Query 047464
Match_columns 94
No_of_seqs 113 out of 350
Neff 5.9
Searched_HMMs 46136
Date Fri Mar 29 11:17:44 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/047464.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/047464hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 smart00079 PBPe Eukaryotic hom 99.2 2.1E-11 4.7E-16 80.5 6.2 76 10-93 1-116 (134)
2 KOG1052 Glutamate-gated kainat 99.2 3.1E-11 6.7E-16 99.0 7.5 88 1-94 432-556 (656)
3 PRK09495 glnH glutamine ABC tr 98.7 7.3E-08 1.6E-12 69.5 6.9 75 9-93 121-226 (247)
4 PF00497 SBP_bac_3: Bacterial 98.5 2.4E-07 5.1E-12 63.7 5.3 75 10-93 101-207 (225)
5 PRK11260 cystine transporter s 98.5 4.7E-07 1E-11 66.2 6.8 74 10-93 140-244 (266)
6 TIGR02995 ectoine_ehuB ectoine 98.4 1.2E-06 2.6E-11 64.5 7.0 60 10-76 132-192 (275)
7 PRK11917 bifunctional adhesin/ 98.4 1.2E-06 2.5E-11 64.7 6.7 76 9-93 138-244 (259)
8 PRK10797 glutamate and asparta 98.4 9.6E-07 2.1E-11 66.8 5.9 76 9-93 143-254 (302)
9 PRK15007 putative ABC transpor 98.3 3E-06 6.5E-11 60.4 6.9 57 10-76 117-173 (243)
10 TIGR01096 3A0103s03R lysine-ar 98.2 4.4E-06 9.5E-11 59.6 6.5 57 11-76 123-179 (250)
11 PRK15010 ABC transporter lysin 98.1 9.9E-06 2.1E-10 59.0 6.9 57 12-76 126-182 (260)
12 TIGR01098 3A0109s03R phosphate 98.1 9.9E-06 2.1E-10 58.2 6.5 79 8-94 130-253 (254)
13 TIGR03870 ABC_MoxJ methanol ox 98.1 1.1E-05 2.3E-10 58.8 6.6 64 10-76 94-169 (246)
14 COG0834 HisJ ABC-type amino ac 98.1 6.3E-06 1.4E-10 59.0 5.2 56 11-76 138-195 (275)
15 TIGR03871 ABC_peri_MoxJ_2 quin 98.1 1.6E-05 3.6E-10 56.3 7.1 64 9-76 92-160 (232)
16 PRK10859 membrane-bound lytic 98.1 1.2E-05 2.7E-10 64.5 6.6 76 9-93 139-249 (482)
17 smart00062 PBPb Bacterial peri 98.0 3.7E-05 8.1E-10 51.0 6.8 59 8-76 95-153 (219)
18 PRK15437 histidine ABC transpo 98.0 3.5E-05 7.6E-10 56.1 6.9 57 12-76 126-182 (259)
19 PF09084 NMT1: NMT1/THI5 like; 97.9 2E-05 4.3E-10 55.4 5.2 64 8-79 82-149 (216)
20 PRK09959 hybrid sensory histid 97.9 2.3E-05 4.9E-10 67.8 5.7 76 8-93 153-261 (1197)
21 cd00134 PBPb Bacterial peripla 97.7 0.00021 4.4E-09 47.7 7.1 59 8-76 94-152 (218)
22 TIGR03427 ABC_peri_uca ABC tra 97.7 4.7E-05 1E-09 59.0 4.0 58 11-76 98-159 (328)
23 PRK11480 tauA taurine transpor 97.6 0.0001 2.2E-09 55.9 5.1 60 9-76 112-175 (320)
24 PRK09959 hybrid sensory histid 97.6 0.00012 2.7E-09 63.3 5.8 71 14-93 401-504 (1197)
25 TIGR01729 taurine_ABC_bnd taur 97.6 0.00016 3.5E-09 53.7 5.5 60 9-76 90-153 (300)
26 KOG1053 Glutamate-gated NMDA-t 97.3 5.1E-05 1.1E-09 66.2 -0.1 70 21-94 688-790 (1258)
27 KOG4440 NMDA selective glutama 97.3 0.0003 6.5E-09 59.9 4.2 91 2-94 666-789 (993)
28 TIGR01728 SsuA_fam ABC transpo 97.2 0.00096 2.1E-08 48.0 5.7 60 8-76 90-154 (288)
29 PRK11553 alkanesulfonate trans 97.2 0.00075 1.6E-08 50.5 5.0 61 8-76 118-182 (314)
30 KOG1054 Glutamate-gated AMPA-t 97.1 0.0003 6.4E-09 59.6 2.7 88 1-94 646-775 (897)
31 TIGR02285 conserved hypothetic 97.0 0.00087 1.9E-08 49.1 4.1 49 21-76 136-189 (268)
32 COG0715 TauA ABC-type nitrate/ 97.0 0.0014 3E-08 49.1 5.0 61 7-76 124-190 (335)
33 TIGR00787 dctP tripartite ATP- 96.9 0.0015 3.2E-08 48.2 4.5 55 9-76 126-180 (257)
34 PF13379 NMT1_2: NMT1-like fam 96.9 0.0017 3.6E-08 47.3 4.6 60 9-76 104-176 (252)
35 TIGR03431 PhnD phosphonate ABC 96.6 0.0064 1.4E-07 44.9 5.6 62 8-76 124-194 (288)
36 PRK00489 hisG ATP phosphoribos 96.5 0.0051 1.1E-07 46.5 4.6 56 9-76 103-158 (287)
37 TIGR02122 TRAP_TAXI TRAP trans 96.3 0.0082 1.8E-07 44.4 4.9 61 8-77 130-197 (320)
38 COG2358 Imp TRAP-type uncharac 96.0 0.017 3.7E-07 45.3 5.6 76 6-88 124-204 (321)
39 TIGR00363 lipoprotein, YaeC fa 95.6 0.037 8.1E-07 41.7 5.7 62 8-76 105-188 (258)
40 PF03480 SBP_bac_7: Bacterial 95.3 0.033 7.2E-07 41.4 4.6 55 9-76 126-180 (286)
41 PRK11063 metQ DL-methionine tr 93.9 0.15 3.2E-06 38.6 5.2 61 9-76 119-201 (271)
42 PF12974 Phosphonate-bd: ABC t 93.7 0.04 8.6E-07 39.7 1.8 61 8-76 94-163 (243)
43 PF03401 TctC: Tripartite tric 93.4 0.41 8.9E-06 35.9 6.9 62 8-76 87-158 (274)
44 PF12727 PBP_like: PBP superfa 92.9 0.43 9.4E-06 34.3 6.0 65 10-76 82-150 (193)
45 COG1910 Periplasmic molybdate- 90.9 0.96 2.1E-05 34.1 6.1 69 5-76 82-156 (223)
46 PF03846 SulA: Cell division i 90.6 0.32 6.8E-06 33.4 3.1 46 30-76 71-116 (119)
47 PF14503 YhfZ_C: YhfZ C-termin 90.1 0.3 6.6E-06 36.8 2.9 51 20-76 113-163 (232)
48 COG4521 TauA ABC-type taurine 86.9 1.3 2.9E-05 34.6 4.5 62 7-76 118-183 (334)
49 PRK11899 prephenate dehydratas 85.8 2.2 4.7E-05 32.7 5.2 48 21-76 4-53 (279)
50 PRK09861 cytoplasmic membrane 85.8 1.9 4.2E-05 32.6 4.9 63 8-76 119-202 (272)
51 COG1638 DctP TRAP-type C4-dica 84.7 1.9 4.1E-05 33.7 4.6 54 10-76 158-211 (332)
52 PF00800 PDT: Prephenate dehyd 82.7 1.2 2.7E-05 31.5 2.6 43 28-76 7-49 (181)
53 PRK11063 metQ DL-methionine tr 79.1 3 6.6E-05 31.5 3.8 48 22-76 33-86 (271)
54 TIGR00363 lipoprotein, YaeC fa 78.7 3 6.5E-05 31.4 3.6 48 22-76 20-73 (258)
55 PLN02317 arogenate dehydratase 78.0 6 0.00013 31.9 5.3 48 21-76 94-143 (382)
56 TIGR00070 hisG ATP phosphoribo 77.7 1.8 3.8E-05 31.4 2.0 65 10-86 100-164 (182)
57 COG3221 PhnD ABC-type phosphat 76.6 6.4 0.00014 30.5 4.9 64 8-76 133-203 (299)
58 TIGR01729 taurine_ABC_bnd taur 75.4 3 6.6E-05 30.8 2.8 47 23-76 2-54 (300)
59 smart00851 MGS MGS-like domain 75.4 13 0.00028 23.0 5.4 54 15-77 7-62 (90)
60 TIGR00623 sula cell division i 74.2 3.6 7.9E-05 29.7 2.9 46 31-77 72-117 (168)
61 PRK10622 pheA bifunctional cho 73.9 8.8 0.00019 30.7 5.2 50 21-76 103-156 (386)
62 PRK10595 SOS cell division inh 73.3 3.6 7.7E-05 29.5 2.6 47 31-78 68-114 (164)
63 PF03180 Lipoprotein_9: NLPA l 72.5 4.7 0.0001 30.2 3.2 46 23-76 2-53 (237)
64 PF13379 NMT1_2: NMT1-like fam 71.4 6.7 0.00015 28.3 3.8 47 22-76 8-62 (252)
65 PF01634 HisG: ATP phosphoribo 70.1 2.1 4.5E-05 30.5 0.8 64 11-85 58-121 (163)
66 TIGR00640 acid_CoA_mut_C methy 69.7 8.3 0.00018 26.2 3.7 40 30-76 20-59 (132)
67 COG2130 Putative NADP-dependen 69.3 11 0.00023 30.1 4.7 54 13-76 169-225 (340)
68 PRK11898 prephenate dehydratas 69.0 9.1 0.0002 29.2 4.2 48 23-76 3-53 (283)
69 PRK09861 cytoplasmic membrane 68.2 6.1 0.00013 29.9 3.1 48 22-76 34-87 (272)
70 PF12974 Phosphonate-bd: ABC t 67.3 5.8 0.00012 28.4 2.7 38 32-76 19-56 (243)
71 COG4663 FcbT1 TRAP-type mannit 66.0 2.5 5.4E-05 33.8 0.6 53 8-75 167-219 (363)
72 cd01422 MGS Methylglyoxal synt 65.9 11 0.00024 24.9 3.7 41 32-76 36-76 (115)
73 PF12916 DUF3834: Protein of u 65.5 5.5 0.00012 29.6 2.3 56 22-84 69-130 (201)
74 COG1732 OpuBC Periplasmic glyc 64.5 16 0.00035 28.7 4.8 59 10-76 151-217 (300)
75 PRK08410 2-hydroxyacid dehydro 63.6 8.2 0.00018 29.6 3.0 28 58-85 238-270 (311)
76 PRK07377 hypothetical protein; 62.4 11 0.00023 27.8 3.2 25 46-76 111-135 (184)
77 PRK03094 hypothetical protein; 62.2 12 0.00027 23.9 3.2 39 22-76 2-41 (80)
78 PF03466 LysR_substrate: LysR 61.1 10 0.00023 24.8 2.8 19 58-76 43-61 (209)
79 COG0077 PheA Prephenate dehydr 61.0 14 0.00031 28.6 3.9 46 23-76 4-52 (279)
80 COG1756 Mra1 Uncharacterized c 60.8 17 0.00036 27.5 4.1 51 27-82 134-184 (223)
81 COG2185 Sbm Methylmalonyl-CoA 59.3 21 0.00046 25.1 4.3 40 30-76 30-69 (143)
82 COG3221 PhnD ABC-type phosphat 58.8 17 0.00036 28.2 4.0 38 32-76 57-94 (299)
83 PF00060 Lig_chan: Ligand-gate 58.0 2.5 5.4E-05 27.7 -0.6 21 1-21 95-115 (148)
84 COG1832 Predicted CoA-binding 57.5 19 0.00041 25.4 3.7 64 11-84 6-86 (140)
85 PF02142 MGS: MGS-like domain 57.4 24 0.00051 22.1 3.9 54 16-76 8-66 (95)
86 COG2107 Predicted periplasmic 55.7 16 0.00035 28.3 3.4 53 14-76 90-142 (272)
87 TIGR01728 SsuA_fam ABC transpo 55.3 14 0.0003 26.2 2.9 24 47-76 33-56 (288)
88 PRK06034 hypothetical protein; 54.6 23 0.00049 27.5 4.1 50 22-78 95-147 (279)
89 TIGR02706 P_butyryltrans phosp 54.4 16 0.00034 28.0 3.2 46 30-76 48-93 (294)
90 cd08486 PBP2_CbnR The C-termin 53.9 18 0.00039 23.9 3.1 19 58-76 38-56 (198)
91 COG3181 Uncharacterized protei 52.2 76 0.0016 25.1 6.7 63 7-76 130-202 (319)
92 COG0111 SerA Phosphoglycerate 51.7 13 0.00028 29.0 2.3 24 58-81 239-263 (324)
93 cd00532 MGS-like MGS-like doma 51.4 55 0.0012 21.1 5.0 55 15-76 19-74 (112)
94 PRK06487 glycerate dehydrogena 50.5 19 0.0004 27.7 3.1 29 58-86 239-273 (317)
95 cd08463 PBP2_DntR_like_4 The C 49.5 26 0.00056 23.4 3.3 19 58-76 38-56 (203)
96 PF03698 UPF0180: Uncharacteri 49.1 24 0.00051 22.5 2.9 39 22-76 2-41 (80)
97 cd01424 MGS_CPS_II Methylglyox 48.7 56 0.0012 20.7 4.7 55 15-77 20-74 (110)
98 cd08462 PBP2_NodD The C-termin 47.9 50 0.0011 21.6 4.5 17 60-76 38-54 (200)
99 PRK12683 transcriptional regul 47.7 9.1 0.0002 28.5 0.9 19 58-76 130-148 (309)
100 cd08421 PBP2_LTTR_like_1 The C 47.7 29 0.00063 22.3 3.3 19 58-76 37-55 (198)
101 TIGR03414 ABC_choline_bnd chol 46.9 60 0.0013 24.5 5.3 60 10-76 105-178 (290)
102 TIGR03339 phn_lysR aminoethylp 46.8 36 0.00077 24.1 3.9 49 22-76 89-139 (279)
103 cd08440 PBP2_LTTR_like_4 TThe 46.6 29 0.00063 22.0 3.1 19 58-76 37-55 (197)
104 PRK06932 glycerate dehydrogena 46.4 20 0.00043 27.6 2.6 28 58-85 239-272 (314)
105 PF04069 OpuAC: Substrate bind 45.3 17 0.00036 26.5 2.0 36 33-76 21-56 (257)
106 PLN02928 oxidoreductase family 43.9 23 0.0005 27.7 2.7 28 58-85 268-301 (347)
107 cd08438 PBP2_CidR The C-termin 43.6 34 0.00074 21.8 3.1 19 58-76 37-55 (197)
108 cd08460 PBP2_DntR_like_1 The C 43.6 57 0.0012 21.2 4.3 16 61-76 39-54 (200)
109 PLN02245 ATP phosphoribosyl tr 43.3 10 0.00022 30.9 0.7 57 10-76 178-242 (403)
110 PF01071 GARS_A: Phosphoribosy 43.0 18 0.00039 26.5 1.8 37 30-73 4-40 (194)
111 PRK11480 tauA taurine transpor 42.7 34 0.00074 25.7 3.4 49 21-76 24-78 (320)
112 COG4623 Predicted soluble lyti 42.3 36 0.00079 28.2 3.6 61 8-76 10-87 (473)
113 cd08420 PBP2_CysL_like C-termi 42.2 37 0.00079 21.6 3.1 19 58-76 37-55 (201)
114 cd08412 PBP2_PAO1_like The C-t 42.0 39 0.00086 21.6 3.2 19 58-76 37-55 (198)
115 cd05466 PBP2_LTTR_substrate Th 41.7 43 0.00092 20.8 3.3 18 59-76 38-55 (197)
116 PRK09189 uroporphyrinogen-III 41.4 58 0.0013 23.4 4.3 57 20-76 117-176 (240)
117 cd08459 PBP2_DntR_NahR_LinR_li 40.7 37 0.00081 22.0 3.0 18 59-76 38-55 (201)
118 cd08415 PBP2_LysR_opines_like 40.1 44 0.00095 21.3 3.2 19 58-76 37-55 (196)
119 PRK15409 bifunctional glyoxyla 39.9 31 0.00066 26.7 2.8 23 58-80 242-265 (323)
120 PRK07574 formate dehydrogenase 39.9 27 0.00058 28.0 2.5 28 58-85 290-323 (385)
121 cd08411 PBP2_OxyR The C-termin 39.9 43 0.00093 21.6 3.2 19 58-76 38-56 (200)
122 PRK00072 hemC porphobilinogen 39.8 33 0.00071 26.8 2.9 17 60-76 63-79 (295)
123 PF02826 2-Hacid_dh_C: D-isome 39.5 30 0.00065 24.0 2.5 24 58-81 133-157 (178)
124 cd01423 MGS_CPS_I_III Methylgl 39.1 84 0.0018 20.1 4.5 59 15-77 20-78 (116)
125 cd08447 PBP2_LTTR_aromatics_li 38.9 48 0.001 21.3 3.3 19 58-76 37-55 (198)
126 COG0120 RpiA Ribose 5-phosphat 38.8 47 0.001 25.1 3.6 54 17-76 17-83 (227)
127 TIGR03061 pip_yhgE_Nterm YhgE/ 38.7 1E+02 0.0022 21.0 5.0 23 58-81 84-106 (164)
128 TIGR03730 tungstate_WtpA tungs 38.1 23 0.0005 26.9 1.8 26 45-76 176-201 (273)
129 cd08467 PBP2_SyrM The C-termin 38.0 39 0.00085 22.1 2.8 18 59-76 38-55 (200)
130 PRK04148 hypothetical protein; 37.4 51 0.0011 22.7 3.3 44 23-76 22-65 (134)
131 cd08425 PBP2_CynR The C-termin 37.1 53 0.0011 21.1 3.3 19 58-76 38-56 (197)
132 cd08445 PBP2_BenM_CatM_CatR Th 36.5 48 0.001 21.7 3.0 19 58-76 38-56 (203)
133 PRK11242 DNA-binding transcrip 36.4 48 0.001 23.9 3.2 19 58-76 128-146 (296)
134 PF00107 ADH_zinc_N: Zinc-bind 35.8 56 0.0012 20.6 3.2 50 22-78 16-66 (130)
135 cd08426 PBP2_LTTR_like_5 The C 35.6 50 0.0011 21.2 3.0 19 58-76 37-55 (199)
136 cd08466 PBP2_LeuO The C-termin 35.6 55 0.0012 21.1 3.2 19 58-76 37-55 (200)
137 cd08413 PBP2_CysB_like The C-t 35.3 51 0.0011 21.5 3.0 18 59-76 38-55 (198)
138 PRK07742 phosphate butyryltran 34.6 43 0.00093 25.6 2.8 45 32-77 52-97 (299)
139 cd08441 PBP2_MetR The C-termin 34.2 59 0.0013 21.0 3.1 19 58-76 37-55 (198)
140 cd08448 PBP2_LTTR_aromatics_li 33.9 63 0.0014 20.5 3.2 19 58-76 37-55 (197)
141 COG0715 TauA ABC-type nitrate/ 33.8 27 0.00059 25.9 1.6 35 35-76 54-88 (335)
142 PRK15469 ghrA bifunctional gly 33.2 42 0.00091 25.9 2.6 23 58-80 232-255 (312)
143 cd08442 PBP2_YofA_SoxR_like Th 33.1 66 0.0014 20.4 3.2 19 58-76 37-55 (193)
144 TIGR03427 ABC_peri_uca ABC tra 32.8 25 0.00055 27.2 1.3 34 35-76 29-62 (328)
145 PRK11119 proX glycine betaine 32.7 88 0.0019 24.3 4.3 60 10-76 128-208 (331)
146 TIGR01327 PGDH D-3-phosphoglyc 32.6 45 0.00097 27.5 2.8 28 58-85 235-267 (525)
147 PLN03139 formate dehydrogenase 32.6 39 0.00085 27.1 2.4 29 58-86 297-331 (386)
148 PF02621 VitK2_biosynth: Menaq 32.6 1.1E+02 0.0024 22.6 4.7 55 13-76 86-140 (251)
149 cd08452 PBP2_AlsR The C-termin 32.5 65 0.0014 21.0 3.1 19 58-76 37-55 (197)
150 PF01379 Porphobil_deam: Porph 32.0 40 0.00086 25.1 2.2 17 60-76 60-76 (215)
151 PRK13978 ribose-5-phosphate is 31.2 1.1E+02 0.0024 22.9 4.5 22 16-37 17-38 (228)
152 PRK13243 glyoxylate reductase; 31.2 46 0.001 25.7 2.5 23 58-80 246-269 (333)
153 cd08417 PBP2_Nitroaromatics_li 30.7 71 0.0015 20.5 3.1 19 58-76 37-55 (200)
154 PRK00702 ribose-5-phosphate is 30.2 91 0.002 23.0 3.9 46 16-68 16-64 (220)
155 PRK05752 uroporphyrinogen-III 30.1 1.3E+02 0.0027 22.0 4.6 57 20-76 129-188 (255)
156 cd08458 PBP2_NocR The C-termin 30.1 71 0.0015 20.7 3.0 19 58-76 37-55 (196)
157 PF02602 HEM4: Uroporphyrinoge 30.1 19 0.0004 25.4 0.2 51 20-76 116-174 (231)
158 cd08461 PBP2_DntR_like_3 The C 29.8 60 0.0013 20.9 2.6 18 59-76 38-55 (198)
159 PF13531 SBP_bac_11: Bacterial 29.6 54 0.0012 22.9 2.5 60 10-76 92-164 (230)
160 cd08419 PBP2_CbbR_RubisCO_like 29.4 82 0.0018 20.0 3.2 19 58-76 36-54 (197)
161 TIGR01309 L30P_arch 50S riboso 29.3 54 0.0012 23.1 2.4 15 58-72 90-104 (152)
162 PF04796 RepA_C: Plasmid encod 29.1 80 0.0017 22.4 3.3 35 29-70 29-65 (161)
163 PF01795 Methyltransf_5: MraW 28.8 79 0.0017 24.8 3.5 54 21-76 45-99 (310)
164 cd08416 PBP2_MdcR The C-termin 28.7 81 0.0018 20.2 3.1 18 59-76 38-55 (199)
165 COG0725 ModA ABC-type molybdat 28.4 1.3E+02 0.0029 22.5 4.6 59 11-76 124-192 (258)
166 cd00494 HMBS Hydroxymethylbila 28.4 65 0.0014 25.1 2.9 16 61-76 60-75 (292)
167 PLN02384 ribose-5-phosphate is 28.3 1.3E+02 0.0028 23.2 4.5 18 20-37 49-66 (264)
168 cd08446 PBP2_Chlorocatechol Th 28.0 88 0.0019 20.1 3.2 18 59-76 39-56 (198)
169 PRK09906 DNA-binding transcrip 28.0 81 0.0017 22.8 3.2 18 59-76 128-145 (296)
170 COG0181 HemC Porphobilinogen d 27.9 49 0.0011 26.1 2.2 17 60-76 62-78 (307)
171 cd08433 PBP2_Nac The C-teminal 27.6 81 0.0018 20.2 2.9 19 58-76 37-55 (198)
172 PRK05234 mgsA methylglyoxal sy 27.6 1E+02 0.0023 21.1 3.6 41 32-76 41-81 (142)
173 cd08456 PBP2_LysR The C-termin 27.4 89 0.0019 19.9 3.1 18 59-76 38-55 (196)
174 PRK04171 ribosome biogenesis p 26.9 75 0.0016 23.9 2.9 35 46-82 148-182 (222)
175 cd08450 PBP2_HcaR The C-termin 26.9 94 0.002 19.8 3.2 18 59-76 38-55 (196)
176 COG0560 SerB Phosphoserine pho 26.5 1E+02 0.0022 22.4 3.5 32 13-44 85-118 (212)
177 PRK05659 sulfur carrier protei 26.5 81 0.0018 18.1 2.5 26 20-46 6-31 (66)
178 PRK06049 rpl30p 50S ribosomal 26.4 65 0.0014 22.8 2.4 15 57-71 91-105 (154)
179 COG0151 PurD Phosphoribosylami 26.3 87 0.0019 25.9 3.4 40 30-76 105-144 (428)
180 cd08185 Fe-ADH1 Iron-containin 26.2 96 0.0021 24.1 3.6 58 18-76 22-89 (380)
181 COG1110 Reverse gyrase [DNA re 26.2 75 0.0016 29.4 3.2 35 32-76 354-389 (1187)
182 COG5404 SulA SOS-response cell 26.2 48 0.001 23.8 1.7 47 29-76 72-118 (169)
183 PRK11013 DNA-binding transcrip 26.2 81 0.0017 23.2 3.0 19 58-76 131-149 (309)
184 cd08414 PBP2_LTTR_aromatics_li 26.0 95 0.0021 19.7 3.0 18 59-76 38-55 (197)
185 PRK09860 putative alcohol dehy 25.9 1E+02 0.0023 24.2 3.8 59 17-76 26-94 (383)
186 PRK08190 bifunctional enoyl-Co 25.9 81 0.0018 25.6 3.2 42 34-76 215-256 (466)
187 TIGR00212 hemC porphobilinogen 25.7 78 0.0017 24.7 2.9 16 61-76 60-75 (292)
188 PRK10859 membrane-bound lytic 25.6 1.2E+02 0.0025 24.6 4.0 58 12-76 34-107 (482)
189 COG0040 HisG ATP phosphoribosy 25.6 65 0.0014 25.2 2.5 64 11-85 107-170 (290)
190 PLN02691 porphobilinogen deami 25.4 75 0.0016 25.5 2.8 16 61-76 107-122 (351)
191 smart00094 TR_FER Transferrin. 25.4 66 0.0014 25.3 2.5 19 58-76 36-54 (332)
192 COG2104 ThiS Sulfur transfer p 25.3 84 0.0018 19.1 2.5 26 20-46 8-33 (68)
193 PF13407 Peripla_BP_4: Peripla 24.6 1.5E+02 0.0033 20.6 4.1 37 33-76 198-235 (257)
194 PRK13583 hisG ATP phosphoribos 24.5 33 0.00072 25.8 0.7 57 10-76 110-177 (228)
195 COG1732 OpuBC Periplasmic glyc 24.5 1.1E+02 0.0023 24.2 3.5 36 34-76 54-89 (300)
196 PRK07696 sulfur carrier protei 24.1 94 0.002 18.4 2.5 27 20-47 6-33 (67)
197 cd02072 Glm_B12_BD B12 binding 23.9 1.6E+02 0.0035 20.1 3.9 19 58-76 38-56 (128)
198 PF02571 CbiJ: Precorrin-6x re 23.5 1.4E+02 0.003 22.4 3.8 68 15-91 17-84 (249)
199 PRK15408 autoinducer 2-binding 23.5 1.1E+02 0.0024 23.3 3.5 37 33-76 225-261 (336)
200 TIGR03261 phnS2 putative 2-ami 23.5 1.4E+02 0.0031 22.3 4.0 19 58-76 202-220 (334)
201 PF04422 FrhB_FdhB_N: Coenzyme 23.2 84 0.0018 19.4 2.3 16 63-78 28-43 (82)
202 PLN02344 chorismate mutase 22.8 20 0.00042 28.0 -0.9 36 21-63 74-109 (284)
203 COG1464 NlpA ABC-type metal io 22.7 53 0.0011 25.4 1.5 48 21-76 30-84 (268)
204 PRK10837 putative DNA-binding 22.6 1.1E+02 0.0024 21.9 3.1 19 58-76 126-144 (290)
205 PF00885 DMRL_synthase: 6,7-di 22.0 95 0.0021 21.4 2.5 62 21-83 3-77 (144)
206 COG0745 OmpR Response regulato 21.7 1.4E+02 0.0031 21.8 3.6 41 31-82 15-57 (229)
207 cd08469 PBP2_PnbR The C-termin 21.6 1.3E+02 0.0027 19.9 3.1 19 58-76 37-55 (221)
208 PF03607 DCX: Doublecortin; I 21.2 45 0.00098 19.5 0.7 21 10-30 38-58 (60)
209 smart00537 DCX Domain in the D 21.2 64 0.0014 20.3 1.4 23 9-31 61-83 (89)
210 PRK12679 cbl transcriptional r 21.0 1.2E+02 0.0026 22.5 3.1 19 58-76 130-148 (316)
211 cd08465 PBP2_ToxR The C-termin 20.5 1.2E+02 0.0026 19.8 2.8 19 58-76 37-55 (200)
212 PRK11151 DNA-binding transcrip 20.5 1.4E+02 0.003 21.7 3.3 19 58-76 128-146 (305)
213 KOG1198 Zinc-binding oxidoredu 20.5 3.3E+02 0.0071 21.4 5.5 50 17-76 178-231 (347)
214 cd06273 PBP1_GntR_like_1 This 20.5 98 0.0021 21.6 2.4 38 35-76 24-61 (268)
215 KOG3127 Deoxycytidylate deamin 20.5 2.1E+02 0.0045 21.8 4.2 35 49-83 56-112 (230)
216 COG4034 Uncharacterized protei 20.2 1.2E+02 0.0027 24.0 3.0 47 47-93 107-166 (328)
217 PF01693 Cauli_VI: Caulimoviru 20.1 1.7E+02 0.0036 15.9 2.8 36 21-64 8-43 (44)
218 PRK11074 putative DNA-binding 20.1 1.2E+02 0.0025 22.2 2.8 19 58-76 129-147 (300)
No 1
>smart00079 PBPe Eukaryotic homologues of bacterial periplasmic substrate binding proteins. Prokaryotic homologues are represented by a separate alignment: PBPb
Probab=99.24 E-value=2.1e-11 Score=80.50 Aligned_cols=76 Identities=21% Similarity=0.302 Sum_probs=64.6
Q ss_pred CCCChhHHHhC-CCeeeecCCccHHHHHHHhhCCCC----------CCcccccCCCCCCChhhHHHHHhcCCeeEEEE--
Q 047464 10 STVDIKTLQRR-NAAVGCNGNSFIIRYLINVLNFKP----------GSNKKINAKNGYNSITSYPMAFESGDIAAAFL-- 76 (94)
Q Consensus 10 ~i~~i~dL~~~-~~~VG~~~gSf~~~~L~~~~~~~~----------~~i~~~~~~~~~~s~~~~~~aL~~g~i~A~v~-- 76 (94)
+|++++||+.+ +++||++.||+...|+.+ ..... .+++.|+ +.++++++|.+|+ ||++.
T Consensus 1 ~i~~~~dl~~~~~~~vgv~~gs~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~------~~~~~~~~l~~g~-da~v~d~ 72 (134)
T smart00079 1 PITSVEDLAKQTKIEYGTIRGSSTLAFFKR-SGNPEYSRMWNYMSASPSVFVK------SYAEGVQRVRVSN-YAFLMES 72 (134)
T ss_pred CCCChHHHhhCCCccceEecCchHHHHHHh-CCChHHHHHHHHHHhCCCCCCC------CHHHHHHHHHcCC-CEEEeeh
Confidence 37899999943 379999999999999987 43320 2566777 9999999999999 99998
Q ss_pred ---------------------------eecCCCCChHHhHHHhh
Q 047464 77 ---------------------------VFPRGSPLALDISEAIL 93 (94)
Q Consensus 77 ---------------------------afpkGSpL~~dvn~aiL 93 (94)
|||||++|++.||++|.
T Consensus 73 ~~~~~~~~~~~~~~~~~~~~~~~~~~ia~~k~~~l~~~vn~~l~ 116 (134)
T smart00079 73 TYLDYELSQNCDLMTVGENFGRKGYGIAFPKGSPLRDDLSRAIL 116 (134)
T ss_pred HhHHHHHhCCCCeEEcCcccCCCceEEEecCCCHHHHHHHHHHH
Confidence 99999999999999986
No 2
>KOG1052 consensus Glutamate-gated kainate-type ion channel receptor subunit GluR5 and related subunits [Inorganic ion transport and metabolism; Amino acid transport and metabolism; Signal transduction mechanisms]
Probab=99.22 E-value=3.1e-11 Score=98.95 Aligned_cols=88 Identities=34% Similarity=0.392 Sum_probs=78.1
Q ss_pred CccccccCCCCCChhHHH-hCCCeeeecCCccHHHHHHHh---hCCCCC-CcccccCCCCCCChhhHHHHHhcC---Cee
Q 047464 1 MLTVSRLQPSTVDIKTLQ-RRNAAVGCNGNSFIIRYLINV---LNFKPG-SNKKINAKNGYNSITSYPMAFESG---DIA 72 (94)
Q Consensus 1 mLTV~~l~~~i~~i~dL~-~~~~~VG~~~gSf~~~~L~~~---~~~~~~-~i~~~~~~~~~~s~~~~~~aL~~g---~i~ 72 (94)
+||+++++++|++++||. .++..+|++.|++...|+.+. ..+..+ +.+.+. +++++.+++++| +++
T Consensus 432 ~Lt~~~~~~~i~~~~dL~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~------~~~e~~~~v~~~~~~~~~ 505 (656)
T KOG1052|consen 432 FLTVPRLRSPIDSLDDLADQSNIPYGTQRGSFTRIYLEESEDMWAFKVSQRSVPLA------SPEEGVERVRKGPSGGYA 505 (656)
T ss_pred HhcccccCCcccCHHHHHHhcCCeEEEEecchHHHHHHHHHHHHhhhccCCCccCC------CHHHHHHHHHcCCCCceE
Confidence 699999999999999999 489999999999999999885 445544 555666 999999999999 588
Q ss_pred EEEE-----------------------------eecCCCCChHHhHHHhhC
Q 047464 73 AAFL-----------------------------VFPRGSPLALDISEAILK 94 (94)
Q Consensus 73 A~v~-----------------------------afpkGSpL~~dvn~aiL~ 94 (94)
+++. ||||||||+.++|++||+
T Consensus 506 ~~~~~~~~~~~~~~~~~c~~~~v~~~~~~~~~~~~~~~Spl~~~is~~Il~ 556 (656)
T KOG1052|consen 506 FASDELYLAYLFLRDEICDLTEVGEPFLYKGYGAFPKGSPLRSLISRAILK 556 (656)
T ss_pred EEeccHHHHHHHhhcCCCceEEeCCcccCCCcceecCCCccHHHHHHHHHh
Confidence 8888 999999999999999984
No 3
>PRK09495 glnH glutamine ABC transporter periplasmic protein; Reviewed
Probab=98.68 E-value=7.3e-08 Score=69.52 Aligned_cols=75 Identities=19% Similarity=0.290 Sum_probs=65.0
Q ss_pred CCCCChhHHHhCCCeeeecCCccHHHHHHHhhCCCCCCcccccCCCCCCChhhHHHHHhcCCeeEEEE------------
Q 047464 9 PSTVDIKTLQRRNAAVGCNGNSFIIRYLINVLNFKPGSNKKINAKNGYNSITSYPMAFESGDIAAAFL------------ 76 (94)
Q Consensus 9 ~~i~~i~dL~~~~~~VG~~~gSf~~~~L~~~~~~~~~~i~~~~~~~~~~s~~~~~~aL~~g~i~A~v~------------ 76 (94)
+.+.+++||+ |++||+..||....|+.. . .+..+++.++ +.++..++|.+|+|||++.
T Consensus 121 ~~~~~~~dL~--g~~I~v~~g~~~~~~l~~-~-~~~~~i~~~~------~~~~~~~~L~~grvDa~i~~~~~~~~~~~~~ 190 (247)
T PRK09495 121 NDIKSVKDLD--GKVVAVKSGTGSVDYAKA-N-IKTKDLRQFP------NIDNAYLELGTGRADAVLHDTPNILYFIKTA 190 (247)
T ss_pred CCCCChHHhC--CCEEEEecCchHHHHHHh-c-CCCCceEEcC------CHHHHHHHHHcCceeEEEeChHHHHHHHHhC
Confidence 3589999998 799999999999999977 3 3334677788 9999999999999999987
Q ss_pred -------------------eecCCCCChHHhHHHhh
Q 047464 77 -------------------VFPRGSPLALDISEAIL 93 (94)
Q Consensus 77 -------------------afpkGSpL~~dvn~aiL 93 (94)
||+++++|++.+|++|.
T Consensus 191 ~~~~~~~~~~~~~~~~~~~a~~~~~~l~~~~n~al~ 226 (247)
T PRK09495 191 GNGQFKAVGDSLEAQQYGIAFPKGSELREKVNGALK 226 (247)
T ss_pred CCCceEEecCcccccceEEEEcCcHHHHHHHHHHHH
Confidence 89999999999999885
No 4
>PF00497 SBP_bac_3: Bacterial extracellular solute-binding proteins, family 3; InterPro: IPR001638 Bacterial high affinity transport systems are involved in active transport of solutes across the cytoplasmic membrane. The protein components of these traffic systems include one or two transmembrane protein components, one or two membrane-associated ATP-binding proteins (ABC transporters; see IPR003439 from INTERPRO) and a high affinity periplasmic solute-binding protein. The latter are thought to bind the substrate in the vicinity of the inner membrane, and to transfer it to a complex of inner membrane proteins for concentration into the cytoplasm. In Gram-positive bacteria which are surrounded by a single membrane and have therefore no periplasmic region, the equivalent proteins are bound to the membrane via an N-terminal lipid anchor. These homologue proteins do not play an integral role in the transport process per se, but probably serve as receptors to trigger or initiate translocation of the solute throught the membrane by binding to external sites of the integral membrane proteins of the efflux system. In addition, at least some solute-binding proteins function in the initiation of sensory transduction pathways. On the basis of sequence similarities, the vast majority of these solute-binding proteins can be grouped [] into eight families or clusters, which generally correlate with the nature of the solute bound. Family 3 groups together specific amino acids and opine-binding periplasmic proteins and a periplasmic homologue with catalytic activity.; GO: 0005215 transporter activity, 0006810 transport, 0030288 outer membrane-bounded periplasmic space; PDB: 3N26_A 3QAX_A 3I6V_A 2VHA_B 2IA4_B 2Q89_A 2Q88_A 2YJP_C 1II5_A 1IIW_A ....
Probab=98.50 E-value=2.4e-07 Score=63.66 Aligned_cols=75 Identities=19% Similarity=0.140 Sum_probs=61.1
Q ss_pred CCCChhHHHhCCCeeeecCCccHHHHHHHhhCCCCCCcccccCCCCCCChhhHHHHHhcCCeeEEEE-------------
Q 047464 10 STVDIKTLQRRNAAVGCNGNSFIIRYLINVLNFKPGSNKKINAKNGYNSITSYPMAFESGDIAAAFL------------- 76 (94)
Q Consensus 10 ~i~~i~dL~~~~~~VG~~~gSf~~~~L~~~~~~~~~~i~~~~~~~~~~s~~~~~~aL~~g~i~A~v~------------- 76 (94)
++++++||. |++||+..|+...+++.+.. -...++..++ +.++++++|.+|++||++.
T Consensus 101 ~~~~~~dl~--~~~i~~~~g~~~~~~l~~~~-~~~~~~~~~~------~~~~~~~~l~~g~~d~~i~~~~~~~~~~~~~~ 171 (225)
T PF00497_consen 101 TIKSLDDLK--GKRIGVVRGSSYADYLKQQY-PSNINIVEVD------SPEEALEALLSGRIDAFIVDESTAEYLLKRHP 171 (225)
T ss_dssp SHSSGGGGT--TSEEEEETTSHHHHHHHHHT-HHTSEEEEES------SHHHHHHHHHTTSSSEEEEEHHHHHHHHHHTT
T ss_pred cccchhhhc--CcccccccchhHHHHhhhhc-cchhhhcccc------cHHHHHHHHhcCCeeeeeccchhhhhhhhhcc
Confidence 456777996 79999999999999988732 1123677899 9999999999999999998
Q ss_pred ------------------ee-cCCCCChHHhHHHhh
Q 047464 77 ------------------VF-PRGSPLALDISEAIL 93 (94)
Q Consensus 77 ------------------af-pkGSpL~~dvn~aiL 93 (94)
++ |++++|+..+|++|.
T Consensus 172 ~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~n~~i~ 207 (225)
T PF00497_consen 172 LENIVVIPPPISPSPVYFAVRKKNPELLEIFNKAIR 207 (225)
T ss_dssp TCEEEEEEEEEEEEEEEEEEETTTHHHHHHHHHHHH
T ss_pred cccccccccccccceeEEeecccccHHHHHHHHHHH
Confidence 44 556779999999985
No 5
>PRK11260 cystine transporter subunit; Provisional
Probab=98.49 E-value=4.7e-07 Score=66.20 Aligned_cols=74 Identities=16% Similarity=0.216 Sum_probs=63.4
Q ss_pred CCCChhHHHhCCCeeeecCCccHHHHHHHhhCCCCCCcccccCCCCCCChhhHHHHHhcCCeeEEEE-------------
Q 047464 10 STVDIKTLQRRNAAVGCNGNSFIIRYLINVLNFKPGSNKKINAKNGYNSITSYPMAFESGDIAAAFL------------- 76 (94)
Q Consensus 10 ~i~~i~dL~~~~~~VG~~~gSf~~~~L~~~~~~~~~~i~~~~~~~~~~s~~~~~~aL~~g~i~A~v~------------- 76 (94)
.+.+++||+ |++||+..|+....|+.+ . +...++..|+ +.++++++|.+|+||+++.
T Consensus 140 ~~~~~~dL~--g~~Igv~~G~~~~~~l~~-~-~~~~~i~~~~------~~~~~l~~L~~GrvD~~i~d~~~~~~~~~~~~ 209 (266)
T PRK11260 140 TIKTAADLK--GKKVGVGLGTNYEQWLRQ-N-VQGVDVRTYD------DDPTKYQDLRVGRIDAILVDRLAALDLVKKTN 209 (266)
T ss_pred CCCCHHHcC--CCEEEEecCCcHHHHHHH-h-CCCCceEecC------CHHHHHHHHHcCCCCEEEechHHHHHHHHhCC
Confidence 478899997 799999999999999976 3 4445688888 9999999999999999998
Q ss_pred -----------------eecCCCC-ChHHhHHHhh
Q 047464 77 -----------------VFPRGSP-LALDISEAIL 93 (94)
Q Consensus 77 -----------------afpkGSp-L~~dvn~aiL 93 (94)
+|++++| |+..+|++|-
T Consensus 210 ~~~~~~~~~~~~~~~~~~v~~~~~~l~~~ln~~l~ 244 (266)
T PRK11260 210 DTLAVAGEAFSRQESGVALRKGNPDLLKAVNQAIA 244 (266)
T ss_pred CcceecCCccccCceEEEEeCCCHHHHHHHHHHHH
Confidence 8888875 8999998874
No 6
>TIGR02995 ectoine_ehuB ectoine/hydroxyectoine ABC transporter solute-binding protein. Members of this family are the extracellular solute-binding proteins of ABC transporters that closely resemble amino acid transporters. The member from Sinorhizobium meliloti is involved in ectoine uptake, both for osmoprotection and for catabolism. All other members of the seed alignment are found associated with ectoine catabolic genes.
Probab=98.39 E-value=1.2e-06 Score=64.54 Aligned_cols=60 Identities=13% Similarity=0.043 Sum_probs=51.4
Q ss_pred CCCChhHHHh-CCCeeeecCCccHHHHHHHhhCCCCCCcccccCCCCCCChhhHHHHHhcCCeeEEEE
Q 047464 10 STVDIKTLQR-RNAAVGCNGNSFIIRYLINVLNFKPGSNKKINAKNGYNSITSYPMAFESGDIAAAFL 76 (94)
Q Consensus 10 ~i~~i~dL~~-~~~~VG~~~gSf~~~~L~~~~~~~~~~i~~~~~~~~~~s~~~~~~aL~~g~i~A~v~ 76 (94)
.+.+++||.. .|.+||+..|++..++|.+ .+++..++..|+ +.++.+++|.+|+|||++.
T Consensus 132 ~i~~~~dl~~~~g~~Igv~~g~~~~~~l~~-~~~~~~~i~~~~------~~~~~i~~L~~grvDa~i~ 192 (275)
T TIGR02995 132 GLKSYKDIAKNPDAKIAAPGGGTEEKLARE-AGVKREQIIVVP------DGQSGLKMVQDGRADAYSL 192 (275)
T ss_pred CCCCHHHhccCCCceEEEeCCcHHHHHHHH-cCCChhhEEEeC------CHHHHHHHHHcCCCCEEec
Confidence 3678899864 3789999999999999987 666555677888 9999999999999999987
No 7
>PRK11917 bifunctional adhesin/ABC transporter aspartate/glutamate-binding protein; Reviewed
Probab=98.38 E-value=1.2e-06 Score=64.67 Aligned_cols=76 Identities=11% Similarity=0.138 Sum_probs=61.7
Q ss_pred CCCCChhHHHhCCCeeeecCCccHHHHHHHhh---CCCCCCcccccCCCCCCChhhHHHHHhcCCeeEEEE---------
Q 047464 9 PSTVDIKTLQRRNAAVGCNGNSFIIRYLINVL---NFKPGSNKKINAKNGYNSITSYPMAFESGDIAAAFL--------- 76 (94)
Q Consensus 9 ~~i~~i~dL~~~~~~VG~~~gSf~~~~L~~~~---~~~~~~i~~~~~~~~~~s~~~~~~aL~~g~i~A~v~--------- 76 (94)
..+++++||+ |++||+..||...+++.+.+ +++ .++..|+ +..+..++|.+|++||++.
T Consensus 138 ~~~~s~~dL~--g~~V~v~~gs~~~~~l~~~~~~~~~~-~~~~~~~------~~~~~~~~l~~GrvDa~~~d~~~~~~~~ 208 (259)
T PRK11917 138 KNYKSLADMK--GANIGVAQAATTKKAIGEAAKKIGID-VKFSEFP------DYPSIKAALDAKRVDAFSVDKSILLGYV 208 (259)
T ss_pred CCCCCHHHhC--CCeEEEecCCcHHHHHHHhhHhcCCc-eeEEecC------CHHHHHHHHHcCCCcEEEecHHHHHHhh
Confidence 4588999998 79999999999887665422 221 2455677 9999999999999999987
Q ss_pred ------------------eecCCCC-ChHHhHHHhh
Q 047464 77 ------------------VFPRGSP-LALDISEAIL 93 (94)
Q Consensus 77 ------------------afpkGSp-L~~dvn~aiL 93 (94)
|+|||++ |+..||++|.
T Consensus 209 ~~~~~~~~~~~~~~~~~~a~~k~~~~l~~~ln~~l~ 244 (259)
T PRK11917 209 DDKSEILPDSFEPQSYGIVTKKDDPAFAKYVDDFVK 244 (259)
T ss_pred hcCCeecCCcCCCCceEEEEeCCCHHHHHHHHHHHH
Confidence 8999976 8999999874
No 8
>PRK10797 glutamate and aspartate transporter subunit; Provisional
Probab=98.36 E-value=9.6e-07 Score=66.79 Aligned_cols=76 Identities=17% Similarity=0.119 Sum_probs=63.8
Q ss_pred CCCCChhHHHhCCCeeeecCCccHHHHHHHhhC---CCCCCcccccCCCCCCChhhHHHHHhcCCeeEEEE---------
Q 047464 9 PSTVDIKTLQRRNAAVGCNGNSFIIRYLINVLN---FKPGSNKKINAKNGYNSITSYPMAFESGDIAAAFL--------- 76 (94)
Q Consensus 9 ~~i~~i~dL~~~~~~VG~~~gSf~~~~L~~~~~---~~~~~i~~~~~~~~~~s~~~~~~aL~~g~i~A~v~--------- 76 (94)
..+++++||+ |++||++.||...++|.+ +. ....++..++ +.++.+++|.+|++||++.
T Consensus 143 ~~i~sl~dL~--Gk~V~v~~gs~~~~~l~~-~~~~~~~~~~i~~~~------~~~~~l~~L~~GrvDa~i~d~~~~~~~~ 213 (302)
T PRK10797 143 GDIKDFADLK--GKAVVVTSGTTSEVLLNK-LNEEQKMNMRIISAK------DHGDSFRTLESGRAVAFMMDDALLAGER 213 (302)
T ss_pred CCCCChHHcC--CCEEEEeCCCcHHHHHHH-HhhhcCCceEEEEeC------CHHHHHHHHHcCCceEEEccHHHHHHHH
Confidence 4589999998 799999999999999876 32 1123677788 9999999999999999887
Q ss_pred -----------------------eecCCCC-ChHHhHHHhh
Q 047464 77 -----------------------VFPRGSP-LALDISEAIL 93 (94)
Q Consensus 77 -----------------------afpkGSp-L~~dvn~aiL 93 (94)
+|++++| |+..+|++|.
T Consensus 214 ~~~~~~~~l~i~~~~~~~~~~~~a~~k~~~~L~~~in~~L~ 254 (302)
T PRK10797 214 AKAKKPDNWEIVGKPQSQEAYGCMLRKDDPQFKKLMDDTIA 254 (302)
T ss_pred HcCCCCcceEECCccCCcCceeEEEeCCCHHHHHHHHHHHH
Confidence 7888875 8999998875
No 9
>PRK15007 putative ABC transporter arginine-biding protein; Provisional
Probab=98.29 E-value=3e-06 Score=60.44 Aligned_cols=57 Identities=14% Similarity=0.265 Sum_probs=48.0
Q ss_pred CCCChhHHHhCCCeeeecCCccHHHHHHHhhCCCCCCcccccCCCCCCChhhHHHHHhcCCeeEEEE
Q 047464 10 STVDIKTLQRRNAAVGCNGNSFIIRYLINVLNFKPGSNKKINAKNGYNSITSYPMAFESGDIAAAFL 76 (94)
Q Consensus 10 ~i~~i~dL~~~~~~VG~~~gSf~~~~L~~~~~~~~~~i~~~~~~~~~~s~~~~~~aL~~g~i~A~v~ 76 (94)
.+.+++||+ |++||+..|++..+|+.+. +..-.+..|+ +.++..++|.+|++||++.
T Consensus 117 ~~~~~~dL~--g~~Igv~~g~~~~~~l~~~--~~~~~~~~~~------~~~~~~~~L~~grvDa~i~ 173 (243)
T PRK15007 117 KYTSVDQLK--GKKVGVQNGTTHQKFIMDK--HPEITTVPYD------SYQNAKLDLQNGRIDAVFG 173 (243)
T ss_pred CCCCHHHhC--CCeEEEecCcHHHHHHHHh--CCCCeEEEcC------CHHHHHHHHHcCCCCEEEe
Confidence 478899997 7999999999999998863 3323566688 9999999999999999986
No 10
>TIGR01096 3A0103s03R lysine-arginine-ornithine-binding periplasmic protein.
Probab=98.22 E-value=4.4e-06 Score=59.57 Aligned_cols=57 Identities=19% Similarity=0.266 Sum_probs=47.6
Q ss_pred CCChhHHHhCCCeeeecCCccHHHHHHHhhCCCCCCcccccCCCCCCChhhHHHHHhcCCeeEEEE
Q 047464 11 TVDIKTLQRRNAAVGCNGNSFIIRYLINVLNFKPGSNKKINAKNGYNSITSYPMAFESGDIAAAFL 76 (94)
Q Consensus 11 i~~i~dL~~~~~~VG~~~gSf~~~~L~~~~~~~~~~i~~~~~~~~~~s~~~~~~aL~~g~i~A~v~ 76 (94)
..+++||. |++||+..|+....|+.+.+.. ..++..+. +.+++.++|.+|++|+++.
T Consensus 123 ~~~~~dl~--g~~i~~~~g~~~~~~l~~~~~~-~~~~~~~~------s~~~~~~~L~~g~vD~~v~ 179 (250)
T TIGR01096 123 AKTLEDLD--GKTVGVQSGTTHEQYLKDYFKP-GVDIVEYD------SYDNANMDLKAGRIDAVFT 179 (250)
T ss_pred CCChHHcC--CCEEEEecCchHHHHHHHhccC-CcEEEEcC------CHHHHHHHHHcCCCCEEEe
Confidence 46788997 7999999999999999874321 23567788 9999999999999999988
No 11
>PRK15010 ABC transporter lysine/arginine/ornithine binding periplasmic protein; Provisional
Probab=98.13 E-value=9.9e-06 Score=59.01 Aligned_cols=57 Identities=16% Similarity=0.072 Sum_probs=45.1
Q ss_pred CChhHHHhCCCeeeecCCccHHHHHHHhhCCCCCCcccccCCCCCCChhhHHHHHhcCCeeEEEE
Q 047464 12 VDIKTLQRRNAAVGCNGNSFIIRYLINVLNFKPGSNKKINAKNGYNSITSYPMAFESGDIAAAFL 76 (94)
Q Consensus 12 ~~i~dL~~~~~~VG~~~gSf~~~~L~~~~~~~~~~i~~~~~~~~~~s~~~~~~aL~~g~i~A~v~ 76 (94)
.+++||. |++||+..||....|+.+.+.-..-++..++ +.++.+++|.+|++||++.
T Consensus 126 ~~~~dl~--g~~Igv~~gs~~~~~~~~~~~~~~~~~~~~~------~~~~~~~~l~~griDa~i~ 182 (260)
T PRK15010 126 PTLDSLK--GKHVGVLQGSTQEAYANETWRSKGVDVVAYA------NQDLVYSDLAAGRLDAALQ 182 (260)
T ss_pred CChhHcC--CCEEEEecCchHHHHHHHhcccCCceEEecC------CHHHHHHHHHcCCccEEEe
Confidence 4789997 7999999999988888763321112455577 9999999999999999986
No 12
>TIGR01098 3A0109s03R phosphate/phosphite/phosphonate ABC transporters, periplasmic binding protein. A subset of this model in which nearly all members exhibit genomic context with elements of phosphonate metabolism, particularly the C-P lyase system has been built (TIGR03431) as an equivalog. Nevertheless, there are members of this subfamily (TIGR01098) which show up sporadically on a phylogenetic tree that also show phosphonate context and are most likely competent to transport phosphonates.
Probab=98.11 E-value=9.9e-06 Score=58.25 Aligned_cols=79 Identities=18% Similarity=0.155 Sum_probs=58.8
Q ss_pred CCCCCChhHHHhCCCeeeecC-CccH-----HHHHHHhhCCCCC----CcccccCCCCCCChhhHHHHHhcCCeeEEEE-
Q 047464 8 QPSTVDIKTLQRRNAAVGCNG-NSFI-----IRYLINVLNFKPG----SNKKINAKNGYNSITSYPMAFESGDIAAAFL- 76 (94)
Q Consensus 8 ~~~i~~i~dL~~~~~~VG~~~-gSf~-----~~~L~~~~~~~~~----~i~~~~~~~~~~s~~~~~~aL~~g~i~A~v~- 76 (94)
...+++++||+ |++||+.. +++. ..+|.+..++++. .+..+. +.++..++|.+|++||++.
T Consensus 130 d~~i~~~~dL~--gk~I~~~~~~s~~~~~~~~~~l~~~~~~~~~~~~~~i~~~~------~~~~~~~al~~G~~Da~~~~ 201 (254)
T TIGR01098 130 DSPIKSLKDLK--GKTFAFGDPASTSGYLVPRYQLKKEGGLDADGFFSEVVFSG------SHDASALAVANGKVDAATNN 201 (254)
T ss_pred CCCCCChHHhc--CCEEEeeCCCCccchHhHHHHHHHhcCCChHHhhhheeecC------chHHHHHHHHcCCCCeEEec
Confidence 34589999997 79999975 4443 3455554554432 344455 6789999999999999998
Q ss_pred --------------------------------eecCC-CC-ChHHhHHHhhC
Q 047464 77 --------------------------------VFPRG-SP-LALDISEAILK 94 (94)
Q Consensus 77 --------------------------------afpkG-Sp-L~~dvn~aiL~ 94 (94)
+++++ .+ |.+.||++|++
T Consensus 202 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~~l~~ 253 (254)
T TIGR01098 202 SSAIGRLKKRGPSDMKKVRVIWKSPLIPNDPIAVRKDLPPELKEKIRDAFLT 253 (254)
T ss_pred HHHHHHHHHhCccchhheEEEEecCCCCCCCEEEECCCCHHHHHHHHHHHhh
Confidence 88888 54 99999999874
No 13
>TIGR03870 ABC_MoxJ methanol oxidation system protein MoxJ. This predicted periplasmic protein, called MoxJ or MxaJ, is required for methanol oxidation in Methylobacterium extorquens. Two differing lines of evidence suggest two different roles. Forming one view, homology suggests it is the substrate-binding protein of an ABC transporter associated with methanol oxidation. The gene, furthermore, is found regular in genomes with, and only two or three genes away from, a corresponding permease and ATP-binding cassette gene pair. The other view is that this protein is an accessory factor or additional subunit of methanol dehydrogenase itself. Mutational studies show a dependence on this protein for expression of the PQQ-dependent, two-subunit methanol dehydrogenase (MxaF and MxaI) in Methylobacterium extorquens, as if it is a chaperone for enzyme assembly or a third subunit. A homologous N-terminal sequence was found in Paracoccus denitrificans as a 32Kd third subunit. This protein may, in
Probab=98.10 E-value=1.1e-05 Score=58.81 Aligned_cols=64 Identities=14% Similarity=0.060 Sum_probs=43.4
Q ss_pred CCCChhH--HHhCCC-eeeecCCccHHHHHHHhhCCC------CCCccccc-CCCCCC--ChhhHHHHHhcCCeeEEEE
Q 047464 10 STVDIKT--LQRRNA-AVGCNGNSFIIRYLINVLNFK------PGSNKKIN-AKNGYN--SITSYPMAFESGDIAAAFL 76 (94)
Q Consensus 10 ~i~~i~d--L~~~~~-~VG~~~gSf~~~~L~~~~~~~------~~~i~~~~-~~~~~~--s~~~~~~aL~~g~i~A~v~ 76 (94)
.+++++| |+ |+ +||++.||+...++.+ ++.. ...+..|. +...|. +.++.+++|.+|+|||++.
T Consensus 94 ~~~~~~d~~L~--g~~~vgv~~gs~~~~~l~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~aL~~GrvDa~i~ 169 (246)
T TIGR03870 94 DIKSWNDPRLK--KVSKIGVIFGSPAETMLKQ-IGRYEDNFAYLYSLVNFKSPRNQYTQIDPRKLVSEVATGKADLAVA 169 (246)
T ss_pred CCCCccchhhc--cCceEEEecCChHHHHHHh-cCccccccccccccccccCcccccccCCHHHHHHHHHcCCCCEEEe
Confidence 4677754 77 77 9999999999999987 4311 01223332 111122 3578899999999999987
No 14
>COG0834 HisJ ABC-type amino acid transport/signal transduction systems, periplasmic component/domain [Amino acid transport and metabolism / Signal transduction mechanisms]
Probab=98.10 E-value=6.3e-06 Score=59.00 Aligned_cols=56 Identities=13% Similarity=0.032 Sum_probs=46.2
Q ss_pred CCChhHHHhCCCeeeecCCcc--HHHHHHHhhCCCCCCcccccCCCCCCChhhHHHHHhcCCeeEEEE
Q 047464 11 TVDIKTLQRRNAAVGCNGNSF--IIRYLINVLNFKPGSNKKINAKNGYNSITSYPMAFESGDIAAAFL 76 (94)
Q Consensus 11 i~~i~dL~~~~~~VG~~~gSf--~~~~L~~~~~~~~~~i~~~~~~~~~~s~~~~~~aL~~g~i~A~v~ 76 (94)
+.+++||+ |++||++.||+ ...++... .....+..|+ +..+.+++|++|++||++.
T Consensus 138 ~~~~~DL~--gk~v~v~~gt~~~~~~~~~~~--~~~~~~~~~~------~~~~~~~al~~Gr~Da~~~ 195 (275)
T COG0834 138 IKSLEDLK--GKKVGVQLGTTDEAEEKAKKP--GPNAKIVAYD------SNAEALLALKNGRADAVVS 195 (275)
T ss_pred cCCHHHhC--CCEEEEEcCcchhHHHHHhhc--cCCceEEeeC------CHHHHHHHHHcCCccEEEc
Confidence 67999999 79999999999 55555442 2224678888 9999999999999999997
No 15
>TIGR03871 ABC_peri_MoxJ_2 quinoprotein dehydrogenase-associated probable ABC transporter substrate-binding protein. This protein family, a sister family to TIGR03870, is found more broadly. It occurs a range of PQQ-biosynthesizing species, not just in known methanotrophs. Interpretation of evidence by homology and by direct experimental work suggest two different roles. By homology, this family appears to be the periplasmic substrate-binding protein of an ABC transport family. However, mutational studies and direct characterization for some sequences related to this family suggests this family may act as a maturation chaperone or additional subunit of a methanol dehydrogenase-like enzyme.
Probab=98.08 E-value=1.6e-05 Score=56.26 Aligned_cols=64 Identities=9% Similarity=0.080 Sum_probs=47.5
Q ss_pred CCCCChhH--HHhCCCeeeecCCccHHHHHHHhhCCCCCCcccccCCC---CCCChhhHHHHHhcCCeeEEEE
Q 047464 9 PSTVDIKT--LQRRNAAVGCNGNSFIIRYLINVLNFKPGSNKKINAKN---GYNSITSYPMAFESGDIAAAFL 76 (94)
Q Consensus 9 ~~i~~i~d--L~~~~~~VG~~~gSf~~~~L~~~~~~~~~~i~~~~~~~---~~~s~~~~~~aL~~g~i~A~v~ 76 (94)
..+++++| |. |++||+..||...++|.. .++. .+++.|.... ...+.++.+++|.+|++||++.
T Consensus 92 ~~~~~~~d~~l~--g~~V~v~~g~~~~~~l~~-~~~~-~~~~~~~~~~~~~~~~~~~~~~~~l~~G~~Da~i~ 160 (232)
T TIGR03871 92 LDVKSLDDPRLK--KLRIGVFAGTPPAHWLAR-HGLV-ENVVGYSLFGDYRPESPPGRMVEDLAAGEIDVAIV 160 (232)
T ss_pred ccccchhhhhhc--CCeEEEEcCChHHHHHHh-cCcc-cccccccccccccccCCHHHHHHHHHcCCcCEEEe
Confidence 35788888 66 799999999999999987 6653 2333332111 1237899999999999999987
No 16
>PRK10859 membrane-bound lytic transglycosylase F; Provisional
Probab=98.05 E-value=1.2e-05 Score=64.53 Aligned_cols=76 Identities=13% Similarity=0.099 Sum_probs=60.2
Q ss_pred CCCCChhHHHhCCCeeeecCCccHHHHHHHhhCC--CCCCc--ccccCCCCCCChhhHHHHHhcCCeeEEEE--------
Q 047464 9 PSTVDIKTLQRRNAAVGCNGNSFIIRYLINVLNF--KPGSN--KKINAKNGYNSITSYPMAFESGDIAAAFL-------- 76 (94)
Q Consensus 9 ~~i~~i~dL~~~~~~VG~~~gSf~~~~L~~~~~~--~~~~i--~~~~~~~~~~s~~~~~~aL~~g~i~A~v~-------- 76 (94)
+.+++++||+ |++||+..||...+.|.+ ++. ..-.+ ..+. +.++.+++|.+|+|||++.
T Consensus 139 ~~i~~l~dL~--Gk~I~V~~gS~~~~~L~~-l~~~~p~i~~~~~~~~------s~~e~l~aL~~G~iDa~v~d~~~~~~~ 209 (482)
T PRK10859 139 PRPRSLGDLK--GGTLTVAAGSSHVETLQE-LKKKYPELSWEESDDK------DSEELLEQVAEGKIDYTIADSVEISLN 209 (482)
T ss_pred CCCCCHHHhC--CCeEEEECCCcHHHHHHH-HHHhCCCceEEecCCC------CHHHHHHHHHCCCCCEEEECcHHHHHH
Confidence 4588999998 899999999999998876 322 11122 2355 9999999999999999998
Q ss_pred ---------------------eecCC-CC-ChHHhHHHhh
Q 047464 77 ---------------------VFPRG-SP-LALDISEAIL 93 (94)
Q Consensus 77 ---------------------afpkG-Sp-L~~dvn~aiL 93 (94)
||+|+ +| |+..+|++|-
T Consensus 210 ~~~~p~l~v~~~l~~~~~~~~av~k~~~~~L~~~ln~~L~ 249 (482)
T PRK10859 210 QRYHPELAVAFDLTDEQPVAWALPPSGDDSLYAALLDFFN 249 (482)
T ss_pred HHhCCCceeeeecCCCceeEEEEeCCCCHHHHHHHHHHHH
Confidence 88884 44 9999999874
No 17
>smart00062 PBPb Bacterial periplasmic substrate-binding proteins. bacterial proteins, eukaryotic ones are in PBPe
Probab=97.97 E-value=3.7e-05 Score=50.99 Aligned_cols=59 Identities=15% Similarity=0.138 Sum_probs=48.7
Q ss_pred CCCCCChhHHHhCCCeeeecCCccHHHHHHHhhCCCCCCcccccCCCCCCChhhHHHHHhcCCeeEEEE
Q 047464 8 QPSTVDIKTLQRRNAAVGCNGNSFIIRYLINVLNFKPGSNKKINAKNGYNSITSYPMAFESGDIAAAFL 76 (94)
Q Consensus 8 ~~~i~~i~dL~~~~~~VG~~~gSf~~~~L~~~~~~~~~~i~~~~~~~~~~s~~~~~~aL~~g~i~A~v~ 76 (94)
...+.+++||+ |++||...|+....++.. . .....+..+. +.++.+.+|.+|++||++.
T Consensus 95 ~~~~~~~~dL~--g~~i~~~~g~~~~~~~~~-~-~~~~~~~~~~------~~~~~~~~l~~g~~d~~~~ 153 (219)
T smart00062 95 DSPIKSLEDLK--GKKVAVVAGTTGEELLKK-L-YPEAKIVSYD------SQAEALAALKAGRADAAVA 153 (219)
T ss_pred CCCCCChHHhC--CCEEEEecCccHHHHHHH-h-CCCceEEEcC------CHHHHHHHhhcCcccEEEe
Confidence 34589999997 799999999999998877 4 2223566677 8999999999999999998
No 18
>PRK15437 histidine ABC transporter substrate-binding protein HisJ; Provisional
Probab=97.95 E-value=3.5e-05 Score=56.10 Aligned_cols=57 Identities=16% Similarity=0.071 Sum_probs=45.6
Q ss_pred CChhHHHhCCCeeeecCCccHHHHHHHhhCCCCCCcccccCCCCCCChhhHHHHHhcCCeeEEEE
Q 047464 12 VDIKTLQRRNAAVGCNGNSFIIRYLINVLNFKPGSNKKINAKNGYNSITSYPMAFESGDIAAAFL 76 (94)
Q Consensus 12 ~~i~dL~~~~~~VG~~~gSf~~~~L~~~~~~~~~~i~~~~~~~~~~s~~~~~~aL~~g~i~A~v~ 76 (94)
.+++||+ |++||+..||+...|+.+.......++..+. +.++.+++|.+|+||+++.
T Consensus 126 ~~~~dl~--g~~Igv~~g~~~~~~~~~~~~~~~~~~~~~~------~~~~~i~~L~~grvD~~v~ 182 (259)
T PRK15437 126 PTVESLK--GKRVGVLQGTTQETFGNEHWAPKGIEIVSYQ------GQDNIYSDLTAGRIDAAFQ 182 (259)
T ss_pred CChHHhC--CCEEEEecCcHHHHHHHhhccccCceEEecC------CHHHHHHHHHcCCccEEEe
Confidence 4789997 7999999999999888763211112466677 9999999999999999886
No 19
>PF09084 NMT1: NMT1/THI5 like; InterPro: IPR015168 This entry is found in the NMT1 and THI5 proteins. These proteins are proposed to be required for the biosynthesis of the pyrimidine moiety of thiamine [, , ]. They are regulated by thiamine []. ; PDB: 2X26_A 3E4R_A 3KSJ_A 3KSX_A 3UIF_A 4DDD_A 1US4_A 1US5_A 3IX1_B 2X7P_A ....
Probab=97.94 E-value=2e-05 Score=55.41 Aligned_cols=64 Identities=22% Similarity=0.264 Sum_probs=46.8
Q ss_pred CCCCCChhHHHhCCCeeeecCCccHH----HHHHHhhCCCCCCcccccCCCCCCChhhHHHHHhcCCeeEEEEeec
Q 047464 8 QPSTVDIKTLQRRNAAVGCNGNSFII----RYLINVLNFKPGSNKKINAKNGYNSITSYPMAFESGDIAAAFLVFP 79 (94)
Q Consensus 8 ~~~i~~i~dL~~~~~~VG~~~gSf~~----~~L~~~~~~~~~~i~~~~~~~~~~s~~~~~~aL~~g~i~A~v~afp 79 (94)
.+.|++++||+ |++||+..||... .+|++ .|++.++++..+ -+..+...+|.+|++||++..+|
T Consensus 82 ~s~i~~~~DLk--GK~i~v~~~s~~~~~~~~~l~~-~g~~~~~v~~v~-----~~~~~~~~al~~g~vDa~~~~~~ 149 (216)
T PF09084_consen 82 DSGIKSPADLK--GKKIGVSRGSSSEYFLRALLKK-NGIDPDDVKIVN-----LGPPELAQALLSGQVDAAILWYP 149 (216)
T ss_dssp TTS-SSGGGGT--TSEEEESTTSHHHHHHHHHHHH-TTT-GGGSEEEE-----S-HHHHHHHHHTTSSSEEEEEEE
T ss_pred cCCCCCHHHhC--CCEEEEecCcchhHHHHHHHHH-hccccccceeee-----eehhhhhhhhhcCCCCEEEEccC
Confidence 45699999999 8999999987554 45555 888877777654 03567777999999999995444
No 20
>PRK09959 hybrid sensory histidine kinase in two-component regulatory system with EvgA; Provisional
Probab=97.89 E-value=2.3e-05 Score=67.76 Aligned_cols=76 Identities=8% Similarity=-0.027 Sum_probs=63.5
Q ss_pred CCCCCChhHHHhCCCeeeecCCccHHHHHHHhhCCCCCCcccccCCCCCCChhhHHHHHhcCCeeEEEE-----------
Q 047464 8 QPSTVDIKTLQRRNAAVGCNGNSFIIRYLINVLNFKPGSNKKINAKNGYNSITSYPMAFESGDIAAAFL----------- 76 (94)
Q Consensus 8 ~~~i~~i~dL~~~~~~VG~~~gSf~~~~L~~~~~~~~~~i~~~~~~~~~~s~~~~~~aL~~g~i~A~v~----------- 76 (94)
...++++++|+ +++||.+.|++..+++.+. ++..+++.|+ |.+++++|+.+|++||++.
T Consensus 153 ~~~~~~~~~l~--~~~i~~~~g~~~~~~~~~~--~p~~~i~~~~------s~~~al~av~~G~~Da~i~~~~~~~~~i~~ 222 (1197)
T PRK09959 153 HDSMRPLTSSK--PVNIARVANYPPDEVIHQS--FPKATIISFT------NLYQALASVSAGQNDYFIGSNIITSSMISR 222 (1197)
T ss_pred CCCCCCccccc--CeEEEEeCCCCCHHHHHHh--CCCCEEEeCC------CHHHHHHHHHcCCCCEEEccHHHHHHHHhc
Confidence 34567788887 7999999999999999873 5556788999 9999999999999999998
Q ss_pred ---------------------eecCCCC-ChHHhHHHhh
Q 047464 77 ---------------------VFPRGSP-LALDISEAIL 93 (94)
Q Consensus 77 ---------------------afpkGSp-L~~dvn~aiL 93 (94)
+.+|+.| |..-||++|-
T Consensus 223 ~~~~~l~~~~~~~~~~~~~~~~~~~~~~~L~~~lnkal~ 261 (1197)
T PRK09959 223 YFTHSLNVVKYYNSPRQYNFFLTRKESVILNEVLNRFVD 261 (1197)
T ss_pred ccccceEEEeeccCCCCceeEEEcCCcHHHHHHHHHHHH
Confidence 5677877 6666799874
No 21
>cd00134 PBPb Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and inorganic ions. PBPs have two cell-membrane translocation functions: bind substrate, and interact with the membrane bound complex. A diverse group of periplasmic transport receptors for lysine/arginine/ornithine (LAO), glutamine, histidine, sulfate, phosphate, molybdate, and methanol are included in the PBPb CD.
Probab=97.71 E-value=0.00021 Score=47.65 Aligned_cols=59 Identities=19% Similarity=0.209 Sum_probs=49.1
Q ss_pred CCCCCChhHHHhCCCeeeecCCccHHHHHHHhhCCCCCCcccccCCCCCCChhhHHHHHhcCCeeEEEE
Q 047464 8 QPSTVDIKTLQRRNAAVGCNGNSFIIRYLINVLNFKPGSNKKINAKNGYNSITSYPMAFESGDIAAAFL 76 (94)
Q Consensus 8 ~~~i~~i~dL~~~~~~VG~~~gSf~~~~L~~~~~~~~~~i~~~~~~~~~~s~~~~~~aL~~g~i~A~v~ 76 (94)
...+.+++||+ |++||+..|+....++.+.+. ...+..++ +.++.++.|.+|++||++.
T Consensus 94 ~~~~~~~~dl~--g~~i~~~~~~~~~~~~~~~~~--~~~~~~~~------~~~~~~~~l~~g~~d~~~~ 152 (218)
T cd00134 94 GSPIKSVKDLK--GKKVAVQKGSTAEKYLKKALP--EAKVVSYD------DNAEALAALENGRADAVIV 152 (218)
T ss_pred CCCCCChHHhC--CCEEEEEcCchHHHHHHHhCC--cccEEEeC------CHHHHHHHHHcCCccEEEe
Confidence 34567899998 799999999998888887443 24577788 9999999999999999998
No 22
>TIGR03427 ABC_peri_uca ABC transporter periplasmic binding protein, urea carboxylase region. Members of this family are ABC transporter periplasmic binding proteins associated with the urea carboxylase/allophanate hydrolase pathway, an alternative to urease for urea degradation. The protein is restricted to bacteria with the pathway, with its gene close to the urea carboxylase and allophanate hydrolase genes. The substrate for this transporter therefore is likely to be urea or a compound from which urea is easily derived.
Probab=97.68 E-value=4.7e-05 Score=58.98 Aligned_cols=58 Identities=21% Similarity=0.161 Sum_probs=46.6
Q ss_pred CCChhHHHhCCCeeeecCCccHH----HHHHHhhCCCCCCcccccCCCCCCChhhHHHHHhcCCeeEEEE
Q 047464 11 TVDIKTLQRRNAAVGCNGNSFII----RYLINVLNFKPGSNKKINAKNGYNSITSYPMAFESGDIAAAFL 76 (94)
Q Consensus 11 i~~i~dL~~~~~~VG~~~gSf~~----~~L~~~~~~~~~~i~~~~~~~~~~s~~~~~~aL~~g~i~A~v~ 76 (94)
|++++||+ |++||+..||... ..|++ .|++++.+...+ -++.++..||.+|+|||++.
T Consensus 98 i~svaDLK--GKkIav~~gs~~~~ll~~aL~~-aGL~~~DV~~v~-----~~~~d~~aAl~~G~VDAa~~ 159 (328)
T TIGR03427 98 GKSLADLK--GQKVNLVELSVSHYLLARALES-VGLSEKDVKVVN-----TSDADIVAAFITKDVTAVVT 159 (328)
T ss_pred CCCHHHcC--CCEEeccCCChHHHHHHHHHHH-cCCCHHHeEEEe-----CChHHHHHHHhcCCCcEEEE
Confidence 89999999 8999999999876 45555 777665555533 15678899999999999987
No 23
>PRK11480 tauA taurine transporter substrate binding subunit; Provisional
Probab=97.63 E-value=0.0001 Score=55.90 Aligned_cols=60 Identities=20% Similarity=0.215 Sum_probs=47.1
Q ss_pred CCCCChhHHHhCCCeeeecCCccHH----HHHHHhhCCCCCCcccccCCCCCCChhhHHHHHhcCCeeEEEE
Q 047464 9 PSTVDIKTLQRRNAAVGCNGNSFII----RYLINVLNFKPGSNKKINAKNGYNSITSYPMAFESGDIAAAFL 76 (94)
Q Consensus 9 ~~i~~i~dL~~~~~~VG~~~gSf~~----~~L~~~~~~~~~~i~~~~~~~~~~s~~~~~~aL~~g~i~A~v~ 76 (94)
+.|++++||+ |++||+..+|+.. .+|++ .|++++.++..+ -.+.+...+|.+|+|||++.
T Consensus 112 ~~I~s~~DLk--GK~Iav~~~s~~~~~l~~~L~~-~Gl~~~dv~~v~-----~~~~~~~~Al~~G~VDAa~~ 175 (320)
T PRK11480 112 KTISKPEDLI--GKRIAVPFISTTHYSLLAALKH-WGIKPGQVEIVN-----LQPPAIIAAWQRGDIDGAYV 175 (320)
T ss_pred CCCCChHHcC--CCEEecCCCCchHHHHHHHHHH-cCCCHhheEEEE-----CCcHHHHHHHHcCCcCEEEE
Confidence 4599999999 8999998887654 35655 888877766533 14678899999999999987
No 24
>PRK09959 hybrid sensory histidine kinase in two-component regulatory system with EvgA; Provisional
Probab=97.60 E-value=0.00012 Score=63.28 Aligned_cols=71 Identities=21% Similarity=0.249 Sum_probs=58.9
Q ss_pred hhHHHhCCCeeeecCCccHHHHHHHhhCCCCCCcccccCCCCCCChhhHHHHHhcCCeeEEEE-----------------
Q 047464 14 IKTLQRRNAAVGCNGNSFIIRYLINVLNFKPGSNKKINAKNGYNSITSYPMAFESGDIAAAFL----------------- 76 (94)
Q Consensus 14 i~dL~~~~~~VG~~~gSf~~~~L~~~~~~~~~~i~~~~~~~~~~s~~~~~~aL~~g~i~A~v~----------------- 76 (94)
+.++. .|++||+..|+...+++.+. ++..+++.|+ +.++++++|.+|++||++.
T Consensus 401 ~~~~~-~g~~vav~~g~~~~~~~~~~--~p~~~~~~~~------~~~~~l~av~~G~~Da~i~~~~~~~~~~~~~~~~~l 471 (1197)
T PRK09959 401 EQTLK-KGMKVAIPYYYELHSQLKEM--YPEVEWIKVD------NASAAFHKVKEGELDALVATQLNSRYMIDHYYPNEL 471 (1197)
T ss_pred ccccc-cCCEEEEeCCcchHHHHHHH--CCCcEEEEcC------CHHHHHHHHHcCCCCEEehhhHHHHHHHHhcccccc
Confidence 34454 48999999999999988763 3334788899 9999999999999999987
Q ss_pred ---------------eecCCCC-ChHHhHHHhh
Q 047464 77 ---------------VFPRGSP-LALDISEAIL 93 (94)
Q Consensus 77 ---------------afpkGSp-L~~dvn~aiL 93 (94)
|++|+.| |+.-||++|.
T Consensus 472 ~~~~~~~~~~~~~~~av~k~~~~L~~~lnk~l~ 504 (1197)
T PRK09959 472 YHFLIPGVPNASLSFAFPRGEPELKDIINKALN 504 (1197)
T ss_pred eeeecCCCCchheEEeeCCCCHHHHHHHHHHHH
Confidence 7888876 8999999874
No 25
>TIGR01729 taurine_ABC_bnd taurine ABC transporter, periplasmic binding protein. This model identifies a cluster of ABC transporter periplasmic substrate binding proteins, apparently specific for taurine. Transport systems for taurine (NH2-CH2-CH2-SO3H), sulfonates, and sulfate esters import sulfur when sulfate levels are low. The most closely related proteins outside this family are putative aliphatic sulfonate binding proteins (TIGR01728).
Probab=97.58 E-value=0.00016 Score=53.73 Aligned_cols=60 Identities=20% Similarity=0.161 Sum_probs=46.0
Q ss_pred CCCCChhHHHhCCCeeeecCCccHHH----HHHHhhCCCCCCcccccCCCCCCChhhHHHHHhcCCeeEEEE
Q 047464 9 PSTVDIKTLQRRNAAVGCNGNSFIIR----YLINVLNFKPGSNKKINAKNGYNSITSYPMAFESGDIAAAFL 76 (94)
Q Consensus 9 ~~i~~i~dL~~~~~~VG~~~gSf~~~----~L~~~~~~~~~~i~~~~~~~~~~s~~~~~~aL~~g~i~A~v~ 76 (94)
+.|++++||+ |++||+..||.... +|+. .|+++..+.... -++.+...+|.+|+|||++.
T Consensus 90 s~I~s~~DLk--GK~Igv~~~s~~~~~l~~~L~~-~Gl~~~dv~~v~-----~~~~~~~~al~~G~vDa~~~ 153 (300)
T TIGR01729 90 SGIEKPEDLK--GKNVAVPFVSTTHYSLLAALKH-WKTDPREVNILN-----LKPPQIVAAWQRGDIDAAYV 153 (300)
T ss_pred CCCCChhHcC--CCEEEeCCCCcHHHHHHHHHHH-cCCChhheEEEe-----cCcHHHHHHHHcCCcCEEEE
Confidence 4589999999 89999998886553 5554 677665554432 14678999999999999987
No 26
>KOG1053 consensus Glutamate-gated NMDA-type ion channel receptor subunit GRIN2A and related subunits [Inorganic ion transport and metabolism; Amino acid transport and metabolism; Signal transduction mechanisms]
Probab=97.31 E-value=5.1e-05 Score=66.21 Aligned_cols=70 Identities=19% Similarity=0.168 Sum_probs=55.3
Q ss_pred CCeeeecCCccHHHHHHHhhCCCCCCcccccCCCCCCChhhHHHHHhcCCeeEEEE------------------------
Q 047464 21 NAAVGCNGNSFIIRYLINVLNFKPGSNKKINAKNGYNSITSYPMAFESGDIAAAFL------------------------ 76 (94)
Q Consensus 21 ~~~VG~~~gSf~~~~L~~~~~~~~~~i~~~~~~~~~~s~~~~~~aL~~g~i~A~v~------------------------ 76 (94)
..+.|++.++...+++++.+--=.+-++.|+ -..+++++..|++|+.||++|
T Consensus 688 pFRFGTVpngSTE~niR~Nyp~MHeYM~kyN----q~~v~dal~sLK~gKLDAFIyDaAVLnY~agkDegCKLvTIGsgK 763 (1258)
T KOG1053|consen 688 PFRFGTVPNGSTERNIRSNYPEMHEYMVKYN----QPGVEDALESLKNGKLDAFIYDAAVLNYMAGKDEGCKLVTIGSGK 763 (1258)
T ss_pred CcccccCCCCchhhhHHhccHHHHHHHHHhc----cCchHHHHHHHhcccchhHHHHHHHHHHhhccCCCceEEEecCCc
Confidence 5689999999999888763211111244455 348899999999999999999
Q ss_pred ---------eecCCCCChHHhHHHhhC
Q 047464 77 ---------VFPRGSPLALDISEAILK 94 (94)
Q Consensus 77 ---------afpkGSpL~~dvn~aiL~ 94 (94)
|||||||+...|+.+||.
T Consensus 764 vFAttGYGIal~k~Spwkr~IdlallQ 790 (1258)
T KOG1053|consen 764 VFATTGYGIALPKNSPWKRQIDLALLQ 790 (1258)
T ss_pred eeeecceeeecCCCCcchhhHHHHHHH
Confidence 999999999999999984
No 27
>KOG4440 consensus NMDA selective glutamate-gated ion channel receptor subunit GRIN1 [Inorganic ion transport and metabolism; Amino acid transport and metabolism; Signal transduction mechanisms]
Probab=97.29 E-value=0.0003 Score=59.92 Aligned_cols=91 Identities=20% Similarity=0.256 Sum_probs=68.3
Q ss_pred ccccccCCCCCChhHHH--h--CCCeeeecCCccHHHHHHHhhCCCCCCcccccCCCCCCChhhHHHHHhcCCeeEEEE-
Q 047464 2 LTVSRLQPSTVDIKTLQ--R--RNAAVGCNGNSFIIRYLINVLNFKPGSNKKINAKNGYNSITSYPMAFESGDIAAAFL- 76 (94)
Q Consensus 2 LTV~~l~~~i~~i~dL~--~--~~~~VG~~~gSf~~~~L~~~~~~~~~~i~~~~~~~~~~s~~~~~~aL~~g~i~A~v~- 76 (94)
|-..|-+..+++|.|=. + .+..-|++.+|.+..|.+..-... +.++.-. ++.|.+.+|+.+++++|+.+|++-
T Consensus 666 LVLdrPe~~ltGinDpRLRNps~nf~~aTVk~SsVd~YFrRqVELS-~MyR~ME-~hNy~~A~eAiq~v~~gkL~AFIWD 743 (993)
T KOG4440|consen 666 LVLDRPEERLTGINDPRLRNPSDNFIYATVKQSSVDIYFRRQVELS-TMYRHME-KHNYESAAEAIQAVRDGKLHAFIWD 743 (993)
T ss_pred eeecCccccccCCCCccccCcccceeEEEecCccHHHHHHHHhHHH-HHHHhhh-hcchhhHHHHHHHHHcCceeEEEee
Confidence 44566666677777743 2 346789999999999987643221 1123222 445669999999999999999987
Q ss_pred ----------------------------eecCCCCChHHhHHHhhC
Q 047464 77 ----------------------------VFPRGSPLALDISEAILK 94 (94)
Q Consensus 77 ----------------------------afpkGSpL~~dvn~aiL~ 94 (94)
.++||||+.+.|.-|||+
T Consensus 744 S~rLEfEAs~~CeLvT~GeLFgRSgyGIGlqK~SPWt~~vtlaIL~ 789 (993)
T KOG4440|consen 744 SARLEFEASQKCELVTTGELFGRSGYGIGLQKDSPWTQNVTLAILK 789 (993)
T ss_pred cceeeehhhcccceEeccccccccccccccccCCCCcchhhHHHHH
Confidence 899999999999999985
No 28
>TIGR01728 SsuA_fam ABC transporter, substrate-binding protein, aliphatic sulfonates family. Members of this family are substrate-binding periplasmic proteins of ABC transporters. This subfamily includes SsuA, a member of a transporter operon needed to obtain sulfur from aliphatic sulfonates. Related proteins outside the scope of this model include taurine (NH2-CH2-CH2-S03H) binding proteins, the probable sulfate ester binding protein AtsR, and the probable aromatic sulfonate binding protein AsfC. All these families make sulfur available when Cys and sulfate levels are low. Please note that phylogenetic analysis by neighbor-joining suggests that a number of sequences belonging to this family have been excluded because of scoring lower than taurine-binding proteins.
Probab=97.21 E-value=0.00096 Score=47.98 Aligned_cols=60 Identities=10% Similarity=0.065 Sum_probs=45.0
Q ss_pred CCCCCChhHHHhCCCeeeecCCccHHH----HHHHhhCCCCCCccc-ccCCCCCCChhhHHHHHhcCCeeEEEE
Q 047464 8 QPSTVDIKTLQRRNAAVGCNGNSFIIR----YLINVLNFKPGSNKK-INAKNGYNSITSYPMAFESGDIAAAFL 76 (94)
Q Consensus 8 ~~~i~~i~dL~~~~~~VG~~~gSf~~~----~L~~~~~~~~~~i~~-~~~~~~~~s~~~~~~aL~~g~i~A~v~ 76 (94)
.+.|++++||+ |++||+..|+.... +|.. .|++...+.. +. +..+..++|.+|++||++.
T Consensus 90 ~~~i~s~~dL~--Gk~i~~~~~~~~~~~~~~~l~~-~G~~~~~v~~~~~------~~~~~~~al~~g~vda~~~ 154 (288)
T TIGR01728 90 GSPIRTVADLK--GKRIAVPKGGSGHDLLLRALLK-AGLSGDDVTILYL------GPSDARAAFAAGQVDAWAI 154 (288)
T ss_pred CCCCCCHHHcC--CCEEEecCCccHHHHHHHHHHH-cCCCccceeEEec------CcHHHHHHHHCCCCCEEEe
Confidence 35689999999 79999988875543 4444 5776554433 34 6678899999999999988
No 29
>PRK11553 alkanesulfonate transporter substrate-binding subunit; Provisional
Probab=97.19 E-value=0.00075 Score=50.48 Aligned_cols=61 Identities=15% Similarity=0.145 Sum_probs=46.0
Q ss_pred CCCCCChhHHHhCCCeeeecCCccHHHHHHHh---hCCCCCCcc-cccCCCCCCChhhHHHHHhcCCeeEEEE
Q 047464 8 QPSTVDIKTLQRRNAAVGCNGNSFIIRYLINV---LNFKPGSNK-KINAKNGYNSITSYPMAFESGDIAAAFL 76 (94)
Q Consensus 8 ~~~i~~i~dL~~~~~~VG~~~gSf~~~~L~~~---~~~~~~~i~-~~~~~~~~~s~~~~~~aL~~g~i~A~v~ 76 (94)
.+.+++++||+ |++||+..||....++... .|++...+. .+. +..+...+|.+|+|||++.
T Consensus 118 ~s~i~s~~dL~--Gk~I~~~~gs~~~~~l~~~l~~~g~~~~dv~~v~~------~~~~~~~al~~G~vDa~~~ 182 (314)
T PRK11553 118 NSPIKTVADLK--GHKVAFQKGSSSHNLLLRALRKAGLKFTDIQPTYL------TPADARAAFQQGNVDAWAI 182 (314)
T ss_pred CCCCCCHHHhC--CCEEeecCCCcHHHHHHHHHHHcCCCHHHeEEEec------ChHHHHHHHHcCCCCEEEE
Confidence 45688999999 7999999998887654432 555443432 344 7778899999999999986
No 30
>KOG1054 consensus Glutamate-gated AMPA-type ion channel receptor subunit GluR2 and related subunits [Inorganic ion transport and metabolism; Amino acid transport and metabolism; Signal transduction mechanisms]
Probab=97.14 E-value=0.0003 Score=59.63 Aligned_cols=88 Identities=18% Similarity=0.175 Sum_probs=59.9
Q ss_pred CccccccCCCCCChhHHHh-CCCeeeecCCccHHHHHHHhhCCCCCCccccc----------CCCCCCChhhHHHHHhc-
Q 047464 1 MLTVSRLQPSTVDIKTLQR-RNAAVGCNGNSFIIRYLINVLNFKPGSNKKIN----------AKNGYNSITSYPMAFES- 68 (94)
Q Consensus 1 mLTV~~l~~~i~~i~dL~~-~~~~VG~~~gSf~~~~L~~~~~~~~~~i~~~~----------~~~~~~s~~~~~~aL~~- 68 (94)
+|||.|+.++|.++|||.+ +...-|++.|...++|.+. - .+..|. |+---.|..|.....+.
T Consensus 646 FLTvErMvsPIESaEDLAkQteIaYGt~~~GSTkeFFr~-S-----kiavy~kMW~yM~SaepsVFv~t~aeGv~rVRks 719 (897)
T KOG1054|consen 646 FLTVERMVSPIESAEDLAKQTEIAYGTLDSGSTKEFFRR-S-----KIAVYEKMWTYMKSAEPSVFVRTTAEGVARVRKS 719 (897)
T ss_pred HHhHHhhcCcchhHHHHhhcceeeeeecCCCchHHHHhh-h-----hHHHHHHHHHHHhcCCcceeeehhhhHHHHHHhc
Confidence 5899999999999999997 4457888888777777654 1 222221 11112255566666653
Q ss_pred -CCeeEEEE-----------------------------eecCCCCChHHhHHHhhC
Q 047464 69 -GDIAAAFL-----------------------------VFPRGSPLALDISEAILK 94 (94)
Q Consensus 69 -g~i~A~v~-----------------------------afpkGSpL~~dvn~aiL~ 94 (94)
|+-+.... |-|+||.|+..||-|+|+
T Consensus 720 KGkyAfLLEsTmNey~eqRkPCDTMKVGgNLds~GYGiATp~Gsslr~~vNLAvLk 775 (897)
T KOG1054|consen 720 KGKYAFLLESTMNEYIEQRKPCDTMKVGGNLDSKGYGIATPKGSSLRNAVNLAVLK 775 (897)
T ss_pred CCceEeehHhhhhhhhhccCCccceecccccCCcceeecCCCCcccccchhhhhhh
Confidence 33322222 999999999999999985
No 31
>TIGR02285 conserved hypothetical protein. Members of this family are found in several Proteobacteria, including Pseudomonas putida KT2440, Bdellovibrio bacteriovorus HD100 (three members), Aeromonas hydrophila, and Chromobacterium violaceum ATCC 12472. The function is unknown.
Probab=97.03 E-value=0.00087 Score=49.06 Aligned_cols=49 Identities=8% Similarity=0.054 Sum_probs=35.4
Q ss_pred CCeeeecCCccH----HHHHHHhhCCCC-CCcccccCCCCCCChhhHHHHHhcCCeeEEEE
Q 047464 21 NAAVGCNGNSFI----IRYLINVLNFKP-GSNKKINAKNGYNSITSYPMAFESGDIAAAFL 76 (94)
Q Consensus 21 ~~~VG~~~gSf~----~~~L~~~~~~~~-~~i~~~~~~~~~~s~~~~~~aL~~g~i~A~v~ 76 (94)
|++||++.|+.. .+++++ .++.. .++..++ +.++.+++|.+|+|||++.
T Consensus 136 g~~vgv~~g~~~~~~~~~~~~~-~~~~~~~~~~~~~------~~~~~~~~L~~GrvD~~v~ 189 (268)
T TIGR02285 136 KKRLGVIASRSYGQQIDDILSD-SGYQHNTRIIGNA------AMGNLFKMLEKGRVNYTLA 189 (268)
T ss_pred CeEEEEecceeccHHHHHHHHh-CCcccceeeeccc------hHHHHHHHHHcCCccEEEe
Confidence 789999998765 344544 44321 1344566 8888999999999999987
No 32
>COG0715 TauA ABC-type nitrate/sulfonate/bicarbonate transport systems, periplasmic components [Inorganic ion transport and metabolism]
Probab=97.01 E-value=0.0014 Score=49.09 Aligned_cols=61 Identities=13% Similarity=0.091 Sum_probs=46.9
Q ss_pred cCCCCCChhHHHhCCCeeeecCCcc-H----HHHHHHhhCCCCCCccc-ccCCCCCCChhhHHHHHhcCCeeEEEE
Q 047464 7 LQPSTVDIKTLQRRNAAVGCNGNSF-I----IRYLINVLNFKPGSNKK-INAKNGYNSITSYPMAFESGDIAAAFL 76 (94)
Q Consensus 7 l~~~i~~i~dL~~~~~~VG~~~gSf-~----~~~L~~~~~~~~~~i~~-~~~~~~~~s~~~~~~aL~~g~i~A~v~ 76 (94)
-.+.+++++||+ |++||+..++. . +.+|.. .|++++.+.. +- .+.++..+|.+|+|||++.
T Consensus 124 ~~~~i~~~adlk--Gk~vg~~~~~~~~~~~l~~~L~~-~Gl~~~dv~~v~~------~~~~~~~al~~g~vda~~~ 190 (335)
T COG0715 124 KDSGIKSVADLK--GKKVGVPFGGSTSDFLLRYALAK-AGLDPDDVELVNL------PPADAVAALAAGQVDAFVV 190 (335)
T ss_pred cCCCcccccCCC--CceEEEeCCCchHHHHHHHHHHH-cCCCcccceEEee------CcHHHHHHHhcCCcceEEe
Confidence 356689999998 89999999875 2 234444 8998888763 33 4568999999999999766
No 33
>TIGR00787 dctP tripartite ATP-independent periplasmic transporter solute receptor, DctP family. TRAP-T (Tripartite ATP-independent Periplasmic Transporter) family proteins generally consist of three components, and these systems have so far been found in Gram-negative bacteria, Gram-postive bacteria and archaea. The best characterized example is the DctPQM system of Rhodobacter capsulatus, a C4 dicarboxylate (malate, fumarate, succinate) transporter. This model represents the DctP family, one of at least three major families of extracytoplasmic solute receptor for TRAP family transporters. Other are the SnoM family (see pfam03480) and TAXI (TRAP-associated extracytoplasmic immunogenic) family.
Probab=96.93 E-value=0.0015 Score=48.17 Aligned_cols=55 Identities=7% Similarity=0.019 Sum_probs=47.2
Q ss_pred CCCCChhHHHhCCCeeeecCCccHHHHHHHhhCCCCCCcccccCCCCCCChhhHHHHHhcCCeeEEEE
Q 047464 9 PSTVDIKTLQRRNAAVGCNGNSFIIRYLINVLNFKPGSNKKINAKNGYNSITSYPMAFESGDIAAAFL 76 (94)
Q Consensus 9 ~~i~~i~dL~~~~~~VG~~~gSf~~~~L~~~~~~~~~~i~~~~~~~~~~s~~~~~~aL~~g~i~A~v~ 76 (94)
.+|++++||+ |++|++..++...++++. +|.. .. +- +..|.+.||++|.||+++.
T Consensus 126 ~~i~s~~Dl~--G~kir~~~~~~~~~~~~~-~Ga~---~v-~~------~~~e~~~aL~~G~vDg~~~ 180 (257)
T TIGR00787 126 KPITKPEDLK--GLKIRIPNSPMNEAQFKA-LGAN---PE-PM------AFSEVYTALQTGVVDGQEN 180 (257)
T ss_pred CccCChHHhC--CCEEecCCCHHHHHHHHH-cCCc---cc-cc------CHHHHHHHHHcCCcccccC
Confidence 4589999999 899999998888999988 7763 33 55 7889999999999999887
No 34
>PF13379 NMT1_2: NMT1-like family; PDB: 2G29_A 3UN6_A 2I4C_A 2I49_A 2I4B_A 2I48_A 3QSL_A.
Probab=96.90 E-value=0.0017 Score=47.32 Aligned_cols=60 Identities=17% Similarity=0.206 Sum_probs=41.5
Q ss_pred CCCCChhHHHh-----CCCeeee-cCCccHH----HHHHHhhCCCC-CC--cccccCCCCCCChhhHHHHHhcCCeeEEE
Q 047464 9 PSTVDIKTLQR-----RNAAVGC-NGNSFII----RYLINVLNFKP-GS--NKKINAKNGYNSITSYPMAFESGDIAAAF 75 (94)
Q Consensus 9 ~~i~~i~dL~~-----~~~~VG~-~~gSf~~----~~L~~~~~~~~-~~--i~~~~~~~~~~s~~~~~~aL~~g~i~A~v 75 (94)
+.+++++||.. .|++||+ ..||... .+|++ .|+++ .. +..++ . .++.++|++|+|||++
T Consensus 104 ~~~~~~~dl~~~~~~~kGk~i~~~~~gs~~~~~l~~~l~~-~Gl~~~~dv~~~~~~------~-~~~~~al~~g~iDa~~ 175 (252)
T PF13379_consen 104 SDIKSLADLIKKRKAQKGKKIAVPFPGSTHDMLLRYLLKK-AGLDPKDDVTLVNVP------P-PEMVAALRAGEIDAAV 175 (252)
T ss_dssp STTCCGHHHHHTCCSCSTEEEEESSTTSHHHHHHHHHHHH-TT--TTTSSEEEE--------G-HHHHHHHHTTS-SEEE
T ss_pred CCccCHHHHHhhhcccCCcEEEEcCCCCHHHHHHHHHHHh-CCCCcccceEEEecC------H-HHHHHHHhCCCcCEEE
Confidence 67999999921 3899999 6677553 34444 88987 44 44455 4 9999999999999999
Q ss_pred E
Q 047464 76 L 76 (94)
Q Consensus 76 ~ 76 (94)
.
T Consensus 176 ~ 176 (252)
T PF13379_consen 176 L 176 (252)
T ss_dssp E
T ss_pred e
Confidence 8
No 35
>TIGR03431 PhnD phosphonate ABC transporter, periplasmic phosphonate binding protein. Note that this model does not identify all phnD-subfamily genes with evident phosphonate context, but all sequences above the trusted context may be inferred to bind phosphonate compounds even in the absence of such context. Furthermore, there is ample evidence to suggest that many other members of the TIGR01098 subfamily have a different primary function.
Probab=96.57 E-value=0.0064 Score=44.92 Aligned_cols=62 Identities=21% Similarity=0.223 Sum_probs=40.6
Q ss_pred CCCCCChhHHHhCCCeeeec-CCccHHH-----HHHHhhCCCCCC---cccccCCCCCCChhhHHHHHhcCCeeEEEE
Q 047464 8 QPSTVDIKTLQRRNAAVGCN-GNSFIIR-----YLINVLNFKPGS---NKKINAKNGYNSITSYPMAFESGDIAAAFL 76 (94)
Q Consensus 8 ~~~i~~i~dL~~~~~~VG~~-~gSf~~~-----~L~~~~~~~~~~---i~~~~~~~~~~s~~~~~~aL~~g~i~A~v~ 76 (94)
.+.+++++||+ |++||+. .||+... ++.+..|.+... ...|. .+.++..++|.+|++||++.
T Consensus 124 ds~i~sl~DL~--Gk~v~~~~~~s~~~~~~~~~~l~~~~g~~~~~~~~~v~~~-----~~~~~~~~al~~G~vDa~~~ 194 (288)
T TIGR03431 124 DSPIKSLEDLK--GKTFGFVDPNSTSGFLVPSYYLFKKNGIKPKEYFKKVTFS-----GSHEAAILAVANGTVDAATT 194 (288)
T ss_pred CCCCCcHHHhC--CCEEEeeCCCcchhhHHHHHHHHHhcCCChHHhHHhheec-----CchHHHHHHHHcCCCCeEec
Confidence 34589999997 8999975 4555432 232324553222 11222 15788999999999999997
No 36
>PRK00489 hisG ATP phosphoribosyltransferase; Reviewed
Probab=96.46 E-value=0.0051 Score=46.46 Aligned_cols=56 Identities=13% Similarity=0.094 Sum_probs=46.3
Q ss_pred CCCCChhHHHhCCCeeeecCCccHHHHHHHhhCCCCCCcccccCCCCCCChhhHHHHHhcCCeeEEEE
Q 047464 9 PSTVDIKTLQRRNAAVGCNGNSFIIRYLINVLNFKPGSNKKINAKNGYNSITSYPMAFESGDIAAAFL 76 (94)
Q Consensus 9 ~~i~~i~dL~~~~~~VG~~~gSf~~~~L~~~~~~~~~~i~~~~~~~~~~s~~~~~~aL~~g~i~A~v~ 76 (94)
..+++++||+ |++||+..+....+|+.+ .|++ .+++.|. +..+. ++..|.+||+++
T Consensus 103 ~~i~sl~DL~--Gk~ia~~~~~~~~~~l~~-~gi~-~~iv~~~------gs~ea--a~~~G~aDaivd 158 (287)
T PRK00489 103 SDWQGVEDLA--GKRIATSYPNLTRRYLAE-KGID-AEVVELS------GAVEV--APRLGLADAIVD 158 (287)
T ss_pred CCCCChHHhC--CCEEEEcCcHHHHHHHHH-cCCc-eEEEECC------Cchhh--hhcCCcccEEEe
Confidence 4589999998 799999999999999998 8884 3566666 55554 788899999998
No 37
>TIGR02122 TRAP_TAXI TRAP transporter solute receptor, TAXI family. This family is one of at least three major families of extracytoplasmic solute receptor (ESR) for TRAP (Tripartite ATP-independent Periplasmic Transporter) transporters. The others are the DctP (TIGR00787) and SmoM (pfam03480) families. These transporters are secondary (driven by an ion gradient) but composed of three polypeptides, although in some species the 4-TM and 12-TM integral membrane proteins are fused. Substrates for this transporter family are not fully characterized but, besides C4 dicarboxylates, may include mannitol and other compounds.
Probab=96.31 E-value=0.0082 Score=44.36 Aligned_cols=61 Identities=16% Similarity=0.120 Sum_probs=44.1
Q ss_pred CCCCCChhHHHhCCCeeeecCC-ccH----HHHHHHhhCCCCCCc--ccccCCCCCCChhhHHHHHhcCCeeEEEEe
Q 047464 8 QPSTVDIKTLQRRNAAVGCNGN-SFI----IRYLINVLNFKPGSN--KKINAKNGYNSITSYPMAFESGDIAAAFLV 77 (94)
Q Consensus 8 ~~~i~~i~dL~~~~~~VG~~~g-Sf~----~~~L~~~~~~~~~~i--~~~~~~~~~~s~~~~~~aL~~g~i~A~v~a 77 (94)
...+++++||+ |++|++..+ |.. ..+++. .|+++..+ ..|. +..+...+|.+|+|||++..
T Consensus 130 d~~i~sl~dL~--gk~v~~~~~~s~~~~~~~~~l~~-~G~~~~~~~~v~~~------~~~~~~~al~~G~vDa~~~~ 197 (320)
T TIGR02122 130 DSGIKTVADLK--GKRVAVGAPGSGTELNARAVLKA-AGLTYDDVKKVEYL------GYAEAADALKDGKIDAAFYT 197 (320)
T ss_pred CCCCCcHHHcC--CCEEecCCCCcchHHHHHHHHHH-cCCCHHHccchhcC------CHHHHHHHHHCCCccEEEEe
Confidence 34588999998 688888643 333 234444 77764444 4566 88999999999999999984
No 38
>COG2358 Imp TRAP-type uncharacterized transport system, periplasmic component [General function prediction only]
Probab=96.02 E-value=0.017 Score=45.33 Aligned_cols=76 Identities=21% Similarity=0.160 Sum_probs=46.8
Q ss_pred ccCCCCCChhHHHhCCCeeeec-CCcc----HHHHHHHhhCCCCCCcccccCCCCCCChhhHHHHHhcCCeeEEEEeecC
Q 047464 6 RLQPSTVDIKTLQRRNAAVGCN-GNSF----IIRYLINVLNFKPGSNKKINAKNGYNSITSYPMAFESGDIAAAFLVFPR 80 (94)
Q Consensus 6 ~l~~~i~~i~dL~~~~~~VG~~-~gSf----~~~~L~~~~~~~~~~i~~~~~~~~~~s~~~~~~aL~~g~i~A~v~afpk 80 (94)
|=...|++++||+ |++|++- -||- .+..|+ .+|+..+.+..-- .| ...+..++|++|.|||+|++-+-
T Consensus 124 r~d~~Ikti~DL~--GKrV~iG~~gSgt~~~a~~il~-a~Gi~~~~~~~~~---~~-~~a~~~~~l~~g~iDA~~~~~G~ 196 (321)
T COG2358 124 RKDAGIKTIADLK--GKRVAIGPPGSGTEATARQILE-ALGITYDDYELDL---GL-GDAESADALKNGTIDAAFYVAGV 196 (321)
T ss_pred ecCCCcceehhcC--CCEEeecCCCCccHHHHHHHHH-HcCCCCcchhhhh---hc-CchhhHHHhhCCcccEEEEecCC
Confidence 3345699999999 7887762 2332 234444 4888655544411 01 23445788999999999995444
Q ss_pred CCCChHHh
Q 047464 81 GSPLALDI 88 (94)
Q Consensus 81 GSpL~~dv 88 (94)
.+|...++
T Consensus 197 p~~ai~el 204 (321)
T COG2358 197 PNPAISEL 204 (321)
T ss_pred CCccHHHH
Confidence 44444443
No 39
>TIGR00363 lipoprotein, YaeC family. This family of putative lipoproteins contains a consensus site for lipoprotein signal sequence cleavage. Included in this family is the E. coli hypothetical protein yaeC. About half of the proteins between the noise and trusted cutoffs contain the consensus lipoprotein signature and may belong to this family.
Probab=95.58 E-value=0.037 Score=41.71 Aligned_cols=62 Identities=15% Similarity=0.200 Sum_probs=44.1
Q ss_pred CCCCCChhHHHhCCCeeeecCCccHHH----HHHHhhCCC------------------CCCcccccCCCCCCChhhHHHH
Q 047464 8 QPSTVDIKTLQRRNAAVGCNGNSFIIR----YLINVLNFK------------------PGSNKKINAKNGYNSITSYPMA 65 (94)
Q Consensus 8 ~~~i~~i~dL~~~~~~VG~~~gSf~~~----~L~~~~~~~------------------~~~i~~~~~~~~~~s~~~~~~a 65 (94)
++++++++||+. |++|++.++.+-.. .|++ .|+- +.+++-.. -...+...+
T Consensus 105 s~~~~sl~dlk~-G~~IAip~d~~n~~raL~~L~~-aGLi~l~~~~~~~~t~~DI~~n~~~v~~ve-----l~~~~~~~a 177 (258)
T TIGR00363 105 SKKIKNVNELQD-GAKVAVPNDPTNLGRALLLLQK-QGLIKLKDGNGLLPTVLDIVENPKKLNITE-----LETSQLPRA 177 (258)
T ss_pred CcCCCCHHHcCC-CCEEEEeCCcchHHHHHHHHHH-cCCceecCCCCCcCChhhhhcCCCCCEEEE-----cCHHHHHHH
Confidence 457999999986 89999988765433 3555 6662 44433311 135668899
Q ss_pred HhcCCeeEEEE
Q 047464 66 FESGDIAAAFL 76 (94)
Q Consensus 66 L~~g~i~A~v~ 76 (94)
|.+|++||++.
T Consensus 178 l~~g~vDaa~v 188 (258)
T TIGR00363 178 LDDPKVDLAVI 188 (258)
T ss_pred hhcccccEEEE
Confidence 99999999998
No 40
>PF03480 SBP_bac_7: Bacterial extracellular solute-binding protein, family 7; InterPro: IPR018389 This family of proteins are involved in binding extracellular solutes for transport across the bacterial cytoplasmic membrane. This family includes a C4-dicarboxylate-binding protein DctP [, ] and the sialic acid-binding protein SiaP. The structure of the SiaP receptor has revealed an overall topology similar to ATP binding cassette ESR (extracytoplasmic solute receptors) proteins []. Upon binding of sialic acid, SiaP undergoes domain closure about a hinge region and kinking of an alpha-helix hinge component [].; GO: 0006810 transport, 0030288 outer membrane-bounded periplasmic space; PDB: 2HZK_C 2HZL_B 2HPG_C 2XWI_A 2XWK_A 2WX9_A 2CEY_A 2WYP_A 3B50_A 2CEX_B ....
Probab=95.33 E-value=0.033 Score=41.45 Aligned_cols=55 Identities=13% Similarity=0.123 Sum_probs=43.9
Q ss_pred CCCCChhHHHhCCCeeeecCCccHHHHHHHhhCCCCCCcccccCCCCCCChhhHHHHHhcCCeeEEEE
Q 047464 9 PSTVDIKTLQRRNAAVGCNGNSFIIRYLINVLNFKPGSNKKINAKNGYNSITSYPMAFESGDIAAAFL 76 (94)
Q Consensus 9 ~~i~~i~dL~~~~~~VG~~~gSf~~~~L~~~~~~~~~~i~~~~~~~~~~s~~~~~~aL~~g~i~A~v~ 76 (94)
..|++++||+ |.++.+..+.....+++. +|.. -...+ ..|.+.+|++|.||++..
T Consensus 126 ~pi~s~~Dlk--G~kiR~~~~~~~~~~~~~-lGa~---pv~ip-------~~evy~aLq~G~vDg~~~ 180 (286)
T PF03480_consen 126 KPIRSPEDLK--GLKIRVPGSPVMSDFFEA-LGAS---PVPIP-------WSEVYQALQQGVVDGAEN 180 (286)
T ss_dssp S--SSGGGGT--TEEEEETSSHHHHHHHHH-CTSE---EEE-T-------GGGHHHHHHTTSSSEEEE
T ss_pred cCCccHhhHh--hCeEEecCCHHHHHHHHH-cCCe---eecCc-------HHHHHHHHhcCCcCeEec
Confidence 4699999999 799999977777888887 9883 44444 678999999999999988
No 41
>PRK11063 metQ DL-methionine transporter substrate-binding subunit; Provisional
Probab=93.86 E-value=0.15 Score=38.58 Aligned_cols=61 Identities=18% Similarity=0.279 Sum_probs=40.9
Q ss_pred CCCCChhHHHhCCCeeeecC-CccHHH---HHHHhhCC------------------CCCCcccccCCCCCCChhhHHHHH
Q 047464 9 PSTVDIKTLQRRNAAVGCNG-NSFIIR---YLINVLNF------------------KPGSNKKINAKNGYNSITSYPMAF 66 (94)
Q Consensus 9 ~~i~~i~dL~~~~~~VG~~~-gSf~~~---~L~~~~~~------------------~~~~i~~~~~~~~~~s~~~~~~aL 66 (94)
..+++++||+. |++|++.+ .+...+ +|++ .|+ ++.+++-.. -...+...+|
T Consensus 119 ~~i~si~DL~~-Gk~IAip~d~~n~~r~L~lL~~-~Gli~l~~~~~~~~t~~di~~n~~~v~~v~-----~~~~~~~~al 191 (271)
T PRK11063 119 KKIKSLDELQD-GSQVAVPNDPTNLGRSLLLLQK-VGLIKLKDGVGLLPTVLDIVENPKNLKIVE-----LEAPQLPRSL 191 (271)
T ss_pred cCCCCHHHhcC-CCEEEecCCCccHHHHHHHHHH-CCCEEecCCCCCCCCHHHHhcCCCCCEEEE-----CcHHHHHHhc
Confidence 45999999986 89999986 433333 3333 444 222333222 1456788999
Q ss_pred hcCCeeEEEE
Q 047464 67 ESGDIAAAFL 76 (94)
Q Consensus 67 ~~g~i~A~v~ 76 (94)
.+|++||++-
T Consensus 192 ~~g~vDaa~i 201 (271)
T PRK11063 192 DDAQIALAVI 201 (271)
T ss_pred ccccccEEEE
Confidence 9999999998
No 42
>PF12974 Phosphonate-bd: ABC transporter, phosphonate, periplasmic substrate-binding protein ; PDB: 3N5L_B 3QUJ_C 3P7I_A 3QK6_A 3S4U_A.
Probab=93.73 E-value=0.04 Score=39.71 Aligned_cols=61 Identities=21% Similarity=0.266 Sum_probs=38.2
Q ss_pred CCCCCChhHHHhCCCeeeecCCc-cH----HHH-HHHhhCCCCC---CcccccCCCCCCChhhHHHHHhcCCeeEEEE
Q 047464 8 QPSTVDIKTLQRRNAAVGCNGNS-FI----IRY-LINVLNFKPG---SNKKINAKNGYNSITSYPMAFESGDIAAAFL 76 (94)
Q Consensus 8 ~~~i~~i~dL~~~~~~VG~~~gS-f~----~~~-L~~~~~~~~~---~i~~~~~~~~~~s~~~~~~aL~~g~i~A~v~ 76 (94)
.+.|++++||+ |++||+...+ ++ ..+ |.+..|++.. ...... +.+..+.+|.+|++||++.
T Consensus 94 ds~i~~l~dL~--Gk~v~~~~~~s~sg~l~~~~~L~~~~Gl~~~~~~~~~~~~------~~~~~~~~l~~G~~Da~~~ 163 (243)
T PF12974_consen 94 DSPITSLADLK--GKRVAFPDPSSTSGYLIPRYELLREAGLDPGDDFKQVFVG------SHDAVLEALLNGKADAAAI 163 (243)
T ss_dssp TSS--SHHHHG--GSEEEEE-TT-TTTTHHHHHHTCCCCT--HHHHSSEEEEE-------HHHHHHHHHTTSSSEEEE
T ss_pred CCCCCChhhcC--CCEEEEecCCccHHHHHHHHHHHHHcCCChhHceeEEEeC------CHHHHHHHHHcCCccEEEE
Confidence 45689999998 7999995544 22 333 3123666532 122345 8889999999999999998
No 43
>PF03401 TctC: Tripartite tricarboxylate transporter family receptor; InterPro: IPR005064 Bordetella pertussis, the causative agent of human whooping cough (pertussis), is an obligate human pathogen with diverse high-affinity transport systems for the assimilation of iron, a biometal that is essential for growth []. Periplasmic binding proteins of a new family, particularly well represented in this organism (and more generally in beta-proteobacteria), have been called Bug receptors []. They adopt a characteristic Venus flytrap fold with two globular domains bisected by a ligand-binding cleft. The family is specific for carboxylated solutes, with a characteristic mode of binding involving two highly conserved beta strand-beta turn-alpha helix motifs originating from each domain. These two motifs form hydrogen bonds with a carboxylate group of the ligand, both directly and via conserved water molecules, and have thus been termed the carboxylate pincers. Domain 1 recognises the ligand and the carboxylate group serves as an initial anchoring point. Domain 2 discriminates between productively and non-productively bound ligands as proper interactions with this domain is needed for the of the closed conformation []. BugE has a glutamate bound ligand. No charged residues are involved in glutamate binding by BugE, unlike what has been described for all glutamate receptors reported so far. The Bug architecture is highly conserved despite limited sequence identity [].; GO: 0030288 outer membrane-bounded periplasmic space; PDB: 2QPQ_C 2DVZ_A 2F5X_A.
Probab=93.44 E-value=0.41 Score=35.93 Aligned_cols=62 Identities=18% Similarity=0.173 Sum_probs=41.7
Q ss_pred CCCCCChhHHHh----C--CCeeeecC-Ccc---HHHHHHHhhCCCCCCcccccCCCCCCChhhHHHHHhcCCeeEEEE
Q 047464 8 QPSTVDIKTLQR----R--NAAVGCNG-NSF---IIRYLINVLNFKPGSNKKINAKNGYNSITSYPMAFESGDIAAAFL 76 (94)
Q Consensus 8 ~~~i~~i~dL~~----~--~~~VG~~~-gSf---~~~~L~~~~~~~~~~i~~~~~~~~~~s~~~~~~aL~~g~i~A~v~ 76 (94)
.+.+++++||.. + ...+|+.+ ||. ....|.+..|++ -+..+|. +-.+...+|..|+||+.+.
T Consensus 87 dsp~~t~~eli~~ak~~p~~~~~g~~g~g~~~hl~~~~l~~~~G~~-~~~Vpy~------G~~~~~~allgG~vd~~~~ 158 (274)
T PF03401_consen 87 DSPYKTLEELIEYAKANPGKLTFGSSGPGSSDHLAAALLAKAAGIK-FTHVPYD------GGAEALTALLGGHVDAAFG 158 (274)
T ss_dssp TSS-SSHHHHHHHHHCSCCC-EEEESSTTSHHHHHHHHHHHHHT----EEEE-S------SHHHHHHHHHTTSSSEEEE
T ss_pred CCccccHHHHHHHHHhCCCCeEEEecCCCchHHHHHHHHHHHhCCc-eEEEEeC------CccHHHHHHhCCeeeEEee
Confidence 566899999852 1 25778874 443 335556668885 2455677 9999999999999999998
No 44
>PF12727 PBP_like: PBP superfamily domain; InterPro: IPR024370 This entry represents members of the periplasmic binding domain superfamily []. It is often associated with a helix-turn-helix domain.
Probab=92.85 E-value=0.43 Score=34.30 Aligned_cols=65 Identities=14% Similarity=0.043 Sum_probs=50.9
Q ss_pred CCCChhHHHhCC-CeeeecCCccHHHHHHHh---hCCCCCCcccccCCCCCCChhhHHHHHhcCCeeEEEE
Q 047464 10 STVDIKTLQRRN-AAVGCNGNSFIIRYLINV---LNFKPGSNKKINAKNGYNSITSYPMAFESGDIAAAFL 76 (94)
Q Consensus 10 ~i~~i~dL~~~~-~~VG~~~gSf~~~~L~~~---~~~~~~~i~~~~~~~~~~s~~~~~~aL~~g~i~A~v~ 76 (94)
.|++++||.+.+ ..|+=+.||-.+.++... .|++++.++.|. +...|-.+...++.+|..|+-|.
T Consensus 82 ~i~~~~dL~~~~~r~vnR~~GSGtR~l~d~~l~~~gi~~~~i~gy~--~~~~th~~vA~aVa~G~AD~G~g 150 (193)
T PF12727_consen 82 GITSLEDLADPGLRFVNRQPGSGTRILFDQLLAEEGIDPEDIPGYA--QEANTHLAVAAAVASGKADAGIG 150 (193)
T ss_pred cCCCHHHhccCCcEEEECCCCCHHHHHHHHHHHHcCCChhhCCCcc--ccccChHHHHHHHHcCCCCEEee
Confidence 499999997545 467778889888766543 467877888886 44557788899999999999988
No 45
>COG1910 Periplasmic molybdate-binding protein/domain [Inorganic ion transport and metabolism]
Probab=90.89 E-value=0.96 Score=34.08 Aligned_cols=69 Identities=23% Similarity=0.186 Sum_probs=49.8
Q ss_pred cccCCC-CCChhHHHhCC-CeeeecCCccHHH----HHHHhhCCCCCCcccccCCCCCCChhhHHHHHhcCCeeEEEE
Q 047464 5 SRLQPS-TVDIKTLQRRN-AAVGCNGNSFIIR----YLINVLNFKPGSNKKINAKNGYNSITSYPMAFESGDIAAAFL 76 (94)
Q Consensus 5 ~~l~~~-i~~i~dL~~~~-~~VG~~~gSf~~~----~L~~~~~~~~~~i~~~~~~~~~~s~~~~~~aL~~g~i~A~v~ 76 (94)
++=.|. |++++||.+.+ ..|==++||=.+. +|.+ ++..+..|+.|. ..-+|-+..+.+..+|+.||-|.
T Consensus 82 ~~gnpk~i~~~edl~~~d~~fVNR~rGSGTR~LlD~~L~~-~~~~~~~I~GY~--~e~~th~avA~aVa~G~AD~GvG 156 (223)
T COG1910 82 QKGNPKNISSLEDLLRKDLRFVNRNRGSGTRILLDELLGE-LNILPDSIKGYS--DEATTHDAVASAVASGRADAGVG 156 (223)
T ss_pred ecCCCCccccHHHHhhcCcEEEecCCCccHHHHHHHHHHH-cCcCchhcCCcc--ccccccHHHHHHHHcCCCCcccc
Confidence 333344 99999999743 2455567887764 3444 778888899998 33346677788999999999998
No 46
>PF03846 SulA: Cell division inhibitor SulA; InterPro: IPR004596 All proteins in this family for which the functions are known are cell division inhibitors. In Escherichia coli, SulA is one of the SOS regulated genes. Accumulation of SulA causes rapid cessation of cell division and the appearance of long, non-septate filaments. In the presence of GTP, SulA binds a polymerisation-competent form of ftsZ in a 1:1 ratio, thus inhibiting ftsZ polymerisation and therefore preventing it from participating in the assembly of the Z ring. This mechanism prevents the premature segregation of damaged DNA to daughter cells during cell division. The expression of SulA is repressed by LexA. The N terminus of SulA may be involved in recognising the cell division apparatus.; GO: 0009432 SOS response, 0051782 negative regulation of cell division, 0009276 Gram-negative-bacterium-type cell wall; PDB: 1OFU_X 1OFT_A.
Probab=90.65 E-value=0.32 Score=33.41 Aligned_cols=46 Identities=13% Similarity=0.212 Sum_probs=36.5
Q ss_pred ccHHHHHHHhhCCCCCCcccccCCCCCCChhhHHHHHhcCCeeEEEE
Q 047464 30 SFIIRYLINVLNFKPGSNKKINAKNGYNSITSYPMAFESGDIAAAFL 76 (94)
Q Consensus 30 Sf~~~~L~~~~~~~~~~i~~~~~~~~~~s~~~~~~aL~~g~i~A~v~ 76 (94)
...+.+|++ -|++.+++-...|.+...+.+.+-+||+.|+..||+.
T Consensus 71 ~ls~~wL~~-aGl~~~kvl~l~~~~~~~tl~amekAL~sGn~s~Vl~ 116 (119)
T PF03846_consen 71 KLSRQWLQQ-AGLPLEKVLQLHPRNPQSTLEAMEKALRSGNYSAVLG 116 (119)
T ss_dssp TS-HHHHHH-TT--CCCEEEE--SSTTHHHHHHHHHHHHT-EEEEEE
T ss_pred ccCHHHHHH-cCCChhHeEEeCCCCcccHHHHHHHHHHhCCCeEEEE
Confidence 456789998 9999999999999999999999999999999999985
No 47
>PF14503 YhfZ_C: YhfZ C-terminal domain; PDB: 2OZZ_B.
Probab=90.07 E-value=0.3 Score=36.79 Aligned_cols=51 Identities=20% Similarity=0.221 Sum_probs=31.5
Q ss_pred CCCeeeecCCccHHHHHHHhhCCCCCCcccccCCCCCCChhhHHHHHhcCCeeEEEE
Q 047464 20 RNAAVGCNGNSFIIRYLINVLNFKPGSNKKINAKNGYNSITSYPMAFESGDIAAAFL 76 (94)
Q Consensus 20 ~~~~VG~~~gSf~~~~L~~~~~~~~~~i~~~~~~~~~~s~~~~~~aL~~g~i~A~v~ 76 (94)
.|.+||+...|.=+..|.+ .-|...++.-.. -+-.+.+..|.+|.|||+|-
T Consensus 113 dGmRVGiD~~S~Dq~~LT~-~~~~gk~Ve~Ve-----i~Y~q~~~~l~~g~IDA~IW 163 (232)
T PF14503_consen 113 DGMRVGIDPSSIDQKILTE-AEFEGKNVEFVE-----IPYNQLLELLRSGEIDAAIW 163 (232)
T ss_dssp ---EEEE-TT-HHHHHHHH-HHHTTS--EEEE-------HHHHHHHHHHTS--EEEE
T ss_pred eeeEeecCCCCccHHHHHH-HHhCCCceEEEE-----ecHHHHHHHHHCCCccEEEE
Confidence 3899999999998888887 446555544322 13568889999999999998
No 48
>COG4521 TauA ABC-type taurine transport system, periplasmic component [Inorganic ion transport and metabolism]
Probab=86.89 E-value=1.3 Score=34.56 Aligned_cols=62 Identities=18% Similarity=0.188 Sum_probs=47.7
Q ss_pred cCCCCCChhHHHhCCCeeeecCCccHH----HHHHHhhCCCCCCcccccCCCCCCChhhHHHHHhcCCeeEEEE
Q 047464 7 LQPSTVDIKTLQRRNAAVGCNGNSFII----RYLINVLNFKPGSNKKINAKNGYNSITSYPMAFESGDIAAAFL 76 (94)
Q Consensus 7 l~~~i~~i~dL~~~~~~VG~~~gSf~~----~~L~~~~~~~~~~i~~~~~~~~~~s~~~~~~aL~~g~i~A~v~ 76 (94)
=.+.|...+||+ |++|++-==|+.- --|+. .++++..+...+ -.+.+...|.++|.||+++-
T Consensus 118 ~gsgI~kpeDL~--GK~iavPFvSTtHysLLaaLkh-w~idp~~V~IlN-----l~Pp~IaAAwqRGDIDgAyV 183 (334)
T COG4521 118 KGSGIEKPEDLI--GKRIAVPFVSTTHYSLLAALKH-WGIDPGQVEILN-----LQPPAIAAAWQRGDIDGAYV 183 (334)
T ss_pred cCCCcCChHHhc--cCeeccceeehhHHHHHHHHHH-cCCCccceeEec-----cCCHHHHHHHHcCCCCceee
Confidence 355788999999 7999986555442 24555 899988877766 24778899999999999886
No 49
>PRK11899 prephenate dehydratase; Provisional
Probab=85.82 E-value=2.2 Score=32.75 Aligned_cols=48 Identities=13% Similarity=0.032 Sum_probs=39.1
Q ss_pred CCeeeec--CCccHHHHHHHhhCCCCCCcccccCCCCCCChhhHHHHHhcCCeeEEEE
Q 047464 21 NAAVGCN--GNSFIIRYLINVLNFKPGSNKKINAKNGYNSITSYPMAFESGDIAAAFL 76 (94)
Q Consensus 21 ~~~VG~~--~gSf~~~~L~~~~~~~~~~i~~~~~~~~~~s~~~~~~aL~~g~i~A~v~ 76 (94)
..+|||+ .|||+.....+. |....+..+. |.++..+|+.+|.+|-.|.
T Consensus 4 ~~kvaylGp~GsfS~~Aa~~~--~~~~~~v~~~------s~~~vf~av~~g~~d~gVv 53 (279)
T PRK11899 4 TNRIAFQGEPGANSHLACRDA--FPDMEPLPCA------TFEDAFEAVESGEADLAMI 53 (279)
T ss_pred CCEEEEECCCCCHHHHHHHHh--cCcCceeecC------CHHHHHHHHHCCCCCEEEE
Confidence 4679996 589999988774 3334677788 9999999999999998776
No 50
>PRK09861 cytoplasmic membrane lipoprotein-28; Provisional
Probab=85.78 E-value=1.9 Score=32.63 Aligned_cols=63 Identities=10% Similarity=0.155 Sum_probs=40.7
Q ss_pred CCCCCChhHHHhCCCeeeecC--CccHHHHH-HHhhC---------CC---------CCCcccccCCCCCCChhhHHHHH
Q 047464 8 QPSTVDIKTLQRRNAAVGCNG--NSFIIRYL-INVLN---------FK---------PGSNKKINAKNGYNSITSYPMAF 66 (94)
Q Consensus 8 ~~~i~~i~dL~~~~~~VG~~~--gSf~~~~L-~~~~~---------~~---------~~~i~~~~~~~~~~s~~~~~~aL 66 (94)
+..+++++||+. |++|++.+ +..++-.+ .+..| .. +.+++-.. -...+...+|
T Consensus 119 s~~iksl~DL~~-Ga~IAipnd~~n~~ral~lL~~agli~l~~~~g~~~t~~di~~np~~l~~ve-----~~~~q~~~al 192 (272)
T PRK09861 119 SKKIKTVAQIKE-GATVAIPNDPTNLGRALLLLQKEKLITLKEGKGLLPTALDITDNPRHLQIME-----LEGAQLPRVL 192 (272)
T ss_pred ccCCCCHHHcCC-CCEEEEeCCCccHHHHHHHHHHCCCEEEcCCCCCCCCHhHHhcCCCCCEEEE-----cCHHHhHhhc
Confidence 456999999986 89999987 44444322 12133 11 12222211 1466789999
Q ss_pred hcCCeeEEEE
Q 047464 67 ESGDIAAAFL 76 (94)
Q Consensus 67 ~~g~i~A~v~ 76 (94)
.+|++||++.
T Consensus 193 ~dg~vD~a~i 202 (272)
T PRK09861 193 DDPKVDVAII 202 (272)
T ss_pred cCcccCEEEE
Confidence 9999999998
No 51
>COG1638 DctP TRAP-type C4-dicarboxylate transport system, periplasmic component [Carbohydrate transport and metabolism]
Probab=84.70 E-value=1.9 Score=33.69 Aligned_cols=54 Identities=9% Similarity=0.155 Sum_probs=45.2
Q ss_pred CCCChhHHHhCCCeeeecCCccHHHHHHHhhCCCCCCcccccCCCCCCChhhHHHHHhcCCeeEEEE
Q 047464 10 STVDIKTLQRRNAAVGCNGNSFIIRYLINVLNFKPGSNKKINAKNGYNSITSYPMAFESGDIAAAFL 76 (94)
Q Consensus 10 ~i~~i~dL~~~~~~VG~~~gSf~~~~L~~~~~~~~~~i~~~~~~~~~~s~~~~~~aL~~g~i~A~v~ 76 (94)
+|+.++||+ |.++=+........+.+. +|.++.. .+ ..|.+.||+.|.||+.=.
T Consensus 158 PI~~peDlk--GlkiRv~~s~~~~~~~~a-~GA~P~p---m~-------f~Evy~aLqtGvVDGqEn 211 (332)
T COG1638 158 PIKTPEDLK--GLKIRVPQSPLLLAMFKA-LGANPTP---MP-------FAEVYTALQTGVVDGQEN 211 (332)
T ss_pred CCCChHHhC--CCeeecCCCHHHHHHHHH-cCCCCCC---CC-------HHHHHHHHHcCCcccccC
Confidence 799999999 899999999999999888 9995433 33 668889999999998644
No 52
>PF00800 PDT: Prephenate dehydratase Caution this is only a partial structure.; InterPro: IPR001086 Prephenate dehydratase (4.2.1.51 from EC, PDT) catalyses the decarboxylation of prephenate to phenylpyruvate. In microorganisms it is part of the terminal pathway of phenylalanine biosynthesis. In some bacteria such as Escherichia coli PDT is part of a bifunctional enzyme (P-protein) that also catalyses the transformation of chorismate into prephenate (chorismate mutase, IPR002701 from INTERPRO, 5.4.99.5 from EC) while in other bacteria it is a monofunctional enzyme. The sequence of monofunctional PDT aligns well with the C-terminal part of P-proteins [].; GO: 0004664 prephenate dehydratase activity, 0009094 L-phenylalanine biosynthetic process; PDB: 3MWB_B 2QMX_A 2QMW_A 3LUY_A.
Probab=82.75 E-value=1.2 Score=31.48 Aligned_cols=43 Identities=12% Similarity=0.014 Sum_probs=36.4
Q ss_pred CCccHHHHHHHhhCCCCCCcccccCCCCCCChhhHHHHHhcCCeeEEEE
Q 047464 28 GNSFIIRYLINVLNFKPGSNKKINAKNGYNSITSYPMAFESGDIAAAFL 76 (94)
Q Consensus 28 ~gSf~~~~L~~~~~~~~~~i~~~~~~~~~~s~~~~~~aL~~g~i~A~v~ 76 (94)
.|||+......-++.+...+..+. |.++.++++.+|++|..|.
T Consensus 7 ~GT~S~~Aa~~~~~~~~~~~~~~~------s~~~v~~av~~~~~d~~vv 49 (181)
T PF00800_consen 7 EGTFSHEAAQQYFGGPDAEIVPCD------SFEEVFDAVEEGEADYGVV 49 (181)
T ss_dssp TTSHHHHHHCCCCTTTCSEEEEES------SHHHHHHHHHCTSSSEEEE
T ss_pred CCCHHHHHHHHHHHhhccceEecC------CHHHHHHHHHcCCCceEEE
Confidence 589999988773324666799999 9999999999999999887
No 53
>PRK11063 metQ DL-methionine transporter substrate-binding subunit; Provisional
Probab=79.14 E-value=3 Score=31.47 Aligned_cols=48 Identities=17% Similarity=0.052 Sum_probs=35.6
Q ss_pred CeeeecCCccH------HHHHHHhhCCCCCCcccccCCCCCCChhhHHHHHhcCCeeEEEE
Q 047464 22 AAVGCNGNSFI------IRYLINVLNFKPGSNKKINAKNGYNSITSYPMAFESGDIAAAFL 76 (94)
Q Consensus 22 ~~VG~~~gSf~------~~~L~~~~~~~~~~i~~~~~~~~~~s~~~~~~aL~~g~i~A~v~ 76 (94)
.+||+..++.. ...+++..|++ -.++.|+ +..+..+||.+|+||+.+.
T Consensus 33 I~IG~~~~~~~~~~~~~~~~l~~~~G~~-Vel~~f~------~~~~~~~ALa~GdID~~~~ 86 (271)
T PRK11063 33 IKVGVIVGAEQQVAEVAQKVAKEKYGLD-VELVTFN------DYVLPNEALSKGDIDANAF 86 (271)
T ss_pred EEEEeCCCChHHHHHHHHHHHHHhcCCe-EEEEEec------CcHHHHHHHHcCCcceecc
Confidence 78999887763 33444434764 4577788 8888999999999999665
No 54
>TIGR00363 lipoprotein, YaeC family. This family of putative lipoproteins contains a consensus site for lipoprotein signal sequence cleavage. Included in this family is the E. coli hypothetical protein yaeC. About half of the proteins between the noise and trusted cutoffs contain the consensus lipoprotein signature and may belong to this family.
Probab=78.69 E-value=3 Score=31.42 Aligned_cols=48 Identities=15% Similarity=0.068 Sum_probs=34.5
Q ss_pred CeeeecCCccHH------HHHHHhhCCCCCCcccccCCCCCCChhhHHHHHhcCCeeEEEE
Q 047464 22 AAVGCNGNSFII------RYLINVLNFKPGSNKKINAKNGYNSITSYPMAFESGDIAAAFL 76 (94)
Q Consensus 22 ~~VG~~~gSf~~------~~L~~~~~~~~~~i~~~~~~~~~~s~~~~~~aL~~g~i~A~v~ 76 (94)
.+||+..++... +.+.+..|++ -+++.|+ +..+..+||.+|+||+.+.
T Consensus 20 l~vG~~~~~~~~~~~~~~~~~~~~~G~~-Ve~~~f~------d~~~~~~Al~~G~ID~~~~ 73 (258)
T TIGR00363 20 IKVGVISGAEQQVAEVAAKVAKEKYGLD-VELVEFN------DYALPNEAVSKGDLDANAF 73 (258)
T ss_pred EEEEeCCCChHHHHHHHHHHHHHhcCCE-EEEEEeC------CcHHHHHHHHcCCCCeEec
Confidence 689998776542 2222225663 3466788 8889999999999999876
No 55
>PLN02317 arogenate dehydratase
Probab=77.99 E-value=6 Score=31.88 Aligned_cols=48 Identities=10% Similarity=-0.045 Sum_probs=39.6
Q ss_pred CCeeeec--CCccHHHHHHHhhCCCCCCcccccCCCCCCChhhHHHHHhcCCeeEEEE
Q 047464 21 NAAVGCN--GNSFIIRYLINVLNFKPGSNKKINAKNGYNSITSYPMAFESGDIAAAFL 76 (94)
Q Consensus 21 ~~~VG~~--~gSf~~~~L~~~~~~~~~~i~~~~~~~~~~s~~~~~~aL~~g~i~A~v~ 76 (94)
..+|+|+ .|||+.....+. |....+..+. +.++.++|+++|.+|-.|.
T Consensus 94 ~~rVaylGp~GtfSe~AA~~~--f~~~e~vp~~------sf~~vf~AVe~g~ad~gVv 143 (382)
T PLN02317 94 KLRVAYQGVPGAYSEAAARKA--YPNCEAVPCE------QFEAAFQAVELWLADRAVL 143 (382)
T ss_pred CcEEEEECCCcCHHHHHHHHh--hCcCceeecC------CHHHHHHHHHCCCCCEEEE
Confidence 4789996 589999988774 3334677888 9999999999999998876
No 56
>TIGR00070 hisG ATP phosphoribosyltransferase. Members of this family from B. subtilis, Aquifex aeolicus, and Synechocystis PCC6803 (and related taxa) lack the C-terminal third of the sequence. The sole homolog from Archaeoglobus fulgidus lacks the N-terminal 50 residues (as reported) and is otherwise atypical of the rest of the family. This model excludes the C-terminal extension.
Probab=77.65 E-value=1.8 Score=31.45 Aligned_cols=65 Identities=15% Similarity=0.102 Sum_probs=49.3
Q ss_pred CCCChhHHHhCCCeeeecCCccHHHHHHHhhCCCCCCcccccCCCCCCChhhHHHHHhcCCeeEEEEeecCCCCChH
Q 047464 10 STVDIKTLQRRNAAVGCNGNSFIIRYLINVLNFKPGSNKKINAKNGYNSITSYPMAFESGDIAAAFLVFPRGSPLAL 86 (94)
Q Consensus 10 ~i~~i~dL~~~~~~VG~~~gSf~~~~L~~~~~~~~~~i~~~~~~~~~~s~~~~~~aL~~g~i~A~v~afpkGSpL~~ 86 (94)
.+.+++||+ +++|++---..+++|+.+ .|++-.=++.+. |.|- |-.-|-.||+|+..--|+.|++
T Consensus 100 ~~~~~~~l~--~~rIATkyp~i~~~~f~~-~Gi~v~ii~l~G------svE~---aP~~GlaD~IvDiv~TG~TL~~ 164 (182)
T TIGR00070 100 DISSVEDLK--GKRIATKYPNLARRYFEK-KGIDVEIIKLNG------SVEL---APLLGLADAIVDIVSTGTTLRE 164 (182)
T ss_pred CCCChHHhC--CCEEEECCHHHHHHHHHH-cCCeEEEEECcc------eeec---ccCCCceeEEEEEeCCHHHHHH
Confidence 477889998 799999888899999998 899644455566 7765 3448999999996666655543
No 57
>COG3221 PhnD ABC-type phosphate/phosphonate transport system, periplasmic component [Inorganic ion transport and metabolism]
Probab=76.60 E-value=6.4 Score=30.49 Aligned_cols=64 Identities=13% Similarity=0.174 Sum_probs=43.3
Q ss_pred CCCCCChhHHHhCCCeeeecCCccHH------HHHHHhhCCCCCCcccccCCCCCCC-hhhHHHHHhcCCeeEEEE
Q 047464 8 QPSTVDIKTLQRRNAAVGCNGNSFII------RYLINVLNFKPGSNKKINAKNGYNS-ITSYPMAFESGDIAAAFL 76 (94)
Q Consensus 8 ~~~i~~i~dL~~~~~~VG~~~gSf~~------~~L~~~~~~~~~~i~~~~~~~~~~s-~~~~~~aL~~g~i~A~v~ 76 (94)
.+.|++++||+ |+++|+..=+... .||.+..++++ ..|--+-.|.. -+..+.++.||++|++..
T Consensus 133 ds~i~sl~dlk--gk~~af~d~~StSG~l~P~~~L~~~g~~d~---~~~f~~v~~~G~H~~a~~aV~nG~vDva~~ 203 (299)
T COG3221 133 DSPIKSLEDLK--GKRFAFGDPDSTSGYLFPLYYLAKEGGIDP---DKFFGEVIFSGGHDAAVLAVANGQVDVAAV 203 (299)
T ss_pred CCCcchHHHhc--CCeEeccCCCcchhhHhHHHHHHHhcCCCh---hhhhceeeccChHHHHHHHHHcCCceEEec
Confidence 57799999999 8999997654443 45666333432 11211222335 788899999999999987
No 58
>TIGR01729 taurine_ABC_bnd taurine ABC transporter, periplasmic binding protein. This model identifies a cluster of ABC transporter periplasmic substrate binding proteins, apparently specific for taurine. Transport systems for taurine (NH2-CH2-CH2-SO3H), sulfonates, and sulfate esters import sulfur when sulfate levels are low. The most closely related proteins outside this family are putative aliphatic sulfonate binding proteins (TIGR01728).
Probab=75.44 E-value=3 Score=30.81 Aligned_cols=47 Identities=15% Similarity=0.113 Sum_probs=33.1
Q ss_pred eeeecCCccHHH------HHHHhhCCCCCCcccccCCCCCCChhhHHHHHhcCCeeEEEE
Q 047464 23 AVGCNGNSFIIR------YLINVLNFKPGSNKKINAKNGYNSITSYPMAFESGDIAAAFL 76 (94)
Q Consensus 23 ~VG~~~gSf~~~------~L~~~~~~~~~~i~~~~~~~~~~s~~~~~~aL~~g~i~A~v~ 76 (94)
+|||+.+....- ++.+.+|++ -+++.|. +..+..++|.+|++|.++.
T Consensus 2 ~~~~~~~~~p~~va~~~G~~~k~~Gl~-Ve~~~~~------~~~~~~~al~~G~iD~~~~ 54 (300)
T TIGR01729 2 TVGYQTIVEPFKVAQADGAAAKEAGAT-IDWRKFD------SGADISTALASGNVPIGVI 54 (300)
T ss_pred EEEecCCCCHHHHHHHcCchHHhcCCe-eEEEecC------cHHHHHHHHHcCCCCEecc
Confidence 688988763221 333335663 3566788 8889999999999998875
No 59
>smart00851 MGS MGS-like domain. This domain composes the whole protein of methylglyoxal synthetase and the domain is also found in Carbamoyl phosphate synthetase (CPS) where it forms a regulatory domain that binds to the allosteric effector ornithine. This family also includes inosicase. The known structures in this family show a common phosphate binding site PUBMED:10526357.
Probab=75.43 E-value=13 Score=23.00 Aligned_cols=54 Identities=15% Similarity=0.169 Sum_probs=35.1
Q ss_pred hHHHhCCCeeeecCCccHHHHHHHhhCCCCC-Cc-ccccCCCCCCChhhHHHHHhcCCeeEEEEe
Q 047464 15 KTLQRRNAAVGCNGNSFIIRYLINVLNFKPG-SN-KKINAKNGYNSITSYPMAFESGDIAAAFLV 77 (94)
Q Consensus 15 ~dL~~~~~~VG~~~gSf~~~~L~~~~~~~~~-~i-~~~~~~~~~~s~~~~~~aL~~g~i~A~v~a 77 (94)
+.|.+-|..+=.-.|+ .+||++ .|++-. .+ +.+. ..+...+.+++|+||.||.-
T Consensus 7 ~~l~~lG~~i~AT~gT--a~~L~~-~Gi~~~~~~~ki~~------~~~~i~~~i~~g~id~VIn~ 62 (90)
T smart00851 7 KRLAELGFELVATGGT--AKFLRE-AGLPVKTLHPKVHG------GILAILDLIKNGEIDLVINT 62 (90)
T ss_pred HHHHHCCCEEEEccHH--HHHHHH-CCCcceeccCCCCC------CCHHHHHHhcCCCeEEEEEC
Confidence 4456567776444443 589988 888532 11 1223 34568889999999999983
No 60
>TIGR00623 sula cell division inhibitor SulA. All proteins in this family for which the functions are known are cell division inhibitors. In E. coli, SulA is one of the SOS regulated genes.
Probab=74.25 E-value=3.6 Score=29.69 Aligned_cols=46 Identities=11% Similarity=0.109 Sum_probs=39.9
Q ss_pred cHHHHHHHhhCCCCCCcccccCCCCCCChhhHHHHHhcCCeeEEEEe
Q 047464 31 FIIRYLINVLNFKPGSNKKINAKNGYNSITSYPMAFESGDIAAAFLV 77 (94)
Q Consensus 31 f~~~~L~~~~~~~~~~i~~~~~~~~~~s~~~~~~aL~~g~i~A~v~a 77 (94)
....+|.+ .|++..++....+.+..++.+.+-++|++|...||+.=
T Consensus 72 ~~~~~L~~-~Gl~l~rvlli~~~~~~d~lwa~EQaLrSG~c~aVL~W 117 (168)
T TIGR00623 72 LSKEWVQS-SGLPLTKVMQISQLSPCNTVESMIRALRTGNYSVVIGW 117 (168)
T ss_pred cCHHHHHH-cCCChhHEEEEecCCchhHHHHHHHHHHhCCCcEEEec
Confidence 45788988 99999998888777777789999999999999999983
No 61
>PRK10622 pheA bifunctional chorismate mutase/prephenate dehydratase; Provisional
Probab=73.87 E-value=8.8 Score=30.68 Aligned_cols=50 Identities=12% Similarity=-0.038 Sum_probs=37.0
Q ss_pred CCeeeec--CCccHHHHHHHhhCCCCCCc--ccccCCCCCCChhhHHHHHhcCCeeEEEE
Q 047464 21 NAAVGCN--GNSFIIRYLINVLNFKPGSN--KKINAKNGYNSITSYPMAFESGDIAAAFL 76 (94)
Q Consensus 21 ~~~VG~~--~gSf~~~~L~~~~~~~~~~i--~~~~~~~~~~s~~~~~~aL~~g~i~A~v~ 76 (94)
..+|||+ .|||+...+...++...... ..|+ |.++..+|+.+|.+|..|.
T Consensus 103 ~~~va~lGp~GtfSh~Aa~~~~~~~~~~~~~~~~~------s~~~v~~av~~g~~d~gVv 156 (386)
T PRK10622 103 SARIAFLGPKGSYSHLAARQYAARHFEQFIESGCA------KFADIFNQVETGQADYAVL 156 (386)
T ss_pred cceEEEECCCCcHHHHHHHHhhccccccccccCCC------CHHHHHHHHHCCCCCEEEE
Confidence 4679997 58999988877333210122 2566 9999999999999998876
No 62
>PRK10595 SOS cell division inhibitor; Provisional
Probab=73.28 E-value=3.6 Score=29.54 Aligned_cols=47 Identities=6% Similarity=0.113 Sum_probs=40.0
Q ss_pred cHHHHHHHhhCCCCCCcccccCCCCCCChhhHHHHHhcCCeeEEEEee
Q 047464 31 FIIRYLINVLNFKPGSNKKINAKNGYNSITSYPMAFESGDIAAAFLVF 78 (94)
Q Consensus 31 f~~~~L~~~~~~~~~~i~~~~~~~~~~s~~~~~~aL~~g~i~A~v~af 78 (94)
-...+|.. .|++..++....|.+.....+.+-++|++|...||+.=+
T Consensus 68 p~~~~L~~-~Gl~l~rvl~v~~~~~~d~Lwa~EqaLrsG~~~aVL~Wl 114 (164)
T PRK10595 68 LSREWLQA-SGLPLTKVMQLSQLSPCHTVEAMERALRTGNYSVVLGWL 114 (164)
T ss_pred CCHHHHHH-cCCCcccEEEEecCCcHHHHHHHHHHHhhCCCcEEEECC
Confidence 44678888 999999998888777777888888999999999999833
No 63
>PF03180 Lipoprotein_9: NLPA lipoprotein; InterPro: IPR004872 This family of bacterial lipoproteins contains several antigenic members, that may be involved in bacterial virulence. Their precise function is unknown. However they are probably distantly related to IPR001638 from INTERPRO which are solute binding proteins.; PDB: 4EF2_A 4EF1_B 3GXA_C 3IR1_D 3TQW_A 3K2D_B 3UP9_A 1XS5_A 1P99_A.
Probab=72.54 E-value=4.7 Score=30.19 Aligned_cols=46 Identities=15% Similarity=0.153 Sum_probs=33.6
Q ss_pred eeeecCCccHH------HHHHHhhCCCCCCcccccCCCCCCChhhHHHHHhcCCeeEEEE
Q 047464 23 AVGCNGNSFII------RYLINVLNFKPGSNKKINAKNGYNSITSYPMAFESGDIAAAFL 76 (94)
Q Consensus 23 ~VG~~~gSf~~------~~L~~~~~~~~~~i~~~~~~~~~~s~~~~~~aL~~g~i~A~v~ 76 (94)
+||+..|+... +.+++ .|++ -.++.|+ +..+...||.+|+|||-++
T Consensus 2 kIG~~~~~~~~i~~~v~~~~~~-~Gi~-vevv~f~------D~~~~N~AL~~G~iDaN~f 53 (237)
T PF03180_consen 2 KIGVTPGPDAEILEAVKEKLKK-KGID-VEVVEFS------DYVQPNEALADGEIDANFF 53 (237)
T ss_dssp EEEEETTCHHHHHHHHHHHHHH-TTEE-EEEEEES------STTHHHHHHHTTSSSEEEE
T ss_pred EEEEeCCCHHHHHHHHHHHHHh-cCCe-EEEEEec------chhhcChHHHCCCcceecc
Confidence 57888776543 33444 5553 2467788 8888889999999999998
No 64
>PF13379 NMT1_2: NMT1-like family; PDB: 2G29_A 3UN6_A 2I4C_A 2I49_A 2I4B_A 2I48_A 3QSL_A.
Probab=71.37 E-value=6.7 Score=28.31 Aligned_cols=47 Identities=15% Similarity=0.097 Sum_probs=36.5
Q ss_pred CeeeecCCccHHH--------HHHHhhCCCCCCcccccCCCCCCChhhHHHHHhcCCeeEEEE
Q 047464 22 AAVGCNGNSFIIR--------YLINVLNFKPGSNKKINAKNGYNSITSYPMAFESGDIAAAFL 76 (94)
Q Consensus 22 ~~VG~~~gSf~~~--------~L~~~~~~~~~~i~~~~~~~~~~s~~~~~~aL~~g~i~A~v~ 76 (94)
.+||+........ |+++ .|++ -+++.|. +..+..++|.+|++|+.+.
T Consensus 8 l~ig~~~~~~~~p~~~a~~~g~f~~-~G~~-ve~~~~~------~g~~~~~al~~G~iD~a~~ 62 (252)
T PF13379_consen 8 LRIGYLPGPDYAPLYVAQEKGLFEK-EGLD-VEWVQFA------SGADILEALAAGEIDIAFV 62 (252)
T ss_dssp EEEEETSSGGGHHHHHHHHTTHHHH-TTSC-EEEEEES------SHHHHHHHHHCTSSSEEEE
T ss_pred EEEEeecchHHHHHHHHHHcChHHH-cCCE-EEEEEcC------CHHHHHHHHHcCCCCEEEe
Confidence 5788888776332 4444 6775 4677899 9999999999999999886
No 65
>PF01634 HisG: ATP phosphoribosyltransferase; InterPro: IPR013820 ATP phosphoribosyltransferase (2.4.2.17 from EC) is the enzyme that catalyzes the first step in the biosynthesis of histidine in bacteria, fungi and plants as shown below. It is a member of the larger phosphoribosyltransferase superfamily of enzymes which catalyse the condensation of 5-phospho-alpha-D-ribose 1-diphosphate with nitrogenous bases in the presence of divalent metal ions []. ATP + 5-phospho-alpha-D-ribose 1-diphosphate = 1-(5-phospho-D-ribosyl)-ATP + diphosphate Histidine biosynthesis is an energetically expensive process and ATP phosphoribosyltransferase activity is subject to control at several levels. Transcriptional regulation is based primarily on nutrient conditions and determines the amount of enzyme present in the cell, while feedback inihibition rapidly modulates activity in response to cellular conditions. The enzyme has been shown to be inhibited by 1-(5-phospho-D-ribosyl)-ATP, histidine, ppGpp (a signal associated with adverse environmental conditions) and ADP and AMP (which reflect the overall energy status of the cell). As this pathway of histidine biosynthesis is present only in prokayrotes, plants and fungi, this enzyme is a promising target for the development of novel antimicrobial compounds and herbicides. ATP phosphoribosyltransferase is found in two distinct forms: a long form containing two catalytic domains and a C-terminal regulatory domain, and a short form in which the regulatory domain is missing. The long form is catalytically competent, but in organisms with the short form, a histidyl-tRNA synthetase paralogue, HisZ, is required for enzyme activity []. This entry represents the catalytic region of this enzyme. The structures of the long form enzymes from Escherichia coli (P60757 from SWISSPROT) and Mycobacterium tuberculosis (P60759 from SWISSPROT) have been determined [, ]. The enzyme itself exists in equilibrium between an active dimeric form, an inactive hexameric form and higher aggregates. Interconversion between the various forms is largely reversible and is influenced by the binding of the natural substrates and inhibitors of the enzyme. The two catalytic domains are linked by a two-stranded beta-sheet and togther form a "periplasmic binding protein fold". A crevice between these domains contains the active site. The C-terminal domain is not directly involved in catalysis but appears to be involved the formation of hexamers, induced by the binding of inhibitors such as histidine to the enzyme, thus regulating activity.; GO: 0003879 ATP phosphoribosyltransferase activity, 0000105 histidine biosynthetic process, 0005737 cytoplasm; PDB: 1VE4_A 2VD3_B 1NH7_A 1NH8_A 1Z7N_G 1Z7M_E 1O64_A 1O63_A 1USY_F 1Q1K_A ....
Probab=70.06 E-value=2.1 Score=30.54 Aligned_cols=64 Identities=14% Similarity=0.099 Sum_probs=47.0
Q ss_pred CCChhHHHhCCCeeeecCCccHHHHHHHhhCCCCCCcccccCCCCCCChhhHHHHHhcCCeeEEEEeecCCCCCh
Q 047464 11 TVDIKTLQRRNAAVGCNGNSFIIRYLINVLNFKPGSNKKINAKNGYNSITSYPMAFESGDIAAAFLVFPRGSPLA 85 (94)
Q Consensus 11 i~~i~dL~~~~~~VG~~~gSf~~~~L~~~~~~~~~~i~~~~~~~~~~s~~~~~~aL~~g~i~A~v~afpkGSpL~ 85 (94)
+.+++||.+ +.+|++--=-.+++|+.+ .|++-.-++.+. +.|-+ -.-|-.||+|+..--|+.|+
T Consensus 58 ~~~~~~l~~-~~rIATkyp~l~~~yf~~-~g~~~~ii~l~G------svE~a---p~~glAD~IvDiv~TG~TLr 121 (163)
T PF01634_consen 58 YKSVEDLKA-GLRIATKYPNLTRRYFAE-KGINVEIIKLSG------SVELA---PPLGLADAIVDIVETGTTLR 121 (163)
T ss_dssp GCCGGGGSS-TEEEEES-HHHHHHHHHH-CT-EEEEEE-SS-------TTHH---HHTTSSSEEEEEESSSHHHH
T ss_pred CCCHHHhcc-CCEEEECCHHHHHHHHHH-cCCcEEEEEccC------Ccccc---CCCCCCCEEEEeccCcHHHH
Confidence 678889986 699999988899999999 888655567777 88864 45788999999555555544
No 66
>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=69.75 E-value=8.3 Score=26.20 Aligned_cols=40 Identities=10% Similarity=0.069 Sum_probs=30.5
Q ss_pred ccHHHHHHHhhCCCCCCcccccCCCCCCChhhHHHHHhcCCeeEEEE
Q 047464 30 SFIIRYLINVLNFKPGSNKKINAKNGYNSITSYPMAFESGDIAAAFL 76 (94)
Q Consensus 30 Sf~~~~L~~~~~~~~~~i~~~~~~~~~~s~~~~~~aL~~g~i~A~v~ 76 (94)
.|+..+|.. .||.--..-.+. +++++.++...-+.|+++.
T Consensus 20 ~iv~~~l~~-~GfeVi~lg~~~------s~e~~v~aa~e~~adii~i 59 (132)
T TIGR00640 20 KVIATAYAD-LGFDVDVGPLFQ------TPEEIARQAVEADVHVVGV 59 (132)
T ss_pred HHHHHHHHh-CCcEEEECCCCC------CHHHHHHHHHHcCCCEEEE
Confidence 377788887 888544445566 8899988888888888887
No 67
>COG2130 Putative NADP-dependent oxidoreductases [General function prediction only]
Probab=69.34 E-value=11 Score=30.11 Aligned_cols=54 Identities=20% Similarity=0.306 Sum_probs=41.9
Q ss_pred ChhHHHhCCCeeeecCCccHHHHHHHhhCCCCCCcccccCCCCCCChhhHHHHHhc---CCeeEEEE
Q 047464 13 DIKTLQRRNAAVGCNGNSFIIRYLINVLNFKPGSNKKINAKNGYNSITSYPMAFES---GDIAAAFL 76 (94)
Q Consensus 13 ~i~dL~~~~~~VG~~~gSf~~~~L~~~~~~~~~~i~~~~~~~~~~s~~~~~~aL~~---g~i~A~v~ 76 (94)
.+..|+. ...||..+|-==.+||.+++||+ ....|. +. ++.++|.. .+||..|+
T Consensus 169 QiAKlkG-~rVVGiaGg~eK~~~l~~~lGfD--~~idyk------~~-d~~~~L~~a~P~GIDvyfe 225 (340)
T COG2130 169 QIAKLKG-CRVVGIAGGAEKCDFLTEELGFD--AGIDYK------AE-DFAQALKEACPKGIDVYFE 225 (340)
T ss_pred HHHHhhC-CeEEEecCCHHHHHHHHHhcCCc--eeeecC------cc-cHHHHHHHHCCCCeEEEEE
Confidence 4555664 46788888877789999999996 677777 54 77777775 88999999
No 68
>PRK11898 prephenate dehydratase; Provisional
Probab=68.97 E-value=9.1 Score=29.20 Aligned_cols=48 Identities=15% Similarity=0.142 Sum_probs=36.7
Q ss_pred eeeec--CCccHHHHHHHhhCC-CCCCcccccCCCCCCChhhHHHHHhcCCeeEEEE
Q 047464 23 AVGCN--GNSFIIRYLINVLNF-KPGSNKKINAKNGYNSITSYPMAFESGDIAAAFL 76 (94)
Q Consensus 23 ~VG~~--~gSf~~~~L~~~~~~-~~~~i~~~~~~~~~~s~~~~~~aL~~g~i~A~v~ 76 (94)
+|+|+ .|||+.......++- ....+..+. |.++.++++.+|.+|..|.
T Consensus 3 ~va~lGp~Gs~s~~Aa~~~~~~~~~~~~~~~~------s~~~v~~av~~~~~d~gvv 53 (283)
T PRK11898 3 KIAYLGPEGTFTEAAALKFFPADGEAELVPYD------SIPDVLDAVEAGEVDYAVV 53 (283)
T ss_pred EEEEECCCCCHHHHHHHHhhccccccceEecC------CHHHHHHHHHcCCCCEEEE
Confidence 47775 489998887773322 124678888 9999999999999997776
No 69
>PRK09861 cytoplasmic membrane lipoprotein-28; Provisional
Probab=68.23 E-value=6.1 Score=29.94 Aligned_cols=48 Identities=10% Similarity=-0.000 Sum_probs=34.2
Q ss_pred CeeeecCCcc------HHHHHHHhhCCCCCCcccccCCCCCCChhhHHHHHhcCCeeEEEE
Q 047464 22 AAVGCNGNSF------IIRYLINVLNFKPGSNKKINAKNGYNSITSYPMAFESGDIAAAFL 76 (94)
Q Consensus 22 ~~VG~~~gSf------~~~~L~~~~~~~~~~i~~~~~~~~~~s~~~~~~aL~~g~i~A~v~ 76 (94)
.+||+..++. +.+++++..|++ -.+..|+ ..-.+..||.+|+||+.+.
T Consensus 34 LkVG~~~~~~~~~~e~a~~~~k~~~G~~-Velv~fs------d~~~~n~AL~~G~ID~n~~ 87 (272)
T PRK09861 34 IKVGVINGAEQDVAEVAKKVAKEKYGLD-VELVGFS------GSLLPNDATNHGELDANVF 87 (272)
T ss_pred EEEEEcCCchHHHHHHHHHHHHHcCCCe-EEEEecC------chhhHHHHHHcCCcceehh
Confidence 6899987755 344554423663 2455677 7777889999999999887
No 70
>PF12974 Phosphonate-bd: ABC transporter, phosphonate, periplasmic substrate-binding protein ; PDB: 3N5L_B 3QUJ_C 3P7I_A 3QK6_A 3S4U_A.
Probab=67.30 E-value=5.8 Score=28.38 Aligned_cols=38 Identities=24% Similarity=0.352 Sum_probs=28.6
Q ss_pred HHHHHHHhhCCCCCCcccccCCCCCCChhhHHHHHhcCCeeEEEE
Q 047464 32 IIRYLINVLNFKPGSNKKINAKNGYNSITSYPMAFESGDIAAAFL 76 (94)
Q Consensus 32 ~~~~L~~~~~~~~~~i~~~~~~~~~~s~~~~~~aL~~g~i~A~v~ 76 (94)
..+||.+.+|.+ -.++.+. +..++.+++++|++|.++.
T Consensus 19 l~~~L~~~~g~~-v~~~~~~------~~~~~~~~l~~g~~D~~~~ 56 (243)
T PF12974_consen 19 LADYLSKQLGVP-VELVPAD------DYAEFIEALRSGEIDLAFM 56 (243)
T ss_dssp HHHHHHHHHTSE-EEEE--S------SHHHHHHHHHTTS-SEEE-
T ss_pred HHHHHHHHhCCC-EEEEEcC------CHHHHHHHHHcCCccEEEE
Confidence 347888888884 4566777 9999999999999999998
No 71
>COG4663 FcbT1 TRAP-type mannitol/chloroaromatic compound transport system, periplasmic component [Secondary metabolites biosynthesis, transport, and catabolism]
Probab=65.99 E-value=2.5 Score=33.75 Aligned_cols=53 Identities=19% Similarity=0.184 Sum_probs=36.2
Q ss_pred CCCCCChhHHHhCCCeeeecCCccHHHHHHHhhCCCCCCcccccCCCCCCChhhHHHHHhcCCeeEEE
Q 047464 8 QPSTVDIKTLQRRNAAVGCNGNSFIIRYLINVLNFKPGSNKKINAKNGYNSITSYPMAFESGDIAAAF 75 (94)
Q Consensus 8 ~~~i~~i~dL~~~~~~VG~~~gSf~~~~L~~~~~~~~~~i~~~~~~~~~~s~~~~~~aL~~g~i~A~v 75 (94)
+..|++++||+.-+.+|+ -|+-+-+.+ +|..+..|.. -|..-||++|.|||+=
T Consensus 167 rKeI~sv~DLkGLKMRI~----G~aG~V~~k-LGv~pq~iag----------Geiy~ALerGtIDAaE 219 (363)
T COG4663 167 RKEINSVEDLKGLKMRIP----GFAGQVMAK-LGVVPQQIAG----------GEIYPALERGTIDAAE 219 (363)
T ss_pred hhhccchhhhccceeecc----ccHHHHHHH-hCCCccccCC----------cceehhhhcccccHHH
Confidence 345899999995444443 466677777 9996555542 3344589999999973
No 72
>cd01422 MGS Methylglyoxal synthase catalyzes the enolization of dihydroxyacetone phosphate (DHAP) to produce methylglyoxal. The first part of the catalytic mechanism is believed to be similar to TIM (triosephosphate isomerase) in that both enzymes utilize DHAP to form an ene-diolate phosphate intermediate. In MGS, the second catalytic step is characterized by the elimination of phosphate and collapse of the enediolate to form methylglyoxal instead of reprotonation to form the isomer glyceraldehyde 3-phosphate, as in TIM. This is the first reaction in the methylglyoxal bypass of the Embden-Myerhoff glycolytic pathway and is believed to provide physiological benefits under non-ideal growth conditions in bacteria.
Probab=65.92 E-value=11 Score=24.86 Aligned_cols=41 Identities=12% Similarity=0.091 Sum_probs=28.0
Q ss_pred HHHHHHHhhCCCCCCcccccCCCCCCChhhHHHHHhcCCeeEEEE
Q 047464 32 IIRYLINVLNFKPGSNKKINAKNGYNSITSYPMAFESGDIAAAFL 76 (94)
Q Consensus 32 ~~~~L~~~~~~~~~~i~~~~~~~~~~s~~~~~~aL~~g~i~A~v~ 76 (94)
..+||++..|++-+.+ ...|.++ -++..+.+++|+||.|+.
T Consensus 36 Ta~~L~~~~Gi~v~~v-k~~~~~g---~~~i~~~i~~g~i~~VIn 76 (115)
T cd01422 36 TGLLIQEATGLTVNRM-KSGPLGG---DQQIGALIAEGEIDAVIF 76 (115)
T ss_pred HHHHHHHhhCCcEEEE-ecCCCCc---hhHHHHHHHcCceeEEEE
Confidence 3467776578864455 4432333 366888999999999998
No 73
>PF12916 DUF3834: Protein of unknown function (DUF3834); InterPro: IPR024533 This family is likely to be related to solute-binding lipo-proteins.; PDB: 3MST_A.
Probab=65.51 E-value=5.5 Score=29.60 Aligned_cols=56 Identities=9% Similarity=0.185 Sum_probs=31.1
Q ss_pred CeeeecCCccHHHHHHHh----hCCCCCCcccccCCCCCCChhhHHHHHhcCCeeEEEE--eecCCCCC
Q 047464 22 AAVGCNGNSFIIRYLINV----LNFKPGSNKKINAKNGYNSITSYPMAFESGDIAAAFL--VFPRGSPL 84 (94)
Q Consensus 22 ~~VG~~~gSf~~~~L~~~----~~~~~~~i~~~~~~~~~~s~~~~~~aL~~g~i~A~v~--afpkGSpL 84 (94)
.++|+-+--.+.++|.+. .|. ...+.-.+ +.++..+.|.+|++|++|. +|.+|--+
T Consensus 69 ~rI~vwRkGsaADvl~Ral~d~~~~-~~EvVytd------D~~~i~~Ml~~g~vdsAVv~~~~~~G~~f 130 (201)
T PF12916_consen 69 PRIAVWRKGSAADVLTRALLDLKGI-KAEVVYTD------DMSEIVKMLNEGEVDSAVVGSEFSKGETF 130 (201)
T ss_dssp SEEEESSTTSHHHHHHHHHHHHH---T-EEEE---------HHHHHHHHHTT-E--EEEETTT---EEH
T ss_pred ceEEEEecccHHHHHHHHHHhhccc-cceeEEec------CHHHHHHHHhcCceeeeeecchhccchhH
Confidence 488887666666655542 222 13466566 9999999999999998888 66666444
No 74
>COG1732 OpuBC Periplasmic glycine betaine/choline-binding (lipo)protein of an ABC-type transport system (osmoprotectant binding protein) [Cell envelope biogenesis, outer membrane]
Probab=64.51 E-value=16 Score=28.69 Aligned_cols=59 Identities=19% Similarity=0.188 Sum_probs=37.8
Q ss_pred CCCChhHHHh-CC-CeeeecCCccHH-----HHHHHhhCCCCCC-cccccCCCCCCChhhHHHHHhcCCeeEEEE
Q 047464 10 STVDIKTLQR-RN-AAVGCNGNSFII-----RYLINVLNFKPGS-NKKINAKNGYNSITSYPMAFESGDIAAAFL 76 (94)
Q Consensus 10 ~i~~i~dL~~-~~-~~VG~~~gSf~~-----~~L~~~~~~~~~~-i~~~~~~~~~~s~~~~~~aL~~g~i~A~v~ 76 (94)
.++++.||.+ .+ .+-|. ...|.. .-|++.+||+-.+ ++..+ +--..+|+.+|.+||+.-
T Consensus 151 ~i~TiSDLak~~~~l~~g~-~~eF~~R~DG~~~l~k~Yg~~~~~~~~~m~-------~gl~y~Al~~g~~d~~~~ 217 (300)
T COG1732 151 NLETISDLAKHSNQLKLGA-DSEFAERADGLPALQKAYGFDFKPDLRTMD-------GGLTYQALKNGTVDAADA 217 (300)
T ss_pred CCccHHHHHHhhhhceecC-ChhhhccccccHHHHHHhCCccCCCceecC-------chHHHHHHHcCCCCeEee
Confidence 4788888885 22 23332 222322 3456668887555 55555 337789999999999877
No 75
>PRK08410 2-hydroxyacid dehydrogenase; Provisional
Probab=63.61 E-value=8.2 Score=29.61 Aligned_cols=28 Identities=25% Similarity=0.352 Sum_probs=22.3
Q ss_pred ChhhHHHHHhcCCeeEEEEeec-----CCCCCh
Q 047464 58 SITSYPMAFESGDIAAAFLVFP-----RGSPLA 85 (94)
Q Consensus 58 s~~~~~~aL~~g~i~A~v~afp-----kGSpL~ 85 (94)
+.++..+||++|.|.|++|+|. .++||.
T Consensus 238 De~AL~~AL~~g~i~AaLDV~~~EP~~~~~pL~ 270 (311)
T PRK08410 238 NEKDLAKALDEKDIYAGLDVLEKEPMEKNHPLL 270 (311)
T ss_pred CHHHHHHHHHcCCeEEEEecCCCCCCCCCChhh
Confidence 4678889999999998899774 456765
No 76
>PRK07377 hypothetical protein; Provisional
Probab=62.41 E-value=11 Score=27.75 Aligned_cols=25 Identities=12% Similarity=0.123 Sum_probs=22.1
Q ss_pred CcccccCCCCCCChhhHHHHHhcCCeeEEEE
Q 047464 46 SNKKINAKNGYNSITSYPMAFESGDIAAAFL 76 (94)
Q Consensus 46 ~i~~~~~~~~~~s~~~~~~aL~~g~i~A~v~ 76 (94)
.+..|. +.++..+||.+|+|+++..
T Consensus 111 Elv~y~------~~~~l~~aL~~~eVh~~c~ 135 (184)
T PRK07377 111 ELVVYP------DLQALEQALRDKEVHAICL 135 (184)
T ss_pred eEEecC------CHHHHHHHHhcCCccEEec
Confidence 356688 9999999999999999987
No 77
>PRK03094 hypothetical protein; Provisional
Probab=62.20 E-value=12 Score=23.87 Aligned_cols=39 Identities=10% Similarity=0.169 Sum_probs=27.6
Q ss_pred CeeeecCC-ccHHHHHHHhhCCCCCCcccccCCCCCCChhhHHHHHhcCCeeEEEE
Q 047464 22 AAVGCNGN-SFIIRYLINVLNFKPGSNKKINAKNGYNSITSYPMAFESGDIAAAFL 76 (94)
Q Consensus 22 ~~VG~~~g-Sf~~~~L~~~~~~~~~~i~~~~~~~~~~s~~~~~~aL~~g~i~A~v~ 76 (94)
++||+-.| |.++++|++ .|+. +..+. +..+ ...+||+|.
T Consensus 2 ~kIaVE~~Ls~i~~~L~~-~GYe---Vv~l~------~~~~------~~~~Da~Vi 41 (80)
T PRK03094 2 AKIGVEQSLTDVQQALKQ-KGYE---VVQLR------SEQD------AQGCDCCVV 41 (80)
T ss_pred CeEEeecCcHHHHHHHHH-CCCE---EEecC------cccc------cCCcCEEEE
Confidence 46888777 788999998 8994 55444 3222 247899988
No 78
>PF03466 LysR_substrate: LysR substrate binding domain; InterPro: IPR005119 The structure of this domain is known and is similar to the periplasmic binding proteins []. This domain is found in members of the LysR family of prokaryotic transcriptional regulatory proteins IPR000847 from INTERPRO which share sequence similarities over approximately 280 residues including a putative helix-turn-helix DNA-binding motif at their N terminus.; PDB: 3ONM_B 3FZJ_J 3FXR_B 3N6T_A 3FXQ_A 3FXU_A 3N6U_A 2QSX_B 3HO7_B 1IZ1_B ....
Probab=61.06 E-value=10 Score=24.79 Aligned_cols=19 Identities=21% Similarity=0.247 Sum_probs=17.0
Q ss_pred ChhhHHHHHhcCCeeEEEE
Q 047464 58 SITSYPMAFESGDIAAAFL 76 (94)
Q Consensus 58 s~~~~~~aL~~g~i~A~v~ 76 (94)
+.++..+.|.+|++|.+|.
T Consensus 43 ~~~~~~~~l~~g~~Dl~i~ 61 (209)
T PF03466_consen 43 DSDELIEALRSGELDLAIT 61 (209)
T ss_dssp SHHHHHHHHHTTSSSEEEE
T ss_pred cchhhhHHHhcccccEEEE
Confidence 4578899999999999999
No 79
>COG0077 PheA Prephenate dehydratase [Amino acid transport and metabolism]
Probab=60.96 E-value=14 Score=28.58 Aligned_cols=46 Identities=13% Similarity=0.146 Sum_probs=35.5
Q ss_pred eeee--cCCccHHHHHHHhhCCCC-CCcccccCCCCCCChhhHHHHHhcCCeeEEEE
Q 047464 23 AVGC--NGNSFIIRYLINVLNFKP-GSNKKINAKNGYNSITSYPMAFESGDIAAAFL 76 (94)
Q Consensus 23 ~VG~--~~gSf~~~~L~~~~~~~~-~~i~~~~~~~~~~s~~~~~~aL~~g~i~A~v~ 76 (94)
+|+| -.|||+.....+. |.. ....++. |++|.++|+++|.+|-.|-
T Consensus 4 ~iayLGP~Gtfs~~Aa~~~--f~~~~~~~p~~------ti~evf~ave~g~aD~gVV 52 (279)
T COG0077 4 KIAYLGPEGTFSEQAARKL--FGSGAELLPCS------TIEDVFKAVENGEADYGVV 52 (279)
T ss_pred eeEEeCCCccHHHHHHHHh--ccccceeccCC------CHHHHHHHHHcCCCceEEE
Confidence 4555 3589999988763 332 3566777 9999999999999998876
No 80
>COG1756 Mra1 Uncharacterized conserved protein [Function unknown]
Probab=60.76 E-value=17 Score=27.52 Aligned_cols=51 Identities=18% Similarity=0.121 Sum_probs=39.5
Q ss_pred cCCccHHHHHHHhhCCCCCCcccccCCCCCCChhhHHHHHhcCCeeEEEEeecCCC
Q 047464 27 NGNSFIIRYLINVLNFKPGSNKKINAKNGYNSITSYPMAFESGDIAAAFLVFPRGS 82 (94)
Q Consensus 27 ~~gSf~~~~L~~~~~~~~~~i~~~~~~~~~~s~~~~~~aL~~g~i~A~v~afpkGS 82 (94)
+......++|.. .+ .....+.++-....+.++...+..+ |..+|++||.|.
T Consensus 134 v~~~~l~d~l~~-~~---~~~ill~e~G~~~~p~~~~~~l~~~-i~v~iG~fp~Gd 184 (223)
T COG1756 134 VEKNPLTDLLPE-NN---KVTILLHEKGELIPPKELISLLLKG-IAVIIGGFPHGD 184 (223)
T ss_pred eecCcHHHhccc-cC---ceEEEEcCCCCccCHHHHHhhhccC-ceEEEeccCCCc
Confidence 344456676665 43 2566788888888999999999888 999999999995
No 81
>COG2185 Sbm Methylmalonyl-CoA mutase, C-terminal domain/subunit (cobalamin-binding) [Lipid metabolism]
Probab=59.33 E-value=21 Score=25.08 Aligned_cols=40 Identities=15% Similarity=0.028 Sum_probs=33.3
Q ss_pred ccHHHHHHHhhCCCCCCcccccCCCCCCChhhHHHHHhcCCeeEEEE
Q 047464 30 SFIIRYLINVLNFKPGSNKKINAKNGYNSITSYPMAFESGDIAAAFL 76 (94)
Q Consensus 30 Sf~~~~L~~~~~~~~~~i~~~~~~~~~~s~~~~~~aL~~g~i~A~v~ 76 (94)
.|+.+.|.+ .||.--..-.+. |++|+.++-....+++++.
T Consensus 30 kvia~~l~d-~GfeVi~~g~~~------tp~e~v~aA~~~dv~vIgv 69 (143)
T COG2185 30 KVIARALAD-AGFEVINLGLFQ------TPEEAVRAAVEEDVDVIGV 69 (143)
T ss_pred HHHHHHHHh-CCceEEecCCcC------CHHHHHHHHHhcCCCEEEE
Confidence 466788888 999765666688 9999999999999998887
No 82
>COG3221 PhnD ABC-type phosphate/phosphonate transport system, periplasmic component [Inorganic ion transport and metabolism]
Probab=58.83 E-value=17 Score=28.20 Aligned_cols=38 Identities=18% Similarity=0.252 Sum_probs=29.1
Q ss_pred HHHHHHHhhCCCCCCcccccCCCCCCChhhHHHHHhcCCeeEEEE
Q 047464 32 IIRYLINVLNFKPGSNKKINAKNGYNSITSYPMAFESGDIAAAFL 76 (94)
Q Consensus 32 ~~~~L~~~~~~~~~~i~~~~~~~~~~s~~~~~~aL~~g~i~A~v~ 76 (94)
..+||.+.+|++ +..|- .++.....++|.+|++|.+.+
T Consensus 57 l~~~L~~~lG~~---V~~~~----a~dy~~vieal~~g~~D~A~~ 94 (299)
T COG3221 57 LADYLEKELGIP---VEFFV----ATDYAAVIEALRAGQVDIAWL 94 (299)
T ss_pred HHHHHHHHhCCc---eEEEe----cccHHHHHHHHhCCCeeEEec
Confidence 346999999995 44433 227788889999999998777
No 83
>PF00060 Lig_chan: Ligand-gated ion channel; InterPro: IPR001320 The ability of synapses to modify their synaptic strength in response to activity is a fundamental property of the nervous system and may be an essential component of learning and memory. There are three classes of ionotropic glutamate receptor, namely NMDA (N-methyl-D-aspartate), AMPA (alpha-amino-3-hydroxy-5-methyl-4-isoxazole-4-propionic acid) and kainate receptors. They are believed to play critical roles in synaptic plasticity. At many synapses in the brain, transient activation of NMDA receptors leads to a persistent modification in the strength of synaptic transmission mediated by AMPA receptors and kainate receptors can act as the induction trigger for long-term changes in synaptic transmission [].; GO: 0004970 ionotropic glutamate receptor activity, 0005234 extracellular-glutamate-gated ion channel activity, 0016020 membrane; PDB: 3FAT_A 3KFM_A 3KEI_A 3EN3_A 3EPE_B 3FAS_A 2F34_A 3C34_B 3S2V_A 3GBB_B ....
Probab=58.04 E-value=2.5 Score=27.67 Aligned_cols=21 Identities=24% Similarity=0.471 Sum_probs=17.5
Q ss_pred CccccccCCCCCChhHHHhCC
Q 047464 1 MLTVSRLQPSTVDIKTLQRRN 21 (94)
Q Consensus 1 mLTV~~l~~~i~~i~dL~~~~ 21 (94)
+||+++.++.|++++||.+++
T Consensus 95 ~Lt~~~~~~~i~sl~dL~~~~ 115 (148)
T PF00060_consen 95 FLTVPKYEPPIDSLEDLANSG 115 (148)
T ss_dssp HHHCHHHTSS-SSHHHHHTHS
T ss_pred HhcccCcCCCCCCHHHHHHCC
Confidence 378999999999999999765
No 84
>COG1832 Predicted CoA-binding protein [General function prediction only]
Probab=57.49 E-value=19 Score=25.38 Aligned_cols=64 Identities=23% Similarity=0.364 Sum_probs=42.0
Q ss_pred CCChhHHHhCCCeeeecCCc--------cHHHHHHHhhCCCCCCcccccCC---------CCCCChhhHHHHHhcCCeeE
Q 047464 11 TVDIKTLQRRNAAVGCNGNS--------FIIRYLINVLNFKPGSNKKINAK---------NGYNSITSYPMAFESGDIAA 73 (94)
Q Consensus 11 i~~i~dL~~~~~~VG~~~gS--------f~~~~L~~~~~~~~~~i~~~~~~---------~~~~s~~~~~~aL~~g~i~A 73 (94)
..++.+..++-+.|++++-| .+..||.+ .|+ ++-+.+|+ --|.|+.|.. ..||.
T Consensus 6 ~~~i~~iL~~~K~IAvVG~S~~P~r~sy~V~kyL~~-~GY---~ViPVNP~~~~~eiLG~k~y~sL~dIp-----e~IDi 76 (140)
T COG1832 6 EEDIAEILKSAKTIAVVGASDKPDRPSYRVAKYLQQ-KGY---RVIPVNPKLAGEEILGEKVYPSLADIP-----EPIDI 76 (140)
T ss_pred HHHHHHHHHhCceEEEEecCCCCCccHHHHHHHHHH-CCC---EEEeeCcccchHHhcCchhhhcHHhCC-----CCCcE
Confidence 34455555557888888766 35689998 898 78888872 3466666544 56774
Q ss_pred EEEeecCCCCC
Q 047464 74 AFLVFPRGSPL 84 (94)
Q Consensus 74 ~v~afpkGSpL 84 (94)
|++|++..-+
T Consensus 77 -VdvFR~~e~~ 86 (140)
T COG1832 77 -VDVFRRSEAA 86 (140)
T ss_pred -EEEecChhhh
Confidence 5577765433
No 85
>PF02142 MGS: MGS-like domain This is a subfamily of this family; InterPro: IPR011607 This domain composes the whole protein of methylglyoxal synthetase and the domain is also found in carbamoyl phosphate synthetase (CPS) where it forms a regulatory domain that binds to the allosteric effector ornithine. The known structures in this domain show a common phosphate binding site []. ; PDB: 4A1O_A 3ZZM_A 1ZCZ_A 1M6V_C 1CS0_C 1C30_E 1C3O_G 1BXR_A 1T36_E 1A9X_A ....
Probab=57.43 E-value=24 Score=22.12 Aligned_cols=54 Identities=11% Similarity=0.097 Sum_probs=30.2
Q ss_pred HHHhCCCeeeecCCccHHHHHHHhhCCCCCCc-ccccCCCCCCChhh----HHHHHhcCCeeEEEE
Q 047464 16 TLQRRNAAVGCNGNSFIIRYLINVLNFKPGSN-KKINAKNGYNSITS----YPMAFESGDIAAAFL 76 (94)
Q Consensus 16 dL~~~~~~VG~~~gSf~~~~L~~~~~~~~~~i-~~~~~~~~~~s~~~----~~~aL~~g~i~A~v~ 76 (94)
.|.+-|..+=.-.|+ .+||++ .|++-.++ .... .....+ ..+.+++|+||.||.
T Consensus 8 ~l~~lG~~i~AT~gT--a~~L~~-~Gi~~~~v~~~~~----~~~~~~g~~~i~~~i~~~~IdlVIn 66 (95)
T PF02142_consen 8 RLAELGFEIYATEGT--AKFLKE-HGIEVTEVVNKIG----EGESPDGRVQIMDLIKNGKIDLVIN 66 (95)
T ss_dssp HHHHTTSEEEEEHHH--HHHHHH-TT--EEECCEEHS----TG-GGTHCHHHHHHHHTTSEEEEEE
T ss_pred HHHHCCCEEEEChHH--HHHHHH-cCCCceeeeeecc----cCccCCchhHHHHHHHcCCeEEEEE
Confidence 445445444333333 488987 99962223 2222 002234 889999999998887
No 86
>COG2107 Predicted periplasmic solute-binding protein [General function prediction only]
Probab=55.72 E-value=16 Score=28.30 Aligned_cols=53 Identities=19% Similarity=0.243 Sum_probs=39.8
Q ss_pred hhHHHhCCCeeeecCCccHHHHHHHhhCCCCCCcccccCCCCCCChhhHHHHHhcCCeeEEEE
Q 047464 14 IKTLQRRNAAVGCNGNSFIIRYLINVLNFKPGSNKKINAKNGYNSITSYPMAFESGDIAAAFL 76 (94)
Q Consensus 14 i~dL~~~~~~VG~~~gSf~~~~L~~~~~~~~~~i~~~~~~~~~~s~~~~~~aL~~g~i~A~v~ 76 (94)
+.+|+ +++|++.+--+..-.|-. +-....++..- ..++...|..+|.|||-+.
T Consensus 90 ~~~l~--~~rvavpG~~TTA~lL~r-l~~p~~~~V~m-------~fdeI~~Avl~G~VDaGvl 142 (272)
T COG2107 90 VKDLK--GKRVAVPGEMTTAALLFR-LAYPKAEIVYM-------PFDEIIPAVLEGKVDAGVL 142 (272)
T ss_pred ccccc--cceEecCCcccHHHHHHH-HhCCCceEEEe-------eHHHHHHHHHcCCCccceE
Confidence 34466 799999998888887777 54554444433 4789999999999999877
No 87
>TIGR01728 SsuA_fam ABC transporter, substrate-binding protein, aliphatic sulfonates family. Members of this family are substrate-binding periplasmic proteins of ABC transporters. This subfamily includes SsuA, a member of a transporter operon needed to obtain sulfur from aliphatic sulfonates. Related proteins outside the scope of this model include taurine (NH2-CH2-CH2-S03H) binding proteins, the probable sulfate ester binding protein AtsR, and the probable aromatic sulfonate binding protein AsfC. All these families make sulfur available when Cys and sulfate levels are low. Please note that phylogenetic analysis by neighbor-joining suggests that a number of sequences belonging to this family have been excluded because of scoring lower than taurine-binding proteins.
Probab=55.28 E-value=14 Score=26.25 Aligned_cols=24 Identities=8% Similarity=0.099 Sum_probs=19.2
Q ss_pred cccccCCCCCCChhhHHHHHhcCCeeEEEE
Q 047464 47 NKKINAKNGYNSITSYPMAFESGDIAAAFL 76 (94)
Q Consensus 47 i~~~~~~~~~~s~~~~~~aL~~g~i~A~v~ 76 (94)
+..++ +..+..++|.+|++|.++.
T Consensus 33 ~~~~~------~~~~~~~~l~~G~~D~~~~ 56 (288)
T TIGR01728 33 WVEFP------AGPPALEALGAGSLDFGYI 56 (288)
T ss_pred EEecC------CCcHHHHHHhcCCcccccc
Confidence 55566 7778899999999999765
No 88
>PRK06034 hypothetical protein; Provisional
Probab=54.61 E-value=23 Score=27.49 Aligned_cols=50 Identities=10% Similarity=-0.043 Sum_probs=39.7
Q ss_pred Cee-eec--CCccHHHHHHHhhCCCCCCcccccCCCCCCChhhHHHHHhcCCeeEEEEee
Q 047464 22 AAV-GCN--GNSFIIRYLINVLNFKPGSNKKINAKNGYNSITSYPMAFESGDIAAAFLVF 78 (94)
Q Consensus 22 ~~V-G~~--~gSf~~~~L~~~~~~~~~~i~~~~~~~~~~s~~~~~~aL~~g~i~A~v~af 78 (94)
..| +|+ .|||+.+...+.+|+. .....+. |.++.++++.+|++|-.|.-+
T Consensus 95 ~~V~a~lG~~gs~s~~AA~~~FG~s-~~~~~~~------s~~dVf~AV~~g~adyGVVPI 147 (279)
T PRK06034 95 FSVHADGSGGEAAMRDSARFHFGFT-VPYVPHF------SAQAVVEAVARSKGDLGLVSL 147 (279)
T ss_pred ceEEEEeCCccHHHHHHHHHHhccc-cCCccCC------CHHHHHHHHHcCCCCEEEEEC
Confidence 558 785 5789999998877764 3455577 999999999999999888743
No 89
>TIGR02706 P_butyryltrans phosphate butyryltransferase. Members of this family are phosphate butyryltransferase, also called phosphotransbutyrylase. In general, this enzyme is found in butyrate-producing anaerobic bacteria, encoded next to the gene for butyrate kinase. Together, these two enzymes represent what may be the less common of two pathways for butyrate production from butyryl-CoA. The alternative is transfer of the CoA group to acetate by butyryl-CoA:acetate CoA transferase. Cutoffs for this model are set such that the homolog from Thermotoga maritima, whose activity on butyryl-CoA is only 30 % of its activity with acetyl-CoA, scores in the zone between trusted and noice cutoffs.
Probab=54.43 E-value=16 Score=27.99 Aligned_cols=46 Identities=9% Similarity=-0.010 Sum_probs=34.8
Q ss_pred ccHHHHHHHhhCCCCCCcccccCCCCCCChhhHHHHHhcCCeeEEEE
Q 047464 30 SFIIRYLINVLNFKPGSNKKINAKNGYNSITSYPMAFESGDIAAAFL 76 (94)
Q Consensus 30 Sf~~~~L~~~~~~~~~~i~~~~~~~~~~s~~~~~~aL~~g~i~A~v~ 76 (94)
.-+++.+.. ++++..++...++++.-.+...+.+.+++|++|++|-
T Consensus 48 ~~I~~~~~~-~~l~~~~ieIi~~~~~~~s~~~a~~lv~~G~aD~~vs 93 (294)
T TIGR02706 48 EKINEIAKK-IGMNLDDVEIVNAPSPKKAALLAVRLVSTGKADMLMK 93 (294)
T ss_pred HHHHHHHHH-cCCCccCcEEECCCCcHHHHHHHHHHHHCCCCCEEEe
Confidence 344566665 6776667777887766667778888999999999997
No 90
>cd08486 PBP2_CbnR The C-terminal substrate binding domain of LysR-type transcriptional regulator, CbnR, involved in the chlorocatechol catabolism, contains the type 2 periplasmic binding fold. This CD represents the substrate binding domain of LysR-type regulator CbnR which is involved in the regulation of chlorocatechol breakdown. The chlorocatechol-degradative pathway is often found in bacteria that can use chlorinated aromatic compounds as carbon and energy sources. CbnR is found in the 3-chlorobenzoate degradative bacterium Ralstonia eutropha NH9 and forms a tetramer. CbnR activates the expression of the cbnABCD genes, which are responsible for the degradation of chlorocatechol converted from 3-chlorobenzoate and are transcribed divergently from cbnR. The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccha
Probab=53.94 E-value=18 Score=23.89 Aligned_cols=19 Identities=16% Similarity=0.181 Sum_probs=16.9
Q ss_pred ChhhHHHHHhcCCeeEEEE
Q 047464 58 SITSYPMAFESGDIAAAFL 76 (94)
Q Consensus 58 s~~~~~~aL~~g~i~A~v~ 76 (94)
+..+..+.|.+|++|++|.
T Consensus 38 ~~~~l~~~l~~g~~D~~~~ 56 (198)
T cd08486 38 TKDEQVEGLLAGTIHVGFS 56 (198)
T ss_pred CHHHHHHHHHcCCceEEEe
Confidence 5678899999999999987
No 91
>COG3181 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=52.18 E-value=76 Score=25.08 Aligned_cols=63 Identities=13% Similarity=0.048 Sum_probs=41.4
Q ss_pred cCCCCCChhHHHh----CCCeeeecCCcc-HH-----HHHHHhhCCCCCCcccccCCCCCCChhhHHHHHhcCCeeEEEE
Q 047464 7 LQPSTVDIKTLQR----RNAAVGCNGNSF-II-----RYLINVLNFKPGSNKKINAKNGYNSITSYPMAFESGDIAAAFL 76 (94)
Q Consensus 7 l~~~i~~i~dL~~----~~~~VG~~~gSf-~~-----~~L~~~~~~~~~~i~~~~~~~~~~s~~~~~~aL~~g~i~A~v~ 76 (94)
-.+..++++||.. +...|-+-+++. .. .-+.+..|++ -+..+|+ .-.+...+|..|+|||.+.
T Consensus 130 ~~s~~~t~~dlv~~~k~~p~~v~~~~~g~Gs~dhl~~~~~~k~~Gi~-~~~Vpy~------g~gea~taLlgg~v~a~~~ 202 (319)
T COG3181 130 ADSPYKTLKDLVAYAKADPGSVIGGGSGLGSADHLAGALFAKAAGIK-ITYVPYK------GGGEALTALLGGHVDAGST 202 (319)
T ss_pred CCCCcccHHHHHHHHHhCCCeEEecCCCCCcHHHHHHHHHHHHhCCc-eeEEeec------CccHHHHHHhcCceeeeec
Confidence 3566788888863 222344444444 11 2223337773 4566777 9999999999999999998
No 92
>COG0111 SerA Phosphoglycerate dehydrogenase and related dehydrogenases [Amino acid transport and metabolism]
Probab=51.72 E-value=13 Score=29.04 Aligned_cols=24 Identities=38% Similarity=0.432 Sum_probs=19.8
Q ss_pred ChhhHHHHHhcCCee-EEEEeecCC
Q 047464 58 SITSYPMAFESGDIA-AAFLVFPRG 81 (94)
Q Consensus 58 s~~~~~~aL~~g~i~-A~v~afpkG 81 (94)
+.+..++||++|.|. |++|+|++-
T Consensus 239 de~aL~~AL~~G~i~gA~lDVf~~E 263 (324)
T COG0111 239 DEDALLAALDSGKIAGAALDVFEEE 263 (324)
T ss_pred cHHHHHHHHHcCCcceEEecCCCCC
Confidence 467888999999999 788888655
No 93
>cd00532 MGS-like MGS-like domain. This domain composes the whole protein of methylglyoxal synthetase, which catalyzes the enolization of dihydroxyacetone phosphate (DHAP) to produce methylglyoxal. The family also includes the C-terminal domain in carbamoyl phosphate synthetase (CPS) where it catalyzes the last phosphorylation of a coaboxyphosphate intermediate to form the product carbamoyl phosphate and may also play a regulatory role. This family also includes inosine monophosphate cyclohydrolase. The known structures in this family show a common phosphate binding site.
Probab=51.39 E-value=55 Score=21.07 Aligned_cols=55 Identities=13% Similarity=0.126 Sum_probs=34.4
Q ss_pred hHHHhCCCeeeecCCccHHHHHHHhhCCCCCCcccccCCCCCCChhhHHHHHhc-CCeeEEEE
Q 047464 15 KTLQRRNAAVGCNGNSFIIRYLINVLNFKPGSNKKINAKNGYNSITSYPMAFES-GDIAAAFL 76 (94)
Q Consensus 15 ~dL~~~~~~VG~~~gSf~~~~L~~~~~~~~~~i~~~~~~~~~~s~~~~~~aL~~-g~i~A~v~ 76 (94)
..|...|..+=+-.| ...||++ .|++-..+...+ +. .-++..+.+++ |+||.++.
T Consensus 19 ~~l~~~G~~i~AT~g--Ta~~L~~-~Gi~~~~v~~~~-~~---g~~~i~~~i~~~g~idlVIn 74 (112)
T cd00532 19 PKLSSDGFPLFATGG--TSRVLAD-AGIPVRAVSKRH-ED---GEPTVDAAIAEKGKFDVVIN 74 (112)
T ss_pred HHHHHCCCEEEECcH--HHHHHHH-cCCceEEEEecC-CC---CCcHHHHHHhCCCCEEEEEE
Confidence 345555666633333 4678888 888644444332 10 12558889999 99999987
No 94
>PRK06487 glycerate dehydrogenase; Provisional
Probab=50.51 E-value=19 Score=27.74 Aligned_cols=29 Identities=31% Similarity=0.377 Sum_probs=22.2
Q ss_pred ChhhHHHHHhcCCee-EEEEee-----cCCCCChH
Q 047464 58 SITSYPMAFESGDIA-AAFLVF-----PRGSPLAL 86 (94)
Q Consensus 58 s~~~~~~aL~~g~i~-A~v~af-----pkGSpL~~ 86 (94)
+.++..+||++|.|. |++|+| |.++||..
T Consensus 239 de~AL~~AL~~g~i~gAaLDVf~~EP~~~~~pl~~ 273 (317)
T PRK06487 239 DEQALADALRSGHLGGAATDVLSVEPPVNGNPLLA 273 (317)
T ss_pred CHHHHHHHHHcCCeeEEEeecCCCCCCCCCCchhh
Confidence 367888999999998 667777 45677763
No 95
>cd08463 PBP2_DntR_like_4 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator similar to DntR, which is involved in the catabolism of dinitrotoluene; contains the type 2 periplasmic binding fold. This CD includes an uncharacterized LysR-type transcriptional regulator similar to DntR, NahR, and LinR, which are involved in the degradation of aromatic compounds. The transcription of the genes encoding enzymes involved in such degradation is regulated and expression of these enzymes is enhanced by inducers, which are either an intermediate in the metabolic pathway or compounds to be degraded. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytra
Probab=49.48 E-value=26 Score=23.38 Aligned_cols=19 Identities=21% Similarity=0.254 Sum_probs=16.3
Q ss_pred ChhhHHHHHhcCCeeEEEE
Q 047464 58 SITSYPMAFESGDIAAAFL 76 (94)
Q Consensus 58 s~~~~~~aL~~g~i~A~v~ 76 (94)
+.++..+.|.+|++|.+|.
T Consensus 38 ~~~~l~~~L~~g~lDl~i~ 56 (203)
T cd08463 38 PDFDYERALASGELDLVIG 56 (203)
T ss_pred cchhHHHHHhcCCeeEEEe
Confidence 3467899999999999996
No 96
>PF03698 UPF0180: Uncharacterised protein family (UPF0180); InterPro: IPR005370 The members of this family are small uncharacterised proteins.
Probab=49.10 E-value=24 Score=22.48 Aligned_cols=39 Identities=8% Similarity=0.124 Sum_probs=27.5
Q ss_pred CeeeecCC-ccHHHHHHHhhCCCCCCcccccCCCCCCChhhHHHHHhcCCeeEEEE
Q 047464 22 AAVGCNGN-SFIIRYLINVLNFKPGSNKKINAKNGYNSITSYPMAFESGDIAAAFL 76 (94)
Q Consensus 22 ~~VG~~~g-Sf~~~~L~~~~~~~~~~i~~~~~~~~~~s~~~~~~aL~~g~i~A~v~ 76 (94)
++||+..| |-++++|.+ .|+ .+..+. +.+ ....+||+|.
T Consensus 2 kkIAVE~~Ls~v~~~L~~-~Gy---eVv~l~------~~~------~~~~~daiVv 41 (80)
T PF03698_consen 2 KKIAVEEGLSNVKEALRE-KGY---EVVDLE------NEQ------DLQNVDAIVV 41 (80)
T ss_pred CeEEecCCchHHHHHHHH-CCC---EEEecC------Ccc------ccCCcCEEEE
Confidence 57888877 788899998 899 455555 322 1236888887
No 97
>cd01424 MGS_CPS_II Methylglyoxal synthase-like domain from type II glutamine-dependent carbamoyl phosphate synthetase (CSP). CSP, a CarA and CarB heterodimer, catalyzes the production of carbamoyl phosphate which is subsequently employed in the metabolic pathways responsible for the synthesis of pyrimidine nucleotides or arginine. The MGS-like domain is the C-terminal domain of CarB and appears to play a regulatory role in CPS function by binding allosteric effector molecules, including UMP and ornithine.
Probab=48.70 E-value=56 Score=20.74 Aligned_cols=55 Identities=13% Similarity=0.135 Sum_probs=34.6
Q ss_pred hHHHhCCCeeeecCCccHHHHHHHhhCCCCCCcccccCCCCCCChhhHHHHHhcCCeeEEEEe
Q 047464 15 KTLQRRNAAVGCNGNSFIIRYLINVLNFKPGSNKKINAKNGYNSITSYPMAFESGDIAAAFLV 77 (94)
Q Consensus 15 ~dL~~~~~~VG~~~gSf~~~~L~~~~~~~~~~i~~~~~~~~~~s~~~~~~aL~~g~i~A~v~a 77 (94)
+.|.+.|..+=.-.| ...||++ .|++-..+.... ..-++..+.+++|++|.++..
T Consensus 20 ~~l~~~G~~l~aT~g--T~~~l~~-~gi~~~~v~~~~-----~~~~~i~~~i~~~~id~vIn~ 74 (110)
T cd01424 20 KRLAELGFKLVATEG--TAKYLQE-AGIPVEVVNKVS-----EGRPNIVDLIKNGEIQLVINT 74 (110)
T ss_pred HHHHHCCCEEEEchH--HHHHHHH-cCCeEEEEeecC-----CCchhHHHHHHcCCeEEEEEC
Confidence 445555666643333 4568888 788533333331 033667888999999999984
No 98
>cd08462 PBP2_NodD The C-terminal substsrate binding domain of NodD family of LysR-type transcriptional regulators that regulates the expression of nodulation (nod) genes; contains the type 2 periplasmic binding fold. The nodulation (nod) genes in soil bacteria play important roles in the development of nodules. nod genes are involved in synthesis of Nod factors that are required for bacterial entry into root hairs. Thirteen nod genes have been identified and are classified into five transcription units: nodD, nodABCIJ, nodFEL, nodMNT, and nodO. NodD is negatively auto-regulates its own expression of nodD gene, while other nod genes are inducible and positively regulated by NodD in the presence of flavonoids released by plant roots. This substrate-binding domain has significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. T
Probab=47.87 E-value=50 Score=21.55 Aligned_cols=17 Identities=12% Similarity=0.153 Sum_probs=15.3
Q ss_pred hhHHHHHhcCCeeEEEE
Q 047464 60 TSYPMAFESGDIAAAFL 76 (94)
Q Consensus 60 ~~~~~aL~~g~i~A~v~ 76 (94)
.+..+.|.+|++|.+|.
T Consensus 38 ~~~~~~l~~g~~D~~i~ 54 (200)
T cd08462 38 DQPHELLERGEVDLLIA 54 (200)
T ss_pred hhHHHHHhcCCeeEEEe
Confidence 38899999999999997
No 99
>PRK12683 transcriptional regulator CysB-like protein; Reviewed
Probab=47.67 E-value=9.1 Score=28.48 Aligned_cols=19 Identities=11% Similarity=0.081 Sum_probs=16.9
Q ss_pred ChhhHHHHHhcCCeeEEEE
Q 047464 58 SITSYPMAFESGDIAAAFL 76 (94)
Q Consensus 58 s~~~~~~aL~~g~i~A~v~ 76 (94)
+.++..+.|.+|++|.++.
T Consensus 130 ~~~~~~~~L~~~~~D~~i~ 148 (309)
T PRK12683 130 SPQEIAEMLLNGEADIGIA 148 (309)
T ss_pred CHHHHHHHHHcCCccEEEe
Confidence 5788899999999999886
No 100
>cd08421 PBP2_LTTR_like_1 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator, contains the type 2 periplasmic binding fold. LysR-transcriptional regulators comprise the largest family of prokaryotic transcription factor. Homologs of some of LTTRs with similar domain organizations are also found in the archaea and eukaryotic organisms. The LTTRs are composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcriptional repressor undergoes a conformational change upon substrate binding which in turn changes the DNA binding affinity of the repressor. The genes controlled by the LTTRs have diverse functi
Probab=47.65 E-value=29 Score=22.33 Aligned_cols=19 Identities=11% Similarity=0.055 Sum_probs=16.2
Q ss_pred ChhhHHHHHhcCCeeEEEE
Q 047464 58 SITSYPMAFESGDIAAAFL 76 (94)
Q Consensus 58 s~~~~~~aL~~g~i~A~v~ 76 (94)
+.++..+.|.+|++|++|.
T Consensus 37 ~~~~~~~~l~~~~~D~~i~ 55 (198)
T cd08421 37 LSADIVRAVAEGRADLGIV 55 (198)
T ss_pred CcHHHHHHHhcCCceEEEE
Confidence 4567788999999999887
No 101
>TIGR03414 ABC_choline_bnd choline ABC transporter, periplasmic binding protein. Partial phylogenetic profiling (PubMed:16930487) vs. the genome property of glycine betaine biosynthesis from choline consistently reveals a member of this ABC transporter periplasmic binding protein as the best match, save for the betaine biosynthesis enzymes themselves. Genomes often carry several paralogs, one encoded together with the permease and ATP-binding components and another encoded next to a choline-sulfatase gene, suggesting that different members of this protein family interact with shared components and give some flexibility in substrate. Of two members from Sinorhizobium meliloti 1021, one designated ChoX has been shown experimentally to bind choline (though not various related compounds such as betaine) and to be required for about 60 % of choline uptake. Members of this protein have an invariant Cys residue near the N-terminus and likely are lipoproteins.
Probab=46.92 E-value=60 Score=24.51 Aligned_cols=60 Identities=8% Similarity=0.015 Sum_probs=37.2
Q ss_pred CCCChhHHHhC-----CCeeeecCCccHHHHHHH-----hhCCCCCCcccccCCCCCCChh----hHHHHHhcCCeeEEE
Q 047464 10 STVDIKTLQRR-----NAAVGCNGNSFIIRYLIN-----VLNFKPGSNKKINAKNGYNSIT----SYPMAFESGDIAAAF 75 (94)
Q Consensus 10 ~i~~i~dL~~~-----~~~VG~~~gSf~~~~L~~-----~~~~~~~~i~~~~~~~~~~s~~----~~~~aL~~g~i~A~v 75 (94)
.|++|+||++. |+..||-.|+.....+.+ .+|++ .++... + |.. +...|+++|+.+++.
T Consensus 105 ~i~sisDL~~~a~~f~g~~~g~~~g~~~~~~~~~~~~~~~ygL~--~~~~~~---~--s~~a~~a~~~~A~~~~e~~v~~ 177 (290)
T TIGR03414 105 GLKSFADIAKFKDKLDGKIYGIEPGNDGNRLIQKMIDKNAFGLG--GFKLVE---S--SEAGMLAQVARAVKRKEWVVFL 177 (290)
T ss_pred CCCCHHHHhhHHHhcCCEEEcccCChhHHHHHHHHHhhccCCCC--CceEee---c--CHHHHHHHHHHHHHCCCCEEEE
Confidence 58999999852 556899888765433322 25553 233332 0 222 235788999998887
Q ss_pred E
Q 047464 76 L 76 (94)
Q Consensus 76 ~ 76 (94)
.
T Consensus 178 ~ 178 (290)
T TIGR03414 178 G 178 (290)
T ss_pred E
Confidence 6
No 102
>TIGR03339 phn_lysR aminoethylphosphonate catabolism associated LysR family transcriptional regulator. This group of sequences represents a number of related clades with numerous examples of members adjacent to operons for the degradation of 2-aminoethylphosphonate (AEP) in Pseudomonas, Ralstonia, Bordetella and Burkholderia species. These are transcriptional regulators of the LysR family which contain a helix-turn-helix (HTH) domain (pfam00126) and a periplasmic substrate-binding protein-like domain (pfam03466).
Probab=46.79 E-value=36 Score=24.12 Aligned_cols=49 Identities=6% Similarity=0.044 Sum_probs=31.4
Q ss_pred CeeeecCCccHHHHHHHhhC-CCCCCcccc-cCCCCCCChhhHHHHHhcCCeeEEEE
Q 047464 22 AAVGCNGNSFIIRYLINVLN-FKPGSNKKI-NAKNGYNSITSYPMAFESGDIAAAFL 76 (94)
Q Consensus 22 ~~VG~~~gSf~~~~L~~~~~-~~~~~i~~~-~~~~~~~s~~~~~~aL~~g~i~A~v~ 76 (94)
.+||+....+....+.+... .+.-++... . +.++..+.|.+|++|.++.
T Consensus 89 l~ig~~~~~~~~~~l~~~~~~~p~v~l~i~~~------~~~~~~~~l~~g~~Dl~i~ 139 (279)
T TIGR03339 89 LRIAATAPYYVLDLVARFRQRYPGIEVSVRIG------NSQEVLQALQSYRVDVAVS 139 (279)
T ss_pred EEEeCchHHHHHHHHHHHHHHCCCcEEEEEEC------CHHHHHHHHHcCCCcEEEE
Confidence 57888754455555554221 222344443 4 5677889999999999996
No 103
>cd08440 PBP2_LTTR_like_4 TThe C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator, contains the type 2 periplasmic binding fold. LysR-transcriptional regulators comprise the largest family of prokaryotic transcription factor. Homologs of some of LTTRs with similar domain organizations are also found in the archaea and eukaryotic organisms. The LTTRs are composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcriptional repressor undergoes a conformational change upon substrate binding which in turn changes the DNA binding affinity of the repressor. The genes controlled by the LTTRs have diverse funct
Probab=46.57 E-value=29 Score=22.02 Aligned_cols=19 Identities=21% Similarity=0.139 Sum_probs=16.0
Q ss_pred ChhhHHHHHhcCCeeEEEE
Q 047464 58 SITSYPMAFESGDIAAAFL 76 (94)
Q Consensus 58 s~~~~~~aL~~g~i~A~v~ 76 (94)
+..+..+.|.+|++|.+|.
T Consensus 37 ~~~~~~~~l~~g~~D~~i~ 55 (197)
T cd08440 37 SAEQVIEAVRSGEVDFGIG 55 (197)
T ss_pred ChHHHHHHHHcCCccEEEE
Confidence 3567788999999999887
No 104
>PRK06932 glycerate dehydrogenase; Provisional
Probab=46.36 E-value=20 Score=27.58 Aligned_cols=28 Identities=36% Similarity=0.456 Sum_probs=21.9
Q ss_pred ChhhHHHHHhcCCee-EEEEee-----cCCCCCh
Q 047464 58 SITSYPMAFESGDIA-AAFLVF-----PRGSPLA 85 (94)
Q Consensus 58 s~~~~~~aL~~g~i~-A~v~af-----pkGSpL~ 85 (94)
+.++..+||++|.|. |+.|+| |.++||.
T Consensus 239 de~AL~~aL~~g~i~gAaLDV~~~EP~~~~~pl~ 272 (314)
T PRK06932 239 DEQALLDALENGKIAGAALDVLVKEPPEKDNPLI 272 (314)
T ss_pred CHHHHHHHHHcCCccEEEEecCCCCCCCCCChhh
Confidence 477888999999997 678888 3457775
No 105
>PF04069 OpuAC: Substrate binding domain of ABC-type glycine betaine transport system; InterPro: IPR007210 This domain is a part of a high affinity multicomponent binding-protein-dependent transport system involved in bacterial osmoregulation. This domain is often fused to the permease component of the transporter complex. It is often found in integral membrane proteins or proteins predicted to be attached to the membrane by a lipid anchor. Glycine betaine is involved in protection from high osmolarity environments for example in Bacillus subtilis []. OpuBC is closely related and involved in choline transport. Choline is necessary for the biosynthesis of glycine betaine []. L-carnitine is important for osmoregulation in Listeria monocytogenes. This domain is found also in proteins binding l-proline (ProX), histidine (HisX) and taurine (TauA).; GO: 0005215 transporter activity, 0005488 binding, 0006810 transport; PDB: 3R6U_A 3TMG_C 3MAM_A 1SW5_C 1SW4_B 1SW1_A 1SW2_A 3O66_A 1R9Q_A 1R9L_A ....
Probab=45.27 E-value=17 Score=26.51 Aligned_cols=36 Identities=19% Similarity=0.083 Sum_probs=29.4
Q ss_pred HHHHHHhhCCCCCCcccccCCCCCCChhhHHHHHhcCCeeEEEE
Q 047464 33 IRYLINVLNFKPGSNKKINAKNGYNSITSYPMAFESGDIAAAFL 76 (94)
Q Consensus 33 ~~~L~~~~~~~~~~i~~~~~~~~~~s~~~~~~aL~~g~i~A~v~ 76 (94)
...|++ .|+ ..++...+ +......+|.+|.||++..
T Consensus 21 ~~~Le~-~G~-~v~~~~~~------~~~~~~~al~~G~iD~~~~ 56 (257)
T PF04069_consen 21 AQLLEA-AGY-VVEVVNLG------STPVIFAALASGDIDIYPE 56 (257)
T ss_dssp HHHHHH-TTE-EEEEEEES------SHHHHHHHHHTTSSSEEEE
T ss_pred HHHHHH-CCC-eEEEecCC------chHHHHHHHHCCCCeEEhh
Confidence 356666 688 56777788 8788999999999999995
No 106
>PLN02928 oxidoreductase family protein
Probab=43.85 E-value=23 Score=27.65 Aligned_cols=28 Identities=25% Similarity=0.297 Sum_probs=21.5
Q ss_pred ChhhHHHHHhcCCee-EEEEee-----cCCCCCh
Q 047464 58 SITSYPMAFESGDIA-AAFLVF-----PRGSPLA 85 (94)
Q Consensus 58 s~~~~~~aL~~g~i~-A~v~af-----pkGSpL~ 85 (94)
+.++.++||++|.|. |++|+| |.++||.
T Consensus 268 de~AL~~AL~~g~i~gAaLDV~~~EP~~~~~pL~ 301 (347)
T PLN02928 268 DYDAVLAALESGHLGGLAIDVAWSEPFDPDDPIL 301 (347)
T ss_pred CHHHHHHHHHcCCeeEEEEccCCCCCCCCCChhh
Confidence 577888999999996 667776 4556664
No 107
>cd08438 PBP2_CidR The C-terminal substrate binding domain of LysR-like transcriptional regulator CidR, contains the type 2 periplasmic binding fold. This CD includes the substrate binding domain of CidR which positively up-regulates the expression of cidABC operon in the presence of acetic acid produced by the metabolism of excess glucose. The CidR affects the control of murein hydrolase activity by enhancing cidABC expression in the presence of acetic acid. Thus, up-regulation of cidABC expression results in increased murein hydrolase activity. This substrate binding domain has significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate
Probab=43.62 E-value=34 Score=21.81 Aligned_cols=19 Identities=11% Similarity=0.111 Sum_probs=16.1
Q ss_pred ChhhHHHHHhcCCeeEEEE
Q 047464 58 SITSYPMAFESGDIAAAFL 76 (94)
Q Consensus 58 s~~~~~~aL~~g~i~A~v~ 76 (94)
+.++..+.|.+|++|.+|.
T Consensus 37 ~~~~~~~~L~~~~~Dl~i~ 55 (197)
T cd08438 37 GGKKVEQAVLNGELDVGIT 55 (197)
T ss_pred CcHHHHHHHHcCCCCEEEE
Confidence 4566778999999999987
No 108
>cd08460 PBP2_DntR_like_1 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator similar to DntR, which is involved in the catabolism of dinitrotoluene; contains the type 2 periplasmic binding fold. This CD includes an uncharacterized LysR-type transcriptional regulator similar to DntR, NahR, and LinR, which are involved in the degradation of aromatic compounds. The transcription of the genes encoding enzymes involved in such degradation is regulated and expression of these enzymes is enhanced by inducers, which are either an intermediate in the metabolic pathway or compounds to be degraded. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytra
Probab=43.56 E-value=57 Score=21.20 Aligned_cols=16 Identities=19% Similarity=0.063 Sum_probs=14.4
Q ss_pred hHHHHHhcCCeeEEEE
Q 047464 61 SYPMAFESGDIAAAFL 76 (94)
Q Consensus 61 ~~~~aL~~g~i~A~v~ 76 (94)
+..+.|.+|++|++|.
T Consensus 39 ~~~~~l~~g~~D~~i~ 54 (200)
T cd08460 39 KDVDALREGRIDLEIG 54 (200)
T ss_pred hHHHHHHCCCccEEEe
Confidence 6788999999999986
No 109
>PLN02245 ATP phosphoribosyl transferase
Probab=43.35 E-value=10 Score=30.88 Aligned_cols=57 Identities=16% Similarity=0.073 Sum_probs=40.3
Q ss_pred CCCChhHHHh-------CCCeeeecCCccHHHHHHHhhCCCCCCc-ccccCCCCCCChhhHHHHHhcCCeeEEEE
Q 047464 10 STVDIKTLQR-------RNAAVGCNGNSFIIRYLINVLNFKPGSN-KKINAKNGYNSITSYPMAFESGDIAAAFL 76 (94)
Q Consensus 10 ~i~~i~dL~~-------~~~~VG~~~gSf~~~~L~~~~~~~~~~i-~~~~~~~~~~s~~~~~~aL~~g~i~A~v~ 76 (94)
.+.+++||.. ..++|++--=-.+++|+.+ .|++.-.+ +.+. +.|- |-.-|-.||+++
T Consensus 178 ~~~s~~dL~g~~~~~~~~~~RIATkYp~ltr~ff~~-~Gv~~v~Iv~l~G------AvE~---AP~lGlADaIvD 242 (403)
T PLN02245 178 NINSLKELAQMPQWTEERPLRVVTGFTYLGPKFMKD-NGFKHVTFSTADG------ALEA---APAMGIADAILD 242 (403)
T ss_pred ccCCHHHhcccccccccCceEEEeCCHHHHHHHHHH-cCCCeEEEEECcC------ceec---ccccCchhhhcc
Confidence 4788899983 1279999888899999998 89953343 3455 5554 445567777777
No 110
>PF01071 GARS_A: Phosphoribosylglycinamide synthetase, ATP-grasp (A) domain; InterPro: IPR020561 Phosphoribosylglycinamide synthetase (6.3.4.13 from EC) (GARS) (phosphoribosylamine glycine ligase) [] catalyses the second step in the de novo biosynthesis of purine. The reaction catalysed by phosphoribosylglycinamide synthetase is the ATP-dependent addition of 5-phosphoribosylamine to glycine to form 5'phosphoribosylglycinamide: ATP + 5-phosphoribosylamine + glycine = ADP + Pi + 5'-phosphoribosylglycinamide In bacteria, GARS is a monofunctional enzyme (encoded by the purD gene). In yeast, GARS is part of a bifunctional enzyme (encoded by the ADE5/7 gene) in conjunction with phosphoribosylformylglycinamidine cyclo-ligase (AIRS) (IPR000728 from INTERPRO). In higher eukaryotes, GARS is part of a trifunctional enzyme in conjunction with AIRS (IPR000728 from INTERPRO) and with phosphoribosylglycinamide formyltransferase (GART) (), forming GARS-AIRS-GART. This entry represents the A-domain of the enzyme, and is related to the ATP-grasp domain of biotin carboxylase/carbamoyl phosphate synthetase.; PDB: 1GSO_A 3LP8_A 2IP4_A 1VKZ_A 2QK4_A 2XD4_A 2XCL_A 3MJF_A 2YRW_A 2YS6_A ....
Probab=43.00 E-value=18 Score=26.46 Aligned_cols=37 Identities=11% Similarity=0.087 Sum_probs=28.7
Q ss_pred ccHHHHHHHhhCCCCCCcccccCCCCCCChhhHHHHHhcCCeeE
Q 047464 30 SFIIRYLINVLNFKPGSNKKINAKNGYNSITSYPMAFESGDIAA 73 (94)
Q Consensus 30 Sf~~~~L~~~~~~~~~~i~~~~~~~~~~s~~~~~~aL~~g~i~A 73 (94)
+|+++|+++ +||+-.+.+.|. +.+++.+.+++-.-..
T Consensus 4 ~faK~fm~~-~~IPTa~~~~f~------~~~~A~~~l~~~~~p~ 40 (194)
T PF01071_consen 4 SFAKEFMKR-YGIPTAKYKVFT------DYEEALEYLEEQGYPY 40 (194)
T ss_dssp HHHHHHHHH-TT-SB--EEEES------SHHHHHHHHHHHSSSE
T ss_pred HHHHHHHHH-cCCCCCCeeEEC------CHHHHHHHHHhcCCCc
Confidence 588999998 999988999999 9999999888655444
No 111
>PRK11480 tauA taurine transporter substrate binding subunit; Provisional
Probab=42.73 E-value=34 Score=25.73 Aligned_cols=49 Identities=20% Similarity=0.135 Sum_probs=33.3
Q ss_pred CCeeeecCCccHHH------HHHHhhCCCCCCcccccCCCCCCChhhHHHHHhcCCeeEEEE
Q 047464 21 NAAVGCNGNSFIIR------YLINVLNFKPGSNKKINAKNGYNSITSYPMAFESGDIAAAFL 76 (94)
Q Consensus 21 ~~~VG~~~gSf~~~------~L~~~~~~~~~~i~~~~~~~~~~s~~~~~~aL~~g~i~A~v~ 76 (94)
..+|||..++-..- ++.+..|++ -.++.+. +..+..++|.+|++|..+.
T Consensus 24 ~v~~~y~~~~~~~~vA~~~g~f~~~~Gl~-Ve~~~~~------~~~~~~~al~~G~~D~a~~ 78 (320)
T PRK11480 24 NVTVAYQTSAEPAKVAQADNTFAKESGAT-VDWRKFD------SGASIVRALASGDVQIGNL 78 (320)
T ss_pred eEEEEecCCCcHHHHHHHcCchHHHcCCe-eEEEEeC------CHHHHHHHHHCCCCCEECc
Confidence 57899987654222 222224553 3466678 8889999999999998754
No 112
>COG4623 Predicted soluble lytic transglycosylase fused to an ABC-type amino acid-binding protein [Cell envelope biogenesis, outer membrane]
Probab=42.28 E-value=36 Score=28.18 Aligned_cols=61 Identities=20% Similarity=0.197 Sum_probs=41.9
Q ss_pred CCCCCChhHHHhCCC-eeeecCCcc----------------HHHHHHHhhCCCCCCcccccCCCCCCChhhHHHHHhcCC
Q 047464 8 QPSTVDIKTLQRRNA-AVGCNGNSF----------------IIRYLINVLNFKPGSNKKINAKNGYNSITSYPMAFESGD 70 (94)
Q Consensus 8 ~~~i~~i~dL~~~~~-~VG~~~gSf----------------~~~~L~~~~~~~~~~i~~~~~~~~~~s~~~~~~aL~~g~ 70 (94)
++.-.+++..++.|. +||+.+.-. ++.|... +|.+ =++.+.+ ++++.+.+|.+|+
T Consensus 10 ~~ee~~l~~Iq~rGvLrV~tinsp~sy~~~~~~p~G~eYelak~Fa~y-LgV~-Lki~~~~------n~dqLf~aL~ng~ 81 (473)
T COG4623 10 QPEENDLAAIQARGVLRVSTINSPLSYFEDKGGPTGLEYELAKAFADY-LGVK-LKIIPAD------NIDQLFDALDNGN 81 (473)
T ss_pred CcccchHHHHHhcCeEEEEeecCccceeccCCCccchhHHHHHHHHHH-hCCe-EEEEecC------CHHHHHHHHhCCC
Confidence 455677888888775 888865421 2234444 7763 2466677 8999999999999
Q ss_pred eeEEEE
Q 047464 71 IAAAFL 76 (94)
Q Consensus 71 i~A~v~ 76 (94)
+|.+--
T Consensus 82 ~DL~Aa 87 (473)
T COG4623 82 ADLAAA 87 (473)
T ss_pred cceecc
Confidence 886643
No 113
>cd08420 PBP2_CysL_like C-terminal substrate binding domain of LysR-type transcriptional regulator CysL, which activates the transcription of the cysJI operon encoding sulfite reductase, contains the type 2 periplasmic binding fold. CysL, also known as YwfK, is a regular of sulfur metabolism in Bacillus subtilis. Sulfur is required for the synthesis of proteins and essential cofactors in all living organism. Sulfur can be assimilated either from inorganic sources (sulfate and thiosulfate), or from organic sources (sulfate esters, sulfamates, and sulfonates). CysL activates the transcription of the cysJI operon encoding sulfite reductase, which reduces sulfite to sulfide. Both cysL mutant and cysJI mutant are unable to grow using sulfate or sulfite as the sulfur source. Like other LysR-type regulators, CysL also negatively regulates its own transcription. In Escherichia coli, three LysR-type activators are involved in the regulation of sulfur metabolism: CysB, Cbl and MetR. The topology
Probab=42.22 E-value=37 Score=21.60 Aligned_cols=19 Identities=11% Similarity=0.200 Sum_probs=16.1
Q ss_pred ChhhHHHHHhcCCeeEEEE
Q 047464 58 SITSYPMAFESGDIAAAFL 76 (94)
Q Consensus 58 s~~~~~~aL~~g~i~A~v~ 76 (94)
+..+..++|.+|++|.+|.
T Consensus 37 ~~~~~~~~l~~g~~D~~i~ 55 (201)
T cd08420 37 NTEEIAERVLDGEIDLGLV 55 (201)
T ss_pred CcHHHHHHHHCCCccEEEe
Confidence 4567788999999999887
No 114
>cd08412 PBP2_PAO1_like The C-terminal substrate-binding domain of putative LysR-type transcriptional regulator PAO1-like, a member of the type 2 periplasmic binding fold protein superfamily. This family includes the C-terminal substrate domain of a putative LysR-type transcriptional regulator from the plant pathogen Pseudomonas aeruginosa PAO1and its closely related homologs. The LysR-type transcriptional regulators (LTTRs) are composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcriptional repressor undergoes a conformational change upon substrate binding which in turn changes the DNA binding affinity of the repressor. The genes controll
Probab=41.98 E-value=39 Score=21.60 Aligned_cols=19 Identities=16% Similarity=0.272 Sum_probs=16.0
Q ss_pred ChhhHHHHHhcCCeeEEEE
Q 047464 58 SITSYPMAFESGDIAAAFL 76 (94)
Q Consensus 58 s~~~~~~aL~~g~i~A~v~ 76 (94)
+.++..+.|.+|++|.+|.
T Consensus 37 ~~~~~~~~l~~~~~D~~i~ 55 (198)
T cd08412 37 NQEELEEGLRSGELDLALT 55 (198)
T ss_pred CHHHHHHHHHcCCCcEEEE
Confidence 4567788999999999987
No 115
>cd05466 PBP2_LTTR_substrate The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily. This model and hierarchy represent the the substrate-binding domain of the LysR-type transcriptional regulators that form the largest family of prokaryotic transcription factor. Homologs of some of LTTRs with similar domain organizations are also found in the archaea and eukaryotic organisms. The LTTRs are composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcriptional repressor undergoes a conformational change upon substrate binding which in turn changes the DNA bin
Probab=41.71 E-value=43 Score=20.82 Aligned_cols=18 Identities=17% Similarity=0.246 Sum_probs=15.4
Q ss_pred hhhHHHHHhcCCeeEEEE
Q 047464 59 ITSYPMAFESGDIAAAFL 76 (94)
Q Consensus 59 ~~~~~~aL~~g~i~A~v~ 76 (94)
.++..+.|.+|++|.+|.
T Consensus 38 ~~~~~~~l~~g~~D~~i~ 55 (197)
T cd05466 38 SSELLEALLEGELDLAIV 55 (197)
T ss_pred hHHHHHHHHcCCceEEEE
Confidence 456788999999999997
No 116
>PRK09189 uroporphyrinogen-III synthase; Validated
Probab=41.44 E-value=58 Score=23.41 Aligned_cols=57 Identities=7% Similarity=-0.099 Sum_probs=37.8
Q ss_pred CCCeeeecCCccHHHHHHHh---hCCCCCCcccccCCCCCCChhhHHHHHhcCCeeEEEE
Q 047464 20 RNAAVGCNGNSFIIRYLINV---LNFKPGSNKKINAKNGYNSITSYPMAFESGDIAAAFL 76 (94)
Q Consensus 20 ~~~~VG~~~gSf~~~~L~~~---~~~~~~~i~~~~~~~~~~s~~~~~~aL~~g~i~A~v~ 76 (94)
.+++|-+..|.-.++.|.+. .|+.-..+..|..+......++..+++.++++|+++.
T Consensus 117 ~~~~vL~~rg~~~r~~l~~~L~~~G~~v~~~~vY~~~~~~~~~~~~~~~l~~~~~d~i~f 176 (240)
T PRK09189 117 PTARLLYLAGRPRAPVFEDRLAAAGIPFRVAECYDMLPVMYSPATLSAILGGAPFDAVLL 176 (240)
T ss_pred CCCcEEEeccCcccchhHHHHHhCCCeeEEEEEEEeecCCCChHHHHHHHhcCCCCEEEE
Confidence 46788888877555444332 5665555666764433344566778889999999988
No 117
>cd08459 PBP2_DntR_NahR_LinR_like The C-terminal substrate binding domain of LysR-type transcriptional regulators that are involved in the catabolism of dinitrotoluene, naphthalene and gamma-hexachlorohexane; contains the type 2 periplasmic binding fold. This CD includes LysR-like bacterial transcriptional regulators, DntR, NahR, and LinR, which are involved in the degradation of aromatic compounds. The transcription of the genes encoding enzymes involved in such degradation is regulated and expression of these enzymes is enhanced by inducers, which are either an intermediate in the metabolic pathway or compounds to be degraded. DntR from Burkholderia species controls genes encoding enzymes for oxidative degradation of the nitro-aromatic compound 2,4-dinitrotoluene. The active form of DntR is homotetrameric, consisting of a dimer of dimers. NahR is a salicylate-dependent transcription activator of the nah and sal operons for naphthalene degradation. Salicylic acid is an intermediate o
Probab=40.68 E-value=37 Score=21.99 Aligned_cols=18 Identities=33% Similarity=0.405 Sum_probs=15.3
Q ss_pred hhhHHHHHhcCCeeEEEE
Q 047464 59 ITSYPMAFESGDIAAAFL 76 (94)
Q Consensus 59 ~~~~~~aL~~g~i~A~v~ 76 (94)
.++..+.|.+|++|++|.
T Consensus 38 ~~~~~~~l~~g~~D~~i~ 55 (201)
T cd08459 38 VDELEEALESGEIDLAIG 55 (201)
T ss_pred ccCHHHHhhCCCceEEEE
Confidence 456778999999999997
No 118
>cd08415 PBP2_LysR_opines_like The C-terminal substrate-domain of LysR-type transcriptional regulators involved in the catabolism of opines and that of related regulators, contains the type 2 periplasmic binding fold. This CD includes the C-terminal substrate-domain of LysR-type transcriptional regulators, OccR and NocR, involved in the catabolism of opines and that of LysR for lysine biosynthesis which clustered together in phylogenetic trees. Opines, such as octopine and nopaline, are low molecular weight compounds found in plant crown gall tumors that are produced by the parasitic bacterium Agrobacterium. There are at least 30 different opines identified so far. Opines are utilized by tumor-colonizing bacteria as a source of carbon, nitrogen, and energy. NocR and OccR belong to the family of LysR-type transcriptional regulators that positively regulates the catabolism of nopaline and octopine, respectively. Both nopaline and octopalin are arginine derivatives. In Agrobacterium tumefa
Probab=40.14 E-value=44 Score=21.35 Aligned_cols=19 Identities=21% Similarity=0.123 Sum_probs=15.9
Q ss_pred ChhhHHHHHhcCCeeEEEE
Q 047464 58 SITSYPMAFESGDIAAAFL 76 (94)
Q Consensus 58 s~~~~~~aL~~g~i~A~v~ 76 (94)
+.++..+.|.+|++|.+|.
T Consensus 37 ~~~~~~~~l~~~~~Dl~i~ 55 (196)
T cd08415 37 SSSTVVEAVLSGQADLGLA 55 (196)
T ss_pred chHHHHHHHHcCCccEEEE
Confidence 4567788999999999997
No 119
>PRK15409 bifunctional glyoxylate/hydroxypyruvate reductase B; Provisional
Probab=39.93 E-value=31 Score=26.74 Aligned_cols=23 Identities=26% Similarity=0.394 Sum_probs=18.5
Q ss_pred ChhhHHHHHhcCCee-EEEEeecC
Q 047464 58 SITSYPMAFESGDIA-AAFLVFPR 80 (94)
Q Consensus 58 s~~~~~~aL~~g~i~-A~v~afpk 80 (94)
+.++..+||++|.|. |+.|+|+.
T Consensus 242 de~AL~~AL~~g~i~gAaLDVf~~ 265 (323)
T PRK15409 242 DENALIAALQKGEIHAAGLDVFEQ 265 (323)
T ss_pred CHHHHHHHHHcCCeeEEEeecCCC
Confidence 477888999999997 66787753
No 120
>PRK07574 formate dehydrogenase; Provisional
Probab=39.92 E-value=27 Score=27.99 Aligned_cols=28 Identities=32% Similarity=0.337 Sum_probs=21.7
Q ss_pred ChhhHHHHHhcCCee-EEEEee-----cCCCCCh
Q 047464 58 SITSYPMAFESGDIA-AAFLVF-----PRGSPLA 85 (94)
Q Consensus 58 s~~~~~~aL~~g~i~-A~v~af-----pkGSpL~ 85 (94)
+.++..+||++|.|. |+.|+| |+++||.
T Consensus 290 De~AL~~AL~sG~i~GAaLDV~~~EPlp~d~pL~ 323 (385)
T PRK07574 290 DRDAVVRALESGHLAGYAGDVWFPQPAPADHPWR 323 (385)
T ss_pred hHHHHHHHHHhCCccEEEEecCCCCCCCCCChHH
Confidence 478888999999997 667876 4566764
No 121
>cd08411 PBP2_OxyR The C-terminal substrate-binding domain of the LysR-type transcriptional regulator OxyR, a member of the type 2 periplasmic binding fold protein superfamily. OxyR senses hydrogen peroxide and is activated through the formation of an intramolecular disulfide bond. The OxyR activation induces the transcription of genes necessary for the bacterial defense against oxidative stress. The OxyR of LysR-type transcriptional regulator family is composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcriptional repressor undergoes a conformational change upon substrate binding which in turn changes the DNA binding affinity of the repre
Probab=39.86 E-value=43 Score=21.60 Aligned_cols=19 Identities=26% Similarity=0.384 Sum_probs=16.2
Q ss_pred ChhhHHHHHhcCCeeEEEE
Q 047464 58 SITSYPMAFESGDIAAAFL 76 (94)
Q Consensus 58 s~~~~~~aL~~g~i~A~v~ 76 (94)
+.++..+.|.+|++|.+|.
T Consensus 38 ~~~~~~~~l~~~~~Dl~i~ 56 (200)
T cd08411 38 QTERLLEKLRSGELDAALL 56 (200)
T ss_pred cHHHHHHHHHcCCccEEEE
Confidence 4577789999999999886
No 122
>PRK00072 hemC porphobilinogen deaminase; Reviewed
Probab=39.80 E-value=33 Score=26.79 Aligned_cols=17 Identities=24% Similarity=0.245 Sum_probs=14.5
Q ss_pred hhHHHHHhcCCeeEEEE
Q 047464 60 TSYPMAFESGDIAAAFL 76 (94)
Q Consensus 60 ~~~~~aL~~g~i~A~v~ 76 (94)
.|.-+||.+|+||.+|+
T Consensus 63 kele~aLl~g~iDiAVH 79 (295)
T PRK00072 63 KELEEALLEGEIDIAVH 79 (295)
T ss_pred HHHHHHHHcCCCCEEEe
Confidence 35557899999999999
No 123
>PF02826 2-Hacid_dh_C: D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain; InterPro: IPR006140 A number of NAD-dependent 2-hydroxyacid dehydrogenases which seem to be specific for the D-isomer of their substrate have been shown to be functionally and structurally related. All contain a glycine-rich region located in the central section of these enzymes, this region corresponds to the NAD-binding domain. The catalytic domain is described in IPR006139 from INTERPRO ; GO: 0016616 oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor, 0048037 cofactor binding, 0055114 oxidation-reduction process; PDB: 3JTM_A 3NAQ_B 3N7U_J 3KB6_B 3GG9_A 1QP8_B 2CUK_C 2W2L_D 2W2K_A 1WWK_A ....
Probab=39.46 E-value=30 Score=24.04 Aligned_cols=24 Identities=42% Similarity=0.394 Sum_probs=18.4
Q ss_pred ChhhHHHHHhcCCee-EEEEeecCC
Q 047464 58 SITSYPMAFESGDIA-AAFLVFPRG 81 (94)
Q Consensus 58 s~~~~~~aL~~g~i~-A~v~afpkG 81 (94)
+.++..+||++|.+. |++|+|+..
T Consensus 133 de~aL~~aL~~g~i~ga~lDV~~~E 157 (178)
T PF02826_consen 133 DEDALLDALESGKIAGAALDVFEPE 157 (178)
T ss_dssp -HHHHHHHHHTTSEEEEEESS-SSS
T ss_pred hhhHHHHHHhhccCceEEEECCCCC
Confidence 577899999999999 677777664
No 124
>cd01423 MGS_CPS_I_III Methylglyoxal synthase-like domain found in pyr1 and URA1-like carbamoyl phosphate synthetases (CPS), including ammonia-dependent CPS Type I, and glutamine-dependent CPS Type III. These are multidomain proteins, in which MGS is the C-terminal domain.
Probab=39.06 E-value=84 Score=20.14 Aligned_cols=59 Identities=10% Similarity=0.070 Sum_probs=34.7
Q ss_pred hHHHhCCCeeeecCCccHHHHHHHhhCCCCCCcccccCCCCCCChhhHHHHHhcCCeeEEEEe
Q 047464 15 KTLQRRNAAVGCNGNSFIIRYLINVLNFKPGSNKKINAKNGYNSITSYPMAFESGDIAAAFLV 77 (94)
Q Consensus 15 ~dL~~~~~~VG~~~gSf~~~~L~~~~~~~~~~i~~~~~~~~~~s~~~~~~aL~~g~i~A~v~a 77 (94)
+-|.+.|..|-.-.| ..+||.+ .|++...+..+. +.+-...+...+.+++|+||.|+..
T Consensus 20 ~~l~~~G~~i~aT~g--Ta~~L~~-~gi~~~~v~~~~-~~~~~~~~~i~~~i~~~~idlVIn~ 78 (116)
T cd01423 20 QKLSKLGYKLYATEG--TADFLLE-NGIPVTPVAWPS-EEPQNDKPSLRELLAEGKIDLVINL 78 (116)
T ss_pred HHHHHCCCEEEEccH--HHHHHHH-cCCCceEeeecc-CCCCCCchhHHHHHHcCCceEEEEC
Confidence 345555677644333 3467876 888544443332 0000012667888999999999984
No 125
>cd08447 PBP2_LTTR_aromatics_like_1 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator similar to regulators involved in the catabolism of aromatic compounds, contains type 2 periplasmic binding fold. This CD represents the substrate binding domain of an uncharacterized LysR-type regulator similar to CbnR which is involved in the regulation of chlorocatechol breakdown. The transcription of the genes encoding enzymes involved in such degradation is regulated and expression of these enzymes is enhanced by inducers, which are either an intermediate in the metabolic pathway or compounds to be degraded. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Ve
Probab=38.94 E-value=48 Score=21.27 Aligned_cols=19 Identities=37% Similarity=0.363 Sum_probs=16.2
Q ss_pred ChhhHHHHHhcCCeeEEEE
Q 047464 58 SITSYPMAFESGDIAAAFL 76 (94)
Q Consensus 58 s~~~~~~aL~~g~i~A~v~ 76 (94)
+.++..+.|.+|++|.+|.
T Consensus 37 ~~~~~~~~l~~g~~D~~i~ 55 (198)
T cd08447 37 VTTDQIEALESGRIDLGLL 55 (198)
T ss_pred CHHHHHHHHHcCCceEEEe
Confidence 4567888999999999987
No 126
>COG0120 RpiA Ribose 5-phosphate isomerase [Carbohydrate transport and metabolism]
Probab=38.78 E-value=47 Score=25.08 Aligned_cols=54 Identities=17% Similarity=0.143 Sum_probs=34.8
Q ss_pred HHhCCCeeeecCCccHHHHHHHhhC--CCC-CCcccccCCCCCCChhhHHHHHhcC----------CeeEEEE
Q 047464 17 LQRRNAAVGCNGNSFIIRYLINVLN--FKP-GSNKKINAKNGYNSITSYPMAFESG----------DIAAAFL 76 (94)
Q Consensus 17 L~~~~~~VG~~~gSf~~~~L~~~~~--~~~-~~i~~~~~~~~~~s~~~~~~aL~~g----------~i~A~v~ 76 (94)
+..+|..||.-.||++..|++. +| ... ..+...+ +|.+....+-+.| .+|.+|+
T Consensus 17 ~v~~gmviGlGTGST~~~fI~~-Lg~~~~~e~~i~~V~-----TS~~t~~l~~~~GI~v~~l~~~~~lDl~iD 83 (227)
T COG0120 17 YVKDGMVIGLGTGSTAAYFIEA-LGRRVKGELDIGGVP-----TSFQTEELARELGIPVSSLNEVDSLDLAID 83 (227)
T ss_pred HhcCCCEEEEcCcHHHHHHHHH-HHHhhccCccEEEEe-----CCHHHHHHHHHcCCeecCccccCccceEee
Confidence 3445899999999999998887 76 222 2566666 2333333333333 4777777
No 127
>TIGR03061 pip_yhgE_Nterm YhgE/Pip N-terminal domain. This family contains the N-terminal domain of a family of multiple membrane-spanning proteins of Gram-positive bacteria. One member was shown to be a host protein essential for phage infection, so many members of this family are called "phage infection protein". A separate model, TIGR03062, represents the conserved C-terminal domain. The domains are separated by regions highly variable in both length and sequence, often containing extended heptad repeats as described in model TIGR03057.
Probab=38.68 E-value=1e+02 Score=21.01 Aligned_cols=23 Identities=13% Similarity=0.190 Sum_probs=19.8
Q ss_pred ChhhHHHHHhcCCeeEEEEeecCC
Q 047464 58 SITSYPMAFESGDIAAAFLVFPRG 81 (94)
Q Consensus 58 s~~~~~~aL~~g~i~A~v~afpkG 81 (94)
+.+++-++|.+|+++|++. +|+|
T Consensus 84 ~~~ea~~~l~~g~~~~~iv-IP~~ 106 (164)
T TIGR03061 84 SAKEAEKGLADGKYYMVIT-IPED 106 (164)
T ss_pred CHHHHHHHhHcCcEEEEEE-ECcc
Confidence 7899999999999999985 5555
No 128
>TIGR03730 tungstate_WtpA tungstate ABC transporter binding protein WtpA. Members of this protein family are tungstate (and, more weakly, molybdate) binding proteins of tungstate(/molybdate) ABC transporters, as first characterized in Pyrococcus furiosus. Model seed members and cutoffs, pending experimental evidence for more distant homologs, were chosen such that this model identifies select archaeal proteins, excluding weaker archaeal and all bacterial homologs. Note that this family is homologous to molybdate transporters, and that at least one other family of tungstate transporter binding protein, TupA, also exists.
Probab=38.07 E-value=23 Score=26.89 Aligned_cols=26 Identities=23% Similarity=0.162 Sum_probs=21.8
Q ss_pred CCcccccCCCCCCChhhHHHHHhcCCeeEEEE
Q 047464 45 GSNKKINAKNGYNSITSYPMAFESGDIAAAFL 76 (94)
Q Consensus 45 ~~i~~~~~~~~~~s~~~~~~aL~~g~i~A~v~ 76 (94)
+++..-. +..+.+..+.+|++|+.|.
T Consensus 176 ~k~~~~~------~v~~~~~~v~sG~aD~g~v 201 (273)
T TIGR03730 176 SKIFIRP------KEVELLSLLESGEIDYAFI 201 (273)
T ss_pred cceeecC------chHhHHHHHHCCCCcEEEE
Confidence 4555555 8999999999999999987
No 129
>cd08467 PBP2_SyrM The C-terminal substrate binding of LysR-type symbiotic regulator SyrM, which activates expression of nodulation gene NodD3, contains the type 2 periplasmic binding fold. Rhizobium is a nitrogen fixing bacteria present in the roots of leguminous plants, which fixes atmospheric nitrogen to the soil. Most Rhizobium species possess multiple nodulation (nod) genes for the development of nodules. For example, Rhizobium meliloti possesses three copies of nodD genes. NodD1 and NodD2 activate nod operons when Rhizobium is exposed to inducers synthesized by the host plant, while NodD3 acts independent of plant inducers and requires the symbiotic regulator SyrM for nod gene expression. SyrM activates the expression of the regulatory nodulation gene nodD3. In turn, NodD3 activates expression of syrM. In addition, SyrM is involved in exopolysaccharide synthesis. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are
Probab=37.98 E-value=39 Score=22.13 Aligned_cols=18 Identities=22% Similarity=0.062 Sum_probs=15.2
Q ss_pred hhhHHHHHhcCCeeEEEE
Q 047464 59 ITSYPMAFESGDIAAAFL 76 (94)
Q Consensus 59 ~~~~~~aL~~g~i~A~v~ 76 (94)
..+..+.|.+|++|.+|.
T Consensus 38 ~~~~~~~l~~g~~D~~i~ 55 (200)
T cd08467 38 DDLAERGLEQGTIDLAVG 55 (200)
T ss_pred cccHHHHhhCCCcCEEEe
Confidence 346788999999999996
No 130
>PRK04148 hypothetical protein; Provisional
Probab=37.40 E-value=51 Score=22.75 Aligned_cols=44 Identities=11% Similarity=-0.080 Sum_probs=32.6
Q ss_pred eeeecCCccHHHHHHHhhCCCCCCcccccCCCCCCChhhHHHHHhcCCeeEEEE
Q 047464 23 AVGCNGNSFIIRYLINVLNFKPGSNKKINAKNGYNSITSYPMAFESGDIAAAFL 76 (94)
Q Consensus 23 ~VG~~~gSf~~~~L~~~~~~~~~~i~~~~~~~~~~s~~~~~~aL~~g~i~A~v~ 76 (94)
-|||-.|.-+...|.+ .|+ .+...+ .-++..+..+...++++++
T Consensus 22 eIG~GfG~~vA~~L~~-~G~---~ViaID------i~~~aV~~a~~~~~~~v~d 65 (134)
T PRK04148 22 ELGIGFYFKVAKKLKE-SGF---DVIVID------INEKAVEKAKKLGLNAFVD 65 (134)
T ss_pred EEEecCCHHHHHHHHH-CCC---EEEEEE------CCHHHHHHHHHhCCeEEEC
Confidence 5788766546677877 787 688787 6677777777777888887
No 131
>cd08425 PBP2_CynR The C-terminal substrate-binding domain of the LysR-type transcriptional regulator CynR, contains the type 2 periplasmic binding fold. CynR is a LysR-like transcriptional regulator of the cyn operon, which encodes genes that allow cyanate to be used as a sole source of nitrogen. The operon includes three genes in the following order: cynT (cyanate permease), cynS (cyanase), and cynX (a protein of unknown function). CynR negatively regulates its own expression independently of cyanate. CynR binds to DNA and induces bending of DNA in the presence or absence of cyanate, but the amount of bending is decreased by cyanate. The CynR of LysR-type transcriptional regulator family is composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding
Probab=37.14 E-value=53 Score=21.10 Aligned_cols=19 Identities=5% Similarity=0.048 Sum_probs=15.8
Q ss_pred ChhhHHHHHhcCCeeEEEE
Q 047464 58 SITSYPMAFESGDIAAAFL 76 (94)
Q Consensus 58 s~~~~~~aL~~g~i~A~v~ 76 (94)
+..+..+.|.+|++|.+|.
T Consensus 38 ~~~~~~~~l~~g~~Dl~i~ 56 (197)
T cd08425 38 PQERIEAALADDRLDLGIA 56 (197)
T ss_pred cHHHHHHHHHcCCccEEEE
Confidence 3466778999999999997
No 132
>cd08445 PBP2_BenM_CatM_CatR The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in benzoate catabolism; contains the type 2 periplasmic binding fold. This CD includes the C-terminal of LysR-type transcription regulators, BenM, CatM, and CatR, which are involved in the benzoate catabolism. The BenM and CatM are paralogs with overlapping functions. BenM responds synergistically to two effectors, benzoate and cis,cis-muconate, to activate expression of the benABCDE operon which is involved in benzoate catabolism, while CatM responses only to muconate. BenM and CatM share high protein sequence identity and bind to the operator-promoter regions that have similar DNA sequences. In Pseudomonas species, phenolic compounds are converted by different enzymes to central intermediates, such as protocatechuate and catechols. Generally, unsubstituted compounds, such as benzoate, are metabolized by an ortho-cleavage pathway. The catBCA operon encodes three enzymes
Probab=36.45 E-value=48 Score=21.65 Aligned_cols=19 Identities=21% Similarity=0.244 Sum_probs=16.4
Q ss_pred ChhhHHHHHhcCCeeEEEE
Q 047464 58 SITSYPMAFESGDIAAAFL 76 (94)
Q Consensus 58 s~~~~~~aL~~g~i~A~v~ 76 (94)
+.++..+.|.+|++|.+|.
T Consensus 38 ~~~~~~~~l~~~~~Dl~i~ 56 (203)
T cd08445 38 TTVQQIEALKEGRIDVGFG 56 (203)
T ss_pred ChHHHHHHHHcCCCcEEEe
Confidence 3678888999999999996
No 133
>PRK11242 DNA-binding transcriptional regulator CynR; Provisional
Probab=36.41 E-value=48 Score=23.88 Aligned_cols=19 Identities=5% Similarity=0.092 Sum_probs=16.5
Q ss_pred ChhhHHHHHhcCCeeEEEE
Q 047464 58 SITSYPMAFESGDIAAAFL 76 (94)
Q Consensus 58 s~~~~~~aL~~g~i~A~v~ 76 (94)
+..+..++|.+|++|.+|.
T Consensus 128 ~~~~~~~~l~~g~~Dl~i~ 146 (296)
T PRK11242 128 SQERIEALLADDELDVGIA 146 (296)
T ss_pred CHHHHHHHHHCCCCcEEEE
Confidence 4577788999999999997
No 134
>PF00107 ADH_zinc_N: Zinc-binding dehydrogenase; InterPro: IPR013149 Alcohol dehydrogenase (1.1.1.1 from EC) (ADH) catalyzes the reversible oxidation of alcohols to their corresponding acetaldehyde or ketone with the concomitant reduction of NAD: alcohol + NAD = aldehyde or ketone + NADH Currently three structurally and catalytically different types of alcohol dehydrogenases are known: Zinc-containing 'long-chain' alcohol dehydrogenases. Insect-type, or 'short-chain' alcohol dehydrogenases. Iron-containing alcohol dehydrogenases. Zinc-containing ADH's [, ] are dimeric or tetrameric enzymes that bind two atoms of zinc per subunit. One of the zinc atom is essential for catalytic activity while the other is not. Both zinc atoms are coordinated by either cysteine or histidine residues; the catalytic zinc is coordinated by two cysteines and one histidine. Zinc-containing ADH's are found in bacteria, mammals, plants, and in fungi. In many species there is more than one isozyme (for example, humans have at least six isozymes, yeast have three, etc.). A number of other zinc-dependent dehydrogenases are closely related to zinc ADH [] and are included in this family. Sorbitol dehydrogenase (1.1.1.14 from EC) L-threonine 3-dehydrogenase (1.1.1.103 from EC) Glutathione-dependent formaldehyde dehydrogenase (1.1.1.284 from EC) Mannitol dehydrogenase (1.1.1.255 from EC) In addition, this family includes NADP-dependent quinone oxidoreductase (1.6.5.5 from EC), an enzyme found in bacteria (gene qor), in yeast and in mammals where, in some species such as rodents, it has been recruited as an eye lens protein and is known as zeta-crystallin []. The sequence of quinone oxidoreductase is distantly related to that other zinc-containing alcohol dehydrogenases and it lacks the zinc-ligand residues. The torpedo fish and mammalian synaptic vesicle membrane protein vat-1 is related to qor. This entry represents the cofactor-binding domain of these enzymes, which is normally found towards the C terminus. Structural studies indicate that it forms a classical Rossman fold that reversibly binds NAD(H) [, , ].; GO: 0008270 zinc ion binding, 0016491 oxidoreductase activity, 0055114 oxidation-reduction process; PDB: 3PI7_A 3COS_D 1VJ1_A 2ZB3_A 1PIW_B 1Q1N_A 1PS0_A 2EER_B 3KRT_A 1ZSY_A ....
Probab=35.83 E-value=56 Score=20.58 Aligned_cols=50 Identities=4% Similarity=0.027 Sum_probs=32.9
Q ss_pred CeeeecCCccHHHHHHHhhCCCCCCcccccCCCCCCChhhHHHHHhcC-CeeEEEEee
Q 047464 22 AAVGCNGNSFIIRYLINVLNFKPGSNKKINAKNGYNSITSYPMAFESG-DIAAAFLVF 78 (94)
Q Consensus 22 ~~VG~~~gSf~~~~L~~~~~~~~~~i~~~~~~~~~~s~~~~~~aL~~g-~i~A~v~af 78 (94)
..|++.....-.+++++ +|.+ .+-.+..+ +..+.++++.+| ++|++|++.
T Consensus 16 ~vi~~~~~~~k~~~~~~-~Ga~--~~~~~~~~----~~~~~i~~~~~~~~~d~vid~~ 66 (130)
T PF00107_consen 16 KVIATDRSEEKLELAKE-LGAD--HVIDYSDD----DFVEQIRELTGGRGVDVVIDCV 66 (130)
T ss_dssp EEEEEESSHHHHHHHHH-TTES--EEEETTTS----SHHHHHHHHTTTSSEEEEEESS
T ss_pred EEEEEECCHHHHHHHHh-hccc--cccccccc----ccccccccccccccceEEEEec
Confidence 34677777777888887 8864 44444411 255666666666 899999943
No 135
>cd08426 PBP2_LTTR_like_5 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator, contains the type 2 periplasmic binding fold. LysR-transcriptional regulators comprise the largest family of prokaryotic transcription factor. Homologs of some of LTTRs with similar domain organizations are also found in the archaea and eukaryotic organisms. The LTTRs are composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcriptional repressor undergoes a conformational change upon substrate binding which in turn changes the DNA binding affinity of the repressor. The genes controlled by the LTTRs have diverse functi
Probab=35.65 E-value=50 Score=21.18 Aligned_cols=19 Identities=21% Similarity=0.141 Sum_probs=16.1
Q ss_pred ChhhHHHHHhcCCeeEEEE
Q 047464 58 SITSYPMAFESGDIAAAFL 76 (94)
Q Consensus 58 s~~~~~~aL~~g~i~A~v~ 76 (94)
+.++..+.|.+|++|++|.
T Consensus 37 ~~~~~~~~l~~~~~D~~i~ 55 (199)
T cd08426 37 STADVLEAVLSGEADIGLA 55 (199)
T ss_pred CcHHHHHHHHCCCccEEEe
Confidence 3467788999999999987
No 136
>cd08466 PBP2_LeuO The C-terminal substrate binding domain of LysR-type transcriptional regulator LeuO, an activator of leucine synthesis operon, contains the type 2 periplasmic binding fold. LeuO, a LysR-type transcriptional regulator, was originally identified as an activator of the leucine synthesis operon (leuABCD). Subsequently, LeuO was found to be not a specific regulator of the leu gene but a global regulator of unrelated various genes. LeuO activates bglGFB (utilization of beta-D-glucoside) and represses cadCBA (lysine decarboxylation) and dsrA (encoding a regulatory small RNA for translational control of rpoS and hns). LeuO also regulates the yjjQ-bglJ operon which coding for a LuxR-type transcription factor. In Salmonella enterica serovar Typhi, LeuO is a positive regulator of ompS1 (encoding an outer membrane), ompS2 (encoding a pathogenicity determinant), and assT, while LeuO represses the expression of OmpX and Tpx. Both osmS1 and osmS2 influence virulence in the mouse mo
Probab=35.56 E-value=55 Score=21.10 Aligned_cols=19 Identities=5% Similarity=-0.094 Sum_probs=15.9
Q ss_pred ChhhHHHHHhcCCeeEEEE
Q 047464 58 SITSYPMAFESGDIAAAFL 76 (94)
Q Consensus 58 s~~~~~~aL~~g~i~A~v~ 76 (94)
+.++..+.|.+|++|.+|.
T Consensus 37 ~~~~~~~~l~~g~~Dl~i~ 55 (200)
T cd08466 37 SEEDLFEDLRLQEVDLVID 55 (200)
T ss_pred chHhHHHHHHcCCccEEEe
Confidence 4557788999999999886
No 137
>cd08413 PBP2_CysB_like The C-terminal substrate domain of LysR-type transcriptional regulators CysB-like contains type 2 periplasmic binding fold. CysB is a transcriptional activator of genes involved in sulfate and thiosulfate transport, sulfate reduction, and cysteine synthesis. In Escherichia coli, the regulation of transcription in response to sulfur source is attributed to two transcriptional regulators, CysB and Cbl. CysB, in association with Cbl, downregulates the expression of ssuEADCB operon which is required for the utilization of sulfur from aliphatic sulfonates, in the presence of cysteine. Also, Cbl and CysB together directly function as transcriptional activators of tauABCD genes, which are required for utilization of taurine as sulfur source for growth. Like many other members of the LTTR family, CysB is composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-bi
Probab=35.26 E-value=51 Score=21.54 Aligned_cols=18 Identities=11% Similarity=0.058 Sum_probs=15.3
Q ss_pred hhhHHHHHhcCCeeEEEE
Q 047464 59 ITSYPMAFESGDIAAAFL 76 (94)
Q Consensus 59 ~~~~~~aL~~g~i~A~v~ 76 (94)
..+..+.|.+|++|.+|.
T Consensus 38 ~~~~~~~l~~g~~D~~i~ 55 (198)
T cd08413 38 PSQIAEMVLKGEADIAIA 55 (198)
T ss_pred HHHHHHHHHcCCCCEEEE
Confidence 456788999999999887
No 138
>PRK07742 phosphate butyryltransferase; Validated
Probab=34.61 E-value=43 Score=25.63 Aligned_cols=45 Identities=13% Similarity=0.102 Sum_probs=30.3
Q ss_pred HHHHHHHhhCC-CCCCcccccCCCCCCChhhHHHHHhcCCeeEEEEe
Q 047464 32 IIRYLINVLNF-KPGSNKKINAKNGYNSITSYPMAFESGDIAAAFLV 77 (94)
Q Consensus 32 ~~~~L~~~~~~-~~~~i~~~~~~~~~~s~~~~~~aL~~g~i~A~v~a 77 (94)
+.+.+.+ +|+ +..++..++|++.-.+...+.+.+++|++|++|-+
T Consensus 52 I~~~~~~-~~l~~~~~~~Ii~~~~~~~s~~~a~~lV~~G~aD~lvsG 97 (299)
T PRK07742 52 IMGMLQE-HGLQTSEHIEIIHAQSSAEAAELAVKAVRNGEADVLMKG 97 (299)
T ss_pred HHHHHHH-CCCCCCCCcEEECCCCHHHHHHHHHHHHHCCCCCEEEEC
Confidence 3455555 666 45567777765543345566788899999999973
No 139
>cd08441 PBP2_MetR The C-terminal substrate binding domain of LysR-type transcriptional regulator metR, which regulates the expression of methionine biosynthetic genes, contains type 2 periplasmic binding fold. MetR, a member of the LysR family, is a positive regulator for the metA, metE, metF, and metH genes. The sulfur-containing amino acid methionine is the universal initiator of protein synthesis in all known organisms and its derivative S-adenosylmethionine (SAM) and autoinducer-2 (AI-2) are involved in various cellular processes. SAM plays a central role as methyl donor in methylation reactions, which are essential for the biosynthesis of phospholipids, proteins, DNA and RNA. The interspecies signaling molecule AI-2 is involved in cell-cell communication process (quorum sensing) and gene regulation in bacteria. Although methionine biosynthetic enzymes and metabolic pathways are well conserved in bacteria, the regulation of methionine biosynthesis involves various regulatory mecha
Probab=34.15 E-value=59 Score=20.97 Aligned_cols=19 Identities=11% Similarity=-0.045 Sum_probs=16.0
Q ss_pred ChhhHHHHHhcCCeeEEEE
Q 047464 58 SITSYPMAFESGDIAAAFL 76 (94)
Q Consensus 58 s~~~~~~aL~~g~i~A~v~ 76 (94)
+..+..+.|.+|++|.++.
T Consensus 37 ~~~~~~~~l~~g~~Dl~i~ 55 (198)
T cd08441 37 FHFDPLPALLRGELDLVIT 55 (198)
T ss_pred CchhHHHHHHcCCceEEEe
Confidence 3457788999999999987
No 140
>cd08448 PBP2_LTTR_aromatics_like_2 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator similar to regulators involved in the catabolism of aromatic compounds, contains type 2 periplasmic binding fold. This CD represents the substrate binding domain of an uncharacterized LysR-type regulator similar to CbnR which is involved in the regulation of chlorocatechol breakdown. The transcription of the genes encoding enzymes involved in such degradation is regulated and expression of these enzymes is enhanced by inducers, which are either an intermediate in the metabolic pathway or compounds to be degraded. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Ve
Probab=33.87 E-value=63 Score=20.54 Aligned_cols=19 Identities=21% Similarity=0.286 Sum_probs=16.2
Q ss_pred ChhhHHHHHhcCCeeEEEE
Q 047464 58 SITSYPMAFESGDIAAAFL 76 (94)
Q Consensus 58 s~~~~~~aL~~g~i~A~v~ 76 (94)
+..+..+.|.+|++|.+|.
T Consensus 37 ~~~~~~~~l~~~~~Di~i~ 55 (197)
T cd08448 37 SSAEQIEALLRGELDLGFV 55 (197)
T ss_pred CHHHHHHHHHcCCcceEEE
Confidence 4567889999999999986
No 141
>COG0715 TauA ABC-type nitrate/sulfonate/bicarbonate transport systems, periplasmic components [Inorganic ion transport and metabolism]
Probab=33.80 E-value=27 Score=25.87 Aligned_cols=35 Identities=9% Similarity=0.060 Sum_probs=28.2
Q ss_pred HHHHhhCCCCCCcccccCCCCCCChhhHHHHHhcCCeeEEEE
Q 047464 35 YLINVLNFKPGSNKKINAKNGYNSITSYPMAFESGDIAAAFL 76 (94)
Q Consensus 35 ~L~~~~~~~~~~i~~~~~~~~~~s~~~~~~aL~~g~i~A~v~ 76 (94)
|.++ .|++.-.++.+. +..+..++|.+|.+|.+++
T Consensus 54 ~f~~-~Gl~~v~~~~~~------~~~~~~~~l~~G~~D~a~~ 88 (335)
T COG0715 54 FFKK-EGLDDVELVEFT------GGAPVLEALAAGALDFAVY 88 (335)
T ss_pred hHhH-hCCCceEEEEcC------CChHHHHHHhcCCcCcccc
Confidence 5555 666445678888 9999999999999999975
No 142
>PRK15469 ghrA bifunctional glyoxylate/hydroxypyruvate reductase A; Provisional
Probab=33.24 E-value=42 Score=25.85 Aligned_cols=23 Identities=30% Similarity=0.408 Sum_probs=18.1
Q ss_pred ChhhHHHHHhcCCee-EEEEeecC
Q 047464 58 SITSYPMAFESGDIA-AAFLVFPR 80 (94)
Q Consensus 58 s~~~~~~aL~~g~i~-A~v~afpk 80 (94)
+.++..+||++|.|. |+.|+|.+
T Consensus 232 de~aL~~aL~~g~i~gaalDVf~~ 255 (312)
T PRK15469 232 VEDDLLAALDSGKVKGAMLDVFSR 255 (312)
T ss_pred CHHHHHHHHhcCCeeeEEecCCCC
Confidence 477888999999997 56777743
No 143
>cd08442 PBP2_YofA_SoxR_like The C-terminal substrate binding domain of LysR-type transcriptional regulators, YofA and SoxR, contains the type 2 periplasmic binding fold. YofA is a LysR-like transcriptional regulator of cell growth in Bacillus subtillis. YofA controls cell viability and the formation of constrictions during cell division. YofaA positively regulates expression of the cell division gene ftsW, and thus is essential for cell viability during stationary-phase growth of Bacillus substilis. YofA shows significant homology to SoxR from Arthrobacter sp. TE1826. SoxR is a negative regulator for the sarcosine oxidase gene soxA. Sarcosine oxidase catalyzes the oxidative demethylation of sarcosine, which is involved in the metabolism of creatine and choline. The topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides
Probab=33.06 E-value=66 Score=20.40 Aligned_cols=19 Identities=21% Similarity=0.312 Sum_probs=15.8
Q ss_pred ChhhHHHHHhcCCeeEEEE
Q 047464 58 SITSYPMAFESGDIAAAFL 76 (94)
Q Consensus 58 s~~~~~~aL~~g~i~A~v~ 76 (94)
+.++..+.|.+|++|.+|.
T Consensus 37 ~~~~~~~~l~~g~~Dl~i~ 55 (193)
T cd08442 37 TTGALIQAVLEGRLDGAFV 55 (193)
T ss_pred CcHHHHHHHHCCCccEEEE
Confidence 4567788899999999887
No 144
>TIGR03427 ABC_peri_uca ABC transporter periplasmic binding protein, urea carboxylase region. Members of this family are ABC transporter periplasmic binding proteins associated with the urea carboxylase/allophanate hydrolase pathway, an alternative to urease for urea degradation. The protein is restricted to bacteria with the pathway, with its gene close to the urea carboxylase and allophanate hydrolase genes. The substrate for this transporter therefore is likely to be urea or a compound from which urea is easily derived.
Probab=32.82 E-value=25 Score=27.20 Aligned_cols=34 Identities=9% Similarity=0.111 Sum_probs=24.7
Q ss_pred HHHHhhCCCCCCcccccCCCCCCChhhHHHHHhcCCeeEEEE
Q 047464 35 YLINVLNFKPGSNKKINAKNGYNSITSYPMAFESGDIAAAFL 76 (94)
Q Consensus 35 ~L~~~~~~~~~~i~~~~~~~~~~s~~~~~~aL~~g~i~A~v~ 76 (94)
++.+ .|++ -++..|+ +..+.+.||.+|.||+...
T Consensus 29 ~l~~-~Gl~-Ve~~~f~------~~~~~l~Al~aG~iD~~~~ 62 (328)
T TIGR03427 29 WADK-YGIT-IEVVQIN------DYVESINQYTAGKFDGCTM 62 (328)
T ss_pred hHHH-cCCe-EEEEECC------ChHHHHHHHHcCCCCEEee
Confidence 3444 4542 2466788 9999999999999997654
No 145
>PRK11119 proX glycine betaine transporter periplasmic subunit; Provisional
Probab=32.69 E-value=88 Score=24.33 Aligned_cols=60 Identities=10% Similarity=0.170 Sum_probs=37.2
Q ss_pred CCCChhHHHh-------------CCCeeeecCCccHHHHHH---HhhCCCCCCcccccCCCCCCC-----hhhHHHHHhc
Q 047464 10 STVDIKTLQR-------------RNAAVGCNGNSFIIRYLI---NVLNFKPGSNKKINAKNGYNS-----ITSYPMAFES 68 (94)
Q Consensus 10 ~i~~i~dL~~-------------~~~~VG~~~gSf~~~~L~---~~~~~~~~~i~~~~~~~~~~s-----~~~~~~aL~~ 68 (94)
.|++++||++ .|..+||..|+.+.+... +.+|.+. .+.... + ..+...|.++
T Consensus 128 gI~Si~DL~~~~~a~~F~~e~~gkg~i~g~~~G~~~~~~~~~~l~~yGL~~-~~~~~~------~S~aam~a~l~~A~~~ 200 (331)
T PRK11119 128 NITNIAQLKDPKIAKLFDTNGDGKADLTGCNPGWGCEAVINHQLKAYGLED-TVTHNQ------GNYAALMADTIARYKE 200 (331)
T ss_pred CCCCHHHhCCcHHHHhcCCCCCCCcceECCCCCccccHHHHHHHHhcCCCc-ceeECC------CCHHHHHHHHHHHHHc
Confidence 4899999982 123899999987766422 2366631 133322 3 2344567778
Q ss_pred CCeeEEEE
Q 047464 69 GDIAAAFL 76 (94)
Q Consensus 69 g~i~A~v~ 76 (94)
|+..++.+
T Consensus 201 ~epiv~~~ 208 (331)
T PRK11119 201 GKPVLYYT 208 (331)
T ss_pred CCCEEEEE
Confidence 88777766
No 146
>TIGR01327 PGDH D-3-phosphoglycerate dehydrogenase. This model represents a long form of D-3-phosphoglycerate dehydrogenase, the serA gene of one pathway of serine biosynthesis. Shorter forms, scoring between trusted and noise cutoff, include SerA from E. coli.
Probab=32.61 E-value=45 Score=27.51 Aligned_cols=28 Identities=32% Similarity=0.451 Sum_probs=21.2
Q ss_pred ChhhHHHHHhcCCee-EEEEeecC----CCCCh
Q 047464 58 SITSYPMAFESGDIA-AAFLVFPR----GSPLA 85 (94)
Q Consensus 58 s~~~~~~aL~~g~i~-A~v~afpk----GSpL~ 85 (94)
+.++..+||++|.|. |++|+|.. ++||.
T Consensus 235 de~aL~~aL~~g~i~gAaLDVf~~EP~~~~pL~ 267 (525)
T TIGR01327 235 DEAALYEALEEGHVRAAALDVFEKEPPTDNPLF 267 (525)
T ss_pred CHHHHHHHHHcCCeeEEEEecCCCCCCCCChhh
Confidence 577888999999997 66788843 45654
No 147
>PLN03139 formate dehydrogenase; Provisional
Probab=32.59 E-value=39 Score=27.09 Aligned_cols=29 Identities=24% Similarity=0.292 Sum_probs=21.9
Q ss_pred ChhhHHHHHhcCCee-EEEEee-----cCCCCChH
Q 047464 58 SITSYPMAFESGDIA-AAFLVF-----PRGSPLAL 86 (94)
Q Consensus 58 s~~~~~~aL~~g~i~-A~v~af-----pkGSpL~~ 86 (94)
+.++..+||++|.|. |+.|+| |+++||..
T Consensus 297 De~AL~~AL~sG~l~GAaLDV~~~EPlp~d~pL~~ 331 (386)
T PLN03139 297 DTQAVADACSSGHIGGYGGDVWYPQPAPKDHPWRY 331 (386)
T ss_pred hHHHHHHHHHcCCceEEEEcCCCCCCCCCCChhhc
Confidence 578888999999998 567766 45667653
No 148
>PF02621 VitK2_biosynth: Menaquinone biosynthesis; InterPro: IPR003773 This entry describes proteins of unknown function, which appear to be putative periplasmic binding proteins.; PDB: 3A3U_A 2CZL_A 1ZBM_A 2NXO_C 2I6E_E.
Probab=32.58 E-value=1.1e+02 Score=22.59 Aligned_cols=55 Identities=22% Similarity=0.219 Sum_probs=34.3
Q ss_pred ChhHHHhCCCeeeecCCccHHHHHHHhhCCCCCCcccccCCCCCCChhhHHHHHhcCCeeEEEE
Q 047464 13 DIKTLQRRNAAVGCNGNSFIIRYLINVLNFKPGSNKKINAKNGYNSITSYPMAFESGDIAAAFL 76 (94)
Q Consensus 13 ~i~dL~~~~~~VG~~~gSf~~~~L~~~~~~~~~~i~~~~~~~~~~s~~~~~~aL~~g~i~A~v~ 76 (94)
.+++|. |++|++.+.|.....|.+.+--+.-..+... .. ++...++.+|. ||++.
T Consensus 86 p~~~l~--~~~ial~~~S~TS~~Llrill~~~~~p~~~~-----~~-~~~~~~~~~~~-da~Ll 140 (251)
T PF02621_consen 86 PIEELD--GKKIALTGESTTSVALLRILLEEFYKPEYVP-----MP-DDIPPAMLAGA-DAALL 140 (251)
T ss_dssp -CCC-T--TSEEEESTTTSHHHHHHHHHHCCTT--EEEE-----E--CGHHHHHHTTS-SEEEE
T ss_pred ChHHcC--CCeEEcCCCCHHHHHHHHHHHHhccccceee-----cC-chhhHHhhcCC-CEEEE
Confidence 356677 5799999999988777765422100001112 13 67788899999 88888
No 149
>cd08452 PBP2_AlsR The C-terminal substrate binding domain of LysR-type trnascriptional regulator AlsR, which regulates acetoin formation under stationary phase growth conditions; contains the type 2 periplasmic binding fold. AlsR is responsible for activating the expression of the acetoin operon (alsSD) in response to inducing signals such as glucose and acetate. Like many other LysR family proteins, AlsR is transcribed divergently from the alsSD operon. The alsS gene encodes acetolactate synthase, an enzyme involved in the production of acetoin in cells of stationary-phase. AlsS catalyzes the conversion of two pyruvate molecules to acetolactate and carbon dioxide. Acetolactate is then converted to acetoin at low pH by acetolactate decarboxylase which encoded by the alsD gene. Acetoin is an important physiological metabolite excreted by many microorganisms grown on glucose or other fermentable carbon sources. This substrate-binding domain shows significant homology to the type 2 perip
Probab=32.46 E-value=65 Score=20.95 Aligned_cols=19 Identities=26% Similarity=0.274 Sum_probs=16.3
Q ss_pred ChhhHHHHHhcCCeeEEEE
Q 047464 58 SITSYPMAFESGDIAAAFL 76 (94)
Q Consensus 58 s~~~~~~aL~~g~i~A~v~ 76 (94)
+..+..+.|.+|++|.+|.
T Consensus 37 ~~~~~~~~l~~~~~Dl~i~ 55 (197)
T cd08452 37 SSPDQVEELLKGRIDIGFL 55 (197)
T ss_pred ChHHHHHHHHCCCccEEEe
Confidence 4577889999999999887
No 150
>PF01379 Porphobil_deam: Porphobilinogen deaminase, dipyromethane cofactor binding domain; InterPro: IPR022417 Tetrapyrroles are large macrocyclic compounds derived from a common biosynthetic pathway []. The end-product, uroporphyrinogen III, is used to synthesise a number of important molecules, including vitamin B12, haem, sirohaem, chlorophyll, coenzyme F430 and phytochromobilin []. The first stage in tetrapyrrole synthesis is the synthesis of 5-aminoaevulinic acid ALA via two possible routes: (1) condensation of succinyl CoA and glycine (C4 pathway) using ALA synthase (2.3.1.37 from EC), or (2) decarboxylation of glutamate (C5 pathway) via three different enzymes, glutamyl-tRNA synthetase (6.1.1.17 from EC) to charge a tRNA with glutamate, glutamyl-tRNA reductase (1.2.1.70 from EC) to reduce glutamyl-tRNA to glutamate-1-semialdehyde (GSA), and GSA aminotransferase (5.4.3.8 from EC) to catalyse a transamination reaction to produce ALA. The second stage is to convert ALA to uroporphyrinogen III, the first macrocyclic tetrapyrrolic structure in the pathway. This is achieved by the action of three enzymes in one common pathway: porphobilinogen (PBG) synthase (or ALA dehydratase, 4.2.1.24 from EC) to condense two ALA molecules to generate porphobilinogen; hydroxymethylbilane synthase (or PBG deaminase, 2.5.1.61 from EC) to polymerise four PBG molecules into preuroporphyrinogen (tetrapyrrole structure); and uroporphyrinogen III synthase (4.2.1.75 from EC) to link two pyrrole units together (rings A and D) to yield uroporphyrinogen III. Uroporphyrinogen III is the first branch point of the pathway. To synthesise cobalamin (vitamin B12), sirohaem, and coenzyme F430, uroporphyrinogen III needs to be converted into precorrin-2 by the action of uroporphyrinogen III methyltransferase (2.1.1.107 from EC). To synthesise haem and chlorophyll, uroporphyrinogen III needs to be decarboxylated into coproporphyrinogen III by the action of uroporphyrinogen III decarboxylase (4.1.1.37 from EC) []. Porphobilinogen deaminase (also known as hydroxymethylbilane synthase, 2.5.1.61 from EC) functions during the second stage of tetrapyrrole biosynthesis. This enzyme catalyses the polymerisation of four PBG molecules into the tetrapyrrole structure, preuroporphyrinogen, with the concomitant release of four molecules of ammonia. This enzyme uses a unique dipyrro-methane cofactor made from two molecules of PBG, which is covalently attached to a cysteine side chain. The tetrapyrrole product is synthesized in an ordered, sequential fashion, by initial attachment of the first pyrrole unit (ring A) to the cofactor, followed by subsequent additions of the remaining pyrrole units (rings B, C, D) to the growing pyrrole chain []. The link between the pyrrole ring and the cofactor is broken once all the pyrroles have been added. This enzyme is folded into three distinct domains that enclose a single, large active site that makes use of an aspartic acid as its one essential catalytic residue, acting as a general acid/base during catalysis [, ]. A deficiency of hydroxymethylbilane synthase is implicated in the neuropathic disease, Acute Intermittent Porphyria (AIP) []. This entry represents the N-terminal domains 1 and 2 of porphobilinogen deaminase, an enzyme involved in tetrapyrrole biosynthesis. The structure of this domain consists of a duplication of two similar intertwined domains with three layers of (a/b/a) each. Porphobilinogen deaminase has a three-domain structure. Domains 1 (N-terminal) and 2 are duplications with the same structure, resembling the transferrins and periplasmic binding proteins. The dipyrromethane cofactor is covalently linked to domain 3 (C-terminal), but is bound by extensive salt-bridges and hydrogen-bonds within the cleft between domains 1 and 2, at a position corresponding to the binding sites for small-molecule ligands in the analogous proteins []. The enzyme has a single catalytic site, and the flexibility between domains is thought to aid elongation of the polypyrrole product in the active-site cleft of the enzyme.; GO: 0033014 tetrapyrrole biosynthetic process; PDB: 1GTK_A 1AH5_A 2YPN_A 1PDA_A 1YPN_A 3EQ1_B 3ECR_A.
Probab=31.97 E-value=40 Score=25.14 Aligned_cols=17 Identities=24% Similarity=0.251 Sum_probs=14.3
Q ss_pred hhHHHHHhcCCeeEEEE
Q 047464 60 TSYPMAFESGDIAAAFL 76 (94)
Q Consensus 60 ~~~~~aL~~g~i~A~v~ 76 (94)
.|.-+||.+|+||.+|+
T Consensus 60 kele~aLl~g~iDiAVH 76 (215)
T PF01379_consen 60 KELEEALLDGEIDIAVH 76 (215)
T ss_dssp HHHHHHHHTTS-SEEEE
T ss_pred HHHHHHHHcCCccEEEe
Confidence 56678999999999999
No 151
>PRK13978 ribose-5-phosphate isomerase A; Provisional
Probab=31.19 E-value=1.1e+02 Score=22.94 Aligned_cols=22 Identities=14% Similarity=0.084 Sum_probs=17.3
Q ss_pred HHHhCCCeeeecCCccHHHHHH
Q 047464 16 TLQRRNAAVGCNGNSFIIRYLI 37 (94)
Q Consensus 16 dL~~~~~~VG~~~gSf~~~~L~ 37 (94)
++.++|..||.-.||++.-+++
T Consensus 17 ~~V~~gmvvGLGTGSTv~~~i~ 38 (228)
T PRK13978 17 SQINGDMTLGIGTGSTMELLLP 38 (228)
T ss_pred HhCCCCCEEEeCchHHHHHHHH
Confidence 3455799999999999985554
No 152
>PRK13243 glyoxylate reductase; Reviewed
Probab=31.19 E-value=46 Score=25.74 Aligned_cols=23 Identities=30% Similarity=0.330 Sum_probs=18.3
Q ss_pred ChhhHHHHHhcCCee-EEEEeecC
Q 047464 58 SITSYPMAFESGDIA-AAFLVFPR 80 (94)
Q Consensus 58 s~~~~~~aL~~g~i~-A~v~afpk 80 (94)
+.++..+||++|.|. |++|+|+.
T Consensus 246 d~~aL~~aL~~g~i~gAaLDV~~~ 269 (333)
T PRK13243 246 DTKALVKALKEGWIAGAGLDVFEE 269 (333)
T ss_pred CHHHHHHHHHcCCeEEEEeccCCC
Confidence 577888999999997 55778844
No 153
>cd08417 PBP2_Nitroaromatics_like The C-terminal substrate binding domain of LysR-type transcriptional regulators that involved in the catabolism of nitroaromatic/naphthalene compounds and that of related regulators; contains the type 2 periplasmic binding fold. This CD includes the C-terminal substrate binding domain of LysR-type transcriptional regulators involved in the catabolism of dinitrotoluene and similar compounds, such as DntR, NahR, and LinR. The transcription of the genes encoding enzymes involved in such degradation is regulated and expression of these enzymes is enhanced by inducers, which are either an intermediate in the metabolic pathway or compounds to be degraded. Also included are related LysR-type regulators clustered together in phylogenetic trees, including NodD, ToxR, LeuO, SyrM, TdcA, and PnbR. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrate
Probab=30.69 E-value=71 Score=20.48 Aligned_cols=19 Identities=32% Similarity=0.302 Sum_probs=16.1
Q ss_pred ChhhHHHHHhcCCeeEEEE
Q 047464 58 SITSYPMAFESGDIAAAFL 76 (94)
Q Consensus 58 s~~~~~~aL~~g~i~A~v~ 76 (94)
+.++..+.|.+|++|.+|.
T Consensus 37 ~~~~~~~~l~~g~~D~~i~ 55 (200)
T cd08417 37 DRDDLEEALESGEIDLAIG 55 (200)
T ss_pred CHHHHHHHHHcCCCCEEEe
Confidence 4457788999999999998
No 154
>PRK00702 ribose-5-phosphate isomerase A; Provisional
Probab=30.17 E-value=91 Score=23.04 Aligned_cols=46 Identities=9% Similarity=-0.047 Sum_probs=29.0
Q ss_pred HHHhCCCeeeecCCccHHHHHHHhhCCCC---CCcccccCCCCCCChhhHHHHHhc
Q 047464 16 TLQRRNAAVGCNGNSFIIRYLINVLNFKP---GSNKKINAKNGYNSITSYPMAFES 68 (94)
Q Consensus 16 dL~~~~~~VG~~~gSf~~~~L~~~~~~~~---~~i~~~~~~~~~~s~~~~~~aL~~ 68 (94)
++.+.|..||...||++..+++. ++-.. -++..++ +-......+.+
T Consensus 16 ~lI~dg~~IgLgsGST~~~l~~~-L~~~~~~~~~itvVt------~S~~~a~~l~~ 64 (220)
T PRK00702 16 EYVEDGMIVGLGTGSTAAYFIDA-LGERVKEGLIIGGVP------TSEASTELAKE 64 (220)
T ss_pred HhCCCCCEEEECCcHHHHHHHHH-HHhhhccCCCEEEEC------CcHHHHHHHHh
Confidence 45567899999999999765554 43211 1356666 55555555554
No 155
>PRK05752 uroporphyrinogen-III synthase; Validated
Probab=30.15 E-value=1.3e+02 Score=21.96 Aligned_cols=57 Identities=5% Similarity=-0.192 Sum_probs=38.1
Q ss_pred CCCeeeecCCccHHHHHHHh---hCCCCCCcccccCCCCCCChhhHHHHHhcCCeeEEEE
Q 047464 20 RNAAVGCNGNSFIIRYLINV---LNFKPGSNKKINAKNGYNSITSYPMAFESGDIAAAFL 76 (94)
Q Consensus 20 ~~~~VG~~~gSf~~~~L~~~---~~~~~~~i~~~~~~~~~~s~~~~~~aL~~g~i~A~v~ 76 (94)
.+.+|-+..|.-.++.|.+. .|+.-..+..|..+..-...++..+.+..|.+|+++.
T Consensus 129 ~~~~vLi~rg~~~r~~L~~~L~~~G~~v~~~~vY~~~~~~~~~~~~~~~~~~~~~d~v~f 188 (255)
T PRK05752 129 PDPRVLIMRGEGGRELLAERLREQGASVDYLELYRRCLPDYPAGTLLQRVEAERLNGLVV 188 (255)
T ss_pred CCCEEEEEccCccHHHHHHHHHHCCCEEeEEEEEeecCCCCCHHHHHHHHHhCCCCEEEE
Confidence 46788888888777666554 4665445555652222223456778889999999988
No 156
>cd08458 PBP2_NocR The C-terminal substrate-domain of LysR-type transcriptional regulator, NocR, involved in the catabolism of nopaline, contains the type 2 periplasmic binding fold. This CD includes the C-terminal substrate-domain of LysR-type transcriptional regulator NocR, which is involved in the catabolism of nopaline. Opines are low molecular weight compounds found in plant crown gall tumors produced by the parasitic bacterium Agrobacterium. There are at least 30 different opines identified so far. Opines are utilized by tumor-colonizing bacteria as a source of carbon, nitrogen, and energy. In Agrobacterium tumefaciens, NocR regulates expression of the divergently transcribed nocB and nocR genes of the nopaline catabolism (noc) region. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, an
Probab=30.15 E-value=71 Score=20.74 Aligned_cols=19 Identities=0% Similarity=-0.202 Sum_probs=15.9
Q ss_pred ChhhHHHHHhcCCeeEEEE
Q 047464 58 SITSYPMAFESGDIAAAFL 76 (94)
Q Consensus 58 s~~~~~~aL~~g~i~A~v~ 76 (94)
+.++..+.|.+|++|.+|.
T Consensus 37 ~~~~~~~~l~~g~~Dl~i~ 55 (196)
T cd08458 37 PSQTVLELVSLQHYDLGIS 55 (196)
T ss_pred ChHHHHHHHHcCCCCEEEE
Confidence 4566788999999999887
No 157
>PF02602 HEM4: Uroporphyrinogen-III synthase HemD; InterPro: IPR003754 Tetrapyrroles are large macrocyclic compounds derived from a common biosynthetic pathway []. The end-product, uroporphyrinogen III, is used to synthesise a number of important molecules, including vitamin B12, haem, sirohaem, chlorophyll, coenzyme F430 and phytochromobilin []. The first stage in tetrapyrrole synthesis is the synthesis of 5-aminoaevulinic acid ALA via two possible routes: (1) condensation of succinyl CoA and glycine (C4 pathway) using ALA synthase (2.3.1.37 from EC), or (2) decarboxylation of glutamate (C5 pathway) via three different enzymes, glutamyl-tRNA synthetase (6.1.1.17 from EC) to charge a tRNA with glutamate, glutamyl-tRNA reductase (1.2.1.70 from EC) to reduce glutamyl-tRNA to glutamate-1-semialdehyde (GSA), and GSA aminotransferase (5.4.3.8 from EC) to catalyse a transamination reaction to produce ALA. The second stage is to convert ALA to uroporphyrinogen III, the first macrocyclic tetrapyrrolic structure in the pathway. This is achieved by the action of three enzymes in one common pathway: porphobilinogen (PBG) synthase (or ALA dehydratase, 4.2.1.24 from EC) to condense two ALA molecules to generate porphobilinogen; hydroxymethylbilane synthase (or PBG deaminase, 2.5.1.61 from EC) to polymerise four PBG molecules into preuroporphyrinogen (tetrapyrrole structure); and uroporphyrinogen III synthase (4.2.1.75 from EC) to link two pyrrole units together (rings A and D) to yield uroporphyrinogen III. Uroporphyrinogen III is the first branch point of the pathway. To synthesise cobalamin (vitamin B12), sirohaem, and coenzyme F430, uroporphyrinogen III needs to be converted into precorrin-2 by the action of uroporphyrinogen III methyltransferase (2.1.1.107 from EC). To synthesise haem and chlorophyll, uroporphyrinogen III needs to be decarboxylated into coproporphyrinogen III by the action of uroporphyrinogen III decarboxylase (4.1.1.37 from EC) []. This entry represents uroporphyrinogen III synthase (4.2.1.75 from EC) which functions during the second stage of tetrapyrrole biosynthesis. This enzyme catalyses the inversion of the final pyrrole unit (ring D) of the linear tetrapyrrole molecule, linking it to the first pyrrole unit (ring A), thereby generating a large macrocyclic structure called uroporphyrinogen III []. The enzyme folds into two alpha/beta domains connected by a beta-ladder, the active site being located between the two domains []. Congenital erythropoietic porphyria (CEP) is an autosomal recessive inborn error of metabolism that results from the markedly deficient activity of uroporphyrinogen III synthase []. ; GO: 0004852 uroporphyrinogen-III synthase activity, 0033014 tetrapyrrole biosynthetic process; PDB: 1WD7_B 1WCX_A 1WCW_A 3D8R_A 3D8T_B 3D8S_A 3D8N_A 3RE1_A 3MW8_A 3P9Z_A ....
Probab=30.05 E-value=19 Score=25.39 Aligned_cols=51 Identities=16% Similarity=0.025 Sum_probs=37.8
Q ss_pred CCCeeeecCCccHHHHHHHhh---CCCCCCcccccCCCCCCC-----hhhHHHHHhcCCeeEEEE
Q 047464 20 RNAAVGCNGNSFIIRYLINVL---NFKPGSNKKINAKNGYNS-----ITSYPMAFESGDIAAAFL 76 (94)
Q Consensus 20 ~~~~VG~~~gSf~~~~L~~~~---~~~~~~i~~~~~~~~~~s-----~~~~~~aL~~g~i~A~v~ 76 (94)
.+.+|-+..|.-...+|.+.+ |+.-..+..|. + .++..+.|..+++|+++.
T Consensus 116 ~~~~vl~~~g~~~~~~l~~~L~~~g~~v~~~~vY~------~~~~~~~~~~~~~l~~~~~~~v~f 174 (231)
T PF02602_consen 116 RGKRVLILRGEGGRPDLPEKLREAGIEVTEVIVYE------TPPEELSPELKEALDRGEIDAVVF 174 (231)
T ss_dssp TTEEEEEEESSSSCHHHHHHHHHTTEEEEEEECEE------EEEHHHHHHHHHHHHHTTTSEEEE
T ss_pred CCCeEEEEcCCCccHHHHHHHHHCCCeEEEEEEee------cccccchHHHHHHHHcCCCCEEEE
Confidence 357899988877766666555 66545666677 6 566778888999999998
No 158
>cd08461 PBP2_DntR_like_3 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator similar to DntR, which is involved in the catabolism of dinitrotoluene; contains the type 2 periplasmic binding fold. This CD includes an uncharacterized LysR-type transcriptional regulator similar to DntR, NahR, and LinR, which are involved in the degradation of aromatic compounds. The transcription of the genes encoding enzymes involved in such degradation is regulated and expression of these enzymes is enhanced by inducers, which are either an intermediate in the metabolic pathway or compounds to be degraded. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytra
Probab=29.79 E-value=60 Score=20.86 Aligned_cols=18 Identities=17% Similarity=0.318 Sum_probs=15.3
Q ss_pred hhhHHHHHhcCCeeEEEE
Q 047464 59 ITSYPMAFESGDIAAAFL 76 (94)
Q Consensus 59 ~~~~~~aL~~g~i~A~v~ 76 (94)
.++..+.|.+|++|.+|.
T Consensus 38 ~~~~~~~l~~~~~Di~i~ 55 (198)
T cd08461 38 SDNLEAQLERGEVDLALT 55 (198)
T ss_pred cccHHHHHhcCCCcEEEe
Confidence 456788999999999886
No 159
>PF13531 SBP_bac_11: Bacterial extracellular solute-binding protein; PDB: 2HXW_B 3FJG_C 3FJM_B 3FJ7_B 3FIR_B 3AXF_C 1WOD_A 1AMF_A 3R26_A 1SBP_A ....
Probab=29.55 E-value=54 Score=22.93 Aligned_cols=60 Identities=13% Similarity=0.071 Sum_probs=37.7
Q ss_pred CCCChhHHHhCCCeeeecCCc---cH---HHHHHHhhC---CC---CCCcc-cccCCCCCCChhhHHHHHhcCCeeEEEE
Q 047464 10 STVDIKTLQRRNAAVGCNGNS---FI---IRYLINVLN---FK---PGSNK-KINAKNGYNSITSYPMAFESGDIAAAFL 76 (94)
Q Consensus 10 ~i~~i~dL~~~~~~VG~~~gS---f~---~~~L~~~~~---~~---~~~i~-~~~~~~~~~s~~~~~~aL~~g~i~A~v~ 76 (94)
.+++++||.+.+.+||+..-+ .+ ..++.+ .| +- .+++. ..+ +..+...++.+|++|+.|.
T Consensus 92 ~~~~~~dL~~~~~~i~~~dP~~s~~g~~~~~~l~~-~g~~~~~~~l~~~~~~~~~------~~~~~~~~v~~g~~d~~~~ 164 (230)
T PF13531_consen 92 GIRSWADLAQPGLRIAIPDPSTSPSGLAALQVLAA-AGGQELLDALQKNIVQYVP------STSQVLSAVASGEADAGIV 164 (230)
T ss_dssp STTCHHHHCSTT--EEEE-TTTTHHHHHHHHHHHH-HTHCHHHHHHHHTEEEEES------SHHHHHHHHHTTSSSEEEE
T ss_pred ccCCHHHHhhccCEEEecCcccChhhHHHHHHHHH-cccHHHHHHHHHhCccccc------chHHHHHHHHcCCCcceee
Confidence 588999999877799997632 11 223333 33 00 11333 344 7889999999999999987
No 160
>cd08419 PBP2_CbbR_RubisCO_like The C-terminal substrate binding of LysR-type transcriptional regulator (CbbR) of RubisCO operon, which is involved in the carbon dioxide fixation, contains the type 2 periplasmic binding fold. CbbR, a LysR-type transcriptional regulator, is required to activate expression of RubisCO, one of two unique enzymes in the Calvin-Benson-Bassham (CBB) cycle pathway. All plants, cyanobacteria, and many autotrophic bacteria use the CBB cycle to fix carbon dioxide. Thus, this cycle plays an essential role in assimilating CO2 into organic carbon on earth. The key CBB cycle enzyme is ribulose 1,5-bisphosphate carboxylase/oxygenase (RubisCO), which catalyzes the actual CO2 fixation reaction. The CO2 concentration affects the expression of RubisCO genes. It has also shown that NADPH enhances the DNA-binding ability of the CbbR. RubisCO is composed of eight large (CbbL) and eight small subunits (CbbS). The topology of this substrate-binding domain is most similar to t
Probab=29.37 E-value=82 Score=19.97 Aligned_cols=19 Identities=5% Similarity=-0.013 Sum_probs=16.1
Q ss_pred ChhhHHHHHhcCCeeEEEE
Q 047464 58 SITSYPMAFESGDIAAAFL 76 (94)
Q Consensus 58 s~~~~~~aL~~g~i~A~v~ 76 (94)
+.++..+.|.+|++|.+|.
T Consensus 36 ~~~~~~~~l~~g~~Dl~i~ 54 (197)
T cd08419 36 NREQVLERLADNEDDLAIM 54 (197)
T ss_pred CHHHHHHHHhcCCccEEEe
Confidence 4566788999999999987
No 161
>TIGR01309 L30P_arch 50S ribosomal protein L30P, archaeal. This model represents the archaeal ribosomal protein similar to longer (~ 250 residue) eukaryotic 60S ribosomal protein L7 and to the much shorter (~ 60 residue) bacterial 50S ribosomal protein L30. Protein naming follows the SwissProt designation as L30P, while the gene symbol rpmD follows TIGR usage.
Probab=29.29 E-value=54 Score=23.13 Aligned_cols=15 Identities=27% Similarity=0.445 Sum_probs=13.2
Q ss_pred ChhhHHHHHhcCCee
Q 047464 58 SITSYPMAFESGDIA 72 (94)
Q Consensus 58 s~~~~~~aL~~g~i~ 72 (94)
+++|..+++.+|+..
T Consensus 90 ~iedl~~~i~~~~~~ 104 (152)
T TIGR01309 90 SVDELAKALVEGEIK 104 (152)
T ss_pred cHHHHHHHHHcCCCC
Confidence 999999999998743
No 162
>PF04796 RepA_C: Plasmid encoded RepA protein; InterPro: IPR006881 This is a family of plasmid encoded proteins involved in plasmid replication. The role of RepA in the replication process is not clearly understood [].
Probab=29.10 E-value=80 Score=22.41 Aligned_cols=35 Identities=11% Similarity=0.189 Sum_probs=23.7
Q ss_pred CccHHHHHHHhhCCCCCCcc--cccCCCCCCChhhHHHHHhcCC
Q 047464 29 NSFIIRYLINVLNFKPGSNK--KINAKNGYNSITSYPMAFESGD 70 (94)
Q Consensus 29 gSf~~~~L~~~~~~~~~~i~--~~~~~~~~~s~~~~~~aL~~g~ 70 (94)
|.+..+||++ +|++...=+ .|. .+-+-+++|.+=.
T Consensus 29 G~S~~~flr~-lG~~~tGG~~g~~~------~lreQ~~rL~~~~ 65 (161)
T PF04796_consen 29 GRSLSEFLRR-LGLSPTGGRRGTIT------RLREQMERLFACR 65 (161)
T ss_pred ccCHHHHHHH-hCCCCCCCCcccHH------HHHHHHHHHHhhe
Confidence 5777889988 999742222 344 7888888886533
No 163
>PF01795 Methyltransf_5: MraW methylase family; InterPro: IPR002903 This is a family of S-adenosyl-L-methionine-dependent methyltransferases, which are found primarily, though not exclusively, in bacteria. The Escherichia coli protein is essential and has been linked to peptidoglycan biosynthesis [, ].; GO: 0008168 methyltransferase activity; PDB: 1N2X_A 1M6Y_A 1WG8_A 3TKA_A.
Probab=28.83 E-value=79 Score=24.82 Aligned_cols=54 Identities=7% Similarity=0.119 Sum_probs=35.9
Q ss_pred CCeeeecCCccHHHHHHHhhCCCCCCcccccCCCCCCChhhHHHHH-hcCCeeEEEE
Q 047464 21 NAAVGCNGNSFIIRYLINVLNFKPGSNKKINAKNGYNSITSYPMAF-ESGDIAAAFL 76 (94)
Q Consensus 21 ~~~VG~~~gSf~~~~L~~~~~~~~~~i~~~~~~~~~~s~~~~~~aL-~~g~i~A~v~ 76 (94)
+..+|+.....+..+..+.+.--..++..+. ..|....+++..+ .-+++|+++.
T Consensus 45 ~~li~~DrD~~a~~~a~~~l~~~~~r~~~~~--~~F~~l~~~l~~~~~~~~~dgiL~ 99 (310)
T PF01795_consen 45 GRLIGIDRDPEALERAKERLKKFDDRFIFIH--GNFSNLDEYLKELNGINKVDGILF 99 (310)
T ss_dssp -EEEEEES-HHHHHHHHCCTCCCCTTEEEEE--S-GGGHHHHHHHTTTTS-EEEEEE
T ss_pred CeEEEecCCHHHHHHHHHHHhhccceEEEEe--ccHHHHHHHHHHccCCCccCEEEE
Confidence 7899999999999888765543244555433 2233788888887 6678999998
No 164
>cd08416 PBP2_MdcR The C-terminal substrate-binding domian of LysR-type transcriptional regulator MdcR, which involved in the malonate catabolism contains the type 2 periplasmic binding fold. This family includes the C-terminal substrate binding domain of LysR-type transcriptional regulator (LTTR) MdcR that controls the expression of the malonate decarboxylase (mdc) genes. Like other members of the LTTRs, MdcR is a positive regulatory protein for its target promoter and composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins (PBP2). The PBP2 are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these dom
Probab=28.68 E-value=81 Score=20.18 Aligned_cols=18 Identities=11% Similarity=0.272 Sum_probs=14.7
Q ss_pred hhhHHHHHhcCCeeEEEE
Q 047464 59 ITSYPMAFESGDIAAAFL 76 (94)
Q Consensus 59 ~~~~~~aL~~g~i~A~v~ 76 (94)
..+..+.|.+|++|+++.
T Consensus 38 ~~~~~~~l~~~~~Dl~i~ 55 (199)
T cd08416 38 NKDLLKKLKDGELDAILV 55 (199)
T ss_pred cHHHHHHHhCCCCCEEEE
Confidence 445678899999999996
No 165
>COG0725 ModA ABC-type molybdate transport system, periplasmic component [Inorganic ion transport and metabolism]
Probab=28.39 E-value=1.3e+02 Score=22.54 Aligned_cols=59 Identities=12% Similarity=0.115 Sum_probs=42.9
Q ss_pred CCChhHHHh-CCCeeeecC------CccHHHHHHHhhCCCCC---CcccccCCCCCCChhhHHHHHhcCCeeEEEE
Q 047464 11 TVDIKTLQR-RNAAVGCNG------NSFIIRYLINVLNFKPG---SNKKINAKNGYNSITSYPMAFESGDIAAAFL 76 (94)
Q Consensus 11 i~~i~dL~~-~~~~VG~~~------gSf~~~~L~~~~~~~~~---~i~~~~~~~~~~s~~~~~~aL~~g~i~A~v~ 76 (94)
+.++++|.. .+.++|.-. |-.+.+.|+. +|+-.. ++..-+ +..+.+.-+.+|++|+.|-
T Consensus 124 ~~~~~~l~~~~~~~lai~~p~~~P~G~ya~~~l~~-~g~~~~~~~k~v~~~------~v~~~l~~V~~G~ad~g~v 192 (258)
T COG0725 124 IESLEDLLERPDVRLAIGDPKTVPAGKYAKEALEL-LGLWYTLKDKLVLAT------NVRQALAYVETGEADAGFV 192 (258)
T ss_pred cccHHHHhcCcCcEEEecCCCCCCchHHHHHHHHH-hchhhhccccEEecC------cHHHHHHHHHcCCCCeEEE
Confidence 344778886 467777755 6677777877 777522 445556 8888999999999999886
No 166
>cd00494 HMBS Hydroxymethylbilane synthase (HMBS), also known as porphobilinogen deaminase (PBGD), is an intermediate enzyme in the biosynthetic pathway of tetrapyrrolic ring systems, such as heme, chlorophylls, and vitamin B12. HMBS catalyzes the conversion of porphobilinogen (PBG) into hydroxymethylbilane (HMB). HMBS consists of three domains, and is believed to bind substrate through a hinge-bending motion of domains I and II. HMBS is found in all organisms except viruses.
Probab=28.38 E-value=65 Score=25.10 Aligned_cols=16 Identities=25% Similarity=0.264 Sum_probs=14.1
Q ss_pred hHHHHHhcCCeeEEEE
Q 047464 61 SYPMAFESGDIAAAFL 76 (94)
Q Consensus 61 ~~~~aL~~g~i~A~v~ 76 (94)
|.-+||.+|+||.+|+
T Consensus 60 ele~aLl~g~iDiAVH 75 (292)
T cd00494 60 ELEEALLNGEIDLAVH 75 (292)
T ss_pred HHHHHHHcCCCCEEEe
Confidence 5567999999999999
No 167
>PLN02384 ribose-5-phosphate isomerase
Probab=28.30 E-value=1.3e+02 Score=23.19 Aligned_cols=18 Identities=11% Similarity=-0.003 Sum_probs=15.3
Q ss_pred CCCeeeecCCccHHHHHH
Q 047464 20 RNAAVGCNGNSFIIRYLI 37 (94)
Q Consensus 20 ~~~~VG~~~gSf~~~~L~ 37 (94)
+|..||.-.||++.-+++
T Consensus 49 ~gmvVGLGTGSTv~~~I~ 66 (264)
T PLN02384 49 SGMVLGLGTGSTAKHAVD 66 (264)
T ss_pred CCCEEEecchHHHHHHHH
Confidence 799999999999885554
No 168
>cd08446 PBP2_Chlorocatechol The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in the chlorocatechol catabolism, contains the type 2 periplasmic binding fold. This CD includes the substrate binding domain of LysR-type regulators CbnR, ClcR and TfdR, which are involved in the regulation of chlorocatechol breakdown. The chlorocatechol-degradative pathway is often found in bacteria that can use chlorinated aromatic compounds as carbon and energy sources. CbnR is found in the 3-chlorobenzoate degradative bacterium Ralstonia eutropha NH9 and forms a tetramer. CbnR activates the expression of the cbnABCD genes, which are responsible for the degradation of chlorocatechol converted from 3-chlorobenzoate and are transcribed divergently from cbnR. In soil bacterium Pseudomonas putida, the 3-chlorocatechol-degradative pathway is encoded by clcABD operon, which requires the divergently transcribed clcR for activation. TfdR is involved in the activation of tf
Probab=27.99 E-value=88 Score=20.05 Aligned_cols=18 Identities=22% Similarity=0.178 Sum_probs=15.0
Q ss_pred hhhHHHHHhcCCeeEEEE
Q 047464 59 ITSYPMAFESGDIAAAFL 76 (94)
Q Consensus 59 ~~~~~~aL~~g~i~A~v~ 76 (94)
.++..+.|.+|++|.++.
T Consensus 39 ~~~~~~~l~~~~~Dl~i~ 56 (198)
T cd08446 39 KDEQIEALRAGRIHIGFG 56 (198)
T ss_pred HHHHHHHHHCCCccEEEE
Confidence 456778999999999986
No 169
>PRK09906 DNA-binding transcriptional regulator HcaR; Provisional
Probab=27.97 E-value=81 Score=22.78 Aligned_cols=18 Identities=17% Similarity=0.407 Sum_probs=15.8
Q ss_pred hhhHHHHHhcCCeeEEEE
Q 047464 59 ITSYPMAFESGDIAAAFL 76 (94)
Q Consensus 59 ~~~~~~aL~~g~i~A~v~ 76 (94)
.++..+.|.+|++|.+|.
T Consensus 128 ~~~~~~~l~~~~~D~~i~ 145 (296)
T PRK09906 128 TTQQEEKLRRGELDVGFM 145 (296)
T ss_pred cHHHHHHHHcCCeeEEEe
Confidence 466788999999999997
No 170
>COG0181 HemC Porphobilinogen deaminase [Coenzyme metabolism]
Probab=27.90 E-value=49 Score=26.13 Aligned_cols=17 Identities=24% Similarity=0.264 Sum_probs=15.0
Q ss_pred hhHHHHHhcCCeeEEEE
Q 047464 60 TSYPMAFESGDIAAAFL 76 (94)
Q Consensus 60 ~~~~~aL~~g~i~A~v~ 76 (94)
.|.-++|.+|.||.+|+
T Consensus 62 kEle~all~g~~DiAVH 78 (307)
T COG0181 62 KELEQALLEGEIDIAVH 78 (307)
T ss_pred HHHHHHHHcCCCCEEEe
Confidence 56668899999999999
No 171
>cd08433 PBP2_Nac The C-teminal substrate binding domain of LysR-like nitrogen assimilation control (NAC) protein, contains the type 2 periplasmic binding fold. The NAC is a LysR-type transcription regulator that activates expression of operons such as hut (histidine utilization) and ure (urea utilization), allowing use of non-preferred (poor) nitrogen sources, and represses expression of operons, such as glutamate dehydrogenase (gdh), allowing assimilation of the preferred nitrogen source. The expression of the nac gene is fully dependent on the nitrogen regulatory system (NTR) and the sigma54-containing RNA polymerase (sigma54-RNAP). In response to nitrogen starvation, NTR system activates the expression of nac, and NAC activates the expression of hut, ure, and put (proline utilization). NAC is not involved in the transcription of Sigma70-RNAP operons such as glnA, which directly respond by the NTR system, but activates the transcription of sigma70-RNAP dependent operons such as hut.
Probab=27.62 E-value=81 Score=20.23 Aligned_cols=19 Identities=16% Similarity=0.055 Sum_probs=16.0
Q ss_pred ChhhHHHHHhcCCeeEEEE
Q 047464 58 SITSYPMAFESGDIAAAFL 76 (94)
Q Consensus 58 s~~~~~~aL~~g~i~A~v~ 76 (94)
+..+..+.|.+|++|.+|.
T Consensus 37 ~~~~~~~~l~~~~~D~~i~ 55 (198)
T cd08433 37 LSGHLLEWLLNGRLDLALL 55 (198)
T ss_pred CcHHHHHHHhCCCCcEEEE
Confidence 4567788999999999987
No 172
>PRK05234 mgsA methylglyoxal synthase; Validated
Probab=27.62 E-value=1e+02 Score=21.12 Aligned_cols=41 Identities=7% Similarity=-0.011 Sum_probs=25.9
Q ss_pred HHHHHHHhhCCCCCCcccccCCCCCCChhhHHHHHhcCCeeEEEE
Q 047464 32 IIRYLINVLNFKPGSNKKINAKNGYNSITSYPMAFESGDIAAAFL 76 (94)
Q Consensus 32 ~~~~L~~~~~~~~~~i~~~~~~~~~~s~~~~~~aL~~g~i~A~v~ 76 (94)
...||++..|++-..+ ...|+.+ -.+..+.+++|+|++|+.
T Consensus 41 Ta~~L~~~~Gi~v~~v-i~~~~gg---~~~i~~~I~~g~i~lVIn 81 (142)
T PRK05234 41 TGGLIQEATGLDVTRL-LSGPLGG---DQQIGALIAEGKIDMLIF 81 (142)
T ss_pred HHHHHHhccCCeeEEE-EcCCCCC---chhHHHHHHcCceeEEEE
Confidence 4567887238853333 1221111 256888999999999998
No 173
>cd08456 PBP2_LysR The C-terminal substrate binding domain of LysR, transcriptional regulator for lysine biosynthesis, contains the type 2 periplasmic binding fold. LysR, the transcriptional activator of lysA encoding diaminopimelate decarboxylase, catalyses the decarboxylation of diaminopimelate to produce lysine. The LysR-transcriptional regulators comprise the largest family of prokaryotic transcription factor. Homologs of some of LTTRs with similar domain organizations are also found in the archaea and eukaryotic organisms. The LTTRs are composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcriptional repressor undergoes a conformational
Probab=27.38 E-value=89 Score=19.92 Aligned_cols=18 Identities=0% Similarity=-0.025 Sum_probs=14.8
Q ss_pred hhhHHHHHhcCCeeEEEE
Q 047464 59 ITSYPMAFESGDIAAAFL 76 (94)
Q Consensus 59 ~~~~~~aL~~g~i~A~v~ 76 (94)
..+..+.|.+|++|.+|.
T Consensus 38 ~~~~~~~l~~g~~Dl~i~ 55 (196)
T cd08456 38 SPTVEQWLSAQQCDLGLV 55 (196)
T ss_pred HHHHHHHHHcCCccEEEE
Confidence 455678899999999997
No 174
>PRK04171 ribosome biogenesis protein; Provisional
Probab=26.92 E-value=75 Score=23.86 Aligned_cols=35 Identities=20% Similarity=0.196 Sum_probs=25.1
Q ss_pred CcccccCCCCCCChhhHHHHHhcCCeeEEEEeecCCC
Q 047464 46 SNKKINAKNGYNSITSYPMAFESGDIAAAFLVFPRGS 82 (94)
Q Consensus 46 ~i~~~~~~~~~~s~~~~~~aL~~g~i~A~v~afpkGS 82 (94)
++..+.....-.++.++.. .+..+-.+|+|||+|.
T Consensus 148 ~~i~lS~~g~~~~~~~~~~--~~~~~~~vIGaf~hG~ 182 (222)
T PRK04171 148 RIILLSEKGELVKPKELGK--ENENIAVGIGGFPHGD 182 (222)
T ss_pred cEEEECCCCcccCHHHHhh--ccCCcEEEEccccCCC
Confidence 4444554445557777766 5778989999999996
No 175
>cd08450 PBP2_HcaR The C-terminal substrate binding domain of LysR-type transcriptional regulator HcaR in involved in 3-phenylpropionic acid catabolism, contains the type2 periplasmic binding fold. HcaR, a member of the LysR family of transcriptional regulators, controls the expression of the hcA1, A2, B, C, and D operon, encoding for the 3-phenylpropionate dioxygenase complex and 3-phenylpropionate-2',3'-dihydrodiol dehydrogenase, that oxidizes 3-phenylpropionate to 3-(2,3-dihydroxyphenyl) propionate. Dioxygenases play an important role in protecting the cell against the toxic effects of dioxygen. The expression of hcaR is negatively auto-regulated, as for other members of the LysR family, and is strongly repressed in the presence of glucose. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, an
Probab=26.90 E-value=94 Score=19.79 Aligned_cols=18 Identities=22% Similarity=0.388 Sum_probs=15.0
Q ss_pred hhhHHHHHhcCCeeEEEE
Q 047464 59 ITSYPMAFESGDIAAAFL 76 (94)
Q Consensus 59 ~~~~~~aL~~g~i~A~v~ 76 (94)
..+..+.|.+|++|.+|.
T Consensus 38 ~~~~~~~l~~~~~Dl~i~ 55 (196)
T cd08450 38 SPQLAEALMRGKLDVAFM 55 (196)
T ss_pred hHHHHHHHhcCCccEEEE
Confidence 456678999999999886
No 176
>COG0560 SerB Phosphoserine phosphatase [Amino acid transport and metabolism]
Probab=26.55 E-value=1e+02 Score=22.35 Aligned_cols=32 Identities=16% Similarity=0.147 Sum_probs=25.1
Q ss_pred ChhHHHhCCCeeeecCCccH--HHHHHHhhCCCC
Q 047464 13 DIKTLQRRNAAVGCNGNSFI--IRYLINVLNFKP 44 (94)
Q Consensus 13 ~i~dL~~~~~~VG~~~gSf~--~~~L~~~~~~~~ 44 (94)
=++.|+..|.+|.+.+|||. .+.+.+.+|++.
T Consensus 85 lv~~lk~~G~~v~iiSgg~~~lv~~ia~~lg~d~ 118 (212)
T COG0560 85 LVAALKAAGAKVVIISGGFTFLVEPIAERLGIDY 118 (212)
T ss_pred HHHHHHHCCCEEEEEcCChHHHHHHHHHHhCCch
Confidence 35778889999999999987 355666688863
No 177
>PRK05659 sulfur carrier protein ThiS; Validated
Probab=26.49 E-value=81 Score=18.15 Aligned_cols=26 Identities=4% Similarity=-0.058 Sum_probs=20.1
Q ss_pred CCCeeeecCCccHHHHHHHhhCCCCCC
Q 047464 20 RNAAVGCNGNSFIIRYLINVLNFKPGS 46 (94)
Q Consensus 20 ~~~~VG~~~gSf~~~~L~~~~~~~~~~ 46 (94)
+|+.+-+..|.++.++|.. +++++..
T Consensus 6 NG~~~~~~~~~tl~~lL~~-l~~~~~~ 31 (66)
T PRK05659 6 NGEPRELPDGESVAALLAR-EGLAGRR 31 (66)
T ss_pred CCeEEEcCCCCCHHHHHHh-cCCCCCe
Confidence 4677777888889998887 8886554
No 178
>PRK06049 rpl30p 50S ribosomal protein L30P; Reviewed
Probab=26.41 E-value=65 Score=22.75 Aligned_cols=15 Identities=33% Similarity=0.508 Sum_probs=13.1
Q ss_pred CChhhHHHHHhcCCe
Q 047464 57 NSITSYPMAFESGDI 71 (94)
Q Consensus 57 ~s~~~~~~aL~~g~i 71 (94)
.+++|..+++.+|+.
T Consensus 91 ~~iedl~~~i~~~~~ 105 (154)
T PRK06049 91 DSIEELAEALVEGEI 105 (154)
T ss_pred ccHHHHHHHHHhCCC
Confidence 399999999999874
No 179
>COG0151 PurD Phosphoribosylamine-glycine ligase [Nucleotide transport and metabolism]
Probab=26.29 E-value=87 Score=25.88 Aligned_cols=40 Identities=3% Similarity=0.042 Sum_probs=33.0
Q ss_pred ccHHHHHHHhhCCCCCCcccccCCCCCCChhhHHHHHhcCCeeEEEE
Q 047464 30 SFIIRYLINVLNFKPGSNKKINAKNGYNSITSYPMAFESGDIAAAFL 76 (94)
Q Consensus 30 Sf~~~~L~~~~~~~~~~i~~~~~~~~~~s~~~~~~aL~~g~i~A~v~ 76 (94)
+|+++|+++ +||+..+.+.|+ +++++..-+..-+--.||-
T Consensus 105 ~faK~fm~k-~~IPta~y~~f~------~~e~a~ayi~~~g~piVVK 144 (428)
T COG0151 105 AFAKDFMKK-YGIPTAEYEVFT------DPEEAKAYIDEKGAPIVVK 144 (428)
T ss_pred HHHHHHHHH-cCCCcccccccC------CHHHHHHHHHHcCCCEEEe
Confidence 588999998 999988899999 9999988888766554443
No 180
>cd08185 Fe-ADH1 Iron-containing alcohol dehydrogenases-like. Iron-containing alcohol dehydrogenases-like (ADH). Alcohol dehydrogenase catalyzes the reduction of acetaldehyde to alcohol with NADP as cofactor. Its activity requires iron ions. The protein structure represents a dehydroquinate synthase fold and is a member of the iron-containing alcohol dehydrogenase-like family. They are distinct from other alcohol dehydrogenases which contain different protein domains. Proteins of this family have not been characterized. Their specific function is unknown. They are present in bacteria and archaea.
Probab=26.19 E-value=96 Score=24.15 Aligned_cols=58 Identities=5% Similarity=-0.127 Sum_probs=36.7
Q ss_pred HhCCCeeeecCCccH----------HHHHHHhhCCCCCCcccccCCCCCCChhhHHHHHhcCCeeEEEE
Q 047464 18 QRRNAAVGCNGNSFI----------IRYLINVLNFKPGSNKKINAKNGYNSITSYPMAFESGDIAAAFL 76 (94)
Q Consensus 18 ~~~~~~VG~~~gSf~----------~~~L~~~~~~~~~~i~~~~~~~~~~s~~~~~~aL~~g~i~A~v~ 76 (94)
++.|++|=.+.|.++ .+.|++ .|+.-.-+..+.|+-++.++++..+.++..++|++|.
T Consensus 22 ~~~g~r~livt~~~~~~~~g~~~~v~~~L~~-~~~~~~~~~~v~~~p~~~~v~~~~~~~~~~~~D~Iia 89 (380)
T cd08185 22 LKPGKKALIVTGNGSSKKTGYLDRVIELLKQ-AGVEVVVFDKVEPNPTTTTVMEGAALAREEGCDFVVG 89 (380)
T ss_pred HhcCCeEEEEeCCCchhhccHHHHHHHHHHH-cCCeEEEeCCccCCCCHHHHHHHHHHHHHcCCCEEEE
Confidence 333567777666543 123333 3443112234556777788999999999999999997
No 181
>COG1110 Reverse gyrase [DNA replication, recombination, and repair]
Probab=26.19 E-value=75 Score=29.38 Aligned_cols=35 Identities=17% Similarity=0.252 Sum_probs=28.2
Q ss_pred HHHHHHHhhCCCCCCcccccCCCCCCCh-hhHHHHHhcCCeeEEEE
Q 047464 32 IIRYLINVLNFKPGSNKKINAKNGYNSI-TSYPMAFESGDIAAAFL 76 (94)
Q Consensus 32 ~~~~L~~~~~~~~~~i~~~~~~~~~~s~-~~~~~aL~~g~i~A~v~ 76 (94)
..+||++ .|| +...+. +. .+.++.|+.|+||..|.
T Consensus 354 l~e~Lr~-~Gi---~a~~~~------a~~~~~le~F~~GeidvLVG 389 (1187)
T COG1110 354 LAEYLRS-HGI---NAELIH------AEKEEALEDFEEGEVDVLVG 389 (1187)
T ss_pred HHHHHHh-cCc---eEEEee------ccchhhhhhhccCceeEEEE
Confidence 3468888 899 566665 33 88899999999999998
No 182
>COG5404 SulA SOS-response cell division inhibitor, blocks FtsZ ring formation [Cell division and chromosome partitioning]
Probab=26.18 E-value=48 Score=23.79 Aligned_cols=47 Identities=9% Similarity=0.115 Sum_probs=36.6
Q ss_pred CccHHHHHHHhhCCCCCCcccccCCCCCCChhhHHHHHhcCCeeEEEE
Q 047464 29 NSFIIRYLINVLNFKPGSNKKINAKNGYNSITSYPMAFESGDIAAAFL 76 (94)
Q Consensus 29 gSf~~~~L~~~~~~~~~~i~~~~~~~~~~s~~~~~~aL~~g~i~A~v~ 76 (94)
.+.+.+||+. -|.+-.++......+.-.+++.+.+||+-|+-..|+.
T Consensus 72 qkLsreWl~~-sGLp~~kv~ql~q~~p~~tle~m~~ALrtGnysvVig 118 (169)
T COG5404 72 QKLSREWLQA-SGLPLTKVMQLSQLSPCHTVESMVRALRTGNYSVVIG 118 (169)
T ss_pred HHHHHHHHHH-cCCCHHHHHHHhhcCcHHHHHHHHHHHHcCCceEEEe
Confidence 3456678877 7777666666665556669999999999999999998
No 183
>PRK11013 DNA-binding transcriptional regulator LysR; Provisional
Probab=26.18 E-value=81 Score=23.21 Aligned_cols=19 Identities=0% Similarity=-0.176 Sum_probs=15.5
Q ss_pred ChhhHHHHHhcCCeeEEEE
Q 047464 58 SITSYPMAFESGDIAAAFL 76 (94)
Q Consensus 58 s~~~~~~aL~~g~i~A~v~ 76 (94)
+.++..+.|.+|++|.+|.
T Consensus 131 ~~~~~~~~l~~~~~Dl~i~ 149 (309)
T PRK11013 131 ESPLLEEWLSAQRHDLGLT 149 (309)
T ss_pred CHHHHHHHHHcCCCCEEEE
Confidence 3455668999999999987
No 184
>cd08414 PBP2_LTTR_aromatics_like The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in the catabolism of aromatic compounds and that of other related regulators, contains type 2 periplasmic binding fold. This CD includes the C-terminal substrate binding domain of LTTRs involved in degradation of aromatic compounds, such as CbnR, BenM, CatM, ClcR and TfdR, as well as that of other transcriptional regulators clustered together in phylogenetic trees, including XapR, HcaR, MprR, IlvR, BudR, AlsR, LysR, and OccR. The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they ca
Probab=25.98 E-value=95 Score=19.67 Aligned_cols=18 Identities=17% Similarity=0.340 Sum_probs=15.7
Q ss_pred hhhHHHHHhcCCeeEEEE
Q 047464 59 ITSYPMAFESGDIAAAFL 76 (94)
Q Consensus 59 ~~~~~~aL~~g~i~A~v~ 76 (94)
.++..+.|.+|++|.++.
T Consensus 38 ~~~~~~~l~~~~~Dl~i~ 55 (197)
T cd08414 38 TAEQLEALRAGRLDVGFV 55 (197)
T ss_pred hHHHHHHHHcCCccEEEE
Confidence 467888999999999887
No 185
>PRK09860 putative alcohol dehydrogenase; Provisional
Probab=25.95 E-value=1e+02 Score=24.17 Aligned_cols=59 Identities=3% Similarity=-0.031 Sum_probs=37.1
Q ss_pred HHhCC-CeeeecCCccHH---------HHHHHhhCCCCCCcccccCCCCCCChhhHHHHHhcCCeeEEEE
Q 047464 17 LQRRN-AAVGCNGNSFII---------RYLINVLNFKPGSNKKINAKNGYNSITSYPMAFESGDIAAAFL 76 (94)
Q Consensus 17 L~~~~-~~VG~~~gSf~~---------~~L~~~~~~~~~~i~~~~~~~~~~s~~~~~~aL~~g~i~A~v~ 76 (94)
+++.| ++|-.+.|.+.. +.|++ .|+...-+-...|+-++.++++..+..+..++|++|.
T Consensus 26 ~~~~g~~~~livt~~~~~~~g~~~~v~~~L~~-~~i~~~~f~~v~~np~~~~v~~~~~~~~~~~~D~Iia 94 (383)
T PRK09860 26 MADYGFTRTLIVTDNMLTKLGMAGDVQKALEE-RNIFSVIYDGTQPNPTTENVAAGLKLLKENNCDSVIS 94 (383)
T ss_pred HHhcCCCEEEEEcCcchhhCccHHHHHHHHHH-cCCeEEEeCCCCCCcCHHHHHHHHHHHHHcCCCEEEE
Confidence 44445 677777776542 23333 4452112223445667778889999999999999997
No 186
>PRK08190 bifunctional enoyl-CoA hydratase/phosphate acetyltransferase; Validated
Probab=25.91 E-value=81 Score=25.64 Aligned_cols=42 Identities=5% Similarity=0.033 Sum_probs=29.9
Q ss_pred HHHHHhhCCCCCCcccccCCCCCCChhhHHHHHhcCCeeEEEE
Q 047464 34 RYLINVLNFKPGSNKKINAKNGYNSITSYPMAFESGDIAAAFL 76 (94)
Q Consensus 34 ~~L~~~~~~~~~~i~~~~~~~~~~s~~~~~~aL~~g~i~A~v~ 76 (94)
+.+.+ +|++.+++...++++.-.+...+.+.+++|++|+++-
T Consensus 215 ~~~~~-~g~~~~~~eIi~~~~~~~s~~~a~~lv~~G~aD~~v~ 256 (466)
T PRK08190 215 AAAEE-AGLDLSGVRIVDVPHSHAAAARAVALARAGEVEALMK 256 (466)
T ss_pred HHHHH-cCCCcCCCEEECCCCCHHHHHHHHHHHHCCCCCEEEe
Confidence 33443 5665556777776665455677888899999999997
No 187
>TIGR00212 hemC porphobilinogen deaminase. Biosynthesis of cofactors, prosthetic groups, and carriers: Heme and porphyrin
Probab=25.68 E-value=78 Score=24.66 Aligned_cols=16 Identities=25% Similarity=0.277 Sum_probs=14.2
Q ss_pred hHHHHHhcCCeeEEEE
Q 047464 61 SYPMAFESGDIAAAFL 76 (94)
Q Consensus 61 ~~~~aL~~g~i~A~v~ 76 (94)
|.-+||.+|+||.+|+
T Consensus 60 ele~aLl~g~iDiAVH 75 (292)
T TIGR00212 60 ELEQALLDGEIDLAVH 75 (292)
T ss_pred HHHHHHhcCCCCEEEe
Confidence 5567999999999999
No 188
>PRK10859 membrane-bound lytic transglycosylase F; Provisional
Probab=25.62 E-value=1.2e+02 Score=24.58 Aligned_cols=58 Identities=19% Similarity=0.185 Sum_probs=37.2
Q ss_pred CChhHHHhCC-CeeeecCCccH------------HHHHH---HhhCCCCCCcccccCCCCCCChhhHHHHHhcCCeeEEE
Q 047464 12 VDIKTLQRRN-AAVGCNGNSFI------------IRYLI---NVLNFKPGSNKKINAKNGYNSITSYPMAFESGDIAAAF 75 (94)
Q Consensus 12 ~~i~dL~~~~-~~VG~~~gSf~------------~~~L~---~~~~~~~~~i~~~~~~~~~~s~~~~~~aL~~g~i~A~v 75 (94)
++++.++.+| .+||+....+. .+++. +.+|++ -+++.+. +.++...+|++|++|.++
T Consensus 34 ~~l~~I~~~g~LrVg~~~~P~~~~~~~~~~~G~~~DLl~~ia~~LGv~-~e~v~~~------~~~~ll~aL~~G~iDi~~ 106 (482)
T PRK10859 34 NQLEQIQERGELRVGTINSPLTYYIGNDGPTGFEYELAKRFADYLGVK-LEIKVRD------NISQLFDALDKGKADLAA 106 (482)
T ss_pred ccHHHHHhCCEEEEEEecCCCeeEecCCCcccHHHHHHHHHHHHhCCc-EEEEecC------CHHHHHHHHhCCCCCEEe
Confidence 5677787766 47787654321 12222 336663 2344566 899999999999999665
Q ss_pred E
Q 047464 76 L 76 (94)
Q Consensus 76 ~ 76 (94)
.
T Consensus 107 ~ 107 (482)
T PRK10859 107 A 107 (482)
T ss_pred c
Confidence 3
No 189
>COG0040 HisG ATP phosphoribosyltransferase [Amino acid transport and metabolism]
Probab=25.56 E-value=65 Score=25.17 Aligned_cols=64 Identities=16% Similarity=0.118 Sum_probs=47.0
Q ss_pred CCChhHHHhCCCeeeecCCccHHHHHHHhhCCCCCCcccccCCCCCCChhhHHHHHhcCCeeEEEEeecCCCCCh
Q 047464 11 TVDIKTLQRRNAAVGCNGNSFIIRYLINVLNFKPGSNKKINAKNGYNSITSYPMAFESGDIAAAFLVFPRGSPLA 85 (94)
Q Consensus 11 i~~i~dL~~~~~~VG~~~gSf~~~~L~~~~~~~~~~i~~~~~~~~~~s~~~~~~aL~~g~i~A~v~afpkGSpL~ 85 (94)
.++.+||+.. .+|++--=-.+++|+++ .|++-.-++... |.|- |-.-|-.||+++...-|+.|.
T Consensus 107 ~~~~~~l~~~-~rIATkYp~l~~~yf~~-~g~~~~Ii~l~G------svE~---aP~~GlADaIvDivsTG~TLk 170 (290)
T COG0040 107 YTSPEDLKGR-LRIATKYPNLARKYFAE-KGIDVEIIKLSG------SVEL---APALGLADAIVDIVSTGTTLK 170 (290)
T ss_pred ccChhHhcCC-ceEEEccHHHHHHHHHH-cCceEEEEEccC------cEee---ccccCccceEEEeecCCHhHH
Confidence 6788889843 58888777778899987 888655566667 7775 445688999999655665554
No 190
>PLN02691 porphobilinogen deaminase
Probab=25.42 E-value=75 Score=25.50 Aligned_cols=16 Identities=31% Similarity=0.198 Sum_probs=14.4
Q ss_pred hHHHHHhcCCeeEEEE
Q 047464 61 SYPMAFESGDIAAAFL 76 (94)
Q Consensus 61 ~~~~aL~~g~i~A~v~ 76 (94)
|.-+||.+|+||.+|+
T Consensus 107 ele~aLl~g~iDiAVH 122 (351)
T PLN02691 107 EIDDALLSGRIDIAVH 122 (351)
T ss_pred HHHHHHHcCCCCEEEe
Confidence 5668999999999999
No 191
>smart00094 TR_FER Transferrin.
Probab=25.39 E-value=66 Score=25.28 Aligned_cols=19 Identities=26% Similarity=0.263 Sum_probs=16.8
Q ss_pred ChhhHHHHHhcCCeeEEEE
Q 047464 58 SITSYPMAFESGDIAAAFL 76 (94)
Q Consensus 58 s~~~~~~aL~~g~i~A~v~ 76 (94)
|.+++++++++|++|+++.
T Consensus 36 s~~~Ci~~I~~g~AD~a~l 54 (332)
T smart00094 36 STEECIKAIQKGEADAVTL 54 (332)
T ss_pred CHHHHHHHHHCCCCCEEEE
Confidence 7888899999999998887
No 192
>COG2104 ThiS Sulfur transfer protein involved in thiamine biosynthesis [Coenzyme metabolism]
Probab=25.31 E-value=84 Score=19.14 Aligned_cols=26 Identities=15% Similarity=0.267 Sum_probs=21.4
Q ss_pred CCCeeeecCCccHHHHHHHhhCCCCCC
Q 047464 20 RNAAVGCNGNSFIIRYLINVLNFKPGS 46 (94)
Q Consensus 20 ~~~~VG~~~gSf~~~~L~~~~~~~~~~ 46 (94)
+|+.+=|..+++..++|.+ ++|++..
T Consensus 8 ng~~~e~~~~~tv~dLL~~-l~~~~~~ 33 (68)
T COG2104 8 NGKEVEIAEGTTVADLLAQ-LGLNPEG 33 (68)
T ss_pred CCEEEEcCCCCcHHHHHHH-hCCCCce
Confidence 3788888888999999998 9997554
No 193
>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=24.64 E-value=1.5e+02 Score=20.62 Aligned_cols=37 Identities=14% Similarity=0.012 Sum_probs=30.0
Q ss_pred HHHHHHhhCCCCCC-cccccCCCCCCChhhHHHHHhcCCeeEEEE
Q 047464 33 IRYLINVLNFKPGS-NKKINAKNGYNSITSYPMAFESGDIAAAFL 76 (94)
Q Consensus 33 ~~~L~~~~~~~~~~-i~~~~~~~~~~s~~~~~~aL~~g~i~A~v~ 76 (94)
.+.|++ .|....- +..++ ..++..+++++|.+.|.+.
T Consensus 198 ~~al~~-~g~~~~~~v~g~d------~~~~~~~~i~~g~~~a~v~ 235 (257)
T PF13407_consen 198 AQALQQ-AGRAGKVIVVGFD------GSPEALEAIKDGNITATVG 235 (257)
T ss_dssp HHHHHH-TTCTTTSEEEEEE------CHHHHHHHHHTTSSSEEEE
T ss_pred HHHHHH-cCCcccceeecCC------CCHHHHHHHHCCCCeEEEe
Confidence 477887 8875333 77788 9999999999999998776
No 194
>PRK13583 hisG ATP phosphoribosyltransferase catalytic subunit; Provisional
Probab=24.51 E-value=33 Score=25.77 Aligned_cols=57 Identities=9% Similarity=0.071 Sum_probs=39.1
Q ss_pred CCCChhHHH----------hCCCeeeecCCccHHHHHHHhhCCCC-CCcccccCCCCCCChhhHHHHHhcCCeeEEEE
Q 047464 10 STVDIKTLQ----------RRNAAVGCNGNSFIIRYLINVLNFKP-GSNKKINAKNGYNSITSYPMAFESGDIAAAFL 76 (94)
Q Consensus 10 ~i~~i~dL~----------~~~~~VG~~~gSf~~~~L~~~~~~~~-~~i~~~~~~~~~~s~~~~~~aL~~g~i~A~v~ 76 (94)
.+.+++||. ....+|++--=-.+++|+.+ .|++. .=++.+. |.|- |-.-|-.||+|+
T Consensus 110 ~~~~~~dl~~~~~~~~~~~g~~~RIATkYp~it~~yf~~-~Gv~~~~Iv~l~G------svEl---aP~~GlAD~IvD 177 (228)
T PRK13583 110 DVDTMADLDDVAADFRARHGRRLRIATKYWRLTQQFLSQ-KGVQDYRIVESLG------ATEG---APANGSAEIIVD 177 (228)
T ss_pred ccCCHHHhhhhhhhhhhccCCceEEEeCCHHHHHHHHHH-cCCceeEEEECCC------ceec---ccccCcchhhhh
Confidence 367778886 12268999888889999988 89863 3345566 6665 344566677776
No 195
>COG1732 OpuBC Periplasmic glycine betaine/choline-binding (lipo)protein of an ABC-type transport system (osmoprotectant binding protein) [Cell envelope biogenesis, outer membrane]
Probab=24.48 E-value=1.1e+02 Score=24.16 Aligned_cols=36 Identities=19% Similarity=0.136 Sum_probs=28.2
Q ss_pred HHHHHhhCCCCCCcccccCCCCCCChhhHHHHHhcCCeeEEEE
Q 047464 34 RYLINVLNFKPGSNKKINAKNGYNSITSYPMAFESGDIAAAFL 76 (94)
Q Consensus 34 ~~L~~~~~~~~~~i~~~~~~~~~~s~~~~~~aL~~g~i~A~v~ 76 (94)
+.|++ .|++-.....+. +..=...||.+|+||....
T Consensus 54 ~lle~-~~~kv~~~~~lG------~t~v~~~Al~~G~IDiYpE 89 (300)
T COG1732 54 QLLEK-NGIKVEDKTGLG------GTAVVRNALKSGDIDIYPE 89 (300)
T ss_pred HHHHh-cCCceeeccCCC------chHHHHHHHHcCCCCeEee
Confidence 45555 477666666677 8888899999999999977
No 196
>PRK07696 sulfur carrier protein ThiS; Provisional
Probab=24.08 E-value=94 Score=18.44 Aligned_cols=27 Identities=7% Similarity=0.105 Sum_probs=18.4
Q ss_pred CCCeeeecCC-ccHHHHHHHhhCCCCCCc
Q 047464 20 RNAAVGCNGN-SFIIRYLINVLNFKPGSN 47 (94)
Q Consensus 20 ~~~~VG~~~g-Sf~~~~L~~~~~~~~~~i 47 (94)
||+..-+..+ +++.++|.. +++++..+
T Consensus 6 NG~~~~~~~~~~tv~~lL~~-l~~~~~~v 33 (67)
T PRK07696 6 NGNQIEVPESVKTVAELLTH-LELDNKIV 33 (67)
T ss_pred CCEEEEcCCCcccHHHHHHH-cCCCCCeE
Confidence 3666666666 678888877 88865443
No 197
>cd02072 Glm_B12_BD B12 binding domain of glutamate mutase (Glm). Glutamate mutase catalysis the conversion of (S)-glutamate with (2S,3S)-3-methylaspartate. The rearrangement reaction is initiated by the extraction of a hydrogen from the protein-bound substrate by a 5'-desoxyadenosyl radical, which is generated by the homolytic cleavage of the organometallic bond of the cofactor B12. Glm is a heterotetrameric molecule consisting of two alpha and two epsilon polypeptide chains.
Probab=23.93 E-value=1.6e+02 Score=20.06 Aligned_cols=19 Identities=16% Similarity=0.066 Sum_probs=10.3
Q ss_pred ChhhHHHHHhcCCeeEEEE
Q 047464 58 SITSYPMAFESGDIAAAFL 76 (94)
Q Consensus 58 s~~~~~~aL~~g~i~A~v~ 76 (94)
+++++.++-..-+.|++..
T Consensus 38 ~~e~~v~aa~~~~adiVgl 56 (128)
T cd02072 38 PQEEFIDAAIETDADAILV 56 (128)
T ss_pred CHHHHHHHHHHcCCCEEEE
Confidence 5555555555555555544
No 198
>PF02571 CbiJ: Precorrin-6x reductase CbiJ/CobK; InterPro: IPR003723 Cobalamin (vitamin B12) is a structurally complex cofactor, consisting of a modified tetrapyrrole with a centrally chelated cobalt. Cobalamin is usually found in one of two biologically active forms: methylcobalamin and adocobalamin. Most prokaryotes, as well as animals, have cobalamin-dependent enzymes, whereas plants and fungi do not appear to use it. In bacteria and archaea, these include methionine synthase, ribonucleotide reductase, glutamate and methylmalonyl-CoA mutases, ethanolamine ammonia lyase, and diol dehydratase []. In mammals, cobalamin is obtained through the diet, and is required for methionine synthase and methylmalonyl-CoA mutase []. There are at least two distinct cobalamin biosynthetic pathways in bacteria []: Aerobic pathway that requires oxygen and in which cobalt is inserted late in the pathway []; found in Pseudomonas denitrificans and Rhodobacter capsulatus. Anaerobic pathway in which cobalt insertion is the first committed step towards cobalamin synthesis []; found in Salmonella typhimurium, Bacillus megaterium, and Propionibacterium freudenreichii subsp. shermanii. Either pathway can be divided into two parts: (1) corrin ring synthesis (differs in aerobic and anaerobic pathways) and (2) adenosylation of corrin ring, attachment of aminopropanol arm, and assembly of the nucleotide loop (common to both pathways) []. There are about 30 enzymes involved in either pathway, where those involved in the aerobic pathway are prefixed Cob and those of the anaerobic pathway Cbi. Several of these enzymes are pathway-specific: CbiD, CbiG, and CbiK are specific to the anaerobic route of S. typhimurium, whereas CobE, CobF, CobG, CobN, CobS, CobT, and CobW are unique to the aerobic pathway of P. denitrificans. This entry represents CobK and CbiJ precorrin-6x reductase (1.3.1.54 from EC). In the aerobic pathway, CobK catalyses the reduction of the macrocycle of precorrin-6X to produce precorrin-6Y; while in the anaerobic pathway CbiJ catalyses the reduction of the macrocycle of cobalt-precorrin-6X into cobalt-precorrin-6Y [, ].; GO: 0016994 precorrin-6A reductase activity, 0009236 cobalamin biosynthetic process, 0055114 oxidation-reduction process
Probab=23.50 E-value=1.4e+02 Score=22.40 Aligned_cols=68 Identities=15% Similarity=0.066 Sum_probs=39.0
Q ss_pred hHHHhCCCeeeecCCccHHHHHHHhhCCCCCCcccccCCCCCCChhhHHHHHhcCCeeEEEEeecCCCCChHHhHHH
Q 047464 15 KTLQRRNAAVGCNGNSFIIRYLINVLNFKPGSNKKINAKNGYNSITSYPMAFESGDIAAAFLVFPRGSPLALDISEA 91 (94)
Q Consensus 15 ~dL~~~~~~VG~~~gSf~~~~L~~~~~~~~~~i~~~~~~~~~~s~~~~~~aL~~g~i~A~v~afpkGSpL~~dvn~a 91 (94)
+.|...|..+-++.-|.+.+.+......-.-++..+. +.+++.+-++..+|+++|||= -|.+..||+.
T Consensus 17 ~~L~~~g~v~~sv~t~~g~~~~~~~~~~~~v~~G~lg------~~~~l~~~l~~~~i~~vIDAT---HPfA~~is~n 84 (249)
T PF02571_consen 17 ERLAEAGYVIVSVATSYGGELLKPELPGLEVRVGRLG------DEEGLAEFLRENGIDAVIDAT---HPFAAEISQN 84 (249)
T ss_pred HHHHhcCCEEEEEEhhhhHhhhccccCCceEEECCCC------CHHHHHHHHHhCCCcEEEECC---CchHHHHHHH
Confidence 4566555423334444444444321122223455676 788888999999999999942 2455555543
No 199
>PRK15408 autoinducer 2-binding protein lsrB; Provisional
Probab=23.49 E-value=1.1e+02 Score=23.33 Aligned_cols=37 Identities=11% Similarity=-0.055 Sum_probs=28.1
Q ss_pred HHHHHHhhCCCCCCcccccCCCCCCChhhHHHHHhcCCeeEEEE
Q 047464 33 IRYLINVLNFKPGSNKKINAKNGYNSITSYPMAFESGDIAAAFL 76 (94)
Q Consensus 33 ~~~L~~~~~~~~~~i~~~~~~~~~~s~~~~~~aL~~g~i~A~v~ 76 (94)
.+.+++ .|...-.+..|+ ++++..+++++|.|++.+.
T Consensus 225 ~~Al~~-~g~~~v~VvG~D------~~~~~~~~i~~G~i~~~~~ 261 (336)
T PRK15408 225 AQAAEN-LKRDKVAIVGFS------TPNVMRPYVKRGTVKEFGL 261 (336)
T ss_pred HHHHHh-CCCCCEEEEEeC------CcHHHHHHHhcCCcceEEe
Confidence 466666 665422356688 9999999999999999886
No 200
>TIGR03261 phnS2 putative 2-aminoethylphosphonate ABC transporter, periplasmic 2-aminoethylphosphonate-binding protein. This ABC transporter extracellular solute-binding protein is found in a number of genomes in operon-like contexts strongly suggesting a substrate specificity for 2-aminoethylphosphonate (2-AEP). The characterized PhnSTUV system is absent in the genomes in which this system is found. These genomes encode systems for the catabolism of 2-AEP, making the need for a 2-AEP-specific transporter likely.
Probab=23.46 E-value=1.4e+02 Score=22.27 Aligned_cols=19 Identities=11% Similarity=-0.081 Sum_probs=15.8
Q ss_pred ChhhHHHHHhcCCeeEEEE
Q 047464 58 SITSYPMAFESGDIAAAFL 76 (94)
Q Consensus 58 s~~~~~~aL~~g~i~A~v~ 76 (94)
+..+..+++.+|++++.+.
T Consensus 202 s~~~~~~~v~~Ge~~i~~~ 220 (334)
T TIGR03261 202 SGSKPCKLAGMGEFPIGIS 220 (334)
T ss_pred CChHHHHHHhCCCceEEEE
Confidence 5667788999999998875
No 201
>PF04422 FrhB_FdhB_N: Coenzyme F420 hydrogenase/dehydrogenase, beta subunit N-term; InterPro: IPR007516 Coenzyme F420 hydrogenase (1.12.99.1 from EC) reduces the low-potential two-electron acceptor coenzyme F420. This entry contains the N termini of F420 hydrogenase and dehydrogenase beta subunits [, ]. The N terminus of Methanobacterium formicicum formate dehydrogenase beta chain (1.2.1.2 from EC, P06130 from SWISSPROT) is also represented in this entry []. This region is often found in association with the 4Fe-4S binding domain, fer4 (IPR001450 from INTERPRO), and the C terminus IPR007525 from INTERPRO.
Probab=23.15 E-value=84 Score=19.38 Aligned_cols=16 Identities=25% Similarity=0.268 Sum_probs=13.0
Q ss_pred HHHHhcCCeeEEEEee
Q 047464 63 PMAFESGDIAAAFLVF 78 (94)
Q Consensus 63 ~~aL~~g~i~A~v~af 78 (94)
..+|++|.||++|.+=
T Consensus 28 ~~lLe~g~Vd~vv~~~ 43 (82)
T PF04422_consen 28 AYLLESGLVDGVVVVG 43 (82)
T ss_pred HHHHHcCCceEEEEEe
Confidence 4578999999999844
No 202
>PLN02344 chorismate mutase
Probab=22.82 E-value=20 Score=28.04 Aligned_cols=36 Identities=11% Similarity=0.002 Sum_probs=27.6
Q ss_pred CCeeeecCCccHHHHHHHhhCCCCCCcccccCCCCCCChhhHH
Q 047464 21 NAAVGCNGNSFIIRYLINVLNFKPGSNKKINAKNGYNSITSYP 63 (94)
Q Consensus 21 ~~~VG~~~gSf~~~~L~~~~~~~~~~i~~~~~~~~~~s~~~~~ 63 (94)
+..++...|||..-+|.+...++ +++++|. |++|++
T Consensus 74 ~~~~~~f~gS~le~~l~etE~lh-a~vrRY~------sPDE~P 109 (284)
T PLN02344 74 AFGVPGFHGSLVEFMVRETEALH-AKVGRYK------SPDEHP 109 (284)
T ss_pred CcCCCCCCccHHHHHHHHHHHHH-HhhcccC------CCCcCC
Confidence 34566778899999998755443 6899999 999853
No 203
>COG1464 NlpA ABC-type metal ion transport system, periplasmic component/surface antigen [Inorganic ion transport and metabolism]
Probab=22.66 E-value=53 Score=25.43 Aligned_cols=48 Identities=19% Similarity=0.156 Sum_probs=31.9
Q ss_pred CCeeeecCCccHHH-------HHHHhhCCCCCCcccccCCCCCCChhhHHHHHhcCCeeEEEE
Q 047464 21 NAAVGCNGNSFIIR-------YLINVLNFKPGSNKKINAKNGYNSITSYPMAFESGDIAAAFL 76 (94)
Q Consensus 21 ~~~VG~~~gSf~~~-------~L~~~~~~~~~~i~~~~~~~~~~s~~~~~~aL~~g~i~A~v~ 76 (94)
...||.-.+...+- -+++ .|++ =.|+.|+ +|..+. .||.+|+|||=.+
T Consensus 30 ~I~vg~~~~p~a~ile~~~k~~~~k-~Gi~-l~i~~Ft---DY~~PN---~AL~~gdiDaN~F 84 (268)
T COG1464 30 TIKVGATPGPHAEILEVVVKPALKK-KGLD-LKIVEFT---DYVQPN---EALADGDIDANAF 84 (268)
T ss_pred cEEEeecCCchHHHHHHHHHHHHHh-cCce-EEEEEec---CCcchh---HHHhcCCccchhh
Confidence 36788887776543 2223 5663 2467787 555555 5999999999776
No 204
>PRK10837 putative DNA-binding transcriptional regulator; Provisional
Probab=22.60 E-value=1.1e+02 Score=21.90 Aligned_cols=19 Identities=5% Similarity=-0.073 Sum_probs=16.5
Q ss_pred ChhhHHHHHhcCCeeEEEE
Q 047464 58 SITSYPMAFESGDIAAAFL 76 (94)
Q Consensus 58 s~~~~~~aL~~g~i~A~v~ 76 (94)
+.++..+.|.+|++|.++.
T Consensus 126 ~~~~~~~~l~~g~~Di~i~ 144 (290)
T PRK10837 126 NSQDVINAVLDFRVDIGLI 144 (290)
T ss_pred CHHHHHHHHHhCCceEEEe
Confidence 5677889999999999986
No 205
>PF00885 DMRL_synthase: 6,7-dimethyl-8-ribityllumazine synthase; InterPro: IPR002180 6,7-dimethyl-8-ribityllumazine synthase (riboflavin synthase) catalyses the biosynthesis of riboflavin according to the reaction: 2 6,7-dimethyl-8-(1-D-ribityl)lumazine = riboflavin + 4-(1-D-ribitylamino)-5-amino-2,6-dihydroxypyrimidine. The biosynthesis of one riboflavin molecule requires one molecule of GTP and two molecules of ribulose 5-phosphate as substrates. The final step in the biosynthesis of the vitamin involves the dismutation of 6,7-dimethyl-8-ribityllumazine catalyzed by riboflavin synthase. The second product, 5-amino-6-ribitylamino-2,4(1H,3H)-pyrimidinedione, is recycled in the biosynthetic pathway by 6,7-dimethyl-8-ribityllumazine synthase []. N-[2,4-dioxo-6-d-ribitylamino-1,2,3,4-tetrahydropyrimidin-5-yl]oxalamic acid derivatives inhibit riboflavin synthase []. This family includes the beta chain of 6,7-dimethyl-8-ribityllumazine synthase 2.5.1.9 from EC. The family also includes a subfamily of distant archaebacterial proteins that may also have the same function for example O28856 from SWISSPROT.; GO: 0009231 riboflavin biosynthetic process, 0009349 riboflavin synthase complex; PDB: 2O6H_D 1C41_C 2OBX_H 1VSX_H 1VSW_3 3JV8_C 3MK3_r 3NQ4_G 2A58_A 2A57_D ....
Probab=21.96 E-value=95 Score=21.44 Aligned_cols=62 Identities=15% Similarity=0.070 Sum_probs=33.4
Q ss_pred CCeeeecCCccHH-----------HHHHHhhCCCCCCcccccCCCCCCChhhHHHHHhcCCeeEEEE--eecCCCC
Q 047464 21 NAAVGCNGNSFII-----------RYLINVLNFKPGSNKKINAKNGYNSITSYPMAFESGDIAAAFL--VFPRGSP 83 (94)
Q Consensus 21 ~~~VG~~~gSf~~-----------~~L~~~~~~~~~~i~~~~~~~~~~s~~~~~~aL~~g~i~A~v~--afpkGSp 83 (94)
+.+||.+...|-. +.|.. .|+.+.++..|.---.|.-|-..-..+++|+.||++- +.=||..
T Consensus 3 ~~ri~IV~s~~n~~i~~~ll~~a~~~l~~-~g~~~~~i~~~~VPGa~ElP~a~~~l~~~~~~Davi~lG~VI~G~T 77 (144)
T PF00885_consen 3 GLRIAIVVSRFNEEITDRLLEGALEELKR-HGVAEENIEVIRVPGAFELPLAAKRLAESGRYDAVIALGCVIRGET 77 (144)
T ss_dssp TEEEEEEEESTTHHHHHHHHHHHHHHHHH-TTTTGGCEEEEEESSGGGHHHHHHHHHHCSTESEEEEEEEEE--SS
T ss_pred CCEEEEEEEeccHHHHHHHHHHHHHHHHH-cCCCccceEEEEcCCHHHHHHHHHHHhcccCccEEEEeccccCCCc
Confidence 4566666666543 34444 6665555554431222224444556667899999987 4445543
No 206
>COG0745 OmpR Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]
Probab=21.71 E-value=1.4e+02 Score=21.82 Aligned_cols=41 Identities=12% Similarity=0.082 Sum_probs=32.5
Q ss_pred cHHHHHHHhhCCCCCCcccccCCCCCCChhhHHHHHhcCCeeEEEE--eecCCC
Q 047464 31 FIIRYLINVLNFKPGSNKKINAKNGYNSITSYPMAFESGDIAAAFL--VFPRGS 82 (94)
Q Consensus 31 f~~~~L~~~~~~~~~~i~~~~~~~~~~s~~~~~~aL~~g~i~A~v~--afpkGS 82 (94)
+...+|.. .|| ....+. +.+++..++... .|.++. .+|..+
T Consensus 15 ~l~~~L~~-~g~---~v~~~~------~~~~a~~~~~~~-~dlviLD~~lP~~d 57 (229)
T COG0745 15 LLKEYLEE-EGY---EVDVAA------DGEEALEAAREQ-PDLVLLDLMLPDLD 57 (229)
T ss_pred HHHHHHHH-CCC---EEEEEC------CHHHHHHHHhcC-CCEEEEECCCCCCC
Confidence 45577777 788 677788 889999999988 999998 777544
No 207
>cd08469 PBP2_PnbR The C-terminal substrate binding domain of LysR-type transcriptional regulator PnbR, which is involved in regulating the pnb genes encoding enzymes for 4-nitrobenzoate catabolism, contains the type 2 periplasmic binding fold. PnbR is the regulator of one or both of the two pnb genes that encoding enzymes for 4-nitrobenzoate catabolism. In Pseudomonas putida strain, pnbA encodes a 4-nitrobenzoate reductase, which is responsible for catalyzing the direct reduction of 4-nitrobenzoate to 4-hydroxylaminobenzoate, and pnbB encodes a 4-hydroxylaminobenzoate lyase, which catalyzes the conversion of 4-hydroxylaminobenzoate to 3, 4-dihydroxybenzoic acid and ammonium. The topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft bet
Probab=21.58 E-value=1.3e+02 Score=19.94 Aligned_cols=19 Identities=11% Similarity=0.081 Sum_probs=15.4
Q ss_pred ChhhHHHHHhcCCeeEEEE
Q 047464 58 SITSYPMAFESGDIAAAFL 76 (94)
Q Consensus 58 s~~~~~~aL~~g~i~A~v~ 76 (94)
+..+..+.|.+|++|.+|.
T Consensus 37 ~~~~~~~~l~~g~~Di~i~ 55 (221)
T cd08469 37 TRLDLAEQLDLGRIDLVIG 55 (221)
T ss_pred ChhhHHHHHHCCCccEEEe
Confidence 3446778899999999996
No 208
>PF03607 DCX: Doublecortin; InterPro: IPR003533 X-linked lissencephaly is a severe brain malformation affecting males. Recently it has been demonstrated that the doublecortin gene is implicated in this disorder []. Doublecortin was found to bind to the microtubule cytoskeleton. In vivo and in vitro assays show that Doublecortin stabilises microtubules and causes bundling []. Doublecortin is a basic protein with an iso-electric point of 10, typical of microtubule-binding proteins. However, its sequence contains no known microtubule-binding domain(s). The detailed sequence analysis of Doublecortin and Doublecortin-like proteins allowed the identification of an evolutionarily conserved Doublecortin (DC) domain. This domain is found in the N terminus of proteins and consists of one or two tandemly repeated copies of an around 80 amino acids region. It has been suggested that the first DC domain of Doublecortin binds tubulin and enhances microtubule polymerisation []. Some proteins known to contain a DC domain are listed below: Doublecortin. It is required for neuronal migration []. A large number of point mutations in the human DCX gene leading to lissencephaly are located within the DC domains []. Human serine/threonine-protein kinase DCAMKL1. It is a probable kinase that may be involved in a calcium-signaling pathway controling neuronal migration in the developing brain []. Retinitis pigmentosa 1 protein. It could play a role in the differentiation of photoreceptor cells. Mutation in the human RP1 gene cause retinitis pigmentosa of type 1 []. ; GO: 0035556 intracellular signal transduction; PDB: 1UF0_A 1MG4_A 1MFW_A 2DNF_A 2XRP_I 2BQQ_A 1MJD_A.
Probab=21.22 E-value=45 Score=19.46 Aligned_cols=21 Identities=10% Similarity=0.164 Sum_probs=15.0
Q ss_pred CCCChhHHHhCCCeeeecCCc
Q 047464 10 STVDIKTLQRRNAAVGCNGNS 30 (94)
Q Consensus 10 ~i~~i~dL~~~~~~VG~~~gS 30 (94)
.|+++++|...+..|.|-...
T Consensus 38 ~V~~l~~l~dg~~yVa~g~e~ 58 (60)
T PF03607_consen 38 RVKSLDELEDGGSYVASGREP 58 (60)
T ss_dssp EESSGGGS-TTEEEEEESSSS
T ss_pred EeCCHHHHCCCCEEEEEcCCc
Confidence 489999999877788875443
No 209
>smart00537 DCX Domain in the Doublecortin (DCX) gene product. Tandemly-repeated domain in doublin, the Doublecortin gene product. Proposed to bind tubulin. Doublecortin (DCX) is mutated in human X-linked neuronal migration defects.
Probab=21.20 E-value=64 Score=20.34 Aligned_cols=23 Identities=13% Similarity=0.280 Sum_probs=18.0
Q ss_pred CCCCChhHHHhCCCeeeecCCcc
Q 047464 9 PSTVDIKTLQRRNAAVGCNGNSF 31 (94)
Q Consensus 9 ~~i~~i~dL~~~~~~VG~~~gSf 31 (94)
..|++++||...+..|.|....|
T Consensus 61 ~~v~~l~~l~~g~~yVa~g~e~f 83 (89)
T smart00537 61 KKVTSLDELEDGGSYVASGTEAF 83 (89)
T ss_pred CEECCHHHhCcCCEEEEEcCCcc
Confidence 34899999998777888876655
No 210
>PRK12679 cbl transcriptional regulator Cbl; Reviewed
Probab=20.99 E-value=1.2e+02 Score=22.46 Aligned_cols=19 Identities=5% Similarity=0.163 Sum_probs=16.4
Q ss_pred ChhhHHHHHhcCCeeEEEE
Q 047464 58 SITSYPMAFESGDIAAAFL 76 (94)
Q Consensus 58 s~~~~~~aL~~g~i~A~v~ 76 (94)
+..+..+.|.+|++|.+|.
T Consensus 130 ~~~~~~~~L~~g~~Dl~i~ 148 (316)
T PRK12679 130 TPQEIATLLQNGEADIGIA 148 (316)
T ss_pred CHHHHHHHHHcCCCCEEEe
Confidence 4667889999999999886
No 211
>cd08465 PBP2_ToxR The C-terminal substrate binding domain of LysR-type transcriptional regulator ToxR regulates the expression of the toxoflavin biosynthesis genes; contains the type 2 periplasmic bindinig fold. In soil bacterium Burkholderia glumae, ToxR regulates the toxABCDE and toxFGHI operons in the presence of toxoflavin as a coinducer. Additionally, the expression of both operons requires a transcriptional activator, ToxJ, whose expression is regulated by the TofI or TofR quorum-sensing system. The biosynthesis of toxoflavin is suggested to be synthesized in a pathway common to the synthesis of riboflavin. The topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After
Probab=20.54 E-value=1.2e+02 Score=19.80 Aligned_cols=19 Identities=21% Similarity=0.174 Sum_probs=16.7
Q ss_pred ChhhHHHHHhcCCeeEEEE
Q 047464 58 SITSYPMAFESGDIAAAFL 76 (94)
Q Consensus 58 s~~~~~~aL~~g~i~A~v~ 76 (94)
+.++..+.|.+|++|.+|.
T Consensus 37 ~~~~~~~~L~~g~~Dl~i~ 55 (200)
T cd08465 37 SREAMLAQVADGEIDLALG 55 (200)
T ss_pred ChHhHHHHHHCCCccEEEe
Confidence 5677889999999999986
No 212
>PRK11151 DNA-binding transcriptional regulator OxyR; Provisional
Probab=20.53 E-value=1.4e+02 Score=21.70 Aligned_cols=19 Identities=21% Similarity=0.364 Sum_probs=16.7
Q ss_pred ChhhHHHHHhcCCeeEEEE
Q 047464 58 SITSYPMAFESGDIAAAFL 76 (94)
Q Consensus 58 s~~~~~~aL~~g~i~A~v~ 76 (94)
+.++..+.|.+|.+|.+|.
T Consensus 128 ~~~~~~~~l~~g~~Dl~i~ 146 (305)
T PRK11151 128 QTHQLLAQLDSGKLDCAIL 146 (305)
T ss_pred CHHHHHHHHHcCCccEEEE
Confidence 4678889999999999997
No 213
>KOG1198 consensus Zinc-binding oxidoreductase [Energy production and conversion; General function prediction only]
Probab=20.50 E-value=3.3e+02 Score=21.37 Aligned_cols=50 Identities=4% Similarity=-0.047 Sum_probs=34.3
Q ss_pred HHhCC-CeeeecCCccHHHHHHHhhCCCCCCcccccCCCCCCChhhHHHHHhc---CCeeEEEE
Q 047464 17 LQRRN-AAVGCNGNSFIIRYLINVLNFKPGSNKKINAKNGYNSITSYPMAFES---GDIAAAFL 76 (94)
Q Consensus 17 L~~~~-~~VG~~~gSf~~~~L~~~~~~~~~~i~~~~~~~~~~s~~~~~~aL~~---g~i~A~v~ 76 (94)
.+..+ ..|.+..+.-..++++. +|-+ .+..|+ + +++.+.+++ +++|.+|+
T Consensus 178 Ak~~~~~~v~t~~s~e~~~l~k~-lGAd--~vvdy~------~-~~~~e~~kk~~~~~~DvVlD 231 (347)
T KOG1198|consen 178 AKHAGAIKVVTACSKEKLELVKK-LGAD--EVVDYK------D-ENVVELIKKYTGKGVDVVLD 231 (347)
T ss_pred HHhcCCcEEEEEcccchHHHHHH-cCCc--EeecCC------C-HHHHHHHHhhcCCCccEEEE
Confidence 44445 56666666667777776 7764 677777 6 556666654 67999999
No 214
>cd06273 PBP1_GntR_like_1 This group includes the ligand-binding domain of putative DNA transcription repressors which are highly similar to that of the repressor specific for gluconate (GntR), a member of the LacI-GalR family of bacterial transcription regulators. This group includes the ligand-binding domain of putative DNA transcription repressors which are highly similar to that of the repressor specific for gluconate (GntR), a member of the LacI-GalR family of bacterial transcription regulators. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational
Probab=20.47 E-value=98 Score=21.56 Aligned_cols=38 Identities=5% Similarity=-0.038 Sum_probs=23.5
Q ss_pred HHHHhhCCCCCCcccccCCCCCCChhhHHHHHhcCCeeEEEE
Q 047464 35 YLINVLNFKPGSNKKINAKNGYNSITSYPMAFESGDIAAAFL 76 (94)
Q Consensus 35 ~L~~~~~~~~~~i~~~~~~~~~~s~~~~~~aL~~g~i~A~v~ 76 (94)
.+++ +|+ .+..++.+++.....++.+.|.+.++|+++.
T Consensus 24 ~~~~-~g~---~~~~~~~~~~~~~~~~~~~~l~~~~vdgiii 61 (268)
T cd06273 24 TLAA-HGY---TLLVASSGYDLDREYAQARKLLERGVDGLAL 61 (268)
T ss_pred HHHH-CCC---EEEEecCCCCHHHHHHHHHHHHhcCCCEEEE
Confidence 3444 565 4545554444444456777788888998886
No 215
>KOG3127 consensus Deoxycytidylate deaminase [Nucleotide transport and metabolism]
Probab=20.46 E-value=2.1e+02 Score=21.80 Aligned_cols=35 Identities=34% Similarity=0.578 Sum_probs=25.8
Q ss_pred cccCCCCCCChhhHHHHHh----------cCCeeEEEE------------eecCCCC
Q 047464 49 KINAKNGYNSITSYPMAFE----------SGDIAAAFL------------VFPRGSP 83 (94)
Q Consensus 49 ~~~~~~~~~s~~~~~~aL~----------~g~i~A~v~------------afpkGSp 83 (94)
++.+.|+|.+-++|.+++. +-+|.|.+. +||.|+.
T Consensus 56 ~~~k~~~~lswd~yFM~iA~LsA~RSkDpntqVGaCiv~~~n~iVg~GYNgfP~gc~ 112 (230)
T KOG3127|consen 56 PFLKRNGYLSWDDYFMAIAFLSAKRSKDPNTQVGACIVDRENRIVGTGYNGFPRGCS 112 (230)
T ss_pred cccccccCccHHHHHHHHHHHHHHhccCcccceeeEEEcCCCEEEEeccCCCcCCCC
Confidence 3457788999999999875 345776554 9999953
No 216
>COG4034 Uncharacterized protein conserved in archaea [Function unknown]
Probab=20.19 E-value=1.2e+02 Score=24.00 Aligned_cols=47 Identities=26% Similarity=0.217 Sum_probs=34.3
Q ss_pred cccccCCCCCCChhhHHHHHhcC-CeeEEEE------eecCC------CCChHHhHHHhh
Q 047464 47 NKKINAKNGYNSITSYPMAFESG-DIAAAFL------VFPRG------SPLALDISEAIL 93 (94)
Q Consensus 47 i~~~~~~~~~~s~~~~~~aL~~g-~i~A~v~------afpkG------SpL~~dvn~aiL 93 (94)
+...+-..++.-+.+.+++|.+. ++|++|. |+-+| |||+.-|+-+-|
T Consensus 107 ~v~v~~~~gv~gl~e~lk~lv~~~~id~IvgvD~GGDaLa~GcEe~l~SPLaDai~lasL 166 (328)
T COG4034 107 AVAVDLVDGVRGLAEGLKALVEKEGIDLIVGVDVGGDALAVGCEEGLRSPLADAISLASL 166 (328)
T ss_pred eEEEeccCCcccHHHHHHHHHHhhCccEEEEeccCccceeccccccccchHHHHHHHHHH
Confidence 34444455666889999999874 6999998 55554 899988887654
No 217
>PF01693 Cauli_VI: Caulimovirus viroplasmin; InterPro: IPR011320 This entry represents the N-terminal domain of RNase HI, which has a 3-layer alpha/beta/alpha structure []. This domain is lacking in retroviral and prokaryotic enzymes, but shows a striking structural similarity to the ribosomal protein L9 N-terminal domain, and may function as a regulatory RNA-binding module. However, the topology of this domain differs from structures of known RNA binding domains such as the double-stranded RNA binding domain (dsRBD), the hnRNP K homology (KH) domain and the RNP motif. Eukaryotic RNases HI possess either one or two copies of this small N-terminal domain, in addition to the well-conserved catalytic RNase H domain. RNase HI belongs to the family of ribonuclease H enzymes that recognise RNA:DNA hybrids and degrade the RNA component. ; PDB: 1QHK_A 3BSU_C.
Probab=20.07 E-value=1.7e+02 Score=15.88 Aligned_cols=36 Identities=8% Similarity=-0.035 Sum_probs=22.4
Q ss_pred CCeeeecCCccHHHHHHHhhCCCCCCcccccCCCCCCChhhHHH
Q 047464 21 NAAVGCNGNSFIIRYLINVLNFKPGSNKKINAKNGYNSITSYPM 64 (94)
Q Consensus 21 ~~~VG~~~gSf~~~~L~~~~~~~~~~i~~~~~~~~~~s~~~~~~ 64 (94)
|...|+- +.-.+....+.|++....+.|. |.+|+.+
T Consensus 8 G~~~GIy--~~W~~~~~~v~g~~ga~~k~F~------t~~eA~~ 43 (44)
T PF01693_consen 8 GRQPGIY--TSWAECKKQVSGYPGAIYKSFK------TREEAEE 43 (44)
T ss_dssp SSS-EEE--CCHHHHHHHCTT-TT-EEEEES------SHHHHHH
T ss_pred CCCCCeE--CCHHHHHHHhCCCCCceECCcC------CHHHHhh
Confidence 4555666 2225555667889888899999 9888653
No 218
>PRK11074 putative DNA-binding transcriptional regulator; Provisional
Probab=20.06 E-value=1.2e+02 Score=22.18 Aligned_cols=19 Identities=16% Similarity=0.072 Sum_probs=16.1
Q ss_pred ChhhHHHHHhcCCeeEEEE
Q 047464 58 SITSYPMAFESGDIAAAFL 76 (94)
Q Consensus 58 s~~~~~~aL~~g~i~A~v~ 76 (94)
+.++..+.|.+|++|.+|.
T Consensus 129 ~~~~~~~~l~~g~~Dl~i~ 147 (300)
T PRK11074 129 VFNGVWDALADGRVDIAIG 147 (300)
T ss_pred hhhHHHHHHHCCCCCEEEe
Confidence 4566788999999999995
Done!