Query 043606
Match_columns 101
No_of_seqs 106 out of 676
Neff 5.6
Searched_HMMs 46136
Date Fri Mar 29 06:34:54 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/043606.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/043606hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PTZ00129 40S ribosomal protein 100.0 1E-43 2.3E-48 255.1 12.9 99 1-99 51-149 (149)
2 PRK09607 rps11p 30S ribosomal 100.0 4.4E-42 9.5E-47 242.8 13.2 100 1-101 32-132 (132)
3 COG0100 RpsK Ribosomal protein 100.0 1.5E-38 3.3E-43 223.8 11.3 89 1-98 41-129 (129)
4 PF00411 Ribosomal_S11: Riboso 100.0 3.9E-38 8.5E-43 215.7 9.4 87 2-97 24-110 (110)
5 PRK05309 30S ribosomal protein 100.0 1E-37 2.2E-42 219.3 11.6 88 2-98 41-128 (128)
6 TIGR03632 bact_S11 30S ribosom 100.0 1.1E-36 2.4E-41 208.3 11.1 85 2-95 24-108 (108)
7 TIGR03628 arch_S11P archaeal r 100.0 1.2E-35 2.7E-40 205.5 11.6 88 2-90 26-114 (114)
8 PTZ00090 40S ribosomal protein 100.0 2.3E-34 5.1E-39 217.1 11.1 86 3-98 145-233 (233)
9 CHL00041 rps11 ribosomal prote 100.0 1.3E-32 2.7E-37 190.5 10.6 80 2-90 37-116 (116)
10 KOG0408 Mitochondrial/chloropl 100.0 5.3E-32 1.1E-36 197.7 9.1 88 2-98 103-190 (190)
11 KOG0407 40S ribosomal protein 100.0 2.8E-29 6E-34 174.4 10.9 101 1-101 39-139 (139)
12 PRK08569 rpl18p 50S ribosomal 92.7 1.1 2.3E-05 33.9 8.1 67 20-99 78-144 (193)
13 cd00432 Ribosomal_L18_L5e Ribo 91.0 1.6 3.5E-05 28.9 6.8 61 6-74 40-103 (103)
14 PF00861 Ribosomal_L18p: Ribos 91.0 0.52 1.1E-05 32.4 4.5 49 20-76 69-119 (119)
15 TIGR00060 L18_bact ribosomal p 87.0 4.8 0.0001 27.9 7.0 51 18-75 62-113 (114)
16 PRK05593 rplR 50S ribosomal pr 86.6 2.9 6.2E-05 29.0 5.7 51 18-75 65-116 (117)
17 CHL00139 rpl18 ribosomal prote 85.8 2.1 4.5E-05 29.4 4.6 50 19-75 58-108 (109)
18 COG0256 RplR Ribosomal protein 85.6 3.1 6.6E-05 29.4 5.5 48 21-76 76-125 (125)
19 cd05313 NAD_bind_2_Glu_DH NAD( 79.8 5.1 0.00011 31.1 5.3 61 18-87 15-75 (254)
20 PRK13260 2,3-diketo-L-gulonate 79.8 16 0.00034 29.4 8.2 73 11-92 78-152 (332)
21 TIGR03175 AllD ureidoglycolate 79.2 20 0.00044 29.0 8.7 73 11-92 78-152 (349)
22 PF02615 Ldh_2: Malate/L-lacta 73.1 25 0.00053 28.3 7.6 72 11-91 78-151 (335)
23 PLN00105 malate/L-lactate dehy 73.0 41 0.0009 27.0 8.9 74 11-92 67-142 (330)
24 PRK15025 ureidoglycolate dehyd 71.2 47 0.001 26.9 8.9 73 11-92 78-152 (349)
25 PRK10098 putative dehydrogenas 71.0 34 0.00074 27.7 8.1 73 11-92 82-158 (350)
26 TIGR03694 exosort_acyl putativ 70.2 18 0.00039 27.4 6.0 58 20-93 153-210 (241)
27 cd01076 NAD_bind_1_Glu_DH NAD( 68.9 14 0.00031 27.8 5.2 60 18-87 8-68 (227)
28 COG2099 CobK Precorrin-6x redu 68.2 8.5 0.00018 30.3 3.9 27 19-46 74-100 (257)
29 PF13420 Acetyltransf_4: Acety 67.4 33 0.00072 22.7 6.7 47 23-80 93-140 (155)
30 PRK13490 chemoreceptor glutami 65.9 39 0.00084 24.5 6.8 57 20-78 63-130 (162)
31 PRK07757 acetyltransferase; Pr 65.6 16 0.00035 24.3 4.5 54 22-92 82-135 (152)
32 PF00583 Acetyltransf_1: Acety 65.5 25 0.00054 20.6 5.4 41 24-75 43-83 (83)
33 PF13302 Acetyltransf_3: Acety 65.3 30 0.00065 22.2 5.7 46 18-75 96-142 (142)
34 PF02601 Exonuc_VII_L: Exonucl 64.7 26 0.00056 27.1 6.0 54 23-78 56-112 (319)
35 PRK14834 undecaprenyl pyrophos 64.5 65 0.0014 25.0 8.2 60 23-87 42-115 (249)
36 PRK14840 undecaprenyl pyrophos 62.6 71 0.0015 24.8 8.1 61 22-87 49-123 (250)
37 PRK14829 undecaprenyl pyrophos 62.1 49 0.0011 25.5 7.1 60 22-86 41-114 (243)
38 TIGR01575 rimI ribosomal-prote 61.9 37 0.0008 21.3 6.3 48 22-81 71-118 (131)
39 cd05211 NAD_bind_Glu_Leu_Phe_V 61.2 24 0.00053 26.4 5.2 55 21-85 3-58 (217)
40 PRK13488 chemoreceptor glutami 59.4 49 0.0011 23.8 6.3 57 20-78 60-125 (157)
41 PRK14841 undecaprenyl pyrophos 58.8 81 0.0018 24.2 7.9 61 22-87 30-104 (233)
42 COG0241 HisB Histidinol phosph 58.5 50 0.0011 24.5 6.3 58 31-95 39-108 (181)
43 PRK13491 chemoreceptor glutami 58.1 42 0.00092 25.4 6.0 57 20-78 71-133 (199)
44 PTZ00349 dehydrodolichyl dipho 58.1 81 0.0017 25.6 7.9 61 22-87 46-123 (322)
45 KOG3551 Syntrophins (type beta 57.8 9.2 0.0002 32.3 2.5 79 6-89 94-179 (506)
46 TIGR01917 gly_red_sel_B glycin 57.6 47 0.001 28.0 6.6 54 24-86 321-377 (431)
47 COG1433 Uncharacterized conser 57.3 29 0.00064 24.1 4.7 40 28-80 54-93 (121)
48 TIGR02382 wecD_rffC TDP-D-fuco 57.2 48 0.001 23.4 6.0 45 22-78 140-184 (191)
49 COG3981 Predicted acetyltransf 57.1 70 0.0015 23.9 6.8 40 7-48 98-139 (174)
50 PRK10809 ribosomal-protein-S5- 56.9 64 0.0014 22.5 7.1 48 22-81 120-168 (194)
51 PTZ00079 NADP-specific glutama 56.7 40 0.00087 28.5 6.1 63 16-87 212-274 (454)
52 PLN02477 glutamate dehydrogena 56.3 37 0.00079 28.2 5.8 60 18-87 183-243 (410)
53 PRK09491 rimI ribosomal-protei 56.2 56 0.0012 21.5 7.9 54 19-84 77-130 (146)
54 TIGR01918 various_sel_PB selen 56.2 51 0.0011 27.8 6.6 55 24-87 321-378 (431)
55 PRK14837 undecaprenyl pyrophos 56.2 91 0.002 24.0 7.9 61 22-87 33-107 (230)
56 PRK13498 chemoreceptor glutami 56.1 46 0.001 24.3 5.7 58 19-78 64-133 (167)
57 TIGR00587 nfo apurinic endonuc 55.5 33 0.00072 26.0 5.1 64 29-92 14-78 (274)
58 PRK14831 undecaprenyl pyrophos 55.5 91 0.002 24.1 7.6 60 23-87 48-121 (249)
59 cd04516 TBP_eukaryotes eukaryo 55.2 27 0.00059 25.5 4.4 37 3-42 51-87 (174)
60 PRK01060 endonuclease IV; Prov 53.8 39 0.00084 25.2 5.2 62 29-90 15-77 (281)
61 COG1570 XseA Exonuclease VII, 53.5 28 0.0006 29.4 4.7 54 23-78 177-230 (440)
62 cd04518 TBP_archaea archaeal T 53.3 30 0.00065 25.3 4.4 37 3-42 51-87 (174)
63 PF02878 PGM_PMM_I: Phosphoglu 52.9 15 0.00033 25.0 2.6 61 19-86 18-80 (137)
64 PTZ00032 60S ribosomal protein 52.2 32 0.0007 26.4 4.5 29 18-46 159-187 (211)
65 PRK00394 transcription factor; 52.0 34 0.00074 25.1 4.5 37 3-42 50-86 (179)
66 PLN00062 TATA-box-binding prot 51.2 34 0.00074 25.2 4.4 35 3-40 51-85 (179)
67 TIGR03234 OH-pyruv-isom hydrox 50.2 63 0.0014 23.7 5.8 43 29-80 17-59 (254)
68 cd05801 PGM_like3 This bacteri 49.7 86 0.0019 26.3 7.1 74 8-86 24-102 (522)
69 PF00044 Gp_dh_N: Glyceraldehy 49.5 21 0.00046 25.4 3.0 29 56-84 6-35 (151)
70 cd05799 PGM2 This CD includes 49.5 70 0.0015 26.3 6.4 73 10-87 7-87 (487)
71 PRK13489 chemoreceptor glutami 49.3 67 0.0015 24.9 5.9 57 20-78 79-143 (233)
72 cd04517 TLF TBP-like factors ( 48.4 41 0.0009 24.5 4.5 37 3-42 51-87 (174)
73 PRK13487 chemoreceptor glutami 47.9 80 0.0017 23.8 6.0 58 19-78 80-145 (201)
74 PF13207 AAA_17: AAA domain; P 47.6 33 0.00073 21.9 3.6 25 58-82 8-33 (121)
75 PRK14836 undecaprenyl pyrophos 47.3 1E+02 0.0022 23.9 6.7 60 23-87 42-115 (253)
76 PRK10240 undecaprenyl pyrophos 47.2 1.2E+02 0.0027 23.1 7.1 60 23-87 21-94 (229)
77 PRK12360 4-hydroxy-3-methylbut 47.1 67 0.0014 25.4 5.7 39 30-77 45-95 (281)
78 PRK09414 glutamate dehydrogena 46.9 55 0.0012 27.5 5.5 60 16-85 207-267 (445)
79 PLN00124 succinyl-CoA ligase [ 46.7 69 0.0015 26.6 6.0 48 25-82 361-409 (422)
80 PLN02891 IMP cyclohydrolase 46.0 27 0.00059 30.3 3.6 42 29-87 36-77 (547)
81 PRK14832 undecaprenyl pyrophos 45.7 1.4E+02 0.0031 23.2 8.2 60 23-87 46-119 (253)
82 PRK13495 chemoreceptor glutami 45.6 91 0.002 22.6 5.8 57 20-78 60-123 (159)
83 cd00652 TBP_TLF TATA box bindi 45.5 47 0.001 24.2 4.4 37 3-42 51-87 (174)
84 PRK14830 undecaprenyl pyrophos 44.4 1.5E+02 0.0032 23.0 8.0 60 23-87 50-123 (251)
85 PRK14030 glutamate dehydrogena 44.0 70 0.0015 26.9 5.7 63 16-88 203-266 (445)
86 PRK06920 dnaE DNA polymerase I 43.8 21 0.00045 33.3 2.7 44 26-88 324-367 (1107)
87 PRK13493 chemoreceptor glutami 43.6 1E+02 0.0023 23.4 6.1 58 19-78 94-157 (213)
88 PRK07564 phosphoglucomutase; V 43.4 1.1E+02 0.0024 25.8 6.8 74 8-86 41-119 (543)
89 TIGR00055 uppS undecaprenyl di 43.1 1.5E+02 0.0032 22.7 8.1 61 22-87 26-100 (226)
90 PF00208 ELFV_dehydrog: Glutam 43.1 36 0.00078 26.0 3.6 59 18-85 8-67 (244)
91 PRK09542 manB phosphomannomuta 42.9 1E+02 0.0022 25.2 6.4 63 18-87 13-76 (445)
92 PF08901 DUF1847: Protein of u 42.7 60 0.0013 23.8 4.5 44 28-80 43-88 (157)
93 PRK10887 glmM phosphoglucosami 42.6 1.9E+02 0.004 23.6 8.2 76 3-86 3-79 (443)
94 PRK13210 putative L-xylulose 5 42.6 94 0.002 23.0 5.7 52 28-80 18-72 (284)
95 PRK08356 hypothetical protein; 42.5 54 0.0012 23.4 4.3 36 39-81 2-37 (195)
96 PRK05673 dnaE DNA polymerase I 42.4 22 0.00048 33.1 2.7 44 26-88 339-382 (1135)
97 PRK09989 hypothetical protein; 42.1 92 0.002 23.0 5.6 43 29-80 18-60 (258)
98 PF02776 TPP_enzyme_N: Thiamin 41.9 91 0.002 21.7 5.3 44 27-81 3-47 (172)
99 PRK00286 xseA exodeoxyribonucl 41.8 59 0.0013 26.4 4.9 53 23-78 177-229 (438)
100 cd07039 TPP_PYR_POX Pyrimidine 41.3 1E+02 0.0022 21.7 5.5 45 27-82 2-47 (164)
101 PRK04266 fibrillarin; Provisio 40.6 1.2E+02 0.0026 22.7 6.1 60 27-88 158-217 (226)
102 PRK10975 TDP-fucosamine acetyl 40.1 1.3E+02 0.0028 21.1 7.2 46 22-79 143-188 (194)
103 PRK03624 putative acetyltransf 39.8 96 0.0021 19.5 6.2 48 19-78 82-129 (140)
104 PF01121 CoaE: Dephospho-CoA k 39.4 80 0.0017 22.9 4.8 24 56-79 7-30 (180)
105 TIGR00715 precor6x_red precorr 39.0 57 0.0012 25.1 4.1 28 18-46 72-99 (256)
106 PRK06826 dnaE DNA polymerase I 38.8 26 0.00055 32.8 2.5 45 25-88 338-382 (1151)
107 PF02571 CbiJ: Precorrin-6x re 38.6 44 0.00096 25.6 3.5 27 19-46 74-100 (249)
108 PF05677 DUF818: Chlamydia CHL 38.6 2.1E+02 0.0046 23.7 7.5 59 19-85 189-255 (365)
109 PRK14828 undecaprenyl pyrophos 38.4 1.2E+02 0.0027 23.5 6.0 59 23-87 55-125 (256)
110 PRK08057 cobalt-precorrin-6x r 38.2 44 0.00096 25.6 3.4 27 19-46 73-99 (248)
111 TIGR00542 hxl6Piso_put hexulos 38.2 91 0.002 23.3 5.1 51 29-80 19-72 (279)
112 PRK13494 chemoreceptor glutami 37.8 1.4E+02 0.003 21.8 5.8 57 20-78 69-132 (163)
113 TIGR00594 polc DNA-directed DN 37.4 28 0.00062 32.0 2.6 45 25-88 342-386 (1022)
114 PRK07135 dnaE DNA polymerase I 37.4 25 0.00055 32.3 2.2 45 25-88 272-316 (973)
115 PF03198 Glyco_hydro_72: Gluca 37.3 79 0.0017 25.6 4.8 53 21-83 48-100 (314)
116 PRK07199 phosphoribosylpyropho 37.1 1.8E+02 0.0038 22.9 6.7 51 29-88 228-278 (301)
117 TIGR00237 xseA exodeoxyribonuc 37.0 92 0.002 25.7 5.3 54 23-78 171-224 (432)
118 PRK15490 Vi polysaccharide bio 36.8 93 0.002 27.2 5.5 74 3-83 164-240 (578)
119 PF02222 ATP-grasp: ATP-grasp 36.7 61 0.0013 23.5 3.8 42 24-88 122-163 (172)
120 PRK07374 dnaE DNA polymerase I 36.6 31 0.00066 32.4 2.7 44 26-88 350-393 (1170)
121 PTZ00069 60S ribosomal protein 36.5 84 0.0018 25.3 4.8 72 10-94 86-183 (300)
122 PF01255 Prenyltransf: Putativ 36.3 1.8E+02 0.004 21.7 6.8 59 23-86 22-96 (223)
123 PRK14842 undecaprenyl pyrophos 36.1 2E+02 0.0044 22.2 8.1 60 23-87 36-109 (241)
124 PRK07279 dnaE DNA polymerase I 36.1 32 0.00069 31.9 2.7 45 25-88 280-324 (1034)
125 COG1184 GCD2 Translation initi 36.1 1.4E+02 0.0031 24.0 6.1 50 26-82 130-179 (301)
126 PRK14839 undecaprenyl pyrophos 36.0 2.1E+02 0.0045 22.2 8.1 60 23-87 37-110 (239)
127 COG1751 Uncharacterized conser 35.7 1.9E+02 0.0041 21.7 6.6 45 27-83 15-61 (186)
128 cd01421 IMPCH Inosine monophos 35.2 76 0.0016 23.8 4.2 42 29-87 14-55 (187)
129 cd01853 Toc34_like Toc34-like 35.1 1.4E+02 0.0031 22.6 5.8 49 18-73 7-55 (249)
130 PRK04143 hypothetical protein; 34.8 42 0.00092 26.2 2.9 37 4-47 208-244 (264)
131 PRK14320 glmM phosphoglucosami 34.3 1.3E+02 0.0029 24.4 5.8 62 19-86 19-81 (443)
132 COG0057 GapA Glyceraldehyde-3- 34.2 55 0.0012 26.7 3.5 33 43-84 2-37 (335)
133 PRK02269 ribose-phosphate pyro 34.1 2.4E+02 0.0052 22.4 7.2 51 29-88 234-284 (320)
134 cd05800 PGM_like2 This PGM-lik 33.8 1.1E+02 0.0024 24.9 5.3 63 19-86 16-80 (461)
135 PRK14731 coaE dephospho-CoA ki 33.8 1.1E+02 0.0024 22.2 4.8 31 42-79 5-35 (208)
136 PRK14031 glutamate dehydrogena 33.7 1.4E+02 0.0029 25.2 5.8 60 15-83 202-261 (444)
137 PRK13209 L-xylulose 5-phosphat 33.6 2E+02 0.0043 21.3 6.8 51 29-80 24-77 (283)
138 COG0237 CoaE Dephospho-CoA kin 33.2 43 0.00094 24.9 2.6 28 56-83 9-36 (201)
139 cd02904 Macro_H2A_like Macro d 33.1 61 0.0013 24.0 3.4 38 4-47 135-175 (186)
140 TIGR00511 ribulose_e2b2 ribose 33.1 1.8E+02 0.0039 22.8 6.2 49 27-82 127-175 (301)
141 TIGR00355 purH phosphoribosyla 33.0 1.2E+02 0.0026 26.2 5.5 42 29-87 14-55 (511)
142 PRK01045 ispH 4-hydroxy-3-meth 32.7 1.5E+02 0.0032 23.6 5.7 38 31-77 45-92 (298)
143 PRK05898 dnaE DNA polymerase I 32.3 37 0.0008 31.4 2.4 45 25-88 274-318 (971)
144 TIGR01455 glmM phosphoglucosam 32.3 1.3E+02 0.0028 24.5 5.4 63 18-86 14-78 (443)
145 PF00352 TBP: Transcription fa 32.2 96 0.0021 19.6 3.8 34 3-39 53-86 (86)
146 PF13344 Hydrolase_6: Haloacid 32.2 90 0.002 20.2 3.8 37 31-76 22-58 (101)
147 PRK06371 translation initiatio 32.1 1.7E+02 0.0037 23.7 6.0 50 27-82 156-205 (329)
148 PRK14835 undecaprenyl pyrophos 31.9 2.6E+02 0.0055 22.1 7.7 60 23-87 69-144 (275)
149 KOG0747 Putative NAD+-dependen 31.6 1.3E+02 0.0027 24.7 5.1 30 19-48 154-185 (331)
150 COG0027 PurT Formate-dependent 31.5 1.2E+02 0.0027 25.2 5.1 25 24-48 248-272 (394)
151 PRK14324 glmM phosphoglucosami 31.4 1.7E+02 0.0037 23.9 6.0 63 18-86 16-79 (446)
152 PRK08334 translation initiatio 31.2 1.9E+02 0.0041 23.7 6.1 51 26-82 178-228 (356)
153 cd03089 PMM_PGM The phosphoman 31.1 1.6E+02 0.0035 23.9 5.8 62 18-86 14-76 (443)
154 TIGR00512 salvage_mtnA S-methy 31.1 1.7E+02 0.0037 23.6 5.8 50 27-82 166-215 (331)
155 COG1670 RimL Acetyltransferase 30.9 1.6E+02 0.0034 19.3 5.5 51 18-80 108-159 (187)
156 PRK08535 translation initiatio 30.8 2E+02 0.0043 22.7 6.1 50 26-82 131-180 (310)
157 PRK15425 gapA glyceraldehyde-3 30.8 66 0.0014 26.0 3.4 34 43-85 3-38 (331)
158 PRK14827 undecaprenyl pyrophos 30.7 2.8E+02 0.0061 22.1 7.8 60 23-87 95-168 (296)
159 TIGR00829 FRU PTS system, fruc 30.5 1.2E+02 0.0025 19.5 4.0 52 23-83 12-63 (85)
160 TIGR03585 PseH pseudaminic aci 30.4 1.6E+02 0.0034 19.2 6.2 42 27-79 96-138 (156)
161 PRK08322 acetolactate synthase 30.3 1.1E+02 0.0024 25.4 4.8 46 27-83 3-48 (547)
162 PRK10151 ribosomal-protein-L7/ 30.2 1.8E+02 0.0039 19.8 7.1 50 19-80 106-156 (179)
163 PRK09997 hydroxypyruvate isome 29.9 2E+02 0.0044 21.2 5.8 42 29-79 18-59 (258)
164 cd04908 ACT_Bt0572_1 N-termina 29.9 91 0.002 18.2 3.2 13 67-79 20-32 (66)
165 KOG3302 TATA-box binding prote 29.9 1.1E+02 0.0024 23.3 4.3 37 3-42 72-108 (200)
166 PLN02371 phosphoglucosamine mu 29.8 1.5E+02 0.0032 25.4 5.6 63 18-86 87-155 (583)
167 PF03975 CheD: CheD chemotacti 29.7 90 0.002 20.9 3.5 58 19-78 15-82 (114)
168 PRK13371 4-hydroxy-3-methylbut 29.6 1.8E+02 0.0038 24.3 5.8 41 31-83 83-139 (387)
169 PRK09532 DNA polymerase III su 29.4 49 0.0011 30.1 2.7 45 25-88 347-391 (874)
170 PF01261 AP_endonuc_2: Xylose 29.0 59 0.0013 22.3 2.6 43 33-82 2-49 (213)
171 COG3916 LasI N-acyl-L-homoseri 28.9 2.3E+02 0.0049 21.7 5.9 51 20-85 119-169 (209)
172 COG2101 SPT15 TATA-box binding 28.9 1.1E+02 0.0023 23.1 4.0 36 2-40 149-184 (185)
173 PF13380 CoA_binding_2: CoA bi 28.7 1.8E+02 0.0039 19.3 4.8 38 29-77 69-106 (116)
174 PF08924 DUF1906: Domain of un 28.2 97 0.0021 21.5 3.6 52 30-82 8-60 (136)
175 cd00475 CIS_IPPS Cis (Z)-Isopr 27.7 2.7E+02 0.0059 21.1 7.9 61 22-87 27-101 (221)
176 PF04312 DUF460: Protein of un 27.6 1.2E+02 0.0025 21.9 3.9 29 59-87 62-90 (138)
177 KOG1602 Cis-prenyltransferase 27.4 3.2E+02 0.007 21.8 7.2 59 23-86 64-139 (271)
178 cd07038 TPP_PYR_PDC_IPDC_like 27.1 1.8E+02 0.004 20.3 4.9 42 30-82 2-44 (162)
179 PF14124 DUF4291: Domain of un 26.9 18 0.0004 27.1 -0.3 26 59-87 132-157 (181)
180 PRK03092 ribose-phosphate pyro 26.9 3.1E+02 0.0068 21.5 6.7 51 29-88 218-268 (304)
181 PRK00881 purH bifunctional pho 26.9 1.7E+02 0.0036 25.3 5.3 42 29-87 18-59 (513)
182 PF14057 GGGtGRT: GGGtGRT prot 26.6 1.6E+02 0.0034 23.7 4.8 48 20-77 124-171 (328)
183 COG0587 DnaE DNA polymerase II 26.5 32 0.0007 32.2 1.1 42 28-88 343-384 (1139)
184 PRK09856 fructoselysine 3-epim 26.5 2.6E+02 0.0057 20.5 5.8 61 28-89 15-77 (275)
185 TIGR01132 pgm phosphoglucomuta 26.2 2.8E+02 0.006 23.5 6.5 63 19-86 55-120 (543)
186 PRK10146 aminoalkylphosphonic 26.2 1.9E+02 0.004 18.6 5.6 44 22-77 93-136 (144)
187 PRK14833 undecaprenyl pyrophos 26.1 3E+02 0.0066 21.1 6.8 60 23-87 32-105 (233)
188 PRK05720 mtnA methylthioribose 26.1 2.6E+02 0.0057 22.6 6.1 49 28-82 167-215 (344)
189 PRK06965 acetolactate synthase 26.1 1.6E+02 0.0036 24.8 5.2 54 18-82 14-68 (587)
190 COG4130 Predicted sugar epimer 26.1 2.7E+02 0.0059 22.0 5.9 54 29-85 20-74 (272)
191 PRK08617 acetolactate synthase 26.0 1.7E+02 0.0038 24.3 5.2 47 26-83 6-52 (552)
192 PRK08978 acetolactate synthase 25.6 1.6E+02 0.0034 24.6 4.9 46 26-82 2-47 (548)
193 PRK00394 transcription factor; 25.3 1.5E+02 0.0033 21.6 4.3 35 3-40 143-177 (179)
194 PF13523 Acetyltransf_8: Acety 25.1 2.1E+02 0.0045 18.8 6.5 49 22-82 95-144 (152)
195 PLN02821 1-hydroxy-2-methyl-2- 25.1 2E+02 0.0044 24.5 5.5 41 31-83 151-207 (460)
196 COG1636 Uncharacterized protei 25.0 34 0.00073 26.1 0.8 53 26-89 97-149 (204)
197 TIGR03457 sulphoacet_xsc sulfo 24.9 1.9E+02 0.0041 24.3 5.3 46 26-82 3-48 (579)
198 PRK09875 putative hydrolase; P 24.9 1.3E+02 0.0029 23.6 4.1 38 32-78 40-79 (292)
199 COG0194 Gmk Guanylate kinase [ 24.7 2.9E+02 0.0062 20.9 5.7 40 43-89 5-44 (191)
200 TIGR03849 arch_ComA phosphosul 24.6 3.3E+02 0.0071 21.1 6.2 46 24-77 69-117 (237)
201 cd01577 IPMI_Swivel Aconatase- 24.3 89 0.0019 20.7 2.6 24 55-78 26-49 (91)
202 PRK07729 glyceraldehyde-3-phos 24.1 1E+02 0.0022 25.1 3.4 29 56-85 8-38 (343)
203 KOG3139 N-acetyltransferase [G 24.1 2.9E+02 0.0063 20.4 5.5 42 24-76 102-143 (165)
204 COG1710 Uncharacterized protei 24.0 1E+02 0.0022 22.0 3.0 54 26-87 64-123 (139)
205 COG0462 PrsA Phosphoribosylpyr 24.0 2.5E+02 0.0054 22.7 5.6 48 30-86 232-279 (314)
206 PF07693 KAP_NTPase: KAP famil 23.9 2.4E+02 0.0051 21.2 5.3 37 28-71 5-42 (325)
207 cd05802 GlmM GlmM is a bacteri 23.8 2.5E+02 0.0054 22.7 5.7 63 18-86 14-77 (434)
208 PRK08335 translation initiatio 23.7 3.3E+02 0.0071 21.4 6.1 50 27-83 121-170 (275)
209 COG3911 Predicted ATPase [Gene 23.7 77 0.0017 23.7 2.4 22 56-77 16-37 (183)
210 TIGR00524 eIF-2B_rel eIF-2B al 23.7 2.5E+02 0.0054 22.2 5.5 51 26-82 137-187 (303)
211 TIGR02406 ectoine_EctA L-2,4-d 23.6 2.5E+02 0.0053 19.1 5.8 46 19-76 80-125 (157)
212 cd05803 PGM_like4 This PGM-lik 23.5 3E+02 0.0065 22.3 6.1 61 19-86 15-77 (445)
213 COG4782 Uncharacterized protei 23.3 2.1E+02 0.0046 23.8 5.1 57 3-71 152-211 (377)
214 PRK14733 coaE dephospho-CoA ki 23.2 2.2E+02 0.0048 21.1 4.9 31 41-78 5-36 (204)
215 PF09499 RE_ApaLI: ApaLI-like 23.2 1.4E+02 0.003 22.6 3.7 27 31-67 134-160 (191)
216 PRK09732 hypothetical protein; 23.1 2.5E+02 0.0053 19.7 4.9 34 19-53 7-40 (134)
217 PRK02458 ribose-phosphate pyro 23.1 3.9E+02 0.0084 21.2 6.8 50 29-87 235-284 (323)
218 cd06422 NTP_transferase_like_1 22.9 1.3E+02 0.0029 21.3 3.5 53 18-81 23-77 (221)
219 PF00490 ALAD: Delta-aminolevu 22.8 3.3E+02 0.0071 22.2 6.1 58 30-87 61-124 (324)
220 PF14877 mIF3: Mitochondrial t 22.8 2.4E+02 0.0051 21.1 4.9 56 23-87 14-80 (181)
221 cd05569 PTS_IIB_fructose PTS_I 22.8 2.1E+02 0.0045 18.4 4.2 25 24-49 14-38 (96)
222 PRK06036 translation initiatio 22.6 3E+02 0.0064 22.3 5.8 50 27-82 167-216 (339)
223 cd01075 NAD_bind_Leu_Phe_Val_D 22.5 2.1E+02 0.0046 20.8 4.6 55 20-84 5-61 (200)
224 cd03088 ManB ManB is a bacteri 22.3 4E+02 0.0086 21.8 6.6 62 18-86 13-76 (459)
225 cd00019 AP2Ec AP endonuclease 22.3 2.4E+02 0.0051 21.0 5.0 22 29-50 13-34 (279)
226 PF00765 Autoind_synth: Autoin 22.2 3.1E+02 0.0068 19.9 5.5 45 23-81 113-157 (182)
227 PRK13497 chemoreceptor glutami 22.2 1.8E+02 0.0039 21.6 4.2 57 20-78 68-130 (184)
228 PF11547 E3_UbLigase_EDD: E3 u 22.2 69 0.0015 19.4 1.6 19 58-76 21-39 (53)
229 PF09338 Gly_reductase: Glycin 22.2 4.1E+02 0.009 22.5 6.7 49 26-82 290-341 (428)
230 COG0630 VirB11 Type IV secreto 22.1 2E+02 0.0043 22.6 4.7 30 56-85 150-182 (312)
231 PRK15414 phosphomannomutase Cp 22.1 2.2E+02 0.0047 23.4 5.0 60 18-86 19-78 (456)
232 PRK10427 putative PTS system f 22.0 1.9E+02 0.0041 19.6 4.0 27 23-50 17-43 (114)
233 cd02022 DPCK Dephospho-coenzym 22.0 86 0.0019 22.0 2.4 28 56-83 6-33 (179)
234 cd08192 Fe-ADH7 Iron-containin 22.0 3.8E+02 0.0082 21.1 6.3 54 28-86 12-65 (370)
235 PF05673 DUF815: Protein of un 21.7 3E+02 0.0065 21.5 5.5 36 38-80 48-87 (249)
236 COG1964 Predicted Fe-S oxidore 21.6 2E+02 0.0043 24.7 4.7 50 30-87 129-181 (475)
237 PRK07449 2-succinyl-5-enolpyru 21.5 3.1E+02 0.0067 22.8 5.9 49 24-83 8-57 (568)
238 PRK06546 pyruvate dehydrogenas 21.4 1.8E+02 0.0039 24.6 4.6 47 25-82 3-50 (578)
239 PRK12677 xylose isomerase; Pro 21.4 3.4E+02 0.0074 22.1 6.0 47 29-80 34-87 (384)
240 COG2518 Pcm Protein-L-isoaspar 21.4 3.7E+02 0.0081 20.4 6.2 46 30-79 109-169 (209)
241 COG1109 {ManB} Phosphomannomut 21.4 3.7E+02 0.008 22.1 6.3 63 18-86 22-84 (464)
242 TIGR00216 ispH_lytB (E)-4-hydr 21.4 3.4E+02 0.0073 21.4 5.8 38 31-77 44-92 (280)
243 PRK01259 ribose-phosphate pyro 21.3 4E+02 0.0086 21.0 6.2 51 29-88 225-275 (309)
244 COG5628 Predicted acetyltransf 21.3 91 0.002 22.4 2.3 31 55-85 77-109 (143)
245 PF01713 Smr: Smr domain; Int 21.0 2.1E+02 0.0046 17.4 7.4 65 21-88 8-74 (83)
246 PRK01184 hypothetical protein; 20.9 1.7E+02 0.0036 20.3 3.7 27 56-82 8-34 (184)
247 PF02789 Peptidase_M17_N: Cyto 20.7 2.2E+02 0.0048 18.2 4.1 30 18-47 65-94 (126)
248 PHA02588 cd deoxycytidylate de 20.7 3.3E+02 0.0072 19.6 5.5 41 32-81 115-155 (168)
249 PRK14737 gmk guanylate kinase; 20.7 1.9E+02 0.0042 20.7 4.0 30 58-87 13-43 (186)
250 PF08903 DUF1846: Domain of un 20.6 1.5E+02 0.0032 25.5 3.8 25 20-44 113-137 (491)
251 PF02367 UPF0079: Uncharacteri 20.6 2.5E+02 0.0055 19.3 4.5 35 27-72 4-38 (123)
252 PRK13834 putative autoinducer 20.5 3.6E+02 0.0078 19.9 6.0 47 23-83 123-169 (207)
253 KOG1447 GTP-specific succinyl- 20.5 3.2E+02 0.007 22.4 5.5 47 27-83 354-401 (412)
254 PRK15454 ethanol dehydrogenase 20.3 3.7E+02 0.008 21.7 6.0 55 28-87 37-91 (395)
255 PRK14318 glmM phosphoglucosami 20.2 3.8E+02 0.0082 21.8 6.1 75 4-86 5-84 (448)
256 PRK14314 glmM phosphoglucosami 20.1 4.8E+02 0.01 21.2 7.8 76 3-86 5-82 (450)
257 PRK09936 hypothetical protein; 20.1 3.7E+02 0.0081 21.6 5.8 46 29-77 41-89 (296)
258 PF00158 Sigma54_activat: Sigm 20.0 2.3E+02 0.005 20.0 4.3 37 29-72 9-45 (168)
No 1
>PTZ00129 40S ribosomal protein S14; Provisional
Probab=100.00 E-value=1e-43 Score=255.10 Aligned_cols=99 Identities=88% Similarity=1.295 Sum_probs=97.0
Q ss_pred CceeeeeccceeeccCCCCcHHHHHHHHHHHHHHHHHcCCcEEEEEEeecCCCcccCCCCChHHHHHHHHhCCCeEEEEE
Q 043606 1 ETLERITGGMKVKADRDESSPYAAMLAAQDVSQRCKERGITALHIKLRATGGNKTKTPGPGAQSALRALARSGMKIGRIE 80 (101)
Q Consensus 1 ~t~~~SsG~~gfKg~r~k~t~~Aa~~a~~~~~~~~~~~gi~~v~V~lrg~~g~~~kG~G~gr~~~lr~l~~~gl~I~~I~ 80 (101)
|++|.|+|++|||+.++|+||||||.|+|+++++|+++||+.|+|+|||+|||.++|+|+||++|||+|+++||+|.+|+
T Consensus 51 ~~~w~SsG~~gfKg~r~KsTpyAAq~aa~~~a~k~~~~Gi~~v~V~vr~~gg~~~kg~GpGr~~airaL~~~glkI~~I~ 130 (149)
T PTZ00129 51 ETLVRVTGGMKVKADRDESSPYAAMMAAQDVAARCKELGINALHIKLRATGGVRTKTPGPGAQAALRALARAGLKIGRIE 130 (149)
T ss_pred EEEEEecCcceecccccCCCHHHHHHHHHHHHHHHHHcCCeEEEEEEEecCCCCCCCCCCCHHHHHHHHHHCCCEEEEEE
Confidence 57899999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ecCCCCCCCCCCCCCCCCC
Q 043606 81 DVTPIPTDSTRRKGGRRGR 99 (101)
Q Consensus 81 D~TpiphNGcR~~K~RR~~ 99 (101)
|+||+|||||||||+||.|
T Consensus 131 DvTPiPhNGcRppk~RR~r 149 (149)
T PTZ00129 131 DVTPIPTDSTRRKGGRRGR 149 (149)
T ss_pred ecCCCCCCCCCCCCCCCCC
Confidence 9999999999999999976
No 2
>PRK09607 rps11p 30S ribosomal protein S11P; Reviewed
Probab=100.00 E-value=4.4e-42 Score=242.76 Aligned_cols=100 Identities=61% Similarity=0.973 Sum_probs=93.9
Q ss_pred Cceeee-eccceeeccCCCCcHHHHHHHHHHHHHHHHHcCCcEEEEEEeecCCCcccCCCCChHHHHHHHHhCCCeEEEE
Q 043606 1 ETLERI-TGGMKVKADRDESSPYAAMLAAQDVSQRCKERGITALHIKLRATGGNKTKTPGPGAQSALRALARSGMKIGRI 79 (101)
Q Consensus 1 ~t~~~S-sG~~gfKg~r~k~t~~Aa~~a~~~~~~~~~~~gi~~v~V~lrg~~g~~~kG~G~gr~~~lr~l~~~gl~I~~I 79 (101)
|+++|+ +|.+||+|.+ |+||||||.|+|+++++|+++||+.|+|+|+|+|||..+-+|+||++||++|+++||+|.+|
T Consensus 32 ~~~~~~S~G~~g~kg~k-K~TpyAAq~aae~~~~~~~~~Gi~~v~v~vkG~Ggn~~~~~G~Gr~~airal~~~glkI~~I 110 (132)
T PRK09607 32 ETIAKSSGGMVVKADRD-ESSPYAAMQAAEKAAEDAKEKGITGVHIKVRAPGGNGQKSPGPGAQAAIRALARAGLRIGRI 110 (132)
T ss_pred EEEEEecCcceeeCCCc-cCCHHHHHHHHHHHHHHHHHcCCcEEEEEEEecCCCCCcCCCCcHHHHHHHHHHCCCEEEEE
Confidence 366665 5556788887 99999999999999999999999999999999999999999999999999999999999999
Q ss_pred EecCCCCCCCCCCCCCCCCCCC
Q 043606 80 EDVTPIPTDSTRRKGGRRGRRL 101 (101)
Q Consensus 80 ~D~TpiphNGcR~~K~RR~~~~ 101 (101)
+|+||+|||||||||+||+|||
T Consensus 111 ~DvTpiPhNGCRp~K~RR~r~~ 132 (132)
T PRK09607 111 EDVTPIPHDGTRPPGGRRGRRV 132 (132)
T ss_pred EEcCCCCCCCCCCCCCCCCCCC
Confidence 9999999999999999999996
No 3
>COG0100 RpsK Ribosomal protein S11 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=1.5e-38 Score=223.77 Aligned_cols=89 Identities=49% Similarity=0.800 Sum_probs=86.4
Q ss_pred CceeeeeccceeeccCCCCcHHHHHHHHHHHHHHHHHcCCcEEEEEEeecCCCcccCCCCChHHHHHHHHhCCCeEEEEE
Q 043606 1 ETLERITGGMKVKADRDESSPYAAMLAAQDVSQRCKERGITALHIKLRATGGNKTKTPGPGAQSALRALARSGMKIGRIE 80 (101)
Q Consensus 1 ~t~~~SsG~~gfKg~r~k~t~~Aa~~a~~~~~~~~~~~gi~~v~V~lrg~~g~~~kG~G~gr~~~lr~l~~~gl~I~~I~ 80 (101)
|++|.|+|++|||+++ |+||||||.|++.+++.++++|++.|+|+| +|||+||++|||+|+.+|++|.+|+
T Consensus 41 ~i~wassG~~gfk~~r-k~tpyAA~~aa~~aa~~a~e~Gi~~v~v~v--------kgpG~GreaAiraL~~ag~~i~~I~ 111 (129)
T COG0100 41 VIIWASSGGMGFKGSR-KSTPYAAQLAAEDAAKKAKEHGIKSVEVKV--------KGPGPGREAAIRALAAAGLKITRIE 111 (129)
T ss_pred EEEEEecCCceEcCCC-CCCHHHHHHHHHHHHHHHHHhCccEEEEEE--------ECCCCcHHHHHHHHHHccceEEEEE
Confidence 5789999999999999 999999999999999999999999999999 7899999999999999999999999
Q ss_pred ecCCCCCCCCCCCCCCCC
Q 043606 81 DVTPIPTDSTRRKGGRRG 98 (101)
Q Consensus 81 D~TpiphNGcR~~K~RR~ 98 (101)
|+||+|||||||||+||+
T Consensus 112 DvTPiphnG~Rppk~RR~ 129 (129)
T COG0100 112 DVTPIPHNGCRPPKRRRV 129 (129)
T ss_pred EcCCCCCCCCCCCCCCCC
Confidence 999999999999999985
No 4
>PF00411 Ribosomal_S11: Ribosomal protein S11; InterPro: IPR001971 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. Ribosomal protein S11 [] plays an essential role in selecting the correct tRNA in protein biosynthesis. It is located on the large lobe of the small ribosomal subunit. On the basis of sequence similarities, S11 belongs to a family of bacterial, archaeal and eukaryotic ribosomal proteins [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 2YKR_K 3U5C_O 3O2Z_H 3IZB_K 3U5G_O 3O30_H 1S1H_K 3BBN_K 2XZN_K 2XZM_K ....
Probab=100.00 E-value=3.9e-38 Score=215.72 Aligned_cols=87 Identities=44% Similarity=0.697 Sum_probs=80.9
Q ss_pred ceeeeeccceeeccCCCCcHHHHHHHHHHHHHHHHHcCCcEEEEEEeecCCCcccCCCCChHHHHHHHHhCCCeEEEEEe
Q 043606 2 TLERITGGMKVKADRDESSPYAAMLAAQDVSQRCKERGITALHIKLRATGGNKTKTPGPGAQSALRALARSGMKIGRIED 81 (101)
Q Consensus 2 t~~~SsG~~gfKg~r~k~t~~Aa~~a~~~~~~~~~~~gi~~v~V~lrg~~g~~~kG~G~gr~~~lr~l~~~gl~I~~I~D 81 (101)
.+|.|+|++|||+++ |+||||||++++.++++|+++|++.|+|+| +|+|+||+++|++|+.+|++|.+|+|
T Consensus 24 ~~~~S~G~~gfK~~r-k~t~~Aa~~~a~~~~~~~~~~gi~~v~v~i--------kG~g~gr~~~lk~l~~~gl~I~~I~D 94 (110)
T PF00411_consen 24 LFWSSAGSLGFKGAR-KSTPYAAQQAAEKIAKKAKELGIKTVRVKI--------KGFGPGREAALKALKKSGLKIVSITD 94 (110)
T ss_dssp EEEEETTTSSTTTTC-GSSHHHHHHHHHHHHHHHHCTTEEEEEEEE--------ESSSTTHHHHHHHHHHTTSEEEEEEE
T ss_pred EEEEecccccccccc-ccCHHHHHHHHHHHHHHHHHcCCeEEEEEE--------cCCCccHHHHHHHHHhcCCEEEEEEe
Confidence 578999999999999 999999999999999999999999999999 78999999999999999999999999
Q ss_pred cCCCCCCCCCCCCCCC
Q 043606 82 VTPIPTDSTRRKGGRR 97 (101)
Q Consensus 82 ~TpiphNGcR~~K~RR 97 (101)
+||+|||||||||+||
T Consensus 95 ~T~iphnGcR~kK~RR 110 (110)
T PF00411_consen 95 VTPIPHNGCRPKKKRR 110 (110)
T ss_dssp ETT--SSSS--TTTTT
T ss_pred ecCCCCCCCCCCCCCC
Confidence 9999999999999998
No 5
>PRK05309 30S ribosomal protein S11; Validated
Probab=100.00 E-value=1e-37 Score=219.31 Aligned_cols=88 Identities=40% Similarity=0.677 Sum_probs=84.5
Q ss_pred ceeeeeccceeeccCCCCcHHHHHHHHHHHHHHHHHcCCcEEEEEEeecCCCcccCCCCChHHHHHHHHhCCCeEEEEEe
Q 043606 2 TLERITGGMKVKADRDESSPYAAMLAAQDVSQRCKERGITALHIKLRATGGNKTKTPGPGAQSALRALARSGMKIGRIED 81 (101)
Q Consensus 2 t~~~SsG~~gfKg~r~k~t~~Aa~~a~~~~~~~~~~~gi~~v~V~lrg~~g~~~kG~G~gr~~~lr~l~~~gl~I~~I~D 81 (101)
.+|.|+|.+||||.+ |+||||||.+++.++++++++||+.|+|+| +|+|+||+++|++|+.+|++|.+|+|
T Consensus 41 ~~~~S~G~~gfKg~r-K~T~~Aa~~aa~~~~~~~~~~gi~~v~v~i--------kG~G~Gr~~air~L~~~glkI~~I~D 111 (128)
T PRK05309 41 ISWASAGGLGFKGSR-KSTPYAAQVAAEDAAKKAKEHGMKTVEVFV--------KGPGSGRESAIRALQAAGLEVTSIKD 111 (128)
T ss_pred EEEEecCccEeCCCc-cCCHHHHHHHHHHHHHHHHHcCCcEEEEEE--------ECCCCcHHHHHHHHHHCCCEEEEEEE
Confidence 457799999999999 999999999999999999999999999999 78999999999999999999999999
Q ss_pred cCCCCCCCCCCCCCCCC
Q 043606 82 VTPIPTDSTRRKGGRRG 98 (101)
Q Consensus 82 ~TpiphNGcR~~K~RR~ 98 (101)
+||+|||||||||+||+
T Consensus 112 ~TpiphNGcR~~K~RRv 128 (128)
T PRK05309 112 VTPIPHNGCRPPKRRRV 128 (128)
T ss_pred cCCCCCCCcCcCCCCCC
Confidence 99999999999999985
No 6
>TIGR03632 bact_S11 30S ribosomal protein S11. This model describes the bacterial 30S ribosomal protein S11. Cutoffs are set such that the model excludes archaeal and eukaryotic ribosomal proteins, but many chloroplast and mitochondrial equivalents of S11 are detected.
Probab=100.00 E-value=1.1e-36 Score=208.34 Aligned_cols=85 Identities=38% Similarity=0.636 Sum_probs=81.8
Q ss_pred ceeeeeccceeeccCCCCcHHHHHHHHHHHHHHHHHcCCcEEEEEEeecCCCcccCCCCChHHHHHHHHhCCCeEEEEEe
Q 043606 2 TLERITGGMKVKADRDESSPYAAMLAAQDVSQRCKERGITALHIKLRATGGNKTKTPGPGAQSALRALARSGMKIGRIED 81 (101)
Q Consensus 2 t~~~SsG~~gfKg~r~k~t~~Aa~~a~~~~~~~~~~~gi~~v~V~lrg~~g~~~kG~G~gr~~~lr~l~~~gl~I~~I~D 81 (101)
..|.|+|++||||.+ |+||||||.++|.++++++++||+.|+|++ +|+|+||+++|++|+++|++|.+|+|
T Consensus 24 ~~~~S~G~~gfkg~r-k~t~~Aa~~~a~~~~~~~~~~gi~~v~v~~--------kG~G~gr~~~ir~l~~~glkI~~I~D 94 (108)
T TIGR03632 24 LSWASAGAVGFKGSK-KSTPYAAQLAAEDAAKKAKEFGMKTVDVYV--------KGPGAGRESAIRALQAAGLEVTSIKD 94 (108)
T ss_pred EEEEecCceeeCCCc-cCCHHHHHHHHHHHHHHHHHcCCcEEEEEE--------ECCCCcHHHHHHHHHHCCCEEEEEEE
Confidence 467799999999999 999999999999999999999999999999 78999999999999999999999999
Q ss_pred cCCCCCCCCCCCCC
Q 043606 82 VTPIPTDSTRRKGG 95 (101)
Q Consensus 82 ~TpiphNGcR~~K~ 95 (101)
+||+|||||||||+
T Consensus 95 ~T~iphNGcR~~K~ 108 (108)
T TIGR03632 95 VTPIPHNGCRPPKR 108 (108)
T ss_pred cCCCCCCCcCCCCC
Confidence 99999999999984
No 7
>TIGR03628 arch_S11P archaeal ribosomal protein S11P. This model describes exclusively the archaeal ribosomal protein S11P. It excludes homologous ribosomal proteins S14 from eukaryotes and S11 from bacteria.
Probab=100.00 E-value=1.2e-35 Score=205.51 Aligned_cols=88 Identities=63% Similarity=0.949 Sum_probs=83.2
Q ss_pred ceee-eeccceeeccCCCCcHHHHHHHHHHHHHHHHHcCCcEEEEEEeecCCCcccCCCCChHHHHHHHHhCCCeEEEEE
Q 043606 2 TLER-ITGGMKVKADRDESSPYAAMLAAQDVSQRCKERGITALHIKLRATGGNKTKTPGPGAQSALRALARSGMKIGRIE 80 (101)
Q Consensus 2 t~~~-SsG~~gfKg~r~k~t~~Aa~~a~~~~~~~~~~~gi~~v~V~lrg~~g~~~kG~G~gr~~~lr~l~~~gl~I~~I~ 80 (101)
+++| |+|.+|||+.+ |+||||||.|+|+++++|+++||+.|+|+|+|.|||.++.+|+||++|||+|+++||+|.+|+
T Consensus 26 ~~~~~S~G~~g~kg~k-k~TpyAAq~aa~~~~~~~~~~Gi~~v~v~ikG~gg~~~~~~G~Gr~~air~l~~~glkI~~I~ 104 (114)
T TIGR03628 26 TIARSSGGMVVKADRD-ESSPYAAMQAAGRAAEKAKERGITGLHIKVRAPGGNGQKSPGPGAQAAIRALARAGLRIGRIE 104 (114)
T ss_pred EEEEecCcceEeCCCc-cCCHHHHHHHHHHHHHHHHHcCCcEEEEEEEecCCCCCCCCCCcHHHHHHHHHHCCCEEEEEE
Confidence 4555 56667888888 999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ecCCCCCCCC
Q 043606 81 DVTPIPTDST 90 (101)
Q Consensus 81 D~TpiphNGc 90 (101)
|+||+|||||
T Consensus 105 DvTpiPhNGC 114 (114)
T TIGR03628 105 DVTPIPHDGT 114 (114)
T ss_pred EcCCCCCCCC
Confidence 9999999999
No 8
>PTZ00090 40S ribosomal protein S11; Provisional
Probab=100.00 E-value=2.3e-34 Score=217.12 Aligned_cols=86 Identities=19% Similarity=0.397 Sum_probs=81.6
Q ss_pred eeeeeccceeeccCCCCcHHHHHHHHHHHHHHHHHcCCcEEEEEEeecCCCcccCCCCChHHHHHHHHhCCCeEEEEEec
Q 043606 3 LERITGGMKVKADRDESSPYAAMLAAQDVSQRCKERGITALHIKLRATGGNKTKTPGPGAQSALRALARSGMKIGRIEDV 82 (101)
Q Consensus 3 ~~~SsG~~gfKg~r~k~t~~Aa~~a~~~~~~~~~~~gi~~v~V~lrg~~g~~~kG~G~gr~~~lr~l~~~gl~I~~I~D~ 82 (101)
.|.|+|.+||||++ |+||||||.|+|+++++|+++||+.|+|.| +|+| +||+|||+|+.+||+|.+|.|+
T Consensus 145 ~WSSAG~~GFKGsK-KsTpfAAQ~aae~aakka~~~GIk~V~V~v--------KGpG-gREtALRaL~~~GLkIt~I~Dv 214 (233)
T PTZ00090 145 FGSFAGNVGFRKKL-QQSERCAYRIGENIAKKCRRLGIFAVDIKF--------RRIM-RVETVLQAFYANGLQVTQIIHE 214 (233)
T ss_pred EEEcccccCcccCc-cCCHHHHHHHHHHHHHHHHHcCCeEEEEEE--------eCCC-hHHHHHHHHHHCCCEEEEEEEC
Confidence 56789999999999 999999999999999999999999999999 7788 6999999999999999999999
Q ss_pred CCCCC---CCCCCCCCCCC
Q 043606 83 TPIPT---DSTRRKGGRRG 98 (101)
Q Consensus 83 Tpiph---NGcR~~K~RR~ 98 (101)
||+|| |||||||+||+
T Consensus 215 TpiPHNG~NGCRPpKKRRV 233 (233)
T PTZ00090 215 PRLPKCGLNAVKPRKRRRV 233 (233)
T ss_pred CCCCcCCCCCCCCCCCCCC
Confidence 99999 55999999885
No 9
>CHL00041 rps11 ribosomal protein S11
Probab=100.00 E-value=1.3e-32 Score=190.52 Aligned_cols=80 Identities=34% Similarity=0.588 Sum_probs=77.1
Q ss_pred ceeeeeccceeeccCCCCcHHHHHHHHHHHHHHHHHcCCcEEEEEEeecCCCcccCCCCChHHHHHHHHhCCCeEEEEEe
Q 043606 2 TLERITGGMKVKADRDESSPYAAMLAAQDVSQRCKERGITALHIKLRATGGNKTKTPGPGAQSALRALARSGMKIGRIED 81 (101)
Q Consensus 2 t~~~SsG~~gfKg~r~k~t~~Aa~~a~~~~~~~~~~~gi~~v~V~lrg~~g~~~kG~G~gr~~~lr~l~~~gl~I~~I~D 81 (101)
..|.|+|++||||++ |+||||||.++|+++++++++||+.|+|++ +|+|+||+++|++|+++|++|.+|+|
T Consensus 37 l~~~S~G~~gfKg~r-K~T~~Aa~~~a~~~~~~~~~~gi~~v~I~i--------kG~G~Gr~~~ir~l~~~glkI~~I~D 107 (116)
T CHL00041 37 ISWSSAGACGFKGAR-KGTPFAAQTAAENAIRTVIDQGMKRAEVMI--------KGPGLGRDTALRAIRRSGLKLSSIRD 107 (116)
T ss_pred EEEEecCceeeCCCc-cCCHHHHHHHHHHHHHHHHHcCCcEEEEEE--------ECCCCcHHHHHHHHHHCCCEEEEEEE
Confidence 356789999999999 999999999999999999999999999999 78999999999999999999999999
Q ss_pred cCCCCCCCC
Q 043606 82 VTPIPTDST 90 (101)
Q Consensus 82 ~TpiphNGc 90 (101)
+||+|||||
T Consensus 108 ~TpiphNGC 116 (116)
T CHL00041 108 VTPMPHNGC 116 (116)
T ss_pred cCCCCCCCC
Confidence 999999999
No 10
>KOG0408 consensus Mitochondrial/chloroplast ribosomal protein S11 [Translation, ribosomal structure and biogenesis]
Probab=99.97 E-value=5.3e-32 Score=197.73 Aligned_cols=88 Identities=30% Similarity=0.457 Sum_probs=84.8
Q ss_pred ceeeeeccceeeccCCCCcHHHHHHHHHHHHHHHHHcCCcEEEEEEeecCCCcccCCCCChHHHHHHHHhCCCeEEEEEe
Q 043606 2 TLERITGGMKVKADRDESSPYAAMLAAQDVSQRCKERGITALHIKLRATGGNKTKTPGPGAQSALRALARSGMKIGRIED 81 (101)
Q Consensus 2 t~~~SsG~~gfKg~r~k~t~~Aa~~a~~~~~~~~~~~gi~~v~V~lrg~~g~~~kG~G~gr~~~lr~l~~~gl~I~~I~D 81 (101)
.+|.|||.+||++.| |+|++|||.++-.++++++++|+..|+|.+ ||+||||++||++|...||.|++|+|
T Consensus 103 i~~~ScgteGFrntr-kgT~iAaQtaavaa~~r~v~~G~~~vrV~V--------kGlGpGRmsa~kgl~m~Gl~vvsItD 173 (190)
T KOG0408|consen 103 ISWSSCGTEGFRNTR-KGTPIAAQTAAVAAIRRAVDQGMQTVRVRV--------KGLGPGRMSALKGLRMGGLLVVSITD 173 (190)
T ss_pred EEEeecccccccccc-cCCchhHHHHHHHHHHHHHHhcceEEEEEE--------ecCCccHHHHHhhhhhcceEEEEeec
Confidence 357799999999999 999999999999999999999999999999 88999999999999999999999999
Q ss_pred cCCCCCCCCCCCCCCCC
Q 043606 82 VTPIPTDSTRRKGGRRG 98 (101)
Q Consensus 82 ~TpiphNGcR~~K~RR~ 98 (101)
.||+|||||||+|+||.
T Consensus 174 ~Tp~~~ng~RPrK~Rrl 190 (190)
T KOG0408|consen 174 NTPMPHNGCRPRKKRRL 190 (190)
T ss_pred CCcCCCCCCCccccccC
Confidence 99999999999999984
No 11
>KOG0407 consensus 40S ribosomal protein S14 [Translation, ribosomal structure and biogenesis]
Probab=99.96 E-value=2.8e-29 Score=174.45 Aligned_cols=101 Identities=90% Similarity=1.316 Sum_probs=99.6
Q ss_pred CceeeeeccceeeccCCCCcHHHHHHHHHHHHHHHHHcCCcEEEEEEeecCCCcccCCCCChHHHHHHHHhCCCeEEEEE
Q 043606 1 ETLERITGGMKVKADRDESSPYAAMLAAQDVSQRCKERGITALHIKLRATGGNKTKTPGPGAQSALRALARSGMKIGRIE 80 (101)
Q Consensus 1 ~t~~~SsG~~gfKg~r~k~t~~Aa~~a~~~~~~~~~~~gi~~v~V~lrg~~g~~~kG~G~gr~~~lr~l~~~gl~I~~I~ 80 (101)
||+....|+|..|..++.++||||++||+.++.+|+++||+.+||+||++||++.+.+|||.+++||+|.++|++|..|+
T Consensus 39 eti~rvtggmkvkadrdesspyaamlaaqdva~kck~~gi~alh~klratgg~ktktpgpgaqsalralar~gmrigrie 118 (139)
T KOG0407|consen 39 ETIVRVTGGMKVKADRDESSPYAAMLAAQDVAAKCKELGITALHIKLRATGGTKTKTPGPGAQSALRALARSGMRIGRIE 118 (139)
T ss_pred eEEEEecCCeEEecccccCChHHHHHHHHHHHHHHHhcCeeEEEEEEEecCCcccCCCCccHHHHHHHHHHhcceeeeec
Confidence 78999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ecCCCCCCCCCCCCCCCCCCC
Q 043606 81 DVTPIPTDSTRRKGGRRGRRL 101 (101)
Q Consensus 81 D~TpiphNGcR~~K~RR~~~~ 101 (101)
|+||+|.+-.|.+..||.||+
T Consensus 119 dvtpip~d~trrkggrrgrrl 139 (139)
T KOG0407|consen 119 DVTPIPSDSTRRKGGRRGRRL 139 (139)
T ss_pred ccccCCccchhhccCcccccC
Confidence 999999999999999999986
No 12
>PRK08569 rpl18p 50S ribosomal protein L18P; Reviewed
Probab=92.73 E-value=1.1 Score=33.86 Aligned_cols=67 Identities=19% Similarity=0.291 Sum_probs=48.2
Q ss_pred cHHHHHHHHHHHHHHHHHcCCcEEEEEEeecCCCcccCCCCChHHHHHHHHhCCCeEEEEEecCCCCCCCCCCCCCCCCC
Q 043606 20 SPYAAMLAAQDVSQRCKERGITALHIKLRATGGNKTKTPGPGAQSALRALARSGMKIGRIEDVTPIPTDSTRRKGGRRGR 99 (101)
Q Consensus 20 t~~Aa~~a~~~~~~~~~~~gi~~v~V~lrg~~g~~~kG~G~gr~~~lr~l~~~gl~I~~I~D~TpiphNGcR~~K~RR~~ 99 (101)
.--||..+++.+++++++.|++.+.+-. ||...+ .|--=.+++++...+||+ +|||-.|.|---|.+
T Consensus 78 N~~AAy~vG~llA~ral~kGi~~vvfDr---Gg~~yh-~gGRV~A~akgArd~GL~---------fPh~~~~~p~~~ri~ 144 (193)
T PRK08569 78 NTPAAYLTGLLAGKKALKAGVEEAVLDI---GLHRPT-KGSRVFAALKGAIDAGLE---------IPHGEEVLPDEDRIR 144 (193)
T ss_pred CHHHHHHHHHHHHHHHHHCCCCEEEEec---CCcccc-CCccHHHHHHHHHHcCCc---------CCCCCCcCCCccccc
Confidence 3448888999999999999999988776 222222 111234577888889997 499988888765543
No 13
>cd00432 Ribosomal_L18_L5e Ribosomal L18/L5e: L18 (L5e) is a ribosomal protein found in the central protuberance (CP) of the large subunit. L18 binds 5S rRNA and induces a conformational change that stimulates the binding of L5 to 5S rRNA. Association of 5S rRNA with 23S rRNA depends on the binding of L18 and L5 to 5S rRNA. L18/L5e is generally described as L18 in prokaryotes and archaea, and as L5e (or L5) in eukaryotes. In bacteria, the CP proteins L5, L18, and L25 are required for the ribosome to incorporate 5S rRNA into the large subunit, one of the last steps in ribosome assembly. In archaea, both L18 and L5 bind 5S rRNA; in eukaryotes, only the L18 homolog (L5e) binds 5S rRNA but a homolog to L5 is also identified.
Probab=90.99 E-value=1.6 Score=28.89 Aligned_cols=61 Identities=18% Similarity=0.194 Sum_probs=40.0
Q ss_pred eeccceeecc-CCCCcHHHHHHHHHHHHHHHHHcCCcEEEEEEeecCCCcccCCC-CChH-HHHHHHHhCCC
Q 043606 6 ITGGMKVKAD-RDESSPYAAMLAAQDVSQRCKERGITALHIKLRATGGNKTKTPG-PGAQ-SALRALARSGM 74 (101)
Q Consensus 6 SsG~~gfKg~-r~k~t~~Aa~~a~~~~~~~~~~~gi~~v~V~lrg~~g~~~kG~G-~gr~-~~lr~l~~~gl 74 (101)
|+-...+++. .....-.||..+++.++++|++.|+..+.+-. .+.- -||. +++.++...||
T Consensus 40 st~e~~~~~~~~~~~n~~aA~~vG~~la~r~~~~gi~~vv~D~--------~~~~~~grv~a~~~~~r~~Gl 103 (103)
T cd00432 40 STLELAIKGVLGSGNNVEAAYLVGRLLAKRALEKGIKKVVFDR--------GGYRYHGRVKALAKGAREGGL 103 (103)
T ss_pred ecCchhhcccccCCCcHHHHHHHHHHHHHHHHHCCCCEEEEeC--------CCcccccHHHHHHHHHHHcCC
Confidence 3333444442 22456678999999999999999999988876 2222 2343 45566766664
No 14
>PF00861 Ribosomal_L18p: Ribosomal L18p/L5e family; InterPro: IPR005484 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This family includes L18 from bacteria and L5 from eukaryotes. The ribosomal 5S RNA is the only known rRNA species to bind a ribosomal protein before its assembly into the ribosomal subunits []. In eukaryotes, the 5S rRNA molecule binds one protein species, a 34kDa protein which has been implicated in the intracellular transport of 5 S rRNA, while in bacteria it binds two or three different protein species []. ; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 4A1E_M 4A1C_M 4A1A_M 4A17_M 3IZR_Q 3O58_E 1S1I_E 3IZS_Q 3O5H_E 1KQS_M ....
Probab=90.95 E-value=0.52 Score=32.42 Aligned_cols=49 Identities=18% Similarity=0.236 Sum_probs=36.1
Q ss_pred cHHHHHHHHHHHHHHHHHcCCcEEEEEEeecCCCcccCCCC-Ch-HHHHHHHHhCCCeE
Q 043606 20 SPYAAMLAAQDVSQRCKERGITALHIKLRATGGNKTKTPGP-GA-QSALRALARSGMKI 76 (101)
Q Consensus 20 t~~Aa~~a~~~~~~~~~~~gi~~v~V~lrg~~g~~~kG~G~-gr-~~~lr~l~~~gl~I 76 (101)
.--||..+++.++++|++.|+..|.+-. .|+-. || .+++.++...||+|
T Consensus 69 n~~aa~~vG~lla~ra~~~gi~~v~fdr--------~~~~y~grv~a~~~~~re~Gl~f 119 (119)
T PF00861_consen 69 NVEAAYLVGELLAKRALEKGIAKVVFDR--------GGYKYHGRVKALADGAREGGLEF 119 (119)
T ss_dssp SHHHHHHHHHHHHHHHHHTTSSEEEECT--------STSSSSSHHHHHHHHHHHTTCB-
T ss_pred CEehHHHHHHHHHHHHHHcCCcEEEEcC--------CCCcccHHHHHHHHHHHHcCCCC
Confidence 4558899999999999999998887765 33222 34 34667888889875
No 15
>TIGR00060 L18_bact ribosomal protein L18, bacterial type. The archaeal and eukaryotic type rpL18 is not detectable under this model.
Probab=87.01 E-value=4.8 Score=27.89 Aligned_cols=51 Identities=27% Similarity=0.351 Sum_probs=35.3
Q ss_pred CCcHHHHHHHHHHHHHHHHHcCCcEEEEEEeecCCCcccCCCCChHH-HHHHHHhCCCe
Q 043606 18 ESSPYAAMLAAQDVSQRCKERGITALHIKLRATGGNKTKTPGPGAQS-ALRALARSGMK 75 (101)
Q Consensus 18 k~t~~Aa~~a~~~~~~~~~~~gi~~v~V~lrg~~g~~~kG~G~gr~~-~lr~l~~~gl~ 75 (101)
..+--||..+++.++++|++.||+.|..-- +|-.. -||-. +..++...||+
T Consensus 62 ~~n~~aA~~vG~~la~ra~~~gi~~vvfDr---gg~~Y----hGrv~A~a~~aRe~Gl~ 113 (114)
T TIGR00060 62 TGNKDAAKKVGKLVAERLKEKGIKDVVFDR---GGYKY----HGRVAALAEAAREAGLN 113 (114)
T ss_pred CCCHHHHHHHHHHHHHHHHHCCCCEEEEeC---CCCcc----hHHHHHHHHHHHHhCCC
Confidence 445568899999999999999999986553 22222 24543 44666777876
No 16
>PRK05593 rplR 50S ribosomal protein L18; Reviewed
Probab=86.62 E-value=2.9 Score=28.98 Aligned_cols=51 Identities=25% Similarity=0.377 Sum_probs=35.4
Q ss_pred CCcHHHHHHHHHHHHHHHHHcCCcEEEEEEeecCCCcccCCCCCh-HHHHHHHHhCCCe
Q 043606 18 ESSPYAAMLAAQDVSQRCKERGITALHIKLRATGGNKTKTPGPGA-QSALRALARSGMK 75 (101)
Q Consensus 18 k~t~~Aa~~a~~~~~~~~~~~gi~~v~V~lrg~~g~~~kG~G~gr-~~~lr~l~~~gl~ 75 (101)
...--||..+++.++++|++.||+.+..-- +|...+ || .+++.++..+||+
T Consensus 65 ~~n~~aa~~vG~~la~ra~~~gi~~vvfDr---g~~~yh----GrV~a~a~~are~Gl~ 116 (117)
T PRK05593 65 GGNKEAAKKVGKLIAERAKAKGIKQVVFDR---GGYKYH----GRVKALADAAREAGLK 116 (117)
T ss_pred CCCHHHHHHHHHHHHHHHHHCCCCEEEEcC---CCCccc----HHHHHHHHHHHHhCCC
Confidence 445568899999999999999999975553 222222 23 3455667777876
No 17
>CHL00139 rpl18 ribosomal protein L18; Validated
Probab=85.77 E-value=2.1 Score=29.35 Aligned_cols=50 Identities=24% Similarity=0.393 Sum_probs=34.5
Q ss_pred CcHHHHHHHHHHHHHHHHHcCCcEEEEEEeecCCCcccCCCCCh-HHHHHHHHhCCCe
Q 043606 19 SSPYAAMLAAQDVSQRCKERGITALHIKLRATGGNKTKTPGPGA-QSALRALARSGMK 75 (101)
Q Consensus 19 ~t~~Aa~~a~~~~~~~~~~~gi~~v~V~lrg~~g~~~kG~G~gr-~~~lr~l~~~gl~ 75 (101)
..--||..+++.++++|++.||+.|..-- +|.... || .+++.++..+||+
T Consensus 58 ~n~~aA~~vG~lla~ra~~~gi~~vvfDr---gg~~yh----GrV~a~a~~are~GL~ 108 (109)
T CHL00139 58 STCDASKLVGQKLAKKSLKKGITKVVFDR---GGKLYH----GRIKALAEAAREAGLQ 108 (109)
T ss_pred CCHHHHHHHHHHHHHHHHHCCCCEEEEcC---CCCccc----hHHHHHHHHHHHhCCC
Confidence 34458888999999999999999986663 222211 33 3455667777876
No 18
>COG0256 RplR Ribosomal protein L18 [Translation, ribosomal structure and biogenesis]
Probab=85.58 E-value=3.1 Score=29.41 Aligned_cols=48 Identities=17% Similarity=0.214 Sum_probs=34.6
Q ss_pred HHHHHHHHHHHHHHHHHcCCcEEEEEEeecCCCcccCCCC-ChHH-HHHHHHhCCCeE
Q 043606 21 PYAAMLAAQDVSQRCKERGITALHIKLRATGGNKTKTPGP-GAQS-ALRALARSGMKI 76 (101)
Q Consensus 21 ~~Aa~~a~~~~~~~~~~~gi~~v~V~lrg~~g~~~kG~G~-gr~~-~lr~l~~~gl~I 76 (101)
--||..+++.+++++++.||+.+.+-. .|+=+ ||-. ++++...+||+|
T Consensus 76 ~~aA~~vG~lia~ra~~kgi~~vVfdr--------~g~~yhgRV~Ala~~AreaGL~f 125 (125)
T COG0256 76 TEAAYLVGKLIAERALAKGIEEVVFDR--------GGYKYHGRVAALADGAREAGLEF 125 (125)
T ss_pred HHHHHHHHHHHHHHHHHcCCcEEEEcC--------CCCCcchHHHHHHHHHHHcCcCC
Confidence 448888999999999999999999665 44443 3433 445566678764
No 19
>cd05313 NAD_bind_2_Glu_DH NAD(P) binding domain of glutamate dehydrogenase, subgroup 2. Amino acid dehydrogenase (DH) is a widely distributed family of enzymes that catalyzes the oxidative deamination of an amino acid to its keto acid and ammonia with concomitant reduction of NADP+. Glutamate DH is a multidomain enzyme that catalyzes the reaction from glutamate to 2-oxyoglutarate and ammonia in the presence of NAD or NADP. It is present in all organisms. Enzymes involved in ammonia asimilation are typically NADP+-dependent, while those involved in glutamate catabolism are generally NAD+-dependent. Amino acid DH-like NAD(P)-binding domains are members of the Rossmann fold superfamily and include glutamate, leucine, and phenylalanine DHs, methylene tetrahydrofolate DH, methylene-tetrahydromethanopterin DH, methylene-tetrahydropholate DH/cyclohydrolase, Shikimate DH-like proteins, malate oxidoreductases, and glutamyl tRNA reductase. Amino acid DHs catalyze the deamination of amino acids t
Probab=79.83 E-value=5.1 Score=31.14 Aligned_cols=61 Identities=16% Similarity=0.212 Sum_probs=44.3
Q ss_pred CCcHHHHHHHHHHHHHHHHHcCCcEEEEEEeecCCCcccCCCCChHHHHHHHHhCCCeEEEEEecCCCCC
Q 043606 18 ESSPYAAMLAAQDVSQRCKERGITALHIKLRATGGNKTKTPGPGAQSALRALARSGMKIGRIEDVTPIPT 87 (101)
Q Consensus 18 k~t~~Aa~~a~~~~~~~~~~~gi~~v~V~lrg~~g~~~kG~G~gr~~~lr~l~~~gl~I~~I~D~Tpiph 87 (101)
..|-|....+++.+++.. +..++-..|-| .|||.-=..+.+.|...|.+|+-|.|.+-.-|
T Consensus 15 ~aTg~Gv~~~~~~~~~~~-~~~l~g~~vaI--------qGfGnVG~~~a~~L~e~GakvvaVsD~~G~i~ 75 (254)
T cd05313 15 EATGYGLVYFVEEMLKDR-NETLKGKRVAI--------SGSGNVAQYAAEKLLELGAKVVTLSDSKGYVY 75 (254)
T ss_pred chhHHHHHHHHHHHHHhc-CCCcCCCEEEE--------ECCCHHHHHHHHHHHHCCCEEEEEECCCceEE
Confidence 667777766666555544 45566789999 78996444566788999999999999665444
No 20
>PRK13260 2,3-diketo-L-gulonate reductase; Provisional
Probab=79.75 E-value=16 Score=29.44 Aligned_cols=73 Identities=12% Similarity=0.086 Sum_probs=57.2
Q ss_pred eeeccCCCCcHHHHHHHHHHHHHHHHHcCCcEEEEEEeecCCCcccCCCCChHHHHHHHHhCCCeEEEEEecCCC--CCC
Q 043606 11 KVKADRDESSPYAAMLAAQDVSQRCKERGITALHIKLRATGGNKTKTPGPGAQSALRALARSGMKIGRIEDVTPI--PTD 88 (101)
Q Consensus 11 gfKg~r~k~t~~Aa~~a~~~~~~~~~~~gi~~v~V~lrg~~g~~~kG~G~gr~~~lr~l~~~gl~I~~I~D~Tpi--phN 88 (101)
-+.+.. --.++++..+.+.++++|++.|+-.|.|+= ++.+|..-..+.++.. .|+-=+...+..|. ||+
T Consensus 78 ~~Dg~~-g~G~~~~~~am~~aiekAr~~Gi~~v~vrn-------s~H~G~~g~y~~~aa~-~G~igi~~tn~~~~vaP~G 148 (332)
T PRK13260 78 QWDAQR-AIGNLTAKKMMDRAIELARDHGIGLVALRN-------ANHWMRGGSYGWQAAE-KGYIGICWTNSIAVMPPWG 148 (332)
T ss_pred EEECCC-CchHHHHHHHHHHHHHHHHHhCEEEEEEcC-------CCchhhHHHHHHHHHH-CCCEEEEEeCCCCeeCCCC
Confidence 466666 778999999999999999999999988874 4789988888877544 67666666776665 888
Q ss_pred CCCC
Q 043606 89 STRR 92 (101)
Q Consensus 89 GcR~ 92 (101)
|-+|
T Consensus 149 g~~~ 152 (332)
T PRK13260 149 AKEC 152 (332)
T ss_pred CCCC
Confidence 8554
No 21
>TIGR03175 AllD ureidoglycolate dehydrogenase. This enzyme converts ureidoglycolate to oxalureate in the non-urea-forming catabolism of allantoin (GenProp0687). The pathway has been characterized in E. coli and is observed in the genomes of Entercoccus faecalis and Bacillus licheniformis.
Probab=79.22 E-value=20 Score=29.01 Aligned_cols=73 Identities=19% Similarity=0.216 Sum_probs=57.7
Q ss_pred eeeccCCCCcHHHHHHHHHHHHHHHHHcCCcEEEEEEeecCCCcccCCCCChHHHHHHHHhCCCeEEEEEecCCC--CCC
Q 043606 11 KVKADRDESSPYAAMLAAQDVSQRCKERGITALHIKLRATGGNKTKTPGPGAQSALRALARSGMKIGRIEDVTPI--PTD 88 (101)
Q Consensus 11 gfKg~r~k~t~~Aa~~a~~~~~~~~~~~gi~~v~V~lrg~~g~~~kG~G~gr~~~lr~l~~~gl~I~~I~D~Tpi--phN 88 (101)
-+.+.. ---++++..+.+.++++|++.|+-.|.|+= ++.+|.--..+.++.. .|+-=+...+..|. ||+
T Consensus 78 ~vDg~~-g~G~~a~~~Am~~aiekAr~~Gi~~v~v~n-------s~H~G~~g~Y~~~aa~-~G~Igi~~tNs~~~vaP~G 148 (349)
T TIGR03175 78 IFHGDN-GAGQVAAKMAMEHAIEIAKKSGVAVVGISR-------MSHSGALSYFVRQAAE-QGMVALSMCQSDPMVVPFG 148 (349)
T ss_pred EEECCC-CchHHHHHHHHHHHHHHHHHhCEEEEEecC-------CCccccHHHHHHHHHH-CCCEEEEEeCCCCeeCCCC
Confidence 466666 778999999999999999999999988874 4789998888877665 67666666666665 888
Q ss_pred CCCC
Q 043606 89 STRR 92 (101)
Q Consensus 89 GcR~ 92 (101)
|-+|
T Consensus 149 G~~~ 152 (349)
T TIGR03175 149 GTDI 152 (349)
T ss_pred CCCC
Confidence 8554
No 22
>PF02615 Ldh_2: Malate/L-lactate dehydrogenase; InterPro: IPR003767 The malate dehydrogenase (MDH) of some extremophilies is more similar to the L-lactate dehydrogenases (L-LDH) 1.1.1.27 from EC from various sources than to other MDHs []. This family consists of bacterial and archaeal malate/L-lactate dehydrogenases. The archaebacterial malate dehydrogenase 1.1.1.37 from EC, 1.1.1.82 from EC deviates from the eubacterial and eukaryotic enzymes having a low selectivity for the coenzyme (NAD(H) or NADP(H)) and catalyzing the reduction of oxalacetate to malate more efficiently than the reverse reaction [].; GO: 0016491 oxidoreductase activity, 0008152 metabolic process, 0055114 oxidation-reduction process; PDB: 1VBI_A 2G8Y_B 2X06_H 1Z2I_B 1X0A_A 1V9N_A 1XRH_G 3I0P_A 2CWH_B 2CWF_B ....
Probab=73.06 E-value=25 Score=28.29 Aligned_cols=72 Identities=24% Similarity=0.242 Sum_probs=52.7
Q ss_pred eeeccCCCCcHHHHHHHHHHHHHHHHHcCCcEEEEEEeecCCCcccCCCCChHHHHHHHHhCCCeEEEEEecCCC--CCC
Q 043606 11 KVKADRDESSPYAAMLAAQDVSQRCKERGITALHIKLRATGGNKTKTPGPGAQSALRALARSGMKIGRIEDVTPI--PTD 88 (101)
Q Consensus 11 gfKg~r~k~t~~Aa~~a~~~~~~~~~~~gi~~v~V~lrg~~g~~~kG~G~gr~~~lr~l~~~gl~I~~I~D~Tpi--phN 88 (101)
-+.+.. ---++++..|.+.++++|++.|+-.|.|+= ++.+|..-..+.++.. .|+-=+...+..|. ||+
T Consensus 78 ~vDg~~-g~G~~~~~~A~~~aiekA~~~Gia~v~vrn-------s~H~G~~g~y~~~aa~-~G~Igi~~tn~~p~vaP~G 148 (335)
T PF02615_consen 78 VVDGDN-GFGQVAAKFAMELAIEKAKEHGIAAVAVRN-------SNHFGALGYYAEMAAE-QGMIGIAFTNTPPLVAPFG 148 (335)
T ss_dssp EEEETT-BBHHHHHHHHHHHHHHHHHHHSEEEEEEEE-------EE--S-THHHHHHHHH-TTSEEEEEEEESSEB--TT
T ss_pred EEECCC-CccHHHHHHHHHHHHHHHHHcCEEEEEEec-------CCCCCccHHHHHHHHH-CCCEEEEecCCCCcccCCC
Confidence 455666 678899999999999999999999888875 3789998888877555 67666666666665 887
Q ss_pred CCC
Q 043606 89 STR 91 (101)
Q Consensus 89 GcR 91 (101)
|-+
T Consensus 149 g~~ 151 (335)
T PF02615_consen 149 GRE 151 (335)
T ss_dssp BSS
T ss_pred CCC
Confidence 744
No 23
>PLN00105 malate/L-lactate dehydrogenase; Provisional
Probab=73.02 E-value=41 Score=26.99 Aligned_cols=74 Identities=11% Similarity=0.105 Sum_probs=56.5
Q ss_pred eeeccCCCCcHHHHHHHHHHHHHHHHHcCCcEEEEEEeecCCCcccCCCCChHHHHHHHHhCCCeEEEEEecCCC--CCC
Q 043606 11 KVKADRDESSPYAAMLAAQDVSQRCKERGITALHIKLRATGGNKTKTPGPGAQSALRALARSGMKIGRIEDVTPI--PTD 88 (101)
Q Consensus 11 gfKg~r~k~t~~Aa~~a~~~~~~~~~~~gi~~v~V~lrg~~g~~~kG~G~gr~~~lr~l~~~gl~I~~I~D~Tpi--phN 88 (101)
-+.+.. ---++++..+.+.++++|++.|+-.|.|+= -++.+|.--..+.++.+ .|+--+...+..|. ||+
T Consensus 67 ~vDg~~-g~G~~~~~~am~~aiekAr~~Gi~~v~vrn------~S~H~G~~g~y~~~aa~-~Gligi~~tN~~~~vaP~G 138 (330)
T PLN00105 67 AVDGNK-NAGMLVLHHAMDMAIDKAKTHGVGIVGTCN------TSTSTGALGYYAEKVAQ-QGLIGLVFANSPEFVAPAG 138 (330)
T ss_pred EEECCC-CccHHHHHHHHHHHHHHHHHhCEEEEEEeC------CcCCccchHHHHHHHHH-CCCeEEEEeCCCCeeCCCC
Confidence 466666 778999999999999999999999888873 02678987777766544 67776677776665 888
Q ss_pred CCCC
Q 043606 89 STRR 92 (101)
Q Consensus 89 GcR~ 92 (101)
|-+|
T Consensus 139 G~~~ 142 (330)
T PLN00105 139 GIEP 142 (330)
T ss_pred CCCC
Confidence 8554
No 24
>PRK15025 ureidoglycolate dehydrogenase; Provisional
Probab=71.16 E-value=47 Score=26.92 Aligned_cols=73 Identities=16% Similarity=0.210 Sum_probs=56.6
Q ss_pred eeeccCCCCcHHHHHHHHHHHHHHHHHcCCcEEEEEEeecCCCcccCCCCChHHHHHHHHhCCCeEEEEEecCCC--CCC
Q 043606 11 KVKADRDESSPYAAMLAAQDVSQRCKERGITALHIKLRATGGNKTKTPGPGAQSALRALARSGMKIGRIEDVTPI--PTD 88 (101)
Q Consensus 11 gfKg~r~k~t~~Aa~~a~~~~~~~~~~~gi~~v~V~lrg~~g~~~kG~G~gr~~~lr~l~~~gl~I~~I~D~Tpi--phN 88 (101)
-+.+.. --.++++..+.+.++++|++.|+-.|.|+= ++.+|..-..+.++.. .|+-=+..++..|. ||+
T Consensus 78 ~vDg~~-g~G~~a~~~Am~~aiekA~~~Gi~~v~vrn-------S~H~G~~g~y~~~aa~-~Gligi~~tns~~~vaP~G 148 (349)
T PRK15025 78 ILHADN-AAGQVAAKMGMEHAIETAKQNGVAVVGISR-------MGHSGAISYFVQQAAR-AGLIGLSMCQSDPMVVPFG 148 (349)
T ss_pred EEECCC-CchHHHHHHHHHHHHHHHHHhCEEEEEEeC-------CCccccHHHHHHHHHH-CCCEEEEEeCCCCeeCCCC
Confidence 455666 778999999999999999999999888874 4889998888877555 67666666666665 787
Q ss_pred CCCC
Q 043606 89 STRR 92 (101)
Q Consensus 89 GcR~ 92 (101)
|-+|
T Consensus 149 g~~~ 152 (349)
T PRK15025 149 GAEI 152 (349)
T ss_pred CCCC
Confidence 7443
No 25
>PRK10098 putative dehydrogenase; Provisional
Probab=70.99 E-value=34 Score=27.68 Aligned_cols=73 Identities=19% Similarity=0.179 Sum_probs=55.1
Q ss_pred eeeccCCCCcHHHHHHHHHHHHHHHHHcCCcEEEEEEeecCCCcccCCCCChHHHHHHHHhCCCeEEEEEecC----CCC
Q 043606 11 KVKADRDESSPYAAMLAAQDVSQRCKERGITALHIKLRATGGNKTKTPGPGAQSALRALARSGMKIGRIEDVT----PIP 86 (101)
Q Consensus 11 gfKg~r~k~t~~Aa~~a~~~~~~~~~~~gi~~v~V~lrg~~g~~~kG~G~gr~~~lr~l~~~gl~I~~I~D~T----pip 86 (101)
-+.+.. ---++++..+.+.++++|++.|+-.|.|+= ++.+|.--..+.++.. .|+-=+...+.+ -.|
T Consensus 82 ~vDg~~-g~G~~a~~~Am~~aie~Ar~~Gi~~v~vrn-------S~H~G~~g~y~~~aa~-~G~igi~~tN~~s~~~vaP 152 (350)
T PRK10098 82 TLDGDR-GFGQVVAHEAMALGIERARQHGICAVALRN-------SHHIGRIGHWAEQCAA-AGLVSIHFVNVVGDPMVAP 152 (350)
T ss_pred EEECCC-CccHHHHHHHHHHHHHHHHHhCEEEEEEec-------CCCccchHHHHHHHHH-CCCEEEEEecCCCCceecC
Confidence 355555 668899999999999999999999888875 4889998888877555 676555566633 348
Q ss_pred CCCCCC
Q 043606 87 TDSTRR 92 (101)
Q Consensus 87 hNGcR~ 92 (101)
|+|-+|
T Consensus 153 ~Gg~~~ 158 (350)
T PRK10098 153 FHGRDS 158 (350)
T ss_pred CCCCCC
Confidence 888554
No 26
>TIGR03694 exosort_acyl putative PEP-CTERM/exosortase system-associated acyltransferase. Members of this protein family are restricted to bacterial species with the PEP-CTERM/exosortase system predicted to act in exopolysaccharide-associated protein targeting. PSI-BLAST and CDD reveal relationships to the acyltransferase family that includes N-acyl-L-homoserine lactone synthetase. Several members of this family may be found in a single genome. These proteins likely contribute to chemical modifications in exopolysaccharide and biofilm structural material production.
Probab=70.20 E-value=18 Score=27.44 Aligned_cols=58 Identities=17% Similarity=0.206 Sum_probs=45.5
Q ss_pred cHHHHHHHHHHHHHHHHHcCCcEEEEEEeecCCCcccCCCCChHHHHHHHHhCCCeEEEEEecCCCCCCCCCCC
Q 043606 20 SPYAAMLAAQDVSQRCKERGITALHIKLRATGGNKTKTPGPGAQSALRALARSGMKIGRIEDVTPIPTDSTRRK 93 (101)
Q Consensus 20 t~~Aa~~a~~~~~~~~~~~gi~~v~V~lrg~~g~~~kG~G~gr~~~lr~l~~~gl~I~~I~D~TpiphNGcR~~ 93 (101)
.++.+......+++.|...||+.+...+ .-...+.|.+.|+.+..|-+ |+.|+|.|.|
T Consensus 153 ~~~~~~~L~~~~~~~a~~~Gi~~~~~v~--------------~~~l~r~l~r~G~~~~~lG~--~~~~~G~r~p 210 (241)
T TIGR03694 153 FPHIPLGLYLGLIALSSANGITHWYAIM--------------EPRLARLLSRFGIQFRQVGP--PVDYHGLRAP 210 (241)
T ss_pred CchHHHHHHHHHHHHHHHCCCcEEEEEe--------------CHHHHHHHHHhCCceEEcCC--CeeECcEecc
Confidence 3556666677789999999999999888 22577889999999998886 5567787643
No 27
>cd01076 NAD_bind_1_Glu_DH NAD(P) binding domain of glutamate dehydrogenase, subgroup 1. Amino acid dehydrogenase (DH) is a widely distributed family of enzymes that catalyzes the oxidative deamination of an amino acid to its keto acid and ammonia with concomitant reduction of NADP+. Glutamate DH is a multidomain enzyme that catalyzes the reaction from glutamate to 2-oxyoglutarate and ammonia in the presence of NAD or NADP. It is present in all organisms. Enzymes involved in ammonia assimilation are typically NADP+-dependent, while those involved in glutamate catabolism are generally NAD+-dependent. Amino acid DH-like NAD(P)-binding domains are members of the Rossmann fold superfamily and include glutamate, leucine, and phenylalanine DHs, methylene tetrahydrofolate DH, methylene-tetrahydromethanopterin DH, methylene-tetrahydropholate DH/cyclohydrolase, Shikimate DH-like proteins, malate oxidoreductases, and glutamyl tRNA reductase. Amino acid DHs catalyze the deamination of amino acids
Probab=68.87 E-value=14 Score=27.79 Aligned_cols=60 Identities=18% Similarity=0.295 Sum_probs=42.9
Q ss_pred CCcHHHHHHHHHHHHHHHHHcCCcEEEEEEeecCCCcccCCCC-ChHHHHHHHHhCCCeEEEEEecCCCCC
Q 043606 18 ESSPYAAMLAAQDVSQRCKERGITALHIKLRATGGNKTKTPGP-GAQSALRALARSGMKIGRIEDVTPIPT 87 (101)
Q Consensus 18 k~t~~Aa~~a~~~~~~~~~~~gi~~v~V~lrg~~g~~~kG~G~-gr~~~lr~l~~~gl~I~~I~D~Tpiph 87 (101)
..|-|....+.+.+++... ..+...+|-| .|+|. |+..+ +.|.+.|.+|+.|.|.+..=|
T Consensus 8 ~~Tg~Gv~~~~~~~~~~~~-~~l~~~~v~I--------~G~G~VG~~~a-~~L~~~g~~vv~v~D~~g~~~ 68 (227)
T cd01076 8 EATGRGVAYATREALKKLG-IGLAGARVAI--------QGFGNVGSHAA-RFLHEAGAKVVAVSDSDGTIY 68 (227)
T ss_pred ccchHHHHHHHHHHHHhcC-CCccCCEEEE--------ECCCHHHHHHH-HHHHHCCCEEEEEECCCCeEE
Confidence 6677777767666655542 4577788889 77885 66554 678889999999999864433
No 28
>COG2099 CobK Precorrin-6x reductase [Coenzyme metabolism]
Probab=68.17 E-value=8.5 Score=30.29 Aligned_cols=27 Identities=37% Similarity=0.634 Sum_probs=23.1
Q ss_pred CcHHHHHHHHHHHHHHHHHcCCcEEEEE
Q 043606 19 SSPYAAMLAAQDVSQRCKERGITALHIK 46 (101)
Q Consensus 19 ~t~~Aa~~a~~~~~~~~~~~gi~~v~V~ 46 (101)
+=||||+ +.+++++-|++.|+..+...
T Consensus 74 THPyAa~-iS~Na~~aake~gipy~r~e 100 (257)
T COG2099 74 THPYAAR-ISQNAARAAKETGIPYLRLE 100 (257)
T ss_pred CChHHHH-HHHHHHHHHHHhCCcEEEEE
Confidence 4699999 55789999999999988765
No 29
>PF13420 Acetyltransf_4: Acetyltransferase (GNAT) domain; PDB: 3DR8_A 3DR6_A 2AE6_B 2JLM_C 2J8R_A 1YVO_B 2J8M_A 2J8N_A 2BL1_A 3IWG_A ....
Probab=67.38 E-value=33 Score=22.65 Aligned_cols=47 Identities=13% Similarity=0.146 Sum_probs=35.0
Q ss_pred HHHHHHHHHHHHH-HHcCCcEEEEEEeecCCCcccCCCCChHHHHHHHHhCCCeEEEEE
Q 043606 23 AAMLAAQDVSQRC-KERGITALHIKLRATGGNKTKTPGPGAQSALRALARSGMKIGRIE 80 (101)
Q Consensus 23 Aa~~a~~~~~~~~-~~~gi~~v~V~lrg~~g~~~kG~G~gr~~~lr~l~~~gl~I~~I~ 80 (101)
.+..+.+.+.+.| .++|++.|.+.+- .....+++.+++.|+++....
T Consensus 93 ig~~l~~~l~~~af~~~~~~~i~~~v~-----------~~N~~~i~~~~~~GF~~~g~~ 140 (155)
T PF13420_consen 93 IGRKLLDELIEYAFKELGIHKIYLEVF-----------SSNEKAINFYKKLGFEEEGEL 140 (155)
T ss_dssp HHHHHHHHHHHHH-HHTT-CEEEEEEE-----------TT-HHHHHHHHHTTEEEEEEE
T ss_pred HHHHHHHHHHHHhhhccCeEEEEEEEe-----------cCCHHHHHHHHhCCCEEEEEE
Confidence 3444667788899 9999999999993 226688899999999887553
No 30
>PRK13490 chemoreceptor glutamine deamidase CheD; Provisional
Probab=65.85 E-value=39 Score=24.50 Aligned_cols=57 Identities=16% Similarity=0.185 Sum_probs=40.8
Q ss_pred cHHHHHHHHHHHHHHHHHcCCc--EEEEEEeecCCCcccC------CCC---ChHHHHHHHHhCCCeEEE
Q 043606 20 SPYAAMLAAQDVSQRCKERGIT--ALHIKLRATGGNKTKT------PGP---GAQSALRALARSGMKIGR 78 (101)
Q Consensus 20 t~~Aa~~a~~~~~~~~~~~gi~--~v~V~lrg~~g~~~kG------~G~---gr~~~lr~l~~~gl~I~~ 78 (101)
.-||- .|.+.+++.+.++|.+ .++++|-| |++-+.+ ++. +-++|.+.|.+.||.|..
T Consensus 63 ~rY~d-~ai~~Li~~m~~~Ga~~~~l~aKifG-GA~m~~~~~~~~~~~IG~rNv~~a~~~L~~~gI~i~a 130 (162)
T PRK13490 63 MKFAD-LAIPILIEKMEKLGANKRNLKAKIAG-GASMFNFSDKSMVMDIGNRNGKAVKKKLKELSIPILA 130 (162)
T ss_pred ccCHH-HHHHHHHHHHHHcCCCHHHEEEEEEe-CccccCCCCccccCChhHHHHHHHHHHHHHcCCcEEE
Confidence 44654 4668899999999977 57788866 5554442 222 456788889999999875
No 31
>PRK07757 acetyltransferase; Provisional
Probab=65.58 E-value=16 Score=24.31 Aligned_cols=54 Identities=11% Similarity=0.104 Sum_probs=39.7
Q ss_pred HHHHHHHHHHHHHHHHcCCcEEEEEEeecCCCcccCCCCChHHHHHHHHhCCCeEEEEEecCCCCCCCCCC
Q 043606 22 YAAMLAAQDVSQRCKERGITALHIKLRATGGNKTKTPGPGAQSALRALARSGMKIGRIEDVTPIPTDSTRR 92 (101)
Q Consensus 22 ~Aa~~a~~~~~~~~~~~gi~~v~V~lrg~~g~~~kG~G~gr~~~lr~l~~~gl~I~~I~D~TpiphNGcR~ 92 (101)
++..+. +.+.+.+.+.|+..+.+.. . ..+-.++.|++...-.|..+.-||+|+.
T Consensus 82 lg~~Ll-~~l~~~a~~~g~~~i~~~~--------~--------~~~~Y~k~GF~~~~~~~~~~~~~~~~~~ 135 (152)
T PRK07757 82 IGRMLV-EACLEEARELGVKRVFALT--------Y--------QPEFFEKLGFREVDKEALPQKVWADCIK 135 (152)
T ss_pred HHHHHH-HHHHHHHHhCCCCeEEEEe--------C--------cHHHHHHCCCEEcccccCChhHHhcCcc
Confidence 444433 4567788888999876655 1 2356788899999888888888999974
No 32
>PF00583 Acetyltransf_1: Acetyltransferase (GNAT) family; InterPro: IPR000182 The N-acetyltransferases (NAT) (EC 2.3.1.-) are enzymes that use acetyl coenzyme A (CoA) to transfer an acetyl group to a substrate, a reaction implicated in various functions from bacterial antibiotic resistance to mammalian circadian rhythm and chromatin remodeling. The Gcn5-related N-acetyltransferases (GNAT) catalyze the transfer of the acetyl from the CoA donor to a primary amine of the acceptor. The GNAT proteins share a domain composed of four conserved sequence motifs A-D [, ]. This GNAT domain is named after yeast GCN5 (from General Control Nonrepressed) and related histone acetyltransferases (HATs) like Hat1 and PCAF. HATs acetylate lysine residues of amino terminal histone tails, resulting in transcription activation. Another category of GNAT, the aminoglycoside N-acetyltransferases, confer antibiotic resistance by catalyzing the acetylation of amino groups in aminoglycoside antibiotics []. GNAT proteins can also have anabolic and catabolic functions in both prokaryotes and eukaryotes [, , , , ]. The acetyltransferase/GNAT domain forms a structurally conserved fold of 6 to 7 beta strands (B) and 4 helices (H) in the topology B1-H1-H2-B2-B3-B4-H3-B5-H4-B6, followed by a C-terminal strand which may be from the same monomer or contributed by another [, ]. Motifs D (B2-B3), A (B4-H3) and B (B5-H4) are collectively called the HAT core [, , ], while the N-terminal motif C (B1-H1) is less conserved. Some proteins known to contain a GNAT domain: Yeast GCN5 and Hat1, which are histone acetyltransferases (EC 2.3.1.48). Human PCAF, a histone acetyltransferase. Mammalian serotonin N-acetyltransferase (SNAT) or arylalkylamine NAT (AANAT), which acetylates serotonin into a circadian neurohormone that may participate in light-dark rhythms, and human mood and behavior. Mammalian glucosamine 6-phosphate N-acetyltransferase (GNA1) (EC 2.3.1.4). Escherichia coli rimI and rimJ, which acetylate the N-terminal alanine of ribosomal proteins S18 and S5, respectively (EC 2.3.1.128). Mycobacterium tuberculosis aminoglycoside 2'-N-acetyltransferase (aac), which acetylates the 2' hydroxyl or amino group of a broad spectrum of aminoglycoside antibiotics. Bacillus subtilis bltD and paiA, which acetylate spermine and spermidine. This entry represents the entire GNAT domain.; GO: 0008080 N-acetyltransferase activity, 0008152 metabolic process; PDB: 3T9Y_A 2R7H_B 2OZH_A 1Y9W_B 1VKC_B 2OH1_C 3R9E_B 3R9G_B 3R9F_A 3R96_A ....
Probab=65.51 E-value=25 Score=20.55 Aligned_cols=41 Identities=20% Similarity=0.356 Sum_probs=31.1
Q ss_pred HHHHHHHHHHHHHHcCCcEEEEEEeecCCCcccCCCCChHHHHHHHHhCCCe
Q 043606 24 AMLAAQDVSQRCKERGITALHIKLRATGGNKTKTPGPGAQSALRALARSGMK 75 (101)
Q Consensus 24 a~~a~~~~~~~~~~~gi~~v~V~lrg~~g~~~kG~G~gr~~~lr~l~~~gl~ 75 (101)
+....+.+.+.+++.|+..|.+.+ .+....+++.+.+.|++
T Consensus 43 g~~L~~~~~~~~~~~g~~~i~~~~-----------~~~n~~~~~~~~k~Gf~ 83 (83)
T PF00583_consen 43 GSKLLQAAEEWARKRGIKRIYLDV-----------SPDNPAARRFYEKLGFE 83 (83)
T ss_dssp HHHHHHHHHHHHHHTTESEEEEEE-----------ETTGHHHHHHHHHTTEE
T ss_pred chhhhhhhhhhHHhcCccEEEEEE-----------eCCCHHHHHHHHHcCCC
Confidence 344456788899999999999998 55566788877777753
No 33
>PF13302 Acetyltransf_3: Acetyltransferase (GNAT) domain; PDB: 3TTH_C 3JUW_A 2ZXV_A 2Z0Z_A 2VI7_B 3EG7_F 1YRE_C 3IGR_B 3FBU_A 2FCK_A ....
Probab=65.26 E-value=30 Score=22.24 Aligned_cols=46 Identities=13% Similarity=0.215 Sum_probs=33.5
Q ss_pred CCcHHHHHHHHHHHHHHH-HHcCCcEEEEEEeecCCCcccCCCCChHHHHHHHHhCCCe
Q 043606 18 ESSPYAAMLAAQDVSQRC-KERGITALHIKLRATGGNKTKTPGPGAQSALRALARSGMK 75 (101)
Q Consensus 18 k~t~~Aa~~a~~~~~~~~-~~~gi~~v~V~lrg~~g~~~kG~G~gr~~~lr~l~~~gl~ 75 (101)
.+.-|+...+ ..+.+.+ .++++..|.+.+ -+.-..+++.+.+.|++
T Consensus 96 ~g~G~~~~~~-~~~~~~~~~~~~~~~i~a~~-----------~~~N~~s~~~~~k~GF~ 142 (142)
T PF13302_consen 96 RGKGYGTEAL-KLLLDWAFEELGLHRIIATV-----------MADNEASRRLLEKLGFE 142 (142)
T ss_dssp TTSSHHHHHH-HHHHHHHHHTSTSSEEEEEE-----------ETT-HHHHHHHHHTT-E
T ss_pred HhhhHHHHHH-HHHHHHHHhcCCcEEEEEEE-----------CcCCHHHHHHHHHcCCC
Confidence 4556776655 4577777 689999999999 45567888999988874
No 34
>PF02601 Exonuc_VII_L: Exonuclease VII, large subunit; InterPro: IPR020579 Exonuclease VII 3.1.11.6 from EC is composed of two nonidentical subunits; one large subunit and 4 small ones []. Exonuclease VII catalyses exonucleolytic cleavage in either 5'-3' or 3'-5' direction to yield 5'-phosphomononucleotides. The large subunit also contains the OB-fold domains (IPR004365 from INTERPRO) that bind to nucleic acids at the N terminus. This entry represents Exonuclease VII, large subunit, C-terminal. ; GO: 0008855 exodeoxyribonuclease VII activity
Probab=64.72 E-value=26 Score=27.13 Aligned_cols=54 Identities=22% Similarity=0.206 Sum_probs=38.9
Q ss_pred HHHHHHHHHHHHHHHcC---CcEEEEEEeecCCCcccCCCCChHHHHHHHHhCCCeEEE
Q 043606 23 AAMLAAQDVSQRCKERG---ITALHIKLRATGGNKTKTPGPGAQSALRALARSGMKIGR 78 (101)
Q Consensus 23 Aa~~a~~~~~~~~~~~g---i~~v~V~lrg~~g~~~kG~G~gr~~~lr~l~~~gl~I~~ 78 (101)
|+..+++ .++.+.+.+ --.|.|.+|| ||+..--+-.+-+.+.+++..+.+.|++
T Consensus 56 A~~~I~~-al~~~~~~~~~~~~Dviii~RG-GGs~eDL~~FN~e~varai~~~~~Pvis 112 (319)
T PF02601_consen 56 AAASIVS-ALRKANEMGQADDFDVIIIIRG-GGSIEDLWAFNDEEVARAIAASPIPVIS 112 (319)
T ss_pred hHHHHHH-HHHHHHhccccccccEEEEecC-CCChHHhcccChHHHHHHHHhCCCCEEE
Confidence 5555554 455565555 2357777888 7777777778999999999999888864
No 35
>PRK14834 undecaprenyl pyrophosphate synthase; Provisional
Probab=64.52 E-value=65 Score=24.99 Aligned_cols=60 Identities=22% Similarity=0.241 Sum_probs=40.9
Q ss_pred HHHHHHHHHHHHHHHcCCcEEEEEEeecCCCcccCCCCChHH--------------HHHHHHhCCCeEEEEEecCCCCC
Q 043606 23 AAMLAAQDVSQRCKERGITALHIKLRATGGNKTKTPGPGAQS--------------ALRALARSGMKIGRIEDVTPIPT 87 (101)
Q Consensus 23 Aa~~a~~~~~~~~~~~gi~~v~V~lrg~~g~~~kG~G~gr~~--------------~lr~l~~~gl~I~~I~D~Tpiph 87 (101)
+.......+++.|.++||+.|.|+.--+ ..+..-.+- .+..|...|++|..|-|...+|-
T Consensus 42 ~G~~~l~~i~~~c~~lgI~~lTvYaFS~-----eN~~R~~~EV~~Lm~L~~~~l~~~~~~~~~~~iri~viGd~~~Lp~ 115 (249)
T PRK14834 42 AGVEALRRVVRAAGELGIGYLTLFAFSS-----ENWSRPASEVSDLFGLLRLFIRRDLAELHRNGVRVRVIGERAGLEA 115 (249)
T ss_pred HHHHHHHHHHHHHHHcCCCEEEEEEEec-----cccCCCHHHHHHHHHHHHHHHHHHHHHHHHCCcEEEEEcChhhCCH
Confidence 4445557788999999999999999543 333322210 11234457999999999998884
No 36
>PRK14840 undecaprenyl pyrophosphate synthase; Provisional
Probab=62.60 E-value=71 Score=24.84 Aligned_cols=61 Identities=16% Similarity=0.254 Sum_probs=41.3
Q ss_pred HHHHHHHHHHHHHHHHcCCcEEEEEEeecCCCcccCCCCChHHH--------------HHHHHhCCCeEEEEEecCCCCC
Q 043606 22 YAAMLAAQDVSQRCKERGITALHIKLRATGGNKTKTPGPGAQSA--------------LRALARSGMKIGRIEDVTPIPT 87 (101)
Q Consensus 22 ~Aa~~a~~~~~~~~~~~gi~~v~V~lrg~~g~~~kG~G~gr~~~--------------lr~l~~~gl~I~~I~D~Tpiph 87 (101)
.+...+.+.+++.|.++||+.|.|+.--+ -.+..-.+=+ +..+.+.|++|..|-|...+|-
T Consensus 49 ~~G~~~l~~v~~~c~~~GIk~lTvYaFS~-----EN~~R~~~EV~~Lm~L~~~~l~~~~~~~~~~~irvr~iGd~~~Lp~ 123 (250)
T PRK14840 49 YYGAKSLPQIVDTALHLGIEVLTLFAFST-----ENFSRSKEEVAELFSLFNSQLDSQLPYLHENEIRLRCIGDLSKLPQ 123 (250)
T ss_pred HHHHHHHHHHHHHHHHcCCCEEEEEEeeh-----hhcCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCEEEEEeChhhCCH
Confidence 34445567788889999999999998643 3343222211 1123456999999999998884
No 37
>PRK14829 undecaprenyl pyrophosphate synthase; Provisional
Probab=62.14 E-value=49 Score=25.48 Aligned_cols=60 Identities=15% Similarity=0.047 Sum_probs=40.1
Q ss_pred HHHHHHHHHHHHHHHHcCCcEEEEEEeecCCCcccCCCCChH------HH--------HHHHHhCCCeEEEEEecCCCC
Q 043606 22 YAAMLAAQDVSQRCKERGITALHIKLRATGGNKTKTPGPGAQ------SA--------LRALARSGMKIGRIEDVTPIP 86 (101)
Q Consensus 22 ~Aa~~a~~~~~~~~~~~gi~~v~V~lrg~~g~~~kG~G~gr~------~~--------lr~l~~~gl~I~~I~D~Tpip 86 (101)
.+...+...+++.|.++||+.|.|+.--+ .| +..-++ .. +..+.+.|++|..|-|...+|
T Consensus 41 ~~G~~~l~~iv~~c~~~gI~~vTvYaFS~-eN----~kR~~~Ev~~lm~L~~~~l~~~~~~~~~~~iri~~iG~~~~Lp 114 (243)
T PRK14829 41 KAGEPVLFDVVAGAIEAGVPYLSLYTFST-EN----WKRSPDEVRFLMGFSRDVIHRRREQMDEWGVRVRWSGRRPRLW 114 (243)
T ss_pred HHHHHHHHHHHHHHHHcCCCEEEEeeecc-hh----hCCCHHHHHHHHHHHHHHHHHHHHHHHHcCcEEEEEechhhCC
Confidence 34445567788899999999999998432 22 222221 11 122456799999999999888
No 38
>TIGR01575 rimI ribosomal-protein-alanine acetyltransferase. Members of this model belong to the GCN5-related N-acetyltransferase (GNAT) superfamily. This model covers prokarotes and the archaea. The seed contains a characterized accession for Gram negative E. coli. An untraceable characterized accession (PIR|S66013) for Gram positive B. subtilis scores well (205.0) in the full alignment. Characterized members are lacking in the archaea. Noise cutoff (72.4) was set to exclude M. loti paralog of rimI. Trusted cutoff (80.0) was set at next highest scoring member in the mini-database.
Probab=61.94 E-value=37 Score=21.27 Aligned_cols=48 Identities=13% Similarity=0.203 Sum_probs=34.5
Q ss_pred HHHHHHHHHHHHHHHHcCCcEEEEEEeecCCCcccCCCCChHHHHHHHHhCCCeEEEEEe
Q 043606 22 YAAMLAAQDVSQRCKERGITALHIKLRATGGNKTKTPGPGAQSALRALARSGMKIGRIED 81 (101)
Q Consensus 22 ~Aa~~a~~~~~~~~~~~gi~~v~V~lrg~~g~~~kG~G~gr~~~lr~l~~~gl~I~~I~D 81 (101)
++.+ +.+.+.+.+.+.++..+.+.+ .+....+++.+++.|+++....+
T Consensus 71 ~g~~-ll~~~~~~~~~~~~~~i~~~~-----------~~~n~~~~~~y~~~Gf~~~~~~~ 118 (131)
T TIGR01575 71 IGRA-LLRELIDEAKGRGVNEIFLEV-----------RVSNIAAQALYKKLGFNEIAIRR 118 (131)
T ss_pred HHHH-HHHHHHHHHHHcCCCeEEEEE-----------ecccHHHHHHHHHcCCCcccccc
Confidence 4444 335677788888999888887 23345678889999998876654
No 39
>cd05211 NAD_bind_Glu_Leu_Phe_Val NAD(P) binding domain of glutamate dehydrogenase, leucine dehydrogenase, phenylalanine dehydrogenase, and valine dehydrogenase. Amino acid dehydrogenase (DH) is a widely distributed family of enzymes that catalyzes the oxidative deamination of an amino acid to its keto acid and ammonia with concomitant reduction of NAD(P)+. This subfamily includes glutamate, leucine, phenylalanine, and valine DHs. Glutamate DH is a multi-domain enzyme that catalyzes the reaction from glutamate to 2-oxyoglutarate and ammonia in the presence of NAD or NADP. It is present in all organisms. Enzymes involved in ammonia assimilation are typically NADP+-dependent, while those involved in glutamate catabolism are generally NAD+-dependent. As in other NAD+-dependent DHs, monomers in this family have 2 domains separated by a deep cleft. Here the c-terminal domain contains a modified NAD-binding Rossmann fold with 7 rather than the usual 6 beta strands and one strand anti-parral
Probab=61.25 E-value=24 Score=26.37 Aligned_cols=55 Identities=18% Similarity=0.267 Sum_probs=37.1
Q ss_pred HHHHHHHHHHHHHHHHHcCCcEEEEEEeecCCCcccCCCC-ChHHHHHHHHhCCCeEEEEEecCCC
Q 043606 21 PYAAMLAAQDVSQRCKERGITALHIKLRATGGNKTKTPGP-GAQSALRALARSGMKIGRIEDVTPI 85 (101)
Q Consensus 21 ~~Aa~~a~~~~~~~~~~~gi~~v~V~lrg~~g~~~kG~G~-gr~~~lr~l~~~gl~I~~I~D~Tpi 85 (101)
-|....+.+.+++... ..+...+|-| .|||. |+. +.+.|.+.|.+++.|.|....
T Consensus 3 g~Gv~~~~~~~~~~~~-~~l~g~~vaI--------qGfGnVG~~-~a~~L~~~G~~vV~vsD~~g~ 58 (217)
T cd05211 3 GYGVVVAMKAAMKHLG-DSLEGLTVAV--------QGLGNVGWG-LAKKLAEEGGKVLAVSDPDGY 58 (217)
T ss_pred hhHHHHHHHHHHHHcC-CCcCCCEEEE--------ECCCHHHHH-HHHHHHHcCCEEEEEEcCCCc
Confidence 3444444444443332 4566788999 78885 664 457788899999999998774
No 40
>PRK13488 chemoreceptor glutamine deamidase CheD; Provisional
Probab=59.38 E-value=49 Score=23.84 Aligned_cols=57 Identities=25% Similarity=0.269 Sum_probs=39.4
Q ss_pred cHHHHHHHHHHHHHHHHHcCCcE--EEEEEeecCCCcccC------CC-CChHHHHHHHHhCCCeEEE
Q 043606 20 SPYAAMLAAQDVSQRCKERGITA--LHIKLRATGGNKTKT------PG-PGAQSALRALARSGMKIGR 78 (101)
Q Consensus 20 t~~Aa~~a~~~~~~~~~~~gi~~--v~V~lrg~~g~~~kG------~G-~gr~~~lr~l~~~gl~I~~ 78 (101)
.-||- .|.+.+++.+.++|.+. +++++-| |++-+.+ +| .+-+.|.+.|++.||+|..
T Consensus 60 ~rY~d-~ai~~li~~m~~~Ga~~~~l~akifG-GA~m~~~~~~~~~IG~rNi~~a~~~L~~~gi~i~a 125 (157)
T PRK13488 60 GKYAD-TAIPLLIEEMVKLGARKSKLEAKLAG-GAAMFDFSSNNLNIGERNIESAKETLKKLGIRIVA 125 (157)
T ss_pred cccHH-HHHHHHHHHHHHcCCCHHHEEEEEEe-CcccccCCCccCChHHHHHHHHHHHHHHCCCcEEE
Confidence 34654 46688999999998764 7777765 5554442 22 2456788889999999875
No 41
>PRK14841 undecaprenyl pyrophosphate synthase; Provisional
Probab=58.79 E-value=81 Score=24.20 Aligned_cols=61 Identities=13% Similarity=0.095 Sum_probs=41.0
Q ss_pred HHHHHHHHHHHHHHHHcCCcEEEEEEeecCCCcccCCCCChHH---H-----------HHHHHhCCCeEEEEEecCCCCC
Q 043606 22 YAAMLAAQDVSQRCKERGITALHIKLRATGGNKTKTPGPGAQS---A-----------LRALARSGMKIGRIEDVTPIPT 87 (101)
Q Consensus 22 ~Aa~~a~~~~~~~~~~~gi~~v~V~lrg~~g~~~kG~G~gr~~---~-----------lr~l~~~gl~I~~I~D~Tpiph 87 (101)
.+...+...+++.|.++||+.|.|+.--+ ..+..-.+= . +..+.+.|++|..|-|.+.+|-
T Consensus 30 ~~G~~~l~~i~~~~~~lgIk~lTvYaFS~-----eN~~R~~~Ev~~Lm~L~~~~l~~~~~~~~~~~irvr~iG~~~~Lp~ 104 (233)
T PRK14841 30 QRGAEVLHNTVKWSLELGIKYLTAFSFST-----ENWKRPKEEVEFLMDLFVQMIDREMELLRRERVRVRILGRKEGLPE 104 (233)
T ss_pred HHHHHHHHHHHHHHHHcCCCEEEEEeeeH-----hhcCCCHHHHHHHHHHHHHHHHHHHHHHHHcCcEEEEEeChhhCCH
Confidence 34555667788899999999999998533 223221111 1 1223457999999999998884
No 42
>COG0241 HisB Histidinol phosphatase and related phosphatases [Amino acid transport and metabolism]
Probab=58.53 E-value=50 Score=24.46 Aligned_cols=58 Identities=21% Similarity=0.233 Sum_probs=36.6
Q ss_pred HHHHHHHcCCcEEEEEEeecCCCcccCCCCChHH----------HHHHHHhCCCeEEEEEecCCCCC--CCCCCCCC
Q 043606 31 VSQRCKERGITALHIKLRATGGNKTKTPGPGAQS----------ALRALARSGMKIGRIEDVTPIPT--DSTRRKGG 95 (101)
Q Consensus 31 ~~~~~~~~gi~~v~V~lrg~~g~~~kG~G~gr~~----------~lr~l~~~gl~I~~I~D~Tpiph--NGcR~~K~ 95 (101)
+..+..+.|+.-|.|.-. .|+|.|-.+ .+..|.+.|++|..|-=---.|- +.||+||.
T Consensus 39 al~~l~~~gy~lVvvTNQ-------sGi~rgyf~~~~f~~~~~~m~~~l~~~gv~id~i~~Cph~p~~~c~cRKP~~ 108 (181)
T COG0241 39 ALLKLQRAGYKLVVVTNQ-------SGIGRGYFTEADFDKLHNKMLKILASQGVKIDGILYCPHHPEDNCDCRKPKP 108 (181)
T ss_pred HHHHHHhCCCeEEEEECC-------CCccccCccHHHHHHHHHHHHHHHHHcCCccceEEECCCCCCCCCcccCCCh
Confidence 455667889998888875 567765432 23345566876665544333333 68999874
No 43
>PRK13491 chemoreceptor glutamine deamidase CheD; Provisional
Probab=58.11 E-value=42 Score=25.39 Aligned_cols=57 Identities=21% Similarity=0.212 Sum_probs=40.5
Q ss_pred cHHHHHHHHHHHHHHHHHcCCc--EEEEEEeecCCCcccC---CC-CChHHHHHHHHhCCCeEEE
Q 043606 20 SPYAAMLAAQDVSQRCKERGIT--ALHIKLRATGGNKTKT---PG-PGAQSALRALARSGMKIGR 78 (101)
Q Consensus 20 t~~Aa~~a~~~~~~~~~~~gi~--~v~V~lrg~~g~~~kG---~G-~gr~~~lr~l~~~gl~I~~ 78 (101)
.-||-. |.+.+++.+.++|.+ .+.++|-| |++-+.+ +| .+-+.|.+.|.+.||.|..
T Consensus 71 ~rYgd~-Ai~~Li~~m~~~Ga~~~~L~AKifG-GA~M~~~~~~IG~rNie~a~~~L~~~GI~iva 133 (199)
T PRK13491 71 LRYGSH-AMELLINALLKLGAARQRIEAKIFG-GAMMTPQLGAIGQANAAFARRYLRDEGIRCTA 133 (199)
T ss_pred cccHHH-HHHHHHHHHHHcCCCHHHeEEEEEe-CcccccccccHHHHHHHHHHHHHHHcCCcEEE
Confidence 446544 667899999999977 57777765 5554543 33 2556788889999999875
No 44
>PTZ00349 dehydrodolichyl diphosphate synthetase; Provisional
Probab=58.06 E-value=81 Score=25.62 Aligned_cols=61 Identities=13% Similarity=0.138 Sum_probs=41.8
Q ss_pred HHHHHHHHHHHHHHHHcCCcEEEEEEeecCCCcccCCCCC-hHH------H----------HHHHHhCCCeEEEEEecCC
Q 043606 22 YAAMLAAQDVSQRCKERGITALHIKLRATGGNKTKTPGPG-AQS------A----------LRALARSGMKIGRIEDVTP 84 (101)
Q Consensus 22 ~Aa~~a~~~~~~~~~~~gi~~v~V~lrg~~g~~~kG~G~g-r~~------~----------lr~l~~~gl~I~~I~D~Tp 84 (101)
.+...+...+++.|.++||+.|.|+.--+ -.+..- .|. . +.-|.+.|++|..|-|.+.
T Consensus 46 ~~G~~~l~~il~~c~~lGIk~lTlYAFSt-----ENwkRp~~EV~~Lm~L~~~~l~~~~~~~~~l~~~~irirviGd~~~ 120 (322)
T PTZ00349 46 FMGSKALIQIIEICIKLKIKILSVFSFSL-----LNYNRSPEEIHFLFYLNLLILINEDFFFKFIKDNKIKIKIIGNLSY 120 (322)
T ss_pred HHHHHHHHHHHHHHHHcCCCEEEEEEeeh-----hhhCCCHHHHHHHHHHHHHHHHHhhhhHHHHHHCCCEEEEEeChhh
Confidence 34455667788999999999999998543 223221 222 0 1334567999999999998
Q ss_pred CCC
Q 043606 85 IPT 87 (101)
Q Consensus 85 iph 87 (101)
+|-
T Consensus 121 Lp~ 123 (322)
T PTZ00349 121 IND 123 (322)
T ss_pred CCH
Confidence 884
No 45
>KOG3551 consensus Syntrophins (type beta) [Extracellular structures]
Probab=57.77 E-value=9.2 Score=32.31 Aligned_cols=79 Identities=16% Similarity=0.276 Sum_probs=51.5
Q ss_pred eeccce--eeccCCCCcHHHHHHHHHH-HHHHHHHcCCcEEEEEEeecCCCcccCCCCChHHHHHHHHhCC----CeEEE
Q 043606 6 ITGGMK--VKADRDESSPYAAMLAAQD-VSQRCKERGITALHIKLRATGGNKTKTPGPGAQSALRALARSG----MKIGR 78 (101)
Q Consensus 6 SsG~~g--fKg~r~k~t~~Aa~~a~~~-~~~~~~~~gi~~v~V~lrg~~g~~~kG~G~gr~~~lr~l~~~g----l~I~~ 78 (101)
-+|++| -||.|.-.-|.-...+..- +++....+=+..+.+.++|+ .--..--+-|+++|+++| +++-.
T Consensus 94 d~gGLGISIKGGreNkMPIlISKIFkGlAADQt~aL~~gDaIlSVNG~-----dL~~AtHdeAVqaLKraGkeV~levKy 168 (506)
T KOG3551|consen 94 DAGGLGISIKGGRENKMPILISKIFKGLAADQTGALFLGDAILSVNGE-----DLRDATHDEAVQALKRAGKEVLLEVKY 168 (506)
T ss_pred cCCcceEEeecCcccCCceehhHhccccccccccceeeccEEEEecch-----hhhhcchHHHHHHHHhhCceeeeeeee
Confidence 356665 7888866666544443321 23344456677788899543 223344567999999997 67779
Q ss_pred EEecCCCCCCC
Q 043606 79 IEDVTPIPTDS 89 (101)
Q Consensus 79 I~D~TpiphNG 89 (101)
++|+||+=|++
T Consensus 169 ~REvtPy~kk~ 179 (506)
T KOG3551|consen 169 MREVTPYFKKE 179 (506)
T ss_pred ehhcchhhccC
Confidence 99999976643
No 46
>TIGR01917 gly_red_sel_B glycine reductase, selenoprotein B. Glycine reductase is a complex with two selenoprotein subunits, A and B. This model represents the glycine reductase selenoprotein B. Closely related to it, but excluded from this model, are selenoprotein B subunits of betaine reductase and sarcosine reductase. All contain selenocysteine incorporated during translation at a specific UGA codon.
Probab=57.62 E-value=47 Score=28.04 Aligned_cols=54 Identities=24% Similarity=0.378 Sum_probs=42.0
Q ss_pred HHHHHHHHHHHHHHcCCcEEEEEEeecCCCcccCCCCCh---HHHHHHHHhCCCeEEEEEecCCCC
Q 043606 24 AMLAAQDVSQRCKERGITALHIKLRATGGNKTKTPGPGA---QSALRALARSGMKIGRIEDVTPIP 86 (101)
Q Consensus 24 a~~a~~~~~~~~~~~gi~~v~V~lrg~~g~~~kG~G~gr---~~~lr~l~~~gl~I~~I~D~Tpip 86 (101)
++..++.|++++++-|+..|.+.= .-|.-- -+..|.|.++||.++.|..++||.
T Consensus 321 a~~~g~eIa~~Lk~dgVDAvILts---------tCgtCtrcga~m~keiE~~GIPvV~i~~~~pI~ 377 (431)
T TIGR01917 321 SKQFAKEFSKELLAAGVDAVILTS---------TUGTCTRCGATMVKEIERAGIPVVHICTVTPIA 377 (431)
T ss_pred HHHHHHHHHHHHHHcCCCEEEEcC---------CCCcchhHHHHHHHHHHHcCCCEEEEeechhHH
Confidence 444677799999999999877652 344432 246789999999999999999984
No 47
>COG1433 Uncharacterized conserved protein [Function unknown]
Probab=57.25 E-value=29 Score=24.13 Aligned_cols=40 Identities=20% Similarity=0.338 Sum_probs=29.0
Q ss_pred HHHHHHHHHHcCCcEEEEEEeecCCCcccCCCCChHHHHHHHHhCCCeEEEEE
Q 043606 28 AQDVSQRCKERGITALHIKLRATGGNKTKTPGPGAQSALRALARSGMKIGRIE 80 (101)
Q Consensus 28 ~~~~~~~~~~~gi~~v~V~lrg~~g~~~kG~G~gr~~~lr~l~~~gl~I~~I~ 80 (101)
+..+++.++++|++-|.+ .++|++ ++..|+..|++|....
T Consensus 54 G~~~a~~l~~~gvdvvi~----------~~iG~~---a~~~l~~~GIkv~~~~ 93 (121)
T COG1433 54 GIRIAELLVDEGVDVVIA----------SNIGPN---AYNALKAAGIKVYVAP 93 (121)
T ss_pred hHHHHHHHHHcCCCEEEE----------CccCHH---HHHHHHHcCcEEEecC
Confidence 345788899999986554 447774 5666788899988654
No 48
>TIGR02382 wecD_rffC TDP-D-fucosamine acetyltransferase. This model represents the WecD protein (Formerly RffC) for the biosynthesis of enterobacterial common antigen (ECA), an outer leaflet, outer membrane glycolipid with a trisaccharide repeat unit. WecD is a member of the GNAT family of acetytransferases (pfam00583).
Probab=57.23 E-value=48 Score=23.37 Aligned_cols=45 Identities=33% Similarity=0.440 Sum_probs=33.8
Q ss_pred HHHHHHHHHHHHHHHHcCCcEEEEEEeecCCCcccCCCCChHHHHHHHHhCCCeEEE
Q 043606 22 YAAMLAAQDVSQRCKERGITALHIKLRATGGNKTKTPGPGAQSALRALARSGMKIGR 78 (101)
Q Consensus 22 ~Aa~~a~~~~~~~~~~~gi~~v~V~lrg~~g~~~kG~G~gr~~~lr~l~~~gl~I~~ 78 (101)
|+.+ +.+.+.+.+.++|+..|.+.+ ...-..+++...+.|+++..
T Consensus 140 ~G~~-ll~~~~~~a~~~g~~~I~l~v-----------~~~N~~A~~~Y~klGF~~~~ 184 (191)
T TIGR02382 140 IGAE-LMQTALNWCYARGLTRLRVAT-----------QMGNTAALRLYIRSGANIES 184 (191)
T ss_pred HHHH-HHHHHHHHHHHcCCCEEEEEe-----------CCCCHHHHHHHHHcCCcccc
Confidence 5554 446688888999999999998 34446788888888987643
No 49
>COG3981 Predicted acetyltransferase [General function prediction only]
Probab=57.10 E-value=70 Score=23.85 Aligned_cols=40 Identities=15% Similarity=0.251 Sum_probs=28.2
Q ss_pred eccceee--ccCCCCcHHHHHHHHHHHHHHHHHcCCcEEEEEEe
Q 043606 7 TGGMKVK--ADRDESSPYAAMLAAQDVSQRCKERGITALHIKLR 48 (101)
Q Consensus 7 sG~~gfK--g~r~k~t~~Aa~~a~~~~~~~~~~~gi~~v~V~lr 48 (101)
.|-+||- -+. +.--||-+.. ..++++|+++||+.|-|...
T Consensus 98 gGHIGY~VrPse-R~KGYA~emL-kl~L~~ar~lgi~~Vlvtcd 139 (174)
T COG3981 98 GGHIGYSVRPSE-RRKGYAKEML-KLALEKARELGIKKVLVTCD 139 (174)
T ss_pred CCcccceeChhh-hccCHHHHHH-HHHHHHHHHcCCCeEEEEeC
Confidence 5666653 222 3344666655 66899999999999999993
No 50
>PRK10809 ribosomal-protein-S5-alanine N-acetyltransferase; Provisional
Probab=56.86 E-value=64 Score=22.45 Aligned_cols=48 Identities=15% Similarity=0.099 Sum_probs=35.7
Q ss_pred HHHHHHHHHHHHHHHH-cCCcEEEEEEeecCCCcccCCCCChHHHHHHHHhCCCeEEEEEe
Q 043606 22 YAAMLAAQDVSQRCKE-RGITALHIKLRATGGNKTKTPGPGAQSALRALARSGMKIGRIED 81 (101)
Q Consensus 22 ~Aa~~a~~~~~~~~~~-~gi~~v~V~lrg~~g~~~kG~G~gr~~~lr~l~~~gl~I~~I~D 81 (101)
|+.. +.+.+++.+.+ +|++.|.+.+ -+....+++.+.+.|++..-+..
T Consensus 120 ~~~e-a~~~ll~~~~~~l~l~~i~~~v-----------~~~N~~S~~l~ek~Gf~~~g~~~ 168 (194)
T PRK10809 120 LMFE-ALQAAIRYMQRQQHMHRIMANY-----------MPHNKRSGDLLARLGFEKEGYAK 168 (194)
T ss_pred HHHH-HHHHHHHHHHhcCCceEEEEEe-----------eCCCHHHHHHHHHCCCcEEeeec
Confidence 4444 44667888866 7999999999 44466788999999998765543
No 51
>PTZ00079 NADP-specific glutamate dehydrogenase; Provisional
Probab=56.67 E-value=40 Score=28.49 Aligned_cols=63 Identities=19% Similarity=0.242 Sum_probs=46.8
Q ss_pred CCCCcHHHHHHHHHHHHHHHHHcCCcEEEEEEeecCCCcccCCCCChHHHHHHHHhCCCeEEEEEecCCCCC
Q 043606 16 RDESSPYAAMLAAQDVSQRCKERGITALHIKLRATGGNKTKTPGPGAQSALRALARSGMKIGRIEDVTPIPT 87 (101)
Q Consensus 16 r~k~t~~Aa~~a~~~~~~~~~~~gi~~v~V~lrg~~g~~~kG~G~gr~~~lr~l~~~gl~I~~I~D~Tpiph 87 (101)
+...|-|....+++.+++.. ...++-.+|-| .|+|-=-..+.+.|.+.|-+|+.|.|..-.=|
T Consensus 212 r~eATG~Gv~~~~~~~l~~~-~~~l~Gk~VaV--------qG~GnVg~~aa~~L~e~GakVVavSD~~G~iy 274 (454)
T PTZ00079 212 RPEATGYGLVYFVLEVLKKL-NDSLEGKTVVV--------SGSGNVAQYAVEKLLQLGAKVLTMSDSDGYIH 274 (454)
T ss_pred CCcccHHHHHHHHHHHHHHc-CCCcCCCEEEE--------ECCCHHHHHHHHHHHHCCCEEEEEEcCCCcEE
Confidence 34678888887777666554 45577788999 78886445556778889999999999985444
No 52
>PLN02477 glutamate dehydrogenase
Probab=56.28 E-value=37 Score=28.17 Aligned_cols=60 Identities=17% Similarity=0.254 Sum_probs=42.9
Q ss_pred CCcHHHHHHHHHHHHHHHHHcCCcEEEEEEeecCCCcccCCCC-ChHHHHHHHHhCCCeEEEEEecCCCCC
Q 043606 18 ESSPYAAMLAAQDVSQRCKERGITALHIKLRATGGNKTKTPGP-GAQSALRALARSGMKIGRIEDVTPIPT 87 (101)
Q Consensus 18 k~t~~Aa~~a~~~~~~~~~~~gi~~v~V~lrg~~g~~~kG~G~-gr~~~lr~l~~~gl~I~~I~D~Tpiph 87 (101)
..|-|....+++.+++. ....++-.+|-| .|||. |+..+ +.|.+.|.+|+.|.|.+-.-|
T Consensus 183 ~aTg~Gv~~~~~~~~~~-~g~~l~g~~VaI--------qGfGnVG~~~A-~~L~e~GakVVaVsD~~G~iy 243 (410)
T PLN02477 183 AATGRGVVFATEALLAE-HGKSIAGQTFVI--------QGFGNVGSWAA-QLIHEKGGKIVAVSDITGAVK 243 (410)
T ss_pred ccchHHHHHHHHHHHHH-cCCCccCCEEEE--------ECCCHHHHHHH-HHHHHcCCEEEEEECCCCeEE
Confidence 66777777666665554 223456688999 78886 66555 788999999999999874433
No 53
>PRK09491 rimI ribosomal-protein-alanine N-acetyltransferase; Provisional
Probab=56.23 E-value=56 Score=21.54 Aligned_cols=54 Identities=13% Similarity=0.190 Sum_probs=38.4
Q ss_pred CcHHHHHHHHHHHHHHHHHcCCcEEEEEEeecCCCcccCCCCChHHHHHHHHhCCCeEEEEEecCC
Q 043606 19 SSPYAAMLAAQDVSQRCKERGITALHIKLRATGGNKTKTPGPGAQSALRALARSGMKIGRIEDVTP 84 (101)
Q Consensus 19 ~t~~Aa~~a~~~~~~~~~~~gi~~v~V~lrg~~g~~~kG~G~gr~~~lr~l~~~gl~I~~I~D~Tp 84 (101)
+.=++... .+.+.+.+.+.++..+.+.+ -.....+++.+.+.|++...+.....
T Consensus 77 g~G~g~~l-l~~~~~~~~~~~~~~~~~~~-----------~~~N~~a~~~y~k~Gf~~~~~~~~~~ 130 (146)
T PRK09491 77 RQGLGRAL-LEHLIDELEKRGVATLWLEV-----------RASNAAAIALYESLGFNEVTIRRNYY 130 (146)
T ss_pred cCCHHHHH-HHHHHHHHHHCCCcEEEEEE-----------ccCCHHHHHHHHHcCCEEeeeeeccc
Confidence 33444443 45677788889999988877 23346789999999999887665553
No 54
>TIGR01918 various_sel_PB selenoprotein B, glycine/betaine/sarcosine/D-proline reductase family. This model represents selenoprotein B of glycine reductase, sarcosine reductase, betaine reductase, D-proline reductase, and perhaps others. This model is built in fragment mode to assist in recognizing fragmentary translations. All members are expected to contain an internal TGA codon, encoding selenocysteine, which may be misinterpreted as a stop codon.
Probab=56.22 E-value=51 Score=27.82 Aligned_cols=55 Identities=20% Similarity=0.338 Sum_probs=42.3
Q ss_pred HHHHHHHHHHHHHHcCCcEEEEEEeecCCCcccCCCCCh---HHHHHHHHhCCCeEEEEEecCCCCC
Q 043606 24 AMLAAQDVSQRCKERGITALHIKLRATGGNKTKTPGPGA---QSALRALARSGMKIGRIEDVTPIPT 87 (101)
Q Consensus 24 a~~a~~~~~~~~~~~gi~~v~V~lrg~~g~~~kG~G~gr---~~~lr~l~~~gl~I~~I~D~Tpiph 87 (101)
+...+..|++++++-|+..|.+.= .-|.-- -+..|.|.++||.++.|..+|||..
T Consensus 321 a~~~g~eIa~~Lk~dgVDAVILTs---------tCgtC~r~~a~m~keiE~~GiPvv~~~~~~pis~ 378 (431)
T TIGR01918 321 SKQFAKEFVVELKQGGVDAVILTS---------TUGTCTRCGATMVKEIERAGIPVVHMCTVIPIAL 378 (431)
T ss_pred HHHHHHHHHHHHHHcCCCEEEEcC---------CCCcchhHHHHHHHHHHHcCCCEEEEeecccHhh
Confidence 346677899999999999877652 344422 2467889999999999999999854
No 55
>PRK14837 undecaprenyl pyrophosphate synthase; Provisional
Probab=56.20 E-value=91 Score=23.98 Aligned_cols=61 Identities=13% Similarity=0.162 Sum_probs=41.8
Q ss_pred HHHHHHHHHHHHHHHHcCCcEEEEEEeecCCCcccCCCCChH-H-H------------HHHHHhCCCeEEEEEecCCCCC
Q 043606 22 YAAMLAAQDVSQRCKERGITALHIKLRATGGNKTKTPGPGAQ-S-A------------LRALARSGMKIGRIEDVTPIPT 87 (101)
Q Consensus 22 ~Aa~~a~~~~~~~~~~~gi~~v~V~lrg~~g~~~kG~G~gr~-~-~------------lr~l~~~gl~I~~I~D~Tpiph 87 (101)
.+...+...+++.|.++||+.|.|+.--+ ..+..-.+ . . +.-|...|++|..|-|.+.+|-
T Consensus 33 ~~G~~~~~~i~~~c~~~GI~~lT~YaFS~-----EN~~Rp~~EV~~Lm~L~~~~l~~~~~~~~~~~irvr~iGd~~~Lp~ 107 (230)
T PRK14837 33 KEGLKRAKEIVKHSLKLGIKYLSLYVFST-----ENWNRTDSEIEHLMFLIADYLSSEFNFYKKNNIKIIVSGDIESLSE 107 (230)
T ss_pred HHHHHHHHHHHHHHHHcCCCEEEEEEeeh-----hhcCCCHHHHHHHHHHHHHHHHHHHHHHHHCCcEEEEEcChhhCCH
Confidence 45555667789999999999999998543 33332221 1 1 1123456999999999999884
No 56
>PRK13498 chemoreceptor glutamine deamidase CheD; Provisional
Probab=56.12 E-value=46 Score=24.26 Aligned_cols=58 Identities=21% Similarity=0.292 Sum_probs=40.5
Q ss_pred CcHHHHHHHHHHHHHHHHHcCCc--EEEEEEeecCCCcccC-------CCC---ChHHHHHHHHhCCCeEEE
Q 043606 19 SSPYAAMLAAQDVSQRCKERGIT--ALHIKLRATGGNKTKT-------PGP---GAQSALRALARSGMKIGR 78 (101)
Q Consensus 19 ~t~~Aa~~a~~~~~~~~~~~gi~--~v~V~lrg~~g~~~kG-------~G~---gr~~~lr~l~~~gl~I~~ 78 (101)
..-||-. |.+.+++.+.++|.+ .+.+++-| |++-+.+ +.. +-+.|.+.|++.||.|..
T Consensus 64 ~~rY~d~-ai~~Ll~~m~~~Ga~~~~l~aKifG-GA~m~~~~~~~~~~~~IG~rNi~~a~~~L~~~gi~i~a 133 (167)
T PRK13498 64 DGRYADE-AMELLIRHALANGTPPEDYQVKLFG-GGNMFPELQQDLHTLNVADKNIHAALALAEQNGLHLKA 133 (167)
T ss_pred CcCcHHH-HHHHHHHHHHHcCCCHHHEEEEEEE-CcccccccccCcccCChHHHHHHHHHHHHHHCCCcEEE
Confidence 3447554 668899999999977 57788866 4554442 233 446688889999999874
No 57
>TIGR00587 nfo apurinic endonuclease (APN1). All proteins in this family for which functions are known are 5' AP endonculeases that are used in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=55.54 E-value=33 Score=26.04 Aligned_cols=64 Identities=16% Similarity=0.047 Sum_probs=42.0
Q ss_pred HHHHHHHHHcCCcEEEEEEeecCCCcccCCCCChHHHHH-HHHhCCCeEEEEEecCCCCCCCCCC
Q 043606 29 QDVSQRCKERGITALHIKLRATGGNKTKTPGPGAQSALR-ALARSGMKIGRIEDVTPIPTDSTRR 92 (101)
Q Consensus 29 ~~~~~~~~~~gi~~v~V~lrg~~g~~~kG~G~gr~~~lr-~l~~~gl~I~~I~D~TpiphNGcR~ 92 (101)
..+++.+.++|+..+.|.++.|.+...+-+.......++ .+...++.+..|.--.|++.|-|=|
T Consensus 14 ~~a~~~~~~~G~~~~qif~~~P~~w~~~~~~~~~~~~~~~~~~~~~~~~~~i~~Hapy~iNlas~ 78 (274)
T TIGR00587 14 QAAYNRAAEIGATAFMFFLKSPRWWRRPMLEEEVIDWFKAALETNKNLSQIVLVHAPYLINLASP 78 (274)
T ss_pred HHHHHHHHHhCCCEEEEEecCccccCCCCCCHHHHHHHHHHHHHcCCCCcceeccCCeeeecCCC
Confidence 457889999999999999976644444433344444554 3666777755555556666676654
No 58
>PRK14831 undecaprenyl pyrophosphate synthase; Provisional
Probab=55.49 E-value=91 Score=24.13 Aligned_cols=60 Identities=25% Similarity=0.358 Sum_probs=39.5
Q ss_pred HHHHHHHHHHHHHHHcCCcEEEEEEeecCCCcccCCCCCh-HH--H-----------HHHHHhCCCeEEEEEecCCCCC
Q 043606 23 AAMLAAQDVSQRCKERGITALHIKLRATGGNKTKTPGPGA-QS--A-----------LRALARSGMKIGRIEDVTPIPT 87 (101)
Q Consensus 23 Aa~~a~~~~~~~~~~~gi~~v~V~lrg~~g~~~kG~G~gr-~~--~-----------lr~l~~~gl~I~~I~D~Tpiph 87 (101)
+...+...+++.|.++||+.|.|+.--+ -.+..-. |. . +..+...|++|..|-|.+.+|-
T Consensus 48 ~G~~~l~~i~~~c~~~GI~~vT~yaFS~-----eN~kR~~~Ev~~Lm~L~~~~l~~~~~~~~~~~iri~~iG~~~~Lp~ 121 (249)
T PRK14831 48 RGVDALKDLLRCCKDWGIGALTAYAFST-----ENWSRPLEEVNFLMTLFERVLRRELEELMEENVRIRFVGDLDPLPK 121 (249)
T ss_pred HHHHHHHHHHHHHHHcCCCEEEEeecch-----hhhCcCHHHHHHHHHHHHHHHHHHHHHHHHCCcEEEEEechhhCCH
Confidence 4444556788899999999999998432 1222221 00 1 1234567999999999988874
No 59
>cd04516 TBP_eukaryotes eukaryotic TATA box binding protein (TBP): Present in archaea and eukaryotes, TBPs are transcription factors that recognize promoters and initiate transcription. TBP has been shown to be an essential component of three different transcription initiation complexes: SL1, TFIID and TFIIIB, directing transcription by RNA polymerases I, II and III, respectively. TBP binds directly to the TATA box promoter element, where it nucleates polymerase assembly, thus defining the transcription start site. TBP's binding in the minor groove induces a dramatic DNA bending while its own structure barely changes. The conserved core domain of TBP, which binds to the TATA box, has a bipartite structure, with intramolecular symmetry generating a saddle-shaped structure that sits astride the DNA.
Probab=55.17 E-value=27 Score=25.53 Aligned_cols=37 Identities=24% Similarity=0.241 Sum_probs=31.5
Q ss_pred eeeeeccceeeccCCCCcHHHHHHHHHHHHHHHHHcCCcE
Q 043606 3 LERITGGMKVKADRDESSPYAAMLAAQDVSQRCKERGITA 42 (101)
Q Consensus 3 ~~~SsG~~gfKg~r~k~t~~Aa~~a~~~~~~~~~~~gi~~ 42 (101)
+.+++|-+-..|++ +.-.+..|++.+++.+.++|++.
T Consensus 51 lIF~SGKiviTGak---s~e~a~~a~~~i~~~L~~~g~~~ 87 (174)
T cd04516 51 LIFSSGKMVCTGAK---SEDDSKLAARKYARIIQKLGFPA 87 (174)
T ss_pred EEECCCeEEEEecC---CHHHHHHHHHHHHHHHHHcCCCC
Confidence 56789999999998 77788889999999999998653
No 60
>PRK01060 endonuclease IV; Provisional
Probab=53.79 E-value=39 Score=25.16 Aligned_cols=62 Identities=16% Similarity=0.018 Sum_probs=33.9
Q ss_pred HHHHHHHHHcCCcEEEEEEeecCCCcccCCCCChHH-HHHHHHhCCCeEEEEEecCCCCCCCC
Q 043606 29 QDVSQRCKERGITALHIKLRATGGNKTKTPGPGAQS-ALRALARSGMKIGRIEDVTPIPTDST 90 (101)
Q Consensus 29 ~~~~~~~~~~gi~~v~V~lrg~~g~~~kG~G~gr~~-~lr~l~~~gl~I~~I~D~TpiphNGc 90 (101)
+.+++.+.++|+..|++.+..+..-...-..+..-. .-+.+...|+.|..+.=-.|.+.|=|
T Consensus 15 ~~~l~~~~~~G~d~vEl~~~~p~~~~~~~~~~~~~~~lk~~~~~~gl~~~~~~~h~~~~~nl~ 77 (281)
T PRK01060 15 EGAVAEAAEIGANAFMIFTGNPQQWKRKPLEELNIEAFKAACEKYGISPEDILVHAPYLINLG 77 (281)
T ss_pred HHHHHHHHHcCCCEEEEECCCCCCCcCCCCCHHHHHHHHHHHHHcCCCCCceEEecceEecCC
Confidence 567889999999999999843311000000011112 33456678998754443345444433
No 61
>COG1570 XseA Exonuclease VII, large subunit [DNA replication, recombination, and repair]
Probab=53.45 E-value=28 Score=29.40 Aligned_cols=54 Identities=24% Similarity=0.230 Sum_probs=42.6
Q ss_pred HHHHHHHHHHHHHHHcCCcEEEEEEeecCCCcccCCCCChHHHHHHHHhCCCeEEE
Q 043606 23 AAMLAAQDVSQRCKERGITALHIKLRATGGNKTKTPGPGAQSALRALARSGMKIGR 78 (101)
Q Consensus 23 Aa~~a~~~~~~~~~~~gi~~v~V~lrg~~g~~~kG~G~gr~~~lr~l~~~gl~I~~ 78 (101)
|+..+++ +++.+.+++--.|-|.-|| ||+----+..+-|.+.|++..+.+.|+|
T Consensus 177 A~~eIv~-aI~~an~~~~~DvlIVaRG-GGSiEDLW~FNdE~vaRAi~~s~iPvIS 230 (440)
T COG1570 177 AAEEIVE-AIERANQRGDVDVLIVARG-GGSIEDLWAFNDEIVARAIAASRIPVIS 230 (440)
T ss_pred cHHHHHH-HHHHhhccCCCCEEEEecC-cchHHHHhccChHHHHHHHHhCCCCeEe
Confidence 5666665 5777877776667777777 7777777889999999999999998876
No 62
>cd04518 TBP_archaea archaeal TATA box binding protein (TBP): TBPs are transcription factors present in archaea and eukaryotes, that recognize promoters and initiate transcription. TBP has been shown to be an essential component of three different transcription initiation complexes: SL1, TFIID and TFIIIB, directing transcription by RNA polymerases I, II and III, respectively. TBP binds directly to the TATA box promoter element, where it nucleates polymerase assembly, thus defining the transcription start site. TBP's binding in the minor groove induces a dramatic DNA bending while its own structure barely changes. The conserved core domain of TBP, which binds to the TATA box, has a bipartite structure, with intramolecular symmetry generating a saddle-shaped structure that sits astride the DNA.
Probab=53.30 E-value=30 Score=25.32 Aligned_cols=37 Identities=22% Similarity=0.241 Sum_probs=32.2
Q ss_pred eeeeeccceeeccCCCCcHHHHHHHHHHHHHHHHHcCCcE
Q 043606 3 LERITGGMKVKADRDESSPYAAMLAAQDVSQRCKERGITA 42 (101)
Q Consensus 3 ~~~SsG~~gfKg~r~k~t~~Aa~~a~~~~~~~~~~~gi~~ 42 (101)
+.+++|-+-..|.+ +.-.+..|++++++.++++|++.
T Consensus 51 lIF~SGKiv~tGak---s~~~a~~a~~~~~~~L~~~g~~~ 87 (174)
T cd04518 51 LIFRSGKMVCTGAK---SVEDLHRAVKEIIKKLKDYGIKV 87 (174)
T ss_pred EEECCCeEEEEccC---CHHHHHHHHHHHHHHHHhcCCCc
Confidence 45789999999999 88889999999999999999664
No 63
>PF02878 PGM_PMM_I: Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain I; InterPro: IPR005844 The alpha-D-phosphohexomutase superfamily is composed of four related enzymes, each of which catalyses a phosphoryl transfer on their sugar substrates: phosphoglucomutase (PGM), phosphoglucomutase/phosphomannomutase (PGM/PMM), phosphoglucosamine mutase (PNGM), and phosphoacetylglucosamine mutase (PAGM) []. PGM (5.4.2.2 from EC) converts D-glucose 1-phosphate into D-glucose 6-phosphate, and participates in both the breakdown and synthesis of glucose []. PGM/PMM (5.4.2.2 from EC; 5.4.2.8 from EC) are primarily bacterial enzymes that use either glucose or mannose as substrate, participating in the biosynthesis of a variety of carbohydrates such as lipopolysaccharides and alginate [, ]. Both PNGM (5.4.2.3 from EC) and PAGM (5.4.2.10 from EC) are involved in the biosynthesis of UDP-N-acetylglucosamine [, ]. Despite differences in substrate specificity, these enzymes share a similar catalytic mechanism, converting 1-phospho-sugars to 6-phospho-sugars via a biphosphorylated 1,6-phospho-sugar. The active enzyme is phosphorylated at a conserved serine residue and binds one magnesium ion; residues around the active site serine are well conserved among family members. The reaction mechanism involves phosphoryl transfer from the phosphoserine to the substrate to create a biophosphorylated sugar, followed by a phosphoryl transfer from the substrate back to the enzyme []. The structures of PGM and PGM/PMM have been determined, and were found to be very similar in topology. These enzymes are both composed of four domains and a large central active site cleft, where each domain contains residues essential for catalysis and/or substrate recognition. Domain I contains the catalytic phosphoserine, domain II contains a metal-binding loop to coordinate the magnesium ion, domain III contains the sugar-binding loop that recognises the two different binding orientations of the 1- and 6-phospho-sugars, and domain IV contains a phosphate-binding site required for orienting the incoming phospho-sugar substrate. This entry represents domain I found in alpha-D-phosphohexomutase enzymes. This domain has a 3-layer alpha/beta/alpha topology.; GO: 0016868 intramolecular transferase activity, phosphotransferases, 0005975 carbohydrate metabolic process; PDB: 3I3W_B 1WQA_C 1KFQ_B 1KFI_A 2Z0F_A 2FKM_X 3C04_A 1K2Y_X 1P5G_X 2H4L_X ....
Probab=52.89 E-value=15 Score=24.96 Aligned_cols=61 Identities=20% Similarity=0.215 Sum_probs=40.4
Q ss_pred CcHHHHHHHHHHHHHHHHHc-CCcEEEEEEeecCCCcccCCC-CChHHHHHHHHhCCCeEEEEEecCCCC
Q 043606 19 SSPYAAMLAAQDVSQRCKER-GITALHIKLRATGGNKTKTPG-PGAQSALRALARSGMKIGRIEDVTPIP 86 (101)
Q Consensus 19 ~t~~Aa~~a~~~~~~~~~~~-gi~~v~V~lrg~~g~~~kG~G-~gr~~~lr~l~~~gl~I~~I~D~Tpip 86 (101)
-||..+...+..+++.+.+. .-..|.|=-.. +-.+ .-.+.+..+|...|++|..+. .+|.|
T Consensus 18 lt~~~~~~~~~a~~~~~~~~~~~~~VvVg~D~------R~~s~~~~~~~~~~l~~~G~~V~~~g-~~~tP 80 (137)
T PF02878_consen 18 LTPEFAARLAQAFASYLKEKGNGSRVVVGRDT------RPSSPMLAKALAAGLRANGVDVIDIG-LVPTP 80 (137)
T ss_dssp BSHHHHHHHHHHHHHHHHHTTTSSEEEEEE-S------STTHHHHHHHHHHHHHHTTEEEEEEE-EB-HH
T ss_pred CCHHHHHHHHHHHHHhhcccCCCCeEEEEEcc------cCCHHHHHHHHHHHHhhccccccccc-ccCcH
Confidence 69999999999999888875 33344444321 1111 235567788889999999887 55554
No 64
>PTZ00032 60S ribosomal protein L18; Provisional
Probab=52.22 E-value=32 Score=26.38 Aligned_cols=29 Identities=14% Similarity=0.227 Sum_probs=25.4
Q ss_pred CCcHHHHHHHHHHHHHHHHHcCCcEEEEE
Q 043606 18 ESSPYAAMLAAQDVSQRCKERGITALHIK 46 (101)
Q Consensus 18 k~t~~Aa~~a~~~~~~~~~~~gi~~v~V~ 46 (101)
.++--||..+++.++++|.+.||+.|..-
T Consensus 159 g~nieaA~~VGk~IAerAl~kGI~kVvFD 187 (211)
T PTZ00032 159 GGTIKAAYELGKLIGRKALSKGISKVRFD 187 (211)
T ss_pred CCcHHHHHHHHHHHHHHHHHCCCCEEEEe
Confidence 55778999999999999999999987665
No 65
>PRK00394 transcription factor; Reviewed
Probab=51.99 E-value=34 Score=25.07 Aligned_cols=37 Identities=22% Similarity=0.158 Sum_probs=32.3
Q ss_pred eeeeeccceeeccCCCCcHHHHHHHHHHHHHHHHHcCCcE
Q 043606 3 LERITGGMKVKADRDESSPYAAMLAAQDVSQRCKERGITA 42 (101)
Q Consensus 3 ~~~SsG~~gfKg~r~k~t~~Aa~~a~~~~~~~~~~~gi~~ 42 (101)
+.+++|-+-..|++ +.-.+..|++.+++.++++|++.
T Consensus 50 lIf~sGKiv~tGa~---S~~~a~~a~~~~~~~l~~~g~~~ 86 (179)
T PRK00394 50 LIFRSGKVVCTGAK---SVEDLHEAVKIIIKKLKELGIKV 86 (179)
T ss_pred EEEcCCcEEEEccC---CHHHHHHHHHHHHHHHHHcCCCc
Confidence 45789999999998 78889999999999999999765
No 66
>PLN00062 TATA-box-binding protein; Provisional
Probab=51.17 E-value=34 Score=25.19 Aligned_cols=35 Identities=23% Similarity=0.246 Sum_probs=30.6
Q ss_pred eeeeeccceeeccCCCCcHHHHHHHHHHHHHHHHHcCC
Q 043606 3 LERITGGMKVKADRDESSPYAAMLAAQDVSQRCKERGI 40 (101)
Q Consensus 3 ~~~SsG~~gfKg~r~k~t~~Aa~~a~~~~~~~~~~~gi 40 (101)
+.+++|-+-..|++ +.-.+..|++++++.+.++|+
T Consensus 51 lIF~SGKiviTGak---s~e~a~~a~~~~~~~L~~lg~ 85 (179)
T PLN00062 51 LIFASGKMVCTGAK---SEHDSKLAARKYARIIQKLGF 85 (179)
T ss_pred EEECCCeEEEEecC---CHHHHHHHHHHHHHHHHHcCC
Confidence 45789999999998 777888899999999999997
No 67
>TIGR03234 OH-pyruv-isom hydroxypyruvate isomerase. This enzyme interconverts tartronate semi-aldehyde (TSA, aka 2-hydroxy 3-oxopropionate) and hydroxypyruvate. The E. coli enzyme has been characterized and found to be specific for TSA, contain no cofactors, and have a rather high Km for hydroxypyruvate of 12.5 mM. The gene is ofter found in association with glyoxalate carboligase (which produces TSA), but has been shown to have no effect on growth on glyoxalate when knocked out. This is consistent with the fact that the gene for tartronate semialdehyde reductase (glxR) is also associated and may have primary responsibility for the catabolism of TSA.
Probab=50.16 E-value=63 Score=23.70 Aligned_cols=43 Identities=14% Similarity=0.100 Sum_probs=33.0
Q ss_pred HHHHHHHHHcCCcEEEEEEeecCCCcccCCCCChHHHHHHHHhCCCeEEEEE
Q 043606 29 QDVSQRCKERGITALHIKLRATGGNKTKTPGPGAQSALRALARSGMKIGRIE 80 (101)
Q Consensus 29 ~~~~~~~~~~gi~~v~V~lrg~~g~~~kG~G~gr~~~lr~l~~~gl~I~~I~ 80 (101)
+.+++.+.++|+..|++... .....+.+.+.|...||+|..+.
T Consensus 17 ~e~~~~~~e~G~~~vEl~~~---------~~~~~~~l~~~l~~~gl~v~~~~ 59 (254)
T TIGR03234 17 LERFAAAAQAGFTGVEYLFP---------YDWDAEALKARLAAAGLEQVLFN 59 (254)
T ss_pred HHHHHHHHHcCCCEEEecCC---------ccCCHHHHHHHHHHcCCeEEEEe
Confidence 55788889999999999751 13345566677888999999885
No 68
>cd05801 PGM_like3 This bacterial PGM-like (phosphoglucomutase-like) protein of unknown function belongs to the alpha-D-phosphohexomutase superfamily. The alpha-D-phosphohexomutases include several related enzymes that catalyze a reversible intramolecular phosphoryl transfer on their sugar substrates. Other members of this superfamily include phosphoglucosamine mutase (PNGM), phosphoacetylglucosamine mutase (PAGM), the bacterial phosphomannomutase ManB, the bacterial phosphoglucosamine mutase GlmM, and the bifunctional phosphomannomutase/phosphoglucomutase (PMM/PGM). Each of these enzymes has four domains with a centrally located active site formed by four loops, one from each domain. All four domains are included in this alignment model.
Probab=49.75 E-value=86 Score=26.28 Aligned_cols=74 Identities=22% Similarity=0.283 Sum_probs=47.3
Q ss_pred ccceeeccC--CCCcHHHHHHHHHHHHHHHHHcCC-cEEEEEEeecCCCcccCCCCChHHHHHHHHhCCCeEEEEEe--c
Q 043606 8 GGMKVKADR--DESSPYAAMLAAQDVSQRCKERGI-TALHIKLRATGGNKTKTPGPGAQSALRALARSGMKIGRIED--V 82 (101)
Q Consensus 8 G~~gfKg~r--~k~t~~Aa~~a~~~~~~~~~~~gi-~~v~V~lrg~~g~~~kG~G~gr~~~lr~l~~~gl~I~~I~D--~ 82 (101)
|.-|..|.- ..-|++-++.+++.+++.+.+.+. ..|.|---.+ ..-.+-.+.++.+|..+|++|....| .
T Consensus 24 GT~GiRG~~g~~~lt~~~v~~i~~a~~~~l~~~~~~~~VvVg~D~R-----~~S~~~~~~~~~gL~s~Gi~V~~~~~~g~ 98 (522)
T cd05801 24 GTSGHRGSSLKGSFNEAHILAISQAICDYRKSQGITGPLFLGKDTH-----ALSEPAFISALEVLAANGVEVIIQQNDGY 98 (522)
T ss_pred EcccccCccCCCchhHHHHHHHHHHHHHHHHhhCCCCeEEEEeCCC-----cCCHHHHHHHHHHHHHCCCEEEEeCCCCC
Confidence 334455422 146999999999988988876553 2344443211 11234455677899999999998876 5
Q ss_pred CCCC
Q 043606 83 TPIP 86 (101)
Q Consensus 83 Tpip 86 (101)
+|.|
T Consensus 99 ~pTP 102 (522)
T cd05801 99 TPTP 102 (522)
T ss_pred CCch
Confidence 6666
No 69
>PF00044 Gp_dh_N: Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain; InterPro: IPR020828 Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) plays an important role in glycolysis and gluconeogenesis [] by reversibly catalysing the oxidation and phosphorylation of D-glyceraldehyde-3-phosphate to 1,3-diphospho-glycerate. The enzyme exists as a tetramer of identical subunits, each containing 2 conserved functional domains: an NAD-binding domain, and a highly conserved catalytic domain []. The enzyme has been found to bind to actin and tropomyosin, and may thus have a role in cytoskeleton assembly. Alternatively, the cytoskeleton may provide a framework for precise positioning of the glycolytic enzymes, thus permitting efficient passage of metabolites from enzyme to enzyme []. GAPDH displays diverse non-glycolytic functions as well, its role depending upon its subcellular location. For instance, the translocation of GAPDH to the nucleus acts as a signalling mechanism for programmed cell death, or apoptosis []. The accumulation of GAPDH within the nucleus is involved in the induction of apoptosis, where GAPDH functions in the activation of transcription. The presence of GAPDH is associated with the synthesis of pro-apoptotic proteins like BAX, c-JUN and GAPDH itself. GAPDH has been implicated in certain neurological diseases: GAPDH is able to bind to the gene products from neurodegenerative disorders such as Huntington's disease, Alzheimer's disease, Parkinson's disease and Machado-Joseph disease through stretches encoded by their CAG repeats. Abnormal neuronal apoptosis is associated with these diseases. Propargylamines such as deprenyl increase neuronal survival by interfering with apoptosis signalling pathways via their binding to GAPDH, which decreases the synthesis of pro-apoptotic proteins []. This entry represents the N-terminal domain which is a Rossmann NAD(P) binding fold.; GO: 0016620 oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor, 0055114 oxidation-reduction process; PDB: 2G82_Q 1CER_R 1ZNQ_Q 3GPD_G 1U8F_R 3DOC_B 2YYY_A 1GPD_G 4GPD_1 2I5P_O ....
Probab=49.47 E-value=21 Score=25.43 Aligned_cols=29 Identities=24% Similarity=0.323 Sum_probs=22.0
Q ss_pred cCCCC-ChHHHHHHHHhCCCeEEEEEecCC
Q 043606 56 KTPGP-GAQSALRALARSGMKIGRIEDVTP 84 (101)
Q Consensus 56 kG~G~-gr~~~lr~l~~~gl~I~~I~D~Tp 84 (101)
+|||. ||..+--++.+..++|+-|.|..+
T Consensus 6 NGfGRIGR~v~r~~~~~~~~evvaInd~~~ 35 (151)
T PF00044_consen 6 NGFGRIGRLVLRAALDQPDIEVVAINDPAP 35 (151)
T ss_dssp ESTSHHHHHHHHHHHTSTTEEEEEEEESSS
T ss_pred ECCCcccHHHHHhhcccceEEEEEEecccc
Confidence 78995 776554445567899999999874
No 70
>cd05799 PGM2 This CD includes PGM2 (phosphoglucomutase 2) and PGM2L1 (phosphoglucomutase 2-like 1). The mammalian PGM2 is thought to be a phosphopentomutase that catalyzes the conversion of the nucleoside breakdown products, ribose-1-phosphate and deoxyribose-1-phosphate to the corresponding 5-phosphopentoses. PGM2L1 is thought to catalyze the 1,3-bisphosphoglycerate-dependent synthesis of glucose 1,6-bisphosphate and other aldose-bisphosphates that serve as cofactors for several sugar phosphomutases and possibly also as regulators of glycolytic enzymes. PGM2 and PGM2L1 belong to the alpha-D-phosphohexomutase superfamily which includes several related enzymes that catalyze a reversible intramolecular phosphoryl transfer on their sugar substrates. Other members of this superfamily include phosphoglucosamine mutase (PNGM), phosphoacetylglucosamine mutase (PAGM), the bacterial phosphomannomutase ManB, the bacterial phosphoglucosamine mutase GlmM, and the bifunctional phosphomannomutase/ph
Probab=49.45 E-value=70 Score=26.32 Aligned_cols=73 Identities=19% Similarity=0.300 Sum_probs=46.2
Q ss_pred ceeeccCCC----CcHHHHHHHHHHHHHHHHHcCC----cEEEEEEeecCCCcccCCCCChHHHHHHHHhCCCeEEEEEe
Q 043606 10 MKVKADRDE----SSPYAAMLAAQDVSQRCKERGI----TALHIKLRATGGNKTKTPGPGAQSALRALARSGMKIGRIED 81 (101)
Q Consensus 10 ~gfKg~r~k----~t~~Aa~~a~~~~~~~~~~~gi----~~v~V~lrg~~g~~~kG~G~gr~~~lr~l~~~gl~I~~I~D 81 (101)
-|..|.--. -|+..+..+++.++..+.+.+. ..|.|---. +..+. .=.++++.+|...|++|..+.+
T Consensus 7 ~giRg~~~~~~~~l~~~~~~~l~~a~~~~l~~~~~~~~~~~V~Vg~D~----R~~s~-~~~~a~~~gL~s~Gi~V~~~g~ 81 (487)
T cd05799 7 AGLRGKMGAGTNRMNDYTVRQATQGLANYLKKKGPDAKNRGVVIGYDS----RHNSR-EFAELTAAVLAANGIKVYLFDD 81 (487)
T ss_pred cccccccCCCCccccHHHHHHHHHHHHHHHHHhcccccCCeEEEEcCC----CCChH-HHHHHHHHHHHHCCCEEEEeCC
Confidence 345554433 4778888888888888775431 334333211 11111 1256777888999999999998
Q ss_pred cCCCCC
Q 043606 82 VTPIPT 87 (101)
Q Consensus 82 ~Tpiph 87 (101)
.+|.|-
T Consensus 82 ~~ptP~ 87 (487)
T cd05799 82 LRPTPL 87 (487)
T ss_pred CCCCcH
Confidence 888883
No 71
>PRK13489 chemoreceptor glutamine deamidase CheD; Provisional
Probab=49.27 E-value=67 Score=24.88 Aligned_cols=57 Identities=19% Similarity=0.129 Sum_probs=40.8
Q ss_pred cHHHHHHHHHHHHHHHHHcCCc--EEEEEEeecCCCcccC---CCC---ChHHHHHHHHhCCCeEEE
Q 043606 20 SPYAAMLAAQDVSQRCKERGIT--ALHIKLRATGGNKTKT---PGP---GAQSALRALARSGMKIGR 78 (101)
Q Consensus 20 t~~Aa~~a~~~~~~~~~~~gi~--~v~V~lrg~~g~~~kG---~G~---gr~~~lr~l~~~gl~I~~ 78 (101)
.-|+.. +.+.+++.+.++|.. .+.++|-| |++-+.+ ++. +-+.+.+.|...||.|+.
T Consensus 79 ~rYgd~-Ame~Li~~m~~~Ga~r~~L~AKifG-GA~m~~~~~~~~IG~RNieaa~~~L~~~gI~Iva 143 (233)
T PRK13489 79 MRYGAY-AMEVLINELIKAGGRRERFEAKVFG-GAAVLAGMTTINIGDRNADFVRRYLALERIRITA 143 (233)
T ss_pred cccHHH-HHHHHHHHHHHcCCCHHHEEEEEEE-CccccCCCCcCChhHHHHHHHHHHHHHcCCcEEE
Confidence 457655 568899999999977 57777766 5655553 233 345678889999999875
No 72
>cd04517 TLF TBP-like factors (TLF; also called TLP, TRF, TRP), which are found in most metazoans. TLFs and TBPs have well-conserved core domains; however, they only share about 60% similarity. TLFs, like TBPs, interact with TFIIA and TFIIB, which are part of the basal transcription machinery. Yet, in contrast to TBPs, TLFs seem not to interact with the TATA-box and even have a negative effect on the transcription of TATA-containing promoters. Recent results indicate that TLFs are involved in the transcription via TATA-less promoters.
Probab=48.38 E-value=41 Score=24.50 Aligned_cols=37 Identities=16% Similarity=0.156 Sum_probs=31.8
Q ss_pred eeeeeccceeeccCCCCcHHHHHHHHHHHHHHHHHcCCcE
Q 043606 3 LERITGGMKVKADRDESSPYAAMLAAQDVSQRCKERGITA 42 (101)
Q Consensus 3 ~~~SsG~~gfKg~r~k~t~~Aa~~a~~~~~~~~~~~gi~~ 42 (101)
+.+++|.+--.|.+ +.-.+..|++.+++.++++|++.
T Consensus 51 lIF~sGKiviTGak---s~~~~~~a~~~~~~~l~~~g~~~ 87 (174)
T cd04517 51 SVWSSGKITITGAT---SEEEAKQAARRAARLLQKLGFKV 87 (174)
T ss_pred EEECCCeEEEEccC---CHHHHHHHHHHHHHHHHHcCCCc
Confidence 45789999999998 77788889999999999998765
No 73
>PRK13487 chemoreceptor glutamine deamidase CheD; Provisional
Probab=47.87 E-value=80 Score=23.76 Aligned_cols=58 Identities=21% Similarity=0.182 Sum_probs=39.8
Q ss_pred CcHHHHHHHHHHHHHHHHHcCCcE--EEEEEeecCCCcccC---CCC---ChHHHHHHHHhCCCeEEE
Q 043606 19 SSPYAAMLAAQDVSQRCKERGITA--LHIKLRATGGNKTKT---PGP---GAQSALRALARSGMKIGR 78 (101)
Q Consensus 19 ~t~~Aa~~a~~~~~~~~~~~gi~~--v~V~lrg~~g~~~kG---~G~---gr~~~lr~l~~~gl~I~~ 78 (101)
..-||-. |.+.+++.+.++|... ++++|-| |++-+.+ ++. +-+.+.+.|.+.||.|+.
T Consensus 80 ~~rY~d~-A~~~Li~~m~~~Ga~~~~l~aKlfG-GA~m~~~~~~~~IG~rNi~~a~~~L~~~gI~iva 145 (201)
T PRK13487 80 SARYGSY-AMELLINDLLKLGARRENLEAKVFG-GGNVLRGFTSMNVGERNAEFVRDYLQTERIPIVA 145 (201)
T ss_pred CcccHHH-HHHHHHHHHHHcCCCHHHEEEEEEe-CCcccCCCccCCchHHHHHHHHHHHHHcCCcEEE
Confidence 3446554 6688999999998764 7777765 5555542 233 445678889999999875
No 74
>PF13207 AAA_17: AAA domain; PDB: 3AKC_A 3AKE_A 3AKD_A 2QL6_G 2QT1_A 2QSZ_A 2QSY_A 2QT0_A 2QG6_A 2P0E_A ....
Probab=47.58 E-value=33 Score=21.87 Aligned_cols=25 Identities=28% Similarity=0.628 Sum_probs=22.5
Q ss_pred CCCChHHHHHHHHhC-CCeEEEEEec
Q 043606 58 PGPGAQSALRALARS-GMKIGRIEDV 82 (101)
Q Consensus 58 ~G~gr~~~lr~l~~~-gl~I~~I~D~ 82 (101)
+|.|+.+..+.|.+. |+.++++.|+
T Consensus 8 ~gsGKST~a~~La~~~~~~~i~~d~~ 33 (121)
T PF13207_consen 8 PGSGKSTLAKELAERLGFPVISMDDL 33 (121)
T ss_dssp TTSSHHHHHHHHHHHHTCEEEEEHHH
T ss_pred CCCCHHHHHHHHHHHHCCeEEEecce
Confidence 899999999999986 9999988883
No 75
>PRK14836 undecaprenyl pyrophosphate synthase; Provisional
Probab=47.32 E-value=1e+02 Score=23.95 Aligned_cols=60 Identities=22% Similarity=0.298 Sum_probs=40.4
Q ss_pred HHHHHHHHHHHHHHHcCCcEEEEEEeecCCCcccCCCCChHHH--------------HHHHHhCCCeEEEEEecCCCCC
Q 043606 23 AAMLAAQDVSQRCKERGITALHIKLRATGGNKTKTPGPGAQSA--------------LRALARSGMKIGRIEDVTPIPT 87 (101)
Q Consensus 23 Aa~~a~~~~~~~~~~~gi~~v~V~lrg~~g~~~kG~G~gr~~~--------------lr~l~~~gl~I~~I~D~Tpiph 87 (101)
+...++..+++.|.++||+.|.|+.--+ ..+..-.+-+ +.-+...|++|..|-|.+++|-
T Consensus 42 ~G~~~~~~iv~~c~~~gI~~lTvYaFS~-----eN~~R~~~EV~~Lm~l~~~~l~~~~~~~~~~~irv~viG~~~~Lp~ 115 (253)
T PRK14836 42 AGVRAVRRTIEFCLEKGIEMLTLFAFSS-----ENWLRPADEVSALMELFLKALDREVDKLHRNGIRVRFIGDRSRLSP 115 (253)
T ss_pred HHHHHHHHHHHHHHHcCCCEEehhHhhh-----hhcCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCEEEEEeccccCCH
Confidence 4444567788999999999999987432 3333222211 1123447999999999999884
No 76
>PRK10240 undecaprenyl pyrophosphate synthase; Provisional
Probab=47.20 E-value=1.2e+02 Score=23.12 Aligned_cols=60 Identities=17% Similarity=0.221 Sum_probs=40.1
Q ss_pred HHHHHHHHHHHHHHHcCCcEEEEEEeecCCCcccCCCCCh-HH--H-----------HHHHHhCCCeEEEEEecCCCCC
Q 043606 23 AAMLAAQDVSQRCKERGITALHIKLRATGGNKTKTPGPGA-QS--A-----------LRALARSGMKIGRIEDVTPIPT 87 (101)
Q Consensus 23 Aa~~a~~~~~~~~~~~gi~~v~V~lrg~~g~~~kG~G~gr-~~--~-----------lr~l~~~gl~I~~I~D~Tpiph 87 (101)
+.......+++.|.++||+.|.|+.--+ ..+..-. |. . +..+...+++|..|-|.+.+|-
T Consensus 21 ~G~~~l~~i~~~c~~~GI~~lT~yaFS~-----eN~~R~~~Ev~~Lm~l~~~~l~~~~~~~~~~~i~vr~iG~~~~Lp~ 94 (229)
T PRK10240 21 AGAKSVRRAVSFAANNGIEALTLYAFSS-----ENWNRPAQEVSALMELFVWALDSEVKSLHRHNVRLRIIGDTSRFNS 94 (229)
T ss_pred HHHHHHHHHHHHHHHcCCCEEEEEeeeh-----hhcCcCHHHHHHHHHHHHHHHHHHHHHHHHCCcEEEEEeChhhCCH
Confidence 4445557788999999999999998543 2332211 11 1 1123456899999999999884
No 77
>PRK12360 4-hydroxy-3-methylbut-2-enyl diphosphate reductase; Provisional
Probab=47.07 E-value=67 Score=25.36 Aligned_cols=39 Identities=18% Similarity=0.374 Sum_probs=28.3
Q ss_pred HHHHHHHHcCCcEE------------EEEEeecCCCcccCCCCChHHHHHHHHhCCCeEE
Q 043606 30 DVSQRCKERGITAL------------HIKLRATGGNKTKTPGPGAQSALRALARSGMKIG 77 (101)
Q Consensus 30 ~~~~~~~~~gi~~v------------~V~lrg~~g~~~kG~G~gr~~~lr~l~~~gl~I~ 77 (101)
.+.+++.++|+..| .|.||+ +|..+ .....+.+.|++|+
T Consensus 45 ~Vv~~L~~~Gv~~v~~~~~~~v~~~~~ViirA------HGv~~---~~~~~~~~~g~~vi 95 (281)
T PRK12360 45 QVVSDLEEKGVKTIEESEIDSLKEGDVVIIRS------HGVSK---KVYKDLKDKGLEII 95 (281)
T ss_pred HHHHHHHHCcCEEECcCchhhCCCCCEEEEeC------CCCCH---HHHHHHHHCCCeEE
Confidence 34667788999988 588876 77666 45566777787765
No 78
>PRK09414 glutamate dehydrogenase; Provisional
Probab=46.91 E-value=55 Score=27.46 Aligned_cols=60 Identities=15% Similarity=0.225 Sum_probs=43.7
Q ss_pred CCCCcHHHHHHHHHHHHHHHHHcCCcEEEEEEeecCCCcccCCCC-ChHHHHHHHHhCCCeEEEEEecCCC
Q 043606 16 RDESSPYAAMLAAQDVSQRCKERGITALHIKLRATGGNKTKTPGP-GAQSALRALARSGMKIGRIEDVTPI 85 (101)
Q Consensus 16 r~k~t~~Aa~~a~~~~~~~~~~~gi~~v~V~lrg~~g~~~kG~G~-gr~~~lr~l~~~gl~I~~I~D~Tpi 85 (101)
+...|-|....+++.+++.. ...++-.+|-| .|||- |+. +.+.|...|.+|+-|.|.+-.
T Consensus 207 r~~aTg~Gv~~~~~~~~~~~-~~~l~g~rVaI--------qGfGnVG~~-~A~~L~~~GakVVavsDs~G~ 267 (445)
T PRK09414 207 RTEATGYGLVYFAEEMLKAR-GDSFEGKRVVV--------SGSGNVAIY-AIEKAQQLGAKVVTCSDSSGY 267 (445)
T ss_pred CCCcccHHHHHHHHHHHHhc-CCCcCCCEEEE--------ECCCHHHHH-HHHHHHHCCCEEEEEEcCCce
Confidence 44678887777776666553 44577789999 78885 554 447788899999999995543
No 79
>PLN00124 succinyl-CoA ligase [GDP-forming] subunit beta; Provisional
Probab=46.69 E-value=69 Score=26.65 Aligned_cols=48 Identities=27% Similarity=0.436 Sum_probs=35.9
Q ss_pred HHHHHHHHHHHHHcCCc-EEEEEEeecCCCcccCCCCChHHHHHHHHhCCCeEEEEEec
Q 043606 25 MLAAQDVSQRCKERGIT-ALHIKLRATGGNKTKTPGPGAQSALRALARSGMKIGRIEDV 82 (101)
Q Consensus 25 ~~a~~~~~~~~~~~gi~-~v~V~lrg~~g~~~kG~G~gr~~~lr~l~~~gl~I~~I~D~ 82 (101)
..+|+-+++.+++++++ .+.|++ -|++.+-..+.|..+|++|..-.|.
T Consensus 361 d~iA~gii~a~~~~~~~~pivvRl----------~Gtn~~~g~~~l~~~~~~~~~~~~l 409 (422)
T PLN00124 361 DVIASGIVNAAKQVGLKVPLVVRL----------EGTNVDQGKRILKESGMTLITAEDL 409 (422)
T ss_pred HHHHHHHHHHHHhcCCCCcEEEEc----------CCCCHHHHHHHHHhCCCCeEEcCCH
Confidence 44667778888887765 355555 4788899999999999988766654
No 80
>PLN02891 IMP cyclohydrolase
Probab=45.98 E-value=27 Score=30.29 Aligned_cols=42 Identities=24% Similarity=0.438 Sum_probs=32.2
Q ss_pred HHHHHHHHHcCCcEEEEEEeecCCCcccCCCCChHHHHHHHHhCCCeEEEEEecCCCCC
Q 043606 29 QDVSQRCKERGITALHIKLRATGGNKTKTPGPGAQSALRALARSGMKIGRIEDVTPIPT 87 (101)
Q Consensus 29 ~~~~~~~~~~gi~~v~V~lrg~~g~~~kG~G~gr~~~lr~l~~~gl~I~~I~D~Tpiph 87 (101)
+.+++.+.++|++-+. .| | .-+.|+.+|+++..|.|+|..|.
T Consensus 36 ~~fAk~L~~~gveIiS-----------Tg-G-----Tak~L~e~Gi~v~~Vsd~TgfPE 77 (547)
T PLN02891 36 ALLANGLQELGYTIVS-----------TG-G-----TASALEAAGVSVTKVEELTNFPE 77 (547)
T ss_pred HHHHHHHHHCCCEEEE-----------cc-h-----HHHHHHHcCCceeeHHhccCCch
Confidence 4577888888877332 11 2 34889999999999999999997
No 81
>PRK14832 undecaprenyl pyrophosphate synthase; Provisional
Probab=45.73 E-value=1.4e+02 Score=23.20 Aligned_cols=60 Identities=23% Similarity=0.369 Sum_probs=40.2
Q ss_pred HHHHHHHHHHHHHHHcCCcEEEEEEeecCCCcccCCCCChH-H-------------HHHHHHhCCCeEEEEEecCCCCC
Q 043606 23 AAMLAAQDVSQRCKERGITALHIKLRATGGNKTKTPGPGAQ-S-------------ALRALARSGMKIGRIEDVTPIPT 87 (101)
Q Consensus 23 Aa~~a~~~~~~~~~~~gi~~v~V~lrg~~g~~~kG~G~gr~-~-------------~lr~l~~~gl~I~~I~D~Tpiph 87 (101)
+...+...+++.|.++||+.|.|+.--+ ..+..-.+ . .+..+...|+.|..|-|...+|-
T Consensus 46 ~G~~~l~~i~~~c~~~gI~~lTvyaFS~-----EN~~Rp~~EV~~Lm~L~~~~l~~~~~~~~~~~irv~~iGd~~~Lp~ 119 (253)
T PRK14832 46 QGARTLKELLRCCKDWGIKALTAYAFST-----ENWQRPIEEVDFLMLLFERLLRRELAQMHREGVRISFIGDLSALPK 119 (253)
T ss_pred HHHHHHHHHHHHHHHcCCCEEEEEEeeh-----hhcCCCHHHHHHHHHHHHHHHHHHHHHHHhcCCEEEEEeCchhCCH
Confidence 4444556788889999999999998543 33332221 1 11224456999999999988884
No 82
>PRK13495 chemoreceptor glutamine deamidase CheD; Provisional
Probab=45.56 E-value=91 Score=22.56 Aligned_cols=57 Identities=19% Similarity=0.289 Sum_probs=39.4
Q ss_pred cHHHHHHHHHHHHHHHHHcCCcE--EEEEEeecCCCcccC--CCC---ChHHHHHHHHhCCCeEEE
Q 043606 20 SPYAAMLAAQDVSQRCKERGITA--LHIKLRATGGNKTKT--PGP---GAQSALRALARSGMKIGR 78 (101)
Q Consensus 20 t~~Aa~~a~~~~~~~~~~~gi~~--v~V~lrg~~g~~~kG--~G~---gr~~~lr~l~~~gl~I~~ 78 (101)
.-||-. |.+.+++.+.++|.+. +++++-| |++-+.. ++. +-+.|.+.|.+.||.|..
T Consensus 60 ~rY~d~-ai~~Li~~m~~~Ga~~~~l~aKifG-GA~m~~~~~~~IG~rNi~~a~~~L~~~gI~i~a 123 (159)
T PRK13495 60 GKYADT-AIKTLVEELKKMGAKVERLEAKIAG-GASMFESSGMNIGARNVEAVKKHLKDFGIKLVA 123 (159)
T ss_pred ccCHHH-HHHHHHHHHHHcCCCHHHEEEEEEe-CCccCCCCCCChHHHHHHHHHHHHHHcCCcEEE
Confidence 446554 6688999999998764 7777765 5554442 333 445678888999999875
No 83
>cd00652 TBP_TLF TATA box binding protein (TBP): Present in archaea and eukaryotes, TBPs are transcription factors that recognize promoters and initiate transcription. TBP has been shown to be an essential component of three different transcription initiation complexes: SL1, TFIID and TFIIIB, directing transcription by RNA polymerases I, II and III, respectively. TBP binds directly to the TATA box promoter element, where it nucleates polymerase assembly, thus defining the transcription start site. TBP's binding in the minor groove induces a dramatic DNA bending while its own structure barely changes. The conserved core domain of TBP, which binds to the TATA box, has a bipartite structure, with intramolecular symmetry generating a saddle-shaped structure that sits astride the DNA. New members of the TBP family, called TBP-like proteins (TBLP, TLF, TLP) or TBP-related factors (TRF1, TRF2,TRP), are similar to the core domain of TBPs, with identical or chemically similar amino acids at many
Probab=45.47 E-value=47 Score=24.15 Aligned_cols=37 Identities=24% Similarity=0.258 Sum_probs=32.2
Q ss_pred eeeeeccceeeccCCCCcHHHHHHHHHHHHHHHHHcCCcE
Q 043606 3 LERITGGMKVKADRDESSPYAAMLAAQDVSQRCKERGITA 42 (101)
Q Consensus 3 ~~~SsG~~gfKg~r~k~t~~Aa~~a~~~~~~~~~~~gi~~ 42 (101)
+.+++|-+-..|++ +.-.+..+++.+++.++++|++.
T Consensus 51 lIf~sGKivitGak---s~~~~~~a~~~~~~~L~~~g~~~ 87 (174)
T cd00652 51 LIFSSGKMVITGAK---SEEDAKLAARKYARILQKLGFPV 87 (174)
T ss_pred EEECCCEEEEEecC---CHHHHHHHHHHHHHHHHHcCCCc
Confidence 45789999999998 77888999999999999999776
No 84
>PRK14830 undecaprenyl pyrophosphate synthase; Provisional
Probab=44.35 E-value=1.5e+02 Score=22.98 Aligned_cols=60 Identities=18% Similarity=0.257 Sum_probs=40.4
Q ss_pred HHHHHHHHHHHHHHHcCCcEEEEEEeecCCCcccCCCCChH---HH-----------HHHHHhCCCeEEEEEecCCCCC
Q 043606 23 AAMLAAQDVSQRCKERGITALHIKLRATGGNKTKTPGPGAQ---SA-----------LRALARSGMKIGRIEDVTPIPT 87 (101)
Q Consensus 23 Aa~~a~~~~~~~~~~~gi~~v~V~lrg~~g~~~kG~G~gr~---~~-----------lr~l~~~gl~I~~I~D~Tpiph 87 (101)
+.......+++-|.++||+.|.|+.--+ ..+..-.+ .. +..+...+++|..|-|.+.+|-
T Consensus 50 ~G~~~l~~~l~~c~~~GI~~vTvYaFS~-----eN~~R~~~Ev~~Lm~l~~~~l~~~~~~~~~~~iri~viG~~~~Lp~ 123 (251)
T PRK14830 50 AGMDTVKKITKAASELGVKVLTLYAFST-----ENWKRPKDEVKFLMNLPVEFLDKFVPELIENNVKVNVIGDTDRLPE 123 (251)
T ss_pred HHHHHHHHHHHHHHHcCCCEEEEEEEeh-----hhcCCCHHHHHHHHHHHHHHHHHHHHHHHHcCCEEEEEcChhhCCH
Confidence 4444667788999999999999998432 33332222 11 1223457999999999998873
No 85
>PRK14030 glutamate dehydrogenase; Provisional
Probab=43.95 E-value=70 Score=26.94 Aligned_cols=63 Identities=16% Similarity=0.153 Sum_probs=44.8
Q ss_pred CCCCcHHHHHHHHHHHHHHHHHcCCcEEEEEEeecCCCcccCCCC-ChHHHHHHHHhCCCeEEEEEecCCCCCC
Q 043606 16 RDESSPYAAMLAAQDVSQRCKERGITALHIKLRATGGNKTKTPGP-GAQSALRALARSGMKIGRIEDVTPIPTD 88 (101)
Q Consensus 16 r~k~t~~Aa~~a~~~~~~~~~~~gi~~v~V~lrg~~g~~~kG~G~-gr~~~lr~l~~~gl~I~~I~D~TpiphN 88 (101)
+...|-|....+++.+++.. ...++-.+|-| .|+|- |..+| +.|...|-+|+.|.|.+-.=||
T Consensus 203 r~~ATg~Gv~~~~~~~~~~~-g~~l~g~~vaI--------QGfGnVG~~aA-~~L~e~GakvVavSD~~G~i~d 266 (445)
T PRK14030 203 RPEATGFGALYFVHQMLETK-GIDIKGKTVAI--------SGFGNVAWGAA-TKATELGAKVVTISGPDGYIYD 266 (445)
T ss_pred CCCccHHHHHHHHHHHHHHc-CCCcCCCEEEE--------ECCCHHHHHHH-HHHHHCCCEEEEEEcCCceEEC
Confidence 33668887777776665544 23466788999 78885 55555 6688899999999998765443
No 86
>PRK06920 dnaE DNA polymerase III DnaE; Reviewed
Probab=43.83 E-value=21 Score=33.32 Aligned_cols=44 Identities=34% Similarity=0.450 Sum_probs=32.4
Q ss_pred HHHHHHHHHHHHcCCcEEEEEEeecCCCcccCCCCChHHHHHHHHhCCCeEEEEEecCCCCCC
Q 043606 26 LAAQDVSQRCKERGITALHIKLRATGGNKTKTPGPGAQSALRALARSGMKIGRIEDVTPIPTD 88 (101)
Q Consensus 26 ~a~~~~~~~~~~~gi~~v~V~lrg~~g~~~kG~G~gr~~~lr~l~~~gl~I~~I~D~TpiphN 88 (101)
++...+++.|++.||. .||||=+|--.|-. ..+.|+|+-|++||
T Consensus 324 LIV~D~i~~Ak~~gI~----------------VGPGRGSaAGSLVa---Y~LgIT~VDPl~y~ 367 (1107)
T PRK06920 324 LIVWDFMKYAHENHIL----------------TGPGRGSAAGSLVS---YVLEITDIDPIEYD 367 (1107)
T ss_pred HHHHHHHHHHHHCCCE----------------eCCCcchHHHHHHH---HHhCCCccCccccC
Confidence 4555677888887765 37777777777764 45668999999996
No 87
>PRK13493 chemoreceptor glutamine deamidase CheD; Provisional
Probab=43.61 E-value=1e+02 Score=23.38 Aligned_cols=58 Identities=22% Similarity=0.241 Sum_probs=40.4
Q ss_pred CcHHHHHHHHHHHHHHHHHcCCc--EEEEEEeecCCCcccC---CC-CChHHHHHHHHhCCCeEEE
Q 043606 19 SSPYAAMLAAQDVSQRCKERGIT--ALHIKLRATGGNKTKT---PG-PGAQSALRALARSGMKIGR 78 (101)
Q Consensus 19 ~t~~Aa~~a~~~~~~~~~~~gi~--~v~V~lrg~~g~~~kG---~G-~gr~~~lr~l~~~gl~I~~ 78 (101)
..-|+-. |.+.+++.+.++|.. .++++|-| |+|-+.+ +| .+-+.|.+.|.+.||+|..
T Consensus 94 ~~rY~d~-Am~~Li~~m~~~Ga~~~~l~aKifG-GA~m~~~~~~IG~rNi~~a~~~L~~~gI~Iva 157 (213)
T PRK13493 94 SSRYGCY-AMEVLINRLLSMGAERERLKFKLFG-GAHLMGYQSLVGEKNVEFVLEYAKREKLNVVA 157 (213)
T ss_pred ccccHHH-HHHHHHHHHHHcCCCHHHeEEEEEe-CcccccccccHhHHHHHHHHHHHHHcCCcEEE
Confidence 3456554 668899999999877 57777766 4554432 33 2456788889999999875
No 88
>PRK07564 phosphoglucomutase; Validated
Probab=43.36 E-value=1.1e+02 Score=25.84 Aligned_cols=74 Identities=23% Similarity=0.296 Sum_probs=46.5
Q ss_pred ccceeeccC--CCCcHHHHHHHHHHHHHHHHHcCCc-EEEEEEeecCCCcccCCCCChHHHHHHHHhCCCeEEEEEe--c
Q 043606 8 GGMKVKADR--DESSPYAAMLAAQDVSQRCKERGIT-ALHIKLRATGGNKTKTPGPGAQSALRALARSGMKIGRIED--V 82 (101)
Q Consensus 8 G~~gfKg~r--~k~t~~Aa~~a~~~~~~~~~~~gi~-~v~V~lrg~~g~~~kG~G~gr~~~lr~l~~~gl~I~~I~D--~ 82 (101)
|.-|+.|-- ..-|+.-++.+++.+++.+.+.+.+ .|.|---. +..+ -.=.++++.+|..+|++|..+.| .
T Consensus 41 GT~GiRg~~~~~~lt~~~v~~i~~a~a~~~~~~~~~~~VvVG~D~----R~~S-~~~a~a~a~gL~s~Gi~V~~~~~~g~ 115 (543)
T PRK07564 41 GTSGHRGSSLQPSFNENHILAIFQAICEYRGKQGITGPLFVGGDT----HALS-EPAIQSALEVLAANGVGVVIVGRGGY 115 (543)
T ss_pred cccccccccCCCCcCHHHHHHHHHHHHHHHHhcCCCCeEEEEecC----CcCC-HHHHHHHHHHHHHCCCEEEEeCCCCc
Confidence 334555422 1468888998988888888765532 24444321 1111 12356788899999999999976 5
Q ss_pred CCCC
Q 043606 83 TPIP 86 (101)
Q Consensus 83 Tpip 86 (101)
+|.|
T Consensus 116 ~pTP 119 (543)
T PRK07564 116 TPTP 119 (543)
T ss_pred CCch
Confidence 6666
No 89
>TIGR00055 uppS undecaprenyl diphosphate synthase. Alternate name: undecaprenyl pyrophosphate synthetase. Activity has been demonstrated experimentally for members of this family from Micrococcus luteus, E. coli, Haemophilus influenzae, and Streptococcus pneumoniae.
Probab=43.14 E-value=1.5e+02 Score=22.68 Aligned_cols=61 Identities=18% Similarity=0.259 Sum_probs=41.2
Q ss_pred HHHHHHHHHHHHHHHHcCCcEEEEEEeecCCCcccCCCCCh-HH-HH------------HHHHhCCCeEEEEEecCCCCC
Q 043606 22 YAAMLAAQDVSQRCKERGITALHIKLRATGGNKTKTPGPGA-QS-AL------------RALARSGMKIGRIEDVTPIPT 87 (101)
Q Consensus 22 ~Aa~~a~~~~~~~~~~~gi~~v~V~lrg~~g~~~kG~G~gr-~~-~l------------r~l~~~gl~I~~I~D~Tpiph 87 (101)
.+...+...+++.|.++||+.|.|+.--+ ..+..-. |. .| .-|...|++|..|-|.+.+|-
T Consensus 26 ~~G~~~~~~v~~~c~~~GI~~lT~yaFSt-----EN~~Rp~~EV~~Lm~L~~~~l~~~~~~~~~~~irvr~iGd~~~Lp~ 100 (226)
T TIGR00055 26 KAGVKSLRRILRWCANLGVECLTLYAFST-----ENWKRPKEEVDFLMELFEKKLDREVKELHRYNVRIRIIGDLSLLSK 100 (226)
T ss_pred HHHHHHHHHHHHHHHHcCCCEEEEEEeeh-----hhcCcCHHHHHHHHHHHHHHHHHHHHHHHHCCCEEEEEeChhhCCH
Confidence 34555667788999999999999998543 2232211 11 11 123456999999999999884
No 90
>PF00208 ELFV_dehydrog: Glutamate/Leucine/Phenylalanine/Valine dehydrogenase; InterPro: IPR006096 Glutamate, leucine, phenylalanine and valine dehydrogenases are structurally and functionally related. They contain a Gly-rich region containing a conserved Lys residue, which has been implicated in the catalytic activity, in each case a reversible oxidative deamination reaction. Glutamate dehydrogenases (1.4.1.2 from EC, 1.4.1.3 from EC, and 1.4.1.4 from EC) (GluDH) are enzymes that catalyse the NAD- and/or NADP-dependent reversible deamination of L-glutamate into alpha-ketoglutarate [, ]. GluDH isozymes are generally involved with either ammonia assimilation or glutamate catabolism. Two separate enzymes are present in yeasts: the NADP-dependent enzyme, which catalyses the amination of alpha-ketoglutarate to L-glutamate; and the NAD-dependent enzyme, which catalyses the reverse reaction [] - this form links the L-amino acids with the Krebs cycle, which provides a major pathway for metabolic interconversion of alpha-amino acids and alpha- keto acids []. Leucine dehydrogenase (1.4.1.9 from EC) (LeuDH) is a NAD-dependent enzyme that catalyses the reversible deamination of leucine and several other aliphatic amino acids to their keto analogues []. Each subunit of this octameric enzyme from Bacillus sphaericus contains 364 amino acids and folds into two domains, separated by a deep cleft. The nicotinamide ring of the NAD+ cofactor binds deep in this cleft, which is thought to close during the hydride transfer step of the catalytic cycle. Phenylalanine dehydrogenase (1.4.1.20 from EC) (PheDH) is na NAD-dependent enzyme that catalyses the reversible deamidation of L-phenylalanine into phenyl-pyruvate []. Valine dehydrogenase (1.4.1.8 from EC) (ValDH) is an NADP-dependent enzyme that catalyses the reversible deamidation of L-valine into 3-methyl-2-oxobutanoate []. This entry represents the C-terminal domain of these proteins.; GO: 0016491 oxidoreductase activity, 0006520 cellular amino acid metabolic process, 0055114 oxidation-reduction process; PDB: 1LEH_A 3AOG_D 3AOE_A 2YFQ_B 2YFH_B 1HRD_A 1K89_A 1AUP_A 1BGV_A 1B26_C ....
Probab=43.06 E-value=36 Score=25.97 Aligned_cols=59 Identities=20% Similarity=0.295 Sum_probs=39.7
Q ss_pred CCcHHHHHHHHHHHHHHHHHcCCcEEEEEEeecCCCcccCCCC-ChHHHHHHHHhCCCeEEEEEecCCC
Q 043606 18 ESSPYAAMLAAQDVSQRCKERGITALHIKLRATGGNKTKTPGP-GAQSALRALARSGMKIGRIEDVTPI 85 (101)
Q Consensus 18 k~t~~Aa~~a~~~~~~~~~~~gi~~v~V~lrg~~g~~~kG~G~-gr~~~lr~l~~~gl~I~~I~D~Tpi 85 (101)
..|-|....+.+.+++.+....++..+|-| .|||. |. .+.+.|.+.|.+|+-|.|.+..
T Consensus 8 ~aTg~GV~~~~~~~~~~~~~~~l~g~~v~I--------qGfG~VG~-~~a~~l~~~Ga~vv~vsD~~G~ 67 (244)
T PF00208_consen 8 EATGYGVAYAIEAALEHLGGDSLEGKRVAI--------QGFGNVGS-HAARFLAELGAKVVAVSDSSGA 67 (244)
T ss_dssp THHHHHHHHHHHHHHHHTTCHSSTTCEEEE--------EESSHHHH-HHHHHHHHTTEEEEEEEESSEE
T ss_pred cchHHHHHHHHHHHHHHcCCCCcCCCEEEE--------ECCCHHHH-HHHHHHHHcCCEEEEEecCceE
Confidence 455566555555555552222366788999 77885 54 4557788889999999997643
No 91
>PRK09542 manB phosphomannomutase/phosphoglucomutase; Reviewed
Probab=42.86 E-value=1e+02 Score=25.21 Aligned_cols=63 Identities=11% Similarity=0.124 Sum_probs=42.8
Q ss_pred CCcHHHHHHHHHHHHHHHHHcCCcEEEEEEeecCCCcccCCC-CChHHHHHHHHhCCCeEEEEEecCCCCC
Q 043606 18 ESSPYAAMLAAQDVSQRCKERGITALHIKLRATGGNKTKTPG-PGAQSALRALARSGMKIGRIEDVTPIPT 87 (101)
Q Consensus 18 k~t~~Aa~~a~~~~~~~~~~~gi~~v~V~lrg~~g~~~kG~G-~gr~~~lr~l~~~gl~I~~I~D~Tpiph 87 (101)
.-||.-+..++..+++.+.+.+-..|.|---. +-.+ .=..+++.+|...|++|..+ +.+|.|-
T Consensus 13 ~lt~~~v~~l~~a~~~~l~~~~~~~VvVg~D~------R~~s~~l~~a~~~gL~s~G~~V~~l-g~~pTP~ 76 (445)
T PRK09542 13 QIDEDLVRDVGAAFARLMRAEGATTVVIGHDM------RDSSPELAAAFAEGVTAQGLDVVRI-GLASTDQ 76 (445)
T ss_pred CcCHHHHHHHHHHHHHHHHHcCCCeEEEEeCC------CCCHHHHHHHHHHHHHHCCCEEEEe-CCCCCHH
Confidence 36888888888888888776543445444321 1111 12566788899999999999 6888884
No 92
>PF08901 DUF1847: Protein of unknown function (DUF1847); InterPro: IPR014997 This group of proteins are functionally uncharacterised. They contain 4 N-terminal cysteines that may form a zinc-binding domain.
Probab=42.67 E-value=60 Score=23.81 Aligned_cols=44 Identities=14% Similarity=0.260 Sum_probs=34.6
Q ss_pred HHHHHHHHHHcCCcEEEEEEeecCCCcccCCCCChHH--HHHHHHhCCCeEEEEE
Q 043606 28 AQDVSQRCKERGITALHIKLRATGGNKTKTPGPGAQS--ALRALARSGMKIGRIE 80 (101)
Q Consensus 28 ~~~~~~~~~~~gi~~v~V~lrg~~g~~~kG~G~gr~~--~lr~l~~~gl~I~~I~ 80 (101)
.|.+++.|+.+|++.|=|-+ =+|.-+++ .-+.|...|+.+.++.
T Consensus 43 veEiieFak~mgykkiGiAf---------CiGL~~EA~~~~~iL~~~gFev~sV~ 88 (157)
T PF08901_consen 43 VEEIIEFAKRMGYKKIGIAF---------CIGLRKEARILAKILEANGFEVYSVC 88 (157)
T ss_pred HHHHHHHHHHcCCCeeeehh---------hHhHHHHHHHHHHHHHHCCCEEEEEE
Confidence 46789999999999988876 35776665 4466888999999874
No 93
>PRK10887 glmM phosphoglucosamine mutase; Provisional
Probab=42.60 E-value=1.9e+02 Score=23.60 Aligned_cols=76 Identities=13% Similarity=0.079 Sum_probs=46.6
Q ss_pred eeeeeccceeeccCCCCcHHHHHHHHHHHHHHHHHcCCcEEEEEEeecCCCcccCCCC-ChHHHHHHHHhCCCeEEEEEe
Q 043606 3 LERITGGMKVKADRDESSPYAAMLAAQDVSQRCKERGITALHIKLRATGGNKTKTPGP-GAQSALRALARSGMKIGRIED 81 (101)
Q Consensus 3 ~~~SsG~~gfKg~r~k~t~~Aa~~a~~~~~~~~~~~gi~~v~V~lrg~~g~~~kG~G~-gr~~~lr~l~~~gl~I~~I~D 81 (101)
++-..|--|.-+.- .-||.-+...+..++..+.+.+-..|.|---. +-.++ =..+++.+|..+|++|..+ .
T Consensus 3 ~Fgt~GiRG~~~~~-~ltpe~~~~lg~a~a~~l~~~~~~~VvVg~D~------R~ss~~l~~a~~~gL~s~Gv~V~~~-g 74 (443)
T PRK10887 3 YFGTDGIRGKVGQA-PITPDFVLKLGWAAGKVLARQGRPKVLIGKDT------RISGYMLESALEAGLAAAGVDVLLT-G 74 (443)
T ss_pred ccCCCccceecCCC-CCCHHHHHHHHHHHHHHHHhCCCCcEEEEeCC------CCCHHHHHHHHHHHHHHCCCeEEEE-C
Confidence 44445554544432 35887777777777877765443445444321 11121 1457788899999999998 6
Q ss_pred cCCCC
Q 043606 82 VTPIP 86 (101)
Q Consensus 82 ~Tpip 86 (101)
.+|.|
T Consensus 75 ~~pTP 79 (443)
T PRK10887 75 PMPTP 79 (443)
T ss_pred CcChH
Confidence 77777
No 94
>PRK13210 putative L-xylulose 5-phosphate 3-epimerase; Reviewed
Probab=42.57 E-value=94 Score=22.96 Aligned_cols=52 Identities=13% Similarity=0.175 Sum_probs=32.8
Q ss_pred HHHHHHHHHHcCCcEEEEEEeecCCCccc--CCCCC-hHHHHHHHHhCCCeEEEEE
Q 043606 28 AQDVSQRCKERGITALHIKLRATGGNKTK--TPGPG-AQSALRALARSGMKIGRIE 80 (101)
Q Consensus 28 ~~~~~~~~~~~gi~~v~V~lrg~~g~~~k--G~G~g-r~~~lr~l~~~gl~I~~I~ 80 (101)
-+.+++.+.++|+..|++.+..+. .... .+... ...+-+.|...||+|.++.
T Consensus 18 ~~e~~~~~~~~G~~~iEl~~~~~~-~~~~~~~~~~~~~~~l~~~l~~~Gl~i~~~~ 72 (284)
T PRK13210 18 WEERLVFAKELGFDFVEMSVDESD-ERLARLDWSKEERLSLVKAIYETGVRIPSMC 72 (284)
T ss_pred HHHHHHHHHHcCCCeEEEecCCcc-cccccccCCHHHHHHHHHHHHHcCCCceEEe
Confidence 356788999999999999873210 0000 11222 2334556788899999884
No 95
>PRK08356 hypothetical protein; Provisional
Probab=42.48 E-value=54 Score=23.38 Aligned_cols=36 Identities=11% Similarity=0.217 Sum_probs=25.6
Q ss_pred CCcEEEEEEeecCCCcccCCCCChHHHHHHHHhCCCeEEEEEe
Q 043606 39 GITALHIKLRATGGNKTKTPGPGAQSALRALARSGMKIGRIED 81 (101)
Q Consensus 39 gi~~v~V~lrg~~g~~~kG~G~gr~~~lr~l~~~gl~I~~I~D 81 (101)
|.....|.|-| .+|.|+.++-+.|...|+.+++..|
T Consensus 2 ~~~~~~i~~~G-------~~gsGK~t~a~~l~~~g~~~is~~~ 37 (195)
T PRK08356 2 GVEKMIVGVVG-------KIAAGKTTVAKFFEEKGFCRVSCSD 37 (195)
T ss_pred CCCcEEEEEEC-------CCCCCHHHHHHHHHHCCCcEEeCCC
Confidence 34444566644 3899999999999887887666554
No 96
>PRK05673 dnaE DNA polymerase III subunit alpha; Validated
Probab=42.40 E-value=22 Score=33.14 Aligned_cols=44 Identities=32% Similarity=0.430 Sum_probs=32.3
Q ss_pred HHHHHHHHHHHHcCCcEEEEEEeecCCCcccCCCCChHHHHHHHHhCCCeEEEEEecCCCCCC
Q 043606 26 LAAQDVSQRCKERGITALHIKLRATGGNKTKTPGPGAQSALRALARSGMKIGRIEDVTPIPTD 88 (101)
Q Consensus 26 ~a~~~~~~~~~~~gi~~v~V~lrg~~g~~~kG~G~gr~~~lr~l~~~gl~I~~I~D~TpiphN 88 (101)
++...+++.|++.||. .||||=+|--.|-. ..+.|+|+-|++||
T Consensus 339 LIV~D~i~~Ak~~gI~----------------vGpGRGSaAGSLVa---Y~LgIT~vDPl~y~ 382 (1135)
T PRK05673 339 LIVADFIQWAKDNGIP----------------VGPGRGSGAGSLVA---YALGITDLDPLRFG 382 (1135)
T ss_pred HHHHHHHHHHHHCCCe----------------eCCCCchHHHHHHH---HHhcCCccCccccC
Confidence 4555677788887765 37777777777764 45678999999996
No 97
>PRK09989 hypothetical protein; Provisional
Probab=42.06 E-value=92 Score=23.02 Aligned_cols=43 Identities=7% Similarity=0.132 Sum_probs=32.1
Q ss_pred HHHHHHHHHcCCcEEEEEEeecCCCcccCCCCChHHHHHHHHhCCCeEEEEE
Q 043606 29 QDVSQRCKERGITALHIKLRATGGNKTKTPGPGAQSALRALARSGMKIGRIE 80 (101)
Q Consensus 29 ~~~~~~~~~~gi~~v~V~lrg~~g~~~kG~G~gr~~~lr~l~~~gl~I~~I~ 80 (101)
+..++.+.++|++.|++.. + .+...+-+.+.|...||++..+.
T Consensus 18 ~~~l~~~~~~Gfd~VEl~~--~-------~~~~~~~~~~~l~~~Gl~v~~~~ 60 (258)
T PRK09989 18 IERFAAARKAGFDAVEFLF--P-------YDYSTLQIQKQLEQNHLTLALFN 60 (258)
T ss_pred HHHHHHHHHcCCCEEEECC--c-------ccCCHHHHHHHHHHcCCcEEEec
Confidence 4568889999999999854 1 23345556677888999999875
No 98
>PF02776 TPP_enzyme_N: Thiamine pyrophosphate enzyme, N-terminal TPP binding domain; InterPro: IPR012001 A number of enzymes require thiamine pyrophosphate (TPP) (vitamin B1) as a cofactor. It has been shown [] that some of these enzymes are structurally related. This represents the N-terminal TPP binding domain of TPP enzymes.; GO: 0030976 thiamine pyrophosphate binding; PDB: 3HWX_1 3FLM_B 3HWW_A 2JLC_A 2JLA_A 2VBG_A 2VBF_B 2Q29_A 2Q27_B 2Q28_B ....
Probab=41.91 E-value=91 Score=21.74 Aligned_cols=44 Identities=27% Similarity=0.471 Sum_probs=31.9
Q ss_pred HHHHHHHHHHHcCCcEEEEEEeecCCCcccCCCCChHHHHHHHHhC-CCeEEEEEe
Q 043606 27 AAQDVSQRCKERGITALHIKLRATGGNKTKTPGPGAQSALRALARS-GMKIGRIED 81 (101)
Q Consensus 27 a~~~~~~~~~~~gi~~v~V~lrg~~g~~~kG~G~gr~~~lr~l~~~-gl~I~~I~D 81 (101)
.++.+++.+++.|++.|--. +|.+-...+.+|... +++++...+
T Consensus 3 ~~~~l~~~L~~~Gv~~vfgv-----------pG~~~~~l~~al~~~~~i~~i~~~~ 47 (172)
T PF02776_consen 3 GAEALAEALKANGVTHVFGV-----------PGSGNLPLLDALEKSPGIRFIPVRH 47 (172)
T ss_dssp HHHHHHHHHHHTT-SEEEEE-------------GGGHHHHHHHHHTTTSEEEE-SS
T ss_pred HHHHHHHHHHHCCCeEEEEE-----------eChhHhHHHHHhhhhcceeeecccC
Confidence 56889999999999986444 477777899999998 688776543
No 99
>PRK00286 xseA exodeoxyribonuclease VII large subunit; Reviewed
Probab=41.78 E-value=59 Score=26.44 Aligned_cols=53 Identities=25% Similarity=0.263 Sum_probs=37.3
Q ss_pred HHHHHHHHHHHHHHHcCCcEEEEEEeecCCCcccCCCCChHHHHHHHHhCCCeEEE
Q 043606 23 AAMLAAQDVSQRCKERGITALHIKLRATGGNKTKTPGPGAQSALRALARSGMKIGR 78 (101)
Q Consensus 23 Aa~~a~~~~~~~~~~~gi~~v~V~lrg~~g~~~kG~G~gr~~~lr~l~~~gl~I~~ 78 (101)
|+..+++. ++.+.+.+ -.|.|..|| ||...--+-.+-+.+.+++..+.+.|++
T Consensus 177 A~~~i~~a-l~~~~~~~-~Dviii~RG-GGS~eDL~~Fn~e~v~~ai~~~~~Pvis 229 (438)
T PRK00286 177 AAASIVAA-IERANARG-EDVLIVARG-GGSLEDLWAFNDEAVARAIAASRIPVIS 229 (438)
T ss_pred HHHHHHHH-HHHhcCCC-CCEEEEecC-CCCHHHhhccCcHHHHHHHHcCCCCEEE
Confidence 55555543 34455455 467888887 6666666667889999999999888874
No 100
>cd07039 TPP_PYR_POX Pyrimidine (PYR) binding domain of POX. Thiamine pyrophosphate (TPP family), pyrimidine (PYR) binding domain of pyruvate oxidase (POX) subfamily. The PYR domain is found in many key metabolic enzymes which use TPP (also known as thiamine diphosphate) as a cofactor. TPP binds in the cleft formed by a PYR domain and a PP domain. The PYR domain, binds the aminopyrimidine ring of TPP, the PP domain binds the diphosphate residue. The PYR and PP domains have a common fold, but do not share strong sequence conservation. The PP domain is not included in this sub-family. Most TPP-dependent enzymes have the PYR and PP domains on the same subunit although these domains can be alternatively arranged in the primary structure. TPP-dependent enzymes are multisubunit proteins, the smallest catalytic unit being a dimer-of-active sites. Lactobacillus plantarum POX is a homotetramer (dimer-of-homodimers), having two active sites per homodimer lying between PYR and PP domains of differ
Probab=41.30 E-value=1e+02 Score=21.69 Aligned_cols=45 Identities=16% Similarity=0.256 Sum_probs=33.7
Q ss_pred HHHHHHHHHHHcCCcEEEEEEeecCCCcccCCCCChHHHHHHHHh-CCCeEEEEEec
Q 043606 27 AAQDVSQRCKERGITALHIKLRATGGNKTKTPGPGAQSALRALAR-SGMKIGRIEDV 82 (101)
Q Consensus 27 a~~~~~~~~~~~gi~~v~V~lrg~~g~~~kG~G~gr~~~lr~l~~-~gl~I~~I~D~ 82 (101)
.++.+++.+++.|++.|--. +|..-...+.+|.+ .+++++...+.
T Consensus 2 ~~~~l~~~L~~~Gv~~vFgi-----------pG~~~~~l~~al~~~~~i~~v~~rhE 47 (164)
T cd07039 2 VADVIVETLENWGVKRVYGI-----------PGDSINGLMDALRREGKIEFIQVRHE 47 (164)
T ss_pred HHHHHHHHHHHCCCCEEEEc-----------CCCchHHHHHHHhhcCCCeEEEeCCH
Confidence 46788999999999976544 47767788889876 57887766553
No 101
>PRK04266 fibrillarin; Provisional
Probab=40.62 E-value=1.2e+02 Score=22.69 Aligned_cols=60 Identities=28% Similarity=0.352 Sum_probs=33.5
Q ss_pred HHHHHHHHHHHcCCcEEEEEEeecCCCcccCCCCChHHHHHHHHhCCCeEEEEEecCCCCCC
Q 043606 27 AAQDVSQRCKERGITALHIKLRATGGNKTKTPGPGAQSALRALARSGMKIGRIEDVTPIPTD 88 (101)
Q Consensus 27 a~~~~~~~~~~~gi~~v~V~lrg~~g~~~kG~G~gr~~~lr~l~~~gl~I~~I~D~TpiphN 88 (101)
+.+.+.+.++.-|.=-|.|..+. =++.+.+..=.+..++.|..+|+++....|.+|...|
T Consensus 158 ~L~~~~r~LKpGG~lvI~v~~~~--~d~~~~~~~~~~~~~~~l~~aGF~~i~~~~l~p~~~~ 217 (226)
T PRK04266 158 AIDNAEFFLKDGGYLLLAIKARS--IDVTKDPKEIFKEEIRKLEEGGFEILEVVDLEPYHKD 217 (226)
T ss_pred HHHHHHHhcCCCcEEEEEEeccc--ccCcCCHHHHHHHHHHHHHHcCCeEEEEEcCCCCcCC
Confidence 33444555555565555555421 0111111100122568899999999999999888544
No 102
>PRK10975 TDP-fucosamine acetyltransferase; Provisional
Probab=40.08 E-value=1.3e+02 Score=21.09 Aligned_cols=46 Identities=33% Similarity=0.440 Sum_probs=33.1
Q ss_pred HHHHHHHHHHHHHHHHcCCcEEEEEEeecCCCcccCCCCChHHHHHHHHhCCCeEEEE
Q 043606 22 YAAMLAAQDVSQRCKERGITALHIKLRATGGNKTKTPGPGAQSALRALARSGMKIGRI 79 (101)
Q Consensus 22 ~Aa~~a~~~~~~~~~~~gi~~v~V~lrg~~g~~~kG~G~gr~~~lr~l~~~gl~I~~I 79 (101)
++.. +.+.+.+.+.+.|++.+.+.+ -.....+++..++.|+....+
T Consensus 143 ig~~-Ll~~~~~~a~~~g~~~i~l~v-----------~~~N~~a~~~yek~Gf~~~~~ 188 (194)
T PRK10975 143 IGAR-LMQAALNWCQARGLTRLRVAT-----------QMGNLAALRLYIRSGANIEST 188 (194)
T ss_pred HHHH-HHHHHHHHHHHcCCCEEEEEe-----------CCCcHHHHHHHHHCCCeEeEE
Confidence 4444 345677888889999998887 233457888889999887654
No 103
>PRK03624 putative acetyltransferase; Provisional
Probab=39.81 E-value=96 Score=19.48 Aligned_cols=48 Identities=8% Similarity=0.142 Sum_probs=34.1
Q ss_pred CcHHHHHHHHHHHHHHHHHcCCcEEEEEEeecCCCcccCCCCChHHHHHHHHhCCCeEEE
Q 043606 19 SSPYAAMLAAQDVSQRCKERGITALHIKLRATGGNKTKTPGPGAQSALRALARSGMKIGR 78 (101)
Q Consensus 19 ~t~~Aa~~a~~~~~~~~~~~gi~~v~V~lrg~~g~~~kG~G~gr~~~lr~l~~~gl~I~~ 78 (101)
+.=++.. +.+.+.+.+.+++++.+.+.+ -..-..+++...+.|+....
T Consensus 82 g~Gig~~-ll~~~~~~~~~~~~~~~~~~~-----------~~~N~~~~~~y~k~GF~~~~ 129 (140)
T PRK03624 82 GRGIGRA-LVARLEKKLIARGCPKINLQV-----------REDNDAVLGFYEALGYEEQD 129 (140)
T ss_pred CCCHHHH-HHHHHHHHHHHCCCCEEEEEE-----------ecCcHHHHHHHHHcCCcccc
Confidence 3345554 445677888899999999888 23345678888889988654
No 104
>PF01121 CoaE: Dephospho-CoA kinase; InterPro: IPR001977 This family contains dephospho-CoA kinases (2.7.1.24 from EC), which catalyzes the final step in CoA biosynthesis, the phosphorylation of the 3'-hydroxyl group of ribose using ATP as a phosphate donor. The crystal structures of a number of the proteins in this entry have been determined, including the structure of the protein from Haemophilus influenzae to 2.0-A resolution in a comlex with ATP. The protein consists of three domains: the nucleotide-binding domain with a five-stranded parallel beta-sheet, the substrate-binding alpha-helical domain, and the lid domain formed by a pair of alpha-helices; the overall topology of the protein resembles the structures of other nucleotide kinases [].; GO: 0004140 dephospho-CoA kinase activity, 0005524 ATP binding, 0015937 coenzyme A biosynthetic process; PDB: 1VHL_A 1N3B_A 1VIY_A 1VHT_B 1T3H_B 1UF9_C 2F6R_A 2GRJ_D 2IF2_C 1JJV_A.
Probab=39.44 E-value=80 Score=22.86 Aligned_cols=24 Identities=21% Similarity=0.277 Sum_probs=20.2
Q ss_pred cCCCCChHHHHHHHHhCCCeEEEE
Q 043606 56 KTPGPGAQSALRALARSGMKIGRI 79 (101)
Q Consensus 56 kG~G~gr~~~lr~l~~~gl~I~~I 79 (101)
-|+|.|+.++.+.|+..|+.+.+-
T Consensus 7 G~igsGKStv~~~l~~~G~~vida 30 (180)
T PF01121_consen 7 GGIGSGKSTVSKILAELGFPVIDA 30 (180)
T ss_dssp ESTTSSHHHHHHHHHHTT-EEEEH
T ss_pred CCCcCCHHHHHHHHHHCCCCEECc
Confidence 479999999999999999988753
No 105
>TIGR00715 precor6x_red precorrin-6x reductase. This enzyme was found to be a monomer by gel filtration.
Probab=38.99 E-value=57 Score=25.12 Aligned_cols=28 Identities=29% Similarity=0.577 Sum_probs=23.4
Q ss_pred CCcHHHHHHHHHHHHHHHHHcCCcEEEEE
Q 043606 18 ESSPYAAMLAAQDVSQRCKERGITALHIK 46 (101)
Q Consensus 18 k~t~~Aa~~a~~~~~~~~~~~gi~~v~V~ 46 (101)
-..|||++ +.+++.+-|.++|+..+++.
T Consensus 72 AtHPfA~~-is~~a~~a~~~~~ipylR~e 99 (256)
T TIGR00715 72 ATHPFAAQ-ITTNATAVCKELGIPYVRFE 99 (256)
T ss_pred cCCHHHHH-HHHHHHHHHHHhCCcEEEEE
Confidence 35799887 55789999999999999884
No 106
>PRK06826 dnaE DNA polymerase III DnaE; Reviewed
Probab=38.81 E-value=26 Score=32.82 Aligned_cols=45 Identities=31% Similarity=0.414 Sum_probs=33.1
Q ss_pred HHHHHHHHHHHHHcCCcEEEEEEeecCCCcccCCCCChHHHHHHHHhCCCeEEEEEecCCCCCC
Q 043606 25 MLAAQDVSQRCKERGITALHIKLRATGGNKTKTPGPGAQSALRALARSGMKIGRIEDVTPIPTD 88 (101)
Q Consensus 25 ~~a~~~~~~~~~~~gi~~v~V~lrg~~g~~~kG~G~gr~~~lr~l~~~gl~I~~I~D~TpiphN 88 (101)
.+++..+++.|++.||. .||||=+|--.|-. ..+.|+|+-|++||
T Consensus 338 FLIV~D~i~~Ak~~gI~----------------vGpGRGSaAGSLVa---Y~LgIT~VDPl~y~ 382 (1151)
T PRK06826 338 FLIVWDFIRFARENGIM----------------VGPGRGSAAGSLVA---YTLGITKIDPIKYN 382 (1151)
T ss_pred HHHHHHHHHHHHHCCCe----------------eCCCcccHHHHHHH---HHhCCCccCccccC
Confidence 34556778888888765 47777777777764 45668999999996
No 107
>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=38.64 E-value=44 Score=25.62 Aligned_cols=27 Identities=33% Similarity=0.646 Sum_probs=22.4
Q ss_pred CcHHHHHHHHHHHHHHHHHcCCcEEEEE
Q 043606 19 SSPYAAMLAAQDVSQRCKERGITALHIK 46 (101)
Q Consensus 19 ~t~~Aa~~a~~~~~~~~~~~gi~~v~V~ 46 (101)
.=|||++ +.+++.+-|.++|+..+++.
T Consensus 74 THPfA~~-is~na~~a~~~~~ipylR~e 100 (249)
T PF02571_consen 74 THPFAAE-ISQNAIEACRELGIPYLRFE 100 (249)
T ss_pred CCchHHH-HHHHHHHHHhhcCcceEEEE
Confidence 4589888 45789999999999998865
No 108
>PF05677 DUF818: Chlamydia CHLPS protein (DUF818); InterPro: IPR008536 This family of unknown function includes several Chlamydia CHLPS proteins and Legionella SidB proteins.
Probab=38.60 E-value=2.1e+02 Score=23.72 Aligned_cols=59 Identities=20% Similarity=0.151 Sum_probs=44.3
Q ss_pred CcHHHHHHHHHHHHHHHHH--cCCcEEEEEEeecCCCcccCCCCChHHHHHHHHhC------CCeEEEEEecCCC
Q 043606 19 SSPYAAMLAAQDVSQRCKE--RGITALHIKLRATGGNKTKTPGPGAQSALRALARS------GMKIGRIEDVTPI 85 (101)
Q Consensus 19 ~t~~Aa~~a~~~~~~~~~~--~gi~~v~V~lrg~~g~~~kG~G~gr~~~lr~l~~~------gl~I~~I~D~Tpi 85 (101)
.++.+-..+++.+++.+.+ .|++.=+|.+ .|...|--.+=.+|++. |++-..|.|.|+-
T Consensus 189 ~s~~dLv~~~~a~v~yL~d~~~G~ka~~Ii~--------yG~SLGG~Vqa~AL~~~~~~~~dgi~~~~ikDRsfs 255 (365)
T PF05677_consen 189 PSRKDLVKDYQACVRYLRDEEQGPKAKNIIL--------YGHSLGGGVQAEALKKEVLKGSDGIRWFLIKDRSFS 255 (365)
T ss_pred CCHHHHHHHHHHHHHHHHhcccCCChheEEE--------eeccccHHHHHHHHHhcccccCCCeeEEEEecCCcc
Confidence 4677777778899999985 8999999999 55555554443466653 7888899999875
No 109
>PRK14828 undecaprenyl pyrophosphate synthase; Provisional
Probab=38.43 E-value=1.2e+02 Score=23.48 Aligned_cols=59 Identities=14% Similarity=0.275 Sum_probs=38.3
Q ss_pred HHHHHHHHHHHHHHHcCCcEEEEEEeecCCCcccCCCCChHHHHHH------------HHhCCCeEEEEEecCCCCC
Q 043606 23 AAMLAAQDVSQRCKERGITALHIKLRATGGNKTKTPGPGAQSALRA------------LARSGMKIGRIEDVTPIPT 87 (101)
Q Consensus 23 Aa~~a~~~~~~~~~~~gi~~v~V~lrg~~g~~~kG~G~gr~~~lr~------------l~~~gl~I~~I~D~Tpiph 87 (101)
++..+...+++.|.++||+.|.|+.--+ ..+..-. .-+.. +...+++|..|-|.+.+|-
T Consensus 55 ~G~~~l~~~~~~~~~~gIk~lTvYaFS~-----eN~~R~~-~Ev~~Lm~L~~~~l~~~~~~~~irv~~iG~~~~lp~ 125 (256)
T PRK14828 55 AGAAKIGEFLGWCDETDVNVVTLYLLST-----DNLGRPS-EELNPLLDIIEDVVRQLAPDGRWRVRHVGSLDLLPA 125 (256)
T ss_pred HHHHHHHHHHHHHHHcCCCEEEEEEEEh-----hhcCCCH-HHHHHHHHHHHHHHHHHHHhCCeEEEEECChhhCCH
Confidence 4555567788999999999999988543 2222211 11111 1245788888888888874
No 110
>PRK08057 cobalt-precorrin-6x reductase; Reviewed
Probab=38.22 E-value=44 Score=25.63 Aligned_cols=27 Identities=30% Similarity=0.690 Sum_probs=22.4
Q ss_pred CcHHHHHHHHHHHHHHHHHcCCcEEEEE
Q 043606 19 SSPYAAMLAAQDVSQRCKERGITALHIK 46 (101)
Q Consensus 19 ~t~~Aa~~a~~~~~~~~~~~gi~~v~V~ 46 (101)
+=|||++. .+++.+-|.++|++.++..
T Consensus 73 THPfA~~i-s~~a~~ac~~~~ipyiR~e 99 (248)
T PRK08057 73 THPYAAQI-SANAAAACRALGIPYLRLE 99 (248)
T ss_pred CCccHHHH-HHHHHHHHHHhCCcEEEEe
Confidence 45898885 4689999999999998875
No 111
>TIGR00542 hxl6Piso_put hexulose-6-phosphate isomerase, putative. This family is conserved at better than 40 % identity among the four known examples from three species: Escherichia coli (SgbU and SgaU), Haemophilus influenzae, and Mycoplasma pneumoniae. The rarity of the family, high level of conservation, and proposed catabolic role suggests lateral transfer may be a part of the evolutionary history of this protein.
Probab=38.22 E-value=91 Score=23.29 Aligned_cols=51 Identities=14% Similarity=0.195 Sum_probs=31.5
Q ss_pred HHHHHHHHHcCCcEEEEEEeecCCCccc--CCCCCh-HHHHHHHHhCCCeEEEEE
Q 043606 29 QDVSQRCKERGITALHIKLRATGGNKTK--TPGPGA-QSALRALARSGMKIGRIE 80 (101)
Q Consensus 29 ~~~~~~~~~~gi~~v~V~lrg~~g~~~k--G~G~gr-~~~lr~l~~~gl~I~~I~ 80 (101)
+.+++.+.+.|+..|+|-+... ..+.. .+.+.. +...+.|.+.||+|.++.
T Consensus 19 ~e~l~~~~~~G~~~VEl~~~~~-~~~~~~~~~~~~~~~~~~~~l~~~gl~i~~~~ 72 (279)
T TIGR00542 19 LERLQLAKTCGFDFVEMSVDET-DDRLSRLDWSREQRLALVNAIIETGVRIPSMC 72 (279)
T ss_pred HHHHHHHHHcCCCEEEEecCCc-cchhhccCCCHHHHHHHHHHHHHcCCCceeee
Confidence 5577889999999999987321 00000 111222 234456778899999884
No 112
>PRK13494 chemoreceptor glutamine deamidase CheD; Provisional
Probab=37.76 E-value=1.4e+02 Score=21.77 Aligned_cols=57 Identities=23% Similarity=0.244 Sum_probs=40.0
Q ss_pred cHHHHHHHHHHHHHHHHHcCCc--EEEEEEeecCCCcccC--CCC---ChHHHHHHHHhCCCeEEE
Q 043606 20 SPYAAMLAAQDVSQRCKERGIT--ALHIKLRATGGNKTKT--PGP---GAQSALRALARSGMKIGR 78 (101)
Q Consensus 20 t~~Aa~~a~~~~~~~~~~~gi~--~v~V~lrg~~g~~~kG--~G~---gr~~~lr~l~~~gl~I~~ 78 (101)
..|| ..|.+.+++.+.++|.+ .+++++-| |++=+.. ++. +-+.|.+.|.+.||.|+.
T Consensus 69 ~rY~-d~ai~~Ll~~m~~~Ga~~~~l~aKifG-Ga~m~~~~~~~IG~rNv~~a~~~L~~~gI~i~a 132 (163)
T PRK13494 69 GRYG-VYAIPMLIDAMLENGASKSNLKAKLFG-GTNFMAKGTIKVGLENSEFAVNTLNKYGIPILA 132 (163)
T ss_pred cccH-HHHHHHHHHHHHHcCCCHHHeEEEEEe-CcccCCcccCChHHHHHHHHHHHHHHcCCcEEE
Confidence 4475 45668899999999876 57777766 5554441 333 445688889999999875
No 113
>TIGR00594 polc DNA-directed DNA polymerase III (polc). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=37.43 E-value=28 Score=32.02 Aligned_cols=45 Identities=33% Similarity=0.483 Sum_probs=32.5
Q ss_pred HHHHHHHHHHHHHcCCcEEEEEEeecCCCcccCCCCChHHHHHHHHhCCCeEEEEEecCCCCCC
Q 043606 25 MLAAQDVSQRCKERGITALHIKLRATGGNKTKTPGPGAQSALRALARSGMKIGRIEDVTPIPTD 88 (101)
Q Consensus 25 ~~a~~~~~~~~~~~gi~~v~V~lrg~~g~~~kG~G~gr~~~lr~l~~~gl~I~~I~D~TpiphN 88 (101)
.++...+++.|++.||. .||||=+|--.|-. ..+-|+|+-|++||
T Consensus 342 FLIV~D~v~~Ar~~gI~----------------vGpGRGSaAgSlVa---Y~LgIT~VDPl~~~ 386 (1022)
T TIGR00594 342 FLIVWDFIKWAKDHGIP----------------VGPGRGSAAGSLVA---YALKITDIDPIKHG 386 (1022)
T ss_pred HHHHHHHHHHHHHCCCe----------------eCCCCChHHHHHHH---HHhcCCccCccccC
Confidence 34555677788887754 37777777777764 45678999999996
No 114
>PRK07135 dnaE DNA polymerase III DnaE; Validated
Probab=37.36 E-value=25 Score=32.35 Aligned_cols=45 Identities=29% Similarity=0.400 Sum_probs=32.1
Q ss_pred HHHHHHHHHHHHHcCCcEEEEEEeecCCCcccCCCCChHHHHHHHHhCCCeEEEEEecCCCCCC
Q 043606 25 MLAAQDVSQRCKERGITALHIKLRATGGNKTKTPGPGAQSALRALARSGMKIGRIEDVTPIPTD 88 (101)
Q Consensus 25 ~~a~~~~~~~~~~~gi~~v~V~lrg~~g~~~kG~G~gr~~~lr~l~~~gl~I~~I~D~TpiphN 88 (101)
.+++..+++.|++.||. .||||=+|--.|-. ..+-|+|+-|++||
T Consensus 272 FLIV~D~v~~Ak~~gI~----------------vGpGRGSaAGSLVa---Y~LgIT~VDPl~y~ 316 (973)
T PRK07135 272 FLIIWDFIKWARKNKIS----------------IGPGRGSASGSLVS---YLLNITSVNPLKYD 316 (973)
T ss_pred HHHHHHHHHHHHHCCce----------------eCCCCcchHHHHHH---HHhcCCccCccccC
Confidence 34556677888887765 37777777666764 45668999999996
No 115
>PF03198 Glyco_hydro_72: Glucanosyltransferase; InterPro: IPR004886 This family is a group of yeast glycolipid proteins anchored to the membrane. It includes Candida albicans (Yeast) pH-regulated protein, which is required for apical growth and plays a role in morphogenesis and Saccharomyces cerevisiae glycolipid anchored surface protein.; PDB: 2W61_A 2W62_A 2W63_A.
Probab=37.31 E-value=79 Score=25.58 Aligned_cols=53 Identities=25% Similarity=0.341 Sum_probs=32.7
Q ss_pred HHHHHHHHHHHHHHHHHcCCcEEEEEEeecCCCcccCCCCChHHHHHHHHhCCCeEEEEEecC
Q 043606 21 PYAAMLAAQDVSQRCKERGITALHIKLRATGGNKTKTPGPGAQSALRALARSGMKIGRIEDVT 83 (101)
Q Consensus 21 ~~Aa~~a~~~~~~~~~~~gi~~v~V~lrg~~g~~~kG~G~gr~~~lr~l~~~gl~I~~I~D~T 83 (101)
|.|=..+-+.=+..+++||++.|+|+- =-+-..-+.++++|..+||.+ |.|+.
T Consensus 48 PLad~~~C~rDi~~l~~LgiNtIRVY~--------vdp~~nHd~CM~~~~~aGIYv--i~Dl~ 100 (314)
T PF03198_consen 48 PLADPEACKRDIPLLKELGINTIRVYS--------VDPSKNHDECMSAFADAGIYV--ILDLN 100 (314)
T ss_dssp GGG-HHHHHHHHHHHHHHT-SEEEES-----------TTS--HHHHHHHHHTT-EE--EEES-
T ss_pred cccCHHHHHHhHHHHHHcCCCEEEEEE--------eCCCCCHHHHHHHHHhCCCEE--EEecC
Confidence 333334445556788999999999987 335567788999999999765 45554
No 116
>PRK07199 phosphoribosylpyrophosphate synthetase; Provisional
Probab=37.07 E-value=1.8e+02 Score=22.89 Aligned_cols=51 Identities=20% Similarity=0.272 Sum_probs=39.8
Q ss_pred HHHHHHHHHcCCcEEEEEEeecCCCcccCCCCChHHHHHHHHhCCCeEEEEEecCCCCCC
Q 043606 29 QDVSQRCKERGITALHIKLRATGGNKTKTPGPGAQSALRALARSGMKIGRIEDVTPIPTD 88 (101)
Q Consensus 29 ~~~~~~~~~~gi~~v~V~lrg~~g~~~kG~G~gr~~~lr~l~~~gl~I~~I~D~TpiphN 88 (101)
..+++.+++.|-+.|.+..- +|+=.+ .++.-|..+++.=+.++|.-|.|++
T Consensus 228 ~~aa~~Lk~~GA~~V~~~~t-------Hgvfs~--~a~~~l~~~~i~~iv~Tdti~~~~~ 278 (301)
T PRK07199 228 IEAARQLRAAGAASPDCVVV-------HALFAG--DAYSALAAAGIARVVSTDTVPHPSN 278 (301)
T ss_pred HHHHHHHHHCCCcEEEEEEE-------eeeCCh--HHHHHHHhCCCCEEEEeCCccCCCC
Confidence 35688889999999998882 664443 4677788899999999999887754
No 117
>TIGR00237 xseA exodeoxyribonuclease VII, large subunit. This family consist of exodeoxyribonuclease VII, large subunit XseA which catalyses exonucleolytic cleavage in either the 5'-3' or 3'-5' direction to yield 5'-phosphomononucleotides. Exonuclease VII consists of one large subunit and four small subunits.
Probab=36.97 E-value=92 Score=25.69 Aligned_cols=54 Identities=17% Similarity=0.086 Sum_probs=38.0
Q ss_pred HHHHHHHHHHHHHHHcCCcEEEEEEeecCCCcccCCCCChHHHHHHHHhCCCeEEE
Q 043606 23 AAMLAAQDVSQRCKERGITALHIKLRATGGNKTKTPGPGAQSALRALARSGMKIGR 78 (101)
Q Consensus 23 Aa~~a~~~~~~~~~~~gi~~v~V~lrg~~g~~~kG~G~gr~~~lr~l~~~gl~I~~ 78 (101)
|+..++.. ++.+.+.+--.|.|..|| ||...--+..+-+.+.+++..+.+.|++
T Consensus 171 a~~~i~~a-l~~~~~~~~~dviii~RG-GGs~eDL~~Fn~e~~~rai~~~~~Pvis 224 (432)
T TIGR00237 171 AVQSIVES-IELANTKNECDVLIVGRG-GGSLEDLWSFNDEKVARAIFLSKIPIIS 224 (432)
T ss_pred HHHHHHHH-HHHhhcCCCCCEEEEecC-CCCHHHhhhcCcHHHHHHHHcCCCCEEE
Confidence 45555443 334443332367788888 7777777888999999999999888875
No 118
>PRK15490 Vi polysaccharide biosynthesis protein TviE; Provisional
Probab=36.82 E-value=93 Score=27.18 Aligned_cols=74 Identities=20% Similarity=0.268 Sum_probs=50.2
Q ss_pred eeeeeccceeeccCCCCcHHHHHHHHHHHHHHHHHcCC---cEEEEEEeecCCCcccCCCCChHHHHHHHHhCCCeEEEE
Q 043606 3 LERITGGMKVKADRDESSPYAAMLAAQDVSQRCKERGI---TALHIKLRATGGNKTKTPGPGAQSALRALARSGMKIGRI 79 (101)
Q Consensus 3 ~~~SsG~~gfKg~r~k~t~~Aa~~a~~~~~~~~~~~gi---~~v~V~lrg~~g~~~kG~G~gr~~~lr~l~~~gl~I~~I 79 (101)
+++.+|++|--|.-+.-+..|...+ .++-|+-+--|+ ..|.+.+|- =-++.|.+..+..+..+++.+.+|
T Consensus 164 ~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~------~~~~~~~~~~~~~~~~~~~~~~~~ 236 (578)
T PRK15490 164 LALCTGSLGSGGAERQISRLAIEIA-RKYRQKGKIGGLKVEEPVELIIRS------LTPELRQDFFLKEVLEEQVEVLEI 236 (578)
T ss_pred eEEEecCCCCCchHHHHHHHHHHHH-HHHHhcccccccccccceeEEEee------cCcccCcchhHHHHHhcCCceEEe
Confidence 5677888888887755554444333 222222221122 368888853 457889999999999999999999
Q ss_pred EecC
Q 043606 80 EDVT 83 (101)
Q Consensus 80 ~D~T 83 (101)
.|++
T Consensus 237 ~~~~ 240 (578)
T PRK15490 237 AKIT 240 (578)
T ss_pred eccc
Confidence 9998
No 119
>PF02222 ATP-grasp: ATP-grasp domain; InterPro: IPR003135 The ATP-grasp domain has an unusual nucleotide-binding fold, also referred to as palmate, and is found in a superfamily of enzymes including D-alanine-D-alanine ligase, glutathione synthetase, biotin carboxylase, and carbamoyl phosphate synthetase, the ribosomal protein S6 modification enzyme (RimK), urea amidolyase, tubulin-tyrosine ligase, and three enzymes of purine biosynthesis. This family does not contain all known ATP-grasp domain members. All the enzymes of this family possess ATP-dependent carboxylate-amine ligase activity, and their catalytic mechanisms are likely to include acylphosphate intermediates.; PDB: 3K5H_C 3K5I_C 3AX6_A 3Q2O_B 3QFF_B 3R5H_A 3ORQ_B 3ORR_B 4E4T_B 2Z04_A ....
Probab=36.67 E-value=61 Score=23.46 Aligned_cols=42 Identities=17% Similarity=0.302 Sum_probs=24.3
Q ss_pred HHHHHHHHHHHHHHcCCcEEEEEEeecCCCcccCCCCChHHHHHHHHhCCCeEEEEEecCCCCCC
Q 043606 24 AMLAAQDVSQRCKERGITALHIKLRATGGNKTKTPGPGAQSALRALARSGMKIGRIEDVTPIPTD 88 (101)
Q Consensus 24 a~~a~~~~~~~~~~~gi~~v~V~lrg~~g~~~kG~G~gr~~~lr~l~~~gl~I~~I~D~TpiphN 88 (101)
|+.+|..+++.+.-.|+-.|+..+.. .| .-+.|.++.|-|||
T Consensus 122 a~~ia~~i~~~l~~vGv~~VE~Fv~~----------------------~g-~~v~vNEiaPRpHn 163 (172)
T PF02222_consen 122 AKEIARKIAEALDYVGVLAVEFFVTK----------------------DG-DEVLVNEIAPRPHN 163 (172)
T ss_dssp HHHHHHHHHHHHTSSEEEEEEEEEET----------------------TS-TEEEEEEEESS--G
T ss_pred HHHHHHHHHHHcCcEEEEEEEEEEec----------------------CC-CEEEEEeccCCccC
Confidence 33444444444444677788888821 11 14678889999998
No 120
>PRK07374 dnaE DNA polymerase III subunit alpha; Validated
Probab=36.55 E-value=31 Score=32.40 Aligned_cols=44 Identities=30% Similarity=0.430 Sum_probs=32.1
Q ss_pred HHHHHHHHHHHHcCCcEEEEEEeecCCCcccCCCCChHHHHHHHHhCCCeEEEEEecCCCCCC
Q 043606 26 LAAQDVSQRCKERGITALHIKLRATGGNKTKTPGPGAQSALRALARSGMKIGRIEDVTPIPTD 88 (101)
Q Consensus 26 ~a~~~~~~~~~~~gi~~v~V~lrg~~g~~~kG~G~gr~~~lr~l~~~gl~I~~I~D~TpiphN 88 (101)
++...+++.|++.||. .||||=+|--.|-. ..+.|+|+-|++||
T Consensus 350 LIV~D~i~~Ak~~gI~----------------vGPGRGSaAGSLVa---Y~LgIT~VDPl~y~ 393 (1170)
T PRK07374 350 LVVWDYIRFAREQGIP----------------VGPGRGSAAGSLVA---YALGITNIDPVKNG 393 (1170)
T ss_pred HHHHHHHHHHHHCCCe----------------eCCCCchHHHHHHH---HHhcCCccCccccC
Confidence 4555677788887754 37777777777764 45678999999996
No 121
>PTZ00069 60S ribosomal protein L5; Provisional
Probab=36.54 E-value=84 Score=25.35 Aligned_cols=72 Identities=21% Similarity=0.290 Sum_probs=43.9
Q ss_pred ceeeccCCCCcHHHHHHHHHHHHHHHHHc--------CCcEE------------------EEEEeecCCCcccCCCCChH
Q 043606 10 MKVKADRDESSPYAAMLAAQDVSQRCKER--------GITAL------------------HIKLRATGGNKTKTPGPGAQ 63 (101)
Q Consensus 10 ~gfKg~r~k~t~~Aa~~a~~~~~~~~~~~--------gi~~v------------------~V~lrg~~g~~~kG~G~gr~ 63 (101)
.|++++. ..+| ||.+++..++.++... |+..+ ...|. -|-.....|.--.
T Consensus 86 yG~k~gl-~N~~-AAY~TGlL~arR~L~kl~ld~~y~G~~e~~g~~y~v~e~~~~~~rpf~a~LD--iGL~rtt~G~RVF 161 (300)
T PTZ00069 86 FGIPVGL-TNYA-AAYATGLLLARRLLKKLGLDKQFEGVKEADGEYYHVDEEDDEERRPFKAILD--VGLARTTTGNRVF 161 (300)
T ss_pred cCcCCCC-ccHH-HHHHHHHHHHHHHHHhhcccccccCcccccCcccccccccccCCCCceEEEe--eccccCCCCceee
Confidence 4888888 6666 6777888888888765 55211 11110 0000122333334
Q ss_pred HHHHHHHhCCCeEEEEEecCCCCCCCCCCCC
Q 043606 64 SALRALARSGMKIGRIEDVTPIPTDSTRRKG 94 (101)
Q Consensus 64 ~~lr~l~~~gl~I~~I~D~TpiphNGcR~~K 94 (101)
+||++....||. |||+-.|-|.
T Consensus 162 aalKGa~DgGl~---------IPhs~~rfpg 183 (300)
T PTZ00069 162 GALKGAVDGGLH---------IPHSPNRFPG 183 (300)
T ss_pred eehhcccccCcc---------cCCCCCcCCC
Confidence 588888888986 5999888775
No 122
>PF01255 Prenyltransf: Putative undecaprenyl diphosphate synthase; InterPro: IPR001441 Synonym(s): Di-trans-poly-cis-undecaprenyl-diphosphate synthase, Undecaprenyl pyrophosphate synthetase, Undecaprenyl pyrophosphate synthase, UPP synthetase Di-trans-poly-cis-decaprenylcistransferase (2.5.1.31 from EC) (UPP synthetase) generates undecaprenyl pyrophosphate (UPP) from isopentenyl pyrophosphate (IPP) []. This bacterial enzyme is also found in archaebacteria and in a number of uncharacterised proteins including some from yeasts. This entry also matches related enzymes that transfer alkyl groups, such as dehydrodolichyl diphosphate synthase.; GO: 0016765 transferase activity, transferring alkyl or aryl (other than methyl) groups; PDB: 2D2R_B 2DTN_B 1F75_B 1X07_A 2E9D_A 1JP3_A 3QAS_A 1X09_A 1V7U_B 2E9A_A ....
Probab=36.28 E-value=1.8e+02 Score=21.70 Aligned_cols=59 Identities=19% Similarity=0.333 Sum_probs=36.0
Q ss_pred HHHHHHHHHHHHHHHcCCcEEEEEEeecCCCcccCCCCChHH---HHHHH-----------H--hCCCeEEEEEecCCCC
Q 043606 23 AAMLAAQDVSQRCKERGITALHIKLRATGGNKTKTPGPGAQS---ALRAL-----------A--RSGMKIGRIEDVTPIP 86 (101)
Q Consensus 23 Aa~~a~~~~~~~~~~~gi~~v~V~lrg~~g~~~kG~G~gr~~---~lr~l-----------~--~~gl~I~~I~D~Tpip 86 (101)
+.......+++.|.++||+.|.|+.--+ ..+..-.+= .+..+ . +.|+.|..|-|.+.+|
T Consensus 22 ~G~~~l~~i~~~~~~~gI~~lTvYaFS~-----eN~~R~~~EV~~Lm~l~~~~l~~~~~~~~~~~~~irvr~iGd~~~Lp 96 (223)
T PF01255_consen 22 AGAEKLKEIVEWCLELGIKYLTVYAFST-----ENWKRPKEEVDALMDLFERYLRELIDELNFHKNGIRVRVIGDLSLLP 96 (223)
T ss_dssp HHHHHHHHHHHHHHHCT-SEEEEEEEET-----TGGGS-HHHHHHHHHHHHHHHHHHHHHHH--HTTEEEEEES-GGGS-
T ss_pred HHHHHHHHHHHHHHHcCCCEEEEEEecc-----hhhcCCHHHHHHHHHHHHHHHHHHhhhcchhhcCeeEEEEeccCcCC
Confidence 3444556788899999999999998543 233322211 11111 1 4689999999999887
No 123
>PRK14842 undecaprenyl pyrophosphate synthase; Provisional
Probab=36.14 E-value=2e+02 Score=22.18 Aligned_cols=60 Identities=12% Similarity=0.132 Sum_probs=39.7
Q ss_pred HHHHHHHHHHHHHHHcCCcEEEEEEeecCCCcccCCCCChHH--H------------HHHHHhCCCeEEEEEecCCCCC
Q 043606 23 AAMLAAQDVSQRCKERGITALHIKLRATGGNKTKTPGPGAQS--A------------LRALARSGMKIGRIEDVTPIPT 87 (101)
Q Consensus 23 Aa~~a~~~~~~~~~~~gi~~v~V~lrg~~g~~~kG~G~gr~~--~------------lr~l~~~gl~I~~I~D~Tpiph 87 (101)
+.......+++.|.++||+.|.|+.--+ ..+..-.+= . +.-+.+.|++|..|-|.+.+|-
T Consensus 36 ~G~~~l~~i~~~c~~lgI~~vTvYaFS~-----eN~~R~~~EV~~Lm~L~~~~l~~~~~~~~~~~irv~~iG~~~~Lp~ 109 (241)
T PRK14842 36 EGANAIDRLMDASLEYGLKNISLYAFST-----ENWKRPITEIRSIFGLLVEFIETRLDTIHARGIRIHHSGSRKKLTR 109 (241)
T ss_pred HHHHHHHHHHHHHHHcCCCEEEEEEeeh-----hhcCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCEEEEEeChhhCCH
Confidence 4444556788899999999999998543 333322111 1 1122356999999999998874
No 124
>PRK07279 dnaE DNA polymerase III DnaE; Reviewed
Probab=36.10 E-value=32 Score=31.94 Aligned_cols=45 Identities=22% Similarity=0.273 Sum_probs=32.8
Q ss_pred HHHHHHHHHHHHHcCCcEEEEEEeecCCCcccCCCCChHHHHHHHHhCCCeEEEEEecCCCCCC
Q 043606 25 MLAAQDVSQRCKERGITALHIKLRATGGNKTKTPGPGAQSALRALARSGMKIGRIEDVTPIPTD 88 (101)
Q Consensus 25 ~~a~~~~~~~~~~~gi~~v~V~lrg~~g~~~kG~G~gr~~~lr~l~~~gl~I~~I~D~TpiphN 88 (101)
-++...+++.|++.||. .||||=+|-=.|-. ..+.|+|+-|+.||
T Consensus 280 FLIV~D~i~~Ak~~gI~----------------vGPGRGSaAGSLVa---Y~LgIT~vDPl~y~ 324 (1034)
T PRK07279 280 FLIVWDLLRFGRSQGYY----------------MGMGRGSAAGSLVA---YALDITGIDPVKHN 324 (1034)
T ss_pred hHHHHHHHHHHHhCCce----------------eCCCCchHHHHHHH---HHhcCCccCccccC
Confidence 34556778888888765 37777777777764 45678999999996
No 125
>COG1184 GCD2 Translation initiation factor 2B subunit, eIF-2B alpha/beta/delta family [Translation, ribosomal structure and biogenesis]
Probab=36.10 E-value=1.4e+02 Score=23.96 Aligned_cols=50 Identities=22% Similarity=0.388 Sum_probs=34.6
Q ss_pred HHHHHHHHHHHHcCCcEEEEEEeecCCCcccCCCCChHHHHHHHHhCCCeEEEEEec
Q 043606 26 LAAQDVSQRCKERGITALHIKLRATGGNKTKTPGPGAQSALRALARSGMKIGRIEDV 82 (101)
Q Consensus 26 ~a~~~~~~~~~~~gi~~v~V~lrg~~g~~~kG~G~gr~~~lr~l~~~gl~I~~I~D~ 82 (101)
.++..++..|.+.+.+ +.|.+-= ++=-+.|+..+ +.|.++|+.++-|.|-
T Consensus 130 ~~v~~~l~~A~~~~k~-~~V~VtE-----SRP~~eG~~~a-k~L~~~gI~~~~I~Ds 179 (301)
T COG1184 130 KTVLEVLKTAADRGKR-FKVIVTE-----SRPRGEGRIMA-KELRQSGIPVTVIVDS 179 (301)
T ss_pred HHHHHHHHHhhhcCCc-eEEEEEc-----CCCcchHHHHH-HHHHHcCCceEEEech
Confidence 4556678888888877 5555521 12123577666 8899999999999984
No 126
>PRK14839 undecaprenyl pyrophosphate synthase; Provisional
Probab=35.98 E-value=2.1e+02 Score=22.21 Aligned_cols=60 Identities=22% Similarity=0.268 Sum_probs=39.8
Q ss_pred HHHHHHHHHHHHHHHcCCcEEEEEEeecCCCcccCCCCChHH--H------------HHHHHhCCCeEEEEEecCCCCC
Q 043606 23 AAMLAAQDVSQRCKERGITALHIKLRATGGNKTKTPGPGAQS--A------------LRALARSGMKIGRIEDVTPIPT 87 (101)
Q Consensus 23 Aa~~a~~~~~~~~~~~gi~~v~V~lrg~~g~~~kG~G~gr~~--~------------lr~l~~~gl~I~~I~D~Tpiph 87 (101)
+...+...+++.|.++||+.|.|+.--+ ..+..-.+= . +..+.+.|++|..|-|.+.+|-
T Consensus 37 ~G~~~l~~i~~~c~~~GI~~lTvYaFS~-----EN~~R~~~EV~~Lm~L~~~~l~~~~~~~~~~~irvr~iGd~~~Lp~ 110 (239)
T PRK14839 37 AGVEAIRRVVEAAPDLGIGTLTLYAFSS-----DNWRRPAAEVGGLMRLLRAYLRNETERLARNGVRLTVIGRRDRLPD 110 (239)
T ss_pred HHHHHHHHHHHHHHHcCCCEEEEEEech-----hhcCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCEEEEEeChhhCCH
Confidence 4444556788899999999999998543 223221111 1 1123446999999999998884
No 127
>COG1751 Uncharacterized conserved protein [Function unknown]
Probab=35.73 E-value=1.9e+02 Score=21.67 Aligned_cols=45 Identities=24% Similarity=0.341 Sum_probs=32.2
Q ss_pred HHHHHHHHHHHcCCcEEEEEEeecCCCcccCCCCChHHHHHHHHhC--CCeEEEEEecC
Q 043606 27 AAQDVSQRCKERGITALHIKLRATGGNKTKTPGPGAQSALRALARS--GMKIGRIEDVT 83 (101)
Q Consensus 27 a~~~~~~~~~~~gi~~v~V~lrg~~g~~~kG~G~gr~~~lr~l~~~--gl~I~~I~D~T 83 (101)
+-+.++++|+++|++.+.|-= ..| ++|+++|... .++|+.++.-+
T Consensus 15 tle~a~erA~elgik~~vVAS---------~tG---~tA~k~lemveg~lkvVvVthh~ 61 (186)
T COG1751 15 TLEIAVERAKELGIKHIVVAS---------STG---YTALKALEMVEGDLKVVVVTHHA 61 (186)
T ss_pred HHHHHHHHHHhcCcceEEEEe---------ccc---HHHHHHHHhcccCceEEEEEeec
Confidence 446678899999999887765 123 4788887653 38888887533
No 128
>cd01421 IMPCH Inosine monophosphate cyclohydrolase domain. This is the N-terminal domain in the purine biosynthesis pathway protein ATIC (purH). The bifunctional ATIC protein contains a C-terminal ATIC formylase domain that formylates 5-aminoimidazole-4-carboxamide-ribonucleotide. The IMPCH domain then converts the formyl-5-aminoimidazole-4-carboxamide-ribonucleotide to inosine monophosphate. This is the final step in de novo purine production.
Probab=35.21 E-value=76 Score=23.78 Aligned_cols=42 Identities=21% Similarity=0.416 Sum_probs=32.5
Q ss_pred HHHHHHHHHcCCcEEEEEEeecCCCcccCCCCChHHHHHHHHhCCCeEEEEEecCCCCC
Q 043606 29 QDVSQRCKERGITALHIKLRATGGNKTKTPGPGAQSALRALARSGMKIGRIEDVTPIPT 87 (101)
Q Consensus 29 ~~~~~~~~~~gi~~v~V~lrg~~g~~~kG~G~gr~~~lr~l~~~gl~I~~I~D~Tpiph 87 (101)
..+++++.++|++-+ +| .| .-+.|+..|+.+..|.++|..|.
T Consensus 14 ~~lAk~L~~lGf~I~-----AT-----~G-------TAk~L~e~GI~v~~V~k~TgfpE 55 (187)
T cd01421 14 VEFAKELVELGVEIL-----ST-----GG-------TAKFLKEAGIPVTDVSDITGFPE 55 (187)
T ss_pred HHHHHHHHHCCCEEE-----Ec-----cH-------HHHHHHHcCCeEEEhhhccCCcH
Confidence 457888899998832 22 11 33789999999999999999986
No 129
>cd01853 Toc34_like Toc34-like (Translocon at the Outer-envelope membrane of Chloroplasts). This family contains several Toc proteins, including Toc34, Toc33, Toc120, Toc159, Toc86, Toc125, and Toc90. The Toc complex at the outer envelope membrane of chloroplasts is a molecular machine of ~500 kDa that contains a single Toc159 protein, four Toc75 molecules, and four or five copies of Toc34. Toc64 and Toc12 are associated with the translocon, but do not appear to be part of the core complex. The Toc translocon initiates the import of nuclear-encoded preproteins from the cytosol into the organelle. Toc34 and Toc159 are both GTPases, while Toc75 is a beta-barrel integral membrane protein. Toc159 is equally distributed between a soluble cytoplasmic form and a membrane-inserted form, suggesting that assembly of the Toc complex is dynamic. Toc34 and Toc75 act sequentially to mediate docking and insertion of Toc159 resulting in assembly of the functional translocon.
Probab=35.11 E-value=1.4e+02 Score=22.64 Aligned_cols=49 Identities=22% Similarity=0.204 Sum_probs=39.8
Q ss_pred CCcHHHHHHHHHHHHHHHHHcCCcEEEEEEeecCCCcccCCCCChHHHHHHHHhCC
Q 043606 18 ESSPYAAMLAAQDVSQRCKERGITALHIKLRATGGNKTKTPGPGAQSALRALARSG 73 (101)
Q Consensus 18 k~t~~Aa~~a~~~~~~~~~~~gi~~v~V~lrg~~g~~~kG~G~gr~~~lr~l~~~g 73 (101)
...|-|++..+..+..+..+..-..+.|.|=|. .|.|+-+.+.+|....
T Consensus 7 ~~~~~~~~~~~~~~~~~~~~~~~~~~~IllvG~-------tGvGKSSliNaLlg~~ 55 (249)
T cd01853 7 QFFPDAAQTKALELEAKGKEELDFSLTILVLGK-------TGVGKSSTINSIFGER 55 (249)
T ss_pred ccCcHHHHHHHHHHHHHhhhhccCCeEEEEECC-------CCCcHHHHHHHHhCCC
Confidence 457889999998888888887788888888653 6899999999998653
No 130
>PRK04143 hypothetical protein; Provisional
Probab=34.78 E-value=42 Score=26.21 Aligned_cols=37 Identities=24% Similarity=0.184 Sum_probs=27.7
Q ss_pred eeeeccceeeccCCCCcHHHHHHHHHHHHHHHHHcCCcEEEEEE
Q 043606 4 ERITGGMKVKADRDESSPYAAMLAAQDVSQRCKERGITALHIKL 47 (101)
Q Consensus 4 ~~SsG~~gfKg~r~k~t~~Aa~~a~~~~~~~~~~~gi~~v~V~l 47 (101)
+.|+|..||.... ||+.+.+.+.+.+.+..-. .+|.+
T Consensus 208 ~IsTGi~gfP~~~------aA~ia~~tv~~fl~~~~~~-~~Vif 244 (264)
T PRK04143 208 CISTGVFGFPKEE------AAEIAIKTVLSWLKENPSK-LKVVF 244 (264)
T ss_pred cccCCCCCCCHHH------HHHHHHHHHHHHHHhCCCC-CEEEE
Confidence 4588999999888 8999988888888775432 34444
No 131
>PRK14320 glmM phosphoglucosamine mutase; Provisional
Probab=34.34 E-value=1.3e+02 Score=24.44 Aligned_cols=62 Identities=10% Similarity=0.106 Sum_probs=39.5
Q ss_pred CcHHHHHHHHHHHHHHHHHcCC-cEEEEEEeecCCCcccCCCCChHHHHHHHHhCCCeEEEEEecCCCC
Q 043606 19 SSPYAAMLAAQDVSQRCKERGI-TALHIKLRATGGNKTKTPGPGAQSALRALARSGMKIGRIEDVTPIP 86 (101)
Q Consensus 19 ~t~~Aa~~a~~~~~~~~~~~gi-~~v~V~lrg~~g~~~kG~G~gr~~~lr~l~~~gl~I~~I~D~Tpip 86 (101)
-||..+..++..++..+.+.+- ..|.|---. +..+. .=..++..+|..+|++|..+ +.+|.|
T Consensus 19 ltpe~~~~lg~a~g~~l~~~~~~~~VvVg~D~----R~ss~-~l~~a~~~gL~s~G~~V~d~-g~~pTP 81 (443)
T PRK14320 19 ITVEFTQKLGNAVGSLINQKNYPKFVIVGQDT----RSSGG-FLKFALVSGLNAAGIDVLDL-GVVPTP 81 (443)
T ss_pred CCHHHHHHHHHHHHHhHhhCCCCCeEEEEECC----CcCHH-HHHHHHHHHHHHCCCEEEEe-cccCch
Confidence 6888888888877877755442 224433311 11111 12455678899999999988 788877
No 132
>COG0057 GapA Glyceraldehyde-3-phosphate dehydrogenase/erythrose-4-phosphate dehydrogenase [Carbohydrate transport and metabolism]
Probab=34.21 E-value=55 Score=26.75 Aligned_cols=33 Identities=24% Similarity=0.386 Sum_probs=24.1
Q ss_pred EEEEEeecCCCcccCCCC-ChHHHHHHHHh-C-CCeEEEEEecCC
Q 043606 43 LHIKLRATGGNKTKTPGP-GAQSALRALAR-S-GMKIGRIEDVTP 84 (101)
Q Consensus 43 v~V~lrg~~g~~~kG~G~-gr~~~lr~l~~-~-gl~I~~I~D~Tp 84 (101)
+.|-| +|||. ||..+ |++.. . .++|+-|.|.|+
T Consensus 2 ikV~I--------NGfGrIGR~v~-ra~~~~~~dieVVaInd~t~ 37 (335)
T COG0057 2 IKVAI--------NGFGRIGRLVA-RAALERDGDIEVVAINDLTD 37 (335)
T ss_pred cEEEE--------ecCcHHHHHHH-HHHHhCCCCeEEEEEecCCC
Confidence 45667 88995 88655 66555 4 499999999665
No 133
>PRK02269 ribose-phosphate pyrophosphokinase; Provisional
Probab=34.06 E-value=2.4e+02 Score=22.36 Aligned_cols=51 Identities=18% Similarity=0.206 Sum_probs=40.0
Q ss_pred HHHHHHHHHcCCcEEEEEEeecCCCcccCCCCChHHHHHHHHhCCCeEEEEEecCCCCCC
Q 043606 29 QDVSQRCKERGITALHIKLRATGGNKTKTPGPGAQSALRALARSGMKIGRIEDVTPIPTD 88 (101)
Q Consensus 29 ~~~~~~~~~~gi~~v~V~lrg~~g~~~kG~G~gr~~~lr~l~~~gl~I~~I~D~TpiphN 88 (101)
..+++.+++.|-+.|.+..- +|+=.+ -++.-|..+++.=+-++|.-|.|..
T Consensus 234 ~~aa~~Lk~~GA~~V~~~~t-------Hglf~~--~a~~~l~~~~i~~iv~Tdti~~~~~ 284 (320)
T PRK02269 234 CHAADALAEAGATEVYASCT-------HPVLSG--PALDNIQKSAIEKLVVLDTIYLPEE 284 (320)
T ss_pred HHHHHHHHHCCCCEEEEEEE-------CcccCc--hHHHHHHhCCCCEEEEeCCCCCccc
Confidence 45788899999999999882 654443 4666688899999999999887765
No 134
>cd05800 PGM_like2 This PGM-like (phosphoglucomutase-like) protein of unknown function belongs to the alpha-D-phosphohexomutase superfamily and is found in both archaea and bacteria. The alpha-D-phosphohexomutases include several related enzymes that catalyze a reversible intramolecular phosphoryl transfer on their sugar substrates. Other members of this superfamily include phosphoglucosamine mutase (PNGM), phosphoacetylglucosamine mutase (PAGM), the bacterial phosphomannomutase ManB, the bacterial phosphoglucosamine mutase GlmM, and the bifunctional phosphomannomutase/phosphoglucomutase (PMM/PGM). Each of these enzymes has four structural domains (subdomains) with a centrally located active site formed by four loops, one from each subdomain. All four subdomains are included in this alignment model.
Probab=33.85 E-value=1.1e+02 Score=24.87 Aligned_cols=63 Identities=17% Similarity=0.165 Sum_probs=40.5
Q ss_pred CcHHHHHHHHHHHHHHHHHc--CCcEEEEEEeecCCCcccCCCCChHHHHHHHHhCCCeEEEEEecCCCC
Q 043606 19 SSPYAAMLAAQDVSQRCKER--GITALHIKLRATGGNKTKTPGPGAQSALRALARSGMKIGRIEDVTPIP 86 (101)
Q Consensus 19 ~t~~Aa~~a~~~~~~~~~~~--gi~~v~V~lrg~~g~~~kG~G~gr~~~lr~l~~~gl~I~~I~D~Tpip 86 (101)
-||.-+...+..++..+.+. +-..|.|---. +..+ -.=.++++.+|...|++|..+.+..|.|
T Consensus 16 lt~~~~~~lg~a~~~~l~~~~~~~~~Vvvg~D~----R~ss-~~l~~a~~~gL~s~G~~V~~~~g~~pTP 80 (461)
T cd05800 16 FTFENVRRVAQAIADYLKEEGGGGRGVVVGYDT----RFLS-EEFARAVAEVLAANGIDVYLSDRPVPTP 80 (461)
T ss_pred ccHHHHHHHHHHHHHHHHHhCCCCCeEEEEeCC----CcCc-HHHHHHHHHHHHHCCCEEEEcCCCCCch
Confidence 57777777777778777653 22334443311 1111 1125678888999999999997788877
No 135
>PRK14731 coaE dephospho-CoA kinase; Provisional
Probab=33.80 E-value=1.1e+02 Score=22.21 Aligned_cols=31 Identities=19% Similarity=0.266 Sum_probs=24.4
Q ss_pred EEEEEEeecCCCcccCCCCChHHHHHHHHhCCCeEEEE
Q 043606 42 ALHIKLRATGGNKTKTPGPGAQSALRALARSGMKIGRI 79 (101)
Q Consensus 42 ~v~V~lrg~~g~~~kG~G~gr~~~lr~l~~~gl~I~~I 79 (101)
.+.|-|- -++|.|+.++.+.|...|+.+..-
T Consensus 5 ~~~igit-------G~igsGKSt~~~~l~~~g~~v~d~ 35 (208)
T PRK14731 5 PFLVGVT-------GGIGSGKSTVCRFLAEMGCELFEA 35 (208)
T ss_pred CEEEEEE-------CCCCCCHHHHHHHHHHCCCeEEec
Confidence 3455664 369999999999999999888763
No 136
>PRK14031 glutamate dehydrogenase; Provisional
Probab=33.67 E-value=1.4e+02 Score=25.22 Aligned_cols=60 Identities=15% Similarity=0.136 Sum_probs=42.3
Q ss_pred cCCCCcHHHHHHHHHHHHHHHHHcCCcEEEEEEeecCCCcccCCCCChHHHHHHHHhCCCeEEEEEecC
Q 043606 15 DRDESSPYAAMLAAQDVSQRCKERGITALHIKLRATGGNKTKTPGPGAQSALRALARSGMKIGRIEDVT 83 (101)
Q Consensus 15 ~r~k~t~~Aa~~a~~~~~~~~~~~gi~~v~V~lrg~~g~~~kG~G~gr~~~lr~l~~~gl~I~~I~D~T 83 (101)
.+...|-|....+++.+++.. ...++-..|-| .|+|.=-..+.+.|...|-+|+-|.|..
T Consensus 202 ~r~~aTg~Gv~~~~~~~~~~~-g~~l~g~rVaV--------QGfGNVG~~aA~~L~e~GAkVVaVSD~~ 261 (444)
T PRK14031 202 IRPEATGYGNIYFLMEMLKTK-GTDLKGKVCLV--------SGSGNVAQYTAEKVLELGGKVVTMSDSD 261 (444)
T ss_pred CCCcccHHHHHHHHHHHHHhc-CCCcCCCEEEE--------ECCCHHHHHHHHHHHHCCCEEEEEECCC
Confidence 333677777776666655544 33467788999 7788644455677888999999999943
No 137
>PRK13209 L-xylulose 5-phosphate 3-epimerase; Reviewed
Probab=33.56 E-value=2e+02 Score=21.33 Aligned_cols=51 Identities=10% Similarity=0.183 Sum_probs=31.1
Q ss_pred HHHHHHHHHcCCcEEEEEEeecCCCcccCCCCC---hHHHHHHHHhCCCeEEEEE
Q 043606 29 QDVSQRCKERGITALHIKLRATGGNKTKTPGPG---AQSALRALARSGMKIGRIE 80 (101)
Q Consensus 29 ~~~~~~~~~~gi~~v~V~lrg~~g~~~kG~G~g---r~~~lr~l~~~gl~I~~I~ 80 (101)
+..++.++++|+..|++.+.... ......+.. .+.+-+.+...||+|..+.
T Consensus 24 ~e~~~~~~~~G~~~iEl~~~~~~-~~~~~~~~~~~~~~~l~~~l~~~gl~i~~~~ 77 (283)
T PRK13209 24 LEKLAIAKTAGFDFVEMSVDESD-ERLARLDWSREQRLALVNALVETGFRVNSMC 77 (283)
T ss_pred HHHHHHHHHcCCCeEEEecCccc-cchhccCCCHHHHHHHHHHHHHcCCceeEEe
Confidence 45677889999999999873210 000111112 2234455678899998875
No 138
>COG0237 CoaE Dephospho-CoA kinase [Coenzyme metabolism]
Probab=33.19 E-value=43 Score=24.88 Aligned_cols=28 Identities=25% Similarity=0.383 Sum_probs=23.9
Q ss_pred cCCCCChHHHHHHHHhCCCeEEEEEecC
Q 043606 56 KTPGPGAQSALRALARSGMKIGRIEDVT 83 (101)
Q Consensus 56 kG~G~gr~~~lr~l~~~gl~I~~I~D~T 83 (101)
-|+|.|+.++.+.|+..|+.++.--|+.
T Consensus 9 G~igsGKStva~~~~~~G~~vidaD~v~ 36 (201)
T COG0237 9 GGIGSGKSTVAKILAELGFPVIDADDVA 36 (201)
T ss_pred cCCCCCHHHHHHHHHHcCCeEEEccHHH
Confidence 4799999999999999889998766554
No 139
>cd02904 Macro_H2A_like Macro domain, Macro_H2A_like family. The macro domain is a high-affinity ADP-ribose binding module found in a variety of proteins as a stand-alone domain or in combination with other domains like in histone macroH2A and some PARPs (poly ADP-ribose polymerases). Some macro domains recognize poly ADP-ribose as a ligand. Previously identified as displaying an Appr-1"-p (ADP-ribose-1"-monophosphate) processing activity, the macro domain may play roles in distinct ADP-ribose pathways, such as the ADP-ribosylation of proteins, an important post-translational modification which occurs in DNA repair, transcription, chromatin biology, and long-term memory formation, among other processes. Members of this family are similar to macroH2A, a variant of the major-type core histone H2A, which contains an N-terminal H2A domain and a C-terminal nonhistone macro domain. Histone macroH2A is enriched on the inactive X chromosome of mammalian female cells. It does not bind poly ADP-r
Probab=33.11 E-value=61 Score=23.99 Aligned_cols=38 Identities=18% Similarity=0.137 Sum_probs=28.2
Q ss_pred eeeeccceeeccCCCCcHHHHHHHHHHHHHHHHHc---CCcEEEEEE
Q 043606 4 ERITGGMKVKADRDESSPYAAMLAAQDVSQRCKER---GITALHIKL 47 (101)
Q Consensus 4 ~~SsG~~gfKg~r~k~t~~Aa~~a~~~~~~~~~~~---gi~~v~V~l 47 (101)
+.|+|..||.... ||+.+.+.+.+.+.+. .++.|.+.+
T Consensus 135 aIstG~~g~P~~~------aA~i~~~~i~~~l~~~~~~~l~~I~fv~ 175 (186)
T cd02904 135 SLPSGRNGFPKQT------AAQLILKAISSYFVSTMSSSIKQIYFVL 175 (186)
T ss_pred CcccCCCCCCHHH------HHHHHHHHHHHHHHhcCCCCccEEEEEE
Confidence 3578888998877 8888888888877753 356666665
No 140
>TIGR00511 ribulose_e2b2 ribose-1,5-bisphosphate isomerase, e2b2 family. The delineation of this family was based originally, in part, on a discussion and neighbor-joining phylogenetic study by Kyrpides and Woese of archaeal and other proteins homologous to the alpha, beta, and delta subunits of eukaryotic initiation factor 2B (eIF-2B), a five-subunit molecule that catalyzes GTP recycling for eIF-2. Recently, Sato, et al. assigned the function ribulose-1,5 bisphosphate isomerase.
Probab=33.08 E-value=1.8e+02 Score=22.83 Aligned_cols=49 Identities=24% Similarity=0.308 Sum_probs=33.1
Q ss_pred HHHHHHHHHHHcCCcEEEEEEeecCCCcccCCCCChHHHHHHHHhCCCeEEEEEec
Q 043606 27 AAQDVSQRCKERGITALHIKLRATGGNKTKTPGPGAQSALRALARSGMKIGRIEDV 82 (101)
Q Consensus 27 a~~~~~~~~~~~gi~~v~V~lrg~~g~~~kG~G~gr~~~lr~l~~~gl~I~~I~D~ 82 (101)
+++.++..+.+.|.+ ++|.+-- +.=.+.|+..+ +.|.+.|+.++.|.|-
T Consensus 127 tv~~~l~~a~~~~~~-f~V~v~E-----srP~~~G~~~a-~~L~~~gI~vtlI~Ds 175 (301)
T TIGR00511 127 AALSVIKTAFEQGKD-IEVIATE-----TRPRKQGHITA-KELRDYGIPVTLIVDS 175 (301)
T ss_pred HHHHHHHHHHHcCCc-EEEEEec-----CCCcchHHHHH-HHHHHCCCCEEEEehh
Confidence 455677777777754 5565521 13345677666 6799999999999984
No 141
>TIGR00355 purH phosphoribosylaminoimidazolecarboxamide formyltransferase/IMP cyclohydrolase. Involved in purine ribonucleotide biosynthesis. The IMP cyclohydrolase activity is in the N-terminal region.
Probab=33.04 E-value=1.2e+02 Score=26.19 Aligned_cols=42 Identities=26% Similarity=0.424 Sum_probs=32.6
Q ss_pred HHHHHHHHHcCCcEEEEEEeecCCCcccCCCCChHHHHHHHHhCCCeEEEEEecCCCCC
Q 043606 29 QDVSQRCKERGITALHIKLRATGGNKTKTPGPGAQSALRALARSGMKIGRIEDVTPIPT 87 (101)
Q Consensus 29 ~~~~~~~~~~gi~~v~V~lrg~~g~~~kG~G~gr~~~lr~l~~~gl~I~~I~D~Tpiph 87 (101)
..+++++.++|++-+ -- .| .-+.|+..|+++..|.|+|..|.
T Consensus 14 v~lAk~L~~lGfeIi--AT--------gG-------Tak~L~e~GI~v~~Vsk~TgfPE 55 (511)
T TIGR00355 14 VEFAQGLVERGVELL--ST--------GG-------TAKLLAEAGVPVTEVSDYTGFPE 55 (511)
T ss_pred HHHHHHHHHCCCEEE--Ee--------ch-------HHHHHHHCCCeEEEeecccCCch
Confidence 457888889998842 22 11 34789999999999999999986
No 142
>PRK01045 ispH 4-hydroxy-3-methylbut-2-enyl diphosphate reductase; Reviewed
Probab=32.71 E-value=1.5e+02 Score=23.61 Aligned_cols=38 Identities=16% Similarity=0.281 Sum_probs=25.4
Q ss_pred HHHHHHHcCCcEE----------EEEEeecCCCcccCCCCChHHHHHHHHhCCCeEE
Q 043606 31 VSQRCKERGITAL----------HIKLRATGGNKTKTPGPGAQSALRALARSGMKIG 77 (101)
Q Consensus 31 ~~~~~~~~gi~~v----------~V~lrg~~g~~~kG~G~gr~~~lr~l~~~gl~I~ 77 (101)
+.+.+.++|+..| .|.||+ +|..+ .....|.+.|++|+
T Consensus 45 vv~~L~~~GV~~v~~~~~v~~~~~ViirA------HGv~~---~~~~~~~~~g~~vi 92 (298)
T PRK01045 45 VVERLEKKGAIFVEELDEVPDGAIVIFSA------HGVSP---AVREEAKERGLTVI 92 (298)
T ss_pred HHHHHHHCCCEEecCcccCCCCCEEEEeC------CCCCH---HHHHHHHHCCCeEE
Confidence 4556778888776 377765 66665 45566777787764
No 143
>PRK05898 dnaE DNA polymerase III DnaE; Validated
Probab=32.27 E-value=37 Score=31.37 Aligned_cols=45 Identities=33% Similarity=0.449 Sum_probs=32.4
Q ss_pred HHHHHHHHHHHHHcCCcEEEEEEeecCCCcccCCCCChHHHHHHHHhCCCeEEEEEecCCCCCC
Q 043606 25 MLAAQDVSQRCKERGITALHIKLRATGGNKTKTPGPGAQSALRALARSGMKIGRIEDVTPIPTD 88 (101)
Q Consensus 25 ~~a~~~~~~~~~~~gi~~v~V~lrg~~g~~~kG~G~gr~~~lr~l~~~gl~I~~I~D~TpiphN 88 (101)
-++...+++.|++.||. .||||=+|--.|-. ..+-|+|+-|+.||
T Consensus 274 FLIV~D~i~~Ar~~gI~----------------vGpGRGSAAGSLVa---Y~LgIT~VDPl~~~ 318 (971)
T PRK05898 274 FLIVYDFINFAKSNGII----------------IGPGRGSAAGSLIA---YLLHITDIDPIKYN 318 (971)
T ss_pred HHHHHHHHHHHHHCCce----------------eCCCCccHHHHHHH---HHhcCCccCccccC
Confidence 34556678888887754 37777777776764 45668999999996
No 144
>TIGR01455 glmM phosphoglucosamine mutase. This model describes GlmM, phosphoglucosamine mutase, also designated in MrsA and YhbF E. coli, UreC in Helicobacter pylori, and femR315 or FemD in Staphlococcus aureus. It converts glucosamine-6-phosphate to glucosamine-1-phosphate as part of the pathway toward UDP-N-acetylglucosamine for peptidoglycan and lipopolysaccharides.
Probab=32.27 E-value=1.3e+02 Score=24.51 Aligned_cols=63 Identities=11% Similarity=0.081 Sum_probs=41.6
Q ss_pred CCcHHHHHHHHHHHHHHHHHcCC--cEEEEEEeecCCCcccCCCCChHHHHHHHHhCCCeEEEEEecCCCC
Q 043606 18 ESSPYAAMLAAQDVSQRCKERGI--TALHIKLRATGGNKTKTPGPGAQSALRALARSGMKIGRIEDVTPIP 86 (101)
Q Consensus 18 k~t~~Aa~~a~~~~~~~~~~~gi--~~v~V~lrg~~g~~~kG~G~gr~~~lr~l~~~gl~I~~I~D~Tpip 86 (101)
.-||.-+...+..++..+.+.+. +.|.|---. +..+. .=.++++.+|..+|++|..+ +.+|.|
T Consensus 14 ~ltp~~~~~l~~a~~~~l~~~~~~~~~V~Vg~D~----R~~s~-~l~~a~~~gL~s~G~~V~~~-g~~pTP 78 (443)
T TIGR01455 14 PLTAELALLLGAAAGRVLRQGRDTAPRVVIGKDT----RLSGY-MLENALAAGLNSAGVDVLLL-GPLPTP 78 (443)
T ss_pred CCCHHHHHHHHHHHHHHHHhcCCCCCeEEEEeCC----CcChH-HHHHHHHHHHHHCCCeEEEe-CCcCcH
Confidence 36888888888888887765432 234444321 11111 12566788899999999999 688888
No 145
>PF00352 TBP: Transcription factor TFIID (or TATA-binding protein, TBP); InterPro: IPR000814 The TATA-box binding protein (TBP) is required for the initiation of transcription by RNA polymerases I, II and III, from promoters with or without a TATA box [, ]. TBP associates with a host of factors, including the general transcription factors TFIIA, -B, -D, -E, and -H, to form huge multi-subunit pre-initiation complexes on the core promoter. Through its association with different transcription factors, TBP can initiate transcription from different RNA polymerases. There are several related TBPs, including TBP-like (TBPL) proteins []. The C-terminal core of TBP (~180 residues) is highly conserved and contains two 77-amino acid repeats that produce a saddle-shaped structure that straddles the DNA; this region binds to the TATA box and interacts with transcription factors and regulatory proteins []. By contrast, the N-terminal region varies in both length and sequence.; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent, 0006367 transcription initiation from RNA polymerase II promoter; PDB: 1D3U_A 1PCZ_B 1AIS_A 1NGM_A 1TBP_A 1TBA_B 1YTB_A 1RM1_A 1YTF_A 1NH2_A ....
Probab=32.20 E-value=96 Score=19.58 Aligned_cols=34 Identities=18% Similarity=0.158 Sum_probs=27.1
Q ss_pred eeeeeccceeeccCCCCcHHHHHHHHHHHHHHHHHcC
Q 043606 3 LERITGGMKVKADRDESSPYAAMLAAQDVSQRCKERG 39 (101)
Q Consensus 3 ~~~SsG~~gfKg~r~k~t~~Aa~~a~~~~~~~~~~~g 39 (101)
+..++|.+--.|++ ++-.+..|.+.+...+.++|
T Consensus 53 ~IF~sGki~itGak---s~~~~~~a~~~i~~~L~~~~ 86 (86)
T PF00352_consen 53 LIFSSGKIVITGAK---SEEEAKKAIEKILPILQKLG 86 (86)
T ss_dssp EEETTSEEEEEEES---SHHHHHHHHHHHHHHHHHTT
T ss_pred EEEcCCEEEEEecC---CHHHHHHHHHHHHHHHHHcC
Confidence 34678888888888 77788888888988888765
No 146
>PF13344 Hydrolase_6: Haloacid dehalogenase-like hydrolase; PDB: 2HO4_B 1YV9_A 1WVI_B 3EPR_A 2P27_A 2OYC_A 2CFT_A 2P69_A 2CFS_A 2CFR_A ....
Probab=32.20 E-value=90 Score=20.22 Aligned_cols=37 Identities=14% Similarity=0.302 Sum_probs=19.8
Q ss_pred HHHHHHHcCCcEEEEEEeecCCCcccCCCCChHHHHHHHHhCCCeE
Q 043606 31 VSQRCKERGITALHIKLRATGGNKTKTPGPGAQSALRALARSGMKI 76 (101)
Q Consensus 31 ~~~~~~~~gi~~v~V~lrg~~g~~~kG~G~gr~~~lr~l~~~gl~I 76 (101)
+++.+++.|++.+-| = +....-++...+-|...|+.+
T Consensus 22 ~l~~L~~~g~~~~~l-T--------Nns~~s~~~~~~~L~~~Gi~~ 58 (101)
T PF13344_consen 22 ALDALRERGKPVVFL-T--------NNSSRSREEYAKKLKKLGIPV 58 (101)
T ss_dssp HHHHHHHTTSEEEEE-E--------S-SSS-HHHHHHHHHHTTTT-
T ss_pred HHHHHHHcCCCEEEE-e--------CCCCCCHHHHHHHHHhcCcCC
Confidence 455666666553322 2 445555666667777777664
No 147
>PRK06371 translation initiation factor IF-2B subunit alpha; Provisional
Probab=32.15 E-value=1.7e+02 Score=23.68 Aligned_cols=50 Identities=20% Similarity=0.225 Sum_probs=34.8
Q ss_pred HHHHHHHHHHHcCCcEEEEEEeecCCCcccCCCCChHHHHHHHHhCCCeEEEEEec
Q 043606 27 AAQDVSQRCKERGITALHIKLRATGGNKTKTPGPGAQSALRALARSGMKIGRIEDV 82 (101)
Q Consensus 27 a~~~~~~~~~~~gi~~v~V~lrg~~g~~~kG~G~gr~~~lr~l~~~gl~I~~I~D~ 82 (101)
++..++..|.+.|.+ ++|.+-- +.=.+.|..-..+.|.+.|+.+..|.|-
T Consensus 156 Tal~~l~~A~~~gk~-f~V~v~E-----sRP~~qG~rlta~eL~~~GI~vtlI~Ds 205 (329)
T PRK06371 156 TALAPIRIAHRNGKN-IFVFVDE-----TRPRLQGARLTAWELAQEGIDHAIIADN 205 (329)
T ss_pred hHHHHHHHHHHcCCe-eEEEECC-----CCCcchHHHHHHHHHHHCCCCEEEEccc
Confidence 456677888888865 6777721 2334566654457799999999999984
No 148
>PRK14835 undecaprenyl pyrophosphate synthase; Provisional
Probab=31.89 E-value=2.6e+02 Score=22.06 Aligned_cols=60 Identities=20% Similarity=0.280 Sum_probs=38.4
Q ss_pred HHHHHHHHHHHHHHHcCCcEEEEEEeecCCCcccCCCCChH--HHH--------H------HHHhCCCeEEEEEecCCCC
Q 043606 23 AAMLAAQDVSQRCKERGITALHIKLRATGGNKTKTPGPGAQ--SAL--------R------ALARSGMKIGRIEDVTPIP 86 (101)
Q Consensus 23 Aa~~a~~~~~~~~~~~gi~~v~V~lrg~~g~~~kG~G~gr~--~~l--------r------~l~~~gl~I~~I~D~Tpip 86 (101)
++..+...+++.|.++||+.|.|+.--+ ..+..-.+ ..| + .|...|++|..|-|...+|
T Consensus 69 ~G~~~l~~i~~~c~~lGIk~lTvYaFS~-----EN~~R~~~EV~~Lm~L~~~~l~~~~~~~~~~~~~irir~iGd~~~Lp 143 (275)
T PRK14835 69 FGVQKAYEVLEWCLELGIPTVTIWVFST-----DNFSRSPAEVETLMNLFEREARRMAVDPRIHANRVRVRAIGRHDGFP 143 (275)
T ss_pred HHHHHHHHHHHHHHHcCCCEEEEEEEEc-----cccCCCHHHHHHHHHHHHHHHHHHhchhhhhhCCeEEEEecChhhCC
Confidence 3444556788899999999999988543 22321111 111 1 1334589999999988887
Q ss_pred C
Q 043606 87 T 87 (101)
Q Consensus 87 h 87 (101)
-
T Consensus 144 ~ 144 (275)
T PRK14835 144 P 144 (275)
T ss_pred H
Confidence 4
No 149
>KOG0747 consensus Putative NAD+-dependent epimerases [Carbohydrate transport and metabolism]
Probab=31.64 E-value=1.3e+02 Score=24.65 Aligned_cols=30 Identities=23% Similarity=0.463 Sum_probs=22.1
Q ss_pred CcHHHHHHHH-HHHHHHH-HHcCCcEEEEEEe
Q 043606 19 SSPYAAMLAA-QDVSQRC-KERGITALHIKLR 48 (101)
Q Consensus 19 ~t~~Aa~~a~-~~~~~~~-~~~gi~~v~V~lr 48 (101)
.+||||..|| |.+.+.- .++|+..+.+++.
T Consensus 154 tnpyAasKaAaE~~v~Sy~~sy~lpvv~~R~n 185 (331)
T KOG0747|consen 154 TNPYAASKAAAEMLVRSYGRSYGLPVVTTRMN 185 (331)
T ss_pred CCchHHHHHHHHHHHHHHhhccCCcEEEEecc
Confidence 4899998877 5444443 5689999999884
No 150
>COG0027 PurT Formate-dependent phosphoribosylglycinamide formyltransferase (GAR transformylase) [Nucleotide transport and metabolism]
Probab=31.50 E-value=1.2e+02 Score=25.16 Aligned_cols=25 Identities=20% Similarity=0.301 Sum_probs=15.3
Q ss_pred HHHHHHHHHHHHHHcCCcEEEEEEe
Q 043606 24 AMLAAQDVSQRCKERGITALHIKLR 48 (101)
Q Consensus 24 a~~a~~~~~~~~~~~gi~~v~V~lr 48 (101)
|+.+|+.+.+.+=-+|+.-|++.+.
T Consensus 248 A~~IA~~vt~aLGG~GiFGVElfv~ 272 (394)
T COG0027 248 AQSIAKRVTDALGGRGLFGVELFVK 272 (394)
T ss_pred HHHHHHHHHHhhcCccceeEEEEEe
Confidence 3344444444444478999999994
No 151
>PRK14324 glmM phosphoglucosamine mutase; Provisional
Probab=31.42 E-value=1.7e+02 Score=23.89 Aligned_cols=63 Identities=16% Similarity=0.192 Sum_probs=41.2
Q ss_pred CCcHHHHHHHHHHHHHHHHHcCC-cEEEEEEeecCCCcccCCCCChHHHHHHHHhCCCeEEEEEecCCCC
Q 043606 18 ESSPYAAMLAAQDVSQRCKERGI-TALHIKLRATGGNKTKTPGPGAQSALRALARSGMKIGRIEDVTPIP 86 (101)
Q Consensus 18 k~t~~Aa~~a~~~~~~~~~~~gi-~~v~V~lrg~~g~~~kG~G~gr~~~lr~l~~~gl~I~~I~D~Tpip 86 (101)
.-||.-+..++..+++.+.+.+. ..|.|---. +..+.- =..++..+|..+|++|..+ ..+|.|
T Consensus 16 ~lt~~~~~~lg~a~g~~l~~~~~~~~V~Vg~D~----R~ss~~-l~~a~~~gL~s~G~~V~~~-g~~pTP 79 (446)
T PRK14324 16 KLTAFLAMRLAMAAGIYFKKHSITNKILVGKDT----RRSGYM-IENALVSGLTSVGYNVIQI-GPMPTP 79 (446)
T ss_pred CcCHHHHHHHHHHHHHHHHhCCCCCeEEEEeCC----CcCHHH-HHHHHHHHHHHCCCeEEEe-cCccHH
Confidence 46888888888877888776553 234443311 112211 2445678889999999988 678777
No 152
>PRK08334 translation initiation factor IF-2B subunit beta; Validated
Probab=31.20 E-value=1.9e+02 Score=23.73 Aligned_cols=51 Identities=16% Similarity=0.116 Sum_probs=35.7
Q ss_pred HHHHHHHHHHHHcCCcEEEEEEeecCCCcccCCCCChHHHHHHHHhCCCeEEEEEec
Q 043606 26 LAAQDVSQRCKERGITALHIKLRATGGNKTKTPGPGAQSALRALARSGMKIGRIEDV 82 (101)
Q Consensus 26 ~a~~~~~~~~~~~gi~~v~V~lrg~~g~~~kG~G~gr~~~lr~l~~~gl~I~~I~D~ 82 (101)
-++..++..+.+.|. .++|.+- -+.=...|...+-..|.+.|+.++.|.|-
T Consensus 178 gTal~vi~~A~~~gk-~~~V~v~-----EtRP~~qG~rlta~eL~~~GI~vtlI~Ds 228 (356)
T PRK08334 178 GTVGAVLRVMHKDGT-LKLLWVD-----ETRPVLQGARLSAWEYHYDGIPLKLISDN 228 (356)
T ss_pred chHHHHHHHHHHcCC-eEEEEEC-----CCCchhhHHHHHHHHHHHCCCCEEEEehh
Confidence 345667888888884 5666662 12334567666557799999999999995
No 153
>cd03089 PMM_PGM The phosphomannomutase/phosphoglucomutase (PMM/PGM) bifunctional enzyme catalyzes the reversible conversion of 1-phospho to 6-phospho-sugars (e.g. between mannose-1-phosphate and mannose-6-phosphate or glucose-1-phosphate and glucose-6-phosphate) via a bisphosphorylated sugar intermediate. The reaction involves two phosphoryl transfers, with an intervening 180 degree reorientation of the reaction intermediate during catalysis. Reorientation of the intermediate occurs without dissociation from the active site of the enzyme and is thus, a simple example of processivity, as defined by multiple rounds of catalysis without release of substrate. Glucose-6-phosphate and glucose-1-phosphate are known to be utilized for energy metabolism and cell surface construction, respectively. PMM/PGM belongs to the alpha-D-phosphohexomutase superfamily which includes several related enzymes that catalyze a reversible intramolecular phosphoryl transfer on their sugar substrates. Other membe
Probab=31.08 E-value=1.6e+02 Score=23.90 Aligned_cols=62 Identities=16% Similarity=0.214 Sum_probs=41.5
Q ss_pred CCcHHHHHHHHHHHHHHHHHcCCcEEEEEEeecCCCcccCCC-CChHHHHHHHHhCCCeEEEEEecCCCC
Q 043606 18 ESSPYAAMLAAQDVSQRCKERGITALHIKLRATGGNKTKTPG-PGAQSALRALARSGMKIGRIEDVTPIP 86 (101)
Q Consensus 18 k~t~~Aa~~a~~~~~~~~~~~gi~~v~V~lrg~~g~~~kG~G-~gr~~~lr~l~~~gl~I~~I~D~Tpip 86 (101)
.-||.-+..++..+++.+.+.+-..|.|---. +-.+ .-.+++..+|...|++|..+ +.+|.|
T Consensus 14 ~lt~~~v~~l~~a~~~~l~~~~~~~VvVg~D~------R~~s~~~~~a~~~gL~s~G~~V~~~-g~~pTP 76 (443)
T cd03089 14 ELTEEIAYAIGRAFGSWLLEKGAKKVVVGRDG------RLSSPELAAALIEGLLAAGCDVIDI-GLVPTP 76 (443)
T ss_pred ccCHHHHHHHHHHHHHHHHhcCCCeEEEEECC------CCCHHHHHHHHHHHHHHcCCcEEEe-CCcchH
Confidence 46888888888877888765433334433311 1112 23556778889999999998 788887
No 154
>TIGR00512 salvage_mtnA S-methyl-5-thioribose-1-phosphate isomerase. The delineation of this family was based in part on a discussion and neighbor-joining phylogenetic study, by Kyrpides and Woese, of archaeal and other proteins homologous to the alpha, beta, and delta subunits of eukaryotic initiation factor 2B (eIF-2B), a five-subunit molecule that catalyzes GTP recycling for eIF-2. This clade is now recognized to include the methionine salvage pathway enzyme MtnA.
Probab=31.06 E-value=1.7e+02 Score=23.59 Aligned_cols=50 Identities=24% Similarity=0.276 Sum_probs=33.6
Q ss_pred HHHHHHHHHHHcCCcEEEEEEeecCCCcccCCCCChHHHHHHHHhCCCeEEEEEec
Q 043606 27 AAQDVSQRCKERGITALHIKLRATGGNKTKTPGPGAQSALRALARSGMKIGRIEDV 82 (101)
Q Consensus 27 a~~~~~~~~~~~gi~~v~V~lrg~~g~~~kG~G~gr~~~lr~l~~~gl~I~~I~D~ 82 (101)
++..++..+.+.|.. ++|.+-- +.=...|..-..+.|.+.|+.+..|.|-
T Consensus 166 tal~~l~~A~~~g~~-~~V~v~E-----srP~~qG~rlta~~L~~~GI~vtlI~Ds 215 (331)
T TIGR00512 166 TALGVIRSAHEKGRL-EHVYADE-----TRPRLQGARLTAWELVQEGIPATLITDS 215 (331)
T ss_pred hHHHHHHHHHHcCCc-eEEEECC-----CCchhhHHHHHHHHHHHCCCCEEEEccc
Confidence 345677788888844 6666621 1223556644457799999999999984
No 155
>COG1670 RimL Acetyltransferases, including N-acetylases of ribosomal proteins [Translation, ribosomal structure and biogenesis]
Probab=30.86 E-value=1.6e+02 Score=19.35 Aligned_cols=51 Identities=14% Similarity=0.247 Sum_probs=35.9
Q ss_pred CCcHHHHHHHHHHHHHHHHH-cCCcEEEEEEeecCCCcccCCCCChHHHHHHHHhCCCeEEEEE
Q 043606 18 ESSPYAAMLAAQDVSQRCKE-RGITALHIKLRATGGNKTKTPGPGAQSALRALARSGMKIGRIE 80 (101)
Q Consensus 18 k~t~~Aa~~a~~~~~~~~~~-~gi~~v~V~lrg~~g~~~kG~G~gr~~~lr~l~~~gl~I~~I~ 80 (101)
.+.-||...+ ..+.+.+-+ +++..|...+ -+.-+.+++.+.+.|++..-..
T Consensus 108 ~g~G~~tea~-~~~l~~~f~~~~l~ri~~~~-----------~~~N~~S~rv~ek~Gf~~eg~~ 159 (187)
T COG1670 108 WGKGYATEAL-RALLDYAFEELGLHRIEATV-----------DPENEASIRVYEKLGFRLEGEL 159 (187)
T ss_pred hcCchHHHHH-HHHHHHhhhhcCceEEEEEe-----------cCCCHHHHHHHHHcCChhhhhh
Confidence 4555666544 445666544 9999999998 4556789999999997665443
No 156
>PRK08535 translation initiation factor IF-2B subunit delta; Provisional
Probab=30.84 E-value=2e+02 Score=22.69 Aligned_cols=50 Identities=26% Similarity=0.349 Sum_probs=33.2
Q ss_pred HHHHHHHHHHHHcCCcEEEEEEeecCCCcccCCCCChHHHHHHHHhCCCeEEEEEec
Q 043606 26 LAAQDVSQRCKERGITALHIKLRATGGNKTKTPGPGAQSALRALARSGMKIGRIEDV 82 (101)
Q Consensus 26 ~a~~~~~~~~~~~gi~~v~V~lrg~~g~~~kG~G~gr~~~lr~l~~~gl~I~~I~D~ 82 (101)
.+++.++..+.+.|.+ ++|.+-- +.=.+.|+..+ +.|.+.|+.++.|.|-
T Consensus 131 ~tv~~~l~~A~~~~k~-~~V~v~E-----srP~~~G~~~a-~~L~~~GI~vtlI~Ds 180 (310)
T PRK08535 131 SAALSVIKTAHEQGKD-IEVIATE-----TRPRNQGHITA-KELAEYGIPVTLIVDS 180 (310)
T ss_pred HHHHHHHHHHHHCCCe-EEEEEec-----CCchhhHHHHH-HHHHHCCCCEEEEehh
Confidence 3556677777777754 5555521 12234676665 6789999999999984
No 157
>PRK15425 gapA glyceraldehyde-3-phosphate dehydrogenase A; Provisional
Probab=30.76 E-value=66 Score=25.97 Aligned_cols=34 Identities=26% Similarity=0.403 Sum_probs=24.8
Q ss_pred EEEEEeecCCCcccCCCC-ChHHHHHHH-HhCCCeEEEEEecCCC
Q 043606 43 LHIKLRATGGNKTKTPGP-GAQSALRAL-ARSGMKIGRIEDVTPI 85 (101)
Q Consensus 43 v~V~lrg~~g~~~kG~G~-gr~~~lr~l-~~~gl~I~~I~D~Tpi 85 (101)
+.|-| +|||. || .++|++ .+..++|+-|-|.+..
T Consensus 3 ~~i~i--------nGfGRIGr-~~~r~~~~~~~~~vvaiNd~~~~ 38 (331)
T PRK15425 3 IKVGI--------NGFGRIGR-IVFRAAQKRSDIEIVAINDLLDA 38 (331)
T ss_pred eEEEE--------EeeChHHH-HHHHHHHHCCCCEEEEEecCCCH
Confidence 46667 78885 65 566775 4568999999997653
No 158
>PRK14827 undecaprenyl pyrophosphate synthase; Provisional
Probab=30.70 E-value=2.8e+02 Score=22.15 Aligned_cols=60 Identities=17% Similarity=0.132 Sum_probs=39.6
Q ss_pred HHHHHHHHHHHHHHHcCCcEEEEEEeecCCCcccCCCCChHH----------H----HHHHHhCCCeEEEEEecCCCCC
Q 043606 23 AAMLAAQDVSQRCKERGITALHIKLRATGGNKTKTPGPGAQS----------A----LRALARSGMKIGRIEDVTPIPT 87 (101)
Q Consensus 23 Aa~~a~~~~~~~~~~~gi~~v~V~lrg~~g~~~kG~G~gr~~----------~----lr~l~~~gl~I~~I~D~Tpiph 87 (101)
+...+...+++-|.++||+.|.|+---+ .|| ..-++= . +..|.+.|++|..|-|.+.+|-
T Consensus 95 ~G~~~l~~v~~~c~~lGI~~lTvYaFSt-EN~----kR~~~EV~~Lm~L~~~~l~~~~~~~~~~~irir~iG~~~~Lp~ 168 (296)
T PRK14827 95 MGEAVVIDIACGAIELGIKWLSLYAFST-ENW----KRSPEEVRFLMGFNRDVVRRRRDNLNKMGVRIRWVGSRPRLWR 168 (296)
T ss_pred HHHHHHHHHHHHHHHcCCCEEEEeeecc-hhh----cCCHHHHHHHHHHHHHHHHHHHHHHHHCCcEEEEEechhhCCH
Confidence 3444556778889999999999998532 222 221111 0 1224557999999999998884
No 159
>TIGR00829 FRU PTS system, fructose-specific, IIB component. Bacterial PTS transporters transport and concomitantly phosphorylate their sugar substrates, and typically consist of multiple subunits or protein domains. The Fru family is a large and complex family which includes several sequenced fructose and mannitol-specific permeases as well as several PTS components of unknown specificities. The fructose components of this family phosphorylate fructose on the 1-position. The Fru family PTS systems typically have 3 domains, IIA, IIB and IIC, which may be found as 1 or more proteins. The fructose and mannitol transporters form separate phylogenetic clusters in this family. This family is specific for the IIB domain of the fructose PTS transporters.
Probab=30.51 E-value=1.2e+02 Score=19.49 Aligned_cols=52 Identities=15% Similarity=0.261 Sum_probs=31.9
Q ss_pred HHHHHHHHHHHHHHHcCCcEEEEEEeecCCCcccCCCCChHHHHHHHHhCCCeEEEEEecC
Q 043606 23 AAMLAAQDVSQRCKERGITALHIKLRATGGNKTKTPGPGAQSALRALARSGMKIGRIEDVT 83 (101)
Q Consensus 23 Aa~~a~~~~~~~~~~~gi~~v~V~lrg~~g~~~kG~G~gr~~~lr~l~~~gl~I~~I~D~T 83 (101)
.+++|++.+.+.++++|+. +.|..+|. .|.-....-..+..+. -|+.+.|+.
T Consensus 12 ht~lAae~L~~aA~~~G~~-i~VE~qg~-------~g~~~~lt~~~i~~Ad-~viia~d~~ 63 (85)
T TIGR00829 12 HTFMAAEALEKAAKKRGWE-VKVETQGS-------VGAQNALTAEDIAAAD-GVILAADRE 63 (85)
T ss_pred HHHHHHHHHHHHHHHCCCe-EEEEecCC-------cCccCCCCHHHHHhCC-EEEEeccCC
Confidence 4567888888889999997 88888653 2222211225566664 444555553
No 160
>TIGR03585 PseH pseudaminic acid biosynthesis N-acetyl transferase. Sequences in this family are members of the pfam00583 (GNAT) superfamily of acetyltransferases and are proposed to perform a N-acetylation step in the process of pseudaminic acid biosynthesis in Campylobacter species. This gene is commonly observed in apparent operons with other genes responsible for the biosynthesis of pseudaminic acid and as a component of flagellar and exopolysaccharide biosynthesis loci. Significantly, many genomes containing other components of this pathway lack this gene, indicating that some other N-acetyl transferases may be incolved and/or the step is optional, resulting in a non-acetylated pseudaminic acid variant sugar.
Probab=30.41 E-value=1.6e+02 Score=19.23 Aligned_cols=42 Identities=12% Similarity=0.147 Sum_probs=31.0
Q ss_pred HHHHHHHHHH-HcCCcEEEEEEeecCCCcccCCCCChHHHHHHHHhCCCeEEEE
Q 043606 27 AAQDVSQRCK-ERGITALHIKLRATGGNKTKTPGPGAQSALRALARSGMKIGRI 79 (101)
Q Consensus 27 a~~~~~~~~~-~~gi~~v~V~lrg~~g~~~kG~G~gr~~~lr~l~~~gl~I~~I 79 (101)
+.+.+.+.+. ++++..|.+.+ -.....+++.+++.|++...+
T Consensus 96 ~~~~~~~~a~~~~~~~~i~~~v-----------~~~N~~s~~~y~k~Gf~~~g~ 138 (156)
T TIGR03585 96 LEEAALEYAFEHLGLHKLSLEV-----------LEFNNKALKLYEKFGFEREGV 138 (156)
T ss_pred HHHHHHHHHHhhCCeeEEEEEE-----------eccCHHHHHHHHHcCCeEeee
Confidence 3455677766 47999999988 445668889999999876543
No 161
>PRK08322 acetolactate synthase; Reviewed
Probab=30.31 E-value=1.1e+02 Score=25.36 Aligned_cols=46 Identities=22% Similarity=0.201 Sum_probs=36.2
Q ss_pred HHHHHHHHHHHcCCcEEEEEEeecCCCcccCCCCChHHHHHHHHhCCCeEEEEEecC
Q 043606 27 AAQDVSQRCKERGITALHIKLRATGGNKTKTPGPGAQSALRALARSGMKIGRIEDVT 83 (101)
Q Consensus 27 a~~~~~~~~~~~gi~~v~V~lrg~~g~~~kG~G~gr~~~lr~l~~~gl~I~~I~D~T 83 (101)
+++.+++.++++|++.|-.. +|..-...+.+|.+.+++++...|..
T Consensus 3 ~~~~l~~~L~~~Gv~~vFg~-----------pG~~~~~l~dal~~~~i~~i~~~hE~ 48 (547)
T PRK08322 3 AADLFVKCLENEGVEYIFGI-----------PGEENLDLLEALRDSSIKLILTRHEQ 48 (547)
T ss_pred HHHHHHHHHHHcCCCEEEeC-----------CCcchHHHHHHHHhcCCcEEEeccHH
Confidence 56889999999999977654 46667778899977888888776643
No 162
>PRK10151 ribosomal-protein-L7/L12-serine acetyltransferase; Provisional
Probab=30.19 E-value=1.8e+02 Score=19.79 Aligned_cols=50 Identities=10% Similarity=0.074 Sum_probs=35.9
Q ss_pred CcHHHHHHHHHHHHHHHH-HcCCcEEEEEEeecCCCcccCCCCChHHHHHHHHhCCCeEEEEE
Q 043606 19 SSPYAAMLAAQDVSQRCK-ERGITALHIKLRATGGNKTKTPGPGAQSALRALARSGMKIGRIE 80 (101)
Q Consensus 19 ~t~~Aa~~a~~~~~~~~~-~~gi~~v~V~lrg~~g~~~kG~G~gr~~~lr~l~~~gl~I~~I~ 80 (101)
+.-||.+.+ ..+++.+. ++++..|.+.+ -.+-..+.+.+.+.|++..-+.
T Consensus 106 g~G~~tea~-~~l~~~~~~~~~~~ri~~~v-----------~~~N~~S~~v~ek~Gf~~~g~~ 156 (179)
T PRK10151 106 GQGIISQAL-QALIHHYAQSGELRRFVIKC-----------RVDNPASNQVALRNGFTLEGCL 156 (179)
T ss_pred CCcHHHHHH-HHHHHHHHhhCCccEEEEEE-----------cCCCHHHHHHHHHCCCEEEeEe
Confidence 445666644 45677675 47899999988 3456678899999999876554
No 163
>PRK09997 hydroxypyruvate isomerase; Provisional
Probab=29.94 E-value=2e+02 Score=21.17 Aligned_cols=42 Identities=7% Similarity=0.041 Sum_probs=31.2
Q ss_pred HHHHHHHHHcCCcEEEEEEeecCCCcccCCCCChHHHHHHHHhCCCeEEEE
Q 043606 29 QDVSQRCKERGITALHIKLRATGGNKTKTPGPGAQSALRALARSGMKIGRI 79 (101)
Q Consensus 29 ~~~~~~~~~~gi~~v~V~lrg~~g~~~kG~G~gr~~~lr~l~~~gl~I~~I 79 (101)
+..++++.+.|+..|++.. + ....-+...+.|...||++...
T Consensus 18 ~~~l~~~a~~Gf~~VEl~~--~-------~~~~~~~~~~~l~~~gl~~~~~ 59 (258)
T PRK09997 18 LARFEKAAQCGFRGVEFMF--P-------YDYDIEELKQVLASNKLEHTLH 59 (258)
T ss_pred HHHHHHHHHhCCCEEEEcC--C-------CCCCHHHHHHHHHHcCCcEEEE
Confidence 4568899999999999843 1 2345566667788899999763
No 164
>cd04908 ACT_Bt0572_1 N-terminal ACT domain of a novel protein composed almost entirely of two tandem ACT domains. Included in this CD is the N-terminal ACT domain of a novel protein composed almost entirely of two tandem ACT domains as seen in the uncharacterized structure (pdb 2F06) of the Bt0572 protein from Bacteroides thetaiotaomicron and related ACT domains. These tandem ACT domain proteins belong to the superfamily of ACT regulatory domains.
Probab=29.94 E-value=91 Score=18.19 Aligned_cols=13 Identities=23% Similarity=0.547 Sum_probs=6.3
Q ss_pred HHHHhCCCeEEEE
Q 043606 67 RALARSGMKIGRI 79 (101)
Q Consensus 67 r~l~~~gl~I~~I 79 (101)
..|.+.|++|.++
T Consensus 20 ~~l~~~~inI~~i 32 (66)
T cd04908 20 EILSEAGINIRAL 32 (66)
T ss_pred HHHHHCCCCEEEE
Confidence 4444455555444
No 165
>KOG3302 consensus TATA-box binding protein (TBP), component of TFIID and TFIIIB [Transcription]
Probab=29.86 E-value=1.1e+02 Score=23.28 Aligned_cols=37 Identities=22% Similarity=0.223 Sum_probs=31.1
Q ss_pred eeeeeccceeeccCCCCcHHHHHHHHHHHHHHHHHcCCcE
Q 043606 3 LERITGGMKVKADRDESSPYAAMLAAQDVSQRCKERGITA 42 (101)
Q Consensus 3 ~~~SsG~~gfKg~r~k~t~~Aa~~a~~~~~~~~~~~gi~~ 42 (101)
+.+|+|-+--.|++ +.-.|..++.++++.+..+|++.
T Consensus 72 ~I~ssGKi~ctgA~---se~~ar~aark~aRilqkLgf~~ 108 (200)
T KOG3302|consen 72 LIFSSGKIVCTGAK---SEDSARLAARKYARILQKLGFPV 108 (200)
T ss_pred EEecCCcEEEeccC---CHHHHHHHHHHHHHHHHHcCCCc
Confidence 46789998888888 77789999999999999998763
No 166
>PLN02371 phosphoglucosamine mutase family protein
Probab=29.78 E-value=1.5e+02 Score=25.40 Aligned_cols=63 Identities=16% Similarity=0.256 Sum_probs=40.6
Q ss_pred CCcHHHHHHHHHHHHHHHHHc----CC--cEEEEEEeecCCCcccCCCCChHHHHHHHHhCCCeEEEEEecCCCC
Q 043606 18 ESSPYAAMLAAQDVSQRCKER----GI--TALHIKLRATGGNKTKTPGPGAQSALRALARSGMKIGRIEDVTPIP 86 (101)
Q Consensus 18 k~t~~Aa~~a~~~~~~~~~~~----gi--~~v~V~lrg~~g~~~kG~G~gr~~~lr~l~~~gl~I~~I~D~Tpip 86 (101)
.-||..+..++..+++.+.+. +- ..|.|--- ++..+. .=..++..+|..+|++|..+ +.+|.|
T Consensus 87 ~lTpe~v~~ig~A~a~~l~~~~~~~~~~~~~VvVG~D----~R~sS~-~l~~a~a~gL~s~Gi~V~~~-g~~pTP 155 (583)
T PLN02371 87 TLTPPAVEAIGAAFAEWLLEKKKADGSGELRVSVGRD----PRISGP-RLADAVFAGLASAGLDVVDM-GLATTP 155 (583)
T ss_pred CCCHHHHHHHHHHHHHHHHhhcccccCCCCeEEEEeC----CCCChH-HHHHHHHHHHHHCCCEEEEe-cccCch
Confidence 479999999998888887653 11 23333321 111211 12456778899999999977 677777
No 167
>PF03975 CheD: CheD chemotactic sensory transduction; InterPro: IPR005659 CheD deamidates glutamine residues to glutamate on methyl-accepting chemotaxis receptors (MCPs). CheD-mediated MCP deamidation is required for productive communication of the conformational signals of the chemoreceptors to the cheA kinase []. CheC is a CheY-P phosphatase (CheY controls flagellar rotation and is activated by phosphorylation). The activity of CheC is enhanced by its interaction with CheD, forming a CheC-CheD heterodimer. It is suggested that CheC exerts its effect on MCP methylation in Bacillus subtilis by controlling the binding of CheD to the MCPs [].; GO: 0050568 protein-glutamine glutaminase activity, 0006935 chemotaxis; PDB: 2F9Z_D.
Probab=29.67 E-value=90 Score=20.90 Aligned_cols=58 Identities=24% Similarity=0.269 Sum_probs=32.9
Q ss_pred CcHHHHHHHHHHHHHHHHHcCC--cEEEEEEeecCCCcccC-----CCC---ChHHHHHHHHhCCCeEEE
Q 043606 19 SSPYAAMLAAQDVSQRCKERGI--TALHIKLRATGGNKTKT-----PGP---GAQSALRALARSGMKIGR 78 (101)
Q Consensus 19 ~t~~Aa~~a~~~~~~~~~~~gi--~~v~V~lrg~~g~~~kG-----~G~---gr~~~lr~l~~~gl~I~~ 78 (101)
..-|+-. |.+.+++.+..+|. ..+.++|-| |++-+.+ +.. +-+.|.+.|.+.||.|..
T Consensus 15 ~~rY~d~-ai~~ll~~m~~~Ga~~~~l~aklfG-Ga~m~~~~~~~~~~IG~rNv~~a~~~L~~~gi~I~a 82 (114)
T PF03975_consen 15 PGRYGDT-AIELLLDEMEKRGARPSRLEAKLFG-GANMFPGMNSSSFNIGERNVEAARELLAEEGIPIVA 82 (114)
T ss_dssp CCCBHHH-HHHHHHHHHHTTT--GGG-EEEEEE-----S------SS-HHHHHHHHHHHHHHHTT--EEE
T ss_pred CccCHHH-HHHHHHHHHHHcCCCHHHeEEEEee-CcccccccccccCCHHHHHHHHHHHHHHHCCCcEEE
Confidence 3445544 55788888888875 558888876 5555551 222 345678888999999875
No 168
>PRK13371 4-hydroxy-3-methylbut-2-enyl diphosphate reductase; Provisional
Probab=29.56 E-value=1.8e+02 Score=24.26 Aligned_cols=41 Identities=27% Similarity=0.333 Sum_probs=27.6
Q ss_pred HHHHHHHcCCcEEE----------------EEEeecCCCcccCCCCChHHHHHHHHhCCCeEEEEEecC
Q 043606 31 VSQRCKERGITALH----------------IKLRATGGNKTKTPGPGAQSALRALARSGMKIGRIEDVT 83 (101)
Q Consensus 31 ~~~~~~~~gi~~v~----------------V~lrg~~g~~~kG~G~gr~~~lr~l~~~gl~I~~I~D~T 83 (101)
+.+.+.++|+..|. |.|++ +|..+ .....|+..|++|+ |.|
T Consensus 83 Vv~~L~~~Gv~~v~~~~~~~~~~~v~~~~~VIIrA------HGv~~---~v~~~~~~rgl~ii---DAT 139 (387)
T PRK13371 83 VNQHLREMGVRFIPVEKGVKDFSVVTPGDVVILPA------FGATV---QEMQLLNEKGCHIV---DTT 139 (387)
T ss_pred HHHHHHhCCCEEEcCcCcccchhcCCCCCEEEEeC------CCCCH---HHHHHHHHCCCeEE---ecC
Confidence 45566788998883 77765 65555 45566777888876 554
No 169
>PRK09532 DNA polymerase III subunit alpha; Reviewed
Probab=29.37 E-value=49 Score=30.06 Aligned_cols=45 Identities=24% Similarity=0.397 Sum_probs=32.4
Q ss_pred HHHHHHHHHHHHHcCCcEEEEEEeecCCCcccCCCCChHHHHHHHHhCCCeEEEEEecCCCCCC
Q 043606 25 MLAAQDVSQRCKERGITALHIKLRATGGNKTKTPGPGAQSALRALARSGMKIGRIEDVTPIPTD 88 (101)
Q Consensus 25 ~~a~~~~~~~~~~~gi~~v~V~lrg~~g~~~kG~G~gr~~~lr~l~~~gl~I~~I~D~TpiphN 88 (101)
.++...+++.|++.||. .||||=+|--.|.. ..+-|+|+-|+.||
T Consensus 347 FLIV~D~v~~Ar~~gi~----------------VGpGRGSAAGSLVa---Y~LgIT~VDPl~~~ 391 (874)
T PRK09532 347 FLVVWDYIKYARDNNIP----------------VGPGRGSAAGSLVA---YCLKITNIDPVHHG 391 (874)
T ss_pred HHHHHHHHHHHHhCCce----------------ecCCcccHHHHHHH---HHhcCCccCccccC
Confidence 34556677888887754 37777777777774 45568899999986
No 170
>PF01261 AP_endonuc_2: Xylose isomerase-like TIM barrel; InterPro: IPR012307 This TIM alpha/beta barrel structure is found in xylose isomerase (P19148 from SWISSPROT) and in endonuclease IV (P12638 from SWISSPROT, 3.1.21.2 from EC). This domain is also found in the N termini of bacterial myo-inositol catabolism proteins. These are involved in the myo-inositol catabolism pathway, and is required for growth on myo-inositol in Rhizobium leguminosarum bv. viciae []. ; PDB: 3KWS_B 3DX5_A 3CQH_B 3CQI_A 3CQK_A 3CQJ_B 2G0W_B 1DXI_A 2ZDS_D 3TVA_B ....
Probab=29.00 E-value=59 Score=22.25 Aligned_cols=43 Identities=19% Similarity=0.291 Sum_probs=27.4
Q ss_pred HHHHHcCCcEEEEEEeecCCCcccCCCCC-----hHHHHHHHHhCCCeEEEEEec
Q 043606 33 QRCKERGITALHIKLRATGGNKTKTPGPG-----AQSALRALARSGMKIGRIEDV 82 (101)
Q Consensus 33 ~~~~~~gi~~v~V~lrg~~g~~~kG~G~g-----r~~~lr~l~~~gl~I~~I~D~ 82 (101)
+.+.++|+..|++.+.- ..... .+...+.+.+.|++|..+.=.
T Consensus 2 ~~~~~~G~~~vE~~~~~-------~~~~~~~~~~~~~~~~~~~~~gl~i~~~~~~ 49 (213)
T PF01261_consen 2 EAAAEAGFDGVELRFDD-------GQPWDEKDDEAEELRRLLEDYGLKIASLHPP 49 (213)
T ss_dssp HHHHHTTHSEEEEEHHH-------HSHHTHHHHHHHHHHHHHHHTTCEEEEEEEE
T ss_pred hHHHHcCCCEEEEecCC-------CcccccchHHHHHHHHHHHHcCCeEEEEecc
Confidence 46777888888888732 22221 345666677788887776533
No 171
>COG3916 LasI N-acyl-L-homoserine lactone synthetase [Signal transduction mechanisms / Secondary metabolites biosynthesis, transport, and catabolism]
Probab=28.91 E-value=2.3e+02 Score=21.75 Aligned_cols=51 Identities=29% Similarity=0.303 Sum_probs=38.6
Q ss_pred cHHHHHHHHHHHHHHHHHcCCcEEEEEEeecCCCcccCCCCChHHHHHHHHhCCCeEEEEEecCCC
Q 043606 20 SPYAAMLAAQDVSQRCKERGITALHIKLRATGGNKTKTPGPGAQSALRALARSGMKIGRIEDVTPI 85 (101)
Q Consensus 20 t~~Aa~~a~~~~~~~~~~~gi~~v~V~lrg~~g~~~kG~G~gr~~~lr~l~~~gl~I~~I~D~Tpi 85 (101)
++ |+....--+++.+...|++.|.... -....+.|.++|+.+..|-|...+
T Consensus 119 ~~-a~~el~~g~ie~a~~~G~~~IvtVt--------------~~~meril~r~Gw~~~riG~~~~i 169 (209)
T COG3916 119 SP-AAYELFAGMIEYALARGITGIVTVT--------------DTGMERILRRAGWPLTRIGPPLTI 169 (209)
T ss_pred cH-HHHHHHHHHHHHHHHcCCceEEEEE--------------chHHHHHHHHcCCCeEEcCCceee
Confidence 44 4444445689999999999998887 224678899999999988876554
No 172
>COG2101 SPT15 TATA-box binding protein (TBP), component of TFIID and TFIIIB [Transcription]
Probab=28.86 E-value=1.1e+02 Score=23.10 Aligned_cols=36 Identities=22% Similarity=0.254 Sum_probs=30.6
Q ss_pred ceeeeeccceeeccCCCCcHHHHHHHHHHHHHHHHHcCC
Q 043606 2 TLERITGGMKVKADRDESSPYAAMLAAQDVSQRCKERGI 40 (101)
Q Consensus 2 t~~~SsG~~gfKg~r~k~t~~Aa~~a~~~~~~~~~~~gi 40 (101)
.|..+||-+.-.|++ ++--+..|.+++.+++.++|.
T Consensus 149 ~LiF~SGK~ViTGaK---~~ed~~~Av~~i~~~L~elgl 184 (185)
T COG2101 149 LLLFGSGKLVITGAK---SEEDAEQAVEKIQSRLEELGL 184 (185)
T ss_pred EEEecCCcEEEecCC---CHHHHHHHHHHHHHHHHHhcc
Confidence 356789999999998 777888899999999999874
No 173
>PF13380 CoA_binding_2: CoA binding domain; PDB: 3FF4_A 2D5A_A 2D59_A 2E6U_X 1IUL_A 1IUK_A 1Y81_A 2DUW_A.
Probab=28.71 E-value=1.8e+02 Score=19.33 Aligned_cols=38 Identities=13% Similarity=0.375 Sum_probs=25.7
Q ss_pred HHHHHHHHHcCCcEEEEEEeecCCCcccCCCCChHHHHHHHHhCCCeEE
Q 043606 29 QDVSQRCKERGITALHIKLRATGGNKTKTPGPGAQSALRALARSGMKIG 77 (101)
Q Consensus 29 ~~~~~~~~~~gi~~v~V~lrg~~g~~~kG~G~gr~~~lr~l~~~gl~I~ 77 (101)
..+.+.+.++|++.+-+.- |.-.+.+++..+..|+.|+
T Consensus 69 ~~~v~~~~~~g~~~v~~~~-----------g~~~~~~~~~a~~~gi~vi 106 (116)
T PF13380_consen 69 PEIVDEAAALGVKAVWLQP-----------GAESEELIEAAREAGIRVI 106 (116)
T ss_dssp HHHHHHHHHHT-SEEEE-T-----------TS--HHHHHHHHHTT-EEE
T ss_pred HHHHHHHHHcCCCEEEEEc-----------chHHHHHHHHHHHcCCEEE
Confidence 4578899999999776664 4556678888888898875
No 174
>PF08924 DUF1906: Domain of unknown function (DUF1906); InterPro: IPR015020 This entry represents a family of uncharacterised hypothetical bacterial proteins. ; PDB: 1SFS_A.
Probab=28.23 E-value=97 Score=21.48 Aligned_cols=52 Identities=17% Similarity=0.208 Sum_probs=27.0
Q ss_pred HHHHHHHHcCCcEEEEEEeecCCCcc-cCCCCChHHHHHHHHhCCCeEEEEEec
Q 043606 30 DVSQRCKERGITALHIKLRATGGNKT-KTPGPGAQSALRALARSGMKIGRIEDV 82 (101)
Q Consensus 30 ~~~~~~~~~gi~~v~V~lrg~~g~~~-kG~G~gr~~~lr~l~~~gl~I~~I~D~ 82 (101)
..++.+++.|+..|-.+|-+..+.-. ....+ ...=++.|...||+|..|-..
T Consensus 8 ~~~~~l~~aGy~~VgrYl~~~~~~~~~~~k~L-t~~e~~~i~~~Gl~i~pIyq~ 60 (136)
T PF08924_consen 8 ASAQALKAAGYRAVGRYLSGSRGGCAMRQKNL-TAGEVQDIRAAGLRIFPIYQG 60 (136)
T ss_dssp HHHHHHHHT---SEEEESS-BTTTB-----B---HHHHHHHHHTT-EEEEEE--
T ss_pred HHHHHHHHCCCCEEEEEcCCCCCCcccccCCC-CHHHHHHHHHCCCEEEEEEec
Confidence 45667789999999999954322211 00111 123457788999999998654
No 175
>cd00475 CIS_IPPS Cis (Z)-Isoprenyl Diphosphate Synthases (cis-IPPS); homodimers which catalyze the successive 1'-4 condensation of the isopentenyl diphosphate (IPP) molecule to trans,trans-farnesyl diphosphate (FPP) or to cis,trans-FPP to form long-chain polyprenyl diphosphates. A few can also catalyze the condensation of IPP to trans-geranyl diphosphate to form the short-chain cis,trans- FPP. In prokaryotes, the cis-IPPS, undecaprenyl diphosphate synthase (UPP synthase) catalyzes the formation of the carrier lipid UPP in bacterial cell wall peptidooglycan biosynthesis. Similarly, in eukaryotes, the cis-IPPS, dehydrodolichyl diphosphate (dedol-PP) synthase catalyzes the formation of the polyisoprenoid glycosyl carrier lipid dolichyl monophosphate. cis-IPPS are mechanistically and structurally distinct from trans-IPPS, lacking the DDXXD motifs, yet requiring Mg2+ for activity.
Probab=27.66 E-value=2.7e+02 Score=21.06 Aligned_cols=61 Identities=21% Similarity=0.320 Sum_probs=39.7
Q ss_pred HHHHHHHHHHHHHHHHcCCcEEEEEEeecCCCcccCCCCC-hHH-H------------HHHHHhCCCeEEEEEecCCCCC
Q 043606 22 YAAMLAAQDVSQRCKERGITALHIKLRATGGNKTKTPGPG-AQS-A------------LRALARSGMKIGRIEDVTPIPT 87 (101)
Q Consensus 22 ~Aa~~a~~~~~~~~~~~gi~~v~V~lrg~~g~~~kG~G~g-r~~-~------------lr~l~~~gl~I~~I~D~Tpiph 87 (101)
.+...+...+++.|.++||+.|.|+.--+ ..+..- .|. . +..+...+++|..|-|.+.+|-
T Consensus 27 ~~G~~~~~~i~~~~~~~gI~~lTvyaFS~-----eN~~R~~~EV~~Lm~l~~~~l~~~~~~~~~~~i~vr~iGd~~~Lp~ 101 (221)
T cd00475 27 KAGAEKLRDILRWCLELGVKEVTLYAFST-----ENWKRPKEEVDFLMELFRDVLRRILKELEKLGVRIRIIGDLSLLPE 101 (221)
T ss_pred HHHHHHHHHHHHHHHHcCCCEEEEEeech-----hhhCcCHHHHHHHHHHHHHHHHHHHHHHHHCCcEEEEEeChhhCCH
Confidence 34445556788899999999999997543 222211 111 1 1112346899999999998884
No 176
>PF04312 DUF460: Protein of unknown function (DUF460); InterPro: IPR007408 This is an archaeal protein of unknown function.
Probab=27.55 E-value=1.2e+02 Score=21.86 Aligned_cols=29 Identities=17% Similarity=0.263 Sum_probs=26.1
Q ss_pred CCChHHHHHHHHhCCCeEEEEEecCCCCC
Q 043606 59 GPGAQSALRALARSGMKIGRIEDVTPIPT 87 (101)
Q Consensus 59 G~gr~~~lr~l~~~gl~I~~I~D~Tpiph 87 (101)
+..+.-+|..+.+.|-.|+-=+|++|.|.
T Consensus 62 ~~~~~evi~~I~~~G~PviVAtDV~p~P~ 90 (138)
T PF04312_consen 62 NMSRSEVIEWISEYGKPVIVATDVSPPPE 90 (138)
T ss_pred CCCHHHHHHHHHHcCCEEEEEecCCCCcH
Confidence 56677899999999999999999999985
No 177
>KOG1602 consensus Cis-prenyltransferase [Lipid transport and metabolism]
Probab=27.40 E-value=3.2e+02 Score=21.78 Aligned_cols=59 Identities=22% Similarity=0.365 Sum_probs=41.0
Q ss_pred HHHHHHHHHHHHHHHcCCcEEEEEEeecCCCcccCCCCChHHH---------------HH--HHHhCCCeEEEEEecCCC
Q 043606 23 AAMLAAQDVSQRCKERGITALHIKLRATGGNKTKTPGPGAQSA---------------LR--ALARSGMKIGRIEDVTPI 85 (101)
Q Consensus 23 Aa~~a~~~~~~~~~~~gi~~v~V~lrg~~g~~~kG~G~gr~~~---------------lr--~l~~~gl~I~~I~D~Tpi 85 (101)
|.-.+-..+++.|.++||+.|.++--.. ..|....+=+ .+ -+.+.|+.|..|-|.+-+
T Consensus 64 aGf~~l~~ile~C~~lGI~~vT~fAFSi-----eNFkRs~eEVd~LM~L~~~k~~~~~~~~~~~~~~gvririiGdlslL 138 (271)
T KOG1602|consen 64 AGFEALKEILELCKELGIKEVTVFAFSI-----ENFKRSPEEVDGLMDLALEKIERLLEQGEKLDKYGVRIRVIGDLSLL 138 (271)
T ss_pred HHHHHHHHHHHHHHHcCCcEEEEEEEeh-----hhhCCCHHHHHHHHHHHHHHHHHHHHHhhhhhhcCeEEEEEcchhhC
Confidence 5555556789999999999999997543 4444444321 01 123469999999999888
Q ss_pred C
Q 043606 86 P 86 (101)
Q Consensus 86 p 86 (101)
|
T Consensus 139 ~ 139 (271)
T KOG1602|consen 139 P 139 (271)
T ss_pred C
Confidence 7
No 178
>cd07038 TPP_PYR_PDC_IPDC_like Pyrimidine (PYR) binding domain of pyruvate decarboxylase (PDC), indolepyruvate decarboxylase (IPDC) and related proteins. Thiamine pyrophosphate (TPP family), pyrimidine (PYR) binding domain of pyruvate decarboxylase (PDC) and indolepyruvate decarboxylase (IPDC) subfamily. The PYR domain is found in many key metabolic enzymes which use TPP (also known as thiamine diphosphate) as a cofactor. TPP binds in the cleft formed by a PYR domain and a PP domain. The PYR domain, binds the aminopyrimidine ring of TPP, the PP domain binds the diphosphate residue. The PYR and PP domains have a common fold, but do not share strong sequence conservation. The PP domain is not included in this sub-family. Most TPP-dependent enzymes have the PYR and PP domains on the same subunit although these domains can be alternatively arranged in the primary structure. TPP-dependent enzymes are multisubunit proteins, the smallest catalytic unit being a dimer-of-active sites, for many
Probab=27.13 E-value=1.8e+02 Score=20.28 Aligned_cols=42 Identities=17% Similarity=0.134 Sum_probs=30.8
Q ss_pred HHHHHHHHcCCcEEEEEEeecCCCcccCCCCChHHHHHHHHhC-CCeEEEEEec
Q 043606 30 DVSQRCKERGITALHIKLRATGGNKTKTPGPGAQSALRALARS-GMKIGRIEDV 82 (101)
Q Consensus 30 ~~~~~~~~~gi~~v~V~lrg~~g~~~kG~G~gr~~~lr~l~~~-gl~I~~I~D~ 82 (101)
.+++.++++|++.|--.. |..-...+.+|.+. +++++...|.
T Consensus 2 ~l~~~L~~~Gi~~vFg~p-----------G~~~~~l~~al~~~~~i~~i~~rhE 44 (162)
T cd07038 2 YLLERLKQLGVKHVFGVP-----------GDYNLPLLDAIEENPGLRWVGNCNE 44 (162)
T ss_pred HHHHHHHHcCCCEEEEeC-----------CccHHHHHHHHhhcCCceEEeeCCH
Confidence 477889999999765544 66666788888654 7888877654
No 179
>PF14124 DUF4291: Domain of unknown function (DUF4291)
Probab=26.90 E-value=18 Score=27.06 Aligned_cols=26 Identities=35% Similarity=0.419 Sum_probs=16.4
Q ss_pred CCChHHHHHHHHhCCCeEEEEEecCCCCC
Q 043606 59 GPGAQSALRALARSGMKIGRIEDVTPIPT 87 (101)
Q Consensus 59 G~gr~~~lr~l~~~gl~I~~I~D~Tpiph 87 (101)
|...+.+-+ ... -=|+.|+|+||.-|
T Consensus 132 Gl~g~~~~~-y~~--eWiv~I~DiT~~v~ 157 (181)
T PF14124_consen 132 GLRGEAVRR-YAD--EWIVSIEDITPLVR 157 (181)
T ss_pred cCCHHHHHH-hHh--hcEEeeEECCHHHH
Confidence 554444433 332 36899999999754
No 180
>PRK03092 ribose-phosphate pyrophosphokinase; Provisional
Probab=26.86 E-value=3.1e+02 Score=21.50 Aligned_cols=51 Identities=22% Similarity=0.256 Sum_probs=39.8
Q ss_pred HHHHHHHHHcCCcEEEEEEeecCCCcccCCCCChHHHHHHHHhCCCeEEEEEecCCCCCC
Q 043606 29 QDVSQRCKERGITALHIKLRATGGNKTKTPGPGAQSALRALARSGMKIGRIEDVTPIPTD 88 (101)
Q Consensus 29 ~~~~~~~~~~gi~~v~V~lrg~~g~~~kG~G~gr~~~lr~l~~~gl~I~~I~D~TpiphN 88 (101)
..+++.++++|-+.|.+..- +|+-. ..++..|..+++.=+.++|.-|.|.+
T Consensus 218 ~~aa~~Lk~~Ga~~I~~~~t-------H~v~~--~~a~~~l~~~~~~~i~~t~tip~~~~ 268 (304)
T PRK03092 218 AGAVRALKEAGAKDVIIAAT-------HGVLS--GPAAERLKNCGAREVVVTDTLPIPEE 268 (304)
T ss_pred HHHHHHHHhcCCCeEEEEEE-------cccCC--hHHHHHHHHCCCCEEEEeeeeccchh
Confidence 35678889999999998882 55443 34777788899999999999887765
No 181
>PRK00881 purH bifunctional phosphoribosylaminoimidazolecarboxamide formyltransferase/IMP cyclohydrolase; Provisional
Probab=26.86 E-value=1.7e+02 Score=25.30 Aligned_cols=42 Identities=26% Similarity=0.447 Sum_probs=32.6
Q ss_pred HHHHHHHHHcCCcEEEEEEeecCCCcccCCCCChHHHHHHHHhCCCeEEEEEecCCCCC
Q 043606 29 QDVSQRCKERGITALHIKLRATGGNKTKTPGPGAQSALRALARSGMKIGRIEDVTPIPT 87 (101)
Q Consensus 29 ~~~~~~~~~~gi~~v~V~lrg~~g~~~kG~G~gr~~~lr~l~~~gl~I~~I~D~Tpiph 87 (101)
..+++++.++|++-+ +| .| .-+.|+..|+++..|.++|..|.
T Consensus 18 v~lAk~L~~lGfeI~-----AT-----~G-------Tak~L~e~GI~v~~V~k~TgfpE 59 (513)
T PRK00881 18 VEFAKALVELGVEIL-----ST-----GG-------TAKLLAEAGIPVTEVSDVTGFPE 59 (513)
T ss_pred HHHHHHHHHCCCEEE-----Ec-----ch-------HHHHHHHCCCeeEEeecccCCch
Confidence 457888899998842 11 11 33789999999999999999986
No 182
>PF14057 GGGtGRT: GGGtGRT protein
Probab=26.62 E-value=1.6e+02 Score=23.72 Aligned_cols=48 Identities=19% Similarity=0.237 Sum_probs=34.0
Q ss_pred cHHHHHHHHHHHHHHHHHcCCcEEEEEEeecCCCcccCCCCChHHHHHHHHhCCCeEE
Q 043606 20 SPYAAMLAAQDVSQRCKERGITALHIKLRATGGNKTKTPGPGAQSALRALARSGMKIG 77 (101)
Q Consensus 20 t~~Aa~~a~~~~~~~~~~~gi~~v~V~lrg~~g~~~kG~G~gr~~~lr~l~~~gl~I~ 77 (101)
-.|||-.-|..|++.+....-+.+.|.| + |+|++++.-.-.-.|+.-+
T Consensus 124 ESFAAAEGAIgIa~~AnK~Rk~PLrVIL--------n--GLGKDAA~iIsRinGFTyV 171 (328)
T PF14057_consen 124 ESFAAAEGAIGIARNANKVRKEPLRVIL--------N--GLGKDAAYIISRINGFTYV 171 (328)
T ss_pred hhhhhhcchHHHHHhhchhhcCCeeeee--------c--ccchhHHHHHHHhcCceEE
Confidence 4677777777889888888889999999 4 6667777443333455443
No 183
>COG0587 DnaE DNA polymerase III, alpha subunit [DNA replication, recombination, and repair]
Probab=26.49 E-value=32 Score=32.24 Aligned_cols=42 Identities=31% Similarity=0.445 Sum_probs=28.7
Q ss_pred HHHHHHHHHHcCCcEEEEEEeecCCCcccCCCCChHHHHHHHHhCCCeEEEEEecCCCCCC
Q 043606 28 AQDVSQRCKERGITALHIKLRATGGNKTKTPGPGAQSALRALARSGMKIGRIEDVTPIPTD 88 (101)
Q Consensus 28 ~~~~~~~~~~~gi~~v~V~lrg~~g~~~kG~G~gr~~~lr~l~~~gl~I~~I~D~TpiphN 88 (101)
...+++.|++.||. .||||=++-=.|-. ..+-|+|+-|+.||
T Consensus 343 V~D~I~~Ak~~gI~----------------vGPGRGSaAGSLVa---Y~L~IT~IDPl~~~ 384 (1139)
T COG0587 343 VWDFIKFARDNGIP----------------VGPGRGSAAGSLVA---YALGITDIDPLKYD 384 (1139)
T ss_pred HHHHHHHHHHCCCc----------------cCCCCcchHHHHHH---HHhcCCCcCccccC
Confidence 34556666666665 47777777666664 34568899999996
No 184
>PRK09856 fructoselysine 3-epimerase; Provisional
Probab=26.46 E-value=2.6e+02 Score=20.54 Aligned_cols=61 Identities=11% Similarity=0.001 Sum_probs=33.8
Q ss_pred HHHHHHHHHHcCCcEEEEEEeecCCCcccCCCC-ChHHHHHHHHhCCCeEEEEEec-CCCCCCC
Q 043606 28 AQDVSQRCKERGITALHIKLRATGGNKTKTPGP-GAQSALRALARSGMKIGRIEDV-TPIPTDS 89 (101)
Q Consensus 28 ~~~~~~~~~~~gi~~v~V~lrg~~g~~~kG~G~-gr~~~lr~l~~~gl~I~~I~D~-TpiphNG 89 (101)
.+..++.+.++|+..|++...-+ -.....+.. ..+..-+.+...||+|.++.-. ...|+|.
T Consensus 15 l~~~l~~~~~~G~~~vEl~~~~~-~~~~~~~~~~~~~~l~~~~~~~gl~v~s~~~~~~~~~~~~ 77 (275)
T PRK09856 15 IEHAFRDASELGYDGIEIWGGRP-HAFAPDLKAGGIKQIKALAQTYQMPIIGYTPETNGYPYNM 77 (275)
T ss_pred HHHHHHHHHHcCCCEEEEccCCc-cccccccCchHHHHHHHHHHHcCCeEEEecCcccCcCccc
Confidence 35678899999999999953100 000000111 1233334566789999887532 2345553
No 185
>TIGR01132 pgm phosphoglucomutase, alpha-D-glucose phosphate-specific. This enzyme interconverts alpha-D-glucose-1-P and alpha-D-glucose-6-P.
Probab=26.19 E-value=2.8e+02 Score=23.46 Aligned_cols=63 Identities=25% Similarity=0.313 Sum_probs=41.3
Q ss_pred CcHHHHHHHHHHHHHHHHHcCC-cEEEEEEeecCCCcccCCCCChHHHHHHHHhCCCeEEEEEe--cCCCC
Q 043606 19 SSPYAAMLAAQDVSQRCKERGI-TALHIKLRATGGNKTKTPGPGAQSALRALARSGMKIGRIED--VTPIP 86 (101)
Q Consensus 19 ~t~~Aa~~a~~~~~~~~~~~gi-~~v~V~lrg~~g~~~kG~G~gr~~~lr~l~~~gl~I~~I~D--~Tpip 86 (101)
-|+..+..+++.+++.+.+.+. ..|.|---. +..+. .=.++++.+|..+|++|..+.| ..|.|
T Consensus 55 lt~~~~~~i~~a~a~~~~~~~~~~~VvVG~D~----R~sS~-~~~~a~a~gL~s~Gi~V~~~~~~G~~pTP 120 (543)
T TIGR01132 55 FNEPHILAIAQAIAEYRAAQGITGPLYIGKDT----HALSE-PAFISVLEVLAANGVEVIVQENNGFTPTP 120 (543)
T ss_pred cCHHHHHHHHHHHHHHHHHhCCCCcEEEEeCC----CcCCH-HHHHHHHHHHHHCCCEEEEeCCCCcCCch
Confidence 6889999999887888876663 223333311 11111 1245677889999999999866 46665
No 186
>PRK10146 aminoalkylphosphonic acid N-acetyltransferase; Provisional
Probab=26.16 E-value=1.9e+02 Score=18.61 Aligned_cols=44 Identities=14% Similarity=0.155 Sum_probs=30.4
Q ss_pred HHHHHHHHHHHHHHHHcCCcEEEEEEeecCCCcccCCCCChHHHHHHHHhCCCeEE
Q 043606 22 YAAMLAAQDVSQRCKERGITALHIKLRATGGNKTKTPGPGAQSALRALARSGMKIG 77 (101)
Q Consensus 22 ~Aa~~a~~~~~~~~~~~gi~~v~V~lrg~~g~~~kG~G~gr~~~lr~l~~~gl~I~ 77 (101)
++..+. +.+.+.|++.|++.+.+.. ..-...|++--.+.|+...
T Consensus 93 iG~~Ll-~~~~~~a~~~~~~~i~l~~-----------~~~n~~a~~fY~~~Gf~~~ 136 (144)
T PRK10146 93 VGSKLL-AWAEEEARQAGAEMTELST-----------NVKRHDAHRFYLREGYEQS 136 (144)
T ss_pred HHHHHH-HHHHHHHHHcCCcEEEEec-----------CCCchHHHHHHHHcCCchh
Confidence 444444 5678888889999998887 3334567777777777543
No 187
>PRK14833 undecaprenyl pyrophosphate synthase; Provisional
Probab=26.11 E-value=3e+02 Score=21.05 Aligned_cols=60 Identities=10% Similarity=0.175 Sum_probs=39.2
Q ss_pred HHHHHHHHHHHHHHHcCCcEEEEEEeecCCCcccCCCCChH-H-HH------------HHHHhCCCeEEEEEecCCCCC
Q 043606 23 AAMLAAQDVSQRCKERGITALHIKLRATGGNKTKTPGPGAQ-S-AL------------RALARSGMKIGRIEDVTPIPT 87 (101)
Q Consensus 23 Aa~~a~~~~~~~~~~~gi~~v~V~lrg~~g~~~kG~G~gr~-~-~l------------r~l~~~gl~I~~I~D~Tpiph 87 (101)
+...+...+++.|.++||+.|.|+.--+ ..+..-.+ . .| ..+...|++|..|-|...+|-
T Consensus 32 ~G~~~l~~~~~~c~~~gI~~lTvyaFS~-----eN~~R~~~Ev~~Lm~L~~~~l~~~~~~~~~~~irvr~iG~~~~Lp~ 105 (233)
T PRK14833 32 KGVKTLREITIWCANHKLECLTLYAFST-----ENWKRPKSEVDFLMKLLKKYLKDERSTYLENNIRFKAIGDLEGFSK 105 (233)
T ss_pred HHHHHHHHHHHHHHHcCCCEEEEeecch-----hhcCcCHHHHHHHHHHHHHHHHHHHHHHHhCCcEEEEEeChhhCCH
Confidence 4445556788899999999999998532 23332121 1 11 112345899999999988874
No 188
>PRK05720 mtnA methylthioribose-1-phosphate isomerase; Reviewed
Probab=26.11 E-value=2.6e+02 Score=22.61 Aligned_cols=49 Identities=27% Similarity=0.341 Sum_probs=33.2
Q ss_pred HHHHHHHHHHcCCcEEEEEEeecCCCcccCCCCChHHHHHHHHhCCCeEEEEEec
Q 043606 28 AQDVSQRCKERGITALHIKLRATGGNKTKTPGPGAQSALRALARSGMKIGRIEDV 82 (101)
Q Consensus 28 ~~~~~~~~~~~gi~~v~V~lrg~~g~~~kG~G~gr~~~lr~l~~~gl~I~~I~D~ 82 (101)
+..++..+.+.|.+ ++|.+-- +.=...|..-..+.|.+.|+.++.|.|-
T Consensus 167 al~~i~~A~~~gk~-~~V~v~E-----sRP~~qG~~lta~eL~~~GI~vtlI~Ds 215 (344)
T PRK05720 167 ALAPIYAAKEKGID-IHVYADE-----TRPRLQGARLTAWELYQAGIDVTVITDN 215 (344)
T ss_pred HHHHHHHHHHcCCc-eEEEEcC-----CCChhhhHHHHHHHHHHCCCCEEEEccc
Confidence 44567777777765 5666621 1334567655557799999999999985
No 189
>PRK06965 acetolactate synthase 3 catalytic subunit; Validated
Probab=26.07 E-value=1.6e+02 Score=24.81 Aligned_cols=54 Identities=15% Similarity=0.143 Sum_probs=40.3
Q ss_pred CCcHHHHHHHHHHHHHHHHHcCCcEEEEEEeecCCCcccCCCCChHHHHHHHHh-CCCeEEEEEec
Q 043606 18 ESSPYAAMLAAQDVSQRCKERGITALHIKLRATGGNKTKTPGPGAQSALRALAR-SGMKIGRIEDV 82 (101)
Q Consensus 18 k~t~~Aa~~a~~~~~~~~~~~gi~~v~V~lrg~~g~~~kG~G~gr~~~lr~l~~-~gl~I~~I~D~ 82 (101)
-+-|.+-+..++.+++.++++|++.|--. +|-.-...+.+|.. .+++++...+.
T Consensus 14 ~~~~~~~~~~a~~l~~~L~~~GV~~vFgv-----------pG~~~~~l~dal~~~~~i~~i~~rhE 68 (587)
T PRK06965 14 LSPPAADSIGAEILMKALAAEGVEFIWGY-----------PGGAVLYIYDELYKQDKIQHVLVRHE 68 (587)
T ss_pred cCCCchhccHHHHHHHHHHHcCCCEEEec-----------CCcchHHHHHHHhhcCCCeEEEeCCH
Confidence 35567777788999999999999977553 46556678888865 47887766553
No 190
>COG4130 Predicted sugar epimerase [Carbohydrate transport and metabolism]
Probab=26.07 E-value=2.7e+02 Score=22.01 Aligned_cols=54 Identities=19% Similarity=0.306 Sum_probs=35.9
Q ss_pred HHHHHHHHHcCCcEEEEEEeecCCCcccCCCCChHHHHHHHHh-CCCeEEEEEecCCC
Q 043606 29 QDVSQRCKERGITALHIKLRATGGNKTKTPGPGAQSALRALAR-SGMKIGRIEDVTPI 85 (101)
Q Consensus 29 ~~~~~~~~~~gi~~v~V~lrg~~g~~~kG~G~gr~~~lr~l~~-~gl~I~~I~D~Tpi 85 (101)
+.....++++|+..|+|+=.=+++.-..|..+ ..+|++.. .|+.|++|.-.-|.
T Consensus 20 ~affa~ak~lg~s~VeiRndl~~~~I~dg~p~---a~vka~Aek~Gl~IvSINAlypF 74 (272)
T COG4130 20 EAFFALAKRLGLSKVEIRNDLPSNAIADGTPA---AEVKALAEKAGLTIVSINALYPF 74 (272)
T ss_pred HHHHHHHHHcCcceeEEecCCCcccccCCCCH---HHHHHHHHHcCcEEEEeeccccc
Confidence 45667899999999999853222222233333 46788754 69999999766443
No 191
>PRK08617 acetolactate synthase; Reviewed
Probab=26.01 E-value=1.7e+02 Score=24.29 Aligned_cols=47 Identities=19% Similarity=0.199 Sum_probs=36.7
Q ss_pred HHHHHHHHHHHHcCCcEEEEEEeecCCCcccCCCCChHHHHHHHHhCCCeEEEEEecC
Q 043606 26 LAAQDVSQRCKERGITALHIKLRATGGNKTKTPGPGAQSALRALARSGMKIGRIEDVT 83 (101)
Q Consensus 26 ~a~~~~~~~~~~~gi~~v~V~lrg~~g~~~kG~G~gr~~~lr~l~~~gl~I~~I~D~T 83 (101)
..++.+++.++++|++.|-.. +|-.-...+.+|...+++++...|..
T Consensus 6 ~~~~~l~~~L~~~GV~~vFg~-----------pG~~~~~l~~al~~~~i~~i~~~hE~ 52 (552)
T PRK08617 6 YGADLVVDSLINQGVKYVFGI-----------PGAKIDRVFDALEDSGPELIVTRHEQ 52 (552)
T ss_pred cHHHHHHHHHHHcCCCEEEeC-----------CCccHHHHHHHHhhCCCCEEEeccHH
Confidence 456888999999999976544 46667778999987889888877754
No 192
>PRK08978 acetolactate synthase 2 catalytic subunit; Reviewed
Probab=25.62 E-value=1.6e+02 Score=24.55 Aligned_cols=46 Identities=20% Similarity=0.167 Sum_probs=34.8
Q ss_pred HHHHHHHHHHHHcCCcEEEEEEeecCCCcccCCCCChHHHHHHHHhCCCeEEEEEec
Q 043606 26 LAAQDVSQRCKERGITALHIKLRATGGNKTKTPGPGAQSALRALARSGMKIGRIEDV 82 (101)
Q Consensus 26 ~a~~~~~~~~~~~gi~~v~V~lrg~~g~~~kG~G~gr~~~lr~l~~~gl~I~~I~D~ 82 (101)
..++.+++.+++.|++.|-.. +|-.-...+.+|...+++++...|.
T Consensus 2 ~~~~~l~~~L~~~Gv~~vFg~-----------pG~~~~~l~~al~~~~i~~v~~~hE 47 (548)
T PRK08978 2 NGAQWVVHALRAQGVDTVFGY-----------PGGAIMPVYDALYDGGVEHLLCRHE 47 (548)
T ss_pred cHHHHHHHHHHHcCCCEEEeC-----------CCcchHHHHHHHHhcCCeEEEeccH
Confidence 357889999999999977554 3665667888887778888776654
No 193
>PRK00394 transcription factor; Reviewed
Probab=25.28 E-value=1.5e+02 Score=21.62 Aligned_cols=35 Identities=20% Similarity=0.243 Sum_probs=30.0
Q ss_pred eeeeeccceeeccCCCCcHHHHHHHHHHHHHHHHHcCC
Q 043606 3 LERITGGMKVKADRDESSPYAAMLAAQDVSQRCKERGI 40 (101)
Q Consensus 3 ~~~SsG~~gfKg~r~k~t~~Aa~~a~~~~~~~~~~~gi 40 (101)
+..++|-+-..|++ +.--++.|.+.+...+.++|.
T Consensus 143 lIF~SGKvvitGak---s~~~~~~a~~~i~~~l~~~g~ 177 (179)
T PRK00394 143 LLFGSGKLVITGAK---SEEDAEKAVEKILEKLEELGL 177 (179)
T ss_pred EEEcCCEEEEEecC---CHHHHHHHHHHHHHHHHHcCC
Confidence 45689999999999 777888899999999988875
No 194
>PF13523 Acetyltransf_8: Acetyltransferase (GNAT) domain; PDB: 2VQY_A 2BUE_A 1V0C_A 1YK3_D 2PR8_A 2QIR_A 2PRB_A 2QML_A 2PC1_A.
Probab=25.13 E-value=2.1e+02 Score=18.84 Aligned_cols=49 Identities=10% Similarity=0.145 Sum_probs=31.5
Q ss_pred HHHHHHHHHHHHHHHHc-CCcEEEEEEeecCCCcccCCCCChHHHHHHHHhCCCeEEEEEec
Q 043606 22 YAAMLAAQDVSQRCKER-GITALHIKLRATGGNKTKTPGPGAQSALRALARSGMKIGRIEDV 82 (101)
Q Consensus 22 ~Aa~~a~~~~~~~~~~~-gi~~v~V~lrg~~g~~~kG~G~gr~~~lr~l~~~gl~I~~I~D~ 82 (101)
++.... ..+++.+.+. ++..|.+-+ ...-..+++.+++.|+......+.
T Consensus 95 ~g~~~~-~~~~~~~~~~~~~~~i~~~~-----------~~~N~~~~~~~~k~GF~~~g~~~~ 144 (152)
T PF13523_consen 95 LGKAML-RALIEFLFEDPGVDRIVLDP-----------HEDNTRAIRLYEKAGFRKVGEFEF 144 (152)
T ss_dssp HHHHHH-HHHHHHHHTSTT--EEEEEE-----------BTT-HHHHHHHHHTT-EEEEEEEE
T ss_pred HHHHHH-HHHHHHHHhCCCCCEEEEec-----------CcCCHHHHHHHHHcCCEEeeEEEC
Confidence 444333 4456666654 788888888 445567999999999998877763
No 195
>PLN02821 1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate reductase
Probab=25.10 E-value=2e+02 Score=24.50 Aligned_cols=41 Identities=22% Similarity=0.306 Sum_probs=26.8
Q ss_pred HHHHHHHcCCcEEE----------------EEEeecCCCcccCCCCChHHHHHHHHhCCCeEEEEEecC
Q 043606 31 VSQRCKERGITALH----------------IKLRATGGNKTKTPGPGAQSALRALARSGMKIGRIEDVT 83 (101)
Q Consensus 31 ~~~~~~~~gi~~v~----------------V~lrg~~g~~~kG~G~gr~~~lr~l~~~gl~I~~I~D~T 83 (101)
+.+.+.++|+..|. |.|++ .|..+ ..+..|...|++|+ |.|
T Consensus 151 Vv~~L~~~GV~~I~~~~~~~~~~~v~~gdvVIirA------HGvs~---~~~~~l~~kg~~IV---DaT 207 (460)
T PLN02821 151 VNKRLEEMNVQFIEVEEGGKDFSVVGEGDVVILPA------FGASV---EEMQTLNDKNVQIV---DTT 207 (460)
T ss_pred HHHHHHHCCCEEecccccccccccCCCCCEEEEeC------CCCCH---HHHHHHHHCCCeEE---ecC
Confidence 35567789998885 55544 44333 45566788888876 655
No 196
>COG1636 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=24.96 E-value=34 Score=26.13 Aligned_cols=53 Identities=15% Similarity=0.309 Sum_probs=41.5
Q ss_pred HHHHHHHHHHHHcCCcEEEEEEeecCCCcccCCCCChHHHHHHHHhCCCeEEEEEecCCCCCCC
Q 043606 26 LAAQDVSQRCKERGITALHIKLRATGGNKTKTPGPGAQSALRALARSGMKIGRIEDVTPIPTDS 89 (101)
Q Consensus 26 ~a~~~~~~~~~~~gi~~v~V~lrg~~g~~~kG~G~gr~~~lr~l~~~gl~I~~I~D~TpiphNG 89 (101)
.--+..+++|.++|++.+.=.| ++.|-+ -+..|...|..+....||+-+|.|.
T Consensus 97 ~Rle~tA~~A~e~G~d~ftttL---------~iSp~K--n~~qin~~G~~~~k~y~V~yl~~df 149 (204)
T COG1636 97 MRLEKTAKKAKELGFDVFTTTL---------LISPKK--NMNQINEIGERAAKPYGVVYLPSNF 149 (204)
T ss_pred HHHHHHHHHHHHcCCchhhhhe---------ecCccc--CHHHHHHHhHHhhcccCceecCccc
Confidence 3346789999999999877666 234433 4567888999999999999999987
No 197
>TIGR03457 sulphoacet_xsc sulfoacetaldehyde acetyltransferase. Members of this protein family are sulfoacetaldehyde acetyltransferase, an enzyme of taurine utilization. Taurine, or 2-aminoethanesulfonate, can be used by bacteria as a source of carbon, nitrogen, and sulfur.
Probab=24.92 E-value=1.9e+02 Score=24.33 Aligned_cols=46 Identities=11% Similarity=0.122 Sum_probs=35.1
Q ss_pred HHHHHHHHHHHHcCCcEEEEEEeecCCCcccCCCCChHHHHHHHHhCCCeEEEEEec
Q 043606 26 LAAQDVSQRCKERGITALHIKLRATGGNKTKTPGPGAQSALRALARSGMKIGRIEDV 82 (101)
Q Consensus 26 ~a~~~~~~~~~~~gi~~v~V~lrg~~g~~~kG~G~gr~~~lr~l~~~gl~I~~I~D~ 82 (101)
.+++.+++.++++|++.|--. +|-.-...+.+|...+++.+...+.
T Consensus 3 ~~~~~l~~~L~~~GV~~vFGi-----------pG~~~~~l~dal~~~~i~~i~~rhE 48 (579)
T TIGR03457 3 TPSEAFVEVLVANGVTHAFGI-----------MGSAFMDAMDLFPPAGIRFIPVVHE 48 (579)
T ss_pred cHHHHHHHHHHHCCCCEEEEc-----------cCcchHHHHHHHhhcCCeEEEeccH
Confidence 356888999999999976544 3666667888998788888877664
No 198
>PRK09875 putative hydrolase; Provisional
Probab=24.91 E-value=1.3e+02 Score=23.59 Aligned_cols=38 Identities=13% Similarity=0.273 Sum_probs=27.0
Q ss_pred HHHHHHcCCcEEEEEEeecCCCcccCCCCChHH-HHHHHH-hCCCeEEE
Q 043606 32 SQRCKERGITALHIKLRATGGNKTKTPGPGAQS-ALRALA-RSGMKIGR 78 (101)
Q Consensus 32 ~~~~~~~gi~~v~V~lrg~~g~~~kG~G~gr~~-~lr~l~-~~gl~I~~ 78 (101)
+...++.|...| |-+ ..+|.||+. .|+.|. ++|++|+.
T Consensus 40 l~~~~~~Gg~ti-Vd~--------T~~g~GRd~~~l~~is~~tgv~Iv~ 79 (292)
T PRK09875 40 MNDLMTRGVRNV-IEM--------TNRYMGRNAQFMLDVMRETGINVVA 79 (292)
T ss_pred HHHHHHhCCCeE-Eec--------CCCccCcCHHHHHHHHHHhCCcEEE
Confidence 344667899987 666 668888887 455554 46998875
No 199
>COG0194 Gmk Guanylate kinase [Nucleotide transport and metabolism]
Probab=24.74 E-value=2.9e+02 Score=20.86 Aligned_cols=40 Identities=23% Similarity=0.249 Sum_probs=28.3
Q ss_pred EEEEEeecCCCcccCCCCChHHHHHHHHhCCCeEEEEEecCCCCCCC
Q 043606 43 LHIKLRATGGNKTKTPGPGAQSALRALARSGMKIGRIEDVTPIPTDS 89 (101)
Q Consensus 43 v~V~lrg~~g~~~kG~G~gr~~~lr~l~~~gl~I~~I~D~TpiphNG 89 (101)
..+.|.|| -|.|+.++++.|...----.||.-.|.-|-+|
T Consensus 5 ~l~vlsgP-------SG~GKsTl~k~L~~~~~l~~SVS~TTR~pR~g 44 (191)
T COG0194 5 LLIVLSGP-------SGVGKSTLVKALLEDDKLRFSVSATTRKPRPG 44 (191)
T ss_pred eEEEEECC-------CCCCHHHHHHHHHhhcCeEEEEEeccCCCCCC
Confidence 34566554 47899999999987653335788888877655
No 200
>TIGR03849 arch_ComA phosphosulfolactate synthase. This model finds the ComA (Coenzyme M biosynthesis A) protein, phosphosulfolactate synthase, in methanogenic archaea. The ComABC pathway is one of at least two pathways to the intermediate sulfopyruvate. Coenzyme M occurs rarely and sporadically outside of the archaea, as for expoxide metabolism in Xanthobacter autotrophicus Py2, but candidate phosphosulfolactate synthases from that and other species occur fall below the cutoff and outside the scope of this model. This model deliberately is narrower in scope than pfam02679.
Probab=24.60 E-value=3.3e+02 Score=21.09 Aligned_cols=46 Identities=13% Similarity=0.132 Sum_probs=31.0
Q ss_pred HHHHHHHHHHHHHHcCCcEEEEEEeecCCCcccCCCCCh---HHHHHHHHhCCCeEE
Q 043606 24 AMLAAQDVSQRCKERGITALHIKLRATGGNKTKTPGPGA---QSALRALARSGMKIG 77 (101)
Q Consensus 24 a~~a~~~~~~~~~~~gi~~v~V~lrg~~g~~~kG~G~gr---~~~lr~l~~~gl~I~ 77 (101)
+|...+...+.|+++|+..|+|.- --+.... ...|+.+++.|+++.
T Consensus 69 ~q~~~~~Yl~~~k~lGf~~IEiS~--------G~~~i~~~~~~rlI~~~~~~g~~v~ 117 (237)
T TIGR03849 69 SKGKFDEYLNECDELGFEAVEISD--------GSMEISLEERCNLIERAKDNGFMVL 117 (237)
T ss_pred HhhhHHHHHHHHHHcCCCEEEEcC--------CccCCCHHHHHHHHHHHHhCCCeEe
Confidence 344456667799999999999875 1134433 345666677788776
No 201
>cd01577 IPMI_Swivel Aconatase-like swivel domain of 3-isopropylmalate dehydratase and related uncharacterized proteins. 3-isopropylmalate dehydratase catalyzes the isomerization between 2-isopropylmalate and 3-isopropylmalate, via the formation of 2-isopropylmaleate 3-isopropylmalate. IPMI is involved in fungal and bacterial leucine biosynthesis and is also found in eukaryotes. This is the aconitase-like swivel domain, which is believed to undergo swivelling conformational change in the enzyme mechanism.
Probab=24.31 E-value=89 Score=20.70 Aligned_cols=24 Identities=21% Similarity=0.167 Sum_probs=19.5
Q ss_pred ccCCCCChHHHHHHHHhCCCeEEE
Q 043606 55 TKTPGPGAQSALRALARSGMKIGR 78 (101)
Q Consensus 55 ~kG~G~gr~~~lr~l~~~gl~I~~ 78 (101)
.-|.|.-||.|..+|+..|++.+-
T Consensus 26 nfG~GSSRE~A~~al~~~Gi~avi 49 (91)
T cd01577 26 NFGCGSSREHAPWALKDAGIRAVI 49 (91)
T ss_pred cccCCCcHHHHHHHHHHhCCCEEE
Confidence 356677899999999999988654
No 202
>PRK07729 glyceraldehyde-3-phosphate dehydrogenase; Validated
Probab=24.13 E-value=1e+02 Score=25.10 Aligned_cols=29 Identities=24% Similarity=0.283 Sum_probs=21.5
Q ss_pred cCCCC-ChHHHHHHH-HhCCCeEEEEEecCCC
Q 043606 56 KTPGP-GAQSALRAL-ARSGMKIGRIEDVTPI 85 (101)
Q Consensus 56 kG~G~-gr~~~lr~l-~~~gl~I~~I~D~Tpi 85 (101)
+|||. || .++|++ .+..++|+-|-|.+..
T Consensus 8 NGfGRIGR-~~~r~~~~~~~~~vvaINd~~~~ 38 (343)
T PRK07729 8 NGFGRIGR-MVFRKAIKESAFEIVAINASYPS 38 (343)
T ss_pred ECcChHHH-HHHHHHhhcCCcEEEEecCCCCH
Confidence 88996 65 566774 4567999999997653
No 203
>KOG3139 consensus N-acetyltransferase [General function prediction only]
Probab=24.07 E-value=2.9e+02 Score=20.42 Aligned_cols=42 Identities=19% Similarity=0.218 Sum_probs=32.7
Q ss_pred HHHHHHHHHHHHHHcCCcEEEEEEeecCCCcccCCCCChHHHHHHHHhCCCeE
Q 043606 24 AMLAAQDVSQRCKERGITALHIKLRATGGNKTKTPGPGAQSALRALARSGMKI 76 (101)
Q Consensus 24 a~~a~~~~~~~~~~~gi~~v~V~lrg~~g~~~kG~G~gr~~~lr~l~~~gl~I 76 (101)
|....+.+++.+.+.|+..|.+.- ..-..+|++--++-|++-
T Consensus 102 g~aLvr~aId~m~~~g~~eVvLeT-----------e~~n~~A~~LY~sLGF~r 143 (165)
T KOG3139|consen 102 GKALVRKAIDAMRSRGYSEVVLET-----------EVTNLSALRLYESLGFKR 143 (165)
T ss_pred HHHHHHHHHHHHHHCCCcEEEEec-----------cccchHHHHHHHhcCceE
Confidence 455567789999999999999887 555778988777777654
No 204
>COG1710 Uncharacterized protein conserved in archaea [Function unknown]
Probab=24.04 E-value=1e+02 Score=22.00 Aligned_cols=54 Identities=22% Similarity=0.355 Sum_probs=36.7
Q ss_pred HHHHHHHHHHHHcCCcEEEEEEeecCCCcccCCCCChHH------HHHHHHhCCCeEEEEEecCCCCC
Q 043606 26 LAAQDVSQRCKERGITALHIKLRATGGNKTKTPGPGAQS------ALRALARSGMKIGRIEDVTPIPT 87 (101)
Q Consensus 26 ~a~~~~~~~~~~~gi~~v~V~lrg~~g~~~kG~G~gr~~------~lr~l~~~gl~I~~I~D~Tpiph 87 (101)
...+++.+...++|++-+-|.++| -|.-+.. .++-+.++|..-..|...+.||.
T Consensus 64 k~skkvlkaleq~gI~vIPvk~Kg--------rGrprkyd~~t~~~i~emlr~gk~preIsk~lGIpi 123 (139)
T COG1710 64 KVSKKVLKALEQMGIKVIPVKLKG--------RGRPRKYDRNTLLRIREMLRNGKTPREISKDLGIPI 123 (139)
T ss_pred HHHHHHHHHHHhCCceEeeeeecC--------CCCCcccchhHHHHHHHHHHcCCCHHHHHHhhCCch
Confidence 455677888888999999999944 3432222 55666677777666666666664
No 205
>COG0462 PrsA Phosphoribosylpyrophosphate synthetase [Nucleotide transport and metabolism / Amino acid transport and metabolism]
Probab=24.01 E-value=2.5e+02 Score=22.74 Aligned_cols=48 Identities=23% Similarity=0.280 Sum_probs=40.0
Q ss_pred HHHHHHHHcCCcEEEEEEeecCCCcccCCCCChHHHHHHHHhCCCeEEEEEecCCCC
Q 043606 30 DVSQRCKERGITALHIKLRATGGNKTKTPGPGAQSALRALARSGMKIGRIEDVTPIP 86 (101)
Q Consensus 30 ~~~~~~~~~gi~~v~V~lrg~~g~~~kG~G~gr~~~lr~l~~~gl~I~~I~D~Tpip 86 (101)
++++.++++|-+.|.+..- +|+-. ..+++.|..+.++=+-++|..|.|
T Consensus 232 ~Aa~~Lk~~GAk~V~a~~t-------H~vfs--~~a~~~l~~~~i~~vivTnTi~~~ 279 (314)
T COG0462 232 KAAKALKERGAKKVYAAAT-------HGVFS--GAALERLEASAIDEVIVTDTIPLP 279 (314)
T ss_pred HHHHHHHHCCCCeEEEEEE-------chhhC--hHHHHHHhcCCCCEEEEeCCcccc
Confidence 4677889999999999983 66555 679999998879999999998887
No 206
>PF07693 KAP_NTPase: KAP family P-loop domain; InterPro: IPR011646 The KAP (after Kidins220/ARMS and PifA) family of predicted NTPases are sporadically distributed across a wide phylogenetic range in bacteria and in animals. Many of the prokaryotic KAP NTPases are encoded in plasmids and tend to undergo disruption to form pseudogenes. A unique feature of all eukaryotic and certain bacterial KAP NTPases is the presence of two or four transmembrane helices inserted into the P-loop NTPase domain. These transmembrane helices anchor KAP NTPases in the membrane such that the P-loop domain is located on the intracellular side [].
Probab=23.94 E-value=2.4e+02 Score=21.20 Aligned_cols=37 Identities=24% Similarity=0.235 Sum_probs=27.0
Q ss_pred HHHHHHHHHHcC-CcEEEEEEeecCCCcccCCCCChHHHHHHHHh
Q 043606 28 AQDVSQRCKERG-ITALHIKLRATGGNKTKTPGPGAQSALRALAR 71 (101)
Q Consensus 28 ~~~~~~~~~~~g-i~~v~V~lrg~~g~~~kG~G~gr~~~lr~l~~ 71 (101)
|+.+++.+.+.. -..+.|-|.|+ +|.|+.+.|+.|+.
T Consensus 5 a~~la~~I~~~~~~~~~~IgL~G~-------WGsGKSs~l~~l~~ 42 (325)
T PF07693_consen 5 AKALAEIIKNPDSDDPFVIGLYGE-------WGSGKSSFLNMLKE 42 (325)
T ss_pred HHHHHHHHhccCCCCCeEEEEECC-------CCCCHHHHHHHHHH
Confidence 345555565543 66788888663 99999999998865
No 207
>cd05802 GlmM GlmM is a bacterial phosphoglucosamine mutase (PNGM) that belongs to the alpha-D-phosphohexomutase superfamily. It is required for the interconversion of glucosamine-6-phosphate and glucosamine-1-phosphate in the biosynthetic pathway of UDP-N-acetylglucosamine, an essential precursor to components of the cell envelope. In order to be active, GlmM must be phosphorylated, which can occur via autophosphorylation or by the Ser/Thr kinase StkP. GlmM functions in a classical ping-pong bi-bi mechanism with glucosamine-1,6-diphosphate as an intermediate. Other members of the alpha-D-phosphohexomutase superfamily include phosphoglucosamine mutase (PNGM), phosphoacetylglucosamine mutase (PAGM), the bacterial phosphomannomutase ManB, and the bifunctional phosphomannomutase/phosphoglucomutase (PMM/PGM). Each of these enzymes has four domains with a centrally located active site formed by four loops, one from each domain. All four domains are included in this alignment model.
Probab=23.75 E-value=2.5e+02 Score=22.69 Aligned_cols=63 Identities=14% Similarity=0.143 Sum_probs=40.6
Q ss_pred CCcHHHHHHHHHHHHHHHHHcCC-cEEEEEEeecCCCcccCCCCChHHHHHHHHhCCCeEEEEEecCCCC
Q 043606 18 ESSPYAAMLAAQDVSQRCKERGI-TALHIKLRATGGNKTKTPGPGAQSALRALARSGMKIGRIEDVTPIP 86 (101)
Q Consensus 18 k~t~~Aa~~a~~~~~~~~~~~gi-~~v~V~lrg~~g~~~kG~G~gr~~~lr~l~~~gl~I~~I~D~Tpip 86 (101)
.-||..+...+..++..+.+.+- ..|.|---. +..+ -.=.++++.+|..+|++|..+ ..+|.|
T Consensus 14 ~lt~e~~~~lg~a~~~~l~~~~~~~~VvVg~D~----R~ss-~~l~~a~~~gL~s~G~~V~~~-g~~pTP 77 (434)
T cd05802 14 PLTPELALKLGRAAGKVLGKGGGRPKVLIGKDT----RISG-YMLESALAAGLTSAGVDVLLL-GVIPTP 77 (434)
T ss_pred CCCHHHHHHHHHHHHHHHHhcCCCCeEEEEECC----CCCH-HHHHHHHHHHHHHCCCcEEEE-cccchH
Confidence 46888888888888887765432 334444321 1111 112566778889999999998 578777
No 208
>PRK08335 translation initiation factor IF-2B subunit alpha; Validated
Probab=23.72 E-value=3.3e+02 Score=21.40 Aligned_cols=50 Identities=18% Similarity=0.258 Sum_probs=34.5
Q ss_pred HHHHHHHHHHHcCCcEEEEEEeecCCCcccCCCCChHHHHHHHHhCCCeEEEEEecC
Q 043606 27 AAQDVSQRCKERGITALHIKLRATGGNKTKTPGPGAQSALRALARSGMKIGRIEDVT 83 (101)
Q Consensus 27 a~~~~~~~~~~~gi~~v~V~lrg~~g~~~kG~G~gr~~~lr~l~~~gl~I~~I~D~T 83 (101)
++..++..+.+.|.. ++|.+-- +.=...|+.. .+.|.+.|+.+..|.|-.
T Consensus 121 tv~~~l~~A~~~gk~-~~V~v~E-----srP~~qG~~l-a~eL~~~GI~vtlI~Dsa 170 (275)
T PRK08335 121 AVLEILKTAKRKGKR-FKVILTE-----SAPDYEGLAL-ANELEFLGIEFEVITDAQ 170 (275)
T ss_pred HHHHHHHHHHHcCCc-eEEEEec-----CCCchhHHHH-HHHHHHCCCCEEEEeccH
Confidence 556677778777754 5555521 1334568777 688999999999999853
No 209
>COG3911 Predicted ATPase [General function prediction only]
Probab=23.70 E-value=77 Score=23.73 Aligned_cols=22 Identities=41% Similarity=0.617 Sum_probs=19.1
Q ss_pred cCCCCChHHHHHHHHhCCCeEE
Q 043606 56 KTPGPGAQSALRALARSGMKIG 77 (101)
Q Consensus 56 kG~G~gr~~~lr~l~~~gl~I~ 77 (101)
-|+|.|+.+.|.+|.+.|+-..
T Consensus 16 GgpGaGKTtLL~aLa~~Gfatv 37 (183)
T COG3911 16 GGPGAGKTTLLAALARAGFATV 37 (183)
T ss_pred CCCCCcHHHHHHHHHHcCceee
Confidence 5899999999999999986544
No 210
>TIGR00524 eIF-2B_rel eIF-2B alpha/beta/delta-related uncharacterized proteins. This model, eIF-2B_rel, describes half of a superfamily, where the other half consists of eukaryotic translation initiation factor 2B (eIF-2B) subunits alpha, beta, and delta. It is unclear whether the eIF-2B_rel set is monophyletic, or whether they are all more closely related to each other than to any eIF-2B subunit because the eIF-2B clade is highly derived. Members of this branch of the family are all uncharacterized with respect to function and are found in the Archaea, Bacteria, and Eukarya, although a number are described as putative translation intiation factor components. Proteins found by eIF-2B_rel include at least three clades, including a set of uncharacterized eukaryotic proteins, a set found in some but not all Archaea, and a set universal so far among the Archaea and closely related to several uncharacterized bacterial proteins.
Probab=23.68 E-value=2.5e+02 Score=22.16 Aligned_cols=51 Identities=20% Similarity=0.246 Sum_probs=33.3
Q ss_pred HHHHHHHHHHHHcCCcEEEEEEeecCCCcccCCCCChHHHHHHHHhCCCeEEEEEec
Q 043606 26 LAAQDVSQRCKERGITALHIKLRATGGNKTKTPGPGAQSALRALARSGMKIGRIEDV 82 (101)
Q Consensus 26 ~a~~~~~~~~~~~gi~~v~V~lrg~~g~~~kG~G~gr~~~lr~l~~~gl~I~~I~D~ 82 (101)
.+++.++..|.+.|.+ ++|.+-- +.-.+.|.....+.|.+.|+.+..|.|-
T Consensus 137 ~tv~~~l~~A~~~g~~-~~V~v~E-----srP~~~G~~~~a~~L~~~gI~vtlI~Ds 187 (303)
T TIGR00524 137 GTALGVIRSAWEDGKR-IRVIACE-----TRPRNQGSRLTAWELMQDGIDVTLITDS 187 (303)
T ss_pred chHHHHHHHHHHcCCc-eEEEECC-----CCCccchHHHHHHHHHHCCCCEEEEChh
Confidence 3455677778777755 5555521 1334567334447799999999999884
No 211
>TIGR02406 ectoine_EctA L-2,4-diaminobutyric acid acetyltransferase. This enzyme family is the EctA of ectoine biosynthesis. Ectoine is a compatible solute, analagous to trehalose, betaines, etc., found often in halotolerant organisms. EctA is L-2,4-diaminobutyric acid acetyltransferase, also called DABA acetyltransferase.
Probab=23.64 E-value=2.5e+02 Score=19.15 Aligned_cols=46 Identities=13% Similarity=0.142 Sum_probs=31.9
Q ss_pred CcHHHHHHHHHHHHHHHHHcCCcEEEEEEeecCCCcccCCCCChHHHHHHHHhCCCeE
Q 043606 19 SSPYAAMLAAQDVSQRCKERGITALHIKLRATGGNKTKTPGPGAQSALRALARSGMKI 76 (101)
Q Consensus 19 ~t~~Aa~~a~~~~~~~~~~~gi~~v~V~lrg~~g~~~kG~G~gr~~~lr~l~~~gl~I 76 (101)
+.=|+.++ .+.+.+.+++.++..+.+.+ -.....+++...+.|++.
T Consensus 80 g~GiG~~L-~~~l~~~a~~~~~~~i~~~v-----------~~~N~~a~~ly~k~G~~~ 125 (157)
T TIGR02406 80 GKGLARRL-LEALLERVACERVRHLETTI-----------TPDNQASRALFKALARRR 125 (157)
T ss_pred cCcHHHHH-HHHHHHHHHhCCCCEEEEEE-----------cCCCHHHHHHHHHhCccc
Confidence 33455554 45678888889998888777 455667888778777643
No 212
>cd05803 PGM_like4 This PGM-like (phosphoglucomutase-like) domain is located C-terminal to a mannose-1-phosphate guanyltransferase domain in a protein of unknown function that is found in both prokaryotes and eukaryotes. This domain belongs to the alpha-D-phosphohexomutase superfamily which includes several related enzymes that catalyze a reversible intramolecular phosphoryl transfer on their sugar substrates. Members of this superfamily include the phosphoglucomutases (PGM1 and PGM2), phosphoglucosamine mutase (PNGM), phosphoacetylglucosamine mutase (PAGM), the bacterial phosphomannomutase ManB, the bacterial phosphoglucosamine mutase GlmM, and the bifunctional phosphomannomutase/phosphoglucomutase (PMM/PGM). Each of these enzymes has four domains with a centrally located active site formed by four loops, one from each domain. All four domains are included in this alignment model.
Probab=23.50 E-value=3e+02 Score=22.35 Aligned_cols=61 Identities=15% Similarity=0.189 Sum_probs=41.0
Q ss_pred CcHHHHHHHHHHHHHHHHHcCC-cEEEEEEeecCCCcccCCC-CChHHHHHHHHhCCCeEEEEEecCCCC
Q 043606 19 SSPYAAMLAAQDVSQRCKERGI-TALHIKLRATGGNKTKTPG-PGAQSALRALARSGMKIGRIEDVTPIP 86 (101)
Q Consensus 19 ~t~~Aa~~a~~~~~~~~~~~gi-~~v~V~lrg~~g~~~kG~G-~gr~~~lr~l~~~gl~I~~I~D~Tpip 86 (101)
-||.-+...+..+++.+.+.+- ..|.|---. +-.+ .=+++++.+|...|++|..+ +.+|.|
T Consensus 15 lt~~~v~~l~~a~~~~l~~~~~~~~Vvvg~D~------R~~s~~l~~a~~~gL~~~G~~V~~~-g~~pTP 77 (445)
T cd05803 15 LTPEVITRYVAAFATWQPERTKGGKIVVGRDG------RPSGPMLEKIVIGALLACGCDVIDL-GIAPTP 77 (445)
T ss_pred CCHHHHHHHHHHHHHHHHhcCCCCeEEEEeCC------CCCHHHHHHHHHHHHHHCCCeEEEe-CCCCch
Confidence 6888888888888888776442 334443311 1112 23567888899999999998 478877
No 213
>COG4782 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=23.32 E-value=2.1e+02 Score=23.83 Aligned_cols=57 Identities=16% Similarity=0.227 Sum_probs=39.0
Q ss_pred eee-eecc-ceeeccCCCCcHHHHHHHHHHHHHHH-HHcCCcEEEEEEeecCCCcccCCCCChHHHHHHHHh
Q 043606 3 LER-ITGG-MKVKADRDESSPYAAMLAAQDVSQRC-KERGITALHIKLRATGGNKTKTPGPGAQSALRALAR 71 (101)
Q Consensus 3 ~~~-SsG~-~gfKg~r~k~t~~Aa~~a~~~~~~~~-~~~gi~~v~V~lrg~~g~~~kG~G~gr~~~lr~l~~ 71 (101)
++| |.|+ +||--.| .++.|+.-..+ .+++.+ .+...+.|+|.- + .+|-..+..+|++
T Consensus 152 FSWPS~g~l~~Yn~Dr-eS~~~Sr~aLe-~~lr~La~~~~~~~I~ilA--------H--SMGtwl~~e~LrQ 211 (377)
T COG4782 152 FSWPSRGSLLGYNYDR-ESTNYSRPALE-RLLRYLATDKPVKRIYLLA--------H--SMGTWLLMEALRQ 211 (377)
T ss_pred EEcCCCCeeeecccch-hhhhhhHHHHH-HHHHHHHhCCCCceEEEEE--------e--cchHHHHHHHHHH
Confidence 344 5555 4888888 89998877664 556655 456699999988 5 4455566666654
No 214
>PRK14733 coaE dephospho-CoA kinase; Provisional
Probab=23.24 E-value=2.2e+02 Score=21.10 Aligned_cols=31 Identities=16% Similarity=0.195 Sum_probs=23.6
Q ss_pred cEEEEEEeecCCCcccCCCCChHHHHHHHHh-CCCeEEE
Q 043606 41 TALHIKLRATGGNKTKTPGPGAQSALRALAR-SGMKIGR 78 (101)
Q Consensus 41 ~~v~V~lrg~~g~~~kG~G~gr~~~lr~l~~-~gl~I~~ 78 (101)
..+.|-|- -|+|.|+.++.+.|.. .|+.+..
T Consensus 5 ~~~~IglT-------G~iGsGKStv~~~l~~~lg~~vid 36 (204)
T PRK14733 5 NTYPIGIT-------GGIASGKSTATRILKEKLNLNVVC 36 (204)
T ss_pred ceEEEEEE-------CCCCCCHHHHHHHHHHHcCCeEEe
Confidence 34556674 4799999999999986 6888654
No 215
>PF09499 RE_ApaLI: ApaLI-like restriction endonuclease; InterPro: IPR019036 There are four classes of restriction endonucleases: types I, II,III and IV. All types of enzymes recognise specific short DNA sequences and carry out the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. They differ in their recognition sequence, subunit composition, cleavage position, and cofactor requirements [, ], as summarised below: Type I enzymes (3.1.21.3 from EC) cleave at sites remote from recognition site; require both ATP and S-adenosyl-L-methionine to function; multifunctional protein with both restriction and methylase (2.1.1.72 from EC) activities. Type II enzymes (3.1.21.4 from EC) cleave within or at short specific distances from recognition site; most require magnesium; single function (restriction) enzymes independent of methylase. Type III enzymes (3.1.21.5 from EC) cleave at sites a short distance from recognition site; require ATP (but doesn't hydrolyse it); S-adenosyl-L-methionine stimulates reaction but is not required; exists as part of a complex with a modification methylase methylase (2.1.1.72 from EC). Type IV enzymes target methylated DNA. Type II restriction endonucleases (3.1.21.4 from EC) are components of prokaryotic DNA restriction-modification mechanisms that protect the organism against invading foreign DNA. These site-specific deoxyribonucleases catalyse the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. Of the 3000 restriction endonucleases that have been characterised, most are homodimeric or tetrameric enzymes that cleave target DNA at sequence-specific sites close to the recognition site. For homodimeric enzymes, the recognition site is usually a palindromic sequence 4-8 bp in length. Most enzymes require magnesium ions as a cofactor for catalysis. Although they can vary in their mode of recognition, many restriction endonucleases share a similar structural core comprising four beta-strands and one alpha-helix, as well as a similar mechanism of cleavage, suggesting a common ancestral origin []. However, there is still considerable diversity amongst restriction endonucleases [, ]. The target site recognition process triggers large conformational changes of the enzyme and the target DNA, leading to the activation of the catalytic centres. Like other DNA binding proteins, restriction enzymes are capable of non-specific DNA binding as well, which is the prerequisite for efficient target site location by facilitated diffusion. Non-specific binding usually does not involve interactions with the bases but only with the DNA backbone []. This entry includes R.ApaLI and R.XbaI restriction endonucleases. ApaLI recognises and cleaves the sequence GTGCAC.
Probab=23.20 E-value=1.4e+02 Score=22.61 Aligned_cols=27 Identities=22% Similarity=0.295 Sum_probs=23.4
Q ss_pred HHHHHHHcCCcEEEEEEeecCCCcccCCCCChHHHHH
Q 043606 31 VSQRCKERGITALHIKLRATGGNKTKTPGPGAQSALR 67 (101)
Q Consensus 31 ~~~~~~~~gi~~v~V~lrg~~g~~~kG~G~gr~~~lr 67 (101)
-++-+++.|+++|.|++ +-|.|..++|
T Consensus 134 rikvi~~aGy~PIrimf----------~~P~r~~~~~ 160 (191)
T PF09499_consen 134 RIKVIKSAGYKPIRIMF----------YYPNREQAIR 160 (191)
T ss_pred HHHHHHHCCCcceEEEE----------eCCCHHHHHH
Confidence 36678889999999999 7899999985
No 216
>PRK09732 hypothetical protein; Provisional
Probab=23.09 E-value=2.5e+02 Score=19.69 Aligned_cols=34 Identities=15% Similarity=0.181 Sum_probs=26.0
Q ss_pred CcHHHHHHHHHHHHHHHHHcCCcEEEEEEeecCCC
Q 043606 19 SSPYAAMLAAQDVSQRCKERGITALHIKLRATGGN 53 (101)
Q Consensus 19 ~t~~Aa~~a~~~~~~~~~~~gi~~v~V~lrg~~g~ 53 (101)
-|.-.|+.+++...++|.++|+. |.|-|=.++|+
T Consensus 7 Ltl~~A~~~~~aA~~~A~~~g~~-v~iaVvD~~G~ 40 (134)
T PRK09732 7 LSQQMASAIIAAGQEEAQKNNWS-VSIAVADDGGH 40 (134)
T ss_pred CCHHHHHHHHHHHHHHHHHhCCC-EEEEEEcCCCC
Confidence 46678889999999999999985 66655555555
No 217
>PRK02458 ribose-phosphate pyrophosphokinase; Provisional
Probab=23.08 E-value=3.9e+02 Score=21.24 Aligned_cols=50 Identities=14% Similarity=0.113 Sum_probs=38.9
Q ss_pred HHHHHHHHHcCCcEEEEEEeecCCCcccCCCCChHHHHHHHHhCCCeEEEEEecCCCCC
Q 043606 29 QDVSQRCKERGITALHIKLRATGGNKTKTPGPGAQSALRALARSGMKIGRIEDVTPIPT 87 (101)
Q Consensus 29 ~~~~~~~~~~gi~~v~V~lrg~~g~~~kG~G~gr~~~lr~l~~~gl~I~~I~D~Tpiph 87 (101)
..+++.+++.|-+.|.+.+- +|+=.| .|..-|..+++.=+.++|.-|.|+
T Consensus 235 ~~aa~~Lk~~GA~~V~~~~t-------Hgif~~--~a~~~l~~s~i~~iv~TdTi~~~~ 284 (323)
T PRK02458 235 AEAAKIVEREGATEIYAVAS-------HGLFAG--GAAEVLENAPIKEILVTDSVATKE 284 (323)
T ss_pred HHHHHHHHhCCCCcEEEEEE-------ChhcCc--hHHHHHhhCCCCEEEEECCcCCch
Confidence 35788899999999999882 664444 367779889999999999876554
No 218
>cd06422 NTP_transferase_like_1 NTP_transferase_like_1 is a member of the nucleotidyl transferase family. This is a subfamily of nucleotidyl transferases. Nucleotidyl transferases transfer nucleotides onto phosphosugars. The activated sugars are precursors for synthesis of lipopolysaccharide, glycolipids and polysaccharides. Other subfamilies of nucleotidyl transferases include Alpha-D-Glucose-1-Phosphate Cytidylyltransferase, Mannose-1-phosphate guanyltransferase, and Glucose-1-phosphate thymidylyltransferase.
Probab=22.86 E-value=1.3e+02 Score=21.31 Aligned_cols=53 Identities=17% Similarity=0.159 Sum_probs=37.4
Q ss_pred CCcHHHHHHHHHHHHHHHHHcCCcEEEEEEeecCCCcccCCCCChHHHHHHHHh--CCCeEEEEEe
Q 043606 18 ESSPYAAMLAAQDVSQRCKERGITALHIKLRATGGNKTKTPGPGAQSALRALAR--SGMKIGRIED 81 (101)
Q Consensus 18 k~t~~Aa~~a~~~~~~~~~~~gi~~v~V~lrg~~g~~~kG~G~gr~~~lr~l~~--~gl~I~~I~D 81 (101)
-.-|++.+...+.+++.+.+.|++.|.|.+ +...+.....|.. .++.|..+.+
T Consensus 23 ~llpi~g~~li~~~l~~l~~~gi~~i~iv~-----------~~~~~~i~~~~~~~~~~~~i~~~~~ 77 (221)
T cd06422 23 PLVPVAGKPLIDHALDRLAAAGIRRIVVNT-----------HHLADQIEAHLGDSRFGLRITISDE 77 (221)
T ss_pred ceeeECCEEHHHHHHHHHHHCCCCEEEEEc-----------cCCHHHHHHHHhcccCCceEEEecC
Confidence 456677777888899999999999998876 4444555555543 4677766544
No 219
>PF00490 ALAD: Delta-aminolevulinic acid dehydratase; InterPro: IPR001731 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 porphobilinogen (PBG) synthase (PBGS, or 5-aminoaevulinic acid dehydratase, or ALAD, 4.2.1.24 from EC), which functions during the second stage of tetrapyrrole biosynthesis. This enzyme catalyses a Knorr-type condensation reaction between two molecules of ALA to generate porphobilinogen, the pyrrolic building block used in later steps []. The structure of the enzyme is based on a TIM barrel topology made up of eight identical subunits, where each subunit binds to a metal ion that is essential for activity, usually zinc (in yeast, mammals and certain bacteria) or magnesium (in plants and other bacteria). A lysine has been implicated in the catalytic mechanism []. The lack of PBGS enzyme causes a rare porphyric disorder known as ALAD porphyria, which appears to involve conformational changes in the enzyme [.; GO: 0004655 porphobilinogen synthase activity, 0046872 metal ion binding, 0033014 tetrapyrrole biosynthetic process; PDB: 2C1H_A 1W1Z_A 1GZG_B 1W5O_B 1W5Q_B 2C18_A 1B4K_A 2C19_B 1W56_B 2C13_B ....
Probab=22.81 E-value=3.3e+02 Score=22.23 Aligned_cols=58 Identities=21% Similarity=0.194 Sum_probs=36.0
Q ss_pred HHHHHHHHcCCcEEEEEE------eecCCCcccCCCCChHHHHHHHHhCCCeEEEEEecCCCCC
Q 043606 30 DVSQRCKERGITALHIKL------RATGGNKTKTPGPGAQSALRALARSGMKIGRIEDVTPIPT 87 (101)
Q Consensus 30 ~~~~~~~~~gi~~v~V~l------rg~~g~~~kG~G~gr~~~lr~l~~~gl~I~~I~D~Tpiph 87 (101)
..++.+.++||+.|.+.= |.+.|+..-...-=-.-+|+.|+..-..+.-|.|+.--||
T Consensus 61 ~~v~~~~~~GI~~v~lFgvi~~~~Kd~~gs~a~~~~g~v~~air~iK~~~pdl~vi~Dvclc~Y 124 (324)
T PF00490_consen 61 KEVEEAVDLGIRAVILFGVIDPSKKDEEGSEAYNPDGLVQRAIRAIKKAFPDLLVITDVCLCEY 124 (324)
T ss_dssp HHHHHHHHTT--EEEEEEE-SCSC-BSS-GGGGSTTSHHHHHHHHHHHHSTTSEEEEEE-STTT
T ss_pred HHHHHHHHCCCCEEEEEeeCCcccCCcchhcccCCCChHHHHHHHHHHhCCCcEEEEecccccc
Confidence 467889999999988743 3333322211221134588889888788999999987775
No 220
>PF14877 mIF3: Mitochondrial translation initiation factor
Probab=22.78 E-value=2.4e+02 Score=21.11 Aligned_cols=56 Identities=21% Similarity=0.244 Sum_probs=36.2
Q ss_pred HHHHHHHHHHHHHHHcCCcEEEEEEeecCCCcccCCCCC--hHHHHHHH------HhCCCeEEEEEecC---CCCC
Q 043606 23 AAMLAAQDVSQRCKERGITALHIKLRATGGNKTKTPGPG--AQSALRAL------ARSGMKIGRIEDVT---PIPT 87 (101)
Q Consensus 23 Aa~~a~~~~~~~~~~~gi~~v~V~lrg~~g~~~kG~G~g--r~~~lr~l------~~~gl~I~~I~D~T---piph 87 (101)
-||.|+..+++++.++.-+...-.|. |..+ .++-|+-+ ...||.|+.+.+.+ ++|.
T Consensus 14 ~aq~A~~svi~ki~~~n~~g~Vk~in---------p~t~~Le~~~l~~~~~~lDL~~~Gl~iV~~~~~~~~~~lPL 80 (181)
T PF14877_consen 14 RAQEAANSVISKIFKINPNGKVKFIN---------PETNKLEESNLRDIAKGLDLSKHGLQIVNSEKDQKGRDLPL 80 (181)
T ss_pred HHHHHHHHHHHHHHhhCCCCeEEEEc---------CCCCcceeeeHHHHHHhCCccccceEEecccccCCCCcCce
Confidence 57888888999998877665444442 2222 22333333 44699999999887 6663
No 221
>cd05569 PTS_IIB_fructose PTS_IIB_fructose: subunit IIB of enzyme II (EII) of the fructose-specific phosphoenolpyruvate:carbohydrate phosphotransferase system (PTS). In this system, EII (also referred to as FruAB) is a fructose-specific permease made up of two proteins (FruA and FruB) each containing 3 domains. The FruA protein contains two tandem nonidentical IIB domains and a C-terminal IIC transmembrane domain. Both IIB domains of FruA are included in this alignment. The FruB protein (also referred to as diphosphoryl transfer protein) contains a IIA domain, a domain of unknown function, and an Hpr-like domain called FPr (fructose-inducible HPr). This familiy also includes the IIB domains of several fructose-like PTS permeases including the Frv permease encoded by the frvABXR operon, the Frw permease encoded by the frwACBD operon, the Frx permease encoded by the hrsA gene, and the Fry permease encoded by the fryABC (ypdDGH) operon. FruAB takes up exogenous fructose, releasing the 1-p
Probab=22.75 E-value=2.1e+02 Score=18.44 Aligned_cols=25 Identities=16% Similarity=0.376 Sum_probs=20.0
Q ss_pred HHHHHHHHHHHHHHcCCcEEEEEEee
Q 043606 24 AMLAAQDVSQRCKERGITALHIKLRA 49 (101)
Q Consensus 24 a~~a~~~~~~~~~~~gi~~v~V~lrg 49 (101)
+..+++.+-+.++++|+. +.|..++
T Consensus 14 s~laa~~L~~aa~~~g~~-~~ve~~~ 38 (96)
T cd05569 14 TYMAAEALEKAAKKLGWE-IKVETQG 38 (96)
T ss_pred HHHHHHHHHHHHHHCCCe-EEEEEec
Confidence 456778888999999998 7777754
No 222
>PRK06036 translation initiation factor IF-2B subunit alpha; Provisional
Probab=22.58 E-value=3e+02 Score=22.32 Aligned_cols=50 Identities=18% Similarity=0.246 Sum_probs=33.1
Q ss_pred HHHHHHHHHHHcCCcEEEEEEeecCCCcccCCCCChHHHHHHHHhCCCeEEEEEec
Q 043606 27 AAQDVSQRCKERGITALHIKLRATGGNKTKTPGPGAQSALRALARSGMKIGRIEDV 82 (101)
Q Consensus 27 a~~~~~~~~~~~gi~~v~V~lrg~~g~~~kG~G~gr~~~lr~l~~~gl~I~~I~D~ 82 (101)
++..++..+.+.|.+ ++|.+-- +.=.+.|..-.-..|.+.|+.++.|.|-
T Consensus 167 Tal~~l~~A~~~gk~-~~V~v~E-----tRP~~qG~rlta~eL~~~GI~vtlI~Ds 216 (339)
T PRK06036 167 TALGVIRSAVEQGKE-IKVIACE-----TRPLNQGSRLTTWELMQDNIPVTLITDS 216 (339)
T ss_pred hHHHHHHHHHHcCCc-eEEEEcC-----CCchhhHHHHHHHHHHHcCCCEEEEehh
Confidence 345577788777754 6666621 1334566554447788999999999984
No 223
>cd01075 NAD_bind_Leu_Phe_Val_DH NAD(P) binding domain of leucine dehydrogenase, phenylalanine dehydrogenase, and valine dehydrogenase. Amino acid dehydrogenase (DH) is a widely distributed family of enzymes that catalyzes the oxidative deamination of an amino acid to its keto acid and ammonia with concomitant reduction of NADP+. For example, leucine DH catalyzes the reversible oxidative deamination of L-leucine and several other straight or branched chain amino acids to the corresponding 2-oxoacid derivative. Amino acid DH -like NAD(P)-binding domains are members of the Rossmann fold superfamily and include glutamate, leucine, and phenylalanine DHs, methylene tetrahydrofolate DH, methylene-tetrahydromethanopterin DH, methylene-tetrahydropholate DH/cyclohydrolase, Shikimate DH-like proteins, malate oxidoreductases, and glutamyl tRNA reductase. Amino acid DHs catalyze the deamination of amino acids to keto acids with NAD(P)+ as a cofactor. The NAD(P)-binding Rossmann fold superfamily inc
Probab=22.48 E-value=2.1e+02 Score=20.77 Aligned_cols=55 Identities=15% Similarity=0.316 Sum_probs=31.4
Q ss_pred cHHHHHHHHHHHHHHH-HHcCCcEEEEEEeecCCCcccCCCC-ChHHHHHHHHhCCCeEEEEEecCC
Q 043606 20 SPYAAMLAAQDVSQRC-KERGITALHIKLRATGGNKTKTPGP-GAQSALRALARSGMKIGRIEDVTP 84 (101)
Q Consensus 20 t~~Aa~~a~~~~~~~~-~~~gi~~v~V~lrg~~g~~~kG~G~-gr~~~lr~l~~~gl~I~~I~D~Tp 84 (101)
|-|....+.+.+++.. -...++--.|-| -|+|. |+. +.+.|.+.|.+|+ +.|..+
T Consensus 5 Tg~Gv~~~~~~~~~~~~~~~~l~gk~v~I--------~G~G~vG~~-~A~~L~~~G~~Vv-v~D~~~ 61 (200)
T cd01075 5 TAYGVFLGMKAAAEHLLGTDSLEGKTVAV--------QGLGKVGYK-LAEHLLEEGAKLI-VADINE 61 (200)
T ss_pred hHHHHHHHHHHHHHHhcCCCCCCCCEEEE--------ECCCHHHHH-HHHHHHHCCCEEE-EEcCCH
Confidence 4444444444444443 122344456777 55663 554 4567888999998 777653
No 224
>cd03088 ManB ManB is a bacterial phosphomannomutase (PMM) that catalyzes the conversion of mannose 6-phosphate to mannose-1-phosphate in the second of three steps in the GDP-mannose pathway, in which GDP-D-mannose is synthesized from fructose-6-phosphate. In Mycobacterium tuberculosis, the causative agent of tuberculosis, PMM is involved in the biosynthesis of mannosylated lipoglycans that participate in the association of mycobacteria with host macrophage phagocytic receptors. ManB belongs to the the alpha-D-phosphohexomutase superfamily which includes several related enzymes that catalyze a reversible intramolecular phosphoryl transfer on their sugar substrates. Other members of this superfamily include the phosphoglucomutases (PGM1 and PGM2), phosphoglucosamine mutase (PNGM), phosphoacetylglucosamine mutase (PAGM), the bacterial phosphoglucosamine mutase GlmM, and the bifunctional phosphomannomutase/phosphoglucomutase (PMM/PGM). Each of these enzymes has four domains with a centrall
Probab=22.30 E-value=4e+02 Score=21.83 Aligned_cols=62 Identities=11% Similarity=0.142 Sum_probs=39.7
Q ss_pred CCcHHHHHHHHHHHHHHHHHc-CCcEEEEEEeecCCCcccCCC-CChHHHHHHHHhCCCeEEEEEecCCCC
Q 043606 18 ESSPYAAMLAAQDVSQRCKER-GITALHIKLRATGGNKTKTPG-PGAQSALRALARSGMKIGRIEDVTPIP 86 (101)
Q Consensus 18 k~t~~Aa~~a~~~~~~~~~~~-gi~~v~V~lrg~~g~~~kG~G-~gr~~~lr~l~~~gl~I~~I~D~Tpip 86 (101)
.-||.-+..+++.+++.+... +-..|.|---. +-.+ .=..++..+|...|++|..+ ..+|.|
T Consensus 13 ~ltpe~~~~l~~a~~~~l~~~~~~~~VvVG~D~------R~~s~~l~~a~~~gL~~~Gv~V~~~-g~~pTP 76 (459)
T cd03088 13 DLTDEVCYAYTRAFLQHLESKFPGDTVAVGRDL------RPSSPRIAAACAAALRDAGFRVVDC-GAVPTP 76 (459)
T ss_pred cCCHHHHHHHHHHHHHHHHHhCCCCeEEEEeCC------CcchHHHHHHHHHHHHHCCCEEEEe-CCCCCH
Confidence 468888888888778777542 22334443311 1111 12456777888999999988 688877
No 225
>cd00019 AP2Ec AP endonuclease family 2; These endonucleases play a role in DNA repair. Cleave phosphodiester bonds at apurinic or apyrimidinic sites; the alignment also contains hexulose-6-phosphate isomerases, enzymes that catalyze the epimerization of D-arabino-6-hexulose 3-phosphate to D-fructose 6-phosphate, via cleaving the phosphoesterbond with the sugar.
Probab=22.29 E-value=2.4e+02 Score=20.96 Aligned_cols=22 Identities=23% Similarity=0.368 Sum_probs=18.4
Q ss_pred HHHHHHHHHcCCcEEEEEEeec
Q 043606 29 QDVSQRCKERGITALHIKLRAT 50 (101)
Q Consensus 29 ~~~~~~~~~~gi~~v~V~lrg~ 50 (101)
+...+.++++|+..|+|.+...
T Consensus 13 ~~~l~~a~~~G~d~vEl~~~~~ 34 (279)
T cd00019 13 ENALKRAKEIGFDTVAMFLGNP 34 (279)
T ss_pred HHHHHHHHHcCCCEEEEEcCCC
Confidence 5678899999999999998543
No 226
>PF00765 Autoind_synth: Autoinducer synthetase; InterPro: IPR001690 Bacterial species have many methods of controlling gene expression and cell growth. Regulation of gene expression in response to changes in cell density is termed quorum sensing [, ]. Quorum-sensing bacteria produce, release and respond to hormone-like molecules (autoinducers) that accumulate in the external environment as the cell population grows. Once a threshold of these molecules is reached, a signal transduction cascade is triggered that ultimately leads to behavioural changes in the bacterium []. Autoinducers are thus clearly important mediators of molecular communication. Conjugal transfer of Agrobacterium octopine-type Ti plasmids is activated by octopine, a metabolite released from plant tumours []. Octopine causes conjugal donors to secrete a pheromone, Agrobacterium autoinducer (AAI), and exogenous AAI further stimulates conjugation. The putative AAI synthase and an AAI-responsive transcriptional regulator have been found to be encoded by the Ti plasmid traI and traR genes, respectively. TraR and TraI are similar to the LuxR and LuxI regulatory proteins of Vibrio fischeri, and AAI is similar in structure to the diffusable V. fischeri autoinducer, the inducing ligand of LuxR. TraR activates target genes in the presence of AAI and also activates traR and traI themselves, creating two positive-feedback loops. TraR-AAI-mediated activation in wild-type Agrobacterium strains is enhanced by culturing on solid media, suggesting a possible role in cell density sensing []. Production of light by the marine bacterium V. fischeri and by recombinant hosts containing cloned lux genes is controlled by the density of the culture []. Density-dependent regulation of lux gene expression has been shown to require a locus consisting of the luxR and luxI genes. In these and other Gram-negative bacteria, N-(3-oxohexanoyl)-L-homoserine lactone (OHHL) acts as the autoinducer by binding to transcriptional regulatory proteins and activating them []. OHHL and related molecules, such as N-butanoyl- (BHL), N-hexanoyl- (HHL) and N-oxododecanoyl- (PAI) homoserine lactones, are produced by a family of proteins that share a high level of sequence similarity. Proteins which currently members of this family include: luxI from V. fischeri. ahyI and asaI from Aeromonas species, which synthesize BHL and whose targets are ahyR and asaR respectively. carI from Erwinia carotovora. The target of OHHL is carR which activates genes involved in the biosynthesis of carbapenem antibiotics. eagI from Enterobacter agglomerans. The target of OHHL is not yet known. esaI from Erwinia stewartii. expI from Erwinia carotovora. lasI from Pseudomonas aeruginosa, which synthesizes PAI and whose target is lasR which activates the transcription of the elastase gene. rhlI (or vsmI) from P. aeruginosa, which synthesizes BHL and HHL and whose target is rhlR. swrI from Serratia liquefaciens, which synthesizes BHL. yenI from Yersinia enterocolitica. ; GO: 0007165 signal transduction; PDB: 3P2H_A 3P2F_A 1KZF_A 1K4J_A 1RO5_A.
Probab=22.21 E-value=3.1e+02 Score=19.85 Aligned_cols=45 Identities=18% Similarity=0.192 Sum_probs=33.4
Q ss_pred HHHHHHHHHHHHHHHcCCcEEEEEEeecCCCcccCCCCChHHHHHHHHhCCCeEEEEEe
Q 043606 23 AAMLAAQDVSQRCKERGITALHIKLRATGGNKTKTPGPGAQSALRALARSGMKIGRIED 81 (101)
Q Consensus 23 Aa~~a~~~~~~~~~~~gi~~v~V~lrg~~g~~~kG~G~gr~~~lr~l~~~gl~I~~I~D 81 (101)
++......+.+.|.+.|++.+...+. ....+.|.+.|+.+..|-.
T Consensus 113 ~~~~L~~~~~e~a~~~gi~~~v~V~~--------------~~~~r~l~r~G~~~~~lG~ 157 (182)
T PF00765_consen 113 VTMELLLGMVEFALSNGIRHIVGVVD--------------PAMERILRRAGWPVRRLGP 157 (182)
T ss_dssp HHHHHHHHHHHHHHCTT-SEEEEEEE--------------HHHHHHHHHCT-EEEESSE
T ss_pred HHHHHHHHHHHHHHHCCCCEEEEEEC--------------hHHHHHHHHcCCceEECCC
Confidence 44445556899999999999998882 3478889999999887655
No 227
>PRK13497 chemoreceptor glutamine deamidase CheD; Provisional
Probab=22.18 E-value=1.8e+02 Score=21.56 Aligned_cols=57 Identities=18% Similarity=0.242 Sum_probs=38.7
Q ss_pred cHHHHHHHHHHHHHHHHHcCCcE--EEEEEeecCCCccc---CCC-CChHHHHHHHHhCCCeEEE
Q 043606 20 SPYAAMLAAQDVSQRCKERGITA--LHIKLRATGGNKTK---TPG-PGAQSALRALARSGMKIGR 78 (101)
Q Consensus 20 t~~Aa~~a~~~~~~~~~~~gi~~--v~V~lrg~~g~~~k---G~G-~gr~~~lr~l~~~gl~I~~ 78 (101)
.-||-. |.+.+++.+.++|... +.++|-| |++-+. .+| .+-++|.+.|.+.||+|..
T Consensus 68 ~rY~d~-ai~~Li~~m~~~Ga~~~~l~aKifG-GA~m~~~~~~IG~rNi~~a~~~L~~~gI~i~a 130 (184)
T PRK13497 68 TRYGVH-LMELLINGLLKQGARRDRLEAKIFG-GAKTIATFSNVGEQNAAFAMQFLRDEGIPVVG 130 (184)
T ss_pred cchHHH-HHHHHHHHHHHcCCCHHHEEEEEEe-CchhccccccHHHHHHHHHHHHHHHcCCcEEE
Confidence 446544 6688999999998764 6777755 444332 233 2456788889999999875
No 228
>PF11547 E3_UbLigase_EDD: E3 ubiquitin ligase EDD; InterPro: IPR024725 EDD, the ER ubiquitin ligase from the HECT ligases, contains an N-terminal ubiquitin-associated (UBA) domain which binds ubiquitin. Ubiquitin is recognised by helices alpha-1 and -3 in in the UBA domain. EDD is involved in DNA damage repair pathways and binds to mono-ubiquitinated proteins [].; GO: 0043130 ubiquitin binding; PDB: 2QHO_H.
Probab=22.17 E-value=69 Score=19.36 Aligned_cols=19 Identities=21% Similarity=0.506 Sum_probs=14.8
Q ss_pred CCCChHHHHHHHHhCCCeE
Q 043606 58 PGPGAQSALRALARSGMKI 76 (101)
Q Consensus 58 ~G~gr~~~lr~l~~~gl~I 76 (101)
.|.-|+.++|-|++.++.+
T Consensus 21 qgksR~vIirELqrTnLdV 39 (53)
T PF11547_consen 21 QGKSRNVIIRELQRTNLDV 39 (53)
T ss_dssp TTS-HHHHHHHHHHTTT-H
T ss_pred cCCcHHHHHHHHHHhcccH
Confidence 4788999999999988764
No 229
>PF09338 Gly_reductase: Glycine/sarcosine/betaine reductase component B subunits; InterPro: IPR015417 This is a family of glycine reductase, sarcosine reductase and betaine reductases. These enzymes catalyse the following reactions: sarcosine reductase: Acetyl phosphate + methylamine + thioredoxin disulphide = N-methylglycine + phosphate + thioredoxin. glycine reductase: Acetyl phosphate + NH3 + thioredoxin disulphide = glycine + phosphate + thioredoxin. betaine reductase: Acetyl phosphate + trimethylamine + thioredoxin disulphide = N,N,N-trimethylglycine + phosphate + thioredoxin. ; GO: 0050485 oxidoreductase activity, acting on X-H and Y-H to form an X-Y bond, with a disulfide as acceptor, 0055114 oxidation-reduction process
Probab=22.16 E-value=4.1e+02 Score=22.46 Aligned_cols=49 Identities=14% Similarity=0.184 Sum_probs=36.4
Q ss_pred HHHHHHHHHHHHcCCcEEEEEEeecCCCcccCCCC-ChH--HHHHHHHhCCCeEEEEEec
Q 043606 26 LAAQDVSQRCKERGITALHIKLRATGGNKTKTPGP-GAQ--SALRALARSGMKIGRIEDV 82 (101)
Q Consensus 26 ~a~~~~~~~~~~~gi~~v~V~lrg~~g~~~kG~G~-gr~--~~lr~l~~~gl~I~~I~D~ 82 (101)
..++.+++-|+.||..-+.|.- -|+|- --+ ..++.|...|++.+-|+|.
T Consensus 290 r~s~~~~~la~~LgaDGaIvs~--------eG~GN~d~D~~~~~~~~e~~GIktV~it~e 341 (428)
T PF09338_consen 290 RVSQRAAKLAEMLGADGAIVSE--------EGFGNPDVDFAMNIEEIEKRGIKTVGITDE 341 (428)
T ss_pred HHHHHHHHHHHHhCCCEEEEEe--------cCCCchhHHHHHHHHHHHHCCCCEEEecce
Confidence 3445566677889999999999 66773 222 3567788899999999873
No 230
>COG0630 VirB11 Type IV secretory pathway, VirB11 components, and related ATPases involved in archaeal flagella biosynthesis [Cell motility and secretion / Intracellular trafficking and secretion]
Probab=22.09 E-value=2e+02 Score=22.63 Aligned_cols=30 Identities=27% Similarity=0.299 Sum_probs=25.8
Q ss_pred cCCCCChHHHHHHHHhC---CCeEEEEEecCCC
Q 043606 56 KTPGPGAQSALRALARS---GMKIGRIEDVTPI 85 (101)
Q Consensus 56 kG~G~gr~~~lr~l~~~---gl~I~~I~D~Tpi 85 (101)
-+.|.|+.+.|.+|... ..+|+.|+|...+
T Consensus 150 G~t~sGKTt~lnall~~Ip~~~rivtIEdt~E~ 182 (312)
T COG0630 150 GGTASGKTTLLNALLDFIPPEERIVTIEDTPEL 182 (312)
T ss_pred CCCCCCHHHHHHHHHHhCCchhcEEEEeccccc
Confidence 46899999999998763 7899999999877
No 231
>PRK15414 phosphomannomutase CpsG; Provisional
Probab=22.09 E-value=2.2e+02 Score=23.39 Aligned_cols=60 Identities=10% Similarity=0.060 Sum_probs=39.3
Q ss_pred CCcHHHHHHHHHHHHHHHHHcCCcEEEEEEeecCCCcccCCCCChHHHHHHHHhCCCeEEEEEecCCCC
Q 043606 18 ESSPYAAMLAAQDVSQRCKERGITALHIKLRATGGNKTKTPGPGAQSALRALARSGMKIGRIEDVTPIP 86 (101)
Q Consensus 18 k~t~~Aa~~a~~~~~~~~~~~gi~~v~V~lrg~~g~~~kG~G~gr~~~lr~l~~~gl~I~~I~D~Tpip 86 (101)
.-||.-+..++..++..+.+ ..|.|---. +..+. .=..++..+|...|++|..+ +.+|.|
T Consensus 19 ~lt~~~~~~~~~a~a~~l~~---~~VvVg~D~----R~ss~-~l~~a~a~gL~s~Gi~V~~~-g~~pTP 78 (456)
T PRK15414 19 ELNEDIAWRIGRAYGEFLKP---KTIVLGGDV----RLTSE-TLKLALAKGLQDAGVDVLDI-GMSGTE 78 (456)
T ss_pred CcCHHHHHHHHHHHHHHhcC---CeEEEEECC----CCChH-HHHHHHHHHHHHCCCeEEEe-CCcChH
Confidence 36888888888877776642 234443211 11111 23566778889999999999 788888
No 232
>PRK10427 putative PTS system fructose-like transporter subunit EIIB; Provisional
Probab=22.02 E-value=1.9e+02 Score=19.62 Aligned_cols=27 Identities=15% Similarity=0.315 Sum_probs=21.3
Q ss_pred HHHHHHHHHHHHHHHcCCcEEEEEEeec
Q 043606 23 AAMLAAQDVSQRCKERGITALHIKLRAT 50 (101)
Q Consensus 23 Aa~~a~~~~~~~~~~~gi~~v~V~lrg~ 50 (101)
.+..|++.+.+.++++|+. +.|..+|.
T Consensus 17 ht~lAAeaL~kAA~~~G~~-i~VE~qg~ 43 (114)
T PRK10427 17 HTYMAAERLEKLCQLEKWG-VKIETQGA 43 (114)
T ss_pred HHHHHHHHHHHHHHHCCCe-EEEEecCC
Confidence 4567888888888999987 88888653
No 233
>cd02022 DPCK Dephospho-coenzyme A kinase (DPCK, EC 2.7.1.24) catalyzes the phosphorylation of dephosphocoenzyme A (dCoA) to yield CoA, which is the final step in CoA biosynthesis.
Probab=21.96 E-value=86 Score=22.02 Aligned_cols=28 Identities=14% Similarity=0.303 Sum_probs=22.9
Q ss_pred cCCCCChHHHHHHHHhCCCeEEEEEecC
Q 043606 56 KTPGPGAQSALRALARSGMKIGRIEDVT 83 (101)
Q Consensus 56 kG~G~gr~~~lr~l~~~gl~I~~I~D~T 83 (101)
-++|.|+.++.+.|.+.|+.+.+.-++.
T Consensus 6 G~~gsGKst~~~~l~~~g~~~i~~D~~~ 33 (179)
T cd02022 6 GGIGSGKSTVAKLLKELGIPVIDADKIA 33 (179)
T ss_pred CCCCCCHHHHHHHHHHCCCCEEecCHHH
Confidence 3699999999999999898887765543
No 234
>cd08192 Fe-ADH7 Iron-containing alcohol dehydrogenases-like, involved in the linear alkylbenzenesulfonate (LAS) degradation pathway. NAD-dependent iron-containing alcohol dehydrogenase-like. Proteins in this family are NAD-dependent alcohol dehydrogenases which are involved in the linear alkylbenzenesulfonate (LAS) degradation pathway. They catalyze the oxidation of beta-hydroxy CoA ester to beta-oxo CoA ester, which then be subject to CoA-dependent thiolysis to yield acetyl-CoA and 6-C8-SPC-CoA. The major laundry surfactant in worldwide use is commercial linear alkylbenzenesulfonate (LAS) which contains 20 congeners of linear alkanes (C10 to C13). LAS is fully biodegradable in oxic environments. Degradation involves microbial communities. Parvibaculum lavamentivorans DS-1T is a representative member of many heterotrophic, LAS-degrading communities, in which it catalyzes the first steps of LAS degradation. Strain DS-1T is a small heterotrophic bacterium able to omega-oxygenate the comm
Probab=21.95 E-value=3.8e+02 Score=21.14 Aligned_cols=54 Identities=22% Similarity=0.368 Sum_probs=33.2
Q ss_pred HHHHHHHHHHcCCcEEEEEEeecCCCcccCCCCChHHHHHHHHhCCCeEEEEEecCCCC
Q 043606 28 AQDVSQRCKERGITALHIKLRATGGNKTKTPGPGAQSALRALARSGMKIGRIEDVTPIP 86 (101)
Q Consensus 28 ~~~~~~~~~~~gi~~v~V~lrg~~g~~~kG~G~gr~~~lr~l~~~gl~I~~I~D~Tpip 86 (101)
.+.+.+.+.++|.+.+-|.. + ....-.|. -+-+...|...|+.+..+.++.|-|
T Consensus 12 ~~~l~~~l~~~g~~~~liv~-~---~~~~~~~~-~~~v~~~L~~~g~~~~~~~~v~~~p 65 (370)
T cd08192 12 IKELPAECAELGIKRPLIVT-D---PGLAALGL-VARVLALLEDAGLAAALFDEVPPNP 65 (370)
T ss_pred HHHHHHHHHHcCCCeEEEEc-C---cchhhCcc-HHHHHHHHHHcCCeEEEeCCCCCCC
Confidence 34567778888887766654 1 11122233 3346778888899887666665544
No 235
>PF05673 DUF815: Protein of unknown function (DUF815); InterPro: IPR008533 This domain consists of several bacterial proteins of unknown function.
Probab=21.70 E-value=3e+02 Score=21.53 Aligned_cols=36 Identities=25% Similarity=0.497 Sum_probs=28.6
Q ss_pred cCCcEEEEEEeecCCCcccCCCCChHHHHHHHHh----CCCeEEEEE
Q 043606 38 RGITALHIKLRATGGNKTKTPGPGAQSALRALAR----SGMKIGRIE 80 (101)
Q Consensus 38 ~gi~~v~V~lrg~~g~~~kG~G~gr~~~lr~l~~----~gl~I~~I~ 80 (101)
.|....+|.|-|+ -|.|+.+.+|+|.. .|+.++.|.
T Consensus 48 ~G~pannvLL~G~-------rGtGKSSlVkall~~y~~~GLRlIev~ 87 (249)
T PF05673_consen 48 QGLPANNVLLWGA-------RGTGKSSLVKALLNEYADQGLRLIEVS 87 (249)
T ss_pred cCCCCcceEEecC-------CCCCHHHHHHHHHHHHhhcCceEEEEC
Confidence 5889999999664 57888999999854 588888774
No 236
>COG1964 Predicted Fe-S oxidoreductases [General function prediction only]
Probab=21.56 E-value=2e+02 Score=24.74 Aligned_cols=50 Identities=14% Similarity=0.259 Sum_probs=36.3
Q ss_pred HHHHHHHHcCCcEEEEEEeecCCCcccCCCCCh-HHHHHHHHhCCCeEEE--EEecCCCCC
Q 043606 30 DVSQRCKERGITALHIKLRATGGNKTKTPGPGA-QSALRALARSGMKIGR--IEDVTPIPT 87 (101)
Q Consensus 30 ~~~~~~~~~gi~~v~V~lrg~~g~~~kG~G~gr-~~~lr~l~~~gl~I~~--I~D~Tpiph 87 (101)
.+++.|.+.|+++|.+-. +|+-.++ ....+.|..+|+..+. -.++||-||
T Consensus 129 eiv~~a~e~g~~hVqinT--------nGirlA~~~~~~~~l~~ag~~tvYlsFDG~~e~~~ 181 (475)
T COG1964 129 EIIKIAREEGYDHVQLNT--------NGIRLAFDPEYVKKLREAGVNTVYLSFDGVTPKTN 181 (475)
T ss_pred HHHHHHhhcCccEEEEcc--------CceeeccCHHHHHHHHhcCCcEEEEecCCCCCCch
Confidence 367888999999999998 5565555 3355889999977664 446666554
No 237
>PRK07449 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase; Validated
Probab=21.53 E-value=3.1e+02 Score=22.85 Aligned_cols=49 Identities=16% Similarity=0.124 Sum_probs=36.6
Q ss_pred HHHHHHHHHHHHHHcCCcEEEEEEeecCCCcccCCCCChHHHHHHHHh-CCCeEEEEEecC
Q 043606 24 AMLAAQDVSQRCKERGITALHIKLRATGGNKTKTPGPGAQSALRALAR-SGMKIGRIEDVT 83 (101)
Q Consensus 24 a~~a~~~~~~~~~~~gi~~v~V~lrg~~g~~~kG~G~gr~~~lr~l~~-~gl~I~~I~D~T 83 (101)
.+.+++.+++.++++|++.|-..- |-.-...+.+|.. .+++.+...|..
T Consensus 8 ~~~~a~~l~~~L~~~GV~~vFgvp-----------G~~~~~l~~~l~~~~~i~~v~~~hE~ 57 (568)
T PRK07449 8 NTLWAAVILEELTRLGVRHVVIAP-----------GSRSTPLTLAAAEHPRLRLHTHFDER 57 (568)
T ss_pred HHHHHHHHHHHHHHcCCCEEEECC-----------CCccHHHHHHHHhCCCcEEEeecCcc
Confidence 377889999999999999765543 6656678888855 478887766643
No 238
>PRK06546 pyruvate dehydrogenase; Provisional
Probab=21.44 E-value=1.8e+02 Score=24.55 Aligned_cols=47 Identities=13% Similarity=0.204 Sum_probs=35.6
Q ss_pred HHHHHHHHHHHHHcCCcEEEEEEeecCCCcccCCCCChHHHHHHHHhC-CCeEEEEEec
Q 043606 25 MLAAQDVSQRCKERGITALHIKLRATGGNKTKTPGPGAQSALRALARS-GMKIGRIEDV 82 (101)
Q Consensus 25 ~~a~~~~~~~~~~~gi~~v~V~lrg~~g~~~kG~G~gr~~~lr~l~~~-gl~I~~I~D~ 82 (101)
..+++.+++.+.++|++.|--. +|-.-...+.+|.++ +++.+...+.
T Consensus 3 ~t~~~~l~~~L~~~GV~~vFg~-----------pG~~~~~l~dal~~~~~i~~i~~rhE 50 (578)
T PRK06546 3 KTVAEQLVEQLVAAGVKRIYGI-----------VGDSLNPIVDAVRRTGGIEWVHVRHE 50 (578)
T ss_pred ccHHHHHHHHHHHcCCCEEEEC-----------CCCchHHHHHHHhccCCCeEEEeCcH
Confidence 4567889999999999976544 477677899999776 7777766543
No 239
>PRK12677 xylose isomerase; Provisional
Probab=21.43 E-value=3.4e+02 Score=22.06 Aligned_cols=47 Identities=13% Similarity=0.165 Sum_probs=31.2
Q ss_pred HHHHHHHHHcCCcEEEEEEeecCCCcccCCCCC-------hHHHHHHHHhCCCeEEEEE
Q 043606 29 QDVSQRCKERGITALHIKLRATGGNKTKTPGPG-------AQSALRALARSGMKIGRIE 80 (101)
Q Consensus 29 ~~~~~~~~~~gi~~v~V~lrg~~g~~~kG~G~g-------r~~~lr~l~~~gl~I~~I~ 80 (101)
+.+++++.++|+..|+++.... --++.- .+-+.+.|...||+|..|.
T Consensus 34 ~E~v~~~a~~Gf~gVElh~~~l-----~p~~~~~~~~~~~~~~lk~~l~~~GL~v~~v~ 87 (384)
T PRK12677 34 VEAVHKLAELGAYGVTFHDDDL-----VPFGATDAERDRIIKRFKKALDETGLVVPMVT 87 (384)
T ss_pred HHHHHHHHHhCCCEEEeccccc-----CCCCCChhhhHHHHHHHHHHHHHcCCeeEEEe
Confidence 4578899999999999985110 112221 2345556778899999886
No 240
>COG2518 Pcm Protein-L-isoaspartate carboxylmethyltransferase [Posttranslational modification, protein turnover, chaperones]
Probab=21.42 E-value=3.7e+02 Score=20.40 Aligned_cols=46 Identities=15% Similarity=0.208 Sum_probs=31.6
Q ss_pred HHHHHHHHcCCcEEEEEEeecCCCcccCCCCCh---------------HHHHHHHHhCCCeEEEE
Q 043606 30 DVSQRCKERGITALHIKLRATGGNKTKTPGPGA---------------QSALRALARSGMKIGRI 79 (101)
Q Consensus 30 ~~~~~~~~~gi~~v~V~lrg~~g~~~kG~G~gr---------------~~~lr~l~~~gl~I~~I 79 (101)
.+-+.+..+|+..|+|.. |++++|+-... ++.+..|+..|.-|.-|
T Consensus 109 ~A~~~L~~lg~~nV~v~~----gDG~~G~~~~aPyD~I~Vtaaa~~vP~~Ll~QL~~gGrlv~Pv 169 (209)
T COG2518 109 QARRNLETLGYENVTVRH----GDGSKGWPEEAPYDRIIVTAAAPEVPEALLDQLKPGGRLVIPV 169 (209)
T ss_pred HHHHHHHHcCCCceEEEE----CCcccCCCCCCCcCEEEEeeccCCCCHHHHHhcccCCEEEEEE
Confidence 334446779998898888 77888866544 56677777766555444
No 241
>COG1109 {ManB} Phosphomannomutase [Carbohydrate transport and metabolism]
Probab=21.40 E-value=3.7e+02 Score=22.13 Aligned_cols=63 Identities=14% Similarity=0.260 Sum_probs=44.1
Q ss_pred CCcHHHHHHHHHHHHHHHHHcCCcEEEEEEeecCCCcccCCCCChHHHHHHHHhCCCeEEEEEecCCCC
Q 043606 18 ESSPYAAMLAAQDVSQRCKERGITALHIKLRATGGNKTKTPGPGAQSALRALARSGMKIGRIEDVTPIP 86 (101)
Q Consensus 18 k~t~~Aa~~a~~~~~~~~~~~gi~~v~V~lrg~~g~~~kG~G~gr~~~lr~l~~~gl~I~~I~D~Tpip 86 (101)
.-||+-+..++..+++.+.+.+-..|.|---. +..+. .-..++..+|...|+++..+- .+|.|
T Consensus 22 ~lt~~~~~~~g~a~~~~l~~~~~~~VvVG~D~----R~ss~-~~~~a~~~gl~~~G~~v~~~g-~~pTP 84 (464)
T COG1109 22 ELTPEFALKLGRALGSVLRKKGAPKVVVGRDT----RLSSE-MLAAALAAGLTSAGIDVYDLG-LVPTP 84 (464)
T ss_pred CcCHHHHHHHHHHHHHHHhhcCCCeEEEEecC----CCCHH-HHHHHHHHHHHHCCCeEEEeC-CCCCH
Confidence 78999999999999999887222345544321 12221 235567788999999999999 77776
No 242
>TIGR00216 ispH_lytB (E)-4-hydroxy-3-methyl-but-2-enyl pyrophosphate reductase (IPP and DMAPP forming). Escherichia coli LytB protein had been found to regulate the activity of RelA (guanosine 3',5'-bispyrophosphate synthetase I), which in turn controls the level of a regulatory metabolite. It is involved in penicillin tolerance and the stringent response.
Probab=21.36 E-value=3.4e+02 Score=21.42 Aligned_cols=38 Identities=26% Similarity=0.477 Sum_probs=23.1
Q ss_pred HHHHHHHcCCcEE-----------EEEEeecCCCcccCCCCChHHHHHHHHhCCCeEE
Q 043606 31 VSQRCKERGITAL-----------HIKLRATGGNKTKTPGPGAQSALRALARSGMKIG 77 (101)
Q Consensus 31 ~~~~~~~~gi~~v-----------~V~lrg~~g~~~kG~G~gr~~~lr~l~~~gl~I~ 77 (101)
+.+.+.++|+..+ .|.||+ +|..+ .....|.+.|++|+
T Consensus 44 Vv~~L~~~Gv~~~v~~~~~v~~~~~ViirA------HGv~~---~~~~~~~~~gl~vi 92 (280)
T TIGR00216 44 VVERLRERGVFFFLEDLDEVAAGDTVIIRA------HGVPP---EVREELEKKGLEVI 92 (280)
T ss_pred HHHHHHHCCCEEeecCcccCCCCCEEEEeC------CCCCH---HHHHHHHHCCCeEE
Confidence 4556677886222 367765 66655 45566777777754
No 243
>PRK01259 ribose-phosphate pyrophosphokinase; Provisional
Probab=21.30 E-value=4e+02 Score=20.96 Aligned_cols=51 Identities=18% Similarity=0.231 Sum_probs=39.4
Q ss_pred HHHHHHHHHcCCcEEEEEEeecCCCcccCCCCChHHHHHHHHhCCCeEEEEEecCCCCCC
Q 043606 29 QDVSQRCKERGITALHIKLRATGGNKTKTPGPGAQSALRALARSGMKIGRIEDVTPIPTD 88 (101)
Q Consensus 29 ~~~~~~~~~~gi~~v~V~lrg~~g~~~kG~G~gr~~~lr~l~~~gl~I~~I~D~TpiphN 88 (101)
..+++.+++.|-+.|.+..- +|+-.+ -++..|..+++.-+..+|.-|.|.+
T Consensus 225 ~~a~~~l~~~Ga~~v~~~~t-------H~i~~~--~a~~~l~~~~~~~iv~t~ti~~~~~ 275 (309)
T PRK01259 225 CKAAEALKERGAKSVYAYAT-------HPVLSG--GAIERIENSVIDELVVTDSIPLSEE 275 (309)
T ss_pred HHHHHHHHccCCCEEEEEEE-------eeeCCh--HHHHHHhcCCCCEEEEecCcccchh
Confidence 45678889999999998872 454433 4667788889999999999888866
No 244
>COG5628 Predicted acetyltransferase [General function prediction only]
Probab=21.25 E-value=91 Score=22.42 Aligned_cols=31 Identities=16% Similarity=0.315 Sum_probs=21.9
Q ss_pred ccCCCCChHHHHHHHHhC--CCeEEEEEecCCC
Q 043606 55 TKTPGPGAQSALRALARS--GMKIGRIEDVTPI 85 (101)
Q Consensus 55 ~kG~G~gr~~~lr~l~~~--gl~I~~I~D~Tpi 85 (101)
.++-|.||++|=+.+... -..|..|.+.+|.
T Consensus 77 ~~~~GvGR~aaK~If~~~~g~w~Va~i~EN~PA 109 (143)
T COG5628 77 HRRRGVGRAAAKAIFGSAWGVWQVATVRENTPA 109 (143)
T ss_pred hhccchhHHHHHHHHHHhhceEEEEEeccCChh
Confidence 478899998886655543 3677777777773
No 245
>PF01713 Smr: Smr domain; InterPro: IPR002625 This family includes the Smr (Small MutS Related) proteins, and the C-terminal region of the MutS2 protein. It has been suggested that this domain interacts with the MutS1 (P23909 from SWISSPROT) protein in the case of Smr proteins and with the N-terminal MutS related region of MutS2, P94545 from SWISSPROT [].; PDB: 3QD7_X 2D9I_A 3FAU_A 2VKC_A 2ZQE_A.
Probab=20.97 E-value=2.1e+02 Score=17.44 Aligned_cols=65 Identities=23% Similarity=0.271 Sum_probs=37.0
Q ss_pred HHHHHHHHHHHHHHHHHcCCcEEEEEEeecCCCcccCCCCChHHHHHHHHh--CCCeEEEEEecCCCCCC
Q 043606 21 PYAAMLAAQDVSQRCKERGITALHIKLRATGGNKTKTPGPGAQSALRALAR--SGMKIGRIEDVTPIPTD 88 (101)
Q Consensus 21 ~~Aa~~a~~~~~~~~~~~gi~~v~V~lrg~~g~~~kG~G~gr~~~lr~l~~--~gl~I~~I~D~TpiphN 88 (101)
.--|..+.+..++.+.+.+++.+.|.- |.| +-+. -|.=+..+.+.|.+ .--.|..+.+..|-+.|
T Consensus 8 ~~eA~~~l~~~l~~~~~~~~~~~~II~-G~G-~hS~-~g~Lk~~V~~~L~~~~~~~~v~~~~~~~~~~g~ 74 (83)
T PF01713_consen 8 VEEALRALEEFLDEARQRGIRELRIIT-GKG-NHSK-GGVLKRAVRRWLEEGYQYEEVLAYRDAEPEDGN 74 (83)
T ss_dssp HHHHHHHHHHHHHHHHHTTHSEEEEE---ST-CTCC-TSHHHHHHHHHHHHTHCCTTEEEEEE--CCCTG
T ss_pred HHHHHHHHHHHHHHHHHcCCCEEEEEe-ccC-CCCC-CCcHHHHHHHHHHhhhccchhheeeecCCCCCC
Confidence 345666777888899999999999765 321 1110 12225556666654 12456677777666655
No 246
>PRK01184 hypothetical protein; Provisional
Probab=20.90 E-value=1.7e+02 Score=20.26 Aligned_cols=27 Identities=22% Similarity=0.361 Sum_probs=21.2
Q ss_pred cCCCCChHHHHHHHHhCCCeEEEEEec
Q 043606 56 KTPGPGAQSALRALARSGMKIGRIEDV 82 (101)
Q Consensus 56 kG~G~gr~~~lr~l~~~gl~I~~I~D~ 82 (101)
-++|.|+.++-+.++..|+.+.+.-|+
T Consensus 8 G~~GsGKsT~a~~~~~~g~~~i~~~d~ 34 (184)
T PRK01184 8 GMPGSGKGEFSKIAREMGIPVVVMGDV 34 (184)
T ss_pred CCCCCCHHHHHHHHHHcCCcEEEhhHH
Confidence 358999999878777789888887554
No 247
>PF02789 Peptidase_M17_N: Cytosol aminopeptidase family, N-terminal domain; InterPro: IPR008283 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Metalloproteases are the most diverse of the four main types of protease, with more than 50 families identified to date. In these enzymes, a divalent cation, usually zinc, activates the water molecule. The metal ion is held in place by amino acid ligands, usually three in number. The known metal ligands are His, Glu, Asp or Lys and at least one other residue is required for catalysis, which may play an electrophillic role. Of the known metalloproteases, around half contain an HEXXH motif, which has been shown in crystallographic studies to form part of the metal-binding site []. The HEXXH motif is relatively common, but can be more stringently defined for metalloproteases as 'abXHEbbHbc', where 'a' is most often valine or threonine and forms part of the S1' subsite in thermolysin and neprilysin, 'b' is an uncharged residue, and 'c' a hydrophobic residue. Proline is never found in this site, possibly because it would break the helical structure adopted by this motif in metalloproteases []. This group of metallopeptidases belong to the MEROPS peptidase family M17 (leucyl aminopeptidase family, clan MF), the type example being leucyl aminopeptidase from Bos taurus (Bovine). Aminopeptidases are exopeptidases involved in the processing and regular turnover of intracellular proteins, although their precise role in cellular metabolism is unclear [, ]. Leucine aminopeptidases cleave leucine residues from the N-terminal of polypeptide chains, but substantial rates are evident for all amino acids []. The enzymes exist as homo-hexamers, comprising 2 trimers stacked on top of one another []. Each monomer binds 2 zinc ions and folds into 2 alpha/beta-type quasi-spherical globular domains, producing a comma-like shape []. The N-terminal 150 residues form a 5-stranded beta-sheet with 4 parallel and 1 anti-parallel strand sandwiched between 4 alpha-helices []. An alpha-helix extends into the C-terminal domain, which comprises a central 8-stranded saddle-shaped beta-sheet sandwiched between groups of helices, forming the monomer hydrophobic core []. A 3-stranded beta-sheet resides on the surface of the monomer, where it interacts with other members of the hexamer []. The two zinc ions and the active site are entirely located in the C-terminal catalytic domain [].; GO: 0004177 aminopeptidase activity, 0006508 proteolysis, 0005622 intracellular; PDB: 3PEI_A 1GYT_C 3JRU_A 3H8F_D 3H8G_F 3H8E_A 3KZW_L 1LAP_A 1LAN_A 1LCP_B ....
Probab=20.73 E-value=2.2e+02 Score=18.24 Aligned_cols=30 Identities=13% Similarity=0.138 Sum_probs=26.3
Q ss_pred CCcHHHHHHHHHHHHHHHHHcCCcEEEEEE
Q 043606 18 ESSPYAAMLAAQDVSQRCKERGITALHIKL 47 (101)
Q Consensus 18 k~t~~Aa~~a~~~~~~~~~~~gi~~v~V~l 47 (101)
+-++-....++-.+++.+.+.+++.+.|.+
T Consensus 65 ~~~~~~~r~a~~~~~~~l~~~~~~~v~i~l 94 (126)
T PF02789_consen 65 KLTAESLRKAGAAAARALKKLKVKSVAIDL 94 (126)
T ss_dssp GBCHHHHHHHHHHHHHHHHHTT-SEEEEEG
T ss_pred cCCHHHHHHHHHHHHHHHhhCCceEEEEeC
Confidence 568888899998999999999999999998
No 248
>PHA02588 cd deoxycytidylate deaminase; Provisional
Probab=20.67 E-value=3.3e+02 Score=19.56 Aligned_cols=41 Identities=20% Similarity=0.184 Sum_probs=25.7
Q ss_pred HHHHHHcCCcEEEEEEeecCCCcccCCCCChHHHHHHHHhCCCeEEEEEe
Q 043606 32 SQRCKERGITALHIKLRATGGNKTKTPGPGAQSALRALARSGMKIGRIED 81 (101)
Q Consensus 32 ~~~~~~~gi~~v~V~lrg~~g~~~kG~G~gr~~~lr~l~~~gl~I~~I~D 81 (101)
+..+.+.||+.|.+-- . ....-...+..|.++|++|..+.+
T Consensus 115 a~aI~~~gI~rVvy~~--------~-~~~~~~~~~~~L~~~Gi~v~~~~~ 155 (168)
T PHA02588 115 AKAIAQSGIKKLVYCE--------K-YDRNGPGWDDILRKSGIEVIQIPK 155 (168)
T ss_pred HHHHHHhCCCEEEEee--------c-cCCCcHHHHHHHHHCCCEEEEeCH
Confidence 3344567888876554 1 222223357888999999887644
No 249
>PRK14737 gmk guanylate kinase; Provisional
Probab=20.66 E-value=1.9e+02 Score=20.74 Aligned_cols=30 Identities=23% Similarity=0.288 Sum_probs=19.6
Q ss_pred CCCChHHHHHHHHhCCCe-EEEEEecCCCCC
Q 043606 58 PGPGAQSALRALARSGMK-IGRIEDVTPIPT 87 (101)
Q Consensus 58 ~G~gr~~~lr~l~~~gl~-I~~I~D~Tpiph 87 (101)
.|.|+.++++.|.+..-. ..+|..+|.-|-
T Consensus 13 sG~GK~tl~~~l~~~~~~~~~~v~~TTR~~r 43 (186)
T PRK14737 13 AGGGKSTIIQALLEEHPDFLFSISCTTRAPR 43 (186)
T ss_pred CCCCHHHHHHHHHhcCCccccccCccCCCCC
Confidence 689999999999775322 234455554443
No 250
>PF08903 DUF1846: Domain of unknown function (DUF1846); InterPro: IPR014999 This group of proteins are functionally uncharacterised. ; PDB: 3BH1_B.
Probab=20.64 E-value=1.5e+02 Score=25.46 Aligned_cols=25 Identities=20% Similarity=0.329 Sum_probs=18.2
Q ss_pred cHHHHHHHHHHHHHHHHHcCCcEEE
Q 043606 20 SPYAAMLAAQDVSQRCKERGITALH 44 (101)
Q Consensus 20 t~~Aa~~a~~~~~~~~~~~gi~~v~ 44 (101)
|.|..|-+|+.+.+++..+||+.-.
T Consensus 113 T~y~~q~~a~~F~~kLe~~gIkvy~ 137 (491)
T PF08903_consen 113 TQYEGQPAADAFKNKLERLGIKVYR 137 (491)
T ss_dssp ECE-T-HHHHHHHHHHHTTT-EEEE
T ss_pred EecCCCHHHHHHHHHHHHCCCcEEE
Confidence 6678888999999999999988643
No 251
>PF02367 UPF0079: Uncharacterised P-loop hydrolase UPF0079; InterPro: IPR003442 This group consists of bacterial proteins, which contain a P-loop. They are probably essential to bacteria as members are found in all genomes so far sequenced and no equivalent genes have been found in the archaea and eukaryotes, suggesting the protein may be involved in cell wall biosynthesis. The sequence of YjeE, from Haemophilus influenzae, has been determined to 1.7-A resolution. The protein has a nucleotide-binding fold with a four-stranded parallel beta-sheet flanked by antiparallel beta-strands on each side. The topology of the beta-sheet is unique among P-loop proteins and has features of different families of enzymes. ADP has been shown to bind to the P-loop in the presence of Mg2+ and ATPase activity has been confirmed by kinetic measurements [].; PDB: 1HTW_A 1FL9_A.
Probab=20.59 E-value=2.5e+02 Score=19.26 Aligned_cols=35 Identities=31% Similarity=0.364 Sum_probs=23.5
Q ss_pred HHHHHHHHHHHcCCcEEEEEEeecCCCcccCCCCChHHHHHHHHhC
Q 043606 27 AAQDVSQRCKERGITALHIKLRATGGNKTKTPGPGAQSALRALARS 72 (101)
Q Consensus 27 a~~~~~~~~~~~gi~~v~V~lrg~~g~~~kG~G~gr~~~lr~l~~~ 72 (101)
.|+.+++.++ ..-.|.+.|. +|.|+.+..|+|.++
T Consensus 4 la~~l~~~l~----~g~vi~L~Gd-------LGaGKTtf~r~l~~~ 38 (123)
T PF02367_consen 4 LAKKLAQILK----PGDVILLSGD-------LGAGKTTFVRGLARA 38 (123)
T ss_dssp HHHHHHHHHS----S-EEEEEEES-------TTSSHHHHHHHHHHH
T ss_pred HHHHHHHhCC----CCCEEEEECC-------CCCCHHHHHHHHHHH
Confidence 3445554442 2345778664 899999999999764
No 252
>PRK13834 putative autoinducer synthesis protein; Provisional
Probab=20.53 E-value=3.6e+02 Score=19.89 Aligned_cols=47 Identities=19% Similarity=0.227 Sum_probs=35.8
Q ss_pred HHHHHHHHHHHHHHHcCCcEEEEEEeecCCCcccCCCCChHHHHHHHHhCCCeEEEEEecC
Q 043606 23 AAMLAAQDVSQRCKERGITALHIKLRATGGNKTKTPGPGAQSALRALARSGMKIGRIEDVT 83 (101)
Q Consensus 23 Aa~~a~~~~~~~~~~~gi~~v~V~lrg~~g~~~kG~G~gr~~~lr~l~~~gl~I~~I~D~T 83 (101)
........+.+.+.+.|++.+...+ -....+.|.+.|+.+..|-+..
T Consensus 123 ~~~~L~~~~~~~a~~~Gi~~~~~v~--------------~~~~~r~l~r~G~~~~~lG~~~ 169 (207)
T PRK13834 123 ATLTMFAGIIEWSMANGYTEIVTAT--------------DLRFERILARAGWPMQRLGEPK 169 (207)
T ss_pred HHHHHHHHHHHHHHHCCCCEEEEEE--------------CHHHHHHHHHcCCCeEECCCCE
Confidence 3444455689999999999998888 2246788999999998877644
No 253
>KOG1447 consensus GTP-specific succinyl-CoA synthetase, beta subunit [Energy production and conversion]
Probab=20.52 E-value=3.2e+02 Score=22.45 Aligned_cols=47 Identities=26% Similarity=0.487 Sum_probs=33.5
Q ss_pred HHHHHHHHHHHcCCc-EEEEEEeecCCCcccCCCCChHHHHHHHHhCCCeEEEEEecC
Q 043606 27 AAQDVSQRCKERGIT-ALHIKLRATGGNKTKTPGPGAQSALRALARSGMKIGRIEDVT 83 (101)
Q Consensus 27 a~~~~~~~~~~~gi~-~v~V~lrg~~g~~~kG~G~gr~~~lr~l~~~gl~I~~I~D~T 83 (101)
+|.-+...+.+++++ .+.|++ -|.+-+.|-+.|..+||+|..-.|.-
T Consensus 354 IANGiv~A~~kl~LnVPlVVRL----------EGTNV~~A~~Ilk~SGLpI~tA~dLd 401 (412)
T KOG1447|consen 354 IANGIVKACRKLELNVPLVVRL----------EGTNVQEAQKILKKSGLPITTAIDLD 401 (412)
T ss_pred HhhHHHHHHHhhcCCCcEEEEE----------cCCCHHHHHHHHHhcCCceeeccchH
Confidence 444566667766665 266777 25667788899999999999877653
No 254
>PRK15454 ethanol dehydrogenase EutG; Provisional
Probab=20.34 E-value=3.7e+02 Score=21.72 Aligned_cols=55 Identities=18% Similarity=0.233 Sum_probs=35.1
Q ss_pred HHHHHHHHHHcCCcEEEEEEeecCCCcccCCCCChHHHHHHHHhCCCeEEEEEecCCCCC
Q 043606 28 AQDVSQRCKERGITALHIKLRATGGNKTKTPGPGAQSALRALARSGMKIGRIEDVTPIPT 87 (101)
Q Consensus 28 ~~~~~~~~~~~gi~~v~V~lrg~~g~~~kG~G~gr~~~lr~l~~~gl~I~~I~D~Tpiph 87 (101)
.+++.+.++++|.+.+-|.- + ......|. -+.+...|...|+.+....+++|-|.
T Consensus 37 ~~~l~~~~~~~g~~~~lvv~-~---~~~~~~g~-~~~v~~~L~~~gi~~~~~~~v~~~P~ 91 (395)
T PRK15454 37 VSSCGQQAQTRGLKHLFVMA-D---SFLHQAGM-TAGLTRSLAVKGIAMTLWPCPVGEPC 91 (395)
T ss_pred HHHHHHHHHhcCCCEEEEEc-C---cchhhCcc-HHHHHHHHHHcCCeEEEECCCCCCcC
Confidence 35677788888987666653 1 11122233 23477889999998876667777663
No 255
>PRK14318 glmM phosphoglucosamine mutase; Provisional
Probab=20.22 E-value=3.8e+02 Score=21.84 Aligned_cols=75 Identities=15% Similarity=0.147 Sum_probs=44.9
Q ss_pred eeeeccceeeccCCCCcHHHHHHHHHHHHHHHHHcC-----CcEEEEEEeecCCCcccCCCCChHHHHHHHHhCCCeEEE
Q 043606 4 ERITGGMKVKADRDESSPYAAMLAAQDVSQRCKERG-----ITALHIKLRATGGNKTKTPGPGAQSALRALARSGMKIGR 78 (101)
Q Consensus 4 ~~SsG~~gfKg~r~k~t~~Aa~~a~~~~~~~~~~~g-----i~~v~V~lrg~~g~~~kG~G~gr~~~lr~l~~~gl~I~~ 78 (101)
+-..|--|.-+ . .-||..+...+..++..+.+.+ -..|.|---. +..+. .=.++++.+|..+|++|..
T Consensus 5 Fg~~giRG~~~-~-~ltpe~~~~lg~a~~~~l~~~~~~~~~~~~VvVg~D~----R~ss~-~l~~a~~~gL~s~G~~V~~ 77 (448)
T PRK14318 5 FGTDGVRGLAN-R-DLTAELALALGAAAARVLGHAGRPGGRRPVAVVGRDP----RASGE-FLEAAVSAGLASAGVDVLR 77 (448)
T ss_pred cCCCCcceecC-C-ccCHHHHHHHHHHHHHHHHhcccccCCCCeEEEEeCC----CcCHH-HHHHHHHHHHHHCCCEEEE
Confidence 33444444333 2 4799888888887787776543 2335444321 11111 1245677778899999998
Q ss_pred EEecCCCC
Q 043606 79 IEDVTPIP 86 (101)
Q Consensus 79 I~D~Tpip 86 (101)
+ ..+|.|
T Consensus 78 ~-g~~pTP 84 (448)
T PRK14318 78 V-GVLPTP 84 (448)
T ss_pred e-cccCch
Confidence 8 477777
No 256
>PRK14314 glmM phosphoglucosamine mutase; Provisional
Probab=20.14 E-value=4.8e+02 Score=21.23 Aligned_cols=76 Identities=12% Similarity=0.065 Sum_probs=46.4
Q ss_pred eeeeeccceeeccCCCCcHHHHHHHHHHHHHHHHHcCC-cEEEEEEeecCCCcccCCC-CChHHHHHHHHhCCCeEEEEE
Q 043606 3 LERITGGMKVKADRDESSPYAAMLAAQDVSQRCKERGI-TALHIKLRATGGNKTKTPG-PGAQSALRALARSGMKIGRIE 80 (101)
Q Consensus 3 ~~~SsG~~gfKg~r~k~t~~Aa~~a~~~~~~~~~~~gi-~~v~V~lrg~~g~~~kG~G-~gr~~~lr~l~~~gl~I~~I~ 80 (101)
++-..|--|.-+.. .-||.-+..++..+++.+...+- ..|.|---. +-.+ .=.++++.+|..+|++|..+
T Consensus 5 ~Fgt~GiRG~~~~~-~lt~e~~~~l~~a~~~~l~~~~~~~~VvVg~D~------R~~s~~l~~a~~~gL~s~Gv~V~~~- 76 (450)
T PRK14314 5 LFGTDGVRGRANVY-PMTAEMALQLGRAAAYVFRNGSGRHRVVIGKDT------RLSGYMFENALIAGLCSMGVDVLLV- 76 (450)
T ss_pred eeCCCCcceecCCC-CCCHHHHHHHHHHHHHHHHhcCCCCcEEEEeCC------CcChHHHHHHHHHHHHHCCCeEEEe-
Confidence 34444444444422 36888888888888887764331 234443321 1122 12556778899999999998
Q ss_pred ecCCCC
Q 043606 81 DVTPIP 86 (101)
Q Consensus 81 D~Tpip 86 (101)
+.+|.|
T Consensus 77 g~~ptP 82 (450)
T PRK14314 77 GPLPTP 82 (450)
T ss_pred cccCCH
Confidence 688877
No 257
>PRK09936 hypothetical protein; Provisional
Probab=20.11 E-value=3.7e+02 Score=21.64 Aligned_cols=46 Identities=15% Similarity=0.212 Sum_probs=30.5
Q ss_pred HHHHHHHHHcCCcEEEEEEeecCCCcccCCCCChHHHHHH---HHhCCCeEE
Q 043606 29 QDVSQRCKERGITALHIKLRATGGNKTKTPGPGAQSALRA---LARSGMKIG 77 (101)
Q Consensus 29 ~~~~~~~~~~gi~~v~V~lrg~~g~~~kG~G~gr~~~lr~---l~~~gl~I~ 77 (101)
+.+.+..+.+|++.|.|-+.+.|++ -||--+-...+. -+..|++|.
T Consensus 41 q~~~~~~~~~G~~tLivQWt~yG~~---~fg~~~g~La~~l~~A~~~Gl~v~ 89 (296)
T PRK09936 41 QGLWSQLRLQGFDTLVVQWTRYGDA---DFGGQRGWLAKRLAAAQQAGLKLV 89 (296)
T ss_pred HHHHHHHHHcCCcEEEEEeeeccCC---CcccchHHHHHHHHHHHHcCCEEE
Confidence 4567788999999999999877444 233323333333 355688886
No 258
>PF00158 Sigma54_activat: Sigma-54 interaction domain; InterPro: IPR002078 Some bacterial regulatory proteins activate the expression of genes from promoters recognised by core RNA polymerase associated with the alternative sigma-54 factor. These have a conserved domain of about 230 residues involved in the ATP-dependent [, ] interaction with sigma-54. About half of the proteins in which this domain is found (algB, dcdT, flbD, hoxA, hupR1, hydG, ntrC, pgtA and pilR) belong to signal transduction two-component systems [] and possess a domain that can be phosphorylated by a sensor-kinase protein in their N-terminal section. Almost all of these proteins possess a helix-turn-helix DNA-binding domain in their C-terminal section. The domain which interacts with the sigma-54 factor has an ATPase activity. This may be required to promote a conformational change necessary for the interaction []. The domain contains an atypical ATP-binding motif A (P-loop) as well as a form of motif B. The two ATP-binding motifs are located in the N-terminal section of the domain.; GO: 0005524 ATP binding, 0008134 transcription factor binding, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 1NY6_K 3M0E_G 1NY5_A 1OJL_A 3DZD_B 2C9C_A 2C98_A 2C96_A 2BJV_A 2C99_A ....
Probab=20.00 E-value=2.3e+02 Score=20.05 Aligned_cols=37 Identities=16% Similarity=0.333 Sum_probs=28.2
Q ss_pred HHHHHHHHHcCCcEEEEEEeecCCCcccCCCCChHHHHHHHHhC
Q 043606 29 QDVSQRCKERGITALHIKLRATGGNKTKTPGPGAQSALRALARS 72 (101)
Q Consensus 29 ~~~~~~~~~~gi~~v~V~lrg~~g~~~kG~G~gr~~~lr~l~~~ 72 (101)
..+.+.++...-....|.|-|+ .|.|++.+-++|...
T Consensus 9 ~~~~~~~~~~a~~~~pVlI~GE-------~GtGK~~lA~~IH~~ 45 (168)
T PF00158_consen 9 KRLREQAKRAASSDLPVLITGE-------TGTGKELLARAIHNN 45 (168)
T ss_dssp HHHHHHHHHHTTSTS-EEEECS-------TTSSHHHHHHHHHHC
T ss_pred HHHHHHHHHHhCCCCCEEEEcC-------CCCcHHHHHHHHHHh
Confidence 4566677776677799999776 789999999999764
Done!