sum_probs=21.9
Q ss_pred HHHHHHHcHHHHHHhCCCCeEEEEEc
Q 041692 37 TRSFVERNYKELKTLNPKLPILIREC 62 (73)
Q Consensus 37 ~R~Fl~~~l~~fk~~NP~v~i~v~~~ 62 (73)
...++...+.+|.+++|++.|.+...
T Consensus 11 ~~~~l~~~i~~f~~~~P~v~i~~~~~ 36 (195)
T cd08482 11 LMRWLIPRLPAFQAALPDIDLQLSAS 36 (195)
T ss_pred HHHHHHhhHHHHHHHCCCceEEEEec
Confidence 45778888999999999999998754
No 51
>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=49.08 E-value=29 Score=21.39 Aligned_cols=25 Identities=16% Similarity=0.340 Sum_probs=21.8
Q ss_pred HHHHHHcHHHHHHhCCCCeEEEEEc
Q 041692 38 RSFVERNYKELKTLNPKLPILIREC 62 (73)
Q Consensus 38 R~Fl~~~l~~fk~~NP~v~i~v~~~ 62 (73)
..|+...+..|.+++|++.|.+...
T Consensus 12 ~~~l~~~l~~~~~~~P~i~l~i~~~ 36 (200)
T cd08453 12 YSVLPELVRRFREAYPDVELQLREA 36 (200)
T ss_pred hHHHHHHHHHHHHhCCCceEEEEeC
Confidence 4678899999999999999999764
No 52
>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=49.05 E-value=30 Score=21.17 Aligned_cols=27 Identities=15% Similarity=0.223 Sum_probs=22.9
Q ss_pred HHHHHHHHcHHHHHHhCCCCeEEEEEc
Q 041692 36 STRSFVERNYKELKTLNPKLPILIREC 62 (73)
Q Consensus 36 G~R~Fl~~~l~~fk~~NP~v~i~v~~~ 62 (73)
....++...+.+|.+.+|++.|.+.+.
T Consensus 11 ~~~~~l~~~l~~~~~~~P~v~i~i~~~ 37 (197)
T cd08425 11 FTAYLIGPLIDRFHARYPGIALSLREM 37 (197)
T ss_pred hhhhhhHHHHHHHHHHCCCcEEEEEEC
Confidence 456677899999999999999999764
No 53
>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=48.76 E-value=41 Score=20.57 Aligned_cols=25 Identities=8% Similarity=0.151 Sum_probs=21.3
Q ss_pred HHHHHHHcHHHHHHhCCCCeEEEEE
Q 041692 37 TRSFVERNYKELKTLNPKLPILIRE 61 (73)
Q Consensus 37 ~R~Fl~~~l~~fk~~NP~v~i~v~~ 61 (73)
...++-..+..|.+++|++.|.+..
T Consensus 12 ~~~~l~~~l~~~~~~~P~i~v~~~~ 36 (202)
T cd08472 12 ARLLLIPALPDFLARYPDIELDLGV 36 (202)
T ss_pred HHHHHHHHHHHHHHHCCCcEEEEEE
Confidence 3567788999999999999999864
No 54
>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=48.08 E-value=33 Score=21.33 Aligned_cols=25 Identities=12% Similarity=0.250 Sum_probs=21.7
Q ss_pred HHHHHHcHHHHHHhCCCCeEEEEEc
Q 041692 38 RSFVERNYKELKTLNPKLPILIREC 62 (73)
Q Consensus 38 R~Fl~~~l~~fk~~NP~v~i~v~~~ 62 (73)
..++...+.+|.+.+|++.|.+.+.
T Consensus 13 ~~~l~~~l~~~~~~~P~i~l~i~~~ 37 (203)
T cd08445 13 YGLLPELIRRFRQAAPDVEIELIEM 37 (203)
T ss_pred HhHHHHHHHHHHHHCCCeEEEEEeC
Confidence 5678899999999999999998764
No 55
>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=47.94 E-value=32 Score=20.98 Aligned_cols=24 Identities=17% Similarity=0.349 Sum_probs=20.8
Q ss_pred HHHHHcHHHHHHhCCCCeEEEEEc
Q 041692 39 SFVERNYKELKTLNPKLPILIREC 62 (73)
Q Consensus 39 ~Fl~~~l~~fk~~NP~v~i~v~~~ 62 (73)
.++...+.+|.+.+|++.|.+...
T Consensus 13 ~~l~~~l~~~~~~~P~i~i~~~~~ 36 (198)
T cd08421 13 EFLPEDLASFLAAHPDVRIDLEER 36 (198)
T ss_pred hhhHHHHHHHHHHCCCceEEEEec
Confidence 467889999999999999998764
No 56
>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=47.87 E-value=34 Score=20.86 Aligned_cols=26 Identities=15% Similarity=0.346 Sum_probs=21.6
Q ss_pred HHHHHHHcHHHHHHhCCCCeEEEEEc
Q 041692 37 TRSFVERNYKELKTLNPKLPILIREC 62 (73)
Q Consensus 37 ~R~Fl~~~l~~fk~~NP~v~i~v~~~ 62 (73)
...++...+.+|.+++|++.+.+...
T Consensus 11 ~~~~l~~~l~~f~~~~P~i~l~i~~~ 36 (189)
T cd08487 11 AVGWLLPRLAEFRQLHPFIELRLRTN 36 (189)
T ss_pred HHHHHhHHHHHHHHHCCCceEEeeec
Confidence 35677778999999999999998763
No 57
>PRK14003 potassium-transporting ATPase subunit C; Provisional
Probab=47.68 E-value=33 Score=24.48 Aligned_cols=43 Identities=14% Similarity=0.279 Sum_probs=34.8
Q ss_pred CCCCCCCHHHHHHHHHcHHHHHHhCCCC--eEEEEEcCCCCCEEE
Q 041692 28 CQTSPSSSSTRSFVERNYKELKTLNPKL--PILIRECSGIEPQLW 70 (73)
Q Consensus 28 C~~~~SS~G~R~Fl~~~l~~fk~~NP~v--~i~v~~~~g~~P~l~ 70 (73)
++-++++.-+.+-++.....|+++||.. ..++.-.+|-+|+|.
T Consensus 93 SNl~psnp~l~~~v~~r~~~~~~~~~~pp~DlVTaSgSGLDPhIS 137 (194)
T PRK14003 93 SNLAPSNPALIERIKEEANRLQDAGIQPTADLVYTSGSGLDPHIS 137 (194)
T ss_pred cCCCCCCHHHHHHHHHHHHHHHHcCCCCChhheecccccCCCCCC
Confidence 4567888889999999999999999654 566677778899874
No 58
>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=47.11 E-value=38 Score=20.49 Aligned_cols=28 Identities=4% Similarity=0.193 Sum_probs=22.5
Q ss_pred HHHHHHHHcHHHHHHhCCCCeEEEEEcC
Q 041692 36 STRSFVERNYKELKTLNPKLPILIRECS 63 (73)
Q Consensus 36 G~R~Fl~~~l~~fk~~NP~v~i~v~~~~ 63 (73)
..-.++...+.+|.+.+|++.|.+.+..
T Consensus 10 ~~~~~l~~~l~~~~~~~P~v~i~~~~~~ 37 (194)
T cd08432 10 FAARWLIPRLARFQARHPDIDLRLSTSD 37 (194)
T ss_pred HHHHHHHHHhHHHHHHCCCeEEEEEecC
Confidence 3455677889999999999999997643
No 59
>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=47.09 E-value=16 Score=22.30 Aligned_cols=26 Identities=15% Similarity=0.317 Sum_probs=21.6
Q ss_pred HHHHHHHcHHHHHHhCCCCeEEEEEc
Q 041692 37 TRSFVERNYKELKTLNPKLPILIREC 62 (73)
Q Consensus 37 ~R~Fl~~~l~~fk~~NP~v~i~v~~~ 62 (73)
...++...+..|.+++|++.|.+...
T Consensus 11 ~~~~l~~~l~~~~~~~P~i~l~i~~~ 36 (196)
T cd08415 11 ALSLLPRAIARFRARHPDVRISLHTL 36 (196)
T ss_pred cccccHHHHHHHHHHCCCcEEEEEec
Confidence 34567788999999999999998865
No 60
>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=47.07 E-value=41 Score=20.52 Aligned_cols=25 Identities=4% Similarity=0.187 Sum_probs=21.3
Q ss_pred HHHHHHcHHHHHHhCCCCeEEEEEc
Q 041692 38 RSFVERNYKELKTLNPKLPILIREC 62 (73)
Q Consensus 38 R~Fl~~~l~~fk~~NP~v~i~v~~~ 62 (73)
..++...+.+|.+++|++.|.+...
T Consensus 15 ~~~l~~~l~~~~~~~P~i~i~~~~~ 39 (202)
T cd08473 15 QELLAPLLPRFMAAYPQVRLQLEAT 39 (202)
T ss_pred HHHHHHHHHHHHHHCCCeEEEEEEc
Confidence 4567889999999999999998764
No 61
>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=46.54 E-value=27 Score=21.15 Aligned_cols=24 Identities=4% Similarity=0.036 Sum_probs=20.0
Q ss_pred HHHHHHcHHHHHHhCCCCeEEEEE
Q 041692 38 RSFVERNYKELKTLNPKLPILIRE 61 (73)
Q Consensus 38 R~Fl~~~l~~fk~~NP~v~i~v~~ 61 (73)
-.++-..+.+|.+.+|++.|.+..
T Consensus 11 ~~~l~~~l~~~~~~~P~v~i~~~~ 34 (197)
T cd08476 11 GGLLLPVLAAFMQRYPEIELDLDF 34 (197)
T ss_pred HHHHHHHHHHHHHHCCCeEEEEEe
Confidence 356667899999999999999854
No 62
>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=46.52 E-value=28 Score=21.00 Aligned_cols=25 Identities=12% Similarity=0.103 Sum_probs=21.3
Q ss_pred HHHHHHcHHHHHHhCCCCeEEEEEc
Q 041692 38 RSFVERNYKELKTLNPKLPILIREC 62 (73)
Q Consensus 38 R~Fl~~~l~~fk~~NP~v~i~v~~~ 62 (73)
..++...+.+|++++|++.|.+...
T Consensus 13 ~~~l~~~l~~~~~~~P~v~i~i~~~ 37 (197)
T cd08422 13 RLHLAPLLAEFLARYPDVRLELVLS 37 (197)
T ss_pred HHHHHHHHHHHHHhCCceEEEEecC
Confidence 4567889999999999999999753
No 63
>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=46.52 E-value=40 Score=20.69 Aligned_cols=26 Identities=8% Similarity=0.075 Sum_probs=21.9
Q ss_pred HHHHHHHcHHHHHHhCCCCeEEEEEc
Q 041692 37 TRSFVERNYKELKTLNPKLPILIREC 62 (73)
Q Consensus 37 ~R~Fl~~~l~~fk~~NP~v~i~v~~~ 62 (73)
...++...+..|++++|++.|.+...
T Consensus 14 ~~~~l~~~l~~~~~~~P~v~i~~~~~ 39 (202)
T cd08474 14 ARLLLAPLLARFLARYPDIRLELVVD 39 (202)
T ss_pred HHHHHHHHHHHHHHHCCCeEEEEEec
Confidence 35677889999999999999999753
No 64
>PRK13997 potassium-transporting ATPase subunit C; Provisional
Probab=46.42 E-value=23 Score=25.25 Aligned_cols=43 Identities=30% Similarity=0.530 Sum_probs=33.7
Q ss_pred CCCCCCCHHHHHHHHHcHHHHHHhCCC-----CeE--EEEEcCCCCCEEE
Q 041692 28 CQTSPSSSSTRSFVERNYKELKTLNPK-----LPI--LIRECSGIEPQLW 70 (73)
Q Consensus 28 C~~~~SS~G~R~Fl~~~l~~fk~~NP~-----v~i--~v~~~~g~~P~l~ 70 (73)
++-++++.-+.+-++.....|++.||. ||. .+.-.+|-+|+|.
T Consensus 87 SNl~psnp~l~~~v~~r~~~~~~~~~~~~~~~vP~DlVTaSgSGLDPhIS 136 (193)
T PRK13997 87 NNYAPSNPDLEKRVEKSIEEWKKQNPSVPVTEVPIDLVTNSGSGLDPDIS 136 (193)
T ss_pred cCCCCCCHHHHHHHHHHHHHHHHhCCCCCCCCCCHHHHhccccCCCCCCC
Confidence 567889999999999999999999985 443 3445567788774
No 65
>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=46.40 E-value=34 Score=20.80 Aligned_cols=25 Identities=12% Similarity=0.181 Sum_probs=21.5
Q ss_pred HHHHHHcHHHHHHhCCCCeEEEEEc
Q 041692 38 RSFVERNYKELKTLNPKLPILIREC 62 (73)
Q Consensus 38 R~Fl~~~l~~fk~~NP~v~i~v~~~ 62 (73)
..++...+..|.+.+|++.|.+...
T Consensus 12 ~~~l~~~l~~~~~~~P~i~i~~~~~ 36 (197)
T cd08449 12 WGGLGPALRRFKRQYPNVTVRFHEL 36 (197)
T ss_pred hhhHHHHHHHHHHHCCCeEEEEEEC
Confidence 4677889999999999999998753
No 66
>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=46.30 E-value=33 Score=20.83 Aligned_cols=25 Identities=20% Similarity=0.344 Sum_probs=21.6
Q ss_pred HHHHHHcHHHHHHhCCCCeEEEEEc
Q 041692 38 RSFVERNYKELKTLNPKLPILIREC 62 (73)
Q Consensus 38 R~Fl~~~l~~fk~~NP~v~i~v~~~ 62 (73)
..|+...+.+|.+.+|++.|.+...
T Consensus 12 ~~~l~~~l~~~~~~~P~i~l~~~~~ 36 (195)
T cd08427 12 TGLLPRALARLRRRHPDLEVHIVPG 36 (195)
T ss_pred HHHhHHHHHHHHHHCCCceEEEEeC
Confidence 4677889999999999999998764
No 67
>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=46.10 E-value=29 Score=21.35 Aligned_cols=25 Identities=4% Similarity=0.135 Sum_probs=21.4
Q ss_pred HHHHHHHcHHHHHHhCCCCeEEEEE
Q 041692 37 TRSFVERNYKELKTLNPKLPILIRE 61 (73)
Q Consensus 37 ~R~Fl~~~l~~fk~~NP~v~i~v~~ 61 (73)
...++-..+..|.+++|++.|.+..
T Consensus 14 ~~~~l~~~l~~f~~~~P~v~i~~~~ 38 (199)
T cd08478 14 VLHLLAPLIAKFRERYPDIELELVS 38 (199)
T ss_pred HHHHHHHHHHHHHHHCCCeEEEEEe
Confidence 4567889999999999999999863
No 68
>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=46.04 E-value=47 Score=20.36 Aligned_cols=24 Identities=4% Similarity=0.152 Sum_probs=20.3
Q ss_pred HHHHHcHHHHHHhCCCCeEEEEEc
Q 041692 39 SFVERNYKELKTLNPKLPILIREC 62 (73)
Q Consensus 39 ~Fl~~~l~~fk~~NP~v~i~v~~~ 62 (73)
.++...+.+|.+++|++.|.+...
T Consensus 13 ~~~~~~l~~~~~~~P~i~i~i~~~ 36 (198)
T cd08441 13 DWLMPVLDQFRERWPDVELDLSSG 36 (198)
T ss_pred hhhHHHHHHHHHhCCCeEEEEEeC
Confidence 467788899999999999998764
No 69
>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=45.77 E-value=24 Score=25.03 Aligned_cols=43 Identities=19% Similarity=0.342 Sum_probs=33.4
Q ss_pred CCCCCCCHHHHHHHHHcHHHHHHhCCC----CeE--EEEEcCCCCCEEE
Q 041692 28 CQTSPSSSSTRSFVERNYKELKTLNPK----LPI--LIRECSGIEPQLW 70 (73)
Q Consensus 28 C~~~~SS~G~R~Fl~~~l~~fk~~NP~----v~i--~v~~~~g~~P~l~ 70 (73)
++-++|+.-+.+-|+.....|++.||. ||+ ++.-.+|-+|+|.
T Consensus 84 SNl~psnp~l~~~v~~r~~~~~~~~~~~~~~vP~DlvTaSgSGLDPhIS 132 (187)
T TIGR00681 84 SNLAPSNPDLLSRIAARVEAQRLENLDAAVQVPVDLVTSSGSGLDPHIS 132 (187)
T ss_pred cCCCCCCHHHHHHHHHHHHHHHHhCCCCCCCCCHHHHhcccccCCCCCC
Confidence 567888999999999999999999984 553 3344567788764
No 70
>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=45.42 E-value=37 Score=20.52 Aligned_cols=25 Identities=16% Similarity=0.247 Sum_probs=21.7
Q ss_pred HHHHHHcHHHHHHhCCCCeEEEEEc
Q 041692 38 RSFVERNYKELKTLNPKLPILIREC 62 (73)
Q Consensus 38 R~Fl~~~l~~fk~~NP~v~i~v~~~ 62 (73)
..|+...+..|.+.+|++.|.+...
T Consensus 11 ~~~l~~~l~~~~~~~P~i~l~i~~~ 35 (197)
T cd08419 11 KYFAPRLLGAFCRRHPGVEVSLRVG 35 (197)
T ss_pred HhHhhHHHHHHHHHCCCceEEEEEC
Confidence 4677889999999999999998764
No 71
>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=45.12 E-value=32 Score=21.30 Aligned_cols=27 Identities=11% Similarity=0.247 Sum_probs=22.3
Q ss_pred HHHHHHHcHHHHHHhCCCCeEEEEEcC
Q 041692 37 TRSFVERNYKELKTLNPKLPILIRECS 63 (73)
Q Consensus 37 ~R~Fl~~~l~~fk~~NP~v~i~v~~~~ 63 (73)
...++...+.+|++.+|++.|.+....
T Consensus 11 ~~~~l~~~l~~f~~~~P~v~i~~~~~~ 37 (196)
T cd08458 11 ALSFMSGVIQTFIADRPDVSVYLDTVP 37 (196)
T ss_pred hhhhhHHHHHHHHHHCCCcEEEEeccC
Confidence 456788899999999999999887643
No 72
>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=44.67 E-value=34 Score=20.68 Aligned_cols=26 Identities=8% Similarity=0.059 Sum_probs=21.7
Q ss_pred HHHHHHcHHHHHHhCCCCeEEEEEcC
Q 041692 38 RSFVERNYKELKTLNPKLPILIRECS 63 (73)
Q Consensus 38 R~Fl~~~l~~fk~~NP~v~i~v~~~~ 63 (73)
..++...+..|.+++|++.|.+....
T Consensus 12 ~~~l~~~l~~~~~~~P~i~l~i~~~~ 37 (193)
T cd08442 12 AVRLPPLLAAYHARYPKVDLSLSTGT 37 (193)
T ss_pred hhhhHHHHHHHHHHCCCceEEEEeCC
Confidence 35677889999999999999998643
No 73
>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=44.30 E-value=46 Score=20.28 Aligned_cols=26 Identities=23% Similarity=0.418 Sum_probs=21.8
Q ss_pred HHHHHHHcHHHHHHhCCCCeEEEEEc
Q 041692 37 TRSFVERNYKELKTLNPKLPILIREC 62 (73)
Q Consensus 37 ~R~Fl~~~l~~fk~~NP~v~i~v~~~ 62 (73)
...++...+..|.+++|++.|.+...
T Consensus 11 ~~~~l~~~l~~~~~~~P~i~v~~~~~ 36 (198)
T cd08447 11 AYSFLPRLLAAARAALPDVDLVLREM 36 (198)
T ss_pred HHHHHHHHHHHHHHHCCCeEEEEEeC
Confidence 35667889999999999999998764
No 74
>PRK00286 xseA exodeoxyribonuclease VII large subunit; Reviewed
Probab=43.70 E-value=36 Score=25.89 Aligned_cols=37 Identities=22% Similarity=0.394 Sum_probs=27.1
Q ss_pred cceEEEEeCCCCCCCHHHHHHHHHcHHHHHHhCCCCeEEEEEcC
Q 041692 20 MKELRILLCQTSPSSSSTRSFVERNYKELKTLNPKLPILIRECS 63 (73)
Q Consensus 20 Lk~l~~~yC~~~~SS~G~R~Fl~~~l~~fk~~NP~v~i~v~~~~ 63 (73)
-++|=+. ||++++|++||+.. +.+.+|.+.|++-+..
T Consensus 135 p~~I~vi---Ts~~gAa~~D~~~~----~~~r~p~~~~~~~~~~ 171 (438)
T PRK00286 135 PKRIGVI---TSPTGAAIRDILTV----LRRRFPLVEVIIYPTL 171 (438)
T ss_pred CCEEEEE---eCCccHHHHHHHHH----HHhcCCCCeEEEecCc
Confidence 4455555 56678999999864 4577899999887764
No 75
>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=43.66 E-value=37 Score=26.22 Aligned_cols=37 Identities=22% Similarity=0.341 Sum_probs=27.1
Q ss_pred cceEEEEeCCCCCCCHHHHHHHHHcHHHHHHhCCCCeEEEEEcC
Q 041692 20 MKELRILLCQTSPSSSSTRSFVERNYKELKTLNPKLPILIRECS 63 (73)
Q Consensus 20 Lk~l~~~yC~~~~SS~G~R~Fl~~~l~~fk~~NP~v~i~v~~~~ 63 (73)
-++|=+. ||++++|++||+. .+++.+|.+.|.+-+..
T Consensus 129 p~~i~vi---ts~~~aa~~D~~~----~~~~r~p~~~~~~~~~~ 165 (432)
T TIGR00237 129 PKRVGVI---TSQTGAALADILH----ILKRRDPSLKVVIYPTL 165 (432)
T ss_pred CCEEEEE---eCCccHHHHHHHH----HHHhhCCCceEEEeccc
Confidence 3444444 6778999999975 46777899999887653
No 76
>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=43.57 E-value=51 Score=20.11 Aligned_cols=25 Identities=12% Similarity=0.101 Sum_probs=21.3
Q ss_pred HHHHHHHcHHHHHHhCCCCeEEEEE
Q 041692 37 TRSFVERNYKELKTLNPKLPILIRE 61 (73)
Q Consensus 37 ~R~Fl~~~l~~fk~~NP~v~i~v~~ 61 (73)
...++...+..|.+.+|++.|.+..
T Consensus 12 ~~~~l~~~l~~~~~~~P~v~i~i~~ 36 (201)
T cd08471 12 GRLHVLPIITDFLDAYPEVSVRLLL 36 (201)
T ss_pred HHHHHHHHHHHHHHHCCCcEEEEEE
Confidence 3467788999999999999999875
No 77
>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=43.56 E-value=42 Score=20.55 Aligned_cols=25 Identities=16% Similarity=0.259 Sum_probs=21.1
Q ss_pred HHHHHHcHHHHHHhCCCCeEEEEEc
Q 041692 38 RSFVERNYKELKTLNPKLPILIREC 62 (73)
Q Consensus 38 R~Fl~~~l~~fk~~NP~v~i~v~~~ 62 (73)
-.++...+.+|.+++|++.|.+...
T Consensus 13 ~~~l~~~i~~~~~~~P~v~l~i~~~ 37 (198)
T cd08446 13 LDTVPRLLRAFLTARPDVTVSLHNM 37 (198)
T ss_pred HHHHHHHHHHHHHHCCCeEEEEeeC
Confidence 4577888999999999999998764
No 78
>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=43.41 E-value=41 Score=20.43 Aligned_cols=25 Identities=4% Similarity=0.179 Sum_probs=21.2
Q ss_pred HHHHHHHcHHHHHHhCCCCeEEEEE
Q 041692 37 TRSFVERNYKELKTLNPKLPILIRE 61 (73)
Q Consensus 37 ~R~Fl~~~l~~fk~~NP~v~i~v~~ 61 (73)
...++...+.+|.+++|++.|.+..
T Consensus 11 ~~~~l~~~l~~~~~~~P~i~l~~~~ 35 (190)
T cd08483 11 ASNWLMPRLGSFWAKHPEIELSLLP 35 (190)
T ss_pred HHhhHHhhHHHHHHHCCCceEEEEe
Confidence 4567778899999999999999874
No 79
>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=43.40 E-value=42 Score=20.56 Aligned_cols=24 Identities=29% Similarity=0.434 Sum_probs=20.3
Q ss_pred HHHHHcHHHHHHhCCCCeEEEEEc
Q 041692 39 SFVERNYKELKTLNPKLPILIREC 62 (73)
Q Consensus 39 ~Fl~~~l~~fk~~NP~v~i~v~~~ 62 (73)
.++..-+.+|.+++|++.|.+...
T Consensus 14 ~~l~~~l~~~~~~~P~i~i~i~~~ 37 (200)
T cd08411 14 YLLPRLLPALRQAYPKLRLYLRED 37 (200)
T ss_pred hhhHHHHHHHHHHCCCcEEEEEeC
Confidence 467888999999999999998753
No 80
>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=43.36 E-value=52 Score=20.22 Aligned_cols=26 Identities=19% Similarity=0.250 Sum_probs=21.8
Q ss_pred HHHHHHcHHHHHHhCCCCeEEEEEcC
Q 041692 38 RSFVERNYKELKTLNPKLPILIRECS 63 (73)
Q Consensus 38 R~Fl~~~l~~fk~~NP~v~i~v~~~~ 63 (73)
..|+...+.+|.+.+|++.|.+....
T Consensus 12 ~~~l~~~l~~~~~~~P~v~v~i~~~~ 37 (201)
T cd08459 12 MYFLPRLLAALREVAPGVRIETVRLP 37 (201)
T ss_pred HHHHHHHHHHHHHHCCCCeEEEEecC
Confidence 45678899999999999999998653
No 81
>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=42.86 E-value=68 Score=18.64 Aligned_cols=38 Identities=18% Similarity=0.250 Sum_probs=23.5
Q ss_pred EEEEeCCCCCCCHHHHHHHHHcHHHHHHhCCCCeEEEEEcCC
Q 041692 23 LRILLCQTSPSSSSTRSFVERNYKELKTLNPKLPILIRECSG 64 (73)
Q Consensus 23 l~~~yC~~~~SS~G~R~Fl~~~l~~fk~~NP~v~i~v~~~~g 64 (73)
|++.||...+ ..+--.++. .++....|+..+.+...++
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 3456667887766665443
No 82
>PRK00315 potassium-transporting ATPase subunit C; Reviewed
Probab=42.36 E-value=28 Score=24.76 Aligned_cols=43 Identities=21% Similarity=0.483 Sum_probs=33.2
Q ss_pred CCCCCCCHHHHHHHHHcHHHHHHhCCC----CeE--EEEEcCCCCCEEE
Q 041692 28 CQTSPSSSSTRSFVERNYKELKTLNPK----LPI--LIRECSGIEPQLW 70 (73)
Q Consensus 28 C~~~~SS~G~R~Fl~~~l~~fk~~NP~----v~i--~v~~~~g~~P~l~ 70 (73)
++-++++.-+.+-++.....|+++||. ||. ++.-.+|-+|+|.
T Consensus 86 SNl~psnp~l~~~v~~r~~~~~~~~~~~~~~vP~DlvTaSgSGLDPhIS 134 (193)
T PRK00315 86 SNLAPSNPALDDAIKARVAALRAANPGASSPVPVDLVTASGSGLDPHIS 134 (193)
T ss_pred cCCCCCCHHHHHHHHHHHHHHHHhCCCCCCCCCHHHHhccccCCCCCCC
Confidence 567788889999999999999999984 553 3344567788764
No 83
>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=42.23 E-value=46 Score=21.03 Aligned_cols=26 Identities=19% Similarity=0.304 Sum_probs=22.1
Q ss_pred HHHHHHcHHHHHHhCCCCeEEEEEcC
Q 041692 38 RSFVERNYKELKTLNPKLPILIRECS 63 (73)
Q Consensus 38 R~Fl~~~l~~fk~~NP~v~i~v~~~~ 63 (73)
..++...+.+|.+++|++.|.+....
T Consensus 12 ~~~l~~~l~~f~~~~P~v~l~i~~~~ 37 (221)
T cd08469 12 AVLLPALVRRLETEAPGIDLRIRPVT 37 (221)
T ss_pred HHHHHHHHHHHHHHCCCcEEEEeeCC
Confidence 46778899999999999999998654
No 84
>PRK13999 potassium-transporting ATPase subunit C; Provisional
Probab=42.19 E-value=30 Score=24.83 Aligned_cols=43 Identities=26% Similarity=0.498 Sum_probs=33.3
Q ss_pred CCCCCCCHHHHHHHHHcHHHHHHhCC--CCeE--EEEEcCCCCCEEE
Q 041692 28 CQTSPSSSSTRSFVERNYKELKTLNP--KLPI--LIRECSGIEPQLW 70 (73)
Q Consensus 28 C~~~~SS~G~R~Fl~~~l~~fk~~NP--~v~i--~v~~~~g~~P~l~ 70 (73)
++-++++.-+.+-|+.....|+++|| .||+ ++.-.+|-+|+|.
T Consensus 97 SNlgpsnp~L~~~v~~r~~~~~~~~~~~~vP~DlvTaSgSGLDPhIS 143 (201)
T PRK13999 97 SNLGPTSKALADRVKEDVDALKAENPGAPVPVDLVTTSGSGLDPDIS 143 (201)
T ss_pred cCCCCCCHHHHHHHHHHHHHHHHhCCCCCCCHHHHhcccccCCCCCC
Confidence 46678888899999999999999998 5653 3445567788774
No 85
>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=41.89 E-value=46 Score=20.75 Aligned_cols=26 Identities=8% Similarity=0.153 Sum_probs=21.9
Q ss_pred HHHHHHHcHHHHHHhCCCCeEEEEEc
Q 041692 37 TRSFVERNYKELKTLNPKLPILIREC 62 (73)
Q Consensus 37 ~R~Fl~~~l~~fk~~NP~v~i~v~~~ 62 (73)
.-.++...+..|.+.+|++.|.+...
T Consensus 12 ~~~~l~~~l~~~~~~~P~i~l~~~~~ 37 (198)
T cd08485 12 VLHTLPLLLRQLLSVAPSATVSLTQM 37 (198)
T ss_pred hhHHHHHHHHHHHHhCCCcEEEEEEC
Confidence 34577888999999999999999764
No 86
>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=41.54 E-value=72 Score=19.68 Aligned_cols=33 Identities=3% Similarity=-0.095 Sum_probs=23.6
Q ss_pred EEEEeCCCCCCCHHHHHHHHHcHHHHHHhCCCCeEEE
Q 041692 23 LRILLCQTSPSSSSTRSFVERNYKELKTLNPKLPILI 59 (73)
Q Consensus 23 l~~~yC~~~~SS~G~R~Fl~~~l~~fk~~NP~v~i~v 59 (73)
|...|.+|++.++-+...| .++++++|++.|+-
T Consensus 26 vV~f~a~~c~~C~~~~p~l----~~la~~~~~i~f~~ 58 (113)
T cd02989 26 VCHFYHPEFFRCKIMDKHL----EILAKKHLETKFIK 58 (113)
T ss_pred EEEEECCCCccHHHHHHHH----HHHHHHcCCCEEEE
Confidence 5677889999999776654 45566778876644
No 87
>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=41.53 E-value=32 Score=21.06 Aligned_cols=25 Identities=12% Similarity=0.150 Sum_probs=20.7
Q ss_pred HHHHHHcHHHHHHhCCCCeEEEEEc
Q 041692 38 RSFVERNYKELKTLNPKLPILIREC 62 (73)
Q Consensus 38 R~Fl~~~l~~fk~~NP~v~i~v~~~ 62 (73)
..++...+..|.+.+|++.|.+...
T Consensus 12 ~~~l~~~l~~~~~~~P~i~i~~~~~ 36 (198)
T cd08433 12 SVLAVPLLRAVRRRYPGIRLRIVEG 36 (198)
T ss_pred hhcchHHHHHHHHHCCCcEEEEEec
Confidence 4566788899999999999999864
No 88
>PF06244 DUF1014: Protein of unknown function (DUF1014); InterPro: IPR010422 This family consists of several hypothetical eukaryotic proteins of unknown function.
Probab=41.48 E-value=22 Score=23.50 Aligned_cols=20 Identities=45% Similarity=0.605 Sum_probs=17.0
Q ss_pred HHHHHHHcHHHHHHhCCCCe
Q 041692 37 TRSFVERNYKELKTLNPKLP 56 (73)
Q Consensus 37 ~R~Fl~~~l~~fk~~NP~v~ 56 (73)
-..|-+..||.|+..||++-
T Consensus 80 y~afeE~~Lp~lK~E~PgLr 99 (122)
T PF06244_consen 80 YKAFEERRLPELKEENPGLR 99 (122)
T ss_pred HHHHHHHHhHHHHhhCCCch
Confidence 35677899999999999874
No 89
>cd08480 PBP2_CrgA_like_10 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold. This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 10. The LTTRs are acting as both auto-repressors and activators of target promoters, controlling operons involved in a wide variety of cellular processes such as amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to name a few. In contrast to the tetrameric form of other LTTRs, CrgA from Neisseria meningitides assembles into an octameric ring, which can bind up to four 63-bp DNA oligonucleotides. Phylogenetic cluster analysis showed that the CrgA-like regulators form a subclass of the LTTRs that function as octamers. The CrgA is an auto-repressor of its own gene
Probab=41.22 E-value=46 Score=20.61 Aligned_cols=25 Identities=8% Similarity=0.070 Sum_probs=21.0
Q ss_pred HHHHHHHcHHHHHHhCCCCeEEEEE
Q 041692 37 TRSFVERNYKELKTLNPKLPILIRE 61 (73)
Q Consensus 37 ~R~Fl~~~l~~fk~~NP~v~i~v~~ 61 (73)
...|+...+.+|.+++|++.|.+..
T Consensus 12 ~~~~l~~~l~~~~~~~P~i~i~i~~ 36 (198)
T cd08480 12 GTHFLLPLLPAFLARYPEILVDLSL 36 (198)
T ss_pred HhHhhHHHHHHHHHHCCCeEEEEEe
Confidence 3467788999999999999998864
No 90
>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=41.02 E-value=44 Score=20.81 Aligned_cols=27 Identities=15% Similarity=0.193 Sum_probs=22.0
Q ss_pred HHHHHHHcHHHHHHhCCCCeEEEEEcC
Q 041692 37 TRSFVERNYKELKTLNPKLPILIRECS 63 (73)
Q Consensus 37 ~R~Fl~~~l~~fk~~NP~v~i~v~~~~ 63 (73)
...++..-+..|.+++|++.|.+....
T Consensus 11 ~~~~l~~~l~~~~~~~P~i~l~~~~~~ 37 (200)
T cd08467 11 EVALLPRLAPRLRERAPGLDLRLCPIG 37 (200)
T ss_pred HHHHHHHHHHHHHhhCCCCEEEEecCC
Confidence 356677888999999999999987653
No 91
>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=40.79 E-value=46 Score=20.24 Aligned_cols=25 Identities=24% Similarity=0.203 Sum_probs=21.2
Q ss_pred HHHHHHHcHHHHHHhCCCCeEEEEE
Q 041692 37 TRSFVERNYKELKTLNPKLPILIRE 61 (73)
Q Consensus 37 ~R~Fl~~~l~~fk~~NP~v~i~v~~ 61 (73)
...++...+..|.+++|++.|.+..
T Consensus 12 ~~~~l~~~l~~~~~~~P~v~i~i~~ 36 (199)
T cd08475 12 GRLCVAPLLLELARRHPELELELSF 36 (199)
T ss_pred HHhhHHHHHHHHHHHCCCeEEEEEe
Confidence 3567788899999999999999864
No 92
>PRK14001 potassium-transporting ATPase subunit C; Provisional
Probab=40.33 E-value=33 Score=24.34 Aligned_cols=43 Identities=16% Similarity=0.323 Sum_probs=33.4
Q ss_pred CCCCCCCHHHHHHHHHcHHHHHHhCCC-----CeE--EEEEcCCCCCEEE
Q 041692 28 CQTSPSSSSTRSFVERNYKELKTLNPK-----LPI--LIRECSGIEPQLW 70 (73)
Q Consensus 28 C~~~~SS~G~R~Fl~~~l~~fk~~NP~-----v~i--~v~~~~g~~P~l~ 70 (73)
++.++++.-+.+-++.....|.++||. ||+ ++.-.+|-+|+|.
T Consensus 85 SNl~psnp~l~~~v~~r~~~~~~~~~~~~~~~vP~DlvTaSgSGLDPhIS 134 (189)
T PRK14001 85 SNLGPTNEKLLAAVAERVTAYRKENNLPADTLVPVDAVTGSGSGLDPAIS 134 (189)
T ss_pred cCCCCCCHHHHHHHHHHHHHHHHhCCCccCCCCCHHHHhcccccCCCCCC
Confidence 567888999999999999999999984 443 3445567788774
No 93
>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=40.05 E-value=51 Score=20.10 Aligned_cols=25 Identities=8% Similarity=0.073 Sum_probs=21.2
Q ss_pred HHHHHHcHHHHHHhCCCCeEEEEEc
Q 041692 38 RSFVERNYKELKTLNPKLPILIREC 62 (73)
Q Consensus 38 R~Fl~~~l~~fk~~NP~v~i~v~~~ 62 (73)
..++...+..|.+.+|++.|.+...
T Consensus 12 ~~~~~~~i~~~~~~~P~i~l~~~~~ 36 (200)
T cd08417 12 ALLLPPLLARLRQEAPGVRLRFVPL 36 (200)
T ss_pred HHHHHHHHHHHHhhCCCeEEEeccC
Confidence 4677888999999999999998754
No 94
>PTZ00062 glutaredoxin; Provisional
Probab=39.93 E-value=83 Score=22.12 Aligned_cols=37 Identities=14% Similarity=0.157 Sum_probs=27.5
Q ss_pred EEEEe-CCCCCCCHHHHHHHHHcHHHHHHhCCCCeEEEEEcC
Q 041692 23 LRILL-CQTSPSSSSTRSFVERNYKELKTLNPKLPILIRECS 63 (73)
Q Consensus 23 l~~~y-C~~~~SS~G~R~Fl~~~l~~fk~~NP~v~i~v~~~~ 63 (73)
+.|.| -+|.+.++-|. .-++++++++|++.|+...+.
T Consensus 20 ~vl~f~a~w~~~C~~m~----~vl~~l~~~~~~~~F~~V~~d 57 (204)
T PTZ00062 20 LVLYVKSSKEPEYEQLM----DVCNALVEDFPSLEFYVVNLA 57 (204)
T ss_pred EEEEEeCCCCcchHHHH----HHHHHHHHHCCCcEEEEEccc
Confidence 44555 88899888554 566788889999998876654
No 95
>COG2871 NqrF Na+-transporting NADH:ubiquinone oxidoreductase, subunit NqrF [Energy production and conversion]
Probab=39.83 E-value=58 Score=25.44 Aligned_cols=37 Identities=14% Similarity=0.335 Sum_probs=28.3
Q ss_pred ceEEEEeCCCCCCCHHHHHHH-HHcHHHHHHhCCCCeEEEEEc
Q 041692 21 KELRILLCQTSPSSSSTRSFV-ERNYKELKTLNPKLPILIREC 62 (73)
Q Consensus 21 k~l~~~yC~~~~SS~G~R~Fl-~~~l~~fk~~NP~v~i~v~~~ 62 (73)
++|+|+|= -+..|+-+ +..|+.++++||++.-++...
T Consensus 305 Rkis~WYG-----ARS~rE~fY~Ed~d~L~ae~pNF~wH~aLS 342 (410)
T COG2871 305 RKISFWYG-----ARSLREMFYQEDFDQLQAENPNFHWHLALS 342 (410)
T ss_pred ceeeeeec-----cchHHHhHHHHHHHHHHhhCCCcEEEEEec
Confidence 57889883 34466655 789999999999998777543
No 96
>KOG0863 consensus 20S proteasome, regulatory subunit alpha type PSMA1/PRE5 [Posttranslational modification, protein turnover, chaperones]
Probab=39.83 E-value=18 Score=26.87 Aligned_cols=24 Identities=33% Similarity=0.648 Sum_probs=20.6
Q ss_pred CCCCHHHHHHHHHcHHHHHHhCCC
Q 041692 31 SPSSSSTRSFVERNYKELKTLNPK 54 (73)
Q Consensus 31 ~~SS~G~R~Fl~~~l~~fk~~NP~ 54 (73)
|.-|++.|.||+.++.+|-+.+|.
T Consensus 162 GsRSQsARTyLEr~~e~f~~~~~e 185 (264)
T KOG0863|consen 162 GSRSQSARTYLERNLEEFEDSSPE 185 (264)
T ss_pred ccchhhHHHHHHHHHHHHhcCCHH
Confidence 447999999999999999887764
No 97
>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=39.78 E-value=29 Score=21.15 Aligned_cols=25 Identities=16% Similarity=0.336 Sum_probs=21.1
Q ss_pred HHHHHHcHHHHHHhCCCCeEEEEEc
Q 041692 38 RSFVERNYKELKTLNPKLPILIREC 62 (73)
Q Consensus 38 R~Fl~~~l~~fk~~NP~v~i~v~~~ 62 (73)
..|+...+..|.+.+|++.|.+...
T Consensus 12 ~~~l~~~l~~~~~~~P~v~l~~~~~ 36 (199)
T cd08430 12 YSFLPPILERFRAQHPQVEIKLHTG 36 (199)
T ss_pred eeeccHHHHHHHHHCCCceEEEEeC
Confidence 3567788999999999999999764
No 98
>PLN02757 sirohydrochlorine ferrochelatase
Probab=39.61 E-value=26 Score=23.52 Aligned_cols=31 Identities=13% Similarity=0.135 Sum_probs=20.2
Q ss_pred HHHHHcHHHHHHhCCCCeEEEEEcCCCCCEE
Q 041692 39 SFVERNYKELKTLNPKLPILIRECSGIEPQL 69 (73)
Q Consensus 39 ~Fl~~~l~~fk~~NP~v~i~v~~~~g~~P~l 69 (73)
+=|...+.++++.+|++.|.+-+--|.||.|
T Consensus 90 ~DIp~~v~~~~~~~p~~~i~~~~pLG~~p~l 120 (154)
T PLN02757 90 EDIPALTAEAAKEHPGVKYLVTAPIGLHELM 120 (154)
T ss_pred hHHHHHHHHHHHHCCCcEEEECCCCCCCHHH
Confidence 3344455567777777777777666777654
No 99
>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=39.31 E-value=24 Score=24.65 Aligned_cols=19 Identities=21% Similarity=0.550 Sum_probs=16.9
Q ss_pred HHHHHHcHHHHHHhCCCCe
Q 041692 38 RSFVERNYKELKTLNPKLP 56 (73)
Q Consensus 38 R~Fl~~~l~~fk~~NP~v~ 56 (73)
-.|+...+..+|..||++.
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 100
>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=39.21 E-value=60 Score=20.11 Aligned_cols=26 Identities=4% Similarity=0.002 Sum_probs=22.0
Q ss_pred HHHHHHHcHHHHHHhCCCCeEEEEEc
Q 041692 37 TRSFVERNYKELKTLNPKLPILIREC 62 (73)
Q Consensus 37 ~R~Fl~~~l~~fk~~NP~v~i~v~~~ 62 (73)
...|+-.-+..|++.+|++.|.+...
T Consensus 11 ~~~~l~~~i~~~~~~~P~i~l~i~~~ 36 (200)
T cd08462 11 ITVLLPPVIERVAREAPGVRFELLPP 36 (200)
T ss_pred HHHHHHHHHHHHHHHCCCCEEEEecC
Confidence 45677889999999999999999764
No 101
>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=38.74 E-value=87 Score=18.71 Aligned_cols=36 Identities=8% Similarity=0.158 Sum_probs=28.8
Q ss_pred EEEEeCCCCCCCHHHHHHHHHcHHHHHHhCCCCeEEEEEc
Q 041692 23 LRILLCQTSPSSSSTRSFVERNYKELKTLNPKLPILIREC 62 (73)
Q Consensus 23 l~~~yC~~~~SS~G~R~Fl~~~l~~fk~~NP~v~i~v~~~ 62 (73)
|.+..-++.+...-+..++ .+++..+|.+.+.+...
T Consensus 16 i~~F~~~~C~~C~~~~~~~----~~l~~~~~~i~~~~vd~ 51 (89)
T cd03026 16 FETYVSLSCHNCPDVVQAL----NLMAVLNPNIEHEMIDG 51 (89)
T ss_pred EEEEECCCCCCcHHHHHHH----HHHHHHCCCceEEEEEh
Confidence 7777778888888887776 67788899999888664
No 102
>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=38.34 E-value=37 Score=20.66 Aligned_cols=23 Identities=13% Similarity=0.342 Sum_probs=20.0
Q ss_pred HHHHcHHHHHHhCCCCeEEEEEc
Q 041692 40 FVERNYKELKTLNPKLPILIREC 62 (73)
Q Consensus 40 Fl~~~l~~fk~~NP~v~i~v~~~ 62 (73)
++...+..|++.+|++.|.+...
T Consensus 15 ~l~~~l~~~~~~~P~i~l~i~~~ 37 (199)
T cd08451 15 LVPGLIRRFREAYPDVELTLEEA 37 (199)
T ss_pred ccHHHHHHHHHHCCCcEEEEecC
Confidence 66788999999999999998764
No 103
>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=38.20 E-value=33 Score=21.26 Aligned_cols=21 Identities=33% Similarity=0.433 Sum_probs=18.0
Q ss_pred HHcHHHHHHhCCCCeEEEEEc
Q 041692 42 ERNYKELKTLNPKLPILIREC 62 (73)
Q Consensus 42 ~~~l~~fk~~NP~v~i~v~~~ 62 (73)
.+.|.++|+++|+..+.++-.
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 467899999999999998864
No 104
>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=37.74 E-value=65 Score=20.00 Aligned_cols=26 Identities=15% Similarity=0.267 Sum_probs=21.1
Q ss_pred HHHHHHcHHHHHHhCCCCeEEEEEcC
Q 041692 38 RSFVERNYKELKTLNPKLPILIRECS 63 (73)
Q Consensus 38 R~Fl~~~l~~fk~~NP~v~i~v~~~~ 63 (73)
..++...+..|.+.+|++.|.+....
T Consensus 12 ~~~l~~~l~~~~~~~P~v~i~~~~~~ 37 (202)
T cd08468 12 LAVMPRLMARLEELAPSVRLNLVHAE 37 (202)
T ss_pred HHHhHHHHHHHHhhCCCCEEEEEECC
Confidence 45678888999999999999888653
No 105
>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=37.68 E-value=87 Score=18.38 Aligned_cols=32 Identities=16% Similarity=0.264 Sum_probs=24.2
Q ss_pred EEEEeCCCCCCCHHHHHHHHHcHHHHHHhCCCC
Q 041692 23 LRILLCQTSPSSSSTRSFVERNYKELKTLNPKL 55 (73)
Q Consensus 23 l~~~yC~~~~SS~G~R~Fl~~~l~~fk~~NP~v 55 (73)
|.+.+ ..-.-+.++++|+++.+..+.+-.|.+
T Consensus 3 i~i~~-~~~~~t~~l~~~i~~k~~kl~k~~~~i 34 (95)
T TIGR00741 3 INITG-KNVEITEALREYVEEKLARLERYFTHI 34 (95)
T ss_pred EEEEE-eccccCHHHHHHHHHHHHHHHHhcCCC
Confidence 34444 455568999999999999898888764
No 106
>PRK14002 potassium-transporting ATPase subunit C; Provisional
Probab=37.65 E-value=34 Score=24.22 Aligned_cols=43 Identities=19% Similarity=0.379 Sum_probs=33.3
Q ss_pred CCCCCCCHHHHHHHHHcHHHHHHhCCC-----Ce--EEEEEcCCCCCEEE
Q 041692 28 CQTSPSSSSTRSFVERNYKELKTLNPK-----LP--ILIRECSGIEPQLW 70 (73)
Q Consensus 28 C~~~~SS~G~R~Fl~~~l~~fk~~NP~-----v~--i~v~~~~g~~P~l~ 70 (73)
++-++++.-+.+-++.....|.++||+ || ..+.-.+|-+|+|.
T Consensus 81 SNl~psnp~L~~~v~~r~~~~~~~~~~~~~~~vP~DlvTaSgSGLDPhIS 130 (186)
T PRK14002 81 SNKGPSNPEYLAEVQARIDTFLVHHPYLSRKDIPAEMVTASGSGLDPNIS 130 (186)
T ss_pred cCCCCCCHHHHHHHHHHHHHHHHhCCCCCCCCCCHHHHhccccCCCCCCC
Confidence 567888999999999999999999986 44 33445567788764
No 107
>PF02638 DUF187: Glycosyl hydrolase like GH101; InterPro: IPR003790 This entry describes proteins of unknown function.
Probab=36.66 E-value=59 Score=23.97 Aligned_cols=30 Identities=23% Similarity=0.455 Sum_probs=25.3
Q ss_pred CHHHHHHHHHcHHHHHHhCCCCeEEEEEcC
Q 041692 34 SSSTRSFVERNYKELKTLNPKLPILIRECS 63 (73)
Q Consensus 34 S~G~R~Fl~~~l~~fk~~NP~v~i~v~~~~ 63 (73)
..-+-+||++-+..+|+.||.+.|-|-+..
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 345778899999999999999999987753
No 108
>PLN02958 diacylglycerol kinase/D-erythro-sphingosine kinase
Probab=36.35 E-value=81 Score=24.78 Aligned_cols=44 Identities=16% Similarity=0.139 Sum_probs=35.5
Q ss_pred ceEEEEeCCCCCCCHHHHHHHHHcHHHHHHhCCCCeEEEEEcCC
Q 041692 21 KELRILLCQTSPSSSSTRSFVERNYKELKTLNPKLPILIRECSG 64 (73)
Q Consensus 21 k~l~~~yC~~~~SS~G~R~Fl~~~l~~fk~~NP~v~i~v~~~~g 64 (73)
+++-|.+.+.+|.-++.+.|...--+.|++.+-.+.+.+.+.+|
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 67889999999999988887777777888888777777766654
No 109
>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=35.79 E-value=10 Score=17.26 Aligned_cols=20 Identities=10% Similarity=0.164 Sum_probs=12.7
Q ss_pred cccceEEEEeCCCCCCCHHHHH
Q 041692 18 RSMKELRILLCQTSPSSSSTRS 39 (73)
Q Consensus 18 ~qLk~l~~~yC~~~~SS~G~R~ 39 (73)
++|+.|.|.+|+-+ ..|+..
T Consensus 2 ~~L~~L~l~~n~i~--~~g~~~ 21 (24)
T PF13516_consen 2 PNLETLDLSNNQIT--DEGASA 21 (24)
T ss_dssp TT-SEEE-TSSBEH--HHHHHH
T ss_pred CCCCEEEccCCcCC--HHHHHH
Confidence 47889999998854 566554
No 110
>PRK10974 glycerol-3-phosphate transporter periplasmic binding protein; Provisional
Probab=35.70 E-value=62 Score=23.98 Aligned_cols=36 Identities=11% Similarity=0.065 Sum_probs=25.6
Q ss_pred eEEEEeCCCCCCCHHHHHHHHHcHHHHHHhCCCCeEEEEE
Q 041692 22 ELRILLCQTSPSSSSTRSFVERNYKELKTLNPKLPILIRE 61 (73)
Q Consensus 22 ~l~~~yC~~~~SS~G~R~Fl~~~l~~fk~~NP~v~i~v~~ 61 (73)
+|+|.. .+++ .-.+.++....+|.++||++.|.+..
T Consensus 27 ~i~~W~-~~~~---~~~~~~~~~~~~F~~~~p~i~V~~~~ 62 (438)
T PRK10974 27 EIPFWH-SMEG---ELGKEVDSLAQRFNASQPDYKIVPVY 62 (438)
T ss_pred eEEEec-CCCC---hhHHHHHHHHHHHHHhCCCeEEEEee
Confidence 566664 2222 23467889999999999999987754
No 111
>smart00367 LRR_CC Leucine-rich repeat - CC (cysteine-containing) subfamily.
Probab=35.43 E-value=28 Score=16.14 Aligned_cols=23 Identities=13% Similarity=0.368 Sum_probs=17.0
Q ss_pred cccceEEEEeCCCCCCCHHHHHHH
Q 041692 18 RSMKELRILLCQTSPSSSSTRSFV 41 (73)
Q Consensus 18 ~qLk~l~~~yC~~~~SS~G~R~Fl 41 (73)
++|++|.|..|..= +..|++.+.
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 57999999999842 567776553
No 112
>cd03076 GST_N_Pi GST_N family, Class Pi 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. 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. Class Pi GST is a homodimeric eukaryotic protein. The human GSTP1 is mainly found in erythrocytes, kidney, placenta and fetal liver. It is involved in stress responses and in cellular proliferation pathways as an inhibitor of JNK (c-Jun N-terminal kinase). Following oxidative stress, monomeric GSTP1 dissociates from JNK and dimerizes, losing its ability to bind JNK and causing an increase in JNK activity, thereby promoting apoptosis. GSTP1 is expressed in various tumors and is the predominant GST in a w
Probab=35.43 E-value=83 Score=17.51 Aligned_cols=37 Identities=14% Similarity=0.188 Sum_probs=23.6
Q ss_pred EEEEeCCCCCCCHHHHHHHH-Hc-------------HHHHHHhCC--CCeEEE
Q 041692 23 LRILLCQTSPSSSSTRSFVE-RN-------------YKELKTLNP--KLPILI 59 (73)
Q Consensus 23 l~~~yC~~~~SS~G~R~Fl~-~~-------------l~~fk~~NP--~v~i~v 59 (73)
++|.|.+.++.|+-+|-++. .. -++|++.|| ++|+++
T Consensus 2 ~~Ly~~~~~~~~~~v~~~L~~~~i~~e~~~v~~~~~~~~~~~~~p~~~vP~l~ 54 (73)
T cd03076 2 YTLTYFPVRGRAEAIRLLLADQGISWEEERVTYEEWQESLKPKMLFGQLPCFK 54 (73)
T ss_pred cEEEEeCCcchHHHHHHHHHHcCCCCEEEEecHHHhhhhhhccCCCCCCCEEE
Confidence 46677777777777777774 12 234667777 366664
No 113
>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=35.39 E-value=44 Score=22.39 Aligned_cols=23 Identities=13% Similarity=0.187 Sum_probs=19.4
Q ss_pred HHHHcH-HHHHHhCCCCeEEEEEc
Q 041692 40 FVERNY-KELKTLNPKLPILIREC 62 (73)
Q Consensus 40 Fl~~~l-~~fk~~NP~v~i~v~~~ 62 (73)
+++..+ .+|.+.||++.|.+...
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 677777 88999999999998765
No 114
>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=35.10 E-value=67 Score=20.27 Aligned_cols=24 Identities=13% Similarity=0.166 Sum_probs=20.9
Q ss_pred HHHHHHcHHHHHHhCCCCeEEEEE
Q 041692 38 RSFVERNYKELKTLNPKLPILIRE 61 (73)
Q Consensus 38 R~Fl~~~l~~fk~~NP~v~i~v~~ 61 (73)
-.++...+..|.+.+|++.|.+.+
T Consensus 12 ~~~~~~~l~~~~~~~P~~~v~~~~ 35 (203)
T cd08463 12 ALFLPELVARFRREAPGARLEIHP 35 (203)
T ss_pred HHHhHHHHHHHHHHCCCCEEEEEe
Confidence 356788999999999999999986
No 115
>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=35.03 E-value=96 Score=18.10 Aligned_cols=27 Identities=11% Similarity=0.313 Sum_probs=20.1
Q ss_pred CCCCCCHHHHHHHHHcHHHHHHhCCCC
Q 041692 29 QTSPSSSSTRSFVERNYKELKTLNPKL 55 (73)
Q Consensus 29 ~~~~SS~G~R~Fl~~~l~~fk~~NP~v 55 (73)
.+-.-+..+++||++.+..|.+-.|.+
T Consensus 7 ~~~~~t~~l~~~i~~kl~kl~~~~~~i 33 (97)
T PF02482_consen 7 RNFELTDALREYIEEKLEKLERFFDDI 33 (97)
T ss_dssp CSS---HHHHHHHHHHHHHHHTTSSC-
T ss_pred EcccCCHHHHHHHHHHHHHHHhhcCCC
Confidence 555678999999999999999988755
No 116
>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=34.66 E-value=1.1e+02 Score=18.78 Aligned_cols=55 Identities=16% Similarity=0.207 Sum_probs=33.4
Q ss_pred hhhccccccceEEE-EeCCCCCCCHHHHHHHHHcHHHHHHhCCCCeEEEEEcCCCCCEEE
Q 041692 12 WRGQLSRSMKELRI-LLCQTSPSSSSTRSFVERNYKELKTLNPKLPILIRECSGIEPQLW 70 (73)
Q Consensus 12 ~rg~~~~qLk~l~~-~yC~~~~SS~G~R~Fl~~~l~~fk~~NP~v~i~v~~~~g~~P~l~ 70 (73)
.++.|..-=+.+.| .|.+.+..|.=+++|++ +++..+|.+.+.+......-|.+.
T Consensus 10 L~~~f~~l~~pV~l~~f~~~~~~~~e~~~ll~----e~a~lSdkI~~~~~~~~~~~P~~~ 65 (94)
T cd02974 10 LKAYLERLENPVELVASLDDSEKSAELLELLE----EIASLSDKITLEEDNDDERKPSFS 65 (94)
T ss_pred HHHHHHhCCCCEEEEEEeCCCcchHHHHHHHH----HHHHhCCceEEEEecCCCCCCEEE
Confidence 45555432233555 34455577777777765 889999998887765433346544
No 117
>KOG1909 consensus Ran GTPase-activating protein [RNA processing and modification; Nuclear structure; Signal transduction mechanisms]
Probab=34.53 E-value=49 Score=25.96 Aligned_cols=44 Identities=25% Similarity=0.385 Sum_probs=32.3
Q ss_pred HhHhh-hccccccceEEEEeCCCCCCCHHHHHHHHHcHHHHHHhCCCCeEEE
Q 041692 9 EMAWR-GQLSRSMKELRILLCQTSPSSSSTRSFVERNYKELKTLNPKLPILI 59 (73)
Q Consensus 9 ~Ms~r-g~~~~qLk~l~~~yC~~~~SS~G~R~Fl~~~l~~fk~~NP~v~i~v 59 (73)
.||-- ..| ++|++|.|.||.-. +.|+-.|+. .|+..||.+++.-
T Consensus 232 ~LakaL~s~-~~L~El~l~dcll~--~~Ga~a~~~----al~~~~p~L~vl~ 276 (382)
T KOG1909|consen 232 ALAKALSSW-PHLRELNLGDCLLE--NEGAIAFVD----ALKESAPSLEVLE 276 (382)
T ss_pred HHHHHhccc-chheeecccccccc--cccHHHHHH----HHhccCCCCceec
Confidence 45433 344 48999999999985 889888874 5667789888653
No 118
>COG0607 PspE Rhodanese-related sulfurtransferase [Inorganic ion transport and metabolism]
Probab=34.51 E-value=61 Score=18.80 Aligned_cols=23 Identities=9% Similarity=0.271 Sum_probs=19.7
Q ss_pred ceEEEEeCCCCCCCHHHHHHHHH
Q 041692 21 KELRILLCQTSPSSSSTRSFVER 43 (73)
Q Consensus 21 k~l~~~yC~~~~SS~G~R~Fl~~ 43 (73)
.+-.+.||..|..|.-+-.+|.+
T Consensus 61 ~~~ivv~C~~G~rS~~aa~~L~~ 83 (110)
T COG0607 61 DDPIVVYCASGVRSAAAAAALKL 83 (110)
T ss_pred CCeEEEEeCCCCChHHHHHHHHH
Confidence 46778999999999999888864
No 119
>PRK13994 potassium-transporting ATPase subunit C; Provisional
Probab=34.39 E-value=40 Score=24.56 Aligned_cols=43 Identities=19% Similarity=0.329 Sum_probs=32.5
Q ss_pred CCCCCCCHHHHHHHHHcHHHHHHhC--CC-------Ce--EEEEEcCCCCCEEE
Q 041692 28 CQTSPSSSSTRSFVERNYKELKTLN--PK-------LP--ILIRECSGIEPQLW 70 (73)
Q Consensus 28 C~~~~SS~G~R~Fl~~~l~~fk~~N--P~-------v~--i~v~~~~g~~P~l~ 70 (73)
++.++++.-+.+.|+.....|++.| |. || ..+.-.+|-+|+|.
T Consensus 111 SNlgpsnp~L~~~v~~r~~~~~~~~~~p~~~~~~~~VP~DlVTaSGSGLDPhIS 164 (222)
T PRK13994 111 TNRSADNEELIQWVKDAKAAVVEDNSVPGYEVKPSDVPADAVTSSGSGLDPDIS 164 (222)
T ss_pred cCCCCCCHHHHHHHHHHHHHHHHhCCCCccccCCCCCCHHHHhcccccCCCCCC
Confidence 5678889999999999999999999 45 33 23344567788764
No 120
>TIGR02200 GlrX_actino Glutaredoxin-like protein. This family of glutaredoxin-like proteins is limited to the Actinobacteria and contains the conserved CxxC motif.
Probab=34.36 E-value=46 Score=18.06 Aligned_cols=21 Identities=0% Similarity=-0.043 Sum_probs=17.9
Q ss_pred EEEEeCCCCCCCHHHHHHHHH
Q 041692 23 LRILLCQTSPSSSSTRSFVER 43 (73)
Q Consensus 23 l~~~yC~~~~SS~G~R~Fl~~ 43 (73)
+++.+-.|++.++-++.||..
T Consensus 2 v~ly~~~~C~~C~~~~~~L~~ 22 (77)
T TIGR02200 2 ITVYGTTWCGYCAQLMRTLDK 22 (77)
T ss_pred EEEEECCCChhHHHHHHHHHH
Confidence 677888899999999999964
No 121
>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=33.84 E-value=71 Score=19.43 Aligned_cols=26 Identities=12% Similarity=0.281 Sum_probs=21.6
Q ss_pred HHHHHHHcHHHHHHhCCCCeEEEEEc
Q 041692 37 TRSFVERNYKELKTLNPKLPILIREC 62 (73)
Q Consensus 37 ~R~Fl~~~l~~fk~~NP~v~i~v~~~ 62 (73)
...++...+.+|.+.+|++.|.+...
T Consensus 11 ~~~~l~~~l~~f~~~~P~i~l~~~~~ 36 (189)
T cd08484 11 AVGWLLPRLAEFRQLHPFIDLRLSTN 36 (189)
T ss_pred HHHHHHhhhHHHHHHCCCceEEEecc
Confidence 35677788999999999999998754
No 122
>PRK13995 potassium-transporting ATPase subunit C; Provisional
Probab=33.21 E-value=48 Score=23.82 Aligned_cols=43 Identities=21% Similarity=0.461 Sum_probs=32.7
Q ss_pred CCCCCCCHHHHHHHHHcHHHHHHhCCC-----CeE--EEEEcCCCCCEEE
Q 041692 28 CQTSPSSSSTRSFVERNYKELKTLNPK-----LPI--LIRECSGIEPQLW 70 (73)
Q Consensus 28 C~~~~SS~G~R~Fl~~~l~~fk~~NP~-----v~i--~v~~~~g~~P~l~ 70 (73)
++-++++.-+.+-|++....|++.||. ||+ ++.-.+|-+|+|.
T Consensus 95 SNlgpsnp~L~~~v~~r~~~~~~~~p~~~~~~vP~DlvTaSgSGLDPhIS 144 (203)
T PRK13995 95 QNYAPTNPELHDRVQKDIDKFLKTNPTVKKEDIPTDLLTASGSGLDPHIS 144 (203)
T ss_pred cCCCCCCHHHHHHHHHHHHHHHHhCCCCCCCCCCHHHHhccccCCCCCCC
Confidence 466788888999999999999999985 443 3344567788764
No 123
>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=32.76 E-value=86 Score=18.04 Aligned_cols=34 Identities=18% Similarity=0.087 Sum_probs=28.7
Q ss_pred CCCCCCHHHHHHHHHcHHHHHHhCCCCeEEEEEc
Q 041692 29 QTSPSSSSTRSFVERNYKELKTLNPKLPILIREC 62 (73)
Q Consensus 29 ~~~~SS~G~R~Fl~~~l~~fk~~NP~v~i~v~~~ 62 (73)
.|..=|.|.|..+.+.+..+-+++|.++|.+-..
T Consensus 27 ~w~~~s~~~r~~~g~~F~~~V~~~~~~~i~~~~k 60 (70)
T PF07205_consen 27 EWNTLSRAERQSLGRAFLYEVKQGPIVRIKIIGK 60 (70)
T ss_pred hhhhCCHHHHHHHHHHHHHHHHhCCCCceEEEee
Confidence 3566799999999999999999999998777543
No 124
>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=32.57 E-value=56 Score=18.97 Aligned_cols=37 Identities=14% Similarity=0.195 Sum_probs=22.9
Q ss_pred eEEEEeCCCCCCCHHHHHHHHHcHHHHHHhCCC--CeEEEEEc
Q 041692 22 ELRILLCQTSPSSSSTRSFVERNYKELKTLNPK--LPILIREC 62 (73)
Q Consensus 22 ~l~~~yC~~~~SS~G~R~Fl~~~l~~fk~~NP~--v~i~v~~~ 62 (73)
+|.+.||...+-..-.-++ -..+....|+ ..|...+.
T Consensus 2 ~V~IeYC~~C~~~~~a~~l----~~~l~~~fp~~~~~v~~~~~ 40 (76)
T PF10262_consen 2 KVTIEYCTSCGYRPRALEL----AQELLQTFPDRIAEVELSPG 40 (76)
T ss_dssp EEEEEEETTTTCHHHHHHH----HHHHHHHSTTTCSEEEEEEE
T ss_pred EEEEEECCCCCCHHHHHHH----HHHHHHHCCCcceEEEEEec
Confidence 6899999988654443222 2345556677 66666553
No 125
>cd08413 PBP2_CysB_like The C-terminal substrate domain of LysR-type transcriptional regulators CysB-like contains type 2 periplasmic binding fold. CysB is a transcriptional activator of genes involved in sulfate and thiosulfate transport, sulfate reduction, and cysteine synthesis. In Escherichia coli, the regulation of transcription in response to sulfur source is attributed to two transcriptional regulators, CysB and Cbl. CysB, in association with Cbl, downregulates the expression of ssuEADCB operon which is required for the utilization of sulfur from aliphatic sulfonates, in the presence of cysteine. Also, Cbl and CysB together directly function as transcriptional activators of tauABCD genes, which are required for utilization of taurine as sulfur source for growth. Like many other members of the LTTR family, CysB is composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-bi
Probab=32.30 E-value=52 Score=20.45 Aligned_cols=25 Identities=12% Similarity=0.228 Sum_probs=20.3
Q ss_pred HHHHHHcHHHHHHhCCCCeEEEEEc
Q 041692 38 RSFVERNYKELKTLNPKLPILIREC 62 (73)
Q Consensus 38 R~Fl~~~l~~fk~~NP~v~i~v~~~ 62 (73)
..++...+..|.+++|++.|.+...
T Consensus 12 ~~~l~~~l~~~~~~~P~i~v~~~~~ 36 (198)
T cd08413 12 RYVLPPVIAAFRKRYPKVKLSLHQG 36 (198)
T ss_pred hhhccHHHHHHHHhCCceEEEEEeC
Confidence 4566788889999999999888764
No 126
>TIGR00269 conserved hypothetical protein TIGR00269.
Probab=32.22 E-value=43 Score=20.82 Aligned_cols=27 Identities=26% Similarity=0.363 Sum_probs=21.5
Q ss_pred CCCCCCCHHHHHHHHHcHHHHHHhCCCCe
Q 041692 28 CQTSPSSSSTRSFVERNYKELKTLNPKLP 56 (73)
Q Consensus 28 C~~~~SS~G~R~Fl~~~l~~fk~~NP~v~ 56 (73)
|+. +....|..+.+.|.++.+.||++.
T Consensus 31 CP~--~~~a~R~~~k~~L~~LE~~~P~~k 57 (104)
T TIGR00269 31 CPY--SSLSVRARIRDFLYDLENKKPGVK 57 (104)
T ss_pred CCC--CCCCchHHHHHHHHHHHHHCcChH
Confidence 554 345679999999999999999874
No 127
>TIGR02036 dsdC D-serine deaminase transcriptional activator. This family, part of the LysR family of transcriptional regulators, activates transcription of the gene for D-serine deaminase, dsdA. Trusted members of this family so far are found adjacent to dsdA and only in Gammaproteobacteria, including E. coli, Vibrio cholerae, and Colwellia psychrerythraea.
Probab=32.16 E-value=86 Score=21.95 Aligned_cols=38 Identities=5% Similarity=0.142 Sum_probs=28.2
Q ss_pred ceEEEEeCCCCCCCHHHHHHHHHcHHHHHHhCCCCeEEEEEcC
Q 041692 21 KELRILLCQTSPSSSSTRSFVERNYKELKTLNPKLPILIRECS 63 (73)
Q Consensus 21 k~l~~~yC~~~~SS~G~R~Fl~~~l~~fk~~NP~v~i~v~~~~ 63 (73)
-.|++-.+.+ -...|+-..+..|.+++|++.|.+....
T Consensus 96 g~l~i~~~~~-----~~~~~l~~~l~~f~~~~P~i~l~l~~~~ 133 (302)
T TIGR02036 96 GTLTLYSRPS-----FAQCWLVPRIGDFTRRYPSISLTVLTGN 133 (302)
T ss_pred CeEEEEechH-----HHHHHHHHHHHHHHHHCCCceEEEEeCC
Confidence 4577764322 2356778899999999999999987654
No 128
>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=32.07 E-value=97 Score=19.80 Aligned_cols=37 Identities=30% Similarity=0.432 Sum_probs=24.8
Q ss_pred CCCCCCCHHHHHHHHHcHHHHHHhCCCCeEEEEEcCCCCC
Q 041692 28 CQTSPSSSSTRSFVERNYKELKTLNPKLPILIRECSGIEP 67 (73)
Q Consensus 28 C~~~~SS~G~R~Fl~~~l~~fk~~NP~v~i~v~~~~g~~P 67 (73)
|=+-+||+-+-+||+- .+++..|+.+|.++-.--.+|
T Consensus 12 CVn~PsSkeTyeWL~a---al~RKyp~~~f~~~YiDi~~p 48 (93)
T PF07315_consen 12 CVNAPSSKETYEWLEA---ALKRKYPDQPFEFTYIDIENP 48 (93)
T ss_dssp GSSS--HHHHHHHHHH---HHHHH-TTS-EEEEEEETTT-
T ss_pred hcCCCCchhHHHHHHH---HHhCcCCCCceEEEEEecCCC
Confidence 6678999999999985 568899999998876543333
No 129
>KOG1454 consensus Predicted hydrolase/acyltransferase (alpha/beta hydrolase superfamily) [General function prediction only]
Probab=32.05 E-value=46 Score=24.63 Aligned_cols=26 Identities=27% Similarity=0.271 Sum_probs=23.1
Q ss_pred cHHHHHHhCCCCeEEEEEcCCCCCEE
Q 041692 44 NYKELKTLNPKLPILIRECSGIEPQL 69 (73)
Q Consensus 44 ~l~~fk~~NP~v~i~v~~~~g~~P~l 69 (73)
.-..+++++|++++++-+.-|.+|++
T Consensus 282 ~~~~~~~~~pn~~~~~I~~~gH~~h~ 307 (326)
T KOG1454|consen 282 LAEELKKKLPNAELVEIPGAGHLPHL 307 (326)
T ss_pred HHHHHHhhCCCceEEEeCCCCccccc
Confidence 56688999999999999998999987
No 130
>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=31.96 E-value=1.3e+02 Score=21.98 Aligned_cols=25 Identities=4% Similarity=0.054 Sum_probs=20.8
Q ss_pred HHHHHHcHHHHHHhCCCCeEEEEEc
Q 041692 38 RSFVERNYKELKTLNPKLPILIREC 62 (73)
Q Consensus 38 R~Fl~~~l~~fk~~NP~v~i~v~~~ 62 (73)
.+.++..+.+|.++||++.|.+...
T Consensus 47 ~~~~~~~~~~F~~~~~~i~V~~~~~ 71 (437)
T TIGR03850 47 TKMWEEVVEAFEKSHEGVKVELTVS 71 (437)
T ss_pred HHHHHHHHHHHHHHCCCceEEEEeC
Confidence 3567888899999999999988754
No 131
>PRK10680 molybdopterin biosynthesis protein MoeA; Provisional
Probab=31.81 E-value=33 Score=26.48 Aligned_cols=38 Identities=13% Similarity=0.268 Sum_probs=26.4
Q ss_pred CCCCCHHHHHHHHHcHHHHHHhCCCCeE-EEEEcCCCCCEEEEe
Q 041692 30 TSPSSSSTRSFVERNYKELKTLNPKLPI-LIRECSGIEPQLWAR 72 (73)
Q Consensus 30 ~~~SS~G~R~Fl~~~l~~fk~~NP~v~i-~v~~~~g~~P~l~a~ 72 (73)
+||+|.|-+||+..-+.++- .+.| -|.-+|| .|...|.
T Consensus 250 tGG~S~G~~D~~~~al~~lG----~~~f~~v~~kPG-kp~~~g~ 288 (411)
T PRK10680 250 SGGVSVGEADYTKTILEELG----EIAFWKLAIKPG-KPFAFGK 288 (411)
T ss_pred cCCCCCCCcchHHHHHHhcC----cEEEEEEEEecC-cceEEEE
Confidence 59999999999998777653 3333 3555677 6665543
No 132
>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=31.50 E-value=57 Score=19.30 Aligned_cols=26 Identities=8% Similarity=0.412 Sum_probs=19.6
Q ss_pred HHHHHHHHHcHHHHHHhCCCCeEEEE
Q 041692 35 SSTRSFVERNYKELKTLNPKLPILIR 60 (73)
Q Consensus 35 ~G~R~Fl~~~l~~fk~~NP~v~i~v~ 60 (73)
.-+++|+++-..-+++.+|..+|.+-
T Consensus 38 ~~~~~~l~~~~~~iR~~dP~~pvt~g 63 (88)
T PF12876_consen 38 EAYAEWLKEAFRWIRAVDPSQPVTSG 63 (88)
T ss_dssp HHHHHHHHHHHHHHHTT-TTS-EE--
T ss_pred HHHHHHHHHHHHHHHHhCCCCcEEee
Confidence 55789999999999999999998764
No 133
>COG1570 XseA Exonuclease VII, large subunit [DNA replication, recombination, and repair]
Probab=31.46 E-value=73 Score=25.38 Aligned_cols=30 Identities=20% Similarity=0.391 Sum_probs=25.0
Q ss_pred CCCCCHHHHHHHHHcHHHHHHhCCCCeEEEEEcC
Q 041692 30 TSPSSSSTRSFVERNYKELKTLNPKLPILIRECS 63 (73)
Q Consensus 30 ~~~SS~G~R~Fl~~~l~~fk~~NP~v~i~v~~~~ 63 (73)
||++++.+||++. .+++..|.++|+|-|..
T Consensus 142 TS~tgAairDIl~----~~~rR~P~~~viv~pt~ 171 (440)
T COG1570 142 TSPTGAALRDILH----TLSRRFPSVEVIVYPTL 171 (440)
T ss_pred cCCchHHHHHHHH----HHHhhCCCCeEEEEecc
Confidence 6788999999886 47889999999997753
No 134
>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=31.32 E-value=59 Score=18.58 Aligned_cols=41 Identities=15% Similarity=0.177 Sum_probs=29.4
Q ss_pred eEEEEeCCCCCCCHHHHHHHHHcHHHHHHhCCCCeEEEEEc
Q 041692 22 ELRILLCQTSPSSSSTRSFVERNYKELKTLNPKLPILIREC 62 (73)
Q Consensus 22 ~l~~~yC~~~~SS~G~R~Fl~~~l~~fk~~NP~v~i~v~~~ 62 (73)
-|...|-+|.+.++.+..-+.+...+++..+|.+.|....+
T Consensus 19 ~lv~f~a~wC~~C~~~~p~~~~~~~~~~~~~~~~~~~~vd~ 59 (102)
T cd03005 19 HFVKFFAPWCGHCKRLAPTWEQLAKKFNNENPSVKIAKVDC 59 (102)
T ss_pred EEEEEECCCCHHHHHhCHHHHHHHHHHhccCCcEEEEEEEC
Confidence 56777888999999887777776666666566676655443
No 135
>PF13552 DUF4127: Protein of unknown function (DUF4127)
Probab=31.12 E-value=43 Score=26.51 Aligned_cols=18 Identities=44% Similarity=0.674 Sum_probs=15.9
Q ss_pred HcHHHHHHhCCCCeEEEE
Q 041692 43 RNYKELKTLNPKLPILIR 60 (73)
Q Consensus 43 ~~l~~fk~~NP~v~i~v~ 60 (73)
+.+.+|++.||+++|++-
T Consensus 92 ~~l~~lk~~~p~~~iyaf 109 (497)
T PF13552_consen 92 ERLRELKARNPNLPIYAF 109 (497)
T ss_pred HHHHHHHHHCCCCeEEEE
Confidence 678999999999999873
No 136
>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=30.97 E-value=43 Score=20.58 Aligned_cols=26 Identities=19% Similarity=0.330 Sum_probs=20.9
Q ss_pred HHHHHHHcHHHHHHhCCCCeEEEEEc
Q 041692 37 TRSFVERNYKELKTLNPKLPILIREC 62 (73)
Q Consensus 37 ~R~Fl~~~l~~fk~~NP~v~i~v~~~ 62 (73)
...++...+.+|.+.+|++.|.+...
T Consensus 11 ~~~~l~~~l~~~~~~~P~i~l~~~~~ 36 (196)
T cd08457 11 ANGFLPRFLAAFLRLRPNLHLSLMGL 36 (196)
T ss_pred hccccHHHHHHHHHHCCCeEEEEEec
Confidence 34566788889999999999988764
No 137
>PRK10696 tRNA 2-thiocytidine biosynthesis protein TtcA; Provisional
Probab=30.28 E-value=55 Score=23.13 Aligned_cols=25 Identities=12% Similarity=0.106 Sum_probs=20.7
Q ss_pred CCHHHHHHHHHcHHHHHHhCCCCeE
Q 041692 33 SSSSTRSFVERNYKELKTLNPKLPI 57 (73)
Q Consensus 33 SS~G~R~Fl~~~l~~fk~~NP~v~i 57 (73)
....+|+.+++-++.+.+.||++..
T Consensus 206 ~~~~~R~~ir~~l~~L~~~~P~~~~ 230 (258)
T PRK10696 206 QENLQRQVVKEMLRDWEKEYPGRIE 230 (258)
T ss_pred CchhHHHHHHHHHHHHHHHCccHHH
Confidence 3455899999999999999998753
No 138
>PRK10597 DNA damage-inducible protein I; Provisional
Probab=29.46 E-value=1.4e+02 Score=18.35 Aligned_cols=43 Identities=12% Similarity=0.223 Sum_probs=35.0
Q ss_pred eEEEEeCCCCCCCHHHHHHHHH-cHHHHHHhCCCCe--EEEEEcCC
Q 041692 22 ELRILLCQTSPSSSSTRSFVER-NYKELKTLNPKLP--ILIRECSG 64 (73)
Q Consensus 22 ~l~~~yC~~~~SS~G~R~Fl~~-~l~~fk~~NP~v~--i~v~~~~g 64 (73)
+|-+.|-...+-+.|+.+-|+. ....+....|++. |.|+....
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 4667788878888999999975 5668999999998 88887654
No 139
>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=29.35 E-value=1.4e+02 Score=21.68 Aligned_cols=35 Identities=20% Similarity=0.138 Sum_probs=26.8
Q ss_pred EEEeCCCCCCCHHHHHHHHHcHHHHHHhCCCCeEEEE
Q 041692 24 RILLCQTSPSSSSTRSFVERNYKELKTLNPKLPILIR 60 (73)
Q Consensus 24 ~~~yC~~~~SS~G~R~Fl~~~l~~fk~~NP~v~i~v~ 60 (73)
+|.+||+.|...... +...+..+++..|+++|.+.
T Consensus 163 ~i~l~DT~G~~~P~~--v~~l~~~l~~~~~~~~i~~H 197 (280)
T cd07945 163 RIMLPDTLGILSPFE--TYTYISDMVKRYPNLHFDFH 197 (280)
T ss_pred EEEecCCCCCCCHHH--HHHHHHHHHhhCCCCeEEEE
Confidence 688999998877765 55666777788888887664
No 140
>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=28.89 E-value=88 Score=21.84 Aligned_cols=27 Identities=7% Similarity=0.172 Sum_probs=22.3
Q ss_pred HHHHHHHcHHHHHHhCCCCeEEEEEcC
Q 041692 37 TRSFVERNYKELKTLNPKLPILIRECS 63 (73)
Q Consensus 37 ~R~Fl~~~l~~fk~~NP~v~i~v~~~~ 63 (73)
...++..-+.++++.||+..|.|++-|
T Consensus 138 ~~~~~~~~l~~~~~~~p~~~lvvK~HP 164 (269)
T PF05159_consen 138 SQADFLDMLESFAKENPDAKLVVKPHP 164 (269)
T ss_pred cHhHHHHHHHHHHHHCCCCEEEEEECc
Confidence 455667788899999999999999855
No 141
>PRK09375 quinolinate synthetase; Provisional
Probab=28.42 E-value=83 Score=23.85 Aligned_cols=34 Identities=18% Similarity=0.172 Sum_probs=27.5
Q ss_pred eCCCCCCCHHHHHHHHHc-------------HHHHHHhCCCCeEEEE
Q 041692 27 LCQTSPSSSSTRSFVERN-------------YKELKTLNPKLPILIR 60 (73)
Q Consensus 27 yC~~~~SS~G~R~Fl~~~-------------l~~fk~~NP~v~i~v~ 60 (73)
.+|.-|||.||-+|+++. ...++++||+-.|+.-
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 578899999999999643 4578888999988853
No 142
>PRK14690 molybdopterin biosynthesis protein MoeA; Provisional
Probab=28.29 E-value=34 Score=26.49 Aligned_cols=39 Identities=15% Similarity=0.098 Sum_probs=27.0
Q ss_pred CCCCCHHHHHHHHHcHHHHHHhCCCCeEEEEEcCCCCCEEEEe
Q 041692 30 TSPSSSSTRSFVERNYKELKTLNPKLPILIRECSGIEPQLWAR 72 (73)
Q Consensus 30 ~~~SS~G~R~Fl~~~l~~fk~~NP~v~i~v~~~~g~~P~l~a~ 72 (73)
+||+|.|-+||+..-+.++- -.+..-|..++| .|.+.|.
T Consensus 266 TGG~S~G~~D~v~~~l~~~G---~~~~~~v~mkPG-kp~~~~~ 304 (419)
T PRK14690 266 SGGASAGDEDHVSALLREAG---AMQSWRIALKPG-RPLALGL 304 (419)
T ss_pred cCCccCCCcchHHHHHHhcC---CEEEcceeecCC-CceEEEE
Confidence 48999999999998877763 122245566677 4766654
No 143
>cd03051 GST_N_GTT2_like GST_N family, Saccharomyces cerevisiae GTT2-like subfamily; composed of predominantly uncharacterized proteins with similarity to the S. cerevisiae GST protein, GTT2. GSTs are cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of glutathione (GSH) with a wide range of endogenous and xenobiotic alkylating agents, including carcinogens, therapeutic drugs, environmental toxins and products of oxidative stress. GSTs also show GSH peroxidase activity and are involved in the synthesis of prostaglandins and leukotrienes. The GST fold contains an N-terminal TRX-fold domain and a C-terminal alpha helical domain, with an active site located in a cleft between the two domains. GTT2, a homodimer, exhibits GST activity with standard substrates. Strains with deleted GTT2 genes are viable but exhibit increased sensitivity to heat shock.
Probab=28.12 E-value=1e+02 Score=16.37 Aligned_cols=19 Identities=21% Similarity=0.443 Sum_probs=12.4
Q ss_pred EEEeCCCCCCCHHHHHHHH
Q 041692 24 RILLCQTSPSSSSTRSFVE 42 (73)
Q Consensus 24 ~~~yC~~~~SS~G~R~Fl~ 42 (73)
+|....+++.|+-+|-++.
T Consensus 2 ~Ly~~~~s~~~~~~~~~L~ 20 (74)
T cd03051 2 KLYDSPTAPNPRRVRIFLA 20 (74)
T ss_pred EEEeCCCCcchHHHHHHHH
Confidence 4555566677777777764
No 144
>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=28.00 E-value=51 Score=18.72 Aligned_cols=18 Identities=17% Similarity=0.202 Sum_probs=14.3
Q ss_pred HHHHcHHHHHHhCCCCeE
Q 041692 40 FVERNYKELKTLNPKLPI 57 (73)
Q Consensus 40 Fl~~~l~~fk~~NP~v~i 57 (73)
|+...-..++++||++.+
T Consensus 12 F~~~~r~~~~~~~p~~~~ 29 (72)
T cd01388 12 FSKRHRRKVLQEYPLKEN 29 (72)
T ss_pred HHHHHHHHHHHHCCCCCH
Confidence 556788899999999753
No 145
>PRK10470 ribosome hibernation promoting factor HPF; Provisional
Probab=28.00 E-value=87 Score=18.72 Aligned_cols=25 Identities=16% Similarity=0.353 Sum_probs=20.9
Q ss_pred CCCCHHHHHHHHHcHHHHHHhCCCC
Q 041692 31 SPSSSSTRSFVERNYKELKTLNPKL 55 (73)
Q Consensus 31 ~~SS~G~R~Fl~~~l~~fk~~NP~v 55 (73)
-.-+.++|+|+++.+..+.+-.+.+
T Consensus 10 i~~t~al~~~v~~kl~kL~r~~~~i 34 (95)
T PRK10470 10 VEITEALREFVTAKFAKLEQYFDRI 34 (95)
T ss_pred eccCHHHHHHHHHHHHHHHHhcCCC
Confidence 3468999999999999998888765
No 146
>PRK09508 leuO leucine transcriptional activator; Reviewed
Probab=27.93 E-value=1.1e+02 Score=21.49 Aligned_cols=26 Identities=8% Similarity=0.395 Sum_probs=22.8
Q ss_pred HHHHHHcHHHHHHhCCCCeEEEEEcC
Q 041692 38 RSFVERNYKELKTLNPKLPILIRECS 63 (73)
Q Consensus 38 R~Fl~~~l~~fk~~NP~v~i~v~~~~ 63 (73)
..|+...+.+|.+++|++.|.+....
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 147
>KOG1806 consensus DEAD box containing helicases [Replication, recombination and repair]
Probab=27.86 E-value=52 Score=29.45 Aligned_cols=50 Identities=20% Similarity=0.268 Sum_probs=38.4
Q ss_pred EEEeCCCCCCCHHHHHHHHHcHHHHHHhCCCCeEEEEE-------------cCCCCCEEEEeC
Q 041692 24 RILLCQTSPSSSSTRSFVERNYKELKTLNPKLPILIRE-------------CSGIEPQLWARY 73 (73)
Q Consensus 24 ~~~yC~~~~SS~G~R~Fl~~~l~~fk~~NP~v~i~v~~-------------~~g~~P~l~a~Y 73 (73)
...=|+.+.+-.|-|+|+.+.+.+|++.-=-+-+++++ ..|..|.-+++|
T Consensus 494 ~kv~ad~~~~~~~eRh~~~nli~~f~k~~~~~Li~i~P~e~~~~~~~~~~~~eg~vp~~~v~y 556 (1320)
T KOG1806|consen 494 QKVTADVTLSRPGERHSILNLIENFKKHDVLFLIYIRPMEPKGLEGNALDPLEGRVPLTYVRY 556 (1320)
T ss_pred hhhhhhccccCcchHHHHHHHHHHhhhcCeeEEEEeccCcccCcccccccccccccCcccchh
Confidence 34458889999999999999999999865555566777 567777766655
No 148
>PRK10837 putative DNA-binding transcriptional regulator; Provisional
Probab=27.83 E-value=98 Score=21.09 Aligned_cols=25 Identities=12% Similarity=0.185 Sum_probs=21.5
Q ss_pred HHHHHHcHHHHHHhCCCCeEEEEEc
Q 041692 38 RSFVERNYKELKTLNPKLPILIREC 62 (73)
Q Consensus 38 R~Fl~~~l~~fk~~NP~v~i~v~~~ 62 (73)
..++...+..|.+++|++.|.+...
T Consensus 101 ~~~~~~~l~~~~~~~P~i~i~v~~~ 125 (290)
T PRK10837 101 NYILPAMIARYRRDYPQLPLELSVG 125 (290)
T ss_pred hhhhHHHHHHHHHHCCCceEEEEEC
Confidence 4667889999999999999999764
No 149
>smart00579 FBD domain in FBox and BRCT domain containing plant proteins.
Probab=27.49 E-value=97 Score=17.32 Aligned_cols=40 Identities=10% Similarity=0.120 Sum_probs=25.2
Q ss_pred ccccceEEEEeCCCCCCCHHHHHHHHHcHHHHHHhCCCCeEEE
Q 041692 17 SRSMKELRILLCQTSPSSSSTRSFVERNYKELKTLNPKLPILI 59 (73)
Q Consensus 17 ~~qLk~l~~~yC~~~~SS~G~R~Fl~~~l~~fk~~NP~v~i~v 59 (73)
.+.|+++++...++... +.. -+.+.+..+.+..+...|.+
T Consensus 32 a~~Lk~~~i~~~~~~~~--~~~-~i~~~L~~~~~aS~~c~i~~ 71 (72)
T smart00579 32 APCLKKLTISVETSDDD--EKL-EILKELLSLPRASSSCQVQF 71 (72)
T ss_pred chhheEEEEEeecCCcc--HHH-HHHHHHHhCcCCCCceEEEe
Confidence 45789999988776532 233 33456777766667666543
No 150
>PRK13337 putative lipid kinase; Reviewed
Probab=27.38 E-value=1.7e+02 Score=20.98 Aligned_cols=43 Identities=16% Similarity=0.144 Sum_probs=29.4
Q ss_pred ceEEEEeCCCCCCCHHHHHHHHHcHHHHHHhCCCCeEEEEEcCC
Q 041692 21 KELRILLCQTSPSSSSTRSFVERNYKELKTLNPKLPILIRECSG 64 (73)
Q Consensus 21 k~l~~~yC~~~~SS~G~R~Fl~~~l~~fk~~NP~v~i~v~~~~g 64 (73)
+++.|.|++.+|+.++.+.+ ..-...+.+.+-.+.++..+..+
T Consensus 2 ~r~~~I~Np~aG~~~~~~~~-~~~~~~l~~~~~~~~~~~t~~~~ 44 (304)
T PRK13337 2 KRARIIYNPTSGRELFKKNL-PDVLQKLEQAGYETSAHATTGPG 44 (304)
T ss_pred ceEEEEECCcccchhHHHHH-HHHHHHHHHcCCEEEEEEecCCC
Confidence 57889999999998877764 33344566777666665555443
No 151
>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=27.24 E-value=1e+02 Score=19.43 Aligned_cols=38 Identities=18% Similarity=0.330 Sum_probs=26.3
Q ss_pred ccceEEEEeCCCCCCCHHHHHHHHHcHHHHHHhCCCCeEEEEE
Q 041692 19 SMKELRILLCQTSPSSSSTRSFVERNYKELKTLNPKLPILIRE 61 (73)
Q Consensus 19 qLk~l~~~yC~~~~SS~G~R~Fl~~~l~~fk~~NP~v~i~v~~ 61 (73)
...++.+.||+++-....+.+|++.....+ +++|.+-.
T Consensus 22 ~~~~~~vv~~dtg~e~p~t~~~~~~~~~~~-----~~~i~~~~ 59 (174)
T PF01507_consen 22 AGRKVPVVFIDTGYEFPETYEFVDELAKRY-----GIPIIVYR 59 (174)
T ss_dssp HHTTCEEEEEE-STB-HHHHHHHHHHHHHT-----TCEEEEEE
T ss_pred hcCCCcEEEEecCccCHHHHHHHHHHHhhh-----hhhhhhcc
Confidence 344457999999999999999998765555 66655543
No 152
>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=26.97 E-value=86 Score=18.26 Aligned_cols=20 Identities=15% Similarity=0.242 Sum_probs=14.4
Q ss_pred EEEEeCCCCCCCHHHHHHHH
Q 041692 23 LRILLCQTSPSSSSTRSFVE 42 (73)
Q Consensus 23 l~~~yC~~~~SS~G~R~Fl~ 42 (73)
-.+.||..|..|.-+-..|.
T Consensus 63 ~ivv~C~~G~rs~~aa~~L~ 82 (100)
T cd01523 63 EVTVICAKEGSSQFVAELLA 82 (100)
T ss_pred eEEEEcCCCCcHHHHHHHHH
Confidence 34569999988876666654
No 153
>COG4097 Predicted ferric reductase [Inorganic ion transport and metabolism]
Probab=26.87 E-value=73 Score=25.41 Aligned_cols=43 Identities=14% Similarity=0.274 Sum_probs=30.0
Q ss_pred ceEEEEeCCCCCCCHHHHHHH-HHcHHHHHHhCCCCeEEEEEcCCCCCEE
Q 041692 21 KELRILLCQTSPSSSSTRSFV-ERNYKELKTLNPKLPILIRECSGIEPQL 69 (73)
Q Consensus 21 k~l~~~yC~~~~SS~G~R~Fl-~~~l~~fk~~NP~v~i~v~~~~g~~P~l 69 (73)
+-+-|.||-.+ --+=+ .+.+.++++.||++++.+-- ++..|++
T Consensus 344 ~~V~L~Y~~~n-----~e~~~y~~eLr~~~qkl~~~~lHiiD-Ss~~g~l 387 (438)
T COG4097 344 PPVHLFYCSRN-----WEEALYAEELRALAQKLPNVVLHIID-SSKDGYL 387 (438)
T ss_pred CceEEEEEecC-----CchhHHHHHHHHHHhcCCCeEEEEec-CCCCCcc
Confidence 34789999654 22333 46788899999999999943 4446665
No 154
>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=26.57 E-value=1.3e+02 Score=20.17 Aligned_cols=34 Identities=9% Similarity=0.050 Sum_probs=23.1
Q ss_pred EEEeCCCCCCCHHHHHHHHHcHHHHHHhCCCCeEEEEE
Q 041692 24 RILLCQTSPSSSSTRSFVERNYKELKTLNPKLPILIRE 61 (73)
Q Consensus 24 ~~~yC~~~~SS~G~R~Fl~~~l~~fk~~NP~v~i~v~~ 61 (73)
...|-+|.+.++- +...|..+++.+|.+.|.-..
T Consensus 88 V~Fya~wc~~Ck~----m~~~l~~LA~~~~~vkF~kVd 121 (175)
T cd02987 88 VHIYEPGIPGCAA----LNSSLLCLAAEYPAVKFCKIR 121 (175)
T ss_pred EEEECCCCchHHH----HHHHHHHHHHHCCCeEEEEEe
Confidence 3345567777774 455677888899998875443
No 155
>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=26.51 E-value=97 Score=18.03 Aligned_cols=25 Identities=16% Similarity=0.349 Sum_probs=20.4
Q ss_pred CCCCHHHHHHHHHcHHHHHHhCCCC
Q 041692 31 SPSSSSTRSFVERNYKELKTLNPKL 55 (73)
Q Consensus 31 ~~SS~G~R~Fl~~~l~~fk~~NP~v 55 (73)
-.-|..+++||++.+..+.+-.+++
T Consensus 9 ~~~t~al~~~i~~k~~kl~r~~~~i 33 (93)
T cd00552 9 IEVTDALREYVEEKLEKLEKYFDRI 33 (93)
T ss_pred ccCCHHHHHHHHHHHHHHHHhcCCC
Confidence 3458999999999888888888754
No 156
>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=26.42 E-value=33 Score=14.76 Aligned_cols=11 Identities=9% Similarity=0.226 Sum_probs=7.6
Q ss_pred ccceEEEEeCC
Q 041692 19 SMKELRILLCQ 29 (73)
Q Consensus 19 qLk~l~~~yC~ 29 (73)
.|+.|.+..|+
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 57888888886
No 157
>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=26.37 E-value=84 Score=16.45 Aligned_cols=21 Identities=5% Similarity=0.328 Sum_probs=17.9
Q ss_pred EEEEeCCCCCCCHHHHHHHHH
Q 041692 23 LRILLCQTSPSSSSTRSFVER 43 (73)
Q Consensus 23 l~~~yC~~~~SS~G~R~Fl~~ 43 (73)
|++.+-+|++.++-++.++..
T Consensus 2 i~lf~~~~C~~C~~~~~~l~~ 22 (74)
T TIGR02196 2 VKVYTTPWCPPCKKAKEYLTS 22 (74)
T ss_pred EEEEcCCCChhHHHHHHHHHH
Confidence 678888899999999998864
No 158
>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=26.26 E-value=59 Score=17.76 Aligned_cols=15 Identities=27% Similarity=0.262 Sum_probs=11.0
Q ss_pred HcHHHHHHhCCCCeE
Q 041692 43 RNYKELKTLNPKLPI 57 (73)
Q Consensus 43 ~~l~~fk~~NP~v~i 57 (73)
..+.+.+..||-+++
T Consensus 33 ~~i~~~~~eNP~Le~ 47 (49)
T PF00309_consen 33 EYIEEEAEENPFLEV 47 (49)
T ss_pred HHHHHHHHhCcCccc
Confidence 445667889998875
No 159
>COG0279 GmhA Phosphoheptose isomerase [Carbohydrate transport and metabolism]
Probab=26.16 E-value=97 Score=21.89 Aligned_cols=36 Identities=19% Similarity=0.449 Sum_probs=32.0
Q ss_pred EEEeCCCCCCCHHHHHHHHHcHHHHHHhCCCCeEEE
Q 041692 24 RILLCQTSPSSSSTRSFVERNYKELKTLNPKLPILI 59 (73)
Q Consensus 24 ~~~yC~~~~SS~G~R~Fl~~~l~~fk~~NP~v~i~v 59 (73)
.+.-|-.|||..-+-.|..+....|.++-|.+|-..
T Consensus 43 Kvl~cGNGgSaadAqHfaael~gRf~~eR~~lpaIa 78 (176)
T COG0279 43 KVLACGNGGSAADAQHFAAELTGRFEKERPSLPAIA 78 (176)
T ss_pred EEEEECCCcchhhHHHHHHHHhhHHHhcCCCCCeeE
Confidence 356899999999999999999999999999998544
No 160
>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=26.12 E-value=66 Score=17.52 Aligned_cols=18 Identities=33% Similarity=0.499 Sum_probs=14.9
Q ss_pred HHHHHcHHHHHHhCCCCe
Q 041692 39 SFVERNYKELKTLNPKLP 56 (73)
Q Consensus 39 ~Fl~~~l~~fk~~NP~v~ 56 (73)
-|.......++..||+..
T Consensus 10 lf~~~~~~~~k~~~p~~~ 27 (69)
T PF00505_consen 10 LFCKEKRAKLKEENPDLS 27 (69)
T ss_dssp HHHHHHHHHHHHHSTTST
T ss_pred HHHHHHHHHHHHHhcccc
Confidence 366788999999999875
No 161
>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=26.07 E-value=50 Score=19.45 Aligned_cols=15 Identities=27% Similarity=0.446 Sum_probs=11.9
Q ss_pred HHcHHHHHHhCCCCe
Q 041692 42 ERNYKELKTLNPKLP 56 (73)
Q Consensus 42 ~~~l~~fk~~NP~v~ 56 (73)
.+-+.+|+..||.++
T Consensus 8 TqFl~~lk~~~Pele 22 (60)
T PF11943_consen 8 TQFLNQLKAKHPELE 22 (60)
T ss_pred HHHHHHHHHhCCchH
Confidence 456778999999875
No 162
>PRK11914 diacylglycerol kinase; Reviewed
Probab=25.93 E-value=1.3e+02 Score=21.43 Aligned_cols=42 Identities=12% Similarity=0.161 Sum_probs=28.5
Q ss_pred ccceEEEEeCCCCCCCHHHHHHHHHcHHHHHHhCCCCeEEEEE
Q 041692 19 SMKELRILLCQTSPSSSSTRSFVERNYKELKTLNPKLPILIRE 61 (73)
Q Consensus 19 qLk~l~~~yC~~~~SS~G~R~Fl~~~l~~fk~~NP~v~i~v~~ 61 (73)
+.+++.|.|++.+|+.++.+.+ .+....|++.+..+.+...+
T Consensus 7 ~~~~~~iI~NP~sG~g~~~~~~-~~~~~~l~~~g~~~~~~~t~ 48 (306)
T PRK11914 7 EIGKVTVLTNPLSGHGAAPHAA-ERAIARLHHRGVDVVEIVGT 48 (306)
T ss_pred CCceEEEEECCCCCCCcHHHHH-HHHHHHHHHcCCeEEEEEeC
Confidence 3478899999999987776654 33345677777666554443
No 163
>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=25.88 E-value=95 Score=23.02 Aligned_cols=25 Identities=8% Similarity=0.109 Sum_probs=20.8
Q ss_pred HHHHHHcHHHHHHhCCCCeEEEEEc
Q 041692 38 RSFVERNYKELKTLNPKLPILIREC 62 (73)
Q Consensus 38 R~Fl~~~l~~fk~~NP~v~i~v~~~ 62 (73)
-++++....+|.++||+|.|.+...
T Consensus 53 ~~~~~~~~~~F~~~~p~i~V~~~~~ 77 (450)
T TIGR03851 53 DDYAKDAEPLYKKKYPGATVKVSPT 77 (450)
T ss_pred HHHHHHHHHHHHHHCCCcEEEEeec
Confidence 3578888899999999999988643
No 164
>TIGR03341 YhgI_GntY IscR-regulated protein YhgI. IscR (TIGR02010) is an iron-sulfur cluster-binding transcriptional regulator (see Genome Property GenProp0138). Members of this protein family include YhgI, whose expression is under control of IscR, and show sequence similarity to IscA, a known protein of iron-sulfur cluster biosynthesis. These two lines of evidence strongly suggest a role as an iron-sulfur cluster biosynthesis protein. An older study designated this protein GntY and suggested a role for it and for the product of an adjacent gene, based on complementation studies, in gluconate utilization.
Probab=25.67 E-value=59 Score=22.59 Aligned_cols=38 Identities=13% Similarity=0.130 Sum_probs=24.4
Q ss_pred CCCCCCCHH-HHHHHHHcHHHHHHhCCC---CeEEEEEcCCCCCE
Q 041692 28 CQTSPSSSS-TRSFVERNYKELKTLNPK---LPILIRECSGIEPQ 68 (73)
Q Consensus 28 C~~~~SS~G-~R~Fl~~~l~~fk~~NP~---v~i~v~~~~g~~P~ 68 (73)
|...++|.- +++.|++.| +..-|. |.-.+.+..|.||+
T Consensus 148 C~gC~~s~~Tl~~~ie~~l---~~~~p~v~~V~~~~~~~~~~~~~ 189 (190)
T TIGR03341 148 CNGCSMVDVTLKDGVEKTL---LERFPELKGVRDATDHTRGEHSY 189 (190)
T ss_pred CCCCcchHHHHHHHHHHHH---HHhCCCcceEEEecCccccCCCC
Confidence 777776654 467777655 444454 44455677899986
No 165
>PHA00684 hypothetical protein
Probab=25.35 E-value=85 Score=21.15 Aligned_cols=28 Identities=14% Similarity=0.237 Sum_probs=21.1
Q ss_pred HHHHHHHHcHHHHHHhCCCCeEEEEEcCC
Q 041692 36 STRSFVERNYKELKTLNPKLPILIRECSG 64 (73)
Q Consensus 36 G~R~Fl~~~l~~fk~~NP~v~i~v~~~~g 64 (73)
-+|.+|+ .+.+|+++||+..|.|.+--+
T Consensus 57 ~I~~~V~-~Fi~ya~~hp~~~F~VT~IGC 84 (128)
T PHA00684 57 DIGAAVN-RFIAYATAHPHLNFQVTRVGC 84 (128)
T ss_pred HHHHHHH-HHHHHHHhCCCcEEEeeeecc
Confidence 3555554 467899999999999987643
No 166
>PRK11716 DNA-binding transcriptional regulator IlvY; Provisional
Probab=25.06 E-value=1.3e+02 Score=19.98 Aligned_cols=25 Identities=12% Similarity=0.158 Sum_probs=21.6
Q ss_pred HHHHHHcHHHHHHhCCCCeEEEEEc
Q 041692 38 RSFVERNYKELKTLNPKLPILIREC 62 (73)
Q Consensus 38 R~Fl~~~l~~fk~~NP~v~i~v~~~ 62 (73)
..++..-+..|.+.+|++.|.+...
T Consensus 79 ~~~~~~~l~~~~~~~p~i~l~i~~~ 103 (269)
T PRK11716 79 YSHLPPILDRFRAEHPLVEIKLTTG 103 (269)
T ss_pred HHHHHHHHHHHHHHCCCeEEEEEEC
Confidence 4677889999999999999998764
No 167
>PRK14491 putative bifunctional molybdopterin-guanine dinucleotide biosynthesis protein MobB/MoeA; Provisional
Probab=25.05 E-value=53 Score=26.61 Aligned_cols=37 Identities=14% Similarity=0.305 Sum_probs=26.1
Q ss_pred CCCCCHHHHHHHHHcHHHHHHhCCCCeEE-EEEcCCCCCEEEE
Q 041692 30 TSPSSSSTRSFVERNYKELKTLNPKLPIL-IRECSGIEPQLWA 71 (73)
Q Consensus 30 ~~~SS~G~R~Fl~~~l~~fk~~NP~v~i~-v~~~~g~~P~l~a 71 (73)
+||+|.|-+||+..-+..+. .+.|. |.-++| .|.+.|
T Consensus 440 tGG~s~G~~D~~~~al~~lG----~i~f~~v~~kPG-kp~~~g 477 (597)
T PRK14491 440 SGGVSVGDADYIKTALAKLG----QIDFWRINMRPG-RPLAFG 477 (597)
T ss_pred cCCccCCCcccHHHHHHhcC----cEEEEEEEeecC-CcEEEE
Confidence 59999999999987766653 44443 566677 566554
No 168
>PRK12681 cysB transcriptional regulator CysB; Reviewed
Probab=24.99 E-value=1.2e+02 Score=21.77 Aligned_cols=37 Identities=14% Similarity=0.169 Sum_probs=28.4
Q ss_pred ceEEEEeCCCCCCCHHHHHHHHHcHHHHHHhCCCCeEEEEEc
Q 041692 21 KELRILLCQTSPSSSSTRSFVERNYKELKTLNPKLPILIREC 62 (73)
Q Consensus 21 k~l~~~yC~~~~SS~G~R~Fl~~~l~~fk~~NP~v~i~v~~~ 62 (73)
..|+|-... .-...++...+..|.+.+|++.|.+...
T Consensus 93 g~l~Ig~~~-----~~~~~~l~~~l~~f~~~~P~i~i~i~~~ 129 (324)
T PRK12681 93 GSLYIATTH-----TQARYALPPVIKGFIERYPRVSLHMHQG 129 (324)
T ss_pred CeEEEEech-----hHHHHhhHHHHHHHHHHCCCcEEEEEeC
Confidence 457775543 2345688899999999999999999765
No 169
>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=24.96 E-value=51 Score=20.78 Aligned_cols=29 Identities=21% Similarity=0.327 Sum_probs=24.3
Q ss_pred CCCHHHHHHHHHcHHHHHHhCCCCeEEEE
Q 041692 32 PSSSSTRSFVERNYKELKTLNPKLPILIR 60 (73)
Q Consensus 32 ~SS~G~R~Fl~~~l~~fk~~NP~v~i~v~ 60 (73)
|.-..+-+|++.+.+.+.+.|+++.|.++
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 45677889999999999999999987653
No 170
>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=24.91 E-value=44 Score=18.70 Aligned_cols=20 Identities=5% Similarity=0.275 Sum_probs=16.5
Q ss_pred HHHHHHHHcHHHHHHhCCCC
Q 041692 36 STRSFVERNYKELKTLNPKL 55 (73)
Q Consensus 36 G~R~Fl~~~l~~fk~~NP~v 55 (73)
-+++||.+-|......+|.+
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 47899999999999999875
No 171
>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=24.81 E-value=2.4e+02 Score=19.75 Aligned_cols=39 Identities=18% Similarity=0.309 Sum_probs=28.2
Q ss_pred EEEEeCCCCCC-CHHHHHHHHHcHHHHHHhCC-CCeEEEEE
Q 041692 23 LRILLCQTSPS-SSSTRSFVERNYKELKTLNP-KLPILIRE 61 (73)
Q Consensus 23 l~~~yC~~~~S-S~G~R~Fl~~~l~~fk~~NP-~v~i~v~~ 61 (73)
|++.+...-+. -...+.-+...|.++++.|| ++.+.+.-
T Consensus 29 i~~~~s~~l~~~~~~~~~~v~~lL~~y~~~s~g~i~v~~iD 69 (271)
T PF09822_consen 29 ITVYFSRELPPELSPLRKQVRDLLDEYARYSPGKIKVEFID 69 (271)
T ss_pred EEEEECCCcchhhhHHHHHHHHHHHHHHHhCCCceEEEEEC
Confidence 56666653333 45667777889999999999 88887653
No 172
>PRK13055 putative lipid kinase; Reviewed
Probab=24.15 E-value=2.5e+02 Score=20.60 Aligned_cols=40 Identities=15% Similarity=0.114 Sum_probs=28.3
Q ss_pred ceEEEEeCCCCCCCHHHHHHHHHcHHHHHHhCCCCeEEEEE
Q 041692 21 KELRILLCQTSPSSSSTRSFVERNYKELKTLNPKLPILIRE 61 (73)
Q Consensus 21 k~l~~~yC~~~~SS~G~R~Fl~~~l~~fk~~NP~v~i~v~~ 61 (73)
+++.|.+++.+|+.++.+. +.+-...|.+.+-.+.++...
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 173
>PRK11151 DNA-binding transcriptional regulator OxyR; Provisional
Probab=24.11 E-value=1.5e+02 Score=20.61 Aligned_cols=26 Identities=19% Similarity=0.238 Sum_probs=22.4
Q ss_pred HHHHHHHcHHHHHHhCCCCeEEEEEc
Q 041692 37 TRSFVERNYKELKTLNPKLPILIREC 62 (73)
Q Consensus 37 ~R~Fl~~~l~~fk~~NP~v~i~v~~~ 62 (73)
...++...+.+|.+.+|++.|.+...
T Consensus 102 ~~~~~~~~l~~~~~~~P~v~i~~~~~ 127 (305)
T PRK11151 102 GPYLLPHIIPMLHQTFPKLEMYLHEA 127 (305)
T ss_pred HHHHHHHHHHHHHHHCCCcEEEEEeC
Confidence 45788889999999999999999865
No 174
>COG0694 Thioredoxin-like proteins and domains [Posttranslational modification, protein turnover, chaperones]
Probab=24.04 E-value=75 Score=20.03 Aligned_cols=24 Identities=38% Similarity=0.515 Sum_probs=17.3
Q ss_pred eCCCCCCCHHH-HHHHHHcHHHHHH
Q 041692 27 LCQTSPSSSST-RSFVERNYKELKT 50 (73)
Q Consensus 27 yC~~~~SS~G~-R~Fl~~~l~~fk~ 50 (73)
-|...+||.+. .+-|++.|.++--
T Consensus 52 aC~gC~sS~~TLk~gIE~~L~~~i~ 76 (93)
T COG0694 52 ACSGCPSSTVTLKNGIERQLKEEIP 76 (93)
T ss_pred cCCCCcccHHHHHHHHHHHHHHhCC
Confidence 49999999887 5557877765543
No 175
>PF13890 Rab3-GTPase_cat: Rab3 GTPase-activating protein catalytic subunit
Probab=23.96 E-value=63 Score=22.37 Aligned_cols=19 Identities=16% Similarity=0.233 Sum_probs=14.5
Q ss_pred HHHHHcHHHHHHhCCCCeE
Q 041692 39 SFVERNYKELKTLNPKLPI 57 (73)
Q Consensus 39 ~Fl~~~l~~fk~~NP~v~i 57 (73)
+-|-+....||.+||...|
T Consensus 71 ~~LlSDM~aFKAANpg~vf 89 (164)
T PF13890_consen 71 ASLLSDMQAFKAANPGCVF 89 (164)
T ss_pred HHHHHHHHHHHhcCCCcch
Confidence 3444577899999999875
No 176
>PF14363 AAA_assoc: Domain associated at C-terminal with AAA
Probab=23.91 E-value=1.3e+02 Score=18.33 Aligned_cols=29 Identities=28% Similarity=0.532 Sum_probs=23.4
Q ss_pred HHHHHHHHcHHH-HH-HhCCCCeEEEEEcCC
Q 041692 36 STRSFVERNYKE-LK-TLNPKLPILIRECSG 64 (73)
Q Consensus 36 G~R~Fl~~~l~~-fk-~~NP~v~i~v~~~~g 64 (73)
.+|+||.+.+.. |. .-+|.+.|.|.+-.|
T Consensus 5 ~lr~~~~~~~~~~~~~~~s~~~ti~I~E~~g 35 (98)
T PF14363_consen 5 ELRSYLRSLLRRLFSSRFSPYLTIVIPEFDG 35 (98)
T ss_pred HHHHHHHHHHHHHHhccCCCcEEEEEEeCCC
Confidence 689999887755 55 688999999988776
No 177
>PRK09791 putative DNA-binding transcriptional regulator; Provisional
Probab=23.72 E-value=1.3e+02 Score=20.85 Aligned_cols=39 Identities=15% Similarity=0.221 Sum_probs=29.1
Q ss_pred ccceEEEEeCCCCCCCHHHHHHHHHcHHHHHHhCCCCeEEEEEc
Q 041692 19 SMKELRILLCQTSPSSSSTRSFVERNYKELKTLNPKLPILIREC 62 (73)
Q Consensus 19 qLk~l~~~yC~~~~SS~G~R~Fl~~~l~~fk~~NP~v~i~v~~~ 62 (73)
+-..|++-..+. -...++...+..|.+.+|++.|.++..
T Consensus 93 ~~g~l~I~~~~~-----~~~~~l~~~l~~~~~~~p~i~~~~~~~ 131 (302)
T PRK09791 93 LAGQINIGMGAS-----IARSLMPAVISRFHQQHPQVKVRIMEG 131 (302)
T ss_pred cceEEEEEechH-----HHHhhhHHHHHHHHHHCCCeEEEEEeC
Confidence 345667665443 245677889999999999999999864
No 178
>KOG4131 consensus Ngg1-interacting factor 3 protein NIF3L1 [General function prediction only]
Probab=23.62 E-value=1.5e+02 Score=22.26 Aligned_cols=56 Identities=16% Similarity=0.363 Sum_probs=41.7
Q ss_pred HhHhhhccccccceEEEEeCCCCCCCHHHHHHHHHcHHHHHHhCCCCeEEEEEcCCCCCE
Q 041692 9 EMAWRGQLSRSMKELRILLCQTSPSSSSTRSFVERNYKELKTLNPKLPILIRECSGIEPQ 68 (73)
Q Consensus 9 ~Ms~rg~~~~qLk~l~~~yC~~~~SS~G~R~Fl~~~l~~fk~~NP~v~i~v~~~~g~~P~ 68 (73)
+||.--++...-+=+++-.|++|.+-+| ||...-+.++.+-+.-+|.|.+-- ++|.
T Consensus 214 EmSHH~vL~~~~~g~sVilc~HSNtERg---fL~d~~~kl~~~l~~~~v~vS~~D-~DPl 269 (272)
T KOG4131|consen 214 EMSHHDVLDAAANGISVILCEHSNTERG---FLSDLCDKLASSLEEEEVIVSKMD-KDPL 269 (272)
T ss_pred cccHHHHHHHHHcCCeEEEecCCCccch---hHHHHHHHHHhhCCcceEEEeecC-CCCc
Confidence 5777777766666789999999777655 888877888888888777776554 4664
No 179
>PRK09801 transcriptional activator TtdR; Provisional
Probab=23.56 E-value=1.5e+02 Score=20.92 Aligned_cols=28 Identities=21% Similarity=0.214 Sum_probs=22.9
Q ss_pred HHHHHHHHHcHHHHHHhCCCCeEEEEEc
Q 041692 35 SSTRSFVERNYKELKTLNPKLPILIREC 62 (73)
Q Consensus 35 ~G~R~Fl~~~l~~fk~~NP~v~i~v~~~ 62 (73)
.-...|+-..+..|.+.+|++.|.+...
T Consensus 105 ~~~~~~l~~~l~~f~~~~P~i~l~i~~~ 132 (310)
T PRK09801 105 GFGRSHIAPAITELMRNYPELQVHFELF 132 (310)
T ss_pred HHHHHHHHHHHHHHHHHCCCeEEEEEec
Confidence 3345678889999999999999998754
No 180
>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=23.48 E-value=76 Score=22.82 Aligned_cols=20 Identities=20% Similarity=0.371 Sum_probs=17.0
Q ss_pred HcHHHHHHhCCCCeEEEEEc
Q 041692 43 RNYKELKTLNPKLPILIREC 62 (73)
Q Consensus 43 ~~l~~fk~~NP~v~i~v~~~ 62 (73)
+.+.++|++||++.+++--.
T Consensus 59 ~~~~~lK~~~p~lKvllSiG 78 (253)
T cd06544 59 EAVKSIKAQHPNVKVVISIG 78 (253)
T ss_pred HHHHHHHHhCCCcEEEEEeC
Confidence 47889999999999998654
No 181
>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=23.45 E-value=29 Score=20.76 Aligned_cols=35 Identities=14% Similarity=0.222 Sum_probs=25.2
Q ss_pred HHHHHHHHHcHHHHHHhCCCCeEEEEEcCCCCCEE
Q 041692 35 SSTRSFVERNYKELKTLNPKLPILIRECSGIEPQL 69 (73)
Q Consensus 35 ~G~R~Fl~~~l~~fk~~NP~v~i~v~~~~g~~P~l 69 (73)
.-++.=|.+.+..++...|++.|.+-+-=|.||.|
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 44454466788889999999999998888888865
No 182
>PRK11074 putative DNA-binding transcriptional regulator; Provisional
Probab=23.45 E-value=1.1e+02 Score=21.35 Aligned_cols=39 Identities=10% Similarity=0.037 Sum_probs=30.6
Q ss_pred ccceEEEEeCCCCCCCHHHHHHHHHcHHHHHHhCCCCeEEEEEc
Q 041692 19 SMKELRILLCQTSPSSSSTRSFVERNYKELKTLNPKLPILIREC 62 (73)
Q Consensus 19 qLk~l~~~yC~~~~SS~G~R~Fl~~~l~~fk~~NP~v~i~v~~~ 62 (73)
.-..|+|-..+.. +..++...+..|++.+|++.|.+...
T Consensus 90 ~~g~l~Ig~~~~~-----~~~~l~~~l~~~~~~~p~i~i~i~~~ 128 (300)
T PRK11074 90 WRGQLSIAVDNIV-----RPDRTRQLIVDFYRHFDDVELIIRQE 128 (300)
T ss_pred CCceEEEEEcCcc-----chhHHHHHHHHHHHhCCCceEEEEeh
Confidence 3467888865543 35788899999999999999998764
No 183
>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=23.36 E-value=1.3e+02 Score=16.01 Aligned_cols=36 Identities=14% Similarity=0.369 Sum_probs=25.6
Q ss_pred eEEEEeCCCCCCCHHHHHHHHHcHHHHHHhCCCCeEEEEE
Q 041692 22 ELRILLCQTSPSSSSTRSFVERNYKELKTLNPKLPILIRE 61 (73)
Q Consensus 22 ~l~~~yC~~~~SS~G~R~Fl~~~l~~fk~~NP~v~i~v~~ 61 (73)
+|.+.+-+|.+.+.=++.+++ +++..+|++++....
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 467778888888877777654 455667888776544
No 184
>COG1393 ArsC Arsenate reductase and related proteins, glutaredoxin family [Inorganic ion transport and metabolism]
Probab=23.28 E-value=78 Score=20.32 Aligned_cols=23 Identities=9% Similarity=0.159 Sum_probs=17.6
Q ss_pred eEEEEeCCCCCCCHHHHHHHHHc
Q 041692 22 ELRILLCQTSPSSSSTRSFVERN 44 (73)
Q Consensus 22 ~l~~~yC~~~~SS~G~R~Fl~~~ 44 (73)
-|+|...+.+++|+-+++||+++
T Consensus 2 ~itiy~~p~C~t~rka~~~L~~~ 24 (117)
T COG1393 2 MITIYGNPNCSTCRKALAWLEEH 24 (117)
T ss_pred eEEEEeCCCChHHHHHHHHHHHc
Confidence 36777778888888888888654
No 185
>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=23.23 E-value=2.3e+02 Score=19.22 Aligned_cols=32 Identities=9% Similarity=0.022 Sum_probs=26.3
Q ss_pred HHHHcHHHHHHhCCCCeEEEEEcCCCCCEEEE
Q 041692 40 FVERNYKELKTLNPKLPILIRECSGIEPQLWA 71 (73)
Q Consensus 40 Fl~~~l~~fk~~NP~v~i~v~~~~g~~P~l~a 71 (73)
++..-+|+++++.|+-++.+.-.....|.+..
T Consensus 48 ~~~~~iP~l~~~yPn~~~~L~i~~~~~P~v~i 79 (202)
T smart00329 48 CFGTLVPEVAEQYPDSTLQLEISVLSPPRVTL 79 (202)
T ss_pred HHHHHHHHHHHHCCCCcEEEEEEeCCCCEEEE
Confidence 77788899999999988777777767888764
No 186
>PRK03601 transcriptional regulator HdfR; Provisional
Probab=22.97 E-value=1.7e+02 Score=20.15 Aligned_cols=27 Identities=11% Similarity=-0.026 Sum_probs=22.6
Q ss_pred HHHHHHHcHHHHHHhCCCCeEEEEEcC
Q 041692 37 TRSFVERNYKELKTLNPKLPILIRECS 63 (73)
Q Consensus 37 ~R~Fl~~~l~~fk~~NP~v~i~v~~~~ 63 (73)
...++...+..|.+.+|++.|.+....
T Consensus 100 ~~~~l~~~l~~f~~~~P~v~v~~~~~~ 126 (275)
T PRK03601 100 WECMLTPWLGRLYQNQEALQFEARIAQ 126 (275)
T ss_pred HHHHHHHHHHHHHHhCCCcEEEEEECC
Confidence 367778999999999999999886643
No 187
>PRK15421 DNA-binding transcriptional regulator MetR; Provisional
Probab=22.87 E-value=1.4e+02 Score=21.23 Aligned_cols=25 Identities=4% Similarity=0.147 Sum_probs=21.9
Q ss_pred HHHHHHcHHHHHHhCCCCeEEEEEc
Q 041692 38 RSFVERNYKELKTLNPKLPILIREC 62 (73)
Q Consensus 38 R~Fl~~~l~~fk~~NP~v~i~v~~~ 62 (73)
..|+...+..|++.+|++.|.+.+.
T Consensus 101 ~~~l~~~l~~~~~~~P~i~l~~~~~ 125 (317)
T PRK15421 101 IQWLTPALENFHKNWPQVEMDFKSG 125 (317)
T ss_pred HHHHHHHHHHHHHHCCCceEEEEeC
Confidence 4688889999999999999999765
No 188
>PRK10086 DNA-binding transcriptional regulator DsdC; Provisional
Probab=22.83 E-value=1.6e+02 Score=20.70 Aligned_cols=28 Identities=7% Similarity=0.203 Sum_probs=23.6
Q ss_pred HHHHHHHHcHHHHHHhCCCCeEEEEEcC
Q 041692 36 STRSFVERNYKELKTLNPKLPILIRECS 63 (73)
Q Consensus 36 G~R~Fl~~~l~~fk~~NP~v~i~v~~~~ 63 (73)
-...++...+..|.+.+|++.|.+....
T Consensus 112 ~~~~~l~~~l~~f~~~~P~i~i~~~~~~ 139 (311)
T PRK10086 112 IAQCWLVPRLADFTRRYPSISLTILTGN 139 (311)
T ss_pred HHHHHHHHHHHHHHHHCCCeEEEEEeCC
Confidence 3567888999999999999999988654
No 189
>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=22.70 E-value=1e+02 Score=16.13 Aligned_cols=21 Identities=14% Similarity=0.388 Sum_probs=15.0
Q ss_pred EEEEeCCCCCCCHHHHHHHHH
Q 041692 23 LRILLCQTSPSSSSTRSFVER 43 (73)
Q Consensus 23 l~~~yC~~~~SS~G~R~Fl~~ 43 (73)
+++.+..+++.+.-++.++..
T Consensus 2 v~l~~~~~c~~c~~~~~~l~~ 22 (73)
T cd02976 2 VTVYTKPDCPYCKATKRFLDE 22 (73)
T ss_pred EEEEeCCCChhHHHHHHHHHH
Confidence 566677777778888777753
No 190
>PRK10341 DNA-binding transcriptional activator TdcA; Provisional
Probab=22.66 E-value=1.6e+02 Score=20.69 Aligned_cols=38 Identities=13% Similarity=0.170 Sum_probs=27.8
Q ss_pred ceEEEEeCCCCCCCHHHHHHHHHcHHHHHHhCCCCeEEEEEcC
Q 041692 21 KELRILLCQTSPSSSSTRSFVERNYKELKTLNPKLPILIRECS 63 (73)
Q Consensus 21 k~l~~~yC~~~~SS~G~R~Fl~~~l~~fk~~NP~v~i~v~~~~ 63 (73)
..|++-.+.. -...|+...+..|.+.+|++.|.+....
T Consensus 97 ~~l~ig~~~~-----~~~~~l~~~l~~~~~~~p~v~i~~~~~~ 134 (312)
T PRK10341 97 VDVSFGFPSL-----IGFTFMSDMINKFKEVFPKAQVSMYEAQ 134 (312)
T ss_pred eEEEEEechH-----HhHhhHHHHHHHHHHhCCCCEEEEEeCC
Confidence 4567655432 2345778899999999999999987653
No 191
>PRK14997 LysR family transcriptional regulator; Provisional
Probab=22.47 E-value=1.6e+02 Score=20.36 Aligned_cols=38 Identities=5% Similarity=0.067 Sum_probs=27.4
Q ss_pred ceEEEEeCCCCCCCHHHHHHHHHcHHHHHHhCCCCeEEEEEcC
Q 041692 21 KELRILLCQTSPSSSSTRSFVERNYKELKTLNPKLPILIRECS 63 (73)
Q Consensus 21 k~l~~~yC~~~~SS~G~R~Fl~~~l~~fk~~NP~v~i~v~~~~ 63 (73)
..|+|-...+ -...++...+.+|.+++|++.|.+....
T Consensus 92 g~lrIg~~~~-----~~~~~l~~~l~~~~~~~P~i~i~~~~~~ 129 (301)
T PRK14997 92 GIVKLTCPVT-----LLHVHIGPMLAKFMARYPDVSLQLEATN 129 (301)
T ss_pred eeEEEECcHH-----HHHHHHHHHHHHHHHHCCCeEEEEEecC
Confidence 4566654322 2346778899999999999999987643
No 192
>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=22.47 E-value=1.3e+02 Score=22.44 Aligned_cols=35 Identities=17% Similarity=0.147 Sum_probs=28.2
Q ss_pred EeCCCCCCCHHHHHHHHHc-------------HHHHHHhCCCCeEEEE
Q 041692 26 LLCQTSPSSSSTRSFVERN-------------YKELKTLNPKLPILIR 60 (73)
Q Consensus 26 ~yC~~~~SS~G~R~Fl~~~-------------l~~fk~~NP~v~i~v~ 60 (73)
..||.-|||.||-+|+++. +..+++.+|+-.|+.-
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 4688899999999999765 5678889999866554
No 193
>PRK11139 DNA-binding transcriptional activator GcvA; Provisional
Probab=22.44 E-value=1.3e+02 Score=20.72 Aligned_cols=25 Identities=4% Similarity=0.272 Sum_probs=21.8
Q ss_pred HHHHHHcHHHHHHhCCCCeEEEEEc
Q 041692 38 RSFVERNYKELKTLNPKLPILIREC 62 (73)
Q Consensus 38 R~Fl~~~l~~fk~~NP~v~i~v~~~ 62 (73)
..||...+.+|.+.+|++.|.+...
T Consensus 106 ~~~l~~~l~~f~~~~p~i~i~l~~~ 130 (297)
T PRK11139 106 IQWLVPRLSSFNEAHPDIDVRLKAV 130 (297)
T ss_pred HHHHHHHHHHHHHHCCCceEEEEeC
Confidence 5788889999999999999999753
No 194
>PF05725 FNIP: FNIP Repeat; InterPro: IPR008615 This repeat is approximately 22 residues long and is only found in Dictyostelium discoideum (Slime mould). It appears to be related to IPR001611 from INTERPRO. The alignment consists of two tandem repeats. It is termed the FNIP repeat after the pattern of conserved residues.
Probab=22.15 E-value=60 Score=16.94 Aligned_cols=16 Identities=31% Similarity=0.389 Sum_probs=10.7
Q ss_pred hhccccccceEEEEeC
Q 041692 13 RGQLSRSMKELRILLC 28 (73)
Q Consensus 13 rg~~~~qLk~l~~~yC 28 (73)
.|+++..|+.|.|.++
T Consensus 29 ~~~lP~sl~~L~fg~~ 44 (44)
T PF05725_consen 29 PGSLPNSLKSLSFGYF 44 (44)
T ss_pred CCccCCCceEEEeeCC
Confidence 5667777777777553
No 195
>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=22.08 E-value=90 Score=22.08 Aligned_cols=43 Identities=28% Similarity=0.509 Sum_probs=31.0
Q ss_pred CCCCCCCHHHHHHHHHcHHHHHHhCCC----Ce--EEEEEcCCCCCEEE
Q 041692 28 CQTSPSSSSTRSFVERNYKELKTLNPK----LP--ILIRECSGIEPQLW 70 (73)
Q Consensus 28 C~~~~SS~G~R~Fl~~~l~~fk~~NP~----v~--i~v~~~~g~~P~l~ 70 (73)
.+-|+++.-+++=+++....|+++||. +| .+..-.+|-+|+|.
T Consensus 85 SNl~psn~~l~~~v~~~~~~~~~~~~~~~~~vP~dlvtaSgSGLDP~IS 133 (188)
T PF02669_consen 85 SNLGPSNPELRERVEERIAALRKENPVAPSPVPADLVTASGSGLDPHIS 133 (188)
T ss_pred ccCCCCChHHHHHHHHHHHHHHhhcccCCCCCCHHHHhcccccCCCCcC
Confidence 356777888999999999999999833 23 23345567788764
No 196
>KOG0026 consensus Anthranilate synthase, beta chain [Amino acid transport and metabolism]
Probab=22.02 E-value=72 Score=22.99 Aligned_cols=23 Identities=43% Similarity=0.640 Sum_probs=18.6
Q ss_pred cHHHHHHhCCCCeEEEEEcCCCCCE
Q 041692 44 NYKELKTLNPKLPILIRECSGIEPQ 68 (73)
Q Consensus 44 ~l~~fk~~NP~v~i~v~~~~g~~P~ 68 (73)
..+++++.||.. +++.|.+| ||.
T Consensus 55 TV~El~~~NP~~-LliSPGPG-~P~ 77 (223)
T KOG0026|consen 55 TVEELKRKNPRG-LLISPGPG-TPQ 77 (223)
T ss_pred cHHHHhhcCCCe-EEecCCCC-CCc
Confidence 578999999974 67888888 775
No 197
>PRK11233 nitrogen assimilation transcriptional regulator; Provisional
Probab=21.89 E-value=1.9e+02 Score=20.14 Aligned_cols=27 Identities=15% Similarity=0.213 Sum_probs=22.5
Q ss_pred HHHHHHHcHHHHHHhCCCCeEEEEEcC
Q 041692 37 TRSFVERNYKELKTLNPKLPILIRECS 63 (73)
Q Consensus 37 ~R~Fl~~~l~~fk~~NP~v~i~v~~~~ 63 (73)
.+.++...+.+|.+.+|++.|.+....
T Consensus 103 ~~~~~~~~l~~~~~~~p~i~l~~~~~~ 129 (305)
T PRK11233 103 ASSLTMPLLQAVRAEFPGIVLYLHENS 129 (305)
T ss_pred hHHHHHHHHHHHHHHCCCcEEEEEECC
Confidence 467777889999999999999887643
No 198
>PF13589 HATPase_c_3: Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase; PDB: 3IED_A 2XCM_B 2JKI_B 3OPD_A 2O1V_B 2GQP_A 2O1W_C 1YT2_A 1TC6_A 2H8M_B ....
Probab=21.88 E-value=2.2e+02 Score=17.96 Aligned_cols=35 Identities=17% Similarity=0.116 Sum_probs=26.4
Q ss_pred CHHHHHHHHHcHHHHHHhCCCCeEEEEEcCCCCCEEEE
Q 041692 34 SSSTRSFVERNYKELKTLNPKLPILIRECSGIEPQLWA 71 (73)
Q Consensus 34 S~G~R~Fl~~~l~~fk~~NP~v~i~v~~~~g~~P~l~a 71 (73)
-..++++|.+.++.-+.. |.|.+....+..+.+..
T Consensus 4 ~~al~ElI~Ns~DA~a~~---I~I~i~~~~~~~~~i~I 38 (137)
T PF13589_consen 4 EDALRELIDNSIDAGATN---IKISIDEDKKGERYIVI 38 (137)
T ss_dssp THHHHHHHHHHHHHHHHH---EEEEEEEETTTTTEEEE
T ss_pred HHHHHHHHHHHHHccCCE---EEEEEEcCCCCCcEEEE
Confidence 357899999999998888 77777776544555554
No 199
>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=21.88 E-value=1.6e+02 Score=21.37 Aligned_cols=30 Identities=17% Similarity=0.247 Sum_probs=22.9
Q ss_pred HHHHHHHHHcHHHHHHhCCCCeEEEEEcCC
Q 041692 35 SSTRSFVERNYKELKTLNPKLPILIRECSG 64 (73)
Q Consensus 35 ~G~R~Fl~~~l~~fk~~NP~v~i~v~~~~g 64 (73)
.-+.+-++..+..+++-||++.|.+.-.|=
T Consensus 148 ~ei~~~l~~~~~~l~~~nP~~kiilTVSPV 177 (251)
T PF08885_consen 148 EEILEDLEAIIDLLRSINPDIKIILTVSPV 177 (251)
T ss_pred HHHHHHHHHHHHHHHhhCCCceEEEEeccc
Confidence 344556677788899999999988877663
No 200
>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=21.75 E-value=1.5e+02 Score=16.12 Aligned_cols=27 Identities=22% Similarity=0.415 Sum_probs=21.7
Q ss_pred eEEEEeCCCCCCCHHHHHHHHHcHHHH
Q 041692 22 ELRILLCQTSPSSSSTRSFVERNYKEL 48 (73)
Q Consensus 22 ~l~~~yC~~~~SS~G~R~Fl~~~l~~f 48 (73)
.|.+.+.+|.+.++-+...+++...++
T Consensus 2 ~v~~f~~~~C~~C~~~~~~l~~l~~~~ 28 (82)
T TIGR00411 2 KIELFTSPTCPYCPAAKRVVEEVAKEM 28 (82)
T ss_pred EEEEEECCCCcchHHHHHHHHHHHHHh
Confidence 467888999999999999887665554
No 201
>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=21.73 E-value=1.8e+02 Score=16.83 Aligned_cols=33 Identities=21% Similarity=0.339 Sum_probs=20.7
Q ss_pred HHHHHHHHcHHHHHHhCCCCeEEEEEcCCCCCE
Q 041692 36 STRSFVERNYKELKTLNPKLPILIRECSGIEPQ 68 (73)
Q Consensus 36 G~R~Fl~~~l~~fk~~NP~v~i~v~~~~g~~P~ 68 (73)
...+.+......+++..|..++.+--....+|.
T Consensus 14 ~~~~~~~~~~~~l~~~~~~~~v~~a~~~~~~P~ 46 (101)
T cd03409 14 PYKKDIEAQAHNLAESLPDFPYYVGFQSGLGPD 46 (101)
T ss_pred cHHHHHHHHHHHHHHHCCCCCEEEEEECCCCCC
Confidence 566677777777777777666665444433443
No 202
>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=21.64 E-value=77 Score=20.39 Aligned_cols=15 Identities=13% Similarity=0.200 Sum_probs=13.1
Q ss_pred HHHHHHHHHcHHHHH
Q 041692 35 SSTRSFVERNYKELK 49 (73)
Q Consensus 35 ~G~R~Fl~~~l~~fk 49 (73)
.|+|+||...+.+..
T Consensus 68 ~g~R~~IKe~~~E~s 82 (98)
T PF11247_consen 68 QGIREAIKEMLSEYS 82 (98)
T ss_pred HHHHHHHHHHHHHhc
Confidence 689999998888876
No 203
>PRK15317 alkyl hydroperoxide reductase subunit F; Provisional
Probab=21.25 E-value=1.7e+02 Score=22.61 Aligned_cols=38 Identities=8% Similarity=0.182 Sum_probs=29.4
Q ss_pred eEEEEeCCCCCCCHHHHHHHHHcHHHHHHhCCCCeEEEEEcC
Q 041692 22 ELRILLCQTSPSSSSTRSFVERNYKELKTLNPKLPILIRECS 63 (73)
Q Consensus 22 ~l~~~yC~~~~SS~G~R~Fl~~~l~~fk~~NP~v~i~v~~~~ 63 (73)
.|.+.+..+++-+..+.+-+ ..||..||++.+.+-+..
T Consensus 119 ~i~~fv~~~Cp~Cp~~v~~~----~~~a~~~~~i~~~~id~~ 156 (517)
T PRK15317 119 HFETYVSLSCHNCPDVVQAL----NLMAVLNPNITHTMIDGA 156 (517)
T ss_pred EEEEEEcCCCCCcHHHHHHH----HHHHHhCCCceEEEEEch
Confidence 37778888888888776655 778999999998877543
No 204
>cd01844 SGNH_hydrolase_like_6 SGNH_hydrolase subfamily. SGNH hydrolases are a diverse family of lipases and esterases. The tertiary fold of the enzyme is substantially different from that of the alpha/beta hydrolase family and unique among all known hydrolases; its active site closely resembles the Ser-His-Asp(Glu) triad found in other serine hydrolases.
Probab=21.21 E-value=2.4e+02 Score=18.06 Aligned_cols=40 Identities=25% Similarity=0.400 Sum_probs=26.2
Q ss_pred eEEEEeCCCCCCCHHH--HHHHHHcHHHHHHhCCCCeEEEEE
Q 041692 22 ELRILLCQTSPSSSST--RSFVERNYKELKTLNPKLPILIRE 61 (73)
Q Consensus 22 ~l~~~yC~~~~SS~G~--R~Fl~~~l~~fk~~NP~v~i~v~~ 61 (73)
.+.+..+-+.....+. ++-+.+-+..+++.+|.++|.+..
T Consensus 59 d~vii~~G~ND~~~~~~~~~~~~~~i~~i~~~~p~~~iil~~ 100 (177)
T cd01844 59 DLYIIDCGPNIVGAEAMVRERLGPLVKGLRETHPDTPILLVS 100 (177)
T ss_pred CEEEEEeccCCCccHHHHHHHHHHHHHHHHHHCcCCCEEEEe
Confidence 4555555555555564 344456788889999999877643
No 205
>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=21.18 E-value=2e+02 Score=17.26 Aligned_cols=33 Identities=15% Similarity=0.135 Sum_probs=23.2
Q ss_pred EEEEeCCCCCCCHHHHHHHHHcHHHHHHhCCCCeEEE
Q 041692 23 LRILLCQTSPSSSSTRSFVERNYKELKTLNPKLPILI 59 (73)
Q Consensus 23 l~~~yC~~~~SS~G~R~Fl~~~l~~fk~~NP~v~i~v 59 (73)
|...|-+|.+.++-+.. .+.++++++|++.|..
T Consensus 28 vv~F~a~~c~~C~~l~~----~l~~la~~~~~v~f~~ 60 (113)
T cd02957 28 VVHFYEPGFPRCKILDS----HLEELAAKYPETKFVK 60 (113)
T ss_pred EEEEeCCCCCcHHHHHH----HHHHHHHHCCCcEEEE
Confidence 45677789998986554 5566777788876543
No 206
>PF09345 DUF1987: Domain of unknown function (DUF1987); InterPro: IPR018530 This family of proteins are functionally uncharacterised.
Probab=20.94 E-value=1.7e+02 Score=18.41 Aligned_cols=34 Identities=15% Similarity=0.179 Sum_probs=22.6
Q ss_pred EEEEeCCCCCCCHHHHHHHHHcHHHHHHhCCCCeEE
Q 041692 23 LRILLCQTSPSSSSTRSFVERNYKELKTLNPKLPIL 58 (73)
Q Consensus 23 l~~~yC~~~~SS~G~R~Fl~~~l~~fk~~NP~v~i~ 58 (73)
+.|.|=++| ||+.+-+.++ .|.+.+++...|.|.
T Consensus 49 ~~L~YfNTS-Ssk~l~~i~~-~Le~~~~~g~~V~v~ 82 (99)
T PF09345_consen 49 FKLSYFNTS-SSKALMDIFD-LLEDAAQKGGKVTVN 82 (99)
T ss_pred EEEEEEecH-hHHHHHHHHH-HHHHHHhcCCcEEEE
Confidence 556666765 7777777664 566667777776654
No 207
>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=20.93 E-value=29 Score=23.26 Aligned_cols=41 Identities=12% Similarity=0.333 Sum_probs=35.2
Q ss_pred CCHHHHHHHHHcHHHHHHhCCCCeEEEEEcCCCCCEEEEeC
Q 041692 33 SSSSTRSFVERNYKELKTLNPKLPILIRECSGIEPQLWARY 73 (73)
Q Consensus 33 SS~G~R~Fl~~~l~~fk~~NP~v~i~v~~~~g~~P~l~a~Y 73 (73)
|-.|.|.|=.+.+.++--+..+..+.++|....+|++...|
T Consensus 30 STTGFrTfsTn~lvnIi~aTth~vvvvkEakstn~hi~v~f 70 (130)
T PF02960_consen 30 STTGFRTFSTNSLVNIIHATTHDVVVVKEAKSTNPHIQVHF 70 (130)
T ss_pred cccceEEEecccccceecccccceEEEEEeecCCceEEeee
Confidence 44688999989888898899999999999999999987643
No 208
>KOG3170 consensus Conserved phosducin-like protein [Signal transduction mechanisms]
Probab=20.78 E-value=3.3e+02 Score=20.09 Aligned_cols=47 Identities=13% Similarity=0.161 Sum_probs=35.4
Q ss_pred HHHhHhhhccccccceEEEEeCCCCCCCHHHHHHHHHcHHHHHHhCCCCeEEEEEc
Q 041692 7 EREMAWRGQLSRSMKELRILLCQTSPSSSSTRSFVERNYKELKTLNPKLPILIREC 62 (73)
Q Consensus 7 ~~~Ms~rg~~~~qLk~l~~~yC~~~~SS~G~R~Fl~~~l~~fk~~NP~v~i~v~~~ 62 (73)
|=--|..|+| +.++.-.. |...=..|.+.+..++...|++.|+--+.
T Consensus 104 EVT~As~gvw------VvvhLy~~---gvp~c~Ll~~~l~~la~kfp~iKFVki~a 150 (240)
T KOG3170|consen 104 EVTKASEGVW------VVVHLYKQ---GVPLCALLSHHLQSLACKFPQIKFVKIPA 150 (240)
T ss_pred HHHhccCccE------EEEEeecc---ccHHHHHHHHHHHHHhhcCCcceEEeccc
Confidence 3334566777 66776665 56777889999999999999999876554
No 209
>PF03562 MltA: MltA specific insert domain; InterPro: IPR005300 This group of proteins includes MltA; a membrane-bound, murein degrading transglycosylase enzyme which plays an important role in the controlled growth of the stress-bearing sacculus of Escherichia coli [, ].; GO: 0004553 hydrolase activity, hydrolyzing O-glycosyl compounds; PDB: 2PI8_D 2AE0_X 2PIC_A 2GAE_A 2PJJ_A 3CZB_A 2G6G_A 2PNW_A 2G5D_A.
Probab=20.59 E-value=1.2e+02 Score=20.82 Aligned_cols=28 Identities=21% Similarity=0.293 Sum_probs=18.6
Q ss_pred CCCCCHHHHHHHHH---cHHHHHHhCCCCeE
Q 041692 30 TSPSSSSTRSFVER---NYKELKTLNPKLPI 57 (73)
Q Consensus 30 ~~~SS~G~R~Fl~~---~l~~fk~~NP~v~i 57 (73)
..-|=.++|+|+.+ ...++-..||..+|
T Consensus 126 ~~~Smq~Ir~wl~~~P~~~~~ll~~N~syVF 156 (158)
T PF03562_consen 126 EQMSMQAIRAWLRAHPEEADELLNQNPSYVF 156 (158)
T ss_dssp TS-SHHHHHHHHHHTGGGHHHHHTTS---EE
T ss_pred hhCCHHHHHHHHHHCHHHHHHHHHhCCCceE
Confidence 33466899999974 67788889999876
No 210
>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=20.53 E-value=2.5e+02 Score=20.03 Aligned_cols=35 Identities=23% Similarity=0.439 Sum_probs=25.0
Q ss_pred EEEeCCCCCCCHHHHHHHHHcHHHHHHhCCCCeEEEE
Q 041692 24 RILLCQTSPSSSSTRSFVERNYKELKTLNPKLPILIR 60 (73)
Q Consensus 24 ~~~yC~~~~SS~G~R~Fl~~~l~~fk~~NP~v~i~v~ 60 (73)
+|.+||+.|....-+ +.+.+..+++..|+++|.+.
T Consensus 167 ~i~l~DT~G~~~P~~--v~~lv~~l~~~~~~~~l~~H 201 (273)
T cd07941 167 WLVLCDTNGGTLPHE--IAEIVKEVRERLPGVPLGIH 201 (273)
T ss_pred EEEEecCCCCCCHHH--HHHHHHHHHHhCCCCeeEEE
Confidence 577899988766543 55666777777788777664
No 211
>PRK11013 DNA-binding transcriptional regulator LysR; Provisional
Probab=20.51 E-value=1.8e+02 Score=20.33 Aligned_cols=38 Identities=13% Similarity=0.112 Sum_probs=27.7
Q ss_pred ceEEEEeCCCCCCCHHHHHHHHHcHHHHHHhCCCCeEEEEEcC
Q 041692 21 KELRILLCQTSPSSSSTRSFVERNYKELKTLNPKLPILIRECS 63 (73)
Q Consensus 21 k~l~~~yC~~~~SS~G~R~Fl~~~l~~fk~~NP~v~i~v~~~~ 63 (73)
..|++-..+.. ...++...+..|.+.+|++.|.+....
T Consensus 94 g~l~I~~~~~~-----~~~~l~~~l~~~~~~~P~v~i~i~~~~ 131 (309)
T PRK11013 94 GQLSIACLPVF-----SQSLLPGLCQPFLARYPDVSLNIVPQE 131 (309)
T ss_pred CcEEEEEcHHH-----HHhhHHHHHHHHHHHCCCCeEEEEeCC
Confidence 45666543321 245778999999999999999998654
No 212
>COG0007 CysG Uroporphyrinogen-III methylase [Coenzyme metabolism]
Probab=20.50 E-value=1.4e+02 Score=21.87 Aligned_cols=33 Identities=18% Similarity=0.303 Sum_probs=25.5
Q ss_pred HHHHHHHHcHHHHHHhCCCCeEEEEEcCCCCCEEEEe
Q 041692 36 STRSFVERNYKELKTLNPKLPILIRECSGIEPQLWAR 72 (73)
Q Consensus 36 G~R~Fl~~~l~~fk~~NP~v~i~v~~~~g~~P~l~a~ 72 (73)
..-+-|.+.+.+++++. ...||...| +|+++++
T Consensus 65 ~~q~eIn~~lv~~a~~G---~~VVRLKgG-DP~iFGR 97 (244)
T COG0007 65 KPQDEINALLVELAREG---KRVVRLKGG-DPYIFGR 97 (244)
T ss_pred CCHHHHHHHHHHHHhcC---CeEEEecCC-CCCeecC
Confidence 34567888899999985 566777777 9999875
No 213
>PRK12684 transcriptional regulator CysB-like protein; Reviewed
Probab=20.42 E-value=1.8e+02 Score=20.46 Aligned_cols=38 Identities=26% Similarity=0.295 Sum_probs=28.2
Q ss_pred ceEEEEeCCCCCCCHHHHHHHHHcHHHHHHhCCCCeEEEEEcC
Q 041692 21 KELRILLCQTSPSSSSTRSFVERNYKELKTLNPKLPILIRECS 63 (73)
Q Consensus 21 k~l~~~yC~~~~SS~G~R~Fl~~~l~~fk~~NP~v~i~v~~~~ 63 (73)
..|+|-. +......++...+..|.+.+|++.|.+....
T Consensus 93 g~l~Ig~-----~~~~~~~~l~~~l~~~~~~~p~i~l~~~~~~ 130 (313)
T PRK12684 93 GNLTIAT-----THTQARYALPAAIKEFKKRYPKVRLSILQGS 130 (313)
T ss_pred CeEEEEe-----chHHHHHHhHHHHHHHHHHCCCceEEEEeCC
Confidence 4566654 2344567778899999999999999987643
No 214
>PF01076 Mob_Pre: Plasmid recombination enzyme; InterPro: IPR001668 With some plasmids, recombination can occur in a site specific manner that is independent of RecA. In such cases, the recombination event requires another protein called Pre. Pre is a plasmid recombination enzyme. This protein is also known as Mob (conjugative mobilisation) [].; GO: 0003677 DNA binding, 0006310 DNA recombination, 0005727 extrachromosomal circular DNA
Probab=20.26 E-value=2.7e+02 Score=18.96 Aligned_cols=51 Identities=10% Similarity=0.095 Sum_probs=32.5
Q ss_pred ceEEEEeCCC---CCCCHHHHHHHHHcHHHHHHhCCCC-eE-EEEEcCCCCCEEEE
Q 041692 21 KELRILLCQT---SPSSSSTRSFVERNYKELKTLNPKL-PI-LIRECSGIEPQLWA 71 (73)
Q Consensus 21 k~l~~~yC~~---~~SS~G~R~Fl~~~l~~fk~~NP~v-~i-~v~~~~g~~P~l~a 71 (73)
-++.|...+. ..+-.=..+|++..+..|++.+|.. .| -+...-...|++-+
T Consensus 81 ~e~iit~~~e~~~~~~~e~~~~~~~~~~~~~~~r~g~~ni~~a~vH~DE~tPH~H~ 136 (196)
T PF01076_consen 81 IEFIITASPEFFNDLDPEQQKRWFEDSLEWLQERYGNENIVSAVVHLDETTPHMHF 136 (196)
T ss_pred EEEEEeCChHHhcchhhHHHHHHHHHHHHHHHHHCCchhEEEEEEECCCCCcceEE
Confidence 3455554431 2233447899999999999999933 33 34555566887765
No 215
>PF14606 Lipase_GDSL_3: GDSL-like Lipase/Acylhydrolase family; PDB: 3SKV_B.
Probab=20.23 E-value=1.5e+02 Score=20.66 Aligned_cols=32 Identities=22% Similarity=0.277 Sum_probs=21.4
Q ss_pred CCCHHHHHHHHHcHHHHHHhCCCCeEEEEEcC
Q 041692 32 PSSSSTRSFVERNYKELKTLNPKLPILIRECS 63 (73)
Q Consensus 32 ~SS~G~R~Fl~~~l~~fk~~NP~v~i~v~~~~ 63 (73)
.+-.-+++=+...+..+.+.+|.+||++.+..
T Consensus 71 ~~~~~~~~~~~~fv~~iR~~hP~tPIllv~~~ 102 (178)
T PF14606_consen 71 MSPEEFRERLDGFVKTIREAHPDTPILLVSPI 102 (178)
T ss_dssp CCTTTHHHHHHHHHHHHHTT-SSS-EEEEE--
T ss_pred CCHHHHHHHHHHHHHHHHHhCCCCCEEEEecC
Confidence 44555566666788899999999999987743
No 216
>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=20.17 E-value=2.3e+02 Score=17.48 Aligned_cols=38 Identities=8% Similarity=0.200 Sum_probs=26.6
Q ss_pred eEEEEeCCCCCCCHHHHHHHHHcHHHHHHhCCCCeEEEEEc
Q 041692 22 ELRILLCQTSPSSSSTRSFVERNYKELKTLNPKLPILIREC 62 (73)
Q Consensus 22 ~l~~~yC~~~~SS~G~R~Fl~~~l~~fk~~NP~v~i~v~~~ 62 (73)
++-|.+.+.+|..++. | ++-.+.|+.....+.+...+.
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 4668889999999988 4 556666777766665555443
No 217
>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=20.01 E-value=1.2e+02 Score=15.71 Aligned_cols=21 Identities=14% Similarity=0.300 Sum_probs=14.4
Q ss_pred EEEEeCCCCCCCHHHHHHHHH
Q 041692 23 LRILLCQTSPSSSSTRSFVER 43 (73)
Q Consensus 23 l~~~yC~~~~SS~G~R~Fl~~ 43 (73)
|++..-++.+.++.++.+|..
T Consensus 2 v~ly~~~~Cp~C~~~~~~L~~ 22 (72)
T cd02066 2 VVVFSKSTCPYCKRAKRLLES 22 (72)
T ss_pred EEEEECCCCHHHHHHHHHHHH
Confidence 445555677778888888753
Done!