Query 014409
Match_columns 425
No_of_seqs 184 out of 585
Neff 6.9
Searched_HMMs 46136
Date Fri Mar 29 04:51:19 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/014409.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/014409hhsearch_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 4E-106 9E-111 838.0 32.6 399 1-418 87-496 (496)
2 KOG2648 Diphthamide biosynthes 100.0 5.7E-96 1E-100 732.5 30.3 370 1-418 83-453 (453)
3 TIGR00322 diphth2_R diphthamid 100.0 1.2E-80 2.6E-85 620.8 29.0 278 1-308 52-330 (332)
4 PF01866 Diphthamide_syn: Puta 100.0 4.3E-80 9.3E-85 613.6 23.3 278 1-307 26-306 (307)
5 TIGR03682 arCOG04112 arCOG0411 100.0 3.8E-77 8.2E-82 590.5 27.8 271 1-307 34-306 (308)
6 COG1736 DPH2 Diphthamide synth 100.0 1.4E-64 3E-69 500.7 26.2 278 1-308 57-335 (347)
7 PRK09492 treR trehalose repres 76.8 8.3 0.00018 37.6 7.3 77 206-284 60-143 (315)
8 cd06280 PBP1_LacI_like_4 Ligan 76.5 5 0.00011 37.9 5.5 59 210-269 1-65 (263)
9 cd06289 PBP1_MalI_like Ligand- 71.0 9.1 0.0002 35.9 5.7 75 210-285 1-84 (268)
10 cd06293 PBP1_LacI_like_11 Liga 70.6 8.5 0.00019 36.4 5.5 61 210-271 1-67 (269)
11 COG1609 PurR Transcriptional r 69.0 13 0.00029 37.3 6.8 62 205-267 55-122 (333)
12 cd06272 PBP1_hexuronate_repres 68.9 8.3 0.00018 36.3 5.0 74 210-285 1-79 (261)
13 PF00919 UPF0004: Uncharacteri 66.9 7.6 0.00016 32.2 3.7 70 193-264 21-97 (98)
14 cd06274 PBP1_FruR Ligand bindi 66.4 12 0.00026 35.3 5.5 61 210-271 1-67 (264)
15 cd06279 PBP1_LacI_like_3 Ligan 66.2 11 0.00023 36.2 5.2 61 210-271 1-68 (283)
16 PRK07188 nicotinate phosphorib 65.1 14 0.0003 37.9 5.9 43 222-264 261-308 (352)
17 cd06295 PBP1_CelR Ligand bindi 64.5 10 0.00022 36.0 4.7 64 207-270 2-75 (275)
18 cd06315 PBP1_ABC_sugar_binding 63.8 9.8 0.00021 36.6 4.5 76 209-285 1-86 (280)
19 cd06271 PBP1_AglR_RafR_like Li 63.7 20 0.00044 33.5 6.5 77 210-286 1-88 (268)
20 cd01536 PBP1_ABC_sugar_binding 63.4 14 0.0003 34.4 5.3 75 210-286 1-86 (267)
21 TIGR02990 ectoine_eutA ectoine 63.0 22 0.00047 34.4 6.6 81 204-290 116-216 (239)
22 TIGR02405 trehalos_R_Ecol treh 62.1 24 0.00051 34.5 6.9 63 206-269 57-125 (311)
23 COG5136 U1 snRNP-specific prot 61.5 8.7 0.00019 34.7 3.2 67 191-272 28-94 (188)
24 cd06298 PBP1_CcpA_like Ligand- 61.5 17 0.00037 34.1 5.6 58 210-269 1-65 (268)
25 cd06273 PBP1_GntR_like_1 This 61.4 11 0.00025 35.3 4.4 75 210-286 1-84 (268)
26 cd06310 PBP1_ABC_sugar_binding 61.1 10 0.00022 35.9 4.0 76 210-285 1-87 (273)
27 cd06270 PBP1_GalS_like Ligand 61.0 25 0.00055 33.1 6.7 59 210-270 1-66 (268)
28 cd06277 PBP1_LacI_like_1 Ligan 60.7 25 0.00053 33.2 6.6 73 211-285 2-85 (268)
29 cd06281 PBP1_LacI_like_5 Ligan 58.8 19 0.00041 34.0 5.4 60 210-270 1-66 (269)
30 TIGR01753 flav_short flavodoxi 58.6 35 0.00076 29.0 6.6 55 211-270 1-55 (140)
31 PF00532 Peripla_BP_1: Peripla 58.5 12 0.00026 36.5 4.1 61 209-271 2-68 (279)
32 cd01542 PBP1_TreR_like Ligand- 58.5 18 0.0004 33.7 5.2 75 210-286 1-84 (259)
33 cd06283 PBP1_RegR_EndR_KdgR_li 58.5 31 0.00068 32.2 6.8 74 210-285 1-83 (267)
34 PRK12321 cobN cobaltochelatase 58.4 6.4 0.00014 46.1 2.3 28 17-44 522-567 (1100)
35 PRK10653 D-ribose transporter 57.7 12 0.00027 36.2 4.0 63 206-269 24-92 (295)
36 PRK10014 DNA-binding transcrip 57.3 31 0.00067 34.0 6.8 79 205-285 61-149 (342)
37 cd06290 PBP1_LacI_like_9 Ligan 56.9 20 0.00043 33.7 5.2 59 210-269 1-65 (265)
38 PRK11303 DNA-binding transcrip 56.4 30 0.00066 33.8 6.6 62 206-269 59-127 (328)
39 cd06291 PBP1_Qymf_like Ligand 56.1 25 0.00055 33.0 5.7 59 210-269 1-65 (265)
40 cd01538 PBP1_ABC_xylose_bindin 55.0 13 0.00028 35.8 3.6 75 210-285 1-85 (288)
41 PRK05723 flavodoxin; Provision 54.8 38 0.00082 30.2 6.3 55 210-269 2-56 (151)
42 PRK14987 gluconate operon tran 53.3 32 0.00069 33.8 6.1 79 206-285 61-147 (331)
43 cd06299 PBP1_LacI_like_13 Liga 52.9 41 0.0009 31.4 6.7 60 210-271 1-67 (265)
44 PRK06703 flavodoxin; Provision 52.8 46 0.001 29.1 6.5 56 210-270 3-58 (151)
45 PRK11041 DNA-binding transcrip 52.8 48 0.001 31.9 7.3 62 205-268 32-100 (309)
46 PLN03069 magnesiumprotoporphyr 52.1 9.7 0.00021 45.2 2.5 28 17-44 600-645 (1220)
47 TIGR02417 fruct_sucro_rep D-fr 52.1 36 0.00079 33.3 6.3 62 206-268 58-125 (327)
48 cd06316 PBP1_ABC_sugar_binding 52.0 17 0.00038 35.0 4.0 75 210-284 1-85 (294)
49 PRK07308 flavodoxin; Validated 51.9 61 0.0013 28.2 7.1 57 210-271 3-59 (146)
50 cd06292 PBP1_LacI_like_10 Liga 51.8 36 0.00079 32.0 6.1 57 210-268 1-64 (273)
51 cd05569 PTS_IIB_fructose PTS_I 51.7 57 0.0012 26.7 6.4 68 211-284 2-76 (96)
52 cd01574 PBP1_LacI Ligand-bindi 51.6 27 0.00059 32.7 5.1 61 210-271 1-68 (264)
53 PRK10703 DNA-binding transcrip 51.6 37 0.0008 33.4 6.3 63 205-268 56-124 (341)
54 PLN03241 magnesium chelatase s 51.5 10 0.00022 45.5 2.5 28 17-44 663-708 (1353)
55 COG2984 ABC-type uncharacteriz 51.3 58 0.0013 32.9 7.4 110 195-310 145-265 (322)
56 PRK13405 bchH magnesium chelat 50.7 10 0.00023 44.8 2.4 28 17-44 593-638 (1209)
57 TIGR02257 cobalto_cobN cobalto 50.4 10 0.00023 44.5 2.4 28 17-44 535-580 (1122)
58 cd06297 PBP1_LacI_like_12 Liga 50.3 27 0.00059 33.1 5.0 62 210-271 1-67 (269)
59 PRK05989 cobN cobaltochelatase 50.3 10 0.00022 45.2 2.3 28 17-44 541-586 (1244)
60 PRK12493 magnesium chelatase s 50.0 10 0.00022 45.3 2.3 28 17-44 587-632 (1310)
61 PRK09004 FMN-binding protein M 49.8 46 0.00099 29.4 6.0 53 210-269 3-55 (146)
62 TIGR02025 BchH magnesium chela 49.8 10 0.00023 44.9 2.3 28 17-44 573-618 (1216)
63 cd06282 PBP1_GntR_like_2 Ligan 49.3 35 0.00075 31.8 5.5 75 210-286 1-85 (266)
64 cd06286 PBP1_CcpB_like Ligand- 49.2 31 0.00067 32.2 5.1 59 210-270 1-66 (260)
65 cd06284 PBP1_LacI_like_6 Ligan 49.2 48 0.001 30.9 6.4 59 210-269 1-65 (267)
66 cd06278 PBP1_LacI_like_2 Ligan 49.1 43 0.00094 31.2 6.1 61 210-270 1-65 (266)
67 cd01545 PBP1_SalR Ligand-bindi 48.5 59 0.0013 30.4 6.9 59 210-269 1-66 (270)
68 cd06296 PBP1_CatR_like Ligand- 48.2 55 0.0012 30.6 6.7 59 210-269 1-65 (270)
69 PRK10423 transcriptional repre 48.0 65 0.0014 31.4 7.4 64 205-269 53-122 (327)
70 cd06285 PBP1_LacI_like_7 Ligan 47.4 37 0.0008 31.9 5.4 60 210-270 1-66 (265)
71 cd06318 PBP1_ABC_sugar_binding 47.4 26 0.00057 33.2 4.4 75 210-285 1-85 (282)
72 TIGR01481 ccpA catabolite cont 47.3 61 0.0013 31.6 7.1 61 207-269 58-125 (329)
73 PRK09526 lacI lac repressor; R 46.9 64 0.0014 31.7 7.2 61 206-266 61-127 (342)
74 COG2185 Sbm Methylmalonyl-CoA 46.6 27 0.00058 31.2 3.9 53 205-258 59-112 (143)
75 PRK08105 flavodoxin; Provision 46.5 47 0.001 29.4 5.6 41 209-250 2-42 (149)
76 COG1429 CobN Cobalamin biosynt 46.3 12 0.00026 44.9 2.2 25 20-44 555-597 (1388)
77 PRK10427 putative PTS system f 46.3 56 0.0012 27.9 5.7 61 208-271 3-69 (114)
78 PF00258 Flavodoxin_1: Flavodo 46.1 39 0.00085 29.0 4.9 54 213-269 1-54 (143)
79 TIGR00829 FRU PTS system, fruc 46.0 48 0.001 26.6 5.0 68 212-284 2-76 (85)
80 KOG0781 Signal recognition par 45.9 1.2E+02 0.0026 32.6 9.0 69 201-270 458-542 (587)
81 TIGR00640 acid_CoA_mut_C methy 45.9 59 0.0013 28.3 5.9 64 207-273 53-119 (132)
82 PRK05569 flavodoxin; Provision 45.1 96 0.0021 26.5 7.2 56 210-270 3-58 (141)
83 PF00885 DMRL_synthase: 6,7-di 44.4 50 0.0011 29.4 5.3 61 208-268 3-71 (144)
84 cd06307 PBP1_uncharacterized_s 43.6 23 0.00051 33.5 3.3 76 210-285 1-88 (275)
85 PF00731 AIRC: AIR carboxylase 42.7 71 0.0015 28.7 6.0 72 210-284 2-82 (150)
86 cd06300 PBP1_ABC_sugar_binding 42.4 37 0.0008 32.0 4.5 77 210-286 1-91 (272)
87 cd06312 PBP1_ABC_sugar_binding 42.0 34 0.00073 32.4 4.2 60 210-269 1-67 (271)
88 cd01575 PBP1_GntR Ligand-bindi 41.4 53 0.0011 30.6 5.4 76 210-286 1-84 (268)
89 PRK09271 flavodoxin; Provision 41.0 91 0.002 27.7 6.6 58 210-269 2-60 (160)
90 PRK10339 DNA-binding transcrip 40.6 49 0.0011 32.4 5.2 58 207-268 62-123 (327)
91 PF03698 UPF0180: Uncharacteri 40.5 63 0.0014 25.9 4.8 56 228-290 11-72 (80)
92 PF01729 QRPTase_C: Quinolinat 40.4 36 0.00077 31.1 3.8 63 201-267 92-156 (169)
93 PF02514 CobN-Mg_chel: CobN/Ma 39.9 17 0.00038 42.7 2.1 93 171-267 716-817 (1098)
94 TIGR00288 conserved hypothetic 39.9 95 0.0021 28.2 6.4 53 206-267 104-156 (160)
95 cd06321 PBP1_ABC_sugar_binding 39.5 38 0.00082 31.9 4.1 59 210-268 1-66 (271)
96 cd06302 PBP1_LsrB_Quorum_Sensi 39.4 54 0.0012 31.8 5.2 59 210-268 1-65 (298)
97 TIGR01754 flav_RNR ribonucleot 39.0 61 0.0013 28.0 5.0 57 210-269 2-59 (140)
98 TIGR01579 MiaB-like-C MiaB-lik 38.9 32 0.0007 35.7 3.7 66 199-265 25-93 (414)
99 COG0716 FldA Flavodoxins [Ener 38.8 1E+02 0.0023 27.0 6.5 59 209-271 2-60 (151)
100 cd04502 SGNH_hydrolase_like_7 38.5 1.6E+02 0.0036 25.7 7.9 55 193-247 36-96 (171)
101 PF04392 ABC_sub_bind: ABC tra 38.3 90 0.0019 30.5 6.6 113 193-310 115-237 (294)
102 PRK09426 methylmalonyl-CoA mut 38.1 61 0.0013 36.5 5.9 71 201-274 625-700 (714)
103 cd01571 NAPRTase_B Nicotinate 38.0 69 0.0015 32.0 5.7 59 209-267 211-274 (302)
104 cd06275 PBP1_PurR Ligand-bindi 37.4 1.2E+02 0.0025 28.4 7.1 60 210-270 1-66 (269)
105 cd02071 MM_CoA_mut_B12_BD meth 37.2 88 0.0019 26.5 5.6 62 205-270 48-113 (122)
106 cd01543 PBP1_XylR Ligand-bindi 37.2 58 0.0013 30.6 4.9 55 210-267 1-58 (265)
107 cd01452 VWA_26S_proteasome_sub 37.1 74 0.0016 29.6 5.4 49 209-258 108-158 (187)
108 COG1736 DPH2 Diphthamide synth 36.9 4.1E+02 0.0088 27.3 11.1 168 47-274 8-175 (347)
109 cd05013 SIS_RpiR RpiR-like pro 36.7 1.7E+02 0.0036 24.2 7.3 68 201-272 6-73 (139)
110 cd06319 PBP1_ABC_sugar_binding 36.4 68 0.0015 30.2 5.3 74 210-285 1-85 (277)
111 cd06294 PBP1_ycjW_transcriptio 36.2 77 0.0017 29.6 5.6 59 210-268 1-69 (270)
112 PRK10936 TMAO reductase system 36.1 51 0.0011 32.9 4.6 79 206-284 44-132 (343)
113 cd06306 PBP1_TorT-like TorT-li 34.8 49 0.0011 31.3 4.1 77 210-286 1-87 (268)
114 PRK14571 D-alanyl-alanine synt 34.5 1.3E+02 0.0027 29.5 7.0 76 210-286 2-85 (299)
115 cd06317 PBP1_ABC_sugar_binding 34.2 66 0.0014 30.1 4.8 59 210-269 1-66 (275)
116 TIGR02634 xylF D-xylose ABC tr 34.2 43 0.00094 32.7 3.6 60 211-271 1-66 (302)
117 PF00205 TPP_enzyme_M: Thiamin 34.0 28 0.00061 29.9 2.0 46 201-248 4-49 (137)
118 PRK15395 methyl-galactoside AB 33.9 64 0.0014 32.0 4.9 64 206-269 22-91 (330)
119 PRK05568 flavodoxin; Provision 33.7 2E+02 0.0044 24.5 7.5 56 210-270 3-58 (142)
120 cd06325 PBP1_ABC_uncharacteriz 33.7 1E+02 0.0022 29.1 6.0 75 210-286 1-87 (281)
121 PRK12359 flavodoxin FldB; Prov 33.4 1.3E+02 0.0029 27.4 6.4 53 210-270 2-55 (172)
122 PRK11104 hemG protoporphyrinog 33.1 73 0.0016 29.0 4.7 54 210-269 2-55 (177)
123 PF12641 Flavodoxin_3: Flavodo 33.1 89 0.0019 28.2 5.2 96 147-257 37-140 (160)
124 cd06305 PBP1_methylthioribose_ 32.9 84 0.0018 29.4 5.3 58 210-268 1-64 (273)
125 cd01537 PBP1_Repressors_Sugar_ 32.6 98 0.0021 28.3 5.6 74 210-285 1-84 (264)
126 cd06288 PBP1_sucrose_transcrip 32.6 91 0.002 29.1 5.5 59 210-269 1-66 (269)
127 cd06320 PBP1_allose_binding Pe 32.6 80 0.0017 29.7 5.1 74 210-284 1-86 (275)
128 PF10657 RC-P840_PscD: Photosy 32.2 47 0.001 28.8 2.9 35 259-310 74-108 (144)
129 PRK09701 D-allose transporter 32.2 96 0.0021 30.4 5.7 64 204-267 20-90 (311)
130 PRK09240 thiH thiamine biosynt 31.7 1.1E+02 0.0024 31.4 6.2 57 195-252 201-263 (371)
131 cd01540 PBP1_arabinose_binding 31.6 75 0.0016 30.2 4.8 58 210-269 1-64 (289)
132 PRK10727 DNA-binding transcrip 31.4 1.7E+02 0.0037 28.8 7.4 62 207-269 58-125 (343)
133 cd01473 vWA_CTRP CTRP for CS 31.3 1.1E+02 0.0025 28.1 5.7 50 208-258 108-159 (192)
134 PF02514 CobN-Mg_chel: CobN/Ma 31.2 66 0.0014 38.0 4.9 113 174-289 40-168 (1098)
135 PRK08091 ribulose-phosphate 3- 30.8 1.6E+02 0.0034 28.4 6.7 60 207-266 140-207 (228)
136 cd06304 PBP1_BmpA_like Peripla 29.9 97 0.0021 29.2 5.2 57 210-268 1-65 (260)
137 PRK10355 xylF D-xylose transpo 29.7 1.1E+02 0.0024 30.4 5.8 64 207-271 24-93 (330)
138 TIGR01574 miaB-methiolase tRNA 29.6 63 0.0014 33.9 4.1 15 250-264 85-100 (438)
139 cd06309 PBP1_YtfQ_like Peripla 29.4 50 0.0011 31.2 3.1 59 210-269 1-65 (273)
140 cd05566 PTS_IIB_galactitol PTS 29.4 2.1E+02 0.0045 22.4 6.3 54 214-270 5-58 (89)
141 PRK08883 ribulose-phosphate 3- 29.2 70 0.0015 30.4 4.0 104 149-267 83-196 (220)
142 cd06322 PBP1_ABC_sugar_binding 28.9 70 0.0015 29.9 4.0 75 210-286 1-86 (267)
143 PF14538 Raptor_N: Raptor N-te 28.7 1.3E+02 0.0028 27.1 5.4 51 22-80 92-148 (154)
144 PRK09267 flavodoxin FldA; Vali 28.3 1.2E+02 0.0026 27.0 5.2 53 210-269 3-55 (169)
145 cd01539 PBP1_GGBP Periplasmic 28.1 52 0.0011 32.0 3.0 59 210-269 1-67 (303)
146 cd01541 PBP1_AraR Ligand-bindi 27.8 1.2E+02 0.0026 28.5 5.4 55 210-266 1-62 (273)
147 PRK05452 anaerobic nitric oxid 27.7 2.3E+02 0.0049 30.3 8.0 114 191-311 235-360 (479)
148 COG0622 Predicted phosphoester 27.7 54 0.0012 30.0 2.8 74 1-76 7-91 (172)
149 PRK00061 ribH 6,7-dimethyl-8-r 27.0 1.6E+02 0.0034 26.6 5.6 61 209-269 13-81 (154)
150 PRK09613 thiH thiamine biosynt 26.5 80 0.0017 33.7 4.2 58 195-253 218-281 (469)
151 KOG1736 Glia maturation factor 26.5 58 0.0013 28.3 2.6 61 238-299 38-112 (143)
152 PF02302 PTS_IIB: PTS system, 26.5 1.9E+02 0.0041 22.5 5.6 56 213-272 3-58 (90)
153 PRK02910 light-independent pro 26.5 1.8E+02 0.004 31.3 7.0 76 209-285 159-238 (519)
154 cd03819 GT1_WavL_like This fam 26.5 1.2E+02 0.0027 29.3 5.4 41 228-270 233-275 (355)
155 cd06267 PBP1_LacI_sugar_bindin 26.4 1.2E+02 0.0026 27.8 5.0 31 211-241 2-32 (264)
156 PRK14336 (dimethylallyl)adenos 26.2 1.4E+02 0.003 31.2 5.9 14 260-273 124-139 (418)
157 TIGR02014 BchZ chlorophyllide 25.7 1.1E+02 0.0023 32.8 5.0 77 207-284 151-227 (468)
158 PRK14057 epimerase; Provisiona 25.6 1.9E+02 0.0042 28.3 6.3 60 207-266 154-221 (254)
159 cd06324 PBP1_ABC_sugar_binding 25.1 94 0.002 30.2 4.3 58 210-268 1-67 (305)
160 PRK10401 DNA-binding transcrip 25.0 3.5E+02 0.0075 26.6 8.4 61 206-268 57-124 (346)
161 PF06414 Zeta_toxin: Zeta toxi 24.9 3.6E+02 0.0078 24.6 7.9 49 196-247 80-128 (199)
162 TIGR00147 lipid kinase, YegS/R 24.9 2.3E+02 0.0049 27.6 6.9 37 210-246 3-40 (293)
163 cd06314 PBP1_tmGBP Periplasmic 24.8 1.1E+02 0.0023 28.9 4.5 59 210-269 1-65 (271)
164 PF02593 dTMP_synthase: Thymid 24.8 1.2E+02 0.0025 29.1 4.5 40 199-240 66-105 (217)
165 COG0529 CysC Adenylylsulfate k 24.5 1.8E+02 0.0039 27.2 5.5 38 208-245 21-58 (197)
166 cd02036 MinD Bacterial cell di 24.5 2.7E+02 0.0059 24.2 6.8 59 213-271 3-73 (179)
167 TIGR01012 Sa_S2_E_A ribosomal 24.4 1.6E+02 0.0034 27.7 5.3 51 25-78 14-73 (196)
168 TIGR01501 MthylAspMutase methy 24.4 1.5E+02 0.0032 26.1 4.9 44 202-248 45-90 (134)
169 TIGR01931 cysJ sulfite reducta 24.2 1.4E+02 0.003 32.9 5.7 49 208-257 58-106 (597)
170 TIGR02955 TMAO_TorT TMAO reduc 24.2 1.7E+02 0.0037 28.2 5.8 61 210-270 1-68 (295)
171 PRK08662 nicotinate phosphorib 24.1 1.5E+02 0.0033 30.2 5.6 55 209-263 227-285 (343)
172 COG0041 PurE Phosphoribosylcar 23.9 2E+02 0.0043 26.1 5.5 60 210-272 4-68 (162)
173 cd06323 PBP1_ribose_binding Pe 23.8 85 0.0018 29.2 3.5 57 210-267 1-63 (268)
174 PRK11921 metallo-beta-lactamas 23.4 2.2E+02 0.0047 29.4 6.7 77 191-270 231-310 (394)
175 KOG3360 Acylphosphatase [Energ 22.7 2E+02 0.0043 24.0 4.8 44 197-240 23-72 (98)
176 cd06276 PBP1_FucR_like Ligand- 22.6 1.9E+02 0.004 27.2 5.7 56 211-269 2-62 (247)
177 TIGR01162 purE phosphoribosyla 22.5 1.7E+02 0.0036 26.6 4.9 71 211-284 1-80 (156)
178 PRK15408 autoinducer 2-binding 22.5 1E+02 0.0023 30.9 4.1 63 207-269 22-90 (336)
179 PRK04020 rps2P 30S ribosomal p 22.4 1.7E+02 0.0037 27.6 5.2 50 25-77 20-78 (204)
180 TIGR01007 eps_fam capsular exo 22.4 2.3E+02 0.0051 25.8 6.1 50 197-247 6-55 (204)
181 PRK06756 flavodoxin; Provision 22.3 3.2E+02 0.0069 23.6 6.7 56 210-270 3-59 (148)
182 TIGR02363 dhaK1 dihydroxyaceto 22.2 2.4E+02 0.0052 28.7 6.5 45 205-249 249-296 (329)
183 PF01583 APS_kinase: Adenylyls 22.1 1.6E+02 0.0034 26.6 4.7 37 211-247 3-39 (156)
184 cd01450 vWFA_subfamily_ECM Von 22.0 2.2E+02 0.0048 24.1 5.6 67 193-260 84-154 (161)
185 cd06308 PBP1_sensor_kinase_lik 22.0 1.9E+02 0.0042 27.0 5.7 59 210-269 1-66 (270)
186 PRK14339 (dimethylallyl)adenos 22.0 1.8E+02 0.0038 30.4 5.7 6 173-178 29-34 (420)
187 TIGR01205 D_ala_D_alaTIGR D-al 21.7 2.9E+02 0.0064 26.9 7.0 77 210-286 1-95 (315)
188 PLN02404 6,7-dimethyl-8-ribity 21.6 1.6E+02 0.0035 26.1 4.5 61 209-269 8-76 (141)
189 cd01981 Pchlide_reductase_B Pc 21.5 2.1E+02 0.0045 29.8 6.2 78 208-286 162-243 (430)
190 PF12163 HobA: DNA replication 21.1 99 0.0022 28.6 3.2 147 47-212 25-176 (180)
191 TIGR02883 spore_cwlD N-acetylm 21.0 2E+02 0.0043 26.3 5.3 47 223-269 28-93 (189)
192 cd02072 Glm_B12_BD B12 binding 20.6 1.8E+02 0.0038 25.4 4.5 40 207-249 50-89 (128)
193 PRK08745 ribulose-phosphate 3- 20.6 1.3E+02 0.0027 28.8 3.9 82 170-266 110-199 (223)
194 cd06320 PBP1_allose_binding Pe 20.4 4.4E+02 0.0095 24.6 7.8 45 207-251 121-166 (275)
195 PRK06455 riboflavin synthase; 20.4 2.9E+02 0.0062 25.0 5.9 58 209-269 2-66 (155)
196 cd07945 DRE_TIM_CMS Leptospira 20.2 84 0.0018 31.0 2.8 87 201-293 79-182 (280)
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=4.1e-106 Score=837.98 Aligned_cols=399 Identities=30% Similarity=0.488 Sum_probs=322.8
Q ss_pred CCCCCccCCccChhhhcccCCcEEEEecCCCCCCCCCCCeEEEccccCCChHHHHHHHhhhhcCCCCcEEEEecccchhh
Q 014409 1 MADTTYGSCCVDEVGASHVDADCVIHYGHTCLSPTSTLPAFFVFGKASINTSNCIENLSKHALTNGKPILVLYGLEYAHA 80 (425)
Q Consensus 1 LaDtsYGsCCVDevaA~hv~aD~iVHyGhaClsp~~~lpviYVf~~~~ld~~~~~~~~~~~~~~~~~~v~l~~dvqy~~~ 80 (425)
|||||||||||||+||+|++||+|||||||||+|++++||+|||++.++|++++++.+++.+++..++|+|++|+||.|+
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 79999999999999999999999999999999999999999999999999999999998776655568999999999999
Q ss_pred hHHHHHHHHhhccCCCCCcceeeeeecceeeeecCCCCCCCCCCCCCCcccccccCccccCCCccCccceEEEEEcCCch
Q 014409 81 IPHIREAVKVASSSYGSGLKLEINFADVMCTVITPSKDHKSLCGPAGGCTRHTIGGLVWNIPDRKKMEEHLLFWIGSDNS 160 (425)
Q Consensus 81 l~~l~~~L~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~g~~~gc~~~~~~~~~~~~~~~~~~~~~~i~~Ig~~~~ 160 (425)
++++++.|++.....+ ...++.++ ...|.. ....++++||++.... +...+++.+||||++.+
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 1123678999865432 12334667999999777
Q ss_pred -hhhHHHhhcC-C-ceEEEecCCCCccccccCc-HHHHHHHHHHHHHHHhcCCeEEEEEcCCcccCcHHHHHHHHHHHHH
Q 014409 161 -AFANVVLTFN-G-CEIVRYDATEERLLTDVSQ-PLKILKRRYYLVEKAKDANIIGVLVGTLGVAGYLHMIHQMKELITK 236 (425)
Q Consensus 161 -~l~~l~l~~~-~-~~v~~yDP~~~~~~~~~~~-~~r~L~rRy~~I~ka~~A~~iGIlvgTl~~q~~~~~i~~Lk~li~~ 236 (425)
+|++++|+++ . +++|+|||+++++..+... ++|+|||||++|+|||+|++||||||||++|+|++++++|+++|++
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 8888988643 4 5799999999998766545 8899999999999999999999999999999999999999999999
Q ss_pred cCCcEEEEEcCCCCHHHhcCCCCCCEEEEecCCCcccccccCCCCcccCHHHHHHhhCCCCccccceeeccccccCCCC-
Q 014409 237 AGKKAYTLVMGKPNPAKLANFPECDVFINVSCAQTALLDSKEFLAPVITPFEAMLAFGRGTQWTGAYVMEFRDLMSSSP- 315 (425)
Q Consensus 237 ~GKk~Y~~~vgkln~aKLaNF~eID~fV~vaCPr~si~d~~ef~kPViTP~ElevAL~~~~~W~g~y~~Df~~ll~~~~- 315 (425)
+|||+|+|+||||||+|||||++||+||+|||||++|+|+++|+||||||||++|||+.+.+|.++|..+|..+.+...
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 9999999999999999999999999999999999999999999999999999999999887899999888887764311
Q ss_pred -----CCCCCccccCccccccCccccccCCCCCCchhhhhHHHHhhhhhhhhhhccCCCCceeecccchHHHHhhcCCcc
Q 014409 316 -----VEGSDQAEEARFSFLKGGYVEDVAQPENGEEEKEGALALANAAEKALQLRDRSLDPIVKGTAKSGAEYFVSRSYH 390 (425)
Q Consensus 316 -----~~~~~~~~~p~fslitG~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~s~~a~~l~~Rtw~ 390 (425)
.+..+++++|+||||||+|++++++++....... ....+..+.+++.+.+++.+++++++|+||+||++||||
T Consensus 390 ~~~~~~~~~~~~~~p~fslitG~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~s~~a~~l~~Rtw~ 467 (496)
T TIGR00272 390 QDTISPSTTSDEAAPEFSLIRGKYTSTSRPLRALTHLEL--EAADNDDSKQSTTRHTASGAVIKGTVSTSASALQNRSWK 467 (496)
T ss_pred cccCCCccccccCCCceeccccceeecCCccchhhhccc--cccCCCCccceeecccCcceeeccccccHHHHhhcCcee
Confidence 1112234689999999999998887652111100 000012234455554434366778899999999999999
Q ss_pred CCCCCCCC-CCCcccccCCccccccccCC
Q 014409 391 GLEMQCNS-SSPEPYAIGRSGKASGYDDE 418 (425)
Q Consensus 391 GL~~~~~~-~~~~~~~~GrsGiA~gY~~e 418 (425)
|||+++|+ ++++.++||||||||||+++
T Consensus 468 GL~~~~~~~~~~a~~~eGrsGIA~gY~~~ 496 (496)
T TIGR00272 468 GLGDDVDSTEVDAKIEEGISGIARGYGGD 496 (496)
T ss_pred CCCCCcCCCCCcceeecCCccccccCCCC
Confidence 99999976 45799999999999999865
No 2
>KOG2648 consensus Diphthamide biosynthesis protein [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=5.7e-96 Score=732.45 Aligned_cols=370 Identities=36% Similarity=0.608 Sum_probs=309.7
Q ss_pred CCCCCccCCccChhhhcccCCcEEEEecCCCCCCCCCCCe-EEEccccCCChHHHHHHHhhhhcCCCCcEEEEecccchh
Q 014409 1 MADTTYGSCCVDEVGASHVDADCVIHYGHTCLSPTSTLPA-FFVFGKASINTSNCIENLSKHALTNGKPILVLYGLEYAH 79 (425)
Q Consensus 1 LaDtsYGsCCVDevaA~hv~aD~iVHyGhaClsp~~~lpv-iYVf~~~~ld~~~~~~~~~~~~~~~~~~v~l~~dvqy~~ 79 (425)
||||+||||||||+||+|++||+|||||||||+|++++|+ +|||++++||++++++.|+..+++..++|++++++||+|
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 999999999999999999998887777999999999999
Q ss_pred hhHHHHHHHHhhccCCCCCcceeeeeecceeeeecCCCCCCCCCCCCCCcccccccCccccCCCccCccceEEEEEcCCc
Q 014409 80 AIPHIREAVKVASSSYGSGLKLEINFADVMCTVITPSKDHKSLCGPAGGCTRHTIGGLVWNIPDRKKMEEHLLFWIGSDN 159 (425)
Q Consensus 80 ~l~~l~~~L~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~g~~~gc~~~~~~~~~~~~~~~~~~~~~~i~~Ig~~~ 159 (425)
.++++++.|...... .++. -|+.+ +.+++.++|||.+...+ . .++.+++|||++.
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 1221 23322 56688999998765432 1 3466899999999
Q ss_pred hhhhHHHhhcCCceEEEecCCCCccccccCcHHHHHHHHHHHHHHHhcCCeEEEEEcCCcccCcHHHHHHHHHHHHHcCC
Q 014409 160 SAFANVVLTFNGCEIVRYDATEERLLTDVSQPLKILKRRYYLVEKAKDANIIGVLVGTLGVAGYLHMIHQMKELITKAGK 239 (425)
Q Consensus 160 ~~l~~l~l~~~~~~v~~yDP~~~~~~~~~~~~~r~L~rRy~~I~ka~~A~~iGIlvgTl~~q~~~~~i~~Lk~li~~~GK 239 (425)
+|+...|+..+.+++++|||+++++..|.+++.++++|||++|||||+|++||||+||||+|+|++++++|+++|+++||
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 99988888888999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cEEEEEcCCCCHHHhcCCCCCCEEEEecCCCcccccccCCCCcccCHHHHHHhhCCCCccccceeeccccccCCCCCCCC
Q 014409 240 KAYTLVMGKPNPAKLANFPECDVFINVSCAQTALLDSKEFLAPVITPFEAMLAFGRGTQWTGAYVMEFRDLMSSSPVEGS 319 (425)
Q Consensus 240 k~Y~~~vgkln~aKLaNF~eID~fV~vaCPr~si~d~~ef~kPViTP~ElevAL~~~~~W~g~y~~Df~~ll~~~~~~~~ 319 (425)
|+|+++||||||+|||||+||||||++||||++++|+++|+||||||||+++||++. .|+++|..+|...+.+...
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 999999999999999999999999999999999999999999999999999999997 9999999999887653321
Q ss_pred CccccCccccccCccccccCCCCCCchhhhhHHHHhhhhhhhhhhccCCCCceeecccchHHHHhhcCCccCCCCCCCCC
Q 014409 320 DQAEEARFSFLKGGYVEDVAQPENGEEEKEGALALANAAEKALQLRDRSLDPIVKGTAKSGAEYFVSRSYHGLEMQCNSS 399 (425)
Q Consensus 320 ~~~~~p~fslitG~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~s~~a~~l~~Rtw~GL~~~~~~~ 399 (425)
+.+++ +..+|.|.++.......... .+. .+..... .+..++++.||++|+||||+++.+++
T Consensus 374 -~~~~~--~~~~~d~pm~~~~~~~~~~~------~~~--------~~~~~~~--~~~~~~a~~~~~~rsw~gLd~~~~~~ 434 (453)
T KOG2648|consen 374 -ESEFH--SSELGDYPMDYYSLGSLGPP------PAW--------TSSNDHG--AGESSPAISFLQNRSWQGLDPRLGQT 434 (453)
T ss_pred -ccccc--ccccccCcccccccccCCcC------ccc--------CCccccc--ccccccccchhccccccCCCcCCCCC
Confidence 11122 14455554332221100000 000 0000000 12335788899999999999999999
Q ss_pred CCcccccCCccccccccCC
Q 014409 400 SPEPYAIGRSGKASGYDDE 418 (425)
Q Consensus 400 ~~~~~~~GrsGiA~gY~~e 418 (425)
++++..+||||||+||.+|
T Consensus 435 ~~~~~~~Grsgia~gy~~~ 453 (453)
T KOG2648|consen 435 PPTKLVSGRSGIAIGYSDE 453 (453)
T ss_pred CccchhccccccccccCCC
Confidence 9999999999999999875
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=1.2e-80 Score=620.77 Aligned_cols=278 Identities=23% Similarity=0.437 Sum_probs=249.6
Q ss_pred CCCCCccCCccChhhhcccCCcEEEEecCCCCCCCC-CCCeEEEccccCCChHHHHHHHhhhhcCCCCcEEEEecccchh
Q 014409 1 MADTTYGSCCVDEVGASHVDADCVIHYGHTCLSPTS-TLPAFFVFGKASINTSNCIENLSKHALTNGKPILVLYGLEYAH 79 (425)
Q Consensus 1 LaDtsYGsCCVDevaA~hv~aD~iVHyGhaClsp~~-~lpviYVf~~~~ld~~~~~~~~~~~~~~~~~~v~l~~dvqy~~ 79 (425)
|||||||||||||++|+|++||+|||||||||+|+. ++||+|||++.++|++++++.+.+.+.+ .++|+|++|+||.|
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 9999999999999999999999887654 46899999999999
Q ss_pred hhHHHHHHHHhhccCCCCCcceeeeeecceeeeecCCCCCCCCCCCCCCcccccccCccccCCCccCccceEEEEEcCCc
Q 014409 80 AIPHIREAVKVASSSYGSGLKLEINFADVMCTVITPSKDHKSLCGPAGGCTRHTIGGLVWNIPDRKKMEEHLLFWIGSDN 159 (425)
Q Consensus 80 ~l~~l~~~L~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~g~~~gc~~~~~~~~~~~~~~~~~~~~~~i~~Ig~~~ 159 (425)
.++++++.|++.|++ +.++ .....+..+|+++||++..+.+ .+.+ .++|||+|.
T Consensus 131 ~~~~~~~~L~~~g~~--------v~i~--------~~~~~~~~~g~vLGC~~~~~~~--------~~~d--~~l~vg~g~ 184 (332)
T TIGR00322 131 KLHSVRDKLLNEGHE--------VYIG--------PPQGKPLSRGQVLGCNSEVLRG--------EQAD--AMVFIGDGR 184 (332)
T ss_pred HHHHHHHHHHhcCce--------EEEe--------cCccCCCCCccccCCCcCCCCC--------CCCC--EEEEEcCCc
Confidence 999999999887642 2221 1123456799999998754421 1222 788999999
Q ss_pred hhhhHHHhhcCCceEEEecCCCCccccccCcHHHHHHHHHHHHHHHhcCCeEEEEEcCCcccCcHHHHHHHHHHHHHcCC
Q 014409 160 SAFANVVLTFNGCEIVRYDATEERLLTDVSQPLKILKRRYYLVEKAKDANIIGVLVGTLGVAGYLHMIHQMKELITKAGK 239 (425)
Q Consensus 160 ~~l~~l~l~~~~~~v~~yDP~~~~~~~~~~~~~r~L~rRy~~I~ka~~A~~iGIlvgTl~~q~~~~~i~~Lk~li~~~GK 239 (425)
||+++++|. +++++|+|||+++++..+..+.+|+|||||++|+||++|++||||+|||++|+|++++++|+++|+++||
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 5889999999999987776779999999999999999999999999999999999999999999999999
Q ss_pred cEEEEEcCCCCHHHhcCCCCCCEEEEecCCCcccccccCCCCcccCHHHHHHhhCCCCccccceeeccc
Q 014409 240 KAYTLVMGKPNPAKLANFPECDVFINVSCAQTALLDSKEFLAPVITPFEAMLAFGRGTQWTGAYVMEFR 308 (425)
Q Consensus 240 k~Y~~~vgkln~aKLaNF~eID~fV~vaCPr~si~d~~ef~kPViTP~ElevAL~~~~~W~g~y~~Df~ 308 (425)
|+|+|+||+|||+||+||+|||+||++||||++|||+++|+||||||||++|||+. +.|. .|+||+.
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 4696 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=4.3e-80 Score=613.55 Aligned_cols=278 Identities=40% Similarity=0.754 Sum_probs=193.7
Q ss_pred CCCCCccCCccChhhhcccCCcEEEEecCCCCCCCC-CCCeEEEccccCCChHHHHHHHhhhhcCCCCcEEEEecccchh
Q 014409 1 MADTTYGSCCVDEVGASHVDADCVIHYGHTCLSPTS-TLPAFFVFGKASINTSNCIENLSKHALTNGKPILVLYGLEYAH 79 (425)
Q Consensus 1 LaDtsYGsCCVDevaA~hv~aD~iVHyGhaClsp~~-~lpviYVf~~~~ld~~~~~~~~~~~~~~~~~~v~l~~dvqy~~ 79 (425)
||||||||||||+++|+|++||+|||||||||+++. ++||+|||++.++|++++++.+.+.+.+ .++|+|++|+||.|
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 9999999999999999999999988776 58999999999999
Q ss_pred hhHHHHHHHHhhccCCCCCcceeeeeecceeeeecCCCCCCCCCCCCCCcccccccCccccCCCccCccceEEEEEcCCc
Q 014409 80 AIPHIREAVKVASSSYGSGLKLEINFADVMCTVITPSKDHKSLCGPAGGCTRHTIGGLVWNIPDRKKMEEHLLFWIGSDN 159 (425)
Q Consensus 80 ~l~~l~~~L~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~g~~~gc~~~~~~~~~~~~~~~~~~~~~~i~~Ig~~~ 159 (425)
.++++++.|++.+.. ..+ ..+...+..+|+++||+...+... .+++.++|||+|.
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 222334467899999987655310 3456899999999
Q ss_pred hhhhHHHhhcCCceEEEecCCCCccccc--cCcHHHHHHHHHHHHHHHhcCCeEEEEEcCCcccCcHHHHHHHHHHHHHc
Q 014409 160 SAFANVVLTFNGCEIVRYDATEERLLTD--VSQPLKILKRRYYLVEKAKDANIIGVLVGTLGVAGYLHMIHQMKELITKA 237 (425)
Q Consensus 160 ~~l~~l~l~~~~~~v~~yDP~~~~~~~~--~~~~~r~L~rRy~~I~ka~~A~~iGIlvgTl~~q~~~~~i~~Lk~li~~~ 237 (425)
||+++++|+ +++++|+|||++++...+ ..+.+|+|||||++|+||++|++||||+|||++|+|++++++|+++|+++
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 889999999997665555 45689999999999999999999999999999999999999999999999
Q ss_pred CCcEEEEEcCCCCHHHhcCCCCCCEEEEecCCCcccccccCCCCcccCHHHHHHhhCCCCccccceeecc
Q 014409 238 GKKAYTLVMGKPNPAKLANFPECDVFINVSCAQTALLDSKEFLAPVITPFEAMLAFGRGTQWTGAYVMEF 307 (425)
Q Consensus 238 GKk~Y~~~vgkln~aKLaNF~eID~fV~vaCPr~si~d~~ef~kPViTP~ElevAL~~~~~W~g~y~~Df 307 (425)
|||+|+|+||++||+||+||+|||+||++||||+++||+++|+||||||||++|||+... | ++|.|||
T Consensus 239 gkk~y~~~~~~i~~~kL~nf~eid~fV~~aCPr~~idd~~~f~kPvltP~E~~~al~~~~-~-~~Y~~D~ 306 (307)
T PF01866_consen 239 GKKSYTLSVGEINPAKLANFPEIDAFVQIACPRLSIDDSKDFYKPVLTPYELEVALNERE-W-GEYPMDE 306 (307)
T ss_dssp T-EEEEEEESS--GGGGTTS---SEEEE-S-THHHHT--S--SS-EE-HHHHHHHTTS-S----S-----
T ss_pred CCEEEEEEECCCCHHHHhcCcccCEEEEecCCCcccCchhhcCCcccCHHHHHHHhCCcc-c-CcCCCCc
Confidence 999999999999999999999999999999999999999999999999999999999743 5 7999997
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=3.8e-77 Score=590.46 Aligned_cols=271 Identities=21% Similarity=0.387 Sum_probs=240.2
Q ss_pred CCCCCccCCcc-ChhhhcccCCcEEEEecCCCCC-CCCCCCeEEEccccCCChHHHHHHHhhhhcCCCCcEEEEecccch
Q 014409 1 MADTTYGSCCV-DEVGASHVDADCVIHYGHTCLS-PTSTLPAFFVFGKASINTSNCIENLSKHALTNGKPILVLYGLEYA 78 (425)
Q Consensus 1 LaDtsYGsCCV-DevaA~hv~aD~iVHyGhaCls-p~~~lpviYVf~~~~ld~~~~~~~~~~~~~~~~~~v~l~~dvqy~ 78 (425)
||||||||||| |++|++| ||+|||||||||+ +++++||+|||++.++|++++++.+.+.+. .++|+|++|+||.
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 588999999999999999988887776553 3689999999999
Q ss_pred hhhHHHHHHHHhhccCCCCCcceeeeeecceeeeecCCCCCCCCCCCCCCcccccccCccccCCCccCccceEEEEEcCC
Q 014409 79 HAIPHIREAVKVASSSYGSGLKLEINFADVMCTVITPSKDHKSLCGPAGGCTRHTIGGLVWNIPDRKKMEEHLLFWIGSD 158 (425)
Q Consensus 79 ~~l~~l~~~L~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~g~~~gc~~~~~~~~~~~~~~~~~~~~~~i~~Ig~~ 158 (425)
|.++++++.|++.|+ ++.++ .....+..+|+++||++.... +.+. ..++|||+|
T Consensus 110 ~~~~~v~~~L~~~g~--------~v~i~--------~~~~~~~~~g~vlGC~~~~~~--------~~~~--d~~~~vg~g 163 (308)
T TIGR03682 110 HLLEKVKEILEERGI--------EVVIG--------KGDGRVTYPGQVLGCNFSAAR--------SVDA--DAFLFVGTG 163 (308)
T ss_pred HHHHHHHHHHHHcCc--------eEEec--------CCCCCCCCCceeeCccccCCC--------CCCc--cEEEEEcCC
Confidence 999999999998764 23332 112335668999999865431 1122 378899999
Q ss_pred chhhhHHHhhcCCceEEEecCCCCccccccCcHHHHHHHHHHHHHHHhcCCeEEEEEcCCcccCcHHHHHHHHHHHHHcC
Q 014409 159 NSAFANVVLTFNGCEIVRYDATEERLLTDVSQPLKILKRRYYLVEKAKDANIIGVLVGTLGVAGYLHMIHQMKELITKAG 238 (425)
Q Consensus 159 ~~~l~~l~l~~~~~~v~~yDP~~~~~~~~~~~~~r~L~rRy~~I~ka~~A~~iGIlvgTl~~q~~~~~i~~Lk~li~~~G 238 (425)
.||+++++| ++++++|+|||+++++..+..+.+|+|||||++|+||++|++||||+|||++|+|++++++|+++|+++|
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 7899999999999998777667999999999999999999999999999999999999999999999999
Q ss_pred CcEEEEEcCCCCHHHhcCCCCCCEEEEecCCCcccccccCCCCcccCHHHHHHhhCCCCccccceeecc
Q 014409 239 KKAYTLVMGKPNPAKLANFPECDVFINVSCAQTALLDSKEFLAPVITPFEAMLAFGRGTQWTGAYVMEF 307 (425)
Q Consensus 239 Kk~Y~~~vgkln~aKLaNF~eID~fV~vaCPr~si~d~~ef~kPViTP~ElevAL~~~~~W~g~y~~Df 307 (425)
||+|+|+||+|||+||+|| +||+||++||||+++||+++|+||||||||+++||+. ++| |++|+
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 6999999999999999999999999999999999997 789 99885
No 6
>COG1736 DPH2 Diphthamide synthase subunit DPH2 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=1.4e-64 Score=500.68 Aligned_cols=278 Identities=24% Similarity=0.490 Sum_probs=247.2
Q ss_pred CCCCCccCCccChhhhcccCCcEEEEecCCCCCC-CCCCCeEEEccccCCChHHHHHHHhhhhcCCCCcEEEEecccchh
Q 014409 1 MADTTYGSCCVDEVGASHVDADCVIHYGHTCLSP-TSTLPAFFVFGKASINTSNCIENLSKHALTNGKPILVLYGLEYAH 79 (425)
Q Consensus 1 LaDtsYGsCCVDevaA~hv~aD~iVHyGhaClsp-~~~lpviYVf~~~~ld~~~~~~~~~~~~~~~~~~v~l~~dvqy~~ 79 (425)
+|||+|||||||+.+|+|+ ||+||||||||+++ ...+||+|||...++|++..++.+...+.+..++|++++++||.|
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 678999999999999999998888775555556799999999999
Q ss_pred hhHHHHHHHHhhccCCCCCcceeeeeecceeeeecCCCCCCCCCCCCCCcccccccCccccCCCccCccceEEEEEcCCc
Q 014409 80 AIPHIREAVKVASSSYGSGLKLEINFADVMCTVITPSKDHKSLCGPAGGCTRHTIGGLVWNIPDRKKMEEHLLFWIGSDN 159 (425)
Q Consensus 80 ~l~~l~~~L~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~g~~~gc~~~~~~~~~~~~~~~~~~~~~~i~~Ig~~~ 159 (425)
.++++++.|+..|. ++.+ .+.+....++||++||++..+.+ .+.-.++|||+|.
T Consensus 136 ~l~~~k~~L~~~g~--------~v~i--------~~~~~r~~~~gqVLGC~~~~~~~----------~~~d~~l~vg~G~ 189 (347)
T COG1736 136 LLEEVKEILEGRGY--------EVVI--------GRGQTRPAYPGQVLGCNFSVLEG----------VDADAVLYVGSGR 189 (347)
T ss_pred HHHHHHHHhhcCCe--------EEEE--------eCCCCcccCcceeeccccccCCc----------cccceEEEEcCCc
Confidence 99999999998764 2222 33344477899999998765432 1233788999999
Q ss_pred hhhhHHHhhcCCceEEEecCCCCccccccCcHHHHHHHHHHHHHHHhcCCeEEEEEcCCcccCcHHHHHHHHHHHHHcCC
Q 014409 160 SAFANVVLTFNGCEIVRYDATEERLLTDVSQPLKILKRRYYLVEKAKDANIIGVLVGTLGVAGYLHMIHQMKELITKAGK 239 (425)
Q Consensus 160 ~~l~~l~l~~~~~~v~~yDP~~~~~~~~~~~~~r~L~rRy~~I~ka~~A~~iGIlvgTl~~q~~~~~i~~Lk~li~~~GK 239 (425)
||++++++. +.++|++|||+++++.......++++|+||+.|+||++|++||||+||+++|+++++++.|.++++++||
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 999998888 8899999999999987766668999999999999999999999999999999999999999999999999
Q ss_pred cEEEEEcCCCCHHHhcCCCCCCEEEEecCCCcccccccCCCCcccCHHHHHHhhCCCCccccceeeccc
Q 014409 240 KAYTLVMGKPNPAKLANFPECDVFINVSCAQTALLDSKEFLAPVITPFEAMLAFGRGTQWTGAYVMEFR 308 (425)
Q Consensus 240 k~Y~~~vgkln~aKLaNF~eID~fV~vaCPr~si~d~~ef~kPViTP~ElevAL~~~~~W~g~y~~Df~ 308 (425)
++|+|+|+++||+||+||.+||+||++||||+++||..+|+||||||+|+++||+. +.| .+|.+|+-
T Consensus 269 ~~~li~~~~i~p~~L~~f~~iD~~v~taCPRi~iDd~~~f~kPlLTP~E~~~~l~~-~~~-~~y~~Dei 335 (347)
T COG1736 269 EVYLIVVDEISPDKLANFDDIDAFVNTACPRIPIDDGDRFKKPLLTPYEFEIALGW-RSD-ERYAFDEI 335 (347)
T ss_pred ceEEEEecCCCHHHHhcccceeEEEEecCCCcccchHhhhCCcccChHHHHHhhcc-Ccc-ccccccee
Confidence 99999999999999999999999999999999999999999999999999999982 333 68888863
No 7
>PRK09492 treR trehalose repressor; Provisional
Probab=76.84 E-value=8.3 Score=37.59 Aligned_cols=77 Identities=13% Similarity=0.162 Sum_probs=50.9
Q ss_pred hcCCeEEEEEcCCcccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHHH-------hcCCCCCCEEEEecCCCcccccccC
Q 014409 206 KDANIIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAK-------LANFPECDVFINVSCAQTALLDSKE 278 (425)
Q Consensus 206 ~~A~~iGIlvgTl~~q~~~~~i~~Lk~li~~~GKk~Y~~~vgkln~aK-------LaNF~eID~fV~vaCPr~si~d~~e 278 (425)
+..++||+|+.++.-..+..+++.+.+.++++|....++.. .-++++ |.+. .+|.+|+.++..........
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 45579999999887677889999999999999977644433 334433 2332 59999998753211222234
Q ss_pred CCCccc
Q 014409 279 FLAPVI 284 (425)
Q Consensus 279 f~kPVi 284 (425)
+.+|++
T Consensus 138 ~~~pvv 143 (315)
T PRK09492 138 WQDKLV 143 (315)
T ss_pred cCCCEE
Confidence 456665
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=76.52 E-value=5 Score=37.91 Aligned_cols=59 Identities=14% Similarity=0.190 Sum_probs=45.0
Q ss_pred eEEEEEcCCcccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHHHhcC----C--CCCCEEEEecCC
Q 014409 210 IIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKLAN----F--PECDVFINVSCA 269 (425)
Q Consensus 210 ~iGIlvgTl~~q~~~~~i~~Lk~li~~~GKk~Y~~~vgkln~aKLaN----F--~eID~fV~vaCP 269 (425)
+||+|+..+....+..+++.+.+.+++.|.+..+ ....-++++... + ..+|.+++.+|.
T Consensus 1 ~Ig~i~p~~~~~~~~~~~~~i~~~~~~~g~~~~~-~~~~~~~~~~~~~i~~l~~~~~dgiii~~~~ 65 (263)
T cd06280 1 TVGLIVADIRNPFFTAVSRAVEDAAYRAGLRVIL-CNTDEDPEKEAMYLELMEEERVTGVIFAPTR 65 (263)
T ss_pred CEEEEecccccccHHHHHHHHHHHHHHCCCEEEE-EeCCCCHHHHHHHHHHHHhCCCCEEEEeCCC
Confidence 5899999988788899999999999999977644 444455554322 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=70.98 E-value=9.1 Score=35.90 Aligned_cols=75 Identities=16% Similarity=0.195 Sum_probs=52.3
Q ss_pred eEEEEEcCCcccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHHHh----cCC--CCCCEEEEecCCCcccc---cccCCC
Q 014409 210 IIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKL----ANF--PECDVFINVSCAQTALL---DSKEFL 280 (425)
Q Consensus 210 ~iGIlvgTl~~q~~~~~i~~Lk~li~~~GKk~Y~~~vgkln~aKL----aNF--~eID~fV~vaCPr~si~---d~~ef~ 280 (425)
+||+|+....-..+..+++.+++.+++.|.+..++ .+.-++++. .++ ..+|++++.+|...... ..+...
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 58999988877777889999999999999876544 445555542 222 36999999999765422 223445
Q ss_pred CcccC
Q 014409 281 APVIT 285 (425)
Q Consensus 281 kPViT 285 (425)
.|+|+
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=70.62 E-value=8.5 Score=36.38 Aligned_cols=61 Identities=15% Similarity=0.178 Sum_probs=45.5
Q ss_pred eEEEEEcCCcccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHHHhcC----C--CCCCEEEEecCCCc
Q 014409 210 IIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKLAN----F--PECDVFINVSCAQT 271 (425)
Q Consensus 210 ~iGIlvgTl~~q~~~~~i~~Lk~li~~~GKk~Y~~~vgkln~aKLaN----F--~eID~fV~vaCPr~ 271 (425)
+||+|+..+.-..+..+++.+.+.++++|....++... -++++... + ..+|++++.+|+..
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 58999988776677899999999999999887666444 35543322 1 25999999998743
No 11
>COG1609 PurR Transcriptional regulators [Transcription]
Probab=69.00 E-value=13 Score=37.33 Aligned_cols=62 Identities=16% Similarity=0.247 Sum_probs=52.2
Q ss_pred HhcCCeEEEEEcCCcccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHHHhc----CC--CCCCEEEEec
Q 014409 205 AKDANIIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKLA----NF--PECDVFINVS 267 (425)
Q Consensus 205 a~~A~~iGIlvgTl~~q~~~~~i~~Lk~li~~~GKk~Y~~~vgkln~aKLa----NF--~eID~fV~va 267 (425)
.+..++||+|+..+.-..|.++++.+.+.++++|+...+...+. ++++.. ++ ..+|.+|+.+
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 44688999999998888899999999999999999998888887 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=68.95 E-value=8.3 Score=36.29 Aligned_cols=74 Identities=16% Similarity=0.247 Sum_probs=49.5
Q ss_pred eEEEEEcCCcccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHHHhc-CC--CCCCEEEEecCCCccc--ccccCCCCccc
Q 014409 210 IIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKLA-NF--PECDVFINVSCAQTAL--LDSKEFLAPVI 284 (425)
Q Consensus 210 ~iGIlvgTl~~q~~~~~i~~Lk~li~~~GKk~Y~~~vgkln~aKLa-NF--~eID~fV~vaCPr~si--~d~~ef~kPVi 284 (425)
+||+++.++....+..+++.+++.++++|....+.... +++... .+ ..+|+.++.+|....- ....+...|+|
T Consensus 1 ~igvv~~~~~~~~~~~~~~gi~~~~~~~g~~~~~~~~~--~~~~~~~~l~~~~vdgii~~~~~~~~~~~~~~~~~~ipvV 78 (261)
T cd06272 1 TIGLIWPSVSRVALTELVTGINQAISKNGYNMNVSITP--SLAEAEDLFKENRFDGVIIFGESASDVEYLYKIKLAIPVV 78 (261)
T ss_pred CEEEEecCCCchhHHHHHHHHHHHHHHcCCEEEEEecc--cHHHHHHHHHHcCcCEEEEeCCCCChHHHHHHHHcCCCEE
Confidence 58999998887788899999999999999776666554 333221 12 2699999988753221 12233445665
Q ss_pred C
Q 014409 285 T 285 (425)
Q Consensus 285 T 285 (425)
+
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=66.86 E-value=7.6 Score=32.19 Aligned_cols=70 Identities=23% Similarity=0.369 Sum_probs=48.2
Q ss_pred HHHHHH-HHHHHHHhcCCeEEEEEcCCcccCc--HHHHHHHHHHHHHcCCcEEEEEcC---CCCHHHhcCC-CCCCEEE
Q 014409 193 KILKRR-YYLVEKAKDANIIGVLVGTLGVAGY--LHMIHQMKELITKAGKKAYTLVMG---KPNPAKLANF-PECDVFI 264 (425)
Q Consensus 193 r~L~rR-y~~I~ka~~A~~iGIlvgTl~~q~~--~~~i~~Lk~li~~~GKk~Y~~~vg---kln~aKLaNF-~eID~fV 264 (425)
..|.++ |..++.-.+|..+ |++|=++... .+++++|+++.+...++..+++.| ...+++|... |++|+|+
T Consensus 21 ~~l~~~G~~~~~~~e~AD~i--iiNTC~V~~~Ae~k~~~~i~~l~~~~~~~~~ivv~GC~aq~~~~~l~~~~p~vd~v~ 97 (98)
T PF00919_consen 21 SILQAAGYEIVDDPEEADVI--IINTCTVRESAEQKSRNRIRKLKKLKKPGAKIVVTGCMAQRYGEELKKEFPEVDLVV 97 (98)
T ss_pred HHHHhcCCeeecccccCCEE--EEEcCCCCcHHHHHHHHHHHHHHHhcCCCCEEEEEeCccccChHHHHhhCCCeEEEe
Confidence 334444 5556666789986 5555555444 688888888887765667788887 5567888775 6688875
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=66.43 E-value=12 Score=35.27 Aligned_cols=61 Identities=13% Similarity=0.287 Sum_probs=44.7
Q ss_pred eEEEEEcCCcccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHHHhcC----C--CCCCEEEEecCCCc
Q 014409 210 IIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKLAN----F--PECDVFINVSCAQT 271 (425)
Q Consensus 210 ~iGIlvgTl~~q~~~~~i~~Lk~li~~~GKk~Y~~~vgkln~aKLaN----F--~eID~fV~vaCPr~ 271 (425)
+||+|+..+....+..+++.+.+.+++.|....++.. .-++++... + ..+|++++.++...
T Consensus 1 ~igvi~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~-~~~~~~~~~~i~~l~~~~vdgiii~~~~~~ 67 (264)
T cd06274 1 TIGLIIPDLENRSFARIAKRLEALARERGYQLLIACS-DDDPETERETVETLIARQVDALIVAGSLPP 67 (264)
T ss_pred CEEEEeccccCchHHHHHHHHHHHHHHCCCEEEEEeC-CCCHHHHHHHHHHHHHcCCCEEEEcCCCCc
Confidence 4899999888888889999999999998877544433 345554321 1 16899999988643
No 15
>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=66.19 E-value=11 Score=36.23 Aligned_cols=61 Identities=16% Similarity=0.195 Sum_probs=42.5
Q ss_pred eEEEEEcC-----CcccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHHHhcCC--CCCCEEEEecCCCc
Q 014409 210 IIGVLVGT-----LGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKLANF--PECDVFINVSCAQT 271 (425)
Q Consensus 210 ~iGIlvgT-----l~~q~~~~~i~~Lk~li~~~GKk~Y~~~vgkln~aKLaNF--~eID~fV~vaCPr~ 271 (425)
+||+|+-+ ..-..+..+++.+.+.+++.|....++.... ....+.++ ..+|.+++.+|+..
T Consensus 1 ~igvi~p~~~~~~~~~~~~~~~~~gi~~~a~~~g~~~~~~~~~~-~~~~~~~~~~~~~dgiii~~~~~~ 68 (283)
T cd06279 1 AVGVVLTDSLSYAFSDPVASQFLAGVAEVLDAAGVNLLLLPASS-EDSDSALVVSALVDGFIVYGVPRD 68 (283)
T ss_pred CEEEEeCCcccccccCccHHHHHHHHHHHHHHCCCEEEEecCcc-HHHHHHHHHhcCCCEEEEeCCCCC
Confidence 48888866 4455667899999999999988776665543 22223232 26899999998754
No 16
>PRK07188 nicotinate phosphoribosyltransferase; Provisional
Probab=65.06 E-value=14 Score=37.89 Aligned_cols=43 Identities=16% Similarity=0.317 Sum_probs=37.5
Q ss_pred CcHHHHHHHHHHHHHcC-CcEEEEEcCCCCHHHhcCCC----CCCEEE
Q 014409 222 GYLHMIHQMKELITKAG-KKAYTLVMGKPNPAKLANFP----ECDVFI 264 (425)
Q Consensus 222 ~~~~~i~~Lk~li~~~G-Kk~Y~~~vgkln~aKLaNF~----eID~fV 264 (425)
...++++++++.|.++| .+.-+++.|-+|+.+++.|. .||+|=
T Consensus 261 ~~~~l~~~vr~~Ld~~g~~~vkI~aSgGine~~I~~~~~~g~piD~~G 308 (352)
T PRK07188 261 VNPELIKALRKALDENGGKHVKIIVSSGFDAKKIREFEAQNVPVDIYG 308 (352)
T ss_pred ccHHHHHHHHHHHhhCCCCCcEEEEeCCCCHHHHHHHHHcCCCccEEe
Confidence 45899999999999999 78889999999999999984 378773
No 17
>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=64.50 E-value=10 Score=35.97 Aligned_cols=64 Identities=14% Similarity=0.254 Sum_probs=45.3
Q ss_pred cCCeEEEEEcC-------CcccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHHHhcCC---CCCCEEEEecCCC
Q 014409 207 DANIIGVLVGT-------LGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKLANF---PECDVFINVSCAQ 270 (425)
Q Consensus 207 ~A~~iGIlvgT-------l~~q~~~~~i~~Lk~li~~~GKk~Y~~~vgkln~aKLaNF---~eID~fV~vaCPr 270 (425)
..++||||+.. +.-..+..+++.+++.+++.|.+..++..+.-...++..+ ..+|++|+.+|..
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 45789999964 4444577899999999999999987776654323333221 3699999988753
No 18
>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=63.79 E-value=9.8 Score=36.56 Aligned_cols=76 Identities=16% Similarity=0.081 Sum_probs=51.2
Q ss_pred CeEEEEEcCCcccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHHHh----cCC--CCCCEEEEecCCCccc----ccccC
Q 014409 209 NIIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKL----ANF--PECDVFINVSCAQTAL----LDSKE 278 (425)
Q Consensus 209 ~~iGIlvgTl~~q~~~~~i~~Lk~li~~~GKk~Y~~~vgkln~aKL----aNF--~eID~fV~vaCPr~si----~d~~e 278 (425)
++||+|+.++.-..+..+++.+.+.+++.|....+ .-+.-++++. .+| ..+|.+|++++..... ...++
T Consensus 1 ~~ig~i~~~~~~~~~~~~~~gi~~~a~~~gy~~~~-~~~~~~~~~~~~~i~~l~~~~vdgiil~~~~~~~~~~~~~~~~~ 79 (280)
T cd06315 1 KNIIFVASDLKNGGILGVGEGVREAAKAIGWNLRI-LDGRGSEAGQAAALNQAIALKPDGIVLGGVDAAELQAELELAQK 79 (280)
T ss_pred CeEEEEecccCCcHHHHHHHHHHHHHHHcCcEEEE-ECCCCCHHHHHHHHHHHHHcCCCEEEEcCCCHHHHHHHHHHHHH
Confidence 57999999988777889999999999999976433 3344565543 222 2689999998653321 22334
Q ss_pred CCCcccC
Q 014409 279 FLAPVIT 285 (425)
Q Consensus 279 f~kPViT 285 (425)
...|||.
T Consensus 80 ~~iPvV~ 86 (280)
T cd06315 80 AGIPVVG 86 (280)
T ss_pred CCCCEEE
Confidence 4566654
No 19
>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=63.67 E-value=20 Score=33.48 Aligned_cols=77 Identities=18% Similarity=0.178 Sum_probs=48.4
Q ss_pred eEEEEEcC----CcccCcHHHHHHHHHHHHHcCCcEEEEEcCCC-CH----HHhcCCCCCCEEEEecCCCcc--cccccC
Q 014409 210 IIGVLVGT----LGVAGYLHMIHQMKELITKAGKKAYTLVMGKP-NP----AKLANFPECDVFINVSCAQTA--LLDSKE 278 (425)
Q Consensus 210 ~iGIlvgT----l~~q~~~~~i~~Lk~li~~~GKk~Y~~~vgkl-n~----aKLaNF~eID~fV~vaCPr~s--i~d~~e 278 (425)
.||+|+.+ .+-..+..+++.+.+.+++.|....++....- +. .++.+-..+|++|+.+|.... +....+
T Consensus 1 ~igvi~p~~~~~~~~~~~~~~~~~i~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~vdgiii~~~~~~~~~~~~~~~ 80 (268)
T cd06271 1 AIGLVLPTGEREEGDPFFAEFLSGLSEALAEHGYDLVLLPVDPDEDPLEVYRRLVESGLVDGVIISRTRPDDPRVALLLE 80 (268)
T ss_pred CeEEEeCCcccccCCccHHHHHHHHHHHHHHCCceEEEecCCCcHHHHHHHHHHHHcCCCCEEEEecCCCCChHHHHHHh
Confidence 48999977 34566788999999999999988766665432 11 222222369999998875331 111223
Q ss_pred CCCcccCH
Q 014409 279 FLAPVITP 286 (425)
Q Consensus 279 f~kPViTP 286 (425)
-..|+|..
T Consensus 81 ~~ipvV~~ 88 (268)
T cd06271 81 RGFPFVTH 88 (268)
T ss_pred cCCCEEEE
Confidence 34576653
No 20
>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=63.39 E-value=14 Score=34.43 Aligned_cols=75 Identities=21% Similarity=0.181 Sum_probs=49.6
Q ss_pred eEEEEEcCCcccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHHH-------hcCCCCCCEEEEecCCCcc----cccccC
Q 014409 210 IIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAK-------LANFPECDVFINVSCAQTA----LLDSKE 278 (425)
Q Consensus 210 ~iGIlvgTl~~q~~~~~i~~Lk~li~~~GKk~Y~~~vgkln~aK-------LaNF~eID~fV~vaCPr~s----i~d~~e 278 (425)
+||+|+....-..+..+++.+++.++++|.+.-++.... ++++ |.+- ++|++++.++.... +...++
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 588888766566778899999999999887765555543 5543 3333 68999888775332 222334
Q ss_pred CCCcccCH
Q 014409 279 FLAPVITP 286 (425)
Q Consensus 279 f~kPViTP 286 (425)
...|+|+.
T Consensus 79 ~~ip~V~~ 86 (267)
T cd01536 79 AGIPVVTV 86 (267)
T ss_pred CCCcEEEe
Confidence 45677654
No 21
>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=63.01 E-value=22 Score=34.41 Aligned_cols=81 Identities=17% Similarity=0.224 Sum_probs=60.1
Q ss_pred HHhcCCeEEEEEcCCcccCcHHHHHHHHHHHHHcCCcEEEE---------EcCCCCHHHhcC------CCCCCEEEEecC
Q 014409 204 KAKDANIIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTL---------VMGKPNPAKLAN------FPECDVFINVSC 268 (425)
Q Consensus 204 ka~~A~~iGIlvgTl~~q~~~~~i~~Lk~li~~~GKk~Y~~---------~vgkln~aKLaN------F~eID~fV~vaC 268 (425)
++.++++|+|+- -+-.++-+++++-++++|...--+ .++++.|+-+.. .++.|+.++. |
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 466899999874 355688899999999999988766 577788887633 3578887665 8
Q ss_pred CCccccc-----ccCCCCcccCHHHHH
Q 014409 269 AQTALLD-----SKEFLAPVITPFEAM 290 (425)
Q Consensus 269 Pr~si~d-----~~ef~kPViTP~Ele 290 (425)
=-....+ ..++-|||||.--+.
T Consensus 190 TnLrt~~vi~~lE~~lGkPVlsSNqat 216 (239)
T TIGR02990 190 TALRAATCAQRIEQAIGKPVVTSNQAT 216 (239)
T ss_pred CCchhHHHHHHHHHHHCCCEEEHHHHH
Confidence 8775433 456899999875544
No 22
>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=62.14 E-value=24 Score=34.51 Aligned_cols=63 Identities=14% Similarity=0.156 Sum_probs=44.1
Q ss_pred hcCCeEEEEEcCCcccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHHHhc----CC--CCCCEEEEecCC
Q 014409 206 KDANIIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKLA----NF--PECDVFINVSCA 269 (425)
Q Consensus 206 ~~A~~iGIlvgTl~~q~~~~~i~~Lk~li~~~GKk~Y~~~vgkln~aKLa----NF--~eID~fV~vaCP 269 (425)
+..++||+|+..+.--.+..+++.+.+.++++|....++. ..-++++.. .+ ..+|.+|+++..
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 4567999999876655677899999999999998855443 334454322 11 259999998653
No 23
>COG5136 U1 snRNP-specific protein C [RNA processing and modification]
Probab=61.53 E-value=8.7 Score=34.69 Aligned_cols=67 Identities=21% Similarity=0.263 Sum_probs=51.5
Q ss_pred HHHHHHHHHHHHHHHhcCCeEEEEEcCCcccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHHHhcCCCCCCEEEEecCCC
Q 014409 191 PLKILKRRYYLVEKAKDANIIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKLANFPECDVFINVSCAQ 270 (425)
Q Consensus 191 ~~r~L~rRy~~I~ka~~A~~iGIlvgTl~~q~~~~~i~~Lk~li~~~GKk~Y~~~vgkln~aKLaNF~eID~fV~vaCPr 270 (425)
.+-++|+.-+.+++|+|- .+-..++.+-|+.+|-|.--..-+.....+.-.|+.+|-+.+++||+
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 12234555677788988888888889999998899999999999998
Q ss_pred cc
Q 014409 271 TA 272 (425)
Q Consensus 271 ~s 272 (425)
-.
T Consensus 93 pp 94 (188)
T COG5136 93 PP 94 (188)
T ss_pred CC
Confidence 65
No 24
>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=61.51 E-value=17 Score=34.10 Aligned_cols=58 Identities=10% Similarity=0.147 Sum_probs=43.1
Q ss_pred eEEEEEcCCcccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHH-------HhcCCCCCCEEEEecCC
Q 014409 210 IIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPA-------KLANFPECDVFINVSCA 269 (425)
Q Consensus 210 ~iGIlvgTl~~q~~~~~i~~Lk~li~~~GKk~Y~~~vgkln~a-------KLaNF~eID~fV~vaCP 269 (425)
+||+|+..+.-..+..+++.+++.+++.|....++. ..-+++ +|.+ ..+|++|+.+++
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 489999888778888999999999999988765553 444443 2222 368999998765
No 25
>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=61.41 E-value=11 Score=35.34 Aligned_cols=75 Identities=19% Similarity=0.163 Sum_probs=50.0
Q ss_pred eEEEEEcCCcccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHH-------HhcCCCCCCEEEEecCCCcc--cccccCCC
Q 014409 210 IIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPA-------KLANFPECDVFINVSCAQTA--LLDSKEFL 280 (425)
Q Consensus 210 ~iGIlvgTl~~q~~~~~i~~Lk~li~~~GKk~Y~~~vgkln~a-------KLaNF~eID~fV~vaCPr~s--i~d~~ef~ 280 (425)
+||+++..+.-..|..+++.+.+.+++.|....++ -+.-+++ +|.+- .+|+++++++.... +...++-.
T Consensus 1 ~i~vv~p~~~~~~~~~~~~~i~~~~~~~g~~~~~~-~~~~~~~~~~~~~~~l~~~-~vdgiii~~~~~~~~~~~~l~~~~ 78 (268)
T cd06273 1 TIGAIVPTLDNAIFARVIQAFQETLAAHGYTLLVA-SSGYDLDREYAQARKLLER-GVDGLALIGLDHSPALLDLLARRG 78 (268)
T ss_pred CeEEEeCCCCCchHHHHHHHHHHHHHHCCCEEEEe-cCCCCHHHHHHHHHHHHhc-CCCEEEEeCCCCCHHHHHHHHhCC
Confidence 58999988877788999999999999999665443 2333443 33333 69999998875321 11223345
Q ss_pred CcccCH
Q 014409 281 APVITP 286 (425)
Q Consensus 281 kPViTP 286 (425)
.|+|+.
T Consensus 79 iPvv~~ 84 (268)
T cd06273 79 VPYVAT 84 (268)
T ss_pred CCEEEE
Confidence 677764
No 26
>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=61.13 E-value=10 Score=35.89 Aligned_cols=76 Identities=14% Similarity=0.068 Sum_probs=49.8
Q ss_pred eEEEEEcCCcccCcHHHHHHHHHHHHHcCCcEEEEEcC-CCCHHHhc----CC--CCCCEEEEecCCCcccc----cccC
Q 014409 210 IIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMG-KPNPAKLA----NF--PECDVFINVSCAQTALL----DSKE 278 (425)
Q Consensus 210 ~iGIlvgTl~~q~~~~~i~~Lk~li~~~GKk~Y~~~vg-kln~aKLa----NF--~eID~fV~vaCPr~si~----d~~e 278 (425)
+||+|+.++.-..+..+++.+++.++++|.+..++... .=++++.. ++ ..+|.+|+.++...... ....
T Consensus 1 ~Igvi~~~~~~~~~~~~~~g~~~~~~~~g~~~~~~~~~~~~~~~~~~~~i~~l~~~~vdgvii~~~~~~~~~~~l~~~~~ 80 (273)
T cd06310 1 KIALVPKGTTSDFWQAVKAGAEAAAKELGVKVTFQGPASETDVAGQVNLLENAIARGPDAILLAPTDAKALVPPLKEAKD 80 (273)
T ss_pred CeEEEecCCCcHHHHHHHHHHHHHHHHcCCEEEEecCccCCCHHHHHHHHHHHHHhCCCEEEEcCCChhhhHHHHHHHHH
Confidence 48999998877778899999999999999876555332 23554321 21 26899998877653222 1233
Q ss_pred CCCcccC
Q 014409 279 FLAPVIT 285 (425)
Q Consensus 279 f~kPViT 285 (425)
...|+|+
T Consensus 81 ~~ipvV~ 87 (273)
T cd06310 81 AGIPVVL 87 (273)
T ss_pred CCCCEEE
Confidence 4457765
No 27
>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=61.05 E-value=25 Score=33.07 Aligned_cols=59 Identities=27% Similarity=0.366 Sum_probs=44.6
Q ss_pred eEEEEEcCCcccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHHH-------hcCCCCCCEEEEecCCC
Q 014409 210 IIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAK-------LANFPECDVFINVSCAQ 270 (425)
Q Consensus 210 ~iGIlvgTl~~q~~~~~i~~Lk~li~~~GKk~Y~~~vgkln~aK-------LaNF~eID~fV~vaCPr 270 (425)
+||+|+..+.-..+..+++.+++.++++|.+.-++. +.-++++ |.+ ..+|++|+.+|..
T Consensus 1 ~igvi~p~~~~~~~~~~~~g~~~~a~~~g~~~~~~~-~~~~~~~~~~~i~~~~~-~~vdgii~~~~~~ 66 (268)
T cd06270 1 TIGLVVSDLDGPFFGPLLSGVESVARKAGKHLIITA-GHHSAEKEREAIEFLLE-RRCDALILHSKAL 66 (268)
T ss_pred CEEEEEccccCcchHHHHHHHHHHHHHCCCEEEEEe-CCCchHHHHHHHHHHHH-cCCCEEEEecCCC
Confidence 489999998888889999999999999998765443 3444443 223 2699999998853
No 28
>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=60.73 E-value=25 Score=33.17 Aligned_cols=73 Identities=19% Similarity=0.247 Sum_probs=50.3
Q ss_pred EEEEEcC---CcccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHHH-------hcCCCCCCEEEEecCCCcccc-cccCC
Q 014409 211 IGVLVGT---LGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAK-------LANFPECDVFINVSCAQTALL-DSKEF 279 (425)
Q Consensus 211 iGIlvgT---l~~q~~~~~i~~Lk~li~~~GKk~Y~~~vgkln~aK-------LaNF~eID~fV~vaCPr~si~-d~~ef 279 (425)
||+|+.+ ++-..+..+++.+++.+++.|.+..+...+. +.++ |.+ ..+|++|+.++...+.. ..++-
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 5667788999999999999998887776653 3321 222 26999999887654322 22333
Q ss_pred CCcccC
Q 014409 280 LAPVIT 285 (425)
Q Consensus 280 ~kPViT 285 (425)
..|+|+
T Consensus 80 ~ipvV~ 85 (268)
T cd06277 80 GIPFVL 85 (268)
T ss_pred CCCEEE
Confidence 457664
No 29
>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=58.81 E-value=19 Score=34.01 Aligned_cols=60 Identities=17% Similarity=0.206 Sum_probs=44.1
Q ss_pred eEEEEEcCCcccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHHHhc----CC--CCCCEEEEecCCC
Q 014409 210 IIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKLA----NF--PECDVFINVSCAQ 270 (425)
Q Consensus 210 ~iGIlvgTl~~q~~~~~i~~Lk~li~~~GKk~Y~~~vgkln~aKLa----NF--~eID~fV~vaCPr 270 (425)
+||+|+....-..+..+++.+.+.+++.|....+. ...-++++.. .+ ..+|++++.+|..
T Consensus 1 ~Igvv~~~~~~~~~~~~~~~i~~~a~~~g~~~~~~-~~~~~~~~~~~~i~~l~~~~vdgii~~~~~~ 66 (269)
T cd06281 1 TIGCLVSDITNPLLAQLFSGAEDRLRAAGYSLLIA-NSLNDPERELEILRSFEQRRMDGIIIAPGDE 66 (269)
T ss_pred CEEEEecCCccccHHHHHHHHHHHHHHcCCEEEEE-eCCCChHHHHHHHHHHHHcCCCEEEEecCCC
Confidence 58999988877788899999999999999885443 3444554321 12 2699999998853
No 30
>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=58.62 E-value=35 Score=28.97 Aligned_cols=55 Identities=16% Similarity=0.284 Sum_probs=43.3
Q ss_pred EEEEEcCCcccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHHHhcCCCCCCEEEEecCCC
Q 014409 211 IGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKLANFPECDVFINVSCAQ 270 (425)
Q Consensus 211 iGIlvgTl~~q~~~~~i~~Lk~li~~~GKk~Y~~~vgkln~aKLaNF~eID~fV~vaCPr 270 (425)
|-|+.+|.. .+...+++.|.+.+.+.|.+.-++-+.+.++.+|.+ .|.+|+ ++|-
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 577899999999999999999999999999988866 465544 4443
No 31
>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=58.53 E-value=12 Score=36.51 Aligned_cols=61 Identities=20% Similarity=0.251 Sum_probs=47.9
Q ss_pred CeEEEEEcCCcccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHHH------hcCCCCCCEEEEecCCCc
Q 014409 209 NIIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAK------LANFPECDVFINVSCAQT 271 (425)
Q Consensus 209 ~~iGIlvgTl~~q~~~~~i~~Lk~li~~~GKk~Y~~~vgkln~aK------LaNF~eID~fV~vaCPr~ 271 (425)
++||+|+..+.-..+.++++-+.+.++++|....++..+. ++++ |.+- .+|.+|+.+....
T Consensus 2 ~~IGvivp~~~npff~~ii~gIe~~a~~~Gy~l~l~~t~~-~~~~e~~i~~l~~~-~vDGiI~~s~~~~ 68 (279)
T PF00532_consen 2 KTIGVIVPDISNPFFAEIIRGIEQEAREHGYQLLLCNTGD-DEEKEEYIELLLQR-RVDGIILASSEND 68 (279)
T ss_dssp CEEEEEESSSTSHHHHHHHHHHHHHHHHTTCEEEEEEETT-THHHHHHHHHHHHT-TSSEEEEESSSCT
T ss_pred CEEEEEECCCCCcHHHHHHHHHHHHHHHcCCEEEEecCCC-chHHHHHHHHHHhc-CCCEEEEecccCC
Confidence 6899999999988899999999999999999887766663 3332 2232 6999999955443
No 32
>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=58.48 E-value=18 Score=33.70 Aligned_cols=75 Identities=20% Similarity=0.214 Sum_probs=50.9
Q ss_pred eEEEEEcCCcccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHHH-------hcCCCCCCEEEEecCCCc-cc-ccccCCC
Q 014409 210 IIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAK-------LANFPECDVFINVSCAQT-AL-LDSKEFL 280 (425)
Q Consensus 210 ~iGIlvgTl~~q~~~~~i~~Lk~li~~~GKk~Y~~~vgkln~aK-------LaNF~eID~fV~vaCPr~-si-~d~~ef~ 280 (425)
+||+|+....-..+..+++.+++.+++.|.+..++. ..-++++ |.+ ..+|++|++++... .+ ...++..
T Consensus 1 ~igvv~~~~~~~~~~~~~~gi~~~~~~~g~~~~~~~-~~~~~~~~~~~i~~l~~-~~~dgii~~~~~~~~~~~~~~~~~~ 78 (259)
T cd01542 1 LIGVIVPRLDSFSTSRTVKGILAALYENGYQMLLMN-TNFSIEKEIEALELLAR-QKVDGIILLATTITDEHREAIKKLN 78 (259)
T ss_pred CeEEEecCCccchHHHHHHHHHHHHHHCCCEEEEEe-CCCCHHHHHHHHHHHHh-cCCCEEEEeCCCCCHHHHHHHhcCC
Confidence 489999887766778999999999999998865543 3445544 223 36999999876432 11 2234455
Q ss_pred CcccCH
Q 014409 281 APVITP 286 (425)
Q Consensus 281 kPViTP 286 (425)
.|||+-
T Consensus 79 ipvv~~ 84 (259)
T cd01542 79 VPVVVV 84 (259)
T ss_pred CCEEEE
Confidence 687753
No 33
>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=58.46 E-value=31 Score=32.16 Aligned_cols=74 Identities=16% Similarity=0.238 Sum_probs=49.6
Q ss_pred eEEEEEcCCcccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHHH-------hcCCCCCCEEEEecCCCcc--cccccCCC
Q 014409 210 IIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAK-------LANFPECDVFINVSCAQTA--LLDSKEFL 280 (425)
Q Consensus 210 ~iGIlvgTl~~q~~~~~i~~Lk~li~~~GKk~Y~~~vgkln~aK-------LaNF~eID~fV~vaCPr~s--i~d~~ef~ 280 (425)
+||+|+....-..+..+++.+++.+++.|....++. ..-++++ |.+- .+|.+++.++.... +...++-.
T Consensus 1 ~igvi~~~~~~~~~~~~~~~i~~~a~~~g~~~~~~~-~~~~~~~~~~~~~~l~~~-~~dgiii~~~~~~~~~l~~~~~~~ 78 (267)
T cd06283 1 LIGVIVADITNPFSSLVLKGIEDVCRAHGYQVLVCN-SDNDPEKEKEYLESLLAY-QVDGLIVNPTGNNKELYQRLAKNG 78 (267)
T ss_pred CEEEEecCCccccHHHHHHHHHHHHHHcCCEEEEEc-CCCCHHHHHHHHHHHHHc-CcCEEEEeCCCCChHHHHHHhcCC
Confidence 589999887777888999999999999997764443 3334443 3332 68999998764332 12223445
Q ss_pred CcccC
Q 014409 281 APVIT 285 (425)
Q Consensus 281 kPViT 285 (425)
.|||+
T Consensus 79 ipvV~ 83 (267)
T cd06283 79 KPVVL 83 (267)
T ss_pred CCEEE
Confidence 57665
No 34
>PRK12321 cobN cobaltochelatase subunit CobN; Reviewed
Probab=58.44 E-value=6.4 Score=46.11 Aligned_cols=28 Identities=36% Similarity=0.805 Sum_probs=0.0
Q ss_pred cccCCcEEEEec-CC---------------CCCCC--CCCCeEEEc
Q 014409 17 SHVDADCVIHYG-HT---------------CLSPT--STLPAFFVF 44 (425)
Q Consensus 17 ~hv~aD~iVHyG-ha---------------Clsp~--~~lpviYVf 44 (425)
++++||+|||+| |- |.+.. ..+|.+|.|
T Consensus 522 ~~~~ADAiiH~GtHGtlEwLPGK~vgLS~~c~Pd~lig~lP~iYpy 567 (1100)
T PRK12321 522 REVGVDALIHLGAHGTLEWLPGKAVALSPACWPEALTGALPVIYPF 567 (1100)
T ss_pred hhcCCCEEEECCCCcccccCCCccccCCcccChHHHhCCCCEEEEE
No 35
>PRK10653 D-ribose transporter subunit RbsB; Provisional
Probab=57.71 E-value=12 Score=36.17 Aligned_cols=63 Identities=17% Similarity=0.199 Sum_probs=45.6
Q ss_pred hcCCeEEEEEcCCcccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHHHhc----CC--CCCCEEEEecCC
Q 014409 206 KDANIIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKLA----NF--PECDVFINVSCA 269 (425)
Q Consensus 206 ~~A~~iGIlvgTl~~q~~~~~i~~Lk~li~~~GKk~Y~~~vgkln~aKLa----NF--~eID~fV~vaCP 269 (425)
++.++||+|+.++.-..+..+++.+++.++++|.+..++..+ -++++.. ++ ..+|+.++.++.
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 467899999998877778899999999999999777655443 2344332 22 258888887654
No 36
>PRK10014 DNA-binding transcriptional repressor MalI; Provisional
Probab=57.34 E-value=31 Score=33.98 Aligned_cols=79 Identities=22% Similarity=0.311 Sum_probs=53.4
Q ss_pred HhcCCeEEEEEcCCcccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHHH-------hcCCCCCCEEEEecCCCcc--c-c
Q 014409 205 AKDANIIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAK-------LANFPECDVFINVSCAQTA--L-L 274 (425)
Q Consensus 205 a~~A~~iGIlvgTl~~q~~~~~i~~Lk~li~~~GKk~Y~~~vgkln~aK-------LaNF~eID~fV~vaCPr~s--i-~ 274 (425)
.+..++||+|+..+.-..+..+++.+.+.++++|...+++..+ -++++ |.+- .+|++++.+..... + .
T Consensus 61 ~~~~~~Igvv~~~~~~~~~~~i~~gi~~~a~~~g~~~~~~~~~-~~~~~~~~~~~~l~~~-~vdgiIi~~~~~~~~~~~~ 138 (342)
T PRK10014 61 GGQSGVIGLIVRDLSAPFYAELTAGLTEALEAQGRMVFLLQGG-KDGEQLAQRFSTLLNQ-GVDGVVIAGAAGSSDDLRE 138 (342)
T ss_pred cCCCCEEEEEeCCCccchHHHHHHHHHHHHHHcCCEEEEEeCC-CCHHHHHHHHHHHHhC-CCCEEEEeCCCCCcHHHHH
Confidence 3456799999998877778899999999999999776655433 34443 3232 58999998765321 1 1
Q ss_pred cccCCCCcccC
Q 014409 275 DSKEFLAPVIT 285 (425)
Q Consensus 275 d~~ef~kPViT 285 (425)
..++...|+|+
T Consensus 139 ~l~~~~iPvV~ 149 (342)
T PRK10014 139 MAEEKGIPVVF 149 (342)
T ss_pred HHhhcCCCEEE
Confidence 23345567775
No 37
>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=56.91 E-value=20 Score=33.68 Aligned_cols=59 Identities=19% Similarity=0.233 Sum_probs=43.2
Q ss_pred eEEEEEcCCcccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHHHhc----CC--CCCCEEEEecCC
Q 014409 210 IIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKLA----NF--PECDVFINVSCA 269 (425)
Q Consensus 210 ~iGIlvgTl~~q~~~~~i~~Lk~li~~~GKk~Y~~~vgkln~aKLa----NF--~eID~fV~vaCP 269 (425)
+||+|+..+.-..+..+++.+.+.+++.|....++. ..-++++.. ++ ..+|.+++.+|.
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 589999888777778899999999999997654433 455665432 22 158999999875
No 38
>PRK11303 DNA-binding transcriptional regulator FruR; Provisional
Probab=56.41 E-value=30 Score=33.82 Aligned_cols=62 Identities=15% Similarity=0.253 Sum_probs=45.0
Q ss_pred hcCCeEEEEEcCCcccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHHH-------hcCCCCCCEEEEecCC
Q 014409 206 KDANIIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAK-------LANFPECDVFINVSCA 269 (425)
Q Consensus 206 ~~A~~iGIlvgTl~~q~~~~~i~~Lk~li~~~GKk~Y~~~vgkln~aK-------LaNF~eID~fV~vaCP 269 (425)
+..++||+|+..+.-..+..+++.+.+.++++|....++..+ -++++ |.+- .+|.+++.++.
T Consensus 59 ~~~~~Igvv~~~~~~~~~~~l~~gi~~~~~~~g~~~~~~~~~-~~~~~~~~~~~~l~~~-~vdgiIi~~~~ 127 (328)
T PRK11303 59 GRTRSIGLIIPDLENTSYARIAKYLERQARQRGYQLLIACSD-DQPDNEMRCAEHLLQR-QVDALIVSTSL 127 (328)
T ss_pred CCCceEEEEeCCCCCchHHHHHHHHHHHHHHcCCEEEEEeCC-CCHHHHHHHHHHHHHc-CCCEEEEcCCC
Confidence 346799999988776778899999999999999886655443 23332 2232 68999997763
No 39
>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=56.12 E-value=25 Score=32.97 Aligned_cols=59 Identities=19% Similarity=0.268 Sum_probs=42.1
Q ss_pred eEEEEEcCCcccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHHHhcCC------CCCCEEEEecCC
Q 014409 210 IIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKLANF------PECDVFINVSCA 269 (425)
Q Consensus 210 ~iGIlvgTl~~q~~~~~i~~Lk~li~~~GKk~Y~~~vgkln~aKLaNF------~eID~fV~vaCP 269 (425)
+||+|+..+..-.+..+++.+++.+++.|.+..++.. .-++++-..+ ..+|++|+.++.
T Consensus 1 ~I~vi~~~~~~~~~~~~~~gi~~~~~~~g~~~~~~~~-~~~~~~~~~~i~~~~~~~~dgiii~~~~ 65 (265)
T cd06291 1 LIGLIVPTISNPFFSELARAVEKELYKKGYKLILCNS-DNDPEKEREYLEMLRQNQVDGIIAGTHN 65 (265)
T ss_pred CEEEEECCCCChhHHHHHHHHHHHHHHCCCeEEEecC-CccHHHHHHHHHHHHHcCCCEEEEecCC
Confidence 5899998888777889999999999999977654433 3344432221 158999998874
No 40
>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=55.04 E-value=13 Score=35.84 Aligned_cols=75 Identities=19% Similarity=0.233 Sum_probs=47.4
Q ss_pred eEEEEEcCCcccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHHHhc----CC--CCCCEEEEecCCCcc----cccccCC
Q 014409 210 IIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKLA----NF--PECDVFINVSCAQTA----LLDSKEF 279 (425)
Q Consensus 210 ~iGIlvgTl~~q~~~~~i~~Lk~li~~~GKk~Y~~~vgkln~aKLa----NF--~eID~fV~vaCPr~s----i~d~~ef 279 (425)
+||+|+....-..+..+++.+++.+++.|....++..+ -++++.. ++ ..+|.+++++|.... +...++.
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 47888887765566788888888888888776655443 3555421 11 258988888875432 1123445
Q ss_pred CCcccC
Q 014409 280 LAPVIT 285 (425)
Q Consensus 280 ~kPViT 285 (425)
-.|||+
T Consensus 80 ~ipvV~ 85 (288)
T cd01538 80 GIPVIA 85 (288)
T ss_pred CCCEEE
Confidence 567764
No 41
>PRK05723 flavodoxin; Provisional
Probab=54.77 E-value=38 Score=30.21 Aligned_cols=55 Identities=15% Similarity=0.205 Sum_probs=40.8
Q ss_pred eEEEEEcCCcccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHHHhcCCCCCCEEEEecCC
Q 014409 210 IIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKLANFPECDVFINVSCA 269 (425)
Q Consensus 210 ~iGIlvgTl~~q~~~~~i~~Lk~li~~~GKk~Y~~~vgkln~aKLaNF~eID~fV~vaCP 269 (425)
.++|+.||-+| +...++++|.+.+++.|.+...+ ...+++.|..+ +.|.. ++.|+
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 68999999864 56789999999999999988653 45777888777 34543 44444
No 42
>PRK14987 gluconate operon transcriptional regulator; Provisional
Probab=53.34 E-value=32 Score=33.84 Aligned_cols=79 Identities=19% Similarity=0.224 Sum_probs=51.1
Q ss_pred hcCCeEEEEEcCCcccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHHH----hcCC--CCCCEEEEecCCCcc--ccccc
Q 014409 206 KDANIIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAK----LANF--PECDVFINVSCAQTA--LLDSK 277 (425)
Q Consensus 206 ~~A~~iGIlvgTl~~q~~~~~i~~Lk~li~~~GKk~Y~~~vgkln~aK----LaNF--~eID~fV~vaCPr~s--i~d~~ 277 (425)
+..++||+++..+.-..+..+++.+.+.++++|.+..+...+ -++++ +.++ ..+|.+++.++.... +....
T Consensus 61 ~~~~~Igvi~~~~~~~~~~~~~~gi~~~~~~~g~~~~~~~~~-~~~~~~~~~~~~~~~~~vdgiI~~~~~~~~~~~~~l~ 139 (331)
T PRK14987 61 ATSRAIGVLLPSLTNQVFAEVLRGIESVTDAHGYQTMLAHYG-YKPEMEQERLESMLSWNIDGLILTERTHTPRTLKMIE 139 (331)
T ss_pred CCCCEEEEEeCCCcchhHHHHHHHHHHHHHHCCCEEEEecCC-CCHHHHHHHHHHHHhcCCCEEEEcCCCCCHHHHHHHH
Confidence 456799999998877778899999999999999776544333 23322 2222 269999997653221 11123
Q ss_pred CCCCcccC
Q 014409 278 EFLAPVIT 285 (425)
Q Consensus 278 ef~kPViT 285 (425)
+...|+|+
T Consensus 140 ~~~iPvV~ 147 (331)
T PRK14987 140 VAGIPVVE 147 (331)
T ss_pred hCCCCEEE
Confidence 34557664
No 43
>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=52.93 E-value=41 Score=31.41 Aligned_cols=60 Identities=22% Similarity=0.271 Sum_probs=43.6
Q ss_pred eEEEEEcCCcccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHHH-------hcCCCCCCEEEEecCCCc
Q 014409 210 IIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAK-------LANFPECDVFINVSCAQT 271 (425)
Q Consensus 210 ~iGIlvgTl~~q~~~~~i~~Lk~li~~~GKk~Y~~~vgkln~aK-------LaNF~eID~fV~vaCPr~ 271 (425)
+||+|+....-..+..+++.+++.+++.|....++.... ++++ |.+- .+|.+++.++...
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 589999877666778899999999999998777765532 4432 3333 5899999887543
No 44
>PRK06703 flavodoxin; Provisional
Probab=52.79 E-value=46 Score=29.11 Aligned_cols=56 Identities=11% Similarity=0.049 Sum_probs=43.1
Q ss_pred eEEEEEcCCcccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHHHhcCCCCCCEEEEecCCC
Q 014409 210 IIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKLANFPECDVFINVSCAQ 270 (425)
Q Consensus 210 ~iGIlvgTl~~q~~~~~i~~Lk~li~~~GKk~Y~~~vgkln~aKLaNF~eID~fV~vaCPr 270 (425)
.+.|+.+|.. -+...+++.|.+.|.+.|.+.-++-+.+..+..|.+ .|. |+++||=
T Consensus 3 kv~IiY~S~t-GnT~~iA~~ia~~l~~~g~~v~~~~~~~~~~~~l~~---~d~-viigspt 58 (151)
T PRK06703 3 KILIAYASMS-GNTEDIADLIKVSLDAFDHEVVLQEMDGMDAEELLA---YDG-IILGSYT 58 (151)
T ss_pred eEEEEEECCC-chHHHHHHHHHHHHHhcCCceEEEehhhCCHHHHhc---CCc-EEEEECC
Confidence 5789999954 567899999999999999998888888887776654 455 4455553
No 45
>PRK11041 DNA-binding transcriptional regulator CytR; Provisional
Probab=52.78 E-value=48 Score=31.95 Aligned_cols=62 Identities=10% Similarity=0.099 Sum_probs=45.4
Q ss_pred HhcCCeEEEEEcCCcccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHHH-------hcCCCCCCEEEEecC
Q 014409 205 AKDANIIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAK-------LANFPECDVFINVSC 268 (425)
Q Consensus 205 a~~A~~iGIlvgTl~~q~~~~~i~~Lk~li~~~GKk~Y~~~vgkln~aK-------LaNF~eID~fV~vaC 268 (425)
....++||+|+..+.-..+..+++.+++.+++.|....++.... +.++ |.. ..+|.+++.++
T Consensus 32 ~~~~~~ig~v~~~~~~~~~~~~~~gi~~~~~~~g~~~~~~~~~~-~~~~~~~~i~~l~~-~~vDgiIi~~~ 100 (309)
T PRK11041 32 RNESRTILVIVPDICDPFFSEIIRGIEVTAAEHGYLVLIGDCAH-QNQQEKTFVNLIIT-KQIDGMLLLGS 100 (309)
T ss_pred cCCCcEEEEEeCCCcCccHHHHHHHHHHHHHHCCCEEEEEeCCC-ChHHHHHHHHHHHH-cCCCEEEEecC
Confidence 34568999999887767788999999999999998776654332 3332 222 26899999876
No 46
>PLN03069 magnesiumprotoporphyrin-IX chelatase subunit H; Provisional
Probab=52.14 E-value=9.7 Score=45.19 Aligned_cols=28 Identities=29% Similarity=0.782 Sum_probs=0.0
Q ss_pred cccCCcEEEEec-CC---------------CCCC--CCCCCeEEEc
Q 014409 17 SHVDADCVIHYG-HT---------------CLSP--TSTLPAFFVF 44 (425)
Q Consensus 17 ~hv~aD~iVHyG-ha---------------Clsp--~~~lpviYVf 44 (425)
+..+||+||||| |- |.+. ...+|.||.|
T Consensus 600 ~~F~ADAviH~GtHGtlEwLPGK~vGLS~~cwPd~liGdlPniY~Y 645 (1220)
T PLN03069 600 KIFKADAVLHFGTHGSLEFMPGKQVGMSDACYPDSLIGNIPNVYYY 645 (1220)
T ss_pred hhcCCCEEEEcCCCCCcccCCCccccCCcccChHHHhCCCCEEeEE
No 47
>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=52.11 E-value=36 Score=33.28 Aligned_cols=62 Identities=21% Similarity=0.423 Sum_probs=45.6
Q ss_pred hcCCeEEEEEcCCcccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHHH----hcCC--CCCCEEEEecC
Q 014409 206 KDANIIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAK----LANF--PECDVFINVSC 268 (425)
Q Consensus 206 ~~A~~iGIlvgTl~~q~~~~~i~~Lk~li~~~GKk~Y~~~vgkln~aK----LaNF--~eID~fV~vaC 268 (425)
+..++||+++..+.-..+..+++.+.+.++++|....+...+. ++++ +.++ ..+|..|+.++
T Consensus 58 ~~~~~Igvi~~~~~~~~~~~~~~~i~~~~~~~gy~~~i~~~~~-~~~~~~~~~~~l~~~~vdgiIi~~~ 125 (327)
T TIGR02417 58 GRSRTIGLVIPDLENYSYARIAKELEQQCREAGYQLLIACSDD-NPDQEKVVIENLLARQVDALIVASC 125 (327)
T ss_pred CCCceEEEEeCCCCCccHHHHHHHHHHHHHHCCCEEEEEeCCC-CHHHHHHHHHHHHHcCCCEEEEeCC
Confidence 3467999999888777888999999999999998876655543 4432 2222 26899888765
No 48
>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=52.02 E-value=17 Score=34.96 Aligned_cols=75 Identities=15% Similarity=0.138 Sum_probs=46.9
Q ss_pred eEEEEEcCCcccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHHHhc----CC--CCCCEEEEecCCCcccc----cccCC
Q 014409 210 IIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKLA----NF--PECDVFINVSCAQTALL----DSKEF 279 (425)
Q Consensus 210 ~iGIlvgTl~~q~~~~~i~~Lk~li~~~GKk~Y~~~vgkln~aKLa----NF--~eID~fV~vaCPr~si~----d~~ef 279 (425)
+||+|+.++.-..+..+++.+++.+++.|.....+..++-++++.. .+ ..+|.+|+.+|.....+ ..++.
T Consensus 1 ~i~~i~~~~~~~~~~~~~~gi~~~a~~~g~~~~~~~~~~~~~~~~~~~l~~~~~~~~dgiii~~~~~~~~~~~i~~~~~~ 80 (294)
T cd06316 1 KAAIVMHTSGSDWSNAQVRGAKDEFAKLGIEVVATTDAQFDPAKQVADIETTISQKPDIIISIPVDPVSTAAAYKKVAEA 80 (294)
T ss_pred CeEEEecCCCChHHHHHHHHHHHHHHHcCCEEEEecCCCCCHHHHHHHHHHHHHhCCCEEEEcCCCchhhhHHHHHHHHc
Confidence 4788888766445567888888889888877654434555554321 11 25899999887643222 23344
Q ss_pred CCccc
Q 014409 280 LAPVI 284 (425)
Q Consensus 280 ~kPVi 284 (425)
-.|||
T Consensus 81 ~iPvV 85 (294)
T cd06316 81 GIKLV 85 (294)
T ss_pred CCcEE
Confidence 45665
No 49
>PRK07308 flavodoxin; Validated
Probab=51.92 E-value=61 Score=28.20 Aligned_cols=57 Identities=5% Similarity=0.105 Sum_probs=43.8
Q ss_pred eEEEEEcCCcccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHHHhcCCCCCCEEEEecCCCc
Q 014409 210 IIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKLANFPECDVFINVSCAQT 271 (425)
Q Consensus 210 ~iGIlvgTl~~q~~~~~i~~Lk~li~~~GKk~Y~~~vgkln~aKLaNF~eID~fV~vaCPr~ 271 (425)
.+-|+-+|.. -+...+++.|.+.+++.|...-++-+.+..+..|.. .|++++ +||--
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 4678999965 567899999999999999888778888877776644 466554 88764
No 50
>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=51.77 E-value=36 Score=32.03 Aligned_cols=57 Identities=12% Similarity=0.139 Sum_probs=41.7
Q ss_pred eEEEEEcCCcccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHHH-------hcCCCCCCEEEEecC
Q 014409 210 IIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAK-------LANFPECDVFINVSC 268 (425)
Q Consensus 210 ~iGIlvgTl~~q~~~~~i~~Lk~li~~~GKk~Y~~~vgkln~aK-------LaNF~eID~fV~vaC 268 (425)
.||+|+..+.--.+..+++.+.+.+++.|....++. ..-++++ |.+ ..+|..+++++
T Consensus 1 ~Igvi~~~~~~~~~~~~~~gi~~~~~~~g~~~~~~~-~~~~~~~~~~~i~~l~~-~~vdgiIi~~~ 64 (273)
T cd06292 1 LVGLLVPELSNPIFPAFAEAIEAALAQYGYTVLLCN-TYRGGVSEADYVEDLLA-RGVRGVVFISS 64 (273)
T ss_pred CEEEEeCCCcCchHHHHHHHHHHHHHHCCCEEEEEe-CCCChHHHHHHHHHHHH-cCCCEEEEeCC
Confidence 489999988877888999999999999997764433 3334432 223 26899999865
No 51
>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=51.72 E-value=57 Score=26.70 Aligned_cols=68 Identities=18% Similarity=0.171 Sum_probs=49.2
Q ss_pred EEEEEcCCcccCcHHHHHHHHHHHHHcCCcEEEEE------cCCCCHHHhcCCCCCCEEEEecCCCcccccccCC-CCcc
Q 014409 211 IGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLV------MGKPNPAKLANFPECDVFINVSCAQTALLDSKEF-LAPV 283 (425)
Q Consensus 211 iGIlvgTl~~q~~~~~i~~Lk~li~~~GKk~Y~~~------vgkln~aKLaNF~eID~fV~vaCPr~si~d~~ef-~kPV 283 (425)
++|+.+.-|.....-+.+.|++.++++|.+.-+-. .+.++.+.++ +.|.+++++..... + .+| -||+
T Consensus 2 ~~i~ac~~G~a~s~laa~~L~~aa~~~g~~~~ve~~~~~g~~~~l~~~~i~---~Ad~vi~~~~~~~~--~-~rf~gk~v 75 (96)
T cd05569 2 VAVTACPTGIAHTYMAAEALEKAAKKLGWEIKVETQGSLGIENELTAEDIA---EADAVILAADVPVD--D-ERFAGKRV 75 (96)
T ss_pred EEEEECCCchhHHHHHHHHHHHHHHHCCCeEEEEEecCcCccCcCCHHHHh---hCCEEEEecCCCCc--h-hhhCCCeE
Confidence 57788888888888899999999999999966443 3345555554 45999999998743 3 333 3565
Q ss_pred c
Q 014409 284 I 284 (425)
Q Consensus 284 i 284 (425)
+
T Consensus 76 ~ 76 (96)
T cd05569 76 Y 76 (96)
T ss_pred E
Confidence 4
No 52
>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=51.64 E-value=27 Score=32.67 Aligned_cols=61 Identities=16% Similarity=0.182 Sum_probs=44.1
Q ss_pred eEEEEEcCCcccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHH---H----hcCCCCCCEEEEecCCCc
Q 014409 210 IIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPA---K----LANFPECDVFINVSCAQT 271 (425)
Q Consensus 210 ~iGIlvgTl~~q~~~~~i~~Lk~li~~~GKk~Y~~~vgkln~a---K----LaNF~eID~fV~vaCPr~ 271 (425)
+||+|+.+..-..+..+++.+++.+++.|....++..+.-.++ + |.+- .+|+.++.+|...
T Consensus 1 ~i~vi~~~~~~~~~~~~~~gi~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~-~vdgiii~~~~~~ 68 (264)
T cd01574 1 TIGVVTTDLALHGPSSTLAAIESAAREAGYAVTLSMLAEADEEALRAAVRRLLAQ-RVDGVIVNAPLDD 68 (264)
T ss_pred CEEEEeCCCCcccHHHHHHHHHHHHHHCCCeEEEEeCCCCchHHHHHHHHHHHhc-CCCEEEEeCCCCC
Confidence 5899998877667789999999999999988766655433322 1 2222 5999999887543
No 53
>PRK10703 DNA-binding transcriptional repressor PurR; Provisional
Probab=51.60 E-value=37 Score=33.45 Aligned_cols=63 Identities=13% Similarity=0.125 Sum_probs=46.2
Q ss_pred HhcCCeEEEEEcCCcccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHHHhcC----C--CCCCEEEEecC
Q 014409 205 AKDANIIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKLAN----F--PECDVFINVSC 268 (425)
Q Consensus 205 a~~A~~iGIlvgTl~~q~~~~~i~~Lk~li~~~GKk~Y~~~vgkln~aKLaN----F--~eID~fV~vaC 268 (425)
.+..++||+|+..+.-..+..+++.+.+.+++.|.+.+++..+ -++++..+ + ..+|++++.+.
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 3456799999998877778899999999999999887766543 34544221 1 15899988764
No 54
>PLN03241 magnesium chelatase subunit H; Provisional
Probab=51.55 E-value=10 Score=45.47 Aligned_cols=28 Identities=39% Similarity=0.710 Sum_probs=0.0
Q ss_pred cccCCcEEEEec-CC---------------CCCC--CCCCCeEEEc
Q 014409 17 SHVDADCVIHYG-HT---------------CLSP--TSTLPAFFVF 44 (425)
Q Consensus 17 ~hv~aD~iVHyG-ha---------------Clsp--~~~lpviYVf 44 (425)
+..+||+||||| |- |.+. ...+|.||+|
T Consensus 663 ~~F~ADAvIHfGtHGtLEwLPGK~vGLS~~cwPd~LiGdlPniY~Y 708 (1353)
T PLN03241 663 DGYGADAVIHFGMHGTVEWLPGQPLGNDRLSWSDELLGGLPNVYVY 708 (1353)
T ss_pred cccCCCeEEEccCCcCcccCCCccccCCcccChHHHhCCCCEEEEE
No 55
>COG2984 ABC-type uncharacterized transport system, periplasmic component [General function prediction only]
Probab=51.25 E-value=58 Score=32.90 Aligned_cols=110 Identities=21% Similarity=0.299 Sum_probs=73.2
Q ss_pred HHHHHHHHHHH-hcCCeEEEEEcCCcccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCH--HHhcCC-CCCCEEEEecCCC
Q 014409 195 LKRRYYLVEKA-KDANIIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNP--AKLANF-PECDVFINVSCAQ 270 (425)
Q Consensus 195 L~rRy~~I~ka-~~A~~iGIlvgTl~~q~~~~~i~~Lk~li~~~GKk~Y~~~vgkln~--aKLaNF-~eID~fV~vaCPr 270 (425)
+.++..+|.+. =+|++||++-+. +-++...+++.|++.++++|.+.+...+.+.|. .-..+. ...|++..- |--
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 222 (322)
T COG2984 145 VAQQIELIKALLPNAKSIGVLYNP-GEANSVSLVEELKKEARKAGLEVVEAAVTSVNDIPRAVQALLGKVDVIYIP-TDN 222 (322)
T ss_pred HHHHHHHHHHhCCCCeeEEEEeCC-CCcccHHHHHHHHHHHHHCCCEEEEEecCcccccHHHHHHhcCCCcEEEEe-cch
Confidence 45666666644 469999999987 457999999999999999999999999988873 333344 357766443 222
Q ss_pred c------ccc-cccCCCCcccCHHHHHHhhCCCCccccceeeccccc
Q 014409 271 T------ALL-DSKEFLAPVITPFEAMLAFGRGTQWTGAYVMEFRDL 310 (425)
Q Consensus 271 ~------si~-d~~ef~kPViTP~ElevAL~~~~~W~g~y~~Df~~l 310 (425)
+ ++. -......||+++-+-.+-=+. .-.+-.||.++
T Consensus 223 ~i~s~~~~l~~~a~~~kiPli~sd~~~V~~Ga----~aA~gvdy~~~ 265 (322)
T COG2984 223 LIVSAIESLLQVANKAKIPLIASDTSSVKEGA----LAALGVDYKDL 265 (322)
T ss_pred HHHHHHHHHHHHHHHhCCCeecCCHHHHhcCc----ceeeccCHHHH
Confidence 2 111 244567788877766554222 13445555554
No 56
>PRK13405 bchH magnesium chelatase subunit H; Provisional
Probab=50.69 E-value=10 Score=44.83 Aligned_cols=28 Identities=32% Similarity=0.844 Sum_probs=0.0
Q ss_pred cccCCcEEEEec-CC---------------CCCC--CCCCCeEEEc
Q 014409 17 SHVDADCVIHYG-HT---------------CLSP--TSTLPAFFVF 44 (425)
Q Consensus 17 ~hv~aD~iVHyG-ha---------------Clsp--~~~lpviYVf 44 (425)
+..+||+||||| |- |.+. ...+|.||.|
T Consensus 593 ~~F~ADAviH~GtHGtlEwLPGK~vGLS~~cwPd~liGdlP~iY~Y 638 (1209)
T PRK13405 593 EDFGADAVLHFGTHGALEFMPGKQAGLSAACWPDRLIGDLPNVYLY 638 (1209)
T ss_pred hhcCCCEEEECCCCcccccCCCccccCCcccChHHHhCCCCEEEEE
No 57
>TIGR02257 cobalto_cobN cobaltochelatase, CobN subunit.
Probab=50.41 E-value=10 Score=44.50 Aligned_cols=28 Identities=32% Similarity=0.761 Sum_probs=0.0
Q ss_pred cccCCcEEEEec-CC---------------CCCCC--CCCCeEEEc
Q 014409 17 SHVDADCVIHYG-HT---------------CLSPT--STLPAFFVF 44 (425)
Q Consensus 17 ~hv~aD~iVHyG-ha---------------Clsp~--~~lpviYVf 44 (425)
+..+||+|||+| |- |.+.. ..+|.||.|
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 58
>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=50.31 E-value=27 Score=33.13 Aligned_cols=62 Identities=13% Similarity=0.061 Sum_probs=43.2
Q ss_pred eEEEEEcCCcccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCH--HHhcC-C--CCCCEEEEecCCCc
Q 014409 210 IIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNP--AKLAN-F--PECDVFINVSCAQT 271 (425)
Q Consensus 210 ~iGIlvgTl~~q~~~~~i~~Lk~li~~~GKk~Y~~~vgkln~--aKLaN-F--~eID~fV~vaCPr~ 271 (425)
+||+|+..+....+..+++.+.+.+++.|....+........ +.+.+ + ..+|.+++.++...
T Consensus 1 ~Igvi~p~~~~~~~~~~~~~i~~~~~~~gy~~~~~~~~~~~~~~~~~~~~l~~~~vdgvi~~~~~~~ 67 (269)
T cd06297 1 TISVLLPVVATEFYRRLLEGIEGALLEQRYDLALFPLLSLARLKRYLESTTLAYLTDGLLLASYDLT 67 (269)
T ss_pred CEEEEeCCCcChhHHHHHHHHHHHHHHCCCEEEEEeCCCcHHHHHHHHHHHHhcCCCEEEEecCccC
Confidence 589999877767788999999999999998877766553211 11211 2 14899999876533
No 59
>PRK05989 cobN cobaltochelatase subunit CobN; Reviewed
Probab=50.30 E-value=10 Score=45.16 Aligned_cols=28 Identities=36% Similarity=0.771 Sum_probs=0.0
Q ss_pred cccCCcEEEEec-CC---------------CCCCC--CCCCeEEEc
Q 014409 17 SHVDADCVIHYG-HT---------------CLSPT--STLPAFFVF 44 (425)
Q Consensus 17 ~hv~aD~iVHyG-ha---------------Clsp~--~~lpviYVf 44 (425)
+..+||+|||+| |- |.+.. ..+|.||.|
T Consensus 541 ~~f~ADAiIH~GtHGtlEwLPGK~vgLS~~c~Pd~llgdlP~iYpY 586 (1244)
T PRK05989 541 EGFGADAVVHVGKHGNLEWLPGKSVGLSADCYPDAALGDLPHLYPF 586 (1244)
T ss_pred hhcCCCEEEECCCCcccccCCCccccCCcccChHHHhCCCCEEEEE
No 60
>PRK12493 magnesium chelatase subunit H; Provisional
Probab=50.02 E-value=10 Score=45.31 Aligned_cols=28 Identities=36% Similarity=0.852 Sum_probs=0.0
Q ss_pred cccCCcEEEEec-CC---------------CCCCC--CCCCeEEEc
Q 014409 17 SHVDADCVIHYG-HT---------------CLSPT--STLPAFFVF 44 (425)
Q Consensus 17 ~hv~aD~iVHyG-ha---------------Clsp~--~~lpviYVf 44 (425)
+..+||+||||| |- |.+.. ..+|.||.|
T Consensus 587 ~~F~ADAviH~GtHGtlEwLPGK~vGLS~~cwPd~liG~lP~iY~Y 632 (1310)
T PRK12493 587 KVWGADAVLHFGTHGALEFMPGKQMGMSASCWPDRLIGSLPNFYYY 632 (1310)
T ss_pred hhcCCCEEEECCCCcCcccCCCccccCCcccChHHHhCCCCEEeEE
No 61
>PRK09004 FMN-binding protein MioC; Provisional
Probab=49.80 E-value=46 Score=29.39 Aligned_cols=53 Identities=17% Similarity=0.122 Sum_probs=38.1
Q ss_pred eEEEEEcCCcccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHHHhcCCCCCCEEEEecCC
Q 014409 210 IIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKLANFPECDVFINVSCA 269 (425)
Q Consensus 210 ~iGIlvgTl~~q~~~~~i~~Lk~li~~~GKk~Y~~~vgkln~aKLaNF~eID~fV~vaCP 269 (425)
++.|+.||-+| +...++++|.+.+++.|.+..++-+. .++.| ++.|.+ ++.||
T Consensus 3 ~i~I~ygS~tG-nae~~A~~l~~~~~~~g~~~~~~~~~--~~~~l---~~~~~l-i~~~s 55 (146)
T PRK09004 3 DITLISGSTLG-GAEYVADHLAEKLEEAGFSTETLHGP--LLDDL---SASGLW-LIVTS 55 (146)
T ss_pred eEEEEEEcCch-HHHHHHHHHHHHHHHcCCceEEeccC--CHHHh---ccCCeE-EEEEC
Confidence 68899999874 66789999999999999988765543 34544 444554 44444
No 62
>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=49.75 E-value=10 Score=44.87 Aligned_cols=28 Identities=36% Similarity=0.946 Sum_probs=0.0
Q ss_pred cccCCcEEEEec-CC---------------CCCCC--CCCCeEEEc
Q 014409 17 SHVDADCVIHYG-HT---------------CLSPT--STLPAFFVF 44 (425)
Q Consensus 17 ~hv~aD~iVHyG-ha---------------Clsp~--~~lpviYVf 44 (425)
+..+||+||||| |- |.+.. ..+|.+|+|
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 63
>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=49.27 E-value=35 Score=31.84 Aligned_cols=75 Identities=15% Similarity=0.148 Sum_probs=49.1
Q ss_pred eEEEEEcCCcccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHHH-------hcCCCCCCEEEEecCCCcc---cccccCC
Q 014409 210 IIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAK-------LANFPECDVFINVSCAQTA---LLDSKEF 279 (425)
Q Consensus 210 ~iGIlvgTl~~q~~~~~i~~Lk~li~~~GKk~Y~~~vgkln~aK-------LaNF~eID~fV~vaCPr~s---i~d~~ef 279 (425)
+||+++.....-.+..+++.+.+.+++.|.+..++..+ -++.+ |.+. .+|+.|+..+-... +....+.
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 58999988776667889999999999988777665443 34433 3332 68999887663221 1233445
Q ss_pred CCcccCH
Q 014409 280 LAPVITP 286 (425)
Q Consensus 280 ~kPViTP 286 (425)
..|+|+.
T Consensus 79 ~ipvV~~ 85 (266)
T cd06282 79 RVPYVLA 85 (266)
T ss_pred CCCEEEE
Confidence 5677655
No 64
>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=49.24 E-value=31 Score=32.23 Aligned_cols=59 Identities=19% Similarity=0.213 Sum_probs=44.7
Q ss_pred eEEEEEcCCcccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHHHh-------cCCCCCCEEEEecCCC
Q 014409 210 IIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKL-------ANFPECDVFINVSCAQ 270 (425)
Q Consensus 210 ~iGIlvgTl~~q~~~~~i~~Lk~li~~~GKk~Y~~~vgkln~aKL-------aNF~eID~fV~vaCPr 270 (425)
+||+|+...+-..+..+++.+++.+++.|....++. ..-++++. .+ ..+|++++.+|..
T Consensus 1 ~i~~i~~~~~~~~~~~i~~gi~~~~~~~g~~~~~~~-~~~~~~~~~~~i~~l~~-~~vdgiii~~~~~ 66 (260)
T cd06286 1 TIGVVLPYINHPYFSQLVDGIEKAALKHGYKVVLLQ-TNYDKEKELEYLELLKT-KQVDGLILCSREN 66 (260)
T ss_pred CEEEEeCCCCCchHHHHHHHHHHHHHHcCCEEEEEe-CCCChHHHHHHHHHHHH-cCCCEEEEeCCCC
Confidence 589999988877889999999999999998776554 34455433 22 2699999988743
No 65
>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=49.16 E-value=48 Score=30.90 Aligned_cols=59 Identities=15% Similarity=0.235 Sum_probs=44.8
Q ss_pred eEEEEEcCCcccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHHHhcCC------CCCCEEEEecCC
Q 014409 210 IIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKLANF------PECDVFINVSCA 269 (425)
Q Consensus 210 ~iGIlvgTl~~q~~~~~i~~Lk~li~~~GKk~Y~~~vgkln~aKLaNF------~eID~fV~vaCP 269 (425)
.||+|+.+++-..+..+++.+++.++++|.+..++.. .-++++..+. ..+|++++.+|.
T Consensus 1 ~i~~v~~~~~~~~~~~~~~~i~~~~~~~g~~~~~~~~-~~~~~~~~~~~~~~~~~~vdgiii~~~~ 65 (267)
T cd06284 1 MILVLVPDIANPFFSEILKGIEDEAREAGYGVLLGDT-RSDPEREQEYLDLLRRKQADGIILLDGS 65 (267)
T ss_pred CEEEEECCCCCccHHHHHHHHHHHHHHcCCeEEEecC-CCChHHHHHHHHHHHHcCCCEEEEecCC
Confidence 3789999988888899999999999999988765544 3455543322 268999998764
No 66
>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=49.13 E-value=43 Score=31.16 Aligned_cols=61 Identities=18% Similarity=0.242 Sum_probs=41.6
Q ss_pred eEEEEEcCCcccCcHHHHHHHHHHHHHcCCcEEEEEcCCCC-HHH-hcCC--CCCCEEEEecCCC
Q 014409 210 IIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPN-PAK-LANF--PECDVFINVSCAQ 270 (425)
Q Consensus 210 ~iGIlvgTl~~q~~~~~i~~Lk~li~~~GKk~Y~~~vgkln-~aK-LaNF--~eID~fV~vaCPr 270 (425)
+||+++....-..+..+++.+.+.+++.|.+...+....-. ..+ +.++ ..+|.+|+.+|..
T Consensus 1 ~I~~i~~~~~~~~~~~~~~~i~~~~~~~g~~~~~~~~~~~~~~~~~i~~~~~~~vdgiii~~~~~ 65 (266)
T cd06278 1 LIGVVVADLDNPFYSELLEALSRALQARGYQPLLINTDDDEDLDAALRQLLQYRVDGVIVTSGTL 65 (266)
T ss_pred CEEEEeCCCCCchHHHHHHHHHHHHHHCCCeEEEEcCCCCHHHHHHHHHHHHcCCCEEEEecCCC
Confidence 58899887766677789999999999999886555444221 111 1122 2689999988753
No 67
>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=48.53 E-value=59 Score=30.39 Aligned_cols=59 Identities=15% Similarity=0.078 Sum_probs=44.0
Q ss_pred eEEEEEcCCcccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCH-------HHhcCCCCCCEEEEecCC
Q 014409 210 IIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNP-------AKLANFPECDVFINVSCA 269 (425)
Q Consensus 210 ~iGIlvgTl~~q~~~~~i~~Lk~li~~~GKk~Y~~~vgkln~-------aKLaNF~eID~fV~vaCP 269 (425)
+||+++....-..+..+++-+++.+++.|....++..+.-.. ..|.+ ..+|+++++++-
T Consensus 1 ~I~vi~~~~~~~~~~~~~~gi~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~l~~-~~vdgiii~~~~ 66 (270)
T cd01545 1 LIGLLYDNPSPGYVSEIQLGALDACRDTGYQLVIEPCDSGSPDLAERVRALLQR-SRVDGVILTPPL 66 (270)
T ss_pred CEEEEEcCCCcccHHHHHHHHHHHHHhCCCeEEEEeCCCCchHHHHHHHHHHHH-CCCCEEEEeCCC
Confidence 589999888777888999999999999998877766654332 11222 368999998774
No 68
>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=48.21 E-value=55 Score=30.63 Aligned_cols=59 Identities=15% Similarity=0.121 Sum_probs=41.2
Q ss_pred eEEEEEcCCcccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHHHh----cCC--CCCCEEEEecCC
Q 014409 210 IIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKL----ANF--PECDVFINVSCA 269 (425)
Q Consensus 210 ~iGIlvgTl~~q~~~~~i~~Lk~li~~~GKk~Y~~~vgkln~aKL----aNF--~eID~fV~vaCP 269 (425)
+||||+.++.-..+..+++.+++.+++.|.+..++.. .-++++. .++ ..+|..+++++-
T Consensus 1 ~i~vi~~~~~~~~~~~~~~gi~~~~~~~g~~~~~~~~-~~~~~~~~~~i~~l~~~~~dgiii~~~~ 65 (270)
T cd06296 1 LIGLVFPDLDSPWASEVLRGVEEAAAAAGYDVVLSES-GRRTSPERQWVERLSARRTDGVILVTPE 65 (270)
T ss_pred CeEEEECCCCCccHHHHHHHHHHHHHHcCCeEEEecC-CCchHHHHHHHHHHHHcCCCEEEEecCC
Confidence 4899998888788889999999999999877655443 3333222 112 258998887653
No 69
>PRK10423 transcriptional repressor RbsR; Provisional
Probab=48.03 E-value=65 Score=31.36 Aligned_cols=64 Identities=9% Similarity=0.145 Sum_probs=46.5
Q ss_pred HhcCCeEEEEEcCCcccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHHHh----cCC--CCCCEEEEecCC
Q 014409 205 AKDANIIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKL----ANF--PECDVFINVSCA 269 (425)
Q Consensus 205 a~~A~~iGIlvgTl~~q~~~~~i~~Lk~li~~~GKk~Y~~~vgkln~aKL----aNF--~eID~fV~vaCP 269 (425)
.+..++||+|+....-..|..+++.+.+.+++.|.+..++..+ -++++. .+| ..+|.+++.+..
T Consensus 53 ~~~~~~Igvi~~~~~~~~~~~~~~gi~~~~~~~g~~~~~~~~~-~~~~~~~~~~~~l~~~~vdGiI~~~~~ 122 (327)
T PRK10423 53 LNQTRTIGMLITASTNPFYSELVRGVERSCFERGYSLVLCNTE-GDEQRMNRNLETLMQKRVDGLLLLCTE 122 (327)
T ss_pred hCCCCeEEEEeCCCCCCcHHHHHHHHHHHHHHcCCEEEEEeCC-CCHHHHHHHHHHHHHcCCCEEEEeCCC
Confidence 3466899999998877788899999999999999876554433 344332 222 269999987654
No 70
>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=47.44 E-value=37 Score=31.89 Aligned_cols=60 Identities=22% Similarity=0.211 Sum_probs=43.1
Q ss_pred eEEEEEcCCcccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHHHhc----CC--CCCCEEEEecCCC
Q 014409 210 IIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKLA----NF--PECDVFINVSCAQ 270 (425)
Q Consensus 210 ~iGIlvgTl~~q~~~~~i~~Lk~li~~~GKk~Y~~~vgkln~aKLa----NF--~eID~fV~vaCPr 270 (425)
+||+|+....-..+..+++.+.+.+++.|.+..++ .+.-++++.. .+ ..+|.+++.+|..
T Consensus 1 ~igvi~p~~~~~~~~~~~~gi~~~~~~~~~~~~~~-~~~~~~~~~~~~i~~l~~~~~dgiii~~~~~ 66 (265)
T cd06285 1 TIGVLVPRLTDTVMATMYEGIEEAAAERGYSTFVA-NTGDNPDAQRRAIEMLLDRRVDGLILGDARS 66 (265)
T ss_pred CEEEEeCCCCCccHHHHHHHHHHHHHHCCCEEEEE-eCCCCHHHHHHHHHHHHHcCCCEEEEecCCC
Confidence 58999988877777899999999999999886443 4444554321 11 1589999877653
No 71
>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=47.42 E-value=26 Score=33.20 Aligned_cols=75 Identities=17% Similarity=0.176 Sum_probs=48.4
Q ss_pred eEEEEEcCCcccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHHH----hcCC--CCCCEEEEecCCCccccc----ccCC
Q 014409 210 IIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAK----LANF--PECDVFINVSCAQTALLD----SKEF 279 (425)
Q Consensus 210 ~iGIlvgTl~~q~~~~~i~~Lk~li~~~GKk~Y~~~vgkln~aK----LaNF--~eID~fV~vaCPr~si~d----~~ef 279 (425)
+||+|+.++....+..+++.+.+.+++.|.+..++. ..-++++ |.++ ..+|++++.+|...+..+ .++.
T Consensus 1 ~igv~~~~~~~~~~~~~~~~i~~~~~~~g~~v~~~~-~~~~~~~~~~~i~~~~~~~~Dgiii~~~~~~~~~~~i~~~~~~ 79 (282)
T cd06318 1 KIGFSQYTLNSPFFAALTEAAKAHAKALGYELISTD-AQGDLTKQIADVEDLLTRGVNVLIINPVDPEGLVPAVAAAKAA 79 (282)
T ss_pred CeeEEeccccCHHHHHHHHHHHHHHHHcCCEEEEEc-CCCCHHHHHHHHHHHHHcCCCEEEEecCCccchHHHHHHHHHC
Confidence 589999888777778999999999999987654432 2334432 2222 268999987765332211 2345
Q ss_pred CCcccC
Q 014409 280 LAPVIT 285 (425)
Q Consensus 280 ~kPViT 285 (425)
-.|||+
T Consensus 80 ~iPvV~ 85 (282)
T cd06318 80 GVPVVV 85 (282)
T ss_pred CCCEEE
Confidence 567764
No 72
>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=47.34 E-value=61 Score=31.63 Aligned_cols=61 Identities=15% Similarity=0.223 Sum_probs=44.7
Q ss_pred cCCeEEEEEcCCcccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHHH-------hcCCCCCCEEEEecCC
Q 014409 207 DANIIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAK-------LANFPECDVFINVSCA 269 (425)
Q Consensus 207 ~A~~iGIlvgTl~~q~~~~~i~~Lk~li~~~GKk~Y~~~vgkln~aK-------LaNF~eID~fV~vaCP 269 (425)
..++||+++..+.-..+..+++.+.+.++++|.+..++.. .-++++ |.+ ..+|.+|++++.
T Consensus 58 ~~~~Igvv~~~~~~~f~~~l~~~i~~~~~~~g~~~~i~~~-~~~~~~~~~~~~~l~~-~~vdGiIi~~~~ 125 (329)
T TIGR01481 58 RTTTVGVIIPDISNIYYAELARGIEDIATMYKYNIILSNS-DEDPEKEVQVLNTLLS-KQVDGIIFMGGT 125 (329)
T ss_pred CCCEEEEEeCCCCchhHHHHHHHHHHHHHHcCCEEEEEeC-CCCHHHHHHHHHHHHh-CCCCEEEEeCCC
Confidence 4679999998877677889999999999999987655432 333332 222 269999998764
No 73
>PRK09526 lacI lac repressor; Reviewed
Probab=46.95 E-value=64 Score=31.72 Aligned_cols=61 Identities=11% Similarity=0.137 Sum_probs=45.1
Q ss_pred hcCCeEEEEEcCCcccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHHH----hcCC--CCCCEEEEe
Q 014409 206 KDANIIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAK----LANF--PECDVFINV 266 (425)
Q Consensus 206 ~~A~~iGIlvgTl~~q~~~~~i~~Lk~li~~~GKk~Y~~~vgkln~aK----LaNF--~eID~fV~v 266 (425)
+..++||+++..+.-..+..+++.+.+.+++.|....++..+.-++++ |.++ ..+|.+++.
T Consensus 61 ~~~~~Igvv~~~~~~~~~~~~~~gi~~~a~~~g~~~~i~~~~~~~~~~~~~~l~~l~~~~vdGiii~ 127 (342)
T PRK09526 61 KQSLTIGLATTSLALHAPSQIAAAIKSRADQLGYSVVISMVERSGVEACQAAVNELLAQRVSGVIIN 127 (342)
T ss_pred CCCceEEEEeCCCCcccHHHHHHHHHHHHHHCCCEEEEEeCCCChHHHHHHHHHHHHhcCCCEEEEe
Confidence 356799999998877777899999999999999887766555433322 2233 269999886
No 74
>COG2185 Sbm Methylmalonyl-CoA mutase, C-terminal domain/subunit (cobalamin-binding) [Lipid metabolism]
Probab=46.60 E-value=27 Score=31.15 Aligned_cols=53 Identities=21% Similarity=0.344 Sum_probs=39.2
Q ss_pred HhcCCeEEEEEcCCcccCcHHHHHHHHHHHHHcCCcEEEEEc-CCCCHHHhcCCC
Q 014409 205 AKDANIIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVM-GKPNPAKLANFP 258 (425)
Q Consensus 205 a~~A~~iGIlvgTl~~q~~~~~i~~Lk~li~~~GKk~Y~~~v-gkln~aKLaNF~ 258 (425)
|.+...=.|.|+++. .+|++++..+.+.|+++|.+.-++++ |.+.|+.+.+|.
T Consensus 59 A~~~dv~vIgvSsl~-g~h~~l~~~lve~lre~G~~~i~v~~GGvip~~d~~~l~ 112 (143)
T COG2185 59 AVEEDVDVIGVSSLD-GGHLTLVPGLVEALREAGVEDILVVVGGVIPPGDYQELK 112 (143)
T ss_pred HHhcCCCEEEEEecc-chHHHHHHHHHHHHHHhCCcceEEeecCccCchhHHHHH
Confidence 444444456667776 78999999999999999998888555 577777755553
No 75
>PRK08105 flavodoxin; Provisional
Probab=46.51 E-value=47 Score=29.39 Aligned_cols=41 Identities=17% Similarity=0.255 Sum_probs=33.6
Q ss_pred CeEEEEEcCCcccCcHHHHHHHHHHHHHcCCcEEEEEcCCCC
Q 014409 209 NIIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPN 250 (425)
Q Consensus 209 ~~iGIlvgTl~~q~~~~~i~~Lk~li~~~GKk~Y~~~vgkln 250 (425)
++++|+.||-+| +...++++|.+.+++.|.++-++-+..+.
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 368999999864 56789999999999999998877766543
No 76
>COG1429 CobN Cobalamin biosynthesis protein CobN and related Mg-chelatases [Coenzyme metabolism]
Probab=46.33 E-value=12 Score=44.94 Aligned_cols=25 Identities=32% Similarity=0.675 Sum_probs=0.0
Q ss_pred CCcEEEEec-C---------------CCCCCC--CCCCeEEEc
Q 014409 20 DADCVIHYG-H---------------TCLSPT--STLPAFFVF 44 (425)
Q Consensus 20 ~aD~iVHyG-h---------------aClsp~--~~lpviYVf 44 (425)
+||+|||+| | .|.+.+ ..+|.||.|
T Consensus 555 ~ADAvVHvGtHGTlEWLPGK~vgLs~~d~P~illgdlP~iYpY 597 (1388)
T COG1429 555 GADAVVHVGTHGTLEWLPGKEVGLSREDFPDILLGDLPNIYPY 597 (1388)
T ss_pred CCCeEEEccCccCcccCCCccccCChhhchHHhhCCCCeEEEE
No 77
>PRK10427 putative PTS system fructose-like transporter subunit EIIB; Provisional
Probab=46.28 E-value=56 Score=27.86 Aligned_cols=61 Identities=13% Similarity=0.097 Sum_probs=49.2
Q ss_pred CCeEEEEEcCCcccCcHHHHHHHHHHHHHcCCcEE------EEEcCCCCHHHhcCCCCCCEEEEecCCCc
Q 014409 208 ANIIGVLVGTLGVAGYLHMIHQMKELITKAGKKAY------TLVMGKPNPAKLANFPECDVFINVSCAQT 271 (425)
Q Consensus 208 A~~iGIlvgTl~~q~~~~~i~~Lk~li~~~GKk~Y------~~~vgkln~aKLaNF~eID~fV~vaCPr~ 271 (425)
.+.++|.-+.-|.....-..+.|++..++.|.... .=+.+.++++.++. .|.+++++....
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 46788888888888888889999999999999888 44556677777765 589999988764
No 78
>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=46.06 E-value=39 Score=28.97 Aligned_cols=54 Identities=11% Similarity=0.236 Sum_probs=39.7
Q ss_pred EEEcCCcccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHHHhcCCCCCCEEEEecCC
Q 014409 213 VLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKLANFPECDVFINVSCA 269 (425)
Q Consensus 213 IlvgTl~~q~~~~~i~~Lk~li~~~GKk~Y~~~vgkln~aKLaNF~eID~fV~vaCP 269 (425)
|+-+|.. -+...++++|.+.++++|.+..++-+...+.. +..+.+-+.+ +++||
T Consensus 1 I~Y~S~t-G~te~~A~~ia~~l~~~g~~~~~~~~~~~~~~-~~~~~~~~~~-i~~~s 54 (143)
T PF00258_consen 1 IVYGSMT-GNTEKMAEAIAEGLRERGVEVRVVDLDDFDDS-PSDLSEYDLL-IFGVS 54 (143)
T ss_dssp EEEETSS-SHHHHHHHHHHHHHHHTTSEEEEEEGGGSCHH-HHHHCTTSEE-EEEEE
T ss_pred CEEECCc-hhHHHHHHHHHHHHHHcCCceeeechhhhhhh-hhhhhhhcee-eEeec
Confidence 5667765 35678999999999999999999999999966 3233334554 44444
No 79
>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=46.04 E-value=48 Score=26.65 Aligned_cols=68 Identities=16% Similarity=0.119 Sum_probs=46.4
Q ss_pred EEEEcCCcccCcHHHHHHHHHHHHHcCCcEE------EEEcCCCCHHHhcCCCCCCEEEEecCCCcccccccCCC-Cccc
Q 014409 212 GVLVGTLGVAGYLHMIHQMKELITKAGKKAY------TLVMGKPNPAKLANFPECDVFINVSCAQTALLDSKEFL-APVI 284 (425)
Q Consensus 212 GIlvgTl~~q~~~~~i~~Lk~li~~~GKk~Y------~~~vgkln~aKLaNF~eID~fV~vaCPr~si~d~~ef~-kPVi 284 (425)
+|.-+.-|.....-..+.|++..++.|.... .=+.+.++.+.++. .|++++++... +++.++|. ||++
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---ADGVILAADRE--IDLSRRFAGKNVY 76 (85)
T ss_pred EEecCCCcHHHHHHHHHHHHHHHHHCCCeEEEEecCCcCccCCCCHHHHHh---CCEEEEeccCC--CchhhhcCCCeEE
Confidence 4555555666667778899999999998877 34455677776654 58999998876 34444353 6664
No 80
>KOG0781 consensus Signal recognition particle receptor, alpha subunit [Intracellular trafficking, secretion, and vesicular transport]
Probab=45.94 E-value=1.2e+02 Score=32.61 Aligned_cols=69 Identities=17% Similarity=0.256 Sum_probs=49.7
Q ss_pred HHHHHhcCCeEEEEEcCCcc-cCcHHHHHHHHHHHHHcCCcEEEEEcCC-----CCHHHhcCCC----------CCCEEE
Q 014409 201 LVEKAKDANIIGVLVGTLGV-AGYLHMIHQMKELITKAGKKAYTLVMGK-----PNPAKLANFP----------ECDVFI 264 (425)
Q Consensus 201 ~I~ka~~A~~iGIlvgTl~~-q~~~~~i~~Lk~li~~~GKk~Y~~~vgk-----ln~aKLaNF~----------eID~fV 264 (425)
+|+.|++-.-=-|||-|-|+ ++...+...|.++++.+--. -+|.||+ =.++.|.+|. -||.|+
T Consensus 458 AI~~a~~~gfDVvLiDTAGR~~~~~~lm~~l~k~~~~~~pd-~i~~vgealvg~dsv~q~~~fn~al~~~~~~r~id~~~ 536 (587)
T KOG0781|consen 458 AIQEARNQGFDVVLIDTAGRMHNNAPLMTSLAKLIKVNKPD-LILFVGEALVGNDSVDQLKKFNRALADHSTPRLIDGIL 536 (587)
T ss_pred HHHHHHhcCCCEEEEeccccccCChhHHHHHHHHHhcCCCc-eEEEehhhhhCcHHHHHHHHHHHHHhcCCCccccceEE
Confidence 57777777766799999986 78889999999998875544 4555554 4455554442 488888
Q ss_pred EecCCC
Q 014409 265 NVSCAQ 270 (425)
Q Consensus 265 ~vaCPr 270 (425)
++-|.-
T Consensus 537 ltk~dt 542 (587)
T KOG0781|consen 537 LTKFDT 542 (587)
T ss_pred EEeccc
Confidence 888865
No 81
>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=45.86 E-value=59 Score=28.35 Aligned_cols=64 Identities=17% Similarity=0.374 Sum_probs=43.1
Q ss_pred cCCeEEEEEcCCcccCcHHHHHHHHHHHHHcCCcEEEEEcCC-CCHHHhcCCC--CCCEEEEecCCCccc
Q 014409 207 DANIIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGK-PNPAKLANFP--ECDVFINVSCAQTAL 273 (425)
Q Consensus 207 ~A~~iGIlvgTl~~q~~~~~i~~Lk~li~~~GKk~Y~~~vgk-ln~aKLaNF~--eID~fV~vaCPr~si 273 (425)
+|..+|| +++. ..|++.+..+.+.|+++|.....+++|- +-.+..+.|. .+|.|+-.++|-..+
T Consensus 53 ~adii~i--Ssl~-~~~~~~~~~~~~~L~~~g~~~i~vivGG~~~~~~~~~l~~~Gvd~~~~~gt~~~~i 119 (132)
T TIGR00640 53 DVHVVGV--SSLA-GGHLTLVPALRKELDKLGRPDILVVVGGVIPPQDFDELKEMGVAEIFGPGTPIPES 119 (132)
T ss_pred CCCEEEE--cCch-hhhHHHHHHHHHHHHhcCCCCCEEEEeCCCChHhHHHHHHCCCCEEECCCCCHHHH
Confidence 4555544 6654 6789999999999999998666777773 2233344442 588888777765433
No 82
>PRK05569 flavodoxin; Provisional
Probab=45.06 E-value=96 Score=26.55 Aligned_cols=56 Identities=7% Similarity=0.104 Sum_probs=41.4
Q ss_pred eEEEEEcCCcccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHHHhcCCCCCCEEEEecCCC
Q 014409 210 IIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKLANFPECDVFINVSCAQ 270 (425)
Q Consensus 210 ~iGIlvgTl~~q~~~~~i~~Lk~li~~~GKk~Y~~~vgkln~aKLaNF~eID~fV~vaCPr 270 (425)
.+.|+-+|. --+...+++.+.+.+++.|...-++-+.+.++.++. +.|. |+++||=
T Consensus 3 ki~iiY~S~-tGnT~~iA~~i~~~~~~~g~~v~~~~~~~~~~~~~~---~~d~-iilgsPt 58 (141)
T PRK05569 3 KVSIIYWSC-GGNVEVLANTIADGAKEAGAEVTIKHVADAKVEDVL---EADA-VAFGSPS 58 (141)
T ss_pred eEEEEEECC-CCHHHHHHHHHHHHHHhCCCeEEEEECCcCCHHHHh---hCCE-EEEECCC
Confidence 567888885 356789999999999999988777777777776554 4455 5566664
No 83
>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=44.45 E-value=50 Score=29.37 Aligned_cols=61 Identities=15% Similarity=0.184 Sum_probs=43.5
Q ss_pred CCeEEEEEcCCcccCcHHHHHHHHHHHHHcCC---cEEEEEcCCCC-----HHHhcCCCCCCEEEEecC
Q 014409 208 ANIIGVLVGTLGVAGYLHMIHQMKELITKAGK---KAYTLVMGKPN-----PAKLANFPECDVFINVSC 268 (425)
Q Consensus 208 A~~iGIlvgTl~~q~~~~~i~~Lk~li~~~GK---k~Y~~~vgkln-----~aKLaNF~eID~fV~vaC 268 (425)
.-+||||++.-...---.+++...+.|+++|- ...++.|--.- ..+|++...+|++|.+||
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 34789999876544444555666778888886 66676665332 467777778999999998
No 84
>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=43.59 E-value=23 Score=33.53 Aligned_cols=76 Identities=16% Similarity=0.123 Sum_probs=47.7
Q ss_pred eEEEEEcCCcccCcHHHHHHHHHHHHHcCCcEEEEEc---CCCCHHHh----cCCC-CCCEEEEecCCCccc----cccc
Q 014409 210 IIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVM---GKPNPAKL----ANFP-ECDVFINVSCAQTAL----LDSK 277 (425)
Q Consensus 210 ~iGIlvgTl~~q~~~~~i~~Lk~li~~~GKk~Y~~~v---gkln~aKL----aNF~-eID~fV~vaCPr~si----~d~~ 277 (425)
+||+|+....-..+..+++.+.+.+++.|...++... ..-++++. .++. .+|++++++...... ....
T Consensus 1 ~ig~v~~~~~~~~~~~~~~~i~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~i~~~~~~vdgiii~~~~~~~~~~~i~~~~ 80 (275)
T cd06307 1 RLGFLLPKGSNAFYRELAAALEAAAAAFPDARIRVRIHFVESFDPAALAAALLRLGARSDGVALVAPDHPQVRAAVARLA 80 (275)
T ss_pred CeEEEeCCCCChHHHHHHHHHHHHHhhhhccCceEEEEEccCCCHHHHHHHHHHHHhcCCEEEEeCCCcHHHHHHHHHHH
Confidence 5889998877777788889999988888877665543 22344322 2222 589988877553321 1123
Q ss_pred CCCCcccC
Q 014409 278 EFLAPVIT 285 (425)
Q Consensus 278 ef~kPViT 285 (425)
+.-.|||+
T Consensus 81 ~~~ipvV~ 88 (275)
T cd06307 81 AAGVPVVT 88 (275)
T ss_pred HCCCcEEE
Confidence 34557764
No 85
>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=42.65 E-value=71 Score=28.69 Aligned_cols=72 Identities=22% Similarity=0.328 Sum_probs=45.1
Q ss_pred eEEEEEcCCcccCcHHHHHHHHHHHHHcCCcEEEEEcC-CCCHHHhcCC------CCCCEEEEecCCCccccc--ccCCC
Q 014409 210 IIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMG-KPNPAKLANF------PECDVFINVSCAQTALLD--SKEFL 280 (425)
Q Consensus 210 ~iGIlvgTl~~q~~~~~i~~Lk~li~~~GKk~Y~~~vg-kln~aKLaNF------~eID~fV~vaCPr~si~d--~~ef~ 280 (425)
.++||.|+ ..=+.+.+..++.|++-|..+-+-+.+ .=+|++|..| .++|+||.+|==..+|-- ...-.
T Consensus 2 ~V~Ii~gs---~SD~~~~~~a~~~L~~~gi~~~~~V~saHR~p~~l~~~~~~~~~~~~~viIa~AG~~a~Lpgvva~~t~ 78 (150)
T PF00731_consen 2 KVAIIMGS---TSDLPIAEEAAKTLEEFGIPYEVRVASAHRTPERLLEFVKEYEARGADVIIAVAGMSAALPGVVASLTT 78 (150)
T ss_dssp EEEEEESS---GGGHHHHHHHHHHHHHTT-EEEEEE--TTTSHHHHHHHHHHTTTTTESEEEEEEESS--HHHHHHHHSS
T ss_pred eEEEEeCC---HHHHHHHHHHHHHHHHcCCCEEEEEEeccCCHHHHHHHHHHhccCCCEEEEEECCCcccchhhheeccC
Confidence 58899988 456788899999999999877665555 4567777554 247888877765555421 11235
Q ss_pred Cccc
Q 014409 281 APVI 284 (425)
Q Consensus 281 kPVi 284 (425)
+|||
T Consensus 79 ~PVI 82 (150)
T PF00731_consen 79 LPVI 82 (150)
T ss_dssp S-EE
T ss_pred CCEE
Confidence 6665
No 86
>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=42.38 E-value=37 Score=32.02 Aligned_cols=77 Identities=19% Similarity=0.173 Sum_probs=48.3
Q ss_pred eEEEEEcCCcccCcHHHHHHHHHHHHHc---CCcE-EEEEcCCCCHHHhcCC------CCCCEEEEecCCCcccc----c
Q 014409 210 IIGVLVGTLGVAGYLHMIHQMKELITKA---GKKA-YTLVMGKPNPAKLANF------PECDVFINVSCAQTALL----D 275 (425)
Q Consensus 210 ~iGIlvgTl~~q~~~~~i~~Lk~li~~~---GKk~-Y~~~vgkln~aKLaNF------~eID~fV~vaCPr~si~----d 275 (425)
+||+++.......+..+++.+.+.+++. |.+. .++.-+.-++++..+. ..+|++|+.++-...+. -
T Consensus 1 ~Ig~i~~~~~~~~~~~~~~~i~~~~~~~~~~g~~~~l~i~~~~~~~~~~~~~~~~~~~~~vdgiIi~~~~~~~~~~~l~~ 80 (272)
T cd06300 1 KIGLSNSYAGNTWRAQMLDEFKAQAKELKKAGLISEFIVTSADGDVAQQIADIRNLIAQGVDAIIINPASPTALNPVIEE 80 (272)
T ss_pred CeEEeccccCChHHHHHHHHHHHHHHhhhccCCeeEEEEecCCCCHHHHHHHHHHHHHcCCCEEEEeCCChhhhHHHHHH
Confidence 4889998877667778999999999888 7653 3444455555543221 26899999776433222 1
Q ss_pred ccCCCCcccCH
Q 014409 276 SKEFLAPVITP 286 (425)
Q Consensus 276 ~~ef~kPViTP 286 (425)
.++...|||+.
T Consensus 81 ~~~~~iPvv~~ 91 (272)
T cd06300 81 ACEAGIPVVSF 91 (272)
T ss_pred HHHCCCeEEEE
Confidence 23445576653
No 87
>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=42.01 E-value=34 Score=32.40 Aligned_cols=60 Identities=10% Similarity=-0.024 Sum_probs=40.8
Q ss_pred eEEEEEcCC-cccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHHHhcCC------CCCCEEEEecCC
Q 014409 210 IIGVLVGTL-GVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKLANF------PECDVFINVSCA 269 (425)
Q Consensus 210 ~iGIlvgTl-~~q~~~~~i~~Lk~li~~~GKk~Y~~~vgkln~aKLaNF------~eID~fV~vaCP 269 (425)
+||+|+..+ .-..+..+++.+++.+++.|....++....-++++.... ..+|++|+.++.
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 556667888999999998887766554443355544221 268998887754
No 88
>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=41.40 E-value=53 Score=30.63 Aligned_cols=76 Identities=14% Similarity=0.158 Sum_probs=50.7
Q ss_pred eEEEEEcCCcccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHHHhc----CC--CCCCEEEEecCCCc-ccc-cccCCCC
Q 014409 210 IIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKLA----NF--PECDVFINVSCAQT-ALL-DSKEFLA 281 (425)
Q Consensus 210 ~iGIlvgTl~~q~~~~~i~~Lk~li~~~GKk~Y~~~vgkln~aKLa----NF--~eID~fV~vaCPr~-si~-d~~ef~k 281 (425)
+||+|+.......+..+++.+.+.+++.|.+..++.. .-++++.. .+ ..+|+.+++++... ... -......
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 5899998888788899999999999999988665443 44554432 11 26899999887543 111 1123345
Q ss_pred cccCH
Q 014409 282 PVITP 286 (425)
Q Consensus 282 PViTP 286 (425)
|||+-
T Consensus 80 pvv~~ 84 (268)
T cd01575 80 PVVEI 84 (268)
T ss_pred CEEEE
Confidence 77643
No 89
>PRK09271 flavodoxin; Provisional
Probab=41.02 E-value=91 Score=27.72 Aligned_cols=58 Identities=12% Similarity=0.098 Sum_probs=39.0
Q ss_pred eEEEEEcCCcccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHHH-hcCCCCCCEEEEecCC
Q 014409 210 IIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAK-LANFPECDVFINVSCA 269 (425)
Q Consensus 210 ~iGIlvgTl~~q~~~~~i~~Lk~li~~~GKk~Y~~~vgkln~aK-LaNF~eID~fV~vaCP 269 (425)
.+.|+.+|.. -+...++++|.+.|++.|.+.-+.-+....... ..++.+.|++++ +||
T Consensus 2 kv~IvY~S~t-GnTe~~A~~ia~~l~~~g~~v~~~~~~~~~~~~~~~~~~~~d~vil-gt~ 60 (160)
T PRK09271 2 RILLAYASLS-GNTREVAREIEERCEEAGHEVDWVETDVQTLAEYPLDPEDYDLYLL-GTW 60 (160)
T ss_pred eEEEEEEcCC-chHHHHHHHHHHHHHhCCCeeEEEecccccccccccCcccCCEEEE-ECc
Confidence 4679999976 467899999999999999877555554433222 224445566555 444
No 90
>PRK10339 DNA-binding transcriptional repressor EbgR; Provisional
Probab=40.62 E-value=49 Score=32.44 Aligned_cols=58 Identities=12% Similarity=0.111 Sum_probs=40.5
Q ss_pred cCCeEEEEEc----CCcccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHHHhcCCCCCCEEEEecC
Q 014409 207 DANIIGVLVG----TLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKLANFPECDVFINVSC 268 (425)
Q Consensus 207 ~A~~iGIlvg----Tl~~q~~~~~i~~Lk~li~~~GKk~Y~~~vgkln~aKLaNF~eID~fV~vaC 268 (425)
...++|||+. ++.-..+..+++.+.+.++++|.+..+..-.+ .. .....+|.++++++
T Consensus 62 ~~~~i~v~~~~~~~~~~~~f~~~l~~~i~~~~~~~g~~~~~~~~~~--~~--~~~~~vDgiI~~~~ 123 (327)
T PRK10339 62 QHHILAIYSYQQELEINDPYYLAIRHGIETQCEKLGIELTNCYEHS--GL--PDIKNVTGILIVGK 123 (327)
T ss_pred cccEEEEEEccccccccCchHHHHHHHHHHHHHHCCCEEEEeeccc--cc--cccccCCEEEEeCC
Confidence 4568899884 55556677899999999999997754432222 11 12357999999875
No 91
>PF03698 UPF0180: Uncharacterised protein family (UPF0180); InterPro: IPR005370 The members of this family are small uncharacterised proteins.
Probab=40.48 E-value=63 Score=25.90 Aligned_cols=56 Identities=18% Similarity=0.230 Sum_probs=38.1
Q ss_pred HHHHHHHHHcCCcEEEEEcCCCCHHHhcCCCCCCEEEEecCCCcccc-cccCCCCccc-----CHHHHH
Q 014409 228 HQMKELITKAGKKAYTLVMGKPNPAKLANFPECDVFINVSCAQTALL-DSKEFLAPVI-----TPFEAM 290 (425)
Q Consensus 228 ~~Lk~li~~~GKk~Y~~~vgkln~aKLaNF~eID~fV~vaCPr~si~-d~~ef~kPVi-----TP~Ele 290 (425)
..+++.|+++|.+...+-- .+ ++..+||.|+.+=..+-+- ....+.-||| ||.|..
T Consensus 11 s~v~~~L~~~GyeVv~l~~----~~---~~~~~daiVvtG~~~n~mg~~d~~~~~pVInA~G~T~eEI~ 72 (80)
T PF03698_consen 11 SNVKEALREKGYEVVDLEN----EQ---DLQNVDAIVVTGQDTNMMGIQDTSTKVPVINASGLTAEEIV 72 (80)
T ss_pred hHHHHHHHHCCCEEEecCC----cc---ccCCcCEEEEECCCcccccccccccCceEEecCCCCHHHHH
Confidence 4788899999988665541 11 4567999999997776432 1235677885 666654
No 92
>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=40.40 E-value=36 Score=31.12 Aligned_cols=63 Identities=14% Similarity=0.129 Sum_probs=46.8
Q ss_pred HHHHHhcCCeEEEEEcCCcccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHHHhcCCC--CCCEEEEec
Q 014409 201 LVEKAKDANIIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKLANFP--ECDVFINVS 267 (425)
Q Consensus 201 ~I~ka~~A~~iGIlvgTl~~q~~~~~i~~Lk~li~~~GKk~Y~~~vgkln~aKLaNF~--eID~fV~va 267 (425)
-.++|.+++.=+|.+=+.+ ++.++++.+.++..+.+.-+.+.|.+|++.+.+|. .+|++++-+
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 3445677887778887764 47777777777888999999999999999998885 578777654
No 93
>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=39.91 E-value=17 Score=42.71 Aligned_cols=93 Identities=18% Similarity=0.189 Sum_probs=44.1
Q ss_pred CceEEEecCCCCcc--cccc-CcHHHHHHHHHHHHHHHhcCCeEEEEE-cCCcccCcHHHHHHHHHHHHHcCCcEEEEEc
Q 014409 171 GCEIVRYDATEERL--LTDV-SQPLKILKRRYYLVEKAKDANIIGVLV-GTLGVAGYLHMIHQMKELITKAGKKAYTLVM 246 (425)
Q Consensus 171 ~~~v~~yDP~~~~~--~~~~-~~~~r~L~rRy~~I~ka~~A~~iGIlv-gTl~~q~~~~~i~~Lk~li~~~GKk~Y~~~v 246 (425)
+..+|.+||..--- ..+. ......|.+||..=+ =+-=++||+++ ||=.....=..+.. .|.--|-|..-=..
T Consensus 716 GrN~y~~Dp~~iPt~~A~~~G~~la~~ll~~y~~~~-g~yPe~v~~vlW~~~t~rt~G~~~aq---il~llGv~Pvw~~~ 791 (1098)
T PF02514_consen 716 GRNFYSFDPRKIPTPAAWEVGKKLAEQLLERYREEH-GRYPEKVAFVLWGTETMRTGGEDIAQ---ILYLLGVRPVWDSS 791 (1098)
T ss_pred CCcccccCcccccCHHHHHHHHHHHHHHHHHHHHhc-CCCCceeEEEEEecchhhcCCHHHHH---HHHhcCceeccCCC
Confidence 45688888876421 1111 112233444554333 33346777665 33332222233333 33334554433233
Q ss_pred CCC-----CHHHhcCCCCCCEEEEec
Q 014409 247 GKP-----NPAKLANFPECDVFINVS 267 (425)
Q Consensus 247 gkl-----n~aKLaNF~eID~fV~va 267 (425)
|++ -|-.-.+-|-|||.|.++
T Consensus 792 grv~~~e~iPl~eL~RPRIDV~~~~s 817 (1098)
T PF02514_consen 792 GRVSGVELIPLEELGRPRIDVVVRIS 817 (1098)
T ss_pred CCCCCceeccHHHcCCCCeeEEEecc
Confidence 333 244444677889888865
No 94
>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=39.91 E-value=95 Score=28.22 Aligned_cols=53 Identities=19% Similarity=0.310 Sum_probs=42.0
Q ss_pred hcCCeEEEEEcCCcccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHHHhcCCCCCCEEEEec
Q 014409 206 KDANIIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKLANFPECDVFINVS 267 (425)
Q Consensus 206 ~~A~~iGIlvgTl~~q~~~~~i~~Lk~li~~~GKk~Y~~~vgkln~aKLaNF~eID~fV~va 267 (425)
.+..+|.|+-|- ..+..++++|| +.||+.+.+.+.+.++.-|.|= .|-|+-+.
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 567788777765 77888887766 6799999999888899999885 77887654
No 95
>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=39.49 E-value=38 Score=31.91 Aligned_cols=59 Identities=19% Similarity=0.195 Sum_probs=38.5
Q ss_pred eEEEEEcCCcccCcHHHHHHHHHHHHHcCCcEEEEE-cCCCCHHHhcCC------CCCCEEEEecC
Q 014409 210 IIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLV-MGKPNPAKLANF------PECDVFINVSC 268 (425)
Q Consensus 210 ~iGIlvgTl~~q~~~~~i~~Lk~li~~~GKk~Y~~~-vgkln~aKLaNF------~eID~fV~vaC 268 (425)
+||+|+.++.-..+..+++.+.+.+++.|..+-++. -+.-++++.... ..+|.+|+.+.
T Consensus 1 ~Ig~v~~~~~~~~~~~~~~gi~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~dgiIi~~~ 66 (271)
T cd06321 1 KIGVSVGDLGNPFFVALAKGAEAAAKKLNPGVKVTVVSADYDLNKQVSQIDNFIAAKVDLILLNAV 66 (271)
T ss_pred CeEEEecccCCHHHHHHHHHHHHHHHHhCCCeEEEEccCCCCHHHHHHHHHHHHHhCCCEEEEeCC
Confidence 589999888777778999999999998554433332 233344433221 15888888653
No 96
>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=39.39 E-value=54 Score=31.78 Aligned_cols=59 Identities=17% Similarity=0.151 Sum_probs=41.1
Q ss_pred eEEEEEcCCcccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHHHhc----CC--CCCCEEEEecC
Q 014409 210 IIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKLA----NF--PECDVFINVSC 268 (425)
Q Consensus 210 ~iGIlvgTl~~q~~~~~i~~Lk~li~~~GKk~Y~~~vgkln~aKLa----NF--~eID~fV~vaC 268 (425)
+||+|+.+.+-..+..+++.+++.+++.|.+..++.-..-++++-. ++ ..+|.+|+.+.
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 5888888877777788999999999998876555434445554332 22 25899888764
No 97
>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=39.03 E-value=61 Score=28.05 Aligned_cols=57 Identities=12% Similarity=0.051 Sum_probs=35.3
Q ss_pred eEEEEEcCCcccCcHHHHHHHHHHHHHcCCcEE-EEEcCCCCHHHhcCCCCCCEEEEecCC
Q 014409 210 IIGVLVGTLGVAGYLHMIHQMKELITKAGKKAY-TLVMGKPNPAKLANFPECDVFINVSCA 269 (425)
Q Consensus 210 ~iGIlvgTl~~q~~~~~i~~Lk~li~~~GKk~Y-~~~vgkln~aKLaNF~eID~fV~vaCP 269 (425)
.+.||.+|..| +...++++|.+.+...|.+.- ++-+.+++.. ..++.+.|++ +++||
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 46789999763 578899999999998887653 2223332211 1234455664 44554
No 98
>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=38.92 E-value=32 Score=35.67 Aligned_cols=66 Identities=18% Similarity=0.324 Sum_probs=36.4
Q ss_pred HHHHHHHhcCCeEEEEEcCCcccCcHHHHHHHHHHHHHcCCcEEEEEcC---CCCHHHhcCCCCCCEEEE
Q 014409 199 YYLVEKAKDANIIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMG---KPNPAKLANFPECDVFIN 265 (425)
Q Consensus 199 y~~I~ka~~A~~iGIlvgTl~~q~~~~~i~~Lk~li~~~GKk~Y~~~vg---kln~aKLaNF~eID~fV~ 265 (425)
|..+....+|..++|=..|...+.-...++.+++ +++.|++..+++.| ...|+.+..++++|++|-
T Consensus 25 ~~~~~~~~~aD~v~intctv~~~a~~~~~~~i~~-~k~~~p~~~vvvgGc~a~~~~ee~~~~~~vD~vv~ 93 (414)
T TIGR01579 25 YEVVPDEDKADVYIINTCTVTAKADSKARRAIRR-ARRQNPTAKIIVTGCYAQSNPKELADLKDVDLVLG 93 (414)
T ss_pred CEECCCcccCCEEEEeccccchHHHHHHHHHHHH-HHhhCCCcEEEEECCccccCHHHHhcCCCCcEEEC
Confidence 4444444567775544444332222334444433 35566666666666 346777777788887763
No 99
>COG0716 FldA Flavodoxins [Energy production and conversion]
Probab=38.83 E-value=1e+02 Score=27.00 Aligned_cols=59 Identities=10% Similarity=0.000 Sum_probs=42.8
Q ss_pred CeEEEEEcCCcccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHHHhcCCCCCCEEEEecCCCc
Q 014409 209 NIIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKLANFPECDVFINVSCAQT 271 (425)
Q Consensus 209 ~~iGIlvgTl~~q~~~~~i~~Lk~li~~~GKk~Y~~~vgkln~aKLaNF~eID~fV~vaCPr~ 271 (425)
..++|+-+|.+ -|...++++|++.|.+.|.+. ++-...-....+. + ..|.+++..++-.
T Consensus 2 ~ki~Ivy~S~t-GnTe~vA~~i~~~l~~~~~~~-~~~~~~~~~~~~~-~-~~d~~~~g~~t~~ 60 (151)
T COG0716 2 MKILIVYGSRT-GNTEKVAEIIAEELGADGFEV-DIDIRPGIKDDLL-E-SYDELLLGTPTWG 60 (151)
T ss_pred CeEEEEEEcCC-CcHHHHHHHHHHHhccCCceE-EEeecCCcchhhh-c-cCCEEEEEeCCCC
Confidence 36899999987 578899999999999999998 4444443333332 2 4577777777654
No 100
>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=38.48 E-value=1.6e+02 Score=25.73 Aligned_cols=55 Identities=5% Similarity=-0.041 Sum_probs=30.0
Q ss_pred HHHHHHHHHHHHHhcCCeEEEEEcCCc------ccCcHHHHHHHHHHHHHcCCcEEEEEcC
Q 014409 193 KILKRRYYLVEKAKDANIIGVLVGTLG------VAGYLHMIHQMKELITKAGKKAYTLVMG 247 (425)
Q Consensus 193 r~L~rRy~~I~ka~~A~~iGIlvgTl~------~q~~~~~i~~Lk~li~~~GKk~Y~~~vg 247 (425)
..+..|......+...+.+-|.+||=- .+.+.+-++.+-+.+++++.+.-+++++
T Consensus 36 ~~~~~~~~~~~~~~~p~~vvi~~G~ND~~~~~~~~~~~~~~~~lv~~i~~~~~~~~iil~~ 96 (171)
T cd04502 36 ADCLHYFDRLVLPYQPRRVVLYAGDNDLASGRTPEEVLRDFRELVNRIRAKLPDTPIAIIS 96 (171)
T ss_pred HHHHHHHHhhhccCCCCEEEEEEecCcccCCCCHHHHHHHHHHHHHHHHHHCCCCcEEEEE
Confidence 344556555545557788888888833 2334444455555555554444444443
No 101
>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=38.33 E-value=90 Score=30.53 Aligned_cols=113 Identities=19% Similarity=0.257 Sum_probs=66.8
Q ss_pred HHHHHHHHHHHHHh-cCCeEEEEEcCCcccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCH--HHhcCC-CCCCEEEEecC
Q 014409 193 KILKRRYYLVEKAK-DANIIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNP--AKLANF-PECDVFINVSC 268 (425)
Q Consensus 193 r~L~rRy~~I~ka~-~A~~iGIlvgTl~~q~~~~~i~~Lk~li~~~GKk~Y~~~vgkln~--aKLaNF-~eID~fV~vaC 268 (425)
..+.++..++.+.. +++++|+|...- -.+....++.+++..++.|.+...+.+...+. ..+..+ ...|++++...
T Consensus 115 ~~~~~~l~l~~~l~P~~k~igvl~~~~-~~~~~~~~~~~~~~a~~~g~~l~~~~v~~~~~~~~~~~~l~~~~da~~~~~~ 193 (294)
T PF04392_consen 115 PPIEKQLELIKKLFPDAKRIGVLYDPS-EPNSVAQIEQLRKAAKKLGIELVEIPVPSSEDLEQALEALAEKVDALYLLPD 193 (294)
T ss_dssp --HHHHHHHHHHHSTT--EEEEEEETT--HHHHHHHHHHHHHHHHTT-EEEEEEESSGGGHHHHHHHHCTT-SEEEE-S-
T ss_pred cCHHHHHHHHHHhCCCCCEEEEEecCC-CccHHHHHHHHHHHHHHcCCEEEEEecCcHhHHHHHHHHhhccCCEEEEECC
Confidence 45677888888886 799999999764 34567889999999999999999888887663 223333 35898887654
Q ss_pred CCcc-----cc-cccCCCCcccCHHHHHHhhCCCCccccceeeccccc
Q 014409 269 AQTA-----LL-DSKEFLAPVITPFEAMLAFGRGTQWTGAYVMEFRDL 310 (425)
Q Consensus 269 Pr~s-----i~-d~~ef~kPViTP~ElevAL~~~~~W~g~y~~Df~~l 310 (425)
+-.. +. -..+...||++.++..+--+ .-+.+..|+.++
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 3210 11 13456778887776665432 234566666655
No 102
>PRK09426 methylmalonyl-CoA mutase; Reviewed
Probab=38.14 E-value=61 Score=36.49 Aligned_cols=71 Identities=17% Similarity=0.284 Sum_probs=47.2
Q ss_pred HHHHHhc--CCeEEEEEcCCcccCcHHHHHHHHHHHHHcCCcEE-EEEcCCCCHHHhcCC--CCCCEEEEecCCCcccc
Q 014409 201 LVEKAKD--ANIIGVLVGTLGVAGYLHMIHQMKELITKAGKKAY-TLVMGKPNPAKLANF--PECDVFINVSCAQTALL 274 (425)
Q Consensus 201 ~I~ka~~--A~~iGIlvgTl~~q~~~~~i~~Lk~li~~~GKk~Y-~~~vgkln~aKLaNF--~eID~fV~vaCPr~si~ 274 (425)
.++.|++ +.+++| +++. ..|.+.+..+.+.|+++|.+.. +++=|++-++....+ ..+|.|+-.+|+-..++
T Consensus 625 ~v~aa~~~~a~ivvl--cs~d-~~~~e~~~~l~~~Lk~~G~~~v~vl~GG~~~~~~~~~l~~aGvD~~i~~g~d~~~~L 700 (714)
T PRK09426 625 AARQAVENDVHVVGV--SSLA-AGHKTLVPALIEALKKLGREDIMVVVGGVIPPQDYDFLYEAGVAAIFGPGTVIADAA 700 (714)
T ss_pred HHHHHHHcCCCEEEE--eccc-hhhHHHHHHHHHHHHhcCCCCcEEEEeCCCChhhHHHHHhCCCCEEECCCCCHHHHH
Confidence 3444444 555544 4432 7899999999999999998655 444456445433322 27999999999866554
No 103
>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=37.95 E-value=69 Score=32.04 Aligned_cols=59 Identities=17% Similarity=0.225 Sum_probs=44.3
Q ss_pred CeEEEEEcCCcc--cCcHHHHHHHHHHHHHcC-CcEEEEEcCCCCHHHhcCCC--CCCEEEEec
Q 014409 209 NIIGVLVGTLGV--AGYLHMIHQMKELITKAG-KKAYTLVMGKPNPAKLANFP--ECDVFINVS 267 (425)
Q Consensus 209 ~~iGIlvgTl~~--q~~~~~i~~Lk~li~~~G-Kk~Y~~~vgkln~aKLaNF~--eID~fV~va 267 (425)
+..+|.+=+.+. -...+.++++++.++..| .+.-+.+.|.+|++++++|. .+|++=+-+
T Consensus 211 ~~d~I~lDn~~~~~G~~~~~~~~~~~~l~~~g~~~~~ieaSGgI~~~~i~~~a~~gvD~isvGs 274 (302)
T cd01571 211 KLDGVRLDTPSSRRGVFRYLIREVRWALDIRGYKHVKIFVSGGLDEEDIKELEDVGVDAFGVGT 274 (302)
T ss_pred CCcEEEECCCCCCCCCHHHHHHHHHHHHHhCCCCCeEEEEeCCCCHHHHHHHHHcCCCEEECCc
Confidence 356777777541 225677899999999987 66788999999999999885 588774433
No 104
>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=37.36 E-value=1.2e+02 Score=28.35 Aligned_cols=60 Identities=13% Similarity=0.189 Sum_probs=42.3
Q ss_pred eEEEEEcCCcccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHHHhc----CC--CCCCEEEEecCCC
Q 014409 210 IIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKLA----NF--PECDVFINVSCAQ 270 (425)
Q Consensus 210 ~iGIlvgTl~~q~~~~~i~~Lk~li~~~GKk~Y~~~vgkln~aKLa----NF--~eID~fV~vaCPr 270 (425)
+||+|+.+..-..+..+++.+++.+++.|....++. ..=++++.. ++ ..+|.+|+.++..
T Consensus 1 ~igvi~~~~~~~~~~~~~~gi~~~~~~~g~~~~~~~-~~~~~~~~~~~i~~l~~~~vdgiii~~~~~ 66 (269)
T cd06275 1 TIGMLVTTSTNPFFAEVVRGVEQYCYRQGYNLILCN-TEGDPERQRSYLRMLAQKRVDGLLVMCSEY 66 (269)
T ss_pred CEEEEeCCCCcchHHHHHHHHHHHHHHcCCEEEEEe-CCCChHHHHHHHHHHHHcCCCEEEEecCCC
Confidence 489999887767778899999999999987655433 333554321 22 2689999988753
No 105
>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=37.21 E-value=88 Score=26.50 Aligned_cols=62 Identities=18% Similarity=0.339 Sum_probs=42.4
Q ss_pred HhcCCeEEEEEcCCcccCcHHHHHHHHHHHHHcCC-cEEEEEcCCCCHHH---hcCCCCCCEEEEecCCC
Q 014409 205 AKDANIIGVLVGTLGVAGYLHMIHQMKELITKAGK-KAYTLVMGKPNPAK---LANFPECDVFINVSCAQ 270 (425)
Q Consensus 205 a~~A~~iGIlvgTl~~q~~~~~i~~Lk~li~~~GK-k~Y~~~vgkln~aK---LaNF~eID~fV~vaCPr 270 (425)
..+|..++| +.+ ...+.+.++.+.+.|++.|. +..+++-|...++. |... .+|.|+-.+|+-
T Consensus 48 ~~~~d~V~i--S~~-~~~~~~~~~~~~~~L~~~~~~~i~i~~GG~~~~~~~~~~~~~-G~d~~~~~~~~~ 113 (122)
T cd02071 48 QEDVDVIGL--SSL-SGGHMTLFPEVIELLRELGAGDILVVGGGIIPPEDYELLKEM-GVAEIFGPGTSI 113 (122)
T ss_pred HcCCCEEEE--ccc-chhhHHHHHHHHHHHHhcCCCCCEEEEECCCCHHHHHHHHHC-CCCEEECCCCCH
Confidence 446777666 333 36788888999999999988 44455555555554 3344 599999888774
No 106
>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=37.18 E-value=58 Score=30.64 Aligned_cols=55 Identities=13% Similarity=0.027 Sum_probs=33.7
Q ss_pred eEEEEEcCCcccCcHHHHHHHHHHHHH-cCCcEEEEEcCCC--CHHHhcCCCCCCEEEEec
Q 014409 210 IIGVLVGTLGVAGYLHMIHQMKELITK-AGKKAYTLVMGKP--NPAKLANFPECDVFINVS 267 (425)
Q Consensus 210 ~iGIlvgTl~~q~~~~~i~~Lk~li~~-~GKk~Y~~~vgkl--n~aKLaNF~eID~fV~va 267 (425)
+||+|+.+ +--.+..+++.+.+.+++ .|....+.. +.. -...|.+. .+|.+++.+
T Consensus 1 ~ig~i~~~-~~~~~~~~~~gi~~~~~~~~g~~~~~~~-~~~~~~~~~l~~~-~vdGiI~~~ 58 (265)
T cd01543 1 RVALLVET-SSSYGRGVLRGIARYAREHGPWSIYLEP-RGLQEPLRWLKDW-QGDGIIARI 58 (265)
T ss_pred CeEEEecc-cchhhHHHHHHHHHHHHhcCCeEEEEec-ccchhhhhhcccc-ccceEEEEC
Confidence 48999974 345667888888888888 555543322 211 01223333 689998865
No 107
>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=37.12 E-value=74 Score=29.59 Aligned_cols=49 Identities=18% Similarity=0.179 Sum_probs=37.3
Q ss_pred CeEEEEEcCCcccCcHHHHHHHHHHHHHcCCcEEEEEcCC--CCHHHhcCCC
Q 014409 209 NIIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGK--PNPAKLANFP 258 (425)
Q Consensus 209 ~~iGIlvgTl~~q~~~~~i~~Lk~li~~~GKk~Y~~~vgk--ln~aKLaNF~ 258 (425)
+.+=|++|+.+-. ...-+..+-+.++++|.+.+++.+|+ -|++||..|-
T Consensus 108 ~rivi~v~S~~~~-d~~~i~~~~~~lkk~~I~v~vI~~G~~~~~~~~l~~~~ 158 (187)
T cd01452 108 QRIVAFVGSPIEE-DEKDLVKLAKRLKKNNVSVDIINFGEIDDNTEKLTAFI 158 (187)
T ss_pred ceEEEEEecCCcC-CHHHHHHHHHHHHHcCCeEEEEEeCCCCCCHHHHHHHH
Confidence 4788999998654 44334456677788999999999995 4788998873
No 108
>COG1736 DPH2 Diphthamide synthase subunit DPH2 [Translation, ribosomal structure and biogenesis]
Probab=36.87 E-value=4.1e+02 Score=27.30 Aligned_cols=168 Identities=16% Similarity=0.248 Sum_probs=90.7
Q ss_pred cCCChHHHHHHHhhhhcCCCCcEEEEecccchhhhHHHHHHHHhhccCCCCCcceeeeeecceeeeecCCCCCCCCCCCC
Q 014409 47 ASINTSNCIENLSKHALTNGKPILVLYGLEYAHAIPHIREAVKVASSSYGSGLKLEINFADVMCTVITPSKDHKSLCGPA 126 (425)
Q Consensus 47 ~~ld~~~~~~~~~~~~~~~~~~v~l~~dvqy~~~l~~l~~~L~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~g~~ 126 (425)
..+|.+.++..+++. ..++|+|-+.--..+...++.+.|++... .++.+.. +|.-
T Consensus 8 ~~~e~~~iv~~ir~~---~ak~V~LQ~PeGLk~~~~~ia~~le~~~~-------~~v~i~g------d~~y--------- 62 (347)
T COG1736 8 YNYEIEEIVREIRRL---GAKRVLLQFPEGLKRYAIEIADILEANLG-------AEVIISG------DPVY--------- 62 (347)
T ss_pred eecchhHHHHHHHhC---CCceEEEECChHHHHHHHHHHHHHHHhhC-------ceEEEeC------Cccc---------
Confidence 345677778777754 35789998888888888899999988621 2222210 1110
Q ss_pred CCcccccccCccccCCCccCccceEEEEEcCCchhhhHHHhhcCCceEEEecCCCCccccccCcHHHHHHHHHHHHHHHh
Q 014409 127 GGCTRHTIGGLVWNIPDRKKMEEHLLFWIGSDNSAFANVVLTFNGCEIVRYDATEERLLTDVSQPLKILKRRYYLVEKAK 206 (425)
Q Consensus 127 ~gc~~~~~~~~~~~~~~~~~~~~~~i~~Ig~~~~~l~~l~l~~~~~~v~~yDP~~~~~~~~~~~~~r~L~rRy~~I~ka~ 206 (425)
+.|.-... . .... .-.++|+|..... + ..++.. ..|=|...++ +...+...=-..++ +
T Consensus 63 GACdi~~~-----~---a~~~-~D~iVH~GHs~l~--~--~~~~~~--Viyv~~~~~~-----d~~~~~~~~~~~l~--~ 120 (347)
T COG1736 63 GACDIDDL-----K---AKDV-VDLIVHYGHSCLP--P--VEYELP--VIYVFAFSRV-----DVDLVVLEATRELK--K 120 (347)
T ss_pred ccccCCHH-----H---Hhhc-ccEEEEcccccCC--C--cCCCCc--EEEeeccccc-----chhHHHHHhhHhhc--c
Confidence 22321000 0 0011 1278999987632 1 111111 2222222221 12221111111222 2
Q ss_pred cCCeEEEEEcCCcccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHHHhcCCCCCCEEEEecCCCcccc
Q 014409 207 DANIIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKLANFPECDVFINVSCAQTALL 274 (425)
Q Consensus 207 ~A~~iGIlvgTl~~q~~~~~i~~Lk~li~~~GKk~Y~~~vgkln~aKLaNF~eID~fV~vaCPr~si~ 274 (425)
..+.||++. | ..+...++.+++.|+..|. .+++++.+-- .++. ..++||.-.++.
T Consensus 121 ~~r~I~li~-t---~q~~~~l~~~k~~L~~~g~---~v~i~~~~~r-~~~~-----gqVLGC~~~~~~ 175 (347)
T COG1736 121 GSRRIGLIT-T---AQHVHLLEEVKEILEGRGY---EVVIGRGQTR-PAYP-----GQVLGCNFSVLE 175 (347)
T ss_pred CCceEEEEe-c---ccchhHHHHHHHHhhcCCe---EEEEeCCCCc-ccCc-----ceeeccccccCC
Confidence 455687766 3 5677888999999998776 8888888765 4443 345677666654
No 109
>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=36.66 E-value=1.7e+02 Score=24.23 Aligned_cols=68 Identities=19% Similarity=0.150 Sum_probs=46.8
Q ss_pred HHHHHhcCCeEEEEEcCCcccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHHHhcCCCCCCEEEEecCCCcc
Q 014409 201 LVEKAKDANIIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKLANFPECDVFINVSCAQTA 272 (425)
Q Consensus 201 ~I~ka~~A~~iGIlvgTl~~q~~~~~i~~Lk~li~~~GKk~Y~~~vgkln~aKLaNF~eID~fV~vaCPr~s 272 (425)
.++...+++++ +++|+ .....+.+.++..++..|+..+.+.=......-+.+..+=|++++++-...+
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 34445666775 66666 3466789999999999999888764444444444455667899988877653
No 110
>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=36.37 E-value=68 Score=30.15 Aligned_cols=74 Identities=16% Similarity=0.127 Sum_probs=48.2
Q ss_pred eEEEEEcCCcccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHH-------HhcCCCCCCEEEEecCCCc---c-cccccC
Q 014409 210 IIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPA-------KLANFPECDVFINVSCAQT---A-LLDSKE 278 (425)
Q Consensus 210 ~iGIlvgTl~~q~~~~~i~~Lk~li~~~GKk~Y~~~vgkln~a-------KLaNF~eID~fV~vaCPr~---s-i~d~~e 278 (425)
.||+|+..+.-..+..+++.+++.+++.|.+..++ -+.=+++ +|.+ ..+|.+|+.++... . +....+
T Consensus 1 ~i~vi~~~~~~~~~~~~~~~i~~~~~~~g~~~~~~-~~~~~~~~~~~~i~~~~~-~~~dgiii~~~~~~~~~~~l~~~~~ 78 (277)
T cd06319 1 QIAYIVSDLRIPFWQIMGRGVKSKAKALGYDAVEL-SAENSAKKELENLRTAID-KGVSGIIISPTNSSAAVTLLKLAAQ 78 (277)
T ss_pred CeEEEeCCCCchHHHHHHHHHHHHHHhcCCeEEEe-cCCCCHHHHHHHHHHHHh-cCCCEEEEcCCchhhhHHHHHHHHH
Confidence 37888888777777899999999999988766543 2333433 2333 36899988776422 1 222345
Q ss_pred CCCcccC
Q 014409 279 FLAPVIT 285 (425)
Q Consensus 279 f~kPViT 285 (425)
...|||+
T Consensus 79 ~~ipvV~ 85 (277)
T cd06319 79 AKIPVVI 85 (277)
T ss_pred CCCCEEE
Confidence 5668876
No 111
>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=36.24 E-value=77 Score=29.58 Aligned_cols=59 Identities=12% Similarity=0.200 Sum_probs=36.5
Q ss_pred eEEEEEcC-----CcccCcHHHHHHHHHHHHHcCCcEEEEEcCCCC--HHHhcCC---CCCCEEEEecC
Q 014409 210 IIGVLVGT-----LGVAGYLHMIHQMKELITKAGKKAYTLVMGKPN--PAKLANF---PECDVFINVSC 268 (425)
Q Consensus 210 ~iGIlvgT-----l~~q~~~~~i~~Lk~li~~~GKk~Y~~~vgkln--~aKLaNF---~eID~fV~vaC 268 (425)
+||+|+.. +.-..+..+++.+++.+++.|.+..+....... ...+.++ ..+|++|+++.
T Consensus 1 ~igli~p~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~dgiii~~~ 69 (270)
T cd06294 1 TIGVVLPPSADEAFQNPFFIEVLRGISAVANENGYDISLATGKNEEELLEEVKKMIQQKRVDGFILLYS 69 (270)
T ss_pred CEEEEeCCccccCcCCCCHHHHHHHHHHHHHHCCCEEEEecCCCcHHHHHHHHHHHHHcCcCEEEEecC
Confidence 47888875 445567788999999999988775433222211 1122221 24899888764
No 112
>PRK10936 TMAO reductase system periplasmic protein TorT; Provisional
Probab=36.14 E-value=51 Score=32.92 Aligned_cols=79 Identities=23% Similarity=0.122 Sum_probs=49.8
Q ss_pred hcCCeEEEEEcCCcccCcHHHHHHHHHHHHHcCCcEEEEEcC-CCCHHHh----cCC--CCCCEEEEecCCCcccc---c
Q 014409 206 KDANIIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMG-KPNPAKL----ANF--PECDVFINVSCAQTALL---D 275 (425)
Q Consensus 206 ~~A~~iGIlvgTl~~q~~~~~i~~Lk~li~~~GKk~Y~~~vg-kln~aKL----aNF--~eID~fV~vaCPr~si~---d 275 (425)
+..++||+|+.++.-..+..+++.+++.+++.|.+.-++... .-+.++. .++ ..+|++|+.+.....+. .
T Consensus 44 r~t~~Igvv~p~~~~~f~~~~~~gi~~aa~~~G~~l~i~~~~~~~~~~~q~~~i~~l~~~~vdgIIl~~~~~~~~~~~l~ 123 (343)
T PRK10936 44 KKAWKLCALYPHLKDSYWLSVNYGMVEEAKRLGVDLKVLEAGGYYNLAKQQQQLEQCVAWGADAILLGAVTPDGLNPDLE 123 (343)
T ss_pred CCCeEEEEEecCCCchHHHHHHHHHHHHHHHhCCEEEEEcCCCCCCHHHHHHHHHHHHHhCCCEEEEeCCChHHhHHHHH
Confidence 347899999988776667788999999999999765554332 2333333 222 25899998764433211 2
Q ss_pred ccCCCCccc
Q 014409 276 SKEFLAPVI 284 (425)
Q Consensus 276 ~~ef~kPVi 284 (425)
.++-..|||
T Consensus 124 ~~~~giPvV 132 (343)
T PRK10936 124 LQAANIPVI 132 (343)
T ss_pred HHHCCCCEE
Confidence 234445665
No 113
>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=34.77 E-value=49 Score=31.34 Aligned_cols=77 Identities=26% Similarity=0.218 Sum_probs=49.7
Q ss_pred eEEEEEcCCcccCcHHHHHHHHHHHHHcCCcEEEEEcCC-CCHH----HhcCC--CCCCEEEEecCCCccc---ccccCC
Q 014409 210 IIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGK-PNPA----KLANF--PECDVFINVSCAQTAL---LDSKEF 279 (425)
Q Consensus 210 ~iGIlvgTl~~q~~~~~i~~Lk~li~~~GKk~Y~~~vgk-ln~a----KLaNF--~eID~fV~vaCPr~si---~d~~ef 279 (425)
+||||+..+....+..++..+++.+++.|.+..++..+. -+++ .+.++ ..+|..++.+...... .....-
T Consensus 1 ~Igvi~~~~~~~f~~~~~~gi~~~a~~~g~~~~~~~~~~~~~~~~~~~~i~~~~~~~vdgiI~~~~~~~~~~~~~~~~~~ 80 (268)
T cd06306 1 KLCVLYPHLKDAYWLSVNYGMVEEAKRLGVSLKLLEAGGYPNLAKQIAQLEDCAAWGADAILLGAVSPDGLNEILQQVAA 80 (268)
T ss_pred CeEEEcCCCCCHHHHHHHHHHHHHHHHcCCEEEEecCCCCCCHHHHHHHHHHHHHcCCCEEEEcCCChhhHHHHHHHHHC
Confidence 589999988777888999999999999998765554332 2332 22222 2689999887643322 222334
Q ss_pred CCcccCH
Q 014409 280 LAPVITP 286 (425)
Q Consensus 280 ~kPViTP 286 (425)
-.|||+-
T Consensus 81 giPvV~~ 87 (268)
T cd06306 81 SIPVIAL 87 (268)
T ss_pred CCCEEEe
Confidence 4577643
No 114
>PRK14571 D-alanyl-alanine synthetase A; Provisional
Probab=34.54 E-value=1.3e+02 Score=29.54 Aligned_cols=76 Identities=14% Similarity=0.050 Sum_probs=52.7
Q ss_pred eEEEEEcCCccc--CcHHHHHHHHHHHHHcCCcEEEEEcCCCCHHHhcCCCCCCEEEEecCCCccccc------ccCCCC
Q 014409 210 IIGVLVGTLGVA--GYLHMIHQMKELITKAGKKAYTLVMGKPNPAKLANFPECDVFINVSCAQTALLD------SKEFLA 281 (425)
Q Consensus 210 ~iGIlvgTl~~q--~~~~~i~~Lk~li~~~GKk~Y~~~vgkln~aKLaNF~eID~fV~vaCPr~si~d------~~ef~k 281 (425)
+|+||.|-.+.. -.+...+.+.+-|++.|.+...+-+.+--..++....++|+ |+..|+...-.| ...+-.
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 589999998854 44678889999999999999988777655556655667884 455665432112 124667
Q ss_pred cccCH
Q 014409 282 PVITP 286 (425)
Q Consensus 282 PViTP 286 (425)
|.+.+
T Consensus 81 p~~G~ 85 (299)
T PRK14571 81 RYTGS 85 (299)
T ss_pred CccCC
Confidence 88744
No 115
>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=34.19 E-value=66 Score=30.12 Aligned_cols=59 Identities=14% Similarity=0.066 Sum_probs=37.2
Q ss_pred eEEEEEcCC-cccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHHHhcCC------CCCCEEEEecCC
Q 014409 210 IIGVLVGTL-GVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKLANF------PECDVFINVSCA 269 (425)
Q Consensus 210 ~iGIlvgTl-~~q~~~~~i~~Lk~li~~~GKk~Y~~~vgkln~aKLaNF------~eID~fV~vaCP 269 (425)
+||+|+.++ ....+..+++.+++.++++|....++ -..-++++.... ..+|++++.++-
T Consensus 1 ~i~vi~p~~~~~~~~~~~~~g~~~~~~~~g~~~~~~-~~~~~~~~~~~~~~~l~~~~vdgiii~~~~ 66 (275)
T cd06317 1 TIGYTQNNVGSHSYQTTYNKAFQAAAEEDGVEVIVL-DANGDVARQAAQVEDLIAQKVDGIILWPTD 66 (275)
T ss_pred CeEEEecccCCCHHHHHHHHHHHHHHHhcCCEEEEE-cCCcCHHHHHHHHHHHHHcCCCEEEEecCC
Confidence 478888776 55566778888888888888765443 333344333111 257888887764
No 116
>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=34.16 E-value=43 Score=32.67 Aligned_cols=60 Identities=20% Similarity=0.241 Sum_probs=41.6
Q ss_pred EEEEEcCCcccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHHHhc----CC--CCCCEEEEecCCCc
Q 014409 211 IGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKLA----NF--PECDVFINVSCAQT 271 (425)
Q Consensus 211 iGIlvgTl~~q~~~~~i~~Lk~li~~~GKk~Y~~~vgkln~aKLa----NF--~eID~fV~vaCPr~ 271 (425)
||+++.++...-+..+.+-+++.+++.|....+... .-++++.. +| ..+|++++.++...
T Consensus 1 ig~~~~~~~~~~~~~~~~~i~~~a~~~g~~v~~~~~-~~~~~~q~~~i~~l~~~~vDgIIi~~~~~~ 66 (302)
T TIGR02634 1 IGVSIDDLRLERWQKDRDIFVAAAESLGAKVFVQSA-NGNEAKQISQIENLIARGVDVLVIIPQNGQ 66 (302)
T ss_pred CeeecCccchhhHHHHHHHHHHHHHhcCCEEEEEeC-CCCHHHHHHHHHHHHHcCCCEEEEeCCChh
Confidence 588888888777888888888888888876655433 34554332 22 25899888877543
No 117
>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=34.04 E-value=28 Score=29.91 Aligned_cols=46 Identities=26% Similarity=0.213 Sum_probs=35.3
Q ss_pred HHHHHhcCCeEEEEEcCCcccCcHHHHHHHHHHHHHcCCcEEEEEcCC
Q 014409 201 LVEKAKDANIIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGK 248 (425)
Q Consensus 201 ~I~ka~~A~~iGIlvgTl~~q~~~~~i~~Lk~li~~~GKk~Y~~~vgk 248 (425)
..+..+.|++--||+|.. ..+....+.+++++++.|-..++-.++|
T Consensus 4 ~~~~L~~A~rP~il~G~g--~~~~~a~~~l~~lae~~~~Pv~~t~~~k 49 (137)
T PF00205_consen 4 AADLLSSAKRPVILAGRG--ARRSGAAEELRELAEKLGIPVATTPMGK 49 (137)
T ss_dssp HHHHHHH-SSEEEEE-HH--HHHTTCHHHHHHHHHHHTSEEEEEGGGT
T ss_pred HHHHHHhCCCEEEEEcCC--cChhhHHHHHHHHHHHHCCCEEecCccc
Confidence 566788899999999984 3344667888899999999999888887
No 118
>PRK15395 methyl-galactoside ABC transporter galactose-binding periplasmic protein MglB; Provisional
Probab=33.87 E-value=64 Score=32.03 Aligned_cols=64 Identities=6% Similarity=-0.046 Sum_probs=40.1
Q ss_pred hcCCeEEEEEcCCcccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHH----HhcCCC--CCCEEEEecCC
Q 014409 206 KDANIIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPA----KLANFP--ECDVFINVSCA 269 (425)
Q Consensus 206 ~~A~~iGIlvgTl~~q~~~~~i~~Lk~li~~~GKk~Y~~~vgkln~a----KLaNF~--eID~fV~vaCP 269 (425)
+.-++||+++..++...+..+++.+.+.++++|....++..+.-++. .+.++. .+|.+++.+++
T Consensus 22 ~~~~~Igvv~~~~~~~f~~~~~~gi~~~a~~~g~~~~~~~~~~~~~~~~~~~i~~l~~~~vdgiIi~~~~ 91 (330)
T PRK15395 22 AADTRIGVTIYKYDDNFMSVVRKAIEKDAKAAPDVQLLMNDSQNDQSKQNDQIDVLLAKGVKALAINLVD 91 (330)
T ss_pred cCCceEEEEEecCcchHHHHHHHHHHHHHHhcCCeEEEEecCCCCHHHHHHHHHHHHHcCCCEEEEeccC
Confidence 33478888888777667778888888888887643333333333332 222332 58888887655
No 119
>PRK05568 flavodoxin; Provisional
Probab=33.69 E-value=2e+02 Score=24.48 Aligned_cols=56 Identities=13% Similarity=0.141 Sum_probs=43.0
Q ss_pred eEEEEEcCCcccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHHHhcCCCCCCEEEEecCCC
Q 014409 210 IIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKLANFPECDVFINVSCAQ 270 (425)
Q Consensus 210 ~iGIlvgTl~~q~~~~~i~~Lk~li~~~GKk~Y~~~vgkln~aKLaNF~eID~fV~vaCPr 270 (425)
.+.|+-.|.. -+...+++.|.+-+++.|-..-++-+.+.+..+|.+ .|. |++++|=
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 4678888854 567899999999999999988888888888776654 464 5566664
No 120
>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=33.65 E-value=1e+02 Score=29.05 Aligned_cols=75 Identities=12% Similarity=0.121 Sum_probs=46.9
Q ss_pred eEEEEEcCCcccCcHHHHHHHHHHHHHcCCc----EEEEEcC-CCCHH-------HhcCCCCCCEEEEecCCCccccccc
Q 014409 210 IIGVLVGTLGVAGYLHMIHQMKELITKAGKK----AYTLVMG-KPNPA-------KLANFPECDVFINVSCAQTALLDSK 277 (425)
Q Consensus 210 ~iGIlvgTl~~q~~~~~i~~Lk~li~~~GKk----~Y~~~vg-kln~a-------KLaNF~eID~fV~vaCPr~si~d~~ 277 (425)
+||+++. ..-..+..+++.+++.++++|.. .-+++.. .-+++ +|.+- .+|.+|+.+++-....-..
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 5889885 66567789999999999999863 3333332 33343 45553 6899999876522111122
Q ss_pred CCCCcccCH
Q 014409 278 EFLAPVITP 286 (425)
Q Consensus 278 ef~kPViTP 286 (425)
..-.|||..
T Consensus 79 ~~~iPvV~~ 87 (281)
T cd06325 79 TKDIPIVFT 87 (281)
T ss_pred CCCCCEEEE
Confidence 345588755
No 121
>PRK12359 flavodoxin FldB; Provisional
Probab=33.42 E-value=1.3e+02 Score=27.42 Aligned_cols=53 Identities=13% Similarity=0.252 Sum_probs=39.3
Q ss_pred eEEEEEcCCcccCcHHHHHHHHHHHHHcCC-cEEEEEcCCCCHHHhcCCCCCCEEEEecCCC
Q 014409 210 IIGVLVGTLGVAGYLHMIHQMKELITKAGK-KAYTLVMGKPNPAKLANFPECDVFINVSCAQ 270 (425)
Q Consensus 210 ~iGIlvgTl~~q~~~~~i~~Lk~li~~~GK-k~Y~~~vgkln~aKLaNF~eID~fV~vaCPr 270 (425)
.++|+-+|.+ -+...++++|++.+ |. ..-++-+.+..+..|.++ | +++++||=
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 46788888888776 43 356677788888777665 4 67788886
No 122
>PRK11104 hemG protoporphyrinogen oxidase; Provisional
Probab=33.13 E-value=73 Score=29.02 Aligned_cols=54 Identities=6% Similarity=0.120 Sum_probs=37.6
Q ss_pred eEEEEEcCCcccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHHHhcCCCCCCEEEEecCC
Q 014409 210 IIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKLANFPECDVFINVSCA 269 (425)
Q Consensus 210 ~iGIlvgTl~~q~~~~~i~~Lk~li~~~GKk~Y~~~vgkln~aKLaNF~eID~fV~vaCP 269 (425)
.+.|+-+|.. -+...+++.|.+.|.. |..+-++-+.+.... ++.+.|. |++++|
T Consensus 2 kilIvY~S~~-G~T~~iA~~Ia~~l~~-g~~v~~~~~~~~~~~---~l~~yD~-vIlGsp 55 (177)
T PRK11104 2 KTLILYSSRD-GQTRKIASYIASELKE-GIQCDVVNLHRIEEP---DLSDYDR-VVIGAS 55 (177)
T ss_pred cEEEEEECCC-ChHHHHHHHHHHHhCC-CCeEEEEEhhhcCcc---CHHHCCE-EEEECc
Confidence 3578888865 4567889999999887 877666666655543 3445687 566666
No 123
>PF12641 Flavodoxin_3: Flavodoxin domain
Probab=33.07 E-value=89 Score=28.23 Aligned_cols=96 Identities=19% Similarity=0.276 Sum_probs=48.2
Q ss_pred ccceEEEEEcCCc------hhhhHHHhhcCCceEEEecCCCCccccccCcHHHHHHHHHHHHHHHhcCCeEEEEEcCCcc
Q 014409 147 MEEHLLFWIGSDN------SAFANVVLTFNGCEIVRYDATEERLLTDVSQPLKILKRRYYLVEKAKDANIIGVLVGTLGV 220 (425)
Q Consensus 147 ~~~~~i~~Ig~~~------~~l~~l~l~~~~~~v~~yDP~~~~~~~~~~~~~r~L~rRy~~I~ka~~A~~iGIlvgTl~~ 220 (425)
+++|-++|+|..- ..+..++-.+.+++|+.|-..-.-. . +...++-...++++.+.+ -.++|+.--
T Consensus 37 ~~~yD~i~lG~w~d~G~~d~~~~~fl~~l~~KkV~lF~T~G~~~--~----s~~~~~~~~~~~~~~~~~--~~~lg~f~C 108 (160)
T PF12641_consen 37 LEDYDLIFLGFWIDKGTPDKDMKEFLKKLKGKKVALFGTAGAGP--D----SEYAKKILKNVEALLPKG--NEILGTFMC 108 (160)
T ss_pred CCCCCEEEEEcCccCCCCCHHHHHHHHHccCCeEEEEEecCCCC--c----hHHHHHHHHHHHHhhccC--CeecceEEe
Confidence 4567788888543 2344445455667777776553211 1 112222333334443433 344444444
Q ss_pred cC--cHHHHHHHHHHHHHcCCcEEEEEcCCCCHHHhcCC
Q 014409 221 AG--YLHMIHQMKELITKAGKKAYTLVMGKPNPAKLANF 257 (425)
Q Consensus 221 q~--~~~~i~~Lk~li~~~GKk~Y~~~vgkln~aKLaNF 257 (425)
|| -..+++++++++...... +.+++.++||
T Consensus 109 qGk~~~~~~e~~~~~~~~~~~~-------~~~~~~~~~~ 140 (160)
T PF12641_consen 109 QGKMDPKVIEKYKKMLPKNPPH-------AMTPERLARF 140 (160)
T ss_pred CCcCCHHHHHHHHhccCCCCCC-------cccHHHHHHH
Confidence 44 457777777764433222 4445555555
No 124
>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=32.87 E-value=84 Score=29.44 Aligned_cols=58 Identities=16% Similarity=-0.054 Sum_probs=39.7
Q ss_pred eEEEEEcCCcccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHHHhcC----C--CCCCEEEEecC
Q 014409 210 IIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKLAN----F--PECDVFINVSC 268 (425)
Q Consensus 210 ~iGIlvgTl~~q~~~~~i~~Lk~li~~~GKk~Y~~~vgkln~aKLaN----F--~eID~fV~vaC 268 (425)
+||+|+.++.-..+..+++.+.+.+++.|.+..++ -..-++++-.+ + ..+|++|+.+.
T Consensus 1 ~Ig~i~~~~~~~~~~~~~~gi~~~~~~~g~~~~~~-~~~~~~~~~~~~l~~~~~~~vdgii~~~~ 64 (273)
T cd06305 1 RIAVVRYGGSGDFDQAYLAGTKAEAEALGGDLRVY-DAGGDDAKQADQIDQAIAQKVDAIIIQHG 64 (273)
T ss_pred CeEEEeecCCCcHHHHHHHHHHHHHHHcCCEEEEE-CCCCCHHHHHHHHHHHHHcCCCEEEEecC
Confidence 47888888766666788888888888888775544 34555654322 1 25888888653
No 125
>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=32.63 E-value=98 Score=28.28 Aligned_cols=74 Identities=22% Similarity=0.192 Sum_probs=45.2
Q ss_pred eEEEEEcCCcccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHH-------HhcCCCCCCEEEEecCCCccc---ccccCC
Q 014409 210 IIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPA-------KLANFPECDVFINVSCAQTAL---LDSKEF 279 (425)
Q Consensus 210 ~iGIlvgTl~~q~~~~~i~~Lk~li~~~GKk~Y~~~vgkln~a-------KLaNF~eID~fV~vaCPr~si---~d~~ef 279 (425)
+||++.....-..+..+++-+++.+++.|.+.-++-.+ -+++ +|.+- .+|++|..+|....+ ....+-
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 47888866545566788888888888888765444333 2332 23332 688888888876553 222334
Q ss_pred CCcccC
Q 014409 280 LAPVIT 285 (425)
Q Consensus 280 ~kPViT 285 (425)
..|+|+
T Consensus 79 ~ip~v~ 84 (264)
T cd01537 79 GIPVVL 84 (264)
T ss_pred CCCEEE
Confidence 456664
No 126
>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=32.60 E-value=91 Score=29.07 Aligned_cols=59 Identities=10% Similarity=0.080 Sum_probs=41.4
Q ss_pred eEEEEEcCC-cccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHHHh----cCC--CCCCEEEEecCC
Q 014409 210 IIGVLVGTL-GVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKL----ANF--PECDVFINVSCA 269 (425)
Q Consensus 210 ~iGIlvgTl-~~q~~~~~i~~Lk~li~~~GKk~Y~~~vgkln~aKL----aNF--~eID~fV~vaCP 269 (425)
+||+|+-.. .-..+..+++.+++.+++.|....++. ..-++++. .++ ..+|..++.++.
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 556667899999999999997764443 34444322 222 258999998764
No 127
>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=32.58 E-value=80 Score=29.75 Aligned_cols=74 Identities=15% Similarity=0.100 Sum_probs=43.7
Q ss_pred eEEEEEcCCcccCcHHHHHHHHHHHHHcCCcEEEEEcC-CCCHHH-------hcCCCCCCEEEEecCCCccc----cccc
Q 014409 210 IIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMG-KPNPAK-------LANFPECDVFINVSCAQTAL----LDSK 277 (425)
Q Consensus 210 ~iGIlvgTl~~q~~~~~i~~Lk~li~~~GKk~Y~~~vg-kln~aK-------LaNF~eID~fV~vaCPr~si----~d~~ 277 (425)
.||+|+..+.--.+..+++.+++.+++.|...-++... .-++++ |.+- .+|+.|+.++....+ ...+
T Consensus 1 ~igvi~~~~~~~~~~~~~~gi~~~~~~~g~~~~~~~~~~~~~~~~~~~~i~~l~~~-~vdgiIi~~~~~~~~~~~~~~~~ 79 (275)
T cd06320 1 KYGVVLKTLSNEFWRSLKEGYENEAKKLGVSVDIQAAPSEGDQQGQLSIAENMINK-GYKGLLFSPISDVNLVPAVERAK 79 (275)
T ss_pred CeeEEEecCCCHHHHHHHHHHHHHHHHhCCeEEEEccCCCCCHHHHHHHHHHHHHh-CCCEEEECCCChHHhHHHHHHHH
Confidence 37888877766666788888888888888765444332 223332 2222 578888765543222 1223
Q ss_pred CCCCccc
Q 014409 278 EFLAPVI 284 (425)
Q Consensus 278 ef~kPVi 284 (425)
+...|||
T Consensus 80 ~~~iPvV 86 (275)
T cd06320 80 KKGIPVV 86 (275)
T ss_pred HCCCeEE
Confidence 4555766
No 128
>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=32.20 E-value=47 Score=28.75 Aligned_cols=35 Identities=17% Similarity=0.384 Sum_probs=25.2
Q ss_pred CCCEEEEecCCCcccccccCCCCcccCHHHHHHhhCCCCccccceeeccccc
Q 014409 259 ECDVFINVSCAQTALLDSKEFLAPVITPFEAMLAFGRGTQWTGAYVMEFRDL 310 (425)
Q Consensus 259 eID~fV~vaCPr~si~d~~ef~kPViTP~ElevAL~~~~~W~g~y~~Df~~l 310 (425)
||++||++.=|-++|+-.+. + +.. ...|++||+.=
T Consensus 74 eIel~VLttqpDIai~l~~k------------V-ldn----EnRYViDFD~R 108 (144)
T PF10657_consen 74 EIELFVLTTQPDIAINLQQK------------V-LDN----ENRYVIDFDKR 108 (144)
T ss_pred ceEEEEEccCCCeeechhhh------------h-hcc----cceEEEeccCC
Confidence 89999999999999873221 1 222 26899999653
No 129
>PRK09701 D-allose transporter subunit; Provisional
Probab=32.18 E-value=96 Score=30.35 Aligned_cols=64 Identities=11% Similarity=0.076 Sum_probs=44.0
Q ss_pred HHhcCCeEEEEEcCCcccCcHHHHHHHHHHHHHcCCcEEEEE-cCCCCHHH----hcCC--CCCCEEEEec
Q 014409 204 KAKDANIIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLV-MGKPNPAK----LANF--PECDVFINVS 267 (425)
Q Consensus 204 ka~~A~~iGIlvgTl~~q~~~~~i~~Lk~li~~~GKk~Y~~~-vgkln~aK----LaNF--~eID~fV~va 267 (425)
.|.-|.+||+|+.++.-..+..+++.+++.+++.|....++. -+.-++++ |.+| ..+|.+|+.+
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 355577999999887766678899999999998887766543 23334433 3344 2589888864
No 130
>PRK09240 thiH thiamine biosynthesis protein ThiH; Reviewed
Probab=31.74 E-value=1.1e+02 Score=31.41 Aligned_cols=57 Identities=23% Similarity=0.288 Sum_probs=45.0
Q ss_pred HHHHHHHHHHHhcCCe----EEEEEcCCcccC--cHHHHHHHHHHHHHcCCcEEEEEcCCCCHH
Q 014409 195 LKRRYYLVEKAKDANI----IGVLVGTLGVAG--YLHMIHQMKELITKAGKKAYTLVMGKPNPA 252 (425)
Q Consensus 195 L~rRy~~I~ka~~A~~----iGIlvgTl~~q~--~~~~i~~Lk~li~~~GKk~Y~~~vgkln~a 252 (425)
...|...++.|++|+. .|+|+|. +... ...++.+|+.|=...++..+.+.+..++|.
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 5689999999999963 7899985 4333 567788888887778888888888888876
No 131
>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=31.58 E-value=75 Score=30.19 Aligned_cols=58 Identities=14% Similarity=0.079 Sum_probs=40.0
Q ss_pred eEEEEEcCCcccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHHHhc----CC--CCCCEEEEecCC
Q 014409 210 IIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKLA----NF--PECDVFINVSCA 269 (425)
Q Consensus 210 ~iGIlvgTl~~q~~~~~i~~Lk~li~~~GKk~Y~~~vgkln~aKLa----NF--~eID~fV~vaCP 269 (425)
+||+|+.++....+..+++.+.+.+++.|.+.-++. .. ++++.. ++ ..+|.+|+.++.
T Consensus 1 ~Ig~v~~~~~~~~~~~~~~gi~~~~~~~g~~~~~~~-~~-~~~~~~~~i~~~~~~~~dgiii~~~~ 64 (289)
T cd01540 1 KIGFIVKQPEEPWFQTEWKFAKKAAKEKGFTVVKID-VP-DGEKVLSAIDNLGAQGAKGFVICVPD 64 (289)
T ss_pred CeeeecCCCCCcHHHHHHHHHHHHHHHcCCEEEEcc-CC-CHHHHHHHHHHHHHcCCCEEEEccCc
Confidence 588899887767788899999999999886643332 33 554332 11 258999987763
No 132
>PRK10727 DNA-binding transcriptional regulator GalR; Provisional
Probab=31.39 E-value=1.7e+02 Score=28.81 Aligned_cols=62 Identities=15% Similarity=0.279 Sum_probs=43.7
Q ss_pred cCCeEEEEEcCCcccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHHH----hcCC--CCCCEEEEecCC
Q 014409 207 DANIIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAK----LANF--PECDVFINVSCA 269 (425)
Q Consensus 207 ~A~~iGIlvgTl~~q~~~~~i~~Lk~li~~~GKk~Y~~~vgkln~aK----LaNF--~eID~fV~vaCP 269 (425)
..++||+++.++.-..+..+++.+.+.++++|....+.. +.-++++ +.++ ..+|.+++.++.
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 467999999988777788999999999999997654332 3333332 2222 268999988653
No 133
>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=31.26 E-value=1.1e+02 Score=28.07 Aligned_cols=50 Identities=18% Similarity=0.175 Sum_probs=36.9
Q ss_pred CCeEEEEEcCCcccCc--HHHHHHHHHHHHHcCCcEEEEEcCCCCHHHhcCCC
Q 014409 208 ANIIGVLVGTLGVAGY--LHMIHQMKELITKAGKKAYTLVMGKPNPAKLANFP 258 (425)
Q Consensus 208 A~~iGIlvgTl~~q~~--~~~i~~Lk~li~~~GKk~Y~~~vgkln~aKLaNF~ 258 (425)
+..+.||+ |=|.... ..-+....+.++++|.+.|++-||..+.++|....
T Consensus 108 ~~kv~Ill-TDG~s~~~~~~~~~~~a~~lk~~gV~i~~vGiG~~~~~el~~ia 159 (192)
T cd01473 108 APKVTMLF-TDGNDTSASKKELQDISLLYKEENVKLLVVGVGAASENKLKLLA 159 (192)
T ss_pred CCeEEEEE-ecCCCCCcchhhHHHHHHHHHHCCCEEEEEEeccccHHHHHHhc
Confidence 47787777 4344432 23456667788999999999999999988887664
No 134
>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=31.16 E-value=66 Score=38.03 Aligned_cols=113 Identities=15% Similarity=0.216 Sum_probs=71.2
Q ss_pred EEEecCCCCccccccCcHHHHHHHHHHHHHHHhcCCeEEEEEcCCcc-cCcHHHHHHHHHHHHHcCCcEEEEEcCC--CC
Q 014409 174 IVRYDATEERLLTDVSQPLKILKRRYYLVEKAKDANIIGVLVGTLGV-AGYLHMIHQMKELITKAGKKAYTLVMGK--PN 250 (425)
Q Consensus 174 v~~yDP~~~~~~~~~~~~~r~L~rRy~~I~ka~~A~~iGIlvgTl~~-q~~~~~i~~Lk~li~~~GKk~Y~~~vgk--ln 250 (425)
.-.|.|....+.....+..++.+.|-. -.-++.+||||+..--. .+....++.|-+.|+++|-.++.++..- -.
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 356666665443322222222222211 13468999999976543 5678999999999999999999988653 33
Q ss_pred HHHhcC-C-----CCCCEEEEecCCCccc-------ccccCCCCcccCHHHH
Q 014409 251 PAKLAN-F-----PECDVFINVSCAQTAL-------LDSKEFLAPVITPFEA 289 (425)
Q Consensus 251 ~aKLaN-F-----~eID~fV~vaCPr~si-------~d~~ef~kPViTP~El 289 (425)
...+.. | +.||+.|.+.+=++.- ...++..-|||.+.-+
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 333422 3 2499999988866543 2345677888877543
No 135
>PRK08091 ribulose-phosphate 3-epimerase; Validated
Probab=30.85 E-value=1.6e+02 Score=28.37 Aligned_cols=60 Identities=8% Similarity=0.031 Sum_probs=38.6
Q ss_pred cCCeEEEEEcCCc--ccCcH-H---HHHHHHHHHHHcCCcEEEEEcCCCCHHHhcCCC--CCCEEEEe
Q 014409 207 DANIIGVLVGTLG--VAGYL-H---MIHQMKELITKAGKKAYTLVMGKPNPAKLANFP--ECDVFINV 266 (425)
Q Consensus 207 ~A~~iGIlvgTl~--~q~~~-~---~i~~Lk~li~~~GKk~Y~~~vgkln~aKLaNF~--eID~fV~v 266 (425)
....+=|..-..| ||.+. . =+++++++++++|.+.-+-+=|-+|.+-+.-.. ++|+||.=
T Consensus 140 ~vD~VLiMtV~PGfgGQ~f~~~~l~KI~~lr~~~~~~~~~~~IeVDGGI~~~ti~~l~~aGaD~~V~G 207 (228)
T PRK08091 140 QIDLIQILTLDPRTGTKAPSDLILDRVIQVENRLGNRRVEKLISIDGSMTLELASYLKQHQIDWVVSG 207 (228)
T ss_pred hcCEEEEEEECCCCCCccccHHHHHHHHHHHHHHHhcCCCceEEEECCCCHHHHHHHHHCCCCEEEEC
Confidence 4555555444444 67665 3 455556677777777666777789988665442 58988873
No 136
>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=29.91 E-value=97 Score=29.18 Aligned_cols=57 Identities=7% Similarity=0.018 Sum_probs=37.9
Q ss_pred eEEEEEcC--CcccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHHHhc----CC--CCCCEEEEecC
Q 014409 210 IIGVLVGT--LGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKLA----NF--PECDVFINVSC 268 (425)
Q Consensus 210 ~iGIlvgT--l~~q~~~~~i~~Lk~li~~~GKk~Y~~~vgkln~aKLa----NF--~eID~fV~vaC 268 (425)
+||+|+.. ++...+..+++.+++.+++.|....+.... ++++.. ++ ..+|.++++++
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 555677788899999999888765554333 444432 22 14898888653
No 137
>PRK10355 xylF D-xylose transporter subunit XylF; Provisional
Probab=29.73 E-value=1.1e+02 Score=30.39 Aligned_cols=64 Identities=14% Similarity=0.193 Sum_probs=47.4
Q ss_pred cCCeEEEEEcCCcccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHHHh----cCC--CCCCEEEEecCCCc
Q 014409 207 DANIIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKL----ANF--PECDVFINVSCAQT 271 (425)
Q Consensus 207 ~A~~iGIlvgTl~~q~~~~~i~~Lk~li~~~GKk~Y~~~vgkln~aKL----aNF--~eID~fV~vaCPr~ 271 (425)
++.+||+++..+.-..+..+++-+++.+++.|....+.. +.-++++. .++ ..+|.+|++++...
T Consensus 24 ~~~~Ig~i~~~~~~~f~~~~~~gi~~~a~~~g~~l~i~~-~~~~~~~~~~~i~~l~~~~vDGiIi~~~~~~ 93 (330)
T PRK10355 24 KEVKIGMAIDDLRLERWQKDRDIFVKKAESLGAKVFVQS-ANGNEETQMSQIENMINRGVDVLVIIPYNGQ 93 (330)
T ss_pred CCceEEEEecCCCchHHHHHHHHHHHHHHHcCCEEEEEC-CCCCHHHHHHHHHHHHHcCCCEEEEeCCChh
Confidence 468999999998888888999999999999997766543 33455433 222 26999999877543
No 138
>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=29.62 E-value=63 Score=33.91 Aligned_cols=15 Identities=13% Similarity=0.126 Sum_probs=6.8
Q ss_pred CHHHhc-CCCCCCEEE
Q 014409 250 NPAKLA-NFPECDVFI 264 (425)
Q Consensus 250 n~aKLa-NF~eID~fV 264 (425)
.++++. .++++|.+|
T Consensus 85 ~~~~~~~~~~~vd~v~ 100 (438)
T TIGR01574 85 LGNEIFQRAPYVDFVF 100 (438)
T ss_pred cHHHHHhcCCCCcEEE
Confidence 344443 245555554
No 139
>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=29.42 E-value=50 Score=31.16 Aligned_cols=59 Identities=12% Similarity=-0.003 Sum_probs=36.9
Q ss_pred eEEEEEcCCcccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHHHhcCC------CCCCEEEEecCC
Q 014409 210 IIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKLANF------PECDVFINVSCA 269 (425)
Q Consensus 210 ~iGIlvgTl~~q~~~~~i~~Lk~li~~~GKk~Y~~~vgkln~aKLaNF------~eID~fV~vaCP 269 (425)
+||+++=...-..+..+++.+.+.++++|.+..+..... +.++-.+. ..+|.+|+.++-
T Consensus 1 ~~g~~~~~~~~~~~~~~~~~~~~~a~~~g~~~~~~~~~~-~~~~~~~~i~~l~~~~vdgiIi~~~~ 65 (273)
T cd06309 1 TVGFSQVGAESPWRTAETKSIKDAAEKRGFDLKFADAQQ-KQENQISAIRSFIAQGVDVIILAPVV 65 (273)
T ss_pred CeeeccCCCCCHHHHHHHHHHHHHHHhcCCEEEEeCCCC-CHHHHHHHHHHHHHcCCCEEEEcCCc
Confidence 477777766656667788888888888877766654432 34322111 157888776643
No 140
>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=29.41 E-value=2.1e+02 Score=22.44 Aligned_cols=54 Identities=17% Similarity=0.153 Sum_probs=30.1
Q ss_pred EEcCCcccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHHHhcCCCCCCEEEEecCCC
Q 014409 214 LVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKLANFPECDVFINVSCAQ 270 (425)
Q Consensus 214 lvgTl~~q~~~~~i~~Lk~li~~~GKk~Y~~~vgkln~aKLaNF~eID~fV~vaCPr 270 (425)
+|..-|..-..-+..+|++.+.+.|....+-.++.-.... ...++| +|+++.|-
T Consensus 5 ivC~~G~~tS~~l~~~i~~~~~~~~i~~~v~~~~~~~~~~--~~~~~D-liist~~~ 58 (89)
T cd05566 5 VACGTGVATSTVVASKVKELLKENGIDVKVEQCKIAEVPS--LLDDAD-LIVSTTKV 58 (89)
T ss_pred EECCCCccHHHHHHHHHHHHHHHCCCceEEEEecHHHhhc--ccCCCc-EEEEcCCc
Confidence 3444344444578899999998888754443222222221 234678 55555554
No 141
>PRK08883 ribulose-phosphate 3-epimerase; Provisional
Probab=29.22 E-value=70 Score=30.44 Aligned_cols=104 Identities=11% Similarity=0.215 Sum_probs=59.0
Q ss_pred ceEEEEEcCCc-h-hhhHHHhhcCCceEEEecCCCCccccccCcHHHHHHHHHHHHHHHhcCCeEEEEEcC--CcccCcH
Q 014409 149 EHLLFWIGSDN-S-AFANVVLTFNGCEIVRYDATEERLLTDVSQPLKILKRRYYLVEKAKDANIIGVLVGT--LGVAGYL 224 (425)
Q Consensus 149 ~~~i~~Ig~~~-~-~l~~l~l~~~~~~v~~yDP~~~~~~~~~~~~~r~L~rRy~~I~ka~~A~~iGIlvgT--l~~q~~~ 224 (425)
++..||+-... . ..++..-...-+.-..++|.|.-- .+. . + +.....|=|.--. .++|.+.
T Consensus 83 d~i~~H~Ea~~~~~~~l~~ik~~g~k~GlalnP~Tp~~---------~i~-~--~---l~~~D~vlvMtV~PGfgGq~fi 147 (220)
T PRK08883 83 SMITFHVEASEHVDRTLQLIKEHGCQAGVVLNPATPLH---------HLE-Y--I---MDKVDLILLMSVNPGFGGQSFI 147 (220)
T ss_pred CEEEEcccCcccHHHHHHHHHHcCCcEEEEeCCCCCHH---------HHH-H--H---HHhCCeEEEEEecCCCCCceec
Confidence 34556665322 1 122222233345678889888531 111 1 1 2244444332222 2456664
Q ss_pred ----HHHHHHHHHHHHcCCcEEEEEcCCCCHHHhcCCC--CCCEEEEec
Q 014409 225 ----HMIHQMKELITKAGKKAYTLVMGKPNPAKLANFP--ECDVFINVS 267 (425)
Q Consensus 225 ----~~i~~Lk~li~~~GKk~Y~~~vgkln~aKLaNF~--eID~fV~va 267 (425)
+-++++++++.++|.+.-+.+-|-+|++.+.... +.|++|+.+
T Consensus 148 ~~~lekI~~l~~~~~~~~~~~~I~vdGGI~~eni~~l~~aGAd~vVvGS 196 (220)
T PRK08883 148 PHTLDKLRAVRKMIDESGRDIRLEIDGGVKVDNIREIAEAGADMFVAGS 196 (220)
T ss_pred HhHHHHHHHHHHHHHhcCCCeeEEEECCCCHHHHHHHHHcCCCEEEEeH
Confidence 4567777777777877778899999988776553 589999873
No 142
>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=28.86 E-value=70 Score=29.90 Aligned_cols=75 Identities=20% Similarity=0.199 Sum_probs=46.3
Q ss_pred eEEEEEcCCcccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHHHh-------cCCCCCCEEEEecCCCcccc----cccC
Q 014409 210 IIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKL-------ANFPECDVFINVSCAQTALL----DSKE 278 (425)
Q Consensus 210 ~iGIlvgTl~~q~~~~~i~~Lk~li~~~GKk~Y~~~vgkln~aKL-------aNF~eID~fV~vaCPr~si~----d~~e 278 (425)
+||+++.+..-..+..+++.+++.+++.|....+.. +.-++++- .+- .+|++|+.++...... ..++
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 478888887766667888999999998886654432 33344432 222 5899988776432211 1234
Q ss_pred CCCcccCH
Q 014409 279 FLAPVITP 286 (425)
Q Consensus 279 f~kPViTP 286 (425)
...|+|+.
T Consensus 79 ~~ipvV~~ 86 (267)
T cd06322 79 AGIPVITV 86 (267)
T ss_pred CCCCEEEE
Confidence 45566654
No 143
>PF14538 Raptor_N: Raptor N-terminal CASPase like domain
Probab=28.68 E-value=1.3e+02 Score=27.10 Aligned_cols=51 Identities=25% Similarity=0.472 Sum_probs=31.9
Q ss_pred cEEEEe-cCCCCCCCCCCCeEEEccccC-----CChHHHHHHHhhhhcCCCCcEEEEecccchhh
Q 014409 22 DCVIHY-GHTCLSPTSTLPAFFVFGKAS-----INTSNCIENLSKHALTNGKPILVLYGLEYAHA 80 (425)
Q Consensus 22 D~iVHy-GhaClsp~~~lpviYVf~~~~-----ld~~~~~~~~~~~~~~~~~~v~l~~dvqy~~~ 80 (425)
=+|+|| ||-+-.|++. -=|++|.+.. +.+..+.+.+ +.+.+.+.|-..+-.
T Consensus 92 RvLFHYnGhGvP~Pt~~-GeIw~f~~~~tqyip~si~dL~~~l-------g~Psi~V~DC~~AG~ 148 (154)
T PF14538_consen 92 RVLFHYNGHGVPRPTEN-GEIWVFNKNYTQYIPLSIYDLQSWL-------GSPSIYVFDCSNAGS 148 (154)
T ss_pred eEEEEECCCCCCCCCCC-CeEEEEcCCCCcceEEEHHHHHHhc-------CCCEEEEEECCcHHH
Confidence 479999 8998766642 3688888633 4444333322 346777778666543
No 144
>PRK09267 flavodoxin FldA; Validated
Probab=28.34 E-value=1.2e+02 Score=26.97 Aligned_cols=53 Identities=13% Similarity=0.232 Sum_probs=35.6
Q ss_pred eEEEEEcCCcccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHHHhcCCCCCCEEEEecCC
Q 014409 210 IIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKLANFPECDVFINVSCA 269 (425)
Q Consensus 210 ~iGIlvgTl~~q~~~~~i~~Lk~li~~~GKk~Y~~~vgkln~aKLaNF~eID~fV~vaCP 269 (425)
.+.|+-+|.. -+...++++|.+.+.. ...-++-+.+.++..|. +.|+ |++++|
T Consensus 3 ki~IiY~S~t-GnT~~vA~~Ia~~l~~--~~~~~~~~~~~~~~~l~---~~d~-vi~g~p 55 (169)
T PRK09267 3 KIGIFFGSDT-GNTEDIAKMIQKKLGK--DVADVVDIAKASKEDFE---AYDL-LILGIP 55 (169)
T ss_pred eEEEEEECCC-ChHHHHHHHHHHHhCC--CceEEEEhhhCCHhhHh---hCCE-EEEEec
Confidence 5789999976 3567888888888763 35566667777665554 4576 445544
No 145
>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=28.14 E-value=52 Score=32.02 Aligned_cols=59 Identities=10% Similarity=0.050 Sum_probs=37.2
Q ss_pred eEEEEEcCCcccCcHHHHHHHHHHHHH--cCCcEEEEEcCCCCHHH----hcCC--CCCCEEEEecCC
Q 014409 210 IIGVLVGTLGVAGYLHMIHQMKELITK--AGKKAYTLVMGKPNPAK----LANF--PECDVFINVSCA 269 (425)
Q Consensus 210 ~iGIlvgTl~~q~~~~~i~~Lk~li~~--~GKk~Y~~~vgkln~aK----LaNF--~eID~fV~vaCP 269 (425)
+||+|+..+.-..+..+++.|.+.+++ .|.+...+ -..-++++ |.++ ..+|.+|+.++.
T Consensus 1 ~Igviv~~~~~~~~~~~~~gi~~~a~~~~~g~~~~~~-~~~~~~~~q~~~i~~l~~~~vdgiii~~~~ 67 (303)
T cd01539 1 KIGVFLYKFDDTFISLVRKNLEDIQKENGGKVEFTFY-DAKNNQSTQNEQIDTALAKGVDLLAVNLVD 67 (303)
T ss_pred CeEEEeeCCCChHHHHHHHHHHHHHHhhCCCeeEEEe-cCCCCHHHHHHHHHHHHHcCCCEEEEecCc
Confidence 478888887766677888888888888 45443322 23334432 2222 268988887654
No 146
>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=27.79 E-value=1.2e+02 Score=28.47 Aligned_cols=55 Identities=15% Similarity=0.212 Sum_probs=39.9
Q ss_pred eEEEEEcCCcccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHH-------HhcCCCCCCEEEEe
Q 014409 210 IIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPA-------KLANFPECDVFINV 266 (425)
Q Consensus 210 ~iGIlvgTl~~q~~~~~i~~Lk~li~~~GKk~Y~~~vgkln~a-------KLaNF~eID~fV~v 266 (425)
+||+++.++.-..+..+++.+.+.+++.|....+... .-+++ .|.+- .+|++++.
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 4789998887677788999999999999887755443 44553 23333 68999885
No 147
>PRK05452 anaerobic nitric oxide reductase flavorubredoxin; Provisional
Probab=27.73 E-value=2.3e+02 Score=30.25 Aligned_cols=114 Identities=11% Similarity=0.167 Sum_probs=71.1
Q ss_pred HHHHHHHHHHHHHHHhcCCeEEEEEcCCcccCcHHHHHHHHHHHHHc--CCcEEEEEcCCCCHHHhcC-CCCCCEEEEec
Q 014409 191 PLKILKRRYYLVEKAKDANIIGVLVGTLGVAGYLHMIHQMKELITKA--GKKAYTLVMGKPNPAKLAN-FPECDVFINVS 267 (425)
Q Consensus 191 ~~r~L~rRy~~I~ka~~A~~iGIlvgTl~~q~~~~~i~~Lk~li~~~--GKk~Y~~~vgkln~aKLaN-F~eID~fV~va 267 (425)
..+++ ++|....+-+..+.+-|+-.|.. -+...+++.+.+-++++ |.++-++-+...+++.|.+ +.+.|+ |+++
T Consensus 235 ~~~~l-~~Y~~~~~~~~~~kv~IvY~S~~-GnTe~mA~~ia~gl~~~g~gv~v~~~~v~~~~~~~i~~~~~~ad~-vilG 311 (479)
T PRK05452 235 PTQIV-ELYLKWAADYQEDRITIFYDTMS-NNTRMMADAIAQGIAEVDPRVAVKIFNVARSDKNEILTNVFRSKG-VLVG 311 (479)
T ss_pred HHHHH-HHHHHHhhccCcCcEEEEEECCc-cHHHHHHHHHHHHHHhhCCCceEEEEECCCCCHHHHHhHHhhCCE-EEEE
Confidence 33433 34554444434577889998875 45679999999999987 5677788889999988753 446774 6677
Q ss_pred CCCcccccccCCCCcccCHHHHHHhhCC---------CCccccceeecccccc
Q 014409 268 CAQTALLDSKEFLAPVITPFEAMLAFGR---------GTQWTGAYVMEFRDLM 311 (425)
Q Consensus 268 CPr~si~d~~ef~kPViTP~ElevAL~~---------~~~W~g~y~~Df~~ll 311 (425)
||=. ....+. |+...++....+.. .-.|.|.+.-.+.+.|
T Consensus 312 spT~---~~~~~p-~~~~fl~~l~~~~l~gK~~~vFGSygw~g~a~~~~~~~l 360 (479)
T PRK05452 312 SSTM---NNVMMP-KIAGLLEEITGLRFRNKRASAFGSHGWSGGAVDRLSTRL 360 (479)
T ss_pred CCcc---CCcchH-HHHHHHHHhhccCcCCCEEEEEECCCcCcHHHHHHHHHH
Confidence 7753 222233 55555555433321 1256666655554444
No 148
>COG0622 Predicted phosphoesterase [General function prediction only]
Probab=27.67 E-value=54 Score=30.03 Aligned_cols=74 Identities=20% Similarity=0.175 Sum_probs=42.0
Q ss_pred CCCCCccCCccChhh--hcccCCcEEEEecCCCCCCC-----C--CCCeEEEccccCCChHHHHHHHhh--hhcCCCCcE
Q 014409 1 MADTTYGSCCVDEVG--ASHVDADCVIHYGHTCLSPT-----S--TLPAFFVFGKASINTSNCIENLSK--HALTNGKPI 69 (425)
Q Consensus 1 LaDtsYGsCCVDeva--A~hv~aD~iVHyGhaClsp~-----~--~lpviYVf~~~~ld~~~~~~~~~~--~~~~~~~~v 69 (425)
|+||=.-.|++.... ...-++|+|||-|+.=.+.+ . .-++++|+|+-..+... +.+.. .+.-.+.++
T Consensus 7 iSDtH~~~~~~~~~~~~~~~~~~d~vih~GD~~~~~~~~~l~~~~~~~i~~V~GN~D~~~~~--~~~p~~~~~~~~g~ki 84 (172)
T COG0622 7 ISDTHGPLRAIEKALKIFNLEKVDAVIHAGDSTSPFTLDALEGGLAAKLIAVRGNCDGEVDQ--EELPEELVLEVGGVKI 84 (172)
T ss_pred EeccCCChhhhhHHHHHhhhcCCCEEEECCCcCCccchHHhhcccccceEEEEccCCCcccc--ccCChhHeEEECCEEE
Confidence 467777776543332 23458999999999855432 1 34678999976554321 11110 111223578
Q ss_pred EEEeccc
Q 014409 70 LVLYGLE 76 (425)
Q Consensus 70 ~l~~dvq 76 (425)
.++-.=+
T Consensus 85 ~l~HGh~ 91 (172)
T COG0622 85 FLTHGHL 91 (172)
T ss_pred EEECCCc
Confidence 8876633
No 149
>PRK00061 ribH 6,7-dimethyl-8-ribityllumazine synthase; Provisional
Probab=27.01 E-value=1.6e+02 Score=26.61 Aligned_cols=61 Identities=15% Similarity=0.135 Sum_probs=39.9
Q ss_pred CeEEEEEcCCcccCcHHHHHHHHHHHHHcCC---cEEEEEcCC---C--CHHHhcCCCCCCEEEEecCC
Q 014409 209 NIIGVLVGTLGVAGYLHMIHQMKELITKAGK---KAYTLVMGK---P--NPAKLANFPECDVFINVSCA 269 (425)
Q Consensus 209 ~~iGIlvgTl~~q~~~~~i~~Lk~li~~~GK---k~Y~~~vgk---l--n~aKLaNF~eID~fV~vaCP 269 (425)
-+|+||++...-.-.-.+++...+.|++.|. ...++.|-- | -..+|++-.++|++|.+||-
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 4889999775443334666666778888883 333343321 1 12467766679999999997
No 150
>PRK09613 thiH thiamine biosynthesis protein ThiH; Reviewed
Probab=26.54 E-value=80 Score=33.68 Aligned_cols=58 Identities=28% Similarity=0.367 Sum_probs=43.5
Q ss_pred HHHHHHHHHHHhcCCe----EEEEEcCCccc--CcHHHHHHHHHHHHHcCCcEEEEEcCCCCHHH
Q 014409 195 LKRRYYLVEKAKDANI----IGVLVGTLGVA--GYLHMIHQMKELITKAGKKAYTLVMGKPNPAK 253 (425)
Q Consensus 195 L~rRy~~I~ka~~A~~----iGIlvgTl~~q--~~~~~i~~Lk~li~~~GKk~Y~~~vgkln~aK 253 (425)
...|...+++|++|+. .|+|+| |+.+ ..+.++-+++.|=+.-|-...+++|..+.|++
T Consensus 218 y~~Rl~t~~rA~~aGi~~Vg~G~L~G-Lge~~~E~~~l~~hl~~L~~~~gvgp~tIsvprl~P~~ 281 (469)
T PRK09613 218 YDWRLTAMDRAMEAGIDDVGIGVLFG-LYDYKFEVLGLLMHAEHLEERFGVGPHTISVPRLRPAD 281 (469)
T ss_pred HHHHHHHHHHHHHcCCCeeCeEEEEc-CCCCHHHHHHHHHHHHHHHHhhCCCCccccccceecCC
Confidence 5689999999999976 499999 6654 44667777777766666666778888777764
No 151
>KOG1736 consensus Glia maturation factor beta [Extracellular structures]
Probab=26.51 E-value=58 Score=28.33 Aligned_cols=61 Identities=25% Similarity=0.413 Sum_probs=45.8
Q ss_pred CCcEEEEEcC-----CCCHHHhcC-CCC-CCEEEEecCCCccccccc-------CCCCcccCHHHHHHhhCCCCcc
Q 014409 238 GKKAYTLVMG-----KPNPAKLAN-FPE-CDVFINVSCAQTALLDSK-------EFLAPVITPFEAMLAFGRGTQW 299 (425)
Q Consensus 238 GKk~Y~~~vg-----kln~aKLaN-F~e-ID~fV~vaCPr~si~d~~-------ef~kPViTP~ElevAL~~~~~W 299 (425)
-|..|.+++. .++|..||. +|| =-=||++|-|-.. +|++ =|++|+.+|.|..|.......|
T Consensus 38 dK~~~eiV~d~Eeld~is~eEladeLpe~~PRFvl~sYpt~t-~DGr~stPL~~Iyw~P~~~~~e~~MmYAgak~~ 112 (143)
T KOG1736|consen 38 DKDSYEIVLDEEELDEISPEELADELPERQPRFVLYSYPTTT-DDGRVSTPLCFIYWSPVGCKPEQQMMYAGAKNM 112 (143)
T ss_pred cCCceEeecCHHHhccCChHHHHhhccccCCcEEEEECcccc-cCCcccccEEEEEecCccCCHHHHHHHHHHHHH
Confidence 3777888877 788888875 454 3579999999765 3433 2899999999999987665556
No 152
>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=26.47 E-value=1.9e+02 Score=22.53 Aligned_cols=56 Identities=16% Similarity=0.242 Sum_probs=34.8
Q ss_pred EEEcCCcccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHHHhcCCCCCCEEEEecCCCcc
Q 014409 213 VLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKLANFPECDVFINVSCAQTA 272 (425)
Q Consensus 213 IlvgTl~~q~~~~~i~~Lk~li~~~GKk~Y~~~vgkln~aKLaNF~eID~fV~vaCPr~s 272 (425)
+++..-|.....-+.++|++.+++.|...-.............+ ++|+++.. |+..
T Consensus 3 lvvC~~Gi~TS~~~~~~i~~~~~~~gi~~~~~~~~~~~~~~~~~--~~D~il~~--~~i~ 58 (90)
T PF02302_consen 3 LVVCGSGIGTSLMVANKIKKALKELGIEVEVSAGSILEVEEIAD--DADLILLT--PQIA 58 (90)
T ss_dssp EEEESSSSHHHHHHHHHHHHHHHHTTECEEEEEEETTTHHHHHT--T-SEEEEE--ESSG
T ss_pred EEECCChHHHHHHHHHHHHHHHHhccCceEEEEecccccccccC--CCcEEEEc--Cccc
Confidence 34444444444445599999999999877777777444444433 46887654 4444
No 153
>PRK02910 light-independent protochlorophyllide reductase subunit B; Provisional
Probab=26.46 E-value=1.8e+02 Score=31.27 Aligned_cols=76 Identities=16% Similarity=0.130 Sum_probs=55.0
Q ss_pred CeEEEEEcCCcccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHHHhcCCCCCCEEEEecCCCccccc----ccCCCCccc
Q 014409 209 NIIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKLANFPECDVFINVSCAQTALLD----SKEFLAPVI 284 (425)
Q Consensus 209 ~~iGIlvgTl~~q~~~~~i~~Lk~li~~~GKk~Y~~~vgkln~aKLaNF~eID~fV~vaCPr~si~d----~~ef~kPVi 284 (425)
+.|-||=.+..+-+...=+..|+++|+.-|.+.-.+.-+.-+++.|.+.++.++= ++-||+.+..- .++|-.|.+
T Consensus 159 ~~VNIiG~~~l~f~~~~D~~EikrlL~~~Gi~vn~v~p~g~s~~di~~l~~A~~n-ivl~~~~g~~~A~~Lee~fGiP~i 237 (519)
T PRK02910 159 PSVNLLGPTALGFHHRDDLTELRRLLATLGIDVNVVAPLGASPADLKRLPAAWFN-VVLYREIGESAARYLEREFGQPYV 237 (519)
T ss_pred CeEEEEecCccCCCChhHHHHHHHHHHHcCCeEEEEeCCCCCHHHHHhcccCcEE-EEeCHHHHHHHHHHHHHHhCCccc
Confidence 4566665544334445666779999999999998888888999999999876553 34499865431 356888887
Q ss_pred C
Q 014409 285 T 285 (425)
Q Consensus 285 T 285 (425)
.
T Consensus 238 ~ 238 (519)
T PRK02910 238 K 238 (519)
T ss_pred c
Confidence 4
No 154
>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=26.45 E-value=1.2e+02 Score=29.35 Aligned_cols=41 Identities=17% Similarity=0.358 Sum_probs=19.3
Q ss_pred HHHHHHHHHcCCcEEEEEcCCCCHHHhcC-CCCCCEEEEec-CCC
Q 014409 228 HQMKELITKAGKKAYTLVMGKPNPAKLAN-FPECDVFINVS-CAQ 270 (425)
Q Consensus 228 ~~Lk~li~~~GKk~Y~~~vgkln~aKLaN-F~eID~fV~va-CPr 270 (425)
+.+++++++.+.+..+..+|.. +.+.. +...|++|..+ +++
T Consensus 233 ~~~~~~~~~~~~~~~v~~~g~~--~~~~~~l~~ad~~i~ps~~~e 275 (355)
T cd03819 233 AELLELIKRLGLQDRVTFVGHC--SDMPAAYALADIVVSASTEPE 275 (355)
T ss_pred HHHHHHHHHcCCcceEEEcCCc--ccHHHHHHhCCEEEecCCCCC
Confidence 3344444444444444444441 11211 22367777776 665
No 155
>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=26.40 E-value=1.2e+02 Score=27.79 Aligned_cols=31 Identities=23% Similarity=0.405 Sum_probs=15.5
Q ss_pred EEEEEcCCcccCcHHHHHHHHHHHHHcCCcE
Q 014409 211 IGVLVGTLGVAGYLHMIHQMKELITKAGKKA 241 (425)
Q Consensus 211 iGIlvgTl~~q~~~~~i~~Lk~li~~~GKk~ 241 (425)
||+++-+.....+..+++.+++.+++.|.+.
T Consensus 2 i~~v~~~~~~~~~~~~~~g~~~~~~~~g~~~ 32 (264)
T cd06267 2 IGVIVPDISNPFFAELLRGIEEAAREAGYSV 32 (264)
T ss_pred EEEEECCCCCHHHHHHHHHHHHHHHHcCCEE
Confidence 4555544444444455555555555555443
No 156
>PRK14336 (dimethylallyl)adenosine tRNA methylthiotransferase; Provisional
Probab=26.17 E-value=1.4e+02 Score=31.16 Aligned_cols=14 Identities=7% Similarity=0.150 Sum_probs=8.1
Q ss_pred CCEEE--EecCCCccc
Q 014409 260 CDVFI--NVSCAQTAL 273 (425)
Q Consensus 260 ID~fV--~vaCPr~si 273 (425)
.-+|| .-|||..+-
T Consensus 124 ~~a~i~i~rGC~~~Cs 139 (418)
T PRK14336 124 VSANVTIMQGCDNFCT 139 (418)
T ss_pred eEEEEEeccCCCCCCc
Confidence 34553 457887653
No 157
>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=25.74 E-value=1.1e+02 Score=32.75 Aligned_cols=77 Identities=10% Similarity=0.121 Sum_probs=60.1
Q ss_pred cCCeEEEEEcCCcccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHHHhcCCCCCCEEEEecCCCcccccccCCCCccc
Q 014409 207 DANIIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKLANFPECDVFINVSCAQTALLDSKEFLAPVI 284 (425)
Q Consensus 207 ~A~~iGIlvgTl~~q~~~~~i~~Lk~li~~~GKk~Y~~~vgkln~aKLaNF~eID~fV~vaCPr~si~d~~ef~kPVi 284 (425)
+.+.|-||=.+-+.-++..=++.||++|+.-|-+...+.-+.-+.+.|.+.++-++=+++ |++.+..-.++|-.|-+
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 345677776555555667777899999999999999999999999999999887776666 88765554556777765
No 158
>PRK14057 epimerase; Provisional
Probab=25.60 E-value=1.9e+02 Score=28.29 Aligned_cols=60 Identities=15% Similarity=0.176 Sum_probs=38.1
Q ss_pred cCCeEEEEEcCCc--ccCcH-H---HHHHHHHHHHHcCCcEEEEEcCCCCHHHhcCC--CCCCEEEEe
Q 014409 207 DANIIGVLVGTLG--VAGYL-H---MIHQMKELITKAGKKAYTLVMGKPNPAKLANF--PECDVFINV 266 (425)
Q Consensus 207 ~A~~iGIlvgTl~--~q~~~-~---~i~~Lk~li~~~GKk~Y~~~vgkln~aKLaNF--~eID~fV~v 266 (425)
....|=|.--..| ||.+. . =++++++++.++|.+.-+-+=|-+|.+.+.-. .++|+||.=
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 3445444444433 67765 3 44555567777777766677788998866544 268999885
No 159
>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=25.11 E-value=94 Score=30.16 Aligned_cols=58 Identities=10% Similarity=-0.015 Sum_probs=35.8
Q ss_pred eEEEEEcCC-cccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHHHh----cCC--C--CCCEEEEecC
Q 014409 210 IIGVLVGTL-GVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKL----ANF--P--ECDVFINVSC 268 (425)
Q Consensus 210 ~iGIlvgTl-~~q~~~~~i~~Lk~li~~~GKk~Y~~~vgkln~aKL----aNF--~--eID~fV~vaC 268 (425)
.||+|+..+ .-..+..+++.+++.+++.|....+...+ -++++- .+| . .+|++|+.+.
T Consensus 1 ~Igvi~~~~~~~~~~~~~~~gi~~~~~~~g~~v~~~~~~-~~~~~~~~~i~~~~~~~~~vdgiIi~~~ 67 (305)
T cd06324 1 SVVFLNPGKSDEPFWNSVARFMQAAADDLGIELEVLYAE-RDRFLMLQQARTILQRPDKPDALIFTNE 67 (305)
T ss_pred CeEEecCCCCCCcHHHHHHHHHHHHHHhcCCeEEEEeCC-CCHHHHHHHHHHHHHhccCCCEEEEcCC
Confidence 378888776 55556778888888888877765554333 233322 122 2 5888888654
No 160
>PRK10401 DNA-binding transcriptional regulator GalS; Provisional
Probab=25.02 E-value=3.5e+02 Score=26.61 Aligned_cols=61 Identities=18% Similarity=0.188 Sum_probs=43.1
Q ss_pred hcCCeEEEEEcCCcccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHHH-------hcCCCCCCEEEEecC
Q 014409 206 KDANIIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAK-------LANFPECDVFINVSC 268 (425)
Q Consensus 206 ~~A~~iGIlvgTl~~q~~~~~i~~Lk~li~~~GKk~Y~~~vgkln~aK-------LaNF~eID~fV~vaC 268 (425)
+..++||+++..+.-..+..+++.+.+.++++|....+. -..-++++ |.+ ..+|.+++++.
T Consensus 57 ~~~~~Igvi~~~~~~~f~~~l~~gi~~~~~~~gy~~~~~-~~~~~~~~~~~~i~~l~~-~~vdGiIi~~~ 124 (346)
T PRK10401 57 QVSDTIGVVVMDVSDAFFGALVKAVDLVAQQHQKYVLIG-NSYHEAEKERHAIEVLIR-QRCNALIVHSK 124 (346)
T ss_pred CCCCEEEEEeCCCCCccHHHHHHHHHHHHHHCCCEEEEE-cCCCChHHHHHHHHHHHh-cCCCEEEEeCC
Confidence 346789999988877778899999999999998764432 22333333 222 25999999864
No 161
>PF06414 Zeta_toxin: Zeta toxin; InterPro: IPR010488 This entry represents a domain originally identified in bacterial zeta toxin proteins, where it comprises the whole protein []. It has subsequently been found in a number of other proteins, such as polynucleotide kinase and 2',3'-cyclic-nucleotide 3'-phosphodiesterase. It appears to function as a kinase domain [, ].; GO: 0005524 ATP binding, 0016301 kinase activity; PDB: 2P5T_H 1GVN_B 3Q8X_D.
Probab=24.93 E-value=3.6e+02 Score=24.60 Aligned_cols=49 Identities=18% Similarity=0.146 Sum_probs=29.1
Q ss_pred HHHHHHHHHHhcCCeEEEEEcCCcccCcHHHHHHHHHHHHHcCCcEEEEEcC
Q 014409 196 KRRYYLVEKAKDANIIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMG 247 (425)
Q Consensus 196 ~rRy~~I~ka~~A~~iGIlvgTl~~q~~~~~i~~Lk~li~~~GKk~Y~~~vg 247 (425)
+....++++|.+.+.==|+=+|++...+ +.++.+.++++|.+..+++|+
T Consensus 80 ~~~~~~~~~a~~~~~nii~E~tl~~~~~---~~~~~~~~k~~GY~v~l~~v~ 128 (199)
T PF06414_consen 80 RLAEKLIEYAIENRYNIIFEGTLSNPSK---LRKLIREAKAAGYKVELYYVA 128 (199)
T ss_dssp HHHHHHHHHHHHCT--EEEE--TTSSHH---HHHHHHHHHCTT-EEEEEEE-
T ss_pred HHHHHHHHHHHHcCCCEEEecCCCChhH---HHHHHHHHHcCCceEEEEEEE
Confidence 3445678888888887777888875433 334556666788887776665
No 162
>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=24.91 E-value=2.3e+02 Score=27.59 Aligned_cols=37 Identities=8% Similarity=0.040 Sum_probs=20.3
Q ss_pred eEEEEEcCCcccCc-HHHHHHHHHHHHHcCCcEEEEEc
Q 014409 210 IIGVLVGTLGVAGY-LHMIHQMKELITKAGKKAYTLVM 246 (425)
Q Consensus 210 ~iGIlvgTl~~q~~-~~~i~~Lk~li~~~GKk~Y~~~v 246 (425)
+++||++..++.+. ....+++++.++++|.++.++..
T Consensus 3 ~~~ii~Np~sg~~~~~~~~~~i~~~l~~~~~~~~~~~t 40 (293)
T TIGR00147 3 EAPAILNPTAGKSNDNKPLREVIMLLREEGMEIHVRVT 40 (293)
T ss_pred eEEEEECCCccchhhHHHHHHHHHHHHHCCCEEEEEEe
Confidence 45666666555432 34555666666666665544443
No 163
>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=24.83 E-value=1.1e+02 Score=28.89 Aligned_cols=59 Identities=10% Similarity=-0.024 Sum_probs=34.4
Q ss_pred eEEEEEcCCcccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHHHh----cCC--CCCCEEEEecCC
Q 014409 210 IIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKL----ANF--PECDVFINVSCA 269 (425)
Q Consensus 210 ~iGIlvgTl~~q~~~~~i~~Lk~li~~~GKk~Y~~~vgkln~aKL----aNF--~eID~fV~vaCP 269 (425)
+||+|+.. .--.+..+++.+.+.+++.|.+.-++.-..-++++. .++ ..+|.+++.++-
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 47777743 334567888888888888886654443232233322 122 158888887653
No 164
>PF02593 dTMP_synthase: Thymidylate synthase; InterPro: IPR003745 This entry describes proteins of unknown function.
Probab=24.78 E-value=1.2e+02 Score=29.10 Aligned_cols=40 Identities=28% Similarity=0.328 Sum_probs=32.6
Q ss_pred HHHHHHHhcCCeEEEEEcCCcccCcHHHHHHHHHHHHHcCCc
Q 014409 199 YYLVEKAKDANIIGVLVGTLGVAGYLHMIHQMKELITKAGKK 240 (425)
Q Consensus 199 y~~I~ka~~A~~iGIlvgTl~~q~~~~~i~~Lk~li~~~GKk 240 (425)
|.++.+|++++.-+|||++-.+. +.+.+.|++.+++.|..
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 45777788899999999998766 88899999998876643
No 165
>COG0529 CysC Adenylylsulfate kinase and related kinases [Inorganic ion transport and metabolism]
Probab=24.54 E-value=1.8e+02 Score=27.23 Aligned_cols=38 Identities=16% Similarity=0.155 Sum_probs=33.2
Q ss_pred CCeEEEEEcCCcccCcHHHHHHHHHHHHHcCCcEEEEE
Q 014409 208 ANIIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLV 245 (425)
Q Consensus 208 A~~iGIlvgTl~~q~~~~~i~~Lk~li~~~GKk~Y~~~ 245 (425)
.+-+-|-+.-|+++|=-.+.+.|.+.|.+.|+.+|++=
T Consensus 21 ~~~~viW~TGLSGsGKSTiA~ale~~L~~~G~~~y~LD 58 (197)
T COG0529 21 QKGAVIWFTGLSGSGKSTIANALEEKLFAKGYHVYLLD 58 (197)
T ss_pred CCCeEEEeecCCCCCHHHHHHHHHHHHHHcCCeEEEec
Confidence 34456778889999999999999999999999999874
No 166
>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=24.47 E-value=2.7e+02 Score=24.22 Aligned_cols=59 Identities=12% Similarity=0.114 Sum_probs=42.5
Q ss_pred EEEcCCcccCcHHHHHHHHHHHHHcCCcEEEEEcCC--CCHHHhcCC--------CCCC--EEEEecCCCc
Q 014409 213 VLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGK--PNPAKLANF--------PECD--VFINVSCAQT 271 (425)
Q Consensus 213 IlvgTl~~q~~~~~i~~Lk~li~~~GKk~Y~~~vgk--ln~aKLaNF--------~eID--~fV~vaCPr~ 271 (425)
.+++.+||.|--.+.-+|-..+.++|+|..++=.+- .|...+... .++- =||++-||..
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 468899999999999999999999999998886653 355444221 1111 3777778754
No 167
>TIGR01012 Sa_S2_E_A ribosomal protein Sa(cytosolic)/S2(archaeal). TIGR01011 describes the related protein of organelles and bacteria.
Probab=24.41 E-value=1.6e+02 Score=27.71 Aligned_cols=51 Identities=22% Similarity=0.268 Sum_probs=30.8
Q ss_pred EEecCCCCCCCCCCCeEEEccccC-----CChHHHHHHHhhhh----cCCCCcEEEEecccch
Q 014409 25 IHYGHTCLSPTSTLPAFFVFGKAS-----INTSNCIENLSKHA----LTNGKPILVLYGLEYA 78 (425)
Q Consensus 25 VHyGhaClsp~~~lpviYVf~~~~-----ld~~~~~~~~~~~~----~~~~~~v~l~~dvqy~ 78 (425)
|||||.-.+|-- --|+|++.+ ||+++..+.++... .-..++|+++.+-.+.
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 1114578888775543
No 168
>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=24.40 E-value=1.5e+02 Score=26.06 Aligned_cols=44 Identities=20% Similarity=0.148 Sum_probs=30.3
Q ss_pred HHHHhc--CCeEEEEEcCCcccCcHHHHHHHHHHHHHcCCcEEEEEcCC
Q 014409 202 VEKAKD--ANIIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGK 248 (425)
Q Consensus 202 I~ka~~--A~~iGIlvgTl~~q~~~~~i~~Lk~li~~~GKk~Y~~~vgk 248 (425)
++.|++ |..+|+ ++|.+ ..+..+.++.++|+++|-+...+++|-
T Consensus 45 v~aa~~~~adiVgl--S~l~~-~~~~~~~~~~~~l~~~gl~~~~vivGG 90 (134)
T TIGR01501 45 IKAAIETKADAILV--SSLYG-HGEIDCKGLRQKCDEAGLEGILLYVGG 90 (134)
T ss_pred HHHHHHcCCCEEEE--ecccc-cCHHHHHHHHHHHHHCCCCCCEEEecC
Confidence 344444 666554 77765 556677888899999987666677776
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=24.20 E-value=1.4e+02 Score=32.86 Aligned_cols=49 Identities=12% Similarity=0.074 Sum_probs=42.9
Q ss_pred CCeEEEEEcCCcccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHHHhcCC
Q 014409 208 ANIIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKLANF 257 (425)
Q Consensus 208 A~~iGIlvgTl~~q~~~~~i~~Lk~li~~~GKk~Y~~~vgkln~aKLaNF 257 (425)
++.+.||.||-+| +...++++|.+.++++|..+.+..|+...+..|.+.
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 6789999999764 557899999999999999999999999998888776
No 170
>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=24.18 E-value=1.7e+02 Score=28.21 Aligned_cols=61 Identities=20% Similarity=0.133 Sum_probs=39.6
Q ss_pred eEEEEEcCCcccCcHHHHHHHHHHHHHcCCcEEEEEcCC-CCHHHh----cCC--CCCCEEEEecCCC
Q 014409 210 IIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGK-PNPAKL----ANF--PECDVFINVSCAQ 270 (425)
Q Consensus 210 ~iGIlvgTl~~q~~~~~i~~Lk~li~~~GKk~Y~~~vgk-ln~aKL----aNF--~eID~fV~vaCPr 270 (425)
.+|+|+.++.-..+..+++.+.+.++++|....++..+. -++++. .++ ..+|++++.++..
T Consensus 1 ~igvvvp~~~n~f~~~~~~gi~~~a~~~g~~v~~~~~~~~~~~~~~~~~i~~l~~~~vDgiIi~~~~~ 68 (295)
T TIGR02955 1 KLCALYPHLKDSYWLSINYGMVEQAKHLGVELKVLEAGGYPNLDKQLAQIEQCKSWGADAILLGTVSP 68 (295)
T ss_pred CeeEEecCCCcHHHHHHHHHHHHHHHHhCCEEEEEcCCCCCCHHHHHHHHHHHHHcCCCEEEEecCCh
Confidence 378888877666667788888888888887776655431 233322 122 2588888876543
No 171
>PRK08662 nicotinate phosphoribosyltransferase; Reviewed
Probab=24.05 E-value=1.5e+02 Score=30.17 Aligned_cols=55 Identities=16% Similarity=0.368 Sum_probs=41.8
Q ss_pred CeEEEEEcCCcc--cCcHHHHHHHHHHHHHcC-CcEEEEEcCCCCHHHhcCCCC-CCEE
Q 014409 209 NIIGVLVGTLGV--AGYLHMIHQMKELITKAG-KKAYTLVMGKPNPAKLANFPE-CDVF 263 (425)
Q Consensus 209 ~~iGIlvgTl~~--q~~~~~i~~Lk~li~~~G-Kk~Y~~~vgkln~aKLaNF~e-ID~f 263 (425)
+.-||.+=+.+. ..-..+++++++.+++.| .+.-+.+.|.+|++++++|.+ +|+|
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 456788888764 555677788888888887 467888899999999988743 5555
No 172
>COG0041 PurE Phosphoribosylcarboxyaminoimidazole (NCAIR) mutase [Nucleotide transport and metabolism]
Probab=23.91 E-value=2e+02 Score=26.10 Aligned_cols=60 Identities=18% Similarity=0.316 Sum_probs=43.5
Q ss_pred eEEEEEcCCcccCcHHHHHHHHHHHHHcCCcEEEEEc-CCCCHHHhcCCC----CCCEEEEecCCCcc
Q 014409 210 IIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVM-GKPNPAKLANFP----ECDVFINVSCAQTA 272 (425)
Q Consensus 210 ~iGIlvgTl~~q~~~~~i~~Lk~li~~~GKk~Y~~~v-gkln~aKLaNF~----eID~fV~vaCPr~s 272 (425)
.+|||.|+. .-+++.++--+.|++-|..+-.-++ -.=||++|-.|. +-++=|++|..-.+
T Consensus 4 ~V~IIMGS~---SD~~~mk~Aa~~L~~fgi~ye~~VvSAHRTPe~m~~ya~~a~~~g~~viIAgAGgA 68 (162)
T COG0041 4 KVGIIMGSK---SDWDTMKKAAEILEEFGVPYEVRVVSAHRTPEKMFEYAEEAEERGVKVIIAGAGGA 68 (162)
T ss_pred eEEEEecCc---chHHHHHHHHHHHHHcCCCeEEEEEeccCCHHHHHHHHHHHHHCCCeEEEecCcch
Confidence 799999995 4577888888999999998876444 478899998775 23333555555443
No 173
>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=23.77 E-value=85 Score=29.19 Aligned_cols=57 Identities=21% Similarity=0.223 Sum_probs=33.4
Q ss_pred eEEEEEcCCcccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHHHhcC----C--CCCCEEEEec
Q 014409 210 IIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKLAN----F--PECDVFINVS 267 (425)
Q Consensus 210 ~iGIlvgTl~~q~~~~~i~~Lk~li~~~GKk~Y~~~vgkln~aKLaN----F--~eID~fV~va 267 (425)
+||+|+.++.-..+..+++.+.+.+++.|...-++ -..-++++..+ + ..+|++++.+
T Consensus 1 ~I~vv~~~~~~~~~~~~~~~i~~~~~~~g~~v~~~-~~~~~~~~~~~~~~~~~~~~~dgii~~~ 63 (268)
T cd06323 1 TIGLSVSTLNNPFFVTLKDGAQKEAKELGYELTVL-DAQNDAAKQLNDIEDLITRGVDAIIINP 63 (268)
T ss_pred CeeEecccccCHHHHHHHHHHHHHHHHcCceEEec-CCCCCHHHHHHHHHHHHHcCCCEEEEcC
Confidence 46777777765666777788888887776444322 22334543211 1 1477777654
No 174
>PRK11921 metallo-beta-lactamase/flavodoxin domain-containing protein; Provisional
Probab=23.35 E-value=2.2e+02 Score=29.37 Aligned_cols=77 Identities=16% Similarity=0.205 Sum_probs=56.6
Q ss_pred HHHHHHHHHHHHHHHhcCCeEEEEEcCCcccCcHHHHHHHHHHHH--HcCCcEEEEEcCCCCHHHhcC-CCCCCEEEEec
Q 014409 191 PLKILKRRYYLVEKAKDANIIGVLVGTLGVAGYLHMIHQMKELIT--KAGKKAYTLVMGKPNPAKLAN-FPECDVFINVS 267 (425)
Q Consensus 191 ~~r~L~rRy~~I~ka~~A~~iGIlvgTl~~q~~~~~i~~Lk~li~--~~GKk~Y~~~vgkln~aKLaN-F~eID~fV~va 267 (425)
..+++ ++|....+-+.-+.+.|+-+|.. -+...+++.+.+-++ +.|-++-++-+.+..++.+++ +.+.|++| ++
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 44444 45665555566788999999976 467899999999998 678888888899999888765 34567755 45
Q ss_pred CCC
Q 014409 268 CAQ 270 (425)
Q Consensus 268 CPr 270 (425)
||-
T Consensus 308 spT 310 (394)
T PRK11921 308 SST 310 (394)
T ss_pred CCC
Confidence 554
No 175
>KOG3360 consensus Acylphosphatase [Energy production and conversion]
Probab=22.66 E-value=2e+02 Score=23.99 Aligned_cols=44 Identities=23% Similarity=0.300 Sum_probs=37.3
Q ss_pred HHHHHHHHHhcCCeEEEEEcCCc------ccCcHHHHHHHHHHHHHcCCc
Q 014409 197 RRYYLVEKAKDANIIGVLVGTLG------VAGYLHMIHQMKELITKAGKK 240 (425)
Q Consensus 197 rRy~~I~ka~~A~~iGIlvgTl~------~q~~~~~i~~Lk~li~~~GKk 240 (425)
-|.+...+|+...+.|-+.+|.- .++-++.++.++++|..+|-.
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 36778889999999999998865 478899999999999987753
No 176
>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=22.59 E-value=1.9e+02 Score=27.21 Aligned_cols=56 Identities=9% Similarity=0.070 Sum_probs=37.9
Q ss_pred EEEEEcCCcccCcHHHHHHHHHHHHHcC-CcEEEEEcCCCCHH-Hh---cCCCCCCEEEEecCC
Q 014409 211 IGVLVGTLGVAGYLHMIHQMKELITKAG-KKAYTLVMGKPNPA-KL---ANFPECDVFINVSCA 269 (425)
Q Consensus 211 iGIlvgTl~~q~~~~~i~~Lk~li~~~G-Kk~Y~~~vgkln~a-KL---aNF~eID~fV~vaCP 269 (425)
+.|+++.+ -..+..++..|.+.++++| ....+...+. ... .+ .+ ..+|.+|++++.
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 56888888 4667789999999999999 5444433333 221 11 12 368999998865
No 177
>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=22.53 E-value=1.7e+02 Score=26.56 Aligned_cols=71 Identities=17% Similarity=0.277 Sum_probs=49.4
Q ss_pred EEEEEcCCcccCcHHHHHHHHHHHHHcCCcEEEEEcC-CCCHHHhcCCC------CCCEEEEecCCCcccc--cccCCCC
Q 014409 211 IGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMG-KPNPAKLANFP------ECDVFINVSCAQTALL--DSKEFLA 281 (425)
Q Consensus 211 iGIlvgTl~~q~~~~~i~~Lk~li~~~GKk~Y~~~vg-kln~aKLaNF~------eID~fV~vaCPr~si~--d~~ef~k 281 (425)
+|||.|+ ..=+++.+...+.|++-|..+-+-+.+ .=+|++|..|. ++++||.+|==...|- -...-.+
T Consensus 1 V~IimGS---~SD~~~~~~a~~~L~~~gi~~dv~V~SaHRtp~~~~~~~~~a~~~g~~viIa~AG~aa~Lpgvva~~t~~ 77 (156)
T TIGR01162 1 VGIIMGS---DSDLPTMKKAADILEEFGIPYELRVVSAHRTPELMLEYAKEAEERGIKVIIAGAGGAAHLPGMVAALTPL 77 (156)
T ss_pred CEEEECc---HhhHHHHHHHHHHHHHcCCCeEEEEECcccCHHHHHHHHHHHHHCCCeEEEEeCCccchhHHHHHhccCC
Confidence 5788887 445778888889999999886554444 56788887774 5788877766555543 2344567
Q ss_pred ccc
Q 014409 282 PVI 284 (425)
Q Consensus 282 PVi 284 (425)
|||
T Consensus 78 PVI 80 (156)
T TIGR01162 78 PVI 80 (156)
T ss_pred CEE
Confidence 776
No 178
>PRK15408 autoinducer 2-binding protein lsrB; Provisional
Probab=22.52 E-value=1e+02 Score=30.90 Aligned_cols=63 Identities=17% Similarity=0.106 Sum_probs=38.0
Q ss_pred cCCeEEEEEcCCcccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHHHh----cCC--CCCCEEEEecCC
Q 014409 207 DANIIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKL----ANF--PECDVFINVSCA 269 (425)
Q Consensus 207 ~A~~iGIlvgTl~~q~~~~~i~~Lk~li~~~GKk~Y~~~vgkln~aKL----aNF--~eID~fV~vaCP 269 (425)
.+.+|++++.+++...+..+.+-+++.++++|.+..+..-..-++++- .++ ..+|+.|+.++-
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 456788777777666666777777777777775554322233344332 223 257887776543
No 179
>PRK04020 rps2P 30S ribosomal protein S2; Provisional
Probab=22.44 E-value=1.7e+02 Score=27.65 Aligned_cols=50 Identities=18% Similarity=0.274 Sum_probs=29.6
Q ss_pred EEecCCCCCCCCCCCeEEEccccC-----CChHHHHHHHhhhh----cCCCCcEEEEecccc
Q 014409 25 IHYGHTCLSPTSTLPAFFVFGKAS-----INTSNCIENLSKHA----LTNGKPILVLYGLEY 77 (425)
Q Consensus 25 VHyGhaClsp~~~lpviYVf~~~~-----ld~~~~~~~~~~~~----~~~~~~v~l~~dvqy 77 (425)
+||||.=.+|-- --|||+..+ ||++...+.+...+ ....++|+++.+-++
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 699997444422 227777542 48877666665432 113457877777543
No 180
>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=22.37 E-value=2.3e+02 Score=25.78 Aligned_cols=50 Identities=10% Similarity=0.074 Sum_probs=37.5
Q ss_pred HHHHHHHHHhcCCeEEEEEcCCcccCcHHHHHHHHHHHHHcCCcEEEEEcC
Q 014409 197 RRYYLVEKAKDANIIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMG 247 (425)
Q Consensus 197 rRy~~I~ka~~A~~iGIlvgTl~~q~~~~~i~~Lk~li~~~GKk~Y~~~vg 247 (425)
-|..+.....+.++| .+.|.+++.+--.+.-.|-..+.++|++.-++=.+
T Consensus 6 l~~~l~~~~~~~kvI-~v~s~kgG~GKTt~a~~LA~~la~~G~rVllID~D 55 (204)
T TIGR01007 6 IRTNIQFSGAEIKVL-LITSVKPGEGKSTTSANIAVAFAQAGYKTLLIDGD 55 (204)
T ss_pred HHHHHhhhcCCCcEE-EEecCCCCCCHHHHHHHHHHHHHhCCCeEEEEeCC
Confidence 344455555667777 45778889999999999999999999997666554
No 181
>PRK06756 flavodoxin; Provisional
Probab=22.33 E-value=3.2e+02 Score=23.59 Aligned_cols=56 Identities=7% Similarity=0.124 Sum_probs=38.6
Q ss_pred eEEEEEcCCcccCcHHHHHHHHHHHHHcCCcEEEEEcCCC-CHHHhcCCCCCCEEEEecCCC
Q 014409 210 IIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKP-NPAKLANFPECDVFINVSCAQ 270 (425)
Q Consensus 210 ~iGIlvgTl~~q~~~~~i~~Lk~li~~~GKk~Y~~~vgkl-n~aKLaNF~eID~fV~vaCPr 270 (425)
.+-|+-+|.. -+...+++.|.+.+++.|.+.-++-+.+. ....|. +.|.+ +++||=
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 5778888854 56788999999999999988777666543 234444 45665 455543
No 182
>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=22.25 E-value=2.4e+02 Score=28.72 Aligned_cols=45 Identities=16% Similarity=0.347 Sum_probs=38.2
Q ss_pred HhcCCeEEEEEcCCcccCcHHH---HHHHHHHHHHcCCcEEEEEcCCC
Q 014409 205 AKDANIIGVLVGTLGVAGYLHM---IHQMKELITKAGKKAYTLVMGKP 249 (425)
Q Consensus 205 a~~A~~iGIlvgTl~~q~~~~~---i~~Lk~li~~~GKk~Y~~~vgkl 249 (425)
.++-..+.++|+.||+..++++ .+++.++|+++|.+.+...+|..
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 3455689999999999999864 67888899999999999999864
No 183
>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=22.15 E-value=1.6e+02 Score=26.58 Aligned_cols=37 Identities=16% Similarity=0.191 Sum_probs=31.0
Q ss_pred EEEEEcCCcccCcHHHHHHHHHHHHHcCCcEEEEEcC
Q 014409 211 IGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMG 247 (425)
Q Consensus 211 iGIlvgTl~~q~~~~~i~~Lk~li~~~GKk~Y~~~vg 247 (425)
+-|.+.-|+++|=-.+...|.+.|.+.|+++|.+=..
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 3467778889999999999999999999999998554
No 184
>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=22.05 E-value=2.2e+02 Score=24.06 Aligned_cols=67 Identities=12% Similarity=0.183 Sum_probs=43.4
Q ss_pred HHHHHHHHHHHHHh----cCCeEEEEEcCCcccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHHHhcCCCCC
Q 014409 193 KILKRRYYLVEKAK----DANIIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKLANFPEC 260 (425)
Q Consensus 193 r~L~rRy~~I~ka~----~A~~iGIlvgTl~~q~~~~~i~~Lk~li~~~GKk~Y~~~vgkln~aKLaNF~eI 260 (425)
..|..-+..+.+.. +++.+-||+.. |..+...-...+.+.++++|.+.|+|.+|..+.+.|..+...
T Consensus 84 ~al~~a~~~~~~~~~~~~~~~~~iiliTD-G~~~~~~~~~~~~~~~~~~~v~v~~i~~g~~~~~~l~~la~~ 154 (161)
T cd01450 84 KALQYALEQLFSESNARENVPKVIIVLTD-GRSDDGGDPKEAAAKLKDEGIKVFVVGVGPADEEELREIASC 154 (161)
T ss_pred HHHHHHHHHhcccccccCCCCeEEEEECC-CCCCCCcchHHHHHHHHHCCCEEEEEeccccCHHHHHHHhCC
Confidence 34444444555553 67777777755 222222234555566778899999999999888888887544
No 185
>cd06308 PBP1_sensor_kinase_like Periplasmic binding domain of two-component sensor kinase signaling systems. Periplasmic binding domain of two-component sensor kinase signaling systems, some of which are fused with a C-terminal histidine kinase A domain (HisK) and/or a signal receiver domain (REC). Members of this group share homology with a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily and are predicted to be involved in sensing of environmental stimuli; their substrate specificities, however, are not known in detail.
Probab=21.99 E-value=1.9e+02 Score=27.01 Aligned_cols=59 Identities=15% Similarity=0.113 Sum_probs=38.6
Q ss_pred eEEEEEcCCcccCcHHHHHHHHHHHHHc-CCcEEEEEcCCCCHHHh----cCC--CCCCEEEEecCC
Q 014409 210 IIGVLVGTLGVAGYLHMIHQMKELITKA-GKKAYTLVMGKPNPAKL----ANF--PECDVFINVSCA 269 (425)
Q Consensus 210 ~iGIlvgTl~~q~~~~~i~~Lk~li~~~-GKk~Y~~~vgkln~aKL----aNF--~eID~fV~vaCP 269 (425)
+||+++.++.-..+..+++.+.+.+++. |....++.. .-++++- .++ ..+|++|+.++.
T Consensus 1 ~ig~~~~~~~~~~~~~~~~~i~~~~~~~~g~~~~~~~~-~~~~~~~~~~i~~~~~~~vdgiii~~~~ 66 (270)
T cd06308 1 VIGFSQCNLADPWRAAMNDEIQREASNYPDVELIIADA-ADDNSKQVADIENFIRQGVDLLIISPNE 66 (270)
T ss_pred CEEEEeeCCCCHHHHHHHHHHHHHHHhcCCcEEEEEcC-CCCHHHHHHHHHHHHHhCCCEEEEecCc
Confidence 4889998877666778899998888886 666654433 2234322 221 258988887654
No 186
>PRK14339 (dimethylallyl)adenosine tRNA methylthiotransferase; Provisional
Probab=21.95 E-value=1.8e+02 Score=30.43 Aligned_cols=6 Identities=0% Similarity=0.440 Sum_probs=2.7
Q ss_pred eEEEec
Q 014409 173 EIVRYD 178 (425)
Q Consensus 173 ~v~~yD 178 (425)
.++..|
T Consensus 29 Dv~iiN 34 (420)
T PRK14339 29 DLILIN 34 (420)
T ss_pred CEEEEe
Confidence 344444
No 187
>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=21.67 E-value=2.9e+02 Score=26.93 Aligned_cols=77 Identities=14% Similarity=0.143 Sum_probs=51.4
Q ss_pred eEEEEEcCCcccC--cHHHHHHHHHHHHHcCCcEEEEEcCCCCH-------HHhcCC----CCCCEEEEec---CCCccc
Q 014409 210 IIGVLVGTLGVAG--YLHMIHQMKELITKAGKKAYTLVMGKPNP-------AKLANF----PECDVFINVS---CAQTAL 273 (425)
Q Consensus 210 ~iGIlvgTl~~q~--~~~~i~~Lk~li~~~GKk~Y~~~vgkln~-------aKLaNF----~eID~fV~va---CPr~si 273 (425)
+||||.|-.|-.. .+....++.+-|++.|.+.+.+-+.+.++ +.+.++ .++|+.+.+. ..+.+.
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 47888999999999999999999887432 223321 3688888753 112211
Q ss_pred c--cccCCCCcccCH
Q 014409 274 L--DSKEFLAPVITP 286 (425)
Q Consensus 274 ~--d~~ef~kPViTP 286 (425)
. -...+-.|++.+
T Consensus 81 ~~~~le~~gip~~g~ 95 (315)
T TIGR01205 81 IQGLLELMGIPYTGS 95 (315)
T ss_pred HHHHHHHcCCCccCC
Confidence 1 123456687764
No 188
>PLN02404 6,7-dimethyl-8-ribityllumazine synthase
Probab=21.58 E-value=1.6e+02 Score=26.14 Aligned_cols=61 Identities=15% Similarity=0.160 Sum_probs=38.5
Q ss_pred CeEEEEEcCCcccCcHHHHHHHHHHHHHcCCc---EEEEEc-C--CC--CHHHhcCCCCCCEEEEecCC
Q 014409 209 NIIGVLVGTLGVAGYLHMIHQMKELITKAGKK---AYTLVM-G--KP--NPAKLANFPECDVFINVSCA 269 (425)
Q Consensus 209 ~~iGIlvgTl~~q~~~~~i~~Lk~li~~~GKk---~Y~~~v-g--kl--n~aKLaNF~eID~fV~vaCP 269 (425)
-+||||++...-.-.-.+++-.++.|+++|-+ ..++.| | ++ -..+|+.-.++|++|.++|=
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 58999997654333344555555677888864 344444 2 11 12467766679999999993
No 189
>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=21.54 E-value=2.1e+02 Score=29.78 Aligned_cols=78 Identities=14% Similarity=0.130 Sum_probs=55.4
Q ss_pred CCeEEEEEcCCcccCcHHHHHHHHHHHHHcCCcEEEEEcCCCCHHHhcCCCCCCEEEEecCCCccccc----ccCCCCcc
Q 014409 208 ANIIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKLANFPECDVFINVSCAQTALLD----SKEFLAPV 283 (425)
Q Consensus 208 A~~iGIlvgTl~~q~~~~~i~~Lk~li~~~GKk~Y~~~vgkln~aKLaNF~eID~fV~vaCPr~si~d----~~ef~kPV 283 (425)
.+++-||=.+-..-+...=++.|+++|++.|.+.-.+..+.-+.+.+.+.++.++=++ -||+.+..- .++|-.|.
T Consensus 162 ~~~VNiiG~~~~~~~~~~d~~ei~~lL~~~Gl~v~~~~~~~~~~~~i~~~~~A~lniv-~~~~~~~~~a~~L~~~~GiP~ 240 (430)
T cd01981 162 KPSVNLIGPSSLGFHNRHDCRELKRLLHTLGIEVNVVIPEGASVDDLNELPKAWFNIV-PYREYGLSAALYLEEEFGMPS 240 (430)
T ss_pred CCcEEEEcCCCCCCCCcchHHHHHHHHHHcCCeEEEEEcCCCCHHHHHhhhhCeEEEE-ecHHHHHHHHHHHHHHhCCCe
Confidence 4567666544322233556678899999999999888889999999999987665544 388765432 35688888
Q ss_pred cCH
Q 014409 284 ITP 286 (425)
Q Consensus 284 iTP 286 (425)
+..
T Consensus 241 ~~~ 243 (430)
T cd01981 241 VKI 243 (430)
T ss_pred Eec
Confidence 743
No 190
>PF12163 HobA: DNA replication regulator; InterPro: IPR021011 This family of proteins is found exclusively in epsilon-proteobacteria. Proteins in this family are approximately 180 amino acids in length. The crystal structure of HobA from Helicobacter pylori has been reported at 1.7A resolution; HobA represents a modified Rossmann fold consisting of a five-stranded parallel beta-sheet (beta1-5) flanked on one side by alpha-2, alpha-3 and alpha-6 helices and alpha-4 and alpha-5 on the other. The alpha-1 helix is extended away from and has minimal interaction with the globular part of the protein. Four monomers interact to form a tetrameric molecule. Four calcium atoms bind to the tetramer and these binding sites may have functional relevance. The closest structural homologue of HobA is a sugar isomerase (SIS) domain containing protein, the phosphoheptose isomerase from Pseudomonas aeruginosa. The SIS proteins share strong sequence homology with DiaA from Escherichia coli; yet, HobA and DiaA share no sequence homology []. HobA is a novel protein essential for initiation of H. pylori chromosome replication. It interacts specifically via DnaA with the oriC-DnaA complex. It is possible that HobA is essential for the correct formation and stabilisation of the orisome by facilitating the spatial positioning of DnaA at oriC [].; PDB: 2UVP_D 2WP0_A.
Probab=21.08 E-value=99 Score=28.63 Aligned_cols=147 Identities=12% Similarity=0.082 Sum_probs=69.1
Q ss_pred cCCChHHHHHHHhhhhcCCCCcEEEEecccchhhhHHHHHHHHhhccCCCCCcceeeeeecceeeeecCCCCCCCCCCCC
Q 014409 47 ASINTSNCIENLSKHALTNGKPILVLYGLEYAHAIPHIREAVKVASSSYGSGLKLEINFADVMCTVITPSKDHKSLCGPA 126 (425)
Q Consensus 47 ~~ld~~~~~~~~~~~~~~~~~~v~l~~dvqy~~~l~~l~~~L~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~g~~ 126 (425)
...+..+++.+..+...+ ++.++|++|-+-.+-.+.+-..+......- +-+-+-++. ..-|.-.. ..+++.
T Consensus 25 ~R~eW~pl~a~~l~~il~-G~s~iliTD~~R~WF~~Yil~~IN~~~~~R-----P~lPi~~l~--~l~p~~~~-~~~~e~ 95 (180)
T PF12163_consen 25 RRFEWTPLIASALSHILN-GGSFILITDEEREWFEEYILSNINNSHKNR-----PLLPIFSLK--SLYPHIDS-IKSKED 95 (180)
T ss_dssp T-STHHHHHHHHHHHHHT-T-EEEEEE-GGGHHHHHHHHHHHS-SSTTS---------EEEST--T-----ST-TS-SS-
T ss_pred HhhhhHHHHHHHHHHHhC-CCeEEEEeCchhHHHHHHHHHhcCcccCCC-----CcceEEecc--cccchhhc-cCchhh
Confidence 456776666544444333 678999999988888887777775332210 000000000 00010000 000000
Q ss_pred --CCcccccccCccccCCCccCccceEEEEEcCCchhhhHHHhhcCCceEEEecCCCCc-ccccc--CcHHHHHHHHHHH
Q 014409 127 --GGCTRHTIGGLVWNIPDRKKMEEHLLFWIGSDNSAFANVVLTFNGCEIVRYDATEER-LLTDV--SQPLKILKRRYYL 201 (425)
Q Consensus 127 --~gc~~~~~~~~~~~~~~~~~~~~~~i~~Ig~~~~~l~~l~l~~~~~~v~~yDP~~~~-~~~~~--~~~~r~L~rRy~~ 201 (425)
+-+..-. .. -.++|.++|||.+......+.+.....=.+.+|-.-.. ..-.+ ...+--|.+=|.+
T Consensus 96 ~~li~DmL~-----is-----f~n~y~fWYIGk~~~~~a~iA~~~~~sflWifDe~~qnsf~L~S~D~~LD~KLLqLykl 165 (180)
T PF12163_consen 96 IALIEDMLS-----IS-----FPNGYFFWYIGKSDDPRAKIAKSKDDSFLWIFDEQLQNSFYLSSSDPLLDIKLLQLYKL 165 (180)
T ss_dssp HHHHHHHHH-----HH-----BSS-EEEEEES--SHHHHHHHTSSS-EEEEESS-SSSSSEE--TT-TTHHHHHHHHHHH
T ss_pred HHHHHHHHH-----hh-----ccCceEEEEecCCCcHHHHHHhcCCCceEEEeccchhcceeeccCCchhhHHHHHHHHH
Confidence 0000000 00 12359999999988666677776656668899985332 11111 1244456677888
Q ss_pred HHHHhcCCeEE
Q 014409 202 VEKAKDANIIG 212 (425)
Q Consensus 202 I~ka~~A~~iG 212 (425)
.+++.+|-.||
T Consensus 166 Fd~sL~AaLfg 176 (180)
T PF12163_consen 166 FDKSLFAALFG 176 (180)
T ss_dssp HHHHHHHHHTT
T ss_pred HHHHHHHHHhh
Confidence 88888875554
No 191
>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=20.95 E-value=2e+02 Score=26.32 Aligned_cols=47 Identities=21% Similarity=0.329 Sum_probs=31.0
Q ss_pred cHHHHHHHHHHHHHcCCcEEEEEcCCCC-------------------HHHhcCCCCCCEEEEecCC
Q 014409 223 YLHMIHQMKELITKAGKKAYTLVMGKPN-------------------PAKLANFPECDVFINVSCA 269 (425)
Q Consensus 223 ~~~~i~~Lk~li~~~GKk~Y~~~vgkln-------------------~aKLaNF~eID~fV~vaCP 269 (425)
.+.+..+|+++|++.|.++++.--+..+ .+++||=...|+||-+=|-
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 4566777777777777777765554433 1345665567888888874
No 192
>cd02072 Glm_B12_BD B12 binding domain of glutamate mutase (Glm). Glutamate mutase catalysis the conversion of (S)-glutamate with (2S,3S)-3-methylaspartate. The rearrangement reaction is initiated by the extraction of a hydrogen from the protein-bound substrate by a 5'-desoxyadenosyl radical, which is generated by the homolytic cleavage of the organometallic bond of the cofactor B12. Glm is a heterotetrameric molecule consisting of two alpha and two epsilon polypeptide chains.
Probab=20.63 E-value=1.8e+02 Score=25.43 Aligned_cols=40 Identities=28% Similarity=0.162 Sum_probs=28.4
Q ss_pred cCCeEEEEEcCCcccCcHHHHHHHHHHHHHcCCcEEEEEcCCC
Q 014409 207 DANIIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKP 249 (425)
Q Consensus 207 ~A~~iGIlvgTl~~q~~~~~i~~Lk~li~~~GKk~Y~~~vgkl 249 (425)
+|..+|+ ++|.+ ..+..++++.++|+++|-+...+++|-.
T Consensus 50 ~adiVgl--S~L~t-~~~~~~~~~~~~l~~~gl~~v~vivGG~ 89 (128)
T cd02072 50 DADAILV--SSLYG-HGEIDCKGLREKCDEAGLKDILLYVGGN 89 (128)
T ss_pred CCCEEEE--ecccc-CCHHHHHHHHHHHHHCCCCCCeEEEECC
Confidence 4666665 77764 4566777888899999975577777764
No 193
>PRK08745 ribulose-phosphate 3-epimerase; Provisional
Probab=20.59 E-value=1.3e+02 Score=28.85 Aligned_cols=82 Identities=10% Similarity=0.103 Sum_probs=51.5
Q ss_pred CCceEEEecCCCCccccccCcHHHHHHHHHHHHHHHhcCCeEEEEEcCCc--ccCcHH----HHHHHHHHHHHcCCcEEE
Q 014409 170 NGCEIVRYDATEERLLTDVSQPLKILKRRYYLVEKAKDANIIGVLVGTLG--VAGYLH----MIHQMKELITKAGKKAYT 243 (425)
Q Consensus 170 ~~~~v~~yDP~~~~~~~~~~~~~r~L~rRy~~I~ka~~A~~iGIlvgTl~--~q~~~~----~i~~Lk~li~~~GKk~Y~ 243 (425)
.-+.-...+|.|.-- ....+ +.....|=|.--..| ||.+.+ -++++++++.++|++.-+
T Consensus 110 g~k~GlalnP~T~~~-----~i~~~----------l~~vD~VlvMtV~PGf~GQ~fi~~~l~KI~~l~~~~~~~~~~~~I 174 (223)
T PRK08745 110 GCQAGLVLNPATPVD-----ILDWV----------LPELDLVLVMSVNPGFGGQAFIPSALDKLRAIRKKIDALGKPIRL 174 (223)
T ss_pred CCceeEEeCCCCCHH-----HHHHH----------HhhcCEEEEEEECCCCCCccccHHHHHHHHHHHHHHHhcCCCeeE
Confidence 334577888887531 01111 335566555554444 677753 556666777777887667
Q ss_pred EEcCCCCHHHhcCCC--CCCEEEEe
Q 014409 244 LVMGKPNPAKLANFP--ECDVFINV 266 (425)
Q Consensus 244 ~~vgkln~aKLaNF~--eID~fV~v 266 (425)
-+=|-+|.+-+.-+. ++|+||.=
T Consensus 175 eVDGGI~~eti~~l~~aGaDi~V~G 199 (223)
T PRK08745 175 EIDGGVKADNIGAIAAAGADTFVAG 199 (223)
T ss_pred EEECCCCHHHHHHHHHcCCCEEEEC
Confidence 777889988775543 58999984
No 194
>cd06320 PBP1_allose_binding Periplasmic allose-binding domain of bacterial transport systems that function as a primary receptor of active transport and chemotaxis. Periplasmic allose-binding domain of bacterial transport systems that function as a primary receptor of active transport and chemotaxis. The members of this group are belonging to a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily. Like other periplasmic receptors of the ABC-type transport systems, the allose-binding protein consists of two alpha/beta domains connected by a three-stranded hinge. This Venus flytrap-like domain undergoes transition from an open to a closed conformational state upon ligand binding.
Probab=20.42 E-value=4.4e+02 Score=24.58 Aligned_cols=45 Identities=16% Similarity=0.174 Sum_probs=28.1
Q ss_pred cCCeEEEEEcCCcccCcHHHHHHHHHHHHHc-CCcEEEEEcCCCCH
Q 014409 207 DANIIGVLVGTLGVAGYLHMIHQMKELITKA-GKKAYTLVMGKPNP 251 (425)
Q Consensus 207 ~A~~iGIlvgTl~~q~~~~~i~~Lk~li~~~-GKk~Y~~~vgkln~ 251 (425)
..+.++++.|.........-.+-+++.++++ |.+......+.-++
T Consensus 121 g~~~i~~l~~~~~~~~~~~r~~g~~~~~~~~~~~~~~~~~~~~~~~ 166 (275)
T cd06320 121 EGGKVAIIEGKAGAFAAEQRTEGFTEAIKKASGIEVVASQPADWDR 166 (275)
T ss_pred CCceEEEEeCCCCCccHHHHHHHHHHHHhhCCCcEEEEecCCCccH
Confidence 4578998887655444445556678888888 76654333344343
No 195
>PRK06455 riboflavin synthase; Provisional
Probab=20.36 E-value=2.9e+02 Score=25.03 Aligned_cols=58 Identities=19% Similarity=0.236 Sum_probs=38.9
Q ss_pred CeEEEEEcCCcccCcHHHHHHHHHHHHHcC--CcEEEEEc-C--CCC--HHHhcCCCCCCEEEEecCC
Q 014409 209 NIIGVLVGTLGVAGYLHMIHQMKELITKAG--KKAYTLVM-G--KPN--PAKLANFPECDVFINVSCA 269 (425)
Q Consensus 209 ~~iGIlvgTl~~q~~~~~i~~Lk~li~~~G--Kk~Y~~~v-g--kln--~aKLaNF~eID~fV~vaCP 269 (425)
.+|||+++|.... .+.+--.+.|+++| -+..++.| | +|- ..||+.=..+|++|.++|+
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 4789999997653 66777778888855 44434433 3 221 2366654579999999998
No 196
>cd07945 DRE_TIM_CMS Leptospira interrogans citramalate synthase (CMS) and related proteins, N-terminal catalytic TIM barrel domain. Citramalate synthase (CMS) catalyzes the conversion of pyruvate and acetyl-CoA to (R)-citramalate in the first dedicated step of the citramalate pathway. Citramalate is only found in Leptospira interrogans and a few other microorganisms. This family belongs to the DRE-TIM metallolyase superfamily. DRE-TIM metallolyases include 2-isopropylmalate synthase (IPMS), alpha-isopropylmalate synthase (LeuA), 3-hydroxy-3-methylglutaryl-CoA lyase, homocitrate synthase, citramalate synthase, 4-hydroxy-2-oxovalerate aldolase, re-citrate synthase, transcarboxylase 5S, pyruvate carboxylase, AksA, and FrbC. These members all share a conserved triose-phosphate isomerase (TIM) barrel domain consisting of a core beta(8)-alpha(8) motif with the eight parallel beta strands forming an enclosed barrel surrounded by eight alpha helices. The domain has a catalytic center con
Probab=20.22 E-value=84 Score=31.00 Aligned_cols=87 Identities=17% Similarity=0.263 Sum_probs=51.0
Q ss_pred HHHHHhcC--CeEEEEEcC----------CcccCcHHHHHHHHHHHHHcCCcEEEEEcC-----CCCHHHhcCCCCCCEE
Q 014409 201 LVEKAKDA--NIIGVLVGT----------LGVAGYLHMIHQMKELITKAGKKAYTLVMG-----KPNPAKLANFPECDVF 263 (425)
Q Consensus 201 ~I~ka~~A--~~iGIlvgT----------l~~q~~~~~i~~Lk~li~~~GKk~Y~~~vg-----kln~aKLaNF~eID~f 263 (425)
-++.|+++ +.+.|.+++ .+....++.+..+-+..+++|.+.-.-... +.+|+.+..+ ++.+
T Consensus 79 ~~~~A~~~g~~~i~i~~~~S~~h~~~~~~~t~~e~l~~~~~~i~~a~~~G~~v~~~~~d~~~~~r~~~~~~~~~--~~~~ 156 (280)
T cd07945 79 SVDWIKSAGAKVLNLLTKGSLKHCTEQLRKTPEEHFADIREVIEYAIKNGIEVNIYLEDWSNGMRDSPDYVFQL--VDFL 156 (280)
T ss_pred HHHHHHHCCCCEEEEEEeCCHHHHHHHHCcCHHHHHHHHHHHHHHHHhCCCEEEEEEEeCCCCCcCCHHHHHHH--HHHH
Confidence 45566665 778888755 223333444444455556667754333332 6678888766 4445
Q ss_pred EEecCCCcccccccCCCCcccCHHHHHHhh
Q 014409 264 INVSCAQTALLDSKEFLAPVITPFEAMLAF 293 (425)
Q Consensus 264 V~vaCPr~si~d~~ef~kPViTP~ElevAL 293 (425)
.-.+|-+..|-|.-. +.+|.+..-.+
T Consensus 157 ~~~G~~~i~l~DT~G----~~~P~~v~~l~ 182 (280)
T cd07945 157 SDLPIKRIMLPDTLG----ILSPFETYTYI 182 (280)
T ss_pred HHcCCCEEEecCCCC----CCCHHHHHHHH
Confidence 555777777778766 45666654333
Done!