Query psy9334
Match_columns 65
No_of_seqs 123 out of 1084
Neff 5.4
Searched_HMMs 46136
Date Sat Aug 17 00:39:36 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy9334.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/9334hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 COG0473 LeuB Isocitrate/isopro 100.0 1.6E-30 3.5E-35 189.3 5.7 62 4-65 190-251 (348)
2 PRK03437 3-isopropylmalate deh 100.0 1.2E-29 2.5E-34 184.4 5.8 63 3-65 193-255 (344)
3 PLN02329 3-isopropylmalate deh 100.0 8.2E-30 1.8E-34 188.7 4.9 64 2-65 241-304 (409)
4 PRK08194 tartrate dehydrogenas 100.0 1.7E-29 3.6E-34 184.0 5.6 63 3-65 193-255 (352)
5 PLN00123 isocitrate dehydrogen 100.0 2.3E-29 5E-34 184.0 5.7 62 4-65 202-263 (360)
6 TIGR02089 TTC tartrate dehydro 100.0 2.4E-29 5.2E-34 183.1 5.5 63 3-65 196-258 (352)
7 PRK08997 isocitrate dehydrogen 100.0 3.3E-29 7.1E-34 181.5 5.5 63 3-65 180-242 (334)
8 PRK14025 multifunctional 3-iso 100.0 5.9E-29 1.3E-33 180.0 5.5 63 3-65 177-239 (330)
9 PLN00118 isocitrate dehydrogen 100.0 8.3E-29 1.8E-33 181.6 5.2 63 3-65 217-279 (372)
10 TIGR00169 leuB 3-isopropylmala 100.0 1.1E-28 2.3E-33 179.5 5.6 64 2-65 193-256 (349)
11 TIGR00175 mito_nad_idh isocitr 99.9 1.4E-28 3E-33 177.9 5.5 63 3-65 178-240 (333)
12 TIGR02088 LEU3_arch isopropylm 99.9 3.7E-28 8.1E-33 175.2 5.3 60 5-65 175-234 (322)
13 PRK00772 3-isopropylmalate deh 99.9 5.6E-28 1.2E-32 176.3 4.8 64 2-65 196-259 (358)
14 PRK09222 isocitrate dehydrogen 99.9 6.8E-28 1.5E-32 181.2 5.3 63 3-65 182-244 (482)
15 TIGR02924 ICDH_alpha isocitrat 99.9 1.5E-27 3.3E-32 179.1 5.8 62 4-65 179-240 (473)
16 PF00180 Iso_dh: Isocitrate/is 99.9 1E-27 2.2E-32 173.4 3.4 65 1-65 190-255 (348)
17 PRK06451 isocitrate dehydrogen 99.9 1.2E-26 2.7E-31 171.8 5.5 62 4-65 230-312 (412)
18 PRK07006 isocitrate dehydrogen 99.9 2.1E-26 4.5E-31 170.4 5.7 62 4-65 231-312 (409)
19 KOG0785|consensus 99.9 2.3E-26 4.9E-31 167.1 5.4 61 5-65 213-273 (365)
20 TIGR00183 prok_nadp_idh isocit 99.9 7.1E-26 1.5E-30 167.7 5.4 62 4-65 238-319 (416)
21 PRK08299 isocitrate dehydrogen 99.9 5.4E-25 1.2E-29 162.8 5.2 61 4-65 218-285 (402)
22 TIGR00127 nadp_idh_euk isocitr 99.9 8E-25 1.7E-29 162.2 5.9 61 4-65 219-286 (409)
23 PTZ00435 isocitrate dehydrogen 99.9 1.1E-24 2.4E-29 161.6 5.3 61 4-65 221-288 (413)
24 PLN00103 isocitrate dehydrogen 99.9 1.9E-24 4.2E-29 160.2 5.9 61 4-65 222-289 (410)
25 PRK07362 isocitrate dehydrogen 99.9 1.8E-24 4E-29 162.4 5.2 46 20-65 331-376 (474)
26 KOG0784|consensus 99.9 1.5E-23 3.2E-28 153.4 4.6 60 6-65 220-279 (375)
27 PLN00096 isocitrate dehydrogen 99.9 2.9E-23 6.4E-28 153.3 5.2 60 5-65 210-281 (393)
28 PLN03065 isocitrate dehydrogen 99.9 3.6E-22 7.8E-27 150.4 5.6 60 5-65 290-356 (483)
29 KOG0786|consensus 99.9 4.1E-22 8.9E-27 143.4 4.2 63 3-65 196-260 (363)
30 COG0538 Icd Isocitrate dehydro 99.5 1.6E-14 3.5E-19 107.2 5.5 60 6-65 230-308 (407)
31 KOG1526|consensus 97.2 0.00042 9.2E-09 51.7 4.0 58 7-65 233-297 (422)
32 TIGR00651 pta phosphate acetyl 76.1 7.7 0.00017 28.0 4.9 56 8-63 202-267 (303)
33 cd01846 fatty_acyltransferase_ 72.0 4.6 9.9E-05 27.2 2.8 37 8-44 185-221 (270)
34 PF08883 DOPA_dioxygen: Dopa 4 68.2 10 0.00022 23.8 3.6 37 20-57 49-85 (104)
35 KOG0907|consensus 67.5 3.2 6.9E-05 25.6 1.2 43 2-49 35-77 (106)
36 cd08450 PBP2_HcaR The C-termin 66.6 11 0.00023 22.5 3.4 42 5-47 13-55 (196)
37 cd01837 SGNH_plant_lipase_like 66.0 8.2 0.00018 26.9 3.1 37 8-44 222-258 (315)
38 cd05466 PBP2_LTTR_substrate Th 64.5 14 0.0003 21.3 3.5 42 6-48 14-56 (197)
39 TIGR01256 modA molybdenum ABC 63.3 21 0.00045 23.1 4.5 43 6-50 7-51 (216)
40 cd08460 PBP2_DntR_like_1 The C 63.0 19 0.0004 21.8 4.0 43 4-47 12-54 (200)
41 PF08601 PAP1: Transcription f 61.1 6.2 0.00013 29.3 1.9 47 1-54 295-343 (347)
42 PF01547 SBP_bac_1: Bacterial 60.3 19 0.00042 23.5 4.0 42 6-47 9-57 (315)
43 PLN03156 GDSL esterase/lipase; 57.1 17 0.00037 26.4 3.6 37 8-44 253-289 (351)
44 cd08445 PBP2_BenM_CatM_CatR Th 56.7 23 0.0005 21.4 3.7 40 6-47 15-56 (203)
45 cd08486 PBP2_CbnR The C-termin 55.4 32 0.0007 21.0 4.2 40 6-47 15-56 (198)
46 PF01515 PTA_PTB: Phosphate ac 54.9 42 0.00091 24.4 5.2 62 3-64 213-284 (319)
47 cd08448 PBP2_LTTR_aromatics_li 54.2 25 0.00055 20.7 3.5 42 5-48 13-56 (197)
48 PF02608 Bmp: Basic membrane p 51.9 10 0.00022 26.6 1.7 20 4-23 69-88 (306)
49 PRK09653 eutD phosphotransacet 51.5 45 0.00097 24.1 4.9 58 6-63 215-282 (324)
50 cd08438 PBP2_CidR The C-termin 51.3 22 0.00048 21.0 2.9 41 6-47 14-55 (197)
51 cd08470 PBP2_CrgA_like_1 The C 50.8 9 0.00019 23.0 1.1 40 6-48 15-54 (197)
52 PF03466 LysR_substrate: LysR 50.6 25 0.00054 21.2 3.1 44 5-50 19-64 (209)
53 COG4837 Uncharacterized protei 50.5 13 0.00029 23.5 1.8 40 7-48 31-81 (106)
54 cd08439 PBP2_LrhA_like The C-t 50.3 31 0.00067 20.6 3.4 40 6-47 14-55 (185)
55 PRK15381 pathogenicity island 49.9 17 0.00037 27.5 2.6 36 8-43 313-348 (408)
56 cd08446 PBP2_Chlorocatechol Th 49.9 34 0.00074 20.4 3.6 40 7-48 16-57 (198)
57 cd08464 PBP2_DntR_like_2 The C 49.6 23 0.00049 21.1 2.7 40 7-47 15-55 (200)
58 cd08416 PBP2_MdcR The C-termin 49.4 29 0.00062 20.6 3.2 40 6-47 14-55 (199)
59 cd08435 PBP2_GbpR The C-termin 48.9 33 0.00072 20.3 3.4 40 6-47 14-55 (201)
60 cd08478 PBP2_CrgA The C-termin 48.7 12 0.00025 22.6 1.4 39 6-47 17-55 (199)
61 cd08453 PBP2_IlvR The C-termin 48.6 34 0.00074 20.5 3.5 41 5-47 13-55 (200)
62 cd08436 PBP2_LTTR_like_3 The C 48.6 36 0.00079 20.0 3.5 40 6-47 14-55 (194)
63 cd08469 PBP2_PnbR The C-termin 47.6 34 0.00073 21.1 3.4 40 6-47 14-55 (221)
64 TIGR02329 propionate_PrpR prop 47.4 39 0.00083 26.2 4.3 51 7-57 15-70 (526)
65 cd08444 PBP2_Cbl The C-termina 47.2 38 0.00083 20.5 3.6 42 6-48 14-56 (198)
66 cd08462 PBP2_NodD The C-termin 47.1 39 0.00085 20.4 3.6 43 6-49 14-56 (200)
67 cd02957 Phd_like Phosducin (Ph 47.1 24 0.00052 20.9 2.6 29 2-31 38-66 (113)
68 cd08449 PBP2_XapR The C-termin 46.8 40 0.00087 19.9 3.6 41 5-47 13-55 (197)
69 cd08466 PBP2_LeuO The C-termin 46.1 43 0.00094 19.9 3.6 41 6-47 14-55 (200)
70 cd08452 PBP2_AlsR The C-termin 46.0 44 0.00096 20.1 3.7 39 7-47 15-55 (197)
71 cd08437 PBP2_MleR The substrat 45.7 42 0.0009 20.0 3.5 40 6-47 14-55 (198)
72 TIGR03850 bind_CPR_0540 carboh 44.7 51 0.0011 23.5 4.3 45 5-49 48-95 (437)
73 cd08423 PBP2_LTTR_like_6 The C 44.1 42 0.00091 19.8 3.3 42 5-48 13-56 (200)
74 PF12183 NotI: Restriction end 44.1 3.5 7.5E-05 29.5 -1.7 54 2-64 22-78 (254)
75 TIGR02709 branched_ptb branche 43.9 99 0.0022 22.3 5.7 59 2-61 164-232 (271)
76 PF07315 DUF1462: Protein of u 43.6 8.5 0.00018 24.0 0.2 40 7-48 24-74 (93)
77 cd08427 PBP2_LTTR_like_2 The C 43.4 41 0.00088 19.8 3.2 42 5-48 13-56 (195)
78 cd02987 Phd_like_Phd Phosducin 43.2 20 0.00043 23.6 1.9 29 2-31 97-125 (175)
79 cd08441 PBP2_MetR The C-termin 43.1 42 0.00091 20.0 3.2 41 6-47 14-55 (198)
80 COG1653 UgpB ABC-type sugar tr 42.9 65 0.0014 22.1 4.5 47 5-51 46-97 (433)
81 cd08434 PBP2_GltC_like The sub 42.8 52 0.0011 19.2 3.6 41 6-47 14-55 (195)
82 cd08487 PBP2_BlaA The C-termin 42.7 16 0.00036 21.7 1.4 39 6-47 14-52 (189)
83 COG1744 Med Uncharacterized AB 42.6 18 0.00039 26.4 1.8 23 3-25 104-126 (345)
84 PRK12862 malic enzyme; Reviewe 42.5 69 0.0015 26.2 5.1 54 8-61 654-717 (763)
85 cd08451 PBP2_BudR The C-termin 42.2 46 0.001 19.7 3.3 42 6-48 15-57 (199)
86 cd08425 PBP2_CynR The C-termin 41.7 54 0.0012 19.5 3.6 41 6-47 15-56 (197)
87 PRK04168 molybdate ABC transpo 41.6 54 0.0012 23.7 4.1 44 6-49 45-90 (334)
88 COG2227 UbiG 2-polyprenyl-3-me 41.4 39 0.00084 24.2 3.3 24 28-51 111-134 (243)
89 cd08417 PBP2_Nitroaromatics_li 41.3 54 0.0012 19.4 3.5 41 6-48 14-56 (200)
90 PF13174 TPR_6: Tetratricopept 41.3 28 0.00061 15.5 1.8 13 8-20 20-32 (33)
91 cd08442 PBP2_YofA_SoxR_like Th 41.2 46 0.001 19.5 3.2 40 6-47 14-55 (193)
92 TIGR03401 cyanamide_fam HD dom 41.1 36 0.00078 23.6 3.0 34 9-42 176-209 (228)
93 PF04155 Ground-like: Ground-l 40.7 53 0.0012 18.7 3.3 13 39-51 40-52 (76)
94 cd08477 PBP2_CrgA_like_8 The C 40.4 27 0.0006 20.7 2.1 38 7-47 16-53 (197)
95 cd08415 PBP2_LysR_opines_like 40.1 48 0.001 19.5 3.1 40 6-47 14-55 (196)
96 cd08467 PBP2_SyrM The C-termin 40.0 42 0.00091 20.3 2.9 42 5-47 13-55 (200)
97 cd08418 PBP2_TdcA The C-termin 40.0 62 0.0013 19.1 3.6 41 6-47 14-55 (201)
98 cd08456 PBP2_LysR The C-termin 39.9 55 0.0012 19.3 3.4 42 5-47 13-55 (196)
99 cd08412 PBP2_PAO1_like The C-t 39.5 57 0.0012 19.2 3.4 40 6-47 14-55 (198)
100 cd08420 PBP2_CysL_like C-termi 39.4 53 0.0012 19.2 3.2 42 6-48 14-56 (201)
101 cd02973 TRX_GRX_like Thioredox 39.3 23 0.0005 18.7 1.5 28 2-30 13-40 (67)
102 cd06353 PBP1_BmpA_Med_like Per 39.1 27 0.00058 23.9 2.1 19 5-23 66-84 (258)
103 COG4989 Predicted oxidoreducta 38.7 50 0.0011 24.4 3.5 40 8-51 227-266 (298)
104 cd08422 PBP2_CrgA_like The C-t 38.2 31 0.00067 20.3 2.1 40 6-48 15-54 (197)
105 PRK00536 speE spermidine synth 38.1 35 0.00077 24.3 2.6 17 35-51 132-149 (262)
106 cd08431 PBP2_HupR The C-termin 38.1 43 0.00093 19.9 2.7 40 6-47 14-55 (195)
107 PF04255 DUF433: Protein of un 37.3 20 0.00044 19.4 1.1 16 10-25 33-48 (56)
108 PTZ00062 glutaredoxin; Provisi 36.5 28 0.00061 23.8 1.9 27 2-29 31-57 (204)
109 cd08447 PBP2_LTTR_aromatics_li 36.1 74 0.0016 18.8 3.5 40 6-47 14-55 (198)
110 cd02989 Phd_like_TxnDC9 Phosdu 36.1 24 0.00052 21.3 1.4 28 2-30 36-63 (113)
111 cd02988 Phd_like_VIAF Phosduci 35.9 38 0.00083 22.7 2.4 29 2-31 116-144 (192)
112 PF08242 Methyltransf_12: Meth 35.4 14 0.0003 21.0 0.2 15 40-54 65-79 (99)
113 PF01523 PmbA_TldD: Putative m 35.2 9.5 0.00021 26.0 -0.6 23 38-60 205-227 (293)
114 cd08458 PBP2_NocR The C-termin 35.0 83 0.0018 18.9 3.7 41 6-47 14-55 (196)
115 cd08461 PBP2_DntR_like_3 The C 34.9 44 0.00095 19.9 2.4 41 6-48 14-56 (198)
116 cd08421 PBP2_LTTR_like_1 The C 34.4 68 0.0015 19.0 3.2 41 6-47 14-55 (198)
117 TIGR03851 chitin_NgcE carbohyd 34.4 98 0.0021 22.3 4.5 42 7-48 56-100 (450)
118 cd08475 PBP2_CrgA_like_6 The C 34.0 54 0.0012 19.4 2.7 38 7-47 16-53 (199)
119 cd08414 PBP2_LTTR_aromatics_li 33.9 92 0.002 18.2 3.7 40 6-47 14-55 (197)
120 cd08440 PBP2_LTTR_like_4 TThe 33.9 79 0.0017 18.4 3.4 39 7-47 15-55 (197)
121 cd08324 CARD_NOD1_CARD4 Caspas 33.4 27 0.00059 21.4 1.3 21 2-22 61-81 (85)
122 cd08468 PBP2_Pa0477 The C-term 33.3 70 0.0015 19.3 3.1 41 5-47 13-55 (202)
123 PF09986 DUF2225: Uncharacteri 32.5 23 0.0005 24.2 1.0 14 37-50 41-54 (214)
124 TIGR03730 tungstate_WtpA tungs 32.5 86 0.0019 22.2 3.9 45 6-50 14-60 (273)
125 PRK11716 DNA-binding transcrip 32.4 82 0.0018 20.4 3.5 41 6-48 81-123 (269)
126 cd08433 PBP2_Nac The C-teminal 32.4 66 0.0014 19.1 2.9 40 7-47 15-55 (198)
127 PRK10721 hypothetical protein; 32.1 1E+02 0.0022 18.1 3.5 21 8-28 9-29 (66)
128 cd01483 E1_enzyme_family Super 31.5 40 0.00087 20.7 1.9 39 10-48 58-96 (143)
129 COG0800 Eda 2-keto-3-deoxy-6-p 31.5 1.4E+02 0.0031 20.9 4.7 49 5-55 49-99 (211)
130 PF06481 COX_ARM: COX Aromatic 31.4 40 0.00086 17.8 1.6 27 30-56 9-40 (47)
131 PRK12861 malic enzyme; Reviewe 30.9 1.2E+02 0.0027 25.0 4.9 57 8-64 655-721 (764)
132 cd03026 AhpF_NTD_C TRX-GRX-lik 30.9 53 0.0012 19.1 2.3 44 2-50 26-69 (89)
133 PRK11151 DNA-binding transcrip 29.9 85 0.0018 21.2 3.4 41 5-47 104-146 (305)
134 cd08429 PBP2_NhaR The C-termin 29.5 1E+02 0.0023 19.0 3.6 41 5-47 13-55 (204)
135 PRK12560 adenine phosphoribosy 29.4 88 0.0019 20.8 3.3 24 39-62 49-72 (187)
136 TIGR03339 phn_lysR aminoethylp 29.3 1.7E+02 0.0036 19.1 4.8 41 6-48 98-140 (279)
137 cd08457 PBP2_OccR The C-termin 29.2 88 0.0019 18.6 3.1 40 7-48 15-56 (196)
138 PRK10974 glycerol-3-phosphate 29.2 1.5E+02 0.0033 21.3 4.8 42 6-47 41-88 (438)
139 KOG0649|consensus 29.1 26 0.00056 26.0 0.8 22 31-54 13-34 (325)
140 KOG3812|consensus 29.0 52 0.0011 25.4 2.4 36 19-54 306-343 (475)
141 TIGR03261 phnS2 putative 2-ami 29.0 1.1E+02 0.0024 21.2 3.9 42 6-48 34-80 (334)
142 COG4635 HemG Flavodoxin [Energ 28.8 43 0.00092 23.1 1.7 40 8-49 15-56 (175)
143 cd08465 PBP2_ToxR The C-termin 28.5 1E+02 0.0022 18.7 3.3 40 6-47 14-55 (200)
144 PRK02277 orotate phosphoribosy 28.5 1.1E+02 0.0023 20.5 3.7 33 29-61 73-105 (200)
145 PRK07232 bifunctional malic en 28.5 1.4E+02 0.0031 24.5 4.9 57 8-64 646-712 (752)
146 cd08413 PBP2_CysB_like The C-t 28.2 1.1E+02 0.0023 18.5 3.4 41 7-48 15-56 (198)
147 TIGR02845 spore_V_AD stage V s 28.2 29 0.00063 25.8 0.9 15 36-50 216-230 (327)
148 COG0421 SpeE Spermidine syntha 27.8 77 0.0017 22.7 3.0 23 26-48 134-156 (282)
149 PRK08304 stage V sporulation p 27.7 30 0.00066 25.9 0.9 15 36-50 222-236 (337)
150 cd06297 PBP1_LacI_like_12 Liga 27.5 1.2E+02 0.0026 19.9 3.7 20 30-49 169-188 (269)
151 cd08419 PBP2_CbbR_RubisCO_like 27.4 1.1E+02 0.0024 17.9 3.2 39 7-47 14-54 (197)
152 PRK11482 putative DNA-binding 27.3 1.5E+02 0.0032 20.6 4.3 40 6-47 131-170 (317)
153 PRK11013 DNA-binding transcrip 27.2 1.2E+02 0.0026 20.7 3.8 42 6-48 108-150 (309)
154 cd03412 CbiK_N Anaerobic cobal 27.2 93 0.002 19.3 3.0 24 6-29 18-41 (127)
155 TIGR00477 tehB tellurite resis 27.1 52 0.0011 21.5 1.9 14 39-52 92-105 (195)
156 cd08426 PBP2_LTTR_like_5 The C 27.1 1E+02 0.0022 18.2 3.1 39 7-47 15-55 (199)
157 PRK12682 transcriptional regul 27.0 1.1E+02 0.0025 20.7 3.7 41 6-48 107-149 (309)
158 PRK10216 DNA-binding transcrip 27.0 85 0.0018 21.5 3.0 43 4-47 109-151 (319)
159 PF12847 Methyltransf_18: Meth 26.7 43 0.00092 19.0 1.3 38 8-49 38-78 (112)
160 cd08430 PBP2_IlvY The C-termin 26.3 1.1E+02 0.0024 17.9 3.1 39 8-48 16-56 (199)
161 PRK12404 stage V sporulation p 26.2 32 0.0007 25.7 0.8 15 36-50 220-234 (334)
162 PRK09791 putative DNA-binding 26.2 1.2E+02 0.0025 20.5 3.5 40 6-47 109-150 (302)
163 TIGR03807 RR_fam_repeat putati 26.1 34 0.00073 16.7 0.6 11 41-51 13-23 (27)
164 PRK10797 glutamate and asparta 26.0 1E+02 0.0022 21.5 3.3 42 6-47 69-112 (302)
165 PF06506 PrpR_N: Propionate ca 25.9 74 0.0016 20.6 2.5 44 14-57 2-50 (176)
166 PHA03058 Hypothetical protein; 25.8 1.3E+02 0.0029 19.5 3.6 32 9-40 44-87 (124)
167 cd08485 PBP2_ClcR The C-termin 25.6 1.6E+02 0.0035 17.7 4.6 40 7-48 16-57 (198)
168 PRK06934 flavodoxin; Provision 25.2 55 0.0012 22.8 1.8 21 34-54 122-144 (221)
169 PF13531 SBP_bac_11: Bacterial 25.2 58 0.0013 21.1 1.9 41 7-49 13-55 (230)
170 COG1412 Uncharacterized protei 24.8 1.3E+02 0.0029 19.5 3.5 37 10-49 69-105 (136)
171 COG3186 Phenylalanine-4-hydrox 24.8 40 0.00086 24.8 1.1 37 20-56 106-148 (291)
172 cd02985 TRX_CDSP32 TRX family, 24.8 44 0.00095 19.5 1.1 27 2-29 29-55 (103)
173 cd05568 PTS_IIB_bgl_like PTS_I 24.7 1.3E+02 0.0028 16.4 3.4 38 10-50 17-55 (85)
174 PRK15421 DNA-binding transcrip 24.6 1.3E+02 0.0027 20.9 3.6 43 5-49 102-146 (317)
175 cd08411 PBP2_OxyR The C-termin 24.5 1.6E+02 0.0035 17.4 4.5 38 8-47 17-56 (200)
176 cd03073 PDI_b'_ERp72_ERp57 PDI 24.5 54 0.0012 20.0 1.5 27 5-31 34-60 (111)
177 PRK08349 hypothetical protein; 24.5 1.3E+02 0.0028 19.7 3.4 17 2-18 88-104 (198)
178 TIGR00595 priA primosomal prot 24.4 1.3E+02 0.0028 23.1 3.9 43 8-51 272-322 (505)
179 cd08432 PBP2_GcdR_TrpI_HvrB_Am 24.4 54 0.0012 19.3 1.5 38 7-47 15-52 (194)
180 KOG3673|consensus 24.3 75 0.0016 26.2 2.6 39 23-62 236-278 (845)
181 KOG0230|consensus 23.8 34 0.00073 30.5 0.6 16 36-51 1426-1446(1598)
182 cd08481 PBP2_GcdR_like The C-t 23.7 63 0.0014 19.0 1.7 37 8-47 16-52 (194)
183 cd01840 SGNH_hydrolase_yrhL_li 23.4 84 0.0018 19.4 2.3 32 6-42 96-127 (150)
184 cd08443 PBP2_CysB The C-termin 23.2 1.3E+02 0.0028 18.1 3.1 38 8-47 16-55 (198)
185 COG0312 TldD Predicted Zn-depe 23.2 37 0.00081 25.2 0.7 21 39-59 226-246 (454)
186 PF05047 L51_S25_CI-B8: Mitoch 23.1 66 0.0014 16.7 1.5 23 4-26 2-24 (52)
187 PRK12680 transcriptional regul 23.1 1.3E+02 0.0029 21.0 3.4 42 5-48 106-149 (327)
188 cd08479 PBP2_CrgA_like_9 The C 23.0 89 0.0019 18.5 2.3 40 6-48 15-54 (198)
189 TIGR03412 iscX_yfhJ FeS assemb 23.0 1.7E+02 0.0036 17.0 3.4 35 8-43 6-40 (63)
190 PF07451 SpoVAD: Stage V sporu 22.8 36 0.00079 25.5 0.6 15 36-50 217-231 (329)
191 cd08488 PBP2_AmpR The C-termin 22.8 85 0.0018 18.7 2.2 39 6-47 14-52 (191)
192 smart00828 PKS_MT Methyltransf 22.5 35 0.00077 22.2 0.4 15 39-53 65-79 (224)
193 cd03710 BipA_TypA_C BipA_TypA_ 22.4 59 0.0013 18.3 1.3 20 41-60 5-24 (79)
194 cd02440 AdoMet_MTases S-adenos 22.3 89 0.0019 16.2 2.0 17 37-53 62-78 (107)
195 COG1383 RPS17A Ribosomal prote 22.3 51 0.0011 19.7 1.0 15 7-21 9-23 (74)
196 cd04098 eEF2_C_snRNP eEF2_C_sn 22.2 41 0.00088 19.2 0.6 20 41-60 5-24 (80)
197 PRK03601 transcriptional regul 22.2 1.5E+02 0.0033 19.8 3.5 41 7-49 104-146 (275)
198 cd08473 PBP2_CrgA_like_4 The C 22.1 94 0.002 18.3 2.2 38 7-47 18-55 (202)
199 cd06308 PBP1_sensor_kinase_lik 22.0 2.4E+02 0.0051 18.3 4.6 19 31-49 172-190 (270)
200 cd02954 DIM1 Dim1 family; Dim1 22.0 59 0.0013 20.3 1.4 28 2-30 28-56 (114)
201 PRK00455 pyrE orotate phosphor 21.9 1.8E+02 0.004 19.1 3.8 37 24-60 47-83 (202)
202 cd08471 PBP2_CrgA_like_2 The C 21.7 96 0.0021 18.3 2.2 39 6-47 15-53 (201)
203 cd08483 PBP2_HvrB The C-termin 21.6 90 0.002 18.3 2.1 39 6-47 14-52 (190)
204 PF06325 PrmA: Ribosomal prote 21.4 52 0.0011 23.8 1.1 22 40-62 224-245 (295)
205 cd05132 RasGAP_GAPA GAPA is an 21.4 1.1E+02 0.0023 22.2 2.8 41 5-45 149-196 (331)
206 PRK10682 putrescine transporte 21.3 1.1E+02 0.0025 21.6 2.9 42 9-51 44-88 (370)
207 KOG2765|consensus 21.3 56 0.0012 25.3 1.3 21 39-59 314-334 (416)
208 PRK10735 tldD protease TldD; P 21.3 80 0.0017 24.2 2.2 21 39-59 245-265 (481)
209 KOG4720|consensus 21.2 64 0.0014 24.6 1.6 19 1-19 167-185 (391)
210 PF10719 ComFB: Late competenc 21.0 1.7E+02 0.0038 16.8 3.2 32 11-42 13-45 (85)
211 cd08472 PBP2_CrgA_like_3 The C 21.0 1E+02 0.0023 18.2 2.3 39 6-47 15-53 (202)
212 cd06320 PBP1_allose_binding Pe 20.9 2.5E+02 0.0054 18.2 4.8 19 31-49 172-190 (275)
213 COG0280 Pta Phosphotransacetyl 20.9 2.6E+02 0.0057 20.8 4.7 60 5-64 215-285 (327)
214 PRK11074 putative DNA-binding 20.8 2.7E+02 0.0058 18.8 4.5 43 4-47 104-147 (300)
215 COG2264 PrmA Ribosomal protein 20.7 70 0.0015 23.4 1.7 20 40-60 228-247 (300)
216 PRK15408 autoinducer 2-binding 20.7 3.2E+02 0.0069 19.4 5.1 46 6-51 165-219 (336)
217 TIGR02174 CXXU_selWTH selT/sel 20.7 89 0.0019 17.6 1.8 31 9-46 17-47 (72)
218 cd08480 PBP2_CrgA_like_10 The 20.7 1E+02 0.0022 18.5 2.2 38 8-48 17-54 (198)
219 PRK01581 speE spermidine synth 20.6 1.3E+02 0.0028 22.8 3.1 22 26-48 212-233 (374)
220 PHA02096 hypothetical protein 20.5 57 0.0012 20.3 1.0 17 37-53 9-25 (103)
221 TIGR02424 TF_pcaQ pca operon t 20.4 1.7E+02 0.0037 19.5 3.5 43 4-47 105-148 (300)
222 COG0583 LysR Transcriptional r 20.3 2.6E+02 0.0056 18.1 4.7 40 7-48 107-146 (297)
223 PF01739 CheR: CheR methyltran 20.1 50 0.0011 22.3 0.8 15 37-51 132-146 (196)
224 PF01075 Glyco_transf_9: Glyco 20.1 71 0.0015 20.9 1.5 25 38-64 9-33 (247)
225 CHL00180 rbcR LysR transcripti 20.0 2E+02 0.0044 19.4 3.8 42 6-48 109-151 (305)
226 PTZ00051 thioredoxin; Provisio 20.0 1E+02 0.0022 17.1 2.0 27 2-29 32-58 (98)
227 cd06323 PBP1_ribose_binding Pe 20.0 2.5E+02 0.0054 17.9 5.0 19 32-50 172-190 (268)
No 1
>COG0473 LeuB Isocitrate/isopropylmalate dehydrogenase [Amino acid transport and metabolism]
Probab=99.96 E-value=1.6e-30 Score=189.34 Aligned_cols=62 Identities=39% Similarity=0.690 Sum_probs=60.8
Q ss_pred hchHHHHHHHHHhhCCCceechhhHHHHHHHHhhCCCCccEEecCCchHHHHHhhhhhccCC
Q psy9334 4 RFGYPNLGQTMAKLYPKIQFEQMIVDNCTMQIVSNPHQFDVMVMPNLYGNIVDNLASDIKGS 65 (65)
Q Consensus 4 ~~~f~~~~~eva~~ypdV~~~~~~vDa~~~~lv~~P~~fDVIV~~Nl~GDIlSD~aa~l~Gg 65 (65)
+.+|+++++|+|++||||+++|+|||+++||||++|++||||||+|||||||||+||+|+||
T Consensus 190 ~~lwrev~~eva~~yPdv~~~~~~VD~aam~lV~~P~~FDViVt~NlFGDILSD~aa~l~Gs 251 (348)
T COG0473 190 DGLWREVVEEVAKEYPDVELDHMYVDAAAMQLVRNPEQFDVIVTSNLFGDILSDEAAALTGS 251 (348)
T ss_pred hHHHHHHHHHHhhcCCCcchhHHhHHHHHHHHhhCccccCEEEEccchhHHHHhHHHHhcCc
Confidence 57999999999999999999999999999999999999999999999999999999999997
No 2
>PRK03437 3-isopropylmalate dehydrogenase; Provisional
Probab=99.96 E-value=1.2e-29 Score=184.38 Aligned_cols=63 Identities=30% Similarity=0.561 Sum_probs=61.5
Q ss_pred hhchHHHHHHHHHhhCCCceechhhHHHHHHHHhhCCCCccEEecCCchHHHHHhhhhhccCC
Q psy9334 3 CRFGYPNLGQTMAKLYPKIQFEQMIVDNCTMQIVSNPHQFDVMVMPNLYGNIVDNLASDIKGS 65 (65)
Q Consensus 3 ~~~~f~~~~~eva~~ypdV~~~~~~vDa~~~~lv~~P~~fDVIV~~Nl~GDIlSD~aa~l~Gg 65 (65)
.+.+|+++++|+|++||+|++++++||++||+||++|++||||||+|||||||||++|+++||
T Consensus 193 t~glf~~~~~eva~~ypdV~~~~~~vDa~~~~Lv~~P~~fDVIVt~NlfGDILSDlaa~l~Gg 255 (344)
T PRK03437 193 AGDLWQRTVDEVAAEYPDVTVDYQHVDAATIFMVTDPSRFDVIVTDNLFGDIITDLAAAVTGG 255 (344)
T ss_pred cchHHHHHHHHHHhhCCCceEeehhHHHHHHHHhcCcccCcEEEEcccchhhhhHHHHHhcCC
Confidence 467999999999999999999999999999999999999999999999999999999999997
No 3
>PLN02329 3-isopropylmalate dehydrogenase
Probab=99.96 E-value=8.2e-30 Score=188.67 Aligned_cols=64 Identities=34% Similarity=0.631 Sum_probs=62.0
Q ss_pred chhchHHHHHHHHHhhCCCceechhhHHHHHHHHhhCCCCccEEecCCchHHHHHhhhhhccCC
Q psy9334 2 PCRFGYPNLGQTMAKLYPKIQFEQMIVDNCTMQIVSNPHQFDVMVMPNLYGNIVDNLASDIKGS 65 (65)
Q Consensus 2 ~~~~~f~~~~~eva~~ypdV~~~~~~vDa~~~~lv~~P~~fDVIV~~Nl~GDIlSD~aa~l~Gg 65 (65)
..+.+|+++++|+|++||+|++++++||+++|+||+||++||||||+|||||||||++|+|+||
T Consensus 241 ~t~~lf~~~~~evA~eyPdV~~~~~~VDa~a~~LV~~P~~FDVIVt~NLfGDILSDlaa~l~Gg 304 (409)
T PLN02329 241 DASILWRKRVTALASEYPDVELSHMYVDNAAMQLIRDPKQFDTIVTNNIFGDILSDEASMITGS 304 (409)
T ss_pred cchHHHHHHHHHHHhhCCCcccchhHHHHHHHHHhcCchhCCEEEEcCcccccccHHHHHhcCC
Confidence 4567999999999999999999999999999999999999999999999999999999999997
No 4
>PRK08194 tartrate dehydrogenase; Provisional
Probab=99.96 E-value=1.7e-29 Score=184.00 Aligned_cols=63 Identities=30% Similarity=0.525 Sum_probs=61.6
Q ss_pred hhchHHHHHHHHHhhCCCceechhhHHHHHHHHhhCCCCccEEecCCchHHHHHhhhhhccCC
Q psy9334 3 CRFGYPNLGQTMAKLYPKIQFEQMIVDNCTMQIVSNPHQFDVMVMPNLYGNIVDNLASDIKGS 65 (65)
Q Consensus 3 ~~~~f~~~~~eva~~ypdV~~~~~~vDa~~~~lv~~P~~fDVIV~~Nl~GDIlSD~aa~l~Gg 65 (65)
.+.+|+++++|+|++||+|++++++||++||+||++|++||||||+|||||||||++|+++||
T Consensus 193 t~~lf~~~~~eva~~yp~V~~~~~~vDa~~~~Lv~~P~~fDVIVt~NlfGDILSDlaa~l~Gs 255 (352)
T PRK08194 193 SMPFWDEVFQEVGKDYPEIETDSQHIDALAAFFVTRPEEFDVIVASNLFGDILTDIGAAIMGS 255 (352)
T ss_pred hHHHHHHHHHHHHhhCCCceeeehhHHHHHHHHhhChhhCcEEEEccchHHHHhHHHHHhcCC
Confidence 568999999999999999999999999999999999999999999999999999999999997
No 5
>PLN00123 isocitrate dehydrogenase (NAD+)
Probab=99.96 E-value=2.3e-29 Score=183.96 Aligned_cols=62 Identities=52% Similarity=0.851 Sum_probs=60.6
Q ss_pred hchHHHHHHHHHhhCCCceechhhHHHHHHHHhhCCCCccEEecCCchHHHHHhhhhhccCC
Q psy9334 4 RFGYPNLGQTMAKLYPKIQFEQMIVDNCTMQIVSNPHQFDVMVMPNLYGNIVDNLASDIKGS 65 (65)
Q Consensus 4 ~~~f~~~~~eva~~ypdV~~~~~~vDa~~~~lv~~P~~fDVIV~~Nl~GDIlSD~aa~l~Gg 65 (65)
..+|+++++|+|++||+|++++++||++||+||++|++||||||+|||||||||++|+|+||
T Consensus 202 ~glf~~~~~eva~eyPdV~~~~~~VDa~~~~Lv~~P~~fDViVt~NlfGDILSDlaa~l~Gg 263 (360)
T PLN00123 202 DGLFLESCREVAKKYPGIKYNEIIVDNCCMQLVSKPEQFDVMVTPNLYGNLVANTAAGIAGG 263 (360)
T ss_pred hhHHHHHHHHHHhhCCCceEeeeeHHHHHHHHhhCcccCcEEEEcCcccchhhhHHHHhcCC
Confidence 46899999999999999999999999999999999999999999999999999999999997
No 6
>TIGR02089 TTC tartrate dehydrogenase. Tartrate dehydrogenase catalyzes the oxidation of both meso- and (+)-tartrate as well as a D-malate. These enzymes are closely related to the 3-isopropylmalate and isohomocitrate dehydrogenases found in TIGR00169 and TIGR02088, respectively.
Probab=99.95 E-value=2.4e-29 Score=183.07 Aligned_cols=63 Identities=27% Similarity=0.532 Sum_probs=61.5
Q ss_pred hhchHHHHHHHHHhhCCCceechhhHHHHHHHHhhCCCCccEEecCCchHHHHHhhhhhccCC
Q psy9334 3 CRFGYPNLGQTMAKLYPKIQFEQMIVDNCTMQIVSNPHQFDVMVMPNLYGNIVDNLASDIKGS 65 (65)
Q Consensus 3 ~~~~f~~~~~eva~~ypdV~~~~~~vDa~~~~lv~~P~~fDVIV~~Nl~GDIlSD~aa~l~Gg 65 (65)
.+.+|+++++|+|++||+|++++++||+++|+|+++|++||||||+|||||||||++|+++||
T Consensus 196 t~~lf~~~~~eva~~yp~v~~~~~~vD~~~~~lv~~P~~fDVivt~NlfGDILSD~aa~l~Gg 258 (352)
T TIGR02089 196 SMPFWDEVFAEVAAEYPDVEWDSYHIDALAARFVLKPETFDVIVASNLFGDILSDLGAALMGS 258 (352)
T ss_pred hhHHHHHHHHHHHhhCCCceEeeehHHHHHHHHhcChhhCcEEEecccchhhhhHHHHHhcCC
Confidence 567999999999999999999999999999999999999999999999999999999999997
No 7
>PRK08997 isocitrate dehydrogenase; Provisional
Probab=99.95 E-value=3.3e-29 Score=181.54 Aligned_cols=63 Identities=41% Similarity=0.722 Sum_probs=61.3
Q ss_pred hhchHHHHHHHHHhhCCCceechhhHHHHHHHHhhCCCCccEEecCCchHHHHHhhhhhccCC
Q psy9334 3 CRFGYPNLGQTMAKLYPKIQFEQMIVDNCTMQIVSNPHQFDVMVMPNLYGNIVDNLASDIKGS 65 (65)
Q Consensus 3 ~~~~f~~~~~eva~~ypdV~~~~~~vDa~~~~lv~~P~~fDVIV~~Nl~GDIlSD~aa~l~Gg 65 (65)
+..+|+++++|+|++||+|++++++||+++|+|+++|++||||||+|||||||||++|+++||
T Consensus 180 t~glf~~~~~eva~~yP~V~~~~~~vDa~~~~lv~~P~~fdVivt~NlfGDILSDlaa~l~Gg 242 (334)
T PRK08997 180 TSGLFLKVAREVALRYPDIEFEEMIVDATCMQLVMNPEQFDVIVTTNLFGDILSDLCAGLVGG 242 (334)
T ss_pred hhHHHHHHHHHHHhhCCCeEEEeeeHHHHHHHHhhCcccCcEEEEcCcccchhhHHHHHhcCC
Confidence 467999999999999999999999999999999999999999999999999999999999997
No 8
>PRK14025 multifunctional 3-isopropylmalate dehydrogenase/D-malate dehydrogenase; Provisional
Probab=99.95 E-value=5.9e-29 Score=179.98 Aligned_cols=63 Identities=33% Similarity=0.523 Sum_probs=61.2
Q ss_pred hhchHHHHHHHHHhhCCCceechhhHHHHHHHHhhCCCCccEEecCCchHHHHHhhhhhccCC
Q psy9334 3 CRFGYPNLGQTMAKLYPKIQFEQMIVDNCTMQIVSNPHQFDVMVMPNLYGNIVDNLASDIKGS 65 (65)
Q Consensus 3 ~~~~f~~~~~eva~~ypdV~~~~~~vDa~~~~lv~~P~~fDVIV~~Nl~GDIlSD~aa~l~Gg 65 (65)
...+|+++++|+|++||+|++++++||++||+|+++|++||||||+|||||||||++|+++||
T Consensus 177 t~glf~e~~~eva~~yp~i~~~~~~vDa~~~~lv~~P~~fDVivt~NlfGDILSDlaa~l~Gg 239 (330)
T PRK14025 177 TDGLFKKTFYEVAKEYPDIKAEDYYVDAMNMYIITRPQTFDVVVTSNLFGDILSDGAAGLVGG 239 (330)
T ss_pred hhHHHHHHHHHHHhhCCCeEEEeeeHHHHHHHHhcCcccCcEEEEcCcccchhhHHHHHhcCC
Confidence 457899999999999999999999999999999999999999999999999999999999997
No 9
>PLN00118 isocitrate dehydrogenase (NAD+)
Probab=99.95 E-value=8.3e-29 Score=181.59 Aligned_cols=63 Identities=41% Similarity=0.800 Sum_probs=61.2
Q ss_pred hhchHHHHHHHHHhhCCCceechhhHHHHHHHHhhCCCCccEEecCCchHHHHHhhhhhccCC
Q psy9334 3 CRFGYPNLGQTMAKLYPKIQFEQMIVDNCTMQIVSNPHQFDVMVMPNLYGNIVDNLASDIKGS 65 (65)
Q Consensus 3 ~~~~f~~~~~eva~~ypdV~~~~~~vDa~~~~lv~~P~~fDVIV~~Nl~GDIlSD~aa~l~Gg 65 (65)
...+|+++++|++++||+|++++++||++||+|+++|++||||||+|||||||||++|+++||
T Consensus 217 tdglf~e~~~eva~eyPdI~~~~~~VDa~a~~Lv~~P~~fDViVt~NLfGDILSDlaa~l~Gg 279 (372)
T PLN00118 217 TDGLFLKCCREVAEKYPEIVYEEVIIDNCCMMLVKNPALFDVLVMPNLYGDIISDLCAGLIGG 279 (372)
T ss_pred hhHHHHHHHHHHHhhCCCceEEeeeHHHHHHHhccCcccCcEEEEcCcccchhhHHHHHhcCC
Confidence 457899999999999999999999999999999999999999999999999999999999997
No 10
>TIGR00169 leuB 3-isopropylmalate dehydrogenase. This model will not find all isopropylmalate dehydrogenases; the enzyme from Sulfolobus sp. strain 7 is more similar to mitochondrial NAD-dependent isocitrate dehydrogenases than to other known isopropylmalate dehydrogenases and was omitted to improve the specificity of the model. It scores below the cutoff and below some enzymes known not to be isopropylmalate dehydrogenase.
Probab=99.95 E-value=1.1e-28 Score=179.51 Aligned_cols=64 Identities=38% Similarity=0.619 Sum_probs=61.6
Q ss_pred chhchHHHHHHHHHhhCCCceechhhHHHHHHHHhhCCCCccEEecCCchHHHHHhhhhhccCC
Q psy9334 2 PCRFGYPNLGQTMAKLYPKIQFEQMIVDNCTMQIVSNPHQFDVMVMPNLYGNIVDNLASDIKGS 65 (65)
Q Consensus 2 ~~~~~f~~~~~eva~~ypdV~~~~~~vDa~~~~lv~~P~~fDVIV~~Nl~GDIlSD~aa~l~Gg 65 (65)
....+|+++++|+|++||+|++++++||+++++|+++|++||||||+|||||||||++|+++||
T Consensus 193 kt~glf~~~~~eva~~yP~I~~~~~~vDa~~~~Lv~~P~~fDViv~~NlfGDILSDlaa~l~Gg 256 (349)
T TIGR00169 193 ESSRLWRKTVEEIAKEYPDVELEHQYIDNAAMQLVKSPTQFDVVVTGNIFGDILSDEASVIPGS 256 (349)
T ss_pred chhHHHHHHHHHHHhhCCCceEEeeeHHHHHHHHHhCccCceEEEEcCcccchhhHHHHHhcCC
Confidence 3457999999999999999999999999999999999999999999999999999999999997
No 11
>TIGR00175 mito_nad_idh isocitrate dehydrogenase, NAD-dependent, mitochondrial type. The NADP-dependent IDH of Thermus aquaticus thermophilus strain HB8 resembles these NAD-dependent IDH, except for the residues involved in cofactor specificity, much more closely than it resembles other prokaryotic NADP-dependent IDH, including that of Thermus aquaticus strain YT1.
Probab=99.95 E-value=1.4e-28 Score=177.91 Aligned_cols=63 Identities=56% Similarity=0.863 Sum_probs=61.0
Q ss_pred hhchHHHHHHHHHhhCCCceechhhHHHHHHHHhhCCCCccEEecCCchHHHHHhhhhhccCC
Q psy9334 3 CRFGYPNLGQTMAKLYPKIQFEQMIVDNCTMQIVSNPHQFDVMVMPNLYGNIVDNLASDIKGS 65 (65)
Q Consensus 3 ~~~~f~~~~~eva~~ypdV~~~~~~vDa~~~~lv~~P~~fDVIV~~Nl~GDIlSD~aa~l~Gg 65 (65)
...+|+++++|+|++||+|++++++||+++|+|+++|++||||||+|||||||||++|+++||
T Consensus 178 t~glf~~~~~eva~~yp~v~~~~~~vDa~~~~lv~~P~~fdViVt~NlfGDILSDlaa~l~Gs 240 (333)
T TIGR00175 178 ADGLFLNVCREVAKEYPDITFESMIVDNTCMQLVSRPSQFDVMVMPNLYGNILSNLGAGLVGG 240 (333)
T ss_pred hHHHHHHHHHHHHHHCCCCeeeeeeHHHHHHHHhcCcccccEEEEccccchhhhHHHHHhcCC
Confidence 356899999999999999999999999999999999999999999999999999999999997
No 12
>TIGR02088 LEU3_arch isopropylmalate/isohomocitrate dehydrogenases. This family is closely related to both the LeuB genes found in TIGR00169 and the mitochondrial eukaryotic isocitrate dehydratases found in TIGR00175. All of these are included within the broader subfamily model, pfam00180.
Probab=99.95 E-value=3.7e-28 Score=175.22 Aligned_cols=60 Identities=35% Similarity=0.692 Sum_probs=58.9
Q ss_pred chHHHHHHHHHhhCCCceechhhHHHHHHHHhhCCCCccEEecCCchHHHHHhhhhhccCC
Q psy9334 5 FGYPNLGQTMAKLYPKIQFEQMIVDNCTMQIVSNPHQFDVMVMPNLYGNIVDNLASDIKGS 65 (65)
Q Consensus 5 ~~f~~~~~eva~~ypdV~~~~~~vDa~~~~lv~~P~~fDVIV~~Nl~GDIlSD~aa~l~Gg 65 (65)
.+|+++++|+|++|| |++++++||++||+|+++|++||||||+|||||||||++|+++||
T Consensus 175 glf~~~~~eva~~yp-v~~~~~~vDa~~~~lv~~P~~fdViv~~NlfGDIlSDlaa~l~Gg 234 (322)
T TIGR02088 175 GLFREVCREIAKRYG-VEYRDMYVDSAAMNLVKDPWRFDVIVTTNMFGDILSDLASALAGS 234 (322)
T ss_pred HHHHHHHHHHHHhCC-eeeeeeeHHHHHHHHhhCCcCceEEEecCcccchhhHHHHhhcCC
Confidence 489999999999999 999999999999999999999999999999999999999999997
No 13
>PRK00772 3-isopropylmalate dehydrogenase; Provisional
Probab=99.94 E-value=5.6e-28 Score=176.30 Aligned_cols=64 Identities=39% Similarity=0.660 Sum_probs=61.9
Q ss_pred chhchHHHHHHHHHhhCCCceechhhHHHHHHHHhhCCCCccEEecCCchHHHHHhhhhhccCC
Q psy9334 2 PCRFGYPNLGQTMAKLYPKIQFEQMIVDNCTMQIVSNPHQFDVMVMPNLYGNIVDNLASDIKGS 65 (65)
Q Consensus 2 ~~~~~f~~~~~eva~~ypdV~~~~~~vDa~~~~lv~~P~~fDVIV~~Nl~GDIlSD~aa~l~Gg 65 (65)
....+|+++++|+|++||+|++++++||+++++|+++|++||||||+|||||||||++|+++||
T Consensus 196 ~~~glf~~~~~eva~eyp~i~~~~~~vDa~~~~lv~~P~~fDViv~~NlfGDIlSDlaa~l~Gg 259 (358)
T PRK00772 196 ESSRLWREVVTEVAKEYPDVELSHMYVDNAAMQLVRNPKQFDVIVTENLFGDILSDEAAMLTGS 259 (358)
T ss_pred ccchHHHHHHHHHHhHCCCceEEEEeHHHHHHHHhhCcccCeEEeecCcccccccHHHHHhcCC
Confidence 4567999999999999999999999999999999999999999999999999999999999997
No 14
>PRK09222 isocitrate dehydrogenase; Validated
Probab=99.94 E-value=6.8e-28 Score=181.24 Aligned_cols=63 Identities=40% Similarity=0.685 Sum_probs=61.1
Q ss_pred hhchHHHHHHHHHhhCCCceechhhHHHHHHHHhhCCCCccEEecCCchHHHHHhhhhhccCC
Q psy9334 3 CRFGYPNLGQTMAKLYPKIQFEQMIVDNCTMQIVSNPHQFDVMVMPNLYGNIVDNLASDIKGS 65 (65)
Q Consensus 3 ~~~~f~~~~~eva~~ypdV~~~~~~vDa~~~~lv~~P~~fDVIV~~Nl~GDIlSD~aa~l~Gg 65 (65)
...+|+++++|+|++||+|++++++||+++|+|+++|++||||||+|||||||||++|+++||
T Consensus 182 tdglf~~v~~eva~eyPdI~~~~~~VDa~a~~Lv~~P~~FDVIVt~NLfGDILSDlaa~l~Gs 244 (482)
T PRK09222 182 TDGLFHKVFDEIAKEYPDIEAEHYIVDIGAARLATNPENFDVIVTPNLYGDILSDIAAEISGS 244 (482)
T ss_pred cchHHHHHHHHHHhhCCCceEeeeeHHHHHHHHhcCcccceEEEEcccccchhhHHHHHhcCC
Confidence 456899999999999999999999999999999999999999999999999999999999997
No 15
>TIGR02924 ICDH_alpha isocitrate dehydrogenase. This family of mainly alphaproteobacterial enzymes is a member of the isocitrate/isopropylmalate dehydrogenase superfamily described by pfam00180. Every member of the seed of this model appears to have a TCA cycle lacking only a determined isocitrate dehydrogenase. The precise identity of the cofactor (NADH -- 1.1.1.41 vs. NADPH -- 1.1.1.42) is unclear.
Probab=99.94 E-value=1.5e-27 Score=179.05 Aligned_cols=62 Identities=39% Similarity=0.671 Sum_probs=60.6
Q ss_pred hchHHHHHHHHHhhCCCceechhhHHHHHHHHhhCCCCccEEecCCchHHHHHhhhhhccCC
Q psy9334 4 RFGYPNLGQTMAKLYPKIQFEQMIVDNCTMQIVSNPHQFDVMVMPNLYGNIVDNLASDIKGS 65 (65)
Q Consensus 4 ~~~f~~~~~eva~~ypdV~~~~~~vDa~~~~lv~~P~~fDVIV~~Nl~GDIlSD~aa~l~Gg 65 (65)
..+|+++++|+|++||+|++++++||+++|+|+++|++||||||+|||||||||++|+++||
T Consensus 179 dglf~e~~~eva~eyPdI~~e~~~VDa~a~~Lv~~P~~FDVIVt~NLfGDILSDlaA~l~Gs 240 (473)
T TIGR02924 179 DGIFHKIFDKIAAEYPDIESEHYIVDIGMARLATNPENFDVIVTPNLYGDILSDVAAEISGS 240 (473)
T ss_pred chhHHHHHHHHHhhCCCcEEeeHHHHHHHHHHhhCcccceEEEEccccchhhhHHHHHhcCC
Confidence 46899999999999999999999999999999999999999999999999999999999997
No 16
>PF00180 Iso_dh: Isocitrate/isopropylmalate dehydrogenase; InterPro: IPR024084 Isocitrate dehydrogenase (IDH) [, ] is an important enzyme of carbohydrate metabolism which catalyses the oxidative decarboxylation of isocitrate into alpha-ketoglutarate. IDH is either dependent on NAD+ (1.1.1.41 from EC) or on NADP+ (1.1.1.42 from EC). In eukaryotes there are at least three isozymes of IDH: two are located in the mitochondrial matrix (one NAD+-dependent, the other NADP+-dependent), while the third one (also NADP+-dependent) is cytoplasmic. In Escherichia coli the activity of a NADP+-dependent form of the enzyme is controlled by the phosphorylation of a serine residue; the phosphorylated form of IDH is completely inactivated. 3-isopropylmalate dehydrogenase (1.1.1.85 from EC) (IMDH) [, ] catalyses the third step in the biosynthesis of leucine in bacteria and fungi, the oxidative decarboxylation of 3-isopropylmalate into 2-oxo-4-methylvalerate. Tartrate dehydrogenase (1.1.1.93 from EC) [] catalyses the reduction of tartrate to oxaloglycolate. These enzymes are evolutionary related. To this family also belongs the enzyme tartrate dehydrogenase, which shows strong homology to prokaryotic isopropylmalate dehydrogenases and, to a lesser extent, isocitrate dehydrogenase []. This entry represents a structural domain found in all types of isocitrate dehydrogenase, and in isopropylmalate dehydrogenase and tartrate dehydrogenase. The crystal structure of Escherichia coli isopropylmalate dehydrogenase has been described []. ; GO: 0016616 oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor, 0055114 oxidation-reduction process; PDB: 1WAL_A 1CNZ_B 2D4V_C 1CM7_A 4AOY_D 3FMX_X 3FLK_C 1A05_A 1X0L_B 4F7I_D ....
Probab=99.94 E-value=1e-27 Score=173.39 Aligned_cols=65 Identities=43% Similarity=0.749 Sum_probs=61.9
Q ss_pred CchhchHHHHHHHHHh-hCCCceechhhHHHHHHHHhhCCCCccEEecCCchHHHHHhhhhhccCC
Q psy9334 1 MPCRFGYPNLGQTMAK-LYPKIQFEQMIVDNCTMQIVSNPHQFDVMVMPNLYGNIVDNLASDIKGS 65 (65)
Q Consensus 1 ~~~~~~f~~~~~eva~-~ypdV~~~~~~vDa~~~~lv~~P~~fDVIV~~Nl~GDIlSD~aa~l~Gg 65 (65)
|+.+.+|+++++|+++ +||+|++++++||+++++|+++|++||||||+|||||||||++++++||
T Consensus 190 l~~~~lf~~~~~eva~~~yp~I~~~~~~vD~~~~~Lv~~P~~fdViv~~Nl~GDIlSDl~a~l~G~ 255 (348)
T PF00180_consen 190 LKSTDLFREVFQEVAKQEYPDIEVEHMLVDAAAMQLVKNPEQFDVIVTPNLFGDILSDLAAGLVGG 255 (348)
T ss_dssp STTHHHHHHHHHHHHHHTHTTSEEEEEEHHHHHHHHHHSGGGESEEEEEHHHHHHHHHHHHHHHTS
T ss_pred hHHHHHHHHHHHHHHHhhcceeEeeeeechhhhheeecCCcceeEEeecchhHHHHHHHhhhcCCC
Confidence 3455699999999999 9999999999999999999999999999999999999999999999997
No 17
>PRK06451 isocitrate dehydrogenase; Validated
Probab=99.93 E-value=1.2e-26 Score=171.80 Aligned_cols=62 Identities=21% Similarity=0.450 Sum_probs=59.2
Q ss_pred hchHHHHHHHHHh-hCCC--------------------ceechhhHHHHHHHHhhCCCCccEEecCCchHHHHHhhhhhc
Q psy9334 4 RFGYPNLGQTMAK-LYPK--------------------IQFEQMIVDNCTMQIVSNPHQFDVMVMPNLYGNIVDNLASDI 62 (65)
Q Consensus 4 ~~~f~~~~~eva~-~ypd--------------------V~~~~~~vDa~~~~lv~~P~~fDVIV~~Nl~GDIlSD~aa~l 62 (65)
..+|+++++|+++ +||+ |++++++||++||+||++|++||||||+|||||||||++|++
T Consensus 230 ~glf~~~~~eva~~eypd~~~~~~~~~~~y~~~~~~~~I~~~~~~vDa~~~~Lv~~P~~FDVivt~NlfGDILSDlaa~l 309 (412)
T PRK06451 230 EGAFREWAYEVALKEFRDYVVTEEEVTKNYNGVPPSGKVIINDRIADNMFQQIIIRPDEYDIILAPNVNGDYISDAAGAL 309 (412)
T ss_pred hhhHHHHHHHHHHHhCCcccccccchhhccccccccCceEEEeeeHHHHHHHHhcCcccCcEEEEcCcccchhhHHHHHh
Confidence 4589999999997 7995 999999999999999999999999999999999999999999
Q ss_pred cCC
Q psy9334 63 KGS 65 (65)
Q Consensus 63 ~Gg 65 (65)
+||
T Consensus 310 ~Gg 312 (412)
T PRK06451 310 VGN 312 (412)
T ss_pred cCc
Confidence 997
No 18
>PRK07006 isocitrate dehydrogenase; Reviewed
Probab=99.93 E-value=2.1e-26 Score=170.40 Aligned_cols=62 Identities=23% Similarity=0.401 Sum_probs=58.8
Q ss_pred hchHHHHHHHHHh-hC-------------------CCceechhhHHHHHHHHhhCCCCccEEecCCchHHHHHhhhhhcc
Q psy9334 4 RFGYPNLGQTMAK-LY-------------------PKIQFEQMIVDNCTMQIVSNPHQFDVMVMPNLYGNIVDNLASDIK 63 (65)
Q Consensus 4 ~~~f~~~~~eva~-~y-------------------pdV~~~~~~vDa~~~~lv~~P~~fDVIV~~Nl~GDIlSD~aa~l~ 63 (65)
.-+|++++.|+|+ +| |+|++++++||++||+||++|++||||||+|||||||||++|+++
T Consensus 231 dglf~~~~~eva~~ey~~~~~~~~~~~~~~~~~~~p~v~~~~~~vDa~~~~lv~~P~~fDVIvt~NlfGDILSDlaa~l~ 310 (409)
T PRK07006 231 EGAFKDWGYQLAEEEFGDELIDGGPWDKIKNPETGKEIIVKDSIADAFLQQILLRPAEYDVIATMNLNGDYISDALAAQV 310 (409)
T ss_pred hHHHHHHHHHHHHHHhhhhhhccccccccccccCCCCceeehHHHHHHHHHHhhCcccCcEEEEcCcccchhhHHHHHhc
Confidence 4579998889998 68 899999999999999999999999999999999999999999999
Q ss_pred CC
Q psy9334 64 GS 65 (65)
Q Consensus 64 Gg 65 (65)
||
T Consensus 311 Gg 312 (409)
T PRK07006 311 GG 312 (409)
T ss_pred Cc
Confidence 97
No 19
>KOG0785|consensus
Probab=99.93 E-value=2.3e-26 Score=167.14 Aligned_cols=61 Identities=41% Similarity=0.798 Sum_probs=59.6
Q ss_pred chHHHHHHHHHhhCCCceechhhHHHHHHHHhhCCCCccEEecCCchHHHHHhhhhhccCC
Q psy9334 5 FGYPNLGQTMAKLYPKIQFEQMIVDNCTMQIVSNPHQFDVMVMPNLYGNIVDNLASDIKGS 65 (65)
Q Consensus 5 ~~f~~~~~eva~~ypdV~~~~~~vDa~~~~lv~~P~~fDVIV~~Nl~GDIlSD~aa~l~Gg 65 (65)
-+|+++|+|++++||||++|++|+|++|++|+++|..|||+|+||||||||||+||||+||
T Consensus 213 GLFle~cre~a~~y~dI~~eE~~lDt~~l~lv~~P~~~DVlV~PNLYGDIlSD~~agLvGg 273 (365)
T KOG0785|consen 213 GLFLECCREVAKKYPDIKFEEQYLDTCCLKLVRNPSCFDVLVMPNLYGDILSDLCAGLVGG 273 (365)
T ss_pred hHHHHHHHHHhhhCCccchhHHHHHHHHHHHhcCchhceEEeccchhHHHHHHHHHHhccC
Confidence 3799999999999999999999999999999999999999999999999999999999997
No 20
>TIGR00183 prok_nadp_idh isocitrate dehydrogenase, NADP-dependent, prokaryotic type. Prokaryotic NADP-dependent isocitrate dehydrogenases resemble their NAD-dependent counterparts and 3-isopropylmalate dehydrogenase (an NAD-dependent enzyme) more closely than they resemble eukaryotic NADP-dependent isocitrate dehydrogenases.
Probab=99.92 E-value=7.1e-26 Score=167.71 Aligned_cols=62 Identities=24% Similarity=0.440 Sum_probs=58.6
Q ss_pred hchHHHHHHHHHh-hC-------------------CCceechhhHHHHHHHHhhCCCCccEEecCCchHHHHHhhhhhcc
Q psy9334 4 RFGYPNLGQTMAK-LY-------------------PKIQFEQMIVDNCTMQIVSNPHQFDVMVMPNLYGNIVDNLASDIK 63 (65)
Q Consensus 4 ~~~f~~~~~eva~-~y-------------------pdV~~~~~~vDa~~~~lv~~P~~fDVIV~~Nl~GDIlSD~aa~l~ 63 (65)
..+|++++.|+|+ +| |+|++++++||+++|+||++|++||||||+|||||||||++|+++
T Consensus 238 dglf~e~~~eva~~ey~~~~~~~~lw~~~~~p~~~p~I~~~~~~vDa~~~~lv~~P~~fDVivt~NlfGDILSDlaa~l~ 317 (416)
T TIGR00183 238 EGAFRDWGYELAKKEFGAECITWGLWDKYKNPNPGKEIVIKDRIADAFLQQILTRPDEYDVIATMNLNGDYISDALAAQV 317 (416)
T ss_pred hhhHHHHHHHHHHHHHhHhhhhccccccccCcccCCceeEeehhHHHHHHHHhhCcccCcEEEEcCcccchhhHHHHHhc
Confidence 4579998889999 57 499999999999999999999999999999999999999999999
Q ss_pred CC
Q psy9334 64 GS 65 (65)
Q Consensus 64 Gg 65 (65)
||
T Consensus 318 Gs 319 (416)
T TIGR00183 318 GG 319 (416)
T ss_pred Cc
Confidence 97
No 21
>PRK08299 isocitrate dehydrogenase; Validated
Probab=99.91 E-value=5.4e-25 Score=162.81 Aligned_cols=61 Identities=15% Similarity=0.230 Sum_probs=58.5
Q ss_pred hchHHHHHHHHHh-hCC------CceechhhHHHHHHHHhhCCCCccEEecCCchHHHHHhhhhhccCC
Q psy9334 4 RFGYPNLGQTMAK-LYP------KIQFEQMIVDNCTMQIVSNPHQFDVMVMPNLYGNIVDNLASDIKGS 65 (65)
Q Consensus 4 ~~~f~~~~~eva~-~yp------dV~~~~~~vDa~~~~lv~~P~~fDVIV~~Nl~GDIlSD~aa~l~Gg 65 (65)
..+|+++++|+|+ +|| +|++++++||++||+||++|++| ||||+|||||||||++|+++||
T Consensus 218 ~glf~~~~~evA~~~yp~~~~~~~i~~~~~~vDa~~~~lv~~P~~f-Vivt~NlfGDIlSDlaa~l~Gg 285 (402)
T PRK08299 218 DGRFKDIFQEVYEAEFKEKFEAAGITYEHRLIDDMVASALKWEGGY-VWACKNYDGDVQSDTVAQGFGS 285 (402)
T ss_pred hHHHHHHHHHHHHHhCccccccCcEEEEEeeHHHHHHHHHhCcCCc-EEEEeccccchhhhHHHhhcCC
Confidence 4689999999995 899 59999999999999999999999 9999999999999999999998
No 22
>TIGR00127 nadp_idh_euk isocitrate dehydrogenase, NADP-dependent, eukaryotic type. This model does not discriminate cytosolic, mitochondrial, and chloroplast proteins. However, the model starts very near the amino end of the cytosolic form; the finding of additional amino-terminal sequence may indicate a transit peptide.
Probab=99.91 E-value=8e-25 Score=162.21 Aligned_cols=61 Identities=18% Similarity=0.297 Sum_probs=58.3
Q ss_pred hchHHHHHHHHH-hhCC------CceechhhHHHHHHHHhhCCCCccEEecCCchHHHHHhhhhhccCC
Q psy9334 4 RFGYPNLGQTMA-KLYP------KIQFEQMIVDNCTMQIVSNPHQFDVMVMPNLYGNIVDNLASDIKGS 65 (65)
Q Consensus 4 ~~~f~~~~~eva-~~yp------dV~~~~~~vDa~~~~lv~~P~~fDVIV~~Nl~GDIlSD~aa~l~Gg 65 (65)
..+|+++++|++ ++|| +|++++++||++||+||++|++| ||||+|||||||||++|+++||
T Consensus 219 dglf~~~~~eva~~eYp~~~~~~~I~~~~~lVDa~~m~lv~~P~~f-Viv~~NlfGDIlSDlaA~l~Gs 286 (409)
T TIGR00127 219 DGRFKDIFQEVYEAQYKSKFEALGIWYEHRLIDDMVAQALKSEGGF-IWACKNYDGDVQSDIVAQGFGS 286 (409)
T ss_pred hHHHHHHHHHHHHHhCcccccCCCEEEEEeeHHHHHHHHhhCCCCc-EEEecccchHHHHHHHHHhcCc
Confidence 357999999996 7999 89999999999999999999999 9999999999999999999997
No 23
>PTZ00435 isocitrate dehydrogenase; Provisional
Probab=99.90 E-value=1.1e-24 Score=161.62 Aligned_cols=61 Identities=18% Similarity=0.309 Sum_probs=58.6
Q ss_pred hchHHHHHHHHHh-hCC------CceechhhHHHHHHHHhhCCCCccEEecCCchHHHHHhhhhhccCC
Q psy9334 4 RFGYPNLGQTMAK-LYP------KIQFEQMIVDNCTMQIVSNPHQFDVMVMPNLYGNIVDNLASDIKGS 65 (65)
Q Consensus 4 ~~~f~~~~~eva~-~yp------dV~~~~~~vDa~~~~lv~~P~~fDVIV~~Nl~GDIlSD~aa~l~Gg 65 (65)
..+|+++++|+|+ +|| +|++++++||++||+||++|++| ||||+|||||||||++|+++||
T Consensus 221 dglf~~~~~eva~~eYpe~~~~~~I~~~~~lVDa~~m~lv~~P~~f-ViV~~NlfGDIlSDlaA~l~Gg 288 (413)
T PTZ00435 221 DGRFKDIFQEIYDEEYKAKFEKAGLWYEHRLIDDMVAQAIKSEGGF-VWACKNYDGDVQSDIVAQGYGS 288 (413)
T ss_pred HHHHHHHHHHHHHHhCccccccCCEEEEEeeHHHHHHHHhhCCCCe-EEEeecccchhhhHHHHHhcCc
Confidence 4689999999996 699 89999999999999999999999 9999999999999999999998
No 24
>PLN00103 isocitrate dehydrogenase (NADP+); Provisional
Probab=99.90 E-value=1.9e-24 Score=160.18 Aligned_cols=61 Identities=15% Similarity=0.245 Sum_probs=58.1
Q ss_pred hchHHHHHHHHHh-----hCC--CceechhhHHHHHHHHhhCCCCccEEecCCchHHHHHhhhhhccCC
Q psy9334 4 RFGYPNLGQTMAK-----LYP--KIQFEQMIVDNCTMQIVSNPHQFDVMVMPNLYGNIVDNLASDIKGS 65 (65)
Q Consensus 4 ~~~f~~~~~eva~-----~yp--dV~~~~~~vDa~~~~lv~~P~~fDVIV~~Nl~GDIlSD~aa~l~Gg 65 (65)
..+|+++++|+++ +|| +|++++++||++||+|+++|++| ||||+|||||||||++|+++||
T Consensus 222 dglf~~~~~eva~~~~~~eyp~~~I~~~~~lVDa~a~~lv~~P~~f-Viv~~NLfGDIlSDlaA~l~Gs 289 (410)
T PLN00103 222 DGRFKDIFQEVYEAQWKSKFEAAGIWYEHRLIDDMVAYALKSEGGY-VWACKNYDGDVQSDFLAQGFGS 289 (410)
T ss_pred HHHHHHHHHHHHHhhhhhhCCCCceEEEEeEHHHHHHHHhcCCCCC-EEEEcccchHHHHHHHHHhcCc
Confidence 3579999999996 799 79999999999999999999999 9999999999999999999998
No 25
>PRK07362 isocitrate dehydrogenase; Validated
Probab=99.90 E-value=1.8e-24 Score=162.39 Aligned_cols=46 Identities=26% Similarity=0.507 Sum_probs=44.4
Q ss_pred CceechhhHHHHHHHHhhCCCCccEEecCCchHHHHHhhhhhccCC
Q psy9334 20 KIQFEQMIVDNCTMQIVSNPHQFDVMVMPNLYGNIVDNLASDIKGS 65 (65)
Q Consensus 20 dV~~~~~~vDa~~~~lv~~P~~fDVIV~~Nl~GDIlSD~aa~l~Gg 65 (65)
+|+++++++|+++|||+++|++||||||+|||||||||++|+|+||
T Consensus 331 ~v~~~~~~vDa~a~~lv~~P~~FDVIVt~NLfGDILSDlaA~lvGg 376 (474)
T PRK07362 331 KVLVDDRIADSIFQQIQTRPQEYSILATLNLNGDYISDAAAAIVGG 376 (474)
T ss_pred cceeehHHHHHHHHHHHhChhhCCEEEEccccchhhhHHHHHhcCC
Confidence 4778999999999999999999999999999999999999999998
No 26
>KOG0784|consensus
Probab=99.88 E-value=1.5e-23 Score=153.41 Aligned_cols=60 Identities=58% Similarity=0.939 Sum_probs=59.1
Q ss_pred hHHHHHHHHHhhCCCceechhhHHHHHHHHhhCCCCccEEecCCchHHHHHhhhhhccCC
Q psy9334 6 GYPNLGQTMAKLYPKIQFEQMIVDNCTMQIVSNPHQFDVMVMPNLYGNIVDNLASDIKGS 65 (65)
Q Consensus 6 ~f~~~~~eva~~ypdV~~~~~~vDa~~~~lv~~P~~fDVIV~~Nl~GDIlSD~aa~l~Gg 65 (65)
+|+++|+|+|+.||+|++|.++||++||||+++|++|||+|+|||||.|||++||||+||
T Consensus 220 lFle~~~eva~~Yp~I~~e~miVDN~~MQlvs~P~qFDvmv~pnlYgniisNiaaGlvGG 279 (375)
T KOG0784|consen 220 LFLESCQEVAKKYPDITFEEMIVDNACMQLVSRPQQFDVMVMPNLYGNIISNIAAGLVGG 279 (375)
T ss_pred hHHHHHHHHHhcCCCccHHHhhHHHhHHHhhcCchheeeEechHHHHHHHHHHHHHhcCC
Confidence 799999999999999999999999999999999999999999999999999999999997
No 27
>PLN00096 isocitrate dehydrogenase (NADP+); Provisional
Probab=99.88 E-value=2.9e-23 Score=153.32 Aligned_cols=60 Identities=13% Similarity=0.141 Sum_probs=56.0
Q ss_pred chHHHHHHHHH-hhC-----------CCceechhhHHHHHHHHhhCCCCccEEecCCchHHHHHhhhhhccCC
Q psy9334 5 FGYPNLGQTMA-KLY-----------PKIQFEQMIVDNCTMQIVSNPHQFDVMVMPNLYGNIVDNLASDIKGS 65 (65)
Q Consensus 5 ~~f~~~~~eva-~~y-----------pdV~~~~~~vDa~~~~lv~~P~~fDVIV~~Nl~GDIlSD~aa~l~Gg 65 (65)
.+|+ +++|++ ++| |+|+++|++||+++|+||++|++||||||+|||||||||++|+++||
T Consensus 210 g~f~-if~eVa~~eyk~~f~~~~~~~p~V~~e~~lIDa~~~qlVk~P~~fdViv~~NlfGDIlSDlaA~l~Gs 281 (393)
T PLN00096 210 PFWE-IMKKVFDEEFKSKFVDKGVMKSGDELVHLLSDAATMKLVVWTDGGFGMAAHNYDGDVLTDELAQVHKS 281 (393)
T ss_pred HHHH-HHHHHHHHHHhhhhhhcccCCCceEEEeeeHHHHHHHHHhCcccCCEEEECcccchHHHHHHHHhcCC
Confidence 4676 888887 777 77999999999999999999999999999999999999999999997
No 28
>PLN03065 isocitrate dehydrogenase (NADP+); Provisional
Probab=99.86 E-value=3.6e-22 Score=150.44 Aligned_cols=60 Identities=18% Similarity=0.279 Sum_probs=56.9
Q ss_pred chHHHHHHHHH-----hhCC--CceechhhHHHHHHHHhhCCCCccEEecCCchHHHHHhhhhhccCC
Q psy9334 5 FGYPNLGQTMA-----KLYP--KIQFEQMIVDNCTMQIVSNPHQFDVMVMPNLYGNIVDNLASDIKGS 65 (65)
Q Consensus 5 ~~f~~~~~eva-----~~yp--dV~~~~~~vDa~~~~lv~~P~~fDVIV~~Nl~GDIlSD~aa~l~Gg 65 (65)
-+|+++++|++ ++|| +|+++|++||+++|+|+++|++| |+||+|+||||+||++|+++||
T Consensus 290 GlF~dif~eVa~~eyk~~yp~~~I~~e~~lIDa~~~~lvk~P~~F-Viv~~NlfGDIlSDl~A~l~Gs 356 (483)
T PLN03065 290 GRFKDIFQEVYEEQWKQKFEEHSIWYEHRLIDDMVAYAVKSEGGY-VWACKNYDGDVQSDLLAQGFGS 356 (483)
T ss_pred HHHHHHHHHHHHHhhhhcCCCCCceEEeeeHHHHHHHHHhCCCCc-EEEeeccchhhhhHHHHHhcCc
Confidence 47999999998 4599 69999999999999999999999 9999999999999999999997
No 29
>KOG0786|consensus
Probab=99.85 E-value=4.1e-22 Score=143.42 Aligned_cols=63 Identities=27% Similarity=0.552 Sum_probs=59.4
Q ss_pred hhchHHHHHH-HHHhhCCCceechhhHHHHHHHHhhCCCCcc-EEecCCchHHHHHhhhhhccCC
Q psy9334 3 CRFGYPNLGQ-TMAKLYPKIQFEQMIVDNCTMQIVSNPHQFD-VMVMPNLYGNIVDNLASDIKGS 65 (65)
Q Consensus 3 ~~~~f~~~~~-eva~~ypdV~~~~~~vDa~~~~lv~~P~~fD-VIV~~Nl~GDIlSD~aa~l~Gg 65 (65)
.|++||+.+. .++.|||++++.||+||+++|+||++|++|| +|||.|+|||||||.++.+.||
T Consensus 196 aSrLWRKtV~~~~k~EyP~l~l~hqliDsAAM~Lvk~P~~lng~ivT~NiFGDIiSDEASvIpGS 260 (363)
T KOG0786|consen 196 ASRLWRKTVTKALKSEYPDLELSHQLIDSAAMQLVKDPKQLNGTIVTNNIFGDIISDEASVIPGS 260 (363)
T ss_pred HHHHHHHHHHHHHHhhCCCcchhhhhhhHHHHHHhcCchhcCceEEeccchhhhhccccccccCc
Confidence 4789999887 4588999999999999999999999999999 9999999999999999999986
No 30
>COG0538 Icd Isocitrate dehydrogenases [Energy production and conversion]
Probab=99.52 E-value=1.6e-14 Score=107.18 Aligned_cols=60 Identities=23% Similarity=0.426 Sum_probs=55.4
Q ss_pred hHHHHHHHHHhhC---------------CC----ceechhhHHHHHHHHhhCCCCccEEecCCchHHHHHhhhhhccCC
Q psy9334 6 GYPNLGQTMAKLY---------------PK----IQFEQMIVDNCTMQIVSNPHQFDVMVMPNLYGNIVDNLASDIKGS 65 (65)
Q Consensus 6 ~f~~~~~eva~~y---------------pd----V~~~~~~vDa~~~~lv~~P~~fDVIV~~Nl~GDIlSD~aa~l~Gg 65 (65)
.|++++.|+|+++ .+ |.++++++|+|.+|++++|..||||.|.|+.||++||.+|+.+||
T Consensus 230 aFkdw~yeva~~~ef~~~~~~~~~~~~~~~~~gkI~~~driaD~mlqQil~r~~eydViA~~NlnGDy~SDa~Aa~vGg 308 (407)
T COG0538 230 AFKDWGYEVAEEEEFGDEVVTGKEKFELKGPKGKIVYKDRIADDMLQQILLRPGEYDVIATKNLNGDYISDALAAQVGG 308 (407)
T ss_pred hHHHHHHHHHhhhcccccccccchhhhccCcCceEEEehhhHHHHHHHHhcCCCCceEEEeccCCccHHHHHHHHhcCC
Confidence 5899999998863 13 999999999999999999999999999999999999999999997
No 31
>KOG1526|consensus
Probab=97.23 E-value=0.00042 Score=51.69 Aligned_cols=58 Identities=22% Similarity=0.383 Sum_probs=49.9
Q ss_pred HHHHHHHHH-hhCC------CceechhhHHHHHHHHhhCCCCccEEecCCchHHHHHhhhhhccCC
Q psy9334 7 YPNLGQTMA-KLYP------KIQFEQMIVDNCTMQIVSNPHQFDVMVMPNLYGNIVDNLASDIKGS 65 (65)
Q Consensus 7 f~~~~~eva-~~yp------dV~~~~~~vDa~~~~lv~~P~~fDVIV~~Nl~GDIlSD~aa~l~Gg 65 (65)
|+++++|+- ++|. .|-+||++||.|.++.++.-..| |..+-|--||+-||..|+=-||
T Consensus 233 FKdiFqeiye~~yk~kfe~~~IwYEHRLIDDmVAqa~KS~GGf-vwAcKNYDGDVqSD~vAQg~GS 297 (422)
T KOG1526|consen 233 FKDIFQEIYEKQYKSKFEALGIWYEHRLIDDMVAQAMKSEGGF-VWACKNYDGDVQSDIVAQGYGS 297 (422)
T ss_pred HHHHHHHHHHHHHHHHHHhhcchhhhhhHHHHHHHHHhcCCce-EEEeecCCCchhhhHHHhcccc
Confidence 677777773 3343 69999999999999999999999 9999999999999999876665
No 32
>TIGR00651 pta phosphate acetyltransferase. Model contains a gene from E.coli coding for ethanolamine utilization protein (euti) and also contains similarity to malate oxidoreductases
Probab=76.06 E-value=7.7 Score=28.00 Aligned_cols=56 Identities=18% Similarity=0.313 Sum_probs=34.0
Q ss_pred HHHHHHHHhhCCCceech-hhHHHHHHHHhh------C--CCCccEEecCCch-HHHHHhhhhhcc
Q psy9334 8 PNLGQTMAKLYPKIQFEQ-MIVDNCTMQIVS------N--PHQFDVMVMPNLY-GNIVDNLASDIK 63 (65)
Q Consensus 8 ~~~~~eva~~ypdV~~~~-~~vDa~~~~lv~------~--P~~fDVIV~~Nl~-GDIlSD~aa~l~ 63 (65)
++.++-+.+++|++.++- +-+|++.-.=+. . -++-||+|+||++ |+|+--+.-.+.
T Consensus 202 ~eA~~l~~~~~~~~~vdG~l~~D~Al~~~~a~~K~~~s~v~G~AdvLV~Pnl~aGNi~~K~~~~~~ 267 (303)
T TIGR00651 202 REATRIAKEKRPDLTIDGELQFDAAFVEKVAEKKAPNSPVAGSANVFVFPDLDAGNIGYKIVQRLG 267 (303)
T ss_pred HHHHHHHhccCCCeEEEecCchhhhCCHHHHHhhCCCCccCCcCCEEEeCCchHHHHHHHHHHHhc
Confidence 444444444688876653 344766533111 1 3567999999999 888766554443
No 33
>cd01846 fatty_acyltransferase_like Fatty acyltransferase-like subfamily of the SGNH hydrolases, 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. Might catalyze fatty acid transfer between phosphatidylcholine and sterols.
Probab=72.04 E-value=4.6 Score=27.17 Aligned_cols=37 Identities=11% Similarity=0.148 Sum_probs=30.7
Q ss_pred HHHHHHHHhhCCCceechhhHHHHHHHHhhCCCCccE
Q psy9334 8 PNLGQTMAKLYPKIQFEQMIVDNCTMQIVSNPHQFDV 44 (65)
Q Consensus 8 ~~~~~eva~~ypdV~~~~~~vDa~~~~lv~~P~~fDV 44 (65)
++.+++++++||+.++...-+.++...++.+|..|..
T Consensus 185 ~~~l~~l~~~~~~~~i~~~D~~~~~~~~~~~p~~yGf 221 (270)
T cd01846 185 AEKLAELKAQHPGVNILLFDTNALFNDILDNPAAYGF 221 (270)
T ss_pred HHHHHHHHHhCCCCeEEEEEhHHHHHHHHhCHHhcCC
Confidence 4556677778999988888888999999999998863
No 34
>PF08883 DOPA_dioxygen: Dopa 4,5-dioxygenase family; InterPro: IPR014980 This family of proteins is related to P87064 from SWISSPROT a DOPA 4,5-dioxygenase that is involved in synthesis of betalain. DOPA-dioxygenase is the key enzyme involved in betalain biosynthesis. It converts 3,4-dihydroxyphenylalanine to betalamic acid, a yellow chromophore. ; PDB: 2NYH_A 2P8I_C.
Probab=68.23 E-value=10 Score=23.77 Aligned_cols=37 Identities=16% Similarity=0.319 Sum_probs=26.8
Q ss_pred CceechhhHHHHHHHHhhCCCCccEEecCCchHHHHHh
Q psy9334 20 KIQFEQMIVDNCTMQIVSNPHQFDVMVMPNLYGNIVDN 57 (65)
Q Consensus 20 dV~~~~~~vDa~~~~lv~~P~~fDVIV~~Nl~GDIlSD 57 (65)
+|.+.....+...-+|..|-+.++|+|-||- ||=+.|
T Consensus 49 ev~f~~~~f~~~v~Wl~~nrg~LsVLiHP~T-g~dl~D 85 (104)
T PF08883_consen 49 EVDFPPEQFAEVVPWLMLNRGGLSVLIHPNT-GDDLRD 85 (104)
T ss_dssp EEEE-HHHHHHHHHHHHHH-TT--EEEEEES-S-HHHH
T ss_pred EEEcCHHHHHHHHHHHHHhCCCceEEEcCCC-Cchhhh
Confidence 3677778889999999999999999999998 665555
No 35
>KOG0907|consensus
Probab=67.54 E-value=3.2 Score=25.59 Aligned_cols=43 Identities=30% Similarity=0.592 Sum_probs=29.2
Q ss_pred chhchHHHHHHHHHhhCCCceechhhHHHHHHHHhhCCCCccEEecCC
Q psy9334 2 PCRFGYPNLGQTMAKLYPKIQFEQMIVDNCTMQIVSNPHQFDVMVMPN 49 (65)
Q Consensus 2 ~~~~~f~~~~~eva~~ypdV~~~~~~vDa~~~~lv~~P~~fDVIV~~N 49 (65)
||+.+.- ...++|++||++.+=..-+|. +..+.. .|.|-.+|.
T Consensus 35 PCk~i~P-~~~~La~~y~~v~Flkvdvde-~~~~~~---~~~V~~~PT 77 (106)
T KOG0907|consen 35 PCKAIAP-KFEKLAEKYPDVVFLKVDVDE-LEEVAK---EFNVKAMPT 77 (106)
T ss_pred chhhhhh-HHHHHHHHCCCCEEEEEeccc-CHhHHH---hcCceEeeE
Confidence 7877766 566899999998888888887 433332 344555544
No 36
>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=66.57 E-value=11 Score=22.49 Aligned_cols=42 Identities=14% Similarity=0.136 Sum_probs=26.5
Q ss_pred chHHHHHHHHHhhCCCceechhhHHH-HHHHHhhCCCCccEEec
Q psy9334 5 FGYPNLGQTMAKLYPKIQFEQMIVDN-CTMQIVSNPHQFDVMVM 47 (65)
Q Consensus 5 ~~f~~~~~eva~~ypdV~~~~~~vDa-~~~~lv~~P~~fDVIV~ 47 (65)
..+-+...+..++||+++++-..... -..+.+.+ +++|+.++
T Consensus 13 ~~l~~~l~~~~~~~P~i~l~i~~~~~~~~~~~l~~-~~~Dl~i~ 55 (196)
T cd08450 13 QWLPEVLPILREEHPDLDVELSSLFSPQLAEALMR-GKLDVAFM 55 (196)
T ss_pred hhHHHHHHHHHhhCCCcEEEEEecChHHHHHHHhc-CCccEEEE
Confidence 34567888889999998887654322 22233333 57787664
No 37
>cd01837 SGNH_plant_lipase_like SGNH_plant_lipase_like, a plant specific subfamily of the SGNH-family of hydrolases, 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=65.98 E-value=8.2 Score=26.94 Aligned_cols=37 Identities=16% Similarity=0.345 Sum_probs=28.7
Q ss_pred HHHHHHHHhhCCCceechhhHHHHHHHHhhCCCCccE
Q psy9334 8 PNLGQTMAKLYPKIQFEQMIVDNCTMQIVSNPHQFDV 44 (65)
Q Consensus 8 ~~~~~eva~~ypdV~~~~~~vDa~~~~lv~~P~~fDV 44 (65)
++..++++++||++++-..-+-++...++.||.+|..
T Consensus 222 ~~~l~~l~~~~~~~~i~~~D~y~~~~~i~~np~~yGf 258 (315)
T cd01837 222 KKLLAELRRELPGAKFVYADIYNALLDLIQNPAKYGF 258 (315)
T ss_pred HHHHHHHHhcCCCcEEEEEehhHHHHHHHhChhhcCC
Confidence 3455666778899887766666888999999998863
No 38
>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=64.50 E-value=14 Score=21.30 Aligned_cols=42 Identities=12% Similarity=0.256 Sum_probs=26.5
Q ss_pred hHHHHHHHHHhhCCCceechhhHHH-HHHHHhhCCCCccEEecC
Q psy9334 6 GYPNLGQTMAKLYPKIQFEQMIVDN-CTMQIVSNPHQFDVMVMP 48 (65)
Q Consensus 6 ~f~~~~~eva~~ypdV~~~~~~vDa-~~~~lv~~P~~fDVIV~~ 48 (65)
.+.+...+..++||+++++-...+. -..+.+.+ ++.|+.++.
T Consensus 14 ~l~~~i~~~~~~~p~i~i~~~~~~~~~~~~~l~~-g~~D~~i~~ 56 (197)
T cd05466 14 LLPPLLAAFRQRYPGVELSLVEGGSSELLEALLE-GELDLAIVA 56 (197)
T ss_pred HhHHHHHHHHHHCCCCEEEEEECChHHHHHHHHc-CCceEEEEc
Confidence 4456777888899998888665433 12233333 458877764
No 39
>TIGR01256 modA molybdenum ABC transporter, periplasmic molybdate-binding protein. The model describes the molybdate ABC transporter periplasmic binding protein in bacteria and archae. Several of the periplasmic receptors constitute a diverse class of binding proteins that differ widely in size, sequence and ligand specificity. It has been shown experimentally by radioactive labeling that ModA represent hydrophylioc periplasmic-binding protein in gram-negative organisms and its counterpart in gram-positive organisms is a lipoprotein. The other components of the system include the ModB, an integral membrane protein and ModC the ATP-binding subunit. Invariably almost all of them display a common beta/alpha folding motif and have similar tertiary structures consisting of two globular domains.
Probab=63.34 E-value=21 Score=23.07 Aligned_cols=43 Identities=9% Similarity=0.053 Sum_probs=26.3
Q ss_pred hHHHHHHHHHhhCCCceechhh--HHHHHHHHhhCCCCccEEecCCc
Q psy9334 6 GYPNLGQTMAKLYPKIQFEQMI--VDNCTMQIVSNPHQFDVMVMPNL 50 (65)
Q Consensus 6 ~f~~~~~eva~~ypdV~~~~~~--vDa~~~~lv~~P~~fDVIV~~Nl 50 (65)
.+.++..+..+++| ++++..+ -..+..++..+|. .||+++.+.
T Consensus 7 ~~~~~~~~f~~~~g-i~V~~~~~gs~~l~~~l~~~~~-aDv~~~~~~ 51 (216)
T TIGR01256 7 ALKEIAKQFEKRTG-NKVVFSFGSSGTLYTQIENGAP-ADLFISADN 51 (216)
T ss_pred HHHHHHHHHHHhhC-CeEEEEeCChHHHHHHHHcCCC-CcEEEECCH
Confidence 34555666666666 6665543 3345566666554 999998763
No 40
>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=63.00 E-value=19 Score=21.81 Aligned_cols=43 Identities=12% Similarity=0.088 Sum_probs=27.7
Q ss_pred hchHHHHHHHHHhhCCCceechhhHHHHHHHHhhCCCCccEEec
Q psy9334 4 RFGYPNLGQTMAKLYPKIQFEQMIVDNCTMQIVSNPHQFDVMVM 47 (65)
Q Consensus 4 ~~~f~~~~~eva~~ypdV~~~~~~vDa~~~~lv~~P~~fDVIV~ 47 (65)
....-+...+..++||+++++-..-..-..+.+.+ ++.|+.+.
T Consensus 12 ~~~l~~~l~~~~~~~P~v~v~l~~~~~~~~~~l~~-g~~D~~i~ 54 (200)
T cd08460 12 AAFGPALLAAVAAEAPGVRLRFVPESDKDVDALRE-GRIDLEIG 54 (200)
T ss_pred HHHHHHHHHHHHHHCCCCEEEEecCchhHHHHHHC-CCccEEEe
Confidence 33455778888999999887765322233444444 68887775
No 41
>PF08601 PAP1: Transcription factor PAP1; InterPro: IPR013910 The transcription factor Pap1 regulates antioxidant-gene transcription in response to H2O2 []. This region is cysteine rich. Alkylation of cysteine residues following treatment with a cysteine alkylating agent can mask the accessibility of the nuclear exporter Crm1, triggering nuclear accumulation and Pap1 dependent transcriptional expression []. ; PDB: 1SSE_B.
Probab=61.08 E-value=6.2 Score=29.26 Aligned_cols=47 Identities=15% Similarity=0.224 Sum_probs=27.1
Q ss_pred CchhchHHHHHHHHHhhCCCceechhhHHHHHHHHhhCCCCcc--EEecCCchHHH
Q psy9334 1 MPCRFGYPNLGQTMAKLYPKIQFEQMIVDNCTMQIVSNPHQFD--VMVMPNLYGNI 54 (65)
Q Consensus 1 ~~~~~~f~~~~~eva~~ypdV~~~~~~vDa~~~~lv~~P~~fD--VIV~~Nl~GDI 54 (65)
|-|+.+|+++-. +|.. .+.-||.+|.+|.++-+.=+ |||-+-=+-+|
T Consensus 295 l~Cs~Iw~~i~~-----~p~~--~~~did~lc~el~~kakcs~~g~vv~~~dv~~~ 343 (347)
T PF08601_consen 295 LKCSEIWDRIQS-----HPKF--GEIDIDGLCSELKKKAKCSESGVVVDEKDVQKI 343 (347)
T ss_dssp E-HHHHHHHHHT------S----SS--HHHHHHHHTTT--EETTEE-EEHHHHHHH
T ss_pred ccHHHHHHHHHh-----CCcc--cccchHHHHHHHHHhCccCCCCceecHHHHHHH
Confidence 469999997753 4654 78889999999998866433 66654433333
No 42
>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=60.29 E-value=19 Score=23.49 Aligned_cols=42 Identities=21% Similarity=0.364 Sum_probs=27.6
Q ss_pred hHHHHH-HHHHhhCCCceechhhH--HHHH----HHHhhCCCCccEEec
Q psy9334 6 GYPNLG-QTMAKLYPKIQFEQMIV--DNCT----MQIVSNPHQFDVMVM 47 (65)
Q Consensus 6 ~f~~~~-~eva~~ypdV~~~~~~v--Da~~----~~lv~~P~~fDVIV~ 47 (65)
.|.+.+ ++..+++|+|+++...+ +... ..+...-.-+||+.+
T Consensus 9 ~~~~~~~~~f~k~~~~i~V~~~~~~~~~~~~~~~~~~~sg~~p~Dv~~~ 57 (315)
T PF01547_consen 9 ALQELIIEEFEKEHPGIKVEIEFIPWDDYQQKLNTALASGDAPYDVIFI 57 (315)
T ss_dssp HHHHHHHHHHHHHHTTEEEEEEEETHHHHHHHHHHHHHTTGSSESEEEE
T ss_pred HHHHHHHHHHHHHCCCcEEEEEECCCccHHHHHHHHHHcCCChhheEEe
Confidence 466666 77777789999988766 3332 244444434499988
No 43
>PLN03156 GDSL esterase/lipase; Provisional
Probab=57.10 E-value=17 Score=26.43 Aligned_cols=37 Identities=24% Similarity=0.306 Sum_probs=27.5
Q ss_pred HHHHHHHHhhCCCceechhhHHHHHHHHhhCCCCccE
Q psy9334 8 PNLGQTMAKLYPKIQFEQMIVDNCTMQIVSNPHQFDV 44 (65)
Q Consensus 8 ~~~~~eva~~ypdV~~~~~~vDa~~~~lv~~P~~fDV 44 (65)
++..+++.+++|++++-..-+=++...++.||.+|..
T Consensus 253 ~~~l~~L~~~~pg~~i~~~D~y~~~~~ii~nP~~yGf 289 (351)
T PLN03156 253 EKLVTKLNKELPGIKLVFSNPYDIFMQIIRNPSAYGF 289 (351)
T ss_pred HHHHHHHHHhCCCCeEEEEehHHHHHHHHhCccccCc
Confidence 3455566778999877665556777889999999863
No 44
>cd08445 PBP2_BenM_CatM_CatR The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in benzoate catabolism; contains the type 2 periplasmic binding fold. This CD includes the C-terminal of LysR-type transcription regulators, BenM, CatM, and CatR, which are involved in the benzoate catabolism. The BenM and CatM are paralogs with overlapping functions. BenM responds synergistically to two effectors, benzoate and cis,cis-muconate, to activate expression of the benABCDE operon which is involved in benzoate catabolism, while CatM responses only to muconate. BenM and CatM share high protein sequence identity and bind to the operator-promoter regions that have similar DNA sequences. In Pseudomonas species, phenolic compounds are converted by different enzymes to central intermediates, such as protocatechuate and catechols. Generally, unsubstituted compounds, such as benzoate, are metabolized by an ortho-cleavage pathway. The catBCA operon encodes three enzymes
Probab=56.69 E-value=23 Score=21.44 Aligned_cols=40 Identities=15% Similarity=0.135 Sum_probs=25.4
Q ss_pred hHHHHHHHHHhhCCCceechhh--HHHHHHHHhhCCCCccEEec
Q psy9334 6 GYPNLGQTMAKLYPKIQFEQMI--VDNCTMQIVSNPHQFDVMVM 47 (65)
Q Consensus 6 ~f~~~~~eva~~ypdV~~~~~~--vDa~~~~lv~~P~~fDVIV~ 47 (65)
..-+...+..++||+++++-.. -+.....+.+ +++|+.+.
T Consensus 15 ~l~~~l~~~~~~~P~i~l~i~~~~~~~~~~~l~~--~~~Dl~i~ 56 (203)
T cd08445 15 LLPELIRRFRQAAPDVEIELIEMTTVQQIEALKE--GRIDVGFG 56 (203)
T ss_pred HHHHHHHHHHHHCCCeEEEEEeCChHHHHHHHHc--CCCcEEEe
Confidence 3456778888999998877553 3333333332 55787665
No 45
>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=55.44 E-value=32 Score=20.97 Aligned_cols=40 Identities=13% Similarity=0.052 Sum_probs=25.2
Q ss_pred hHHHHHHHHHhhCCCceechh--hHHHHHHHHhhCCCCccEEec
Q psy9334 6 GYPNLGQTMAKLYPKIQFEQM--IVDNCTMQIVSNPHQFDVMVM 47 (65)
Q Consensus 6 ~f~~~~~eva~~ypdV~~~~~--~vDa~~~~lv~~P~~fDVIV~ 47 (65)
....+..+..++||+|+++-. .-+.+ ++.+.+ +++|+.+.
T Consensus 15 ~l~~~l~~f~~~~P~v~i~i~~~~~~~l-~~~l~~-g~~D~~~~ 56 (198)
T cd08486 15 SLPLLLRAFLTSTPTATVSLTHMTKDEQ-VEGLLA-GTIHVGFS 56 (198)
T ss_pred HHHHHHHHHHHhCCCeEEEEEECCHHHH-HHHHHc-CCceEEEe
Confidence 455677888899999887643 33333 333333 67787665
No 46
>PF01515 PTA_PTB: Phosphate acetyl/butaryl transferase; InterPro: IPR002505 This entry contains both phosphate acetyltransferase 2.3.1.8 from EC: Acetyl-CoA + phosphate = CoA + acetyl phosphate and phosphate butaryltransferase 2.3.1.19 from EC: Butanoyl-CoA + phosphate = CoA + butanoyl phosphate These enzymes catalyse the transfer of an acetyl or butaryl group to orthophosphate.; GO: 0016746 transferase activity, transferring acyl groups, 0008152 metabolic process; PDB: 2AF3_D 1QZT_D 2AF4_D 1VMI_A 3UF6_B 3U9E_A 3TNG_A 4E4R_A 1R5J_A 1YCO_A ....
Probab=54.92 E-value=42 Score=24.38 Aligned_cols=62 Identities=21% Similarity=0.282 Sum_probs=36.4
Q ss_pred hhchHHHHHHHHHhhCCCceec-hhhHHHHHHHHhhC--------CCCccEEecCCch-HHHHHhhhhhccC
Q psy9334 3 CRFGYPNLGQTMAKLYPKIQFE-QMIVDNCTMQIVSN--------PHQFDVMVMPNLY-GNIVDNLASDIKG 64 (65)
Q Consensus 3 ~~~~f~~~~~eva~~ypdV~~~-~~~vDa~~~~lv~~--------P~~fDVIV~~Nl~-GDIlSD~aa~l~G 64 (65)
...--++..+-+.+.+|+..++ ++-+|++.-.=+.. -++-||+|.|||- |+|+--+...+.|
T Consensus 213 s~~~~~~a~~~~~~~~~~~~vdGe~q~D~Al~~~~~~~k~~~s~v~G~AnvLIfPnl~agNi~~K~l~~~~~ 284 (319)
T PF01515_consen 213 STDKVREAVEIAREKQPDLIVDGEMQFDAALSPEVAAKKYPFSPVAGDANVLIFPNLEAGNIAYKLLQRLGG 284 (319)
T ss_dssp HHHHHHHHHHHHHHHCTTSEEEEEE-HHHHH-HHHHHHHSTTSSTTTC-SEEE-SSHHHHHHHHHHHHHTTT
T ss_pred hHHHHHHHHHHHHhhCCCceecCccccchhcCHHHHHHhCCCCccCCcCCEEEeCChhHhHHHHHHHHHhhC
Confidence 3334445555555668987766 45678776322221 3467999999997 8887766555444
No 47
>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=54.20 E-value=25 Score=20.73 Aligned_cols=42 Identities=14% Similarity=0.220 Sum_probs=25.1
Q ss_pred chHHHHHHHHHhhCCCceechhh--HHHHHHHHhhCCCCccEEecC
Q psy9334 5 FGYPNLGQTMAKLYPKIQFEQMI--VDNCTMQIVSNPHQFDVMVMP 48 (65)
Q Consensus 5 ~~f~~~~~eva~~ypdV~~~~~~--vDa~~~~lv~~P~~fDVIV~~ 48 (65)
...-....++.++||+++++-.. -+... +.+.+ +++|+.++.
T Consensus 13 ~~l~~~l~~~~~~~P~i~i~i~~~~~~~~~-~~l~~-~~~Di~i~~ 56 (197)
T cd08448 13 RGLPRILRAFRAEYPGIEVALHEMSSAEQI-EALLR-GELDLGFVH 56 (197)
T ss_pred HHHHHHHHHHHHHCCCCeEEEEeCCHHHHH-HHHHc-CCcceEEEe
Confidence 34456778888999998877543 22222 33333 457876653
No 48
>PF02608 Bmp: Basic membrane protein; InterPro: IPR003760 This is a family of basic membrane lipoproteins from Borrelia and various putative lipoproteins from other bacteria. All of these proteins are outer membrane proteins and are thus antigenic in nature when possessed by the pathogenic members of the family []. The Bacillus subtilis degR, a positive regulator of the production of degradative enzymes, is also a member of this group [].; GO: 0005886 plasma membrane; PDB: 2HQB_A 3S99_A 2FQW_A 2FQY_A 2FQX_A.
Probab=51.93 E-value=10 Score=26.63 Aligned_cols=20 Identities=40% Similarity=0.680 Sum_probs=15.4
Q ss_pred hchHHHHHHHHHhhCCCcee
Q psy9334 4 RFGYPNLGQTMAKLYPKIQF 23 (65)
Q Consensus 4 ~~~f~~~~~eva~~ypdV~~ 23 (65)
+..|.+.+.++|++||++++
T Consensus 69 g~~~~~~~~~vA~~yPd~~F 88 (306)
T PF02608_consen 69 GFEYSDALQEVAKEYPDTKF 88 (306)
T ss_dssp SGGGHHHHHHHHTC-TTSEE
T ss_pred cHHHHHHHHHHHHHCCCCEE
Confidence 45677889999999999865
No 49
>PRK09653 eutD phosphotransacetylase; Reviewed
Probab=51.46 E-value=45 Score=24.09 Aligned_cols=58 Identities=19% Similarity=0.342 Sum_probs=35.4
Q ss_pred hHHHHHHHHHhhCCCceec-hhhHHHHHHH-H--hhC-----CCCccEEecCCch-HHHHHhhhhhcc
Q psy9334 6 GYPNLGQTMAKLYPKIQFE-QMIVDNCTMQ-I--VSN-----PHQFDVMVMPNLY-GNIVDNLASDIK 63 (65)
Q Consensus 6 ~f~~~~~eva~~ypdV~~~-~~~vDa~~~~-l--v~~-----P~~fDVIV~~Nl~-GDIlSD~aa~l~ 63 (65)
.-++..+-+.+++|+..++ ++-+|++.-. . .+- -++-||+|.||+- |+|+--+...+.
T Consensus 215 ~~~ea~~ll~~~~~~~~vdGel~~D~A~~~~~~~~k~~~s~v~G~AnvLi~P~l~agNi~yK~l~~~~ 282 (324)
T PRK09653 215 KVQEATEIAKELAPDLKIDGELQFDAAFVPEVAAKKAPGSPVAGKANVFVFPSLEAGNIGYKIAQRLG 282 (324)
T ss_pred HHHHHHHHHHhhCCCCeEEecchHHHhCCHHHHHhhCCCCccCCcCCEEEcCChHHhHHHHHHHHHhc
Confidence 3445555555568887665 3455877422 1 122 3456999999998 888766554443
No 50
>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=51.32 E-value=22 Score=20.98 Aligned_cols=41 Identities=24% Similarity=0.296 Sum_probs=25.4
Q ss_pred hHHHHHHHHHhhCCCceechhhHHHH-HHHHhhCCCCccEEec
Q psy9334 6 GYPNLGQTMAKLYPKIQFEQMIVDNC-TMQIVSNPHQFDVMVM 47 (65)
Q Consensus 6 ~f~~~~~eva~~ypdV~~~~~~vDa~-~~~lv~~P~~fDVIV~ 47 (65)
.+.+...++.++||+++++-..-+.. ....+.+ +++|+.+.
T Consensus 14 ~l~~~l~~~~~~~p~v~i~i~~~~~~~~~~~L~~-~~~Dl~i~ 55 (197)
T cd08438 14 LFAPLLAAFRQRYPNIELELVEYGGKKVEQAVLN-GELDVGIT 55 (197)
T ss_pred hcHHHHHHHHHHCcCeEEEEEEcCcHHHHHHHHc-CCCCEEEE
Confidence 44577888899999988776532221 2233333 45787665
No 51
>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=50.84 E-value=9 Score=22.96 Aligned_cols=40 Identities=20% Similarity=0.377 Sum_probs=26.6
Q ss_pred hHHHHHHHHHhhCCCceechhhHHHHHHHHhhCCCCccEEecC
Q psy9334 6 GYPNLGQTMAKLYPKIQFEQMIVDNCTMQIVSNPHQFDVMVMP 48 (65)
Q Consensus 6 ~f~~~~~eva~~ypdV~~~~~~vDa~~~~lv~~P~~fDVIV~~ 48 (65)
..-+...+..++||+|+++-..-+. ..+++.+ ++|+.++.
T Consensus 15 ~l~~~l~~f~~~~P~v~l~i~~~~~-~~~~~~~--~~D~~i~~ 54 (197)
T cd08470 15 FIAPLVNDFMQRYPKLEVDIELTNR-VVDLVSE--GFDLAIRL 54 (197)
T ss_pred HHHHHHHHHHHHCCCeEEEEEecCC-ccchhcc--CccEEEEc
Confidence 3457788889999998887653222 3455543 59987764
No 52
>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=50.62 E-value=25 Score=21.18 Aligned_cols=44 Identities=16% Similarity=0.117 Sum_probs=29.0
Q ss_pred chHHHHHHHHHhhCCCceechhhHH--HHHHHHhhCCCCccEEecCCc
Q psy9334 5 FGYPNLGQTMAKLYPKIQFEQMIVD--NCTMQIVSNPHQFDVMVMPNL 50 (65)
Q Consensus 5 ~~f~~~~~eva~~ypdV~~~~~~vD--a~~~~lv~~P~~fDVIV~~Nl 50 (65)
..+-+...+..++||+++++-...+ .+..+| .+ ++.|+.++..-
T Consensus 19 ~~l~~~l~~~~~~~P~i~i~~~~~~~~~~~~~l-~~-g~~Dl~i~~~~ 64 (209)
T PF03466_consen 19 SLLPPLLAEFRERHPNIRIEIREGDSDELIEAL-RS-GELDLAITFGP 64 (209)
T ss_dssp HTHHHHHHHHHHHSTTEEEEEEEESHHHHHHHH-HT-TSSSEEEESSS
T ss_pred HHHHHHHHHHHHHCCCcEEEEEeccchhhhHHH-hc-ccccEEEEEee
Confidence 3455778888999999887766555 333333 33 66787776543
No 53
>COG4837 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=50.49 E-value=13 Score=23.51 Aligned_cols=40 Identities=15% Similarity=0.343 Sum_probs=25.9
Q ss_pred HHHHHHHHHhhCCCceechhhHHH-----------HHHHHhhCCCCccEEecC
Q psy9334 7 YPNLGQTMAKLYPKIQFEQMIVDN-----------CTMQIVSNPHQFDVMVMP 48 (65)
Q Consensus 7 f~~~~~eva~~ypdV~~~~~~vDa-----------~~~~lv~~P~~fDVIV~~ 48 (65)
|++.+ +.++||+..++.+|||- ++-++.++-.-|=+||.+
T Consensus 31 WLeaa--lkRKyp~~~F~~~YiDI~n~~~e~~~~~~aekI~~dey~YPlivve 81 (106)
T COG4837 31 WLEAA--LKRKYPNQPFKYTYIDITNPPLEDHDLQFAEKIEQDEYFYPLIVVE 81 (106)
T ss_pred HHHHH--HhccCCCCCcEEEEEEcCCCccHHHHHHHHHHHhcccccceEEEEc
Confidence 55554 45789999999999886 344555554445455544
No 54
>cd08439 PBP2_LrhA_like The C-terminal substrate domain of LysR-like regulator LrhA (LysR homologue A) and that of closely related homologs, contains the type 2 periplasmic binding fold. This CD represents the LrhA subfamily of LysR-like bacterial transcriptional regulators, including LrhA, HexA, PecT, and DgdR. LrhA is involved in control of the transcription of flagellar, motility, and chemotaxis genes by regulating the synthesis and concentration of FlhD(2)C(2), the master regulator for the expression of flagellar and chemotaxis genes. The LrhA protein has strong homology to HexA and PecT from plant pathogenic bacteria, in which HexA and PecT act as repressors of motility and of virulence factors, such as exoenzymes required for lytic reactions. DgdR also shares similar characteristics to those of LrhA, HexA and PecT. The topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a vari
Probab=50.34 E-value=31 Score=20.60 Aligned_cols=40 Identities=18% Similarity=0.287 Sum_probs=25.5
Q ss_pred hHHHHHHHHHhhCCCceechhhH--HHHHHHHhhCCCCccEEec
Q psy9334 6 GYPNLGQTMAKLYPKIQFEQMIV--DNCTMQIVSNPHQFDVMVM 47 (65)
Q Consensus 6 ~f~~~~~eva~~ypdV~~~~~~v--Da~~~~lv~~P~~fDVIV~ 47 (65)
..-+...+..++||+|+++-... +.+..+|.+ +++|+.+.
T Consensus 14 ~l~~~l~~~~~~~P~v~i~~~~~~~~~~~~~l~~--~~~Dl~i~ 55 (185)
T cd08439 14 ILPFLLNRFASVYPRLAIEVVCKRTPRLMEMLER--GEVDLALI 55 (185)
T ss_pred HHHHHHHHHHHHCCCeEEEEEECChHHHHHHHHC--CCCcEEEE
Confidence 44567788889999988876643 233333333 56787665
No 55
>PRK15381 pathogenicity island 2 effector protein SseJ; Provisional
Probab=49.90 E-value=17 Score=27.48 Aligned_cols=36 Identities=8% Similarity=0.104 Sum_probs=28.2
Q ss_pred HHHHHHHHhhCCCceechhhHHHHHHHHhhCCCCcc
Q psy9334 8 PNLGQTMAKLYPKIQFEQMIVDNCTMQIVSNPHQFD 43 (65)
Q Consensus 8 ~~~~~eva~~ypdV~~~~~~vDa~~~~lv~~P~~fD 43 (65)
++..+++.+++|++++-..-+=++.++++.+|..|-
T Consensus 313 ~~~L~~L~~~~pg~~ivy~D~y~~~~~ii~nP~~yG 348 (408)
T PRK15381 313 KTNVEELKEKYPQHKICYYETADAFKVIMEAASNIG 348 (408)
T ss_pred HHHHHHHHHhCCCCEEEEEEhHHHHHHHHhCHHhcC
Confidence 455666777899988776666677799999999876
No 56
>cd08446 PBP2_Chlorocatechol The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in the chlorocatechol catabolism, contains the type 2 periplasmic binding fold. This CD includes the substrate binding domain of LysR-type regulators CbnR, ClcR and TfdR, which are involved in the regulation of chlorocatechol breakdown. The chlorocatechol-degradative pathway is often found in bacteria that can use chlorinated aromatic compounds as carbon and energy sources. CbnR is found in the 3-chlorobenzoate degradative bacterium Ralstonia eutropha NH9 and forms a tetramer. CbnR activates the expression of the cbnABCD genes, which are responsible for the degradation of chlorocatechol converted from 3-chlorobenzoate and are transcribed divergently from cbnR. In soil bacterium Pseudomonas putida, the 3-chlorocatechol-degradative pathway is encoded by clcABD operon, which requires the divergently transcribed clcR for activation. TfdR is involved in the activation of tf
Probab=49.88 E-value=34 Score=20.38 Aligned_cols=40 Identities=10% Similarity=0.106 Sum_probs=25.4
Q ss_pred HHHHHHHHHhhCCCceechhhH--HHHHHHHhhCCCCccEEecC
Q psy9334 7 YPNLGQTMAKLYPKIQFEQMIV--DNCTMQIVSNPHQFDVMVMP 48 (65)
Q Consensus 7 f~~~~~eva~~ypdV~~~~~~v--Da~~~~lv~~P~~fDVIV~~ 48 (65)
.-++..++.++||+++++-..- +....+|.. +++|+.++.
T Consensus 16 l~~~i~~~~~~~P~v~l~i~~~~~~~~~~~l~~--~~~Dl~i~~ 57 (198)
T cd08446 16 VPRLLRAFLTARPDVTVSLHNMTKDEQIEALRA--GRIHIGFGR 57 (198)
T ss_pred HHHHHHHHHHHCCCeEEEEeeCCHHHHHHHHHC--CCccEEEEe
Confidence 3467788889999988876542 233334444 367876653
No 57
>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=49.61 E-value=23 Score=21.14 Aligned_cols=40 Identities=15% Similarity=0.184 Sum_probs=24.5
Q ss_pred HHHHHHHHHhhCCCceechhhHHHH-HHHHhhCCCCccEEec
Q psy9334 7 YPNLGQTMAKLYPKIQFEQMIVDNC-TMQIVSNPHQFDVMVM 47 (65)
Q Consensus 7 f~~~~~eva~~ypdV~~~~~~vDa~-~~~lv~~P~~fDVIV~ 47 (65)
.-+...+..++||+|+++-..-+.. ..+.+.+ ++.|+.+.
T Consensus 15 l~~~l~~~~~~~P~v~l~i~~~~~~~~~~~l~~-g~~D~~i~ 55 (200)
T cd08464 15 APPLLAALRAEAPGVRLVFRQVDPFNVGDMLDR-GEIDLAIG 55 (200)
T ss_pred HHHHHHHHHHHCCCcEEEEecCCcccHHHHHhc-CcccEEEe
Confidence 3466788899999988876543221 1233332 56787765
No 58
>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=49.38 E-value=29 Score=20.65 Aligned_cols=40 Identities=13% Similarity=0.242 Sum_probs=24.9
Q ss_pred hHHHHHHHHHhhCCCceechhhHHH--HHHHHhhCCCCccEEec
Q psy9334 6 GYPNLGQTMAKLYPKIQFEQMIVDN--CTMQIVSNPHQFDVMVM 47 (65)
Q Consensus 6 ~f~~~~~eva~~ypdV~~~~~~vDa--~~~~lv~~P~~fDVIV~ 47 (65)
...+...++.++||+++++-..-+. ...+|.. +++|+.++
T Consensus 14 ~l~~~l~~~~~~~P~i~l~i~~~~~~~~~~~l~~--~~~Dl~i~ 55 (199)
T cd08416 14 TVPRIIMGLKLRRPELDIELTLGSNKDLLKKLKD--GELDAILV 55 (199)
T ss_pred hhHHHHHHHHHhCCCeEEEEEEcCcHHHHHHHhC--CCCCEEEE
Confidence 3456778889999988877654332 2233333 46777665
No 59
>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=48.87 E-value=33 Score=20.25 Aligned_cols=40 Identities=10% Similarity=0.105 Sum_probs=24.7
Q ss_pred hHHHHHHHHHhhCCCceechhh--HHHHHHHHhhCCCCccEEec
Q psy9334 6 GYPNLGQTMAKLYPKIQFEQMI--VDNCTMQIVSNPHQFDVMVM 47 (65)
Q Consensus 6 ~f~~~~~eva~~ypdV~~~~~~--vDa~~~~lv~~P~~fDVIV~ 47 (65)
.+.+...++.++||+++++-.. -+....+|.. +++|+.++
T Consensus 14 ~l~~~l~~~~~~~P~v~i~i~~~~~~~~~~~l~~--~~~Dl~i~ 55 (201)
T cd08435 14 LLPPAIARLLARHPRLTVRVVEGTSDELLEGLRA--GELDLAIG 55 (201)
T ss_pred HHHHHHHHHHHHCCCeEEEEEeCCHHHHHHHHHc--CCccEEEE
Confidence 4556778888999998877543 2233233322 46787664
No 60
>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=48.71 E-value=12 Score=22.58 Aligned_cols=39 Identities=18% Similarity=0.336 Sum_probs=25.8
Q ss_pred hHHHHHHHHHhhCCCceechhhHHHHHHHHhhCCCCccEEec
Q psy9334 6 GYPNLGQTMAKLYPKIQFEQMIVDNCTMQIVSNPHQFDVMVM 47 (65)
Q Consensus 6 ~f~~~~~eva~~ypdV~~~~~~vDa~~~~lv~~P~~fDVIV~ 47 (65)
.+-+...+..++||+|+++-.. .....++. + ++.|+.++
T Consensus 17 ~l~~~l~~f~~~~P~v~i~~~~-~~~~~~l~-~-~~~D~~i~ 55 (199)
T cd08478 17 LLAPLIAKFRERYPDIELELVS-NEGIIDLI-E-RKTDVAIR 55 (199)
T ss_pred HHHHHHHHHHHHCCCeEEEEEe-ccccccch-h-ccccEEEE
Confidence 3456778888999998887652 33334444 3 68887665
No 61
>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=48.62 E-value=34 Score=20.47 Aligned_cols=41 Identities=15% Similarity=0.248 Sum_probs=25.6
Q ss_pred chHHHHHHHHHhhCCCceechhhH--HHHHHHHhhCCCCccEEec
Q psy9334 5 FGYPNLGQTMAKLYPKIQFEQMIV--DNCTMQIVSNPHQFDVMVM 47 (65)
Q Consensus 5 ~~f~~~~~eva~~ypdV~~~~~~v--Da~~~~lv~~P~~fDVIV~ 47 (65)
...-.+..+..++||+|+++-... +... ..+.+ +++|+.+.
T Consensus 13 ~~l~~~l~~~~~~~P~i~l~i~~~~~~~~~-~~l~~-g~~D~~i~ 55 (200)
T cd08453 13 SVLPELVRRFREAYPDVELQLREATSDVQL-EALLA-GEIDAGIV 55 (200)
T ss_pred HHHHHHHHHHHHhCCCceEEEEeCCHHHHH-HHHHc-CCCCEEEE
Confidence 344567788889999887766532 2333 33333 47887664
No 62
>cd08436 PBP2_LTTR_like_3 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator, contains the type 2 periplasmic binding fold. LysR-transcriptional regulators comprise the largest family of prokaryotic transcription factor. Homologs of some of LTTRs with similar domain organizations are also found in the archaea and eukaryotic organisms. The LTTRs are composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcriptional repressor undergoes a conformational change upon substrate binding which in turn changes the DNA binding affinity of the repressor. The genes controlled by the LTTRs have diverse functi
Probab=48.57 E-value=36 Score=19.96 Aligned_cols=40 Identities=13% Similarity=0.243 Sum_probs=25.0
Q ss_pred hHHHHHHHHHhhCCCceechhhH--HHHHHHHhhCCCCccEEec
Q psy9334 6 GYPNLGQTMAKLYPKIQFEQMIV--DNCTMQIVSNPHQFDVMVM 47 (65)
Q Consensus 6 ~f~~~~~eva~~ypdV~~~~~~v--Da~~~~lv~~P~~fDVIV~ 47 (65)
.+.+...+..++||+++++-..- +.....| . -++.|+.++
T Consensus 14 ~l~~~l~~~~~~~P~v~i~i~~~~~~~~~~~l-~-~~~~Dl~i~ 55 (194)
T cd08436 14 DLPELLARFHRRHPGVDIRLRQAGSDDLLAAV-R-EGRLDLAFV 55 (194)
T ss_pred HHHHHHHHHHHHCCCcEEEEecCCHHHHHHHH-H-cCCccEEEE
Confidence 45567788889999988876543 2222233 2 256776654
No 63
>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=47.56 E-value=34 Score=21.08 Aligned_cols=40 Identities=18% Similarity=0.165 Sum_probs=26.1
Q ss_pred hHHHHHHHHHhhCCCceechhhHHH--HHHHHhhCCCCccEEec
Q psy9334 6 GYPNLGQTMAKLYPKIQFEQMIVDN--CTMQIVSNPHQFDVMVM 47 (65)
Q Consensus 6 ~f~~~~~eva~~ypdV~~~~~~vDa--~~~~lv~~P~~fDVIV~ 47 (65)
..-++..+..++||+++++-...+. +..+|. + +++|+.++
T Consensus 14 ~l~~~l~~f~~~~P~v~l~i~~~~~~~~~~~l~-~-g~~Di~i~ 55 (221)
T cd08469 14 LLPALVRRLETEAPGIDLRIRPVTRLDLAEQLD-L-GRIDLVIG 55 (221)
T ss_pred HHHHHHHHHHHHCCCcEEEEeeCChhhHHHHHH-C-CCccEEEe
Confidence 3456777888899998877654443 333443 3 57887775
No 64
>TIGR02329 propionate_PrpR propionate catabolism operon regulatory protein PrpR. At least five distinct pathways exists for the catabolism of propionate by way of propionyl-CoA. Members of this family represent the transcriptional regulatory protein PrpR, whose gene is found in most cases divergently transcribed from an operon for the methylcitric acid cycle of propionate catabolism. 2-methylcitric acid, a catabolite by this pathway, is a coactivator of PrpR.
Probab=47.39 E-value=39 Score=26.24 Aligned_cols=51 Identities=18% Similarity=0.181 Sum_probs=33.3
Q ss_pred HHHHHHHHHhhCCC---ceechhhHHHHHHHH--hhCCCCccEEecCCchHHHHHh
Q psy9334 7 YPNLGQTMAKLYPK---IQFEQMIVDNCTMQI--VSNPHQFDVMVMPNLYGNIVDN 57 (65)
Q Consensus 7 f~~~~~eva~~ypd---V~~~~~~vDa~~~~l--v~~P~~fDVIV~~Nl~GDIlSD 57 (65)
+++.+++++++|++ +.+..-..+...... -...+.+|||++----+.+|-.
T Consensus 15 l~~~~~~i~~~~~~~~~~~v~~~~~~~~~~~a~~~~~~~~~dviIsrG~ta~~i~~ 70 (526)
T TIGR02329 15 LFDLFRDIAPEFDHRANITPIQLGFEDAVREIRQRLGAERCDVVVAGGSNGAYLKS 70 (526)
T ss_pred HHHHHHHHHHhCCCCceEEEEeccHHHHHHHHHHHHHhCCCcEEEECchHHHHHHH
Confidence 67899999999987 444444444443322 1225679999997776666654
No 65
>cd08444 PBP2_Cbl The C-terminal substrate binding domain of LysR-type transcriptional regulator Cbl, which is required for expression of sulfate starvation-inducible (ssi) genes, contains the type 2 periplasmic binding fold. Cbl is a member of the LysR transcriptional regulators that comprise the largest family of prokaryotic transcription factor. Cbl shows high sequence similarity to CysB, the LysR-type transcriptional activator of genes involved in sulfate and thiosulfate transport, sulfate reduction, and cysteine synthesis. In Escherichia coli, the function of Cbl is required for expression of sulfate starvation-inducible (ssi) genes, coupled with the biosynthesis of cysteine from the organic sulfur sources (sulfonates). The ssi genes include the ssuEADCB and tauABCD operons encoding uptake systems for organosulfur compounds, aliphatic sulfonates, and taurine. The genes in these operons encode an ABC-type transport system required for uptake of aliphatic sulfonates and a desulfonati
Probab=47.24 E-value=38 Score=20.49 Aligned_cols=42 Identities=12% Similarity=0.182 Sum_probs=25.7
Q ss_pred hHHHHHHHHHhhCCCceechhhHHHH-HHHHhhCCCCccEEecC
Q psy9334 6 GYPNLGQTMAKLYPKIQFEQMIVDNC-TMQIVSNPHQFDVMVMP 48 (65)
Q Consensus 6 ~f~~~~~eva~~ypdV~~~~~~vDa~-~~~lv~~P~~fDVIV~~ 48 (65)
.+-+...+..++||+|+++-...+.- ..+.+. -+++|+.++.
T Consensus 14 ~l~~~l~~~~~~~P~v~l~i~~~~~~~~~~~l~-~g~~Dl~i~~ 56 (198)
T cd08444 14 ALPWVVQAFKEQFPNVHLVLHQGSPEEIASMLA-NGQADIGIAT 56 (198)
T ss_pred hhhHHHHHHHHHCCCeEEEEEeCCHHHHHHHHH-CCCccEEEec
Confidence 45567788889999887776543321 223333 3667876653
No 66
>cd08462 PBP2_NodD The C-terminal substsrate binding domain of NodD family of LysR-type transcriptional regulators that regulates the expression of nodulation (nod) genes; contains the type 2 periplasmic binding fold. The nodulation (nod) genes in soil bacteria play important roles in the development of nodules. nod genes are involved in synthesis of Nod factors that are required for bacterial entry into root hairs. Thirteen nod genes have been identified and are classified into five transcription units: nodD, nodABCIJ, nodFEL, nodMNT, and nodO. NodD is negatively auto-regulates its own expression of nodD gene, while other nod genes are inducible and positively regulated by NodD in the presence of flavonoids released by plant roots. This substrate-binding domain has significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. T
Probab=47.10 E-value=39 Score=20.40 Aligned_cols=43 Identities=19% Similarity=0.404 Sum_probs=26.3
Q ss_pred hHHHHHHHHHhhCCCceechhhHHHHHHHHhhCCCCccEEecCC
Q psy9334 6 GYPNLGQTMAKLYPKIQFEQMIVDNCTMQIVSNPHQFDVMVMPN 49 (65)
Q Consensus 6 ~f~~~~~eva~~ypdV~~~~~~vDa~~~~lv~~P~~fDVIV~~N 49 (65)
..-....+..++||+++++-.....-....+.+ ++.|+.+...
T Consensus 14 ~l~~~i~~~~~~~P~i~l~i~~~~~~~~~~l~~-g~~D~~i~~~ 56 (200)
T cd08462 14 LLPPVIERVAREAPGVRFELLPPDDQPHELLER-GEVDLLIAPE 56 (200)
T ss_pred HHHHHHHHHHHHCCCCEEEEecCChhHHHHHhc-CCeeEEEecC
Confidence 344567778889998877665322233344444 5788777643
No 67
>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=47.08 E-value=24 Score=20.91 Aligned_cols=29 Identities=17% Similarity=0.465 Sum_probs=21.0
Q ss_pred chhchHHHHHHHHHhhCCCceechhhHHHH
Q psy9334 2 PCRFGYPNLGQTMAKLYPKIQFEQMIVDNC 31 (65)
Q Consensus 2 ~~~~~f~~~~~eva~~ypdV~~~~~~vDa~ 31 (65)
||+. .....+++|++||++.+-...+|..
T Consensus 38 ~C~~-l~~~l~~la~~~~~v~f~~vd~~~~ 66 (113)
T cd02957 38 RCKI-LDSHLEELAAKYPETKFVKINAEKA 66 (113)
T ss_pred cHHH-HHHHHHHHHHHCCCcEEEEEEchhh
Confidence 5664 4557788999999987766666654
No 68
>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=46.84 E-value=40 Score=19.89 Aligned_cols=41 Identities=12% Similarity=0.182 Sum_probs=25.7
Q ss_pred chHHHHHHHHHhhCCCceechhh--HHHHHHHHhhCCCCccEEec
Q psy9334 5 FGYPNLGQTMAKLYPKIQFEQMI--VDNCTMQIVSNPHQFDVMVM 47 (65)
Q Consensus 5 ~~f~~~~~eva~~ypdV~~~~~~--vDa~~~~lv~~P~~fDVIV~ 47 (65)
..+.....+..+.||+++++-.. -+.....|.. +++|+.+.
T Consensus 13 ~~l~~~l~~~~~~~P~i~i~~~~~~~~~~~~~l~~--~~~Dl~i~ 55 (197)
T cd08449 13 GGLGPALRRFKRQYPNVTVRFHELSPEAQKAALLS--KRIDLGFV 55 (197)
T ss_pred hhHHHHHHHHHHHCCCeEEEEEECCHHHHHHHHhC--CCccEEEe
Confidence 34556778888999998877543 2333333333 56787664
No 69
>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=46.08 E-value=43 Score=19.94 Aligned_cols=41 Identities=15% Similarity=0.216 Sum_probs=25.9
Q ss_pred hHHHHHHHHHhhCCCceechhhHHH-HHHHHhhCCCCccEEec
Q psy9334 6 GYPNLGQTMAKLYPKIQFEQMIVDN-CTMQIVSNPHQFDVMVM 47 (65)
Q Consensus 6 ~f~~~~~eva~~ypdV~~~~~~vDa-~~~~lv~~P~~fDVIV~ 47 (65)
..-+...+..++||+++++-..-.. -....+.+ +++|+.+.
T Consensus 14 ~l~~~l~~f~~~~P~v~l~~~~~~~~~~~~~l~~-g~~Dl~i~ 55 (200)
T cd08466 14 LLPRLLARLKQLAPNISLRESPSSEEDLFEDLRL-QEVDLVID 55 (200)
T ss_pred HHHHHHHHHHHHCCCCEEEEecCchHhHHHHHHc-CCccEEEe
Confidence 3456777888999998877654322 22344444 67887664
No 70
>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=45.96 E-value=44 Score=20.12 Aligned_cols=39 Identities=13% Similarity=0.290 Sum_probs=23.9
Q ss_pred HHHHHHHHHhhCCCceechhh--HHHHHHHHhhCCCCccEEec
Q psy9334 7 YPNLGQTMAKLYPKIQFEQMI--VDNCTMQIVSNPHQFDVMVM 47 (65)
Q Consensus 7 f~~~~~eva~~ypdV~~~~~~--vDa~~~~lv~~P~~fDVIV~ 47 (65)
.-+...+..++||+++++-.. -+.....|.+ ++.|+.+.
T Consensus 15 l~~~l~~~~~~~P~v~i~i~~~~~~~~~~~l~~--~~~Dl~i~ 55 (197)
T cd08452 15 LPPIVREYRKKFPSVKVELRELSSPDQVEELLK--GRIDIGFL 55 (197)
T ss_pred HHHHHHHHHHHCCCcEEEEEecChHHHHHHHHC--CCccEEEe
Confidence 346777888999988776543 3333333433 36776554
No 71
>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=45.67 E-value=42 Score=20.05 Aligned_cols=40 Identities=18% Similarity=0.276 Sum_probs=25.3
Q ss_pred hHHHHHHHHHhhCCCceechhhH--HHHHHHHhhCCCCccEEec
Q psy9334 6 GYPNLGQTMAKLYPKIQFEQMIV--DNCTMQIVSNPHQFDVMVM 47 (65)
Q Consensus 6 ~f~~~~~eva~~ypdV~~~~~~v--Da~~~~lv~~P~~fDVIV~ 47 (65)
.+-+...+..++||+++++-... +.....|. + +++|+.++
T Consensus 14 ~l~~~l~~~~~~~P~v~i~~~~~~~~~~~~~l~-~-g~~Dl~i~ 55 (198)
T cd08437 14 YFPKLAKDLIKTGLMIQIDTYEGGSAELLEQLL-Q-GDLDIALL 55 (198)
T ss_pred HhHHHHHHHHHhCCceEEEEEEcCHHHHHHHHH-c-CCCCEEEe
Confidence 34567788889999988776533 33333343 3 46887664
No 72
>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=44.67 E-value=51 Score=23.49 Aligned_cols=45 Identities=11% Similarity=0.107 Sum_probs=29.9
Q ss_pred chHHHHHHHHHhhCCCceechhhHHHHH---HHHhhCCCCccEEecCC
Q psy9334 5 FGYPNLGQTMAKLYPKIQFEQMIVDNCT---MQIVSNPHQFDVMVMPN 49 (65)
Q Consensus 5 ~~f~~~~~eva~~ypdV~~~~~~vDa~~---~~lv~~P~~fDVIV~~N 49 (65)
..|.+++++..+++|+|+++...+.... ...++.-.-.||+...+
T Consensus 48 ~~~~~~~~~F~~~~~~i~V~~~~~~~~~~kl~~~~~sg~~PDi~~~~~ 95 (437)
T TIGR03850 48 KMWEEVVEAFEKSHEGVKVELTVSKNLEDVITPQIQAGDYPDVVYLAT 95 (437)
T ss_pred HHHHHHHHHHHHHCCCceEEEEeCccHHHHHHHHHhCCCCCCEEEeCC
Confidence 3577888888888999998876543222 22333346689988764
No 73
>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=44.14 E-value=42 Score=19.78 Aligned_cols=42 Identities=10% Similarity=0.089 Sum_probs=26.7
Q ss_pred chHHHHHHHHHhhCCCceechhhHH--HHHHHHhhCCCCccEEecC
Q psy9334 5 FGYPNLGQTMAKLYPKIQFEQMIVD--NCTMQIVSNPHQFDVMVMP 48 (65)
Q Consensus 5 ~~f~~~~~eva~~ypdV~~~~~~vD--a~~~~lv~~P~~fDVIV~~ 48 (65)
..+-+...+..++||+++++-.... ... ..+.+ +++|+.++.
T Consensus 13 ~~l~~~l~~~~~~~P~i~i~~~~~~~~~~~-~~l~~-~~~Dl~i~~ 56 (200)
T cd08423 13 ALLPPALAALRARHPGLEVRLREAEPPESL-DALRA-GELDLAVVF 56 (200)
T ss_pred HhhhHHHHHHHHhCCCCeEEEEeCCHHHHH-HHHhc-CCccEEEEe
Confidence 3456788889999999877765432 333 33333 467866653
No 74
>PF12183 NotI: Restriction endonuclease NotI; InterPro: IPR022009 This family of proteins is found in bacteria. Proteins in this family are typically between 270 and 341 amino acids in length. There is a conserved CPF sequence motif. The type IIP restriction enzyme, NotI, is a homodimer that recognises the 8 bp DNA sequence 5'-GC/GGCCGC-3' and cleaves both strands of DNA to create 5', 4 base cohesive overhangs. ; PDB: 3C25_B 3BVQ_A.
Probab=44.07 E-value=3.5 Score=29.50 Aligned_cols=54 Identities=19% Similarity=0.166 Sum_probs=26.9
Q ss_pred chhchHHHHHHHHHhhCCCceechhhHHHHHHHHhhCCCCccEEecCCch---HHHHHhhhhhccC
Q psy9334 2 PCRFGYPNLGQTMAKLYPKIQFEQMIVDNCTMQIVSNPHQFDVMVMPNLY---GNIVDNLASDIKG 64 (65)
Q Consensus 2 ~~~~~f~~~~~eva~~ypdV~~~~~~vDa~~~~lv~~P~~fDVIV~~Nl~---GDIlSD~aa~l~G 64 (65)
+|.++ .+.|.++.+.-|++.+-..-| +.+..-++||+||.| ++|++|.+.-+.|
T Consensus 22 ~CPF~-~~~c~K~~k~~~~~~~GvCSV--------r~~~~~~~IvCP~R~~~~~~i~~~v~~~~f~ 78 (254)
T PF12183_consen 22 QCPFL-DKKCPKCSKSKAGIPIGVCSV--------RGKDGTPWIVCPIRFAEDYQIFIDVAHKLFG 78 (254)
T ss_dssp B-HHH-HHSSS--B--S-GGGTTEEEE--------ETTEEEEEE--GGG-G--HHHHHHHHHHHHT
T ss_pred CCCCC-CCcccccccCCCCCcCceEEE--------EcCCCCeEEECCCccccccHHHHHHHHHHhc
Confidence 45555 555555555544333222222 367777899999998 5688887765544
No 75
>TIGR02709 branched_ptb branched-chain phosphotransacylase. This model distinguishes branched-chain phosphotransacylases like that of Enterococcus faecalis from closely related subfamilies of phosphate butyryltransferase (EC 2.3.1.19) (TIGR02706) and phosphate acetyltransferase (EC 2.3.1.8) (TIGR00651). Members of this family and of TIGR02706 show considerable crossreactivity, and the occurrence of a member of either family near an apparent leucine dehydrogenase will suggest activity on branched chain-acyl-CoA compounds.
Probab=43.92 E-value=99 Score=22.28 Aligned_cols=59 Identities=17% Similarity=0.142 Sum_probs=32.9
Q ss_pred chhchHHHHHHHHHhhCCCceechh-hHHHHHHH-H-----hhCC--CCccEEecCCch-HHHHHhhhhh
Q psy9334 2 PCRFGYPNLGQTMAKLYPKIQFEQM-IVDNCTMQ-I-----VSNP--HQFDVMVMPNLY-GNIVDNLASD 61 (65)
Q Consensus 2 ~~~~~f~~~~~eva~~ypdV~~~~~-~vDa~~~~-l-----v~~P--~~fDVIV~~Nl~-GDIlSD~aa~ 61 (65)
|.+..-++..+. +++-|+..++-. -+|++.-. . +..| ++-||+|.||+- |+|+--....
T Consensus 164 ~st~~a~~l~~~-~~~~~~~~vdGpl~~D~Al~~e~a~~K~~~s~vaG~AniLI~PnleaGNi~yK~l~~ 232 (271)
T TIGR02709 164 PSSVLAKEVTAH-FNDQQEATVFGPLSLDLATSEEAVAHKRYSGPIMGDADILVVPTIDVGNCLYKSLTL 232 (271)
T ss_pred chHHHHHHHHHH-HHhCCCCEEEecCchhhhcCHHHHHhhCCCCCCCCcCCEEEcCChHHHHHHHHHHHH
Confidence 334443344433 333377666543 35666422 2 2223 577999999997 8887665433
No 76
>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=43.62 E-value=8.5 Score=23.98 Aligned_cols=40 Identities=18% Similarity=0.412 Sum_probs=21.8
Q ss_pred HHHHHHHHHhhCCCceechhhHH-----------HHHHHHhhCCCCccEEecC
Q psy9334 7 YPNLGQTMAKLYPKIQFEQMIVD-----------NCTMQIVSNPHQFDVMVMP 48 (65)
Q Consensus 7 f~~~~~eva~~ypdV~~~~~~vD-----------a~~~~lv~~P~~fDVIV~~ 48 (65)
|++.+ +.++||+..++..||| ..+.+++.+---|=+|+..
T Consensus 24 WL~aa--l~RKyp~~~f~~~YiDi~~p~~~~~~~~~a~~I~ede~fYPlV~i~ 74 (93)
T PF07315_consen 24 WLEAA--LKRKYPDQPFEFTYIDIENPPENDHDQQFAERILEDELFYPLVVIN 74 (93)
T ss_dssp HHHHH--HHHH-TTS-EEEEEEETTT----HHHHHHHHHHHTTSS-SSEEEET
T ss_pred HHHHH--HhCcCCCCceEEEEEecCCCCccHHHHHHHHHHHhcccccceEEEC
Confidence 66554 4678999888777776 3444555444444454443
No 77
>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=43.43 E-value=41 Score=19.84 Aligned_cols=42 Identities=7% Similarity=0.091 Sum_probs=26.1
Q ss_pred chHHHHHHHHHhhCCCceechhh--HHHHHHHHhhCCCCccEEecC
Q psy9334 5 FGYPNLGQTMAKLYPKIQFEQMI--VDNCTMQIVSNPHQFDVMVMP 48 (65)
Q Consensus 5 ~~f~~~~~eva~~ypdV~~~~~~--vDa~~~~lv~~P~~fDVIV~~ 48 (65)
..+-+...+..++||+++++-.. -+.....|.. ++.|+.++.
T Consensus 13 ~~l~~~l~~~~~~~P~i~l~~~~~~~~~~~~~l~~--g~~Dl~i~~ 56 (195)
T cd08427 13 GLLPRALARLRRRHPDLEVHIVPGLSAELLARVDA--GELDAAIVV 56 (195)
T ss_pred HHhHHHHHHHHHHCCCceEEEEeCCcHHHHHHHHC--CCCCEEEEc
Confidence 34456778888999998776543 3344334433 467876653
No 78
>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=43.16 E-value=20 Score=23.59 Aligned_cols=29 Identities=17% Similarity=0.243 Sum_probs=22.0
Q ss_pred chhchHHHHHHHHHhhCCCceechhhHHHH
Q psy9334 2 PCRFGYPNLGQTMAKLYPKIQFEQMIVDNC 31 (65)
Q Consensus 2 ~~~~~f~~~~~eva~~ypdV~~~~~~vDa~ 31 (65)
||+.+ ....+++|++||.+++-...+|..
T Consensus 97 ~Ck~m-~~~l~~LA~~~~~vkF~kVd~d~~ 125 (175)
T cd02987 97 GCAAL-NSSLLCLAAEYPAVKFCKIRASAT 125 (175)
T ss_pred hHHHH-HHHHHHHHHHCCCeEEEEEeccch
Confidence 56644 457788999999988888877763
No 79
>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=43.12 E-value=42 Score=20.04 Aligned_cols=41 Identities=5% Similarity=0.107 Sum_probs=25.2
Q ss_pred hHHHHHHHHHhhCCCceechhhHHH-HHHHHhhCCCCccEEec
Q psy9334 6 GYPNLGQTMAKLYPKIQFEQMIVDN-CTMQIVSNPHQFDVMVM 47 (65)
Q Consensus 6 ~f~~~~~eva~~ypdV~~~~~~vDa-~~~~lv~~P~~fDVIV~ 47 (65)
.+-....++.++||+++++-..... -..+.+.+ ++.|+.+.
T Consensus 14 ~~~~~l~~~~~~~P~i~i~i~~~~~~~~~~~l~~-g~~Dl~i~ 55 (198)
T cd08441 14 WLMPVLDQFRERWPDVELDLSSGFHFDPLPALLR-GELDLVIT 55 (198)
T ss_pred hhHHHHHHHHHhCCCeEEEEEeCCchhHHHHHHc-CCceEEEe
Confidence 4456778889999998877553322 22333333 55776664
No 80
>COG1653 UgpB ABC-type sugar transport system, periplasmic component [Carbohydrate transport and metabolism]
Probab=42.87 E-value=65 Score=22.13 Aligned_cols=47 Identities=15% Similarity=0.168 Sum_probs=31.3
Q ss_pred chHHHHHHHHHhhCCCceechhhHH--HHHHHHhhC---CCCccEEecCCch
Q psy9334 5 FGYPNLGQTMAKLYPKIQFEQMIVD--NCTMQIVSN---PHQFDVMVMPNLY 51 (65)
Q Consensus 5 ~~f~~~~~eva~~ypdV~~~~~~vD--a~~~~lv~~---P~~fDVIV~~Nl~ 51 (65)
..+++++.+.-+++|+|+++...+. ....++... -...||+...+.+
T Consensus 46 ~~~~~~i~~f~~~~p~ikv~~~~~~~~~~~~~l~~~~~ag~~PDv~~~~~~~ 97 (433)
T COG1653 46 DALEELIKEFEKENPGIKVKVVNVPGDDYLQKLLTALASGDAPDVVQLDPEW 97 (433)
T ss_pred HHHHHHHHHHHHhCCCeEEEEEecCcHHHHHHHHHHHhcCCCCCeEEeccch
Confidence 5677888888899999888887764 233333332 3334988887633
No 81
>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=42.76 E-value=52 Score=19.22 Aligned_cols=41 Identities=22% Similarity=0.330 Sum_probs=25.3
Q ss_pred hHHHHHHHHHhhCCCceechhhHHH-HHHHHhhCCCCccEEec
Q psy9334 6 GYPNLGQTMAKLYPKIQFEQMIVDN-CTMQIVSNPHQFDVMVM 47 (65)
Q Consensus 6 ~f~~~~~eva~~ypdV~~~~~~vDa-~~~~lv~~P~~fDVIV~ 47 (65)
.......+..+.||+++++-..... -..+.+.+ ++.|+.+.
T Consensus 14 ~l~~~l~~~~~~~P~i~i~i~~~~~~~~~~~l~~-~~~Dl~i~ 55 (195)
T cd08434 14 LVPDLIRAFRKEYPNVTFELHQGSTDELLDDLKN-GELDLALC 55 (195)
T ss_pred hhHHHHHHHHHhCCCeEEEEecCcHHHHHHHHHc-CCccEEEE
Confidence 4456778888899998877654322 22333443 36786664
No 82
>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=42.68 E-value=16 Score=21.70 Aligned_cols=39 Identities=13% Similarity=0.146 Sum_probs=25.3
Q ss_pred hHHHHHHHHHhhCCCceechhhHHHHHHHHhhCCCCccEEec
Q psy9334 6 GYPNLGQTMAKLYPKIQFEQMIVDNCTMQIVSNPHQFDVMVM 47 (65)
Q Consensus 6 ~f~~~~~eva~~ypdV~~~~~~vDa~~~~lv~~P~~fDVIV~ 47 (65)
.+-....+..++||+++++-..-+.. .+++++ ++|+.++
T Consensus 14 ~l~~~l~~f~~~~P~i~l~i~~~~~~-~~~~~~--~~Dl~i~ 52 (189)
T cd08487 14 WLLPRLAEFRQLHPFIELRLRTNNNV-VDLATE--GLDFAIR 52 (189)
T ss_pred HHhHHHHHHHHHCCCceEEeeecCCc-cccccC--CcCEEEE
Confidence 34466778888999988775433333 355554 4897765
No 83
>COG1744 Med Uncharacterized ABC-type transport system, periplasmic component/surface lipoprotein [General function prediction only]
Probab=42.59 E-value=18 Score=26.43 Aligned_cols=23 Identities=22% Similarity=0.499 Sum_probs=18.6
Q ss_pred hhchHHHHHHHHHhhCCCceech
Q psy9334 3 CRFGYPNLGQTMAKLYPKIQFEQ 25 (65)
Q Consensus 3 ~~~~f~~~~~eva~~ypdV~~~~ 25 (65)
.+..|.+..+++|++||++.+.+
T Consensus 104 ~gf~~~d~~~~va~~~Pd~~F~i 126 (345)
T COG1744 104 TGFAFSDALEKVAAEYPDVKFVI 126 (345)
T ss_pred eccchhhHHHHHHHHCCCCEEEE
Confidence 35678899999999999987654
No 84
>PRK12862 malic enzyme; Reviewed
Probab=42.45 E-value=69 Score=26.24 Aligned_cols=54 Identities=22% Similarity=0.348 Sum_probs=34.8
Q ss_pred HHHHHHHHhhCCCceec-hhhHHHHHHHHhhC---C-----CCccEEecCCch-HHHHHhhhhh
Q psy9334 8 PNLGQTMAKLYPKIQFE-QMIVDNCTMQIVSN---P-----HQFDVMVMPNLY-GNIVDNLASD 61 (65)
Q Consensus 8 ~~~~~eva~~ypdV~~~-~~~vDa~~~~lv~~---P-----~~fDVIV~~Nl~-GDIlSD~aa~ 61 (65)
++..+.+.+++|++.++ ++-.|++...=++. | +.+|++|+||+- |.|.--+..-
T Consensus 654 ~pAiellr~~~~g~~VdGPl~aDtAf~~~~~~~K~~~s~vaG~aDvLV~P~~DqGNI~~Kll~f 717 (763)
T PRK12862 654 REALEILRERAPDLEVDGEMHGDAALDEELRDRIFPDSRLEGEANLLVFPNLDAANIAYNLLKT 717 (763)
T ss_pred HHHHHHHHhcCCCcEEEcCCCHHHHcCHHHHhhcCCCCccCCCCCEEEecChhHhhHHHHHHHH
Confidence 45555566678887665 45568876443332 2 349999999986 7776555433
No 85
>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=42.24 E-value=46 Score=19.66 Aligned_cols=42 Identities=12% Similarity=0.286 Sum_probs=25.8
Q ss_pred hHHHHHHHHHhhCCCceechhhHHHH-HHHHhhCCCCccEEecC
Q psy9334 6 GYPNLGQTMAKLYPKIQFEQMIVDNC-TMQIVSNPHQFDVMVMP 48 (65)
Q Consensus 6 ~f~~~~~eva~~ypdV~~~~~~vDa~-~~~lv~~P~~fDVIV~~ 48 (65)
++-+..++..++||+++++-..-+.- ..+.+.+ ++.|+.++.
T Consensus 15 ~l~~~l~~~~~~~P~i~l~i~~~~~~~~~~~l~~-g~~Dl~i~~ 57 (199)
T cd08451 15 LVPGLIRRFREAYPDVELTLEEANTAELLEALRE-GRLDAAFVR 57 (199)
T ss_pred ccHHHHHHHHHHCCCcEEEEecCChHHHHHHHHC-CCccEEEEe
Confidence 45567888999999887776543221 2233333 367876653
No 86
>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=41.68 E-value=54 Score=19.46 Aligned_cols=41 Identities=12% Similarity=0.128 Sum_probs=25.8
Q ss_pred hHHHHHHHHHhhCCCceechhhHH-HHHHHHhhCCCCccEEec
Q psy9334 6 GYPNLGQTMAKLYPKIQFEQMIVD-NCTMQIVSNPHQFDVMVM 47 (65)
Q Consensus 6 ~f~~~~~eva~~ypdV~~~~~~vD-a~~~~lv~~P~~fDVIV~ 47 (65)
.+-+...+..++||+++++-...+ .-..+.+.+ +++|+.++
T Consensus 15 ~l~~~l~~~~~~~P~v~i~i~~~~~~~~~~~l~~-g~~Dl~i~ 56 (197)
T cd08425 15 LIGPLIDRFHARYPGIALSLREMPQERIEAALAD-DRLDLGIA 56 (197)
T ss_pred hhHHHHHHHHHHCCCcEEEEEECcHHHHHHHHHc-CCccEEEE
Confidence 345677788889999887765432 223344444 46887765
No 87
>PRK04168 molybdate ABC transporter periplasmic substrate-binding protein; Provisional
Probab=41.61 E-value=54 Score=23.73 Aligned_cols=44 Identities=11% Similarity=0.290 Sum_probs=30.5
Q ss_pred hHHHHHHHHHhhCCCceechhhHHH--HHHHHhhCCCCccEEecCC
Q psy9334 6 GYPNLGQTMAKLYPKIQFEQMIVDN--CTMQIVSNPHQFDVMVMPN 49 (65)
Q Consensus 6 ~f~~~~~eva~~ypdV~~~~~~vDa--~~~~lv~~P~~fDVIV~~N 49 (65)
.+.++.+...+++|+++++..+--+ +..|+..+-..+||.++-|
T Consensus 45 ~l~~i~~~fe~~~~gv~v~~~~~gSg~L~~QI~e~Gap~DVfisAd 90 (334)
T PRK04168 45 PFEEYEKEFEAYHPNVDVQREAGGSVKCVRKITELGKKADIMASAD 90 (334)
T ss_pred HHHHHHHHHHHhCCCeeEEEEeCcHHHHHHHHHhcCCCCCEEEECc
Confidence 3555666666678888887766654 5677754456699988877
No 88
>COG2227 UbiG 2-polyprenyl-3-methyl-5-hydroxy-6-metoxy-1,4-benzoquinol methylase [Coenzyme metabolism]
Probab=41.44 E-value=39 Score=24.24 Aligned_cols=24 Identities=21% Similarity=0.246 Sum_probs=17.7
Q ss_pred HHHHHHHHhhCCCCccEEecCCch
Q psy9334 28 VDNCTMQIVSNPHQFDVMVMPNLY 51 (65)
Q Consensus 28 vDa~~~~lv~~P~~fDVIV~~Nl~ 51 (65)
.-.++..|...-++||||++--+.
T Consensus 111 ~~~~~edl~~~~~~FDvV~cmEVl 134 (243)
T COG2227 111 RQATVEDLASAGGQFDVVTCMEVL 134 (243)
T ss_pred hhhhHHHHHhcCCCccEEEEhhHH
Confidence 335566777777999999986554
No 89
>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=41.32 E-value=54 Score=19.42 Aligned_cols=41 Identities=12% Similarity=0.195 Sum_probs=25.7
Q ss_pred hHHHHHHHHHhhCCCceechhhHH--HHHHHHhhCCCCccEEecC
Q psy9334 6 GYPNLGQTMAKLYPKIQFEQMIVD--NCTMQIVSNPHQFDVMVMP 48 (65)
Q Consensus 6 ~f~~~~~eva~~ypdV~~~~~~vD--a~~~~lv~~P~~fDVIV~~ 48 (65)
.+.....++.++||+++++-..-+ ....+| .+ +++|+.++.
T Consensus 14 ~~~~~i~~~~~~~P~i~l~~~~~~~~~~~~~l-~~-g~~D~~i~~ 56 (200)
T cd08417 14 LLPPLLARLRQEAPGVRLRFVPLDRDDLEEAL-ES-GEIDLAIGV 56 (200)
T ss_pred HHHHHHHHHHhhCCCeEEEeccCCHHHHHHHH-Hc-CCCCEEEee
Confidence 344677888899999877765433 333334 33 368876653
No 90
>PF13174 TPR_6: Tetratricopeptide repeat; PDB: 3QKY_A 2XEV_A 3URZ_B 2Q7F_A.
Probab=41.28 E-value=28 Score=15.47 Aligned_cols=13 Identities=31% Similarity=0.373 Sum_probs=9.4
Q ss_pred HHHHHHHHhhCCC
Q psy9334 8 PNLGQTMAKLYPK 20 (65)
Q Consensus 8 ~~~~~eva~~ypd 20 (65)
.+..+++.++||+
T Consensus 20 ~~~~~~~~~~~P~ 32 (33)
T PF13174_consen 20 IEYFQRLIKRYPD 32 (33)
T ss_dssp HHHHHHHHHHSTT
T ss_pred HHHHHHHHHHCcC
Confidence 3567777888886
No 91
>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=41.15 E-value=46 Score=19.54 Aligned_cols=40 Identities=15% Similarity=0.224 Sum_probs=24.8
Q ss_pred hHHHHHHHHHhhCCCceechhhHH--HHHHHHhhCCCCccEEec
Q psy9334 6 GYPNLGQTMAKLYPKIQFEQMIVD--NCTMQIVSNPHQFDVMVM 47 (65)
Q Consensus 6 ~f~~~~~eva~~ypdV~~~~~~vD--a~~~~lv~~P~~fDVIV~ 47 (65)
.+-....++.++||+|+++-...+ ....+|. + +++|+.++
T Consensus 14 ~l~~~l~~~~~~~P~i~l~i~~~~~~~~~~~l~-~-g~~Dl~i~ 55 (193)
T cd08442 14 RLPPLLAAYHARYPKVDLSLSTGTTGALIQAVL-E-GRLDGAFV 55 (193)
T ss_pred hhHHHHHHHHHHCCCceEEEEeCCcHHHHHHHH-C-CCccEEEE
Confidence 345677888899999887765433 2222332 2 56787665
No 92
>TIGR03401 cyanamide_fam HD domain protein, cyanamide hydratase family. Members of this protein family are known, so far, in the Ascomycota, a branch of the Fungi, and contain an HD domain (pfam01966), found typically in various metal-dependent phosphohydrolases. The only characterized member of this family, from the soil fungus Myrothecium verrucaria, is cyanamide hydratase (EC 4.2.1.69), a zinc-containing homohexamer that adds water to the fertilizer cyanamide (NCNH2), a nitrile compound, to produce urea (NH2-CO-NH2). Homologs are likely to be nitrile hydratases.
Probab=41.13 E-value=36 Score=23.61 Aligned_cols=34 Identities=9% Similarity=0.176 Sum_probs=30.2
Q ss_pred HHHHHHHhhCCCceechhhHHHHHHHHhhCCCCc
Q psy9334 9 NLGQTMAKLYPKIQFEQMIVDNCTMQIVSNPHQF 42 (65)
Q Consensus 9 ~~~~eva~~ypdV~~~~~~vDa~~~~lv~~P~~f 42 (65)
+..++|-+.||...+...++++....+-.+|+.-
T Consensus 176 ~~~~~v~~~~PR~~~~~~~~~~~~~~~~~kP~~~ 209 (228)
T TIGR03401 176 DTVDAVNEAYPRHGWSSCFASTIRKENELKPWCH 209 (228)
T ss_pred HHHHHHHHHCCchhHHHHHHHHHHHHHccCCCcc
Confidence 4567888999999999999999999999999853
No 93
>PF04155 Ground-like: Ground-like domain; InterPro: IPR007284 This group of proteins contain one or more copies of the ground-like domain, which are specific to Caenorhabditis elegans and Caenorhabditis briggsae. It has been proposed that the ground-like domain containing proteins may bind and modulate the activity of Patched-like membrane molecules, reminiscent of the modulating activities of neuropeptides [].
Probab=40.69 E-value=53 Score=18.67 Aligned_cols=13 Identities=15% Similarity=0.319 Sum_probs=11.4
Q ss_pred CCCccEEecCCch
Q psy9334 39 PHQFDVMVMPNLY 51 (65)
Q Consensus 39 P~~fDVIV~~Nl~ 51 (65)
|.+|+||++++-|
T Consensus 40 ~~~f~vIcs~~~F 52 (76)
T PF04155_consen 40 GGSFEVICSEGDF 52 (76)
T ss_pred CCCEEEEEeCCCc
Confidence 6699999999877
No 94
>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=40.42 E-value=27 Score=20.70 Aligned_cols=38 Identities=16% Similarity=0.316 Sum_probs=25.2
Q ss_pred HHHHHHHHHhhCCCceechhhHHHHHHHHhhCCCCccEEec
Q psy9334 7 YPNLGQTMAKLYPKIQFEQMIVDNCTMQIVSNPHQFDVMVM 47 (65)
Q Consensus 7 f~~~~~eva~~ypdV~~~~~~vDa~~~~lv~~P~~fDVIV~ 47 (65)
.-+...+..++||+++++-..-+. ..+++. ++.|+.++
T Consensus 16 l~~~l~~~~~~~P~i~l~i~~~~~-~~~~~~--~~~D~~i~ 53 (197)
T cd08477 16 LTPALAEYLARYPDVRVDLVLSDR-LVDLVE--EGFDAAFR 53 (197)
T ss_pred HHHHHHHHHHHCCCcEEEEEecCC-cchhhh--cCccEEEE
Confidence 346778888999998887653222 344554 35898775
No 95
>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=40.06 E-value=48 Score=19.54 Aligned_cols=40 Identities=13% Similarity=0.125 Sum_probs=24.6
Q ss_pred hHHHHHHHHHhhCCCceechhhHH--HHHHHHhhCCCCccEEec
Q psy9334 6 GYPNLGQTMAKLYPKIQFEQMIVD--NCTMQIVSNPHQFDVMVM 47 (65)
Q Consensus 6 ~f~~~~~eva~~ypdV~~~~~~vD--a~~~~lv~~P~~fDVIV~ 47 (65)
.......++.++||+++++-...+ .....|.+ +++|+.++
T Consensus 14 ~l~~~l~~~~~~~P~i~l~i~~~~~~~~~~~l~~--~~~Dl~i~ 55 (196)
T cd08415 14 LLPRAIARFRARHPDVRISLHTLSSSTVVEAVLS--GQADLGLA 55 (196)
T ss_pred ccHHHHHHHHHHCCCcEEEEEecchHHHHHHHHc--CCccEEEE
Confidence 344677888889999887765443 23333333 46786654
No 96
>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=40.00 E-value=42 Score=20.34 Aligned_cols=42 Identities=12% Similarity=0.155 Sum_probs=26.5
Q ss_pred chHHHHHHHHHhhCCCceechhhHHH-HHHHHhhCCCCccEEec
Q psy9334 5 FGYPNLGQTMAKLYPKIQFEQMIVDN-CTMQIVSNPHQFDVMVM 47 (65)
Q Consensus 5 ~~f~~~~~eva~~ypdV~~~~~~vDa-~~~~lv~~P~~fDVIV~ 47 (65)
.+..+...+..++||+++++-...+. .....+.+ ++.|+.++
T Consensus 13 ~~l~~~l~~~~~~~P~i~l~~~~~~~~~~~~~l~~-g~~D~~i~ 55 (200)
T cd08467 13 ALLPRLAPRLRERAPGLDLRLCPIGDDLAERGLEQ-GTIDLAVG 55 (200)
T ss_pred HHHHHHHHHHHhhCCCCEEEEecCCcccHHHHhhC-CCcCEEEe
Confidence 34456778889999998877654333 22333333 56787765
No 97
>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=39.97 E-value=62 Score=19.13 Aligned_cols=41 Identities=10% Similarity=0.161 Sum_probs=26.2
Q ss_pred hHHHHHHHHHhhCCCceechhhHHH-HHHHHhhCCCCccEEec
Q psy9334 6 GYPNLGQTMAKLYPKIQFEQMIVDN-CTMQIVSNPHQFDVMVM 47 (65)
Q Consensus 6 ~f~~~~~eva~~ypdV~~~~~~vDa-~~~~lv~~P~~fDVIV~ 47 (65)
..-+...+..+.||+++++-..... -....+.+ ++.|+.++
T Consensus 14 ~l~~~l~~~~~~~P~i~l~i~~~~~~~~~~~l~~-g~~Dl~i~ 55 (201)
T cd08418 14 LMPAVINRFKEQFPDVQISIYEGQLSSLLPELRD-GRLDFAIG 55 (201)
T ss_pred hhHHHHHHHHHHCCCceEEEEeCcHHHHHHHHHc-CCCcEEEE
Confidence 3446677888899998887664322 22344444 57887775
No 98
>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=39.95 E-value=55 Score=19.33 Aligned_cols=42 Identities=17% Similarity=0.121 Sum_probs=25.8
Q ss_pred chHHHHHHHHHhhCCCceechhhHHHH-HHHHhhCCCCccEEec
Q psy9334 5 FGYPNLGQTMAKLYPKIQFEQMIVDNC-TMQIVSNPHQFDVMVM 47 (65)
Q Consensus 5 ~~f~~~~~eva~~ypdV~~~~~~vDa~-~~~lv~~P~~fDVIV~ 47 (65)
..+-+...++.+.||+++++-...+.. ..+.+.+ ++.|+.++
T Consensus 13 ~~l~~~l~~~~~~~P~i~~~i~~~~~~~~~~~l~~-g~~Dl~i~ 55 (196)
T cd08456 13 SFLPRAIKAFLQRHPDVTISIHTRDSPTVEQWLSA-QQCDLGLV 55 (196)
T ss_pred hhHHHHHHHHHHHCCCcEEEEEeCCHHHHHHHHHc-CCccEEEE
Confidence 345577888899999887776643332 2233333 46776654
No 99
>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=39.53 E-value=57 Score=19.24 Aligned_cols=40 Identities=15% Similarity=0.255 Sum_probs=25.3
Q ss_pred hHHHHHHHHHhhCCCceechhhHH--HHHHHHhhCCCCccEEec
Q psy9334 6 GYPNLGQTMAKLYPKIQFEQMIVD--NCTMQIVSNPHQFDVMVM 47 (65)
Q Consensus 6 ~f~~~~~eva~~ypdV~~~~~~vD--a~~~~lv~~P~~fDVIV~ 47 (65)
..-+...+..++||+++++-...+ .+..+|.+ ++.|+.++
T Consensus 14 ~l~~~l~~~~~~~P~i~l~i~~~~~~~~~~~l~~--~~~D~~i~ 55 (198)
T cd08412 14 YLPGLLRRFREAYPGVEVRVVEGNQEELEEGLRS--GELDLALT 55 (198)
T ss_pred hhHHHHHHHHHHCCCcEEEEEECCHHHHHHHHHc--CCCcEEEE
Confidence 344677788899999887765432 23333433 57787665
No 100
>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=39.38 E-value=53 Score=19.21 Aligned_cols=42 Identities=19% Similarity=0.264 Sum_probs=25.3
Q ss_pred hHHHHHHHHHhhCCCceechhhHHH-HHHHHhhCCCCccEEecC
Q psy9334 6 GYPNLGQTMAKLYPKIQFEQMIVDN-CTMQIVSNPHQFDVMVMP 48 (65)
Q Consensus 6 ~f~~~~~eva~~ypdV~~~~~~vDa-~~~~lv~~P~~fDVIV~~ 48 (65)
...+...+..+.||+++++-...+. -....+.+ ++.|+.++.
T Consensus 14 ~l~~~l~~~~~~~P~~~l~~~~~~~~~~~~~l~~-g~~D~~i~~ 56 (201)
T cd08420 14 LLPRLLARFRKRYPEVRVSLTIGNTEEIAERVLD-GEIDLGLVE 56 (201)
T ss_pred hhHHHHHHHHHHCCCceEEEEeCCcHHHHHHHHC-CCccEEEec
Confidence 4456777888899998776543222 12333333 467876654
No 101
>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=39.32 E-value=23 Score=18.68 Aligned_cols=28 Identities=21% Similarity=0.259 Sum_probs=19.9
Q ss_pred chhchHHHHHHHHHhhCCCceechhhHHH
Q psy9334 2 PCRFGYPNLGQTMAKLYPKIQFEQMIVDN 30 (65)
Q Consensus 2 ~~~~~f~~~~~eva~~ypdV~~~~~~vDa 30 (65)
+|... ++..+++++++|++++....+|.
T Consensus 13 ~C~~~-~~~l~~l~~~~~~i~~~~id~~~ 40 (67)
T cd02973 13 YCPDA-VQAANRIAALNPNISAEMIDAAE 40 (67)
T ss_pred CcHHH-HHHHHHHHHhCCceEEEEEEccc
Confidence 45433 55777888888988888777664
No 102
>cd06353 PBP1_BmpA_Med_like Periplasmic binding domain of the basic membrane lipoprotein Med in Bacillus and its close homologs from other bacteria and Archaea. Periplasmic binding domain of the basic membrane lipoprotein Med in Bacillus and its close homologs from other bacteria and Archaea. Med, a cell-surface localized protein, which regulates the competence transcription factor gene comK in Bacillus subtilis, lacks the DNA binding domain when compared with structures of transcription regulators from the LacI family. Nevertheless, Med has significant overall sequence homology to various periplasmic substrate-binding proteins. Moreover, the structure of Med shows a striking similarity to PnrA, a periplasmic nucleoside binding protein of an ATP-binding cassette transport system. Members of this group contain the type I periplasmic sugar-binding protein-like fold.
Probab=39.08 E-value=27 Score=23.89 Aligned_cols=19 Identities=37% Similarity=0.845 Sum_probs=14.9
Q ss_pred chHHHHHHHHHhhCCCcee
Q psy9334 5 FGYPNLGQTMAKLYPKIQF 23 (65)
Q Consensus 5 ~~f~~~~~eva~~ypdV~~ 23 (65)
..+.+.+.++|++||++.+
T Consensus 66 ~~~~~~~~~vA~~~p~~~F 84 (258)
T cd06353 66 FGFMDAALKVAKEYPDVKF 84 (258)
T ss_pred hhhhHHHHHHHHHCCCCEE
Confidence 4567888899999998764
No 103
>COG4989 Predicted oxidoreductase [General function prediction only]
Probab=38.71 E-value=50 Score=24.42 Aligned_cols=40 Identities=8% Similarity=0.120 Sum_probs=28.8
Q ss_pred HHHHHHHHhhCCCceechhhHHHHHHHHhhCCCCccEEecCCch
Q psy9334 8 PNLGQTMAKLYPKIQFEQMIVDNCTMQIVSNPHQFDVMVMPNLY 51 (65)
Q Consensus 8 ~~~~~eva~~ypdV~~~~~~vDa~~~~lv~~P~~fDVIV~~Nl~ 51 (65)
+++.+++|++|.-+..+. .+.+||++.|.++--||-++--
T Consensus 227 ~~~l~~ia~e~ga~s~~~----VaiAWllR~Pa~~~PiiGt~~~ 266 (298)
T COG4989 227 RKVLDRIAEEYGAVSITA----VAIAWLLRHPAKPQPIIGTGNL 266 (298)
T ss_pred HHHHHHHHHHhCcccHHH----HHHHHHHhCcCcccceecCCCH
Confidence 456677788886555443 4568999999999977766543
No 104
>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=38.20 E-value=31 Score=20.26 Aligned_cols=40 Identities=20% Similarity=0.390 Sum_probs=25.7
Q ss_pred hHHHHHHHHHhhCCCceechhhHHHHHHHHhhCCCCccEEecC
Q psy9334 6 GYPNLGQTMAKLYPKIQFEQMIVDNCTMQIVSNPHQFDVMVMP 48 (65)
Q Consensus 6 ~f~~~~~eva~~ypdV~~~~~~vDa~~~~lv~~P~~fDVIV~~ 48 (65)
..-+...++.++||+++++-..-+. ..+++. ++.|+.++.
T Consensus 15 ~l~~~l~~~~~~~P~v~i~i~~~~~-~~~l~~--~~~D~~i~~ 54 (197)
T cd08422 15 HLAPLLAEFLARYPDVRLELVLSDR-LVDLVE--EGFDLAIRI 54 (197)
T ss_pred HHHHHHHHHHHhCCceEEEEecCcc-ccchhh--cCccEEEEe
Confidence 3456778889999998876653332 234444 358976653
No 105
>PRK00536 speE spermidine synthase; Provisional
Probab=38.15 E-value=35 Score=24.26 Aligned_cols=17 Identities=6% Similarity=0.206 Sum_probs=12.2
Q ss_pred HhhC-CCCccEEecCCch
Q psy9334 35 IVSN-PHQFDVMVMPNLY 51 (65)
Q Consensus 35 lv~~-P~~fDVIV~~Nl~ 51 (65)
+..+ +++||||+...+|
T Consensus 132 ~~~~~~~~fDVIIvDs~~ 149 (262)
T PRK00536 132 LLDLDIKKYDLIICLQEP 149 (262)
T ss_pred hhhccCCcCCEEEEcCCC
Confidence 4443 4899999988655
No 106
>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=38.09 E-value=43 Score=19.93 Aligned_cols=40 Identities=8% Similarity=-0.056 Sum_probs=24.0
Q ss_pred hHHHHHHHHHhhCCCceechhhH--HHHHHHHhhCCCCccEEec
Q psy9334 6 GYPNLGQTMAKLYPKIQFEQMIV--DNCTMQIVSNPHQFDVMVM 47 (65)
Q Consensus 6 ~f~~~~~eva~~ypdV~~~~~~v--Da~~~~lv~~P~~fDVIV~ 47 (65)
..-....+..++||+++++-... +.....|. -++.|+.+.
T Consensus 14 ~l~~~l~~~~~~~P~v~i~i~~~~~~~~~~~l~--~g~~D~~i~ 55 (195)
T cd08431 14 PLYPLIAEFYQLNKATRIRLSEEVLGGTWDALA--SGRADLVIG 55 (195)
T ss_pred HHHHHHHHHHHHCCCCceEEEEeccchHHHHHh--CCCCCEEEE
Confidence 34567788889999987765432 22323322 456676664
No 107
>PF04255 DUF433: Protein of unknown function (DUF433); InterPro: IPR007367 This is a family of uncharacterised proteins.; PDB: 2GA1_B.
Probab=37.25 E-value=20 Score=19.45 Aligned_cols=16 Identities=25% Similarity=0.517 Sum_probs=10.6
Q ss_pred HHHHHHhhCCCceech
Q psy9334 10 LGQTMAKLYPKIQFEQ 25 (65)
Q Consensus 10 ~~~eva~~ypdV~~~~ 25 (65)
..+|++++||+++.+.
T Consensus 33 s~eeI~~~yp~Lt~~~ 48 (56)
T PF04255_consen 33 SPEEIAEDYPSLTLED 48 (56)
T ss_dssp -HHHHHHHSTT--HHH
T ss_pred CHHHHHHHCCCCCHHH
Confidence 5678999999987554
No 108
>PTZ00062 glutaredoxin; Provisional
Probab=36.51 E-value=28 Score=23.84 Aligned_cols=27 Identities=7% Similarity=0.246 Sum_probs=20.2
Q ss_pred chhchHHHHHHHHHhhCCCceechhhHH
Q psy9334 2 PCRFGYPNLGQTMAKLYPKIQFEQMIVD 29 (65)
Q Consensus 2 ~~~~~f~~~~~eva~~ypdV~~~~~~vD 29 (65)
||+ ....+..+++++||++.+-....|
T Consensus 31 ~C~-~m~~vl~~l~~~~~~~~F~~V~~d 57 (204)
T PTZ00062 31 EYE-QLMDVCNALVEDFPSLEFYVVNLA 57 (204)
T ss_pred chH-HHHHHHHHHHHHCCCcEEEEEccc
Confidence 455 446788999999999877766655
No 109
>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=36.13 E-value=74 Score=18.81 Aligned_cols=40 Identities=13% Similarity=0.174 Sum_probs=25.0
Q ss_pred hHHHHHHHHHhhCCCceechh--hHHHHHHHHhhCCCCccEEec
Q psy9334 6 GYPNLGQTMAKLYPKIQFEQM--IVDNCTMQIVSNPHQFDVMVM 47 (65)
Q Consensus 6 ~f~~~~~eva~~ypdV~~~~~--~vDa~~~~lv~~P~~fDVIV~ 47 (65)
..-+...+..+.||+++++-. .-+....+|.. +++|+.++
T Consensus 14 ~l~~~l~~~~~~~P~i~v~~~~~~~~~~~~~l~~--g~~D~~i~ 55 (198)
T cd08447 14 FLPRLLAAARAALPDVDLVLREMVTTDQIEALES--GRIDLGLL 55 (198)
T ss_pred HHHHHHHHHHHHCCCeEEEEEeCCHHHHHHHHHc--CCceEEEe
Confidence 344677788889999887653 33344444443 55677665
No 110
>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=36.12 E-value=24 Score=21.28 Aligned_cols=28 Identities=14% Similarity=0.189 Sum_probs=19.9
Q ss_pred chhchHHHHHHHHHhhCCCceechhhHHH
Q psy9334 2 PCRFGYPNLGQTMAKLYPKIQFEQMIVDN 30 (65)
Q Consensus 2 ~~~~~f~~~~~eva~~ypdV~~~~~~vDa 30 (65)
||+.+- ...++++++||++++-...+|.
T Consensus 36 ~C~~~~-p~l~~la~~~~~i~f~~Vd~~~ 63 (113)
T cd02989 36 RCKIMD-KHLEILAKKHLETKFIKVNAEK 63 (113)
T ss_pred cHHHHH-HHHHHHHHHcCCCEEEEEEccc
Confidence 566544 4778889999988776665555
No 111
>cd02988 Phd_like_VIAF Phosducin (Phd)-like family, Viral inhibitor of apoptosis (IAP)-associated factor (VIAF) subfamily; VIAF is a Phd-like protein that functions in caspase activation during apoptosis. It was identified as an IAP binding protein through a screen of a human B-cell library using a prototype IAP. VIAF lacks a consensus IAP binding motif and while it does not function as an IAP antagonist, it still plays a regulatory role in the complete activation of caspases. VIAF itself is a substrate for IAP-mediated ubiquitination, suggesting that it may be a target of IAPs in the prevention of cell death. The similarity of VIAF to Phd points to a potential role distinct from apoptosis regulation. Phd functions as a cytosolic regulator of G protein by specifically binding to G protein betagamma (Gbg)-subunits. The C-terminal domain of Phd adopts a thioredoxin fold, but it does not contain a CXXC motif. Phd interacts with G protein beta mostly through the N-terminal helical domain.
Probab=35.87 E-value=38 Score=22.69 Aligned_cols=29 Identities=24% Similarity=0.618 Sum_probs=22.8
Q ss_pred chhchHHHHHHHHHhhCCCceechhhHHHH
Q psy9334 2 PCRFGYPNLGQTMAKLYPKIQFEQMIVDNC 31 (65)
Q Consensus 2 ~~~~~f~~~~~eva~~ypdV~~~~~~vDa~ 31 (65)
||+. .....+++|++||++++-...+|.+
T Consensus 116 ~C~~-m~~~l~~LA~k~~~vkFvkI~ad~~ 144 (192)
T cd02988 116 LCRL-LNQHLSELARKFPDTKFVKIISTQC 144 (192)
T ss_pred hHHH-HHHHHHHHHHHCCCCEEEEEEhHHh
Confidence 4554 3557888999999999988888875
No 112
>PF08242 Methyltransf_12: Methyltransferase domain; InterPro: IPR013217 Methyl transfer from the ubiquitous donor S-adenosyl-L-methionine (SAM) to either nitrogen, oxygen or carbon atoms is frequently employed in diverse organisms ranging from bacteria to plants and mammals. The reaction is catalyzed by methyltransferases (Mtases) and modifies DNA, RNA, proteins and small molecules, such as catechol for regulatory purposes. The various aspects of the role of DNA methylation in prokaryotic restriction-modification systems and in a number of cellular processes in eukaryotes including gene regulation and differentiation is well documented. This entry represents a methyltransferase domain found in a large variety of SAM-dependent methyltransferases including, but not limited to: Hexaprenyldihydroxybenzoate methyltransferase (2.1.1.114 from EC), a mitochodrial enzyme involved in ubiquinone biosynthesis [] Fatty acid synthase (2.3.1.85 from EC), a biosynthetic enzyme catalysing the formation of long-chain fatty acids Glycine N-methyltransferase (2.1.1.20 from EC) which catalyses the SAM-dependent methylation of glycine to form sarcosine and may play a role in regulating the methylation potential of the cell [] Enniatin synthetase, involved in non-ribosomal biosynthesis of cyclohexadepsipeptidase, enniatin [] Histamine N-methyltransferase (2.1.1.8 from EC), a SAM-dependent histamine-inactivating enzyme [] A probable cobalt-precorrin-6Y C(15)-methyltransferase thought to be involved in adenosylcobalamin biosynthesis [] Structural studies show that this domain forms the Rossman-like alpha-beta fold typical of SAM-dependent methyltransferases [, , ].; PDB: 2VZ8_A 2VZ9_A.
Probab=35.43 E-value=14 Score=21.00 Aligned_cols=15 Identities=27% Similarity=0.600 Sum_probs=8.1
Q ss_pred CCccEEecCCchHHH
Q psy9334 40 HQFDVMVMPNLYGNI 54 (65)
Q Consensus 40 ~~fDVIV~~Nl~GDI 54 (65)
++||+|++.|.+--+
T Consensus 65 ~~fD~V~~~~vl~~l 79 (99)
T PF08242_consen 65 ESFDLVVASNVLHHL 79 (99)
T ss_dssp ---SEEEEE-TTS--
T ss_pred cccceehhhhhHhhh
Confidence 699999999887655
No 113
>PF01523 PmbA_TldD: Putative modulator of DNA gyrase; InterPro: IPR002510 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. The peptidases families associated with clan U- have an unknown catalytic mechanism as the protein fold of the active site domain and the active site residues have not been reported. This group of peptidases belong to MEROPS peptidase family U62 (clan U-). The type example is microcin-processing peptidase 1 from Escherichia coli, which is the product of the gene PmbA. It has been suggests that the pmbA gene product acts to inhibit the interaction between the letD protein and the A subunit of DNA gyrase. The letA (ccdA) and letD (ccdB) genes of the F plasmid, located just outside the sequence essential for F-plasmid replication, contribute to stable maintenance of the plasmid in E. coli cells. The letD gene product acts to inhibit partitioning of chromosomal DNA and cell division by inhibiting DNA gyrase activity, whereas the letA gene product acts to reverse the inhibitory activity of the letD gene product []. It has also been proposed that PmbA facilitates the secretion of microcin B17 (MccB17) the by completing its maturation []. Microcin B17 (MccB17) is a peptide antibiotic produced by E. coli strains harbouring plasmid pMccB17. ; PDB: 1VPB_A 1VL4_A 3TV9_A 3QTD_B.
Probab=35.16 E-value=9.5 Score=25.98 Aligned_cols=23 Identities=13% Similarity=0.374 Sum_probs=18.5
Q ss_pred CCCCccEEecCCchHHHHHhhhh
Q psy9334 38 NPHQFDVMVMPNLYGNIVDNLAS 60 (65)
Q Consensus 38 ~P~~fDVIV~~Nl~GDIlSD~aa 60 (65)
.|.+|+||++|...|+++....+
T Consensus 205 ~~g~y~Vil~p~a~~~ll~~~~~ 227 (293)
T PF01523_consen 205 PSGKYPVILSPEAAGELLHEAFG 227 (293)
T ss_dssp -SEEEEEEE-HHHHHHHHHHHHH
T ss_pred CCCeEEEEECcHHHHHHHHHHhh
Confidence 37899999999999999996654
No 114
>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=34.99 E-value=83 Score=18.86 Aligned_cols=41 Identities=17% Similarity=0.160 Sum_probs=24.2
Q ss_pred hHHHHHHHHHhhCCCceechhhHHHH-HHHHhhCCCCccEEec
Q psy9334 6 GYPNLGQTMAKLYPKIQFEQMIVDNC-TMQIVSNPHQFDVMVM 47 (65)
Q Consensus 6 ~f~~~~~eva~~ypdV~~~~~~vDa~-~~~lv~~P~~fDVIV~ 47 (65)
..-+...+..+.||+++++-..-+.. ..+.+.+ +++|+.+.
T Consensus 14 ~l~~~l~~f~~~~P~v~i~~~~~~~~~~~~~l~~-g~~Dl~i~ 55 (196)
T cd08458 14 FMSGVIQTFIADRPDVSVYLDTVPSQTVLELVSL-QHYDLGIS 55 (196)
T ss_pred hhHHHHHHHHHHCCCcEEEEeccChHHHHHHHHc-CCCCEEEE
Confidence 33467788888999887765433322 2233332 57786554
No 115
>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=34.92 E-value=44 Score=19.87 Aligned_cols=41 Identities=15% Similarity=0.158 Sum_probs=25.6
Q ss_pred hHHHHHHHHHhhCCCceechhhH--HHHHHHHhhCCCCccEEecC
Q psy9334 6 GYPNLGQTMAKLYPKIQFEQMIV--DNCTMQIVSNPHQFDVMVMP 48 (65)
Q Consensus 6 ~f~~~~~eva~~ypdV~~~~~~v--Da~~~~lv~~P~~fDVIV~~ 48 (65)
.+-+...+..++||+|+++-... +.. .+.+.+ ++.|+.+..
T Consensus 14 ~l~~~l~~f~~~~P~v~i~i~~~~~~~~-~~~l~~-~~~Di~i~~ 56 (198)
T cd08461 14 ILPPLLAALRQEAPGVRVAIRDLESDNL-EAQLER-GEVDLALTT 56 (198)
T ss_pred HhHHHHHHHHHHCCCcEEEEeeCCcccH-HHHHhc-CCCcEEEec
Confidence 34567778889999988776532 223 333333 678877653
No 116
>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=34.44 E-value=68 Score=18.97 Aligned_cols=41 Identities=10% Similarity=0.051 Sum_probs=24.6
Q ss_pred hHHHHHHHHHhhCCCceechhhHH-HHHHHHhhCCCCccEEec
Q psy9334 6 GYPNLGQTMAKLYPKIQFEQMIVD-NCTMQIVSNPHQFDVMVM 47 (65)
Q Consensus 6 ~f~~~~~eva~~ypdV~~~~~~vD-a~~~~lv~~P~~fDVIV~ 47 (65)
..-....+..+.||+++++-.... .-..+.+.+ +++|+.++
T Consensus 14 ~l~~~l~~~~~~~P~i~i~~~~~~~~~~~~~l~~-~~~D~~i~ 55 (198)
T cd08421 14 FLPEDLASFLAAHPDVRIDLEERLSADIVRAVAE-GRADLGIV 55 (198)
T ss_pred hhHHHHHHHHHHCCCceEEEEecCcHHHHHHHhc-CCceEEEE
Confidence 344677888889999887754321 122333333 56787665
No 117
>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=34.36 E-value=98 Score=22.32 Aligned_cols=42 Identities=12% Similarity=0.081 Sum_probs=29.0
Q ss_pred HHHHHHHHHhhCCCceechhhHHHHHHHHh---hCCCCccEEecC
Q psy9334 7 YPNLGQTMAKLYPKIQFEQMIVDNCTMQIV---SNPHQFDVMVMP 48 (65)
Q Consensus 7 f~~~~~eva~~ypdV~~~~~~vDa~~~~lv---~~P~~fDVIV~~ 48 (65)
+.++..+..++||+|+++...++....+|. .--+-.||+-..
T Consensus 56 ~~~~~~~F~~~~p~i~V~~~~~~~~~~kl~~~~asg~~PDi~~~~ 100 (450)
T TIGR03851 56 AKDAEPLYKKKYPGATVKVSPTQKIAPQLQPRFAGGNPPDLIDNS 100 (450)
T ss_pred HHHHHHHHHHHCCCcEEEEeechhhHHHHHHHHhCCCCCcEEeec
Confidence 455667777889999999887776555543 334567988653
No 118
>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=33.99 E-value=54 Score=19.37 Aligned_cols=38 Identities=18% Similarity=0.309 Sum_probs=24.9
Q ss_pred HHHHHHHHHhhCCCceechhhHHHHHHHHhhCCCCccEEec
Q psy9334 7 YPNLGQTMAKLYPKIQFEQMIVDNCTMQIVSNPHQFDVMVM 47 (65)
Q Consensus 7 f~~~~~eva~~ypdV~~~~~~vDa~~~~lv~~P~~fDVIV~ 47 (65)
.-+...++.++||+++++-..-+. ..+++.+ + .|+.+.
T Consensus 16 l~~~l~~~~~~~P~v~i~i~~~~~-~~~~l~~-~-~D~~i~ 53 (199)
T cd08475 16 VAPLLLELARRHPELELELSFSDR-FVDLIEE-G-IDLAVR 53 (199)
T ss_pred HHHHHHHHHHHCCCeEEEEEeccc-hhhHhhc-C-ccEEEE
Confidence 345677888899998888653233 3445553 4 898774
No 119
>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=33.88 E-value=92 Score=18.22 Aligned_cols=40 Identities=18% Similarity=0.270 Sum_probs=24.4
Q ss_pred hHHHHHHHHHhhCCCceechhhH--HHHHHHHhhCCCCccEEec
Q psy9334 6 GYPNLGQTMAKLYPKIQFEQMIV--DNCTMQIVSNPHQFDVMVM 47 (65)
Q Consensus 6 ~f~~~~~eva~~ypdV~~~~~~v--Da~~~~lv~~P~~fDVIV~ 47 (65)
.+.....+..++||+++++-... +... ..+++ ++.|+.+.
T Consensus 14 ~l~~~l~~~~~~~p~i~i~i~~~~~~~~~-~~l~~-~~~Dl~i~ 55 (197)
T cd08414 14 LLPRLLRRFRARYPDVELELREMTTAEQL-EALRA-GRLDVGFV 55 (197)
T ss_pred HHHHHHHHHHHHCCCcEEEEecCChHHHH-HHHHc-CCccEEEE
Confidence 45567788888999887775432 2333 33333 44776554
No 120
>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=33.85 E-value=79 Score=18.38 Aligned_cols=39 Identities=15% Similarity=0.214 Sum_probs=23.6
Q ss_pred HHHHHHHHHhhCCCceechhhH--HHHHHHHhhCCCCccEEec
Q psy9334 7 YPNLGQTMAKLYPKIQFEQMIV--DNCTMQIVSNPHQFDVMVM 47 (65)
Q Consensus 7 f~~~~~eva~~ypdV~~~~~~v--Da~~~~lv~~P~~fDVIV~ 47 (65)
..+...+..++||+++++-... +.. .+.+.+ +++|+.++
T Consensus 15 l~~~l~~~~~~~p~v~i~i~~~~~~~~-~~~l~~-g~~D~~i~ 55 (197)
T cd08440 15 LPPVLAAFRRRHPGIRVRLRDVSAEQV-IEAVRS-GEVDFGIG 55 (197)
T ss_pred HHHHHHHHHHhCCCcEEEEEeCChHHH-HHHHHc-CCccEEEE
Confidence 3467778888999988775432 222 233333 45786665
No 121
>cd08324 CARD_NOD1_CARD4 Caspase activation and recruitment domain similar to that found in NOD1. Caspase activation and recruitment domain (CARD) found in human NOD1 (CARD4) and similar proteins. NOD1 is a member of the Nod-like receptor (NLR) family, which plays a central role in the innate immune response. NLRs typically contain an N-terminal effector domain, a central nucleotide-binding domain and a C-terminal ligand-binding region of several leucine-rich repeats (LRRs). In NOD1, as well as NOD2, the N-terminal effector domain is a CARD. Nod1-CARD has been shown to interact with the CARD domain of the downstream effector RICK (RIP2, CARDIAK), a serine/threonine kinase. In general, CARDs are death domains (DDs) found associated with caspases. They are known to be important in the signaling pathways for apoptosis, inflammation, and host-defense mechanisms. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form hom
Probab=33.42 E-value=27 Score=21.39 Aligned_cols=21 Identities=19% Similarity=0.167 Sum_probs=17.9
Q ss_pred chhchHHHHHHHHHhhCCCce
Q psy9334 2 PCRFGYPNLGQTMAKLYPKIQ 22 (65)
Q Consensus 2 ~~~~~f~~~~~eva~~ypdV~ 22 (65)
-|+..|..+-++++..|+|..
T Consensus 61 ~~k~~F~~iL~e~~~~y~~~~ 81 (85)
T cd08324 61 EVSEYFLYLLQQLADAYVDLR 81 (85)
T ss_pred hHHHHHHHHHHHHHHhhhhhh
Confidence 488899999999999998753
No 122
>cd08468 PBP2_Pa0477 The C-terminal substrate biniding domain of an uncharacterized LysR-like transcriptional regulator Pa0477 related to DntR, contains the type 2 periplasmic binding fold. LysR-type transcriptional regulator Pa0477 is related to DntR, which controls genes encoding enzymes for oxidative degradation of the nitro-aromatic compound 2,4-dinitrotoluene. The transcription of the genes encoding enzymes involved in such degradation is regulated and expression of these enzymes is enhanced by inducers, which are either an intermediate in the metabolic pathway or compounds to be degraded. The topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their spec
Probab=33.25 E-value=70 Score=19.31 Aligned_cols=41 Identities=12% Similarity=0.155 Sum_probs=25.6
Q ss_pred chHHHHHHHHHhhCCCceechhh--HHHHHHHHhhCCCCccEEec
Q psy9334 5 FGYPNLGQTMAKLYPKIQFEQMI--VDNCTMQIVSNPHQFDVMVM 47 (65)
Q Consensus 5 ~~f~~~~~eva~~ypdV~~~~~~--vDa~~~~lv~~P~~fDVIV~ 47 (65)
...-+...+..++||+++++-.. -+.....|.. ++.|..+.
T Consensus 13 ~~l~~~l~~~~~~~P~v~i~~~~~~~~~~~~~l~~--g~~Dl~i~ 55 (202)
T cd08468 13 AVMPRLMARLEELAPSVRLNLVHAEQKLPLDALLA--GEIDFALG 55 (202)
T ss_pred HHhHHHHHHHHhhCCCCEEEEEECChHhHHHHHHC--CCccEEEe
Confidence 44567788889999987765553 3333333333 56776654
No 123
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=32.55 E-value=23 Score=24.19 Aligned_cols=14 Identities=36% Similarity=0.617 Sum_probs=12.5
Q ss_pred hCCCCccEEecCCc
Q psy9334 37 SNPHQFDVMVMPNL 50 (65)
Q Consensus 37 ~~P~~fDVIV~~Nl 50 (65)
-||--|+|+|+||=
T Consensus 41 vnP~~Y~V~vCP~C 54 (214)
T PF09986_consen 41 VNPLFYEVWVCPHC 54 (214)
T ss_pred CCCeeeeEEECCCC
Confidence 68999999999983
No 124
>TIGR03730 tungstate_WtpA tungstate ABC transporter binding protein WtpA. Members of this protein family are tungstate (and, more weakly, molybdate) binding proteins of tungstate(/molybdate) ABC transporters, as first characterized in Pyrococcus furiosus. Model seed members and cutoffs, pending experimental evidence for more distant homologs, were chosen such that this model identifies select archaeal proteins, excluding weaker archaeal and all bacterial homologs. Note that this family is homologous to molybdate transporters, and that at least one other family of tungstate transporter binding protein, TupA, also exists.
Probab=32.46 E-value=86 Score=22.17 Aligned_cols=45 Identities=7% Similarity=0.209 Sum_probs=29.0
Q ss_pred hHHHHHHHHHhhCCCceechhhHHH--HHHHHhhCCCCccEEecCCc
Q psy9334 6 GYPNLGQTMAKLYPKIQFEQMIVDN--CTMQIVSNPHQFDVMVMPNL 50 (65)
Q Consensus 6 ~f~~~~~eva~~ypdV~~~~~~vDa--~~~~lv~~P~~fDVIV~~Nl 50 (65)
-+.++..+..+++|+++++-.+--+ +..|+..+-..+||.++-|.
T Consensus 14 ~~~ei~~~Fe~~~~gvkv~~~~~gSg~L~~Qi~e~Gap~DVfisAd~ 60 (273)
T TIGR03730 14 PFEEMEKEFEAKHPNVDVQREAAGSVAAVRKITELGKPADILASADY 60 (273)
T ss_pred HHHHHHHHHHhhCCCceEEEEeCcHHHHHHHHHHcCCCeeEEEeCCH
Confidence 3455555555667888887776443 33444447778999888773
No 125
>PRK11716 DNA-binding transcriptional regulator IlvY; Provisional
Probab=32.41 E-value=82 Score=20.40 Aligned_cols=41 Identities=10% Similarity=0.181 Sum_probs=26.2
Q ss_pred hHHHHHHHHHhhCCCceechhh--HHHHHHHHhhCCCCccEEecC
Q psy9334 6 GYPNLGQTMAKLYPKIQFEQMI--VDNCTMQIVSNPHQFDVMVMP 48 (65)
Q Consensus 6 ~f~~~~~eva~~ypdV~~~~~~--vDa~~~~lv~~P~~fDVIV~~ 48 (65)
.+.+......++||+|+++-.. .+....+|.+ +++|+.++.
T Consensus 81 ~~~~~l~~~~~~~p~i~l~i~~~~~~~~~~~l~~--~~~D~~i~~ 123 (269)
T PRK11716 81 HLPPILDRFRAEHPLVEIKLTTGDAADAVEKVQS--GEADLAIAA 123 (269)
T ss_pred HHHHHHHHHHHHCCCeEEEEEECCHHHHHHHHHC--CCccEEEEe
Confidence 3456778888999998777543 3333444444 467876653
No 126
>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=32.37 E-value=66 Score=19.09 Aligned_cols=40 Identities=13% Similarity=0.189 Sum_probs=23.8
Q ss_pred HHHHHHHHHhhCCCceechhhHHH-HHHHHhhCCCCccEEec
Q psy9334 7 YPNLGQTMAKLYPKIQFEQMIVDN-CTMQIVSNPHQFDVMVM 47 (65)
Q Consensus 7 f~~~~~eva~~ypdV~~~~~~vDa-~~~~lv~~P~~fDVIV~ 47 (65)
+-+...+..++||+++++-...+. -+...+. -++.|+.++
T Consensus 15 l~~~l~~~~~~~P~i~i~~~~~~~~~~~~~l~-~~~~D~~i~ 55 (198)
T cd08433 15 AVPLLRAVRRRYPGIRLRIVEGLSGHLLEWLL-NGRLDLALL 55 (198)
T ss_pred chHHHHHHHHHCCCcEEEEEecCcHHHHHHHh-CCCCcEEEE
Confidence 346777888899988777653321 2223332 355786665
No 127
>PRK10721 hypothetical protein; Provisional
Probab=32.11 E-value=1e+02 Score=18.07 Aligned_cols=21 Identities=14% Similarity=0.444 Sum_probs=15.1
Q ss_pred HHHHHHHHhhCCCceechhhH
Q psy9334 8 PNLGQTMAKLYPKIQFEQMIV 28 (65)
Q Consensus 8 ~~~~~eva~~ypdV~~~~~~v 28 (65)
++++.+....||++.-...-.
T Consensus 9 ~dIA~~L~e~~Pd~DP~~vrF 29 (66)
T PRK10721 9 REIGEALYDAYPDLDPKTVRF 29 (66)
T ss_pred HHHHHHHHHHCCCCCCCEeeh
Confidence 468889999999975444433
No 128
>cd01483 E1_enzyme_family Superfamily of activating enzymes (E1) of the ubiquitin-like proteins. This family includes classical ubiquitin-activating enzymes E1, ubiquitin-like (ubl) activating enzymes and other mechanistic homologes, like MoeB, Thif1 and others. The common reaction mechanism catalyzed by MoeB, ThiF and the E1 enzymes begins with a nucleophilic attack of the C-terminal carboxylate of MoaD, ThiS and ubiquitin, respectively, on the alpha-phosphate of an ATP molecule bound at the active site of the activating enzymes, leading to the formation of a high-energy acyladenylate intermediate and subsequently to the formation of a thiocarboxylate at the C termini of MoaD and ThiS.
Probab=31.55 E-value=40 Score=20.68 Aligned_cols=39 Identities=8% Similarity=0.106 Sum_probs=20.2
Q ss_pred HHHHHHhhCCCceechhhHHHHHHHHhhCCCCccEEecC
Q psy9334 10 LGQTMAKLYPKIQFEQMIVDNCTMQIVSNPHQFDVMVMP 48 (65)
Q Consensus 10 ~~~eva~~ypdV~~~~~~vDa~~~~lv~~P~~fDVIV~~ 48 (65)
.++++.+.+|+++++......-.........+||+||..
T Consensus 58 ~~~~l~~~~p~v~i~~~~~~~~~~~~~~~~~~~diVi~~ 96 (143)
T cd01483 58 AARRLNELNPGVNVTAVPEGISEDNLDDFLDGVDLVIDA 96 (143)
T ss_pred HHHHHHHHCCCcEEEEEeeecChhhHHHHhcCCCEEEEC
Confidence 345556667887765433221111123334678977754
No 129
>COG0800 Eda 2-keto-3-deoxy-6-phosphogluconate aldolase [Carbohydrate transport and metabolism]
Probab=31.47 E-value=1.4e+02 Score=20.90 Aligned_cols=49 Identities=16% Similarity=0.203 Sum_probs=30.7
Q ss_pred chHHHHHHHHHhhCCCceec--hhhHHHHHHHHhhCCCCccEEecCCchHHHH
Q psy9334 5 FGYPNLGQTMAKLYPKIQFE--QMIVDNCTMQIVSNPHQFDVMVMPNLYGNIV 55 (65)
Q Consensus 5 ~~f~~~~~eva~~ypdV~~~--~~~vDa~~~~lv~~P~~fDVIV~~Nl~GDIl 55 (65)
.-|.+..++++++||++-+- ..+=..-..+.+..-.+ -||+||+.-+++
T Consensus 49 p~a~e~I~~l~~~~p~~lIGAGTVL~~~q~~~a~~aGa~--fiVsP~~~~ev~ 99 (211)
T COG0800 49 PAALEAIRALAKEFPEALIGAGTVLNPEQARQAIAAGAQ--FIVSPGLNPEVA 99 (211)
T ss_pred CCHHHHHHHHHHhCcccEEccccccCHHHHHHHHHcCCC--EEECCCCCHHHH
Confidence 45778899999999964321 11112223455555554 499999986665
No 130
>PF06481 COX_ARM: COX Aromatic Rich Motif; InterPro: IPR010514 COX2 (Cytochrome O ubiquinol OXidase 2) is a major component of the respiratory complex during vegetative growth. It transfers electrons from a quinol to the binuclear centre of the catalytic subunit 1. The function of this region is not known.; GO: 0008827 cytochrome o ubiquinol oxidase activity, 0022900 electron transport chain, 0055114 oxidation-reduction process, 0016021 integral to membrane; PDB: 1CYX_A 1CYW_A 1FFT_G.
Probab=31.44 E-value=40 Score=17.83 Aligned_cols=27 Identities=22% Similarity=0.430 Sum_probs=15.3
Q ss_pred HHHHHHhhCCCCccEE-----ecCCchHHHHH
Q psy9334 30 NCTMQIVSNPHQFDVM-----VMPNLYGNIVD 56 (65)
Q Consensus 30 a~~~~lv~~P~~fDVI-----V~~Nl~GDIlS 56 (65)
...+.-+..|..-+-+ |-++||.+|+-
T Consensus 9 ~~~Y~~La~PS~~~pv~yfssv~p~LF~~Iv~ 40 (47)
T PF06481_consen 9 MASYDELAKPSENNPVTYFSSVEPGLFDDIVM 40 (47)
T ss_dssp HHHHHHHCSS-SS--SEEES-B-TTHHHHHHH
T ss_pred HHHHHHHHCcCcCCCceeeccCCHHHHHHHHH
Confidence 3344455566666644 78999999875
No 131
>PRK12861 malic enzyme; Reviewed
Probab=30.94 E-value=1.2e+02 Score=24.99 Aligned_cols=57 Identities=21% Similarity=0.248 Sum_probs=36.0
Q ss_pred HHHHHHHHhhCCCceec-hhhHHHHHHHHhhC--------CCCccEEecCCc-hHHHHHhhhhhccC
Q psy9334 8 PNLGQTMAKLYPKIQFE-QMIVDNCTMQIVSN--------PHQFDVMVMPNL-YGNIVDNLASDIKG 64 (65)
Q Consensus 8 ~~~~~eva~~ypdV~~~-~~~vDa~~~~lv~~--------P~~fDVIV~~Nl-~GDIlSD~aa~l~G 64 (65)
+++.+-+.+++|+..++ ++-.|++.-.-+++ -++-||+|.||+ =|+|+-.+.-.+.|
T Consensus 655 ~eA~~l~~~~~pd~~vdGemq~DaAl~~e~a~~K~p~s~vaG~ANVLVfPnLeAGNI~yKll~~l~g 721 (764)
T PRK12861 655 RRALEIVREQAPDLEADGEMHGDCALDEGLRARLLPMSPLKGAANLLVCPNVDAGNIAYNLLKTEAG 721 (764)
T ss_pred HHHHHHHHhhCCCcEEEecCcHHHhCCHHHHHhcCCCCcCCCcCCEEEECCcchhhHHHHHHHHHcC
Confidence 44444445568987665 34567665332211 356789999999 79998877655543
No 132
>cd03026 AhpF_NTD_C TRX-GRX-like family, Alkyl hydroperoxide reductase F subunit (AhpF) N-terminal domain (NTD) subfamily, C-terminal TRX-fold subdomain; AhpF is a homodimeric flavoenzyme which catalyzes the NADH-dependent reduction of the peroxiredoxin AhpC, which then reduces hydrogen peroxide and organic hydroperoxides. AhpF contains an NTD containing two contiguous TRX-fold subdomains similar to Pyrococcus furiosus protein disulfide oxidoreductase (PfPDO). It also contains a catalytic core similar to TRX reductase containing FAD and NADH binding domains with an active site disulfide. The proposed mechanism of action of AhpF is similar to a TRX/TRX reductase system. The flow of reducing equivalents goes from NADH - catalytic core of AhpF - NTD of AhpF - AhpC - peroxide substrates. The catalytic CXXC motif of the NTD of AhpF is contained in its C-terminal TRX subdomain.
Probab=30.92 E-value=53 Score=19.14 Aligned_cols=44 Identities=23% Similarity=0.190 Sum_probs=27.3
Q ss_pred chhchHHHHHHHHHhhCCCceechhhHHHHHHHHhhCCCCccEEecCCc
Q psy9334 2 PCRFGYPNLGQTMAKLYPKIQFEQMIVDNCTMQIVSNPHQFDVMVMPNL 50 (65)
Q Consensus 2 ~~~~~f~~~~~eva~~ypdV~~~~~~vDa~~~~lv~~P~~fDVIV~~Nl 50 (65)
+|+.. .+.++++++++|+|+++..-+|..-- +. ++|+|.=.|.+
T Consensus 26 ~C~~~-~~~~~~l~~~~~~i~~~~vd~~~~~e-~a---~~~~V~~vPt~ 69 (89)
T cd03026 26 NCPDV-VQALNLMAVLNPNIEHEMIDGALFQD-EV---EERGIMSVPAI 69 (89)
T ss_pred CcHHH-HHHHHHHHHHCCCceEEEEEhHhCHH-HH---HHcCCccCCEE
Confidence 45533 45678899999999888877774421 11 25555544444
No 133
>PRK11151 DNA-binding transcriptional regulator OxyR; Provisional
Probab=29.91 E-value=85 Score=21.19 Aligned_cols=41 Identities=15% Similarity=0.305 Sum_probs=25.4
Q ss_pred chHHHHHHHHHhhCCCceechhh--HHHHHHHHhhCCCCccEEec
Q psy9334 5 FGYPNLGQTMAKLYPKIQFEQMI--VDNCTMQIVSNPHQFDVMVM 47 (65)
Q Consensus 5 ~~f~~~~~eva~~ypdV~~~~~~--vDa~~~~lv~~P~~fDVIV~ 47 (65)
..+.....+..++||+|+++-.. -+.....|.. +++|+++.
T Consensus 104 ~~~~~~l~~~~~~~P~v~i~~~~~~~~~~~~~l~~--g~~Dl~i~ 146 (305)
T PRK11151 104 YLLPHIIPMLHQTFPKLEMYLHEAQTHQLLAQLDS--GKLDCAIL 146 (305)
T ss_pred HHHHHHHHHHHHHCCCcEEEEEeCCHHHHHHHHHc--CCccEEEE
Confidence 34456777888899998877654 3333333333 36776664
No 134
>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=29.51 E-value=1e+02 Score=19.03 Aligned_cols=41 Identities=12% Similarity=0.079 Sum_probs=24.2
Q ss_pred chHHHHHHHHHhhCCCceechhh--HHHHHHHHhhCCCCccEEec
Q psy9334 5 FGYPNLGQTMAKLYPKIQFEQMI--VDNCTMQIVSNPHQFDVMVM 47 (65)
Q Consensus 5 ~~f~~~~~eva~~ypdV~~~~~~--vDa~~~~lv~~P~~fDVIV~ 47 (65)
....+...+..++||+|+++-.- -+.....|. =++.|+.++
T Consensus 13 ~~l~~~l~~f~~~~P~v~l~i~~~~~~~~~~~L~--~~~~D~~i~ 55 (204)
T cd08429 13 SIAYRLLEPAMDLHEPIRLVCREGKLEQLLADLA--LHRLDMVLA 55 (204)
T ss_pred HHHHHHHHHHHHhCCCcEEEEEeCCHHHHHHHHH--cCCccEEEe
Confidence 34456777888899987765543 333333332 266776554
No 135
>PRK12560 adenine phosphoribosyltransferase; Provisional
Probab=29.36 E-value=88 Score=20.81 Aligned_cols=24 Identities=17% Similarity=0.126 Sum_probs=19.4
Q ss_pred CCCccEEecCCchHHHHHhhhhhc
Q psy9334 39 PHQFDVMVMPNLYGNIVDNLASDI 62 (65)
Q Consensus 39 P~~fDVIV~~Nl~GDIlSD~aa~l 62 (65)
+.+||+|+++-.=|-.++-..|..
T Consensus 49 ~~~~D~Ivg~e~~Gi~lA~~vA~~ 72 (187)
T PRK12560 49 DKDIDKIVTEEDKGAPLATPVSLL 72 (187)
T ss_pred CCCCCEEEEEccccHHHHHHHHHh
Confidence 668999999999888887766554
No 136
>TIGR03339 phn_lysR aminoethylphosphonate catabolism associated LysR family transcriptional regulator. This group of sequences represents a number of related clades with numerous examples of members adjacent to operons for the degradation of 2-aminoethylphosphonate (AEP) in Pseudomonas, Ralstonia, Bordetella and Burkholderia species. These are transcriptional regulators of the LysR family which contain a helix-turn-helix (HTH) domain (pfam00126) and a periplasmic substrate-binding protein-like domain (pfam03466).
Probab=29.32 E-value=1.7e+02 Score=19.10 Aligned_cols=41 Identities=20% Similarity=0.191 Sum_probs=25.8
Q ss_pred hHHHHHHHHHhhCCCceechh--hHHHHHHHHhhCCCCccEEecC
Q psy9334 6 GYPNLGQTMAKLYPKIQFEQM--IVDNCTMQIVSNPHQFDVMVMP 48 (65)
Q Consensus 6 ~f~~~~~eva~~ypdV~~~~~--~vDa~~~~lv~~P~~fDVIV~~ 48 (65)
.+.....+..++||+++++-. ..+... +.+.+ +++|+.+..
T Consensus 98 ~~~~~l~~~~~~~p~v~l~i~~~~~~~~~-~~l~~-g~~Dl~i~~ 140 (279)
T TIGR03339 98 YVLDLVARFRQRYPGIEVSVRIGNSQEVL-QALQS-YRVDVAVSS 140 (279)
T ss_pred HHHHHHHHHHHHCCCcEEEEEECCHHHHH-HHHHc-CCCcEEEEe
Confidence 445677788889998777654 333333 44444 568877754
No 137
>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=29.19 E-value=88 Score=18.62 Aligned_cols=40 Identities=15% Similarity=0.289 Sum_probs=24.1
Q ss_pred HHHHHHHHHhhCCCceechhhH--HHHHHHHhhCCCCccEEecC
Q psy9334 7 YPNLGQTMAKLYPKIQFEQMIV--DNCTMQIVSNPHQFDVMVMP 48 (65)
Q Consensus 7 f~~~~~eva~~ypdV~~~~~~v--Da~~~~lv~~P~~fDVIV~~ 48 (65)
.-+...+..++||+++++-... +... +.+.+ ++.|+.++.
T Consensus 15 l~~~l~~~~~~~P~i~l~~~~~~~~~~~-~~l~~-~~~Dl~i~~ 56 (196)
T cd08457 15 LPRFLAAFLRLRPNLHLSLMGLSSSQVL-EAVAS-GRADLGIAD 56 (196)
T ss_pred cHHHHHHHHHHCCCeEEEEEecCcHHHH-HHHHc-CCccEEEec
Confidence 4467778888999888775543 3333 33333 456765553
No 138
>PRK10974 glycerol-3-phosphate transporter periplasmic binding protein; Provisional
Probab=29.17 E-value=1.5e+02 Score=21.29 Aligned_cols=42 Identities=10% Similarity=0.106 Sum_probs=25.9
Q ss_pred hHHHHHHHHHhhCCCceechhhHHH---HHHHHhh---CCCCccEEec
Q psy9334 6 GYPNLGQTMAKLYPKIQFEQMIVDN---CTMQIVS---NPHQFDVMVM 47 (65)
Q Consensus 6 ~f~~~~~eva~~ypdV~~~~~~vDa---~~~~lv~---~P~~fDVIV~ 47 (65)
.+++.+++..+++|+|+++....+. ....++. .-.-.||+..
T Consensus 41 ~~~~~~~~F~~~~p~i~V~~~~~~~~~~~~~~~~~a~~~g~~PDv~~~ 88 (438)
T PRK10974 41 EVDSLAQRFNASQPDYKIVPVYKGNYEQSLAAGIAAFRSGNAPAILQV 88 (438)
T ss_pred HHHHHHHHHHHhCCCeEEEEeeeccHHHHHHHHHHHHhCCCCCeEEEE
Confidence 4667888888889999988764432 2222222 2344688754
No 139
>KOG0649|consensus
Probab=29.13 E-value=26 Score=26.00 Aligned_cols=22 Identities=32% Similarity=0.584 Sum_probs=18.3
Q ss_pred HHHHHhhCCCCccEEecCCchHHH
Q psy9334 31 CTMQIVSNPHQFDVMVMPNLYGNI 54 (65)
Q Consensus 31 ~~~~lv~~P~~fDVIV~~Nl~GDI 54 (65)
...+-+.-|.+| +++.|+||||
T Consensus 13 vf~qa~sp~~~~--l~agn~~G~i 34 (325)
T KOG0649|consen 13 VFAQAISPSKQY--LFAGNLFGDI 34 (325)
T ss_pred HHHHhhCCcceE--EEEecCCCeE
Confidence 345677889988 9999999998
No 140
>KOG3812|consensus
Probab=28.98 E-value=52 Score=25.44 Aligned_cols=36 Identities=22% Similarity=0.306 Sum_probs=26.1
Q ss_pred CCceechhhHHHHHHH-Hhh-CCCCccEEecCCchHHH
Q psy9334 19 PKIQFEQMIVDNCTMQ-IVS-NPHQFDVMVMPNLYGNI 54 (65)
Q Consensus 19 pdV~~~~~~vDa~~~~-lv~-~P~~fDVIV~~Nl~GDI 54 (65)
..-...++.++-++.. |.+ -|+.||||+-+|-.-|-
T Consensus 306 Gksq~K~lnvq~va~~klaQc~~e~FdvildENqLedA 343 (475)
T KOG3812|consen 306 GKSQSKHLNVQMVAADKLAQCPPEGFDVILDENQLEDA 343 (475)
T ss_pred CchhhhhchHhhhhcchhhhCChhhhheeeccccHHHH
Confidence 3446778888877743 333 28999999999987664
No 141
>TIGR03261 phnS2 putative 2-aminoethylphosphonate ABC transporter, periplasmic 2-aminoethylphosphonate-binding protein. This ABC transporter extracellular solute-binding protein is found in a number of genomes in operon-like contexts strongly suggesting a substrate specificity for 2-aminoethylphosphonate (2-AEP). The characterized PhnSTUV system is absent in the genomes in which this system is found. These genomes encode systems for the catabolism of 2-AEP, making the need for a 2-AEP-specific transporter likely.
Probab=28.96 E-value=1.1e+02 Score=21.24 Aligned_cols=42 Identities=21% Similarity=0.235 Sum_probs=26.1
Q ss_pred hHHHHHHHHHhhCCCceechhhHH--HHHHHHhh---CCCCccEEecC
Q psy9334 6 GYPNLGQTMAKLYPKIQFEQMIVD--NCTMQIVS---NPHQFDVMVMP 48 (65)
Q Consensus 6 ~f~~~~~eva~~ypdV~~~~~~vD--a~~~~lv~---~P~~fDVIV~~ 48 (65)
.+..+.++..++||+|+++....+ .+..++.. +| ..||+.+.
T Consensus 34 ~~~~l~~~Fe~~~pgi~V~~~~~~s~~~~~kl~ae~~~~-~~Dvv~~~ 80 (334)
T TIGR03261 34 LIAKYKDAFEKVNPDIKINWVRDSTGIITAKLLAEKNNP-QADVVWGL 80 (334)
T ss_pred HHHHHHHHHHHHCCCceEEEEECChHHHHHHHHHHhhCC-CCCEEEec
Confidence 345566677788999888765432 23344542 34 58998753
No 142
>COG4635 HemG Flavodoxin [Energy production and conversion / Coenzyme metabolism]
Probab=28.84 E-value=43 Score=23.05 Aligned_cols=40 Identities=13% Similarity=0.172 Sum_probs=21.6
Q ss_pred HHHHHHHHhhCCCceechhhHHHHHHHHh-hCCCCcc-EEecCC
Q psy9334 8 PNLGQTMAKLYPKIQFEQMIVDNCTMQIV-SNPHQFD-VMVMPN 49 (65)
Q Consensus 8 ~~~~~eva~~ypdV~~~~~~vDa~~~~lv-~~P~~fD-VIV~~N 49 (65)
+++++.+|..-++--.+-.+.|.- ++. -+++.|| ||+...
T Consensus 15 ~kIA~~iA~~L~e~g~qvdi~dl~--~~~~~~l~~ydavVIgAs 56 (175)
T COG4635 15 RKIAEYIASHLRESGIQVDIQDLH--AVEEPALEDYDAVVIGAS 56 (175)
T ss_pred HHHHHHHHHHhhhcCCeeeeeehh--hhhccChhhCceEEEecc
Confidence 467777777655322222233333 222 4899999 444433
No 143
>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=28.54 E-value=1e+02 Score=18.69 Aligned_cols=40 Identities=15% Similarity=0.192 Sum_probs=24.8
Q ss_pred hHHHHHHHHHhhCCCceechhhH--HHHHHHHhhCCCCccEEec
Q psy9334 6 GYPNLGQTMAKLYPKIQFEQMIV--DNCTMQIVSNPHQFDVMVM 47 (65)
Q Consensus 6 ~f~~~~~eva~~ypdV~~~~~~v--Da~~~~lv~~P~~fDVIV~ 47 (65)
...+...+..+.||+|+++-..- +....+|.. +++|..++
T Consensus 14 ~l~~~l~~f~~~~P~i~l~i~~~~~~~~~~~L~~--g~~Dl~i~ 55 (200)
T cd08465 14 VLPALMRQLRAEAPGIDLAVSQASREAMLAQVAD--GEIDLALG 55 (200)
T ss_pred hhhHHHHHHHHHCCCcEEEEecCChHhHHHHHHC--CCccEEEe
Confidence 34467777888999998876532 333334433 46776654
No 144
>PRK02277 orotate phosphoribosyltransferase-like protein; Provisional
Probab=28.50 E-value=1.1e+02 Score=20.48 Aligned_cols=33 Identities=18% Similarity=0.161 Sum_probs=22.3
Q ss_pred HHHHHHHhhCCCCccEEecCCchHHHHHhhhhh
Q psy9334 29 DNCTMQIVSNPHQFDVMVMPNLYGNIVDNLASD 61 (65)
Q Consensus 29 Da~~~~lv~~P~~fDVIV~~Nl~GDIlSD~aa~ 61 (65)
+.++..+-.+..++|+||+.-.=|-.++...|.
T Consensus 73 ~~la~~i~~~~~~~D~Ivgi~~gG~~~A~~lA~ 105 (200)
T PRK02277 73 SAMADMLEKEDEEVDVVVGIAKSGVPLATLVAD 105 (200)
T ss_pred HHHHHHHHhcCCCCCEEEeeccCCHHHHHHHHH
Confidence 344444434567899999998888777665554
No 145
>PRK07232 bifunctional malic enzyme oxidoreductase/phosphotransacetylase; Reviewed
Probab=28.46 E-value=1.4e+02 Score=24.50 Aligned_cols=57 Identities=25% Similarity=0.345 Sum_probs=34.9
Q ss_pred HHHHHHHHhhCCCceech-hhHHHHHHHHhhC--------CCCccEEecCCch-HHHHHhhhhhccC
Q psy9334 8 PNLGQTMAKLYPKIQFEQ-MIVDNCTMQIVSN--------PHQFDVMVMPNLY-GNIVDNLASDIKG 64 (65)
Q Consensus 8 ~~~~~eva~~ypdV~~~~-~~vDa~~~~lv~~--------P~~fDVIV~~Nl~-GDIlSD~aa~l~G 64 (65)
++..+.+.+++|++.++- +-+|++.-.-+.+ -++-||+|.||+- |+|+--+..-+.|
T Consensus 646 reA~~llk~~~~~l~~dGemq~D~Al~~~va~~K~p~s~vaG~ANVLIfPdLeaGNI~yKllq~l~g 712 (752)
T PRK07232 646 REAVELLRERAPDLEVDGEMHGDAALNEEIRKDLYPFSRLKGPANVLVMPNLEAANISYNLLKELGG 712 (752)
T ss_pred HHHHHHHHhhCCCcEEEEechHHHhCCHHHHHhhCCCCccCCcCCEEEeCCchhhHHHHHHHHHhcC
Confidence 344444455678877664 4467664222221 3456899999998 8888776655443
No 146
>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=28.17 E-value=1.1e+02 Score=18.46 Aligned_cols=41 Identities=17% Similarity=0.270 Sum_probs=25.4
Q ss_pred HHHHHHHHHhhCCCceechhhHHH-HHHHHhhCCCCccEEecC
Q psy9334 7 YPNLGQTMAKLYPKIQFEQMIVDN-CTMQIVSNPHQFDVMVMP 48 (65)
Q Consensus 7 f~~~~~eva~~ypdV~~~~~~vDa-~~~~lv~~P~~fDVIV~~ 48 (65)
.-+...+..++||+|+++-..-+. -..+.+.+ ++.|+.++.
T Consensus 15 l~~~l~~~~~~~P~i~v~~~~~~~~~~~~~l~~-g~~D~~i~~ 56 (198)
T cd08413 15 LPPVIAAFRKRYPKVKLSLHQGTPSQIAEMVLK-GEADIAIAT 56 (198)
T ss_pred ccHHHHHHHHhCCceEEEEEeCCHHHHHHHHHc-CCCCEEEEc
Confidence 345677888999998887665432 22333333 667866653
No 147
>TIGR02845 spore_V_AD stage V sporulation protein AD. Bacillus and Clostridium species contain about 10 % dipicolinic acid (pyridine-2,6-dicarboxylic acid) by weight. This protein family, SpoVAD, belongs to the spoVA operon that is suggested to act in the transport of dipicolinic acid (DPA) from the mother cell, where DPA is synthesized, to the forespore, a process essential to sporulation. Members of this protein family are found, so far, in exactly those species believed capable of endospore formation.
Probab=28.16 E-value=29 Score=25.81 Aligned_cols=15 Identities=20% Similarity=0.410 Sum_probs=12.8
Q ss_pred hhCCCCccEEecCCc
Q psy9334 36 VSNPHQFDVMVMPNL 50 (65)
Q Consensus 36 v~~P~~fDVIV~~Nl 50 (65)
=++|+.||.|||..|
T Consensus 216 ~~~~~~yd~i~tgdl 230 (327)
T TIGR02845 216 GRSVDDYDLIVTGDL 230 (327)
T ss_pred CCChhhccEEEecch
Confidence 357999999999876
No 148
>COG0421 SpeE Spermidine synthase [Amino acid transport and metabolism]
Probab=27.83 E-value=77 Score=22.74 Aligned_cols=23 Identities=22% Similarity=0.471 Sum_probs=16.8
Q ss_pred hhHHHHHHHHhhCCCCccEEecC
Q psy9334 26 MIVDNCTMQIVSNPHQFDVMVMP 48 (65)
Q Consensus 26 ~~vDa~~~~lv~~P~~fDVIV~~ 48 (65)
..+|.....+=+.++.||||+..
T Consensus 134 i~i~Dg~~~v~~~~~~fDvIi~D 156 (282)
T COG0421 134 IIIDDGVEFLRDCEEKFDVIIVD 156 (282)
T ss_pred EEeccHHHHHHhCCCcCCEEEEc
Confidence 45666666776778889999864
No 149
>PRK08304 stage V sporulation protein AD; Validated
Probab=27.68 E-value=30 Score=25.85 Aligned_cols=15 Identities=27% Similarity=0.618 Sum_probs=12.8
Q ss_pred hhCCCCccEEecCCc
Q psy9334 36 VSNPHQFDVMVMPNL 50 (65)
Q Consensus 36 v~~P~~fDVIV~~Nl 50 (65)
=++|+.||.|||..|
T Consensus 222 ~~~~~~yDli~tGDl 236 (337)
T PRK08304 222 GRSPEDYDLIVTGDL 236 (337)
T ss_pred CCChhhccEEEEcch
Confidence 367999999999876
No 150
>cd06297 PBP1_LacI_like_12 Ligand-binding domain of uncharacterized transcription regulators from Thermus thermophilus and close homologs. Ligand-binding domain of uncharacterized transcription regulators from Thermus thermophilus and close homologs from other bacteria. This group belongs to the the LacI-GalR family repressors that are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding.
Probab=27.48 E-value=1.2e+02 Score=19.90 Aligned_cols=20 Identities=0% Similarity=-0.076 Sum_probs=15.0
Q ss_pred HHHHHHhhCCCCccEEecCC
Q psy9334 30 NCTMQIVSNPHQFDVMVMPN 49 (65)
Q Consensus 30 a~~~~lv~~P~~fDVIV~~N 49 (65)
..+.+++++..++|.|++.|
T Consensus 169 ~~~~~~l~~~~~~~ai~~~~ 188 (269)
T cd06297 169 LAMRHLLEKASPPLAVFASA 188 (269)
T ss_pred HHHHHHHcCCCCCcEEEEcC
Confidence 45567777655799999987
No 151
>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=27.39 E-value=1.1e+02 Score=17.90 Aligned_cols=39 Identities=13% Similarity=0.269 Sum_probs=23.2
Q ss_pred HHHHHHHHHhhCCCceechhh--HHHHHHHHhhCCCCccEEec
Q psy9334 7 YPNLGQTMAKLYPKIQFEQMI--VDNCTMQIVSNPHQFDVMVM 47 (65)
Q Consensus 7 f~~~~~eva~~ypdV~~~~~~--vDa~~~~lv~~P~~fDVIV~ 47 (65)
.-....++.++||+++++-.. -+.....|.+ ++.|+.+.
T Consensus 14 l~~~l~~~~~~~P~i~l~i~~~~~~~~~~~l~~--g~~Dl~i~ 54 (197)
T cd08419 14 APRLLGAFCRRHPGVEVSLRVGNREQVLERLAD--NEDDLAIM 54 (197)
T ss_pred hhHHHHHHHHHCCCceEEEEECCHHHHHHHHhc--CCccEEEe
Confidence 345677788899998776553 2223333333 46776664
No 152
>PRK11482 putative DNA-binding transcriptional regulator; Provisional
Probab=27.33 E-value=1.5e+02 Score=20.57 Aligned_cols=40 Identities=18% Similarity=0.365 Sum_probs=25.3
Q ss_pred hHHHHHHHHHhhCCCceechhhHHHHHHHHhhCCCCccEEec
Q psy9334 6 GYPNLGQTMAKLYPKIQFEQMIVDNCTMQIVSNPHQFDVMVM 47 (65)
Q Consensus 6 ~f~~~~~eva~~ypdV~~~~~~vDa~~~~lv~~P~~fDVIV~ 47 (65)
+.-.....+.+.||+++++....+.....|.+ +++|+.+.
T Consensus 131 ~l~~~l~~f~~~~P~i~i~~~~~~~~~~~l~~--g~~Dl~i~ 170 (317)
T PRK11482 131 VMPVIYQAIKTHYPQLLLRNIPISDAENQLSQ--FQTDLIID 170 (317)
T ss_pred HHHHHHHHHHHHCCCCEEEEecchhHHHHHHC--CCcCEEEe
Confidence 34456677888999998874433444343333 46787765
No 153
>PRK11013 DNA-binding transcriptional regulator LysR; Provisional
Probab=27.18 E-value=1.2e+02 Score=20.69 Aligned_cols=42 Identities=14% Similarity=0.280 Sum_probs=27.5
Q ss_pred hHHHHHHHHHhhCCCceechhhHHHHHH-HHhhCCCCccEEecC
Q psy9334 6 GYPNLGQTMAKLYPKIQFEQMIVDNCTM-QIVSNPHQFDVMVMP 48 (65)
Q Consensus 6 ~f~~~~~eva~~ypdV~~~~~~vDa~~~-~lv~~P~~fDVIV~~ 48 (65)
.+-+...+..++||+++++-...+..-. ..+ .=.++|+.+..
T Consensus 108 ~l~~~l~~~~~~~P~v~i~i~~~~~~~~~~~l-~~~~~Dl~i~~ 150 (309)
T PRK11013 108 LLPGLCQPFLARYPDVSLNIVPQESPLLEEWL-SAQRHDLGLTE 150 (309)
T ss_pred hHHHHHHHHHHHCCCCeEEEEeCCHHHHHHHH-HcCCCCEEEEc
Confidence 4456777888899999888876655432 222 24567766654
No 154
>cd03412 CbiK_N Anaerobic cobalamin biosynthetic cobalt chelatase (CbiK), N-terminal domain. CbiK is part of the cobalt-early path for cobalamin biosynthesis. It catalyzes the insertion of cobalt into the oxidized form of precorrin-2, factor II (sirohydrochlorin), the second step of the anaerobic branch of vitamin B12 biosynthesis. CbiK belongs to the class II family of chelatases and is a homomeric enzyme that does not require ATP for its enzymatic activity.
Probab=27.16 E-value=93 Score=19.30 Aligned_cols=24 Identities=4% Similarity=0.174 Sum_probs=17.4
Q ss_pred hHHHHHHHHHhhCCCceechhhHH
Q psy9334 6 GYPNLGQTMAKLYPKIQFEQMIVD 29 (65)
Q Consensus 6 ~f~~~~~eva~~ypdV~~~~~~vD 29 (65)
-+..+.+++++.||+..++.-+..
T Consensus 18 ~~~~i~~~l~~~~p~~~V~~afts 41 (127)
T cd03412 18 TIDAIEDKVRAAFPDYEVRWAFTS 41 (127)
T ss_pred HHHHHHHHHHHHCCCCeEEEEecH
Confidence 466778888888998766655544
No 155
>TIGR00477 tehB tellurite resistance protein TehB. Part of a tellurite-reducing operon tehA and tehB
Probab=27.13 E-value=52 Score=21.49 Aligned_cols=14 Identities=7% Similarity=0.306 Sum_probs=10.7
Q ss_pred CCCccEEecCCchH
Q psy9334 39 PHQFDVMVMPNLYG 52 (65)
Q Consensus 39 P~~fDVIV~~Nl~G 52 (65)
|.+||+|++.+.|.
T Consensus 92 ~~~fD~I~~~~~~~ 105 (195)
T TIGR00477 92 NEDYDFIFSTVVFM 105 (195)
T ss_pred cCCCCEEEEecccc
Confidence 46799999887663
No 156
>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=27.08 E-value=1e+02 Score=18.20 Aligned_cols=39 Identities=18% Similarity=0.319 Sum_probs=23.3
Q ss_pred HHHHHHHHHhhCCCceechhh--HHHHHHHHhhCCCCccEEec
Q psy9334 7 YPNLGQTMAKLYPKIQFEQMI--VDNCTMQIVSNPHQFDVMVM 47 (65)
Q Consensus 7 f~~~~~eva~~ypdV~~~~~~--vDa~~~~lv~~P~~fDVIV~ 47 (65)
..+...+..++||+++++-.. -+....+|.. +++|+.++
T Consensus 15 l~~~l~~~~~~~P~i~l~i~~~~~~~~~~~l~~--~~~D~~i~ 55 (199)
T cd08426 15 LPSLIARFRQRYPGVFFTVDVASTADVLEAVLS--GEADIGLA 55 (199)
T ss_pred HHHHHHHHHHhCCCeEEEEEeCCcHHHHHHHHC--CCccEEEe
Confidence 456778888999987776543 2333333333 55665554
No 157
>PRK12682 transcriptional regulator CysB-like protein; Reviewed
Probab=27.01 E-value=1.1e+02 Score=20.70 Aligned_cols=41 Identities=20% Similarity=0.319 Sum_probs=25.1
Q ss_pred hHHHHHHHHHhhCCCceechhh--HHHHHHHHhhCCCCccEEecC
Q psy9334 6 GYPNLGQTMAKLYPKIQFEQMI--VDNCTMQIVSNPHQFDVMVMP 48 (65)
Q Consensus 6 ~f~~~~~eva~~ypdV~~~~~~--vDa~~~~lv~~P~~fDVIV~~ 48 (65)
.+-+...+..++||+++++-.. .+.....|.. +++|+.++.
T Consensus 107 ~l~~~l~~~~~~~P~i~i~i~~~~~~~~~~~l~~--g~~D~~i~~ 149 (309)
T PRK12682 107 VLPRVVAAFRKRYPKVNLSLHQGSPDEIARMVIS--GEADIGIAT 149 (309)
T ss_pred HHHHHHHHHHHhCCCeEEEEecCCHHHHHHHHHc--CCccEEEec
Confidence 3446777888999988776543 3334333333 457876653
No 158
>PRK10216 DNA-binding transcriptional regulator YidZ; Provisional
Probab=26.96 E-value=85 Score=21.50 Aligned_cols=43 Identities=12% Similarity=0.181 Sum_probs=26.6
Q ss_pred hchHHHHHHHHHhhCCCceechhhHHHHHHHHhhCCCCccEEec
Q psy9334 4 RFGYPNLGQTMAKLYPKIQFEQMIVDNCTMQIVSNPHQFDVMVM 47 (65)
Q Consensus 4 ~~~f~~~~~eva~~ypdV~~~~~~vDa~~~~lv~~P~~fDVIV~ 47 (65)
...+-.+..+..++||+++++-...+.-..+.+.+ +++|+.+.
T Consensus 109 ~~~~~~~l~~f~~~~P~v~v~i~~~~~~~~~~l~~-g~~D~~i~ 151 (319)
T PRK10216 109 MIMLNALSKRIYQRYPQATIKLRNWDYDSLDAITR-GEVDIGFT 151 (319)
T ss_pred HHHHHHHHHHHHHHCCCCEEEEEeCCcchHHHHhc-CCccEEEe
Confidence 34556778888899999877765322222344444 47886554
No 159
>PF12847 Methyltransf_18: Methyltransferase domain; PDB: 3G2Q_A 3G2O_A 3G2M_B 3G2P_B 3D2L_B 1IM8_B 3NJR_A 3E05_H 3EVZ_A 3HM2_A ....
Probab=26.70 E-value=43 Score=19.04 Aligned_cols=38 Identities=16% Similarity=0.079 Sum_probs=22.9
Q ss_pred HHHHHHHHhh---CCCceechhhHHHHHHHHhhCCCCccEEecCC
Q psy9334 8 PNLGQTMAKL---YPKIQFEQMIVDNCTMQIVSNPHQFDVMVMPN 49 (65)
Q Consensus 8 ~~~~~eva~~---ypdV~~~~~~vDa~~~~lv~~P~~fDVIV~~N 49 (65)
.+.+++-+++ -+.|++.+.-+ ......+++||+|++.+
T Consensus 38 ~~~a~~~~~~~~~~~~i~~~~~d~----~~~~~~~~~~D~v~~~~ 78 (112)
T PF12847_consen 38 LEIARERAAEEGLSDRITFVQGDA----EFDPDFLEPFDLVICSG 78 (112)
T ss_dssp HHHHHHHHHHTTTTTTEEEEESCC----HGGTTTSSCEEEEEECS
T ss_pred HHHHHHHHHhcCCCCCeEEEECcc----ccCcccCCCCCEEEECC
Confidence 3445554421 24455544332 45667788899999999
No 160
>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=26.26 E-value=1.1e+02 Score=17.94 Aligned_cols=39 Identities=10% Similarity=0.254 Sum_probs=24.0
Q ss_pred HHHHHHHHhhCCCceechhhH--HHHHHHHhhCCCCccEEecC
Q psy9334 8 PNLGQTMAKLYPKIQFEQMIV--DNCTMQIVSNPHQFDVMVMP 48 (65)
Q Consensus 8 ~~~~~eva~~ypdV~~~~~~v--Da~~~~lv~~P~~fDVIV~~ 48 (65)
.....+..+.||+++++-..- +....+|. + ++.|+.++.
T Consensus 16 ~~~l~~~~~~~P~v~l~~~~~~~~~~~~~l~-~-g~~Dl~i~~ 56 (199)
T cd08430 16 PPILERFRAQHPQVEIKLHTGDPADAIDKVL-N-GEADIAIAA 56 (199)
T ss_pred cHHHHHHHHHCCCceEEEEeCCHHHHHHHHH-C-CCCCEEEEe
Confidence 456778888999888776532 22233333 3 467876653
No 161
>PRK12404 stage V sporulation protein AD; Provisional
Probab=26.19 E-value=32 Score=25.73 Aligned_cols=15 Identities=20% Similarity=0.419 Sum_probs=12.8
Q ss_pred hhCCCCccEEecCCc
Q psy9334 36 VSNPHQFDVMVMPNL 50 (65)
Q Consensus 36 v~~P~~fDVIV~~Nl 50 (65)
=++|+.||.|||..|
T Consensus 220 ~~~~~~yDlI~TGDL 234 (334)
T PRK12404 220 QIDASYYDLIVTGDL 234 (334)
T ss_pred CCChhhccEEEEcch
Confidence 467999999999876
No 162
>PRK09791 putative DNA-binding transcriptional regulator; Provisional
Probab=26.17 E-value=1.2e+02 Score=20.49 Aligned_cols=40 Identities=10% Similarity=0.130 Sum_probs=25.9
Q ss_pred hHHHHHHHHHhhCCCceechhhHHH--HHHHHhhCCCCccEEec
Q psy9334 6 GYPNLGQTMAKLYPKIQFEQMIVDN--CTMQIVSNPHQFDVMVM 47 (65)
Q Consensus 6 ~f~~~~~eva~~ypdV~~~~~~vDa--~~~~lv~~P~~fDVIV~ 47 (65)
.+-....+..++||+++++-...+. ....| .-++.|+.++
T Consensus 109 ~l~~~l~~~~~~~p~i~~~~~~~~~~~~~~~l--~~g~~Di~i~ 150 (302)
T PRK09791 109 LMPAVISRFHQQHPQVKVRIMEGQLVSMINEL--RQGELDFTIN 150 (302)
T ss_pred hhHHHHHHHHHHCCCeEEEEEeCChHHHHHHH--HCCCccEEEE
Confidence 3446777888999998877665332 22222 3668888665
No 163
>TIGR03807 RR_fam_repeat putative cofactor-binding repeat. This model describes a small repeat found in a family of proteins that crosses the plasma membrane by twin-arginine translation, which usually signifies the presence of a bound cofactor. This repeat shows similarity to the beta-helical repeat, in which three beta-strands per repeat wind once per repeat around in a right-handed helical stack of parallel beta structure.
Probab=26.08 E-value=34 Score=16.69 Aligned_cols=11 Identities=36% Similarity=0.643 Sum_probs=8.6
Q ss_pred CccEEecCCch
Q psy9334 41 QFDVMVMPNLY 51 (65)
Q Consensus 41 ~fDVIV~~Nl~ 51 (65)
+||++|+.|.-
T Consensus 13 ~~d~~vsGNvI 23 (27)
T TIGR03807 13 EFDAVVTGNVI 23 (27)
T ss_pred eeeeEEeccee
Confidence 57899998863
No 164
>PRK10797 glutamate and aspartate transporter subunit; Provisional
Probab=25.95 E-value=1e+02 Score=21.47 Aligned_cols=42 Identities=12% Similarity=0.086 Sum_probs=23.3
Q ss_pred hHHHHHHHHHhhC--CCceechhhHHHHHHHHhhCCCCccEEec
Q psy9334 6 GYPNLGQTMAKLY--PKIQFEQMIVDNCTMQIVSNPHQFDVMVM 47 (65)
Q Consensus 6 ~f~~~~~eva~~y--pdV~~~~~~vDa~~~~lv~~P~~fDVIV~ 47 (65)
+.+.++++++++- ++++++..-......-...+++++|++.+
T Consensus 69 l~~~ia~~l~~~lg~~~~~~~~v~~~~~~~i~~L~~G~~Di~~~ 112 (302)
T PRK10797 69 YSNAIVEAVKKKLNKPDLQVKLIPITSQNRIPLLQNGTFDFECG 112 (302)
T ss_pred HHHHHHHHHHHhhCCCCceEEEEEcChHhHHHHHHCCCccEEec
Confidence 4455677776653 35555555443222334446788998653
No 165
>PF06506 PrpR_N: Propionate catabolism activator; InterPro: IPR010524 Two-component signal transduction systems enable bacteria to sense, respond, and adapt to a wide range of environments, stressors, and growth conditions []. Some bacteria can contain up to as many as 200 two-component systems that need tight regulation to prevent unwanted cross-talk []. These pathways have been adapted to response to a wide variety of stimuli, including nutrients, cellular redox state, changes in osmolarity, quorum signals, antibiotics, and more []. Two-component systems are comprised of a sensor histidine kinase (HK) and its cognate response regulator (RR) []. The HK catalyses its own auto-phosphorylation followed by the transfer of the phosphoryl group to the receiver domain on RR; phosphorylation of the RR usually activates an attached output domain, which can then effect changes in cellular physiology, often by regulating gene expression. Some HK are bifunctional, catalysing both the phosphorylation and dephosphorylation of their cognate RR. The input stimuli can regulate either the kinase or phosphatase activity of the bifunctional HK. A variant of the two-component system is the phospho-relay system. Here a hybrid HK auto-phosphorylates and then transfers the phosphoryl group to an internal receiver domain, rather than to a separate RR protein. The phosphoryl group is then shuttled to histidine phosphotransferase (HPT) and subsequently to a terminal RR, which can evoke the desired response [, ]. This entry represents a domain found at the N terminus of several sigma54- dependent transcriptional activators including PrpR, which activates catabolism of propionate. In Salmonella enterica subsp. enterica serovar Typhimurium, PrpR acts as a sensor of 2-methylcitrate (2-MC), an intermediate of the 2-methylcitric acid cycle used by this bacterium to convert propionate to pyruvate []. ; GO: 0000156 two-component response regulator activity, 0003677 DNA binding, 0005524 ATP binding, 0000160 two-component signal transduction system (phosphorelay); PDB: 2Q5C_A 2PJU_A.
Probab=25.92 E-value=74 Score=20.56 Aligned_cols=44 Identities=14% Similarity=0.219 Sum_probs=25.6
Q ss_pred HHhhCC---CceechhhHHHHHHHHhh--CCCCccEEecCCchHHHHHh
Q psy9334 14 MAKLYP---KIQFEQMIVDNCTMQIVS--NPHQFDVMVMPNLYGNIVDN 57 (65)
Q Consensus 14 va~~yp---dV~~~~~~vDa~~~~lv~--~P~~fDVIV~~Nl~GDIlSD 57 (65)
++++|. +|.+..-..|......-+ ..+.+|||++---.+..|..
T Consensus 2 i~~e~~~~~~i~v~~~~~e~~v~~a~~~~~~~g~dViIsRG~ta~~lr~ 50 (176)
T PF06506_consen 2 IAKEYEDEAEIDVIEASLEEAVEEARQLLESEGADVIISRGGTAELLRK 50 (176)
T ss_dssp HHCCCTTTSEEEEEE--HHHHHHHHHHHHTTTT-SEEEEEHHHHHHHHC
T ss_pred chhhhCCCceEEEEEecHHHHHHHHHHhhHhcCCeEEEECCHHHHHHHH
Confidence 677777 466656566655432222 45888999987766666654
No 166
>PHA03058 Hypothetical protein; Provisional
Probab=25.80 E-value=1.3e+02 Score=19.53 Aligned_cols=32 Identities=19% Similarity=0.352 Sum_probs=25.3
Q ss_pred HHHHHHHhhCCCce------------echhhHHHHHHHHhhCCC
Q psy9334 9 NLGQTMAKLYPKIQ------------FEQMIVDNCTMQIVSNPH 40 (65)
Q Consensus 9 ~~~~eva~~ypdV~------------~~~~~vDa~~~~lv~~P~ 40 (65)
+.|.++.+.||++. -+..|||....+.++|-.
T Consensus 44 DlA~Ki~~~Y~g~~~iyFl~kv~~~ipn~~yv~s~L~r~i~~~~ 87 (124)
T PHA03058 44 DLAEKISEKYPGIRSIYFLKKVISEIPNTEYVDSLLSRAIKDFN 87 (124)
T ss_pred HHHHHHHHHCCCcchHHHHHHHHHhCCchHHHHHHHHHHHHhcC
Confidence 46788888999753 366799999999998866
No 167
>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=25.61 E-value=1.6e+02 Score=17.71 Aligned_cols=40 Identities=10% Similarity=0.056 Sum_probs=25.1
Q ss_pred HHHHHHHHHhhCCCceechh--hHHHHHHHHhhCCCCccEEecC
Q psy9334 7 YPNLGQTMAKLYPKIQFEQM--IVDNCTMQIVSNPHQFDVMVMP 48 (65)
Q Consensus 7 f~~~~~eva~~ypdV~~~~~--~vDa~~~~lv~~P~~fDVIV~~ 48 (65)
.-....+..++||+++++-. .-+.....|.. ++.|+.+..
T Consensus 16 l~~~l~~~~~~~P~i~l~~~~~~~~~~~~~l~~--~~~D~~i~~ 57 (198)
T cd08485 16 LPLLLRQLLSVAPSATVSLTQMSKNRQIEALDA--GTIDIGFGR 57 (198)
T ss_pred HHHHHHHHHHhCCCcEEEEEECCHHHHHHHHHc--CCccEEEec
Confidence 44566778889999888765 33444334433 467876553
No 168
>PRK06934 flavodoxin; Provisional
Probab=25.20 E-value=55 Score=22.81 Aligned_cols=21 Identities=14% Similarity=0.333 Sum_probs=15.9
Q ss_pred HHhhCCCCcc--EEecCCchHHH
Q psy9334 34 QIVSNPHQFD--VMVMPNLYGNI 54 (65)
Q Consensus 34 ~lv~~P~~fD--VIV~~Nl~GDI 54 (65)
..+.+..+|| +|.+|+++|.+
T Consensus 122 ~~~~dl~~YD~I~IG~PIWwg~~ 144 (221)
T PRK06934 122 EKIQNLADYDQIFIGYPIWWYKM 144 (221)
T ss_pred HHHHhHHhCCEEEEEcchhhccc
Confidence 4457788999 67789998864
No 169
>PF13531 SBP_bac_11: Bacterial extracellular solute-binding protein; PDB: 2HXW_B 3FJG_C 3FJM_B 3FJ7_B 3FIR_B 3AXF_C 1WOD_A 1AMF_A 3R26_A 1SBP_A ....
Probab=25.17 E-value=58 Score=21.10 Aligned_cols=41 Identities=15% Similarity=0.216 Sum_probs=24.1
Q ss_pred HHHHHHHHHhhCCCceechhhH--HHHHHHHhhCCCCccEEecCC
Q psy9334 7 YPNLGQTMAKLYPKIQFEQMIV--DNCTMQIVSNPHQFDVMVMPN 49 (65)
Q Consensus 7 f~~~~~eva~~ypdV~~~~~~v--Da~~~~lv~~P~~fDVIV~~N 49 (65)
+++++++.. ++|+++++-... ..+..+|...+ ++||++..+
T Consensus 13 ~~~l~~~f~-~~~g~~v~v~~~~s~~~~~~l~~g~-~~Dv~~~~~ 55 (230)
T PF13531_consen 13 LEELAEAFE-KQPGIKVEVSFGGSGELVRRLQAGK-KPDVFIPAS 55 (230)
T ss_dssp HHHHHHHHH-HHHCEEEEEEEECHHHHHHHHHTT--S-SEEEESS
T ss_pred HHHHHHHHH-hccCCeEEEEECChHHHHHHHhcCC-CceEEEECC
Confidence 445555553 357666655543 34445665556 999999987
No 170
>COG1412 Uncharacterized proteins of PilT N-term./Vapc superfamily [General function prediction only]
Probab=24.85 E-value=1.3e+02 Score=19.52 Aligned_cols=37 Identities=16% Similarity=0.198 Sum_probs=26.5
Q ss_pred HHHHHHhhCCCceechhhHHHHHHHHhhCCCCccEEecCC
Q psy9334 10 LGQTMAKLYPKIQFEQMIVDNCTMQIVSNPHQFDVMVMPN 49 (65)
Q Consensus 10 ~~~eva~~ypdV~~~~~~vDa~~~~lv~~P~~fDVIV~~N 49 (65)
++...++.++-+.. ..+.|-+..+.+..-+ -++|++|
T Consensus 69 ia~~~~er~~~~~~-~~~aDe~i~~~a~~~~--~~iVaTn 105 (136)
T COG1412 69 IALKYAERLECIHK-GRYADECLLEAALKHG--RYIVATN 105 (136)
T ss_pred HHHHHhhccCcccc-CCChHHHHHHHHHHcC--CEEEEeC
Confidence 45556777877776 7777888888777655 4777777
No 171
>COG3186 Phenylalanine-4-hydroxylase [Amino acid transport and metabolism]
Probab=24.83 E-value=40 Score=24.84 Aligned_cols=37 Identities=11% Similarity=0.321 Sum_probs=28.4
Q ss_pred CceechhhHHHHH------HHHhhCCCCccEEecCCchHHHHH
Q psy9334 20 KIQFEQMIVDNCT------MQIVSNPHQFDVMVMPNLYGNIVD 56 (65)
Q Consensus 20 dV~~~~~~vDa~~------~~lv~~P~~fDVIV~~Nl~GDIlS 56 (65)
...-.+.+.|-++ .+.++.|+++|-+..|.+|=|++.
T Consensus 106 glvp~~~ff~lLanrrFPva~~mRt~~eldylqePD~fHdvfG 148 (291)
T COG3186 106 GLVPFDVFFDLLANRRFPVATFMRTPDELDYLQEPDIFHDVFG 148 (291)
T ss_pred ccCChHHHHHHHhhccCcHHHHhcCHhhcccccCccHHHHHhc
Confidence 3344455555554 688999999999999999999864
No 172
>cd02985 TRX_CDSP32 TRX family, chloroplastic drought-induced stress protein of 32 kD (CDSP32); CDSP32 is composed of two TRX domains, a C-terminal TRX domain which contains a redox active CXXC motif and an N-terminal TRX-like domain which contains an SXXS sequence instead of the redox active motif. CDSP32 is a stress-inducible TRX, i.e., it acts as a TRX by reducing protein disulfides and is induced by environmental and oxidative stress conditions. It plays a critical role in plastid defense against oxidative damage, a role related to its function as a physiological electron donor to BAS1, a plastidic 2-cys peroxiredoxin. Plants lacking CDSP32 exhibit decreased photosystem II photochemical efficiencies and chlorophyll retention compared to WT controls, as well as an increased proportion of BAS1 in its overoxidized monomeric form.
Probab=24.78 E-value=44 Score=19.46 Aligned_cols=27 Identities=15% Similarity=0.094 Sum_probs=18.1
Q ss_pred chhchHHHHHHHHHhhCCCceechhhHH
Q psy9334 2 PCRFGYPNLGQTMAKLYPKIQFEQMIVD 29 (65)
Q Consensus 2 ~~~~~f~~~~~eva~~ypdV~~~~~~vD 29 (65)
||+.+. ...++++++|+++.+-...+|
T Consensus 29 ~C~~~~-p~l~~la~~~~~v~~~~vd~d 55 (103)
T cd02985 29 PSVKIY-PTMVKLSRTCNDVVFLLVNGD 55 (103)
T ss_pred hHHHHh-HHHHHHHHHCCCCEEEEEECC
Confidence 677664 466678889987665544444
No 173
>cd05568 PTS_IIB_bgl_like PTS_IIB_bgl_like: the PTS (phosphotransferase system) IIB domain of a family of sensory systems composed of a membrane-bound sugar-sensor (similar to BglF) and a transcription antiterminator (similar to BglG) which regulate expression of genes involved in sugar utilization. The domain architecture of the IIB-containing protein includes a region N-terminal to the IIB domain which is homologous to the BglG transcription antiterminator with an RNA-binding domain followed by two homologous domains, PRD1 and PRD2 (PTS Regulation Domains). C-terminal to the IIB domain is a domain similar to the PTS IIA domain. In this system, the BglG-like region and the IIB and IIA-like domains are all expressed together as a single multidomain protein. The IIB domain fold includes a central four-stranded parallel open twisted beta-sheet flanked by alpha-helices on both sides. The seven major PTS systems with this IIB fold include this sensory system with similarity to the bacterial
Probab=24.71 E-value=1.3e+02 Score=16.37 Aligned_cols=38 Identities=16% Similarity=0.418 Sum_probs=20.7
Q ss_pred HHHHHHhhCCCceechhhHHHHHHHHhh-CCCCccEEecCCc
Q psy9334 10 LGQTMAKLYPKIQFEQMIVDNCTMQIVS-NPHQFDVMVMPNL 50 (65)
Q Consensus 10 ~~~eva~~ypdV~~~~~~vDa~~~~lv~-~P~~fDVIV~~Nl 50 (65)
...++.+.||+...-.. +.. .++-. +..++|.|+|+--
T Consensus 17 l~~~l~~~~~~~~~v~~-~~~--~~~~~~~~~~~DlIitT~~ 55 (85)
T cd05568 17 LKSKLKKLFPEIEIIDV-ISL--RELEEVDLDDYDLIISTVP 55 (85)
T ss_pred HHHHHHHHCCCceEEEE-EeH--HHHhhCcccCCCEEEEccc
Confidence 44556667876544211 111 12222 4788999988764
No 174
>PRK15421 DNA-binding transcriptional regulator MetR; Provisional
Probab=24.64 E-value=1.3e+02 Score=20.89 Aligned_cols=43 Identities=7% Similarity=0.108 Sum_probs=26.4
Q ss_pred chHHHHHHHHHhhCCCceechhhH--HHHHHHHhhCCCCccEEecCC
Q psy9334 5 FGYPNLGQTMAKLYPKIQFEQMIV--DNCTMQIVSNPHQFDVMVMPN 49 (65)
Q Consensus 5 ~~f~~~~~eva~~ypdV~~~~~~v--Da~~~~lv~~P~~fDVIV~~N 49 (65)
..+.+...+..++||+|.++-... +... ..+.+ +++|+.++..
T Consensus 102 ~~l~~~l~~~~~~~P~i~l~~~~~~~~~~~-~~L~~-g~~Dl~i~~~ 146 (317)
T PRK15421 102 QWLTPALENFHKNWPQVEMDFKSGVTFDPQ-PALQQ-GELDLVMTSD 146 (317)
T ss_pred HHHHHHHHHHHHHCCCceEEEEeCccHHHH-HHHHC-CCcCEEEecC
Confidence 345567788888999988876433 2232 33333 5578666543
No 175
>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=24.52 E-value=1.6e+02 Score=17.37 Aligned_cols=38 Identities=18% Similarity=0.355 Sum_probs=23.7
Q ss_pred HHHHHHHHhhCCCceechhh--HHHHHHHHhhCCCCccEEec
Q psy9334 8 PNLGQTMAKLYPKIQFEQMI--VDNCTMQIVSNPHQFDVMVM 47 (65)
Q Consensus 8 ~~~~~eva~~ypdV~~~~~~--vDa~~~~lv~~P~~fDVIV~ 47 (65)
-+...+..++||+++++-.. -+.....|.. ++.|+.++
T Consensus 17 ~~~l~~~~~~~P~i~i~i~~~~~~~~~~~l~~--~~~Dl~i~ 56 (200)
T cd08411 17 PRLLPALRQAYPKLRLYLREDQTERLLEKLRS--GELDAALL 56 (200)
T ss_pred HHHHHHHHHHCCCcEEEEEeCcHHHHHHHHHc--CCccEEEE
Confidence 45677888899998777553 2333333333 56787664
No 176
>cd03073 PDI_b'_ERp72_ERp57 PDIb' family, ERp72 and ERp57 subfamily, second redox inactive TRX-like domain b'; ERp72 and ER57 are involved in oxidative protein folding in the ER, like PDI. They exhibit both disulfide oxidase and reductase functions, by catalyzing the formation of disulfide bonds of newly synthesized polypeptides and acting as isomerases to correct any non-native disulfide bonds. They also display chaperone activity to prevent protein aggregation and facilitate the folding of newly synthesized proteins. ERp57 contains two redox-active TRX (a) domains and two redox inactive TRX-like (b) domains. It shares the same domain arrangement of abb'a' as PDI, but lacks the C-terminal acid-rich region (c domain) that is present in PDI. ERp72 contains one additional redox-active TRX (a) domain at the N-terminus with a molecular structure of a"abb'a'. ERp57 interacts with the lectin chaperones, calnexin and calreticulin, and specifically promotes the oxidative folding of glycoprotei
Probab=24.48 E-value=54 Score=19.99 Aligned_cols=27 Identities=19% Similarity=0.171 Sum_probs=18.9
Q ss_pred chHHHHHHHHHhhCCCceechhhHHHH
Q psy9334 5 FGYPNLGQTMAKLYPKIQFEQMIVDNC 31 (65)
Q Consensus 5 ~~f~~~~~eva~~ypdV~~~~~~vDa~ 31 (65)
.-|++..+++|++|.+-++.-.++|+-
T Consensus 34 ~~~~~~~~~vAk~fk~gki~Fv~~D~~ 60 (111)
T cd03073 34 NYWRNRVLKVAKDFPDRKLNFAVADKE 60 (111)
T ss_pred HHHHHHHHHHHHHCcCCeEEEEEEcHH
Confidence 458999999999998223445555544
No 177
>PRK08349 hypothetical protein; Validated
Probab=24.46 E-value=1.3e+02 Score=19.72 Aligned_cols=17 Identities=12% Similarity=0.262 Sum_probs=12.3
Q ss_pred chhchHHHHHHHHHhhC
Q psy9334 2 PCRFGYPNLGQTMAKLY 18 (65)
Q Consensus 2 ~~~~~f~~~~~eva~~y 18 (65)
||+.+++..+.+.|+++
T Consensus 88 ~cr~~~~~~a~~~A~~~ 104 (198)
T PRK08349 88 FCKYTMYRKAERIAHEI 104 (198)
T ss_pred HHHHHHHHHHHHHHHHc
Confidence 57777777777777653
No 178
>TIGR00595 priA primosomal protein N'. All proteins in this family for which functions are known are components of the primosome which is involved in replication, repair, and recombination.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=24.42 E-value=1.3e+02 Score=23.06 Aligned_cols=43 Identities=14% Similarity=0.342 Sum_probs=28.5
Q ss_pred HHHHHHHHhhCCCceechhhHHHH--------HHHHhhCCCCccEEecCCch
Q psy9334 8 PNLGQTMAKLYPKIQFEQMIVDNC--------TMQIVSNPHQFDVMVMPNLY 51 (65)
Q Consensus 8 ~~~~~eva~~ypdV~~~~~~vDa~--------~~~lv~~P~~fDVIV~~Nl~ 51 (65)
.++.+++.+.||+..+..+.-|.. .++-++ -.++|++|++.+.
T Consensus 272 e~~~e~l~~~fp~~~v~~~d~d~~~~~~~~~~~l~~f~-~g~~~ILVgT~~i 322 (505)
T TIGR00595 272 EQVEEELAKLFPGARIARIDSDTTSRKGAHEALLNQFA-NGKADILIGTQMI 322 (505)
T ss_pred HHHHHHHHhhCCCCcEEEEecccccCccHHHHHHHHHh-cCCCCEEEeCccc
Confidence 567788888899877665544432 122233 3678999999875
No 179
>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=24.39 E-value=54 Score=19.28 Aligned_cols=38 Identities=11% Similarity=0.055 Sum_probs=24.9
Q ss_pred HHHHHHHHHhhCCCceechhhHHHHHHHHhhCCCCccEEec
Q psy9334 7 YPNLGQTMAKLYPKIQFEQMIVDNCTMQIVSNPHQFDVMVM 47 (65)
Q Consensus 7 f~~~~~eva~~ypdV~~~~~~vDa~~~~lv~~P~~fDVIV~ 47 (65)
......+..+.||+++++-..-+ . ...+.+ ++.|+.++
T Consensus 15 l~~~l~~~~~~~P~v~i~~~~~~-~-~~~l~~-g~~D~~i~ 52 (194)
T cd08432 15 LIPRLARFQARHPDIDLRLSTSD-R-LVDFAR-EGIDLAIR 52 (194)
T ss_pred HHHHhHHHHHHCCCeEEEEEecC-C-cccccc-ccccEEEE
Confidence 34566778888999888876544 2 333344 57887665
No 180
>KOG3673|consensus
Probab=24.30 E-value=75 Score=26.18 Aligned_cols=39 Identities=13% Similarity=0.154 Sum_probs=28.5
Q ss_pred echhhHHHHHHHHhhCCCCcc--EEecCCchHH--HHHhhhhhc
Q psy9334 23 FEQMIVDNCTMQIVSNPHQFD--VMVMPNLYGN--IVDNLASDI 62 (65)
Q Consensus 23 ~~~~~vDa~~~~lv~~P~~fD--VIV~~Nl~GD--IlSD~aa~l 62 (65)
+.--.+|.++-+|.+||...= -.|++|. -+ ..+|+|||=
T Consensus 236 mKmANmD~i~d~mftNpRdp~g~~lva~~~-~eLlYFaDvCAGP 278 (845)
T KOG3673|consen 236 MKMANMDKIYDWMFTNPRDPLGESLVAENV-EELLYFADVCAGP 278 (845)
T ss_pred HHhhhHHHHHHHHhCCCCCcccCccccccH-HHHHHHHhhhcCC
Confidence 344578999999999999542 7788874 22 268899883
No 181
>KOG0230|consensus
Probab=23.76 E-value=34 Score=30.50 Aligned_cols=16 Identities=56% Similarity=0.835 Sum_probs=13.4
Q ss_pred hhCCCCc-----cEEecCCch
Q psy9334 36 VSNPHQF-----DVMVMPNLY 51 (65)
Q Consensus 36 v~~P~~f-----DVIV~~Nl~ 51 (65)
+++|... ||+|++|||
T Consensus 1426 vK~~~sgke~K~DvmVMENLf 1446 (1598)
T KOG0230|consen 1426 VKSPKSGKETKMDVMVMENLF 1446 (1598)
T ss_pred EecCCCCceeEeeeeeehhhh
Confidence 5677776 999999998
No 182
>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=23.66 E-value=63 Score=18.95 Aligned_cols=37 Identities=16% Similarity=0.062 Sum_probs=24.0
Q ss_pred HHHHHHHHhhCCCceechhhHHHHHHHHhhCCCCccEEec
Q psy9334 8 PNLGQTMAKLYPKIQFEQMIVDNCTMQIVSNPHQFDVMVM 47 (65)
Q Consensus 8 ~~~~~eva~~ypdV~~~~~~vDa~~~~lv~~P~~fDVIV~ 47 (65)
.....+..++||+|+++-..-+.. ..+.+ ++.|+.++
T Consensus 16 ~~~l~~f~~~~P~i~i~i~~~~~~--~~l~~-~~~Dl~l~ 52 (194)
T cd08481 16 IPRLPDFLARHPDITVNLVTRDEP--FDFSQ-GSFDAAIH 52 (194)
T ss_pred HhhhhHHHHHCCCceEEEEecccc--cCccc-CCCCEEEE
Confidence 356678888999988875543322 23333 68898775
No 183
>cd01840 SGNH_hydrolase_yrhL_like yrhL-like subfamily of SGNH-hydrolases, 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. Most members of this sub-family appear to co-occur with N-terminal acyltransferase domains. Might be involved in lipid metabolism.
Probab=23.37 E-value=84 Score=19.36 Aligned_cols=32 Identities=16% Similarity=0.168 Sum_probs=20.7
Q ss_pred hHHHHHHHHHhhCCCceechhhHHHHHHHHhhCCCCc
Q psy9334 6 GYPNLGQTMAKLYPKIQFEQMIVDNCTMQIVSNPHQF 42 (65)
Q Consensus 6 ~f~~~~~eva~~ypdV~~~~~~vDa~~~~lv~~P~~f 42 (65)
-|.+..+++|++||.+.+-+.+ .. +..+|+.|
T Consensus 96 ~~n~~~~~~a~~~~~v~~id~~--~~---~~~~~~~~ 127 (150)
T cd01840 96 DVNAYLLDAAKKYKNVTIIDWY--KA---AKGHPDWF 127 (150)
T ss_pred HHHHHHHHHHHHCCCcEEecHH--HH---hcccchhh
Confidence 4567788889999988776643 11 22467655
No 184
>cd08443 PBP2_CysB The C-terminal substrate domain of LysR-type transcriptional regulator CysB contains type 2 periplasmic binding fold. CysB is a transcriptional activator of genes involved in sulfate and thiosulfate transport, sulfate reduction, and cysteine synthesis. In Escherichia coli, the regulation of transcription in response to sulfur source is attributed to two transcriptional regulators, CysB and Cbl. CysB, in association with Cbl, downregulates the expression of ssuEADCB operon which is required for the utilization of sulfur from aliphatic sulfonates, in the presence of cysteine. Also, Cbl and CysB together directly function as transcriptional activators of tauABCD genes, which are required for utilization of taurine as sulfur source for growth. Like many other members of the LTTR family, CysB is composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding speci
Probab=23.20 E-value=1.3e+02 Score=18.13 Aligned_cols=38 Identities=11% Similarity=0.219 Sum_probs=23.2
Q ss_pred HHHHHHHHhhCCCceechhhH--HHHHHHHhhCCCCccEEec
Q psy9334 8 PNLGQTMAKLYPKIQFEQMIV--DNCTMQIVSNPHQFDVMVM 47 (65)
Q Consensus 8 ~~~~~eva~~ypdV~~~~~~v--Da~~~~lv~~P~~fDVIV~ 47 (65)
-+...+..++||+++++-..- +.....|.. ++.|+.++
T Consensus 16 ~~~l~~f~~~~P~~~i~i~~~~~~~~~~~l~~--g~~Dl~i~ 55 (198)
T cd08443 16 PPVIKGFIERYPRVSLQMHQGSPTQIAEMVSK--GLVDFAIA 55 (198)
T ss_pred cHHHHHHHHHCCCeEEEEEeCCHHHHHHHHHC--CCccEEEE
Confidence 456777888999887765433 333333333 46786664
No 185
>COG0312 TldD Predicted Zn-dependent proteases and their inactivated homologs [General function prediction only]
Probab=23.15 E-value=37 Score=25.23 Aligned_cols=21 Identities=14% Similarity=0.385 Sum_probs=17.7
Q ss_pred CCCccEEecCCchHHHHHhhh
Q psy9334 39 PHQFDVMVMPNLYGNIVDNLA 59 (65)
Q Consensus 39 P~~fDVIV~~Nl~GDIlSD~a 59 (65)
+.+|+||..|...|.+++...
T Consensus 226 ~g~~~VIl~p~~~~~llhea~ 246 (454)
T COG0312 226 SGRYPVILSPEAAGVLLHEAL 246 (454)
T ss_pred CCcccEEECCCchheeeehhh
Confidence 567999999999999998443
No 186
>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=23.09 E-value=66 Score=16.73 Aligned_cols=23 Identities=30% Similarity=0.182 Sum_probs=16.1
Q ss_pred hchHHHHHHHHHhhCCCceechh
Q psy9334 4 RFGYPNLGQTMAKLYPKIQFEQM 26 (65)
Q Consensus 4 ~~~f~~~~~eva~~ypdV~~~~~ 26 (65)
|.+|++-.-.++...|+|++...
T Consensus 2 R~F~~~~lp~l~~~NP~v~~~v~ 24 (52)
T PF05047_consen 2 RDFLKNNLPTLKYHNPQVQFEVR 24 (52)
T ss_dssp HHHHHHTHHHHHHHSTT--EEEE
T ss_pred HhHHHHhHHHHHHHCCCcEEEEE
Confidence 56677778888888999887653
No 187
>PRK12680 transcriptional regulator CysB-like protein; Reviewed
Probab=23.07 E-value=1.3e+02 Score=21.00 Aligned_cols=42 Identities=12% Similarity=0.219 Sum_probs=25.2
Q ss_pred chHHHHHHHHHhhCCCceechh--hHHHHHHHHhhCCCCccEEecC
Q psy9334 5 FGYPNLGQTMAKLYPKIQFEQM--IVDNCTMQIVSNPHQFDVMVMP 48 (65)
Q Consensus 5 ~~f~~~~~eva~~ypdV~~~~~--~vDa~~~~lv~~P~~fDVIV~~ 48 (65)
.++.+......+.||+|.++-. .-+.....|.. +++|+.++.
T Consensus 106 ~~l~~~l~~f~~~~P~v~i~l~~~~~~~~~~~l~~--g~~Dl~i~~ 149 (327)
T PRK12680 106 FVLPPAVAQIKQAYPQVSVHLQQAAESAALDLLGQ--GDADIAIVS 149 (327)
T ss_pred HhhHHHHHHHHHHCCCcEEEEEeCChHHHHHHHHC--CCCcEEEEe
Confidence 3455777888899998776644 33344333332 346766653
No 188
>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=23.00 E-value=89 Score=18.51 Aligned_cols=40 Identities=18% Similarity=0.231 Sum_probs=25.0
Q ss_pred hHHHHHHHHHhhCCCceechhhHHHHHHHHhhCCCCccEEecC
Q psy9334 6 GYPNLGQTMAKLYPKIQFEQMIVDNCTMQIVSNPHQFDVMVMP 48 (65)
Q Consensus 6 ~f~~~~~eva~~ypdV~~~~~~vDa~~~~lv~~P~~fDVIV~~ 48 (65)
..-+...+..++||+++++-..-+. .+.+.+ ++.|+.++.
T Consensus 15 ~l~~~l~~f~~~~P~i~i~~~~~~~--~~~l~~-g~~Dl~i~~ 54 (198)
T cd08479 15 HIAPALSDFAKRYPELEVQLELTDR--PVDLVE-EGFDLDIRV 54 (198)
T ss_pred HHHHHHHHHHHHCCCeEEEEEecCc--cccccc-cCccEEEEc
Confidence 3346778889999998887553222 233344 478876653
No 189
>TIGR03412 iscX_yfhJ FeS assembly protein IscX. Members of this protein family are YfhJ, a protein of the ISC system for iron-sulfur cluster assembly. Other genes in the system include iscSUA, hscBA, and fdx.
Probab=22.96 E-value=1.7e+02 Score=16.96 Aligned_cols=35 Identities=17% Similarity=0.233 Sum_probs=20.8
Q ss_pred HHHHHHHHhhCCCceechhhHHHHHHHHhhCCCCcc
Q psy9334 8 PNLGQTMAKLYPKIQFEQMIVDNCTMQIVSNPHQFD 43 (65)
Q Consensus 8 ~~~~~eva~~ypdV~~~~~~vDa~~~~lv~~P~~fD 43 (65)
+++|.+..+.||++.-...-.-.+ .++|..-..||
T Consensus 6 ~eIA~~L~e~~pd~dp~~vrFtdL-~~wV~~L~~Fd 40 (63)
T TIGR03412 6 QEIAIALAEAHPDVDPKTVRFTDL-HQWVLELPGFD 40 (63)
T ss_pred HHHHHHHHHHCCCCCcceeeHHHH-HHHHHhCcCcC
Confidence 478889999999975444333333 34444444443
No 190
>PF07451 SpoVAD: Stage V sporulation protein AD (SpoVAD); InterPro: IPR010894 This family contains the bacterial stage V sporulation protein AD (SpoVAD), which is approximately 340 residues long. This is one of six proteins encoded by the spoVA operon, which is transcribed exclusively in the forespore at about the time of dipicolinic acid (DPA) synthesis in the mother cell. The functions of the proteins encoded by the spoVA operon are unknown, but it has been suggested they are involved in DPA transport during sporulation [].; PDB: 3LMA_D 3LM6_A.
Probab=22.80 E-value=36 Score=25.50 Aligned_cols=15 Identities=27% Similarity=0.618 Sum_probs=9.9
Q ss_pred hhCCCCccEEecCCc
Q psy9334 36 VSNPHQFDVMVMPNL 50 (65)
Q Consensus 36 v~~P~~fDVIV~~Nl 50 (65)
=++|..||.|||..|
T Consensus 217 g~~p~dYDlIvTGDL 231 (329)
T PF07451_consen 217 GRSPDDYDLIVTGDL 231 (329)
T ss_dssp T--GGG-SEEEESS-
T ss_pred CCChhhcCeEEecch
Confidence 356999999999876
No 191
>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=22.79 E-value=85 Score=18.73 Aligned_cols=39 Identities=13% Similarity=0.060 Sum_probs=23.9
Q ss_pred hHHHHHHHHHhhCCCceechhhHHHHHHHHhhCCCCccEEec
Q psy9334 6 GYPNLGQTMAKLYPKIQFEQMIVDNCTMQIVSNPHQFDVMVM 47 (65)
Q Consensus 6 ~f~~~~~eva~~ypdV~~~~~~vDa~~~~lv~~P~~fDVIV~ 47 (65)
.+-....+..++||+++++-..-+.. ..+.. .+.|+.++
T Consensus 14 ~l~~~l~~f~~~~P~v~i~~~~~~~~-~~l~~--~~~D~~i~ 52 (191)
T cd08488 14 WLLPRLADFQNRHPFIDLRLSTNNNR-VDIAA--EGLDYAIR 52 (191)
T ss_pred HHHhHHHHHHHHCCCcEEEEEecCCc-cccCC--CCccEEEE
Confidence 34567788889999988876533322 23333 35776554
No 192
>smart00828 PKS_MT Methyltransferase in polyketide synthase (PKS) enzymes.
Probab=22.49 E-value=35 Score=22.21 Aligned_cols=15 Identities=13% Similarity=0.352 Sum_probs=12.1
Q ss_pred CCCccEEecCCchHH
Q psy9334 39 PHQFDVMVMPNLYGN 53 (65)
Q Consensus 39 P~~fDVIV~~Nl~GD 53 (65)
|..||+|++.+++..
T Consensus 65 ~~~fD~I~~~~~l~~ 79 (224)
T smart00828 65 PDTYDLVFGFEVIHH 79 (224)
T ss_pred CCCCCEeehHHHHHh
Confidence 578999999887753
No 193
>cd03710 BipA_TypA_C BipA_TypA_C: a C-terminal portion of BipA or TypA having homology to the C terminal domains of the elongation factors EF-G and EF-2. A member of the ribosome binding GTPase superfamily, BipA is widely distributed in bacteria and plants. BipA is a highly conserved protein with global regulatory properties in Escherichia coli. BipA is phosphorylated on a tyrosine residue under some cellular conditions. Mutants show altered regulation of some pathways. BipA functions as a translation factor that is required specifically for the expression of the transcriptional modulator Fis. BipA binds to ribosomes at a site that coincides with that of EF-G and has a GTPase activity that is sensitive to high GDP:GTP ratios and, is stimulated by 70S ribosomes programmed with mRNA and aminoacylated tRNAs. The growth rate-dependent induction of BipA allows the efficient expression of Fis, thereby modulating a range of downstream processes, including DNA metabolism and type III secreti
Probab=22.44 E-value=59 Score=18.33 Aligned_cols=20 Identities=15% Similarity=0.399 Sum_probs=15.3
Q ss_pred CccEEecCCchHHHHHhhhh
Q psy9334 41 QFDVMVMPNLYGNIVDNLAS 60 (65)
Q Consensus 41 ~fDVIV~~Nl~GDIlSD~aa 60 (65)
++.|.+-++.-|++++|+..
T Consensus 5 ~v~I~~P~~~~g~V~~~l~~ 24 (79)
T cd03710 5 ELTIDVPEEYSGAVIEKLGK 24 (79)
T ss_pred EEEEEeCchhhHHHHHHHHh
Confidence 35577777788999999874
No 194
>cd02440 AdoMet_MTases S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy). There are at least five structurally distinct families of AdoMet-MTases, class I being the largest and most diverse. Within this class enzymes can be classified by different substrate specificities (small molecules, lipids, nucleic acids, etc.) and different target atoms for methylation (nitrogen, oxygen, carbon, sulfur, etc.).
Probab=22.30 E-value=89 Score=16.17 Aligned_cols=17 Identities=18% Similarity=0.296 Sum_probs=13.6
Q ss_pred hCCCCccEEecCCchHH
Q psy9334 37 SNPHQFDVMVMPNLYGN 53 (65)
Q Consensus 37 ~~P~~fDVIV~~Nl~GD 53 (65)
..+.+||+|++.+.+..
T Consensus 62 ~~~~~~d~i~~~~~~~~ 78 (107)
T cd02440 62 EADESFDVIISDPPLHH 78 (107)
T ss_pred ccCCceEEEEEccceee
Confidence 36788999999988754
No 195
>COG1383 RPS17A Ribosomal protein S17E [Translation, ribosomal structure and biogenesis]
Probab=22.25 E-value=51 Score=19.74 Aligned_cols=15 Identities=13% Similarity=0.315 Sum_probs=12.5
Q ss_pred HHHHHHHHHhhCCCc
Q psy9334 7 YPNLGQTMAKLYPKI 21 (65)
Q Consensus 7 f~~~~~eva~~ypdV 21 (65)
-+++++++.+.||+.
T Consensus 9 vKR~a~el~ekY~~~ 23 (74)
T COG1383 9 VKRTARELIEKYPDK 23 (74)
T ss_pred HHHHHHHHHHHhHHH
Confidence 467999999999974
No 196
>cd04098 eEF2_C_snRNP eEF2_C_snRNP: This family includes a C-terminal portion of the spliceosomal human 116kD U5 small nuclear ribonucleoprotein (snRNP) protein (U5-116 kD) and, its yeast counterpart Snu114p. This domain is homologous to the C-terminal domain of the eukaryotic translational elongation factor EF-2. Yeast Snu114p is essential for cell viability and for splicing in vivo. U5-116 kD binds GTP. Experiments suggest that GTP binding and probably GTP hydrolysis is important for the function of the U5-116 kD/Snu114p. In complex with GTP, EF-2 promotes the translocation step of translation. During translocation the peptidyl-tRNA is moved from the A site to the P site, the uncharged tRNA from the P site to the E-site and, the mRNA is shifted one codon relative to the ribosome.
Probab=22.23 E-value=41 Score=19.22 Aligned_cols=20 Identities=5% Similarity=0.207 Sum_probs=15.7
Q ss_pred CccEEecCCchHHHHHhhhh
Q psy9334 41 QFDVMVMPNLYGNIVDNLAS 60 (65)
Q Consensus 41 ~fDVIV~~Nl~GDIlSD~aa 60 (65)
.++|.+-....|++++|+..
T Consensus 5 ~~ei~~p~~~~g~v~~~L~~ 24 (80)
T cd04098 5 EVEITCPADAVSAVYEVLSR 24 (80)
T ss_pred EEEEEECHHHHhHHHHHHhh
Confidence 45677778888999999864
No 197
>PRK03601 transcriptional regulator HdfR; Provisional
Probab=22.15 E-value=1.5e+02 Score=19.82 Aligned_cols=41 Identities=15% Similarity=0.168 Sum_probs=24.3
Q ss_pred HHHHHHHHHhhCCCceechh--hHHHHHHHHhhCCCCccEEecCC
Q psy9334 7 YPNLGQTMAKLYPKIQFEQM--IVDNCTMQIVSNPHQFDVMVMPN 49 (65)
Q Consensus 7 f~~~~~eva~~ypdV~~~~~--~vDa~~~~lv~~P~~fDVIV~~N 49 (65)
.-....+..+.||+++++-. .-+.+...|.. +++|+.++..
T Consensus 104 l~~~l~~f~~~~P~v~v~~~~~~~~~~~~~l~~--g~~Dl~i~~~ 146 (275)
T PRK03601 104 LTPWLGRLYQNQEALQFEARIAQRQSLVKQLHE--RQLDLLITTE 146 (275)
T ss_pred HHHHHHHHHHhCCCcEEEEEECChHHHHHHHHc--CCCCEEEEcC
Confidence 34567777889999887642 33333333333 4568777644
No 198
>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=22.08 E-value=94 Score=18.32 Aligned_cols=38 Identities=13% Similarity=0.319 Sum_probs=24.2
Q ss_pred HHHHHHHHHhhCCCceechhhHHHHHHHHhhCCCCccEEec
Q psy9334 7 YPNLGQTMAKLYPKIQFEQMIVDNCTMQIVSNPHQFDVMVM 47 (65)
Q Consensus 7 f~~~~~eva~~ypdV~~~~~~vDa~~~~lv~~P~~fDVIV~ 47 (65)
.-+...+..++||+++++-..-+.. .++. + ++.|+.+.
T Consensus 18 l~~~l~~~~~~~P~i~i~~~~~~~~-~~~~-~-~~~D~~i~ 55 (202)
T cd08473 18 LAPLLPRFMAAYPQVRLQLEATNRR-VDLI-E-EGIDVALR 55 (202)
T ss_pred HHHHHHHHHHHCCCeEEEEEEcCCc-cccc-c-cCccEEEE
Confidence 3467788889999988775433322 3444 3 46887664
No 199
>cd06308 PBP1_sensor_kinase_like Periplasmic binding domain of two-component sensor kinase signaling systems. Periplasmic binding domain of two-component sensor kinase signaling systems, some of which are fused with a C-terminal histidine kinase A domain (HisK) and/or a signal receiver domain (REC). Members of this group share homology with a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily and are predicted to be involved in sensing of environmental stimuli; their substrate specificities, however, are not known in detail.
Probab=21.99 E-value=2.4e+02 Score=18.32 Aligned_cols=19 Identities=11% Similarity=0.172 Sum_probs=12.8
Q ss_pred HHHHHhhCCCCccEEecCC
Q psy9334 31 CTMQIVSNPHQFDVMVMPN 49 (65)
Q Consensus 31 ~~~~lv~~P~~fDVIV~~N 49 (65)
.+.++++....+|.|++.|
T Consensus 172 ~~~~~l~~~~~~~aI~~~~ 190 (270)
T cd06308 172 KMEELLQANPDIDLVYAHN 190 (270)
T ss_pred HHHHHHHhCCCCcEEEeCC
Confidence 4556665544789888865
No 200
>cd02954 DIM1 Dim1 family; Dim1 is also referred to as U5 small nuclear ribonucleoprotein particle (snRNP)-specific 15kD protein. It is a component of U5 snRNP, which pre-assembles with U4/U6 snRNPs to form a [U4/U6:U5] tri-snRNP complex required for pre-mRNA splicing. Dim1 interacts with multiple splicing-associated proteins, suggesting that it functions at multiple control points in the splicing of pre-mRNA as part of a large spliceosomal complex involving many protein-protein interactions. U5 snRNP contains seven core proteins (common to all snRNPs) and nine U5-specific proteins, one of which is Dim1. Dim1 adopts a thioredoxin fold but does not contain the redox active CXXC motif. It is essential for G2/M phase transition, as a consequence to its role in pre-mRNA splicing.
Probab=21.98 E-value=59 Score=20.34 Aligned_cols=28 Identities=11% Similarity=0.032 Sum_probs=18.0
Q ss_pred chhchHHHHHHHHHhhCCC-ceechhhHHH
Q psy9334 2 PCRFGYPNLGQTMAKLYPK-IQFEQMIVDN 30 (65)
Q Consensus 2 ~~~~~f~~~~~eva~~ypd-V~~~~~~vDa 30 (65)
||+.+ .....+++++|++ +.+-...+|.
T Consensus 28 pCk~m-~P~le~la~~~~~~v~f~kVDvD~ 56 (114)
T cd02954 28 VCMQM-DEVLAKIAEDVSNFAVIYLVDIDE 56 (114)
T ss_pred hHHHH-HHHHHHHHHHccCceEEEEEECCC
Confidence 67644 4578888999987 3544444443
No 201
>PRK00455 pyrE orotate phosphoribosyltransferase; Validated
Probab=21.89 E-value=1.8e+02 Score=19.15 Aligned_cols=37 Identities=16% Similarity=0.111 Sum_probs=24.6
Q ss_pred chhhHHHHHHHHhhCCCCccEEecCCchHHHHHhhhh
Q psy9334 24 EQMIVDNCTMQIVSNPHQFDVMVMPNLYGNIVDNLAS 60 (65)
Q Consensus 24 ~~~~vDa~~~~lv~~P~~fDVIV~~Nl~GDIlSD~aa 60 (65)
-+..++.++.++..+-..+|+||++-.=|=.++...|
T Consensus 47 ~~~~~~~la~~i~~~~~~~d~Ivgi~~gG~~~A~~la 83 (202)
T PRK00455 47 LALLGRFLAEAIKDSGIEFDVVAGPATGGIPLAAAVA 83 (202)
T ss_pred HHHHHHHHHHHHHhcCCCCCEEEecccCcHHHHHHHH
Confidence 3455666666665555589999998776666655444
No 202
>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=21.68 E-value=96 Score=18.34 Aligned_cols=39 Identities=15% Similarity=0.336 Sum_probs=24.8
Q ss_pred hHHHHHHHHHhhCCCceechhhHHHHHHHHhhCCCCccEEec
Q psy9334 6 GYPNLGQTMAKLYPKIQFEQMIVDNCTMQIVSNPHQFDVMVM 47 (65)
Q Consensus 6 ~f~~~~~eva~~ypdV~~~~~~vDa~~~~lv~~P~~fDVIV~ 47 (65)
..-....+..+.||+|+++-..-+. ..+++. ++.|+.++
T Consensus 15 ~l~~~l~~~~~~~P~v~i~i~~~~~-~~~~~~--~~~Dl~i~ 53 (201)
T cd08471 15 HVLPIITDFLDAYPEVSVRLLLLDR-VVNLLE--EGVDVAVR 53 (201)
T ss_pred HHHHHHHHHHHHCCCcEEEEEEcCc-cchhhc--ccccEEEE
Confidence 3446777888899998887543232 334444 37887665
No 203
>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=21.63 E-value=90 Score=18.33 Aligned_cols=39 Identities=10% Similarity=0.032 Sum_probs=24.0
Q ss_pred hHHHHHHHHHhhCCCceechhhHHHHHHHHhhCCCCccEEec
Q psy9334 6 GYPNLGQTMAKLYPKIQFEQMIVDNCTMQIVSNPHQFDVMVM 47 (65)
Q Consensus 6 ~f~~~~~eva~~ypdV~~~~~~vDa~~~~lv~~P~~fDVIV~ 47 (65)
.+.....+..+.||+++++-..-+. ...+.+ ++.|+.++
T Consensus 14 ~l~~~l~~~~~~~P~i~l~~~~~~~--~~~l~~-g~~Dl~i~ 52 (190)
T cd08483 14 WLMPRLGSFWAKHPEIELSLLPSAD--LVDLRP-DGIDVAIR 52 (190)
T ss_pred hHHhhHHHHHHHCCCceEEEEecCC--cCCCCC-CCcCEEEE
Confidence 3446677888899998877643222 222333 57887665
No 204
>PF06325 PrmA: Ribosomal protein L11 methyltransferase (PrmA); InterPro: IPR010456 This family consists of several Ribosomal protein L11 methyltransferase sequences. Its genetic determinant is prmA, which forms a bifunctional operon with the downstream panF gene []. The role of L11 methylation in ribosome function is, as yet, unknown. Deletion of the prmA gene in Escherichia coli showed no obvious effect [] except for the production of undermethylated forms of L11 []. Methylation is the most common post-transcriptional modification to ribosomal proteins in all organisms. PrmA is the only bacterial enzyme that catalyses the methylation of a ribosomal protein [].; GO: 0008276 protein methyltransferase activity, 0006479 protein methylation, 0005737 cytoplasm; PDB: 3GRZ_B 1F3L_A 2NXJ_B 3CJT_I 3CJQ_G 2NXE_A 2NXC_A 2ZBP_A 3EGV_A 3CJS_A ....
Probab=21.39 E-value=52 Score=23.75 Aligned_cols=22 Identities=36% Similarity=0.674 Sum_probs=15.8
Q ss_pred CCccEEecCCchHHHHHhhhhhc
Q psy9334 40 HQFDVMVMPNLYGNIVDNLASDI 62 (65)
Q Consensus 40 ~~fDVIV~~Nl~GDIlSD~aa~l 62 (65)
++||+||+ |+..++|-.++..+
T Consensus 224 ~~~dlvvA-NI~~~vL~~l~~~~ 245 (295)
T PF06325_consen 224 GKFDLVVA-NILADVLLELAPDI 245 (295)
T ss_dssp S-EEEEEE-ES-HHHHHHHHHHC
T ss_pred ccCCEEEE-CCCHHHHHHHHHHH
Confidence 89999884 88888888777554
No 205
>cd05132 RasGAP_GAPA GAPA is an IQGAP-related protein and is predicted to bind to small GTPases, which are yet to be identified. IQGAP proteins are integral components of cytoskeletal regulation. Results from truncated GAPAs indicated that almost the entire region of GAPA homologous to IQGAP is required for cytokinesis in Dictyostelium. More members of the IQGAP family are emerging, and evidence suggests that there are both similarities and differences in their function.
Probab=21.36 E-value=1.1e+02 Score=22.17 Aligned_cols=41 Identities=5% Similarity=0.131 Sum_probs=22.6
Q ss_pred chHHHHHHHHHhhCCCceec-------hhhHHHHHHHHhhCCCCccEE
Q psy9334 5 FGYPNLGQTMAKLYPKIQFE-------QMIVDNCTMQIVSNPHQFDVM 45 (65)
Q Consensus 5 ~~f~~~~~eva~~ypdV~~~-------~~~vDa~~~~lv~~P~~fDVI 45 (65)
.+++.+-+.+.+.||+..-+ ..+.-....--+.+|+.|+++
T Consensus 149 ~i~~~l~~~~~~kfp~~~~~~~~~~vg~flflRfi~PAIvsP~~fgl~ 196 (331)
T cd05132 149 WICKQIRSLTKRKFPSATDAEICSLIGYFFFLRFINPAIVTPQAYMLV 196 (331)
T ss_pred HHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHhhHHhcCchhcCCc
Confidence 34444444556679976521 122233334456779999876
No 206
>PRK10682 putrescine transporter subunit: periplasmic-binding component of ABC superfamily; Provisional
Probab=21.34 E-value=1.1e+02 Score=21.56 Aligned_cols=42 Identities=12% Similarity=0.162 Sum_probs=26.0
Q ss_pred HHHHHHHhhCCCceechhhH---HHHHHHHhhCCCCccEEecCCch
Q psy9334 9 NLGQTMAKLYPKIQFEQMIV---DNCTMQIVSNPHQFDVMVMPNLY 51 (65)
Q Consensus 9 ~~~~eva~~ypdV~~~~~~v---Da~~~~lv~~P~~fDVIV~~Nl~ 51 (65)
+++.+..+++ +|+++.... +.+..++......+||+...+.+
T Consensus 44 ~~i~~Fe~~~-gi~V~~~~~~~~~~~~~kl~a~~~~~Dvv~~~~~~ 88 (370)
T PRK10682 44 DTVANFEKET-GIKVVYDVFDSNEVLEGKLMAGSTGFDLVVPSASF 88 (370)
T ss_pred HHHHHHHHHH-CCEEEEEecCCHHHHHHHHHcCCCCCcEEEECHHH
Confidence 3455555665 787776443 34555666666679998866533
No 207
>KOG2765|consensus
Probab=21.32 E-value=56 Score=25.26 Aligned_cols=21 Identities=33% Similarity=0.635 Sum_probs=18.3
Q ss_pred CCCccEEecCCchHHHHHhhh
Q psy9334 39 PHQFDVMVMPNLYGNIVDNLA 59 (65)
Q Consensus 39 P~~fDVIV~~Nl~GDIlSD~a 59 (65)
-.+|+.||..|+-|.++||-.
T Consensus 314 ~~q~~~vv~~~ligtvvSDyl 334 (416)
T KOG2765|consen 314 STQFSLVVFNNLIGTVVSDYL 334 (416)
T ss_pred CceeEeeeHhhHHHHHHHHHH
Confidence 357889999999999999964
No 208
>PRK10735 tldD protease TldD; Provisional
Probab=21.27 E-value=80 Score=24.16 Aligned_cols=21 Identities=10% Similarity=0.148 Sum_probs=18.7
Q ss_pred CCCccEEecCCchHHHHHhhh
Q psy9334 39 PHQFDVMVMPNLYGNIVDNLA 59 (65)
Q Consensus 39 P~~fDVIV~~Nl~GDIlSD~a 59 (65)
+.+|+||+.|...|.++....
T Consensus 245 ~g~y~VIl~p~~~~~ll~~~~ 265 (481)
T PRK10735 245 AGTMPVVLGAGWPGVLLHEAV 265 (481)
T ss_pred CceeeEEECCcHHHHHHHHHh
Confidence 789999999999999998744
No 209
>KOG4720|consensus
Probab=21.21 E-value=64 Score=24.64 Aligned_cols=19 Identities=21% Similarity=0.149 Sum_probs=16.4
Q ss_pred CchhchHHHHHHHHHhhCC
Q psy9334 1 MPCRFGYPNLGQTMAKLYP 19 (65)
Q Consensus 1 ~~~~~~f~~~~~eva~~yp 19 (65)
|-|+.+|+.+|+++||-+.
T Consensus 167 mr~pki~~lIAr~mak~H~ 185 (391)
T KOG4720|consen 167 MREPKIFRLIARRMAKIHS 185 (391)
T ss_pred ccChHHHHHHHHHHHHhhe
Confidence 5688999999999999764
No 210
>PF10719 ComFB: Late competence development protein ComFB; InterPro: IPR019657 Competence is the ability of a cell to take up exogenous DNA from its environment, resulting in transformation. It is widespread among bacteria and is probably an important mechanism for the horizontal transfer of genes. Cells that take up DNA inevitably acquire the nucleotides the DNA consists of, and, because nucleotides are needed for DNA and RNA synthesis and are expensive to synthesise, these may make a significant contribution to the cell's energy budget []. The lateral gene transfer caused by competence also contributes to the genetic diversity that makes evolution possible. DNA usually becomes available by the death and lysis of other cells. Competent bacteria use components of extracellular filaments called type 4 pili to create pores in their membranes and pull DNA through the pores into the cytoplasm. This process, including the development of competence and the expression of the uptake machinery, is regulated in response to cell-cell signalling and/or nutritional conditions []. The development of genetic competence in Bacillus subtilis is a highly regulated adaptive response to stationary-phase stress. For competence to develop, the transcriptional regulator, ComK, must be activated. ComK is required for the expression of genes encoding proteins that function in DNA uptake. In log-phase cultures, ComK is inactive in a complex with MecA and ClpC. The comS gene is induced in response to high culture cell density and nutritional stress and its product functions to release active ComK from the complex. ComK then stimulates the transcription initiation of its own gene as well as that of the late competence operons []. The comF locus has three open reading frames and is driven by a single sigma A-like promoter in front of comFORF1. It is dependent on early regulatory competence genes and is only expressed in competence medium. ComFORF1 is similar to an extensive family of ATP-dependent RNA/DNA helicases with closer similarity to the DEAD protein subfamily and to the PriA protein in Escherichia coli. ComFORF1 late gene product plays an essential role during the binding and uptake events involved in B. subtilis transformation []. ComFB is the second protein encoded within the late competence locus ComF []. The function of ComFB within late competence development is not known.
Probab=21.02 E-value=1.7e+02 Score=16.78 Aligned_cols=32 Identities=16% Similarity=0.342 Sum_probs=25.0
Q ss_pred HHHHHhhCCCc-eechhhHHHHHHHHhhCCCCc
Q psy9334 11 GQTMAKLYPKI-QFEQMIVDNCTMQIVSNPHQF 42 (65)
Q Consensus 11 ~~eva~~ypdV-~~~~~~vDa~~~~lv~~P~~f 42 (65)
..++.+++|+. .-+....|.+|.-|=+=|-+|
T Consensus 13 l~~~l~~~~~~c~c~~c~~Dv~alaLN~LPPrY 45 (85)
T PF10719_consen 13 LDEYLEEYPDFCTCEDCLADVAALALNRLPPRY 45 (85)
T ss_pred HHHHHHhccccCCcHHHHHHHHHHHHcCCCCeE
Confidence 33444678887 788899999998888878877
No 211
>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=20.99 E-value=1e+02 Score=18.20 Aligned_cols=39 Identities=13% Similarity=0.244 Sum_probs=25.5
Q ss_pred hHHHHHHHHHhhCCCceechhhHHHHHHHHhhCCCCccEEec
Q psy9334 6 GYPNLGQTMAKLYPKIQFEQMIVDNCTMQIVSNPHQFDVMVM 47 (65)
Q Consensus 6 ~f~~~~~eva~~ypdV~~~~~~vDa~~~~lv~~P~~fDVIV~ 47 (65)
..-+...+..++||+++++-..-+. ..+++++ +.|+.++
T Consensus 15 ~l~~~l~~~~~~~P~i~v~~~~~~~-~~~~l~~--~~D~~i~ 53 (202)
T cd08472 15 LLIPALPDFLARYPDIELDLGVSDR-PVDLIRE--GVDCVIR 53 (202)
T ss_pred HHHHHHHHHHHHCCCcEEEEEECCC-cchhhcc--cccEEEE
Confidence 3446778889999998887543222 3455553 4897775
No 212
>cd06320 PBP1_allose_binding Periplasmic allose-binding domain of bacterial transport systems that function as a primary receptor of active transport and chemotaxis. Periplasmic allose-binding domain of bacterial transport systems that function as a primary receptor of active transport and chemotaxis. The members of this group are belonging to a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily. Like other periplasmic receptors of the ABC-type transport systems, the allose-binding protein consists of two alpha/beta domains connected by a three-stranded hinge. This Venus flytrap-like domain undergoes transition from an open to a closed conformational state upon ligand binding.
Probab=20.92 E-value=2.5e+02 Score=18.20 Aligned_cols=19 Identities=11% Similarity=0.198 Sum_probs=13.7
Q ss_pred HHHHHhhCCCCccEEecCC
Q psy9334 31 CTMQIVSNPHQFDVMVMPN 49 (65)
Q Consensus 31 ~~~~lv~~P~~fDVIV~~N 49 (65)
...++++++.++|.|++.|
T Consensus 172 ~~~~~l~~~~~~~ai~~~~ 190 (275)
T cd06320 172 VATTILQRNPDLKAIYCNN 190 (275)
T ss_pred HHHHHHHhCCCccEEEECC
Confidence 4456776666789998876
No 213
>COG0280 Pta Phosphotransacetylase [Energy production and conversion]
Probab=20.86 E-value=2.6e+02 Score=20.76 Aligned_cols=60 Identities=22% Similarity=0.372 Sum_probs=36.7
Q ss_pred chHHHHHHHHHhhCC-Cceec-hhhHHHHHHHHhhC---C-----CCccEEecCCch-HHHHHhhhhhccC
Q psy9334 5 FGYPNLGQTMAKLYP-KIQFE-QMIVDNCTMQIVSN---P-----HQFDVMVMPNLY-GNIVDNLASDIKG 64 (65)
Q Consensus 5 ~~f~~~~~eva~~yp-dV~~~-~~~vDa~~~~lv~~---P-----~~fDVIV~~Nl~-GDIlSD~aa~l~G 64 (65)
.--++..+-+.+..| |..++ ++-.|++.-+=+++ | .+-+|.|.|||- |+|.--+.-.+.|
T Consensus 215 ~kv~ea~~i~~~~~~~dl~vDGelq~DaA~~~~va~~k~p~s~vaG~ANvlVfP~LeagNI~yK~lq~~~~ 285 (327)
T COG0280 215 DKVREATKILRERAPPDLEVDGELQFDAALVEKVAAKKAPDSPLAGSANVLVFPDLEAGNIGYKLLQRLGG 285 (327)
T ss_pred HHHHHHHHHHHhcCCccceeccCcchhhhcCHHHHHhhCCCCCcCCCCCEEEcCCchHHHHHHHHHHHhcC
Confidence 334444444444567 66665 45677776533332 3 456799999998 8887766654443
No 214
>PRK11074 putative DNA-binding transcriptional regulator; Provisional
Probab=20.81 E-value=2.7e+02 Score=18.78 Aligned_cols=43 Identities=7% Similarity=0.013 Sum_probs=25.9
Q ss_pred hchHHHHHHHHHhhCCCceechhhHH-HHHHHHhhCCCCccEEec
Q psy9334 4 RFGYPNLGQTMAKLYPKIQFEQMIVD-NCTMQIVSNPHQFDVMVM 47 (65)
Q Consensus 4 ~~~f~~~~~eva~~ypdV~~~~~~vD-a~~~~lv~~P~~fDVIV~ 47 (65)
...+.+...+..++||+++++-..-+ .-+.+.+.+ ++.|+.+.
T Consensus 104 ~~~l~~~l~~~~~~~p~i~i~i~~~~~~~~~~~l~~-g~~Dl~i~ 147 (300)
T PRK11074 104 PDRTRQLIVDFYRHFDDVELIIRQEVFNGVWDALAD-GRVDIAIG 147 (300)
T ss_pred hhHHHHHHHHHHHhCCCceEEEEehhhhHHHHHHHC-CCCCEEEe
Confidence 44566778888899999776654322 222344433 34786664
No 215
>COG2264 PrmA Ribosomal protein L11 methylase [Translation, ribosomal structure and biogenesis]
Probab=20.72 E-value=70 Score=23.43 Aligned_cols=20 Identities=35% Similarity=0.607 Sum_probs=13.9
Q ss_pred CCccEEecCCchHHHHHhhhh
Q psy9334 40 HQFDVMVMPNLYGNIVDNLAS 60 (65)
Q Consensus 40 ~~fDVIV~~Nl~GDIlSD~aa 60 (65)
+.|||||+ |+.-++|--++.
T Consensus 228 ~~~DvIVA-NILA~vl~~La~ 247 (300)
T COG2264 228 GPFDVIVA-NILAEVLVELAP 247 (300)
T ss_pred CcccEEEe-hhhHHHHHHHHH
Confidence 48999998 566666655543
No 216
>PRK15408 autoinducer 2-binding protein lsrB; Provisional
Probab=20.71 E-value=3.2e+02 Score=19.38 Aligned_cols=46 Identities=13% Similarity=0.202 Sum_probs=25.9
Q ss_pred hHHHHHHHH-HhhCCCcee-chhh----HHH---HHHHHhhCCCCccEEecCCch
Q psy9334 6 GYPNLGQTM-AKLYPKIQF-EQMI----VDN---CTMQIVSNPHQFDVMVMPNLY 51 (65)
Q Consensus 6 ~f~~~~~ev-a~~ypdV~~-~~~~----vDa---~~~~lv~~P~~fDVIV~~Nl~ 51 (65)
.|.+-+++. +++||++++ ...+ .+. .+..+++.-.+.|.|++.|-.
T Consensus 165 ~r~~g~~~~l~~~~p~~~vv~~~~~~~d~~~a~~~~~~lL~~~pdi~aI~~~~~~ 219 (336)
T PRK15408 165 QWVKEAKAKIAKEHPGWEIVTTQFGYNDATKSLQTAEGILKAYPDLDAIIAPDAN 219 (336)
T ss_pred HHHHHHHHHHHhhCCCCEEEeecCCCCcHHHHHHHHHHHHHHCCCCcEEEECCCc
Confidence 465555553 467998765 2111 121 334555543368999998754
No 217
>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=20.68 E-value=89 Score=17.64 Aligned_cols=31 Identities=23% Similarity=0.344 Sum_probs=18.9
Q ss_pred HHHHHHHhhCCCceechhhHHHHHHHHhhCCCCccEEe
Q psy9334 9 NLGQTMAKLYPKIQFEQMIVDNCTMQIVSNPHQFDVMV 46 (65)
Q Consensus 9 ~~~~eva~~ypdV~~~~~~vDa~~~~lv~~P~~fDVIV 46 (65)
...+++.+.||+..++.... -.+...|+|-|
T Consensus 17 ~l~q~L~~~Fp~~~v~~~~~-------~~~~G~Fev~~ 47 (72)
T TIGR02174 17 WLKQELLEEFPDLEIEGENT-------PPTTGAFEVTV 47 (72)
T ss_pred HHHHHHHHHCCCCeeEEeee-------cCCCcEEEEEE
Confidence 45556666799854443222 24678888876
No 218
>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=20.65 E-value=1e+02 Score=18.48 Aligned_cols=38 Identities=18% Similarity=0.311 Sum_probs=24.7
Q ss_pred HHHHHHHHhhCCCceechhhHHHHHHHHhhCCCCccEEecC
Q psy9334 8 PNLGQTMAKLYPKIQFEQMIVDNCTMQIVSNPHQFDVMVMP 48 (65)
Q Consensus 8 ~~~~~eva~~ypdV~~~~~~vDa~~~~lv~~P~~fDVIV~~ 48 (65)
-....+..++||+|+++-..-+.. .++. + ++.|+.++.
T Consensus 17 ~~~l~~~~~~~P~i~i~i~~~~~~-~~~~-~-~~~D~~i~~ 54 (198)
T cd08480 17 LPLLPAFLARYPEILVDLSLTDEV-VDLL-A-ERTDVAIRV 54 (198)
T ss_pred HHHHHHHHHHCCCeEEEEEecCCc-cccc-c-ccccEEEEe
Confidence 366778889999998875432332 3444 3 588877653
No 219
>PRK01581 speE spermidine synthase; Validated
Probab=20.61 E-value=1.3e+02 Score=22.83 Aligned_cols=22 Identities=18% Similarity=0.321 Sum_probs=14.5
Q ss_pred hhHHHHHHHHhhCCCCccEEecC
Q psy9334 26 MIVDNCTMQIVSNPHQFDVMVMP 48 (65)
Q Consensus 26 ~~vDa~~~~lv~~P~~fDVIV~~ 48 (65)
..-|+. ..+-..+++||||+..
T Consensus 212 vi~Da~-~fL~~~~~~YDVIIvD 233 (374)
T PRK01581 212 HVCDAK-EFLSSPSSLYDVIIID 233 (374)
T ss_pred EECcHH-HHHHhcCCCccEEEEc
Confidence 445555 3444567899999976
No 220
>PHA02096 hypothetical protein
Probab=20.48 E-value=57 Score=20.27 Aligned_cols=17 Identities=35% Similarity=0.491 Sum_probs=14.9
Q ss_pred hCCCCccEEecCCchHH
Q psy9334 37 SNPHQFDVMVMPNLYGN 53 (65)
Q Consensus 37 ~~P~~fDVIV~~Nl~GD 53 (65)
++|+.|=-.|..||||-
T Consensus 9 kd~egfchfv~gnl~g~ 25 (103)
T PHA02096 9 KDPEGFCHFVSGNLHGA 25 (103)
T ss_pred cCCCceeEeecCccccc
Confidence 57999999999999984
No 221
>TIGR02424 TF_pcaQ pca operon transcription factor PcaQ. Members of this family are LysR-family transcription factors associated with operons for catabolism of protocatechuate. Members occur only in Proteobacteria.
Probab=20.44 E-value=1.7e+02 Score=19.54 Aligned_cols=43 Identities=14% Similarity=0.165 Sum_probs=27.0
Q ss_pred hchHHHHHHHHHhhCCCceechhhHHHH-HHHHhhCCCCccEEec
Q psy9334 4 RFGYPNLGQTMAKLYPKIQFEQMIVDNC-TMQIVSNPHQFDVMVM 47 (65)
Q Consensus 4 ~~~f~~~~~eva~~ypdV~~~~~~vDa~-~~~lv~~P~~fDVIV~ 47 (65)
...+-....+..++||+++++-...+.. ..+.+.+ +++|+.++
T Consensus 105 ~~~~~~~l~~~~~~~P~~~i~~~~~~~~~~~~~l~~-g~~D~~i~ 148 (300)
T TIGR02424 105 ARLMPEVVKRFLARAPRLRVRIMTGPNAYLLDQLRV-GALDLVVG 148 (300)
T ss_pred HhhhHHHHHHHHHhCCCcEEEEEeCchHHHHHHHHC-CCCCEEEE
Confidence 3455677788889999988776643332 2233332 57887774
No 222
>COG0583 LysR Transcriptional regulator [Transcription]
Probab=20.26 E-value=2.6e+02 Score=18.10 Aligned_cols=40 Identities=23% Similarity=0.352 Sum_probs=28.3
Q ss_pred HHHHHHHHHhhCCCceechhhHHHHHHHHhhCCCCccEEecC
Q psy9334 7 YPNLGQTMAKLYPKIQFEQMIVDNCTMQIVSNPHQFDVMVMP 48 (65)
Q Consensus 7 f~~~~~eva~~ypdV~~~~~~vDa~~~~lv~~P~~fDVIV~~ 48 (65)
+-....+..++||++.++....+.....|. -.+.|+.+..
T Consensus 107 l~~~l~~~~~~~P~~~~~~~~~~~~~~~l~--~~~~D~~i~~ 146 (297)
T COG0583 107 LPPLLARFRARYPEIELELGTSDRLLEDLV--EGELDLAIRA 146 (297)
T ss_pred hHHHHHHHHHhCCCeEEEeCchHHHHHHHH--cCCCCEEEec
Confidence 446777788899999888877777444444 5667866655
No 223
>PF01739 CheR: CheR methyltransferase, SAM binding domain; InterPro: IPR022642 Methyl transfer from the ubiquitous S-adenosyl-L-methionine (AdoMet) to either nitrogen, oxygen or carbon atoms is frequently employed in diverse organisms ranging from bacteria to plants and mammals. The reaction is catalysed by methyltransferases (Mtases) and modifies DNA, RNA, proteins and small molecules, such as catechol for regulatory purposes. The various aspects of the role of DNA methylation in prokaryotic restriction-modification systems and in a number of cellular processes in eukaryotes including gene regulation and differentiation is well documented. Three classes of DNA Mtases transfer the methyl group from AdoMet to the target base to form either N-6-methyladenine, or N-4-methylcytosine, or C-5- methylcytosine. In C-5-cytosine Mtases, ten conserved motifs are arranged in the same order []. Motif I (a glycine-rich or closely related consensus sequence; FAGxGG in M.HhaI []), shared by other AdoMet-Mtases [], is part of the cofactor binding site and motif IV (PCQ) is part of the catalytic site. In contrast, sequence comparison among N-6-adenine and N-4-cytosine Mtases indicated two of the conserved segments [], although more conserved segments may be present. One of them corresponds to motif I in C-5-cytosine Mtases, and the other is named (D/N/S)PP(Y/F). Crystal structures are known for a number of Mtases [, , , ]. The cofactor binding sites are almost identical and the essential catalytic amino acids coincide. The comparable protein folding and the existence of equivalent amino acids in similar secondary and tertiary positions indicate that many (if not all) AdoMet-Mtases have a common catalytic domain structure. This permits tertiary structure prediction of other DNA, RNA, protein, and small-molecule AdoMet-Mtases from their amino acid sequences []. Flagellated bacteria swim towards favourable chemicals and away from deleterious ones. Sensing of chemoeffector gradients involves chemotaxis receptors, transmembrane (TM) proteins that detect stimuli through their periplasmic domains and transduce the signals via their cytoplasmic domains []. Signalling outputs from these receptors are influenced both by the binding of the chemoeffector ligand to their periplasmic domains and by methylation of specific glutamate residues on their cytoplasmic domains. Methylation is catalysed by CheR, an S-adenosylmethionine-dependent methyltransferase [], which reversibly methylates specific glutamate residues within a coiled coil region, to form gamma-glutamyl methyl ester residues [, ]. The structure of the Salmonella typhimurium chemotaxis receptor methyltransferase CheR, bound to S-adenosylhomocysteine, has been determined to a resolution of 2.0 A []. The structure reveals CheR to be a two-domain protein, with a smaller N-terminal helical domain linked via a single polypeptide connection to a larger C-terminal alpha/beta domain. The C-terminal domain has the characteristics of a nucleotide-binding fold, with an insertion of a small anti-parallel beta-sheet subdomain. The S-adenosylhomocysteine-binding site is formed mainly by the large domain, with contributions from residues within the N-terminal domain and the linker region []. CheR proteins are part of the chemotaxis signaling mechanism which methylates the chemotaxis receptor at specific glutamate residues. This entry refers to the C-terminal SAM-binding domain of the CherR-type MCP methyltransferases, which are found in bacteria, archaea and green plants. This entry is found in association with PF03705 from PFAM. ; PDB: 1AF7_A 1BC5_A.
Probab=20.11 E-value=50 Score=22.29 Aligned_cols=15 Identities=20% Similarity=0.350 Sum_probs=8.4
Q ss_pred hCCCCccEEecCCch
Q psy9334 37 SNPHQFDVMVMPNLY 51 (65)
Q Consensus 37 ~~P~~fDVIV~~Nl~ 51 (65)
..+.+||+|++=|++
T Consensus 132 ~~~~~fD~I~CRNVl 146 (196)
T PF01739_consen 132 PPFGRFDLIFCRNVL 146 (196)
T ss_dssp -----EEEEEE-SSG
T ss_pred cccCCccEEEecCEE
Confidence 357899999999986
No 224
>PF01075 Glyco_transf_9: Glycosyltransferase family 9 (heptosyltransferase); InterPro: IPR002201 The biosynthesis of disaccharides, oligosaccharides and polysaccharides involves the action of hundreds of different glycosyltransferases. These enzymes catalyse the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming glycosidic bonds. A classification of glycosyltransferases using nucleotide diphospho-sugar, nucleotide monophospho-sugar and sugar phosphates (2.4.1.- from EC) and related proteins into distinct sequence based families has been described []. This classification is available on the CAZy (CArbohydrate-Active EnZymes) web site. The same three-dimensional fold is expected to occur within each of the families. Because 3-D structures are better conserved than sequences, several of the families defined on the basis of sequence similarities may have similar 3-D structures and therefore form 'clans'. Glycosyltransferase family 9 GT9 from CAZY comprises enzymes with two known activity; lipopolysaccharide N-acetylglucosaminyltransferase (2.4.1.56 from EC), heptosyltransferase (2.4 from EC). Heptosyltransferase I is thought to add L-glycero-D-manno-heptose to the inner 3-deoxy-D-manno-octulosonic acid (Kdo) residue of the lipopolysaccharide core []. Heptosyltransferase II is a glycosyltransferase involved in the synthesis of the inner core region of lipopolysaccharide []. Lipopolysaccharide is a major component of the outer leaflet of the outer membrane in Gram-negative bacteria. It is composed of three domains; lipid A, Core oligosaccharide and the O-antigen. These enzymes transfer heptose to the lipopolysaccharide core [].; GO: 0016757 transferase activity, transferring glycosyl groups, 0008152 metabolic process; PDB: 1PSW_A 2H1F_A 2GT1_A 3TOV_A 2H1H_A.
Probab=20.07 E-value=71 Score=20.93 Aligned_cols=25 Identities=20% Similarity=0.494 Sum_probs=12.8
Q ss_pred CCCCccEEecCCchHHHHHhhhhhccC
Q psy9334 38 NPHQFDVMVMPNLYGNIVDNLASDIKG 64 (65)
Q Consensus 38 ~P~~fDVIV~~Nl~GDIlSD~aa~l~G 64 (65)
+.++||+++- +.++.-|-..+.+.|
T Consensus 9 r~~~yD~vid--~~~~~~s~~l~~~~~ 33 (247)
T PF01075_consen 9 RKEKYDLVID--LQGSFRSALLARLSG 33 (247)
T ss_dssp CTSB-SEEEE---S-SHHHHHHTCCCS
T ss_pred hCCCCCEEEE--CCCCccHHHHHHHHh
Confidence 4677897763 455556655554443
No 225
>CHL00180 rbcR LysR transcriptional regulator; Provisional
Probab=20.04 E-value=2e+02 Score=19.45 Aligned_cols=42 Identities=21% Similarity=0.280 Sum_probs=25.8
Q ss_pred hHHHHHHHHHhhCCCceechhhHH-HHHHHHhhCCCCccEEecC
Q psy9334 6 GYPNLGQTMAKLYPKIQFEQMIVD-NCTMQIVSNPHQFDVMVMP 48 (65)
Q Consensus 6 ~f~~~~~eva~~ypdV~~~~~~vD-a~~~~lv~~P~~fDVIV~~ 48 (65)
.+-....+..+.||+|+++-...+ ....+.+.+- ++|+.++.
T Consensus 109 ~~~~~l~~~~~~~P~v~i~~~~~~~~~~~~~l~~g-~~Dl~i~~ 151 (305)
T CHL00180 109 LMPRLIGLFRQRYPQINVQLQVHSTRRIAWNVANG-QIDIAIVG 151 (305)
T ss_pred HHHHHHHHHHHHCCCceEEEEeCCHHHHHHHHHcC-CccEEEEc
Confidence 334667778889999877754422 3333444443 58877764
No 226
>PTZ00051 thioredoxin; Provisional
Probab=20.02 E-value=1e+02 Score=17.14 Aligned_cols=27 Identities=30% Similarity=0.443 Sum_probs=17.2
Q ss_pred chhchHHHHHHHHHhhCCCceechhhHH
Q psy9334 2 PCRFGYPNLGQTMAKLYPKIQFEQMIVD 29 (65)
Q Consensus 2 ~~~~~f~~~~~eva~~ypdV~~~~~~vD 29 (65)
||+.+. ...++++++++++.+-...+|
T Consensus 32 ~C~~~~-~~l~~l~~~~~~~~~~~vd~~ 58 (98)
T PTZ00051 32 PCKRIA-PFYEECSKEYTKMVFVKVDVD 58 (98)
T ss_pred HHHHHh-HHHHHHHHHcCCcEEEEEECc
Confidence 566554 456678888888766544444
No 227
>cd06323 PBP1_ribose_binding Periplasmic sugar-binding domain of the thermophilic Thermoanaerobacter tengcongensis ribose binding protein (ttRBP) and its mesophilic homologs. Periplasmic sugar-binding domain of the thermophilic Thermoanaerobacter tengcongensis ribose binding protein (ttRBP) and its mesophilic homologs. Members of this group are belonging to the type I periplasmic binding protein superfamily, whose members are involved in chemotaxis, ATP-binding cassette transport, and intercellular communication in central nervous system. The thermophilic and mesophilic ribose-binding proteins are structurally very similar, but differ substantially in thermal stability.
Probab=20.02 E-value=2.5e+02 Score=17.89 Aligned_cols=19 Identities=11% Similarity=0.025 Sum_probs=13.3
Q ss_pred HHHHhhCCCCccEEecCCc
Q psy9334 32 TMQIVSNPHQFDVMVMPNL 50 (65)
Q Consensus 32 ~~~lv~~P~~fDVIV~~Nl 50 (65)
+.++++++..+|.|++.|=
T Consensus 172 ~~~~l~~~~~~~ai~~~~d 190 (268)
T cd06323 172 MENILQAHPDIKGVFAQND 190 (268)
T ss_pred HHHHHHHCCCcCEEEEcCC
Confidence 4566666667898888763
Done!