Query 014264
Match_columns 427
No_of_seqs 180 out of 587
Neff 6.8
Searched_HMMs 46136
Date Fri Mar 29 03:26:44 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/014264.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/014264hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 TIGR00272 DPH2 diphthamide bio 100.0 1E-103 3E-108 820.0 32.7 399 1-420 87-496 (496)
2 KOG2648 Diphthamide biosynthes 100.0 4.9E-94 1.1E-98 719.6 30.3 370 1-420 83-453 (453)
3 TIGR00322 diphth2_R diphthamid 100.0 8.6E-80 1.9E-84 615.5 29.4 278 1-308 52-330 (332)
4 PF01866 Diphthamide_syn: Puta 100.0 3.6E-79 7.7E-84 607.7 23.1 279 1-308 26-307 (307)
5 TIGR03682 arCOG04112 arCOG0411 100.0 2.3E-76 5E-81 585.6 28.1 271 1-307 34-306 (308)
6 COG1736 DPH2 Diphthamide synth 100.0 6.9E-64 1.5E-68 496.5 27.1 280 1-310 57-337 (347)
7 PRK09492 treR trehalose repres 78.3 7.3 0.00016 38.0 7.4 78 206-285 60-144 (315)
8 cd06280 PBP1_LacI_like_4 Ligan 77.9 4.4 9.6E-05 38.3 5.6 59 210-269 1-65 (263)
9 cd06289 PBP1_MalI_like Ligand- 74.2 7 0.00015 36.7 5.8 75 210-285 1-84 (268)
10 cd06293 PBP1_LacI_like_11 Liga 73.6 6.8 0.00015 37.1 5.6 61 210-271 1-67 (269)
11 COG1609 PurR Transcriptional r 70.9 12 0.00026 37.7 6.9 62 205-267 55-122 (333)
12 cd06272 PBP1_hexuronate_repres 70.3 7.6 0.00017 36.6 5.1 74 210-285 1-79 (261)
13 PF00919 UPF0004: Uncharacteri 69.9 6.4 0.00014 32.7 3.9 71 194-264 22-97 (98)
14 cd06274 PBP1_FruR Ligand bindi 69.6 9.5 0.00021 36.0 5.6 76 210-286 1-84 (264)
15 cd06295 PBP1_CelR Ligand bindi 68.9 7.8 0.00017 36.8 4.8 64 207-270 2-75 (275)
16 cd06279 PBP1_LacI_like_3 Ligan 68.8 9.1 0.0002 36.8 5.3 61 210-271 1-68 (283)
17 cd06271 PBP1_AglR_RafR_like Li 66.9 17 0.00036 34.1 6.6 77 210-286 1-88 (268)
18 COG5136 U1 snRNP-specific prot 66.7 6.1 0.00013 35.7 3.2 67 191-272 28-94 (188)
19 cd06273 PBP1_GntR_like_1 This 66.6 8.2 0.00018 36.4 4.4 75 210-286 1-84 (268)
20 cd06270 PBP1_GalS_like Ligand 65.6 13 0.00028 35.2 5.6 60 210-271 1-67 (268)
21 cd06298 PBP1_CcpA_like Ligand- 65.6 13 0.00029 34.9 5.6 58 210-269 1-65 (268)
22 cd01536 PBP1_ABC_sugar_binding 65.5 12 0.00027 34.8 5.4 75 210-286 1-86 (267)
23 PF00532 Peripla_BP_1: Peripla 65.5 8 0.00017 37.8 4.2 61 209-271 2-68 (279)
24 cd06315 PBP1_ABC_sugar_binding 65.4 9 0.0002 36.9 4.5 76 209-285 1-86 (280)
25 PRK07188 nicotinate phosphorib 65.3 14 0.0003 38.0 6.0 42 222-263 261-307 (352)
26 cd06277 PBP1_LacI_like_1 Ligan 64.2 20 0.00044 33.8 6.7 73 211-285 2-85 (268)
27 PF04392 ABC_sub_bind: ABC tra 63.8 9.9 0.00021 37.4 4.5 113 193-310 115-237 (294)
28 TIGR02405 trehalos_R_Ecol treh 63.5 17 0.00036 35.6 6.1 63 206-269 57-125 (311)
29 TIGR01753 flav_short flavodoxi 63.4 27 0.00057 29.8 6.7 55 211-270 1-55 (140)
30 cd06310 PBP1_ABC_sugar_binding 62.5 9.4 0.0002 36.1 4.0 76 210-285 1-87 (273)
31 cd05569 PTS_IIB_fructose PTS_I 62.0 31 0.00067 28.3 6.5 59 211-272 2-66 (96)
32 cd06283 PBP1_RegR_EndR_KdgR_li 61.5 26 0.00057 32.7 6.9 74 210-285 1-83 (267)
33 cd01542 PBP1_TreR_like Ligand- 61.4 16 0.00034 34.2 5.3 75 210-286 1-84 (259)
34 cd06281 PBP1_LacI_like_5 Ligan 60.8 17 0.00037 34.4 5.5 76 210-286 1-85 (269)
35 PRK10014 DNA-binding transcrip 60.8 26 0.00057 34.5 7.0 79 205-285 61-149 (342)
36 PRK10653 D-ribose transporter 60.4 11 0.00023 36.6 4.1 63 206-269 24-92 (295)
37 PRK11303 DNA-binding transcrip 59.6 26 0.00056 34.3 6.7 62 206-269 59-127 (328)
38 PRK12321 cobN cobaltochelatase 59.5 6 0.00013 46.4 2.4 28 17-44 522-567 (1100)
39 cd06290 PBP1_LacI_like_9 Ligan 58.9 18 0.00039 34.0 5.3 59 210-269 1-65 (265)
40 cd01545 PBP1_SalR Ligand-bindi 58.5 27 0.00059 32.8 6.4 59 210-269 1-66 (270)
41 PRK07308 flavodoxin; Validated 58.4 43 0.00094 29.2 7.2 57 210-271 3-59 (146)
42 cd06291 PBP1_Qymf_like Ligand 58.4 25 0.00054 33.0 6.2 59 210-269 1-65 (265)
43 PRK14987 gluconate operon tran 58.1 25 0.00053 34.7 6.2 79 206-285 61-147 (331)
44 cd01538 PBP1_ABC_xylose_bindin 57.7 12 0.00025 36.3 3.8 75 210-285 1-85 (288)
45 PRK06703 flavodoxin; Provision 57.5 37 0.0008 29.8 6.7 55 210-269 3-57 (151)
46 cd06299 PBP1_LacI_like_13 Liga 56.9 33 0.00072 32.1 6.7 60 210-271 1-67 (265)
47 cd06292 PBP1_LacI_like_10 Liga 56.7 27 0.0006 32.9 6.1 57 210-268 1-64 (273)
48 PRK05723 flavodoxin; Provision 56.1 37 0.00081 30.3 6.5 55 210-269 2-56 (151)
49 cd06316 PBP1_ABC_sugar_binding 55.7 14 0.00031 35.6 4.0 76 210-285 1-86 (294)
50 PRK10703 DNA-binding transcrip 55.2 31 0.00068 34.0 6.5 63 205-268 56-124 (341)
51 cd01574 PBP1_LacI Ligand-bindi 54.7 23 0.0005 33.2 5.2 75 210-285 1-84 (264)
52 TIGR02417 fruct_sucro_rep D-fr 54.5 48 0.001 32.5 7.6 62 206-268 58-125 (327)
53 PRK09004 FMN-binding protein M 54.4 37 0.00081 30.0 6.2 54 209-269 2-55 (146)
54 cd06282 PBP1_GntR_like_2 Ligan 54.1 27 0.00058 32.6 5.5 75 210-286 1-85 (266)
55 PRK08105 flavodoxin; Provision 53.5 35 0.00075 30.3 5.8 41 209-250 2-42 (149)
56 TIGR00829 FRU PTS system, fruc 52.8 34 0.00075 27.6 5.1 68 212-284 2-76 (85)
57 PLN03241 magnesium chelatase s 52.7 9.4 0.0002 45.7 2.5 28 17-44 663-708 (1353)
58 cd06286 PBP1_CcpB_like Ligand- 52.6 26 0.00057 32.8 5.2 59 210-270 1-66 (260)
59 cd06278 PBP1_LacI_like_2 Ligan 52.5 37 0.00079 31.7 6.2 60 210-270 1-65 (266)
60 cd06297 PBP1_LacI_like_12 Liga 52.5 25 0.00053 33.4 5.1 76 210-285 1-83 (269)
61 PRK11041 DNA-binding transcrip 52.2 52 0.0011 31.8 7.4 61 206-268 33-100 (309)
62 cd06296 PBP1_CatR_like Ligand- 52.2 45 0.00097 31.3 6.8 59 210-269 1-65 (270)
63 PLN03069 magnesiumprotoporphyr 52.1 9.4 0.0002 45.3 2.4 28 17-44 600-645 (1220)
64 TIGR02257 cobalto_cobN cobalto 51.8 9.7 0.00021 44.8 2.4 28 17-44 535-580 (1122)
65 cd06285 PBP1_LacI_like_7 Ligan 51.7 29 0.00064 32.6 5.4 60 210-270 1-66 (265)
66 PRK05989 cobN cobaltochelatase 51.7 9.4 0.0002 45.5 2.3 28 17-44 541-586 (1244)
67 cd06318 PBP1_ABC_sugar_binding 51.7 21 0.00046 33.9 4.4 75 210-285 1-85 (282)
68 cd06284 PBP1_LacI_like_6 Ligan 51.5 43 0.00093 31.3 6.5 59 210-269 1-65 (267)
69 PRK12493 magnesium chelatase s 51.3 9.6 0.00021 45.6 2.3 28 18-45 588-633 (1310)
70 PF00258 Flavodoxin_1: Flavodo 51.2 31 0.00067 29.7 5.1 54 213-269 1-54 (143)
71 COG2984 ABC-type uncharacteriz 51.1 58 0.0013 32.9 7.5 111 195-310 145-265 (322)
72 TIGR02025 BchH magnesium chela 51.1 9.7 0.00021 45.2 2.3 28 17-44 573-618 (1216)
73 PRK13405 bchH magnesium chelat 50.8 10 0.00022 45.0 2.4 28 17-44 593-638 (1209)
74 TIGR01481 ccpA catabolite cont 50.7 53 0.0012 32.1 7.3 77 207-285 58-143 (329)
75 PRK10423 transcriptional repre 50.5 58 0.0013 31.7 7.5 64 205-269 53-122 (327)
76 COG2185 Sbm Methylmalonyl-CoA 49.6 23 0.0005 31.6 3.9 56 202-258 56-112 (143)
77 TIGR02990 ectoine_eutA ectoine 48.8 71 0.0015 30.9 7.5 81 204-290 116-216 (239)
78 COG1429 CobN Cobalamin biosynt 47.5 11 0.00025 45.2 2.2 25 20-44 555-597 (1388)
79 PRK09526 lacI lac repressor; R 47.1 96 0.0021 30.5 8.5 62 206-267 61-128 (342)
80 PF03698 UPF0180: Uncharacteri 46.5 45 0.00098 26.8 4.8 58 228-292 11-74 (80)
81 COG0716 FldA Flavodoxins [Ener 46.1 72 0.0016 28.1 6.7 60 209-272 2-61 (151)
82 PF00885 DMRL_synthase: 6,7-di 46.1 50 0.0011 29.4 5.6 61 208-268 3-71 (144)
83 cd06312 PBP1_ABC_sugar_binding 46.0 27 0.00059 33.1 4.2 60 210-269 1-67 (271)
84 PF00731 AIRC: AIR carboxylase 45.3 64 0.0014 29.0 6.1 72 210-284 2-82 (150)
85 PRK10339 DNA-binding transcrip 43.9 42 0.00092 32.9 5.4 75 207-285 62-141 (327)
86 cd06307 PBP1_uncharacterized_s 43.9 28 0.0006 33.0 3.9 76 210-285 1-88 (275)
87 TIGR01754 flav_RNR ribonucleot 43.8 48 0.001 28.8 5.1 57 210-269 2-59 (140)
88 PF01729 QRPTase_C: Quinolinat 43.7 30 0.00065 31.7 3.9 63 201-267 92-156 (169)
89 cd01575 PBP1_GntR Ligand-bindi 43.7 47 0.001 31.0 5.4 76 210-286 1-84 (268)
90 cd01571 NAPRTase_B Nicotinate 43.6 47 0.001 33.2 5.6 57 209-265 211-272 (302)
91 cd01540 PBP1_arabinose_binding 43.4 22 0.00047 34.0 3.1 74 210-285 1-84 (289)
92 PRK09271 flavodoxin; Provision 43.2 82 0.0018 28.1 6.6 57 210-267 2-59 (160)
93 PRK12359 flavodoxin FldB; Prov 42.7 82 0.0018 28.9 6.6 53 210-270 2-55 (172)
94 cd05013 SIS_RpiR RpiR-like pro 42.4 1.3E+02 0.0027 25.0 7.5 68 201-272 6-73 (139)
95 cd06302 PBP1_LsrB_Quorum_Sensi 42.0 48 0.001 32.2 5.3 59 210-268 1-65 (298)
96 cd02071 MM_CoA_mut_B12_BD meth 41.8 65 0.0014 27.4 5.5 62 205-270 48-113 (122)
97 TIGR01579 MiaB-like-C MiaB-lik 41.8 29 0.00062 36.1 3.9 65 199-264 25-92 (414)
98 cd06294 PBP1_ycjW_transcriptio 41.7 57 0.0012 30.5 5.7 59 210-268 1-69 (270)
99 PF02514 CobN-Mg_chel: CobN/Ma 41.5 16 0.00034 43.1 2.1 93 171-267 716-817 (1098)
100 cd06300 PBP1_ABC_sugar_binding 41.1 41 0.00088 31.8 4.6 77 210-286 1-91 (272)
101 cd01452 VWA_26S_proteasome_sub 41.1 59 0.0013 30.3 5.4 49 209-258 108-158 (187)
102 cd06275 PBP1_PurR Ligand-bindi 40.8 97 0.0021 28.9 7.1 60 210-270 1-66 (269)
103 TIGR00640 acid_CoA_mut_C methy 40.5 66 0.0014 28.1 5.4 72 201-273 45-119 (132)
104 PRK05568 flavodoxin; Provision 40.2 1.4E+02 0.0031 25.5 7.6 56 210-270 3-58 (142)
105 PRK09426 methylmalonyl-CoA mut 39.9 54 0.0012 37.0 5.8 73 201-274 625-700 (714)
106 PF00205 TPP_enzyme_M: Thiamin 39.8 20 0.00044 30.9 2.1 46 201-248 4-49 (137)
107 TIGR02634 xylF D-xylose ABC tr 39.7 32 0.00069 33.6 3.7 74 211-285 1-84 (302)
108 cd06319 PBP1_ABC_sugar_binding 39.5 58 0.0013 30.6 5.4 73 211-285 2-85 (277)
109 PRK11104 hemG protoporphyrinog 39.3 53 0.0012 30.0 4.9 54 210-269 2-55 (177)
110 cd01543 PBP1_XylR Ligand-bindi 39.1 52 0.0011 31.0 5.0 55 210-267 1-58 (265)
111 PRK10936 TMAO reductase system 39.0 45 0.00098 33.4 4.8 78 207-284 45-132 (343)
112 cd06321 PBP1_ABC_sugar_binding 38.7 32 0.00069 32.5 3.4 59 210-268 1-66 (271)
113 TIGR02955 TMAO_TorT TMAO reduc 38.0 58 0.0013 31.5 5.2 62 210-271 1-69 (295)
114 cd06320 PBP1_allose_binding Pe 38.0 59 0.0013 30.7 5.2 74 210-284 1-86 (275)
115 PRK08662 nicotinate phosphorib 37.8 54 0.0012 33.5 5.1 55 209-263 227-285 (343)
116 cd01537 PBP1_Repressors_Sugar_ 37.3 77 0.0017 29.0 5.7 74 210-285 1-84 (264)
117 PRK10427 putative PTS system f 37.2 1.1E+02 0.0024 26.2 6.1 61 208-271 3-69 (114)
118 cd06306 PBP1_TorT-like TorT-li 37.1 44 0.00095 31.7 4.1 77 210-286 1-87 (268)
119 TIGR00288 conserved hypothetic 36.6 1.2E+02 0.0026 27.7 6.5 53 206-267 104-156 (160)
120 PRK14571 D-alanyl-alanine synt 36.4 1.1E+02 0.0025 29.9 7.1 76 210-286 2-85 (299)
121 cd05566 PTS_IIB_galactitol PTS 36.4 1.4E+02 0.0031 23.5 6.4 56 213-271 4-59 (89)
122 cd04502 SGNH_hydrolase_like_7 36.4 1.7E+02 0.0037 25.6 7.6 55 193-247 36-96 (171)
123 PRK08091 ribulose-phosphate 3- 35.5 1.2E+02 0.0026 29.2 6.7 59 207-265 140-206 (228)
124 PRK15395 methyl-galactoside AB 35.5 62 0.0013 32.2 5.0 63 207-269 23-91 (330)
125 KOG0781 Signal recognition par 35.4 3.1E+02 0.0068 29.6 10.1 70 200-270 457-542 (587)
126 PF02514 CobN-Mg_chel: CobN/Ma 35.2 51 0.0011 39.0 4.9 113 174-289 40-168 (1098)
127 cd06325 PBP1_ABC_uncharacteriz 35.0 93 0.002 29.3 6.1 75 210-286 1-87 (281)
128 PRK05452 anaerobic nitric oxid 34.8 1.5E+02 0.0033 31.6 8.1 96 191-293 235-333 (479)
129 PRK09267 flavodoxin FldA; Vali 34.5 88 0.0019 27.9 5.4 53 210-269 3-55 (169)
130 PRK10355 xylF D-xylose transpo 34.4 88 0.0019 31.2 6.0 64 207-271 24-93 (330)
131 PRK09701 D-allose transporter 34.3 1E+02 0.0022 30.2 6.3 64 204-267 20-90 (311)
132 cd06317 PBP1_ABC_sugar_binding 34.1 57 0.0012 30.6 4.3 59 210-269 1-66 (275)
133 TIGR01574 miaB-methiolase tRNA 34.0 50 0.0011 34.7 4.3 15 250-264 85-100 (438)
134 cd06308 PBP1_sensor_kinase_lik 33.9 69 0.0015 30.2 4.9 59 210-269 1-66 (270)
135 cd06305 PBP1_methylthioribose_ 33.5 82 0.0018 29.5 5.4 58 210-268 1-64 (273)
136 cd06267 PBP1_LacI_sugar_bindin 33.1 75 0.0016 29.2 4.9 32 211-242 2-33 (264)
137 PRK02910 light-independent pro 32.5 1.3E+02 0.0027 32.6 7.1 76 209-285 159-238 (519)
138 COG1736 DPH2 Diphthamide synth 32.4 4.6E+02 0.01 26.9 10.6 168 47-274 8-175 (347)
139 PRK10727 DNA-binding transcrip 32.4 1.7E+02 0.0036 28.9 7.6 62 207-269 58-125 (343)
140 cd06309 PBP1_YtfQ_like Peripla 32.2 43 0.00094 31.6 3.2 59 210-269 1-65 (273)
141 cd01541 PBP1_AraR Ligand-bindi 32.0 94 0.002 29.2 5.5 55 210-266 1-62 (273)
142 cd06304 PBP1_BmpA_like Peripla 31.4 89 0.0019 29.5 5.2 57 210-268 1-65 (260)
143 cd01539 PBP1_GGBP Periplasmic 31.0 45 0.00097 32.5 3.1 59 210-269 1-67 (303)
144 cd02036 MinD Bacterial cell di 30.9 1.9E+02 0.004 25.4 7.0 59 213-271 3-73 (179)
145 cd06288 PBP1_sucrose_transcrip 30.8 1.7E+02 0.0036 27.2 7.0 59 210-269 1-66 (269)
146 PRK05569 flavodoxin; Provision 30.7 2.5E+02 0.0054 24.0 7.5 56 210-270 3-58 (141)
147 PRK00061 ribH 6,7-dimethyl-8-r 30.3 1.4E+02 0.0029 27.0 5.8 61 209-269 13-81 (154)
148 cd06322 PBP1_ABC_sugar_binding 30.2 58 0.0013 30.5 3.7 75 210-286 1-86 (267)
149 PRK08883 ribulose-phosphate 3- 30.2 75 0.0016 30.3 4.4 84 169-267 105-196 (220)
150 COG0529 CysC Adenylylsulfate k 29.3 1.3E+02 0.0029 28.1 5.6 40 208-247 21-60 (197)
151 PRK14057 epimerase; Provisiona 29.0 1.5E+02 0.0033 29.0 6.3 60 207-266 154-221 (254)
152 cd06324 PBP1_ABC_sugar_binding 28.9 75 0.0016 30.9 4.3 58 210-268 1-67 (305)
153 TIGR02014 BchZ chlorophyllide 28.8 87 0.0019 33.4 5.0 77 207-284 151-227 (468)
154 cd01473 vWA_CTRP CTRP for CS 28.4 1.9E+02 0.0041 26.6 6.7 50 208-258 108-159 (192)
155 PLN02404 6,7-dimethyl-8-ribity 28.2 1.8E+02 0.004 25.8 6.2 61 209-269 8-76 (141)
156 cd06323 PBP1_ribose_binding Pe 28.1 56 0.0012 30.5 3.2 57 210-267 1-63 (268)
157 cd06314 PBP1_tmGBP Periplasmic 27.8 91 0.002 29.4 4.6 59 210-269 1-65 (271)
158 PRK06756 flavodoxin; Provision 27.2 2.4E+02 0.0052 24.4 6.9 56 210-270 3-59 (148)
159 cd06276 PBP1_FucR_like Ligand- 27.2 1.4E+02 0.0031 28.1 5.8 56 211-269 2-62 (247)
160 PRK10401 DNA-binding transcrip 27.1 3.1E+02 0.0067 27.0 8.5 61 206-268 57-124 (346)
161 cd03819 GT1_WavL_like This fam 26.3 1.3E+02 0.0027 29.3 5.4 43 227-271 232-276 (355)
162 PF14538 Raptor_N: Raptor N-te 26.3 1.5E+02 0.0032 26.7 5.4 50 22-79 92-147 (154)
163 PRK11921 metallo-beta-lactamas 26.2 1.8E+02 0.004 29.9 6.8 77 191-270 231-310 (394)
164 PRK15408 autoinducer 2-binding 26.0 86 0.0019 31.6 4.2 63 207-269 22-90 (336)
165 PF02593 dTMP_synthase: Thymid 25.7 1.1E+02 0.0023 29.4 4.5 40 199-240 66-105 (217)
166 PF09547 Spore_IV_A: Stage IV 25.7 1.1E+02 0.0023 32.6 4.8 71 205-276 141-225 (492)
167 TIGR01012 Sa_S2_E_A ribosomal 25.6 1.4E+02 0.0031 28.0 5.3 51 25-78 14-73 (196)
168 COG0041 PurE Phosphoribosylcar 25.5 1.8E+02 0.0039 26.4 5.6 60 210-272 4-68 (162)
169 TIGR01931 cysJ sulfite reducta 25.2 1.4E+02 0.0031 32.8 6.0 49 208-257 58-106 (597)
170 TIGR01007 eps_fam capsular exo 24.8 2E+02 0.0043 26.3 6.2 51 197-248 6-56 (204)
171 cd01981 Pchlide_reductase_B Pc 24.6 1.5E+02 0.0033 30.8 5.9 79 207-286 161-243 (430)
172 TIGR02883 spore_cwlD N-acetylm 24.3 1.6E+02 0.0035 27.0 5.4 47 223-269 28-93 (189)
173 TIGR01205 D_ala_D_alaTIGR D-al 24.3 2.4E+02 0.0052 27.6 7.0 77 210-286 1-95 (315)
174 PRK14336 (dimethylallyl)adenos 24.2 1.7E+02 0.0036 30.7 6.1 10 264-273 130-139 (418)
175 TIGR00147 lipid kinase, YegS/R 23.9 2.5E+02 0.0053 27.4 7.0 35 210-244 3-38 (293)
176 PRK09240 thiH thiamine biosynt 23.7 1.9E+02 0.0041 29.7 6.3 57 195-252 201-263 (371)
177 TIGR01501 MthylAspMutase methy 23.7 1.5E+02 0.0033 26.0 4.8 45 201-248 44-90 (134)
178 cd01450 vWFA_subfamily_ECM Von 23.5 2.7E+02 0.0059 23.5 6.5 68 192-260 83-154 (161)
179 PF02302 PTS_IIB: PTS system, 23.4 2.6E+02 0.0056 21.8 5.8 57 213-273 3-59 (90)
180 PF01583 APS_kinase: Adenylyls 23.4 1.8E+02 0.004 26.2 5.4 37 211-247 3-39 (156)
181 TIGR01162 purE phosphoribosyla 23.3 1.6E+02 0.0035 26.7 4.9 71 211-284 1-80 (156)
182 cd01025 TOPRIM_recR TOPRIM_rec 23.2 2.7E+02 0.0059 23.7 6.1 54 201-254 48-101 (112)
183 TIGR02363 dhaK1 dihydroxyaceto 23.1 2.3E+02 0.005 28.9 6.5 45 205-249 249-296 (329)
184 PRK04020 rps2P 30S ribosomal p 23.0 1.6E+02 0.0036 27.8 5.2 50 25-77 20-78 (204)
185 PRK10310 PTS system galactitol 22.9 2.1E+02 0.0046 23.2 5.3 52 213-267 6-58 (94)
186 PRK12493 magnesium chelatase s 22.8 1.8E+02 0.0039 35.2 6.6 61 208-268 253-324 (1310)
187 cd06320 PBP1_allose_binding Pe 22.3 3.9E+02 0.0084 25.0 7.9 50 202-251 116-166 (275)
188 PF02233 PNTB: NAD(P) transhyd 22.3 92 0.002 33.2 3.6 66 201-270 300-393 (463)
189 cd01982 Chlide_reductase_Z Chl 22.2 1.2E+02 0.0025 31.9 4.4 77 207-284 154-230 (412)
190 COG0622 Predicted phosphoester 22.1 80 0.0017 29.0 2.8 74 1-76 7-91 (172)
191 KOG4175 Tryptophan synthase al 22.0 1.9E+02 0.004 27.7 5.2 63 200-266 114-177 (268)
192 PF10657 RC-P840_PscD: Photosy 21.9 93 0.002 27.1 2.9 36 258-310 73-108 (144)
193 PRK06455 riboflavin synthase; 21.8 2.7E+02 0.0058 25.3 6.0 58 209-269 2-66 (155)
194 PRK08745 ribulose-phosphate 3- 21.5 1.2E+02 0.0025 29.1 4.0 81 170-265 110-198 (223)
195 TIGR01752 flav_long flavodoxin 21.4 2.2E+02 0.0047 25.5 5.6 53 210-269 1-53 (167)
196 PF13671 AAA_33: AAA domain; P 21.4 4.7E+02 0.01 21.8 7.5 45 199-246 60-104 (143)
197 cd03142 GATase1_ThuA Type 1 gl 21.3 2.4E+02 0.0051 26.9 6.0 44 226-272 24-71 (215)
198 KOG3360 Acylphosphatase [Energ 21.3 2.2E+02 0.0047 23.8 4.8 44 197-240 23-72 (98)
199 cd02042 ParA ParA and ParB of 21.2 3.2E+02 0.007 21.7 6.1 48 213-271 3-50 (104)
200 PRK14340 (dimethylallyl)adenos 21.1 1.2E+02 0.0026 32.1 4.3 29 236-264 74-106 (445)
201 PF00781 DAGK_cat: Diacylglyce 21.1 3E+02 0.0064 23.3 6.1 37 211-248 2-38 (130)
202 PF06283 ThuA: Trehalose utili 20.7 1.2E+02 0.0026 28.3 3.9 59 211-272 2-65 (217)
203 PRK11404 putative PTS system 20.7 2.2E+02 0.0048 30.6 6.2 73 209-284 5-84 (482)
204 cd06301 PBP1_rhizopine_binding 20.7 1.4E+02 0.0031 27.9 4.4 59 210-269 1-66 (272)
205 PRK00782 hypothetical protein; 20.7 1.9E+02 0.0041 28.3 5.3 46 206-251 136-181 (267)
206 PRK14814 NADH dehydrogenase su 20.6 1.9E+02 0.0041 27.0 4.9 13 259-272 131-143 (186)
207 TIGR02362 dhaK1b probable dihy 20.3 2.9E+02 0.0063 28.1 6.6 46 204-249 244-292 (326)
208 cd06354 PBP1_BmpA_PnrA_like Pe 20.3 2.6E+02 0.0056 26.5 6.2 58 210-269 1-67 (265)
209 PRK10953 cysJ sulfite reductas 20.3 2.1E+02 0.0046 31.5 6.2 51 206-257 59-109 (600)
210 PRK03501 ppnK inorganic polyph 20.2 2.1E+02 0.0046 28.1 5.5 32 209-242 3-34 (264)
211 COG1445 FrwB Phosphotransferas 20.1 3.2E+02 0.0069 23.8 5.9 72 209-285 3-81 (122)
No 1
>TIGR00272 DPH2 diphthamide biosynthesis protein 2. This protein has been shown in Saccharomyces cerevisiae to be one of several required for the modification of a particular histidine residue of translation elongation factor 2 to diphthamide. This modified site can then become the target for ADP-ribosylation by diphtheria toxin.
Probab=100.00 E-value=1.4e-103 Score=819.98 Aligned_cols=399 Identities=30% Similarity=0.494 Sum_probs=321.4
Q ss_pred CCCCcccccccChhhhcccCCcEEEEecCCCCCCCCCCCeEEEccccCCChHHHHHHHhhhhcCCCCcEEEEecccchhh
Q 014264 1 MADTTYGSCCVDEVGASHVDADCVIHYGHTCLSPTSTLPAFFVFGKASINTSNCIENLSKHALTNGKPILVLYGLEYAHA 80 (427)
Q Consensus 1 LaDtsYGsCCVDevaA~hv~aD~iVHyGhaCls~~~~lpv~YVf~~~~ld~~~~~~~l~~~~~~~~~~v~l~~dvqy~~~ 80 (427)
|||||||||||||+||+|++||+|||||||||+|++++||+|||++.++|++++++.+++.+++..++|+|++|+||.|+
T Consensus 87 laDtsYGaCCVDevaA~hv~aD~iVHyGhsCLsp~~~lPviYVf~~~~~d~~~~~~~~~~~~~~~~~kV~l~~dvqy~~~ 166 (496)
T TIGR00272 87 LADTAYSSCCVDEVAAEHVHAEAVVHFGDACLSAIQNLPVVYVFGTPPIDLALVVENFQRAFPDLSSKICLMADAPFSKH 166 (496)
T ss_pred EeCCcccccccCHHHHhhcCCCEEEEeCCCCCCCCCCCCEEEEeccCCCCHHHHHHHHHHhccccCCeEEEEEchhHHHH
Confidence 79999999999999999999999999999999999999999999999999999999998776654568999999999999
Q ss_pred hHHHHHHHHhhccCCCCCcceeeeeecceeeeecCCCCCCCCCCCCCCcccccccCcccccCCccCccceEEEEEcCCcc
Q 014264 81 IPHIREAVKVASSSYGSGLKLEINFADVMCTVITPSKDHKSLCGPAGGCTRHTIGGLVWNIPDRKKMEEHLLFWIGSDNS 160 (427)
Q Consensus 81 l~~l~~~L~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~g~~~gc~~~~~~~~~~~~~~~~~~~~~~i~~Ig~~~~ 160 (427)
++++++.|++.....+ ...++.++ ...|.. ....++++||++.... +...+++.+||||++.+
T Consensus 167 ~~~l~~~L~~~~~~~~--~~~~~~~~-----~~~~~~--~~~~~~vlGc~~~~~~--------~~~~~~~~~l~IG~~~~ 229 (496)
T TIGR00272 167 QSQLYNILKEVLPGDL--HYTNIIYP-----QVNTSA--VEEKFVTIGRTFHVPE--------DVDQQEKNLVLFGQHSS 229 (496)
T ss_pred HHHHHHHHHhhccccc--cccceecc-----cccccc--CCCCceecCccccCcc--------ccccccceEEEEcCCCc
Confidence 9999999986432100 01112221 112221 1124678999865432 12334667999999777
Q ss_pred -hhhHHHhhcC-C-ceEEEecCCCCceecccCc-HHHHHHHHHHHHHHHhcCCeEEEEEcCCcccCcHHHHHHHHHHHHH
Q 014264 161 -AFANVVLTFN-G-CEIVRYDATEERLLTDVSQ-PLKILKRRYYLVEKAKDANIIGVLVGTLGVAGYLHMIHQMKELITK 236 (427)
Q Consensus 161 -~l~~l~l~~~-~-~~v~~yDP~~~~~~~~~~~-~~r~L~rRy~~I~ka~~A~~iGIlvgTl~~q~~~~~i~~l~~li~~ 236 (427)
+|++++|+++ . ++||+|||+++++..+... ++|+|||||++|+|||+|++||||||||++|+|++++++|+++|++
T Consensus 230 g~f~~l~l~~~~~~~~v~~~dP~~~~~~~~~~~~~~~~L~rRy~~I~kA~~A~~~GIlVgTL~~q~~~~ii~~l~~li~~ 309 (496)
T TIGR00272 230 EDLHLIHLTTYQDLSTVFQFVPIFDPILPESVTGPFPSLRRRYKLVHVARDAGCIGIVVGTLGVRNTRETINELRKMIKT 309 (496)
T ss_pred hhhhHhhhhcCCCCCceEEECCCCCcceecccchHHHHHHHHHHHHHHHhcCCEEEEEEecCccCCCHHHHHHHHHHHHH
Confidence 8889988643 4 6799999999998766545 8999999999999999999999999999999999999999999999
Q ss_pred cCCcEEEEEcCCCCHHHHcCCCCCCEEEEecCCCcccccccCCCCcccCHHHHHHhhCCCCccccceeeccccccCCC--
Q 014264 237 AGKKAYTLVMGKPNPAKLANFPECDVFINVSCAQTALLDSKEFLAPVITPFEAMLAFGRGTQWTGAYVMEFRDLMSSS-- 314 (427)
Q Consensus 237 ~GKK~y~~~vgkln~aKLaNF~eiD~fVlvaCPr~si~d~~~f~kPvlTP~El~~aL~~~~~w~g~y~~Df~~~l~~~-- 314 (427)
+|||+|+|+||||||+|||||++||+||+|||||++|+|+++|+||||||||++|||+.+.+|.++|..+|..+.+..
T Consensus 310 ~GkK~yl~~vgkinpaKLaNF~eID~fV~vaCPr~sidd~~~F~KPVlTP~ElelAL~~~~~w~~~~~~~~~~~~~~~~~ 389 (496)
T TIGR00272 310 AGKKHYLFVVGKPNPAKLANFEDIDIFVLLGCSQSGIIDSNEFYRPIVTPFELNLALSEEVTWVVDFRDSIDEIEQLLGG 389 (496)
T ss_pred cCCcEEEEEeCCCCHHHHhCCCCCCEEEEccCCCcccccHhhCCCceecHHHHHHHhCCcccccchHHHHhhhhhhcccc
Confidence 999999999999999999999999999999999999999999999999999999999987789999988888775421
Q ss_pred C----CCCCCcccccccccccCccccccCCCCCCCcchhhhhHHHHhhhhhhhhhhccCCCcceeecccchHHHHhhcCC
Q 014264 315 P----VEGSDQAEEARFSFLKGGYVEDVAQPETENGEEEKEGALALANAAEKALQLRDRSLDPIVKGTAKSGAEYFVSRS 390 (427)
Q Consensus 315 ~----~~~~~~~~~p~fslitG~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~s~~a~~L~~Rt 390 (427)
. .+..+++++|+||||||+|++++++++...+.+... ..+..+.+++.+.+.+.+++++++|+||+||++||
T Consensus 390 ~~~~~~~~~~~~~~p~fslitG~~~~~~~~~~~~~~~~~~~----~~~~~~~~~~~~~~~~~~~~~~~~s~~a~~l~~Rt 465 (496)
T TIGR00272 390 QDTISPSTTSDEAAPEFSLIRGKYTSTSRPLRALTHLELEA----ADNDDSKQSTTRHTASGAVIKGTVSTSASALQNRS 465 (496)
T ss_pred cccCCCccccccCCCceeccccceeecCCccchhhhccccc----cCCCCccceeecccCcceeeccccccHHHHhhcCc
Confidence 1 111223468999999999998877754222111000 00112234544444333566788899999999999
Q ss_pred cccCCCCCCC-CCCcccccCCcccccCccCC
Q 014264 391 YHGLEMQCNS-SSPEPYAIGRSGKASGYDDE 420 (427)
Q Consensus 391 ~~GL~~~~g~-~~~~~~~~Gr~GiA~~Y~~e 420 (427)
|||||+++|+ ++++.++|||+||||||+++
T Consensus 466 w~GL~~~~~~~~~~a~~~eGrsGIA~gY~~~ 496 (496)
T TIGR00272 466 WKGLGDDVDSTEVDAKIEEGISGIARGYGGD 496 (496)
T ss_pred eeCCCCCcCCCCCcceeecCCccccccCCCC
Confidence 9999999976 45789999999999999865
No 2
>KOG2648 consensus Diphthamide biosynthesis protein [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=4.9e-94 Score=719.64 Aligned_cols=370 Identities=36% Similarity=0.611 Sum_probs=307.8
Q ss_pred CCCCcccccccChhhhcccCCcEEEEecCCCCCCCCCCCe-EEEccccCCChHHHHHHHhhhhcCCCCcEEEEecccchh
Q 014264 1 MADTTYGSCCVDEVGASHVDADCVIHYGHTCLSPTSTLPA-FFVFGKASINTSNCIENLSKHALTNGKPILVLYGLEYAH 79 (427)
Q Consensus 1 LaDtsYGsCCVDevaA~hv~aD~iVHyGhaCls~~~~lpv-~YVf~~~~ld~~~~~~~l~~~~~~~~~~v~l~~dvqy~~ 79 (427)
|||||||||||||+||+|++||+|||||||||+|++++|+ +|||++++||++++++.|+..+++..++|++++++||.|
T Consensus 83 LaDttYGsCCVDevaA~h~~ad~lVHyG~aCLsp~~~~~~~lYVf~~i~Idl~~~~~~l~~~~~~~~~~I~l~~~i~f~~ 162 (453)
T KOG2648|consen 83 LGDTTYGSCCVDEVAAEHLDADALVHYGHACLSPIDRLPVVLYVFVDIPIDLDHLVKSLQRNFPQLISQIVLLGTIQFAH 162 (453)
T ss_pred EecCcccccccchHHHhhcCCCEEEEecccccCccccCCceEEEeecccccHHHHHHHHHhhcccccceeEEeechhhhH
Confidence 7999999999999999999999999999999999999998 999999999999999999998877667899999999999
Q ss_pred hhHHHHHHHHhhccCCCCCcceeeeeecceeeeecCCCCCCCCCCCCCCcccccccCcccccCCccCccceEEEEEcCCc
Q 014264 80 AIPHIREAVKVASSSYGSGLKLEINFADVMCTVITPSKDHKSLCGPAGGCTRHTIGGLVWNIPDRKKMEEHLLFWIGSDN 159 (427)
Q Consensus 80 ~l~~l~~~L~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~g~~~gc~~~~~~~~~~~~~~~~~~~~~~i~~Ig~~~ 159 (427)
.++++++.|+..... .++. -|+.+ +.+++.++|||.+...+ . .+..+++|||+++
T Consensus 163 ~l~~~~~~L~~~~~~------~~~i---------~Pq~~-p~s~~e~lG~t~p~~~~--------~-~~~~~li~iGD~~ 217 (453)
T KOG2648|consen 163 SLEALATELKEELLD------LEVI---------LPQFK-PLSPGEVLGCTSPLLEG--------R-EEYDALIFIGDGR 217 (453)
T ss_pred HHHHHHHHHhhccCc------eEEe---------ccCCC-CCCCccccceeccCCCC--------c-cccceEEEecCCC
Confidence 999999999876421 1222 23322 55688999998765432 1 3456899999999
Q ss_pred chhhHHHhhcCCceEEEecCCCCceecccCcHHHHHHHHHHHHHHHhcCCeEEEEEcCCcccCcHHHHHHHHHHHHHcCC
Q 014264 160 SAFANVVLTFNGCEIVRYDATEERLLTDVSQPLKILKRRYYLVEKAKDANIIGVLVGTLGVAGYLHMIHQMKELITKAGK 239 (427)
Q Consensus 160 ~~l~~l~l~~~~~~v~~yDP~~~~~~~~~~~~~r~L~rRy~~I~ka~~A~~iGIlvgTl~~q~~~~~i~~l~~li~~~GK 239 (427)
||+...|+..+..++++|||+++++..|..++.++++|||++|||||+|++||||+||||+|+|++++++|+++|+++||
T Consensus 218 ~~le~~mi~np~~~~~~ydp~s~kl~~E~y~~~~m~~rR~~~vekardA~~iGlivGTLG~qg~~~vl~~L~~~~~~~Gk 297 (453)
T KOG2648|consen 218 FHLESSMIANPGLPAYRYDPYSKKLTRESYDHSRMLRRRYYLVEKARDARTIGLIVGTLGRQGNREVLEHLRKLLKAAGK 297 (453)
T ss_pred cchhHHHHhCCCCCeEEeCCccCceeecccchHHHHHHHHHHHHHHhcCCeEEEEEecccccCCHHHHHHHHHHHHHcCC
Confidence 99998888888999999999999999999899999999999999999999999999999999999999999999999999
Q ss_pred cEEEEEcCCCCHHHHcCCCCCCEEEEecCCCcccccccCCCCcccCHHHHHHhhCCCCccccceeeccccccCCCCCCCC
Q 014264 240 KAYTLVMGKPNPAKLANFPECDVFINVSCAQTALLDSKEFLAPVITPFEAMLAFGRGTQWTGAYVMEFRDLMSSSPVEGS 319 (427)
Q Consensus 240 K~y~~~vgkln~aKLaNF~eiD~fVlvaCPr~si~d~~~f~kPvlTP~El~~aL~~~~~w~g~y~~Df~~~l~~~~~~~~ 319 (427)
|+|+|+||||||+|||||++|||||++||||+++||+++|+||||||||+++||++. .|+++|..+|.........
T Consensus 298 k~y~l~~g~inPaKLAnF~eIDvfV~iaCp~lsid~s~~F~kPiltPfEa~~Al~~~-~W~~~~~~~~~~~~~~~~~--- 373 (453)
T KOG2648|consen 298 KSYVLALGEINPAKLANFPEIDVFVQIACPRLSIDWSKEFYKPLLTPFEAEVALNPI-AWTGDYLAPFVTAIKLLLK--- 373 (453)
T ss_pred ceEEEEecCCCHHHhcCCccccEEEEEeCcccchhhhhhhccccccHHHHHHhcCcc-ccCCccccchhhHHhhhhc---
Confidence 999999999999999999999999999999999999999999999999999999986 9999999999877543221
Q ss_pred CcccccccccccCccccccCCCCCCCcchhhhhHHHHhhhhhhhhhhccCCCcceeecccchHHHHhhcCCcccCCCCCC
Q 014264 320 DQAEEARFSFLKGGYVEDVAQPETENGEEEKEGALALANAAEKALQLRDRSLDPIVKGTAKSGAEYFVSRSYHGLEMQCN 399 (427)
Q Consensus 320 ~~~~~p~fslitG~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~s~~a~~L~~Rt~~GL~~~~g 399 (427)
+.+++ +...|.|.++.......... .+...+ . ..+ .+-.++++.||++|+||||+++.+
T Consensus 374 -~~~~~--~~~~~d~pm~~~~~~~~~~~--------~~~~~~-----~-~~~----~~~~~~a~~~~~~rsw~gLd~~~~ 432 (453)
T KOG2648|consen 374 -ESEFH--SSELGDYPMDYYSLGSLGPP--------PAWTSS-----N-DHG----AGESSPAISFLQNRSWQGLDPRLG 432 (453)
T ss_pred -ccccc--ccccccCcccccccccCCcC--------cccCCc-----c-ccc----ccccccccchhccccccCCCcCCC
Confidence 11111 13445443332221100000 000000 0 000 122356778899999999999999
Q ss_pred CCCCcccccCCcccccCccCC
Q 014264 400 SSSPEPYAIGRSGKASGYDDE 420 (427)
Q Consensus 400 ~~~~~~~~~Gr~GiA~~Y~~e 420 (427)
++++++..+||||||+||.+|
T Consensus 433 ~~~~~~~~~Grsgia~gy~~~ 453 (453)
T KOG2648|consen 433 QTPPTKLVSGRSGIAIGYSDE 453 (453)
T ss_pred CCCccchhccccccccccCCC
Confidence 999999999999999999875
No 3
>TIGR00322 diphth2_R diphthamide biosynthesis protein 2-related domain. Because archaeal species are known to have the diphthamide modification to the conserved His of archaeal and eukaryotic EF-2, it may be that the lone homolog of YKL191W in M. jannaschii, A. fulgidus, and M. thermoautotrophicum is orthologous. However, each of these is considerably shorter than YKL191W and seems more closely related to the uncharacterized protein YIL103W than to YKL191W.
Probab=100.00 E-value=8.6e-80 Score=615.46 Aligned_cols=278 Identities=24% Similarity=0.441 Sum_probs=249.4
Q ss_pred CCCCcccccccChhhhcccCCcEEEEecCCCCCCCC-CCCeEEEccccCCChHHHHHHHhhhhcCCCCcEEEEecccchh
Q 014264 1 MADTTYGSCCVDEVGASHVDADCVIHYGHTCLSPTS-TLPAFFVFGKASINTSNCIENLSKHALTNGKPILVLYGLEYAH 79 (427)
Q Consensus 1 LaDtsYGsCCVDevaA~hv~aD~iVHyGhaCls~~~-~lpv~YVf~~~~ld~~~~~~~l~~~~~~~~~~v~l~~dvqy~~ 79 (427)
|||||||||||||++|+|++||+|||||||||+|+. ++||+|||++.++|++++++.+.+.+.+ .++|+|++|+||.|
T Consensus 52 laD~~YGaCcvdd~~a~~~~aD~iVHyGHscl~~~~~~~pv~yVf~~~~~d~~~~~~~~~~~~~~-~~~i~l~~tiq~~~ 130 (332)
T TIGR00322 52 SGDTSFGACDIDDFTARALDVDLIVHYAHTPLVPDDVEIKVLYVPVTINIEYDHIIKTLQDNFPK-GRRIATIGTAQFNH 130 (332)
T ss_pred EcCCceecCCCCHHHHhhcCCCEEEEcCCCCCCcccCCCCEEEEEccCCCCHHHHHHHHHHHcCC-CCeEEEEECHHHHH
Confidence 799999999999999999999999999999999988 8999999999999999999999877654 45899999999999
Q ss_pred hhHHHHHHHHhhccCCCCCcceeeeeecceeeeecCCCCCCCCCCCCCCcccccccCcccccCCccCccceEEEEEcCCc
Q 014264 80 AIPHIREAVKVASSSYGSGLKLEINFADVMCTVITPSKDHKSLCGPAGGCTRHTIGGLVWNIPDRKKMEEHLLFWIGSDN 159 (427)
Q Consensus 80 ~l~~l~~~L~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~g~~~gc~~~~~~~~~~~~~~~~~~~~~~i~~Ig~~~ 159 (427)
+++++++.|++.|+ ++.++ .....+..+|+++||++..+.+ .+.+ .++|||+|.
T Consensus 131 ~~~~~~~~L~~~g~--------~v~i~--------~~~~~~~~~g~vLGC~~~~~~~--------~~~d--~~l~vg~g~ 184 (332)
T TIGR00322 131 KLHSVRDKLLNEGH--------EVYIG--------PPQGKPLSRGQVLGCNSEVLRG--------EQAD--AMVFIGDGR 184 (332)
T ss_pred HHHHHHHHHHhcCc--------eEEEe--------cCccCCCCCccccCCCcCCCCC--------CCCC--EEEEEcCCc
Confidence 99999999988764 22221 1123446799999998754321 1222 788999999
Q ss_pred chhhHHHhhcCCceEEEecCCCCceecccCcHHHHHHHHHHHHHHHhcCCeEEEEEcCCcccCcHHHHHHHHHHHHHcCC
Q 014264 160 SAFANVVLTFNGCEIVRYDATEERLLTDVSQPLKILKRRYYLVEKAKDANIIGVLVGTLGVAGYLHMIHQMKELITKAGK 239 (427)
Q Consensus 160 ~~l~~l~l~~~~~~v~~yDP~~~~~~~~~~~~~r~L~rRy~~I~ka~~A~~iGIlvgTl~~q~~~~~i~~l~~li~~~GK 239 (427)
||+++++|. ++++||+|||+++++..+..+.+|+|||||++|+||++|++||||+|||++|+|++++++|+++|+++||
T Consensus 185 FH~~~~~l~-~~~~v~~~DP~s~~~~~~~~~~~~~l~rR~~~I~ka~~A~~vGIlvgTl~~q~~~~~~~~l~~ll~~~gk 263 (332)
T TIGR00322 185 FHPLGAAIH-TEKEVFKYDPYSGEFTRIGEDAKQFVKVRALAISKARKGKKFGVVLSSKGGQGRLRLAKNLKKNLEEAGK 263 (332)
T ss_pred chHHHHHHH-cCCcEEEECCCCCceeEccccHHHHHHHHHHHHHHHhcCCEEEEEEecCccCCCHHHHHHHHHHHHHcCC
Confidence 999999995 5899999999999987776679999999999999999999999999999999999999999999999999
Q ss_pred cEEEEEcCCCCHHHHcCCCCCCEEEEecCCCcccccccCCCCcccCHHHHHHhhCCCCccccceeeccc
Q 014264 240 KAYTLVMGKPNPAKLANFPECDVFINVSCAQTALLDSKEFLAPVITPFEAMLAFGRGTQWTGAYVMEFR 308 (427)
Q Consensus 240 K~y~~~vgkln~aKLaNF~eiD~fVlvaCPr~si~d~~~f~kPvlTP~El~~aL~~~~~w~g~y~~Df~ 308 (427)
|+|+|+||+|||+||+||++||+||++||||++|||+++|+||||||||+++||+. +.|. .|+||+.
T Consensus 264 k~y~i~~~~in~~kL~nf~eiD~fV~~aCPr~sidd~~~f~kPvlTP~E~e~al~~-~~~~-~y~~d~~ 330 (332)
T TIGR00322 264 TVLIILLSNVSPAKLLMFDQIDVFVQVACPRIAIDDGYLFNKPLLTPYEFELLLKK-RVEK-YYPMDEI 330 (332)
T ss_pred cEEEEEeCCCCHHHHhCCCCcCEEEEecCCCceecchhhcCCccccHHHHHHHhCc-cccc-cCCCcee
Confidence 99999999999999999999999999999999999999999999999999999997 5696 5999974
No 4
>PF01866 Diphthamide_syn: Putative diphthamide synthesis protein; InterPro: IPR002728 Members of this family include Q16439 from SWISSPROT, a candidate tumour suppressor gene [], and DPH2 from yeast P32461 from SWISSPROT [], which confers resistance to diphtheria toxin and has been found to be involved in diphthamide synthesis. Diphtheria toxin inhibits eukaryotic protein synthesis by ADP-ribosylating diphthamide, a posttranslationally modified histidine residue present in EF2. The exact function of the members of this family is unknown.; GO: 0017183 peptidyl-diphthamide biosynthetic process from peptidyl-histidine, 0005737 cytoplasm; PDB: 3LZD_B 3LZC_A.
Probab=100.00 E-value=3.6e-79 Score=607.68 Aligned_cols=279 Identities=40% Similarity=0.748 Sum_probs=193.4
Q ss_pred CCCCcccccccChhhhcccCCcEEEEecCCCCCCCC-CCCeEEEccccCCChHHHHHHHhhhhcCCCCcEEEEecccchh
Q 014264 1 MADTTYGSCCVDEVGASHVDADCVIHYGHTCLSPTS-TLPAFFVFGKASINTSNCIENLSKHALTNGKPILVLYGLEYAH 79 (427)
Q Consensus 1 LaDtsYGsCCVDevaA~hv~aD~iVHyGhaCls~~~-~lpv~YVf~~~~ld~~~~~~~l~~~~~~~~~~v~l~~dvqy~~ 79 (427)
||||||||||||+++|+|++||+||||||||+++++ ++||+|||++.++|++++++.+.+.+.. .++|+|++|+||.|
T Consensus 26 laDttYGaCcvD~~~a~h~~aD~IVH~Ghscl~~~~~~ipviyV~~~~~id~~~~~~~~~~~~~~-~~~i~l~~~vqy~~ 104 (307)
T PF01866_consen 26 LADTTYGACCVDEVAAEHVGADLIVHYGHSCLSPTKPRIPVIYVFVEINIDVEHLVESLKEEFKK-KKKIVLLTDVQYAH 104 (307)
T ss_dssp E-S-B--TTS--HHHHHHTT-SEEEEEE----S----SS-EEEEE--B-S-HHHHHHHTHHHHHT--SEEEEEE-GGGGG
T ss_pred EeCCcccCCCcCHHHHhhcCCcEEEECCCCCCCcccccCceEEEeccCCCCHHHHHHHHHHhccC-CceEEEEEehhHHH
Confidence 699999999999999999999999999999999975 8999999999999999999999988776 58999999999999
Q ss_pred hhHHHHHHHHhhccCCCCCcceeeeeecceeeeecCCCCCCCCCCCCCCcccccccCcccccCCccCccceEEEEEcCCc
Q 014264 80 AIPHIREAVKVASSSYGSGLKLEINFADVMCTVITPSKDHKSLCGPAGGCTRHTIGGLVWNIPDRKKMEEHLLFWIGSDN 159 (427)
Q Consensus 80 ~l~~l~~~L~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~g~~~gc~~~~~~~~~~~~~~~~~~~~~~i~~Ig~~~ 159 (427)
.++++++.|++.+.. ..+ ......+..+|+++||+...+... .+++.++|||+|.
T Consensus 105 ~~~~~~~~L~~~g~~--------~~i--------~~~~~~~~~~g~vlGc~~~~~~~~---------~~~~~~l~IG~g~ 159 (307)
T PF01866_consen 105 ALEELKEILREKGFE--------VVI--------GIPQNRPLSPGQVLGCTYPSADSL---------DDDDAILFIGGGR 159 (307)
T ss_dssp GHHHHHHHHHHTT-E--------EE-------------TT-SSTTB-BTTB-GGG-S-----------S-SEEEEESSSS
T ss_pred HHHHHHHHHHHhccc--------ccc--------cCCccccCCcccccCCccCccccc---------ccccEEEEEcCCc
Confidence 999999999996531 111 112233456899999987655310 2456899999999
Q ss_pred chhhHHHhhcCCceEEEecCCCCceecc--cCcHHHHHHHHHHHHHHHhcCCeEEEEEcCCcccCcHHHHHHHHHHHHHc
Q 014264 160 SAFANVVLTFNGCEIVRYDATEERLLTD--VSQPLKILKRRYYLVEKAKDANIIGVLVGTLGVAGYLHMIHQMKELITKA 237 (427)
Q Consensus 160 ~~l~~l~l~~~~~~v~~yDP~~~~~~~~--~~~~~r~L~rRy~~I~ka~~A~~iGIlvgTl~~q~~~~~i~~l~~li~~~ 237 (427)
||+++++|+ ++++||+|||++++...+ ..+.+|+|||||++|+||++|++||||+|||++|+|++++++|+++|+++
T Consensus 160 fh~~~l~l~-~~~~v~~~dP~~~~~~~e~~~~~~~~~l~~R~~~i~ka~~a~~~GIiv~tl~~q~~~~~~~~l~~~l~~~ 238 (307)
T PF01866_consen 160 FHLLGLMLS-PGKPVYRYDPYSKTLSVEDISYDIERLLRRRYALIEKAKDAKTFGIIVGTLGGQGYLELIKRLKKLLKKA 238 (307)
T ss_dssp HHHHHHHHH-H-SEEEEE-TT--T--EEE----THHHHHHHHHHHHHHTT--EEEEEEE-STTT--HHHHHHHHHHHHHT
T ss_pred hHHHHHHHh-cCCCEEEeCCCcccceeecccccHHHHHHHHHHHHHHHhcCCEEEEEEecCCCCCCHHHHHHHHHHHHHc
Confidence 999999999 899999999996665544 45689999999999999999999999999999999999999999999999
Q ss_pred CCcEEEEEcCCCCHHHHcCCCCCCEEEEecCCCcccccccCCCCcccCHHHHHHhhCCCCccccceeeccc
Q 014264 238 GKKAYTLVMGKPNPAKLANFPECDVFINVSCAQTALLDSKEFLAPVITPFEAMLAFGRGTQWTGAYVMEFR 308 (427)
Q Consensus 238 GKK~y~~~vgkln~aKLaNF~eiD~fVlvaCPr~si~d~~~f~kPvlTP~El~~aL~~~~~w~g~y~~Df~ 308 (427)
|||+|+|+||+|||+||+||+|||+||++||||+++||+++|+||||||||+++||+... | ++|+|||.
T Consensus 239 gkk~y~~~~~~i~~~kL~nf~eid~fV~~aCPr~~idd~~~f~kPvltP~E~~~al~~~~-~-~~Y~~D~~ 307 (307)
T PF01866_consen 239 GKKSYTLSVGEINPAKLANFPEIDAFVQIACPRLSIDDSKDFYKPVLTPYELEVALNERE-W-GEYPMDEI 307 (307)
T ss_dssp T-EEEEEEESS--GGGGTTS---SEEEE-S-THHHHT--S--SS-EE-HHHHHHHTTS-S----S------
T ss_pred CCEEEEEEECCCCHHHHhcCcccCEEEEecCCCcccCchhhcCCcccCHHHHHHHhCCcc-c-CcCCCCcC
Confidence 999999999999999999999999999999999999999999999999999999999743 5 69999983
No 5
>TIGR03682 arCOG04112 arCOG04112 universal archaeal diphthamide biosynthesis domain protein. This family of proteins has been observed universally in archaeal genomes and contains a match to the TIGR00322 model for the diphthamide biosynthesis protein 2-related domain.
Probab=100.00 E-value=2.3e-76 Score=585.65 Aligned_cols=271 Identities=21% Similarity=0.388 Sum_probs=239.8
Q ss_pred CCCCccccccc-ChhhhcccCCcEEEEecCCCCC-CCCCCCeEEEccccCCChHHHHHHHhhhhcCCCCcEEEEecccch
Q 014264 1 MADTTYGSCCV-DEVGASHVDADCVIHYGHTCLS-PTSTLPAFFVFGKASINTSNCIENLSKHALTNGKPILVLYGLEYA 78 (427)
Q Consensus 1 LaDtsYGsCCV-DevaA~hv~aD~iVHyGhaCls-~~~~lpv~YVf~~~~ld~~~~~~~l~~~~~~~~~~v~l~~dvqy~ 78 (427)
||||||||||| |++|++| ||+|||||||||+ +++++||+|||++.++|++++++++.+.+. .++|+|++|+||.
T Consensus 34 ~gD~tYGaCcV~D~~a~~~--~D~iVH~GHscl~~~~~~~pv~yV~~~~~~d~~~~~~~~~~~~~--~~~v~l~~tiq~~ 109 (308)
T TIGR03682 34 SGEPCYGACDLADDEALEL--VDLIVHFGHSPLPNVKPEIPVIFIEARSDVDVEEVIEKALEELK--GRRIGLVTTAQHV 109 (308)
T ss_pred EcCCceeeccCChHHHHhc--CCEEEEcCCCCCCcccCCCCEEEEEecCCcCHHHHHHHHHHHCC--CCeEEEEEcHHhH
Confidence 69999999999 8887665 9999999999999 588999999999999999988887766553 3689999999999
Q ss_pred hhhHHHHHHHHhhccCCCCCcceeeeeecceeeeecCCCCCCCCCCCCCCcccccccCcccccCCccCccceEEEEEcCC
Q 014264 79 HAIPHIREAVKVASSSYGSGLKLEINFADVMCTVITPSKDHKSLCGPAGGCTRHTIGGLVWNIPDRKKMEEHLLFWIGSD 158 (427)
Q Consensus 79 ~~l~~l~~~L~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~g~~~gc~~~~~~~~~~~~~~~~~~~~~~i~~Ig~~ 158 (427)
|.++++++.|++.|+ ++.++. ....+..+|+++||++.... +.+. ..++|||+|
T Consensus 110 ~~~~~v~~~L~~~g~--------~v~i~~--------~~~~~~~~g~vlGC~~~~~~--------~~~~--d~~~~vg~g 163 (308)
T TIGR03682 110 HLLEKVKEILEERGI--------EVVIGK--------GDGRVTYPGQVLGCNFSAAR--------SVDA--DAFLFVGTG 163 (308)
T ss_pred HHHHHHHHHHHHcCc--------eEEecC--------CCCCCCCCceeeCccccCCC--------CCCc--cEEEEEcCC
Confidence 999999999998764 233321 12234568999999865431 1122 278899999
Q ss_pred cchhhHHHhhcCCceEEEecCCCCceecccCcHHHHHHHHHHHHHHHhcCCeEEEEEcCCcccCcHHHHHHHHHHHHHcC
Q 014264 159 NSAFANVVLTFNGCEIVRYDATEERLLTDVSQPLKILKRRYYLVEKAKDANIIGVLVGTLGVAGYLHMIHQMKELITKAG 238 (427)
Q Consensus 159 ~~~l~~l~l~~~~~~v~~yDP~~~~~~~~~~~~~r~L~rRy~~I~ka~~A~~iGIlvgTl~~q~~~~~i~~l~~li~~~G 238 (427)
.||+++++| +++++||+|||+++++..+..+++|+|||||++|+||++|++||||+|||++|+|++++++|+++|+++|
T Consensus 164 ~Fh~~~l~l-~~~~~v~~~DP~~~~~~~~~~~~~~~l~~R~~~I~ka~~A~~vGIlvgTl~~q~~~~~~~~l~~ll~~~g 242 (308)
T TIGR03682 164 LFHPLGLAL-ATNKPVYAADPFSGEVEDIEAEIDKFLRVRYARISKALDAKKFGILVSTKKGQRRPELAEELKKLLEELG 242 (308)
T ss_pred cchHHHHHh-ccCCcEEEECCCCCceEeechhHHHHHHHHHHHHHHHhhCCeEEEEEEccCcCCCHHHHHHHHHHHHHcC
Confidence 999999988 7899999999999998776667999999999999999999999999999999999999999999999999
Q ss_pred CcEEEEEcCCCCHHHHcCCCCCCEEEEecCCCcccccccCCCCcccCHHHHHHhhCCCCccccceeecc
Q 014264 239 KKAYTLVMGKPNPAKLANFPECDVFINVSCAQTALLDSKEFLAPVITPFEAMLAFGRGTQWTGAYVMEF 307 (427)
Q Consensus 239 KK~y~~~vgkln~aKLaNF~eiD~fVlvaCPr~si~d~~~f~kPvlTP~El~~aL~~~~~w~g~y~~Df 307 (427)
||+|+|+||+|||+||+|| +||+||++||||+++||+++|+||||||||+++||+. ++| |+||+
T Consensus 243 kk~y~i~~~~in~~kL~nf-~iD~fV~~aCPr~sidd~~~f~kPvlTP~E~~~al~~-~~~---y~~D~ 306 (308)
T TIGR03682 243 KEALLILLDNISPDQLRNL-DFDAYVNTACPRIAIDDYARFKKPVLTPQEFEIVLGK-RSE---YVFDE 306 (308)
T ss_pred CeEEEEEeCCCCHHHHhcC-CcCEEEEccCCCcccccHhhCCCcccCHHHHHHHhCC-Ccc---ccCCc
Confidence 9999999999999999999 6999999999999999999999999999999999998 789 99885
No 6
>COG1736 DPH2 Diphthamide synthase subunit DPH2 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=6.9e-64 Score=496.47 Aligned_cols=280 Identities=24% Similarity=0.474 Sum_probs=247.8
Q ss_pred CCCCcccccccChhhhcccCCcEEEEecCCCCCC-CCCCCeEEEccccCCChHHHHHHHhhhhcCCCCcEEEEecccchh
Q 014264 1 MADTTYGSCCVDEVGASHVDADCVIHYGHTCLSP-TSTLPAFFVFGKASINTSNCIENLSKHALTNGKPILVLYGLEYAH 79 (427)
Q Consensus 1 LaDtsYGsCCVDevaA~hv~aD~iVHyGhaCls~-~~~lpv~YVf~~~~ld~~~~~~~l~~~~~~~~~~v~l~~dvqy~~ 79 (427)
+|||+|||||||+.+|+|+ ||+||||||||+++ ...+||+|||...++|++..++.+...+.+..++|++++++||.|
T Consensus 57 ~gd~~yGACdi~~~~a~~~-~D~iVH~GHs~l~~~~~~~~Viyv~~~~~~d~~~~~~~~~~~l~~~~r~I~li~t~q~~~ 135 (347)
T COG1736 57 SGDPVYGACDIDDLKAKDV-VDLIVHYGHSCLPPVEYELPVIYVFAFSRVDVDLVVLEATRELKKGSRRIGLITTAQHVH 135 (347)
T ss_pred eCCcccccccCCHHHHhhc-ccEEEEcccccCCCcCCCCcEEEeecccccchhHHHHHhhHhhccCCceEEEEecccchh
Confidence 5899999999999999999 99999999999997 578999999999999999988877775555566899999999999
Q ss_pred hhHHHHHHHHhhccCCCCCcceeeeeecceeeeecCCCCCCCCCCCCCCcccccccCcccccCCccCccceEEEEEcCCc
Q 014264 80 AIPHIREAVKVASSSYGSGLKLEINFADVMCTVITPSKDHKSLCGPAGGCTRHTIGGLVWNIPDRKKMEEHLLFWIGSDN 159 (427)
Q Consensus 80 ~l~~l~~~L~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~g~~~gc~~~~~~~~~~~~~~~~~~~~~~i~~Ig~~~ 159 (427)
.++++++.|+..|. ++.+ .+.+.....+||++||+++.+.+ . +.-.++|||+|.
T Consensus 136 ~l~~~k~~L~~~g~--------~v~i--------~~~~~r~~~~gqVLGC~~~~~~~--------~--~~d~~l~vg~G~ 189 (347)
T COG1736 136 LLEEVKEILEGRGY--------EVVI--------GRGQTRPAYPGQVLGCNFSVLEG--------V--DADAVLYVGSGR 189 (347)
T ss_pred HHHHHHHHhhcCCe--------EEEE--------eCCCCcccCcceeeccccccCCc--------c--ccceEEEEcCCc
Confidence 99999999998764 2222 23334467899999999765432 1 233788999999
Q ss_pred chhhHHHhhcCCceEEEecCCCCceecccCcHHHHHHHHHHHHHHHhcCCeEEEEEcCCcccCcHHHHHHHHHHHHHcCC
Q 014264 160 SAFANVVLTFNGCEIVRYDATEERLLTDVSQPLKILKRRYYLVEKAKDANIIGVLVGTLGVAGYLHMIHQMKELITKAGK 239 (427)
Q Consensus 160 ~~l~~l~l~~~~~~v~~yDP~~~~~~~~~~~~~r~L~rRy~~I~ka~~A~~iGIlvgTl~~q~~~~~i~~l~~li~~~GK 239 (427)
||++++++. +.++|++|||+++.+.+.....++++|+||+.|+||++|++||||+||+++|+++++++.|.++++++||
T Consensus 190 FH~lg~~i~-~~~~v~~~dP~s~~~~~~~~~~~~~l~~R~~~i~~a~~a~~~giiv~tk~gQ~r~~~~~~l~k~~~~~g~ 268 (347)
T COG1736 190 FHPLGLAIR-TEKPVFAIDPYSGKVREEDPEADRFLRKRYAAISKALDAKSFGIIVSTKGGQRRLEVARELVKLLKEAGK 268 (347)
T ss_pred cChhhcccc-cCCcEEEEcCCCCceeecchhhhHHHHHHHHHHHHHhcCCeEEEEEecccccCcHHHHHHHHHHHHHcCC
Confidence 999988888 8999999999999987666668999999999999999999999999999999999999999999999999
Q ss_pred cEEEEEcCCCCHHHHcCCCCCCEEEEecCCCcccccccCCCCcccCHHHHHHhhCCCCccccceeeccccc
Q 014264 240 KAYTLVMGKPNPAKLANFPECDVFINVSCAQTALLDSKEFLAPVITPFEAMLAFGRGTQWTGAYVMEFRDL 310 (427)
Q Consensus 240 K~y~~~vgkln~aKLaNF~eiD~fVlvaCPr~si~d~~~f~kPvlTP~El~~aL~~~~~w~g~y~~Df~~~ 310 (427)
++|+|+|+++||+||+||.+||+||++||||++|||...|+||||||+|++++|+. +.| .+|.||.-.-
T Consensus 269 ~~~li~~~~i~p~~L~~f~~iD~~v~taCPRi~iDd~~~f~kPlLTP~E~~~~l~~-~~~-~~y~~Dei~~ 337 (347)
T COG1736 269 EVYLIVVDEISPDKLANFDDIDAFVNTACPRIPIDDGDRFKKPLLTPYEFEIALGW-RSD-ERYAFDEIVG 337 (347)
T ss_pred ceEEEEecCCCHHHHhcccceeEEEEecCCCcccchHhhhCCcccChHHHHHhhcc-Ccc-cccccceeec
Confidence 99999999999999999999999999999999999999999999999999999992 333 6898886443
No 7
>PRK09492 treR trehalose repressor; Provisional
Probab=78.29 E-value=7.3 Score=38.03 Aligned_cols=78 Identities=13% Similarity=0.154 Sum_probs=51.6
Q ss_pred hcCCeEEEEEcCCcccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHHH-------HcCCCCCCEEEEecCCCcccccccC
Q 014264 206 KDANIIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAK-------LANFPECDVFINVSCAQTALLDSKE 278 (427)
Q Consensus 206 ~~A~~iGIlvgTl~~q~~~~~i~~l~~li~~~GKK~y~~~vgkln~aK-------LaNF~eiD~fVlvaCPr~si~d~~~ 278 (427)
+..++||+|+..+.-..+..+++.+.+.++++|....++.. .-++++ |.+. .+|.+|+.++..........
T Consensus 60 ~~~~~Ig~i~~~~~~~~~~~~~~~i~~~~~~~gy~~~~~~~-~~~~~~~~~~~~~l~~~-~vdgiIi~~~~~~~~~~l~~ 137 (315)
T PRK09492 60 QSDKVVGIIVSRLDSLSENQAVRTMLPAFYEQGYDPIIMES-QFSPEKVNEHLGVLKRR-NVDGVILFGFTGITEEMLAP 137 (315)
T ss_pred CCCCeEEEEecCCcCcccHHHHHHHHHHHHHcCCeEEEEec-CCChHHHHHHHHHHHhc-CCCEEEEeCCCcccHHHHHh
Confidence 45579999999887777889999999999999987655443 334433 2332 59999998753222222234
Q ss_pred CCCcccC
Q 014264 279 FLAPVIT 285 (427)
Q Consensus 279 f~kPvlT 285 (427)
+.+|++.
T Consensus 138 ~~~pvv~ 144 (315)
T PRK09492 138 WQDKLVL 144 (315)
T ss_pred cCCCEEE
Confidence 4566553
No 8
>cd06280 PBP1_LacI_like_4 Ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. This group includes the ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. The LacI-GalR family repressors 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 affinity of the repressor.
Probab=77.91 E-value=4.4 Score=38.31 Aligned_cols=59 Identities=14% Similarity=0.181 Sum_probs=45.2
Q ss_pred eEEEEEcCCcccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHHHHcC----C--CCCCEEEEecCC
Q 014264 210 IIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKLAN----F--PECDVFINVSCA 269 (427)
Q Consensus 210 ~iGIlvgTl~~q~~~~~i~~l~~li~~~GKK~y~~~vgkln~aKLaN----F--~eiD~fVlvaCP 269 (427)
+||+|+..+....+..+++.+.+.+++.|.+..++ ...-++++... + ..+|.+++.+|.
T Consensus 1 ~Ig~i~p~~~~~~~~~~~~~i~~~~~~~g~~~~~~-~~~~~~~~~~~~i~~l~~~~~dgiii~~~~ 65 (263)
T cd06280 1 TVGLIVADIRNPFFTAVSRAVEDAAYRAGLRVILC-NTDEDPEKEAMYLELMEEERVTGVIFAPTR 65 (263)
T ss_pred CEEEEecccccccHHHHHHHHHHHHHHCCCEEEEE-eCCCCHHHHHHHHHHHHhCCCCEEEEeCCC
Confidence 58999999888889999999999999999887544 44445554322 1 269999998875
No 9
>cd06289 PBP1_MalI_like Ligand-binding domain of MalI, a transcription regulator of the maltose system of Escherichia coli and its close homologs from other bacteria. This group includes the ligand-binding domain of MalI, a transcription regulator of the maltose system of Escherichia coli and its close homologs from other bacteria. They are members of the LacI-GalR family of repressor proteins which 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 affinity of the repressor.
Probab=74.23 E-value=7 Score=36.70 Aligned_cols=75 Identities=16% Similarity=0.195 Sum_probs=52.7
Q ss_pred eEEEEEcCCcccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHHHH----cCC--CCCCEEEEecCCCcccc---cccCCC
Q 014264 210 IIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKL----ANF--PECDVFINVSCAQTALL---DSKEFL 280 (427)
Q Consensus 210 ~iGIlvgTl~~q~~~~~i~~l~~li~~~GKK~y~~~vgkln~aKL----aNF--~eiD~fVlvaCPr~si~---d~~~f~ 280 (427)
+||+|+....-..+..+++.+++.+++.|.+..++ .+.-++++. .++ ..+|++++.+|...... ..+...
T Consensus 1 ~I~vi~~~~~~~~~~~~~~g~~~~a~~~g~~~~~~-~~~~~~~~~~~~i~~~~~~~vdgiii~~~~~~~~~~~~~~~~~~ 79 (268)
T cd06289 1 TIGLVINDLTNPFFAELAAGLEEVLEEAGYTVFLA-NSGEDVERQEQLLSTMLEHGVAGIILCPAAGTSPDLLKRLAESG 79 (268)
T ss_pred CEEEEecCCCcchHHHHHHHHHHHHHHcCCeEEEe-cCCCChHHHHHHHHHHHHcCCCEEEEeCCCCccHHHHHHHHhcC
Confidence 58999988877778889999999999999876544 444555532 222 36999999999765422 233445
Q ss_pred CcccC
Q 014264 281 APVIT 285 (427)
Q Consensus 281 kPvlT 285 (427)
.|+|+
T Consensus 80 ipvV~ 84 (268)
T cd06289 80 IPVVL 84 (268)
T ss_pred CCEEE
Confidence 67775
No 10
>cd06293 PBP1_LacI_like_11 Ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. This group includes the ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. The LacI-GalR family repressors 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 affinity of the repressor.
Probab=73.63 E-value=6.8 Score=37.12 Aligned_cols=61 Identities=15% Similarity=0.178 Sum_probs=45.8
Q ss_pred eEEEEEcCCcccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHHHHcC----C--CCCCEEEEecCCCc
Q 014264 210 IIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKLAN----F--PECDVFINVSCAQT 271 (427)
Q Consensus 210 ~iGIlvgTl~~q~~~~~i~~l~~li~~~GKK~y~~~vgkln~aKLaN----F--~eiD~fVlvaCPr~ 271 (427)
+||+|+..+.-..+..+++.+.+.++++|....++..+ -++++... + ..+|.+++.+|+..
T Consensus 1 ~Ig~i~~~~~~~~~~~~~~gi~~~~~~~gy~v~~~~~~-~~~~~~~~~i~~~~~~~~dgiii~~~~~~ 67 (269)
T cd06293 1 TIGLVVPDIANPFFAELADAVEEEADARGLSLVLCATR-NRPERELTYLRWLDTNHVDGLIFVTNRPD 67 (269)
T ss_pred CEEEEeCCCCCCcHHHHHHHHHHHHHHCCCEEEEEeCC-CCHHHHHHHHHHHHHCCCCEEEEeCCCCC
Confidence 58999988876777899999999999999888666544 35543221 1 26999999998744
No 11
>COG1609 PurR Transcriptional regulators [Transcription]
Probab=70.90 E-value=12 Score=37.71 Aligned_cols=62 Identities=16% Similarity=0.247 Sum_probs=52.3
Q ss_pred HhcCCeEEEEEcCCcccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHHHHc----CC--CCCCEEEEec
Q 014264 205 AKDANIIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKLA----NF--PECDVFINVS 267 (427)
Q Consensus 205 a~~A~~iGIlvgTl~~q~~~~~i~~l~~li~~~GKK~y~~~vgkln~aKLa----NF--~eiD~fVlva 267 (427)
.+..++||+|+..+.-..|.++++.+.+.++++|+...+...+. ++++.. ++ ..+|.+|+.+
T Consensus 55 ~~~s~~Ig~i~p~~~~~~~~~i~~gi~~~~~~~gy~~~l~~~~~-~~~~e~~~~~~l~~~~vdGiIi~~ 122 (333)
T COG1609 55 TGRTKTIGLVVPDITNPFFAEILKGIEEAAREAGYSLLLANTDD-DPEKEREYLETLLQKRVDGLILLG 122 (333)
T ss_pred hCCCCEEEEEeCCCCCchHHHHHHHHHHHHHHcCCEEEEECCCC-CHHHHHHHHHHHHHcCCCEEEEec
Confidence 34678999999999888999999999999999999998888887 666532 22 2699999998
No 12
>cd06272 PBP1_hexuronate_repressor_like Ligand-binding domain of DNA transcription repressor for the hexuronate utilization operon from Bacillus species and its close homologs from other bacteria, all of which are a member of the LacI-GalR family of bacterial transcription regulators. Ligand-binding domain of DNA transcription repressor for the hexuronate utilization operon from Bacillus species and its close homologs from other bacteria, all of which are a member of the LacI-GalR family of bacterial transcription regulators. The LacI-GalR family repressors 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
Probab=70.27 E-value=7.6 Score=36.56 Aligned_cols=74 Identities=16% Similarity=0.247 Sum_probs=50.2
Q ss_pred eEEEEEcCCcccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHHHHc-CC--CCCCEEEEecCCCccc--ccccCCCCccc
Q 014264 210 IIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKLA-NF--PECDVFINVSCAQTAL--LDSKEFLAPVI 284 (427)
Q Consensus 210 ~iGIlvgTl~~q~~~~~i~~l~~li~~~GKK~y~~~vgkln~aKLa-NF--~eiD~fVlvaCPr~si--~d~~~f~kPvl 284 (427)
+||+|+.++....+..+++.+++.++++|....+.... +++... .+ ..+|..|+.+|....- ....+...|+|
T Consensus 1 ~igvv~~~~~~~~~~~~~~gi~~~~~~~g~~~~~~~~~--~~~~~~~~l~~~~vdgii~~~~~~~~~~~~~~~~~~ipvV 78 (261)
T cd06272 1 TIGLIWPSVSRVALTELVTGINQAISKNGYNMNVSITP--SLAEAEDLFKENRFDGVIIFGESASDVEYLYKIKLAIPVV 78 (261)
T ss_pred CEEEEecCCCchhHHHHHHHHHHHHHHcCCEEEEEecc--cHHHHHHHHHHcCcCEEEEeCCCCChHHHHHHHHcCCCEE
Confidence 58999998888888899999999999999887666554 333221 12 2699999988753221 12234456665
Q ss_pred C
Q 014264 285 T 285 (427)
Q Consensus 285 T 285 (427)
+
T Consensus 79 ~ 79 (261)
T cd06272 79 S 79 (261)
T ss_pred E
Confidence 4
No 13
>PF00919 UPF0004: Uncharacterized protein family UPF0004; InterPro: IPR013848 The methylthiotransferase (MTTase) or miaB-like family is named after the (dimethylallyl)adenosine tRNA MTTase miaB protein, which catalyses a C-H to C-S bond conversion in the methylthiolation of tRNA. A related bacterial enzyme rimO performs a similar methylthiolation, but on a protein substrate. RimO acts on the ribosomal protein S12 and forms a separate MTTase subfamily. The miaB-subfamily includes mammalian CDK5 regulatory subunit-associated proteins and similar proteins in other eukaryotes. Two other subfamilies, yqeV and CDKAL1, are named after a Bacillus subtilis and a human protein, respectively. While yqeV-like proteins are found in bacteria, CDKAL1 subfamily members occur in eukaryotes and in archaebacteria. The likely MTTases from these 4 subfamilies contain an N-terminal MTTase domain, a central radical generating fold and a C-terminal TRAM domain (see PDOC50926 from PROSITEDOC). The core forms a radical SAM fold (or AdoMet radical), containing a cysteine motif CxxxCxxC that binds a [4Fe-4S] cluster [, , ]. A reducing equivalent from the [4Fe-4S]+ cluster is used to cleave S-adenosylmethionine (SAM) to generate methionine and a 5'-deoxyadenosyl radical. The latter is thought to produce a reactive substrate radical that is amenable to sulphur insertion [, ]. The N-terminal MTTase domain contains 3 cysteines that bind a second [4Fe-4S] cluster, in addition to the radical-generating [4Fe-4S] cluster, which could be involved in the thiolation reaction. The C-terminal TRAM domain is not shared with other radical SAM proteins outside the MTTase family. The TRAM domain can bind to RNA substrate and seems to be important for substrate recognition. The tertiary structure of the central radical SAM fold has six beta/alpha motifs resembling a three-quarter TIM barrel core (see PDOC00155 from PROSITEDOC) []. The N-terminal MTTase domain might form an additional [beta/alpha]2 TIM barrel unit []. ; GO: 0003824 catalytic activity, 0051539 4 iron, 4 sulfur cluster binding, 0009451 RNA modification
Probab=69.86 E-value=6.4 Score=32.69 Aligned_cols=71 Identities=21% Similarity=0.305 Sum_probs=49.7
Q ss_pred HHHHH-HHHHHHHhcCCeEEEEEcCCcccCcHHHHHHHHHHHHHcCCcEEEEEcC---CCCHHHHcCC-CCCCEEE
Q 014264 194 ILKRR-YYLVEKAKDANIIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMG---KPNPAKLANF-PECDVFI 264 (427)
Q Consensus 194 ~L~rR-y~~I~ka~~A~~iGIlvgTl~~q~~~~~i~~l~~li~~~GKK~y~~~vg---kln~aKLaNF-~eiD~fV 264 (427)
.|.++ |..++...+|..+-|--.|..-+--.+++++|+++.+...++..+++.| ...+++|... |++|+|+
T Consensus 22 ~l~~~G~~~~~~~e~AD~iiiNTC~V~~~Ae~k~~~~i~~l~~~~~~~~~ivv~GC~aq~~~~~l~~~~p~vd~v~ 97 (98)
T PF00919_consen 22 ILQAAGYEIVDDPEEADVIIINTCTVRESAEQKSRNRIRKLKKLKKPGAKIVVTGCMAQRYGEELKKEFPEVDLVV 97 (98)
T ss_pred HHHhcCCeeecccccCCEEEEEcCCCCcHHHHHHHHHHHHHHHhcCCCCEEEEEeCccccChHHHHhhCCCeEEEe
Confidence 34444 5566666789988665555555556688888888877765667788888 5567888775 5688875
No 14
>cd06274 PBP1_FruR Ligand binding domain of DNA transcription repressor specific for fructose (FruR) and its close homologs. Ligand binding domain of DNA transcription repressor specific for fructose (FruR) and its close homologs, all of which are a member of the LacI-GalR family of bacterial transcription regulators. The LacI-GalR family repressors 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 members of the type I periplasmic binding protein superfamily. 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 affinity of the repressor
Probab=69.59 E-value=9.5 Score=35.98 Aligned_cols=76 Identities=13% Similarity=0.227 Sum_probs=50.9
Q ss_pred eEEEEEcCCcccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHHHHcC----C--CCCCEEEEecCCCccc--ccccCCCC
Q 014264 210 IIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKLAN----F--PECDVFINVSCAQTAL--LDSKEFLA 281 (427)
Q Consensus 210 ~iGIlvgTl~~q~~~~~i~~l~~li~~~GKK~y~~~vgkln~aKLaN----F--~eiD~fVlvaCPr~si--~d~~~f~k 281 (427)
+||+|+..+....+..+++.+.+.+++.|....++.. .-++++... + ..+|++++.++...+. ....+-..
T Consensus 1 ~igvi~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~-~~~~~~~~~~i~~l~~~~vdgiii~~~~~~~~~~~~~~~~~i 79 (264)
T cd06274 1 TIGLIIPDLENRSFARIAKRLEALARERGYQLLIACS-DDDPETERETVETLIARQVDALIVAGSLPPDDPYYLCQKAGL 79 (264)
T ss_pred CEEEEeccccCchHHHHHHHHHHHHHHCCCEEEEEeC-CCCHHHHHHHHHHHHHcCCCEEEEcCCCCchHHHHHHHhcCC
Confidence 4899999888888889999999999999887655443 335554321 1 2689999998864331 12223345
Q ss_pred cccCH
Q 014264 282 PVITP 286 (427)
Q Consensus 282 PvlTP 286 (427)
|||+-
T Consensus 80 pvV~~ 84 (264)
T cd06274 80 PVVAL 84 (264)
T ss_pred CEEEe
Confidence 66543
No 15
>cd06295 PBP1_CelR Ligand binding domain of a transcription regulator of cellulose genes, CelR, which is highly homologous to the LacI-GalR family of bacterial transcription regulators. This group includes the ligand binding domain of a transcription regulator of cellulose genes, CelR, which is highly homologous to the LacI-GalR family of bacterial transcription regulators. The binding of CelR to the celE promoter is inhibited specifically by cellobiose. The LacI-GalR family repressors 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 chang
Probab=68.90 E-value=7.8 Score=36.83 Aligned_cols=64 Identities=14% Similarity=0.254 Sum_probs=45.8
Q ss_pred cCCeEEEEEcC-------CcccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHHHHcCC---CCCCEEEEecCCC
Q 014264 207 DANIIGVLVGT-------LGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKLANF---PECDVFINVSCAQ 270 (427)
Q Consensus 207 ~A~~iGIlvgT-------l~~q~~~~~i~~l~~li~~~GKK~y~~~vgkln~aKLaNF---~eiD~fVlvaCPr 270 (427)
..++||||+-. +.-..+..+++.+++.+++.|.+..++..+.-...++..+ ..+|++|+.+|..
T Consensus 2 ~s~~i~vi~p~~~~~~~~~~~~~~~~~~~gi~~~~~~~g~~~~v~~~~~~~~~~~~~~l~~~~~dgiii~~~~~ 75 (275)
T cd06295 2 RTDTIALVVPEPHERDQSFSDPFFLSLLGGIADALAERGYDLLLSFVSSPDRDWLARYLASGRADGVILIGQHD 75 (275)
T ss_pred CceEEEEEecCccccccccCCchHHHHHHHHHHHHHHcCCEEEEEeCCchhHHHHHHHHHhCCCCEEEEeCCCC
Confidence 46789999964 4445677899999999999999988776654323333221 3699999988753
No 16
>cd06279 PBP1_LacI_like_3 Ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. This group includes the ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. The LacI-GalR family repressors 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 affinity of the repressor.
Probab=68.77 E-value=9.1 Score=36.79 Aligned_cols=61 Identities=16% Similarity=0.195 Sum_probs=43.0
Q ss_pred eEEEEEcC-----CcccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHHHHcCC--CCCCEEEEecCCCc
Q 014264 210 IIGVLVGT-----LGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKLANF--PECDVFINVSCAQT 271 (427)
Q Consensus 210 ~iGIlvgT-----l~~q~~~~~i~~l~~li~~~GKK~y~~~vgkln~aKLaNF--~eiD~fVlvaCPr~ 271 (427)
+||+|+-+ ..-..+..+++.+.+.+++.|....++.... ....+.++ ..+|.+++.+|+..
T Consensus 1 ~igvi~p~~~~~~~~~~~~~~~~~gi~~~a~~~g~~~~~~~~~~-~~~~~~~~~~~~~dgiii~~~~~~ 68 (283)
T cd06279 1 AVGVVLTDSLSYAFSDPVASQFLAGVAEVLDAAGVNLLLLPASS-EDSDSALVVSALVDGFIVYGVPRD 68 (283)
T ss_pred CEEEEeCCcccccccCccHHHHHHHHHHHHHHCCCEEEEecCcc-HHHHHHHHHhcCCCEEEEeCCCCC
Confidence 47888876 4556667899999999999998877665543 22223232 26899999998754
No 17
>cd06271 PBP1_AglR_RafR_like Ligand-binding domain of DNA transcription repressors specific for raffinose (RafR) and alpha-glucosides (AglR) which are members of the LacI-GalR family of bacterial transcription regulators. Ligand-binding domain of DNA transcription repressors specific for raffinose (RafR) and alpha-glucosides (AglR) which are members of the LacI-GalR family of bacterial transcription regulators. The LacI-GalR family repressors 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 affinity of the represso
Probab=66.86 E-value=17 Score=34.10 Aligned_cols=77 Identities=18% Similarity=0.178 Sum_probs=48.9
Q ss_pred eEEEEEcC----CcccCcHHHHHHHHHHHHHcCCcEEEEEcCCC-CH----HHHcCCCCCCEEEEecCCCcc--cccccC
Q 014264 210 IIGVLVGT----LGVAGYLHMIHQMKELITKAGKKAYTLVMGKP-NP----AKLANFPECDVFINVSCAQTA--LLDSKE 278 (427)
Q Consensus 210 ~iGIlvgT----l~~q~~~~~i~~l~~li~~~GKK~y~~~vgkl-n~----aKLaNF~eiD~fVlvaCPr~s--i~d~~~ 278 (427)
.||+|+.+ .+-..+..+++.+.+.+++.|....++....- +. .++.+-..+|++|+.+|.... +....+
T Consensus 1 ~igvi~p~~~~~~~~~~~~~~~~~i~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~vdgiii~~~~~~~~~~~~~~~ 80 (268)
T cd06271 1 AIGLVLPTGEREEGDPFFAEFLSGLSEALAEHGYDLVLLPVDPDEDPLEVYRRLVESGLVDGVIISRTRPDDPRVALLLE 80 (268)
T ss_pred CeEEEeCCcccccCCccHHHHHHHHHHHHHHCCceEEEecCCCcHHHHHHHHHHHHcCCCCEEEEecCCCCChHHHHHHh
Confidence 47999977 34577788999999999999988776665432 11 222222369999998875332 111223
Q ss_pred CCCcccCH
Q 014264 279 FLAPVITP 286 (427)
Q Consensus 279 f~kPvlTP 286 (427)
-..|+|..
T Consensus 81 ~~ipvV~~ 88 (268)
T cd06271 81 RGFPFVTH 88 (268)
T ss_pred cCCCEEEE
Confidence 44576653
No 18
>COG5136 U1 snRNP-specific protein C [RNA processing and modification]
Probab=66.74 E-value=6.1 Score=35.73 Aligned_cols=67 Identities=21% Similarity=0.263 Sum_probs=51.3
Q ss_pred HHHHHHHHHHHHHHHhcCCeEEEEEcCCcccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHHHHcCCCCCCEEEEecCCC
Q 014264 191 PLKILKRRYYLVEKAKDANIIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKLANFPECDVFINVSCAQ 270 (427)
Q Consensus 191 ~~r~L~rRy~~I~ka~~A~~iGIlvgTl~~q~~~~~i~~l~~li~~~GKK~y~~~vgkln~aKLaNF~eiD~fVlvaCPr 270 (427)
.+-.+|+.-+.+++|+|- .+-...+.+-|+.+|-|+--..-+.....+.-.|+.+|-+-+++||+
T Consensus 28 ~~H~~~~~dYY~~~a~di---------------~~e~~~~lr~i~~~G~kv~c~gnks~~~p~~~a~~p~d~~~nL~~p~ 92 (188)
T COG5136 28 AKHGLMRKDYYMEMAEDI---------------AAEMASILRDIKTAGEKVECEGNKSTSYPPFPAFPPGDFYLNLALPE 92 (188)
T ss_pred HHHHHHHHHHHHHHHHHH---------------HHHHHHHHHHHhhcCceEEeccCCccCCCCcccCCccchhhhccCCC
Confidence 345677777788888741 12234555667788989888888889999998899999999999998
Q ss_pred cc
Q 014264 271 TA 272 (427)
Q Consensus 271 ~s 272 (427)
-.
T Consensus 93 pp 94 (188)
T COG5136 93 PP 94 (188)
T ss_pred CC
Confidence 76
No 19
>cd06273 PBP1_GntR_like_1 This group includes the ligand-binding domain of putative DNA transcription repressors which are highly similar to that of the repressor specific for gluconate (GntR), a member of the LacI-GalR family of bacterial transcription regulators. This group includes the ligand-binding domain of putative DNA transcription repressors which are highly similar to that of the repressor specific for gluconate (GntR), a member of the LacI-GalR family of bacterial transcription regulators. The LacI-GalR family repressors 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
Probab=66.56 E-value=8.2 Score=36.37 Aligned_cols=75 Identities=19% Similarity=0.165 Sum_probs=50.6
Q ss_pred eEEEEEcCCcccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHH-------HHcCCCCCCEEEEecCCCcc--cccccCCC
Q 014264 210 IIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPA-------KLANFPECDVFINVSCAQTA--LLDSKEFL 280 (427)
Q Consensus 210 ~iGIlvgTl~~q~~~~~i~~l~~li~~~GKK~y~~~vgkln~a-------KLaNF~eiD~fVlvaCPr~s--i~d~~~f~ 280 (427)
+||+|+..+.-..|..+++.+.+.+++.|....++. ++-+++ +|.+- .+|+++++++.... +...++-.
T Consensus 1 ~i~vv~p~~~~~~~~~~~~~i~~~~~~~g~~~~~~~-~~~~~~~~~~~~~~l~~~-~vdgiii~~~~~~~~~~~~l~~~~ 78 (268)
T cd06273 1 TIGAIVPTLDNAIFARVIQAFQETLAAHGYTLLVAS-SGYDLDREYAQARKLLER-GVDGLALIGLDHSPALLDLLARRG 78 (268)
T ss_pred CeEEEeCCCCCchHHHHHHHHHHHHHHCCCEEEEec-CCCCHHHHHHHHHHHHhc-CCCEEEEeCCCCCHHHHHHHHhCC
Confidence 589999888878889999999999999996665433 333443 33332 69999998875321 11223445
Q ss_pred CcccCH
Q 014264 281 APVITP 286 (427)
Q Consensus 281 kPvlTP 286 (427)
.|+|+.
T Consensus 79 iPvv~~ 84 (268)
T cd06273 79 VPYVAT 84 (268)
T ss_pred CCEEEE
Confidence 677764
No 20
>cd06270 PBP1_GalS_like Ligand binding domain of DNA transcription iso-repressor GalS, which is one of two regulatory proteins involved in galactose transport and metabolism. Ligand binding domain of DNA transcription iso-repressor GalS, which is one of two regulatory proteins involved in galactose transport and metabolism. Transcription of the galactose regulon genes is regulated by Gal iso-repressor (GalS) and Gal repressor (GalR) in different ways, but both repressors recognize the same DNA binding site in the absence of D-galactose. GalS is a dimeric protein like GalR,and its major role is in regulating expression of the high-affinity galactose transporter encoded by the mgl operon, whereas GalR is the exclusive regulator of galactose permease, the low-affinity galactose transporter. GalS and GalR are members of the LacI-GalR family of transcription regulators and both contain the type I periplasmic binding protein-like fold. Hence, they are homologous to the periplasmic sugar bindi
Probab=65.57 E-value=13 Score=35.18 Aligned_cols=60 Identities=27% Similarity=0.369 Sum_probs=45.2
Q ss_pred eEEEEEcCCcccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHHH-------HcCCCCCCEEEEecCCCc
Q 014264 210 IIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAK-------LANFPECDVFINVSCAQT 271 (427)
Q Consensus 210 ~iGIlvgTl~~q~~~~~i~~l~~li~~~GKK~y~~~vgkln~aK-------LaNF~eiD~fVlvaCPr~ 271 (427)
+||+|+..+.-..+..+++.+++.++++|.+..++. +.-++++ |.+ ..+|++|+.+|...
T Consensus 1 ~igvi~p~~~~~~~~~~~~g~~~~a~~~g~~~~~~~-~~~~~~~~~~~i~~~~~-~~vdgii~~~~~~~ 67 (268)
T cd06270 1 TIGLVVSDLDGPFFGPLLSGVESVARKAGKHLIITA-GHHSAEKEREAIEFLLE-RRCDALILHSKALS 67 (268)
T ss_pred CEEEEEccccCcchHHHHHHHHHHHHHCCCEEEEEe-CCCchHHHHHHHHHHHH-cCCCEEEEecCCCC
Confidence 489999999888899999999999999998866543 3334442 233 36999999988533
No 21
>cd06298 PBP1_CcpA_like Ligand-binding domain of the catabolite control protein A (CcpA), which functions as the major transcriptional regulator of carbon catabolite repression/regulation. Ligand-binding domain of the catabolite control protein A (CcpA), which functions as the major transcriptional regulator of carbon catabolite repression/regulation (CCR), a process in which enzymes necessary for the metabolism of alternative sugars are inhibited in the presence of glucose. In gram-positive bacteria, CCR is controlled by HPr, a phosphoenolpyruvate:sugar phsophotrasnferase system (PTS) and a transcriptional regulator CcpA. Moreover, CcpA can regulate sporulation and antibiotic resistance as well as play a role in virulence development of certain pathogens such as the group A streptococcus. The ligand binding domain of CcpA is a member of the LacI-GalR family of bacterial transcription regulators.
Probab=65.57 E-value=13 Score=34.88 Aligned_cols=58 Identities=10% Similarity=0.147 Sum_probs=43.4
Q ss_pred eEEEEEcCCcccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHH-------HHcCCCCCCEEEEecCC
Q 014264 210 IIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPA-------KLANFPECDVFINVSCA 269 (427)
Q Consensus 210 ~iGIlvgTl~~q~~~~~i~~l~~li~~~GKK~y~~~vgkln~a-------KLaNF~eiD~fVlvaCP 269 (427)
+||+|+..+.-..+..+++.+++.+++.|....++. ..-+++ +|.+ ..+|++|+.+++
T Consensus 1 ~i~vi~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~-~~~~~~~~~~~i~~l~~-~~vdgiii~~~~ 65 (268)
T cd06298 1 TVGVIIPDITNSYFAELARGIDDIATMYKYNIILSN-SDNDKEKELKVLNNLLA-KQVDGIIFMGGK 65 (268)
T ss_pred CEEEEECCCcchHHHHHHHHHHHHHHHcCCeEEEEe-CCCCHHHHHHHHHHHHH-hcCCEEEEeCCC
Confidence 489999888878888999999999999998866554 343443 2332 368999998765
No 22
>cd01536 PBP1_ABC_sugar_binding_like Periplasmic sugar-binding domain of active transport systems that are members of the type I periplasmic binding protein (PBP1) superfamily. Periplasmic sugar-binding domain of active transport systems that are members of the type I periplasmic binding protein (PBP1) superfamily. The members of this family function as the primary receptors for chemotaxis and transport of many sugar based solutes in bacteria and archaea. The sugar binding domain is also homologous to the ligand-binding domain of eukaryotic receptors such as glutamate receptor (GluR) and DNA-binding transcriptional repressors such as LacI and GalR. Moreover, this periplasmic binding domain, also known as Venus flytrap domain, undergoes transition from an open to a closed conformational state upon the binding of ligands such as lactose, ribose, fructose, xylose, arabinose, galactose/glucose, and other sugars. This family also includes the periplasmic binding domain of autoinducer-2 (AI-2
Probab=65.47 E-value=12 Score=34.80 Aligned_cols=75 Identities=21% Similarity=0.181 Sum_probs=49.4
Q ss_pred eEEEEEcCCcccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHHH-------HcCCCCCCEEEEecCCCcc----cccccC
Q 014264 210 IIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAK-------LANFPECDVFINVSCAQTA----LLDSKE 278 (427)
Q Consensus 210 ~iGIlvgTl~~q~~~~~i~~l~~li~~~GKK~y~~~vgkln~aK-------LaNF~eiD~fVlvaCPr~s----i~d~~~ 278 (427)
+||+|+....-..+..+++.+++.++++|.+.-++.... ++++ |.+- ++|.+++.++.... +...++
T Consensus 1 ~ig~i~p~~~~~~~~~~~~~~~~~a~~~g~~~~~~~~~~-~~~~~~~~~~~l~~~-~vdgvi~~~~~~~~~~~~~~~l~~ 78 (267)
T cd01536 1 KIGLVVPSLNNPFWQAMNKGAEAAAKELGVELIVLDAQN-DVSKQIQQIEDLIAQ-GVDGIIISPVDSAALTPALKKANA 78 (267)
T ss_pred CEEEEeccccCHHHHHHHHHHHHHHHhcCceEEEECCCC-CHHHHHHHHHHHHHc-CCCEEEEeCCCchhHHHHHHHHHH
Confidence 578888766666778899999999998887766655543 5543 3333 68999888775332 222334
Q ss_pred CCCcccCH
Q 014264 279 FLAPVITP 286 (427)
Q Consensus 279 f~kPvlTP 286 (427)
...|+|+.
T Consensus 79 ~~ip~V~~ 86 (267)
T cd01536 79 AGIPVVTV 86 (267)
T ss_pred CCCcEEEe
Confidence 45676654
No 23
>PF00532 Peripla_BP_1: Periplasmic binding proteins and sugar binding domain of LacI family; InterPro: IPR001761 This family includes the periplasmic binding proteins, and the LacI family transcriptional regulators. The periplasmic binding proteins are the primary receptors for chemotaxis and transport of many sugar based solutes. The LacI family of proteins consist of transcriptional regulators related to the lac repressor. In this case, generally the sugar binding domain binds a sugar which changes the DNA binding activity of the repressor domain (lacI) [, ].; PDB: 1BAP_A 7ABP_A 6ABP_A 1ABF_A 5ABP_A 2WRZ_B 9ABP_A 1APB_A 1ABE_A 8ABP_A ....
Probab=65.46 E-value=8 Score=37.83 Aligned_cols=61 Identities=20% Similarity=0.236 Sum_probs=48.4
Q ss_pred CeEEEEEcCCcccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHHH------HcCCCCCCEEEEecCCCc
Q 014264 209 NIIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAK------LANFPECDVFINVSCAQT 271 (427)
Q Consensus 209 ~~iGIlvgTl~~q~~~~~i~~l~~li~~~GKK~y~~~vgkln~aK------LaNF~eiD~fVlvaCPr~ 271 (427)
++||+|+..+.-..+.++++-+.+.++++|....++..++= +++ |.+- .+|.+|+.+....
T Consensus 2 ~~IGvivp~~~npff~~ii~gIe~~a~~~Gy~l~l~~t~~~-~~~e~~i~~l~~~-~vDGiI~~s~~~~ 68 (279)
T PF00532_consen 2 KTIGVIVPDISNPFFAEIIRGIEQEAREHGYQLLLCNTGDD-EEKEEYIELLLQR-RVDGIILASSEND 68 (279)
T ss_dssp CEEEEEESSSTSHHHHHHHHHHHHHHHHTTCEEEEEEETTT-HHHHHHHHHHHHT-TSSEEEEESSSCT
T ss_pred CEEEEEECCCCCcHHHHHHHHHHHHHHHcCCEEEEecCCCc-hHHHHHHHHHHhc-CCCEEEEecccCC
Confidence 68999999999999999999999999999998877766643 332 2232 6999999955444
No 24
>cd06315 PBP1_ABC_sugar_binding_like_6 Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems. Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily, which consists of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis.
Probab=65.43 E-value=9 Score=36.86 Aligned_cols=76 Identities=17% Similarity=0.090 Sum_probs=51.8
Q ss_pred CeEEEEEcCCcccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHHHH----cCC--CCCCEEEEecCCCcc----cccccC
Q 014264 209 NIIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKL----ANF--PECDVFINVSCAQTA----LLDSKE 278 (427)
Q Consensus 209 ~~iGIlvgTl~~q~~~~~i~~l~~li~~~GKK~y~~~vgkln~aKL----aNF--~eiD~fVlvaCPr~s----i~d~~~ 278 (427)
++||+|+.++.-..+..+++.+.+.+++.|....+. -+.-++++. .+| ..+|.+|++++.... +...++
T Consensus 1 ~~ig~i~~~~~~~~~~~~~~gi~~~a~~~gy~~~~~-~~~~~~~~~~~~i~~l~~~~vdgiil~~~~~~~~~~~~~~~~~ 79 (280)
T cd06315 1 KNIIFVASDLKNGGILGVGEGVREAAKAIGWNLRIL-DGRGSEAGQAAALNQAIALKPDGIVLGGVDAAELQAELELAQK 79 (280)
T ss_pred CeEEEEecccCCcHHHHHHHHHHHHHHHcCcEEEEE-CCCCCHHHHHHHHHHHHHcCCCEEEEcCCCHHHHHHHHHHHHH
Confidence 579999999888788899999999999999765443 344455542 222 269999999865332 122334
Q ss_pred CCCcccC
Q 014264 279 FLAPVIT 285 (427)
Q Consensus 279 f~kPvlT 285 (427)
...|+|.
T Consensus 80 ~~iPvV~ 86 (280)
T cd06315 80 AGIPVVG 86 (280)
T ss_pred CCCCEEE
Confidence 4567654
No 25
>PRK07188 nicotinate phosphoribosyltransferase; Provisional
Probab=65.31 E-value=14 Score=37.96 Aligned_cols=42 Identities=17% Similarity=0.360 Sum_probs=37.1
Q ss_pred CcHHHHHHHHHHHHHcC-CcEEEEEcCCCCHHHHcCCC----CCCEE
Q 014264 222 GYLHMIHQMKELITKAG-KKAYTLVMGKPNPAKLANFP----ECDVF 263 (427)
Q Consensus 222 ~~~~~i~~l~~li~~~G-KK~y~~~vgkln~aKLaNF~----eiD~f 263 (427)
....+++++++.|.++| .++-+++.|.+|+++++.|. .||+|
T Consensus 261 ~~~~l~~~vr~~Ld~~g~~~vkI~aSgGine~~I~~~~~~g~piD~~ 307 (352)
T PRK07188 261 VNPELIKALRKALDENGGKHVKIIVSSGFDAKKIREFEAQNVPVDIY 307 (352)
T ss_pred ccHHHHHHHHHHHhhCCCCCcEEEEeCCCCHHHHHHHHHcCCCccEE
Confidence 45899999999999999 88889999999999999984 26777
No 26
>cd06277 PBP1_LacI_like_1 Ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. This group includes the ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. The LacI-GalR family repressors 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 affinity of the repressor.
Probab=64.23 E-value=20 Score=33.79 Aligned_cols=73 Identities=19% Similarity=0.227 Sum_probs=51.0
Q ss_pred EEEEEcC---CcccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHH-------HHcCCCCCCEEEEecCCCcccc-cccCC
Q 014264 211 IGVLVGT---LGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPA-------KLANFPECDVFINVSCAQTALL-DSKEF 279 (427)
Q Consensus 211 iGIlvgT---l~~q~~~~~i~~l~~li~~~GKK~y~~~vgkln~a-------KLaNF~eiD~fVlvaCPr~si~-d~~~f 279 (427)
||+|+.+ ++-..+..+++.+++.+++.|.+..+...+. +.+ .|.+ ..+|.+|+.++...+.. ..++-
T Consensus 2 vgv~~~~~~~~~~~~~~~~~~~i~~~~~~~g~~~~~~~~~~-~~~~~~~~~~~l~~-~~vdgiii~~~~~~~~~~~l~~~ 79 (268)
T cd06277 2 IGLIASKRILNSPAFYSEIYRAIEEEAKKYGYNLILKFVSD-EDEEEFELPSFLED-GKVDGIILLGGISTEYIKEIKEL 79 (268)
T ss_pred eEEEEeccccccCCcHHHHHHHHHHHHHHcCCEEEEEeCCC-ChHHHHHHHHHHHH-CCCCEEEEeCCCChHHHHHHhhc
Confidence 7999988 6777788999999999999999887777663 332 1222 26999999887654432 22334
Q ss_pred CCcccC
Q 014264 280 LAPVIT 285 (427)
Q Consensus 280 ~kPvlT 285 (427)
..|+|+
T Consensus 80 ~ipvV~ 85 (268)
T cd06277 80 GIPFVL 85 (268)
T ss_pred CCCEEE
Confidence 457664
No 27
>PF04392 ABC_sub_bind: ABC transporter substrate binding protein; InterPro: IPR007487 ABC transporters belong to the ATP-Binding Cassette (ABC) superfamily, which uses the hydrolysis of ATP to energize diverse biological systems. ABC transporters are minimally constituted of two conserved regions: a highly conserved ATP binding cassette (ABC) and a less conserved transmembrane domain (TMD). These regions can be found on the same protein or on two different ones. Most ABC transporters function as a dimer and therefore are constituted of four domains, two ABC modules and two TMDs. This family contains many hypothetical proteins and some ABC transporter substrate binding proteins.; PDB: 3LFT_A 3LKV_A.
Probab=63.82 E-value=9.9 Score=37.41 Aligned_cols=113 Identities=19% Similarity=0.260 Sum_probs=68.7
Q ss_pred HHHHHHHHHHHHHh-cCCeEEEEEcCCcccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCH--HHHcCC-CCCCEEEEecC
Q 014264 193 KILKRRYYLVEKAK-DANIIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNP--AKLANF-PECDVFINVSC 268 (427)
Q Consensus 193 r~L~rRy~~I~ka~-~A~~iGIlvgTl~~q~~~~~i~~l~~li~~~GKK~y~~~vgkln~--aKLaNF-~eiD~fVlvaC 268 (427)
..+.++..++.+.. +++++|+|...-. .+....++.+++..++.|.+.+.+.+...+. ..+..+ ..+|++++...
T Consensus 115 ~~~~~~l~l~~~l~P~~k~igvl~~~~~-~~~~~~~~~~~~~a~~~g~~l~~~~v~~~~~~~~~~~~l~~~~da~~~~~~ 193 (294)
T PF04392_consen 115 PPIEKQLELIKKLFPDAKRIGVLYDPSE-PNSVAQIEQLRKAAKKLGIELVEIPVPSSEDLEQALEALAEKVDALYLLPD 193 (294)
T ss_dssp --HHHHHHHHHHHSTT--EEEEEEETT--HHHHHHHHHHHHHHHHTT-EEEEEEESSGGGHHHHHHHHCTT-SEEEE-S-
T ss_pred cCHHHHHHHHHHhCCCCCEEEEEecCCC-ccHHHHHHHHHHHHHHcCCEEEEEecCcHhHHHHHHHHhhccCCEEEEECC
Confidence 45677888888886 7899999998643 4567788999999999999999999887663 223333 35898888754
Q ss_pred CCcc-----cc-cccCCCCcccCHHHHHHhhCCCCccccceeeccccc
Q 014264 269 AQTA-----LL-DSKEFLAPVITPFEAMLAFGRGTQWTGAYVMEFRDL 310 (427)
Q Consensus 269 Pr~s-----i~-d~~~f~kPvlTP~El~~aL~~~~~w~g~y~~Df~~~ 310 (427)
+-.. +. -..+...||++.++..+.-| .-+-|..|+.++
T Consensus 194 ~~~~~~~~~i~~~~~~~~iPv~~~~~~~v~~G----al~~~~~~~~~~ 237 (294)
T PF04392_consen 194 NLVDSNFEAILQLANEAKIPVFGSSDFYVKAG----ALGGYSVDYYEQ 237 (294)
T ss_dssp HHHHHTHHHHHHHCCCTT--EEESSHHHHCTT-----SEEEE--HHHH
T ss_pred cchHhHHHHHHHHHHhcCCCEEECCHHHhcCC----cEEEEccCHHHH
Confidence 3111 11 13567788888887766533 235566777665
No 28
>TIGR02405 trehalos_R_Ecol trehalose operon repressor, proteobacterial. This family consists of repressors of the LacI family typically associated with trehalose utilization operons. Trehalose is imported as trehalose-6-phosphate and then hydrolyzed by alpha,alpha-phosphotrehalase to glucose and glucose-6-P. This family includes repressors mostly from Gammaproteobacteria and does not include the GntR family TreR of Bacillus subtilis
Probab=63.53 E-value=17 Score=35.60 Aligned_cols=63 Identities=14% Similarity=0.156 Sum_probs=44.3
Q ss_pred hcCCeEEEEEcCCcccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHHHHc----CC--CCCCEEEEecCC
Q 014264 206 KDANIIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKLA----NF--PECDVFINVSCA 269 (427)
Q Consensus 206 ~~A~~iGIlvgTl~~q~~~~~i~~l~~li~~~GKK~y~~~vgkln~aKLa----NF--~eiD~fVlvaCP 269 (427)
+..++||+|+..+.--.+..+++.+.+.++++|....++. ..-++++.. .+ ..+|.+|+++..
T Consensus 57 ~~~~~Ig~i~~~~~~~~~~~~~~~i~~~~~~~gy~~~i~~-~~~~~~~~~~~~~~l~~~~vdGvIi~~~~ 125 (311)
T TIGR02405 57 GSDKVVAVIVSRLDSPSENLAVSGMLPVFYTAGYDPIIME-SQFSPQLTNEHLSVLQKRNVDGVILFGFT 125 (311)
T ss_pred CCCCEEEEEeCCcccccHHHHHHHHHHHHHHCCCeEEEec-CCCChHHHHHHHHHHHhcCCCEEEEeCCC
Confidence 4557999999876656677899999999999998865543 334444321 11 259999998653
No 29
>TIGR01753 flav_short flavodoxin, short chain. Flavodoxins are small redox-active proteins with a flavin mononucleotide (FMN) prosthetic group. They can act in nitrogen fixation by nitrogenase, in sulfite reduction, and light-dependent NADP+ reduction in during photosynthesis, among other roles. This model describes the short chain type. Many of these are involved in sulfite reduction.
Probab=63.43 E-value=27 Score=29.77 Aligned_cols=55 Identities=16% Similarity=0.284 Sum_probs=43.7
Q ss_pred EEEEEcCCcccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHHHHcCCCCCCEEEEecCCC
Q 014264 211 IGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKLANFPECDVFINVSCAQ 270 (427)
Q Consensus 211 iGIlvgTl~~q~~~~~i~~l~~li~~~GKK~y~~~vgkln~aKLaNF~eiD~fVlvaCPr 270 (427)
|-|+.+|.. -+...+++.|.+.+++.|.++-++-+.+.++.+|.+ .|.+|+ ++|-
T Consensus 1 v~Iiy~S~t-GnT~~~A~~i~~~~~~~g~~v~~~~~~~~~~~~l~~---~d~iil-gspt 55 (140)
T TIGR01753 1 ILIVYASMT-GNTEEMANIIAEGLKEAGAEVDLLEVADADAEDLLS---YDAVLL-GCST 55 (140)
T ss_pred CEEEEECCC-cHHHHHHHHHHHHHHhcCCeEEEEEcccCCHHHHhc---CCEEEE-EcCC
Confidence 357888864 578899999999999999999999999999988866 466544 4443
No 30
>cd06310 PBP1_ABC_sugar_binding_like_2 Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems. Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily, which consists of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis.
Probab=62.46 E-value=9.4 Score=36.14 Aligned_cols=76 Identities=14% Similarity=0.068 Sum_probs=50.0
Q ss_pred eEEEEEcCCcccCcHHHHHHHHHHHHHcCCcEEEEEcC-CCCHHHHc----CC--CCCCEEEEecCCCcccc----cccC
Q 014264 210 IIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMG-KPNPAKLA----NF--PECDVFINVSCAQTALL----DSKE 278 (427)
Q Consensus 210 ~iGIlvgTl~~q~~~~~i~~l~~li~~~GKK~y~~~vg-kln~aKLa----NF--~eiD~fVlvaCPr~si~----d~~~ 278 (427)
+||+|+.++.-..+..+++.+++.++++|.+..++..+ .=++++.. ++ ..+|.+|+.++...... ....
T Consensus 1 ~Igvi~~~~~~~~~~~~~~g~~~~~~~~g~~~~~~~~~~~~~~~~~~~~i~~l~~~~vdgvii~~~~~~~~~~~l~~~~~ 80 (273)
T cd06310 1 KIALVPKGTTSDFWQAVKAGAEAAAKELGVKVTFQGPASETDVAGQVNLLENAIARGPDAILLAPTDAKALVPPLKEAKD 80 (273)
T ss_pred CeEEEecCCCcHHHHHHHHHHHHHHHHcCCEEEEecCccCCCHHHHHHHHHHHHHhCCCEEEEcCCChhhhHHHHHHHHH
Confidence 48999998877778899999999999999876655432 23544321 11 26899998877653222 1233
Q ss_pred CCCcccC
Q 014264 279 FLAPVIT 285 (427)
Q Consensus 279 f~kPvlT 285 (427)
...|+|+
T Consensus 81 ~~ipvV~ 87 (273)
T cd06310 81 AGIPVVL 87 (273)
T ss_pred CCCCEEE
Confidence 4457665
No 31
>cd05569 PTS_IIB_fructose PTS_IIB_fructose: subunit IIB of enzyme II (EII) of the fructose-specific phosphoenolpyruvate:carbohydrate phosphotransferase system (PTS). In this system, EII (also referred to as FruAB) is a fructose-specific permease made up of two proteins (FruA and FruB) each containing 3 domains. The FruA protein contains two tandem nonidentical IIB domains and a C-terminal IIC transmembrane domain. Both IIB domains of FruA are included in this alignment. The FruB protein (also referred to as diphosphoryl transfer protein) contains a IIA domain, a domain of unknown function, and an Hpr-like domain called FPr (fructose-inducible HPr). This familiy also includes the IIB domains of several fructose-like PTS permeases including the Frv permease encoded by the frvABXR operon, the Frw permease encoded by the frwACBD operon, the Frx permease encoded by the hrsA gene, and the Fry permease encoded by the fryABC (ypdDGH) operon. FruAB takes up exogenous fructose, releasing the 1-p
Probab=62.04 E-value=31 Score=28.33 Aligned_cols=59 Identities=15% Similarity=0.144 Sum_probs=46.2
Q ss_pred EEEEEcCCcccCcHHHHHHHHHHHHHcCCcEEEEEc------CCCCHHHHcCCCCCCEEEEecCCCcc
Q 014264 211 IGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVM------GKPNPAKLANFPECDVFINVSCAQTA 272 (427)
Q Consensus 211 iGIlvgTl~~q~~~~~i~~l~~li~~~GKK~y~~~v------gkln~aKLaNF~eiD~fVlvaCPr~s 272 (427)
++|+.+.-|.....-+.+.|++.++++|.+.-+-.- +.++.+.++ +.|.+++++.....
T Consensus 2 ~~i~ac~~G~a~s~laa~~L~~aa~~~g~~~~ve~~~~~g~~~~l~~~~i~---~Ad~vi~~~~~~~~ 66 (96)
T cd05569 2 VAVTACPTGIAHTYMAAEALEKAAKKLGWEIKVETQGSLGIENELTAEDIA---EADAVILAADVPVD 66 (96)
T ss_pred EEEEECCCchhHHHHHHHHHHHHHHHCCCeEEEEEecCcCccCcCCHHHHh---hCCEEEEecCCCCc
Confidence 678888888888899999999999999999764433 345555554 46999999998753
No 32
>cd06283 PBP1_RegR_EndR_KdgR_like Ligand-binding domain of DNA transcription repressor RegR and other putative regulators such as KdgR and EndR. Ligand-binding domain of DNA transcription repressor RegR and other putative regulators such as KdgR and EndR, all of which are members of the LacI-GalR family of bacterial transcription regulators. RegR regulates bacterial competence and the expression of virulence factors, including hyaluronidase. The LacI-GalR family repressors 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 b
Probab=61.50 E-value=26 Score=32.71 Aligned_cols=74 Identities=16% Similarity=0.230 Sum_probs=50.1
Q ss_pred eEEEEEcCCcccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHHH-------HcCCCCCCEEEEecCCCcc--cccccCCC
Q 014264 210 IIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAK-------LANFPECDVFINVSCAQTA--LLDSKEFL 280 (427)
Q Consensus 210 ~iGIlvgTl~~q~~~~~i~~l~~li~~~GKK~y~~~vgkln~aK-------LaNF~eiD~fVlvaCPr~s--i~d~~~f~ 280 (427)
+||+|+....-..+..+++.+++.+++.|....++.. +-+++. |.+- .+|.+++.++.... +...++-.
T Consensus 1 ~igvi~~~~~~~~~~~~~~~i~~~a~~~g~~~~~~~~-~~~~~~~~~~~~~l~~~-~~dgiii~~~~~~~~~l~~~~~~~ 78 (267)
T cd06283 1 LIGVIVADITNPFSSLVLKGIEDVCRAHGYQVLVCNS-DNDPEKEKEYLESLLAY-QVDGLIVNPTGNNKELYQRLAKNG 78 (267)
T ss_pred CEEEEecCCccccHHHHHHHHHHHHHHcCCEEEEEcC-CCCHHHHHHHHHHHHHc-CcCEEEEeCCCCChHHHHHHhcCC
Confidence 5899998887788889999999999999977654443 334443 3332 68999998764332 12223445
Q ss_pred CcccC
Q 014264 281 APVIT 285 (427)
Q Consensus 281 kPvlT 285 (427)
.|||+
T Consensus 79 ipvV~ 83 (267)
T cd06283 79 KPVVL 83 (267)
T ss_pred CCEEE
Confidence 57665
No 33
>cd01542 PBP1_TreR_like Ligand-binding domain of DNA transcription repressor specific for trehalose (TreR) which is a member of the LacI-GalR family of bacterial transcription regulators. Ligand-binding domain of DNA transcription repressor specific for trehalose (TreR) which is a member of the LacI-GalR family of bacterial transcription regulators. The ligand-binding domain of TreR is structurally homologous to the periplasmic sugar-binding domain of ABC-type transporters and both domains contain the type I periplasmic binding protein-like fold. The LacI-GalR family repressors 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 type I periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding wh
Probab=61.42 E-value=16 Score=34.21 Aligned_cols=75 Identities=20% Similarity=0.216 Sum_probs=51.3
Q ss_pred eEEEEEcCCcccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHHH-------HcCCCCCCEEEEecCCCc-cc-ccccCCC
Q 014264 210 IIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAK-------LANFPECDVFINVSCAQT-AL-LDSKEFL 280 (427)
Q Consensus 210 ~iGIlvgTl~~q~~~~~i~~l~~li~~~GKK~y~~~vgkln~aK-------LaNF~eiD~fVlvaCPr~-si-~d~~~f~ 280 (427)
+||+|+....-..+..+++.+++.+++.|.+..++.. .-++++ |.+ ..+|++|++++... .+ ...++..
T Consensus 1 ~igvv~~~~~~~~~~~~~~gi~~~~~~~g~~~~~~~~-~~~~~~~~~~i~~l~~-~~~dgii~~~~~~~~~~~~~~~~~~ 78 (259)
T cd01542 1 LIGVIVPRLDSFSTSRTVKGILAALYENGYQMLLMNT-NFSIEKEIEALELLAR-QKVDGIILLATTITDEHREAIKKLN 78 (259)
T ss_pred CeEEEecCCccchHHHHHHHHHHHHHHCCCEEEEEeC-CCCHHHHHHHHHHHHh-cCCCEEEEeCCCCCHHHHHHHhcCC
Confidence 4899998887677789999999999999988755543 445543 233 36999999876432 11 2234455
Q ss_pred CcccCH
Q 014264 281 APVITP 286 (427)
Q Consensus 281 kPvlTP 286 (427)
.|||+-
T Consensus 79 ipvv~~ 84 (259)
T cd01542 79 VPVVVV 84 (259)
T ss_pred CCEEEE
Confidence 687753
No 34
>cd06281 PBP1_LacI_like_5 Ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. This group includes the ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. The LacI-GalR family repressors 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 affinity of the repressor.
Probab=60.77 E-value=17 Score=34.36 Aligned_cols=76 Identities=16% Similarity=0.205 Sum_probs=50.5
Q ss_pred eEEEEEcCCcccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHHHHc----CC--CCCCEEEEecCCCcc--cc-cccCCC
Q 014264 210 IIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKLA----NF--PECDVFINVSCAQTA--LL-DSKEFL 280 (427)
Q Consensus 210 ~iGIlvgTl~~q~~~~~i~~l~~li~~~GKK~y~~~vgkln~aKLa----NF--~eiD~fVlvaCPr~s--i~-d~~~f~ 280 (427)
+||+|+....-..+..+++.+.+.+++.|....+. ...-++++.. .+ ..+|.+++.+|.... +. ..++..
T Consensus 1 ~Igvv~~~~~~~~~~~~~~~i~~~a~~~g~~~~~~-~~~~~~~~~~~~i~~l~~~~vdgii~~~~~~~~~~~~~~~~~~~ 79 (269)
T cd06281 1 TIGCLVSDITNPLLAQLFSGAEDRLRAAGYSLLIA-NSLNDPERELEILRSFEQRRMDGIIIAPGDERDPELVDALASLD 79 (269)
T ss_pred CEEEEecCCccccHHHHHHHHHHHHHHcCCEEEEE-eCCCChHHHHHHHHHHHHcCCCEEEEecCCCCcHHHHHHHHhCC
Confidence 58999988887888899999999999999886544 3444554321 12 269999999885321 11 123334
Q ss_pred CcccCH
Q 014264 281 APVITP 286 (427)
Q Consensus 281 kPvlTP 286 (427)
.|||+-
T Consensus 80 ipvV~i 85 (269)
T cd06281 80 LPIVLL 85 (269)
T ss_pred CCEEEE
Confidence 576554
No 35
>PRK10014 DNA-binding transcriptional repressor MalI; Provisional
Probab=60.76 E-value=26 Score=34.54 Aligned_cols=79 Identities=20% Similarity=0.295 Sum_probs=54.0
Q ss_pred HhcCCeEEEEEcCCcccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHHH-------HcCCCCCCEEEEecCCCcc---cc
Q 014264 205 AKDANIIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAK-------LANFPECDVFINVSCAQTA---LL 274 (427)
Q Consensus 205 a~~A~~iGIlvgTl~~q~~~~~i~~l~~li~~~GKK~y~~~vgkln~aK-------LaNF~eiD~fVlvaCPr~s---i~ 274 (427)
.+..++||+|+..+.-..+..+++.+.+.++++|...+++..+ -++++ |.+ ..+|.+++.+..... +.
T Consensus 61 ~~~~~~Igvv~~~~~~~~~~~i~~gi~~~a~~~g~~~~~~~~~-~~~~~~~~~~~~l~~-~~vdgiIi~~~~~~~~~~~~ 138 (342)
T PRK10014 61 GGQSGVIGLIVRDLSAPFYAELTAGLTEALEAQGRMVFLLQGG-KDGEQLAQRFSTLLN-QGVDGVVIAGAAGSSDDLRE 138 (342)
T ss_pred cCCCCEEEEEeCCCccchHHHHHHHHHHHHHHcCCEEEEEeCC-CCHHHHHHHHHHHHh-CCCCEEEEeCCCCCcHHHHH
Confidence 3456799999998877788899999999999999877655443 34432 323 269999998765321 11
Q ss_pred cccCCCCcccC
Q 014264 275 DSKEFLAPVIT 285 (427)
Q Consensus 275 d~~~f~kPvlT 285 (427)
..++...|+|+
T Consensus 139 ~l~~~~iPvV~ 149 (342)
T PRK10014 139 MAEEKGIPVVF 149 (342)
T ss_pred HHhhcCCCEEE
Confidence 23445567775
No 36
>PRK10653 D-ribose transporter subunit RbsB; Provisional
Probab=60.39 E-value=11 Score=36.62 Aligned_cols=63 Identities=17% Similarity=0.199 Sum_probs=45.8
Q ss_pred hcCCeEEEEEcCCcccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHHHHc----CC--CCCCEEEEecCC
Q 014264 206 KDANIIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKLA----NF--PECDVFINVSCA 269 (427)
Q Consensus 206 ~~A~~iGIlvgTl~~q~~~~~i~~l~~li~~~GKK~y~~~vgkln~aKLa----NF--~eiD~fVlvaCP 269 (427)
++.++||+|+.++.-..+..+++.+++.++++|.+..++..+ -++++.. ++ ..+|+.++.++.
T Consensus 24 ~~~~~I~vi~~~~~~~f~~~~~~~i~~~~~~~G~~~~~~~~~-~d~~~~~~~~~~l~~~~~dgiii~~~~ 92 (295)
T PRK10653 24 MAKDTIALVVSTLNNPFFVSLKDGAQKEADKLGYNLVVLDSQ-NNPAKELANVQDLTVRGTKILLINPTD 92 (295)
T ss_pred ccCCeEEEEecCCCChHHHHHHHHHHHHHHHcCCeEEEecCC-CCHHHHHHHHHHHHHcCCCEEEEcCCC
Confidence 467899999998887788899999999999999887665443 2343322 22 258988887654
No 37
>PRK11303 DNA-binding transcriptional regulator FruR; Provisional
Probab=59.56 E-value=26 Score=34.34 Aligned_cols=62 Identities=15% Similarity=0.259 Sum_probs=45.4
Q ss_pred hcCCeEEEEEcCCcccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHHH-------HcCCCCCCEEEEecCC
Q 014264 206 KDANIIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAK-------LANFPECDVFINVSCA 269 (427)
Q Consensus 206 ~~A~~iGIlvgTl~~q~~~~~i~~l~~li~~~GKK~y~~~vgkln~aK-------LaNF~eiD~fVlvaCP 269 (427)
+..++||+|+..+.-..+..+++.+.+.++++|....++..+. ++++ |.+- .+|.+++.++.
T Consensus 59 ~~~~~Igvv~~~~~~~~~~~l~~gi~~~~~~~g~~~~~~~~~~-~~~~~~~~~~~l~~~-~vdgiIi~~~~ 127 (328)
T PRK11303 59 GRTRSIGLIIPDLENTSYARIAKYLERQARQRGYQLLIACSDD-QPDNEMRCAEHLLQR-QVDALIVSTSL 127 (328)
T ss_pred CCCceEEEEeCCCCCchHHHHHHHHHHHHHHcCCEEEEEeCCC-CHHHHHHHHHHHHHc-CCCEEEEcCCC
Confidence 3467999999887777788999999999999998876654432 3332 2232 69999997763
No 38
>PRK12321 cobN cobaltochelatase subunit CobN; Reviewed
Probab=59.46 E-value=6 Score=46.36 Aligned_cols=28 Identities=36% Similarity=0.805 Sum_probs=0.0
Q ss_pred cccCCcEEEEec-CC---------------CCCCC--CCCCeEEEc
Q 014264 17 SHVDADCVIHYG-HT---------------CLSPT--STLPAFFVF 44 (427)
Q Consensus 17 ~hv~aD~iVHyG-ha---------------Cls~~--~~lpv~YVf 44 (427)
++++||+|||+| |- |.+.. ..+|.+|.|
T Consensus 522 ~~~~ADAiiH~GtHGtlEwLPGK~vgLS~~c~Pd~lig~lP~iYpy 567 (1100)
T PRK12321 522 REVGVDALIHLGAHGTLEWLPGKAVALSPACWPEALTGALPVIYPF 567 (1100)
T ss_pred hhcCCCEEEECCCCcccccCCCccccCCcccChHHHhCCCCEEEEE
No 39
>cd06290 PBP1_LacI_like_9 Ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. This group includes the ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. The LacI-GalR family repressors 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 affinity of the repressor.
Probab=58.92 E-value=18 Score=34.00 Aligned_cols=59 Identities=19% Similarity=0.233 Sum_probs=43.6
Q ss_pred eEEEEEcCCcccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHHHHc----CC--CCCCEEEEecCC
Q 014264 210 IIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKLA----NF--PECDVFINVSCA 269 (427)
Q Consensus 210 ~iGIlvgTl~~q~~~~~i~~l~~li~~~GKK~y~~~vgkln~aKLa----NF--~eiD~fVlvaCP 269 (427)
+||+|+..+.-..+..+++.+.+.+++.|....++. ..-++++.. ++ ..+|.+++.+|.
T Consensus 1 ~i~vi~~~~~~~~~~~~~~gi~~~~~~~gy~~~~~~-~~~~~~~~~~~i~~l~~~~~dgiii~~~~ 65 (265)
T cd06290 1 TIGVLTQDFASPFYGRILKGMERGLNGSGYSPIIAT-GHWNQSRELEALELLKSRRVDALILLGGD 65 (265)
T ss_pred CEEEEECCCCCchHHHHHHHHHHHHHHCCCEEEEEe-CCCCHHHHHHHHHHHHHCCCCEEEEeCCC
Confidence 589999888877888899999999999997765543 445664332 22 158999999875
No 40
>cd01545 PBP1_SalR Ligand-binding domain of DNA transcription repressor SalR, a member of the LacI-GalR family of bacterial transcription regulators. Ligand-binding domain of DNA transcription repressor SalR, a member of the LacI-GalR family of bacterial transcription regulators. The SalR binds to glucose based compound Salicin which is chemically related to aspirin. The ligand-binding of SalR is structurally homologous to the periplasmic sugar-binding domain of ABC-transporters and both domains contain the type I periplasmic binding protein-like fold. The LacI-GalR family repressors 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 type I periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand bind
Probab=58.51 E-value=27 Score=32.75 Aligned_cols=59 Identities=15% Similarity=0.078 Sum_probs=44.4
Q ss_pred eEEEEEcCCcccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCH-------HHHcCCCCCCEEEEecCC
Q 014264 210 IIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNP-------AKLANFPECDVFINVSCA 269 (427)
Q Consensus 210 ~iGIlvgTl~~q~~~~~i~~l~~li~~~GKK~y~~~vgkln~-------aKLaNF~eiD~fVlvaCP 269 (427)
+||+|+....-..+..+++-+++.+++.|....++..+.-.+ ..|.+ ..+|+++++.+-
T Consensus 1 ~I~vi~~~~~~~~~~~~~~gi~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~l~~-~~vdgiii~~~~ 66 (270)
T cd01545 1 LIGLLYDNPSPGYVSEIQLGALDACRDTGYQLVIEPCDSGSPDLAERVRALLQR-SRVDGVILTPPL 66 (270)
T ss_pred CEEEEEcCCCcccHHHHHHHHHHHHHhCCCeEEEEeCCCCchHHHHHHHHHHHH-CCCCEEEEeCCC
Confidence 589999888878888999999999999998887776654332 11222 368999998774
No 41
>PRK07308 flavodoxin; Validated
Probab=58.43 E-value=43 Score=29.18 Aligned_cols=57 Identities=5% Similarity=0.105 Sum_probs=44.5
Q ss_pred eEEEEEcCCcccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHHHHcCCCCCCEEEEecCCCc
Q 014264 210 IIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKLANFPECDVFINVSCAQT 271 (427)
Q Consensus 210 ~iGIlvgTl~~q~~~~~i~~l~~li~~~GKK~y~~~vgkln~aKLaNF~eiD~fVlvaCPr~ 271 (427)
.+-|+.+|.. -+...+++.|.+.+++.|..+-++-+.+..+..|.. .|++++ +||-.
T Consensus 3 ~~~IvY~S~t-GnTe~iA~~ia~~l~~~g~~~~~~~~~~~~~~~l~~---~d~vi~-g~~t~ 59 (146)
T PRK07308 3 LAKIVYASMT-GNTEEIADIVADKLRELGHDVDVDECTTVDASDFED---ADIAIV-ATYTY 59 (146)
T ss_pred eEEEEEECCC-chHHHHHHHHHHHHHhCCCceEEEecccCCHhHhcc---CCEEEE-EeCcc
Confidence 4778999966 467899999999999999988888888887776644 466555 88765
No 42
>cd06291 PBP1_Qymf_like Ligand binding domain of the lacI-like transcription regulator from a novel metal-reducing bacterium Alkaliphilus Metalliredigens (strain Qymf) and its close homologs. This group includes the ligand binding domain of the lacI-like transcription regulator from a novel metal-reducing bacterium Alkaliphilus Metalliredigens (strain Qymf) and its close homologs. Qymf is a strict anaerobe that could be grown in the presence of borax and its cells are straight rods that produce endospores. This group is a member of 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
Probab=58.41 E-value=25 Score=33.02 Aligned_cols=59 Identities=19% Similarity=0.266 Sum_probs=42.3
Q ss_pred eEEEEEcCCcccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHHHHcCC------CCCCEEEEecCC
Q 014264 210 IIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKLANF------PECDVFINVSCA 269 (427)
Q Consensus 210 ~iGIlvgTl~~q~~~~~i~~l~~li~~~GKK~y~~~vgkln~aKLaNF------~eiD~fVlvaCP 269 (427)
+||+|+..+....+..+++.+++.+++.|.+..++..+ -++++-..+ ..+|++|+.++.
T Consensus 1 ~I~vi~~~~~~~~~~~~~~gi~~~~~~~g~~~~~~~~~-~~~~~~~~~i~~~~~~~~dgiii~~~~ 65 (265)
T cd06291 1 LIGLIVPTISNPFFSELARAVEKELYKKGYKLILCNSD-NDPEKEREYLEMLRQNQVDGIIAGTHN 65 (265)
T ss_pred CEEEEECCCCChhHHHHHHHHHHHHHHCCCeEEEecCC-ccHHHHHHHHHHHHHcCCCEEEEecCC
Confidence 58999988887788899999999999999876544333 344432211 158999998874
No 43
>PRK14987 gluconate operon transcriptional regulator; Provisional
Probab=58.06 E-value=25 Score=34.67 Aligned_cols=79 Identities=19% Similarity=0.224 Sum_probs=51.8
Q ss_pred hcCCeEEEEEcCCcccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHHH----HcCC--CCCCEEEEecCCCcc--ccccc
Q 014264 206 KDANIIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAK----LANF--PECDVFINVSCAQTA--LLDSK 277 (427)
Q Consensus 206 ~~A~~iGIlvgTl~~q~~~~~i~~l~~li~~~GKK~y~~~vgkln~aK----LaNF--~eiD~fVlvaCPr~s--i~d~~ 277 (427)
+..++||+|+..+.-..+..+++.+.+.++++|.+..+...+ -++++ +.++ ..+|.+|+.++.... +....
T Consensus 61 ~~~~~Igvi~~~~~~~~~~~~~~gi~~~~~~~g~~~~~~~~~-~~~~~~~~~~~~~~~~~vdgiI~~~~~~~~~~~~~l~ 139 (331)
T PRK14987 61 ATSRAIGVLLPSLTNQVFAEVLRGIESVTDAHGYQTMLAHYG-YKPEMEQERLESMLSWNIDGLILTERTHTPRTLKMIE 139 (331)
T ss_pred CCCCEEEEEeCCCcchhHHHHHHHHHHHHHHCCCEEEEecCC-CCHHHHHHHHHHHHhcCCCEEEEcCCCCCHHHHHHHH
Confidence 456799999998877788899999999999999776554433 23322 2222 269999997653221 11123
Q ss_pred CCCCcccC
Q 014264 278 EFLAPVIT 285 (427)
Q Consensus 278 ~f~kPvlT 285 (427)
+...|+|+
T Consensus 140 ~~~iPvV~ 147 (331)
T PRK14987 140 VAGIPVVE 147 (331)
T ss_pred hCCCCEEE
Confidence 44567664
No 44
>cd01538 PBP1_ABC_xylose_binding Periplasmic xylose-binding component of the ABC-type transport systems that belong to a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein (PBP1) superfamily. Periplasmic xylose-binding component of the ABC-type transport systems that belong to a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein (PBP1) superfamily, which consists of two alpha/beta globular domains connected by a three-stranded hinge. This Venus flytrap-like domain undergoes a transition from an open to a closed conformational state upon ligand binding. Moreover, the periplasmic xylose-binding protein is homologous to the ligand-binding domain of eukaryotic receptors such as glutamate receptor (GluR) and DNA-binding transcriptional repressors such as LacI and GalR.
Probab=57.69 E-value=12 Score=36.25 Aligned_cols=75 Identities=19% Similarity=0.233 Sum_probs=47.5
Q ss_pred eEEEEEcCCcccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHHHHc----CC--CCCCEEEEecCCCcc----cccccCC
Q 014264 210 IIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKLA----NF--PECDVFINVSCAQTA----LLDSKEF 279 (427)
Q Consensus 210 ~iGIlvgTl~~q~~~~~i~~l~~li~~~GKK~y~~~vgkln~aKLa----NF--~eiD~fVlvaCPr~s----i~d~~~f 279 (427)
+||+|+....-..+..+++.+++.+++.|....++..+ -++++.. ++ ..+|.+|+++|.... +...++.
T Consensus 1 ~I~vi~~~~~~~~~~~~~~gi~~~a~~~g~~~~~~~~~-~~~~~~~~~i~~~~~~~vdgiii~~~~~~~~~~~l~~l~~~ 79 (288)
T cd01538 1 KIGLSLPTKTEERWIRDRPNFEAALKELGAEVIVQNAN-GDPAKQISQIENMIAKGVDVLVIAPVDGEALASAVEKAADA 79 (288)
T ss_pred CeEEEEeCCCcHHHHHHHHHHHHHHHHcCCEEEEECCC-CCHHHHHHHHHHHHHcCCCEEEEecCChhhHHHHHHHHHHC
Confidence 47888887766667788888888888888776655443 3555421 11 258888888875432 1122345
Q ss_pred CCcccC
Q 014264 280 LAPVIT 285 (427)
Q Consensus 280 ~kPvlT 285 (427)
..|||+
T Consensus 80 ~ipvV~ 85 (288)
T cd01538 80 GIPVIA 85 (288)
T ss_pred CCCEEE
Confidence 567665
No 45
>PRK06703 flavodoxin; Provisional
Probab=57.45 E-value=37 Score=29.76 Aligned_cols=55 Identities=9% Similarity=0.032 Sum_probs=43.2
Q ss_pred eEEEEEcCCcccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHHHHcCCCCCCEEEEecCC
Q 014264 210 IIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKLANFPECDVFINVSCA 269 (427)
Q Consensus 210 ~iGIlvgTl~~q~~~~~i~~l~~li~~~GKK~y~~~vgkln~aKLaNF~eiD~fVlvaCP 269 (427)
.+.|+.+|.. -+...+++.|.+.|.+.|.++-++-+.+..+..|.+ .|.+ +++||
T Consensus 3 kv~IiY~S~t-GnT~~iA~~ia~~l~~~g~~v~~~~~~~~~~~~l~~---~d~v-iigsp 57 (151)
T PRK06703 3 KILIAYASMS-GNTEDIADLIKVSLDAFDHEVVLQEMDGMDAEELLA---YDGI-ILGSY 57 (151)
T ss_pred eEEEEEECCC-chHHHHHHHHHHHHHhcCCceEEEehhhCCHHHHhc---CCcE-EEEEC
Confidence 5789999965 568899999999999999998888888887776654 4654 44555
No 46
>cd06299 PBP1_LacI_like_13 Ligand-binding domain of DNA-binding regulatory protein from Corynebacterium glutamicum which has a unique ability to produce significant amounts of L-glutamate directly from cheap sugar and ammonia. This group includes the ligand-binding domain of DNA-binding regulatory protein from Corynebacterium glutamicum which has a unique ability to produce significant amounts of L-glutamate directly from cheap sugar and ammonia. This regulatory protein is a member of the LacI-GalR family of bacterial transcription repressors. The LacI-GalR family repressors 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 trans
Probab=56.91 E-value=33 Score=32.12 Aligned_cols=60 Identities=22% Similarity=0.271 Sum_probs=43.8
Q ss_pred eEEEEEcCCcccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHHH-------HcCCCCCCEEEEecCCCc
Q 014264 210 IIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAK-------LANFPECDVFINVSCAQT 271 (427)
Q Consensus 210 ~iGIlvgTl~~q~~~~~i~~l~~li~~~GKK~y~~~vgkln~aK-------LaNF~eiD~fVlvaCPr~ 271 (427)
+||+|+....-..+..+++.+++.+++.|....++.... ++++ |.+- .+|.+++.++...
T Consensus 1 ~igvv~~~~~~~~~~~~~~gi~~~~~~~g~~~~~~~~~~-~~~~~~~~~~~l~~~-~vdgiIi~~~~~~ 67 (265)
T cd06299 1 TIGVIVPDIRNPYFASLATAIQDAASAAGYSTIIGNSDE-NPETENRYLDNLLSQ-RVDGIIVVPHEQS 67 (265)
T ss_pred CEEEEecCCCCccHHHHHHHHHHHHHHcCCEEEEEeCCC-CHHHHHHHHHHHHhc-CCCEEEEcCCCCC
Confidence 589999877666778899999999999998877765542 4432 3332 5899999887544
No 47
>cd06292 PBP1_LacI_like_10 Ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. This group includes the ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. The LacI-GalR family repressors 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 affinity of the repressor.
Probab=56.73 E-value=27 Score=32.90 Aligned_cols=57 Identities=12% Similarity=0.142 Sum_probs=42.2
Q ss_pred eEEEEEcCCcccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHHH-------HcCCCCCCEEEEecC
Q 014264 210 IIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAK-------LANFPECDVFINVSC 268 (427)
Q Consensus 210 ~iGIlvgTl~~q~~~~~i~~l~~li~~~GKK~y~~~vgkln~aK-------LaNF~eiD~fVlvaC 268 (427)
.||+|+..+.--.+..+++.+.+.+++.|....++.. .-++++ |.+ ..+|..+++++
T Consensus 1 ~Igvi~~~~~~~~~~~~~~gi~~~~~~~g~~~~~~~~-~~~~~~~~~~i~~l~~-~~vdgiIi~~~ 64 (273)
T cd06292 1 LVGLLVPELSNPIFPAFAEAIEAALAQYGYTVLLCNT-YRGGVSEADYVEDLLA-RGVRGVVFISS 64 (273)
T ss_pred CEEEEeCCCcCchHHHHHHHHHHHHHHCCCEEEEEeC-CCChHHHHHHHHHHHH-cCCCEEEEeCC
Confidence 4899999888778889999999999999987654433 334432 223 26899999865
No 48
>PRK05723 flavodoxin; Provisional
Probab=56.12 E-value=37 Score=30.32 Aligned_cols=55 Identities=15% Similarity=0.205 Sum_probs=41.3
Q ss_pred eEEEEEcCCcccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHHHHcCCCCCCEEEEecCC
Q 014264 210 IIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKLANFPECDVFINVSCA 269 (427)
Q Consensus 210 ~iGIlvgTl~~q~~~~~i~~l~~li~~~GKK~y~~~vgkln~aKLaNF~eiD~fVlvaCP 269 (427)
.++|+.||-+| +...++++|.+.++++|.++.++ ...++..|..+ +.|.. ++.|+
T Consensus 2 ~i~I~ygS~tG-~ae~~A~~la~~l~~~g~~~~~~--~~~~~~~~~~~-~~~~l-i~~~s 56 (151)
T PRK05723 2 KVAILSGSVYG-TAEEVARHAESLLKAAGFEAWHN--PRASLQDLQAF-APEAL-LAVTS 56 (151)
T ss_pred eEEEEEEcCch-HHHHHHHHHHHHHHHCCCceeec--CcCCHhHHHhC-CCCeE-EEEEC
Confidence 68999999885 57799999999999999988663 45777888777 34543 44444
No 49
>cd06316 PBP1_ABC_sugar_binding_like_7 Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems. Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily, which consists of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis.
Probab=55.71 E-value=14 Score=35.62 Aligned_cols=76 Identities=14% Similarity=0.126 Sum_probs=47.3
Q ss_pred eEEEEEcCCcccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHHHHc----CC--CCCCEEEEecCCCcccc----cccCC
Q 014264 210 IIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKLA----NF--PECDVFINVSCAQTALL----DSKEF 279 (427)
Q Consensus 210 ~iGIlvgTl~~q~~~~~i~~l~~li~~~GKK~y~~~vgkln~aKLa----NF--~eiD~fVlvaCPr~si~----d~~~f 279 (427)
+||+|+.++.-..+..+++.+++.+++.|.....+..++-++++.. .+ ..+|.+|+.+|.....+ ..++.
T Consensus 1 ~i~~i~~~~~~~~~~~~~~gi~~~a~~~g~~~~~~~~~~~~~~~~~~~l~~~~~~~~dgiii~~~~~~~~~~~i~~~~~~ 80 (294)
T cd06316 1 KAAIVMHTSGSDWSNAQVRGAKDEFAKLGIEVVATTDAQFDPAKQVADIETTISQKPDIIISIPVDPVSTAAAYKKVAEA 80 (294)
T ss_pred CeEEEecCCCChHHHHHHHHHHHHHHHcCCEEEEecCCCCCHHHHHHHHHHHHHhCCCEEEEcCCCchhhhHHHHHHHHc
Confidence 4788888776455567888888888888877654444555554321 11 25899998887643222 22344
Q ss_pred CCcccC
Q 014264 280 LAPVIT 285 (427)
Q Consensus 280 ~kPvlT 285 (427)
..|||.
T Consensus 81 ~iPvV~ 86 (294)
T cd06316 81 GIKLVF 86 (294)
T ss_pred CCcEEE
Confidence 556653
No 50
>PRK10703 DNA-binding transcriptional repressor PurR; Provisional
Probab=55.18 E-value=31 Score=34.01 Aligned_cols=63 Identities=13% Similarity=0.125 Sum_probs=46.5
Q ss_pred HhcCCeEEEEEcCCcccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHHHHcC----C--CCCCEEEEecC
Q 014264 205 AKDANIIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKLAN----F--PECDVFINVSC 268 (427)
Q Consensus 205 a~~A~~iGIlvgTl~~q~~~~~i~~l~~li~~~GKK~y~~~vgkln~aKLaN----F--~eiD~fVlvaC 268 (427)
.+..++||+|+..+.-..+..+++.+.+.+++.|.+.+++..+ -++++..+ + ..+|.+++.+.
T Consensus 56 ~~~~~~i~vi~~~~~~~~~~~~~~gi~~~~~~~g~~~~~~~~~-~~~~~~~~~i~~l~~~~vdgiii~~~ 124 (341)
T PRK10703 56 VNHTKSIGLLATSSEAPYFAEIIEAVEKNCYQKGYTLILCNAW-NNLEKQRAYLSMLAQKRVDGLLVMCS 124 (341)
T ss_pred hCCCCeEEEEeCCCCCchHHHHHHHHHHHHHHCCCEEEEEeCC-CCHHHHHHHHHHHHHcCCCEEEEecC
Confidence 3456799999998887788899999999999999887766543 34443211 1 25899988764
No 51
>cd01574 PBP1_LacI Ligand-binding domain of DNA transcription repressor LacI specific for lactose, a member of the LacI-GalR family of bacterial transcription regulators. Ligand-binding domain of DNA transcription repressor LacI specific for lactose, a member of the LacI-GalR family of bacterial transcription regulators. The ligand-binding domain of LacI is structurally homologous to the periplasmic sugar-binding domain of ABC-type transporters and both domains contain the type I periplasmic binding protein-like fold. The LacI-GalR family repressors 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 type I periplasmic binding proteins. 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 b
Probab=54.73 E-value=23 Score=33.19 Aligned_cols=75 Identities=19% Similarity=0.195 Sum_probs=49.9
Q ss_pred eEEEEEcCCcccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHH---H----HcCCCCCCEEEEecCCCccc--ccccCCC
Q 014264 210 IIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPA---K----LANFPECDVFINVSCAQTAL--LDSKEFL 280 (427)
Q Consensus 210 ~iGIlvgTl~~q~~~~~i~~l~~li~~~GKK~y~~~vgkln~a---K----LaNF~eiD~fVlvaCPr~si--~d~~~f~ 280 (427)
+||+|+.+..-..+..+++.+++.+++.|....++..+.-.++ + |.+ ..+|..++.+|..... ....+-.
T Consensus 1 ~i~vi~~~~~~~~~~~~~~gi~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~-~~vdgiii~~~~~~~~~~~~~~~~~ 79 (264)
T cd01574 1 TIGVVTTDLALHGPSSTLAAIESAAREAGYAVTLSMLAEADEEALRAAVRRLLA-QRVDGVIVNAPLDDADAALAAAPAD 79 (264)
T ss_pred CEEEEeCCCCcccHHHHHHHHHHHHHHCCCeEEEEeCCCCchHHHHHHHHHHHh-cCCCEEEEeCCCCChHHHHHHHhcC
Confidence 5899998877677889999999999999988766665543322 1 222 2599999998854432 1122233
Q ss_pred CcccC
Q 014264 281 APVIT 285 (427)
Q Consensus 281 kPvlT 285 (427)
.|+|+
T Consensus 80 ipvv~ 84 (264)
T cd01574 80 VPVVF 84 (264)
T ss_pred CCEEE
Confidence 56655
No 52
>TIGR02417 fruct_sucro_rep D-fructose-responsive transcription factor. Members of this family belong the lacI helix-turn-helix family (pfam00356) of DNA-binding transcriptional regulators. All members are from the proteobacteria. Characterized members act as positive and negative transcriptional regulators of fructose and sucrose transport and metabolism. Sucrose is a disaccharide composed of fructose and glucose; D-fructose-1-phosphate rather than an intact sucrose moiety has been shown to act as the inducer.
Probab=54.53 E-value=48 Score=32.48 Aligned_cols=62 Identities=21% Similarity=0.423 Sum_probs=46.1
Q ss_pred hcCCeEEEEEcCCcccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHHH----HcCC--CCCCEEEEecC
Q 014264 206 KDANIIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAK----LANF--PECDVFINVSC 268 (427)
Q Consensus 206 ~~A~~iGIlvgTl~~q~~~~~i~~l~~li~~~GKK~y~~~vgkln~aK----LaNF--~eiD~fVlvaC 268 (427)
+..++||+++..+.-..+..+++.+.+.++++|....+...+. ++++ +.++ ..+|..|+.++
T Consensus 58 ~~~~~Igvi~~~~~~~~~~~~~~~i~~~~~~~gy~~~i~~~~~-~~~~~~~~~~~l~~~~vdgiIi~~~ 125 (327)
T TIGR02417 58 GRSRTIGLVIPDLENYSYARIAKELEQQCREAGYQLLIACSDD-NPDQEKVVIENLLARQVDALIVASC 125 (327)
T ss_pred CCCceEEEEeCCCCCccHHHHHHHHHHHHHHCCCEEEEEeCCC-CHHHHHHHHHHHHHcCCCEEEEeCC
Confidence 3467999999888777889999999999999998887665543 4432 2222 26999888765
No 53
>PRK09004 FMN-binding protein MioC; Provisional
Probab=54.44 E-value=37 Score=30.01 Aligned_cols=54 Identities=17% Similarity=0.154 Sum_probs=39.0
Q ss_pred CeEEEEEcCCcccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHHHHcCCCCCCEEEEecCC
Q 014264 209 NIIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKLANFPECDVFINVSCA 269 (427)
Q Consensus 209 ~~iGIlvgTl~~q~~~~~i~~l~~li~~~GKK~y~~~vgkln~aKLaNF~eiD~fVlvaCP 269 (427)
+++.|+.||-+| +...++++|.+.+++.|.++.++-+. .++.| ++.|.+| +.||
T Consensus 2 ~~i~I~ygS~tG-nae~~A~~l~~~~~~~g~~~~~~~~~--~~~~l---~~~~~li-~~~s 55 (146)
T PRK09004 2 ADITLISGSTLG-GAEYVADHLAEKLEEAGFSTETLHGP--LLDDL---SASGLWL-IVTS 55 (146)
T ss_pred CeEEEEEEcCch-HHHHHHHHHHHHHHHcCCceEEeccC--CHHHh---ccCCeEE-EEEC
Confidence 368999999885 57899999999999999998776543 34544 4456544 4444
No 54
>cd06282 PBP1_GntR_like_2 Ligand-binding domain of putative DNA transcription repressors highly similar to that of the repressor specific for gluconate (GntR) which is a member of the LacI-GalR family of bacterial transcription regulators. This group includes the ligand-binding domain of putative DNA transcription repressors highly similar to that of the repressor specific for gluconate (GntR) which is a member of the LacI-GalR family of bacterial transcription regulators. The LacI-GalR family repressors 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
Probab=54.09 E-value=27 Score=32.65 Aligned_cols=75 Identities=15% Similarity=0.148 Sum_probs=49.4
Q ss_pred eEEEEEcCCcccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHHH-------HcCCCCCCEEEEecCCCcc---cccccCC
Q 014264 210 IIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAK-------LANFPECDVFINVSCAQTA---LLDSKEF 279 (427)
Q Consensus 210 ~iGIlvgTl~~q~~~~~i~~l~~li~~~GKK~y~~~vgkln~aK-------LaNF~eiD~fVlvaCPr~s---i~d~~~f 279 (427)
+||+|+.....-.+..+++.+.+.+++.|.+..++..+ -++.+ |.+. .+|+.|+..+-... +....+.
T Consensus 1 ~igvv~~~~~~~~~~~~~~~i~~~~~~~g~~~~~~~~~-~~~~~~~~~~~~l~~~-~vdgiii~~~~~~~~~~~~~~~~~ 78 (266)
T cd06282 1 TVGVVLPSLANPVFAECVQGIQEEARAAGYSLLLATTD-YDAEREADAVETLLRQ-RVDGLILTVADAATSPALDLLDAE 78 (266)
T ss_pred CeEEEeCCCCcchHHHHHHHHHHHHHHCCCEEEEeeCC-CCHHHHHHHHHHHHhc-CCCEEEEecCCCCchHHHHHHhhC
Confidence 58999988776677889999999999988877765543 33332 3332 68999887663221 1233445
Q ss_pred CCcccCH
Q 014264 280 LAPVITP 286 (427)
Q Consensus 280 ~kPvlTP 286 (427)
..|+|+.
T Consensus 79 ~ipvV~~ 85 (266)
T cd06282 79 RVPYVLA 85 (266)
T ss_pred CCCEEEE
Confidence 6677655
No 55
>PRK08105 flavodoxin; Provisional
Probab=53.54 E-value=35 Score=30.31 Aligned_cols=41 Identities=17% Similarity=0.255 Sum_probs=34.4
Q ss_pred CeEEEEEcCCcccCcHHHHHHHHHHHHHcCCcEEEEEcCCCC
Q 014264 209 NIIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPN 250 (427)
Q Consensus 209 ~~iGIlvgTl~~q~~~~~i~~l~~li~~~GKK~y~~~vgkln 250 (427)
++++|+.||-+| +...++++|.+.+++.|.++.++-+..+.
T Consensus 2 ~~i~I~YgS~tG-nte~~A~~l~~~l~~~g~~~~~~~~~~~~ 42 (149)
T PRK08105 2 AKVGIFVGTVYG-NALLVAEEAEAILTAQGHEVTLFEDPELS 42 (149)
T ss_pred CeEEEEEEcCch-HHHHHHHHHHHHHHhCCCceEEechhhCC
Confidence 468999999885 57789999999999999998887776554
No 56
>TIGR00829 FRU PTS system, fructose-specific, IIB component. Bacterial PTS transporters transport and concomitantly phosphorylate their sugar substrates, and typically consist of multiple subunits or protein domains. The Fru family is a large and complex family which includes several sequenced fructose and mannitol-specific permeases as well as several PTS components of unknown specificities. The fructose components of this family phosphorylate fructose on the 1-position. The Fru family PTS systems typically have 3 domains, IIA, IIB and IIC, which may be found as 1 or more proteins. The fructose and mannitol transporters form separate phylogenetic clusters in this family. This family is specific for the IIB domain of the fructose PTS transporters.
Probab=52.83 E-value=34 Score=27.57 Aligned_cols=68 Identities=16% Similarity=0.087 Sum_probs=47.7
Q ss_pred EEEEcCCcccCcHHHHHHHHHHHHHcCCcEE------EEEcCCCCHHHHcCCCCCCEEEEecCCCcccccccCC-CCccc
Q 014264 212 GVLVGTLGVAGYLHMIHQMKELITKAGKKAY------TLVMGKPNPAKLANFPECDVFINVSCAQTALLDSKEF-LAPVI 284 (427)
Q Consensus 212 GIlvgTl~~q~~~~~i~~l~~li~~~GKK~y------~~~vgkln~aKLaNF~eiD~fVlvaCPr~si~d~~~f-~kPvl 284 (427)
+|.-+.-|.....-..+.|++..++.|.... .-+.+.++.+.++. .|++++++.... ++.++| -||++
T Consensus 2 ~vtacp~G~Aht~lAae~L~~aA~~~G~~i~VE~qg~~g~~~~lt~~~i~~---Ad~viia~d~~~--~~~~rf~gk~v~ 76 (85)
T TIGR00829 2 AVTACPTGIAHTFMAAEALEKAAKKRGWEVKVETQGSVGAQNALTAEDIAA---ADGVILAADREI--DLSRRFAGKNVY 76 (85)
T ss_pred EEecCCCcHHHHHHHHHHHHHHHHHCCCeEEEEecCCcCccCCCCHHHHHh---CCEEEEeccCCC--chhhhcCCCeEE
Confidence 4556666777778888999999999999877 44445666676654 599999988763 334435 35654
No 57
>PLN03241 magnesium chelatase subunit H; Provisional
Probab=52.67 E-value=9.4 Score=45.73 Aligned_cols=28 Identities=39% Similarity=0.710 Sum_probs=0.0
Q ss_pred cccCCcEEEEec-CC---------------CCCC--CCCCCeEEEc
Q 014264 17 SHVDADCVIHYG-HT---------------CLSP--TSTLPAFFVF 44 (427)
Q Consensus 17 ~hv~aD~iVHyG-ha---------------Cls~--~~~lpv~YVf 44 (427)
+..+||+||||| |- |.+. +..+|.+|+|
T Consensus 663 ~~F~ADAvIHfGtHGtLEwLPGK~vGLS~~cwPd~LiGdlPniY~Y 708 (1353)
T PLN03241 663 DGYGADAVIHFGMHGTVEWLPGQPLGNDRLSWSDELLGGLPNVYVY 708 (1353)
T ss_pred cccCCCeEEEccCCcCcccCCCccccCCcccChHHHhCCCCEEEEE
No 58
>cd06286 PBP1_CcpB_like Ligand-binding domain of a novel transcription factor implicated in catabolite repression in Bacillus and Clostridium species. This group includes the ligand-binding domain of a novel transcription factor implicated in catabolite repression in Bacillus and Clostridium species. CcpB is 30% identical in sequence to CcpA which functions as the major transcriptional regulator of carbon catabolite repression/regulation (CCR), a process in which enzymes necessary for the metabolism of alternative sugars are inhibited in the presence of glucose. Like CcpA, the DNA-binding protein CcpB exerts its catabolite-repressing effect by a mechanism dependent on the presence of HPr(Ser-P), the small phosphocarrier proteins of the phosphoenolpyruvate-sugar phosphotransferase system, but with a less significant degree.
Probab=52.60 E-value=26 Score=32.77 Aligned_cols=59 Identities=19% Similarity=0.215 Sum_probs=45.3
Q ss_pred eEEEEEcCCcccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHHHH-------cCCCCCCEEEEecCCC
Q 014264 210 IIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKL-------ANFPECDVFINVSCAQ 270 (427)
Q Consensus 210 ~iGIlvgTl~~q~~~~~i~~l~~li~~~GKK~y~~~vgkln~aKL-------aNF~eiD~fVlvaCPr 270 (427)
+||+|+....-..+..+++.+++.+++.|....++.. .-++++. .+ ..+|.+++.+|..
T Consensus 1 ~i~~i~~~~~~~~~~~i~~gi~~~~~~~g~~~~~~~~-~~~~~~~~~~i~~l~~-~~vdgiii~~~~~ 66 (260)
T cd06286 1 TIGVVLPYINHPYFSQLVDGIEKAALKHGYKVVLLQT-NYDKEKELEYLELLKT-KQVDGLILCSREN 66 (260)
T ss_pred CEEEEeCCCCCchHHHHHHHHHHHHHHcCCEEEEEeC-CCChHHHHHHHHHHHH-cCCCEEEEeCCCC
Confidence 5899999888888999999999999999988765543 4455432 22 2699999988743
No 59
>cd06278 PBP1_LacI_like_2 Ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. This group includes the ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. The LacI-GalR family repressors 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 affinity of the repressor.
Probab=52.50 E-value=37 Score=31.71 Aligned_cols=60 Identities=18% Similarity=0.242 Sum_probs=41.5
Q ss_pred eEEEEEcCCcccCcHHHHHHHHHHHHHcCCcEEEEEcCCCC-HH----HHcCCCCCCEEEEecCCC
Q 014264 210 IIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPN-PA----KLANFPECDVFINVSCAQ 270 (427)
Q Consensus 210 ~iGIlvgTl~~q~~~~~i~~l~~li~~~GKK~y~~~vgkln-~a----KLaNF~eiD~fVlvaCPr 270 (427)
+||+++....-..+..+++.+.+.+++.|.+..++....-. .. ++.. ..+|.+|+.+|..
T Consensus 1 ~I~~i~~~~~~~~~~~~~~~i~~~~~~~g~~~~~~~~~~~~~~~~~i~~~~~-~~vdgiii~~~~~ 65 (266)
T cd06278 1 LIGVVVADLDNPFYSELLEALSRALQARGYQPLLINTDDDEDLDAALRQLLQ-YRVDGVIVTSGTL 65 (266)
T ss_pred CEEEEeCCCCCchHHHHHHHHHHHHHHCCCeEEEEcCCCCHHHHHHHHHHHH-cCCCEEEEecCCC
Confidence 47888887766677788999999999999887655444221 11 2222 2689999988753
No 60
>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=52.48 E-value=25 Score=33.45 Aligned_cols=76 Identities=13% Similarity=0.047 Sum_probs=49.0
Q ss_pred eEEEEEcCCcccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCH--HHHcC-C--CCCCEEEEecCCCccc--ccccCCCCc
Q 014264 210 IIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNP--AKLAN-F--PECDVFINVSCAQTAL--LDSKEFLAP 282 (427)
Q Consensus 210 ~iGIlvgTl~~q~~~~~i~~l~~li~~~GKK~y~~~vgkln~--aKLaN-F--~eiD~fVlvaCPr~si--~d~~~f~kP 282 (427)
+||+|+..+....+..+++.+.+.+++.|....+........ +.+.+ + ..+|.+++.++....- ...++...|
T Consensus 1 ~Igvi~p~~~~~~~~~~~~~i~~~~~~~gy~~~~~~~~~~~~~~~~~~~~l~~~~vdgvi~~~~~~~~~~~~~l~~~~iP 80 (269)
T cd06297 1 TISVLLPVVATEFYRRLLEGIEGALLEQRYDLALFPLLSLARLKRYLESTTLAYLTDGLLLASYDLTERLAERRLPTERP 80 (269)
T ss_pred CEEEEeCCCcChhHHHHHHHHHHHHHHCCCEEEEEeCCCcHHHHHHHHHHHHhcCCCEEEEecCccChHHHHHHhhcCCC
Confidence 489999877777788999999999999998877766553211 11211 2 1489999987753321 112334456
Q ss_pred ccC
Q 014264 283 VIT 285 (427)
Q Consensus 283 vlT 285 (427)
+|+
T Consensus 81 vv~ 83 (269)
T cd06297 81 VVL 83 (269)
T ss_pred EEE
Confidence 554
No 61
>PRK11041 DNA-binding transcriptional regulator CytR; Provisional
Probab=52.24 E-value=52 Score=31.77 Aligned_cols=61 Identities=10% Similarity=0.104 Sum_probs=45.4
Q ss_pred hcCCeEEEEEcCCcccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHHH-------HcCCCCCCEEEEecC
Q 014264 206 KDANIIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAK-------LANFPECDVFINVSC 268 (427)
Q Consensus 206 ~~A~~iGIlvgTl~~q~~~~~i~~l~~li~~~GKK~y~~~vgkln~aK-------LaNF~eiD~fVlvaC 268 (427)
++.++||+|+..+.-..+..+++.+.+.+++.|....+..... +.++ |.. ..+|.+++.++
T Consensus 33 ~~~~~ig~v~~~~~~~~~~~~~~gi~~~~~~~g~~~~~~~~~~-~~~~~~~~i~~l~~-~~vDgiIi~~~ 100 (309)
T PRK11041 33 NESRTILVIVPDICDPFFSEIIRGIEVTAAEHGYLVLIGDCAH-QNQQEKTFVNLIIT-KQIDGMLLLGS 100 (309)
T ss_pred CCCcEEEEEeCCCcCccHHHHHHHHHHHHHHCCCEEEEEeCCC-ChHHHHHHHHHHHH-cCCCEEEEecC
Confidence 3568999999887767788999999999999998876654432 3332 222 26999999876
No 62
>cd06296 PBP1_CatR_like Ligand-binding domain of a LacI-like transcriptional regulator, CatR which is involved in catechol degradation. This group includes the ligand-binding domain of a LacI-like transcriptional regulator, CatR which is involved in catechol degradation. 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 affinity of the repressor.
Probab=52.19 E-value=45 Score=31.29 Aligned_cols=59 Identities=17% Similarity=0.164 Sum_probs=41.3
Q ss_pred eEEEEEcCCcccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHHHH----cCC--CCCCEEEEecCC
Q 014264 210 IIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKL----ANF--PECDVFINVSCA 269 (427)
Q Consensus 210 ~iGIlvgTl~~q~~~~~i~~l~~li~~~GKK~y~~~vgkln~aKL----aNF--~eiD~fVlvaCP 269 (427)
+||||+..+.-..+..+++.+++.+++.|.+..++... -++++. .++ ..+|..|++++-
T Consensus 1 ~i~vi~~~~~~~~~~~~~~gi~~~~~~~g~~~~~~~~~-~~~~~~~~~i~~l~~~~~dgiii~~~~ 65 (270)
T cd06296 1 LIGLVFPDLDSPWASEVLRGVEEAAAAAGYDVVLSESG-RRTSPERQWVERLSARRTDGVILVTPE 65 (270)
T ss_pred CeEEEECCCCCccHHHHHHHHHHHHHHcCCeEEEecCC-CchHHHHHHHHHHHHcCCCEEEEecCC
Confidence 48999988887888899999999999998776555443 333222 112 258988887653
No 63
>PLN03069 magnesiumprotoporphyrin-IX chelatase subunit H; Provisional
Probab=52.09 E-value=9.4 Score=45.34 Aligned_cols=28 Identities=29% Similarity=0.807 Sum_probs=0.0
Q ss_pred cccCCcEEEEec-CC---------------CCCCC--CCCCeEEEc
Q 014264 17 SHVDADCVIHYG-HT---------------CLSPT--STLPAFFVF 44 (427)
Q Consensus 17 ~hv~aD~iVHyG-ha---------------Cls~~--~~lpv~YVf 44 (427)
+..+||+||||| |- |.+.. ..+|.+|.|
T Consensus 600 ~~F~ADAviH~GtHGtlEwLPGK~vGLS~~cwPd~liGdlPniY~Y 645 (1220)
T PLN03069 600 KIFKADAVLHFGTHGSLEFMPGKQVGMSDACYPDSLIGNIPNVYYY 645 (1220)
T ss_pred hhcCCCEEEEcCCCCCcccCCCccccCCcccChHHHhCCCCEEeEE
No 64
>TIGR02257 cobalto_cobN cobaltochelatase, CobN subunit.
Probab=51.80 E-value=9.7 Score=44.81 Aligned_cols=28 Identities=32% Similarity=0.761 Sum_probs=0.0
Q ss_pred cccCCcEEEEec-CC---------------CCCCC--CCCCeEEEc
Q 014264 17 SHVDADCVIHYG-HT---------------CLSPT--STLPAFFVF 44 (427)
Q Consensus 17 ~hv~aD~iVHyG-ha---------------Cls~~--~~lpv~YVf 44 (427)
+..+||+|||+| |- |.+.. ..+|.+|.|
T Consensus 535 ~~f~ADAiIH~GtHGtlEwLPGK~vgLS~~c~Pd~lig~lP~iYpy 580 (1122)
T TIGR02257 535 KVFGADAIVHVGKHGTLEWLPGKGVGLSETCFPEIVLGPLPHIYPF 580 (1122)
T ss_pred hhcCCCEEEECCCCcCcccCCCccccCCcccChHHHhCCCCEEEEE
No 65
>cd06285 PBP1_LacI_like_7 Ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. This group includes the ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. The LacI-GalR family repressors 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 affinity of the repressor.
Probab=51.70 E-value=29 Score=32.60 Aligned_cols=60 Identities=22% Similarity=0.211 Sum_probs=43.3
Q ss_pred eEEEEEcCCcccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHHHHc----CC--CCCCEEEEecCCC
Q 014264 210 IIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKLA----NF--PECDVFINVSCAQ 270 (427)
Q Consensus 210 ~iGIlvgTl~~q~~~~~i~~l~~li~~~GKK~y~~~vgkln~aKLa----NF--~eiD~fVlvaCPr 270 (427)
+||+|+....-..+..+++.+.+.+++.|.+..++ .+.-++++.. .+ ..+|.+++..|..
T Consensus 1 ~igvi~p~~~~~~~~~~~~gi~~~~~~~~~~~~~~-~~~~~~~~~~~~i~~l~~~~~dgiii~~~~~ 66 (265)
T cd06285 1 TIGVLVPRLTDTVMATMYEGIEEAAAERGYSTFVA-NTGDNPDAQRRAIEMLLDRRVDGLILGDARS 66 (265)
T ss_pred CEEEEeCCCCCccHHHHHHHHHHHHHHCCCEEEEE-eCCCCHHHHHHHHHHHHHcCCCEEEEecCCC
Confidence 58999998877788899999999999999886543 4444554321 11 2589999877653
No 66
>PRK05989 cobN cobaltochelatase subunit CobN; Reviewed
Probab=51.66 E-value=9.4 Score=45.47 Aligned_cols=28 Identities=36% Similarity=0.771 Sum_probs=0.0
Q ss_pred cccCCcEEEEec-CC---------------CCCCC--CCCCeEEEc
Q 014264 17 SHVDADCVIHYG-HT---------------CLSPT--STLPAFFVF 44 (427)
Q Consensus 17 ~hv~aD~iVHyG-ha---------------Cls~~--~~lpv~YVf 44 (427)
+..+||+|||+| |- |.+.. ..+|.+|.|
T Consensus 541 ~~f~ADAiIH~GtHGtlEwLPGK~vgLS~~c~Pd~llgdlP~iYpY 586 (1244)
T PRK05989 541 EGFGADAVVHVGKHGNLEWLPGKSVGLSADCYPDAALGDLPHLYPF 586 (1244)
T ss_pred hhcCCCEEEECCCCcccccCCCccccCCcccChHHHhCCCCEEEEE
No 67
>cd06318 PBP1_ABC_sugar_binding_like_9 Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems. Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily, which consists of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis.
Probab=51.65 E-value=21 Score=33.90 Aligned_cols=75 Identities=17% Similarity=0.172 Sum_probs=48.9
Q ss_pred eEEEEEcCCcccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHHH----HcCC--CCCCEEEEecCCCcccc----cccCC
Q 014264 210 IIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAK----LANF--PECDVFINVSCAQTALL----DSKEF 279 (427)
Q Consensus 210 ~iGIlvgTl~~q~~~~~i~~l~~li~~~GKK~y~~~vgkln~aK----LaNF--~eiD~fVlvaCPr~si~----d~~~f 279 (427)
+||+|+.++....+..+++.+.+.+++.|.+..+... .-++++ |.++ ..+|++++.+|...+.. ..++.
T Consensus 1 ~igv~~~~~~~~~~~~~~~~i~~~~~~~g~~v~~~~~-~~~~~~~~~~i~~~~~~~~Dgiii~~~~~~~~~~~i~~~~~~ 79 (282)
T cd06318 1 KIGFSQYTLNSPFFAALTEAAKAHAKALGYELISTDA-QGDLTKQIADVEDLLTRGVNVLIINPVDPEGLVPAVAAAKAA 79 (282)
T ss_pred CeeEEeccccCHHHHHHHHHHHHHHHHcCCEEEEEcC-CCCHHHHHHHHHHHHHcCCCEEEEecCCccchHHHHHHHHHC
Confidence 5899998888777889999999999999987654332 334432 2222 26899998876533221 12345
Q ss_pred CCcccC
Q 014264 280 LAPVIT 285 (427)
Q Consensus 280 ~kPvlT 285 (427)
-.|||+
T Consensus 80 ~iPvV~ 85 (282)
T cd06318 80 GVPVVV 85 (282)
T ss_pred CCCEEE
Confidence 567664
No 68
>cd06284 PBP1_LacI_like_6 Ligand-binding domain of an uncharacterized transcription regulator from Actinobacillus succinogenes and its close homologs from other bacteria. This group includes the ligand-binding domain of an uncharacterized transcription regulator from Actinobacillus succinogenes and its close homologs from other bacteria. This group belongs to the the LacI-GalR family repressors and 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=51.52 E-value=43 Score=31.26 Aligned_cols=59 Identities=15% Similarity=0.214 Sum_probs=44.8
Q ss_pred eEEEEEcCCcccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHHHHcCC------CCCCEEEEecCC
Q 014264 210 IIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKLANF------PECDVFINVSCA 269 (427)
Q Consensus 210 ~iGIlvgTl~~q~~~~~i~~l~~li~~~GKK~y~~~vgkln~aKLaNF------~eiD~fVlvaCP 269 (427)
.||+|+.+++-..+..+++.+++.++++|.+..++..+ -++++..+. ..+|++++.+|.
T Consensus 1 ~i~~v~~~~~~~~~~~~~~~i~~~~~~~g~~~~~~~~~-~~~~~~~~~~~~~~~~~vdgiii~~~~ 65 (267)
T cd06284 1 MILVLVPDIANPFFSEILKGIEDEAREAGYGVLLGDTR-SDPEREQEYLDLLRRKQADGIILLDGS 65 (267)
T ss_pred CEEEEECCCCCccHHHHHHHHHHHHHHcCCeEEEecCC-CChHHHHHHHHHHHHcCCCEEEEecCC
Confidence 37899999888888899999999999999887665543 455543222 268999998764
No 69
>PRK12493 magnesium chelatase subunit H; Provisional
Probab=51.30 E-value=9.6 Score=45.60 Aligned_cols=28 Identities=36% Similarity=0.852 Sum_probs=21.0
Q ss_pred ccCCcEEEEec-CC---------------CCCC--CCCCCeEEEcc
Q 014264 18 HVDADCVIHYG-HT---------------CLSP--TSTLPAFFVFG 45 (427)
Q Consensus 18 hv~aD~iVHyG-ha---------------Cls~--~~~lpv~YVf~ 45 (427)
..+||+||||| |- |.+. +..+|.+|.|.
T Consensus 588 ~F~ADAviH~GtHGtlEwLPGK~vGLS~~cwPd~liG~lP~iY~Yi 633 (1310)
T PRK12493 588 VWGADAVLHFGTHGALEFMPGKQMGMSASCWPDRLIGSLPNFYYYA 633 (1310)
T ss_pred hcCCCEEEECCCCcCcccCCCccccCCcccChHHHhCCCCEEeEEe
Confidence 35899999999 64 4433 24789999994
No 70
>PF00258 Flavodoxin_1: Flavodoxin; InterPro: IPR008254 This domain is found in a number of proteins including flavodoxin and nitric-oxide synthase. Flavodoxins are electron-transfer proteins that function in various electron transport systems. They bind one FMN molecule, which serves as a redox-active prosthetic group [] and are functionally interchangeable with ferredoxins. They have been isolated from prokaryotes, cyanobacteria, and some eukaryotic algae. Nitric oxide synthase (1.14.13.39 from EC) produces nitric oxide from L-arginie and NADPH. Nitric oxide acts as a messenger molecule in the body.; GO: 0010181 FMN binding, 0016491 oxidoreductase activity; PDB: 2WC1_A 2FVX_A 2FOX_A 6NUL_A 1FVX_A 2FAX_A 1FLN_A 1FLA_A 4NLL_A 2FDX_A ....
Probab=51.16 E-value=31 Score=29.67 Aligned_cols=54 Identities=13% Similarity=0.254 Sum_probs=40.1
Q ss_pred EEEcCCcccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHHHHcCCCCCCEEEEecCC
Q 014264 213 VLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKLANFPECDVFINVSCA 269 (427)
Q Consensus 213 IlvgTl~~q~~~~~i~~l~~li~~~GKK~y~~~vgkln~aKLaNF~eiD~fVlvaCP 269 (427)
|+-+|..| +...+++.|.+.++++|.++.++-+.+.+.. +..+.+.+.++ ++||
T Consensus 1 I~Y~S~tG-~te~~A~~ia~~l~~~g~~~~~~~~~~~~~~-~~~~~~~~~~i-~~~s 54 (143)
T PF00258_consen 1 IVYGSMTG-NTEKMAEAIAEGLRERGVEVRVVDLDDFDDS-PSDLSEYDLLI-FGVS 54 (143)
T ss_dssp EEEETSSS-HHHHHHHHHHHHHHHTTSEEEEEEGGGSCHH-HHHHCTTSEEE-EEEE
T ss_pred CEEECCch-hHHHHHHHHHHHHHHcCCceeeechhhhhhh-hhhhhhhceee-Eeec
Confidence 56777763 5678999999999999999999999999966 33333445544 4444
No 71
>COG2984 ABC-type uncharacterized transport system, periplasmic component [General function prediction only]
Probab=51.15 E-value=58 Score=32.94 Aligned_cols=111 Identities=21% Similarity=0.285 Sum_probs=74.4
Q ss_pred HHHHHHHHHHH-hcCCeEEEEEcCCcccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCH--HHHcCC-CCCCEEEEecCCC
Q 014264 195 LKRRYYLVEKA-KDANIIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNP--AKLANF-PECDVFINVSCAQ 270 (427)
Q Consensus 195 L~rRy~~I~ka-~~A~~iGIlvgTl~~q~~~~~i~~l~~li~~~GKK~y~~~vgkln~--aKLaNF-~eiD~fVlvaCPr 270 (427)
+.++..+|++. =+|++||++-+. +-++...+++.+++.++++|.+.+...+.+.|. .-..+. ..+|++..-.-+-
T Consensus 145 v~q~i~lik~~~Pnak~Igv~Y~p-~E~ns~~l~eelk~~A~~~Gl~vve~~v~~~ndi~~a~~~l~g~~d~i~~p~dn~ 223 (322)
T COG2984 145 VAQQIELIKALLPNAKSIGVLYNP-GEANSVSLVEELKKEARKAGLEVVEAAVTSVNDIPRAVQALLGKVDVIYIPTDNL 223 (322)
T ss_pred HHHHHHHHHHhCCCCeeEEEEeCC-CCcccHHHHHHHHHHHHHCCCEEEEEecCcccccHHHHHHhcCCCcEEEEecchH
Confidence 45666677654 469999999987 447899999999999999999999999988873 333444 3577765432221
Q ss_pred cc-----cc-cccCCCCcccCHHHHHHhhCCCCccccceeeccccc
Q 014264 271 TA-----LL-DSKEFLAPVITPFEAMLAFGRGTQWTGAYVMEFRDL 310 (427)
Q Consensus 271 ~s-----i~-d~~~f~kPvlTP~El~~aL~~~~~w~g~y~~Df~~~ 310 (427)
.. +. -......||+++-+-.+-=|. --.+-+||.++
T Consensus 224 i~s~~~~l~~~a~~~kiPli~sd~~~V~~Ga----~aA~gvdy~~~ 265 (322)
T COG2984 224 IVSAIESLLQVANKAKIPLIASDTSSVKEGA----LAALGVDYKDL 265 (322)
T ss_pred HHHHHHHHHHHHHHhCCCeecCCHHHHhcCc----ceeeccCHHHH
Confidence 10 11 244567788888776665332 13455566654
No 72
>TIGR02025 BchH magnesium chelatase, H subunit. This model represents the H subunit of the magnesium chelatase complex responsible for magnesium insertion into the protoporphyrin IX ring in the biosynthesis of both chlorophyll and bacteriochlorophyll. In chlorophyll-utilizing species, this gene is known as ChlH, while in bacteriochlorophyll-utilizing spoecies it is called BchH. Subunit H is the largest (~140kDa) of the three subunits (the others being BchD/ChlD and BchI/ChlI), and is known to bind protoporphyrin IX. Subunit H is homologous to the CobN subunit of cobaltochelatase and by anology with that enzyme, subunit H is believed to also bind the magnesium ion which is inserted into the ring. In conjunction with the hydrolysis of ATP by subunits I and D, a conformation change is believed to happen in subunit H causing the magnesium ion insertion into the distorted protoporphyrin ring.
Probab=51.15 E-value=9.7 Score=45.18 Aligned_cols=28 Identities=36% Similarity=0.946 Sum_probs=0.0
Q ss_pred cccCCcEEEEec-CC---------------CCCCC--CCCCeEEEc
Q 014264 17 SHVDADCVIHYG-HT---------------CLSPT--STLPAFFVF 44 (427)
Q Consensus 17 ~hv~aD~iVHyG-ha---------------Cls~~--~~lpv~YVf 44 (427)
+..+||+||||| |- |.+.. ..+|.+|+|
T Consensus 573 ~~f~ADAviH~GtHGtlEwLPGK~~GLS~~cwPd~liG~lP~iY~Y 618 (1216)
T TIGR02025 573 RDFKADAVLHFGTHGSLEFMPGKQTGLTGECWPDRLLGDLPNFYIY 618 (1216)
T ss_pred hhcCCCEEEECCCCcCcccCCCccccCCcccChHHHhCCCCEEeEE
No 73
>PRK13405 bchH magnesium chelatase subunit H; Provisional
Probab=50.80 E-value=10 Score=45.01 Aligned_cols=28 Identities=32% Similarity=0.848 Sum_probs=0.0
Q ss_pred cccCCcEEEEec-CC---------------CCCCC--CCCCeEEEc
Q 014264 17 SHVDADCVIHYG-HT---------------CLSPT--STLPAFFVF 44 (427)
Q Consensus 17 ~hv~aD~iVHyG-ha---------------Cls~~--~~lpv~YVf 44 (427)
+..+||+||||| |- |.+.. ..+|.+|.|
T Consensus 593 ~~F~ADAviH~GtHGtlEwLPGK~vGLS~~cwPd~liGdlP~iY~Y 638 (1209)
T PRK13405 593 EDFGADAVLHFGTHGALEFMPGKQAGLSAACWPDRLIGDLPNVYLY 638 (1209)
T ss_pred hhcCCCEEEECCCCcccccCCCccccCCcccChHHHhCCCCEEEEE
No 74
>TIGR01481 ccpA catabolite control protein A. Catabolite control protein A is a LacI family global transcriptional regulator found in Gram-positive bacteria. CcpA is involved in repressing carbohydrate utilization genes [ex: alpha-amylase (amyE), acetyl-coenzyme A synthase (acsA)] and in activating genes involved in transporting excess carbon from the cell [ex: acetate kinase (ackA), alpha-acetolactate synthase (alsS)]. Additionally, disruption of CcpA in Bacillus megaterium, Staphylococcus xylosus, Lactobacillus casei and Lactocacillus pentosus also decreases growth rate, which suggests CcpA is involved in the regulation of other metabolic pathways.
Probab=50.70 E-value=53 Score=32.12 Aligned_cols=77 Identities=17% Similarity=0.220 Sum_probs=51.3
Q ss_pred cCCeEEEEEcCCcccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHHH-------HcCCCCCCEEEEecCCCcc-c-cccc
Q 014264 207 DANIIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAK-------LANFPECDVFINVSCAQTA-L-LDSK 277 (427)
Q Consensus 207 ~A~~iGIlvgTl~~q~~~~~i~~l~~li~~~GKK~y~~~vgkln~aK-------LaNF~eiD~fVlvaCPr~s-i-~d~~ 277 (427)
..++||+++..+.-..+..+++.+.+.++++|.+..+... .-++++ |.+ ..+|.+|++++.... + ....
T Consensus 58 ~~~~Igvv~~~~~~~f~~~l~~~i~~~~~~~g~~~~i~~~-~~~~~~~~~~~~~l~~-~~vdGiIi~~~~~~~~~~~~l~ 135 (329)
T TIGR01481 58 RTTTVGVIIPDISNIYYAELARGIEDIATMYKYNIILSNS-DEDPEKEVQVLNTLLS-KQVDGIIFMGGTITEKLREEFS 135 (329)
T ss_pred CCCEEEEEeCCCCchhHHHHHHHHHHHHHHcCCEEEEEeC-CCCHHHHHHHHHHHHh-CCCCEEEEeCCCCChHHHHHHH
Confidence 4579999998887777889999999999999987755433 333332 222 369999998764321 1 1123
Q ss_pred CCCCcccC
Q 014264 278 EFLAPVIT 285 (427)
Q Consensus 278 ~f~kPvlT 285 (427)
+...|+|.
T Consensus 136 ~~~iPvV~ 143 (329)
T TIGR01481 136 RSPVPVVL 143 (329)
T ss_pred hcCCCEEE
Confidence 34567663
No 75
>PRK10423 transcriptional repressor RbsR; Provisional
Probab=50.50 E-value=58 Score=31.74 Aligned_cols=64 Identities=9% Similarity=0.145 Sum_probs=46.9
Q ss_pred HhcCCeEEEEEcCCcccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHHHH----cCC--CCCCEEEEecCC
Q 014264 205 AKDANIIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKL----ANF--PECDVFINVSCA 269 (427)
Q Consensus 205 a~~A~~iGIlvgTl~~q~~~~~i~~l~~li~~~GKK~y~~~vgkln~aKL----aNF--~eiD~fVlvaCP 269 (427)
.+..++||+|+....-..|..+++.+.+.+++.|.+..++..+ -++++. .+| ..+|.+|+.+..
T Consensus 53 ~~~~~~Igvi~~~~~~~~~~~~~~gi~~~~~~~g~~~~~~~~~-~~~~~~~~~~~~l~~~~vdGiI~~~~~ 122 (327)
T PRK10423 53 LNQTRTIGMLITASTNPFYSELVRGVERSCFERGYSLVLCNTE-GDEQRMNRNLETLMQKRVDGLLLLCTE 122 (327)
T ss_pred hCCCCeEEEEeCCCCCCcHHHHHHHHHHHHHHcCCEEEEEeCC-CCHHHHHHHHHHHHHcCCCEEEEeCCC
Confidence 3466899999998877888999999999999999886655443 344322 222 269999987654
No 76
>COG2185 Sbm Methylmalonyl-CoA mutase, C-terminal domain/subunit (cobalamin-binding) [Lipid metabolism]
Probab=49.57 E-value=23 Score=31.63 Aligned_cols=56 Identities=21% Similarity=0.346 Sum_probs=41.6
Q ss_pred HHHHhcCCeEEEEEcCCcccCcHHHHHHHHHHHHHcCCcEEEEEc-CCCCHHHHcCCC
Q 014264 202 VEKAKDANIIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVM-GKPNPAKLANFP 258 (427)
Q Consensus 202 I~ka~~A~~iGIlvgTl~~q~~~~~i~~l~~li~~~GKK~y~~~v-gkln~aKLaNF~ 258 (427)
+..|.+...=.|.|+.+. .+|+.++..+.+.|+++|....++++ |.|.|+.+.+|.
T Consensus 56 v~aA~~~dv~vIgvSsl~-g~h~~l~~~lve~lre~G~~~i~v~~GGvip~~d~~~l~ 112 (143)
T COG2185 56 VRAAVEEDVDVIGVSSLD-GGHLTLVPGLVEALREAGVEDILVVVGGVIPPGDYQELK 112 (143)
T ss_pred HHHHHhcCCCEEEEEecc-chHHHHHHHHHHHHHHhCCcceEEeecCccCchhHHHHH
Confidence 334444455556778877 78999999999999999998888555 577788765554
No 77
>TIGR02990 ectoine_eutA ectoine utilization protein EutA. Members of this protein family are EutA, a predicted arylmalonate decarboxylase found in a conserved ectoine utilization operon of species that include Sinorhizobium meliloti 1021 (where it is known to be induced by ectoine), Mesorhizobium loti and Silicibacter pomeroyi. It is missing from two other species with the other ectoine transport and utilization genes: Pseudomonas putida and Agrobacterium tumefaciens.
Probab=48.78 E-value=71 Score=30.88 Aligned_cols=81 Identities=17% Similarity=0.224 Sum_probs=59.9
Q ss_pred HHhcCCeEEEEEcCCcccCcHHHHHHHHHHHHHcCCcEEEE---------EcCCCCHHHHcC------CCCCCEEEEecC
Q 014264 204 KAKDANIIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTL---------VMGKPNPAKLAN------FPECDVFINVSC 268 (427)
Q Consensus 204 ka~~A~~iGIlvgTl~~q~~~~~i~~l~~li~~~GKK~y~~---------~vgkln~aKLaN------F~eiD~fVlvaC 268 (427)
++.++++|+|+- -+-.++-+++++-++++|..+--+ .++++.|+-+.. -++.|+.++. |
T Consensus 116 ~alg~~RIalvT-----PY~~~v~~~~~~~l~~~G~eV~~~~~~~~~~~~~ia~i~p~~i~~~~~~~~~~~aDAifis-C 189 (239)
T TIGR02990 116 AALGVRRISLLT-----PYTPETSRPMAQYFAVRGFEIVNFTCLGLTDDREMARISPDCIVEAALAAFDPDADALFLS-C 189 (239)
T ss_pred HHcCCCEEEEEC-----CCcHHHHHHHHHHHHhCCcEEeeeeccCCCCCceeeecCHHHHHHHHHHhcCCCCCEEEEe-C
Confidence 455899999874 245588889999999999998776 577788887633 3578887665 8
Q ss_pred CCccccc-----ccCCCCcccCHHHHH
Q 014264 269 AQTALLD-----SKEFLAPVITPFEAM 290 (427)
Q Consensus 269 Pr~si~d-----~~~f~kPvlTP~El~ 290 (427)
=-..-.+ ..++-|||||.--+.
T Consensus 190 TnLrt~~vi~~lE~~lGkPVlsSNqat 216 (239)
T TIGR02990 190 TALRAATCAQRIEQAIGKPVVTSNQAT 216 (239)
T ss_pred CCchhHHHHHHHHHHHCCCEEEHHHHH
Confidence 8776433 356899999876554
No 78
>COG1429 CobN Cobalamin biosynthesis protein CobN and related Mg-chelatases [Coenzyme metabolism]
Probab=47.47 E-value=11 Score=45.22 Aligned_cols=25 Identities=32% Similarity=0.675 Sum_probs=0.0
Q ss_pred CCcEEEEec-C---------------CCCCCC--CCCCeEEEc
Q 014264 20 DADCVIHYG-H---------------TCLSPT--STLPAFFVF 44 (427)
Q Consensus 20 ~aD~iVHyG-h---------------aCls~~--~~lpv~YVf 44 (427)
+||+|||+| | .|.+.+ ..+|.+|.|
T Consensus 555 ~ADAvVHvGtHGTlEWLPGK~vgLs~~d~P~illgdlP~iYpY 597 (1388)
T COG1429 555 GADAVVHVGTHGTLEWLPGKEVGLSREDFPDILLGDLPNIYPY 597 (1388)
T ss_pred CCCeEEEccCccCcccCCCccccCChhhchHHhhCCCCeEEEE
No 79
>PRK09526 lacI lac repressor; Reviewed
Probab=47.10 E-value=96 Score=30.45 Aligned_cols=62 Identities=11% Similarity=0.129 Sum_probs=45.8
Q ss_pred hcCCeEEEEEcCCcccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHHH----HcCC--CCCCEEEEec
Q 014264 206 KDANIIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAK----LANF--PECDVFINVS 267 (427)
Q Consensus 206 ~~A~~iGIlvgTl~~q~~~~~i~~l~~li~~~GKK~y~~~vgkln~aK----LaNF--~eiD~fVlva 267 (427)
+..++||+++..+.-..+..+++.+.+.+++.|....++..+.-++++ |.++ ..+|.+++.+
T Consensus 61 ~~~~~Igvv~~~~~~~~~~~~~~gi~~~a~~~g~~~~i~~~~~~~~~~~~~~l~~l~~~~vdGiii~~ 128 (342)
T PRK09526 61 KQSLTIGLATTSLALHAPSQIAAAIKSRADQLGYSVVISMVERSGVEACQAAVNELLAQRVSGVIINV 128 (342)
T ss_pred CCCceEEEEeCCCCcccHHHHHHHHHHHHHHCCCEEEEEeCCCChHHHHHHHHHHHHhcCCCEEEEec
Confidence 346799999998877778899999999999999887776655433322 2233 2699998863
No 80
>PF03698 UPF0180: Uncharacterised protein family (UPF0180); InterPro: IPR005370 The members of this family are small uncharacterised proteins.
Probab=46.55 E-value=45 Score=26.80 Aligned_cols=58 Identities=19% Similarity=0.247 Sum_probs=39.0
Q ss_pred HHHHHHHHHcCCcEEEEEcCCCCHHHHcCCCCCCEEEEecCCCcccc-cccCCCCccc-----CHHHHHHh
Q 014264 228 HQMKELITKAGKKAYTLVMGKPNPAKLANFPECDVFINVSCAQTALL-DSKEFLAPVI-----TPFEAMLA 292 (427)
Q Consensus 228 ~~l~~li~~~GKK~y~~~vgkln~aKLaNF~eiD~fVlvaCPr~si~-d~~~f~kPvl-----TP~El~~a 292 (427)
..+++.|+++|.++..+- +.+ ++..+||.|+.+=..+-+- ....+..||| ||.|..=.
T Consensus 11 s~v~~~L~~~GyeVv~l~----~~~---~~~~~daiVvtG~~~n~mg~~d~~~~~pVInA~G~T~eEI~~~ 74 (80)
T PF03698_consen 11 SNVKEALREKGYEVVDLE----NEQ---DLQNVDAIVVTGQDTNMMGIQDTSTKVPVINASGLTAEEIVQE 74 (80)
T ss_pred hHHHHHHHHCCCEEEecC----Ccc---ccCCcCEEEEECCCcccccccccccCceEEecCCCCHHHHHHH
Confidence 478889999999966554 222 4567999999997776432 1234677885 56665433
No 81
>COG0716 FldA Flavodoxins [Energy production and conversion]
Probab=46.12 E-value=72 Score=28.10 Aligned_cols=60 Identities=12% Similarity=0.014 Sum_probs=44.4
Q ss_pred CeEEEEEcCCcccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHHHHcCCCCCCEEEEecCCCcc
Q 014264 209 NIIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKLANFPECDVFINVSCAQTA 272 (427)
Q Consensus 209 ~~iGIlvgTl~~q~~~~~i~~l~~li~~~GKK~y~~~vgkln~aKLaNF~eiD~fVlvaCPr~s 272 (427)
..++|+.+|.+ -+...+++.|++.|.+.|.+. .+....-....+. + ..|.+++.+++-..
T Consensus 2 ~ki~Ivy~S~t-GnTe~vA~~i~~~l~~~~~~~-~~~~~~~~~~~~~-~-~~d~~~~g~~t~~~ 61 (151)
T COG0716 2 MKILIVYGSRT-GNTEKVAEIIAEELGADGFEV-DIDIRPGIKDDLL-E-SYDELLLGTPTWGA 61 (151)
T ss_pred CeEEEEEEcCC-CcHHHHHHHHHHHhccCCceE-EEeecCCcchhhh-c-cCCEEEEEeCCCCC
Confidence 46899999998 578899999999999999998 4444444444333 2 45888887777553
No 82
>PF00885 DMRL_synthase: 6,7-dimethyl-8-ribityllumazine synthase; InterPro: IPR002180 6,7-dimethyl-8-ribityllumazine synthase (riboflavin synthase) catalyses the biosynthesis of riboflavin according to the reaction: 2 6,7-dimethyl-8-(1-D-ribityl)lumazine = riboflavin + 4-(1-D-ribitylamino)-5-amino-2,6-dihydroxypyrimidine. The biosynthesis of one riboflavin molecule requires one molecule of GTP and two molecules of ribulose 5-phosphate as substrates. The final step in the biosynthesis of the vitamin involves the dismutation of 6,7-dimethyl-8-ribityllumazine catalyzed by riboflavin synthase. The second product, 5-amino-6-ribitylamino-2,4(1H,3H)-pyrimidinedione, is recycled in the biosynthetic pathway by 6,7-dimethyl-8-ribityllumazine synthase []. N-[2,4-dioxo-6-d-ribitylamino-1,2,3,4-tetrahydropyrimidin-5-yl]oxalamic acid derivatives inhibit riboflavin synthase []. This family includes the beta chain of 6,7-dimethyl-8-ribityllumazine synthase 2.5.1.9 from EC. The family also includes a subfamily of distant archaebacterial proteins that may also have the same function for example O28856 from SWISSPROT.; GO: 0009231 riboflavin biosynthetic process, 0009349 riboflavin synthase complex; PDB: 2O6H_D 1C41_C 2OBX_H 1VSX_H 1VSW_3 3JV8_C 3MK3_r 3NQ4_G 2A58_A 2A57_D ....
Probab=46.08 E-value=50 Score=29.39 Aligned_cols=61 Identities=15% Similarity=0.184 Sum_probs=44.0
Q ss_pred CCeEEEEEcCCcccCcHHHHHHHHHHHHHcCC---cEEEEEcCCCC-----HHHHcCCCCCCEEEEecC
Q 014264 208 ANIIGVLVGTLGVAGYLHMIHQMKELITKAGK---KAYTLVMGKPN-----PAKLANFPECDVFINVSC 268 (427)
Q Consensus 208 A~~iGIlvgTl~~q~~~~~i~~l~~li~~~GK---K~y~~~vgkln-----~aKLaNF~eiD~fVlvaC 268 (427)
.-+||||++.-...---.+++...+.|+++|- ...++.|--.. ..+|++...+|++|.+||
T Consensus 3 ~~ri~IV~s~~n~~i~~~ll~~a~~~l~~~g~~~~~i~~~~VPGa~ElP~a~~~l~~~~~~Davi~lG~ 71 (144)
T PF00885_consen 3 GLRIAIVVSRFNEEITDRLLEGALEELKRHGVAEENIEVIRVPGAFELPLAAKRLAESGRYDAVIALGC 71 (144)
T ss_dssp TEEEEEEEESTTHHHHHHHHHHHHHHHHHTTTTGGCEEEEEESSGGGHHHHHHHHHHCSTESEEEEEEE
T ss_pred CCEEEEEEEeccHHHHHHHHHHHHHHHHHcCCCccceEEEEcCCHHHHHHHHHHHhcccCccEEEEecc
Confidence 34789999976544444555556778888886 66777765433 467777778999999998
No 83
>cd06312 PBP1_ABC_sugar_binding_like_4 Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems. Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily, which consists of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis.
Probab=46.01 E-value=27 Score=33.06 Aligned_cols=60 Identities=10% Similarity=-0.024 Sum_probs=41.4
Q ss_pred eEEEEEcCC-cccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHHHHcCC------CCCCEEEEecCC
Q 014264 210 IIGVLVGTL-GVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKLANF------PECDVFINVSCA 269 (427)
Q Consensus 210 ~iGIlvgTl-~~q~~~~~i~~l~~li~~~GKK~y~~~vgkln~aKLaNF------~eiD~fVlvaCP 269 (427)
+||+|+... .-..+..+++.+++.+++.|....++....-++++.... ..+|.+|+.++.
T Consensus 1 ~i~~i~~~~~~~~~~~~~~~g~~~~~~~~g~~v~~~~~~~~~~~~~~~~i~~l~~~~vdgiii~~~~ 67 (271)
T cd06312 1 KIAFVTHGPAGDPFWTVVKNGAEDAAKDLGVDVEYRGPETFDVADMARLIEAAIAAKPDGIVVTIPD 67 (271)
T ss_pred CEEEecCCCCCCcHHHHHHHHHHHHHHHhCCEEEEECCCCCCHHHHHHHHHHHHHhCCCEEEEeCCC
Confidence 478888766 556777888999999999888776655543355544221 268999887754
No 84
>PF00731 AIRC: AIR carboxylase; InterPro: IPR000031 Phosphoribosylaminoimidazole carboxylase is a fusion protein in plants and fungi, but consists of two non-interacting proteins in bacteria, PurK and PurE. PurK, N5-carboxyaminoimidazole ribonucleotide (N5_CAIR) synthetase, catalyzes the conversion of 5-aminoimidazole ribonucleotide (AIR), ATP, and bicarbonate to N5-CAIR, ADP, and Pi. PurE converts N5-CAIR to CAIR, the sixth step of de novo purine biosynthesis. In the presence of high concentrations of bicarbonate, PurE is reported able to convert AIR to CAIR directly and without ATP. Some members of this family contain two copies of this domain []. The crystal structure of PurE indicates a unique quaternary structure that confirms the octameric nature of the enzyme [].; GO: 0004638 phosphoribosylaminoimidazole carboxylase activity, 0006189 'de novo' IMP biosynthetic process; PDB: 3TRH_O 2YWX_A 2NSL_A 1D7A_A 2NSJ_A 1QCZ_A 2ATE_A 2NSH_A 3RG8_C 3RGG_D ....
Probab=45.35 E-value=64 Score=29.04 Aligned_cols=72 Identities=22% Similarity=0.320 Sum_probs=46.1
Q ss_pred eEEEEEcCCcccCcHHHHHHHHHHHHHcCCcEEEEEcC-CCCHHHHcCC------CCCCEEEEecCCCccccc--ccCCC
Q 014264 210 IIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMG-KPNPAKLANF------PECDVFINVSCAQTALLD--SKEFL 280 (427)
Q Consensus 210 ~iGIlvgTl~~q~~~~~i~~l~~li~~~GKK~y~~~vg-kln~aKLaNF------~eiD~fVlvaCPr~si~d--~~~f~ 280 (427)
.++||.|+.+ -+.+.+..++.|++-|..+-+-+.+ .=+|++|..| .++|+||-+|==...|-- ...-.
T Consensus 2 ~V~Ii~gs~S---D~~~~~~a~~~L~~~gi~~~~~V~saHR~p~~l~~~~~~~~~~~~~viIa~AG~~a~Lpgvva~~t~ 78 (150)
T PF00731_consen 2 KVAIIMGSTS---DLPIAEEAAKTLEEFGIPYEVRVASAHRTPERLLEFVKEYEARGADVIIAVAGMSAALPGVVASLTT 78 (150)
T ss_dssp EEEEEESSGG---GHHHHHHHHHHHHHTT-EEEEEE--TTTSHHHHHHHHHHTTTTTESEEEEEEESS--HHHHHHHHSS
T ss_pred eEEEEeCCHH---HHHHHHHHHHHHHHcCCCEEEEEEeccCCHHHHHHHHHHhccCCCEEEEEECCCcccchhhheeccC
Confidence 5889999754 7888899999999999877666665 4567777554 257888887766655421 12235
Q ss_pred Cccc
Q 014264 281 APVI 284 (427)
Q Consensus 281 kPvl 284 (427)
+|||
T Consensus 79 ~PVI 82 (150)
T PF00731_consen 79 LPVI 82 (150)
T ss_dssp S-EE
T ss_pred CCEE
Confidence 6655
No 85
>PRK10339 DNA-binding transcriptional repressor EbgR; Provisional
Probab=43.88 E-value=42 Score=32.95 Aligned_cols=75 Identities=12% Similarity=0.112 Sum_probs=47.1
Q ss_pred cCCeEEEEEc----CCcccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHHHHcCCCCCCEEEEecCCCccc-ccccCCCC
Q 014264 207 DANIIGVLVG----TLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKLANFPECDVFINVSCAQTAL-LDSKEFLA 281 (427)
Q Consensus 207 ~A~~iGIlvg----Tl~~q~~~~~i~~l~~li~~~GKK~y~~~vgkln~aKLaNF~eiD~fVlvaCPr~si-~d~~~f~k 281 (427)
...++|||+. ++.-..+..+++.+.+.++++|....+..-.+ .+ .....+|.++++++....+ ....+...
T Consensus 62 ~~~~i~v~~~~~~~~~~~~f~~~l~~~i~~~~~~~g~~~~~~~~~~--~~--~~~~~vDgiI~~~~~~~~~~~~l~~~~~ 137 (327)
T PRK10339 62 QHHILAIYSYQQELEINDPYYLAIRHGIETQCEKLGIELTNCYEHS--GL--PDIKNVTGILIVGKPTPALRAAASALTD 137 (327)
T ss_pred cccEEEEEEccccccccCchHHHHHHHHHHHHHHCCCEEEEeeccc--cc--cccccCCEEEEeCCCCHHHHHHHHhcCC
Confidence 4568899884 55656777899999999999998865433222 11 1235799999987522111 12233455
Q ss_pred cccC
Q 014264 282 PVIT 285 (427)
Q Consensus 282 PvlT 285 (427)
|||+
T Consensus 138 pvV~ 141 (327)
T PRK10339 138 NICF 141 (327)
T ss_pred CEEE
Confidence 7654
No 86
>cd06307 PBP1_uncharacterized_sugar_binding Periplasmic sugar-binding domain of uncharacterized transport systems. Periplasmic sugar-binding domain of uncharacterized transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein (PBP1) superfamily. The members of this group are predicted to be involved in the transport of sugar-containing molecules across cellular and organellar membranes.
Probab=43.88 E-value=28 Score=33.03 Aligned_cols=76 Identities=16% Similarity=0.123 Sum_probs=47.0
Q ss_pred eEEEEEcCCcccCcHHHHHHHHHHHHHcCCcEEEEEc---CCCCHHHH----cCCC-CCCEEEEecCCCccc----cccc
Q 014264 210 IIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVM---GKPNPAKL----ANFP-ECDVFINVSCAQTAL----LDSK 277 (427)
Q Consensus 210 ~iGIlvgTl~~q~~~~~i~~l~~li~~~GKK~y~~~v---gkln~aKL----aNF~-eiD~fVlvaCPr~si----~d~~ 277 (427)
+||+|+....-..+..+++.+.+.+++.|...++... ..-++++. .++. .+|++|+++...... ....
T Consensus 1 ~ig~v~~~~~~~~~~~~~~~i~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~i~~~~~~vdgiii~~~~~~~~~~~i~~~~ 80 (275)
T cd06307 1 RLGFLLPKGSNAFYRELAAALEAAAAAFPDARIRVRIHFVESFDPAALAAALLRLGARSDGVALVAPDHPQVRAAVARLA 80 (275)
T ss_pred CeEEEeCCCCChHHHHHHHHHHHHHhhhhccCceEEEEEccCCCHHHHHHHHHHHHhcCCEEEEeCCCcHHHHHHHHHHH
Confidence 4788888877777778888888888888876665543 22334322 2222 588888877543321 1123
Q ss_pred CCCCcccC
Q 014264 278 EFLAPVIT 285 (427)
Q Consensus 278 ~f~kPvlT 285 (427)
+...|||+
T Consensus 81 ~~~ipvV~ 88 (275)
T cd06307 81 AAGVPVVT 88 (275)
T ss_pred HCCCcEEE
Confidence 34557664
No 87
>TIGR01754 flav_RNR ribonucleotide reductase-associated flavodoxin, putative. This model represents a family of proteins found immediately downstream of ribonucleotide reductase genes in Xyella fastidiosa and some Gram-positive bacteria. It appears to be a highly divergent flavodoxin of the short chain type, more like the flavodoxins of the sulfate-reducing genus Desulfovibrio than like the NifF flavodoxins associated with nitrogen fixation.
Probab=43.83 E-value=48 Score=28.76 Aligned_cols=57 Identities=12% Similarity=0.051 Sum_probs=36.0
Q ss_pred eEEEEEcCCcccCcHHHHHHHHHHHHHcCCcEE-EEEcCCCCHHHHcCCCCCCEEEEecCC
Q 014264 210 IIGVLVGTLGVAGYLHMIHQMKELITKAGKKAY-TLVMGKPNPAKLANFPECDVFINVSCA 269 (427)
Q Consensus 210 ~iGIlvgTl~~q~~~~~i~~l~~li~~~GKK~y-~~~vgkln~aKLaNF~eiD~fVlvaCP 269 (427)
.+.||.+|..| +...++++|.+.++..|.++- ++-+.+++.. ..++.+.|++ +++||
T Consensus 2 ~i~IiY~S~tG-nTe~iA~~ia~~l~~~g~~v~~~~~~~~~~~~-~~~~~~~d~i-ilgs~ 59 (140)
T TIGR01754 2 RILLAYLSLSG-NTEEVAFMIQDYLQKDGHEVDILHRIGTLADA-PLDPENYDLV-FLGTW 59 (140)
T ss_pred eEEEEEECCCC-hHHHHHHHHHHHHhhCCeeEEecccccccccC-cCChhhCCEE-EEEcC
Confidence 46799999774 578899999999998887653 2223432211 1234455764 45554
No 88
>PF01729 QRPTase_C: Quinolinate phosphoribosyl transferase, C-terminal domain; InterPro: IPR002638 Quinolinate phosphoribosyl transferase (QPRTase) or nicotinate-nucleotide pyrophosphorylase 2.4.2.19 from EC is involved in the de novo synthesis of NAD in both prokaryotes and eukaryotes. It catalyses the reaction of quinolinic acid with 5-phosphoribosyl-1-pyrophosphate (PRPP) in the presence of Mg2+ to give rise to nicotinic acid mononucleotide (NaMN), pyrophosphate and carbon dioxide [, ]. Unlike IPR004393 from INTERPRO, this domain also includes the molybdenum transport system protein ModD.; GO: 0004514 nicotinate-nucleotide diphosphorylase (carboxylating) activity, 0009435 NAD biosynthetic process; PDB: 3C2O_A 3C2F_A 3C2E_A 3C2R_A 3C2V_A 1QPN_E 1QPO_A 1QPQ_F 1QPR_E 2I14_D ....
Probab=43.75 E-value=30 Score=31.66 Aligned_cols=63 Identities=14% Similarity=0.129 Sum_probs=47.1
Q ss_pred HHHHHhcCCeEEEEEcCCcccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHHHHcCCC--CCCEEEEec
Q 014264 201 LVEKAKDANIIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKLANFP--ECDVFINVS 267 (427)
Q Consensus 201 ~I~ka~~A~~iGIlvgTl~~q~~~~~i~~l~~li~~~GKK~y~~~vgkln~aKLaNF~--eiD~fVlva 267 (427)
..++|.+++.=+|.+=+.+ ++.++++.+.++..+.++-+.+.|.+|++.+.+|. .+|++++-+
T Consensus 92 e~~ea~~~g~d~I~lD~~~----~~~~~~~v~~l~~~~~~v~ie~SGGI~~~ni~~ya~~gvD~isvg~ 156 (169)
T PF01729_consen 92 EAEEALEAGADIIMLDNMS----PEDLKEAVEELRELNPRVKIEASGGITLENIAEYAKTGVDVISVGS 156 (169)
T ss_dssp HHHHHHHTT-SEEEEES-C----HHHHHHHHHHHHHHTTTSEEEEESSSSTTTHHHHHHTT-SEEEECH
T ss_pred HHHHHHHhCCCEEEecCcC----HHHHHHHHHHHhhcCCcEEEEEECCCCHHHHHHHHhcCCCEEEcCh
Confidence 4456667887778888764 57777777777888889999999999999998885 578877654
No 89
>cd01575 PBP1_GntR Ligand-binding domain of DNA transcription repressor GntR specific for gluconate, a member of the LacI-GalR family of bacterial transcription regulators. This group represents the ligand-binding domain of DNA transcription repressor GntR specific for gluconate, a member of the LacI-GalR family of bacterial transcription regulators. The ligand-binding domain of GntR is structurally homologous to the periplasmic sugar-binding domain of ABC-type transporters and both domains contain the type I periplasmic binding protein-like fold. The LacI-GalR family repressors 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 type I periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding,
Probab=43.69 E-value=47 Score=31.00 Aligned_cols=76 Identities=14% Similarity=0.158 Sum_probs=51.4
Q ss_pred eEEEEEcCCcccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHHHHc----CC--CCCCEEEEecCCCc-ccc-cccCCCC
Q 014264 210 IIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKLA----NF--PECDVFINVSCAQT-ALL-DSKEFLA 281 (427)
Q Consensus 210 ~iGIlvgTl~~q~~~~~i~~l~~li~~~GKK~y~~~vgkln~aKLa----NF--~eiD~fVlvaCPr~-si~-d~~~f~k 281 (427)
+||+|+.......+..+++.+.+.+++.|.+..++.. .-++++.. .+ ..+|..+++++... ... .......
T Consensus 1 ~Ig~i~~~~~~~~~~~~~~gi~~~~~~~g~~~~~~~~-~~~~~~~~~~~~~l~~~~vdgiii~~~~~~~~~~~~~~~~~i 79 (268)
T cd01575 1 LVAVLVPSLSNSVFADVLQGISDVLEAAGYQLLLGNT-GYSPEREEELLRTLLSRRPAGLILTGLEHTERTRQLLRAAGI 79 (268)
T ss_pred CEEEEeCCCcchhHHHHHHHHHHHHHHcCCEEEEecC-CCCchhHHHHHHHHHHcCCCEEEEeCCCCCHHHHHHHHhcCC
Confidence 5899998888888899999999999999988766544 44554432 11 26999999887543 111 1123345
Q ss_pred cccCH
Q 014264 282 PVITP 286 (427)
Q Consensus 282 PvlTP 286 (427)
|||+-
T Consensus 80 pvv~~ 84 (268)
T cd01575 80 PVVEI 84 (268)
T ss_pred CEEEE
Confidence 76653
No 90
>cd01571 NAPRTase_B Nicotinate phosphoribosyltransferase (NAPRTase), subgroup B. Nicotinate phosphoribosyltransferase catalyses the formation of NAMN and PPi from 5-phosphoribosy -1-pyrophosphate (PRPP) and nicotinic acid, this is the first, and also rate limiting, reaction in the NAD salvage synthesis. This salvage pathway serves to recycle NAD degradation products.
Probab=43.62 E-value=47 Score=33.23 Aligned_cols=57 Identities=18% Similarity=0.237 Sum_probs=43.4
Q ss_pred CeEEEEEcCCc--ccCcHHHHHHHHHHHHHcC-CcEEEEEcCCCCHHHHcCCC--CCCEEEE
Q 014264 209 NIIGVLVGTLG--VAGYLHMIHQMKELITKAG-KKAYTLVMGKPNPAKLANFP--ECDVFIN 265 (427)
Q Consensus 209 ~~iGIlvgTl~--~q~~~~~i~~l~~li~~~G-KK~y~~~vgkln~aKLaNF~--eiD~fVl 265 (427)
+..+|.+=+.+ .-..++.++++++.++..| .+.-+.+.|.||++++.+|. +||++=+
T Consensus 211 ~~d~I~lDn~~~~~G~~~~~~~~~~~~l~~~g~~~~~ieaSGgI~~~~i~~~a~~gvD~isv 272 (302)
T cd01571 211 KLDGVRLDTPSSRRGVFRYLIREVRWALDIRGYKHVKIFVSGGLDEEDIKELEDVGVDAFGV 272 (302)
T ss_pred CCcEEEECCCCCCCCCHHHHHHHHHHHHHhCCCCCeEEEEeCCCCHHHHHHHHHcCCCEEEC
Confidence 35677777753 1226677899999999887 67889999999999999885 4787633
No 91
>cd01540 PBP1_arabinose_binding Periplasmic L-arabinose-binding protein (ABP), a member of a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily. Periplasmic L-arabinose-binding protein (ABP), a member of a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily. ABP is only involved in transport contrary to other related sugar-binding proteins such as the glucose/galactose-binding protein (GGBP) and the ribose-binding protein (RBP), both of which are involved in chemotaxis as well as transport. The periplasmic ABP consists of two alpha/beta globular domains connected by a three-stranded hinge, a Venus flytrap-like domain, which undergoes a transition from an open to a closed conformational state upon ligand binding. Moreover, ABP is homologous to the ligand-binding domain of eukaryotic receptors such as metabotropic glutamate receptor (mGluR) and DNA-binding transcriptional repressors such a
Probab=43.44 E-value=22 Score=34.01 Aligned_cols=74 Identities=14% Similarity=0.112 Sum_probs=46.6
Q ss_pred eEEEEEcCCcccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHHHHc----CC--CCCCEEEEecCCC-cc---cccccCC
Q 014264 210 IIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKLA----NF--PECDVFINVSCAQ-TA---LLDSKEF 279 (427)
Q Consensus 210 ~iGIlvgTl~~q~~~~~i~~l~~li~~~GKK~y~~~vgkln~aKLa----NF--~eiD~fVlvaCPr-~s---i~d~~~f 279 (427)
+||+|+..+....+..+++.+.+.+++.|.+..++. .. ++++.. ++ ..+|.+|+.++.. .. +...++.
T Consensus 1 ~Ig~v~~~~~~~~~~~~~~gi~~~~~~~g~~~~~~~-~~-~~~~~~~~i~~~~~~~~dgiii~~~~~~~~~~~~~~~~~~ 78 (289)
T cd01540 1 KIGFIVKQPEEPWFQTEWKFAKKAAKEKGFTVVKID-VP-DGEKVLSAIDNLGAQGAKGFVICVPDVKLGPAIVAKAKAY 78 (289)
T ss_pred CeeeecCCCCCcHHHHHHHHHHHHHHHcCCEEEEcc-CC-CHHHHHHHHHHHHHcCCCEEEEccCchhhhHHHHHHHHhC
Confidence 578888887777788889999999999887754332 33 554332 11 2589999877631 11 1122345
Q ss_pred CCcccC
Q 014264 280 LAPVIT 285 (427)
Q Consensus 280 ~kPvlT 285 (427)
-.|||+
T Consensus 79 ~iPvV~ 84 (289)
T cd01540 79 NMKVVA 84 (289)
T ss_pred CCeEEE
Confidence 567664
No 92
>PRK09271 flavodoxin; Provisional
Probab=43.21 E-value=82 Score=28.07 Aligned_cols=57 Identities=12% Similarity=0.089 Sum_probs=38.7
Q ss_pred eEEEEEcCCcccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHHH-HcCCCCCCEEEEec
Q 014264 210 IIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAK-LANFPECDVFINVS 267 (427)
Q Consensus 210 ~iGIlvgTl~~q~~~~~i~~l~~li~~~GKK~y~~~vgkln~aK-LaNF~eiD~fVlva 267 (427)
++.|+.+|..| +...++++|.+.|+..|.++-+.-+....... ...+.+.|++++.+
T Consensus 2 kv~IvY~S~tG-nTe~~A~~ia~~l~~~g~~v~~~~~~~~~~~~~~~~~~~~d~vilgt 59 (160)
T PRK09271 2 RILLAYASLSG-NTREVAREIEERCEEAGHEVDWVETDVQTLAEYPLDPEDYDLYLLGT 59 (160)
T ss_pred eEEEEEEcCCc-hHHHHHHHHHHHHHhCCCeeEEEecccccccccccCcccCCEEEEEC
Confidence 46899999874 67899999999999999887555554433222 22444556655544
No 93
>PRK12359 flavodoxin FldB; Provisional
Probab=42.70 E-value=82 Score=28.86 Aligned_cols=53 Identities=13% Similarity=0.252 Sum_probs=39.7
Q ss_pred eEEEEEcCCcccCcHHHHHHHHHHHHHcCC-cEEEEEcCCCCHHHHcCCCCCCEEEEecCCC
Q 014264 210 IIGVLVGTLGVAGYLHMIHQMKELITKAGK-KAYTLVMGKPNPAKLANFPECDVFINVSCAQ 270 (427)
Q Consensus 210 ~iGIlvgTl~~q~~~~~i~~l~~li~~~GK-K~y~~~vgkln~aKLaNF~eiD~fVlvaCPr 270 (427)
+++|+-+|.+ -+...++++|++.+ |. .+-++-+.+..++.|.++ | +|+++||=
T Consensus 2 ki~I~Y~S~T-GNTe~vAe~I~~~l---g~~~v~v~~i~~~~~~~l~~y---D-~iIlG~pT 55 (172)
T PRK12359 2 KIGLFYGSST-CYTEMAAEKIRDII---GEELVDLHNLKDDPPKLMEQY---D-VLILGIPT 55 (172)
T ss_pred eEEEEEECCC-CHHHHHHHHHHHHh---CCCeEEEEEcccCChhHHccC---C-EEEEEecc
Confidence 5799999987 46788899888776 43 356777788888777665 5 67788885
No 94
>cd05013 SIS_RpiR RpiR-like protein. RpiR contains a SIS (Sugar ISomerase) domain, which is found in many phosphosugar isomerases and phosphosugar binding proteins. In E. coli, rpiR negatively regulates the expression of rpiB gene. Both rpiB and rpiA are ribose phosphate isomerases that catalyze the reversible reactions of ribose 5-phosphate into ribulose 5-phosphate.
Probab=42.38 E-value=1.3e+02 Score=25.03 Aligned_cols=68 Identities=19% Similarity=0.150 Sum_probs=47.5
Q ss_pred HHHHHhcCCeEEEEEcCCcccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHHHHcCCCCCCEEEEecCCCcc
Q 014264 201 LVEKAKDANIIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKLANFPECDVFINVSCAQTA 272 (427)
Q Consensus 201 ~I~ka~~A~~iGIlvgTl~~q~~~~~i~~l~~li~~~GKK~y~~~vgkln~aKLaNF~eiD~fVlvaCPr~s 272 (427)
.++...+++++ +++|+ .....+.+.++..++..|+.++.+.-......-+.+..+=|++++++-...+
T Consensus 6 ~~~~i~~~~~i-~i~g~---g~s~~~a~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~iS~~g~~ 73 (139)
T cd05013 6 AVDLLAKARRI-YIFGV---GSSGLVAEYLAYKLLRLGKPVVLLSDPHLQLMSAANLTPGDVVIAISFSGET 73 (139)
T ss_pred HHHHHHhCCEE-EEEEc---CchHHHHHHHHHHHHHcCCceEEecCHHHHHHHHHcCCCCCEEEEEeCCCCC
Confidence 44555667776 66665 3466789999999999999888764444444444456667899988877664
No 95
>cd06302 PBP1_LsrB_Quorum_Sensing Periplasmic binding domain of autoinducer-2 (AI-2) receptor LsrB from Salmonella typhimurium and its close homologs. Periplasmic binding domain of autoinducer-2 (AI-2) receptor LsrB from Salmonella typhimurium and its close homologs from other bacteria. The members of this group are homologous to a family of periplasmic pentose/hexose sugar-binding proteins that function as the primary receptors for chemotaxis and transporters of many sugar based solutes in bacteria and archaea and that are a member of the type I periplasmic binding protein superfamily. LsrB binds a chemically distinct form of the AI-2 signal that lacks boron, in contrast to the Vibrio harveyi AI-2 signaling molecule that has an unusual furanosyl borate diester. Hence, many bacteria coordinate their gene expression according to the local density of their population by producing species specific AI-2. This process of quorum sensing allows LsrB to function as a periplasmic AI-2 binding p
Probab=41.95 E-value=48 Score=32.20 Aligned_cols=59 Identities=17% Similarity=0.151 Sum_probs=41.6
Q ss_pred eEEEEEcCCcccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHHHHc----CC--CCCCEEEEecC
Q 014264 210 IIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKLA----NF--PECDVFINVSC 268 (427)
Q Consensus 210 ~iGIlvgTl~~q~~~~~i~~l~~li~~~GKK~y~~~vgkln~aKLa----NF--~eiD~fVlvaC 268 (427)
+||+|+.+.+-..+..+++.+++.+++.|.+..++.-..-++++-. ++ ..+|.+|+++.
T Consensus 1 ~I~vi~~~~~~~f~~~i~~gi~~~a~~~g~~v~~~~~~~~d~~~~~~~i~~~~~~~~DgiIi~~~ 65 (298)
T cd06302 1 TIAFVPKVTGIPYFNRMEEGAKEAAKELGVDAIYVGPTTADAAGQVQIIEDLIAQGVDAIAVVPN 65 (298)
T ss_pred CEEEEEcCCCChHHHHHHHHHHHHHHHhCCeEEEECCCCCCHHHHHHHHHHHHhcCCCEEEEecC
Confidence 5888888877777888999999999998877665434445554332 22 25899888764
No 96
>cd02071 MM_CoA_mut_B12_BD methylmalonyl CoA mutase B12 binding domain. This domain binds to B12 (adenosylcobamide), which initiates the conversion of succinyl CoA and methylmalonyl CoA by forming an adenosyl radical, which then undergoes a rearrangement exchanging a hydrogen atom with a group attached to a neighboring carbon atom. This family is present in both mammals and bacteria. Bacterial members are heterodimers and involved in the fermentation of pyruvate to propionate. Mammalian members are homodimers and responsible for the conversion of odd-chain fatty acids and branched-chain amino acids via propionyl CoA to succinyl CoA for further degradation.
Probab=41.84 E-value=65 Score=27.38 Aligned_cols=62 Identities=18% Similarity=0.346 Sum_probs=41.7
Q ss_pred HhcCCeEEEEEcCCcccCcHHHHHHHHHHHHHcCC-cEEEEEcCCCCHHH---HcCCCCCCEEEEecCCC
Q 014264 205 AKDANIIGVLVGTLGVAGYLHMIHQMKELITKAGK-KAYTLVMGKPNPAK---LANFPECDVFINVSCAQ 270 (427)
Q Consensus 205 a~~A~~iGIlvgTl~~q~~~~~i~~l~~li~~~GK-K~y~~~vgkln~aK---LaNF~eiD~fVlvaCPr 270 (427)
..++..++| +.+. ..+.+.++.+.+.|++.|. +..+++-|...++. |... .+|.|+-.+|+-
T Consensus 48 ~~~~d~V~i--S~~~-~~~~~~~~~~~~~L~~~~~~~i~i~~GG~~~~~~~~~~~~~-G~d~~~~~~~~~ 113 (122)
T cd02071 48 QEDVDVIGL--SSLS-GGHMTLFPEVIELLRELGAGDILVVGGGIIPPEDYELLKEM-GVAEIFGPGTSI 113 (122)
T ss_pred HcCCCEEEE--cccc-hhhHHHHHHHHHHHHhcCCCCCEEEEECCCCHHHHHHHHHC-CCCEEECCCCCH
Confidence 345666655 4433 6788888999999999988 55555555555554 4444 599998888763
No 97
>TIGR01579 MiaB-like-C MiaB-like tRNA modifying enzyme. This clade is a member of a subfamily (TIGR00089) and spans low GC Gram positive bacteria, alpha and epsilon proteobacteria, Campylobacter, Porphyromonas, Aquifex, Thermotoga, Chlamydia, Treponema and Fusobacterium.
Probab=41.76 E-value=29 Score=36.09 Aligned_cols=65 Identities=18% Similarity=0.327 Sum_probs=35.1
Q ss_pred HHHHHHHhcCCeEEEEEcCCcccCcHHHHHHHHHHHHHcCCcEEEEEcC---CCCHHHHcCCCCCCEEE
Q 014264 199 YYLVEKAKDANIIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMG---KPNPAKLANFPECDVFI 264 (427)
Q Consensus 199 y~~I~ka~~A~~iGIlvgTl~~q~~~~~i~~l~~li~~~GKK~y~~~vg---kln~aKLaNF~eiD~fV 264 (427)
|..+....+|..++|=..|...+.-...++.+++ +++.+++..+++.| ...|+.+..++++|++|
T Consensus 25 ~~~~~~~~~aD~v~intctv~~~a~~~~~~~i~~-~k~~~p~~~vvvgGc~a~~~~ee~~~~~~vD~vv 92 (414)
T TIGR01579 25 YEVVPDEDKADVYIINTCTVTAKADSKARRAIRR-ARRQNPTAKIIVTGCYAQSNPKELADLKDVDLVL 92 (414)
T ss_pred CEECCCcccCCEEEEeccccchHHHHHHHHHHHH-HHhhCCCcEEEEECCccccCHHHHhcCCCCcEEE
Confidence 3344444456766554444433222334444433 35566666666666 34677777777777776
No 98
>cd06294 PBP1_ycjW_transcription_regulator_like Ligand-binding domain of uncharacterized transcription regulator ycjW which is a member of the LacI-GalR family repressors. This group includes the ligand-binding domain of uncharacterized transcription regulator ycjW which is a member of 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 affinity of the repressor.
Probab=41.73 E-value=57 Score=30.50 Aligned_cols=59 Identities=12% Similarity=0.200 Sum_probs=37.1
Q ss_pred eEEEEEcC-----CcccCcHHHHHHHHHHHHHcCCcEEEEEcCCCC--HHHHcCC---CCCCEEEEecC
Q 014264 210 IIGVLVGT-----LGVAGYLHMIHQMKELITKAGKKAYTLVMGKPN--PAKLANF---PECDVFINVSC 268 (427)
Q Consensus 210 ~iGIlvgT-----l~~q~~~~~i~~l~~li~~~GKK~y~~~vgkln--~aKLaNF---~eiD~fVlvaC 268 (427)
+||+|+.. +.-..+..+++.+++.+++.|.+..+....... ...+.++ ..+|++|+++.
T Consensus 1 ~igli~p~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~dgiii~~~ 69 (270)
T cd06294 1 TIGVVLPPSADEAFQNPFFIEVLRGISAVANENGYDISLATGKNEEELLEEVKKMIQQKRVDGFILLYS 69 (270)
T ss_pred CEEEEeCCccccCcCCCCHHHHHHHHHHHHHHCCCEEEEecCCCcHHHHHHHHHHHHHcCcCEEEEecC
Confidence 47888875 455667788899999999998776543332211 1122221 24899888764
No 99
>PF02514 CobN-Mg_chel: CobN/Magnesium Chelatase; InterPro: IPR003672 This family contains a domain common to the cobN protein and to magnesium protoporphyrin chelatase. CobN may play a role in cobalt insertion reactions and is implicated in the conversion of precorrin-2 to cobyrinic acid in cobalamin biosynthesis []. Magnesium protoporphyrin chelatase is involved in chlorophyll biosynthesis as the third subunit of light-independent protochlorophyllide reductase in bacteria and plants [].; GO: 0009058 biosynthetic process
Probab=41.51 E-value=16 Score=43.08 Aligned_cols=93 Identities=19% Similarity=0.189 Sum_probs=45.8
Q ss_pred CceEEEecCCCCce--eccc-CcHHHHHHHHHHHHHHHhcCCeEEEEE-cCCcccCcHHHHHHHHHHHHHcCCcEEEEEc
Q 014264 171 GCEIVRYDATEERL--LTDV-SQPLKILKRRYYLVEKAKDANIIGVLV-GTLGVAGYLHMIHQMKELITKAGKKAYTLVM 246 (427)
Q Consensus 171 ~~~v~~yDP~~~~~--~~~~-~~~~r~L~rRy~~I~ka~~A~~iGIlv-gTl~~q~~~~~i~~l~~li~~~GKK~y~~~v 246 (427)
+..+|.+||..--- ..+. ......|.+||..=+ =+-=+++|+++ ||=.....-..+..+-.+ -|-|..-=..
T Consensus 716 GrN~y~~Dp~~iPt~~A~~~G~~la~~ll~~y~~~~-g~yPe~v~~vlW~~~t~rt~G~~~aqil~l---lGv~Pvw~~~ 791 (1098)
T PF02514_consen 716 GRNFYSFDPRKIPTPAAWEVGKKLAEQLLERYREEH-GRYPEKVAFVLWGTETMRTGGEDIAQILYL---LGVRPVWDSS 791 (1098)
T ss_pred CCcccccCcccccCHHHHHHHHHHHHHHHHHHHHhc-CCCCceeEEEEEecchhhcCCHHHHHHHHh---cCceeccCCC
Confidence 55689999986421 1111 122233444554333 33346788666 443333333434333333 3444332233
Q ss_pred CCC-----CHHHHcCCCCCCEEEEec
Q 014264 247 GKP-----NPAKLANFPECDVFINVS 267 (427)
Q Consensus 247 gkl-----n~aKLaNF~eiD~fVlva 267 (427)
|++ -|-.-.+-|.|||.|.++
T Consensus 792 grv~~~e~iPl~eL~RPRIDV~~~~s 817 (1098)
T PF02514_consen 792 GRVSGVELIPLEELGRPRIDVVVRIS 817 (1098)
T ss_pred CCCCCceeccHHHcCCCCeeEEEecc
Confidence 333 244444678899998875
No 100
>cd06300 PBP1_ABC_sugar_binding_like_1 Periplasmic sugar-binding component of uncharacterized ABC-type transport systems that are members of the pentose/hexose sugar-binding protein family of the type I periplasmic binding protein superfamily. Periplasmic sugar-binding component of uncharacterized ABC-type transport systems that are members of the pentose/hexose sugar-binding protein family of the type I periplasmic binding protein superfamily, which consists of two alpha/beta globular 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. Members of this group are predicted to be involved in the transport of sugar-containing molecules across cellular and organellar membranes; however their substrate specificity is not known in detail.
Probab=41.09 E-value=41 Score=31.75 Aligned_cols=77 Identities=19% Similarity=0.173 Sum_probs=48.0
Q ss_pred eEEEEEcCCcccCcHHHHHHHHHHHHHc---CCcE-EEEEcCCCCHHHHcCC------CCCCEEEEecCCCcccc----c
Q 014264 210 IIGVLVGTLGVAGYLHMIHQMKELITKA---GKKA-YTLVMGKPNPAKLANF------PECDVFINVSCAQTALL----D 275 (427)
Q Consensus 210 ~iGIlvgTl~~q~~~~~i~~l~~li~~~---GKK~-y~~~vgkln~aKLaNF------~eiD~fVlvaCPr~si~----d 275 (427)
+||+++.......+..+++.+.+.+++. |.+. .++.-+.-++++..+. ..+|.+|+.++-...+. -
T Consensus 1 ~Ig~i~~~~~~~~~~~~~~~i~~~~~~~~~~g~~~~l~i~~~~~~~~~~~~~~~~~~~~~vdgiIi~~~~~~~~~~~l~~ 80 (272)
T cd06300 1 KIGLSNSYAGNTWRAQMLDEFKAQAKELKKAGLISEFIVTSADGDVAQQIADIRNLIAQGVDAIIINPASPTALNPVIEE 80 (272)
T ss_pred CeEEeccccCChHHHHHHHHHHHHHHhhhccCCeeEEEEecCCCCHHHHHHHHHHHHHcCCCEEEEeCCChhhhHHHHHH
Confidence 4788998877777778899999988888 7653 3444445455543211 26899998776433222 2
Q ss_pred ccCCCCcccCH
Q 014264 276 SKEFLAPVITP 286 (427)
Q Consensus 276 ~~~f~kPvlTP 286 (427)
.++...|||+.
T Consensus 81 ~~~~~iPvv~~ 91 (272)
T cd06300 81 ACEAGIPVVSF 91 (272)
T ss_pred HHHCCCeEEEE
Confidence 23445576653
No 101
>cd01452 VWA_26S_proteasome_subunit 26S proteasome plays a major role in eukaryotic protein breakdown, especially for ubiquitin-tagged proteins. It is an ATP-dependent protease responsible for the bulk of non-lysosomal proteolysis in eukaryotes, often using covalent modification of proteins by ubiquitylation. It consists of a 20S proteolytic core particle (CP) and a 19S regulatory particle (RP). The CP is an ATP independent peptidase consisting of hydrolyzing activities. One or both ends of CP carry the RP that confers both ubiquitin and ATP dependence to the 26S proteosome. The RP's proposed functions include recognition of substrates and translocation of these to CP for proteolysis. The RP can dissociate into a stable lid and base subcomplexes. The base is composed of three non-ATPase subunits (Rpn 1, 2 and 10). A single residue in the vWA domain of Rpn10 has been implicated to be responsible for stabilizing the lid-base association.
Probab=41.09 E-value=59 Score=30.30 Aligned_cols=49 Identities=18% Similarity=0.204 Sum_probs=37.5
Q ss_pred CeEEEEEcCCcccCcHHHHHHHHHHHHHcCCcEEEEEcCC--CCHHHHcCCC
Q 014264 209 NIIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGK--PNPAKLANFP 258 (427)
Q Consensus 209 ~~iGIlvgTl~~q~~~~~i~~l~~li~~~GKK~y~~~vgk--ln~aKLaNF~ 258 (427)
+.+-|++|+.+-..-.. +..+.+.++++|-+++++.+|+ -|++||..|-
T Consensus 108 ~rivi~v~S~~~~d~~~-i~~~~~~lkk~~I~v~vI~~G~~~~~~~~l~~~~ 158 (187)
T cd01452 108 QRIVAFVGSPIEEDEKD-LVKLAKRLKKNNVSVDIINFGEIDDNTEKLTAFI 158 (187)
T ss_pred ceEEEEEecCCcCCHHH-HHHHHHHHHHcCCeEEEEEeCCCCCCHHHHHHHH
Confidence 47889999987554444 4456667788999999999995 5788998874
No 102
>cd06275 PBP1_PurR Ligand-binding domain of purine repressor, PurR, which functions as the master regulatory protein of de novo purine nucleotide biosynthesis in Escherichia coli. Ligand-binding domain of purine repressor, PurR, which functions as the master regulatory protein of de novo purine nucleotide biosynthesis in Escherichia coli. This dimeric PurR belongs to the LacI-GalR family of transcription regulators and is activated to bind to DNA operator sites by initially binding either of high affinity corepressors, hypoxanthine or guanine. PurR is composed of two functional domains: aan 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 purine transcription repressor undergoes a
Probab=40.80 E-value=97 Score=28.95 Aligned_cols=60 Identities=13% Similarity=0.191 Sum_probs=42.8
Q ss_pred eEEEEEcCCcccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHHHHc----CC--CCCCEEEEecCCC
Q 014264 210 IIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKLA----NF--PECDVFINVSCAQ 270 (427)
Q Consensus 210 ~iGIlvgTl~~q~~~~~i~~l~~li~~~GKK~y~~~vgkln~aKLa----NF--~eiD~fVlvaCPr 270 (427)
+||+|+.+..-..+..+++.+++.+++.|....++.. .=++++.. ++ ..+|.+|+.++..
T Consensus 1 ~igvi~~~~~~~~~~~~~~gi~~~~~~~g~~~~~~~~-~~~~~~~~~~i~~l~~~~vdgiii~~~~~ 66 (269)
T cd06275 1 TIGMLVTTSTNPFFAEVVRGVEQYCYRQGYNLILCNT-EGDPERQRSYLRMLAQKRVDGLLVMCSEY 66 (269)
T ss_pred CEEEEeCCCCcchHHHHHHHHHHHHHHcCCEEEEEeC-CCChHHHHHHHHHHHHcCCCEEEEecCCC
Confidence 4899998877677888999999999999977654433 33454321 22 2689999988753
No 103
>TIGR00640 acid_CoA_mut_C methylmalonyl-CoA mutase C-terminal domain. Methylmalonyl-CoA mutase (EC 5.4.99.2) catalyzes a reversible isomerization between L-methylmalonyl-CoA and succinyl-CoA. The enzyme uses an adenosylcobalamin cofactor. It may be a homodimer, as in mitochondrion, or a heterodimer with partially homologous beta chain that does not bind the adenosylcobalamin cofactor, as in Propionibacterium freudenreichii. The most similar archaeal sequences are separate chains, such as AF2215 and AF2219 of Archaeoglobus fulgidus, that correspond roughly to the first 500 and last 130 residues, respectively of known methylmalonyl-CoA mutases. This model describes the C-terminal domain subfamily. In a neighbor-joining tree (methylaspartate mutase S chain as the outgroup), AF2219 branches with a coenzyme B12-dependent enzyme known not to be 5.4.99.2.
Probab=40.52 E-value=66 Score=28.07 Aligned_cols=72 Identities=17% Similarity=0.289 Sum_probs=46.7
Q ss_pred HHHHHhcCCeEEEEEcCCcccCcHHHHHHHHHHHHHcCCcEEEEEcCC-CCHHHHcCCC--CCCEEEEecCCCccc
Q 014264 201 LVEKAKDANIIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGK-PNPAKLANFP--ECDVFINVSCAQTAL 273 (427)
Q Consensus 201 ~I~ka~~A~~iGIlvgTl~~q~~~~~i~~l~~li~~~GKK~y~~~vgk-ln~aKLaNF~--eiD~fVlvaCPr~si 273 (427)
.++.|++.+.=.|.++++. ..|.+.+..+.+.|+++|.....+++|- +-.+..+.|. .+|.|+-.++|-..+
T Consensus 45 ~v~aa~e~~adii~iSsl~-~~~~~~~~~~~~~L~~~g~~~i~vivGG~~~~~~~~~l~~~Gvd~~~~~gt~~~~i 119 (132)
T TIGR00640 45 IARQAVEADVHVVGVSSLA-GGHLTLVPALRKELDKLGRPDILVVVGGVIPPQDFDELKEMGVAEIFGPGTPIPES 119 (132)
T ss_pred HHHHHHHcCCCEEEEcCch-hhhHHHHHHHHHHHHhcCCCCCEEEEeCCCChHhHHHHHHCCCCEEECCCCCHHHH
Confidence 4455555444444456665 6788999999999999998666677773 3233344443 588888777765443
No 104
>PRK05568 flavodoxin; Provisional
Probab=40.21 E-value=1.4e+02 Score=25.48 Aligned_cols=56 Identities=13% Similarity=0.141 Sum_probs=43.7
Q ss_pred eEEEEEcCCcccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHHHHcCCCCCCEEEEecCCC
Q 014264 210 IIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKLANFPECDVFINVSCAQ 270 (427)
Q Consensus 210 ~iGIlvgTl~~q~~~~~i~~l~~li~~~GKK~y~~~vgkln~aKLaNF~eiD~fVlvaCPr 270 (427)
.+.|+-.|.. -+...+++.|.+-+++.|-.+-++-+.+.+..+|.+ .|. |++++|=
T Consensus 3 ~~~IvY~S~~-GnT~~~a~~i~~~~~~~g~~v~~~~~~~~~~~~~~~---~d~-iilgsp~ 58 (142)
T PRK05568 3 KINIIYWSGT-GNTEAMANLIAEGAKENGAEVKLLNVSEASVDDVKG---ADV-VALGSPA 58 (142)
T ss_pred eEEEEEECCC-chHHHHHHHHHHHHHHCCCeEEEEECCCCCHHHHHh---CCE-EEEECCc
Confidence 5778888865 567899999999999999998888888888776654 465 5566664
No 105
>PRK09426 methylmalonyl-CoA mutase; Reviewed
Probab=39.89 E-value=54 Score=36.95 Aligned_cols=73 Identities=16% Similarity=0.205 Sum_probs=48.4
Q ss_pred HHHHHhcCCeEEEEEcCCcccCcHHHHHHHHHHHHHcCCcEE-EEEcCCCCHHHHcCC--CCCCEEEEecCCCcccc
Q 014264 201 LVEKAKDANIIGVLVGTLGVAGYLHMIHQMKELITKAGKKAY-TLVMGKPNPAKLANF--PECDVFINVSCAQTALL 274 (427)
Q Consensus 201 ~I~ka~~A~~iGIlvgTl~~q~~~~~i~~l~~li~~~GKK~y-~~~vgkln~aKLaNF--~eiD~fVlvaCPr~si~ 274 (427)
.++.|++.+.=.|+++++. ..|.+.+..+.+.|+++|.+-. +++=|++-++....+ .++|.|+-.+|+-..++
T Consensus 625 ~v~aa~~~~a~ivvlcs~d-~~~~e~~~~l~~~Lk~~G~~~v~vl~GG~~~~~~~~~l~~aGvD~~i~~g~d~~~~L 700 (714)
T PRK09426 625 AARQAVENDVHVVGVSSLA-AGHKTLVPALIEALKKLGREDIMVVVGGVIPPQDYDFLYEAGVAAIFGPGTVIADAA 700 (714)
T ss_pred HHHHHHHcCCCEEEEeccc-hhhHHHHHHHHHHHHhcCCCCcEEEEeCCCChhhHHHHHhCCCCEEECCCCCHHHHH
Confidence 4555555443334445544 6799999999999999998644 444456445433322 27999999999866654
No 106
>PF00205 TPP_enzyme_M: Thiamine pyrophosphate enzyme, central domain; InterPro: IPR012000 A number of enzymes require thiamine pyrophosphate (TPP) (vitamin B1) as a cofactor. It has been shown [] that some of these enzymes are structurally related. This central domain of TPP enzymes contains a 2-fold Rossman fold. ; GO: 0000287 magnesium ion binding, 0030976 thiamine pyrophosphate binding; PDB: 1OZH_C 1OZF_B 1OZG_B 2Q29_B 2Q28_A 2Q27_B 1OVM_B 1PVD_A 1PYD_B 2VK1_C ....
Probab=39.81 E-value=20 Score=30.85 Aligned_cols=46 Identities=24% Similarity=0.200 Sum_probs=35.8
Q ss_pred HHHHHhcCCeEEEEEcCCcccCcHHHHHHHHHHHHHcCCcEEEEEcCC
Q 014264 201 LVEKAKDANIIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGK 248 (427)
Q Consensus 201 ~I~ka~~A~~iGIlvgTl~~q~~~~~i~~l~~li~~~GKK~y~~~vgk 248 (427)
..+..+.|++--||+|... .+....+.+++++++.|-.+++-.++|
T Consensus 4 ~~~~L~~A~rP~il~G~g~--~~~~a~~~l~~lae~~~~Pv~~t~~~k 49 (137)
T PF00205_consen 4 AADLLSSAKRPVILAGRGA--RRSGAAEELRELAEKLGIPVATTPMGK 49 (137)
T ss_dssp HHHHHHH-SSEEEEE-HHH--HHTTCHHHHHHHHHHHTSEEEEEGGGT
T ss_pred HHHHHHhCCCEEEEEcCCc--ChhhHHHHHHHHHHHHCCCEEecCccc
Confidence 5677888999999999743 344677889999999999999888886
No 107
>TIGR02634 xylF D-xylose ABC transporter, substrate-binding protein. Members of this family are periplasmic (when in Gram-negative bacteria) binding proteins for D-xylose import by a high-affinity ATP-binding cassette (ABC) transporter.
Probab=39.73 E-value=32 Score=33.64 Aligned_cols=74 Identities=20% Similarity=0.238 Sum_probs=48.4
Q ss_pred EEEEEcCCcccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHHHH----cCC--CCCCEEEEecCCCccccc----ccCCC
Q 014264 211 IGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKL----ANF--PECDVFINVSCAQTALLD----SKEFL 280 (427)
Q Consensus 211 iGIlvgTl~~q~~~~~i~~l~~li~~~GKK~y~~~vgkln~aKL----aNF--~eiD~fVlvaCPr~si~d----~~~f~ 280 (427)
||+++.++.-.-+..+.+-+++.+++.|....+... .-++++. .+| ..+|++++.++....+.+ .++-.
T Consensus 1 ig~~~~~~~~~~~~~~~~~i~~~a~~~g~~v~~~~~-~~~~~~q~~~i~~l~~~~vDgIIi~~~~~~~~~~~l~~~~~~~ 79 (302)
T TIGR02634 1 IGVSIDDLRLERWQKDRDIFVAAAESLGAKVFVQSA-NGNEAKQISQIENLIARGVDVLVIIPQNGQVLSNAVQEAKDEG 79 (302)
T ss_pred CeeecCccchhhHHHHHHHHHHHHHhcCCEEEEEeC-CCCHHHHHHHHHHHHHcCCCEEEEeCCChhHHHHHHHHHHHCC
Confidence 588888888888888889999999998877655433 3454433 222 258999988775442221 23344
Q ss_pred CcccC
Q 014264 281 APVIT 285 (427)
Q Consensus 281 kPvlT 285 (427)
.|||+
T Consensus 80 iPvV~ 84 (302)
T TIGR02634 80 IKVVA 84 (302)
T ss_pred CeEEE
Confidence 56654
No 108
>cd06319 PBP1_ABC_sugar_binding_like_10 Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems. Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily, which consists of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis.
Probab=39.51 E-value=58 Score=30.63 Aligned_cols=73 Identities=18% Similarity=0.148 Sum_probs=47.8
Q ss_pred EEEEEcCCcccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHH-------HHcCCCCCCEEEEecCCCcc----cccccCC
Q 014264 211 IGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPA-------KLANFPECDVFINVSCAQTA----LLDSKEF 279 (427)
Q Consensus 211 iGIlvgTl~~q~~~~~i~~l~~li~~~GKK~y~~~vgkln~a-------KLaNF~eiD~fVlvaCPr~s----i~d~~~f 279 (427)
||+|+..+.-..+..+++.+++.+++.|.+..++. ++=+++ +|.+ ..+|.+|+.++.... +...++.
T Consensus 2 i~vi~~~~~~~~~~~~~~~i~~~~~~~g~~~~~~~-~~~~~~~~~~~i~~~~~-~~~dgiii~~~~~~~~~~~l~~~~~~ 79 (277)
T cd06319 2 IAYIVSDLRIPFWQIMGRGVKSKAKALGYDAVELS-AENSAKKELENLRTAID-KGVSGIIISPTNSSAAVTLLKLAAQA 79 (277)
T ss_pred eEEEeCCCCchHHHHHHHHHHHHHHhcCCeEEEec-CCCCHHHHHHHHHHHHh-cCCCEEEEcCCchhhhHHHHHHHHHC
Confidence 78888887777788899999999999887765442 333433 2333 368999887764221 2223455
Q ss_pred CCcccC
Q 014264 280 LAPVIT 285 (427)
Q Consensus 280 ~kPvlT 285 (427)
..|||+
T Consensus 80 ~ipvV~ 85 (277)
T cd06319 80 KIPVVI 85 (277)
T ss_pred CCCEEE
Confidence 667776
No 109
>PRK11104 hemG protoporphyrinogen oxidase; Provisional
Probab=39.29 E-value=53 Score=29.98 Aligned_cols=54 Identities=6% Similarity=0.097 Sum_probs=38.6
Q ss_pred eEEEEEcCCcccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHHHHcCCCCCCEEEEecCC
Q 014264 210 IIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKLANFPECDVFINVSCA 269 (427)
Q Consensus 210 ~iGIlvgTl~~q~~~~~i~~l~~li~~~GKK~y~~~vgkln~aKLaNF~eiD~fVlvaCP 269 (427)
.+.|+-+|..| +...+++.|.+.|.. |..+-++-+.+.... ++.+.|. |++++|
T Consensus 2 kilIvY~S~~G-~T~~iA~~Ia~~l~~-g~~v~~~~~~~~~~~---~l~~yD~-vIlGsp 55 (177)
T PRK11104 2 KTLILYSSRDG-QTRKIASYIASELKE-GIQCDVVNLHRIEEP---DLSDYDR-VVIGAS 55 (177)
T ss_pred cEEEEEECCCC-hHHHHHHHHHHHhCC-CCeEEEEEhhhcCcc---CHHHCCE-EEEECc
Confidence 36788898774 577889999999987 877766666665543 3445687 666666
No 110
>cd01543 PBP1_XylR Ligand-binding domain of DNA transcription repressor specific for xylose (XylR). Ligand-binding domain of DNA transcription repressor specific for xylose (XylR), a member of the LacI-GalR family of bacterial transcription regulators. The ligand-binding domain of XylR is structurally homologous to the periplasmic sugar-binding domain of ABC-type transporters and both domains contain the type I periplasmic binding protein-like fold. The LacI-GalR family repressors 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 type I periplasmic binding proteins. 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 affinity of the repressor.
Probab=39.05 E-value=52 Score=30.98 Aligned_cols=55 Identities=13% Similarity=0.016 Sum_probs=33.9
Q ss_pred eEEEEEcCCcccCcHHHHHHHHHHHHH-cCCcEEEEEcCCCCHHHHcCCC--CCCEEEEec
Q 014264 210 IIGVLVGTLGVAGYLHMIHQMKELITK-AGKKAYTLVMGKPNPAKLANFP--ECDVFINVS 267 (427)
Q Consensus 210 ~iGIlvgTl~~q~~~~~i~~l~~li~~-~GKK~y~~~vgkln~aKLaNF~--eiD~fVlva 267 (427)
.||+|+.+ +--.+..+++.+.+.+++ .|....+.. +.. ..-+.++. .+|.+++..
T Consensus 1 ~ig~i~~~-~~~~~~~~~~gi~~~~~~~~g~~~~~~~-~~~-~~~~~~l~~~~vdGiI~~~ 58 (265)
T cd01543 1 RVALLVET-SSSYGRGVLRGIARYAREHGPWSIYLEP-RGL-QEPLRWLKDWQGDGIIARI 58 (265)
T ss_pred CeEEEecc-cchhhHHHHHHHHHHHHhcCCeEEEEec-ccc-hhhhhhccccccceEEEEC
Confidence 47899974 345667888888888888 555544332 211 22222232 689998865
No 111
>PRK10936 TMAO reductase system periplasmic protein TorT; Provisional
Probab=39.04 E-value=45 Score=33.36 Aligned_cols=78 Identities=22% Similarity=0.110 Sum_probs=50.1
Q ss_pred cCCeEEEEEcCCcccCcHHHHHHHHHHHHHcCCcEEEEEcC-CCCHHHH----cCC--CCCCEEEEecCCCcccc---cc
Q 014264 207 DANIIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMG-KPNPAKL----ANF--PECDVFINVSCAQTALL---DS 276 (427)
Q Consensus 207 ~A~~iGIlvgTl~~q~~~~~i~~l~~li~~~GKK~y~~~vg-kln~aKL----aNF--~eiD~fVlvaCPr~si~---d~ 276 (427)
..++||+|+.++.-..+..+++.+++.+++.|.+..++... .-+.++. .++ ..+|.+|+.+.....+. ..
T Consensus 45 ~t~~Igvv~p~~~~~f~~~~~~gi~~aa~~~G~~l~i~~~~~~~~~~~q~~~i~~l~~~~vdgIIl~~~~~~~~~~~l~~ 124 (343)
T PRK10936 45 KAWKLCALYPHLKDSYWLSVNYGMVEEAKRLGVDLKVLEAGGYYNLAKQQQQLEQCVAWGADAILLGAVTPDGLNPDLEL 124 (343)
T ss_pred CCeEEEEEecCCCchHHHHHHHHHHHHHHHhCCEEEEEcCCCCCCHHHHHHHHHHHHHhCCCEEEEeCCChHHhHHHHHH
Confidence 47899999988776777788899999999999775555432 2333333 222 25899998764433211 22
Q ss_pred cCCCCccc
Q 014264 277 KEFLAPVI 284 (427)
Q Consensus 277 ~~f~kPvl 284 (427)
++-..|||
T Consensus 125 ~~~giPvV 132 (343)
T PRK10936 125 QAANIPVI 132 (343)
T ss_pred HHCCCCEE
Confidence 34455665
No 112
>cd06321 PBP1_ABC_sugar_binding_like_11 Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems. This group includes the periplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily, which consist of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis.
Probab=38.71 E-value=32 Score=32.50 Aligned_cols=59 Identities=19% Similarity=0.195 Sum_probs=38.2
Q ss_pred eEEEEEcCCcccCcHHHHHHHHHHHHHcCCcEEEEE-cCCCCHHHHcCC------CCCCEEEEecC
Q 014264 210 IIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLV-MGKPNPAKLANF------PECDVFINVSC 268 (427)
Q Consensus 210 ~iGIlvgTl~~q~~~~~i~~l~~li~~~GKK~y~~~-vgkln~aKLaNF------~eiD~fVlvaC 268 (427)
+||+|+.++.-..+..+++.+.+.+++.|..+-++. -+.-++++.... ..+|.+|+.+.
T Consensus 1 ~Ig~v~~~~~~~~~~~~~~gi~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~dgiIi~~~ 66 (271)
T cd06321 1 KIGVSVGDLGNPFFVALAKGAEAAAKKLNPGVKVTVVSADYDLNKQVSQIDNFIAAKVDLILLNAV 66 (271)
T ss_pred CeEEEecccCCHHHHHHHHHHHHHHHHhCCCeEEEEccCCCCHHHHHHHHHHHHHhCCCEEEEeCC
Confidence 488999888777788899999999998554433332 233344433221 25888887653
No 113
>TIGR02955 TMAO_TorT TMAO reductase system periplasmic protein TorT. Members of this family are the periplasmic protein TorT which, together with the the TorS/TorR histidine kinase/response regulator system, regulates expression of the torCAD operon for trimethylamine N-oxide reductase (TMAO reductase). It appears to bind an inducer for TMAO reductase, and shows homology to a periplasmic D-ribose binding protein.
Probab=37.97 E-value=58 Score=31.53 Aligned_cols=62 Identities=19% Similarity=0.131 Sum_probs=40.7
Q ss_pred eEEEEEcCCcccCcHHHHHHHHHHHHHcCCcEEEEEcCC-CCHHHH----cCC--CCCCEEEEecCCCc
Q 014264 210 IIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGK-PNPAKL----ANF--PECDVFINVSCAQT 271 (427)
Q Consensus 210 ~iGIlvgTl~~q~~~~~i~~l~~li~~~GKK~y~~~vgk-ln~aKL----aNF--~eiD~fVlvaCPr~ 271 (427)
++|+|+.++.-..+..+++.+.+.++++|....+...+. -++++. .++ ..+|.+|+.++...
T Consensus 1 ~igvvvp~~~n~f~~~~~~gi~~~a~~~g~~v~~~~~~~~~~~~~~~~~i~~l~~~~vDgiIi~~~~~~ 69 (295)
T TIGR02955 1 KLCALYPHLKDSYWLSINYGMVEQAKHLGVELKVLEAGGYPNLDKQLAQIEQCKSWGADAILLGTVSPE 69 (295)
T ss_pred CeeEEecCCCcHHHHHHHHHHHHHHHHhCCEEEEEcCCCCCCHHHHHHHHHHHHHcCCCEEEEecCChh
Confidence 378888887766777888888888888888776665541 233322 122 25888888776433
No 114
>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=37.96 E-value=59 Score=30.68 Aligned_cols=74 Identities=15% Similarity=0.100 Sum_probs=44.4
Q ss_pred eEEEEEcCCcccCcHHHHHHHHHHHHHcCCcEEEEEcC-CCCHHH-------HcCCCCCCEEEEecCCCccc----cccc
Q 014264 210 IIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMG-KPNPAK-------LANFPECDVFINVSCAQTAL----LDSK 277 (427)
Q Consensus 210 ~iGIlvgTl~~q~~~~~i~~l~~li~~~GKK~y~~~vg-kln~aK-------LaNF~eiD~fVlvaCPr~si----~d~~ 277 (427)
+||+|+..+.--.+..+++.+++.++++|...-++... .-++++ |.+- .+|+.|+.++....+ ...+
T Consensus 1 ~igvi~~~~~~~~~~~~~~gi~~~~~~~g~~~~~~~~~~~~~~~~~~~~i~~l~~~-~vdgiIi~~~~~~~~~~~~~~~~ 79 (275)
T cd06320 1 KYGVVLKTLSNEFWRSLKEGYENEAKKLGVSVDIQAAPSEGDQQGQLSIAENMINK-GYKGLLFSPISDVNLVPAVERAK 79 (275)
T ss_pred CeeEEEecCCCHHHHHHHHHHHHHHHHhCCeEEEEccCCCCCHHHHHHHHHHHHHh-CCCEEEECCCChHHhHHHHHHHH
Confidence 47888877766667788888888888888765544432 223332 2222 588888765543222 1223
Q ss_pred CCCCccc
Q 014264 278 EFLAPVI 284 (427)
Q Consensus 278 ~f~kPvl 284 (427)
+...|||
T Consensus 80 ~~~iPvV 86 (275)
T cd06320 80 KKGIPVV 86 (275)
T ss_pred HCCCeEE
Confidence 4556766
No 115
>PRK08662 nicotinate phosphoribosyltransferase; Reviewed
Probab=37.80 E-value=54 Score=33.48 Aligned_cols=55 Identities=16% Similarity=0.368 Sum_probs=41.9
Q ss_pred CeEEEEEcCCcc--cCcHHHHHHHHHHHHHcC-CcEEEEEcCCCCHHHHcCCCC-CCEE
Q 014264 209 NIIGVLVGTLGV--AGYLHMIHQMKELITKAG-KKAYTLVMGKPNPAKLANFPE-CDVF 263 (427)
Q Consensus 209 ~~iGIlvgTl~~--q~~~~~i~~l~~li~~~G-KK~y~~~vgkln~aKLaNF~e-iD~f 263 (427)
+..||.+=+.+. ..-..+++++++.+++.| .+.-+.+.|.||++++++|.+ +|+|
T Consensus 227 ~~d~I~LDn~~~~~g~l~~~v~~vr~~ld~~g~~~v~IeaSGgI~~~ni~~ya~~vD~i 285 (343)
T PRK08662 227 RLDGVRLDTPSSRRGNFRKIVREVRWTLDIRGYEHVKIFVSGGLDPERIRELRDVVDGF 285 (343)
T ss_pred cCCEEEcCCCCCCCccHHHHHHHHHHHHHhcCCCCeEEEEeCCCCHHHHHHHHHhCCEE
Confidence 456788887763 556677788888888887 468889999999999988743 5554
No 116
>cd01537 PBP1_Repressors_Sugar_Binding_like Ligand-binding domain of the LacI-GalR family of transcription regulators and the sugar-binding domain of ABC-type transport systems. Ligand-binding domain of the LacI-GalR family of transcription regulators and the sugar-binding domain of ABC-type transport systems, all of which contain the type I periplasmic binding protein-like fold. Their specific ligands include lactose, ribose, fructose, xylose, arabinose, galactose/glucose, and other sugars. The LacI family of proteins consists of transcriptional regulators related to the lac repressor; in general the sugar binding domain in this family binds a sugar, which in turn changes the DNA binding activity of the repressor domain. The core structure of the periplasmic binding proteins is classified into two types and they differ in number and order of beta strands in each domain: type I, which has six beta strands, and type II, which has five beta strands. These two distinct structural arrangem
Probab=37.30 E-value=77 Score=29.04 Aligned_cols=74 Identities=22% Similarity=0.192 Sum_probs=45.3
Q ss_pred eEEEEEcCCcccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHH-------HHcCCCCCCEEEEecCCCccc---ccccCC
Q 014264 210 IIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPA-------KLANFPECDVFINVSCAQTAL---LDSKEF 279 (427)
Q Consensus 210 ~iGIlvgTl~~q~~~~~i~~l~~li~~~GKK~y~~~vgkln~a-------KLaNF~eiD~fVlvaCPr~si---~d~~~f 279 (427)
+||++.....-..+..+++-+++.+++.|.+..++-.+ -+++ +|.+- .+|++|..+|....+ ....+-
T Consensus 1 ~ig~v~~~~~~~~~~~~~~g~~~~~~~~g~~l~~~~~~-~~~~~~~~~~~~~~~~-~~d~ii~~~~~~~~~~~~~~l~~~ 78 (264)
T cd01537 1 TIGVLVPDLDNPFFAQVLKGIEEAAKAAGYQVLLANSQ-NDAEKQLSALENLIAR-GVDGIIIAPSDLTAPTIVKLARKA 78 (264)
T ss_pred CeEEEEcCCCChHHHHHHHHHHHHHHHcCCeEEEEeCC-CCHHHHHHHHHHHHHc-CCCEEEEecCCCcchhHHHHhhhc
Confidence 36777766545566788888888888888765444333 2332 23332 688888888875553 222334
Q ss_pred CCcccC
Q 014264 280 LAPVIT 285 (427)
Q Consensus 280 ~kPvlT 285 (427)
..|+|+
T Consensus 79 ~ip~v~ 84 (264)
T cd01537 79 GIPVVL 84 (264)
T ss_pred CCCEEE
Confidence 556655
No 117
>PRK10427 putative PTS system fructose-like transporter subunit EIIB; Provisional
Probab=37.20 E-value=1.1e+02 Score=26.16 Aligned_cols=61 Identities=13% Similarity=0.097 Sum_probs=50.2
Q ss_pred CCeEEEEEcCCcccCcHHHHHHHHHHHHHcCCcEE------EEEcCCCCHHHHcCCCCCCEEEEecCCCc
Q 014264 208 ANIIGVLVGTLGVAGYLHMIHQMKELITKAGKKAY------TLVMGKPNPAKLANFPECDVFINVSCAQT 271 (427)
Q Consensus 208 A~~iGIlvgTl~~q~~~~~i~~l~~li~~~GKK~y------~~~vgkln~aKLaNF~eiD~fVlvaCPr~ 271 (427)
.+.++|.-+.-|.....-..+.|++..++.|.+.. .-+.+.++++.++. .|.+++++....
T Consensus 3 mkivaVtacp~GiAht~lAAeaL~kAA~~~G~~i~VE~qg~~g~~~~lt~~~i~~---Ad~VIia~d~~~ 69 (114)
T PRK10427 3 AYLVAVTACVSGVAHTYMAAERLEKLCQLEKWGVKIETQGALGTENRLTDEDIRR---ADVVLLITDIEL 69 (114)
T ss_pred ceEEEEeeCCCcHHHHHHHHHHHHHHHHHCCCeEEEEecCCcCcCCCCCHHHHHh---CCEEEEEecCCC
Confidence 46888888889999999999999999999999988 44555677777755 599999998764
No 118
>cd06306 PBP1_TorT-like TorT-like proteins, a periplasmic binding protein family that activates induction of the Tor respiratory system upon trimethylamine N-oxide (TMAO) electron-acceptor binding in bacteria. TorT-like proteins, a periplasmic binding protein family that activates induction of the Tor respiratory system upon trimethylamine N-oxide (TMAO) electron-acceptor binding in bacteria. The Tor respiratory system is consists of three proteins (TorC, TorA, and TorD) and is induced in the presence of TMAO. The TMAO control is tightly regulated by three proteins: TorS, TorT, and TorR. Thus, the disruption of any of these proteins can abolish the Tor respiratory induction. TorT shares homology with the sugar-binding domain of the type I periplasmic binding proteins. The members of TorT-like family bind TMAO or related compounds and are predicted to be involved in signal transduction and/or substrate transport.
Probab=37.05 E-value=44 Score=31.72 Aligned_cols=77 Identities=26% Similarity=0.218 Sum_probs=50.2
Q ss_pred eEEEEEcCCcccCcHHHHHHHHHHHHHcCCcEEEEEcCC-CCHH----HHcCC--CCCCEEEEecCCCccc---ccccCC
Q 014264 210 IIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGK-PNPA----KLANF--PECDVFINVSCAQTAL---LDSKEF 279 (427)
Q Consensus 210 ~iGIlvgTl~~q~~~~~i~~l~~li~~~GKK~y~~~vgk-ln~a----KLaNF--~eiD~fVlvaCPr~si---~d~~~f 279 (427)
+||||+..+....+..++..+++.+++.|.+..++..+. -+++ .+.++ ..+|..++.+...... ...+.-
T Consensus 1 ~Igvi~~~~~~~f~~~~~~gi~~~a~~~g~~~~~~~~~~~~~~~~~~~~i~~~~~~~vdgiI~~~~~~~~~~~~~~~~~~ 80 (268)
T cd06306 1 KLCVLYPHLKDAYWLSVNYGMVEEAKRLGVSLKLLEAGGYPNLAKQIAQLEDCAAWGADAILLGAVSPDGLNEILQQVAA 80 (268)
T ss_pred CeEEEcCCCCCHHHHHHHHHHHHHHHHcCCEEEEecCCCCCCHHHHHHHHHHHHHcCCCEEEEcCCChhhHHHHHHHHHC
Confidence 489999988878888999999999999998766654332 2332 22222 2689999887643322 222334
Q ss_pred CCcccCH
Q 014264 280 LAPVITP 286 (427)
Q Consensus 280 ~kPvlTP 286 (427)
-.|||+-
T Consensus 81 giPvV~~ 87 (268)
T cd06306 81 SIPVIAL 87 (268)
T ss_pred CCCEEEe
Confidence 4577654
No 119
>TIGR00288 conserved hypothetical protein TIGR00288. This family of orthologs is restricted to but universal among the completed archaeal genomes so far. Eubacterial proteins showing at least local homology include slr1870 from Synechocystis PCC6803 and two proteins from Aquifex aeolicusr, none of which is characterized.
Probab=36.57 E-value=1.2e+02 Score=27.67 Aligned_cols=53 Identities=19% Similarity=0.310 Sum_probs=41.1
Q ss_pred hcCCeEEEEEcCCcccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHHHHcCCCCCCEEEEec
Q 014264 206 KDANIIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKLANFPECDVFINVS 267 (427)
Q Consensus 206 ~~A~~iGIlvgTl~~q~~~~~i~~l~~li~~~GKK~y~~~vgkln~aKLaNF~eiD~fVlva 267 (427)
.+..+|.|+-|- ..+..++++|| +.||+++.+.+.+.++.-|.|= .|-||-+.
T Consensus 104 ~~iD~~vLvSgD---~DF~~Lv~~lr----e~G~~V~v~g~~~~ts~~L~~a--cd~FI~L~ 156 (160)
T TIGR00288 104 PNIDAVALVTRD---ADFLPVINKAK----ENGKETIVIGAEPGFSTALQNS--ADIAIILG 156 (160)
T ss_pred CCCCEEEEEecc---HhHHHHHHHHH----HCCCEEEEEeCCCCChHHHHHh--cCeEEeCC
Confidence 667888777664 66777776665 6799999999888899999885 78887654
No 120
>PRK14571 D-alanyl-alanine synthetase A; Provisional
Probab=36.41 E-value=1.1e+02 Score=29.91 Aligned_cols=76 Identities=14% Similarity=0.050 Sum_probs=52.3
Q ss_pred eEEEEEcCCcc--cCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHHHHcCCCCCCEEEEecCCCccccc------ccCCCC
Q 014264 210 IIGVLVGTLGV--AGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKLANFPECDVFINVSCAQTALLD------SKEFLA 281 (427)
Q Consensus 210 ~iGIlvgTl~~--q~~~~~i~~l~~li~~~GKK~y~~~vgkln~aKLaNF~eiD~fVlvaCPr~si~d------~~~f~k 281 (427)
+|+||.|-.+. .-.+...+.+.+-|++.|.++..+-+.+--..++....++|+ |+..|+...-.| ...+-.
T Consensus 2 ~v~v~~gg~s~e~~~sl~s~~~i~~al~~~g~~~~~i~~~~~~~~~~~~~~~~D~-v~~~~~g~~ge~~~~~~~le~~gi 80 (299)
T PRK14571 2 RVALLMGGVSREREISLRSGERVKKALEKLGYEVTVFDVDEDFLKKVDQLKSFDV-VFNVLHGTFGEDGTLQAILDFLGI 80 (299)
T ss_pred eEEEEeCCCCCCccchHHHHHHHHHHHHHcCCeEEEEccCchHHHHhhhccCCCE-EEEeCCCCCCCccHHHHHHHHcCC
Confidence 58999999885 445677888999999999999998877655566666667884 455665431112 124667
Q ss_pred cccCH
Q 014264 282 PVITP 286 (427)
Q Consensus 282 PvlTP 286 (427)
|.+.+
T Consensus 81 p~~G~ 85 (299)
T PRK14571 81 RYTGS 85 (299)
T ss_pred CccCC
Confidence 77754
No 121
>cd05566 PTS_IIB_galactitol PTS_IIB_galactitol: subunit IIB of enzyme II (EII) of the galactitol-specific phosphoenolpyruvate:carbohydrate phosphotransferase system (PTS). In this system, EII is a galactitol-specific permease with two cytoplasmic domains (IIA and IIB) and a transmembrane channel IIC domain that are expressed on three distinct polypeptide chains, in contrast to other PTS sugar transporters. The three genes encoding these subunits (gatA, gatB, and gatC) comprise the gatCBA operon. Galactitol PTS permease takes up exogenous galactitol, releasing the phosphate ester into the cytoplasm in preparation for oxidation and further metabolism via a modified glycolytic pathway called the tagatose-6-phosphate glycolytic pathway. 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 galactitol, chitobiose/lichenan, ascorbate, lactose, mannitol, fructose, and
Probab=36.41 E-value=1.4e+02 Score=23.47 Aligned_cols=56 Identities=16% Similarity=0.159 Sum_probs=31.9
Q ss_pred EEEcCCcccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHHHHcCCCCCCEEEEecCCCc
Q 014264 213 VLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKLANFPECDVFINVSCAQT 271 (427)
Q Consensus 213 IlvgTl~~q~~~~~i~~l~~li~~~GKK~y~~~vgkln~aKLaNF~eiD~fVlvaCPr~ 271 (427)
++|+.-|.....-+..+|++.+.+.+....+-.++.-.... ...++| +|+++.|-.
T Consensus 4 livC~~G~~tS~~l~~~i~~~~~~~~i~~~v~~~~~~~~~~--~~~~~D-liist~~~~ 59 (89)
T cd05566 4 LVACGTGVATSTVVASKVKELLKENGIDVKVEQCKIAEVPS--LLDDAD-LIVSTTKVP 59 (89)
T ss_pred EEECCCCccHHHHHHHHHHHHHHHCCCceEEEEecHHHhhc--ccCCCc-EEEEcCCcC
Confidence 34454454455688999999998888754443223222121 244678 555555543
No 122
>cd04502 SGNH_hydrolase_like_7 Members of the SGNH-hydrolase superfamily, a diverse family of lipases and esterases. The tertiary fold of the enzyme is substantially different from that of the alpha/beta hydrolase family and unique among all known hydrolases; its active site closely resembles the Ser-His-Asp(Glu) triad from other serine hydrolases, but may lack the carboxlic acid.
Probab=36.37 E-value=1.7e+02 Score=25.64 Aligned_cols=55 Identities=5% Similarity=-0.041 Sum_probs=29.7
Q ss_pred HHHHHHHHHHHHHhcCCeEEEEEcCCc------ccCcHHHHHHHHHHHHHcCCcEEEEEcC
Q 014264 193 KILKRRYYLVEKAKDANIIGVLVGTLG------VAGYLHMIHQMKELITKAGKKAYTLVMG 247 (427)
Q Consensus 193 r~L~rRy~~I~ka~~A~~iGIlvgTl~------~q~~~~~i~~l~~li~~~GKK~y~~~vg 247 (427)
.-+..|......+...+.+-|.+||-- .+.+.+-++.+-+.+++++.+.-+++++
T Consensus 36 ~~~~~~~~~~~~~~~p~~vvi~~G~ND~~~~~~~~~~~~~~~~lv~~i~~~~~~~~iil~~ 96 (171)
T cd04502 36 ADCLHYFDRLVLPYQPRRVVLYAGDNDLASGRTPEEVLRDFRELVNRIRAKLPDTPIAIIS 96 (171)
T ss_pred HHHHHHHHhhhccCCCCEEEEEEecCcccCCCCHHHHHHHHHHHHHHHHHHCCCCcEEEEE
Confidence 334455555544556788888888843 2334444455555555554444444443
No 123
>PRK08091 ribulose-phosphate 3-epimerase; Validated
Probab=35.48 E-value=1.2e+02 Score=29.23 Aligned_cols=59 Identities=8% Similarity=0.050 Sum_probs=38.0
Q ss_pred cCCeEEEEEcCCc--ccCcH-H---HHHHHHHHHHHcCCcEEEEEcCCCCHHHHcCCC--CCCEEEE
Q 014264 207 DANIIGVLVGTLG--VAGYL-H---MIHQMKELITKAGKKAYTLVMGKPNPAKLANFP--ECDVFIN 265 (427)
Q Consensus 207 ~A~~iGIlvgTl~--~q~~~-~---~i~~l~~li~~~GKK~y~~~vgkln~aKLaNF~--eiD~fVl 265 (427)
....+=|..-..| ||.+. . -+++++++++++|.++.+-+=|-+|.+-+.-.. ++|+||.
T Consensus 140 ~vD~VLiMtV~PGfgGQ~f~~~~l~KI~~lr~~~~~~~~~~~IeVDGGI~~~ti~~l~~aGaD~~V~ 206 (228)
T PRK08091 140 QIDLIQILTLDPRTGTKAPSDLILDRVIQVENRLGNRRVEKLISIDGSMTLELASYLKQHQIDWVVS 206 (228)
T ss_pred hcCEEEEEEECCCCCCccccHHHHHHHHHHHHHHHhcCCCceEEEECCCCHHHHHHHHHCCCCEEEE
Confidence 3555544444444 66665 3 455555677777777667777889988665442 5898876
No 124
>PRK15395 methyl-galactoside ABC transporter galactose-binding periplasmic protein MglB; Provisional
Probab=35.45 E-value=62 Score=32.19 Aligned_cols=63 Identities=6% Similarity=-0.044 Sum_probs=38.8
Q ss_pred cCCeEEEEEcCCcccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHH----HHcCCC--CCCEEEEecCC
Q 014264 207 DANIIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPA----KLANFP--ECDVFINVSCA 269 (427)
Q Consensus 207 ~A~~iGIlvgTl~~q~~~~~i~~l~~li~~~GKK~y~~~vgkln~a----KLaNF~--eiD~fVlvaCP 269 (427)
.-++||+++..++...+..+++.+.+.++++|.-..++..+.-++. .+.++. .+|.+++.+++
T Consensus 23 ~~~~Igvv~~~~~~~f~~~~~~gi~~~a~~~g~~~~~~~~~~~~~~~~~~~i~~l~~~~vdgiIi~~~~ 91 (330)
T PRK15395 23 ADTRIGVTIYKYDDNFMSVVRKAIEKDAKAAPDVQLLMNDSQNDQSKQNDQIDVLLAKGVKALAINLVD 91 (330)
T ss_pred CCceEEEEEecCcchHHHHHHHHHHHHHHhcCCeEEEEecCCCCHHHHHHHHHHHHHcCCCEEEEeccC
Confidence 3477888887777667778888888888887632223323333332 222332 58888887655
No 125
>KOG0781 consensus Signal recognition particle receptor, alpha subunit [Intracellular trafficking, secretion, and vesicular transport]
Probab=35.45 E-value=3.1e+02 Score=29.63 Aligned_cols=70 Identities=19% Similarity=0.267 Sum_probs=50.0
Q ss_pred HHHHHHhcCCeEEEEEcCCcc-cCcHHHHHHHHHHHHHcCCcEEEEEcCCC-----CHHHHcCC-------C---CCCEE
Q 014264 200 YLVEKAKDANIIGVLVGTLGV-AGYLHMIHQMKELITKAGKKAYTLVMGKP-----NPAKLANF-------P---ECDVF 263 (427)
Q Consensus 200 ~~I~ka~~A~~iGIlvgTl~~-q~~~~~i~~l~~li~~~GKK~y~~~vgkl-----n~aKLaNF-------~---eiD~f 263 (427)
.+|+.|++-.-=-|||-|-|+ ++...+...|.++++.+ +.-.+|+||+- ..+.|.+| + -||.|
T Consensus 457 ~AI~~a~~~gfDVvLiDTAGR~~~~~~lm~~l~k~~~~~-~pd~i~~vgealvg~dsv~q~~~fn~al~~~~~~r~id~~ 535 (587)
T KOG0781|consen 457 EAIQEARNQGFDVVLIDTAGRMHNNAPLMTSLAKLIKVN-KPDLILFVGEALVGNDSVDQLKKFNRALADHSTPRLIDGI 535 (587)
T ss_pred HHHHHHHhcCCCEEEEeccccccCChhHHHHHHHHHhcC-CCceEEEehhhhhCcHHHHHHHHHHHHHhcCCCccccceE
Confidence 467778877777789999996 78889999999888764 55556666643 44444444 2 38888
Q ss_pred EEecCCC
Q 014264 264 INVSCAQ 270 (427)
Q Consensus 264 VlvaCPr 270 (427)
+++-|.-
T Consensus 536 ~ltk~dt 542 (587)
T KOG0781|consen 536 LLTKFDT 542 (587)
T ss_pred EEEeccc
Confidence 8888764
No 126
>PF02514 CobN-Mg_chel: CobN/Magnesium Chelatase; InterPro: IPR003672 This family contains a domain common to the cobN protein and to magnesium protoporphyrin chelatase. CobN may play a role in cobalt insertion reactions and is implicated in the conversion of precorrin-2 to cobyrinic acid in cobalamin biosynthesis []. Magnesium protoporphyrin chelatase is involved in chlorophyll biosynthesis as the third subunit of light-independent protochlorophyllide reductase in bacteria and plants [].; GO: 0009058 biosynthetic process
Probab=35.16 E-value=51 Score=38.96 Aligned_cols=113 Identities=14% Similarity=0.186 Sum_probs=71.3
Q ss_pred EEEecCCCCceecccCcHHHHHHHHHHHHHHHhcCCeEEEEEcCCcc-cCcHHHHHHHHHHHHHcCCcEEEEEcCC--CC
Q 014264 174 IVRYDATEERLLTDVSQPLKILKRRYYLVEKAKDANIIGVLVGTLGV-AGYLHMIHQMKELITKAGKKAYTLVMGK--PN 250 (427)
Q Consensus 174 v~~yDP~~~~~~~~~~~~~r~L~rRy~~I~ka~~A~~iGIlvgTl~~-q~~~~~i~~l~~li~~~GKK~y~~~vgk--ln 250 (427)
.-.|.|....+.....+..++.+.|-. -.-++.+||||+..--. .+....++.|.+.|+++|-.++.++..- -.
T Consensus 40 ~GiYhPd~~~~f~~~~eYl~w~~~~~~---~~~~~P~VgIlfyrs~~~~g~~~~vdaLI~~LE~~G~nvipvf~~~~~~~ 116 (1098)
T PF02514_consen 40 NGIYHPDAGRVFESLEEYLAWYRKRGR---YDPNRPTVGILFYRSYWLSGNTAVVDALIRALEERGLNVIPVFCSSGPDS 116 (1098)
T ss_pred eEEEeeccccccCCHHHHHHHHhhhcc---cCCCCCEEEEEeehhhhhcCCcHHHHHHHHHHHHCCCeEEEEEecCccch
Confidence 356666665543322112222222111 23468999999975543 5678899999999999999999999653 33
Q ss_pred HHHHcC-CC-----CCCEEEEecCCCccc-------ccccCCCCcccCHHHH
Q 014264 251 PAKLAN-FP-----ECDVFINVSCAQTAL-------LDSKEFLAPVITPFEA 289 (427)
Q Consensus 251 ~aKLaN-F~-----eiD~fVlvaCPr~si-------~d~~~f~kPvlTP~El 289 (427)
...+.. |. .||+.|.+.+=++.- ...++...|||.+.-+
T Consensus 117 ~~~i~~~f~~~g~~~vDaIIn~~~f~l~~~~~~~~~~~L~~LnVPVlq~i~~ 168 (1098)
T PF02514_consen 117 QEAIEDYFMDDGKPRVDAIINLTGFSLGGGPAGGAIELLKELNVPVLQAITL 168 (1098)
T ss_pred HHHHHHHHhhcCCCCceEEEEcCccccCCCCcchhHHHHHHCCCCEEEeecc
Confidence 333322 32 499999888866543 2345678888877543
No 127
>cd06325 PBP1_ABC_uncharacterized_transporter Type I periplasmic ligand-binding domain of uncharacterized ABC-type transport systems that are predicted to be involved in the uptake of amino acids, peptides, or inorganic ions. This group includes the type I periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type transport systems that are predicted to be involved in the uptake of amino acids, peptides, or inorganic ions. This subgroup has high sequence similarity to members of the family of hydrophobic amino acid transporters (HAAT), such as leucine/isoleucine/valine binding protein (LIVBP); its ligand specificity has not been determined experimentally.
Probab=35.05 E-value=93 Score=29.29 Aligned_cols=75 Identities=11% Similarity=0.110 Sum_probs=47.0
Q ss_pred eEEEEEcCCcccCcHHHHHHHHHHHHHcCC----cEEEEEcC-CCCHH-------HHcCCCCCCEEEEecCCCccccccc
Q 014264 210 IIGVLVGTLGVAGYLHMIHQMKELITKAGK----KAYTLVMG-KPNPA-------KLANFPECDVFINVSCAQTALLDSK 277 (427)
Q Consensus 210 ~iGIlvgTl~~q~~~~~i~~l~~li~~~GK----K~y~~~vg-kln~a-------KLaNF~eiD~fVlvaCPr~si~d~~ 277 (427)
+||+++. ..-..+..+++.+++.++++|. +.-+++.. .-+++ +|.+- .+|.+|+.+++-....-..
T Consensus 1 ~igv~~~-~~~~~~~~~~~gi~~~~~~~g~~~g~~v~l~~~~~~~~~~~~~~~~~~l~~~-~vd~iI~~~~~~~~~~~~~ 78 (281)
T cd06325 1 KVGILQL-VEHPALDAARKGFKDGLKEAGYKEGKNVKIDYQNAQGDQSNLPTIARKFVAD-KPDLIVAIATPAAQAAANA 78 (281)
T ss_pred CeEEecC-CCCcchHHHHHHHHHHHHHhCccCCceEEEEEecCCCCHHHHHHHHHHHHhc-CCCEEEEcCcHHHHHHHHc
Confidence 4788885 6656778899999999999986 33444432 22333 45553 6899999876522111122
Q ss_pred CCCCcccCH
Q 014264 278 EFLAPVITP 286 (427)
Q Consensus 278 ~f~kPvlTP 286 (427)
....|||..
T Consensus 79 ~~~iPvV~~ 87 (281)
T cd06325 79 TKDIPIVFT 87 (281)
T ss_pred CCCCCEEEE
Confidence 345687765
No 128
>PRK05452 anaerobic nitric oxide reductase flavorubredoxin; Provisional
Probab=34.77 E-value=1.5e+02 Score=31.57 Aligned_cols=96 Identities=9% Similarity=0.136 Sum_probs=62.9
Q ss_pred HHHHHHHHHHHHHHHhcCCeEEEEEcCCcccCcHHHHHHHHHHHHHc--CCcEEEEEcCCCCHHHHcC-CCCCCEEEEec
Q 014264 191 PLKILKRRYYLVEKAKDANIIGVLVGTLGVAGYLHMIHQMKELITKA--GKKAYTLVMGKPNPAKLAN-FPECDVFINVS 267 (427)
Q Consensus 191 ~~r~L~rRy~~I~ka~~A~~iGIlvgTl~~q~~~~~i~~l~~li~~~--GKK~y~~~vgkln~aKLaN-F~eiD~fVlva 267 (427)
..++++ +|....+-+..+.+-|+-.|.. -+...+++.|.+-+++. |.++-++-+.+.+++.|.+ +.+.|+ |+++
T Consensus 235 ~~~~l~-~Y~~~~~~~~~~kv~IvY~S~~-GnTe~mA~~ia~gl~~~g~gv~v~~~~v~~~~~~~i~~~~~~ad~-vilG 311 (479)
T PRK05452 235 PTQIVE-LYLKWAADYQEDRITIFYDTMS-NNTRMMADAIAQGIAEVDPRVAVKIFNVARSDKNEILTNVFRSKG-VLVG 311 (479)
T ss_pred HHHHHH-HHHHHhhccCcCcEEEEEECCc-cHHHHHHHHHHHHHHhhCCCceEEEEECCCCCHHHHHhHHhhCCE-EEEE
Confidence 334443 4544444434577889999877 45779999999999987 5677888899999988753 446774 6777
Q ss_pred CCCcccccccCCCCcccCHHHHHHhh
Q 014264 268 CAQTALLDSKEFLAPVITPFEAMLAF 293 (427)
Q Consensus 268 CPr~si~d~~~f~kPvlTP~El~~aL 293 (427)
||=. ....+. |+...++....+
T Consensus 312 spT~---~~~~~p-~~~~fl~~l~~~ 333 (479)
T PRK05452 312 SSTM---NNVMMP-KIAGLLEEITGL 333 (479)
T ss_pred CCcc---CCcchH-HHHHHHHHhhcc
Confidence 7753 122232 555555554333
No 129
>PRK09267 flavodoxin FldA; Validated
Probab=34.45 E-value=88 Score=27.91 Aligned_cols=53 Identities=13% Similarity=0.203 Sum_probs=36.5
Q ss_pred eEEEEEcCCcccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHHHHcCCCCCCEEEEecCC
Q 014264 210 IIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKLANFPECDVFINVSCA 269 (427)
Q Consensus 210 ~iGIlvgTl~~q~~~~~i~~l~~li~~~GKK~y~~~vgkln~aKLaNF~eiD~fVlvaCP 269 (427)
.+.|+-+|..| +...+++.|.+.+.. ..+-++-+.+.++..|. +.|++ ++++|
T Consensus 3 ki~IiY~S~tG-nT~~vA~~Ia~~l~~--~~~~~~~~~~~~~~~l~---~~d~v-i~g~p 55 (169)
T PRK09267 3 KIGIFFGSDTG-NTEDIAKMIQKKLGK--DVADVVDIAKASKEDFE---AYDLL-ILGIP 55 (169)
T ss_pred eEEEEEECCCC-hHHHHHHHHHHHhCC--CceEEEEhhhCCHhhHh---hCCEE-EEEec
Confidence 57899999774 577888888888863 35566777777666554 45774 45544
No 130
>PRK10355 xylF D-xylose transporter subunit XylF; Provisional
Probab=34.35 E-value=88 Score=31.20 Aligned_cols=64 Identities=14% Similarity=0.187 Sum_probs=48.0
Q ss_pred cCCeEEEEEcCCcccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHHHH----cCC--CCCCEEEEecCCCc
Q 014264 207 DANIIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKL----ANF--PECDVFINVSCAQT 271 (427)
Q Consensus 207 ~A~~iGIlvgTl~~q~~~~~i~~l~~li~~~GKK~y~~~vgkln~aKL----aNF--~eiD~fVlvaCPr~ 271 (427)
++.+||+++..+.-..+..+++-+++.++++|....+... .-++++. .++ ..+|.+|++++...
T Consensus 24 ~~~~Ig~i~~~~~~~f~~~~~~gi~~~a~~~g~~l~i~~~-~~~~~~~~~~i~~l~~~~vDGiIi~~~~~~ 93 (330)
T PRK10355 24 KEVKIGMAIDDLRLERWQKDRDIFVKKAESLGAKVFVQSA-NGNEETQMSQIENMINRGVDVLVIIPYNGQ 93 (330)
T ss_pred CCceEEEEecCCCchHHHHHHHHHHHHHHHcCCEEEEECC-CCCHHHHHHHHHHHHHcCCCEEEEeCCChh
Confidence 4689999999998888899999999999999988665533 3455433 222 26999999877543
No 131
>PRK09701 D-allose transporter subunit; Provisional
Probab=34.27 E-value=1e+02 Score=30.21 Aligned_cols=64 Identities=11% Similarity=0.076 Sum_probs=43.8
Q ss_pred HHhcCCeEEEEEcCCcccCcHHHHHHHHHHHHHcCCcEEEEE-cCCCCHHH----HcCC--CCCCEEEEec
Q 014264 204 KAKDANIIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLV-MGKPNPAK----LANF--PECDVFINVS 267 (427)
Q Consensus 204 ka~~A~~iGIlvgTl~~q~~~~~i~~l~~li~~~GKK~y~~~-vgkln~aK----LaNF--~eiD~fVlva 267 (427)
.|.-|.+||+|+.++.-..+..+++.+++.+++.|....++. -+.-++++ |.+| ..+|.+|+.+
T Consensus 20 ~~~~~~~Igvi~~~~~~~f~~~~~~gi~~~a~~~g~~v~~~~~~~~~~~~~~~~~i~~l~~~~vDgiIi~~ 90 (311)
T PRK09701 20 SAFAAAEYAVVLKTLSNPFWVDMKKGIEDEAKTLGVSVDIFASPSEGDFQSQLQLFEDLSNKNYKGIAFAP 90 (311)
T ss_pred hhccCCeEEEEeCCCCCHHHHHHHHHHHHHHHHcCCeEEEecCCCCCCHHHHHHHHHHHHHcCCCEEEEeC
Confidence 445567999999887766777889999999998887766553 22334332 3333 2589888864
No 132
>cd06317 PBP1_ABC_sugar_binding_like_8 Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems. Pperiplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily, which consists of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis.
Probab=34.12 E-value=57 Score=30.63 Aligned_cols=59 Identities=14% Similarity=0.093 Sum_probs=36.8
Q ss_pred eEEEEEcCC-cccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHHHHcC----C--CCCCEEEEecCC
Q 014264 210 IIGVLVGTL-GVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKLAN----F--PECDVFINVSCA 269 (427)
Q Consensus 210 ~iGIlvgTl-~~q~~~~~i~~l~~li~~~GKK~y~~~vgkln~aKLaN----F--~eiD~fVlvaCP 269 (427)
+||+|+-++ ....+..+++.+++.++++|....++. ..-++++... + ..+|.+|+.++-
T Consensus 1 ~i~vi~p~~~~~~~~~~~~~g~~~~~~~~g~~~~~~~-~~~~~~~~~~~~~~l~~~~vdgiii~~~~ 66 (275)
T cd06317 1 TIGYTQNNVGSHSYQTTYNKAFQAAAEEDGVEVIVLD-ANGDVARQAAQVEDLIAQKVDGIILWPTD 66 (275)
T ss_pred CeEEEecccCCCHHHHHHHHHHHHHHHhcCCEEEEEc-CCcCHHHHHHHHHHHHHcCCCEEEEecCC
Confidence 477777776 556666778888888888877655433 3334433211 1 257888887764
No 133
>TIGR01574 miaB-methiolase tRNA-N(6)-(isopentenyl)adenosine-37 thiotransferase enzyme MiaB. Hits to this model span all major groups of bacteria and eukaryotes, but not archaea, which are known to lack this particular tRNA modification. The enzyme from Thermotoga maritima has been cloned, expressed, spectroscopically characterized and shown to complement the E. coli MiaB enzyme.
Probab=34.00 E-value=50 Score=34.68 Aligned_cols=15 Identities=13% Similarity=0.126 Sum_probs=6.6
Q ss_pred CHHHHc-CCCCCCEEE
Q 014264 250 NPAKLA-NFPECDVFI 264 (427)
Q Consensus 250 n~aKLa-NF~eiD~fV 264 (427)
.++++. .+++||.+|
T Consensus 85 ~~~~~~~~~~~vd~v~ 100 (438)
T TIGR01574 85 LGNEIFQRAPYVDFVF 100 (438)
T ss_pred cHHHHHhcCCCCcEEE
Confidence 344443 244555444
No 134
>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=33.86 E-value=69 Score=30.17 Aligned_cols=59 Identities=15% Similarity=0.113 Sum_probs=39.0
Q ss_pred eEEEEEcCCcccCcHHHHHHHHHHHHHc-CCcEEEEEcCCCCHHHH----cCC--CCCCEEEEecCC
Q 014264 210 IIGVLVGTLGVAGYLHMIHQMKELITKA-GKKAYTLVMGKPNPAKL----ANF--PECDVFINVSCA 269 (427)
Q Consensus 210 ~iGIlvgTl~~q~~~~~i~~l~~li~~~-GKK~y~~~vgkln~aKL----aNF--~eiD~fVlvaCP 269 (427)
+||+|+..+.-..+..+++.+.+.+++. |....++.. .-++++- .++ ..+|++|+.++.
T Consensus 1 ~ig~~~~~~~~~~~~~~~~~i~~~~~~~~g~~~~~~~~-~~~~~~~~~~i~~~~~~~vdgiii~~~~ 66 (270)
T cd06308 1 VIGFSQCNLADPWRAAMNDEIQREASNYPDVELIIADA-ADDNSKQVADIENFIRQGVDLLIISPNE 66 (270)
T ss_pred CEEEEeeCCCCHHHHHHHHHHHHHHHhcCCcEEEEEcC-CCCHHHHHHHHHHHHHhCCCEEEEecCc
Confidence 4789998877666778889998888886 766654433 2233222 221 258988887654
No 135
>cd06305 PBP1_methylthioribose_binding_like Methylthioribose-binding protein-like of ABC-type transport systems that belong to a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein (PBP1) superfamily. Methylthioribose-binding protein-like of ABC-type transport systems that belong to a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein (PBP1) superfamily, which consists of two alpha/beta globular 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. The sugar-binding domain of the periplasmic proteins in this group is also homologous to the ligand-binding domain of eukaryotic receptors such as metabotropic glutamate receptor (mGluR), DNA-binding transcriptional repressors such as LacI and GalR.
Probab=33.48 E-value=82 Score=29.52 Aligned_cols=58 Identities=16% Similarity=-0.053 Sum_probs=39.6
Q ss_pred eEEEEEcCCcccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHHHHcC----C--CCCCEEEEecC
Q 014264 210 IIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKLAN----F--PECDVFINVSC 268 (427)
Q Consensus 210 ~iGIlvgTl~~q~~~~~i~~l~~li~~~GKK~y~~~vgkln~aKLaN----F--~eiD~fVlvaC 268 (427)
+||+|+.++.-..+..+++.+.+.+++.|.+..++. ..-++++-.+ + ..+|++|+.+.
T Consensus 1 ~Ig~i~~~~~~~~~~~~~~gi~~~~~~~g~~~~~~~-~~~~~~~~~~~l~~~~~~~vdgii~~~~ 64 (273)
T cd06305 1 RIAVVRYGGSGDFDQAYLAGTKAEAEALGGDLRVYD-AGGDDAKQADQIDQAIAQKVDAIIIQHG 64 (273)
T ss_pred CeEEEeecCCCcHHHHHHHHHHHHHHHcCCEEEEEC-CCCCHHHHHHHHHHHHHcCCCEEEEecC
Confidence 478888887766677888888888888888765543 4445554321 1 25888888653
No 136
>cd06267 PBP1_LacI_sugar_binding_like Ligand binding domain of the LacI tanscriptional regulator family belonging to the type I periplasmic-binding fold protein superfamily. Ligand binding domain of the LacI tanscriptional regulator family belonging to the type I periplasmic-binding fold protein superfamily. In most cases, ligands are monosaccharide including lactose, ribose, fructose, xylose, arabinose, galactose/glucose, and other sugars. The LacI family of proteins consists of transcriptional regulators related to the lac repressor. In this case, the domain sugar binding changes the DNA binding activity of the repressor domain.
Probab=33.07 E-value=75 Score=29.17 Aligned_cols=32 Identities=22% Similarity=0.393 Sum_probs=15.4
Q ss_pred EEEEEcCCcccCcHHHHHHHHHHHHHcCCcEE
Q 014264 211 IGVLVGTLGVAGYLHMIHQMKELITKAGKKAY 242 (427)
Q Consensus 211 iGIlvgTl~~q~~~~~i~~l~~li~~~GKK~y 242 (427)
||+++-+.....+..+.+.+++.+++.|.+..
T Consensus 2 i~~v~~~~~~~~~~~~~~g~~~~~~~~g~~~~ 33 (264)
T cd06267 2 IGVIVPDISNPFFAELLRGIEEAAREAGYSVL 33 (264)
T ss_pred EEEEECCCCCHHHHHHHHHHHHHHHHcCCEEE
Confidence 44444444444444555555555555554443
No 137
>PRK02910 light-independent protochlorophyllide reductase subunit B; Provisional
Probab=32.52 E-value=1.3e+02 Score=32.56 Aligned_cols=76 Identities=16% Similarity=0.153 Sum_probs=55.3
Q ss_pred CeEEEEEcCCcccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHHHHcCCCCCCEEEEecCCCccccc----ccCCCCccc
Q 014264 209 NIIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKLANFPECDVFINVSCAQTALLD----SKEFLAPVI 284 (427)
Q Consensus 209 ~~iGIlvgTl~~q~~~~~i~~l~~li~~~GKK~y~~~vgkln~aKLaNF~eiD~fVlvaCPr~si~d----~~~f~kPvl 284 (427)
+.|-||=.+..+-+.+.=+..|+++|+.-|-++-.+.-+.-+.+.|.+.++.++=| +-||+.+..- .++|-.|.+
T Consensus 159 ~~VNIiG~~~l~f~~~~D~~EikrlL~~~Gi~vn~v~p~g~s~~di~~l~~A~~ni-vl~~~~g~~~A~~Lee~fGiP~i 237 (519)
T PRK02910 159 PSVNLLGPTALGFHHRDDLTELRRLLATLGIDVNVVAPLGASPADLKRLPAAWFNV-VLYREIGESAARYLEREFGQPYV 237 (519)
T ss_pred CeEEEEecCccCCCChhHHHHHHHHHHHcCCeEEEEeCCCCCHHHHHhcccCcEEE-EeCHHHHHHHHHHHHHHhCCccc
Confidence 45666655443344456667799999999999998888999999999998765543 3499866431 356888876
Q ss_pred C
Q 014264 285 T 285 (427)
Q Consensus 285 T 285 (427)
.
T Consensus 238 ~ 238 (519)
T PRK02910 238 K 238 (519)
T ss_pred c
Confidence 4
No 138
>COG1736 DPH2 Diphthamide synthase subunit DPH2 [Translation, ribosomal structure and biogenesis]
Probab=32.40 E-value=4.6e+02 Score=26.95 Aligned_cols=168 Identities=16% Similarity=0.253 Sum_probs=89.8
Q ss_pred cCCChHHHHHHHhhhhcCCCCcEEEEecccchhhhHHHHHHHHhhccCCCCCcceeeeeecceeeeecCCCCCCCCCCCC
Q 014264 47 ASINTSNCIENLSKHALTNGKPILVLYGLEYAHAIPHIREAVKVASSSYGSGLKLEINFADVMCTVITPSKDHKSLCGPA 126 (427)
Q Consensus 47 ~~ld~~~~~~~l~~~~~~~~~~v~l~~dvqy~~~l~~l~~~L~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~g~~ 126 (427)
.++|.+.++..+++. +.++|+|-+.--..+...++.+.|++.. + .++.+.. +|.-
T Consensus 8 ~~~e~~~iv~~ir~~---~ak~V~LQ~PeGLk~~~~~ia~~le~~~---~----~~v~i~g------d~~y--------- 62 (347)
T COG1736 8 YNYEIEEIVREIRRL---GAKRVLLQFPEGLKRYAIEIADILEANL---G----AEVIISG------DPVY--------- 62 (347)
T ss_pred eecchhHHHHHHHhC---CCceEEEECChHHHHHHHHHHHHHHHhh---C----ceEEEeC------Cccc---------
Confidence 345677777777653 3578999888888888889999998862 1 2222210 1110
Q ss_pred CCcccccccCcccccCCccCccceEEEEEcCCcchhhHHHhhcCCceEEEecCCCCceecccCcHHHHHHHHHHHHHHHh
Q 014264 127 GGCTRHTIGGLVWNIPDRKKMEEHLLFWIGSDNSAFANVVLTFNGCEIVRYDATEERLLTDVSQPLKILKRRYYLVEKAK 206 (427)
Q Consensus 127 ~gc~~~~~~~~~~~~~~~~~~~~~~i~~Ig~~~~~l~~l~l~~~~~~v~~yDP~~~~~~~~~~~~~r~L~rRy~~I~ka~ 206 (427)
+.|..... . .... .-.+||+|..... + ..++.. ..|=|...++ +...+...=-..+++
T Consensus 63 GACdi~~~-----~---a~~~-~D~iVH~GHs~l~--~--~~~~~~--Viyv~~~~~~-----d~~~~~~~~~~~l~~-- 120 (347)
T COG1736 63 GACDIDDL-----K---AKDV-VDLIVHYGHSCLP--P--VEYELP--VIYVFAFSRV-----DVDLVVLEATRELKK-- 120 (347)
T ss_pred ccccCCHH-----H---Hhhc-ccEEEEcccccCC--C--cCCCCc--EEEeeccccc-----chhHHHHHhhHhhcc--
Confidence 23421100 0 0011 1278999987622 1 111111 2222332221 122222111112222
Q ss_pred cCCeEEEEEcCCcccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHHHHcCCCCCCEEEEecCCCcccc
Q 014264 207 DANIIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKLANFPECDVFINVSCAQTALL 274 (427)
Q Consensus 207 ~A~~iGIlvgTl~~q~~~~~i~~l~~li~~~GKK~y~~~vgkln~aKLaNF~eiD~fVlvaCPr~si~ 274 (427)
..+.||++.. ..+...++.+++.|+..|. .+++++.+-- .++. ..++||.-.++.
T Consensus 121 ~~r~I~li~t----~q~~~~l~~~k~~L~~~g~---~v~i~~~~~r-~~~~-----gqVLGC~~~~~~ 175 (347)
T COG1736 121 GSRRIGLITT----AQHVHLLEEVKEILEGRGY---EVVIGRGQTR-PAYP-----GQVLGCNFSVLE 175 (347)
T ss_pred CCceEEEEec----ccchhHHHHHHHHhhcCCe---EEEEeCCCCc-ccCc-----ceeeccccccCC
Confidence 4566887765 4577889999999998776 7777877654 3333 234666655554
No 139
>PRK10727 DNA-binding transcriptional regulator GalR; Provisional
Probab=32.38 E-value=1.7e+02 Score=28.92 Aligned_cols=62 Identities=15% Similarity=0.279 Sum_probs=44.0
Q ss_pred cCCeEEEEEcCCcccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHHH----HcCC--CCCCEEEEecCC
Q 014264 207 DANIIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAK----LANF--PECDVFINVSCA 269 (427)
Q Consensus 207 ~A~~iGIlvgTl~~q~~~~~i~~l~~li~~~GKK~y~~~vgkln~aK----LaNF--~eiD~fVlvaCP 269 (427)
..++||+++..+.-..+..+++.+.+.++++|....+.. +.-++++ +.++ ..+|.+++.++.
T Consensus 58 ~~~~Igvi~~~~~~~f~~~~~~gi~~~~~~~g~~~~~~~-~~~~~~~~~~~i~~l~~~~vdgiIi~~~~ 125 (343)
T PRK10727 58 STETVGLVVGDVSDPFFGAMVKAVEQVAYHTGNFLLIGN-GYHNEQKERQAIEQLIRHRCAALVVHAKM 125 (343)
T ss_pred CCCeEEEEeCCCCcchHHHHHHHHHHHHHHcCCEEEEEe-CCCCHHHHHHHHHHHHhcCCCEEEEecCC
Confidence 467999999988777888999999999999997754432 3333322 2222 269999988653
No 140
>cd06309 PBP1_YtfQ_like Periplasmic binding domain of ABC-type YtfQ-like transport systems. Periplasmic binding domain of ABC-type YtfQ-like transport systems. The YtfQ protein from Escherichia coli is up-regulated under glucose-limited conditions and shares homology with a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily. Members of this group are predicted to be involved in the transport of sugar-containing molecules across cellular and organellar membranes; however their ligand specificity is not determined experimentally.
Probab=32.15 E-value=43 Score=31.64 Aligned_cols=59 Identities=12% Similarity=-0.003 Sum_probs=36.9
Q ss_pred eEEEEEcCCcccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHHHHcCC------CCCCEEEEecCC
Q 014264 210 IIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKLANF------PECDVFINVSCA 269 (427)
Q Consensus 210 ~iGIlvgTl~~q~~~~~i~~l~~li~~~GKK~y~~~vgkln~aKLaNF------~eiD~fVlvaCP 269 (427)
+||+++=...-..+..+++.+.+.++++|.+..+..... ++++-.+. ..+|.+|+.++-
T Consensus 1 ~~g~~~~~~~~~~~~~~~~~~~~~a~~~g~~~~~~~~~~-~~~~~~~~i~~l~~~~vdgiIi~~~~ 65 (273)
T cd06309 1 TVGFSQVGAESPWRTAETKSIKDAAEKRGFDLKFADAQQ-KQENQISAIRSFIAQGVDVIILAPVV 65 (273)
T ss_pred CeeeccCCCCCHHHHHHHHHHHHHHHhcCCEEEEeCCCC-CHHHHHHHHHHHHHcCCCEEEEcCCc
Confidence 467777766666667788888888888877766654432 33322111 257888776643
No 141
>cd01541 PBP1_AraR Ligand-binding domain of DNA transcription repressor specific for arabinose (AraR) which is a member of the LacI-GalR family of bacterial transcription regulators. Ligand-binding domain of DNA transcription repressor specific for arabinose (AraR) which is a member of the LacI-GalR family of bacterial transcription regulators. The ligand-binding domain of AraR is structurally homologous to the periplasmic sugar-binding domain of ABC-type transporters and both domains contain the type I periplasmic binding protein-like fold. The LacI-GalR family repressors 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 type I periplasmic binding proteins. 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 i
Probab=31.99 E-value=94 Score=29.25 Aligned_cols=55 Identities=15% Similarity=0.212 Sum_probs=40.5
Q ss_pred eEEEEEcCCcccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHH-------HHcCCCCCCEEEEe
Q 014264 210 IIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPA-------KLANFPECDVFINV 266 (427)
Q Consensus 210 ~iGIlvgTl~~q~~~~~i~~l~~li~~~GKK~y~~~vgkln~a-------KLaNF~eiD~fVlv 266 (427)
+||+++.++.-..+..+++.+.+.++++|....+... +-+++ .|.+- .+|.+++.
T Consensus 1 ~igvv~~~~~~~~~~~~~~gi~~~~~~~g~~~~~~~~-~~~~~~~~~~i~~l~~~-~vdgii~~ 62 (273)
T cd01541 1 NIGVITTYISDYIFPSIIRGIESVLSEKGYSLLLAST-NNDPERERKCLENMLSQ-GIDGLIIE 62 (273)
T ss_pred CeEEEeCCccchhHHHHHHHHHHHHHHcCCEEEEEeC-CCCHHHHHHHHHHHHHc-CCCEEEEe
Confidence 4789998888777889999999999999988765443 34553 23343 68999885
No 142
>cd06304 PBP1_BmpA_like Periplasmic binding component of a family of basic membrane lipoproteins from Borrelia and various putative lipoproteins from other bacteria. Periplasmic binding component of a family of basic membrane lipoproteins from Borrelia and various putative lipoproteins from other bacteria. These outer membrane proteins include Med, a cell-surface localized protein regulating the competence transcription factor gene comK in Bacillus subtilis, and PnrA, a periplasmic purine nucleoside binding protein of an ATP-binding cassette (ABC) transport system in Treponema pallidum. All contain the type I periplasmic sugar-binding protein-like fold.
Probab=31.43 E-value=89 Score=29.47 Aligned_cols=57 Identities=7% Similarity=0.018 Sum_probs=37.8
Q ss_pred eEEEEEcC--CcccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHHHHc----CC--CCCCEEEEecC
Q 014264 210 IIGVLVGT--LGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKLA----NF--PECDVFINVSC 268 (427)
Q Consensus 210 ~iGIlvgT--l~~q~~~~~i~~l~~li~~~GKK~y~~~vgkln~aKLa----NF--~eiD~fVlvaC 268 (427)
+||+|+.. ++...+..+++.+.+.+++.|....+.... ++++.. ++ ..+|.++++++
T Consensus 1 ~Igvi~~~~~~~~~f~~~l~~gi~~~~~~~gy~~~~~~~~--~~~~~~~~~~~l~~~~vdgiii~~~ 65 (260)
T cd06304 1 KVALVYDGGGGDKSFNQSAYEGLEKAEKELGVEVKYVESV--EDADYEPNLRQLAAQGYDLIFGVGF 65 (260)
T ss_pred CEEEEecCCCCcchHHHHHHHHHHHHHHhcCceEEEEecC--CHHHHHHHHHHHHHcCCCEEEECCc
Confidence 47888864 555677788889999888888775554433 444332 22 24888888653
No 143
>cd01539 PBP1_GGBP Periplasmic glucose/galactose-binding protein (GGBP) involved in chemotaxis towards, and active transport of, glucose and galactose in various bacterial species. Periplasmic glucose/galactose-binding protein (GGBP) involved in chemotaxis towards, and active transport of, glucose and galactose in various bacterial species. GGBP is a member of the pentose/hexose sugar-binding protein family of the type I periplasmic binding protein superfamily which consists of two alpha/beta globular 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. Moreover, the periplasmic GGBP is homologous to the ligand-binding domain of eukaryotic receptors such as glutamate receptor (GluR) and DNA-binding transcriptional repressors such as LacI and GalR.
Probab=30.98 E-value=45 Score=32.51 Aligned_cols=59 Identities=10% Similarity=0.050 Sum_probs=37.0
Q ss_pred eEEEEEcCCcccCcHHHHHHHHHHHHH--cCCcEEEEEcCCCCHHH----HcCC--CCCCEEEEecCC
Q 014264 210 IIGVLVGTLGVAGYLHMIHQMKELITK--AGKKAYTLVMGKPNPAK----LANF--PECDVFINVSCA 269 (427)
Q Consensus 210 ~iGIlvgTl~~q~~~~~i~~l~~li~~--~GKK~y~~~vgkln~aK----LaNF--~eiD~fVlvaCP 269 (427)
+||+|+..+.-..+..+++.|.+.+++ .|.+..++. ..-++++ |.++ ..+|.+|+.++.
T Consensus 1 ~Igviv~~~~~~~~~~~~~gi~~~a~~~~~g~~~~~~~-~~~~~~~q~~~i~~l~~~~vdgiii~~~~ 67 (303)
T cd01539 1 KIGVFLYKFDDTFISLVRKNLEDIQKENGGKVEFTFYD-AKNNQSTQNEQIDTALAKGVDLLAVNLVD 67 (303)
T ss_pred CeEEEeeCCCChHHHHHHHHHHHHHHhhCCCeeEEEec-CCCCHHHHHHHHHHHHHcCCCEEEEecCc
Confidence 478888887766777888888888888 554433332 2334432 2222 268888887654
No 144
>cd02036 MinD Bacterial cell division requires the formation of a septum at mid-cell. The site is determined by the min operon products MinC, MinD and MinE. MinC is a nonspecific inhibitor of the septum protein FtsZ. MinE is the supressor of MinC. MinD plays a pivotal role, selecting the mid-cell over other sites through the activation and regulation of MinC and MinE. MinD is a membrane-associated ATPase, related to nitrogenase iron protein. More distantly related proteins include flagellar biosynthesis proteins and ParA chromosome partitioning proteins. MinD is a monomer.
Probab=30.93 E-value=1.9e+02 Score=25.37 Aligned_cols=59 Identities=12% Similarity=0.117 Sum_probs=43.3
Q ss_pred EEEcCCcccCcHHHHHHHHHHHHHcCCcEEEEEcCC--CCHHHHcCCC--------CCC--EEEEecCCCc
Q 014264 213 VLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGK--PNPAKLANFP--------ECD--VFINVSCAQT 271 (427)
Q Consensus 213 IlvgTl~~q~~~~~i~~l~~li~~~GKK~y~~~vgk--ln~aKLaNF~--------eiD--~fVlvaCPr~ 271 (427)
.+++.+||.|--.+.-.|-..+.++|+|+.++=.+- .|...+.... ++- =||++-||-.
T Consensus 3 ~v~~~kgG~GKtt~a~~la~~l~~~g~~vllvD~D~~~~~~~~~~~~~~~~~~~~~~~~~~d~viiD~p~~ 73 (179)
T cd02036 3 VVTSGKGGVGKTTTTANLGTALAQLGYKVVLIDADLGLRNLDLILGLENRVVYTLHDVLAGDYILIDSPAG 73 (179)
T ss_pred EEeeCCCCCCHHHHHHHHHHHHHhCCCeEEEEeCCCCCCCchhhccccccCCcchhhcccCCEEEEECCCC
Confidence 478899999999999999999999999999986663 3555542221 111 3788888754
No 145
>cd06288 PBP1_sucrose_transcription_regulator Ligand-binding domain of DNA-binding regulatory proteins specific to sucrose that are members of the LacI-GalR family of bacterial transcription repressors. This group includes the ligand-binding domain of DNA-binding regulatory proteins specific to sucrose that are members of the LacI-GalR family of bacterial transcription repressors. The LacI-GalR family repressors 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 affinity of the repressor.
Probab=30.76 E-value=1.7e+02 Score=27.24 Aligned_cols=59 Identities=10% Similarity=0.080 Sum_probs=41.6
Q ss_pred eEEEEEcCC-cccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHHHH----cCC--CCCCEEEEecCC
Q 014264 210 IIGVLVGTL-GVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKL----ANF--PECDVFINVSCA 269 (427)
Q Consensus 210 ~iGIlvgTl-~~q~~~~~i~~l~~li~~~GKK~y~~~vgkln~aKL----aNF--~eiD~fVlvaCP 269 (427)
+||+|+-.. .-..+..+++.+++.+++.|....++. ..-++++. .++ ..+|..++.++.
T Consensus 1 ~ig~v~~~~~~~~~~~~~~~~i~~~~~~~g~~~~~~~-~~~~~~~~~~~~~~l~~~~~dgiii~~~~ 66 (269)
T cd06288 1 TIGLISDEIATTPFAVEIILGAQDAAREHGYLLLVVN-TGGDDELEAEAVEALLDHRVDGIIYATMY 66 (269)
T ss_pred CeEEEeCCCCCCccHHHHHHHHHHHHHHCCCEEEEEe-CCCCHHHHHHHHHHHHHcCCCEEEEecCC
Confidence 589999877 566677899999999999997765543 34344322 222 258999998864
No 146
>PRK05569 flavodoxin; Provisional
Probab=30.68 E-value=2.5e+02 Score=23.96 Aligned_cols=56 Identities=9% Similarity=0.163 Sum_probs=42.0
Q ss_pred eEEEEEcCCcccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHHHHcCCCCCCEEEEecCCC
Q 014264 210 IIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKLANFPECDVFINVSCAQ 270 (427)
Q Consensus 210 ~iGIlvgTl~~q~~~~~i~~l~~li~~~GKK~y~~~vgkln~aKLaNF~eiD~fVlvaCPr 270 (427)
.+.|+-+|.. -+...+++.|.+.+++.|..+-++-+.+..+.++. +.|. |+++||=
T Consensus 3 ki~iiY~S~t-GnT~~iA~~i~~~~~~~g~~v~~~~~~~~~~~~~~---~~d~-iilgsPt 58 (141)
T PRK05569 3 KVSIIYWSCG-GNVEVLANTIADGAKEAGAEVTIKHVADAKVEDVL---EADA-VAFGSPS 58 (141)
T ss_pred eEEEEEECCC-CHHHHHHHHHHHHHHhCCCeEEEEECCcCCHHHHh---hCCE-EEEECCC
Confidence 5778888853 57789999999999999988777777777776554 4465 5566663
No 147
>PRK00061 ribH 6,7-dimethyl-8-ribityllumazine synthase; Provisional
Probab=30.32 E-value=1.4e+02 Score=27.02 Aligned_cols=61 Identities=15% Similarity=0.132 Sum_probs=40.6
Q ss_pred CeEEEEEcCCcccCcHHHHHHHHHHHHHcCC---cEEEEEcCC---CC--HHHHcCCCCCCEEEEecCC
Q 014264 209 NIIGVLVGTLGVAGYLHMIHQMKELITKAGK---KAYTLVMGK---PN--PAKLANFPECDVFINVSCA 269 (427)
Q Consensus 209 ~~iGIlvgTl~~q~~~~~i~~l~~li~~~GK---K~y~~~vgk---ln--~aKLaNF~eiD~fVlvaCP 269 (427)
-+|+||++.-...-.-.+++...+.|++.|. ...++.|-- |- ..+|++-.++|++|-++|-
T Consensus 13 ~riaIV~s~~n~~i~~~l~~ga~~~l~~~gv~~~~i~v~~VPGa~EiP~a~~~l~~~~~~DavIalG~V 81 (154)
T PRK00061 13 LRIGIVVARFNDFITDALLEGALDALKRHGVSEENIDVVRVPGAFEIPLAAKKLAESGKYDAVIALGAV 81 (154)
T ss_pred CEEEEEEecCcHHHHHHHHHHHHHHHHHcCCCccceEEEECCCHHHHHHHHHHHHHcCCCCEEEEEeeE
Confidence 4899999875444344566666778888883 334444431 11 2467766679999999997
No 148
>cd06322 PBP1_ABC_sugar_binding_like_12 Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems. This group includes the periplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily, which consist of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis.
Probab=30.24 E-value=58 Score=30.53 Aligned_cols=75 Identities=20% Similarity=0.199 Sum_probs=46.1
Q ss_pred eEEEEEcCCcccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHHHH-------cCCCCCCEEEEecCCCcccc----cccC
Q 014264 210 IIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKL-------ANFPECDVFINVSCAQTALL----DSKE 278 (427)
Q Consensus 210 ~iGIlvgTl~~q~~~~~i~~l~~li~~~GKK~y~~~vgkln~aKL-------aNF~eiD~fVlvaCPr~si~----d~~~ 278 (427)
+||+++-+..-..+..+++.+++.+++.|....+.. +.-++++- .+- .+|++|+.++...... ..++
T Consensus 1 ~i~~~~~~~~~~~~~~~~~~i~~~~~~~g~~~~i~~-~~~~~~~~~~~~~~~~~~-~vdgiii~~~~~~~~~~~~~~~~~ 78 (267)
T cd06322 1 VIGASLLTQQHPFYIELANAMKEEAKKQKVNLIVSI-ANQDLNKQLSDVEDFITK-KVDAIVLSPVDSKGIRAAIAKAKK 78 (267)
T ss_pred CeeEeecCcccHHHHHHHHHHHHHHHhcCCEEEEec-CCCCHHHHHHHHHHHHHc-CCCEEEEcCCChhhhHHHHHHHHH
Confidence 478888887766677888888888888887664433 33344332 222 5898888776432211 1233
Q ss_pred CCCcccCH
Q 014264 279 FLAPVITP 286 (427)
Q Consensus 279 f~kPvlTP 286 (427)
...|+|+.
T Consensus 79 ~~ipvV~~ 86 (267)
T cd06322 79 AGIPVITV 86 (267)
T ss_pred CCCCEEEE
Confidence 45566654
No 149
>PRK08883 ribulose-phosphate 3-epimerase; Provisional
Probab=30.18 E-value=75 Score=30.28 Aligned_cols=84 Identities=13% Similarity=0.255 Sum_probs=51.5
Q ss_pred cCCceEEEecCCCCceecccCcHHHHHHHHHHHHHHHhcCCeEEEEEc--CCcccCcH----HHHHHHHHHHHHcCCcEE
Q 014264 169 FNGCEIVRYDATEERLLTDVSQPLKILKRRYYLVEKAKDANIIGVLVG--TLGVAGYL----HMIHQMKELITKAGKKAY 242 (427)
Q Consensus 169 ~~~~~v~~yDP~~~~~~~~~~~~~r~L~rRy~~I~ka~~A~~iGIlvg--Tl~~q~~~----~~i~~l~~li~~~GKK~y 242 (427)
...+.-..++|.|.-- .+ + .+ +.....|=|.-- ..++|.+. +-+++++++++++|...-
T Consensus 105 ~g~k~GlalnP~Tp~~---------~i--~-~~---l~~~D~vlvMtV~PGfgGq~fi~~~lekI~~l~~~~~~~~~~~~ 169 (220)
T PRK08883 105 HGCQAGVVLNPATPLH---------HL--E-YI---MDKVDLILLMSVNPGFGGQSFIPHTLDKLRAVRKMIDESGRDIR 169 (220)
T ss_pred cCCcEEEEeCCCCCHH---------HH--H-HH---HHhCCeEEEEEecCCCCCceecHhHHHHHHHHHHHHHhcCCCee
Confidence 3445678899988531 11 1 11 223444433222 23455554 356677777777787777
Q ss_pred EEEcCCCCHHHHcCCC--CCCEEEEec
Q 014264 243 TLVMGKPNPAKLANFP--ECDVFINVS 267 (427)
Q Consensus 243 ~~~vgkln~aKLaNF~--eiD~fVlva 267 (427)
+.+-|-+|++.+.... ++|++|+.+
T Consensus 170 I~vdGGI~~eni~~l~~aGAd~vVvGS 196 (220)
T PRK08883 170 LEIDGGVKVDNIREIAEAGADMFVAGS 196 (220)
T ss_pred EEEECCCCHHHHHHHHHcCCCEEEEeH
Confidence 8899999988776553 589998873
No 150
>COG0529 CysC Adenylylsulfate kinase and related kinases [Inorganic ion transport and metabolism]
Probab=29.27 E-value=1.3e+02 Score=28.14 Aligned_cols=40 Identities=15% Similarity=0.119 Sum_probs=34.5
Q ss_pred CCeEEEEEcCCcccCcHHHHHHHHHHHHHcCCcEEEEEcC
Q 014264 208 ANIIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMG 247 (427)
Q Consensus 208 A~~iGIlvgTl~~q~~~~~i~~l~~li~~~GKK~y~~~vg 247 (427)
.+-+-|-+.-|+++|=-.+++.|.+.|.+.|+.+|++==+
T Consensus 21 ~~~~viW~TGLSGsGKSTiA~ale~~L~~~G~~~y~LDGD 60 (197)
T COG0529 21 QKGAVIWFTGLSGSGKSTIANALEEKLFAKGYHVYLLDGD 60 (197)
T ss_pred CCCeEEEeecCCCCCHHHHHHHHHHHHHHcCCeEEEecCh
Confidence 3456678889999999999999999999999999987533
No 151
>PRK14057 epimerase; Provisional
Probab=29.03 E-value=1.5e+02 Score=29.03 Aligned_cols=60 Identities=15% Similarity=0.176 Sum_probs=37.8
Q ss_pred cCCeEEEEEcCCc--ccCcH-H---HHHHHHHHHHHcCCcEEEEEcCCCCHHHHcCC--CCCCEEEEe
Q 014264 207 DANIIGVLVGTLG--VAGYL-H---MIHQMKELITKAGKKAYTLVMGKPNPAKLANF--PECDVFINV 266 (427)
Q Consensus 207 ~A~~iGIlvgTl~--~q~~~-~---~i~~l~~li~~~GKK~y~~~vgkln~aKLaNF--~eiD~fVlv 266 (427)
....|=|.--.-| ||.+. . -+++++++++++|.++-+-+=|-+|.+.+.-. .++|+||.=
T Consensus 154 ~vD~VLvMtV~PGfgGQ~Fi~~~l~KI~~lr~~~~~~~~~~~IeVDGGI~~~ti~~l~~aGad~~V~G 221 (254)
T PRK14057 154 DVEVIQLLAVNPGYGSKMRSSDLHERVAQLLCLLGDKREGKIIVIDGSLTQDQLPSLIAQGIDRVVSG 221 (254)
T ss_pred hCCEEEEEEECCCCCchhccHHHHHHHHHHHHHHHhcCCCceEEEECCCCHHHHHHHHHCCCCEEEEC
Confidence 3445544443333 66665 3 44555567777777766777788998866544 268988874
No 152
>cd06324 PBP1_ABC_sugar_binding_like_13 Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems. This group includes the periplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily, which consists of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis.
Probab=28.88 E-value=75 Score=30.92 Aligned_cols=58 Identities=10% Similarity=0.005 Sum_probs=35.5
Q ss_pred eEEEEEcCC-cccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHHHH----cCC--C--CCCEEEEecC
Q 014264 210 IIGVLVGTL-GVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKL----ANF--P--ECDVFINVSC 268 (427)
Q Consensus 210 ~iGIlvgTl-~~q~~~~~i~~l~~li~~~GKK~y~~~vgkln~aKL----aNF--~--eiD~fVlvaC 268 (427)
.||+|+..+ .-..+..+++.+++.+++.|....+...+. ++++- .+| . .+|.+|+.+.
T Consensus 1 ~Igvi~~~~~~~~~~~~~~~gi~~~~~~~g~~v~~~~~~~-~~~~~~~~i~~~~~~~~~vdgiIi~~~ 67 (305)
T cd06324 1 SVVFLNPGKSDEPFWNSVARFMQAAADDLGIELEVLYAER-DRFLMLQQARTILQRPDKPDALIFTNE 67 (305)
T ss_pred CeEEecCCCCCCcHHHHHHHHHHHHHHhcCCeEEEEeCCC-CHHHHHHHHHHHHHhccCCCEEEEcCC
Confidence 367888776 555666777788888888777765544332 33222 122 2 5788887654
No 153
>TIGR02014 BchZ chlorophyllide reductase subunit Z. This model represents the Z subunit of the three-subunit enzyme, (bacterio)chlorophyllide reductase. This enzyme is responsible for the reduction of the chlorin B-ring and is closely related to the protochlorophyllide reductase complex which reduces the D-ring. Both of these complexes in turn are homologous to nitrogenase.
Probab=28.77 E-value=87 Score=33.42 Aligned_cols=77 Identities=10% Similarity=0.121 Sum_probs=60.2
Q ss_pred cCCeEEEEEcCCcccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHHHHcCCCCCCEEEEecCCCcccccccCCCCccc
Q 014264 207 DANIIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKLANFPECDVFINVSCAQTALLDSKEFLAPVI 284 (427)
Q Consensus 207 ~A~~iGIlvgTl~~q~~~~~i~~l~~li~~~GKK~y~~~vgkln~aKLaNF~eiD~fVlvaCPr~si~d~~~f~kPvl 284 (427)
+.+.|-||=.+-+.-+++.=++.||++|+.-|-++..+.-+.-+.+.|.+.++.++=+++ |++.+..-.++|-.|-+
T Consensus 151 ~~~~VNIiG~~~g~~~~~~Dl~ElkrlL~~~Gi~vn~v~~~Gtsv~di~~l~~A~~nIv~-~~~~a~~L~e~~GvP~l 227 (468)
T TIGR02014 151 AKPRVNIIGPTYGCFNMPSDLAEIRRLVEGIGAEVAHVYPLGSHLAEITKLKNADANIVM-YREFGRGLAEKLGKPYL 227 (468)
T ss_pred CCCeEEEECCCcCcCCChhHHHHHHHHHHHcCCcEEEEcCCcCCHHHHHhhccCcEEEee-cHHHHHHHHHHHCCCcc
Confidence 346677776555555667777899999999999999999999999999999988777776 88766554556777754
No 154
>cd01473 vWA_CTRP CTRP for CS protein-TRAP-related protein: Adhesion of Plasmodium to host cells is an important phenomenon in parasite invasion and in malaria associated pathology.CTRP encodes a protein containing a putative signal sequence followed by a long extracellular region of 1990 amino acids, a transmembrane domain, and a short cytoplasmic segment. The extracellular region of CTRP contains two separated adhesive domains. The first domain contains six 210-amino acid-long homologous VWA domain repeats. The second domain contains seven repeats of 87-60 amino acids in length, which share similarities with the thrombospondin type 1 domain found in a variety of adhesive molecules. Finally, CTRP also contains consensus motifs found in the superfamily of haematopoietin receptors. The VWA domains in these proteins likely mediate protein-protein interactions.
Probab=28.37 E-value=1.9e+02 Score=26.59 Aligned_cols=50 Identities=16% Similarity=0.178 Sum_probs=36.2
Q ss_pred CCeEEEEEcCCcccCc--HHHHHHHHHHHHHcCCcEEEEEcCCCCHHHHcCCC
Q 014264 208 ANIIGVLVGTLGVAGY--LHMIHQMKELITKAGKKAYTLVMGKPNPAKLANFP 258 (427)
Q Consensus 208 A~~iGIlvgTl~~q~~--~~~i~~l~~li~~~GKK~y~~~vgkln~aKLaNF~ 258 (427)
+..+.||+.- |.... ..-+....+.++++|-+.|++-||..+.+.|..+.
T Consensus 108 ~~kv~IllTD-G~s~~~~~~~~~~~a~~lk~~gV~i~~vGiG~~~~~el~~ia 159 (192)
T cd01473 108 APKVTMLFTD-GNDTSASKKELQDISLLYKEENVKLLVVGVGAASENKLKLLA 159 (192)
T ss_pred CCeEEEEEec-CCCCCcchhhHHHHHHHHHHCCCEEEEEEeccccHHHHHHhc
Confidence 4777666654 33322 23456667788999999999999999988887764
No 155
>PLN02404 6,7-dimethyl-8-ribityllumazine synthase
Probab=28.16 E-value=1.8e+02 Score=25.84 Aligned_cols=61 Identities=13% Similarity=0.122 Sum_probs=38.6
Q ss_pred CeEEEEEcCCcccCcHHHHHHHHHHHHHcCCc---EEEEEcC---CCC--HHHHcCCCCCCEEEEecCC
Q 014264 209 NIIGVLVGTLGVAGYLHMIHQMKELITKAGKK---AYTLVMG---KPN--PAKLANFPECDVFINVSCA 269 (427)
Q Consensus 209 ~~iGIlvgTl~~q~~~~~i~~l~~li~~~GKK---~y~~~vg---kln--~aKLaNF~eiD~fVlvaCP 269 (427)
-+||||++...-.-.-.+++-.++.|+++|-+ ..++.|= ++- ..+|+.-.++|++|-++|=
T Consensus 8 ~ri~IV~s~fn~~I~~~Ll~ga~~~l~~~gv~~~~i~v~~VPGa~EiP~a~~~l~~s~~~DavIaLG~V 76 (141)
T PLN02404 8 LRFGVVVARFNEIITKNLLEGALETFKRYSVKEENIDVVWVPGSFEIPVVAQRLAKSGKYDAILCIGAV 76 (141)
T ss_pred CEEEEEEecCcHHHHHHHHHHHHHHHHHcCCCccceEEEEcCcHHHHHHHHHHHHhcCCCCEEEEEEEE
Confidence 58999998654333334444455677788854 4555442 221 2567766679999999993
No 156
>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=28.13 E-value=56 Score=30.48 Aligned_cols=57 Identities=21% Similarity=0.223 Sum_probs=32.7
Q ss_pred eEEEEEcCCcccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHHHHcC----C--CCCCEEEEec
Q 014264 210 IIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKLAN----F--PECDVFINVS 267 (427)
Q Consensus 210 ~iGIlvgTl~~q~~~~~i~~l~~li~~~GKK~y~~~vgkln~aKLaN----F--~eiD~fVlva 267 (427)
+||+|+.++.-..+..+++.+.+.+++.|....++. ..-++++..+ + ..+|.+++.+
T Consensus 1 ~I~vv~~~~~~~~~~~~~~~i~~~~~~~g~~v~~~~-~~~~~~~~~~~~~~~~~~~~dgii~~~ 63 (268)
T cd06323 1 TIGLSVSTLNNPFFVTLKDGAQKEAKELGYELTVLD-AQNDAAKQLNDIEDLITRGVDAIIINP 63 (268)
T ss_pred CeeEecccccCHHHHHHHHHHHHHHHHcCceEEecC-CCCCHHHHHHHHHHHHHcCCCEEEEcC
Confidence 367777776666667777777777777765543322 2334443211 1 1467766653
No 157
>cd06314 PBP1_tmGBP Periplasmic sugar-binding domain of Thermotoga maritima glucose-binding protein (tmGBP) and its close homologs. Periplasmic sugar-binding domain of Thermotoga maritima glucose-binding protein (tmGBP) and its close homologs from other bacteria. They are a member of the type I periplasmic binding protein superfamily which consists of two domains connected by a three-stranded hinge. TmGBP is specific for glucose and its binding pocket is buried at the interface of the two domains. TmGBP also exhibits high thermostability and the highest structural similarity to E. coli glucose binding protein (ecGBP).
Probab=27.75 E-value=91 Score=29.41 Aligned_cols=59 Identities=10% Similarity=-0.024 Sum_probs=34.9
Q ss_pred eEEEEEcCCcccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHHHH----cCC--CCCCEEEEecCC
Q 014264 210 IIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKL----ANF--PECDVFINVSCA 269 (427)
Q Consensus 210 ~iGIlvgTl~~q~~~~~i~~l~~li~~~GKK~y~~~vgkln~aKL----aNF--~eiD~fVlvaCP 269 (427)
+||+|+.. .--.+..+++.+.+.+++.|.+..++.-..-++++. .++ ..+|.+++..+-
T Consensus 1 ~i~~v~~~-~~~~~~~~~~gi~~~~~~~g~~~~~~~~~~~~~~~~~~~i~~l~~~~vDgiIi~~~~ 65 (271)
T cd06314 1 TIAVVTNG-ASPFWKIAEAGVKAAGKELGVDVEFVVPQQGTVNAQLRMLEDLIAEGVDGIAISPID 65 (271)
T ss_pred CeEEEcCC-CcHHHHHHHHHHHHHHHHcCCeEEEeCCCCCCHHHHHHHHHHHHhcCCCEEEEecCC
Confidence 46777743 335567888888888888887655443232233322 122 258888887653
No 158
>PRK06756 flavodoxin; Provisional
Probab=27.15 E-value=2.4e+02 Score=24.40 Aligned_cols=56 Identities=7% Similarity=0.124 Sum_probs=39.2
Q ss_pred eEEEEEcCCcccCcHHHHHHHHHHHHHcCCcEEEEEcCCC-CHHHHcCCCCCCEEEEecCCC
Q 014264 210 IIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKP-NPAKLANFPECDVFINVSCAQ 270 (427)
Q Consensus 210 ~iGIlvgTl~~q~~~~~i~~l~~li~~~GKK~y~~~vgkl-n~aKLaNF~eiD~fVlvaCPr 270 (427)
.+.||-+|.. -+...+++.|.+.+++.|.++-++-+.+. ....|. +.|.+ +++||=
T Consensus 3 kv~IiY~S~t-GnTe~vA~~ia~~l~~~g~~v~~~~~~~~~~~~~~~---~~d~v-i~gspt 59 (148)
T PRK06756 3 KLVMIFASMS-GNTEEMADHIAGVIRETENEIEVIDIMDSPEASILE---QYDGI-ILGAYT 59 (148)
T ss_pred eEEEEEECCC-chHHHHHHHHHHHHhhcCCeEEEeehhccCCHHHHh---cCCeE-EEEeCC
Confidence 5778888865 56788999999999999988877766543 234444 45665 455543
No 159
>cd06276 PBP1_FucR_like Ligand-binding domain of a transcription repressor, FucR, which functions as a molecular sensor of L-fucose availability. Ligand-binding domain of a transcription repressor, FucR, which functions as a molecular sensor of L-fucose availability. FcuR acts as an inducer of fucRRIAK and as a corepressor of another locus that regulates production of fucosylated glycans. FcuR and its close homologs in this group are a member of 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 t
Probab=27.15 E-value=1.4e+02 Score=28.08 Aligned_cols=56 Identities=9% Similarity=0.070 Sum_probs=38.9
Q ss_pred EEEEEcCCcccCcHHHHHHHHHHHHHcC-CcEEEEEcCCCCHH-HH---cCCCCCCEEEEecCC
Q 014264 211 IGVLVGTLGVAGYLHMIHQMKELITKAG-KKAYTLVMGKPNPA-KL---ANFPECDVFINVSCA 269 (427)
Q Consensus 211 iGIlvgTl~~q~~~~~i~~l~~li~~~G-KK~y~~~vgkln~a-KL---aNF~eiD~fVlvaCP 269 (427)
+.|++..+ -..+..++..|.+.++++| ....+...++ ... .+ .+ ..+|.+|++++.
T Consensus 2 ~~~~~~~~-~~~~~~~~~~i~~~l~~~g~~~l~~~~~~~-~~~~~~~~~~~-~~vdGvIi~~~~ 62 (247)
T cd06276 2 ILLLLNKL-SSFKEIIYNSFVNTLGKNAQVDLYFHHYNE-DLFKNIISNTK-GKYSGYVVMPHF 62 (247)
T ss_pred EEEEEecC-chHHHHHHHHHHHHHHhcCcEEEEEEcCch-HHHHHHHHHHh-cCCCEEEEecCC
Confidence 67888888 5667789999999999999 5555444443 221 11 12 369999998875
No 160
>PRK10401 DNA-binding transcriptional regulator GalS; Provisional
Probab=27.11 E-value=3.1e+02 Score=26.98 Aligned_cols=61 Identities=18% Similarity=0.188 Sum_probs=43.5
Q ss_pred hcCCeEEEEEcCCcccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHHH-------HcCCCCCCEEEEecC
Q 014264 206 KDANIIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAK-------LANFPECDVFINVSC 268 (427)
Q Consensus 206 ~~A~~iGIlvgTl~~q~~~~~i~~l~~li~~~GKK~y~~~vgkln~aK-------LaNF~eiD~fVlvaC 268 (427)
+..++||+++..+.-..+..+++.+.+.++++|....+.. ..-++++ |.+ ..+|.+++++.
T Consensus 57 ~~~~~Igvi~~~~~~~f~~~l~~gi~~~~~~~gy~~~~~~-~~~~~~~~~~~i~~l~~-~~vdGiIi~~~ 124 (346)
T PRK10401 57 QVSDTIGVVVMDVSDAFFGALVKAVDLVAQQHQKYVLIGN-SYHEAEKERHAIEVLIR-QRCNALIVHSK 124 (346)
T ss_pred CCCCEEEEEeCCCCCccHHHHHHHHHHHHHHCCCEEEEEc-CCCChHHHHHHHHHHHh-cCCCEEEEeCC
Confidence 3467899999888777888999999999999987754332 2223332 222 25999999864
No 161
>cd03819 GT1_WavL_like This family is most closely related to the GT1 family of glycosyltransferases. WavL in Vibrio cholerae has been shown to be involved in the biosynthesis of the lipopolysaccharide core.
Probab=26.34 E-value=1.3e+02 Score=29.31 Aligned_cols=43 Identities=16% Similarity=0.341 Sum_probs=20.7
Q ss_pred HHHHHHHHHHcCCcEEEEEcCCCCHHHHcC-CCCCCEEEEec-CCCc
Q 014264 227 IHQMKELITKAGKKAYTLVMGKPNPAKLAN-FPECDVFINVS-CAQT 271 (427)
Q Consensus 227 i~~l~~li~~~GKK~y~~~vgkln~aKLaN-F~eiD~fVlva-CPr~ 271 (427)
.+.+++++++.+.+-.+.++|.. +.+.. +...|+||+.+ ++++
T Consensus 232 ~~~~~~~~~~~~~~~~v~~~g~~--~~~~~~l~~ad~~i~ps~~~e~ 276 (355)
T cd03819 232 YAELLELIKRLGLQDRVTFVGHC--SDMPAAYALADIVVSASTEPEA 276 (355)
T ss_pred HHHHHHHHHHcCCcceEEEcCCc--ccHHHHHHhCCEEEecCCCCCC
Confidence 33444445555544444445541 11211 22468888777 6653
No 162
>PF14538 Raptor_N: Raptor N-terminal CASPase like domain
Probab=26.29 E-value=1.5e+02 Score=26.70 Aligned_cols=50 Identities=26% Similarity=0.474 Sum_probs=31.4
Q ss_pred cEEEEe-cCCCCCCCCCCCeEEEccccC-----CChHHHHHHHhhhhcCCCCcEEEEecccchh
Q 014264 22 DCVIHY-GHTCLSPTSTLPAFFVFGKAS-----INTSNCIENLSKHALTNGKPILVLYGLEYAH 79 (427)
Q Consensus 22 D~iVHy-GhaCls~~~~lpv~YVf~~~~-----ld~~~~~~~l~~~~~~~~~~v~l~~dvqy~~ 79 (427)
=+|+|| ||-+-.|++. -=|++|.+.. +.+..+.+.+ +.+.+.+.|-..+-
T Consensus 92 RvLFHYnGhGvP~Pt~~-GeIw~f~~~~tqyip~si~dL~~~l-------g~Psi~V~DC~~AG 147 (154)
T PF14538_consen 92 RVLFHYNGHGVPRPTEN-GEIWVFNKNYTQYIPLSIYDLQSWL-------GSPSIYVFDCSNAG 147 (154)
T ss_pred eEEEEECCCCCCCCCCC-CeEEEEcCCCCcceEEEHHHHHHhc-------CCCEEEEEECCcHH
Confidence 479999 8998766542 4688888633 4444333322 34677778866543
No 163
>PRK11921 metallo-beta-lactamase/flavodoxin domain-containing protein; Provisional
Probab=26.17 E-value=1.8e+02 Score=29.92 Aligned_cols=77 Identities=16% Similarity=0.205 Sum_probs=56.9
Q ss_pred HHHHHHHHHHHHHHHhcCCeEEEEEcCCcccCcHHHHHHHHHHHH--HcCCcEEEEEcCCCCHHHHcC-CCCCCEEEEec
Q 014264 191 PLKILKRRYYLVEKAKDANIIGVLVGTLGVAGYLHMIHQMKELIT--KAGKKAYTLVMGKPNPAKLAN-FPECDVFINVS 267 (427)
Q Consensus 191 ~~r~L~rRy~~I~ka~~A~~iGIlvgTl~~q~~~~~i~~l~~li~--~~GKK~y~~~vgkln~aKLaN-F~eiD~fVlva 267 (427)
..+++ ++|....+-+.-+.+.|+-+|.. -+...+++.+.+-++ ..|-++-++-+.+..++.+++ +.+.|++| ++
T Consensus 231 ~~~~~-~~Y~~~~~~~~~~kv~IvY~S~~-GnTe~mA~~ia~g~~~~~~g~~v~~~~~~~~~~~~i~~~~~~~d~ii-~G 307 (394)
T PRK11921 231 PLQIV-EKYLEWAANYQENQVTILYDTMW-NSTRRMAEAIAEGIKKANKDVTVKLYNSAKSDKNDIITEVFKSKAIL-VG 307 (394)
T ss_pred HHHHH-HHHHHHhhcCCcCcEEEEEECCc-hHHHHHHHHHHHHHhhcCCCCeEEEEECCCCCHHHHHHHHHhCCEEE-EE
Confidence 34444 45655555566788999999987 467899999999998 678888888999999888764 34567755 55
Q ss_pred CCC
Q 014264 268 CAQ 270 (427)
Q Consensus 268 CPr 270 (427)
||-
T Consensus 308 spT 310 (394)
T PRK11921 308 SST 310 (394)
T ss_pred CCC
Confidence 664
No 164
>PRK15408 autoinducer 2-binding protein lsrB; Provisional
Probab=25.98 E-value=86 Score=31.57 Aligned_cols=63 Identities=17% Similarity=0.106 Sum_probs=38.7
Q ss_pred cCCeEEEEEcCCcccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHHHH----cCC--CCCCEEEEecCC
Q 014264 207 DANIIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKL----ANF--PECDVFINVSCA 269 (427)
Q Consensus 207 ~A~~iGIlvgTl~~q~~~~~i~~l~~li~~~GKK~y~~~vgkln~aKL----aNF--~eiD~fVlvaCP 269 (427)
.+.+|++++.+++-..+..+.+-+++.++++|.+..+..-..-++++- .++ ..+|+.|+.++-
T Consensus 22 ~~~~i~~v~k~~~~pf~~~~~~Gi~~aa~~~G~~v~~~~~~~~d~~~q~~~i~~li~~~vdgIiv~~~d 90 (336)
T PRK15408 22 AAERIAFIPKLVGVGFFTSGGNGAKEAGKELGVDVTYDGPTEPSVSGQVQLINNFVNQGYNAIIVSAVS 90 (336)
T ss_pred CCcEEEEEECCCCCHHHHHHHHHHHHHHHHhCCEEEEECCCCCCHHHHHHHHHHHHHcCCCEEEEecCC
Confidence 456788888777766666777778888887776554322233344332 233 257888776543
No 165
>PF02593 dTMP_synthase: Thymidylate synthase; InterPro: IPR003745 This entry describes proteins of unknown function.
Probab=25.72 E-value=1.1e+02 Score=29.39 Aligned_cols=40 Identities=28% Similarity=0.328 Sum_probs=32.8
Q ss_pred HHHHHHHhcCCeEEEEEcCCcccCcHHHHHHHHHHHHHcCCc
Q 014264 199 YYLVEKAKDANIIGVLVGTLGVAGYLHMIHQMKELITKAGKK 240 (427)
Q Consensus 199 y~~I~ka~~A~~iGIlvgTl~~q~~~~~i~~l~~li~~~GKK 240 (427)
|.++.+|++++.-+|||++-.+. +.+.+.|++.+++.|..
T Consensus 66 ~~l~~~~~e~g~kavIvp~~~~~--~g~~~~lk~~~e~~gi~ 105 (217)
T PF02593_consen 66 YELPEIAKEAGVKAVIVPSESPK--PGLRRQLKKQLEEFGIE 105 (217)
T ss_pred HHHHHHHHHcCCCEEEEecCCCc--cchHHHHHHHHHhcCce
Confidence 46788888899999999988776 88889999888876644
No 166
>PF09547 Spore_IV_A: Stage IV sporulation protein A (spore_IV_A); InterPro: IPR014201 This entry is designated stage IV sporulation protein A. It acts in the mother cell compartment and plays a role in spore coat morphogenesis []. A comparative genome analysis of all sequenced genomes of Firmicutes shows that the proteins are strictly conserved among the sub-set of endospore-forming species.
Probab=25.71 E-value=1.1e+02 Score=32.60 Aligned_cols=71 Identities=28% Similarity=0.417 Sum_probs=49.1
Q ss_pred HhcCCeEEEEEcCCc------ccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCH-----HHHcC-CC-CCCEE-EEecCCC
Q 014264 205 AKDANIIGVLVGTLG------VAGYLHMIHQMKELITKAGKKAYTLVMGKPNP-----AKLAN-FP-ECDVF-INVSCAQ 270 (427)
Q Consensus 205 a~~A~~iGIlvgTl~------~q~~~~~i~~l~~li~~~GKK~y~~~vgkln~-----aKLaN-F~-eiD~f-VlvaCPr 270 (427)
..+=.+|||||.|=| +.+|.+.=++..+.||+-||.+.++ ++-..| .+|+. +. ..|+= +-+.|-+
T Consensus 141 I~dHSTIGiVVTTDGSi~dipRe~Y~eAEervI~ELk~igKPFvil-lNs~~P~s~et~~L~~eL~ekY~vpVlpvnc~~ 219 (492)
T PF09547_consen 141 ITDHSTIGIVVTTDGSITDIPRENYVEAEERVIEELKEIGKPFVIL-LNSTKPYSEETQELAEELEEKYDVPVLPVNCEQ 219 (492)
T ss_pred eccCCceeEEEecCCCccCCChHHHHHHHHHHHHHHHHhCCCEEEE-EeCCCCCCHHHHHHHHHHHHHhCCcEEEeehHH
Confidence 456789999998754 8999999999999999999875544 443333 23332 11 24443 4578988
Q ss_pred cccccc
Q 014264 271 TALLDS 276 (427)
Q Consensus 271 ~si~d~ 276 (427)
..-.|-
T Consensus 220 l~~~DI 225 (492)
T PF09547_consen 220 LREEDI 225 (492)
T ss_pred cCHHHH
Confidence 877663
No 167
>TIGR01012 Sa_S2_E_A ribosomal protein Sa(cytosolic)/S2(archaeal). TIGR01011 describes the related protein of organelles and bacteria.
Probab=25.55 E-value=1.4e+02 Score=28.04 Aligned_cols=51 Identities=22% Similarity=0.268 Sum_probs=30.5
Q ss_pred EEecCCCCCCCCCCCeEEEccccC-----CChHHHHHHHhhhh----cCCCCcEEEEecccch
Q 014264 25 IHYGHTCLSPTSTLPAFFVFGKAS-----INTSNCIENLSKHA----LTNGKPILVLYGLEYA 78 (427)
Q Consensus 25 VHyGhaCls~~~~lpv~YVf~~~~-----ld~~~~~~~l~~~~----~~~~~~v~l~~dvqy~ 78 (427)
|||||.-.+|-- --|+|++.+ ||+++..+.|+... .-..++|+++.+-.+.
T Consensus 14 vH~Gh~~~np~M---~~yI~~~r~~gi~IIdL~kT~~~L~~A~~~i~~i~~~~ILfVgtk~~~ 73 (196)
T TIGR01012 14 VHIGTQNKTKDM---EKFIYKVRSDGLYVLDLRKTDERLRVAAKFLVRIEPEDILVVSARIYG 73 (196)
T ss_pred eecCCCcCCCCC---ccceeeecCCCCEEEcHHHHHHHHHHHHHHHHHhhCCeEEEEecCHHH
Confidence 899997444421 128887653 57877666665432 0114578887775543
No 168
>COG0041 PurE Phosphoribosylcarboxyaminoimidazole (NCAIR) mutase [Nucleotide transport and metabolism]
Probab=25.47 E-value=1.8e+02 Score=26.42 Aligned_cols=60 Identities=18% Similarity=0.315 Sum_probs=44.4
Q ss_pred eEEEEEcCCcccCcHHHHHHHHHHHHHcCCcEEEEEcC-CCCHHHHcCCC----CCCEEEEecCCCcc
Q 014264 210 IIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMG-KPNPAKLANFP----ECDVFINVSCAQTA 272 (427)
Q Consensus 210 ~iGIlvgTl~~q~~~~~i~~l~~li~~~GKK~y~~~vg-kln~aKLaNF~----eiD~fVlvaCPr~s 272 (427)
.+|||.|+.+ -+++.+..-+.|++-|..+-.-+++ .=||++|..|. +=++=|++|..-.+
T Consensus 4 ~V~IIMGS~S---D~~~mk~Aa~~L~~fgi~ye~~VvSAHRTPe~m~~ya~~a~~~g~~viIAgAGgA 68 (162)
T COG0041 4 KVGIIMGSKS---DWDTMKKAAEILEEFGVPYEVRVVSAHRTPEKMFEYAEEAEERGVKVIIAGAGGA 68 (162)
T ss_pred eEEEEecCcc---hHHHHHHHHHHHHHcCCCeEEEEEeccCCHHHHHHHHHHHHHCCCeEEEecCcch
Confidence 7999999965 6788888889999999987765555 77899997774 22344555555444
No 169
>TIGR01931 cysJ sulfite reductase [NADPH] flavoprotein, alpha-component. This model describes an NADPH-dependent sulfite reductase flavoprotein subunit. Most members of this family are found in Cys biosynthesis gene clusters. The closest homologs below the trusted cutoff are designated as subunits nitrate reductase.
Probab=25.23 E-value=1.4e+02 Score=32.77 Aligned_cols=49 Identities=12% Similarity=0.074 Sum_probs=43.3
Q ss_pred CCeEEEEEcCCcccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHHHHcCC
Q 014264 208 ANIIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKLANF 257 (427)
Q Consensus 208 A~~iGIlvgTl~~q~~~~~i~~l~~li~~~GKK~y~~~vgkln~aKLaNF 257 (427)
++.+.|+.||-+| +...++++|.+.++++|..+.+..|+...+..|.+.
T Consensus 58 ~~~i~IlygSqTG-nae~~A~~l~~~l~~~g~~~~v~~~~d~~~~~l~~~ 106 (597)
T TIGR01931 58 EKRVTILYGSQTG-NARRLAKRLAEKLEAAGFSVRLSSADDYKFKQLKKE 106 (597)
T ss_pred CCeEEEEEECCch-HHHHHHHHHHHHHHhCCCccEEechHHCCHhhcccC
Confidence 6789999999875 567899999999999999999999999998888776
No 170
>TIGR01007 eps_fam capsular exopolysaccharide family. This model describes the capsular exopolysaccharide proteins in bacteria. The exopolysaccharide gene cluster consists of several genes which encode a number of proteins which regulate the exoploysaccharide biosynthesis(EPS). Atleast 13 genes espA to espM in streptococcus species seem to direct the EPS proteins and all of which share high homology. Functional roles were characterized by gene disruption experiments which resulted in exopolysaccharide-deficient phenotypes.
Probab=24.81 E-value=2e+02 Score=26.27 Aligned_cols=51 Identities=10% Similarity=0.064 Sum_probs=38.9
Q ss_pred HHHHHHHHHhcCCeEEEEEcCCcccCcHHHHHHHHHHHHHcCCcEEEEEcCC
Q 014264 197 RRYYLVEKAKDANIIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGK 248 (427)
Q Consensus 197 rRy~~I~ka~~A~~iGIlvgTl~~q~~~~~i~~l~~li~~~GKK~y~~~vgk 248 (427)
-|..+.-...+.++| .+.+.+++.|--.+.-.|-..+.++|+++.++=.+-
T Consensus 6 l~~~l~~~~~~~kvI-~v~s~kgG~GKTt~a~~LA~~la~~G~rVllID~D~ 56 (204)
T TIGR01007 6 IRTNIQFSGAEIKVL-LITSVKPGEGKSTTSANIAVAFAQAGYKTLLIDGDM 56 (204)
T ss_pred HHHHHhhhcCCCcEE-EEecCCCCCCHHHHHHHHHHHHHhCCCeEEEEeCCC
Confidence 344555555667777 568888999999999999999999999987776653
No 171
>cd01981 Pchlide_reductase_B Pchlide_reductase_B: B protein of the NB protein complex of Protochlorophyllide (Pchlide)_reductase. Pchlide reductase catalyzes the reductive formation of chlorophyllide (chlide) from protochlorophyllide (pchlide) during biosynthesis of chlorophylls and bacteriochlorophylls. This group contains both the light-independent Pchlide reductase (DPOR) and light-dependent Pchlide reductase (LPOR). Angiosperms contain only LPOR, cyanobacteria, algae and gymnosperms contain both DPOR and LPOR, primitive anoxygenic photosynthetic bacteria contain only DPOR. NB is structurally similar to the FeMo protein of nitrogenase, forming an N2B2 heterotetramer. N and B are homologous to the FeMo alpha and beta subunits respectively. Also in common with nitrogenase in vitro DPOR activity requires ATP hydrolysis and dithoionite or ferredoxin as electron donor. The NB protein complex may serve as a catalytic site for Pchlide reduction similar to MoFe for nitrogen reduction.
Probab=24.62 E-value=1.5e+02 Score=30.85 Aligned_cols=79 Identities=14% Similarity=0.140 Sum_probs=56.4
Q ss_pred cCCeEEEEEcCCcccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHHHHcCCCCCCEEEEecCCCccccc----ccCCCCc
Q 014264 207 DANIIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKLANFPECDVFINVSCAQTALLD----SKEFLAP 282 (427)
Q Consensus 207 ~A~~iGIlvgTl~~q~~~~~i~~l~~li~~~GKK~y~~~vgkln~aKLaNF~eiD~fVlvaCPr~si~d----~~~f~kP 282 (427)
..+++-||=.+-..-+...=++.|+++|+..|.++-.++.+.-+.+.+.+.++.++=++ -||+.+... .+.|-.|
T Consensus 161 ~~~~VNiiG~~~~~~~~~~d~~ei~~lL~~~Gl~v~~~~~~~~~~~~i~~~~~A~lniv-~~~~~~~~~a~~L~~~~GiP 239 (430)
T cd01981 161 EKPSVNLIGPSSLGFHNRHDCRELKRLLHTLGIEVNVVIPEGASVDDLNELPKAWFNIV-PYREYGLSAALYLEEEFGMP 239 (430)
T ss_pred CCCcEEEEcCCCCCCCCcchHHHHHHHHHHcCCeEEEEEcCCCCHHHHHhhhhCeEEEE-ecHHHHHHHHHHHHHHhCCC
Confidence 34567666444322233556678999999999999998989999999999987666554 388765442 3568888
Q ss_pred ccCH
Q 014264 283 VITP 286 (427)
Q Consensus 283 vlTP 286 (427)
.+..
T Consensus 240 ~~~~ 243 (430)
T cd01981 240 SVKI 243 (430)
T ss_pred eEec
Confidence 7743
No 172
>TIGR02883 spore_cwlD N-acetylmuramoyl-L-alanine amidase CwlD. Members of this protein family are the CwlD family of N-acetylmuramoyl-L-alanine amidase. This family has been called the germination-specific N-acetylmuramoyl-L-alanine amidase. CwlD is required, along with the putative deactylase PdaA, to make muramic delta-lactam, a novel peptidoglycan constituent found only in spores. CwlD mutants show a germination defect.
Probab=24.30 E-value=1.6e+02 Score=27.02 Aligned_cols=47 Identities=21% Similarity=0.319 Sum_probs=32.8
Q ss_pred cHHHHHHHHHHHHHcCCcEEEEEcCCCCH-------------------HHHcCCCCCCEEEEecCC
Q 014264 223 YLHMIHQMKELITKAGKKAYTLVMGKPNP-------------------AKLANFPECDVFINVSCA 269 (427)
Q Consensus 223 ~~~~i~~l~~li~~~GKK~y~~~vgkln~-------------------aKLaNF~eiD~fVlvaCP 269 (427)
.+.+..+|+++|++.|.++++.--+..+. .++||=...|+||-+=|-
T Consensus 28 ~l~ia~~l~~~L~~~G~~V~ltr~~d~~~~~~~~~~~~~~~~~~L~~R~~~An~~~adlfiSiH~N 93 (189)
T TIGR02883 28 TLEIALKLKDYLQEQGALVVMTREDDSDLASEGTKGYSRRKIEDLRKRVKLINESEADLFISIHLN 93 (189)
T ss_pred HHHHHHHHHHHHHhCCCEEEEEecCCcCccccccccccccccCCHHHHHHHHHhcCCCEEEEEecC
Confidence 45677788888888888877766654431 345665568999988885
No 173
>TIGR01205 D_ala_D_alaTIGR D-alanine--D-alanine ligase. but a number of antibiotic resistance proteins score above the trusted cutoff of this model.
Probab=24.27 E-value=2.4e+02 Score=27.60 Aligned_cols=77 Identities=16% Similarity=0.171 Sum_probs=51.6
Q ss_pred eEEEEEcCCcccC--cHHHHHHHHHHHHHcCCcEEEEEcCCCC-------HHHHcCC----CCCCEEEEecC---CCccc
Q 014264 210 IIGVLVGTLGVAG--YLHMIHQMKELITKAGKKAYTLVMGKPN-------PAKLANF----PECDVFINVSC---AQTAL 273 (427)
Q Consensus 210 ~iGIlvgTl~~q~--~~~~i~~l~~li~~~GKK~y~~~vgkln-------~aKLaNF----~eiD~fVlvaC---Pr~si 273 (427)
+||||.|-.+-.. .+.....+.+-|++.|.+++.+.+.+.+ .+.+.++ .++|+.+.+.= .+.+.
T Consensus 1 ~~~~~~gg~s~e~~~s~~s~~~i~~al~~~g~~v~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~D~v~~~~~g~~~~~~~ 80 (315)
T TIGR01205 1 RVAVLFGGKSAEHEISLVSAAAVLKALRDLGYDVYPVDIDKMGSWTYKDLPQLILELGALLEGIDVVFPVLHGRYGEDGT 80 (315)
T ss_pred CEEEEeCCCCCCeeeeHHHHHHHHHHHhhcCCEEEEEeecCCccccccchHHHHhhccccCCCCCEEEEecCCCCCCCcH
Confidence 4899999998755 4788889999999999999999988743 2233321 36898887541 12221
Q ss_pred c--cccCCCCcccCH
Q 014264 274 L--DSKEFLAPVITP 286 (427)
Q Consensus 274 ~--d~~~f~kPvlTP 286 (427)
. ....+-.|++.+
T Consensus 81 ~~~~le~~gip~~g~ 95 (315)
T TIGR01205 81 IQGLLELMGIPYTGS 95 (315)
T ss_pred HHHHHHHcCCCccCC
Confidence 1 123456677765
No 174
>PRK14336 (dimethylallyl)adenosine tRNA methylthiotransferase; Provisional
Probab=24.21 E-value=1.7e+02 Score=30.65 Aligned_cols=10 Identities=20% Similarity=0.322 Sum_probs=6.3
Q ss_pred EEecCCCccc
Q 014264 264 INVSCAQTAL 273 (427)
Q Consensus 264 VlvaCPr~si 273 (427)
|.-|||..+-
T Consensus 130 i~rGC~~~Cs 139 (418)
T PRK14336 130 IMQGCDNFCT 139 (418)
T ss_pred eccCCCCCCc
Confidence 4457887653
No 175
>TIGR00147 lipid kinase, YegS/Rv2252/BmrU family. The E. coli member of this family, YegS has been purified and shown to have phosphatidylglycerol kinase activity. The member from M. tuberculosis, Rv2252, has diacylglycerol kinase activity. BmrU from B. subtilis is in an operon with multidrug efflux transporter Bmr, but is uncharacterized.
Probab=23.93 E-value=2.5e+02 Score=27.39 Aligned_cols=35 Identities=6% Similarity=0.016 Sum_probs=15.4
Q ss_pred eEEEEEcCCcccCc-HHHHHHHHHHHHHcCCcEEEE
Q 014264 210 IIGVLVGTLGVAGY-LHMIHQMKELITKAGKKAYTL 244 (427)
Q Consensus 210 ~iGIlvgTl~~q~~-~~~i~~l~~li~~~GKK~y~~ 244 (427)
+++||++..++.+. ....+++++.++++|.++.++
T Consensus 3 ~~~ii~Np~sg~~~~~~~~~~i~~~l~~~~~~~~~~ 38 (293)
T TIGR00147 3 EAPAILNPTAGKSNDNKPLREVIMLLREEGMEIHVR 38 (293)
T ss_pred eEEEEECCCccchhhHHHHHHHHHHHHHCCCEEEEE
Confidence 44455554444322 234444444445555444333
No 176
>PRK09240 thiH thiamine biosynthesis protein ThiH; Reviewed
Probab=23.75 E-value=1.9e+02 Score=29.74 Aligned_cols=57 Identities=23% Similarity=0.288 Sum_probs=43.5
Q ss_pred HHHHHHHHHHHhcCCe----EEEEEcCCcccC--cHHHHHHHHHHHHHcCCcEEEEEcCCCCHH
Q 014264 195 LKRRYYLVEKAKDANI----IGVLVGTLGVAG--YLHMIHQMKELITKAGKKAYTLVMGKPNPA 252 (427)
Q Consensus 195 L~rRy~~I~ka~~A~~----iGIlvgTl~~q~--~~~~i~~l~~li~~~GKK~y~~~vgkln~a 252 (427)
...|...++.|++|.. .|+|+|. +... ...++.+|+.|=...++..+.+.+..++|.
T Consensus 201 ~~~rl~~i~~a~~aG~~~v~~g~i~Gl-ge~~~d~~~~a~~l~~L~~~~~~~~~sv~~~~l~P~ 263 (371)
T PRK09240 201 FEYRLETPERAGRAGIRKIGLGALLGL-SDWRTDALMTALHLRYLQRKYWQAEYSISFPRLRPC 263 (371)
T ss_pred HHHHHHHHHHHHHcCCCeeceEEEecC-CccHHHHHHHHHHHHHHHHhCCCCceeeecCccccC
Confidence 5688999999999863 7899984 4322 556677777777777887788888888776
No 177
>TIGR01501 MthylAspMutase methylaspartate mutase, S subunit. This model represents the S (sigma) subunit of methylaspartate mutase (glutamate mutase), a cobalamin-dependent enzyme that catalyzes the first step in a pathway of glutamate fermentation.
Probab=23.74 E-value=1.5e+02 Score=26.04 Aligned_cols=45 Identities=20% Similarity=0.159 Sum_probs=30.6
Q ss_pred HHHHHhc--CCeEEEEEcCCcccCcHHHHHHHHHHHHHcCCcEEEEEcCC
Q 014264 201 LVEKAKD--ANIIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGK 248 (427)
Q Consensus 201 ~I~ka~~--A~~iGIlvgTl~~q~~~~~i~~l~~li~~~GKK~y~~~vgk 248 (427)
.++.|++ |..+| +++|.+ ..+..+.++.++|+++|-+...+++|-
T Consensus 44 ~v~aa~~~~adiVg--lS~l~~-~~~~~~~~~~~~l~~~gl~~~~vivGG 90 (134)
T TIGR01501 44 FIKAAIETKADAIL--VSSLYG-HGEIDCKGLRQKCDEAGLEGILLYVGG 90 (134)
T ss_pred HHHHHHHcCCCEEE--Eecccc-cCHHHHHHHHHHHHHCCCCCCEEEecC
Confidence 3445555 55555 477775 456667788889999987655677776
No 178
>cd01450 vWFA_subfamily_ECM Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A
Probab=23.51 E-value=2.7e+02 Score=23.50 Aligned_cols=68 Identities=10% Similarity=0.110 Sum_probs=44.0
Q ss_pred HHHHHHHHHHHHHHh----cCCeEEEEEcCCcccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHHHHcCCCCC
Q 014264 192 LKILKRRYYLVEKAK----DANIIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKLANFPEC 260 (427)
Q Consensus 192 ~r~L~rRy~~I~ka~----~A~~iGIlvgTl~~q~~~~~i~~l~~li~~~GKK~y~~~vgkln~aKLaNF~ei 260 (427)
...|..-+..+.+.. +++.+-||++.-. .+...-...+.+.++++|-+.|+|.+|..+.+.|..|...
T Consensus 83 ~~al~~a~~~~~~~~~~~~~~~~~iiliTDG~-~~~~~~~~~~~~~~~~~~v~v~~i~~g~~~~~~l~~la~~ 154 (161)
T cd01450 83 GKALQYALEQLFSESNARENVPKVIIVLTDGR-SDDGGDPKEAAAKLKDEGIKVFVVGVGPADEEELREIASC 154 (161)
T ss_pred HHHHHHHHHHhcccccccCCCCeEEEEECCCC-CCCCcchHHHHHHHHHCCCEEEEEeccccCHHHHHHHhCC
Confidence 344444444555553 6777777776532 2221234555566778899999999999888888887654
No 179
>PF02302 PTS_IIB: PTS system, Lactose/Cellobiose specific IIB subunit; InterPro: IPR003501 The bacterial phosphoenolpyruvate: sugar phosphotransferase system (PTS) is a multi-protein system involved in the regulation of a variety of metabolic and transcriptional processes. The lactose/cellobiose-specific family are one of four structurally and functionally distinct group IIB PTS system cytoplasmic enzymes. The fold of IIB cellobiose shows similar structure to mammalian tyrosine phosphatases. This signature is often found downstream of IPR003352 from INTERPRO.; GO: 0008982 protein-N(PI)-phosphohistidine-sugar phosphotransferase activity, 0009401 phosphoenolpyruvate-dependent sugar phosphotransferase system; PDB: 1TVM_A 2WY2_D 1IIB_A 2WWV_D 1H9C_A 1E2B_A 2L2Q_A 2KYR_A 3CZC_A 3NBM_A ....
Probab=23.43 E-value=2.6e+02 Score=21.78 Aligned_cols=57 Identities=16% Similarity=0.238 Sum_probs=36.8
Q ss_pred EEEcCCcccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHHHHcCCCCCCEEEEecCCCccc
Q 014264 213 VLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKLANFPECDVFINVSCAQTAL 273 (427)
Q Consensus 213 IlvgTl~~q~~~~~i~~l~~li~~~GKK~y~~~vgkln~aKLaNF~eiD~fVlvaCPr~si 273 (427)
++++.-|.....-+.++|++.+++.|.................+ ++|+++.. |+...
T Consensus 3 lvvC~~Gi~TS~~~~~~i~~~~~~~gi~~~~~~~~~~~~~~~~~--~~D~il~~--~~i~~ 59 (90)
T PF02302_consen 3 LVVCGSGIGTSLMVANKIKKALKELGIEVEVSAGSILEVEEIAD--DADLILLT--PQIAY 59 (90)
T ss_dssp EEEESSSSHHHHHHHHHHHHHHHHTTECEEEEEEETTTHHHHHT--T-SEEEEE--ESSGG
T ss_pred EEECCChHHHHHHHHHHHHHHHHhccCceEEEEecccccccccC--CCcEEEEc--Cccch
Confidence 45555555555556699999999999887777777444444333 46887654 45543
No 180
>PF01583 APS_kinase: Adenylylsulphate kinase; InterPro: IPR002891 Protein phosphorylation, which plays a key role in most cellular activities, is a reversible process mediated by protein kinases and phosphoprotein phosphatases. Protein kinases catalyse the transfer of the gamma phosphate from nucleotide triphosphates (often ATP) to one or more amino acid residues in a protein substrate side chain, resulting in a conformational change affecting protein function. Phosphoprotein phosphatases catalyse the reverse process. Protein kinases fall into three broad classes, characterised with respect to substrate specificity []: Serine/threonine-protein kinases Tyrosine-protein kinases Dual specific protein kinases (e.g. MEK - phosphorylates both Thr and Tyr on target proteins) Protein kinase function has been evolutionarily conserved from Escherichia coli to human []. Protein kinases play a role in a multitude of cellular processes, including division, proliferation, apoptosis, and differentiation []. Phosphorylation usually results in a functional change of the target protein by changing enzyme activity, cellular location, or association with other proteins. The catalytic subunits of protein kinases are highly conserved, and several structures have been solved [], leading to large screens to develop kinase-specific inhibitors for the treatments of a number of diseases []. This domain contains an ATP binding P-loop motif [].; GO: 0005524 ATP binding, 0016301 kinase activity, 0016772 transferase activity, transferring phosphorus-containing groups, 0000103 sulfate assimilation; PDB: 1M7H_B 1M7G_B 3CR7_B 1D6J_A 2OFW_G 1X6V_B 1XNJ_A 1XJQ_B 2PEY_A 2PEZ_B ....
Probab=23.36 E-value=1.8e+02 Score=26.22 Aligned_cols=37 Identities=16% Similarity=0.191 Sum_probs=31.5
Q ss_pred EEEEEcCCcccCcHHHHHHHHHHHHHcCCcEEEEEcC
Q 014264 211 IGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMG 247 (427)
Q Consensus 211 iGIlvgTl~~q~~~~~i~~l~~li~~~GKK~y~~~vg 247 (427)
+-|.+.-|++.|=-.+...|.+.|++.|+++|++=.+
T Consensus 3 ~vIwltGlsGsGKtTlA~~L~~~L~~~g~~~~~LDgD 39 (156)
T PF01583_consen 3 FVIWLTGLSGSGKTTLARALERRLFARGIKVYLLDGD 39 (156)
T ss_dssp EEEEEESSTTSSHHHHHHHHHHHHHHTTS-EEEEEHH
T ss_pred EEEEEECCCCCCHHHHHHHHHHHHHHcCCcEEEecCc
Confidence 3477788899999999999999999999999998654
No 181
>TIGR01162 purE phosphoribosylaminoimidazole carboxylase, PurE protein. Phosphoribosylaminoimidazole carboxylase is a fusion protein in plants and fungi, but consists of two non-interacting proteins in bacteria, PurK and PurE. This model represents PurK, an N5-CAIR mutase.
Probab=23.33 E-value=1.6e+02 Score=26.72 Aligned_cols=71 Identities=17% Similarity=0.259 Sum_probs=50.7
Q ss_pred EEEEEcCCcccCcHHHHHHHHHHHHHcCCcEEEEEcC-CCCHHHHcCCC------CCCEEEEecCCCcccc--cccCCCC
Q 014264 211 IGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMG-KPNPAKLANFP------ECDVFINVSCAQTALL--DSKEFLA 281 (427)
Q Consensus 211 iGIlvgTl~~q~~~~~i~~l~~li~~~GKK~y~~~vg-kln~aKLaNF~------eiD~fVlvaCPr~si~--d~~~f~k 281 (427)
+|||.|+.+ -+++.+...+.|++-|..+-+-+.+ .=+|++|..|. ++++||-+|=-...|- -...-.+
T Consensus 1 V~IimGS~S---D~~~~~~a~~~L~~~gi~~dv~V~SaHRtp~~~~~~~~~a~~~g~~viIa~AG~aa~Lpgvva~~t~~ 77 (156)
T TIGR01162 1 VGIIMGSDS---DLPTMKKAADILEEFGIPYELRVVSAHRTPELMLEYAKEAEERGIKVIIAGAGGAAHLPGMVAALTPL 77 (156)
T ss_pred CEEEECcHh---hHHHHHHHHHHHHHcCCCeEEEEECcccCHHHHHHHHHHHHHCCCeEEEEeCCccchhHHHHHhccCC
Confidence 578888744 7788889999999999886555555 56788888773 5788887776665553 2344567
Q ss_pred ccc
Q 014264 282 PVI 284 (427)
Q Consensus 282 Pvl 284 (427)
|||
T Consensus 78 PVI 80 (156)
T TIGR01162 78 PVI 80 (156)
T ss_pred CEE
Confidence 766
No 182
>cd01025 TOPRIM_recR TOPRIM_recR: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the type found in Escherichia coli RecR. RecR participates in the RecFOR pathway of homologous recombinational repair in prokaryotes. This pathway provides a single-stranded DNA molecule coated with RecA to allow invasion of a homologous molecule. The RecFOR system directs the loading of RecA onto gapped DNA coated with SSB protein. The TOPRIM domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD). In RecR sequences this glutamate in the first turn of the TOPRIM domain is semiconserved, the DXD motif is not conserved.
Probab=23.19 E-value=2.7e+02 Score=23.73 Aligned_cols=54 Identities=20% Similarity=0.233 Sum_probs=40.8
Q ss_pred HHHHHhcCCeEEEEEcCCcccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHHHH
Q 014264 201 LVEKAKDANIIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKL 254 (427)
Q Consensus 201 ~I~ka~~A~~iGIlvgTl~~q~~~~~i~~l~~li~~~GKK~y~~~vgkln~aKL 254 (427)
+++++++.++==||+.|-.-----.+...|+++|+..+.|+..+..|=+-=.-|
T Consensus 48 L~~ri~~~~i~EVIlA~~pt~EGe~Ta~yi~~~l~~~~~kvsRlA~GiP~G~~l 101 (112)
T cd01025 48 LLERIAKGQVKEVILATNPTVEGEATALYIAKLLKDFGVKVTRLAQGIPVGGEL 101 (112)
T ss_pred HHHHHhcCCCcEEEEecCCCchHHHHHHHHHHHHhHcCCCeEEEEEcCCCCcce
Confidence 445666766666778777666666778899999999999999999887654433
No 183
>TIGR02363 dhaK1 dihydroxyacetone kinase, DhaK subunit. Two types of dihydroxyacetone kinase (glycerone kinase) are described. In yeast and a few bacteria, e.g. Citrobacter freundii, the enzyme is a single chain that uses ATP as phosphoryl donor and is designated EC 2.7.1.29. By contract, E. coli and many other bacterial species have a multisubunit form (EC 2.7.1.-) with a phosphoprotein donor related to PTS transport proteins. This family represents the DhaK subunit of the latter type of dihydroxyacetone kinase, but it specifically excludes the DhaK paralog DhaK2 (TIGR02362) found in the same operon as DhaK and DhaK in the Firmicutes.
Probab=23.11 E-value=2.3e+02 Score=28.88 Aligned_cols=45 Identities=16% Similarity=0.347 Sum_probs=38.4
Q ss_pred HhcCCeEEEEEcCCcccCcHHH---HHHHHHHHHHcCCcEEEEEcCCC
Q 014264 205 AKDANIIGVLVGTLGVAGYLHM---IHQMKELITKAGKKAYTLVMGKP 249 (427)
Q Consensus 205 a~~A~~iGIlvgTl~~q~~~~~---i~~l~~li~~~GKK~y~~~vgkl 249 (427)
.++-..+.++|+.||+..++++ .+.+.++|+++|.+.+...+|..
T Consensus 249 ~~~gd~v~vlvN~LG~ts~lEl~i~~~~v~~~L~~~gi~v~r~~vG~~ 296 (329)
T TIGR02363 249 LQSGDRVIVLVNGMGATPLMELYIFYNDVQRLLEQRGVNVARTLVGNY 296 (329)
T ss_pred CCCCCeEEEEEeCCCCCCHHHHHHHHHHHHHHHHHCCCEEEEEEeecc
Confidence 3455689999999999999975 67888889999999999999975
No 184
>PRK04020 rps2P 30S ribosomal protein S2; Provisional
Probab=23.03 E-value=1.6e+02 Score=27.81 Aligned_cols=50 Identities=18% Similarity=0.274 Sum_probs=29.2
Q ss_pred EEecCCCCCCCCCCCeEEEccccC-----CChHHHHHHHhhhh----cCCCCcEEEEecccc
Q 014264 25 IHYGHTCLSPTSTLPAFFVFGKAS-----INTSNCIENLSKHA----LTNGKPILVLYGLEY 77 (427)
Q Consensus 25 VHyGhaCls~~~~lpv~YVf~~~~-----ld~~~~~~~l~~~~----~~~~~~v~l~~dvqy 77 (427)
+||||.=..|-- --|+|+..+ ||+++..+.++..+ ....++|+++.+-++
T Consensus 20 ~H~Gh~~~np~M---k~yIyg~r~~gi~IIdL~kT~~~L~~A~~~i~~~~~~~ILfVgTk~~ 78 (204)
T PRK04020 20 VHIGTQQKTKDM---ERFIYRVRPDGLYVLDVRKTDERIRIAAKFLSRYEPEKILVVSSRQY 78 (204)
T ss_pred eEcCCCcCCCCC---cccEeeecCCCCEEEcHHHHHHHHHHHHHHHHHhcCCeEEEEeCCHH
Confidence 699997444421 127777542 48877666665432 113457877777543
No 185
>PRK10310 PTS system galactitol-specific transporter subunit IIB; Provisional
Probab=22.93 E-value=2.1e+02 Score=23.24 Aligned_cols=52 Identities=12% Similarity=0.130 Sum_probs=34.5
Q ss_pred EEEcCCcccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHHHHcCC-CCCCEEEEec
Q 014264 213 VLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKLANF-PECDVFINVS 267 (427)
Q Consensus 213 IlvgTl~~q~~~~~i~~l~~li~~~GKK~y~~~vgkln~aKLaNF-~eiD~fVlva 267 (427)
++++.-|..-..-+..++++.++++|..+-+.. ..++ .+.+. .++|++|.+.
T Consensus 6 LvvCgsG~~TS~m~~~ki~~~l~~~gi~~~v~~-~~~~--e~~~~~~~~D~iv~t~ 58 (94)
T PRK10310 6 IVACGGAVATSTMAAEEIKELCQSHNIPVELIQ-CRVN--EIETYMDGVHLICTTA 58 (94)
T ss_pred EEECCCchhHHHHHHHHHHHHHHHCCCeEEEEE-ecHH--HHhhhcCCCCEEEECC
Confidence 466666666666778999999999999754444 3333 33331 3579887665
No 186
>PRK12493 magnesium chelatase subunit H; Provisional
Probab=22.82 E-value=1.8e+02 Score=35.21 Aligned_cols=61 Identities=15% Similarity=0.212 Sum_probs=45.6
Q ss_pred CCeEEEEEcCCc-ccCcHHHHHHHHHHHHHcCCcEEEEEcCCCC-----HHHHcCC-----CCCCEEEEecC
Q 014264 208 ANIIGVLVGTLG-VAGYLHMIHQMKELITKAGKKAYTLVMGKPN-----PAKLANF-----PECDVFINVSC 268 (427)
Q Consensus 208 A~~iGIlvgTl~-~q~~~~~i~~l~~li~~~GKK~y~~~vgkln-----~aKLaNF-----~eiD~fVlvaC 268 (427)
+.+||||+-..- ..+....++.|.+.|+++|-.++.++++-+. ..-+.+. +.||+.|.+..
T Consensus 253 ~p~Vgil~~r~~~~~~d~~~~dalI~~LE~~G~~vipvf~~gl~~~~~v~~~~~~~~~~~~~~vDaiI~~t~ 324 (1310)
T PRK12493 253 APTVGLLLQRTHLLTGNDAHYVALIQELEARGARVIPAYAGGLDFRKPVEAFFYDPGNPDTPLVDLVVSLTG 324 (1310)
T ss_pred CCEEEEEEchhhhhcCCcHHHHHHHHHHHHCCCeEEEEEecCcccchHHHHHHHhhcccCCCCccEEEEcCc
Confidence 789999996544 3568889999999999999999999887554 2333331 35898886644
No 187
>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=22.33 E-value=3.9e+02 Score=24.97 Aligned_cols=50 Identities=16% Similarity=0.206 Sum_probs=30.9
Q ss_pred HHHHhcCCeEEEEEcCCcccCcHHHHHHHHHHHHHc-CCcEEEEEcCCCCH
Q 014264 202 VEKAKDANIIGVLVGTLGVAGYLHMIHQMKELITKA-GKKAYTLVMGKPNP 251 (427)
Q Consensus 202 I~ka~~A~~iGIlvgTl~~q~~~~~i~~l~~li~~~-GKK~y~~~vgkln~ 251 (427)
+++....+.++++.|.........-.+-+++.++++ |.+......+..++
T Consensus 116 ~~~~~g~~~i~~l~~~~~~~~~~~r~~g~~~~~~~~~~~~~~~~~~~~~~~ 166 (275)
T cd06320 116 IDKLAEGGKVAIIEGKAGAFAAEQRTEGFTEAIKKASGIEVVASQPADWDR 166 (275)
T ss_pred HHHhCCCceEEEEeCCCCCccHHHHHHHHHHHHhhCCCcEEEEecCCCccH
Confidence 334335578999887655444455566778888888 77654444444443
No 188
>PF02233 PNTB: NAD(P) transhydrogenase beta subunit; InterPro: IPR012136 NAD(P) transhydrogenase catalyses the transfer of reducing equivalents between NAD(H) and NADP(H), coupled to the translocation of protons across a membrane []. It is an integral membrane protein found in most organisms except for yeasts, plants and some bacterial species. In bacterial species it is located in the cytoplasmic membrane, while in mitochondria it is located in the inner membrane. Under most physiological conditions this enzyme synthesises NADPH, driven by consumption of the proton electrochemical gradient. The resulting NADPH is subsequently used for biosynthetic reactions or the reduction of glutathione. The global structure of this enzyme is similar in all organisms, consisting of three distinct domains, though the polypeptide composition can vary. Domain I binds NAD(+)/NADH, domain II is a hydrophobic membrane-spanning domain, and domain III binds NADP(+)/NADPH. Domain I is composed of two subdomains, both of which form a Rossman fold, while domain III consists of a single Rossman fold where the NADP(+) is flipped relative to the normal orientation of bound nucleotides within the Rossman fold [, , ]. Several residues within these domains are thought to make functionally important interdomain contacts for hydride transfer between these domains []. Proton translocation occurs through domain II and is thought to induce conformational changes which are transmitted across domain III to the site of hydride transfer between domains I and III. This entry represents the beta subunit found in bacterial two-subunit NADP(H) transhydrogenases. This subunit forms domain III and part of the transmembrane domain II. ; GO: 0008750 NAD(P)+ transhydrogenase (AB-specific) activity, 0050661 NADP binding, 0055114 oxidation-reduction process, 0016021 integral to membrane; PDB: 1PT9_A 1DJL_A 1U31_B 2BRU_C 1PTJ_C 1HZZ_C 2FRD_C 2FSV_C 1XLT_C 1U2G_C ....
Probab=22.26 E-value=92 Score=33.22 Aligned_cols=66 Identities=23% Similarity=0.424 Sum_probs=48.3
Q ss_pred HHHHHhcCCeEEEEEcC-CcccCcHHHHHHHHHHHHHcCCcEE---------------------------EEEcCCCCHH
Q 014264 201 LVEKAKDANIIGVLVGT-LGVAGYLHMIHQMKELITKAGKKAY---------------------------TLVMGKPNPA 252 (427)
Q Consensus 201 ~I~ka~~A~~iGIlvgT-l~~q~~~~~i~~l~~li~~~GKK~y---------------------------~~~vgkln~a 252 (427)
..+...+|+++-|+=|- +-++.-...++.|-++|+++|+++- ++-|.++|++
T Consensus 300 ~a~~l~~A~~VvIVPGYGmAvAqAQ~~v~el~~~L~~~G~~V~faIHPVAGRMPGHMNVLLAEa~VpYd~~~emdeiN~~ 379 (463)
T PF02233_consen 300 VAEMLANAKKVVIVPGYGMAVAQAQHAVAELADLLEERGVEVKFAIHPVAGRMPGHMNVLLAEANVPYDIVKEMDEINPD 379 (463)
T ss_dssp HHHHHHH-SEEEEEESHHHHHCTTHHHHHHHHHHHHHTT-EEEEEE-TTSSSSTTHHHHHHHHCT--GGGEEEHHHHGGG
T ss_pred HHHHHHhcCceEEecCchHHHHHHHHHHHHHHHHHHhCCCEEEEEeccccCCCCCcceEEEEecCCCHHHHhhhhhcccc
Confidence 45566789999887763 3356777889999999999999875 5667777765
Q ss_pred HHcCCCCCCEEEEecCCC
Q 014264 253 KLANFPECDVFINVSCAQ 270 (427)
Q Consensus 253 KLaNF~eiD~fVlvaCPr 270 (427)
|++.|+-++++-..
T Consensus 380 ----f~~~Dv~lViGAND 393 (463)
T PF02233_consen 380 ----FPDTDVVLVIGAND 393 (463)
T ss_dssp ----GGG-SEEEEES-SG
T ss_pred ----hhcCCEEEEecccc
Confidence 99999999998653
No 189
>cd01982 Chlide_reductase_Z Chlide_reductase_Z : Z subunit of chlorophyllide (chlide) reductase (BchZ). Chlide reductase participates in photosynthetic pigment synthesis playing a role in the conversion of chlorophylls(Chl) into bacteriochlorophylls (BChl). Chlide reductase catalyzes the reduction of the B-ring of the tetrapyrolle. Chlide reductase is a three subunit enzyme (subunits are designated BchX, BchY and BchZ). The similarity between these three subunits and the subunits for nitrogenase suggests that BchX serves as an electron donor for the BchY-BchY catalytic subunits.
Probab=22.20 E-value=1.2e+02 Score=31.91 Aligned_cols=77 Identities=10% Similarity=0.135 Sum_probs=57.1
Q ss_pred cCCeEEEEEcCCcccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHHHHcCCCCCCEEEEecCCCcccccccCCCCccc
Q 014264 207 DANIIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKLANFPECDVFINVSCAQTALLDSKEFLAPVI 284 (427)
Q Consensus 207 ~A~~iGIlvgTl~~q~~~~~i~~l~~li~~~GKK~y~~~vgkln~aKLaNF~eiD~fVlvaCPr~si~d~~~f~kPvl 284 (427)
+...|-||=.+.+--+.+.=++.||++|+.-|-++..+.-+.-+.+.|...++.++=+++ |++.+-.-.+.|-.|.+
T Consensus 154 ~~~~VNIIG~~~g~~~~~gDl~ElkrLLe~~Gl~vn~v~~~gt~l~eI~~l~~A~lniv~-~~~~g~~L~e~~giPy~ 230 (412)
T cd01982 154 RKGTVNIIGPSYGCFNSPSDLAEVKRLVTGIGAEVNHVYPFESHLAEIPKLKNAAVNVVM-YREFGRGLAEDLGRPYL 230 (412)
T ss_pred CCCeEEEECCCcCcCCCHHHHHHHHHHHHHcCCcEEEECCCCCCHHHHHhhccCCEEEEe-CHHHHHHHHHHHCcCeE
Confidence 346687775555555567788999999999999999898899999999999988877776 66544332334555543
No 190
>COG0622 Predicted phosphoesterase [General function prediction only]
Probab=22.11 E-value=80 Score=28.98 Aligned_cols=74 Identities=20% Similarity=0.153 Sum_probs=41.7
Q ss_pred CCCCcccccccChhh--hcccCCcEEEEecCCCCCCC----C---CCCeEEEccccCCChHH--HHHHHhhhhcCCCCcE
Q 014264 1 MADTTYGSCCVDEVG--ASHVDADCVIHYGHTCLSPT----S---TLPAFFVFGKASINTSN--CIENLSKHALTNGKPI 69 (427)
Q Consensus 1 LaDtsYGsCCVDeva--A~hv~aD~iVHyGhaCls~~----~---~lpv~YVf~~~~ld~~~--~~~~l~~~~~~~~~~v 69 (427)
|+||=.-.|++.... ...-++|+|||-|+.=.+.+ . .-++++|+|+-..+... +=+... +.-.+.++
T Consensus 7 iSDtH~~~~~~~~~~~~~~~~~~d~vih~GD~~~~~~~~~l~~~~~~~i~~V~GN~D~~~~~~~~p~~~~--~~~~g~ki 84 (172)
T COG0622 7 ISDTHGPLRAIEKALKIFNLEKVDAVIHAGDSTSPFTLDALEGGLAAKLIAVRGNCDGEVDQEELPEELV--LEVGGVKI 84 (172)
T ss_pred EeccCCChhhhhHHHHHhhhcCCCEEEECCCcCCccchHHhhcccccceEEEEccCCCccccccCChhHe--EEECCEEE
Confidence 456666666543222 33568999999999855432 1 24678999976554321 111111 11234578
Q ss_pred EEEeccc
Q 014264 70 LVLYGLE 76 (427)
Q Consensus 70 ~l~~dvq 76 (427)
.++-.=+
T Consensus 85 ~l~HGh~ 91 (172)
T COG0622 85 FLTHGHL 91 (172)
T ss_pred EEECCCc
Confidence 8876633
No 191
>KOG4175 consensus Tryptophan synthase alpha chain [Amino acid transport and metabolism]
Probab=22.04 E-value=1.9e+02 Score=27.65 Aligned_cols=63 Identities=22% Similarity=0.277 Sum_probs=48.0
Q ss_pred HHHHHHhcCCeEEEEEcCCcccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHHHHcCCCC-CCEEEEe
Q 014264 200 YLVEKAKDANIIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKLANFPE-CDVFINV 266 (427)
Q Consensus 200 ~~I~ka~~A~~iGIlvgTl~~q~~~~~i~~l~~li~~~GKK~y~~~vgkln~aKLaNF~e-iD~fVlv 266 (427)
..|++|++|..=|.||--|. ++-...+|+.++++|.....++.---+-+++.-+.+ .|-||.+
T Consensus 114 ~~iq~ak~aGanGfiivDlP----pEEa~~~Rne~~k~gislvpLvaPsTtdeRmell~~~adsFiYv 177 (268)
T KOG4175|consen 114 NYIQVAKNAGANGFIIVDLP----PEEAETLRNEARKHGISLVPLVAPSTTDERMELLVEAADSFIYV 177 (268)
T ss_pred HHHHHHHhcCCCceEeccCC----hHHHHHHHHHHHhcCceEEEeeCCCChHHHHHHHHHhhcceEEE
Confidence 46999999999999998776 677788999999999987777766666666654443 3666554
No 192
>PF10657 RC-P840_PscD: Photosystem P840 reaction centre protein PscD; InterPro: IPR019608 Oxygenic photosynthesis uses two multi-subunit photosystems (I and II) located in the cell membranes of cyanobacteria and in the thylakoid membranes of chloroplasts in plants and algae. Photosystem II (PSII) has a P680 reaction centre containing chlorophyll 'a' that uses light energy to carry out the oxidation (splitting) of water molecules, and to produce ATP via a proton pump. Photosystem I (PSI) has a P700 reaction centre containing chlorophyll that takes the electron and associated hydrogen donated from PSII to reduce NADP+ to NADPH. Both ATP and NADPH are subsequently used in the light-independent reactions to convert carbon dioxide to glucose using the hydrogen atom extracted from water by PSII, releasing oxygen as a by-product. The photosynthetic reaction centres (RCs) of aerotolerant organisms contain a heterodimeric core, built up of two strongly homologous polypeptides each of which contributes five transmembrane peptide helices to hold a pseudo-symmetric double set of redox components. Two molecules of PscD are housed within a subunit. PscD may be involved in stabilising the PscB component since it is found to co-precipitate with FMO (Fenna-Mathews-Olson BChl a-protein) and PscB. It may also be involved in the interaction with ferredoxin [].
Probab=21.95 E-value=93 Score=27.05 Aligned_cols=36 Identities=17% Similarity=0.343 Sum_probs=25.6
Q ss_pred CCCCEEEEecCCCcccccccCCCCcccCHHHHHHhhCCCCccccceeeccccc
Q 014264 258 PECDVFINVSCAQTALLDSKEFLAPVITPFEAMLAFGRGTQWTGAYVMEFRDL 310 (427)
Q Consensus 258 ~eiD~fVlvaCPr~si~d~~~f~kPvlTP~El~~aL~~~~~w~g~y~~Df~~~ 310 (427)
.||++||++.-|-++|+-.+. .|.. ..+|++||+.=
T Consensus 73 geIel~VLttqpDIai~l~~k-------------Vldn----EnRYViDFD~R 108 (144)
T PF10657_consen 73 GEIELFVLTTQPDIAINLQQK-------------VLDN----ENRYVIDFDKR 108 (144)
T ss_pred CceEEEEEccCCCeeechhhh-------------hhcc----cceEEEeccCC
Confidence 489999999999999873221 1222 25899999753
No 193
>PRK06455 riboflavin synthase; Provisional
Probab=21.78 E-value=2.7e+02 Score=25.28 Aligned_cols=58 Identities=19% Similarity=0.236 Sum_probs=39.8
Q ss_pred CeEEEEEcCCcccCcHHHHHHHHHHHHHcC--CcEEEEEc-C--CCC--HHHHcCCCCCCEEEEecCC
Q 014264 209 NIIGVLVGTLGVAGYLHMIHQMKELITKAG--KKAYTLVM-G--KPN--PAKLANFPECDVFINVSCA 269 (427)
Q Consensus 209 ~~iGIlvgTl~~q~~~~~i~~l~~li~~~G--KK~y~~~v-g--kln--~aKLaNF~eiD~fVlvaCP 269 (427)
.+|||+++|.... .+.+-..+.|+++| -+..++.| | +|- ..||+.=..+|++|-++|+
T Consensus 2 ~kigIV~s~fn~~---~L~~gAi~~L~~~g~~~~I~v~~VPGa~ELP~aakkL~~~~~yDaVIaLG~V 66 (155)
T PRK06455 2 MKIGIADTTFARV---DMGSAAIDELRKLDPSAKIIRYTVPGIKDLPVAAKKLIEEEGCDIVMALGMP 66 (155)
T ss_pred cEEEEEEEecchH---HHHHHHHHHHHhcCCCCceEEEECCCHHHHHHHHHHHHhcCCCCEEEEecce
Confidence 4799999997653 67788888888855 44444433 3 221 2366654579999999998
No 194
>PRK08745 ribulose-phosphate 3-epimerase; Provisional
Probab=21.54 E-value=1.2e+02 Score=29.08 Aligned_cols=81 Identities=10% Similarity=0.158 Sum_probs=51.1
Q ss_pred CCceEEEecCCCCceecccCcHHHHHHHHHHHHHHHhcCCeEEEEEcCCc--ccCcHH----HHHHHHHHHHHcCCcEEE
Q 014264 170 NGCEIVRYDATEERLLTDVSQPLKILKRRYYLVEKAKDANIIGVLVGTLG--VAGYLH----MIHQMKELITKAGKKAYT 243 (427)
Q Consensus 170 ~~~~v~~yDP~~~~~~~~~~~~~r~L~rRy~~I~ka~~A~~iGIlvgTl~--~q~~~~----~i~~l~~li~~~GKK~y~ 243 (427)
.-+.-...+|.|.-- .. ++ + +.....+=|.-...| ||.+.+ -++++++++.++|++.-+
T Consensus 110 g~k~GlalnP~T~~~-----~i------~~-~---l~~vD~VlvMtV~PGf~GQ~fi~~~l~KI~~l~~~~~~~~~~~~I 174 (223)
T PRK08745 110 GCQAGLVLNPATPVD-----IL------DW-V---LPELDLVLVMSVNPGFGGQAFIPSALDKLRAIRKKIDALGKPIRL 174 (223)
T ss_pred CCceeEEeCCCCCHH-----HH------HH-H---HhhcCEEEEEEECCCCCCccccHHHHHHHHHHHHHHHhcCCCeeE
Confidence 345678888887531 01 11 1 235566655544444 666653 556666777777888777
Q ss_pred EEcCCCCHHHHcCCC--CCCEEEE
Q 014264 244 LVMGKPNPAKLANFP--ECDVFIN 265 (427)
Q Consensus 244 ~~vgkln~aKLaNF~--eiD~fVl 265 (427)
-+=|-+|.+-+.-+. ++|+||.
T Consensus 175 eVDGGI~~eti~~l~~aGaDi~V~ 198 (223)
T PRK08745 175 EIDGGVKADNIGAIAAAGADTFVA 198 (223)
T ss_pred EEECCCCHHHHHHHHHcCCCEEEE
Confidence 777889988775543 5899987
No 195
>TIGR01752 flav_long flavodoxin, long chain. Flavodoxins are small redox-active proteins with a flavin mononucleotide (FMN) prosthetic group. They can act in nitrogen fixation by nitrogenase, in sulfite reduction, and light-dependent NADP+ reduction in during photosynthesis, among other roles. This model describes the long chain type, typical for nitrogen fixation but associated with pyruvate formate-lyase activation and cobalamin-dependent methionine synthase activity in E. coli.
Probab=21.44 E-value=2.2e+02 Score=25.47 Aligned_cols=53 Identities=13% Similarity=0.243 Sum_probs=36.4
Q ss_pred eEEEEEcCCcccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHHHHcCCCCCCEEEEecCC
Q 014264 210 IIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKLANFPECDVFINVSCA 269 (427)
Q Consensus 210 ~iGIlvgTl~~q~~~~~i~~l~~li~~~GKK~y~~~vgkln~aKLaNF~eiD~fVlvaCP 269 (427)
+++|+-+|.. -+...++++|.+.|.. ..+-++-+.+.+++.|.++ |.+ ++++|
T Consensus 1 ~i~IiY~S~t-GnTe~vA~~Ia~~l~~--~~~~i~~~~~~~~~~l~~~---d~i-i~gsp 53 (167)
T TIGR01752 1 KIGIFYGTDT-GNTEGIAEKIQKELGE--DDVDVFNIAKASKEDLNAY---DKL-ILGTP 53 (167)
T ss_pred CEEEEEECCC-ChHHHHHHHHHHHhCC--CceEEEEcccCCHhHHhhC---CEE-EEEec
Confidence 3688889854 5678889999888763 3456777788777766554 554 44444
No 196
>PF13671 AAA_33: AAA domain; PDB: 1LTQ_A 2IA5_K 1RC8_A 1LY1_A 1RRC_A 1RPZ_A 3ZVM_A 1YJ5_A 3ZVL_A 3U7E_B ....
Probab=21.43 E-value=4.7e+02 Score=21.81 Aligned_cols=45 Identities=18% Similarity=0.037 Sum_probs=31.8
Q ss_pred HHHHHHHhcCCeEEEEEcCCcccCcHHHHHHHHHHHHHcCCcEEEEEc
Q 014264 199 YYLVEKAKDANIIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVM 246 (427)
Q Consensus 199 y~~I~ka~~A~~iGIlvgTl~~q~~~~~i~~l~~li~~~GKK~y~~~v 246 (427)
+..+.++...+.-.||-+|.. +..-...+.+++++.|.+.+++.+
T Consensus 60 ~~~~~~~l~~g~~~vvd~~~~---~~~~r~~~~~~~~~~~~~~~~v~l 104 (143)
T PF13671_consen 60 NAAIRKALRNGNSVVVDNTNL---SREERARLRELARKHGYPVRVVYL 104 (143)
T ss_dssp HHHHHHHHHTT-EEEEESS-----SHHHHHHHHHHHHHCTEEEEEEEE
T ss_pred HHHHHHHHHcCCCceeccCcC---CHHHHHHHHHHHHHcCCeEEEEEE
Confidence 356667777787777777754 345567888999999988888877
No 197
>cd03142 GATase1_ThuA Type 1 glutamine amidotransferase (GATase1)-like domain found in Sinorhizobium meliloti Rm1021 ThuA (SmThuA). Type 1 glutamine amidotransferase (GATase1)-like domain found in Sinorhizobium meliloti Rm1021 ThuA (SmThuA). This group includes proteins similar to SmThuA which plays a role in a major pathway for trehalose catabolism. SmThuA is induced by trehalose but not by related structurally similar disaccharides like sucrose or maltose. Proteins in this group lack the catalytic triad of typical GATase1 domains: a His replaces the reactive Cys found in the sharp turn between a beta strand and an alpha helix termed the nucleophile elbow. S. meliloti Rm1021 thuA mutants are impaired in competitive colonization of Medicago sativa roots but are more competitive than the wild-type Rml021 in infecting alfalfa roots and forming nitrogen-fixing nodules.
Probab=21.34 E-value=2.4e+02 Score=26.90 Aligned_cols=44 Identities=16% Similarity=0.130 Sum_probs=34.1
Q ss_pred HHHHHHHHHHHcCCcEEEEEcCC----CCHHHHcCCCCCCEEEEecCCCcc
Q 014264 226 MIHQMKELITKAGKKAYTLVMGK----PNPAKLANFPECDVFINVSCAQTA 272 (427)
Q Consensus 226 ~i~~l~~li~~~GKK~y~~~vgk----ln~aKLaNF~eiD~fVlvaCPr~s 272 (427)
|=..++.+|++.|.++-+-.... +|+++|+.+ |+.|..+|.-..
T Consensus 24 ~~~~~~~~L~~~gf~V~~~~~~d~~~~~~~~~L~~~---D~lV~~~~~~~~ 71 (215)
T cd03142 24 MHGTIAAALAEYGFDVQTATLDEPEHGLTEEVLAET---DVLLWWGHIAHD 71 (215)
T ss_pred HHHHHHHHHHhcCcEEEEEeccCccccCCHhHHhcC---CEEEEeCCCCcC
Confidence 45678888999998877655655 678888776 999999998644
No 198
>KOG3360 consensus Acylphosphatase [Energy production and conversion]
Probab=21.31 E-value=2.2e+02 Score=23.82 Aligned_cols=44 Identities=23% Similarity=0.300 Sum_probs=37.9
Q ss_pred HHHHHHHHHhcCCeEEEEEcCCc------ccCcHHHHHHHHHHHHHcCCc
Q 014264 197 RRYYLVEKAKDANIIGVLVGTLG------VAGYLHMIHQMKELITKAGKK 240 (427)
Q Consensus 197 rRy~~I~ka~~A~~iGIlvgTl~------~q~~~~~i~~l~~li~~~GKK 240 (427)
-|.+...+|+.....|-+.+|.- .++-++.++.++++|..+|-.
T Consensus 23 fr~~t~~~a~~lGlrGWv~Nt~~GtvkG~leGp~~~vd~mk~wl~~~gsP 72 (98)
T KOG3360|consen 23 FRKHTLDEAKKLGLRGWVMNTSEGTVKGQLEGPPEKVDEMKEWLLTRGSP 72 (98)
T ss_pred hhHHHHHHHHhhcceEEEEecCCceEEEEEeCCHHHHHHHHHHHHhcCCh
Confidence 36688999999999999998865 478899999999999988754
No 199
>cd02042 ParA ParA and ParB of Caulobacter crescentus belong to a conserved family of bacterial proteins implicated in chromosome segregation. ParB binds to DNA sequences adjacent to the origin of replication and localizes to opposite cell poles shortly following the initiation of DNA replication. ParB regulates the ParA ATPase activity by promoting nucleotide exchange in a fashion reminiscent of the exchange factors of eukaryotic G proteins. ADP-bound ParA binds single-stranded DNA, whereas the ATP-bound form dissociates ParB from its DNA binding sites. Increasing the fraction of ParA-ADP in the cell inhibits cell division, suggesting that this simple nucleotide switch may regulate cytokinesis. ParA shares sequence similarity to a conserved and widespread family of ATPases which includes the repA protein of the repABC operon in R. etli Sym plasmid. This operon is involved in the plasmid replication and partition.
Probab=21.16 E-value=3.2e+02 Score=21.69 Aligned_cols=48 Identities=13% Similarity=0.312 Sum_probs=38.6
Q ss_pred EEEcCCcccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHHHHcCCCCCCEEEEecCCCc
Q 014264 213 VLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKLANFPECDVFINVSCAQT 271 (427)
Q Consensus 213 IlvgTl~~q~~~~~i~~l~~li~~~GKK~y~~~vgkln~aKLaNF~eiD~fVlvaCPr~ 271 (427)
.+.|.+||-|--.+...|-..+.++|+++.++-.+.- | | ||++-||..
T Consensus 3 ~~~~~kgG~Gkst~~~~la~~~~~~~~~vl~~d~d~~-------~---d-~viiD~p~~ 50 (104)
T cd02042 3 AVANQKGGVGKTTTAVNLAAALARRGKRVLLIDLDPQ-------Y---D-YIIIDTPPS 50 (104)
T ss_pred EEEeCCCCcCHHHHHHHHHHHHHhCCCcEEEEeCCCC-------C---C-EEEEeCcCC
Confidence 3677899999999999999999999999877776543 3 3 788888875
No 200
>PRK14340 (dimethylallyl)adenosine tRNA methylthiotransferase; Provisional
Probab=21.13 E-value=1.2e+02 Score=32.07 Aligned_cols=29 Identities=21% Similarity=0.285 Sum_probs=14.4
Q ss_pred HcCCcEEEEEcCC---CCHHHHcC-CCCCCEEE
Q 014264 236 KAGKKAYTLVMGK---PNPAKLAN-FPECDVFI 264 (427)
Q Consensus 236 ~~GKK~y~~~vgk---ln~aKLaN-F~eiD~fV 264 (427)
+.+.+.-+++.|- ..++.|.. ||+||+++
T Consensus 74 ~~~~~~~ivv~GC~a~~~~~e~~~~~p~vd~v~ 106 (445)
T PRK14340 74 RRRKGLLVGVLGCVPQYEREEMFSMFPVIDFLA 106 (445)
T ss_pred hcCCCCEEEEeCcccccchHHHHhhCCCCcEEE
Confidence 3444445555553 23444543 56666555
No 201
>PF00781 DAGK_cat: Diacylglycerol kinase catalytic domain; InterPro: IPR001206 The DAG-kinase catalytic domain or DAGKc domain is present in mammalian lipid kinases, such as diacylglycerol (DAG), ceramide and sphingosine kinases, as well as in related bacterial proteins [, ]. Eukaryotic DAG-kinase (2.7.1.107 from EC) catalyses the phosphorylation of DAG to phosphatidic acid, thus modulating the balance between the two signaling lipids. At least ten different isoforms have been identified in mammals, which form 5 groups characterised by different functional domains, such as the calcium-binding EF hand (see PDOC00018 from PROSITEDOC), PH (see PDOC50003 from PROSITEDOC), SAM (see PDOC50105 from PROSITEDOC) , DAG/PE-binding C1 domain (see PDOC00379 from PROSITEDOC) and ankyrin repeats (see PDOC50088 from PROSITEDOC) []. In bacteria, an integral membrane DAG kinase forms a homotrimeric protein that lacks the DAGKc domain (see PDOC00820 from PROSITEDOC). In contrast, the bacterial yegS protein is a soluble cytosolic protein that contains the DAGKc domain in the N-terminal part. YegS is a lipid kinase with two structural domains, wherein the active site is located in the interdomain cleft, C-terminal to the DAGKc domain which forms an alpha/beta fold []. The tertiary structure resembles that of NAD kinases and contains a metal-binding site in the C-terminal region [, ]. This domain is usually associated with an accessory domain (see IPR000756 from INTERPRO).; GO: 0004143 diacylglycerol kinase activity, 0007205 activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway; PDB: 2JGR_A 2BON_A 3T5P_D 3S40_A 2P1R_A 2QV7_A 2QVL_A.
Probab=21.05 E-value=3e+02 Score=23.26 Aligned_cols=37 Identities=11% Similarity=0.127 Sum_probs=29.7
Q ss_pred EEEEEcCCcccCcHHHHHHHHHHHHHcCCcEEEEEcCC
Q 014264 211 IGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGK 248 (427)
Q Consensus 211 iGIlvgTl~~q~~~~~i~~l~~li~~~GKK~y~~~vgk 248 (427)
+.||++.+++.+.-. ++++++.+++++..+-++....
T Consensus 2 ~~vi~Np~sG~~~~~-~~~v~~~l~~~~~~~~~~~t~~ 38 (130)
T PF00781_consen 2 VLVIINPKSGGGRAK-WKKVEPALRAAGIDYEVIETES 38 (130)
T ss_dssp EEEEEETTSTTSHHH-HHHHHHHHHHTTCEEEEEEESS
T ss_pred EEEEECCCCCCCchh-HHHHHHHHHHcCCceEEEEEec
Confidence 678999999988888 7899999999887765555544
No 202
>PF06283 ThuA: Trehalose utilisation; PDB: 4E5V_A 1T0B_A.
Probab=20.70 E-value=1.2e+02 Score=28.25 Aligned_cols=59 Identities=14% Similarity=0.153 Sum_probs=33.1
Q ss_pred EEEEEcC-CcccCc--HHHHHHHHHHHHH-cCCcEEEEE-cCCCCHHHHcCCCCCCEEEEecCCCcc
Q 014264 211 IGVLVGT-LGVAGY--LHMIHQMKELITK-AGKKAYTLV-MGKPNPAKLANFPECDVFINVSCAQTA 272 (427)
Q Consensus 211 iGIlvgT-l~~q~~--~~~i~~l~~li~~-~GKK~y~~~-vgkln~aKLaNF~eiD~fVlvaCPr~s 272 (427)
|=|+-|+ -+.+.. ....+.|++++++ .|.++-... ...++++.| .++|+.|+..|....
T Consensus 2 vLi~~g~~~~~~h~~~~~~~~~l~~ll~~~~~~~v~~~~~~~~~~~~~L---~~~Dvvv~~~~~~~~ 65 (217)
T PF06283_consen 2 VLIFSGGWSGYRHDSIPAAKKALAQLLEESEGFEVTVTEDPDDLTPENL---KGYDVVVFYNTGGDE 65 (217)
T ss_dssp EEEEES-SHHHCSHHHHHHHHHHHHHHHHTTCEEEEECCSGGCTSHHCH---CT-SEEEEE-SSCCG
T ss_pred EEEEeCCcCCccCccHHHHHHHHHHHhccCCCEEEEEEeCcccCChhHh---cCCCEEEEECCCCCc
Confidence 3355555 233333 4788888899985 344432111 234666655 456999999999433
No 203
>PRK11404 putative PTS system transporter subunits IIBC; Provisional
Probab=20.69 E-value=2.2e+02 Score=30.57 Aligned_cols=73 Identities=15% Similarity=0.134 Sum_probs=53.2
Q ss_pred CeEEEEEcCCcccCcHHHHHHHHHHHHHcCCcEE------EEEcCCCCHHHHcCCCCCCEEEEecCCCcccccccCC-CC
Q 014264 209 NIIGVLVGTLGVAGYLHMIHQMKELITKAGKKAY------TLVMGKPNPAKLANFPECDVFINVSCAQTALLDSKEF-LA 281 (427)
Q Consensus 209 ~~iGIlvgTl~~q~~~~~i~~l~~li~~~GKK~y------~~~vgkln~aKLaNF~eiD~fVlvaCPr~si~d~~~f-~k 281 (427)
+.++|.-+.-+.++..-..+.|++..++.|.+.- .=+.+.++++.+++ .|..++.+.-.....|..+| -|
T Consensus 5 kivaVtacp~GiAht~mAaeaL~~aA~~~G~~i~VEtqg~~g~~~~lt~~~i~~---Ad~VIia~d~~~~~~d~~rF~gk 81 (482)
T PRK11404 5 RIVAITNCPAGIAHTYMVAEALEQKARSLGHTIKVETQGSSGVENRLSSEEIAA---ADYVILATGRGLSGDDRARFAGK 81 (482)
T ss_pred eEEEEecCCCcHHHHHHHHHHHHHHHHHCCCeEEEEecCCccCCCCCCHHHHHh---CCEEEEeeccccCccccccccCC
Confidence 6778888888888888899999999999999877 44455677777765 48888887754444444444 35
Q ss_pred ccc
Q 014264 282 PVI 284 (427)
Q Consensus 282 Pvl 284 (427)
|++
T Consensus 82 ~v~ 84 (482)
T PRK11404 82 KVY 84 (482)
T ss_pred ceE
Confidence 553
No 204
>cd06301 PBP1_rhizopine_binding_like Periplasmic binding proteins specific to rhizopines. Periplasmic binding proteins specific to rhizopines, which are simple sugar-like compounds produced in the nodules induced by the symbiotic root nodule bacteria, such as Rhizobium and Sinorhizobium. Rhizopine-binding-like proteins from other bacteria are also included. Two inositol based rhizopine compounds are known to date: L-3-O-methly-scyllo-inosamine (3-O-MSI) and scyllo-inosamine. Bacterial strains that can metabolize rhizopine have a greater competitive advantage in nodulation and rhizopine synthesis is regulated by NifA/NtrA regulatory transcription activators which are maximally expressed at the onset of nitrogen fixation in bacteroids. The members of this group belong to the pentose/hexose sugar-binding protein family of the type I periplasmic binding protein superfamily.
Probab=20.68 E-value=1.4e+02 Score=27.93 Aligned_cols=59 Identities=22% Similarity=0.158 Sum_probs=32.8
Q ss_pred eEEEEEcCCcccCcHHHHHHHHHHHHH-cCCcEEEEEcCCCCHHHHcC----C--CCCCEEEEecCC
Q 014264 210 IIGVLVGTLGVAGYLHMIHQMKELITK-AGKKAYTLVMGKPNPAKLAN----F--PECDVFINVSCA 269 (427)
Q Consensus 210 ~iGIlvgTl~~q~~~~~i~~l~~li~~-~GKK~y~~~vgkln~aKLaN----F--~eiD~fVlvaCP 269 (427)
+||+|+....-..+..+++.+.+.+++ .|.+..+. -+.-++++..+ + ..+|.+|+.++-
T Consensus 1 ~igvi~~~~~~~~~~~~~~gi~~~~~~~~~~~~~~~-~~~~~~~~~~~~i~~l~~~~vdgiii~~~~ 66 (272)
T cd06301 1 KIGVSMANFDDNFLTLLRNAMKEHAKVLGGVELQFE-DAKNDVATQLSQVENFIAQGVDAIIVVPVD 66 (272)
T ss_pred CeeEeecccCCHHHHHHHHHHHHHHHHcCCcEEEEe-CCCCCHHHHHHHHHHHHHcCCCEEEEecCc
Confidence 367777666555556677777777776 55544332 22334433321 1 157777776654
No 205
>PRK00782 hypothetical protein; Provisional
Probab=20.66 E-value=1.9e+02 Score=28.29 Aligned_cols=46 Identities=20% Similarity=0.208 Sum_probs=39.8
Q ss_pred hcCCeEEEEEcCCcccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCH
Q 014264 206 KDANIIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNP 251 (427)
Q Consensus 206 ~~A~~iGIlvgTl~~q~~~~~i~~l~~li~~~GKK~y~~~vgkln~ 251 (427)
.+.++|=|++|..+.+.-.++.+.|.+.+++.++++.+|..+.++=
T Consensus 136 ~~~~iVPI~vg~~~~~~~~~lg~~L~~~~~~~~~~vliIaSsDlSH 181 (267)
T PRK00782 136 KDFKIVPICLGMQDEETAREVGEAIAEAIEELGKKVVVIASSDFTH 181 (267)
T ss_pred CCCeEEEEEcCCCCHHHHHHHHHHHHHHHHhcCCCEEEEEeCCCcC
Confidence 5889999999998877777888888888888899999888888874
No 206
>PRK14814 NADH dehydrogenase subunit B; Provisional
Probab=20.55 E-value=1.9e+02 Score=27.03 Aligned_cols=13 Identities=23% Similarity=0.534 Sum_probs=9.4
Q ss_pred CCCEEEEecCCCcc
Q 014264 259 ECDVFINVSCAQTA 272 (427)
Q Consensus 259 eiD~fVlvaCPr~s 272 (427)
.||+| +=+||-..
T Consensus 131 pVDv~-IPGCPP~P 143 (186)
T PRK14814 131 PVDVY-VPGCPPRP 143 (186)
T ss_pred cccEE-ecCCCCCH
Confidence 56776 78999664
No 207
>TIGR02362 dhaK1b probable dihydroxyacetone kinase DhaK1b subunit. Two types of dihydroxyacetone kinase (glycerone kinase) are described. In yeast and a few bacteria, e.g. Citrobacter freundii, the enzyme is a single chain that uses ATP as phosphoryl donor and is designated EC 2.7.1.29. By contract, E. coli and many other bacterial species have a multisubunit form with a phosphoprotein donor related to PTS transport proteins. This family represents a protein, unique to the Firmicutes (low GC Gram-positives), that appears to be a divergent second copy of the K subunit of that complex; its gene is always found in operons with the other three proteins of the complex.
Probab=20.30 E-value=2.9e+02 Score=28.12 Aligned_cols=46 Identities=17% Similarity=0.190 Sum_probs=38.8
Q ss_pred HHhcCCeEEEEEcCCcccCcHHH---HHHHHHHHHHcCCcEEEEEcCCC
Q 014264 204 KAKDANIIGVLVGTLGVAGYLHM---IHQMKELITKAGKKAYTLVMGKP 249 (427)
Q Consensus 204 ka~~A~~iGIlvgTl~~q~~~~~---i~~l~~li~~~GKK~y~~~vgkl 249 (427)
+.++-..+.++|+.||+-.++++ .+.+.++|+++|.+.+.+.+|..
T Consensus 244 ~~~~gd~v~vlvN~LG~t~~lEl~i~~~~v~~~L~~~gi~v~r~~vG~~ 292 (326)
T TIGR02362 244 RWQADDHYAVLVNNLGGTTPMEQMVFNNDVHELLALEALHLPFIKVGTF 292 (326)
T ss_pred CCCCCCEEEEEecCCCCCCHHHHHHHHHHHHHHHHHCCCEEEEeEeecc
Confidence 33455789999999999999875 67888889999999999999965
No 208
>cd06354 PBP1_BmpA_PnrA_like Periplasmic binding domain of basic membrane lipoprotein, PnrA, in Treponema pallidum and its homologs from other bacteria and Archaea. Periplasmic binding domain of basic membrane lipoprotein, PnrA, in Treponema pallidum and its homologs from other bacteria and Archaea. The PnrA lipoprotein, also known as Tp0319 or TmpC, represents a novel family of bacterial purine nucleoside receptor encoded within an ATP-binding cassette (ABC) transport system (pnrABCDE). It shows a striking structural similarity to another basic membrane lipoprotein Med which regulates the competence transcription factor gene, comK, in Bacillus subtilis. The members of PnrA-like subgroup are likely to have similar nucleoside-binding functions and a similar type I periplasmic sugar-binding protein-like fold.
Probab=20.30 E-value=2.6e+02 Score=26.50 Aligned_cols=58 Identities=9% Similarity=0.059 Sum_probs=37.4
Q ss_pred eEEEEEcC---CcccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHHH----HcCC--CCCCEEEEecCC
Q 014264 210 IIGVLVGT---LGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAK----LANF--PECDVFINVSCA 269 (427)
Q Consensus 210 ~iGIlvgT---l~~q~~~~~i~~l~~li~~~GKK~y~~~vgkln~aK----LaNF--~eiD~fVlvaCP 269 (427)
+||+|+.. +.-..+..+++.+.+.+++.|....+.... ++++ +.++ ..+|.+|++++.
T Consensus 1 ~I~~i~~~~~~~~~~f~~~~~~gi~~~~~~~gy~~~i~~~~--~~~~~~~~i~~l~~~~vdgiI~~~~~ 67 (265)
T cd06354 1 KVALVTDVGGLGDKSFNQSAWEGLERAAKELGIEYKYVESK--SDADYEPNLEQLADAGYDLIVGVGFL 67 (265)
T ss_pred CEEEEeCCCCcCchhHHHHHHHHHHHHHHHcCCeEEEEecC--CHHHHHHHHHHHHhCCCCEEEEcCcc
Confidence 36777754 455667788888888888888776665443 3321 2222 158888887654
No 209
>PRK10953 cysJ sulfite reductase subunit alpha; Provisional
Probab=20.29 E-value=2.1e+02 Score=31.51 Aligned_cols=51 Identities=10% Similarity=0.034 Sum_probs=43.7
Q ss_pred hcCCeEEEEEcCCcccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHHHHcCC
Q 014264 206 KDANIIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKLANF 257 (427)
Q Consensus 206 ~~A~~iGIlvgTl~~q~~~~~i~~l~~li~~~GKK~y~~~vgkln~aKLaNF 257 (427)
..++.+.||.||-+| +-..++++|.+.++++|..+-++.|+...+..|...
T Consensus 59 ~~~~~v~IlygSqTG-nae~lA~~la~~l~~~g~~~~v~~~~d~~~~~L~~~ 109 (600)
T PRK10953 59 AEMPGITLISASQTG-NARRVAEQLRDDLLAAKLNVNLVNAGDYKFKQIAQE 109 (600)
T ss_pred CCCCeEEEEEEcCch-HHHHHHHHHHHHHHhCCCCcEEechHhCCHhHhccC
Confidence 346789999999874 567899999999999999999999999988877665
No 210
>PRK03501 ppnK inorganic polyphosphate/ATP-NAD kinase; Provisional
Probab=20.18 E-value=2.1e+02 Score=28.07 Aligned_cols=32 Identities=6% Similarity=0.041 Sum_probs=25.7
Q ss_pred CeEEEEEcCCcccCcHHHHHHHHHHHHHcCCcEE
Q 014264 209 NIIGVLVGTLGVAGYLHMIHQMKELITKAGKKAY 242 (427)
Q Consensus 209 ~~iGIlvgTl~~q~~~~~i~~l~~li~~~GKK~y 242 (427)
+.+||+..... ...+++++++++++++|..++
T Consensus 3 ~~i~iv~~~~~--~a~~~~~~l~~~l~~~g~~~~ 34 (264)
T PRK03501 3 RNLFFFYKRDK--ELVEKVKPLKKIAEEYGFTVV 34 (264)
T ss_pred cEEEEEECCCH--HHHHHHHHHHHHHHHCCCEEE
Confidence 47888887655 677899999999999997654
No 211
>COG1445 FrwB Phosphotransferase system fructose-specific component IIB [Carbohydrate transport and metabolism]
Probab=20.13 E-value=3.2e+02 Score=23.79 Aligned_cols=72 Identities=19% Similarity=0.217 Sum_probs=53.9
Q ss_pred CeEEEEEcCCcccCcHHHHHHHHHHHHHcCCcEEEE------EcCCCCHHHHcCCCCCCEEEEecCCCcccccccCC-CC
Q 014264 209 NIIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTL------VMGKPNPAKLANFPECDVFINVSCAQTALLDSKEF-LA 281 (427)
Q Consensus 209 ~~iGIlvgTl~~q~~~~~i~~l~~li~~~GKK~y~~------~vgkln~aKLaNF~eiD~fVlvaCPr~si~d~~~f-~k 281 (427)
+.++|=-+.-|++......+.|++..++.|.+..+= +-++|+++.+++= |+ |+++|-.. ++..+.| -|
T Consensus 3 ~IVAVTACPtGIAHTyMAAeaLe~~A~~~g~~IKVETqGs~G~eN~LT~edI~~A---d~-VI~AaD~~-i~~~~ff~gk 77 (122)
T COG1445 3 KIVAVTACPTGIAHTYMAAEALEKAAKKLGVEIKVETQGAVGIENRLTAEDIAAA---DV-VILAADIE-VDLSRFFAGK 77 (122)
T ss_pred cEEEEecCCchHHHHHHHHHHHHHHHHHcCCeEEEEcCCcccccCcCCHHHHHhC---CE-EEEEeccc-ccHhHhhcCC
Confidence 567788888899999999999999999999887654 3458899988775 44 56666654 3445556 78
Q ss_pred cccC
Q 014264 282 PVIT 285 (427)
Q Consensus 282 PvlT 285 (427)
||+-
T Consensus 78 ~vi~ 81 (122)
T COG1445 78 PVIE 81 (122)
T ss_pred eEEE
Confidence 8763
Done!