Query 001724
Match_columns 1020
No_of_seqs 193 out of 739
Neff 4.1
Searched_HMMs 46136
Date Fri Mar 29 07:48:49 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/001724.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/001724hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 TIGR00288 conserved hypothetic 99.9 1E-23 2.3E-28 211.8 14.7 134 48-193 21-156 (160)
2 PF01936 NYN: NYN domain; Int 99.9 5.5E-23 1.2E-27 196.5 5.8 135 51-193 1-146 (146)
3 cd06167 LabA_like LabA_like pr 99.8 8E-20 1.7E-24 177.3 11.3 140 50-191 1-148 (149)
4 PF14418 OHA: OST-HTH Associat 98.9 2.6E-10 5.7E-15 102.7 2.0 61 619-680 10-70 (75)
5 PF12872 OST-HTH: OST-HTH/LOTU 98.9 3E-09 6.6E-14 93.0 5.6 67 256-322 4-74 (74)
6 COG1432 Uncharacterized conser 98.9 8.8E-09 1.9E-13 106.1 9.8 148 49-198 5-166 (181)
7 PF12872 OST-HTH: OST-HTH/LOTU 97.7 6.2E-05 1.3E-09 66.0 4.9 55 740-795 3-60 (74)
8 COG4634 Uncharacterized protei 91.7 0.73 1.6E-05 45.3 7.8 71 101-179 10-81 (113)
9 PRK00124 hypothetical protein; 83.3 5.6 0.00012 41.2 8.5 96 54-179 3-99 (151)
10 PF04263 TPK_catalytic: Thiami 77.5 11 0.00024 37.4 8.2 76 92-173 39-121 (123)
11 cd05013 SIS_RpiR RpiR-like pro 67.7 76 0.0016 29.9 11.1 103 79-192 6-111 (139)
12 cd00431 cysteine_hydrolases Cy 64.4 68 0.0015 31.8 10.5 118 53-175 2-143 (161)
13 PF09419 PGP_phosphatase: Mito 63.9 69 0.0015 33.8 10.8 115 49-172 39-163 (168)
14 COG1671 Uncharacterized protei 62.6 32 0.0007 35.8 7.9 89 52-172 2-90 (150)
15 TIGR01378 thi_PPkinase thiamin 61.5 50 0.0011 35.2 9.5 81 92-177 40-127 (203)
16 TIGR02417 fruct_sucro_rep D-fr 55.3 1.4E+02 0.003 32.7 11.9 100 71-175 32-148 (327)
17 cd01537 PBP1_Repressors_Sugar_ 54.5 1.4E+02 0.003 30.4 11.0 73 102-177 138-215 (264)
18 PRK11303 DNA-binding transcrip 52.0 1.6E+02 0.0035 32.2 11.6 99 72-175 34-149 (328)
19 cd06319 PBP1_ABC_sugar_binding 51.8 2.1E+02 0.0046 30.0 12.1 75 102-179 145-222 (277)
20 PRK10014 DNA-binding transcrip 51.0 1.6E+02 0.0035 32.4 11.5 100 71-175 36-152 (342)
21 PRK09426 methylmalonyl-CoA mut 50.2 1.1E+02 0.0023 39.0 11.1 88 74-169 570-663 (714)
22 TIGR02634 xylF D-xylose ABC tr 48.1 60 0.0013 35.6 7.7 68 103-175 19-87 (302)
23 cd06306 PBP1_TorT-like TorT-li 47.9 49 0.0011 35.2 6.8 69 104-175 21-89 (268)
24 cd06324 PBP1_ABC_sugar_binding 47.3 2.4E+02 0.0052 30.8 12.1 113 68-184 117-246 (305)
25 cd06311 PBP1_ABC_sugar_binding 46.6 1.9E+02 0.0041 30.6 10.8 78 103-183 147-226 (274)
26 PRK14987 gluconate operon tran 46.2 2.1E+02 0.0045 31.4 11.5 98 71-174 35-149 (331)
27 COG1564 THI80 Thiamine pyropho 45.9 80 0.0017 34.6 8.0 79 91-175 45-130 (212)
28 cd05014 SIS_Kpsf KpsF-like pro 45.3 71 0.0015 30.4 6.8 48 144-192 48-98 (128)
29 PF13768 VWA_3: von Willebrand 45.2 1.3E+02 0.0028 29.6 8.9 45 51-98 2-46 (155)
30 cd07995 TPK Thiamine pyrophosp 45.1 1.3E+02 0.0028 32.0 9.4 79 92-175 44-129 (208)
31 PF07283 TrbH: Conjugal transf 44.9 53 0.0011 33.1 6.0 51 126-176 4-58 (121)
32 PRK11041 DNA-binding transcrip 44.4 1.2E+02 0.0026 32.6 9.2 97 68-169 135-238 (309)
33 cd06305 PBP1_methylthioribose_ 44.0 62 0.0013 33.9 6.7 67 104-175 21-88 (273)
34 cd01539 PBP1_GGBP Periplasmic 43.6 60 0.0013 35.4 6.8 45 130-175 45-90 (303)
35 cd06320 PBP1_allose_binding Pe 43.0 2.8E+02 0.0061 29.2 11.5 77 102-181 142-221 (275)
36 PRK10703 DNA-binding transcrip 42.5 2.6E+02 0.0056 30.8 11.5 98 72-175 32-147 (341)
37 PRK11302 DNA-binding transcrip 42.4 2.4E+02 0.0052 30.8 11.1 103 76-192 118-225 (284)
38 PRK10401 DNA-binding transcrip 42.2 1.2E+02 0.0027 33.5 9.0 65 102-170 196-263 (346)
39 PRK10653 D-ribose transporter 42.0 4.4E+02 0.0095 28.5 13.0 76 102-181 168-245 (295)
40 cd06322 PBP1_ABC_sugar_binding 41.4 3.5E+02 0.0076 28.3 11.8 76 102-181 140-217 (267)
41 PRK10997 yieM hypothetical pro 41.1 7.2E+02 0.016 30.7 15.6 142 45-197 319-478 (487)
42 cd06309 PBP1_YtfQ_like Peripla 41.0 1E+02 0.0022 32.6 7.8 68 103-175 20-88 (273)
43 cd06316 PBP1_ABC_sugar_binding 39.8 77 0.0017 34.1 6.8 68 104-175 21-89 (294)
44 cd01453 vWA_transcription_fact 39.4 2.7E+02 0.0059 29.1 10.5 129 51-186 5-155 (183)
45 cd05006 SIS_GmhA Phosphoheptos 39.0 3.4E+02 0.0073 27.8 11.0 48 144-192 102-152 (177)
46 PRK11337 DNA-binding transcrip 38.8 2.9E+02 0.0064 30.5 11.2 105 76-191 130-237 (292)
47 PRK11557 putative DNA-binding 38.2 2.3E+02 0.0049 31.0 10.2 105 76-191 118-225 (278)
48 cd06310 PBP1_ABC_sugar_binding 38.2 84 0.0018 33.0 6.7 69 104-175 21-90 (273)
49 cd05005 SIS_PHI Hexulose-6-pho 37.2 2.5E+02 0.0055 28.8 9.8 100 76-191 23-125 (179)
50 cd06312 PBP1_ABC_sugar_binding 37.1 1E+02 0.0022 32.6 7.1 68 104-175 22-90 (271)
51 cd01536 PBP1_ABC_sugar_binding 36.8 4.2E+02 0.0091 27.2 11.4 76 102-180 141-219 (267)
52 TIGR03127 RuMP_HxlB 6-phospho 36.7 2.2E+02 0.0047 29.2 9.2 100 76-191 20-122 (179)
53 cd01477 vWA_F09G8-8_type VWA F 36.5 4.5E+02 0.0098 27.9 11.7 121 48-173 18-167 (193)
54 TIGR03436 acidobact_VWFA VWFA- 36.4 4.7E+02 0.01 28.9 12.3 122 49-174 53-201 (296)
55 PRK10355 xylF D-xylose transpo 35.5 1.2E+02 0.0026 34.1 7.7 67 104-175 47-114 (330)
56 cd06274 PBP1_FruR Ligand bindi 35.3 1.1E+02 0.0023 32.1 6.9 67 104-176 21-87 (264)
57 cd06310 PBP1_ABC_sugar_binding 34.6 5.1E+02 0.011 27.2 11.8 74 102-179 143-220 (273)
58 cd01538 PBP1_ABC_xylose_bindin 34.5 1.2E+02 0.0026 32.6 7.3 42 133-175 46-88 (288)
59 PLN02905 beta-amylase 34.4 89 0.0019 39.2 6.8 92 598-692 62-172 (702)
60 cd06300 PBP1_ABC_sugar_binding 34.4 4.3E+02 0.0093 27.8 11.2 65 102-171 145-211 (272)
61 cd06318 PBP1_ABC_sugar_binding 34.3 1.3E+02 0.0027 31.9 7.3 42 133-175 46-88 (282)
62 cd06303 PBP1_LuxPQ_Quorum_Sens 34.1 1E+02 0.0022 33.0 6.6 41 132-173 50-90 (280)
63 PRK11440 putative hydrolase; P 33.8 3E+02 0.0065 28.5 9.7 125 49-174 7-153 (188)
64 cd01391 Periplasmic_Binding_Pr 33.6 3E+02 0.0065 27.5 9.5 106 69-179 108-220 (269)
65 cd06313 PBP1_ABC_sugar_binding 33.4 1.1E+02 0.0025 32.6 6.8 68 103-175 20-88 (272)
66 cd06302 PBP1_LsrB_Quorum_Sensi 33.4 1.3E+02 0.0027 32.8 7.2 67 104-175 21-89 (298)
67 cd06303 PBP1_LuxPQ_Quorum_Sens 33.3 4.3E+02 0.0093 28.3 11.2 80 103-186 151-234 (280)
68 cd06288 PBP1_sucrose_transcrip 33.3 3.5E+02 0.0076 28.2 10.3 64 103-169 137-202 (269)
69 PF12075 KN_motif: KN motif; 33.1 13 0.00029 30.6 -0.1 13 771-783 8-20 (39)
70 cd01460 vWA_midasin VWA_Midasi 32.7 3.4E+02 0.0074 30.7 10.5 130 44-174 55-201 (266)
71 cd01014 nicotinamidase_related 32.6 2.6E+02 0.0057 28.1 8.9 35 53-87 2-39 (155)
72 PRK13883 conjugal transfer pro 32.3 97 0.0021 32.4 5.8 51 126-176 32-86 (151)
73 PLN02714 thiamin pyrophosphoki 32.3 1.9E+02 0.0042 31.6 8.4 81 92-176 57-147 (229)
74 cd06324 PBP1_ABC_sugar_binding 32.3 1.2E+02 0.0027 33.0 7.0 44 132-175 46-90 (305)
75 cd01545 PBP1_SalR Ligand-bindi 32.2 1.3E+02 0.0028 31.4 6.8 45 130-175 44-88 (270)
76 cd01012 YcaC_related YcaC rela 32.0 3.1E+02 0.0068 27.6 9.3 114 53-175 2-121 (157)
77 cd06281 PBP1_LacI_like_5 Ligan 31.8 1.3E+02 0.0029 31.6 7.0 41 134-175 47-87 (269)
78 PRK15482 transcriptional regul 31.4 3.7E+02 0.008 29.7 10.5 104 77-191 126-232 (285)
79 cd01542 PBP1_TreR_like Ligand- 31.3 1.4E+02 0.003 31.0 6.9 66 104-175 21-86 (259)
80 KOG0919 C-5 cytosine-specific 31.2 40 0.00087 37.9 3.0 38 738-775 104-144 (338)
81 cd06296 PBP1_CatR_like Ligand- 31.2 6.2E+02 0.013 26.5 11.7 127 53-181 81-219 (270)
82 cd06286 PBP1_CcpB_like Ligand- 31.0 3.1E+02 0.0067 28.6 9.4 64 103-169 135-200 (260)
83 cd06289 PBP1_MalI_like Ligand- 30.9 1.4E+02 0.0031 31.0 6.9 43 131-174 44-86 (268)
84 TIGR01481 ccpA catabolite cont 30.9 5.3E+02 0.012 28.2 11.6 99 71-175 31-146 (329)
85 cd06270 PBP1_GalS_like Ligand 30.8 2.5E+02 0.0053 29.5 8.7 63 103-169 137-202 (268)
86 cd06320 PBP1_allose_binding Pe 30.7 1.5E+02 0.0032 31.3 7.0 44 131-175 46-90 (275)
87 cd06314 PBP1_tmGBP Periplasmic 30.4 1.4E+02 0.003 31.6 6.8 44 130-175 43-87 (271)
88 cd07018 S49_SppA_67K_type Sign 30.3 1.4E+02 0.003 32.2 6.8 68 124-191 27-104 (222)
89 PRK09526 lacI lac repressor; R 30.2 3E+02 0.0066 30.2 9.6 65 103-170 202-266 (342)
90 cd06290 PBP1_LacI_like_9 Ligan 30.0 2.5E+02 0.0054 29.3 8.6 63 103-169 136-201 (265)
91 PRK01045 ispH 4-hydroxy-3-meth 29.8 1.3E+02 0.0028 34.6 6.7 102 72-181 15-127 (298)
92 cd06281 PBP1_LacI_like_5 Ligan 29.6 1.7E+02 0.0036 30.9 7.2 63 102-169 136-201 (269)
93 cd06299 PBP1_LacI_like_13 Liga 29.6 1.6E+02 0.0034 30.8 6.9 66 104-175 21-86 (265)
94 cd06272 PBP1_hexuronate_repres 29.5 3.5E+02 0.0076 28.3 9.5 73 103-179 132-211 (261)
95 PF13407 Peripla_BP_4: Peripla 29.5 1.4E+02 0.0031 31.2 6.6 69 103-176 19-89 (257)
96 cd06268 PBP1_ABC_transporter_L 29.3 4.9E+02 0.011 27.0 10.5 96 74-175 123-222 (298)
97 cd06321 PBP1_ABC_sugar_binding 28.8 1.7E+02 0.0037 30.7 7.1 41 134-175 49-90 (271)
98 PF00857 Isochorismatase: Isoc 28.8 1.4E+02 0.0029 30.0 6.1 116 53-174 3-144 (174)
99 cd06323 PBP1_ribose_binding Pe 28.6 6.8E+02 0.015 26.0 11.5 74 103-179 142-217 (268)
100 KOG2961 Predicted hydrolase (H 28.6 2.9E+02 0.0062 29.6 8.3 114 51-172 43-166 (190)
101 TIGR02955 TMAO_TorT TMAO reduc 28.5 6.4E+02 0.014 27.4 11.6 76 103-183 146-224 (295)
102 cd06337 PBP1_ABC_ligand_bindin 28.4 2.5E+02 0.0054 31.6 8.7 63 105-172 169-232 (357)
103 PLN02342 ornithine carbamoyltr 28.4 5E+02 0.011 30.5 11.3 110 53-177 114-228 (348)
104 cd06282 PBP1_GntR_like_2 Ligan 28.0 1.7E+02 0.0038 30.3 6.9 42 133-175 46-87 (266)
105 cd06322 PBP1_ABC_sugar_binding 28.0 1.6E+02 0.0035 30.8 6.8 42 132-174 45-87 (267)
106 cd01536 PBP1_ABC_sugar_binding 27.9 1.8E+02 0.004 29.9 7.0 67 104-175 21-88 (267)
107 cd06317 PBP1_ABC_sugar_binding 27.4 1.9E+02 0.004 30.3 7.1 65 106-175 24-89 (275)
108 COG0794 GutQ Predicted sugar p 27.4 3.1E+02 0.0068 30.1 8.8 96 85-191 38-136 (202)
109 PF02739 5_3_exonuc_N: 5'-3' e 27.1 88 0.0019 32.7 4.5 61 105-175 92-152 (169)
110 TIGR00642 mmCoA_mut_beta methy 27.0 1.6E+02 0.0034 37.1 7.3 104 81-192 489-601 (619)
111 cd06275 PBP1_PurR Ligand-bindi 27.0 3.6E+02 0.0077 28.2 9.1 64 102-169 137-203 (269)
112 PF03033 Glyco_transf_28: Glyc 26.3 1.4E+02 0.003 28.5 5.5 36 156-191 15-50 (139)
113 PRK11609 nicotinamidase/pyrazi 26.0 7.8E+02 0.017 26.0 11.4 41 51-91 3-47 (212)
114 cd01540 PBP1_arabinose_binding 26.0 6E+02 0.013 27.0 10.7 64 102-168 150-218 (289)
115 PF09314 DUF1972: Domain of un 25.9 5.6E+02 0.012 27.6 10.2 103 63-173 12-124 (185)
116 cd06278 PBP1_LacI_like_2 Ligan 25.8 6.4E+02 0.014 26.1 10.6 63 103-168 136-199 (266)
117 cd06309 PBP1_YtfQ_like Peripla 25.6 8.1E+02 0.018 25.8 12.6 93 87-182 123-227 (273)
118 PRK10423 transcriptional repre 25.5 3E+02 0.0065 30.0 8.5 65 103-170 195-261 (327)
119 cd06301 PBP1_rhizopine_binding 25.5 2.3E+02 0.0051 29.7 7.4 44 131-175 45-89 (272)
120 cd06317 PBP1_ABC_sugar_binding 25.4 6.7E+02 0.014 26.2 10.7 75 102-179 145-224 (275)
121 cd06287 PBP1_LacI_like_8 Ligan 25.0 4.8E+02 0.01 28.0 9.8 65 103-169 139-203 (269)
122 cd01574 PBP1_LacI Ligand-bindi 25.0 5.6E+02 0.012 26.7 10.0 73 103-179 137-213 (264)
123 cd06291 PBP1_Qymf_like Ligand 25.0 1.6E+02 0.0036 30.7 6.1 63 104-175 21-83 (265)
124 cd06270 PBP1_GalS_like Ligand 24.9 2.1E+02 0.0045 30.1 6.9 66 104-175 21-86 (268)
125 PTZ00441 sporozoite surface pr 24.8 1E+03 0.023 30.0 13.5 29 146-174 151-185 (576)
126 cd06308 PBP1_sensor_kinase_lik 24.7 7.3E+02 0.016 26.1 10.9 63 103-168 143-206 (270)
127 PRK09701 D-allose transporter 24.6 8.1E+02 0.018 27.0 11.7 75 102-180 176-254 (311)
128 PF05991 NYN_YacP: YacP-like N 24.5 2.9E+02 0.0062 28.8 7.7 54 110-171 65-118 (166)
129 COG1737 RpiR Transcriptional r 24.4 5.4E+02 0.012 28.7 10.3 89 91-191 133-227 (281)
130 COG1609 PurR Transcriptional r 24.1 8.5E+02 0.019 27.7 12.0 98 72-175 31-145 (333)
131 COG2179 Predicted hydrolase of 24.1 2.7E+02 0.0059 29.9 7.4 123 49-184 26-148 (175)
132 cd06267 PBP1_LacI_sugar_bindin 23.9 4.6E+02 0.0099 26.8 9.0 107 74-181 102-218 (264)
133 cd06319 PBP1_ABC_sugar_binding 23.7 2.1E+02 0.0046 30.0 6.7 67 104-175 21-88 (277)
134 cd06283 PBP1_RegR_EndR_KdgR_li 23.6 2.5E+02 0.0055 29.1 7.2 42 132-175 45-86 (267)
135 PRK10653 D-ribose transporter 23.6 2E+02 0.0042 31.2 6.6 43 132-175 72-115 (295)
136 TIGR02990 ectoine_eutA ectoine 23.4 3.4E+02 0.0075 30.0 8.4 95 73-171 108-210 (239)
137 cd06308 PBP1_sensor_kinase_lik 23.3 2.2E+02 0.0048 30.0 6.8 42 133-175 47-89 (270)
138 cd01822 Lysophospholipase_L1_l 23.3 6.4E+02 0.014 24.8 9.7 60 112-175 36-109 (177)
139 cd06323 PBP1_ribose_binding Pe 23.2 2.3E+02 0.0051 29.4 6.9 68 103-175 20-88 (268)
140 PRK15408 autoinducer 2-binding 23.0 2.3E+02 0.0049 32.3 7.2 70 102-176 43-114 (336)
141 PRK09701 D-allose transporter 23.0 2.4E+02 0.0053 31.0 7.3 69 104-175 46-115 (311)
142 PF13607 Succ_CoA_lig: Succiny 23.0 1.8E+02 0.0038 29.7 5.7 73 104-179 17-93 (138)
143 TIGR00393 kpsF KpsF/GutQ famil 23.0 2.2E+02 0.0047 30.8 6.7 95 87-192 1-98 (268)
144 TIGR00216 ispH_lytB (E)-4-hydr 22.9 2.1E+02 0.0046 32.6 6.8 102 72-181 14-127 (280)
145 PRK10423 transcriptional repre 22.7 9.2E+02 0.02 26.2 11.6 98 71-174 28-143 (327)
146 PRK12360 4-hydroxy-3-methylbut 22.6 2.1E+02 0.0046 32.7 6.7 102 72-181 15-130 (281)
147 cd06336 PBP1_ABC_ligand_bindin 22.6 6E+02 0.013 28.4 10.3 80 87-170 137-221 (347)
148 PRK13937 phosphoheptose isomer 22.5 6.2E+02 0.013 26.5 9.8 49 143-192 106-157 (188)
149 cd01575 PBP1_GntR Ligand-bindi 22.4 8.8E+02 0.019 25.1 11.0 133 46-179 75-216 (268)
150 PF01239 PPTA: Protein prenylt 22.1 97 0.0021 23.3 2.8 28 745-772 4-31 (31)
151 PF01380 SIS: SIS domain SIS d 22.0 2.6E+02 0.0055 26.4 6.3 47 144-191 54-103 (131)
152 cd06360 PBP1_alkylbenzenes_lik 21.7 5.3E+02 0.011 28.1 9.5 68 103-174 153-222 (336)
153 cd06333 PBP1_ABC-type_HAAT_lik 21.7 3.7E+02 0.0081 29.2 8.3 64 103-173 152-218 (312)
154 cd06311 PBP1_ABC_sugar_binding 21.6 2.8E+02 0.0061 29.2 7.2 45 130-175 48-93 (274)
155 PF00532 Peripla_BP_1: Peripla 21.6 3.6E+02 0.0077 29.7 8.2 66 104-176 23-88 (279)
156 cd01461 vWA_interalpha_trypsin 21.5 7.8E+02 0.017 24.1 11.0 46 50-97 3-48 (171)
157 cd01540 PBP1_arabinose_binding 21.4 2.6E+02 0.0057 29.7 6.9 66 104-175 21-87 (289)
158 cd01545 PBP1_SalR Ligand-bindi 21.2 6.7E+02 0.014 26.1 9.7 64 103-169 139-204 (270)
159 cd06297 PBP1_LacI_like_12 Liga 21.1 9.1E+02 0.02 25.6 10.9 64 102-168 139-204 (269)
160 COG0451 WcaG Nucleoside-diphos 21.1 1.2E+02 0.0025 32.6 4.3 30 148-177 3-34 (314)
161 TIGR00658 orni_carb_tr ornithi 21.1 8.1E+02 0.017 28.1 11.0 110 53-177 68-182 (304)
162 cd06291 PBP1_Qymf_like Ligand 21.1 5.6E+02 0.012 26.7 9.2 74 102-179 133-212 (265)
163 TIGR00640 acid_CoA_mut_C methy 20.8 4.6E+02 0.0099 26.5 8.0 74 87-168 3-82 (132)
164 cd01541 PBP1_AraR Ligand-bindi 20.7 2.8E+02 0.006 29.2 6.9 66 105-175 22-91 (273)
165 PRK02240 GTP cyclohydrolase II 20.7 4.6E+02 0.0099 29.8 8.7 80 89-186 7-101 (254)
166 PRK13835 conjugal transfer pro 20.5 2.2E+02 0.0047 29.8 5.7 47 126-172 38-87 (145)
167 cd06315 PBP1_ABC_sugar_binding 20.4 3.5E+02 0.0075 29.0 7.6 43 132-175 46-89 (280)
168 PRK10014 DNA-binding transcrip 20.4 5.3E+02 0.011 28.3 9.2 64 103-170 203-269 (342)
169 PF12683 DUF3798: Protein of u 20.3 1.6E+02 0.0036 33.5 5.2 71 130-200 49-121 (275)
170 PRK15395 methyl-galactoside AB 20.1 9.3E+02 0.02 26.9 11.2 74 103-179 183-261 (330)
171 cd06295 PBP1_CelR Ligand bindi 20.1 2.7E+02 0.006 29.3 6.7 32 143-175 64-95 (275)
172 PRK11543 gutQ D-arabinose 5-ph 20.0 5.1E+02 0.011 28.9 9.1 95 87-192 43-140 (321)
No 1
>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=99.91 E-value=1e-23 Score=211.81 Aligned_cols=134 Identities=16% Similarity=0.162 Sum_probs=114.3
Q ss_pred CCCeEEEEEecCCCCCCCCCChhhHHHHHHHHHHHhCCCCceEE-EEeecccccchhhHHHhhhcCCceeeccCCCccch
Q 001724 48 KNVRVSVWWDFENCNLPAGVNAFKVAHTITAAIRANGIKGPVTI-TAFGDVVQMSRANQEVLSSTGINIAHVPHGGKNSA 126 (1020)
Q Consensus 48 ~~~rVAVFWDiENcpiP~g~d~~~Va~nI~~aLrelG~~GpVtI-RAYGDws~~~k~~qe~L~ssGI~LihvP~ggKNAA 126 (1020)
...+||||||++|++. ..+ ..+++.+++.+..+|.|++ |+||||.. ...+++.|...||+++.+ |+++
T Consensus 21 ~~~riAvfID~~Nv~~-~~~-----~~d~~~i~~~ls~~G~i~~~R~Y~~a~a-~~~l~~~l~~~Gf~pv~~----kG~~ 89 (160)
T TIGR00288 21 GEKKIGLLVDGPNMLR-KEF-----NIDLDEIREILSEYGDIKIGKVLLNQYA-SDKLIEAVVNQGFEPIIV----AGDV 89 (160)
T ss_pred CCCcEEEEEeCCccCh-hhh-----ccCHHHHHHHHHhcCCeEEEEEEechhc-cHHHHHHHHHCCceEEEe----cCcc
Confidence 3578999999999973 211 1235666777778899999 99999744 346889999999998753 5689
Q ss_pred hhHHHHHHHHHHHhCCCCcEEEEEeCCcchHHHHHHHHhCCCEEEEec-CCchhHHHHhhcceEEecc
Q 001724 127 DRSLLVDLMYWVSQNPPPAHLFLISGDRDFASVLHRLRMNNYNILLAS-RESASNVLCSAASVMWNWD 193 (1020)
Q Consensus 127 Di~LiIDaMd~a~~nP~pdtFVLISGDsDFtpLL~RLRerGynVILag-p~kTpeaL~sAcd~Fw~we 193 (1020)
|+.|+||||+++|. +.+|+|||||||+||++|+.+||++|+.|++++ +.+||..|+++||+|+++.
T Consensus 90 Dv~laIDame~~~~-~~iD~~vLvSgD~DF~~Lv~~lre~G~~V~v~g~~~~ts~~L~~acd~FI~L~ 156 (160)
T TIGR00288 90 DVRMAVEAMELIYN-PNIDAVALVTRDADFLPVINKAKENGKETIVIGAEPGFSTALQNSADIAIILG 156 (160)
T ss_pred cHHHHHHHHHHhcc-CCCCEEEEEeccHhHHHHHHHHHHCCCEEEEEeCCCCChHHHHHhcCeEEeCC
Confidence 99999999999996 679999999999999999999999999999988 6689999999999999865
No 2
>PF01936 NYN: NYN domain; InterPro: IPR021139 This highly conserved domain has no known function. However it contains many conserved aspartates, suggesting an enzymatic function such as an endonuclease or glycosyl hydrolase.; PDB: 2QIP_A.
Probab=99.87 E-value=5.5e-23 Score=196.53 Aligned_cols=135 Identities=33% Similarity=0.548 Sum_probs=94.7
Q ss_pred eEEEEEecCCCCCCCC---CChhhHHHHHHHHHHHhCCCCce-EEEEeecccccc-hhhHHHhhhcCCceeeccC-----
Q 001724 51 RVSVWWDFENCNLPAG---VNAFKVAHTITAAIRANGIKGPV-TITAFGDVVQMS-RANQEVLSSTGINIAHVPH----- 120 (1020)
Q Consensus 51 rVAVFWDiENcpiP~g---~d~~~Va~nI~~aLrelG~~GpV-tIRAYGDws~~~-k~~qe~L~ssGI~LihvP~----- 120 (1020)
|||||||+|||++|.+ + ....+++.+..+|++ .+++|++|.... ..+++.|...||.+.+++.
T Consensus 1 rvavfvD~eN~~~~~~~~~~-------~~~~l~~~i~~~~~~~~~~~y~~~~~~~~~~~~~~L~~~g~~v~~~~~~~~~~ 73 (146)
T PF01936_consen 1 RVAVFVDGENLYIPLKRWDI-------DFERLLEEIRKYGPLVRIRAYGNWDDPNQKSFQEALQRAGIKVRHFPLRKRGG 73 (146)
T ss_dssp EEEEEEEHHHHHHHHHSS-B--------HHHHHHHHTTTEEEEEEEEEE----HHHHHHHHHHHHHT-EEEE------S-
T ss_pred CEEEEEEhHhCchhhCCCCC-------CHHHHHHHHHhcCCeEEEEEEeeccccchhhHHHHHHhCeeeEEeeecccccc
Confidence 7999999999998643 2 334445555557888 459999976543 5678999999998888876
Q ss_pred CCccchhhHHHHHHHHHHHhCCCCcEEEEEeCCcchHHHHHHHHhCCCEEEEec-CCchhHHHHhhcceEEecc
Q 001724 121 GGKNSADRSLLVDLMYWVSQNPPPAHLFLISGDRDFASVLHRLRMNNYNILLAS-RESASNVLCSAASVMWNWD 193 (1020)
Q Consensus 121 ggKNAADi~LiIDaMd~a~~nP~pdtFVLISGDsDFtpLL~RLRerGynVILag-p~kTpeaL~sAcd~Fw~we 193 (1020)
.+|+++|..|++|||.++++++ +++|||||||+||++++.+||++|++|++++ +..++..|+++||.|+..|
T Consensus 74 ~~k~~~D~~l~~d~~~~~~~~~-~d~ivLvSgD~Df~~~v~~l~~~g~~V~v~~~~~~~s~~L~~~ad~f~~~~ 146 (146)
T PF01936_consen 74 GGKKGVDVALAVDILELAYENP-PDTIVLVSGDSDFAPLVRKLRERGKRVIVVGAEDSASEALRSAADEFISIE 146 (146)
T ss_dssp --S---HHHHHHHHHHHG--GG--SEEEEE---GGGHHHHHHHHHH--EEEEEE-GGGS-HHHHHHSSEEEE--
T ss_pred cccCCcHHHHHHHHHHHhhccC-CCEEEEEECcHHHHHHHHHHHHcCCEEEEEEeCCCCCHHHHHhcCEEEeCC
Confidence 5899999999999999999876 5999999999999999999999999999988 6789999999999999864
No 3
>cd06167 LabA_like LabA_like proteins. A well conserved group of bacterial proteins with no defined function. LabA, a member from Synechococcus elongatus PCC 7942, has been shown to play a role in cyanobacterial circadian timing. It is required for negative feedback regulation of the autokinase/autophosphatase KaiC, a central component of the circadian clock system. In particular, LabA seems necessary for KaiC-dependent repression of gene expression.
Probab=99.81 E-value=8e-20 Score=177.27 Aligned_cols=140 Identities=23% Similarity=0.285 Sum_probs=114.0
Q ss_pred CeEEEEEecCCCCCCCCCChhhHHHHHHHHHHHhCCCCceEE-EEeecccc--cchhhHHHhhhcCCceeeccC----CC
Q 001724 50 VRVSVWWDFENCNLPAGVNAFKVAHTITAAIRANGIKGPVTI-TAFGDVVQ--MSRANQEVLSSTGINIAHVPH----GG 122 (1020)
Q Consensus 50 ~rVAVFWDiENcpiP~g~d~~~Va~nI~~aLrelG~~GpVtI-RAYGDws~--~~k~~qe~L~ssGI~LihvP~----gg 122 (1020)
.+++||||+||+........ .....+.++++.+...|.+.. |+|++|.. ....|.++|...|+.+++++. .+
T Consensus 1 ~r~~ifiD~~Nl~~~~~~~~-~~~~d~~~l~~~~~~~~~~~~~r~y~~~~~~~~~~~~~~~L~~~g~~~~~~~~~~~~~~ 79 (149)
T cd06167 1 KRVAVFIDGENLYYSLRDLG-GKRFDYRKLLEFLRDGGEIVLARAYGNWTSPERQRGFLDALRRLGFEPIQKPLRTRGSG 79 (149)
T ss_pred CeEEEEEeHHHHHHHHHHhc-CCCcCHHHHHHHHHhCCeEEEEEEEEecCCchhHHHHHHHHHHCCcEEEEEcceecCCc
Confidence 37999999999975221000 001234455555544466655 99999985 446789999999999999885 67
Q ss_pred ccchhhHHHHHHHHHHHhCCCCcEEEEEeCCcchHHHHHHHHhCCCEEEEecCC-chhHHHHhhcceEEe
Q 001724 123 KNSADRSLLVDLMYWVSQNPPPAHLFLISGDRDFASVLHRLRMNNYNILLASRE-SASNVLCSAASVMWN 191 (1020)
Q Consensus 123 KNAADi~LiIDaMd~a~~nP~pdtFVLISGDsDFtpLL~RLRerGynVILagp~-kTpeaL~sAcd~Fw~ 191 (1020)
||++|+.|++||+++++++ .+++|||||||+||++++.+||++|++|++++.. .++..|..+||+|+.
T Consensus 80 ~~~~D~~l~~d~~~~~~~~-~~d~ivLvSgD~Df~~~i~~lr~~G~~V~v~~~~~~~s~~L~~~~d~f~~ 148 (149)
T cd06167 80 KKGVDVALAIDALELAYKR-RIDTIVLVSGDSDFVPLVERLRELGKRVIVVGFEAKTSRELRKAADRFID 148 (149)
T ss_pred ccCccHHHHHHHHHHhhhc-CCCEEEEEECCccHHHHHHHHHHcCCEEEEEccCccChHHHHHhCCcccc
Confidence 9999999999999999998 6999999999999999999999999999998876 899999999998865
No 4
>PF14418 OHA: OST-HTH Associated domain
Probab=98.94 E-value=2.6e-10 Score=102.68 Aligned_cols=61 Identities=36% Similarity=0.373 Sum_probs=57.6
Q ss_pred ccHHHHHHHHHhcCCccccCCCccchhHHHHHHHhhhhhhhhCCCCCCCceeeccccccccC
Q 001724 619 RTRKQMAESLKEEGPLVLRDLSECDLLDLVDLMILEKKWVEEYPSEKSPFKLSGLVRKKSSL 680 (1020)
Q Consensus 619 ktRE~~ah~Lq~~gp~~lr~L~e~~~~qLV~llisEKKWieE~pS~~fpF~lt~p~~~~~~~ 680 (1020)
+.|+.||+.||+.||..||+|+..+|+|||+|+|++|||+ +.++..+||..++.+..+...
T Consensus 10 ~gRY~~A~~Lk~~gp~~lr~l~Lg~i~~iVqlai~~k~l~-y~~~~l~P~~~~~~~a~s~~~ 70 (75)
T PF14418_consen 10 GGRYGMAQFLKKRGPPFLRSLSLGDICHIVQLAISKKKLI-YENSNLKPFCISQKVANSFLG 70 (75)
T ss_pred CcHHHHHHHHHhcCchhhcCCcHHHHHHHHHHHHhCCeee-eCCCccccHHHHHHHHHhhhc
Confidence 7899999999999999999999999999999999999999 999999999999988777653
No 5
>PF12872 OST-HTH: OST-HTH/LOTUS domain; PDB: 2KPM_A 3S93_B 3RCO_A 2KZV_A.
Probab=98.86 E-value=3e-09 Score=93.02 Aligned_cols=67 Identities=24% Similarity=0.434 Sum_probs=52.8
Q ss_pred HHHHHHHHHHHHhC---CCccchHHHHHHHhcCCCCCCCCccChhhHHHHHHhCCcceEee-cCCCCcEEE
Q 001724 256 KSVVRQIRYILKSY---PEGIFITELRAELSKSPVTIDKDLYGYKKFSRFLLSMPNILRLQ-PEPDGQFLV 322 (1020)
Q Consensus 256 k~lvk~Ir~iL~s~---~G~VsLs~Lg~~Lkk~~PdFD~R~YGykKFSdLL~s~p~~vev~-~~g~g~~~V 322 (1020)
+.+.++|++++.+. .||++++.|+..+++..|+||++.|||.+|++||++++++|++. ...+++++|
T Consensus 4 ~~~~~~l~~ll~~~~~~~g~v~ls~l~~~~~~~~~~f~~~~yG~~~l~~ll~~~~~~~~i~~~~~g~~~~v 74 (74)
T PF12872_consen 4 EELKKLLRELLESQKGEDGWVSLSQLGQEYKKKYPDFDPRDYGFSSLSELLESLPDVVEIEERQHGGQVYV 74 (74)
T ss_dssp HHHHHHHHHHHHHTCTTTSSEEHHHHHHHHHHHHTT--TCCTTSSSHHHHHHT-TTTEEEEEEECCCC---
T ss_pred HHHHHHHHHHHHhCcCCCceEEHHHHHHHHHHHCCCCCccccCCCcHHHHHHhCCCeEEEeeeCCCCcCCC
Confidence 45788888888554 35999999999999999999999999999999999999999994 456667665
No 6
>COG1432 Uncharacterized conserved protein [Function unknown]
Probab=98.86 E-value=8.8e-09 Score=106.09 Aligned_cols=148 Identities=18% Similarity=0.152 Sum_probs=101.0
Q ss_pred CCeEEEEEecCCCCCCCCCChhhHHHHHHHHHHHhCCCCceE-EEEeeccccc---chhh--HHHhhhcCCceeeccC--
Q 001724 49 NVRVSVWWDFENCNLPAGVNAFKVAHTITAAIRANGIKGPVT-ITAFGDVVQM---SRAN--QEVLSSTGINIAHVPH-- 120 (1020)
Q Consensus 49 ~~rVAVFWDiENcpiP~g~d~~~Va~nI~~aLrelG~~GpVt-IRAYGDws~~---~k~~--qe~L~ssGI~LihvP~-- 120 (1020)
..++++|+|..|.+.-.. ....+.-....+|+.....+.+. +..|.-+... .... ...+...|+.++..+.
T Consensus 5 ~~~i~~~id~~n~~~~~~-~~~~~~~d~~~ll~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~v~~~~~~~ 83 (181)
T COG1432 5 VDRIALFIDGKNLYASQR-KNLGILIDYRKLLRKELKRIYLYEAAPYTAEYGDIEIQEVFLNEYELRSDGFTVVTSNLDG 83 (181)
T ss_pred ccceeEEeehhhhHHHHH-HhcCcccCHHHHHHHHhcCceEEEEeehhhccccchhhhheecHHHHhhcCcEEEeccccc
Confidence 468999999999865321 01111112334455443222222 2444333222 2211 2256677777665433
Q ss_pred -----CCccchhhHHHHHHHHHHHhCCCCcEEEEEeCCcchHHHHHHHHhCCCEEEEec-CCchhHHHHhhcceEEeccc
Q 001724 121 -----GGKNSADRSLLVDLMYWVSQNPPPAHLFLISGDRDFASVLHRLRMNNYNILLAS-RESASNVLCSAASVMWNWDS 194 (1020)
Q Consensus 121 -----ggKNAADi~LiIDaMd~a~~nP~pdtFVLISGDsDFtpLL~RLRerGynVILag-p~kTpeaL~sAcd~Fw~wes 194 (1020)
..|-.-|+.|.+|||.+++. +.+++++|+|||.||.|++..++++|..|++++ ...++..|.++||.|+.+..
T Consensus 84 ~~~~~~~k~~vDv~la~D~~~l~~~-~~~D~ivl~SgD~DF~p~v~~~~~~G~rv~v~~~~~~~s~~L~~~aD~~i~L~~ 162 (181)
T COG1432 84 FTDLRITKGDVDVELAVDAMELADK-KNVDTIVLFSGDGDFIPLVEAARDKGKRVEVAGIEPMTSSDLRNAADYYIDLKS 162 (181)
T ss_pred cCcccccccCcchhhHHHHHHhhcc-cCCCEEEEEcCCccHHHHHHHHHHcCCEEEEEecCCcCHHHHHHhhcceEEchh
Confidence 23455699999999999985 579999999999999999999999999999875 45799999999999999887
Q ss_pred hhhh
Q 001724 195 LLRK 198 (1020)
Q Consensus 195 Ll~g 198 (1020)
+...
T Consensus 163 ~~~~ 166 (181)
T COG1432 163 LEEA 166 (181)
T ss_pred hhhh
Confidence 7643
No 7
>PF12872 OST-HTH: OST-HTH/LOTUS domain; PDB: 2KPM_A 3S93_B 3RCO_A 2KZV_A.
Probab=97.65 E-value=6.2e-05 Score=66.00 Aligned_cols=55 Identities=25% Similarity=0.477 Sum_probs=46.8
Q ss_pred HHHHHHHHHHHHHhCCC---CccchhhHHHHHHHhcccccccccchhhhhhHHhhcCcc
Q 001724 740 LADCQKLVDEILKEYPE---GYNMRGFRQLFIERYGYHLDIQKLGYQKLGTLLQIMPGV 795 (1020)
Q Consensus 740 l~Dc~KLvkeil~e~p~---Gyni~~Frk~F~~~ygy~ld~~klgy~kl~sllqimpgv 795 (1020)
|..+.++|.++|.+.++ +.+++.|+..+..+| +++|++.+||.+|..||+-||++
T Consensus 3 ~~~~~~~l~~ll~~~~~~~g~v~ls~l~~~~~~~~-~~f~~~~yG~~~l~~ll~~~~~~ 60 (74)
T PF12872_consen 3 LEELKKLLRELLESQKGEDGWVSLSQLGQEYKKKY-PDFDPRDYGFSSLSELLESLPDV 60 (74)
T ss_dssp -HHHHHHHHHHHHHTCTTTSSEEHHHHHHHHHHHH-TT--TCCTTSSSHHHHHHT-TTT
T ss_pred HHHHHHHHHHHHHhCcCCCceEEHHHHHHHHHHHC-CCCCccccCCCcHHHHHHhCCCe
Confidence 56788999999966654 699999999999999 99999999999999999999997
No 8
>COG4634 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=91.71 E-value=0.73 Score=45.29 Aligned_cols=71 Identities=17% Similarity=0.299 Sum_probs=49.1
Q ss_pred chhhHHHhhhcCCceeeccC-CCccchhhHHHHHHHHHHHhCCCCcEEEEEeCCcchHHHHHHHHhCCCEEEEecCCchh
Q 001724 101 SRANQEVLSSTGINIAHVPH-GGKNSADRSLLVDLMYWVSQNPPPAHLFLISGDRDFASVLHRLRMNNYNILLASRESAS 179 (1020)
Q Consensus 101 ~k~~qe~L~ssGI~LihvP~-ggKNAADi~LiIDaMd~a~~nP~pdtFVLISGDsDFtpLL~RLRerGynVILagp~kTp 179 (1020)
+..+.+-|...||.-+|+-. +-+||+| +.++.+++. +++||||-|+||..|+.++-.-=+-|.+-+..-++
T Consensus 10 p~rlad~l~~~g~e~~h~r~lg~~da~D----~EI~a~A~~----~~~iivTkDsDF~~la~~~G~Ppki~wLr~gNvs~ 81 (113)
T COG4634 10 PPRLADWLPMAGIEAVHWRDLGLRDATD----IEIWAYARR----NNRIIVTKDSDFADLALTLGSPPKIVWLRCGNVST 81 (113)
T ss_pred ChHHHHHhhhcccceeeecccCcCCCcc----HHHHHHHHh----cCcEEEEcCccHHHHHHHcCCCCeEEEEEecCCCH
Confidence 34466778889999999865 5599998 445566654 57999999999987766654444444454443333
No 9
>PRK00124 hypothetical protein; Validated
Probab=83.34 E-value=5.6 Score=41.19 Aligned_cols=96 Identities=18% Similarity=0.190 Sum_probs=58.5
Q ss_pred EEEecCCCCCCCCCChhhHHHHHHHHHHHhCCCCceEEEEeecccccchhhHHHhhhcCCceeeccCCCccchhhHHHHH
Q 001724 54 VWWDFENCNLPAGVNAFKVAHTITAAIRANGIKGPVTITAFGDVVQMSRANQEVLSSTGINIAHVPHGGKNSADRSLLVD 133 (1020)
Q Consensus 54 VFWDiENcpiP~g~d~~~Va~nI~~aLrelG~~GpVtIRAYGDws~~~k~~qe~L~ssGI~LihvP~ggKNAADi~LiID 133 (1020)
||+|+|-||+ ...|.++-++.+ +.+.++++.+.... .=.+..|+.++|+. |.+++|..|+
T Consensus 3 I~VDADACPV---------k~~i~r~a~r~~----i~v~~Vas~n~~~~----~~~~~~v~~v~V~~-g~D~AD~~Iv-- 62 (151)
T PRK00124 3 IYVDADACPV---------KDIIIRVAERHG----IPVTLVASFNHFLR----VPYSPFIRTVYVDA-GFDAADNEIV-- 62 (151)
T ss_pred EEEECCCCcH---------HHHHHHHHHHHC----CeEEEEEeCCcccC----CCCCCceEEEEeCC-CCChHHHHHH--
Confidence 9999999995 233434444433 44566665544211 01134577788885 6889995554
Q ss_pred HHHHHHhCCCCcEEEEEeCCcchHHHHHHHHhCCCEEEEe-cCCchh
Q 001724 134 LMYWVSQNPPPAHLFLISGDRDFASVLHRLRMNNYNILLA-SRESAS 179 (1020)
Q Consensus 134 aMd~a~~nP~pdtFVLISGDsDFtpLL~RLRerGynVILa-gp~kTp 179 (1020)
++- -.+=++||.|- +|+.++-.+|..|+-- |..-++
T Consensus 63 ------~~~-~~gDiVIT~Di---~LAa~~l~Kga~vl~prG~~yt~ 99 (151)
T PRK00124 63 ------QLA-EKGDIVITQDY---GLAALALEKGAIVLNPRGYIYTN 99 (151)
T ss_pred ------HhC-CCCCEEEeCCH---HHHHHHHHCCCEEECCCCcCCCH
Confidence 221 22356788885 7888889999988843 333344
No 10
>PF04263 TPK_catalytic: Thiamin pyrophosphokinase, catalytic domain; InterPro: IPR007371 Thiamin pyrophosphokinase (TPK, 2.7.6.2 from EC) catalyzes the transfer of a pyrophosphate group from ATP to vitamin B1 (thiamin) to form the coenzyme thiamin pyrophosphate (TPP). Thus, TPK is important for the formation of a coenzyme required for central metabolic functions. The structure of thiamin pyrophosphokinase suggests that the enzyme may operate by a mechanism of pyrophosphoryl transfer similar to those described for pyrophosphokinases functioning in nucleotide biosynthesis [].; GO: 0004788 thiamine diphosphokinase activity, 0005524 ATP binding, 0009229 thiamine diphosphate biosynthetic process; PDB: 2F17_B 1IG3_B 3S4Y_B 2OMK_B 1IG0_A 3MEL_B 3CQ9_A 3LM8_B 3K94_B 3L8M_B ....
Probab=77.49 E-value=11 Score=37.39 Aligned_cols=76 Identities=22% Similarity=0.379 Sum_probs=54.0
Q ss_pred EEeecccccchhhHHHhhhcCCceeeccCCCccchhhHHHHHHHHHHHhCCCCcEEEEEeCCc---c--hH--HHHHHHH
Q 001724 92 TAFGDVVQMSRANQEVLSSTGINIAHVPHGGKNSADRSLLVDLMYWVSQNPPPAHLFLISGDR---D--FA--SVLHRLR 164 (1020)
Q Consensus 92 RAYGDws~~~k~~qe~L~ssGI~LihvP~ggKNAADi~LiIDaMd~a~~nP~pdtFVLISGDs---D--Ft--pLL~RLR 164 (1020)
-+.||+.......++.+...|+.+++.| .|+.+|..++++.+ .+. .++.++|+-+=+ | ++ .+|.+++
T Consensus 39 ~iiGDfDSi~~~~~~~~~~~~~~~~~~p--~kD~TD~e~Al~~~---~~~-~~~~i~v~Ga~GgR~DH~lanl~~l~~~~ 112 (123)
T PF04263_consen 39 LIIGDFDSISPEVLEFYKSKGVEIIHFP--EKDYTDLEKALEYA---IEQ-GPDEIIVLGALGGRFDHTLANLNLLYKYK 112 (123)
T ss_dssp EEEC-SSSS-HHHHHHHHHCTTEEEEE---STTS-HHHHHHHHH---HHT-TTSEEEEES-SSSSHHHHHHHHHHHHHHH
T ss_pred EEEecCCCCChHHHHHHHhhccceeccc--ccccCHHHHHHHHH---HHC-CCCEEEEEecCCCcHHHHHHHHHHHHHHH
Confidence 8899999988777888888999999999 69999999888866 443 467766664333 3 22 5566667
Q ss_pred hCCCEEEEe
Q 001724 165 MNNYNILLA 173 (1020)
Q Consensus 165 erGynVILa 173 (1020)
+.|.+|+++
T Consensus 113 ~~~~~i~li 121 (123)
T PF04263_consen 113 KRGIKIVLI 121 (123)
T ss_dssp TTTSEEEEE
T ss_pred HcCCeEEEE
Confidence 789999876
No 11
>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=67.69 E-value=76 Score=29.86 Aligned_cols=103 Identities=11% Similarity=0.039 Sum_probs=56.8
Q ss_pred HHHHhCCCCceEEEEeecccccchhhHHHhhhcCCceeeccCCCccchhhHHHHHHHHHHHhCCCCcEEEEEeCCc---c
Q 001724 79 AIRANGIKGPVTITAFGDVVQMSRANQEVLSSTGINIAHVPHGGKNSADRSLLVDLMYWVSQNPPPAHLFLISGDR---D 155 (1020)
Q Consensus 79 aLrelG~~GpVtIRAYGDws~~~k~~qe~L~ssGI~LihvP~ggKNAADi~LiIDaMd~a~~nP~pdtFVLISGDs---D 155 (1020)
+.+.+...++|-+.+.|.-.......+..|...|.....++.. ......+ ... ..-+.+++||-.+ +
T Consensus 6 ~~~~i~~~~~i~i~g~g~s~~~a~~~~~~l~~~~~~~~~~~~~-------~~~~~~~--~~~-~~~~~~i~iS~~g~~~~ 75 (139)
T cd05013 6 AVDLLAKARRIYIFGVGSSGLVAEYLAYKLLRLGKPVVLLSDP-------HLQLMSA--ANL-TPGDVVIAISFSGETKE 75 (139)
T ss_pred HHHHHHhCCEEEEEEcCchHHHHHHHHHHHHHcCCceEEecCH-------HHHHHHH--HcC-CCCCEEEEEeCCCCCHH
Confidence 3333333355555555543223344566677777654443321 1111111 111 2346677776554 3
Q ss_pred hHHHHHHHHhCCCEEEEecCCchhHHHHhhcceEEec
Q 001724 156 FASVLHRLRMNNYNILLASRESASNVLCSAASVMWNW 192 (1020)
Q Consensus 156 FtpLL~RLRerGynVILagp~kTpeaL~sAcd~Fw~w 192 (1020)
...++..++++|..|++++.... ..+...||..+..
T Consensus 76 ~~~~~~~a~~~g~~iv~iT~~~~-~~l~~~~d~~i~~ 111 (139)
T cd05013 76 TVEAAEIAKERGAKVIAITDSAN-SPLAKLADIVLLV 111 (139)
T ss_pred HHHHHHHHHHcCCeEEEEcCCCC-ChhHHhcCEEEEc
Confidence 66788899999999998876543 3455677766654
No 12
>cd00431 cysteine_hydrolases Cysteine hydrolases; This family contains amidohydrolases, like CSHase (N-carbamoylsarcosine amidohydrolase), involved in creatine metabolism and nicotinamidase, converting nicotinamide to nicotinic acid and ammonia in the pyridine nucleotide cycle. It also contains isochorismatase, an enzyme that catalyzes the conversion of isochorismate to 2,3-dihydroxybenzoate and pyruvate, via the hydrolysis of the vinyl ether bond, and other related enzymes with unknown function.
Probab=64.36 E-value=68 Score=31.78 Aligned_cols=118 Identities=14% Similarity=0.063 Sum_probs=62.3
Q ss_pred EEEEecCCCCCCCCC----ChhhHHHHHHHHHHHhCCCCceEE--EEeeccccc--------------c--hhhHHHhhh
Q 001724 53 SVWWDFENCNLPAGV----NAFKVAHTITAAIRANGIKGPVTI--TAFGDVVQM--------------S--RANQEVLSS 110 (1020)
Q Consensus 53 AVFWDiENcpiP~g~----d~~~Va~nI~~aLrelG~~GpVtI--RAYGDws~~--------------~--k~~qe~L~s 110 (1020)
-|.||+.|--...+. ....+..+|..+++.+...|...| +-+...... . ..+...|.-
T Consensus 2 LliID~Q~~f~~~~~~~~~~~~~~~~~i~~l~~~ar~~~~~vi~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~~l~~ 81 (161)
T cd00431 2 LLVVDMQNDFVPGGGLLLPGADELVPNINRLLAAARAAGIPVIFTRDWHPPDDPEFAELLWPPHCVKGTEGAELVPELAP 81 (161)
T ss_pred EEEEECcccCcCCCCCcCccHHHHHHHHHHHHHHHHHcCCeEEEEEeeecCCCcccccccCcccccCCCchhhcchhhCC
Confidence 478999997654432 245666788888777755564333 443332110 0 011122211
Q ss_pred cCCceeeccCCCccchhhHHHHHHHHHHHhCCCCcEEEEEeCCcchH--HHHHHHHhCCCEEEEecC
Q 001724 111 TGINIAHVPHGGKNSADRSLLVDLMYWVSQNPPPAHLFLISGDRDFA--SVLHRLRMNNYNILLASR 175 (1020)
Q Consensus 111 sGI~LihvP~ggKNAADi~LiIDaMd~a~~nP~pdtFVLISGDsDFt--pLL~RLRerGynVILagp 175 (1020)
..-. .+. .|+..+.----++..++..+ .+++++|+--..++. ..+..+.++||+|+++..
T Consensus 82 ~~~~--~~i--~K~~~saf~~t~l~~~L~~~-~i~~vil~G~~t~~CV~~T~~~a~~~G~~v~vi~D 143 (161)
T cd00431 82 LPDD--LVI--EKTRYSAFYGTDLDELLRER-GIDTLVVCGIATDICVLATARDALDLGYRVIVVED 143 (161)
T ss_pred CCCC--EEE--ecCCcCCccCCCHHHHHHHC-CCCEEEEEecCcChhHHHHHHHHHHCCCEEEEehh
Confidence 0000 111 12222211112455677765 588888886666654 556777788999998643
No 13
>PF09419 PGP_phosphatase: Mitochondrial PGP phosphatase; InterPro: IPR010021 This group of hypothetical proteins is a part of the IIIA subfamily of the haloacid dehalogenase (HAD) superfamily of hydrolases. All characterised members of this subfamily and most characterised members of the HAD superfamily are phosphatases. HAD superfamily phosphatases contain active site residues in several conserved catalytic motifs [], all of which are found conserved here. This family consists of sequences from fungi, plants, cyanobacteria, Gram-positive bacteria and Deinococcus. There is presently no characterisation of any sequence in this family.
Probab=63.93 E-value=69 Score=33.79 Aligned_cols=115 Identities=17% Similarity=0.252 Sum_probs=59.8
Q ss_pred CCeEEEEEecCCCCCCCCCChhhHHHHHHHHHHHhC-CCCceEEEEeecc----cccc-hhhHHHhhhcCCce-eeccCC
Q 001724 49 NVRVSVWWDFENCNLPAGVNAFKVAHTITAAIRANG-IKGPVTITAFGDV----VQMS-RANQEVLSSTGINI-AHVPHG 121 (1020)
Q Consensus 49 ~~rVAVFWDiENcpiP~g~d~~~Va~nI~~aLrelG-~~GpVtIRAYGDw----s~~~-k~~qe~L~ssGI~L-ihvP~g 121 (1020)
..-=+|..|.|||=.+.+-+ .+.+.+...++++- .+|.-.|-++-|- .... ......-...||.+ .|. .
T Consensus 39 ~Gik~li~DkDNTL~~~~~~--~i~~~~~~~~~~l~~~~~~~~v~IvSNsaGs~~d~~~~~a~~~~~~lgIpvl~h~-~- 114 (168)
T PF09419_consen 39 KGIKALIFDKDNTLTPPYED--EIPPEYAEWLNELKKQFGKDRVLIVSNSAGSSDDPDGERAEALEKALGIPVLRHR-A- 114 (168)
T ss_pred cCceEEEEcCCCCCCCCCcC--cCCHHHHHHHHHHHHHCCCCeEEEEECCCCcccCccHHHHHHHHHhhCCcEEEeC-C-
Confidence 34468999999998755422 23333444444442 2232123333222 2211 11222234678874 453 1
Q ss_pred CccchhhHHHHHHHHHHHhCC---CCcEEEEEeCCcchHHHHHHHHhCCCEEEE
Q 001724 122 GKNSADRSLLVDLMYWVSQNP---PPAHLFLISGDRDFASVLHRLRMNNYNILL 172 (1020)
Q Consensus 122 gKNAADi~LiIDaMd~a~~nP---~pdtFVLISGDsDFtpLL~RLRerGynVIL 172 (1020)
.|-. -.-+++.++..++ .|..++ |-||+=||.++.--|+-.|.|++
T Consensus 115 kKP~----~~~~i~~~~~~~~~~~~p~eia-vIGDrl~TDVl~gN~~G~~tilv 163 (168)
T PF09419_consen 115 KKPG----CFREILKYFKCQKVVTSPSEIA-VIGDRLFTDVLMGNRMGSYTILV 163 (168)
T ss_pred CCCc----cHHHHHHHHhhccCCCCchhEE-EEcchHHHHHHHhhccCceEEEE
Confidence 1221 2236666665542 244544 44999999999888876677664
No 14
>COG1671 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=62.64 E-value=32 Score=35.82 Aligned_cols=89 Identities=17% Similarity=0.248 Sum_probs=54.2
Q ss_pred EEEEEecCCCCCCCCCChhhHHHHHHHHHHHhCCCCceEEEEeecccccchhhHHHhhhcCCceeeccCCCccchhhHHH
Q 001724 52 VSVWWDFENCNLPAGVNAFKVAHTITAAIRANGIKGPVTITAFGDVVQMSRANQEVLSSTGINIAHVPHGGKNSADRSLL 131 (1020)
Q Consensus 52 VAVFWDiENcpiP~g~d~~~Va~nI~~aLrelG~~GpVtIRAYGDws~~~k~~qe~L~ssGI~LihvP~ggKNAADi~Li 131 (1020)
.-||+|+|-||+ ..-|.++.+++| +.++..+|..... .....|..+.+-. |.+++|..|+
T Consensus 2 ~~I~VDADACPV---------k~~i~r~A~r~~----~~v~~Van~~~~~------~~~~~i~~v~V~~-g~DaaD~~Iv 61 (150)
T COG1671 2 MTIWVDADACPV---------KDEIYRVAERMG----LKVTFVANFPHRV------PPSPEIRTVVVDA-GFDAADDWIV 61 (150)
T ss_pred ceEEEeCCCCch---------HHHHHHHHHHhC----CeEEEEeCCCccC------CCCCceeEEEecC-CcchHHHHHH
Confidence 358999999995 244555556654 2345555553321 1344555555544 6889996554
Q ss_pred HHHHHHHHhCCCCcEEEEEeCCcchHHHHHHHHhCCCEEEE
Q 001724 132 VDLMYWVSQNPPPAHLFLISGDRDFASVLHRLRMNNYNILL 172 (1020)
Q Consensus 132 IDaMd~a~~nP~pdtFVLISGDsDFtpLL~RLRerGynVIL 172 (1020)
++ .=.+=++||-|- +|+.+|-..|-.|+-
T Consensus 62 --------~~-a~~gDlVVT~Di---~LA~~ll~kg~~v~~ 90 (150)
T COG1671 62 --------NL-AEKGDLVVTADI---PLASLLLDKGAAVLN 90 (150)
T ss_pred --------Hh-CCCCCEEEECch---HHHHHHHhcCCEEEC
Confidence 22 122336778886 566778888888884
No 15
>TIGR01378 thi_PPkinase thiamine pyrophosphokinase. This model has been revised. Originally, it described strictly eukaryotic thiamine pyrophosphokinase. However, it is now expanded to include also homologous enzymes, apparently functionally equivalent, from species that rely on thiamine pyrophosphokinase rather than thiamine-monophosphate kinase (TIGR01379) to produce the active TPP cofactor. This includes the thiamine pyrophosphokinase from Bacillus subtilis, previously designated YloS.
Probab=61.51 E-value=50 Score=35.20 Aligned_cols=81 Identities=17% Similarity=0.365 Sum_probs=56.6
Q ss_pred EEeecccccchhhHHHhhhcCCceeeccCCCccchhhHHHHHHHHHHHhCCCCcEEEEE--eCCc-c--hH--HHHHHHH
Q 001724 92 TAFGDVVQMSRANQEVLSSTGINIAHVPHGGKNSADRSLLVDLMYWVSQNPPPAHLFLI--SGDR-D--FA--SVLHRLR 164 (1020)
Q Consensus 92 RAYGDws~~~k~~qe~L~ssGI~LihvP~ggKNAADi~LiIDaMd~a~~nP~pdtFVLI--SGDs-D--Ft--pLL~RLR 164 (1020)
-+.||+.......++.+...++.++..|. -|+.||..+++. ++.++ .++.++|+ +|.+ | ++ .+|.+++
T Consensus 40 ~iiGDfDSi~~~~~~~~~~~~~~~~~~~~-eKD~TD~e~Al~---~~~~~-~~~~i~i~Ga~GgR~DH~lani~~L~~~~ 114 (203)
T TIGR01378 40 LIVGDFDSIDEEELDFYKKAGVKIIVFPP-EKDTTDLELALK---YALER-GADEITILGATGGRLDHTLANLNLLLEYA 114 (203)
T ss_pred EEEeCcccCCHHHHHHHHHcCCceEEcCC-CCCCCHHHHHHH---HHHHC-CCCEEEEEcCCCCcHHHHHHHHHHHHHHH
Confidence 88899999887777778888998877766 499999888764 55555 36777776 4444 4 33 3444455
Q ss_pred hCCCEEEEecCCc
Q 001724 165 MNNYNILLASRES 177 (1020)
Q Consensus 165 erGynVILagp~k 177 (1020)
..|..|+++.+..
T Consensus 115 ~~~~~i~l~d~~~ 127 (203)
T TIGR01378 115 KRGIKVRLIDEQN 127 (203)
T ss_pred hcCCeEEEEcCCc
Confidence 5788888776543
No 16
>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=55.29 E-value=1.4e+02 Score=32.67 Aligned_cols=100 Identities=11% Similarity=0.128 Sum_probs=63.0
Q ss_pred hHHHHHHHHHHHhCCCCce-----------EE-EEeeccccc-----chhhHHHhhhcCCceeeccCCCccchhhHHHHH
Q 001724 71 KVAHTITAAIRANGIKGPV-----------TI-TAFGDVVQM-----SRANQEVLSSTGINIAHVPHGGKNSADRSLLVD 133 (1020)
Q Consensus 71 ~Va~nI~~aLrelG~~GpV-----------tI-RAYGDws~~-----~k~~qe~L~ssGI~LihvP~ggKNAADi~LiID 133 (1020)
.....|.++++++||.-.. +| -+..++... -..+.+.+...|+.+..+.... |......
T Consensus 32 ~tr~rV~~~a~~lgY~pn~~a~~l~~~~~~~Igvi~~~~~~~~~~~~~~~i~~~~~~~gy~~~i~~~~~----~~~~~~~ 107 (327)
T TIGR02417 32 ETVERVMAVVREQGYQPNIHAASLRAGRSRTIGLVIPDLENYSYARIAKELEQQCREAGYQLLIACSDD----NPDQEKV 107 (327)
T ss_pred HHHHHHHHHHHHhCCCCCHHHHHhhcCCCceEEEEeCCCCCccHHHHHHHHHHHHHHCCCEEEEEeCCC----CHHHHHH
Confidence 3446788899999985421 23 333344332 1345667788999887655422 1123344
Q ss_pred HHHHHHhCCCCcEEEEEeCCcchHHHHHHHHhCCCEEEEecC
Q 001724 134 LMYWVSQNPPPAHLFLISGDRDFASVLHRLRMNNYNILLASR 175 (1020)
Q Consensus 134 aMd~a~~nP~pdtFVLISGDsDFtpLL~RLRerGynVILagp 175 (1020)
++..+..+ .+++++|+..+.+....+..|+..|..|+++..
T Consensus 108 ~~~~l~~~-~vdgiIi~~~~~~~~~~~~~l~~~~iPvV~~~~ 148 (327)
T TIGR02417 108 VIENLLAR-QVDALIVASCMPPEDAYYQKLQNEGLPVVALDR 148 (327)
T ss_pred HHHHHHHc-CCCEEEEeCCCCCChHHHHHHHhcCCCEEEEcc
Confidence 55556655 499999887665345778889999998887764
No 17
>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=54.46 E-value=1.4e+02 Score=30.41 Aligned_cols=73 Identities=19% Similarity=0.272 Sum_probs=42.1
Q ss_pred hhhHHHhhhcC-CceeeccCCCccchhhHHHHHHHHHHHhCCCCcEEEEEeCCcchHHHHHHHHhCCCE----EEEecCC
Q 001724 102 RANQEVLSSTG-INIAHVPHGGKNSADRSLLVDLMYWVSQNPPPAHLFLISGDRDFASVLHRLRMNNYN----ILLASRE 176 (1020)
Q Consensus 102 k~~qe~L~ssG-I~LihvP~ggKNAADi~LiIDaMd~a~~nP~pdtFVLISGDsDFtpLL~RLRerGyn----VILagp~ 176 (1020)
..++..+...| +.+..+.....+..+ ..-.+..|+..+|.++.++ +.+|.....++..+++.|++ |.+++-.
T Consensus 138 ~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~l~~~~~~~~i~-~~~~~~a~~~~~~~~~~g~~i~~~i~i~~~d 214 (264)
T cd01537 138 AGFKDALKEAGPIEIVLVQEGDWDAEK--GYQAAEELLTAHPDPTAIF-AANDDMALGALRALREAGLRVPDDISVIGFD 214 (264)
T ss_pred HHHHHHHHHcCCcChhhhccCCCCHHH--HHHHHHHHHhcCCCCCEEE-EcCcHHHHHHHHHHHHhCCCCCCCeEEEeec
Confidence 34666777777 555444332223222 3444556666666555554 45665556788999999874 5454433
Q ss_pred c
Q 001724 177 S 177 (1020)
Q Consensus 177 k 177 (1020)
.
T Consensus 215 ~ 215 (264)
T cd01537 215 G 215 (264)
T ss_pred C
Confidence 3
No 18
>PRK11303 DNA-binding transcriptional regulator FruR; Provisional
Probab=51.96 E-value=1.6e+02 Score=32.16 Aligned_cols=99 Identities=11% Similarity=0.098 Sum_probs=61.9
Q ss_pred HHHHHHHHHHHhCCCCce-----------EE-EEeeccccc-----chhhHHHhhhcCCceeeccCCCccchhhHHHHHH
Q 001724 72 VAHTITAAIRANGIKGPV-----------TI-TAFGDVVQM-----SRANQEVLSSTGINIAHVPHGGKNSADRSLLVDL 134 (1020)
Q Consensus 72 Va~nI~~aLrelG~~GpV-----------tI-RAYGDws~~-----~k~~qe~L~ssGI~LihvP~ggKNAADi~LiIDa 134 (1020)
....|.++++++||.-.. +| -+..++... -..+.+++...|+.+..+.... |..-..++
T Consensus 34 tr~rV~~~a~elgY~pn~~a~~l~~~~~~~Igvv~~~~~~~~~~~l~~gi~~~~~~~g~~~~~~~~~~----~~~~~~~~ 109 (328)
T PRK11303 34 TVEKVMAVVREHNYHPNAVAAGLRAGRTRSIGLIIPDLENTSYARIAKYLERQARQRGYQLLIACSDD----QPDNEMRC 109 (328)
T ss_pred HHHHHHHHHHHhCCCCCHHHHHhhcCCCceEEEEeCCCCCchHHHHHHHHHHHHHHcCCEEEEEeCCC----CHHHHHHH
Confidence 446788889999875321 23 222333321 1345667788999887654322 11223456
Q ss_pred HHHHHhCCCCcEEEEEeCCcchHHHHHHHHhCCCEEEEecC
Q 001724 135 MYWVSQNPPPAHLFLISGDRDFASVLHRLRMNNYNILLASR 175 (1020)
Q Consensus 135 Md~a~~nP~pdtFVLISGDsDFtpLL~RLRerGynVILagp 175 (1020)
+.++... .+++++|++.+.+-...+..|.+.|..|+++..
T Consensus 110 ~~~l~~~-~vdgiIi~~~~~~~~~~~~~l~~~~iPvV~v~~ 149 (328)
T PRK11303 110 AEHLLQR-QVDALIVSTSLPPEHPFYQRLQNDGLPIIALDR 149 (328)
T ss_pred HHHHHHc-CCCEEEEcCCCCCChHHHHHHHhcCCCEEEECC
Confidence 6666654 599999987654445677888889999987764
No 19
>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=51.81 E-value=2.1e+02 Score=30.02 Aligned_cols=75 Identities=15% Similarity=0.255 Sum_probs=43.4
Q ss_pred hhhHHHhhhcCCceeeccCCCccchhhHHHHHHH-HHHHhCCCCcEEEEEeCCcchHHHHHHHHhCCCE--EEEecCCch
Q 001724 102 RANQEVLSSTGINIAHVPHGGKNSADRSLLVDLM-YWVSQNPPPAHLFLISGDRDFASVLHRLRMNNYN--ILLASRESA 178 (1020)
Q Consensus 102 k~~qe~L~ssGI~LihvP~ggKNAADi~LiIDaM-d~a~~nP~pdtFVLISGDsDFtpLL~RLRerGyn--VILagp~kT 178 (1020)
.++++.|...|+.+..+...+....+ -..+++ .++..+|.++. +++.+|.--..++..|+++|+. |.+++-..+
T Consensus 145 ~gf~~~l~~~~~~~~~~~~~~~~~~~--~~~~~~~~~l~~~~~~~a-i~~~~d~~a~g~~~al~~~g~~~di~vvg~d~~ 221 (277)
T cd06319 145 KGFKEAMKEAGCDLAGIRQQKDFSYQ--ETFDYTNDLLTANPDIRA-IWLQGSDRYQGALDAIATAGKTGKVLLICFDAE 221 (277)
T ss_pred HHHHHHHHhcCCceEeeccCCCCCHH--HHHHHHHHHHHhCCCCCE-EEECCCccchHHHHHHHHcCCCCCEEEEEcCCC
Confidence 35788899999875543221211112 233444 34545665644 4445666556899999999975 555544444
Q ss_pred h
Q 001724 179 S 179 (1020)
Q Consensus 179 p 179 (1020)
+
T Consensus 222 ~ 222 (277)
T cd06319 222 P 222 (277)
T ss_pred H
Confidence 4
No 20
>PRK10014 DNA-binding transcriptional repressor MalI; Provisional
Probab=51.02 E-value=1.6e+02 Score=32.36 Aligned_cols=100 Identities=14% Similarity=0.127 Sum_probs=64.9
Q ss_pred hHHHHHHHHHHHhCCCCce-----------EE-EEeeccccc-----chhhHHHhhhcCCceeeccCCCccchhhHHHHH
Q 001724 71 KVAHTITAAIRANGIKGPV-----------TI-TAFGDVVQM-----SRANQEVLSSTGINIAHVPHGGKNSADRSLLVD 133 (1020)
Q Consensus 71 ~Va~nI~~aLrelG~~GpV-----------tI-RAYGDws~~-----~k~~qe~L~ssGI~LihvP~ggKNAADi~LiID 133 (1020)
.....|.++++++||.-.. +| -++.++... -..+.+++...|..+.-+.... |..-..+
T Consensus 36 ~tr~~V~~~a~elgY~p~~~a~~l~~~~~~~Igvv~~~~~~~~~~~i~~gi~~~a~~~g~~~~~~~~~~----~~~~~~~ 111 (342)
T PRK10014 36 ATGERVNQAIEELGFVRNRQASALRGGQSGVIGLIVRDLSAPFYAELTAGLTEALEAQGRMVFLLQGGK----DGEQLAQ 111 (342)
T ss_pred HHHHHHHHHHHHhCCCcCHHHHhhccCCCCEEEEEeCCCccchHHHHHHHHHHHHHHcCCEEEEEeCCC----CHHHHHH
Confidence 3446788888888875421 23 334444332 1345667888898776554422 2223456
Q ss_pred HHHHHHhCCCCcEEEEEeCCcchHHHHHHHHhCCCEEEEecC
Q 001724 134 LMYWVSQNPPPAHLFLISGDRDFASVLHRLRMNNYNILLASR 175 (1020)
Q Consensus 134 aMd~a~~nP~pdtFVLISGDsDFtpLL~RLRerGynVILagp 175 (1020)
++..+... .+++|+|+..+.....++..|++.|..|+++..
T Consensus 112 ~~~~l~~~-~vdgiIi~~~~~~~~~~~~~l~~~~iPvV~~~~ 152 (342)
T PRK10014 112 RFSTLLNQ-GVDGVVIAGAAGSSDDLREMAEEKGIPVVFASR 152 (342)
T ss_pred HHHHHHhC-CCCEEEEeCCCCCcHHHHHHHhhcCCCEEEEec
Confidence 66666664 499999988776667889999999999987753
No 21
>PRK09426 methylmalonyl-CoA mutase; Reviewed
Probab=50.15 E-value=1.1e+02 Score=39.05 Aligned_cols=88 Identities=10% Similarity=0.053 Sum_probs=55.6
Q ss_pred HHHHHHHHHhCCCCceEE-EEeecccccchhh-HHHhhhcCCceeeccCCCccchhhHHHHHHHHHHHhCCCCcEEEEEe
Q 001724 74 HTITAAIRANGIKGPVTI-TAFGDVVQMSRAN-QEVLSSTGINIAHVPHGGKNSADRSLLVDLMYWVSQNPPPAHLFLIS 151 (1020)
Q Consensus 74 ~nI~~aLrelG~~GpVtI-RAYGDws~~~k~~-qe~L~ssGI~LihvP~ggKNAADi~LiIDaMd~a~~nP~pdtFVLIS 151 (1020)
......+...|..++|.+ +.-+|-......+ ...|...||++++-. +-...+ ++.+.+..+ .++.+||.|
T Consensus 570 ~~~~~~~~~~g~rpkV~LatlG~d~H~~ra~fv~~~l~~~GfeV~~~~--~~~s~e-----~~v~aa~~~-~a~ivvlcs 641 (714)
T PRK09426 570 ALVEAFAEAEGRRPRILVAKMGQDGHDRGAKVIATAFADLGFDVDIGP--LFQTPE-----EAARQAVEN-DVHVVGVSS 641 (714)
T ss_pred HHHHHHHHhcCCCceEEEEecCCcchhHhHHHHHHHHHhCCeeEecCC--CCCCHH-----HHHHHHHHc-CCCEEEEec
Confidence 334444455677788877 7777743333333 567889999995421 111222 344455554 488999999
Q ss_pred CCcc----hHHHHHHHHhCCCE
Q 001724 152 GDRD----FASVLHRLRMNNYN 169 (1020)
Q Consensus 152 GDsD----FtpLL~RLRerGyn 169 (1020)
.|.+ +..++..||+.|..
T Consensus 642 ~d~~~~e~~~~l~~~Lk~~G~~ 663 (714)
T PRK09426 642 LAAGHKTLVPALIEALKKLGRE 663 (714)
T ss_pred cchhhHHHHHHHHHHHHhcCCC
Confidence 8975 45888899999863
No 22
>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=48.14 E-value=60 Score=35.59 Aligned_cols=68 Identities=9% Similarity=0.121 Sum_probs=47.7
Q ss_pred hhHHHhhhcCCceeeccCCCccchhhHHHHHHHHHHHhCCCCcEEEEEeCCcc-hHHHHHHHHhCCCEEEEecC
Q 001724 103 ANQEVLSSTGINIAHVPHGGKNSADRSLLVDLMYWVSQNPPPAHLFLISGDRD-FASVLHRLRMNNYNILLASR 175 (1020)
Q Consensus 103 ~~qe~L~ssGI~LihvP~ggKNAADi~LiIDaMd~a~~nP~pdtFVLISGDsD-FtpLL~RLRerGynVILagp 175 (1020)
..++++...|+.++.+.... |.....++++.+... .+|+|+|++.|.. ..+.+.+|++.|..|+++..
T Consensus 19 ~i~~~a~~~g~~v~~~~~~~----~~~~q~~~i~~l~~~-~vDgIIi~~~~~~~~~~~l~~~~~~~iPvV~~d~ 87 (302)
T TIGR02634 19 IFVAAAESLGAKVFVQSANG----NEAKQISQIENLIAR-GVDVLVIIPQNGQVLSNAVQEAKDEGIKVVAYDR 87 (302)
T ss_pred HHHHHHHhcCCEEEEEeCCC----CHHHHHHHHHHHHHc-CCCEEEEeCCChhHHHHHHHHHHHCCCeEEEecC
Confidence 45566777777776654422 223445666666654 5999999988865 47888999999999998754
No 23
>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=47.89 E-value=49 Score=35.15 Aligned_cols=69 Identities=9% Similarity=0.018 Sum_probs=44.5
Q ss_pred hHHHhhhcCCceeeccCCCccchhhHHHHHHHHHHHhCCCCcEEEEEeCCcchHHHHHHHHhCCCEEEEecC
Q 001724 104 NQEVLSSTGINIAHVPHGGKNSADRSLLVDLMYWVSQNPPPAHLFLISGDRDFASVLHRLRMNNYNILLASR 175 (1020)
Q Consensus 104 ~qe~L~ssGI~LihvP~ggKNAADi~LiIDaMd~a~~nP~pdtFVLISGDsDFtpLL~RLRerGynVILagp 175 (1020)
..+++...|+.++.+...+.+. ..-.+.+++.+... .+|+++|+..+.+....+.+++.+|..|+++..
T Consensus 21 i~~~a~~~g~~~~~~~~~~~~~--~~~~~~~i~~~~~~-~vdgiI~~~~~~~~~~~~~~~~~~giPvV~~~~ 89 (268)
T cd06306 21 MVEEAKRLGVSLKLLEAGGYPN--LAKQIAQLEDCAAW-GADAILLGAVSPDGLNEILQQVAASIPVIALVN 89 (268)
T ss_pred HHHHHHHcCCEEEEecCCCCCC--HHHHHHHHHHHHHc-CCCEEEEcCCChhhHHHHHHHHHCCCCEEEecc
Confidence 4455666677666654332221 22344566666665 599999998887653357888999999987643
No 24
>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=47.34 E-value=2.4e+02 Score=30.78 Aligned_cols=113 Identities=13% Similarity=0.167 Sum_probs=59.5
Q ss_pred ChhhHHHHHHHHHHHhCCC-----CceEE-EEeecccccc-----hhhHHHhhhcC-CceeeccCCCccchhhHHHHHHH
Q 001724 68 NAFKVAHTITAAIRANGIK-----GPVTI-TAFGDVVQMS-----RANQEVLSSTG-INIAHVPHGGKNSADRSLLVDLM 135 (1020)
Q Consensus 68 d~~~Va~nI~~aLrelG~~-----GpVtI-RAYGDws~~~-----k~~qe~L~ssG-I~LihvP~ggKNAADi~LiIDaM 135 (1020)
+.+.....+...|-+.|+. |.+.| -+.|.-.... .++++.|..+| +.+..+..+.- ..+ -..+++
T Consensus 117 d~~~~g~~~~~~l~~~g~~~~~~~g~~~i~~i~~~~~~~~~~~R~~Gf~~~~~~~g~~~~~~~~~~~~-~~~--~~~~~~ 193 (305)
T cd06324 117 NDEEAGYLMAEALISQARSVQAPGGRIDLLAISGDPTTPAAILREAGLRRALAEHPDVRLRQVVYAGW-SED--EAYEQA 193 (305)
T ss_pred CcHHHHHHHHHHHHHHhhcccCCCCceeEEEEeCCCCChHHHHHHHHHHHHHHHCCCceEeeeecCCC-CHH--HHHHHH
Confidence 4344444444555555544 44444 3334332211 34677888887 44433222221 111 223333
Q ss_pred H-HHHhCCCCcEEEEEeCCcchHHHHHHHHhCCCE----EEEecCCchhHHHHh
Q 001724 136 Y-WVSQNPPPAHLFLISGDRDFASVLHRLRMNNYN----ILLASRESASNVLCS 184 (1020)
Q Consensus 136 d-~a~~nP~pdtFVLISGDsDFtpLL~RLRerGyn----VILagp~kTpeaL~s 184 (1020)
. ++..+|.++.|+ ..+|.-=..+++-|+++|+. |.+++-..++..+..
T Consensus 194 ~~~l~~~~~~~ai~-~~~d~~A~g~~~al~~~g~~vp~di~vig~D~~~~~~~~ 246 (305)
T cd06324 194 ENLLKRYPDVRLIW-AANDQMAFGALRAAKEAGRKPGRDVLFGGVNWSPEALRA 246 (305)
T ss_pred HHHHHHCCCccEEE-ECCchHHHHHHHHHHHcCCCcCCCEEEEecCCCHHHHHH
Confidence 3 444566677544 55666656899999999965 556665666665443
No 25
>cd06311 PBP1_ABC_sugar_binding_like_3 Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems. Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily, which consists of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis.
Probab=46.63 E-value=1.9e+02 Score=30.59 Aligned_cols=78 Identities=10% Similarity=0.094 Sum_probs=45.5
Q ss_pred hhHHHhhhcCCceeeccCCCccchhhHHHHHHHHHHHhCCCCcEEEEEeCCcchHHHHHHHHhCCCE--EEEecCCchhH
Q 001724 103 ANQEVLSSTGINIAHVPHGGKNSADRSLLVDLMYWVSQNPPPAHLFLISGDRDFASVLHRLRMNNYN--ILLASRESASN 180 (1020)
Q Consensus 103 ~~qe~L~ssGI~LihvP~ggKNAADi~LiIDaMd~a~~nP~pdtFVLISGDsDFtpLL~RLRerGyn--VILagp~kTpe 180 (1020)
.+++.|..+|++++......- ..+ ...--+-.|+..+|.++. +++.+|.-...++..|++.|+. |.+++-..+|.
T Consensus 147 gf~~~l~~~~~~~~~~~~~~~-~~~-~~~~~~~~~l~~~~~~~a-i~~~~d~~a~g~~~al~~~g~~~~~~ivg~d~~~~ 223 (274)
T cd06311 147 AFDAAIAKYPIKILDRQYANW-NRD-DAFSVMQDLLTKFPKIDA-VWAHDDDMAVGVLAAIKQAGRTDIKFVVGGAGSKD 223 (274)
T ss_pred HHHHHHhhCCcEEEeccCCCC-cHH-HHHHHHHHHHHhCCCcCE-EEECCCcHHHHHHHHHHHcCCCCCceEEEeCCCHH
Confidence 467788888877655322111 111 112223345656676665 4556666677899999999874 55555444665
Q ss_pred HHH
Q 001724 181 VLC 183 (1020)
Q Consensus 181 aL~ 183 (1020)
.+.
T Consensus 224 ~~~ 226 (274)
T cd06311 224 MIK 226 (274)
T ss_pred HHH
Confidence 553
No 26
>PRK14987 gluconate operon transcriptional regulator; Provisional
Probab=46.17 E-value=2.1e+02 Score=31.43 Aligned_cols=98 Identities=12% Similarity=0.078 Sum_probs=61.8
Q ss_pred hHHHHHHHHHHHhCCCCce-----------EE-EEeeccccc-----chhhHHHhhhcCCceeeccCCCccchhhHHHHH
Q 001724 71 KVAHTITAAIRANGIKGPV-----------TI-TAFGDVVQM-----SRANQEVLSSTGINIAHVPHGGKNSADRSLLVD 133 (1020)
Q Consensus 71 ~Va~nI~~aLrelG~~GpV-----------tI-RAYGDws~~-----~k~~qe~L~ssGI~LihvP~ggKNAADi~LiID 133 (1020)
.....|.++.+++||.-.. +| -++-++... -....+.+...|+.++.++... |.....+
T Consensus 35 ~tr~rV~~~a~elgY~pn~~a~~l~~~~~~~Igvi~~~~~~~~~~~~~~gi~~~~~~~g~~~~~~~~~~----~~~~~~~ 110 (331)
T PRK14987 35 ALRGKIAAALDELGYIPNRAPDILSNATSRAIGVLLPSLTNQVFAEVLRGIESVTDAHGYQTMLAHYGY----KPEMEQE 110 (331)
T ss_pred HHHHHHHHHHHHhCCCccHHHHHHhhCCCCEEEEEeCCCcchhHHHHHHHHHHHHHHCCCEEEEecCCC----CHHHHHH
Confidence 4557788999999985321 23 233344321 2345667888999887655432 1223345
Q ss_pred HHHHHHhCCCCcEEEEEeCCcchHHHHHHHHhCCCEEEEec
Q 001724 134 LMYWVSQNPPPAHLFLISGDRDFASVLHRLRMNNYNILLAS 174 (1020)
Q Consensus 134 aMd~a~~nP~pdtFVLISGDsDFtpLL~RLRerGynVILag 174 (1020)
+++.+..+ .+++++|+..+.+ ...+..|++.|..|+++.
T Consensus 111 ~~~~~~~~-~vdgiI~~~~~~~-~~~~~~l~~~~iPvV~~~ 149 (331)
T PRK14987 111 RLESMLSW-NIDGLILTERTHT-PRTLKMIEVAGIPVVELM 149 (331)
T ss_pred HHHHHHhc-CCCEEEEcCCCCC-HHHHHHHHhCCCCEEEEe
Confidence 66666654 5999999864432 467788889999988764
No 27
>COG1564 THI80 Thiamine pyrophosphokinase [Coenzyme metabolism]
Probab=45.90 E-value=80 Score=34.60 Aligned_cols=79 Identities=23% Similarity=0.269 Sum_probs=57.3
Q ss_pred EEEeecccccchhhHHHhhhcCCceeeccCCCccchhhHHHHHHHHHHHhCCCCcEEEEE--eCCc-c----hHHHHHHH
Q 001724 91 ITAFGDVVQMSRANQEVLSSTGINIAHVPHGGKNSADRSLLVDLMYWVSQNPPPAHLFLI--SGDR-D----FASVLHRL 163 (1020)
Q Consensus 91 IRAYGDws~~~k~~qe~L~ssGI~LihvP~ggKNAADi~LiIDaMd~a~~nP~pdtFVLI--SGDs-D----FtpLL~RL 163 (1020)
--++||+.......++.+...++. +.+| .-||.+|-.++++ ++..+. ++.++++ .|.+ | ...|+.++
T Consensus 45 ~~~vGDfDSv~~e~~~~~~~~~~~-~~f~-~eKd~TD~elAl~---~a~e~g-~d~i~i~Ga~GGR~DH~l~nl~ll~~~ 118 (212)
T COG1564 45 DLAVGDFDSVSEELLAYYKEKTVT-IKFP-AEKDSTDLELALD---EALERG-ADEIVILGALGGRLDHALANLFLLLRP 118 (212)
T ss_pred cEEEecccccCHHHHHHHhhcCcc-eecC-hhhccchHHHHHH---HHHHcC-CCEEEEEecCCChHHHHHHHHHHHHhh
Confidence 389999999888788888888877 3334 4699999888766 666653 6888888 5554 3 34666677
Q ss_pred HhCCCEEEEecC
Q 001724 164 RMNNYNILLASR 175 (1020)
Q Consensus 164 RerGynVILagp 175 (1020)
-.+|.+|.+.-.
T Consensus 119 ~~~~~~i~l~~~ 130 (212)
T COG1564 119 AKSGFKITLISG 130 (212)
T ss_pred hhccceEEEecC
Confidence 667888877644
No 28
>cd05014 SIS_Kpsf KpsF-like protein. KpsF is an arabinose-5-phosphate isomerase which contains SIS (Sugar ISomerase) domains. SIS domains are found in many phosphosugar isomerases and phosphosugar binding proteins. KpsF catalyzes the reversible reaction of ribulose 5-phosphate to arabinose 5-phosphate. This is the second step in the CMP-Kdo biosynthesis pathway.
Probab=45.27 E-value=71 Score=30.41 Aligned_cols=48 Identities=17% Similarity=0.252 Sum_probs=34.8
Q ss_pred CcEEEEEeCC---cchHHHHHHHHhCCCEEEEecCCchhHHHHhhcceEEec
Q 001724 144 PAHLFLISGD---RDFASVLHRLRMNNYNILLASRESASNVLCSAASVMWNW 192 (1020)
Q Consensus 144 pdtFVLISGD---sDFtpLL~RLRerGynVILagp~kTpeaL~sAcd~Fw~w 192 (1020)
-|.+++||-- .+...+++.+|++|..|++++....+ .|...||..+.+
T Consensus 48 ~d~vi~iS~sG~t~~~~~~~~~a~~~g~~vi~iT~~~~s-~la~~ad~~l~~ 98 (128)
T cd05014 48 GDVVIAISNSGETDELLNLLPHLKRRGAPIIAITGNPNS-TLAKLSDVVLDL 98 (128)
T ss_pred CCEEEEEeCCCCCHHHHHHHHHHHHCCCeEEEEeCCCCC-chhhhCCEEEEC
Confidence 4667777644 36889999999999999988765443 455568866654
No 29
>PF13768 VWA_3: von Willebrand factor type A domain
Probab=45.25 E-value=1.3e+02 Score=29.60 Aligned_cols=45 Identities=22% Similarity=0.184 Sum_probs=33.2
Q ss_pred eEEEEEecCCCCCCCCCChhhHHHHHHHHHHHhCCCCceEEEEeeccc
Q 001724 51 RVSVWWDFENCNLPAGVNAFKVAHTITAAIRANGIKGPVTITAFGDVV 98 (1020)
Q Consensus 51 rVAVFWDiENcpiP~g~d~~~Va~nI~~aLrelG~~GpVtIRAYGDws 98 (1020)
+|.+++|.-.-.... . ..+...+..+|+.++..-.+.|-+||+-.
T Consensus 2 ~vvilvD~S~Sm~g~--~-~~~k~al~~~l~~L~~~d~fnii~f~~~~ 46 (155)
T PF13768_consen 2 DVVILVDTSGSMSGE--K-ELVKDALRAILRSLPPGDRFNIIAFGSSV 46 (155)
T ss_pred eEEEEEeCCCCCCCc--H-HHHHHHHHHHHHhCCCCCEEEEEEeCCEe
Confidence 588899987765422 2 45667888899998877778888898843
No 30
>cd07995 TPK Thiamine pyrophosphokinase. Thiamine pyrophosphokinase (TPK, EC:2.7.6.2, also spelled thiamin pyrophosphokinase) catalyzes the transfer of a pyrophosphate group from ATP to vitamin B1 (thiamine) to form the coenzyme thiamine pyrophosphate (TPP). TPP is required for central metabolic functions, and thiamine deficiency is associated with potentially fatal human diseases. The structure of thiamine pyrophosphokinase suggests that the enzyme may operate by a mechanism of pyrophosphoryl transfer similar to those described for pyrophosphokinases functioning in nucleotide biosynthesis.
Probab=45.14 E-value=1.3e+02 Score=32.04 Aligned_cols=79 Identities=22% Similarity=0.351 Sum_probs=55.8
Q ss_pred EEeecccccchhhHHHhhhcCCceeeccCCCccchhhHHHHHHHHHHHhCCCCcEEEEEeCC--c-c--hH--HHHHHHH
Q 001724 92 TAFGDVVQMSRANQEVLSSTGINIAHVPHGGKNSADRSLLVDLMYWVSQNPPPAHLFLISGD--R-D--FA--SVLHRLR 164 (1020)
Q Consensus 92 RAYGDws~~~k~~qe~L~ssGI~LihvP~ggKNAADi~LiIDaMd~a~~nP~pdtFVLISGD--s-D--Ft--pLL~RLR 164 (1020)
-+.||+.......++.+...|+.+++.|. .|+.||..+++. ++.... ++.++|+.+= + | ++ .+|.+.+
T Consensus 44 ~iiGDfDSi~~~~~~~~~~~~~~~~~~p~-~KD~TD~e~Al~---~~~~~~-~~~i~i~Ga~GgR~DH~lani~~l~~~~ 118 (208)
T cd07995 44 LIIGDFDSISPEVLEYYKSKGVEIIHFPD-EKDFTDFEKALK---LALERG-ADEIVILGATGGRLDHTLANLNLLLKYA 118 (208)
T ss_pred EEEecCcCCCHHHHHHHHhcCCeEEECCC-CCCCCHHHHHHH---HHHHcC-CCEEEEEccCCCcHHHHHHHHHHHHHHH
Confidence 78899999887777788888999999987 699999888765 555543 5666666433 3 4 22 3344444
Q ss_pred hCCCEEEEecC
Q 001724 165 MNNYNILLASR 175 (1020)
Q Consensus 165 erGynVILagp 175 (1020)
..+.+|+++..
T Consensus 119 ~~~~~~~l~d~ 129 (208)
T cd07995 119 KDGIKIVLIDE 129 (208)
T ss_pred hcCCeEEEEcC
Confidence 56788887765
No 31
>PF07283 TrbH: Conjugal transfer protein TrbH; InterPro: IPR010837 This entry represents TrbH, a bacterial conjugal transfer protein approximately 150 residues long. TrbH contains a putative membrane lipoprotein lipid attachment site [].
Probab=44.94 E-value=53 Score=33.10 Aligned_cols=51 Identities=20% Similarity=0.350 Sum_probs=38.0
Q ss_pred hhhHHHHHHHHHHHhCCCCc--EEEEEeCCc-chH-HHHHHHHhCCCEEEEecCC
Q 001724 126 ADRSLLVDLMYWVSQNPPPA--HLFLISGDR-DFA-SVLHRLRMNNYNILLASRE 176 (1020)
Q Consensus 126 ADi~LiIDaMd~a~~nP~pd--tFVLISGDs-DFt-pLL~RLRerGynVILagp~ 176 (1020)
.+..|.-||...+...-+|+ +|+|-=.|. .|. .|+..||.+||-|+-..+.
T Consensus 4 ~~~~iA~D~v~qL~~~ypPA~Tt~~L~q~~~d~Fg~aL~~~LR~~GYaV~e~~~~ 58 (121)
T PF07283_consen 4 DAQAIAGDMVSQLAEQYPPAKTTFELKQKDPDPFGQALENALRAKGYAVIEDDPP 58 (121)
T ss_pred HHHHHHHHHHHHHHHhcCCCccEEEEEcCCCChHHHHHHHHHHhcCcEEEecCCc
Confidence 46789999999887754444 488854554 475 7888999999999976554
No 32
>PRK11041 DNA-binding transcriptional regulator CytR; Provisional
Probab=44.39 E-value=1.2e+02 Score=32.61 Aligned_cols=97 Identities=12% Similarity=0.145 Sum_probs=51.0
Q ss_pred ChhhHHHHHHHHHHHhCCCCceEEEEeeccccc-c----hhhHHHhhhcCCceeec-cCCCccchhhHHHHHHH-HHHHh
Q 001724 68 NAFKVAHTITAAIRANGIKGPVTITAFGDVVQM-S----RANQEVLSSTGINIAHV-PHGGKNSADRSLLVDLM-YWVSQ 140 (1020)
Q Consensus 68 d~~~Va~nI~~aLrelG~~GpVtIRAYGDws~~-~----k~~qe~L~ssGI~Lihv-P~ggKNAADi~LiIDaM-d~a~~ 140 (1020)
|.+.....+-..|...| ++.|.+- -|..... . .++++.+...|+.+... ...+-...+. ..+++ .|+..
T Consensus 135 Dn~~~g~~a~~~l~~~G-~~~I~~l-~~~~~~~~~~~R~~Gf~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~l~~ 210 (309)
T PRK11041 135 DNLTAAFEAVNYLHELG-HKRIACI-AGPEEMPLCHYRLQGYVQALRRCGITVDPQYIARGDFTFEA--GAKALKQLLDL 210 (309)
T ss_pred CcHHHHHHHHHHHHHcC-CceEEEE-eCCccccchHHHHHHHHHHHHHcCCCCCHHHeEeCCCCHHH--HHHHHHHHHcC
Confidence 44444444444444455 3555442 1332211 1 35677888888875432 1111122221 22343 34444
Q ss_pred CCCCcEEEEEeCCcchHHHHHHHHhCCCE
Q 001724 141 NPPPAHLFLISGDRDFASVLHRLRMNNYN 169 (1020)
Q Consensus 141 nP~pdtFVLISGDsDFtpLL~RLRerGyn 169 (1020)
++.|++|+ +++|.-...++..|++.|+.
T Consensus 211 ~~~~~ai~-~~~d~~a~gv~~al~~~g~~ 238 (309)
T PRK11041 211 PQPPTAVF-CHSDVMALGALSQAKRMGLR 238 (309)
T ss_pred CCCCCEEE-EcCcHHHHHHHHHHHHcCCC
Confidence 55567655 56787777899999999974
No 33
>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=44.01 E-value=62 Score=33.89 Aligned_cols=67 Identities=10% Similarity=0.115 Sum_probs=42.9
Q ss_pred hHHHhhhcCCceeeccCCCccchhhHHHHHHHHHHHhCCCCcEEEEEeCCcc-hHHHHHHHHhCCCEEEEecC
Q 001724 104 NQEVLSSTGINIAHVPHGGKNSADRSLLVDLMYWVSQNPPPAHLFLISGDRD-FASVLHRLRMNNYNILLASR 175 (1020)
Q Consensus 104 ~qe~L~ssGI~LihvP~ggKNAADi~LiIDaMd~a~~nP~pdtFVLISGDsD-FtpLL~RLRerGynVILagp 175 (1020)
..+++...|+.+.-+.... |......+++.+... .+|+|++...|.+ ....+.+|+++|..|+++..
T Consensus 21 i~~~~~~~g~~~~~~~~~~----~~~~~~~~l~~~~~~-~vdgii~~~~~~~~~~~~i~~~~~~~ipvV~~~~ 88 (273)
T cd06305 21 TKAEAEALGGDLRVYDAGG----DDAKQADQIDQAIAQ-KVDAIIIQHGRAEVLKPWVKRALDAGIPVVAFDV 88 (273)
T ss_pred HHHHHHHcCCEEEEECCCC----CHHHHHHHHHHHHHc-CCCEEEEecCChhhhHHHHHHHHHcCCCEEEecC
Confidence 3445555666555443211 223445556555554 5999999987765 46778999999999887754
No 34
>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=43.56 E-value=60 Score=35.42 Aligned_cols=45 Identities=11% Similarity=0.062 Sum_probs=34.3
Q ss_pred HHHHHHHHHHhCCCCcEEEEEeCCcc-hHHHHHHHHhCCCEEEEecC
Q 001724 130 LLVDLMYWVSQNPPPAHLFLISGDRD-FASVLHRLRMNNYNILLASR 175 (1020)
Q Consensus 130 LiIDaMd~a~~nP~pdtFVLISGDsD-FtpLL~RLRerGynVILagp 175 (1020)
-.+.+++.+..+ .+++|+|+..|.+ +...+.+|++.|..|+++..
T Consensus 45 ~q~~~i~~l~~~-~vdgiii~~~~~~~~~~~~~~~~~~giPvV~~~~ 90 (303)
T cd01539 45 TQNEQIDTALAK-GVDLLAVNLVDPTAAQTVINKAKQKNIPVIFFNR 90 (303)
T ss_pred HHHHHHHHHHHc-CCCEEEEecCchhhHHHHHHHHHHCCCCEEEeCC
Confidence 445666666665 4999999888866 57888999999999987653
No 35
>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=42.98 E-value=2.8e+02 Score=29.21 Aligned_cols=77 Identities=10% Similarity=0.148 Sum_probs=45.9
Q ss_pred hhhHHHhhhc-CCceeeccCCCccchhhHHHHHHHHHHHhCCCCcEEEEEeCCcchHHHHHHHHhCCC--EEEEecCCch
Q 001724 102 RANQEVLSST-GINIAHVPHGGKNSADRSLLVDLMYWVSQNPPPAHLFLISGDRDFASVLHRLRMNNY--NILLASRESA 178 (1020)
Q Consensus 102 k~~qe~L~ss-GI~LihvP~ggKNAADi~LiIDaMd~a~~nP~pdtFVLISGDsDFtpLL~RLRerGy--nVILagp~kT 178 (1020)
.++++.|..+ |+.+.....+..+..+. ..-+-.++..++.++. ++..+|.-...+++.|+++|+ .|.+++-..+
T Consensus 142 ~g~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~l~~~~~~~a-i~~~~d~~a~~~~~al~~~g~~~di~vig~d~~ 218 (275)
T cd06320 142 EGFTEAIKKASGIEVVASQPADWDREKA--YDVATTILQRNPDLKA-IYCNNDTMALGVVEAVKNAGKQGKVLVVGTDGI 218 (275)
T ss_pred HHHHHHHhhCCCcEEEEecCCCccHHHH--HHHHHHHHHhCCCccE-EEECCchhHHHHHHHHHhcCCCCCeEEEecCCC
Confidence 3567788888 98876543322222221 1122234545565654 455677777788899999998 6666665555
Q ss_pred hHH
Q 001724 179 SNV 181 (1020)
Q Consensus 179 pea 181 (1020)
+..
T Consensus 219 ~~~ 221 (275)
T cd06320 219 PEA 221 (275)
T ss_pred HHH
Confidence 543
No 36
>PRK10703 DNA-binding transcriptional repressor PurR; Provisional
Probab=42.46 E-value=2.6e+02 Score=30.80 Aligned_cols=98 Identities=10% Similarity=0.046 Sum_probs=61.7
Q ss_pred HHHHHHHHHHHhCCCCce-----------EE-EEeeccccc-----chhhHHHhhhcCCceeeccCCCccchhhHHHHHH
Q 001724 72 VAHTITAAIRANGIKGPV-----------TI-TAFGDVVQM-----SRANQEVLSSTGINIAHVPHGGKNSADRSLLVDL 134 (1020)
Q Consensus 72 Va~nI~~aLrelG~~GpV-----------tI-RAYGDws~~-----~k~~qe~L~ssGI~LihvP~ggKNAADi~LiIDa 134 (1020)
....|.++++++||.... +| -+..++... -.+..+.+...|+.+.-++... |..-..++
T Consensus 32 tr~~V~~~a~elgY~pn~~a~~l~~~~~~~i~vi~~~~~~~~~~~~~~gi~~~~~~~g~~~~~~~~~~----~~~~~~~~ 107 (341)
T PRK10703 32 TRNAVWAAIKELHYSPSAVARSLKVNHTKSIGLLATSSEAPYFAEIIEAVEKNCYQKGYTLILCNAWN----NLEKQRAY 107 (341)
T ss_pred HHHHHHHHHHHHCCCcCHHHHHHhhCCCCeEEEEeCCCCCchHHHHHHHHHHHHHHCCCEEEEEeCCC----CHHHHHHH
Confidence 346788888999876631 22 222333321 1345667888999877765432 22234555
Q ss_pred HHHHHhCCCCcEEEEEeCCcchHHHHHHHHh-CCCEEEEecC
Q 001724 135 MYWVSQNPPPAHLFLISGDRDFASVLHRLRM-NNYNILLASR 175 (1020)
Q Consensus 135 Md~a~~nP~pdtFVLISGDsDFtpLL~RLRe-rGynVILagp 175 (1020)
++.+..+ .+++|+|...+. ....+.+|++ .|..|+++..
T Consensus 108 i~~l~~~-~vdgiii~~~~~-~~~~~~~l~~~~~iPvV~~d~ 147 (341)
T PRK10703 108 LSMLAQK-RVDGLLVMCSEY-PEPLLAMLEEYRHIPMVVMDW 147 (341)
T ss_pred HHHHHHc-CCCEEEEecCCC-CHHHHHHHHhcCCCCEEEEec
Confidence 5655554 489999877653 4467788888 7998887753
No 37
>PRK11302 DNA-binding transcriptional regulator HexR; Provisional
Probab=42.37 E-value=2.4e+02 Score=30.81 Aligned_cols=103 Identities=15% Similarity=0.145 Sum_probs=56.1
Q ss_pred HHHHHHHhCCCCceEEEEeeccccc--chhhHHHhhhcCCceeeccCCCccchhhHHHHHHHHHHHhCCCCcEEEEEeCC
Q 001724 76 ITAAIRANGIKGPVTITAFGDVVQM--SRANQEVLSSTGINIAHVPHGGKNSADRSLLVDLMYWVSQNPPPAHLFLISGD 153 (1020)
Q Consensus 76 I~~aLrelG~~GpVtIRAYGDws~~--~k~~qe~L~ssGI~LihvP~ggKNAADi~LiIDaMd~a~~nP~pdtFVLISGD 153 (1020)
|.++.+.+...++ |.+||--... .......|...|+...... |..+ ..+....-+ .=|.+++||--
T Consensus 118 i~~~~~~i~~a~~--I~i~G~G~S~~~a~~~~~~l~~~g~~~~~~~-------~~~~--~~~~~~~~~-~~D~vI~iS~s 185 (284)
T PRK11302 118 INRAVDLLTQAKK--ISFFGLGASAAVAHDAQNKFFRFNVPVVYFD-------DIVM--QRMSCMNSS-DGDVVVLISHT 185 (284)
T ss_pred HHHHHHHHHcCCe--EEEEEcchHHHHHHHHHHHHHhcCCceEecC-------CHHH--HHHHHHhCC-CCCEEEEEeCC
Confidence 4444444433344 4445443332 2334445667777655432 2211 111222222 24666666554
Q ss_pred c---chHHHHHHHHhCCCEEEEecCCchhHHHHhhcceEEec
Q 001724 154 R---DFASVLHRLRMNNYNILLASRESASNVLCSAASVMWNW 192 (1020)
Q Consensus 154 s---DFtpLL~RLRerGynVILagp~kTpeaL~sAcd~Fw~w 192 (1020)
+ +...++...|++|..|++++.. . ..+...||..+..
T Consensus 186 G~t~~~~~~~~~ak~~g~~vI~IT~~-~-s~l~~~ad~~l~~ 225 (284)
T PRK11302 186 GRTKSLVELAQLARENGATVIAITSA-G-SPLAREATLALTL 225 (284)
T ss_pred CCCHHHHHHHHHHHHcCCeEEEECCC-C-ChhHHhCCEEEec
Confidence 4 5667888889999999999853 2 3477778876653
No 38
>PRK10401 DNA-binding transcriptional regulator GalS; Provisional
Probab=42.17 E-value=1.2e+02 Score=33.49 Aligned_cols=65 Identities=20% Similarity=0.123 Sum_probs=37.9
Q ss_pred hhhHHHhhhcCCceee--ccCCCccchhhHHHHHHH-HHHHhCCCCcEEEEEeCCcchHHHHHHHHhCCCEE
Q 001724 102 RANQEVLSSTGINIAH--VPHGGKNSADRSLLVDLM-YWVSQNPPPAHLFLISGDRDFASVLHRLRMNNYNI 170 (1020)
Q Consensus 102 k~~qe~L~ssGI~Lih--vP~ggKNAADi~LiIDaM-d~a~~nP~pdtFVLISGDsDFtpLL~RLRerGynV 170 (1020)
.++++.|..+|+.+.. +..+ .. +..-..+++ .|+..++.|+. +++.+|.--..++..|+++|++|
T Consensus 196 ~Gf~~al~~~gi~~~~~~~~~~-~~--~~~~~~~~~~~~l~~~~~~~a-i~~~nd~~A~g~~~al~~~G~~v 263 (346)
T PRK10401 196 AGWMSALKEQGIIPPESWIGTG-TP--DMQGGEAAMVELLGRNLQLTA-VFAYNDNMAAGALTALKDNGIAI 263 (346)
T ss_pred HHHHHHHHHcCCCCChhheecC-CC--ChHHHHHHHHHHHcCCCCCcE-EEECCcHHHHHHHHHHHHcCCCC
Confidence 3578889999986532 2221 11 111112333 44444555664 44567776678999999999853
No 39
>PRK10653 D-ribose transporter subunit RbsB; Provisional
Probab=41.99 E-value=4.4e+02 Score=28.52 Aligned_cols=76 Identities=8% Similarity=0.172 Sum_probs=46.3
Q ss_pred hhhHHHhhhcCCceeeccCCCccchhhHHHHHHH-HHHHhCCCCcEEEEEeCCcchHHHHHHHHhCCC-EEEEecCCchh
Q 001724 102 RANQEVLSSTGINIAHVPHGGKNSADRSLLVDLM-YWVSQNPPPAHLFLISGDRDFASVLHRLRMNNY-NILLASRESAS 179 (1020)
Q Consensus 102 k~~qe~L~ssGI~LihvP~ggKNAADi~LiIDaM-d~a~~nP~pdtFVLISGDsDFtpLL~RLRerGy-nVILagp~kTp 179 (1020)
.++++.|...|+.+.......-+..+ ..+++ .++..+|.| ..++..+|.--..+++.|+++|+ .|-+++-..++
T Consensus 168 ~gf~~al~~~g~~~~~~~~~~~~~~~---~~~~~~~~l~~~~~~-~ai~~~~d~~A~g~l~al~~~G~~dv~vig~d~~~ 243 (295)
T PRK10653 168 EGFKQAVAAHKFNVLASQPADFDRTK---GLNVMQNLLTAHPDV-QAVFAQNDEMALGALRALQTAGKSDVMVVGFDGTP 243 (295)
T ss_pred HHHHHHHhhCCCEEEEecCCCCCHHH---HHHHHHHHHHhCCCc-CEEEECCChhHHHHHHHHHHcCCCceEEEEeCCCH
Confidence 35788899999876543222111111 23333 455455544 44666777766788999999997 67776655555
Q ss_pred HH
Q 001724 180 NV 181 (1020)
Q Consensus 180 ea 181 (1020)
.+
T Consensus 244 ~~ 245 (295)
T PRK10653 244 DG 245 (295)
T ss_pred HH
Confidence 44
No 40
>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=41.38 E-value=3.5e+02 Score=28.27 Aligned_cols=76 Identities=17% Similarity=0.196 Sum_probs=46.1
Q ss_pred hhhHHHhhhc-CCceeeccCCCccchhhHHHHHHHHHHHhCCCCcEEEEEeCCcchHHHHHHHHhCCC-EEEEecCCchh
Q 001724 102 RANQEVLSST-GINIAHVPHGGKNSADRSLLVDLMYWVSQNPPPAHLFLISGDRDFASVLHRLRMNNY-NILLASRESAS 179 (1020)
Q Consensus 102 k~~qe~L~ss-GI~LihvP~ggKNAADi~LiIDaMd~a~~nP~pdtFVLISGDsDFtpLL~RLRerGy-nVILagp~kTp 179 (1020)
.++++.|..+ |+.+....... + .+. ..--+.+|+..+|.++ .+++.+|.-...++..|+++|+ .|.+++-..++
T Consensus 140 ~gf~~~~~~~~~~~~~~~~~~~-~-~~~-~~~~~~~~l~~~~~~~-ai~~~~d~~a~~~~~al~~~g~~di~vvg~d~~~ 215 (267)
T cd06322 140 RGFKEALADYPNIKIVAVQPGI-T-RAE-ALTAAQNILQANPDLD-GIFAFGDDAALGAVSAIKAAGRDNVKVIGFDGMP 215 (267)
T ss_pred HHHHHHHHhCCCcEEEEecCCC-C-hHH-HHHHHHHHHHhCCCCC-EEEEcCCcHHHHHHHHHHHCCCCCeEEEEecCCH
Confidence 3567788888 88876543321 1 121 1112334555566565 5666777777889999999997 55555544444
Q ss_pred HH
Q 001724 180 NV 181 (1020)
Q Consensus 180 ea 181 (1020)
..
T Consensus 216 ~~ 217 (267)
T cd06322 216 EA 217 (267)
T ss_pred HH
Confidence 33
No 41
>PRK10997 yieM hypothetical protein; Provisional
Probab=41.10 E-value=7.2e+02 Score=30.67 Aligned_cols=142 Identities=13% Similarity=0.094 Sum_probs=73.2
Q ss_pred cccCCCeEEEEEecCCCCCCCCCChhhHHHHHHHHHHHhC--CCCceEEEEeeccccc-----chhhHHHhhhcCCceee
Q 001724 45 EESKNVRVSVWWDFENCNLPAGVNAFKVAHTITAAIRANG--IKGPVTITAFGDVVQM-----SRANQEVLSSTGINIAH 117 (1020)
Q Consensus 45 ~es~~~rVAVFWDiENcpiP~g~d~~~Va~nI~~aLrelG--~~GpVtIRAYGDws~~-----~k~~qe~L~ssGI~Lih 117 (1020)
.+.....|.|++|.-.--- |. ...++..+-.+|-.+. ..-.+.+.+|++-... ..+..+.+.... .
T Consensus 319 ~~~~kGpiII~VDtSGSM~--G~-ke~~AkalAaAL~~iAl~q~dr~~li~Fs~~i~~~~l~~~~gl~~ll~fL~----~ 391 (487)
T PRK10997 319 DEQPRGPFIVCVDTSGSMG--GF-NEQCAKAFCLALMRIALAENRRCYIMLFSTEVVTYELTGPDGLEQAIRFLS----Q 391 (487)
T ss_pred cCCCCCcEEEEEECCCCCC--CC-HHHHHHHHHHHHHHHHHhcCCCEEEEEecCCceeeccCCccCHHHHHHHHH----H
Confidence 3455678999999876553 32 2233334333333321 1234455666552221 112222222211 1
Q ss_pred ccCCCccchhhHHHHH-HHHHHHhCCCCcEEEEEeCCcc-------hHHHHHHHHh-CCCEEEEecCC--chhHHHHhhc
Q 001724 118 VPHGGKNSADRSLLVD-LMYWVSQNPPPAHLFLISGDRD-------FASVLHRLRM-NNYNILLASRE--SASNVLCSAA 186 (1020)
Q Consensus 118 vP~ggKNAADi~LiID-aMd~a~~nP~pdtFVLISGDsD-------FtpLL~RLRe-rGynVILagp~--kTpeaL~sAc 186 (1020)
.+.|| ||+.=++. ++..+.....-.+.+||-+|-. +...+.+|++ +|..++++.=+ ..|. +...|
T Consensus 392 ~f~GG---TDl~~aL~~al~~l~~~~~r~adIVVISDF~~~~~~eel~~~L~~Lk~~~~~rf~~l~i~~~~~p~-l~~if 467 (487)
T PRK10997 392 SFRGG---TDLAPCLRAIIEKMQGREWFDADAVVISDFIAQRLPDELVAKVKELQRQHQHRFHAVAMSAHGKPG-IMRIF 467 (487)
T ss_pred hcCCC---CcHHHHHHHHHHHHcccccCCceEEEECCCCCCCChHHHHHHHHHHHHhcCcEEEEEEeCCCCCch-HHHhc
Confidence 22344 45444333 5555544322345566666642 4566778877 78888854322 3444 56889
Q ss_pred ceEEeccchhh
Q 001724 187 SVMWNWDSLLR 197 (1020)
Q Consensus 187 d~Fw~wesLl~ 197 (1020)
|..|.++.=+.
T Consensus 468 D~~W~~d~~~~ 478 (487)
T PRK10997 468 DHIWRFDTGLR 478 (487)
T ss_pred CeeeEecCCch
Confidence 99999885443
No 42
>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=41.03 E-value=1e+02 Score=32.59 Aligned_cols=68 Identities=9% Similarity=0.144 Sum_probs=47.9
Q ss_pred hhHHHhhhcCCceeeccCCCccchhhHHHHHHHHHHHhCCCCcEEEEEeCCcc-hHHHHHHHHhCCCEEEEecC
Q 001724 103 ANQEVLSSTGINIAHVPHGGKNSADRSLLVDLMYWVSQNPPPAHLFLISGDRD-FASVLHRLRMNNYNILLASR 175 (1020)
Q Consensus 103 ~~qe~L~ssGI~LihvP~ggKNAADi~LiIDaMd~a~~nP~pdtFVLISGDsD-FtpLL~RLRerGynVILagp 175 (1020)
...+.+...|++++.+.... |.....+++..+... .+++++|...+.+ +.+.+..|+++|..|+++..
T Consensus 20 ~~~~~a~~~g~~~~~~~~~~----~~~~~~~~i~~l~~~-~vdgiIi~~~~~~~~~~~i~~~~~~~iPvV~~~~ 88 (273)
T cd06309 20 SIKDAAEKRGFDLKFADAQQ----KQENQISAIRSFIAQ-GVDVIILAPVVETGWDPVLKEAKAAGIPVILVDR 88 (273)
T ss_pred HHHHHHHhcCCEEEEeCCCC----CHHHHHHHHHHHHHc-CCCEEEEcCCccccchHHHHHHHHCCCCEEEEec
Confidence 45566777888877765432 233445666666654 4899999877765 57888999999999987764
No 43
>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=39.85 E-value=77 Score=34.08 Aligned_cols=68 Identities=12% Similarity=0.158 Sum_probs=44.7
Q ss_pred hHHHhhhcCCceeeccCCCccchhhHHHHHHHHHHHhCCCCcEEEEEeCCcc-hHHHHHHHHhCCCEEEEecC
Q 001724 104 NQEVLSSTGINIAHVPHGGKNSADRSLLVDLMYWVSQNPPPAHLFLISGDRD-FASVLHRLRMNNYNILLASR 175 (1020)
Q Consensus 104 ~qe~L~ssGI~LihvP~ggKNAADi~LiIDaMd~a~~nP~pdtFVLISGDsD-FtpLL~RLRerGynVILagp 175 (1020)
..+++...|+.++.+..+ .+ +....++++..+..+ .+++|+|...|.+ ....+..|+++|..|+++..
T Consensus 21 i~~~a~~~g~~~~~~~~~-~~--~~~~~~~~l~~~~~~-~~dgiii~~~~~~~~~~~i~~~~~~~iPvV~~~~ 89 (294)
T cd06316 21 AKDEFAKLGIEVVATTDA-QF--DPAKQVADIETTISQ-KPDIIISIPVDPVSTAAAYKKVAEAGIKLVFMDN 89 (294)
T ss_pred HHHHHHHcCCEEEEecCC-CC--CHHHHHHHHHHHHHh-CCCEEEEcCCCchhhhHHHHHHHHcCCcEEEecC
Confidence 445566777776643221 11 223455666666655 4899999887765 46788999999999987753
No 44
>cd01453 vWA_transcription_factor_IIH_type Transcription factors IIH type: TFIIH is a multiprotein complex that is one of the five general transcription factors that binds RNA polymerase II holoenzyme. Orthologues of these genes are found in all completed eukaryotic genomes and all these proteins contain a VWA domain. The p44 subunit of TFIIH functions as a DNA helicase in RNA polymerase II transcription initiation and DNA repair, and its transcriptional activity is dependent on its C-terminal Zn-binding domains. The function of the vWA domain is unclear, but may be involved in complex assembly. The MIDAS motif is not conserved in this sub-group.
Probab=39.42 E-value=2.7e+02 Score=29.07 Aligned_cols=129 Identities=9% Similarity=0.107 Sum_probs=59.0
Q ss_pred eEEEEEecCCCCCCCCCChhhH---HHHHHHHHHHh---CCCCceEEEEe-eccccc--c--hh---hHHHhhhcCCcee
Q 001724 51 RVSVWWDFENCNLPAGVNAFKV---AHTITAAIRAN---GIKGPVTITAF-GDVVQM--S--RA---NQEVLSSTGINIA 116 (1020)
Q Consensus 51 rVAVFWDiENcpiP~g~d~~~V---a~nI~~aLrel---G~~GpVtIRAY-GDws~~--~--k~---~qe~L~ssGI~Li 116 (1020)
.+.|.+|.-+--.-.++.+.++ ...+..+++.. ...++|-+.+| +.-... + .+ +...|.. .
T Consensus 5 ~ivi~lD~S~SM~a~D~~ptRl~~ak~~~~~fi~~~~~~~~~~~vglv~f~~~~a~~~~PlT~D~~~~~~~L~~-----~ 79 (183)
T cd01453 5 HLIIVIDCSRSMEEQDLKPSRLAVVLKLLELFIEEFFDQNPISQLGIISIKNGRAEKLTDLTGNPRKHIQALKT-----A 79 (183)
T ss_pred EEEEEEECcHHHhcCCCCchHHHHHHHHHHHHHHHHhhcCccccEEEEEEcCCccEEEECCCCCHHHHHHHhhc-----c
Confidence 4677777766544344444433 23444444432 23356777777 342221 1 11 2333322 1
Q ss_pred eccCCCccchhhHHHHHHHHHHHhCCC--CcEEEEEeCC-c-----chHHHHHHHHhCCCEEEEecCCchhHHHHhhc
Q 001724 117 HVPHGGKNSADRSLLVDLMYWVSQNPP--PAHLFLISGD-R-----DFASVLHRLRMNNYNILLASRESASNVLCSAA 186 (1020)
Q Consensus 117 hvP~ggKNAADi~LiIDaMd~a~~nP~--pdtFVLISGD-s-----DFtpLL~RLRerGynVILagp~kTpeaL~sAc 186 (1020)
-.+.++.+-.+ +|. .++..+...+. .-.++|+.+| . ++..++..|++.|..|+.++=+.....|...|
T Consensus 80 ~~~~G~t~l~~-aL~-~A~~~l~~~~~~~~~~iiil~sd~~~~~~~~~~~~~~~l~~~~I~v~~IgiG~~~~~L~~ia 155 (183)
T cd01453 80 RECSGEPSLQN-GLE-MALESLKHMPSHGSREVLIIFSSLSTCDPGNIYETIDKLKKENIRVSVIGLSAEMHICKEIC 155 (183)
T ss_pred cCCCCchhHHH-HHH-HHHHHHhcCCccCceEEEEEEcCCCcCChhhHHHHHHHHHHcCcEEEEEEechHHHHHHHHH
Confidence 12333333322 222 22233322121 2235555444 2 35568889999998887543333333444433
No 45
>cd05006 SIS_GmhA Phosphoheptose isomerase is a member of the SIS (Sugar ISomerase) superfamily. Phosphoheptose isomerase catalyzes the isomerization of sedoheptulose 7-phosphate into D-glycero-D-mannoheptose 7-phosphate. This is the first step of the biosynthesis of gram-negative bacteria inner core lipopolysaccharide precursor, L-glycero-D-mannoheptose (Gmh).
Probab=39.03 E-value=3.4e+02 Score=27.84 Aligned_cols=48 Identities=13% Similarity=0.071 Sum_probs=34.1
Q ss_pred CcEEEEEeCCc---chHHHHHHHHhCCCEEEEecCCchhHHHHhhcceEEec
Q 001724 144 PAHLFLISGDR---DFASVLHRLRMNNYNILLASRESASNVLCSAASVMWNW 192 (1020)
Q Consensus 144 pdtFVLISGDs---DFtpLL~RLRerGynVILagp~kTpeaL~sAcd~Fw~w 192 (1020)
-|.+++||.-+ +-..++..++++|..||+++....+ .|...||..+..
T Consensus 102 ~Dv~I~iS~SG~t~~~i~~~~~ak~~Ga~vI~IT~~~~s-~La~~aD~~l~~ 152 (177)
T cd05006 102 GDVLIGISTSGNSPNVLKALEAAKERGMKTIALTGRDGG-KLLELADIEIHV 152 (177)
T ss_pred CCEEEEEeCCCCCHHHHHHHHHHHHCCCEEEEEeCCCCC-chhhhCCEEEEe
Confidence 46677776432 5678889999999999988754333 277778876653
No 46
>PRK11337 DNA-binding transcriptional repressor RpiR; Provisional
Probab=38.79 E-value=2.9e+02 Score=30.48 Aligned_cols=105 Identities=12% Similarity=0.092 Sum_probs=58.0
Q ss_pred HHHHHHHhCCCCceEEEEeecccccchhhHHHhhhcCCceeeccCCCccchhhHHHHHHHHHHHhCCCCcEEEEEeCCc-
Q 001724 76 ITAAIRANGIKGPVTITAFGDVVQMSRANQEVLSSTGINIAHVPHGGKNSADRSLLVDLMYWVSQNPPPAHLFLISGDR- 154 (1020)
Q Consensus 76 I~~aLrelG~~GpVtIRAYGDws~~~k~~qe~L~ssGI~LihvP~ggKNAADi~LiIDaMd~a~~nP~pdtFVLISGDs- 154 (1020)
|.++.+.+..-.+|-|-++|.-......+...|...|+....+. |..+..... ..- .+-|.+++||--+
T Consensus 130 l~~~~~~i~~A~~I~i~G~G~S~~~A~~l~~~l~~~g~~~~~~~-------d~~~~~~~~--~~~-~~~Dl~I~iS~sG~ 199 (292)
T PRK11337 130 FHRAARFFYQARQRDLYGAGGSAAIARDVQHKFLRIGVRCQAYD-------DAHIMLMSA--ALL-QEGDVVLVVSHSGR 199 (292)
T ss_pred HHHHHHHHHcCCeEEEEEecHHHHHHHHHHHHHhhCCCeEEEcC-------CHHHHHHHH--hcC-CCCCEEEEEeCCCC
Confidence 33444444333444445555432233445566777887655432 222322111 111 2356677776553
Q ss_pred --chHHHHHHHHhCCCEEEEecCCchhHHHHhhcceEEe
Q 001724 155 --DFASVLHRLRMNNYNILLASRESASNVLCSAASVMWN 191 (1020)
Q Consensus 155 --DFtpLL~RLRerGynVILagp~kTpeaL~sAcd~Fw~ 191 (1020)
+...++..++++|..|++++....+ .+...||..+.
T Consensus 200 t~~~~~~~~~ak~~g~~ii~IT~~~~s-~la~~ad~~l~ 237 (292)
T PRK11337 200 TSDVIEAVELAKKNGAKIICITNSYHS-PIAKLADYVIC 237 (292)
T ss_pred CHHHHHHHHHHHHCCCeEEEEeCCCCC-hhHHhCCEEEE
Confidence 5678888889999999998865444 34456776664
No 47
>PRK11557 putative DNA-binding transcriptional regulator; Provisional
Probab=38.19 E-value=2.3e+02 Score=31.05 Aligned_cols=105 Identities=15% Similarity=0.091 Sum_probs=58.2
Q ss_pred HHHHHHHhCCCCceEEEEeecccccchhhHHHhhhcCCceeeccCCCccchhhHHHHHHHHHHHhCCCCcEEEEEeCCc-
Q 001724 76 ITAAIRANGIKGPVTITAFGDVVQMSRANQEVLSSTGINIAHVPHGGKNSADRSLLVDLMYWVSQNPPPAHLFLISGDR- 154 (1020)
Q Consensus 76 I~~aLrelG~~GpVtIRAYGDws~~~k~~qe~L~ssGI~LihvP~ggKNAADi~LiIDaMd~a~~nP~pdtFVLISGDs- 154 (1020)
|.++.+.+..-++|-|-+.|.-......+...|...|+..... .|..+...++..+ .+-|.+++||--+
T Consensus 118 l~~~~~~i~~a~~I~i~G~G~s~~~A~~~~~~l~~~g~~~~~~-------~d~~~~~~~~~~~---~~~Dv~I~iS~sg~ 187 (278)
T PRK11557 118 LHECVTMLRSARRIILTGIGASGLVAQNFAWKLMKIGINAVAE-------RDMHALLATVQAL---SPDDLLLAISYSGE 187 (278)
T ss_pred HHHHHHHHhcCCeEEEEecChhHHHHHHHHHHHhhCCCeEEEc-------CChHHHHHHHHhC---CCCCEEEEEcCCCC
Confidence 4444444433445444555532223344566777888765442 1222333332222 3457777776554
Q ss_pred --chHHHHHHHHhCCCEEEEecCCchhHHHHhhcceEEe
Q 001724 155 --DFASVLHRLRMNNYNILLASRESASNVLCSAASVMWN 191 (1020)
Q Consensus 155 --DFtpLL~RLRerGynVILagp~kTpeaL~sAcd~Fw~ 191 (1020)
+...++..+|++|..||+++....+. +...||..++
T Consensus 188 ~~~~~~~~~~ak~~ga~iI~IT~~~~s~-la~~ad~~l~ 225 (278)
T PRK11557 188 RRELNLAADEALRVGAKVLAITGFTPNA-LQQRASHCLY 225 (278)
T ss_pred CHHHHHHHHHHHHcCCCEEEEcCCCCCc-hHHhCCEEEE
Confidence 34577888899999999998654443 3335675554
No 48
>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=38.16 E-value=84 Score=33.00 Aligned_cols=69 Identities=13% Similarity=0.205 Sum_probs=43.2
Q ss_pred hHHHhhhcCCceeeccCCCccchhhHHHHHHHHHHHhCCCCcEEEEEeCCcc-hHHHHHHHHhCCCEEEEecC
Q 001724 104 NQEVLSSTGINIAHVPHGGKNSADRSLLVDLMYWVSQNPPPAHLFLISGDRD-FASVLHRLRMNNYNILLASR 175 (1020)
Q Consensus 104 ~qe~L~ssGI~LihvP~ggKNAADi~LiIDaMd~a~~nP~pdtFVLISGDsD-FtpLL~RLRerGynVILagp 175 (1020)
..+.+...|+.+..+.....+ |..-..++++.+..+ .+++++|++.+.+ ....+.+|+..|..|+++..
T Consensus 21 ~~~~~~~~g~~~~~~~~~~~~--~~~~~~~~i~~l~~~-~vdgvii~~~~~~~~~~~l~~~~~~~ipvV~~~~ 90 (273)
T cd06310 21 AEAAAKELGVKVTFQGPASET--DVAGQVNLLENAIAR-GPDAILLAPTDAKALVPPLKEAKDAGIPVVLIDS 90 (273)
T ss_pred HHHHHHHcCCEEEEecCccCC--CHHHHHHHHHHHHHh-CCCEEEEcCCChhhhHHHHHHHHHCCCCEEEecC
Confidence 344455566665554321111 223445666666654 5999999877643 35688999999998887753
No 49
>cd05005 SIS_PHI Hexulose-6-phosphate isomerase (PHI). PHI is a member of the SIS (Sugar ISomerase domain) superfamily. In the ribulose monophosphate pathway of formaldehyde fixation, hexulose-6-phosphate synthase catalyzes the condensation of ribulose-5-phosphate with formadelhyde to become hexulose-6-phosphate, which is then isomerized to fructose-6-phosphate by PHI.
Probab=37.24 E-value=2.5e+02 Score=28.80 Aligned_cols=100 Identities=18% Similarity=0.151 Sum_probs=56.3
Q ss_pred HHHHHHHhCCCCceEEEEeecccccchhhHHHhhhcCCceeeccCCCccchhhHHHHHHHHHHHhCCCCcEEEEEeCCc-
Q 001724 76 ITAAIRANGIKGPVTITAFGDVVQMSRANQEVLSSTGINIAHVPHGGKNSADRSLLVDLMYWVSQNPPPAHLFLISGDR- 154 (1020)
Q Consensus 76 I~~aLrelG~~GpVtIRAYGDws~~~k~~qe~L~ssGI~LihvP~ggKNAADi~LiIDaMd~a~~nP~pdtFVLISGDs- 154 (1020)
|+++.+.+..-++|-|-+.|.-..........|...|+..+.+.... +..-.+-|.+++||-.+
T Consensus 23 l~~~~~~i~~a~~I~i~G~G~S~~~A~~~~~~l~~~g~~~~~~~~~~---------------~~~~~~~D~vI~iS~sG~ 87 (179)
T cd05005 23 LDKLISAILNAKRIFVYGAGRSGLVAKAFAMRLMHLGLNVYVVGETT---------------TPAIGPGDLLIAISGSGE 87 (179)
T ss_pred HHHHHHHHHhCCeEEEEecChhHHHHHHHHHHHHhCCCeEEEeCCCC---------------CCCCCCCCEEEEEcCCCC
Confidence 44444444333554444444332223445556777888766653210 11112356677776553
Q ss_pred --chHHHHHHHHhCCCEEEEecCCchhHHHHhhcceEEe
Q 001724 155 --DFASVLHRLRMNNYNILLASRESASNVLCSAASVMWN 191 (1020)
Q Consensus 155 --DFtpLL~RLRerGynVILagp~kTpeaL~sAcd~Fw~ 191 (1020)
+...++..+|++|..|++++....+ .|...||..+.
T Consensus 88 t~~~i~~~~~ak~~g~~iI~IT~~~~s-~la~~ad~~l~ 125 (179)
T cd05005 88 TSSVVNAAEKAKKAGAKVVLITSNPDS-PLAKLADVVVV 125 (179)
T ss_pred cHHHHHHHHHHHHCCCeEEEEECCCCC-chHHhCCEEEE
Confidence 5677888899999999988754333 45556776655
No 50
>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=37.10 E-value=1e+02 Score=32.64 Aligned_cols=68 Identities=10% Similarity=0.138 Sum_probs=45.4
Q ss_pred hHHHhhhcCCceeeccCCCccchhhHHHHHHHHHHHhCCCCcEEEEEeCCcc-hHHHHHHHHhCCCEEEEecC
Q 001724 104 NQEVLSSTGINIAHVPHGGKNSADRSLLVDLMYWVSQNPPPAHLFLISGDRD-FASVLHRLRMNNYNILLASR 175 (1020)
Q Consensus 104 ~qe~L~ssGI~LihvP~ggKNAADi~LiIDaMd~a~~nP~pdtFVLISGDsD-FtpLL~RLRerGynVILagp 175 (1020)
+.+++...|+.+.-+.... .|..-.+++++.+... .+++++|+..+.+ +...+..++++|..|+++..
T Consensus 22 ~~~~~~~~g~~v~~~~~~~---~~~~~~~~~i~~l~~~-~vdgiii~~~~~~~~~~~l~~~~~~~ipvV~~~~ 90 (271)
T cd06312 22 AEDAAKDLGVDVEYRGPET---FDVADMARLIEAAIAA-KPDGIVVTIPDPDALDPAIKRAVAAGIPVISFNA 90 (271)
T ss_pred HHHHHHHhCCEEEEECCCC---CCHHHHHHHHHHHHHh-CCCEEEEeCCChHHhHHHHHHHHHCCCeEEEeCC
Confidence 4455556666665544322 1233445666666665 5999999987765 56788999999999988754
No 51
>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=36.83 E-value=4.2e+02 Score=27.25 Aligned_cols=76 Identities=13% Similarity=0.214 Sum_probs=43.9
Q ss_pred hhhHHHhhhc-CCceeeccCCCccchhhHHHHHHHHHHHhCCCCcEEEEEeCCcchHHHHHHHHhCCC--EEEEecCCch
Q 001724 102 RANQEVLSST-GINIAHVPHGGKNSADRSLLVDLMYWVSQNPPPAHLFLISGDRDFASVLHRLRMNNY--NILLASRESA 178 (1020)
Q Consensus 102 k~~qe~L~ss-GI~LihvP~ggKNAADi~LiIDaMd~a~~nP~pdtFVLISGDsDFtpLL~RLRerGy--nVILagp~kT 178 (1020)
..+++.+..+ |+.+..+....-...+ ..--+..|+..+|.++ .+++.+|.....+++.|+++|+ +|-+++-..+
T Consensus 141 ~gf~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~-~i~~~~d~~a~~~~~~l~~~g~~~~i~ivg~d~~ 217 (267)
T cd01536 141 KGFRDALKEYPDIEIVAVQDGNWDREK--ALQAMEDLLQANPDID-AIFAANDSMALGAVAALKAAGRKGDVKIVGVDGS 217 (267)
T ss_pred HHHHHHHHhCCCcEEEEEecCCCcHHH--HHHHHHHHHHhCCCcc-EEEEecCCchHHHHHHHHhcCCCCCceEEecCCC
Confidence 3567788888 4765543222222222 2222344555566554 5666777777788899999997 5555544444
Q ss_pred hH
Q 001724 179 SN 180 (1020)
Q Consensus 179 pe 180 (1020)
+.
T Consensus 218 ~~ 219 (267)
T cd01536 218 PE 219 (267)
T ss_pred hh
Confidence 43
No 52
>TIGR03127 RuMP_HxlB 6-phospho 3-hexuloisomerase. Members of this protein family are 6-phospho 3-hexuloisomerase (PHI), or the PHI domain of a fusion protein. This enzyme is part of the ribulose monophosphate (RuMP) pathway, which in one direction removes the toxic metabolite formaldehyde by assimilation into fructose-6-phosphate. In the other direction, in species lacking a complete pentose phosphate pathway, the RuMP pathway yields ribulose-5-phosphate, necessary for nucleotide biosynthesis, at the cost of also yielding formaldehyde. These latter species tend usually have a formaldehyde-activating enzyme to attach formaldehyde to the C1 carrier tetrahydromethanopterin.
Probab=36.74 E-value=2.2e+02 Score=29.15 Aligned_cols=100 Identities=15% Similarity=0.096 Sum_probs=57.0
Q ss_pred HHHHHHHhCCCCceEEEEeecccccchhhHHHhhhcCCceeeccCCCccchhhHHHHHHHHHHHhCCCCcEEEEEeCCc-
Q 001724 76 ITAAIRANGIKGPVTITAFGDVVQMSRANQEVLSSTGINIAHVPHGGKNSADRSLLVDLMYWVSQNPPPAHLFLISGDR- 154 (1020)
Q Consensus 76 I~~aLrelG~~GpVtIRAYGDws~~~k~~qe~L~ssGI~LihvP~ggKNAADi~LiIDaMd~a~~nP~pdtFVLISGDs- 154 (1020)
|.++.+.+...++|-|-+.|.-......+...|...|+......... ...-.+-|.+++||--+
T Consensus 20 ~~~~~~~l~~a~~I~i~G~G~S~~~A~~~~~~l~~~g~~~~~~~~~~---------------~~~~~~~Dv~I~iS~sG~ 84 (179)
T TIGR03127 20 LDKLADKIIKAKRIFVAGAGRSGLVGKAFAMRLMHLGFNVYVVGETT---------------TPSIKKGDLLIAISGSGE 84 (179)
T ss_pred HHHHHHHHHhCCEEEEEecCHHHHHHHHHHHHHHhCCCeEEEeCCcc---------------cCCCCCCCEEEEEeCCCC
Confidence 44444444334554444444322223445666777887666543210 01112346677777543
Q ss_pred --chHHHHHHHHhCCCEEEEecCCchhHHHHhhcceEEe
Q 001724 155 --DFASVLHRLRMNNYNILLASRESASNVLCSAASVMWN 191 (1020)
Q Consensus 155 --DFtpLL~RLRerGynVILagp~kTpeaL~sAcd~Fw~ 191 (1020)
+-..++..++++|..|++++....+ .+...||..+.
T Consensus 85 t~~~i~~~~~ak~~g~~ii~IT~~~~s-~la~~ad~~l~ 122 (179)
T TIGR03127 85 TESLVTVAKKAKEIGATVAAITTNPES-TLGKLADVVVE 122 (179)
T ss_pred cHHHHHHHHHHHHCCCeEEEEECCCCC-chHHhCCEEEE
Confidence 5667888899999999998765443 34556776554
No 53
>cd01477 vWA_F09G8-8_type VWA F09G8.8 type: 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 mo
Probab=36.51 E-value=4.5e+02 Score=27.90 Aligned_cols=121 Identities=11% Similarity=0.105 Sum_probs=63.0
Q ss_pred CCCeEEEEEecCCCCCCCCCChhhHHHHHHHHHHHhCCC---------CceEEEEeecccccch---------hhHHHhh
Q 001724 48 KNVRVSVWWDFENCNLPAGVNAFKVAHTITAAIRANGIK---------GPVTITAFGDVVQMSR---------ANQEVLS 109 (1020)
Q Consensus 48 ~~~rVAVFWDiENcpiP~g~d~~~Va~nI~~aLrelG~~---------GpVtIRAYGDws~~~k---------~~qe~L~ 109 (1020)
....|.+++|.-+.--+.+ ...+...|..++..+..- -+|-+-.|++...... ....++.
T Consensus 18 ~~~DivfvlD~S~Sm~~~~--f~~~k~fi~~~~~~~~~~~~~~~~~~~~rVGlV~fs~~a~~~~~L~d~~~~~~~~~ai~ 95 (193)
T cd01477 18 LWLDIVFVVDNSKGMTQGG--LWQVRATISSLFGSSSQIGTDYDDPRSTRVGLVTYNSNATVVADLNDLQSFDDLYSQIQ 95 (193)
T ss_pred ceeeEEEEEeCCCCcchhh--HHHHHHHHHHHHhhccccccccCCCCCcEEEEEEccCceEEEEecccccCHHHHHHHHH
Confidence 3467999999988764433 334444555555554432 2555678877654321 1222232
Q ss_pred hcCCceeec-cCCCccch-hhHHHHHHHHHH---HhCCCCcEEEEEeCC------cchHHHHHHHHhCCCEEEEe
Q 001724 110 STGINIAHV-PHGGKNSA-DRSLLVDLMYWV---SQNPPPAHLFLISGD------RDFASVLHRLRMNNYNILLA 173 (1020)
Q Consensus 110 ssGI~Lihv-P~ggKNAA-Di~LiIDaMd~a---~~nP~pdtFVLISGD------sDFtpLL~RLRerGynVILa 173 (1020)
. .+..+ +.++-|.. -+.+...++.-. .+...+-.++||++| .+....+.+||+.|..|+-+
T Consensus 96 ~---~~~~~~~~ggT~ig~aL~~A~~~l~~~~~~~R~~v~kvvIllTDg~~~~~~~~~~~~a~~l~~~GI~i~tV 167 (193)
T cd01477 96 G---SLTDVSSTNASYLDTGLQAAEQMLAAGKRTSRENYKKVVIVFASDYNDEGSNDPRPIAARLKSTGIAIITV 167 (193)
T ss_pred H---HhhccccCCcchHHHHHHHHHHHHHhhhccccCCCCeEEEEEecCccCCCCCCHHHHHHHHHHCCCEEEEE
Confidence 1 11122 22233321 122233322210 001135668888853 25788899999999998844
No 54
>TIGR03436 acidobact_VWFA VWFA-related Acidobacterial domain. Members of this family are bacterial domains that include a region related to the von Willebrand factor type A (VWFA) domain (pfam00092). These domains are restricted to, and have undergone a large paralogous family expansion in, the Acidobacteria, including Solibacter usitatus and Acidobacterium capsulatum ATCC 51196.
Probab=36.41 E-value=4.7e+02 Score=28.91 Aligned_cols=122 Identities=11% Similarity=0.119 Sum_probs=62.6
Q ss_pred CCeEEEEEecCCCCCCCCCChhhHHHHHHHHHHH-hCCCCceEEEEeeccccc-------chhhHHHhhhcCCceee---
Q 001724 49 NVRVSVWWDFENCNLPAGVNAFKVAHTITAAIRA-NGIKGPVTITAFGDVVQM-------SRANQEVLSSTGINIAH--- 117 (1020)
Q Consensus 49 ~~rVAVFWDiENcpiP~g~d~~~Va~nI~~aLre-lG~~GpVtIRAYGDws~~-------~k~~qe~L~ssGI~Lih--- 117 (1020)
...+++++|.-+-... ....+...+..+|+. ++....+.|-.|++.... ...+.+.|.........
T Consensus 53 p~~vvlvlD~SgSM~~---~~~~a~~a~~~~l~~~l~~~d~v~lv~f~~~~~~~~~~t~~~~~l~~~l~~l~~~~~~~~~ 129 (296)
T TIGR03436 53 PLTVGLVIDTSGSMRN---DLDRARAAAIRFLKTVLRPNDRVFVVTFNTRLRLLQDFTSDPRLLEAALNRLKPPLRTDYN 129 (296)
T ss_pred CceEEEEEECCCCchH---HHHHHHHHHHHHHHhhCCCCCEEEEEEeCCceeEeecCCCCHHHHHHHHHhccCCCccccc
Confidence 3679999998886532 122334556666655 455567777888765432 12233444433221000
Q ss_pred ------ccCCCccchhhHHHHHHHHHHHhC----CCCcEEEEEeCCc------chHHHHHHHHhCCCEEEEec
Q 001724 118 ------VPHGGKNSADRSLLVDLMYWVSQN----PPPAHLFLISGDR------DFASVLHRLRMNNYNILLAS 174 (1020)
Q Consensus 118 ------vP~ggKNAADi~LiIDaMd~a~~n----P~pdtFVLISGDs------DFtpLL~RLRerGynVILag 174 (1020)
.+.++.+ -.-+|...++..+... |.--.++|||.-. .+..++.+|+..+..|+.++
T Consensus 130 ~~~~~~~~~g~T~-l~~al~~aa~~~~~~~~~~~p~rk~iIllTDG~~~~~~~~~~~~~~~~~~~~v~vy~I~ 201 (296)
T TIGR03436 130 SSGAFVRDGGGTA-LYDAITLAALEQLANALAGIPGRKALIVISDGGDNRSRDTLERAIDAAQRADVAIYSID 201 (296)
T ss_pred cccccccCCCcch-hHHHHHHHHHHHHHHhhcCCCCCeEEEEEecCCCcchHHHHHHHHHHHHHcCCEEEEec
Confidence 0122222 2223433334443332 2334566666322 25577888888998888554
No 55
>PRK10355 xylF D-xylose transporter subunit XylF; Provisional
Probab=35.49 E-value=1.2e+02 Score=34.13 Aligned_cols=67 Identities=12% Similarity=0.113 Sum_probs=41.5
Q ss_pred hHHHhhhcCCceeeccCCCccchhhHHHHHHHHHHHhCCCCcEEEEEeCCcc-hHHHHHHHHhCCCEEEEecC
Q 001724 104 NQEVLSSTGINIAHVPHGGKNSADRSLLVDLMYWVSQNPPPAHLFLISGDRD-FASVLHRLRMNNYNILLASR 175 (1020)
Q Consensus 104 ~qe~L~ssGI~LihvP~ggKNAADi~LiIDaMd~a~~nP~pdtFVLISGDsD-FtpLL~RLRerGynVILagp 175 (1020)
.++++...|+.+.-+... .| ......++..+... .+|+++|+..+.+ +.+.+..++++|..|+++..
T Consensus 47 i~~~a~~~g~~l~i~~~~-~~---~~~~~~~i~~l~~~-~vDGiIi~~~~~~~~~~~l~~~~~~~iPvV~id~ 114 (330)
T PRK10355 47 FVKKAESLGAKVFVQSAN-GN---EETQMSQIENMINR-GVDVLVIIPYNGQVLSNVIKEAKQEGIKVLAYDR 114 (330)
T ss_pred HHHHHHHcCCEEEEECCC-CC---HHHHHHHHHHHHHc-CCCEEEEeCCChhhHHHHHHHHHHCCCeEEEECC
Confidence 344555555555544322 11 12334455555554 5999999876654 67888899999988888754
No 56
>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=35.33 E-value=1.1e+02 Score=32.09 Aligned_cols=67 Identities=6% Similarity=-0.041 Sum_probs=41.4
Q ss_pred hHHHhhhcCCceeeccCCCccchhhHHHHHHHHHHHhCCCCcEEEEEeCCcchHHHHHHHHhCCCEEEEecCC
Q 001724 104 NQEVLSSTGINIAHVPHGGKNSADRSLLVDLMYWVSQNPPPAHLFLISGDRDFASVLHRLRMNNYNILLASRE 176 (1020)
Q Consensus 104 ~qe~L~ssGI~LihvP~ggKNAADi~LiIDaMd~a~~nP~pdtFVLISGDsDFtpLL~RLRerGynVILagp~ 176 (1020)
..+.+...|+++....... |..-..++++.+..+ .+++++|++.+.+-.. +.+|++.|..|+++...
T Consensus 21 ~~~~~~~~g~~~~~~~~~~----~~~~~~~~i~~l~~~-~vdgiii~~~~~~~~~-~~~~~~~~ipvV~~~~~ 87 (264)
T cd06274 21 LEALARERGYQLLIACSDD----DPETERETVETLIAR-QVDALIVAGSLPPDDP-YYLCQKAGLPVVALDRP 87 (264)
T ss_pred HHHHHHHCCCEEEEEeCCC----CHHHHHHHHHHHHHc-CCCEEEEcCCCCchHH-HHHHHhcCCCEEEecCc
Confidence 4455666676655544322 222344566666654 4899999887654333 67788889888877543
No 57
>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=34.59 E-value=5.1e+02 Score=27.20 Aligned_cols=74 Identities=14% Similarity=0.157 Sum_probs=44.0
Q ss_pred hhhHHHhhhc-CCceeeccCCCccchhhHHHHHHH-HHHHhCCCCcEEEEEeCCcchHHHHHHHHhCCC--EEEEecCCc
Q 001724 102 RANQEVLSST-GINIAHVPHGGKNSADRSLLVDLM-YWVSQNPPPAHLFLISGDRDFASVLHRLRMNNY--NILLASRES 177 (1020)
Q Consensus 102 k~~qe~L~ss-GI~LihvP~ggKNAADi~LiIDaM-d~a~~nP~pdtFVLISGDsDFtpLL~RLRerGy--nVILagp~k 177 (1020)
.+++++|..+ |+.+.......- +..-..+++ .++..++.| ..+++++|.....+++.|++.|+ .|.+++-..
T Consensus 143 ~gf~~a~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~l~~~~~~-~~i~~~~d~~a~g~~~~l~~~g~~~di~vig~d~ 218 (273)
T cd06310 143 EGFLEGLKEYPGIEIVATQYSDS---DYAKALDITEDLLTANPDL-KGIFGANEGSAVGAARAVRQAGKAGKVKVVGFDA 218 (273)
T ss_pred HHHHHHHHhCCCcEEEecccCCc---CHHHHHHHHHHHHHhCCCc-eEEEecCchhHHHHHHHHHhcCCCCCeEEEEeCC
Confidence 3567788888 887654332211 111122333 344445545 45666778878889999999998 455555444
Q ss_pred hh
Q 001724 178 AS 179 (1020)
Q Consensus 178 Tp 179 (1020)
++
T Consensus 219 ~~ 220 (273)
T cd06310 219 SP 220 (273)
T ss_pred Ch
Confidence 44
No 58
>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=34.48 E-value=1.2e+02 Score=32.64 Aligned_cols=42 Identities=12% Similarity=0.101 Sum_probs=31.1
Q ss_pred HHHHHHHhCCCCcEEEEEeCCcc-hHHHHHHHHhCCCEEEEecC
Q 001724 133 DLMYWVSQNPPPAHLFLISGDRD-FASVLHRLRMNNYNILLASR 175 (1020)
Q Consensus 133 DaMd~a~~nP~pdtFVLISGDsD-FtpLL~RLRerGynVILagp 175 (1020)
.++..+... .+++|+|+..|.+ ..+++.+|++.|..|+++..
T Consensus 46 ~~i~~~~~~-~vdgiii~~~~~~~~~~~l~~l~~~~ipvV~~~~ 88 (288)
T cd01538 46 SQIENMIAK-GVDVLVIAPVDGEALASAVEKAADAGIPVIAYDR 88 (288)
T ss_pred HHHHHHHHc-CCCEEEEecCChhhHHHHHHHHHHCCCCEEEECC
Confidence 344434443 5999999987765 57888999999999998754
No 59
>PLN02905 beta-amylase
Probab=34.41 E-value=89 Score=39.22 Aligned_cols=92 Identities=20% Similarity=0.280 Sum_probs=68.1
Q ss_pred hHHHHHHhhcCCCCceeeecccc-------------HHH----HHHHHHhcCCccccCCCccchhHHHHHHHhhhhhhhh
Q 001724 598 FWSDMESFMKSPRGSVIVSQSRT-------------RKQ----MAESLKEEGPLVLRDLSECDLLDLVDLMILEKKWVEE 660 (1020)
Q Consensus 598 fW~~~esfi~~p~Gs~lvS~skt-------------RE~----~ah~Lq~~gp~~lr~L~e~~~~qLV~llisEKKWieE 660 (1020)
|=.-|+.++-||.|. .+-..++ |.. |-++|.++|-..|.- -.|+-+++.-|..|.-|+.|
T Consensus 62 ~~~~~~~~~~~~~~~-~~~~~~~~~ere~~~~rer~rrai~~~i~~glr~~g~~~lp~--~~d~n~v~~~l~~eag~~v~ 138 (702)
T PLN02905 62 HQQSIQEQVGTPGGG-GSRRSRPLEEKERTKLRERHRRAITARILAGLRRHGNYNLRV--RADINDVIAALAREAGWVVL 138 (702)
T ss_pred HHHHHHHhcCCCCCC-ccCCCCchhhhhhhHHHHHHHHHHHHHHHHHHHhhcCCCCCc--ccchHHHHHHHHHhcCcEEc
Confidence 667799999999997 3333333 222 457899999988876 78999999999999999999
Q ss_pred CCCCCCCcee--eccccccccCCCCcCcCccccc
Q 001724 661 YPSEKSPFKL--SGLVRKKSSLDHSHAANGLRSI 692 (1020)
Q Consensus 661 ~pS~~fpF~l--t~p~~~~~~~~~s~~~nGl~s~ 692 (1020)
-+-.+|+.++ ..|...++..-+++.+.+++|+
T Consensus 139 ~dg~~y~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 172 (702)
T PLN02905 139 PDGTTFPSRSQGTRPAGGTSAVAATSSSSHLVSQ 172 (702)
T ss_pred CCCCcccccCCCCCCCCCcccccccccccccccc
Confidence 9999999876 4455555655555555555553
No 60
>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=34.36 E-value=4.3e+02 Score=27.82 Aligned_cols=65 Identities=17% Similarity=0.169 Sum_probs=39.8
Q ss_pred hhhHHHhhhcC-CceeeccCCCccchhhHHHHHHH-HHHHhCCCCcEEEEEeCCcchHHHHHHHHhCCCEEE
Q 001724 102 RANQEVLSSTG-INIAHVPHGGKNSADRSLLVDLM-YWVSQNPPPAHLFLISGDRDFASVLHRLRMNNYNIL 171 (1020)
Q Consensus 102 k~~qe~L~ssG-I~LihvP~ggKNAADi~LiIDaM-d~a~~nP~pdtFVLISGDsDFtpLL~RLRerGynVI 171 (1020)
.++++.|..++ +.+..+....-+..+ ..+++ .++..+|.++ .+++++|. -..+++.|++.|+.|.
T Consensus 145 ~g~~~a~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~l~~~~~~~-~i~~~~d~-A~g~~~al~~~g~~~p 211 (272)
T cd06300 145 AGAKEVLKEYPGIKIVGEVYGDWDQAV---AQKAVADFLASNPDVD-GIWTQGGD-AVGAVQAFEQAGRDIP 211 (272)
T ss_pred HHHHHHHHHCCCcEEEeecCCCCCHHH---HHHHHHHHHHhCCCcC-EEEecCCC-cHHHHHHHHHcCCCCc
Confidence 35778888887 876543222222111 22333 3444566555 56667777 7789999999998654
No 61
>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=34.30 E-value=1.3e+02 Score=31.86 Aligned_cols=42 Identities=5% Similarity=0.013 Sum_probs=30.8
Q ss_pred HHHHHHHhCCCCcEEEEEeCCcc-hHHHHHHHHhCCCEEEEecC
Q 001724 133 DLMYWVSQNPPPAHLFLISGDRD-FASVLHRLRMNNYNILLASR 175 (1020)
Q Consensus 133 DaMd~a~~nP~pdtFVLISGDsD-FtpLL~RLRerGynVILagp 175 (1020)
..++.+... .+|+|+|...|.+ +.+++.++++.|..|+++..
T Consensus 46 ~~i~~~~~~-~~Dgiii~~~~~~~~~~~i~~~~~~~iPvV~~~~ 88 (282)
T cd06318 46 ADVEDLLTR-GVNVLIINPVDPEGLVPAVAAAKAAGVPVVVVDS 88 (282)
T ss_pred HHHHHHHHc-CCCEEEEecCCccchHHHHHHHHHCCCCEEEecC
Confidence 344444443 5999999877754 35788999999999998764
No 62
>cd06303 PBP1_LuxPQ_Quorum_Sensing Periplasmic binding protein (LuxP) of autoinducer-2 (AI-2) receptor LuxPQ from Vibrio harveyi and its close homologs. Periplasmic binding protein (LuxP) of autoinducer-2 (AI-2) receptor LuxPQ from Vibrio harveyi and its close homologs from other bacteria. The members of this group are highly homologous to a family of periplasmic pentose/hexose sugar-binding proteins that function as the primary receptors for chemotaxis and transport of many sugar based solutes in bacteria and archaea, and that are members of the type I periplasmic binding protein superfamily. The Vibrio harveyi AI-2 receptor consists of two polypeptides, LuxP and LuxQ: LuxP is a periplasmic binding protein that binds AI-2 by clamping it between two domains, LuxQ is an integral membrane protein belonging to the two-component sensor kinase family. Unlike AI-2 bound to the LsrB receptor in Salmonella typhimurium, the Vibrio harveyi AI-2 signaling molecule has an unusual furanosyl borate
Probab=34.12 E-value=1e+02 Score=33.01 Aligned_cols=41 Identities=10% Similarity=0.115 Sum_probs=27.4
Q ss_pred HHHHHHHHhCCCCcEEEEEeCCcchHHHHHHHHhCCCEEEEe
Q 001724 132 VDLMYWVSQNPPPAHLFLISGDRDFASVLHRLRMNNYNILLA 173 (1020)
Q Consensus 132 IDaMd~a~~nP~pdtFVLISGDsDFtpLL~RLRerGynVILa 173 (1020)
..+++.+.+. .+|+++|+..+......+.+|.+.+..++++
T Consensus 50 ~~~i~~l~~~-~vDgiIv~~~~~~~~~~~~~l~~~~~p~V~i 90 (280)
T cd06303 50 SQQLNEALQS-KPDYLIFTLDSLRHRKLIERVLASGKTKIIL 90 (280)
T ss_pred HHHHHHHHHc-CCCEEEEcCCchhhHHHHHHHHhCCCCeEEE
Confidence 3455555554 5899988765554567788888888655544
No 63
>PRK11440 putative hydrolase; Provisional
Probab=33.79 E-value=3e+02 Score=28.54 Aligned_cols=125 Identities=15% Similarity=0.094 Sum_probs=60.3
Q ss_pred CCeEEEEEecCCCCCCC--C-CChhhHHHHHHHHHHHhCCCC-ceEE-EE-eeccccc-ch-hhH-----HHhhhcCCce
Q 001724 49 NVRVSVWWDFENCNLPA--G-VNAFKVAHTITAAIRANGIKG-PVTI-TA-FGDVVQM-SR-ANQ-----EVLSSTGINI 115 (1020)
Q Consensus 49 ~~rVAVFWDiENcpiP~--g-~d~~~Va~nI~~aLrelG~~G-pVtI-RA-YGDws~~-~k-~~q-----e~L~ssGI~L 115 (1020)
....-|.||+.|--++. + .....+.++|..+++.+-..| ||.. +. |..+... .. ... ..+...+-++
T Consensus 7 ~~~ALlvID~Qn~f~~~~~~~~~~~~~i~~i~~l~~~ar~~g~pVi~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 86 (188)
T PRK11440 7 KTTALVVIDLQEGILPFAGGPHTADEVVARAARLAAKFRASGSPVVLVRVGWSADYAEALKQPVDAPSPAKVLPENWWQH 86 (188)
T ss_pred CCEEEEEEecccccccCCCCcchHHHHHHHHHHHHHHHHHcCCcEEEEecccCCchhhhccCcccccccccccCCccccc
Confidence 34566899999976532 1 234567788888887775555 3332 32 2111100 00 000 0000000000
Q ss_pred ee--ccC-----CCccchhhHHHHHHHHHHHhCCCCcEEEEEeCCcchH--HHHHHHHhCCCEEEEec
Q 001724 116 AH--VPH-----GGKNSADRSLLVDLMYWVSQNPPPAHLFLISGDRDFA--SVLHRLRMNNYNILLAS 174 (1020)
Q Consensus 116 ih--vP~-----ggKNAADi~LiIDaMd~a~~nP~pdtFVLISGDsDFt--pLL~RLRerGynVILag 174 (1020)
.. .|. -.|+..+.-.-.++-.|+..+ .+++++|+--..++. ..+....++||+|+++.
T Consensus 87 ~~~l~~~~~d~vi~K~~~saF~~T~L~~~L~~~-gi~~lii~Gv~T~~CV~~Ta~~A~~~gy~v~vv~ 153 (188)
T PRK11440 87 PAALGKTDSDIEVTKRQWGAFYGTDLELQLRRR-GIDTIVLCGISTNIGVESTARNAWELGFNLVIAE 153 (188)
T ss_pred CcccCCCCCCEEEecCCcCCCCCCCHHHHHHHC-CCCEEEEeeechhHHHHHHHHHHHHCCCEEEEec
Confidence 00 000 013222211223444555544 588887776666653 55666777899999764
No 64
>cd01391 Periplasmic_Binding_Protein_Type_1 Type 1 periplasmic binding fold superfamily. Type 1 periplasmic binding fold superfamily. This model and hierarchy represent the ligand binding domains of the LacI family of transcriptional regulators, periplasmic binding proteins of the ABC-type transport systems, the family C G-protein couples receptors (GPCRs), membrane bound guanylyl cyclases including the family of natriuretic peptide receptors (NPRs), and the N-terminal leucine/isoleucine/valine- binding protein (LIVBP)-like domains of the ionotropic glutamate receptors (iGluRs). In LacI-like transcriptional regulator and the bacterial periplasmic binding proteins the ligands are monosaccharides including lactose, ribose, fructose, xylose, arabinose, galactose/glucose, and other sugars, with a few exceptions. Periplasmic sugar binding proteins are one of the components of ABC transporters and are involved in the active transport of water-soluble ligands. The LacI family of proteins con
Probab=33.65 E-value=3e+02 Score=27.53 Aligned_cols=106 Identities=16% Similarity=0.244 Sum_probs=55.6
Q ss_pred hhhHHHHHHHHHHHhCCCCceEEEEeecccc-c---chhhHHHhhhcCCceeeccCCCccchhhHHHHHHHHHHHhCCCC
Q 001724 69 AFKVAHTITAAIRANGIKGPVTITAFGDVVQ-M---SRANQEVLSSTGINIAHVPHGGKNSADRSLLVDLMYWVSQNPPP 144 (1020)
Q Consensus 69 ~~~Va~nI~~aLrelG~~GpVtIRAYGDws~-~---~k~~qe~L~ssGI~LihvP~ggKNAADi~LiIDaMd~a~~nP~p 144 (1020)
.......+-..|.+.+ .+.|. -+|++-.. . ...+++.+...|+.+..+....-+. + ...-.+..++..++.+
T Consensus 108 ~~~~~~~~~~~l~~~~-~~~i~-~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~-~~~~~~~~~l~~~~~~ 183 (269)
T cd01391 108 NEQAGEAAAEYLAEKG-WKRVA-LIYGDDGAYGRERLEGFKAALKKAGIEVVAIEYGDLDT-E-KGFQALLQLLKAAPKP 183 (269)
T ss_pred cHHHHHHHHHHHHHhC-CceEE-EEecCCcchhhHHHHHHHHHHHhcCcEEEeccccCCCc-c-ccHHHHHHHHhcCCCC
Confidence 3344445555555555 33433 33333311 1 1346778888887776543322111 1 2333455566555555
Q ss_pred cEEEEEeCCcchHHHHHHHHhCCC---EEEEecCCchh
Q 001724 145 AHLFLISGDRDFASVLHRLRMNNY---NILLASRESAS 179 (1020)
Q Consensus 145 dtFVLISGDsDFtpLL~RLRerGy---nVILagp~kTp 179 (1020)
+.+++ .+|.....++..|++.|+ .+.+++....+
T Consensus 184 ~~i~~-~~~~~a~~~~~~~~~~g~~~~~~~ii~~~~~~ 220 (269)
T cd01391 184 DAIFA-CNDEMAAGALKAAREAGLTPGDISIIGFDGSP 220 (269)
T ss_pred CEEEE-cCchHHHHHHHHHHHcCCCCCCCEEEeccccc
Confidence 55555 455666788899999886 34444443333
No 65
>cd06313 PBP1_ABC_sugar_binding_like_5 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=33.44 E-value=1.1e+02 Score=32.55 Aligned_cols=68 Identities=7% Similarity=-0.012 Sum_probs=46.0
Q ss_pred hhHHHhhhcCCceeeccCCCccchhhHHHHHHHHHHHhCCCCcEEEEEeCCcc-hHHHHHHHHhCCCEEEEecC
Q 001724 103 ANQEVLSSTGINIAHVPHGGKNSADRSLLVDLMYWVSQNPPPAHLFLISGDRD-FASVLHRLRMNNYNILLASR 175 (1020)
Q Consensus 103 ~~qe~L~ssGI~LihvP~ggKNAADi~LiIDaMd~a~~nP~pdtFVLISGDsD-FtpLL~RLRerGynVILagp 175 (1020)
...+.+...|+.++...... |..-..+++..+..+ .+++++|.+.|.+ ..+++.+|.+.|..|+++..
T Consensus 20 gi~~~~~~~G~~~~~~~~~~----d~~~~~~~i~~~~~~-~vdgiii~~~~~~~~~~~i~~~~~~~iPvV~~~~ 88 (272)
T cd06313 20 AADEAGKLLGVDVTWYGGAL----DAVKQVAAIENMASQ-GWDFIAVDPLGIGTLTEAVQKAIARGIPVIDMGT 88 (272)
T ss_pred HHHHHHHHcCCEEEEecCCC----CHHHHHHHHHHHHHc-CCCEEEEcCCChHHhHHHHHHHHHCCCcEEEeCC
Confidence 34556666777766653322 223445566656554 4999999887766 46788999999999998764
No 66
>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=33.43 E-value=1.3e+02 Score=32.84 Aligned_cols=67 Identities=16% Similarity=0.248 Sum_probs=43.6
Q ss_pred hHHHhhhcCCceeec-cCCCccchhhHHHHHHHHHHHhCCCCcEEEEEeCCcc-hHHHHHHHHhCCCEEEEecC
Q 001724 104 NQEVLSSTGINIAHV-PHGGKNSADRSLLVDLMYWVSQNPPPAHLFLISGDRD-FASVLHRLRMNNYNILLASR 175 (1020)
Q Consensus 104 ~qe~L~ssGI~Lihv-P~ggKNAADi~LiIDaMd~a~~nP~pdtFVLISGDsD-FtpLL~RLRerGynVILagp 175 (1020)
.++++...|+.+..+ +.. - |..-..+++..+... .+++++|+..+.+ +..++.+++..|..|+++..
T Consensus 21 i~~~a~~~g~~v~~~~~~~-~---d~~~~~~~i~~~~~~-~~DgiIi~~~~~~~~~~~~~~~~~~~iPvV~v~~ 89 (298)
T cd06302 21 AKEAAKELGVDAIYVGPTT-A---DAAGQVQIIEDLIAQ-GVDAIAVVPNDPDALEPVLKKAREAGIKVVTHDS 89 (298)
T ss_pred HHHHHHHhCCeEEEECCCC-C---CHHHHHHHHHHHHhc-CCCEEEEecCCHHHHHHHHHHHHHCCCeEEEEcC
Confidence 445556666666543 322 1 222344566555554 4899999987765 67888999999999887753
No 67
>cd06303 PBP1_LuxPQ_Quorum_Sensing Periplasmic binding protein (LuxP) of autoinducer-2 (AI-2) receptor LuxPQ from Vibrio harveyi and its close homologs. Periplasmic binding protein (LuxP) of autoinducer-2 (AI-2) receptor LuxPQ from Vibrio harveyi and its close homologs from other bacteria. The members of this group are highly homologous to a family of periplasmic pentose/hexose sugar-binding proteins that function as the primary receptors for chemotaxis and transport of many sugar based solutes in bacteria and archaea, and that are members of the type I periplasmic binding protein superfamily. The Vibrio harveyi AI-2 receptor consists of two polypeptides, LuxP and LuxQ: LuxP is a periplasmic binding protein that binds AI-2 by clamping it between two domains, LuxQ is an integral membrane protein belonging to the two-component sensor kinase family. Unlike AI-2 bound to the LsrB receptor in Salmonella typhimurium, the Vibrio harveyi AI-2 signaling molecule has an unusual furanosyl borate
Probab=33.28 E-value=4.3e+02 Score=28.26 Aligned_cols=80 Identities=10% Similarity=0.005 Sum_probs=47.2
Q ss_pred hhHHHhhhc-CCceeeccCCCccchhhHHHHHHH-HHHHhCCCCcEEEEEeCCcchHHHHHHHHhCCCE--EEEecCCch
Q 001724 103 ANQEVLSST-GINIAHVPHGGKNSADRSLLVDLM-YWVSQNPPPAHLFLISGDRDFASVLHRLRMNNYN--ILLASRESA 178 (1020)
Q Consensus 103 ~~qe~L~ss-GI~LihvP~ggKNAADi~LiIDaM-d~a~~nP~pdtFVLISGDsDFtpLL~RLRerGyn--VILagp~kT 178 (1020)
++++.|..+ |+.+..+..+.-+ .+ -...++ .++..+|.|+. ++..+|.--..++..|+++|+. |.+++-...
T Consensus 151 gf~~al~~~~~~~~~~~~~~~~~-~~--~~~~~~~~~l~~~~~~~a-i~~~nd~~A~g~l~al~~~G~~~dv~vvg~d~~ 226 (280)
T cd06303 151 TFIDCVHARNNWTLTSEFYTDAT-RQ--KAYQATSDILSNNPDVDF-IYACSTDIALGASDALKELGREDDILINGWGGG 226 (280)
T ss_pred HHHHHHHhCCCceEEEeecCCCC-HH--HHHHHHHHHHHhCCCCcE-EEECCcHHHHHHHHHHHHcCCCCCcEEEecCCC
Confidence 567788887 7775543222211 11 112233 34445665654 5567777677899999999974 666665666
Q ss_pred hHHHHhhc
Q 001724 179 SNVLCSAA 186 (1020)
Q Consensus 179 peaL~sAc 186 (1020)
+..+...+
T Consensus 227 ~~~~~~~~ 234 (280)
T cd06303 227 SAELDAIQ 234 (280)
T ss_pred HHHHHHHH
Confidence 66554433
No 68
>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=33.27 E-value=3.5e+02 Score=28.16 Aligned_cols=64 Identities=17% Similarity=0.220 Sum_probs=38.3
Q ss_pred hhHHHhhhcCCceee--ccCCCccchhhHHHHHHHHHHHhCCCCcEEEEEeCCcchHHHHHHHHhCCCE
Q 001724 103 ANQEVLSSTGINIAH--VPHGGKNSADRSLLVDLMYWVSQNPPPAHLFLISGDRDFASVLHRLRMNNYN 169 (1020)
Q Consensus 103 ~~qe~L~ssGI~Lih--vP~ggKNAADi~LiIDaMd~a~~nP~pdtFVLISGDsDFtpLL~RLRerGyn 169 (1020)
++++.+..+|+.+.. +....-+..+ ....+..|+..+|.+++| ++.+|.....++..|++.|+.
T Consensus 137 gf~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~l~~~~~~~ai-~~~~d~~a~~~~~~l~~~g~~ 202 (269)
T cd06288 137 GYRQALAEAGIPFDPDLVVHGDWSADD--GYEAAAALLDLDDRPTAI-FCGNDRMAMGAYQALLERGLR 202 (269)
T ss_pred HHHHHHHHcCCCCCHHHeEeCCCChHH--HHHHHHHHHhCCCCCCEE-EEeCcHHHHHHHHHHHHcCCC
Confidence 467788888875432 2222111111 122234455556666766 567777777899999999973
No 69
>PF12075 KN_motif: KN motif; InterPro: IPR021939 This small motif is found at the N terminus of Kank proteins and has been called the KN (for Kank N-terminal) motif. This protein is found in eukaryotes. Proteins in this family are typically between 413 to 1202 amino acids in length. This protein is found associated with PF00023 from PFAM. This protein has two conserved sequence motifs: TPYG and LDLDF. Kank1 was obtained by positional cloning of a tumor suppressor gene in renal cell carcinoma, while the other members were found by homology search. The family is involved in the regulation of actin polymerisation and cell motility through signaling pathways containing PI3K/Akt and/or unidentified modulators/effectors [].
Probab=33.07 E-value=13 Score=30.62 Aligned_cols=13 Identities=46% Similarity=1.104 Sum_probs=10.8
Q ss_pred hcccccccccchh
Q 001724 771 YGYHLDIQKLGYQ 783 (1020)
Q Consensus 771 ygy~ld~~klgy~ 783 (1020)
||||||+.=|-|-
T Consensus 8 YGyhiDLDFvkyv 20 (39)
T PF12075_consen 8 YGYHIDLDFVKYV 20 (39)
T ss_pred cceeecchHHHHH
Confidence 8999998877764
No 70
>cd01460 vWA_midasin VWA_Midasin: Midasin is a member of the AAA ATPase family. The proteins of this family are unified by their common archetectural organization that is based upon a conserved ATPase domain. The AAA domain of midasin contains six tandem AAA protomers. The AAA domains in midasin is followed by a D/E rich domain that is following by a VWA domain. The members of this subgroup have a conserved MIDAS motif. The function of this domain is not exactly known although it has been speculated to play a crucial role in midasin function.
Probab=32.73 E-value=3.4e+02 Score=30.70 Aligned_cols=130 Identities=16% Similarity=0.195 Sum_probs=69.4
Q ss_pred ccccCCCeEEEEEecCCCCCCCCC--ChhhHHHHHHHHHHHhCCCCceEEEEeecccccchhhHHHhh-hcCCceee---
Q 001724 44 EEESKNVRVSVWWDFENCNLPAGV--NAFKVAHTITAAIRANGIKGPVTITAFGDVVQMSRANQEVLS-STGINIAH--- 117 (1020)
Q Consensus 44 ~~es~~~rVAVFWDiENcpiP~g~--d~~~Va~nI~~aLrelG~~GpVtIRAYGDws~~~k~~qe~L~-ssGI~Lih--- 117 (1020)
.+..+...|.|.+|--+--...+. .+..-...|.++|..+. -|.+.|-+||.--.....+-..+. ..|+.+..
T Consensus 55 kpskr~~qIvlaID~S~SM~~~~~~~~aleak~lIs~al~~Le-~g~vgVv~Fg~~~~~v~Plt~d~~~~a~~~~l~~~~ 133 (266)
T cd01460 55 KPAKRDYQILIAIDDSKSMSENNSKKLALESLCLVSKALTLLE-VGQLGVCSFGEDVQILHPFDEQFSSQSGPRILNQFT 133 (266)
T ss_pred cCCccCceEEEEEecchhcccccccccHHHHHHHHHHHHHhCc-CCcEEEEEeCCCceEeCCCCCCchhhHHHHHhCccc
Confidence 344467789999997665433222 12222345777777664 388888888875432211110110 23443333
Q ss_pred ccCCCccchh-hHHHHHHHHHHHhCCC---CcEEEEEeCCcc--h-----HHHHHHHHhCCCEEEEec
Q 001724 118 VPHGGKNSAD-RSLLVDLMYWVSQNPP---PAHLFLISGDRD--F-----ASVLHRLRMNNYNILLAS 174 (1020)
Q Consensus 118 vP~ggKNAAD-i~LiIDaMd~a~~nP~---pdtFVLISGDsD--F-----tpLL~RLRerGynVILag 174 (1020)
+...+.|-.. +.+.+++++-....+. ...++||-+|+. | ..++++++++|..|+.++
T Consensus 134 f~~~~Tni~~aL~~a~~~f~~~~~~~~s~~~~qlilLISDG~~~~~e~~~~~~~r~a~e~~i~l~~I~ 201 (266)
T cd01460 134 FQQDKTDIANLLKFTAQIFEDARTQSSSGSLWQLLLIISDGRGEFSEGAQKVRLREAREQNVFVVFII 201 (266)
T ss_pred CCCCCCcHHHHHHHHHHHHHhhhccccccccccEEEEEECCCcccCccHHHHHHHHHHHcCCeEEEEE
Confidence 2333444222 3334444433321111 126778878876 4 355888889998888655
No 71
>cd01014 nicotinamidase_related Nicotinamidase_ related amidohydrolases. Cysteine hydrolases of unknown function that share the catalytic triad with other amidohydrolases, like nicotinamidase, which converts nicotinamide to nicotinic acid and ammonia.
Probab=32.60 E-value=2.6e+02 Score=28.09 Aligned_cols=35 Identities=26% Similarity=0.260 Sum_probs=22.3
Q ss_pred EEEEecCCCCCCCC---CChhhHHHHHHHHHHHhCCCC
Q 001724 53 SVWWDFENCNLPAG---VNAFKVAHTITAAIRANGIKG 87 (1020)
Q Consensus 53 AVFWDiENcpiP~g---~d~~~Va~nI~~aLrelG~~G 87 (1020)
-|.+|+.|--+..+ .....+.++|.++++.....|
T Consensus 2 LlviD~Q~~f~~~~~~~~~~~~~v~~i~~li~~~r~~~ 39 (155)
T cd01014 2 LLVIDVQNGYFDGGLPPLNNEAALENIAALIAAARAAG 39 (155)
T ss_pred EEEEeCchhhhCCCCCcCCHHHHHHHHHHHHHHHHHCC
Confidence 37899999654322 135566678888877664445
No 72
>PRK13883 conjugal transfer protein TrbH; Provisional
Probab=32.35 E-value=97 Score=32.44 Aligned_cols=51 Identities=22% Similarity=0.307 Sum_probs=37.6
Q ss_pred hhhHHHHHHHHHHHhCCCCc--EEEEEeCCc-chH-HHHHHHHhCCCEEEEecCC
Q 001724 126 ADRSLLVDLMYWVSQNPPPA--HLFLISGDR-DFA-SVLHRLRMNNYNILLASRE 176 (1020)
Q Consensus 126 ADi~LiIDaMd~a~~nP~pd--tFVLISGDs-DFt-pLL~RLRerGynVILagp~ 176 (1020)
.+..|.-|+...+...-+|+ +|.|--..+ .|. .|+..||..||-|+-..+.
T Consensus 32 ~a~~iA~D~v~qL~~~ypPA~Tt~~l~q~~~D~Fg~aL~~aLR~~GYaV~e~~~~ 86 (151)
T PRK13883 32 DQQKLATDAVQQLATLYPPAQTRFELQQPTPDAFGQALVKALRDKGYALLEYNPA 86 (151)
T ss_pred HHHHHHHHHHHHHHHhCCCcceEEEEecCCCcHHHHHHHHHHHHcCeEEEecCCc
Confidence 46789999999887753343 477766666 585 6788999999999965543
No 73
>PLN02714 thiamin pyrophosphokinase
Probab=32.34 E-value=1.9e+02 Score=31.62 Aligned_cols=81 Identities=19% Similarity=0.347 Sum_probs=52.1
Q ss_pred EEeecccccchhhHHHhhhcCCceeeccCCCccchhhHHHHHHHHHHHhCCC-----CcEEEEE--eCCc-c--hHHHHH
Q 001724 92 TAFGDVVQMSRANQEVLSSTGINIAHVPHGGKNSADRSLLVDLMYWVSQNPP-----PAHLFLI--SGDR-D--FASVLH 161 (1020)
Q Consensus 92 RAYGDws~~~k~~qe~L~ssGI~LihvP~ggKNAADi~LiIDaMd~a~~nP~-----pdtFVLI--SGDs-D--FtpLL~ 161 (1020)
-+.||+.......++.+...|+.+++.|. -|+.||..+++. ++..+.+ .+.|+|+ +|-+ | |+.+..
T Consensus 57 ~iiGDfDSi~~e~~~~~~~~~~~i~~~~~-eKD~TD~e~Al~---~~~~~~~~~~~~~~~I~v~Ga~GGRlDH~laNi~~ 132 (229)
T PLN02714 57 VIKGDMDSIRPEVLDFYSNLGTKIVDESH-DQDTTDLHKCIA---YIRDSTPDLDKSNLCILVLGALGGRFDHEAGNINV 132 (229)
T ss_pred EEEeeccCCCHHHHHHHHHCCCEEEECCC-CcccCHHHHHHH---HHHHhccccccCCceEEEEcccCCchHHHHHHHHH
Confidence 88999999887777788889998877765 599999888875 3433321 2445554 3333 3 444333
Q ss_pred HHHhCCCEEEEecCC
Q 001724 162 RLRMNNYNILLASRE 176 (1020)
Q Consensus 162 RLRerGynVILagp~ 176 (1020)
-++-.+.+|+++...
T Consensus 133 L~~~~~~~i~lid~~ 147 (229)
T PLN02714 133 LYRFPDLRIVLLSDD 147 (229)
T ss_pred HHhcCCceEEEEcCC
Confidence 333355667666544
No 74
>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=32.27 E-value=1.2e+02 Score=32.97 Aligned_cols=44 Identities=11% Similarity=0.121 Sum_probs=30.7
Q ss_pred HHHHHHHHhC-CCCcEEEEEeCCcchHHHHHHHHhCCCEEEEecC
Q 001724 132 VDLMYWVSQN-PPPAHLFLISGDRDFASVLHRLRMNNYNILLASR 175 (1020)
Q Consensus 132 IDaMd~a~~n-P~pdtFVLISGDsDFtpLL~RLRerGynVILagp 175 (1020)
..+++-+..+ ..+++++|.+.+....+++.+|+++|.-|+++..
T Consensus 46 ~~~i~~~~~~~~~vdgiIi~~~~~~~~~~~~~~~~~giPvV~~~~ 90 (305)
T cd06324 46 LQQARTILQRPDKPDALIFTNEKSVAPELLRLAEGAGVKLFLVNS 90 (305)
T ss_pred HHHHHHHHHhccCCCEEEEcCCccchHHHHHHHHhCCCeEEEEec
Confidence 3444444443 1589999977654466788999999999997753
No 75
>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=32.21 E-value=1.3e+02 Score=31.44 Aligned_cols=45 Identities=11% Similarity=0.023 Sum_probs=31.2
Q ss_pred HHHHHHHHHHhCCCCcEEEEEeCCcchHHHHHHHHhCCCEEEEecC
Q 001724 130 LLVDLMYWVSQNPPPAHLFLISGDRDFASVLHRLRMNNYNILLASR 175 (1020)
Q Consensus 130 LiIDaMd~a~~nP~pdtFVLISGDsDFtpLL~RLRerGynVILagp 175 (1020)
...++.+.+..+ .+++++++..+.+...++.+|++.|..|+++..
T Consensus 44 ~~~~~~~~l~~~-~vdgiii~~~~~~~~~~~~~~~~~~ipvv~i~~ 88 (270)
T cd01545 44 LAERVRALLQRS-RVDGVILTPPLSDNPELLDLLDEAGVPYVRIAP 88 (270)
T ss_pred HHHHHHHHHHHC-CCCEEEEeCCCCCccHHHHHHHhcCCCEEEEec
Confidence 334445555443 589998887765556778888889988887654
No 76
>cd01012 YcaC_related YcaC related amidohydrolases; E.coli YcaC is an homooctameric hydrolase with unknown specificity. Despite its weak sequence similarity, it is structurally related to other amidohydrolases and shares conserved active site residues with them. Multimerisation interface seems not to be conserved in all members.
Probab=32.04 E-value=3.1e+02 Score=27.60 Aligned_cols=114 Identities=11% Similarity=0.061 Sum_probs=60.9
Q ss_pred EEEEecCCCCCCCCCChhhHHHHHHHHHHHhCCCC-ceEE-EEeecccccchhhHHHhhh--cCCceeeccCCCccchhh
Q 001724 53 SVWWDFENCNLPAGVNAFKVAHTITAAIRANGIKG-PVTI-TAFGDVVQMSRANQEVLSS--TGINIAHVPHGGKNSADR 128 (1020)
Q Consensus 53 AVFWDiENcpiP~g~d~~~Va~nI~~aLrelG~~G-pVtI-RAYGDws~~~k~~qe~L~s--sGI~LihvP~ggKNAADi 128 (1020)
-|.||+.|-......+...+.++|.++++.....| +|.. +-|..+. ..+...|.. -+-.++. |+..+.
T Consensus 2 LlvID~Q~~f~~~~~~~~~~~~~i~~l~~~ar~~g~pVi~~~~~~~~~---g~~~~~l~~~~~~~~vi~-----K~~~sa 73 (157)
T cd01012 2 LLLVDVQEKLAPAIKSFDELINNTVKLAKAAKLLDVPVILTEQYPKGL---GPTVPELREVFPDAPVIE-----KTSFSC 73 (157)
T ss_pred EEEEeCcHHHHHhhcCHHHHHHHHHHHHHHHHhcCCCEEEEeeCCCCC---CCchHHHHhhCCCCCcee-----cccccC
Confidence 36789988543221235567788888887775556 3433 5453221 123334432 1211111 222111
Q ss_pred HHHHHHHHHHHhCCCCcEEEEEeCCcchH--HHHHHHHhCCCEEEEecC
Q 001724 129 SLLVDLMYWVSQNPPPAHLFLISGDRDFA--SVLHRLRMNNYNILLASR 175 (1020)
Q Consensus 129 ~LiIDaMd~a~~nP~pdtFVLISGDsDFt--pLL~RLRerGynVILagp 175 (1020)
-.--++-.++.. ..+++++|+--..++. ..+..+.++||+|+++..
T Consensus 74 f~~t~L~~~L~~-~gi~~lii~G~~T~~CV~~Ta~~a~~~g~~v~v~~D 121 (157)
T cd01012 74 WEDEAFRKALKA-TGRKQVVLAGLETHVCVLQTALDLLEEGYEVFVVAD 121 (157)
T ss_pred cCCHHHHHHHHh-cCCCEEEEEEeeccHHHHHHHHHHHHCCCEEEEEee
Confidence 111244455554 4588888776666654 556667788999998654
No 77
>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=31.84 E-value=1.3e+02 Score=31.58 Aligned_cols=41 Identities=17% Similarity=0.245 Sum_probs=28.1
Q ss_pred HHHHHHhCCCCcEEEEEeCCcchHHHHHHHHhCCCEEEEecC
Q 001724 134 LMYWVSQNPPPAHLFLISGDRDFASVLHRLRMNNYNILLASR 175 (1020)
Q Consensus 134 aMd~a~~nP~pdtFVLISGDsDFtpLL~RLRerGynVILagp 175 (1020)
+++.+... .++++++++++.+-..++..|+++|..|+++..
T Consensus 47 ~i~~l~~~-~vdgii~~~~~~~~~~~~~~~~~~~ipvV~i~~ 87 (269)
T cd06281 47 ILRSFEQR-RMDGIIIAPGDERDPELVDALASLDLPIVLLDR 87 (269)
T ss_pred HHHHHHHc-CCCEEEEecCCCCcHHHHHHHHhCCCCEEEEec
Confidence 33444443 489988887765555667788888888887753
No 78
>PRK15482 transcriptional regulator MurR; Provisional
Probab=31.35 E-value=3.7e+02 Score=29.72 Aligned_cols=104 Identities=14% Similarity=0.062 Sum_probs=58.3
Q ss_pred HHHHHHhCCCCceEEEEeecccccchhhHHHhhhcCCceeeccCCCccchhhHHHHHHHHHHHhCCCCcEEEEEeCCc--
Q 001724 77 TAAIRANGIKGPVTITAFGDVVQMSRANQEVLSSTGINIAHVPHGGKNSADRSLLVDLMYWVSQNPPPAHLFLISGDR-- 154 (1020)
Q Consensus 77 ~~aLrelG~~GpVtIRAYGDws~~~k~~qe~L~ssGI~LihvP~ggKNAADi~LiIDaMd~a~~nP~pdtFVLISGDs-- 154 (1020)
+.+.+.+..-.+|-|-+.|.-......+...|...|+.+.... |..+...+... -.+=|.+++||--+
T Consensus 126 ~~~~~~i~~A~~I~i~G~G~S~~~A~~l~~~l~~~g~~~~~~~-------d~~~~~~~~~~---~~~~Dv~i~iS~sg~t 195 (285)
T PRK15482 126 QKIIEVISKAPFIQITGLGGSALVGRDLSFKLMKIGYRVACEA-------DTHVQATVSQA---LKKGDVQIAISYSGSK 195 (285)
T ss_pred HHHHHHHHhCCeeEEEEeChhHHHHHHHHHHHHhCCCeeEEec-------cHhHHHHHHhc---CCCCCEEEEEeCCCCC
Confidence 3333333333455455555332233445667777887654432 22222222111 12347777777654
Q ss_pred -chHHHHHHHHhCCCEEEEecCCchhHHHHhhcceEEe
Q 001724 155 -DFASVLHRLRMNNYNILLASRESASNVLCSAASVMWN 191 (1020)
Q Consensus 155 -DFtpLL~RLRerGynVILagp~kTpeaL~sAcd~Fw~ 191 (1020)
+...++..++++|..||+++....+ .|...||..+.
T Consensus 196 ~~~~~~~~~a~~~g~~iI~IT~~~~s-~la~~ad~~l~ 232 (285)
T PRK15482 196 KEIVLCAEAARKQGATVIAITSLADS-PLRRLAHFTLD 232 (285)
T ss_pred HHHHHHHHHHHHCCCEEEEEeCCCCC-chHHhCCEEEE
Confidence 5668888889999999998865443 45566776655
No 79
>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=31.32 E-value=1.4e+02 Score=31.03 Aligned_cols=66 Identities=6% Similarity=0.082 Sum_probs=38.9
Q ss_pred hHHHhhhcCCceeeccCCCccchhhHHHHHHHHHHHhCCCCcEEEEEeCCcchHHHHHHHHhCCCEEEEecC
Q 001724 104 NQEVLSSTGINIAHVPHGGKNSADRSLLVDLMYWVSQNPPPAHLFLISGDRDFASVLHRLRMNNYNILLASR 175 (1020)
Q Consensus 104 ~qe~L~ssGI~LihvP~ggKNAADi~LiIDaMd~a~~nP~pdtFVLISGDsDFtpLL~RLRerGynVILagp 175 (1020)
..+++...|+.++..+.. - |..-.+++++.+... .+++++++..+.+ ..++..|++.|..|+++..
T Consensus 21 i~~~~~~~g~~~~~~~~~-~---~~~~~~~~i~~l~~~-~~dgii~~~~~~~-~~~~~~~~~~~ipvv~~~~ 86 (259)
T cd01542 21 ILAALYENGYQMLLMNTN-F---SIEKEIEALELLARQ-KVDGIILLATTIT-DEHREAIKKLNVPVVVVGQ 86 (259)
T ss_pred HHHHHHHCCCEEEEEeCC-C---CHHHHHHHHHHHHhc-CCCEEEEeCCCCC-HHHHHHHhcCCCCEEEEec
Confidence 444555566665544332 1 122344555555543 5888888866543 4667788888888887754
No 80
>KOG0919 consensus C-5 cytosine-specific DNA methylase [Transcription]
Probab=31.21 E-value=40 Score=37.95 Aligned_cols=38 Identities=37% Similarity=0.690 Sum_probs=33.7
Q ss_pred HHHHHHHHHHHHHHHhCCCCccchhhHHHHH---HHhcccc
Q 001724 738 DILADCQKLVDEILKEYPEGYNMRGFRQLFI---ERYGYHL 775 (1020)
Q Consensus 738 ~il~Dc~KLvkeil~e~p~Gyni~~Frk~F~---~~ygy~l 775 (1020)
+||-.||+|=+=||-|+=.||.-+.-|-+|. ++-|||+
T Consensus 104 ~~lP~~q~LPeYIL~ENVkGFE~S~ar~~~i~~lencGf~~ 144 (338)
T KOG0919|consen 104 GLLPECQELPEYILMENVKGFESSQARNQFIESLENCGFHW 144 (338)
T ss_pred hhhhhhhhhhHHHHHhhcccchhhhHHHHHHHHHHhcCchh
Confidence 4788999999999999999999999999996 5677774
No 81
>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=31.20 E-value=6.2e+02 Score=26.46 Aligned_cols=127 Identities=12% Similarity=0.054 Sum_probs=0.0
Q ss_pred EEEEecCCCCCCC----CCChhhHHHHHHHHHHHhCCCCceEEEEeecccccc----hhhHHHhhhcCCceeeccCCCcc
Q 001724 53 SVWWDFENCNLPA----GVNAFKVAHTITAAIRANGIKGPVTITAFGDVVQMS----RANQEVLSSTGINIAHVPHGGKN 124 (1020)
Q Consensus 53 AVFWDiENcpiP~----g~d~~~Va~nI~~aLrelG~~GpVtIRAYGDws~~~----k~~qe~L~ssGI~LihvP~ggKN 124 (1020)
.|++|....+.+. +.+.+.....+-..|.+.| ++.|.+-......... .++++.|...++.+.......-+
T Consensus 81 vV~i~~~~~~~~~~~~v~~d~~~~~~~a~~~l~~~g-~~~i~~i~~~~~~~~~~~r~~gf~~~~~~~~~~~~~~~~~~~~ 159 (270)
T cd06296 81 FVVVDPAGDPDADVPSVGATNWAGGLAATEHLLELG-HRRIGFITGPPDLLCSRARLDGYRAALAEAGIPVDPALVREGD 159 (270)
T ss_pred EEEEecccCCCCCCCEEEeCcHHHHHHHHHHHHHcC-CCcEEEEcCCCcchhHHHHHHHHHHHHHHcCCCCChHHheeCC
Q ss_pred chhhHHHHHHHHHHHhCCCCcEEEEEeCCcchHHHHHHHHhCCC----EEEEecCCchhHH
Q 001724 125 SADRSLLVDLMYWVSQNPPPAHLFLISGDRDFASVLHRLRMNNY----NILLASRESASNV 181 (1020)
Q Consensus 125 AADi~LiIDaMd~a~~nP~pdtFVLISGDsDFtpLL~RLRerGy----nVILagp~kTpea 181 (1020)
...-...-.+-.|+..+|.|+.|+ +.+|.....+++-|+++|+ .|.+++-..++..
T Consensus 160 ~~~~~~~~~~~~~l~~~~~~~ai~-~~~d~~a~~~~~~l~~~g~~~p~~i~v~~~d~~~~~ 219 (270)
T cd06296 160 FSTESGFRAAAELLALPERPTAIF-AGNDLMALGVYEAARERGLRIPEDLSVVGFDDLPEA 219 (270)
T ss_pred CCHHHHHHHHHHHHhCCCCCcEEE-EcCcHHHHHHHHHHHHhCCCCCCceEEEEECChhhh
No 82
>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=30.97 E-value=3.1e+02 Score=28.56 Aligned_cols=64 Identities=13% Similarity=0.095 Sum_probs=37.0
Q ss_pred hhHHHhhhcCCceee--ccCCCccchhhHHHHHHHHHHHhCCCCcEEEEEeCCcchHHHHHHHHhCCCE
Q 001724 103 ANQEVLSSTGINIAH--VPHGGKNSADRSLLVDLMYWVSQNPPPAHLFLISGDRDFASVLHRLRMNNYN 169 (1020)
Q Consensus 103 ~~qe~L~ssGI~Lih--vP~ggKNAADi~LiIDaMd~a~~nP~pdtFVLISGDsDFtpLL~RLRerGyn 169 (1020)
++++.|..+|+.+.. +..+.-+..+ ..-.+..|+..++.|+. +++.+|.--..++.-|++.|+.
T Consensus 135 Gf~~~l~~~~~~~~~~~i~~~~~~~~~--~~~~~~~~l~~~~~~~a-i~~~~d~~a~~~~~~l~~~g~~ 200 (260)
T cd06286 135 AYKDALEEYGLTPDEEWIFEGCFTIED--GERIGHQLLKMKDRPDA-IFTGSDEVAAGIITEAKKQGIR 200 (260)
T ss_pred HHHHHHHHcCCCCChHheEeCCCCHHH--HHHHHHHHHcCCCCCCE-EEEcchHHHHHHHHHHHHcCCC
Confidence 577888888876532 2221111111 11122334445566674 4567777667899999999984
No 83
>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=30.92 E-value=1.4e+02 Score=30.96 Aligned_cols=43 Identities=16% Similarity=0.199 Sum_probs=29.0
Q ss_pred HHHHHHHHHhCCCCcEEEEEeCCcchHHHHHHHHhCCCEEEEec
Q 001724 131 LVDLMYWVSQNPPPAHLFLISGDRDFASVLHRLRMNNYNILLAS 174 (1020)
Q Consensus 131 iIDaMd~a~~nP~pdtFVLISGDsDFtpLL~RLRerGynVILag 174 (1020)
..++++.+... .+++++|+..+.+-...+.+++..|..|+++.
T Consensus 44 ~~~~i~~~~~~-~vdgiii~~~~~~~~~~~~~~~~~~ipvV~~~ 86 (268)
T cd06289 44 QEQLLSTMLEH-GVAGIILCPAAGTSPDLLKRLAESGIPVVLVA 86 (268)
T ss_pred HHHHHHHHHHc-CCCEEEEeCCCCccHHHHHHHHhcCCCEEEEe
Confidence 44555555554 48888888766543347778888888888664
No 84
>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=30.91 E-value=5.3e+02 Score=28.16 Aligned_cols=99 Identities=11% Similarity=0.171 Sum_probs=59.1
Q ss_pred hHHHHHHHHHHHhCCCCc-----------eEE-EEeeccccc-----chhhHHHhhhcCCceeeccCCCccchhhHHHHH
Q 001724 71 KVAHTITAAIRANGIKGP-----------VTI-TAFGDVVQM-----SRANQEVLSSTGINIAHVPHGGKNSADRSLLVD 133 (1020)
Q Consensus 71 ~Va~nI~~aLrelG~~Gp-----------VtI-RAYGDws~~-----~k~~qe~L~ssGI~LihvP~ggKNAADi~LiID 133 (1020)
.....|.++.+++||.-. -+| -+..++... -..+.+.+...|+.+.-+.... |......
T Consensus 31 ~tr~rV~~~a~~lgY~pn~~a~~l~~~~~~~Igvv~~~~~~~f~~~l~~~i~~~~~~~g~~~~i~~~~~----~~~~~~~ 106 (329)
T TIGR01481 31 ATRKKVLEVIKRLDYRPNAVARGLASKRTTTVGVIIPDISNIYYAELARGIEDIATMYKYNIILSNSDE----DPEKEVQ 106 (329)
T ss_pred HHHHHHHHHHHHHCCCCCHHHHHHhhCCCCEEEEEeCCCCchhHHHHHHHHHHHHHHcCCEEEEEeCCC----CHHHHHH
Confidence 344678889999997531 123 233344332 1235567778888876654321 1223344
Q ss_pred HHHHHHhCCCCcEEEEEeCCcchHHHHHHHHhCCCEEEEecC
Q 001724 134 LMYWVSQNPPPAHLFLISGDRDFASVLHRLRMNNYNILLASR 175 (1020)
Q Consensus 134 aMd~a~~nP~pdtFVLISGDsDFtpLL~RLRerGynVILagp 175 (1020)
++..+..+ .+++++|+..+.+ ..++..|++.|..|+++..
T Consensus 107 ~~~~l~~~-~vdGiIi~~~~~~-~~~~~~l~~~~iPvV~~~~ 146 (329)
T TIGR01481 107 VLNTLLSK-QVDGIIFMGGTIT-EKLREEFSRSPVPVVLAGT 146 (329)
T ss_pred HHHHHHhC-CCCEEEEeCCCCC-hHHHHHHHhcCCCEEEEec
Confidence 55555554 5999999865432 3456778888988887653
No 85
>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=30.82 E-value=2.5e+02 Score=29.53 Aligned_cols=63 Identities=16% Similarity=0.220 Sum_probs=36.3
Q ss_pred hhHHHhhhcCCceee--ccCCCccchhhHHHHHHH-HHHHhCCCCcEEEEEeCCcchHHHHHHHHhCCCE
Q 001724 103 ANQEVLSSTGINIAH--VPHGGKNSADRSLLVDLM-YWVSQNPPPAHLFLISGDRDFASVLHRLRMNNYN 169 (1020)
Q Consensus 103 ~~qe~L~ssGI~Lih--vP~ggKNAADi~LiIDaM-d~a~~nP~pdtFVLISGDsDFtpLL~RLRerGyn 169 (1020)
++++.|...|+.+.. +..+..+. .-..+++ .|+..+|.|+ .++.++|.--..+++.|+++|++
T Consensus 137 gf~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~l~~~~~~~-ai~~~~d~~a~g~~~~l~~~g~~ 202 (268)
T cd06270 137 GYRDALAEAGIALDESLIIEGDFTE---EGGYAAMQELLARGAPFT-AVFCANDEMAAGAISALREHGIS 202 (268)
T ss_pred HHHHHHHHcCCCCCcceEEECCCCH---HHHHHHHHHHHhCCCCCC-EEEEcCcHHHHHHHHHHHHcCCC
Confidence 467788888876522 21111111 1123333 3555566565 44566666667889999999875
No 86
>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=30.71 E-value=1.5e+02 Score=31.32 Aligned_cols=44 Identities=5% Similarity=0.021 Sum_probs=30.6
Q ss_pred HHHHHHHHHhCCCCcEEEEEeCCcc-hHHHHHHHHhCCCEEEEecC
Q 001724 131 LVDLMYWVSQNPPPAHLFLISGDRD-FASVLHRLRMNNYNILLASR 175 (1020)
Q Consensus 131 iIDaMd~a~~nP~pdtFVLISGDsD-FtpLL~RLRerGynVILagp 175 (1020)
...+++.+.++ .+++++|+..+.+ ..+.+..|+++|.-|+++..
T Consensus 46 ~~~~i~~l~~~-~vdgiIi~~~~~~~~~~~~~~~~~~~iPvV~~~~ 90 (275)
T cd06320 46 QLSIAENMINK-GYKGLLFSPISDVNLVPAVERAKKKGIPVVNVND 90 (275)
T ss_pred HHHHHHHHHHh-CCCEEEECCCChHHhHHHHHHHHHCCCeEEEECC
Confidence 34566666655 4899888766654 35677888888988887754
No 87
>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=30.41 E-value=1.4e+02 Score=31.59 Aligned_cols=44 Identities=5% Similarity=0.037 Sum_probs=32.1
Q ss_pred HHHHHHHHHHhCCCCcEEEEEeCCcc-hHHHHHHHHhCCCEEEEecC
Q 001724 130 LLVDLMYWVSQNPPPAHLFLISGDRD-FASVLHRLRMNNYNILLASR 175 (1020)
Q Consensus 130 LiIDaMd~a~~nP~pdtFVLISGDsD-FtpLL~RLRerGynVILagp 175 (1020)
.-.+.++.+.++ .+|+|+|+..|.+ +..++.+|++ |..|+++..
T Consensus 43 ~~~~~i~~l~~~-~vDgiIi~~~~~~~~~~~l~~~~~-~ipvV~~~~ 87 (271)
T cd06314 43 AQLRMLEDLIAE-GVDGIAISPIDPKAVIPALNKAAA-GIKLITTDS 87 (271)
T ss_pred HHHHHHHHHHhc-CCCEEEEecCChhHhHHHHHHHhc-CCCEEEecC
Confidence 344555555554 5999999988754 4688899988 988888754
No 88
>cd07018 S49_SppA_67K_type Signal peptide peptidase A (SppA) 67K type, a serine protease, has catalytic Ser-Lys dyad. Signal peptide peptidase A (SppA; Peptidase S49; Protease IV) 67K type: SppA is found in all three domains of life and is involved in the cleavage of signal peptides after their removal from the precursor proteins by signal peptidases. Members in this subfamily contain an amino-terminal domain in addition to the carboxyl-terminal protease domain that is conserved in all the S49 family members (sometimes referred to as 67K type), similar to E. coli and Arabidopsis thaliana SppA peptidases. Unlike the eukaryotic functional homologs that are proposed to be aspartic proteases, site-directed mutagenesis and sequence analysis have shown that members in this subfamily, mostly bacterial, are serine proteases. The predicted active site serine for members in this family occurs in a transmembrane domain. Mutagenesis studies also suggest that the catalytic center comprises a Ser-Lys
Probab=30.31 E-value=1.4e+02 Score=32.19 Aligned_cols=68 Identities=13% Similarity=0.123 Sum_probs=47.2
Q ss_pred cchhhHHHHHHHHHHHhCCCCcEEEEEeCCcc--------hHHHHHHHHhCCCEEEEecCCchh--HHHHhhcceEEe
Q 001724 124 NSADRSLLVDLMYWVSQNPPPAHLFLISGDRD--------FASVLHRLRMNNYNILLASRESAS--NVLCSAASVMWN 191 (1020)
Q Consensus 124 NAADi~LiIDaMd~a~~nP~pdtFVLISGDsD--------FtpLL~RLRerGynVILagp~kTp--eaL~sAcd~Fw~ 191 (1020)
+.....=++++++.+..+|.+..++|--.... +...+.++|+.|+.|+.+...-++ -.+..+||+.|-
T Consensus 27 ~~~~~~~l~~~l~~a~~d~~ik~vvL~~~s~gg~~~~~~el~~~i~~~~~~~kpVia~~~~~~sggy~lasaad~I~a 104 (222)
T cd07018 27 SELSLRDLLEALEKAAEDDRIKGIVLDLDGLSGGLAKLEELRQALERFRASGKPVIAYADGYSQGQYYLASAADEIYL 104 (222)
T ss_pred CCccHHHHHHHHHHHhcCCCeEEEEEECCCCCCCHHHHHHHHHHHHHHHHhCCeEEEEeCCCCchhhhhhhhCCEEEE
Confidence 34455678889999998888888888754432 445667778889999966554333 346677886654
No 89
>PRK09526 lacI lac repressor; Reviewed
Probab=30.18 E-value=3e+02 Score=30.20 Aligned_cols=65 Identities=18% Similarity=0.217 Sum_probs=38.3
Q ss_pred hhHHHhhhcCCceeeccCCCccchhhHHHHHHHHHHHhCCCCcEEEEEeCCcchHHHHHHHHhCCCEE
Q 001724 103 ANQEVLSSTGINIAHVPHGGKNSADRSLLVDLMYWVSQNPPPAHLFLISGDRDFASVLHRLRMNNYNI 170 (1020)
Q Consensus 103 ~~qe~L~ssGI~LihvP~ggKNAADi~LiIDaMd~a~~nP~pdtFVLISGDsDFtpLL~RLRerGynV 170 (1020)
++++.|...|+.+..+..+.-+ .+. -.-.+..|+..++.|+. +++.+|.-...++..|+++|+.|
T Consensus 202 Gf~~al~~~gi~~~~~~~~~~~-~~~-~~~~~~~~l~~~~~~~a-i~~~~d~~A~g~~~al~~~g~~v 266 (342)
T PRK09526 202 GWLEYLTDYQLQPIAVREGDWS-AMS-GYQQTLQMLREGPVPSA-ILVANDQMALGVLRALHESGLRV 266 (342)
T ss_pred HHHHHHHHcCCCcceEEeCCCc-hHH-HHHHHHHHhcCCCCCcE-EEEcCcHHHHHHHHHHHHcCCCC
Confidence 5788899999976543322211 111 11122344444555664 44567766678999999999853
No 90
>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=30.04 E-value=2.5e+02 Score=29.33 Aligned_cols=63 Identities=10% Similarity=0.174 Sum_probs=36.3
Q ss_pred hhHHHhhhcCCceee--ccCCCccchhhHHHHHHH-HHHHhCCCCcEEEEEeCCcchHHHHHHHHhCCCE
Q 001724 103 ANQEVLSSTGINIAH--VPHGGKNSADRSLLVDLM-YWVSQNPPPAHLFLISGDRDFASVLHRLRMNNYN 169 (1020)
Q Consensus 103 ~~qe~L~ssGI~Lih--vP~ggKNAADi~LiIDaM-d~a~~nP~pdtFVLISGDsDFtpLL~RLRerGyn 169 (1020)
++++.+...|+.+.. +..+. ...+ -..+++ .++..++.|++ +++++|.....++..|++.|+.
T Consensus 136 gf~~~~~~~~~~~~~~~~~~~~-~~~~--~~~~~~~~~l~~~~~~~a-ii~~~~~~a~~~~~~l~~~g~~ 201 (265)
T cd06290 136 GYRKALEEAGLEVQPDLIVQGD-FEEE--SGLEAVEELLQRGPDFTA-IFAANDQTAYGARLALYRRGLR 201 (265)
T ss_pred HHHHHHHHcCCCCCHHHEEecC-CCHH--HHHHHHHHHHcCCCCCCE-EEEcCcHHHHHHHHHHHHcCCC
Confidence 467778788876542 22211 1112 122333 45545666665 3456677677888999999874
No 91
>PRK01045 ispH 4-hydroxy-3-methylbut-2-enyl diphosphate reductase; Reviewed
Probab=29.82 E-value=1.3e+02 Score=34.62 Aligned_cols=102 Identities=19% Similarity=0.175 Sum_probs=53.3
Q ss_pred HHHHHHHHHHHhCCCCceEEEEeecccccchhhHHHhhhcCCceeeccCCCc-cch----hhHHHHHHHHHHHhCCCCcE
Q 001724 72 VAHTITAAIRANGIKGPVTITAFGDVVQMSRANQEVLSSTGINIAHVPHGGK-NSA----DRSLLVDLMYWVSQNPPPAH 146 (1020)
Q Consensus 72 Va~nI~~aLrelG~~GpVtIRAYGDws~~~k~~qe~L~ssGI~LihvP~ggK-NAA----Di~LiIDaMd~a~~nP~pdt 146 (1020)
|..+|+.+.+.+...| -.|..||++-.. ....+.|...||.++.-...-. +++ ---+--..++.|.++.
T Consensus 15 V~rAi~~a~~~~~~~~-~~iytlG~iIHN-~~vv~~L~~~GV~~v~~~~~v~~~~~ViirAHGv~~~~~~~~~~~g---- 88 (298)
T PRK01045 15 VDRAIEIVERALEKYG-APIYVRHEIVHN-RYVVERLEKKGAIFVEELDEVPDGAIVIFSAHGVSPAVREEAKERG---- 88 (298)
T ss_pred HHHHHHHHHHHHHhcC-CCeEEEecCccC-HHHHHHHHHCCCEEecCcccCCCCCEEEEeCCCCCHHHHHHHHHCC----
Confidence 4455655544332222 136888988653 3467789999998775322100 000 0001123334444321
Q ss_pred EEEEeCCc------chHHHHHHHHhCCCEEEEecCCchhHH
Q 001724 147 LFLISGDR------DFASVLHRLRMNNYNILLASRESASNV 181 (1020)
Q Consensus 147 FVLISGDs------DFtpLL~RLRerGynVILagp~kTpea 181 (1020)
+-+| |. ---.++.++.+.||.|+++|....|+.
T Consensus 89 ~~vi--DaTCP~V~k~~~~v~~~~~~Gy~vvi~G~~~HpEv 127 (298)
T PRK01045 89 LTVI--DATCPLVTKVHKEVARMSREGYEIILIGHKGHPEV 127 (298)
T ss_pred CeEE--eCCCccchHHHHHHHHHHhCCCEEEEEeCCCCCee
Confidence 1122 21 122456667778999999988877764
No 92
>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=29.62 E-value=1.7e+02 Score=30.89 Aligned_cols=63 Identities=16% Similarity=0.197 Sum_probs=38.2
Q ss_pred hhhHHHhhhcCCceee--ccCCCccchhhHHHHHHH-HHHHhCCCCcEEEEEeCCcchHHHHHHHHhCCCE
Q 001724 102 RANQEVLSSTGINIAH--VPHGGKNSADRSLLVDLM-YWVSQNPPPAHLFLISGDRDFASVLHRLRMNNYN 169 (1020)
Q Consensus 102 k~~qe~L~ssGI~Lih--vP~ggKNAADi~LiIDaM-d~a~~nP~pdtFVLISGDsDFtpLL~RLRerGyn 169 (1020)
.++++.+...|+.+.. +.... . .+ -..+++ .|+..++.|++++ +++|.--..++..|+++|++
T Consensus 136 ~Gf~~~~~~~~~~~~~~~~~~~~-~-~~--~~~~~~~~~l~~~~~~~ai~-~~~d~~a~g~~~~l~~~g~~ 201 (269)
T cd06281 136 EGYKAAFAAAGLPPDPALVRLST-P-AA--SGFDATRALLALPDRPTAII-AGGTQVLVGVLRALREAGLR 201 (269)
T ss_pred HHHHHHHHHcCCCCCHHHeecCc-H-HH--HHHHHHHHHHcCCCCCcEEE-EcCcHHHHHHHHHHHHcCCC
Confidence 3578888888986521 21211 1 11 123333 4555566678764 56676666889999999974
No 93
>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=29.58 E-value=1.6e+02 Score=30.78 Aligned_cols=66 Identities=9% Similarity=0.081 Sum_probs=37.9
Q ss_pred hHHHhhhcCCceeeccCCCccchhhHHHHHHHHHHHhCCCCcEEEEEeCCcchHHHHHHHHhCCCEEEEecC
Q 001724 104 NQEVLSSTGINIAHVPHGGKNSADRSLLVDLMYWVSQNPPPAHLFLISGDRDFASVLHRLRMNNYNILLASR 175 (1020)
Q Consensus 104 ~qe~L~ssGI~LihvP~ggKNAADi~LiIDaMd~a~~nP~pdtFVLISGDsDFtpLL~RLRerGynVILagp 175 (1020)
..+++...|+.+..+.... |..--.++++.+... .+++++|...+.+- ..+.+|+++|..|+++..
T Consensus 21 i~~~~~~~g~~~~~~~~~~----~~~~~~~~~~~l~~~-~vdgiIi~~~~~~~-~~~~~l~~~~ipvV~~~~ 86 (265)
T cd06299 21 IQDAASAAGYSTIIGNSDE----NPETENRYLDNLLSQ-RVDGIIVVPHEQSA-EQLEDLLKRGIPVVFVDR 86 (265)
T ss_pred HHHHHHHcCCEEEEEeCCC----CHHHHHHHHHHHHhc-CCCEEEEcCCCCCh-HHHHHHHhCCCCEEEEec
Confidence 3444555666555543321 111223455555554 48888887666543 457888888888887654
No 94
>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=29.47 E-value=3.5e+02 Score=28.27 Aligned_cols=73 Identities=16% Similarity=0.158 Sum_probs=41.3
Q ss_pred hhHHHhhhcCCceee--ccCCCccchhhHHHHHHH-HHHHhCCCCcEEEEEeCCcchHHHHHHHHhCCC----EEEEecC
Q 001724 103 ANQEVLSSTGINIAH--VPHGGKNSADRSLLVDLM-YWVSQNPPPAHLFLISGDRDFASVLHRLRMNNY----NILLASR 175 (1020)
Q Consensus 103 ~~qe~L~ssGI~Lih--vP~ggKNAADi~LiIDaM-d~a~~nP~pdtFVLISGDsDFtpLL~RLRerGy----nVILagp 175 (1020)
++++.+...|+.... +.....+ .+ -..+++ .|+..++.|+. +++++|.-...+++.|++.|+ .|.+++-
T Consensus 132 gf~~~~~~~~~~~~~~~~~~~~~~-~~--~~~~~~~~~l~~~~~~~a-i~~~~d~~a~~~~~~l~~~g~~vp~dv~vvg~ 207 (261)
T cd06272 132 GFLETCDENGISISDSHIDVDGLS-AE--GGDNAAKKLLKESDLPTA-IICGSYDIALGVLSALNKQGISIPEDIEIISY 207 (261)
T ss_pred HHHHHHHHcCCCCCHHHeeeCCCC-HH--HHHHHHHHHHcCCCCCCE-EEECCcHHHHHHHHHHHHhCCCCCCceEEEee
Confidence 567788888874322 2221111 11 122333 35545554554 666777777789999999997 4555554
Q ss_pred Cchh
Q 001724 176 ESAS 179 (1020)
Q Consensus 176 ~kTp 179 (1020)
..++
T Consensus 208 d~~~ 211 (261)
T cd06272 208 DNIP 211 (261)
T ss_pred CChh
Confidence 4433
No 95
>PF13407 Peripla_BP_4: Periplasmic binding protein domain; PDB: 3BRS_B 3GBP_A 3GA5_A 1GCG_A 1GCA_A 3H75_A 3D02_A 3L49_B 3EJW_B 3T95_A ....
Probab=29.47 E-value=1.4e+02 Score=31.18 Aligned_cols=69 Identities=9% Similarity=0.132 Sum_probs=50.5
Q ss_pred hhHHHhhhcCCceeec-cCCCccchhhHHHHHHHHHHHhCCCCcEEEEEeCCc-chHHHHHHHHhCCCEEEEecCC
Q 001724 103 ANQEVLSSTGINIAHV-PHGGKNSADRSLLVDLMYWVSQNPPPAHLFLISGDR-DFASVLHRLRMNNYNILLASRE 176 (1020)
Q Consensus 103 ~~qe~L~ssGI~Lihv-P~ggKNAADi~LiIDaMd~a~~nP~pdtFVLISGDs-DFtpLL~RLRerGynVILagp~ 176 (1020)
..+..+...|+.+..+ +... |..-.+++++-+... .+|+|+|...|. ...+++.++++.|..|+.+...
T Consensus 19 g~~~~a~~~g~~~~~~~~~~~----d~~~q~~~i~~~i~~-~~d~Iiv~~~~~~~~~~~l~~~~~~gIpvv~~d~~ 89 (257)
T PF13407_consen 19 GAKAAAKELGYEVEIVFDAQN----DPEEQIEQIEQAISQ-GVDGIIVSPVDPDSLAPFLEKAKAAGIPVVTVDSD 89 (257)
T ss_dssp HHHHHHHHHTCEEEEEEESTT----THHHHHHHHHHHHHT-TESEEEEESSSTTTTHHHHHHHHHTTSEEEEESST
T ss_pred HHHHHHHHcCCEEEEeCCCCC----CHHHHHHHHHHHHHh-cCCEEEecCCCHHHHHHHHHHHhhcCceEEEEecc
Confidence 4455666777776664 3322 335666777777765 499999998887 5789999999999999987554
No 96
>cd06268 PBP1_ABC_transporter_LIVBP_like Periplasmic binding domain of ATP-binding cassette transporter-like systems that belong to the type I periplasmic binding fold protein superfamily. Periplasmic binding domain of ATP-binding cassette transporter-like systems that belong to the type I periplasmic binding fold protein superfamily. They are mostly present in archaea and eubacteria, and are primarily involved in scavenging solutes from the environment. ABC-type transporters couple ATP hydrolysis with the uptake and efflux of a wide range of substrates across bacterial membranes, including amino acids, peptides, lipids and sterols, and various drugs. These systems are comprised of transmembrane domains, nucleotide binding domains, and in most bacterial uptake systems, periplasmic binding proteins (PBPs) which transfer the ligand to the extracellular gate of the transmembrane domains. These PBPs bind their substrates selectively and with high affinity. Members of this group include ABC
Probab=29.25 E-value=4.9e+02 Score=26.98 Aligned_cols=96 Identities=16% Similarity=0.163 Sum_probs=52.2
Q ss_pred HHHHHHHHHhCCCCceEE-EEeeccccc---chhhHHHhhhcCCceeeccCCCccchhhHHHHHHHHHHHhCCCCcEEEE
Q 001724 74 HTITAAIRANGIKGPVTI-TAFGDVVQM---SRANQEVLSSTGINIAHVPHGGKNSADRSLLVDLMYWVSQNPPPAHLFL 149 (1020)
Q Consensus 74 ~nI~~aLrelG~~GpVtI-RAYGDws~~---~k~~qe~L~ssGI~LihvP~ggKNAADi~LiIDaMd~a~~nP~pdtFVL 149 (1020)
..+-..+...+ |.-.| -+|++.... ...+++.+...|++++....-..+..|. .+++.-+... .++.+++
T Consensus 123 ~~~~~~~~~~~--~~~~i~~v~~~~~~~~~~~~~~~~~~~~~g~~i~~~~~~~~~~~~~---~~~~~~l~~~-~~~~vi~ 196 (298)
T cd06268 123 AALADYLAEKG--KVKKVAIIYDDYAYGRGLAAAFREALKKLGGEVVAEETYPPGATDF---SPLIAKLKAA-GPDAVFL 196 (298)
T ss_pred HHHHHHHHHhc--CCCEEEEEEcCCchhHHHHHHHHHHHHHcCCEEEEEeccCCCCccH---HHHHHHHHhc-CCCEEEE
Confidence 34444444443 12233 455554321 1346678888998876532111112332 2223223332 3677766
Q ss_pred EeCCcchHHHHHHHHhCCCEEEEecC
Q 001724 150 ISGDRDFASVLHRLRMNNYNILLASR 175 (1020)
Q Consensus 150 ISGDsDFtpLL~RLRerGynVILagp 175 (1020)
++...+...++..|++.|+.+-+++.
T Consensus 197 ~~~~~~~~~~~~~~~~~g~~~~~~~~ 222 (298)
T cd06268 197 AGYGGDAALFLKQAREAGLKVPIVGG 222 (298)
T ss_pred ccccchHHHHHHHHHHcCCCCcEEec
Confidence 66657889999999999987665543
No 97
>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=28.78 E-value=1.7e+02 Score=30.74 Aligned_cols=41 Identities=10% Similarity=0.056 Sum_probs=29.0
Q ss_pred HHHHHHhCCCCcEEEEEeCCcc-hHHHHHHHHhCCCEEEEecC
Q 001724 134 LMYWVSQNPPPAHLFLISGDRD-FASVLHRLRMNNYNILLASR 175 (1020)
Q Consensus 134 aMd~a~~nP~pdtFVLISGDsD-FtpLL~RLRerGynVILagp 175 (1020)
+++.+... .+++++|.+.|.+ ..+.+.+|+++|..|+.+..
T Consensus 49 ~i~~~~~~-~~dgiIi~~~~~~~~~~~i~~~~~~~ipvv~~~~ 90 (271)
T cd06321 49 QIDNFIAA-KVDLILLNAVDSKGIAPAVKRAQAAGIVVVAVDV 90 (271)
T ss_pred HHHHHHHh-CCCEEEEeCCChhHhHHHHHHHHHCCCeEEEecC
Confidence 33334443 4899988877654 46788889999998887754
No 98
>PF00857 Isochorismatase: Isochorismatase family; InterPro: IPR000868 This is a family of hydrolase enzymes. Isochorismatase, also known as 2,3 dihydro-2,3 dihydroxybenzoate synthase catalyses the conversion of isochorismate, in the presence of water, to 2,3-dihydroxybenzoate and pyruvate (3.3.2.1 from EC).; GO: 0003824 catalytic activity, 0008152 metabolic process; PDB: 1XN4_A 3KL2_F 1YZV_A 3IRV_A 1IM5_A 1ILW_A 3PL1_A 1NF9_A 1NF8_A 1X9G_A ....
Probab=28.75 E-value=1.4e+02 Score=29.99 Aligned_cols=116 Identities=17% Similarity=0.103 Sum_probs=61.7
Q ss_pred EEEEecCCCCCC---CCCChhhHHHHHHHHHHHhCCCC-ceEE-EEeec---ccccc---------------hhhHHHhh
Q 001724 53 SVWWDFENCNLP---AGVNAFKVAHTITAAIRANGIKG-PVTI-TAFGD---VVQMS---------------RANQEVLS 109 (1020)
Q Consensus 53 AVFWDiENcpiP---~g~d~~~Va~nI~~aLrelG~~G-pVtI-RAYGD---ws~~~---------------k~~qe~L~ 109 (1020)
-|.+|+.|-.++ .......+..+|.++++.....| +|.. +.+.. |.... ..+...|.
T Consensus 3 LlvID~Q~~f~~~~~~~~~~~~~i~~i~~l~~~~r~~~~~Vi~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~l~~~l~ 82 (174)
T PF00857_consen 3 LLVIDMQNDFINGSLAPPNAEAIIPNINRLLDAARAAGVPVIHTRDIHDSPHWSGPFEPKPWPPHCIPGSPGAELVPELA 82 (174)
T ss_dssp EEEES-BHHHHTSTTTSTTHHHHHHHHHHHHHHHHHTTEEEEEEEESBSTTTTTTSGGHSCHTSCSBTTSGGGSBHGGGH
T ss_pred EEEEeChhhhhcCCccccCHHHHHHHHHHHHHHHHHhCCCeEEEEeeecccccccccccccccccccCCCCccceeeEee
Confidence 478899886651 22345567778888888775456 3433 55544 11000 01111221
Q ss_pred hc-CCceeeccCCCccchhhHHHHHHHHHHHhCCCCcEEEEEeCCcch--HHHHHHHHhCCCEEEEec
Q 001724 110 ST-GINIAHVPHGGKNSADRSLLVDLMYWVSQNPPPAHLFLISGDRDF--ASVLHRLRMNNYNILLAS 174 (1020)
Q Consensus 110 ss-GI~LihvP~ggKNAADi~LiIDaMd~a~~nP~pdtFVLISGDsDF--tpLL~RLRerGynVILag 174 (1020)
.. +-.++ .|+..+.-.-.|+..|+..+ .+++++|+--..++ ...+..+..+||+|+++.
T Consensus 83 ~~~~~~vi-----~K~~~saf~~t~L~~~L~~~-gi~~vil~G~~t~~CV~~Ta~~a~~~g~~v~v~~ 144 (174)
T PF00857_consen 83 PQPGDPVI-----EKNRYSAFFGTDLDEILRKR-GIDTVILCGVATDVCVLATARDAFDRGYRVIVVE 144 (174)
T ss_dssp CHTTSEEE-----EESSSSTTTTSSHHHHHHHT-TESEEEEEEESTTTHHHHHHHHHHHTT-EEEEEE
T ss_pred cccccceE-----Eeeccccccccccccccccc-ccceEEEcccccCcEEehhHHHHHHCCCEEEEEC
Confidence 11 11111 13322222234666777775 48998888666665 456677778999999764
No 99
>cd06323 PBP1_ribose_binding Periplasmic sugar-binding domain of the thermophilic Thermoanaerobacter tengcongensis ribose binding protein (ttRBP) and its mesophilic homologs. Periplasmic sugar-binding domain of the thermophilic Thermoanaerobacter tengcongensis ribose binding protein (ttRBP) and its mesophilic homologs. Members of this group are belonging to the type I periplasmic binding protein superfamily, whose members are involved in chemotaxis, ATP-binding cassette transport, and intercellular communication in central nervous system. The thermophilic and mesophilic ribose-binding proteins are structurally very similar, but differ substantially in thermal stability.
Probab=28.62 E-value=6.8e+02 Score=25.96 Aligned_cols=74 Identities=11% Similarity=0.147 Sum_probs=42.3
Q ss_pred hhHHHhhh-cCCceeeccCCCccchhhHHHHHHHHHHHhCCCCcEEEEEeCCcchHHHHHHHHhCCC-EEEEecCCchh
Q 001724 103 ANQEVLSS-TGINIAHVPHGGKNSADRSLLVDLMYWVSQNPPPAHLFLISGDRDFASVLHRLRMNNY-NILLASRESAS 179 (1020)
Q Consensus 103 ~~qe~L~s-sGI~LihvP~ggKNAADi~LiIDaMd~a~~nP~pdtFVLISGDsDFtpLL~RLRerGy-nVILagp~kTp 179 (1020)
++++.|.. .|+.+.....+..+..+ ..-.+.+++..+|.++. +++.+|..-..++..|+++|+ .|-+++-...+
T Consensus 142 g~~~~l~~~~~~~~~~~~~~~~~~~~--~~~~~~~~l~~~~~~~a-i~~~~d~~a~~~~~~l~~~g~~di~iig~d~~~ 217 (268)
T cd06323 142 GFHEVVDKYPGLKVVASQPADFDRAK--GLNVMENILQAHPDIKG-VFAQNDEMALGAIEALKAAGKDDVKVVGFDGTP 217 (268)
T ss_pred HHHHHHHhCCCcEEEecccCCCCHHH--HHHHHHHHHHHCCCcCE-EEEcCCchHHHHHHHHHHcCCCCcEEEEeCCCH
Confidence 46777877 48876643332222111 12233455555555554 566666665678899999998 55555544333
No 100
>KOG2961 consensus Predicted hydrolase (HAD superfamily) [General function prediction only]
Probab=28.57 E-value=2.9e+02 Score=29.60 Aligned_cols=114 Identities=18% Similarity=0.253 Sum_probs=65.9
Q ss_pred eEEEEEecCCCC-CCCCCChhhHHHHHHHHHHHh-CCCCceEEEEeecccc----cchhhHH-Hh-hhcCCceeeccCCC
Q 001724 51 RVSVWWDFENCN-LPAGVNAFKVAHTITAAIRAN-GIKGPVTITAFGDVVQ----MSRANQE-VL-SSTGINIAHVPHGG 122 (1020)
Q Consensus 51 rVAVFWDiENcp-iP~g~d~~~Va~nI~~aLrel-G~~GpVtIRAYGDws~----~~k~~qe-~L-~ssGI~LihvP~gg 122 (1020)
==||..|=|||- .|... .|.+....-++++ ..||.-.|-++-|-.- -+..-+. .| +..||.+..-.. .
T Consensus 43 ikavVlDKDNcit~P~~~---~Iwp~~l~~ie~~~~vygek~i~v~SNsaG~~~~D~d~s~Ak~le~k~gIpVlRHs~-k 118 (190)
T KOG2961|consen 43 IKAVVLDKDNCITAPYSL---AIWPPLLPSIERCKAVYGEKDIAVFSNSAGLTEYDHDDSKAKALEAKIGIPVLRHSV-K 118 (190)
T ss_pred ceEEEEcCCCeeeCCccc---ccCchhHHHHHHHHHHhCcccEEEEecCcCccccCCchHHHHHHHHhhCCceEeecc-c
Confidence 358889999993 34432 2322222222222 4567544444433222 1222222 33 347886543111 1
Q ss_pred ccchhhHHHHHHHHHHHhCCCCcE--EEEEeCCcchHHHHHHHHhCCCEEEE
Q 001724 123 KNSADRSLLVDLMYWVSQNPPPAH--LFLISGDRDFASVLHRLRMNNYNILL 172 (1020)
Q Consensus 123 KNAADi~LiIDaMd~a~~nP~pdt--FVLISGDsDFtpLL~RLRerGynVIL 172 (1020)
|-+ .....+++.+.|.++.+ =+|+-||+=|+.++..=+|--+-|.+
T Consensus 119 KP~----ct~E~~~y~~~Nshv~~~se~~~vGDRlfTDI~~aN~mGs~gVw~ 166 (190)
T KOG2961|consen 119 KPA----CTAEEVEYHFGNSHVCTSSELIMVGDRLFTDIVYANRMGSLGVWT 166 (190)
T ss_pred CCC----ccHHHHHHHhCCcccCChhHeEEEccchhhhHhhhhhccceeEEe
Confidence 222 45677889999877665 57778999999999888887777775
No 101
>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=28.51 E-value=6.4e+02 Score=27.39 Aligned_cols=76 Identities=16% Similarity=0.213 Sum_probs=42.9
Q ss_pred hhHHHhhhcCCceeeccCCCccchhhHHHHHHHH-HHHhCCCCcEEEEEeCCcchHHHHHHHHhCC--CEEEEecCCchh
Q 001724 103 ANQEVLSSTGINIAHVPHGGKNSADRSLLVDLMY-WVSQNPPPAHLFLISGDRDFASVLHRLRMNN--YNILLASRESAS 179 (1020)
Q Consensus 103 ~~qe~L~ssGI~LihvP~ggKNAADi~LiIDaMd-~a~~nP~pdtFVLISGDsDFtpLL~RLRerG--ynVILagp~kTp 179 (1020)
++++.|...|+.+..+..+.-+. .-...++. ++..+|.++.| +++|.-=..++..|++.| ..|-+++...+|
T Consensus 146 Gf~~al~~~g~~~~~~~~~~~~~---~~~~~~~~~~L~~~~~~d~i--~~~d~~a~g~l~al~~~g~~~dv~vvg~~~~p 220 (295)
T TIGR02955 146 GFRAALEGSDVEISAILWADNDK---ELQRNLLQDLLKKHPDIDYL--VGSAVAAEAAISELRSLHMTQQIKLVSTYLSH 220 (295)
T ss_pred HHHHHHhcCCcEEEEEecCCCcH---HHHHHHHHHHHHhCCCcCEE--EeccHHHHHHHHHHHhhCccCCeEEEEecCCH
Confidence 57888988898766532222211 12233333 44456667743 556644446777887765 455566655566
Q ss_pred HHHH
Q 001724 180 NVLC 183 (1020)
Q Consensus 180 eaL~ 183 (1020)
..+.
T Consensus 221 ~~~~ 224 (295)
T TIGR02955 221 GVYR 224 (295)
T ss_pred HHHH
Confidence 5554
No 102
>cd06337 PBP1_ABC_ligand_binding_like_4 Type I periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type active transport systems that are predicted to be involved in transport of amino acids, peptides, or inorganic ions. This subgroup includes the type I periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type active transport systems that are predicted to be involved in transport of amino acids, peptides, or inorganic ions. Members of this group are sequence-similar to members of the family of ABC-type hydrophobic amino acid transporters, such as leucine-isoleucine-valine-binding protein (LIVBP); however their ligand specificity has not been determined experimentally.
Probab=28.40 E-value=2.5e+02 Score=31.61 Aligned_cols=63 Identities=11% Similarity=0.111 Sum_probs=41.5
Q ss_pred HHHhhhcCCceeec-cCCCccchhhHHHHHHHHHHHhCCCCcEEEEEeCCcchHHHHHHHHhCCCEEEE
Q 001724 105 QEVLSSTGINIAHV-PHGGKNSADRSLLVDLMYWVSQNPPPAHLFLISGDRDFASVLHRLRMNNYNILL 172 (1020)
Q Consensus 105 qe~L~ssGI~Lihv-P~ggKNAADi~LiIDaMd~a~~nP~pdtFVLISGDsDFtpLL~RLRerGynVIL 172 (1020)
...|...|++++.. ... -+.+|..=.+.-+ .. -.||.+++++...|...+++.+|+.|+++-+
T Consensus 169 ~~~~~~~G~~vv~~~~~~-~~~~D~~~~v~~i--k~--a~pD~v~~~~~~~~~~~~~~~~~~~G~~~~~ 232 (357)
T cd06337 169 PAALADAGYKLVDPGRFE-PGTDDFSSQINAF--KR--EGVDIVTGFAIPPDFATFWRQAAQAGFKPKI 232 (357)
T ss_pred cHHHHhCCcEEecccccC-CCCCcHHHHHHHH--Hh--cCCCEEEeCCCccHHHHHHHHHHHCCCCCCe
Confidence 34667789998742 211 1345755343332 22 2479988888888999999999999987543
No 103
>PLN02342 ornithine carbamoyltransferase
Probab=28.37 E-value=5e+02 Score=30.52 Aligned_cols=110 Identities=8% Similarity=0.103 Sum_probs=60.3
Q ss_pred EEEEecCCCCCCCCCChhhHHHHHHHHHHHhCCCCce-EEEEeecccccchhhHHHhhhcCCceeeccCCCccchhhHHH
Q 001724 53 SVWWDFENCNLPAGVNAFKVAHTITAAIRANGIKGPV-TITAFGDVVQMSRANQEVLSSTGINIAHVPHGGKNSADRSLL 131 (1020)
Q Consensus 53 AVFWDiENcpiP~g~d~~~Va~nI~~aLrelG~~GpV-tIRAYGDws~~~k~~qe~L~ssGI~LihvP~ggKNAADi~Li 131 (1020)
+|++|.....+..|-+ |...++-++.|..+ .+|.|.+- ...+.-...+|.+|..-. +. .==-..+
T Consensus 114 ~i~l~~~~ss~~kGES-------l~DTarvLs~y~D~IviR~~~~~-----~~~~la~~~~vPVINA~~-~~-~HPtQaL 179 (348)
T PLN02342 114 ALYLGPDDIQLGKREE-------TRDIARVLSRYNDIIMARVFAHQ-----DVLDLAEYSSVPVINGLT-DY-NHPCQIM 179 (348)
T ss_pred EEEeCcccccCCCCcC-------HHHHHHHHHHhCCEEEEeCCChH-----HHHHHHHhCCCCEEECCC-CC-CChHHHH
Confidence 4555666665544422 33333444333444 34765322 122222345666665421 11 2235789
Q ss_pred HHHHHHHHhCCCCc--EEEEEeCCcc--hHHHHHHHHhCCCEEEEecCCc
Q 001724 132 VDLMYWVSQNPPPA--HLFLISGDRD--FASVLHRLRMNNYNILLASRES 177 (1020)
Q Consensus 132 IDaMd~a~~nP~pd--tFVLISGDsD--FtpLL~RLRerGynVILagp~k 177 (1020)
.|++.+......++ ++++| ||.. .-.++.-|...|.+|.+++|..
T Consensus 180 aDl~Ti~e~~G~l~glkva~v-GD~~nva~Sli~~~~~~G~~v~~~~P~~ 228 (348)
T PLN02342 180 ADALTIIEHIGRLEGTKVVYV-GDGNNIVHSWLLLAAVLPFHFVCACPKG 228 (348)
T ss_pred HHHHHHHHHhCCcCCCEEEEE-CCCchhHHHHHHHHHHcCCEEEEECCcc
Confidence 99988876555555 35555 8853 3345555677899999999865
No 104
>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=27.99 E-value=1.7e+02 Score=30.30 Aligned_cols=42 Identities=19% Similarity=0.143 Sum_probs=29.1
Q ss_pred HHHHHHHhCCCCcEEEEEeCCcchHHHHHHHHhCCCEEEEecC
Q 001724 133 DLMYWVSQNPPPAHLFLISGDRDFASVLHRLRMNNYNILLASR 175 (1020)
Q Consensus 133 DaMd~a~~nP~pdtFVLISGDsDFtpLL~RLRerGynVILagp 175 (1020)
.++..+... .++++++...+.+....+.+|+++|..|+++..
T Consensus 46 ~~~~~l~~~-~vdgiii~~~~~~~~~~~~~~~~~~ipvV~~~~ 87 (266)
T cd06282 46 DAVETLLRQ-RVDGLILTVADAATSPALDLLDAERVPYVLAYN 87 (266)
T ss_pred HHHHHHHhc-CCCEEEEecCCCCchHHHHHHhhCCCCEEEEec
Confidence 334444443 589998887776555678889999988876653
No 105
>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=27.96 E-value=1.6e+02 Score=30.76 Aligned_cols=42 Identities=5% Similarity=0.041 Sum_probs=29.7
Q ss_pred HHHHHHHHhCCCCcEEEEEeCCcc-hHHHHHHHHhCCCEEEEec
Q 001724 132 VDLMYWVSQNPPPAHLFLISGDRD-FASVLHRLRMNNYNILLAS 174 (1020)
Q Consensus 132 IDaMd~a~~nP~pdtFVLISGDsD-FtpLL~RLRerGynVILag 174 (1020)
..++..+... .+++++++..|.+ +...+.++++.|..|+++.
T Consensus 45 ~~~~~~~~~~-~vdgiii~~~~~~~~~~~~~~~~~~~ipvV~~~ 87 (267)
T cd06322 45 LSDVEDFITK-KVDAIVLSPVDSKGIRAAIAKAKKAGIPVITVD 87 (267)
T ss_pred HHHHHHHHHc-CCCEEEEcCCChhhhHHHHHHHHHCCCCEEEEc
Confidence 3444444444 4899999877654 5777888999998888765
No 106
>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=27.93 E-value=1.8e+02 Score=29.90 Aligned_cols=67 Identities=6% Similarity=0.067 Sum_probs=43.3
Q ss_pred hHHHhhhcCCceeeccCCCccchhhHHHHHHHHHHHhCCCCcEEEEEeCCcchH-HHHHHHHhCCCEEEEecC
Q 001724 104 NQEVLSSTGINIAHVPHGGKNSADRSLLVDLMYWVSQNPPPAHLFLISGDRDFA-SVLHRLRMNNYNILLASR 175 (1020)
Q Consensus 104 ~qe~L~ssGI~LihvP~ggKNAADi~LiIDaMd~a~~nP~pdtFVLISGDsDFt-pLL~RLRerGynVILagp 175 (1020)
...++...|+.+..+.... +. .-..+++..+... .++++++++.+.+.. ..+..|+..|..|+.+..
T Consensus 21 ~~~~a~~~g~~~~~~~~~~-~~---~~~~~~~~~l~~~-~vdgvi~~~~~~~~~~~~~~~l~~~~ip~V~~~~ 88 (267)
T cd01536 21 AEAAAKELGVELIVLDAQN-DV---SKQIQQIEDLIAQ-GVDGIIISPVDSAALTPALKKANAAGIPVVTVDS 88 (267)
T ss_pred HHHHHHhcCceEEEECCCC-CH---HHHHHHHHHHHHc-CCCEEEEeCCCchhHHHHHHHHHHCCCcEEEecC
Confidence 3445555677766655432 11 2234566655554 589999998776553 578899999988887654
No 107
>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=27.43 E-value=1.9e+02 Score=30.33 Aligned_cols=65 Identities=9% Similarity=0.130 Sum_probs=41.1
Q ss_pred HHhhhcCCceeeccCCCccchhhHHHHHHHHHHHhCCCCcEEEEEeCCcch-HHHHHHHHhCCCEEEEecC
Q 001724 106 EVLSSTGINIAHVPHGGKNSADRSLLVDLMYWVSQNPPPAHLFLISGDRDF-ASVLHRLRMNNYNILLASR 175 (1020)
Q Consensus 106 e~L~ssGI~LihvP~ggKNAADi~LiIDaMd~a~~nP~pdtFVLISGDsDF-tpLL~RLRerGynVILagp 175 (1020)
+++...|+.++.+.... |..-.+.++..+.+. .+++++|...+.+. ...+..|+++|..|+++..
T Consensus 24 ~~~~~~g~~~~~~~~~~----~~~~~~~~~~~l~~~-~vdgiii~~~~~~~~~~~l~~~~~~~iPvV~~~~ 89 (275)
T cd06317 24 AAAEEDGVEVIVLDANG----DVARQAAQVEDLIAQ-KVDGIILWPTDGQAYIPGLRKAKQAGIPVVITNS 89 (275)
T ss_pred HHHHhcCCEEEEEcCCc----CHHHHHHHHHHHHHc-CCCEEEEecCCccccHHHHHHHHHCCCcEEEeCC
Confidence 34444555555443221 222334556656555 49999998877664 5788999999999887653
No 108
>COG0794 GutQ Predicted sugar phosphate isomerase involved in capsule formation [Cell envelope biogenesis, outer membrane]
Probab=27.38 E-value=3.1e+02 Score=30.05 Aligned_cols=96 Identities=21% Similarity=0.256 Sum_probs=65.5
Q ss_pred CCCceEEEEeecccccchhhHHHhhhcCCceeeccCCCccchhhHHHHHHHHHHHhCCCCcEEEEEeCCc---chHHHHH
Q 001724 85 IKGPVTITAFGDVVQMSRANQEVLSSTGINIAHVPHGGKNSADRSLLVDLMYWVSQNPPPAHLFLISGDR---DFASVLH 161 (1020)
Q Consensus 85 ~~GpVtIRAYGDws~~~k~~qe~L~ssGI~LihvP~ggKNAADi~LiIDaMd~a~~nP~pdtFVLISGDs---DFtpLL~ 161 (1020)
..|+|.|.--|.--...+.+---|...|.....+-..--.-.|.-|+ .+=|-+++||+-. .-..++.
T Consensus 38 ~~gkv~V~G~GkSG~Igkk~Aa~L~s~G~~a~fv~p~ea~hgdlg~i----------~~~DvviaiS~SGeT~el~~~~~ 107 (202)
T COG0794 38 CKGKVFVTGVGKSGLIGKKFAARLASTGTPAFFVGPAEALHGDLGMI----------TPGDVVIAISGSGETKELLNLAP 107 (202)
T ss_pred cCCcEEEEcCChhHHHHHHHHHHHHccCCceEEecCchhccCCccCC----------CCCCEEEEEeCCCcHHHHHHHHH
Confidence 36777776666655555666667889999887774221111233333 2368899998886 4678899
Q ss_pred HHHhCCCEEEEecCCchhHHHHhhcceEEe
Q 001724 162 RLRMNNYNILLASRESASNVLCSAASVMWN 191 (1020)
Q Consensus 162 RLRerGynVILagp~kTpeaL~sAcd~Fw~ 191 (1020)
.+|+.|-.|+.++....+ .|..++|.++.
T Consensus 108 ~aK~~g~~liaiT~~~~S-sLak~aDvvl~ 136 (202)
T COG0794 108 KAKRLGAKLIAITSNPDS-SLAKAADVVLV 136 (202)
T ss_pred HHHHcCCcEEEEeCCCCC-hHHHhcCeEEE
Confidence 999999999988765554 46677887765
No 109
>PF02739 5_3_exonuc_N: 5'-3' exonuclease, N-terminal resolvase-like domain; InterPro: IPR020046 The N-terminal and internal 5'3'-exonuclease domains are commonly found together, and are most often associated with 5' to 3' nuclease activities. The XPG protein signatures (PDOC00658 from PROSITEDOC) are never found outside the '53EXO' domains. The latter are found in more diverse proteins [, , ]. The number of amino acids that separate the two 53EXO domains, and the presence of accompanying motifs allow the diagnosis of several protein families. In the eubacterial type A DNA-polymerases, the N-terminal and internal domains are separated by a few amino acids, usually four. The pattern DNA_POLYMERASE_A (IPR001098 from INTERPRO) is always present towards the C terminus. Several eukaryotic structure-dependent endonucleases and exonucleases have the 53EXO domains separated by 24 to 27 amino acids, and the XPG protein signatures are always present. In several proteins from herpesviridae, the two 53EXO domains are separated by 50 to 120 amino acids. These proteins are implicated in the inhibition of the expression of the host genes. Eukaryotic DNA repair proteins with 600 to 700 amino acids between the 53_EXO domains all carry the XPG protein signatures. This entry represents the N-terminal resolvase-like domain, which has a 3-layer alpha/beta/alpha core structure and contains an alpha-helical arch [, ].; GO: 0003677 DNA binding, 0008409 5'-3' exonuclease activity; PDB: 1TAQ_A 1BGX_T 1TAU_A 1XO1_B 1EXN_A 1UT8_A 1UT5_B 3H7I_A 3H8J_A 3H8S_A ....
Probab=27.09 E-value=88 Score=32.67 Aligned_cols=61 Identities=25% Similarity=0.427 Sum_probs=35.7
Q ss_pred HHHhhhcCCceeeccCCCccchhhHHHHHHHHHHHhCCCCcEEEEEeCCcchHHHHHHHHhCCCEEEEecC
Q 001724 105 QEVLSSTGINIAHVPHGGKNSADRSLLVDLMYWVSQNPPPAHLFLISGDRDFASVLHRLRMNNYNILLASR 175 (1020)
Q Consensus 105 qe~L~ssGI~LihvP~ggKNAADi~LiIDaMd~a~~nP~pdtFVLISGDsDFtpLL~RLRerGynVILagp 175 (1020)
++.|...||..+..+ |=.| |-.|..=+..+... -..++|||+|.||.-|+. .+.+|.+..+
T Consensus 92 ~~~l~~~gi~~~~~~--g~EA-DDvIatla~~~~~~---~~~v~IvS~DkD~~QLv~----~~~~V~~~~~ 152 (169)
T PF02739_consen 92 KELLEALGIPVLEVP--GYEA-DDVIATLAKKASEE---GFEVIIVSGDKDLLQLVD----ENVNVYLLDP 152 (169)
T ss_dssp HHHHHHTTSEEEEET--TB-H-HHHHHHHHHHHHHT---TCEEEEE-SSGGGGGGTC----S-TSEEEEET
T ss_pred HHHHHHCCCCEecCC--CCcH-HHHHHHHHhhhccC---CCEEEEEcCCCCHHHhcC----CCceEEEeec
Confidence 445667888877766 3444 54444444444432 357999999999987653 2356665544
No 110
>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=27.05 E-value=1.6e+02 Score=37.13 Aligned_cols=104 Identities=16% Similarity=0.150 Sum_probs=63.3
Q ss_pred HHhCCCCceEEEEeecccccc-h-hh-HHHhhhcCCceeeccCCCccchhhHHHHHHHHHHHhCCCCcEEEEEeCCcchH
Q 001724 81 RANGIKGPVTITAFGDVVQMS-R-AN-QEVLSSTGINIAHVPHGGKNSADRSLLVDLMYWVSQNPPPAHLFLISGDRDFA 157 (1020)
Q Consensus 81 relG~~GpVtIRAYGDws~~~-k-~~-qe~L~ssGI~LihvP~ggKNAADi~LiIDaMd~a~~nP~pdtFVLISGDsDFt 157 (1020)
++.|.+-.|-+---|+..... + .+ ..-|..-||+++.-..- . |.. ++...+... ..+.+||+|+|.+|.
T Consensus 489 ~~~g~rP~vfL~~lG~~a~~~aRa~Fa~nff~~gG~~~~~~~~~--~--~~~---~~~~a~~~s-ga~i~viCssD~~Y~ 560 (619)
T TIGR00642 489 TSVGERPKVFLLCLGTLADFGGREGFSSNVWHIAGIDTIQVEGG--T--TAE---IVVEAFKKA-GAQVAVLCSSDKVYA 560 (619)
T ss_pred HhcCCCCeEEEeCCCChHhhccHHHHHHhHHhcCceeeccCCCC--C--CHH---HHHHHHHhc-CCCEEEEeCCCcchH
Confidence 455544344445557766543 2 33 34567788887764321 1 111 333333343 478999999999885
Q ss_pred ----HHHHHHHhCCC-EEEEecCCchhHHHHhh-cceEEec
Q 001724 158 ----SVLHRLRMNNY-NILLASRESASNVLCSA-ASVMWNW 192 (1020)
Q Consensus 158 ----pLL~RLRerGy-nVILagp~kTpeaL~sA-cd~Fw~w 192 (1020)
.++..||+.|. .|+|+|....-+.|..+ .|.|++.
T Consensus 561 ~~a~~~~~al~~ag~~~v~lAG~p~~~~~~~~aGvd~fi~~ 601 (619)
T TIGR00642 561 QQGLEVAKALKAAGAKALYLAGAFKEFGDDAAEAIDGRLFM 601 (619)
T ss_pred HHHHHHHHHHHhCCCCEEEEeCCCcchhhHHhcCCcceeEc
Confidence 67788999885 67789876544445544 5778773
No 111
>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=27.01 E-value=3.6e+02 Score=28.21 Aligned_cols=64 Identities=9% Similarity=0.073 Sum_probs=35.9
Q ss_pred hhhHHHhhhcCCceeec--cCCCccchhhHHHHH-HHHHHHhCCCCcEEEEEeCCcchHHHHHHHHhCCCE
Q 001724 102 RANQEVLSSTGINIAHV--PHGGKNSADRSLLVD-LMYWVSQNPPPAHLFLISGDRDFASVLHRLRMNNYN 169 (1020)
Q Consensus 102 k~~qe~L~ssGI~Lihv--P~ggKNAADi~LiID-aMd~a~~nP~pdtFVLISGDsDFtpLL~RLRerGyn 169 (1020)
.++++.|..+|+.+... ..+.-+ ..-..+ +..|+..+|.++. +++++|.--..++..|+++|+.
T Consensus 137 ~gf~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~l~~~~~~~a-i~~~~d~~a~g~~~~l~~~g~~ 203 (269)
T cd06275 137 AGFRRAMAEAGLPVNPGWIVEGDFE---CEGGYEAMQRLLAQPKRPTA-VFCGNDLMAMGALCAAQEAGLR 203 (269)
T ss_pred HHHHHHHHHcCCCCCHHHhccCCCC---hHHHHHHHHHHHcCCCCCcE-EEECChHHHHHHHHHHHHcCCC
Confidence 35678888889876432 111111 111222 3345555555554 4445565445888999999974
No 112
>PF03033 Glyco_transf_28: Glycosyltransferase family 28 N-terminal domain; InterPro: IPR004276 The biosynthesis of disaccharides, oligosaccharides and polysaccharides involves the action of hundreds of different glycosyltransferases. These enzymes catalyse the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming glycosidic bonds. A classification of glycosyltransferases using nucleotide diphospho-sugar, nucleotide monophospho-sugar and sugar phosphates (2.4.1.- from EC) and related proteins into distinct sequence based families has been described []. This classification is available on the CAZy (CArbohydrate-Active EnZymes) web site. The same three-dimensional fold is expected to occur within each of the families. Because 3-D structures are better conserved than sequences, several of the families defined on the basis of sequence similarities may have similar 3-D structures and therefore form 'clans'. Glycosyltransferase family 28 GT28 from CAZY comprises enzymes with a number of known activities; 1,2-diacylglycerol 3-beta-galactosyltransferase (2.4.1.46 from EC); 1,2-diacylglycerol 3-beta-glucosyltransferase (2.4.1.157 from EC); beta-N-acetylglucosamine transferase (2.4.1 from EC).; GO: 0016758 transferase activity, transferring hexosyl groups, 0005975 carbohydrate metabolic process, 0030259 lipid glycosylation; PDB: 2IYF_B 2YJN_A 2P6P_A 1PNV_A 3H4T_A 3H4I_A 1PN3_B 3IA7_B 1NLM_B 1F0K_B ....
Probab=26.27 E-value=1.4e+02 Score=28.51 Aligned_cols=36 Identities=17% Similarity=0.142 Sum_probs=24.4
Q ss_pred hHHHHHHHHhCCCEEEEecCCchhHHHHhhcceEEe
Q 001724 156 FASVLHRLRMNNYNILLASRESASNVLCSAASVMWN 191 (1020)
Q Consensus 156 FtpLL~RLRerGynVILagp~kTpeaL~sAcd~Fw~ 191 (1020)
|..|...|+++|+.|.++++...-+....+.=.|..
T Consensus 15 ~lala~~L~~rGh~V~~~~~~~~~~~v~~~Gl~~~~ 50 (139)
T PF03033_consen 15 FLALARALRRRGHEVRLATPPDFRERVEAAGLEFVP 50 (139)
T ss_dssp HHHHHHHHHHTT-EEEEEETGGGHHHHHHTT-EEEE
T ss_pred HHHHHHHHhccCCeEEEeecccceecccccCceEEE
Confidence 678999999999999988776554444544444443
No 113
>PRK11609 nicotinamidase/pyrazinamidase; Provisional
Probab=26.01 E-value=7.8e+02 Score=26.01 Aligned_cols=41 Identities=17% Similarity=0.084 Sum_probs=27.2
Q ss_pred eEEEEEecCCCCCCCC----CChhhHHHHHHHHHHHhCCCCceEE
Q 001724 51 RVSVWWDFENCNLPAG----VNAFKVAHTITAAIRANGIKGPVTI 91 (1020)
Q Consensus 51 rVAVFWDiENcpiP~g----~d~~~Va~nI~~aLrelG~~GpVtI 91 (1020)
..-|.||+.|..++.| .....+..+|..+++.+-..|...|
T Consensus 3 ~ALlvID~Qndf~~~g~l~~~~~~~~v~~i~~l~~~ar~~g~pVi 47 (212)
T PRK11609 3 RALLLVDLQNDFCAGGALAVPEGDSTIDVANRLIDWCQSRGIPVI 47 (212)
T ss_pred cEEEEEeCCccCCCCCccccCCHHHHHHHHHHHHHHHHhcCCeEE
Confidence 3568899999766533 2355677788888887655664333
No 114
>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=25.99 E-value=6e+02 Score=27.00 Aligned_cols=64 Identities=16% Similarity=0.188 Sum_probs=37.5
Q ss_pred hhhHHHhhhcCCceee---ccCCCccchhhHHHHHHH-HHHHhCCCCcE-EEEEeCCcchHHHHHHHHhCCC
Q 001724 102 RANQEVLSSTGINIAH---VPHGGKNSADRSLLVDLM-YWVSQNPPPAH-LFLISGDRDFASVLHRLRMNNY 168 (1020)
Q Consensus 102 k~~qe~L~ssGI~Lih---vP~ggKNAADi~LiIDaM-d~a~~nP~pdt-FVLISGDsDFtpLL~RLRerGy 168 (1020)
.++++.|...|+.... ++... .|..-..+++ +++..+|.++. .++..+|.-...++..|+++|+
T Consensus 150 ~G~~~~l~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~l~~~~~~~~~~i~~~~d~~a~g~~~al~~~g~ 218 (289)
T cd01540 150 DGALEALKAPGFPEANIFQAPQKT---TDTEGAFDAAASTLTKNPNVKNWIIYGLNDETVLGAVRATEQSGI 218 (289)
T ss_pred HHHHHHHhcCCCCcceEecccccC---cchhhHHHHHHHHHHhCCCcCeeEEEeCCcHHHHHHHHHHHHcCC
Confidence 3578888888876332 22211 1122233444 34445666776 4445566667788899999887
No 115
>PF09314 DUF1972: Domain of unknown function (DUF1972); InterPro: IPR015393 This domain is functionally uncharacterised and found in bacterial glycosyltransferases and rhamnosyltransferases.
Probab=25.91 E-value=5.6e+02 Score=27.60 Aligned_cols=103 Identities=17% Similarity=0.362 Sum_probs=56.2
Q ss_pred CCCCCChh-hHHHHHHHHHHHhCCCCceEEEEeecccccchhhHHHhhhcCCceeeccCCCccchhhHHHHHHHH-----
Q 001724 63 LPAGVNAF-KVAHTITAAIRANGIKGPVTITAFGDVVQMSRANQEVLSSTGINIAHVPHGGKNSADRSLLVDLMY----- 136 (1020)
Q Consensus 63 iP~g~d~~-~Va~nI~~aLrelG~~GpVtIRAYGDws~~~k~~qe~L~ssGI~LihvP~ggKNAADi~LiIDaMd----- 136 (1020)
+|+.+-++ ..+.++..-|.+. | +.+.+||--...... .-.-.|++++++|... +..=.+|+-|++.
T Consensus 12 IPa~YGGfET~ve~L~~~l~~~---g-~~v~Vyc~~~~~~~~---~~~y~gv~l~~i~~~~-~g~~~si~yd~~sl~~al 83 (185)
T PF09314_consen 12 IPARYGGFETFVEELAPRLVSK---G-IDVTVYCRSDYYPYK---EFEYNGVRLVYIPAPK-NGSAESIIYDFLSLLHAL 83 (185)
T ss_pred CCcccCcHHHHHHHHHHHHhcC---C-ceEEEEEccCCCCCC---CcccCCeEEEEeCCCC-CCchHHHHHHHHHHHHHH
Confidence 45555443 3344444444332 2 457788765433211 2345899999998643 3222355555543
Q ss_pred -HHHhCCCCcEEEEEeCCc---chHHHHHHHHhCCCEEEEe
Q 001724 137 -WVSQNPPPAHLFLISGDR---DFASVLHRLRMNNYNILLA 173 (1020)
Q Consensus 137 -~a~~nP~pdtFVLISGDs---DFtpLL~RLRerGynVILa 173 (1020)
+...+..-..+++|-|-. =|.+++.+|+..|..|++-
T Consensus 84 ~~~~~~~~~~~ii~ilg~~~g~~~~~~~r~~~~~g~~v~vN 124 (185)
T PF09314_consen 84 RFIKQDKIKYDIILILGYGIGPFFLPFLRKLRKKGGKVVVN 124 (185)
T ss_pred HHHhhccccCCEEEEEcCCccHHHHHHHHhhhhcCCcEEEC
Confidence 332221112255555544 3678899999999888864
No 116
>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=25.78 E-value=6.4e+02 Score=26.12 Aligned_cols=63 Identities=13% Similarity=0.189 Sum_probs=36.2
Q ss_pred hhHHHhhhcCCceeeccCCCccchhhHHHHHHHHHHHhCCCCcEEEEEeCCcchHHHHHHHHhC-CC
Q 001724 103 ANQEVLSSTGINIAHVPHGGKNSADRSLLVDLMYWVSQNPPPAHLFLISGDRDFASVLHRLRMN-NY 168 (1020)
Q Consensus 103 ~~qe~L~ssGI~LihvP~ggKNAADi~LiIDaMd~a~~nP~pdtFVLISGDsDFtpLL~RLRer-Gy 168 (1020)
++++.+...|+.+..+..+.-+ .+ ...-.+..|+..+|.|++ +++++|.-...++.-|+++ |+
T Consensus 136 gf~~~~~~~~~~~~~~~~~~~~-~~-~~~~~~~~~l~~~~~~~~-i~~~~~~~a~~~~~~l~~~~~~ 199 (266)
T cd06278 136 GFRDALAAAGVPVVVEEAGDYS-YE-GGYEAARRLLASRPRPDA-IFCANDLLAIGVMDAARQEGGL 199 (266)
T ss_pred HHHHHHHHcCCChhhhccCCCC-HH-HHHHHHHHHHhcCCCCCE-EEEcCcHHHHHHHHHHHHhcCC
Confidence 5677888888875433222111 11 123344567766665664 4455666566788999885 44
No 117
>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=25.60 E-value=8.1e+02 Score=25.83 Aligned_cols=93 Identities=12% Similarity=0.125 Sum_probs=50.8
Q ss_pred CceEE-EEeecccccc-----hhhHHHhhhc-CCceeeccCCCccchhhHHHHHHHHHHHhCC-CCcEEEEEeCCcchHH
Q 001724 87 GPVTI-TAFGDVVQMS-----RANQEVLSST-GINIAHVPHGGKNSADRSLLVDLMYWVSQNP-PPAHLFLISGDRDFAS 158 (1020)
Q Consensus 87 GpVtI-RAYGDws~~~-----k~~qe~L~ss-GI~LihvP~ggKNAADi~LiIDaMd~a~~nP-~pdtFVLISGDsDFtp 158 (1020)
|...| -++|+..... .++++.|..+ ++.+..+..+.. ..+.. .-.+..|+..+| .++ .+++++|.-...
T Consensus 123 g~~~i~~i~~~~~~~~~~~R~~Gf~~~l~~~~~~~~~~~~~~~~-~~~~~-~~~~~~~l~~~~~~~~-aI~~~~d~~a~g 199 (273)
T cd06309 123 GKGNIVELQGTVGSSVAIDRKKGFAEVIKKYPNMKIVASQTGDF-TRAKG-KEVMEALLKAHGDDID-AVYAHNDEMALG 199 (273)
T ss_pred CCceEEEEeCCCCCchHHHHHHHHHHHHHHCCCCEEeeccCCcc-cHHHH-HHHHHHHHHhCCCCcc-EEEECCcHHHHH
Confidence 43344 4456544321 3567788876 466554333221 11211 112334555565 454 456667776668
Q ss_pred HHHHHHhCCCE----EEEecCCchhHHH
Q 001724 159 VLHRLRMNNYN----ILLASRESASNVL 182 (1020)
Q Consensus 159 LL~RLRerGyn----VILagp~kTpeaL 182 (1020)
+++.|++.|++ |-+++-...+..+
T Consensus 200 ~~~a~~~~g~~ip~di~iig~d~~~~~~ 227 (273)
T cd06309 200 AIQAIKAAGKKPGKDIKIVSIDGTKDAF 227 (273)
T ss_pred HHHHHHHcCCCCCCCeEEEecCCCHHHH
Confidence 99999999987 5566655555543
No 118
>PRK10423 transcriptional repressor RbsR; Provisional
Probab=25.54 E-value=3e+02 Score=29.96 Aligned_cols=65 Identities=12% Similarity=0.157 Sum_probs=37.6
Q ss_pred hhHHHhhhcCCceee--ccCCCccchhhHHHHHHHHHHHhCCCCcEEEEEeCCcchHHHHHHHHhCCCEE
Q 001724 103 ANQEVLSSTGINIAH--VPHGGKNSADRSLLVDLMYWVSQNPPPAHLFLISGDRDFASVLHRLRMNNYNI 170 (1020)
Q Consensus 103 ~~qe~L~ssGI~Lih--vP~ggKNAADi~LiIDaMd~a~~nP~pdtFVLISGDsDFtpLL~RLRerGynV 170 (1020)
++++.|..+|+.+.. +..+.- ..+ .-.-.+..|+..++.|+. +++.+|.--..++..|+++|+.|
T Consensus 195 Gf~~al~~~~~~~~~~~~~~~~~-~~~-~~~~~~~~~l~~~~~~~a-i~~~~d~~A~g~~~~l~~~g~~v 261 (327)
T PRK10423 195 GYRAAMKRAGLNIPDGYEVTGDF-EFN-GGFDAMQQLLALPLRPQA-VFTGNDAMAVGVYQALYQAGLSV 261 (327)
T ss_pred HHHHHHHHcCCCCCcceEEeCCC-ChH-HHHHHHHHHhcCCCCCCE-EEEcCcHHHHHHHHHHHHcCCCC
Confidence 578889999986532 112111 111 112233445555555664 44556666668999999999853
No 119
>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=25.52 E-value=2.3e+02 Score=29.67 Aligned_cols=44 Identities=7% Similarity=0.088 Sum_probs=32.1
Q ss_pred HHHHHHHHHhCCCCcEEEEEeCCcch-HHHHHHHHhCCCEEEEecC
Q 001724 131 LVDLMYWVSQNPPPAHLFLISGDRDF-ASVLHRLRMNNYNILLASR 175 (1020)
Q Consensus 131 iIDaMd~a~~nP~pdtFVLISGDsDF-tpLL~RLRerGynVILagp 175 (1020)
...++..+... .+|+++|...+.+. ..++..|.++|..|+++..
T Consensus 45 ~~~~i~~l~~~-~vdgiii~~~~~~~~~~~~~~l~~~~iPvv~~~~ 89 (272)
T cd06301 45 QLSQVENFIAQ-GVDAIIVVPVDTAATAPIVKAANAAGIPLVYVNR 89 (272)
T ss_pred HHHHHHHHHHc-CCCEEEEecCchhhhHHHHHHHHHCCCeEEEecC
Confidence 34455555554 48999998877664 5778889999999997754
No 120
>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=25.41 E-value=6.7e+02 Score=26.21 Aligned_cols=75 Identities=7% Similarity=0.118 Sum_probs=41.8
Q ss_pred hhhHHHhhhcC--CceeeccCCCccchhhHHHHHHHHHHHhC-CCCcEEEEEeCCcchHHHHHHHHhCCC--EEEEecCC
Q 001724 102 RANQEVLSSTG--INIAHVPHGGKNSADRSLLVDLMYWVSQN-PPPAHLFLISGDRDFASVLHRLRMNNY--NILLASRE 176 (1020)
Q Consensus 102 k~~qe~L~ssG--I~LihvP~ggKNAADi~LiIDaMd~a~~n-P~pdtFVLISGDsDFtpLL~RLRerGy--nVILagp~ 176 (1020)
.++++.+...| +.+..+..+.- ..+ ...-.+..++..+ |.|+.|+ +.+|.--..++..|+++|+ .|.+++-.
T Consensus 145 ~g~~~~~~~~~~~~~~~~~~~~~~-~~~-~~~~~~~~~l~~~~~~~~ai~-~~~d~~a~g~~~~l~~~g~~~dv~v~g~d 221 (275)
T cd06317 145 KGFEDELAEVCPGVEVLDTQPADW-DRE-KAQVAMEALITKFGDDIDGVY-AGDDNMARGALNAAKEAGLAGGIVIVGAN 221 (275)
T ss_pred HHHHHHHHhhCCCCEEEeccCCCC-CHH-HHHHHHHHHHHhCCCCccEEE-ECCCcHHHHHHHHHHhcCCcCCcEEEEeC
Confidence 35677888875 44433322111 111 1122334466555 6566655 5666666789999999998 45555444
Q ss_pred chh
Q 001724 177 SAS 179 (1020)
Q Consensus 177 kTp 179 (1020)
.++
T Consensus 222 ~~~ 224 (275)
T cd06317 222 NFA 224 (275)
T ss_pred CCH
Confidence 333
No 121
>cd06287 PBP1_LacI_like_8 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=25.02 E-value=4.8e+02 Score=28.04 Aligned_cols=65 Identities=8% Similarity=0.004 Sum_probs=37.3
Q ss_pred hhHHHhhhcCCceeeccCCCccchhhHHHHHHHHHHHhCCCCcEEEEEeCCcchHHHHHHHHhCCCE
Q 001724 103 ANQEVLSSTGINIAHVPHGGKNSADRSLLVDLMYWVSQNPPPAHLFLISGDRDFASVLHRLRMNNYN 169 (1020)
Q Consensus 103 ~~qe~L~ssGI~LihvP~ggKNAADi~LiIDaMd~a~~nP~pdtFVLISGDsDFtpLL~RLRerGyn 169 (1020)
++++.+...|+.+..+...+....+. -.-.+..|+..++.|+. +++.+|.--..++..|+++|++
T Consensus 139 gf~~a~~~~g~~~~~~~~~~~~~~~~-~~~~~~~~l~~~~~~~a-i~~~~d~~A~gvl~al~~~gl~ 203 (269)
T cd06287 139 AYRAFAAEHGMPPVVLRVDEAGGEEA-GYAACAQLLAQHPDLDA-LCVPVDAFAVGAVRAATELGRA 203 (269)
T ss_pred HHHHHHHHcCCCcceeEecCCCChHH-HHHHHHHHHhCCCCCCE-EEEcCcHHHHHHHHHHHHcCCC
Confidence 56778888888643221111222221 11222345555555654 4456777677899999999985
No 122
>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=24.98 E-value=5.6e+02 Score=26.69 Aligned_cols=73 Identities=14% Similarity=0.115 Sum_probs=42.4
Q ss_pred hhHHHhhhcCCceeeccCCCccchhhHHHHHHHHHHHhCCCCcEEEEEeCCcchHHHHHHHHhCCC----EEEEecCCch
Q 001724 103 ANQEVLSSTGINIAHVPHGGKNSADRSLLVDLMYWVSQNPPPAHLFLISGDRDFASVLHRLRMNNY----NILLASRESA 178 (1020)
Q Consensus 103 ~~qe~L~ssGI~LihvP~ggKNAADi~LiIDaMd~a~~nP~pdtFVLISGDsDFtpLL~RLRerGy----nVILagp~kT 178 (1020)
++++.|...|+.+........+. + -..+++..+...++|++ +++.+|.....++..|+++|+ .|.+++-..+
T Consensus 137 gf~~~l~~~~~~~~~~~~~~~~~-~--~~~~~~~~~l~~~~~~a-i~~~~d~~a~g~~~~~~~~g~~ip~~i~ii~~d~~ 212 (264)
T cd01574 137 GWRAALEAAGIAPPPVLEGDWSA-E--SGYRAGRELLREGDPTA-VFAANDQMALGVLRALHELGLRVPDDVSVVGFDDI 212 (264)
T ss_pred HHHHHHHHCCCCcceeeecCCCH-H--HHHHHHHHHHhCCCCcE-EEEcCcHHHHHHHHHHHHcCCCCccceEEecccCc
Confidence 57888888888765432222111 1 22344443334443554 555677878899999999996 3455554433
Q ss_pred h
Q 001724 179 S 179 (1020)
Q Consensus 179 p 179 (1020)
+
T Consensus 213 ~ 213 (264)
T cd01574 213 P 213 (264)
T ss_pred h
Confidence 3
No 123
>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=24.96 E-value=1.6e+02 Score=30.68 Aligned_cols=63 Identities=11% Similarity=0.086 Sum_probs=39.5
Q ss_pred hHHHhhhcCCceeeccCCCccchhhHHHHHHHHHHHhCCCCcEEEEEeCCcchHHHHHHHHhCCCEEEEecC
Q 001724 104 NQEVLSSTGINIAHVPHGGKNSADRSLLVDLMYWVSQNPPPAHLFLISGDRDFASVLHRLRMNNYNILLASR 175 (1020)
Q Consensus 104 ~qe~L~ssGI~LihvP~ggKNAADi~LiIDaMd~a~~nP~pdtFVLISGDsDFtpLL~RLRerGynVILagp 175 (1020)
.++++...|+.++.+.... |......+++.+... .++++++...|.+ +.+|++.|..|+++..
T Consensus 21 i~~~~~~~g~~~~~~~~~~----~~~~~~~~i~~~~~~-~~dgiii~~~~~~----~~~~~~~gipvv~~~~ 83 (265)
T cd06291 21 VEKELYKKGYKLILCNSDN----DPEKEREYLEMLRQN-QVDGIIAGTHNLG----IEEYENIDLPIVSFDR 83 (265)
T ss_pred HHHHHHHCCCeEEEecCCc----cHHHHHHHHHHHHHc-CCCEEEEecCCcC----HHHHhcCCCCEEEEeC
Confidence 4445556666655443321 122345666676665 4899999887765 3477888988887754
No 124
>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=24.87 E-value=2.1e+02 Score=30.06 Aligned_cols=66 Identities=14% Similarity=0.060 Sum_probs=39.4
Q ss_pred hHHHhhhcCCceeeccCCCccchhhHHHHHHHHHHHhCCCCcEEEEEeCCcchHHHHHHHHhCCCEEEEecC
Q 001724 104 NQEVLSSTGINIAHVPHGGKNSADRSLLVDLMYWVSQNPPPAHLFLISGDRDFASVLHRLRMNNYNILLASR 175 (1020)
Q Consensus 104 ~qe~L~ssGI~LihvP~ggKNAADi~LiIDaMd~a~~nP~pdtFVLISGDsDFtpLL~RLRerGynVILagp 175 (1020)
..+++..+|+.+.-+.... |..-.+++++.+... .+++++++..+.+- ..+.+|+..|..|+++..
T Consensus 21 ~~~~a~~~g~~~~~~~~~~----~~~~~~~~i~~~~~~-~vdgii~~~~~~~~-~~~~~~~~~~ipvV~~~~ 86 (268)
T cd06270 21 VESVARKAGKHLIITAGHH----SAEKEREAIEFLLER-RCDALILHSKALSD-DELIELAAQVPPLVLINR 86 (268)
T ss_pred HHHHHHHCCCEEEEEeCCC----chHHHHHHHHHHHHc-CCCEEEEecCCCCH-HHHHHHhhCCCCEEEEec
Confidence 4445556666655443321 122345666666654 48888887765332 237888888888887653
No 125
>PTZ00441 sporozoite surface protein 2 (SSP2); Provisional
Probab=24.80 E-value=1e+03 Score=30.03 Aligned_cols=29 Identities=14% Similarity=0.172 Sum_probs=19.3
Q ss_pred EEEEEeCCcc------hHHHHHHHHhCCCEEEEec
Q 001724 146 HLFLISGDRD------FASVLHRLRMNNYNILLAS 174 (1020)
Q Consensus 146 tFVLISGDsD------FtpLL~RLRerGynVILag 174 (1020)
.++||-.|.. -...+.+||.+|..|++++
T Consensus 151 KVVILLTDG~sns~~dvleaAq~LR~~GVeI~vIG 185 (576)
T PTZ00441 151 QLVILMTDGIPNSKYRALEESRKLKDRNVKLAVIG 185 (576)
T ss_pred eEEEEEecCCCCCcccHHHHHHHHHHCCCEEEEEE
Confidence 4555555642 2345789999999988544
No 126
>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=24.66 E-value=7.3e+02 Score=26.11 Aligned_cols=63 Identities=16% Similarity=0.089 Sum_probs=39.4
Q ss_pred hhHHHhhhc-CCceeeccCCCccchhhHHHHHHHHHHHhCCCCcEEEEEeCCcchHHHHHHHHhCCC
Q 001724 103 ANQEVLSST-GINIAHVPHGGKNSADRSLLVDLMYWVSQNPPPAHLFLISGDRDFASVLHRLRMNNY 168 (1020)
Q Consensus 103 ~~qe~L~ss-GI~LihvP~ggKNAADi~LiIDaMd~a~~nP~pdtFVLISGDsDFtpLL~RLRerGy 168 (1020)
++++.|..+ |+.+.+...+.-+ .+. -.--+..|+..++.++ .+++.+|.--..++..|++.|+
T Consensus 143 g~~~~l~~~~~~~~~~~~~~~~~-~~~-~~~~~~~~l~~~~~~~-aI~~~~d~~a~g~~~al~~~g~ 206 (270)
T cd06308 143 GFKEALSKYPKIKIVAQQDGDWL-KEK-AEEKMEELLQANPDID-LVYAHNDPMALGAYLAAKRAGR 206 (270)
T ss_pred HHHHHHHHCCCCEEEEecCCCcc-HHH-HHHHHHHHHHhCCCCc-EEEeCCcHHHHHHHHHHHHcCC
Confidence 567788888 8877654432221 111 1122334555566666 4566688777799999999996
No 127
>PRK09701 D-allose transporter subunit; Provisional
Probab=24.65 E-value=8.1e+02 Score=27.01 Aligned_cols=75 Identities=11% Similarity=0.132 Sum_probs=44.3
Q ss_pred hhhHHHhhhcC-CceeeccCCCccchhhHHHHHHH-HHHHhCCCCcEEEEEeCCcchHHHHHHHHhCCC--EEEEecCCc
Q 001724 102 RANQEVLSSTG-INIAHVPHGGKNSADRSLLVDLM-YWVSQNPPPAHLFLISGDRDFASVLHRLRMNNY--NILLASRES 177 (1020)
Q Consensus 102 k~~qe~L~ssG-I~LihvP~ggKNAADi~LiIDaM-d~a~~nP~pdtFVLISGDsDFtpLL~RLRerGy--nVILagp~k 177 (1020)
.++++.|..+| +.+...... ....+ ...+++ .|+..++.|+ .++..+|.-...++..|+++|+ .|.+++-..
T Consensus 176 ~Gf~~al~~~~~~~~~~~~~~-~~~~~--~~~~~~~~ll~~~~~~~-~I~~~~d~~A~g~~~al~~~G~~~dv~vvg~d~ 251 (311)
T PRK09701 176 NGATEAFKKASQIKLVASQPA-DWDRI--KALDVATNVLQRNPNIK-AIYCANDTMAMGVAQAVANAGKTGKVLVVGTDG 251 (311)
T ss_pred HHHHHHHHhCCCcEEEEecCC-CCCHH--HHHHHHHHHHHhCCCCC-EEEECCcchHHHHHHHHHHcCCCCCEEEEEeCC
Confidence 35788888887 765443211 11111 123333 3444555566 4557778888899999999998 365555444
Q ss_pred hhH
Q 001724 178 ASN 180 (1020)
Q Consensus 178 Tpe 180 (1020)
++.
T Consensus 252 ~~~ 254 (311)
T PRK09701 252 IPE 254 (311)
T ss_pred CHH
Confidence 443
No 128
>PF05991 NYN_YacP: YacP-like NYN domain; InterPro: IPR010298 This family consists of several hypothetical bacterial proteins as well as some uncharacterised sequences from Arabidopsis thaliana. The function of this family is unknown.
Probab=24.54 E-value=2.9e+02 Score=28.82 Aligned_cols=54 Identities=19% Similarity=0.353 Sum_probs=34.7
Q ss_pred hcCCceeeccCCCccchhhHHHHHHHHHHHhCCCCcEEEEEeCCcchHHHHHHHHhCCCEEE
Q 001724 110 STGINIAHVPHGGKNSADRSLLVDLMYWVSQNPPPAHLFLISGDRDFASVLHRLRMNNYNIL 171 (1020)
Q Consensus 110 ssGI~LihvP~ggKNAADi~LiIDaMd~a~~nP~pdtFVLISGDsDFtpLL~RLRerGynVI 171 (1020)
..||++++.+.+ ..|| ..|.+++.-+.. .+..+++||+|..-... .+.+|-.++
T Consensus 65 ~~gi~Vvft~~~--~tAD-~~Ie~~v~~~~~--~~~~v~VVTSD~~iq~~---~~~~GA~~i 118 (166)
T PF05991_consen 65 YGGIEVVFTKEG--ETAD-DYIERLVRELKN--RPRQVTVVTSDREIQRA---ARGRGAKRI 118 (166)
T ss_pred eCceEEEECCCC--CCHH-HHHHHHHHHhcc--CCCeEEEEeCCHHHHHH---HhhCCCEEE
Confidence 378888887653 4677 455555444432 26899999999864433 356676665
No 129
>COG1737 RpiR Transcriptional regulators [Transcription]
Probab=24.38 E-value=5.4e+02 Score=28.74 Aligned_cols=89 Identities=11% Similarity=0.120 Sum_probs=53.3
Q ss_pred EEEeeccc--ccchhhHHHhhhcCCceeeccCCCccchhhHHHHHHHHHHHhCCCCcEEEEEeCCc----chHHHHHHHH
Q 001724 91 ITAFGDVV--QMSRANQEVLSSTGINIAHVPHGGKNSADRSLLVDLMYWVSQNPPPAHLFLISGDR----DFASVLHRLR 164 (1020)
Q Consensus 91 IRAYGDws--~~~k~~qe~L~ssGI~LihvP~ggKNAADi~LiIDaMd~a~~nP~pdtFVLISGDs----DFtpLL~RLR 164 (1020)
|-.||--. .........|...|+....+.. ..+.. ++.... . ++-++|+-+-+ +-..++...|
T Consensus 133 I~~~G~g~S~~vA~~~~~~l~~ig~~~~~~~d-------~~~~~-~~~~~~--~-~~Dv~i~iS~sG~t~e~i~~a~~ak 201 (281)
T COG1737 133 IYFFGLGSSGLVASDLAYKLMRIGLNVVALSD-------THGQL-MQLALL--T-PGDVVIAISFSGYTREIVEAAELAK 201 (281)
T ss_pred EEEEEechhHHHHHHHHHHHHHcCCceeEecc-------hHHHH-HHHHhC--C-CCCEEEEEeCCCCcHHHHHHHHHHH
Confidence 45555222 2234567789999998887654 23444 322222 2 44444444444 4557788889
Q ss_pred hCCCEEEEecCCchhHHHHhhcceEEe
Q 001724 165 MNNYNILLASRESASNVLCSAASVMWN 191 (1020)
Q Consensus 165 erGynVILagp~kTpeaL~sAcd~Fw~ 191 (1020)
++|..||.++....+ .|...||..+.
T Consensus 202 ~~ga~vIaiT~~~~s-pla~~Ad~~L~ 227 (281)
T COG1737 202 ERGAKVIAITDSADS-PLAKLADIVLL 227 (281)
T ss_pred HCCCcEEEEcCCCCC-chhhhhceEEe
Confidence 999999998865333 45566775544
No 130
>COG1609 PurR Transcriptional regulators [Transcription]
Probab=24.13 E-value=8.5e+02 Score=27.73 Aligned_cols=98 Identities=18% Similarity=0.220 Sum_probs=64.0
Q ss_pred HHHHHHHHHHHhCCCC----------ce-EE-EEeeccccc-----chhhHHHhhhcCCceeeccCCCccchhhHHHHHH
Q 001724 72 VAHTITAAIRANGIKG----------PV-TI-TAFGDVVQM-----SRANQEVLSSTGINIAHVPHGGKNSADRSLLVDL 134 (1020)
Q Consensus 72 Va~nI~~aLrelG~~G----------pV-tI-RAYGDws~~-----~k~~qe~L~ssGI~LihvP~ggKNAADi~LiIDa 134 (1020)
....|.++.+++||.- .. +| -++-+.+.. -.+..+.+..+|..++-+.... |..-...+
T Consensus 31 Tr~kV~~a~~elgY~pN~~Ar~L~~~~s~~Ig~i~p~~~~~~~~~i~~gi~~~~~~~gy~~~l~~~~~----~~~~e~~~ 106 (333)
T COG1609 31 TREKVLAAIKELGYRPNAVARSLRTGRTKTIGLVVPDITNPFFAEILKGIEEAAREAGYSLLLANTDD----DPEKEREY 106 (333)
T ss_pred HHHHHHHHHHHHCCCCCHHHHHHHhCCCCEEEEEeCCCCCchHHHHHHHHHHHHHHcCCEEEEECCCC----CHHHHHHH
Confidence 4467888889998871 11 23 333344332 1356778899999988877643 23355666
Q ss_pred HHHHHhCCCCcEEEEEeCCcchHHHHHHHHhCCCEEEEecC
Q 001724 135 MYWVSQNPPPAHLFLISGDRDFASVLHRLRMNNYNILLASR 175 (1020)
Q Consensus 135 Md~a~~nP~pdtFVLISGDsDFtpLL~RLRerGynVILagp 175 (1020)
+..+.+. .+|+++|.. -.+-..++..|.+.|..|+++..
T Consensus 107 ~~~l~~~-~vdGiIi~~-~~~~~~~~~~l~~~~~P~V~i~~ 145 (333)
T COG1609 107 LETLLQK-RVDGLILLG-ERPNDSLLELLAAAGIPVVVIDR 145 (333)
T ss_pred HHHHHHc-CCCEEEEec-CCCCHHHHHHHHhcCCCEEEEeC
Confidence 6777765 599999998 22234556677788999887764
No 131
>COG2179 Predicted hydrolase of the HAD superfamily [General function prediction only]
Probab=24.08 E-value=2.7e+02 Score=29.93 Aligned_cols=123 Identities=15% Similarity=0.131 Sum_probs=70.3
Q ss_pred CCeEEEEEecCCCCCCCCCChhhHHHHHHHHHHHhCCCCceEEEEeecccccchhhHHHhhhcCCceeeccCCCccchhh
Q 001724 49 NVRVSVWWDFENCNLPAGVNAFKVAHTITAAIRANGIKGPVTITAFGDVVQMSRANQEVLSSTGINIAHVPHGGKNSADR 128 (1020)
Q Consensus 49 ~~rVAVFWDiENcpiP~g~d~~~Va~nI~~aLrelG~~GpVtIRAYGDws~~~k~~qe~L~ssGI~LihvP~ggKNAADi 128 (1020)
..-.+|+.|.||.-+|-+ .....+.+++.+.++...|. .+.+.-|- ....+...++..||..++- .+|--+-
T Consensus 26 ~Gikgvi~DlDNTLv~wd--~~~~tpe~~~W~~e~k~~gi-~v~vvSNn--~e~RV~~~~~~l~v~fi~~--A~KP~~~- 97 (175)
T COG2179 26 HGIKGVILDLDNTLVPWD--NPDATPELRAWLAELKEAGI-KVVVVSNN--KESRVARAAEKLGVPFIYR--AKKPFGR- 97 (175)
T ss_pred cCCcEEEEeccCceeccc--CCCCCHHHHHHHHHHHhcCC-EEEEEeCC--CHHHHHhhhhhcCCceeec--ccCccHH-
Confidence 456789999999888653 33444666677777655553 33444442 1233455667777776653 1221100
Q ss_pred HHHHHHHHHHHhCCCCcEEEEEeCCcchHHHHHHHHhCCCEEEEecCCchhHHHHh
Q 001724 129 SLLVDLMYWVSQNPPPAHLFLISGDRDFASVLHRLRMNNYNILLASRESASNVLCS 184 (1020)
Q Consensus 129 ~LiIDaMd~a~~nP~pdtFVLISGDsDFtpLL~RLRerGynVILagp~kTpeaL~s 184 (1020)
+ +--||.-+ |-++. =|++-||.=||.++-- ...|+..|++-|-.+|+.+..
T Consensus 98 ~-fr~Al~~m--~l~~~-~vvmVGDqL~TDVlgg-nr~G~~tIlV~Pl~~~d~~~t 148 (175)
T COG2179 98 A-FRRALKEM--NLPPE-EVVMVGDQLFTDVLGG-NRAGMRTILVEPLVAPDGWIT 148 (175)
T ss_pred H-HHHHHHHc--CCChh-HEEEEcchhhhhhhcc-cccCcEEEEEEEeccccchhh
Confidence 0 11111111 22233 3555699999987654 335999999988888877653
No 132
>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=23.92 E-value=4.6e+02 Score=26.78 Aligned_cols=107 Identities=14% Similarity=0.054 Sum_probs=0.0
Q ss_pred HHHHHHHHHhCCCCceEE-EEeecccccc-----hhhHHHhhhcCCceeeccCCCccchhhHHHHHHHHHHHhCCCCcEE
Q 001724 74 HTITAAIRANGIKGPVTI-TAFGDVVQMS-----RANQEVLSSTGINIAHVPHGGKNSADRSLLVDLMYWVSQNPPPAHL 147 (1020)
Q Consensus 74 ~nI~~aLrelG~~GpVtI-RAYGDws~~~-----k~~qe~L~ssGI~LihvP~ggKNAADi~LiIDaMd~a~~nP~pdtF 147 (1020)
.....+.+.+...|.-.| -++++-.... ..+++.+...|+.+.......-+.......--+..++..+|.++.|
T Consensus 102 ~~g~~~~~~l~~~g~~~i~~i~~~~~~~~~~~r~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~i 181 (264)
T cd06267 102 AGAYLAVEHLIELGHRRIAFIGGPPDLSTARERLEGYREALEEAGIPLDEELIVEGDFSEESGYEAARELLASGERPTAI 181 (264)
T ss_pred HHHHHHHHHHHHCCCceEEEecCCCccchHHHHHHHHHHHHHHcCCCCCcceEEecccchhhHHHHHHHHHhcCCCCcEE
Q ss_pred EEEeCCcchHHHHHHHHhCCC----EEEEecCCchhHH
Q 001724 148 FLISGDRDFASVLHRLRMNNY----NILLASRESASNV 181 (1020)
Q Consensus 148 VLISGDsDFtpLL~RLRerGy----nVILagp~kTpea 181 (1020)
+ +.+|.....++..|+++|+ .|.+++-..++..
T Consensus 182 ~-~~~~~~a~~~~~al~~~g~~~~~~i~i~~~d~~~~~ 218 (264)
T cd06267 182 F-AANDLMAIGALRALRELGLRVPEDVSVVGFDDIPLA 218 (264)
T ss_pred E-EcCcHHHHHHHHHHHHhCCCCCCceEEEeeCCCchh
No 133
>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=23.72 E-value=2.1e+02 Score=29.99 Aligned_cols=67 Identities=4% Similarity=0.053 Sum_probs=40.6
Q ss_pred hHHHhhhcCCceeeccCCCccchhhHHHHHHHHHHHhCCCCcEEEEEeCCcc-hHHHHHHHHhCCCEEEEecC
Q 001724 104 NQEVLSSTGINIAHVPHGGKNSADRSLLVDLMYWVSQNPPPAHLFLISGDRD-FASVLHRLRMNNYNILLASR 175 (1020)
Q Consensus 104 ~qe~L~ssGI~LihvP~ggKNAADi~LiIDaMd~a~~nP~pdtFVLISGDsD-FtpLL~RLRerGynVILagp 175 (1020)
..+.+...|+.++-+.... |..-..+++..+... .+++++|.+.+.+ ...++..+++.|..|+++..
T Consensus 21 i~~~~~~~g~~~~~~~~~~----~~~~~~~~i~~~~~~-~~dgiii~~~~~~~~~~~l~~~~~~~ipvV~~~~ 88 (277)
T cd06319 21 VKSKAKALGYDAVELSAEN----SAKKELENLRTAIDK-GVSGIIISPTNSSAAVTLLKLAAQAKIPVVIADI 88 (277)
T ss_pred HHHHHHhcCCeEEEecCCC----CHHHHHHHHHHHHhc-CCCEEEEcCCchhhhHHHHHHHHHCCCCEEEEec
Confidence 3444555666655443321 112233555555443 5999998877766 34778888999988887643
No 134
>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=23.62 E-value=2.5e+02 Score=29.12 Aligned_cols=42 Identities=14% Similarity=0.148 Sum_probs=27.9
Q ss_pred HHHHHHHHhCCCCcEEEEEeCCcchHHHHHHHHhCCCEEEEecC
Q 001724 132 VDLMYWVSQNPPPAHLFLISGDRDFASVLHRLRMNNYNILLASR 175 (1020)
Q Consensus 132 IDaMd~a~~nP~pdtFVLISGDsDFtpLL~RLRerGynVILagp 175 (1020)
..+++.+.. ..+|+++|...|.+- ..+.+|++.|..|+++..
T Consensus 45 ~~~~~~l~~-~~~dgiii~~~~~~~-~~l~~~~~~~ipvV~~~~ 86 (267)
T cd06283 45 KEYLESLLA-YQVDGLIVNPTGNNK-ELYQRLAKNGKPVVLVDR 86 (267)
T ss_pred HHHHHHHHH-cCcCEEEEeCCCCCh-HHHHHHhcCCCCEEEEcC
Confidence 344554444 358888888776553 346788888888887754
No 135
>PRK10653 D-ribose transporter subunit RbsB; Provisional
Probab=23.55 E-value=2e+02 Score=31.18 Aligned_cols=43 Identities=12% Similarity=0.112 Sum_probs=30.2
Q ss_pred HHHHHHHHhCCCCcEEEEEeCCcch-HHHHHHHHhCCCEEEEecC
Q 001724 132 VDLMYWVSQNPPPAHLFLISGDRDF-ASVLHRLRMNNYNILLASR 175 (1020)
Q Consensus 132 IDaMd~a~~nP~pdtFVLISGDsDF-tpLL~RLRerGynVILagp 175 (1020)
..+++.+..+ .+++++|...+.+. ...+..+++.|..|+++..
T Consensus 72 ~~~~~~l~~~-~~dgiii~~~~~~~~~~~l~~~~~~~ipvV~~~~ 115 (295)
T PRK10653 72 LANVQDLTVR-GTKILLINPTDSDAVGNAVKMANQANIPVITLDR 115 (295)
T ss_pred HHHHHHHHHc-CCCEEEEcCCChHHHHHHHHHHHHCCCCEEEEcc
Confidence 4455555554 48888887766554 4778888989998887754
No 136
>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=23.37 E-value=3.4e+02 Score=30.02 Aligned_cols=95 Identities=15% Similarity=0.242 Sum_probs=66.1
Q ss_pred HHHHHHHHHHhCCCCceEE-EEeecccccchhhHHHhhhcCCceeeccC-CCc-cc----hhhHHHHHHHHHHHhCCCCc
Q 001724 73 AHTITAAIRANGIKGPVTI-TAFGDVVQMSRANQEVLSSTGINIAHVPH-GGK-NS----ADRSLLVDLMYWVSQNPPPA 145 (1020)
Q Consensus 73 a~nI~~aLrelG~~GpVtI-RAYGDws~~~k~~qe~L~ssGI~LihvP~-ggK-NA----ADi~LiIDaMd~a~~nP~pd 145 (1020)
...+..+|+.+|. .+|.| .-|-++-. ...++.|...||+++.+-. +.. |. .|-.-+.+++.-+ .+|.+|
T Consensus 108 ~~A~~~AL~alg~-~RIalvTPY~~~v~--~~~~~~l~~~G~eV~~~~~~~~~~~~~ia~i~p~~i~~~~~~~-~~~~aD 183 (239)
T TIGR02990 108 SSAAVDGLAALGV-RRISLLTPYTPETS--RPMAQYFAVRGFEIVNFTCLGLTDDREMARISPDCIVEAALAA-FDPDAD 183 (239)
T ss_pred HHHHHHHHHHcCC-CEEEEECCCcHHHH--HHHHHHHHhCCcEEeeeeccCCCCCceeeecCHHHHHHHHHHh-cCCCCC
Confidence 3567788888875 45655 88877644 3456778899999988632 211 11 2334455555544 367899
Q ss_pred EEEEEeCCcchHHHHHHHHh-CCCEEE
Q 001724 146 HLFLISGDRDFASVLHRLRM-NNYNIL 171 (1020)
Q Consensus 146 tFVLISGDsDFtpLL~RLRe-rGynVI 171 (1020)
.++|....-.-..++.+|.+ .|+-|+
T Consensus 184 AifisCTnLrt~~vi~~lE~~lGkPVl 210 (239)
T TIGR02990 184 ALFLSCTALRAATCAQRIEQAIGKPVV 210 (239)
T ss_pred EEEEeCCCchhHHHHHHHHHHHCCCEE
Confidence 99999888888999999955 699887
No 137
>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=23.32 E-value=2.2e+02 Score=29.95 Aligned_cols=42 Identities=10% Similarity=0.098 Sum_probs=30.7
Q ss_pred HHHHHHHhCCCCcEEEEEeCCcc-hHHHHHHHHhCCCEEEEecC
Q 001724 133 DLMYWVSQNPPPAHLFLISGDRD-FASVLHRLRMNNYNILLASR 175 (1020)
Q Consensus 133 DaMd~a~~nP~pdtFVLISGDsD-FtpLL~RLRerGynVILagp 175 (1020)
.+++.+... .+|+++|...+.+ +.+.+.++++.|..|+++..
T Consensus 47 ~~i~~~~~~-~vdgiii~~~~~~~~~~~~~~~~~~~ipvV~~~~ 89 (270)
T cd06308 47 ADIENFIRQ-GVDLLIISPNEAAPLTPVVEEAYRAGIPVILLDR 89 (270)
T ss_pred HHHHHHHHh-CCCEEEEecCchhhchHHHHHHHHCCCCEEEeCC
Confidence 334444433 4899998877754 57888999999999998764
No 138
>cd01822 Lysophospholipase_L1_like Lysophospholipase L1-like subgroup of SGNH-hydrolases. The best characterized member in this family is TesA, an E. coli periplasmic protein with thioesterase, esterase, arylesterase, protease and lysophospholipase activity.
Probab=23.31 E-value=6.4e+02 Score=24.80 Aligned_cols=60 Identities=15% Similarity=0.293 Sum_probs=34.9
Q ss_pred CCceeeccCCCccchhhHHHHHHH-HHHHhCCCCcEEEEEeCCcc-------------hHHHHHHHHhCCCEEEEecC
Q 001724 112 GINIAHVPHGGKNSADRSLLVDLM-YWVSQNPPPAHLFLISGDRD-------------FASVLHRLRMNNYNILLASR 175 (1020)
Q Consensus 112 GI~LihvP~ggKNAADi~LiIDaM-d~a~~nP~pdtFVLISGDsD-------------FtpLL~RLRerGynVILagp 175 (1020)
++.++..-.+|..+.+. ++.+ .++... .|+.++|.-|--| +..++.++|..|..|++++.
T Consensus 36 ~~~v~n~g~~G~~~~~~---~~~l~~~~~~~-~pd~v~i~~G~ND~~~~~~~~~~~~~l~~li~~~~~~~~~vil~~~ 109 (177)
T cd01822 36 DVTVINAGVSGDTTAGG---LARLPALLAQH-KPDLVILELGGNDGLRGIPPDQTRANLRQMIETAQARGAPVLLVGM 109 (177)
T ss_pred CeEEEecCcCCcccHHH---HHHHHHHHHhc-CCCEEEEeccCcccccCCCHHHHHHHHHHHHHHHHHCCCeEEEEec
Confidence 44555544455555442 2223 233332 4677666655433 46788889999999998753
No 139
>cd06323 PBP1_ribose_binding Periplasmic sugar-binding domain of the thermophilic Thermoanaerobacter tengcongensis ribose binding protein (ttRBP) and its mesophilic homologs. Periplasmic sugar-binding domain of the thermophilic Thermoanaerobacter tengcongensis ribose binding protein (ttRBP) and its mesophilic homologs. Members of this group are belonging to the type I periplasmic binding protein superfamily, whose members are involved in chemotaxis, ATP-binding cassette transport, and intercellular communication in central nervous system. The thermophilic and mesophilic ribose-binding proteins are structurally very similar, but differ substantially in thermal stability.
Probab=23.25 E-value=2.3e+02 Score=29.37 Aligned_cols=68 Identities=10% Similarity=0.097 Sum_probs=42.9
Q ss_pred hhHHHhhhcCCceeeccCCCccchhhHHHHHHHHHHHhCCCCcEEEEEeCCcch-HHHHHHHHhCCCEEEEecC
Q 001724 103 ANQEVLSSTGINIAHVPHGGKNSADRSLLVDLMYWVSQNPPPAHLFLISGDRDF-ASVLHRLRMNNYNILLASR 175 (1020)
Q Consensus 103 ~~qe~L~ssGI~LihvP~ggKNAADi~LiIDaMd~a~~nP~pdtFVLISGDsDF-tpLL~RLRerGynVILagp 175 (1020)
...+.+...|+.+..+... + |..-..+++.-+... .++++++.+.+.+. ...+..|+.+|..|+++..
T Consensus 20 ~i~~~~~~~g~~v~~~~~~--~--~~~~~~~~~~~~~~~-~~dgii~~~~~~~~~~~~l~~l~~~~ipvv~~~~ 88 (268)
T cd06323 20 GAQKEAKELGYELTVLDAQ--N--DAAKQLNDIEDLITR-GVDAIIINPTDSDAVVPAVKAANEAGIPVFTIDR 88 (268)
T ss_pred HHHHHHHHcCceEEecCCC--C--CHHHHHHHHHHHHHc-CCCEEEEcCCChHHHHHHHHHHHHCCCcEEEEcc
Confidence 3455666677776654432 1 222344566655554 48999988766544 3577888889988887754
No 140
>PRK15408 autoinducer 2-binding protein lsrB; Provisional
Probab=23.05 E-value=2.3e+02 Score=32.31 Aligned_cols=70 Identities=14% Similarity=0.152 Sum_probs=48.6
Q ss_pred hhhHHHhhhcCCceeec-cCCCccchhhHHHHHHHHHHHhCCCCcEEEEEeCCcc-hHHHHHHHHhCCCEEEEecCC
Q 001724 102 RANQEVLSSTGINIAHV-PHGGKNSADRSLLVDLMYWVSQNPPPAHLFLISGDRD-FASVLHRLRMNNYNILLASRE 176 (1020)
Q Consensus 102 k~~qe~L~ssGI~Lihv-P~ggKNAADi~LiIDaMd~a~~nP~pdtFVLISGDsD-FtpLL~RLRerGynVILagp~ 176 (1020)
...+++...+|+.++.. +.. + |..--+.+++-+..+ .+++++|+..|.+ +.+.+.++++.|..|+.+-..
T Consensus 43 ~Gi~~aa~~~G~~v~~~~~~~--~--d~~~q~~~i~~li~~-~vdgIiv~~~d~~al~~~l~~a~~~gIpVV~~d~~ 114 (336)
T PRK15408 43 NGAKEAGKELGVDVTYDGPTE--P--SVSGQVQLINNFVNQ-GYNAIIVSAVSPDGLCPALKRAMQRGVKVLTWDSD 114 (336)
T ss_pred HHHHHHHHHhCCEEEEECCCC--C--CHHHHHHHHHHHHHc-CCCEEEEecCCHHHHHHHHHHHHHCCCeEEEeCCC
Confidence 34566777888887752 321 1 222334666666654 4999999887754 679999999999999987643
No 141
>PRK09701 D-allose transporter subunit; Provisional
Probab=23.00 E-value=2.4e+02 Score=31.03 Aligned_cols=69 Identities=6% Similarity=0.004 Sum_probs=41.0
Q ss_pred hHHHhhhcCCceeeccCCCccchhhHHHHHHHHHHHhCCCCcEEEEEeCCcc-hHHHHHHHHhCCCEEEEecC
Q 001724 104 NQEVLSSTGINIAHVPHGGKNSADRSLLVDLMYWVSQNPPPAHLFLISGDRD-FASVLHRLRMNNYNILLASR 175 (1020)
Q Consensus 104 ~qe~L~ssGI~LihvP~ggKNAADi~LiIDaMd~a~~nP~pdtFVLISGDsD-FtpLL~RLRerGynVILagp 175 (1020)
..+++...|+.+.-+.....+. ..-.+.+++-+... .+|+|+|...|.+ -.+.+.++++.|..|+.+..
T Consensus 46 i~~~a~~~g~~v~~~~~~~~~~--~~~~~~~i~~l~~~-~vDgiIi~~~~~~~~~~~l~~~~~~giPvV~~~~ 115 (311)
T PRK09701 46 IEDEAKTLGVSVDIFASPSEGD--FQSQLQLFEDLSNK-NYKGIAFAPLSSVNLVMPVARAWKKGIYLVNLDE 115 (311)
T ss_pred HHHHHHHcCCeEEEecCCCCCC--HHHHHHHHHHHHHc-CCCEEEEeCCChHHHHHHHHHHHHCCCcEEEeCC
Confidence 3445555666655442212222 22345555555554 4899999887754 23556778889999988764
No 142
>PF13607 Succ_CoA_lig: Succinyl-CoA ligase like flavodoxin domain; PDB: 2CSU_A.
Probab=22.99 E-value=1.8e+02 Score=29.67 Aligned_cols=73 Identities=19% Similarity=0.269 Sum_probs=43.6
Q ss_pred hHHHhhhcCCceeeccCCCccchhhHHHHHHHHHHHhCCCCcEEEEEeCC----cchHHHHHHHHhCCCEEEEecCCchh
Q 001724 104 NQEVLSSTGINIAHVPHGGKNSADRSLLVDLMYWVSQNPPPAHLFLISGD----RDFASVLHRLRMNNYNILLASRESAS 179 (1020)
Q Consensus 104 ~qe~L~ssGI~LihvP~ggKNAADi~LiIDaMd~a~~nP~pdtFVLISGD----sDFtpLL~RLRerGynVILagp~kTp 179 (1020)
....+...||-+.++-.-| |.+|. =+.|+|+|+.+.|....++|.--. ..|...+++++.+ +-|++.-.+.++
T Consensus 17 ~~~~~~~~g~g~s~~vs~G-n~~dv-~~~d~l~~~~~D~~t~~I~ly~E~~~d~~~f~~~~~~a~~~-KPVv~lk~Grt~ 93 (138)
T PF13607_consen 17 ILDWAQDRGIGFSYVVSVG-NEADV-DFADLLEYLAEDPDTRVIVLYLEGIGDGRRFLEAARRAARR-KPVVVLKAGRTE 93 (138)
T ss_dssp HHHHHHHTT-EESEEEE-T-T-SSS--HHHHHHHHCT-SS--EEEEEES--S-HHHHHHHHHHHCCC-S-EEEEE-----
T ss_pred HHHHHHHcCCCeeEEEEeC-ccccC-CHHHHHHHHhcCCCCCEEEEEccCCCCHHHHHHHHHHHhcC-CCEEEEeCCCch
Confidence 3445667788777764433 34565 478999999998877777776543 2599999999988 999975444433
No 143
>TIGR00393 kpsF KpsF/GutQ family protein. This model describes a number of closely related proteins with the phosphosugar-binding domain SIS (Sugar ISomerase) followed by two copies of the CBS (named after Cystathionine Beta Synthase) domain. One is GutQ, a protein of the glucitol operon. Another is KpsF, a virulence factor involved in capsular polysialic acid biosynthesis in some pathogenic strains of E. coli.
Probab=22.96 E-value=2.2e+02 Score=30.78 Aligned_cols=95 Identities=16% Similarity=0.197 Sum_probs=54.8
Q ss_pred CceEEEEeecccccchhhHHHhhhcCCceeeccCCCccchhhHHHHHHHHHHHhCCCCcEEEEEeCCc---chHHHHHHH
Q 001724 87 GPVTITAFGDVVQMSRANQEVLSSTGINIAHVPHGGKNSADRSLLVDLMYWVSQNPPPAHLFLISGDR---DFASVLHRL 163 (1020)
Q Consensus 87 GpVtIRAYGDws~~~k~~qe~L~ssGI~LihvP~ggKNAADi~LiIDaMd~a~~nP~pdtFVLISGDs---DFtpLL~RL 163 (1020)
|+|-|-+.|.-......+...|...|+..+.+.. ..+..-+ +..-..-|.+++||-.+ +-..++..+
T Consensus 1 ~rI~i~G~G~S~~~a~~~~~~l~~~g~~~~~~~~-------~~~~~~~---~~~~~~~d~~i~iS~sG~t~~~~~~~~~a 70 (268)
T TIGR00393 1 GKLVIVGIGKSGLIGKKIVATFASTGTPSFFLHP-------TEAMHGD---LGMVEPNDVVLMISYSGESLELLNLIPHL 70 (268)
T ss_pred CcEEEEecChHHHHHHHHHHHHHhcCCceEEeCH-------hHHhhcc---cCCCCCCCEEEEEeCCCCCHHHHHHHHHH
Confidence 4555555553222234456667778877665422 1111100 01112346777777554 566888888
Q ss_pred HhCCCEEEEecCCchhHHHHhhcceEEec
Q 001724 164 RMNNYNILLASRESASNVLCSAASVMWNW 192 (1020)
Q Consensus 164 RerGynVILagp~kTpeaL~sAcd~Fw~w 192 (1020)
|++|..|+.++....+ .|...||..+.+
T Consensus 71 ~~~g~~ii~iT~~~~s-~l~~~~d~~l~~ 98 (268)
T TIGR00393 71 KRLSHKIIAFTGSPNS-SLARAADYVLDI 98 (268)
T ss_pred HHcCCcEEEEECCCCC-cccccCCEEEEc
Confidence 9999999988764433 355568877665
No 144
>TIGR00216 ispH_lytB (E)-4-hydroxy-3-methyl-but-2-enyl pyrophosphate reductase (IPP and DMAPP forming). Escherichia coli LytB protein had been found to regulate the activity of RelA (guanosine 3',5'-bispyrophosphate synthetase I), which in turn controls the level of a regulatory metabolite. It is involved in penicillin tolerance and the stringent response.
Probab=22.87 E-value=2.1e+02 Score=32.57 Aligned_cols=102 Identities=18% Similarity=0.248 Sum_probs=51.2
Q ss_pred HHHHHHHHHHHhCCCCceEEEEeecccccchhhHHHhhhcCC-ceee----ccCCCcc-chhhHHHHHHHHHHHhCCCCc
Q 001724 72 VAHTITAAIRANGIKGPVTITAFGDVVQMSRANQEVLSSTGI-NIAH----VPHGGKN-SADRSLLVDLMYWVSQNPPPA 145 (1020)
Q Consensus 72 Va~nI~~aLrelG~~GpVtIRAYGDws~~~k~~qe~L~ssGI-~Lih----vP~ggKN-AADi~LiIDaMd~a~~nP~pd 145 (1020)
|..+|+.+.+.+...| -.|..||..-.. ....+.|...|| .++. ++.++.= -+---+--+.++.+....
T Consensus 14 V~rAi~~a~~~~~~~~-~~iy~lG~iIHN-~~Vv~~L~~~Gv~~~v~~~~~v~~~~~ViirAHGv~~~~~~~~~~~g--- 88 (280)
T TIGR00216 14 VKRAIQMAEEALKESG-KPVYTLGPIVHN-PQVVERLRERGVFFFLEDLDEVAAGDTVIIRAHGVPPEVREELEKKG--- 88 (280)
T ss_pred HHHHHHHHHHHHhhcC-CCeEEecCCccC-HHHHHHHHHCCCEEeecCcccCCCCCEEEEeCCCCCHHHHHHHHHCC---
Confidence 4455554444332222 236888887543 346678888896 4433 2211000 000001123344444321
Q ss_pred EEEEEeCCc------chHHHHHHHHhCCCEEEEecCCchhHH
Q 001724 146 HLFLISGDR------DFASVLHRLRMNNYNILLASRESASNV 181 (1020)
Q Consensus 146 tFVLISGDs------DFtpLL~RLRerGynVILagp~kTpea 181 (1020)
+-+| |. ---.++.++.+.||.|+++|....|+.
T Consensus 89 -l~vi--DaTCP~V~kv~~~v~~~~~~Gy~iiiiG~~~HpEv 127 (280)
T TIGR00216 89 -LEVI--DATCPLVTKVHNAVKKYAKEGYHVILIGKKNHPEV 127 (280)
T ss_pred -CeEE--eCCCcccHHHHHHHHHHHhCCCEEEEEeCCCCCee
Confidence 1122 22 122556777788999999998887764
No 145
>PRK10423 transcriptional repressor RbsR; Provisional
Probab=22.68 E-value=9.2e+02 Score=26.22 Aligned_cols=98 Identities=13% Similarity=0.144 Sum_probs=56.2
Q ss_pred hHHHHHHHHHHHhCCCCce-----------EE-EEeecccc-----cchhhHHHhhhcCCceeeccCCCccchhhHHHHH
Q 001724 71 KVAHTITAAIRANGIKGPV-----------TI-TAFGDVVQ-----MSRANQEVLSSTGINIAHVPHGGKNSADRSLLVD 133 (1020)
Q Consensus 71 ~Va~nI~~aLrelG~~GpV-----------tI-RAYGDws~-----~~k~~qe~L~ssGI~LihvP~ggKNAADi~LiID 133 (1020)
....+|.++.+++||.-.. +| -+..+... .-.++.+.+...|+.++-+.... |......
T Consensus 28 ~tr~rV~~~a~~lgY~pn~~a~~l~~~~~~~Igvi~~~~~~~~~~~~~~gi~~~~~~~g~~~~~~~~~~----~~~~~~~ 103 (327)
T PRK10423 28 AITAKVEAAIKELNYAPSALARSLKLNQTRTIGMLITASTNPFYSELVRGVERSCFERGYSLVLCNTEG----DEQRMNR 103 (327)
T ss_pred HHHHHHHHHHHHHCCCccHHHHHHhhCCCCeEEEEeCCCCCCcHHHHHHHHHHHHHHcCCEEEEEeCCC----CHHHHHH
Confidence 3446788888888874311 12 22222221 12346678888999877655432 1223345
Q ss_pred HHHHHHhCCCCcEEEEEeCCcchHHHHHHHHh-CCCEEEEec
Q 001724 134 LMYWVSQNPPPAHLFLISGDRDFASVLHRLRM-NNYNILLAS 174 (1020)
Q Consensus 134 aMd~a~~nP~pdtFVLISGDsDFtpLL~RLRe-rGynVILag 174 (1020)
++..+.++ .+|+++|+..+.+... ...|+. .|..|+++.
T Consensus 104 ~~~~l~~~-~vdGiI~~~~~~~~~~-~~~l~~~~~iPvV~i~ 143 (327)
T PRK10423 104 NLETLMQK-RVDGLLLLCTETHQPS-REIMQRYPSVPTVMMD 143 (327)
T ss_pred HHHHHHHc-CCCEEEEeCCCcchhh-HHHHHhcCCCCEEEEC
Confidence 66666654 4999999887754322 222333 477787765
No 146
>PRK12360 4-hydroxy-3-methylbut-2-enyl diphosphate reductase; Provisional
Probab=22.65 E-value=2.1e+02 Score=32.66 Aligned_cols=102 Identities=15% Similarity=0.230 Sum_probs=53.6
Q ss_pred HHHHHHHHHHHhC-CCCceEEEEeecccccchhhHHHhhhcCCcee--e----ccCCCcc-chhhHHHHHHHHHHHhCCC
Q 001724 72 VAHTITAAIRANG-IKGPVTITAFGDVVQMSRANQEVLSSTGINIA--H----VPHGGKN-SADRSLLVDLMYWVSQNPP 143 (1020)
Q Consensus 72 Va~nI~~aLrelG-~~GpVtIRAYGDws~~~k~~qe~L~ssGI~Li--h----vP~ggKN-AADi~LiIDaMd~a~~nP~ 143 (1020)
|..+|+.+.+.+. ..| -.|..||+.-.. ....+.|...||.++ . ++.++.= -+---+--+.++.+....
T Consensus 15 V~rAi~~a~~~~~~~~~-~~vy~lG~iVHN-~~Vv~~L~~~Gv~~v~~~~~~~v~~~~~ViirAHGv~~~~~~~~~~~g- 91 (281)
T PRK12360 15 VKRAIDTAYDEIEKNDG-KKIYTLGPLIHN-NQVVSDLEEKGVKTIEESEIDSLKEGDVVIIRSHGVSKKVYKDLKDKG- 91 (281)
T ss_pred HHHHHHHHHHHHHhcCC-CCeEEecCCcCC-HHHHHHHHHCcCEEECcCchhhCCCCCEEEEeCCCCCHHHHHHHHHCC-
Confidence 4455655544332 223 237889998653 346678999999888 3 2311000 000001123344444321
Q ss_pred CcEEEEEeCCc------chHHHHHHHHhCCCEEEEecCCchhHH
Q 001724 144 PAHLFLISGDR------DFASVLHRLRMNNYNILLASRESASNV 181 (1020)
Q Consensus 144 pdtFVLISGDs------DFtpLL~RLRerGynVILagp~kTpea 181 (1020)
+-+| |. ---.++.++.+.||.|+++|....|+.
T Consensus 92 ---~~vi--DaTCP~V~k~~~~v~~~~~~Gy~iviiG~~~HpEv 130 (281)
T PRK12360 92 ---LEII--DATCPFVKKIQNIVEEYYNKGYSIIIVGDKNHPEV 130 (281)
T ss_pred ---CeEE--eCCCccchHHHHHHHHHHhCCCEEEEEcCCCCcee
Confidence 1122 22 122556777788999999998877764
No 147
>cd06336 PBP1_ABC_ligand_binding_like_3 Type I periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type active transport systems that are predicted to be involved in transport of amino acids, peptides, or inorganic ions. This group includes the type I periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type active transport systems that are predicted to be involved in transport of amino acids, peptides, or inorganic ions. Members of this group are sequence-similar to members of the family of ABC-type hydrophobic amino acid transporters (HAAT), such as leucine-isoleucine-valine-binding protein (LIVBP); however their ligand specificity has not been determined experimentally.
Probab=22.60 E-value=6e+02 Score=28.39 Aligned_cols=80 Identities=14% Similarity=0.063 Sum_probs=50.0
Q ss_pred CceEE-EEeecccccc---hhhHHHhhhcCCceeeccCCCccchhhHHHHHHHHHHHhCCCCcEEEEEeCCc-chHHHHH
Q 001724 87 GPVTI-TAFGDVVQMS---RANQEVLSSTGINIAHVPHGGKNSADRSLLVDLMYWVSQNPPPAHLFLISGDR-DFASVLH 161 (1020)
Q Consensus 87 GpVtI-RAYGDws~~~---k~~qe~L~ssGI~LihvP~ggKNAADi~LiIDaMd~a~~nP~pdtFVLISGDs-DFtpLL~ 161 (1020)
|.-.| -+|.|..... ..+++.|.+.|++++..-.-.-+.+|+. ..+.-+.+ ..++.++|..... +...++.
T Consensus 137 ~~~~v~il~~d~~~g~~~~~~~~~~l~~~G~~vv~~~~~~~~~~D~s---~~i~~i~~-~~~d~v~~~~~~~~~~~~~~~ 212 (347)
T cd06336 137 GGKKVALLGPNDAYGQPWVAAYKAAWEAAGGKVVSEEPYDPGTTDFS---PIVTKLLA-EKPDVIFLGGPSPAPAALVIK 212 (347)
T ss_pred CCceEEEEccCCchhHHHHHHHHHHHHHcCCEEeeecccCCCCcchH---HHHHHHHh-cCCCEEEEcCCCchHHHHHHH
Confidence 43344 5565544322 3467788899998876311111245643 33333333 3589998887777 8999999
Q ss_pred HHHhCCCEE
Q 001724 162 RLRMNNYNI 170 (1020)
Q Consensus 162 RLRerGynV 170 (1020)
.+++.|++.
T Consensus 213 ~~~~~g~~~ 221 (347)
T cd06336 213 QARELGFKG 221 (347)
T ss_pred HHHHcCCCc
Confidence 999999874
No 148
>PRK13937 phosphoheptose isomerase; Provisional
Probab=22.52 E-value=6.2e+02 Score=26.54 Aligned_cols=49 Identities=12% Similarity=0.068 Sum_probs=34.1
Q ss_pred CCcEEEEEeCCc---chHHHHHHHHhCCCEEEEecCCchhHHHHhhcceEEec
Q 001724 143 PPAHLFLISGDR---DFASVLHRLRMNNYNILLASRESASNVLCSAASVMWNW 192 (1020)
Q Consensus 143 ~pdtFVLISGDs---DFtpLL~RLRerGynVILagp~kTpeaL~sAcd~Fw~w 192 (1020)
+-|.+++||.-+ +-..++..++++|..||+++....+ .|...||..+.+
T Consensus 106 ~~Dl~i~iS~sG~t~~~~~~~~~ak~~g~~~I~iT~~~~s-~L~~~ad~~l~~ 157 (188)
T PRK13937 106 PGDVLIGISTSGNSPNVLAALEKARELGMKTIGLTGRDGG-KMKELCDHLLIV 157 (188)
T ss_pred CCCEEEEEeCCCCcHHHHHHHHHHHHCCCeEEEEeCCCCC-hhHHhCCEEEEe
Confidence 347777776443 5668889999999999988764333 455567766653
No 149
>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=22.35 E-value=8.8e+02 Score=25.12 Aligned_cols=133 Identities=14% Similarity=0.083 Sum_probs=0.0
Q ss_pred ccCCCeEEEEEecCCCCCC--CCCChhhHHHHHHHHHHHhCCCCceEEEEeecccccc---hhhHHHhhhcCCceeeccC
Q 001724 46 ESKNVRVSVWWDFENCNLP--AGVNAFKVAHTITAAIRANGIKGPVTITAFGDVVQMS---RANQEVLSSTGINIAHVPH 120 (1020)
Q Consensus 46 es~~~rVAVFWDiENcpiP--~g~d~~~Va~nI~~aLrelG~~GpVtIRAYGDws~~~---k~~qe~L~ssGI~LihvP~ 120 (1020)
......+.++-+....... .+.+.+..+..+-..|.+.|+.-...|..-.+..... .++++.|..+|+.+.....
T Consensus 75 ~~~~ipvv~~~~~~~~~~~~~v~~d~~~~~~~~~~~l~~~g~~~i~~i~~~~~~~~~~~r~~gf~~~l~~~~~~~~~~~~ 154 (268)
T cd01575 75 RAAGIPVVEIMDLPPDPIDMAVGFSHAEAGRAMARHLLARGYRRIGFLGARMDDTRAQQRLEGFRAALRAAGLDPPLVVT 154 (268)
T ss_pred HhcCCCEEEEecCCCCCCCCeEEeCcHHHHHHHHHHHHHCCCCcEEEecCCCCcccHHHHHHHHHHHHHHcCCCCCceeE
Q ss_pred CCccchhhHHHHHHHHHHHhCCCCcEEEEEeCCcchHHHHHHHHhCCC----EEEEecCCchh
Q 001724 121 GGKNSADRSLLVDLMYWVSQNPPPAHLFLISGDRDFASVLHRLRMNNY----NILLASRESAS 179 (1020)
Q Consensus 121 ggKNAADi~LiIDaMd~a~~nP~pdtFVLISGDsDFtpLL~RLRerGy----nVILagp~kTp 179 (1020)
..-+..-..-.-.+..|+..+|.|+.|+ +.+|.-...++..|++.|+ .|.+++-..++
T Consensus 155 ~~~~~~~~~~~~~~~~~l~~~~~~~ai~-~~~d~~a~~~~~~l~~~g~~~p~di~vig~d~~~ 216 (268)
T cd01575 155 TPEPSSFALGRELLAELLARWPDLDAVF-CSNDDLALGALFECQRRGISVPEDIAIAGFGDLE 216 (268)
T ss_pred eccCCCHHHHHHHHHHHHhCCCCCCEEE-ECCcHHHHHHHHHHHHhCCCCCcceEEEecCCch
No 150
>PF01239 PPTA: Protein prenyltransferase alpha subunit repeat; InterPro: IPR002088 Protein prenylation is the posttranslational attachment of either a farnesyl group or a geranylgeranyl group via a thioether linkage (-C-S-C-) to a cysteine at or near the carboxyl terminus of the protein. Farnesyl and geranylgeranyl groups are polyisoprenes, unsaturated hydrocarbons with a multiple of five carbons; the chain is 15 carbons long in the farnesyl moiety and 20 carbons long in the geranylgeranyl moiety. There are three different protein prenyltransferases in humans: farnesyltransferase (FT) and geranylgeranyltransferase 1 (GGT1) share the same motif (the CaaX box) around the cysteine in their substrates, and are thus called CaaX prenyltransferases, whereas geranylgeranyltransferase 2 (GGT2, also called Rab geranylgeranyltransferase) recognises a different motif and is thus called a non-CaaX prenyltransferase. Protein prenyltransferases are currently known only in eukaryotes, but they are widespread, being found in vertebrates, insects, nematodes, plants, fungi and protozoa, including several parasites. Each protein consists of two subunits, alpha and beta; the alpha subunit of FT and GGT1 is encoded by the same gene, FNTA. The alpha subunit is thought to participate in a stable complex with the isoprenyl substrate; the beta subunit binds the peptide substrate. In the alpha subunits of both types of protein prenyltransferases, seven tetratricopeptide repeats are formed by pairs of helices that are stabilised by conserved intercalating residues. The alpha subunits of GGT2 in mammals and plants also have an immunoglobulin-like domain between the fifth and sixth tetratricopeptide repeat, as well as leucine-rich repeats at the carboxyl terminus. The functions of these additional domains in GGT2 are as yet undefined, but they are apparently not directly involved in the interaction with substrates and Rab escort proteins. The tetratricopeptide repeats of the alpha subunit form a right-handed superhelix, which embraces the (alpha-alpha)6 barrel of the beta subunit []. ; GO: 0008318 protein prenyltransferase activity, 0018342 protein prenylation; PDB: 1S63_A 1LD7_A 1LD8_A 2H6G_A 1SA4_A 1MZC_A 1TN6_A 2F0Y_A 2H6H_A 2H6F_A ....
Probab=22.06 E-value=97 Score=23.27 Aligned_cols=28 Identities=14% Similarity=0.503 Sum_probs=25.7
Q ss_pred HHHHHHHHhCCCCccchhhHHHHHHHhc
Q 001724 745 KLVDEILKEYPEGYNMRGFRQLFIERYG 772 (1020)
Q Consensus 745 KLvkeil~e~p~Gyni~~Frk~F~~~yg 772 (1020)
.+++++|..+|.-|.+=..|+.++++++
T Consensus 4 ~~~~~~l~~~pknys~W~yR~~ll~~l~ 31 (31)
T PF01239_consen 4 EFTKKALEKDPKNYSAWNYRRWLLKQLN 31 (31)
T ss_dssp HHHHHHHHHSTTCHHHHHHHHHHHHHHS
T ss_pred HHHHHHHHHCcccccHHHHHHHHHHHcc
Confidence 5889999999999999999999998864
No 151
>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=22.01 E-value=2.6e+02 Score=26.38 Aligned_cols=47 Identities=17% Similarity=0.224 Sum_probs=32.5
Q ss_pred CcEEEEEeCCc---chHHHHHHHHhCCCEEEEecCCchhHHHHhhcceEEe
Q 001724 144 PAHLFLISGDR---DFASVLHRLRMNNYNILLASRESASNVLCSAASVMWN 191 (1020)
Q Consensus 144 pdtFVLISGDs---DFtpLL~RLRerGynVILagp~kTpeaL~sAcd~Fw~ 191 (1020)
=+.++++|-.. +...+++.+|++|..|++++....+ .+...||..+.
T Consensus 54 ~d~vi~is~sg~~~~~~~~~~~ak~~g~~vi~iT~~~~~-~l~~~ad~~l~ 103 (131)
T PF01380_consen 54 DDLVIIISYSGETRELIELLRFAKERGAPVILITSNSES-PLARLADIVLY 103 (131)
T ss_dssp TEEEEEEESSSTTHHHHHHHHHHHHTTSEEEEEESSTTS-HHHHHSSEEEE
T ss_pred cceeEeeeccccchhhhhhhHHHHhcCCeEEEEeCCCCC-chhhhCCEEEE
Confidence 35566676554 5678888889999999988765444 45555676655
No 152
>cd06360 PBP1_alkylbenzenes_like Type I periplasmic binding component of active transport systems that are predicted be involved in anaerobic biodegradation of alkylbenzenes such as toluene and ethylbenzene. This group includes the type I periplasmic binding component of active transport systems that are predicted be involved in anaerobic biodegradation of alkylbenzenes such as toluene and ethylbenzene; their substrate specificity is not well characterized, however.
Probab=21.73 E-value=5.3e+02 Score=28.13 Aligned_cols=68 Identities=13% Similarity=0.158 Sum_probs=44.3
Q ss_pred hhHHHhhhcCCceeeccCCCccchhhHHHHHHHHHHHhCCCCcEEEEEeCCcchHHHHHHHHhCCC--EEEEec
Q 001724 103 ANQEVLSSTGINIAHVPHGGKNSADRSLLVDLMYWVSQNPPPAHLFLISGDRDFASVLHRLRMNNY--NILLAS 174 (1020)
Q Consensus 103 ~~qe~L~ssGI~LihvP~ggKNAADi~LiIDaMd~a~~nP~pdtFVLISGDsDFtpLL~RLRerGy--nVILag 174 (1020)
.++..|...|++++....-.-++.|..=.+.-+ .. ..|+.++++....+...++..++..|+ .+.+++
T Consensus 153 ~~~~~~~~~G~~v~~~~~~~~~~~d~~~~v~~~---~~-~~pd~v~~~~~~~~~~~~~~~~~~~g~~~~~~~~~ 222 (336)
T cd06360 153 GFKEAFTEAGGKIVKELWVPFGTSDFASYLAQI---PD-DVPDAVFVFFAGGDAIKFVKQYDAAGLKAKIPLIG 222 (336)
T ss_pred HHHHHHHHcCCEEEEEEecCCCCcchHHHHHHH---Hh-cCCCEEEEecccccHHHHHHHHHHcCCccCCeEEe
Confidence 467788899998875211111234533222222 22 348999998888899999999999999 655443
No 153
>cd06333 PBP1_ABC-type_HAAT_like Type I periplasmic binding component of ABC (ATPase Binding Cassette)-type transport systems that are predicted to be involved in uptake of amino acids. This subgroup includes the type I periplasmic binding component of ABC (ATPase Binding Cassette)-type transport systems that are predicted to be involved in uptake of amino acids. Members of this subgroup are sequence-similar to members of the family of ABC-type hydrophobic amino acid transporters (HAAT), such as leucine-isoleucine-valine-binding protein (LIVBP); their ligand specificity has not been determined experimentally, however.
Probab=21.65 E-value=3.7e+02 Score=29.18 Aligned_cols=64 Identities=13% Similarity=0.146 Sum_probs=41.6
Q ss_pred hhHHHhhhcCCceeec---cCCCccchhhHHHHHHHHHHHhCCCCcEEEEEeCCcchHHHHHHHHhCCCEEEEe
Q 001724 103 ANQEVLSSTGINIAHV---PHGGKNSADRSLLVDLMYWVSQNPPPAHLFLISGDRDFASVLHRLRMNNYNILLA 173 (1020)
Q Consensus 103 ~~qe~L~ssGI~Lihv---P~ggKNAADi~LiIDaMd~a~~nP~pdtFVLISGDsDFtpLL~RLRerGynVILa 173 (1020)
.+++.+...|+++... +.+. .| ..-.+..+.. ..|+.|++++.+.+-..+++.|++.|+.+-++
T Consensus 152 ~~~~~~~~~G~~v~~~~~~~~~~---~d--~~~~~~~l~~--~~pdaIi~~~~~~~~~~~~~~l~~~g~~~p~~ 218 (312)
T cd06333 152 ELKALAPKYGIEVVADERYGRTD---TS--VTAQLLKIRA--ARPDAVLIWGSGTPAALPAKNLRERGYKGPIY 218 (312)
T ss_pred HHHHHHHHcCCEEEEEEeeCCCC---cC--HHHHHHHHHh--CCCCEEEEecCCcHHHHHHHHHHHcCCCCCEE
Confidence 4677888999987642 2222 23 2222333332 24788888877777778999999999886554
No 154
>cd06311 PBP1_ABC_sugar_binding_like_3 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=21.65 E-value=2.8e+02 Score=29.25 Aligned_cols=45 Identities=4% Similarity=0.040 Sum_probs=33.7
Q ss_pred HHHHHHHHHHhCCCCcEEEEEeCCcc-hHHHHHHHHhCCCEEEEecC
Q 001724 130 LLVDLMYWVSQNPPPAHLFLISGDRD-FASVLHRLRMNNYNILLASR 175 (1020)
Q Consensus 130 LiIDaMd~a~~nP~pdtFVLISGDsD-FtpLL~RLRerGynVILagp 175 (1020)
....+++.+..+ .+|+++|+..|.+ +...+.++++.|..|+.+..
T Consensus 48 ~~~~~~~~l~~~-~vDgiii~~~~~~~~~~~i~~~~~~gIpvV~~d~ 93 (274)
T cd06311 48 QQNAQQDLLINR-KIDALVILPFESAPLTQPVAKAKKAGIFVVVVDR 93 (274)
T ss_pred HHHHHHHHHHHc-CCCEEEEeCCCchhhHHHHHHHHHCCCeEEEEcC
Confidence 445666655554 4899999987765 67888999999999997753
No 155
>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=21.61 E-value=3.6e+02 Score=29.74 Aligned_cols=66 Identities=14% Similarity=0.159 Sum_probs=41.2
Q ss_pred hHHHhhhcCCceeeccCCCccchhhHHHHHHHHHHHhCCCCcEEEEEeCCcchHHHHHHHHhCCCEEEEecCC
Q 001724 104 NQEVLSSTGINIAHVPHGGKNSADRSLLVDLMYWVSQNPPPAHLFLISGDRDFASVLHRLRMNNYNILLASRE 176 (1020)
Q Consensus 104 ~qe~L~ssGI~LihvP~ggKNAADi~LiIDaMd~a~~nP~pdtFVLISGDsDFtpLL~RLRerGynVILagp~ 176 (1020)
..+++...|..++-+..+. ..+ .- .+++.+.++ .+|+|+|.+...++..+.. +.+.|..|+++...
T Consensus 23 Ie~~a~~~Gy~l~l~~t~~--~~~--~e-~~i~~l~~~-~vDGiI~~s~~~~~~~l~~-~~~~~iPvV~~~~~ 88 (279)
T PF00532_consen 23 IEQEAREHGYQLLLCNTGD--DEE--KE-EYIELLLQR-RVDGIILASSENDDEELRR-LIKSGIPVVLIDRY 88 (279)
T ss_dssp HHHHHHHTTCEEEEEEETT--THH--HH-HHHHHHHHT-TSSEEEEESSSCTCHHHHH-HHHTTSEEEEESS-
T ss_pred HHHHHHHcCCEEEEecCCC--chH--HH-HHHHHHHhc-CCCEEEEecccCChHHHHH-HHHcCCCEEEEEec
Confidence 3445555555554443321 112 33 677777776 4999999998888555544 44449999988754
No 156
>cd01461 vWA_interalpha_trypsin_inhibitor vWA_interalpha trypsin inhibitor (ITI): ITI is a glycoprotein composed of three polypeptides- two heavy chains and one light chain (bikunin). Bikunin confers the protease-inhibitor function while the heavy chains are involved in rendering stability to the extracellular matrix by binding to hyaluronic acid. The heavy chains carry the VWA domain with a conserved MIDAS motif. Although the exact role of the VWA domains remains unknown, it has been speculated to be involved in mediating protein-protein interactions with the components of the extracellular matrix.
Probab=21.47 E-value=7.8e+02 Score=24.13 Aligned_cols=46 Identities=13% Similarity=0.055 Sum_probs=29.0
Q ss_pred CeEEEEEecCCCCCCCCCChhhHHHHHHHHHHHhCCCCceEEEEeecc
Q 001724 50 VRVSVWWDFENCNLPAGVNAFKVAHTITAAIRANGIKGPVTITAFGDV 97 (1020)
Q Consensus 50 ~rVAVFWDiENcpiP~g~d~~~Va~nI~~aLrelG~~GpVtIRAYGDw 97 (1020)
.+|.+.||.-.---. .....+...|..++..+..-..+.|.+|++-
T Consensus 3 ~~v~~vlD~S~SM~~--~~~~~~~~al~~~l~~l~~~~~~~l~~Fs~~ 48 (171)
T cd01461 3 KEVVFVIDTSGSMSG--TKIEQTKEALLTALKDLPPGDYFNIIGFSDT 48 (171)
T ss_pred ceEEEEEECCCCCCC--hhHHHHHHHHHHHHHhCCCCCEEEEEEeCCC
Confidence 468899998766532 2233445566667776654445777888664
No 157
>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=21.37 E-value=2.6e+02 Score=29.69 Aligned_cols=66 Identities=5% Similarity=0.187 Sum_probs=40.7
Q ss_pred hHHHhhhcCCceeeccCCCccchhhHHHHHHHHHHHhCCCCcEEEEEeCCcch-HHHHHHHHhCCCEEEEecC
Q 001724 104 NQEVLSSTGINIAHVPHGGKNSADRSLLVDLMYWVSQNPPPAHLFLISGDRDF-ASVLHRLRMNNYNILLASR 175 (1020)
Q Consensus 104 ~qe~L~ssGI~LihvP~ggKNAADi~LiIDaMd~a~~nP~pdtFVLISGDsDF-tpLL~RLRerGynVILagp 175 (1020)
..+++...|+.+..+... +. + -..+++..+... .+++++|...|.++ ..++..|+..|..|+++..
T Consensus 21 i~~~~~~~g~~~~~~~~~--~~-~--~~~~~i~~~~~~-~~dgiii~~~~~~~~~~~~~~~~~~~iPvV~~~~ 87 (289)
T cd01540 21 AKKAAKEKGFTVVKIDVP--DG-E--KVLSAIDNLGAQ-GAKGFVICVPDVKLGPAIVAKAKAYNMKVVAVDD 87 (289)
T ss_pred HHHHHHHcCCEEEEccCC--CH-H--HHHHHHHHHHHc-CCCEEEEccCchhhhHHHHHHHHhCCCeEEEecC
Confidence 344555566555544322 21 1 123344444443 48999999888765 4567889999999998753
No 158
>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=21.17 E-value=6.7e+02 Score=26.14 Aligned_cols=64 Identities=17% Similarity=0.221 Sum_probs=36.2
Q ss_pred hhHHHhhhcCCceeec--cCCCccchhhHHHHHHHHHHHhCCCCcEEEEEeCCcchHHHHHHHHhCCCE
Q 001724 103 ANQEVLSSTGINIAHV--PHGGKNSADRSLLVDLMYWVSQNPPPAHLFLISGDRDFASVLHRLRMNNYN 169 (1020)
Q Consensus 103 ~~qe~L~ssGI~Lihv--P~ggKNAADi~LiIDaMd~a~~nP~pdtFVLISGDsDFtpLL~RLRerGyn 169 (1020)
++++.+...|+.+..+ ..+..+ .+.. .-.+..++..++.++.|+ +++|.-...+++.|++.|+.
T Consensus 139 Gf~~~~~~~~~~~~~~~~~~~~~~-~~~~-~~~~~~~l~~~~~~~~i~-~~~d~~a~~~~~~~~~~g~~ 204 (270)
T cd01545 139 GYRDALAEAGLPLDPELVAQGDFT-FESG-LEAAEALLALPDRPTAIF-ASNDDMAAGVLAVAHRRGLR 204 (270)
T ss_pred HHHHHHHHcCCCCChhhEEeCCCC-hhhH-HHHHHHHHhCCCCCCEEE-EcCcHHHHHHHHHHHHcCCC
Confidence 4677788888876321 111111 1111 122334444456677655 56666566999999999974
No 159
>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=21.13 E-value=9.1e+02 Score=25.58 Aligned_cols=64 Identities=14% Similarity=0.169 Sum_probs=36.3
Q ss_pred hhhHHHhhhcCCceee--ccCCCccchhhHHHHHHHHHHHhCCCCcEEEEEeCCcchHHHHHHHHhCCC
Q 001724 102 RANQEVLSSTGINIAH--VPHGGKNSADRSLLVDLMYWVSQNPPPAHLFLISGDRDFASVLHRLRMNNY 168 (1020)
Q Consensus 102 k~~qe~L~ssGI~Lih--vP~ggKNAADi~LiIDaMd~a~~nP~pdtFVLISGDsDFtpLL~RLRerGy 168 (1020)
.++++.+..+|+.+.. +... ..+.+ .....+..++..++.|+ .+++++|.--..+++.|+++|+
T Consensus 139 ~gf~~~~~~~g~~~~~~~~~~~-~~~~~-~~~~~~~~~l~~~~~~~-ai~~~~d~~a~g~~~~l~~~g~ 204 (269)
T cd06297 139 AGFQQALKDAGRPFSPDLLAIT-DHSEE-GGRLAMRHLLEKASPPL-AVFASADQQALGALQEAVELGL 204 (269)
T ss_pred HHHHHHHHHcCCCCChhhEEeC-CCChh-hHHHHHHHHHcCCCCCc-EEEEcCcHHHHHHHHHHHHcCC
Confidence 3578888888886432 2211 11111 11222334444445454 5556677666689999999987
No 160
>COG0451 WcaG Nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]
Probab=21.12 E-value=1.2e+02 Score=32.64 Aligned_cols=30 Identities=20% Similarity=0.326 Sum_probs=26.5
Q ss_pred EEEeCCcchH--HHHHHHHhCCCEEEEecCCc
Q 001724 148 FLISGDRDFA--SVLHRLRMNNYNILLASRES 177 (1020)
Q Consensus 148 VLISGDsDFt--pLL~RLRerGynVILagp~k 177 (1020)
+||+|-..|. .|+.+|.+.|+.|+++....
T Consensus 3 ILVtG~tGfiG~~l~~~L~~~g~~V~~~~r~~ 34 (314)
T COG0451 3 ILVTGGAGFIGSHLVERLLAAGHDVRGLDRLR 34 (314)
T ss_pred EEEEcCcccHHHHHHHHHHhCCCeEEEEeCCC
Confidence 8999999995 99999999999999987543
No 161
>TIGR00658 orni_carb_tr ornithine carbamoyltransferase. Most OTCases are homotrimers, but the homotrimers are organized into dodecamers built from four trimers in at least two species; the catabolic OTCase of Pseudomonas aeruginosa is allosterically regulated, while OTCase of the extreme thermophile Pyrococcus furiosus shows both allostery and thermophily.
Probab=21.12 E-value=8.1e+02 Score=28.06 Aligned_cols=110 Identities=12% Similarity=0.087 Sum_probs=63.0
Q ss_pred EEEEecCCCCCCCCCChhhHHHHHHHHHHHhCCCCce-EEEEeecccccchhhHHHhhhcCCceeeccCCCccchhhHHH
Q 001724 53 SVWWDFENCNLPAGVNAFKVAHTITAAIRANGIKGPV-TITAFGDVVQMSRANQEVLSSTGINIAHVPHGGKNSADRSLL 131 (1020)
Q Consensus 53 AVFWDiENcpiP~g~d~~~Va~nI~~aLrelG~~GpV-tIRAYGDws~~~k~~qe~L~ssGI~LihvP~ggKNAADi~Li 131 (1020)
+|++|..+..+..|- .|...++-++.|..+ .||...+- .....-...+|.++.. ++...==-..+
T Consensus 68 ~i~l~~~~ss~~kgE-------sl~Dt~~vls~y~D~iv~R~~~~~-----~~~~~a~~~~vPVINa--~~~~~HPtQaL 133 (304)
T TIGR00658 68 PLYLNPNDLQLGRGE-------SIKDTARVLSRYVDGIMARVYKHE-----DVEELAKYASVPVING--LTDLFHPCQAL 133 (304)
T ss_pred EEEeCCccccCCCCC-------CHHHHHHHHHHhCCEEEEECCChH-----HHHHHHHhCCCCEEEC--CCCCCChHHHH
Confidence 455598888775542 233334444434444 44854222 1222223466666654 22223235789
Q ss_pred HHHHHHHHhCCCCcE--EEEEeCCc--chHHHHHHHHhCCCEEEEecCCc
Q 001724 132 VDLMYWVSQNPPPAH--LFLISGDR--DFASVLHRLRMNNYNILLASRES 177 (1020)
Q Consensus 132 IDaMd~a~~nP~pdt--FVLISGDs--DFtpLL~RLRerGynVILagp~k 177 (1020)
.|++.+....+.+++ +++| ||. =.-.++.-|...|.+|.+++|..
T Consensus 134 ~Dl~Ti~e~~g~l~g~~v~~v-Gd~~~v~~Sl~~~l~~~g~~v~~~~P~~ 182 (304)
T TIGR00658 134 ADLLTIIEHFGKLKGVKVVYV-GDGNNVCNSLMLAGAKLGMDVVVATPEG 182 (304)
T ss_pred HHHHHHHHHhCCCCCcEEEEE-eCCCchHHHHHHHHHHcCCEEEEECCch
Confidence 999988765555664 4444 783 23455666677899999999864
No 162
>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=21.08 E-value=5.6e+02 Score=26.75 Aligned_cols=74 Identities=12% Similarity=0.168 Sum_probs=43.1
Q ss_pred hhhHHHhhhcCCceee--ccCCCccchhhHHHHHHHHHHHhCCCCcEEEEEeCCcchHHHHHHHHhCCCE----EEEecC
Q 001724 102 RANQEVLSSTGINIAH--VPHGGKNSADRSLLVDLMYWVSQNPPPAHLFLISGDRDFASVLHRLRMNNYN----ILLASR 175 (1020)
Q Consensus 102 k~~qe~L~ssGI~Lih--vP~ggKNAADi~LiIDaMd~a~~nP~pdtFVLISGDsDFtpLL~RLRerGyn----VILagp 175 (1020)
.++++.|..+|+.+.. +... -+ +..-.-.+..|+..++.++ .+++++|.--..++..|++.|+. |.+++-
T Consensus 133 ~gf~~~l~~~~~~~~~~~~~~~-~~--~~~~~~~~~~~l~~~~~~~-ai~~~~d~~a~~~~~al~~~g~~vp~di~v~g~ 208 (265)
T cd06291 133 EGFLDVLKENGLEVRIIEIQEN-FD--DAEKKEEIKELLEEYPDID-GIFASNDLTAILVLKEAQQRGIRVPEDLQIIGY 208 (265)
T ss_pred HHHHHHHHHcCCCCChheeecc-cc--chHHHHHHHHHHhCCCCCC-EEEECChHHHHHHHHHHHHcCCCCCcceEEecc
Confidence 3577888888886432 2221 11 1112233455676676664 44555666556889999999874 556655
Q ss_pred Cchh
Q 001724 176 ESAS 179 (1020)
Q Consensus 176 ~kTp 179 (1020)
...+
T Consensus 209 d~~~ 212 (265)
T cd06291 209 DGTK 212 (265)
T ss_pred CChH
Confidence 5444
No 163
>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=20.77 E-value=4.6e+02 Score=26.46 Aligned_cols=74 Identities=7% Similarity=-0.067 Sum_probs=49.4
Q ss_pred CceEE-EEeecccccchhh-HHHhhhcCCceeeccCCCccchhhHHHHHHHHHHHhCCCCcEEEEEeCCc----chHHHH
Q 001724 87 GPVTI-TAFGDVVQMSRAN-QEVLSSTGINIAHVPHGGKNSADRSLLVDLMYWVSQNPPPAHLFLISGDR----DFASVL 160 (1020)
Q Consensus 87 GpVtI-RAYGDws~~~k~~-qe~L~ssGI~LihvP~ggKNAADi~LiIDaMd~a~~nP~pdtFVLISGDs----DFtpLL 160 (1020)
.+|.+ +..+|.......+ ...|...|+++++...- .+. -++++.+.++ .++.++|-|-+. .+..++
T Consensus 3 ~~v~~a~~g~D~Hd~g~~iv~~~l~~~GfeVi~lg~~--~s~-----e~~v~aa~e~-~adii~iSsl~~~~~~~~~~~~ 74 (132)
T TIGR00640 3 PRILVAKMGQDGHDRGAKVIATAYADLGFDVDVGPLF--QTP-----EEIARQAVEA-DVHVVGVSSLAGGHLTLVPALR 74 (132)
T ss_pred CEEEEEeeCCCccHHHHHHHHHHHHhCCcEEEECCCC--CCH-----HHHHHHHHHc-CCCEEEEcCchhhhHHHHHHHH
Confidence 34555 7888776655544 56788999999986431 111 1344555555 478888887775 366888
Q ss_pred HHHHhCCC
Q 001724 161 HRLRMNNY 168 (1020)
Q Consensus 161 ~RLRerGy 168 (1020)
..|+++|.
T Consensus 75 ~~L~~~g~ 82 (132)
T TIGR00640 75 KELDKLGR 82 (132)
T ss_pred HHHHhcCC
Confidence 88999876
No 164
>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=20.72 E-value=2.8e+02 Score=29.24 Aligned_cols=66 Identities=11% Similarity=0.059 Sum_probs=37.1
Q ss_pred HHHhhhcCCceeeccCCCccchhhHHHHHHHHHHHhCCCCcEEEEEeCCcc----hHHHHHHHHhCCCEEEEecC
Q 001724 105 QEVLSSTGINIAHVPHGGKNSADRSLLVDLMYWVSQNPPPAHLFLISGDRD----FASVLHRLRMNNYNILLASR 175 (1020)
Q Consensus 105 qe~L~ssGI~LihvP~ggKNAADi~LiIDaMd~a~~nP~pdtFVLISGDsD----FtpLL~RLRerGynVILagp 175 (1020)
.+++...|+.++.+.... |...-.++++-+.+. .+|+++|...+.+ ....+..+++.|.-|+++..
T Consensus 22 ~~~~~~~g~~~~~~~~~~----~~~~~~~~i~~l~~~-~vdgii~~~~~~~~~~~~~~~~~~~~~~~ipvV~~~~ 91 (273)
T cd01541 22 ESVLSEKGYSLLLASTNN----DPERERKCLENMLSQ-GIDGLIIEPTKSALPNPNIDLYLKLEKLGIPYVFINA 91 (273)
T ss_pred HHHHHHcCCEEEEEeCCC----CHHHHHHHHHHHHHc-CCCEEEEeccccccccccHHHHHHHHHCCCCEEEEec
Confidence 444555555555433211 112334445445554 4888888766542 34666778888888887653
No 165
>PRK02240 GTP cyclohydrolase III; Provisional
Probab=20.68 E-value=4.6e+02 Score=29.81 Aligned_cols=80 Identities=15% Similarity=0.164 Sum_probs=53.8
Q ss_pred eEEEEeecccccc---hhh-HHHhhhcCCceeeccCCCccchhhHHHHHHHHHHHhCC------CCcEEEEEeCCc---c
Q 001724 89 VTITAFGDVVQMS---RAN-QEVLSSTGINIAHVPHGGKNSADRSLLVDLMYWVSQNP------PPAHLFLISGDR---D 155 (1020)
Q Consensus 89 VtIRAYGDws~~~---k~~-qe~L~ssGI~LihvP~ggKNAADi~LiIDaMd~a~~nP------~pdtFVLISGDs---D 155 (1020)
|.|.-||-|+-.+ +.| .+.|++ .|..|++.++.... ..|+|+.|+..- +
T Consensus 7 iqid~YgpWT~t~~prRE~dlQ~lQs------------------rLya~L~~~~~~~ggl~Ff~RgDN~iavtNGI~~~~ 68 (254)
T PRK02240 7 IQIDNYGPWTVTPNPRRESDLQALQS------------------RLYADLAQQFGARDGYVFFTRFDNMIAVTNGIDLED 68 (254)
T ss_pred EEecCCCcCcCCCCCccHHHHHHHHH------------------HHHHHHHHHHHhCCCEEEeccCceEEEEcCCCCHHH
Confidence 4468899999764 333 334432 47888888887753 479999998776 7
Q ss_pred hHHHHHHHHhC-CCEEE-EecCCchhHHHHhhc
Q 001724 156 FASVLHRLRMN-NYNIL-LASRESASNVLCSAA 186 (1020)
Q Consensus 156 FtpLL~RLRer-GynVI-Lagp~kTpeaL~sAc 186 (1020)
+..++..++++ +..|= +++-.+||..-...|
T Consensus 69 ~~~i~e~I~n~~PV~ls~GIG~g~TP~eA~~~A 101 (254)
T PRK02240 69 HARIQESIRNRYPVTVSMGIGTAETPYEAQKLA 101 (254)
T ss_pred HHHHHHHHHhcCCCceEEEEEecCCHHHHHHHH
Confidence 88999999885 44443 466677774433334
No 166
>PRK13835 conjugal transfer protein TrbH; Provisional
Probab=20.49 E-value=2.2e+02 Score=29.82 Aligned_cols=47 Identities=15% Similarity=0.241 Sum_probs=34.4
Q ss_pred hhhHHHHHHHHHHHhCCCCc--EEEEEeCCcchH-HHHHHHHhCCCEEEE
Q 001724 126 ADRSLLVDLMYWVSQNPPPA--HLFLISGDRDFA-SVLHRLRMNNYNILL 172 (1020)
Q Consensus 126 ADi~LiIDaMd~a~~nP~pd--tFVLISGDsDFt-pLL~RLRerGynVIL 172 (1020)
++..|.-||+.-+...-+|+ +|.|--....|. .|+..||..||-|+=
T Consensus 38 aa~~iA~D~vsqLae~~pPa~tt~~l~q~~d~Fg~aL~~aLr~~GYaVvt 87 (145)
T PRK13835 38 AASAIAGDMVSRLAEQIGPGTTTIKLKKDTSPFGQALEAALKGWGYAVVT 87 (145)
T ss_pred HHHHHHHHHHHHHHHhcCCCceEEEEeecCcHHHHHHHHHHHhcCeEEee
Confidence 46689999998776643343 466665556796 677889999999993
No 167
>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=20.42 E-value=3.5e+02 Score=29.04 Aligned_cols=43 Identities=9% Similarity=-0.015 Sum_probs=31.3
Q ss_pred HHHHHHHHhCCCCcEEEEEeCCcc-hHHHHHHHHhCCCEEEEecC
Q 001724 132 VDLMYWVSQNPPPAHLFLISGDRD-FASVLHRLRMNNYNILLASR 175 (1020)
Q Consensus 132 IDaMd~a~~nP~pdtFVLISGDsD-FtpLL~RLRerGynVILagp 175 (1020)
+.++..+..+ .+|+++|+..+.+ ..+.+..++..|..|+++..
T Consensus 46 ~~~i~~l~~~-~vdgiil~~~~~~~~~~~~~~~~~~~iPvV~~d~ 89 (280)
T cd06315 46 AAALNQAIAL-KPDGIVLGGVDAAELQAELELAQKAGIPVVGWHA 89 (280)
T ss_pred HHHHHHHHHc-CCCEEEEcCCCHHHHHHHHHHHHHCCCCEEEecC
Confidence 3455555554 4999999988765 35677888888999988754
No 168
>PRK10014 DNA-binding transcriptional repressor MalI; Provisional
Probab=20.40 E-value=5.3e+02 Score=28.35 Aligned_cols=64 Identities=11% Similarity=0.051 Sum_probs=37.0
Q ss_pred hhHHHhhhcCCceee--ccCCCccchhhHHHHHHH-HHHHhCCCCcEEEEEeCCcchHHHHHHHHhCCCEE
Q 001724 103 ANQEVLSSTGINIAH--VPHGGKNSADRSLLVDLM-YWVSQNPPPAHLFLISGDRDFASVLHRLRMNNYNI 170 (1020)
Q Consensus 103 ~~qe~L~ssGI~Lih--vP~ggKNAADi~LiIDaM-d~a~~nP~pdtFVLISGDsDFtpLL~RLRerGynV 170 (1020)
++++.|...|+.+.. +... ....+ -..+++ .|+..+|.|++|+ ..+|.--..+++.|++.|+.|
T Consensus 203 Gf~~al~~~g~~~~~~~~~~~-~~~~~--~~~~~~~~~l~~~~~~~ai~-~~nd~~A~g~~~~l~~~g~~v 269 (342)
T PRK10014 203 GYCATLLKFGLPFHSEWVLEC-TSSQK--QAAEAITALLRHNPTISAVV-CYNETIAMGAWFGLLRAGRQS 269 (342)
T ss_pred HHHHHHHHcCCCCCcceEecC-CCChH--HHHHHHHHHHcCCCCCCEEE-ECCcHHHHHHHHHHHHcCCCC
Confidence 578888889986432 1111 11111 223333 4555566676544 556665567888899988754
No 169
>PF12683 DUF3798: Protein of unknown function (DUF3798); InterPro: IPR024258 This entry represents functionally uncharacterised proteins that are found in bacteria. They are typically between 247 and 417 amino acids in length. Most of the proteins in this entry have an N-terminal lipoprotein attachment site. These proteins have distant similarity to periplasmic ligand binding families suggesting that this family has a similar role.; PDB: 3QI7_A.
Probab=20.27 E-value=1.6e+02 Score=33.53 Aligned_cols=71 Identities=17% Similarity=0.234 Sum_probs=47.5
Q ss_pred HHHHHHHHHHhCCCCcEEEEEeCCcchHHHHHHHHhCCCEEEEe--cCCchhHHHHhhcceEEeccchhhhhc
Q 001724 130 LLVDLMYWVSQNPPPAHLFLISGDRDFASVLHRLRMNNYNILLA--SRESASNVLCSAASVMWNWDSLLRKEN 200 (1020)
Q Consensus 130 LiIDaMd~a~~nP~pdtFVLISGDsDFtpLL~RLRerGynVILa--gp~kTpeaL~sAcd~Fw~wesLl~g~~ 200 (1020)
=+|+=+.-+.+.|..-.+|+.++...-+..++|+|+..-.|+++ .+...|..+..++|..+..+.+.+|..
T Consensus 49 ttIskI~~lAdDp~mKaIVv~q~vpGt~~af~kIkekRpDIl~ia~~~~EDp~~i~~~aDi~~~~D~~~~G~~ 121 (275)
T PF12683_consen 49 TTISKIVSLADDPDMKAIVVSQAVPGTAEAFRKIKEKRPDILLIAGEPHEDPEVISSAADIVVNPDEISRGYT 121 (275)
T ss_dssp HHHHHHHGGGG-TTEEEEEEE-SS---HHHHHHHHHH-TTSEEEESS--S-HHHHHHHSSEEEE--HHHHHHH
T ss_pred HHHHHHHHhccCCCccEEEEeCCCcchHHHHHHHHhcCCCeEEEcCCCcCCHHHHhhccCeEeccchhhccHH
Confidence 44554444445688999999999999999999999988777753 356789999999999999998887743
No 170
>PRK15395 methyl-galactoside ABC transporter galactose-binding periplasmic protein MglB; Provisional
Probab=20.12 E-value=9.3e+02 Score=26.93 Aligned_cols=74 Identities=15% Similarity=0.163 Sum_probs=42.9
Q ss_pred hhHHHhhhcCCceeec-cCCCccchhhHHHHHHH-HHHHhC--CCCcEEEEEeCCcchHHHHHHHHhCCC-EEEEecCCc
Q 001724 103 ANQEVLSSTGINIAHV-PHGGKNSADRSLLVDLM-YWVSQN--PPPAHLFLISGDRDFASVLHRLRMNNY-NILLASRES 177 (1020)
Q Consensus 103 ~~qe~L~ssGI~Lihv-P~ggKNAADi~LiIDaM-d~a~~n--P~pdtFVLISGDsDFtpLL~RLRerGy-nVILagp~k 177 (1020)
.+++.|...|+.+... ...+....+ -..+++ .|+..+ +.|+ .++.++|.--..+++.|+++|+ .|-+++-..
T Consensus 183 G~~~al~~~g~~~~~~~~~~~~~~~~--~a~~~~~~~l~~~~~~~~~-ai~~~~d~~A~gvl~al~~~Gl~~vpVvg~D~ 259 (330)
T PRK15395 183 YVIKELNDKGIKTEQLQLDTAMWDTA--QAKDKMDAWLSGPNANKIE-VVIANNDAMAMGAVEALKAHNKSSIPVFGVDA 259 (330)
T ss_pred HHHHHHHhcCCCeeeeecccCCcCHH--HHHHHHHHHHhhCcCCCee-EEEECCchHHHHHHHHHHhcCCCCCeEEeeCC
Confidence 4677888889875432 112332222 223444 344433 3344 4446677766789999999999 776555444
Q ss_pred hh
Q 001724 178 AS 179 (1020)
Q Consensus 178 Tp 179 (1020)
.+
T Consensus 260 ~~ 261 (330)
T PRK15395 260 LP 261 (330)
T ss_pred CH
Confidence 43
No 171
>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=20.08 E-value=2.7e+02 Score=29.29 Aligned_cols=32 Identities=16% Similarity=0.222 Sum_probs=25.3
Q ss_pred CCcEEEEEeCCcchHHHHHHHHhCCCEEEEecC
Q 001724 143 PPAHLFLISGDRDFASVLHRLRMNNYNILLASR 175 (1020)
Q Consensus 143 ~pdtFVLISGDsDFtpLL~RLRerGynVILagp 175 (1020)
.+|++++++.+.+ ...+.+|++.|..|+++..
T Consensus 64 ~~dgiii~~~~~~-~~~~~~~~~~~ipvV~~~~ 95 (275)
T cd06295 64 RADGVILIGQHDQ-DPLPERLAETGLPFVVWGR 95 (275)
T ss_pred CCCEEEEeCCCCC-hHHHHHHHhCCCCEEEECC
Confidence 4899999876644 4668889999999998764
No 172
>PRK11543 gutQ D-arabinose 5-phosphate isomerase; Provisional
Probab=20.04 E-value=5.1e+02 Score=28.92 Aligned_cols=95 Identities=19% Similarity=0.222 Sum_probs=57.1
Q ss_pred CceEEEEeecccccchhhHHHhhhcCCceeeccCCCccchhhHHHHHHHHHHHhCCCCcEEEEEeCCc---chHHHHHHH
Q 001724 87 GPVTITAFGDVVQMSRANQEVLSSTGINIAHVPHGGKNSADRSLLVDLMYWVSQNPPPAHLFLISGDR---DFASVLHRL 163 (1020)
Q Consensus 87 GpVtIRAYGDws~~~k~~qe~L~ssGI~LihvP~ggKNAADi~LiIDaMd~a~~nP~pdtFVLISGDs---DFtpLL~RL 163 (1020)
++|-|-+.|.-..........|...|+....+.. ..++... +..-.+-|.+++||.-+ +-..++..+
T Consensus 43 ~~I~i~G~G~S~~~A~~~~~~l~~~g~~~~~~~~-------~~~~~~~---~~~~~~~d~~i~iS~sG~t~~~~~~~~~a 112 (321)
T PRK11543 43 GKVVVSGIGKSGHIGKKIAATLASTGTPAFFVHP-------AEALHGD---LGMIESRDVMLFISYSGGAKELDLIIPRL 112 (321)
T ss_pred CcEEEEecChhHHHHHHHHHHHHcCCCceeecCh-------HHHhhCC---cCccCCCCEEEEEeCCCCcHHHHHHHHHH
Confidence 3444555553322335566778888887666532 0111100 01113357788887664 466888889
Q ss_pred HhCCCEEEEecCCchhHHHHhhcceEEec
Q 001724 164 RMNNYNILLASRESASNVLCSAASVMWNW 192 (1020)
Q Consensus 164 RerGynVILagp~kTpeaL~sAcd~Fw~w 192 (1020)
+++|..||+++....+ .|...||..+..
T Consensus 113 k~~g~~vI~iT~~~~s-~la~~ad~~l~~ 140 (321)
T PRK11543 113 EDKSIALLAMTGKPTS-PLGLAAKAVLDI 140 (321)
T ss_pred HHcCCeEEEEECCCCC-hhHHhCCEEEEc
Confidence 9999999988765443 477778877654
Done!