Query 020984
Match_columns 319
No_of_seqs 182 out of 558
Neff 5.6
Searched_HMMs 46136
Date Fri Mar 29 06:42:40 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/020984.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/020984hhsearch_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 2.5E-72 5.4E-77 566.2 22.8 285 16-312 201-496 (496)
2 KOG2648 Diphthamide biosynthes 100.0 1.1E-65 2.3E-70 503.7 21.1 276 2-312 178-453 (453)
3 TIGR00322 diphth2_R diphthamid 100.0 1.1E-50 2.4E-55 391.9 19.4 175 13-200 156-330 (332)
4 PF01866 Diphthamide_syn: Puta 100.0 2.3E-50 4.9E-55 385.7 14.9 176 13-200 130-307 (307)
5 TIGR03682 arCOG04112 arCOG0411 100.0 1.1E-49 2.4E-54 381.6 18.0 170 15-200 138-307 (308)
6 COG1736 DPH2 Diphthamide synth 100.0 1.2E-40 2.5E-45 322.0 17.5 182 12-206 160-341 (347)
7 PRK09492 treR trehalose repres 83.9 4.4 9.6E-05 37.7 7.6 78 98-176 60-143 (315)
8 cd06280 PBP1_LacI_like_4 Ligan 78.1 6.4 0.00014 35.4 6.3 59 102-161 1-65 (263)
9 cd06289 PBP1_MalI_like Ligand- 76.2 6 0.00013 35.3 5.6 75 102-177 1-84 (268)
10 TIGR02990 ectoine_eutA ectoine 74.4 13 0.00029 34.8 7.5 114 63-182 71-216 (239)
11 cd06295 PBP1_CelR Ligand bindi 74.1 5.7 0.00012 35.9 4.9 64 99-162 2-75 (275)
12 cd06279 PBP1_LacI_like_3 Ligan 73.5 6.3 0.00014 36.1 5.1 61 102-163 1-68 (283)
13 TIGR02405 trehalos_R_Ecol treh 73.4 13 0.00027 34.8 7.2 63 98-161 57-125 (311)
14 cd06272 PBP1_hexuronate_repres 72.6 6.4 0.00014 35.3 4.8 58 102-161 1-61 (261)
15 COG2984 ABC-type uncharacteriz 72.6 15 0.00032 36.3 7.5 110 87-202 145-265 (322)
16 COG1609 PurR Transcriptional r 72.5 12 0.00025 36.4 6.9 63 96-159 54-122 (333)
17 cd06274 PBP1_FruR Ligand bindi 72.4 7.8 0.00017 34.8 5.3 60 102-162 1-66 (264)
18 cd01536 PBP1_ABC_sugar_binding 72.0 7.7 0.00017 34.3 5.2 75 102-178 1-86 (267)
19 PF00532 Peripla_BP_1: Peripla 71.4 5.5 0.00012 37.4 4.3 61 101-163 2-68 (279)
20 cd06273 PBP1_GntR_like_1 This 71.2 5.9 0.00013 35.5 4.2 75 102-178 1-84 (268)
21 PRK07188 nicotinate phosphorib 70.8 8.9 0.00019 38.1 5.7 57 99-155 227-307 (352)
22 cd06293 PBP1_LacI_like_11 Liga 70.6 11 0.00025 33.8 6.0 61 102-163 1-67 (269)
23 cd06298 PBP1_CcpA_like Ligand- 69.4 7.1 0.00015 34.9 4.4 59 102-161 1-65 (268)
24 PRK10014 DNA-binding transcrip 69.2 23 0.0005 33.2 8.0 79 98-177 62-149 (342)
25 cd06315 PBP1_ABC_sugar_binding 68.8 7.6 0.00016 35.7 4.5 60 101-161 1-66 (280)
26 cd06271 PBP1_AglR_RafR_like Li 68.7 15 0.00033 32.6 6.4 60 102-161 1-69 (268)
27 cd06270 PBP1_GalS_like Ligand 68.7 10 0.00023 34.0 5.3 59 102-161 1-65 (268)
28 TIGR01753 flav_short flavodoxi 68.7 20 0.00043 29.3 6.6 55 103-162 1-55 (140)
29 PF00919 UPF0004: Uncharacteri 68.1 12 0.00025 30.3 4.9 71 86-156 22-97 (98)
30 cd06277 PBP1_LacI_like_1 Ligan 68.0 17 0.00037 32.7 6.6 73 103-177 2-85 (268)
31 PRK14987 gluconate operon tran 67.3 15 0.00032 34.6 6.2 63 98-161 61-129 (331)
32 cd06281 PBP1_LacI_like_5 Ligan 67.0 11 0.00025 33.9 5.3 59 102-161 1-65 (269)
33 cd06310 PBP1_ABC_sugar_binding 67.0 6.9 0.00015 35.2 3.8 61 102-162 1-68 (273)
34 PRK06703 flavodoxin; Provision 66.9 21 0.00046 30.1 6.6 56 102-162 3-58 (151)
35 PF00731 AIRC: AIR carboxylase 66.3 18 0.0004 31.7 6.1 61 102-165 2-69 (150)
36 cd01542 PBP1_TreR_like Ligand- 66.1 12 0.00025 33.4 5.1 76 102-178 1-84 (259)
37 PRK11303 DNA-binding transcrip 65.0 19 0.00042 33.6 6.5 61 99-161 60-127 (328)
38 cd06291 PBP1_Qymf_like Ligand 63.2 19 0.00041 32.2 5.9 59 102-161 1-65 (265)
39 PRK10423 transcriptional repre 62.9 32 0.00069 32.0 7.6 64 97-161 53-122 (327)
40 PF04392 ABC_sub_bind: ABC tra 62.8 11 0.00024 35.5 4.5 114 84-202 114-237 (294)
41 cd06283 PBP1_RegR_EndR_KdgR_li 62.7 26 0.00056 31.1 6.7 58 102-161 1-65 (267)
42 PF02514 CobN-Mg_chel: CobN/Ma 62.6 12 0.00026 42.5 5.4 112 66-180 40-167 (1098)
43 cd01574 PBP1_LacI Ligand-bindi 62.6 15 0.00032 32.9 5.0 61 102-162 1-67 (264)
44 PF00258 Flavodoxin_1: Flavodo 62.4 17 0.00036 30.2 5.0 54 105-161 1-54 (143)
45 PRK09004 FMN-binding protein M 62.0 25 0.00053 30.2 6.1 55 101-162 2-56 (146)
46 PRK11041 DNA-binding transcrip 61.6 34 0.00075 31.4 7.5 62 98-160 33-100 (309)
47 PRK09526 lacI lac repressor; R 61.5 50 0.0011 31.0 8.7 61 98-158 61-127 (342)
48 cd06316 PBP1_ABC_sugar_binding 61.3 11 0.00024 34.7 4.1 61 102-162 1-67 (294)
49 PRK07308 flavodoxin; Validated 60.9 40 0.00087 28.3 7.2 57 102-163 3-59 (146)
50 cd06292 PBP1_LacI_like_10 Liga 60.9 22 0.00048 31.9 5.9 58 102-160 1-64 (273)
51 PRK05569 flavodoxin; Provision 60.5 40 0.00086 27.9 7.0 57 101-162 2-58 (141)
52 cd01545 PBP1_SalR Ligand-bindi 60.1 32 0.00069 30.7 6.8 60 102-161 1-66 (270)
53 PRK08105 flavodoxin; Provision 60.1 25 0.00054 30.3 5.8 41 101-142 2-42 (149)
54 TIGR02417 fruct_sucro_rep D-fr 59.5 57 0.0012 30.4 8.7 62 98-160 58-125 (327)
55 cd01538 PBP1_ABC_xylose_bindin 59.2 11 0.00023 34.8 3.6 59 102-161 1-65 (288)
56 PRK05568 flavodoxin; Provision 59.1 50 0.0011 27.3 7.4 57 101-162 2-58 (142)
57 PRK10703 DNA-binding transcrip 59.0 26 0.00057 32.9 6.3 62 98-160 57-124 (341)
58 cd06299 PBP1_LacI_like_13 Liga 59.0 31 0.00066 30.8 6.5 60 102-163 1-67 (265)
59 cd06282 PBP1_GntR_like_2 Ligan 58.7 21 0.00045 31.7 5.3 75 102-178 1-85 (266)
60 PRK05723 flavodoxin; Provision 58.3 33 0.00071 29.7 6.3 55 102-161 2-56 (151)
61 PRK14571 D-alanyl-alanine synt 58.3 36 0.00078 32.1 7.1 76 102-178 2-85 (299)
62 PF00885 DMRL_synthase: 6,7-di 57.5 25 0.00054 30.5 5.4 61 100-160 3-71 (144)
63 cd06318 PBP1_ABC_sugar_binding 57.4 15 0.00033 33.2 4.2 59 102-161 1-65 (282)
64 TIGR01481 ccpA catabolite cont 57.0 39 0.00085 31.5 7.1 62 99-161 58-125 (329)
65 cd06278 PBP1_LacI_like_2 Ligan 56.4 25 0.00055 31.2 5.5 60 102-161 1-64 (266)
66 cd06296 PBP1_CatR_like Ligand- 56.4 24 0.00053 31.5 5.4 58 102-160 1-64 (270)
67 PRK10653 D-ribose transporter 56.2 23 0.0005 32.7 5.3 63 98-161 24-92 (295)
68 cd06284 PBP1_LacI_like_6 Ligan 55.9 36 0.00079 30.2 6.4 58 103-161 2-65 (267)
69 COG0041 PurE Phosphoribosylcar 55.5 30 0.00066 30.8 5.5 60 102-164 4-68 (162)
70 TIGR01754 flav_RNR ribonucleot 54.9 27 0.00059 29.3 5.1 57 102-161 2-59 (140)
71 cd06286 PBP1_CcpB_like Ligand- 54.4 32 0.0007 30.6 5.8 59 102-161 1-65 (260)
72 PRK14095 pgi glucose-6-phospha 52.6 95 0.0021 32.8 9.6 51 99-150 202-256 (533)
73 cd06290 PBP1_LacI_like_9 Ligan 52.5 29 0.00063 31.0 5.2 59 102-161 1-65 (265)
74 COG0716 FldA Flavodoxins [Ener 52.3 51 0.0011 28.1 6.4 59 101-163 2-60 (151)
75 PRK09271 flavodoxin; Provision 51.8 55 0.0012 28.2 6.7 58 102-161 2-60 (160)
76 cd06297 PBP1_LacI_like_12 Liga 51.3 23 0.00049 32.1 4.4 60 102-161 1-65 (269)
77 cd05013 SIS_RpiR RpiR-like pro 50.7 80 0.0017 25.1 7.1 68 93-164 6-73 (139)
78 PF00205 TPP_enzyme_M: Thiamin 50.4 8.9 0.00019 31.9 1.4 46 93-140 4-49 (137)
79 PF03698 UPF0180: Uncharacteri 50.2 37 0.0008 26.8 4.7 56 120-182 11-72 (80)
80 cd01543 PBP1_XylR Ligand-bindi 50.0 29 0.00063 31.2 4.8 55 102-159 1-58 (265)
81 cd06275 PBP1_PurR Ligand-bindi 49.8 63 0.0014 28.8 7.0 59 102-161 1-65 (269)
82 cd01575 PBP1_GntR Ligand-bindi 49.5 35 0.00076 30.3 5.2 60 102-162 1-66 (268)
83 PRK10339 DNA-binding transcrip 49.4 34 0.00074 32.1 5.4 58 99-160 62-123 (327)
84 PRK11921 metallo-beta-lactamas 49.3 51 0.0011 32.8 6.8 92 67-163 217-311 (394)
85 PF13964 Kelch_6: Kelch motif 48.8 36 0.00077 23.2 4.1 15 62-76 26-40 (50)
86 cd06302 PBP1_LsrB_Quorum_Sensi 48.5 34 0.00073 31.8 5.1 59 102-160 1-65 (298)
87 COG2185 Sbm Methylmalonyl-CoA 47.8 22 0.00048 31.1 3.5 57 93-150 55-112 (143)
88 TIGR01162 purE phosphoribosyla 47.6 37 0.0008 30.1 4.9 71 103-176 1-80 (156)
89 cd04502 SGNH_hydrolase_like_7 47.3 1.3E+02 0.0027 25.4 8.2 88 44-139 2-96 (171)
90 PF01729 QRPTase_C: Quinolinat 46.3 25 0.00054 31.3 3.7 62 94-159 93-156 (169)
91 PF12641 Flavodoxin_3: Flavodo 46.2 95 0.0021 27.3 7.3 81 39-128 37-126 (160)
92 cd06294 PBP1_ycjW_transcriptio 46.2 47 0.001 29.6 5.5 59 102-160 1-69 (270)
93 cd01452 VWA_26S_proteasome_sub 45.9 48 0.001 30.0 5.5 49 101-150 108-158 (187)
94 cd06285 PBP1_LacI_like_7 Ligan 45.4 54 0.0012 29.3 5.8 59 102-161 1-65 (265)
95 cd06307 PBP1_uncharacterized_s 45.0 29 0.00063 31.3 4.0 60 102-161 1-68 (275)
96 cd00300 LDH_like L-lactate deh 44.9 71 0.0015 30.6 6.8 96 46-141 3-117 (300)
97 PRK05452 anaerobic nitric oxid 44.5 1E+02 0.0022 31.8 8.3 109 67-184 221-332 (479)
98 cd05569 PTS_IIB_fructose PTS_I 44.4 74 0.0016 25.3 5.8 59 103-164 2-66 (96)
99 cd01537 PBP1_Repressors_Sugar_ 44.3 54 0.0012 28.6 5.5 75 102-177 1-84 (264)
100 cd06312 PBP1_ABC_sugar_binding 44.2 48 0.001 29.9 5.3 60 102-161 1-67 (271)
101 PRK11104 hemG protoporphyrinog 43.7 42 0.00092 29.6 4.7 55 102-162 2-56 (177)
102 PRK12359 flavodoxin FldB; Prov 43.5 84 0.0018 28.0 6.6 53 102-162 2-55 (172)
103 PRK00061 ribH 6,7-dimethyl-8-r 43.5 64 0.0014 28.4 5.7 62 100-161 12-81 (154)
104 PRK10727 DNA-binding transcrip 43.2 96 0.0021 29.2 7.4 62 99-161 58-125 (343)
105 PRK10355 xylF D-xylose transpo 42.7 59 0.0013 31.1 5.9 63 99-162 24-92 (330)
106 cd06320 PBP1_allose_binding Pe 42.6 47 0.001 29.9 5.0 59 102-161 1-67 (275)
107 cd06305 PBP1_methylthioribose_ 42.6 51 0.0011 29.4 5.2 57 102-159 1-63 (273)
108 PRK09701 D-allose transporter 42.5 60 0.0013 30.5 5.9 63 97-159 21-90 (311)
109 TIGR01205 D_ala_D_alaTIGR D-al 42.0 86 0.0019 29.4 6.9 58 102-159 1-71 (315)
110 cd01981 Pchlide_reductase_B Pc 42.0 77 0.0017 31.8 6.8 79 99-178 161-243 (430)
111 cd06321 PBP1_ABC_sugar_binding 42.0 35 0.00076 30.6 4.1 58 102-159 1-65 (271)
112 PRK02910 light-independent pro 41.5 67 0.0014 33.4 6.5 77 100-177 158-238 (519)
113 PLN02404 6,7-dimethyl-8-ribity 41.3 96 0.0021 27.0 6.4 62 100-161 7-76 (141)
114 cd06304 PBP1_BmpA_like Peripla 41.0 51 0.0011 29.7 5.0 56 102-159 1-64 (260)
115 cd01473 vWA_CTRP CTRP for CS 40.8 1E+02 0.0022 27.4 6.8 50 100-150 108-159 (192)
116 cd01540 PBP1_arabinose_binding 40.8 45 0.00097 30.3 4.6 57 102-160 1-63 (289)
117 PRK12493 magnesium chelatase s 40.5 72 0.0016 37.2 7.0 61 100-160 253-324 (1310)
118 cd06319 PBP1_ABC_sugar_binding 40.0 33 0.00071 30.8 3.5 73 103-177 2-85 (277)
119 cd06267 PBP1_LacI_sugar_bindin 39.6 53 0.0011 28.7 4.7 11 129-139 54-64 (264)
120 cd06288 PBP1_sucrose_transcrip 39.4 1.1E+02 0.0023 27.2 6.8 59 102-161 1-66 (269)
121 cd01571 NAPRTase_B Nicotinate 39.2 38 0.00083 32.8 4.0 55 101-155 211-270 (302)
122 cd06300 PBP1_ABC_sugar_binding 39.1 65 0.0014 28.9 5.4 59 102-160 1-69 (272)
123 PRK09426 methylmalonyl-CoA mut 39.1 47 0.001 36.2 5.0 71 93-166 625-700 (714)
124 cd02071 MM_CoA_mut_B12_BD meth 39.0 71 0.0015 26.3 5.1 60 99-162 50-113 (122)
125 cd01541 PBP1_AraR Ligand-bindi 38.8 64 0.0014 28.9 5.3 55 102-158 1-62 (273)
126 PRK10401 DNA-binding transcrip 38.8 1.2E+02 0.0027 28.5 7.4 61 99-160 58-124 (346)
127 cd06306 PBP1_TorT-like TorT-li 38.5 40 0.00087 30.5 3.9 60 102-161 1-67 (268)
128 PRK06455 riboflavin synthase; 38.4 1.1E+02 0.0025 27.1 6.5 58 101-161 2-66 (155)
129 TIGR00640 acid_CoA_mut_C methy 38.3 65 0.0014 27.4 4.9 94 54-163 21-117 (132)
130 cd06325 PBP1_ABC_uncharacteriz 38.3 83 0.0018 28.2 5.9 75 102-178 1-87 (281)
131 TIGR02634 xylF D-xylose ABC tr 38.1 37 0.00079 31.8 3.6 59 103-162 1-65 (302)
132 PLN02285 methionyl-tRNA formyl 38.0 70 0.0015 31.4 5.7 64 99-163 35-105 (334)
133 TIGR01579 MiaB-like-C MiaB-lik 37.7 46 0.00099 33.2 4.5 65 91-156 25-92 (414)
134 PF02233 PNTB: NAD(P) transhyd 37.6 23 0.0005 36.6 2.3 85 93-181 300-418 (463)
135 PRK15395 methyl-galactoside AB 36.8 97 0.0021 29.5 6.4 65 97-161 21-91 (330)
136 PRK10936 TMAO reductase system 36.7 81 0.0018 30.2 5.9 65 97-161 43-114 (343)
137 TIGR00288 conserved hypothetic 36.3 1.2E+02 0.0027 26.9 6.4 53 98-159 104-156 (160)
138 cd02036 MinD Bacterial cell di 36.1 1.5E+02 0.0033 24.8 6.9 59 105-163 3-73 (179)
139 cd06308 PBP1_sensor_kinase_lik 35.9 70 0.0015 28.7 5.0 59 102-161 1-66 (270)
140 cd01539 PBP1_GGBP Periplasmic 35.9 33 0.00072 32.0 3.0 59 102-161 1-67 (303)
141 TIGR01278 DPOR_BchB light-inde 35.9 2E+02 0.0044 29.8 8.9 77 99-176 157-237 (511)
142 TIGR02014 BchZ chlorophyllide 35.7 67 0.0015 33.2 5.4 77 99-176 151-227 (468)
143 cd01450 vWFA_subfamily_ECM Von 35.5 1.7E+02 0.0036 23.8 6.9 66 86-152 85-154 (161)
144 PF03358 FMN_red: NADPH-depend 35.5 86 0.0019 26.1 5.2 40 102-141 2-42 (152)
145 PRK09590 celB cellobiose phosp 35.5 1.1E+02 0.0025 25.0 5.7 51 113-165 12-62 (104)
146 KOG0781 Signal recognition par 35.3 2.1E+02 0.0046 30.2 8.7 70 92-162 457-542 (587)
147 PRK13937 phosphoheptose isomer 35.0 1.8E+02 0.0039 25.7 7.4 62 98-166 104-165 (188)
148 PRK06756 flavodoxin; Provision 34.5 1.5E+02 0.0032 24.9 6.5 56 102-162 3-59 (148)
149 TIGR02955 TMAO_TorT TMAO reduc 34.4 93 0.002 28.8 5.7 60 102-161 1-67 (295)
150 COG5136 U1 snRNP-specific prot 34.4 41 0.0009 30.2 3.1 44 121-164 51-94 (188)
151 PF01583 APS_kinase: Adenylyls 34.0 92 0.002 27.4 5.3 39 103-141 3-41 (156)
152 cd06317 PBP1_ABC_sugar_binding 33.7 71 0.0015 28.5 4.7 57 103-160 2-65 (275)
153 PF01177 Asp_Glu_race: Asp/Glu 33.6 1.5E+02 0.0032 26.0 6.7 79 99-183 106-212 (216)
154 TIGR01931 cysJ sulfite reducta 33.5 85 0.0018 33.3 5.8 49 100-149 58-106 (597)
155 COG0529 CysC Adenylylsulfate k 33.0 1E+02 0.0022 28.4 5.3 40 100-139 21-60 (197)
156 PLN03069 magnesiumprotoporphyr 32.3 1.4E+02 0.003 34.8 7.5 62 99-160 265-336 (1220)
157 cd03819 GT1_WavL_like This fam 31.9 82 0.0018 29.1 4.9 43 99-142 183-226 (355)
158 TIGR00114 lumazine-synth 6,7-d 31.8 1.4E+02 0.0031 25.7 6.0 60 102-161 2-69 (138)
159 PF06414 Zeta_toxin: Zeta toxi 31.8 1.7E+02 0.0037 25.8 6.8 86 51-139 28-128 (199)
160 PLN02948 phosphoribosylaminoim 31.7 1.3E+02 0.0028 31.9 6.8 116 58-176 353-492 (577)
161 PRK08662 nicotinate phosphorib 31.7 67 0.0014 31.8 4.4 55 101-155 227-285 (343)
162 TIGR01007 eps_fam capsular exo 31.5 1.6E+02 0.0034 25.9 6.5 56 87-143 4-59 (204)
163 PRK08883 ribulose-phosphate 3- 30.8 74 0.0016 29.4 4.3 49 111-159 142-196 (220)
164 cd05015 SIS_PGI_1 Phosphogluco 30.6 3.4E+02 0.0073 23.3 8.2 47 100-148 73-124 (158)
165 PRK00005 fmt methionyl-tRNA fo 30.5 1.6E+02 0.0035 28.3 6.8 41 121-164 47-91 (309)
166 PRK09267 flavodoxin FldA; Vali 30.4 1E+02 0.0023 26.4 5.0 54 102-162 3-56 (169)
167 PF02302 PTS_IIB: PTS system, 30.4 1.1E+02 0.0024 23.1 4.7 56 106-165 4-59 (90)
168 cd01982 Chlide_reductase_Z Chl 30.3 90 0.0019 31.7 5.2 76 100-176 155-230 (412)
169 cd05566 PTS_IIB_galactitol PTS 29.9 1.6E+02 0.0036 22.3 5.6 56 103-162 3-58 (89)
170 cd05565 PTS_IIB_lactose PTS_II 29.8 1.5E+02 0.0033 24.1 5.5 50 112-165 10-59 (99)
171 cd05291 HicDH_like L-2-hydroxy 29.7 2.3E+02 0.005 27.0 7.7 99 43-141 2-119 (306)
172 PF10657 RC-P840_PscD: Photosy 29.7 45 0.00097 28.7 2.4 85 86-210 28-114 (144)
173 cd06276 PBP1_FucR_like Ligand- 29.6 1E+02 0.0022 27.8 5.1 56 103-161 2-62 (247)
174 cd06354 PBP1_BmpA_PnrA_like Pe 29.5 1.4E+02 0.003 27.2 5.9 58 102-161 1-67 (265)
175 TIGR00147 lipid kinase, YegS/R 29.4 1.9E+02 0.0041 27.1 7.0 36 102-137 3-39 (293)
176 cd06320 PBP1_allose_binding Pe 29.3 3E+02 0.0065 24.6 8.0 93 61-155 80-186 (275)
177 TIGR00853 pts-lac PTS system, 29.2 1.7E+02 0.0036 23.3 5.6 59 101-165 4-62 (95)
178 TIGR01574 miaB-methiolase tRNA 29.2 90 0.0019 31.5 5.0 65 92-156 30-100 (438)
179 PRK13055 putative lipid kinase 29.1 2.2E+02 0.0047 27.6 7.4 31 102-132 4-35 (334)
180 cd03825 GT1_wcfI_like This fam 28.8 1.7E+02 0.0038 26.9 6.5 56 102-157 2-57 (365)
181 PRK14096 pgi glucose-6-phospha 28.7 3.3E+02 0.0072 28.7 9.1 49 100-150 167-220 (528)
182 cd06309 PBP1_YtfQ_like Peripla 28.6 83 0.0018 28.3 4.2 58 102-160 1-64 (273)
183 cd02042 ParA ParA and ParB of 28.6 1.9E+02 0.0042 22.2 5.9 48 105-163 3-50 (104)
184 PRK11914 diacylglycerol kinase 28.4 2E+02 0.0043 27.3 7.0 16 170-185 105-120 (306)
185 cd03801 GT1_YqgM_like This fam 28.4 50 0.0011 29.5 2.7 41 121-161 244-285 (374)
186 cd00316 Oxidoreductase_nitroge 28.4 2.1E+02 0.0047 27.8 7.4 75 98-176 150-228 (399)
187 PF01380 SIS: SIS domain SIS d 28.2 76 0.0017 25.3 3.6 62 97-162 2-64 (131)
188 PRK08091 ribulose-phosphate 3- 28.2 1.8E+02 0.0038 27.3 6.3 46 112-157 155-206 (228)
189 KOG0343 RNA Helicase [RNA proc 28.0 2.7E+02 0.0059 30.1 8.1 89 91-186 330-429 (758)
190 KOG1975 mRNA cap methyltransfe 27.9 1.7E+02 0.0036 29.5 6.3 142 43-203 174-322 (389)
191 PRK10310 PTS system galactitol 27.8 1.5E+02 0.0033 23.4 5.2 52 105-159 6-58 (94)
192 PF00781 DAGK_cat: Diacylglyce 27.7 1.9E+02 0.0041 23.6 5.9 38 102-140 1-38 (130)
193 TIGR01752 flav_long flavodoxin 27.3 1.5E+02 0.0032 25.7 5.4 54 102-162 1-54 (167)
194 CHL00076 chlB photochlorophyll 27.2 5.6E+02 0.012 26.7 10.4 78 99-177 162-243 (513)
195 PLN02334 ribulose-phosphate 3- 27.0 4.8E+02 0.01 23.7 10.5 59 100-159 140-203 (229)
196 PF09547 Spore_IV_A: Stage IV 27.0 1E+02 0.0022 32.0 4.8 71 98-168 142-225 (492)
197 PRK12419 riboflavin synthase s 26.8 1.9E+02 0.0041 25.7 6.0 61 101-161 11-79 (158)
198 TIGR02883 spore_cwlD N-acetylm 26.7 1.4E+02 0.003 26.5 5.2 49 114-162 27-94 (189)
199 TIGR03449 mycothiol_MshA UDP-N 26.6 2.4E+02 0.0053 27.0 7.3 41 120-160 270-311 (405)
200 PRK14733 coaE dephospho-CoA ki 26.6 91 0.002 28.5 4.1 51 114-164 91-141 (204)
201 PF09314 DUF1972: Domain of un 26.5 1.2E+02 0.0027 27.4 4.9 58 105-163 5-66 (185)
202 PLN02204 diacylglycerol kinase 26.1 8.5E+02 0.019 26.3 12.7 76 84-159 142-226 (601)
203 cd06322 PBP1_ABC_sugar_binding 26.0 1.1E+02 0.0024 27.3 4.5 59 102-161 1-65 (267)
204 PRK11557 putative DNA-binding 25.8 1.8E+02 0.004 26.9 6.1 65 93-163 121-187 (278)
205 PLN02949 transferase, transfer 25.2 1.3E+02 0.0029 30.7 5.4 74 101-184 303-377 (463)
206 cd06323 PBP1_ribose_binding Pe 25.1 92 0.002 27.5 3.8 31 103-133 2-32 (268)
207 cd03798 GT1_wlbH_like This fam 25.0 45 0.00098 30.0 1.8 38 123-160 249-287 (377)
208 cd03821 GT1_Bme6_like This fam 25.0 1.7E+02 0.0037 26.4 5.6 34 128-161 257-291 (375)
209 TIGR02363 dhaK1 dihydroxyaceto 24.6 2.6E+02 0.0057 27.7 7.1 46 96-141 248-296 (329)
210 PRK03501 ppnK inorganic polyph 24.4 1.6E+02 0.0036 28.0 5.5 32 101-134 3-34 (264)
211 cd03813 GT1_like_3 This family 24.3 2.4E+02 0.0053 28.4 7.1 57 101-161 324-380 (475)
212 PF02273 Acyl_transf_2: Acyl t 24.1 3E+02 0.0065 26.8 7.1 103 33-143 21-136 (294)
213 PRK10427 putative PTS system f 24.0 2.5E+02 0.0055 23.3 6.0 61 100-163 3-69 (114)
214 cd06314 PBP1_tmGBP Periplasmic 24.0 1.5E+02 0.0032 26.7 5.0 58 102-160 1-64 (271)
215 PF02593 dTMP_synthase: Thymid 23.8 1.1E+02 0.0024 28.6 4.1 37 92-130 67-103 (217)
216 PRK10953 cysJ sulfite reductas 23.7 1.8E+02 0.0039 31.0 6.2 51 98-149 59-109 (600)
217 TIGR00642 mmCoA_mut_beta methy 23.7 1.4E+02 0.003 32.1 5.4 59 102-165 548-608 (619)
218 TIGR03567 FMN_reduc_SsuE FMN r 23.7 3.5E+02 0.0075 23.4 7.1 41 103-143 2-43 (171)
219 PRK01372 ddl D-alanine--D-alan 23.3 3.4E+02 0.0074 25.3 7.5 57 101-158 5-63 (304)
220 COG1429 CobN Cobalamin biosynt 23.3 2.5E+02 0.0055 33.2 7.6 96 67-166 173-276 (1388)
221 PF09861 DUF2088: Domain of un 23.1 1.6E+02 0.0034 27.0 5.0 39 93-132 47-87 (204)
222 PF01344 Kelch_1: Kelch motif; 22.9 65 0.0014 21.3 1.9 14 63-76 27-40 (47)
223 cd05397 NT_Pol-beta-like Nucle 22.9 1.7E+02 0.0036 20.4 4.0 39 117-157 2-42 (49)
224 PRK15408 autoinducer 2-binding 22.8 2E+02 0.0043 27.8 5.9 63 99-161 22-90 (336)
225 PRK03767 NAD(P)H:quinone oxido 22.5 2E+02 0.0044 25.5 5.5 42 102-144 3-45 (200)
226 cd03142 GATase1_ThuA Type 1 gl 22.4 2E+02 0.0043 26.7 5.5 44 117-163 23-70 (215)
227 COG0552 FtsY Signal recognitio 22.4 1.6E+02 0.0035 29.3 5.2 87 90-176 210-315 (340)
228 PRK14336 (dimethylallyl)adenos 22.4 2E+02 0.0043 28.9 6.0 10 156-165 130-139 (418)
229 cd06301 PBP1_rhizopine_binding 22.4 2.1E+02 0.0045 25.5 5.6 57 103-160 2-65 (272)
230 PRK03094 hypothetical protein; 22.3 2.1E+02 0.0044 22.7 4.7 57 120-183 11-73 (80)
231 PRK00945 acetyl-CoA decarbonyl 22.3 2.7E+02 0.0059 25.0 6.2 46 92-138 26-71 (171)
232 cd01481 vWA_collagen_alpha3-VI 22.2 2E+02 0.0043 24.8 5.3 49 99-150 105-153 (165)
233 TIGR03605 antibiot_sagB SagB-t 22.2 4.6E+02 0.0099 22.7 7.6 85 65-151 56-160 (173)
234 PRK05319 rplD 50S ribosomal pr 21.9 6.2E+02 0.013 23.1 8.6 68 83-154 103-173 (205)
235 PF03059 NAS: Nicotianamine sy 21.9 1E+02 0.0022 29.7 3.7 30 43-72 123-155 (276)
236 PRK03708 ppnK inorganic polyph 21.9 2E+02 0.0043 27.5 5.6 98 102-203 2-122 (277)
237 PRK00179 pgi glucose-6-phospha 21.8 9.7E+02 0.021 25.4 11.5 52 99-153 196-255 (548)
238 cd06324 PBP1_ABC_sugar_binding 21.8 1.9E+02 0.0042 26.8 5.4 34 103-136 2-36 (305)
239 PRK15482 transcriptional regul 21.7 3.3E+02 0.0072 25.4 7.0 66 96-165 131-196 (285)
240 PRK14481 dihydroxyacetone kina 21.6 3.2E+02 0.0069 27.2 7.0 46 96-141 247-295 (331)
241 cd03806 GT1_ALG11_like This fa 21.4 1.9E+02 0.0041 28.8 5.5 72 102-183 274-346 (419)
242 TIGR02362 dhaK1b probable dihy 21.4 3.3E+02 0.0072 27.0 7.1 46 96-141 244-292 (326)
243 PRK14483 DhaKLM operon coactiv 21.3 3.2E+02 0.007 27.1 7.0 46 96-141 247-295 (329)
244 PLN02958 diacylglycerol kinase 21.3 9.1E+02 0.02 24.9 10.8 63 96-158 107-175 (481)
245 TIGR01501 MthylAspMutase methy 21.3 1.6E+02 0.0035 25.3 4.4 45 93-140 44-90 (134)
246 PRK15427 colanic acid biosynth 21.2 74 0.0016 31.5 2.6 42 120-161 266-308 (406)
247 cd02040 NifH NifH gene encodes 20.8 1.8E+02 0.0038 26.5 4.9 37 101-139 2-38 (270)
248 cd05402 NT_PAP_TUTase Nucleoti 20.6 2E+02 0.0043 22.8 4.6 47 115-161 2-48 (114)
249 TIGR02257 cobalto_cobN cobalto 20.6 2.3E+02 0.005 32.7 6.5 79 100-178 191-284 (1122)
250 PRK14340 (dimethylallyl)adenos 20.5 1.6E+02 0.0034 30.0 4.9 62 93-156 37-106 (445)
251 PRK10359 lipopolysaccharide co 20.2 1.3E+02 0.0028 28.1 3.9 73 49-133 158-231 (232)
252 TIGR02025 BchH magnesium chela 20.2 2.6E+02 0.0057 32.6 6.9 62 99-160 238-309 (1216)
253 cd00133 PTS_IIB PTS_IIB: subun 20.2 3.1E+02 0.0068 19.5 5.3 47 105-154 3-49 (84)
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=2.5e-72 Score=566.21 Aligned_cols=285 Identities=30% Similarity=0.494 Sum_probs=231.1
Q ss_pred CCCCCcccceeCCeeeecCCCCCCCceeEEEEcCCcc-hHHHHHHhcC-C-CeEEEEcCCCCccccccCc-HHHHHHHHH
Q 020984 16 GPAGGCTRHTIGGLVWNIPDRKKMEEHLLFWIGSDNS-AFANVVLTFN-G-CEIVRYDATEERLLTDVSQ-PLKILKRRY 91 (319)
Q Consensus 16 ~~~~gct~~~i~~~~~~l~~~~~~~~~~i~~Ig~~~~-~l~~l~l~~~-~-~~v~~yDP~s~~~~~e~~~-~~k~l~~R~ 91 (319)
|.++|||.+...+ ...+++.+||||++++ ++.+++|+.+ . +++|+|||+++++..+.++ +.++|||||
T Consensus 201 ~~vlGc~~~~~~~--------~~~~~~~~l~IG~~~~g~f~~l~l~~~~~~~~v~~~dP~~~~~~~~~~~~~~~~L~rRy 272 (496)
T TIGR00272 201 FVTIGRTFHVPED--------VDQQEKNLVLFGQHSSEDLHLIHLTTYQDLSTVFQFVPIFDPILPESVTGPFPSLRRRY 272 (496)
T ss_pred ceecCccccCccc--------cccccceEEEEcCCCchhhhHhhhhcCCCCCceEEECCCCCcceecccchHHHHHHHHH
Confidence 4477777665543 2345678999999777 7777877543 5 6799999999999888766 999999999
Q ss_pred HHHHhhccCCEEEEEEcCCCccCcHHHHHHHHHHHHHhCCcEEEEEcCCCCHHhhcCCCCCCEEEEecCCCcccccccCC
Q 020984 92 YLVEKAKDANIIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKLANFPECDVFINVSCAQTALLDSKEF 171 (319)
Q Consensus 92 ~~I~ka~~a~~iGIivgTl~~q~~~~i~~~l~~ll~~~Gkk~y~i~vg~in~~KLaNf~eID~fV~iaCPr~sidd~~~f 171 (319)
++|+||++|++||||||||++|+|++++++|+++|+++|||+|+|+||+|||+||+||++||+||++||||++|||+++|
T Consensus 273 ~~I~kA~~A~~~GIlVgTL~~q~~~~ii~~l~~li~~~GkK~yl~~vgkinpaKLaNF~eID~fV~vaCPr~sidd~~~F 352 (496)
T TIGR00272 273 KLVHVARDAGCIGIVVGTLGVRNTRETINELRKMIKTAGKKHYLFVVGKPNPAKLANFEDIDIFVLLGCSQSGIIDSNEF 352 (496)
T ss_pred HHHHHHhcCCEEEEEEecCccCCCHHHHHHHHHHHHHcCCcEEEEEeCCCCHHHHhCCCCCCEEEEccCCCcccccHhhC
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCcccCHHHHHHhhCCCCCCCcceeeccccccCC--CC----CCCCCcccccceeeecCceeccCCCCCcCCcchhhhhH
Q 020984 172 LAPVITPFEAMLAFGRGTQWTGAYVMEFRDLMSS--SP----VEGSDQAEEARFSFLKGGYVEDVAQPETENGEEEKEGA 245 (319)
Q Consensus 172 ~kPvlTP~El~vAL~~~~~W~~~y~~Df~~ll~~--~~----~~~~~~~~~p~fslitG~~~~~~~~~~~~~~~~~~~~~ 245 (319)
+||||||||++|||+.+..|.+.|..+|..+... +. .+..+++++|+||||||+|++++++++...+.+...
T Consensus 353 ~KPVlTP~ElelAL~~~~~w~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~fslitG~~~~~~~~~~~~~~~~~~~-- 430 (496)
T TIGR00272 353 YRPIVTPFELNLALSEEVTWVVDFRDSIDEIEQLLGGQDTISPSTTSDEAAPEFSLIRGKYTSTSRPLRALTHLELEA-- 430 (496)
T ss_pred CCceecHHHHHHHhCCcccccchHHHHhhhhhhcccccccCCCccccccCCCceeccccceeecCCccchhhhccccc--
Confidence 9999999999999998777998888888776532 11 111223468999999999999887765222111000
Q ss_pred HHhhhhhhhhhhhccCCCCceeecccChHHHHhhcCccccCCCCCCC-CCCcccccCcccccCCCCCc
Q 020984 246 LALANAAEKALQLRDRSLDPIVKGTAKSGAEYFVSRSYHGLEMQCNS-SSPEPYAIGRSGKASGYDDE 312 (319)
Q Consensus 246 ~~~~~~~~~~l~~~~~~~~~~~~~~~s~~a~~L~~Rtw~GLe~~~g~-~~~~~~~~GrsGIA~gY~~e 312 (319)
.....+.++..+.+...+++++++|+||+||++||||||++++|+ ++++.++|||+||||||++|
T Consensus 431 --~~~~~~~~~~~~~~~~~~~~~~~~s~~a~~l~~Rtw~GL~~~~~~~~~~a~~~eGrsGIA~gY~~~ 496 (496)
T TIGR00272 431 --ADNDDSKQSTTRHTASGAVIKGTVSTSASALQNRSWKGLGDDVDSTEVDAKIEEGISGIARGYGGD 496 (496)
T ss_pred --cCCCCccceeecccCcceeeccccccHHHHhhcCceeCCCCCcCCCCCcceeecCCccccccCCCC
Confidence 001222345444433335667788999999999999999999986 45789999999999999865
No 2
>KOG2648 consensus Diphthamide biosynthesis protein [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=1.1e-65 Score=503.68 Aligned_cols=276 Identities=35% Similarity=0.562 Sum_probs=225.6
Q ss_pred CcccCCCccccccCCCCCCcccceeCCeeeecCCCCCCCceeEEEEcCCcchHHHHHHhcCCCeEEEEcCCCCccccccC
Q 020984 2 CTVITPSKDHKSLCGPAGGCTRHTIGGLVWNIPDRKKMEEHLLFWIGSDNSAFANVVLTFNGCEIVRYDATEERLLTDVS 81 (319)
Q Consensus 2 ~~~~~~~~~~~~~~~~~~gct~~~i~~~~~~l~~~~~~~~~~i~~Ig~~~~~l~~l~l~~~~~~v~~yDP~s~~~~~e~~ 81 (319)
+.|+.|+..--| -|+++|||+|.+.++ .++.++|||||++||++..|+.+|..++|+|||++++++.|.+
T Consensus 178 ~~~i~Pq~~p~s-~~e~lG~t~p~~~~~---------~~~~~li~iGD~~~~le~~mi~np~~~~~~ydp~s~kl~~E~y 247 (453)
T KOG2648|consen 178 LEVILPQFKPLS-PGEVLGCTSPLLEGR---------EEYDALIFIGDGRFHLESSMIANPGLPAYRYDPYSKKLTRESY 247 (453)
T ss_pred eEEeccCCCCCC-CccccceeccCCCCc---------cccceEEEecCCCcchhHHHHhCCCCCeEEeCCccCceeeccc
Confidence 356777777333 788999999999874 4567899999999999999999999999999999999999999
Q ss_pred cHHHHHHHHHHHHHhhccCCEEEEEEcCCCccCcHHHHHHHHHHHHHhCCcEEEEEcCCCCHHhhcCCCCCCEEEEecCC
Q 020984 82 QPLKILKRRYYLVEKAKDANIIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKLANFPECDVFINVSCA 161 (319)
Q Consensus 82 ~~~k~l~~R~~~I~ka~~a~~iGIivgTl~~q~~~~i~~~l~~ll~~~Gkk~y~i~vg~in~~KLaNf~eID~fV~iaCP 161 (319)
++.+|+++||++|+|||+|++||||+||||+|||++++++|+++|+++|||+|+|+||||||+|||||++|||||+||||
T Consensus 248 ~~~~m~~rR~~~vekardA~~iGlivGTLG~qg~~~vl~~L~~~~~~~Gkk~y~l~~g~inPaKLAnF~eIDvfV~iaCp 327 (453)
T KOG2648|consen 248 DHSRMLRRRYYLVEKARDARTIGLIVGTLGRQGNREVLEHLRKLLKAAGKKSYVLALGEINPAKLANFPEIDVFVQIACP 327 (453)
T ss_pred chHHHHHHHHHHHHHHhcCCeEEEEEecccccCCHHHHHHHHHHHHHcCCceEEEEecCCCHHHhcCCccccEEEEEeCc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CcccccccCCCCcccCHHHHHHhhCCCCCCCcceeeccccccCCCCCCCCCcccccceeeecCceeccCCCCCcCCcchh
Q 020984 162 QTALLDSKEFLAPVITPFEAMLAFGRGTQWTGAYVMEFRDLMSSSPVEGSDQAEEARFSFLKGGYVEDVAQPETENGEEE 241 (319)
Q Consensus 162 r~sidd~~~f~kPvlTP~El~vAL~~~~~W~~~y~~Df~~ll~~~~~~~~~~~~~p~fslitG~~~~~~~~~~~~~~~~~ 241 (319)
|+++||+++|+||||||||+++||+.. .|.+.|.++|........ .+.+++. ...|.|-.+..........
T Consensus 328 ~lsid~s~~F~kPiltPfEa~~Al~~~-~W~~~~~~~~~~~~~~~~----~~~~~~~--~~~~d~pm~~~~~~~~~~~-- 398 (453)
T KOG2648|consen 328 RLSIDWSKEFYKPLLTPFEAEVALNPI-AWTGDYLAPFVTAIKLLL----KESEFHS--SELGDYPMDYYSLGSLGPP-- 398 (453)
T ss_pred ccchhhhhhhccccccHHHHHHhcCcc-ccCCccccchhhHHhhhh----ccccccc--cccccCcccccccccCCcC--
Confidence 999999999999999999999999986 999999999977754322 1111111 2334332211111000000
Q ss_pred hhhHHHhhhhhhhhhhhccCCCCceeecccChHHHHhhcCccccCCCCCCCCCCcccccCcccccCCCCCc
Q 020984 242 KEGALALANAAEKALQLRDRSLDPIVKGTAKSGAEYFVSRSYHGLEMQCNSSSPEPYAIGRSGKASGYDDE 312 (319)
Q Consensus 242 ~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~s~~a~~L~~Rtw~GLe~~~g~~~~~~~~~GrsGIA~gY~~e 312 (319)
.+.. +..... .+..++|+.||++|+||||+++.+++++++..+||||||+||.+|
T Consensus 399 ------~~~~--------~~~~~~--~~~~~~a~~~~~~rsw~gLd~~~~~~~~~~~~~Grsgia~gy~~~ 453 (453)
T KOG2648|consen 399 ------PAWT--------SSNDHG--AGESSPAISFLQNRSWQGLDPRLGQTPPTKLVSGRSGIAIGYSDE 453 (453)
T ss_pred ------cccC--------Cccccc--ccccccccchhccccccCCCcCCCCCCccchhccccccccccCCC
Confidence 0000 000000 122356788999999999999999999999999999999999875
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=1.1e-50 Score=391.93 Aligned_cols=175 Identities=24% Similarity=0.399 Sum_probs=162.5
Q ss_pred ccCCCCCCcccceeCCeeeecCCCCCCCceeEEEEcCCcchHHHHHHhcCCCeEEEEcCCCCccccccCcHHHHHHHHHH
Q 020984 13 SLCGPAGGCTRHTIGGLVWNIPDRKKMEEHLLFWIGSDNSAFANVVLTFNGCEIVRYDATEERLLTDVSQPLKILKRRYY 92 (319)
Q Consensus 13 ~~~~~~~gct~~~i~~~~~~l~~~~~~~~~~i~~Ig~~~~~l~~l~l~~~~~~v~~yDP~s~~~~~e~~~~~k~l~~R~~ 92 (319)
.--|+++||+.+.+.+. .. .+++|||+|+||++++||.+ +++||+|||+++++..+..++++++|+||+
T Consensus 156 ~~~g~vLGC~~~~~~~~--------~~--d~~l~vg~g~FH~~~~~l~~-~~~v~~~DP~s~~~~~~~~~~~~~l~rR~~ 224 (332)
T TIGR00322 156 LSRGQVLGCNSEVLRGE--------QA--DAMVFIGDGRFHPLGAAIHT-EKEVFKYDPYSGEFTRIGEDAKQFVKVRAL 224 (332)
T ss_pred CCCccccCCCcCCCCCC--------CC--CEEEEEcCCcchHHHHHHHc-CCcEEEECCCCCceeEccccHHHHHHHHHH
Confidence 34688999998876432 12 37999999999999999965 899999999999998888889999999999
Q ss_pred HHHhhccCCEEEEEEcCCCccCcHHHHHHHHHHHHHhCCcEEEEEcCCCCHHhhcCCCCCCEEEEecCCCcccccccCCC
Q 020984 93 LVEKAKDANIIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKLANFPECDVFINVSCAQTALLDSKEFL 172 (319)
Q Consensus 93 ~I~ka~~a~~iGIivgTl~~q~~~~i~~~l~~ll~~~Gkk~y~i~vg~in~~KLaNf~eID~fV~iaCPr~sidd~~~f~ 172 (319)
+|+||++|++||||+|||++|+|++++++|+++|+++|||+|+|+||+|||+||+||++||+||++||||+++||+++|+
T Consensus 225 ~I~ka~~A~~vGIlvgTl~~q~~~~~~~~l~~ll~~~gkk~y~i~~~~in~~kL~nf~eiD~fV~~aCPr~sidd~~~f~ 304 (332)
T TIGR00322 225 AISKARKGKKFGVVLSSKGGQGRLRLAKNLKKNLEEAGKTVLIILLSNVSPAKLLMFDQIDVFVQVACPRIAIDDGYLFN 304 (332)
T ss_pred HHHHHhcCCEEEEEEecCccCCCHHHHHHHHHHHHHcCCcEEEEEeCCCCHHHHhCCCCcCEEEEecCCCceecchhhcC
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CcccCHHHHHHhhCCCCCCCcceeeccc
Q 020984 173 APVITPFEAMLAFGRGTQWTGAYVMEFR 200 (319)
Q Consensus 173 kPvlTP~El~vAL~~~~~W~~~y~~Df~ 200 (319)
||||||||+++||+. +.|. .|+|||+
T Consensus 305 kPvlTP~E~e~al~~-~~~~-~y~~d~~ 330 (332)
T TIGR00322 305 KPLLTPYEFELLLKK-RVEK-YYPMDEI 330 (332)
T ss_pred CccccHHHHHHHhCc-cccc-cCCCcee
Confidence 999999999999997 5696 5999986
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=2.3e-50 Score=385.74 Aligned_cols=176 Identities=41% Similarity=0.744 Sum_probs=127.9
Q ss_pred ccCCCCCCcccceeCCeeeecCCCCCCCceeEEEEcCCcchHHHHHHhcCCCeEEEEcCCCCccccc--cCcHHHHHHHH
Q 020984 13 SLCGPAGGCTRHTIGGLVWNIPDRKKMEEHLLFWIGSDNSAFANVVLTFNGCEIVRYDATEERLLTD--VSQPLKILKRR 90 (319)
Q Consensus 13 ~~~~~~~gct~~~i~~~~~~l~~~~~~~~~~i~~Ig~~~~~l~~l~l~~~~~~v~~yDP~s~~~~~e--~~~~~k~l~~R 90 (319)
...|+++||+.+.+... .+.+.++|||+|+||+++++|+ +.+++|+|||+++++..+ ..+.+++|++|
T Consensus 130 ~~~g~vlGc~~~~~~~~---------~~~~~~l~IG~g~fh~~~l~l~-~~~~v~~~dP~~~~~~~e~~~~~~~~~l~~R 199 (307)
T PF01866_consen 130 LSPGQVLGCTYPSADSL---------DDDDAILFIGGGRFHLLGLMLS-PGKPVYRYDPYSKTLSVEDISYDIERLLRRR 199 (307)
T ss_dssp SSTTB-BTTB-GGG-S-----------S-SEEEEESSSSHHHHHHHHH-H-SEEEEE-TT--T--EEE----THHHHHHH
T ss_pred CCcccccCCccCccccc---------ccccEEEEEcCCchHHHHHHHh-cCCCEEEeCCCcccceeecccccHHHHHHHH
Confidence 56799999999998863 3457899999999999999999 999999999998777766 56899999999
Q ss_pred HHHHHhhccCCEEEEEEcCCCccCcHHHHHHHHHHHHHhCCcEEEEEcCCCCHHhhcCCCCCCEEEEecCCCcccccccC
Q 020984 91 YYLVEKAKDANIIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKLANFPECDVFINVSCAQTALLDSKE 170 (319)
Q Consensus 91 ~~~I~ka~~a~~iGIivgTl~~q~~~~i~~~l~~ll~~~Gkk~y~i~vg~in~~KLaNf~eID~fV~iaCPr~sidd~~~ 170 (319)
|++|+||++|++||||+|||++|+|+.++++|+++|+++|||+|+|+||+|||+||+||++||+||++||||+++||+++
T Consensus 200 ~~~i~ka~~a~~~GIiv~tl~~q~~~~~~~~l~~~l~~~gkk~y~~~~~~i~~~kL~nf~eid~fV~~aCPr~~idd~~~ 279 (307)
T PF01866_consen 200 YALIEKAKDAKTFGIIVGTLGGQGYLELIKRLKKLLKKAGKKSYTLSVGEINPAKLANFPEIDAFVQIACPRLSIDDSKD 279 (307)
T ss_dssp HHHHHHHTT--EEEEEEE-STTT--HHHHHHHHHHHHHTT-EEEEEEESS--GGGGTTS---SEEEE-S-THHHHT--S-
T ss_pred HHHHHHHhcCCEEEEEEecCCCCCCHHHHHHHHHHHHHcCCEEEEEEECCCCHHHHhcCcccCEEEEecCCCcccCchhh
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCcccCHHHHHHhhCCCCCCCcceeeccc
Q 020984 171 FLAPVITPFEAMLAFGRGTQWTGAYVMEFR 200 (319)
Q Consensus 171 f~kPvlTP~El~vAL~~~~~W~~~y~~Df~ 200 (319)
|+||||||||++|||+.. .| +.|+|||+
T Consensus 280 f~kPvltP~E~~~al~~~-~~-~~Y~~D~~ 307 (307)
T PF01866_consen 280 FYKPVLTPYELEVALNER-EW-GEYPMDEI 307 (307)
T ss_dssp -SS-EE-HHHHHHHTTS--S---S------
T ss_pred cCCcccCHHHHHHHhCCc-cc-CcCCCCcC
Confidence 999999999999999973 35 79999985
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=1.1e-49 Score=381.61 Aligned_cols=170 Identities=24% Similarity=0.378 Sum_probs=158.6
Q ss_pred CCCCCCcccceeCCeeeecCCCCCCCceeEEEEcCCcchHHHHHHhcCCCeEEEEcCCCCccccccCcHHHHHHHHHHHH
Q 020984 15 CGPAGGCTRHTIGGLVWNIPDRKKMEEHLLFWIGSDNSAFANVVLTFNGCEIVRYDATEERLLTDVSQPLKILKRRYYLV 94 (319)
Q Consensus 15 ~~~~~gct~~~i~~~~~~l~~~~~~~~~~i~~Ig~~~~~l~~l~l~~~~~~v~~yDP~s~~~~~e~~~~~k~l~~R~~~I 94 (319)
.|+++||+.+...+. +..+++|||+|+||++.++| +|++++|+|||+++++..+..++++++|+||++|
T Consensus 138 ~g~vlGC~~~~~~~~----------~~d~~~~vg~g~Fh~~~l~l-~~~~~v~~~DP~~~~~~~~~~~~~~~l~~R~~~I 206 (308)
T TIGR03682 138 PGQVLGCNFSAARSV----------DADAFLFVGTGLFHPLGLAL-ATNKPVYAADPFSGEVEDIEAEIDKFLRVRYARI 206 (308)
T ss_pred CceeeCccccCCCCC----------CccEEEEEcCCcchHHHHHh-ccCCcEEEECCCCCceEeechhHHHHHHHHHHHH
Confidence 578899997765431 12379999999999999999 8999999999999999888888999999999999
Q ss_pred HhhccCCEEEEEEcCCCccCcHHHHHHHHHHHHHhCCcEEEEEcCCCCHHhhcCCCCCCEEEEecCCCcccccccCCCCc
Q 020984 95 EKAKDANIIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKLANFPECDVFINVSCAQTALLDSKEFLAP 174 (319)
Q Consensus 95 ~ka~~a~~iGIivgTl~~q~~~~i~~~l~~ll~~~Gkk~y~i~vg~in~~KLaNf~eID~fV~iaCPr~sidd~~~f~kP 174 (319)
+||++|++||||+|||++|+|++++++|+++|+++|||+|+|+||+|||+||+|| +||+||++||||+++||+++|+||
T Consensus 207 ~ka~~A~~vGIlvgTl~~q~~~~~~~~l~~ll~~~gkk~y~i~~~~in~~kL~nf-~iD~fV~~aCPr~sidd~~~f~kP 285 (308)
T TIGR03682 207 SKALDAKKFGILVSTKKGQRRPELAEELKKLLEELGKEALLILLDNISPDQLRNL-DFDAYVNTACPRIAIDDYARFKKP 285 (308)
T ss_pred HHHhhCCeEEEEEEccCcCCCHHHHHHHHHHHHHcCCeEEEEEeCCCCHHHHhcC-CcCEEEEccCCCcccccHhhCCCc
Confidence 9999999999999999999999999999999999999999999999999999999 799999999999999999999999
Q ss_pred ccCHHHHHHhhCCCCCCCcceeeccc
Q 020984 175 VITPFEAMLAFGRGTQWTGAYVMEFR 200 (319)
Q Consensus 175 vlTP~El~vAL~~~~~W~~~y~~Df~ 200 (319)
||||||+++||+. ++| |+||+.
T Consensus 286 vlTP~E~~~al~~-~~~---y~~D~~ 307 (308)
T TIGR03682 286 VLTPQEFEIVLGK-RSE---YVFDEI 307 (308)
T ss_pred ccCHHHHHHHhCC-Ccc---ccCCcc
Confidence 9999999999997 789 999873
No 6
>COG1736 DPH2 Diphthamide synthase subunit DPH2 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=1.2e-40 Score=321.95 Aligned_cols=182 Identities=24% Similarity=0.448 Sum_probs=165.3
Q ss_pred cccCCCCCCcccceeCCeeeecCCCCCCCceeEEEEcCCcchHHHHHHhcCCCeEEEEcCCCCccccccCcHHHHHHHHH
Q 020984 12 KSLCGPAGGCTRHTIGGLVWNIPDRKKMEEHLLFWIGSDNSAFANVVLTFNGCEIVRYDATEERLLTDVSQPLKILKRRY 91 (319)
Q Consensus 12 ~~~~~~~~gct~~~i~~~~~~l~~~~~~~~~~i~~Ig~~~~~l~~l~l~~~~~~v~~yDP~s~~~~~e~~~~~k~l~~R~ 91 (319)
-.--|.++||+.+.+.|. +.-+++|||+|.||++.+++. +.++|++|||+++++..+..++.+++++||
T Consensus 160 ~~~~gqVLGC~~~~~~~~----------~~d~~l~vg~G~FH~lg~~i~-~~~~v~~~dP~s~~~~~~~~~~~~~l~~R~ 228 (347)
T COG1736 160 PAYPGQVLGCNFSVLEGV----------DADAVLYVGSGRFHPLGLAIR-TEKPVFAIDPYSGKVREEDPEADRFLRKRY 228 (347)
T ss_pred ccCcceeeccccccCCcc----------ccceEEEEcCCccChhhcccc-cCCcEEEEcCCCCceeecchhhhHHHHHHH
Confidence 445678889988888761 124789999999999999999 899999999999999888888999999999
Q ss_pred HHHHhhccCCEEEEEEcCCCccCcHHHHHHHHHHHHHhCCcEEEEEcCCCCHHhhcCCCCCCEEEEecCCCcccccccCC
Q 020984 92 YLVEKAKDANIIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKLANFPECDVFINVSCAQTALLDSKEF 171 (319)
Q Consensus 92 ~~I~ka~~a~~iGIivgTl~~q~~~~i~~~l~~ll~~~Gkk~y~i~vg~in~~KLaNf~eID~fV~iaCPr~sidd~~~f 171 (319)
++|.+|++|++||||+||+++|+++++++.|.++++++||++|+|+|+++||+||+||.+||+||++||||+++||+..|
T Consensus 229 ~~i~~a~~a~~~giiv~tk~gQ~r~~~~~~l~k~~~~~g~~~~li~~~~i~p~~L~~f~~iD~~v~taCPRi~iDd~~~f 308 (347)
T COG1736 229 AAISKALDAKSFGIIVSTKGGQRRLEVARELVKLLKEAGKEVYLIVVDEISPDKLANFDDIDAFVNTACPRIPIDDGDRF 308 (347)
T ss_pred HHHHHHhcCCeEEEEEecccccCcHHHHHHHHHHHHHcCCceEEEEecCCCHHHHhcccceeEEEEecCCCcccchHhhh
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCcccCHHHHHHhhCCCCCCCcceeeccccccCCC
Q 020984 172 LAPVITPFEAMLAFGRGTQWTGAYVMEFRDLMSSS 206 (319)
Q Consensus 172 ~kPvlTP~El~vAL~~~~~W~~~y~~Df~~ll~~~ 206 (319)
.||||||+|+++||+. +.| .+|.||+..-.+.+
T Consensus 309 ~kPlLTP~E~~~~l~~-~~~-~~y~~Dei~~~~~~ 341 (347)
T COG1736 309 KKPLLTPYEFEIALGW-RSD-ERYAFDEIVGNDGG 341 (347)
T ss_pred CCcccChHHHHHhhcc-Ccc-cccccceeecCCCC
Confidence 9999999999999992 333 68999886654433
No 7
>PRK09492 treR trehalose repressor; Provisional
Probab=83.86 E-value=4.4 Score=37.68 Aligned_cols=78 Identities=12% Similarity=0.162 Sum_probs=50.6
Q ss_pred ccCCEEEEEEcCCCccCcHHHHHHHHHHHHHhCCcEEEEEcCCCCHHhh----cCC--CCCCEEEEecCCCcccccccCC
Q 020984 98 KDANIIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKL----ANF--PECDVFINVSCAQTALLDSKEF 171 (319)
Q Consensus 98 ~~a~~iGIivgTl~~q~~~~i~~~l~~ll~~~Gkk~y~i~vg~in~~KL----aNf--~eID~fV~iaCPr~sidd~~~f 171 (319)
+..++||+|+..+.-..+..+++.+.+.++++|....++.. .-++++. ..+ ..+|.+|+.++.....+.-..+
T Consensus 60 ~~~~~Ig~i~~~~~~~~~~~~~~~i~~~~~~~gy~~~~~~~-~~~~~~~~~~~~~l~~~~vdgiIi~~~~~~~~~~l~~~ 138 (315)
T PRK09492 60 QSDKVVGIIVSRLDSLSENQAVRTMLPAFYEQGYDPIIMES-QFSPEKVNEHLGVLKRRNVDGVILFGFTGITEEMLAPW 138 (315)
T ss_pred CCCCeEEEEecCCcCcccHHHHHHHHHHHHHcCCeEEEEec-CCChHHHHHHHHHHHhcCCCEEEEeCCCcccHHHHHhc
Confidence 34579999999877677889999999999999987654433 3333322 222 1699999987532222222344
Q ss_pred CCccc
Q 020984 172 LAPVI 176 (319)
Q Consensus 172 ~kPvl 176 (319)
.+|++
T Consensus 139 ~~pvv 143 (315)
T PRK09492 139 QDKLV 143 (315)
T ss_pred CCCEE
Confidence 55654
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=78.14 E-value=6.4 Score=35.43 Aligned_cols=59 Identities=14% Similarity=0.150 Sum_probs=44.6
Q ss_pred EEEEEEcCCCccCcHHHHHHHHHHHHHhCCcEEEEEcCCCCHHhhcC------CCCCCEEEEecCC
Q 020984 102 IIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKLAN------FPECDVFINVSCA 161 (319)
Q Consensus 102 ~iGIivgTl~~q~~~~i~~~l~~ll~~~Gkk~y~i~vg~in~~KLaN------f~eID~fV~iaCP 161 (319)
+||+|+..+....+..+++.+.+.++++|.+..++ ...-++++... =..+|.+|+.+|.
T Consensus 1 ~Ig~i~p~~~~~~~~~~~~~i~~~~~~~g~~~~~~-~~~~~~~~~~~~i~~l~~~~~dgiii~~~~ 65 (263)
T cd06280 1 TVGLIVADIRNPFFTAVSRAVEDAAYRAGLRVILC-NTDEDPEKEAMYLELMEEERVTGVIFAPTR 65 (263)
T ss_pred CEEEEecccccccHHHHHHHHHHHHHHCCCEEEEE-eCCCCHHHHHHHHHHHHhCCCCEEEEeCCC
Confidence 58999999887888899999999999999887544 44445544321 1269999998874
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=76.23 E-value=6 Score=35.27 Aligned_cols=75 Identities=16% Similarity=0.190 Sum_probs=50.8
Q ss_pred EEEEEEcCCCccCcHHHHHHHHHHHHHhCCcEEEEEcCCCCHHhhc----CC--CCCCEEEEecCCCcccc---cccCCC
Q 020984 102 IIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKLA----NF--PECDVFINVSCAQTALL---DSKEFL 172 (319)
Q Consensus 102 ~iGIivgTl~~q~~~~i~~~l~~ll~~~Gkk~y~i~vg~in~~KLa----Nf--~eID~fV~iaCPr~sid---d~~~f~ 172 (319)
+||+|+....-..+..+++.+++.+++.|.+.+++ .+.-++++.. ++ ..+|++++.+|...... ......
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 47999988777777789999999999999876543 4444554322 22 36999999998755322 223345
Q ss_pred CcccC
Q 020984 173 APVIT 177 (319)
Q Consensus 173 kPvlT 177 (319)
.|+|+
T Consensus 80 ipvV~ 84 (268)
T cd06289 80 IPVVL 84 (268)
T ss_pred CCEEE
Confidence 57765
No 10
>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=74.42 E-value=13 Score=34.82 Aligned_cols=114 Identities=16% Similarity=0.218 Sum_probs=75.1
Q ss_pred CCeEEEEcCCCCccccccCcHHHHHHH-HH---------HH--HHhhccCCEEEEEEcCCCccCcHHHHHHHHHHHHHhC
Q 020984 63 GCEIVRYDATEERLLTDVSQPLKILKR-RY---------YL--VEKAKDANIIGVLVGTLGVAGYLHMIHQMKELITKAG 130 (319)
Q Consensus 63 ~~~v~~yDP~s~~~~~e~~~~~k~l~~-R~---------~~--I~ka~~a~~iGIivgTl~~q~~~~i~~~l~~ll~~~G 130 (319)
...+..|.-.+..+..........++. +- +. -.++..+++|+|+. -....+-+++++.++++|
T Consensus 71 ~~dvi~~~cTsgs~~~G~~~~~~~i~~~~~g~p~tt~~~A~~~AL~alg~~RIalvT-----PY~~~v~~~~~~~l~~~G 145 (239)
T TIGR02990 71 ELDVVAYSCTSASVVIGDDEVTRAINAAKPGTPVVTPSSAAVDGLAALGVRRISLLT-----PYTPETSRPMAQYFAVRG 145 (239)
T ss_pred CCCEEEEccchhheecCHHHHHHHHHhcCCCCCeeCHHHHHHHHHHHcCCCEEEEEC-----CCcHHHHHHHHHHHHhCC
Confidence 456888887777654432222222222 10 11 12445689999875 456688889999999999
Q ss_pred CcEEEE---------EcCCCCHHhhcC------CCCCCEEEEecCCCccccc-----ccCCCCcccCHHHHH
Q 020984 131 KKAYTL---------VMGKPNPAKLAN------FPECDVFINVSCAQTALLD-----SKEFLAPVITPFEAM 182 (319)
Q Consensus 131 kk~y~i---------~vg~in~~KLaN------f~eID~fV~iaCPr~sidd-----~~~f~kPvlTP~El~ 182 (319)
.++.-+ .++++.|+-+.. .++.|+.+ ++|=-+...+ ..++.|||||.--+.
T Consensus 146 ~eV~~~~~~~~~~~~~ia~i~p~~i~~~~~~~~~~~aDAif-isCTnLrt~~vi~~lE~~lGkPVlsSNqat 216 (239)
T TIGR02990 146 FEIVNFTCLGLTDDREMARISPDCIVEAALAAFDPDADALF-LSCTALRAATCAQRIEQAIGKPVVTSNQAT 216 (239)
T ss_pred cEEeeeeccCCCCCceeeecCHHHHHHHHHHhcCCCCCEEE-EeCCCchhHHHHHHHHHHHCCCEEEHHHHH
Confidence 998876 466788887652 45789855 5598876433 357899999886554
No 11
>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=74.08 E-value=5.7 Score=35.91 Aligned_cols=64 Identities=14% Similarity=0.238 Sum_probs=45.2
Q ss_pred cCCEEEEEEcC-------CCccCcHHHHHHHHHHHHHhCCcEEEEEcCCCCHHhhcC-C--CCCCEEEEecCCC
Q 020984 99 DANIIGVLVGT-------LGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKLAN-F--PECDVFINVSCAQ 162 (319)
Q Consensus 99 ~a~~iGIivgT-------l~~q~~~~i~~~l~~ll~~~Gkk~y~i~vg~in~~KLaN-f--~eID~fV~iaCPr 162 (319)
..++||||+-. +.-..+..+++.+++.+++.|.+..++..+.-...++.. + ..+|++|+.+|..
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 45789999954 444467788999999999999988777665432333332 1 3799999988753
No 12
>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=73.48 E-value=6.3 Score=36.11 Aligned_cols=61 Identities=16% Similarity=0.195 Sum_probs=41.7
Q ss_pred EEEEEEcC-----CCccCcHHHHHHHHHHHHHhCCcEEEEEcCCCCHHhhcCC--CCCCEEEEecCCCc
Q 020984 102 IIGVLVGT-----LGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKLANF--PECDVFINVSCAQT 163 (319)
Q Consensus 102 ~iGIivgT-----l~~q~~~~i~~~l~~ll~~~Gkk~y~i~vg~in~~KLaNf--~eID~fV~iaCPr~ 163 (319)
+||+|+-+ ..-..+..+++.+++.+++.|....++.... ....+.++ ..+|.+|+.+|+..
T Consensus 1 ~igvi~p~~~~~~~~~~~~~~~~~gi~~~a~~~g~~~~~~~~~~-~~~~~~~~~~~~~dgiii~~~~~~ 68 (283)
T cd06279 1 AVGVVLTDSLSYAFSDPVASQFLAGVAEVLDAAGVNLLLLPASS-EDSDSALVVSALVDGFIVYGVPRD 68 (283)
T ss_pred CEEEEeCCcccccccCccHHHHHHHHHHHHHHCCCEEEEecCcc-HHHHHHHHHhcCCCEEEEeCCCCC
Confidence 47888866 4445667888999999999988776665543 22223232 26899999988754
No 13
>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=73.42 E-value=13 Score=34.81 Aligned_cols=63 Identities=14% Similarity=0.156 Sum_probs=44.2
Q ss_pred ccCCEEEEEEcCCCccCcHHHHHHHHHHHHHhCCcEEEEEcCCCCHHhhc----CC--CCCCEEEEecCC
Q 020984 98 KDANIIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKLA----NF--PECDVFINVSCA 161 (319)
Q Consensus 98 ~~a~~iGIivgTl~~q~~~~i~~~l~~ll~~~Gkk~y~i~vg~in~~KLa----Nf--~eID~fV~iaCP 161 (319)
+..++||+|+..+.-..+..+++.+.+.++++|....++. +.-++++.. .+ ..+|.+|++++.
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 3567999999876656677899999999999998865543 334444322 12 269999998653
No 14
>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=72.61 E-value=6.4 Score=35.27 Aligned_cols=58 Identities=16% Similarity=0.206 Sum_probs=43.0
Q ss_pred EEEEEEcCCCccCcHHHHHHHHHHHHHhCCcEEEEEcCCCCHHhhc-CC--CCCCEEEEecCC
Q 020984 102 IIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKLA-NF--PECDVFINVSCA 161 (319)
Q Consensus 102 ~iGIivgTl~~q~~~~i~~~l~~ll~~~Gkk~y~i~vg~in~~KLa-Nf--~eID~fV~iaCP 161 (319)
+||+|+..+....+..+++.+++.++++|....+.... ++.... .+ ..+|++|+.+|.
T Consensus 1 ~igvv~~~~~~~~~~~~~~gi~~~~~~~g~~~~~~~~~--~~~~~~~~l~~~~vdgii~~~~~ 61 (261)
T cd06272 1 TIGLIWPSVSRVALTELVTGINQAISKNGYNMNVSITP--SLAEAEDLFKENRFDGVIIFGES 61 (261)
T ss_pred CEEEEecCCCchhHHHHHHHHHHHHHHcCCEEEEEecc--cHHHHHHHHHHcCcCEEEEeCCC
Confidence 48999998887888899999999999999776666554 332222 22 269999988774
No 15
>COG2984 ABC-type uncharacterized transport system, periplasmic component [General function prediction only]
Probab=72.58 E-value=15 Score=36.29 Aligned_cols=110 Identities=18% Similarity=0.238 Sum_probs=75.9
Q ss_pred HHHHHHHHHhhc-cCCEEEEEEcCCCccCcHHHHHHHHHHHHHhCCcEEEEEcCCCCHH--hhcCC-CCCCEEEEecCCC
Q 020984 87 LKRRYYLVEKAK-DANIIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPA--KLANF-PECDVFINVSCAQ 162 (319)
Q Consensus 87 l~~R~~~I~ka~-~a~~iGIivgTl~~q~~~~i~~~l~~ll~~~Gkk~y~i~vg~in~~--KLaNf-~eID~fV~iaCPr 162 (319)
+.++..+|.+.. ++++||++.+.- -.+...+++.+++.++++|.+++...+...|.- -..++ ..+|++.. -|-.
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 VAQQIELIKALLPNAKSIGVLYNPG-EANSVSLVEELKKEARKAGLEVVEAAVTSVNDIPRAVQALLGKVDVIYI-PTDN 222 (322)
T ss_pred HHHHHHHHHHhCCCCeeEEEEeCCC-CcccHHHHHHHHHHHHHCCCEEEEEecCcccccHHHHHHhcCCCcEEEE-ecch
Confidence 566777777666 899999999883 478999999999999999999999999777633 33344 46887543 3322
Q ss_pred ccc-------ccccCCCCcccCHHHHHHhhCCCCCCCcceeeccccc
Q 020984 163 TAL-------LDSKEFLAPVITPFEAMLAFGRGTQWTGAYVMEFRDL 202 (319)
Q Consensus 163 ~si-------dd~~~f~kPvlTP~El~vAL~~~~~W~~~y~~Df~~l 202 (319)
+.. --......||+++-+-.|-=|. --.+-.||+++
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 211 1124567788888776665432 13455666664
No 16
>COG1609 PurR Transcriptional regulators [Transcription]
Probab=72.50 E-value=12 Score=36.36 Aligned_cols=63 Identities=16% Similarity=0.258 Sum_probs=51.9
Q ss_pred hhccCCEEEEEEcCCCccCcHHHHHHHHHHHHHhCCcEEEEEcCCCCHHhhc----CC--CCCCEEEEec
Q 020984 96 KAKDANIIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKLA----NF--PECDVFINVS 159 (319)
Q Consensus 96 ka~~a~~iGIivgTl~~q~~~~i~~~l~~ll~~~Gkk~y~i~vg~in~~KLa----Nf--~eID~fV~ia 159 (319)
+.+..++||+|+..+....+.+++..+.+.++++|+...+...+. ++++.. .+ ..+|.+|+.+
T Consensus 54 ~~~~s~~Ig~i~p~~~~~~~~~i~~gi~~~~~~~gy~~~l~~~~~-~~~~e~~~~~~l~~~~vdGiIi~~ 122 (333)
T COG1609 54 RTGRTKTIGLVVPDITNPFFAEILKGIEEAAREAGYSLLLANTDD-DPEKEREYLETLLQKRVDGLILLG 122 (333)
T ss_pred HhCCCCEEEEEeCCCCCchHHHHHHHHHHHHHHcCCEEEEECCCC-CHHHHHHHHHHHHHcCCCEEEEec
Confidence 344678999999998888999999999999999999988888777 666533 22 2799999988
No 17
>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=72.36 E-value=7.8 Score=34.79 Aligned_cols=60 Identities=13% Similarity=0.289 Sum_probs=43.4
Q ss_pred EEEEEEcCCCccCcHHHHHHHHHHHHHhCCcEEEEEcCCCCHHhhc----CC--CCCCEEEEecCCC
Q 020984 102 IIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKLA----NF--PECDVFINVSCAQ 162 (319)
Q Consensus 102 ~iGIivgTl~~q~~~~i~~~l~~ll~~~Gkk~y~i~vg~in~~KLa----Nf--~eID~fV~iaCPr 162 (319)
+||+|+..+....+..+++.+++.++++|....++.. .-++++.. .+ ..+|++|+.+|..
T Consensus 1 ~igvi~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~-~~~~~~~~~~i~~l~~~~vdgiii~~~~~ 66 (264)
T cd06274 1 TIGLIIPDLENRSFARIAKRLEALARERGYQLLIACS-DDDPETERETVETLIARQVDALIVAGSLP 66 (264)
T ss_pred CEEEEeccccCchHHHHHHHHHHHHHHCCCEEEEEeC-CCCHHHHHHHHHHHHHcCCCEEEEcCCCC
Confidence 4899999888888889999999999998877655433 33454322 11 1689999988854
No 18
>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=71.99 E-value=7.7 Score=34.30 Aligned_cols=75 Identities=21% Similarity=0.181 Sum_probs=47.2
Q ss_pred EEEEEEcCCCccCcHHHHHHHHHHHHHhCCcEEEEEcCCCCHHh-------hcCCCCCCEEEEecCCCcc----cccccC
Q 020984 102 IIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAK-------LANFPECDVFINVSCAQTA----LLDSKE 170 (319)
Q Consensus 102 ~iGIivgTl~~q~~~~i~~~l~~ll~~~Gkk~y~i~vg~in~~K-------LaNf~eID~fV~iaCPr~s----idd~~~ 170 (319)
+||+|+.......+..+++.+++.++++|.+..++.... ++++ |.+- ++|++|+.++.... +.....
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 478888766556777888889888888887766655543 4442 2233 68888887765321 222233
Q ss_pred CCCcccCH
Q 020984 171 FLAPVITP 178 (319)
Q Consensus 171 f~kPvlTP 178 (319)
...|+|+.
T Consensus 79 ~~ip~V~~ 86 (267)
T cd01536 79 AGIPVVTV 86 (267)
T ss_pred CCCcEEEe
Confidence 44566553
No 19
>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=71.40 E-value=5.5 Score=37.38 Aligned_cols=61 Identities=20% Similarity=0.236 Sum_probs=47.4
Q ss_pred CEEEEEEcCCCccCcHHHHHHHHHHHHHhCCcEEEEEcCCCCHHh------hcCCCCCCEEEEecCCCc
Q 020984 101 NIIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAK------LANFPECDVFINVSCAQT 163 (319)
Q Consensus 101 ~~iGIivgTl~~q~~~~i~~~l~~ll~~~Gkk~y~i~vg~in~~K------LaNf~eID~fV~iaCPr~ 163 (319)
++||+|+..+.-..+.+++.-+.+.++++|+...++..++= +++ |.+. .||.+|+.+....
T Consensus 2 ~~IGvivp~~~npff~~ii~gIe~~a~~~Gy~l~l~~t~~~-~~~e~~i~~l~~~-~vDGiI~~s~~~~ 68 (279)
T PF00532_consen 2 KTIGVIVPDISNPFFAEIIRGIEQEAREHGYQLLLCNTGDD-EEKEEYIELLLQR-RVDGIILASSEND 68 (279)
T ss_dssp CEEEEEESSSTSHHHHHHHHHHHHHHHHTTCEEEEEEETTT-HHHHHHHHHHHHT-TSSEEEEESSSCT
T ss_pred CEEEEEECCCCCcHHHHHHHHHHHHHHHcCCEEEEecCCCc-hHHHHHHHHHHhc-CCCEEEEecccCC
Confidence 68999999999899999999999999999998877665533 332 2222 7999999854433
No 20
>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=71.20 E-value=5.9 Score=35.52 Aligned_cols=75 Identities=19% Similarity=0.165 Sum_probs=49.1
Q ss_pred EEEEEEcCCCccCcHHHHHHHHHHHHHhCCcEEEEEcCCCCHH-------hhcCCCCCCEEEEecCCCcc--cccccCCC
Q 020984 102 IIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPA-------KLANFPECDVFINVSCAQTA--LLDSKEFL 172 (319)
Q Consensus 102 ~iGIivgTl~~q~~~~i~~~l~~ll~~~Gkk~y~i~vg~in~~-------KLaNf~eID~fV~iaCPr~s--idd~~~f~ 172 (319)
+||+|+..+.-..+..+++.+.+.+++.|....++. ++-+++ +|.+- .+|+++++++.... +..-..-.
T Consensus 1 ~i~vv~p~~~~~~~~~~~~~i~~~~~~~g~~~~~~~-~~~~~~~~~~~~~~l~~~-~vdgiii~~~~~~~~~~~~l~~~~ 78 (268)
T cd06273 1 TIGAIVPTLDNAIFARVIQAFQETLAAHGYTLLVAS-SGYDLDREYAQARKLLER-GVDGLALIGLDHSPALLDLLARRG 78 (268)
T ss_pred CeEEEeCCCCCchHHHHHHHHHHHHHHCCCEEEEec-CCCCHHHHHHHHHHHHhc-CCCEEEEeCCCCCHHHHHHHHhCC
Confidence 589999888777788999999999999996655433 333443 23332 69999988775321 11122345
Q ss_pred CcccCH
Q 020984 173 APVITP 178 (319)
Q Consensus 173 kPvlTP 178 (319)
.|+|..
T Consensus 79 iPvv~~ 84 (268)
T cd06273 79 VPYVAT 84 (268)
T ss_pred CCEEEE
Confidence 677664
No 21
>PRK07188 nicotinate phosphoribosyltransferase; Provisional
Probab=70.82 E-value=8.9 Score=38.14 Aligned_cols=57 Identities=19% Similarity=0.318 Sum_probs=45.2
Q ss_pred cCCEEEEEEcCCCcc-------------------CcHHHHHHHHHHHHHhC-CcEEEEEcCCCCHHhhcCCC----CCCE
Q 020984 99 DANIIGVLVGTLGVA-------------------GYLHMIHQMKELITKAG-KKAYTLVMGKPNPAKLANFP----ECDV 154 (319)
Q Consensus 99 ~a~~iGIivgTl~~q-------------------~~~~i~~~l~~ll~~~G-kk~y~i~vg~in~~KLaNf~----eID~ 154 (319)
..+.+||=+-|-|-| ....+++++++.|.++| .++-+++.|.||+++++.|. .||+
T Consensus 227 g~~l~gVRlDs~gdl~DK~~~~~~~~~~~~~~~G~~~~l~~~vr~~Ld~~g~~~vkI~aSgGine~~I~~~~~~g~piD~ 306 (352)
T PRK07188 227 GDKLKGVRVDTSKNMIDKYFIRHPEVLGTFDPRGVNPELIKALRKALDENGGKHVKIIVSSGFDAKKIREFEAQNVPVDI 306 (352)
T ss_pred CCCccEEEeCCcchHhhhhcccccccccccccccccHHHHHHHHHHHhhCCCCCcEEEEeCCCCHHHHHHHHHcCCCccE
Confidence 467788855553222 46899999999999999 77889999999999999885 2676
Q ss_pred E
Q 020984 155 F 155 (319)
Q Consensus 155 f 155 (319)
|
T Consensus 307 ~ 307 (352)
T PRK07188 307 Y 307 (352)
T ss_pred E
Confidence 5
No 22
>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=70.58 E-value=11 Score=33.82 Aligned_cols=61 Identities=15% Similarity=0.156 Sum_probs=44.7
Q ss_pred EEEEEEcCCCccCcHHHHHHHHHHHHHhCCcEEEEEcCCCCHHhhc----CC--CCCCEEEEecCCCc
Q 020984 102 IIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKLA----NF--PECDVFINVSCAQT 163 (319)
Q Consensus 102 ~iGIivgTl~~q~~~~i~~~l~~ll~~~Gkk~y~i~vg~in~~KLa----Nf--~eID~fV~iaCPr~ 163 (319)
+||+|+..+.-..+..+++.+.+.++++|....++... -++++.. .+ ..+|.+|+.+|+..
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 48999988776667789999999999999887666444 3454322 11 26999999988743
No 23
>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=69.38 E-value=7.1 Score=34.88 Aligned_cols=59 Identities=14% Similarity=0.198 Sum_probs=42.4
Q ss_pred EEEEEEcCCCccCcHHHHHHHHHHHHHhCCcEEEEEcCCCCHHh----hcCC--CCCCEEEEecCC
Q 020984 102 IIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAK----LANF--PECDVFINVSCA 161 (319)
Q Consensus 102 ~iGIivgTl~~q~~~~i~~~l~~ll~~~Gkk~y~i~vg~in~~K----LaNf--~eID~fV~iaCP 161 (319)
+||+|+..+.-..+..+++.+++.++++|....++. ..-+++. +..+ ..+|++|+++|+
T Consensus 1 ~i~vi~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~-~~~~~~~~~~~i~~l~~~~vdgiii~~~~ 65 (268)
T cd06298 1 TVGVIIPDITNSYFAELARGIDDIATMYKYNIILSN-SDNDKEKELKVLNNLLAKQVDGIIFMGGK 65 (268)
T ss_pred CEEEEECCCcchHHHHHHHHHHHHHHHcCCeEEEEe-CCCCHHHHHHHHHHHHHhcCCEEEEeCCC
Confidence 478999888777888899999999999988766554 3334432 2222 279999988764
No 24
>PRK10014 DNA-binding transcriptional repressor MalI; Provisional
Probab=69.17 E-value=23 Score=33.23 Aligned_cols=79 Identities=18% Similarity=0.264 Sum_probs=52.4
Q ss_pred ccCCEEEEEEcCCCccCcHHHHHHHHHHHHHhCCcEEEEEcCCCCHHhh----cCC--CCCCEEEEecCCCcc---cccc
Q 020984 98 KDANIIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKL----ANF--PECDVFINVSCAQTA---LLDS 168 (319)
Q Consensus 98 ~~a~~iGIivgTl~~q~~~~i~~~l~~ll~~~Gkk~y~i~vg~in~~KL----aNf--~eID~fV~iaCPr~s---idd~ 168 (319)
+..++||+|+..+.-..+..+++.+.+.++++|...+++.. .-++++. .++ ..+|.+|+.++.... +...
T Consensus 62 ~~~~~Igvv~~~~~~~~~~~i~~gi~~~a~~~g~~~~~~~~-~~~~~~~~~~~~~l~~~~vdgiIi~~~~~~~~~~~~~l 140 (342)
T PRK10014 62 GQSGVIGLIVRDLSAPFYAELTAGLTEALEAQGRMVFLLQG-GKDGEQLAQRFSTLLNQGVDGVVIAGAAGSSDDLREMA 140 (342)
T ss_pred CCCCEEEEEeCCCccchHHHHHHHHHHHHHHcCCEEEEEeC-CCCHHHHHHHHHHHHhCCCCEEEEeCCCCCcHHHHHHH
Confidence 45679999998887777889999999999999977665543 3344322 122 269999998765321 1122
Q ss_pred cCCCCcccC
Q 020984 169 KEFLAPVIT 177 (319)
Q Consensus 169 ~~f~kPvlT 177 (319)
.....|+|+
T Consensus 141 ~~~~iPvV~ 149 (342)
T PRK10014 141 EEKGIPVVF 149 (342)
T ss_pred hhcCCCEEE
Confidence 344567764
No 25
>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=68.81 E-value=7.6 Score=35.66 Aligned_cols=60 Identities=17% Similarity=0.076 Sum_probs=44.2
Q ss_pred CEEEEEEcCCCccCcHHHHHHHHHHHHHhCCcEEEEEcCCCCHHhh----cCC--CCCCEEEEecCC
Q 020984 101 NIIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKL----ANF--PECDVFINVSCA 161 (319)
Q Consensus 101 ~~iGIivgTl~~q~~~~i~~~l~~ll~~~Gkk~y~i~vg~in~~KL----aNf--~eID~fV~iaCP 161 (319)
++||+|+.++....+..+++.+.+.++++|....+. -+.-++++. .+| ..+|.+|++++.
T Consensus 1 ~~ig~i~~~~~~~~~~~~~~gi~~~a~~~gy~~~~~-~~~~~~~~~~~~i~~l~~~~vdgiil~~~~ 66 (280)
T cd06315 1 KNIIFVASDLKNGGILGVGEGVREAAKAIGWNLRIL-DGRGSEAGQAAALNQAIALKPDGIVLGGVD 66 (280)
T ss_pred CeEEEEecccCCcHHHHHHHHHHHHHHHcCcEEEEE-CCCCCHHHHHHHHHHHHHcCCCEEEEcCCC
Confidence 579999999887788899999999999999765443 344455432 222 279999998764
No 26
>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=68.71 E-value=15 Score=32.63 Aligned_cols=60 Identities=18% Similarity=0.240 Sum_probs=41.1
Q ss_pred EEEEEEcC----CCccCcHHHHHHHHHHHHHhCCcEEEEEcCCC-CH----HhhcCCCCCCEEEEecCC
Q 020984 102 IIGVLVGT----LGVAGYLHMIHQMKELITKAGKKAYTLVMGKP-NP----AKLANFPECDVFINVSCA 161 (319)
Q Consensus 102 ~iGIivgT----l~~q~~~~i~~~l~~ll~~~Gkk~y~i~vg~i-n~----~KLaNf~eID~fV~iaCP 161 (319)
.||||+.. ..-..+..+++.+++.++++|....++....- +. .++.+-..+|++|+.+|.
T Consensus 1 ~igvi~p~~~~~~~~~~~~~~~~~i~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~vdgiii~~~~ 69 (268)
T cd06271 1 AIGLVLPTGEREEGDPFFAEFLSGLSEALAEHGYDLVLLPVDPDEDPLEVYRRLVESGLVDGVIISRTR 69 (268)
T ss_pred CeEEEeCCcccccCCccHHHHHHHHHHHHHHCCceEEEecCCCcHHHHHHHHHHHHcCCCCEEEEecCC
Confidence 37899876 33566778999999999999988766665432 11 122222369999988774
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=68.71 E-value=10 Score=34.03 Aligned_cols=59 Identities=25% Similarity=0.364 Sum_probs=42.8
Q ss_pred EEEEEEcCCCccCcHHHHHHHHHHHHHhCCcEEEEEcCCCCHHh----hcCC--CCCCEEEEecCC
Q 020984 102 IIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAK----LANF--PECDVFINVSCA 161 (319)
Q Consensus 102 ~iGIivgTl~~q~~~~i~~~l~~ll~~~Gkk~y~i~vg~in~~K----LaNf--~eID~fV~iaCP 161 (319)
+||||+..+.-..+..+++.+++.++++|....++. +.-++++ |.++ ..+|++|+.+|.
T Consensus 1 ~igvi~p~~~~~~~~~~~~g~~~~a~~~g~~~~~~~-~~~~~~~~~~~i~~~~~~~vdgii~~~~~ 65 (268)
T cd06270 1 TIGLVVSDLDGPFFGPLLSGVESVARKAGKHLIITA-GHHSAEKEREAIEFLLERRCDALILHSKA 65 (268)
T ss_pred CEEEEEccccCcchHHHHHHHHHHHHHCCCEEEEEe-CCCchHHHHHHHHHHHHcCCCEEEEecCC
Confidence 479999888888888999999999999998766543 3333332 1121 269999998874
No 28
>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=68.68 E-value=20 Score=29.32 Aligned_cols=55 Identities=16% Similarity=0.285 Sum_probs=43.0
Q ss_pred EEEEEcCCCccCcHHHHHHHHHHHHHhCCcEEEEEcCCCCHHhhcCCCCCCEEEEecCCC
Q 020984 103 IGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKLANFPECDVFINVSCAQ 162 (319)
Q Consensus 103 iGIivgTl~~q~~~~i~~~l~~ll~~~Gkk~y~i~vg~in~~KLaNf~eID~fV~iaCPr 162 (319)
|.||.+|. -.+...+++.|.+.+...|.++-++-+.+.++.+|.+ .|.+ ++++|-
T Consensus 1 v~Iiy~S~-tGnT~~~A~~i~~~~~~~g~~v~~~~~~~~~~~~l~~---~d~i-ilgspt 55 (140)
T TIGR01753 1 ILIVYASM-TGNTEEMANIIAEGLKEAGAEVDLLEVADADAEDLLS---YDAV-LLGCST 55 (140)
T ss_pred CEEEEECC-CcHHHHHHHHHHHHHHhcCCeEEEEEcccCCHHHHhc---CCEE-EEEcCC
Confidence 35788885 3667789999999999999999999999998888755 5654 555554
No 29
>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=68.11 E-value=12 Score=30.34 Aligned_cols=71 Identities=21% Similarity=0.305 Sum_probs=48.7
Q ss_pred HHHHH-HHHHHhhccCCEEEEEEcCCCccCcHHHHHHHHHHHHHhCCcEEEEEcC---CCCHHhhcCC-CCCCEEE
Q 020984 86 ILKRR-YYLVEKAKDANIIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMG---KPNPAKLANF-PECDVFI 156 (319)
Q Consensus 86 ~l~~R-~~~I~ka~~a~~iGIivgTl~~q~~~~i~~~l~~ll~~~Gkk~y~i~vg---~in~~KLaNf-~eID~fV 156 (319)
.|..+ |..++...+|..+-|-..+.--+--.+++++|+++.+.......+++.| ...+++|... ++||+|+
T Consensus 22 ~l~~~G~~~~~~~e~AD~iiiNTC~V~~~Ae~k~~~~i~~l~~~~~~~~~ivv~GC~aq~~~~~l~~~~p~vd~v~ 97 (98)
T PF00919_consen 22 ILQAAGYEIVDDPEEADVIIINTCTVRESAEQKSRNRIRKLKKLKKPGAKIVVTGCMAQRYGEELKKEFPEVDLVV 97 (98)
T ss_pred HHHhcCCeeecccccCCEEEEEcCCCCcHHHHHHHHHHHHHHHhcCCCCEEEEEeCccccChHHHHhhCCCeEEEe
Confidence 34444 4455555788988666666655666688888888777664667777766 6667888864 6789875
No 30
>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=67.99 E-value=17 Score=32.67 Aligned_cols=73 Identities=19% Similarity=0.225 Sum_probs=48.6
Q ss_pred EEEEEcC---CCccCcHHHHHHHHHHHHHhCCcEEEEEcCCCCHHh-------hcCCCCCCEEEEecCCCccc-ccccCC
Q 020984 103 IGVLVGT---LGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAK-------LANFPECDVFINVSCAQTAL-LDSKEF 171 (319)
Q Consensus 103 iGIivgT---l~~q~~~~i~~~l~~ll~~~Gkk~y~i~vg~in~~K-------LaNf~eID~fV~iaCPr~si-dd~~~f 171 (319)
||+|+.. +....+..+++.+++.+++.|.+..+...+. +.+. |.+ ..+|++|+.++..... .....-
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 7899988 5677788999999999999998877776653 3321 212 2699999988764432 122233
Q ss_pred CCcccC
Q 020984 172 LAPVIT 177 (319)
Q Consensus 172 ~kPvlT 177 (319)
..|+|+
T Consensus 80 ~ipvV~ 85 (268)
T cd06277 80 GIPFVL 85 (268)
T ss_pred CCCEEE
Confidence 456654
No 31
>PRK14987 gluconate operon transcriptional regulator; Provisional
Probab=67.32 E-value=15 Score=34.56 Aligned_cols=63 Identities=17% Similarity=0.244 Sum_probs=45.2
Q ss_pred ccCCEEEEEEcCCCccCcHHHHHHHHHHHHHhCCcEEEEEcCCCCHHh----hcCC--CCCCEEEEecCC
Q 020984 98 KDANIIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAK----LANF--PECDVFINVSCA 161 (319)
Q Consensus 98 ~~a~~iGIivgTl~~q~~~~i~~~l~~ll~~~Gkk~y~i~vg~in~~K----LaNf--~eID~fV~iaCP 161 (319)
+..++||+|+..+....+..+++.+.+.++++|.+..+...+ -++++ +.++ ..+|.+|+.++.
T Consensus 61 ~~~~~Igvi~~~~~~~~~~~~~~gi~~~~~~~g~~~~~~~~~-~~~~~~~~~~~~~~~~~vdgiI~~~~~ 129 (331)
T PRK14987 61 ATSRAIGVLLPSLTNQVFAEVLRGIESVTDAHGYQTMLAHYG-YKPEMEQERLESMLSWNIDGLILTERT 129 (331)
T ss_pred CCCCEEEEEeCCCcchhHHHHHHHHHHHHHHCCCEEEEecCC-CCHHHHHHHHHHHHhcCCCEEEEcCCC
Confidence 356799999998877778899999999999999776554433 23321 2222 269999987653
No 32
>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=67.01 E-value=11 Score=33.86 Aligned_cols=59 Identities=17% Similarity=0.200 Sum_probs=43.2
Q ss_pred EEEEEEcCCCccCcHHHHHHHHHHHHHhCCcEEEEEcCCCCHHhhc----CC--CCCCEEEEecCC
Q 020984 102 IIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKLA----NF--PECDVFINVSCA 161 (319)
Q Consensus 102 ~iGIivgTl~~q~~~~i~~~l~~ll~~~Gkk~y~i~vg~in~~KLa----Nf--~eID~fV~iaCP 161 (319)
+||+|+....-..+..+++.+.+.+++.|....+. ...-++++.. .+ ..+|.+++.+|.
T Consensus 1 ~Igvv~~~~~~~~~~~~~~~i~~~a~~~g~~~~~~-~~~~~~~~~~~~i~~l~~~~vdgii~~~~~ 65 (269)
T cd06281 1 TIGCLVSDITNPLLAQLFSGAEDRLRAAGYSLLIA-NSLNDPERELEILRSFEQRRMDGIIIAPGD 65 (269)
T ss_pred CEEEEecCCccccHHHHHHHHHHHHHHcCCEEEEE-eCCCChHHHHHHHHHHHHcCCCEEEEecCC
Confidence 48999988877788899999999999999875544 3444554322 22 269999998884
No 33
>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=66.98 E-value=6.9 Score=35.25 Aligned_cols=61 Identities=10% Similarity=-0.043 Sum_probs=42.6
Q ss_pred EEEEEEcCCCccCcHHHHHHHHHHHHHhCCcEEEEEcC-CCCHHhhc----CC--CCCCEEEEecCCC
Q 020984 102 IIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMG-KPNPAKLA----NF--PECDVFINVSCAQ 162 (319)
Q Consensus 102 ~iGIivgTl~~q~~~~i~~~l~~ll~~~Gkk~y~i~vg-~in~~KLa----Nf--~eID~fV~iaCPr 162 (319)
+||||+.++.-..+..+++.+++.++++|.+..++... .=++++.. ++ ..+|.+|+.++..
T Consensus 1 ~Igvi~~~~~~~~~~~~~~g~~~~~~~~g~~~~~~~~~~~~~~~~~~~~i~~l~~~~vdgvii~~~~~ 68 (273)
T cd06310 1 KIALVPKGTTSDFWQAVKAGAEAAAKELGVKVTFQGPASETDVAGQVNLLENAIARGPDAILLAPTDA 68 (273)
T ss_pred CeEEEecCCCcHHHHHHHHHHHHHHHHcCCEEEEecCccCCCHHHHHHHHHHHHHhCCCEEEEcCCCh
Confidence 48999988877778899999999999998876655432 22444321 21 2689988877654
No 34
>PRK06703 flavodoxin; Provisional
Probab=66.86 E-value=21 Score=30.15 Aligned_cols=56 Identities=11% Similarity=0.051 Sum_probs=42.9
Q ss_pred EEEEEEcCCCccCcHHHHHHHHHHHHHhCCcEEEEEcCCCCHHhhcCCCCCCEEEEecCCC
Q 020984 102 IIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKLANFPECDVFINVSCAQ 162 (319)
Q Consensus 102 ~iGIivgTl~~q~~~~i~~~l~~ll~~~Gkk~y~i~vg~in~~KLaNf~eID~fV~iaCPr 162 (319)
++.|+.+|.. -+...+++.|.+.|.+.|.++-++-+.+..+..|. +.|. |+++||-
T Consensus 3 kv~IiY~S~t-GnT~~iA~~ia~~l~~~g~~v~~~~~~~~~~~~l~---~~d~-viigspt 58 (151)
T PRK06703 3 KILIAYASMS-GNTEDIADLIKVSLDAFDHEVVLQEMDGMDAEELL---AYDG-IILGSYT 58 (151)
T ss_pred eEEEEEECCC-chHHHHHHHHHHHHHhcCCceEEEehhhCCHHHHh---cCCc-EEEEECC
Confidence 5789999954 56678999999999999999888888887776654 4454 5556653
No 35
>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=66.26 E-value=18 Score=31.73 Aligned_cols=61 Identities=21% Similarity=0.354 Sum_probs=42.5
Q ss_pred EEEEEEcCCCccCcHHHHHHHHHHHHHhCCcEEEEEcC-CCCHHhhcCC----C--CCCEEEEecCCCccc
Q 020984 102 IIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMG-KPNPAKLANF----P--ECDVFINVSCAQTAL 165 (319)
Q Consensus 102 ~iGIivgTl~~q~~~~i~~~l~~ll~~~Gkk~y~i~vg-~in~~KLaNf----~--eID~fV~iaCPr~si 165 (319)
+++||.|+ ..-+.+++..++.|++.|..+-+-+.+ .-+|++|..| . ++|+||.+|==...+
T Consensus 2 ~V~Ii~gs---~SD~~~~~~a~~~L~~~gi~~~~~V~saHR~p~~l~~~~~~~~~~~~~viIa~AG~~a~L 69 (150)
T PF00731_consen 2 KVAIIMGS---TSDLPIAEEAAKTLEEFGIPYEVRVASAHRTPERLLEFVKEYEARGADVIIAVAGMSAAL 69 (150)
T ss_dssp EEEEEESS---GGGHHHHHHHHHHHHHTT-EEEEEE--TTTSHHHHHHHHHHTTTTTESEEEEEEESS--H
T ss_pred eEEEEeCC---HHHHHHHHHHHHHHHHcCCCEEEEEEeccCCHHHHHHHHHHhccCCCEEEEEECCCcccc
Confidence 68999998 667889999999999999888776666 5567776644 3 578887666544443
No 36
>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=66.12 E-value=12 Score=33.36 Aligned_cols=76 Identities=17% Similarity=0.166 Sum_probs=49.2
Q ss_pred EEEEEEcCCCccCcHHHHHHHHHHHHHhCCcEEEEEcCCCCHHhh----cCC--CCCCEEEEecCCCc-c-cccccCCCC
Q 020984 102 IIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKL----ANF--PECDVFINVSCAQT-A-LLDSKEFLA 173 (319)
Q Consensus 102 ~iGIivgTl~~q~~~~i~~~l~~ll~~~Gkk~y~i~vg~in~~KL----aNf--~eID~fV~iaCPr~-s-idd~~~f~k 173 (319)
+||||+....-..+..+++.+++.+++.|.+..++.. .-++++. .++ ..+|++|++++... . +........
T Consensus 1 ~igvv~~~~~~~~~~~~~~gi~~~~~~~g~~~~~~~~-~~~~~~~~~~i~~l~~~~~dgii~~~~~~~~~~~~~~~~~~i 79 (259)
T cd01542 1 LIGVIVPRLDSFSTSRTVKGILAALYENGYQMLLMNT-NFSIEKEIEALELLARQKVDGIILLATTITDEHREAIKKLNV 79 (259)
T ss_pred CeEEEecCCccchHHHHHHHHHHHHHHCCCEEEEEeC-CCCHHHHHHHHHHHHhcCCCEEEEeCCCCCHHHHHHHhcCCC
Confidence 4789998877667778999999999999988655443 4445432 122 37999999876421 1 122234456
Q ss_pred cccCH
Q 020984 174 PVITP 178 (319)
Q Consensus 174 PvlTP 178 (319)
||++-
T Consensus 80 pvv~~ 84 (259)
T cd01542 80 PVVVV 84 (259)
T ss_pred CEEEE
Confidence 77653
No 37
>PRK11303 DNA-binding transcriptional regulator FruR; Provisional
Probab=65.04 E-value=19 Score=33.58 Aligned_cols=61 Identities=15% Similarity=0.269 Sum_probs=44.7
Q ss_pred cCCEEEEEEcCCCccCcHHHHHHHHHHHHHhCCcEEEEEcCCCCHHh-------hcCCCCCCEEEEecCC
Q 020984 99 DANIIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAK-------LANFPECDVFINVSCA 161 (319)
Q Consensus 99 ~a~~iGIivgTl~~q~~~~i~~~l~~ll~~~Gkk~y~i~vg~in~~K-------LaNf~eID~fV~iaCP 161 (319)
..++||+|+..+.-..+..+++.+.+.++++|....++...+ ++++ |.+- .+|.+|+.++.
T Consensus 60 ~~~~Igvv~~~~~~~~~~~l~~gi~~~~~~~g~~~~~~~~~~-~~~~~~~~~~~l~~~-~vdgiIi~~~~ 127 (328)
T PRK11303 60 RTRSIGLIIPDLENTSYARIAKYLERQARQRGYQLLIACSDD-QPDNEMRCAEHLLQR-QVDALIVSTSL 127 (328)
T ss_pred CCceEEEEeCCCCCchHHHHHHHHHHHHHHcCCEEEEEeCCC-CHHHHHHHHHHHHHc-CCCEEEEcCCC
Confidence 467999999887767788899999999999998876654432 3332 2222 69999887763
No 38
>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=63.23 E-value=19 Score=32.22 Aligned_cols=59 Identities=19% Similarity=0.266 Sum_probs=40.1
Q ss_pred EEEEEEcCCCccCcHHHHHHHHHHHHHhCCcEEEEEcCCCCHHhhcCC------CCCCEEEEecCC
Q 020984 102 IIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKLANF------PECDVFINVSCA 161 (319)
Q Consensus 102 ~iGIivgTl~~q~~~~i~~~l~~ll~~~Gkk~y~i~vg~in~~KLaNf------~eID~fV~iaCP 161 (319)
+||+|+..+....+..+++.+++.++++|.+..++... -++++-..+ ..+|++|+.++.
T Consensus 1 ~I~vi~~~~~~~~~~~~~~gi~~~~~~~g~~~~~~~~~-~~~~~~~~~i~~~~~~~~dgiii~~~~ 65 (265)
T cd06291 1 LIGLIVPTISNPFFSELARAVEKELYKKGYKLILCNSD-NDPEKEREYLEMLRQNQVDGIIAGTHN 65 (265)
T ss_pred CEEEEECCCCChhHHHHHHHHHHHHHHCCCeEEEecCC-ccHHHHHHHHHHHHHcCCCEEEEecCC
Confidence 47888888777777888888888888888776544333 234322211 168888888764
No 39
>PRK10423 transcriptional repressor RbsR; Provisional
Probab=62.91 E-value=32 Score=32.02 Aligned_cols=64 Identities=11% Similarity=0.162 Sum_probs=46.2
Q ss_pred hccCCEEEEEEcCCCccCcHHHHHHHHHHHHHhCCcEEEEEcCCCCHHh----hcCC--CCCCEEEEecCC
Q 020984 97 AKDANIIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAK----LANF--PECDVFINVSCA 161 (319)
Q Consensus 97 a~~a~~iGIivgTl~~q~~~~i~~~l~~ll~~~Gkk~y~i~vg~in~~K----LaNf--~eID~fV~iaCP 161 (319)
.+..++||+|+....-..+..+++.+.+.+++.|.+..++.. .-++++ |.+| ..+|.+|+++..
T Consensus 53 ~~~~~~Igvi~~~~~~~~~~~~~~gi~~~~~~~g~~~~~~~~-~~~~~~~~~~~~~l~~~~vdGiI~~~~~ 122 (327)
T PRK10423 53 LNQTRTIGMLITASTNPFYSELVRGVERSCFERGYSLVLCNT-EGDEQRMNRNLETLMQKRVDGLLLLCTE 122 (327)
T ss_pred hCCCCeEEEEeCCCCCCcHHHHHHHHHHHHHHcCCEEEEEeC-CCCHHHHHHHHHHHHHcCCCEEEEeCCC
Confidence 345689999999887778889999999999999988665443 334432 2222 269999987653
No 40
>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=62.75 E-value=11 Score=35.50 Aligned_cols=114 Identities=18% Similarity=0.244 Sum_probs=68.0
Q ss_pred HHHHHHHHHHHHhhc-cCCEEEEEEcCCCccCcHHHHHHHHHHHHHhCCcEEEEEcCCCCH--HhhcCC-CCCCEEEEec
Q 020984 84 LKILKRRYYLVEKAK-DANIIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNP--AKLANF-PECDVFINVS 159 (319)
Q Consensus 84 ~k~l~~R~~~I~ka~-~a~~iGIivgTl~~q~~~~i~~~l~~ll~~~Gkk~y~i~vg~in~--~KLaNf-~eID~fV~ia 159 (319)
...+.++..++.+.. +++++|+|...-. .+....++.+++.+++.|.+.+.+.+...+. ..+..+ .++|++++..
T Consensus 114 ~~~~~~~l~l~~~l~P~~k~igvl~~~~~-~~~~~~~~~~~~~a~~~g~~l~~~~v~~~~~~~~~~~~l~~~~da~~~~~ 192 (294)
T PF04392_consen 114 RPPIEKQLELIKKLFPDAKRIGVLYDPSE-PNSVAQIEQLRKAAKKLGIELVEIPVPSSEDLEQALEALAEKVDALYLLP 192 (294)
T ss_dssp ---HHHHHHHHHHHSTT--EEEEEEETT--HHHHHHHHHHHHHHHHTT-EEEEEEESSGGGHHHHHHHHCTT-SEEEE-S
T ss_pred CcCHHHHHHHHHHhCCCCCEEEEEecCCC-ccHHHHHHHHHHHHHHcCCEEEEEecCcHhHHHHHHHHhhccCCEEEEEC
Confidence 455677888888887 7999999998643 4567788999999999999999888887663 233333 3689888765
Q ss_pred CCCcc-----c-ccccCCCCcccCHHHHHHhhCCCCCCCcceeeccccc
Q 020984 160 CAQTA-----L-LDSKEFLAPVITPFEAMLAFGRGTQWTGAYVMEFRDL 202 (319)
Q Consensus 160 CPr~s-----i-dd~~~f~kPvlTP~El~vAL~~~~~W~~~y~~Df~~l 202 (319)
.+-.. + ........||++.++..|.-|. -+.|..|++++
T Consensus 193 ~~~~~~~~~~i~~~~~~~~iPv~~~~~~~v~~Ga----l~~~~~~~~~~ 237 (294)
T PF04392_consen 193 DNLVDSNFEAILQLANEAKIPVFGSSDFYVKAGA----LGGYSVDYYEQ 237 (294)
T ss_dssp -HHHHHTHHHHHHHCCCTT--EEESSHHHHCTT-----SEEEE--HHHH
T ss_pred CcchHhHHHHHHHHHHhcCCCEEECCHHHhcCCc----EEEEccCHHHH
Confidence 44211 0 1124567888887776665442 24566677665
No 41
>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=62.73 E-value=26 Score=31.13 Aligned_cols=58 Identities=17% Similarity=0.279 Sum_probs=41.4
Q ss_pred EEEEEEcCCCccCcHHHHHHHHHHHHHhCCcEEEEEcCCCCHHh-------hcCCCCCCEEEEecCC
Q 020984 102 IIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAK-------LANFPECDVFINVSCA 161 (319)
Q Consensus 102 ~iGIivgTl~~q~~~~i~~~l~~ll~~~Gkk~y~i~vg~in~~K-------LaNf~eID~fV~iaCP 161 (319)
+||+|+....-..+..+++.+++.++++|....++.. +-+++. |.+. .+|.+|+.++.
T Consensus 1 ~igvi~~~~~~~~~~~~~~~i~~~a~~~g~~~~~~~~-~~~~~~~~~~~~~l~~~-~~dgiii~~~~ 65 (267)
T cd06283 1 LIGVIVADITNPFSSLVLKGIEDVCRAHGYQVLVCNS-DNDPEKEKEYLESLLAY-QVDGLIVNPTG 65 (267)
T ss_pred CEEEEecCCccccHHHHHHHHHHHHHHcCCEEEEEcC-CCCHHHHHHHHHHHHHc-CcCEEEEeCCC
Confidence 4788998877778888999999999999977654443 334433 2232 68999887764
No 42
>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=62.62 E-value=12 Score=42.54 Aligned_cols=112 Identities=14% Similarity=0.191 Sum_probs=73.2
Q ss_pred EEEEcCCCCccccccCcHHHHHHHHHHHHHhhccCCEEEEEEcCCCc-cCcHHHHHHHHHHHHHhCCcEEEEEcCC--CC
Q 020984 66 IVRYDATEERLLTDVSQPLKILKRRYYLVEKAKDANIIGVLVGTLGV-AGYLHMIHQMKELITKAGKKAYTLVMGK--PN 142 (319)
Q Consensus 66 v~~yDP~s~~~~~e~~~~~k~l~~R~~~I~ka~~a~~iGIivgTl~~-q~~~~i~~~l~~ll~~~Gkk~y~i~vg~--in 142 (319)
.-.|.|....++....+..++.+.|-. -.-++.+||||+..--. .+....++.|.+.|+++|..++.++..- -.
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 578888876654332222222222211 23478999999975443 5678999999999999999999999653 23
Q ss_pred HHhhcC-CC-----CCCEEEEecCCCccc-------ccccCCCCcccCHHH
Q 020984 143 PAKLAN-FP-----ECDVFINVSCAQTAL-------LDSKEFLAPVITPFE 180 (319)
Q Consensus 143 ~~KLaN-f~-----eID~fV~iaCPr~si-------dd~~~f~kPvlTP~E 180 (319)
...+.. |. .||+.|.+.+=++.- ...++..-|||.+.-
T Consensus 117 ~~~i~~~f~~~g~~~vDaIIn~~~f~l~~~~~~~~~~~L~~LnVPVlq~i~ 167 (1098)
T PF02514_consen 117 QEAIEDYFMDDGKPRVDAIINLTGFSLGGGPAGGAIELLKELNVPVLQAIT 167 (1098)
T ss_pred HHHHHHHHhhcCCCCceEEEEcCccccCCCCcchhHHHHHHCCCCEEEeec
Confidence 333332 33 499998888866543 234567888877654
No 43
>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=62.57 E-value=15 Score=32.86 Aligned_cols=61 Identities=15% Similarity=0.201 Sum_probs=43.0
Q ss_pred EEEEEEcCCCccCcHHHHHHHHHHHHHhCCcEEEEEcCCCCHH---h-hcCC--CCCCEEEEecCCC
Q 020984 102 IIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPA---K-LANF--PECDVFINVSCAQ 162 (319)
Q Consensus 102 ~iGIivgTl~~q~~~~i~~~l~~ll~~~Gkk~y~i~vg~in~~---K-LaNf--~eID~fV~iaCPr 162 (319)
+||+|+.+..-..+..+++.+++.+++.|....++....-.++ + +..+ ..+|.+++.+|..
T Consensus 1 ~i~vi~~~~~~~~~~~~~~gi~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~vdgiii~~~~~ 67 (264)
T cd01574 1 TIGVVTTDLALHGPSSTLAAIESAAREAGYAVTLSMLAEADEEALRAAVRRLLAQRVDGVIVNAPLD 67 (264)
T ss_pred CEEEEeCCCCcccHHHHHHHHHHHHHHCCCeEEEEeCCCCchHHHHHHHHHHHhcCCCEEEEeCCCC
Confidence 4889998877667788999999999999988766655543322 1 1122 2699999888743
No 44
>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=62.44 E-value=17 Score=30.16 Aligned_cols=54 Identities=11% Similarity=0.241 Sum_probs=39.9
Q ss_pred EEEcCCCccCcHHHHHHHHHHHHHhCCcEEEEEcCCCCHHhhcCCCCCCEEEEecCC
Q 020984 105 VLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKLANFPECDVFINVSCA 161 (319)
Q Consensus 105 IivgTl~~q~~~~i~~~l~~ll~~~Gkk~y~i~vg~in~~KLaNf~eID~fV~iaCP 161 (319)
|+.+|.. .+...+++.|.+.|+++|.++.++-+.+.+.. +..+.+.+. +++.||
T Consensus 1 I~Y~S~t-G~te~~A~~ia~~l~~~g~~~~~~~~~~~~~~-~~~~~~~~~-~i~~~s 54 (143)
T PF00258_consen 1 IVYGSMT-GNTEKMAEAIAEGLRERGVEVRVVDLDDFDDS-PSDLSEYDL-LIFGVS 54 (143)
T ss_dssp EEEETSS-SHHHHHHHHHHHHHHHTTSEEEEEEGGGSCHH-HHHHCTTSE-EEEEEE
T ss_pred CEEECCc-hhHHHHHHHHHHHHHHcCCceeeechhhhhhh-hhhhhhhce-eeEeec
Confidence 5667764 45568999999999999999999999999966 333334455 455555
No 45
>PRK09004 FMN-binding protein MioC; Provisional
Probab=61.99 E-value=25 Score=30.19 Aligned_cols=55 Identities=15% Similarity=0.100 Sum_probs=38.7
Q ss_pred CEEEEEEcCCCccCcHHHHHHHHHHHHHhCCcEEEEEcCCCCHHhhcCCCCCCEEEEecCCC
Q 020984 101 NIIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKLANFPECDVFINVSCAQ 162 (319)
Q Consensus 101 ~~iGIivgTl~~q~~~~i~~~l~~ll~~~Gkk~y~i~vg~in~~KLaNf~eID~fV~iaCPr 162 (319)
+++.|+.||-. -+...++++|.+.+++.|.++.++-+.. ++. +++.|. +++.||-
T Consensus 2 ~~i~I~ygS~t-Gnae~~A~~l~~~~~~~g~~~~~~~~~~--~~~---l~~~~~-li~~~sT 56 (146)
T PRK09004 2 ADITLISGSTL-GGAEYVADHLAEKLEEAGFSTETLHGPL--LDD---LSASGL-WLIVTST 56 (146)
T ss_pred CeEEEEEEcCc-hHHHHHHHHHHHHHHHcCCceEEeccCC--HHH---hccCCe-EEEEECC
Confidence 36899999976 4567899999999999999887654433 444 455565 4444543
No 46
>PRK11041 DNA-binding transcriptional regulator CytR; Provisional
Probab=61.62 E-value=34 Score=31.42 Aligned_cols=62 Identities=10% Similarity=0.061 Sum_probs=44.9
Q ss_pred ccCCEEEEEEcCCCccCcHHHHHHHHHHHHHhCCcEEEEEcCCCCHHhh----cCC--CCCCEEEEecC
Q 020984 98 KDANIIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKL----ANF--PECDVFINVSC 160 (319)
Q Consensus 98 ~~a~~iGIivgTl~~q~~~~i~~~l~~ll~~~Gkk~y~i~vg~in~~KL----aNf--~eID~fV~iaC 160 (319)
...++||+|+..+.-..+..+++.+++.+++.|....+..... +.++- ..+ ..+|.+++.++
T Consensus 33 ~~~~~ig~v~~~~~~~~~~~~~~gi~~~~~~~g~~~~~~~~~~-~~~~~~~~i~~l~~~~vDgiIi~~~ 100 (309)
T PRK11041 33 NESRTILVIVPDICDPFFSEIIRGIEVTAAEHGYLVLIGDCAH-QNQQEKTFVNLIITKQIDGMLLLGS 100 (309)
T ss_pred CCCcEEEEEeCCCcCccHHHHHHHHHHHHHHCCCEEEEEeCCC-ChHHHHHHHHHHHHcCCCEEEEecC
Confidence 3568999999887767788999999999999998876654432 33221 111 26999999765
No 47
>PRK09526 lacI lac repressor; Reviewed
Probab=61.53 E-value=50 Score=30.97 Aligned_cols=61 Identities=11% Similarity=0.137 Sum_probs=45.2
Q ss_pred ccCCEEEEEEcCCCccCcHHHHHHHHHHHHHhCCcEEEEEcCCCCHH----hhcCC--CCCCEEEEe
Q 020984 98 KDANIIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPA----KLANF--PECDVFINV 158 (319)
Q Consensus 98 ~~a~~iGIivgTl~~q~~~~i~~~l~~ll~~~Gkk~y~i~vg~in~~----KLaNf--~eID~fV~i 158 (319)
+..++||+|+..+....+..+++.+++.++++|....++..+.-+++ .|.++ ..+|.+|+.
T Consensus 61 ~~~~~Igvv~~~~~~~~~~~~~~gi~~~a~~~g~~~~i~~~~~~~~~~~~~~l~~l~~~~vdGiii~ 127 (342)
T PRK09526 61 KQSLTIGLATTSLALHAPSQIAAAIKSRADQLGYSVVISMVERSGVEACQAAVNELLAQRVSGVIIN 127 (342)
T ss_pred CCCceEEEEeCCCCcccHHHHHHHHHHHHHHCCCEEEEEeCCCChHHHHHHHHHHHHhcCCCEEEEe
Confidence 35679999999887777789999999999999988777665543332 23333 269998885
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=61.30 E-value=11 Score=34.66 Aligned_cols=61 Identities=16% Similarity=0.179 Sum_probs=39.9
Q ss_pred EEEEEEcCCCccCcHHHHHHHHHHHHHhCCcEEEEEcCCCCHHhhc----CC--CCCCEEEEecCCC
Q 020984 102 IIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKLA----NF--PECDVFINVSCAQ 162 (319)
Q Consensus 102 ~iGIivgTl~~q~~~~i~~~l~~ll~~~Gkk~y~i~vg~in~~KLa----Nf--~eID~fV~iaCPr 162 (319)
+||+|+..+.-..+..+++.+++.+++.|.....+..++-++++.. .+ ..+|.+|+.+|..
T Consensus 1 ~i~~i~~~~~~~~~~~~~~gi~~~a~~~g~~~~~~~~~~~~~~~~~~~l~~~~~~~~dgiii~~~~~ 67 (294)
T cd06316 1 KAAIVMHTSGSDWSNAQVRGAKDEFAKLGIEVVATTDAQFDPAKQVADIETTISQKPDIIISIPVDP 67 (294)
T ss_pred CeEEEecCCCChHHHHHHHHHHHHHHHcCCEEEEecCCCCCHHHHHHHHHHHHHhCCCEEEEcCCCc
Confidence 4788887765444557888888888888877654434544554321 11 2689888887764
No 49
>PRK07308 flavodoxin; Validated
Probab=60.89 E-value=40 Score=28.33 Aligned_cols=57 Identities=5% Similarity=0.110 Sum_probs=43.4
Q ss_pred EEEEEEcCCCccCcHHHHHHHHHHHHHhCCcEEEEEcCCCCHHhhcCCCCCCEEEEecCCCc
Q 020984 102 IIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKLANFPECDVFINVSCAQT 163 (319)
Q Consensus 102 ~iGIivgTl~~q~~~~i~~~l~~ll~~~Gkk~y~i~vg~in~~KLaNf~eID~fV~iaCPr~ 163 (319)
.+-||.+|.. -+...+++.|.+.|++.|..+-++-+.+..+..|. +.|+ |+++||-.
T Consensus 3 ~~~IvY~S~t-GnTe~iA~~ia~~l~~~g~~~~~~~~~~~~~~~l~---~~d~-vi~g~~t~ 59 (146)
T PRK07308 3 LAKIVYASMT-GNTEEIADIVADKLRELGHDVDVDECTTVDASDFE---DADI-AIVATYTY 59 (146)
T ss_pred eEEEEEECCC-chHHHHHHHHHHHHHhCCCceEEEecccCCHhHhc---cCCE-EEEEeCcc
Confidence 5778999954 56678899999999999988888878877776554 4566 45588865
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=60.87 E-value=22 Score=31.92 Aligned_cols=58 Identities=10% Similarity=0.134 Sum_probs=41.2
Q ss_pred EEEEEEcCCCccCcHHHHHHHHHHHHHhCCcEEEEEcCCCCHHhh----cCC--CCCCEEEEecC
Q 020984 102 IIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKL----ANF--PECDVFINVSC 160 (319)
Q Consensus 102 ~iGIivgTl~~q~~~~i~~~l~~ll~~~Gkk~y~i~vg~in~~KL----aNf--~eID~fV~iaC 160 (319)
.||+|+..+.-..+..+++.+.+.+++.|....++.. .-++++- .++ ..+|..++++|
T Consensus 1 ~Igvi~~~~~~~~~~~~~~gi~~~~~~~g~~~~~~~~-~~~~~~~~~~i~~l~~~~vdgiIi~~~ 64 (273)
T cd06292 1 LVGLLVPELSNPIFPAFAEAIEAALAQYGYTVLLCNT-YRGGVSEADYVEDLLARGVRGVVFISS 64 (273)
T ss_pred CEEEEeCCCcCchHHHHHHHHHHHHHHCCCEEEEEeC-CCChHHHHHHHHHHHHcCCCEEEEeCC
Confidence 4799998888778889999999999999987654433 3344322 122 26899888764
No 51
>PRK05569 flavodoxin; Provisional
Probab=60.50 E-value=40 Score=27.94 Aligned_cols=57 Identities=7% Similarity=0.107 Sum_probs=42.4
Q ss_pred CEEEEEEcCCCccCcHHHHHHHHHHHHHhCCcEEEEEcCCCCHHhhcCCCCCCEEEEecCCC
Q 020984 101 NIIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKLANFPECDVFINVSCAQ 162 (319)
Q Consensus 101 ~~iGIivgTl~~q~~~~i~~~l~~ll~~~Gkk~y~i~vg~in~~KLaNf~eID~fV~iaCPr 162 (319)
.++.||.+|. --+...+++.+.+.+++.|.++-++-+.+..+.++. +.|. |+++||-
T Consensus 2 ~ki~iiY~S~-tGnT~~iA~~i~~~~~~~g~~v~~~~~~~~~~~~~~---~~d~-iilgsPt 58 (141)
T PRK05569 2 KKVSIIYWSC-GGNVEVLANTIADGAKEAGAEVTIKHVADAKVEDVL---EADA-VAFGSPS 58 (141)
T ss_pred CeEEEEEECC-CCHHHHHHHHHHHHHHhCCCeEEEEECCcCCHHHHh---hCCE-EEEECCC
Confidence 3577888885 356679999999999999988777777777665543 5565 6777874
No 52
>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=60.15 E-value=32 Score=30.66 Aligned_cols=60 Identities=12% Similarity=0.083 Sum_probs=42.6
Q ss_pred EEEEEEcCCCccCcHHHHHHHHHHHHHhCCcEEEEEcCCCCH---HhhcC-C--CCCCEEEEecCC
Q 020984 102 IIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNP---AKLAN-F--PECDVFINVSCA 161 (319)
Q Consensus 102 ~iGIivgTl~~q~~~~i~~~l~~ll~~~Gkk~y~i~vg~in~---~KLaN-f--~eID~fV~iaCP 161 (319)
+||+|+....-..+..+++-+++.++++|+...++..+.-.+ ..+.. + ..+|++|++.|-
T Consensus 1 ~I~vi~~~~~~~~~~~~~~gi~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~l~~~~vdgiii~~~~ 66 (270)
T cd01545 1 LIGLLYDNPSPGYVSEIQLGALDACRDTGYQLVIEPCDSGSPDLAERVRALLQRSRVDGVILTPPL 66 (270)
T ss_pred CEEEEEcCCCcccHHHHHHHHHHHHHhCCCeEEEEeCCCCchHHHHHHHHHHHHCCCCEEEEeCCC
Confidence 478999887777888899999999999998877766654332 11111 1 268998888764
No 53
>PRK08105 flavodoxin; Provisional
Probab=60.08 E-value=25 Score=30.26 Aligned_cols=41 Identities=17% Similarity=0.286 Sum_probs=33.7
Q ss_pred CEEEEEEcCCCccCcHHHHHHHHHHHHHhCCcEEEEEcCCCC
Q 020984 101 NIIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPN 142 (319)
Q Consensus 101 ~~iGIivgTl~~q~~~~i~~~l~~ll~~~Gkk~y~i~vg~in 142 (319)
++++|+.||-. -+...++++|.+.|++.|.++.++-+..+.
T Consensus 2 ~~i~I~YgS~t-Gnte~~A~~l~~~l~~~g~~~~~~~~~~~~ 42 (149)
T PRK08105 2 AKVGIFVGTVY-GNALLVAEEAEAILTAQGHEVTLFEDPELS 42 (149)
T ss_pred CeEEEEEEcCc-hHHHHHHHHHHHHHHhCCCceEEechhhCC
Confidence 47899999976 456789999999999999998887776654
No 54
>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=59.55 E-value=57 Score=30.41 Aligned_cols=62 Identities=21% Similarity=0.423 Sum_probs=45.9
Q ss_pred ccCCEEEEEEcCCCccCcHHHHHHHHHHHHHhCCcEEEEEcCCCCHHh----hcCC--CCCCEEEEecC
Q 020984 98 KDANIIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAK----LANF--PECDVFINVSC 160 (319)
Q Consensus 98 ~~a~~iGIivgTl~~q~~~~i~~~l~~ll~~~Gkk~y~i~vg~in~~K----LaNf--~eID~fV~iaC 160 (319)
+..++||+|+..+.-..+..+++.+.+.++++|....+...+. ++++ +.++ ..+|.+|+.++
T Consensus 58 ~~~~~Igvi~~~~~~~~~~~~~~~i~~~~~~~gy~~~i~~~~~-~~~~~~~~~~~l~~~~vdgiIi~~~ 125 (327)
T TIGR02417 58 GRSRTIGLVIPDLENYSYARIAKELEQQCREAGYQLLIACSDD-NPDQEKVVIENLLARQVDALIVASC 125 (327)
T ss_pred CCCceEEEEeCCCCCccHHHHHHHHHHHHHHCCCEEEEEeCCC-CHHHHHHHHHHHHHcCCCEEEEeCC
Confidence 3468999999888777888999999999999998877665543 4432 2222 26999888765
No 55
>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=59.21 E-value=11 Score=34.84 Aligned_cols=59 Identities=17% Similarity=0.226 Sum_probs=36.6
Q ss_pred EEEEEEcCCCccCcHHHHHHHHHHHHHhCCcEEEEEcCCCCHHhhc----CC--CCCCEEEEecCC
Q 020984 102 IIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKLA----NF--PECDVFINVSCA 161 (319)
Q Consensus 102 ~iGIivgTl~~q~~~~i~~~l~~ll~~~Gkk~y~i~vg~in~~KLa----Nf--~eID~fV~iaCP 161 (319)
+||+|+....-..+..+++.+++.++++|....++... -++++.. ++ ..+|.+|+++|.
T Consensus 1 ~I~vi~~~~~~~~~~~~~~gi~~~a~~~g~~~~~~~~~-~~~~~~~~~i~~~~~~~vdgiii~~~~ 65 (288)
T cd01538 1 KIGLSLPTKTEERWIRDRPNFEAALKELGAEVIVQNAN-GDPAKQISQIENMIAKGVDVLVIAPVD 65 (288)
T ss_pred CeEEEEeCCCcHHHHHHHHHHHHHHHHcCCEEEEECCC-CCHHHHHHHHHHHHHcCCCEEEEecCC
Confidence 46777776655556677778888788777765554433 2444321 11 157888877764
No 56
>PRK05568 flavodoxin; Provisional
Probab=59.06 E-value=50 Score=27.30 Aligned_cols=57 Identities=12% Similarity=0.135 Sum_probs=43.2
Q ss_pred CEEEEEEcCCCccCcHHHHHHHHHHHHHhCCcEEEEEcCCCCHHhhcCCCCCCEEEEecCCC
Q 020984 101 NIIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKLANFPECDVFINVSCAQ 162 (319)
Q Consensus 101 ~~iGIivgTl~~q~~~~i~~~l~~ll~~~Gkk~y~i~vg~in~~KLaNf~eID~fV~iaCPr 162 (319)
+.+.|+..|.. -+...+++.|.+.+++.|.++.++-+.+.+..+| .+.|. |++++|=
T Consensus 2 ~~~~IvY~S~~-GnT~~~a~~i~~~~~~~g~~v~~~~~~~~~~~~~---~~~d~-iilgsp~ 58 (142)
T PRK05568 2 KKINIIYWSGT-GNTEAMANLIAEGAKENGAEVKLLNVSEASVDDV---KGADV-VALGSPA 58 (142)
T ss_pred CeEEEEEECCC-chHHHHHHHHHHHHHHCCCeEEEEECCCCCHHHH---HhCCE-EEEECCc
Confidence 35778888843 5667889999999999999888888888777655 35564 6777775
No 57
>PRK10703 DNA-binding transcriptional repressor PurR; Provisional
Probab=59.03 E-value=26 Score=32.91 Aligned_cols=62 Identities=13% Similarity=0.117 Sum_probs=45.5
Q ss_pred ccCCEEEEEEcCCCccCcHHHHHHHHHHHHHhCCcEEEEEcCCCCHHhhc----CC--CCCCEEEEecC
Q 020984 98 KDANIIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKLA----NF--PECDVFINVSC 160 (319)
Q Consensus 98 ~~a~~iGIivgTl~~q~~~~i~~~l~~ll~~~Gkk~y~i~vg~in~~KLa----Nf--~eID~fV~iaC 160 (319)
+..++||+|+..+....+..+++.+++.++++|.+.+++... -++++.. .+ ..+|++++.+.
T Consensus 57 ~~~~~i~vi~~~~~~~~~~~~~~gi~~~~~~~g~~~~~~~~~-~~~~~~~~~i~~l~~~~vdgiii~~~ 124 (341)
T PRK10703 57 NHTKSIGLLATSSEAPYFAEIIEAVEKNCYQKGYTLILCNAW-NNLEKQRAYLSMLAQKRVDGLLVMCS 124 (341)
T ss_pred CCCCeEEEEeCCCCCchHHHHHHHHHHHHHHCCCEEEEEeCC-CCHHHHHHHHHHHHHcCCCEEEEecC
Confidence 356799999998877788899999999999999887766543 3444322 11 26899987664
No 58
>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=58.99 E-value=31 Score=30.76 Aligned_cols=60 Identities=22% Similarity=0.261 Sum_probs=41.2
Q ss_pred EEEEEEcCCCccCcHHHHHHHHHHHHHhCCcEEEEEcCCCCHHh-------hcCCCCCCEEEEecCCCc
Q 020984 102 IIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAK-------LANFPECDVFINVSCAQT 163 (319)
Q Consensus 102 ~iGIivgTl~~q~~~~i~~~l~~ll~~~Gkk~y~i~vg~in~~K-------LaNf~eID~fV~iaCPr~ 163 (319)
+||+|+....-..+..+++.+++.+++.|....++... -++++ |.+- .+|.+++.++...
T Consensus 1 ~igvv~~~~~~~~~~~~~~gi~~~~~~~g~~~~~~~~~-~~~~~~~~~~~~l~~~-~vdgiIi~~~~~~ 67 (265)
T cd06299 1 TIGVIVPDIRNPYFASLATAIQDAASAAGYSTIIGNSD-ENPETENRYLDNLLSQ-RVDGIIVVPHEQS 67 (265)
T ss_pred CEEEEecCCCCccHHHHHHHHHHHHHHcCCEEEEEeCC-CCHHHHHHHHHHHHhc-CCCEEEEcCCCCC
Confidence 47888877665667788888988888888877766543 24432 2222 6898888876533
No 59
>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=58.66 E-value=21 Score=31.72 Aligned_cols=75 Identities=15% Similarity=0.148 Sum_probs=46.1
Q ss_pred EEEEEEcCCCccCcHHHHHHHHHHHHHhCCcEEEEEcCCCCHHh-------hcCCCCCCEEEEecCCCcc---cccccCC
Q 020984 102 IIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAK-------LANFPECDVFINVSCAQTA---LLDSKEF 171 (319)
Q Consensus 102 ~iGIivgTl~~q~~~~i~~~l~~ll~~~Gkk~y~i~vg~in~~K-------LaNf~eID~fV~iaCPr~s---idd~~~f 171 (319)
+||||+.....-.+..+++.+++.++++|....++... -++.+ |.+. .+|+.|+..|-... +....+.
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 47888877766667788888888888888776665442 33332 2232 68888876653221 1222344
Q ss_pred CCcccCH
Q 020984 172 LAPVITP 178 (319)
Q Consensus 172 ~kPvlTP 178 (319)
..|+|+.
T Consensus 79 ~ipvV~~ 85 (266)
T cd06282 79 RVPYVLA 85 (266)
T ss_pred CCCEEEE
Confidence 5566554
No 60
>PRK05723 flavodoxin; Provisional
Probab=58.34 E-value=33 Score=29.73 Aligned_cols=55 Identities=15% Similarity=0.228 Sum_probs=40.0
Q ss_pred EEEEEEcCCCccCcHHHHHHHHHHHHHhCCcEEEEEcCCCCHHhhcCCCCCCEEEEecCC
Q 020984 102 IIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKLANFPECDVFINVSCA 161 (319)
Q Consensus 102 ~iGIivgTl~~q~~~~i~~~l~~ll~~~Gkk~y~i~vg~in~~KLaNf~eID~fV~iaCP 161 (319)
+++|+.||-. -+...++++|.+.|++.|.++.++ ...+...|..+ +.|.+ ++.|+
T Consensus 2 ~i~I~ygS~t-G~ae~~A~~la~~l~~~g~~~~~~--~~~~~~~~~~~-~~~~l-i~~~s 56 (151)
T PRK05723 2 KVAILSGSVY-GTAEEVARHAESLLKAAGFEAWHN--PRASLQDLQAF-APEAL-LAVTS 56 (151)
T ss_pred eEEEEEEcCc-hHHHHHHHHHHHHHHHCCCceeec--CcCCHhHHHhC-CCCeE-EEEEC
Confidence 6899999976 356689999999999999887653 44677777766 34643 44444
No 61
>PRK14571 D-alanyl-alanine synthetase A; Provisional
Probab=58.32 E-value=36 Score=32.13 Aligned_cols=76 Identities=14% Similarity=0.061 Sum_probs=53.5
Q ss_pred EEEEEEcCCCc--cCcHHHHHHHHHHHHHhCCcEEEEEcCCCCHHhhcCCCCCCEEEEecCCCcccccc------cCCCC
Q 020984 102 IIGVLVGTLGV--AGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKLANFPECDVFINVSCAQTALLDS------KEFLA 173 (319)
Q Consensus 102 ~iGIivgTl~~--q~~~~i~~~l~~ll~~~Gkk~y~i~vg~in~~KLaNf~eID~fV~iaCPr~sidd~------~~f~k 173 (319)
+|+||+|..+. .-++...+.+.+-|++.|.++..+-..+-...++....++|+ |...|+...-.|+ ..+..
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 58999999886 556677889999999999999988777655566666667895 5556654321121 24677
Q ss_pred cccCH
Q 020984 174 PVITP 178 (319)
Q Consensus 174 PvlTP 178 (319)
|.+.+
T Consensus 81 p~~G~ 85 (299)
T PRK14571 81 RYTGS 85 (299)
T ss_pred CccCC
Confidence 77744
No 62
>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=57.49 E-value=25 Score=30.50 Aligned_cols=61 Identities=15% Similarity=0.184 Sum_probs=45.5
Q ss_pred CCEEEEEEcCCCccCcHHHHHHHHHHHHHhCC---cEEEEEcCCCC-----HHhhcCCCCCCEEEEecC
Q 020984 100 ANIIGVLVGTLGVAGYLHMIHQMKELITKAGK---KAYTLVMGKPN-----PAKLANFPECDVFINVSC 160 (319)
Q Consensus 100 a~~iGIivgTl~~q~~~~i~~~l~~ll~~~Gk---k~y~i~vg~in-----~~KLaNf~eID~fV~iaC 160 (319)
.-+||||.+.....---.+++...+.|+.+|- ...++.|--.. ..+|++..++|++|.++|
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 45799999886555555666667788889986 66777766544 356777778999999999
No 63
>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=57.38 E-value=15 Score=33.19 Aligned_cols=59 Identities=15% Similarity=0.126 Sum_probs=40.2
Q ss_pred EEEEEEcCCCccCcHHHHHHHHHHHHHhCCcEEEEEcCCCCHHh----hcCC--CCCCEEEEecCC
Q 020984 102 IIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAK----LANF--PECDVFINVSCA 161 (319)
Q Consensus 102 ~iGIivgTl~~q~~~~i~~~l~~ll~~~Gkk~y~i~vg~in~~K----LaNf--~eID~fV~iaCP 161 (319)
+||+|+..+....+..+++.+++.++++|.+..+.. ..-++++ |.++ ..+|++|+.+|.
T Consensus 1 ~igv~~~~~~~~~~~~~~~~i~~~~~~~g~~v~~~~-~~~~~~~~~~~i~~~~~~~~Dgiii~~~~ 65 (282)
T cd06318 1 KIGFSQYTLNSPFFAALTEAAKAHAKALGYELISTD-AQGDLTKQIADVEDLLTRGVNVLIINPVD 65 (282)
T ss_pred CeeEEeccccCHHHHHHHHHHHHHHHHcCCEEEEEc-CCCCHHHHHHHHHHHHHcCCCEEEEecCC
Confidence 478888887767777888899999999887754433 2334432 2222 268988887764
No 64
>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=56.97 E-value=39 Score=31.51 Aligned_cols=62 Identities=15% Similarity=0.233 Sum_probs=44.6
Q ss_pred cCCEEEEEEcCCCccCcHHHHHHHHHHHHHhCCcEEEEEcCCCCHHh----hcCC--CCCCEEEEecCC
Q 020984 99 DANIIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAK----LANF--PECDVFINVSCA 161 (319)
Q Consensus 99 ~a~~iGIivgTl~~q~~~~i~~~l~~ll~~~Gkk~y~i~vg~in~~K----LaNf--~eID~fV~iaCP 161 (319)
..++||+++..+.-..+..++..+++.++++|....+... .-++++ +..+ ..+|.+|++++.
T Consensus 58 ~~~~Igvv~~~~~~~f~~~l~~~i~~~~~~~g~~~~i~~~-~~~~~~~~~~~~~l~~~~vdGiIi~~~~ 125 (329)
T TIGR01481 58 RTTTVGVIIPDISNIYYAELARGIEDIATMYKYNIILSNS-DEDPEKEVQVLNTLLSKQVDGIIFMGGT 125 (329)
T ss_pred CCCEEEEEeCCCCchhHHHHHHHHHHHHHHcCCEEEEEeC-CCCHHHHHHHHHHHHhCCCCEEEEeCCC
Confidence 4679999998877677888999999999999987655433 233332 1122 269999998764
No 65
>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=56.45 E-value=25 Score=31.16 Aligned_cols=60 Identities=18% Similarity=0.255 Sum_probs=39.3
Q ss_pred EEEEEEcCCCccCcHHHHHHHHHHHHHhCCcEEEEEcCCCC-HH-hhcCC--CCCCEEEEecCC
Q 020984 102 IIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPN-PA-KLANF--PECDVFINVSCA 161 (319)
Q Consensus 102 ~iGIivgTl~~q~~~~i~~~l~~ll~~~Gkk~y~i~vg~in-~~-KLaNf--~eID~fV~iaCP 161 (319)
+||+|+....-..+..+++.+.+.+++.|.+..++....-. .. -+.++ ..+|.+|+.+|.
T Consensus 1 ~I~~i~~~~~~~~~~~~~~~i~~~~~~~g~~~~~~~~~~~~~~~~~i~~~~~~~vdgiii~~~~ 64 (266)
T cd06278 1 LIGVVVADLDNPFYSELLEALSRALQARGYQPLLINTDDDEDLDAALRQLLQYRVDGVIVTSGT 64 (266)
T ss_pred CEEEEeCCCCCchHHHHHHHHHHHHHHCCCeEEEEcCCCCHHHHHHHHHHHHcCCCEEEEecCC
Confidence 47888877665667778888888888888876555444221 11 11122 268988888774
No 66
>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=56.42 E-value=24 Score=31.52 Aligned_cols=58 Identities=17% Similarity=0.193 Sum_probs=38.8
Q ss_pred EEEEEEcCCCccCcHHHHHHHHHHHHHhCCcEEEEEcCCCCHHh----hcCC--CCCCEEEEecC
Q 020984 102 IIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAK----LANF--PECDVFINVSC 160 (319)
Q Consensus 102 ~iGIivgTl~~q~~~~i~~~l~~ll~~~Gkk~y~i~vg~in~~K----LaNf--~eID~fV~iaC 160 (319)
+||||+..+....+..+++.+++.+++.|.+..++... -++++ +.++ ..+|..|+.++
T Consensus 1 ~i~vi~~~~~~~~~~~~~~gi~~~~~~~g~~~~~~~~~-~~~~~~~~~i~~l~~~~~dgiii~~~ 64 (270)
T cd06296 1 LIGLVFPDLDSPWASEVLRGVEEAAAAAGYDVVLSESG-RRTSPERQWVERLSARRTDGVILVTP 64 (270)
T ss_pred CeEEEECCCCCccHHHHHHHHHHHHHHcCCeEEEecCC-CchHHHHHHHHHHHHcCCCEEEEecC
Confidence 47888888777788888889988888888776554433 22321 1122 25888887665
No 67
>PRK10653 D-ribose transporter subunit RbsB; Provisional
Probab=56.16 E-value=23 Score=32.71 Aligned_cols=63 Identities=17% Similarity=0.199 Sum_probs=45.1
Q ss_pred ccCCEEEEEEcCCCccCcHHHHHHHHHHHHHhCCcEEEEEcCCCCHHhhc----CC--CCCCEEEEecCC
Q 020984 98 KDANIIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKLA----NF--PECDVFINVSCA 161 (319)
Q Consensus 98 ~~a~~iGIivgTl~~q~~~~i~~~l~~ll~~~Gkk~y~i~vg~in~~KLa----Nf--~eID~fV~iaCP 161 (319)
++.+++|+|+..+.-..+..++..+++.++++|....++... -++++.. ++ ..+|++|+.++.
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 357899999998877778899999999999999887665433 2343222 22 268888876643
No 68
>cd06284 PBP1_LacI_like_6 Ligand-binding domain of an uncharacterized transcription regulator from Actinobacillus succinogenes and its close homologs from other bacteria. This group includes the ligand-binding domain of an uncharacterized transcription regulator from Actinobacillus succinogenes and its close homologs from other bacteria. This group belongs to the the LacI-GalR family repressors and are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding.
Probab=55.95 E-value=36 Score=30.17 Aligned_cols=58 Identities=16% Similarity=0.207 Sum_probs=42.2
Q ss_pred EEEEEcCCCccCcHHHHHHHHHHHHHhCCcEEEEEcCCCCHHhhcC----C--CCCCEEEEecCC
Q 020984 103 IGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKLAN----F--PECDVFINVSCA 161 (319)
Q Consensus 103 iGIivgTl~~q~~~~i~~~l~~ll~~~Gkk~y~i~vg~in~~KLaN----f--~eID~fV~iaCP 161 (319)
||+|+.++.-..+..+++.+++.++++|....++.. .-++++... + ..+|++++..|.
T Consensus 2 i~~v~~~~~~~~~~~~~~~i~~~~~~~g~~~~~~~~-~~~~~~~~~~~~~~~~~~vdgiii~~~~ 65 (267)
T cd06284 2 ILVLVPDIANPFFSEILKGIEDEAREAGYGVLLGDT-RSDPEREQEYLDLLRRKQADGIILLDGS 65 (267)
T ss_pred EEEEECCCCCccHHHHHHHHHHHHHHcCCeEEEecC-CCChHHHHHHHHHHHHcCCCEEEEecCC
Confidence 788888888788888999999999999988765543 345544322 2 268998887764
No 69
>COG0041 PurE Phosphoribosylcarboxyaminoimidazole (NCAIR) mutase [Nucleotide transport and metabolism]
Probab=55.54 E-value=30 Score=30.78 Aligned_cols=60 Identities=18% Similarity=0.325 Sum_probs=45.5
Q ss_pred EEEEEEcCCCccCcHHHHHHHHHHHHHhCCcEEEEEcC-CCCHHhhcCCC----CCCEEEEecCCCcc
Q 020984 102 IIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMG-KPNPAKLANFP----ECDVFINVSCAQTA 164 (319)
Q Consensus 102 ~iGIivgTl~~q~~~~i~~~l~~ll~~~Gkk~y~i~vg-~in~~KLaNf~----eID~fV~iaCPr~s 164 (319)
.+|||+|+ +.-+++++..-+.|++-|..+-.-+++ .=+|++|..|. +-++=|+||+--.+
T Consensus 4 ~V~IIMGS---~SD~~~mk~Aa~~L~~fgi~ye~~VvSAHRTPe~m~~ya~~a~~~g~~viIAgAGgA 68 (162)
T COG0041 4 KVGIIMGS---KSDWDTMKKAAEILEEFGVPYEVRVVSAHRTPEKMFEYAEEAEERGVKVIIAGAGGA 68 (162)
T ss_pred eEEEEecC---cchHHHHHHHHHHHHHcCCCeEEEEEeccCCHHHHHHHHHHHHHCCCeEEEecCcch
Confidence 79999999 567888899999999999998766665 78999998775 23333555555443
No 70
>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=54.95 E-value=27 Score=29.25 Aligned_cols=57 Identities=12% Similarity=0.091 Sum_probs=36.0
Q ss_pred EEEEEEcCCCccCcHHHHHHHHHHHHHhCCcEE-EEEcCCCCHHhhcCCCCCCEEEEecCC
Q 020984 102 IIGVLVGTLGVAGYLHMIHQMKELITKAGKKAY-TLVMGKPNPAKLANFPECDVFINVSCA 161 (319)
Q Consensus 102 ~iGIivgTl~~q~~~~i~~~l~~ll~~~Gkk~y-~i~vg~in~~KLaNf~eID~fV~iaCP 161 (319)
++.||.+|.. -+...+++.|.+.|...|.++- ++-+.+++.. ..++.+.|+ |+++||
T Consensus 2 ~i~IiY~S~t-GnTe~iA~~ia~~l~~~g~~v~~~~~~~~~~~~-~~~~~~~d~-iilgs~ 59 (140)
T TIGR01754 2 RILLAYLSLS-GNTEEVAFMIQDYLQKDGHEVDILHRIGTLADA-PLDPENYDL-VFLGTW 59 (140)
T ss_pred eEEEEEECCC-ChHHHHHHHHHHHHhhCCeeEEecccccccccC-cCChhhCCE-EEEEcC
Confidence 4688999965 3567889999999998887654 2223433221 123445676 555555
No 71
>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=54.43 E-value=32 Score=30.57 Aligned_cols=59 Identities=19% Similarity=0.196 Sum_probs=44.2
Q ss_pred EEEEEEcCCCccCcHHHHHHHHHHHHHhCCcEEEEEcCCCCHHhhc----CC--CCCCEEEEecCC
Q 020984 102 IIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKLA----NF--PECDVFINVSCA 161 (319)
Q Consensus 102 ~iGIivgTl~~q~~~~i~~~l~~ll~~~Gkk~y~i~vg~in~~KLa----Nf--~eID~fV~iaCP 161 (319)
+||+|+.......+..+++.+++.+++.|....++. ..-++++.. .+ ..+|++++..|.
T Consensus 1 ~i~~i~~~~~~~~~~~i~~gi~~~~~~~g~~~~~~~-~~~~~~~~~~~i~~l~~~~vdgiii~~~~ 65 (260)
T cd06286 1 TIGVVLPYINHPYFSQLVDGIEKAALKHGYKVVLLQ-TNYDKEKELEYLELLKTKQVDGLILCSRE 65 (260)
T ss_pred CEEEEeCCCCCchHHHHHHHHHHHHHHcCCEEEEEe-CCCChHHHHHHHHHHHHcCCCEEEEeCCC
Confidence 589999988878888999999999999998876554 344554322 11 269999998774
No 72
>PRK14095 pgi glucose-6-phosphate isomerase; Provisional
Probab=52.65 E-value=95 Score=32.75 Aligned_cols=51 Identities=12% Similarity=0.046 Sum_probs=29.3
Q ss_pred cCCEEEEEEcCCCccCcHH--HHHHHHHHHHHhCC--cEEEEEcCCCCHHhhcCCC
Q 020984 99 DANIIGVLVGTLGVAGYLH--MIHQMKELITKAGK--KAYTLVMGKPNPAKLANFP 150 (319)
Q Consensus 99 ~a~~iGIivgTl~~q~~~~--i~~~l~~ll~~~Gk--k~y~i~vg~in~~KLaNf~ 150 (319)
+..+.-+||.++++..--. -...+++.++++|. ....+.+.. +..+|+.|.
T Consensus 202 dpe~TLfiviSKSGtT~ETl~n~~~~r~wl~~~G~~~~~h~VaVT~-~~s~l~~~~ 256 (533)
T PRK14095 202 DLAKTLFIVVSKSGTTLETAANEEFVRDALKKAGLDYKKHFIAVTS-EGSPMDDES 256 (533)
T ss_pred CcccEEEEEEeCCCCCHHHHHHHHHHHHHHHHcCccccceEEEEEC-CchHHHhhc
Confidence 5567778888887643332 23345677777772 124444444 555677663
No 73
>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=52.46 E-value=29 Score=30.98 Aligned_cols=59 Identities=19% Similarity=0.235 Sum_probs=42.0
Q ss_pred EEEEEEcCCCccCcHHHHHHHHHHHHHhCCcEEEEEcCCCCHHhhc----CCC--CCCEEEEecCC
Q 020984 102 IIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKLA----NFP--ECDVFINVSCA 161 (319)
Q Consensus 102 ~iGIivgTl~~q~~~~i~~~l~~ll~~~Gkk~y~i~vg~in~~KLa----Nf~--eID~fV~iaCP 161 (319)
+||+|+..+.-..+..+++.+++.++++|....++. ..-++++.. ++. .+|.+++.+|.
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 478999887777777889999999999997765543 345554332 221 58999998774
No 74
>COG0716 FldA Flavodoxins [Energy production and conversion]
Probab=52.32 E-value=51 Score=28.08 Aligned_cols=59 Identities=10% Similarity=-0.028 Sum_probs=42.1
Q ss_pred CEEEEEEcCCCccCcHHHHHHHHHHHHHhCCcEEEEEcCCCCHHhhcCCCCCCEEEEecCCCc
Q 020984 101 NIIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKLANFPECDVFINVSCAQT 163 (319)
Q Consensus 101 ~~iGIivgTl~~q~~~~i~~~l~~ll~~~Gkk~y~i~vg~in~~KLaNf~eID~fV~iaCPr~ 163 (319)
.+++|+.+|.. -+...++++|++.|.+.|.+.-+..........+ ...|.+++..++-.
T Consensus 2 ~ki~Ivy~S~t-GnTe~vA~~i~~~l~~~~~~~~~~~~~~~~~~~~---~~~d~~~~g~~t~~ 60 (151)
T COG0716 2 MKILIVYGSRT-GNTEKVAEIIAEELGADGFEVDIDIRPGIKDDLL---ESYDELLLGTPTWG 60 (151)
T ss_pred CeEEEEEEcCC-CcHHHHHHHHHHHhccCCceEEEeecCCcchhhh---ccCCEEEEEeCCCC
Confidence 47899999986 5677899999999999998884444433433333 25677777766654
No 75
>PRK09271 flavodoxin; Provisional
Probab=51.84 E-value=55 Score=28.17 Aligned_cols=58 Identities=12% Similarity=0.059 Sum_probs=38.5
Q ss_pred EEEEEEcCCCccCcHHHHHHHHHHHHHhCCcEEEEEcCCCCHHh-hcCCCCCCEEEEecCC
Q 020984 102 IIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAK-LANFPECDVFINVSCA 161 (319)
Q Consensus 102 ~iGIivgTl~~q~~~~i~~~l~~ll~~~Gkk~y~i~vg~in~~K-LaNf~eID~fV~iaCP 161 (319)
++.|+.+|.. -+...+++.|.+.|+..|.++-+.-+....... ...+.+.|+ |+++||
T Consensus 2 kv~IvY~S~t-GnTe~~A~~ia~~l~~~g~~v~~~~~~~~~~~~~~~~~~~~d~-vilgt~ 60 (160)
T PRK09271 2 RILLAYASLS-GNTREVAREIEERCEEAGHEVDWVETDVQTLAEYPLDPEDYDL-YLLGTW 60 (160)
T ss_pred eEEEEEEcCC-chHHHHHHHHHHHHHhCCCeeEEEecccccccccccCcccCCE-EEEECc
Confidence 5789999975 456789999999999999877555554433222 223445666 455555
No 76
>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=51.26 E-value=23 Score=32.12 Aligned_cols=60 Identities=12% Similarity=0.058 Sum_probs=40.9
Q ss_pred EEEEEEcCCCccCcHHHHHHHHHHHHHhCCcEEEEEcCCCCH--HhhcC-C--CCCCEEEEecCC
Q 020984 102 IIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNP--AKLAN-F--PECDVFINVSCA 161 (319)
Q Consensus 102 ~iGIivgTl~~q~~~~i~~~l~~ll~~~Gkk~y~i~vg~in~--~KLaN-f--~eID~fV~iaCP 161 (319)
+||+|+..+....+..+++.+.+.++++|....+........ +.+.+ + ..+|.+|+.++.
T Consensus 1 ~Igvi~p~~~~~~~~~~~~~i~~~~~~~gy~~~~~~~~~~~~~~~~~~~~l~~~~vdgvi~~~~~ 65 (269)
T cd06297 1 TISVLLPVVATEFYRRLLEGIEGALLEQRYDLALFPLLSLARLKRYLESTTLAYLTDGLLLASYD 65 (269)
T ss_pred CEEEEeCCCcChhHHHHHHHHHHHHHHCCCEEEEEeCCCcHHHHHHHHHHHHhcCCCEEEEecCc
Confidence 478888777666778888999999999888877765543211 11211 2 158998888764
No 77
>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=50.73 E-value=80 Score=25.13 Aligned_cols=68 Identities=19% Similarity=0.150 Sum_probs=47.1
Q ss_pred HHHhhccCCEEEEEEcCCCccCcHHHHHHHHHHHHHhCCcEEEEEcCCCCHHhhcCCCCCCEEEEecCCCcc
Q 020984 93 LVEKAKDANIIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKLANFPECDVFINVSCAQTA 164 (319)
Q Consensus 93 ~I~ka~~a~~iGIivgTl~~q~~~~i~~~l~~ll~~~Gkk~y~i~vg~in~~KLaNf~eID~fV~iaCPr~s 164 (319)
.++...+++++ +++|+ .....+++.++..++..|+.++.+.-.+....-+.+..+=|++|.++....+
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 34444566775 66666 4577899999999999999888764444444444456677888888877664
No 78
>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=50.45 E-value=8.9 Score=31.88 Aligned_cols=46 Identities=24% Similarity=0.200 Sum_probs=34.4
Q ss_pred HHHhhccCCEEEEEEcCCCccCcHHHHHHHHHHHHHhCCcEEEEEcCC
Q 020984 93 LVEKAKDANIIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGK 140 (319)
Q Consensus 93 ~I~ka~~a~~iGIivgTl~~q~~~~i~~~l~~ll~~~Gkk~y~i~vg~ 140 (319)
+.+..++|++-.||+|... .+....+.+++++++.|..+++-.+++
T Consensus 4 ~~~~L~~A~rP~il~G~g~--~~~~a~~~l~~lae~~~~Pv~~t~~~k 49 (137)
T PF00205_consen 4 AADLLSSAKRPVILAGRGA--RRSGAAEELRELAEKLGIPVATTPMGK 49 (137)
T ss_dssp HHHHHHH-SSEEEEE-HHH--HHTTCHHHHHHHHHHHTSEEEEEGGGT
T ss_pred HHHHHHhCCCEEEEEcCCc--ChhhHHHHHHHHHHHHCCCEEecCccc
Confidence 5667778999999999853 333566788899999999998887775
No 79
>PF03698 UPF0180: Uncharacterised protein family (UPF0180); InterPro: IPR005370 The members of this family are small uncharacterised proteins.
Probab=50.19 E-value=37 Score=26.85 Aligned_cols=56 Identities=18% Similarity=0.210 Sum_probs=37.5
Q ss_pred HHHHHHHHHhCCcEEEEEcCCCCHHhhcCCCCCCEEEEecCCCccccc-ccCCCCccc-----CHHHHH
Q 020984 120 HQMKELITKAGKKAYTLVMGKPNPAKLANFPECDVFINVSCAQTALLD-SKEFLAPVI-----TPFEAM 182 (319)
Q Consensus 120 ~~l~~ll~~~Gkk~y~i~vg~in~~KLaNf~eID~fV~iaCPr~sidd-~~~f~kPvl-----TP~El~ 182 (319)
..+++.|+++|+++..+--.. ++..+||.|+.+=..+-+-- ...+..||| ||.|..
T Consensus 11 s~v~~~L~~~GyeVv~l~~~~-------~~~~~daiVvtG~~~n~mg~~d~~~~~pVInA~G~T~eEI~ 72 (80)
T PF03698_consen 11 SNVKEALREKGYEVVDLENEQ-------DLQNVDAIVVTGQDTNMMGIQDTSTKVPVINASGLTAEEIV 72 (80)
T ss_pred hHHHHHHHHCCCEEEecCCcc-------ccCCcCEEEEECCCcccccccccccCceEEecCCCCHHHHH
Confidence 478899999998876554211 46689999999977664321 134566875 555543
No 80
>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=49.98 E-value=29 Score=31.19 Aligned_cols=55 Identities=13% Similarity=0.016 Sum_probs=33.0
Q ss_pred EEEEEEcCCCccCcHHHHHHHHHHHHH-hCCcEEEEEcCCCCHHhhcCCC--CCCEEEEec
Q 020984 102 IIGVLVGTLGVAGYLHMIHQMKELITK-AGKKAYTLVMGKPNPAKLANFP--ECDVFINVS 159 (319)
Q Consensus 102 ~iGIivgTl~~q~~~~i~~~l~~ll~~-~Gkk~y~i~vg~in~~KLaNf~--eID~fV~ia 159 (319)
+||+|+.+ .-..+..+++.+.+.+++ .|....+.. +.. ..-+..+. .+|.+++..
T Consensus 1 ~ig~i~~~-~~~~~~~~~~gi~~~~~~~~g~~~~~~~-~~~-~~~~~~l~~~~vdGiI~~~ 58 (265)
T cd01543 1 RVALLVET-SSSYGRGVLRGIARYAREHGPWSIYLEP-RGL-QEPLRWLKDWQGDGIIARI 58 (265)
T ss_pred CeEEEecc-cchhhHHHHHHHHHHHHhcCCeEEEEec-ccc-hhhhhhccccccceEEEEC
Confidence 47888874 345666888888888888 555543322 211 22222332 689888764
No 81
>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=49.80 E-value=63 Score=28.80 Aligned_cols=59 Identities=14% Similarity=0.204 Sum_probs=40.9
Q ss_pred EEEEEEcCCCccCcHHHHHHHHHHHHHhCCcEEEEEcCCCCHHhhc----CC--CCCCEEEEecCC
Q 020984 102 IIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKLA----NF--PECDVFINVSCA 161 (319)
Q Consensus 102 ~iGIivgTl~~q~~~~i~~~l~~ll~~~Gkk~y~i~vg~in~~KLa----Nf--~eID~fV~iaCP 161 (319)
+||+|+.......+..+++.+++.+++.|....++.. +-++++.. ++ ..+|.+|+.++.
T Consensus 1 ~igvi~~~~~~~~~~~~~~gi~~~~~~~g~~~~~~~~-~~~~~~~~~~i~~l~~~~vdgiii~~~~ 65 (269)
T cd06275 1 TIGMLVTTSTNPFFAEVVRGVEQYCYRQGYNLILCNT-EGDPERQRSYLRMLAQKRVDGLLVMCSE 65 (269)
T ss_pred CEEEEeCCCCcchHHHHHHHHHHHHHHcCCEEEEEeC-CCChHHHHHHHHHHHHcCCCEEEEecCC
Confidence 4889998876667778888999999998877654433 33454321 22 268999888764
No 82
>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=49.45 E-value=35 Score=30.29 Aligned_cols=60 Identities=13% Similarity=0.206 Sum_probs=44.0
Q ss_pred EEEEEEcCCCccCcHHHHHHHHHHHHHhCCcEEEEEcCCCCHHhhc----CC--CCCCEEEEecCCC
Q 020984 102 IIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKLA----NF--PECDVFINVSCAQ 162 (319)
Q Consensus 102 ~iGIivgTl~~q~~~~i~~~l~~ll~~~Gkk~y~i~vg~in~~KLa----Nf--~eID~fV~iaCPr 162 (319)
+||+|+.......+..+++.+.+.+++.|.+..++.. .-++++.. .+ ..+|+.+++++..
T Consensus 1 ~Ig~i~~~~~~~~~~~~~~gi~~~~~~~g~~~~~~~~-~~~~~~~~~~~~~l~~~~vdgiii~~~~~ 66 (268)
T cd01575 1 LVAVLVPSLSNSVFADVLQGISDVLEAAGYQLLLGNT-GYSPEREEELLRTLLSRRPAGLILTGLEH 66 (268)
T ss_pred CEEEEeCCCcchhHHHHHHHHHHHHHHcCCEEEEecC-CCCchhHHHHHHHHHHcCCCEEEEeCCCC
Confidence 4899998887788889999999999999988766443 44444322 11 2699999988653
No 83
>PRK10339 DNA-binding transcriptional repressor EbgR; Provisional
Probab=49.42 E-value=34 Score=32.08 Aligned_cols=58 Identities=12% Similarity=0.111 Sum_probs=40.2
Q ss_pred cCCEEEEEEc----CCCccCcHHHHHHHHHHHHHhCCcEEEEEcCCCCHHhhcCCCCCCEEEEecC
Q 020984 99 DANIIGVLVG----TLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKLANFPECDVFINVSC 160 (319)
Q Consensus 99 ~a~~iGIivg----Tl~~q~~~~i~~~l~~ll~~~Gkk~y~i~vg~in~~KLaNf~eID~fV~iaC 160 (319)
...++|||+. .+.-..+..+++.+.+.++++|....+..-.+ .+ .....+|.++++++
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 4568888874 45556677899999999999998765433221 11 12457999998774
No 84
>PRK11921 metallo-beta-lactamase/flavodoxin domain-containing protein; Provisional
Probab=49.29 E-value=51 Score=32.76 Aligned_cols=92 Identities=15% Similarity=0.156 Sum_probs=61.9
Q ss_pred EEEcCCCCccccccCcHHHHHHHHHHHHHhhccCCEEEEEEcCCCccCcHHHHHHHHHHHH--HhCCcEEEEEcCCCCHH
Q 020984 67 VRYDATEERLLTDVSQPLKILKRRYYLVEKAKDANIIGVLVGTLGVAGYLHMIHQMKELIT--KAGKKAYTLVMGKPNPA 144 (319)
Q Consensus 67 ~~yDP~s~~~~~e~~~~~k~l~~R~~~I~ka~~a~~iGIivgTl~~q~~~~i~~~l~~ll~--~~Gkk~y~i~vg~in~~ 144 (319)
-.+-|.-+.+.+. +..+.+. +|..-.+-+.-+++.||-.|.. -+...+++.+.+-++ ..|.++-++-+.+..++
T Consensus 217 ~~i~p~HG~i~~~--~~~~~~~-~Y~~~~~~~~~~kv~IvY~S~~-GnTe~mA~~ia~g~~~~~~g~~v~~~~~~~~~~~ 292 (394)
T PRK11921 217 DMICPSHGVIWRD--NPLQIVE-KYLEWAANYQENQVTILYDTMW-NSTRRMAEAIAEGIKKANKDVTVKLYNSAKSDKN 292 (394)
T ss_pred CEEEcCCccEEeC--CHHHHHH-HHHHHhhcCCcCcEEEEEECCc-hHHHHHHHHHHHHHhhcCCCCeEEEEECCCCCHH
Confidence 3455554444222 3444443 4555555555688999999975 456688899999888 67888888889999988
Q ss_pred hhcC-CCCCCEEEEecCCCc
Q 020984 145 KLAN-FPECDVFINVSCAQT 163 (319)
Q Consensus 145 KLaN-f~eID~fV~iaCPr~ 163 (319)
.+.+ +.+.|+ ++++||-.
T Consensus 293 ~i~~~~~~~d~-ii~GspT~ 311 (394)
T PRK11921 293 DIITEVFKSKA-ILVGSSTI 311 (394)
T ss_pred HHHHHHHhCCE-EEEECCCc
Confidence 8764 446777 55667753
No 85
>PF13964 Kelch_6: Kelch motif
Probab=48.83 E-value=36 Score=23.20 Aligned_cols=15 Identities=20% Similarity=0.410 Sum_probs=12.1
Q ss_pred CCCeEEEEcCCCCcc
Q 020984 62 NGCEIVRYDATEERL 76 (319)
Q Consensus 62 ~~~~v~~yDP~s~~~ 76 (319)
....+++|||.+++-
T Consensus 26 ~~~~v~~yd~~t~~W 40 (50)
T PF13964_consen 26 YSNDVERYDPETNTW 40 (50)
T ss_pred ccccEEEEcCCCCcE
Confidence 356799999999874
No 86
>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=48.53 E-value=34 Score=31.77 Aligned_cols=59 Identities=17% Similarity=0.151 Sum_probs=40.0
Q ss_pred EEEEEEcCCCccCcHHHHHHHHHHHHHhCCcEEEEEcCCCCHHhhc----CC--CCCCEEEEecC
Q 020984 102 IIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKLA----NF--PECDVFINVSC 160 (319)
Q Consensus 102 ~iGIivgTl~~q~~~~i~~~l~~ll~~~Gkk~y~i~vg~in~~KLa----Nf--~eID~fV~iaC 160 (319)
+||+|+.+..-..+..+++.+++.+++.|.+..++.-+.-++++-. ++ ..+|.+|+.+.
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 5788888777777778888888888888877655434444544322 22 25888888753
No 87
>COG2185 Sbm Methylmalonyl-CoA mutase, C-terminal domain/subunit (cobalamin-binding) [Lipid metabolism]
Probab=47.81 E-value=22 Score=31.10 Aligned_cols=57 Identities=21% Similarity=0.333 Sum_probs=41.4
Q ss_pred HHHhhccCCEEEEEEcCCCccCcHHHHHHHHHHHHHhCCcEEEEEc-CCCCHHhhcCCC
Q 020984 93 LVEKAKDANIIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVM-GKPNPAKLANFP 150 (319)
Q Consensus 93 ~I~ka~~a~~iGIivgTl~~q~~~~i~~~l~~ll~~~Gkk~y~i~v-g~in~~KLaNf~ 150 (319)
.+..|.+...=.|.++++. .++..++..+.+.|+++|.+..++++ |.|.++.+.+|.
T Consensus 55 ~v~aA~~~dv~vIgvSsl~-g~h~~l~~~lve~lre~G~~~i~v~~GGvip~~d~~~l~ 112 (143)
T COG2185 55 AVRAAVEEDVDVIGVSSLD-GGHLTLVPGLVEALREAGVEDILVVVGGVIPPGDYQELK 112 (143)
T ss_pred HHHHHHhcCCCEEEEEecc-chHHHHHHHHHHHHHHhCCcceEEeecCccCchhHHHHH
Confidence 3444544444456677775 78999999999999999999888554 578888765554
No 88
>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=47.57 E-value=37 Score=30.11 Aligned_cols=71 Identities=17% Similarity=0.277 Sum_probs=49.8
Q ss_pred EEEEEcCCCccCcHHHHHHHHHHHHHhCCcEEEEEcC-CCCHHhhcCCC------CCCEEEEecCCCcccc--cccCCCC
Q 020984 103 IGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMG-KPNPAKLANFP------ECDVFINVSCAQTALL--DSKEFLA 173 (319)
Q Consensus 103 iGIivgTl~~q~~~~i~~~l~~ll~~~Gkk~y~i~vg-~in~~KLaNf~------eID~fV~iaCPr~sid--d~~~f~k 173 (319)
+|||+|+ ..-+.+++...+.|++-|..+-+-+.+ .=+|++|..|. ++++||.+|==...+- -...-.+
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 567888999999999999987666655 66788888774 5787776665444432 2233456
Q ss_pred ccc
Q 020984 174 PVI 176 (319)
Q Consensus 174 Pvl 176 (319)
|||
T Consensus 78 PVI 80 (156)
T TIGR01162 78 PVI 80 (156)
T ss_pred CEE
Confidence 665
No 89
>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=47.35 E-value=1.3e+02 Score=25.42 Aligned_cols=88 Identities=8% Similarity=0.084 Sum_probs=42.2
Q ss_pred EEEEcCCcchHHHHHH-hcCCCeEEEEcCCCCccccccCcHHHHHHHHHHHHHhhccCCEEEEEEcCCCc------cCcH
Q 020984 44 LFWIGSDNSAFANVVL-TFNGCEIVRYDATEERLLTDVSQPLKILKRRYYLVEKAKDANIIGVLVGTLGV------AGYL 116 (319)
Q Consensus 44 i~~Ig~~~~~l~~l~l-~~~~~~v~~yDP~s~~~~~e~~~~~k~l~~R~~~I~ka~~a~~iGIivgTl~~------q~~~ 116 (319)
|+|||+-.+..--.+. .++...++ | .-+. -+...-+..|......+.....+-|.+||--. +.+.
T Consensus 2 i~~~g~s~~~~w~~~~~~~~~~~v~--N---~Gi~---G~~~~~~~~~~~~~~~~~~p~~vvi~~G~ND~~~~~~~~~~~ 73 (171)
T cd04502 2 ILFYGSSSIRLWDTLADDLAPLPVV--N---RGFG---GSTLADCLHYFDRLVLPYQPRRVVLYAGDNDLASGRTPEEVL 73 (171)
T ss_pred EEEEcCchhcchhhHHHhCCCCcee--e---cCcc---cchHHHHHHHHHhhhccCCCCEEEEEEecCcccCCCCHHHHH
Confidence 7899988765433222 23332221 1 1110 11223344555555455577888888888442 2233
Q ss_pred HHHHHHHHHHHHhCCcEEEEEcC
Q 020984 117 HMIHQMKELITKAGKKAYTLVMG 139 (319)
Q Consensus 117 ~i~~~l~~ll~~~Gkk~y~i~vg 139 (319)
.-++.+-+.+++++.++.+++++
T Consensus 74 ~~~~~lv~~i~~~~~~~~iil~~ 96 (171)
T cd04502 74 RDFRELVNRIRAKLPDTPIAIIS 96 (171)
T ss_pred HHHHHHHHHHHHHCCCCcEEEEE
Confidence 33444444455554444444443
No 90
>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=46.30 E-value=25 Score=31.25 Aligned_cols=62 Identities=15% Similarity=0.133 Sum_probs=45.3
Q ss_pred HHhhccCCEEEEEEcCCCccCcHHHHHHHHHHHHHhCCcEEEEEcCCCCHHhhcCCC--CCCEEEEec
Q 020984 94 VEKAKDANIIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKLANFP--ECDVFINVS 159 (319)
Q Consensus 94 I~ka~~a~~iGIivgTl~~q~~~~i~~~l~~ll~~~Gkk~y~i~vg~in~~KLaNf~--eID~fV~ia 159 (319)
+++|.++..=+|.+-+. .++.++++.+.|+..+.++.+.+.|.||++.+..|. .||++++-+
T Consensus 93 ~~ea~~~g~d~I~lD~~----~~~~~~~~v~~l~~~~~~v~ie~SGGI~~~ni~~ya~~gvD~isvg~ 156 (169)
T PF01729_consen 93 AEEALEAGADIIMLDNM----SPEDLKEAVEELRELNPRVKIEASGGITLENIAEYAKTGVDVISVGS 156 (169)
T ss_dssp HHHHHHTT-SEEEEES-----CHHHHHHHHHHHHHHTTTSEEEEESSSSTTTHHHHHHTT-SEEEECH
T ss_pred HHHHHHhCCCEEEecCc----CHHHHHHHHHHHhhcCCcEEEEEECCCCHHHHHHHHhcCCCEEEcCh
Confidence 34455566667777775 457777777888888888999999999999999886 578766543
No 91
>PF12641 Flavodoxin_3: Flavodoxin domain
Probab=46.23 E-value=95 Score=27.30 Aligned_cols=81 Identities=20% Similarity=0.272 Sum_probs=45.4
Q ss_pred CCceeEEEEcCC------cchHHHHHHhcCCCeEEEEcCCCCccccccCc-HHHHHHHHHHHHHhhcc--CCEEEEEEcC
Q 020984 39 MEEHLLFWIGSD------NSAFANVVLTFNGCEIVRYDATEERLLTDVSQ-PLKILKRRYYLVEKAKD--ANIIGVLVGT 109 (319)
Q Consensus 39 ~~~~~i~~Ig~~------~~~l~~l~l~~~~~~v~~yDP~s~~~~~e~~~-~~k~l~~R~~~I~ka~~--a~~iGIivgT 109 (319)
+++|.++|||.. ...+..++-...+++|+.|-..-.-- ..+ ..+++. .++++.+ ...+|--+.-
T Consensus 37 ~~~yD~i~lG~w~d~G~~d~~~~~fl~~l~~KkV~lF~T~G~~~---~s~~~~~~~~----~~~~~~~~~~~~lg~f~Cq 109 (160)
T PF12641_consen 37 LEDYDLIFLGFWIDKGTPDKDMKEFLKKLKGKKVALFGTAGAGP---DSEYAKKILK----NVEALLPKGNEILGTFMCQ 109 (160)
T ss_pred CCCCCEEEEEcCccCCCCCHHHHHHHHHccCCeEEEEEecCCCC---chHHHHHHHH----HHHHhhccCCeecceEEeC
Confidence 788999999954 23355566666677888887654321 111 222332 2333322 4444544443
Q ss_pred CCccCcHHHHHHHHHHHHH
Q 020984 110 LGVAGYLHMIHQMKELITK 128 (319)
Q Consensus 110 l~~q~~~~i~~~l~~ll~~ 128 (319)
|+-.+.+++++++++..
T Consensus 110 --Gk~~~~~~e~~~~~~~~ 126 (160)
T PF12641_consen 110 --GKMDPKVIEKYKKMLPK 126 (160)
T ss_pred --CcCCHHHHHHHHhccCC
Confidence 45566778777776443
No 92
>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=46.16 E-value=47 Score=29.59 Aligned_cols=59 Identities=12% Similarity=0.196 Sum_probs=35.4
Q ss_pred EEEEEEcC-----CCccCcHHHHHHHHHHHHHhCCcEEEEEcCCCC--HHhhcC-C--CCCCEEEEecC
Q 020984 102 IIGVLVGT-----LGVAGYLHMIHQMKELITKAGKKAYTLVMGKPN--PAKLAN-F--PECDVFINVSC 160 (319)
Q Consensus 102 ~iGIivgT-----l~~q~~~~i~~~l~~ll~~~Gkk~y~i~vg~in--~~KLaN-f--~eID~fV~iaC 160 (319)
+||+|+.. +.-..+..+++.+++.+++.|.+..+....... ...+.+ + ..+|++|+++.
T Consensus 1 ~igli~p~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~dgiii~~~ 69 (270)
T cd06294 1 TIGVVLPPSADEAFQNPFFIEVLRGISAVANENGYDISLATGKNEEELLEEVKKMIQQKRVDGFILLYS 69 (270)
T ss_pred CEEEEeCCccccCcCCCCHHHHHHHHHHHHHHCCCEEEEecCCCcHHHHHHHHHHHHHcCcCEEEEecC
Confidence 47888865 344566678888888888888776543322211 112222 1 24888888764
No 93
>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=45.90 E-value=48 Score=30.03 Aligned_cols=49 Identities=18% Similarity=0.191 Sum_probs=37.3
Q ss_pred CEEEEEEcCCCccCcHHHHHHHHHHHHHhCCcEEEEEcCCC--CHHhhcCCC
Q 020984 101 NIIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKP--NPAKLANFP 150 (319)
Q Consensus 101 ~~iGIivgTl~~q~~~~i~~~l~~ll~~~Gkk~y~i~vg~i--n~~KLaNf~ 150 (319)
+.+-|++|+.+--.-.. +..+.+.|+++|.++++|.+|+. |.+||..|-
T Consensus 108 ~rivi~v~S~~~~d~~~-i~~~~~~lkk~~I~v~vI~~G~~~~~~~~l~~~~ 158 (187)
T cd01452 108 QRIVAFVGSPIEEDEKD-LVKLAKRLKKNNVSVDIINFGEIDDNTEKLTAFI 158 (187)
T ss_pred ceEEEEEecCCcCCHHH-HHHHHHHHHHcCCeEEEEEeCCCCCCHHHHHHHH
Confidence 48889999986544444 44566778899999999999954 678888773
No 94
>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=45.41 E-value=54 Score=29.28 Aligned_cols=59 Identities=22% Similarity=0.213 Sum_probs=41.4
Q ss_pred EEEEEEcCCCccCcHHHHHHHHHHHHHhCCcEEEEEcCCCCHHhhc----CC--CCCCEEEEecCC
Q 020984 102 IIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKLA----NF--PECDVFINVSCA 161 (319)
Q Consensus 102 ~iGIivgTl~~q~~~~i~~~l~~ll~~~Gkk~y~i~vg~in~~KLa----Nf--~eID~fV~iaCP 161 (319)
+||+|+.......+..+++.+.+.+++.|.+..++ .+.-++++.. .+ ..+|.+++..|-
T Consensus 1 ~igvi~p~~~~~~~~~~~~gi~~~~~~~~~~~~~~-~~~~~~~~~~~~i~~l~~~~~dgiii~~~~ 65 (265)
T cd06285 1 TIGVLVPRLTDTVMATMYEGIEEAAAERGYSTFVA-NTGDNPDAQRRAIEMLLDRRVDGLILGDAR 65 (265)
T ss_pred CEEEEeCCCCCccHHHHHHHHHHHHHHCCCEEEEE-eCCCCHHHHHHHHHHHHHcCCCEEEEecCC
Confidence 48999988877778899999999999999886443 4444444321 11 168998887654
No 95
>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=45.00 E-value=29 Score=31.33 Aligned_cols=60 Identities=15% Similarity=0.106 Sum_probs=37.5
Q ss_pred EEEEEEcCCCccCcHHHHHHHHHHHHHhCCcEEEEEc---CCCCHHh----hcCCC-CCCEEEEecCC
Q 020984 102 IIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVM---GKPNPAK----LANFP-ECDVFINVSCA 161 (319)
Q Consensus 102 ~iGIivgTl~~q~~~~i~~~l~~ll~~~Gkk~y~i~v---g~in~~K----LaNf~-eID~fV~iaCP 161 (319)
+||+|+....-..+..+++.+.+.++++|...+++.. ..-++++ |.++. .+|++|+++..
T Consensus 1 ~ig~v~~~~~~~~~~~~~~~i~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~i~~~~~~vdgiii~~~~ 68 (275)
T cd06307 1 RLGFLLPKGSNAFYRELAAALEAAAAAFPDARIRVRIHFVESFDPAALAAALLRLGARSDGVALVAPD 68 (275)
T ss_pred CeEEEeCCCCChHHHHHHHHHHHHHhhhhccCceEEEEEccCCCHHHHHHHHHHHHhcCCEEEEeCCC
Confidence 4788887776666777888888888887766555432 2223322 22222 68888777654
No 96
>cd00300 LDH_like L-lactate dehydrogenase-like enzymes. Members of this subfamily are tetrameric NAD-dependent 2-hydroxycarboxylate dehydrogenases including LDHs, L-2-hydroxyisocaproate dehydrogenases (L-HicDH), and LDH-like malate dehydrogenases (MDH). Dehydrogenases catalyze the conversion of carbonyl compounds to alcohols or amino acids. LDHs catalyze the last step of glycolysis in which pyruvate is converted to L-lactate. Vertebrate LDHs are non-allosteric, but some bacterial LDHs are activated by an allosteric effector such as fructose-1,6-bisphosphate. L-HicDH catalyzes the conversion of a variety of 2-oxo carboxylic acids with medium-sized aliphatic or aromatic side chains. MDH is one of the key enzymes in the citric acid cycle, facilitating both the conversion of malate to oxaloacetate and replenishing levels of oxalacetate by reductive carboxylation of pyruvate. The LDH-like subfamily is part of the NAD(P)-binding Rossmann fold superfamily, which includes a wide variety of prot
Probab=44.88 E-value=71 Score=30.59 Aligned_cols=96 Identities=24% Similarity=0.245 Sum_probs=58.4
Q ss_pred EEcCCc--chHHHHHHhcCC-CeEEEEcCCCCccccccCcHHHHHHH----HH---HHHHhhccCCEEEEEEcCCCccC-
Q 020984 46 WIGSDN--SAFANVVLTFNG-CEIVRYDATEERLLTDVSQPLKILKR----RY---YLVEKAKDANIIGVLVGTLGVAG- 114 (319)
Q Consensus 46 ~Ig~~~--~~l~~l~l~~~~-~~v~~yDP~s~~~~~e~~~~~k~l~~----R~---~~I~ka~~a~~iGIivgTl~~q~- 114 (319)
-||.|. .++...++..+- ..+..||+...+..-...+...+... +. .-.+.+++|..+-|..|+....+
T Consensus 3 iiGaG~VG~~~a~~l~~~~~~~el~l~D~~~~~~~g~~~DL~~~~~~~~~~~i~~~~~~~~l~~aDiVIitag~p~~~~~ 82 (300)
T cd00300 3 IIGAGNVGAAVAFALIAKGLASELVLVDVNEEKAKGDALDLSHASAFLATGTIVRGGDYADAADADIVVITAGAPRKPGE 82 (300)
T ss_pred EECCCHHHHHHHHHHHhcCCCCEEEEEeCCccHHHHHHHhHHHhccccCCCeEEECCCHHHhCCCCEEEEcCCCCCCCCC
Confidence 355554 444444444443 46999999766543222222222111 11 11357778899888888754333
Q ss_pred --------cHHHHHHHHHHHHHhCCcEEEEEcCCC
Q 020984 115 --------YLHMIHQMKELITKAGKKAYTLVMGKP 141 (319)
Q Consensus 115 --------~~~i~~~l~~ll~~~Gkk~y~i~vg~i 141 (319)
+..+++.+-+.|++++.+..+|+++++
T Consensus 83 ~R~~l~~~n~~i~~~~~~~i~~~~p~~~viv~sNP 117 (300)
T cd00300 83 TRLDLINRNAPILRSVITNLKKYGPDAIILVVSNP 117 (300)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHhCCCeEEEEccCh
Confidence 556777788889999999999999943
No 97
>PRK05452 anaerobic nitric oxide reductase flavorubredoxin; Provisional
Probab=44.46 E-value=1e+02 Score=31.75 Aligned_cols=109 Identities=9% Similarity=0.127 Sum_probs=67.8
Q ss_pred EEEcCCCCccccccCcHHHHHHHHHHHHHhhccCCEEEEEEcCCCccCcHHHHHHHHHHHHHh--CCcEEEEEcCCCCHH
Q 020984 67 VRYDATEERLLTDVSQPLKILKRRYYLVEKAKDANIIGVLVGTLGVAGYLHMIHQMKELITKA--GKKAYTLVMGKPNPA 144 (319)
Q Consensus 67 ~~yDP~s~~~~~e~~~~~k~l~~R~~~I~ka~~a~~iGIivgTl~~q~~~~i~~~l~~ll~~~--Gkk~y~i~vg~in~~ 144 (319)
-.+-|.-+.+.+ .+..++++ +|....+-+..+++-||..|.. .+...+++.|.+-|++. |.++-++-+.+.+++
T Consensus 221 ~~i~p~HG~i~r--~~~~~~l~-~Y~~~~~~~~~~kv~IvY~S~~-GnTe~mA~~ia~gl~~~g~gv~v~~~~v~~~~~~ 296 (479)
T PRK05452 221 DMIATSHGVVWR--DNPTQIVE-LYLKWAADYQEDRITIFYDTMS-NNTRMMADAIAQGIAEVDPRVAVKIFNVARSDKN 296 (479)
T ss_pred CEEECCCCceEe--CCHHHHHH-HHHHHhhccCcCcEEEEEECCc-cHHHHHHHHHHHHHHhhCCCceEEEEECCCCCHH
Confidence 345555444433 23334443 3444443334577889999864 34568899999999987 567788889999988
Q ss_pred hhc-CCCCCCEEEEecCCCcccccccCCCCcccCHHHHHHh
Q 020984 145 KLA-NFPECDVFINVSCAQTALLDSKEFLAPVITPFEAMLA 184 (319)
Q Consensus 145 KLa-Nf~eID~fV~iaCPr~sidd~~~f~kPvlTP~El~vA 184 (319)
.|. .+.+.|+ |+++||=.- .+...|+...++....
T Consensus 297 ~i~~~~~~ad~-vilGspT~~----~~~~p~~~~fl~~l~~ 332 (479)
T PRK05452 297 EILTNVFRSKG-VLVGSSTMN----NVMMPKIAGLLEEITG 332 (479)
T ss_pred HHHhHHhhCCE-EEEECCccC----CcchHHHHHHHHHhhc
Confidence 875 4557785 778888641 2222355555555433
No 98
>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=44.41 E-value=74 Score=25.34 Aligned_cols=59 Identities=14% Similarity=0.122 Sum_probs=45.0
Q ss_pred EEEEEcCCCccCcHHHHHHHHHHHHHhCCcEEEEEc------CCCCHHhhcCCCCCCEEEEecCCCcc
Q 020984 103 IGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVM------GKPNPAKLANFPECDVFINVSCAQTA 164 (319)
Q Consensus 103 iGIivgTl~~q~~~~i~~~l~~ll~~~Gkk~y~i~v------g~in~~KLaNf~eID~fV~iaCPr~s 164 (319)
++|+.+.-|.....-+.+.|++.++++|.+..+-.- +.++.+. ..+.|.+|+++.....
T Consensus 2 ~~i~ac~~G~a~s~laa~~L~~aa~~~g~~~~ve~~~~~g~~~~l~~~~---i~~Ad~vi~~~~~~~~ 66 (96)
T cd05569 2 VAVTACPTGIAHTYMAAEALEKAAKKLGWEIKVETQGSLGIENELTAED---IAEADAVILAADVPVD 66 (96)
T ss_pred EEEEECCCchhHHHHHHHHHHHHHHHCCCeEEEEEecCcCccCcCCHHH---HhhCCEEEEecCCCCc
Confidence 577888888888888999999999999998664433 3344444 4467999999988753
No 99
>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=44.25 E-value=54 Score=28.55 Aligned_cols=75 Identities=21% Similarity=0.198 Sum_probs=0.0
Q ss_pred EEEEEEcCCCccCcHHHHHHHHHHHHHhCCcEEEEEcCCCCHHhhcCCC------CCCEEEEecCCCcc---cccccCCC
Q 020984 102 IIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKLANFP------ECDVFINVSCAQTA---LLDSKEFL 172 (319)
Q Consensus 102 ~iGIivgTl~~q~~~~i~~~l~~ll~~~Gkk~y~i~vg~in~~KLaNf~------eID~fV~iaCPr~s---idd~~~f~ 172 (319)
+||+|+....-..+..+++-+++.+++.|.+..++-.+. ++++....- .+|++|..+|.... ++....-.
T Consensus 1 ~ig~v~~~~~~~~~~~~~~g~~~~~~~~g~~l~~~~~~~-~~~~~~~~~~~~~~~~~d~ii~~~~~~~~~~~~~~l~~~~ 79 (264)
T cd01537 1 TIGVLVPDLDNPFFAQVLKGIEEAAKAAGYQVLLANSQN-DAEKQLSALENLIARGVDGIIIAPSDLTAPTIVKLARKAG 79 (264)
T ss_pred CeEEEEcCCCChHHHHHHHHHHHHHHHcCCeEEEEeCCC-CHHHHHHHHHHHHHcCCCEEEEecCCCcchhHHHHhhhcC
Q ss_pred CcccC
Q 020984 173 APVIT 177 (319)
Q Consensus 173 kPvlT 177 (319)
.|+|.
T Consensus 80 ip~v~ 84 (264)
T cd01537 80 IPVVL 84 (264)
T ss_pred CCEEE
No 100
>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=44.17 E-value=48 Score=29.90 Aligned_cols=60 Identities=10% Similarity=-0.048 Sum_probs=38.8
Q ss_pred EEEEEEcCC-CccCcHHHHHHHHHHHHHhCCcEEEEEcCCCCHHhhcC----C--CCCCEEEEecCC
Q 020984 102 IIGVLVGTL-GVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKLAN----F--PECDVFINVSCA 161 (319)
Q Consensus 102 ~iGIivgTl-~~q~~~~i~~~l~~ll~~~Gkk~y~i~vg~in~~KLaN----f--~eID~fV~iaCP 161 (319)
+||+|+..+ .-..+..+++.+++.++++|....++....-++++... + ..+|++|+.++.
T Consensus 1 ~i~~i~~~~~~~~~~~~~~~g~~~~~~~~g~~v~~~~~~~~~~~~~~~~i~~l~~~~vdgiii~~~~ 67 (271)
T cd06312 1 KIAFVTHGPAGDPFWTVVKNGAEDAAKDLGVDVEYRGPETFDVADMARLIEAAIAAKPDGIVVTIPD 67 (271)
T ss_pred CEEEecCCCCCCcHHHHHHHHHHHHHHHhCCEEEEECCCCCCHHHHHHHHHHHHHhCCCEEEEeCCC
Confidence 467777665 55666678888888888888776655544325543321 1 268888877653
No 101
>PRK11104 hemG protoporphyrinogen oxidase; Provisional
Probab=43.73 E-value=42 Score=29.63 Aligned_cols=55 Identities=5% Similarity=0.106 Sum_probs=38.3
Q ss_pred EEEEEEcCCCccCcHHHHHHHHHHHHHhCCcEEEEEcCCCCHHhhcCCCCCCEEEEecCCC
Q 020984 102 IIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKLANFPECDVFINVSCAQ 162 (319)
Q Consensus 102 ~iGIivgTl~~q~~~~i~~~l~~ll~~~Gkk~y~i~vg~in~~KLaNf~eID~fV~iaCPr 162 (319)
++.|+.+|.. -+...+++.|.+.|.. |..+-++-+.+.... ++.+.|+ |++++|=
T Consensus 2 kilIvY~S~~-G~T~~iA~~Ia~~l~~-g~~v~~~~~~~~~~~---~l~~yD~-vIlGspi 56 (177)
T PRK11104 2 KTLILYSSRD-GQTRKIASYIASELKE-GIQCDVVNLHRIEEP---DLSDYDR-VVIGASI 56 (177)
T ss_pred cEEEEEECCC-ChHHHHHHHHHHHhCC-CCeEEEEEhhhcCcc---CHHHCCE-EEEECcc
Confidence 4678888864 4456788999999987 877766666665433 4556787 6677763
No 102
>PRK12359 flavodoxin FldB; Provisional
Probab=43.48 E-value=84 Score=27.98 Aligned_cols=53 Identities=13% Similarity=0.273 Sum_probs=37.8
Q ss_pred EEEEEEcCCCccCcHHHHHHHHHHHHHhCCc-EEEEEcCCCCHHhhcCCCCCCEEEEecCCC
Q 020984 102 IIGVLVGTLGVAGYLHMIHQMKELITKAGKK-AYTLVMGKPNPAKLANFPECDVFINVSCAQ 162 (319)
Q Consensus 102 ~iGIivgTl~~q~~~~i~~~l~~ll~~~Gkk-~y~i~vg~in~~KLaNf~eID~fV~iaCPr 162 (319)
+++|+-+|.. -+...++++|++.+ |.. +-++-+.+..++.|.++ | +|+++||=
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 5799999976 45668888888766 433 55667777777766554 5 57888886
No 103
>PRK00061 ribH 6,7-dimethyl-8-ribityllumazine synthase; Provisional
Probab=43.47 E-value=64 Score=28.40 Aligned_cols=62 Identities=15% Similarity=0.132 Sum_probs=42.9
Q ss_pred CCEEEEEEcCCCccCcHHHHHHHHHHHHHhCC---cEEEEEcCC---CC--HHhhcCCCCCCEEEEecCC
Q 020984 100 ANIIGVLVGTLGVAGYLHMIHQMKELITKAGK---KAYTLVMGK---PN--PAKLANFPECDVFINVSCA 161 (319)
Q Consensus 100 a~~iGIivgTl~~q~~~~i~~~l~~ll~~~Gk---k~y~i~vg~---in--~~KLaNf~eID~fV~iaCP 161 (319)
.-+|+||.+..-..-.-.+++...+.|++.|. ...++.|-- |- ..+|+.-.++|++|.++|-
T Consensus 12 ~~riaIV~s~~n~~i~~~l~~ga~~~l~~~gv~~~~i~v~~VPGa~EiP~a~~~l~~~~~~DavIalG~V 81 (154)
T PRK00061 12 GLRIGIVVARFNDFITDALLEGALDALKRHGVSEENIDVVRVPGAFEIPLAAKKLAESGKYDAVIALGAV 81 (154)
T ss_pred CCEEEEEEecCcHHHHHHHHHHHHHHHHHcCCCccceEEEECCCHHHHHHHHHHHHHcCCCCEEEEEeeE
Confidence 35899999886544444777777788999993 344444432 21 2467766789999999997
No 104
>PRK10727 DNA-binding transcriptional regulator GalR; Provisional
Probab=43.23 E-value=96 Score=29.24 Aligned_cols=62 Identities=15% Similarity=0.279 Sum_probs=44.0
Q ss_pred cCCEEEEEEcCCCccCcHHHHHHHHHHHHHhCCcEEEEEcCCCCHHh----hcCC--CCCCEEEEecCC
Q 020984 99 DANIIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAK----LANF--PECDVFINVSCA 161 (319)
Q Consensus 99 ~a~~iGIivgTl~~q~~~~i~~~l~~ll~~~Gkk~y~i~vg~in~~K----LaNf--~eID~fV~iaCP 161 (319)
..++||+|+..+.-..+..+++.+++.++++|....+.. +.-++++ +.++ ..+|.+|+.++.
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 468999999988777788999999999999997654432 2333322 2222 269999987653
No 105
>PRK10355 xylF D-xylose transporter subunit XylF; Provisional
Probab=42.66 E-value=59 Score=31.11 Aligned_cols=63 Identities=14% Similarity=0.183 Sum_probs=47.3
Q ss_pred cCCEEEEEEcCCCccCcHHHHHHHHHHHHHhCCcEEEEEcCCCCHHhhc----CCC--CCCEEEEecCCC
Q 020984 99 DANIIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKLA----NFP--ECDVFINVSCAQ 162 (319)
Q Consensus 99 ~a~~iGIivgTl~~q~~~~i~~~l~~ll~~~Gkk~y~i~vg~in~~KLa----Nf~--eID~fV~iaCPr 162 (319)
++.+||+++..+.-..+..+++-+++.++++|....+.. +.-++++.. ++. .+|.+|+.++..
T Consensus 24 ~~~~Ig~i~~~~~~~f~~~~~~gi~~~a~~~g~~l~i~~-~~~~~~~~~~~i~~l~~~~vDGiIi~~~~~ 92 (330)
T PRK10355 24 KEVKIGMAIDDLRLERWQKDRDIFVKKAESLGAKVFVQS-ANGNEETQMSQIENMINRGVDVLVIIPYNG 92 (330)
T ss_pred CCceEEEEecCCCchHHHHHHHHHHHHHHHcCCEEEEEC-CCCCHHHHHHHHHHHHHcCCCEEEEeCCCh
Confidence 478999999998888888999999999999998766543 333554332 222 799999987643
No 106
>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=42.63 E-value=47 Score=29.88 Aligned_cols=59 Identities=12% Similarity=0.054 Sum_probs=36.3
Q ss_pred EEEEEEcCCCccCcHHHHHHHHHHHHHhCCcEEEEEcC-CCCHHh-------hcCCCCCCEEEEecCC
Q 020984 102 IIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMG-KPNPAK-------LANFPECDVFINVSCA 161 (319)
Q Consensus 102 ~iGIivgTl~~q~~~~i~~~l~~ll~~~Gkk~y~i~vg-~in~~K-------LaNf~eID~fV~iaCP 161 (319)
+||+|+..+....+..+++.+++.++++|....++... .-++++ |..- .+|+.|+.++.
T Consensus 1 ~igvi~~~~~~~~~~~~~~gi~~~~~~~g~~~~~~~~~~~~~~~~~~~~i~~l~~~-~vdgiIi~~~~ 67 (275)
T cd06320 1 KYGVVLKTLSNEFWRSLKEGYENEAKKLGVSVDIQAAPSEGDQQGQLSIAENMINK-GYKGLLFSPIS 67 (275)
T ss_pred CeeEEEecCCCHHHHHHHHHHHHHHHHhCCeEEEEccCCCCCHHHHHHHHHHHHHh-CCCEEEECCCC
Confidence 37888877665666777888888888888765544432 223332 2122 57887765543
No 107
>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=42.61 E-value=51 Score=29.45 Aligned_cols=57 Identities=16% Similarity=-0.051 Sum_probs=36.7
Q ss_pred EEEEEEcCCCccCcHHHHHHHHHHHHHhCCcEEEEEcCCCCHHhhc----CC--CCCCEEEEec
Q 020984 102 IIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKLA----NF--PECDVFINVS 159 (319)
Q Consensus 102 ~iGIivgTl~~q~~~~i~~~l~~ll~~~Gkk~y~i~vg~in~~KLa----Nf--~eID~fV~ia 159 (319)
+||+|+..+.-..+..+++.+++.+++.|....++. +.-++++-. ++ ..+|++|+.+
T Consensus 1 ~Ig~i~~~~~~~~~~~~~~gi~~~~~~~g~~~~~~~-~~~~~~~~~~~l~~~~~~~vdgii~~~ 63 (273)
T cd06305 1 RIAVVRYGGSGDFDQAYLAGTKAEAEALGGDLRVYD-AGGDDAKQADQIDQAIAQKVDAIIIQH 63 (273)
T ss_pred CeEEEeecCCCcHHHHHHHHHHHHHHHcCCEEEEEC-CCCCHHHHHHHHHHHHHcCCCEEEEec
Confidence 478888776655666788888888888887755543 444554422 11 1688887765
No 108
>PRK09701 D-allose transporter subunit; Provisional
Probab=42.51 E-value=60 Score=30.46 Aligned_cols=63 Identities=11% Similarity=0.082 Sum_probs=42.7
Q ss_pred hccCCEEEEEEcCCCccCcHHHHHHHHHHHHHhCCcEEEEE-cCCCCHHh----hcCCC--CCCEEEEec
Q 020984 97 AKDANIIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLV-MGKPNPAK----LANFP--ECDVFINVS 159 (319)
Q Consensus 97 a~~a~~iGIivgTl~~q~~~~i~~~l~~ll~~~Gkk~y~i~-vg~in~~K----LaNf~--eID~fV~ia 159 (319)
|.-+.+||+|+..+.-..+..+++.+++.++++|....++. -+.-++++ |.+|- .+|.+|+.+
T Consensus 21 ~~~~~~Igvi~~~~~~~f~~~~~~gi~~~a~~~g~~v~~~~~~~~~~~~~~~~~i~~l~~~~vDgiIi~~ 90 (311)
T PRK09701 21 AFAAAEYAVVLKTLSNPFWVDMKKGIEDEAKTLGVSVDIFASPSEGDFQSQLQLFEDLSNKNYKGIAFAP 90 (311)
T ss_pred hccCCeEEEEeCCCCCHHHHHHHHHHHHHHHHcCCeEEEecCCCCCCHHHHHHHHHHHHHcCCCEEEEeC
Confidence 44567999999887666677889999999998887766553 22333332 33432 589887764
No 109
>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=42.02 E-value=86 Score=29.44 Aligned_cols=58 Identities=19% Similarity=0.244 Sum_probs=43.6
Q ss_pred EEEEEEcCCCccC--cHHHHHHHHHHHHHhCCcEEEEEcCCCC-------HHhhcC----CCCCCEEEEec
Q 020984 102 IIGVLVGTLGVAG--YLHMIHQMKELITKAGKKAYTLVMGKPN-------PAKLAN----FPECDVFINVS 159 (319)
Q Consensus 102 ~iGIivgTl~~q~--~~~i~~~l~~ll~~~Gkk~y~i~vg~in-------~~KLaN----f~eID~fV~ia 159 (319)
+||||.|..+-.. ++.....+.+-|++.|.+++.+.+.+.+ .+.+.. -.++|+.+.+.
T Consensus 1 ~~~~~~gg~s~e~~~s~~s~~~i~~al~~~g~~v~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~D~v~~~~ 71 (315)
T TIGR01205 1 RVAVLFGGKSAEHEISLVSAAAVLKALRDLGYDVYPVDIDKMGSWTYKDLPQLILELGALLEGIDVVFPVL 71 (315)
T ss_pred CEEEEeCCCCCCeeeeHHHHHHHHHHHhhcCCEEEEEeecCCccccccchHHHHhhccccCCCCCEEEEec
Confidence 4899999999755 5788889999999999999999988743 222322 24689877753
No 110
>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=41.99 E-value=77 Score=31.77 Aligned_cols=79 Identities=14% Similarity=0.140 Sum_probs=56.6
Q ss_pred cCCEEEEEEcCCCccCcHHHHHHHHHHHHHhCCcEEEEEcCCCCHHhhcCCCCCCEEEEecCCCccccc----ccCCCCc
Q 020984 99 DANIIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKLANFPECDVFINVSCAQTALLD----SKEFLAP 174 (319)
Q Consensus 99 ~a~~iGIivgTl~~q~~~~i~~~l~~ll~~~Gkk~y~i~vg~in~~KLaNf~eID~fV~iaCPr~sidd----~~~f~kP 174 (319)
..+++-||=.+-.......=++.|+++|++.|.++..++.+.-+.+.|.+.++.++=|+ -||+..... .+.|-.|
T Consensus 161 ~~~~VNiiG~~~~~~~~~~d~~ei~~lL~~~Gl~v~~~~~~~~~~~~i~~~~~A~lniv-~~~~~~~~~a~~L~~~~GiP 239 (430)
T cd01981 161 EKPSVNLIGPSSLGFHNRHDCRELKRLLHTLGIEVNVVIPEGASVDDLNELPKAWFNIV-PYREYGLSAALYLEEEFGMP 239 (430)
T ss_pred CCCcEEEEcCCCCCCCCcchHHHHHHHHHHcCCeEEEEEcCCCCHHHHHhhhhCeEEEE-ecHHHHHHHHHHHHHHhCCC
Confidence 34567666444322233455678899999999999999999999999999988776554 488766543 2578888
Q ss_pred ccCH
Q 020984 175 VITP 178 (319)
Q Consensus 175 vlTP 178 (319)
.+..
T Consensus 240 ~~~~ 243 (430)
T cd01981 240 SVKI 243 (430)
T ss_pred eEec
Confidence 7743
No 111
>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=41.98 E-value=35 Score=30.63 Aligned_cols=58 Identities=21% Similarity=0.271 Sum_probs=34.9
Q ss_pred EEEEEEcCCCccCcHHHHHHHHHHHHHhCCcEEEEEc-CCCCHHhhcC----C--CCCCEEEEec
Q 020984 102 IIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVM-GKPNPAKLAN----F--PECDVFINVS 159 (319)
Q Consensus 102 ~iGIivgTl~~q~~~~i~~~l~~ll~~~Gkk~y~i~v-g~in~~KLaN----f--~eID~fV~ia 159 (319)
+||+|+..+.-..+..+++.+.+.+++.|..+-+++. +.-++++... + ..+|.+|+.+
T Consensus 1 ~Ig~v~~~~~~~~~~~~~~gi~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~dgiIi~~ 65 (271)
T cd06321 1 KIGVSVGDLGNPFFVALAKGAEAAAKKLNPGVKVTVVSADYDLNKQVSQIDNFIAAKVDLILLNA 65 (271)
T ss_pred CeEEEecccCCHHHHHHHHHHHHHHHHhCCCeEEEEccCCCCHHHHHHHHHHHHHhCCCEEEEeC
Confidence 4788888777667778888888888885444333332 2334433321 1 1578877754
No 112
>PRK02910 light-independent protochlorophyllide reductase subunit B; Provisional
Probab=41.52 E-value=67 Score=33.40 Aligned_cols=77 Identities=16% Similarity=0.126 Sum_probs=56.1
Q ss_pred CCEEEEEEcCCCccCcHHHHHHHHHHHHHhCCcEEEEEcCCCCHHhhcCCCCCCEEEEecCCCccccc----ccCCCCcc
Q 020984 100 ANIIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKLANFPECDVFINVSCAQTALLD----SKEFLAPV 175 (319)
Q Consensus 100 a~~iGIivgTl~~q~~~~i~~~l~~ll~~~Gkk~y~i~vg~in~~KLaNf~eID~fV~iaCPr~sidd----~~~f~kPv 175 (319)
...+-||=.+..+-+.+.=+..|+++|+..|.++..+.-+.-+.+.|.+.++.++= ++-||+.+..- .++|..|.
T Consensus 158 ~~~VNIiG~~~l~f~~~~D~~EikrlL~~~Gi~vn~v~p~g~s~~di~~l~~A~~n-ivl~~~~g~~~A~~Lee~fGiP~ 236 (519)
T PRK02910 158 RPSVNLLGPTALGFHHRDDLTELRRLLATLGIDVNVVAPLGASPADLKRLPAAWFN-VVLYREIGESAARYLEREFGQPY 236 (519)
T ss_pred CCeEEEEecCccCCCChhHHHHHHHHHHHcCCeEEEEeCCCCCHHHHHhcccCcEE-EEeCHHHHHHHHHHHHHHhCCcc
Confidence 34566665443334445566779999999999999988899999999999888764 34599865432 35788887
Q ss_pred cC
Q 020984 176 IT 177 (319)
Q Consensus 176 lT 177 (319)
+.
T Consensus 237 i~ 238 (519)
T PRK02910 237 VK 238 (519)
T ss_pred cc
Confidence 64
No 113
>PLN02404 6,7-dimethyl-8-ribityllumazine synthase
Probab=41.27 E-value=96 Score=27.00 Aligned_cols=62 Identities=13% Similarity=0.123 Sum_probs=41.2
Q ss_pred CCEEEEEEcCCCccCcHHHHHHHHHHHHHhCCc---EEEEEcC---CCC--HHhhcCCCCCCEEEEecCC
Q 020984 100 ANIIGVLVGTLGVAGYLHMIHQMKELITKAGKK---AYTLVMG---KPN--PAKLANFPECDVFINVSCA 161 (319)
Q Consensus 100 a~~iGIivgTl~~q~~~~i~~~l~~ll~~~Gkk---~y~i~vg---~in--~~KLaNf~eID~fV~iaCP 161 (319)
.-+||||++..-..-.-.+++-..+.|+++|-+ ..++.|= ||- ..+|+.-.++|++|.++|=
T Consensus 7 ~~ri~IV~s~fn~~I~~~Ll~ga~~~l~~~gv~~~~i~v~~VPGa~EiP~a~~~l~~s~~~DavIaLG~V 76 (141)
T PLN02404 7 GLRFGVVVARFNEIITKNLLEGALETFKRYSVKEENIDVVWVPGSFEIPVVAQRLAKSGKYDAILCIGAV 76 (141)
T ss_pred CCEEEEEEecCcHHHHHHHHHHHHHHHHHcCCCccceEEEEcCcHHHHHHHHHHHHhcCCCCEEEEEEEE
Confidence 468999998755444445555556688888854 4555452 221 2466666689999999994
No 114
>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=40.99 E-value=51 Score=29.75 Aligned_cols=56 Identities=7% Similarity=0.023 Sum_probs=35.5
Q ss_pred EEEEEEcC--CCccCcHHHHHHHHHHHHHhCCcEEEEEcCCCCHHhhc----CC--CCCCEEEEec
Q 020984 102 IIGVLVGT--LGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKLA----NF--PECDVFINVS 159 (319)
Q Consensus 102 ~iGIivgT--l~~q~~~~i~~~l~~ll~~~Gkk~y~i~vg~in~~KLa----Nf--~eID~fV~ia 159 (319)
+||+|+.. +....+..+++.+++.+++.|....+.... ++++.. ++ ..+|.+++++
T Consensus 1 ~Igvi~~~~~~~~~f~~~l~~gi~~~~~~~gy~~~~~~~~--~~~~~~~~~~~l~~~~vdgiii~~ 64 (260)
T cd06304 1 KVALVYDGGGGDKSFNQSAYEGLEKAEKELGVEVKYVESV--EDADYEPNLRQLAAQGYDLIFGVG 64 (260)
T ss_pred CEEEEecCCCCcchHHHHHHHHHHHHHHhcCceEEEEecC--CHHHHHHHHHHHHHcCCCEEEECC
Confidence 47888864 455667788888888888888765554333 444322 22 1588877754
No 115
>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=40.80 E-value=1e+02 Score=27.42 Aligned_cols=50 Identities=16% Similarity=0.178 Sum_probs=36.6
Q ss_pred CCEEEEEEcCCCccCc--HHHHHHHHHHHHHhCCcEEEEEcCCCCHHhhcCCC
Q 020984 100 ANIIGVLVGTLGVAGY--LHMIHQMKELITKAGKKAYTLVMGKPNPAKLANFP 150 (319)
Q Consensus 100 a~~iGIivgTl~~q~~--~~i~~~l~~ll~~~Gkk~y~i~vg~in~~KLaNf~ 150 (319)
++++.||+.- |.... ..-+....+.|+++|.+.|+|-+|..+.+.|..+.
T Consensus 108 ~~kv~IllTD-G~s~~~~~~~~~~~a~~lk~~gV~i~~vGiG~~~~~el~~ia 159 (192)
T cd01473 108 APKVTMLFTD-GNDTSASKKELQDISLLYKEENVKLLVVGVGAASENKLKLLA 159 (192)
T ss_pred CCeEEEEEec-CCCCCcchhhHHHHHHHHHHCCCEEEEEEeccccHHHHHHhc
Confidence 4777666655 33322 23455666788999999999999999998887774
No 116
>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=40.79 E-value=45 Score=30.27 Aligned_cols=57 Identities=14% Similarity=0.082 Sum_probs=36.6
Q ss_pred EEEEEEcCCCccCcHHHHHHHHHHHHHhCCcEEEEEcCCCCHHhhc----CC--CCCCEEEEecC
Q 020984 102 IIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKLA----NF--PECDVFINVSC 160 (319)
Q Consensus 102 ~iGIivgTl~~q~~~~i~~~l~~ll~~~Gkk~y~i~vg~in~~KLa----Nf--~eID~fV~iaC 160 (319)
+||+|+..+....+..+++.+.+.+++.|....++. .. ++++.. ++ ..+|.+|+.++
T Consensus 1 ~Ig~v~~~~~~~~~~~~~~gi~~~~~~~g~~~~~~~-~~-~~~~~~~~i~~~~~~~~dgiii~~~ 63 (289)
T cd01540 1 KIGFIVKQPEEPWFQTEWKFAKKAAKEKGFTVVKID-VP-DGEKVLSAIDNLGAQGAKGFVICVP 63 (289)
T ss_pred CeeeecCCCCCcHHHHHHHHHHHHHHHcCCEEEEcc-CC-CHHHHHHHHHHHHHcCCCEEEEccC
Confidence 478888777666777888888888888886644332 22 444322 11 25888888765
No 117
>PRK12493 magnesium chelatase subunit H; Provisional
Probab=40.50 E-value=72 Score=37.23 Aligned_cols=61 Identities=15% Similarity=0.212 Sum_probs=45.9
Q ss_pred CCEEEEEEcCCC-ccCcHHHHHHHHHHHHHhCCcEEEEEcCCCC-----HHhhcCC-----CCCCEEEEecC
Q 020984 100 ANIIGVLVGTLG-VAGYLHMIHQMKELITKAGKKAYTLVMGKPN-----PAKLANF-----PECDVFINVSC 160 (319)
Q Consensus 100 a~~iGIivgTl~-~q~~~~i~~~l~~ll~~~Gkk~y~i~vg~in-----~~KLaNf-----~eID~fV~iaC 160 (319)
+.+||||+-..- ..+....++.|.+.|+++|..++.++++-+. ...+.+. +.||+.|.+..
T Consensus 253 ~p~Vgil~~r~~~~~~d~~~~dalI~~LE~~G~~vipvf~~gl~~~~~v~~~~~~~~~~~~~~vDaiI~~t~ 324 (1310)
T PRK12493 253 APTVGLLLQRTHLLTGNDAHYVALIQELEARGARVIPAYAGGLDFRKPVEAFFYDPGNPDTPLVDLVVSLTG 324 (1310)
T ss_pred CCEEEEEEchhhhhcCCcHHHHHHHHHHHHCCCeEEEEEecCcccchHHHHHHHhhcccCCCCccEEEEcCc
Confidence 789999996544 3668899999999999999999999887554 2333331 35898886644
No 118
>cd06319 PBP1_ABC_sugar_binding_like_10 Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems. Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily, which consists of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis.
Probab=39.98 E-value=33 Score=30.80 Aligned_cols=73 Identities=18% Similarity=0.148 Sum_probs=44.0
Q ss_pred EEEEEcCCCccCcHHHHHHHHHHHHHhCCcEEEEEcCCCCHH-------hhcCCCCCCEEEEecCCCcc----cccccCC
Q 020984 103 IGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPA-------KLANFPECDVFINVSCAQTA----LLDSKEF 171 (319)
Q Consensus 103 iGIivgTl~~q~~~~i~~~l~~ll~~~Gkk~y~i~vg~in~~-------KLaNf~eID~fV~iaCPr~s----idd~~~f 171 (319)
||+|+..+.-..+..+++.+++.+++.|.+..++. ++-+++ +|.+ ..+|.+|+.++.-.. +......
T Consensus 2 i~vi~~~~~~~~~~~~~~~i~~~~~~~g~~~~~~~-~~~~~~~~~~~i~~~~~-~~~dgiii~~~~~~~~~~~l~~~~~~ 79 (277)
T cd06319 2 IAYIVSDLRIPFWQIMGRGVKSKAKALGYDAVELS-AENSAKKELENLRTAID-KGVSGIIISPTNSSAAVTLLKLAAQA 79 (277)
T ss_pred eEEEeCCCCchHHHHHHHHHHHHHHhcCCeEEEec-CCCCHHHHHHHHHHHHh-cCCCEEEEcCCchhhhHHHHHHHHHC
Confidence 78888777767777888888888888886665442 232332 2222 368888876654211 1222344
Q ss_pred CCcccC
Q 020984 172 LAPVIT 177 (319)
Q Consensus 172 ~kPvlT 177 (319)
..|+|+
T Consensus 80 ~ipvV~ 85 (277)
T cd06319 80 KIPVVI 85 (277)
T ss_pred CCCEEE
Confidence 567665
No 119
>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=39.57 E-value=53 Score=28.68 Aligned_cols=11 Identities=9% Similarity=-0.043 Sum_probs=4.7
Q ss_pred hCCcEEEEEcC
Q 020984 129 AGKKAYTLVMG 139 (319)
Q Consensus 129 ~Gkk~y~i~vg 139 (319)
.+...+++...
T Consensus 54 ~~~d~iii~~~ 64 (264)
T cd06267 54 RRVDGIILAPS 64 (264)
T ss_pred cCcCEEEEecC
Confidence 34444444433
No 120
>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=39.39 E-value=1.1e+02 Score=27.18 Aligned_cols=59 Identities=10% Similarity=0.099 Sum_probs=40.2
Q ss_pred EEEEEEcCC-CccCcHHHHHHHHHHHHHhCCcEEEEEcCCCCHHh----hcCCC--CCCEEEEecCC
Q 020984 102 IIGVLVGTL-GVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAK----LANFP--ECDVFINVSCA 161 (319)
Q Consensus 102 ~iGIivgTl-~~q~~~~i~~~l~~ll~~~Gkk~y~i~vg~in~~K----LaNf~--eID~fV~iaCP 161 (319)
+||+|+-.. .-..+..+++.+++.+++.|....++. ..-++++ +.++. .+|.+|+.++.
T Consensus 1 ~ig~v~~~~~~~~~~~~~~~~i~~~~~~~g~~~~~~~-~~~~~~~~~~~~~~l~~~~~dgiii~~~~ 66 (269)
T cd06288 1 TIGLISDEIATTPFAVEIILGAQDAAREHGYLLLVVN-TGGDDELEAEAVEALLDHRVDGIIYATMY 66 (269)
T ss_pred CeEEEeCCCCCCccHHHHHHHHHHHHHHCCCEEEEEe-CCCCHHHHHHHHHHHHHcCCCEEEEecCC
Confidence 489999876 556666889999999999997765544 3334432 22222 68999988764
No 121
>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=39.21 E-value=38 Score=32.77 Aligned_cols=55 Identities=18% Similarity=0.293 Sum_probs=41.5
Q ss_pred CEEEEEEcCCCc--cCcHHHHHHHHHHHHHhC-CcEEEEEcCCCCHHhhcCCC--CCCEE
Q 020984 101 NIIGVLVGTLGV--AGYLHMIHQMKELITKAG-KKAYTLVMGKPNPAKLANFP--ECDVF 155 (319)
Q Consensus 101 ~~iGIivgTl~~--q~~~~i~~~l~~ll~~~G-kk~y~i~vg~in~~KLaNf~--eID~f 155 (319)
+..+|.+-+.+. -..+..++.+++.|+..| .+.-+++.|.||++++..|. +||++
T Consensus 211 ~~d~I~lDn~~~~~G~~~~~~~~~~~~l~~~g~~~~~ieaSGgI~~~~i~~~a~~gvD~i 270 (302)
T cd01571 211 KLDGVRLDTPSSRRGVFRYLIREVRWALDIRGYKHVKIFVSGGLDEEDIKELEDVGVDAF 270 (302)
T ss_pred CCcEEEECCCCCCCCCHHHHHHHHHHHHHhCCCCCeEEEEeCCCCHHHHHHHHHcCCCEE
Confidence 345677766531 225677889999999887 66778888999999999876 58876
No 122
>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=39.15 E-value=65 Score=28.87 Aligned_cols=59 Identities=15% Similarity=0.173 Sum_probs=37.4
Q ss_pred EEEEEEcCCCccCcHHHHHHHHHHHHHh---CCcE-EEEEcCCCCHHhhcC----C--CCCCEEEEecC
Q 020984 102 IIGVLVGTLGVAGYLHMIHQMKELITKA---GKKA-YTLVMGKPNPAKLAN----F--PECDVFINVSC 160 (319)
Q Consensus 102 ~iGIivgTl~~q~~~~i~~~l~~ll~~~---Gkk~-y~i~vg~in~~KLaN----f--~eID~fV~iaC 160 (319)
+||+|+.......+..+++.+.+.+++. |.+. +++.-+.-++++..+ + ..+|++|+.++
T Consensus 1 ~Ig~i~~~~~~~~~~~~~~~i~~~~~~~~~~g~~~~l~i~~~~~~~~~~~~~~~~~~~~~vdgiIi~~~ 69 (272)
T cd06300 1 KIGLSNSYAGNTWRAQMLDEFKAQAKELKKAGLISEFIVTSADGDVAQQIADIRNLIAQGVDAIIINPA 69 (272)
T ss_pred CeEEeccccCChHHHHHHHHHHHHHHhhhccCCeeEEEEecCCCCHHHHHHHHHHHHHcCCCEEEEeCC
Confidence 4788887776666678888888888887 7643 333334444443321 1 16888888765
No 123
>PRK09426 methylmalonyl-CoA mutase; Reviewed
Probab=39.05 E-value=47 Score=36.17 Aligned_cols=71 Identities=17% Similarity=0.289 Sum_probs=46.7
Q ss_pred HHHhhcc--CCEEEEEEcCCCccCcHHHHHHHHHHHHHhCCcEEEEEcC-CCCHHhhcCCC--CCCEEEEecCCCcccc
Q 020984 93 LVEKAKD--ANIIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMG-KPNPAKLANFP--ECDVFINVSCAQTALL 166 (319)
Q Consensus 93 ~I~ka~~--a~~iGIivgTl~~q~~~~i~~~l~~ll~~~Gkk~y~i~vg-~in~~KLaNf~--eID~fV~iaCPr~sid 166 (319)
.++.|++ +..++ ++++. ..|.+.+..+.+.|+++|.+-..+++| .+-++....+. .||.|+-.+|+-..+.
T Consensus 625 ~v~aa~~~~a~ivv--lcs~d-~~~~e~~~~l~~~Lk~~G~~~v~vl~GG~~~~~~~~~l~~aGvD~~i~~g~d~~~~L 700 (714)
T PRK09426 625 AARQAVENDVHVVG--VSSLA-AGHKTLVPALIEALKKLGREDIMVVVGGVIPPQDYDFLYEAGVAAIFGPGTVIADAA 700 (714)
T ss_pred HHHHHHHcCCCEEE--Eeccc-hhhHHHHHHHHHHHHhcCCCCcEEEEeCCCChhhHHHHHhCCCCEEECCCCCHHHHH
Confidence 4455554 44443 34432 788899999999999999865544444 54554333222 7999999999866543
No 124
>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=38.95 E-value=71 Score=26.28 Aligned_cols=60 Identities=17% Similarity=0.323 Sum_probs=39.8
Q ss_pred cCCEEEEEEcCCCccCcHHHHHHHHHHHHHhCCc-EEEEEcCCCCHHhhc---CCCCCCEEEEecCCC
Q 020984 99 DANIIGVLVGTLGVAGYLHMIHQMKELITKAGKK-AYTLVMGKPNPAKLA---NFPECDVFINVSCAQ 162 (319)
Q Consensus 99 ~a~~iGIivgTl~~q~~~~i~~~l~~ll~~~Gkk-~y~i~vg~in~~KLa---Nf~eID~fV~iaCPr 162 (319)
++..++| +.+. ..+...++.+.+.|++.|.. ..+++-|...++..+ .+ .+|.|+-.+|+-
T Consensus 50 ~~d~V~i--S~~~-~~~~~~~~~~~~~L~~~~~~~i~i~~GG~~~~~~~~~~~~~-G~d~~~~~~~~~ 113 (122)
T cd02071 50 DVDVIGL--SSLS-GGHMTLFPEVIELLRELGAGDILVVGGGIIPPEDYELLKEM-GVAEIFGPGTSI 113 (122)
T ss_pred CCCEEEE--cccc-hhhHHHHHHHHHHHHhcCCCCCEEEEECCCCHHHHHHHHHC-CCCEEECCCCCH
Confidence 5666655 3332 67788889999999999874 444444455555443 44 699998877763
No 125
>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=38.80 E-value=64 Score=28.93 Aligned_cols=55 Identities=15% Similarity=0.223 Sum_probs=37.7
Q ss_pred EEEEEEcCCCccCcHHHHHHHHHHHHHhCCcEEEEEcCCCCHHh-------hcCCCCCCEEEEe
Q 020984 102 IIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAK-------LANFPECDVFINV 158 (319)
Q Consensus 102 ~iGIivgTl~~q~~~~i~~~l~~ll~~~Gkk~y~i~vg~in~~K-------LaNf~eID~fV~i 158 (319)
+||+++.++.-..+..+++.+.+.++++|....+... +-++++ |... .+|++|+.
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 4788888877677778888888888888877755433 334432 3332 68888874
No 126
>PRK10401 DNA-binding transcriptional regulator GalS; Provisional
Probab=38.76 E-value=1.2e+02 Score=28.51 Aligned_cols=61 Identities=16% Similarity=0.144 Sum_probs=43.1
Q ss_pred cCCEEEEEEcCCCccCcHHHHHHHHHHHHHhCCcEEEEEcCCCCHHhh----cCC--CCCCEEEEecC
Q 020984 99 DANIIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKL----ANF--PECDVFINVSC 160 (319)
Q Consensus 99 ~a~~iGIivgTl~~q~~~~i~~~l~~ll~~~Gkk~y~i~vg~in~~KL----aNf--~eID~fV~iaC 160 (319)
..++||+|+..+.-..+..+++.+.+.++++|....+.. ..-++++. ..+ ..+|.+|++++
T Consensus 58 ~~~~Igvi~~~~~~~f~~~l~~gi~~~~~~~gy~~~~~~-~~~~~~~~~~~i~~l~~~~vdGiIi~~~ 124 (346)
T PRK10401 58 VSDTIGVVVMDVSDAFFGALVKAVDLVAQQHQKYVLIGN-SYHEAEKERHAIEVLIRQRCNALIVHSK 124 (346)
T ss_pred CCCEEEEEeCCCCCccHHHHHHHHHHHHHHCCCEEEEEc-CCCChHHHHHHHHHHHhcCCCEEEEeCC
Confidence 467899999888777888999999999999997654332 22233322 222 26999998864
No 127
>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=38.48 E-value=40 Score=30.53 Aligned_cols=60 Identities=25% Similarity=0.191 Sum_probs=41.7
Q ss_pred EEEEEEcCCCccCcHHHHHHHHHHHHHhCCcEEEEEcCC-CCHH----hhcCC--CCCCEEEEecCC
Q 020984 102 IIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGK-PNPA----KLANF--PECDVFINVSCA 161 (319)
Q Consensus 102 ~iGIivgTl~~q~~~~i~~~l~~ll~~~Gkk~y~i~vg~-in~~----KLaNf--~eID~fV~iaCP 161 (319)
+||||+..+....+..++..+++.+++.|.+..++..+. -+++ .+.++ ..+|.+|+.+..
T Consensus 1 ~Igvi~~~~~~~f~~~~~~gi~~~a~~~g~~~~~~~~~~~~~~~~~~~~i~~~~~~~vdgiI~~~~~ 67 (268)
T cd06306 1 KLCVLYPHLKDAYWLSVNYGMVEEAKRLGVSLKLLEAGGYPNLAKQIAQLEDCAAWGADAILLGAVS 67 (268)
T ss_pred CeEEEcCCCCCHHHHHHHHHHHHHHHHcCCEEEEecCCCCCCHHHHHHHHHHHHHcCCCEEEEcCCC
Confidence 489999888777788899999999999997765554332 2332 22222 169999887654
No 128
>PRK06455 riboflavin synthase; Provisional
Probab=38.36 E-value=1.1e+02 Score=27.09 Aligned_cols=58 Identities=17% Similarity=0.179 Sum_probs=40.6
Q ss_pred CEEEEEEcCCCccCcHHHHHHHHHHHHHhC--CcEEEEEcCC---CC--HHhhcCCCCCCEEEEecCC
Q 020984 101 NIIGVLVGTLGVAGYLHMIHQMKELITKAG--KKAYTLVMGK---PN--PAKLANFPECDVFINVSCA 161 (319)
Q Consensus 101 ~~iGIivgTl~~q~~~~i~~~l~~ll~~~G--kk~y~i~vg~---in--~~KLaNf~eID~fV~iaCP 161 (319)
.+|||+.++.... .+.+-..+.|+++| -+..++.|=- |- ..+|+.=.++|++|.++|+
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 5799999997653 67788888888855 4444444432 22 2356544579999999998
No 129
>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=38.34 E-value=65 Score=27.36 Aligned_cols=94 Identities=14% Similarity=0.180 Sum_probs=55.4
Q ss_pred HHHHHHhcCCCeEEEEcCCCCccccccCcHHHHHHHHHHHHHhhccCCEEEEEEcCCCccCcHHHHHHHHHHHHHhCCcE
Q 020984 54 FANVVLTFNGCEIVRYDATEERLLTDVSQPLKILKRRYYLVEKAKDANIIGVLVGTLGVAGYLHMIHQMKELITKAGKKA 133 (319)
Q Consensus 54 l~~l~l~~~~~~v~~yDP~s~~~~~e~~~~~k~l~~R~~~I~ka~~a~~iGIivgTl~~q~~~~i~~~l~~ll~~~Gkk~ 133 (319)
+...+|...+..|+--..+... . ..++.|++.+.=.|.++++. ..+.+.+..+.+.|+++|...
T Consensus 21 iv~~~l~~~GfeVi~lg~~~s~--------e-------~~v~aa~e~~adii~iSsl~-~~~~~~~~~~~~~L~~~g~~~ 84 (132)
T TIGR00640 21 VIATAYADLGFDVDVGPLFQTP--------E-------EIARQAVEADVHVVGVSSLA-GGHLTLVPALRKELDKLGRPD 84 (132)
T ss_pred HHHHHHHhCCcEEEECCCCCCH--------H-------HHHHHHHHcCCCEEEEcCch-hhhHHHHHHHHHHHHhcCCCC
Confidence 4456666666555543333221 1 14455554333334446664 678888999999999998866
Q ss_pred EEEEcCC-CCHHhhcCCC--CCCEEEEecCCCc
Q 020984 134 YTLVMGK-PNPAKLANFP--ECDVFINVSCAQT 163 (319)
Q Consensus 134 y~i~vg~-in~~KLaNf~--eID~fV~iaCPr~ 163 (319)
..+++|- +-++..+.|. .+|.|+-.++|-.
T Consensus 85 i~vivGG~~~~~~~~~l~~~Gvd~~~~~gt~~~ 117 (132)
T TIGR00640 85 ILVVVGGVIPPQDFDELKEMGVAEIFGPGTPIP 117 (132)
T ss_pred CEEEEeCCCChHhHHHHHHCCCCEEECCCCCHH
Confidence 6677773 3333344443 6787776666544
No 130
>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=38.27 E-value=83 Score=28.20 Aligned_cols=75 Identities=11% Similarity=0.110 Sum_probs=45.2
Q ss_pred EEEEEEcCCCccCcHHHHHHHHHHHHHhCC----cEEEEEcC-CCCHH-------hhcCCCCCCEEEEecCCCccccccc
Q 020984 102 IIGVLVGTLGVAGYLHMIHQMKELITKAGK----KAYTLVMG-KPNPA-------KLANFPECDVFINVSCAQTALLDSK 169 (319)
Q Consensus 102 ~iGIivgTl~~q~~~~i~~~l~~ll~~~Gk----k~y~i~vg-~in~~-------KLaNf~eID~fV~iaCPr~sidd~~ 169 (319)
+||||+. ..-..+..+++.+++.++++|. +..+++.+ +-+++ +|.+- .+|.+|.++++-.......
T Consensus 1 ~igv~~~-~~~~~~~~~~~gi~~~~~~~g~~~g~~v~l~~~~~~~~~~~~~~~~~~l~~~-~vd~iI~~~~~~~~~~~~~ 78 (281)
T cd06325 1 KVGILQL-VEHPALDAARKGFKDGLKEAGYKEGKNVKIDYQNAQGDQSNLPTIARKFVAD-KPDLIVAIATPAAQAAANA 78 (281)
T ss_pred CeEEecC-CCCcchHHHHHHHHHHHHHhCccCCceEEEEEecCCCCHHHHHHHHHHHHhc-CCCEEEEcCcHHHHHHHHc
Confidence 4788885 5556777899999999999886 33333332 22333 44443 7899888776421111122
Q ss_pred CCCCcccCH
Q 020984 170 EFLAPVITP 178 (319)
Q Consensus 170 ~f~kPvlTP 178 (319)
....|||..
T Consensus 79 ~~~iPvV~~ 87 (281)
T cd06325 79 TKDIPIVFT 87 (281)
T ss_pred CCCCCEEEE
Confidence 344577654
No 131
>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=38.11 E-value=37 Score=31.78 Aligned_cols=59 Identities=20% Similarity=0.245 Sum_probs=36.8
Q ss_pred EEEEEcCCCccCcHHHHHHHHHHHHHhCCcEEEEEcCCCCHHhhc----CC--CCCCEEEEecCCC
Q 020984 103 IGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKLA----NF--PECDVFINVSCAQ 162 (319)
Q Consensus 103 iGIivgTl~~q~~~~i~~~l~~ll~~~Gkk~y~i~vg~in~~KLa----Nf--~eID~fV~iaCPr 162 (319)
||+++.++.-.-...+.+-+++.+++.|....+... .-++++.. ++ ..+|++|+.++..
T Consensus 1 ig~~~~~~~~~~~~~~~~~i~~~a~~~g~~v~~~~~-~~~~~~q~~~i~~l~~~~vDgIIi~~~~~ 65 (302)
T TIGR02634 1 IGVSIDDLRLERWQKDRDIFVAAAESLGAKVFVQSA-NGNEAKQISQIENLIARGVDVLVIIPQNG 65 (302)
T ss_pred CeeecCccchhhHHHHHHHHHHHHHhcCCEEEEEeC-CCCHHHHHHHHHHHHHcCCCEEEEeCCCh
Confidence 577777777777777777788888877766554432 33444321 22 2578877776643
No 132
>PLN02285 methionyl-tRNA formyltransferase
Probab=37.98 E-value=70 Score=31.42 Aligned_cols=64 Identities=14% Similarity=0.130 Sum_probs=37.1
Q ss_pred cCCEEEEEEcCCCccCcH--HHHHHHHHHHHHhCCcEEEE-EcCCCCH----HhhcCCCCCCEEEEecCCCc
Q 020984 99 DANIIGVLVGTLGVAGYL--HMIHQMKELITKAGKKAYTL-VMGKPNP----AKLANFPECDVFINVSCAQT 163 (319)
Q Consensus 99 ~a~~iGIivgTl~~q~~~--~i~~~l~~ll~~~Gkk~y~i-~vg~in~----~KLaNf~eID~fV~iaCPr~ 163 (319)
...+++||...-...++- -.-.-+++..+++|..++.+ .-.+++. +.|..+ +.|+.|++++.++
T Consensus 35 ~~~iv~Vvt~~~~~~gr~~~~~~~pv~~~A~~~gIp~~~v~~~~~~~~~~~~~~l~~~-~~Dliv~~~~~~i 105 (334)
T PLN02285 35 AFEVAAVVTQPPARRGRGRKLMPSPVAQLALDRGFPPDLIFTPEKAGEEDFLSALREL-QPDLCITAAYGNI 105 (334)
T ss_pred CCeEEEEEeCCCCcccCCcccCCCHHHHHHHHcCCCcceecCccccCCHHHHHHHHhh-CCCEEEhhHhhhh
Confidence 355666666654323221 11223667778888886533 3344442 345555 7899999998776
No 133
>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=37.74 E-value=46 Score=33.20 Aligned_cols=65 Identities=18% Similarity=0.327 Sum_probs=38.1
Q ss_pred HHHHHhhccCCEEEEEEcCCCccCcHHHHHHHHHHHHHhCCcEEEEEcC---CCCHHhhcCCCCCCEEE
Q 020984 91 YYLVEKAKDANIIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMG---KPNPAKLANFPECDVFI 156 (319)
Q Consensus 91 ~~~I~ka~~a~~iGIivgTl~~q~~~~i~~~l~~ll~~~Gkk~y~i~vg---~in~~KLaNf~eID~fV 156 (319)
|..+....+|..++|=..|...+.-.++++.+++ +++.+.+..+++.| ...|+.+..++++|++|
T Consensus 25 ~~~~~~~~~aD~v~intctv~~~a~~~~~~~i~~-~k~~~p~~~vvvgGc~a~~~~ee~~~~~~vD~vv 92 (414)
T TIGR01579 25 YEVVPDEDKADVYIINTCTVTAKADSKARRAIRR-ARRQNPTAKIIVTGCYAQSNPKELADLKDVDLVL 92 (414)
T ss_pred CEECCCcccCCEEEEeccccchHHHHHHHHHHHH-HHhhCCCcEEEEECCccccCHHHHhcCCCCcEEE
Confidence 3344444567776555555443333344444433 35566666666666 45677777788888876
No 134
>PF02233 PNTB: NAD(P) transhydrogenase beta subunit; InterPro: IPR012136 NAD(P) transhydrogenase catalyses the transfer of reducing equivalents between NAD(H) and NADP(H), coupled to the translocation of protons across a membrane []. It is an integral membrane protein found in most organisms except for yeasts, plants and some bacterial species. In bacterial species it is located in the cytoplasmic membrane, while in mitochondria it is located in the inner membrane. Under most physiological conditions this enzyme synthesises NADPH, driven by consumption of the proton electrochemical gradient. The resulting NADPH is subsequently used for biosynthetic reactions or the reduction of glutathione. The global structure of this enzyme is similar in all organisms, consisting of three distinct domains, though the polypeptide composition can vary. Domain I binds NAD(+)/NADH, domain II is a hydrophobic membrane-spanning domain, and domain III binds NADP(+)/NADPH. Domain I is composed of two subdomains, both of which form a Rossman fold, while domain III consists of a single Rossman fold where the NADP(+) is flipped relative to the normal orientation of bound nucleotides within the Rossman fold [, , ]. Several residues within these domains are thought to make functionally important interdomain contacts for hydride transfer between these domains []. Proton translocation occurs through domain II and is thought to induce conformational changes which are transmitted across domain III to the site of hydride transfer between domains I and III. This entry represents the beta subunit found in bacterial two-subunit NADP(H) transhydrogenases. This subunit forms domain III and part of the transmembrane domain II. ; GO: 0008750 NAD(P)+ transhydrogenase (AB-specific) activity, 0050661 NADP binding, 0055114 oxidation-reduction process, 0016021 integral to membrane; PDB: 1PT9_A 1DJL_A 1U31_B 2BRU_C 1PTJ_C 1HZZ_C 2FRD_C 2FSV_C 1XLT_C 1U2G_C ....
Probab=37.64 E-value=23 Score=36.62 Aligned_cols=85 Identities=22% Similarity=0.398 Sum_probs=54.2
Q ss_pred HHHhhccCCEEEEEEcC-CCccCcHHHHHHHHHHHHHhCCcEE---------------------------EEEcCCCCHH
Q 020984 93 LVEKAKDANIIGVLVGT-LGVAGYLHMIHQMKELITKAGKKAY---------------------------TLVMGKPNPA 144 (319)
Q Consensus 93 ~I~ka~~a~~iGIivgT-l~~q~~~~i~~~l~~ll~~~Gkk~y---------------------------~i~vg~in~~ 144 (319)
..+...+|+++-|+=|- +.++.-.+.++.|-++|+++|+++- ++-|.++|++
T Consensus 300 ~a~~l~~A~~VvIVPGYGmAvAqAQ~~v~el~~~L~~~G~~V~faIHPVAGRMPGHMNVLLAEa~VpYd~~~emdeiN~~ 379 (463)
T PF02233_consen 300 VAEMLANAKKVVIVPGYGMAVAQAQHAVAELADLLEERGVEVKFAIHPVAGRMPGHMNVLLAEANVPYDIVKEMDEINPD 379 (463)
T ss_dssp HHHHHHH-SEEEEEESHHHHHCTTHHHHHHHHHHHHHTT-EEEEEE-TTSSSSTTHHHHHHHHCT--GGGEEEHHHHGGG
T ss_pred HHHHHHhcCceEEecCchHHHHHHHHHHHHHHHHHHhCCCEEEEEeccccCCCCCcceEEEEecCCCHHHHhhhhhcccc
Confidence 44556679999777663 3346667788889999999999965 6667788864
Q ss_pred hhcCCCCCCEEEEecCCCcc----ccc--ccCCCCcccCHHHH
Q 020984 145 KLANFPECDVFINVSCAQTA----LLD--SKEFLAPVITPFEA 181 (319)
Q Consensus 145 KLaNf~eID~fV~iaCPr~s----idd--~~~f~kPvlTP~El 181 (319)
|++.|+.++++-.... .+| +.-|--|||..+++
T Consensus 380 ----f~~~Dv~lViGANDvVNPaA~~d~~SpI~GMPil~v~~a 418 (463)
T PF02233_consen 380 ----FPDTDVVLVIGANDVVNPAAREDPNSPIYGMPILEVWKA 418 (463)
T ss_dssp ----GGG-SEEEEES-SGGG-CHHCCSTTSTTTTSS---GGGS
T ss_pred ----hhcCCEEEEeccccccCchhccCCCCCCCCCeecchhhc
Confidence 9999999999865432 121 22377788765553
No 135
>PRK15395 methyl-galactoside ABC transporter galactose-binding periplasmic protein MglB; Provisional
Probab=36.75 E-value=97 Score=29.48 Aligned_cols=65 Identities=8% Similarity=-0.033 Sum_probs=41.9
Q ss_pred hccCCEEEEEEcCCCccCcHHHHHHHHHHHHHhCCcEEEEEcCCCCHH----hhcCCC--CCCEEEEecCC
Q 020984 97 AKDANIIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPA----KLANFP--ECDVFINVSCA 161 (319)
Q Consensus 97 a~~a~~iGIivgTl~~q~~~~i~~~l~~ll~~~Gkk~y~i~vg~in~~----KLaNf~--eID~fV~iaCP 161 (319)
++.-++||+++..++...+..+++.+++.++++|.-..++..+.-++. .+.++. .+|.+|+.+++
T Consensus 21 ~~~~~~Igvv~~~~~~~f~~~~~~gi~~~a~~~g~~~~~~~~~~~~~~~~~~~i~~l~~~~vdgiIi~~~~ 91 (330)
T PRK15395 21 AAADTRIGVTIYKYDDNFMSVVRKAIEKDAKAAPDVQLLMNDSQNDQSKQNDQIDVLLAKGVKALAINLVD 91 (330)
T ss_pred hcCCceEEEEEecCcchHHHHHHHHHHHHHHhcCCeEEEEecCCCCHHHHHHHHHHHHHcCCCEEEEeccC
Confidence 344588999998777677778888888888887632223323333332 233332 68999887665
No 136
>PRK10936 TMAO reductase system periplasmic protein TorT; Provisional
Probab=36.72 E-value=81 Score=30.18 Aligned_cols=65 Identities=23% Similarity=0.097 Sum_probs=44.6
Q ss_pred hccCCEEEEEEcCCCccCcHHHHHHHHHHHHHhCCcEEEEEcC-CCCHHhh----cCC--CCCCEEEEecCC
Q 020984 97 AKDANIIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMG-KPNPAKL----ANF--PECDVFINVSCA 161 (319)
Q Consensus 97 a~~a~~iGIivgTl~~q~~~~i~~~l~~ll~~~Gkk~y~i~vg-~in~~KL----aNf--~eID~fV~iaCP 161 (319)
|+..++||+|+-++.-..+..+++.+++.+++.|.+..++... .-+.++. .++ ..+|++|+.+..
T Consensus 43 Ar~t~~Igvv~p~~~~~f~~~~~~gi~~aa~~~G~~l~i~~~~~~~~~~~q~~~i~~l~~~~vdgIIl~~~~ 114 (343)
T PRK10936 43 AKKAWKLCALYPHLKDSYWLSVNYGMVEEAKRLGVDLKVLEAGGYYNLAKQQQQLEQCVAWGADAILLGAVT 114 (343)
T ss_pred cCCCeEEEEEecCCCchHHHHHHHHHHHHHHHhCCEEEEEcCCCCCCHHHHHHHHHHHHHhCCCEEEEeCCC
Confidence 3457899999988776677788899999999999775555432 2333332 222 268999887543
No 137
>TIGR00288 conserved hypothetical protein TIGR00288. This family of orthologs is restricted to but universal among the completed archaeal genomes so far. Eubacterial proteins showing at least local homology include slr1870 from Synechocystis PCC6803 and two proteins from Aquifex aeolicusr, none of which is characterized.
Probab=36.28 E-value=1.2e+02 Score=26.89 Aligned_cols=53 Identities=17% Similarity=0.290 Sum_probs=38.8
Q ss_pred ccCCEEEEEEcCCCccCcHHHHHHHHHHHHHhCCcEEEEEcCCCCHHhhcCCCCCCEEEEec
Q 020984 98 KDANIIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKLANFPECDVFINVS 159 (319)
Q Consensus 98 ~~a~~iGIivgTl~~q~~~~i~~~l~~ll~~~Gkk~y~i~vg~in~~KLaNf~eID~fV~ia 159 (319)
.+..+|.|+-|- ..+..++++ |+++|++++.+.+...++.-|.|- +|-||-+.
T Consensus 104 ~~iD~~vLvSgD---~DF~~Lv~~----lre~G~~V~v~g~~~~ts~~L~~a--cd~FI~L~ 156 (160)
T TIGR00288 104 PNIDAVALVTRD---ADFLPVINK----AKENGKETIVIGAEPGFSTALQNS--ADIAIILG 156 (160)
T ss_pred CCCCEEEEEecc---HhHHHHHHH----HHHCCCEEEEEeCCCCChHHHHHh--cCeEEeCC
Confidence 556777777665 556565544 557799999999888889888775 77777654
No 138
>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=36.06 E-value=1.5e+02 Score=24.81 Aligned_cols=59 Identities=12% Similarity=0.114 Sum_probs=42.6
Q ss_pred EEEcCCCccCcHHHHHHHHHHHHHhCCcEEEEEcCC--CCHHhhcC--------CCCCC--EEEEecCCCc
Q 020984 105 VLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGK--PNPAKLAN--------FPECD--VFINVSCAQT 163 (319)
Q Consensus 105 IivgTl~~q~~~~i~~~l~~ll~~~Gkk~y~i~vg~--in~~KLaN--------f~eID--~fV~iaCPr~ 163 (319)
.+++.+||.|--.+.-+|-..+.++|+++.++=++- .+-..+.. +.++- =||++-||..
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 578899999999999999999999999999886653 34444321 11211 3788888854
No 139
>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=35.87 E-value=70 Score=28.70 Aligned_cols=59 Identities=15% Similarity=0.138 Sum_probs=36.8
Q ss_pred EEEEEEcCCCccCcHHHHHHHHHHHHHh-CCcEEEEEcCCCCHHh----hcCC--CCCCEEEEecCC
Q 020984 102 IIGVLVGTLGVAGYLHMIHQMKELITKA-GKKAYTLVMGKPNPAK----LANF--PECDVFINVSCA 161 (319)
Q Consensus 102 ~iGIivgTl~~q~~~~i~~~l~~ll~~~-Gkk~y~i~vg~in~~K----LaNf--~eID~fV~iaCP 161 (319)
+||+|+..+.-..+..+++.+.+.+++. |+...++.. .-++++ +.++ ..+|++|+.++.
T Consensus 1 ~ig~~~~~~~~~~~~~~~~~i~~~~~~~~g~~~~~~~~-~~~~~~~~~~i~~~~~~~vdgiii~~~~ 66 (270)
T cd06308 1 VIGFSQCNLADPWRAAMNDEIQREASNYPDVELIIADA-ADDNSKQVADIENFIRQGVDLLIISPNE 66 (270)
T ss_pred CEEEEeeCCCCHHHHHHHHHHHHHHHhcCCcEEEEEcC-CCCHHHHHHHHHHHHHhCCCEEEEecCc
Confidence 4788888776566678888888888885 666654433 223322 2221 168888876653
No 140
>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=35.87 E-value=33 Score=31.95 Aligned_cols=59 Identities=10% Similarity=0.050 Sum_probs=33.7
Q ss_pred EEEEEEcCCCccCcHHHHHHHHHHHHH--hCCcEEEEEcCCCCHHh----hcCC--CCCCEEEEecCC
Q 020984 102 IIGVLVGTLGVAGYLHMIHQMKELITK--AGKKAYTLVMGKPNPAK----LANF--PECDVFINVSCA 161 (319)
Q Consensus 102 ~iGIivgTl~~q~~~~i~~~l~~ll~~--~Gkk~y~i~vg~in~~K----LaNf--~eID~fV~iaCP 161 (319)
+||+|+..+.-..+..+++.+++.+++ .|.+..++. ..-++++ |.++ ..+|.+|+.++.
T Consensus 1 ~Igviv~~~~~~~~~~~~~gi~~~a~~~~~g~~~~~~~-~~~~~~~q~~~i~~l~~~~vdgiii~~~~ 67 (303)
T cd01539 1 KIGVFLYKFDDTFISLVRKNLEDIQKENGGKVEFTFYD-AKNNQSTQNEQIDTALAKGVDLLAVNLVD 67 (303)
T ss_pred CeEEEeeCCCChHHHHHHHHHHHHHHhhCCCeeEEEec-CCCCHHHHHHHHHHHHHcCCCEEEEecCc
Confidence 467777776655666777778877777 444433322 2333331 2222 267887776554
No 141
>TIGR01278 DPOR_BchB light-independent protochlorophyllide reductase, B subunit. This enzyme describes the B subunit of the dark form protochlorophyllide reductase, a nitrogenase-like enzyme. This subunit shows homology to the nitrogenase molybdenum-iron protein. It catalyzes a step in bacteriochlorophyll biosynthesis.
Probab=35.86 E-value=2e+02 Score=29.79 Aligned_cols=77 Identities=16% Similarity=0.135 Sum_probs=54.4
Q ss_pred cCCEEEEEEcCCCccCcHHHHHHHHHHHHHhCCcEEEEEcCCCCHHhhcCCCCCCEEEEecCCCcccc----cccCCCCc
Q 020984 99 DANIIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKLANFPECDVFINVSCAQTALL----DSKEFLAP 174 (319)
Q Consensus 99 ~a~~iGIivgTl~~q~~~~i~~~l~~ll~~~Gkk~y~i~vg~in~~KLaNf~eID~fV~iaCPr~sid----d~~~f~kP 174 (319)
....|-||=.+..+-+.+.=+..|+++|+..|.++..++-+.-+.+.|.+.++.++= ++-||+.... -.+.|..|
T Consensus 157 ~~~~VNIiG~~~l~~~~~~D~~elkrlL~~lGi~vn~v~p~g~s~~dl~~l~~A~~N-Iv~~~~~g~~~A~~Le~~fGiP 235 (511)
T TIGR01278 157 EKPSVNLLGPASLGFHHRHDLIELRRLLKTLGIEVNVVAPWGASIADLARLPAAWLN-ICPYREIGLMAAEYLKEKFGQP 235 (511)
T ss_pred CCCcEEEEeCCCCCCCCHHHHHHHHHHHHHCCCeEEEEeCCCCCHHHHHhcccCcEE-EEechHHHHHHHHHHHHHhCCC
Confidence 345676664443333344556789999999999998888888899999999877653 3459886532 23578888
Q ss_pred cc
Q 020984 175 VI 176 (319)
Q Consensus 175 vl 176 (319)
.+
T Consensus 236 ~i 237 (511)
T TIGR01278 236 YI 237 (511)
T ss_pred cc
Confidence 76
No 142
>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=35.72 E-value=67 Score=33.16 Aligned_cols=77 Identities=10% Similarity=0.121 Sum_probs=59.3
Q ss_pred cCCEEEEEEcCCCccCcHHHHHHHHHHHHHhCCcEEEEEcCCCCHHhhcCCCCCCEEEEecCCCcccccccCCCCccc
Q 020984 99 DANIIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKLANFPECDVFINVSCAQTALLDSKEFLAPVI 176 (319)
Q Consensus 99 ~a~~iGIivgTl~~q~~~~i~~~l~~ll~~~Gkk~y~i~vg~in~~KLaNf~eID~fV~iaCPr~sidd~~~f~kPvl 176 (319)
..+.|-||=.+-+.-+++.=++.||++|+..|.++..+.-+.-+.+.|.+.++.++=|++ |++.+..-.+.|..|.+
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 346677775554455667777889999999999999999999999999999988877776 88755444456777754
No 143
>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=35.51 E-value=1.7e+02 Score=23.78 Aligned_cols=66 Identities=9% Similarity=0.119 Sum_probs=42.8
Q ss_pred HHHHHHHHHHhhc----cCCEEEEEEcCCCccCcHHHHHHHHHHHHHhCCcEEEEEcCCCCHHhhcCCCCC
Q 020984 86 ILKRRYYLVEKAK----DANIIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKLANFPEC 152 (319)
Q Consensus 86 ~l~~R~~~I~ka~----~a~~iGIivgTl~~q~~~~i~~~l~~ll~~~Gkk~y~i~vg~in~~KLaNf~eI 152 (319)
.+..-...+.+.. +++++-||++.-. .+...-...+.+.++++|.+.|+|.+|..+.+.|..|...
T Consensus 85 al~~a~~~~~~~~~~~~~~~~~iiliTDG~-~~~~~~~~~~~~~~~~~~v~v~~i~~g~~~~~~l~~la~~ 154 (161)
T cd01450 85 ALQYALEQLFSESNARENVPKVIIVLTDGR-SDDGGDPKEAAAKLKDEGIKVFVVGVGPADEEELREIASC 154 (161)
T ss_pred HHHHHHHHhcccccccCCCCeEEEEECCCC-CCCCcchHHHHHHHHHCCCEEEEEeccccCHHHHHHHhCC
Confidence 3333344444543 5777777776632 2221234555666778899999999999888888887654
No 144
>PF03358 FMN_red: NADPH-dependent FMN reductase; InterPro: IPR005025 NADPH-dependent FMN reductase (1.5.1.29 from EC) reduces FMN and also reduces riboflavin and FAD, although more slowly. Members of this entry catalyse the reaction NAD(P)H + FMN = NAD(P)(+) + FMNH(2).; PDB: 3SVL_B 3GFS_F 3GFQ_A 1NNI_1 2GSW_B 3GFR_D 1T0I_B 3D7N_A 2R97_A 3B6K_A ....
Probab=35.48 E-value=86 Score=26.08 Aligned_cols=40 Identities=13% Similarity=0.159 Sum_probs=34.3
Q ss_pred EEEEEEcCC-CccCcHHHHHHHHHHHHHhCCcEEEEEcCCC
Q 020984 102 IIGVLVGTL-GVAGYLHMIHQMKELITKAGKKAYTLVMGKP 141 (319)
Q Consensus 102 ~iGIivgTl-~~q~~~~i~~~l~~ll~~~Gkk~y~i~vg~i 141 (319)
+|.||.|+. ...+...+++.+.+.++++|.++-+|-+.+.
T Consensus 2 kilii~gS~r~~~~t~~l~~~~~~~l~~~g~e~~~i~l~~~ 42 (152)
T PF03358_consen 2 KILIINGSPRKNSNTRKLAEAVAEQLEEAGAEVEVIDLADY 42 (152)
T ss_dssp EEEEEESSSSTTSHHHHHHHHHHHHHHHTTEEEEEEECTTS
T ss_pred EEEEEECcCCCCCHHHHHHHHHHHHHHHcCCEEEEEecccc
Confidence 577889998 4566779999999999999999999988886
No 145
>PRK09590 celB cellobiose phosphotransferase system IIB component; Reviewed
Probab=35.46 E-value=1.1e+02 Score=24.96 Aligned_cols=51 Identities=18% Similarity=0.180 Sum_probs=33.2
Q ss_pred cCcHHHHHHHHHHHHHhCCcEEEEEcCCCCHHhhcCCCCCCEEEEecCCCccc
Q 020984 113 AGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKLANFPECDVFINVSCAQTAL 165 (319)
Q Consensus 113 q~~~~i~~~l~~ll~~~Gkk~y~i~vg~in~~KLaNf~eID~fV~iaCPr~si 165 (319)
-..--+++++++.++++|.++-+-..+--+.+...+-.+.| |++..|+.+.
T Consensus 12 ~STSlla~k~k~~~~e~gi~~~i~a~~~~e~~~~~~~~~~D--vIll~PQi~~ 62 (104)
T PRK09590 12 MSSSMMAKKTTEYLKEQGKDIEVDAITATEGEKAIAAAEYD--LYLVSPQTKM 62 (104)
T ss_pred hHHHHHHHHHHHHHHHCCCceEEEEecHHHHHHhhccCCCC--EEEEChHHHH
Confidence 35558999999999999998655444433333322223467 5667788874
No 146
>KOG0781 consensus Signal recognition particle receptor, alpha subunit [Intracellular trafficking, secretion, and vesicular transport]
Probab=35.29 E-value=2.1e+02 Score=30.24 Aligned_cols=70 Identities=17% Similarity=0.243 Sum_probs=49.6
Q ss_pred HHHHhhccCCEEEEEEcCCCc-cCcHHHHHHHHHHHHHhCCcEEEEEcCCC-----CHHhhc-------CCC---CCCEE
Q 020984 92 YLVEKAKDANIIGVLVGTLGV-AGYLHMIHQMKELITKAGKKAYTLVMGKP-----NPAKLA-------NFP---ECDVF 155 (319)
Q Consensus 92 ~~I~ka~~a~~iGIivgTl~~-q~~~~i~~~l~~ll~~~Gkk~y~i~vg~i-----n~~KLa-------Nf~---eID~f 155 (319)
.+|+.|++-.-=-|||-|-|+ |+...++..|.++++. ++.-.+|+||+- +.+.|. +.+ -||.|
T Consensus 457 ~AI~~a~~~gfDVvLiDTAGR~~~~~~lm~~l~k~~~~-~~pd~i~~vgealvg~dsv~q~~~fn~al~~~~~~r~id~~ 535 (587)
T KOG0781|consen 457 EAIQEARNQGFDVVLIDTAGRMHNNAPLMTSLAKLIKV-NKPDLILFVGEALVGNDSVDQLKKFNRALADHSTPRLIDGI 535 (587)
T ss_pred HHHHHHHhcCCCEEEEeccccccCChhHHHHHHHHHhc-CCCceEEEehhhhhCcHHHHHHHHHHHHHhcCCCccccceE
Confidence 467777776666789999997 8888999999888875 455566666653 344443 333 48888
Q ss_pred EEecCCC
Q 020984 156 INVSCAQ 162 (319)
Q Consensus 156 V~iaCPr 162 (319)
+++-|--
T Consensus 536 ~ltk~dt 542 (587)
T KOG0781|consen 536 LLTKFDT 542 (587)
T ss_pred EEEeccc
Confidence 8887764
No 147
>PRK13937 phosphoheptose isomerase; Provisional
Probab=34.98 E-value=1.8e+02 Score=25.72 Aligned_cols=62 Identities=18% Similarity=0.234 Sum_probs=37.8
Q ss_pred ccCCEEEEEEcCCCccCcHHHHHHHHHHHHHhCCcEEEEEcCCCCHHhhcCCCCCCEEEEecCCCcccc
Q 020984 98 KDANIIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKLANFPECDVFINVSCAQTALL 166 (319)
Q Consensus 98 ~~a~~iGIivgTl~~q~~~~i~~~l~~ll~~~Gkk~y~i~vg~in~~KLaNf~eID~fV~iaCPr~sid 166 (319)
...+-+.|+++.-| ...+++ .+-+.++++|.+.+.|.= -....|+.+ .|..+.+.+++..+.
T Consensus 104 ~~~~Dl~i~iS~sG--~t~~~~-~~~~~ak~~g~~~I~iT~--~~~s~L~~~--ad~~l~~~~~e~~~~ 165 (188)
T PRK13937 104 GRPGDVLIGISTSG--NSPNVL-AALEKARELGMKTIGLTG--RDGGKMKEL--CDHLLIVPSDDTPRI 165 (188)
T ss_pred CCCCCEEEEEeCCC--CcHHHH-HHHHHHHHCCCeEEEEeC--CCCChhHHh--CCEEEEeCCCCcHHH
Confidence 45667778887633 334444 455677888866555544 334445554 678888888776543
No 148
>PRK06756 flavodoxin; Provisional
Probab=34.48 E-value=1.5e+02 Score=24.86 Aligned_cols=56 Identities=7% Similarity=0.127 Sum_probs=38.6
Q ss_pred EEEEEEcCCCccCcHHHHHHHHHHHHHhCCcEEEEEcCCC-CHHhhcCCCCCCEEEEecCCC
Q 020984 102 IIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKP-NPAKLANFPECDVFINVSCAQ 162 (319)
Q Consensus 102 ~iGIivgTl~~q~~~~i~~~l~~ll~~~Gkk~y~i~vg~i-n~~KLaNf~eID~fV~iaCPr 162 (319)
++.||.+|.. -+...+++.|.+.|++.|.++-++-+.+. .... +.+.|. |+++||=
T Consensus 3 kv~IiY~S~t-GnTe~vA~~ia~~l~~~g~~v~~~~~~~~~~~~~---~~~~d~-vi~gspt 59 (148)
T PRK06756 3 KLVMIFASMS-GNTEEMADHIAGVIRETENEIEVIDIMDSPEASI---LEQYDG-IILGAYT 59 (148)
T ss_pred eEEEEEECCC-chHHHHHHHHHHHHhhcCCeEEEeehhccCCHHH---HhcCCe-EEEEeCC
Confidence 6788888853 55668899999999999988777766543 2333 445666 4556653
No 149
>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=34.42 E-value=93 Score=28.76 Aligned_cols=60 Identities=20% Similarity=0.137 Sum_probs=37.3
Q ss_pred EEEEEEcCCCccCcHHHHHHHHHHHHHhCCcEEEEEcCC-CCHHhh----cCC--CCCCEEEEecCC
Q 020984 102 IIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGK-PNPAKL----ANF--PECDVFINVSCA 161 (319)
Q Consensus 102 ~iGIivgTl~~q~~~~i~~~l~~ll~~~Gkk~y~i~vg~-in~~KL----aNf--~eID~fV~iaCP 161 (319)
++|+|+.++.-..+..+++.+.+.++++|....+...+. -++++. .++ ..+|++|+.++.
T Consensus 1 ~igvvvp~~~n~f~~~~~~gi~~~a~~~g~~v~~~~~~~~~~~~~~~~~i~~l~~~~vDgiIi~~~~ 67 (295)
T TIGR02955 1 KLCALYPHLKDSYWLSINYGMVEQAKHLGVELKVLEAGGYPNLDKQLAQIEQCKSWGADAILLGTVS 67 (295)
T ss_pred CeeEEecCCCcHHHHHHHHHHHHHHHHhCCEEEEEcCCCCCCHHHHHHHHHHHHHcCCCEEEEecCC
Confidence 367788777666666777778888888777766654431 233222 122 268888877654
No 150
>COG5136 U1 snRNP-specific protein C [RNA processing and modification]
Probab=34.40 E-value=41 Score=30.16 Aligned_cols=44 Identities=18% Similarity=0.261 Sum_probs=35.5
Q ss_pred HHHHHHHHhCCcEEEEEcCCCCHHhhcCCCCCCEEEEecCCCcc
Q 020984 121 QMKELITKAGKKAYTLVMGKPNPAKLANFPECDVFINVSCAQTA 164 (319)
Q Consensus 121 ~l~~ll~~~Gkk~y~i~vg~in~~KLaNf~eID~fV~iaCPr~s 164 (319)
.+.+-++++|-|+--..-+..+..+..-|+.+|.+.+++||+-.
T Consensus 51 ~~lr~i~~~G~kv~c~gnks~~~p~~~a~~p~d~~~nL~~p~pp 94 (188)
T COG5136 51 SILRDIKTAGEKVECEGNKSTSYPPFPAFPPGDFYLNLALPEPP 94 (188)
T ss_pred HHHHHHhhcCceEEeccCCccCCCCcccCCccchhhhccCCCCC
Confidence 34455667788877777788888888889999999999999875
No 151
>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=34.04 E-value=92 Score=27.41 Aligned_cols=39 Identities=15% Similarity=0.169 Sum_probs=32.6
Q ss_pred EEEEEcCCCccCcHHHHHHHHHHHHHhCCcEEEEEcCCC
Q 020984 103 IGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKP 141 (319)
Q Consensus 103 iGIivgTl~~q~~~~i~~~l~~ll~~~Gkk~y~i~vg~i 141 (319)
+-|.+..|++.|=-.+...|.+.|.+.|+++|++=.+++
T Consensus 3 ~vIwltGlsGsGKtTlA~~L~~~L~~~g~~~~~LDgD~l 41 (156)
T PF01583_consen 3 FVIWLTGLSGSGKTTLARALERRLFARGIKVYLLDGDNL 41 (156)
T ss_dssp EEEEEESSTTSSHHHHHHHHHHHHHHTTS-EEEEEHHHH
T ss_pred EEEEEECCCCCCHHHHHHHHHHHHHHcCCcEEEecCcch
Confidence 457788889999999999999999999999999865533
No 152
>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=33.66 E-value=71 Score=28.49 Aligned_cols=57 Identities=14% Similarity=0.101 Sum_probs=30.7
Q ss_pred EEEEEcCC-CccCcHHHHHHHHHHHHHhCCcEEEEEcCCCCHHhhcC----C--CCCCEEEEecC
Q 020984 103 IGVLVGTL-GVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKLAN----F--PECDVFINVSC 160 (319)
Q Consensus 103 iGIivgTl-~~q~~~~i~~~l~~ll~~~Gkk~y~i~vg~in~~KLaN----f--~eID~fV~iaC 160 (319)
||+|+-.+ ....+..+++.+++.++++|....++. +.-++++... + ..+|++|+.++
T Consensus 2 i~vi~p~~~~~~~~~~~~~g~~~~~~~~g~~~~~~~-~~~~~~~~~~~~~~l~~~~vdgiii~~~ 65 (275)
T cd06317 2 IGYTQNNVGSHSYQTTYNKAFQAAAEEDGVEVIVLD-ANGDVARQAAQVEDLIAQKVDGIILWPT 65 (275)
T ss_pred eEEEecccCCCHHHHHHHHHHHHHHHhcCCEEEEEc-CCcCHHHHHHHHHHHHHcCCCEEEEecC
Confidence 56666665 445555666777777777666644432 3333332211 0 15677766655
No 153
>PF01177 Asp_Glu_race: Asp/Glu/Hydantoin racemase; InterPro: IPR015942 This entry represents a group of related proteins that includes aspartate racemase, glutamate racemase, hydantoin racemase and arylmalonate decarboxylase. Aspartate racemase (5.1.1.13 from EC) and glutamate racemase (5.1.1.3 from EC) are two evolutionary related bacterial enzymes that do not seem to require a cofactor for their activity []. Glutamate racemase, which interconverts L-glutamate into D-glutamate, is required for the biosynthesis of peptidoglycan and some peptide-based antibiotics such as gramicidin S. In addition to characterised aspartate and glutamate racemases, this family also includes a hypothetical protein from Erwinia carotovora and one from Escherichia coli (ygeA). Two conserved cysteines are present in the sequence of these enzymes. They are expected to play a role in catalytic activity by acting as bases in proton abstraction from the substrate.; PDB: 3S7Z_A 3S81_C 3OUT_A 3EIS_B 3IXL_A 3IP8_A 2VLB_D 3DTV_A 3IXM_A 3DG9_A ....
Probab=33.63 E-value=1.5e+02 Score=26.04 Aligned_cols=79 Identities=27% Similarity=0.371 Sum_probs=52.0
Q ss_pred cCCEEEEEEcCCCccCcHHHHHHHHHHHHHh-CC--cEEE-E-------E-cCCCCHH----------hhcCCCCCCEEE
Q 020984 99 DANIIGVLVGTLGVAGYLHMIHQMKELITKA-GK--KAYT-L-------V-MGKPNPA----------KLANFPECDVFI 156 (319)
Q Consensus 99 ~a~~iGIivgTl~~q~~~~i~~~l~~ll~~~-Gk--k~y~-i-------~-vg~in~~----------KLaNf~eID~fV 156 (319)
..++||||-. ........+.+.++++ |. .+.- + . .+.++++ +|..-.++|+ |
T Consensus 106 ~~~ri~vl~t-----~~~~~~~~~~~~~~~~~gi~~~~~~~i~~~~~~~~e~~~~~~~~~~~~~~~~~~l~~~~~~d~-i 179 (216)
T PF01177_consen 106 GGKRIGVLTT-----YTTEKSPLYEEFIEEAAGIDDEVVAGIHNAIYDVIELGDIPPEQIEILAEAARELIKEDGADA-I 179 (216)
T ss_dssp TSSEEEEEES-----HHHHHHTHHHHHHHHCTTEECEEEEEEEEEHTHHHHTTCTTHHHHHHHHHHHHHHHHCTTSSE-E
T ss_pred cCCEEEEEec-----CcccchHHHHHHHHHhcCCcHHHHHHHHhhcHHHHhhhcCCHHHHHHHHHHHHHHhccCCCCE-E
Confidence 6889999874 2234445677778887 74 2221 1 1 6788887 2222567888 6
Q ss_pred EecCCCcccc-c-----ccCCCCcccCHHHHHH
Q 020984 157 NVSCAQTALL-D-----SKEFLAPVITPFEAML 183 (319)
Q Consensus 157 ~iaCPr~sid-d-----~~~f~kPvlTP~El~v 183 (319)
+++|-.++.. . ..++..||++|-+..+
T Consensus 180 iLgCt~l~~~~~~~~~l~~~~gipVid~~~~~~ 212 (216)
T PF01177_consen 180 ILGCTHLPLLLGAIEALEEELGIPVIDSNQAAA 212 (216)
T ss_dssp EEESTTGGGGHHHHHHHHHTCSSEEEEHHHHHH
T ss_pred EECCCchHHHHHHHHhhcccCCCEEEccHHHHH
Confidence 6779999954 2 2456899999988754
No 154
>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=33.50 E-value=85 Score=33.27 Aligned_cols=49 Identities=12% Similarity=0.099 Sum_probs=41.8
Q ss_pred CCEEEEEEcCCCccCcHHHHHHHHHHHHHhCCcEEEEEcCCCCHHhhcCC
Q 020984 100 ANIIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKLANF 149 (319)
Q Consensus 100 a~~iGIivgTl~~q~~~~i~~~l~~ll~~~Gkk~y~i~vg~in~~KLaNf 149 (319)
++.+.|+.||-. -+...++++|.+.++++|..+.++.|++..+..|.+.
T Consensus 58 ~~~i~IlygSqT-Gnae~~A~~l~~~l~~~g~~~~v~~~~d~~~~~l~~~ 106 (597)
T TIGR01931 58 EKRVTILYGSQT-GNARRLAKRLAEKLEAAGFSVRLSSADDYKFKQLKKE 106 (597)
T ss_pred CCeEEEEEECCc-hHHHHHHHHHHHHHHhCCCccEEechHHCCHhhcccC
Confidence 678999999975 3456799999999999999999999999988877665
No 155
>COG0529 CysC Adenylylsulfate kinase and related kinases [Inorganic ion transport and metabolism]
Probab=32.98 E-value=1e+02 Score=28.44 Aligned_cols=40 Identities=15% Similarity=0.119 Sum_probs=34.4
Q ss_pred CCEEEEEEcCCCccCcHHHHHHHHHHHHHhCCcEEEEEcC
Q 020984 100 ANIIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMG 139 (319)
Q Consensus 100 a~~iGIivgTl~~q~~~~i~~~l~~ll~~~Gkk~y~i~vg 139 (319)
.+-+-|-+..|++.|--.++..|.+.|.++|+.+|++==+
T Consensus 21 ~~~~viW~TGLSGsGKSTiA~ale~~L~~~G~~~y~LDGD 60 (197)
T COG0529 21 QKGAVIWFTGLSGSGKSTIANALEEKLFAKGYHVYLLDGD 60 (197)
T ss_pred CCCeEEEeecCCCCCHHHHHHHHHHHHHHcCCeEEEecCh
Confidence 3446678899999999999999999999999999987433
No 156
>PLN03069 magnesiumprotoporphyrin-IX chelatase subunit H; Provisional
Probab=32.35 E-value=1.4e+02 Score=34.77 Aligned_cols=62 Identities=16% Similarity=0.218 Sum_probs=45.6
Q ss_pred cCCEEEEEEcCCC-ccCcHHHHHHHHHHHHHhCCcEEEEEcCCCCHH----h--hcC---CCCCCEEEEecC
Q 020984 99 DANIIGVLVGTLG-VAGYLHMIHQMKELITKAGKKAYTLVMGKPNPA----K--LAN---FPECDVFINVSC 160 (319)
Q Consensus 99 ~a~~iGIivgTl~-~q~~~~i~~~l~~ll~~~Gkk~y~i~vg~in~~----K--LaN---f~eID~fV~iaC 160 (319)
++.+||||+...- ..+....++.|.+.|+++|..++.++.+.+... + +.+ =+.||+.|.+..
T Consensus 265 ~~p~Vgil~~r~~~~~~~~~~idalI~~LE~~G~~vipvf~~gl~~~~~~~~~~~~~~~~~~~vDaiIn~tg 336 (1220)
T PLN03069 265 DAPVVGLVLQRSHIVTGDDGHYVAVVMELEARGAKVVPIFAGGLDFSGPVERFFYDPITKKPIVDSVVSLTG 336 (1220)
T ss_pred CCCEEEEEechhhhhcCCcHHHHHHHHHHHHCCCeEEEEEecCccccchHHHHHHhhhcCCCCccEEEECCc
Confidence 4789999997433 467889999999999999999999888765511 1 111 135899886654
No 157
>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=31.89 E-value=82 Score=29.06 Aligned_cols=43 Identities=16% Similarity=0.181 Sum_probs=22.3
Q ss_pred cCCEEEEEEcCCCccC-cHHHHHHHHHHHHHhCCcEEEEEcCCCC
Q 020984 99 DANIIGVLVGTLGVAG-YLHMIHQMKELITKAGKKAYTLVMGKPN 142 (319)
Q Consensus 99 ~a~~iGIivgTl~~q~-~~~i~~~l~~ll~~~Gkk~y~i~vg~in 142 (319)
+.+.+-+.+|.+..+. ...+++.++ .|++.+.....+++|.-+
T Consensus 183 ~~~~~i~~~Gr~~~~Kg~~~li~~~~-~l~~~~~~~~l~ivG~~~ 226 (355)
T cd03819 183 KGKPVILLPGRLTRWKGQEVFIEALA-RLKKDDPDVHLLIVGDAQ 226 (355)
T ss_pred CCceEEEEeeccccccCHHHHHHHHH-HHHhcCCCeEEEEEECCc
Confidence 3445556666665543 334444443 344445566666666543
No 158
>TIGR00114 lumazine-synth 6,7-dimethyl-8-ribityllumazine synthase. Archaeal members of this family are considered putative, although included in the seed and scoring above the trusted cutoff.
Probab=31.83 E-value=1.4e+02 Score=25.73 Aligned_cols=60 Identities=13% Similarity=0.224 Sum_probs=38.9
Q ss_pred EEEEEEcCCCccCcHHHHHHHHHHHHHhCCc---EEEEEcCCCC-----HHhhcCCCCCCEEEEecCC
Q 020984 102 IIGVLVGTLGVAGYLHMIHQMKELITKAGKK---AYTLVMGKPN-----PAKLANFPECDVFINVSCA 161 (319)
Q Consensus 102 ~iGIivgTl~~q~~~~i~~~l~~ll~~~Gkk---~y~i~vg~in-----~~KLaNf~eID~fV~iaCP 161 (319)
+||||++..-..-.-.+++-..+.|+++|.. ..++.|--.. ..+|+.=.++|++|.++|-
T Consensus 2 ri~IV~s~~n~~i~~~L~~ga~~~l~~~g~~~~~i~v~~VPGa~EiP~a~~~l~~~~~~DavI~LG~V 69 (138)
T TIGR00114 2 RVGIVIARFNRDITDMLLKGAIDALKRLGAEVDNIDVIWVPGAFELPLAVKKLAETGKYDAVIALGCV 69 (138)
T ss_pred EEEEEEecCCHHHHHHHHHHHHHHHHHcCCCccceEEEECCcHHHHHHHHHHHHhcCCCCEEEEEeeE
Confidence 6888888755444445555566688888865 2345443222 1356655579999999996
No 159
>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=31.78 E-value=1.7e+02 Score=25.78 Aligned_cols=86 Identities=22% Similarity=0.147 Sum_probs=44.1
Q ss_pred cchHHHHHHhcC-CCeEEEEcCCCCccccccC--------------cHHHHHHHHHHHHHhhccCCEEEEEEcCCCccCc
Q 020984 51 NSAFANVVLTFN-GCEIVRYDATEERLLTDVS--------------QPLKILKRRYYLVEKAKDANIIGVLVGTLGVAGY 115 (319)
Q Consensus 51 ~~~l~~l~l~~~-~~~v~~yDP~s~~~~~e~~--------------~~~k~l~~R~~~I~ka~~a~~iGIivgTl~~q~~ 115 (319)
..++...++.-- ...+...||..-+-....+ ...........++++|.+.+.=-|+=+|++..
T Consensus 28 KSt~~~~~~~~~~~~~~v~i~~D~~r~~~p~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~a~~~~~nii~E~tl~~~-- 105 (199)
T PF06414_consen 28 KSTLARQLLEEFGGGGIVVIDADEFRQFHPDYDELLKADPDEASELTQKEASRLAEKLIEYAIENRYNIIFEGTLSNP-- 105 (199)
T ss_dssp THHHHHHHHHHT-TT-SEEE-GGGGGGGSTTHHHHHHHHCCCTHHHHHHHHHHHHHHHHHHHHHCT--EEEE--TTSS--
T ss_pred HHHHHHHhhhhccCCCeEEEehHHHHHhccchhhhhhhhhhhhHHHHHHHHHHHHHHHHHHHHHcCCCEEEecCCCCh--
Confidence 355555444422 3456777776543222111 01222334456788888887776778888644
Q ss_pred HHHHHHHHHHHHHhCCcEEEEEcC
Q 020984 116 LHMIHQMKELITKAGKKAYTLVMG 139 (319)
Q Consensus 116 ~~i~~~l~~ll~~~Gkk~y~i~vg 139 (319)
..+..+.+.++++|.++.+++|.
T Consensus 106 -~~~~~~~~~~k~~GY~v~l~~v~ 128 (199)
T PF06414_consen 106 -SKLRKLIREAKAAGYKVELYYVA 128 (199)
T ss_dssp -HHHHHHHHHHHCTT-EEEEEEE-
T ss_pred -hHHHHHHHHHHcCCceEEEEEEE
Confidence 44444667777889887777666
No 160
>PLN02948 phosphoribosylaminoimidazole carboxylase
Probab=31.74 E-value=1.3e+02 Score=31.86 Aligned_cols=116 Identities=17% Similarity=0.287 Sum_probs=70.5
Q ss_pred HHhcCCCeEEEEcCCCCc-------cccccCcHHHHHHHHHHHHHhh--------ccCCEEEEEEcCCCccCcHHHHHHH
Q 020984 58 VLTFNGCEIVRYDATEER-------LLTDVSQPLKILKRRYYLVEKA--------KDANIIGVLVGTLGVAGYLHMIHQM 122 (319)
Q Consensus 58 ~l~~~~~~v~~yDP~s~~-------~~~e~~~~~k~l~~R~~~I~ka--------~~a~~iGIivgTl~~q~~~~i~~~l 122 (319)
.+..|+..++.|.....+ +.....+......+-..++... +....||||+|+ ..-+.+++..
T Consensus 353 ~~~~p~~~v~~ygk~~~r~~rkmGhV~~~g~~~~e~~~~~~~~~~~~~~~~~~~~~~~~~v~i~~gs---~sd~~~~~~~ 429 (577)
T PLN02948 353 ALNIPGASVHWYGKPEMRKQRKMGHITVVGPSAAEVEARLDQLLAEESADPDALPKGTPLVGIIMGS---DSDLPTMKDA 429 (577)
T ss_pred HhhCCCCEEEEecCCCCCCCCeeEEEEEecCCHHHHHHHHHHHHhhhccCCCCCCCCCCeEEEEECc---hhhHHHHHHH
Confidence 445677888888652211 1111123444433333333221 124679999998 6788999999
Q ss_pred HHHHHHhCCcEEEEEcC-CCCHHhhcCC------CCCCEEEEecCCCccccc--ccCCCCccc
Q 020984 123 KELITKAGKKAYTLVMG-KPNPAKLANF------PECDVFINVSCAQTALLD--SKEFLAPVI 176 (319)
Q Consensus 123 ~~ll~~~Gkk~y~i~vg-~in~~KLaNf------~eID~fV~iaCPr~sidd--~~~f~kPvl 176 (319)
.+.|++.|.++-+-+.+ .=+|+++..| .++++||.+|==...+-- ...-.+|||
T Consensus 430 ~~~l~~~g~~~~~~v~sahr~~~~~~~~~~~~~~~~~~v~i~~ag~~~~l~~~~a~~t~~pvi 492 (577)
T PLN02948 430 AEILDSFGVPYEVTIVSAHRTPERMFSYARSAHSRGLQVIIAGAGGAAHLPGMVASMTPLPVI 492 (577)
T ss_pred HHHHHHcCCCeEEEEECCccCHHHHHHHHHHHHHCCCCEEEEEcCccccchHHHhhccCCCEE
Confidence 99999999987665555 5678888877 468877665544443321 223455655
No 161
>PRK08662 nicotinate phosphoribosyltransferase; Reviewed
Probab=31.71 E-value=67 Score=31.81 Aligned_cols=55 Identities=16% Similarity=0.368 Sum_probs=40.0
Q ss_pred CEEEEEEcCCCc--cCcHHHHHHHHHHHHHhC-CcEEEEEcCCCCHHhhcCCCC-CCEE
Q 020984 101 NIIGVLVGTLGV--AGYLHMIHQMKELITKAG-KKAYTLVMGKPNPAKLANFPE-CDVF 155 (319)
Q Consensus 101 ~~iGIivgTl~~--q~~~~i~~~l~~ll~~~G-kk~y~i~vg~in~~KLaNf~e-ID~f 155 (319)
...+|.+-+.+. ..-..+++++++.+++.| .+..+.+.|.||++++..|.+ ||+|
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 456777777663 455667777888888887 457788889999999998753 5544
No 162
>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=31.51 E-value=1.6e+02 Score=25.89 Aligned_cols=56 Identities=11% Similarity=0.058 Sum_probs=41.1
Q ss_pred HHHHHHHHHhhccCCEEEEEEcCCCccCcHHHHHHHHHHHHHhCCcEEEEEcCCCCH
Q 020984 87 LKRRYYLVEKAKDANIIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNP 143 (319)
Q Consensus 87 l~~R~~~I~ka~~a~~iGIivgTl~~q~~~~i~~~l~~ll~~~Gkk~y~i~vg~in~ 143 (319)
.+.|..+.....+.++| .|++.+++.|--.+.-.|-..+..+|+++.+|=++--++
T Consensus 4 ~~l~~~l~~~~~~~kvI-~v~s~kgG~GKTt~a~~LA~~la~~G~rVllID~D~~~~ 59 (204)
T TIGR01007 4 NAIRTNIQFSGAEIKVL-LITSVKPGEGKSTTSANIAVAFAQAGYKTLLIDGDMRNS 59 (204)
T ss_pred HHHHHHHhhhcCCCcEE-EEecCCCCCCHHHHHHHHHHHHHhCCCeEEEEeCCCCCh
Confidence 34455555555566766 568888999999999999999999999987776653333
No 163
>PRK08883 ribulose-phosphate 3-epimerase; Provisional
Probab=30.83 E-value=74 Score=29.36 Aligned_cols=49 Identities=14% Similarity=0.367 Sum_probs=35.6
Q ss_pred CccCcH----HHHHHHHHHHHHhCCcEEEEEcCCCCHHhhcCCC--CCCEEEEec
Q 020984 111 GVAGYL----HMIHQMKELITKAGKKAYTLVMGKPNPAKLANFP--ECDVFINVS 159 (319)
Q Consensus 111 ~~q~~~----~i~~~l~~ll~~~Gkk~y~i~vg~in~~KLaNf~--eID~fV~ia 159 (319)
++|.+. +-++++++++.++|.+.-+.+-|-||++.+..+. ++|++|..+
T Consensus 142 gGq~fi~~~lekI~~l~~~~~~~~~~~~I~vdGGI~~eni~~l~~aGAd~vVvGS 196 (220)
T PRK08883 142 GGQSFIPHTLDKLRAVRKMIDESGRDIRLEIDGGVKVDNIREIAEAGADMFVAGS 196 (220)
T ss_pred CCceecHhHHHHHHHHHHHHHhcCCCeeEEEECCCCHHHHHHHHHcCCCEEEEeH
Confidence 355554 3566666677777777778889999998887653 689998863
No 164
>cd05015 SIS_PGI_1 Phosphoglucose isomerase (PGI) contains two SIS (Sugar ISomerase) domains. This classification is based on the alignment of the first SIS domain. PGI is a multifunctional enzyme which as an intracellular dimer catalyzes the reversible isomerization of glucose 6-phosphate to fructose 6-phosphate. As an extracellular protein, PGI also has functions equivalent to neuroleukin (NLK), autocrine motility factor (AMF), and maturation factor (MF). Evidence suggests that PGI, NLK, AMF, and MF are closely related or identical. NLK is a neurotrophic growth factor that promotes regeneration and survival of neurons. The dimeric form of NLK has isomerase function, whereas its monomeric form carries out neurotrophic activity. AMF is a cytokine that stimulates cell migration and metastasis. MF mediates the differentiation of human myeloid leukemic HL-60 cells to terminal monocytic cells.
Probab=30.58 E-value=3.4e+02 Score=23.28 Aligned_cols=47 Identities=15% Similarity=0.131 Sum_probs=25.7
Q ss_pred CCEEEEEEcCCCcc--CcHHHHHHHHHHHHHhC---CcEEEEEcCCCCHHhhcC
Q 020984 100 ANIIGVLVGTLGVA--GYLHMIHQMKELITKAG---KKAYTLVMGKPNPAKLAN 148 (319)
Q Consensus 100 a~~iGIivgTl~~q--~~~~i~~~l~~ll~~~G---kk~y~i~vg~in~~KLaN 148 (319)
.+++ +|+.++++. -....++.++++++++| ....++++.. +...|+.
T Consensus 73 ~~tl-vi~iSkSG~T~Et~~~~~~a~~~l~~~~~~~~~~~~vaiT~-~~s~l~~ 124 (158)
T cd05015 73 ETTL-FIVISKSGTTLETLANARLAREWLEEAGGDDLAKHFVAITD-NGSGLLK 124 (158)
T ss_pred ccEE-EEEEECCcCCHHHHHHHHHHHHHHHHhccccccceEEEEcC-CChHHHH
Confidence 4555 666666553 33455666677777665 3445666666 3334444
No 165
>PRK00005 fmt methionyl-tRNA formyltransferase; Reviewed
Probab=30.51 E-value=1.6e+02 Score=28.32 Aligned_cols=41 Identities=27% Similarity=0.301 Sum_probs=29.0
Q ss_pred HHHHHHHHhCCcEEEEEcCCCC----HHhhcCCCCCCEEEEecCCCcc
Q 020984 121 QMKELITKAGKKAYTLVMGKPN----PAKLANFPECDVFINVSCAQTA 164 (319)
Q Consensus 121 ~l~~ll~~~Gkk~y~i~vg~in----~~KLaNf~eID~fV~iaCPr~s 164 (319)
.+++.++++|..++. ..+++ .+.|.++ +.|+.|.+++.+.-
T Consensus 47 ~v~~~a~~~~Ip~~~--~~~~~~~~~~~~l~~~-~~Dliv~~~~~~ii 91 (309)
T PRK00005 47 PVKQLALEHGIPVLQ--PEKLRDPEFLAELAAL-NADVIVVVAYGQIL 91 (309)
T ss_pred HHHHHHHHcCCCEEC--cCCCCCHHHHHHHHhc-CcCEEEEehhhccc
Confidence 567788888888644 45554 3455566 89999999997663
No 166
>PRK09267 flavodoxin FldA; Validated
Probab=30.44 E-value=1e+02 Score=26.38 Aligned_cols=54 Identities=13% Similarity=0.225 Sum_probs=35.5
Q ss_pred EEEEEEcCCCccCcHHHHHHHHHHHHHhCCcEEEEEcCCCCHHhhcCCCCCCEEEEecCCC
Q 020984 102 IIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKLANFPECDVFINVSCAQ 162 (319)
Q Consensus 102 ~iGIivgTl~~q~~~~i~~~l~~ll~~~Gkk~y~i~vg~in~~KLaNf~eID~fV~iaCPr 162 (319)
++.|+.+|.. -+...+++.|.+.|.. ..+-++-+.+.++..| .+.|+ |++++|-
T Consensus 3 ki~IiY~S~t-GnT~~vA~~Ia~~l~~--~~~~~~~~~~~~~~~l---~~~d~-vi~g~pt 56 (169)
T PRK09267 3 KIGIFFGSDT-GNTEDIAKMIQKKLGK--DVADVVDIAKASKEDF---EAYDL-LILGIPT 56 (169)
T ss_pred eEEEEEECCC-ChHHHHHHHHHHHhCC--CceEEEEhhhCCHhhH---hhCCE-EEEEecC
Confidence 5889999965 3455778888888753 3556666777665544 45676 5555553
No 167
>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=30.42 E-value=1.1e+02 Score=23.12 Aligned_cols=56 Identities=16% Similarity=0.229 Sum_probs=33.4
Q ss_pred EEcCCCccCcHHHHHHHHHHHHHhCCcEEEEEcCCCCHHhhcCCCCCCEEEEecCCCccc
Q 020984 106 LVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKLANFPECDVFINVSCAQTAL 165 (319)
Q Consensus 106 ivgTl~~q~~~~i~~~l~~ll~~~Gkk~y~i~vg~in~~KLaNf~eID~fV~iaCPr~si 165 (319)
++..-|...+.-+.++|++.++++|.+...............+ ++|+++. -|....
T Consensus 4 vvC~~Gi~TS~~~~~~i~~~~~~~gi~~~~~~~~~~~~~~~~~--~~D~il~--~~~i~~ 59 (90)
T PF02302_consen 4 VVCGSGIGTSLMVANKIKKALKELGIEVEVSAGSILEVEEIAD--DADLILL--TPQIAY 59 (90)
T ss_dssp EEESSSSHHHHHHHHHHHHHHHHTTECEEEEEEETTTHHHHHT--T-SEEEE--EESSGG
T ss_pred EECCChHHHHHHHHHHHHHHHHhccCceEEEEecccccccccC--CCcEEEE--cCccch
Confidence 3344343444444499999999999888777777333333322 4787654 455543
No 168
>cd01982 Chlide_reductase_Z Chlide_reductase_Z : Z subunit of chlorophyllide (chlide) reductase (BchZ). Chlide reductase participates in photosynthetic pigment synthesis playing a role in the conversion of chlorophylls(Chl) into bacteriochlorophylls (BChl). Chlide reductase catalyzes the reduction of the B-ring of the tetrapyrolle. Chlide reductase is a three subunit enzyme (subunits are designated BchX, BchY and BchZ). The similarity between these three subunits and the subunits for nitrogenase suggests that BchX serves as an electron donor for the BchY-BchY catalytic subunits.
Probab=30.31 E-value=90 Score=31.72 Aligned_cols=76 Identities=11% Similarity=0.138 Sum_probs=55.8
Q ss_pred CCEEEEEEcCCCccCcHHHHHHHHHHHHHhCCcEEEEEcCCCCHHhhcCCCCCCEEEEecCCCcccccccCCCCccc
Q 020984 100 ANIIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKLANFPECDVFINVSCAQTALLDSKEFLAPVI 176 (319)
Q Consensus 100 a~~iGIivgTl~~q~~~~i~~~l~~ll~~~Gkk~y~i~vg~in~~KLaNf~eID~fV~iaCPr~sidd~~~f~kPvl 176 (319)
...|-||=.+.+--+.+.=++.|+++|+..|.++..+.-+.-+.+.|...++.++=+++ |++.+..-.+.|..|.+
T Consensus 155 ~~~VNIIG~~~g~~~~~gDl~ElkrLLe~~Gl~vn~v~~~gt~l~eI~~l~~A~lniv~-~~~~g~~L~e~~giPy~ 230 (412)
T cd01982 155 KGTVNIIGPSYGCFNSPSDLAEVKRLVTGIGAEVNHVYPFESHLAEIPKLKNAAVNVVM-YREFGRGLAEDLGRPYL 230 (412)
T ss_pred CCeEEEECCCcCcCCCHHHHHHHHHHHHHcCCcEEEECCCCCCHHHHHhhccCCEEEEe-CHHHHHHHHHHHCcCeE
Confidence 35687775554445567778899999999999999898888999999999988877766 76544333334555543
No 169
>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=29.86 E-value=1.6e+02 Score=22.33 Aligned_cols=56 Identities=23% Similarity=0.227 Sum_probs=30.7
Q ss_pred EEEEEcCCCccCcHHHHHHHHHHHHHhCCcEEEEEcCCCCHHhhcCCCCCCEEEEecCCC
Q 020984 103 IGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKLANFPECDVFINVSCAQ 162 (319)
Q Consensus 103 iGIivgTl~~q~~~~i~~~l~~ll~~~Gkk~y~i~vg~in~~KLaNf~eID~fV~iaCPr 162 (319)
+.++.++ |.....-+..+|++.+.+.+....+-.++...... ...++| +|+++.|-
T Consensus 3 ilivC~~-G~~tS~~l~~~i~~~~~~~~i~~~v~~~~~~~~~~--~~~~~D-liist~~~ 58 (89)
T cd05566 3 ILVACGT-GVATSTVVASKVKELLKENGIDVKVEQCKIAEVPS--LLDDAD-LIVSTTKV 58 (89)
T ss_pred EEEECCC-CccHHHHHHHHHHHHHHHCCCceEEEEecHHHhhc--ccCCCc-EEEEcCCc
Confidence 4344443 43344578889999998888764443333222222 244678 45555553
No 170
>cd05565 PTS_IIB_lactose PTS_IIB_lactose: subunit IIB of enzyme II (EII) of the lactose-specific phosphoenolpyruvate:carbohydrate phosphotransferase system (PTS) found in Firmicutes as well as Actinobacteria. In this system, EII is a lactose-specific permease with two cytoplasmic domains (IIA and IIB) and a transmembrane channel IIC domain. The IIC and IIB domains are expressed as a single protein from the lac operon. 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 lactose, chitobiose/lichenan, ascorbate, galactitol, mannitol, fructose, and a sensory system with similarity to the bacterial bgl system.
Probab=29.78 E-value=1.5e+02 Score=24.08 Aligned_cols=50 Identities=12% Similarity=0.021 Sum_probs=33.3
Q ss_pred ccCcHHHHHHHHHHHHHhCCcEEEEEcCCCCHHhhcCCCCCCEEEEecCCCccc
Q 020984 112 VAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKLANFPECDVFINVSCAQTAL 165 (319)
Q Consensus 112 ~q~~~~i~~~l~~ll~~~Gkk~y~i~vg~in~~KLaNf~eID~fV~iaCPr~si 165 (319)
|..+--+++++++.++++|..+.+...+.-..+. +..++|+++ .=|+...
T Consensus 10 GaSSs~la~km~~~a~~~gi~~~i~a~~~~e~~~--~~~~~Dvil--l~PQv~~ 59 (99)
T cd05565 10 GGTSGLLANALNKGAKERGVPLEAAAGAYGSHYD--MIPDYDLVI--LAPQMAS 59 (99)
T ss_pred CCCHHHHHHHHHHHHHHCCCcEEEEEeeHHHHHH--hccCCCEEE--EcChHHH
Confidence 4778889999999999999986655544333222 355678544 4465553
No 171
>cd05291 HicDH_like L-2-hydroxyisocapronate dehydrogenases and some bacterial L-lactate dehydrogenases. L-2-hydroxyisocapronate dehydrogenase (HicDH) catalyzes the conversion of a variety of 2-oxo carboxylic acids with medium-sized aliphatic or aromatic side chains. This subfamily is composed of HicDHs and some bacterial L-lactate dehydrogenases (LDH). LDHs catalyze the last step of glycolysis in which pyruvate is converted to L-lactate. Bacterial LDHs can be non-allosteric or may be activated by an allosteric effector such as fructose-1,6-bisphosphate. Members of this subfamily with known structures such as the HicDH of Lactobacillus confusus, the non-allosteric LDH of Lactobacillus pentosus, and the allosteric LDH of Bacillus stearothermophilus, show that they exist as homotetramers. The HicDH-like subfamily is part of the NAD(P)-binding Rossmann fold superfamily, which includes a wide variety of protein families including the NAD(P)-binding domains of alcohol dehydrogenases, tyrosine
Probab=29.74 E-value=2.3e+02 Score=27.01 Aligned_cols=99 Identities=21% Similarity=0.213 Sum_probs=56.1
Q ss_pred eEEEEcCCc--chHHHHHHhcCC-CeEEEEcCCCCccccccCcHHHHH---H----HHHHHHHhhccCCEEEEEEcCCC-
Q 020984 43 LLFWIGSDN--SAFANVVLTFNG-CEIVRYDATEERLLTDVSQPLKIL---K----RRYYLVEKAKDANIIGVLVGTLG- 111 (319)
Q Consensus 43 ~i~~Ig~~~--~~l~~l~l~~~~-~~v~~yDP~s~~~~~e~~~~~k~l---~----~R~~~I~ka~~a~~iGIivgTl~- 111 (319)
.+..||.|. .++...++...- ..++.||....+......+..... . .+....+.+++|..+-+-.|...
T Consensus 2 kI~IIGaG~vG~~~a~~l~~~g~~~ei~l~D~~~~~~~~~a~dL~~~~~~~~~~~~i~~~~~~~l~~aDIVIitag~~~~ 81 (306)
T cd05291 2 KVVIIGAGHVGSSFAYSLVNQGIADELVLIDINEEKAEGEALDLEDALAFLPSPVKIKAGDYSDCKDADIVVITAGAPQK 81 (306)
T ss_pred EEEEECCCHHHHHHHHHHHhcCCCCEEEEEeCCcchhhHhHhhHHHHhhccCCCeEEEcCCHHHhCCCCEEEEccCCCCC
Confidence 356688775 334444444433 379999986654322222211111 0 01112234567777766665532
Q ss_pred -cc-------CcHHHHHHHHHHHHHhCCcEEEEEcCCC
Q 020984 112 -VA-------GYLHMIHQMKELITKAGKKAYTLVMGKP 141 (319)
Q Consensus 112 -~q-------~~~~i~~~l~~ll~~~Gkk~y~i~vg~i 141 (319)
++ .+..+++.+-+.|++++.+..+++++++
T Consensus 82 ~g~~R~dll~~N~~i~~~~~~~i~~~~~~~~vivvsNP 119 (306)
T cd05291 82 PGETRLDLLEKNAKIMKSIVPKIKASGFDGIFLVASNP 119 (306)
T ss_pred CCCCHHHHHHHHHHHHHHHHHHHHHhCCCeEEEEecCh
Confidence 22 2556677788888899999999999943
No 172
>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=29.68 E-value=45 Score=28.67 Aligned_cols=85 Identities=14% Similarity=0.203 Sum_probs=49.6
Q ss_pred HHHHHHHHHHhhcc--CCEEEEEEcCCCccCcHHHHHHHHHHHHHhCCcEEEEEcCCCCHHhhcCCCCCCEEEEecCCCc
Q 020984 86 ILKRRYYLVEKAKD--ANIIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKLANFPECDVFINVSCAQT 163 (319)
Q Consensus 86 ~l~~R~~~I~ka~~--a~~iGIivgTl~~q~~~~i~~~l~~ll~~~Gkk~y~i~vg~in~~KLaNf~eID~fV~iaCPr~ 163 (319)
..+.-.+.|..|+. -...-|-++.-+|...+.-...+.++|+ + .||++||++.-|-+
T Consensus 28 ~HK~eKYfITsAkRD~~g~Lql~i~pasGrrkLspt~emi~~l~--------------------~-geIel~VLttqpDI 86 (144)
T PF10657_consen 28 VHKAEKYFITSAKRDRYGKLQLTISPASGRRKLSPTPEMIDKLI--------------------S-GEIELFVLTTQPDI 86 (144)
T ss_pred hhhhheeEEeeeecccCCceEEEEecCCCccccCCcHHHHHHHh--------------------c-CceEEEEEccCCCe
Confidence 34444556666663 3455566666555444433333333332 2 27999999999999
Q ss_pred ccccccCCCCcccCHHHHHHhhCCCCCCCcceeeccccccCCCCCCC
Q 020984 164 ALLDSKEFLAPVITPFEAMLAFGRGTQWTGAYVMEFRDLMSSSPVEG 210 (319)
Q Consensus 164 sidd~~~f~kPvlTP~El~vAL~~~~~W~~~y~~Df~~ll~~~~~~~ 210 (319)
+|+-.+. .+.+ ..+|++||+.- +-.|+.
T Consensus 87 ai~l~~k-------------Vldn----EnRYViDFD~R--GvkwTM 114 (144)
T PF10657_consen 87 AINLQQK-------------VLDN----ENRYVIDFDKR--GVKWTM 114 (144)
T ss_pred eechhhh-------------hhcc----cceEEEeccCC--cceeEe
Confidence 9984321 2232 36899999764 345543
No 173
>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=29.56 E-value=1e+02 Score=27.79 Aligned_cols=56 Identities=9% Similarity=0.061 Sum_probs=38.5
Q ss_pred EEEEEcCCCccCcHHHHHHHHHHHHHhC-CcEEEEEcCCCCHH-hhc---CCCCCCEEEEecCC
Q 020984 103 IGVLVGTLGVAGYLHMIHQMKELITKAG-KKAYTLVMGKPNPA-KLA---NFPECDVFINVSCA 161 (319)
Q Consensus 103 iGIivgTl~~q~~~~i~~~l~~ll~~~G-kk~y~i~vg~in~~-KLa---Nf~eID~fV~iaCP 161 (319)
+.|++..+ -..+..++..+.+.++++| +..++...++ .+. .+. + ..+|.+|++++.
T Consensus 2 ~~~~~~~~-~~~~~~~~~~i~~~l~~~g~~~l~~~~~~~-~~~~~~~~~~~-~~vdGvIi~~~~ 62 (247)
T cd06276 2 ILLLLNKL-SSFKEIIYNSFVNTLGKNAQVDLYFHHYNE-DLFKNIISNTK-GKYSGYVVMPHF 62 (247)
T ss_pred EEEEEecC-chHHHHHHHHHHHHHHhcCcEEEEEEcCch-HHHHHHHHHHh-cCCCEEEEecCC
Confidence 67888888 5667789999999999999 5544444443 221 111 2 369999998864
No 174
>cd06354 PBP1_BmpA_PnrA_like Periplasmic binding domain of basic membrane lipoprotein, PnrA, in Treponema pallidum and its homologs from other bacteria and Archaea. Periplasmic binding domain of basic membrane lipoprotein, PnrA, in Treponema pallidum and its homologs from other bacteria and Archaea. The PnrA lipoprotein, also known as Tp0319 or TmpC, represents a novel family of bacterial purine nucleoside receptor encoded within an ATP-binding cassette (ABC) transport system (pnrABCDE). It shows a striking structural similarity to another basic membrane lipoprotein Med which regulates the competence transcription factor gene, comK, in Bacillus subtilis. The members of PnrA-like subgroup are likely to have similar nucleoside-binding functions and a similar type I periplasmic sugar-binding protein-like fold.
Probab=29.51 E-value=1.4e+02 Score=27.16 Aligned_cols=58 Identities=9% Similarity=0.059 Sum_probs=35.9
Q ss_pred EEEEEEcC---CCccCcHHHHHHHHHHHHHhCCcEEEEEcCCCCHHh----hcCCC--CCCEEEEecCC
Q 020984 102 IIGVLVGT---LGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAK----LANFP--ECDVFINVSCA 161 (319)
Q Consensus 102 ~iGIivgT---l~~q~~~~i~~~l~~ll~~~Gkk~y~i~vg~in~~K----LaNf~--eID~fV~iaCP 161 (319)
+||+|+.. +....+..+++.+.+.++++|....++... ++++ +.++. .+|.+|++++.
T Consensus 1 ~I~~i~~~~~~~~~~f~~~~~~gi~~~~~~~gy~~~i~~~~--~~~~~~~~i~~l~~~~vdgiI~~~~~ 67 (265)
T cd06354 1 KVALVTDVGGLGDKSFNQSAWEGLERAAKELGIEYKYVESK--SDADYEPNLEQLADAGYDLIVGVGFL 67 (265)
T ss_pred CEEEEeCCCCcCchhHHHHHHHHHHHHHHHcCCeEEEEecC--CHHHHHHHHHHHHhCCCCEEEEcCcc
Confidence 36777754 445566788888888888888765555433 3221 22222 58888876543
No 175
>TIGR00147 lipid kinase, YegS/Rv2252/BmrU family. The E. coli member of this family, YegS has been purified and shown to have phosphatidylglycerol kinase activity. The member from M. tuberculosis, Rv2252, has diacylglycerol kinase activity. BmrU from B. subtilis is in an operon with multidrug efflux transporter Bmr, but is uncharacterized.
Probab=29.42 E-value=1.9e+02 Score=27.07 Aligned_cols=36 Identities=8% Similarity=0.034 Sum_probs=16.8
Q ss_pred EEEEEEcCCCccC-cHHHHHHHHHHHHHhCCcEEEEE
Q 020984 102 IIGVLVGTLGVAG-YLHMIHQMKELITKAGKKAYTLV 137 (319)
Q Consensus 102 ~iGIivgTl~~q~-~~~i~~~l~~ll~~~Gkk~y~i~ 137 (319)
+++||++..++.+ ..+.++.+++.|+++|.++.++.
T Consensus 3 ~~~ii~Np~sg~~~~~~~~~~i~~~l~~~~~~~~~~~ 39 (293)
T TIGR00147 3 EAPAILNPTAGKSNDNKPLREVIMLLREEGMEIHVRV 39 (293)
T ss_pred eEEEEECCCccchhhHHHHHHHHHHHHHCCCEEEEEE
Confidence 4555555544432 23344455555555555544333
No 176
>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=29.35 E-value=3e+02 Score=24.57 Aligned_cols=93 Identities=15% Similarity=0.132 Sum_probs=49.1
Q ss_pred cCCCeEEEEcCCCC--c---cccccCcHHHHHHHHHHHHHhhccCCEEEEEEcCCCccCcHHHHHHHHHHHHHh-CCcEE
Q 020984 61 FNGCEIVRYDATEE--R---LLTDVSQPLKILKRRYYLVEKAKDANIIGVLVGTLGVAGYLHMIHQMKELITKA-GKKAY 134 (319)
Q Consensus 61 ~~~~~v~~yDP~s~--~---~~~e~~~~~k~l~~R~~~I~ka~~a~~iGIivgTl~~q~~~~i~~~l~~ll~~~-Gkk~y 134 (319)
..+.|+..+|.... . +....+...+... .+++.+....++++++.+.........-.+.+++.++++ |.+..
T Consensus 80 ~~~iPvV~~~~~~~~~~~~~V~~d~~~~g~~~~--~~l~~~~~g~~~i~~l~~~~~~~~~~~r~~g~~~~~~~~~~~~~~ 157 (275)
T cd06320 80 KKGIPVVNVNDKLIPNATAFVGTDNKANGVRGA--EWIIDKLAEGGKVAIIEGKAGAFAAEQRTEGFTEAIKKASGIEVV 157 (275)
T ss_pred HCCCeEEEECCCCCCccceEEecCcHHHHHHHH--HHHHHHhCCCceEEEEeCCCCCccHHHHHHHHHHHHhhCCCcEEE
Confidence 34678888886421 1 1111111222222 123333335679999887655444445556788888888 87755
Q ss_pred EEEcCCCCHH--------hhcCCCCCCEE
Q 020984 135 TLVMGKPNPA--------KLANFPECDVF 155 (319)
Q Consensus 135 ~i~vg~in~~--------KLaNf~eID~f 155 (319)
....+..+++ .|.+.+++|++
T Consensus 158 ~~~~~~~~~~~~~~~~~~~l~~~~~~~ai 186 (275)
T cd06320 158 ASQPADWDREKAYDVATTILQRNPDLKAI 186 (275)
T ss_pred EecCCCccHHHHHHHHHHHHHhCCCccEE
Confidence 4444444432 23345566654
No 177
>TIGR00853 pts-lac PTS system, lactose/cellobiose family IIB component. Bacterial PTS transporters transport and concomitantly phosphorylate their sugar substrates, and typically consist of multiple subunits or protein domains.The Lac family includes several sequenced lactose (b-galactoside) permeases of Gram-positive bacteria as well as those in E. coli. While the Lac family usually consists of two polypeptide components IIA and IICB, the Chb permease of E. coli consists of three IIA, IIB and IIC. This family is specific for the IIB subunit of the Lac PTS family.
Probab=29.24 E-value=1.7e+02 Score=23.34 Aligned_cols=59 Identities=14% Similarity=0.163 Sum_probs=35.5
Q ss_pred CEEEEEEcCCCccCcHHHHHHHHHHHHHhCCcEEEEEcCCCCHHhhcCCCCCCEEEEecCCCccc
Q 020984 101 NIIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKLANFPECDVFINVSCAQTAL 165 (319)
Q Consensus 101 ~~iGIivgTl~~q~~~~i~~~l~~ll~~~Gkk~y~i~vg~in~~KLaNf~eID~fV~iaCPr~si 165 (319)
++|-++.|+ |.. .--+++++++.++++|.++-+...+--..+.. ..+.| +++.-|+...
T Consensus 4 ~~ILl~C~~-G~s-SS~l~~k~~~~~~~~gi~~~v~a~~~~~~~~~--~~~~D--vill~pqi~~ 62 (95)
T TIGR00853 4 TNILLLCAA-GMS-TSLLVNKMNKAAEEYGVPVKIAAGSYGAAGEK--LDDAD--VVLLAPQVAY 62 (95)
T ss_pred cEEEEECCC-chh-HHHHHHHHHHHHHHCCCcEEEEEecHHHHHhh--cCCCC--EEEECchHHH
Confidence 455555555 444 44588999999999999865544443222221 23567 4555677663
No 178
>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=29.23 E-value=90 Score=31.54 Aligned_cols=65 Identities=15% Similarity=0.174 Sum_probs=36.7
Q ss_pred HHHHhhccCCEEEEEEcCCCccCcHHHHHHHHHH--HHHhCCcEEEEEcC---CCCHHhhc-CCCCCCEEE
Q 020984 92 YLVEKAKDANIIGVLVGTLGVAGYLHMIHQMKEL--ITKAGKKAYTLVMG---KPNPAKLA-NFPECDVFI 156 (319)
Q Consensus 92 ~~I~ka~~a~~iGIivgTl~~q~~~~i~~~l~~l--l~~~Gkk~y~i~vg---~in~~KLa-Nf~eID~fV 156 (319)
..+....+|..+.|=..|..-.--.++.+.|..+ +++.+.+..+++.| ...++.+. .+++||++|
T Consensus 30 ~~~~~~~~aDv~iiNTC~v~~~a~~k~~~~i~~~~~~k~~~~~~~ivv~GC~a~~~~~~~~~~~~~vd~v~ 100 (438)
T TIGR01574 30 ALTEDAKEADVLLINTCSVREKAEHKVFGELGGFKKLKKKNPDLIIGVCGCMASHLGNEIFQRAPYVDFVF 100 (438)
T ss_pred EECCCcccCCEEEEeccCeechHHHHHHHHHHHHHHHHhhCCCcEEEEeCccccccHHHHHhcCCCCcEEE
Confidence 3444455677776666665555555555555332 33444455566655 33566665 367788776
No 179
>PRK13055 putative lipid kinase; Reviewed
Probab=29.11 E-value=2.2e+02 Score=27.64 Aligned_cols=31 Identities=6% Similarity=0.127 Sum_probs=15.0
Q ss_pred EEEEEEcCCCccCc-HHHHHHHHHHHHHhCCc
Q 020984 102 IIGVLVGTLGVAGY-LHMIHQMKELITKAGKK 132 (319)
Q Consensus 102 ~iGIivgTl~~q~~-~~i~~~l~~ll~~~Gkk 132 (319)
++.||++..++.+. ...+.++++.|+++|.+
T Consensus 4 r~~iI~NP~sG~~~~~~~~~~i~~~l~~~g~~ 35 (334)
T PRK13055 4 RARLIYNPTSGQEIMKKNVADILDILEQAGYE 35 (334)
T ss_pred eEEEEECCCCCchhHHHHHHHHHHHHHHcCCe
Confidence 44455555544433 34444555555555544
No 180
>cd03825 GT1_wcfI_like This family is most closely related to the GT1 family of glycosyltransferases. wcfI in Bacteroides fragilis has been shown to be involved in the capsular polysaccharide biosynthesis.
Probab=28.79 E-value=1.7e+02 Score=26.85 Aligned_cols=56 Identities=14% Similarity=0.039 Sum_probs=41.2
Q ss_pred EEEEEEcCCCccCcHHHHHHHHHHHHHhCCcEEEEEcCCCCHHhhcCCCCCCEEEE
Q 020984 102 IIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKLANFPECDVFIN 157 (319)
Q Consensus 102 ~iGIivgTl~~q~~~~i~~~l~~ll~~~Gkk~y~i~vg~in~~KLaNf~eID~fV~ 157 (319)
+|.++....+..|....+..+.+.|.++|.++++++.....-.+..+...+|+...
T Consensus 2 kIl~~~~~~~~gG~~~~~~~l~~~l~~~G~~v~v~~~~~~~~~~~~~~~~~diih~ 57 (365)
T cd03825 2 KVLHLNTSDISGGAARAAYRLHRALQAAGVDSTMLVQEKKALISKIEIINADIVHL 57 (365)
T ss_pred eEEEEecCCCCCcHHHHHHHHHHHHHhcCCceeEEEeecchhhhChhcccCCEEEE
Confidence 35566666665777777888888999999999999887765555555667888664
No 181
>PRK14096 pgi glucose-6-phosphate isomerase; Provisional
Probab=28.73 E-value=3.3e+02 Score=28.74 Aligned_cols=49 Identities=14% Similarity=0.045 Sum_probs=27.5
Q ss_pred CCEEEEEEcCCCccCcH--HHHHHHHHHHHHhC---CcEEEEEcCCCCHHhhcCCC
Q 020984 100 ANIIGVLVGTLGVAGYL--HMIHQMKELITKAG---KKAYTLVMGKPNPAKLANFP 150 (319)
Q Consensus 100 a~~iGIivgTl~~q~~~--~i~~~l~~ll~~~G---kk~y~i~vg~in~~KLaNf~ 150 (319)
.++.-+||.++++-.-- .-++.+++.++++| .+ ..|++.. +..+|..|.
T Consensus 167 ~~~TLviViSKSGtT~ET~~n~~~~~~~l~~~G~~~~~-h~VAVT~-~~s~L~~~A 220 (528)
T PRK14096 167 LATTLVVVISKSGGTPETRNGMLEAKAAYEAAGLDFAS-HAVAITM-KGSKLDQLA 220 (528)
T ss_pred CCcEEEEEEeCCCCCHHHHHHHHHHHHHHHhhcccccc-eEEEEEC-CCcHHhhhc
Confidence 45666777777753322 22334456777766 23 3444444 455687775
No 182
>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=28.64 E-value=83 Score=28.27 Aligned_cols=58 Identities=14% Similarity=0.050 Sum_probs=31.6
Q ss_pred EEEEEEcCCCccCcHHHHHHHHHHHHHhCCcEEEEEcCCCCHHhhc----CC--CCCCEEEEecC
Q 020984 102 IIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKLA----NF--PECDVFINVSC 160 (319)
Q Consensus 102 ~iGIivgTl~~q~~~~i~~~l~~ll~~~Gkk~y~i~vg~in~~KLa----Nf--~eID~fV~iaC 160 (319)
+||+|+=...-..+..+++.+++.++++|.+..+..... ++++-. .+ ..+|.+|+.++
T Consensus 1 ~~g~~~~~~~~~~~~~~~~~~~~~a~~~g~~~~~~~~~~-~~~~~~~~i~~l~~~~vdgiIi~~~ 64 (273)
T cd06309 1 TVGFSQVGAESPWRTAETKSIKDAAEKRGFDLKFADAQQ-KQENQISAIRSFIAQGVDVIILAPV 64 (273)
T ss_pred CeeeccCCCCCHHHHHHHHHHHHHHHhcCCEEEEeCCCC-CHHHHHHHHHHHHHcCCCEEEEcCC
Confidence 366666665555556677777777777776655543332 332221 11 14677666543
No 183
>cd02042 ParA ParA and ParB of Caulobacter crescentus belong to a conserved family of bacterial proteins implicated in chromosome segregation. ParB binds to DNA sequences adjacent to the origin of replication and localizes to opposite cell poles shortly following the initiation of DNA replication. ParB regulates the ParA ATPase activity by promoting nucleotide exchange in a fashion reminiscent of the exchange factors of eukaryotic G proteins. ADP-bound ParA binds single-stranded DNA, whereas the ATP-bound form dissociates ParB from its DNA binding sites. Increasing the fraction of ParA-ADP in the cell inhibits cell division, suggesting that this simple nucleotide switch may regulate cytokinesis. ParA shares sequence similarity to a conserved and widespread family of ATPases which includes the repA protein of the repABC operon in R. etli Sym plasmid. This operon is involved in the plasmid replication and partition.
Probab=28.63 E-value=1.9e+02 Score=22.22 Aligned_cols=48 Identities=13% Similarity=0.273 Sum_probs=38.8
Q ss_pred EEEcCCCccCcHHHHHHHHHHHHHhCCcEEEEEcCCCCHHhhcCCCCCCEEEEecCCCc
Q 020984 105 VLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKLANFPECDVFINVSCAQT 163 (319)
Q Consensus 105 IivgTl~~q~~~~i~~~l~~ll~~~Gkk~y~i~vg~in~~KLaNf~eID~fV~iaCPr~ 163 (319)
.+.|.+|+-|-..+...+-..+.++|+++.++-++.- .| ||++-||..
T Consensus 3 ~~~~~kgG~Gkst~~~~la~~~~~~~~~vl~~d~d~~----------~d-~viiD~p~~ 50 (104)
T cd02042 3 AVANQKGGVGKTTTAVNLAAALARRGKRVLLIDLDPQ----------YD-YIIIDTPPS 50 (104)
T ss_pred EEEeCCCCcCHHHHHHHHHHHHHhCCCcEEEEeCCCC----------CC-EEEEeCcCC
Confidence 4678899999999999999999989998777766643 33 788999876
No 184
>PRK11914 diacylglycerol kinase; Reviewed
Probab=28.43 E-value=2e+02 Score=27.26 Aligned_cols=16 Identities=31% Similarity=0.231 Sum_probs=7.4
Q ss_pred CCCCcccCHHHHHHhh
Q 020984 170 EFLAPVITPFEAMLAF 185 (319)
Q Consensus 170 ~f~kPvlTP~El~vAL 185 (319)
.+.-|.-.|.++.-++
T Consensus 105 ~lg~~~~~~~~a~~~i 120 (306)
T PRK11914 105 EFGIPTGDPEAAADVI 120 (306)
T ss_pred HcCCCCCCHHHHHHHH
Confidence 3344433455554444
No 185
>cd03801 GT1_YqgM_like This family is most closely related to the GT1 family of glycosyltransferases and named after YqgM in Bacillus licheniformis about which little is known. Glycosyltransferases catalyze the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming glycosidic bonds. The acceptor molecule can be a lipid, a protein, a heterocyclic compound, or another carbohydrate residue. This group of glycosyltransferases is most closely related to the previously defined glycosyltransferase family 1 (GT1). The members of this family may transfer UDP, ADP, GDP, or CMP linked sugars. The diverse enzymatic activities among members of this family reflect a wide range of biological functions. The protein structure available for this family has the GTB topology, one of the two protein topologies observed for nucleotide-sugar-dependent glycosyltransferases. GTB proteins have distinct N- and C- terminal domains each containing a typical Rossmann fold.
Probab=28.40 E-value=50 Score=29.45 Aligned_cols=41 Identities=20% Similarity=0.283 Sum_probs=22.7
Q ss_pred HHHHHHHHhCCcEEEEEcCCCCHHhhcC-CCCCCEEEEecCC
Q 020984 121 QMKELITKAGKKAYTLVMGKPNPAKLAN-FPECDVFINVSCA 161 (319)
Q Consensus 121 ~l~~ll~~~Gkk~y~i~vg~in~~KLaN-f~eID~fV~iaCP 161 (319)
.+++++++.+....+.+.|.++.+.+.. +...|++|..++.
T Consensus 244 ~~~~~~~~~~~~~~v~~~g~~~~~~~~~~~~~~di~i~~~~~ 285 (374)
T cd03801 244 ELEALAAELGLGDRVTFLGFVPDEDLPALYAAADVFVLPSLY 285 (374)
T ss_pred HHHHHHHHhCCCcceEEEeccChhhHHHHHHhcCEEEecchh
Confidence 3334444445555556666666555554 4467877766554
No 186
>cd00316 Oxidoreductase_nitrogenase The nitrogenase enzyme system catalyzes the ATP-dependent reduction of dinitrogen to ammonia. This group contains both alpha and beta subunits of component 1 of the three known genetically distinct types of nitrogenase systems: a molybdenum-dependent nitrogenase (Mo-nitrogenase), a vanadium-dependent nitrogenase (V-nitrogenase), and an iron-only nitrogenase (Fe-nitrogenase) and, both subunits of Protochlorophyllide (Pchlide) reductase and chlorophyllide (chlide) reductase. The nitrogenase systems consist of component 1 (MoFe protein, VFe protein or, FeFe protein respectively) and, component 2 (Fe protein). The most widespread and best characterized nitrogenase is the Mo-nitrogenase. MoFe is an alpha2beta2 tetramer, the alternative nitrogenases are alpha2beta2delta2 hexamers whose alpha and beta subunits are similar to the alpha and beta subunits of MoFe. For MoFe, each alphabeta pair contains one P-cluster (at the alphabeta interface) and, one molec
Probab=28.39 E-value=2.1e+02 Score=27.76 Aligned_cols=75 Identities=16% Similarity=0.358 Sum_probs=52.4
Q ss_pred ccCCEEEEEEcCCCccCcHHHHHHHHHHHHHhCCcEEEEEcCCCCHHhhcCCCCCCEEEEecCCCcccccc----cCCCC
Q 020984 98 KDANIIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKLANFPECDVFINVSCAQTALLDS----KEFLA 173 (319)
Q Consensus 98 ~~a~~iGIivgTl~~q~~~~i~~~l~~ll~~~Gkk~y~i~vg~in~~KLaNf~eID~fV~iaCPr~sidd~----~~f~k 173 (319)
++.+.+-||-.+ .... .=++.|+++|++.|.++..+.-..-+.+.|.+.++.+.-|+ -||+...... +.|..
T Consensus 150 ~~~~~vNlig~~-~~~~--~d~~el~~ll~~~G~~v~~~~~~~~s~~~i~~~~~A~~nlv-~~~~~g~~~a~~l~~~~g~ 225 (399)
T cd00316 150 TEPGSVNLIGGY-NLGG--GDLRELKRLLEEMGIRVNALFDGGTTVEELRELGNAKLNLV-LCRESGLYLARYLEEKYGI 225 (399)
T ss_pred CCCCcEEEECCC-CCch--hhHHHHHHHHHHcCCcEEEEcCCCCCHHHHHhhccCcEEEE-ecHhHHHHHHHHHHHHhCC
Confidence 345566544433 3343 44678899999999999999988899999999988876555 4886665432 34666
Q ss_pred ccc
Q 020984 174 PVI 176 (319)
Q Consensus 174 Pvl 176 (319)
|.+
T Consensus 226 p~~ 228 (399)
T cd00316 226 PYI 228 (399)
T ss_pred CeE
Confidence 644
No 187
>PF01380 SIS: SIS domain SIS domain web page.; InterPro: IPR001347 The SIS (Sugar ISomerase) domain is a phosphosugar-binding domain [] found in many phosphosugar isomerases and phosphosugar binding proteins. SIS domains are also found in proteins that regulate the expression of genes involved in synthesis of phosphosugars possibly by binding to the end-product of the pathway.; GO: 0005529 sugar binding, 0005975 carbohydrate metabolic process; PDB: 3TBF_C 2V4M_A 2ZJ4_A 2ZJ3_A 3FKJ_A 3ODP_A 3EUA_H 1VIV_A 1M3S_B 1TZB_A ....
Probab=28.18 E-value=76 Score=25.30 Aligned_cols=62 Identities=16% Similarity=0.124 Sum_probs=43.0
Q ss_pred hccCCEEEEEEcCCCccCcHHHHHHHHHHHHHhCCcEEEEEcCCC-CHHhhcCCCCCCEEEEecCCC
Q 020984 97 AKDANIIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKP-NPAKLANFPECDVFINVSCAQ 162 (319)
Q Consensus 97 a~~a~~iGIivgTl~~q~~~~i~~~l~~ll~~~Gkk~y~i~vg~i-n~~KLaNf~eID~fV~iaCPr 162 (319)
..++++| +|+|+ .....+...+..++++.|+.++.+.-... ....+.+..+-|+.|+++=+.
T Consensus 2 i~~~~~i-~i~G~---G~s~~~A~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~d~vi~is~sg 64 (131)
T PF01380_consen 2 IAKAKRI-YIYGS---GSSYGVAQYAALKLQKLGRIVVISYEAGEFFHGPLENLDPDDLVIIISYSG 64 (131)
T ss_dssp HTTSSEE-EEEES---THHHHHHHHHHHHHHHHHSSEEEEEEHHHHHTTGGGGCSTTEEEEEEESSS
T ss_pred CCCCCEE-EEEEc---chHHHHHHHHHHHHHHhcCcceeccchHHHhhhhcccccccceeEeeeccc
Confidence 4566666 56665 44555888899999888888777665544 344477777889999988333
No 188
>PRK08091 ribulose-phosphate 3-epimerase; Validated
Probab=28.15 E-value=1.8e+02 Score=27.32 Aligned_cols=46 Identities=7% Similarity=0.056 Sum_probs=31.2
Q ss_pred ccCcH-HHHH---HHHHHHHHhCCcEEEEEcCCCCHHhhcCCC--CCCEEEE
Q 020984 112 VAGYL-HMIH---QMKELITKAGKKAYTLVMGKPNPAKLANFP--ECDVFIN 157 (319)
Q Consensus 112 ~q~~~-~i~~---~l~~ll~~~Gkk~y~i~vg~in~~KLaNf~--eID~fV~ 157 (319)
+|.+. .+++ +++++++++|.++.+-+=|.+|++.+.... ++|+||.
T Consensus 155 GQ~f~~~~l~KI~~lr~~~~~~~~~~~IeVDGGI~~~ti~~l~~aGaD~~V~ 206 (228)
T PRK08091 155 TKAPSDLILDRVIQVENRLGNRRVEKLISIDGSMTLELASYLKQHQIDWVVS 206 (228)
T ss_pred CccccHHHHHHHHHHHHHHHhcCCCceEEEECCCCHHHHHHHHHCCCCEEEE
Confidence 56655 4444 445566777777666666789998876653 6898775
No 189
>KOG0343 consensus RNA Helicase [RNA processing and modification]
Probab=27.99 E-value=2.7e+02 Score=30.08 Aligned_cols=89 Identities=20% Similarity=0.281 Sum_probs=48.1
Q ss_pred HHHHHhhccCCEEEEEEcCCCccCcHHHHHHHHHHHHHhCCcEEEEEcCCCCHHhhcCCCCCCEEEEecCCCccccc---
Q 020984 91 YYLVEKAKDANIIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKLANFPECDVFINVSCAQTALLD--- 167 (319)
Q Consensus 91 ~~~I~ka~~a~~iGIivgTl~~q~~~~i~~~l~~ll~~~Gkk~y~i~vg~in~~KLaNf~eID~fV~iaCPr~sidd--- 167 (319)
|.+..+.|---.+--|-|+..-..+.++ ..+.+++ +..+++...+ .++=..||-||..||+.||+..-.-
T Consensus 330 ~e~F~rlrpg~~l~~L~G~~~Q~~R~ev---~~~F~~~---~~~vLF~TDv-~aRGLDFpaVdwViQ~DCPedv~tYIHR 402 (758)
T KOG0343|consen 330 YEAFCRLRPGIPLLALHGTMSQKKRIEV---YKKFVRK---RAVVLFCTDV-AARGLDFPAVDWVIQVDCPEDVDTYIHR 402 (758)
T ss_pred HHHHHhcCCCCceeeeccchhHHHHHHH---HHHHHHh---cceEEEeehh-hhccCCCcccceEEEecCchhHHHHHHH
Confidence 4445555544444444454433333333 3344443 3444444444 3333479999999999999875211
Q ss_pred -c--cCCC-----CcccCHHHHHHhhC
Q 020984 168 -S--KEFL-----APVITPFEAMLAFG 186 (319)
Q Consensus 168 -~--~~f~-----kPvlTP~El~vAL~ 186 (319)
+ -.|. --+|||.|-+..+.
T Consensus 403 vGRtAR~~~~G~sll~L~psEeE~~l~ 429 (758)
T KOG0343|consen 403 VGRTARYKERGESLLMLTPSEEEAMLK 429 (758)
T ss_pred hhhhhcccCCCceEEEEcchhHHHHHH
Confidence 1 1222 23799999666653
No 190
>KOG1975 consensus mRNA cap methyltransferase [RNA processing and modification]
Probab=27.88 E-value=1.7e+02 Score=29.47 Aligned_cols=142 Identities=17% Similarity=0.223 Sum_probs=76.9
Q ss_pred eEEEEcCCcchHHHHHHhcCCCeEEEEcCCCCccccccCcHHHHHHHHHHHHHhhccCCEEEEEEcCCCccCcHHHHHHH
Q 020984 43 LLFWIGSDNSAFANVVLTFNGCEIVRYDATEERLLTDVSQPLKILKRRYYLVEKAKDANIIGVLVGTLGVAGYLHMIHQM 122 (319)
Q Consensus 43 ~i~~Ig~~~~~l~~l~l~~~~~~v~~yDP~s~~~~~e~~~~~k~l~~R~~~I~ka~~a~~iGIivgTl~~q~~~~i~~~l 122 (319)
+.|+.||...-.+.-++.++..+ ||--|.++. -.|.....-+.|..+-..|+--+-=|+.+||+ -+.-.|+++|
T Consensus 174 a~f~~~Dc~~~~l~d~~e~~dp~---fDivScQF~-~HYaFetee~ar~~l~Nva~~LkpGG~FIgTi--Pdsd~Ii~rl 247 (389)
T KOG1975|consen 174 AVFIAADCFKERLMDLLEFKDPR---FDIVSCQFA-FHYAFETEESARIALRNVAKCLKPGGVFIGTI--PDSDVIIKRL 247 (389)
T ss_pred eEEEEeccchhHHHHhccCCCCC---cceeeeeee-EeeeeccHHHHHHHHHHHHhhcCCCcEEEEec--CcHHHHHHHH
Confidence 34555555433333344434433 555555532 12322233355666667777778889999997 4666778887
Q ss_pred HHH-HHHhCCcEEEEEcCCCCHHh---hcCCC-CCCEEE--EecCCCcccccccCCCCcccCHHHHHHhhCCCCCCCcce
Q 020984 123 KEL-ITKAGKKAYTLVMGKPNPAK---LANFP-ECDVFI--NVSCAQTALLDSKEFLAPVITPFEAMLAFGRGTQWTGAY 195 (319)
Q Consensus 123 ~~l-l~~~Gkk~y~i~vg~in~~K---LaNf~-eID~fV--~iaCPr~sidd~~~f~kPvlTP~El~vAL~~~~~W~~~y 195 (319)
+.. -+.-|-.+|-|.-. +.+.| +--|. +.+.+. .|.||+- |-||++.+.|..+-...-.|
T Consensus 248 r~~e~~~~gNdiykv~y~-~~~~k~~~~p~fG~kY~F~LedaVdcPEy------------lV~F~~l~~lae~y~LeLv~ 314 (389)
T KOG1975|consen 248 RAGEVERFGNDIYKVTYE-IEFQKEFDVPPFGAKYRFHLEDAVDCPEY------------LVPFPTLVSLAEEYGLELVF 314 (389)
T ss_pred HhccchhhcceeeeEeee-eecccccCCCCccceEEEEcccccCCcce------------eeehHHHHHHHHhcCcEEEE
Confidence 765 22336667544444 22222 22232 122221 3449987 67899999987432222346
Q ss_pred eecccccc
Q 020984 196 VMEFRDLM 203 (319)
Q Consensus 196 ~~Df~~ll 203 (319)
...|-+..
T Consensus 315 ~k~F~df~ 322 (389)
T KOG1975|consen 315 VKPFADFY 322 (389)
T ss_pred eccHHHHH
Confidence 66666654
No 191
>PRK10310 PTS system galactitol-specific transporter subunit IIB; Provisional
Probab=27.75 E-value=1.5e+02 Score=23.43 Aligned_cols=52 Identities=12% Similarity=0.107 Sum_probs=32.6
Q ss_pred EEEcCCCccCcHHHHHHHHHHHHHhCCcEEEEEcCCCCHHhhcC-CCCCCEEEEec
Q 020984 105 VLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKLAN-FPECDVFINVS 159 (319)
Q Consensus 105 IivgTl~~q~~~~i~~~l~~ll~~~Gkk~y~i~vg~in~~KLaN-f~eID~fV~ia 159 (319)
+++..-|..-+.-+..++++.++++|..+-+.- ..++ -+.+ ..++|++|...
T Consensus 6 LvvCgsG~~TS~m~~~ki~~~l~~~gi~~~v~~-~~~~--e~~~~~~~~D~iv~t~ 58 (94)
T PRK10310 6 IVACGGAVATSTMAAEEIKELCQSHNIPVELIQ-CRVN--EIETYMDGVHLICTTA 58 (94)
T ss_pred EEECCCchhHHHHHHHHHHHHHHHCCCeEEEEE-ecHH--HHhhhcCCCCEEEECC
Confidence 445555555555668999999999999755444 3333 2333 13678776554
No 192
>PF00781 DAGK_cat: Diacylglycerol kinase catalytic domain; InterPro: IPR001206 The DAG-kinase catalytic domain or DAGKc domain is present in mammalian lipid kinases, such as diacylglycerol (DAG), ceramide and sphingosine kinases, as well as in related bacterial proteins [, ]. Eukaryotic DAG-kinase (2.7.1.107 from EC) catalyses the phosphorylation of DAG to phosphatidic acid, thus modulating the balance between the two signaling lipids. At least ten different isoforms have been identified in mammals, which form 5 groups characterised by different functional domains, such as the calcium-binding EF hand (see PDOC00018 from PROSITEDOC), PH (see PDOC50003 from PROSITEDOC), SAM (see PDOC50105 from PROSITEDOC) , DAG/PE-binding C1 domain (see PDOC00379 from PROSITEDOC) and ankyrin repeats (see PDOC50088 from PROSITEDOC) []. In bacteria, an integral membrane DAG kinase forms a homotrimeric protein that lacks the DAGKc domain (see PDOC00820 from PROSITEDOC). In contrast, the bacterial yegS protein is a soluble cytosolic protein that contains the DAGKc domain in the N-terminal part. YegS is a lipid kinase with two structural domains, wherein the active site is located in the interdomain cleft, C-terminal to the DAGKc domain which forms an alpha/beta fold []. The tertiary structure resembles that of NAD kinases and contains a metal-binding site in the C-terminal region [, ]. This domain is usually associated with an accessory domain (see IPR000756 from INTERPRO).; GO: 0004143 diacylglycerol kinase activity, 0007205 activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway; PDB: 2JGR_A 2BON_A 3T5P_D 3S40_A 2P1R_A 2QV7_A 2QVL_A.
Probab=27.73 E-value=1.9e+02 Score=23.65 Aligned_cols=38 Identities=11% Similarity=0.106 Sum_probs=30.0
Q ss_pred EEEEEEcCCCccCcHHHHHHHHHHHHHhCCcEEEEEcCC
Q 020984 102 IIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGK 140 (319)
Q Consensus 102 ~iGIivgTl~~q~~~~i~~~l~~ll~~~Gkk~y~i~vg~ 140 (319)
++.||++.+++.+.-. ++++++.+++++..+-++....
T Consensus 1 k~~vi~Np~sG~~~~~-~~~v~~~l~~~~~~~~~~~t~~ 38 (130)
T PF00781_consen 1 KVLVIINPKSGGGRAK-WKKVEPALRAAGIDYEVIETES 38 (130)
T ss_dssp SEEEEEETTSTTSHHH-HHHHHHHHHHTTCEEEEEEESS
T ss_pred CEEEEECCCCCCCchh-HHHHHHHHHHcCCceEEEEEec
Confidence 3678999999988888 7889999999887765555544
No 193
>TIGR01752 flav_long flavodoxin, long chain. Flavodoxins are small redox-active proteins with a flavin mononucleotide (FMN) prosthetic group. They can act in nitrogen fixation by nitrogenase, in sulfite reduction, and light-dependent NADP+ reduction in during photosynthesis, among other roles. This model describes the long chain type, typical for nitrogen fixation but associated with pyruvate formate-lyase activation and cobalamin-dependent methionine synthase activity in E. coli.
Probab=27.27 E-value=1.5e+02 Score=25.69 Aligned_cols=54 Identities=13% Similarity=0.217 Sum_probs=35.3
Q ss_pred EEEEEEcCCCccCcHHHHHHHHHHHHHhCCcEEEEEcCCCCHHhhcCCCCCCEEEEecCCC
Q 020984 102 IIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKLANFPECDVFINVSCAQ 162 (319)
Q Consensus 102 ~iGIivgTl~~q~~~~i~~~l~~ll~~~Gkk~y~i~vg~in~~KLaNf~eID~fV~iaCPr 162 (319)
+++|+.+|. --+...+++.|.+.|.. ..+-++-+.+.+++.|. +.|. |++++|=
T Consensus 1 ~i~IiY~S~-tGnTe~vA~~Ia~~l~~--~~~~i~~~~~~~~~~l~---~~d~-ii~gspt 54 (167)
T TIGR01752 1 KIGIFYGTD-TGNTEGIAEKIQKELGE--DDVDVFNIAKASKEDLN---AYDK-LILGTPT 54 (167)
T ss_pred CEEEEEECC-CChHHHHHHHHHHHhCC--CceEEEEcccCCHhHHh---hCCE-EEEEecC
Confidence 368888884 35666888888888763 34566677777766554 4454 4555553
No 194
>CHL00076 chlB photochlorophyllide reductase subunit B
Probab=27.17 E-value=5.6e+02 Score=26.69 Aligned_cols=78 Identities=19% Similarity=0.192 Sum_probs=54.7
Q ss_pred cCCEEEEEEcCCCccCcHHHHHHHHHHHHHhCCcEEEEEcCCCCHHhhcCCCCCCEEEEecCCCccccc----ccCCCCc
Q 020984 99 DANIIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKLANFPECDVFINVSCAQTALLD----SKEFLAP 174 (319)
Q Consensus 99 ~a~~iGIivgTl~~q~~~~i~~~l~~ll~~~Gkk~y~i~vg~in~~KLaNf~eID~fV~iaCPr~sidd----~~~f~kP 174 (319)
....|-||=.+-..-....=++.|+++|+..|.++-.++-+.-+.+.|.+.++.++=|++ ||+....- .+.|..|
T Consensus 162 ~~~~VNIIG~~~l~f~~~~Dl~eikrLL~~~Gi~vn~v~~~g~sl~di~~~~~A~~NIvl-~~~~g~~~A~~Le~~fgiP 240 (513)
T CHL00076 162 DKPSVNIIGIFTLGFHNQHDCRELKRLLQDLGIEINQIIPEGGSVEDLKNLPKAWFNIVP-YREVGLMTAKYLEKEFGMP 240 (513)
T ss_pred CCCcEEEEecCCCCCCCcchHHHHHHHHHHCCCeEEEEECCCCCHHHHHhcccCcEEEEe-chhhhHHHHHHHHHHhCCC
Confidence 345566664442222223335779999999999999888778899999999988876666 88866432 2467778
Q ss_pred ccC
Q 020984 175 VIT 177 (319)
Q Consensus 175 vlT 177 (319)
.+.
T Consensus 241 ~i~ 243 (513)
T CHL00076 241 YIS 243 (513)
T ss_pred eEe
Confidence 654
No 195
>PLN02334 ribulose-phosphate 3-epimerase
Probab=26.98 E-value=4.8e+02 Score=23.68 Aligned_cols=59 Identities=15% Similarity=0.216 Sum_probs=38.3
Q ss_pred CCEE--EEEEcCCCccCc-HHHHHHHHHHHHHhCCcEEEEEcCCCCHHhhcCCC--CCCEEEEec
Q 020984 100 ANII--GVLVGTLGVAGY-LHMIHQMKELITKAGKKAYTLVMGKPNPAKLANFP--ECDVFINVS 159 (319)
Q Consensus 100 a~~i--GIivgTl~~q~~-~~i~~~l~~ll~~~Gkk~y~i~vg~in~~KLaNf~--eID~fV~ia 159 (319)
+..| |-+.-|.++|.. ...+++++++- +...+.-+.+.|-||++.+..+. ++|.+|+.+
T Consensus 140 ~Dyi~~~~v~pg~~~~~~~~~~~~~i~~~~-~~~~~~~I~a~GGI~~e~i~~l~~aGad~vvvgs 203 (229)
T PLN02334 140 VDMVLVMSVEPGFGGQSFIPSMMDKVRALR-KKYPELDIEVDGGVGPSTIDKAAEAGANVIVAGS 203 (229)
T ss_pred CCEEEEEEEecCCCccccCHHHHHHHHHHH-HhCCCCcEEEeCCCCHHHHHHHHHcCCCEEEECh
Confidence 4544 456666666744 56777776643 33223357788999999887765 588887763
No 196
>PF09547 Spore_IV_A: Stage IV sporulation protein A (spore_IV_A); InterPro: IPR014201 This entry is designated stage IV sporulation protein A. It acts in the mother cell compartment and plays a role in spore coat morphogenesis []. A comparative genome analysis of all sequenced genomes of Firmicutes shows that the proteins are strictly conserved among the sub-set of endospore-forming species.
Probab=26.98 E-value=1e+02 Score=32.04 Aligned_cols=71 Identities=28% Similarity=0.373 Sum_probs=48.9
Q ss_pred ccCCEEEEEEcCC------CccCcHHHHHHHHHHHHHhCCcEEEEEcC-CCCH---HhhcC-CC-CCCEE-EEecCCCcc
Q 020984 98 KDANIIGVLVGTL------GVAGYLHMIHQMKELITKAGKKAYTLVMG-KPNP---AKLAN-FP-ECDVF-INVSCAQTA 164 (319)
Q Consensus 98 ~~a~~iGIivgTl------~~q~~~~i~~~l~~ll~~~Gkk~y~i~vg-~in~---~KLaN-f~-eID~f-V~iaCPr~s 164 (319)
.+-.+|||+|.|= .+.+|.+.=+++.+.|++-||.+.+++=+ ++.- ..|+. +. ..|+= +-+.|-++.
T Consensus 142 ~dHSTIGiVVTTDGSi~dipRe~Y~eAEervI~ELk~igKPFvillNs~~P~s~et~~L~~eL~ekY~vpVlpvnc~~l~ 221 (492)
T PF09547_consen 142 TDHSTIGIVVTTDGSITDIPRENYVEAEERVIEELKEIGKPFVILLNSTKPYSEETQELAEELEEKYDVPVLPVNCEQLR 221 (492)
T ss_pred ccCCceeEEEecCCCccCCChHHHHHHHHHHHHHHHHhCCCEEEEEeCCCCCCHHHHHHHHHHHHHhCCcEEEeehHHcC
Confidence 4668999999774 48999999999999999999886665533 2321 22331 11 24433 467899888
Q ss_pred cccc
Q 020984 165 LLDS 168 (319)
Q Consensus 165 idd~ 168 (319)
-+|-
T Consensus 222 ~~DI 225 (492)
T PF09547_consen 222 EEDI 225 (492)
T ss_pred HHHH
Confidence 7664
No 197
>PRK12419 riboflavin synthase subunit beta; Provisional
Probab=26.82 E-value=1.9e+02 Score=25.70 Aligned_cols=61 Identities=8% Similarity=-0.029 Sum_probs=38.9
Q ss_pred CEEEEEEcCCCccCcHHHHHHHHHHHHHhCCc---EEEEEcCC---CC--HHhhcCCCCCCEEEEecCC
Q 020984 101 NIIGVLVGTLGVAGYLHMIHQMKELITKAGKK---AYTLVMGK---PN--PAKLANFPECDVFINVSCA 161 (319)
Q Consensus 101 ~~iGIivgTl~~q~~~~i~~~l~~ll~~~Gkk---~y~i~vg~---in--~~KLaNf~eID~fV~iaCP 161 (319)
-+|+||++-.--.-.-.+++-..+.|+++|-+ ..++-|=- |- ..+|+.=.++|++|.++|=
T Consensus 11 ~riaIV~srfn~~It~~Ll~gA~~~l~~~G~~~~~i~v~~VPGA~EiP~~a~~l~~~~~yDaiIaLG~V 79 (158)
T PRK12419 11 QRIAFIQARWHADIVDQARKGFVAEIAARGGAASQVDIFDVPGAFEIPLHAQTLAKTGRYAAIVAAALV 79 (158)
T ss_pred CEEEEEEecCCHHHHHHHHHHHHHHHHHcCCCccceEEEECCcHHHHHHHHHHHHhcCCCCEEEEEEEE
Confidence 48999998654444445555556678888843 44443432 21 2456665679999999994
No 198
>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=26.73 E-value=1.4e+02 Score=26.54 Aligned_cols=49 Identities=20% Similarity=0.274 Sum_probs=34.9
Q ss_pred CcHHHHHHHHHHHHHhCCcEEEEEcCCCCH-------------------HhhcCCCCCCEEEEecCCC
Q 020984 114 GYLHMIHQMKELITKAGKKAYTLVMGKPNP-------------------AKLANFPECDVFINVSCAQ 162 (319)
Q Consensus 114 ~~~~i~~~l~~ll~~~Gkk~y~i~vg~in~-------------------~KLaNf~eID~fV~iaCPr 162 (319)
-.+.+..+|+++|+++|.++++.--+..+. ..++|=...|+||-+=|--
T Consensus 27 ~~l~ia~~l~~~L~~~G~~V~ltr~~d~~~~~~~~~~~~~~~~~~L~~R~~~An~~~adlfiSiH~Na 94 (189)
T TIGR02883 27 ITLEIALKLKDYLQEQGALVVMTREDDSDLASEGTKGYSRRKIEDLRKRVKLINESEADLFISIHLNA 94 (189)
T ss_pred HHHHHHHHHHHHHHhCCCEEEEEecCCcCccccccccccccccCCHHHHHHHHHhcCCCEEEEEecCC
Confidence 346778888889999888888766554331 3456655789999888853
No 199
>TIGR03449 mycothiol_MshA UDP-N-acetylglucosamine: 1L-myo-inositol-1-phosphate 1-alpha-D-N-acetylglucosaminyltransferase. Members of this protein family, found exclusively in the Actinobacteria, are MshA, the glycosyltransferase of mycothiol biosynthesis. Mycothiol replaces glutathione in these species.
Probab=26.60 E-value=2.4e+02 Score=26.99 Aligned_cols=41 Identities=20% Similarity=0.253 Sum_probs=25.7
Q ss_pred HHHHHHHHHhCCcEEEEEcCCCCHHhhcC-CCCCCEEEEecC
Q 020984 120 HQMKELITKAGKKAYTLVMGKPNPAKLAN-FPECDVFINVSC 160 (319)
Q Consensus 120 ~~l~~ll~~~Gkk~y~i~vg~in~~KLaN-f~eID~fV~iaC 160 (319)
+.+++++++.|....+.++|.++.+.+.. +...|+||+.+-
T Consensus 270 ~~l~~~~~~~~l~~~v~~~g~~~~~~~~~~l~~ad~~v~ps~ 311 (405)
T TIGR03449 270 DALIELAAELGIADRVRFLPPRPPEELVHVYRAADVVAVPSY 311 (405)
T ss_pred HHHHHHHHHcCCCceEEECCCCCHHHHHHHHHhCCEEEECCC
Confidence 44556666666655666677776666554 446788876543
No 200
>PRK14733 coaE dephospho-CoA kinase; Provisional
Probab=26.56 E-value=91 Score=28.47 Aligned_cols=51 Identities=6% Similarity=0.035 Sum_probs=31.8
Q ss_pred CcHHHHHHHHHHHHHhCCcEEEEEcCCCCHHhhcCCCCCCEEEEecCCCcc
Q 020984 114 GYLHMIHQMKELITKAGKKAYTLVMGKPNPAKLANFPECDVFINVSCAQTA 164 (319)
Q Consensus 114 ~~~~i~~~l~~ll~~~Gkk~y~i~vg~in~~KLaNf~eID~fV~iaCPr~s 164 (319)
-++.+.+.+++.+++.+.+++++-+-=+.+..+.....+|..|.|.||.-.
T Consensus 91 ~HP~V~~~~~~~~~~~~~~~vv~eipLL~E~~~~~~~~~D~vi~V~a~~e~ 141 (204)
T PRK14733 91 LHPVINKEIKKQVKESDTVMTIVDIPLLGPYNFRHYDYLKKVIVIKADLET 141 (204)
T ss_pred hhHHHHHHHHHHHHhcCCCeEEEEechhhhccCchhhhCCEEEEEECCHHH
Confidence 456777778888877655544444444444332222358999999999653
No 201
>PF09314 DUF1972: Domain of unknown function (DUF1972); InterPro: IPR015393 This domain is functionally uncharacterised and found in bacterial glycosyltransferases and rhamnosyltransferases.
Probab=26.46 E-value=1.2e+02 Score=27.37 Aligned_cols=58 Identities=12% Similarity=0.276 Sum_probs=45.6
Q ss_pred EEEcCCCc----cCcHHHHHHHHHHHHHhCCcEEEEEcCCCCHHhhcCCCCCCEEEEecCCCc
Q 020984 105 VLVGTLGV----AGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKLANFPECDVFINVSCAQT 163 (319)
Q Consensus 105 IivgTl~~----q~~~~i~~~l~~ll~~~Gkk~y~i~vg~in~~KLaNf~eID~fV~iaCPr~ 163 (319)
-|+||.|. -|+-..++.|-..+.+.|.++++.-..+-.+.+...+.+++++.+ ..|++
T Consensus 5 aIiGtrGIPa~YGGfET~ve~L~~~l~~~g~~v~Vyc~~~~~~~~~~~y~gv~l~~i-~~~~~ 66 (185)
T PF09314_consen 5 AIIGTRGIPARYGGFETFVEELAPRLVSKGIDVTVYCRSDYYPYKEFEYNGVRLVYI-PAPKN 66 (185)
T ss_pred EEEeCCCCCcccCcHHHHHHHHHHHHhcCCceEEEEEccCCCCCCCcccCCeEEEEe-CCCCC
Confidence 36799886 356688899999998899998888888777788888888998774 55554
No 202
>PLN02204 diacylglycerol kinase
Probab=26.07 E-value=8.5e+02 Score=26.26 Aligned_cols=76 Identities=17% Similarity=0.154 Sum_probs=50.8
Q ss_pred HHHHHHHHHHHH-hhccCCEEEEEEcCCCccCcH-HHHHHHHHHHHHhCCcEEEEEcCCCCHHh-----hcC--CCCCCE
Q 020984 84 LKILKRRYYLVE-KAKDANIIGVLVGTLGVAGYL-HMIHQMKELITKAGKKAYTLVMGKPNPAK-----LAN--FPECDV 154 (319)
Q Consensus 84 ~k~l~~R~~~I~-ka~~a~~iGIivgTl~~q~~~-~i~~~l~~ll~~~Gkk~y~i~vg~in~~K-----LaN--f~eID~ 154 (319)
..+..+=...+. .....+++-+|++..++.+.- ...+.+..+++.+|.++-+++--...-+. +++ ....|.
T Consensus 142 ~~w~~~l~~~l~~~~~r~k~llVivNP~sGkg~~~~~~~~V~p~f~~a~i~~~v~~T~~aghA~d~~~~~~~~~l~~~D~ 221 (601)
T PLN02204 142 QSWVDRLNASLNKEVGRPKNLLVFVHPLSGKGSGSRTWETVSPIFIRAKVKTKVIVTERAGHAFDVMASISNKELKSYDG 221 (601)
T ss_pred HHHHHHHHHHHhhccCCCceEEEEECCCCCCcchHHHHHHHHHHHHHcCCeEEEEEecCcchHHHHHHHHhhhhccCCCE
Confidence 344443333333 445578899999999998764 67889999999999998777766665433 222 345677
Q ss_pred EEEec
Q 020984 155 FINVS 159 (319)
Q Consensus 155 fV~ia 159 (319)
+|.++
T Consensus 222 VVaVG 226 (601)
T PLN02204 222 VIAVG 226 (601)
T ss_pred EEEEc
Confidence 66554
No 203
>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=25.98 E-value=1.1e+02 Score=27.27 Aligned_cols=59 Identities=19% Similarity=0.226 Sum_probs=35.9
Q ss_pred EEEEEEcCCCccCcHHHHHHHHHHHHHhCCcEEEEEcCCCCHHhhc----CC--CCCCEEEEecCC
Q 020984 102 IIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKLA----NF--PECDVFINVSCA 161 (319)
Q Consensus 102 ~iGIivgTl~~q~~~~i~~~l~~ll~~~Gkk~y~i~vg~in~~KLa----Nf--~eID~fV~iaCP 161 (319)
+||+++-+..-..+..+++.+++.+++.|....+.. +.-++++-. ++ ..+|++|+.++.
T Consensus 1 ~i~~~~~~~~~~~~~~~~~~i~~~~~~~g~~~~i~~-~~~~~~~~~~~~~~~~~~~vdgiii~~~~ 65 (267)
T cd06322 1 VIGASLLTQQHPFYIELANAMKEEAKKQKVNLIVSI-ANQDLNKQLSDVEDFITKKVDAIVLSPVD 65 (267)
T ss_pred CeeEeecCcccHHHHHHHHHHHHHHHhcCCEEEEec-CCCCHHHHHHHHHHHHHcCCCEEEEcCCC
Confidence 367788776655666788888888888776654433 333443211 11 158888877653
No 204
>PRK11557 putative DNA-binding transcriptional regulator; Provisional
Probab=25.81 E-value=1.8e+02 Score=26.93 Aligned_cols=65 Identities=17% Similarity=0.152 Sum_probs=44.7
Q ss_pred HHHhhccCCEEEEEEcCCCccCcHHHHHHHHHHHHHhCCcEEEEEcCCC--CHHhhcCCCCCCEEEEecCCCc
Q 020984 93 LVEKAKDANIIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKP--NPAKLANFPECDVFINVSCAQT 163 (319)
Q Consensus 93 ~I~ka~~a~~iGIivgTl~~q~~~~i~~~l~~ll~~~Gkk~y~i~vg~i--n~~KLaNf~eID~fV~iaCPr~ 163 (319)
+++...+|++| .|+|. ..+..+.+.+..+|...|+.++.. +.. ...-+.++.+=|++|.++=++.
T Consensus 121 ~~~~i~~a~~I-~i~G~---G~s~~~A~~~~~~l~~~g~~~~~~--~d~~~~~~~~~~~~~~Dv~I~iS~sg~ 187 (278)
T PRK11557 121 CVTMLRSARRI-ILTGI---GASGLVAQNFAWKLMKIGINAVAE--RDMHALLATVQALSPDDLLLAISYSGE 187 (278)
T ss_pred HHHHHhcCCeE-EEEec---ChhHHHHHHHHHHHhhCCCeEEEc--CChHHHHHHHHhCCCCCEEEEEcCCCC
Confidence 34445678886 44554 356778899999999999988753 443 3345567888899888865443
No 205
>PLN02949 transferase, transferring glycosyl groups
Probab=25.20 E-value=1.3e+02 Score=30.68 Aligned_cols=74 Identities=12% Similarity=0.014 Sum_probs=51.0
Q ss_pred CEEEEEEcCCCccCcHHHHHHHHHHHHHhCCcEEEEEcCCCCHHhhcC-CCCCCEEEEecCCCcccccccCCCCcccCHH
Q 020984 101 NIIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKLAN-FPECDVFINVSCAQTALLDSKEFLAPVITPF 179 (319)
Q Consensus 101 ~~iGIivgTl~~q~~~~i~~~l~~ll~~~Gkk~y~i~vg~in~~KLaN-f~eID~fV~iaCPr~sidd~~~f~kPvlTP~ 179 (319)
+.--+|+|.-..+.+....+.|++++++.|..-.+.++|.++.+.+.+ +...|++|..+.+|. |.. .+-
T Consensus 303 ~~~LvIvG~~~~~~~~~~~~eL~~la~~l~L~~~V~f~g~v~~~el~~ll~~a~~~v~~s~~E~-------FGi---vvl 372 (463)
T PLN02949 303 RPKLQFVGSCRNKEDEERLQKLKDRAKELGLDGDVEFHKNVSYRDLVRLLGGAVAGLHSMIDEH-------FGI---SVV 372 (463)
T ss_pred CcEEEEEeCCCCcccHHHHHHHHHHHHHcCCCCcEEEeCCCCHHHHHHHHHhCcEEEeCCccCC-------CCh---HHH
Confidence 334577776533455566788999999998877777789988777665 567899987654443 433 466
Q ss_pred HHHHh
Q 020984 180 EAMLA 184 (319)
Q Consensus 180 El~vA 184 (319)
|++.+
T Consensus 373 EAMA~ 377 (463)
T PLN02949 373 EYMAA 377 (463)
T ss_pred HHHHc
Confidence 87654
No 206
>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=25.08 E-value=92 Score=27.54 Aligned_cols=31 Identities=19% Similarity=0.255 Sum_probs=20.5
Q ss_pred EEEEEcCCCccCcHHHHHHHHHHHHHhCCcE
Q 020984 103 IGVLVGTLGVAGYLHMIHQMKELITKAGKKA 133 (319)
Q Consensus 103 iGIivgTl~~q~~~~i~~~l~~ll~~~Gkk~ 133 (319)
||+|+..+.-..+..+++.+.+.++++|...
T Consensus 2 I~vv~~~~~~~~~~~~~~~i~~~~~~~g~~v 32 (268)
T cd06323 2 IGLSVSTLNNPFFVTLKDGAQKEAKELGYEL 32 (268)
T ss_pred eeEecccccCHHHHHHHHHHHHHHHHcCceE
Confidence 6677766665566677777777777766544
No 207
>cd03798 GT1_wlbH_like This family is most closely related to the GT1 family of glycosyltransferases. wlbH in Bordetella parapertussis has been shown to be required for the biosynthesis of a trisaccharide that, when attached to the B. pertussis lipopolysaccharide (LPS) core (band B), generates band A LPS.
Probab=25.03 E-value=45 Score=29.97 Aligned_cols=38 Identities=18% Similarity=0.314 Sum_probs=20.0
Q ss_pred HHHHHHhCCcEEEEEcCCCCHHhhcC-CCCCCEEEEecC
Q 020984 123 KELITKAGKKAYTLVMGKPNPAKLAN-FPECDVFINVSC 160 (319)
Q Consensus 123 ~~ll~~~Gkk~y~i~vg~in~~KLaN-f~eID~fV~iaC 160 (319)
++++++.+....+.+.|.++.+.|.. +...|+++..+.
T Consensus 249 ~~~~~~~~~~~~v~~~g~~~~~~~~~~~~~ad~~i~~~~ 287 (377)
T cd03798 249 EALAAELGLEDRVTFLGAVPHEEVPAYYAAADVFVLPSL 287 (377)
T ss_pred HHHHHhcCCcceEEEeCCCCHHHHHHHHHhcCeeecchh
Confidence 33333444444555566666666554 345677665443
No 208
>cd03821 GT1_Bme6_like This family is most closely related to the GT1 family of glycosyltransferases. Bme6 in Brucella melitensis has been shown to be involved in the biosynthesis of a polysaccharide.
Probab=25.00 E-value=1.7e+02 Score=26.38 Aligned_cols=34 Identities=18% Similarity=0.197 Sum_probs=17.8
Q ss_pred HhCCcEEEEEcCCCCHHhhcC-CCCCCEEEEecCC
Q 020984 128 KAGKKAYTLVMGKPNPAKLAN-FPECDVFINVSCA 161 (319)
Q Consensus 128 ~~Gkk~y~i~vg~in~~KLaN-f~eID~fV~iaCP 161 (319)
+.+....+.++|.++.+.+.. +...|++|+.+..
T Consensus 257 ~~~~~~~v~~~g~~~~~~~~~~~~~adv~v~ps~~ 291 (375)
T cd03821 257 ALGLEDRVTFTGMLYGEDKAAALADADLFVLPSHS 291 (375)
T ss_pred hcCccceEEEcCCCChHHHHHHHhhCCEEEecccc
Confidence 334334445555555444443 4467777765554
No 209
>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=24.56 E-value=2.6e+02 Score=27.73 Aligned_cols=46 Identities=15% Similarity=0.331 Sum_probs=38.5
Q ss_pred hhccCCEEEEEEcCCCccCcHHH---HHHHHHHHHHhCCcEEEEEcCCC
Q 020984 96 KAKDANIIGVLVGTLGVAGYLHM---IHQMKELITKAGKKAYTLVMGKP 141 (319)
Q Consensus 96 ka~~a~~iGIivgTl~~q~~~~i---~~~l~~ll~~~Gkk~y~i~vg~i 141 (319)
..++-..+.++|+.||+..++++ .+.+.++|+++|.+.+.+.+|..
T Consensus 248 ~~~~gd~v~vlvN~LG~ts~lEl~i~~~~v~~~L~~~gi~v~r~~vG~~ 296 (329)
T TIGR02363 248 GLQSGDRVIVLVNGMGATPLMELYIFYNDVQRLLEQRGVNVARTLVGNY 296 (329)
T ss_pred CCCCCCeEEEEEeCCCCCCHHHHHHHHHHHHHHHHHCCCEEEEEEeecc
Confidence 33456789999999999998864 57788899999999999999875
No 210
>PRK03501 ppnK inorganic polyphosphate/ATP-NAD kinase; Provisional
Probab=24.44 E-value=1.6e+02 Score=27.99 Aligned_cols=32 Identities=6% Similarity=0.041 Sum_probs=25.5
Q ss_pred CEEEEEEcCCCccCcHHHHHHHHHHHHHhCCcEE
Q 020984 101 NIIGVLVGTLGVAGYLHMIHQMKELITKAGKKAY 134 (319)
Q Consensus 101 ~~iGIivgTl~~q~~~~i~~~l~~ll~~~Gkk~y 134 (319)
+++||+..... ...+++++++++|+++|..++
T Consensus 3 ~~i~iv~~~~~--~a~~~~~~l~~~l~~~g~~~~ 34 (264)
T PRK03501 3 RNLFFFYKRDK--ELVEKVKPLKKIAEEYGFTVV 34 (264)
T ss_pred cEEEEEECCCH--HHHHHHHHHHHHHHHCCCEEE
Confidence 47888877654 777889999999999997654
No 211
>cd03813 GT1_like_3 This family is most closely related to the GT1 family of glycosyltransferases. Glycosyltransferases catalyze the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming glycosidic bonds. The acceptor molecule can be a lipid, a protein, a heterocyclic compound, or another carbohydrate residue. This group of glycosyltransferases is most closely related to the previously defined glycosyltransferase family 1 (GT1). The members of this family may transfer UDP, ADP, GDP, or CMP linked sugars. The diverse enzymatic activities among members of this family reflect a wide range of biological functions. The protein structure available for this family has the GTB topology, one of the two protein topologies observed for nucleotide-sugar-dependent glycosyltransferases. GTB proteins have distinct N- and C- terminal domains each containing a typical Rossmann fold. The two domains have high structural homology despite minimal sequence homolog
Probab=24.29 E-value=2.4e+02 Score=28.38 Aligned_cols=57 Identities=19% Similarity=0.286 Sum_probs=37.5
Q ss_pred CEEEEEEcCCCccCcHHHHHHHHHHHHHhCCcEEEEEcCCCCHHhhcCCCCCCEEEEecCC
Q 020984 101 NIIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKLANFPECDVFINVSCA 161 (319)
Q Consensus 101 ~~iGIivgTl~~q~~~~i~~~l~~ll~~~Gkk~y~i~vg~in~~KLaNf~eID~fV~iaCP 161 (319)
+.-.+|+|.- .......+.+++++++.|..-.+.++|.-+...+ +...|++|+.+..
T Consensus 324 ~~~l~IvG~g--~~~~~~~~e~~~li~~l~l~~~V~f~G~~~v~~~--l~~aDv~vlpS~~ 380 (475)
T cd03813 324 DAEGWVIGPT--DEDPEYAEECRELVESLGLEDNVKFTGFQNVKEY--LPKLDVLVLTSIS 380 (475)
T ss_pred CeEEEEECCC--CcChHHHHHHHHHHHHhCCCCeEEEcCCccHHHH--HHhCCEEEeCchh
Confidence 4555677652 2345666778888888887777777784444443 4579999987643
No 212
>PF02273 Acyl_transf_2: Acyl transferase; InterPro: IPR003157 LuxD proteins are bacterial acyl transferases. Together with an acyl-protein synthetase (LuxE) and reductase (LuxC), they form a multienzyme complex. This complex channels activated fatty acids into the aldehyde substrate for the luciferase-catalyzed bacterial bioluminescence reaction [, ]. ; GO: 0016746 transferase activity, transferring acyl groups, 0006631 fatty acid metabolic process; PDB: 1THT_B.
Probab=24.14 E-value=3e+02 Score=26.77 Aligned_cols=103 Identities=15% Similarity=0.107 Sum_probs=41.1
Q ss_pred cCCCCCCCceeEEEEcCCc------chHHHHHHhcCCCeEEEEcCCCCc------cccccCc-HHHHHHHHHHHHHhhcc
Q 020984 33 IPDRKKMEEHLLFWIGSDN------SAFANVVLTFNGCEIVRYDATEER------LLTDVSQ-PLKILKRRYYLVEKAKD 99 (319)
Q Consensus 33 l~~~~~~~~~~i~~Ig~~~------~~l~~l~l~~~~~~v~~yDP~s~~------~~~e~~~-~~k~l~~R~~~I~ka~~ 99 (319)
.|..+...+...+-|.+|- |.-+...|+.++..|+|||+.... +.+-... -..-|..=+.-+ +.+.
T Consensus 21 ~P~~~~~~~~~tiliA~Gf~rrmdh~agLA~YL~~NGFhViRyDsl~HvGlSsG~I~eftms~g~~sL~~V~dwl-~~~g 99 (294)
T PF02273_consen 21 RPKNNEPKRNNTILIAPGFARRMDHFAGLAEYLSANGFHVIRYDSLNHVGLSSGDINEFTMSIGKASLLTVIDWL-ATRG 99 (294)
T ss_dssp ---TTS---S-EEEEE-TT-GGGGGGHHHHHHHHTTT--EEEE---B-------------HHHHHHHHHHHHHHH-HHTT
T ss_pred CCCCCCcccCCeEEEecchhHHHHHHHHHHHHHhhCCeEEEeccccccccCCCCChhhcchHHhHHHHHHHHHHH-HhcC
Confidence 4666666666777887762 334455677888999999997542 2111111 111111122222 2556
Q ss_pred CCEEEEEEcCCCccCcHHHHHHHHHHHHHhCCcEEEEEcCCCCH
Q 020984 100 ANIIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNP 143 (319)
Q Consensus 100 a~~iGIivgTl~~q~~~~i~~~l~~ll~~~Gkk~y~i~vg~in~ 143 (319)
-..+|+|-.+|+..--..++. +.+..+-+..||-.|.
T Consensus 100 ~~~~GLIAaSLSaRIAy~Va~-------~i~lsfLitaVGVVnl 136 (294)
T PF02273_consen 100 IRRIGLIAASLSARIAYEVAA-------DINLSFLITAVGVVNL 136 (294)
T ss_dssp ---EEEEEETTHHHHHHHHTT-------TS--SEEEEES--S-H
T ss_pred CCcchhhhhhhhHHHHHHHhh-------ccCcceEEEEeeeeeH
Confidence 788999999997533333222 1234455666676663
No 213
>PRK10427 putative PTS system fructose-like transporter subunit EIIB; Provisional
Probab=24.03 E-value=2.5e+02 Score=23.30 Aligned_cols=61 Identities=13% Similarity=0.098 Sum_probs=47.2
Q ss_pred CCEEEEEEcCCCccCcHHHHHHHHHHHHHhCCcEE------EEEcCCCCHHhhcCCCCCCEEEEecCCCc
Q 020984 100 ANIIGVLVGTLGVAGYLHMIHQMKELITKAGKKAY------TLVMGKPNPAKLANFPECDVFINVSCAQT 163 (319)
Q Consensus 100 a~~iGIivgTl~~q~~~~i~~~l~~ll~~~Gkk~y------~i~vg~in~~KLaNf~eID~fV~iaCPr~ 163 (319)
.+.++|.-+.-|.....-..+.|++..++.|.+.. .-+.+.++++.++ ..|.+|+++....
T Consensus 3 mkivaVtacp~GiAht~lAAeaL~kAA~~~G~~i~VE~qg~~g~~~~lt~~~i~---~Ad~VIia~d~~~ 69 (114)
T PRK10427 3 AYLVAVTACVSGVAHTYMAAERLEKLCQLEKWGVKIETQGALGTENRLTDEDIR---RADVVLLITDIEL 69 (114)
T ss_pred ceEEEEeeCCCcHHHHHHHHHHHHHHHHHCCCeEEEEecCCcCcCCCCCHHHHH---hCCEEEEEecCCC
Confidence 46788888888888888888999999999998887 4444556666654 5688888888764
No 214
>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=23.99 E-value=1.5e+02 Score=26.69 Aligned_cols=58 Identities=10% Similarity=-0.023 Sum_probs=31.3
Q ss_pred EEEEEEcCCCccCcHHHHHHHHHHHHHhCCcEEEEEcCCCCHHhh----cCC--CCCCEEEEecC
Q 020984 102 IIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKL----ANF--PECDVFINVSC 160 (319)
Q Consensus 102 ~iGIivgTl~~q~~~~i~~~l~~ll~~~Gkk~y~i~vg~in~~KL----aNf--~eID~fV~iaC 160 (319)
+||+|+.. .--.+..++..+.+.++++|....++.-..-++++. .++ ..+|.+|+..+
T Consensus 1 ~i~~v~~~-~~~~~~~~~~gi~~~~~~~g~~~~~~~~~~~~~~~~~~~i~~l~~~~vDgiIi~~~ 64 (271)
T cd06314 1 TIAVVTNG-ASPFWKIAEAGVKAAGKELGVDVEFVVPQQGTVNAQLRMLEDLIAEGVDGIAISPI 64 (271)
T ss_pred CeEEEcCC-CcHHHHHHHHHHHHHHHHcCCeEEEeCCCCCCHHHHHHHHHHHHhcCCCEEEEecC
Confidence 36666643 234456777777777777776654442222233221 122 15777777654
No 215
>PF02593 dTMP_synthase: Thymidylate synthase; InterPro: IPR003745 This entry describes proteins of unknown function.
Probab=23.80 E-value=1.1e+02 Score=28.57 Aligned_cols=37 Identities=27% Similarity=0.293 Sum_probs=17.0
Q ss_pred HHHHhhccCCEEEEEEcCCCccCcHHHHHHHHHHHHHhC
Q 020984 92 YLVEKAKDANIIGVLVGTLGVAGYLHMIHQMKELITKAG 130 (319)
Q Consensus 92 ~~I~ka~~a~~iGIivgTl~~q~~~~i~~~l~~ll~~~G 130 (319)
.++.+|++++.-+||++.-.+. +.+.+.|++.+++.|
T Consensus 67 ~l~~~~~e~g~kavIvp~~~~~--~g~~~~lk~~~e~~g 103 (217)
T PF02593_consen 67 ELPEIAKEAGVKAVIVPSESPK--PGLRRQLKKQLEEFG 103 (217)
T ss_pred HHHHHHHHcCCCEEEEecCCCc--cchHHHHHHHHHhcC
Confidence 3444444444444455444333 444444555444433
No 216
>PRK10953 cysJ sulfite reductase subunit alpha; Provisional
Probab=23.72 E-value=1.8e+02 Score=31.03 Aligned_cols=51 Identities=10% Similarity=0.059 Sum_probs=42.2
Q ss_pred ccCCEEEEEEcCCCccCcHHHHHHHHHHHHHhCCcEEEEEcCCCCHHhhcCC
Q 020984 98 KDANIIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKLANF 149 (319)
Q Consensus 98 ~~a~~iGIivgTl~~q~~~~i~~~l~~ll~~~Gkk~y~i~vg~in~~KLaNf 149 (319)
..++.+.||.||-. -+...++++|.+.++++|..+-++.|++..+..|...
T Consensus 59 ~~~~~v~IlygSqT-Gnae~lA~~la~~l~~~g~~~~v~~~~d~~~~~L~~~ 109 (600)
T PRK10953 59 AEMPGITLISASQT-GNARRVAEQLRDDLLAAKLNVNLVNAGDYKFKQIAQE 109 (600)
T ss_pred CCCCeEEEEEEcCc-hHHHHHHHHHHHHHHhCCCCcEEechHhCCHhHhccC
Confidence 34678999999975 3456799999999999999999999999988777554
No 217
>TIGR00642 mmCoA_mut_beta methylmalonyl-CoA mutase, heterodimeric type, beta chain. The adenosylcobalamin-binding, catalytic chain of methylmalonyl-CoA mutase may form homodimers, as in mitochondrion and E. coli, or heterodimers with a shorter, homologous chain that does not bind adenosylcobalamin. This model describes this non-catalytic beta chain, as found in the enzyme from Propionibacterium freudenreichii, for which the 3-dimensional structure has been solved.
Probab=23.68 E-value=1.4e+02 Score=32.10 Aligned_cols=59 Identities=14% Similarity=0.098 Sum_probs=46.8
Q ss_pred EEEEEEcCCCccCcHHHHHHHHHHHHHhCCcEEEEEcCCCCHHhhcCCC--CCCEEEEecCCCccc
Q 020984 102 IIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKLANFP--ECDVFINVSCAQTAL 165 (319)
Q Consensus 102 ~iGIivgTl~~q~~~~i~~~l~~ll~~~Gkk~y~i~vg~in~~KLaNf~--eID~fV~iaCPr~si 165 (319)
.|.+|.|| -+.|.+....+-+.|+++|.+ .+++-|++.. +..+. .||-||.+.|.=+..
T Consensus 548 ~i~viCss--D~~Y~~~a~~~~~al~~ag~~-~v~lAG~p~~--~~~~~~aGvd~fi~~g~d~~~~ 608 (619)
T TIGR00642 548 QVAVLCSS--DKVYAQQGLEVAKALKAAGAK-ALYLAGAFKE--FGDDAAEAIDGRLFMKMNVVDT 608 (619)
T ss_pred CEEEEeCC--CcchHHHHHHHHHHHHhCCCC-EEEEeCCCcc--hhhHHhcCCcceeEcCCcHHHH
Confidence 46677777 589999999999999999997 8888899853 43332 799999999976543
No 218
>TIGR03567 FMN_reduc_SsuE FMN reductase, SsuE family. Members of this protein family use NAD(P)H to reduce FMN and regenerate FMNH2. Members include the homodimeric, NAD(P)H-dependent enzyme SsuE from Escherichia coli, which serves as a partner to an FMNH2-dependent alkanesulfonate monooxygenase. It is induced by sulfate starvation. The NADH-dependent enzyme MsuE from Pseudomonas aeruginosa is outside the scope of this model (see model TIGR03566).
Probab=23.66 E-value=3.5e+02 Score=23.38 Aligned_cols=41 Identities=12% Similarity=0.208 Sum_probs=30.8
Q ss_pred EEEEEcCCCc-cCcHHHHHHHHHHHHHhCCcEEEEEcCCCCH
Q 020984 103 IGVLVGTLGV-AGYLHMIHQMKELITKAGKKAYTLVMGKPNP 143 (319)
Q Consensus 103 iGIivgTl~~-q~~~~i~~~l~~ll~~~Gkk~y~i~vg~in~ 143 (319)
|-+|.|++.. ..+..+++.+.+.++++|-++-++-+.++..
T Consensus 2 il~I~gS~r~~S~t~~l~~~~~~~l~~~~~~~~~idl~~l~~ 43 (171)
T TIGR03567 2 VLTLSGSPSTPSRSSALLRHVREALQEQGVEVDHLSVRDLPA 43 (171)
T ss_pred EEEEECCCCCCChHHHHHHHHHHHHHHCCCeEEEEEecCCCh
Confidence 5677888754 4456788999999998888877777776653
No 219
>PRK01372 ddl D-alanine--D-alanine ligase; Reviewed
Probab=23.33 E-value=3.4e+02 Score=25.27 Aligned_cols=57 Identities=21% Similarity=0.207 Sum_probs=40.9
Q ss_pred CEEEEEEcCCCccC--cHHHHHHHHHHHHHhCCcEEEEEcCCCCHHhhcCCCCCCEEEEe
Q 020984 101 NIIGVLVGTLGVAG--YLHMIHQMKELITKAGKKAYTLVMGKPNPAKLANFPECDVFINV 158 (319)
Q Consensus 101 ~~iGIivgTl~~q~--~~~i~~~l~~ll~~~Gkk~y~i~vg~in~~KLaNf~eID~fV~i 158 (319)
.+|+|+.|..+-.. .+.-.+.+.+-|++.|.+++.+...+-....|.. .++|+.+..
T Consensus 5 ~~v~~~~g~~~~~~~~~~~s~~~i~~al~~~g~~v~~i~~~~~~~~~~~~-~~~D~v~~~ 63 (304)
T PRK01372 5 GKVAVLMGGTSAEREVSLNSGAAVLAALREAGYDAHPIDPGEDIAAQLKE-LGFDRVFNA 63 (304)
T ss_pred cEEEEEeCCCCCCceEeHHhHHHHHHHHHHCCCEEEEEecCcchHHHhcc-CCCCEEEEe
Confidence 47899998877543 3456688999999999999988777554444433 378876654
No 220
>COG1429 CobN Cobalamin biosynthesis protein CobN and related Mg-chelatases [Coenzyme metabolism]
Probab=23.27 E-value=2.5e+02 Score=33.16 Aligned_cols=96 Identities=15% Similarity=0.104 Sum_probs=60.7
Q ss_pred EEEcCCCCccccccCcHHHHHHHHHHHHHhhccCCEEEEEEcCCC-ccCcHHHHHHHHHHHHHhCCcEEEEEcCCCC--H
Q 020984 67 VRYDATEERLLTDVSQPLKILKRRYYLVEKAKDANIIGVLVGTLG-VAGYLHMIHQMKELITKAGKKAYTLVMGKPN--P 143 (319)
Q Consensus 67 ~~yDP~s~~~~~e~~~~~k~l~~R~~~I~ka~~a~~iGIivgTl~-~q~~~~i~~~l~~ll~~~Gkk~y~i~vg~in--~ 143 (319)
-.|.|....+... ...+|. .|..-.....+.+|||++-..- ..++...++.|.+.|+++|..+..++..-.. +
T Consensus 173 giyhP~~~~~~~~---~~~yl~-wy~~~~~~~~~ptVgi~~~r~~~~~~~~~~idaLi~~le~rG~nvi~~f~~~~~~~~ 248 (1388)
T COG1429 173 GIYHPDAGEIFEN---LREYLD-WYINGFYDPGAPTVGILFYRTYYTNGNLAPIDALIRALEERGLNVIPVFLSSDALYV 248 (1388)
T ss_pred eEEcCCCcccccc---HHHHHH-HHhhcccCCCCCEEEEEeeeeeeeccccHHHHHHHHHHHHCCCeeEEEEeecCCchh
Confidence 5566666543322 222222 2222234457899999998533 3558899999999999999999988877666 2
Q ss_pred HhhcCCC-----CCCEEEEecCCCcccc
Q 020984 144 AKLANFP-----ECDVFINVSCAQTALL 166 (319)
Q Consensus 144 ~KLaNf~-----eID~fV~iaCPr~sid 166 (319)
.....|. .||+.|.+-+-.+.-.
T Consensus 249 ~~~~~~~~~~~~~vdaii~l~~f~l~~~ 276 (1388)
T COG1429 249 VLRAFFLGLEKVLVDAIISLTGFALNGS 276 (1388)
T ss_pred HHHHhhccccccccceeeeehhhhcCCC
Confidence 3333332 4788776665555443
No 221
>PF09861 DUF2088: Domain of unknown function (DUF2088); InterPro: IPR018657 This domain, found in various hypothetical proteins, has no known function. ; PDB: 2YJG_B.
Probab=23.07 E-value=1.6e+02 Score=26.98 Aligned_cols=39 Identities=23% Similarity=0.192 Sum_probs=26.3
Q ss_pred HHHhhccCCEEEEEE--cCCCccCcHHHHHHHHHHHHHhCCc
Q 020984 93 LVEKAKDANIIGVLV--GTLGVAGYLHMIHQMKELITKAGKK 132 (319)
Q Consensus 93 ~I~ka~~a~~iGIiv--gTl~~q~~~~i~~~l~~ll~~~Gkk 132 (319)
+-+.++..+++.|++ +|.. +....++..|.+.|+++|.+
T Consensus 47 L~~~~~~~~~V~Ivv~D~TRp-~p~~~il~~ll~~L~~~Gv~ 87 (204)
T PF09861_consen 47 LRELVKPGKRVAIVVDDITRP-TPSDLILPALLEELEEAGVK 87 (204)
T ss_dssp HHHHCTT-SEEEEEEE-TTS----HHHHHHHHHHHHHT-T-T
T ss_pred HHHHhCCCCeEEEEeCCCCCC-CCHHHHHHHHHHHHHhcCCC
Confidence 334466679999999 6765 66778999999999988753
No 222
>PF01344 Kelch_1: Kelch motif; InterPro: IPR006652 Kelch is a 50-residue motif, named after the Drosophila mutant in which it was first identified []. This sequence motif represents one beta-sheet blade, and several of these repeats can associate to form a beta-propeller. For instance, the motif appears 6 times in Drosophila egg-chamber regulatory protein, creating a 6-bladed beta-propeller. The motif is also found in mouse protein MIPP [] and in a number of poxviruses. In addition, kelch repeats have been recognised in alpha- and beta-scruin [, ], and in galactose oxidase from the fungus Dactylium dendroides [, ]. The structure of galactose oxidase reveals that the repeated sequence corresponds to a 4-stranded anti-parallel beta-sheet motif that forms the repeat unit in a super-barrel structural fold []. The known functions of kelch-containing proteins are diverse: scruin is an actin cross-linking protein; galactose oxidase catalyses the oxidation of the hydroxyl group at the C6 position in D-galactose; neuraminidase hydrolyses sialic acid residues from glycoproteins; and kelch may have a cytoskeletal function, as it is localised to the actin-rich ring canals that connect the 15 nurse cells to the developing oocyte in Drosophila []. Nevertheless, based on the location of the kelch pattern in the catalytic unit in galactose oxidase, functionally important residues have been predicted in glyoxal oxidase []. This entry represents a type of kelch sequence motif that comprises one beta-sheet blade.; GO: 0005515 protein binding; PDB: 2XN4_A 2WOZ_A 3II7_A 4ASC_A 1U6D_X 1ZGK_A 2FLU_X 2VPJ_A 2DYH_A 1X2R_A ....
Probab=22.92 E-value=65 Score=21.25 Aligned_cols=14 Identities=14% Similarity=0.219 Sum_probs=11.3
Q ss_pred CCeEEEEcCCCCcc
Q 020984 63 GCEIVRYDATEERL 76 (319)
Q Consensus 63 ~~~v~~yDP~s~~~ 76 (319)
...+++|||.+++-
T Consensus 27 ~~~v~~yd~~~~~W 40 (47)
T PF01344_consen 27 TNSVEVYDPETNTW 40 (47)
T ss_dssp EEEEEEEETTTTEE
T ss_pred eeeEEEEeCCCCEE
Confidence 45799999998863
No 223
>cd05397 NT_Pol-beta-like Nucleotidyltransferase (NT) domain of DNA polymerase beta and similar proteins. This superfamily includes the NT domains of DNA polymerase beta and other family X DNA polymerases, as well as the NT domains of Class I and Class II CCA-adding enzymes, RelA- and SpoT-like ppGpp synthetases and hydrolases, 2'5'-oligoadenylate (2-5A)synthetases, Escherichia coli adenylyltransferase (GlnE), Escherichia coli uridylyl transferase (GlnD), poly (A) polymerases, terminal uridylyl transferases, and Staphylococcus aureus kanamycin nucleotidyltransferase, and similar proteins. The Escherichia coli CCA-adding enzyme belongs to this superfamily but is not included as this enzyme lacks the N-terminal helix conserved in the remainder of the superfamily. In the majority of the Pol beta-like superfamily NTs, two carboxylates, Dx[D/E], together with a third more distal carboxylate coordinate two divalent metal cations that are essential for catalysis. These divalent metal ions are
Probab=22.91 E-value=1.7e+02 Score=20.35 Aligned_cols=39 Identities=21% Similarity=0.238 Sum_probs=25.2
Q ss_pred HHHHHHHHHHHHh--CCcEEEEEcCCCCHHhhcCCCCCCEEEE
Q 020984 117 HMIHQMKELITKA--GKKAYTLVMGKPNPAKLANFPECDVFIN 157 (319)
Q Consensus 117 ~i~~~l~~ll~~~--Gkk~y~i~vg~in~~KLaNf~eID~fV~ 157 (319)
++++.+++.+++. .++.| +.|-.-.......++||+.|.
T Consensus 2 ~~l~~i~~~l~~~~~~~~v~--lfGS~arg~~~~~SDIDi~v~ 42 (49)
T cd05397 2 ELLDIIKERLKKLVPGYEIV--VYGSLVRGLLKKSSDIDLACV 42 (49)
T ss_pred HHHHHHHHHHHhhcCCcEEE--EECCcCCCCCCCCCCEEEEEE
Confidence 4677888888877 44444 445544444445668998876
No 224
>PRK15408 autoinducer 2-binding protein lsrB; Provisional
Probab=22.75 E-value=2e+02 Score=27.81 Aligned_cols=63 Identities=17% Similarity=0.130 Sum_probs=40.9
Q ss_pred cCCEEEEEEcCCCccCcHHHHHHHHHHHHHhCCcEEEEEcCCCCHHh----hcCC--CCCCEEEEecCC
Q 020984 99 DANIIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAK----LANF--PECDVFINVSCA 161 (319)
Q Consensus 99 ~a~~iGIivgTl~~q~~~~i~~~l~~ll~~~Gkk~y~i~vg~in~~K----LaNf--~eID~fV~iaCP 161 (319)
.+.+|++|+-+++...+..+.+-+++.++++|.+..+..-++-++++ +.++ ..+|+.|+.++-
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 46788888887776666778888888888888665432223444433 2233 268888886543
No 225
>PRK03767 NAD(P)H:quinone oxidoreductase; Provisional
Probab=22.52 E-value=2e+02 Score=25.54 Aligned_cols=42 Identities=17% Similarity=0.072 Sum_probs=32.6
Q ss_pred EEEEEEcCCCccCcHHHHHHHHHHHHH-hCCcEEEEEcCCCCHH
Q 020984 102 IIGVLVGTLGVAGYLHMIHQMKELITK-AGKKAYTLVMGKPNPA 144 (319)
Q Consensus 102 ~iGIivgTl~~q~~~~i~~~l~~ll~~-~Gkk~y~i~vg~in~~ 144 (319)
+|-||.++.. -+...+++.+.+-+++ .|.++-++-+.+..|.
T Consensus 3 kilIvy~S~~-G~T~~lA~~ia~g~~~~~G~ev~~~~l~~~~~~ 45 (200)
T PRK03767 3 KVLVLYYSMY-GHIETMAEAVAEGAREVAGAEVTIKRVPETVPE 45 (200)
T ss_pred eEEEEEcCCC-CHHHHHHHHHHHHHhhcCCcEEEEEeccccCCH
Confidence 5778888874 5677889999999998 8999888888654433
No 226
>cd03142 GATase1_ThuA Type 1 glutamine amidotransferase (GATase1)-like domain found in Sinorhizobium meliloti Rm1021 ThuA (SmThuA). Type 1 glutamine amidotransferase (GATase1)-like domain found in Sinorhizobium meliloti Rm1021 ThuA (SmThuA). This group includes proteins similar to SmThuA which plays a role in a major pathway for trehalose catabolism. SmThuA is induced by trehalose but not by related structurally similar disaccharides like sucrose or maltose. Proteins in this group lack the catalytic triad of typical GATase1 domains: a His replaces the reactive Cys found in the sharp turn between a beta strand and an alpha helix termed the nucleophile elbow. S. meliloti Rm1021 thuA mutants are impaired in competitive colonization of Medicago sativa roots but are more competitive than the wild-type Rml021 in infecting alfalfa roots and forming nitrogen-fixing nodules.
Probab=22.41 E-value=2e+02 Score=26.65 Aligned_cols=44 Identities=16% Similarity=0.135 Sum_probs=32.8
Q ss_pred HHHHHHHHHHHHhCCcEEEEEcCC----CCHHhhcCCCCCCEEEEecCCCc
Q 020984 117 HMIHQMKELITKAGKKAYTLVMGK----PNPAKLANFPECDVFINVSCAQT 163 (319)
Q Consensus 117 ~i~~~l~~ll~~~Gkk~y~i~vg~----in~~KLaNf~eID~fV~iaCPr~ 163 (319)
.|-..++..|++.|.++.+-.+.+ +++++|+. .|+.|..+|.-.
T Consensus 23 ~~~~~~~~~L~~~gf~V~~~~~~d~~~~~~~~~L~~---~D~lV~~~~~~~ 70 (215)
T cd03142 23 GMHGTIAAALAEYGFDVQTATLDEPEHGLTEEVLAE---TDVLLWWGHIAH 70 (215)
T ss_pred hHHHHHHHHHHhcCcEEEEEeccCccccCCHhHHhc---CCEEEEeCCCCc
Confidence 355678889999998877666655 56776655 589999999864
No 227
>COG0552 FtsY Signal recognition particle GTPase [Intracellular trafficking and secretion]
Probab=22.39 E-value=1.6e+02 Score=29.33 Aligned_cols=87 Identities=22% Similarity=0.235 Sum_probs=61.6
Q ss_pred HHHHHHhhccCCEEEEEEcCCCc-cCcHHHHHHHHHHHHHhCCcEE-----EEEc-------CCCCHHhhcC-CCCCCEE
Q 020984 90 RYYLVEKAKDANIIGVLVGTLGV-AGYLHMIHQMKELITKAGKKAY-----TLVM-------GKPNPAKLAN-FPECDVF 155 (319)
Q Consensus 90 R~~~I~ka~~a~~iGIivgTl~~-q~~~~i~~~l~~ll~~~Gkk~y-----~i~v-------g~in~~KLaN-f~eID~f 155 (319)
=|-+|++|+..+.=-+|+-|-|| |+..++++.|++.-+-.+|..- +|++ +-++-+|.-| .-++|.+
T Consensus 210 afDAi~~Akar~~DvvliDTAGRLhnk~nLM~EL~KI~rV~~k~~~~ap~e~llvlDAttGqnal~QAk~F~eav~l~Gi 289 (340)
T COG0552 210 AFDAIQAAKARGIDVVLIDTAGRLHNKKNLMDELKKIVRVIKKDDPDAPHEILLVLDATTGQNALSQAKIFNEAVGLDGI 289 (340)
T ss_pred HHHHHHHHHHcCCCEEEEeCcccccCchhHHHHHHHHHHHhccccCCCCceEEEEEEcccChhHHHHHHHHHHhcCCceE
Confidence 37789999887777789999988 8888999999888776666543 5665 2455666643 3379999
Q ss_pred EEecCCCcc---ccc--ccCCCCccc
Q 020984 156 INVSCAQTA---LLD--SKEFLAPVI 176 (319)
Q Consensus 156 V~iaCPr~s---idd--~~~f~kPvl 176 (319)
|++=|--.+ +.- ..++..||.
T Consensus 290 IlTKlDgtAKGG~il~I~~~l~~PI~ 315 (340)
T COG0552 290 ILTKLDGTAKGGIILSIAYELGIPIK 315 (340)
T ss_pred EEEecccCCCcceeeeHHHHhCCCEE
Confidence 999886332 222 356777774
No 228
>PRK14336 (dimethylallyl)adenosine tRNA methylthiotransferase; Provisional
Probab=22.38 E-value=2e+02 Score=28.95 Aligned_cols=10 Identities=20% Similarity=0.322 Sum_probs=6.2
Q ss_pred EEecCCCccc
Q 020984 156 INVSCAQTAL 165 (319)
Q Consensus 156 V~iaCPr~si 165 (319)
|+-+||..+-
T Consensus 130 i~rGC~~~Cs 139 (418)
T PRK14336 130 IMQGCDNFCT 139 (418)
T ss_pred eccCCCCCCc
Confidence 3557887654
No 229
>cd06301 PBP1_rhizopine_binding_like Periplasmic binding proteins specific to rhizopines. Periplasmic binding proteins specific to rhizopines, which are simple sugar-like compounds produced in the nodules induced by the symbiotic root nodule bacteria, such as Rhizobium and Sinorhizobium. Rhizopine-binding-like proteins from other bacteria are also included. Two inositol based rhizopine compounds are known to date: L-3-O-methly-scyllo-inosamine (3-O-MSI) and scyllo-inosamine. Bacterial strains that can metabolize rhizopine have a greater competitive advantage in nodulation and rhizopine synthesis is regulated by NifA/NtrA regulatory transcription activators which are maximally expressed at the onset of nitrogen fixation in bacteroids. The members of this group belong to the pentose/hexose sugar-binding protein family of the type I periplasmic binding protein superfamily.
Probab=22.37 E-value=2.1e+02 Score=25.48 Aligned_cols=57 Identities=23% Similarity=0.178 Sum_probs=28.6
Q ss_pred EEEEEcCCCccCcHHHHHHHHHHHHH-hCCcEEEEEcCCCCHHhhcC----C--CCCCEEEEecC
Q 020984 103 IGVLVGTLGVAGYLHMIHQMKELITK-AGKKAYTLVMGKPNPAKLAN----F--PECDVFINVSC 160 (319)
Q Consensus 103 iGIivgTl~~q~~~~i~~~l~~ll~~-~Gkk~y~i~vg~in~~KLaN----f--~eID~fV~iaC 160 (319)
||+|+....-..+..+++.+.+.+++ .|....+. -+.-++++..+ + ..+|.+|+.++
T Consensus 2 igvi~~~~~~~~~~~~~~gi~~~~~~~~~~~~~~~-~~~~~~~~~~~~i~~l~~~~vdgiii~~~ 65 (272)
T cd06301 2 IGVSMANFDDNFLTLLRNAMKEHAKVLGGVELQFE-DAKNDVATQLSQVENFIAQGVDAIIVVPV 65 (272)
T ss_pred eeEeecccCCHHHHHHHHHHHHHHHHcCCcEEEEe-CCCCCHHHHHHHHHHHHHcCCCEEEEecC
Confidence 56666655544555666666666666 55443332 22223332221 1 15677666554
No 230
>PRK03094 hypothetical protein; Provisional
Probab=22.29 E-value=2.1e+02 Score=22.73 Aligned_cols=57 Identities=14% Similarity=0.158 Sum_probs=37.1
Q ss_pred HHHHHHHHHhCCcEEEEEcCCCCHHhhcCCCCCCEEEEecCCCcccccc-cCCCCccc-----CHHHHHH
Q 020984 120 HQMKELITKAGKKAYTLVMGKPNPAKLANFPECDVFINVSCAQTALLDS-KEFLAPVI-----TPFEAML 183 (319)
Q Consensus 120 ~~l~~ll~~~Gkk~y~i~vg~in~~KLaNf~eID~fV~iaCPr~sidd~-~~f~kPvl-----TP~El~v 183 (319)
..|++.|+++|+.+..+- . +. +...+||.|+.+=..+-.--. ..+.-||| ||-|..-
T Consensus 11 s~i~~~L~~~GYeVv~l~--~--~~---~~~~~Da~VitG~d~n~mgi~d~~t~~pVI~A~G~TaeEI~~ 73 (80)
T PRK03094 11 TDVQQALKQKGYEVVQLR--S--EQ---DAQGCDCCVVTGQDSNVMGIADTSTKGSVITASGLTADEICQ 73 (80)
T ss_pred HHHHHHHHHCCCEEEecC--c--cc---ccCCcCEEEEeCCCcceecccccccCCcEEEcCCCCHHHHHH
Confidence 468899999998866553 1 11 135799999999777654322 34667774 5555443
No 231
>PRK00945 acetyl-CoA decarbonylase/synthase complex subunit epsilon; Provisional
Probab=22.26 E-value=2.7e+02 Score=24.96 Aligned_cols=46 Identities=15% Similarity=0.036 Sum_probs=35.6
Q ss_pred HHHHhhccCCEEEEEEcCCCccCcHHHHHHHHHHHHHhCCcEEEEEc
Q 020984 92 YLVEKAKDANIIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVM 138 (319)
Q Consensus 92 ~~I~ka~~a~~iGIivgTl~~q~~~~i~~~l~~ll~~~Gkk~y~i~v 138 (319)
.+.+..++|++--||+|..... ..+..+.+++++++.|..+++-..
T Consensus 26 ~aa~lI~~AKrPlIivG~ga~~-~~ea~e~l~elaEkl~iPVvtT~~ 71 (171)
T PRK00945 26 IAAMMIKKAKRPLLVVGSLLLD-DEELLDRAVKIAKKANIPVAATGG 71 (171)
T ss_pred HHHHHHHhCCCcEEEECcCccc-cchHHHHHHHHHHHHCCCEEEccc
Confidence 3555667889999999986554 367888999999999988776655
No 232
>cd01481 vWA_collagen_alpha3-VI-like VWA_collagen alpha 3(VI) like: The extracellular matrix represents a complex alloy of variable members of diverse protein families defining structural integrity and various physiological functions. The most abundant family is the collagens with more than 20 different collagen types identified thus far. Collagens are centrally involved in the formation of fibrillar and microfibrillar networks of the extracellular matrix, basement membranes as well as other structures of the extracellular matrix. Some collagens have about 15-18 vWA domains in them. The VWA domains present in these collagens mediate protein-protein interactions.
Probab=22.17 E-value=2e+02 Score=24.84 Aligned_cols=49 Identities=12% Similarity=0.123 Sum_probs=35.3
Q ss_pred cCCEEEEEEcCCCccCcHHHHHHHHHHHHHhCCcEEEEEcCCCCHHhhcCCC
Q 020984 99 DANIIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKLANFP 150 (319)
Q Consensus 99 ~a~~iGIivgTl~~q~~~~i~~~l~~ll~~~Gkk~y~i~vg~in~~KLaNf~ 150 (319)
+++++-||+.. ++..-. +...-+.|++.|...|.+-++.++.+.|..+.
T Consensus 105 ~~~kv~vviTd--G~s~d~-~~~~a~~lr~~gv~i~~vG~~~~~~~eL~~ia 153 (165)
T cd01481 105 GVPQFLVLITG--GKSQDD-VERPAVALKRAGIVPFAIGARNADLAELQQIA 153 (165)
T ss_pred CCCeEEEEEeC--CCCcch-HHHHHHHHHHCCcEEEEEeCCcCCHHHHHHHh
Confidence 45677666653 333333 34556788899999999999999999998764
No 233
>TIGR03605 antibiot_sagB SagB-type dehydrogenase domain. SagB of Sterptococcus pyogenes participates in the maturation of streptolysin S from a ribosomally produced precursor polypeptide. Chemically similar systems operate on highly diverse sets of bacteriocin precursors in numerous other bacteria. This model describes a domain within SgaB and homologous regions from other proteins, many of which appear to be involved in biosynthesis of secondary metabolites. While some substrates may be intermediates in non-ribosomal peptide syntheses, others are involved in heterocycle-containing bacteriocin biosynthesis, and can be found near SgaC-like (see TIGR03603, cyclodehydratase) and SgaD-like (see TIGR03604, "docking") proteins. Members of this domain family are heterogeneous in length, as many have a partial second copy of the domain represented here. The incomplete second domain scores below the cutoffs to this model in most cases.
Probab=22.15 E-value=4.6e+02 Score=22.66 Aligned_cols=85 Identities=21% Similarity=0.213 Sum_probs=45.1
Q ss_pred eEEEEcCCCCccccccC---cHHHHHHHHHHHHHhhccCCEEEEEEcCCCcc-------CcH-------HHHHHHHHHHH
Q 020984 65 EIVRYDATEERLLTDVS---QPLKILKRRYYLVEKAKDANIIGVLVGTLGVA-------GYL-------HMIHQMKELIT 127 (319)
Q Consensus 65 ~v~~yDP~s~~~~~e~~---~~~k~l~~R~~~I~ka~~a~~iGIivgTl~~q-------~~~-------~i~~~l~~ll~ 127 (319)
-+|.|||..+.+..... +..+.+..-...-.-+.+|..+-++++...+- .|. .+..++.-...
T Consensus 56 G~Y~Y~p~~h~L~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~iv~~~~~~~~~~~y~~~~~~~~~~daG~~~qnl~LaA~ 135 (173)
T TIGR03605 56 GIYHYDPEEHRLILIRAGEENVDAFLVNALLNTENANTPPIIIFIVARFWKNFWKYGNRGYRLALLDSGIIIQNFYLVAT 135 (173)
T ss_pred eeEEEcCCCCEEEEeeCCccCHHHHHHHHHhCccccccCCEEEEEEEEecccHHHHhHHHHHHHHHHHHHHHHHHHHHHH
Confidence 48999999998764432 23333332211122355677776666655321 111 23334444556
Q ss_pred HhCCcEEEEEcCCCCHHhhc---CCCC
Q 020984 128 KAGKKAYTLVMGKPNPAKLA---NFPE 151 (319)
Q Consensus 128 ~~Gkk~y~i~vg~in~~KLa---Nf~e 151 (319)
..|..+..+. -.+.+++. ++++
T Consensus 136 ~~Glgs~~i~--~f~~~~v~~~L~l~~ 160 (173)
T TIGR03605 136 ALGLGSCAIG--GFDDDYIAELLGLDG 160 (173)
T ss_pred HcCCCeEEEc--cccHHHHHHHhCcCC
Confidence 6787776653 44555544 5665
No 234
>PRK05319 rplD 50S ribosomal protein L4; Provisional
Probab=21.94 E-value=6.2e+02 Score=23.14 Aligned_cols=68 Identities=25% Similarity=0.388 Sum_probs=43.0
Q ss_pred HHHHHHHHHHHHHhhccCCEEEEEEcCCCccCcHHHHHHHHHHHHHhCCcEEEEEcCCCCHH-hhc--CCCCCCE
Q 020984 83 PLKILKRRYYLVEKAKDANIIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPA-KLA--NFPECDV 154 (319)
Q Consensus 83 ~~k~l~~R~~~I~ka~~a~~iGIivgTl~~q~~~~i~~~l~~ll~~~Gkk~y~i~vg~in~~-KLa--Nf~eID~ 154 (319)
-.+.+..|.++-.++++-+. +||..+.... .=.+.+.++|++.|.+..+|++++.+.. .++ |++.+++
T Consensus 103 K~~~lAl~~aLs~k~~~~~l--~Vvd~~~~~~--~KTk~~~~~l~~lg~~~~Lii~~~~~~n~~~a~rNi~~v~v 173 (205)
T PRK05319 103 KVRRLALRSALSEKAREGRL--VVVDDLSLEA--PKTKELAAKLKNLGLKKVLIVTDEVDENLYLSARNLPNVDV 173 (205)
T ss_pred HHHHHHHHHHHHHHHhcCCe--EEEeccccCC--CCHHHHHHHHHHcCCCceEEEECCCchHHHHHHhCCCCcEE
Confidence 45667888888888887665 4666553211 1234466677777866677777765543 222 8887876
No 235
>PF03059 NAS: Nicotianamine synthase protein; InterPro: IPR004298 Nicotianamine synthase 2.5.1.43 from EC catalyzes the trimerization of S-adenosylmethionine to yield one molecule of nicotianamine. Nicotianamine has an important role in plant iron uptake mechanisms. Plants adopt two strategies (termed I and II) of iron acquisition. Strategy I is adopted by all higher plants except graminaceous plants, which adopt strategy II [, ]. In strategy I plants, the role of nicotianamine is not fully determined: possible roles include the formation of more stable complexes with ferrous than with ferric ion, which might serve as a sensor of the physiological status of iron within a plant, or which might be involved in the transport of iron []. In strategy II (graminaceous) plants, nicotianamine is the key intermediate (and nicotianamine synthase the key enzyme) in the synthesis of the mugineic family (the only known family in plants) of phytosiderophores. Phytosiderophores are iron chelators whose secretion by the roots is greatly increased in instances of iron deficiency []. The 3D structures of five example NAS from Methanothermobacter thermautotrophicus reveal the monomer to consist of a five-helical bundle N-terminal domain on top of a classic Rossmann fold C-terminal domain. The N-terminal domain is unique to the NAS family, whereas the C-terminal domain is homologous to the class I family of SAM-dependent methyltransferases. An active site is created at the interface of the two domains, at the rim of a large cavity that corresponds to the nucleotide binding site such as is found in other proteins adopting a Rossmann fold [].; GO: 0030410 nicotianamine synthase activity, 0030418 nicotianamine biosynthetic process; PDB: 3O31_B 3FPH_A 3FPJ_A 3FPE_B 3FPF_B 3FPG_B.
Probab=21.94 E-value=1e+02 Score=29.68 Aligned_cols=30 Identities=23% Similarity=0.375 Sum_probs=18.0
Q ss_pred eEEEEcCCcchHHHHHHhc---CCCeEEEEcCC
Q 020984 43 LLFWIGSDNSAFANVVLTF---NGCEIVRYDAT 72 (319)
Q Consensus 43 ~i~~Ig~~~~~l~~l~l~~---~~~~v~~yDP~ 72 (319)
.++|||.|.+.|+.++|+- ++..|.-||-.
T Consensus 123 rVaFIGSGPLPlT~i~la~~~~~~~~v~~iD~d 155 (276)
T PF03059_consen 123 RVAFIGSGPLPLTSIVLAKQHGPGARVHNIDID 155 (276)
T ss_dssp EEEEE---SS-HHHHHHH--HTT--EEEEEESS
T ss_pred eEEEEcCCCcchHHHHHHHHhCCCCeEEEEeCC
Confidence 7999999999999999873 34556667643
No 236
>PRK03708 ppnK inorganic polyphosphate/ATP-NAD kinase; Provisional
Probab=21.93 E-value=2e+02 Score=27.48 Aligned_cols=98 Identities=14% Similarity=0.211 Sum_probs=56.7
Q ss_pred EEEEEEcCCCccCcHHHHHHHHHHHHHhCCcEEEEEc--CCCCHH---hhcCC--CCCCEEEEec---------------
Q 020984 102 IIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVM--GKPNPA---KLANF--PECDVFINVS--------------- 159 (319)
Q Consensus 102 ~iGIivgTl~~q~~~~i~~~l~~ll~~~Gkk~y~i~v--g~in~~---KLaNf--~eID~fV~ia--------------- 159 (319)
++||+... +.+.-.++++++.+.|+++|.++++... ...... .+.+. .++|+.|.++
T Consensus 2 ~v~iv~~~-~k~~~~~~~~~I~~~L~~~g~~v~v~~~~~~~~~~~~~~~~~~~~~~~~d~vi~iGGDGTlL~a~~~~~~~ 80 (277)
T PRK03708 2 RFGIVARR-DKEEALKLAYRVYDFLKVSGYEVVVDSETYEHLPEFSEEDVLPLEEMDVDFIIAIGGDGTILRIEHKTKKD 80 (277)
T ss_pred EEEEEecC-CCHHHHHHHHHHHHHHHHCCCEEEEecchhhhcCcccccccccccccCCCEEEEEeCcHHHHHHHHhcCCC
Confidence 47777555 4477888999999999999988877531 111110 01111 2578777553
Q ss_pred CCCcccccc-cCCCCcccCHHHHHHhhCCCCCCCcceeecccccc
Q 020984 160 CAQTALLDS-KEFLAPVITPFEAMLAFGRGTQWTGAYVMEFRDLM 203 (319)
Q Consensus 160 CPr~sidd~-~~f~kPvlTP~El~vAL~~~~~W~~~y~~Df~~ll 203 (319)
||-..+--+ ..|... +.|.|+.-+|..- -.|.|..+-..++
T Consensus 81 ~pi~gIn~G~lGFl~~-~~~~~~~~~l~~i--~~g~~~~~~r~~l 122 (277)
T PRK03708 81 IPILGINMGTLGFLTE-VEPEETFFALSRL--LEGDYFIDERIKL 122 (277)
T ss_pred CeEEEEeCCCCCcccc-CCHHHHHHHHHHH--HcCCceEEEeEEE
Confidence 343333333 356664 4588888887531 2345555444444
No 237
>PRK00179 pgi glucose-6-phosphate isomerase; Reviewed
Probab=21.82 E-value=9.7e+02 Score=25.41 Aligned_cols=52 Identities=19% Similarity=0.278 Sum_probs=30.2
Q ss_pred cCCEEEEEEcCCCccCcHHH--HHHHHHHHHHhC------CcEEEEEcCCCCHHhhcCCCCCC
Q 020984 99 DANIIGVLVGTLGVAGYLHM--IHQMKELITKAG------KKAYTLVMGKPNPAKLANFPECD 153 (319)
Q Consensus 99 ~a~~iGIivgTl~~q~~~~i--~~~l~~ll~~~G------kk~y~i~vg~in~~KLaNf~eID 153 (319)
+.++..+||.++++..--.+ ...+++.+++++ .+.++.+.++ ..+++.| .++
T Consensus 196 ~~~~TL~iViSKSgtT~ET~~n~~~~~~~l~~~~~~~~~~~~h~vaVT~~--~~~~~~~-g~~ 255 (548)
T PRK00179 196 DPETTLFIVASKTFTTQETLTNAHSARDWFLAAGGDEAAVAKHFVAVSTN--AEAVAEF-GID 255 (548)
T ss_pred CcccEEEEEEeCCCCCHHHHHHHHHHHHHHHHhcCccccccceEEEEcCC--cHHHHHc-CCc
Confidence 66778888888887554444 445566666543 2234444554 4445555 344
No 238
>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=21.81 E-value=1.9e+02 Score=26.77 Aligned_cols=34 Identities=12% Similarity=-0.009 Sum_probs=20.0
Q ss_pred EEEEEcCC-CccCcHHHHHHHHHHHHHhCCcEEEE
Q 020984 103 IGVLVGTL-GVAGYLHMIHQMKELITKAGKKAYTL 136 (319)
Q Consensus 103 iGIivgTl-~~q~~~~i~~~l~~ll~~~Gkk~y~i 136 (319)
||+|+..+ .-..+..+++.+++.+++.|....+.
T Consensus 2 Igvi~~~~~~~~~~~~~~~gi~~~~~~~g~~v~~~ 36 (305)
T cd06324 2 VVFLNPGKSDEPFWNSVARFMQAAADDLGIELEVL 36 (305)
T ss_pred eEEecCCCCCCcHHHHHHHHHHHHHHhcCCeEEEE
Confidence 56666555 44445566666666666666554443
No 239
>PRK15482 transcriptional regulator MurR; Provisional
Probab=21.70 E-value=3.3e+02 Score=25.42 Aligned_cols=66 Identities=15% Similarity=0.108 Sum_probs=45.2
Q ss_pred hhccCCEEEEEEcCCCccCcHHHHHHHHHHHHHhCCcEEEEEcCCCCHHhhcCCCCCCEEEEecCCCccc
Q 020984 96 KAKDANIIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKLANFPECDVFINVSCAQTAL 165 (319)
Q Consensus 96 ka~~a~~iGIivgTl~~q~~~~i~~~l~~ll~~~Gkk~y~i~vg~in~~KLaNf~eID~fV~iaCPr~si 165 (319)
...+|++| .|+|. .....+.+.+...|...|+.+....-......-..++.+=|++|.++-++.+-
T Consensus 131 ~i~~A~~I-~i~G~---G~S~~~A~~l~~~l~~~g~~~~~~~d~~~~~~~~~~~~~~Dv~i~iS~sg~t~ 196 (285)
T PRK15482 131 VISKAPFI-QITGL---GGSALVGRDLSFKLMKIGYRVACEADTHVQATVSQALKKGDVQIAISYSGSKK 196 (285)
T ss_pred HHHhCCee-EEEEe---ChhHHHHHHHHHHHHhCCCeeEEeccHhHHHHHHhcCCCCCEEEEEeCCCCCH
Confidence 34567775 55655 34567889999999999998776542333233344666779999999887753
No 240
>PRK14481 dihydroxyacetone kinase subunit DhaK; Provisional
Probab=21.65 E-value=3.2e+02 Score=27.16 Aligned_cols=46 Identities=20% Similarity=0.328 Sum_probs=38.5
Q ss_pred hhccCCEEEEEEcCCCccCcHHH---HHHHHHHHHHhCCcEEEEEcCCC
Q 020984 96 KAKDANIIGVLVGTLGVAGYLHM---IHQMKELITKAGKKAYTLVMGKP 141 (319)
Q Consensus 96 ka~~a~~iGIivgTl~~q~~~~i---~~~l~~ll~~~Gkk~y~i~vg~i 141 (319)
+.++...+.++|+.||+...+++ .+++.++|+++|.+.+.+.+|..
T Consensus 247 ~~~~gd~v~lLvN~LG~ts~lEl~i~~~~v~~~L~~~gi~i~r~~vG~~ 295 (331)
T PRK14481 247 KLVAGDEVLVLVNGMGATPLMELYIVYNDVAELLEERGVTVARSLVGNY 295 (331)
T ss_pred CCCCCCeEEEEEeCCCCCcHHHHHHHHHHHHHHHHHCCCEEEEEEeecc
Confidence 44566789999999999888864 57788889999999999999875
No 241
>cd03806 GT1_ALG11_like This family is most closely related to the GT1 family of glycosyltransferases. ALG11 in yeast is involved in adding the final 1,2-linked Man to the Man5GlcNAc2-PP-Dol synthesized on the cytosolic face of the ER. The deletion analysis of ALG11 was shown to block the early steps of core biosynthesis that takes place on the cytoplasmic face of the ER and lead to a defect in the assembly of lipid-linked oligosaccharides.
Probab=21.44 E-value=1.9e+02 Score=28.77 Aligned_cols=72 Identities=17% Similarity=0.135 Sum_probs=48.6
Q ss_pred EEEEEEcCCCccCcHHHHHHHHHHHHHhCCcEEEEEcCCCCHHhhcC-CCCCCEEEEecCCCcccccccCCCCcccCHHH
Q 020984 102 IIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKLAN-FPECDVFINVSCAQTALLDSKEFLAPVITPFE 180 (319)
Q Consensus 102 ~iGIivgTl~~q~~~~i~~~l~~ll~~~Gkk~y~i~vg~in~~KLaN-f~eID~fV~iaCPr~sidd~~~f~kPvlTP~E 180 (319)
.--+|+|.-.........+.|++++++.|..-.+.++|.++.+.+.. +...|++|..+-.+ .|. +++.|
T Consensus 274 ~~lvivG~~~~~~~~~~~~~L~~~~~~l~l~~~V~f~g~v~~~~l~~~l~~adv~v~~s~~E-------~Fg---i~~lE 343 (419)
T cd03806 274 IKLVLIGSCRNEDDEKRVEDLKLLAKELGLEDKVEFVVNAPFEELLEELSTASIGLHTMWNE-------HFG---IGVVE 343 (419)
T ss_pred eEEEEEcCCCCcccHHHHHHHHHHHHHhCCCCeEEEecCCCHHHHHHHHHhCeEEEECCccC-------Ccc---cHHHH
Confidence 45577776332333456778888888888877788888888777765 55789988754332 343 56688
Q ss_pred HHH
Q 020984 181 AML 183 (319)
Q Consensus 181 l~v 183 (319)
++.
T Consensus 344 AMa 346 (419)
T cd03806 344 YMA 346 (419)
T ss_pred HHH
Confidence 744
No 242
>TIGR02362 dhaK1b probable dihydroxyacetone kinase DhaK1b subunit. Two types of dihydroxyacetone kinase (glycerone kinase) are described. In yeast and a few bacteria, e.g. Citrobacter freundii, the enzyme is a single chain that uses ATP as phosphoryl donor and is designated EC 2.7.1.29. By contract, E. coli and many other bacterial species have a multisubunit form with a phosphoprotein donor related to PTS transport proteins. This family represents a protein, unique to the Firmicutes (low GC Gram-positives), that appears to be a divergent second copy of the K subunit of that complex; its gene is always found in operons with the other three proteins of the complex.
Probab=21.40 E-value=3.3e+02 Score=26.98 Aligned_cols=46 Identities=17% Similarity=0.190 Sum_probs=38.5
Q ss_pred hhccCCEEEEEEcCCCccCcHHH---HHHHHHHHHHhCCcEEEEEcCCC
Q 020984 96 KAKDANIIGVLVGTLGVAGYLHM---IHQMKELITKAGKKAYTLVMGKP 141 (319)
Q Consensus 96 ka~~a~~iGIivgTl~~q~~~~i---~~~l~~ll~~~Gkk~y~i~vg~i 141 (319)
+.++-..+.++|+.||.--++++ .+.+.++|+++|.+.+.+.+|..
T Consensus 244 ~~~~gd~v~vlvN~LG~t~~lEl~i~~~~v~~~L~~~gi~v~r~~vG~~ 292 (326)
T TIGR02362 244 RWQADDHYAVLVNNLGGTTPMEQMVFNNDVHELLALEALHLPFIKVGTF 292 (326)
T ss_pred CCCCCCEEEEEecCCCCCCHHHHHHHHHHHHHHHHHCCCEEEEeEeecc
Confidence 34456789999999999888864 57788899999999999999875
No 243
>PRK14483 DhaKLM operon coactivator DhaQ; Provisional
Probab=21.34 E-value=3.2e+02 Score=27.12 Aligned_cols=46 Identities=13% Similarity=0.268 Sum_probs=38.4
Q ss_pred hhccCCEEEEEEcCCCccCcHHH---HHHHHHHHHHhCCcEEEEEcCCC
Q 020984 96 KAKDANIIGVLVGTLGVAGYLHM---IHQMKELITKAGKKAYTLVMGKP 141 (319)
Q Consensus 96 ka~~a~~iGIivgTl~~q~~~~i---~~~l~~ll~~~Gkk~y~i~vg~i 141 (319)
+.++...+.++|+.||+--++++ .+.+.++|+++|.+.+.+.+|..
T Consensus 247 ~~~~gd~v~vlVN~LG~ts~~El~i~~~~v~~~L~~~gi~v~r~~vG~~ 295 (329)
T PRK14483 247 RWQKGDNFILLINGLGATTLMEQYIFANDIRRLLELEGLQITFVKVGTL 295 (329)
T ss_pred CcCCCCeEEEEEeCCCCCcHHHHHHHHHHHHHHHHHCCCEEEEeEeecc
Confidence 33456789999999999888864 57788899999999999999875
No 244
>PLN02958 diacylglycerol kinase/D-erythro-sphingosine kinase
Probab=21.34 E-value=9.1e+02 Score=24.90 Aligned_cols=63 Identities=16% Similarity=0.138 Sum_probs=38.7
Q ss_pred hhccCCEEEEEEcCCCccCcH-HHH-HHHHHHHHHhCCcEEEEEcCCCCHHh-hc---CCCCCCEEEEe
Q 020984 96 KAKDANIIGVLVGTLGVAGYL-HMI-HQMKELITKAGKKAYTLVMGKPNPAK-LA---NFPECDVFINV 158 (319)
Q Consensus 96 ka~~a~~iGIivgTl~~q~~~-~i~-~~l~~ll~~~Gkk~y~i~vg~in~~K-La---Nf~eID~fV~i 158 (319)
..-..+++.||++..++.+.- .+. +.++.+|+++|.++-++.-....-++ ++ .....|..|.+
T Consensus 107 ~~~~~kr~lvIvNP~SGkg~a~k~~~~~v~~~L~~~gi~~~v~~T~~~ghA~~la~~~~~~~~D~VV~v 175 (481)
T PLN02958 107 SLGRPKRLLVFVNPFGGKKSASKIFFDVVKPLLEDADIQLTIQETKYQLHAKEVVRTMDLSKYDGIVCV 175 (481)
T ss_pred hccCCcEEEEEEcCCCCCcchhHHHHHHHHHHHHHcCCeEEEEeccCccHHHHHHHHhhhcCCCEEEEE
Confidence 333467888999988887774 443 46777888888876655544443332 11 22346776644
No 245
>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=21.28 E-value=1.6e+02 Score=25.27 Aligned_cols=45 Identities=20% Similarity=0.159 Sum_probs=30.8
Q ss_pred HHHhhcc--CCEEEEEEcCCCccCcHHHHHHHHHHHHHhCCcEEEEEcCC
Q 020984 93 LVEKAKD--ANIIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGK 140 (319)
Q Consensus 93 ~I~ka~~--a~~iGIivgTl~~q~~~~i~~~l~~ll~~~Gkk~y~i~vg~ 140 (319)
.++.|++ +..+| +++|.+ .....+..+.++|+++|.+...+++|-
T Consensus 44 ~v~aa~~~~adiVg--lS~l~~-~~~~~~~~~~~~l~~~gl~~~~vivGG 90 (134)
T TIGR01501 44 FIKAAIETKADAIL--VSSLYG-HGEIDCKGLRQKCDEAGLEGILLYVGG 90 (134)
T ss_pred HHHHHHHcCCCEEE--Eecccc-cCHHHHHHHHHHHHHCCCCCCEEEecC
Confidence 3455554 56655 477765 455567788899999987666677776
No 246
>PRK15427 colanic acid biosynthesis glycosyltransferase WcaL; Provisional
Probab=21.17 E-value=74 Score=31.48 Aligned_cols=42 Identities=17% Similarity=0.255 Sum_probs=29.9
Q ss_pred HHHHHHHHHhCCcEEEEEcCCCCHHhhcC-CCCCCEEEEecCC
Q 020984 120 HQMKELITKAGKKAYTLVMGKPNPAKLAN-FPECDVFINVSCA 161 (319)
Q Consensus 120 ~~l~~ll~~~Gkk~y~i~vg~in~~KLaN-f~eID~fV~iaCP 161 (319)
+.+++++++.|..-.+.+.|.++.+.+.. +...|+||+-+..
T Consensus 266 ~~l~~~~~~~~l~~~V~~~G~~~~~el~~~l~~aDv~v~pS~~ 308 (406)
T PRK15427 266 RRLRTLIEQYQLEDVVEMPGFKPSHEVKAMLDDADVFLLPSVT 308 (406)
T ss_pred HHHHHHHHHcCCCCeEEEeCCCCHHHHHHHHHhCCEEEECCcc
Confidence 55667777777666677778887666654 4578999987654
No 247
>cd02040 NifH NifH gene encodes component II (iron protein) of nitrogenase. Nitrogenase is responsible for the biological nitrogen fixation, i.e. reduction of molecular nitrogen to ammonia. NifH consists of two oxygen-sensitive metallosulfur proteins: the mollybdenum-iron (alternatively, vanadium-iron or iron-iron) protein (commonly referred to as component 1), and the iron protein (commonly referred to as component 2). The iron protein is a homodimer, with an Fe4S4 cluster bound between the subunits and two ATP-binding domains. It supplies energy by ATP hydrolysis, and transfers electrons from reduced ferredoxin or flavodoxin to component 1 for the reduction of molecular nitrogen to ammonia.
Probab=20.83 E-value=1.8e+02 Score=26.54 Aligned_cols=37 Identities=19% Similarity=0.284 Sum_probs=31.8
Q ss_pred CEEEEEEcCCCccCcHHHHHHHHHHHHHhCCcEEEEEcC
Q 020984 101 NIIGVLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMG 139 (319)
Q Consensus 101 ~~iGIivgTl~~q~~~~i~~~l~~ll~~~Gkk~y~i~vg 139 (319)
++|.|. | +||-|--.+.-.|-..|.+.|+|+.+|=++
T Consensus 2 ~~iav~-~-KGGvGKTT~~~nLA~~La~~G~kVlliD~D 38 (270)
T cd02040 2 RQIAIY-G-KGGIGKSTTTQNLSAALAEMGKKVMIVGCD 38 (270)
T ss_pred cEEEEE-e-CCcCCHHHHHHHHHHHHHhCCCeEEEEEcC
Confidence 567776 6 999999999999999999999998887655
No 248
>cd05402 NT_PAP_TUTase Nucleotidyltransferase (NT) domain of poly(A) polymerases and terminal uridylyl transferases. Poly(A) polymerases (PAPs) catalyze mRNA poly(A) tail synthesis, and terminal uridylyl transferases (TUTases) uridylate RNA. PAPs in this subgroup include human PAP alpha, mouse testis-specific cytoplasmic PAP beta, human nuclear PAP gamma, Saccharomyces cerevisiae PAP1, TRF4 and-5, Schizosaccharomyces pombe caffeine-induced death proteins -1, and -14, Caenorhabditis elegans Germ Line Development-2, and Chlamydomonas reinhardtii MUT68. This family also includes human U6 snRNA-specific TUTase1, and Trypanosoma brucei 3'-TUTase-1,-2, and 4. This family belongs to the Pol beta-like NT superfamily. In the majority of enzymes in this superfamily, two carboxylates, Dx[D/E], together with a third more distal carboxylate, coordinate two divalent metal cations involved in a two-metal ion mechanism of nucleotide addition. For the majority of proteins in this family, these carboxyla
Probab=20.57 E-value=2e+02 Score=22.83 Aligned_cols=47 Identities=13% Similarity=-0.013 Sum_probs=32.9
Q ss_pred cHHHHHHHHHHHHHhCCcEEEEEcCCCCHHhhcCCCCCCEEEEecCC
Q 020984 115 YLHMIHQMKELITKAGKKAYTLVMGKPNPAKLANFPECDVFINVSCA 161 (319)
Q Consensus 115 ~~~i~~~l~~ll~~~Gkk~y~i~vg~in~~KLaNf~eID~fV~iaCP 161 (319)
+..++++|++.+++..-++.+.+.|-.-..--..-.+||+.|....+
T Consensus 2 r~~i~~~l~~~i~~~~~~~~v~~fGS~~~g~~~~~SDiDl~i~~~~~ 48 (114)
T cd05402 2 REEVLDRLQELIKEWFPGAKLYPFGSYVTGLGLPGSDIDLCLLGPNH 48 (114)
T ss_pred HHHHHHHHHHHHHHHCCCCEEEEecccccCCCCCCCCeeEEEEeCCC
Confidence 35788999999999766666666675533222245689999887665
No 249
>TIGR02257 cobalto_cobN cobaltochelatase, CobN subunit.
Probab=20.55 E-value=2.3e+02 Score=32.72 Aligned_cols=79 Identities=15% Similarity=0.209 Sum_probs=51.7
Q ss_pred CCEEEEEEcC-CCccCcHHHHHHHHHHHHHhCCcEEEEEcCCCC----HHhhcC-C--CCCCEEEEecCCCcc-------
Q 020984 100 ANIIGVLVGT-LGVAGYLHMIHQMKELITKAGKKAYTLVMGKPN----PAKLAN-F--PECDVFINVSCAQTA------- 164 (319)
Q Consensus 100 a~~iGIivgT-l~~q~~~~i~~~l~~ll~~~Gkk~y~i~vg~in----~~KLaN-f--~eID~fV~iaCPr~s------- 164 (319)
..++||++-. .-..+....++.|.+.|+++|..++.+++.-+. .+.+.. | ..+|++|.+.+=.++
T Consensus 191 ~p~vgilfyr~~~~~~~~~~idali~~Le~~G~~~ipvf~~sl~~~~~~~~~~~~~~~~~vd~iin~~~F~~~~~~~~~~ 270 (1122)
T TIGR02257 191 GPRVGILFYRSLLLAGDTALIEALIDALRQRGLNPVPIFVSSLKDPAVQAGLLDALKEEDPALIITTTGFASSNEQADNG 270 (1122)
T ss_pred CCEEEEEEehhhhhcCCcHHHHHHHHHHHHCCCeEEEEEeCCCCchhHHHHHHHhccCCCCcEEEECCcccccCCcchhh
Confidence 4789999843 335779999999999999999999988876553 122222 2 248988876332211
Q ss_pred cccccCCCCcccCH
Q 020984 165 LLDSKEFLAPVITP 178 (319)
Q Consensus 165 idd~~~f~kPvlTP 178 (319)
....+....||+.+
T Consensus 271 ~~~l~~l~vPVlq~ 284 (1122)
T TIGR02257 271 ETLWDSLGVPVLQV 284 (1122)
T ss_pred HHHHHHCCCCEEEe
Confidence 11234567777664
No 250
>PRK14340 (dimethylallyl)adenosine tRNA methylthiotransferase; Provisional
Probab=20.52 E-value=1.6e+02 Score=29.99 Aligned_cols=62 Identities=21% Similarity=0.271 Sum_probs=34.7
Q ss_pred HHHhhccCCEEEEEEcCCCc--cCcHHHHHHHHH--HHHHhCCcEEEEEcCC---CCHHhhcC-CCCCCEEE
Q 020984 93 LVEKAKDANIIGVLVGTLGV--AGYLHMIHQMKE--LITKAGKKAYTLVMGK---PNPAKLAN-FPECDVFI 156 (319)
Q Consensus 93 ~I~ka~~a~~iGIivgTl~~--q~~~~i~~~l~~--ll~~~Gkk~y~i~vg~---in~~KLaN-f~eID~fV 156 (319)
.+....+|..+ ||+|=++ .--.++.+.|+. .+++.+.+..+++.|- ..++.|.. +++||+++
T Consensus 37 ~~~~~~~ADvi--iiNTC~v~~~A~~k~~~~i~~~~~~k~~~~~~~ivv~GC~a~~~~~e~~~~~p~vd~v~ 106 (445)
T PRK14340 37 PAASEEDADIV--LLNTCAVRENAVERIGHYLQHLKGAKRRRKGLLVGVLGCVPQYEREEMFSMFPVIDFLA 106 (445)
T ss_pred ECCCcccCCEE--EEEeeeeeccHHHHHHHHHHHHHHHhhcCCCCEEEEeCcccccchHHHHhhCCCCcEEE
Confidence 34444557665 4444443 333344445443 3445566666777663 44666655 78888776
No 251
>PRK10359 lipopolysaccharide core biosynthesis protein; Provisional
Probab=20.24 E-value=1.3e+02 Score=28.14 Aligned_cols=73 Identities=21% Similarity=0.230 Sum_probs=42.6
Q ss_pred CCcchHHHHHHhcCCCeEEEEcCCCCccccccCcHHHHHHHHHHHHHhhccCCEEEEEEcCCCccCcHHHHHHHHHHHHH
Q 020984 49 SDNSAFANVVLTFNGCEIVRYDATEERLLTDVSQPLKILKRRYYLVEKAKDANIIGVLVGTLGVAGYLHMIHQMKELITK 128 (319)
Q Consensus 49 ~~~~~l~~l~l~~~~~~v~~yDP~s~~~~~e~~~~~k~l~~R~~~I~ka~~a~~iGIivgTl~~q~~~~i~~~l~~ll~~ 128 (319)
+++.|+.|+++...+ +...|=-..+...+......+.++|-+.+ .|.+|++-+-- .-..+++++++++
T Consensus 158 H~Dikp~Nili~~~g--i~liDfg~~~~~~e~~a~d~~vler~y~~----~~di~~lg~~~------~~~~~k~~~~~~~ 225 (232)
T PRK10359 158 SGDPHKGNFIVSKNG--LRIIDLSGKRCTAQRKAKDRIDLERHYGI----KNEIKDLGYYL------LIYKKKLRKFIRK 225 (232)
T ss_pred cCCCChHHEEEeCCC--EEEEECCCcccccchhhHHHHHHHhHhcc----cccccceeEee------hHHHHHHHHHHHH
Confidence 356788888876544 77888333333333344666777776553 36666554322 3345677777765
Q ss_pred -hCCcE
Q 020984 129 -AGKKA 133 (319)
Q Consensus 129 -~Gkk~ 133 (319)
+||++
T Consensus 226 ~~~~~~ 231 (232)
T PRK10359 226 LKGKAS 231 (232)
T ss_pred hcCCCC
Confidence 47653
No 252
>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=20.21 E-value=2.6e+02 Score=32.58 Aligned_cols=62 Identities=15% Similarity=0.207 Sum_probs=45.8
Q ss_pred cCCEEEEEEcCCCc-cCcHHHHHHHHHHHHHhCCcEEEEEcCCCCH----H-hhcC--CC--CCCEEEEecC
Q 020984 99 DANIIGVLVGTLGV-AGYLHMIHQMKELITKAGKKAYTLVMGKPNP----A-KLAN--FP--ECDVFINVSC 160 (319)
Q Consensus 99 ~a~~iGIivgTl~~-q~~~~i~~~l~~ll~~~Gkk~y~i~vg~in~----~-KLaN--f~--eID~fV~iaC 160 (319)
++.+||||+-..-. .+....+..|.+.|+++|..++.++.+.+.. . -+.+ +. .||+.|.+.+
T Consensus 238 ~~p~Vgil~~r~~~~~~~~~~~dalI~~lE~~G~~vipvf~~gl~~~~~v~~~~~~~~~~~~~vdaiI~~~g 309 (1216)
T TIGR02025 238 KAPRVGLLLLRKHLLTGNQAHYDNLIRELEAAGLQVVPAFSGGLDGRVAVEDFFMKDSTPSVKVDAVVSLTG 309 (1216)
T ss_pred CCCEEEEEEchhhhhcCCcHHHHHHHHHHHHCCCcEEEEEecCccccHHHHHHHHhcccCCCCccEEEECCc
Confidence 57999999976554 5688999999999999999999988876542 1 1222 22 5898886543
No 253
>cd00133 PTS_IIB PTS_IIB: subunit IIB of enzyme II (EII) is the central energy-coupling domain of the phosphoenolpyruvate:carbohydrate phosphotransferase system (PTS). In the multienzyme PTS complex, EII is a carbohydrate-specific permease consisting of two cytoplasmic domains (IIA and IIB) and a transmembrane channel IIC domain. 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 chitobiose/lichenan, ascorbate, lactose, galactitol, mannitol, fructose, and a sensory system with similarity to the bacterial bgl system. The PTS is found only in bacteria, where it catalyzes the transport and phosphorylation of numerous monosaccharides, disaccharides, polyols, amino sugars, and other sugar derivatives. The four proteins (domains) forming the PTS phosphorylation cascade (EI, HPr, EIIA, and EIIB), can phosphorylate or interact with numerous non-PTS proteins thereby r
Probab=20.18 E-value=3.1e+02 Score=19.50 Aligned_cols=47 Identities=9% Similarity=0.198 Sum_probs=28.7
Q ss_pred EEEcCCCccCcHHHHHHHHHHHHHhCCcEEEEEcCCCCHHhhcCCCCCCE
Q 020984 105 VLVGTLGVAGYLHMIHQMKELITKAGKKAYTLVMGKPNPAKLANFPECDV 154 (319)
Q Consensus 105 IivgTl~~q~~~~i~~~l~~ll~~~Gkk~y~i~vg~in~~KLaNf~eID~ 154 (319)
++++.-|.....-+..+|++.+.+.+.. ..+....+... ....++|+
T Consensus 3 l~vc~~G~~~s~~l~~~l~~~~~~~~~~-~~~~~~~~~~~--~~~~~~dl 49 (84)
T cd00133 3 LVVCGSGIGSSSMLAEKLEKAAKELGIE-VKVEAQGLSEV--IDLADADL 49 (84)
T ss_pred EEECCCcHhHHHHHHHHHHHHHHHCCCe-EEEEEcccchh--hhcCCccE
Confidence 3555545455667788999999888875 44444555441 23345664
Done!