Query 044458
Match_columns 241
No_of_seqs 127 out of 1091
Neff 8.2
Searched_HMMs 46136
Date Fri Mar 29 03:27:43 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/044458.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/044458hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3178 Hydroxyindole-O-methyl 100.0 3.3E-29 7.1E-34 217.3 17.3 217 13-240 2-219 (342)
2 TIGR02716 C20_methyl_CrtF C-20 99.9 2.3E-27 5.1E-32 207.9 14.7 186 29-239 2-190 (306)
3 PF00891 Methyltransf_2: O-met 99.9 7.3E-26 1.6E-30 192.0 9.3 137 101-238 3-140 (241)
4 PF08100 Dimerisation: Dimeris 99.1 1.4E-10 3E-15 74.2 4.4 51 32-83 1-51 (51)
5 PRK06922 hypothetical protein; 98.2 1.7E-06 3.8E-11 82.1 5.4 80 158-238 377-459 (677)
6 PF12847 Methyltransf_18: Meth 98.0 3.6E-06 7.7E-11 62.2 2.3 40 199-238 2-42 (112)
7 PRK14103 trans-aconitate 2-met 97.9 2.3E-05 4.9E-10 67.0 6.6 52 187-239 19-71 (255)
8 PRK01683 trans-aconitate 2-met 97.8 3.5E-05 7.7E-10 65.7 6.2 53 186-239 20-73 (258)
9 PRK08287 cobalt-precorrin-6Y C 97.8 2.1E-05 4.5E-10 64.0 4.3 48 190-238 24-72 (187)
10 COG4106 Tam Trans-aconitate me 97.7 9.4E-05 2E-09 61.2 5.7 58 180-239 14-72 (257)
11 TIGR02469 CbiT precorrin-6Y C5 97.7 8.4E-05 1.8E-09 55.5 5.0 48 189-237 11-59 (124)
12 PRK04457 spermidine synthase; 97.5 7.5E-05 1.6E-09 64.2 3.5 44 197-240 65-109 (262)
13 TIGR02021 BchM-ChlM magnesium 97.5 0.00018 3.9E-09 59.9 5.3 77 160-238 16-94 (219)
14 PRK15001 SAM-dependent 23S rib 97.5 0.00013 2.8E-09 65.9 4.7 50 188-238 219-269 (378)
15 TIGR03587 Pse_Me-ase pseudamin 97.4 0.00017 3.7E-09 59.8 4.6 44 196-239 41-85 (204)
16 PRK00107 gidB 16S rRNA methylt 97.4 0.0002 4.3E-09 58.5 4.9 41 198-238 45-86 (187)
17 PF08242 Methyltransf_12: Meth 97.4 2.9E-05 6.3E-10 56.2 -0.2 37 203-239 1-38 (99)
18 PRK07402 precorrin-6B methylas 97.4 0.00021 4.6E-09 58.5 4.5 49 189-238 32-81 (196)
19 COG2813 RsmC 16S RNA G1207 met 97.4 0.00027 5.9E-09 61.4 5.1 52 187-239 148-200 (300)
20 TIGR02752 MenG_heptapren 2-hep 97.3 0.00028 6E-09 59.1 4.6 50 188-238 36-87 (231)
21 PRK06202 hypothetical protein; 97.3 0.00054 1.2E-08 57.6 6.4 43 197-239 59-106 (232)
22 TIGR00740 methyltransferase, p 97.3 0.00024 5.2E-09 60.0 3.6 42 197-238 52-96 (239)
23 PF05175 MTS: Methyltransferas 97.3 0.00014 3E-09 58.4 1.9 41 198-238 31-72 (170)
24 PRK00121 trmB tRNA (guanine-N( 97.3 0.00033 7.1E-09 57.9 4.1 41 198-238 40-81 (202)
25 PRK11207 tellurite resistance 97.2 0.00034 7.4E-09 57.5 4.0 50 186-238 19-69 (197)
26 TIGR00138 gidB 16S rRNA methyl 97.2 0.0002 4.4E-09 58.2 2.6 39 199-237 43-82 (181)
27 PRK15451 tRNA cmo(5)U34 methyl 97.2 0.00026 5.6E-09 60.3 3.4 42 197-238 55-99 (247)
28 PRK10258 biotin biosynthesis p 97.2 0.00094 2E-08 56.7 6.6 51 186-239 31-82 (251)
29 PRK09489 rsmC 16S ribosomal RN 97.2 0.00049 1.1E-08 61.5 4.7 49 189-238 188-237 (342)
30 PF09339 HTH_IclR: IclR helix- 97.2 0.00013 2.8E-09 46.8 0.7 46 40-91 6-51 (52)
31 PF13649 Methyltransf_25: Meth 97.1 0.00029 6.2E-09 51.3 2.0 37 202-238 1-41 (101)
32 PRK08317 hypothetical protein; 97.1 0.00071 1.5E-08 56.3 4.6 50 188-238 10-61 (241)
33 PRK14121 tRNA (guanine-N(7)-)- 97.1 0.00094 2E-08 60.4 5.5 49 188-237 113-162 (390)
34 COG2890 HemK Methylase of poly 97.1 0.00039 8.4E-09 60.4 2.9 38 201-238 113-151 (280)
35 TIGR03704 PrmC_rel_meth putati 97.1 0.00088 1.9E-08 57.3 4.9 40 199-238 87-127 (251)
36 COG2230 Cfa Cyclopropane fatty 97.0 0.00098 2.1E-08 57.7 5.1 49 186-236 61-110 (283)
37 PRK00216 ubiE ubiquinone/menaq 97.0 0.0019 4.2E-08 53.8 6.5 50 188-238 42-93 (239)
38 TIGR03533 L3_gln_methyl protei 97.0 0.00063 1.4E-08 59.2 3.7 41 198-238 121-162 (284)
39 TIGR00477 tehB tellurite resis 97.0 0.0011 2.3E-08 54.4 4.9 48 187-237 20-68 (195)
40 PRK11036 putative S-adenosyl-L 97.0 0.0013 2.9E-08 56.1 5.5 40 197-238 43-83 (255)
41 PRK00274 ksgA 16S ribosomal RN 97.0 0.0011 2.5E-08 57.2 5.0 49 187-238 32-81 (272)
42 PRK11805 N5-glutamine S-adenos 97.0 0.0006 1.3E-08 60.0 3.2 39 200-238 135-174 (307)
43 COG2242 CobL Precorrin-6B meth 96.9 0.0011 2.4E-08 53.8 4.3 46 191-237 28-74 (187)
44 PLN02244 tocopherol O-methyltr 96.9 0.0011 2.4E-08 59.2 4.7 40 197-237 117-157 (340)
45 PTZ00098 phosphoethanolamine N 96.9 0.0011 2.3E-08 57.1 4.5 50 187-238 42-92 (263)
46 PRK01581 speE spermidine synth 96.9 0.00096 2.1E-08 59.8 4.2 45 197-241 149-194 (374)
47 TIGR03534 RF_mod_PrmC protein- 96.9 0.0014 3E-08 55.3 4.7 41 198-238 87-128 (251)
48 COG2226 UbiE Methylase involve 96.9 0.0017 3.6E-08 55.0 4.9 42 198-239 51-93 (238)
49 smart00550 Zalpha Z-DNA-bindin 96.9 0.0024 5.1E-08 43.4 4.7 60 37-108 6-66 (68)
50 PRK14966 unknown domain/N5-glu 96.8 0.001 2.3E-08 60.6 3.7 42 198-239 251-293 (423)
51 PRK05785 hypothetical protein; 96.8 0.0012 2.6E-08 55.5 3.8 40 199-239 52-92 (226)
52 PRK09328 N5-glutamine S-adenos 96.8 0.0018 3.9E-08 55.6 5.0 43 196-238 106-149 (275)
53 TIGR02072 BioC biotin biosynth 96.8 0.001 2.2E-08 55.4 3.4 39 199-237 35-74 (240)
54 TIGR00536 hemK_fam HemK family 96.8 0.00096 2.1E-08 58.0 3.2 39 200-238 116-155 (284)
55 smart00138 MeTrc Methyltransfe 96.8 0.0067 1.4E-07 52.2 8.4 52 187-239 89-150 (264)
56 smart00346 HTH_ICLR helix_turn 96.8 0.002 4.3E-08 45.8 4.3 58 39-109 7-64 (91)
57 PF02390 Methyltransf_4: Putat 96.8 0.0018 3.8E-08 53.3 4.3 36 200-235 19-55 (195)
58 PLN02366 spermidine synthase 96.8 0.0012 2.7E-08 58.0 3.5 43 197-240 90-134 (308)
59 COG2227 UbiG 2-polyprenyl-3-me 96.8 0.001 2.2E-08 56.0 2.7 40 199-240 60-100 (243)
60 PLN02233 ubiquinone biosynthes 96.7 0.0028 6E-08 54.5 5.5 43 196-238 71-115 (261)
61 PRK11705 cyclopropane fatty ac 96.7 0.0021 4.6E-08 58.3 4.9 50 187-238 157-207 (383)
62 TIGR00080 pimt protein-L-isoas 96.7 0.0024 5.3E-08 53.1 4.9 50 188-238 68-119 (215)
63 PRK01544 bifunctional N5-gluta 96.7 0.0012 2.7E-08 62.0 3.4 40 199-238 139-179 (506)
64 PRK00811 spermidine synthase; 96.7 0.0012 2.6E-08 57.4 3.1 44 197-240 75-119 (283)
65 PF13659 Methyltransf_26: Meth 96.7 0.0017 3.6E-08 48.1 3.4 38 200-238 2-40 (117)
66 PRK07580 Mg-protoporphyrin IX 96.7 0.002 4.3E-08 53.7 4.1 41 196-238 61-102 (230)
67 PLN02336 phosphoethanolamine N 96.7 0.0023 5.1E-08 59.5 4.7 49 188-238 257-306 (475)
68 TIGR01934 MenG_MenH_UbiE ubiqu 96.6 0.0025 5.5E-08 52.5 4.4 49 188-237 30-80 (223)
69 PRK11088 rrmA 23S rRNA methylt 96.6 0.0019 4.1E-08 55.7 3.7 41 198-238 85-129 (272)
70 COG4123 Predicted O-methyltran 96.6 0.0019 4E-08 55.0 3.5 50 189-238 35-85 (248)
71 PF02353 CMAS: Mycolic acid cy 96.6 0.0015 3.3E-08 56.5 2.9 43 186-230 51-93 (273)
72 PRK13944 protein-L-isoaspartat 96.6 0.0039 8.5E-08 51.5 5.0 49 189-238 64-114 (205)
73 PLN02490 MPBQ/MSBQ methyltrans 96.5 0.0044 9.4E-08 55.3 5.1 49 189-238 104-154 (340)
74 PF13679 Methyltransf_32: Meth 96.5 0.0021 4.6E-08 49.9 2.8 42 196-237 23-69 (141)
75 PRK13942 protein-L-isoaspartat 96.5 0.0051 1.1E-07 51.2 5.2 50 188-238 67-118 (212)
76 PLN03075 nicotianamine synthas 96.4 0.0033 7.1E-08 54.9 4.0 43 197-239 122-167 (296)
77 COG1414 IclR Transcriptional r 96.4 0.0037 8.1E-08 53.2 4.2 59 39-110 6-64 (246)
78 TIGR00537 hemK_rel_arch HemK-r 96.4 0.0029 6.2E-08 51.0 3.3 38 199-238 20-58 (179)
79 TIGR02431 pcaR_pcaU beta-ketoa 96.4 0.0034 7.3E-08 53.4 3.8 58 39-111 11-68 (248)
80 PRK12335 tellurite resistance 96.4 0.0033 7.1E-08 54.7 3.8 48 188-238 111-159 (287)
81 COG2264 PrmA Ribosomal protein 96.4 0.0022 4.8E-08 56.0 2.6 61 174-238 141-202 (300)
82 KOG2899 Predicted methyltransf 96.4 0.0029 6.3E-08 53.3 3.1 53 187-239 46-100 (288)
83 PRK00377 cbiT cobalt-precorrin 96.4 0.0046 9.9E-08 50.7 4.3 47 191-238 34-82 (198)
84 PF02082 Rrf2: Transcriptional 96.4 0.0051 1.1E-07 43.3 3.9 56 44-109 15-70 (83)
85 PRK00517 prmA ribosomal protei 96.4 0.0032 7E-08 53.6 3.4 41 197-238 118-159 (250)
86 PF06325 PrmA: Ribosomal prote 96.3 0.002 4.3E-08 56.4 2.0 61 174-238 140-201 (295)
87 TIGR00755 ksgA dimethyladenosi 96.3 0.0059 1.3E-07 52.1 4.8 48 186-236 18-66 (253)
88 PLN02396 hexaprenyldihydroxybe 96.3 0.0027 5.8E-08 56.3 2.5 38 199-238 132-170 (322)
89 PRK03612 spermidine synthase; 96.3 0.0048 1E-07 58.3 4.3 43 197-240 296-340 (521)
90 PRK00050 16S rRNA m(4)C1402 me 96.3 0.0076 1.7E-07 52.7 5.3 53 186-239 8-62 (296)
91 PRK14896 ksgA 16S ribosomal RN 96.3 0.0062 1.3E-07 52.2 4.7 49 186-237 18-67 (258)
92 PF08241 Methyltransf_11: Meth 96.3 0.0026 5.7E-08 44.7 2.0 35 203-238 1-36 (95)
93 KOG1540 Ubiquinone biosynthesi 96.3 0.0078 1.7E-07 51.2 5.1 65 172-239 74-148 (296)
94 PF13489 Methyltransf_23: Meth 96.3 0.013 2.9E-07 45.4 6.2 37 196-234 20-57 (161)
95 KOG2904 Predicted methyltransf 96.2 0.0054 1.2E-07 52.6 3.9 43 196-238 146-189 (328)
96 PRK15068 tRNA mo(5)U34 methylt 96.2 0.0087 1.9E-07 53.1 5.4 41 189-231 114-154 (322)
97 TIGR00406 prmA ribosomal prote 96.2 0.0036 7.7E-08 54.6 2.9 40 198-238 159-199 (288)
98 PHA03411 putative methyltransf 96.2 0.0044 9.4E-08 53.5 3.3 40 199-238 65-105 (279)
99 COG0220 Predicted S-adenosylme 96.2 0.0086 1.9E-07 50.4 5.0 37 199-235 49-86 (227)
100 PF01209 Ubie_methyltran: ubiE 96.2 0.0031 6.8E-08 53.3 2.3 43 196-238 45-89 (233)
101 PRK11569 transcriptional repre 96.1 0.0067 1.5E-07 52.4 4.2 60 38-110 29-88 (274)
102 TIGR00452 methyltransferase, p 96.1 0.01 2.2E-07 52.4 5.3 41 188-230 112-152 (314)
103 PRK14968 putative methyltransf 96.1 0.0061 1.3E-07 48.9 3.4 39 197-237 22-61 (188)
104 TIGR00438 rrmJ cell division p 96.0 0.012 2.6E-07 47.7 5.1 44 189-232 23-67 (188)
105 PRK10163 DNA-binding transcrip 96.0 0.0081 1.8E-07 51.9 4.2 59 39-110 27-85 (271)
106 PRK11727 23S rRNA mA1618 methy 96.0 0.0056 1.2E-07 54.2 3.1 41 198-238 114-155 (321)
107 KOG1270 Methyltransferases [Co 96.0 0.0037 8.1E-08 53.2 1.9 39 200-240 91-130 (282)
108 PF13412 HTH_24: Winged helix- 95.9 0.0083 1.8E-07 37.5 2.9 45 38-89 4-48 (48)
109 PLN02672 methionine S-methyltr 95.9 0.0063 1.4E-07 61.7 3.5 39 200-238 120-159 (1082)
110 PRK09834 DNA-binding transcrip 95.9 0.0096 2.1E-07 51.2 4.2 61 38-111 12-72 (263)
111 PRK11188 rrmJ 23S rRNA methylt 95.9 0.017 3.7E-07 47.9 5.5 43 189-231 42-85 (209)
112 PLN02585 magnesium protoporphy 95.9 0.0057 1.2E-07 54.1 2.8 38 199-238 145-183 (315)
113 PF09012 FeoC: FeoC like trans 95.9 0.0088 1.9E-07 40.6 3.1 43 42-91 5-47 (69)
114 PRK15090 DNA-binding transcrip 95.8 0.01 2.2E-07 50.8 4.0 58 39-110 16-73 (257)
115 PRK14967 putative methyltransf 95.8 0.012 2.5E-07 49.3 4.2 42 196-238 34-76 (223)
116 PRK04266 fibrillarin; Provisio 95.8 0.019 4E-07 48.4 5.3 43 192-235 67-110 (226)
117 TIGR00417 speE spermidine synt 95.8 0.0079 1.7E-07 51.9 3.1 43 197-239 71-114 (270)
118 cd02440 AdoMet_MTases S-adenos 95.8 0.0083 1.8E-07 42.0 2.7 35 201-236 1-36 (107)
119 PHA03412 putative methyltransf 95.7 0.01 2.2E-07 50.2 3.4 40 199-238 50-93 (241)
120 PLN02336 phosphoethanolamine N 95.7 0.015 3.2E-07 54.2 4.9 48 187-237 27-75 (475)
121 PF01022 HTH_5: Bacterial regu 95.7 0.0058 1.3E-07 38.2 1.5 43 39-89 4-46 (47)
122 smart00419 HTH_CRP helix_turn_ 95.7 0.014 3E-07 36.0 3.1 34 54-91 8-41 (48)
123 PRK11873 arsM arsenite S-adeno 95.7 0.012 2.7E-07 50.5 3.9 44 196-239 75-120 (272)
124 PF01978 TrmB: Sugar-specific 95.6 0.0049 1.1E-07 41.6 1.1 47 38-91 9-55 (68)
125 TIGR03840 TMPT_Se_Te thiopurin 95.6 0.023 4.9E-07 47.4 5.2 38 197-236 33-71 (213)
126 TIGR03438 probable methyltrans 95.6 0.01 2.2E-07 52.1 3.1 40 198-237 63-104 (301)
127 cd00092 HTH_CRP helix_turn_hel 95.6 0.018 4E-07 38.2 3.6 44 53-108 24-67 (67)
128 PRK13943 protein-L-isoaspartat 95.6 0.021 4.6E-07 50.6 5.0 50 188-238 71-122 (322)
129 PF12840 HTH_20: Helix-turn-he 95.5 0.01 2.2E-07 39.2 2.2 53 32-91 5-57 (61)
130 PLN02823 spermine synthase 95.5 0.013 2.9E-07 52.2 3.5 44 197-240 102-146 (336)
131 PF08003 Methyltransf_9: Prote 95.5 0.022 4.9E-07 49.7 4.8 42 186-229 104-145 (315)
132 COG1959 Predicted transcriptio 95.5 0.023 5.1E-07 44.7 4.4 56 43-108 14-69 (150)
133 COG0421 SpeE Spermidine syntha 95.4 0.013 2.8E-07 50.9 3.2 45 196-240 74-119 (282)
134 PTZ00338 dimethyladenosine tra 95.3 0.028 6E-07 49.2 5.0 49 186-237 25-74 (294)
135 PRK04148 hypothetical protein; 95.3 0.025 5.5E-07 43.6 4.1 47 189-238 8-56 (134)
136 KOG3010 Methyltransferase [Gen 95.3 0.017 3.6E-07 48.8 3.2 42 198-241 33-75 (261)
137 PF14947 HTH_45: Winged helix- 95.2 0.016 3.5E-07 40.2 2.5 48 53-113 18-65 (77)
138 PRK10901 16S rRNA methyltransf 95.2 0.021 4.6E-07 52.5 3.9 63 174-237 221-284 (427)
139 PRK00536 speE spermidine synth 95.2 0.016 3.5E-07 49.9 2.8 42 197-240 71-113 (262)
140 PRK00312 pcm protein-L-isoaspa 95.1 0.036 7.7E-07 45.8 4.8 47 189-238 70-117 (212)
141 TIGR02010 IscR iron-sulfur clu 95.1 0.034 7.4E-07 42.8 4.3 46 53-108 24-69 (135)
142 KOG1271 Methyltransferases [Ge 95.1 0.026 5.7E-07 45.7 3.6 37 199-236 68-106 (227)
143 PRK13255 thiopurine S-methyltr 95.0 0.046 9.9E-07 45.7 5.2 40 196-237 35-75 (218)
144 PRK13168 rumA 23S rRNA m(5)U19 94.9 0.016 3.6E-07 53.5 2.5 48 188-238 288-336 (443)
145 PRK05134 bifunctional 3-demeth 94.9 0.04 8.6E-07 46.1 4.6 38 198-237 48-86 (233)
146 PF13463 HTH_27: Winged helix 94.9 0.025 5.5E-07 37.7 2.6 51 53-109 17-67 (68)
147 PRK03522 rumB 23S rRNA methylu 94.8 0.032 6.9E-07 49.2 3.9 38 199-238 174-212 (315)
148 TIGR00738 rrf2_super rrf2 fami 94.8 0.046 9.9E-07 41.7 4.3 46 53-108 24-69 (132)
149 PRK10857 DNA-binding transcrip 94.7 0.052 1.1E-06 43.4 4.5 46 53-108 24-69 (164)
150 PF03848 TehB: Tellurite resis 94.7 0.072 1.6E-06 43.7 5.4 46 187-235 20-66 (192)
151 PRK14902 16S rRNA methyltransf 94.7 0.032 7E-07 51.6 3.7 64 174-238 227-292 (444)
152 TIGR00478 tly hemolysin TlyA f 94.7 0.082 1.8E-06 44.6 5.8 43 186-230 63-106 (228)
153 PLN02781 Probable caffeoyl-CoA 94.6 0.056 1.2E-06 45.6 4.8 44 196-239 66-111 (234)
154 smart00347 HTH_MARR helix_turn 94.5 0.042 9E-07 39.2 3.3 47 38-91 11-57 (101)
155 PF07757 AdoMet_MTase: Predict 94.5 0.054 1.2E-06 40.0 3.7 43 185-230 46-88 (112)
156 PRK11050 manganese transport r 94.4 0.21 4.5E-06 39.3 7.3 57 41-112 41-97 (152)
157 TIGR02944 suf_reg_Xantho FeS a 94.4 0.054 1.2E-06 41.3 3.8 55 43-108 15-69 (130)
158 PF04703 FaeA: FaeA-like prote 94.4 0.035 7.5E-07 37.0 2.3 45 41-91 4-48 (62)
159 PRK10909 rsmD 16S rRNA m(2)G96 94.3 0.062 1.3E-06 44.3 4.2 39 199-238 54-93 (199)
160 COG4976 Predicted methyltransf 94.1 0.046 1E-06 46.0 3.1 58 170-230 94-155 (287)
161 PF01564 Spermine_synth: Sperm 94.1 0.02 4.4E-07 48.8 1.0 44 197-240 75-119 (246)
162 COG2263 Predicted RNA methylas 94.1 0.044 9.5E-07 44.7 2.9 40 199-239 46-86 (198)
163 PRK06266 transcription initiat 94.1 0.12 2.6E-06 41.9 5.4 45 40-91 25-69 (178)
164 KOG1541 Predicted protein carb 94.1 0.02 4.3E-07 47.8 0.8 39 198-238 50-89 (270)
165 TIGR01983 UbiG ubiquinone bios 94.0 0.045 9.7E-07 45.3 3.0 38 198-237 45-83 (224)
166 PF04967 HTH_10: HTH DNA bindi 94.0 0.05 1.1E-06 35.0 2.4 43 30-82 5-47 (53)
167 PRK01544 bifunctional N5-gluta 94.0 0.065 1.4E-06 50.5 4.2 33 198-230 347-379 (506)
168 PF13601 HTH_34: Winged helix 94.0 0.035 7.5E-07 38.9 1.8 65 38-111 1-66 (80)
169 COG4742 Predicted transcriptio 93.9 0.067 1.4E-06 45.8 3.8 67 33-116 9-75 (260)
170 PF08220 HTH_DeoR: DeoR-like h 93.9 0.093 2E-06 34.1 3.7 44 41-91 4-47 (57)
171 PF01047 MarR: MarR family; I 93.9 0.036 7.7E-07 36.0 1.6 46 39-91 5-50 (59)
172 KOG3115 Methyltransferase-like 93.8 0.029 6.2E-07 46.3 1.2 33 198-230 60-92 (249)
173 PF12802 MarR_2: MarR family; 93.8 0.043 9.3E-07 35.8 1.9 48 39-91 7-54 (62)
174 PRK10141 DNA-binding transcrip 93.8 0.086 1.9E-06 39.7 3.7 56 29-91 8-63 (117)
175 PF10294 Methyltransf_16: Puta 93.7 0.077 1.7E-06 42.6 3.7 40 197-236 44-83 (173)
176 smart00420 HTH_DEOR helix_turn 93.6 0.12 2.6E-06 32.1 3.8 43 42-91 5-47 (53)
177 smart00344 HTH_ASNC helix_turn 93.5 0.098 2.1E-06 38.3 3.7 46 38-90 4-49 (108)
178 PRK03902 manganese transport t 93.5 0.11 2.4E-06 40.3 4.1 49 53-113 21-69 (142)
179 TIGR02337 HpaR homoprotocatech 93.5 0.14 3E-06 38.3 4.5 68 38-114 29-96 (118)
180 TIGR00563 rsmB ribosomal RNA s 93.4 0.083 1.8E-06 48.6 3.7 51 186-237 227-278 (426)
181 PF01135 PCMT: Protein-L-isoas 93.3 0.088 1.9E-06 43.8 3.5 50 188-238 63-114 (209)
182 TIGR02085 meth_trns_rumB 23S r 93.3 0.057 1.2E-06 48.8 2.5 38 199-238 234-272 (374)
183 KOG3420 Predicted RNA methylas 93.2 0.055 1.2E-06 42.3 1.9 45 191-238 42-88 (185)
184 TIGR00479 rumA 23S rRNA (uraci 93.2 0.07 1.5E-06 49.1 3.0 46 190-238 285-331 (431)
185 TIGR02702 SufR_cyano iron-sulf 93.2 0.16 3.6E-06 41.8 4.9 68 40-114 4-71 (203)
186 TIGR00095 RNA methyltransferas 93.2 0.078 1.7E-06 43.3 2.9 38 199-237 50-88 (189)
187 PF06080 DUF938: Protein of un 93.1 0.11 2.4E-06 42.9 3.7 35 196-230 22-57 (204)
188 PRK11014 transcriptional repre 93.1 0.15 3.2E-06 39.5 4.2 46 53-108 24-69 (141)
189 PRK11920 rirA iron-responsive 93.0 0.15 3.3E-06 40.2 4.2 46 53-108 23-68 (153)
190 TIGR01177 conserved hypothetic 92.9 0.15 3.2E-06 45.3 4.5 46 189-237 174-220 (329)
191 TIGR00122 birA_repr_reg BirA b 92.7 0.2 4.3E-06 33.7 4.0 44 39-90 2-45 (69)
192 PRK15431 ferrous iron transpor 92.6 0.18 3.9E-06 35.0 3.6 43 42-91 7-49 (78)
193 COG2345 Predicted transcriptio 92.5 0.15 3.3E-06 42.5 3.7 64 42-114 16-81 (218)
194 KOG1499 Protein arginine N-met 92.5 0.1 2.2E-06 46.3 2.8 38 199-237 61-98 (346)
195 smart00418 HTH_ARSR helix_turn 92.5 0.21 4.5E-06 32.1 3.7 42 42-91 2-43 (66)
196 PF01728 FtsJ: FtsJ-like methy 92.3 0.16 3.5E-06 40.7 3.6 48 186-233 9-59 (181)
197 TIGR01884 cas_HTH CRISPR locus 92.3 0.22 4.7E-06 41.1 4.4 59 38-109 144-202 (203)
198 COG3355 Predicted transcriptio 92.3 0.17 3.8E-06 38.5 3.5 45 40-91 30-75 (126)
199 PF07381 DUF1495: Winged helix 92.2 0.2 4.4E-06 35.8 3.5 67 36-112 8-85 (90)
200 TIGR00373 conserved hypothetic 92.2 0.2 4.2E-06 39.8 3.8 45 40-91 17-61 (158)
201 COG2518 Pcm Protein-L-isoaspar 92.1 0.2 4.4E-06 41.5 3.9 48 188-238 63-111 (209)
202 PF01638 HxlR: HxlR-like helix 92.0 0.11 2.3E-06 37.1 2.0 63 42-114 10-73 (90)
203 PRK06474 hypothetical protein; 92.0 0.27 5.9E-06 39.8 4.6 77 31-113 5-82 (178)
204 COG4190 Predicted transcriptio 92.0 0.24 5.2E-06 37.8 3.9 54 31-91 58-111 (144)
205 COG1321 TroR Mn-dependent tran 91.9 0.25 5.4E-06 39.1 4.2 50 53-114 23-72 (154)
206 PF08279 HTH_11: HTH domain; 91.9 0.25 5.4E-06 31.5 3.5 42 41-88 4-45 (55)
207 PF08461 HTH_12: Ribonuclease 91.8 0.24 5.2E-06 33.3 3.4 60 42-111 3-63 (66)
208 PF01596 Methyltransf_3: O-met 91.5 0.13 2.9E-06 42.6 2.3 41 198-238 45-87 (205)
209 PF08123 DOT1: Histone methyla 91.4 0.3 6.6E-06 40.5 4.3 48 187-235 32-80 (205)
210 TIGR02143 trmA_only tRNA (urac 91.3 0.17 3.6E-06 45.5 2.9 37 200-238 199-236 (353)
211 PHA00738 putative HTH transcri 91.2 0.31 6.8E-06 36.0 3.7 60 38-109 13-72 (108)
212 PF09243 Rsm22: Mitochondrial 91.1 0.39 8.5E-06 41.5 4.9 48 188-236 24-73 (274)
213 PRK11512 DNA-binding transcrip 91.1 1 2.2E-05 34.7 6.9 45 40-91 43-87 (144)
214 PF04182 B-block_TFIIIC: B-blo 91.0 0.24 5.1E-06 34.1 2.8 49 38-91 3-51 (75)
215 PF01726 LexA_DNA_bind: LexA D 91.0 0.27 5.8E-06 33.0 2.9 35 53-91 24-59 (65)
216 cd00090 HTH_ARSR Arsenical Res 90.9 0.34 7.4E-06 32.1 3.6 45 39-91 9-53 (78)
217 PF05401 NodS: Nodulation prot 90.8 0.13 2.7E-06 42.3 1.5 44 192-238 38-82 (201)
218 PRK14903 16S rRNA methyltransf 90.8 0.3 6.5E-06 45.1 4.1 64 173-237 213-278 (431)
219 KOG2361 Predicted methyltransf 90.8 0.21 4.5E-06 42.3 2.8 41 200-240 73-116 (264)
220 PF06163 DUF977: Bacterial pro 90.7 0.42 9.1E-06 36.2 4.1 50 35-91 10-59 (127)
221 PTZ00146 fibrillarin; Provisio 90.7 0.42 9.1E-06 41.8 4.7 36 196-231 130-166 (293)
222 COG4189 Predicted transcriptio 90.5 0.44 9.6E-06 40.1 4.4 55 30-91 16-70 (308)
223 PF02002 TFIIE_alpha: TFIIE al 90.5 0.22 4.7E-06 36.5 2.4 43 42-91 18-60 (105)
224 PF08784 RPA_C: Replication pr 90.5 0.24 5.2E-06 36.1 2.7 49 38-90 48-97 (102)
225 PF05185 PRMT5: PRMT5 arginine 90.5 0.44 9.6E-06 44.2 5.0 67 160-230 152-222 (448)
226 PF00325 Crp: Bacterial regula 90.3 0.21 4.4E-06 28.6 1.6 31 54-88 2-32 (32)
227 PRK05031 tRNA (uracil-5-)-meth 90.3 0.23 4.9E-06 44.8 2.8 37 200-238 208-245 (362)
228 cd07153 Fur_like Ferric uptake 89.8 0.43 9.2E-06 35.3 3.5 50 40-91 4-54 (116)
229 COG0357 GidB Predicted S-adeno 89.5 0.31 6.7E-06 40.7 2.8 32 199-230 68-99 (215)
230 PRK14901 16S rRNA methyltransf 89.5 0.39 8.4E-06 44.4 3.7 50 187-237 242-293 (434)
231 TIGR00446 nop2p NOL1/NOP2/sun 89.4 0.51 1.1E-05 40.5 4.2 42 196-237 69-112 (264)
232 PF01325 Fe_dep_repress: Iron 89.4 0.39 8.4E-06 31.6 2.7 35 53-91 21-55 (60)
233 PRK14904 16S rRNA methyltransf 89.4 0.39 8.6E-06 44.4 3.7 43 196-238 248-292 (445)
234 PRK11179 DNA-binding transcrip 89.4 0.49 1.1E-05 37.1 3.7 46 38-90 10-55 (153)
235 PF02527 GidB: rRNA small subu 89.4 0.34 7.4E-06 39.4 2.9 30 201-230 51-80 (184)
236 TIGR01610 phage_O_Nterm phage 89.2 0.48 1E-05 34.2 3.3 44 53-107 46-89 (95)
237 PLN02476 O-methyltransferase 89.1 0.36 7.7E-06 41.9 3.0 44 196-239 116-161 (278)
238 smart00345 HTH_GNTR helix_turn 89.1 0.5 1.1E-05 30.1 3.1 35 53-91 18-53 (60)
239 PF03444 HrcA_DNA-bdg: Winged 88.8 1.1 2.5E-05 31.1 4.7 48 53-110 22-69 (78)
240 TIGR00006 S-adenosyl-methyltra 88.8 0.85 1.8E-05 40.1 5.2 52 186-238 9-61 (305)
241 PF05148 Methyltransf_8: Hypot 88.7 1.3 2.8E-05 36.8 5.8 83 138-230 15-101 (219)
242 PRK11169 leucine-responsive tr 88.2 0.53 1.2E-05 37.4 3.3 47 37-90 14-60 (164)
243 smart00529 HTH_DTXR Helix-turn 88.1 0.54 1.2E-05 33.4 3.0 45 57-113 2-46 (96)
244 COG4262 Predicted spermidine s 88.1 0.76 1.6E-05 41.4 4.3 41 197-238 288-330 (508)
245 PF05724 TPMT: Thiopurine S-me 88.0 0.53 1.1E-05 39.4 3.3 40 196-237 35-75 (218)
246 PHA02943 hypothetical protein; 87.4 0.79 1.7E-05 36.0 3.6 43 41-91 15-57 (165)
247 PF12147 Methyltransf_20: Puta 87.4 0.58 1.2E-05 40.8 3.2 40 198-237 135-177 (311)
248 PF00398 RrnaAD: Ribosomal RNA 87.2 0.68 1.5E-05 39.7 3.6 42 186-230 19-60 (262)
249 COG1522 Lrp Transcriptional re 87.2 0.8 1.7E-05 35.5 3.7 47 38-91 9-55 (154)
250 TIGR01889 Staph_reg_Sar staphy 87.2 0.8 1.7E-05 33.7 3.5 49 38-91 26-76 (109)
251 PRK04172 pheS phenylalanyl-tRN 87.1 0.54 1.2E-05 44.1 3.1 66 38-116 7-72 (489)
252 COG4122 Predicted O-methyltran 87.1 0.57 1.2E-05 39.2 2.9 44 196-239 57-102 (219)
253 PRK04338 N(2),N(2)-dimethylgua 87.1 0.58 1.3E-05 42.5 3.2 40 199-238 58-98 (382)
254 COG2512 Predicted membrane-ass 86.7 0.63 1.4E-05 40.0 3.0 47 39-91 197-243 (258)
255 PRK15128 23S rRNA m(5)C1962 me 86.7 0.58 1.3E-05 42.7 3.0 41 197-238 219-260 (396)
256 PF12793 SgrR_N: Sugar transpo 86.5 0.79 1.7E-05 34.4 3.1 35 53-91 18-52 (115)
257 KOG4589 Cell division protein 86.4 1.1 2.3E-05 36.8 3.9 43 191-233 62-105 (232)
258 COG3413 Predicted DNA binding 86.3 0.75 1.6E-05 38.2 3.2 43 29-81 159-201 (215)
259 PRK13256 thiopurine S-methyltr 86.2 1.5 3.2E-05 36.9 4.9 39 197-237 42-81 (226)
260 PF01795 Methyltransf_5: MraW 86.1 1 2.2E-05 39.7 4.1 52 186-238 9-61 (310)
261 PLN02853 Probable phenylalanyl 86.0 0.69 1.5E-05 43.2 3.1 69 37-118 3-73 (492)
262 PF13545 HTH_Crp_2: Crp-like h 85.8 0.55 1.2E-05 31.8 1.9 34 54-91 28-61 (76)
263 PRK03573 transcriptional regul 85.2 1.5 3.3E-05 33.7 4.3 44 42-91 36-79 (144)
264 PRK11783 rlmL 23S rRNA m(2)G24 85.1 0.73 1.6E-05 45.2 3.0 41 198-239 538-579 (702)
265 cd07377 WHTH_GntR Winged helix 85.1 1.2 2.6E-05 28.8 3.2 32 55-90 26-57 (66)
266 PF13730 HTH_36: Helix-turn-he 84.8 0.94 2E-05 28.7 2.5 30 55-88 26-55 (55)
267 PF03141 Methyltransf_29: Puta 84.4 0.79 1.7E-05 42.7 2.7 24 197-220 116-139 (506)
268 PF10007 DUF2250: Uncharacteri 84.1 1.4 3.1E-05 31.6 3.4 47 38-91 8-54 (92)
269 COG1378 Predicted transcriptio 83.8 2 4.3E-05 36.7 4.7 61 39-112 18-78 (247)
270 PRK13509 transcriptional repre 83.8 1.3 2.9E-05 37.7 3.7 45 40-91 8-52 (251)
271 PRK04214 rbn ribonuclease BN/u 83.8 1.4 2.9E-05 40.5 4.0 35 53-91 309-343 (412)
272 PF13404 HTH_AsnC-type: AsnC-t 83.6 1.4 3E-05 26.8 2.7 36 38-80 4-39 (42)
273 PRK14165 winged helix-turn-hel 83.4 1.3 2.7E-05 37.1 3.3 52 53-113 20-71 (217)
274 PF02796 HTH_7: Helix-turn-hel 83.4 1.2 2.5E-05 27.3 2.4 23 54-80 21-43 (45)
275 PF12324 HTH_15: Helix-turn-he 83.4 1 2.2E-05 31.2 2.3 35 42-83 29-63 (77)
276 COG3432 Predicted transcriptio 83.4 0.66 1.4E-05 33.5 1.4 62 42-114 20-82 (95)
277 PF14394 DUF4423: Domain of un 82.9 2.3 5E-05 34.2 4.5 46 55-112 40-87 (171)
278 TIGR00498 lexA SOS regulatory 82.9 2.2 4.8E-05 34.8 4.6 50 38-91 7-59 (199)
279 PF01170 UPF0020: Putative RNA 82.7 1.3 2.9E-05 35.6 3.1 50 188-238 19-78 (179)
280 PTZ00326 phenylalanyl-tRNA syn 82.6 1.4 3E-05 41.4 3.5 70 37-118 6-76 (494)
281 COG0030 KsgA Dimethyladenosine 82.6 2.9 6.2E-05 36.0 5.2 44 186-230 19-62 (259)
282 KOG1661 Protein-L-isoaspartate 82.5 0.81 1.8E-05 38.1 1.8 43 196-238 80-125 (237)
283 COG4565 CitB Response regulato 82.4 1.8 3.9E-05 36.0 3.7 43 42-90 163-205 (224)
284 PRK05638 threonine synthase; V 82.0 1.5 3.2E-05 40.7 3.5 60 41-112 375-436 (442)
285 PF05584 Sulfolobus_pRN: Sulfo 81.9 2.7 5.9E-05 28.7 3.8 43 41-91 9-51 (72)
286 COG1675 TFA1 Transcription ini 81.8 1.9 4.1E-05 34.8 3.6 45 40-91 21-65 (176)
287 COG0293 FtsJ 23S rRNA methylas 81.6 3.7 8.1E-05 34.0 5.4 51 182-232 29-80 (205)
288 PRK10906 DNA-binding transcrip 81.4 1.6 3.5E-05 37.3 3.3 46 39-91 7-52 (252)
289 smart00531 TFIIE Transcription 81.3 1.9 4.2E-05 33.6 3.5 42 40-88 4-45 (147)
290 TIGR02987 met_A_Alw26 type II 81.2 1 2.2E-05 42.6 2.1 40 198-237 31-79 (524)
291 PLN02589 caffeoyl-CoA O-methyl 81.0 1.5 3.2E-05 37.4 2.9 42 197-238 78-121 (247)
292 PF08221 HTH_9: RNA polymerase 81.0 1.4 3.1E-05 29.1 2.2 42 42-90 18-59 (62)
293 COG5631 Predicted transcriptio 80.9 10 0.00022 30.2 7.2 78 24-111 63-147 (199)
294 PRK10870 transcriptional repre 80.6 12 0.00026 30.0 8.0 66 41-113 59-124 (176)
295 COG1510 Predicted transcriptio 80.3 2.2 4.7E-05 34.2 3.4 35 53-91 40-74 (177)
296 PF05206 TRM13: Methyltransfer 80.2 4.2 9.2E-05 34.9 5.5 36 196-231 16-56 (259)
297 PF00392 GntR: Bacterial regul 80.2 1.3 2.8E-05 29.2 1.8 35 53-91 22-57 (64)
298 KOG1500 Protein arginine N-met 80.1 2.2 4.7E-05 38.2 3.6 23 196-219 176-198 (517)
299 PRK09802 DNA-binding transcrip 80.1 1.9 4.1E-05 37.2 3.3 47 38-91 18-64 (269)
300 PF02475 Met_10: Met-10+ like- 80.0 2 4.4E-05 35.4 3.4 41 196-236 99-140 (200)
301 PF09824 ArsR: ArsR transcript 80.0 2.6 5.6E-05 33.2 3.7 57 31-98 11-67 (160)
302 TIGR01321 TrpR trp operon repr 79.1 2.7 5.8E-05 30.3 3.3 40 36-83 41-80 (94)
303 PRK11760 putative 23S rRNA C24 79.0 2.9 6.3E-05 37.5 4.1 37 197-235 210-246 (357)
304 KOG3191 Predicted N6-DNA-methy 78.8 2.3 5E-05 34.7 3.2 38 199-236 44-83 (209)
305 PF00165 HTH_AraC: Bacterial r 78.8 1.9 4.1E-05 25.7 2.1 29 53-85 7-35 (42)
306 PRK10434 srlR DNA-bindng trans 78.0 2.3 4.9E-05 36.4 3.2 46 39-91 7-52 (256)
307 PF13518 HTH_28: Helix-turn-he 77.8 3.4 7.3E-05 25.5 3.2 29 55-87 13-41 (52)
308 PF03291 Pox_MCEL: mRNA cappin 77.8 1.6 3.6E-05 38.8 2.3 63 171-238 38-102 (331)
309 PRK09954 putative kinase; Prov 77.7 3.3 7.2E-05 37.0 4.3 44 39-89 5-48 (362)
310 PHA02701 ORF020 dsRNA-binding 77.5 3.5 7.5E-05 33.4 3.8 49 37-91 4-52 (183)
311 PF13384 HTH_23: Homeodomain-l 77.4 2 4.3E-05 26.6 2.0 39 39-86 7-45 (50)
312 PF05732 RepL: Firmicute plasm 76.8 2.6 5.6E-05 33.7 3.0 44 55-110 76-119 (165)
313 PRK10411 DNA-binding transcrip 76.4 3.5 7.5E-05 34.9 3.8 46 39-91 6-51 (240)
314 PRK04424 fatty acid biosynthes 76.3 2.2 4.8E-05 34.6 2.5 46 39-91 9-54 (185)
315 COG1846 MarR Transcriptional r 75.8 3.7 7.9E-05 29.9 3.4 67 36-111 21-87 (126)
316 PF08280 HTH_Mga: M protein tr 75.7 3.2 7E-05 26.9 2.7 39 38-83 6-44 (59)
317 PRK10046 dpiA two-component re 75.7 3.5 7.6E-05 34.0 3.6 44 41-90 166-209 (225)
318 PRK01381 Trp operon repressor; 74.7 3.8 8.3E-05 29.8 3.1 40 36-83 41-80 (99)
319 PRK13239 alkylmercury lyase; P 74.6 3.6 7.9E-05 34.1 3.3 41 38-85 23-63 (206)
320 COG1733 Predicted transcriptio 74.5 4.8 0.0001 30.4 3.7 76 17-111 12-88 (120)
321 PF05219 DREV: DREV methyltran 74.5 3.5 7.7E-05 35.4 3.3 29 198-226 94-122 (265)
322 PF04072 LCM: Leucine carboxyl 74.3 6.2 0.00013 31.7 4.7 40 197-236 77-116 (183)
323 TIGR03879 near_KaiC_dom probab 74.2 2.2 4.8E-05 29.3 1.7 34 53-90 31-64 (73)
324 COG5459 Predicted rRNA methyla 74.1 1.4 3E-05 39.6 0.8 32 199-230 114-146 (484)
325 KOG0820 Ribosomal RNA adenine 74.0 8.6 0.00019 33.4 5.5 42 186-230 47-88 (315)
326 PHA02591 hypothetical protein; 74.0 5 0.00011 27.8 3.3 32 42-81 51-82 (83)
327 PF02384 N6_Mtase: N-6 DNA Met 73.8 3.2 7E-05 36.2 3.1 41 196-236 44-92 (311)
328 TIGR02787 codY_Gpos GTP-sensin 73.3 12 0.00026 31.9 6.1 45 41-91 187-231 (251)
329 KOG3045 Predicted RNA methylas 72.3 7.1 0.00015 33.7 4.6 52 163-214 141-196 (325)
330 COG1349 GlpR Transcriptional r 72.2 3.7 8E-05 35.0 3.0 45 40-91 8-52 (253)
331 PF07789 DUF1627: Protein of u 72.0 5.7 0.00012 31.0 3.6 46 53-107 5-50 (155)
332 PF02295 z-alpha: Adenosine de 71.8 3.4 7.3E-05 27.7 2.1 60 38-108 5-64 (66)
333 COG0275 Predicted S-adenosylme 71.3 7.2 0.00016 34.3 4.5 53 186-239 12-66 (314)
334 COG2519 GCD14 tRNA(1-methylade 70.7 9 0.0002 32.8 4.9 63 174-237 67-135 (256)
335 PRK12423 LexA repressor; Provi 70.6 5.3 0.00012 32.8 3.5 35 54-91 25-59 (202)
336 PRK11886 bifunctional biotin-- 70.5 6.3 0.00014 34.7 4.1 45 39-90 6-50 (319)
337 PRK11161 fumarate/nitrate redu 70.0 4.2 9.2E-05 33.7 2.8 34 54-91 184-217 (235)
338 PRK13777 transcriptional regul 69.7 6.3 0.00014 32.1 3.7 44 41-91 49-92 (185)
339 PRK11753 DNA-binding transcrip 69.6 5.2 0.00011 32.4 3.3 34 54-91 168-201 (211)
340 PF01475 FUR: Ferric uptake re 69.5 3.7 7.9E-05 30.5 2.1 65 38-108 9-74 (120)
341 PRK11511 DNA-binding transcrip 69.4 7.4 0.00016 29.4 3.8 44 42-90 14-57 (127)
342 PRK11783 rlmL 23S rRNA m(2)G24 69.2 7 0.00015 38.5 4.5 32 186-218 178-210 (702)
343 PRK10219 DNA-binding transcrip 68.8 8.3 0.00018 27.9 3.9 34 53-90 20-53 (107)
344 TIGR02147 Fsuc_second hypothet 68.3 8.8 0.00019 33.2 4.5 47 54-110 137-183 (271)
345 TIGR03697 NtcA_cyano global ni 68.2 5.1 0.00011 31.9 2.9 34 54-91 143-176 (193)
346 PRK09334 30S ribosomal protein 68.0 4.8 0.0001 28.5 2.3 35 53-91 40-74 (86)
347 COG1497 Predicted transcriptio 67.5 6.8 0.00015 33.2 3.4 84 54-151 25-111 (260)
348 PF10668 Phage_terminase: Phag 67.5 7.4 0.00016 25.6 2.9 22 53-78 21-42 (60)
349 PF05331 DUF742: Protein of un 67.1 7.3 0.00016 29.2 3.2 35 53-91 54-88 (114)
350 COG3963 Phospholipid N-methylt 67.1 9.3 0.0002 30.8 4.0 34 185-219 36-69 (194)
351 PF06969 HemN_C: HemN C-termin 67.0 7.4 0.00016 25.5 3.0 46 53-111 19-65 (66)
352 PRK09273 hypothetical protein; 66.8 3.7 8.1E-05 34.0 1.8 41 199-239 63-103 (211)
353 PF13542 HTH_Tnp_ISL3: Helix-t 66.7 9 0.0002 23.7 3.2 36 38-82 16-51 (52)
354 TIGR03826 YvyF flagellar opero 66.6 8.3 0.00018 29.8 3.6 35 41-80 34-68 (137)
355 smart00088 PINT motif in prote 66.0 14 0.00031 25.5 4.5 51 33-90 6-56 (88)
356 smart00753 PAM PCI/PINT associ 66.0 14 0.00031 25.5 4.5 51 33-90 6-56 (88)
357 PRK13918 CRP/FNR family transc 65.9 5.9 0.00013 31.9 2.8 33 54-90 149-181 (202)
358 PF02636 Methyltransf_28: Puta 65.8 6.6 0.00014 33.3 3.2 33 198-230 18-58 (252)
359 PRK11639 zinc uptake transcrip 65.7 7.7 0.00017 31.0 3.4 52 38-91 27-79 (169)
360 PF06406 StbA: StbA protein; 65.0 19 0.0004 31.8 6.0 64 171-234 245-310 (318)
361 TIGR00308 TRM1 tRNA(guanine-26 64.9 6.3 0.00014 35.8 3.0 39 200-238 46-86 (374)
362 PF13936 HTH_38: Helix-turn-he 64.6 9.3 0.0002 23.2 2.9 24 53-80 19-42 (44)
363 PF00126 HTH_1: Bacterial regu 64.4 8.6 0.00019 24.8 2.9 54 39-110 3-59 (60)
364 cd00006 PTS_IIA_man PTS_IIA, P 64.4 15 0.00032 27.4 4.6 48 190-237 51-100 (122)
365 smart00421 HTH_LUXR helix_turn 63.6 10 0.00022 23.3 3.1 25 54-82 18-42 (58)
366 smart00342 HTH_ARAC helix_turn 63.4 8.3 0.00018 25.7 2.8 30 54-87 1-30 (84)
367 TIGR00635 ruvB Holliday juncti 63.4 7.3 0.00016 33.7 3.1 34 53-90 254-288 (305)
368 KOG2651 rRNA adenine N-6-methy 63.3 7.2 0.00016 35.5 3.0 36 196-232 151-186 (476)
369 PRK11642 exoribonuclease R; Pr 63.2 11 0.00024 37.8 4.6 49 41-91 23-71 (813)
370 PLN02668 indole-3-acetate carb 62.5 15 0.00032 33.5 4.9 34 198-231 63-111 (386)
371 PRK09462 fur ferric uptake reg 62.1 13 0.00028 28.8 4.0 53 38-91 18-71 (148)
372 PHA03103 double-strand RNA-bin 61.6 15 0.00033 29.8 4.3 43 42-91 18-60 (183)
373 cd06445 ATase The DNA repair p 61.5 18 0.00038 24.9 4.2 42 41-87 4-45 (79)
374 PF02502 LacAB_rpiB: Ribose/Ga 61.5 4.5 9.7E-05 31.4 1.2 39 202-240 59-97 (140)
375 PF11994 DUF3489: Protein of u 61.3 15 0.00033 25.1 3.6 42 42-90 15-58 (72)
376 COG3695 Predicted methylated D 60.9 12 0.00026 27.3 3.2 51 39-91 8-58 (103)
377 PRK09775 putative DNA-binding 60.8 12 0.00026 34.7 4.2 52 42-108 5-56 (442)
378 PRK09391 fixK transcriptional 60.7 8.1 0.00018 32.1 2.8 33 54-90 179-211 (230)
379 TIGR00589 ogt O-6-methylguanin 60.2 19 0.00041 25.0 4.1 43 38-85 3-45 (80)
380 TIGR00824 EIIA-man PTS system, 59.8 19 0.00041 26.7 4.4 49 189-237 51-101 (116)
381 cd06170 LuxR_C_like C-terminal 59.8 13 0.00028 22.8 3.1 25 54-82 15-39 (57)
382 COG0735 Fur Fe2+/Zn2+ uptake r 59.7 11 0.00024 29.3 3.2 51 39-91 23-74 (145)
383 TIGR02844 spore_III_D sporulat 59.6 12 0.00026 26.2 3.0 31 41-79 10-40 (80)
384 PRK11534 DNA-binding transcrip 59.4 10 0.00023 31.2 3.3 36 52-91 28-63 (224)
385 PF08704 GCD14: tRNA methyltra 59.4 15 0.00033 31.3 4.3 57 173-230 12-73 (247)
386 KOG2187 tRNA uracil-5-methyltr 59.1 6.9 0.00015 36.8 2.2 42 196-239 381-423 (534)
387 PF03374 ANT: Phage antirepres 58.8 13 0.00028 27.1 3.3 41 41-90 13-53 (111)
388 TIGR03338 phnR_burk phosphonat 58.7 10 0.00022 31.0 3.0 36 52-91 32-67 (212)
389 PRK09464 pdhR transcriptional 58.4 12 0.00026 31.5 3.5 35 53-91 32-67 (254)
390 PF03297 Ribosomal_S25: S25 ri 58.3 8 0.00017 28.5 2.0 35 53-91 58-92 (105)
391 PF04539 Sigma70_r3: Sigma-70 58.2 7.6 0.00017 26.3 1.9 34 53-90 19-52 (78)
392 COG1725 Predicted transcriptio 58.2 12 0.00026 28.5 3.0 35 53-91 34-68 (125)
393 TIGR02698 CopY_TcrY copper tra 57.9 15 0.00032 28.0 3.6 51 38-91 5-55 (130)
394 COG2390 DeoR Transcriptional r 57.9 10 0.00022 33.7 3.0 35 53-91 25-59 (321)
395 PF01418 HTH_6: Helix-turn-hel 57.8 14 0.0003 25.3 3.1 31 54-88 34-64 (77)
396 PRK11414 colanic acid/biofilm 57.8 12 0.00026 30.9 3.3 36 52-91 32-67 (221)
397 PF13443 HTH_26: Cro/C1-type H 57.7 7.8 0.00017 25.0 1.8 31 42-80 2-32 (63)
398 PRK00135 scpB segregation and 57.5 13 0.00028 30.4 3.3 41 40-90 93-133 (188)
399 PF00356 LacI: Bacterial regul 57.3 6.4 0.00014 24.4 1.2 11 56-66 1-11 (46)
400 PRK10402 DNA-binding transcrip 57.1 8.7 0.00019 31.8 2.4 34 54-91 169-202 (226)
401 PF00196 GerE: Bacterial regul 57.1 8.3 0.00018 24.6 1.8 37 37-82 6-42 (58)
402 COG1565 Uncharacterized conser 57.0 26 0.00056 31.7 5.4 59 167-230 51-117 (370)
403 PRK10736 hypothetical protein; 57.0 13 0.00027 33.8 3.5 44 40-91 311-354 (374)
404 COG1654 BirA Biotin operon rep 56.9 13 0.00029 25.9 2.9 49 53-112 18-66 (79)
405 COG4901 Ribosomal protein S25 56.9 11 0.00024 27.5 2.5 50 38-91 42-92 (107)
406 PRK13917 plasmid segregation p 56.8 38 0.00082 30.2 6.6 59 174-234 267-325 (344)
407 KOG2165 Anaphase-promoting com 56.7 12 0.00027 36.4 3.5 48 53-108 615-662 (765)
408 PF06971 Put_DNA-bind_N: Putat 56.6 5.3 0.00012 25.2 0.8 33 40-77 15-47 (50)
409 COG1802 GntR Transcriptional r 56.5 13 0.00029 30.8 3.5 36 52-91 37-72 (230)
410 PF11312 DUF3115: Protein of u 56.3 16 0.00034 32.3 3.8 22 199-220 87-108 (315)
411 PF02319 E2F_TDP: E2F/DP famil 56.1 6.2 0.00013 26.7 1.1 37 53-91 23-62 (71)
412 TIGR01764 excise DNA binding d 56.1 11 0.00024 22.5 2.2 22 55-80 2-23 (49)
413 PF04545 Sigma70_r4: Sigma-70, 56.0 12 0.00025 23.1 2.3 26 53-82 19-44 (50)
414 TIGR03329 Phn_aa_oxid putative 56.0 13 0.00029 34.3 3.6 33 200-232 25-59 (460)
415 PF01371 Trp_repressor: Trp re 55.8 15 0.00033 26.1 3.1 40 35-83 34-74 (87)
416 PF04672 Methyltransf_19: S-ad 55.7 26 0.00056 30.3 5.0 41 198-238 68-112 (267)
417 TIGR00689 rpiB_lacA_lacB sugar 55.4 7.6 0.00017 30.3 1.6 38 202-239 58-95 (144)
418 COG4367 Uncharacterized protei 55.3 12 0.00026 26.6 2.4 26 53-82 22-47 (97)
419 PF09821 AAA_assoc_C: C-termin 55.2 10 0.00022 28.6 2.2 46 59-117 2-47 (120)
420 TIGR03433 padR_acidobact trans 55.2 28 0.0006 25.0 4.5 67 42-112 9-79 (100)
421 PRK10430 DNA-binding transcrip 55.1 13 0.00027 30.9 3.1 34 53-90 177-210 (239)
422 TIGR00331 hrcA heat shock gene 55.0 17 0.00037 32.4 4.0 41 44-91 14-56 (337)
423 PRK10225 DNA-binding transcrip 54.9 14 0.00031 31.1 3.4 35 53-91 31-66 (257)
424 TIGR01120 rpiB ribose 5-phosph 54.8 8 0.00017 30.2 1.6 39 201-239 58-96 (143)
425 COG3645 Uncharacterized phage- 54.8 13 0.00029 28.5 2.8 41 41-90 36-76 (135)
426 PRK09990 DNA-binding transcrip 54.7 15 0.00032 30.9 3.5 36 52-91 28-64 (251)
427 PRK04984 fatty acid metabolism 54.6 15 0.00033 30.5 3.5 35 53-91 29-64 (239)
428 PF14338 Mrr_N: Mrr N-terminal 54.5 44 0.00095 23.5 5.4 62 42-114 25-88 (92)
429 PF03428 RP-C: Replication pro 54.2 12 0.00025 30.3 2.6 33 55-91 71-104 (177)
430 cd04762 HTH_MerR-trunc Helix-T 54.0 12 0.00026 22.2 2.1 23 55-81 1-23 (49)
431 PRK10421 DNA-binding transcrip 54.0 16 0.00034 30.9 3.5 35 53-91 24-59 (253)
432 TIGR02812 fadR_gamma fatty aci 53.8 16 0.00035 30.3 3.6 36 52-91 27-63 (235)
433 COG3398 Uncharacterized protei 53.7 29 0.00063 29.1 4.8 48 37-91 101-148 (240)
434 COG3682 Predicted transcriptio 53.4 23 0.0005 26.8 3.9 62 37-108 6-67 (123)
435 PF13814 Replic_Relax: Replica 53.4 17 0.00036 29.1 3.4 59 53-115 8-71 (191)
436 PRK00215 LexA repressor; Valid 53.2 23 0.0005 28.8 4.3 36 53-91 22-57 (205)
437 KOG2793 Putative N2,N2-dimethy 52.9 17 0.00036 31.1 3.4 40 196-236 83-123 (248)
438 COG2186 FadR Transcriptional r 52.8 17 0.00038 30.6 3.6 43 54-107 34-76 (241)
439 PRK13626 transcriptional regul 52.2 11 0.00023 36.0 2.4 35 53-91 22-56 (552)
440 PF07091 FmrO: Ribosomal RNA m 52.1 44 0.00095 28.6 5.8 34 198-231 105-138 (251)
441 PF11972 HTH_13: HTH DNA bindi 52.0 24 0.00051 22.7 3.2 36 42-84 4-39 (54)
442 PRK05571 ribose-5-phosphate is 51.8 9.6 0.00021 29.9 1.7 37 204-240 63-99 (148)
443 PF08281 Sigma70_r4_2: Sigma-7 51.7 15 0.00032 22.9 2.3 25 53-81 25-49 (54)
444 TIGR02531 yecD_yerC TrpR-relat 51.6 18 0.0004 25.7 3.0 34 40-82 41-74 (88)
445 PF13309 HTH_22: HTH domain 51.4 13 0.00028 24.6 2.0 38 31-80 27-64 (64)
446 PF01035 DNA_binding_1: 6-O-me 51.2 14 0.0003 25.9 2.3 42 38-81 3-44 (85)
447 PF12728 HTH_17: Helix-turn-he 50.7 15 0.00032 22.7 2.1 22 55-80 2-23 (51)
448 PF05158 RNA_pol_Rpc34: RNA po 50.7 15 0.00033 32.7 2.9 45 42-91 89-133 (327)
449 KOG2918 Carboxymethyl transfer 49.9 17 0.00037 32.2 3.0 41 196-236 85-127 (335)
450 PF10771 DUF2582: Protein of u 49.8 20 0.00044 23.9 2.8 38 42-86 13-50 (65)
451 TIGR02404 trehalos_R_Bsub treh 49.7 16 0.00036 30.3 2.9 42 55-107 25-66 (233)
452 TIGR03739 PRTRC_D PRTRC system 49.4 65 0.0014 28.3 6.8 46 188-233 263-308 (320)
453 KOG4058 Uncharacterized conser 49.4 15 0.00032 29.1 2.3 47 187-235 62-109 (199)
454 PRK00082 hrcA heat-inducible t 49.3 28 0.00061 31.1 4.5 35 53-91 24-60 (339)
455 PRK13558 bacterio-opsin activa 49.3 17 0.00037 35.1 3.3 45 28-82 610-654 (665)
456 TIGR02325 C_P_lyase_phnF phosp 49.2 17 0.00036 30.2 2.9 43 55-108 33-75 (238)
457 PRK10681 DNA-binding transcrip 48.9 23 0.0005 30.1 3.7 41 39-86 9-49 (252)
458 PRK00080 ruvB Holliday junctio 48.8 17 0.00037 32.0 3.0 35 53-91 275-310 (328)
459 PF04492 Phage_rep_O: Bacterio 48.7 17 0.00037 26.5 2.5 34 53-90 53-86 (100)
460 PRK03837 transcriptional regul 48.6 20 0.00044 29.8 3.3 35 53-91 35-70 (241)
461 PRK15201 fimbriae regulatory p 48.3 22 0.00047 29.0 3.2 35 36-79 135-169 (198)
462 cd06171 Sigma70_r4 Sigma70, re 48.2 24 0.00052 21.0 2.9 25 54-82 26-50 (55)
463 COG2524 Predicted transcriptio 48.0 39 0.00085 29.1 4.8 49 53-111 24-72 (294)
464 PRK11523 DNA-binding transcrip 47.9 22 0.00048 29.9 3.5 35 53-91 30-65 (253)
465 PF07638 Sigma70_ECF: ECF sigm 47.7 21 0.00046 28.6 3.2 35 41-83 142-176 (185)
466 PRK14999 histidine utilization 47.5 18 0.00038 30.4 2.8 43 54-107 35-78 (241)
467 PRK15411 rcsA colanic acid cap 47.4 22 0.00048 29.1 3.3 36 35-79 138-173 (207)
468 COG2169 Ada Adenosine deaminas 47.3 17 0.00038 29.6 2.5 42 43-90 88-129 (187)
469 PF05344 DUF746: Domain of Unk 47.2 24 0.00052 23.6 2.7 29 53-85 12-40 (65)
470 KOG2940 Predicted methyltransf 47.2 13 0.00029 31.6 1.9 31 198-230 72-103 (325)
471 PRK15121 right oriC-binding tr 46.7 27 0.00058 30.1 3.9 59 42-115 10-68 (289)
472 COG0698 RpiB Ribose 5-phosphat 46.7 13 0.00028 29.3 1.6 41 200-240 59-99 (151)
473 PRK04217 hypothetical protein; 46.7 25 0.00054 26.1 3.1 33 41-81 49-81 (110)
474 COG0500 SmtA SAM-dependent met 46.6 26 0.00057 25.0 3.4 28 202-230 52-80 (257)
475 cd04761 HTH_MerR-SF Helix-Turn 46.3 18 0.00039 21.7 2.0 27 55-89 1-27 (49)
476 PF13551 HTH_29: Winged helix- 46.2 29 0.00062 24.8 3.5 30 54-87 11-41 (112)
477 COG2964 Uncharacterized protei 46.1 92 0.002 26.1 6.6 44 31-86 176-219 (220)
478 PRK15418 transcriptional regul 46.0 20 0.00044 31.7 3.0 35 53-91 28-62 (318)
479 PF03514 GRAS: GRAS domain fam 45.5 26 0.00055 31.8 3.6 46 186-232 99-151 (374)
480 PF09681 Phage_rep_org_N: N-te 45.4 25 0.00053 26.6 3.0 48 53-112 52-99 (121)
481 PRK12615 galactose-6-phosphate 45.0 15 0.00031 29.6 1.8 39 202-240 60-98 (171)
482 PF09929 DUF2161: Uncharacteri 44.9 33 0.00072 25.8 3.5 57 31-111 59-115 (118)
483 PF04157 EAP30: EAP30/Vps36 fa 44.8 13 0.00028 31.0 1.6 34 53-90 189-222 (223)
484 PHA01634 hypothetical protein 44.5 17 0.00036 28.1 1.9 21 199-219 29-49 (156)
485 TIGR02018 his_ut_repres histid 44.1 22 0.00047 29.5 2.8 41 56-107 27-67 (230)
486 PRK09764 DNA-binding transcrip 43.7 23 0.0005 29.6 2.9 44 53-107 27-71 (240)
487 PF03965 Penicillinase_R: Peni 43.6 19 0.00041 26.5 2.1 51 38-91 4-54 (115)
488 PHA01080 hypothetical protein 43.5 27 0.00057 24.0 2.5 36 5-40 42-77 (80)
489 PTZ00215 ribose 5-phosphate is 43.4 15 0.00033 28.9 1.6 37 203-239 65-101 (151)
490 COG2344 AT-rich DNA-binding pr 43.3 31 0.00066 28.4 3.3 41 41-86 20-60 (211)
491 KOG1709 Guanidinoacetate methy 43.2 46 0.001 28.1 4.4 43 196-238 99-141 (271)
492 COG4883 Uncharacterized protei 42.9 98 0.0021 27.5 6.6 87 133-219 67-161 (500)
493 PF10078 DUF2316: Uncharacteri 42.8 18 0.00038 25.9 1.7 25 53-81 22-46 (89)
494 COG0640 ArsR Predicted transcr 42.7 43 0.00093 22.7 3.9 53 32-91 20-72 (110)
495 PHA00542 putative Cro-like pro 42.6 30 0.00064 24.0 2.9 24 53-80 30-53 (82)
496 PF01381 HTH_3: Helix-turn-hel 42.6 22 0.00047 22.0 2.0 25 53-81 8-32 (55)
497 KOG2352 Predicted spermine/spe 42.5 8.2 0.00018 36.0 -0.0 72 166-240 266-338 (482)
498 PF03602 Cons_hypoth95: Conser 41.8 18 0.00039 29.2 1.9 36 199-235 43-79 (183)
499 PRK15340 transcriptional regul 41.7 60 0.0013 27.1 5.0 47 39-90 111-157 (216)
500 PRK13503 transcriptional activ 41.7 36 0.00078 28.7 3.9 60 42-116 176-235 (278)
No 1
>KOG3178 consensus Hydroxyindole-O-methyltransferase and related SAM-dependent methyltransferases [General function prediction only]
Probab=99.97 E-value=3.3e-29 Score=217.28 Aligned_cols=217 Identities=53% Similarity=0.858 Sum_probs=192.4
Q ss_pred ccHHHHHHHHHHHhhhHHHHHHHHHHhcChHHHHHhcCCCCCCCHHHHHhhCCC-CCCCCcchHHHHHHHHhcCCccccc
Q 044458 13 SDEEANLFAMQLTSASVLPMVLKSAIELDLLEVIAKAGPGAFMSPKQIASQLPT-KNSDAHILLDRILRLLASYSVLNCS 91 (241)
Q Consensus 13 ~~~~~~~~l~~~~~g~~~~~~L~~a~~lglfd~L~~~~~~~~~t~~eLA~~~g~-~~~~~~~~l~rlLr~L~~~g~l~~~ 91 (241)
+.+++..+++++++++..+++|++|+||||||+|.+++ + ..|||..+.. ++|.++..++|+||.|++.+++++.
T Consensus 2 ~e~~~~l~~~~l~~~~~~~~~lk~A~eL~v~d~l~~~~---~--p~~ia~~l~~~~~~~~p~ll~r~lr~L~s~~i~k~~ 76 (342)
T KOG3178|consen 2 EENEASLRAMRLANGFALPMVLKAACELGVFDILANAG---S--PSEIASLLPTPKNPEAPVLLDRILRLLVSYSILKCR 76 (342)
T ss_pred chhHHHHHHHHHHhhhhhHHHHHHHHHcChHHHHHhCC---C--HHHHHHhccCCCCCCChhHHHHHHHHHHHhhhceee
Confidence 45678899999999999999999999999999999853 2 7777777763 4555888999999999999999986
Q ss_pred cccCCCCccccceecCccccccccCCCCCChHHHHHHhcChhhHHhhhhHHHHHhcCCchhhhhhCCCcccccccCchHH
Q 044458 92 LHTLPDGGVERLYGLAPVCKFLTKNEDGVSLSDICLLCQDKIVMESWYHLKDAVLEGGIPFNMAYGMNAFDYHGKDLRLN 171 (241)
Q Consensus 92 ~~~~~~g~~~~~y~~t~~s~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~~l~~g~~~~~~~~g~~~~e~~~~~~~~~ 171 (241)
. ..+ + .|++++++++++++++..+++.++...+.+..+..|.++.++++.+..+|..++|...|+|...+....
T Consensus 77 ~---~~~--~-~Y~~~~~~~~~l~~~~~~S~a~~~~~~~~~v~~~~w~~l~dai~eg~~~~~~~~G~~l~~~~~~~~~~~ 150 (342)
T KOG3178|consen 77 L---VGG--E-VYSATPVCKYFLKDSGGGSLAPLVLLNTSKVIMNTWQFLKDAILEGGDAFATAHGMMLGGYGGADERFS 150 (342)
T ss_pred e---ecc--e-eeeccchhhhheecCCCCchhHHHHHhcccchhhhHHHHHHHHHhcccCCccccchhhhhhcccccccH
Confidence 2 111 3 899999999776555456899999888888899999999999999999999999988999999988888
Q ss_pred HHHHHHHHhcchhhHHHHHHhcCCCCCCCeEEEecCCchHHHHHHHHHCCCCcEEEccchHHHhcCCCC
Q 044458 172 KIFNNGMFSHSTITMKKFLENYKGFEGLQSVVDVGGGIGASLDMIISKYPSIKGINFDLPHVIQDAPAY 240 (241)
Q Consensus 172 ~~f~~aM~~~~~~~~~~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~DlP~vi~~a~~~ 240 (241)
..|+++|...+....+.+++.|.+|++....||||||.|..+..++..||++++|.+|+|.|++.++.+
T Consensus 151 ~~~~~sm~~l~~~~~~~il~~~~Gf~~v~~avDvGgGiG~v~k~ll~~fp~ik~infdlp~v~~~a~~~ 219 (342)
T KOG3178|consen 151 KDFNGSMSFLSTLVMKKILEVYTGFKGVNVAVDVGGGIGRVLKNLLSKYPHIKGINFDLPFVLAAAPYL 219 (342)
T ss_pred HHHHHHHHHHHHHHHHhhhhhhcccccCceEEEcCCcHhHHHHHHHHhCCCCceeecCHHHHHhhhhhh
Confidence 999999999999988899999988999999999999999999999999999999999999999999876
No 2
>TIGR02716 C20_methyl_CrtF C-20 methyltransferase BchU. Members of this protein family are the S-adenosylmethionine-depenedent C-20 methyltransferase BchU, part of the pathway of bacteriochlorophyll c production in photosynthetic green sulfur bacteria. The position modified by this enzyme represents the difference between bacteriochlorophylls c and d; strains lacking this protein can only produced bacteriochlorophyll d.
Probab=99.95 E-value=2.3e-27 Score=207.92 Aligned_cols=186 Identities=21% Similarity=0.313 Sum_probs=140.1
Q ss_pred HHHHHHHHHHhcChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCcchHHHHHHHHhcCCccccccccCCCCccccceecCc
Q 044458 29 VLPMVLKSAIELDLLEVIAKAGPGAFMSPKQIASQLPTKNSDAHILLDRILRLLASYSVLNCSLHTLPDGGVERLYGLAP 108 (241)
Q Consensus 29 ~~~~~L~~a~~lglfd~L~~~~~~~~~t~~eLA~~~g~~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~g~~~~~y~~t~ 108 (241)
+.+++|++|++|||||+|.+ +|.|++|||+++|+ +++.++||||+|+++|+|++. +++|+||+
T Consensus 2 ~~~~~l~aa~~Lglfd~L~~----gp~t~~eLA~~~~~----~~~~~~~lL~~L~~lgll~~~---------~~~y~~t~ 64 (306)
T TIGR02716 2 IEFSCMKAAIELDLFSHMAE----GPKDLATLAADTGS----VPPRLEMLLETLRQMRVINLE---------DGKWSLTE 64 (306)
T ss_pred chHHHHHHHHHcCcHHHHhc----CCCCHHHHHHHcCC----ChHHHHHHHHHHHhCCCeEec---------CCcEecch
Confidence 45789999999999999987 69999999999999 999999999999999999974 58999999
Q ss_pred cccccccCCCCC---ChHHHHHHhcChhhHHhhhhHHHHHhcCCchhhhhhCCCcccccccCchHHHHHHHHHHhcchhh
Q 044458 109 VCKFLTKNEDGV---SLSDICLLCQDKIVMESWYHLKDAVLEGGIPFNMAYGMNAFDYHGKDLRLNKIFNNGMFSHSTIT 185 (241)
Q Consensus 109 ~s~~l~~~~~~~---~~~~~~~~~~~~~~~~~~~~L~~~l~~g~~~~~~~~g~~~~e~~~~~~~~~~~f~~aM~~~~~~~ 185 (241)
.++.++.+.++. ++..++.+. .......|.+|.+++| ++++|.. .+++.+..++....|...+.......
T Consensus 65 ~~~~~l~~~~~~~~~~~~~~~~~~-~~~~~~~~~~l~~~~r-~~~~~~~-----~~~~~~~~~~~~~~~~~~~~~~~~~~ 137 (306)
T TIGR02716 65 FADYMFSPTPKEPNLHQTPVAKAM-AFLADDFYMGLSQAVR-GQKNFKG-----QVPYPPVTREDNLYFEEIHRSNAKFA 137 (306)
T ss_pred hHHhhccCCccchhhhcCchHHHH-HHHHHHHHHhHHHHhc-CCccccc-----ccCCCCCCHHHHHhHHHHHHhcchhH
Confidence 998555544321 112333332 1123356899999997 4445532 22333333333333443333444455
Q ss_pred HHHHHHhcCCCCCCCeEEEecCCchHHHHHHHHHCCCCcEEEccchHHHhcCCC
Q 044458 186 MKKFLENYKGFEGLQSVVDVGGGIGASLDMIISKYPSIKGINFDLPHVIQDAPA 239 (241)
Q Consensus 186 ~~~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~DlP~vi~~a~~ 239 (241)
.+.+++.++ +++..+|||||||+|.+++.+++++|+++++++|+|++++.+++
T Consensus 138 ~~~l~~~~~-~~~~~~vlDiG~G~G~~~~~~~~~~p~~~~~~~D~~~~~~~a~~ 190 (306)
T TIGR02716 138 IQLLLEEAK-LDGVKKMIDVGGGIGDISAAMLKHFPELDSTILNLPGAIDLVNE 190 (306)
T ss_pred HHHHHHHcC-CCCCCEEEEeCCchhHHHHHHHHHCCCCEEEEEecHHHHHHHHH
Confidence 567788887 98899999999999999999999999999999999999987653
No 3
>PF00891 Methyltransf_2: O-methyltransferase; InterPro: IPR001077 Methyl transfer from the ubiquitous S-adenosyl-L-methionine (AdoMet) to either nitrogen, oxygen or carbon atoms is frequently employed in diverse organisms ranging from bacteria to plants and mammals. The reaction is catalysed by methyltransferases (Mtases) and modifies DNA, RNA, proteins and small molecules, such as catechol for regulatory purposes. The various aspects of the role of DNA methylation in prokaryotic restriction-modification systems and in a number of cellular processes in eukaryotes including gene regulation and differentiation is well documented. Three classes of DNA Mtases transfer the methyl group from AdoMet to the target base to form either N-6-methyladenine, or N-4-methylcytosine, or C-5- methylcytosine. In C-5-cytosine Mtases, ten conserved motifs are arranged in the same order []. Motif I (a glycine-rich or closely related consensus sequence; FAGxGG in M.HhaI []), shared by other AdoMet-Mtases [], is part of the cofactor binding site and motif IV (PCQ) is part of the catalytic site. In contrast, sequence comparison among N-6-adenine and N-4-cytosine Mtases indicated two of the conserved segments [], although more conserved segments may be present. One of them corresponds to motif I in C-5-cytosine Mtases, and the other is named (D/N/S)PP(Y/F). Crystal structures are known for a number of Mtases [, , , ]. The cofactor binding sites are almost identical and the essential catalytic amino acids coincide. The comparable protein folding and the existence of equivalent amino acids in similar secondary and tertiary positions indicate that many (if not all) AdoMet-Mtases have a common catalytic domain structure. This permits tertiary structure prediction of other DNA, RNA, protein, and small-molecule AdoMet-Mtases from their amino acid sequences []. This domain includes a range of O-methyltransferases some of which utilise S-adenosyl methionine as substrate []. In prokaryotes, the major role of DNA methylation is to protect host DNA against degradation by restriction enzymes. In eukaryotes, DNA methylation has been implicated in the control of several cellular processes, including differentiation, gene regulation, and embryonic development. O-methyltransferases have a common catalytic domain structure, which might be universal among S-adenosyl-L-methionine (AdoMet)-dependent methyltransferases []. Comparative analysis of the predicted amino acid sequences of a number of plant O-methyltransferase cDNA clones show that they share some 32-71% sequence identity, and can be grouped according to the different compounds they utilise as substrates [].; GO: 0008171 O-methyltransferase activity; PDB: 1FPQ_A 1FP1_D 3P9K_B 3P9I_D 3P9C_A 3I53_A 3I5U_A 3I64_A 3I58_A 1ZG3_A ....
Probab=99.93 E-value=7.3e-26 Score=191.98 Aligned_cols=137 Identities=33% Similarity=0.609 Sum_probs=120.8
Q ss_pred ccceecCccccccccCCCCCChHHHHHHhcChhhHHhhhhHHHHHhcCCchhhhhhCCCcccccccCchHHHHHHHHHHh
Q 044458 101 ERLYGLAPVCKFLTKNEDGVSLSDICLLCQDKIVMESWYHLKDAVLEGGIPFNMAYGMNAFDYHGKDLRLNKIFNNGMFS 180 (241)
Q Consensus 101 ~~~y~~t~~s~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~~l~~g~~~~~~~~g~~~~e~~~~~~~~~~~f~~aM~~ 180 (241)
++.|+||+.|+.|+.+.+..++..++.++..+..+..|.+|.+++++|+++|+..+|.++|++++++|+..+.|+++|..
T Consensus 3 ~~~y~~t~~s~~ll~~~~~~~~~~~~~~~~~~~~~~~~~~L~~~v~~g~~~~~~~~g~~~~~~~~~~~~~~~~f~~~m~~ 82 (241)
T PF00891_consen 3 GDRYSLTPLSELLLSDHSSPSMRGFVLFMISPELYPAWFRLTEAVRTGKPPFEKAFGTPFFEYLEEDPELAKRFNAAMAE 82 (241)
T ss_dssp TEEEEE-HHHHGGSTTTTTTHHHHHHHHHTCHHHHHGGGGHHHHHHHSS-HHHHHHSS-HHHHHHCSHHHHHHHHHHHHH
T ss_pred CCEEeChHHHHHHhCCCCcCcHHHHHHHhcCHHHHHHHHHHHhhhccCCCHHHHhcCCcHHHhhhhChHHHHHHHHHHHh
Confidence 58999999999777776545788888776678899999999999999999999999988999999999999999999999
Q ss_pred cchhhH-HHHHHhcCCCCCCCeEEEecCCchHHHHHHHHHCCCCcEEEccchHHHhcCC
Q 044458 181 HSTITM-KKFLENYKGFEGLQSVVDVGGGIGASLDMIISKYPSIKGINFDLPHVIQDAP 238 (241)
Q Consensus 181 ~~~~~~-~~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~DlP~vi~~a~ 238 (241)
.+.... +.+...++ |++.++|||||||.|+++.+++++||++++|++|+|+|++.++
T Consensus 83 ~~~~~~~~~~~~~~d-~~~~~~vvDvGGG~G~~~~~l~~~~P~l~~~v~Dlp~v~~~~~ 140 (241)
T PF00891_consen 83 YSRLNAFDILLEAFD-FSGFKTVVDVGGGSGHFAIALARAYPNLRATVFDLPEVIEQAK 140 (241)
T ss_dssp HHHHHHHHHHHHHST-TTTSSEEEEET-TTSHHHHHHHHHSTTSEEEEEE-HHHHCCHH
T ss_pred hhhcchhhhhhcccc-ccCccEEEeccCcchHHHHHHHHHCCCCcceeeccHhhhhccc
Confidence 998877 78888999 9999999999999999999999999999999999999998764
No 4
>PF08100 Dimerisation: Dimerisation domain; InterPro: IPR012967 This domain is found at the N terminus of a variety of plant O-methyltransferases. It has been shown to mediate dimerisation of these proteins [].; GO: 0008168 methyltransferase activity, 0046983 protein dimerization activity; PDB: 1ZGJ_A 1ZG3_A 1ZHF_A 1ZGA_A 2QYO_A 1KYW_A 1KYZ_A 3REO_D 1FPX_A 1FP2_A ....
Probab=99.09 E-value=1.4e-10 Score=74.23 Aligned_cols=51 Identities=49% Similarity=0.748 Sum_probs=43.3
Q ss_pred HHHHHHHhcChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCcchHHHHHHHHh
Q 044458 32 MVLKSAIELDLLEVIAKAGPGAFMSPKQIASQLPTKNSDAHILLDRILRLLA 83 (241)
Q Consensus 32 ~~L~~a~~lglfd~L~~~~~~~~~t~~eLA~~~g~~~~~~~~~l~rlLr~L~ 83 (241)
++|++|+||||||+|.+.| ++++|..||+.++...+|.++..|+|+||+|+
T Consensus 1 MaLk~aveLgI~dii~~~g-~~~ls~~eia~~l~~~~p~~~~~L~RimR~L~ 51 (51)
T PF08100_consen 1 MALKCAVELGIPDIIHNAG-GGPLSLSEIAARLPTSNPSAPPMLDRIMRLLV 51 (51)
T ss_dssp HHHHHHHHTTHHHHHHHHT-TS-BEHHHHHHTSTCT-TTHHHHHHHHHHHHH
T ss_pred CcHHHHHHcCcHHHHHHcC-CCCCCHHHHHHHcCCCCcchHHHHHHHHHHhC
Confidence 6899999999999999986 47999999999999445557889999999985
No 5
>PRK06922 hypothetical protein; Provisional
Probab=98.21 E-value=1.7e-06 Score=82.09 Aligned_cols=80 Identities=23% Similarity=0.269 Sum_probs=61.5
Q ss_pred CCcccccccCchHHHHHHHHHHhcchhh--HHHHHHhcCCCCCCCeEEEecCCchHHHHHHHHHCCCCcEEEccch-HHH
Q 044458 158 MNAFDYHGKDLRLNKIFNNGMFSHSTIT--MKKFLENYKGFEGLQSVVDVGGGIGASLDMIISKYPSIKGINFDLP-HVI 234 (241)
Q Consensus 158 ~~~~e~~~~~~~~~~~f~~aM~~~~~~~--~~~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~DlP-~vi 234 (241)
..+|+++..+++..++|...|....... .......++ |.+..+|||||||+|.++..+++.+|+.+++++|+. .++
T Consensus 377 ~~~fd~fg~r~D~~dRf~~~~~yle~m~~~~~~k~~i~d-~~~g~rVLDIGCGTG~ls~~LA~~~P~~kVtGIDIS~~ML 455 (677)
T PRK06922 377 VLLFDFFGLRKDAYDRFHNEEVYLEHMNSSADDKRIILD-YIKGDTIVDVGAGGGVMLDMIEEETEDKRIYGIDISENVI 455 (677)
T ss_pred hHHHHHhccChhhHhHHHhHHHHHHhccccHHHHHHHhh-hcCCCEEEEeCCCCCHHHHHHHHhCCCCEEEEEECCHHHH
Confidence 3578888888888888888776644432 122234456 767799999999999999999999999999999994 556
Q ss_pred hcCC
Q 044458 235 QDAP 238 (241)
Q Consensus 235 ~~a~ 238 (241)
+.++
T Consensus 456 e~Ar 459 (677)
T PRK06922 456 DTLK 459 (677)
T ss_pred HHHH
Confidence 6554
No 6
>PF12847 Methyltransf_18: Methyltransferase domain; PDB: 3G2Q_A 3G2O_A 3G2M_B 3G2P_B 3D2L_B 1IM8_B 3NJR_A 3E05_H 3EVZ_A 3HM2_A ....
Probab=97.99 E-value=3.6e-06 Score=62.22 Aligned_cols=40 Identities=23% Similarity=0.404 Sum_probs=36.8
Q ss_pred CCeEEEecCCchHHHHHHHHHCCCCcEEEccc-hHHHhcCC
Q 044458 199 LQSVVDVGGGIGASLDMIISKYPSIKGINFDL-PHVIQDAP 238 (241)
Q Consensus 199 ~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-P~vi~~a~ 238 (241)
..+|||||||+|.++..+++.+|+.+++.+|. |+.++.++
T Consensus 2 ~~~vLDlGcG~G~~~~~l~~~~~~~~v~gvD~s~~~~~~a~ 42 (112)
T PF12847_consen 2 GGRVLDLGCGTGRLSIALARLFPGARVVGVDISPEMLEIAR 42 (112)
T ss_dssp TCEEEEETTTTSHHHHHHHHHHTTSEEEEEESSHHHHHHHH
T ss_pred CCEEEEEcCcCCHHHHHHHhcCCCCEEEEEeCCHHHHHHHH
Confidence 36899999999999999999999999999999 88887765
No 7
>PRK14103 trans-aconitate 2-methyltransferase; Provisional
Probab=97.94 E-value=2.3e-05 Score=66.98 Aligned_cols=52 Identities=23% Similarity=0.335 Sum_probs=45.1
Q ss_pred HHHHHhcCCCCCCCeEEEecCCchHHHHHHHHHCCCCcEEEccc-hHHHhcCCC
Q 044458 187 KKFLENYKGFEGLQSVVDVGGGIGASLDMIISKYPSIKGINFDL-PHVIQDAPA 239 (241)
Q Consensus 187 ~~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-P~vi~~a~~ 239 (241)
..+++.++ .....+|||||||+|.++..+++++|+.+++.+|+ |..++.|++
T Consensus 19 ~~ll~~l~-~~~~~~vLDlGcG~G~~~~~l~~~~p~~~v~gvD~s~~~~~~a~~ 71 (255)
T PRK14103 19 YDLLARVG-AERARRVVDLGCGPGNLTRYLARRWPGAVIEALDSSPEMVAAARE 71 (255)
T ss_pred HHHHHhCC-CCCCCEEEEEcCCCCHHHHHHHHHCCCCEEEEEECCHHHHHHHHh
Confidence 46677776 66779999999999999999999999999999999 888877654
No 8
>PRK01683 trans-aconitate 2-methyltransferase; Provisional
Probab=97.84 E-value=3.5e-05 Score=65.73 Aligned_cols=53 Identities=25% Similarity=0.527 Sum_probs=45.3
Q ss_pred HHHHHHhcCCCCCCCeEEEecCCchHHHHHHHHHCCCCcEEEccc-hHHHhcCCC
Q 044458 186 MKKFLENYKGFEGLQSVVDVGGGIGASLDMIISKYPSIKGINFDL-PHVIQDAPA 239 (241)
Q Consensus 186 ~~~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-P~vi~~a~~ 239 (241)
...++..++ .....+|||||||.|.++..+++.+|+.+++.+|+ |..++.+++
T Consensus 20 ~~~ll~~~~-~~~~~~vLDiGcG~G~~~~~la~~~~~~~v~gvD~s~~~i~~a~~ 73 (258)
T PRK01683 20 ARDLLARVP-LENPRYVVDLGCGPGNSTELLVERWPAARITGIDSSPAMLAEARS 73 (258)
T ss_pred HHHHHhhCC-CcCCCEEEEEcccCCHHHHHHHHHCCCCEEEEEECCHHHHHHHHH
Confidence 446677776 77789999999999999999999999999999999 777776653
No 9
>PRK08287 cobalt-precorrin-6Y C(15)-methyltransferase; Validated
Probab=97.82 E-value=2.1e-05 Score=63.98 Aligned_cols=48 Identities=19% Similarity=0.376 Sum_probs=41.1
Q ss_pred HHhcCCCCCCCeEEEecCCchHHHHHHHHHCCCCcEEEccc-hHHHhcCC
Q 044458 190 LENYKGFEGLQSVVDVGGGIGASLDMIISKYPSIKGINFDL-PHVIQDAP 238 (241)
Q Consensus 190 ~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-P~vi~~a~ 238 (241)
+..++ .....+|||||||+|.++..+++++|+.+++.+|. |..++.++
T Consensus 24 ~~~l~-~~~~~~vLDiG~G~G~~~~~la~~~~~~~v~~vD~s~~~~~~a~ 72 (187)
T PRK08287 24 LSKLE-LHRAKHLIDVGAGTGSVSIEAALQFPSLQVTAIERNPDALRLIK 72 (187)
T ss_pred HHhcC-CCCCCEEEEECCcCCHHHHHHHHHCCCCEEEEEECCHHHHHHHH
Confidence 34455 66678999999999999999999999999999999 77777664
No 10
>COG4106 Tam Trans-aconitate methyltransferase [General function prediction only]
Probab=97.67 E-value=9.4e-05 Score=61.16 Aligned_cols=58 Identities=22% Similarity=0.414 Sum_probs=49.0
Q ss_pred hcchhhHHHHHHhcCCCCCCCeEEEecCCchHHHHHHHHHCCCCcEEEccc-hHHHhcCCC
Q 044458 180 SHSTITMKKFLENYKGFEGLQSVVDVGGGIGASLDMIISKYPSIKGINFDL-PHVIQDAPA 239 (241)
Q Consensus 180 ~~~~~~~~~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-P~vi~~a~~ 239 (241)
..+.. +..+++..+ ......|+|+|||.|.....+++++|....+.+|- |..++.|++
T Consensus 14 eRtRP-a~dLla~Vp-~~~~~~v~DLGCGpGnsTelL~~RwP~A~i~GiDsS~~Mla~Aa~ 72 (257)
T COG4106 14 ERTRP-ARDLLARVP-LERPRRVVDLGCGPGNSTELLARRWPDAVITGIDSSPAMLAKAAQ 72 (257)
T ss_pred hccCc-HHHHHhhCC-ccccceeeecCCCCCHHHHHHHHhCCCCeEeeccCCHHHHHHHHH
Confidence 34444 356777777 88889999999999999999999999999999998 888887754
No 11
>TIGR02469 CbiT precorrin-6Y C5,15-methyltransferase (decarboxylating), CbiT subunit. This model recognizes the CbiT methylase which is responsible, in part (along with CbiE), for methylating precorrin-6y (or cobalt-precorrin-6y) at both the 5 and 15 positions as well as the concomitant decarbozylation at C-12. In many organisms, this protein is fused to the CbiE subunit. The fused protein, when found in organisms catalyzing the oxidative version of the cobalamin biosynthesis pathway, is called CobL.
Probab=97.65 E-value=8.4e-05 Score=55.52 Aligned_cols=48 Identities=15% Similarity=0.183 Sum_probs=39.4
Q ss_pred HHHhcCCCCCCCeEEEecCCchHHHHHHHHHCCCCcEEEccc-hHHHhcC
Q 044458 189 FLENYKGFEGLQSVVDVGGGIGASLDMIISKYPSIKGINFDL-PHVIQDA 237 (241)
Q Consensus 189 ~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-P~vi~~a 237 (241)
++..++ .....+|+|||||.|.++..+++.+|+.+++.+|. +..++.+
T Consensus 11 ~~~~~~-~~~~~~vldlG~G~G~~~~~l~~~~~~~~v~~vD~s~~~~~~a 59 (124)
T TIGR02469 11 TLSKLR-LRPGDVLWDIGAGSGSITIEAARLVPNGRVYAIERNPEALRLI 59 (124)
T ss_pred HHHHcC-CCCCCEEEEeCCCCCHHHHHHHHHCCCceEEEEcCCHHHHHHH
Confidence 444555 55567999999999999999999999999999999 6666554
No 12
>PRK04457 spermidine synthase; Provisional
Probab=97.52 E-value=7.5e-05 Score=64.23 Aligned_cols=44 Identities=23% Similarity=0.358 Sum_probs=39.9
Q ss_pred CCCCeEEEecCCchHHHHHHHHHCCCCcEEEccc-hHHHhcCCCC
Q 044458 197 EGLQSVVDVGGGIGASLDMIISKYPSIKGINFDL-PHVIQDAPAY 240 (241)
Q Consensus 197 ~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-P~vi~~a~~~ 240 (241)
+..++|||||||.|.++..+++.+|+.+++++|+ |++++.|+++
T Consensus 65 ~~~~~vL~IG~G~G~l~~~l~~~~p~~~v~~VEidp~vi~~A~~~ 109 (262)
T PRK04457 65 PRPQHILQIGLGGGSLAKFIYTYLPDTRQTAVEINPQVIAVARNH 109 (262)
T ss_pred CCCCEEEEECCCHhHHHHHHHHhCCCCeEEEEECCHHHHHHHHHH
Confidence 3468999999999999999999999999999999 9999988653
No 13
>TIGR02021 BchM-ChlM magnesium protoporphyrin O-methyltransferase. This model represents the S-adenosylmethionine-dependent O-methyltransferase responsible for methylation of magnesium protoporphyrin IX. This step is essentiasl for the biosynthesis of both chlorophyll and bacteriochlorophyll. This model encompasses two closely related clades, from cyanobacteria (and plants) where it is called ChlM and other photosynthetic bacteria where it is known as BchM.
Probab=97.49 E-value=0.00018 Score=59.93 Aligned_cols=77 Identities=13% Similarity=0.013 Sum_probs=47.8
Q ss_pred cccccccCchHHHHHHHHHHhcchhhHHHHHHhcCC-CCCCCeEEEecCCchHHHHHHHHHCCCCcEEEccc-hHHHhcC
Q 044458 160 AFDYHGKDLRLNKIFNNGMFSHSTITMKKFLENYKG-FEGLQSVVDVGGGIGASLDMIISKYPSIKGINFDL-PHVIQDA 237 (241)
Q Consensus 160 ~~e~~~~~~~~~~~f~~aM~~~~~~~~~~~~~~~~~-~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-P~vi~~a 237 (241)
-|+.+..++.....+...|..........++..... ..+..+|||||||.|.++..+++. +.+++.+|. |+.++.|
T Consensus 16 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~vLDiGcG~G~~~~~la~~--~~~v~gvD~s~~~i~~a 93 (219)
T TIGR02021 16 RWARIYGSGDPVSRVRQTVREGRAAMRRKLLDWLPKDPLKGKRVLDAGCGTGLLSIELAKR--GAIVKAVDISEQMVQMA 93 (219)
T ss_pred HHHHhhCCchhhHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCEEEEEeCCCCHHHHHHHHC--CCEEEEEECCHHHHHHH
Confidence 344444444444455555533222223334433321 345689999999999999999886 457899998 7777766
Q ss_pred C
Q 044458 238 P 238 (241)
Q Consensus 238 ~ 238 (241)
+
T Consensus 94 ~ 94 (219)
T TIGR02021 94 R 94 (219)
T ss_pred H
Confidence 4
No 14
>PRK15001 SAM-dependent 23S ribosomal RNA mG1835 methyltransferase; Provisional
Probab=97.48 E-value=0.00013 Score=65.87 Aligned_cols=50 Identities=22% Similarity=0.281 Sum_probs=40.6
Q ss_pred HHHHhcCCCCCCCeEEEecCCchHHHHHHHHHCCCCcEEEccc-hHHHhcCC
Q 044458 188 KFLENYKGFEGLQSVVDVGGGIGASLDMIISKYPSIKGINFDL-PHVIQDAP 238 (241)
Q Consensus 188 ~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-P~vi~~a~ 238 (241)
-+++.++ .....+|||+|||+|.+++.+++++|+.+++..|. +.+++.++
T Consensus 219 llL~~lp-~~~~~~VLDLGCGtGvi~i~la~~~P~~~V~~vD~S~~Av~~A~ 269 (378)
T PRK15001 219 FFMQHLP-ENLEGEIVDLGCGNGVIGLTLLDKNPQAKVVFVDESPMAVASSR 269 (378)
T ss_pred HHHHhCC-cccCCeEEEEeccccHHHHHHHHhCCCCEEEEEECCHHHHHHHH
Confidence 3455555 33346999999999999999999999999999999 57777664
No 15
>TIGR03587 Pse_Me-ase pseudaminic acid biosynthesis-associated methylase. Members of this small clade are methyltransferases of the pfam08241 family and are observed within operons for the biosynthesis of pseudaminic acid, a component of exopolysaccharide and flagellin glycosyl modifications. Notable among these genomes is Pseudomonas fluorescens PfO-1. Possibly one of the two hydroxyl groups of pseudaminic acid, at positions 4 and 8 is converted to a methoxy group by this enzyme
Probab=97.45 E-value=0.00017 Score=59.76 Aligned_cols=44 Identities=18% Similarity=0.344 Sum_probs=38.9
Q ss_pred CCCCCeEEEecCCchHHHHHHHHHCCCCcEEEccc-hHHHhcCCC
Q 044458 196 FEGLQSVVDVGGGIGASLDMIISKYPSIKGINFDL-PHVIQDAPA 239 (241)
Q Consensus 196 ~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-P~vi~~a~~ 239 (241)
.....+|||||||+|.++..+++..|+.+++.+|+ |+.++.|++
T Consensus 41 ~~~~~~VLDiGCG~G~~~~~L~~~~~~~~v~giDiS~~~l~~A~~ 85 (204)
T TIGR03587 41 LPKIASILELGANIGMNLAALKRLLPFKHIYGVEINEYAVEKAKA 85 (204)
T ss_pred cCCCCcEEEEecCCCHHHHHHHHhCCCCeEEEEECCHHHHHHHHh
Confidence 34567899999999999999999999999999999 888888765
No 16
>PRK00107 gidB 16S rRNA methyltransferase GidB; Reviewed
Probab=97.44 E-value=0.0002 Score=58.54 Aligned_cols=41 Identities=27% Similarity=0.213 Sum_probs=36.3
Q ss_pred CCCeEEEecCCchHHHHHHHHHCCCCcEEEccc-hHHHhcCC
Q 044458 198 GLQSVVDVGGGIGASLDMIISKYPSIKGINFDL-PHVIQDAP 238 (241)
Q Consensus 198 ~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-P~vi~~a~ 238 (241)
...+|||||||+|..+..+++++|+.+++.+|. +..++.|+
T Consensus 45 ~g~~VLDiGcGtG~~al~la~~~~~~~V~giD~s~~~l~~A~ 86 (187)
T PRK00107 45 GGERVLDVGSGAGFPGIPLAIARPELKVTLVDSLGKKIAFLR 86 (187)
T ss_pred CCCeEEEEcCCCCHHHHHHHHHCCCCeEEEEeCcHHHHHHHH
Confidence 368999999999999999999999999999999 67776554
No 17
>PF08242 Methyltransf_12: Methyltransferase domain; InterPro: IPR013217 Methyl transfer from the ubiquitous donor S-adenosyl-L-methionine (SAM) to either nitrogen, oxygen or carbon atoms is frequently employed in diverse organisms ranging from bacteria to plants and mammals. The reaction is catalyzed by methyltransferases (Mtases) and modifies DNA, RNA, proteins and small molecules, such as catechol for regulatory purposes. The various aspects of the role of DNA methylation in prokaryotic restriction-modification systems and in a number of cellular processes in eukaryotes including gene regulation and differentiation is well documented. This entry represents a methyltransferase domain found in a large variety of SAM-dependent methyltransferases including, but not limited to: Hexaprenyldihydroxybenzoate methyltransferase (2.1.1.114 from EC), a mitochodrial enzyme involved in ubiquinone biosynthesis [] Fatty acid synthase (2.3.1.85 from EC), a biosynthetic enzyme catalysing the formation of long-chain fatty acids Glycine N-methyltransferase (2.1.1.20 from EC) which catalyses the SAM-dependent methylation of glycine to form sarcosine and may play a role in regulating the methylation potential of the cell [] Enniatin synthetase, involved in non-ribosomal biosynthesis of cyclohexadepsipeptidase, enniatin [] Histamine N-methyltransferase (2.1.1.8 from EC), a SAM-dependent histamine-inactivating enzyme [] A probable cobalt-precorrin-6Y C(15)-methyltransferase thought to be involved in adenosylcobalamin biosynthesis [] Structural studies show that this domain forms the Rossman-like alpha-beta fold typical of SAM-dependent methyltransferases [, , ].; PDB: 2VZ8_A 2VZ9_A.
Probab=97.43 E-value=2.9e-05 Score=56.21 Aligned_cols=37 Identities=24% Similarity=0.561 Sum_probs=31.6
Q ss_pred EEecCCchHHHHHHHHHCCCCcEEEccc-hHHHhcCCC
Q 044458 203 VDVGGGIGASLDMIISKYPSIKGINFDL-PHVIQDAPA 239 (241)
Q Consensus 203 vDVGGG~G~~~~~l~~~~P~l~~~v~Dl-P~vi~~a~~ 239 (241)
||||||+|.++..+++.+|..+.+..|. |.+++.+++
T Consensus 1 LdiGcG~G~~~~~l~~~~~~~~~~~~D~s~~~l~~a~~ 38 (99)
T PF08242_consen 1 LDIGCGTGRLLRALLEELPDARYTGVDISPSMLERARE 38 (99)
T ss_dssp -EESTTTS-TTTTHHHHC-EEEEEEEESSSSTTSTTCC
T ss_pred CEeCccChHHHHHHHHhCCCCEEEEEECCHHHHHHHHH
Confidence 7999999999999999999999999999 888877765
No 18
>PRK07402 precorrin-6B methylase; Provisional
Probab=97.39 E-value=0.00021 Score=58.53 Aligned_cols=49 Identities=16% Similarity=0.173 Sum_probs=41.4
Q ss_pred HHHhcCCCCCCCeEEEecCCchHHHHHHHHHCCCCcEEEccc-hHHHhcCC
Q 044458 189 FLENYKGFEGLQSVVDVGGGIGASLDMIISKYPSIKGINFDL-PHVIQDAP 238 (241)
Q Consensus 189 ~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-P~vi~~a~ 238 (241)
++..++ .....+|+|||||+|.++..+++..|+.+++.+|+ |+.++.++
T Consensus 32 l~~~l~-~~~~~~VLDiG~G~G~~~~~la~~~~~~~V~~vD~s~~~~~~a~ 81 (196)
T PRK07402 32 LISQLR-LEPDSVLWDIGAGTGTIPVEAGLLCPKGRVIAIERDEEVVNLIR 81 (196)
T ss_pred HHHhcC-CCCCCEEEEeCCCCCHHHHHHHHHCCCCEEEEEeCCHHHHHHHH
Confidence 445555 66678999999999999999999999999999999 88887664
No 19
>COG2813 RsmC 16S RNA G1207 methylase RsmC [Translation, ribosomal structure and biogenesis]
Probab=97.37 E-value=0.00027 Score=61.36 Aligned_cols=52 Identities=23% Similarity=0.251 Sum_probs=42.8
Q ss_pred HHHHHhcCCCCCCCeEEEecCCchHHHHHHHHHCCCCcEEEccc-hHHHhcCCC
Q 044458 187 KKFLENYKGFEGLQSVVDVGGGIGASLDMIISKYPSIKGINFDL-PHVIQDAPA 239 (241)
Q Consensus 187 ~~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-P~vi~~a~~ 239 (241)
+-+++.++ .....+|+|+|||.|.+++.+++.+|+.+.+..|. ..+++.+++
T Consensus 148 ~lLl~~l~-~~~~~~vlDlGCG~Gvlg~~la~~~p~~~vtmvDvn~~Av~~ar~ 200 (300)
T COG2813 148 RLLLETLP-PDLGGKVLDLGCGYGVLGLVLAKKSPQAKLTLVDVNARAVESARK 200 (300)
T ss_pred HHHHHhCC-ccCCCcEEEeCCCccHHHHHHHHhCCCCeEEEEecCHHHHHHHHH
Confidence 45567776 44445999999999999999999999999999999 577776653
No 20
>TIGR02752 MenG_heptapren 2-heptaprenyl-1,4-naphthoquinone methyltransferase. MenG is a generic term for a methyltransferase that catalyzes the last step in menaquinone biosynthesis; the exact enzymatic activity differs for different MenG because the menaquinone differ in their prenoid side chains in different species. Members of this MenG protein family are 2-heptaprenyl-1,4-naphthoquinone methyltransferase, and are found together in operons with the two subunits of the heptaprenyl diphosphate synthase in Bacillus subtilis and related species.
Probab=97.33 E-value=0.00028 Score=59.08 Aligned_cols=50 Identities=14% Similarity=0.149 Sum_probs=40.2
Q ss_pred HHHHhcCCCCCCCeEEEecCCchHHHHHHHHHC-CCCcEEEccc-hHHHhcCC
Q 044458 188 KFLENYKGFEGLQSVVDVGGGIGASLDMIISKY-PSIKGINFDL-PHVIQDAP 238 (241)
Q Consensus 188 ~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~-P~l~~~v~Dl-P~vi~~a~ 238 (241)
.++..++ .....+|||||||+|.++..+++.+ |+.+++.+|+ |..++.++
T Consensus 36 ~~l~~l~-~~~~~~vLDiGcG~G~~~~~la~~~~~~~~v~gvD~s~~~~~~a~ 87 (231)
T TIGR02752 36 DTMKRMN-VQAGTSALDVCCGTADWSIALAEAVGPEGHVIGLDFSENMLSVGR 87 (231)
T ss_pred HHHHhcC-CCCCCEEEEeCCCcCHHHHHHHHHhCCCCEEEEEECCHHHHHHHH
Confidence 3445555 5666899999999999999999986 7789999999 77776554
No 21
>PRK06202 hypothetical protein; Provisional
Probab=97.33 E-value=0.00054 Score=57.56 Aligned_cols=43 Identities=19% Similarity=0.151 Sum_probs=35.7
Q ss_pred CCCCeEEEecCCchHHHHHHHHH----CCCCcEEEccc-hHHHhcCCC
Q 044458 197 EGLQSVVDVGGGIGASLDMIISK----YPSIKGINFDL-PHVIQDAPA 239 (241)
Q Consensus 197 ~~~~~vvDVGGG~G~~~~~l~~~----~P~l~~~v~Dl-P~vi~~a~~ 239 (241)
.+..+|||||||+|.++..+++. .|+.+++.+|+ |..++.|++
T Consensus 59 ~~~~~iLDlGcG~G~~~~~L~~~~~~~g~~~~v~gvD~s~~~l~~a~~ 106 (232)
T PRK06202 59 DRPLTLLDIGCGGGDLAIDLARWARRDGLRLEVTAIDPDPRAVAFARA 106 (232)
T ss_pred CCCcEEEEeccCCCHHHHHHHHHHHhCCCCcEEEEEcCCHHHHHHHHh
Confidence 45689999999999999888764 56789999999 888877653
No 22
>TIGR00740 methyltransferase, putative. A simple BLAST search finds all members of this family and weaker hits to a large number of known and predicted methyltransferases. A single iteration with PSI-BLAST, keeping only clear members of the family, leads to a large number of highly significant hits to a set of known and predicted methyltransferases with a large repertoire of different specifities. This model is restricted to a subfamily found so far only in the Proteobacteria, sharing consistent length, full-length homology, and on average better than 35 % identity. It is reasonable to predict equivalent function within this subfamily.
Probab=97.27 E-value=0.00024 Score=60.01 Aligned_cols=42 Identities=21% Similarity=0.222 Sum_probs=36.7
Q ss_pred CCCCeEEEecCCchHHHHHHHHH--CCCCcEEEccc-hHHHhcCC
Q 044458 197 EGLQSVVDVGGGIGASLDMIISK--YPSIKGINFDL-PHVIQDAP 238 (241)
Q Consensus 197 ~~~~~vvDVGGG~G~~~~~l~~~--~P~l~~~v~Dl-P~vi~~a~ 238 (241)
....+|||||||+|.++..+++. +|+++++.+|+ |.+++.|+
T Consensus 52 ~~~~~iLDlGcG~G~~~~~l~~~~~~p~~~v~gvD~s~~ml~~a~ 96 (239)
T TIGR00740 52 TPDSNVYDLGCSRGAATLSARRNINQPNVKIIGIDNSQPMVERCR 96 (239)
T ss_pred CCCCEEEEecCCCCHHHHHHHHhcCCCCCeEEEEeCCHHHHHHHH
Confidence 34579999999999999999997 48899999999 88887765
No 23
>PF05175 MTS: Methyltransferase small domain; InterPro: IPR007848 This domain is found in ribosomal RNA small subunit methyltransferase C and in other methyltransferases.; GO: 0008168 methyltransferase activity; PDB: 1WY7_A 1DUS_A 2OZV_A 2PJD_A 1VQ1_A 1NV9_A 1SG9_C 1NV8_A 3Q87_B 3DMF_A ....
Probab=97.26 E-value=0.00014 Score=58.39 Aligned_cols=41 Identities=24% Similarity=0.307 Sum_probs=36.5
Q ss_pred CCCeEEEecCCchHHHHHHHHHCCCCcEEEccc-hHHHhcCC
Q 044458 198 GLQSVVDVGGGIGASLDMIISKYPSIKGINFDL-PHVIQDAP 238 (241)
Q Consensus 198 ~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-P~vi~~a~ 238 (241)
...+|||+|||+|.++..+++.+|+.+++..|. |.+++.++
T Consensus 31 ~~~~vLDlG~G~G~i~~~la~~~~~~~v~~vDi~~~a~~~a~ 72 (170)
T PF05175_consen 31 KGGRVLDLGCGSGVISLALAKRGPDAKVTAVDINPDALELAK 72 (170)
T ss_dssp TTCEEEEETSTTSHHHHHHHHTSTCEEEEEEESBHHHHHHHH
T ss_pred cCCeEEEecCChHHHHHHHHHhCCCCEEEEEcCCHHHHHHHH
Confidence 468999999999999999999999999999999 77776553
No 24
>PRK00121 trmB tRNA (guanine-N(7)-)-methyltransferase; Reviewed
Probab=97.26 E-value=0.00033 Score=57.86 Aligned_cols=41 Identities=20% Similarity=0.219 Sum_probs=36.4
Q ss_pred CCCeEEEecCCchHHHHHHHHHCCCCcEEEccc-hHHHhcCC
Q 044458 198 GLQSVVDVGGGIGASLDMIISKYPSIKGINFDL-PHVIQDAP 238 (241)
Q Consensus 198 ~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-P~vi~~a~ 238 (241)
...+|||||||+|.++..+++.+|+.+++..|. |..++.++
T Consensus 40 ~~~~VLDiGcGtG~~~~~la~~~p~~~v~gVD~s~~~i~~a~ 81 (202)
T PRK00121 40 DAPIHLEIGFGKGEFLVEMAKANPDINFIGIEVHEPGVGKAL 81 (202)
T ss_pred CCCeEEEEccCCCHHHHHHHHHCCCccEEEEEechHHHHHHH
Confidence 468999999999999999999999999999999 77776553
No 25
>PRK11207 tellurite resistance protein TehB; Provisional
Probab=97.24 E-value=0.00034 Score=57.48 Aligned_cols=50 Identities=20% Similarity=0.256 Sum_probs=39.6
Q ss_pred HHHHHHhcCCCCCCCeEEEecCCchHHHHHHHHHCCCCcEEEccc-hHHHhcCC
Q 044458 186 MKKFLENYKGFEGLQSVVDVGGGIGASLDMIISKYPSIKGINFDL-PHVIQDAP 238 (241)
Q Consensus 186 ~~~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-P~vi~~a~ 238 (241)
.+.+++.++ .....+|||||||.|.++..++++ ..+++.+|+ |..++.++
T Consensus 19 ~~~l~~~l~-~~~~~~vLDiGcG~G~~a~~La~~--g~~V~gvD~S~~~i~~a~ 69 (197)
T PRK11207 19 HSEVLEAVK-VVKPGKTLDLGCGNGRNSLYLAAN--GFDVTAWDKNPMSIANLE 69 (197)
T ss_pred hHHHHHhcc-cCCCCcEEEECCCCCHHHHHHHHC--CCEEEEEeCCHHHHHHHH
Confidence 356666666 555689999999999999999986 568899999 77776554
No 26
>TIGR00138 gidB 16S rRNA methyltransferase GidB. GidB (glucose-inhibited division protein B) appears to be present and in a single copy in nearly all complete eubacterial genomes. It is missing only from some obligate intracellular species of various lineages (Chlamydiae, Ehrlichia, Wolbachia, Anaplasma, Buchnera, etc.). GidB shows a methytransferase fold in its the crystal structure, and acts as a 7-methylguanosine (m(7)G) methyltransferase, apparently specific to 16S rRNA.
Probab=97.23 E-value=0.0002 Score=58.17 Aligned_cols=39 Identities=18% Similarity=0.171 Sum_probs=34.1
Q ss_pred CCeEEEecCCchHHHHHHHHHCCCCcEEEccc-hHHHhcC
Q 044458 199 LQSVVDVGGGIGASLDMIISKYPSIKGINFDL-PHVIQDA 237 (241)
Q Consensus 199 ~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-P~vi~~a 237 (241)
..+|+|||||+|.++..++..+|+.+++.+|. |..++.+
T Consensus 43 ~~~vLDiGcGtG~~s~~la~~~~~~~V~~iD~s~~~~~~a 82 (181)
T TIGR00138 43 GKKVIDIGSGAGFPGIPLAIARPELKLTLLESNHKKVAFL 82 (181)
T ss_pred CCeEEEecCCCCccHHHHHHHCCCCeEEEEeCcHHHHHHH
Confidence 57999999999999999999999999999999 5555543
No 27
>PRK15451 tRNA cmo(5)U34 methyltransferase; Provisional
Probab=97.23 E-value=0.00026 Score=60.28 Aligned_cols=42 Identities=24% Similarity=0.259 Sum_probs=36.8
Q ss_pred CCCCeEEEecCCchHHHHHHHH--HCCCCcEEEccc-hHHHhcCC
Q 044458 197 EGLQSVVDVGGGIGASLDMIIS--KYPSIKGINFDL-PHVIQDAP 238 (241)
Q Consensus 197 ~~~~~vvDVGGG~G~~~~~l~~--~~P~l~~~v~Dl-P~vi~~a~ 238 (241)
....+|||||||+|..+..+++ .+|+.+++.+|. |..++.|+
T Consensus 55 ~~~~~vLDlGcGtG~~~~~l~~~~~~~~~~v~gvD~S~~ml~~A~ 99 (247)
T PRK15451 55 QPGTQVYDLGCSLGAATLSVRRNIHHDNCKIIAIDNSPAMIERCR 99 (247)
T ss_pred CCCCEEEEEcccCCHHHHHHHHhcCCCCCeEEEEeCCHHHHHHHH
Confidence 3457999999999999999988 479999999999 88888765
No 28
>PRK10258 biotin biosynthesis protein BioC; Provisional
Probab=97.20 E-value=0.00094 Score=56.71 Aligned_cols=51 Identities=20% Similarity=0.243 Sum_probs=38.6
Q ss_pred HHHHHHhcCCCCCCCeEEEecCCchHHHHHHHHHCCCCcEEEccc-hHHHhcCCC
Q 044458 186 MKKFLENYKGFEGLQSVVDVGGGIGASLDMIISKYPSIKGINFDL-PHVIQDAPA 239 (241)
Q Consensus 186 ~~~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-P~vi~~a~~ 239 (241)
+..+++.++ .....+|||||||+|.++..+.+. ..+++..|+ |..++.+++
T Consensus 31 a~~l~~~l~-~~~~~~vLDiGcG~G~~~~~l~~~--~~~v~~~D~s~~~l~~a~~ 82 (251)
T PRK10258 31 ADALLAMLP-QRKFTHVLDAGCGPGWMSRYWRER--GSQVTALDLSPPMLAQARQ 82 (251)
T ss_pred HHHHHHhcC-ccCCCeEEEeeCCCCHHHHHHHHc--CCeEEEEECCHHHHHHHHh
Confidence 344555555 445689999999999999888764 568899999 888776653
No 29
>PRK09489 rsmC 16S ribosomal RNA m2G1207 methyltransferase; Provisional
Probab=97.17 E-value=0.00049 Score=61.46 Aligned_cols=49 Identities=20% Similarity=0.289 Sum_probs=39.0
Q ss_pred HHHhcCCCCCCCeEEEecCCchHHHHHHHHHCCCCcEEEccc-hHHHhcCC
Q 044458 189 FLENYKGFEGLQSVVDVGGGIGASLDMIISKYPSIKGINFDL-PHVIQDAP 238 (241)
Q Consensus 189 ~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-P~vi~~a~ 238 (241)
+++.++ -....+|+|+|||.|.++..+++++|+.+++..|. +.+++.++
T Consensus 188 Ll~~l~-~~~~g~VLDlGCG~G~ls~~la~~~p~~~v~~vDis~~Al~~A~ 237 (342)
T PRK09489 188 LLSTLT-PHTKGKVLDVGCGAGVLSAVLARHSPKIRLTLSDVSAAALESSR 237 (342)
T ss_pred HHHhcc-ccCCCeEEEeccCcCHHHHHHHHhCCCCEEEEEECCHHHHHHHH
Confidence 344444 22345899999999999999999999999999999 66776654
No 30
>PF09339 HTH_IclR: IclR helix-turn-helix domain; InterPro: IPR005471 The many bacterial transcription regulation proteins which bind DNA through a 'helix-turn-helix' motif can be classified into subfamilies on the basis of sequence similarities. One of these subfamilies, called 'iclR', groups several proteins including: gylR, a possible activator protein for the gylABX glycerol operon in Streptomyces. iclR, the repressor of the acetate operon (also known as glyoxylate bypass operon) in Escherichia coli and Salmonella typhimurium. These proteins have a Helix-Turn-Helix motif at the N terminus that is similar to that of other DNA-binding proteins [].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1MKM_A 3MQ0_A 3R4K_A 2G7U_C 2O0Y_C 2XRO_F 2XRN_B 2IA2_D.
Probab=97.17 E-value=0.00013 Score=46.78 Aligned_cols=46 Identities=24% Similarity=0.360 Sum_probs=40.0
Q ss_pred cChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCcchHHHHHHHHhcCCccccc
Q 044458 40 LDLLEVIAKAGPGAFMSPKQIASQLPTKNSDAHILLDRILRLLASYSVLNCS 91 (241)
Q Consensus 40 lglfd~L~~~~~~~~~t~~eLA~~~g~~~~~~~~~l~rlLr~L~~~g~l~~~ 91 (241)
+.|+++|...+ ++.|..|||+++|+ +...+.|+|..|...|++.++
T Consensus 6 l~iL~~l~~~~--~~~t~~eia~~~gl----~~stv~r~L~tL~~~g~v~~d 51 (52)
T PF09339_consen 6 LRILEALAESG--GPLTLSEIARALGL----PKSTVHRLLQTLVEEGYVERD 51 (52)
T ss_dssp HHHHHCHHCTB--SCEEHHHHHHHHTS-----HHHHHHHHHHHHHTTSEEEC
T ss_pred HHHHHHHHcCC--CCCCHHHHHHHHCc----CHHHHHHHHHHHHHCcCeecC
Confidence 45788888865 57899999999999 999999999999999999873
No 31
>PF13649 Methyltransf_25: Methyltransferase domain; PDB: 3BXO_B 3GGD_A 3PX2_A 3PX3_A 3PFH_D 3PFG_A 1Y8C_A.
Probab=97.10 E-value=0.00029 Score=51.26 Aligned_cols=37 Identities=27% Similarity=0.592 Sum_probs=29.4
Q ss_pred EEEecCCchHHHHHHHHHC---CCCcEEEccc-hHHHhcCC
Q 044458 202 VVDVGGGIGASLDMIISKY---PSIKGINFDL-PHVIQDAP 238 (241)
Q Consensus 202 vvDVGGG~G~~~~~l~~~~---P~l~~~v~Dl-P~vi~~a~ 238 (241)
|||+|||+|.....+++.+ |+.+.+.+|+ |+.++.++
T Consensus 1 ILDlgcG~G~~~~~l~~~~~~~~~~~~~gvD~s~~~l~~~~ 41 (101)
T PF13649_consen 1 ILDLGCGTGRVTRALARRFDAGPSSRVIGVDISPEMLELAK 41 (101)
T ss_dssp -EEET-TTSHHHHHHHHHS-----SEEEEEES-HHHHHHHH
T ss_pred CEEeecCCcHHHHHHHHHhhhcccceEEEEECCHHHHHHHH
Confidence 7999999999999999997 6789999998 77777654
No 32
>PRK08317 hypothetical protein; Provisional
Probab=97.08 E-value=0.00071 Score=56.27 Aligned_cols=50 Identities=20% Similarity=0.256 Sum_probs=40.3
Q ss_pred HHHHhcCCCCCCCeEEEecCCchHHHHHHHHHC-CCCcEEEccc-hHHHhcCC
Q 044458 188 KFLENYKGFEGLQSVVDVGGGIGASLDMIISKY-PSIKGINFDL-PHVIQDAP 238 (241)
Q Consensus 188 ~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~-P~l~~~v~Dl-P~vi~~a~ 238 (241)
.++..++ +....+|||||||.|.++..+++.+ |+.+++..|+ |..++.++
T Consensus 10 ~~~~~~~-~~~~~~vLdiG~G~G~~~~~~a~~~~~~~~v~~~d~~~~~~~~a~ 61 (241)
T PRK08317 10 RTFELLA-VQPGDRVLDVGCGPGNDARELARRVGPEGRVVGIDRSEAMLALAK 61 (241)
T ss_pred HHHHHcC-CCCCCEEEEeCCCCCHHHHHHHHhcCCCcEEEEEeCCHHHHHHHH
Confidence 3455566 6777899999999999999999998 7889999999 55555443
No 33
>PRK14121 tRNA (guanine-N(7)-)-methyltransferase; Provisional
Probab=97.08 E-value=0.00094 Score=60.42 Aligned_cols=49 Identities=18% Similarity=0.262 Sum_probs=39.1
Q ss_pred HHHHhcCCCCCCCeEEEecCCchHHHHHHHHHCCCCcEEEccc-hHHHhcC
Q 044458 188 KFLENYKGFEGLQSVVDVGGGIGASLDMIISKYPSIKGINFDL-PHVIQDA 237 (241)
Q Consensus 188 ~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-P~vi~~a 237 (241)
.+++.+. -.....+||||||.|.++..+++++|+..++.+|+ +..++.+
T Consensus 113 ~~~~~~~-~~~~p~vLEIGcGsG~~ll~lA~~~P~~~~iGIEI~~~~i~~a 162 (390)
T PRK14121 113 NFLDFIS-KNQEKILIEIGFGSGRHLLYQAKNNPNKLFIGIEIHTPSIEQV 162 (390)
T ss_pred HHHHHhc-CCCCCeEEEEcCcccHHHHHHHHhCCCCCEEEEECCHHHHHHH
Confidence 3455554 33457999999999999999999999999999998 5565544
No 34
>COG2890 HemK Methylase of polypeptide chain release factors [Translation, ribosomal structure and biogenesis]
Probab=97.07 E-value=0.00039 Score=60.44 Aligned_cols=38 Identities=26% Similarity=0.413 Sum_probs=35.8
Q ss_pred eEEEecCCchHHHHHHHHHCCCCcEEEccc-hHHHhcCC
Q 044458 201 SVVDVGGGIGASLDMIISKYPSIKGINFDL-PHVIQDAP 238 (241)
Q Consensus 201 ~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-P~vi~~a~ 238 (241)
+|+|||+|+|..+++++++.|+++++..|+ |.+++.|+
T Consensus 113 ~ilDlGTGSG~iai~la~~~~~~~V~a~Dis~~Al~~A~ 151 (280)
T COG2890 113 RILDLGTGSGAIAIALAKEGPDAEVIAVDISPDALALAR 151 (280)
T ss_pred cEEEecCChHHHHHHHHhhCcCCeEEEEECCHHHHHHHH
Confidence 899999999999999999999999999999 88888765
No 35
>TIGR03704 PrmC_rel_meth putative protein-(glutamine-N5) methyltransferase, unknown substrate-specific. This protein family is closely related to two different families of protein-(glutamine-N5) methyltransferase. The first is PrmB, which modifies ribosomal protein L3 in some bacteria. The second is PrmC (HemK), which modifies peptide chain release factors 1 and 2 in most bacteria and also in eukaryotes. The glutamine side chain-binding motif NPPY shared by PrmB and PrmC is N[VAT]PY in this family. The protein substrate is unknown.
Probab=97.06 E-value=0.00088 Score=57.26 Aligned_cols=40 Identities=25% Similarity=0.239 Sum_probs=36.5
Q ss_pred CCeEEEecCCchHHHHHHHHHCCCCcEEEccc-hHHHhcCC
Q 044458 199 LQSVVDVGGGIGASLDMIISKYPSIKGINFDL-PHVIQDAP 238 (241)
Q Consensus 199 ~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-P~vi~~a~ 238 (241)
..+|+|+|||+|.++..+++.+|..+++..|. |.+++.|+
T Consensus 87 ~~~vLDlg~GsG~i~l~la~~~~~~~v~~vDis~~al~~A~ 127 (251)
T TIGR03704 87 TLVVVDLCCGSGAVGAALAAALDGIELHAADIDPAAVRCAR 127 (251)
T ss_pred CCEEEEecCchHHHHHHHHHhCCCCEEEEEECCHHHHHHHH
Confidence 46899999999999999999999999999999 88888765
No 36
>COG2230 Cfa Cyclopropane fatty acid synthase and related methyltransferases [Cell envelope biogenesis, outer membrane]
Probab=97.04 E-value=0.00098 Score=57.66 Aligned_cols=49 Identities=16% Similarity=0.284 Sum_probs=42.2
Q ss_pred HHHHHHhcCCCCCCCeEEEecCCchHHHHHHHHHCCCCcEEEccc-hHHHhc
Q 044458 186 MKKFLENYKGFEGLQSVVDVGGGIGASLDMIISKYPSIKGINFDL-PHVIQD 236 (241)
Q Consensus 186 ~~~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-P~vi~~ 236 (241)
.+.+++.+. ++...+|||||||-|.+++..++.| +.+++..+| ++..+.
T Consensus 61 ~~~~~~kl~-L~~G~~lLDiGCGWG~l~~~aA~~y-~v~V~GvTlS~~Q~~~ 110 (283)
T COG2230 61 LDLILEKLG-LKPGMTLLDIGCGWGGLAIYAAEEY-GVTVVGVTLSEEQLAY 110 (283)
T ss_pred HHHHHHhcC-CCCCCEEEEeCCChhHHHHHHHHHc-CCEEEEeeCCHHHHHH
Confidence 457788887 9999999999999999999999999 999999998 444443
No 37
>PRK00216 ubiE ubiquinone/menaquinone biosynthesis methyltransferase; Reviewed
Probab=97.01 E-value=0.0019 Score=53.83 Aligned_cols=50 Identities=12% Similarity=0.106 Sum_probs=39.5
Q ss_pred HHHHhcCCCCCCCeEEEecCCchHHHHHHHHHCC-CCcEEEccc-hHHHhcCC
Q 044458 188 KFLENYKGFEGLQSVVDVGGGIGASLDMIISKYP-SIKGINFDL-PHVIQDAP 238 (241)
Q Consensus 188 ~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P-~l~~~v~Dl-P~vi~~a~ 238 (241)
.++..+. .....+|+|||||.|.++..+++.+| +.++++.|+ |..++.++
T Consensus 42 ~~~~~~~-~~~~~~vldiG~G~G~~~~~l~~~~~~~~~v~~~D~s~~~~~~a~ 93 (239)
T PRK00216 42 KTIKWLG-VRPGDKVLDLACGTGDLAIALAKAVGKTGEVVGLDFSEGMLAVGR 93 (239)
T ss_pred HHHHHhC-CCCCCeEEEeCCCCCHHHHHHHHHcCCCCeEEEEeCCHHHHHHHH
Confidence 3444554 44568999999999999999999998 789999999 56655543
No 38
>TIGR03533 L3_gln_methyl protein-(glutamine-N5) methyltransferase, ribosomal protein L3-specific. Members of this protein family methylate ribosomal protein L3 on a glutamine side chain. This family is related to HemK, a protein-glutamine methyltranferase for peptide chain release factors.
Probab=97.01 E-value=0.00063 Score=59.22 Aligned_cols=41 Identities=17% Similarity=0.272 Sum_probs=37.0
Q ss_pred CCCeEEEecCCchHHHHHHHHHCCCCcEEEccc-hHHHhcCC
Q 044458 198 GLQSVVDVGGGIGASLDMIISKYPSIKGINFDL-PHVIQDAP 238 (241)
Q Consensus 198 ~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-P~vi~~a~ 238 (241)
+..+|+|+|||+|.++..+++.+|+.+++..|+ |.+++.|+
T Consensus 121 ~~~~vLDlG~GsG~i~~~la~~~~~~~v~avDis~~al~~A~ 162 (284)
T TIGR03533 121 PVKRILDLCTGSGCIAIACAYAFPEAEVDAVDISPDALAVAE 162 (284)
T ss_pred CCCEEEEEeCchhHHHHHHHHHCCCCEEEEEECCHHHHHHHH
Confidence 347899999999999999999999999999999 78887665
No 39
>TIGR00477 tehB tellurite resistance protein TehB. Part of a tellurite-reducing operon tehA and tehB
Probab=97.01 E-value=0.0011 Score=54.42 Aligned_cols=48 Identities=19% Similarity=0.157 Sum_probs=37.6
Q ss_pred HHHHHhcCCCCCCCeEEEecCCchHHHHHHHHHCCCCcEEEccc-hHHHhcC
Q 044458 187 KKFLENYKGFEGLQSVVDVGGGIGASLDMIISKYPSIKGINFDL-PHVIQDA 237 (241)
Q Consensus 187 ~~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-P~vi~~a 237 (241)
..++..++ .....+|||||||.|.++..++++ +.+++.+|+ |..++.+
T Consensus 20 ~~l~~~~~-~~~~~~vLDiGcG~G~~a~~la~~--g~~V~~iD~s~~~l~~a 68 (195)
T TIGR00477 20 SAVREAVK-TVAPCKTLDLGCGQGRNSLYLSLA--GYDVRAWDHNPASIASV 68 (195)
T ss_pred HHHHHHhc-cCCCCcEEEeCCCCCHHHHHHHHC--CCeEEEEECCHHHHHHH
Confidence 35555555 444689999999999999999985 568999999 6677654
No 40
>PRK11036 putative S-adenosyl-L-methionine-dependent methyltransferase; Provisional
Probab=96.99 E-value=0.0013 Score=56.09 Aligned_cols=40 Identities=30% Similarity=0.326 Sum_probs=33.9
Q ss_pred CCCCeEEEecCCchHHHHHHHHHCCCCcEEEccc-hHHHhcCC
Q 044458 197 EGLQSVVDVGGGIGASLDMIISKYPSIKGINFDL-PHVIQDAP 238 (241)
Q Consensus 197 ~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-P~vi~~a~ 238 (241)
....+|||||||.|.++..+++. ..+++.+|+ |+.++.|+
T Consensus 43 ~~~~~vLDiGcG~G~~a~~la~~--g~~v~~vD~s~~~l~~a~ 83 (255)
T PRK11036 43 PRPLRVLDAGGGEGQTAIKLAEL--GHQVILCDLSAEMIQRAK 83 (255)
T ss_pred CCCCEEEEeCCCchHHHHHHHHc--CCEEEEEECCHHHHHHHH
Confidence 34579999999999999999987 467899999 78887764
No 41
>PRK00274 ksgA 16S ribosomal RNA methyltransferase KsgA/Dim1 family protein; Reviewed
Probab=96.98 E-value=0.0011 Score=57.19 Aligned_cols=49 Identities=14% Similarity=0.256 Sum_probs=38.9
Q ss_pred HHHHHhcCCCCCCCeEEEecCCchHHHHHHHHHCCCCcEEEccc-hHHHhcCC
Q 044458 187 KKFLENYKGFEGLQSVVDVGGGIGASLDMIISKYPSIKGINFDL-PHVIQDAP 238 (241)
Q Consensus 187 ~~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-P~vi~~a~ 238 (241)
..+++.++ .....+|||||||.|.++..++++.+ +++.+|. |..++.++
T Consensus 32 ~~i~~~l~-~~~~~~VLEiG~G~G~lt~~L~~~~~--~v~avE~d~~~~~~~~ 81 (272)
T PRK00274 32 DKIVDAAG-PQPGDNVLEIGPGLGALTEPLLERAA--KVTAVEIDRDLAPILA 81 (272)
T ss_pred HHHHHhcC-CCCcCeEEEeCCCccHHHHHHHHhCC--cEEEEECCHHHHHHHH
Confidence 45566666 66678999999999999999999987 6788888 66666553
No 42
>PRK11805 N5-glutamine S-adenosyl-L-methionine-dependent methyltransferase; Provisional
Probab=96.96 E-value=0.0006 Score=60.01 Aligned_cols=39 Identities=18% Similarity=0.273 Sum_probs=36.3
Q ss_pred CeEEEecCCchHHHHHHHHHCCCCcEEEccc-hHHHhcCC
Q 044458 200 QSVVDVGGGIGASLDMIISKYPSIKGINFDL-PHVIQDAP 238 (241)
Q Consensus 200 ~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-P~vi~~a~ 238 (241)
.+|+|+|||+|.++..+++.+|+.+++..|+ |.+++.|+
T Consensus 135 ~~VLDlG~GsG~iai~la~~~p~~~V~avDis~~al~~A~ 174 (307)
T PRK11805 135 TRILDLCTGSGCIAIACAYAFPDAEVDAVDISPDALAVAE 174 (307)
T ss_pred CEEEEEechhhHHHHHHHHHCCCCEEEEEeCCHHHHHHHH
Confidence 6899999999999999999999999999999 88887765
No 43
>COG2242 CobL Precorrin-6B methylase 2 [Coenzyme metabolism]
Probab=96.95 E-value=0.0011 Score=53.77 Aligned_cols=46 Identities=15% Similarity=0.107 Sum_probs=38.9
Q ss_pred HhcCCCCCCCeEEEecCCchHHHHHHHHHCCCCcEEEccc-hHHHhcC
Q 044458 191 ENYKGFEGLQSVVDVGGGIGASLDMIISKYPSIKGINFDL-PHVIQDA 237 (241)
Q Consensus 191 ~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-P~vi~~a 237 (241)
..+- .....+++|||||+|..+++++...|+.+++.+|. ++.++..
T Consensus 28 s~L~-~~~g~~l~DIGaGtGsi~iE~a~~~p~~~v~AIe~~~~a~~~~ 74 (187)
T COG2242 28 SKLR-PRPGDRLWDIGAGTGSITIEWALAGPSGRVIAIERDEEALELI 74 (187)
T ss_pred HhhC-CCCCCEEEEeCCCccHHHHHHHHhCCCceEEEEecCHHHHHHH
Confidence 4444 56678999999999999999999999999999998 6666543
No 44
>PLN02244 tocopherol O-methyltransferase
Probab=96.95 E-value=0.0011 Score=59.17 Aligned_cols=40 Identities=33% Similarity=0.452 Sum_probs=34.1
Q ss_pred CCCCeEEEecCCchHHHHHHHHHCCCCcEEEccc-hHHHhcC
Q 044458 197 EGLQSVVDVGGGIGASLDMIISKYPSIKGINFDL-PHVIQDA 237 (241)
Q Consensus 197 ~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-P~vi~~a 237 (241)
....+|||||||.|.++..+++++ +.+++.+|+ |..++.+
T Consensus 117 ~~~~~VLDiGCG~G~~~~~La~~~-g~~v~gvD~s~~~i~~a 157 (340)
T PLN02244 117 KRPKRIVDVGCGIGGSSRYLARKY-GANVKGITLSPVQAARA 157 (340)
T ss_pred CCCCeEEEecCCCCHHHHHHHHhc-CCEEEEEECCHHHHHHH
Confidence 456899999999999999999998 789999999 6666544
No 45
>PTZ00098 phosphoethanolamine N-methyltransferase; Provisional
Probab=96.94 E-value=0.0011 Score=57.06 Aligned_cols=50 Identities=24% Similarity=0.434 Sum_probs=40.7
Q ss_pred HHHHHhcCCCCCCCeEEEecCCchHHHHHHHHHCCCCcEEEccc-hHHHhcCC
Q 044458 187 KKFLENYKGFEGLQSVVDVGGGIGASLDMIISKYPSIKGINFDL-PHVIQDAP 238 (241)
Q Consensus 187 ~~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-P~vi~~a~ 238 (241)
..+++.++ .....+|||||||.|..+..+++.+ +.+++.+|+ |..++.++
T Consensus 42 ~~~l~~l~-l~~~~~VLDiGcG~G~~a~~la~~~-~~~v~giD~s~~~~~~a~ 92 (263)
T PTZ00098 42 TKILSDIE-LNENSKVLDIGSGLGGGCKYINEKY-GAHVHGVDICEKMVNIAK 92 (263)
T ss_pred HHHHHhCC-CCCCCEEEEEcCCCChhhHHHHhhc-CCEEEEEECCHHHHHHHH
Confidence 45666776 7778999999999999999998876 679999999 66666554
No 46
>PRK01581 speE spermidine synthase; Validated
Probab=96.93 E-value=0.00096 Score=59.77 Aligned_cols=45 Identities=24% Similarity=0.264 Sum_probs=37.9
Q ss_pred CCCCeEEEecCCchHHHHHHHHHCCCCcEEEccc-hHHHhcCCCCC
Q 044458 197 EGLQSVVDVGGGIGASLDMIISKYPSIKGINFDL-PHVIQDAPAYP 241 (241)
Q Consensus 197 ~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-P~vi~~a~~~~ 241 (241)
.+.++||+||||.|..+..+++..+..++++.|+ |+|++.|+++|
T Consensus 149 ~~PkrVLIIGgGdG~tlrelLk~~~v~~It~VEIDpeVIelAr~~~ 194 (374)
T PRK01581 149 IDPKRVLILGGGDGLALREVLKYETVLHVDLVDLDGSMINMARNVP 194 (374)
T ss_pred CCCCEEEEECCCHHHHHHHHHhcCCCCeEEEEeCCHHHHHHHHhcc
Confidence 4568999999999999999997555568999999 89999988653
No 47
>TIGR03534 RF_mod_PrmC protein-(glutamine-N5) methyltransferase, release factor-specific. Members of this protein family are HemK (PrmC), a protein once thought to be involved in heme biosynthesis but now recognized to be a protein-glutamine methyltransferase that modifies the peptide chain release factors. All members of the seed alignment are encoded next to the release factor 1 gene (prfA) and confirmed by phylogenetic analysis. SIMBAL analysis (manuscript in prep.) shows the motif [LIV]PRx[DE]TE (in Escherichia coli, IPRPDTE) confers specificity for the release factors rather than for ribosomal protein L3.
Probab=96.89 E-value=0.0014 Score=55.34 Aligned_cols=41 Identities=27% Similarity=0.408 Sum_probs=36.1
Q ss_pred CCCeEEEecCCchHHHHHHHHHCCCCcEEEccc-hHHHhcCC
Q 044458 198 GLQSVVDVGGGIGASLDMIISKYPSIKGINFDL-PHVIQDAP 238 (241)
Q Consensus 198 ~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-P~vi~~a~ 238 (241)
...+|+|+|||+|.++..+++.+|+.+++.+|. |..++.++
T Consensus 87 ~~~~ilDig~G~G~~~~~l~~~~~~~~v~~iD~~~~~~~~a~ 128 (251)
T TIGR03534 87 GPLRVLDLGTGSGAIALALAKERPDARVTAVDISPEALAVAR 128 (251)
T ss_pred CCCeEEEEeCcHhHHHHHHHHHCCCCEEEEEECCHHHHHHHH
Confidence 346899999999999999999999999999998 77776654
No 48
>COG2226 UbiE Methylase involved in ubiquinone/menaquinone biosynthesis [Coenzyme metabolism]
Probab=96.87 E-value=0.0017 Score=55.03 Aligned_cols=42 Identities=17% Similarity=0.214 Sum_probs=37.6
Q ss_pred CCCeEEEecCCchHHHHHHHHHCCCCcEEEccc-hHHHhcCCC
Q 044458 198 GLQSVVDVGGGIGASLDMIISKYPSIKGINFDL-PHVIQDAPA 239 (241)
Q Consensus 198 ~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-P~vi~~a~~ 239 (241)
...+|||||||+|-.+..+++..++.++++.|. +..++.|++
T Consensus 51 ~g~~vLDva~GTGd~a~~~~k~~g~g~v~~~D~s~~ML~~a~~ 93 (238)
T COG2226 51 PGDKVLDVACGTGDMALLLAKSVGTGEVVGLDISESMLEVARE 93 (238)
T ss_pred CCCEEEEecCCccHHHHHHHHhcCCceEEEEECCHHHHHHHHH
Confidence 468999999999999999999999999999999 777777653
No 49
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=96.86 E-value=0.0024 Score=43.38 Aligned_cols=60 Identities=20% Similarity=0.236 Sum_probs=48.2
Q ss_pred HHhcChHHHHHhcCCCC-CCCHHHHHhhCCCCCCCCcchHHHHHHHHhcCCccccccccCCCCccccceecCc
Q 044458 37 AIELDLLEVIAKAGPGA-FMSPKQIASQLPTKNSDAHILLDRILRLLASYSVLNCSLHTLPDGGVERLYGLAP 108 (241)
Q Consensus 37 a~~lglfd~L~~~~~~~-~~t~~eLA~~~g~~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~g~~~~~y~~t~ 108 (241)
..+-.|++.|...| + ++|+.|||+++|+ +...++|+|..|...|++.... .. ++.|.++.
T Consensus 6 ~~~~~IL~~L~~~g--~~~~ta~eLa~~lgl----~~~~v~r~L~~L~~~G~V~~~~---~~---~~~W~i~~ 66 (68)
T smart00550 6 SLEEKILEFLENSG--DETSTALQLAKNLGL----PKKEVNRVLYSLEKKGKVCKQG---GT---PPLWKLTD 66 (68)
T ss_pred HHHHHHHHHHHHCC--CCCcCHHHHHHHHCC----CHHHHHHHHHHHHHCCCEEecC---CC---CCceEeec
Confidence 35567889998864 3 3999999999999 9999999999999999998741 11 46777664
No 50
>PRK14966 unknown domain/N5-glutamine S-adenosyl-L-methionine-dependent methyltransferase fusion protein; Provisional
Probab=96.83 E-value=0.001 Score=60.61 Aligned_cols=42 Identities=24% Similarity=0.243 Sum_probs=37.5
Q ss_pred CCCeEEEecCCchHHHHHHHHHCCCCcEEEccc-hHHHhcCCC
Q 044458 198 GLQSVVDVGGGIGASLDMIISKYPSIKGINFDL-PHVIQDAPA 239 (241)
Q Consensus 198 ~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-P~vi~~a~~ 239 (241)
...+|+|||||+|.++..+++.+|+.+++.+|+ |++++.|++
T Consensus 251 ~~~rVLDLGcGSG~IaiaLA~~~p~a~VtAVDiS~~ALe~Are 293 (423)
T PRK14966 251 ENGRVWDLGTGSGAVAVTVALERPDAFVRASDISPPALETARK 293 (423)
T ss_pred CCCEEEEEeChhhHHHHHHHHhCCCCEEEEEECCHHHHHHHHH
Confidence 346899999999999999999999999999999 888887653
No 51
>PRK05785 hypothetical protein; Provisional
Probab=96.83 E-value=0.0012 Score=55.50 Aligned_cols=40 Identities=15% Similarity=0.197 Sum_probs=35.0
Q ss_pred CCeEEEecCCchHHHHHHHHHCCCCcEEEccc-hHHHhcCCC
Q 044458 199 LQSVVDVGGGIGASLDMIISKYPSIKGINFDL-PHVIQDAPA 239 (241)
Q Consensus 199 ~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-P~vi~~a~~ 239 (241)
..+|||||||+|.++..+++.+ +.+++.+|+ |+.++.|++
T Consensus 52 ~~~VLDlGcGtG~~~~~l~~~~-~~~v~gvD~S~~Ml~~a~~ 92 (226)
T PRK05785 52 PKKVLDVAAGKGELSYHFKKVF-KYYVVALDYAENMLKMNLV 92 (226)
T ss_pred CCeEEEEcCCCCHHHHHHHHhc-CCEEEEECCCHHHHHHHHh
Confidence 5799999999999999999998 678999999 788877653
No 52
>PRK09328 N5-glutamine S-adenosyl-L-methionine-dependent methyltransferase; Provisional
Probab=96.83 E-value=0.0018 Score=55.57 Aligned_cols=43 Identities=23% Similarity=0.345 Sum_probs=37.1
Q ss_pred CCCCCeEEEecCCchHHHHHHHHHCCCCcEEEccc-hHHHhcCC
Q 044458 196 FEGLQSVVDVGGGIGASLDMIISKYPSIKGINFDL-PHVIQDAP 238 (241)
Q Consensus 196 ~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-P~vi~~a~ 238 (241)
.....+|+|+|||+|.++..+++.+|+.+++..|. |..++.++
T Consensus 106 ~~~~~~vLDiG~GsG~~~~~la~~~~~~~v~~iDis~~~l~~a~ 149 (275)
T PRK09328 106 LKEPLRVLDLGTGSGAIALALAKERPDAEVTAVDISPEALAVAR 149 (275)
T ss_pred ccCCCEEEEEcCcHHHHHHHHHHHCCCCEEEEEECCHHHHHHHH
Confidence 34567999999999999999999999999999999 66666554
No 53
>TIGR02072 BioC biotin biosynthesis protein BioC. This enzyme, which is found in biotin biosynthetic gene clusters in proteobacteria, firmicutes, green-sulfur bacteria, fusobacterium and bacteroides, is believed to carry out an enzymatic step prior to the formation of pimeloyl-CoA (although attribution of this annotation is not traceable). The enzyme appears related to methyltransferases by homology.
Probab=96.82 E-value=0.001 Score=55.37 Aligned_cols=39 Identities=26% Similarity=0.508 Sum_probs=34.0
Q ss_pred CCeEEEecCCchHHHHHHHHHCCCCcEEEccc-hHHHhcC
Q 044458 199 LQSVVDVGGGIGASLDMIISKYPSIKGINFDL-PHVIQDA 237 (241)
Q Consensus 199 ~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-P~vi~~a 237 (241)
..+|||||||.|.++..+++.+|+.+++..|. |..++.+
T Consensus 35 ~~~vLDlG~G~G~~~~~l~~~~~~~~~~~~D~~~~~~~~~ 74 (240)
T TIGR02072 35 PASVLDIGCGTGYLTRALLKRFPQAEFIALDISAGMLAQA 74 (240)
T ss_pred CCeEEEECCCccHHHHHHHHhCCCCcEEEEeChHHHHHHH
Confidence 47899999999999999999999999999999 5555443
No 54
>TIGR00536 hemK_fam HemK family putative methylases. The gene hemK from E. coli was found to contribute to heme biosynthesis and originally suggested to be protoporphyrinogen oxidase (Medline 95189105). Functional analysis of the nearest homolog in Saccharomyces cerevisiae, YNL063w, finds it is not protoporphyrinogen oxidase and sequence analysis suggests that HemK homologs have S-adenosyl-methionine-dependent methyltransferase activity (Medline 99237242). Homologs are found, usually in a single copy, in nearly all completed genomes, but varying somewhat in apparent domain architecture. Both E. coli and H. influenzae have two members rather than one. The members from the Mycoplasmas have an additional C-terminal domain.
Probab=96.82 E-value=0.00096 Score=58.00 Aligned_cols=39 Identities=23% Similarity=0.448 Sum_probs=35.8
Q ss_pred CeEEEecCCchHHHHHHHHHCCCCcEEEccc-hHHHhcCC
Q 044458 200 QSVVDVGGGIGASLDMIISKYPSIKGINFDL-PHVIQDAP 238 (241)
Q Consensus 200 ~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-P~vi~~a~ 238 (241)
.+|+|+|||+|.++..+++.+|+.+++..|+ |.+++.|+
T Consensus 116 ~~vLDlG~GsG~i~l~la~~~~~~~v~avDis~~al~~a~ 155 (284)
T TIGR00536 116 LHILDLGTGSGCIALALAYEFPNAEVIAVDISPDALAVAE 155 (284)
T ss_pred CEEEEEeccHhHHHHHHHHHCCCCEEEEEECCHHHHHHHH
Confidence 6899999999999999999999999999999 77877664
No 55
>smart00138 MeTrc Methyltransferase, chemotaxis proteins. Methylates methyl-accepting chemotaxis proteins to form gamma-glutamyl methyl ester residues.
Probab=96.82 E-value=0.0067 Score=52.24 Aligned_cols=52 Identities=13% Similarity=0.220 Sum_probs=38.5
Q ss_pred HHHHHhcCCCCCCCeEEEecCCchH----HHHHHHHHCC-----CCcEEEccc-hHHHhcCCC
Q 044458 187 KKFLENYKGFEGLQSVVDVGGGIGA----SLDMIISKYP-----SIKGINFDL-PHVIQDAPA 239 (241)
Q Consensus 187 ~~~~~~~~~~~~~~~vvDVGGG~G~----~~~~l~~~~P-----~l~~~v~Dl-P~vi~~a~~ 239 (241)
+.+.+.-. .....+|+|+|||+|. +++.+++.+| +.+++..|+ |.+++.|++
T Consensus 89 p~l~~~~~-~~~~~ri~d~GCgtGee~YslA~~l~e~~~~~~~~~~~I~g~Dis~~~L~~Ar~ 150 (264)
T smart00138 89 PLLIASRR-HGRRVRIWSAGCSTGEEPYSLAMLLAETLPKAREPDVKILATDIDLKALEKARA 150 (264)
T ss_pred HHHHHhcC-CCCCEEEEeccccCChHHHHHHHHHHHHhhhcCCCCeEEEEEECCHHHHHHHHc
Confidence 44444333 3455899999999996 6777777766 578999999 888888764
No 56
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=96.80 E-value=0.002 Score=45.79 Aligned_cols=58 Identities=19% Similarity=0.251 Sum_probs=47.7
Q ss_pred hcChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCcchHHHHHHHHhcCCccccccccCCCCccccceecCcc
Q 044458 39 ELDLLEVIAKAGPGAFMSPKQIASQLPTKNSDAHILLDRILRLLASYSVLNCSLHTLPDGGVERLYGLAPV 109 (241)
Q Consensus 39 ~lglfd~L~~~~~~~~~t~~eLA~~~g~~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~g~~~~~y~~t~~ 109 (241)
-+.|++.|...+ ++.|..|||+.+|+ +...+.|.|+.|...|++.... . .+.|++++.
T Consensus 7 ~~~Il~~l~~~~--~~~t~~~ia~~l~i----~~~tv~r~l~~L~~~g~l~~~~---~----~~~y~l~~~ 64 (91)
T smart00346 7 GLAVLRALAEEP--GGLTLAELAERLGL----SKSTAHRLLNTLQELGYVEQDG---Q----NGRYRLGPK 64 (91)
T ss_pred HHHHHHHHHhCC--CCcCHHHHHHHhCC----CHHHHHHHHHHHHHCCCeeecC---C----CCceeecHH
Confidence 356788888753 58999999999999 9999999999999999998741 1 467888763
No 57
>PF02390 Methyltransf_4: Putative methyltransferase ; InterPro: IPR003358 This entry represents tRNA (guanine-N-7) methyltransferase (2.1.1.33 from EC), which catalyses the formation of N(7)-methylguanine at position 46 (m7G46) in tRNA. Capping of the pre-mRNA 5' end by addition a monomethylated guanosine cap (m(7)G) is an essential and the earliest modification in the biogenesis of mRNA []. The reaction is catalysed by three enzymes: triphosphatase, guanylyltransferase, and tRNA (guanine-N-7) methyltransferase [, ].; GO: 0008176 tRNA (guanine-N7-)-methyltransferase activity, 0006400 tRNA modification; PDB: 3DXZ_A 3DXY_A 3DXX_A 3CKK_A 3P2I_B 3P2K_D 3P2E_A 3MTE_B 3PB3_B 1YZH_B ....
Probab=96.78 E-value=0.0018 Score=53.31 Aligned_cols=36 Identities=19% Similarity=0.394 Sum_probs=31.3
Q ss_pred CeEEEecCCchHHHHHHHHHCCCCcEEEccc-hHHHh
Q 044458 200 QSVVDVGGGIGASLDMIISKYPSIKGINFDL-PHVIQ 235 (241)
Q Consensus 200 ~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-P~vi~ 235 (241)
..+||||||.|.+++++++.+|+..++.+|. ...+.
T Consensus 19 ~l~lEIG~G~G~~l~~~A~~~Pd~n~iGiE~~~~~v~ 55 (195)
T PF02390_consen 19 PLILEIGCGKGEFLIELAKRNPDINFIGIEIRKKRVA 55 (195)
T ss_dssp EEEEEET-TTSHHHHHHHHHSTTSEEEEEES-HHHHH
T ss_pred CeEEEecCCCCHHHHHHHHHCCCCCEEEEecchHHHH
Confidence 4999999999999999999999999999998 44443
No 58
>PLN02366 spermidine synthase
Probab=96.76 E-value=0.0012 Score=58.04 Aligned_cols=43 Identities=26% Similarity=0.325 Sum_probs=35.8
Q ss_pred CCCCeEEEecCCchHHHHHHHHHCCCC-cEEEccc-hHHHhcCCCC
Q 044458 197 EGLQSVVDVGGGIGASLDMIISKYPSI-KGINFDL-PHVIQDAPAY 240 (241)
Q Consensus 197 ~~~~~vvDVGGG~G~~~~~l~~~~P~l-~~~v~Dl-P~vi~~a~~~ 240 (241)
++.++||+||||.|.++.++++. |++ ++++.|+ |+|++.+++|
T Consensus 90 ~~pkrVLiIGgG~G~~~rellk~-~~v~~V~~VEiD~~Vi~~ar~~ 134 (308)
T PLN02366 90 PNPKKVLVVGGGDGGVLREIARH-SSVEQIDICEIDKMVIDVSKKF 134 (308)
T ss_pred CCCCeEEEEcCCccHHHHHHHhC-CCCCeEEEEECCHHHHHHHHHh
Confidence 45789999999999999999865 664 6899999 6789888764
No 59
>COG2227 UbiG 2-polyprenyl-3-methyl-5-hydroxy-6-metoxy-1,4-benzoquinol methylase [Coenzyme metabolism]
Probab=96.75 E-value=0.001 Score=56.01 Aligned_cols=40 Identities=23% Similarity=0.096 Sum_probs=35.2
Q ss_pred CCeEEEecCCchHHHHHHHHHCCCCcEEEccc-hHHHhcCCCC
Q 044458 199 LQSVVDVGGGIGASLDMIISKYPSIKGINFDL-PHVIQDAPAY 240 (241)
Q Consensus 199 ~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-P~vi~~a~~~ 240 (241)
-.+|||||||-|.++..+++.- .+++..|+ ++.|+.|+.|
T Consensus 60 g~~vLDvGCGgG~Lse~mAr~G--a~VtgiD~se~~I~~Ak~h 100 (243)
T COG2227 60 GLRVLDVGCGGGILSEPLARLG--ASVTGIDASEKPIEVAKLH 100 (243)
T ss_pred CCeEEEecCCccHhhHHHHHCC--CeeEEecCChHHHHHHHHh
Confidence 4899999999999999999996 77889999 7888888765
No 60
>PLN02233 ubiquinone biosynthesis methyltransferase
Probab=96.74 E-value=0.0028 Score=54.47 Aligned_cols=43 Identities=19% Similarity=0.145 Sum_probs=36.2
Q ss_pred CCCCCeEEEecCCchHHHHHHHHHC-CCCcEEEccc-hHHHhcCC
Q 044458 196 FEGLQSVVDVGGGIGASLDMIISKY-PSIKGINFDL-PHVIQDAP 238 (241)
Q Consensus 196 ~~~~~~vvDVGGG~G~~~~~l~~~~-P~l~~~v~Dl-P~vi~~a~ 238 (241)
.....+|||||||+|.++..+++.+ |+.+++.+|+ |+.++.|+
T Consensus 71 ~~~~~~VLDlGcGtG~~~~~la~~~~~~~~V~gvD~S~~ml~~A~ 115 (261)
T PLN02233 71 AKMGDRVLDLCCGSGDLAFLLSEKVGSDGKVMGLDFSSEQLAVAA 115 (261)
T ss_pred CCCCCEEEEECCcCCHHHHHHHHHhCCCCEEEEEECCHHHHHHHH
Confidence 4556899999999999999999885 6789999999 77777664
No 61
>PRK11705 cyclopropane fatty acyl phospholipid synthase; Provisional
Probab=96.73 E-value=0.0021 Score=58.33 Aligned_cols=50 Identities=14% Similarity=0.222 Sum_probs=40.1
Q ss_pred HHHHHhcCCCCCCCeEEEecCCchHHHHHHHHHCCCCcEEEccc-hHHHhcCC
Q 044458 187 KKFLENYKGFEGLQSVVDVGGGIGASLDMIISKYPSIKGINFDL-PHVIQDAP 238 (241)
Q Consensus 187 ~~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-P~vi~~a~ 238 (241)
..+++.++ .....+|||||||.|.++..+++.+ +++++.+|+ |+.++.|+
T Consensus 157 ~~l~~~l~-l~~g~rVLDIGcG~G~~a~~la~~~-g~~V~giDlS~~~l~~A~ 207 (383)
T PRK11705 157 DLICRKLQ-LKPGMRVLDIGCGWGGLARYAAEHY-GVSVVGVTISAEQQKLAQ 207 (383)
T ss_pred HHHHHHhC-CCCCCEEEEeCCCccHHHHHHHHHC-CCEEEEEeCCHHHHHHHH
Confidence 34556665 6667899999999999999998876 679999999 77776654
No 62
>TIGR00080 pimt protein-L-isoaspartate(D-aspartate) O-methyltransferase. Among the prokaryotes, the gene name is pcm. Among eukaryotes, pimt.
Probab=96.73 E-value=0.0024 Score=53.05 Aligned_cols=50 Identities=14% Similarity=0.199 Sum_probs=39.6
Q ss_pred HHHHhcCCCCCCCeEEEecCCchHHHHHHHHHCC-CCcEEEccc-hHHHhcCC
Q 044458 188 KFLENYKGFEGLQSVVDVGGGIGASLDMIISKYP-SIKGINFDL-PHVIQDAP 238 (241)
Q Consensus 188 ~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P-~l~~~v~Dl-P~vi~~a~ 238 (241)
.+++.++ .....+|||||||+|.++..+++..+ +.+++.+|. |+.++.|+
T Consensus 68 ~~~~~l~-~~~~~~VLDiG~GsG~~a~~la~~~~~~g~V~~vD~~~~~~~~A~ 119 (215)
T TIGR00080 68 MMTELLE-LKPGMKVLEIGTGSGYQAAVLAEIVGRDGLVVSIERIPELAEKAE 119 (215)
T ss_pred HHHHHhC-CCCcCEEEEECCCccHHHHHHHHHhCCCCEEEEEeCCHHHHHHHH
Confidence 4455555 66678999999999999999999865 467888897 77777654
No 63
>PRK01544 bifunctional N5-glutamine S-adenosyl-L-methionine-dependent methyltransferase/tRNA (m7G46) methyltransferase; Reviewed
Probab=96.73 E-value=0.0012 Score=61.98 Aligned_cols=40 Identities=20% Similarity=0.366 Sum_probs=36.5
Q ss_pred CCeEEEecCCchHHHHHHHHHCCCCcEEEccc-hHHHhcCC
Q 044458 199 LQSVVDVGGGIGASLDMIISKYPSIKGINFDL-PHVIQDAP 238 (241)
Q Consensus 199 ~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-P~vi~~a~ 238 (241)
..+|||||||+|.+++.+++.+|+.+++.+|+ |.+++.|+
T Consensus 139 ~~~VLDlG~GsG~iai~la~~~p~~~v~avDis~~al~~A~ 179 (506)
T PRK01544 139 FLNILELGTGSGCIAISLLCELPNANVIATDISLDAIEVAK 179 (506)
T ss_pred CCEEEEccCchhHHHHHHHHHCCCCeEEEEECCHHHHHHHH
Confidence 46899999999999999999999999999999 78887765
No 64
>PRK00811 spermidine synthase; Provisional
Probab=96.72 E-value=0.0012 Score=57.41 Aligned_cols=44 Identities=20% Similarity=0.327 Sum_probs=37.0
Q ss_pred CCCCeEEEecCCchHHHHHHHHHCCCCcEEEccc-hHHHhcCCCC
Q 044458 197 EGLQSVVDVGGGIGASLDMIISKYPSIKGINFDL-PHVIQDAPAY 240 (241)
Q Consensus 197 ~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-P~vi~~a~~~ 240 (241)
++.++|||||||.|..+..+++..+..++++.|+ |++++.++++
T Consensus 75 ~~p~~VL~iG~G~G~~~~~~l~~~~~~~V~~VEid~~vv~~a~~~ 119 (283)
T PRK00811 75 PNPKRVLIIGGGDGGTLREVLKHPSVEKITLVEIDERVVEVCRKY 119 (283)
T ss_pred CCCCEEEEEecCchHHHHHHHcCCCCCEEEEEeCCHHHHHHHHHH
Confidence 3568999999999999999997545567999999 8999888753
No 65
>PF13659 Methyltransf_26: Methyltransferase domain; PDB: 3GJY_A 3LPM_B 2NP6_D 1AQI_B 2ADM_B 2IH2_A 2JG3_A 2IBS_D 2NP7_A 2IBT_A ....
Probab=96.70 E-value=0.0017 Score=48.12 Aligned_cols=38 Identities=24% Similarity=0.351 Sum_probs=33.9
Q ss_pred CeEEEecCCchHHHHHHHHHCCCCcEEEccc-hHHHhcCC
Q 044458 200 QSVVDVGGGIGASLDMIISKYPSIKGINFDL-PHVIQDAP 238 (241)
Q Consensus 200 ~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-P~vi~~a~ 238 (241)
.+|+|+|||+|.++..+++.. ..+++.+|+ |.+++.++
T Consensus 2 ~~vlD~~~G~G~~~~~~~~~~-~~~~~gvdi~~~~~~~a~ 40 (117)
T PF13659_consen 2 DRVLDPGCGSGTFLLAALRRG-AARVTGVDIDPEAVELAR 40 (117)
T ss_dssp EEEEEETSTTCHHHHHHHHHC-TCEEEEEESSHHHHHHHH
T ss_pred CEEEEcCcchHHHHHHHHHHC-CCeEEEEEECHHHHHHHH
Confidence 479999999999999999999 889999999 77777654
No 66
>PRK07580 Mg-protoporphyrin IX methyl transferase; Validated
Probab=96.69 E-value=0.002 Score=53.71 Aligned_cols=41 Identities=20% Similarity=0.280 Sum_probs=33.1
Q ss_pred CCCCCeEEEecCCchHHHHHHHHHCCCCcEEEccc-hHHHhcCC
Q 044458 196 FEGLQSVVDVGGGIGASLDMIISKYPSIKGINFDL-PHVIQDAP 238 (241)
Q Consensus 196 ~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-P~vi~~a~ 238 (241)
.....+|||||||+|.++..+++..+ +++..|+ +..++.|+
T Consensus 61 ~~~~~~vLDvGcG~G~~~~~l~~~~~--~v~~~D~s~~~i~~a~ 102 (230)
T PRK07580 61 DLTGLRILDAGCGVGSLSIPLARRGA--KVVASDISPQMVEEAR 102 (230)
T ss_pred CCCCCEEEEEeCCCCHHHHHHHHcCC--EEEEEECCHHHHHHHH
Confidence 34568999999999999999998764 4899998 67766654
No 67
>PLN02336 phosphoethanolamine N-methyltransferase
Probab=96.66 E-value=0.0023 Score=59.48 Aligned_cols=49 Identities=27% Similarity=0.436 Sum_probs=39.1
Q ss_pred HHHHhcCCCCCCCeEEEecCCchHHHHHHHHHCCCCcEEEccc-hHHHhcCC
Q 044458 188 KFLENYKGFEGLQSVVDVGGGIGASLDMIISKYPSIKGINFDL-PHVIQDAP 238 (241)
Q Consensus 188 ~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-P~vi~~a~ 238 (241)
.+++.++ ++...+|||||||+|..+..+++.+ +.+++.+|+ |..++.|+
T Consensus 257 ~l~~~~~-~~~~~~vLDiGcG~G~~~~~la~~~-~~~v~gvDiS~~~l~~A~ 306 (475)
T PLN02336 257 EFVDKLD-LKPGQKVLDVGCGIGGGDFYMAENF-DVHVVGIDLSVNMISFAL 306 (475)
T ss_pred HHHHhcC-CCCCCEEEEEeccCCHHHHHHHHhc-CCEEEEEECCHHHHHHHH
Confidence 3555555 6667899999999999999998877 789999999 67766653
No 68
>TIGR01934 MenG_MenH_UbiE ubiquinone/menaquinone biosynthesis methyltransferases. Note that a number of non-orthologous genes which are members of pfam03737 have been erroneously annotated as MenG methyltransferases.
Probab=96.64 E-value=0.0025 Score=52.49 Aligned_cols=49 Identities=20% Similarity=0.163 Sum_probs=39.0
Q ss_pred HHHHhcCCCCCCCeEEEecCCchHHHHHHHHHCCC-CcEEEccc-hHHHhcC
Q 044458 188 KFLENYKGFEGLQSVVDVGGGIGASLDMIISKYPS-IKGINFDL-PHVIQDA 237 (241)
Q Consensus 188 ~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~-l~~~v~Dl-P~vi~~a 237 (241)
.++.... .....+|||||||.|.++..+++.+|+ .+++++|. |..++.+
T Consensus 30 ~~~~~~~-~~~~~~vldiG~G~G~~~~~~~~~~~~~~~~~~iD~~~~~~~~~ 80 (223)
T TIGR01934 30 RAVKLIG-VFKGQKVLDVACGTGDLAIELAKSAPDRGKVTGVDFSSEMLEVA 80 (223)
T ss_pred HHHHHhc-cCCCCeEEEeCCCCChhHHHHHHhcCCCceEEEEECCHHHHHHH
Confidence 3344444 446789999999999999999999998 78999999 6666554
No 69
>PRK11088 rrmA 23S rRNA methyltransferase A; Provisional
Probab=96.63 E-value=0.0019 Score=55.69 Aligned_cols=41 Identities=22% Similarity=0.362 Sum_probs=34.5
Q ss_pred CCCeEEEecCCchHHHHHHHHHCCCC---cEEEccc-hHHHhcCC
Q 044458 198 GLQSVVDVGGGIGASLDMIISKYPSI---KGINFDL-PHVIQDAP 238 (241)
Q Consensus 198 ~~~~vvDVGGG~G~~~~~l~~~~P~l---~~~v~Dl-P~vi~~a~ 238 (241)
...+|||||||+|.++..+++.+|+. +++.+|+ |..++.|+
T Consensus 85 ~~~~vLDiGcG~G~~~~~l~~~~~~~~~~~v~giD~s~~~l~~A~ 129 (272)
T PRK11088 85 KATALLDIGCGEGYYTHALADALPEITTMQLFGLDISKVAIKYAA 129 (272)
T ss_pred CCCeEEEECCcCCHHHHHHHHhcccccCCeEEEECCCHHHHHHHH
Confidence 44789999999999999999998864 5799999 77777654
No 70
>COG4123 Predicted O-methyltransferase [General function prediction only]
Probab=96.62 E-value=0.0019 Score=54.95 Aligned_cols=50 Identities=16% Similarity=0.250 Sum_probs=40.2
Q ss_pred HHHhcCCCCCCCeEEEecCCchHHHHHHHHHCCCCcEEEccc-hHHHhcCC
Q 044458 189 FLENYKGFEGLQSVVDVGGGIGASLDMIISKYPSIKGINFDL-PHVIQDAP 238 (241)
Q Consensus 189 ~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-P~vi~~a~ 238 (241)
++..|.......+|+|+|+|.|.++..+++++++.+.+..|+ ++.++.|+
T Consensus 35 LL~~~~~~~~~~~IlDlGaG~G~l~L~la~r~~~a~I~~VEiq~~~a~~A~ 85 (248)
T COG4123 35 LLAAFAPVPKKGRILDLGAGNGALGLLLAQRTEKAKIVGVEIQEEAAEMAQ 85 (248)
T ss_pred HHHhhcccccCCeEEEecCCcCHHHHHHhccCCCCcEEEEEeCHHHHHHHH
Confidence 344443244589999999999999999999999999999999 66666654
No 71
>PF02353 CMAS: Mycolic acid cyclopropane synthetase; InterPro: IPR003333 This entry represents mycolic acid cyclopropane synthases and related enzymes, including CmaA1, CmaA2 (cyclopropane mycolic acid synthase A1 and A2) and MmaA1-4 (methoxymycolic acid synthase A1-4). All are thought to be S-adenosyl-L-methionine (SAM) utilising methyltransferases []. Mycolic acid cyclopropane synthase or cyclopropane-fatty-acyl-phospholipid synthase (CFA synthase) 2.1.1.79 from EC catalyses the reaction: S-adenosyl-L-methionine + phospholipid olefinic fatty acid -> S-adenosyl-L-homocysteine + phospholipid cyclopropane fatty acid. The major mycolic acid produced by Mycobacterium tuberculosis contains two cis-cyclopropanes in the meromycolate chain. Cyclopropanation may contribute to the structural integrity of the cell wall complex [].; GO: 0008610 lipid biosynthetic process; PDB: 3HA5_A 2FK8_A 3HA7_A 3HA3_A 2FK7_A 1KPG_D 1KP9_B 1KPH_D 3VC2_E 3VC1_D ....
Probab=96.60 E-value=0.0015 Score=56.50 Aligned_cols=43 Identities=19% Similarity=0.278 Sum_probs=32.8
Q ss_pred HHHHHHhcCCCCCCCeEEEecCCchHHHHHHHHHCCCCcEEEccc
Q 044458 186 MKKFLENYKGFEGLQSVVDVGGGIGASLDMIISKYPSIKGINFDL 230 (241)
Q Consensus 186 ~~~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl 230 (241)
...+++..+ .+...+|||||||-|.+++.++++| +++++.+.+
T Consensus 51 ~~~~~~~~~-l~~G~~vLDiGcGwG~~~~~~a~~~-g~~v~gitl 93 (273)
T PF02353_consen 51 LDLLCEKLG-LKPGDRVLDIGCGWGGLAIYAAERY-GCHVTGITL 93 (273)
T ss_dssp HHHHHTTTT---TT-EEEEES-TTSHHHHHHHHHH---EEEEEES
T ss_pred HHHHHHHhC-CCCCCEEEEeCCCccHHHHHHHHHc-CcEEEEEEC
Confidence 356677777 8888999999999999999999999 899988888
No 72
>PRK13944 protein-L-isoaspartate O-methyltransferase; Provisional
Probab=96.56 E-value=0.0039 Score=51.48 Aligned_cols=49 Identities=14% Similarity=0.091 Sum_probs=37.7
Q ss_pred HHHhcCCCCCCCeEEEecCCchHHHHHHHHHCC-CCcEEEccc-hHHHhcCC
Q 044458 189 FLENYKGFEGLQSVVDVGGGIGASLDMIISKYP-SIKGINFDL-PHVIQDAP 238 (241)
Q Consensus 189 ~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P-~l~~~v~Dl-P~vi~~a~ 238 (241)
+++.++ .....+|||||||+|..+..+++..+ .-+++.+|. |..++.|+
T Consensus 64 ~~~~l~-~~~~~~VLDiG~GsG~~~~~la~~~~~~g~V~~iD~~~~~~~~a~ 114 (205)
T PRK13944 64 MCELIE-PRPGMKILEVGTGSGYQAAVCAEAIERRGKVYTVEIVKELAIYAA 114 (205)
T ss_pred HHHhcC-CCCCCEEEEECcCccHHHHHHHHhcCCCCEEEEEeCCHHHHHHHH
Confidence 344444 55568999999999999999998875 557899999 67666554
No 73
>PLN02490 MPBQ/MSBQ methyltransferase
Probab=96.49 E-value=0.0044 Score=55.32 Aligned_cols=49 Identities=31% Similarity=0.353 Sum_probs=39.0
Q ss_pred HHHhcCCCC-CCCeEEEecCCchHHHHHHHHHCCCCcEEEccc-hHHHhcCC
Q 044458 189 FLENYKGFE-GLQSVVDVGGGIGASLDMIISKYPSIKGINFDL-PHVIQDAP 238 (241)
Q Consensus 189 ~~~~~~~~~-~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-P~vi~~a~ 238 (241)
+++... +. ...+|||||||+|.++..+++.+|..++++.|+ |..++.++
T Consensus 104 ~l~~~~-l~~~~~~VLDLGcGtG~~~l~La~~~~~~~VtgVD~S~~mL~~A~ 154 (340)
T PLN02490 104 ALEPAD-LSDRNLKVVDVGGGTGFTTLGIVKHVDAKNVTILDQSPHQLAKAK 154 (340)
T ss_pred HHhhcc-cCCCCCEEEEEecCCcHHHHHHHHHCCCCEEEEEECCHHHHHHHH
Confidence 344444 43 357999999999999999999999999999999 67776654
No 74
>PF13679 Methyltransf_32: Methyltransferase domain
Probab=96.48 E-value=0.0021 Score=49.88 Aligned_cols=42 Identities=21% Similarity=0.352 Sum_probs=33.8
Q ss_pred CCCCCeEEEecCCchHHHHHHHHH----CCCCcEEEccc-hHHHhcC
Q 044458 196 FEGLQSVVDVGGGIGASLDMIISK----YPSIKGINFDL-PHVIQDA 237 (241)
Q Consensus 196 ~~~~~~vvDVGGG~G~~~~~l~~~----~P~l~~~v~Dl-P~vi~~a 237 (241)
-.+..+|||+|+|.|+++..++.. .|+++++.+|. ++.++.+
T Consensus 23 ~~~~~~vvD~GsG~GyLs~~La~~l~~~~~~~~v~~iD~~~~~~~~a 69 (141)
T PF13679_consen 23 SKRCITVVDLGSGKGYLSRALAHLLCNSSPNLRVLGIDCNESLVESA 69 (141)
T ss_pred cCCCCEEEEeCCChhHHHHHHHHHHHhcCCCCeEEEEECCcHHHHHH
Confidence 356799999999999999999992 38899999998 4544443
No 75
>PRK13942 protein-L-isoaspartate O-methyltransferase; Provisional
Probab=96.48 E-value=0.0051 Score=51.16 Aligned_cols=50 Identities=18% Similarity=0.243 Sum_probs=39.7
Q ss_pred HHHHhcCCCCCCCeEEEecCCchHHHHHHHHHC-CCCcEEEccc-hHHHhcCC
Q 044458 188 KFLENYKGFEGLQSVVDVGGGIGASLDMIISKY-PSIKGINFDL-PHVIQDAP 238 (241)
Q Consensus 188 ~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~-P~l~~~v~Dl-P~vi~~a~ 238 (241)
.+++.++ .....+|||||||+|.++..+++.. ++.+++.+|. |+.++.++
T Consensus 67 ~~~~~l~-~~~g~~VLdIG~GsG~~t~~la~~~~~~~~V~~vE~~~~~~~~a~ 118 (212)
T PRK13942 67 IMCELLD-LKEGMKVLEIGTGSGYHAAVVAEIVGKSGKVVTIERIPELAEKAK 118 (212)
T ss_pred HHHHHcC-CCCcCEEEEECCcccHHHHHHHHhcCCCCEEEEEeCCHHHHHHHH
Confidence 4455666 6777899999999999999988875 4578899998 77776654
No 76
>PLN03075 nicotianamine synthase; Provisional
Probab=96.44 E-value=0.0033 Score=54.90 Aligned_cols=43 Identities=26% Similarity=0.225 Sum_probs=34.4
Q ss_pred CCCCeEEEecCCch--HHHHHHHHHCCCCcEEEccc-hHHHhcCCC
Q 044458 197 EGLQSVVDVGGGIG--ASLDMIISKYPSIKGINFDL-PHVIQDAPA 239 (241)
Q Consensus 197 ~~~~~vvDVGGG~G--~~~~~l~~~~P~l~~~v~Dl-P~vi~~a~~ 239 (241)
...++|+|||||.| ...+.+++.+|+.+++.+|. |+.++.|++
T Consensus 122 ~~p~~VldIGcGpgpltaiilaa~~~p~~~~~giD~d~~ai~~Ar~ 167 (296)
T PLN03075 122 GVPTKVAFVGSGPLPLTSIVLAKHHLPTTSFHNFDIDPSANDVARR 167 (296)
T ss_pred CCCCEEEEECCCCcHHHHHHHHHhcCCCCEEEEEeCCHHHHHHHHH
Confidence 36799999999988 44444556789999999999 888887764
No 77
>COG1414 IclR Transcriptional regulator [Transcription]
Probab=96.43 E-value=0.0037 Score=53.24 Aligned_cols=59 Identities=20% Similarity=0.317 Sum_probs=49.2
Q ss_pred hcChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCcchHHHHHHHHhcCCccccccccCCCCccccceecCccc
Q 044458 39 ELDLLEVIAKAGPGAFMSPKQIASQLPTKNSDAHILLDRILRLLASYSVLNCSLHTLPDGGVERLYGLAPVC 110 (241)
Q Consensus 39 ~lglfd~L~~~~~~~~~t~~eLA~~~g~~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~g~~~~~y~~t~~s 110 (241)
-+.|+++|...+ .+.++.|||+++|+ +...+.|+|..|+..|++.++. . .++|++++..
T Consensus 6 al~iL~~l~~~~--~~l~l~ela~~~gl----pksT~~RlL~tL~~~G~v~~d~---~----~g~Y~Lg~~~ 64 (246)
T COG1414 6 ALAILDLLAEGP--GGLSLAELAERLGL----PKSTVHRLLQTLVELGYVEQDP---E----DGRYRLGPRL 64 (246)
T ss_pred HHHHHHHHHhCC--CCCCHHHHHHHhCc----CHHHHHHHHHHHHHCCCEEEcC---C----CCcEeehHHH
Confidence 356889998743 45789999999999 9999999999999999999862 1 4789999854
No 78
>TIGR00537 hemK_rel_arch HemK-related putative methylase. The gene hemK from E. coli was found to contribute to heme biosynthesis and originally suggested to be protoporphyrinogen oxidase (Medline 95189105). Functional analysis of the nearest homolog in Saccharomyces cerevisiae, YNL063w, finds it is not protoporphyrinogen oxidase and sequence analysis suggests that HemK homologs have S-adenosyl-methionine-dependent methyltransferase activity (Medline 99237242). Homologs are found, usually in a single copy, in nearly all completed genomes, but varying somewhat in apparent domain architecture. This model represents an archaeal and eukaryotic protein family that lacks an N-terminal domain found in HemK and its eubacterial homologs. It is found in a single copy in the first six completed archaeal and eukaryotic genomes.
Probab=96.42 E-value=0.0029 Score=50.98 Aligned_cols=38 Identities=18% Similarity=0.306 Sum_probs=32.9
Q ss_pred CCeEEEecCCchHHHHHHHHHCCCCcEEEccc-hHHHhcCC
Q 044458 199 LQSVVDVGGGIGASLDMIISKYPSIKGINFDL-PHVIQDAP 238 (241)
Q Consensus 199 ~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-P~vi~~a~ 238 (241)
..+|+|+|||+|.++..+++..+ +++..|+ |..++.++
T Consensus 20 ~~~vLdlG~G~G~~~~~l~~~~~--~v~~vD~s~~~~~~a~ 58 (179)
T TIGR00537 20 PDDVLEIGAGTGLVAIRLKGKGK--CILTTDINPFAVKELR 58 (179)
T ss_pred CCeEEEeCCChhHHHHHHHhcCC--EEEEEECCHHHHHHHH
Confidence 46899999999999999999887 8899998 77777654
No 79
>TIGR02431 pcaR_pcaU beta-ketoadipate pathway transcriptional regulators, PcaR/PcaU/PobR family. Member of this family are IclR-type transcriptional regulators with similar DNA binding sites, able to bind at least three different metabolites related to protocatechuate metabolism. Beta-ketoadipate is the inducer for PcaR, p-hydroxybenzoate for PobR, and protocatechuate for PcaU.
Probab=96.40 E-value=0.0034 Score=53.40 Aligned_cols=58 Identities=17% Similarity=0.233 Sum_probs=49.1
Q ss_pred hcChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCcchHHHHHHHHhcCCccccccccCCCCccccceecCcccc
Q 044458 39 ELDLLEVIAKAGPGAFMSPKQIASQLPTKNSDAHILLDRILRLLASYSVLNCSLHTLPDGGVERLYGLAPVCK 111 (241)
Q Consensus 39 ~lglfd~L~~~~~~~~~t~~eLA~~~g~~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~g~~~~~y~~t~~s~ 111 (241)
-+.|++.|...+ .+.|..|||+.+|+ +...+.|+|..|...|++.++ .+.|++.+...
T Consensus 11 al~IL~~l~~~~--~~~~l~eia~~lgl----pksT~~RlL~tL~~~G~l~~~---------~~~Y~lG~~~~ 68 (248)
T TIGR02431 11 GLAVIEAFGAER--PRLTLTDVAEATGL----TRAAARRFLLTLVELGYVTSD---------GRLFWLTPRVL 68 (248)
T ss_pred HHHHHHHHhcCC--CCCCHHHHHHHHCc----CHHHHHHHHHHHHHCCCEEeC---------CCEEEecHHHH
Confidence 356888887643 68999999999999 899999999999999999863 57899988543
No 80
>PRK12335 tellurite resistance protein TehB; Provisional
Probab=96.40 E-value=0.0033 Score=54.72 Aligned_cols=48 Identities=15% Similarity=0.192 Sum_probs=36.4
Q ss_pred HHHHhcCCCCCCCeEEEecCCchHHHHHHHHHCCCCcEEEccc-hHHHhcCC
Q 044458 188 KFLENYKGFEGLQSVVDVGGGIGASLDMIISKYPSIKGINFDL-PHVIQDAP 238 (241)
Q Consensus 188 ~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-P~vi~~a~ 238 (241)
.++..++ .....+|||||||+|.++..+++. +.+++.+|. |.+++.++
T Consensus 111 ~~~~~~~-~~~~~~vLDlGcG~G~~~~~la~~--g~~V~avD~s~~ai~~~~ 159 (287)
T PRK12335 111 EVLEAVQ-TVKPGKALDLGCGQGRNSLYLALL--GFDVTAVDINQQSLENLQ 159 (287)
T ss_pred HHHHHhh-ccCCCCEEEeCCCCCHHHHHHHHC--CCEEEEEECCHHHHHHHH
Confidence 4444444 334569999999999999999885 578999999 67766543
No 81
>COG2264 PrmA Ribosomal protein L11 methylase [Translation, ribosomal structure and biogenesis]
Probab=96.39 E-value=0.0022 Score=55.96 Aligned_cols=61 Identities=23% Similarity=0.346 Sum_probs=42.1
Q ss_pred HHHHHHhcchhhHHHHHHhcCCCCCCCeEEEecCCchHHHHHHHHHCCCCcEEEccc-hHHHhcCC
Q 044458 174 FNNGMFSHSTITMKKFLENYKGFEGLQSVVDVGGGIGASLDMIISKYPSIKGINFDL-PHVIQDAP 238 (241)
Q Consensus 174 f~~aM~~~~~~~~~~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-P~vi~~a~ 238 (241)
|..+-...+.++. .+++.+. .+..+++|||||+|.++++.++--. -+++..|+ |.+++.|+
T Consensus 141 FGTG~HpTT~lcL-~~Le~~~--~~g~~vlDvGcGSGILaIAa~kLGA-~~v~g~DiDp~AV~aa~ 202 (300)
T COG2264 141 FGTGTHPTTSLCL-EALEKLL--KKGKTVLDVGCGSGILAIAAAKLGA-KKVVGVDIDPQAVEAAR 202 (300)
T ss_pred cCCCCChhHHHHH-HHHHHhh--cCCCEEEEecCChhHHHHHHHHcCC-ceEEEecCCHHHHHHHH
Confidence 5444333333433 3445554 3679999999999999999888633 34788999 88887765
No 82
>KOG2899 consensus Predicted methyltransferase [General function prediction only]
Probab=96.37 E-value=0.0029 Score=53.35 Aligned_cols=53 Identities=19% Similarity=0.234 Sum_probs=44.2
Q ss_pred HHHHHhcC-CCCCCCeEEEecCCchHHHHHHHHHCCCCcEEEccc-hHHHhcCCC
Q 044458 187 KKFLENYK-GFEGLQSVVDVGGGIGASLDMIISKYPSIKGINFDL-PHVIQDAPA 239 (241)
Q Consensus 187 ~~~~~~~~-~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-P~vi~~a~~ 239 (241)
+.++..++ .|-..+.+|||||+.|.+...+++.|-....+.+|+ |.-|+.|++
T Consensus 46 D~rLk~L~~~~f~~~~~LDIGCNsG~lt~~iak~F~~r~iLGvDID~~LI~~Ark 100 (288)
T KOG2899|consen 46 DPRLKVLEKDWFEPKQALDIGCNSGFLTLSIAKDFGPRRILGVDIDPVLIQRARK 100 (288)
T ss_pred ChhhhhccccccCcceeEeccCCcchhHHHHHHhhccceeeEeeccHHHHHHHHH
Confidence 45555553 377789999999999999999999999999999999 677777764
No 83
>PRK00377 cbiT cobalt-precorrin-6Y C(15)-methyltransferase; Provisional
Probab=96.37 E-value=0.0046 Score=50.73 Aligned_cols=47 Identities=15% Similarity=0.107 Sum_probs=38.2
Q ss_pred HhcCCCCCCCeEEEecCCchHHHHHHHHHC-CCCcEEEccc-hHHHhcCC
Q 044458 191 ENYKGFEGLQSVVDVGGGIGASLDMIISKY-PSIKGINFDL-PHVIQDAP 238 (241)
Q Consensus 191 ~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~-P~l~~~v~Dl-P~vi~~a~ 238 (241)
..++ .....+|+|+|||+|.++..+++.. |..+++.+|+ |..++.++
T Consensus 34 ~~l~-~~~~~~vlDlG~GtG~~s~~~a~~~~~~~~v~avD~~~~~~~~a~ 82 (198)
T PRK00377 34 SKLR-LRKGDMILDIGCGTGSVTVEASLLVGETGKVYAVDKDEKAINLTR 82 (198)
T ss_pred HHcC-CCCcCEEEEeCCcCCHHHHHHHHHhCCCCEEEEEECCHHHHHHHH
Confidence 3445 6667899999999999999998864 6788999999 77777654
No 84
>PF02082 Rrf2: Transcriptional regulator; InterPro: IPR000944 The following uncharacterised bacterial proteins have been shown to be evolutionary related, Desulfovibrio vulgaris protein Rrf2; Escherichia coli hypothetical proteins yfhP and yjeB; Bacillus subtilis hypothetical proteins yhdE, yrzC and ywgB; Mycobacterium tuberculosis hypothetical protein Rv1287; and Synechocystis sp. (strain PCC 6803) hypothetical protein slr0846. These are small proteins of 12 to 18kDa which seem to contain a signal sequence, and may represent a family of probable transcriptional regulators.; PDB: 3T8T_A 3T8R_A 3K69_A 3LWF_C 1XD7_A 2Y75_E 1YLF_C.
Probab=96.36 E-value=0.0051 Score=43.29 Aligned_cols=56 Identities=29% Similarity=0.309 Sum_probs=41.3
Q ss_pred HHHHhcCCCCCCCHHHHHhhCCCCCCCCcchHHHHHHHHhcCCccccccccCCCCccccceecCcc
Q 044458 44 EVIAKAGPGAFMSPKQIASQLPTKNSDAHILLDRILRLLASYSVLNCSLHTLPDGGVERLYGLAPV 109 (241)
Q Consensus 44 d~L~~~~~~~~~t~~eLA~~~g~~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~g~~~~~y~~t~~ 109 (241)
-.|+..+++++.|.+|||+.+++ ++..+++++..|...|+++... |. .|.|.++.-
T Consensus 15 ~~la~~~~~~~~s~~eiA~~~~i----~~~~l~kil~~L~~~Gli~s~~-----G~-~GGy~L~~~ 70 (83)
T PF02082_consen 15 LYLARHPDGKPVSSKEIAERLGI----SPSYLRKILQKLKKAGLIESSR-----GR-GGGYRLARP 70 (83)
T ss_dssp HHHHCTTTSC-BEHHHHHHHHTS-----HHHHHHHHHHHHHTTSEEEET-----ST-TSEEEESS-
T ss_pred HHHHhCCCCCCCCHHHHHHHHCc----CHHHHHHHHHHHhhCCeeEecC-----CC-CCceeecCC
Confidence 34444443356999999999999 9999999999999999998642 31 477877753
No 85
>PRK00517 prmA ribosomal protein L11 methyltransferase; Reviewed
Probab=96.36 E-value=0.0032 Score=53.65 Aligned_cols=41 Identities=24% Similarity=0.267 Sum_probs=32.8
Q ss_pred CCCCeEEEecCCchHHHHHHHHHCCCCcEEEccc-hHHHhcCC
Q 044458 197 EGLQSVVDVGGGIGASLDMIISKYPSIKGINFDL-PHVIQDAP 238 (241)
Q Consensus 197 ~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-P~vi~~a~ 238 (241)
....+|+|||||+|.+++.+++..+. +++.+|. |..++.|+
T Consensus 118 ~~~~~VLDiGcGsG~l~i~~~~~g~~-~v~giDis~~~l~~A~ 159 (250)
T PRK00517 118 LPGKTVLDVGCGSGILAIAAAKLGAK-KVLAVDIDPQAVEAAR 159 (250)
T ss_pred CCCCEEEEeCCcHHHHHHHHHHcCCC-eEEEEECCHHHHHHHH
Confidence 34689999999999999987776544 6899999 77777654
No 86
>PF06325 PrmA: Ribosomal protein L11 methyltransferase (PrmA); InterPro: IPR010456 This family consists of several Ribosomal protein L11 methyltransferase sequences. Its genetic determinant is prmA, which forms a bifunctional operon with the downstream panF gene []. The role of L11 methylation in ribosome function is, as yet, unknown. Deletion of the prmA gene in Escherichia coli showed no obvious effect [] except for the production of undermethylated forms of L11 []. Methylation is the most common post-transcriptional modification to ribosomal proteins in all organisms. PrmA is the only bacterial enzyme that catalyses the methylation of a ribosomal protein [].; GO: 0008276 protein methyltransferase activity, 0006479 protein methylation, 0005737 cytoplasm; PDB: 3GRZ_B 1F3L_A 2NXJ_B 3CJT_I 3CJQ_G 2NXE_A 2NXC_A 2ZBP_A 3EGV_A 3CJS_A ....
Probab=96.34 E-value=0.002 Score=56.40 Aligned_cols=61 Identities=25% Similarity=0.367 Sum_probs=41.8
Q ss_pred HHHHHHhcchhhHHHHHHhcCCCCCCCeEEEecCCchHHHHHHHHHCCCCcEEEccc-hHHHhcCC
Q 044458 174 FNNGMFSHSTITMKKFLENYKGFEGLQSVVDVGGGIGASLDMIISKYPSIKGINFDL-PHVIQDAP 238 (241)
Q Consensus 174 f~~aM~~~~~~~~~~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-P~vi~~a~ 238 (241)
|...-...++.... ++..+. .+ ..+|+|||||+|.++++.++.-.. +++.+|. |.+++.|+
T Consensus 140 FGTG~H~TT~lcl~-~l~~~~-~~-g~~vLDvG~GSGILaiaA~klGA~-~v~a~DiDp~Av~~a~ 201 (295)
T PF06325_consen 140 FGTGHHPTTRLCLE-LLEKYV-KP-GKRVLDVGCGSGILAIAAAKLGAK-KVVAIDIDPLAVEAAR 201 (295)
T ss_dssp S-SSHCHHHHHHHH-HHHHHS-ST-TSEEEEES-TTSHHHHHHHHTTBS-EEEEEESSCHHHHHHH
T ss_pred ccCCCCHHHHHHHH-HHHHhc-cC-CCEEEEeCCcHHHHHHHHHHcCCC-eEEEecCCHHHHHHHH
Confidence 55555555555543 334444 33 479999999999999999997443 6899999 77777664
No 87
>TIGR00755 ksgA dimethyladenosine transferase. Alternate name: S-adenosylmethionine--6-N',N'-adenosyl (rRNA) dimethyltransferase
Probab=96.31 E-value=0.0059 Score=52.10 Aligned_cols=48 Identities=17% Similarity=0.351 Sum_probs=37.1
Q ss_pred HHHHHHhcCCCCCCCeEEEecCCchHHHHHHHHHCCCCcEEEccc-hHHHhc
Q 044458 186 MKKFLENYKGFEGLQSVVDVGGGIGASLDMIISKYPSIKGINFDL-PHVIQD 236 (241)
Q Consensus 186 ~~~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-P~vi~~ 236 (241)
...+++..+ +.+..+|+|||||.|.+...++++.+. ++.+|. +..++.
T Consensus 18 ~~~i~~~~~-~~~~~~VLEiG~G~G~lt~~L~~~~~~--v~~iE~d~~~~~~ 66 (253)
T TIGR00755 18 IQKIVEAAN-VLEGDVVLEIGPGLGALTEPLLKRAKK--VTAIEIDPRLAEI 66 (253)
T ss_pred HHHHHHhcC-CCCcCEEEEeCCCCCHHHHHHHHhCCc--EEEEECCHHHHHH
Confidence 345666666 777789999999999999999999975 677777 444443
No 88
>PLN02396 hexaprenyldihydroxybenzoate methyltransferase
Probab=96.28 E-value=0.0027 Score=56.30 Aligned_cols=38 Identities=16% Similarity=0.112 Sum_probs=32.0
Q ss_pred CCeEEEecCCchHHHHHHHHHCCCCcEEEccc-hHHHhcCC
Q 044458 199 LQSVVDVGGGIGASLDMIISKYPSIKGINFDL-PHVIQDAP 238 (241)
Q Consensus 199 ~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-P~vi~~a~ 238 (241)
..+|||||||.|.++..+++ ++.+++.+|. ++.++.|+
T Consensus 132 g~~ILDIGCG~G~~s~~La~--~g~~V~GID~s~~~i~~Ar 170 (322)
T PLN02396 132 GLKFIDIGCGGGLLSEPLAR--MGATVTGVDAVDKNVKIAR 170 (322)
T ss_pred CCEEEEeeCCCCHHHHHHHH--cCCEEEEEeCCHHHHHHHH
Confidence 46999999999999998876 4778999999 77777664
No 89
>PRK03612 spermidine synthase; Provisional
Probab=96.27 E-value=0.0048 Score=58.27 Aligned_cols=43 Identities=28% Similarity=0.424 Sum_probs=37.7
Q ss_pred CCCCeEEEecCCchHHHHHHHHHCCC-CcEEEccc-hHHHhcCCCC
Q 044458 197 EGLQSVVDVGGGIGASLDMIISKYPS-IKGINFDL-PHVIQDAPAY 240 (241)
Q Consensus 197 ~~~~~vvDVGGG~G~~~~~l~~~~P~-l~~~v~Dl-P~vi~~a~~~ 240 (241)
++.++|+|||||.|..+.++++ +|. -++++.|+ |++++.++++
T Consensus 296 ~~~~rVL~IG~G~G~~~~~ll~-~~~v~~v~~VEid~~vi~~ar~~ 340 (521)
T PRK03612 296 ARPRRVLVLGGGDGLALREVLK-YPDVEQVTLVDLDPAMTELARTS 340 (521)
T ss_pred CCCCeEEEEcCCccHHHHHHHh-CCCcCeEEEEECCHHHHHHHHhC
Confidence 4568999999999999999996 676 68999999 9999998874
No 90
>PRK00050 16S rRNA m(4)C1402 methyltranserfase; Provisional
Probab=96.27 E-value=0.0076 Score=52.72 Aligned_cols=53 Identities=19% Similarity=0.177 Sum_probs=43.6
Q ss_pred HHHHHHhcCCCCCCCeEEEecCCchHHHHHHHHHCC-CCcEEEccc-hHHHhcCCC
Q 044458 186 MKKFLENYKGFEGLQSVVDVGGGIGASLDMIISKYP-SIKGINFDL-PHVIQDAPA 239 (241)
Q Consensus 186 ~~~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P-~l~~~v~Dl-P~vi~~a~~ 239 (241)
.+.+++.+. ......+||++||.|.++..+++.+| +.+++.+|. |++++.+++
T Consensus 8 l~Evl~~L~-~~pg~~vlD~TlG~GGhS~~il~~~~~~g~VigiD~D~~al~~ak~ 62 (296)
T PRK00050 8 LDEVVDALA-IKPDGIYVDGTFGGGGHSRAILERLGPKGRLIAIDRDPDAIAAAKD 62 (296)
T ss_pred HHHHHHhhC-CCCCCEEEEeCcCChHHHHHHHHhCCCCCEEEEEcCCHHHHHHHHH
Confidence 356666665 44557999999999999999999996 789999999 888887653
No 91
>PRK14896 ksgA 16S ribosomal RNA methyltransferase KsgA/Dim1 family protein; Provisional
Probab=96.27 E-value=0.0062 Score=52.18 Aligned_cols=49 Identities=20% Similarity=0.289 Sum_probs=37.3
Q ss_pred HHHHHHhcCCCCCCCeEEEecCCchHHHHHHHHHCCCCcEEEccc-hHHHhcC
Q 044458 186 MKKFLENYKGFEGLQSVVDVGGGIGASLDMIISKYPSIKGINFDL-PHVIQDA 237 (241)
Q Consensus 186 ~~~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-P~vi~~a 237 (241)
...+++..+ .....+|||||||.|.++..++++. .+++++|+ +..++.+
T Consensus 18 ~~~iv~~~~-~~~~~~VLEIG~G~G~lt~~L~~~~--~~v~~vEid~~~~~~l 67 (258)
T PRK14896 18 VDRIVEYAE-DTDGDPVLEIGPGKGALTDELAKRA--KKVYAIELDPRLAEFL 67 (258)
T ss_pred HHHHHHhcC-CCCcCeEEEEeCccCHHHHHHHHhC--CEEEEEECCHHHHHHH
Confidence 445566655 5667899999999999999999984 46788888 4555544
No 92
>PF08241 Methyltransf_11: Methyltransferase domain; InterPro: IPR013216 Methyl transfer from the ubiquitous S-adenosyl-L-methionine (SAM) to either nitrogen, oxygen or carbon atoms is frequently employed in diverse organisms ranging from bacteria to plants and mammals. The reaction is catalyzed by methyltransferases (Mtases) and modifies DNA, RNA, proteins and small molecules, such as catechol for regulatory purposes. The various aspects of the role of DNA methylation in prokaryotic restriction-modification systems and in a number of cellular processes in eukaryotes including gene regulation and differentiation is well documented. This entry represents a methyltransferase domain found in a large variety of SAM-dependent methyltransferases including, but not limited to: Arsenite methyltransferase (2.1.1.137 from EC) which converts arsenical compounds to their methylated forms [] Biotin synthesis protein bioC, which is involved in the early stages of biotin biosyntheis [] Arginine N-methyltransferase 1, an arginine-methylating enzyme which acts on residues present in a glycine and argine-rich domain and can methylate histones [] Hexaprenyldihydroxybenzoate methyltransferase (2.1.1.114 from EC), a mitochodrial enzyme involved in ubiquinone biosynthesis [] A probable cobalt-precorrin-6Y C(15)-methyltransferase thought to be involved in adenosylcobalamin biosynthesis [] Sterol 24-C-methyltransferase (2.1.1.41 from EC), shown to participate in ergosterol biosynthesis [] 3-demethylubiquinone-9 3-methyltransferase (2.1.1.64 from EC) involved in ubiquinone biosynthesis [] Structural studies show that this domain forms the Rossman-like alpha-beta fold typical of SAM-dependent methyltransferases [, , ]. ; GO: 0008168 methyltransferase activity, 0008152 metabolic process; PDB: 3CGG_B 3CCF_B 3BKW_B 2PXX_A 3I9F_A 2YQZ_B 2YR0_A 3BUS_A 3EGE_A 3G5L_B ....
Probab=96.27 E-value=0.0026 Score=44.71 Aligned_cols=35 Identities=17% Similarity=0.359 Sum_probs=29.0
Q ss_pred EEecCCchHHHHHHHHHCCCCcEEEccc-hHHHhcCC
Q 044458 203 VDVGGGIGASLDMIISKYPSIKGINFDL-PHVIQDAP 238 (241)
Q Consensus 203 vDVGGG~G~~~~~l~~~~P~l~~~v~Dl-P~vi~~a~ 238 (241)
||||||.|..+..+++. +..+.+..|. +..++.++
T Consensus 1 LdiG~G~G~~~~~l~~~-~~~~v~~~D~~~~~~~~~~ 36 (95)
T PF08241_consen 1 LDIGCGTGRFAAALAKR-GGASVTGIDISEEMLEQAR 36 (95)
T ss_dssp EEET-TTSHHHHHHHHT-TTCEEEEEES-HHHHHHHH
T ss_pred CEecCcCCHHHHHHHhc-cCCEEEEEeCCHHHHHHHH
Confidence 79999999999999999 9999999999 55555543
No 93
>KOG1540 consensus Ubiquinone biosynthesis methyltransferase COQ5 [Coenzyme transport and metabolism]
Probab=96.26 E-value=0.0078 Score=51.19 Aligned_cols=65 Identities=23% Similarity=0.284 Sum_probs=45.9
Q ss_pred HHHHHHHHhcchhhHHHHHHhcCCC---CCCCeEEEecCCchHHHHHHHHHCCC------CcEEEccc-hHHHhcCCC
Q 044458 172 KIFNNGMFSHSTITMKKFLENYKGF---EGLQSVVDVGGGIGASLDMIISKYPS------IKGINFDL-PHVIQDAPA 239 (241)
Q Consensus 172 ~~f~~aM~~~~~~~~~~~~~~~~~~---~~~~~vvDVGGG~G~~~~~l~~~~P~------l~~~v~Dl-P~vi~~a~~ 239 (241)
+..|.+|..-.+ +-|-+.+..+ ...-++|||+||+|-.+..+++.-++ -+++|.|. |+..+.+++
T Consensus 74 D~mND~mSlGiH---RlWKd~~v~~L~p~~~m~~lDvaGGTGDiaFril~~v~s~~~~~~~~V~v~Dinp~mL~vgkq 148 (296)
T KOG1540|consen 74 DIMNDAMSLGIH---RLWKDMFVSKLGPGKGMKVLDVAGGTGDIAFRILRHVKSQFGDRESKVTVLDINPHMLAVGKQ 148 (296)
T ss_pred HHHHHHhhcchh---HHHHHHhhhccCCCCCCeEEEecCCcchhHHHHHHhhccccCCCCceEEEEeCCHHHHHHHHH
Confidence 445666643322 2344444311 23489999999999999999999998 78999999 888776653
No 94
>PF13489 Methyltransf_23: Methyltransferase domain; PDB: 3JWJ_A 3JWH_B 2AOV_B 2AOT_A 1JQD_B 2AOX_A 1JQE_A 2AOU_B 2AOW_A 3DLI_C ....
Probab=96.26 E-value=0.013 Score=45.44 Aligned_cols=37 Identities=24% Similarity=0.422 Sum_probs=30.1
Q ss_pred CCCCCeEEEecCCchHHHHHHHHHCCCCcEEEccc-hHHH
Q 044458 196 FEGLQSVVDVGGGIGASLDMIISKYPSIKGINFDL-PHVI 234 (241)
Q Consensus 196 ~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-P~vi 234 (241)
.....+|||||||.|.++..+.+... +++..|. |..+
T Consensus 20 ~~~~~~vLDiGcG~G~~~~~l~~~~~--~~~g~D~~~~~~ 57 (161)
T PF13489_consen 20 LKPGKRVLDIGCGTGSFLRALAKRGF--EVTGVDISPQMI 57 (161)
T ss_dssp TTTTSEEEEESSTTSHHHHHHHHTTS--EEEEEESSHHHH
T ss_pred cCCCCEEEEEcCCCCHHHHHHHHhCC--EEEEEECCHHHH
Confidence 35678999999999999999977644 8899998 5554
No 95
>KOG2904 consensus Predicted methyltransferase [General function prediction only]
Probab=96.22 E-value=0.0054 Score=52.62 Aligned_cols=43 Identities=21% Similarity=0.271 Sum_probs=37.0
Q ss_pred CCCCCeEEEecCCchHHHHHHHHHCCCCcEEEccc-hHHHhcCC
Q 044458 196 FEGLQSVVDVGGGIGASLDMIISKYPSIKGINFDL-PHVIQDAP 238 (241)
Q Consensus 196 ~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-P~vi~~a~ 238 (241)
+.....++|+|||+|..+..++...|.+++|..|+ +.++..|.
T Consensus 146 ~~~~~~ildlgtGSGaIslsll~~L~~~~v~AiD~S~~Ai~La~ 189 (328)
T KOG2904|consen 146 HSKHTHILDLGTGSGAISLSLLHGLPQCTVTAIDVSKAAIKLAK 189 (328)
T ss_pred hcccceEEEecCCccHHHHHHHhcCCCceEEEEeccHHHHHHHH
Confidence 55567999999999999999999999999999999 56665543
No 96
>PRK15068 tRNA mo(5)U34 methyltransferase; Provisional
Probab=96.20 E-value=0.0087 Score=53.06 Aligned_cols=41 Identities=20% Similarity=0.250 Sum_probs=31.9
Q ss_pred HHHhcCCCCCCCeEEEecCCchHHHHHHHHHCCCCcEEEccch
Q 044458 189 FLENYKGFEGLQSVVDVGGGIGASLDMIISKYPSIKGINFDLP 231 (241)
Q Consensus 189 ~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~DlP 231 (241)
+...++..+ .++|||||||.|.++..+++..+. +++.+|.-
T Consensus 114 l~~~l~~l~-g~~VLDIGCG~G~~~~~la~~g~~-~V~GiD~S 154 (322)
T PRK15068 114 VLPHLSPLK-GRTVLDVGCGNGYHMWRMLGAGAK-LVVGIDPS 154 (322)
T ss_pred HHHhhCCCC-CCEEEEeccCCcHHHHHHHHcCCC-EEEEEcCC
Confidence 344443133 489999999999999999999877 48999973
No 97
>TIGR00406 prmA ribosomal protein L11 methyltransferase. Ribosomal protein L11 methyltransferase is an S-adenosyl-L-methionine-dependent methyltransferase required for the modification of ribosomal protein L11. This protein is found in bacteria and (with a probable transit peptide) in Arabidopsis.
Probab=96.20 E-value=0.0036 Score=54.58 Aligned_cols=40 Identities=25% Similarity=0.348 Sum_probs=31.9
Q ss_pred CCCeEEEecCCchHHHHHHHHHCCCCcEEEccc-hHHHhcCC
Q 044458 198 GLQSVVDVGGGIGASLDMIISKYPSIKGINFDL-PHVIQDAP 238 (241)
Q Consensus 198 ~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-P~vi~~a~ 238 (241)
...+|+|||||+|.+++.+++. +.-+++..|+ |..++.++
T Consensus 159 ~g~~VLDvGcGsG~lai~aa~~-g~~~V~avDid~~al~~a~ 199 (288)
T TIGR00406 159 KDKNVIDVGCGSGILSIAALKL-GAAKVVGIDIDPLAVESAR 199 (288)
T ss_pred CCCEEEEeCCChhHHHHHHHHc-CCCeEEEEECCHHHHHHHH
Confidence 3489999999999999888764 4458999999 66666654
No 98
>PHA03411 putative methyltransferase; Provisional
Probab=96.20 E-value=0.0044 Score=53.55 Aligned_cols=40 Identities=20% Similarity=0.261 Sum_probs=35.4
Q ss_pred CCeEEEecCCchHHHHHHHHHCCCCcEEEccc-hHHHhcCC
Q 044458 199 LQSVVDVGGGIGASLDMIISKYPSIKGINFDL-PHVIQDAP 238 (241)
Q Consensus 199 ~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-P~vi~~a~ 238 (241)
..+|||+|||+|.++..++++.+..+++.+|+ |..++.++
T Consensus 65 ~grVLDLGcGsGilsl~la~r~~~~~V~gVDisp~al~~Ar 105 (279)
T PHA03411 65 TGKVLDLCAGIGRLSFCMLHRCKPEKIVCVELNPEFARIGK 105 (279)
T ss_pred CCeEEEcCCCCCHHHHHHHHhCCCCEEEEEECCHHHHHHHH
Confidence 46899999999999999999988889999999 77777664
No 99
>COG0220 Predicted S-adenosylmethionine-dependent methyltransferase [General function prediction only]
Probab=96.19 E-value=0.0086 Score=50.42 Aligned_cols=37 Identities=19% Similarity=0.294 Sum_probs=32.6
Q ss_pred CCeEEEecCCchHHHHHHHHHCCCCcEEEccc-hHHHh
Q 044458 199 LQSVVDVGGGIGASLDMIISKYPSIKGINFDL-PHVIQ 235 (241)
Q Consensus 199 ~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-P~vi~ 235 (241)
...+|+||||.|.+...+++++|+..++.+|. ..++.
T Consensus 49 ~pi~lEIGfG~G~~l~~~A~~nP~~nfiGiEi~~~~v~ 86 (227)
T COG0220 49 APIVLEIGFGMGEFLVEMAKKNPEKNFLGIEIRVPGVA 86 (227)
T ss_pred CcEEEEECCCCCHHHHHHHHHCCCCCEEEEEEehHHHH
Confidence 36999999999999999999999999999998 44443
No 100
>PF01209 Ubie_methyltran: ubiE/COQ5 methyltransferase family; InterPro: IPR004033 A number of methyltransferases have been shown to share regions of similarities []. Apart from the ubiquinone/menaquinone biosynthesis methyltransferases (for example, the C-methyltransferase from the ubiE gene of Escherichia coli), the ubiquinone biosynthesis methyltransferases (for example, the C-methyltransferase from the COQ5 gene of Saccharomyces cerevisiae) and the menaquinone biosynthesis methyltransferases (for example, the C-methyltransferase from the MENH gene of Bacillus subtilis), this family also includes methyltransferases involved in biotin and sterol biosynthesis and in phosphatidylethanolamine methylation.; GO: 0008168 methyltransferase activity; PDB: 1VL5_C.
Probab=96.16 E-value=0.0031 Score=53.29 Aligned_cols=43 Identities=23% Similarity=0.357 Sum_probs=30.6
Q ss_pred CCCCCeEEEecCCchHHHHHHHHHC-CCCcEEEccc-hHHHhcCC
Q 044458 196 FEGLQSVVDVGGGIGASLDMIISKY-PSIKGINFDL-PHVIQDAP 238 (241)
Q Consensus 196 ~~~~~~vvDVGGG~G~~~~~l~~~~-P~l~~~v~Dl-P~vi~~a~ 238 (241)
.....+|||||||+|.++..+++.. |+.+++..|+ |..++.|+
T Consensus 45 ~~~g~~vLDv~~GtG~~~~~l~~~~~~~~~v~~vD~s~~ML~~a~ 89 (233)
T PF01209_consen 45 LRPGDRVLDVACGTGDVTRELARRVGPNGKVVGVDISPGMLEVAR 89 (233)
T ss_dssp --S--EEEEET-TTSHHHHHHGGGSS---EEEEEES-HHHHHHHH
T ss_pred CCCCCEEEEeCCChHHHHHHHHHHCCCccEEEEecCCHHHHHHHH
Confidence 4456799999999999999999875 6789999999 77777654
No 101
>PRK11569 transcriptional repressor IclR; Provisional
Probab=96.13 E-value=0.0067 Score=52.44 Aligned_cols=60 Identities=17% Similarity=0.153 Sum_probs=49.5
Q ss_pred HhcChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCcchHHHHHHHHhcCCccccccccCCCCccccceecCccc
Q 044458 38 IELDLLEVIAKAGPGAFMSPKQIASQLPTKNSDAHILLDRILRLLASYSVLNCSLHTLPDGGVERLYGLAPVC 110 (241)
Q Consensus 38 ~~lglfd~L~~~~~~~~~t~~eLA~~~g~~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~g~~~~~y~~t~~s 110 (241)
--+.|+++|.+.. ++.|..|||+.+|+ +...+.|+|..|...|++.++. . .++|++.+..
T Consensus 29 ral~IL~~l~~~~--~~~~lseia~~lgl----pksTv~RlL~tL~~~G~l~~~~---~----~~~Y~lG~~l 88 (274)
T PRK11569 29 RGLKLLEWIAESN--GSVALTELAQQAGL----PNSTTHRLLTTMQQQGFVRQVG---E----LGHWAIGAHA 88 (274)
T ss_pred HHHHHHHHHHhCC--CCcCHHHHHHHHCc----CHHHHHHHHHHHHHCCCEEEcC---C----CCeEecCHHH
Confidence 3456788887753 68999999999999 9999999999999999998741 1 5899998754
No 102
>TIGR00452 methyltransferase, putative. Known examples to date are restricted to the proteobacteria.
Probab=96.11 E-value=0.01 Score=52.43 Aligned_cols=41 Identities=17% Similarity=0.216 Sum_probs=31.8
Q ss_pred HHHHhcCCCCCCCeEEEecCCchHHHHHHHHHCCCCcEEEccc
Q 044458 188 KFLENYKGFEGLQSVVDVGGGIGASLDMIISKYPSIKGINFDL 230 (241)
Q Consensus 188 ~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl 230 (241)
.++..++ ....++|+|||||+|.++..+++..++ +++.+|.
T Consensus 112 ~~l~~l~-~~~g~~VLDvGCG~G~~~~~~~~~g~~-~v~GiDp 152 (314)
T TIGR00452 112 RVLPHLS-PLKGRTILDVGCGSGYHMWRMLGHGAK-SLVGIDP 152 (314)
T ss_pred HHHHhcC-CCCCCEEEEeccCCcHHHHHHHHcCCC-EEEEEcC
Confidence 3444443 333589999999999999999988775 6889997
No 103
>PRK14968 putative methyltransferase; Provisional
Probab=96.06 E-value=0.0061 Score=48.92 Aligned_cols=39 Identities=23% Similarity=0.322 Sum_probs=33.2
Q ss_pred CCCCeEEEecCCchHHHHHHHHHCCCCcEEEccc-hHHHhcC
Q 044458 197 EGLQSVVDVGGGIGASLDMIISKYPSIKGINFDL-PHVIQDA 237 (241)
Q Consensus 197 ~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-P~vi~~a 237 (241)
.+..+|||+|||.|.++..+++. +.+++.+|+ |.+++.+
T Consensus 22 ~~~~~vLd~G~G~G~~~~~l~~~--~~~v~~~D~s~~~~~~a 61 (188)
T PRK14968 22 KKGDRVLEVGTGSGIVAIVAAKN--GKKVVGVDINPYAVECA 61 (188)
T ss_pred cCCCEEEEEccccCHHHHHHHhh--cceEEEEECCHHHHHHH
Confidence 34578999999999999999998 678899999 7777655
No 104
>TIGR00438 rrmJ cell division protein FtsJ.
Probab=96.03 E-value=0.012 Score=47.74 Aligned_cols=44 Identities=18% Similarity=0.247 Sum_probs=34.2
Q ss_pred HHHhcCCCCCCCeEEEecCCchHHHHHHHHHC-CCCcEEEccchH
Q 044458 189 FLENYKGFEGLQSVVDVGGGIGASLDMIISKY-PSIKGINFDLPH 232 (241)
Q Consensus 189 ~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~-P~l~~~v~DlP~ 232 (241)
+.+.+.......+|||||||+|.++..+++++ +..+++.+|+-+
T Consensus 23 ~~~~~~~i~~g~~VLDiG~GtG~~~~~l~~~~~~~~~v~~vDis~ 67 (188)
T TIGR00438 23 LNQKFKLIKPGDTVLDLGAAPGGWSQVAVEQVGGKGRVIAVDLQP 67 (188)
T ss_pred HHHHhcccCCCCEEEEecCCCCHHHHHHHHHhCCCceEEEEeccc
Confidence 44445445667899999999999999999887 567788888743
No 105
>PRK10163 DNA-binding transcriptional repressor AllR; Provisional
Probab=96.02 E-value=0.0081 Score=51.86 Aligned_cols=59 Identities=15% Similarity=0.155 Sum_probs=48.8
Q ss_pred hcChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCcchHHHHHHHHhcCCccccccccCCCCccccceecCccc
Q 044458 39 ELDLLEVIAKAGPGAFMSPKQIASQLPTKNSDAHILLDRILRLLASYSVLNCSLHTLPDGGVERLYGLAPVC 110 (241)
Q Consensus 39 ~lglfd~L~~~~~~~~~t~~eLA~~~g~~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~g~~~~~y~~t~~s 110 (241)
-+.|++.|...+ ++.|..|||+.+|+ +...+.|+|..|...|++.++. . .+.|.++...
T Consensus 27 ~l~IL~~~~~~~--~~~tl~eIa~~lgl----pkStv~RlL~tL~~~G~l~~~~---~----~~~Y~lG~~l 85 (271)
T PRK10163 27 GIAILQYLEKSG--GSSSVSDISLNLDL----PLSTTFRLLKVLQAADFVYQDS---Q----LGWWHIGLGV 85 (271)
T ss_pred HHHHHHHHHhCC--CCcCHHHHHHHHCc----CHHHHHHHHHHHHHCCCEEEcC---C----CCeEEecHHH
Confidence 356788887653 57999999999999 9999999999999999998751 1 5789988744
No 106
>PRK11727 23S rRNA mA1618 methyltransferase; Provisional
Probab=95.99 E-value=0.0056 Score=54.16 Aligned_cols=41 Identities=20% Similarity=0.253 Sum_probs=36.3
Q ss_pred CCCeEEEecCCchHHHHHHHHHCCCCcEEEccc-hHHHhcCC
Q 044458 198 GLQSVVDVGGGIGASLDMIISKYPSIKGINFDL-PHVIQDAP 238 (241)
Q Consensus 198 ~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-P~vi~~a~ 238 (241)
...++||||+|+|.....++.+.++.+++..|+ |.+++.|+
T Consensus 114 ~~~~vLDIGtGag~I~~lLa~~~~~~~~~atDId~~Al~~A~ 155 (321)
T PRK11727 114 ANVRVLDIGVGANCIYPLIGVHEYGWRFVGSDIDPQALASAQ 155 (321)
T ss_pred CCceEEEecCCccHHHHHHHhhCCCCEEEEEeCCHHHHHHHH
Confidence 458999999999999988999999999999999 77887765
No 107
>KOG1270 consensus Methyltransferases [Coenzyme transport and metabolism]
Probab=95.98 E-value=0.0037 Score=53.23 Aligned_cols=39 Identities=18% Similarity=0.175 Sum_probs=33.3
Q ss_pred CeEEEecCCchHHHHHHHHHCCCCcEEEccc-hHHHhcCCCC
Q 044458 200 QSVVDVGGGIGASLDMIISKYPSIKGINFDL-PHVIQDAPAY 240 (241)
Q Consensus 200 ~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-P~vi~~a~~~ 240 (241)
.+|||||||.|.++..|++.- ..++..|+ +..|+.|+++
T Consensus 91 ~~ilDvGCGgGLLSepLArlg--a~V~GID~s~~~V~vA~~h 130 (282)
T KOG1270|consen 91 MKILDVGCGGGLLSEPLARLG--AQVTGIDASDDMVEVANEH 130 (282)
T ss_pred ceEEEeccCccccchhhHhhC--CeeEeecccHHHHHHHHHh
Confidence 779999999999999999986 55678898 7888887764
No 108
>PF13412 HTH_24: Winged helix-turn-helix DNA-binding; PDB: 1I1G_B 2IA0_B 3I4P_A 2GQQ_A 2L4A_A 2CFX_B 2DBB_B 2EFO_A 2EFQ_A 2PN6_A ....
Probab=95.94 E-value=0.0083 Score=37.48 Aligned_cols=45 Identities=16% Similarity=0.318 Sum_probs=37.9
Q ss_pred HhcChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCcchHHHHHHHHhcCCccc
Q 044458 38 IELDLLEVIAKAGPGAFMSPKQIASQLPTKNSDAHILLDRILRLLASYSVLN 89 (241)
Q Consensus 38 ~~lglfd~L~~~~~~~~~t~~eLA~~~g~~~~~~~~~l~rlLr~L~~~g~l~ 89 (241)
.+..|+.+|.+. +.+|..|||+.+|+ +...+.+.|+.|...|+++
T Consensus 4 ~~~~Il~~l~~~---~~~t~~ela~~~~i----s~~tv~~~l~~L~~~g~I~ 48 (48)
T PF13412_consen 4 TQRKILNYLREN---PRITQKELAEKLGI----SRSTVNRYLKKLEEKGLIE 48 (48)
T ss_dssp HHHHHHHHHHHC---TTS-HHHHHHHHTS-----HHHHHHHHHHHHHTTSEE
T ss_pred HHHHHHHHHHHc---CCCCHHHHHHHhCC----CHHHHHHHHHHHHHCcCcC
Confidence 356788999885 47999999999999 9999999999999999874
No 109
>PLN02672 methionine S-methyltransferase
Probab=95.93 E-value=0.0063 Score=61.66 Aligned_cols=39 Identities=26% Similarity=0.322 Sum_probs=36.0
Q ss_pred CeEEEecCCchHHHHHHHHHCCCCcEEEccc-hHHHhcCC
Q 044458 200 QSVVDVGGGIGASLDMIISKYPSIKGINFDL-PHVIQDAP 238 (241)
Q Consensus 200 ~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-P~vi~~a~ 238 (241)
.+|+|||||+|.+++.+++.+|+.+++..|+ |.+++.|+
T Consensus 120 ~~VLDlG~GSG~Iai~La~~~~~~~v~avDis~~Al~~A~ 159 (1082)
T PLN02672 120 KTVAELGCGNGWISIAIAEKWLPSKVYGLDINPRAVKVAW 159 (1082)
T ss_pred CEEEEEecchHHHHHHHHHHCCCCEEEEEECCHHHHHHHH
Confidence 6899999999999999999999999999999 88887764
No 110
>PRK09834 DNA-binding transcriptional activator MhpR; Provisional
Probab=95.92 E-value=0.0096 Score=51.15 Aligned_cols=61 Identities=13% Similarity=0.107 Sum_probs=50.1
Q ss_pred HhcChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCcchHHHHHHHHhcCCccccccccCCCCccccceecCcccc
Q 044458 38 IELDLLEVIAKAGPGAFMSPKQIASQLPTKNSDAHILLDRILRLLASYSVLNCSLHTLPDGGVERLYGLAPVCK 111 (241)
Q Consensus 38 ~~lglfd~L~~~~~~~~~t~~eLA~~~g~~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~g~~~~~y~~t~~s~ 111 (241)
--+.|++.|...+ ++.|..|||+.+|+ +...+.|+|+.|...|++.++. + ++.|++++...
T Consensus 12 ral~iL~~l~~~~--~~ls~~eia~~lgl----~kstv~RlL~tL~~~g~v~~~~----~---~~~Y~Lg~~~~ 72 (263)
T PRK09834 12 RGLMVLRALNRLD--GGATVGLLAELTGL----HRTTVRRLLETLQEEGYVRRSA----S---DDSFRLTLKVR 72 (263)
T ss_pred HHHHHHHHHHhcC--CCCCHHHHHHHHCc----CHHHHHHHHHHHHHCCCEEEec----C---CCcEEEcHHHH
Confidence 3456788887653 46999999999999 9999999999999999999751 1 57899997654
No 111
>PRK11188 rrmJ 23S rRNA methyltransferase J; Provisional
Probab=95.90 E-value=0.017 Score=47.91 Aligned_cols=43 Identities=21% Similarity=0.222 Sum_probs=32.5
Q ss_pred HHHhcCCCCCCCeEEEecCCchHHHHHHHHHC-CCCcEEEccch
Q 044458 189 FLENYKGFEGLQSVVDVGGGIGASLDMIISKY-PSIKGINFDLP 231 (241)
Q Consensus 189 ~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~-P~l~~~v~DlP 231 (241)
+.+.|..+....+|||||||+|.++..+++.. +..+++.+|+-
T Consensus 42 ~~~~~~~~~~~~~VLDlG~GtG~~t~~l~~~~~~~~~V~aVDi~ 85 (209)
T PRK11188 42 IQQSDKLFKPGMTVVDLGAAPGGWSQYAVTQIGDKGRVIACDIL 85 (209)
T ss_pred HHHHhccCCCCCEEEEEcccCCHHHHHHHHHcCCCceEEEEecc
Confidence 33444424556799999999999999999986 45678888874
No 112
>PLN02585 magnesium protoporphyrin IX methyltransferase
Probab=95.90 E-value=0.0057 Score=54.05 Aligned_cols=38 Identities=18% Similarity=0.170 Sum_probs=32.2
Q ss_pred CCeEEEecCCchHHHHHHHHHCCCCcEEEccc-hHHHhcCC
Q 044458 199 LQSVVDVGGGIGASLDMIISKYPSIKGINFDL-PHVIQDAP 238 (241)
Q Consensus 199 ~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-P~vi~~a~ 238 (241)
..+|||||||+|.++..+++. +.+++.+|+ |..++.++
T Consensus 145 ~~~VLDlGcGtG~~a~~la~~--g~~V~gvD~S~~ml~~A~ 183 (315)
T PLN02585 145 GVTVCDAGCGTGSLAIPLALE--GAIVSASDISAAMVAEAE 183 (315)
T ss_pred CCEEEEecCCCCHHHHHHHHC--CCEEEEEECCHHHHHHHH
Confidence 479999999999999999986 578999999 66776554
No 113
>PF09012 FeoC: FeoC like transcriptional regulator; InterPro: IPR015102 This entry contains several transcriptional regulators, including FeoC, which contain a HTH motif. FeoC acts as a [Fe-S] dependent transcriptional repressor []. ; PDB: 1XN7_A 2K02_A.
Probab=95.90 E-value=0.0088 Score=40.59 Aligned_cols=43 Identities=9% Similarity=0.129 Sum_probs=36.7
Q ss_pred hHHHHHhcCCCCCCCHHHHHhhCCCCCCCCcchHHHHHHHHhcCCccccc
Q 044458 42 LLEVIAKAGPGAFMSPKQIASQLPTKNSDAHILLDRILRLLASYSVLNCS 91 (241)
Q Consensus 42 lfd~L~~~~~~~~~t~~eLA~~~g~~~~~~~~~l~rlLr~L~~~g~l~~~ 91 (241)
|-++|.+. +.+|..|||.++++ ++..++.+|..|...|.+.+.
T Consensus 5 i~~~l~~~---~~~S~~eLa~~~~~----s~~~ve~mL~~l~~kG~I~~~ 47 (69)
T PF09012_consen 5 IRDYLRER---GRVSLAELAREFGI----SPEAVEAMLEQLIRKGYIRKV 47 (69)
T ss_dssp HHHHHHHS----SEEHHHHHHHTT------HHHHHHHHHHHHCCTSCEEE
T ss_pred HHHHHHHc---CCcCHHHHHHHHCc----CHHHHHHHHHHHHHCCcEEEe
Confidence 56778775 68999999999999 999999999999999999975
No 114
>PRK15090 DNA-binding transcriptional regulator KdgR; Provisional
Probab=95.83 E-value=0.01 Score=50.76 Aligned_cols=58 Identities=9% Similarity=0.153 Sum_probs=48.1
Q ss_pred hcChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCcchHHHHHHHHhcCCccccccccCCCCccccceecCccc
Q 044458 39 ELDLLEVIAKAGPGAFMSPKQIASQLPTKNSDAHILLDRILRLLASYSVLNCSLHTLPDGGVERLYGLAPVC 110 (241)
Q Consensus 39 ~lglfd~L~~~~~~~~~t~~eLA~~~g~~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~g~~~~~y~~t~~s 110 (241)
-+.|++.|... ++.|..|||+.+|+ +...+.|+|+.|...|++.++. . .+.|++.+..
T Consensus 16 ~l~IL~~l~~~---~~l~l~eia~~lgl----~kstv~Rll~tL~~~G~l~~~~---~----~~~Y~lG~~~ 73 (257)
T PRK15090 16 VFGILQALGEE---REIGITELSQRVMM----SKSTVYRFLQTMKTLGYVAQEG---E----SEKYSLTLKL 73 (257)
T ss_pred HHHHHHHhhcC---CCCCHHHHHHHHCc----CHHHHHHHHHHHHHCCCEEEcC---C----CCcEEecHHH
Confidence 35577777763 57999999999999 9999999999999999998751 1 5889999754
No 115
>PRK14967 putative methyltransferase; Provisional
Probab=95.82 E-value=0.012 Score=49.26 Aligned_cols=42 Identities=17% Similarity=0.129 Sum_probs=32.8
Q ss_pred CCCCCeEEEecCCchHHHHHHHHHCCCCcEEEccc-hHHHhcCC
Q 044458 196 FEGLQSVVDVGGGIGASLDMIISKYPSIKGINFDL-PHVIQDAP 238 (241)
Q Consensus 196 ~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-P~vi~~a~ 238 (241)
.....+|||+|||+|.++..+++. +..+++.+|+ |..++.++
T Consensus 34 ~~~~~~vLDlGcG~G~~~~~la~~-~~~~v~~vD~s~~~l~~a~ 76 (223)
T PRK14967 34 LGPGRRVLDLCTGSGALAVAAAAA-GAGSVTAVDISRRAVRSAR 76 (223)
T ss_pred cCCCCeEEEecCCHHHHHHHHHHc-CCCeEEEEECCHHHHHHHH
Confidence 445579999999999999998876 3347899999 66665443
No 116
>PRK04266 fibrillarin; Provisional
Probab=95.78 E-value=0.019 Score=48.38 Aligned_cols=43 Identities=12% Similarity=0.219 Sum_probs=35.4
Q ss_pred hcCCCCCCCeEEEecCCchHHHHHHHHHCCCCcEEEccc-hHHHh
Q 044458 192 NYKGFEGLQSVVDVGGGIGASLDMIISKYPSIKGINFDL-PHVIQ 235 (241)
Q Consensus 192 ~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-P~vi~ 235 (241)
.++ .....+|+|+|||+|.++..+++..++-+++.+|+ |+.++
T Consensus 67 ~l~-i~~g~~VlD~G~G~G~~~~~la~~v~~g~V~avD~~~~ml~ 110 (226)
T PRK04266 67 NFP-IKKGSKVLYLGAASGTTVSHVSDIVEEGVVYAVEFAPRPMR 110 (226)
T ss_pred hCC-CCCCCEEEEEccCCCHHHHHHHHhcCCCeEEEEECCHHHHH
Confidence 355 66678999999999999999999998667899999 64444
No 117
>TIGR00417 speE spermidine synthase. the SpeE subunit of spermidine synthase catalysesthe reaction (putrescine + S-adenosylmethioninamine = spermidine + 5'-methylthioadenosine) and is involved in polyamine biosynthesis and in the biosynthesis of spermidine from arganine. The region between residues 77 and 120 of the seed alignment is thought to be involved in binding to decarboxylated SAM.
Probab=95.78 E-value=0.0079 Score=51.88 Aligned_cols=43 Identities=23% Similarity=0.329 Sum_probs=35.6
Q ss_pred CCCCeEEEecCCchHHHHHHHHHCCCCcEEEccc-hHHHhcCCC
Q 044458 197 EGLQSVVDVGGGIGASLDMIISKYPSIKGINFDL-PHVIQDAPA 239 (241)
Q Consensus 197 ~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-P~vi~~a~~ 239 (241)
++.++||+||||.|.++..+++..+..++++.|+ |.+++.+++
T Consensus 71 ~~p~~VL~iG~G~G~~~~~ll~~~~~~~v~~veid~~vi~~a~~ 114 (270)
T TIGR00417 71 PNPKHVLVIGGGDGGVLREVLKHKSVEKATLVDIDEKVIELSKK 114 (270)
T ss_pred CCCCEEEEEcCCchHHHHHHHhCCCcceEEEEeCCHHHHHHHHH
Confidence 3457999999999999999998766677899999 778777654
No 118
>cd02440 AdoMet_MTases S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy). There are at least five structurally distinct families of AdoMet-MTases, class I being the largest and most diverse. Within this class enzymes can be classified by different substrate specificities (small molecules, lipids, nucleic acids, etc.) and different target atoms for methylation (nitrogen, oxygen, carbon, sulfur, etc.).
Probab=95.77 E-value=0.0083 Score=41.96 Aligned_cols=35 Identities=29% Similarity=0.415 Sum_probs=29.3
Q ss_pred eEEEecCCchHHHHHHHHHCCCCcEEEccc-hHHHhc
Q 044458 201 SVVDVGGGIGASLDMIISKYPSIKGINFDL-PHVIQD 236 (241)
Q Consensus 201 ~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-P~vi~~ 236 (241)
+|+|||||.|.++..+++ .+..+.+.+|+ +..+..
T Consensus 1 ~ildig~G~G~~~~~~~~-~~~~~~~~~d~~~~~~~~ 36 (107)
T cd02440 1 RVLDLGCGTGALALALAS-GPGARVTGVDISPVALEL 36 (107)
T ss_pred CeEEEcCCccHHHHHHhc-CCCCEEEEEeCCHHHHHH
Confidence 589999999999999999 77889999998 444443
No 119
>PHA03412 putative methyltransferase; Provisional
Probab=95.73 E-value=0.01 Score=50.24 Aligned_cols=40 Identities=20% Similarity=0.164 Sum_probs=34.0
Q ss_pred CCeEEEecCCchHHHHHHHHHC---CCCcEEEccc-hHHHhcCC
Q 044458 199 LQSVVDVGGGIGASLDMIISKY---PSIKGINFDL-PHVIQDAP 238 (241)
Q Consensus 199 ~~~vvDVGGG~G~~~~~l~~~~---P~l~~~v~Dl-P~vi~~a~ 238 (241)
..+|||+|||+|.++..++++. +..+++.+|+ |.+++.|+
T Consensus 50 ~grVLDlG~GSG~Lalala~~~~~~~~~~V~aVEID~~Al~~Ar 93 (241)
T PHA03412 50 SGSVVDLCAGIGGLSFAMVHMMMYAKPREIVCVELNHTYYKLGK 93 (241)
T ss_pred CCEEEEccChHHHHHHHHHHhcccCCCcEEEEEECCHHHHHHHH
Confidence 4799999999999999999875 4678999999 77777665
No 120
>PLN02336 phosphoethanolamine N-methyltransferase
Probab=95.73 E-value=0.015 Score=54.19 Aligned_cols=48 Identities=25% Similarity=0.294 Sum_probs=36.7
Q ss_pred HHHHHhcCCCCCCCeEEEecCCchHHHHHHHHHCCCCcEEEccc-hHHHhcC
Q 044458 187 KKFLENYKGFEGLQSVVDVGGGIGASLDMIISKYPSIKGINFDL-PHVIQDA 237 (241)
Q Consensus 187 ~~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-P~vi~~a 237 (241)
..+++.++ .....+|||||||.|.++..+++.+. +++.+|. |..++.+
T Consensus 27 ~~il~~l~-~~~~~~vLDlGcG~G~~~~~la~~~~--~v~giD~s~~~l~~a 75 (475)
T PLN02336 27 PEILSLLP-PYEGKSVLELGAGIGRFTGELAKKAG--QVIALDFIESVIKKN 75 (475)
T ss_pred hHHHhhcC-ccCCCEEEEeCCCcCHHHHHHHhhCC--EEEEEeCCHHHHHHH
Confidence 45555655 44567999999999999999999864 6788898 6666544
No 121
>PF01022 HTH_5: Bacterial regulatory protein, arsR family; InterPro: IPR001845 Bacterial transcription regulatory proteins that bind DNA via a helix-turn-helix (HTH) motif can be grouped into families on the basis of sequence similarities. One such group, termed arsR, includes several proteins that appear to dissociate from DNA in the presence of metal ions: arsR, which functions as a transcriptional repressor of an arsenic resistance operon; smtB from Synechococcus sp. (strain PCC 7942), which acts as a transcriptional repressor of the smtA gene that codes for a metallothionein; cadC, a protein required for cadmium-resistance; and hypothetical protein yqcJ from Bacillus subtilis. The HTH motif is thought to be located in the central part of these proteins []. The motif is characterised by a number of well-conserved residues: at its N-terminal extremity is a cysteine residue; a second Cys is found in arsR and cadC, but not in smtA; and at the C terminus lie one or two histidines. These residues may be involved in metal-binding (Zn in smtB; metal-oxyanions such as arsenite, antimonite and arsenate for arsR; and cadmium for cadC) []. It is believed that binding of a metal ion could induce a conformational change that would prevent the protein from binding DNA []. The crystal structure of the cyanobacterial smtB shows a fold of five alpha-helices (H) and a pair of antiparallel beta-strands (B) in the topology H1-H2-H3-H4-B1-B2-H5. Helices 3 and 4 comprise the helix-turn-helix motif and the beta-sheet is called the wing as in other wHTH, such as the dtxR-type or the merR-type. Helix 4 is termed the recognition helix, like in other HTHs where it binds the DNA major groove. Most arsR/smtB-like metalloregulators form homodimers []. The dimer interface is formed by helix 5 and an N-terminal part []. Two distinct metal-binding sites have been identified. The first site comprises cysteine thiolates located in the HTH in helix 3 and for some cases in the N terminus, called the alpha3(N) site []. The second metal-binding site is located in helix 5 (and C terminus) and is called the alpha5(C) site. The alpha3N site binds large thiophilic, toxic metals including Cd, Pb, and Bi, as in S. aureus cadC. ArsR lacks the N-terminal arm and its alpha3 site coordinates smaller thiophilic ions like As and Sb. The alpha5 site contains carboxylate and imidazole ligands and interacts preferentially with biologically required metal ions including Zn, Co, and Ni. ArsR-type metalloregulators contain one of these sites, both, or other potential metal-binding sites [, ]. Binding of metal ions to these sites leads to allosteric changes that can derepress the operator/promotor DNA. The metal-inducible operons contain one or two imperfect 12-2-12 inverted repeats, which can be recognised by multimeric arsR-type metalloregulators. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3CUO_A 1U2W_C 3F72_C 3F6V_A 3JTH_B 2P4W_B 1KU9_B 2LKP_B 1SMT_A 1R22_B ....
Probab=95.70 E-value=0.0058 Score=38.15 Aligned_cols=43 Identities=14% Similarity=0.304 Sum_probs=37.8
Q ss_pred hcChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCcchHHHHHHHHhcCCccc
Q 044458 39 ELDLLEVIAKAGPGAFMSPKQIASQLPTKNSDAHILLDRILRLLASYSVLN 89 (241)
Q Consensus 39 ~lglfd~L~~~~~~~~~t~~eLA~~~g~~~~~~~~~l~rlLr~L~~~g~l~ 89 (241)
++.|...|.+ ++.++.||++.+|+ +...+.+-|+.|...|+++
T Consensus 4 R~~Il~~L~~----~~~~~~el~~~l~~----s~~~vs~hL~~L~~~glV~ 46 (47)
T PF01022_consen 4 RLRILKLLSE----GPLTVSELAEELGL----SQSTVSHHLKKLREAGLVE 46 (47)
T ss_dssp HHHHHHHHTT----SSEEHHHHHHHHTS-----HHHHHHHHHHHHHTTSEE
T ss_pred HHHHHHHHHh----CCCchhhHHHhccc----cchHHHHHHHHHHHCcCee
Confidence 4567778877 69999999999999 9999999999999999986
No 122
>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein.
Probab=95.67 E-value=0.014 Score=36.05 Aligned_cols=34 Identities=18% Similarity=0.220 Sum_probs=31.9
Q ss_pred CCCHHHHHhhCCCCCCCCcchHHHHHHHHhcCCccccc
Q 044458 54 FMSPKQIASQLPTKNSDAHILLDRILRLLASYSVLNCS 91 (241)
Q Consensus 54 ~~t~~eLA~~~g~~~~~~~~~l~rlLr~L~~~g~l~~~ 91 (241)
+.|..|||+.+++ +...+.+.|+.|...|++...
T Consensus 8 ~~s~~~la~~l~~----s~~tv~~~l~~L~~~g~l~~~ 41 (48)
T smart00419 8 PLTRQEIAELLGL----TRETVSRTLKRLEKEGLISRE 41 (48)
T ss_pred ccCHHHHHHHHCC----CHHHHHHHHHHHHHCCCEEEe
Confidence 6899999999999 999999999999999999863
No 123
>PRK11873 arsM arsenite S-adenosylmethyltransferase; Reviewed
Probab=95.67 E-value=0.012 Score=50.47 Aligned_cols=44 Identities=27% Similarity=0.401 Sum_probs=35.7
Q ss_pred CCCCCeEEEecCCchHHHHHHHHH-CCCCcEEEccc-hHHHhcCCC
Q 044458 196 FEGLQSVVDVGGGIGASLDMIISK-YPSIKGINFDL-PHVIQDAPA 239 (241)
Q Consensus 196 ~~~~~~vvDVGGG~G~~~~~l~~~-~P~l~~~v~Dl-P~vi~~a~~ 239 (241)
.....+|||||||.|..+..+++. .|+.+++.+|+ |..++.|++
T Consensus 75 ~~~g~~VLDiG~G~G~~~~~~a~~~g~~~~v~gvD~s~~~l~~A~~ 120 (272)
T PRK11873 75 LKPGETVLDLGSGGGFDCFLAARRVGPTGKVIGVDMTPEMLAKARA 120 (272)
T ss_pred CCCCCEEEEeCCCCCHHHHHHHHHhCCCCEEEEECCCHHHHHHHHH
Confidence 556689999999999998887776 46678999999 777776653
No 124
>PF01978 TrmB: Sugar-specific transcriptional regulator TrmB; InterPro: IPR002831 TrmB, is a protein of 38,800 apparent molecular weight, that is involved in the maltose-specific regulation of the trehalose/maltose ABC transport operon in Thermococcus litoralis. TrmB has been shown to be a maltose-specific repressor, and this inhibition is counteracted by maltose and trehalose. TrmB binds maltose and trehalose half-maximally at 20 uM and 0.5 mM sugar concentration, respectively []. Other members of this family are annotated as either transcriptional regulators or hypothetical proteins. ; PDB: 2D1H_A 3QPH_A 1SFX_A.
Probab=95.65 E-value=0.0049 Score=41.56 Aligned_cols=47 Identities=17% Similarity=0.184 Sum_probs=40.6
Q ss_pred HhcChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCcchHHHHHHHHhcCCccccc
Q 044458 38 IELDLLEVIAKAGPGAFMSPKQIASQLPTKNSDAHILLDRILRLLASYSVLNCS 91 (241)
Q Consensus 38 ~~lglfd~L~~~~~~~~~t~~eLA~~~g~~~~~~~~~l~rlLr~L~~~g~l~~~ 91 (241)
.|..|+..|-.. ++.|+.|||+.+|+ +...+.+.|+.|...|++...
T Consensus 9 ~E~~vy~~Ll~~---~~~t~~eIa~~l~i----~~~~v~~~L~~L~~~GlV~~~ 55 (68)
T PF01978_consen 9 NEAKVYLALLKN---GPATAEEIAEELGI----SRSTVYRALKSLEEKGLVERE 55 (68)
T ss_dssp HHHHHHHHHHHH---CHEEHHHHHHHHTS----SHHHHHHHHHHHHHTTSEEEE
T ss_pred HHHHHHHHHHHc---CCCCHHHHHHHHCc----CHHHHHHHHHHHHHCCCEEEE
Confidence 455667676553 69999999999999 999999999999999999975
No 125
>TIGR03840 TMPT_Se_Te thiopurine S-methyltransferase, Se/Te detoxification family. Members of this family are thiopurine S-methyltransferase from a branch in which at least some member proteins can perform selenium methylation as a means to detoxify selenium, or perform a related detoxification of tellurium. Note that the EC number definition does not specify a particular thiopurine, but rather represents a class of activity.
Probab=95.63 E-value=0.023 Score=47.40 Aligned_cols=38 Identities=11% Similarity=0.080 Sum_probs=33.0
Q ss_pred CCCCeEEEecCCchHHHHHHHHHCCCCcEEEccc-hHHHhc
Q 044458 197 EGLQSVVDVGGGIGASLDMIISKYPSIKGINFDL-PHVIQD 236 (241)
Q Consensus 197 ~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-P~vi~~ 236 (241)
....+|||+|||.|..+..++++ +.+++.+|+ |..|+.
T Consensus 33 ~~~~rvLd~GCG~G~da~~LA~~--G~~V~gvD~S~~Ai~~ 71 (213)
T TIGR03840 33 PAGARVFVPLCGKSLDLAWLAEQ--GHRVLGVELSEIAVEQ 71 (213)
T ss_pred CCCCeEEEeCCCchhHHHHHHhC--CCeEEEEeCCHHHHHH
Confidence 44579999999999999999985 888999999 777775
No 126
>TIGR03438 probable methyltransferase. This model represents a distinct set of uncharacterized proteins found in the bacteria. Analysis by PSI-BLAST shows remote sequence homology to methyltransferases
Probab=95.61 E-value=0.01 Score=52.11 Aligned_cols=40 Identities=10% Similarity=0.328 Sum_probs=33.7
Q ss_pred CCCeEEEecCCchHHHHHHHHHCC-CCcEEEccc-hHHHhcC
Q 044458 198 GLQSVVDVGGGIGASLDMIISKYP-SIKGINFDL-PHVIQDA 237 (241)
Q Consensus 198 ~~~~vvDVGGG~G~~~~~l~~~~P-~l~~~v~Dl-P~vi~~a 237 (241)
...+|||+|||+|.....++++.+ ..+.+.+|+ ++.++.+
T Consensus 63 ~~~~iLELGcGtG~~t~~Ll~~l~~~~~~~~iDiS~~mL~~a 104 (301)
T TIGR03438 63 AGCELVELGSGSSRKTRLLLDALRQPARYVPIDISADALKES 104 (301)
T ss_pred CCCeEEecCCCcchhHHHHHHhhccCCeEEEEECCHHHHHHH
Confidence 347899999999999999999998 688999999 5555544
No 127
>cd00092 HTH_CRP helix_turn_helix, cAMP Regulatory protein C-terminus; DNA binding domain of prokaryotic regulatory proteins belonging to the catabolite activator protein family.
Probab=95.56 E-value=0.018 Score=38.18 Aligned_cols=44 Identities=18% Similarity=0.244 Sum_probs=38.0
Q ss_pred CCCCHHHHHhhCCCCCCCCcchHHHHHHHHhcCCccccccccCCCCccccceecCc
Q 044458 53 AFMSPKQIASQLPTKNSDAHILLDRILRLLASYSVLNCSLHTLPDGGVERLYGLAP 108 (241)
Q Consensus 53 ~~~t~~eLA~~~g~~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~g~~~~~y~~t~ 108 (241)
.++|..|||+.+|+ +...+.+.|+.|...|++... . .+.|.+++
T Consensus 24 ~~~s~~ela~~~g~----s~~tv~r~l~~L~~~g~i~~~----~----~~~~~l~~ 67 (67)
T cd00092 24 LPLTRQEIADYLGL----TRETVSRTLKELEEEGLISRR----G----RGKYRVNP 67 (67)
T ss_pred CCcCHHHHHHHHCC----CHHHHHHHHHHHHHCCCEEec----C----CCeEEeCC
Confidence 58999999999999 999999999999999999974 1 26777654
No 128
>PRK13943 protein-L-isoaspartate O-methyltransferase; Provisional
Probab=95.56 E-value=0.021 Score=50.59 Aligned_cols=50 Identities=16% Similarity=0.226 Sum_probs=37.8
Q ss_pred HHHHhcCCCCCCCeEEEecCCchHHHHHHHHHCCC-CcEEEccc-hHHHhcCC
Q 044458 188 KFLENYKGFEGLQSVVDVGGGIGASLDMIISKYPS-IKGINFDL-PHVIQDAP 238 (241)
Q Consensus 188 ~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~-l~~~v~Dl-P~vi~~a~ 238 (241)
.+++..+ .+...+|||||||+|.++..+++..+. -+++.+|. |+.++.|+
T Consensus 71 ~ll~~L~-i~~g~~VLDIG~GtG~~a~~LA~~~~~~g~VvgVDis~~~l~~Ar 122 (322)
T PRK13943 71 LFMEWVG-LDKGMRVLEIGGGTGYNAAVMSRVVGEKGLVVSVEYSRKICEIAK 122 (322)
T ss_pred HHHHhcC-CCCCCEEEEEeCCccHHHHHHHHhcCCCCEEEEEECCHHHHHHHH
Confidence 3444445 556689999999999999999998875 46788898 66665543
No 129
>PF12840 HTH_20: Helix-turn-helix domain; PDB: 1ULY_A 2CWE_A 1Y0U_B 2QUF_B 2QLZ_C 2OQG_B 2ZKZ_C 3PQK_A 3PQJ_D 3F6O_B ....
Probab=95.52 E-value=0.01 Score=39.17 Aligned_cols=53 Identities=17% Similarity=0.270 Sum_probs=44.1
Q ss_pred HHHHHHHhcChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCcchHHHHHHHHhcCCccccc
Q 044458 32 MVLKSAIELDLLEVIAKAGPGAFMSPKQIASQLPTKNSDAHILLDRILRLLASYSVLNCS 91 (241)
Q Consensus 32 ~~L~~a~~lglfd~L~~~~~~~~~t~~eLA~~~g~~~~~~~~~l~rlLr~L~~~g~l~~~ 91 (241)
.+|.--.++.|++.|... ++.|+.|||+.+|+ ++..+.+-|+.|...|+++..
T Consensus 5 ~aL~~p~R~~Il~~L~~~---~~~t~~ela~~l~~----~~~t~s~hL~~L~~aGli~~~ 57 (61)
T PF12840_consen 5 KALSDPTRLRILRLLASN---GPMTVSELAEELGI----SQSTVSYHLKKLEEAGLIEVE 57 (61)
T ss_dssp HHHTSHHHHHHHHHHHHC---STBEHHHHHHHHTS-----HHHHHHHHHHHHHTTSEEEE
T ss_pred HHhCCHHHHHHHHHHhcC---CCCCHHHHHHHHCC----CHHHHHHHHHHHHHCCCeEEe
Confidence 455555778888889442 69999999999999 999999999999999999864
No 130
>PLN02823 spermine synthase
Probab=95.50 E-value=0.013 Score=52.21 Aligned_cols=44 Identities=18% Similarity=0.251 Sum_probs=38.1
Q ss_pred CCCCeEEEecCCchHHHHHHHHHCCCCcEEEccc-hHHHhcCCCC
Q 044458 197 EGLQSVVDVGGGIGASLDMIISKYPSIKGINFDL-PHVIQDAPAY 240 (241)
Q Consensus 197 ~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-P~vi~~a~~~ 240 (241)
...++||-||||.|..+..+++..+.-++++.|+ |+|++.+++|
T Consensus 102 ~~pk~VLiiGgG~G~~~re~l~~~~~~~v~~VEiD~~vv~lar~~ 146 (336)
T PLN02823 102 PNPKTVFIMGGGEGSTAREVLRHKTVEKVVMCDIDQEVVDFCRKH 146 (336)
T ss_pred CCCCEEEEECCCchHHHHHHHhCCCCCeEEEEECCHHHHHHHHHh
Confidence 3568999999999999999998666678999999 8999988764
No 131
>PF08003 Methyltransf_9: Protein of unknown function (DUF1698); InterPro: IPR010017 Methyl transfer from the ubiquitous S-adenosyl-L-methionine (AdoMet) to either nitrogen, oxygen or carbon atoms is frequently employed in diverse organisms ranging from bacteria to plants and mammals. The reaction is catalysed by methyltransferases (Mtases) and modifies DNA, RNA, proteins and small molecules, such as catechol for regulatory purposes. The various aspects of the role of DNA methylation in prokaryotic restriction-modification systems and in a number of cellular processes in eukaryotes including gene regulation and differentiation is well documented. Three classes of DNA Mtases transfer the methyl group from AdoMet to the target base to form either N-6-methyladenine, or N-4-methylcytosine, or C-5- methylcytosine. In C-5-cytosine Mtases, ten conserved motifs are arranged in the same order []. Motif I (a glycine-rich or closely related consensus sequence; FAGxGG in M.HhaI []), shared by other AdoMet-Mtases [], is part of the cofactor binding site and motif IV (PCQ) is part of the catalytic site. In contrast, sequence comparison among N-6-adenine and N-4-cytosine Mtases indicated two of the conserved segments [], although more conserved segments may be present. One of them corresponds to motif I in C-5-cytosine Mtases, and the other is named (D/N/S)PP(Y/F). Crystal structures are known for a number of Mtases [, , , ]. The cofactor binding sites are almost identical and the essential catalytic amino acids coincide. The comparable protein folding and the existence of equivalent amino acids in similar secondary and tertiary positions indicate that many (if not all) AdoMet-Mtases have a common catalytic domain structure. This permits tertiary structure prediction of other DNA, RNA, protein, and small-molecule AdoMet-Mtases from their amino acid sequences []. This entry represents a set of bacterial AdoMet-dependent tRNA (mo5U34)-methyltransferases. These enzymes catalyse the conversion of 5-hydroxyuridine (ho5U) to 5-methoxyuridine (mo5U) at the wobble position (34) of tRNA []. The 5-methoxyuridine is subsequently converted to uridine-5-oxyacetic acid, a modified nucleoside that is apparently necessary for the efficient decoding of G-ending Pro, Ala, and Val codons in these organisms [].; GO: 0016300 tRNA (uracil) methyltransferase activity, 0002098 tRNA wobble uridine modification
Probab=95.49 E-value=0.022 Score=49.72 Aligned_cols=42 Identities=19% Similarity=0.309 Sum_probs=30.3
Q ss_pred HHHHHHhcCCCCCCCeEEEecCCchHHHHHHHHHCCCCcEEEcc
Q 044458 186 MKKFLENYKGFEGLQSVVDVGGGIGASLDMIISKYPSIKGINFD 229 (241)
Q Consensus 186 ~~~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~D 229 (241)
.+.+...++.+++ ++|+|||||.|.++..++++-|.. ++.+|
T Consensus 104 W~rl~p~l~~L~g-k~VLDIGC~nGY~~frM~~~GA~~-ViGiD 145 (315)
T PF08003_consen 104 WDRLLPHLPDLKG-KRVLDIGCNNGYYSFRMLGRGAKS-VIGID 145 (315)
T ss_pred HHHHHhhhCCcCC-CEEEEecCCCcHHHHHHhhcCCCE-EEEEC
Confidence 3445555532544 899999999999999999997653 45555
No 132
>COG1959 Predicted transcriptional regulator [Transcription]
Probab=95.45 E-value=0.023 Score=44.70 Aligned_cols=56 Identities=25% Similarity=0.250 Sum_probs=44.0
Q ss_pred HHHHHhcCCCCCCCHHHHHhhCCCCCCCCcchHHHHHHHHhcCCccccccccCCCCccccceecCc
Q 044458 43 LEVIAKAGPGAFMSPKQIASQLPTKNSDAHILLDRILRLLASYSVLNCSLHTLPDGGVERLYGLAP 108 (241)
Q Consensus 43 fd~L~~~~~~~~~t~~eLA~~~g~~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~g~~~~~y~~t~ 108 (241)
.-.|+..+.+++.|+++||+..++ ++.+|+++|..|...|+++-. .|. .|.|.+..
T Consensus 14 L~~LA~~~~~~~~s~~~IA~~~~i----s~~~L~kil~~L~kaGlV~S~-----rG~-~GGy~Lar 69 (150)
T COG1959 14 LLYLALLPGGGPVSSAEIAERQGI----SPSYLEKILSKLRKAGLVKSV-----RGK-GGGYRLAR 69 (150)
T ss_pred HHHHHhCCCCCcccHHHHHHHhCc----CHHHHHHHHHHHHHcCCEEee-----cCC-CCCccCCC
Confidence 334555443348999999999999 999999999999999999864 232 57788775
No 133
>COG0421 SpeE Spermidine synthase [Amino acid transport and metabolism]
Probab=95.44 E-value=0.013 Score=50.93 Aligned_cols=45 Identities=27% Similarity=0.460 Sum_probs=40.7
Q ss_pred CCCCCeEEEecCCchHHHHHHHHHCCCCcEEEccc-hHHHhcCCCC
Q 044458 196 FEGLQSVVDVGGGIGASLDMIISKYPSIKGINFDL-PHVIQDAPAY 240 (241)
Q Consensus 196 ~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-P~vi~~a~~~ 240 (241)
.+..++||=||||.|..+.++++..+--++++.|+ |.||+.+++|
T Consensus 74 h~~pk~VLiiGgGdG~tlRevlkh~~ve~i~~VEID~~Vi~~ar~~ 119 (282)
T COG0421 74 HPNPKRVLIIGGGDGGTLREVLKHLPVERITMVEIDPAVIELARKY 119 (282)
T ss_pred CCCCCeEEEECCCccHHHHHHHhcCCcceEEEEEcCHHHHHHHHHh
Confidence 34558999999999999999999999888999999 9999998876
No 134
>PTZ00338 dimethyladenosine transferase-like protein; Provisional
Probab=95.35 E-value=0.028 Score=49.25 Aligned_cols=49 Identities=18% Similarity=0.438 Sum_probs=36.6
Q ss_pred HHHHHHhcCCCCCCCeEEEecCCchHHHHHHHHHCCCCcEEEccc-hHHHhcC
Q 044458 186 MKKFLENYKGFEGLQSVVDVGGGIGASLDMIISKYPSIKGINFDL-PHVIQDA 237 (241)
Q Consensus 186 ~~~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-P~vi~~a 237 (241)
...+++..+ .....+|+|||||.|.+...+++... +++.+|+ +..++.+
T Consensus 25 ~~~Iv~~~~-~~~~~~VLEIG~G~G~LT~~Ll~~~~--~V~avEiD~~li~~l 74 (294)
T PTZ00338 25 LDKIVEKAA-IKPTDTVLEIGPGTGNLTEKLLQLAK--KVIAIEIDPRMVAEL 74 (294)
T ss_pred HHHHHHhcC-CCCcCEEEEecCchHHHHHHHHHhCC--cEEEEECCHHHHHHH
Confidence 345566665 66678999999999999999999754 5777887 5555543
No 135
>PRK04148 hypothetical protein; Provisional
Probab=95.30 E-value=0.025 Score=43.60 Aligned_cols=47 Identities=19% Similarity=0.272 Sum_probs=33.9
Q ss_pred HHHhcCCCCCCCeEEEecCCchH-HHHHHHHHCCCCcEEEccc-hHHHhcCC
Q 044458 189 FLENYKGFEGLQSVVDVGGGIGA-SLDMIISKYPSIKGINFDL-PHVIQDAP 238 (241)
Q Consensus 189 ~~~~~~~~~~~~~vvDVGGG~G~-~~~~l~~~~P~l~~~v~Dl-P~vi~~a~ 238 (241)
+.+.++ -.+..+++|||+|.|. ++..+.+. +..++..|. |..++.++
T Consensus 8 l~~~~~-~~~~~kileIG~GfG~~vA~~L~~~--G~~ViaIDi~~~aV~~a~ 56 (134)
T PRK04148 8 IAENYE-KGKNKKIVELGIGFYFKVAKKLKES--GFDVIVIDINEKAVEKAK 56 (134)
T ss_pred HHHhcc-cccCCEEEEEEecCCHHHHHHHHHC--CCEEEEEECCHHHHHHHH
Confidence 444454 2334789999999996 77777754 678899998 77776554
No 136
>KOG3010 consensus Methyltransferase [General function prediction only]
Probab=95.26 E-value=0.017 Score=48.77 Aligned_cols=42 Identities=29% Similarity=0.418 Sum_probs=35.0
Q ss_pred CCCeEEEecCCchHHHHHHHHHCCCCcEEEccc-hHHHhcCCCCC
Q 044458 198 GLQSVVDVGGGIGASLDMIISKYPSIKGINFDL-PHVIQDAPAYP 241 (241)
Q Consensus 198 ~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-P~vi~~a~~~~ 241 (241)
+.+.++|||||+|..++.+++.|.++ |.-|. +..++.|+++|
T Consensus 33 ~h~~a~DvG~G~Gqa~~~iae~~k~V--IatD~s~~mL~~a~k~~ 75 (261)
T KOG3010|consen 33 GHRLAWDVGTGNGQAARGIAEHYKEV--IATDVSEAMLKVAKKHP 75 (261)
T ss_pred CcceEEEeccCCCcchHHHHHhhhhh--eeecCCHHHHHHhhcCC
Confidence 44699999999998888888887766 77788 78888888776
No 137
>PF14947 HTH_45: Winged helix-turn-helix; PDB: 1XSX_B 1R7J_A.
Probab=95.20 E-value=0.016 Score=40.19 Aligned_cols=48 Identities=15% Similarity=0.096 Sum_probs=38.7
Q ss_pred CCCCHHHHHhhCCCCCCCCcchHHHHHHHHhcCCccccccccCCCCccccceecCcccccc
Q 044458 53 AFMSPKQIASQLPTKNSDAHILLDRILRLLASYSVLNCSLHTLPDGGVERLYGLAPVCKFL 113 (241)
Q Consensus 53 ~~~t~~eLA~~~g~~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~g~~~~~y~~t~~s~~l 113 (241)
++.+..+|+..+++ +...+.+.|+.|...|++... .+.|.+|+.+.-+
T Consensus 18 ~~~~~t~i~~~~~L----~~~~~~~yL~~L~~~gLI~~~---------~~~Y~lTekG~~~ 65 (77)
T PF14947_consen 18 GGAKKTEIMYKANL----NYSTLKKYLKELEEKGLIKKK---------DGKYRLTEKGKEF 65 (77)
T ss_dssp T-B-HHHHHTTST------HHHHHHHHHHHHHTTSEEEE---------TTEEEE-HHHHHH
T ss_pred CCCCHHHHHHHhCc----CHHHHHHHHHHHHHCcCeeCC---------CCEEEECccHHHH
Confidence 68999999999999 999999999999999999753 6899999988743
No 138
>PRK10901 16S rRNA methyltransferase B; Provisional
Probab=95.17 E-value=0.021 Score=52.54 Aligned_cols=63 Identities=14% Similarity=0.189 Sum_probs=44.9
Q ss_pred HHHHHHhcchhhHHHHHHhcCCCCCCCeEEEecCCchHHHHHHHHHCCCCcEEEccc-hHHHhcC
Q 044458 174 FNNGMFSHSTITMKKFLENYKGFEGLQSVVDVGGGIGASLDMIISKYPSIKGINFDL-PHVIQDA 237 (241)
Q Consensus 174 f~~aM~~~~~~~~~~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-P~vi~~a 237 (241)
|.+..-.........++..++ .....+|+|+|||+|..+..+++..++.+++.+|+ |..++.+
T Consensus 221 ~~~G~~~iQd~~s~~~~~~l~-~~~g~~VLDlgaG~G~~t~~la~~~~~~~v~a~D~s~~~l~~~ 284 (427)
T PRK10901 221 FAEGWVSVQDAAAQLAATLLA-PQNGERVLDACAAPGGKTAHILELAPQAQVVALDIDAQRLERV 284 (427)
T ss_pred hhCceEEEECHHHHHHHHHcC-CCCCCEEEEeCCCCChHHHHHHHHcCCCEEEEEeCCHHHHHHH
Confidence 444433333333334445555 55568999999999999999999998888999999 6666554
No 139
>PRK00536 speE spermidine synthase; Provisional
Probab=95.16 E-value=0.016 Score=49.85 Aligned_cols=42 Identities=10% Similarity=0.017 Sum_probs=37.1
Q ss_pred CCCCeEEEecCCchHHHHHHHHHCCCCcEEEccc-hHHHhcCCCC
Q 044458 197 EGLQSVVDVGGGIGASLDMIISKYPSIKGINFDL-PHVIQDAPAY 240 (241)
Q Consensus 197 ~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-P~vi~~a~~~ 240 (241)
...++||=||||.|..++++++- |. +++..|+ ++||+.+++|
T Consensus 71 ~~pk~VLIiGGGDGg~~REvLkh-~~-~v~mVeID~~Vv~~~k~~ 113 (262)
T PRK00536 71 KELKEVLIVDGFDLELAHQLFKY-DT-HVDFVQADEKILDSFISF 113 (262)
T ss_pred CCCCeEEEEcCCchHHHHHHHCc-CC-eeEEEECCHHHHHHHHHH
Confidence 45799999999999999999987 55 9999999 8899988873
No 140
>PRK00312 pcm protein-L-isoaspartate O-methyltransferase; Reviewed
Probab=95.13 E-value=0.036 Score=45.81 Aligned_cols=47 Identities=13% Similarity=0.189 Sum_probs=34.0
Q ss_pred HHHhcCCCCCCCeEEEecCCchHHHHHHHHHCCCCcEEEccc-hHHHhcCC
Q 044458 189 FLENYKGFEGLQSVVDVGGGIGASLDMIISKYPSIKGINFDL-PHVIQDAP 238 (241)
Q Consensus 189 ~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-P~vi~~a~ 238 (241)
++..++ .....+|||||||+|.++..+++... +++.+|. |..++.++
T Consensus 70 l~~~l~-~~~~~~VLeiG~GsG~~t~~la~~~~--~v~~vd~~~~~~~~a~ 117 (212)
T PRK00312 70 MTELLE-LKPGDRVLEIGTGSGYQAAVLAHLVR--RVFSVERIKTLQWEAK 117 (212)
T ss_pred HHHhcC-CCCCCEEEEECCCccHHHHHHHHHhC--EEEEEeCCHHHHHHHH
Confidence 344455 56678999999999999988777754 5677776 66665543
No 141
>TIGR02010 IscR iron-sulfur cluster assembly transcription factor IscR. This model describes IscR, an iron-sulfur binding transcription factor of the ISC iron-sulfur cluster assembly system.
Probab=95.09 E-value=0.034 Score=42.82 Aligned_cols=46 Identities=13% Similarity=0.153 Sum_probs=38.4
Q ss_pred CCCCHHHHHhhCCCCCCCCcchHHHHHHHHhcCCccccccccCCCCccccceecCc
Q 044458 53 AFMSPKQIASQLPTKNSDAHILLDRILRLLASYSVLNCSLHTLPDGGVERLYGLAP 108 (241)
Q Consensus 53 ~~~t~~eLA~~~g~~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~g~~~~~y~~t~ 108 (241)
++.|.++||+.+++ ++..++++|+.|...|++.... |. .|.|.++.
T Consensus 24 ~~~s~~~ia~~~~i----p~~~l~kil~~L~~~glv~s~~-----G~-~Ggy~l~~ 69 (135)
T TIGR02010 24 GPVTLADISERQGI----SLSYLEQLFAKLRKAGLVKSVR-----GP-GGGYQLGR 69 (135)
T ss_pred CcCcHHHHHHHHCc----CHHHHHHHHHHHHHCCceEEEe-----CC-CCCEeccC
Confidence 58999999999999 9999999999999999997531 21 45677664
No 142
>KOG1271 consensus Methyltransferases [General function prediction only]
Probab=95.07 E-value=0.026 Score=45.75 Aligned_cols=37 Identities=24% Similarity=0.339 Sum_probs=26.0
Q ss_pred CCeEEEecCCchHHHHHHHHH-CCCCcEEEccc-hHHHhc
Q 044458 199 LQSVVDVGGGIGASLDMIISK-YPSIKGINFDL-PHVIQD 236 (241)
Q Consensus 199 ~~~vvDVGGG~G~~~~~l~~~-~P~l~~~v~Dl-P~vi~~ 236 (241)
..+|||+|||.|+++..|++. |++ +-+..|- +.+|+.
T Consensus 68 A~~VlDLGtGNG~~L~~L~~egf~~-~L~GvDYs~~AV~L 106 (227)
T KOG1271|consen 68 ADRVLDLGTGNGHLLFQLAKEGFQS-KLTGVDYSEKAVEL 106 (227)
T ss_pred ccceeeccCCchHHHHHHHHhcCCC-CccccccCHHHHHH
Confidence 349999999999999999885 555 2244454 444444
No 143
>PRK13255 thiopurine S-methyltransferase; Reviewed
Probab=95.04 E-value=0.046 Score=45.73 Aligned_cols=40 Identities=8% Similarity=0.041 Sum_probs=33.3
Q ss_pred CCCCCeEEEecCCchHHHHHHHHHCCCCcEEEccc-hHHHhcC
Q 044458 196 FEGLQSVVDVGGGIGASLDMIISKYPSIKGINFDL-PHVIQDA 237 (241)
Q Consensus 196 ~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-P~vi~~a 237 (241)
.....+|||+|||.|..+..|+++ +.+++.+|+ |.+|+.+
T Consensus 35 ~~~~~rvL~~gCG~G~da~~LA~~--G~~V~avD~s~~Ai~~~ 75 (218)
T PRK13255 35 LPAGSRVLVPLCGKSLDMLWLAEQ--GHEVLGVELSELAVEQF 75 (218)
T ss_pred CCCCCeEEEeCCCChHhHHHHHhC--CCeEEEEccCHHHHHHH
Confidence 344579999999999999999984 888999999 6767643
No 144
>PRK13168 rumA 23S rRNA m(5)U1939 methyltransferase; Reviewed
Probab=94.94 E-value=0.016 Score=53.51 Aligned_cols=48 Identities=15% Similarity=0.097 Sum_probs=36.9
Q ss_pred HHHHhcCCCCCCCeEEEecCCchHHHHHHHHHCCCCcEEEccc-hHHHhcCC
Q 044458 188 KFLENYKGFEGLQSVVDVGGGIGASLDMIISKYPSIKGINFDL-PHVIQDAP 238 (241)
Q Consensus 188 ~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-P~vi~~a~ 238 (241)
.+++.++ .....+|+|+|||+|.++..+++.. .+++.+|. |+.++.|+
T Consensus 288 ~vl~~l~-~~~~~~VLDlgcGtG~~sl~la~~~--~~V~gvD~s~~al~~A~ 336 (443)
T PRK13168 288 RALEWLD-PQPGDRVLDLFCGLGNFTLPLARQA--AEVVGVEGVEAMVERAR 336 (443)
T ss_pred HHHHHhc-CCCCCEEEEEeccCCHHHHHHHHhC--CEEEEEeCCHHHHHHHH
Confidence 3344444 4455799999999999999999886 57889999 77777664
No 145
>PRK05134 bifunctional 3-demethylubiquinone-9 3-methyltransferase/ 2-octaprenyl-6-hydroxy phenol methylase; Provisional
Probab=94.93 E-value=0.04 Score=46.06 Aligned_cols=38 Identities=24% Similarity=0.160 Sum_probs=29.9
Q ss_pred CCCeEEEecCCchHHHHHHHHHCCCCcEEEccc-hHHHhcC
Q 044458 198 GLQSVVDVGGGIGASLDMIISKYPSIKGINFDL-PHVIQDA 237 (241)
Q Consensus 198 ~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-P~vi~~a 237 (241)
...+|||||||.|.++..+++. ..+++..|+ +..++.+
T Consensus 48 ~~~~vLdiG~G~G~~~~~l~~~--~~~v~~iD~s~~~~~~a 86 (233)
T PRK05134 48 FGKRVLDVGCGGGILSESMARL--GADVTGIDASEENIEVA 86 (233)
T ss_pred CCCeEEEeCCCCCHHHHHHHHc--CCeEEEEcCCHHHHHHH
Confidence 4578999999999999988876 467888898 4555443
No 146
>PF13463 HTH_27: Winged helix DNA-binding domain; PDB: 3GFL_A 2YR2_B 3GFM_A 3GFJ_A 3GF2_A 3GEZ_A 2GXG_A 3GFI_A 2EB7_A.
Probab=94.85 E-value=0.025 Score=37.69 Aligned_cols=51 Identities=20% Similarity=0.306 Sum_probs=36.5
Q ss_pred CCCCHHHHHhhCCCCCCCCcchHHHHHHHHhcCCccccccccCCCCccccceecCcc
Q 044458 53 AFMSPKQIASQLPTKNSDAHILLDRILRLLASYSVLNCSLHTLPDGGVERLYGLAPV 109 (241)
Q Consensus 53 ~~~t~~eLA~~~g~~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~g~~~~~y~~t~~ 109 (241)
++.+..+|++.+++ +...+.+.++.|...|++++... +.|+- ...|++|+.
T Consensus 17 ~~~t~~~l~~~~~~----~~~~vs~~i~~L~~~glv~~~~~-~~d~R-~~~~~LT~~ 67 (68)
T PF13463_consen 17 GPMTQSDLAERLGI----SKSTVSRIIKKLEEKGLVEKERD-PHDKR-SKRYRLTPA 67 (68)
T ss_dssp S-BEHHHHHHHTT------HHHHHHHHHHHHHTTSEEEEEE-SSCTT-SEEEEE-HH
T ss_pred CCcCHHHHHHHHCc----CHHHHHHHHHHHHHCCCEEecCC-CCcCC-eeEEEeCCC
Confidence 78999999999999 99999999999999999976421 12221 246777764
No 147
>PRK03522 rumB 23S rRNA methyluridine methyltransferase; Reviewed
Probab=94.82 E-value=0.032 Score=49.23 Aligned_cols=38 Identities=16% Similarity=0.112 Sum_probs=32.3
Q ss_pred CCeEEEecCCchHHHHHHHHHCCCCcEEEccc-hHHHhcCC
Q 044458 199 LQSVVDVGGGIGASLDMIISKYPSIKGINFDL-PHVIQDAP 238 (241)
Q Consensus 199 ~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-P~vi~~a~ 238 (241)
..+|||+|||.|.++..+++. ..+++.+|. |..++.|+
T Consensus 174 ~~~VLDl~cG~G~~sl~la~~--~~~V~gvD~s~~av~~A~ 212 (315)
T PRK03522 174 PRSMWDLFCGVGGFGLHCATP--GMQLTGIEISAEAIACAK 212 (315)
T ss_pred CCEEEEccCCCCHHHHHHHhc--CCEEEEEeCCHHHHHHHH
Confidence 479999999999999999984 467899999 77777664
No 148
>TIGR00738 rrf2_super rrf2 family protein (putative transcriptional regulator). This model represents a superfamily of probable transcriptional regulators. One member, RRF2 of Desulfovibrio vulgaris is an apparent regulatory protein experimentally (MEDLINE:97293189). The N-terminal region appears related to the DNA-binding biotin repressor region of the BirA bifunctional according to results after three rounds of PSI-BLAST with a fairly high stringency.
Probab=94.81 E-value=0.046 Score=41.65 Aligned_cols=46 Identities=28% Similarity=0.323 Sum_probs=37.8
Q ss_pred CCCCHHHHHhhCCCCCCCCcchHHHHHHHHhcCCccccccccCCCCccccceecCc
Q 044458 53 AFMSPKQIASQLPTKNSDAHILLDRILRLLASYSVLNCSLHTLPDGGVERLYGLAP 108 (241)
Q Consensus 53 ~~~t~~eLA~~~g~~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~g~~~~~y~~t~ 108 (241)
++.|.++||+.+++ ++..++++|+.|...|++... .|. .+.|.++.
T Consensus 24 ~~~s~~eia~~~~i----~~~~v~~il~~L~~~gli~~~-----~g~-~ggy~l~~ 69 (132)
T TIGR00738 24 GPVSVKEIAERQGI----SRSYLEKILRTLRRAGLVESV-----RGP-GGGYRLAR 69 (132)
T ss_pred CcCcHHHHHHHHCc----CHHHHHHHHHHHHHCCcEEec-----cCC-CCCccCCC
Confidence 58999999999999 999999999999999999853 121 35676654
No 149
>PRK10857 DNA-binding transcriptional regulator IscR; Provisional
Probab=94.73 E-value=0.052 Score=43.40 Aligned_cols=46 Identities=13% Similarity=0.132 Sum_probs=38.9
Q ss_pred CCCCHHHHHhhCCCCCCCCcchHHHHHHHHhcCCccccccccCCCCccccceecCc
Q 044458 53 AFMSPKQIASQLPTKNSDAHILLDRILRLLASYSVLNCSLHTLPDGGVERLYGLAP 108 (241)
Q Consensus 53 ~~~t~~eLA~~~g~~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~g~~~~~y~~t~ 108 (241)
++.|+++||+++++ ++..++++|+.|...|++.... |. .|.|.+..
T Consensus 24 ~~vs~~eIA~~~~i----p~~~l~kIl~~L~~aGLv~s~r-----G~-~GGy~Lar 69 (164)
T PRK10857 24 GPVPLADISERQGI----SLSYLEQLFSRLRKNGLVSSVR-----GP-GGGYLLGK 69 (164)
T ss_pred CcCcHHHHHHHHCc----CHHHHHHHHHHHHHCCCEEeCC-----CC-CCCeeccC
Confidence 58999999999999 9999999999999999999642 22 46677764
No 150
>PF03848 TehB: Tellurite resistance protein TehB; InterPro: IPR015985 Tellurite resistance protein TehB is part of a tellurite-reducing operon tehA and tehB. When present in high copy number, TehB is responsible for potassium tellurite resistance, probably by increasing the reduction rate of tellurite to metallic tellurium within the bacterium. TehB is a cytoplasmic protein which possesses three conserved motifs (I, II, and III) found in S-adenosyl-L-methionine (SAM)-dependent non-nucleic acid methyltransferases []. Conformational changes in TehB are observed upon binding of both tellurite and SAM, suggesting that TehB utilises a methyltransferase activity in the detoxification of tellurite. This entry represents the methyltransferase domain found in all TehB proteins.; PDB: 2KW5_A 3MER_B 3M70_A 2I6G_A 4DQ0_D 2XVA_B 2XVM_A.
Probab=94.71 E-value=0.072 Score=43.68 Aligned_cols=46 Identities=20% Similarity=0.302 Sum_probs=34.6
Q ss_pred HHHHHhcCCCCCCCeEEEecCCchHHHHHHHHHCCCCcEEEccc-hHHHh
Q 044458 187 KKFLENYKGFEGLQSVVDVGGGIGASLDMIISKYPSIKGINFDL-PHVIQ 235 (241)
Q Consensus 187 ~~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-P~vi~ 235 (241)
+.++...+ .-...++||+|||.|-.+.-|+++ +..++.+|. +..++
T Consensus 20 s~v~~a~~-~~~~g~~LDlgcG~GRNalyLA~~--G~~VtAvD~s~~al~ 66 (192)
T PF03848_consen 20 SEVLEAVP-LLKPGKALDLGCGEGRNALYLASQ--GFDVTAVDISPVALE 66 (192)
T ss_dssp HHHHHHCT-TS-SSEEEEES-TTSHHHHHHHHT--T-EEEEEESSHHHHH
T ss_pred HHHHHHHh-hcCCCcEEEcCCCCcHHHHHHHHC--CCeEEEEECCHHHHH
Confidence 45666666 556789999999999999999998 777888898 44544
No 151
>PRK14902 16S rRNA methyltransferase B; Provisional
Probab=94.69 E-value=0.032 Score=51.58 Aligned_cols=64 Identities=16% Similarity=0.199 Sum_probs=44.3
Q ss_pred HHHHHHhcchhhHHHHHHhcCCCCCCCeEEEecCCchHHHHHHHHHC-CCCcEEEccc-hHHHhcCC
Q 044458 174 FNNGMFSHSTITMKKFLENYKGFEGLQSVVDVGGGIGASLDMIISKY-PSIKGINFDL-PHVIQDAP 238 (241)
Q Consensus 174 f~~aM~~~~~~~~~~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~-P~l~~~v~Dl-P~vi~~a~ 238 (241)
|....-.........+...++ .....+|+|+|||+|..+..+++.. ++.+++.+|+ +..++.++
T Consensus 227 ~~~G~~~~qd~~s~lv~~~l~-~~~g~~VLDlgaG~G~~t~~la~~~~~~~~v~avDi~~~~l~~~~ 292 (444)
T PRK14902 227 FKDGLITIQDESSMLVAPALD-PKGGDTVLDACAAPGGKTTHIAELLKNTGKVVALDIHEHKLKLIE 292 (444)
T ss_pred HhCceEEEEChHHHHHHHHhC-CCCCCEEEEeCCCCCHHHHHHHHHhCCCCEEEEEeCCHHHHHHHH
Confidence 443333333333333444555 5556899999999999999999986 6788999999 77666543
No 152
>TIGR00478 tly hemolysin TlyA family protein. Hemolysins are exotoxins that attack blood cell membranes and cause cell rupture, often by forming a pore in the membrane. At least two members of this protein family have been characterized indirectly as pore-forming hemolysins, one from the spirochete Serpula (Treponema) hyodysenteriae and one from Mycobacterium tuberculosis. However, homology domains in this protein suggest methyltransferase activity (pfam01728) and RNA-binding activity (pfam01479).
Probab=94.66 E-value=0.082 Score=44.58 Aligned_cols=43 Identities=26% Similarity=0.373 Sum_probs=32.6
Q ss_pred HHHHHHhcCCC-CCCCeEEEecCCchHHHHHHHHHCCCCcEEEccc
Q 044458 186 MKKFLENYKGF-EGLQSVVDVGGGIGASLDMIISKYPSIKGINFDL 230 (241)
Q Consensus 186 ~~~~~~~~~~~-~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl 230 (241)
...+++.++ . -...+++|||||+|.++..+++. +--+++..|.
T Consensus 63 L~~~l~~~~-~~~~~~~vlDiG~gtG~~t~~l~~~-ga~~v~avD~ 106 (228)
T TIGR00478 63 LKEALEEFN-IDVKNKIVLDVGSSTGGFTDCALQK-GAKEVYGVDV 106 (228)
T ss_pred HHHHHHhcC-CCCCCCEEEEcccCCCHHHHHHHHc-CCCEEEEEeC
Confidence 345555554 3 24579999999999999999986 4456889998
No 153
>PLN02781 Probable caffeoyl-CoA O-methyltransferase
Probab=94.65 E-value=0.056 Score=45.65 Aligned_cols=44 Identities=14% Similarity=0.104 Sum_probs=36.4
Q ss_pred CCCCCeEEEecCCchHHHHHHHHHCC-CCcEEEccc-hHHHhcCCC
Q 044458 196 FEGLQSVVDVGGGIGASLDMIISKYP-SIKGINFDL-PHVIQDAPA 239 (241)
Q Consensus 196 ~~~~~~vvDVGGG~G~~~~~l~~~~P-~l~~~v~Dl-P~vi~~a~~ 239 (241)
..+.++|||||+|.|..+..+++..| +.+++.+|. |+.++.|++
T Consensus 66 ~~~~~~vLEiGt~~G~s~l~la~~~~~~g~v~tiD~d~~~~~~A~~ 111 (234)
T PLN02781 66 IMNAKNTLEIGVFTGYSLLTTALALPEDGRITAIDIDKEAYEVGLE 111 (234)
T ss_pred HhCCCEEEEecCcccHHHHHHHHhCCCCCEEEEEECCHHHHHHHHH
Confidence 34578999999999999999999865 678999999 677776653
No 154
>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein.
Probab=94.51 E-value=0.042 Score=39.17 Aligned_cols=47 Identities=15% Similarity=0.229 Sum_probs=40.8
Q ss_pred HhcChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCcchHHHHHHHHhcCCccccc
Q 044458 38 IELDLLEVIAKAGPGAFMSPKQIASQLPTKNSDAHILLDRILRLLASYSVLNCS 91 (241)
Q Consensus 38 ~~lglfd~L~~~~~~~~~t~~eLA~~~g~~~~~~~~~l~rlLr~L~~~g~l~~~ 91 (241)
.++.++..|... ++.|..+||+.+++ +...+.+.++-|...|++...
T Consensus 11 ~~~~il~~l~~~---~~~~~~~la~~~~~----s~~~i~~~l~~L~~~g~v~~~ 57 (101)
T smart00347 11 TQFLVLRILYEE---GPLSVSELAKRLGV----SPSTVTRVLDRLEKKGLIRRL 57 (101)
T ss_pred HHHHHHHHHHHc---CCcCHHHHHHHHCC----CchhHHHHHHHHHHCCCeEec
Confidence 356677888764 47999999999999 899999999999999999864
No 155
>PF07757 AdoMet_MTase: Predicted AdoMet-dependent methyltransferase; InterPro: IPR011671 tRNA (uracil-O(2)-)-methyltransferase catalyses the formation of O(2)-methyl-uracil at position 44 (m2U44) in tRNA(Ser) [].; GO: 0008168 methyltransferase activity
Probab=94.49 E-value=0.054 Score=40.04 Aligned_cols=43 Identities=23% Similarity=0.359 Sum_probs=28.2
Q ss_pred hHHHHHHhcCCCCCCCeEEEecCCchHHHHHHHHHCCCCcEEEccc
Q 044458 185 TMKKFLENYKGFEGLQSVVDVGGGIGASLDMIISKYPSIKGINFDL 230 (241)
Q Consensus 185 ~~~~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl 230 (241)
...-|...|. -.....+||||||.|.+.--|.+. +-+|..+|.
T Consensus 46 Li~LW~~~~~-~~~~~~FVDlGCGNGLLV~IL~~E--Gy~G~GiD~ 88 (112)
T PF07757_consen 46 LIELWRDMYG-EQKFQGFVDLGCGNGLLVYILNSE--GYPGWGIDA 88 (112)
T ss_pred HHHHHhcccC-CCCCCceEEccCCchHHHHHHHhC--CCCcccccc
Confidence 3344555554 356789999999999988666553 444555553
No 156
>PRK11050 manganese transport regulator MntR; Provisional
Probab=94.44 E-value=0.21 Score=39.35 Aligned_cols=57 Identities=21% Similarity=0.223 Sum_probs=44.9
Q ss_pred ChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCcchHHHHHHHHhcCCccccccccCCCCccccceecCccccc
Q 044458 41 DLLEVIAKAGPGAFMSPKQIASQLPTKNSDAHILLDRILRLLASYSVLNCSLHTLPDGGVERLYGLAPVCKF 112 (241)
Q Consensus 41 glfd~L~~~~~~~~~t~~eLA~~~g~~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~g~~~~~y~~t~~s~~ 112 (241)
-|..++... ++.+..|||+.+++ +...+.+.++.|...|++... . ...+.+|+.+..
T Consensus 41 ~I~~~l~~~---~~~t~~eLA~~l~i----s~stVsr~l~~Le~~GlI~r~----~----~~~v~LT~~G~~ 97 (152)
T PRK11050 41 LIADLIAEV---GEARQVDIAARLGV----SQPTVAKMLKRLARDGLVEMR----P----YRGVFLTPEGEK 97 (152)
T ss_pred HHHHHHHhc---CCCCHHHHHHHHCC----CHHHHHHHHHHHHHCCCEEEe----c----CCceEECchHHH
Confidence 355666653 58999999999999 999999999999999999864 1 345677776553
No 157
>TIGR02944 suf_reg_Xantho FeS assembly SUF system regulator, gammaproteobacterial. The SUF system is an oxygen-resistant iron-sulfur cluster assembly system found in both aerobes and facultative anaerobes. Its presence appears to be a marker of oxygen tolerance; strict anaerobes and microaerophiles tend to have different FeS cluster biosynthesis systems. Members of this protein family belong to the rrf2 family of transcriptional regulators and are found, typically, as the first gene of a SUF operon. It is found only in a subset of genomes that encode the SUF system, including the genus Xanthomonas. The conserved location suggests an autoregulatory role.
Probab=94.39 E-value=0.054 Score=41.28 Aligned_cols=55 Identities=25% Similarity=0.262 Sum_probs=41.1
Q ss_pred HHHHHhcCCCCCCCHHHHHhhCCCCCCCCcchHHHHHHHHhcCCccccccccCCCCccccceecCc
Q 044458 43 LEVIAKAGPGAFMSPKQIASQLPTKNSDAHILLDRILRLLASYSVLNCSLHTLPDGGVERLYGLAP 108 (241)
Q Consensus 43 fd~L~~~~~~~~~t~~eLA~~~g~~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~g~~~~~y~~t~ 108 (241)
...|+..+ +++.|+.|||+++++ ++..+.++|+.|...|++.... |. .+.|.+..
T Consensus 15 l~~la~~~-~~~~s~~eia~~l~i----s~~~v~~~l~~L~~~Gli~~~~-----g~-~ggy~l~~ 69 (130)
T TIGR02944 15 LTTLAQND-SQPYSAAEIAEQTGL----NAPTVSKILKQLSLAGIVTSKR-----GV-EGGYTLAR 69 (130)
T ss_pred HHHHHhCC-CCCccHHHHHHHHCc----CHHHHHHHHHHHHHCCcEEecC-----CC-CCChhhcC
Confidence 33444332 268999999999999 9999999999999999997531 11 35666644
No 158
>PF04703 FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A.
Probab=94.38 E-value=0.035 Score=36.95 Aligned_cols=45 Identities=20% Similarity=0.183 Sum_probs=37.3
Q ss_pred ChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCcchHHHHHHHHhcCCccccc
Q 044458 41 DLLEVIAKAGPGAFMSPKQIASQLPTKNSDAHILLDRILRLLASYSVLNCS 91 (241)
Q Consensus 41 glfd~L~~~~~~~~~t~~eLA~~~g~~~~~~~~~l~rlLr~L~~~g~l~~~ 91 (241)
.|.+.|.... +|.+..|||+.+|+ +...++++|..|...|.+...
T Consensus 4 ~Il~~i~~~~--~p~~T~eiA~~~gl----s~~~aR~yL~~Le~eG~V~~~ 48 (62)
T PF04703_consen 4 KILEYIKEQN--GPLKTREIADALGL----SIYQARYYLEKLEKEGKVERS 48 (62)
T ss_dssp CHHHHHHHHT--S-EEHHHHHHHHTS-----HHHHHHHHHHHHHCTSEEEE
T ss_pred HHHHHHHHcC--CCCCHHHHHHHhCC----CHHHHHHHHHHHHHCCCEEEe
Confidence 4667777632 69999999999999 999999999999999999864
No 159
>PRK10909 rsmD 16S rRNA m(2)G966-methyltransferase; Provisional
Probab=94.30 E-value=0.062 Score=44.33 Aligned_cols=39 Identities=21% Similarity=0.147 Sum_probs=30.8
Q ss_pred CCeEEEecCCchHHHHHHHHHCCCCcEEEccc-hHHHhcCC
Q 044458 199 LQSVVDVGGGIGASLDMIISKYPSIKGINFDL-PHVIQDAP 238 (241)
Q Consensus 199 ~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-P~vi~~a~ 238 (241)
..+|||+|||+|.++.+++.+.. .+++.+|. |++++.++
T Consensus 54 ~~~vLDl~~GsG~l~l~~lsr~a-~~V~~vE~~~~a~~~a~ 93 (199)
T PRK10909 54 DARCLDCFAGSGALGLEALSRYA-AGATLLEMDRAVAQQLI 93 (199)
T ss_pred CCEEEEcCCCccHHHHHHHHcCC-CEEEEEECCHHHHHHHH
Confidence 46999999999999998766654 57888888 77766553
No 160
>COG4976 Predicted methyltransferase (contains TPR repeat) [General function prediction only]
Probab=94.13 E-value=0.046 Score=45.97 Aligned_cols=58 Identities=10% Similarity=0.269 Sum_probs=38.2
Q ss_pred HHHHHHHHHHhcchhhHHHH----HHhcCCCCCCCeEEEecCCchHHHHHHHHHCCCCcEEEccc
Q 044458 170 LNKIFNNGMFSHSTITMKKF----LENYKGFEGLQSVVDVGGGIGASLDMIISKYPSIKGINFDL 230 (241)
Q Consensus 170 ~~~~f~~aM~~~~~~~~~~~----~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl 230 (241)
.+++|.+.....-....|.. +...+ ...+++++|+|||+|..+.++...--.++ .+|+
T Consensus 94 ~Ae~Fd~~LVdkL~Y~vP~~l~emI~~~~-~g~F~~~lDLGCGTGL~G~~lR~~a~~lt--GvDi 155 (287)
T COG4976 94 YAERFDHILVDKLGYSVPELLAEMIGKAD-LGPFRRMLDLGCGTGLTGEALRDMADRLT--GVDI 155 (287)
T ss_pred HHHHHHHHHHHHhcCccHHHHHHHHHhcc-CCccceeeecccCcCcccHhHHHHHhhcc--CCch
Confidence 35567666654333333333 33444 44589999999999999998887766664 4566
No 161
>PF01564 Spermine_synth: Spermine/spermidine synthase; InterPro: IPR001045 Synonym(s): Spermidine aminopropyltransferase A group of polyamine biosynthetic enzymes involved in the fifth (last) step in the biosynthesis of spermidine from arginine and methionine which includes; spermidine synthase (2.5.1.16 from EC), spermine synthase (2.5.1.22 from EC) and putrescine N-methyltransferase (2.1.1.53 from EC) []. The Thermotoga maritima spermidine synthase monomer consists of two domains: an N-terminal domain composed of six beta-strands, and a Rossmann-like C- terminal domain []. The larger C-terminal catalytic core domain consists of a seven-stranded beta-sheet flanked by nine alpha helices. This domain resembles a topology observed in a number of nucleotide and dinucleotide-binding enzymes, and in S-adenosyl-L-methionine (AdoMet)- dependent methyltransferase (MTases) [].; GO: 0003824 catalytic activity; PDB: 2E5W_C 2ZSU_E 2O0L_B 2O05_B 2O06_B 2O07_B 3RW9_B 2PWP_A 2HTE_B 3RIE_B ....
Probab=94.12 E-value=0.02 Score=48.78 Aligned_cols=44 Identities=23% Similarity=0.388 Sum_probs=36.2
Q ss_pred CCCCeEEEecCCchHHHHHHHHHCCCCcEEEccc-hHHHhcCCCC
Q 044458 197 EGLQSVVDVGGGIGASLDMIISKYPSIKGINFDL-PHVIQDAPAY 240 (241)
Q Consensus 197 ~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-P~vi~~a~~~ 240 (241)
+..++||=||||.|..+.++++..+..++++.|+ |.|++.+++|
T Consensus 75 ~~p~~VLiiGgG~G~~~~ell~~~~~~~i~~VEiD~~Vv~~a~~~ 119 (246)
T PF01564_consen 75 PNPKRVLIIGGGDGGTARELLKHPPVESITVVEIDPEVVELARKY 119 (246)
T ss_dssp SST-EEEEEESTTSHHHHHHTTSTT-SEEEEEES-HHHHHHHHHH
T ss_pred CCcCceEEEcCCChhhhhhhhhcCCcceEEEEecChHHHHHHHHh
Confidence 3579999999999999999987766778999999 8998887653
No 162
>COG2263 Predicted RNA methylase [Translation, ribosomal structure and biogenesis]
Probab=94.12 E-value=0.044 Score=44.66 Aligned_cols=40 Identities=25% Similarity=0.281 Sum_probs=31.6
Q ss_pred CCeEEEecCCchHHHHHHHHHCCCCcEEEccc-hHHHhcCCC
Q 044458 199 LQSVVDVGGGIGASLDMIISKYPSIKGINFDL-PHVIQDAPA 239 (241)
Q Consensus 199 ~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-P~vi~~a~~ 239 (241)
.++|+|+|||+|.+++..+-.-|. +++.+|+ |+.++.+++
T Consensus 46 g~~V~DlG~GTG~La~ga~~lGa~-~V~~vdiD~~a~ei~r~ 86 (198)
T COG2263 46 GKTVLDLGAGTGILAIGAALLGAS-RVLAVDIDPEALEIARA 86 (198)
T ss_pred CCEEEEcCCCcCHHHHHHHhcCCc-EEEEEecCHHHHHHHHH
Confidence 488999999999999988766554 5777888 788876653
No 163
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=94.11 E-value=0.12 Score=41.88 Aligned_cols=45 Identities=18% Similarity=0.213 Sum_probs=40.1
Q ss_pred cChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCcchHHHHHHHHhcCCccccc
Q 044458 40 LDLLEVIAKAGPGAFMSPKQIASQLPTKNSDAHILLDRILRLLASYSVLNCS 91 (241)
Q Consensus 40 lglfd~L~~~~~~~~~t~~eLA~~~g~~~~~~~~~l~rlLr~L~~~g~l~~~ 91 (241)
..|+++|... |.+|.+|||+.+|+ +...+|++|..|...|++...
T Consensus 25 ~~Vl~~L~~~---g~~tdeeLA~~Lgi----~~~~VRk~L~~L~e~gLv~~~ 69 (178)
T PRK06266 25 FEVLKALIKK---GEVTDEEIAEQTGI----KLNTVRKILYKLYDARLADYK 69 (178)
T ss_pred hHHHHHHHHc---CCcCHHHHHHHHCC----CHHHHHHHHHHHHHCCCeEEe
Confidence 3488888875 68999999999999 999999999999999999843
No 164
>KOG1541 consensus Predicted protein carboxyl methylase [General function prediction only]
Probab=94.06 E-value=0.02 Score=47.78 Aligned_cols=39 Identities=23% Similarity=0.389 Sum_probs=31.5
Q ss_pred CCCeEEEecCCchHHHHHHHHHCCCCcEEEccc-hHHHhcCC
Q 044458 198 GLQSVVDVGGGIGASLDMIISKYPSIKGINFDL-PHVIQDAP 238 (241)
Q Consensus 198 ~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-P~vi~~a~ 238 (241)
....|||||||+|..+..+... +...+.+|. |...+.|.
T Consensus 50 ~~~~iLDIGCGsGLSg~vL~~~--Gh~wiGvDiSpsML~~a~ 89 (270)
T KOG1541|consen 50 KSGLILDIGCGSGLSGSVLSDS--GHQWIGVDISPSMLEQAV 89 (270)
T ss_pred CCcEEEEeccCCCcchheeccC--CceEEeecCCHHHHHHHH
Confidence 3799999999999988877665 466799999 78777654
No 165
>TIGR01983 UbiG ubiquinone biosynthesis O-methyltransferase. This model represents an O-methyltransferase believed to act at two points in the ubiquinone biosynthetic pathway in bacteria (UbiG) and fungi (COQ3). A separate methylase (MenG/UbiE) catalyzes the single C-methylation step. The most commonly used names for genes in this family do not indicate whether this gene is an O-methyl, or C-methyl transferase.
Probab=94.05 E-value=0.045 Score=45.32 Aligned_cols=38 Identities=24% Similarity=0.097 Sum_probs=29.9
Q ss_pred CCCeEEEecCCchHHHHHHHHHCCCCcEEEccc-hHHHhcC
Q 044458 198 GLQSVVDVGGGIGASLDMIISKYPSIKGINFDL-PHVIQDA 237 (241)
Q Consensus 198 ~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-P~vi~~a 237 (241)
...+|||||||.|.++..+++..+ +++..|+ |..++.+
T Consensus 45 ~~~~vLdlG~G~G~~~~~l~~~~~--~v~~iD~s~~~~~~a 83 (224)
T TIGR01983 45 FGLRVLDVGCGGGLLSEPLARLGA--NVTGIDASEENIEVA 83 (224)
T ss_pred CCCeEEEECCCCCHHHHHHHhcCC--eEEEEeCCHHHHHHH
Confidence 357999999999999999988654 4888888 4555544
No 166
>PF04967 HTH_10: HTH DNA binding domain; InterPro: IPR007050 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. This entry represents the HTH DNA binding domain found in Halobacterium salinarium (Halobacterium halobium) and described as a putative bacterio-opsin activator.
Probab=94.01 E-value=0.05 Score=34.99 Aligned_cols=43 Identities=23% Similarity=0.280 Sum_probs=34.9
Q ss_pred HHHHHHHHHhcChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCcchHHHHHHHH
Q 044458 30 LPMVLKSAIELDLLEVIAKAGPGAFMSPKQIASQLPTKNSDAHILLDRILRLL 82 (241)
Q Consensus 30 ~~~~L~~a~~lglfd~L~~~~~~~~~t~~eLA~~~g~~~~~~~~~l~rlLr~L 82 (241)
.-.+|.+|++.|.||.= ...|..|||+.+|+ ++..+..-||-.
T Consensus 5 Q~e~L~~A~~~GYfd~P------R~~tl~elA~~lgi----s~st~~~~LRra 47 (53)
T PF04967_consen 5 QREILKAAYELGYFDVP------RRITLEELAEELGI----SKSTVSEHLRRA 47 (53)
T ss_pred HHHHHHHHHHcCCCCCC------CcCCHHHHHHHhCC----CHHHHHHHHHHH
Confidence 45789999999999973 46899999999999 777776666643
No 167
>PRK01544 bifunctional N5-glutamine S-adenosyl-L-methionine-dependent methyltransferase/tRNA (m7G46) methyltransferase; Reviewed
Probab=94.00 E-value=0.065 Score=50.47 Aligned_cols=33 Identities=15% Similarity=0.218 Sum_probs=31.3
Q ss_pred CCCeEEEecCCchHHHHHHHHHCCCCcEEEccc
Q 044458 198 GLQSVVDVGGGIGASLDMIISKYPSIKGINFDL 230 (241)
Q Consensus 198 ~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl 230 (241)
+...+||||||.|.++..+++++|+..++.+|.
T Consensus 347 ~~p~~lEIG~G~G~~~~~~A~~~p~~~~iGiE~ 379 (506)
T PRK01544 347 KRKVFLEIGFGMGEHFINQAKMNPDALFIGVEV 379 (506)
T ss_pred CCceEEEECCCchHHHHHHHHhCCCCCEEEEEe
Confidence 468999999999999999999999999999998
No 168
>PF13601 HTH_34: Winged helix DNA-binding domain; PDB: 1UB9_A.
Probab=93.95 E-value=0.035 Score=38.90 Aligned_cols=65 Identities=14% Similarity=0.180 Sum_probs=46.7
Q ss_pred HhcChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCcchHHHHHHHHhcCCccccccccCCCCcc-ccceecCcccc
Q 044458 38 IELDLLEVIAKAGPGAFMSPKQIASQLPTKNSDAHILLDRILRLLASYSVLNCSLHTLPDGGV-ERLYGLAPVCK 111 (241)
Q Consensus 38 ~~lglfd~L~~~~~~~~~t~~eLA~~~g~~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~g~~-~~~y~~t~~s~ 111 (241)
++++|..+|... +..++.+|.+.+|+ +...+.+-|+.|...|+++.... ..|.. ...|++|+.++
T Consensus 1 vRl~Il~~L~~~---~~~~f~~L~~~l~l----t~g~Ls~hL~~Le~~GyV~~~k~--~~~~~p~t~~~lT~~Gr 66 (80)
T PF13601_consen 1 VRLAILALLYAN---EEATFSELKEELGL----TDGNLSKHLKKLEEAGYVEVEKE--FEGRRPRTWYSLTDKGR 66 (80)
T ss_dssp HHHHHHHHHHHH---SEEEHHHHHHHTT------HHHHHHHHHHHHHTTSEEEEEE---SSS--EEEEEE-HHHH
T ss_pred CHHHHHHHHhhc---CCCCHHHHHHHhCc----CHHHHHHHHHHHHHCCCEEEEEe--ccCCCCeEEEEECHHHH
Confidence 467788888875 58999999999999 99999999999999999986521 11100 12477777665
No 169
>COG4742 Predicted transcriptional regulator [Transcription]
Probab=93.95 E-value=0.067 Score=45.79 Aligned_cols=67 Identities=15% Similarity=0.200 Sum_probs=58.7
Q ss_pred HHHHHHhcChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCcchHHHHHHHHhcCCccccccccCCCCccccceecCccccc
Q 044458 33 VLKSAIELDLLEVIAKAGPGAFMSPKQIASQLPTKNSDAHILLDRILRLLASYSVLNCSLHTLPDGGVERLYGLAPVCKF 112 (241)
Q Consensus 33 ~L~~a~~lglfd~L~~~~~~~~~t~~eLA~~~g~~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~g~~~~~y~~t~~s~~ 112 (241)
.+....+.+|+=.|.+ ||+|.+||-..+++ ++..+..=++-|...|++.+. ++.|++|..++.
T Consensus 9 if~SekRk~lLllL~e----gPkti~EI~~~l~v----s~~ai~pqiKkL~~~~LV~~~---------~~~Y~LS~~G~i 71 (260)
T COG4742 9 LFLSEKRKDLLLLLKE----GPKTIEEIKNELNV----SSSAILPQIKKLKDKGLVVQE---------GDRYSLSSLGKI 71 (260)
T ss_pred HHccHHHHHHHHHHHh----CCCCHHHHHHHhCC----CcHHHHHHHHHHhhCCCEEec---------CCEEEecchHHH
Confidence 4455677888889988 79999999999999 889999999999999999974 699999999998
Q ss_pred cccC
Q 044458 113 LTKN 116 (241)
Q Consensus 113 l~~~ 116 (241)
++..
T Consensus 72 iv~k 75 (260)
T COG4742 72 IVEK 75 (260)
T ss_pred HHHH
Confidence 7765
No 170
>PF08220 HTH_DeoR: DeoR-like helix-turn-helix domain; InterPro: IPR001034 The deoR-type HTH domain is a DNA-binding, helix-turn-helix (HTH) domain of about 50-60 amino acids present in transcription regulators of the deoR family, involved in sugar catabolism. This family of prokaryotic regulators is named after the Escherichia coli protein DeoR, a repressor of the deo operon, which encodes nucleotide and deoxyribonucleotide catabolic enzymes. DeoR also negatively regulates the expression of nupG and tsx, a nucleoside-specific transport protein and a channel-forming protein, respectively. DeoR-like transcription repressors occur in diverse bacteria as regulators of sugar and nucleoside metabolic systems. The effector molecules for deoR-like regulators are generally phosphorylated intermediates of the relevant metabolic pathway. The DNA-binding deoR-type HTH domain occurs usually in the N-terminal part. The C-terminal part can contain an effector-binding domain and/or an oligomerisation domain. DeoR occurs as an octamer, whilst glpR and agaR are tetramers. Several operators may be bound simultaneously, which could facilitate DNA looping [, ].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular
Probab=93.91 E-value=0.093 Score=34.13 Aligned_cols=44 Identities=18% Similarity=0.332 Sum_probs=39.5
Q ss_pred ChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCcchHHHHHHHHhcCCccccc
Q 044458 41 DLLEVIAKAGPGAFMSPKQIASQLPTKNSDAHILLDRILRLLASYSVLNCS 91 (241)
Q Consensus 41 glfd~L~~~~~~~~~t~~eLA~~~g~~~~~~~~~l~rlLr~L~~~g~l~~~ 91 (241)
.|.+.|... +.+|++|||+.+++ ++.-++|=|..|...|++.+.
T Consensus 4 ~Il~~l~~~---~~~s~~ela~~~~V----S~~TiRRDl~~L~~~g~i~r~ 47 (57)
T PF08220_consen 4 QILELLKEK---GKVSVKELAEEFGV----SEMTIRRDLNKLEKQGLIKRT 47 (57)
T ss_pred HHHHHHHHc---CCEEHHHHHHHHCc----CHHHHHHHHHHHHHCCCEEEE
Confidence 367778775 68999999999999 999999999999999999875
No 171
>PF01047 MarR: MarR family; InterPro: IPR000835 The MarR-type HTH domain is a DNA-binding, winged helix-turn-helix (wHTH) domain of about 135 amino acids present in transcription regulators of the MarR/SlyA family, involved in the development of antibiotic resistance. This family of transcription regulators is named after Escherichia coli MarR, a repressor of genes which activate the multiple antibiotic resistance and oxidative stress regulons, and after slyA from Salmonella typhimurium and E. coli, a transcription regulator that is required for virulence and survival in the macrophage environment. Regulators with the MarR-type HTH domain are present in bacteria and archaea and control a variety of biological functions, including resistance to multiple antibiotics, household disinfectants, organic solvents, oxidative stress agents and regulation of the virulence factor synthesis in pathogens of humans and plants. Many of the MarR-like regulators respond to aromatic compounds [, , ]. The crystal structures of MarR, MexR and SlyA have been determined and show a winged HTH DNA-binding core flanked by helices involved in dimerisation. The DNA-binding domains are ascribed to the superfamily of winged helix proteins, containing a three (four)-helix (H) bundle and a three-stranded antiparallel beta-sheet (B) in the topology: H1-(H1')-H2-B1-H3-H4-B2-B3-H5-H6. Helices 3 and 4 comprise the helix-turn-helix motif and the beta-sheet is called the wing. Helix 4 is termed the recognition helix, like in other HTHs where it binds the DNA major groove. The helices 1, 5 and 6 are involved in dimerisation, as most MarR-like transcription regulators form dimers [, ]. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 1JGS_A 2NYX_D 2PEX_B 2PFB_A 3BPX_A 3BPV_A 2BV6_A 3BJA_A 3E6M_B 2ETH_A ....
Probab=93.86 E-value=0.036 Score=35.97 Aligned_cols=46 Identities=13% Similarity=0.314 Sum_probs=38.7
Q ss_pred hcChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCcchHHHHHHHHhcCCccccc
Q 044458 39 ELDLLEVIAKAGPGAFMSPKQIASQLPTKNSDAHILLDRILRLLASYSVLNCS 91 (241)
Q Consensus 39 ~lglfd~L~~~~~~~~~t~~eLA~~~g~~~~~~~~~l~rlLr~L~~~g~l~~~ 91 (241)
++.+...|... ++.|..+||+.+++ +...+.++++.|...|++.+.
T Consensus 5 q~~iL~~l~~~---~~~~~~~la~~~~~----~~~~~t~~i~~L~~~g~I~r~ 50 (59)
T PF01047_consen 5 QFRILRILYEN---GGITQSELAEKLGI----SRSTVTRIIKRLEKKGLIERE 50 (59)
T ss_dssp HHHHHHHHHHH---SSEEHHHHHHHHTS-----HHHHHHHHHHHHHTTSEEEE
T ss_pred HHHHHHHHHHc---CCCCHHHHHHHHCC----ChhHHHHHHHHHHHCCCEEec
Confidence 44456667665 57999999999999 999999999999999999875
No 172
>KOG3115 consensus Methyltransferase-like protein [General function prediction only]
Probab=93.79 E-value=0.029 Score=46.26 Aligned_cols=33 Identities=21% Similarity=0.410 Sum_probs=29.8
Q ss_pred CCCeEEEecCCchHHHHHHHHHCCCCcEEEccc
Q 044458 198 GLQSVVDVGGGIGASLDMIISKYPSIKGINFDL 230 (241)
Q Consensus 198 ~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl 230 (241)
....++|||||-|.+++.+...||+--.+.+++
T Consensus 60 ~kvefaDIGCGyGGLlv~Lsp~fPdtLiLGmEI 92 (249)
T KOG3115|consen 60 KKVEFADIGCGYGGLLMKLAPKFPDTLILGMEI 92 (249)
T ss_pred ccceEEeeccCccchhhhccccCccceeeeehh
Confidence 347899999999999999999999998888777
No 173
>PF12802 MarR_2: MarR family; PDB: 3ECO_B 2QWW_B 3KP6_B 3KP4_B 3KP2_A 3KP5_A 3KP3_B 3KP7_A 3NQO_B 3K0L_B ....
Probab=93.77 E-value=0.043 Score=35.84 Aligned_cols=48 Identities=15% Similarity=0.270 Sum_probs=38.9
Q ss_pred hcChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCcchHHHHHHHHhcCCccccc
Q 044458 39 ELDLLEVIAKAGPGAFMSPKQIASQLPTKNSDAHILLDRILRLLASYSVLNCS 91 (241)
Q Consensus 39 ~lglfd~L~~~~~~~~~t~~eLA~~~g~~~~~~~~~l~rlLr~L~~~g~l~~~ 91 (241)
+..|+-.|...++ ...|..|||+.+++ ++..+.++++.|...|++.+.
T Consensus 7 q~~vL~~l~~~~~-~~~t~~~la~~l~~----~~~~vs~~v~~L~~~Glv~r~ 54 (62)
T PF12802_consen 7 QFRVLMALARHPG-EELTQSELAERLGI----SKSTVSRIVKRLEKKGLVERE 54 (62)
T ss_dssp HHHHHHHHHHSTT-SGEEHHHHHHHHTS-----HHHHHHHHHHHHHTTSEEEE
T ss_pred HHHHHHHHHHCCC-CCcCHHHHHHHHCc----CHHHHHHHHHHHHHCCCEEEe
Confidence 4556677777541 22899999999999 999999999999999999875
No 174
>PRK10141 DNA-binding transcriptional repressor ArsR; Provisional
Probab=93.76 E-value=0.086 Score=39.72 Aligned_cols=56 Identities=16% Similarity=0.198 Sum_probs=48.3
Q ss_pred HHHHHHHHHHhcChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCcchHHHHHHHHhcCCccccc
Q 044458 29 VLPMVLKSAIELDLLEVIAKAGPGAFMSPKQIASQLPTKNSDAHILLDRILRLLASYSVLNCS 91 (241)
Q Consensus 29 ~~~~~L~~a~~lglfd~L~~~~~~~~~t~~eLA~~~g~~~~~~~~~l~rlLr~L~~~g~l~~~ 91 (241)
-.+.+|.--.++.|+..|... ++.++.||++.+++ .+..+.+-|+.|...|++...
T Consensus 8 ~~fkaLadptRl~IL~~L~~~---~~~~v~ela~~l~l----sqstvS~HL~~L~~AGLV~~~ 63 (117)
T PRK10141 8 QLFKILSDETRLGIVLLLRES---GELCVCDLCTALDQ----SQPKISRHLALLRESGLLLDR 63 (117)
T ss_pred HHHHHhCCHHHHHHHHHHHHc---CCcCHHHHHHHHCc----CHHHHHHHHHHHHHCCceEEE
Confidence 345667777888999999763 58999999999999 999999999999999999864
No 175
>PF10294 Methyltransf_16: Putative methyltransferase; InterPro: IPR019410 There are a number of unidentified genes that have a high probability of coding for methyltransferases. They make up approximately 0.6-1.6% of the genes in the yeast, human, mouse, Drosophila melanogaster, Caenorhabditis elegans, Arabidopsis thaliana, and Escherichia coli genomes []. This entry represents putative nicotinamide N-methyltransferases involved in rDNA silencing and in lifespan determination. ; PDB: 3BZB_A.
Probab=93.75 E-value=0.077 Score=42.62 Aligned_cols=40 Identities=15% Similarity=0.146 Sum_probs=30.8
Q ss_pred CCCCeEEEecCCchHHHHHHHHHCCCCcEEEccchHHHhc
Q 044458 197 EGLQSVVDVGGGIGASLDMIISKYPSIKGINFDLPHVIQD 236 (241)
Q Consensus 197 ~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~DlP~vi~~ 236 (241)
...++||++|+|.|..++.+++.++..++++-|.+++++.
T Consensus 44 ~~~~~VLELGaG~Gl~gi~~a~~~~~~~Vv~TD~~~~l~~ 83 (173)
T PF10294_consen 44 FRGKRVLELGAGTGLPGIAAAKLFGAARVVLTDYNEVLEL 83 (173)
T ss_dssp TTTSEEEETT-TTSHHHHHHHHT-T-SEEEEEE-S-HHHH
T ss_pred cCCceEEEECCccchhHHHHHhccCCceEEEeccchhhHH
Confidence 3468999999999999999999988888999999887764
No 176
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=93.64 E-value=0.12 Score=32.13 Aligned_cols=43 Identities=23% Similarity=0.322 Sum_probs=37.5
Q ss_pred hHHHHHhcCCCCCCCHHHHHhhCCCCCCCCcchHHHHHHHHhcCCccccc
Q 044458 42 LLEVIAKAGPGAFMSPKQIASQLPTKNSDAHILLDRILRLLASYSVLNCS 91 (241)
Q Consensus 42 lfd~L~~~~~~~~~t~~eLA~~~g~~~~~~~~~l~rlLr~L~~~g~l~~~ 91 (241)
|++.|... ++.|..+|++.+++ ++..+++.|..|...|++.+.
T Consensus 5 il~~l~~~---~~~s~~~l~~~l~~----s~~tv~~~l~~L~~~g~i~~~ 47 (53)
T smart00420 5 ILELLAQQ---GKVSVEELAELLGV----SEMTIRRDLNKLEEQGLLTRV 47 (53)
T ss_pred HHHHHHHc---CCcCHHHHHHHHCC----CHHHHHHHHHHHHHCCCEEEe
Confidence 56666653 57999999999999 999999999999999999874
No 177
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=93.53 E-value=0.098 Score=38.31 Aligned_cols=46 Identities=20% Similarity=0.247 Sum_probs=41.3
Q ss_pred HhcChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCcchHHHHHHHHhcCCcccc
Q 044458 38 IELDLLEVIAKAGPGAFMSPKQIASQLPTKNSDAHILLDRILRLLASYSVLNC 90 (241)
Q Consensus 38 ~~lglfd~L~~~~~~~~~t~~eLA~~~g~~~~~~~~~l~rlLr~L~~~g~l~~ 90 (241)
.+..|+.+|... ++.|..+||+.+|+ ++..+++.++.|...|++..
T Consensus 4 ~D~~il~~L~~~---~~~~~~~la~~l~~----s~~tv~~~l~~L~~~g~i~~ 49 (108)
T smart00344 4 IDRKILEELQKD---ARISLAELAKKVGL----SPSTVHNRVKRLEEEGVIKG 49 (108)
T ss_pred HHHHHHHHHHHh---CCCCHHHHHHHHCc----CHHHHHHHHHHHHHCCCeec
Confidence 467788889875 58999999999999 99999999999999999984
No 178
>PRK03902 manganese transport transcriptional regulator; Provisional
Probab=93.53 E-value=0.11 Score=40.28 Aligned_cols=49 Identities=18% Similarity=0.158 Sum_probs=41.9
Q ss_pred CCCCHHHHHhhCCCCCCCCcchHHHHHHHHhcCCccccccccCCCCccccceecCcccccc
Q 044458 53 AFMSPKQIASQLPTKNSDAHILLDRILRLLASYSVLNCSLHTLPDGGVERLYGLAPVCKFL 113 (241)
Q Consensus 53 ~~~t~~eLA~~~g~~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~g~~~~~y~~t~~s~~l 113 (241)
++.+..+||+.+++ ++..+.+.++.|...|++... . ...|++|+.++.+
T Consensus 21 ~~~~~~ela~~l~v----s~~svs~~l~~L~~~Gli~~~----~----~~~i~LT~~G~~~ 69 (142)
T PRK03902 21 GYARVSDIAEALSV----HPSSVTKMVQKLDKDEYLIYE----K----YRGLVLTPKGKKI 69 (142)
T ss_pred CCcCHHHHHHHhCC----ChhHHHHHHHHHHHCCCEEEe----c----CceEEECHHHHHH
Confidence 68999999999999 999999999999999999853 1 4678899877643
No 179
>TIGR02337 HpaR homoprotocatechuate degradation operon regulator, HpaR. This Helix-Turn-Helix transcriptional regulator is a member of the MarR family (pfam01047) and is found in association with operons for the degradation of 4-hydroxyphenylacetic acid via homoprotocatechuate.
Probab=93.48 E-value=0.14 Score=38.27 Aligned_cols=68 Identities=21% Similarity=0.140 Sum_probs=49.4
Q ss_pred HhcChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCcchHHHHHHHHhcCCccccccccCCCCccccceecCccccccc
Q 044458 38 IELDLLEVIAKAGPGAFMSPKQIASQLPTKNSDAHILLDRILRLLASYSVLNCSLHTLPDGGVERLYGLAPVCKFLT 114 (241)
Q Consensus 38 ~~lglfd~L~~~~~~~~~t~~eLA~~~g~~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~g~~~~~y~~t~~s~~l~ 114 (241)
.+..|+..|... ++.|..|||+.+++ +...+.++++-|...|++..... +.|. ..-.+.+|+.++.+.
T Consensus 29 ~q~~iL~~l~~~---~~~t~~ela~~~~~----~~~tvs~~l~~Le~~GlI~r~~~-~~D~-R~~~v~LT~~G~~~~ 96 (118)
T TIGR02337 29 QQWRILRILAEQ---GSMEFTQLANQACI----LRPSLTGILARLERDGLVTRLKA-SNDQ-RRVYISLTPKGQALY 96 (118)
T ss_pred HHHHHHHHHHHc---CCcCHHHHHHHhCC----CchhHHHHHHHHHHCCCEEeccC-CCCC-CeeEEEECHhHHHHH
Confidence 344577777764 58999999999999 89999999999999999987521 1111 023677777666433
No 180
>TIGR00563 rsmB ribosomal RNA small subunit methyltransferase RsmB. The seed alignment is built from bacterial sequences only. Eukaryotic homologs include Nop2, a protein required for processing pre-rRNA, that is likely also a rRNA methyltransferase, although the fine specificity may differ. Cutoff scores are set to avoid treating archaeal and eukaroytic homologs automatically as functionally equivalent, although they may have very similar roles.
Probab=93.36 E-value=0.083 Score=48.60 Aligned_cols=51 Identities=12% Similarity=0.193 Sum_probs=39.9
Q ss_pred HHHHHHhcCCCCCCCeEEEecCCchHHHHHHHHHCCCCcEEEccc-hHHHhcC
Q 044458 186 MKKFLENYKGFEGLQSVVDVGGGIGASLDMIISKYPSIKGINFDL-PHVIQDA 237 (241)
Q Consensus 186 ~~~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-P~vi~~a 237 (241)
...++..++ .....+|+|+|||+|..+..+++..++.+++..|. ++.++.+
T Consensus 227 s~~~~~~L~-~~~g~~VLDlcag~G~kt~~la~~~~~~~v~a~D~~~~~l~~~ 278 (426)
T TIGR00563 227 AQWVATWLA-PQNEETILDACAAPGGKTTHILELAPQAQVVALDIHEHRLKRV 278 (426)
T ss_pred HHHHHHHhC-CCCCCeEEEeCCCccHHHHHHHHHcCCCeEEEEeCCHHHHHHH
Confidence 334455555 55568999999999999999999998778899998 6666544
No 181
>PF01135 PCMT: Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT); InterPro: IPR000682 Protein-L-isoaspartate(D-aspartate) O-methyltransferase (2.1.1.77 from EC) (PCMT) [] (which is also known as L-isoaspartyl protein carboxyl methyltransferase) is an enzyme that catalyses the transfer of a methyl group from S-adenosylmethionine to the free carboxyl groups of D-aspartyl or L-isoaspartyl residues in a variety of peptides and proteins. The enzyme does not act on normal L-aspartyl residues L-isoaspartyl and D-aspartyl are the products of the spontaneous deamidation and/or isomerisation of normal L-aspartyl and L-asparaginyl residues in proteins. PCMT plays a role in the repair and/or degradation of these damaged proteins; the enzymatic methyl esterification of the abnormal residues can lead to their conversion to normal L-aspartyl residues. The SAM domain is present in most of these proteins.; GO: 0004719 protein-L-isoaspartate (D-aspartate) O-methyltransferase activity, 0006464 protein modification process; PDB: 3LBF_A 1DL5_B 1JG3_B 1JG2_A 1JG1_A 1JG4_A 2YXE_A 2PBF_B 1VBF_C 1R18_A ....
Probab=93.34 E-value=0.088 Score=43.78 Aligned_cols=50 Identities=16% Similarity=0.308 Sum_probs=35.4
Q ss_pred HHHHhcCCCCCCCeEEEecCCchHHHHHHHHHCCC-CcEEEccc-hHHHhcCC
Q 044458 188 KFLENYKGFEGLQSVVDVGGGIGASLDMIISKYPS-IKGINFDL-PHVIQDAP 238 (241)
Q Consensus 188 ~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~-l~~~v~Dl-P~vi~~a~ 238 (241)
.+++.++ .....+|||||+|+|+++..+++..-. -+++.+|. |..++.|+
T Consensus 63 ~~l~~L~-l~pg~~VLeIGtGsGY~aAlla~lvg~~g~Vv~vE~~~~l~~~A~ 114 (209)
T PF01135_consen 63 RMLEALD-LKPGDRVLEIGTGSGYQAALLAHLVGPVGRVVSVERDPELAERAR 114 (209)
T ss_dssp HHHHHTT-C-TT-EEEEES-TTSHHHHHHHHHHSTTEEEEEEESBHHHHHHHH
T ss_pred HHHHHHh-cCCCCEEEEecCCCcHHHHHHHHhcCccceEEEECccHHHHHHHH
Confidence 4556666 777899999999999999999987543 35777776 66666554
No 182
>TIGR02085 meth_trns_rumB 23S rRNA (uracil-5-)-methyltransferase RumB. This family consists of RNA methyltransferases designated RumB, formerly YbjF. Members act on 23S rRNA U747 and the equivalent position in other proteobacterial species. This family is homologous to the other 23S rRNA methyltransferase RumA and to the tRNA methyltransferase TrmA.
Probab=93.30 E-value=0.057 Score=48.84 Aligned_cols=38 Identities=13% Similarity=0.086 Sum_probs=31.5
Q ss_pred CCeEEEecCCchHHHHHHHHHCCCCcEEEccc-hHHHhcCC
Q 044458 199 LQSVVDVGGGIGASLDMIISKYPSIKGINFDL-PHVIQDAP 238 (241)
Q Consensus 199 ~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-P~vi~~a~ 238 (241)
..+|+|++||+|.++..++.. ..+++..|. |..++.|+
T Consensus 234 ~~~vLDL~cG~G~~~l~la~~--~~~v~~vE~~~~av~~a~ 272 (374)
T TIGR02085 234 VTQMWDLFCGVGGFGLHCAGP--DTQLTGIEIESEAIACAQ 272 (374)
T ss_pred CCEEEEccCCccHHHHHHhhc--CCeEEEEECCHHHHHHHH
Confidence 479999999999999999854 467899998 77777654
No 183
>KOG3420 consensus Predicted RNA methylase [Translation, ribosomal structure and biogenesis]
Probab=93.24 E-value=0.055 Score=42.32 Aligned_cols=45 Identities=24% Similarity=0.415 Sum_probs=33.9
Q ss_pred HhcCCCCCCCeEEEecCCchHHHHHHHHHCCCCc-EEEccc-hHHHhcCC
Q 044458 191 ENYKGFEGLQSVVDVGGGIGASLDMIISKYPSIK-GINFDL-PHVIQDAP 238 (241)
Q Consensus 191 ~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~-~~v~Dl-P~vi~~a~ 238 (241)
.-|..++ .+++.|+|||.|.+. ++-.+|..+ ++.+|+ |++.+.+.
T Consensus 42 ~TygdiE-gkkl~DLgcgcGmLs--~a~sm~~~e~vlGfDIdpeALEIf~ 88 (185)
T KOG3420|consen 42 NTYGDIE-GKKLKDLGCGCGMLS--IAFSMPKNESVLGFDIDPEALEIFT 88 (185)
T ss_pred hhhcccc-CcchhhhcCchhhhH--HHhhcCCCceEEeeecCHHHHHHHh
Confidence 3443244 488999999999999 566777776 799999 88877653
No 184
>TIGR00479 rumA 23S rRNA (uracil-5-)-methyltransferase RumA. This protein family was first proposed to be RNA methyltransferases by homology to the TrmA family. The member from E. coli has now been shown to act as the 23S RNA methyltransferase for the conserved U1939. The gene is now designated rumA and was previously designated ygcA.
Probab=93.23 E-value=0.07 Score=49.08 Aligned_cols=46 Identities=22% Similarity=0.354 Sum_probs=36.0
Q ss_pred HHhcCCCCCCCeEEEecCCchHHHHHHHHHCCCCcEEEccc-hHHHhcCC
Q 044458 190 LENYKGFEGLQSVVDVGGGIGASLDMIISKYPSIKGINFDL-PHVIQDAP 238 (241)
Q Consensus 190 ~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-P~vi~~a~ 238 (241)
.+... ..+..+|+|+|||.|.++..+++... +++.+|. |..++.|+
T Consensus 285 ~~~l~-~~~~~~vLDl~cG~G~~sl~la~~~~--~V~~vE~~~~av~~a~ 331 (431)
T TIGR00479 285 LEALE-LQGEELVVDAYCGVGTFTLPLAKQAK--SVVGIEVVPESVEKAQ 331 (431)
T ss_pred HHHhc-cCCCCEEEEcCCCcCHHHHHHHHhCC--EEEEEEcCHHHHHHHH
Confidence 33334 55568999999999999999998753 6789998 78887665
No 185
>TIGR02702 SufR_cyano iron-sulfur cluster biosynthesis transcriptional regulator SufR. All members of this cyanobacterial protein family are the transcriptional regulator SufR and regulate the SUF system, which makes possible iron-sulfur cluster biosynthesis despite exposure to oxygen. In all cases, the sufR gene is encoded near SUF system genes but in the opposite direction. This DNA-binding protein belongs to the the DeoR family of helix-loop-helix proteins. All members also have a probable metal-binding motif C-X(12)-C-X(13)-C-X(14)-C near the C-terminus.
Probab=93.22 E-value=0.16 Score=41.78 Aligned_cols=68 Identities=16% Similarity=0.133 Sum_probs=48.6
Q ss_pred cChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCcchHHHHHHHHhcCCccccccccCCCCccccceecCccccccc
Q 044458 40 LDLLEVIAKAGPGAFMSPKQIASQLPTKNSDAHILLDRILRLLASYSVLNCSLHTLPDGGVERLYGLAPVCKFLT 114 (241)
Q Consensus 40 lglfd~L~~~~~~~~~t~~eLA~~~g~~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~g~~~~~y~~t~~s~~l~ 114 (241)
..|+..|... ++.|..|||+.+|+ ++..+++.|+.|...|++.........|-..-.|.+|+.+..+.
T Consensus 4 ~~IL~~L~~~---~~~t~~eLA~~lgi----s~~tV~~~L~~Le~~GlV~r~~~~~~~gRp~~~y~LT~~G~~~~ 71 (203)
T TIGR02702 4 EDILSYLLKQ---GQATAAALAEALAI----SPQAVRRHLKDLETEGLIEYEAVVQGMGRPQYHYQLSRQGREQF 71 (203)
T ss_pred HHHHHHHHHc---CCCCHHHHHHHHCc----CHHHHHHHHHHHHHCCCeEEeecccCCCCCceEEEECcchhhhc
Confidence 4567777664 58999999999999 99999999999999999986410001111123478887776433
No 186
>TIGR00095 RNA methyltransferase, RsmD family. This model represents a family of uncharacterized bacterial proteins. Members are present in nearly every complete bacterial genome, always in a single copy. PSI-BLAST analysis shows homology to several families of SAM-dependent methyltransferases, including ribosomal RNA adenine dimethylases.
Probab=93.15 E-value=0.078 Score=43.28 Aligned_cols=38 Identities=16% Similarity=0.003 Sum_probs=31.4
Q ss_pred CCeEEEecCCchHHHHHHHHHCCCCcEEEccc-hHHHhcC
Q 044458 199 LQSVVDVGGGIGASLDMIISKYPSIKGINFDL-PHVIQDA 237 (241)
Q Consensus 199 ~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-P~vi~~a 237 (241)
..+|||++||+|.++.+++.+... +++..|. +.+++.+
T Consensus 50 g~~vLDLfaGsG~lglea~srga~-~v~~vE~~~~a~~~~ 88 (189)
T TIGR00095 50 GAHLLDVFAGSGLLGEEALSRGAK-VAFLEEDDRKANQTL 88 (189)
T ss_pred CCEEEEecCCCcHHHHHHHhCCCC-EEEEEeCCHHHHHHH
Confidence 478999999999999999999764 6888888 5666544
No 187
>PF06080 DUF938: Protein of unknown function (DUF938); InterPro: IPR010342 This family consists of several hypothetical proteins from both prokaryotes and eukaryotes. The function of this family is unknown.
Probab=93.08 E-value=0.11 Score=42.89 Aligned_cols=35 Identities=14% Similarity=0.204 Sum_probs=28.4
Q ss_pred CCCCC-eEEEecCCchHHHHHHHHHCCCCcEEEccc
Q 044458 196 FEGLQ-SVVDVGGGIGASLDMIISKYPSIKGINFDL 230 (241)
Q Consensus 196 ~~~~~-~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl 230 (241)
+.... +||.||+|+|..+..+++.+|+++..-=|.
T Consensus 22 l~~~~~~vLEiaSGtGqHa~~FA~~lP~l~WqPSD~ 57 (204)
T PF06080_consen 22 LPDSGTRVLEIASGTGQHAVYFAQALPHLTWQPSDP 57 (204)
T ss_pred hCccCceEEEEcCCccHHHHHHHHHCCCCEEcCCCC
Confidence 34344 599999999999999999999998654454
No 188
>PRK11014 transcriptional repressor NsrR; Provisional
Probab=93.08 E-value=0.15 Score=39.54 Aligned_cols=46 Identities=11% Similarity=0.093 Sum_probs=38.2
Q ss_pred CCCCHHHHHhhCCCCCCCCcchHHHHHHHHhcCCccccccccCCCCccccceecCc
Q 044458 53 AFMSPKQIASQLPTKNSDAHILLDRILRLLASYSVLNCSLHTLPDGGVERLYGLAP 108 (241)
Q Consensus 53 ~~~t~~eLA~~~g~~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~g~~~~~y~~t~ 108 (241)
.+.|.++||+.+|+ ++..++++|+.|...|++.-.+ |. .|.|.+..
T Consensus 24 ~~~s~~~ia~~~~i----s~~~vrk~l~~L~~~Glv~s~~-----G~-~GG~~l~~ 69 (141)
T PRK11014 24 RMTSISEVTEVYGV----SRNHMVKIINQLSRAGYVTAVR-----GK-NGGIRLGK 69 (141)
T ss_pred CccCHHHHHHHHCc----CHHHHHHHHHHHHhCCEEEEec-----CC-CCCeeecC
Confidence 57899999999999 9999999999999999998642 21 35676653
No 189
>PRK11920 rirA iron-responsive transcriptional regulator; Reviewed
Probab=92.99 E-value=0.15 Score=40.20 Aligned_cols=46 Identities=17% Similarity=0.179 Sum_probs=39.3
Q ss_pred CCCCHHHHHhhCCCCCCCCcchHHHHHHHHhcCCccccccccCCCCccccceecCc
Q 044458 53 AFMSPKQIASQLPTKNSDAHILLDRILRLLASYSVLNCSLHTLPDGGVERLYGLAP 108 (241)
Q Consensus 53 ~~~t~~eLA~~~g~~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~g~~~~~y~~t~ 108 (241)
++.|+++||+..++ ++..|+++|..|...|++.-.+ |. .|.|.++.
T Consensus 23 ~~~s~~eIA~~~~i----s~~~L~kIl~~L~~aGlv~S~r-----G~-~GGy~La~ 68 (153)
T PRK11920 23 KLSRIPEIARAYGV----SELFLFKILQPLVEAGLVETVR-----GR-NGGVRLGR 68 (153)
T ss_pred CcCcHHHHHHHHCc----CHHHHHHHHHHHHHCCCEEeec-----CC-CCCeeecC
Confidence 57899999999999 9999999999999999998642 32 57787765
No 190
>TIGR01177 conserved hypothetical protein TIGR01177. This family is found exclusively in the Archaea.
Probab=92.94 E-value=0.15 Score=45.29 Aligned_cols=46 Identities=20% Similarity=0.076 Sum_probs=34.9
Q ss_pred HHHhcCCCCCCCeEEEecCCchHHHHHHHHHCCCCcEEEccc-hHHHhcC
Q 044458 189 FLENYKGFEGLQSVVDVGGGIGASLDMIISKYPSIKGINFDL-PHVIQDA 237 (241)
Q Consensus 189 ~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-P~vi~~a 237 (241)
++.... +....+|+|+|||+|.++++.+. ...+++..|. |..++.+
T Consensus 174 ~~~l~~-~~~g~~vLDp~cGtG~~lieaa~--~~~~v~g~Di~~~~~~~a 220 (329)
T TIGR01177 174 MVNLAR-VTEGDRVLDPFCGTGGFLIEAGL--MGAKVIGCDIDWKMVAGA 220 (329)
T ss_pred HHHHhC-CCCcCEEEECCCCCCHHHHHHHH--hCCeEEEEcCCHHHHHHH
Confidence 343444 66678999999999999988665 3678899999 6776654
No 191
>TIGR00122 birA_repr_reg BirA biotin operon repressor domain. This model may recognize some other putative repressor proteins, such as DnrO of Streptomyces peucetius with scores below the noise cutoff but with significance shown by low E-value.
Probab=92.74 E-value=0.2 Score=33.69 Aligned_cols=44 Identities=18% Similarity=0.273 Sum_probs=38.3
Q ss_pred hcChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCcchHHHHHHHHhcCCcccc
Q 044458 39 ELDLLEVIAKAGPGAFMSPKQIASQLPTKNSDAHILLDRILRLLASYSVLNC 90 (241)
Q Consensus 39 ~lglfd~L~~~~~~~~~t~~eLA~~~g~~~~~~~~~l~rlLr~L~~~g~l~~ 90 (241)
++.++..|.+ ++.+..+||+.+|+ +...+++-++.|...|+...
T Consensus 2 ~~~il~~L~~----~~~~~~eLa~~l~v----S~~tv~~~l~~L~~~g~~i~ 45 (69)
T TIGR00122 2 PLRLLALLAD----NPFSGEKLGEALGM----SRTAVNKHIQTLREWGVDVL 45 (69)
T ss_pred hHHHHHHHHc----CCcCHHHHHHHHCC----CHHHHHHHHHHHHHCCCeEE
Confidence 4567788876 57899999999999 99999999999999999664
No 192
>PRK15431 ferrous iron transport protein FeoC; Provisional
Probab=92.65 E-value=0.18 Score=35.01 Aligned_cols=43 Identities=21% Similarity=0.247 Sum_probs=38.9
Q ss_pred hHHHHHhcCCCCCCCHHHHHhhCCCCCCCCcchHHHHHHHHhcCCccccc
Q 044458 42 LLEVIAKAGPGAFMSPKQIASQLPTKNSDAHILLDRILRLLASYSVLNCS 91 (241)
Q Consensus 42 lfd~L~~~~~~~~~t~~eLA~~~g~~~~~~~~~l~rlLr~L~~~g~l~~~ 91 (241)
|=|+|... |..++.+||.++++ ++..++-+|..|+.+|-+++.
T Consensus 7 lRd~l~~~---gr~s~~~Ls~~~~~----p~~~VeaMLe~l~~kGkverv 49 (78)
T PRK15431 7 VRDLLALR---GRMEAAQISQTLNT----PQPMINAMLQQLESMGKAVRI 49 (78)
T ss_pred HHHHHHHc---CcccHHHHHHHHCc----CHHHHHHHHHHHHHCCCeEee
Confidence 45788885 68999999999999 999999999999999999875
No 193
>COG2345 Predicted transcriptional regulator [Transcription]
Probab=92.54 E-value=0.15 Score=42.52 Aligned_cols=64 Identities=20% Similarity=0.273 Sum_probs=48.3
Q ss_pred hHHHHHhcCCCCCCCHHHHHhhCCCCCCCCcchHHHHHHHHhcCCccccccccCCC--CccccceecCccccccc
Q 044458 42 LLEVIAKAGPGAFMSPKQIASQLPTKNSDAHILLDRILRLLASYSVLNCSLHTLPD--GGVERLYGLAPVCKFLT 114 (241)
Q Consensus 42 lfd~L~~~~~~~~~t~~eLA~~~g~~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~--g~~~~~y~~t~~s~~l~ 114 (241)
|...|.+. +|+|+.|||+++|+ ++..+++-|..|.+.|++.... ... |=-.-.|++|..++...
T Consensus 16 il~lL~~~---g~~sa~elA~~Lgi----s~~avR~HL~~Le~~Glv~~~~--~~~g~GRP~~~y~Lt~~g~~~f 81 (218)
T COG2345 16 ILELLKKS---GPVSADELAEELGI----SPMAVRRHLDDLEAEGLVEVER--QQGGRGRPAKLYRLTEKGREQF 81 (218)
T ss_pred HHHHHhcc---CCccHHHHHHHhCC----CHHHHHHHHHHHHhCcceeeee--ccCCCCCCceeeeecccchhhc
Confidence 55666654 79999999999999 9999999999999999997541 111 11124789998876433
No 194
>KOG1499 consensus Protein arginine N-methyltransferase PRMT1 and related enzymes [Posttranslational modification, protein turnover, chaperones; Transcription; Signal transduction mechanisms]
Probab=92.48 E-value=0.1 Score=46.34 Aligned_cols=38 Identities=21% Similarity=0.157 Sum_probs=31.5
Q ss_pred CCeEEEecCCchHHHHHHHHHCCCCcEEEccchHHHhcC
Q 044458 199 LQSVVDVGGGIGASLDMIISKYPSIKGINFDLPHVIQDA 237 (241)
Q Consensus 199 ~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~DlP~vi~~a 237 (241)
.+.|+|||||+|.+++-.+++. .-++...|--++++.|
T Consensus 61 dK~VlDVGcGtGILS~F~akAG-A~~V~aVe~S~ia~~a 98 (346)
T KOG1499|consen 61 DKTVLDVGCGTGILSMFAAKAG-ARKVYAVEASSIADFA 98 (346)
T ss_pred CCEEEEcCCCccHHHHHHHHhC-cceEEEEechHHHHHH
Confidence 4999999999999999999988 5567777777666554
No 195
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=92.47 E-value=0.21 Score=32.10 Aligned_cols=42 Identities=14% Similarity=0.225 Sum_probs=36.2
Q ss_pred hHHHHHhcCCCCCCCHHHHHhhCCCCCCCCcchHHHHHHHHhcCCccccc
Q 044458 42 LLEVIAKAGPGAFMSPKQIASQLPTKNSDAHILLDRILRLLASYSVLNCS 91 (241)
Q Consensus 42 lfd~L~~~~~~~~~t~~eLA~~~g~~~~~~~~~l~rlLr~L~~~g~l~~~ 91 (241)
|+..|.. ++.|..+|++.+++ +...+.+.|+.|...|++...
T Consensus 2 il~~l~~----~~~~~~~i~~~l~i----s~~~v~~~l~~L~~~g~i~~~ 43 (66)
T smart00418 2 ILKLLAE----GELCVCELAEILGL----SQSTVSHHLKKLREAGLVESR 43 (66)
T ss_pred HHHHhhc----CCccHHHHHHHHCC----CHHHHHHHHHHHHHCCCeeee
Confidence 4555653 58999999999999 899999999999999999863
No 196
>PF01728 FtsJ: FtsJ-like methyltransferase; InterPro: IPR002877 RrmJ (FtsJ) is a well conserved heat shock protein present in prokaryotes, archaea, and eukaryotes. RrmJ is responsible for methylating 23 S rRNA at position U2552 in the aminoacyl (A)1-site of the ribosome []. U2552 is one of the five universally conserved A-loop residues and has been shown to be methylated at the ribose 2'-OH group in the majority of organisms investigated so far. This suggests that this modification plays an important role in the A-loop function. RrmJ recognises its methylation target only when the 23 S rRNA is present in 50 S ribosomal subunits. This suggests that the RrmJ-mediated methylation must occur late in the maturation process of the ribosome. This is in contrast to other known 23 S rRNA modifications that occur in earlier maturation steps. The 1.5 A crystal structure of RrmJ in complex with its cofactor S-adenosylmethionine revealed that RrmJ has a methyltransferase fold. The active site of RrmJ appears to be formed by a catalytic triad consisting of two lysine residues and the negatively charged aspartate residue. Another highly conserved glutamate residue that is present in the active site of RrmJ appears to play only a minor role in the methyltransfer reaction in vivo []. ; GO: 0003676 nucleic acid binding, 0008168 methyltransferase activity, 0032259 methylation; PDB: 3GCZ_A 2PLW_A 2NYU_A 2OXT_C 3EMD_A 3ELY_A 3ELW_A 3ELU_A 3ELD_A 3EMB_A ....
Probab=92.32 E-value=0.16 Score=40.71 Aligned_cols=48 Identities=21% Similarity=0.336 Sum_probs=36.4
Q ss_pred HHHHHHhcCCCC--CCCeEEEecCCchHHHHHHHHHC-CCCcEEEccchHH
Q 044458 186 MKKFLENYKGFE--GLQSVVDVGGGIGASLDMIISKY-PSIKGINFDLPHV 233 (241)
Q Consensus 186 ~~~~~~~~~~~~--~~~~vvDVGGG~G~~~~~l~~~~-P~l~~~v~DlP~v 233 (241)
...+.+.|+-++ ...++||+|+++|.++..++++. +..+++.+|+...
T Consensus 9 L~ei~~~~~~~~~~~~~~vlDlG~aPGGws~~~~~~~~~~~~v~avDl~~~ 59 (181)
T PF01728_consen 9 LYEIDEKFKIFKPGKGFTVLDLGAAPGGWSQVLLQRGGPAGRVVAVDLGPM 59 (181)
T ss_dssp HHHHHHTTSSS-TTTTEEEEEET-TTSHHHHHHHTSTTTEEEEEEEESSST
T ss_pred HHHHHHHCCCCCcccccEEEEcCCcccceeeeeeecccccceEEEEecccc
Confidence 345566665233 45999999999999999999998 7888999998643
No 197
>TIGR01884 cas_HTH CRISPR locus-related DNA-binding protein. Most but not all examples of this family are associated with CRISPR loci, a combination of DNA repeats and characteristic proteins encoded near the repeat cluster. The C-terminal region of this protein is homologous to DNA-binding helix-turn-helix domains with predicted transcriptional regulatory activity.
Probab=92.28 E-value=0.22 Score=41.07 Aligned_cols=59 Identities=27% Similarity=0.280 Sum_probs=47.0
Q ss_pred HhcChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCcchHHHHHHHHhcCCccccccccCCCCccccceecCcc
Q 044458 38 IELDLLEVIAKAGPGAFMSPKQIASQLPTKNSDAHILLDRILRLLASYSVLNCSLHTLPDGGVERLYGLAPV 109 (241)
Q Consensus 38 ~~lglfd~L~~~~~~~~~t~~eLA~~~g~~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~g~~~~~y~~t~~ 109 (241)
.+..++..|.+. ++.+..|||+.+++ ++..+.|.|+.|...|++.+.. . ....|.+|+.
T Consensus 144 ~~~~IL~~l~~~---g~~s~~eia~~l~i----s~stv~r~L~~Le~~GlI~r~~---~---r~~~~~lT~~ 202 (203)
T TIGR01884 144 EELKVLEVLKAE---GEKSVKNIAKKLGK----SLSTISRHLRELEKKGLVEQKG---R---KGKRYSLTKL 202 (203)
T ss_pred HHHHHHHHHHHc---CCcCHHHHHHHHCc----CHHHHHHHHHHHHHCCCEEEEc---C---CccEEEeCCC
Confidence 345677777764 57999999999999 9999999999999999999751 0 1467777765
No 198
>COG3355 Predicted transcriptional regulator [Transcription]
Probab=92.28 E-value=0.17 Score=38.45 Aligned_cols=45 Identities=11% Similarity=0.184 Sum_probs=38.2
Q ss_pred cChHHHHH-hcCCCCCCCHHHHHhhCCCCCCCCcchHHHHHHHHhcCCccccc
Q 044458 40 LDLLEVIA-KAGPGAFMSPKQIASQLPTKNSDAHILLDRILRLLASYSVLNCS 91 (241)
Q Consensus 40 lglfd~L~-~~~~~~~~t~~eLA~~~g~~~~~~~~~l~rlLr~L~~~g~l~~~ 91 (241)
..++.+|- .+ +|.|.++||+.++. +...+.|-|+-|...|++.+.
T Consensus 30 v~v~~~LL~~~---~~~tvdelae~lnr----~rStv~rsl~~L~~~GlV~Re 75 (126)
T COG3355 30 VEVYKALLEEN---GPLTVDELAEILNR----SRSTVYRSLQNLLEAGLVERE 75 (126)
T ss_pred HHHHHHHHhhc---CCcCHHHHHHHHCc----cHHHHHHHHHHHHHcCCeeee
Confidence 34555554 43 79999999999999 999999999999999999875
No 199
>PF07381 DUF1495: Winged helix DNA-binding domain (DUF1495); InterPro: IPR010863 This family consists of several hypothetical archaeal proteins of around 110 residues in length. The function of this family is unknown, although one sequence (Q8U3W1 from SWISSPROT) is described as a putative HTH transcription regulator.
Probab=92.18 E-value=0.2 Score=35.84 Aligned_cols=67 Identities=21% Similarity=0.192 Sum_probs=52.0
Q ss_pred HHHhcChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCcchHHHHHHH----------HhcCCcc-ccccccCCCCccccce
Q 044458 36 SAIELDLLEVIAKAGPGAFMSPKQIASQLPTKNSDAHILLDRILRL----------LASYSVL-NCSLHTLPDGGVERLY 104 (241)
Q Consensus 36 ~a~~lglfd~L~~~~~~~~~t~~eLA~~~g~~~~~~~~~l~rlLr~----------L~~~g~l-~~~~~~~~~g~~~~~y 104 (241)
+=++..|+..|.+..+ .+.++.|||..+++ ++..+.--|+- |+.+|++ ++. ...| ...|
T Consensus 8 S~~R~~vl~~L~~~yp-~~~~~~eIar~v~~----~~snV~GaL~G~g~rY~~e~SLv~lGLV~~~~---~~~g--~k~Y 77 (90)
T PF07381_consen 8 SKVRKKVLEYLCSIYP-EPAYPSEIARSVGS----DYSNVLGALRGDGKRYNKEDSLVGLGLVEEEE---EKGG--FKYY 77 (90)
T ss_pred HHHHHHHHHHHHHcCC-CcCCHHHHHHHHCC----CHHHHHHHHhcCCCCcCcchhHHHcCCeeEee---ecCC--eeEE
Confidence 4567789999988732 68999999999999 99988887764 8999999 443 1234 5689
Q ss_pred ecCccccc
Q 044458 105 GLAPVCKF 112 (241)
Q Consensus 105 ~~t~~s~~ 112 (241)
++|+.++.
T Consensus 78 ~lT~~G~~ 85 (90)
T PF07381_consen 78 RLTEKGKR 85 (90)
T ss_pred EeChhhhh
Confidence 99987763
No 200
>TIGR00373 conserved hypothetical protein TIGR00373. This family of proteins is, so far, restricted to archaeal genomes. The family appears to be distantly related to the N-terminal region of the eukaryotic transcription initiation factor IIE alpha chain.
Probab=92.15 E-value=0.2 Score=39.83 Aligned_cols=45 Identities=11% Similarity=0.011 Sum_probs=39.1
Q ss_pred cChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCcchHHHHHHHHhcCCccccc
Q 044458 40 LDLLEVIAKAGPGAFMSPKQIASQLPTKNSDAHILLDRILRLLASYSVLNCS 91 (241)
Q Consensus 40 lglfd~L~~~~~~~~~t~~eLA~~~g~~~~~~~~~l~rlLr~L~~~g~l~~~ 91 (241)
..|+++|... +.+|-+|||+.+|+ +...++++|..|...|++...
T Consensus 17 v~Vl~aL~~~---~~~tdEeLa~~Lgi----~~~~VRk~L~~L~e~~Lv~~~ 61 (158)
T TIGR00373 17 GLVLFSLGIK---GEFTDEEISLELGI----KLNEVRKALYALYDAGLADYK 61 (158)
T ss_pred HHHHHHHhcc---CCCCHHHHHHHHCC----CHHHHHHHHHHHHHCCCceee
Confidence 3477888754 68999999999999 999999999999999999643
No 201
>COG2518 Pcm Protein-L-isoaspartate carboxylmethyltransferase [Posttranslational modification, protein turnover, chaperones]
Probab=92.10 E-value=0.2 Score=41.52 Aligned_cols=48 Identities=13% Similarity=0.272 Sum_probs=36.3
Q ss_pred HHHHhcCCCCCCCeEEEecCCchHHHHHHHHHCCCCcEEEccc-hHHHhcCC
Q 044458 188 KFLENYKGFEGLQSVVDVGGGIGASLDMIISKYPSIKGINFDL-PHVIQDAP 238 (241)
Q Consensus 188 ~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-P~vi~~a~ 238 (241)
.+++.++ .+...+||+||+|+|+.+.-+++--- +++.+|+ ++.++.|+
T Consensus 63 ~m~~~L~-~~~g~~VLEIGtGsGY~aAvla~l~~--~V~siEr~~~L~~~A~ 111 (209)
T COG2518 63 RMLQLLE-LKPGDRVLEIGTGSGYQAAVLARLVG--RVVSIERIEELAEQAR 111 (209)
T ss_pred HHHHHhC-CCCCCeEEEECCCchHHHHHHHHHhC--eEEEEEEcHHHHHHHH
Confidence 4456666 77889999999999999998888766 6666676 55555543
No 202
>PF01638 HxlR: HxlR-like helix-turn-helix; InterPro: IPR002577 The hxlR-type HTH domain is a domain of ~90-100 amino acids present in putative transcription regulators with a winged helix-turn-helix (wHTH) structure. The domain is named after Bacillus subtilis hxlR, a transcription activator of the hxlAB operon involved in the detoxification of formaldehyde []. The hxlR-type domain forms the core of putative transcription regulators and of hypothetical proteins occurring in eubacteria as well as in archaea. The sequence and structure of hxlR-type proteins show similarities with the marR-type wHTH []. The crystal structure of ytfH resembles the DNA-binding domains of winged helix proteins, containing a three helix (H) bundle and a three-stranded antiparallel beta-sheet (B) in the topology: H1-H2-B1-H3-H4-B2-B3-H5-H6. This topology corresponds with that of the marR-type DNA-binding domain, wherein helices 3 and 4 comprise the helix-turn-helix motif and the beta-sheet is called the wing. ; PDB: 2F2E_B 3DF8_A 1Z7U_B 1YYV_A 4A5M_D 4A5N_B 2FSW_A 2HZT_D.
Probab=92.04 E-value=0.11 Score=37.12 Aligned_cols=63 Identities=17% Similarity=0.187 Sum_probs=44.5
Q ss_pred hHHHHHhcCCCCCCCHHHHHhhC-CCCCCCCcchHHHHHHHHhcCCccccccccCCCCccccceecCccccccc
Q 044458 42 LLEVIAKAGPGAFMSPKQIASQL-PTKNSDAHILLDRILRLLASYSVLNCSLHTLPDGGVERLYGLAPVCKFLT 114 (241)
Q Consensus 42 lfd~L~~~~~~~~~t~~eLA~~~-g~~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~g~~~~~y~~t~~s~~l~ 114 (241)
|+..|.. |+..+.||.+.+ ++ ++..|.+-|+.|...|++.+... ......-.|++|+.++.|.
T Consensus 10 IL~~l~~----g~~rf~el~~~l~~i----s~~~L~~~L~~L~~~GLv~r~~~--~~~p~~v~Y~LT~~G~~l~ 73 (90)
T PF01638_consen 10 ILRALFQ----GPMRFSELQRRLPGI----SPKVLSQRLKELEEAGLVERRVY--PEVPPRVEYSLTEKGKELL 73 (90)
T ss_dssp HHHHHTT----SSEEHHHHHHHSTTS-----HHHHHHHHHHHHHTTSEEEEEE--SSSSSEEEEEE-HHHHHHH
T ss_pred HHHHHHh----CCCcHHHHHHhcchh----HHHHHHHHHHHHHHcchhhcccc--cCCCCCCccCCCcCHHHHH
Confidence 4445555 699999999999 89 99999999999999999987521 1000023588888777444
No 203
>PRK06474 hypothetical protein; Provisional
Probab=92.03 E-value=0.27 Score=39.76 Aligned_cols=77 Identities=13% Similarity=0.213 Sum_probs=55.7
Q ss_pred HHHHHHHHhcChHHHHHhcCCCCCCCHHHHHhhC-CCCCCCCcchHHHHHHHHhcCCccccccccCCCCccccceecCcc
Q 044458 31 PMVLKSAIELDLLEVIAKAGPGAFMSPKQIASQL-PTKNSDAHILLDRILRLLASYSVLNCSLHTLPDGGVERLYGLAPV 109 (241)
Q Consensus 31 ~~~L~~a~~lglfd~L~~~~~~~~~t~~eLA~~~-g~~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~g~~~~~y~~t~~ 109 (241)
..+|.--.++.|++.|...+ ++.|+.||++.+ ++ +...+.|-|+.|...|++.........|..+..|+++..
T Consensus 5 ~~~La~p~R~~Il~~L~~~~--~~~ta~el~~~l~~i----s~aTvYrhL~~L~e~GLI~~~~~~~~~~~~ek~y~~~~~ 78 (178)
T PRK06474 5 AEILMHPVRMKICQVLMRNK--EGLTPLELVKILKDV----PQATLYRHLQTMVDSGILHVVKEKKVRSVSEKYYAINEE 78 (178)
T ss_pred HHhhCCHHHHHHHHHHHhCC--CCCCHHHHHHHhcCC----CHHHHHHHHHHHHHCCCEEEeecccccCceeEEEEeccc
Confidence 34566667888999998753 359999999999 57 777899999999999999975211012233457888876
Q ss_pred cccc
Q 044458 110 CKFL 113 (241)
Q Consensus 110 s~~l 113 (241)
+-.+
T Consensus 79 ~~~~ 82 (178)
T PRK06474 79 DAKI 82 (178)
T ss_pred eeee
Confidence 5443
No 204
>COG4190 Predicted transcriptional regulator [Transcription]
Probab=92.01 E-value=0.24 Score=37.81 Aligned_cols=54 Identities=24% Similarity=0.216 Sum_probs=45.8
Q ss_pred HHHHHHHHhcChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCcchHHHHHHHHhcCCccccc
Q 044458 31 PMVLKSAIELDLLEVIAKAGPGAFMSPKQIASQLPTKNSDAHILLDRILRLLASYSVLNCS 91 (241)
Q Consensus 31 ~~~L~~a~~lglfd~L~~~~~~~~~t~~eLA~~~g~~~~~~~~~l~rlLr~L~~~g~l~~~ 91 (241)
.+.+.+=-.+.|.+.|+.. +|.|+.|+|+..|- +...+.|-|+.|.-.|++...
T Consensus 58 la~vLsp~nleLl~~Ia~~---~P~Si~ElAe~vgR----dv~nvhr~Ls~l~~~GlI~fe 111 (144)
T COG4190 58 LARVLSPRNLELLELIAQE---EPASINELAELVGR----DVKNVHRTLSTLADLGLIFFE 111 (144)
T ss_pred HHHHhChhHHHHHHHHHhc---CcccHHHHHHHhCc----chHHHHHHHHHHHhcCeEEEe
Confidence 3444444667789999885 69999999999999 999999999999999999863
No 205
>COG1321 TroR Mn-dependent transcriptional regulator [Transcription]
Probab=91.95 E-value=0.25 Score=39.08 Aligned_cols=50 Identities=18% Similarity=0.203 Sum_probs=43.8
Q ss_pred CCCCHHHHHhhCCCCCCCCcchHHHHHHHHhcCCccccccccCCCCccccceecCccccccc
Q 044458 53 AFMSPKQIASQLPTKNSDAHILLDRILRLLASYSVLNCSLHTLPDGGVERLYGLAPVCKFLT 114 (241)
Q Consensus 53 ~~~t~~eLA~~~g~~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~g~~~~~y~~t~~s~~l~ 114 (241)
+++...+||+.+++ .+..+..+++-|...|+++.. + .+.+.+|+.++-+.
T Consensus 23 ~~~~~~diA~~L~V----sp~sVt~ml~rL~~~GlV~~~----~----y~gi~LT~~G~~~a 72 (154)
T COG1321 23 GFARTKDIAERLKV----SPPSVTEMLKRLERLGLVEYE----P----YGGVTLTEKGREKA 72 (154)
T ss_pred CcccHHHHHHHhCC----CcHHHHHHHHHHHHCCCeEEe----c----CCCeEEChhhHHHH
Confidence 78999999999999 999999999999999999985 2 57889998776443
No 206
>PF08279 HTH_11: HTH domain; InterPro: IPR013196 Winged helix DNA-binding proteins share a related winged helix-turn-helix DNA-binding motif, where the "wings", or loops, are small beta-sheets. The winged helix motif consists of two wings (W1, W2), three alpha helices (H1, H2, H3) and three beta-sheets (S1, S2, S3) arranged in the order H1-S1-H2-H3-S2-W1-S3-W2 []. The DNA-recognition helix makes sequence-specific DNA contacts with the major groove of DNA, while the wings make different DNA contacts, often with the minor groove or the backbone of DNA. Several winged-helix proteins display an exposed patch of hydrophobic residues thought to mediate protein-protein interactions. This entry represents a subset of the winged helix domain superfamily which is predominantly found in bacterial proteins, though there are also some archaeal and eukaryotic examples. This domain is commonly found in the biotin (vitamin H) repressor protein BirA which regulates transcription of the biotin operon []. It is also found in other proteins including regulators of amino acid biosynthsis such as LysM [], and regulators of carbohydrate metabolisms such as LicR and FrvR [, ].; PDB: 1HXD_B 2EWN_B 1BIA_A 1BIB_A 1J5Y_A 3V7S_A 3V7C_A 3RKW_A 3RIR_A 3RKX_A ....
Probab=91.93 E-value=0.25 Score=31.48 Aligned_cols=42 Identities=14% Similarity=0.330 Sum_probs=33.8
Q ss_pred ChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCcchHHHHHHHHhcCCcc
Q 044458 41 DLLEVIAKAGPGAFMSPKQIASQLPTKNSDAHILLDRILRLLASYSVL 88 (241)
Q Consensus 41 glfd~L~~~~~~~~~t~~eLA~~~g~~~~~~~~~l~rlLr~L~~~g~l 88 (241)
.|+..|.... +++|.++||+.+++ +.+.+++-+..|...|+.
T Consensus 4 ~il~~L~~~~--~~it~~eLa~~l~v----S~rTi~~~i~~L~~~~~~ 45 (55)
T PF08279_consen 4 QILKLLLESK--EPITAKELAEELGV----SRRTIRRDIKELREWGIP 45 (55)
T ss_dssp HHHHHHHHTT--TSBEHHHHHHHCTS-----HHHHHHHHHHHHHTT-E
T ss_pred HHHHHHHHcC--CCcCHHHHHHHhCC----CHHHHHHHHHHHHHCCCe
Confidence 4667774433 57999999999999 999999999999999933
No 207
>PF08461 HTH_12: Ribonuclease R winged-helix domain; InterPro: IPR013668 This domain is found at the amino terminus of Ribonuclease R and a number of presumed transcriptional regulatory proteins from archaea.
Probab=91.78 E-value=0.24 Score=33.31 Aligned_cols=60 Identities=17% Similarity=0.179 Sum_probs=43.5
Q ss_pred hHHHHHhcCCCCCCCHHHHHhhCCCC-CCCCcchHHHHHHHHhcCCccccccccCCCCccccceecCcccc
Q 044458 42 LLEVIAKAGPGAFMSPKQIASQLPTK-NSDAHILLDRILRLLASYSVLNCSLHTLPDGGVERLYGLAPVCK 111 (241)
Q Consensus 42 lfd~L~~~~~~~~~t~~eLA~~~g~~-~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~g~~~~~y~~t~~s~ 111 (241)
|+++|.+++ +|++..+|++.++.. ....+..++|.|+.|-..|++.+. | -+.+.+|+.+.
T Consensus 3 IL~~L~~~~--~P~g~~~l~~~L~~~g~~~se~avRrrLr~me~~Glt~~~------g--~~G~~iT~~G~ 63 (66)
T PF08461_consen 3 ILRILAESD--KPLGRKQLAEELKLRGEELSEEAVRRRLRAMERDGLTRKV------G--RQGRIITEKGL 63 (66)
T ss_pred HHHHHHHcC--CCCCHHHHHHHHHhcChhhhHHHHHHHHHHHHHCCCcccc------C--CcccccCHHHH
Confidence 567887764 799999999998652 111358899999999999977753 1 23446776553
No 208
>PF01596 Methyltransf_3: O-methyltransferase; InterPro: IPR002935 Members of this family are O-methyltransferases. The family includes also bacterial O-methyltransferases that may be involved in antibiotic production [].; GO: 0008171 O-methyltransferase activity; PDB: 1SUI_C 1SUS_D 3CBG_A 2GPY_B 3TR6_A 2AVD_A 3DUL_B 3DUW_B 2ZTH_A 1VID_A ....
Probab=91.50 E-value=0.13 Score=42.56 Aligned_cols=41 Identities=20% Similarity=0.199 Sum_probs=34.4
Q ss_pred CCCeEEEecCCchHHHHHHHHHCC-CCcEEEccc-hHHHhcCC
Q 044458 198 GLQSVVDVGGGIGASLDMIISKYP-SIKGINFDL-PHVIQDAP 238 (241)
Q Consensus 198 ~~~~vvDVGGG~G~~~~~l~~~~P-~l~~~v~Dl-P~vi~~a~ 238 (241)
+.++||+||++.|+-++.+++..| +.+.+.+|. |+-.+.|+
T Consensus 45 ~~k~vLEIGt~~GySal~la~~l~~~g~i~tiE~~~~~~~~A~ 87 (205)
T PF01596_consen 45 RPKRVLEIGTFTGYSALWLAEALPEDGKITTIEIDPERAEIAR 87 (205)
T ss_dssp T-SEEEEESTTTSHHHHHHHHTSTTTSEEEEEESSHHHHHHHH
T ss_pred CCceEEEeccccccHHHHHHHhhcccceEEEecCcHHHHHHHH
Confidence 479999999999999999999988 578999998 66666554
No 209
>PF08123 DOT1: Histone methylation protein DOT1 ; InterPro: IPR013110 The DOT1 domain regulates gene expression by methylating histone H3 []. H3 methylation by DOT1 has been shown to be required for the DNA damage checkpoint in yeast [].; GO: 0018024 histone-lysine N-methyltransferase activity; PDB: 4ER3_A 4ER6_A 4EQZ_A 1NW3_A 3UWP_A 4ER5_A 3QOX_A 3SX0_A 4ER7_A 3SR4_A ....
Probab=91.37 E-value=0.3 Score=40.45 Aligned_cols=48 Identities=17% Similarity=0.329 Sum_probs=31.0
Q ss_pred HHHHHhcCCCCCCCeEEEecCCchHHHHHHHHHCCCCcEEEccc-hHHHh
Q 044458 187 KKFLENYKGFEGLQSVVDVGGGIGASLDMIISKYPSIKGINFDL-PHVIQ 235 (241)
Q Consensus 187 ~~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-P~vi~ 235 (241)
..+++.++ ......++|||+|.|....+.+-.++=-+++.+++ |...+
T Consensus 32 ~~il~~~~-l~~~dvF~DlGSG~G~~v~~aal~~~~~~~~GIEi~~~~~~ 80 (205)
T PF08123_consen 32 SKILDELN-LTPDDVFYDLGSGVGNVVFQAALQTGCKKSVGIEILPELHD 80 (205)
T ss_dssp HHHHHHTT---TT-EEEEES-TTSHHHHHHHHHH--SEEEEEE-SHHHHH
T ss_pred HHHHHHhC-CCCCCEEEECCCCCCHHHHHHHHHcCCcEEEEEEechHHHH
Confidence 34556666 77778999999999999998887775334888887 44443
No 210
>TIGR02143 trmA_only tRNA (uracil-5-)-methyltransferase. This family consists exclusively of proteins believed to act as tRNA (uracil-5-)-methyltransferase. All members of far are proteobacterial. The seed alignment was taken directly from pfam05958 in Pfam 12.0, but higher cutoffs are used to select only functionally equivalent proteins. Homologous proteins excluded by the higher cutoff scores of this model include other uracil methyltransferases, such as RumA, active on rRNA.
Probab=91.26 E-value=0.17 Score=45.47 Aligned_cols=37 Identities=8% Similarity=0.160 Sum_probs=30.9
Q ss_pred CeEEEecCCchHHHHHHHHHCCCCcEEEccc-hHHHhcCC
Q 044458 200 QSVVDVGGGIGASLDMIISKYPSIKGINFDL-PHVIQDAP 238 (241)
Q Consensus 200 ~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-P~vi~~a~ 238 (241)
.+|||++||+|.++..+++... +++..|. ++.++.|+
T Consensus 199 ~~vlDl~~G~G~~sl~la~~~~--~v~~vE~~~~av~~a~ 236 (353)
T TIGR02143 199 GDLLELYCGNGNFSLALAQNFR--RVLATEIAKPSVNAAQ 236 (353)
T ss_pred CcEEEEeccccHHHHHHHHhCC--EEEEEECCHHHHHHHH
Confidence 4699999999999999998874 7888888 77777654
No 211
>PHA00738 putative HTH transcription regulator
Probab=91.25 E-value=0.31 Score=35.95 Aligned_cols=60 Identities=18% Similarity=0.211 Sum_probs=47.7
Q ss_pred HhcChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCcchHHHHHHHHhcCCccccccccCCCCccccceecCcc
Q 044458 38 IELDLLEVIAKAGPGAFMSPKQIASQLPTKNSDAHILLDRILRLLASYSVLNCSLHTLPDGGVERLYGLAPV 109 (241)
Q Consensus 38 ~~lglfd~L~~~~~~~~~t~~eLA~~~g~~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~g~~~~~y~~t~~ 109 (241)
.++.|++.|... ++.++.+|++.+++ ....+.+-|+.|...|++.... .|. .-.|++++.
T Consensus 13 tRr~IL~lL~~~---e~~~V~eLae~l~l----SQptVS~HLKvLreAGLV~srK----~Gr-~vyY~Ln~~ 72 (108)
T PHA00738 13 LRRKILELIAEN---YILSASLISHTLLL----SYTTVLRHLKILNEQGYIELYK----EGR-TLYAKIREN 72 (108)
T ss_pred HHHHHHHHHHHc---CCccHHHHHHhhCC----CHHHHHHHHHHHHHCCceEEEE----ECC-EEEEEECCC
Confidence 567788999873 47999999999999 9999999999999999998752 232 346666653
No 212
>PF09243 Rsm22: Mitochondrial small ribosomal subunit Rsm22; InterPro: IPR015324 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 [, ]. Rsm22 has been identified as a mitochondrial small ribosomal subunit [] and is a methyltransferase. In Schizosaccharomyces pombe (Fission yeast), Rsm22 is tandemly fused to Cox11 (a factor required for copper insertion into cytochrome oxidase) and the two proteins are proteolytically cleaved after import into the mitochondria []. This entry consists of mitochondrial Rsm22 and homologous sequences from bacteria.; GO: 0008168 methyltransferase activity, 0006412 translation
Probab=91.09 E-value=0.39 Score=41.54 Aligned_cols=48 Identities=27% Similarity=0.406 Sum_probs=35.0
Q ss_pred HHHHhcCCCCCCCeEEEecCCchHHHHHHHHHCCCCc-EEEccc-hHHHhc
Q 044458 188 KFLENYKGFEGLQSVVDVGGGIGASLDMIISKYPSIK-GINFDL-PHVIQD 236 (241)
Q Consensus 188 ~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~-~~v~Dl-P~vi~~ 236 (241)
.+....++| ..++|||+|+|.|...-++.+.+|++. .+.+|. +...+.
T Consensus 24 El~~r~p~f-~P~~vLD~GsGpGta~wAa~~~~~~~~~~~~vd~s~~~~~l 73 (274)
T PF09243_consen 24 ELRKRLPDF-RPRSVLDFGSGPGTALWAAREVWPSLKEYTCVDRSPEMLEL 73 (274)
T ss_pred HHHHhCcCC-CCceEEEecCChHHHHHHHHHHhcCceeeeeecCCHHHHHH
Confidence 333334423 357999999999999999999999765 688887 455443
No 213
>PRK11512 DNA-binding transcriptional repressor MarR; Provisional
Probab=91.09 E-value=1 Score=34.73 Aligned_cols=45 Identities=22% Similarity=0.217 Sum_probs=38.8
Q ss_pred cChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCcchHHHHHHHHhcCCccccc
Q 044458 40 LDLLEVIAKAGPGAFMSPKQIASQLPTKNSDAHILLDRILRLLASYSVLNCS 91 (241)
Q Consensus 40 lglfd~L~~~~~~~~~t~~eLA~~~g~~~~~~~~~l~rlLr~L~~~g~l~~~ 91 (241)
..|+-.|... +++|..|||+.+++ ++..+.++++.|...|++.+.
T Consensus 43 ~~vL~~l~~~---~~~t~~eLa~~l~i----~~~tvsr~l~~Le~~GlI~R~ 87 (144)
T PRK11512 43 FKVLCSIRCA---ACITPVELKKVLSV----DLGALTRMLDRLVCKGWVERL 87 (144)
T ss_pred HHHHHHHHHc---CCCCHHHHHHHHCC----CHHHHHHHHHHHHHCCCEEec
Confidence 3456667653 58999999999999 999999999999999999975
No 214
>PF04182 B-block_TFIIIC: B-block binding subunit of TFIIIC; InterPro: IPR007309 Yeast transcription factor IIIC (TFIIIC) is a multisubunit protein complex that interacts with two control elements of class III promoters called the A and B blocks. This family represents the subunit within TFIIIC involved in B-block binding []. Although defined as a yeast protein, it is also found in a number of other organisms.
Probab=90.99 E-value=0.24 Score=34.12 Aligned_cols=49 Identities=18% Similarity=0.116 Sum_probs=43.1
Q ss_pred HhcChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCcchHHHHHHHHhcCCccccc
Q 044458 38 IELDLLEVIAKAGPGAFMSPKQIASQLPTKNSDAHILLDRILRLLASYSVLNCS 91 (241)
Q Consensus 38 ~~lglfd~L~~~~~~~~~t~~eLA~~~g~~~~~~~~~l~rlLr~L~~~g~l~~~ 91 (241)
.+..+++.|+.+.. .+++-.||++.+|. |++.+...++.|...|++.+.
T Consensus 3 ~~~~~Le~I~rsR~-~Gi~q~~L~~~~~~----D~r~i~~~~k~L~~~gLI~k~ 51 (75)
T PF04182_consen 3 IQYCLLERIARSRY-NGITQSDLSKLLGI----DPRSIFYRLKKLEKKGLIVKQ 51 (75)
T ss_pred hHHHHHHHHHhcCC-CCEehhHHHHHhCC----CchHHHHHHHHHHHCCCEEEE
Confidence 46678889987653 67999999999999 999999999999999999874
No 215
>PF01726 LexA_DNA_bind: LexA DNA binding domain; InterPro: IPR006199 This is the DNA binding domain of the LexA SOS regulon repressor which prevents expression of DNA repair proteins in bacteria. The aligned region contains a variant form of the helix-turn-helix DNA binding motif []. This domain usually at the N terminus is found associated with IPR006198 from INTERPRO the auto-proteolytic domain of LexA 3.4.21.88 from EC.; GO: 0004252 serine-type endopeptidase activity, 0006508 proteolysis; PDB: 1LEA_A 1JHH_A 3JSP_A 1JHF_A 3JSO_B 1LEB_A 3K2Z_A.
Probab=90.96 E-value=0.27 Score=32.97 Aligned_cols=35 Identities=17% Similarity=0.121 Sum_probs=29.7
Q ss_pred CCCCHHHHHhhCCCCCCCC-cchHHHHHHHHhcCCccccc
Q 044458 53 AFMSPKQIASQLPTKNSDA-HILLDRILRLLASYSVLNCS 91 (241)
Q Consensus 53 ~~~t~~eLA~~~g~~~~~~-~~~l~rlLr~L~~~g~l~~~ 91 (241)
-|-|+.|||+.+|+ . +..+.+.|+.|...|++...
T Consensus 24 ~~Pt~rEIa~~~g~----~S~~tv~~~L~~Le~kG~I~r~ 59 (65)
T PF01726_consen 24 YPPTVREIAEALGL----KSTSTVQRHLKALERKGYIRRD 59 (65)
T ss_dssp S---HHHHHHHHTS----SSHHHHHHHHHHHHHTTSEEEG
T ss_pred CCCCHHHHHHHhCC----CChHHHHHHHHHHHHCcCccCC
Confidence 57899999999999 5 88999999999999999974
No 216
>cd00090 HTH_ARSR Arsenical Resistance Operon Repressor and similar prokaryotic, metal regulated homodimeric repressors. ARSR subfamily of helix-turn-helix bacterial transcription regulatory proteins (winged helix topology). Includes several proteins that appear to dissociate from DNA in the presence of metal ions.
Probab=90.95 E-value=0.34 Score=32.06 Aligned_cols=45 Identities=16% Similarity=0.300 Sum_probs=37.8
Q ss_pred hcChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCcchHHHHHHHHhcCCccccc
Q 044458 39 ELDLLEVIAKAGPGAFMSPKQIASQLPTKNSDAHILLDRILRLLASYSVLNCS 91 (241)
Q Consensus 39 ~lglfd~L~~~~~~~~~t~~eLA~~~g~~~~~~~~~l~rlLr~L~~~g~l~~~ 91 (241)
+..|+..|.. ++.+..||++.+++ +...+.+.|+.|...|++...
T Consensus 9 ~~~il~~l~~----~~~~~~ei~~~~~i----~~~~i~~~l~~L~~~g~i~~~ 53 (78)
T cd00090 9 RLRILRLLLE----GPLTVSELAERLGL----SQSTVSRHLKKLEEAGLVESR 53 (78)
T ss_pred HHHHHHHHHH----CCcCHHHHHHHHCc----CHhHHHHHHHHHHHCCCeEEE
Confidence 3446666666 34999999999999 999999999999999999864
No 217
>PF05401 NodS: Nodulation protein S (NodS); InterPro: IPR008715 This entry consists of nodulation S (NodS) proteins. The products of the rhizobial nodulation genes are involved in the biosynthesis of lipochitin oligosaccharides (LCOs), which are host-specific signal molecules required for nodule formation. NodS is an S-adenosyl-L-methionine (SAM)-dependent methyltransferase involved in N methylation of LCOs. NodS uses N-deacetylated chitooligosaccharides, the products of the NodBC proteins, as its methyl acceptors [].; GO: 0008757 S-adenosylmethionine-dependent methyltransferase activity, 0009312 oligosaccharide biosynthetic process, 0009877 nodulation; PDB: 3OFK_D 3OFJ_A.
Probab=90.81 E-value=0.13 Score=42.32 Aligned_cols=44 Identities=16% Similarity=0.322 Sum_probs=34.3
Q ss_pred hcCCCCCCCeEEEecCCchHHHHHHHHHCCCCcEEEccc-hHHHhcCC
Q 044458 192 NYKGFEGLQSVVDVGGGIGASLDMIISKYPSIKGINFDL-PHVIQDAP 238 (241)
Q Consensus 192 ~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-P~vi~~a~ 238 (241)
.++ -..+.++++||||.|.+...|+.+.- +.++.|. |.+++.|+
T Consensus 38 aLp-~~ry~~alEvGCs~G~lT~~LA~rCd--~LlavDis~~Al~~Ar 82 (201)
T PF05401_consen 38 ALP-RRRYRRALEVGCSIGVLTERLAPRCD--RLLAVDISPRALARAR 82 (201)
T ss_dssp HHT-TSSEEEEEEE--TTSHHHHHHGGGEE--EEEEEES-HHHHHHHH
T ss_pred hcC-ccccceeEecCCCccHHHHHHHHhhC--ceEEEeCCHHHHHHHH
Confidence 455 56678999999999999999998863 4688899 88888765
No 218
>PRK14903 16S rRNA methyltransferase B; Provisional
Probab=90.79 E-value=0.3 Score=45.10 Aligned_cols=64 Identities=16% Similarity=0.093 Sum_probs=43.4
Q ss_pred HHHHHHHhcchhhHHHHHHhcCCCCCCCeEEEecCCchHHHHHHHHHC-CCCcEEEccc-hHHHhcC
Q 044458 173 IFNNGMFSHSTITMKKFLENYKGFEGLQSVVDVGGGIGASLDMIISKY-PSIKGINFDL-PHVIQDA 237 (241)
Q Consensus 173 ~f~~aM~~~~~~~~~~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~-P~l~~~v~Dl-P~vi~~a 237 (241)
.|..+.-.........+....+ .....+|+|+|+|+|..+..+++.. +.-+++..|+ +..++.+
T Consensus 213 ~~~~G~~~~Qd~~s~~~~~~l~-~~~g~~VLD~cagpGgkt~~la~~~~~~g~V~a~Dis~~rl~~~ 278 (431)
T PRK14903 213 VIKDGLATVQGESSQIVPLLME-LEPGLRVLDTCAAPGGKTTAIAELMKDQGKILAVDISREKIQLV 278 (431)
T ss_pred HHHCCeEEEECHHHHHHHHHhC-CCCCCEEEEeCCCccHHHHHHHHHcCCCCEEEEEECCHHHHHHH
Confidence 4544443334433333344444 5556899999999999999999986 4568899999 6665544
No 219
>KOG2361 consensus Predicted methyltransferase [General function prediction only]
Probab=90.77 E-value=0.21 Score=42.30 Aligned_cols=41 Identities=22% Similarity=0.476 Sum_probs=36.2
Q ss_pred CeEEEecCCchHHHHHHHHHCCC--CcEEEccc-hHHHhcCCCC
Q 044458 200 QSVVDVGGGIGASLDMIISKYPS--IKGINFDL-PHVIQDAPAY 240 (241)
Q Consensus 200 ~~vvDVGGG~G~~~~~l~~~~P~--l~~~v~Dl-P~vi~~a~~~ 240 (241)
.+|+.||||.|....-+++.+|+ ++....|. |.+|+.-+++
T Consensus 73 ~~ilEvGCGvGNtvfPll~~~~n~~l~v~acDfsp~Ai~~vk~~ 116 (264)
T KOG2361|consen 73 ETILEVGCGVGNTVFPLLKTSPNNRLKVYACDFSPRAIELVKKS 116 (264)
T ss_pred hhheeeccCCCcccchhhhcCCCCCeEEEEcCCChHHHHHHHhc
Confidence 38999999999999999999999 99999999 8888776543
No 220
>PF06163 DUF977: Bacterial protein of unknown function (DUF977); InterPro: IPR010382 This entry consists of several hypothetical bacterial proteins of unknown function.
Probab=90.72 E-value=0.42 Score=36.22 Aligned_cols=50 Identities=16% Similarity=0.248 Sum_probs=43.9
Q ss_pred HHHHhcChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCcchHHHHHHHHhcCCccccc
Q 044458 35 KSAIELDLLEVIAKAGPGAFMSPKQIASQLPTKNSDAHILLDRILRLLASYSVLNCS 91 (241)
Q Consensus 35 ~~a~~lglfd~L~~~~~~~~~t~~eLA~~~g~~~~~~~~~l~rlLr~L~~~g~l~~~ 91 (241)
+..+...|.+.+.+. |.+|..|++..+|+ +-..+++.++.|++.|-|..+
T Consensus 10 r~eLk~rIvElVRe~---GRiTi~ql~~~TGa----sR~Tvk~~lreLVa~G~l~~~ 59 (127)
T PF06163_consen 10 REELKARIVELVREH---GRITIKQLVAKTGA----SRNTVKRYLRELVARGDLYRH 59 (127)
T ss_pred HHHHHHHHHHHHHHc---CCccHHHHHHHHCC----CHHHHHHHHHHHHHcCCeEeC
Confidence 345677788999886 69999999999999 999999999999999988863
No 221
>PTZ00146 fibrillarin; Provisional
Probab=90.70 E-value=0.42 Score=41.78 Aligned_cols=36 Identities=8% Similarity=0.077 Sum_probs=29.6
Q ss_pred CCCCCeEEEecCCchHHHHHHHHHCC-CCcEEEccch
Q 044458 196 FEGLQSVVDVGGGIGASLDMIISKYP-SIKGINFDLP 231 (241)
Q Consensus 196 ~~~~~~vvDVGGG~G~~~~~l~~~~P-~l~~~v~DlP 231 (241)
+..-.+|||+|||+|.++..+++... .=+++.+|+-
T Consensus 130 IkpG~~VLDLGaG~G~~t~~lAdiVG~~G~VyAVD~s 166 (293)
T PTZ00146 130 IKPGSKVLYLGAASGTTVSHVSDLVGPEGVVYAVEFS 166 (293)
T ss_pred cCCCCEEEEeCCcCCHHHHHHHHHhCCCCEEEEEECc
Confidence 55668999999999999999999874 4467888873
No 222
>COG4189 Predicted transcriptional regulator [Transcription]
Probab=90.54 E-value=0.44 Score=40.06 Aligned_cols=55 Identities=13% Similarity=0.270 Sum_probs=49.1
Q ss_pred HHHHHHHHHhcChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCcchHHHHHHHHhcCCccccc
Q 044458 30 LPMVLKSAIELDLLEVIAKAGPGAFMSPKQIASQLPTKNSDAHILLDRILRLLASYSVLNCS 91 (241)
Q Consensus 30 ~~~~L~~a~~lglfd~L~~~~~~~~~t~~eLA~~~g~~~~~~~~~l~rlLr~L~~~g~l~~~ 91 (241)
..++|...++..|.+.|... +|+.+.|||+++|+ +...+..=+..|...|++.-.
T Consensus 16 v~kalaS~vRv~Il~lL~~k---~plNvneiAe~lgL----pqst~s~~ik~Le~aGlirT~ 70 (308)
T COG4189 16 VLKALASKVRVAILQLLHRK---GPLNVNEIAEALGL----PQSTMSANIKVLEKAGLIRTE 70 (308)
T ss_pred HHHHHHHHHHHHHHHHHHHh---CCCCHHHHHHHhCC----chhhhhhhHHHHHhcCceeee
Confidence 45788899999999999986 69999999999999 888889999999999999743
No 223
>PF02002 TFIIE_alpha: TFIIE alpha subunit; InterPro: IPR024550 The general transcription factor TFIIE has an essential role in eukaryotic transcription initiation, together with RNA polymerase II and other general factors. Human TFIIE consists of two subunits, TFIIE-alpha and TFIIE-beta, and joins the preinitiation complex after RNA polymerase II and TFIIF []. This entry represents a helix-turn-helix (HTH) domain found in eukaryotic TFIIE-alpha []. It is also found in proteins from archaebacteria that are presumed to be TFIIE-alpha subunits [], the transcriptional regulator SarR, and also DNA-directed RNA polymerase III subunit Rpc3.; PDB: 1VD4_A 1Q1H_A.
Probab=90.54 E-value=0.22 Score=36.52 Aligned_cols=43 Identities=14% Similarity=0.227 Sum_probs=33.3
Q ss_pred hHHHHHhcCCCCCCCHHHHHhhCCCCCCCCcchHHHHHHHHhcCCccccc
Q 044458 42 LLEVIAKAGPGAFMSPKQIASQLPTKNSDAHILLDRILRLLASYSVLNCS 91 (241)
Q Consensus 42 lfd~L~~~~~~~~~t~~eLA~~~g~~~~~~~~~l~rlLr~L~~~g~l~~~ 91 (241)
|+++|... +.++-++||+.+++ +...++++|..|...|++...
T Consensus 18 Il~~L~~~---~~l~de~la~~~~l----~~~~vRkiL~~L~~~~lv~~~ 60 (105)
T PF02002_consen 18 ILDALLRK---GELTDEDLAKKLGL----KPKEVRKILYKLYEDGLVSYR 60 (105)
T ss_dssp HHHHHHHH-----B-HHHHHHTT-S-----HHHHHHHHHHHHHHSS-EEE
T ss_pred HHHHHHHc---CCcCHHHHHHHhCC----CHHHHHHHHHHHHHCCCeEEE
Confidence 68888764 58999999999999 999999999999999999753
No 224
>PF08784 RPA_C: Replication protein A C terminal; InterPro: IPR014892 This protein corresponds to the C-terminal of the single stranded DNA binding protein RPA (replication protein A). RPA is involved in many DNA metabolic pathways including DNA replication, DNA repair, recombination, cell cycle and DNA damage checkpoints. ; PDB: 1QUQ_C 2PQA_C 3KDF_B 2Z6K_B 2PI2_B 1L1O_E 1DPU_A 1Z1D_A.
Probab=90.54 E-value=0.24 Score=36.05 Aligned_cols=49 Identities=16% Similarity=0.200 Sum_probs=38.9
Q ss_pred HhcChHHHHHh-cCCCCCCCHHHHHhhCCCCCCCCcchHHHHHHHHhcCCcccc
Q 044458 38 IELDLLEVIAK-AGPGAFMSPKQIASQLPTKNSDAHILLDRILRLLASYSVLNC 90 (241)
Q Consensus 38 ~~lglfd~L~~-~~~~~~~t~~eLA~~~g~~~~~~~~~l~rlLr~L~~~g~l~~ 90 (241)
+.-.|++.|.. ...+.++++++|++++++ ++..++..++.|...|++--
T Consensus 48 ~~~~Vl~~i~~~~~~~~Gv~v~~I~~~l~~----~~~~v~~al~~L~~eG~IYs 97 (102)
T PF08784_consen 48 LQDKVLNFIKQQPNSEEGVHVDEIAQQLGM----SENEVRKALDFLSNEGHIYS 97 (102)
T ss_dssp HHHHHHHHHHC----TTTEEHHHHHHHSTS-----HHHHHHHHHHHHHTTSEEE
T ss_pred HHHHHHHHHHhcCCCCCcccHHHHHHHhCc----CHHHHHHHHHHHHhCCeEec
Confidence 45567788876 222367999999999999 99999999999999998864
No 225
>PF05185 PRMT5: PRMT5 arginine-N-methyltransferase; InterPro: IPR007857 The human homologue of Saccharomyces cerevisiae Skb1 (Shk1 kinase-binding protein 1) is a protein methyltransferase []. These proteins seem to play a role in Jak signalling.; GO: 0008168 methyltransferase activity, 0005737 cytoplasm; PDB: 2Y1W_C 2Y1X_D 2V7E_B 2V74_H 3R0Q_G 3B3F_B 3B3J_A 3B3G_A 3UA3_A 3UA4_B ....
Probab=90.51 E-value=0.44 Score=44.20 Aligned_cols=67 Identities=15% Similarity=0.129 Sum_probs=39.0
Q ss_pred cccccccCchHHHHHHHHHHhcchhhHHHHHHhcCCCCCCCeEEEecCCchHHHHHHHHHC----CCCcEEEccc
Q 044458 160 AFDYHGKDLRLNKIFNNGMFSHSTITMKKFLENYKGFEGLQSVVDVGGGIGASLDMIISKY----PSIKGINFDL 230 (241)
Q Consensus 160 ~~e~~~~~~~~~~~f~~aM~~~~~~~~~~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~----P~l~~~v~Dl 230 (241)
.||.+++|+..-+.|.+|+.. .. ......-..-.+.+.|+|||+|+|-++...+++- -..++...+-
T Consensus 152 tYe~fE~D~vKY~~Ye~AI~~---al-~D~~~~~~~~~~~~vVldVGAGrGpL~~~al~A~~~~~~a~~VyAVEk 222 (448)
T PF05185_consen 152 TYEVFEKDPVKYDQYERAIEE---AL-KDRVRKNSYSSKDKVVLDVGAGRGPLSMFALQAGARAGGAVKVYAVEK 222 (448)
T ss_dssp HHHHHCC-HHHHHHHHHHHHH---HH-HHHHTTS-SEETT-EEEEES-TTSHHHHHHHHTTHHHCCESEEEEEES
T ss_pred cHhhHhcCHHHHHHHHHHHHH---HH-HhhhhhccccccceEEEEeCCCccHHHHHHHHHHHHhCCCeEEEEEcC
Confidence 477778888877777777622 11 1222221100135899999999999997776654 3455666554
No 226
>PF00325 Crp: Bacterial regulatory proteins, crp family; InterPro: IPR001808 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. This family groups together a range of proteins, including anr, crp, clp, cysR, fixK, flp, fnr, fnrN, hlyX and ntcA [, ]. Within this family, the HTH motif is situated towards the C terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 2OZ6_A 1CGP_B 2GZW_C 1O3T_B 3ROU_A 2CGP_A 3RDI_A 1I5Z_A 3IYD_H 3FWE_B ....
Probab=90.28 E-value=0.21 Score=28.62 Aligned_cols=31 Identities=26% Similarity=0.321 Sum_probs=25.6
Q ss_pred CCCHHHHHhhCCCCCCCCcchHHHHHHHHhcCCcc
Q 044458 54 FMSPKQIASQLPTKNSDAHILLDRILRLLASYSVL 88 (241)
Q Consensus 54 ~~t~~eLA~~~g~~~~~~~~~l~rlLr~L~~~g~l 88 (241)
++|-.|||+.+|+ ..+-+.|+|..|...|++
T Consensus 2 ~mtr~diA~~lG~----t~ETVSR~l~~l~~~glI 32 (32)
T PF00325_consen 2 PMTRQDIADYLGL----TRETVSRILKKLERQGLI 32 (32)
T ss_dssp E--HHHHHHHHTS-----HHHHHHHHHHHHHTTSE
T ss_pred CcCHHHHHHHhCC----cHHHHHHHHHHHHHcCCC
Confidence 4788999999999 999999999999988874
No 227
>PRK05031 tRNA (uracil-5-)-methyltransferase; Validated
Probab=90.28 E-value=0.23 Score=44.77 Aligned_cols=37 Identities=8% Similarity=0.155 Sum_probs=30.7
Q ss_pred CeEEEecCCchHHHHHHHHHCCCCcEEEccc-hHHHhcCC
Q 044458 200 QSVVDVGGGIGASLDMIISKYPSIKGINFDL-PHVIQDAP 238 (241)
Q Consensus 200 ~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-P~vi~~a~ 238 (241)
.+|+|++||+|.++..+++... +++..|. +..++.++
T Consensus 208 ~~vLDl~~G~G~~sl~la~~~~--~v~~vE~~~~ai~~a~ 245 (362)
T PRK05031 208 GDLLELYCGNGNFTLALARNFR--RVLATEISKPSVAAAQ 245 (362)
T ss_pred CeEEEEeccccHHHHHHHhhCC--EEEEEECCHHHHHHHH
Confidence 5799999999999999998865 6788888 67776654
No 228
>cd07153 Fur_like Ferric uptake regulator(Fur) and related metalloregulatory proteins; typically iron-dependent, DNA-binding repressors and activators. Ferric uptake regulator (Fur) and related metalloregulatory proteins are iron-dependent, DNA-binding repressors and activators mainly involved in iron metabolism. A general model for Fur repression under iron-rich conditions is that activated Fur (a dimer having one Fe2+ coordinated per monomer) binds to specific DNA sequences (Fur boxes) in the promoter region of iron-responsive genes, hindering access of RNA polymerase, and repressing transcription. Positive regulation by Fur can be direct or indirect, as in the Fur repression of an anti-sense regulatory small RNA. Some members sense metal ions other than Fe2+. For example, the zinc uptake regulator (Zur) responds to Zn2+, the manganese uptake regulator (Mur) responds to Mn2+, and the nickel uptake regulator (Nur) responds to Ni2+. Other members sense signals other than metal ions.
Probab=89.78 E-value=0.43 Score=35.33 Aligned_cols=50 Identities=24% Similarity=0.314 Sum_probs=39.5
Q ss_pred cChHHHHHhcCCCCCCCHHHHHhhCCCC-CCCCcchHHHHHHHHhcCCccccc
Q 044458 40 LDLLEVIAKAGPGAFMSPKQIASQLPTK-NSDAHILLDRILRLLASYSVLNCS 91 (241)
Q Consensus 40 lglfd~L~~~~~~~~~t~~eLA~~~g~~-~~~~~~~l~rlLr~L~~~g~l~~~ 91 (241)
.-|++.|...+ ++.|++||.+.+.-. +.++..-+.|.|+.|...|++.+.
T Consensus 4 ~~Il~~l~~~~--~~~sa~ei~~~l~~~~~~i~~~TVYR~L~~L~~~Gli~~~ 54 (116)
T cd07153 4 LAILEVLLESD--GHLTAEEIYERLRKKGPSISLATVYRTLELLEEAGLVREI 54 (116)
T ss_pred HHHHHHHHhCC--CCCCHHHHHHHHHhcCCCCCHHHHHHHHHHHHhCCCEEEE
Confidence 45788887753 689999999998421 112788899999999999999975
No 229
>COG0357 GidB Predicted S-adenosylmethionine-dependent methyltransferase involved in bacterial cell division [Cell envelope biogenesis, outer membrane]
Probab=89.53 E-value=0.31 Score=40.71 Aligned_cols=32 Identities=22% Similarity=0.363 Sum_probs=30.0
Q ss_pred CCeEEEecCCchHHHHHHHHHCCCCcEEEccc
Q 044458 199 LQSVVDVGGGIGASLDMIISKYPSIKGINFDL 230 (241)
Q Consensus 199 ~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl 230 (241)
..+++|||.|.|.=++-++=.+|+++++++|-
T Consensus 68 ~~~~~DIGSGaGfPGipLAI~~p~~~vtLles 99 (215)
T COG0357 68 AKRVLDIGSGAGFPGIPLAIAFPDLKVTLLES 99 (215)
T ss_pred CCEEEEeCCCCCCchhhHHHhccCCcEEEEcc
Confidence 58999999999999999999999999999884
No 230
>PRK14901 16S rRNA methyltransferase B; Provisional
Probab=89.50 E-value=0.39 Score=44.35 Aligned_cols=50 Identities=8% Similarity=-0.046 Sum_probs=37.2
Q ss_pred HHHHHhcCCCCCCCeEEEecCCchHHHHHHHHHCC-CCcEEEccc-hHHHhcC
Q 044458 187 KKFLENYKGFEGLQSVVDVGGGIGASLDMIISKYP-SIKGINFDL-PHVIQDA 237 (241)
Q Consensus 187 ~~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P-~l~~~v~Dl-P~vi~~a 237 (241)
..++..++ .....+|+|+|||+|..+..+++... .-+++.+|. ++.++.+
T Consensus 242 ~l~~~~l~-~~~g~~VLDl~ag~G~kt~~la~~~~~~g~v~a~D~~~~rl~~~ 293 (434)
T PRK14901 242 QLVAPLLD-PQPGEVILDACAAPGGKTTHIAELMGDQGEIWAVDRSASRLKKL 293 (434)
T ss_pred HHHHHHhC-CCCcCEEEEeCCCCchhHHHHHHHhCCCceEEEEcCCHHHHHHH
Confidence 33444455 45568999999999999999999864 457899998 6555544
No 231
>TIGR00446 nop2p NOL1/NOP2/sun family putative RNA methylase.
Probab=89.43 E-value=0.51 Score=40.51 Aligned_cols=42 Identities=10% Similarity=0.019 Sum_probs=33.2
Q ss_pred CCCCCeEEEecCCchHHHHHHHHHCCC-CcEEEccc-hHHHhcC
Q 044458 196 FEGLQSVVDVGGGIGASLDMIISKYPS-IKGINFDL-PHVIQDA 237 (241)
Q Consensus 196 ~~~~~~vvDVGGG~G~~~~~l~~~~P~-l~~~v~Dl-P~vi~~a 237 (241)
-....+|+|+|+|+|..+..+++...+ -+++..|+ +..++.+
T Consensus 69 ~~~g~~VLDl~ag~G~kt~~la~~~~~~g~v~a~D~~~~~l~~~ 112 (264)
T TIGR00446 69 PDPPERVLDMAAAPGGKTTQISALMKNEGAIVANEFSKSRTKVL 112 (264)
T ss_pred CCCcCEEEEECCCchHHHHHHHHHcCCCCEEEEEcCCHHHHHHH
Confidence 344579999999999999999998754 47888998 6655543
No 232
>PF01325 Fe_dep_repress: Iron dependent repressor, N-terminal DNA binding domain; InterPro: IPR022687 The DtxR-type HTH domain is a DNA-binding, winged helix-turn-helix (wHTH) domain of about 65 residues present in metalloregulators of the DtxR/MntR family. The family is named after Corynebacterium diphtheriae DtxR, an iron-specific diphtheria toxin repressor, and Bacillus subtilis MntR, a manganese transport regulator. Iron-responsive metalloregulators such as DtxR and IdeR occur in Gram-positive bacteria of the high GC branch, while manganese-responsive metalloregulators like MntR are described in diverse genera of Gram-positive and Gram-negative bacteria and also in Archaea [].The metalloregulators like DtxR/MntR contain the DNA-binding DtxR-type HTH domain usually in the N-terminal part. The C-terminal part contains a dimerisation domain with two metal-binding sites, although the primary metal-binding site is less conserved in the Mn(II)-regulators. Fe(II)-regulated proteins contain an SH3-like domain as a C-terminal extension, which is absent in Mn(II)-regulated MntR [, ]. Metal-ion dependent regulators orchestrate the virulence of several important human pathogens. The DtxR protein regulates the expression of diphtheria toxinin response to environmental iron concentrations. Furthermore, DtxR and IdeR control iron uptake []. Homeostasis of manganese, which is an essential nutrient, is regulated by MntR. A typical DtxR-type metalloregulator binds two divalent metal effectors per monomer, upon which allosteric changes occur that moderate binding to the cognate DNA operators. Iron-bound DtxR homodimers bind to an interrupted palindrome of 19 bp, protecting a sequence of ~30 bp. The crystal structures of iron-regulated and manganese-regulated repressors show that the DNA binding domain contains three alpha-helices and a pair of antiparallel beta-strands. Helices 2 and 3 comprise the helix-turn-helix motif and the beta-strands are called the wing []. This wHTH topology is similar to the lysR-type HTH (see PDOC00043 from PROSITEDOC). Most DtxR-type metalloregulators bind as dimers to the DNA major groove. Several proteins are known to contain a DtxR-type HTH domain. These include- Corynebacterium diphtheriae DtxR, a diphtheria toxin repressor [], which regulates the expression of the high-affinity iron uptake system, other iron-sensitive genes, and the bacteriophage tox gene. Metal-bound DtxR represses transcription by binding the tox operator; if iron is limiting, conformational changes of the wHTH disrupt DNA-binding and the diphtheria toxin is produced. Mycobacterium tuberculosis IdeR, an iron-dependent regulator that is essential for this pathogen. The regulator represses genes for iron acquisition and activates iron storage genes, and is a positive regulator of oxidative stress responses []. Bacillus subtilis MntR, a manganese transport regulator, binds Mn2+ as an effector and is a transcriptional repressor of transporters for the import of manganese. Treponema pallidum troR, a metal-dependent transcriptional repressor. Archaeoglobus fulgidus MDR1 (troR), a metal-dependent transcriptional repressor, which negatively regulates its own transcription. This entry covers the entire DtxR-type HTH domain.; GO: 0005506 iron ion binding; PDB: 3HRT_B 3HRS_A 3HRU_B 2X4H_D 1ON1_B 2HYF_C 2F5E_A 3R60_B 1ON2_B 2F5F_A ....
Probab=89.43 E-value=0.39 Score=31.61 Aligned_cols=35 Identities=20% Similarity=0.261 Sum_probs=32.3
Q ss_pred CCCCHHHHHhhCCCCCCCCcchHHHHHHHHhcCCccccc
Q 044458 53 AFMSPKQIASQLPTKNSDAHILLDRILRLLASYSVLNCS 91 (241)
Q Consensus 53 ~~~t~~eLA~~~g~~~~~~~~~l~rlLr~L~~~g~l~~~ 91 (241)
++++..+||+.+++ .+..+..+++-|...|+++..
T Consensus 21 ~~v~~~~iA~~L~v----s~~tvt~ml~~L~~~GlV~~~ 55 (60)
T PF01325_consen 21 GPVRTKDIAERLGV----SPPTVTEMLKRLAEKGLVEYE 55 (60)
T ss_dssp SSBBHHHHHHHHTS-----HHHHHHHHHHHHHTTSEEEE
T ss_pred CCccHHHHHHHHCC----ChHHHHHHHHHHHHCCCEEec
Confidence 79999999999999 999999999999999999874
No 233
>PRK14904 16S rRNA methyltransferase B; Provisional
Probab=89.41 E-value=0.39 Score=44.43 Aligned_cols=43 Identities=12% Similarity=0.097 Sum_probs=33.4
Q ss_pred CCCCCeEEEecCCchHHHHHHHHHCC-CCcEEEccc-hHHHhcCC
Q 044458 196 FEGLQSVVDVGGGIGASLDMIISKYP-SIKGINFDL-PHVIQDAP 238 (241)
Q Consensus 196 ~~~~~~vvDVGGG~G~~~~~l~~~~P-~l~~~v~Dl-P~vi~~a~ 238 (241)
.....+|+|+|||+|..+..+++..+ .-+++.+|+ ++.++.++
T Consensus 248 ~~~g~~VLDlgaG~G~kt~~la~~~~~~~~V~avD~s~~~l~~~~ 292 (445)
T PRK14904 248 PQPGSTVLDLCAAPGGKSTFMAELMQNRGQITAVDRYPQKLEKIR 292 (445)
T ss_pred CCCCCEEEEECCCCCHHHHHHHHHhCCCcEEEEEECCHHHHHHHH
Confidence 44458999999999999999888764 457899999 66665543
No 234
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=89.39 E-value=0.49 Score=37.14 Aligned_cols=46 Identities=11% Similarity=0.153 Sum_probs=41.8
Q ss_pred HhcChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCcchHHHHHHHHhcCCcccc
Q 044458 38 IELDLLEVIAKAGPGAFMSPKQIASQLPTKNSDAHILLDRILRLLASYSVLNC 90 (241)
Q Consensus 38 ~~lglfd~L~~~~~~~~~t~~eLA~~~g~~~~~~~~~l~rlLr~L~~~g~l~~ 90 (241)
.+..|.++|..+ +..|..+||+++|+ ++..+++=++-|...|++..
T Consensus 10 ~D~~Il~~Lq~d---~R~s~~eiA~~lgl----S~~tV~~Ri~rL~~~GvI~~ 55 (153)
T PRK11179 10 LDRGILEALMEN---ARTPYAELAKQFGV----SPGTIHVRVEKMKQAGIITG 55 (153)
T ss_pred HHHHHHHHHHHc---CCCCHHHHHHHHCc----CHHHHHHHHHHHHHCCCeee
Confidence 577899999885 68999999999999 99999999999999999974
No 235
>PF02527 GidB: rRNA small subunit methyltransferase G; InterPro: IPR003682 This entry represents a rRNA small subunit methyltransferase G. Previously identified as a glucose-inhibited division protein B that appears to be present and in a single copy in all complete eubacterial genomes so far sequenced. Specifically methylates the N7 position of a guanosine in 16S rRNA [, , ].; GO: 0008649 rRNA methyltransferase activity, 0006364 rRNA processing, 0005737 cytoplasm; PDB: 1XDZ_A 3G88_A 3G8A_B 3G89_B 3G8B_B 1JSX_A.
Probab=89.39 E-value=0.34 Score=39.42 Aligned_cols=30 Identities=20% Similarity=0.270 Sum_probs=27.6
Q ss_pred eEEEecCCchHHHHHHHHHCCCCcEEEccc
Q 044458 201 SVVDVGGGIGASLDMIISKYPSIKGINFDL 230 (241)
Q Consensus 201 ~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl 230 (241)
+++|||.|.|.=++-++=.+|+++++++|-
T Consensus 51 ~~lDiGSGaGfPGipLaI~~p~~~~~LvEs 80 (184)
T PF02527_consen 51 KVLDIGSGAGFPGIPLAIARPDLQVTLVES 80 (184)
T ss_dssp EEEEETSTTTTTHHHHHHH-TTSEEEEEES
T ss_pred eEEecCCCCCChhHHHHHhCCCCcEEEEeC
Confidence 899999999999999999999999999885
No 236
>TIGR01610 phage_O_Nterm phage replication protein O, N-terminal domain. This model represents the N-terminal region of the phage lambda replication protein O and homologous regions of other phage proteins.
Probab=89.21 E-value=0.48 Score=34.16 Aligned_cols=44 Identities=11% Similarity=0.089 Sum_probs=37.8
Q ss_pred CCCCHHHHHhhCCCCCCCCcchHHHHHHHHhcCCccccccccCCCCccccceecC
Q 044458 53 AFMSPKQIASQLPTKNSDAHILLDRILRLLASYSVLNCSLHTLPDGGVERLYGLA 107 (241)
Q Consensus 53 ~~~t~~eLA~~~g~~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~g~~~~~y~~t 107 (241)
.++|-.|||+.+|+ +...+.|.|..|...|++... .| -+.|+.|
T Consensus 46 ~~is~~eLa~~~g~----sr~tVsr~L~~Le~~GlI~r~-----~~--~~~~~~n 89 (95)
T TIGR01610 46 DRVTATVIAELTGL----SRTHVSDAIKSLARRRIIFRQ-----GM--MGIVGVN 89 (95)
T ss_pred CccCHHHHHHHHCc----CHHHHHHHHHHHHHCCCeeee-----cC--CceeecC
Confidence 58999999999999 999999999999999999864 12 3677766
No 237
>PLN02476 O-methyltransferase
Probab=89.08 E-value=0.36 Score=41.93 Aligned_cols=44 Identities=18% Similarity=0.118 Sum_probs=36.1
Q ss_pred CCCCCeEEEecCCchHHHHHHHHHCC-CCcEEEccc-hHHHhcCCC
Q 044458 196 FEGLQSVVDVGGGIGASLDMIISKYP-SIKGINFDL-PHVIQDAPA 239 (241)
Q Consensus 196 ~~~~~~vvDVGGG~G~~~~~l~~~~P-~l~~~v~Dl-P~vi~~a~~ 239 (241)
..+.++||+||.+.|..++.+++.-| +-+.+-+|. |+..+.|++
T Consensus 116 ~~~ak~VLEIGT~tGySal~lA~al~~~G~V~TiE~d~e~~~~Ar~ 161 (278)
T PLN02476 116 ILGAERCIEVGVYTGYSSLAVALVLPESGCLVACERDSNSLEVAKR 161 (278)
T ss_pred hcCCCeEEEecCCCCHHHHHHHHhCCCCCEEEEEECCHHHHHHHHH
Confidence 45689999999999999999999876 557888998 666666643
No 238
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=89.06 E-value=0.5 Score=30.07 Aligned_cols=35 Identities=17% Similarity=0.229 Sum_probs=31.7
Q ss_pred CCC-CHHHHHhhCCCCCCCCcchHHHHHHHHhcCCccccc
Q 044458 53 AFM-SPKQIASQLPTKNSDAHILLDRILRLLASYSVLNCS 91 (241)
Q Consensus 53 ~~~-t~~eLA~~~g~~~~~~~~~l~rlLr~L~~~g~l~~~ 91 (241)
..+ |..|||+.+++ +...+++.|+.|...|++...
T Consensus 18 ~~l~s~~~la~~~~v----s~~tv~~~l~~L~~~g~i~~~ 53 (60)
T smart00345 18 DKLPSERELAAQLGV----SRTTVREALSRLEAEGLVQRR 53 (60)
T ss_pred CcCcCHHHHHHHHCC----CHHHHHHHHHHHHHCCCEEEe
Confidence 356 89999999999 999999999999999999764
No 239
>PF03444 HrcA_DNA-bdg: Winged helix-turn-helix transcription repressor, HrcA DNA-binding; InterPro: IPR005104 Prokaryotic cells have a defence mechanism against a sudden heat-shock stress. Commonly, they induce a set of proteins that protect cellular proteins from being denatured by heat. Among such proteins are the GroE and DnaK chaperones whose transcription is regulated by a heat-shock repressor protein HrcA. HrcA is a winged helix-turn-helix repressor that negatively regulates the transcription of dnaK and groE operons by binding the upstream CIRCE (controlling inverted repeat of chaperone expression) element. In Bacillus subtilis this element is a perfect 9 base pair inverted repeat separated by a 9 base pair spacer. The crystal structure of a heat-inducible transcriptional repressor, HrcA, from Thermotoga maritima has been reported at 2.2A resolution. HrcA is composed of three domains: an N-terminal winged helix-turn-helix domain (WHTH), a GAF-like domain, and an inserted dimerizing domain (IDD). The IDD shows a unique structural fold with an anti-parallel beta-sheet composed of three beta-strands sided by four alpha-helices. HrcA crystallises as a dimer, which is formed through hydrophobic contact between the IDDs and a limited contact that involves conserved residues between the GAF-like domains []. The structural studies suggest that the inactive form of HrcA is the dimer and this is converted to its DNA-binding form by interaction with GroEL, which binds to a conserved C-terminal sequence region [, ]. Comparison of the HrcA-CIRCE complexes from B. subtilis and Bacillus thermoglucosidasius (Geobacillus thermoglucosidasius), which grow at vastly different ranges of temperature shows that the thermostability profiles were consistent with the difference in the growth temperatures suggesting that HrcA can function as a thermosensor to detect temperature changes in cells []. Any increase in temperature causes the dissociation of the HrcA from the CIRCE complex with the concomitant activation of transcription of the groE and dnaK operons. This domain represents the winged helix-turn-helix DNA-binding domain which is located close to the N terminus of HrcA. This domain is also found at the N terminus of a set of uncharacterised proteins that have two C-terminal CBS domains. ; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent
Probab=88.82 E-value=1.1 Score=31.08 Aligned_cols=48 Identities=10% Similarity=-0.004 Sum_probs=38.8
Q ss_pred CCCCHHHHHhhCCCCCCCCcchHHHHHHHHhcCCccccccccCCCCccccceecCccc
Q 044458 53 AFMSPKQIASQLPTKNSDAHILLDRILRLLASYSVLNCSLHTLPDGGVERLYGLAPVC 110 (241)
Q Consensus 53 ~~~t~~eLA~~~g~~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~g~~~~~y~~t~~s 110 (241)
.|+..++||+.++. ++--+|-.|..|..+|+++.. +|. .+.|..|..+
T Consensus 22 ~PVgSk~ia~~l~~----s~aTIRN~M~~Le~lGlve~~-----p~~-s~GriPT~~a 69 (78)
T PF03444_consen 22 EPVGSKTIAEELGR----SPATIRNEMADLEELGLVESQ-----PHP-SGGRIPTDKA 69 (78)
T ss_pred CCcCHHHHHHHHCC----ChHHHHHHHHHHHHCCCccCC-----CCC-CCCCCcCHHH
Confidence 79999999999999 999999999999999999852 121 3556666554
No 240
>TIGR00006 S-adenosyl-methyltransferase MraW. Genetics paper in 1972 links mra cluster to peptidoglycan biosynthesis in E. coli. Seems to be common in proteobacteria.wn.
Probab=88.82 E-value=0.85 Score=40.15 Aligned_cols=52 Identities=19% Similarity=0.248 Sum_probs=43.0
Q ss_pred HHHHHHhcCCCCCCCeEEEecCCchHHHHHHHHHCCCCcEEEccc-hHHHhcCC
Q 044458 186 MKKFLENYKGFEGLQSVVDVGGGIGASLDMIISKYPSIKGINFDL-PHVIQDAP 238 (241)
Q Consensus 186 ~~~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-P~vi~~a~ 238 (241)
.+.+++.+. ......+||.=.|.|..+.+++++.|+.+.+.+|. |.+++.++
T Consensus 9 l~Evl~~L~-~~~ggiyVD~TlG~GGHS~~iL~~l~~g~vigiD~D~~Al~~ak 61 (305)
T TIGR00006 9 LDEVVEGLN-IKPDGIYIDCTLGFGGHSKAILEQLGTGRLIGIDRDPQAIAFAK 61 (305)
T ss_pred HHHHHHhcC-cCCCCEEEEeCCCChHHHHHHHHhCCCCEEEEEcCCHHHHHHHH
Confidence 345666665 45557999999999999999999998889999999 88887764
No 241
>PF05148 Methyltransf_8: Hypothetical methyltransferase; InterPro: IPR007823 This family consists of uncharacterised eukaryotic proteins which are related to S-adenosyl-L-methionine-dependent methyltransferases.; GO: 0008168 methyltransferase activity; PDB: 2ZFU_B.
Probab=88.67 E-value=1.3 Score=36.83 Aligned_cols=83 Identities=19% Similarity=0.198 Sum_probs=40.5
Q ss_pred hhhHHHHHhcCCchhhhhhCCCcccccccCchHHHH----HHHHHHhcchhhHHHHHHhcCCCCCCCeEEEecCCchHHH
Q 044458 138 WYHLKDAVLEGGIPFNMAYGMNAFDYHGKDLRLNKI----FNNGMFSHSTITMKKFLENYKGFEGLQSVVDVGGGIGASL 213 (241)
Q Consensus 138 ~~~L~~~l~~g~~~~~~~~g~~~~e~~~~~~~~~~~----f~~aM~~~~~~~~~~~~~~~~~~~~~~~vvDVGGG~G~~~ 213 (241)
+..|.|.+-+..+. .-++.+.++|+..+. |.+.+..|-....+.+++.+..-+....|.|.|||.+.++
T Consensus 15 FR~lNE~LYT~~s~-------~A~~lf~~dP~~F~~YH~Gfr~Qv~~WP~nPvd~iI~~l~~~~~~~viaD~GCGdA~la 87 (219)
T PF05148_consen 15 FRWLNEQLYTTSSE-------EALKLFQEDPELFDIYHEGFRQQVKKWPVNPVDVIIEWLKKRPKSLVIADFGCGDAKLA 87 (219)
T ss_dssp HHHHHHHHHHS-HH-------HHHHHHHH-HHHHHHHHHHHHHHHCTSSS-HHHHHHHHHCTS-TTS-EEEES-TT-HHH
T ss_pred hHHHHHhHhcCCHH-------HHHHHHHhCHHHHHHHHHHHHHHHhcCCCCcHHHHHHHHHhcCCCEEEEECCCchHHHH
Confidence 44556655543322 122334456654444 4444444444445666666542445689999999999999
Q ss_pred HHHHHHCCCCcEEEccc
Q 044458 214 DMIISKYPSIKGINFDL 230 (241)
Q Consensus 214 ~~l~~~~P~l~~~v~Dl 230 (241)
..+.+. .++--+||
T Consensus 88 ~~~~~~---~~V~SfDL 101 (219)
T PF05148_consen 88 KAVPNK---HKVHSFDL 101 (219)
T ss_dssp HH--S------EEEEES
T ss_pred HhcccC---ceEEEeec
Confidence 766432 34555555
No 242
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=88.18 E-value=0.53 Score=37.39 Aligned_cols=47 Identities=13% Similarity=0.150 Sum_probs=42.4
Q ss_pred HHhcChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCcchHHHHHHHHhcCCcccc
Q 044458 37 AIELDLLEVIAKAGPGAFMSPKQIASQLPTKNSDAHILLDRILRLLASYSVLNC 90 (241)
Q Consensus 37 a~~lglfd~L~~~~~~~~~t~~eLA~~~g~~~~~~~~~l~rlLr~L~~~g~l~~ 90 (241)
..+..|..+|.++ +.+|..|||+++|+ ++..+.+=++-|...|++..
T Consensus 14 ~~D~~IL~~Lq~d---~R~s~~eiA~~lgl----S~~tv~~Ri~rL~~~GvI~~ 60 (164)
T PRK11169 14 RIDRNILNELQKD---GRISNVELSKRVGL----SPTPCLERVRRLERQGFIQG 60 (164)
T ss_pred HHHHHHHHHhccC---CCCCHHHHHHHHCc----CHHHHHHHHHHHHHCCCeEE
Confidence 3678899999885 68999999999999 99999999999999999974
No 243
>smart00529 HTH_DTXR Helix-turn-helix diphteria tox regulatory element. iron dependent repressor
Probab=88.08 E-value=0.54 Score=33.45 Aligned_cols=45 Identities=20% Similarity=0.245 Sum_probs=37.2
Q ss_pred HHHHHhhCCCCCCCCcchHHHHHHHHhcCCccccccccCCCCccccceecCcccccc
Q 044458 57 PKQIASQLPTKNSDAHILLDRILRLLASYSVLNCSLHTLPDGGVERLYGLAPVCKFL 113 (241)
Q Consensus 57 ~~eLA~~~g~~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~g~~~~~y~~t~~s~~l 113 (241)
..+||+.+++ +...+.+.++.|...|++... . ...|.+|+.+..+
T Consensus 2 ~~ela~~l~i----s~stvs~~l~~L~~~glI~r~----~----~~~~~lT~~g~~~ 46 (96)
T smart00529 2 TSEIAERLNV----SPPTVTQMLKKLEKDGLVEYE----P----YRGITLTEKGRRL 46 (96)
T ss_pred HHHHHHHhCC----ChHHHHHHHHHHHHCCCEEEc----C----CCceEechhHHHH
Confidence 4689999999 999999999999999999985 1 3467888766543
No 244
>COG4262 Predicted spermidine synthase with an N-terminal membrane domain [General function prediction only]
Probab=88.06 E-value=0.76 Score=41.39 Aligned_cols=41 Identities=39% Similarity=0.665 Sum_probs=35.0
Q ss_pred CCCCeEEEecCCchHHHHHHHHHCCCC-cEEEccc-hHHHhcCC
Q 044458 197 EGLQSVVDVGGGIGASLDMIISKYPSI-KGINFDL-PHVIQDAP 238 (241)
Q Consensus 197 ~~~~~vvDVGGG~G~~~~~l~~~~P~l-~~~v~Dl-P~vi~~a~ 238 (241)
.+..+++-+|||.|..+++++ +||+. +++..|| |.+|+.++
T Consensus 288 ~~a~~vLvlGGGDGLAlRell-kyP~~~qI~lVdLDP~miela~ 330 (508)
T COG4262 288 RGARSVLVLGGGDGLALRELL-KYPQVEQITLVDLDPRMIELAS 330 (508)
T ss_pred cccceEEEEcCCchHHHHHHH-hCCCcceEEEEecCHHHHHHhh
Confidence 457899999999999998886 57865 6899999 99999876
No 245
>PF05724 TPMT: Thiopurine S-methyltransferase (TPMT); InterPro: IPR008854 This family consists of thiopurine S-methyltransferase proteins from both eukaryotes and prokaryotes. Thiopurine S-methyltransferase (TPMT) is a cytosolic enzyme that catalyses S-methylation of aromatic and heterocyclic sulphydryl compounds, including anticancer and immunosuppressive thiopurines [].; GO: 0008119 thiopurine S-methyltransferase activity, 0008152 metabolic process, 0005737 cytoplasm; PDB: 1PJZ_A 2H11_A 2BZG_A 3LCC_A 3BGD_A 2GB4_A 3BGI_B.
Probab=88.03 E-value=0.53 Score=39.37 Aligned_cols=40 Identities=23% Similarity=0.302 Sum_probs=34.6
Q ss_pred CCCCCeEEEecCCchHHHHHHHHHCCCCcEEEccc-hHHHhcC
Q 044458 196 FEGLQSVVDVGGGIGASLDMIISKYPSIKGINFDL-PHVIQDA 237 (241)
Q Consensus 196 ~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-P~vi~~a 237 (241)
.....+|++.|||.|+.+..|+++ +.+++.+|+ |.+|+.+
T Consensus 35 ~~~~~rvLvPgCG~g~D~~~La~~--G~~VvGvDls~~Ai~~~ 75 (218)
T PF05724_consen 35 LKPGGRVLVPGCGKGYDMLWLAEQ--GHDVVGVDLSPTAIEQA 75 (218)
T ss_dssp TSTSEEEEETTTTTSCHHHHHHHT--TEEEEEEES-HHHHHHH
T ss_pred CCCCCeEEEeCCCChHHHHHHHHC--CCeEEEEecCHHHHHHH
Confidence 455679999999999999999987 678999999 7788765
No 246
>PHA02943 hypothetical protein; Provisional
Probab=87.41 E-value=0.79 Score=35.97 Aligned_cols=43 Identities=21% Similarity=0.244 Sum_probs=38.0
Q ss_pred ChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCcchHHHHHHHHhcCCccccc
Q 044458 41 DLLEVIAKAGPGAFMSPKQIASQLPTKNSDAHILLDRILRLLASYSVLNCS 91 (241)
Q Consensus 41 glfd~L~~~~~~~~~t~~eLA~~~g~~~~~~~~~l~rlLr~L~~~g~l~~~ 91 (241)
.|.+.|.. |..|..|||+++|+ +...++-.|..|...|.+.+.
T Consensus 15 eILE~Lk~----G~~TtseIAkaLGl----S~~qa~~~LyvLErEG~VkrV 57 (165)
T PHA02943 15 KTLRLLAD----GCKTTSRIANKLGV----SHSMARNALYQLAKEGMVLKV 57 (165)
T ss_pred HHHHHHhc----CCccHHHHHHHHCC----CHHHHHHHHHHHHHcCceEEE
Confidence 46777733 68999999999999 999999999999999999975
No 247
>PF12147 Methyltransf_20: Putative methyltransferase; InterPro: IPR022744 This C-terminal region is found in bacteria and eukaryotes and is approximately 110 amino acids in length. It is found in association with PF00561 from PFAM. Many members are annotated as being lysophospholipases, and others as alpha-beta hydrolase fold-containing proteins. This domain belongs to the S-adenosyl-L-methionine-dependent methyltransferases superfamily.
Probab=87.41 E-value=0.58 Score=40.82 Aligned_cols=40 Identities=18% Similarity=0.211 Sum_probs=34.5
Q ss_pred CCCeEEEecCCchHHHHHHHHHCCC--CcEEEccc-hHHHhcC
Q 044458 198 GLQSVVDVGGGIGASLDMIISKYPS--IKGINFDL-PHVIQDA 237 (241)
Q Consensus 198 ~~~~vvDVGGG~G~~~~~l~~~~P~--l~~~v~Dl-P~vi~~a 237 (241)
...+||||.||+|-+...+++.+|. .++.+-|. |.-|+..
T Consensus 135 ~pvrIlDIAaG~GRYvlDal~~~~~~~~~i~LrDys~~Nv~~g 177 (311)
T PF12147_consen 135 RPVRILDIAAGHGRYVLDALEKHPERPDSILLRDYSPINVEKG 177 (311)
T ss_pred CceEEEEeccCCcHHHHHHHHhCCCCCceEEEEeCCHHHHHHH
Confidence 5799999999999999999999998 67888888 6666554
No 248
>PF00398 RrnaAD: Ribosomal RNA adenine dimethylase; InterPro: IPR001737 This family of proteins include rRNA adenine dimethylases (e.g. KsgA) and the Erythromycin resistance methylases (Erm). The bacterial enzyme KsgA catalyses the transfer of a total of four methyl groups from S-adenosyl-l-methionine (S-AdoMet) to two adjacent adenosine bases in 16S rRNA. This enzyme and the resulting modified adenosine bases appear to be conserved in all species of eubacteria, eukaryotes, and archaea, and in eukaryotic organelles. Bacterial resistance to the aminoglycoside antibiotic kasugamycin involves inactivation of KsgA and resulting loss of the dimethylations, with modest consequences to the overall fitness of the organism. In contrast, the yeast ortholog, Dim1, is essential. In Saccharomyces cerevisiae (Baker's yeast), and presumably in other eukaryotes, the enzyme performs a vital role in pre-rRNA processing in addition to its methylating activity. The best conserved region in these enzymes is located in the N-terminal section and corresponds to a region that is probably involved in S-adenosyl methionine (SAM) binding domain. The crystal structure of KsgA from Escherichia coli has been solved to a resolution of 2.1A. It bears a strong similarity to the crystal structure of ErmC' from Bacillus stearothermophilus and a lesser similarity to the yeast mitochondrial transcription factor, sc-mtTFB []. The Erm family of RNA methyltransferases, which methylate a single adenosine base in 23S rRNA confer resistance to the MLS-B group of antibiotics. Despite their sequence similarity, the two enzyme families have strikingly different levels of regulation that remain to be elucidated. Other orthologs, of this family include the yeast and Homo sapiens (Human) mitochondrial transcription factors (MTF1 and h-mtTFB respectively), which are nuclear encoded []. Human-mtTFB is able to stimulate transcription in vitro independently of its S-adenosylmethionine binding and rRNA methyltransferase activity [].; GO: 0000179 rRNA (adenine-N6,N6-)-dimethyltransferase activity, 0008649 rRNA methyltransferase activity, 0000154 rRNA modification; PDB: 3FTF_A 3R9X_B 3FTE_A 3FTC_A 3FTD_A 3GRY_A 3FYC_A 3GRU_A 3FYD_A 3GRV_A ....
Probab=87.25 E-value=0.68 Score=39.66 Aligned_cols=42 Identities=17% Similarity=0.338 Sum_probs=34.6
Q ss_pred HHHHHHhcCCCCCCCeEEEecCCchHHHHHHHHHCCCCcEEEccc
Q 044458 186 MKKFLENYKGFEGLQSVVDVGGGIGASLDMIISKYPSIKGINFDL 230 (241)
Q Consensus 186 ~~~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl 230 (241)
.+.+++..+ ......|||||.|.|.+...|++.. -+.+++|.
T Consensus 19 ~~~Iv~~~~-~~~~~~VlEiGpG~G~lT~~L~~~~--~~v~~vE~ 60 (262)
T PF00398_consen 19 ADKIVDALD-LSEGDTVLEIGPGPGALTRELLKRG--KRVIAVEI 60 (262)
T ss_dssp HHHHHHHHT-CGTTSEEEEESSTTSCCHHHHHHHS--SEEEEEES
T ss_pred HHHHHHhcC-CCCCCEEEEeCCCCccchhhHhccc--CcceeecC
Confidence 456777776 7778999999999999999999998 55666666
No 249
>COG1522 Lrp Transcriptional regulators [Transcription]
Probab=87.20 E-value=0.8 Score=35.51 Aligned_cols=47 Identities=17% Similarity=0.229 Sum_probs=42.1
Q ss_pred HhcChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCcchHHHHHHHHhcCCccccc
Q 044458 38 IELDLLEVIAKAGPGAFMSPKQIASQLPTKNSDAHILLDRILRLLASYSVLNCS 91 (241)
Q Consensus 38 ~~lglfd~L~~~~~~~~~t~~eLA~~~g~~~~~~~~~l~rlLr~L~~~g~l~~~ 91 (241)
.+..|.+.|.+. ++.+..+||+++|+ ++..+.+-++-|...|++...
T Consensus 9 ~D~~IL~~L~~d---~r~~~~eia~~lgl----S~~~v~~Ri~~L~~~GiI~~~ 55 (154)
T COG1522 9 IDRRILRLLQED---ARISNAELAERVGL----SPSTVLRRIKRLEEEGVIKGY 55 (154)
T ss_pred HHHHHHHHHHHh---CCCCHHHHHHHHCC----CHHHHHHHHHHHHHCCceeeE
Confidence 567788999885 68999999999999 999999999999999999864
No 250
>TIGR01889 Staph_reg_Sar staphylococcal accessory regulator family. This model represents a family of transcriptional regulatory proteins in Staphylococcus aureus and Staphylococcus epidermidis. Some members contain two tandem copies of this region. This family is related to the MarR transcriptional regulator family described by pfam model pfam01047.
Probab=87.17 E-value=0.8 Score=33.71 Aligned_cols=49 Identities=18% Similarity=0.209 Sum_probs=39.6
Q ss_pred HhcChHHHHH--hcCCCCCCCHHHHHhhCCCCCCCCcchHHHHHHHHhcCCccccc
Q 044458 38 IELDLLEVIA--KAGPGAFMSPKQIASQLPTKNSDAHILLDRILRLLASYSVLNCS 91 (241)
Q Consensus 38 ~~lglfd~L~--~~~~~~~~t~~eLA~~~g~~~~~~~~~l~rlLr~L~~~g~l~~~ 91 (241)
.++.++..|. ... +++.|..+||+.+++ +...+.++++.|...|++.+.
T Consensus 26 ~q~~vL~~l~~~~~~-~~~~t~~eL~~~l~~----~~stvs~~i~~Le~kg~I~r~ 76 (109)
T TIGR01889 26 EELLILYYLGKLENN-EGKLTLKEIIKEILI----KQSALVKIIKKLSKKGYLSKE 76 (109)
T ss_pred HHHHHHHHHHhhhcc-CCcCcHHHHHHHHCC----CHHHHHHHHHHHHHCCCEecc
Confidence 3445566665 221 268999999999999 999999999999999999875
No 251
>PRK04172 pheS phenylalanyl-tRNA synthetase subunit alpha; Provisional
Probab=87.10 E-value=0.54 Score=44.11 Aligned_cols=66 Identities=15% Similarity=0.136 Sum_probs=52.7
Q ss_pred HhcChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCcchHHHHHHHHhcCCccccccccCCCCccccceecCccccccccC
Q 044458 38 IELDLLEVIAKAGPGAFMSPKQIASQLPTKNSDAHILLDRILRLLASYSVLNCSLHTLPDGGVERLYGLAPVCKFLTKN 116 (241)
Q Consensus 38 ~~lglfd~L~~~~~~~~~t~~eLA~~~g~~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~g~~~~~y~~t~~s~~l~~~ 116 (241)
.+..|...|... ++.|..+||+.+++ ++..+.++++.|.+.|++...+. . ...|.+|+.++.+...
T Consensus 7 ~e~~vL~~L~~~---~~~s~~eLA~~l~l----~~~tVt~~i~~Le~kGlV~~~~~--~----~~~i~LTeeG~~~~~~ 72 (489)
T PRK04172 7 NEKKVLKALKEL---KEATLEELAEKLGL----PPEAVMRAAEWLEEKGLVKVEER--V----EEVYVLTEEGKKYAEE 72 (489)
T ss_pred HHHHHHHHHHhC---CCCCHHHHHHHhCc----CHHHHHHHHHHHHhCCCEEEEee--e----EEEEEECHHHHHHHHh
Confidence 455666777654 58999999999999 99999999999999999987521 1 4689999999855544
No 252
>COG4122 Predicted O-methyltransferase [General function prediction only]
Probab=87.07 E-value=0.57 Score=39.20 Aligned_cols=44 Identities=16% Similarity=0.213 Sum_probs=38.2
Q ss_pred CCCCCeEEEecCCchHHHHHHHHHCC-CCcEEEccc-hHHHhcCCC
Q 044458 196 FEGLQSVVDVGGGIGASLDMIISKYP-SIKGINFDL-PHVIQDAPA 239 (241)
Q Consensus 196 ~~~~~~vvDVGGG~G~~~~~l~~~~P-~l~~~v~Dl-P~vi~~a~~ 239 (241)
.++.++||.||.+.|.-++.++..-| +-+.|-+|+ |+-++.|++
T Consensus 57 ~~~~k~iLEiGT~~GySal~mA~~l~~~g~l~tiE~~~e~~~~A~~ 102 (219)
T COG4122 57 LSGPKRILEIGTAIGYSALWMALALPDDGRLTTIERDEERAEIARE 102 (219)
T ss_pred hcCCceEEEeecccCHHHHHHHhhCCCCCeEEEEeCCHHHHHHHHH
Confidence 55789999999999999999999999 778899999 677766653
No 253
>PRK04338 N(2),N(2)-dimethylguanosine tRNA methyltransferase; Provisional
Probab=87.05 E-value=0.58 Score=42.52 Aligned_cols=40 Identities=18% Similarity=0.008 Sum_probs=34.2
Q ss_pred CCeEEEecCCchHHHHHHHHHCCCCcEEEccc-hHHHhcCC
Q 044458 199 LQSVVDVGGGIGASLDMIISKYPSIKGINFDL-PHVIQDAP 238 (241)
Q Consensus 199 ~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-P~vi~~a~ 238 (241)
..+|+|++||+|.+++.+++..+-.+++..|. |..++.++
T Consensus 58 ~~~vLDl~aGsG~~~l~~a~~~~~~~V~a~Din~~Av~~a~ 98 (382)
T PRK04338 58 RESVLDALSASGIRGIRYALETGVEKVTLNDINPDAVELIK 98 (382)
T ss_pred CCEEEECCCcccHHHHHHHHHCCCCEEEEEeCCHHHHHHHH
Confidence 35899999999999999999888667899999 77877654
No 254
>COG2512 Predicted membrane-associated trancriptional regulator [Transcription]
Probab=86.70 E-value=0.63 Score=39.99 Aligned_cols=47 Identities=21% Similarity=0.386 Sum_probs=42.1
Q ss_pred hcChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCcchHHHHHHHHhcCCccccc
Q 044458 39 ELDLLEVIAKAGPGAFMSPKQIASQLPTKNSDAHILLDRILRLLASYSVLNCS 91 (241)
Q Consensus 39 ~lglfd~L~~~~~~~~~t~~eLA~~~g~~~~~~~~~l~rlLr~L~~~g~l~~~ 91 (241)
|..+.++|.+.| |.++-+||.+++|+ +...+.|+|+-|..+|++++.
T Consensus 197 e~~il~~i~~~G--Gri~Q~eL~r~lgl----sktTvsR~L~~LEk~GlIe~~ 243 (258)
T COG2512 197 EKEILDLIRERG--GRITQAELRRALGL----SKTTVSRILRRLEKRGLIEKE 243 (258)
T ss_pred HHHHHHHHHHhC--CEEeHHHHHHhhCC----ChHHHHHHHHHHHhCCceEEE
Confidence 345888898876 77999999999999 899999999999999999975
No 255
>PRK15128 23S rRNA m(5)C1962 methyltransferase; Provisional
Probab=86.69 E-value=0.58 Score=42.75 Aligned_cols=41 Identities=10% Similarity=-0.030 Sum_probs=31.5
Q ss_pred CCCCeEEEecCCchHHHHHHHHHCCCCcEEEccc-hHHHhcCC
Q 044458 197 EGLQSVVDVGGGIGASLDMIISKYPSIKGINFDL-PHVIQDAP 238 (241)
Q Consensus 197 ~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-P~vi~~a~ 238 (241)
...++|||+|||+|.++++.+.. ...+++.+|+ +..++.|+
T Consensus 219 ~~g~rVLDlfsgtG~~~l~aa~~-ga~~V~~VD~s~~al~~a~ 260 (396)
T PRK15128 219 VENKRVLNCFSYTGGFAVSALMG-GCSQVVSVDTSQEALDIAR 260 (396)
T ss_pred cCCCeEEEeccCCCHHHHHHHhC-CCCEEEEEECCHHHHHHHH
Confidence 34589999999999998876643 3447899999 77777654
No 256
>PF12793 SgrR_N: Sugar transport-related sRNA regulator N-term
Probab=86.48 E-value=0.79 Score=34.38 Aligned_cols=35 Identities=9% Similarity=0.051 Sum_probs=33.2
Q ss_pred CCCCHHHHHhhCCCCCCCCcchHHHHHHHHhcCCccccc
Q 044458 53 AFMSPKQIASQLPTKNSDAHILLDRILRLLASYSVLNCS 91 (241)
Q Consensus 53 ~~~t~~eLA~~~g~~~~~~~~~l~rlLr~L~~~g~l~~~ 91 (241)
.++|++|||+.+.+ +++.++.+|+.|...|.++..
T Consensus 18 ~~vtl~elA~~l~c----S~Rn~r~lLkkm~~~gWi~W~ 52 (115)
T PF12793_consen 18 VEVTLDELAELLFC----SRRNARTLLKKMQEEGWITWQ 52 (115)
T ss_pred cceeHHHHHHHhCC----CHHHHHHHHHHHHHCCCeeee
Confidence 46899999999999 999999999999999999985
No 257
>KOG4589 consensus Cell division protein FtsJ [Cell cycle control, cell division, chromosome partitioning]
Probab=86.38 E-value=1.1 Score=36.79 Aligned_cols=43 Identities=21% Similarity=0.397 Sum_probs=33.3
Q ss_pred HhcCCCCCCCeEEEecCCchHHHHHHHHHC-CCCcEEEccchHH
Q 044458 191 ENYKGFEGLQSVVDVGGGIGASLDMIISKY-PSIKGINFDLPHV 233 (241)
Q Consensus 191 ~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~-P~l~~~v~DlP~v 233 (241)
+.|.-+..-.+|+|+|+..|.++....++- |+=.+...||-.+
T Consensus 62 dKy~~l~p~~~VlD~G~APGsWsQVavqr~~p~g~v~gVDllh~ 105 (232)
T KOG4589|consen 62 DKYRFLRPEDTVLDCGAAPGSWSQVAVQRVNPNGMVLGVDLLHI 105 (232)
T ss_pred hhccccCCCCEEEEccCCCChHHHHHHHhhCCCceEEEEeeeec
Confidence 445424566999999999999998877765 9988888888443
No 258
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=86.29 E-value=0.75 Score=38.20 Aligned_cols=43 Identities=23% Similarity=0.198 Sum_probs=34.2
Q ss_pred HHHHHHHHHHhcChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCcchHHHHHHH
Q 044458 29 VLPMVLKSAIELDLLEVIAKAGPGAFMSPKQIASQLPTKNSDAHILLDRILRL 81 (241)
Q Consensus 29 ~~~~~L~~a~~lglfd~L~~~~~~~~~t~~eLA~~~g~~~~~~~~~l~rlLr~ 81 (241)
..-.+|+.|++.|-||.= ..++..|||+.+|+ .+..+...||-
T Consensus 159 rQ~~vL~~A~~~GYFd~P------R~~~l~dLA~~lGI----Skst~~ehLRr 201 (215)
T COG3413 159 RQLEVLRLAYKMGYFDYP------RRVSLKDLAKELGI----SKSTLSEHLRR 201 (215)
T ss_pred HHHHHHHHHHHcCCCCCC------ccCCHHHHHHHhCC----CHHHHHHHHHH
Confidence 466899999999999982 46999999999999 66555544443
No 259
>PRK13256 thiopurine S-methyltransferase; Reviewed
Probab=86.16 E-value=1.5 Score=36.94 Aligned_cols=39 Identities=15% Similarity=0.168 Sum_probs=33.4
Q ss_pred CCCCeEEEecCCchHHHHHHHHHCCCCcEEEccc-hHHHhcC
Q 044458 197 EGLQSVVDVGGGIGASLDMIISKYPSIKGINFDL-PHVIQDA 237 (241)
Q Consensus 197 ~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-P~vi~~a 237 (241)
....+|++.|||.|..+..|++. +.+++.+|+ |.+|+.+
T Consensus 42 ~~~~rvLvPgCGkg~D~~~LA~~--G~~V~GvDlS~~Ai~~~ 81 (226)
T PRK13256 42 NDSSVCLIPMCGCSIDMLFFLSK--GVKVIGIELSEKAVLSF 81 (226)
T ss_pred CCCCeEEEeCCCChHHHHHHHhC--CCcEEEEecCHHHHHHH
Confidence 34579999999999999999986 677999999 7777764
No 260
>PF01795 Methyltransf_5: MraW methylase family; InterPro: IPR002903 This is a family of S-adenosyl-L-methionine-dependent methyltransferases, which are found primarily, though not exclusively, in bacteria. The Escherichia coli protein is essential and has been linked to peptidoglycan biosynthesis [, ].; GO: 0008168 methyltransferase activity; PDB: 1N2X_A 1M6Y_A 1WG8_A 3TKA_A.
Probab=86.15 E-value=1 Score=39.71 Aligned_cols=52 Identities=27% Similarity=0.296 Sum_probs=39.4
Q ss_pred HHHHHHhcCCCCCCCeEEEecCCchHHHHHHHHHCCCCcEEEccc-hHHHhcCC
Q 044458 186 MKKFLENYKGFEGLQSVVDVGGGIGASLDMIISKYPSIKGINFDL-PHVIQDAP 238 (241)
Q Consensus 186 ~~~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-P~vi~~a~ 238 (241)
...+++.+. ......+||.==|.|.++.++++++|+.+.+.+|. |.+++.|+
T Consensus 9 l~Evl~~L~-~~~~g~~vD~T~G~GGHS~aiL~~~~~~~li~~DrD~~a~~~a~ 61 (310)
T PF01795_consen 9 LKEVLEALN-PKPGGIYVDCTFGGGGHSKAILEKLPNGRLIGIDRDPEALERAK 61 (310)
T ss_dssp HHHHHHHHT---TT-EEEETT-TTSHHHHHHHHT-TT-EEEEEES-HHHHHHHH
T ss_pred HHHHHHhhC-cCCCceEEeecCCcHHHHHHHHHhCCCCeEEEecCCHHHHHHHH
Confidence 456677766 56678999999999999999999999999999999 88886654
No 261
>PLN02853 Probable phenylalanyl-tRNA synthetase alpha chain
Probab=85.97 E-value=0.69 Score=43.20 Aligned_cols=69 Identities=13% Similarity=0.092 Sum_probs=55.4
Q ss_pred HHhcChHHHHHhcCCCCC-CCHHHHHhhCCCCCCCCcchHHHHHHHHhcCCccccccccCCCCccccceecCccccc-cc
Q 044458 37 AIELDLLEVIAKAGPGAF-MSPKQIASQLPTKNSDAHILLDRILRLLASYSVLNCSLHTLPDGGVERLYGLAPVCKF-LT 114 (241)
Q Consensus 37 a~~lglfd~L~~~~~~~~-~t~~eLA~~~g~~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~g~~~~~y~~t~~s~~-l~ 114 (241)
+.+..|...|... ++ .+.++||+.+|+ ++..+.+.+..|.+.|+++.... . ...|.+|+.++. +.
T Consensus 3 ~~e~~iL~~l~~~---~~~~~~~~la~~~g~----~~~~v~~~~~~L~~kg~v~~~~~--~----~~~~~LT~eG~~~l~ 69 (492)
T PLN02853 3 MAEEALLGALSNN---EEISDSGQFAASHGL----DHNEVVGVIKSLHGFRYVDAQDI--K----RETWVLTEEGKKYAA 69 (492)
T ss_pred hHHHHHHHHHHhc---CCCCCHHHHHHHcCC----CHHHHHHHHHHHHhCCCEEEEEE--E----EEEEEECHHHHHHHH
Confidence 4677788888874 34 799999999999 99999999999999999876421 1 689999999984 44
Q ss_pred cCCC
Q 044458 115 KNED 118 (241)
Q Consensus 115 ~~~~ 118 (241)
.+.+
T Consensus 70 ~G~P 73 (492)
T PLN02853 70 EGSP 73 (492)
T ss_pred cCCH
Confidence 4443
No 262
>PF13545 HTH_Crp_2: Crp-like helix-turn-helix domain; PDB: 3LA2_A 3LA3_B 3LA7_A 3B02_A 3E97_A 2H6C_B 1OMI_A 2BGC_H 2BEO_A 2GAU_A ....
Probab=85.78 E-value=0.55 Score=31.80 Aligned_cols=34 Identities=21% Similarity=0.329 Sum_probs=32.1
Q ss_pred CCCHHHHHhhCCCCCCCCcchHHHHHHHHhcCCccccc
Q 044458 54 FMSPKQIASQLPTKNSDAHILLDRILRLLASYSVLNCS 91 (241)
Q Consensus 54 ~~t~~eLA~~~g~~~~~~~~~l~rlLr~L~~~g~l~~~ 91 (241)
+.|-++||..+|+ +...+.|+|+.|...|++...
T Consensus 28 ~lt~~~iA~~~g~----sr~tv~r~l~~l~~~g~I~~~ 61 (76)
T PF13545_consen 28 PLTQEEIADMLGV----SRETVSRILKRLKDEGIIEVK 61 (76)
T ss_dssp ESSHHHHHHHHTS----CHHHHHHHHHHHHHTTSEEEE
T ss_pred cCCHHHHHHHHCC----CHHHHHHHHHHHHHCCCEEEc
Confidence 6899999999999 999999999999999999864
No 263
>PRK03573 transcriptional regulator SlyA; Provisional
Probab=85.16 E-value=1.5 Score=33.67 Aligned_cols=44 Identities=20% Similarity=0.126 Sum_probs=37.2
Q ss_pred hHHHHHhcCCCCCCCHHHHHhhCCCCCCCCcchHHHHHHHHhcCCccccc
Q 044458 42 LLEVIAKAGPGAFMSPKQIASQLPTKNSDAHILLDRILRLLASYSVLNCS 91 (241)
Q Consensus 42 lfd~L~~~~~~~~~t~~eLA~~~g~~~~~~~~~l~rlLr~L~~~g~l~~~ 91 (241)
++..|...+ ++.|..|||+.+++ +...+.++++.|...|++.+.
T Consensus 36 vL~~l~~~~--~~~t~~eLa~~l~~----~~~tvt~~v~~Le~~GlV~r~ 79 (144)
T PRK03573 36 TLHNIHQLP--PEQSQIQLAKAIGI----EQPSLVRTLDQLEEKGLISRQ 79 (144)
T ss_pred HHHHHHHcC--CCCCHHHHHHHhCC----ChhhHHHHHHHHHHCCCEeee
Confidence 455565432 36899999999999 999999999999999999975
No 264
>PRK11783 rlmL 23S rRNA m(2)G2445 methyltransferase; Provisional
Probab=85.14 E-value=0.73 Score=45.24 Aligned_cols=41 Identities=7% Similarity=-0.058 Sum_probs=33.1
Q ss_pred CCCeEEEecCCchHHHHHHHHHCCCCcEEEccc-hHHHhcCCC
Q 044458 198 GLQSVVDVGGGIGASLDMIISKYPSIKGINFDL-PHVIQDAPA 239 (241)
Q Consensus 198 ~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-P~vi~~a~~ 239 (241)
..++|||+|||+|.+++.+++. ..-+++..|+ +.+++.|++
T Consensus 538 ~g~rVLDlf~gtG~~sl~aa~~-Ga~~V~~vD~s~~al~~a~~ 579 (702)
T PRK11783 538 KGKDFLNLFAYTGTASVHAALG-GAKSTTTVDMSNTYLEWAER 579 (702)
T ss_pred CCCeEEEcCCCCCHHHHHHHHC-CCCEEEEEeCCHHHHHHHHH
Confidence 3589999999999999999986 2336899999 777776653
No 265
>cd07377 WHTH_GntR Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators. This CD represents the winged HTH DNA-binding domain of the GntR (named after the gluconate operon repressor in Bacillus subtilis) family of bacterial transcriptional regulators and their putative homologs found in eukaryota and archaea. The GntR family has over 6000 members distributed among almost all bacterial species, which is comprised of FadR, HutC, MocR, YtrA, AraR, PlmA, and other subfamilies for the regulation of the most varied biological process. The monomeric proteins of the GntR family are characterized by two function domains: a small highly conserved winged helix-turn-helix prokaryotic DNA binding domain in the N-terminus, and a very diverse regulatory ligand-binding domain in the C-terminus for effector-binding/oligomerization, which provides the basis for the subfamily classifications. Binding of the effector to GntR-like transcriptional regulators is
Probab=85.08 E-value=1.2 Score=28.84 Aligned_cols=32 Identities=19% Similarity=0.263 Sum_probs=29.8
Q ss_pred CCHHHHHhhCCCCCCCCcchHHHHHHHHhcCCcccc
Q 044458 55 MSPKQIASQLPTKNSDAHILLDRILRLLASYSVLNC 90 (241)
Q Consensus 55 ~t~~eLA~~~g~~~~~~~~~l~rlLr~L~~~g~l~~ 90 (241)
.|..+||+.+++ +...+++.|..|...|++..
T Consensus 26 ~~~~~la~~~~i----s~~~v~~~l~~L~~~G~i~~ 57 (66)
T cd07377 26 PSERELAEELGV----SRTTVREALRELEAEGLVER 57 (66)
T ss_pred CCHHHHHHHHCC----CHHHHHHHHHHHHHCCCEEe
Confidence 459999999999 99999999999999999975
No 266
>PF13730 HTH_36: Helix-turn-helix domain
Probab=84.84 E-value=0.94 Score=28.71 Aligned_cols=30 Identities=17% Similarity=0.266 Sum_probs=27.9
Q ss_pred CCHHHHHhhCCCCCCCCcchHHHHHHHHhcCCcc
Q 044458 55 MSPKQIASQLPTKNSDAHILLDRILRLLASYSVL 88 (241)
Q Consensus 55 ~t~~eLA~~~g~~~~~~~~~l~rlLr~L~~~g~l 88 (241)
.|.+.||+.+|+ ..+.+.+.++.|...|++
T Consensus 26 pS~~~la~~~g~----s~~Tv~~~i~~L~~~G~I 55 (55)
T PF13730_consen 26 PSQETLAKDLGV----SRRTVQRAIKELEEKGLI 55 (55)
T ss_pred cCHHHHHHHHCc----CHHHHHHHHHHHHHCcCC
Confidence 489999999999 999999999999999975
No 267
>PF03141 Methyltransf_29: Putative S-adenosyl-L-methionine-dependent methyltransferase; InterPro: IPR004159 Members of this family of hypothetical plant proteins are putative methyltransferases. ; GO: 0008168 methyltransferase activity
Probab=84.41 E-value=0.79 Score=42.74 Aligned_cols=24 Identities=21% Similarity=0.513 Sum_probs=21.3
Q ss_pred CCCCeEEEecCCchHHHHHHHHHC
Q 044458 197 EGLQSVVDVGGGIGASLDMIISKY 220 (241)
Q Consensus 197 ~~~~~vvDVGGG~G~~~~~l~~~~ 220 (241)
...+++||||||.|.++..++++.
T Consensus 116 g~iR~~LDvGcG~aSF~a~l~~r~ 139 (506)
T PF03141_consen 116 GGIRTALDVGCGVASFGAYLLERN 139 (506)
T ss_pred CceEEEEeccceeehhHHHHhhCC
Confidence 356999999999999999999874
No 268
>PF10007 DUF2250: Uncharacterized protein conserved in archaea (DUF2250); InterPro: IPR019254 Members of this family of hypothetical archaeal proteins have no known function.
Probab=84.07 E-value=1.4 Score=31.61 Aligned_cols=47 Identities=23% Similarity=0.248 Sum_probs=41.4
Q ss_pred HhcChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCcchHHHHHHHHhcCCccccc
Q 044458 38 IELDLLEVIAKAGPGAFMSPKQIASQLPTKNSDAHILLDRILRLLASYSVLNCS 91 (241)
Q Consensus 38 ~~lglfd~L~~~~~~~~~t~~eLA~~~g~~~~~~~~~l~rlLr~L~~~g~l~~~ 91 (241)
.++.|...|... +|-...-||..+++ +...++..|+-|..+|++++.
T Consensus 8 l~~~IL~hl~~~---~~Dy~k~ia~~l~~----~~~~v~~~l~~Le~~GLler~ 54 (92)
T PF10007_consen 8 LDLKILQHLKKA---GPDYAKSIARRLKI----PLEEVREALEKLEEMGLLERV 54 (92)
T ss_pred hHHHHHHHHHHH---CCCcHHHHHHHHCC----CHHHHHHHHHHHHHCCCeEEe
Confidence 356678888876 57899999999999 999999999999999999985
No 269
>COG1378 Predicted transcriptional regulators [Transcription]
Probab=83.82 E-value=2 Score=36.68 Aligned_cols=61 Identities=15% Similarity=0.179 Sum_probs=46.9
Q ss_pred hcChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCcchHHHHHHHHhcCCccccccccCCCCccccceecCccccc
Q 044458 39 ELDLLEVIAKAGPGAFMSPKQIASQLPTKNSDAHILLDRILRLLASYSVLNCSLHTLPDGGVERLYGLAPVCKF 112 (241)
Q Consensus 39 ~lglfd~L~~~~~~~~~t~~eLA~~~g~~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~g~~~~~y~~t~~s~~ 112 (241)
|-.+.-+|-.. |+.|+.|||+.+|+ +...+..+|+.|...|++... .| .+..|+.-+-...
T Consensus 18 Ea~vY~aLl~~---g~~tA~eis~~sgv----P~~kvY~vl~sLe~kG~v~~~-----~g-~P~~y~av~p~~~ 78 (247)
T COG1378 18 EAKVYLALLCL---GEATAKEISEASGV----PRPKVYDVLRSLEKKGLVEVI-----EG-RPKKYRAVPPEEL 78 (247)
T ss_pred HHHHHHHHHHh---CCccHHHHHHHcCC----CchhHHHHHHHHHHCCCEEee-----CC-CCceEEeCCHHHH
Confidence 33455555554 69999999999999 888999999999999999974 12 1678877665443
No 270
>PRK13509 transcriptional repressor UlaR; Provisional
Probab=83.77 E-value=1.3 Score=37.68 Aligned_cols=45 Identities=20% Similarity=0.230 Sum_probs=40.3
Q ss_pred cChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCcchHHHHHHHHhcCCccccc
Q 044458 40 LDLLEVIAKAGPGAFMSPKQIASQLPTKNSDAHILLDRILRLLASYSVLNCS 91 (241)
Q Consensus 40 lglfd~L~~~~~~~~~t~~eLA~~~g~~~~~~~~~l~rlLr~L~~~g~l~~~ 91 (241)
..|.+.|.+. +.++..|||+.+|+ ++.-++|-|+.|...|++.+.
T Consensus 8 ~~Il~~l~~~---~~~~~~ela~~l~v----S~~TirRdL~~Le~~g~i~r~ 52 (251)
T PRK13509 8 QILLELLAQL---GFVTVEKVIERLGI----SPATARRDINKLDESGKLKKV 52 (251)
T ss_pred HHHHHHHHHc---CCcCHHHHHHHHCc----CHHHHHHHHHHHHHCCCEEEe
Confidence 3478888875 68999999999999 999999999999999999875
No 271
>PRK04214 rbn ribonuclease BN/unknown domain fusion protein; Reviewed
Probab=83.77 E-value=1.4 Score=40.51 Aligned_cols=35 Identities=20% Similarity=0.145 Sum_probs=33.1
Q ss_pred CCCCHHHHHhhCCCCCCCCcchHHHHHHHHhcCCccccc
Q 044458 53 AFMSPKQIASQLPTKNSDAHILLDRILRLLASYSVLNCS 91 (241)
Q Consensus 53 ~~~t~~eLA~~~g~~~~~~~~~l~rlLr~L~~~g~l~~~ 91 (241)
++.|.+||++++++ +++.++++|+.|...|++.+.
T Consensus 309 ~~~t~~~La~~l~~----~~~~v~~iL~~L~~agLI~~~ 343 (412)
T PRK04214 309 KALDVDEIRRLEPM----GYDELGELLCELARIGLLRRG 343 (412)
T ss_pred CCCCHHHHHHHhCC----CHHHHHHHHHHHHhCCCeEec
Confidence 68999999999999 999999999999999999864
No 272
>PF13404 HTH_AsnC-type: AsnC-type helix-turn-helix domain; PDB: 2ZNY_E 2ZNZ_G 1RI7_A 2CYY_A 2E1C_A 2VC1_B 2QZ8_A 2W29_C 2IVM_B 2VBX_B ....
Probab=83.56 E-value=1.4 Score=26.76 Aligned_cols=36 Identities=17% Similarity=0.281 Sum_probs=25.8
Q ss_pred HhcChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCcchHHHHHH
Q 044458 38 IELDLLEVIAKAGPGAFMSPKQIASQLPTKNSDAHILLDRILR 80 (241)
Q Consensus 38 ~~lglfd~L~~~~~~~~~t~~eLA~~~g~~~~~~~~~l~rlLr 80 (241)
++..|...|... +..++.+||+.+|+ ++..+.+=++
T Consensus 4 ~D~~Il~~Lq~d---~r~s~~~la~~lgl----S~~~v~~Ri~ 39 (42)
T PF13404_consen 4 LDRKILRLLQED---GRRSYAELAEELGL----SESTVRRRIR 39 (42)
T ss_dssp HHHHHHHHHHH----TTS-HHHHHHHHTS-----HHHHHHHHH
T ss_pred HHHHHHHHHHHc---CCccHHHHHHHHCc----CHHHHHHHHH
Confidence 466788889885 68999999999999 7776554333
No 273
>PRK14165 winged helix-turn-helix domain-containing protein/riboflavin kinase; Provisional
Probab=83.42 E-value=1.3 Score=37.12 Aligned_cols=52 Identities=17% Similarity=0.179 Sum_probs=41.9
Q ss_pred CCCCHHHHHhhCCCCCCCCcchHHHHHHHHhcCCccccccccCCCCccccceecCcccccc
Q 044458 53 AFMSPKQIASQLPTKNSDAHILLDRILRLLASYSVLNCSLHTLPDGGVERLYGLAPVCKFL 113 (241)
Q Consensus 53 ~~~t~~eLA~~~g~~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~g~~~~~y~~t~~s~~l 113 (241)
..+|..|||+.+++ +...+.|.|+.|...|++++... .. ...+++|+.++.+
T Consensus 20 ~~IS~~eLA~~L~i----S~~Tvsr~Lk~LEe~GlI~R~~~--~r---~~~v~LTekG~~l 71 (217)
T PRK14165 20 VKISSSEFANHTGT----SSKTAARILKQLEDEGYITRTIV--PR---GQLITITEKGLDV 71 (217)
T ss_pred CCcCHHHHHHHHCc----CHHHHHHHHHHHHHCCCEEEEEc--CC---ceEEEECHHHHHH
Confidence 46999999999999 99999999999999999987521 11 4577788776633
No 274
>PF02796 HTH_7: Helix-turn-helix domain of resolvase; InterPro: IPR006120 Site-specific recombination plays an important role in DNA rearrangement in prokaryotic organisms. Two types of site-specific recombination are known to occur: Recombination between inverted repeats resulting in the reversal of a DNA segment. Recombination between repeat sequences on two DNA molecules resulting in their cointegration, or between repeats on one DNA molecule resulting in the excision of a DNA fragment. Site-specific recombination is characterised by a strand exchange mechanism that requires no DNA synthesis or high energy cofactor; the phosphodiester bond energy is conserved in a phospho-protein linkage during strand cleavage and re-ligation. Two unrelated families of recombinases are currently known []. The first, called the 'phage integrase' family, groups a number of bacterial phage and yeast plasmid enzymes. The second [], called the 'resolvase' family, groups enzymes which share the following structural characteristics: an N-terminal catalytic and dimerization domain that contains a conserved serine residue involved in the transient covalent attachment to DNA IPR006119 from INTERPRO, and a C-terminal helix-turn-helix DNA-binding domain. ; GO: 0000150 recombinase activity, 0003677 DNA binding, 0006310 DNA recombination; PDB: 1ZR2_A 2GM4_B 1RES_A 1ZR4_A 1RET_A 1GDT_B 2R0Q_C 1JKP_C 1IJW_C 1JJ6_C ....
Probab=83.40 E-value=1.2 Score=27.35 Aligned_cols=23 Identities=30% Similarity=0.226 Sum_probs=17.3
Q ss_pred CCCHHHHHhhCCCCCCCCcchHHHHHH
Q 044458 54 FMSPKQIASQLPTKNSDAHILLDRILR 80 (241)
Q Consensus 54 ~~t~~eLA~~~g~~~~~~~~~l~rlLr 80 (241)
+.|+.+||+.+|+ +..-+.|+|+
T Consensus 21 G~si~~IA~~~gv----sr~TvyR~l~ 43 (45)
T PF02796_consen 21 GMSIAEIAKQFGV----SRSTVYRYLN 43 (45)
T ss_dssp T--HHHHHHHTTS-----HHHHHHHHC
T ss_pred CCCHHHHHHHHCc----CHHHHHHHHh
Confidence 4999999999999 8888888764
No 275
>PF12324 HTH_15: Helix-turn-helix domain of alkylmercury lyase; InterPro: IPR024259 Alkylmercury lyase (EC:4.99.1.2) cleaves the carbon-mercury bond of organomercurials such as phenylmercuric acetate. This entry represents the N-terminal helix-turn-helix domain.; PDB: 3FN8_B 3F2G_B 3F0P_A 3F2F_B 3F2H_A 3F0O_B 1S6L_A.
Probab=83.37 E-value=1 Score=31.17 Aligned_cols=35 Identities=26% Similarity=0.283 Sum_probs=25.1
Q ss_pred hHHHHHhcCCCCCCCHHHHHhhCCCCCCCCcchHHHHHHHHh
Q 044458 42 LLEVIAKAGPGAFMSPKQIASQLPTKNSDAHILLDRILRLLA 83 (241)
Q Consensus 42 lfd~L~~~~~~~~~t~~eLA~~~g~~~~~~~~~l~rlLr~L~ 83 (241)
++..|++ | +|+|..+||.++|. +.+.++..|..+-
T Consensus 29 LLr~LA~-G--~PVt~~~LA~a~g~----~~e~v~~~L~~~p 63 (77)
T PF12324_consen 29 LLRLLAK-G--QPVTVEQLAAALGW----PVEEVRAALAAMP 63 (77)
T ss_dssp HHHHHTT-T--S-B-HHHHHHHHT------HHHHHHHHHH-T
T ss_pred HHHHHHc-C--CCcCHHHHHHHHCC----CHHHHHHHHHhCC
Confidence 7788887 3 79999999999999 8877887777764
No 276
>COG3432 Predicted transcriptional regulator [Transcription]
Probab=83.35 E-value=0.66 Score=33.52 Aligned_cols=62 Identities=10% Similarity=0.148 Sum_probs=46.5
Q ss_pred hHHHHH-hcCCCCCCCHHHHHhhCCCCCCCCcchHHHHHHHHhcCCccccccccCCCCccccceecCccccccc
Q 044458 42 LLEVIA-KAGPGAFMSPKQIASQLPTKNSDAHILLDRILRLLASYSVLNCSLHTLPDGGVERLYGLAPVCKFLT 114 (241)
Q Consensus 42 lfd~L~-~~~~~~~~t~~eLA~~~g~~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~g~~~~~y~~t~~s~~l~ 114 (241)
+||+|. ..+ ++....-|.-.+++ +-+....+++.|+..|++... ++| ....|.+|+.+.-|.
T Consensus 20 i~dIL~~~~~--~~~~~Tri~y~aNl----ny~~~~~yi~~L~~~Gli~~~----~~~-~~~~y~lT~KG~~fl 82 (95)
T COG3432 20 IFDILKAISE--GGIGITRIIYGANL----NYKRAQKYIEMLVEKGLIIKQ----DNG-RRKVYELTEKGKRFL 82 (95)
T ss_pred HHHHHHHhcC--CCCCceeeeeecCc----CHHHHHHHHHHHHhCCCEEec----cCC-ccceEEEChhHHHHH
Confidence 466666 222 68888899999999 999999999999999966654 111 123799999887443
No 277
>PF14394 DUF4423: Domain of unknown function (DUF4423)
Probab=82.90 E-value=2.3 Score=34.16 Aligned_cols=46 Identities=17% Similarity=0.192 Sum_probs=39.5
Q ss_pred CCHHHHHhhC--CCCCCCCcchHHHHHHHHhcCCccccccccCCCCccccceecCccccc
Q 044458 55 MSPKQIASQL--PTKNSDAHILLDRILRLLASYSVLNCSLHTLPDGGVERLYGLAPVCKF 112 (241)
Q Consensus 55 ~t~~eLA~~~--g~~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~g~~~~~y~~t~~s~~ 112 (241)
.+..+||+.+ ++ +..-++.-|+.|..+|++++. | +|.|..|..+-.
T Consensus 40 ~d~~~iak~l~p~i----s~~ev~~sL~~L~~~gli~k~------~--~g~y~~t~~~l~ 87 (171)
T PF14394_consen 40 PDPEWIAKRLRPKI----SAEEVRDSLEFLEKLGLIKKD------G--DGKYVQTDKSLT 87 (171)
T ss_pred CCHHHHHHHhcCCC----CHHHHHHHHHHHHHCCCeEEC------C--CCcEEEecceee
Confidence 4999999999 88 999999999999999999985 1 578988875543
No 278
>TIGR00498 lexA SOS regulatory protein LexA. LexA acts as a homodimer to repress a number of genes involved in the response to DNA damage (SOS response), including itself and RecA. RecA, in the presence of single-stranded DNA, acts as a co-protease to activate a latent autolytic protease activity (EC 3.4.21.88) of LexA, where the active site Ser is part of LexA. The autolytic cleavage site is an Ala-Gly bond in LexA (at position 84-85 in E. coli LexA; this sequence is replaced by Gly-Gly in Synechocystis). The cleavage leads to derepression of the SOS regulon and eventually to DNA repair. LexA in Bacillus subtilis is called DinR. LexA is much less broadly distributed than RecA.
Probab=82.89 E-value=2.2 Score=34.77 Aligned_cols=50 Identities=16% Similarity=0.129 Sum_probs=38.2
Q ss_pred HhcChHHHHHhcC--CCCCCCHHHHHhhCCCCCCCC-cchHHHHHHHHhcCCccccc
Q 044458 38 IELDLLEVIAKAG--PGAFMSPKQIASQLPTKNSDA-HILLDRILRLLASYSVLNCS 91 (241)
Q Consensus 38 ~~lglfd~L~~~~--~~~~~t~~eLA~~~g~~~~~~-~~~l~rlLr~L~~~g~l~~~ 91 (241)
.+..|++.|.+.. .+-+.|..|||+.+|+ + ...+.+.|+.|...|++...
T Consensus 7 ~q~~iL~~l~~~~~~~~~~~~~~ela~~~~~----~s~~tv~~~l~~L~~~g~i~~~ 59 (199)
T TIGR00498 7 RQQEVLDLIRAHIESTGYPPSIREIARAVGL----RSPSAAEEHLKALERKGYIERD 59 (199)
T ss_pred HHHHHHHHHHHHHHhcCCCCcHHHHHHHhCC----CChHHHHHHHHHHHHCCCEecC
Confidence 3445555555310 0146899999999999 8 88999999999999999974
No 279
>PF01170 UPF0020: Putative RNA methylase family UPF0020; InterPro: IPR000241 This domain is probably a methylase. It is associated with the THUMP domain that also occurs with RNA modification domains [].; PDB: 3LDU_A 3LDG_A 3K0B_A 3V8V_B 3V97_A 3TLJ_A 3TM5_B 3TM4_A 3TMA_A.
Probab=82.70 E-value=1.3 Score=35.64 Aligned_cols=50 Identities=22% Similarity=0.149 Sum_probs=36.0
Q ss_pred HHHHhcCCCCCCCeEEEecCCchHHHHHHHHHCCCCc---------EEEccc-hHHHhcCC
Q 044458 188 KFLENYKGFEGLQSVVDVGGGIGASLDMIISKYPSIK---------GINFDL-PHVIQDAP 238 (241)
Q Consensus 188 ~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~---------~~v~Dl-P~vi~~a~ 238 (241)
.++..-. |.....|+|-=||+|+++++.+...+++. ++..|. +.+++.++
T Consensus 19 ~ll~la~-~~~~~~vlDP~CGsGtiliEaa~~~~~~~~~~~~~~~~~~g~Di~~~~v~~a~ 78 (179)
T PF01170_consen 19 ALLNLAG-WRPGDVVLDPFCGSGTILIEAALMGANIPPLNDINELKIIGSDIDPKAVRGAR 78 (179)
T ss_dssp HHHHHTT---TTS-EEETT-TTSHHHHHHHHHHTTTSTTTH-CH--EEEEESSHHHHHHHH
T ss_pred HHHHHhC-CCCCCEEeecCCCCCHHHHHHHHHhhCcccccccccccEEecCCCHHHHHHHH
Confidence 3444444 77778999999999999999988888877 888898 77776543
No 280
>PTZ00326 phenylalanyl-tRNA synthetase alpha chain; Provisional
Probab=82.63 E-value=1.4 Score=41.36 Aligned_cols=70 Identities=13% Similarity=0.148 Sum_probs=55.0
Q ss_pred HHhcChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCcchHHHHHHHHhcCCccccccccCCCCccccceecCccccc-ccc
Q 044458 37 AIELDLLEVIAKAGPGAFMSPKQIASQLPTKNSDAHILLDRILRLLASYSVLNCSLHTLPDGGVERLYGLAPVCKF-LTK 115 (241)
Q Consensus 37 a~~lglfd~L~~~~~~~~~t~~eLA~~~g~~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~g~~~~~y~~t~~s~~-l~~ 115 (241)
..+..|+..|.+.. +..+..+||+.+|+ ++..+.+.+..|.+.|+++.... . ...|.+|+.++. +..
T Consensus 6 ~~e~~iL~~l~~~~--~~~~~~~la~~~~~----~~~~v~~~~~~L~~kg~v~~~~~--~----~~~~~LT~eG~~~~~~ 73 (494)
T PTZ00326 6 LEENTILSKLESEN--EIVNSLALAESLNI----DHQKVVGAIKSLESANYITTEMK--K----SNTWTLTEEGEDYLKN 73 (494)
T ss_pred HHHHHHHHHHHhcC--CCCCHHHHHHHcCC----CHHHHHHHHHHHHhCCCEEEEEE--E----EEEEEECHHHHHHHHc
Confidence 45666778887622 47899999999999 99999999999999999876421 1 689999999984 444
Q ss_pred CCC
Q 044458 116 NED 118 (241)
Q Consensus 116 ~~~ 118 (241)
+.+
T Consensus 74 G~P 76 (494)
T PTZ00326 74 GSP 76 (494)
T ss_pred CCH
Confidence 443
No 281
>COG0030 KsgA Dimethyladenosine transferase (rRNA methylation) [Translation, ribosomal structure and biogenesis]
Probab=82.57 E-value=2.9 Score=35.95 Aligned_cols=44 Identities=20% Similarity=0.438 Sum_probs=35.0
Q ss_pred HHHHHHhcCCCCCCCeEEEecCCchHHHHHHHHHCCCCcEEEccc
Q 044458 186 MKKFLENYKGFEGLQSVVDVGGGIGASLDMIISKYPSIKGINFDL 230 (241)
Q Consensus 186 ~~~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl 230 (241)
.+.+++..+ ......|+.||.|.|.+...++++-..+.++=+|.
T Consensus 19 ~~kIv~~a~-~~~~d~VlEIGpG~GaLT~~Ll~~~~~v~aiEiD~ 62 (259)
T COG0030 19 IDKIVEAAN-ISPGDNVLEIGPGLGALTEPLLERAARVTAIEIDR 62 (259)
T ss_pred HHHHHHhcC-CCCCCeEEEECCCCCHHHHHHHhhcCeEEEEEeCH
Confidence 456777666 55678999999999999999999988866655553
No 282
>KOG1661 consensus Protein-L-isoaspartate(D-aspartate) O-methyltransferase [Posttranslational modification, protein turnover, chaperones]
Probab=82.53 E-value=0.81 Score=38.06 Aligned_cols=43 Identities=16% Similarity=0.184 Sum_probs=30.9
Q ss_pred CCCCCeEEEecCCchHHHHHHHHH--CCCCcEEEccc-hHHHhcCC
Q 044458 196 FEGLQSVVDVGGGIGASLDMIISK--YPSIKGINFDL-PHVIQDAP 238 (241)
Q Consensus 196 ~~~~~~vvDVGGG~G~~~~~l~~~--~P~l~~~v~Dl-P~vi~~a~ 238 (241)
+..-.++||||+|+|.+...+..- -|....+.+|+ |++|+.++
T Consensus 80 L~pG~s~LdvGsGSGYLt~~~~~mvg~~g~~~~GIEh~~eLVe~Sk 125 (237)
T KOG1661|consen 80 LQPGASFLDVGSGSGYLTACFARMVGATGGNVHGIEHIPELVEYSK 125 (237)
T ss_pred hccCcceeecCCCccHHHHHHHHHhcCCCccccchhhhHHHHHHHH
Confidence 445688999999999999877742 23333367777 88888664
No 283
>COG4565 CitB Response regulator of citrate/malate metabolism [Transcription / Signal transduction mechanisms]
Probab=82.36 E-value=1.8 Score=36.03 Aligned_cols=43 Identities=19% Similarity=0.326 Sum_probs=36.4
Q ss_pred hHHHHHhcCCCCCCCHHHHHhhCCCCCCCCcchHHHHHHHHhcCCcccc
Q 044458 42 LLEVIAKAGPGAFMSPKQIASQLPTKNSDAHILLDRILRLLASYSVLNC 90 (241)
Q Consensus 42 lfd~L~~~~~~~~~t~~eLA~~~g~~~~~~~~~l~rlLr~L~~~g~l~~ 90 (241)
|.+.|... +.+.|++|+|+++|+ +.--.||-|.+|+..|++..
T Consensus 163 i~~~~~~~--~~~~Taeela~~~gi----SRvTaRRYLeyl~~~~~l~a 205 (224)
T COG4565 163 VREALKEP--DQELTAEELAQALGI----SRVTARRYLEYLVSNGILEA 205 (224)
T ss_pred HHHHHhCc--CCccCHHHHHHHhCc----cHHHHHHHHHHHHhcCeeeE
Confidence 55566622 268999999999999 88899999999999999985
No 284
>PRK05638 threonine synthase; Validated
Probab=82.04 E-value=1.5 Score=40.66 Aligned_cols=60 Identities=13% Similarity=0.168 Sum_probs=45.8
Q ss_pred ChHHHHHhcCCCCCCCHHHHHhhCC--CCCCCCcchHHHHHHHHhcCCccccccccCCCCccccceecCccccc
Q 044458 41 DLLEVIAKAGPGAFMSPKQIASQLP--TKNSDAHILLDRILRLLASYSVLNCSLHTLPDGGVERLYGLAPVCKF 112 (241)
Q Consensus 41 glfd~L~~~~~~~~~t~~eLA~~~g--~~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~g~~~~~y~~t~~s~~ 112 (241)
.|+..|.+ ++.+.-||++.++ + +...+.+.|+.|...|+++... ..|- .-.|++|+.++.
T Consensus 375 ~IL~~L~~----~~~~~~el~~~l~~~~----s~~~v~~hL~~Le~~GLV~~~~---~~g~-~~~Y~Lt~~g~~ 436 (442)
T PRK05638 375 EILKILSE----REMYGYEIWKALGKPL----KYQAVYQHIKELEELGLIEEAY---RKGR-RVYYKLTEKGRR 436 (442)
T ss_pred HHHHHHhh----CCccHHHHHHHHcccC----CcchHHHHHHHHHHCCCEEEee---cCCC-cEEEEECcHHHH
Confidence 36666765 6899999999998 7 7889999999999999997531 1121 346888887763
No 285
>PF05584 Sulfolobus_pRN: Sulfolobus plasmid regulatory protein; InterPro: IPR008848 This family consists of several plasmid regulatory proteins from the extreme thermophilic and acidophilic archaea Sulfolobus.
Probab=81.91 E-value=2.7 Score=28.72 Aligned_cols=43 Identities=14% Similarity=0.172 Sum_probs=37.9
Q ss_pred ChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCcchHHHHHHHHhcCCccccc
Q 044458 41 DLLEVIAKAGPGAFMSPKQIASQLPTKNSDAHILLDRILRLLASYSVLNCS 91 (241)
Q Consensus 41 glfd~L~~~~~~~~~t~~eLA~~~g~~~~~~~~~l~rlLr~L~~~g~l~~~ 91 (241)
.|...|+. +..|.+||-+.+|+ +...|-..|.-|...|++.+.
T Consensus 9 ~IL~~ls~----~c~TLeeL~ekTgi----~k~~LlV~LsrL~k~GiI~Rk 51 (72)
T PF05584_consen 9 KILIILSK----RCCTLEELEEKTGI----SKNTLLVYLSRLAKRGIIERK 51 (72)
T ss_pred HHHHHHHh----ccCCHHHHHHHHCC----CHHHHHHHHHHHHHCCCeeee
Confidence 35566666 58999999999999 999999999999999999875
No 286
>COG1675 TFA1 Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=81.82 E-value=1.9 Score=34.80 Aligned_cols=45 Identities=13% Similarity=0.191 Sum_probs=39.1
Q ss_pred cChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCcchHHHHHHHHhcCCccccc
Q 044458 40 LDLLEVIAKAGPGAFMSPKQIASQLPTKNSDAHILLDRILRLLASYSVLNCS 91 (241)
Q Consensus 40 lglfd~L~~~~~~~~~t~~eLA~~~g~~~~~~~~~l~rlLr~L~~~g~l~~~ 91 (241)
..|+++|.+. |-.|-++||+.+|+ ...-++|+|..|...|++...
T Consensus 21 ~~v~~~l~~k---ge~tDeela~~l~i----~~~~vrriL~~L~e~~li~~~ 65 (176)
T COG1675 21 VLVVDALLEK---GELTDEELAELLGI----KKNEVRRILYALYEDGLISYR 65 (176)
T ss_pred hHHHHHHHhc---CCcChHHHHHHhCc----cHHHHHHHHHHHHhCCceEEE
Confidence 3477888774 46999999999999 999999999999999999853
No 287
>COG0293 FtsJ 23S rRNA methylase [Translation, ribosomal structure and biogenesis]
Probab=81.60 E-value=3.7 Score=33.99 Aligned_cols=51 Identities=22% Similarity=0.233 Sum_probs=38.1
Q ss_pred chhhHHHHHHhcCCCCCCCeEEEecCCchHHHHHHHHHCCC-CcEEEccchH
Q 044458 182 STITMKKFLENYKGFEGLQSVVDVGGGIGASLDMIISKYPS-IKGINFDLPH 232 (241)
Q Consensus 182 ~~~~~~~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~-l~~~v~DlP~ 232 (241)
+......+.+.|.-+++...|+|+|...|.++..+++.-.. -+++.+|+-+
T Consensus 29 Aa~KL~el~~k~~i~~~~~~ViDLGAAPGgWsQva~~~~~~~~~ivavDi~p 80 (205)
T COG0293 29 AAYKLLELNEKFKLFKPGMVVVDLGAAPGGWSQVAAKKLGAGGKIVAVDILP 80 (205)
T ss_pred HHHHHHHHHHhcCeecCCCEEEEcCCCCCcHHHHHHHHhCCCCcEEEEECcc
Confidence 33444566777765778899999999999999987776554 5678888743
No 288
>PRK10906 DNA-binding transcriptional repressor GlpR; Provisional
Probab=81.35 E-value=1.6 Score=37.26 Aligned_cols=46 Identities=13% Similarity=0.235 Sum_probs=40.8
Q ss_pred hcChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCcchHHHHHHHHhcCCccccc
Q 044458 39 ELDLLEVIAKAGPGAFMSPKQIASQLPTKNSDAHILLDRILRLLASYSVLNCS 91 (241)
Q Consensus 39 ~lglfd~L~~~~~~~~~t~~eLA~~~g~~~~~~~~~l~rlLr~L~~~g~l~~~ 91 (241)
...|.+.|.+. +.+++.|||+.+++ ++.-+||-|..|...|++.+.
T Consensus 7 ~~~Il~~l~~~---~~~~~~ela~~l~v----S~~TiRRdL~~Le~~g~l~r~ 52 (252)
T PRK10906 7 HDAIIELVKQQ---GYVSTEELVEHFSV----SPQTIRRDLNDLAEQNKILRH 52 (252)
T ss_pred HHHHHHHHHHc---CCEeHHHHHHHhCC----CHHHHHHHHHHHHHCCCEEEe
Confidence 34578888775 68999999999999 999999999999999999875
No 289
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=81.29 E-value=1.9 Score=33.61 Aligned_cols=42 Identities=19% Similarity=0.312 Sum_probs=35.8
Q ss_pred cChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCcchHHHHHHHHhcCCcc
Q 044458 40 LDLLEVIAKAGPGAFMSPKQIASQLPTKNSDAHILLDRILRLLASYSVL 88 (241)
Q Consensus 40 lglfd~L~~~~~~~~~t~~eLA~~~g~~~~~~~~~l~rlLr~L~~~g~l 88 (241)
.-|+++|-.. +.+|-+|||+.+|+ +...++++|..|...+++
T Consensus 4 ~~v~d~L~~~---~~~~dedLa~~l~i----~~n~vRkiL~~L~ed~~~ 45 (147)
T smart00531 4 FLVLDALMRN---GCVTEEDLAELLGI----KQKQLRKILYLLYDEKLI 45 (147)
T ss_pred EeehHHHHhc---CCcCHHHHHHHhCC----CHHHHHHHHHHHHhhhcc
Confidence 3578888764 58999999999999 999999999999995544
No 290
>TIGR02987 met_A_Alw26 type II restriction m6 adenine DNA methyltransferase, Alw26I/Eco31I/Esp3I family. Members of this family are the m6-adenine DNA methyltransferase protein, or domain of a fusion protein that also carries m5 cytosine methyltransferase activity, of type II restriction systems of the Alw26I/Eco31I/Esp3I family. A methyltransferase of this family is alway accompanied by a type II restriction endonuclease from the Alw26I/Eco31I/Esp3I family (TIGR02986) and by an adenine-specific modification methyltransferase. Members of this family are unusual in that regions of similarity to homologs outside this family are circularly permuted.
Probab=81.16 E-value=1 Score=42.64 Aligned_cols=40 Identities=15% Similarity=0.214 Sum_probs=31.2
Q ss_pred CCCeEEEecCCchHHHHHHHHHCCC--------CcEEEccc-hHHHhcC
Q 044458 198 GLQSVVDVGGGIGASLDMIISKYPS--------IKGINFDL-PHVIQDA 237 (241)
Q Consensus 198 ~~~~vvDVGGG~G~~~~~l~~~~P~--------l~~~v~Dl-P~vi~~a 237 (241)
...+|+|.+||+|.++.++++..+. +....+|+ |.+++.+
T Consensus 31 ~~~~ilDP~cGsG~fl~~~~~~~~~~~~~~~~~~~i~g~DId~~a~~~a 79 (524)
T TIGR02987 31 TKTKIIDPCCGDGRLIAALLKKNEEINYFKEVELNIYFADIDKTLLKRA 79 (524)
T ss_pred cceEEEeCCCCccHHHHHHHHHHHhcCCcccceeeeeeechhHHHHHHH
Confidence 4579999999999999999988763 45688888 5555443
No 291
>PLN02589 caffeoyl-CoA O-methyltransferase
Probab=80.99 E-value=1.5 Score=37.42 Aligned_cols=42 Identities=17% Similarity=0.109 Sum_probs=34.7
Q ss_pred CCCCeEEEecCCchHHHHHHHHHCC-CCcEEEccc-hHHHhcCC
Q 044458 197 EGLQSVVDVGGGIGASLDMIISKYP-SIKGINFDL-PHVIQDAP 238 (241)
Q Consensus 197 ~~~~~vvDVGGG~G~~~~~l~~~~P-~l~~~v~Dl-P~vi~~a~ 238 (241)
.+.++||+||.+.|.-++.+++..| +-+.+-+|. |+..+.|+
T Consensus 78 ~~ak~iLEiGT~~GySal~la~al~~~g~v~tiE~~~~~~~~Ar 121 (247)
T PLN02589 78 INAKNTMEIGVYTGYSLLATALALPEDGKILAMDINRENYELGL 121 (247)
T ss_pred hCCCEEEEEeChhhHHHHHHHhhCCCCCEEEEEeCCHHHHHHHH
Confidence 4579999999999999999999874 678888888 66666654
No 292
>PF08221 HTH_9: RNA polymerase III subunit RPC82 helix-turn-helix domain; InterPro: IPR013197 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. This family consists of several DNA-directed RNA polymerase III polypeptides which are related to the Saccharomyces cerevisiae (Baker's yeast) RPC82 protein. RNA polymerase C (III) promotes the transcription of tRNA and 5S RNA genes. In S. cerevisiae, the enzyme is composed of 15 subunits, ranging from 10 kDa to about 160 kDa []. This region is probably a DNA-binding helix-turn-helix.; PDB: 2XV4_S 2XUB_A.
Probab=80.96 E-value=1.4 Score=29.11 Aligned_cols=42 Identities=12% Similarity=0.165 Sum_probs=34.3
Q ss_pred hHHHHHhcCCCCCCCHHHHHhhCCCCCCCCcchHHHHHHHHhcCCcccc
Q 044458 42 LLEVIAKAGPGAFMSPKQIASQLPTKNSDAHILLDRILRLLASYSVLNC 90 (241)
Q Consensus 42 lfd~L~~~~~~~~~t~~eLA~~~g~~~~~~~~~l~rlLr~L~~~g~l~~ 90 (241)
|++.|-.. |..|..+|++.+++ +++.++.-|-.|...+++..
T Consensus 18 V~~~Ll~~---G~ltl~~i~~~t~l----~~~~Vk~~L~~LiQh~~v~y 59 (62)
T PF08221_consen 18 VGEVLLSR---GRLTLREIVRRTGL----SPKQVKKALVVLIQHNLVQY 59 (62)
T ss_dssp HHHHHHHC----SEEHHHHHHHHT------HHHHHHHHHHHHHTTSEEE
T ss_pred HHHHHHHc---CCcCHHHHHHHhCC----CHHHHHHHHHHHHHcCCeee
Confidence 56667664 68999999999999 99999999999999999875
No 293
>COG5631 Predicted transcription regulator, contains HTH domain (MarR family) [Transcription]
Probab=80.86 E-value=10 Score=30.20 Aligned_cols=78 Identities=18% Similarity=0.130 Sum_probs=58.1
Q ss_pred HHhhhHHHHHHHHHHhcC-------hHHHHHhcCCCCCCCHHHHHhhCCCCCCCCcchHHHHHHHHhcCCccccccccCC
Q 044458 24 LTSASVLPMVLKSAIELD-------LLEVIAKAGPGAFMSPKQIASQLPTKNSDAHILLDRILRLLASYSVLNCSLHTLP 96 (241)
Q Consensus 24 ~~~g~~~~~~L~~a~~lg-------lfd~L~~~~~~~~~t~~eLA~~~g~~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~ 96 (241)
.+++-|.-.|+.+|.+.+ |...+.-.+ .++++.||+..+++ . |-..+..-||-|...|+++.. .
T Consensus 63 ~Af~rW~vrCmAaag~~~ls~~e~l~lH~irhrd--R~K~laDic~~ln~--e-Dth~itYslrKL~k~gLit~t----~ 133 (199)
T COG5631 63 EAFGRWQVRCMAAAGEFSLSGPENLLLHIIRHRD--RPKSLADICQMLNR--E-DTHNITYSLRKLLKGGLITRT----G 133 (199)
T ss_pred HHHHHHHHHHHHHhcCCCCcchHHHHHHHHhhcC--chhhHHHHHHHhcc--c-cchhHHHHHHHHHhccceecC----C
Confidence 356778888998887766 345555443 79999999999998 1 556788999999999999975 2
Q ss_pred CCccccceecCcccc
Q 044458 97 DGGVERLYGLAPVCK 111 (241)
Q Consensus 97 ~g~~~~~y~~t~~s~ 111 (241)
.|. +-.|..|+.+.
T Consensus 134 ~gk-evTy~vTa~G~ 147 (199)
T COG5631 134 SGK-EVTYEVTALGH 147 (199)
T ss_pred CCc-eEEEEEecchH
Confidence 332 45788877553
No 294
>PRK10870 transcriptional repressor MprA; Provisional
Probab=80.57 E-value=12 Score=29.97 Aligned_cols=66 Identities=12% Similarity=0.018 Sum_probs=45.3
Q ss_pred ChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCcchHHHHHHHHhcCCccccccccCCCCccccceecCcccccc
Q 044458 41 DLLEVIAKAGPGAFMSPKQIASQLPTKNSDAHILLDRILRLLASYSVLNCSLHTLPDGGVERLYGLAPVCKFL 113 (241)
Q Consensus 41 glfd~L~~~~~~~~~t~~eLA~~~g~~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~g~~~~~y~~t~~s~~l 113 (241)
.++-.|...+ ++++|..|||+.+++ +...+.+++.-|...|++.+... +.|+ ..-...+|+.++.+
T Consensus 59 ~iL~~L~~~~-~~~it~~eLa~~l~l----~~~tvsr~v~rLe~kGlV~R~~~-~~Dr-R~~~v~LT~~G~~~ 124 (176)
T PRK10870 59 MALITLESQE-NHSIQPSELSCALGS----SRTNATRIADELEKRGWIERRES-DNDR-RCLHLQLTEKGHEF 124 (176)
T ss_pred HHHHHHhcCC-CCCcCHHHHHHHHCC----CHHHHHHHHHHHHHCCCEEecCC-CCCC-CeeEEEECHHHHHH
Confidence 3555554322 257999999999999 99999999999999999997521 1111 01245566655533
No 295
>COG1510 Predicted transcriptional regulators [Transcription]
Probab=80.33 E-value=2.2 Score=34.24 Aligned_cols=35 Identities=14% Similarity=0.152 Sum_probs=33.2
Q ss_pred CCCCHHHHHhhCCCCCCCCcchHHHHHHHHhcCCccccc
Q 044458 53 AFMSPKQIASQLPTKNSDAHILLDRILRLLASYSVLNCS 91 (241)
Q Consensus 53 ~~~t~~eLA~~~g~~~~~~~~~l~rlLr~L~~~g~l~~~ 91 (241)
+|+|++||++++|+ +...+..-|+-|...+++.+.
T Consensus 40 ~Pmtl~Ei~E~lg~----Sks~vS~~lkkL~~~~lV~~~ 74 (177)
T COG1510 40 KPLTLDEIAEALGM----SKSNVSMGLKKLQDWNLVKKV 74 (177)
T ss_pred CCccHHHHHHHHCC----CcchHHHHHHHHHhcchHHhh
Confidence 79999999999999 888999999999999999875
No 296
>PF05206 TRM13: Methyltransferase TRM13; InterPro: IPR007871 This entry consists of eukaryotic and bacterial proteins that specifically methylates guanosine-4 in various tRNAs with a Gly(CCG), His or Pro signatures []. The alignment contains some conserved cysteines and histidines that might form a zinc binding site.; GO: 0008168 methyltransferase activity, 0008033 tRNA processing
Probab=80.24 E-value=4.2 Score=34.94 Aligned_cols=36 Identities=14% Similarity=0.181 Sum_probs=31.8
Q ss_pred CCCCCeEEEecCCchHHHHHHHHHC-----CCCcEEEccch
Q 044458 196 FEGLQSVVDVGGGIGASLDMIISKY-----PSIKGINFDLP 231 (241)
Q Consensus 196 ~~~~~~vvDVGGG~G~~~~~l~~~~-----P~l~~~v~DlP 231 (241)
+.....+|+.|+|.|.++..+.+.. +..+++++|+-
T Consensus 16 l~~~~~~vEfGaGrg~LS~~v~~~~~~~~~~~~~~~lIDR~ 56 (259)
T PF05206_consen 16 LNPDSCFVEFGAGRGELSRWVAQALQEDKPSNSRFVLIDRA 56 (259)
T ss_pred CCCCCEEEEECCCchHHHHHHHHHhhhcccCCccEEEEecC
Confidence 6677899999999999999999999 56788999983
No 297
>PF00392 GntR: Bacterial regulatory proteins, gntR family; InterPro: IPR000524 Many bacterial transcription regulation proteins bind DNA through a helix-turn-helix (HTH) motif, which can be classified into subfamilies on the basis of sequence similarities. The HTH GntR family has many members distributed among diverse bacterial groups that regulate various biological processes. It was named GntR after the Bacillus subtilis repressor of the gluconate operon []. Family members include GntR, HutC, KorA, NtaR, FadR, ExuR, FarR, DgoR and PhnF. The crystal structure of the FadR protein has been determined []. In general, these proteins contain a DNA-binding HTH domain at the N terminus, and an effector-binding or oligomerisation domain at the C terminus (IPR011711 from INTERPRO). The DNA-binding domain is well conserved in structure for the whole of the GntR family, consisting of a 3-helical bundle core with a small beta-sheet (wing); the GntR winged helix structure is similar to that found in several other transcriptional regulator families. The regions outside the DNA-binding domain are more variable and are consequently used to define GntR subfamilies []. This entry represents the N-terminal DNA-binding domain of the GntR family.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 1HW1_B 1H9T_A 1HW2_A 1H9G_A 1E2X_A 3IHU_A 3C7J_A 2RA5_A 3BY6_C 3IC7_A ....
Probab=80.24 E-value=1.3 Score=29.20 Aligned_cols=35 Identities=14% Similarity=0.230 Sum_probs=30.5
Q ss_pred CCC-CHHHHHhhCCCCCCCCcchHHHHHHHHhcCCccccc
Q 044458 53 AFM-SPKQIASQLPTKNSDAHILLDRILRLLASYSVLNCS 91 (241)
Q Consensus 53 ~~~-t~~eLA~~~g~~~~~~~~~l~rlLr~L~~~g~l~~~ 91 (241)
..+ |..+||+.+++ +..-+++.|+.|...|++...
T Consensus 22 ~~lps~~~la~~~~v----sr~tvr~al~~L~~~g~i~~~ 57 (64)
T PF00392_consen 22 DRLPSERELAERYGV----SRTTVREALRRLEAEGLIERR 57 (64)
T ss_dssp SBE--HHHHHHHHTS-----HHHHHHHHHHHHHTTSEEEE
T ss_pred CEeCCHHHHHHHhcc----CCcHHHHHHHHHHHCCcEEEE
Confidence 467 99999999999 999999999999999999874
No 298
>KOG1500 consensus Protein arginine N-methyltransferase CARM1 [Posttranslational modification, protein turnover, chaperones; Transcription]
Probab=80.06 E-value=2.2 Score=38.16 Aligned_cols=23 Identities=30% Similarity=0.445 Sum_probs=18.1
Q ss_pred CCCCCeEEEecCCchHHHHHHHHH
Q 044458 196 FEGLQSVVDVGGGIGASLDMIISK 219 (241)
Q Consensus 196 ~~~~~~vvDVGGG~G~~~~~l~~~ 219 (241)
|++ +.|||||+|+|.++.-.+++
T Consensus 176 F~~-kiVlDVGaGSGILS~FAaqA 198 (517)
T KOG1500|consen 176 FQD-KIVLDVGAGSGILSFFAAQA 198 (517)
T ss_pred cCC-cEEEEecCCccHHHHHHHHh
Confidence 544 89999999999988665554
No 299
>PRK09802 DNA-binding transcriptional regulator AgaR; Provisional
Probab=80.06 E-value=1.9 Score=37.17 Aligned_cols=47 Identities=4% Similarity=0.105 Sum_probs=41.6
Q ss_pred HhcChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCcchHHHHHHHHhcCCccccc
Q 044458 38 IELDLLEVIAKAGPGAFMSPKQIASQLPTKNSDAHILLDRILRLLASYSVLNCS 91 (241)
Q Consensus 38 ~~lglfd~L~~~~~~~~~t~~eLA~~~g~~~~~~~~~l~rlLr~L~~~g~l~~~ 91 (241)
-...|.+.|... +.+++.|||+.+++ ++.-+||=|..|...|++.+.
T Consensus 18 R~~~Il~~L~~~---~~vtv~eLa~~l~V----S~~TIRRDL~~Le~~G~l~r~ 64 (269)
T PRK09802 18 RREQIIQRLRQQ---GSVQVNDLSALYGV----STVTIRNDLAFLEKQGIAVRA 64 (269)
T ss_pred HHHHHHHHHHHc---CCEeHHHHHHHHCC----CHHHHHHHHHHHHhCCCeEEE
Confidence 345678888875 57999999999999 999999999999999999975
No 300
>PF02475 Met_10: Met-10+ like-protein; InterPro: IPR003402 This entry represents the Trm5 family. Trm5 specifically methylates the N1 position of guanosine-37 in various tRNAs [, , ]. Another members of this family, tRNA wybutosine-synthesizing protein 2 (Tyw2) and its homologues, are S-adenosyl-L-methionine-dependent transferases that act as a component of the wybutosine biosynthesis pathway [, ]. tRNA wybutosine-synthesizing protein 2 was originally thought to be a methyltransferase [].; GO: 0016740 transferase activity; PDB: 3A27_A 2ZZN_B 2YX1_A 2ZZM_A 3AY0_B 3K6R_A 3A26_A 3A25_A.
Probab=80.04 E-value=2 Score=35.38 Aligned_cols=41 Identities=22% Similarity=0.202 Sum_probs=32.0
Q ss_pred CCCCCeEEEecCCchHHHHHHHHHCCCCcEEEccc-hHHHhc
Q 044458 196 FEGLQSVVDVGGGIGASLDMIISKYPSIKGINFDL-PHVIQD 236 (241)
Q Consensus 196 ~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-P~vi~~ 236 (241)
.....+|+|.-||.|.+++.+++..+..+++..|+ |.+++.
T Consensus 99 v~~~e~VlD~faGIG~f~l~~ak~~~~~~V~A~d~Np~a~~~ 140 (200)
T PF02475_consen 99 VKPGEVVLDMFAGIGPFSLPIAKHGKAKRVYAVDLNPDAVEY 140 (200)
T ss_dssp --TT-EEEETT-TTTTTHHHHHHHT-SSEEEEEES-HHHHHH
T ss_pred CCcceEEEEccCCccHHHHHHhhhcCccEEEEecCCHHHHHH
Confidence 34568999999999999999999888888999999 777664
No 301
>PF09824 ArsR: ArsR transcriptional regulator; InterPro: IPR014517 Members of this family of archaeal proteins are conserved transcriptional regulators belonging to the ArsR family.
Probab=79.96 E-value=2.6 Score=33.24 Aligned_cols=57 Identities=11% Similarity=0.203 Sum_probs=45.7
Q ss_pred HHHHHHHHhcChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCcchHHHHHHHHhcCCccccccccCCCC
Q 044458 31 PMVLKSAIELDLLEVIAKAGPGAFMSPKQIASQLPTKNSDAHILLDRILRLLASYSVLNCSLHTLPDG 98 (241)
Q Consensus 31 ~~~L~~a~~lglfd~L~~~~~~~~~t~~eLA~~~g~~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~g 98 (241)
.++......-.||+.|.+ +.+|.+||.+..|- +. ++-|..|-..|+++..++.+++|
T Consensus 11 l~~f~s~~~kkV~~~Ls~----~W~T~~El~e~~G~----d~---~~~L~~LkK~gLiE~qWrmP~pG 67 (160)
T PF09824_consen 11 LQTFNSEVYKKVYDELSK----GWMTEEELEEKYGK----DV---RESLLILKKGGLIESQWRMPEPG 67 (160)
T ss_pred HHHhCCHHHHHHHHHHHh----ccCCHHHHHHHHCc----CH---HHHHHHHHHcCchhhccccCCCC
Confidence 345556677889999998 79999999999997 54 78889999999998766554443
No 302
>TIGR01321 TrpR trp operon repressor, proteobacterial. This model represents TrpR, the repressor of the trp operon. It is found so far only in the gamma subdivision of the proteobacteria and in Chlamydia trachomatis. All members belong to species capable of tryptophan biosynthesis.
Probab=79.08 E-value=2.7 Score=30.34 Aligned_cols=40 Identities=20% Similarity=0.191 Sum_probs=33.3
Q ss_pred HHHhcChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCcchHHHHHHHHh
Q 044458 36 SAIELDLLEVIAKAGPGAFMSPKQIASQLPTKNSDAHILLDRILRLLA 83 (241)
Q Consensus 36 ~a~~lglfd~L~~~~~~~~~t~~eLA~~~g~~~~~~~~~l~rlLr~L~ 83 (241)
.+.+.+|+..|-+ +++|-.|||+.+|+ +...+.|+=+.|.
T Consensus 41 l~~R~~i~~~Ll~----~~~tQrEIa~~lGi----S~atIsR~sn~lk 80 (94)
T TIGR01321 41 LGDRIRIVNELLN----GNMSQREIASKLGV----SIATITRGSNNLK 80 (94)
T ss_pred HHHHHHHHHHHHh----CCCCHHHHHHHhCC----ChhhhhHHHhhcc
Confidence 4567899998876 58999999999999 8878887777665
No 303
>PRK11760 putative 23S rRNA C2498 ribose 2'-O-ribose methyltransferase; Provisional
Probab=78.96 E-value=2.9 Score=37.47 Aligned_cols=37 Identities=16% Similarity=0.118 Sum_probs=30.7
Q ss_pred CCCCeEEEecCCchHHHHHHHHHCCCCcEEEccchHHHh
Q 044458 197 EGLQSVVDVGGGIGASLDMIISKYPSIKGINFDLPHVIQ 235 (241)
Q Consensus 197 ~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~DlP~vi~ 235 (241)
....++||||+++|.+...++++ +.+++.+|.-+..+
T Consensus 210 ~~g~~vlDLGAsPGGWT~~L~~r--G~~V~AVD~g~l~~ 246 (357)
T PRK11760 210 APGMRAVDLGAAPGGWTYQLVRR--GMFVTAVDNGPMAQ 246 (357)
T ss_pred CCCCEEEEeCCCCcHHHHHHHHc--CCEEEEEechhcCH
Confidence 45689999999999999999998 56889999755443
No 304
>KOG3191 consensus Predicted N6-DNA-methyltransferase [Translation, ribosomal structure and biogenesis]
Probab=78.83 E-value=2.3 Score=34.67 Aligned_cols=38 Identities=18% Similarity=0.375 Sum_probs=30.6
Q ss_pred CCeEEEecCCchHHHHHHHHHC-CCCcEEEccc-hHHHhc
Q 044458 199 LQSVVDVGGGIGASLDMIISKY-PSIKGINFDL-PHVIQD 236 (241)
Q Consensus 199 ~~~vvDVGGG~G~~~~~l~~~~-P~l~~~v~Dl-P~vi~~ 236 (241)
...+++||||+|..+..+++.. |+.-..--|+ |++++.
T Consensus 44 ~~i~lEIG~GSGvvstfL~~~i~~~~~~latDiNp~A~~~ 83 (209)
T KOG3191|consen 44 PEICLEIGCGSGVVSTFLASVIGPQALYLATDINPEALEA 83 (209)
T ss_pred ceeEEEecCCcchHHHHHHHhcCCCceEEEecCCHHHHHH
Confidence 6899999999999998887743 6666777888 777665
No 305
>PF00165 HTH_AraC: Bacterial regulatory helix-turn-helix proteins, AraC family; PDB: 1WPK_A 1ZGW_A 1U8B_A.
Probab=78.83 E-value=1.9 Score=25.74 Aligned_cols=29 Identities=14% Similarity=0.159 Sum_probs=22.6
Q ss_pred CCCCHHHHHhhCCCCCCCCcchHHHHHHHHhcC
Q 044458 53 AFMSPKQIASQLPTKNSDAHILLDRILRLLASY 85 (241)
Q Consensus 53 ~~~t~~eLA~~~g~~~~~~~~~l~rlLr~L~~~ 85 (241)
.+.+++|||+.+|+ ++..+.|+++....+
T Consensus 7 ~~~~l~~iA~~~g~----S~~~f~r~Fk~~~g~ 35 (42)
T PF00165_consen 7 QKLTLEDIAEQAGF----SPSYFSRLFKKETGM 35 (42)
T ss_dssp SS--HHHHHHHHTS-----HHHHHHHHHHHTSS
T ss_pred CCCCHHHHHHHHCC----CHHHHHHHHHHHHCc
Confidence 47999999999999 999999999876544
No 306
>PRK10434 srlR DNA-bindng transcriptional repressor SrlR; Provisional
Probab=77.97 E-value=2.3 Score=36.38 Aligned_cols=46 Identities=17% Similarity=0.192 Sum_probs=41.1
Q ss_pred hcChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCcchHHHHHHHHhcCCccccc
Q 044458 39 ELDLLEVIAKAGPGAFMSPKQIASQLPTKNSDAHILLDRILRLLASYSVLNCS 91 (241)
Q Consensus 39 ~lglfd~L~~~~~~~~~t~~eLA~~~g~~~~~~~~~l~rlLr~L~~~g~l~~~ 91 (241)
+..|.+.|.+. +.+++.|||+.+++ ++.-+||=|+.|...|++.+.
T Consensus 7 ~~~Il~~L~~~---~~v~v~eLa~~l~V----S~~TIRRDL~~Le~~g~l~r~ 52 (256)
T PRK10434 7 QAAILEYLQKQ---GKTSVEELAQYFDT----TGTTIRKDLVILEHAGTVIRT 52 (256)
T ss_pred HHHHHHHHHHc---CCEEHHHHHHHHCC----CHHHHHHHHHHHHHCCCEEEE
Confidence 34578889885 68999999999999 999999999999999999875
No 307
>PF13518 HTH_28: Helix-turn-helix domain
Probab=77.83 E-value=3.4 Score=25.51 Aligned_cols=29 Identities=14% Similarity=0.156 Sum_probs=26.8
Q ss_pred CCHHHHHhhCCCCCCCCcchHHHHHHHHhcCCc
Q 044458 55 MSPKQIASQLPTKNSDAHILLDRILRLLASYSV 87 (241)
Q Consensus 55 ~t~~eLA~~~g~~~~~~~~~l~rlLr~L~~~g~ 87 (241)
.|..++|+.+|+ +...+.+|++.....|+
T Consensus 13 ~s~~~~a~~~gi----s~~tv~~w~~~y~~~G~ 41 (52)
T PF13518_consen 13 ESVREIAREFGI----SRSTVYRWIKRYREGGI 41 (52)
T ss_pred CCHHHHHHHHCC----CHhHHHHHHHHHHhcCH
Confidence 499999999999 99999999999988885
No 308
>PF03291 Pox_MCEL: mRNA capping enzyme; InterPro: IPR004971 This is a family of viral mRNA capping enzymes. The enzyme catalyses the first two reactions in the mRNA cap formation pathway. It is a heterodimer consisting of a large and small subunit. This entry is the large subunit. ; GO: 0006370 mRNA capping; PDB: 3EPP_A 3BGV_C 2VDW_C 1RI5_A 1RI3_A 1RI1_A 1Z3C_A 1RI2_A 2HV9_A 1RI4_A.
Probab=77.78 E-value=1.6 Score=38.82 Aligned_cols=63 Identities=25% Similarity=0.285 Sum_probs=38.0
Q ss_pred HHHHHHHHHhcchhhHHHHHHhcCCCCCCCeEEEecCCchHHHHHHHHHCCCCc-EEEccc-hHHHhcCC
Q 044458 171 NKIFNNGMFSHSTITMKKFLENYKGFEGLQSVVDVGGGIGASLDMIISKYPSIK-GINFDL-PHVIQDAP 238 (241)
Q Consensus 171 ~~~f~~aM~~~~~~~~~~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~-~~v~Dl-P~vi~~a~ 238 (241)
.+.|+.++++. .+...+.....-....+|||+|||.|..+.-..++ +++ .+..|+ ++.|++|+
T Consensus 38 lR~fNNwvKs~---LI~~~~~~~~~~~~~~~VLDl~CGkGGDL~Kw~~~--~i~~~vg~Dis~~si~ea~ 102 (331)
T PF03291_consen 38 LRNFNNWVKSV---LIQKYAKKVKQNRPGLTVLDLCCGKGGDLQKWQKA--KIKHYVGIDISEESIEEAR 102 (331)
T ss_dssp HHHHHHHHHHH---HHHHHCHCCCCTTTT-EEEEET-TTTTTHHHHHHT--T-SEEEEEES-HHHHHHHH
T ss_pred HHHHhHHHHHH---HHHHHHHhhhccCCCCeEEEecCCCchhHHHHHhc--CCCEEEEEeCCHHHHHHHH
Confidence 56777776432 12222332210115689999999999988888776 454 588999 56676654
No 309
>PRK09954 putative kinase; Provisional
Probab=77.68 E-value=3.3 Score=36.95 Aligned_cols=44 Identities=14% Similarity=0.234 Sum_probs=39.2
Q ss_pred hcChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCcchHHHHHHHHhcCCccc
Q 044458 39 ELDLLEVIAKAGPGAFMSPKQIASQLPTKNSDAHILLDRILRLLASYSVLN 89 (241)
Q Consensus 39 ~lglfd~L~~~~~~~~~t~~eLA~~~g~~~~~~~~~l~rlLr~L~~~g~l~ 89 (241)
+..|++.|.++ +.+|..|||+.+++ +...+++.++.|...|++.
T Consensus 5 ~~~il~~l~~~---~~~s~~~la~~l~~----s~~~v~~~i~~L~~~g~i~ 48 (362)
T PRK09954 5 EKEILAILRRN---PLIQQNEIADILQI----SRSRVAAHIMDLMRKGRIK 48 (362)
T ss_pred HHHHHHHHHHC---CCCCHHHHHHHHCC----CHHHHHHHHHHHHHCCCcC
Confidence 44588888875 58999999999999 9999999999999999886
No 310
>PHA02701 ORF020 dsRNA-binding PKR inhibitor; Provisional
Probab=77.52 E-value=3.5 Score=33.44 Aligned_cols=49 Identities=20% Similarity=0.306 Sum_probs=42.3
Q ss_pred HHhcChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCcchHHHHHHHHhcCCccccc
Q 044458 37 AIELDLLEVIAKAGPGAFMSPKQIASQLPTKNSDAHILLDRILRLLASYSVLNCS 91 (241)
Q Consensus 37 a~~lglfd~L~~~~~~~~~t~~eLA~~~g~~~~~~~~~l~rlLr~L~~~g~l~~~ 91 (241)
-++..|.|.|...| ...|+-+||+++|+ +.+.+.|-|.-|...|.|...
T Consensus 4 ~~~~~i~~~l~~~~--~~~~a~~i~k~l~i----~k~~vNr~LY~L~~~~~v~~~ 52 (183)
T PHA02701 4 DCASLILTLLSSSG--DKLPAKRIAKELGI----SKHEANRCLYRLLESDAVSCE 52 (183)
T ss_pred hHHHHHHHHHHhcC--CCCcHHHHHHHhCc----cHHHHHHHHHHHhhcCcEecC
Confidence 35678999999874 25999999999999 889999999999999988764
No 311
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=77.40 E-value=2 Score=26.58 Aligned_cols=39 Identities=13% Similarity=0.178 Sum_probs=23.1
Q ss_pred hcChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCcchHHHHHHHHhcCC
Q 044458 39 ELDLLEVIAKAGPGAFMSPKQIASQLPTKNSDAHILLDRILRLLASYS 86 (241)
Q Consensus 39 ~lglfd~L~~~~~~~~~t~~eLA~~~g~~~~~~~~~l~rlLr~L~~~g 86 (241)
++.+...+.+ +.|..+||+.+|+ +..-+.++++.....|
T Consensus 7 R~~ii~l~~~-----G~s~~~ia~~lgv----s~~Tv~~w~kr~~~~G 45 (50)
T PF13384_consen 7 RAQIIRLLRE-----GWSIREIAKRLGV----SRSTVYRWIKRYREEG 45 (50)
T ss_dssp ---HHHHHHH-----T--HHHHHHHHTS-----HHHHHHHHT------
T ss_pred HHHHHHHHHC-----CCCHHHHHHHHCc----CHHHHHHHHHHccccc
Confidence 4455566655 5899999999999 9999999998776655
No 312
>PF05732 RepL: Firmicute plasmid replication protein (RepL); InterPro: IPR008813 This entry consists of proteins thought to be involved in plasmid replication. ; GO: 0006260 DNA replication, 0006276 plasmid maintenance
Probab=76.82 E-value=2.6 Score=33.70 Aligned_cols=44 Identities=18% Similarity=0.277 Sum_probs=38.7
Q ss_pred CCHHHHHhhCCCCCCCCcchHHHHHHHHhcCCccccccccCCCCccccceecCccc
Q 044458 55 MSPKQIASQLPTKNSDAHILLDRILRLLASYSVLNCSLHTLPDGGVERLYGLAPVC 110 (241)
Q Consensus 55 ~t~~eLA~~~g~~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~g~~~~~y~~t~~s 110 (241)
.|..+||+.+|+ +..-+.|.+..|...+++.+. . .+.|.+||.-
T Consensus 76 ~t~~~ia~~l~i----S~~Tv~r~ik~L~e~~iI~k~----~----~G~Y~iNP~~ 119 (165)
T PF05732_consen 76 ATQKEIAEKLGI----SKPTVSRAIKELEEKNIIKKI----R----NGAYMINPNF 119 (165)
T ss_pred eeHHHHHHHhCC----CHHHHHHHHHHHHhCCcEEEc----c----CCeEEECcHH
Confidence 689999999999 899999999999999999875 2 5889988843
No 313
>PRK10411 DNA-binding transcriptional activator FucR; Provisional
Probab=76.43 E-value=3.5 Score=34.93 Aligned_cols=46 Identities=13% Similarity=0.207 Sum_probs=40.1
Q ss_pred hcChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCcchHHHHHHHHhcCCccccc
Q 044458 39 ELDLLEVIAKAGPGAFMSPKQIASQLPTKNSDAHILLDRILRLLASYSVLNCS 91 (241)
Q Consensus 39 ~lglfd~L~~~~~~~~~t~~eLA~~~g~~~~~~~~~l~rlLr~L~~~g~l~~~ 91 (241)
...|.+.|.+. +..+.+|||+.+++ ++.-++|-|..|...|.+...
T Consensus 6 ~~~Il~~l~~~---~~~~~~eLa~~l~V----S~~TiRRdL~~L~~~~~l~r~ 51 (240)
T PRK10411 6 QQAIVDLLLNH---TSLTTEALAEQLNV----SKETIRRDLNELQTQGKILRN 51 (240)
T ss_pred HHHHHHHHHHc---CCCcHHHHHHHHCc----CHHHHHHHHHHHHHCCCEEEe
Confidence 34477888774 68999999999999 999999999999999998764
No 314
>PRK04424 fatty acid biosynthesis transcriptional regulator; Provisional
Probab=76.29 E-value=2.2 Score=34.65 Aligned_cols=46 Identities=13% Similarity=0.108 Sum_probs=40.5
Q ss_pred hcChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCcchHHHHHHHHhcCCccccc
Q 044458 39 ELDLLEVIAKAGPGAFMSPKQIASQLPTKNSDAHILLDRILRLLASYSVLNCS 91 (241)
Q Consensus 39 ~lglfd~L~~~~~~~~~t~~eLA~~~g~~~~~~~~~l~rlLr~L~~~g~l~~~ 91 (241)
+-.|.+.|... +.++.++||+.+++ ++.-+||=|+.|...|++.+.
T Consensus 9 ~~~Il~~l~~~---~~~~~~~La~~~~v----S~~TiRRDl~~L~~~g~~~r~ 54 (185)
T PRK04424 9 QKALQELIEEN---PFITDEELAEKFGV----SIQTIRLDRMELGIPELRERI 54 (185)
T ss_pred HHHHHHHHHHC---CCEEHHHHHHHHCc----CHHHHHHHHHHHhcchHHHHH
Confidence 34577888875 68999999999999 999999999999999999865
No 315
>COG1846 MarR Transcriptional regulators [Transcription]
Probab=75.82 E-value=3.7 Score=29.85 Aligned_cols=67 Identities=18% Similarity=0.204 Sum_probs=46.8
Q ss_pred HHHhcChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCcchHHHHHHHHhcCCccccccccCCCCccccceecCcccc
Q 044458 36 SAIELDLLEVIAKAGPGAFMSPKQIASQLPTKNSDAHILLDRILRLLASYSVLNCSLHTLPDGGVERLYGLAPVCK 111 (241)
Q Consensus 36 ~a~~lglfd~L~~~~~~~~~t~~eLA~~~g~~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~g~~~~~y~~t~~s~ 111 (241)
...+..+...|...+ +.+..+||+.+++ +...+.++++-|...|++..... +.|+ ..-.+.+|+.++
T Consensus 21 t~~q~~~L~~l~~~~---~~~~~~la~~l~i----~~~~vt~~l~~Le~~glv~r~~~-~~Dr-R~~~l~lT~~G~ 87 (126)
T COG1846 21 TPPQYQVLLALYEAG---GITVKELAERLGL----DRSTVTRLLKRLEDKGLIERLRD-PEDR-RAVLVRLTEKGR 87 (126)
T ss_pred CHHHHHHHHHHHHhC---CCcHHHHHHHHCC----CHHHHHHHHHHHHHCCCeeecCC-cccc-ceeeEEECccHH
Confidence 345566777777743 4444999999999 99999999999999999987631 1111 112556666555
No 316
>PF08280 HTH_Mga: M protein trans-acting positive regulator (MGA) HTH domain; InterPro: IPR013199 Mga is a DNA-binding protein that activates the expression of several important virulence genes in group A streptococcus in response to changing environmental conditions [].; PDB: 2WTE_A 3SQN_A.
Probab=75.74 E-value=3.2 Score=26.95 Aligned_cols=39 Identities=23% Similarity=0.364 Sum_probs=32.1
Q ss_pred HhcChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCcchHHHHHHHHh
Q 044458 38 IELDLLEVIAKAGPGAFMSPKQIASQLPTKNSDAHILLDRILRLLA 83 (241)
Q Consensus 38 ~~lglfd~L~~~~~~~~~t~~eLA~~~g~~~~~~~~~l~rlLr~L~ 83 (241)
-++.|++.|-+. +..|++|||+.+++ .++-++.-+..|-
T Consensus 6 rq~~Ll~~L~~~---~~~~~~ela~~l~~----S~rti~~~i~~L~ 44 (59)
T PF08280_consen 6 RQLKLLELLLKN---KWITLKELAKKLNI----SERTIKNDINELN 44 (59)
T ss_dssp HHHHHHHHHHHH---TSBBHHHHHHHCTS-----HHHHHHHHHHHH
T ss_pred HHHHHHHHHHcC---CCCcHHHHHHHHCC----CHHHHHHHHHHHH
Confidence 466788888774 68999999999999 9999988888776
No 317
>PRK10046 dpiA two-component response regulator DpiA; Provisional
Probab=75.66 E-value=3.5 Score=34.00 Aligned_cols=44 Identities=16% Similarity=0.224 Sum_probs=37.2
Q ss_pred ChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCcchHHHHHHHHhcCCcccc
Q 044458 41 DLLEVIAKAGPGAFMSPKQIASQLPTKNSDAHILLDRILRLLASYSVLNC 90 (241)
Q Consensus 41 glfd~L~~~~~~~~~t~~eLA~~~g~~~~~~~~~l~rlLr~L~~~g~l~~ 90 (241)
.|++.+.+.. .+.|.+|||+++++ ++.-+++-+..|+..|++..
T Consensus 166 ~Vl~~~~~g~--~g~s~~eIa~~l~i----S~~Tv~~~~~~~~~~~~~~~ 209 (225)
T PRK10046 166 AVRKLFKEPG--VQHTAETVAQALTI----SRTTARRYLEYCASRHLIIA 209 (225)
T ss_pred HHHHHHHcCC--CCcCHHHHHHHhCc----cHHHHHHHHHHHHhCCeEEE
Confidence 4667776511 26899999999999 99999999999999999986
No 318
>PRK01381 Trp operon repressor; Provisional
Probab=74.69 E-value=3.8 Score=29.81 Aligned_cols=40 Identities=15% Similarity=0.193 Sum_probs=31.5
Q ss_pred HHHhcChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCcchHHHHHHHHh
Q 044458 36 SAIELDLLEVIAKAGPGAFMSPKQIASQLPTKNSDAHILLDRILRLLA 83 (241)
Q Consensus 36 ~a~~lglfd~L~~~~~~~~~t~~eLA~~~g~~~~~~~~~l~rlLr~L~ 83 (241)
.+.+++|+..|-+ |.+|..|||+.+|+ +--.+.|.-+.|-
T Consensus 41 l~~R~~I~~~L~~----g~~sQREIa~~lGv----SiaTITRgsn~Lk 80 (99)
T PRK01381 41 LGTRVRIVEELLR----GELSQREIKQELGV----GIATITRGSNSLK 80 (99)
T ss_pred HHHHHHHHHHHHc----CCcCHHHHHHHhCC----ceeeehhhHHHhc
Confidence 3568899999987 68999999999999 6666666555553
No 319
>PRK13239 alkylmercury lyase; Provisional
Probab=74.56 E-value=3.6 Score=34.07 Aligned_cols=41 Identities=22% Similarity=0.276 Sum_probs=33.2
Q ss_pred HhcChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCcchHHHHHHHHhcC
Q 044458 38 IELDLLEVIAKAGPGAFMSPKQIASQLPTKNSDAHILLDRILRLLASY 85 (241)
Q Consensus 38 ~~lglfd~L~~~~~~~~~t~~eLA~~~g~~~~~~~~~l~rlLr~L~~~ 85 (241)
+..-|+..|++ | .|.|.++||+.+|. +.+.+++.|+.|...
T Consensus 23 ~~~~llr~la~-G--~pvt~~~lA~~~~~----~~~~v~~~L~~l~~~ 63 (206)
T PRK13239 23 LLVPLLRLLAK-G--RPVSVTTLAAALGW----PVEEVEAVLEAMPDT 63 (206)
T ss_pred HHHHHHHHHHc-C--CCCCHHHHHHHhCC----CHHHHHHHHHhCCCe
Confidence 44456777885 3 79999999999999 999899888887644
No 320
>COG1733 Predicted transcriptional regulators [Transcription]
Probab=74.54 E-value=4.8 Score=30.36 Aligned_cols=76 Identities=11% Similarity=0.093 Sum_probs=53.8
Q ss_pred HHHHHHHHHhhhHHHHHHHHHHhcChHHHHHhcCCCCCCCHHHHHhhCC-CCCCCCcchHHHHHHHHhcCCccccccccC
Q 044458 17 ANLFAMQLTSASVLPMVLKSAIELDLLEVIAKAGPGAFMSPKQIASQLP-TKNSDAHILLDRILRLLASYSVLNCSLHTL 95 (241)
Q Consensus 17 ~~~~l~~~~~g~~~~~~L~~a~~lglfd~L~~~~~~~~~t~~eLA~~~g-~~~~~~~~~l~rlLr~L~~~g~l~~~~~~~ 95 (241)
+.....+++.+=|..-.|+...+ |+.-..||-..++ + ++.-|.+-|+.|...|++.+..-..
T Consensus 12 ~~~~~l~~ig~kW~~lIl~~L~~-------------g~~RF~eL~r~i~~I----s~k~Ls~~Lk~Le~~Glv~R~~~~~ 74 (120)
T COG1733 12 PVEEALEVIGGKWTLLILRDLFD-------------GPKRFNELRRSIGGI----SPKMLSRRLKELEEDGLVERVVYPE 74 (120)
T ss_pred CHHHHHHHHcCccHHHHHHHHhc-------------CCCcHHHHHHHcccc----CHHHHHHHHHHHHHCCCEEeeecCC
Confidence 45566677777777766665332 4789999999998 8 9999999999999999998751100
Q ss_pred CCCccccceecCcccc
Q 044458 96 PDGGVERLYGLAPVCK 111 (241)
Q Consensus 96 ~~g~~~~~y~~t~~s~ 111 (241)
.+- .-.|++|+.++
T Consensus 75 ~Pp--rveY~LT~~G~ 88 (120)
T COG1733 75 EPP--RVEYRLTEKGR 88 (120)
T ss_pred CCc--eeEEEEhhhHH
Confidence 000 24677777665
No 321
>PF05219 DREV: DREV methyltransferase; InterPro: IPR007884 This family contains DREV protein homologues from several eukaryotes. The function of this protein is unknown []. However, these proteins appear to be related to other methyltransferases.
Probab=74.45 E-value=3.5 Score=35.38 Aligned_cols=29 Identities=17% Similarity=0.344 Sum_probs=25.4
Q ss_pred CCCeEEEecCCchHHHHHHHHHCCCCcEE
Q 044458 198 GLQSVVDVGGGIGASLDMIISKYPSIKGI 226 (241)
Q Consensus 198 ~~~~vvDVGGG~G~~~~~l~~~~P~l~~~ 226 (241)
+..++||||.|.|.....++..|.++.+|
T Consensus 94 ~~~~lLDlGAGdG~VT~~l~~~f~~v~aT 122 (265)
T PF05219_consen 94 KDKSLLDLGAGDGEVTERLAPLFKEVYAT 122 (265)
T ss_pred cCCceEEecCCCcHHHHHHHhhcceEEee
Confidence 35899999999999999999999887654
No 322
>PF04072 LCM: Leucine carboxyl methyltransferase; InterPro: IPR007213 This entry represents a group of leucine carboxymethyltransferases which methylate the carboxyl group of leucine residues to form alpha-leucine ester residues. It includes LCTM1 which regulates the activity of serine/threonine phosphatase 2A (PP2A) through methylation of the C-terminal leucine residue of the catalytic subunit of PP2A [, , ]. This affects the heteromultimeric composition of PP2A which in turn affects protein recognition and substrate specificity. Like many other methyltransferases LCTM1 uses S-adenosylmethionine (SAM) as the methyl donor. LCTM1 contains the common SAM-dependent methyltransferase core fold, with various insertions and additions creating a specific PP2A binding site []. This entry also contains LCTM2, a homologue of LCTM1 which is not necessary for PP2A methylation and whose function is not clear.; GO: 0008168 methyltransferase activity; PDB: 2UYQ_A 2CKD_B 2UYO_A 2ZZK_B 2ZWA_B 2ZW9_B 1RJE_C 2OB2_B 1RJF_A 1RJD_A ....
Probab=74.31 E-value=6.2 Score=31.72 Aligned_cols=40 Identities=25% Similarity=0.404 Sum_probs=32.1
Q ss_pred CCCCeEEEecCCchHHHHHHHHHCCCCcEEEccchHHHhc
Q 044458 197 EGLQSVVDVGGGIGASLDMIISKYPSIKGINFDLPHVIQD 236 (241)
Q Consensus 197 ~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~DlP~vi~~ 236 (241)
++...||-+|||-=+....+...+++++.+=+|+|+|++.
T Consensus 77 ~~~~qvV~LGaGlDTr~~Rl~~~~~~~~~~evD~p~v~~~ 116 (183)
T PF04072_consen 77 PGARQVVNLGAGLDTRAYRLDNPAGGVRWFEVDLPEVIAL 116 (183)
T ss_dssp TTESEEEEET-TT--HHHHHHHTTTTEEEEEEE-HHHHHH
T ss_pred CCCcEEEEcCCCCCchHHHhhccccceEEEEeCCHHHHHH
Confidence 3456999999999999999999999999999999999875
No 323
>TIGR03879 near_KaiC_dom probable regulatory domain. This model describes a common domain shared by two different families of proteins, each of which occurs regularly next to its corresponding partner family, a probable regulatory with homology to KaiC. By implication, this protein family likely is also involved in sensory transduction and/or regulation.
Probab=74.18 E-value=2.2 Score=29.27 Aligned_cols=34 Identities=18% Similarity=0.016 Sum_probs=30.2
Q ss_pred CCCCHHHHHhhCCCCCCCCcchHHHHHHHHhcCCcccc
Q 044458 53 AFMSPKQIASQLPTKNSDAHILLDRILRLLASYSVLNC 90 (241)
Q Consensus 53 ~~~t~~eLA~~~g~~~~~~~~~l~rlLr~L~~~g~l~~ 90 (241)
...|..|||+.+|+ ++..++..++.+...|.+.+
T Consensus 31 eGlS~kEIAe~LGI----S~~TVk~~l~~~~~~~~~~~ 64 (73)
T TIGR03879 31 AGKTASEIAEELGR----TEQTVRNHLKGETKAGGLVK 64 (73)
T ss_pred cCCCHHHHHHHHCc----CHHHHHHHHhcCcccchHHH
Confidence 36899999999999 99999999999888887753
No 324
>COG5459 Predicted rRNA methylase [Translation, ribosomal structure and biogenesis]
Probab=74.12 E-value=1.4 Score=39.55 Aligned_cols=32 Identities=31% Similarity=0.556 Sum_probs=28.4
Q ss_pred CCeEEEecCCchHHHHHHHHHCCCCc-EEEccc
Q 044458 199 LQSVVDVGGGIGASLDMIISKYPSIK-GINFDL 230 (241)
Q Consensus 199 ~~~vvDVGGG~G~~~~~l~~~~P~l~-~~v~Dl 230 (241)
.++|||||-|.|.-+.++-.-+|+++ +++++.
T Consensus 114 pqsiLDvG~GPgtgl~A~n~i~Pdl~sa~ile~ 146 (484)
T COG5459 114 PQSILDVGAGPGTGLWALNDIWPDLKSAVILEA 146 (484)
T ss_pred cchhhccCCCCchhhhhhcccCCCchhhhhhcc
Confidence 46799999999999999999999998 577776
No 325
>KOG0820 consensus Ribosomal RNA adenine dimethylase [RNA processing and modification]
Probab=74.03 E-value=8.6 Score=33.42 Aligned_cols=42 Identities=17% Similarity=0.321 Sum_probs=33.1
Q ss_pred HHHHHHhcCCCCCCCeEEEecCCchHHHHHHHHHCCCCcEEEccc
Q 044458 186 MKKFLENYKGFEGLQSVVDVGGGIGASLDMIISKYPSIKGINFDL 230 (241)
Q Consensus 186 ~~~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl 230 (241)
.+.++..-+ ......||.||.|+|.+...++++-. +++.+++
T Consensus 47 ~~~I~~ka~-~k~tD~VLEvGPGTGnLT~~lLe~~k--kVvA~E~ 88 (315)
T KOG0820|consen 47 IDQIVEKAD-LKPTDVVLEVGPGTGNLTVKLLEAGK--KVVAVEI 88 (315)
T ss_pred HHHHHhccC-CCCCCEEEEeCCCCCHHHHHHHHhcC--eEEEEec
Confidence 456666666 77889999999999999999999854 4455555
No 326
>PHA02591 hypothetical protein; Provisional
Probab=73.96 E-value=5 Score=27.81 Aligned_cols=32 Identities=22% Similarity=0.180 Sum_probs=26.6
Q ss_pred hHHHHHhcCCCCCCCHHHHHhhCCCCCCCCcchHHHHHHH
Q 044458 42 LLEVIAKAGPGAFMSPKQIASQLPTKNSDAHILLDRILRL 81 (241)
Q Consensus 42 lfd~L~~~~~~~~~t~~eLA~~~g~~~~~~~~~l~rlLr~ 81 (241)
+...|.+ .+.|.++||+.+|+ +...+++.|+.
T Consensus 51 vA~eL~e----qGlSqeqIA~~LGV----sqetVrKYL~~ 82 (83)
T PHA02591 51 VTHELAR----KGFTVEKIASLLGV----SVRKVRRYLES 82 (83)
T ss_pred HHHHHHH----cCCCHHHHHHHhCC----CHHHHHHHHhc
Confidence 4556766 47999999999999 99999988864
No 327
>PF02384 N6_Mtase: N-6 DNA Methylase; InterPro: IPR003356 This domain is fpound in N-6 adenine-specific DNA methylase (2.1.1.72 from EC) from Type I and Type IC restriction systems. These enzymes are responsible for the methylation of specific DNA sequences in order to prevent the host from digesting its own genome via its restriction enzymes. These methylases have the same sequence specificity as their corresponding restriction enzymes. The type I restriction and modification system is composed of three polypeptides R, M and S. The M and S subunits together form a methyltransferase that methylates two adenine residues in complementary strands of a bipartite DNA recognition sequence. In the presence of the R subunit, the complex can also act as an endonuclease, binding to the same target sequence but cutting the DNA some distance from this site. Whether the DNA is cut or modified depends on the methylation state of the target sequence. When the target site is unmodified, the DNA is cut. When the target site is hemimethylated, the complex acts as a maintenance methyltransferase, modifying the DNA so that both strands become methylated.; GO: 0003677 DNA binding, 0008170 N-methyltransferase activity, 0006306 DNA methylation; PDB: 2F8L_A 2Y7C_C 2Y7H_C 2AR0_B 3KHK_A 3LKD_A 2OKC_B.
Probab=73.78 E-value=3.2 Score=36.18 Aligned_cols=41 Identities=20% Similarity=0.191 Sum_probs=31.1
Q ss_pred CCCCCeEEEecCCchHHHHHHHHH-------CCCCcEEEccc-hHHHhc
Q 044458 196 FEGLQSVVDVGGGIGASLDMIISK-------YPSIKGINFDL-PHVIQD 236 (241)
Q Consensus 196 ~~~~~~vvDVGGG~G~~~~~l~~~-------~P~l~~~v~Dl-P~vi~~ 236 (241)
-....+|+|-.||+|.++.++.+. .+..+...+|. |.++..
T Consensus 44 ~~~~~~VlDPacGsG~fL~~~~~~i~~~~~~~~~~~i~G~ei~~~~~~l 92 (311)
T PF02384_consen 44 PKKGDSVLDPACGSGGFLVAAMEYIKEKRNKIKEINIYGIEIDPEAVAL 92 (311)
T ss_dssp T-TTEEEEETT-TTSHHHHHHHHHHHTCHHHHCCEEEEEEES-HHHHHH
T ss_pred ccccceeechhhhHHHHHHHHHHhhcccccccccceeEeecCcHHHHHH
Confidence 445678999999999999998874 58888899998 555443
No 328
>TIGR02787 codY_Gpos GTP-sensing transcriptional pleiotropic repressor CodY. This model represents the full length of CodY, a pleiotropic repressor in Bacillus subtilis and other Firmicutes (low-GC Gram-positive bacteria) that responds to intracellular levels of GTP and branched chain amino acids. The C-terminal helix-turn-helix DNA-binding region is modeled by pfam08222 in Pfam.
Probab=73.33 E-value=12 Score=31.86 Aligned_cols=45 Identities=18% Similarity=0.298 Sum_probs=39.0
Q ss_pred ChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCcchHHHHHHHHhcCCccccc
Q 044458 41 DLLEVIAKAGPGAFMSPKQIASQLPTKNSDAHILLDRILRLLASYSVLNCS 91 (241)
Q Consensus 41 glfd~L~~~~~~~~~t~~eLA~~~g~~~~~~~~~l~rlLr~L~~~g~l~~~ 91 (241)
.|++.|... ++-++..+||+++|+ +...+++=+|.|...|++.-.
T Consensus 187 ~IL~~L~~~--egrlse~eLAerlGV----SRs~ireAlrkLE~aGvIe~r 231 (251)
T TIGR02787 187 HIFEELDGN--EGLLVASKIADRVGI----TRSVIVNALRKLESAGVIESR 231 (251)
T ss_pred HHHHHhccc--cccccHHHHHHHHCC----CHHHHHHHHHHHHHCCCEEec
Confidence 477888652 268999999999999 999999999999999999864
No 329
>KOG3045 consensus Predicted RNA methylase involved in rRNA processing [RNA processing and modification]
Probab=72.28 E-value=7.1 Score=33.72 Aligned_cols=52 Identities=13% Similarity=0.148 Sum_probs=31.6
Q ss_pred ccccCchHHHHHHHHHHh----cchhhHHHHHHhcCCCCCCCeEEEecCCchHHHH
Q 044458 163 YHGKDLRLNKIFNNGMFS----HSTITMKKFLENYKGFEGLQSVVDVGGGIGASLD 214 (241)
Q Consensus 163 ~~~~~~~~~~~f~~aM~~----~~~~~~~~~~~~~~~~~~~~~vvDVGGG~G~~~~ 214 (241)
.+.++|...+.|++.... |-....+.+++.+..-+....|-|+|||.+.++.
T Consensus 141 lfkedp~afdlYH~gfr~QV~kWP~nPld~ii~~ik~r~~~~vIaD~GCGEakiA~ 196 (325)
T KOG3045|consen 141 LFKEDPTAFDLYHAGFRSQVKKWPENPLDVIIRKIKRRPKNIVIADFGCGEAKIAS 196 (325)
T ss_pred HHhcCcHHHHHHHHHHHHHHHhCCCChHHHHHHHHHhCcCceEEEecccchhhhhh
Confidence 344667655555554432 2222344555554323467899999999999886
No 330
>COG1349 GlpR Transcriptional regulators of sugar metabolism [Transcription / Carbohydrate transport and metabolism]
Probab=72.20 E-value=3.7 Score=35.05 Aligned_cols=45 Identities=18% Similarity=0.229 Sum_probs=41.0
Q ss_pred cChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCcchHHHHHHHHhcCCccccc
Q 044458 40 LDLLEVIAKAGPGAFMSPKQIASQLPTKNSDAHILLDRILRLLASYSVLNCS 91 (241)
Q Consensus 40 lglfd~L~~~~~~~~~t~~eLA~~~g~~~~~~~~~l~rlLr~L~~~g~l~~~ 91 (241)
-.|.++|.+. |.++++|||+.+++ ++.-+||=|+.|...|++.+.
T Consensus 8 ~~Il~~l~~~---g~v~v~eLa~~~~V----S~~TIRRDL~~Le~~g~l~R~ 52 (253)
T COG1349 8 QKILELLKEK---GKVSVEELAELFGV----SEMTIRRDLNELEEQGLLLRV 52 (253)
T ss_pred HHHHHHHHHc---CcEEHHHHHHHhCC----CHHHHHHhHHHHHHCCcEEEE
Confidence 3578889885 68999999999999 999999999999999999985
No 331
>PF07789 DUF1627: Protein of unknown function (DUF1627); InterPro: IPR012432 This is a group of sequences found in hypothetical proteins predicted to be expressed in a number of bacterial species. The region in question is approximately 150 amino acid residues long.
Probab=72.01 E-value=5.7 Score=31.02 Aligned_cols=46 Identities=11% Similarity=0.147 Sum_probs=38.2
Q ss_pred CCCCHHHHHhhCCCCCCCCcchHHHHHHHHhcCCccccccccCCCCccccceecC
Q 044458 53 AFMSPKQIASQLPTKNSDAHILLDRILRLLASYSVLNCSLHTLPDGGVERLYGLA 107 (241)
Q Consensus 53 ~~~t~~eLA~~~g~~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~g~~~~~y~~t 107 (241)
|++|.+|||-+.|+ ..+.+-.-|.++++.|-+.+. ..+| .=+|+.+
T Consensus 5 Ga~T~eELA~~FGv----ttRkvaStLa~~ta~Grl~Rv---~q~g--kfRy~iP 50 (155)
T PF07789_consen 5 GAKTAEELAGKFGV----TTRKVASTLAMVTATGRLIRV---NQNG--KFRYCIP 50 (155)
T ss_pred CcccHHHHHHHhCc----chhhhHHHHHHHHhcceeEEe---cCCC--ceEEeCC
Confidence 79999999999999 999999999999999988874 2334 3466664
No 332
>PF02295 z-alpha: Adenosine deaminase z-alpha domain; InterPro: IPR000607 Double-stranded RNA-specific adenosine deaminase (3.5 from EC) converts multiple adenosines to inosines and creates I/U mismatched base pairs in double-helical RNA substrates without apparent sequence specificity. DRADA has been found to modify adenosines in AU-rich regions more frequently, probably due to the relative ease of melting A/U base pairs compared to G/C base pairs. The protein functions to modify viral RNA genomes, and may be responsible for hypermutation of certain negative-stranded viruses. DRADA edits the mRNAs for the glutamate receptor subunits by site-selective adenosine deamination. The DRADA repeat is also found in viral E3 proteins, which contain a double-stranded RNA-binding domain.; GO: 0003723 RNA binding, 0003726 double-stranded RNA adenosine deaminase activity; PDB: 1OYI_A 3EYI_A 2L4M_A 2HEO_D 1J75_A 1SFU_B 3IRR_B 2ACJ_C 3F22_B 2L54_A ....
Probab=71.79 E-value=3.4 Score=27.72 Aligned_cols=60 Identities=18% Similarity=0.206 Sum_probs=40.3
Q ss_pred HhcChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCcchHHHHHHHHhcCCccccccccCCCCccccceecCc
Q 044458 38 IELDLLEVIAKAGPGAFMSPKQIASQLPTKNSDAHILLDRILRLLASYSVLNCSLHTLPDGGVERLYGLAP 108 (241)
Q Consensus 38 ~~lglfd~L~~~~~~~~~t~~eLA~~~g~~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~g~~~~~y~~t~ 108 (241)
.+-.|.++|...| +.++-.||...|++. +..-+.+.|..|...|.+.+.. | .+..|++++
T Consensus 5 ~ee~Il~~L~~~g---~~~a~~ia~~~~L~~--~kk~VN~~LY~L~k~g~v~k~~-----~-~PP~W~l~~ 64 (66)
T PF02295_consen 5 LEEKILDFLKELG---GSTATAIAKALGLSV--PKKEVNRVLYRLEKQGKVCKEG-----G-TPPKWSLTE 64 (66)
T ss_dssp HHHHHHHHHHHHT---SSEEEHHHHHHHHTS---HHHHHHHHHHHHHTTSEEEEC-----S-SSTEEEE-H
T ss_pred HHHHHHHHHHhcC---CccHHHHHHHhCcch--hHHHHHHHHHHHHHCCCEeeCC-----C-CCCceEecc
Confidence 4556888888864 455555555555410 4788999999999999998741 2 267777664
No 333
>COG0275 Predicted S-adenosylmethionine-dependent methyltransferase involved in cell envelope biogenesis [Cell envelope biogenesis, outer membrane]
Probab=71.26 E-value=7.2 Score=34.27 Aligned_cols=53 Identities=23% Similarity=0.238 Sum_probs=44.7
Q ss_pred HHHHHHhcCCCCCCCeEEEecCCchHHHHHHHHHCCCCc-EEEccc-hHHHhcCCC
Q 044458 186 MKKFLENYKGFEGLQSVVDVGGGIGASLDMIISKYPSIK-GINFDL-PHVIQDAPA 239 (241)
Q Consensus 186 ~~~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~-~~v~Dl-P~vi~~a~~ 239 (241)
...+++.+. .......||.==|.|.++.++++++|++. .+.+|. |++++.|++
T Consensus 12 l~E~i~~L~-~~~~giyiD~TlG~GGHS~~iL~~l~~~~~li~~DrD~~Ai~~a~~ 66 (314)
T COG0275 12 LNEVVELLA-PKPDGIYIDGTLGAGGHSRAILEKLPDLGRLIGIDRDPQAIAIAKE 66 (314)
T ss_pred HHHHHHhcc-cCCCcEEEEecCCCcHhHHHHHHhCCCCCeEEEEcCCHHHHHHHHH
Confidence 345666666 56669999999999999999999999987 899999 899988764
No 334
>COG2519 GCD14 tRNA(1-methyladenosine) methyltransferase and related methyltransferases [Translation, ribosomal structure and biogenesis]
Probab=70.70 E-value=9 Score=32.78 Aligned_cols=63 Identities=14% Similarity=0.175 Sum_probs=45.5
Q ss_pred HHHHHHhcchhh----HHHHHHhcCCCCCCCeEEEecCCchHHHHHHHH-HCCCCcEEEccc-hHHHhcC
Q 044458 174 FNNGMFSHSTIT----MKKFLENYKGFEGLQSVVDVGGGIGASLDMIIS-KYPSIKGINFDL-PHVIQDA 237 (241)
Q Consensus 174 f~~aM~~~~~~~----~~~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~-~~P~l~~~v~Dl-P~vi~~a 237 (241)
|...|...++.. +..|+.... .+...+|+|.|-|+|.++..|+. ..|.=+.+.+|. ++-.+.|
T Consensus 67 ~~~~~~R~tQiIyPKD~~~I~~~~g-i~pg~rVlEAGtGSG~lt~~La~~vg~~G~v~tyE~r~d~~k~A 135 (256)
T COG2519 67 YLLSMKRRTQIIYPKDAGYIVARLG-ISPGSRVLEAGTGSGALTAYLARAVGPEGHVTTYEIREDFAKTA 135 (256)
T ss_pred HHHhCcCCCceecCCCHHHHHHHcC-CCCCCEEEEcccCchHHHHHHHHhhCCCceEEEEEecHHHHHHH
Confidence 444476666643 334555555 77889999999999999999997 667778888887 4444433
No 335
>PRK12423 LexA repressor; Provisional
Probab=70.61 E-value=5.3 Score=32.79 Aligned_cols=35 Identities=14% Similarity=0.110 Sum_probs=30.2
Q ss_pred CCCHHHHHhhCCCCCCCCcchHHHHHHHHhcCCccccc
Q 044458 54 FMSPKQIASQLPTKNSDAHILLDRILRLLASYSVLNCS 91 (241)
Q Consensus 54 ~~t~~eLA~~~g~~~~~~~~~l~rlLr~L~~~g~l~~~ 91 (241)
+-|..|||+++|+. ....++.-|+.|...|++...
T Consensus 25 ~Ps~~eia~~~g~~---s~~~v~~~l~~L~~~G~l~~~ 59 (202)
T PRK12423 25 PPSLAEIAQAFGFA---SRSVARKHVQALAEAGLIEVV 59 (202)
T ss_pred CCCHHHHHHHhCCC---ChHHHHHHHHHHHHCCCEEec
Confidence 56999999999940 566789999999999999974
No 336
>PRK11886 bifunctional biotin--[acetyl-CoA-carboxylase] synthetase/biotin operon repressor; Provisional
Probab=70.46 E-value=6.3 Score=34.72 Aligned_cols=45 Identities=20% Similarity=0.296 Sum_probs=38.0
Q ss_pred hcChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCcchHHHHHHHHhcCCcccc
Q 044458 39 ELDLLEVIAKAGPGAFMSPKQIASQLPTKNSDAHILLDRILRLLASYSVLNC 90 (241)
Q Consensus 39 ~lglfd~L~~~~~~~~~t~~eLA~~~g~~~~~~~~~l~rlLr~L~~~g~l~~ 90 (241)
...|.+.|.+. .+.+..+||+++|+ +...+.+.++.|...|+...
T Consensus 6 ~~~il~~L~~~---~~~s~~~LA~~lgv----sr~tV~~~l~~L~~~G~~i~ 50 (319)
T PRK11886 6 MLQLLSLLADG---DFHSGEQLGEELGI----SRAAIWKHIQTLEEWGLDIF 50 (319)
T ss_pred HHHHHHHHHcC---CCcCHHHHHHHHCC----CHHHHHHHHHHHHHCCCceE
Confidence 34577777763 57999999999999 99999999999999999543
No 337
>PRK11161 fumarate/nitrate reduction transcriptional regulator; Provisional
Probab=69.96 E-value=4.2 Score=33.67 Aligned_cols=34 Identities=18% Similarity=0.191 Sum_probs=31.9
Q ss_pred CCCHHHHHhhCCCCCCCCcchHHHHHHHHhcCCccccc
Q 044458 54 FMSPKQIASQLPTKNSDAHILLDRILRLLASYSVLNCS 91 (241)
Q Consensus 54 ~~t~~eLA~~~g~~~~~~~~~l~rlLr~L~~~g~l~~~ 91 (241)
++|-++||+.+|+ ....+.|+|+.|...|++...
T Consensus 184 ~lt~~~iA~~lG~----sr~tvsR~l~~l~~~g~I~~~ 217 (235)
T PRK11161 184 TMTRGDIGNYLGL----TVETISRLLGRFQKSGMLAVK 217 (235)
T ss_pred cccHHHHHHHhCC----cHHHHHHHHHHHHHCCCEEec
Confidence 5899999999999 999999999999999999974
No 338
>PRK13777 transcriptional regulator Hpr; Provisional
Probab=69.72 E-value=6.3 Score=32.09 Aligned_cols=44 Identities=16% Similarity=-0.070 Sum_probs=38.0
Q ss_pred ChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCcchHHHHHHHHhcCCccccc
Q 044458 41 DLLEVIAKAGPGAFMSPKQIASQLPTKNSDAHILLDRILRLLASYSVLNCS 91 (241)
Q Consensus 41 glfd~L~~~~~~~~~t~~eLA~~~g~~~~~~~~~l~rlLr~L~~~g~l~~~ 91 (241)
.|...|... +++|..+||+.+.+ +...+.++++-|...|++.+.
T Consensus 49 ~iL~~L~~~---~~itq~eLa~~l~l----~~sTvtr~l~rLE~kGlI~R~ 92 (185)
T PRK13777 49 HILWIAYHL---KGASISEIAKFGVM----HVSTAFNFSKKLEERGYLTFS 92 (185)
T ss_pred HHHHHHHhC---CCcCHHHHHHHHCC----CHhhHHHHHHHHHHCCCEEec
Confidence 456666664 58999999999999 888999999999999999975
No 339
>PRK11753 DNA-binding transcriptional dual regulator Crp; Provisional
Probab=69.61 E-value=5.2 Score=32.37 Aligned_cols=34 Identities=12% Similarity=0.345 Sum_probs=31.8
Q ss_pred CCCHHHHHhhCCCCCCCCcchHHHHHHHHhcCCccccc
Q 044458 54 FMSPKQIASQLPTKNSDAHILLDRILRLLASYSVLNCS 91 (241)
Q Consensus 54 ~~t~~eLA~~~g~~~~~~~~~l~rlLr~L~~~g~l~~~ 91 (241)
++|-++||+.+|+ .+..+.|+|+.|...|++...
T Consensus 168 ~~t~~~lA~~lG~----tr~tvsR~l~~l~~~gii~~~ 201 (211)
T PRK11753 168 KITRQEIGRIVGC----SREMVGRVLKMLEDQGLISAH 201 (211)
T ss_pred CCCHHHHHHHhCC----CHHHHHHHHHHHHHCCCEEec
Confidence 6888999999999 999999999999999999863
No 340
>PF01475 FUR: Ferric uptake regulator family; InterPro: IPR002481 The Ferric uptake regulator (FUR) family includes metal ion uptake regulator proteins. These are responsible for controlling the intracellular concentration of iron in many bacteria. Although iron is essential for most organisms, high concentrations can be toxic because of the formation of hydroxyl radicals []. FURs can also control zinc homeostasis [] and is the subject of research on the pathogenesis of mycobacteria.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 1MZB_A 2RGV_B 2FE3_B 3F8N_B 3EYY_B 2W57_A 2FU4_A 2O03_A 3MWM_B 2XIG_B ....
Probab=69.48 E-value=3.7 Score=30.55 Aligned_cols=65 Identities=23% Similarity=0.314 Sum_probs=45.3
Q ss_pred HhcChHHHHHhcCCCCCCCHHHHHhhCCCC-CCCCcchHHHHHHHHhcCCccccccccCCCCccccceecCc
Q 044458 38 IELDLLEVIAKAGPGAFMSPKQIASQLPTK-NSDAHILLDRILRLLASYSVLNCSLHTLPDGGVERLYGLAP 108 (241)
Q Consensus 38 ~~lglfd~L~~~~~~~~~t~~eLA~~~g~~-~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~g~~~~~y~~t~ 108 (241)
-+.-|++.|.+.+ ++.|++||-+.+.-. +.++..-+.|.|+.|...|++.+... .+| ...|..+.
T Consensus 9 ~R~~Il~~l~~~~--~~~ta~ei~~~l~~~~~~is~~TVYR~L~~L~e~Gli~~~~~--~~~--~~~Y~~~~ 74 (120)
T PF01475_consen 9 QRLAILELLKESP--EHLTAEEIYDKLRKKGPRISLATVYRTLDLLEEAGLIRKIEF--GDG--ESRYELST 74 (120)
T ss_dssp HHHHHHHHHHHHS--SSEEHHHHHHHHHHTTTT--HHHHHHHHHHHHHTTSEEEEEE--TTS--EEEEEESS
T ss_pred HHHHHHHHHHcCC--CCCCHHHHHHHhhhccCCcCHHHHHHHHHHHHHCCeEEEEEc--CCC--cceEeecC
Confidence 4556888898865 699999999988531 12256679999999999999998631 112 34666554
No 341
>PRK11511 DNA-binding transcriptional activator MarA; Provisional
Probab=69.43 E-value=7.4 Score=29.37 Aligned_cols=44 Identities=14% Similarity=0.136 Sum_probs=35.3
Q ss_pred hHHHHHhcCCCCCCCHHHHHhhCCCCCCCCcchHHHHHHHHhcCCcccc
Q 044458 42 LLEVIAKAGPGAFMSPKQIASQLPTKNSDAHILLDRILRLLASYSVLNC 90 (241)
Q Consensus 42 lfd~L~~~~~~~~~t~~eLA~~~g~~~~~~~~~l~rlLr~L~~~g~l~~ 90 (241)
+.+.|..... .+.|+++||+.+|+ +++.+.|+++....+.+-..
T Consensus 14 ~~~~I~~~~~-~~~sl~~lA~~~g~----S~~~l~r~Fk~~~G~s~~~~ 57 (127)
T PRK11511 14 ILDWIEDNLE-SPLSLEKVSERSGY----SKWHLQRMFKKETGHSLGQY 57 (127)
T ss_pred HHHHHHHhcC-CCCCHHHHHHHHCc----CHHHHHHHHHHHHCcCHHHH
Confidence 3455554432 57999999999999 99999999999888887765
No 342
>PRK11783 rlmL 23S rRNA m(2)G2445 methyltransferase; Provisional
Probab=69.15 E-value=7 Score=38.46 Aligned_cols=32 Identities=16% Similarity=0.050 Sum_probs=23.8
Q ss_pred HHHHHHhcCCC-CCCCeEEEecCCchHHHHHHHH
Q 044458 186 MKKFLENYKGF-EGLQSVVDVGGGIGASLDMIIS 218 (241)
Q Consensus 186 ~~~~~~~~~~~-~~~~~vvDVGGG~G~~~~~l~~ 218 (241)
+..++..-. | .+...++|-.||+|+++++.+.
T Consensus 178 Aaa~l~~a~-w~~~~~~l~DP~CGSGTilIEAa~ 210 (702)
T PRK11783 178 AAAILLRSG-WPQEGTPLLDPMCGSGTLLIEAAM 210 (702)
T ss_pred HHHHHHHcC-CCCCCCeEEccCCCccHHHHHHHH
Confidence 334444434 7 4568999999999999998776
No 343
>PRK10219 DNA-binding transcriptional regulator SoxS; Provisional
Probab=68.79 E-value=8.3 Score=27.88 Aligned_cols=34 Identities=12% Similarity=0.160 Sum_probs=29.7
Q ss_pred CCCCHHHHHhhCCCCCCCCcchHHHHHHHHhcCCcccc
Q 044458 53 AFMSPKQIASQLPTKNSDAHILLDRILRLLASYSVLNC 90 (241)
Q Consensus 53 ~~~t~~eLA~~~g~~~~~~~~~l~rlLr~L~~~g~l~~ 90 (241)
.+.|+++||+.+++ +++.+.|+++....+.+-..
T Consensus 20 ~~~~~~~lA~~~~~----S~~~l~r~f~~~~g~s~~~~ 53 (107)
T PRK10219 20 QPLNIDVVAKKSGY----SKWYLQRMFRTVTHQTLGDY 53 (107)
T ss_pred CCCCHHHHHHHHCC----CHHHHHHHHHHHHCcCHHHH
Confidence 57999999999999 99999999998877766654
No 344
>TIGR02147 Fsuc_second hypothetical protein, TIGR02147. This family consists of the 40 members of a paralogous protein family in the rumen anaerobe Fibrobacter succinogenes S85. Member proteins are about 270 residues long and appear to lack signal sequences and transmembrane helices. The only perfectly conserved residue is a glycine in an otherwise poorly conserved region, suggesting members are not enzymes. The family is not characterized.
Probab=68.34 E-value=8.8 Score=33.23 Aligned_cols=47 Identities=13% Similarity=0.162 Sum_probs=38.2
Q ss_pred CCCHHHHHhhCCCCCCCCcchHHHHHHHHhcCCccccccccCCCCccccceecCccc
Q 044458 54 FMSPKQIASQLPTKNSDAHILLDRILRLLASYSVLNCSLHTLPDGGVERLYGLAPVC 110 (241)
Q Consensus 54 ~~t~~eLA~~~g~~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~g~~~~~y~~t~~s 110 (241)
..+.++||+.|+- +++..-++.-|+.|...|++++. | +|.|..|..+
T Consensus 137 ~~~~~~ia~~l~p--~is~~ev~~sL~~L~~~glikk~------~--~g~y~~t~~~ 183 (271)
T TIGR02147 137 ADDPEELAKRCFP--KISAEQVKESLDLLERLGLIKKN------E--DGFYKQTDKA 183 (271)
T ss_pred CCCHHHHHHHhCC--CCCHHHHHHHHHHHHHCCCeeEC------C--CCcEEeecce
Confidence 4478999999982 22788899999999999999974 2 6889888764
No 345
>TIGR03697 NtcA_cyano global nitrogen regulator NtcA, cyanobacterial. Members of this protein family, found in the cyanobacteria, are the global nitrogen regulator NtcA. This DNA-binding transcriptional regulator is required for expressing many different ammonia-repressible genes. The consensus NtcA-binding site is G T A N(8)T A C.
Probab=68.17 E-value=5.1 Score=31.90 Aligned_cols=34 Identities=18% Similarity=0.287 Sum_probs=32.0
Q ss_pred CCCHHHHHhhCCCCCCCCcchHHHHHHHHhcCCccccc
Q 044458 54 FMSPKQIASQLPTKNSDAHILLDRILRLLASYSVLNCS 91 (241)
Q Consensus 54 ~~t~~eLA~~~g~~~~~~~~~l~rlLr~L~~~g~l~~~ 91 (241)
+.|-+|||+.+|+ ....+.|+|+.|...|++...
T Consensus 143 ~~t~~~iA~~lG~----tretvsR~l~~l~~~g~I~~~ 176 (193)
T TIGR03697 143 RLSHQAIAEAIGS----TRVTITRLLGDLRKKKLISIH 176 (193)
T ss_pred CCCHHHHHHHhCC----cHHHHHHHHHHHHHCCCEEec
Confidence 6899999999999 999999999999999999863
No 346
>PRK09334 30S ribosomal protein S25e; Provisional
Probab=68.01 E-value=4.8 Score=28.54 Aligned_cols=35 Identities=23% Similarity=0.276 Sum_probs=32.1
Q ss_pred CCCCHHHHHhhCCCCCCCCcchHHHHHHHHhcCCccccc
Q 044458 53 AFMSPKQIASQLPTKNSDAHILLDRILRLLASYSVLNCS 91 (241)
Q Consensus 53 ~~~t~~eLA~~~g~~~~~~~~~l~rlLr~L~~~g~l~~~ 91 (241)
.-+|...||+++++ .-...++.||.|...|++...
T Consensus 40 K~ITps~lserlkI----~~SlAr~~Lr~L~~kG~Ik~V 74 (86)
T PRK09334 40 KIVTPYTLASKYGI----KISVAKKVLRELEKRGVLVLY 74 (86)
T ss_pred cEEcHHHHHHHhcc----hHHHHHHHHHHHHHCCCEEEE
Confidence 56999999999999 999999999999999998754
No 347
>COG1497 Predicted transcriptional regulator [Transcription]
Probab=67.48 E-value=6.8 Score=33.22 Aligned_cols=84 Identities=14% Similarity=0.178 Sum_probs=59.1
Q ss_pred CCCHHHHHhhCCCCCCCCcchHHHHHHHHhcCCccccccccCCCCccccceecCcccc-ccccCCCCCChHHHHHHhc-C
Q 044458 54 FMSPKQIASQLPTKNSDAHILLDRILRLLASYSVLNCSLHTLPDGGVERLYGLAPVCK-FLTKNEDGVSLSDICLLCQ-D 131 (241)
Q Consensus 54 ~~t~~eLA~~~g~~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~g~~~~~y~~t~~s~-~l~~~~~~~~~~~~~~~~~-~ 131 (241)
-..-.|||+.+|+ .+..+..-++-|+..|++++. | -++|..|..+. ++...-+ .++.+..... .
T Consensus 25 ~v~q~eIA~~lgi----T~QaVsehiK~Lv~eG~i~~~------g--R~~Y~iTkkG~e~l~~~~~--dlr~f~~ev~~~ 90 (260)
T COG1497 25 RVKQKEIAKKLGI----TLQAVSEHIKELVKEGLIEKE------G--RGEYEITKKGAEWLLEQLS--DLRRFSEEVELV 90 (260)
T ss_pred CCCHHHHHHHcCC----CHHHHHHHHHHHHhccceeec------C--CeeEEEehhHHHHHHHHHH--HHHHHHHHHHHH
Confidence 5899999999999 999999999999999999973 2 46999999986 5554432 3565554431 1
Q ss_pred hhhHHhhhhHHH-HHhcCCch
Q 044458 132 KIVMESWYHLKD-AVLEGGIP 151 (241)
Q Consensus 132 ~~~~~~~~~L~~-~l~~g~~~ 151 (241)
-.+...|..+++ -+++|.+-
T Consensus 91 l~~~~vw~AIA~edI~~Gd~V 111 (260)
T COG1497 91 LDYVMVWTAIAKEDIKEGDTV 111 (260)
T ss_pred HhhHHHHHHhhHhhhccCCEE
Confidence 122335766653 35555543
No 348
>PF10668 Phage_terminase: Phage terminase small subunit; InterPro: IPR018925 This entry describes the terminase small subunit from Enterococcus phage phiFL1A, related proteins in other bacteriophage, and prophage regions of bacterial genomes. Packaging of double-stranded viral DNA concatemers requires interaction of the prohead with virus DNA. This process is mediated by a phage-encoded DNA recognition and terminase protein. The terminase enzymes described so far, which are hetero-oligomers composed of a small and a large subunit, do not have a significant level of sequence homology. The small terminase subunit is thought to form a nucleoprotein structure that helps to position the terminase large subunit at the packaging initiation site [].
Probab=67.45 E-value=7.4 Score=25.63 Aligned_cols=22 Identities=18% Similarity=0.212 Sum_probs=19.5
Q ss_pred CCCCHHHHHhhCCCCCCCCcchHHHH
Q 044458 53 AFMSPKQIASQLPTKNSDAHILLDRI 78 (241)
Q Consensus 53 ~~~t~~eLA~~~g~~~~~~~~~l~rl 78 (241)
|.++..|||+.+|+ ++.-++++
T Consensus 21 g~i~lkdIA~~Lgv----s~~tIr~W 42 (60)
T PF10668_consen 21 GKIKLKDIAEKLGV----SESTIRKW 42 (60)
T ss_pred CCccHHHHHHHHCC----CHHHHHHH
Confidence 78999999999999 88877765
No 349
>PF05331 DUF742: Protein of unknown function (DUF742); InterPro: IPR007995 This family consists of several uncharacterised Streptomyces proteins as well as one from Mycobacterium tuberculosis. The function of these proteins is unknown.
Probab=67.13 E-value=7.3 Score=29.17 Aligned_cols=35 Identities=17% Similarity=0.141 Sum_probs=32.2
Q ss_pred CCCCHHHHHhhCCCCCCCCcchHHHHHHHHhcCCccccc
Q 044458 53 AFMSPKQIASQLPTKNSDAHILLDRILRLLASYSVLNCS 91 (241)
Q Consensus 53 ~~~t~~eLA~~~g~~~~~~~~~l~rlLr~L~~~g~l~~~ 91 (241)
.+.|+.|||..+++ +...++.++.-|...|++...
T Consensus 54 ~~~SVAEiAA~L~l----PlgVvrVLvsDL~~~G~v~v~ 88 (114)
T PF05331_consen 54 RPLSVAEIAARLGL----PLGVVRVLVSDLADAGLVRVR 88 (114)
T ss_pred CCccHHHHHHhhCC----CchhhhhhHHHHHhCCCEEEe
Confidence 48999999999999 888899999999999999864
No 350
>COG3963 Phospholipid N-methyltransferase [Lipid metabolism]
Probab=67.06 E-value=9.3 Score=30.84 Aligned_cols=34 Identities=24% Similarity=0.320 Sum_probs=27.6
Q ss_pred hHHHHHHhcCCCCCCCeEEEecCCchHHHHHHHHH
Q 044458 185 TMKKFLENYKGFEGLQSVVDVGGGIGASLDMIISK 219 (241)
Q Consensus 185 ~~~~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~ 219 (241)
.++.+....+ |++..-|+.+|-|+|.+..+++++
T Consensus 36 lA~~M~s~I~-pesglpVlElGPGTGV~TkaIL~~ 69 (194)
T COG3963 36 LARKMASVID-PESGLPVLELGPGTGVITKAILSR 69 (194)
T ss_pred HHHHHHhccC-cccCCeeEEEcCCccHhHHHHHhc
Confidence 3455566677 999999999999999999887763
No 351
>PF06969 HemN_C: HemN C-terminal domain; InterPro: IPR010723 Proteins containing this domain are all oxygen-independent coproporphyrinogen-III oxidases (HemN). This enzyme catalyses the oxygen-independent conversion of coproporphyrinogen-III to protoporphyrinogen-IX [], one of the last steps in haem biosynthesis. The function of this domain is unclear, but comparison to other proteins containing a radical SAM domain suggest it may be a substrate binding domain.; GO: 0004109 coproporphyrinogen oxidase activity, 0006779 porphyrin-containing compound biosynthetic process, 0055114 oxidation-reduction process, 0005737 cytoplasm; PDB: 1OLT_A.
Probab=67.04 E-value=7.4 Score=25.48 Aligned_cols=46 Identities=9% Similarity=0.033 Sum_probs=34.3
Q ss_pred CCCCHHHHHhhCCCCCCCCc-chHHHHHHHHhcCCccccccccCCCCccccceecCcccc
Q 044458 53 AFMSPKQIASQLPTKNSDAH-ILLDRILRLLASYSVLNCSLHTLPDGGVERLYGLAPVCK 111 (241)
Q Consensus 53 ~~~t~~eLA~~~g~~~~~~~-~~l~rlLr~L~~~g~l~~~~~~~~~g~~~~~y~~t~~s~ 111 (241)
.+++.+++.++.|. +. ......+..+...|+++.. ++++++|+.+.
T Consensus 19 ~Gi~~~~~~~~~g~----~~~~~~~~~l~~l~~~Gll~~~---------~~~l~lT~~G~ 65 (66)
T PF06969_consen 19 EGIDLSEFEQRFGI----DFAEEFQKELEELQEDGLLEID---------GGRLRLTEKGR 65 (66)
T ss_dssp SEEEHHHHHHHTT------THHH-HHHHHHHHHTTSEEE----------SSEEEE-TTTG
T ss_pred CCcCHHHHHHHHCc----CHHHHHHHHHHHHHHCCCEEEe---------CCEEEECcccC
Confidence 47899999999998 53 3447889999999999974 68999998765
No 352
>PRK09273 hypothetical protein; Provisional
Probab=66.83 E-value=3.7 Score=34.04 Aligned_cols=41 Identities=15% Similarity=0.092 Sum_probs=31.7
Q ss_pred CCeEEEecCCchHHHHHHHHHCCCCcEEEccchHHHhcCCC
Q 044458 199 LQSVVDVGGGIGASLDMIISKYPSIKGINFDLPHVIQDAPA 239 (241)
Q Consensus 199 ~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~DlP~vi~~a~~ 239 (241)
.....=++||+|.-..-.+.++|++++-+.--|.....+++
T Consensus 63 ~~d~GIliCGTGiG~siAANK~pGIraalc~d~~sA~lar~ 103 (211)
T PRK09273 63 AVDFVVTGCGTGQGAMLALNSFPGVVCGYCIDPTDAYLFAQ 103 (211)
T ss_pred CCCEEEEEcCcHHHHHHHHhcCCCeEEEEeCCHHHHHHHHH
Confidence 35567789999999999999999999755555666655544
No 353
>PF13542 HTH_Tnp_ISL3: Helix-turn-helix domain of transposase family ISL3
Probab=66.73 E-value=9 Score=23.69 Aligned_cols=36 Identities=22% Similarity=0.275 Sum_probs=28.1
Q ss_pred HhcChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCcchHHHHHHHH
Q 044458 38 IELDLLEVIAKAGPGAFMSPKQIASQLPTKNSDAHILLDRILRLL 82 (241)
Q Consensus 38 ~~lglfd~L~~~~~~~~~t~~eLA~~~g~~~~~~~~~l~rlLr~L 82 (241)
++.-|.+.+.+ ..|..++|+.+|+ +..-+.|+++..
T Consensus 16 ~~~~i~~~~~~-----~~s~~~vA~~~~v----s~~TV~ri~~~~ 51 (52)
T PF13542_consen 16 LEQYILKLLRE-----SRSFKDVARELGV----SWSTVRRIFDRY 51 (52)
T ss_pred HHHHHHHHHhh-----cCCHHHHHHHHCC----CHHHHHHHHHhh
Confidence 34456666654 3799999999999 999999998753
No 354
>TIGR03826 YvyF flagellar operon protein TIGR03826. This gene is found in flagellar operons of Bacillus-related organisms. Its function has not been determined and an official gene symbol has not been assigned, although the gene is designated yvyF in B. subtilus. A tentative assignment as a regulator is suggested in the NCBI record GI:16080597.
Probab=66.65 E-value=8.3 Score=29.84 Aligned_cols=35 Identities=11% Similarity=0.210 Sum_probs=27.2
Q ss_pred ChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCcchHHHHHH
Q 044458 41 DLLEVIAKAGPGAFMSPKQIASQLPTKNSDAHILLDRILR 80 (241)
Q Consensus 41 glfd~L~~~~~~~~~t~~eLA~~~g~~~~~~~~~l~rlLr 80 (241)
.|-+.|.+.+ +...|+.+|++.||+ ++..+.+|+|
T Consensus 34 kV~~yLr~~p-~~~ati~eV~e~tgV----s~~~I~~~Ir 68 (137)
T TIGR03826 34 KVYKFLRKHE-NRQATVSEIVEETGV----SEKLILKFIR 68 (137)
T ss_pred HHHHHHHHCC-CCCCCHHHHHHHHCc----CHHHHHHHHH
Confidence 4667787754 234899999999999 8887777765
No 355
>smart00088 PINT motif in proteasome subunits, Int-6, Nip-1 and TRIP-15. Also called the PCI (Proteasome, COP9, Initiation factor 3) domain. Unknown function.
Probab=65.95 E-value=14 Score=25.46 Aligned_cols=51 Identities=10% Similarity=0.082 Sum_probs=39.8
Q ss_pred HHHHHHhcChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCcchHHHHHHHHhcCCcccc
Q 044458 33 VLKSAIELDLLEVIAKAGPGAFMSPKQIASQLPTKNSDAHILLDRILRLLASYSVLNC 90 (241)
Q Consensus 33 ~L~~a~~lglfd~L~~~~~~~~~t~~eLA~~~g~~~~~~~~~l~rlLr~L~~~g~l~~ 90 (241)
......+..++...... ..++.++||+.+++ +.+.+++++..+...|.+.-
T Consensus 6 l~~~~~~~~l~~l~~~y---~~i~~~~i~~~~~l----~~~~vE~~i~~~i~~~~l~~ 56 (88)
T smart00088 6 LQRKIRLTNLLQLSEPY---SSISLSDLAKLLGL----SVPEVEKLVSKAIRDGEISA 56 (88)
T ss_pred HHHHHHHHHHHHHhHHh---ceeeHHHHHHHhCc----CHHHHHHHHHHHHHCCCeEE
Confidence 34444555566666543 58999999999999 77889999999999998864
No 356
>smart00753 PAM PCI/PINT associated module.
Probab=65.95 E-value=14 Score=25.46 Aligned_cols=51 Identities=10% Similarity=0.082 Sum_probs=39.8
Q ss_pred HHHHHHhcChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCcchHHHHHHHHhcCCcccc
Q 044458 33 VLKSAIELDLLEVIAKAGPGAFMSPKQIASQLPTKNSDAHILLDRILRLLASYSVLNC 90 (241)
Q Consensus 33 ~L~~a~~lglfd~L~~~~~~~~~t~~eLA~~~g~~~~~~~~~l~rlLr~L~~~g~l~~ 90 (241)
......+..++...... ..++.++||+.+++ +.+.+++++..+...|.+.-
T Consensus 6 l~~~~~~~~l~~l~~~y---~~i~~~~i~~~~~l----~~~~vE~~i~~~i~~~~l~~ 56 (88)
T smart00753 6 LQRKIRLTNLLQLSEPY---SSISLSDLAKLLGL----SVPEVEKLVSKAIRDGEISA 56 (88)
T ss_pred HHHHHHHHHHHHHhHHh---ceeeHHHHHHHhCc----CHHHHHHHHHHHHHCCCeEE
Confidence 34444555566666543 58999999999999 77889999999999998864
No 357
>PRK13918 CRP/FNR family transcriptional regulator; Provisional
Probab=65.87 E-value=5.9 Score=31.86 Aligned_cols=33 Identities=6% Similarity=0.232 Sum_probs=31.4
Q ss_pred CCCHHHHHhhCCCCCCCCcchHHHHHHHHhcCCcccc
Q 044458 54 FMSPKQIASQLPTKNSDAHILLDRILRLLASYSVLNC 90 (241)
Q Consensus 54 ~~t~~eLA~~~g~~~~~~~~~l~rlLr~L~~~g~l~~ 90 (241)
++|-++||+.+|+ .+..+.|+|..|...|++..
T Consensus 149 ~~t~~~iA~~lG~----tretvsR~l~~l~~~g~I~~ 181 (202)
T PRK13918 149 YATHDELAAAVGS----VRETVTKVIGELSREGYIRS 181 (202)
T ss_pred cCCHHHHHHHhCc----cHHHHHHHHHHHHHCCCEEc
Confidence 5799999999999 99999999999999999985
No 358
>PF02636 Methyltransf_28: Putative S-adenosyl-L-methionine-dependent methyltransferase; InterPro: IPR003788 This entry describes proteins of unknown function.; PDB: 4F3N_A 1ZKD_B.
Probab=65.78 E-value=6.6 Score=33.27 Aligned_cols=33 Identities=15% Similarity=0.237 Sum_probs=23.9
Q ss_pred CCCeEEEecCCchHHHHHHHHHCCCC--------cEEEccc
Q 044458 198 GLQSVVDVGGGIGASLDMIISKYPSI--------KGINFDL 230 (241)
Q Consensus 198 ~~~~vvDVGGG~G~~~~~l~~~~P~l--------~~~v~Dl 230 (241)
..-+||++|+|+|.++..+++..... +.++.+.
T Consensus 18 ~~~~ivE~GaG~G~La~diL~~l~~~~p~~~~~~~y~ivE~ 58 (252)
T PF02636_consen 18 EPLRIVEIGAGRGTLARDILRYLRKFSPEVYKRLRYHIVEI 58 (252)
T ss_dssp S-EEEEEES-TTSHHHHHHHHHHCCTTHHHHTTCEEEEE-T
T ss_pred cCcEEEEECCCchHHHHHHHHHHHHhChhhhhcceEEEEcC
Confidence 45899999999999999988865544 5666665
No 359
>PRK11639 zinc uptake transcriptional repressor; Provisional
Probab=65.70 E-value=7.7 Score=30.96 Aligned_cols=52 Identities=13% Similarity=0.138 Sum_probs=40.7
Q ss_pred HhcChHHHHHhcCCCCCCCHHHHHhhCCCC-CCCCcchHHHHHHHHhcCCccccc
Q 044458 38 IELDLLEVIAKAGPGAFMSPKQIASQLPTK-NSDAHILLDRILRLLASYSVLNCS 91 (241)
Q Consensus 38 ~~lglfd~L~~~~~~~~~t~~eLA~~~g~~-~~~~~~~l~rlLr~L~~~g~l~~~ 91 (241)
-+.-|+++|...+ ++.|++||.+.+.-. +.++..-+.|.|+.|...|++.+.
T Consensus 27 qR~~IL~~l~~~~--~hlSa~eI~~~L~~~~~~is~aTVYRtL~~L~e~Glv~~~ 79 (169)
T PRK11639 27 QRLEVLRLMSLQP--GAISAYDLLDLLREAEPQAKPPTVYRALDFLLEQGFVHKV 79 (169)
T ss_pred HHHHHHHHHHhcC--CCCCHHHHHHHHHhhCCCCCcchHHHHHHHHHHCCCEEEE
Confidence 4556788887653 689999999988641 223667899999999999999985
No 360
>PF06406 StbA: StbA protein; InterPro: IPR009440 This entry represents bacterial plasmid segregation proteins ParM and StbA []. They are involved in the control of plasmid partition and required for the accurate segregation of the plasmid. ; PDB: 3IKY_C 3IKU_I 2ZGZ_B 1MWM_A 1MWK_A 2ZHC_A 2ZGY_A 2QU4_A.
Probab=64.95 E-value=19 Score=31.77 Aligned_cols=64 Identities=17% Similarity=0.224 Sum_probs=42.0
Q ss_pred HHHHHHHHHhcchhhHHHHHHhcCCCCCCCeEEEecCCchHHHHHHHHHCC--CCcEEEccchHHH
Q 044458 171 NKIFNNGMFSHSTITMKKFLENYKGFEGLQSVVDVGGGIGASLDMIISKYP--SIKGINFDLPHVI 234 (241)
Q Consensus 171 ~~~f~~aM~~~~~~~~~~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P--~l~~~v~DlP~vi 234 (241)
.+...+.+..........+.+.+..+.+..+|+=||||.=.+..++.+.|| +-++++.|-|+..
T Consensus 245 ~~~v~~~i~~~~~~l~~~i~~~~~~~~~~~~I~~vGGGA~ll~~~Ik~~~~~~~~~i~i~~~pqfA 310 (318)
T PF06406_consen 245 IDDVSEVIEEAVEELINRILRELGDFSDIDRIFFVGGGAILLKDAIKEAFPVPNERIVIVDDPQFA 310 (318)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHTTS-S-SEEEEESTTHHHHHHHHHHHHT--GGGEE--SSGGGH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHhhhccCCeEEEECCcHHHHHHHHHHhhCCCCCcEEECCCchhh
Confidence 334444444444444445555543377788999999999999999999987 5678999988754
No 361
>TIGR00308 TRM1 tRNA(guanine-26,N2-N2) methyltransferase. This enzyme is responsible for two methylations of a characteristic guanine of most tRNA molecules. The activity has been demonstrated for eukaryotic and archaeal proteins, which are active when expressed in E. coli, a species that lacks this enzyme. At least one Eubacterium, Aquifex aeolicus, has an ortholog, as do all completed archaeal genomes.
Probab=64.93 E-value=6.3 Score=35.76 Aligned_cols=39 Identities=10% Similarity=0.153 Sum_probs=33.0
Q ss_pred CeEEEecCCchHHHHHHHHHCCCC-cEEEccc-hHHHhcCC
Q 044458 200 QSVVDVGGGIGASLDMIISKYPSI-KGINFDL-PHVIQDAP 238 (241)
Q Consensus 200 ~~vvDVGGG~G~~~~~l~~~~P~l-~~~v~Dl-P~vi~~a~ 238 (241)
.+|||.-+|+|..++..+++-++. +++..|+ |.+++.++
T Consensus 46 ~~vLD~faGsG~rgir~a~e~~ga~~Vv~nD~n~~Av~~i~ 86 (374)
T TIGR00308 46 INIADALSASGIRAIRYAHEIEGVREVFANDINPKAVESIK 86 (374)
T ss_pred CEEEECCCchhHHHHHHHhhCCCCCEEEEEeCCHHHHHHHH
Confidence 589999999999999999987776 4788898 77777553
No 362
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=64.55 E-value=9.3 Score=23.18 Aligned_cols=24 Identities=29% Similarity=0.317 Sum_probs=16.6
Q ss_pred CCCCHHHHHhhCCCCCCCCcchHHHHHH
Q 044458 53 AFMSPKQIASQLPTKNSDAHILLDRILR 80 (241)
Q Consensus 53 ~~~t~~eLA~~~g~~~~~~~~~l~rlLr 80 (241)
.+.|..+||+.+|. ++.-+.+.|+
T Consensus 19 ~G~s~~~IA~~lg~----s~sTV~relk 42 (44)
T PF13936_consen 19 QGMSIREIAKRLGR----SRSTVSRELK 42 (44)
T ss_dssp S---HHHHHHHTT------HHHHHHHHH
T ss_pred cCCCHHHHHHHHCc----CcHHHHHHHh
Confidence 36999999999999 9988888775
No 363
>PF00126 HTH_1: Bacterial regulatory helix-turn-helix protein, lysR family; InterPro: IPR000847 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. One such family, the lysR family, groups together a range of proteins, including ampR, catM, catR, cynR, cysB, gltC, iciA, ilvY, irgB, lysR, metR, mkaC, mleR, nahR, nhaR, nodD, nolR, oxyR, pssR, rbcR, syrM, tcbR, tfdS and trpI [, , , , ]. The majority of these proteins appear to be transcription activators and most are known to negatively regulate their own expression. All possess a potential HTH DNA-binding motif towards their N-termini.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 3T1B_D 3SZP_A 1O7L_C 1B9N_A 1B9M_A 3FZJ_J 3FXR_B 3FXQ_A 3FXU_A 2IJL_B ....
Probab=64.40 E-value=8.6 Score=24.81 Aligned_cols=54 Identities=19% Similarity=0.191 Sum_probs=39.6
Q ss_pred hcChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCcchHHHHHHHHh---cCCccccccccCCCCccccceecCccc
Q 044458 39 ELDLLEVIAKAGPGAFMSPKQIASQLPTKNSDAHILLDRILRLLA---SYSVLNCSLHTLPDGGVERLYGLAPVC 110 (241)
Q Consensus 39 ~lglfd~L~~~~~~~~~t~~eLA~~~g~~~~~~~~~l~rlLr~L~---~~g~l~~~~~~~~~g~~~~~y~~t~~s 110 (241)
++.+|..+.+. .|+..-|+.+++ ++..+.+-++.|. ..-+|.+. .+.+.+|+.+
T Consensus 3 ~l~~f~~v~~~-----gs~~~AA~~l~i----s~~~vs~~i~~LE~~lg~~Lf~r~---------~~~~~lT~~G 59 (60)
T PF00126_consen 3 QLRYFLAVAET-----GSISAAAEELGI----SQSAVSRQIKQLEEELGVPLFERS---------GRGLRLTEAG 59 (60)
T ss_dssp HHHHHHHHHHH-----SSHHHHHHHCTS----SHHHHHHHHHHHHHHHTS-SEEEC---------SSSEEE-HHH
T ss_pred HHHHHHHHHHh-----CCHHHHHHHhhc----cchHHHHHHHHHHHHhCCeEEEEC---------CCCeeEChhh
Confidence 45678888874 499999999999 9999998888884 44577763 3567888765
No 364
>cd00006 PTS_IIA_man PTS_IIA, PTS system, mannose/sorbose specific IIA subunit. The bacterial phosphoenolpyruvate: sugar phosphotransferase system (PTS) is a multi-protein system involved in the regulation of a variety of metabolic and transcriptional processes. This family is one of four structurally and functionally distinct group IIA PTS system cytoplasmic enzymes, necessary for the uptake of carbohydrates across the cytoplasmic membrane and their phosphorylation. IIA subunits receive phosphoryl groups from HPr and transfer them to IIB subunits, which in turn phosphorylate the substrate.
Probab=64.38 E-value=15 Score=27.40 Aligned_cols=48 Identities=21% Similarity=0.326 Sum_probs=33.4
Q ss_pred HHhcCCCCCCCeEEEecCCchH-HHHHHHHHCCCCc-EEEccchHHHhcC
Q 044458 190 LENYKGFEGLQSVVDVGGGIGA-SLDMIISKYPSIK-GINFDLPHVIQDA 237 (241)
Q Consensus 190 ~~~~~~~~~~~~vvDVGGG~G~-~~~~l~~~~P~l~-~~v~DlP~vi~~a 237 (241)
++.++.-++.-.++|+-||+=. .+..+...+++++ ....++|-+++..
T Consensus 51 i~~~~~~~~viil~Dl~GGSp~n~~~~~~~~~~~~~visG~nlpmlle~~ 100 (122)
T cd00006 51 LAELDSGEGVLILTDLFGGSPNNAAARLSMEHPPVEVIAGVNLPMLLEAA 100 (122)
T ss_pred HHHhCCCCcEEEEEeCCCCCHHHHHHHHHhcCCCEEEEEccCHHHHHHHH
Confidence 4445424567889999555554 4566666668887 5899999998764
No 365
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=63.63 E-value=10 Score=23.31 Aligned_cols=25 Identities=20% Similarity=0.196 Sum_probs=21.2
Q ss_pred CCCHHHHHhhCCCCCCCCcchHHHHHHHH
Q 044458 54 FMSPKQIASQLPTKNSDAHILLDRILRLL 82 (241)
Q Consensus 54 ~~t~~eLA~~~g~~~~~~~~~l~rlLr~L 82 (241)
+.+..+||+.+++ +...+++.++.+
T Consensus 18 g~s~~eia~~l~i----s~~tv~~~~~~~ 42 (58)
T smart00421 18 GLTNKEIAERLGI----SEKTVKTHLSNI 42 (58)
T ss_pred CCCHHHHHHHHCC----CHHHHHHHHHHH
Confidence 5899999999999 888887777654
No 366
>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein.
Probab=63.40 E-value=8.3 Score=25.67 Aligned_cols=30 Identities=13% Similarity=0.158 Sum_probs=25.1
Q ss_pred CCCHHHHHhhCCCCCCCCcchHHHHHHHHhcCCc
Q 044458 54 FMSPKQIASQLPTKNSDAHILLDRILRLLASYSV 87 (241)
Q Consensus 54 ~~t~~eLA~~~g~~~~~~~~~l~rlLr~L~~~g~ 87 (241)
+.|+++||+.+|+ ++..+.++++......+
T Consensus 1 ~~~~~~la~~~~~----s~~~l~~~f~~~~~~s~ 30 (84)
T smart00342 1 PLTLEDLAEALGM----SPRHLQRLFKKETGTTP 30 (84)
T ss_pred CCCHHHHHHHhCC----CHHHHHHHHHHHhCcCH
Confidence 3689999999999 99999999887765543
No 367
>TIGR00635 ruvB Holliday junction DNA helicase, RuvB subunit. RuvA specifically binds Holliday junctions as a sandwich of two tetramers and maintains the configuration of the junction. It forms a complex with two hexameric rings of RuvB, the subunit that contains helicase activity. The complex drives ATP-dependent branch migration of the Holliday junction recombination intermediate. The endonuclease RuvC resolves junctions.
Probab=63.37 E-value=7.3 Score=33.72 Aligned_cols=34 Identities=15% Similarity=0.157 Sum_probs=31.8
Q ss_pred CCCCHHHHHhhCCCCCCCCcchHHHHHH-HHhcCCcccc
Q 044458 53 AFMSPKQIASQLPTKNSDAHILLDRILR-LLASYSVLNC 90 (241)
Q Consensus 53 ~~~t~~eLA~~~g~~~~~~~~~l~rlLr-~L~~~g~l~~ 90 (241)
++.++++||+.+|. ++..++++++ .|...|++..
T Consensus 254 ~~~~~~~ia~~lg~----~~~~~~~~~e~~Li~~~li~~ 288 (305)
T TIGR00635 254 GPVGLKTLAAALGE----DADTIEDVYEPYLLQIGFLQR 288 (305)
T ss_pred CcccHHHHHHHhCC----CcchHHHhhhHHHHHcCCccc
Confidence 68999999999999 9999999999 7999999975
No 368
>KOG2651 consensus rRNA adenine N-6-methyltransferase [RNA processing and modification]
Probab=63.30 E-value=7.2 Score=35.47 Aligned_cols=36 Identities=28% Similarity=0.474 Sum_probs=27.5
Q ss_pred CCCCCeEEEecCCchHHHHHHHHHCCCCcEEEccchH
Q 044458 196 FEGLQSVVDVGGGIGASLDMIISKYPSIKGINFDLPH 232 (241)
Q Consensus 196 ~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~DlP~ 232 (241)
|-+...|||||.|.|+++.-+.-.| ++++..+|=.+
T Consensus 151 f~gi~~vvD~GaG~G~LSr~lSl~y-~lsV~aIegsq 186 (476)
T KOG2651|consen 151 FTGIDQVVDVGAGQGHLSRFLSLGY-GLSVKAIEGSQ 186 (476)
T ss_pred hcCCCeeEEcCCCchHHHHHHhhcc-CceEEEeccch
Confidence 7789999999999999998776655 55555555443
No 369
>PRK11642 exoribonuclease R; Provisional
Probab=63.17 E-value=11 Score=37.79 Aligned_cols=49 Identities=22% Similarity=0.206 Sum_probs=37.4
Q ss_pred ChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCcchHHHHHHHHhcCCccccc
Q 044458 41 DLLEVIAKAGPGAFMSPKQIASQLPTKNSDAHILLDRILRLLASYSVLNCS 91 (241)
Q Consensus 41 glfd~L~~~~~~~~~t~~eLA~~~g~~~~~~~~~l~rlLr~L~~~g~l~~~ 91 (241)
.|.+.|...+ +|++..+|+++++++...+...|++.|+.|...|.+.+.
T Consensus 23 ~Il~~l~~~~--~~~~~~~L~~~l~l~~~~~~~~l~~~L~~L~~~g~l~~~ 71 (813)
T PRK11642 23 FILEHLTKRE--KPASREELAVELNIEGEEQLEALRRRLRAMERDGQLVFT 71 (813)
T ss_pred HHHHHHHhcC--CCCCHHHHHHHhCCCChHHHHHHHHHHHHHHHCCCEEEc
Confidence 3677776543 799999999999993211234699999999999999764
No 370
>PLN02668 indole-3-acetate carboxyl methyltransferase
Probab=62.53 E-value=15 Score=33.53 Aligned_cols=34 Identities=24% Similarity=0.295 Sum_probs=24.5
Q ss_pred CCCeEEEecCCchHHHHH--------HHHH-------CCCCcEEEccch
Q 044458 198 GLQSVVDVGGGIGASLDM--------IISK-------YPSIKGINFDLP 231 (241)
Q Consensus 198 ~~~~vvDVGGG~G~~~~~--------l~~~-------~P~l~~~v~DlP 231 (241)
+.-.|+|+|||+|.++.. +.++ -|++++..=|||
T Consensus 63 ~~~~iaDlGcs~G~ntl~~vs~iI~~i~~~~~~~~~~~pe~qv~~nDLP 111 (386)
T PLN02668 63 VPFTAVDLGCSSGSNTIHIIDVIVKHMSKRYESAGLDPPEFSAFFSDLP 111 (386)
T ss_pred cceeEEEecCCCCccHHHHHHHHHHHHHHHhhhcCCCCCcceEEecCCC
Confidence 467899999999966532 2332 357788888888
No 371
>PRK09462 fur ferric uptake regulator; Provisional
Probab=62.10 E-value=13 Score=28.84 Aligned_cols=53 Identities=15% Similarity=0.221 Sum_probs=39.8
Q ss_pred HhcChHHHHHhcCCCCCCCHHHHHhhCCCC-CCCCcchHHHHHHHHhcCCccccc
Q 044458 38 IELDLLEVIAKAGPGAFMSPKQIASQLPTK-NSDAHILLDRILRLLASYSVLNCS 91 (241)
Q Consensus 38 ~~lglfd~L~~~~~~~~~t~~eLA~~~g~~-~~~~~~~l~rlLr~L~~~g~l~~~ 91 (241)
-+.-|++.|.... +++.|++||-+.+.-. +.++..-+.|.|+.|...|++.+.
T Consensus 18 qR~~Il~~l~~~~-~~h~sa~eI~~~l~~~~~~i~~aTVYR~L~~L~e~Gli~~~ 71 (148)
T PRK09462 18 PRLKILEVLQEPD-NHHVSAEDLYKRLIDMGEEIGLATVYRVLNQFDDAGIVTRH 71 (148)
T ss_pred HHHHHHHHHHhCC-CCCCCHHHHHHHHHhhCCCCCHHHHHHHHHHHHHCCCEEEE
Confidence 3455788887532 1589999999887431 223677899999999999999875
No 372
>PHA03103 double-strand RNA-binding protein; Provisional
Probab=61.55 E-value=15 Score=29.83 Aligned_cols=43 Identities=14% Similarity=0.148 Sum_probs=36.7
Q ss_pred hHHHHHhcCCCCCCCHHHHHhhCCCCCCCCcchHHHHHHHHhcCCccccc
Q 044458 42 LLEVIAKAGPGAFMSPKQIASQLPTKNSDAHILLDRILRLLASYSVLNCS 91 (241)
Q Consensus 42 lfd~L~~~~~~~~~t~~eLA~~~g~~~~~~~~~l~rlLr~L~~~g~l~~~ 91 (241)
+.+.|.. ++..|+.+||.++|+ +..-+.|.|.-|...|.+...
T Consensus 18 ~~~~l~~---~~~~~a~~i~~~l~~----~k~~vNr~LY~l~~~~~v~~~ 60 (183)
T PHA03103 18 EVKNLGL---GEGITAIEISRKLNI----EKSEVNKQLYKLQREGMVYMS 60 (183)
T ss_pred HHHHhcc---CCCccHHHHHHHhCC----CHHHHHHHHHHHHhcCceecC
Confidence 4555655 378999999999999 888999999999999999764
No 373
>cd06445 ATase The DNA repair protein O6-alkylguanine-DNA alkyltransferase (ATase; also known as AGT, AGAT and MGMT) reverses O6-alkylation DNA damage by transferring O6-alkyl adducts to an active site cysteine irreversibly, without inducing DNA strand breaks. ATases are specific for repair of guanines with O6-alkyl adducts, however human ATase is not limited to O6-methylguanine, repairing many other adducts at the O6-position of guanine as well. ATase is widely distributed among species. Most ATases have N- and C-terminal domains. The C-terminal domain contains the conserved active-site cysteine motif (PCHR), the O6-alkylguanine binding channel, and the helix-turn-helix (HTH) DNA-binding motif. The active site is located near the recognition helix of the HTH motif. While the C-terminal domain of ATase contains residues that are necessary for DNA binding and alkyl transfer, the function of the N-terminal domain is still unknown. Removal of the N-terminal domain abolishes the activity of
Probab=61.54 E-value=18 Score=24.94 Aligned_cols=42 Identities=19% Similarity=0.101 Sum_probs=29.1
Q ss_pred ChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCcchHHHHHHHHhcCCc
Q 044458 41 DLLEVIAKAGPGAFMSPKQIASQLPTKNSDAHILLDRILRLLASYSV 87 (241)
Q Consensus 41 glfd~L~~~~~~~~~t~~eLA~~~g~~~~~~~~~l~rlLr~L~~~g~ 87 (241)
.|++.+..-|.|.-.|+.+||+.+|. +...+.+=..|....+
T Consensus 4 ~V~~~v~~IP~G~v~TYg~iA~~~g~-----p~~~R~Vg~al~~np~ 45 (79)
T cd06445 4 RVWEALRQIPYGEVTTYGQIAKLAGT-----PKAARAVGSALARNPI 45 (79)
T ss_pred HHHHHHhcCCCCCcCcHHHHHHHHCC-----CCcHHHHHHHHHhCCC
Confidence 46677776665678999999999997 3445555555554443
No 374
>PF02502 LacAB_rpiB: Ribose/Galactose Isomerase; InterPro: IPR003500 This entry represents the sugar isomerase enzymes ribose 5-phosphate isomerase B (rpiB), galactose isomerase subunit A (LacA) and galactose isomerase subunit B (LacB). Galactose-6-phosphate isomerase (5.3.1.26 from EC) is a heteromultimeric protein consisting of subunits LacA and LacB, and catalyses the conversion of D-galactose 6-phosphate to D-tagatose and 6-phosphate in the tagatose 6-phosphate pathway of lactose catabolism []. Galactose-6-phosphate isomerase is induced by galactose or lactose. This entry represents the LacB subunit. Ribose 5-phosphate isomerase (5.3.1.6 from EC) forms a homodimer and catalyses the interconversion of D-ribose 5-phosphate and D-ribulose 5-phosphate in the non-oxidative branch of the pentose phosphate pathway. This reaction permits the synthesis of ribose from other sugars, as well as the recycling of sugars from nucleotide breakdown. Two unrelated enzymes can catalyse this reaction: RpiA (found in most organisms) and RpiB (found in some bacteria and eukaryotes). RpiB is also involved in metabolism of the rare sugar, allose, in addition to ribose sugars. The structures of RpiA and RpiB are distinct, RpiB having a Rossmann-type alpha/beta/alpha sandwich topology [].; GO: 0005975 carbohydrate metabolic process; PDB: 3HEE_A 3HE8_A 3PH3_B 3PH4_B 3ONO_A 4EM8_B 3S5P_B 1O1X_A 2BES_D 2VVP_D ....
Probab=61.46 E-value=4.5 Score=31.43 Aligned_cols=39 Identities=18% Similarity=0.123 Sum_probs=28.0
Q ss_pred EEEecCCchHHHHHHHHHCCCCcEEEccchHHHhcCCCC
Q 044458 202 VVDVGGGIGASLDMIISKYPSIKGINFDLPHVIQDAPAY 240 (241)
Q Consensus 202 vvDVGGG~G~~~~~l~~~~P~l~~~v~DlP~vi~~a~~~ 240 (241)
.-=+.||+|.-..-.+.++|++++.+.--|.....+++|
T Consensus 59 ~GIliCgtGiG~~iaANK~~GIrAa~~~d~~~A~~ar~h 97 (140)
T PF02502_consen 59 RGILICGTGIGMSIAANKVPGIRAALCSDPYSAKMAREH 97 (140)
T ss_dssp EEEEEESSSHHHHHHHHTSTT--EEE-SSHHHHHHHHHT
T ss_pred eEEEEcCCChhhhhHhhcCCCEEEEeeCCHHHHHHHHHh
Confidence 355678888888999999999998777777777666543
No 375
>PF11994 DUF3489: Protein of unknown function (DUF3489); InterPro: IPR021880 This family of proteins is functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 84 to 211 amino acids in length. This protein has a single completely conserved residue W that may be functionally important.
Probab=61.35 E-value=15 Score=25.10 Aligned_cols=42 Identities=10% Similarity=0.015 Sum_probs=32.1
Q ss_pred hHHHHHhcCCCCCCCHHHHHhhCCCCCCCCcchHHHHHHHH--hcCCcccc
Q 044458 42 LLEVIAKAGPGAFMSPKQIASQLPTKNSDAHILLDRILRLL--ASYSVLNC 90 (241)
Q Consensus 42 lfd~L~~~~~~~~~t~~eLA~~~g~~~~~~~~~l~rlLr~L--~~~g~l~~ 90 (241)
|.+.|... ++.|++||++++|+ .++-++-.|--+ -..|+-..
T Consensus 15 li~mL~rp---~GATi~ei~~atGW----q~HTvRgalsg~~kKklGl~i~ 58 (72)
T PF11994_consen 15 LIAMLRRP---EGATIAEICEATGW----QPHTVRGALSGLLKKKLGLTIT 58 (72)
T ss_pred HHHHHcCC---CCCCHHHHHHhhCC----chhhHHHHHHHHHHHhcCcEEE
Confidence 55667653 57999999999999 899888877777 55665543
No 376
>COG3695 Predicted methylated DNA-protein cysteine methyltransferase [DNA replication, recombination, and repair]
Probab=60.87 E-value=12 Score=27.31 Aligned_cols=51 Identities=25% Similarity=0.203 Sum_probs=37.9
Q ss_pred hcChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCcchHHHHHHHHhcCCccccc
Q 044458 39 ELDLLEVIAKAGPGAFMSPKQIASQLPTKNSDAHILLDRILRLLASYSVLNCS 91 (241)
Q Consensus 39 ~lglfd~L~~~~~~~~~t~~eLA~~~g~~~~~~~~~l~rlLr~L~~~g~l~~~ 91 (241)
.-.|++.+..-|.+.-.|+-|||+-.|. |..++-+.++|..|..--.+-..
T Consensus 8 ~~~v~~vv~~IP~GkV~TYGdIA~laG~--p~~ARqVG~il~~l~~~s~lPWh 58 (103)
T COG3695 8 TQRVLDVVAAIPEGKVSTYGDIAKLAGL--PRAARQVGRILKHLPEGSDLPWH 58 (103)
T ss_pred HHHHHHHHHhCCCCceeeHHHHHHHhCC--ChhHHHHHHHHhhCCCCCCCChh
Confidence 3456777776665677999999999999 32488888999888766665443
No 377
>PRK09775 putative DNA-binding transcriptional regulator; Provisional
Probab=60.75 E-value=12 Score=34.72 Aligned_cols=52 Identities=19% Similarity=0.209 Sum_probs=39.0
Q ss_pred hHHHHHhcCCCCCCCHHHHHhhCCCCCCCCcchHHHHHHHHhcCCccccccccCCCCccccceecCc
Q 044458 42 LLEVIAKAGPGAFMSPKQIASQLPTKNSDAHILLDRILRLLASYSVLNCSLHTLPDGGVERLYGLAP 108 (241)
Q Consensus 42 lfd~L~~~~~~~~~t~~eLA~~~g~~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~g~~~~~y~~t~ 108 (241)
|...|.. |+.|+.||++.+|+ +...+.|.|+.| .|+|.... .|- .-+|++..
T Consensus 5 ~~~~L~~----g~~~~~eL~~~l~~----sq~~~s~~L~~L--~~~V~~~~----~gr-~~~Y~l~~ 56 (442)
T PRK09775 5 LTTLLLQ----GPLSAAELAARLGV----SQATLSRLLAAL--GDQVVRFG----KAR-ATRYALLR 56 (442)
T ss_pred HHHHHhc----CCCCHHHHHHHhCC----CHHHHHHHHHHh--hcceeEec----cCc-eEEEEecc
Confidence 4556665 79999999999999 999999999999 77776531 221 35666655
No 378
>PRK09391 fixK transcriptional regulator FixK; Provisional
Probab=60.68 E-value=8.1 Score=32.12 Aligned_cols=33 Identities=24% Similarity=0.213 Sum_probs=31.1
Q ss_pred CCCHHHHHhhCCCCCCCCcchHHHHHHHHhcCCcccc
Q 044458 54 FMSPKQIASQLPTKNSDAHILLDRILRLLASYSVLNC 90 (241)
Q Consensus 54 ~~t~~eLA~~~g~~~~~~~~~l~rlLr~L~~~g~l~~ 90 (241)
+.|-++||+.+|+ .+..+.|+|+.|...|+++.
T Consensus 179 ~lt~~~IA~~lGi----sretlsR~L~~L~~~GlI~~ 211 (230)
T PRK09391 179 PMSRRDIADYLGL----TIETVSRALSQLQDRGLIGL 211 (230)
T ss_pred cCCHHHHHHHHCC----CHHHHHHHHHHHHHCCcEEe
Confidence 5788999999999 99999999999999999985
No 379
>TIGR00589 ogt O-6-methylguanine DNA methyltransferase. All proteins in this family for which functions are known are involved alkyl-DNA transferases which remove alkyl groups from DNA as part of alkylation DNA repair. Some of the proteins in this family are also transcription regulators and have a distinct transcription regulatory domain. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=60.18 E-value=19 Score=25.03 Aligned_cols=43 Identities=9% Similarity=0.023 Sum_probs=29.9
Q ss_pred HhcChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCcchHHHHHHHHhcC
Q 044458 38 IELDLLEVIAKAGPGAFMSPKQIASQLPTKNSDAHILLDRILRLLASY 85 (241)
Q Consensus 38 ~~lglfd~L~~~~~~~~~t~~eLA~~~g~~~~~~~~~l~rlLr~L~~~ 85 (241)
+...|++.|.+-+.+.-.|+.+||+.+|. +...+.+-.+|...
T Consensus 3 f~~~V~~~l~~IP~G~v~TYg~iA~~~g~-----p~~~RaVg~al~~n 45 (80)
T TIGR00589 3 FQQRVWQALRTIPYGETKSYGQLAARIGN-----PKAVRAVGGANGRN 45 (80)
T ss_pred HHHHHHHHHhCCCCCCcCCHHHHHHHhCC-----CChHHHHHHHHHhC
Confidence 34567888887766688999999999996 33444444444443
No 380
>TIGR00824 EIIA-man PTS system, mannose/fructose/sorbose family, IIA component. Bacterial PTS transporters transport and concomitantly phosphorylate their sugar substrates, and typically consist of multiple subunits or protein domains.The Man family is unique in several respects among PTS permease families It is the only PTS family in which members possess a IID protein. It is the only PTS family in which the IIB constituent is phosphorylated on a histidyl rather than a cysteyl residue. Its permease members exhibit broad specificity for a range of sugars, rather than being specific for just one or a few sugars. The mannose permease of E. coli, for example, can transport and phosphorylate glucose, mannose, fructose, glucosamine, N-acetylglucosamine, and other sugars. Other members of this can transport sorbose, fructose and N-acetylglucosamine. This family is specific for the IIA components.
Probab=59.80 E-value=19 Score=26.75 Aligned_cols=49 Identities=22% Similarity=0.278 Sum_probs=34.4
Q ss_pred HHHhcCCCCCCCeEEEecCCchHHH-HHHHHHCCCCc-EEEccchHHHhcC
Q 044458 189 FLENYKGFEGLQSVVDVGGGIGASL-DMIISKYPSIK-GINFDLPHVIQDA 237 (241)
Q Consensus 189 ~~~~~~~~~~~~~vvDVGGG~G~~~-~~l~~~~P~l~-~~v~DlP~vi~~a 237 (241)
+++.++.=.+.-.+.|+=||+-... ..+...+|+++ ....+||-+++.+
T Consensus 51 ~i~~~~~~~~vivltDl~GGSp~n~a~~~~~~~~~~~vIsG~NLpmlle~~ 101 (116)
T TIGR00824 51 ALADLDTEEEVLFLVDIFGGSPYNAAARIIVDKPHMDVIAGVNLPLLLETL 101 (116)
T ss_pred HHHhcCCCCCEEEEEeCCCCCHHHHHHHHHhhcCCEEEEEecCHHHHHHHH
Confidence 3444442345678899977776654 44667889998 4899999998864
No 381
>cd06170 LuxR_C_like C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many are active as homodimers. Many are two domain proteins in which the DNA binding property of the C-terminal DNA binding domain is modulated by modifications of the N-terminal domain. For example in the case of Lux R which participates in the regulation of gene expression in response to fluctuations in cell-population density (quorum-sensing), a signaling molecule, the pheromone Acyl HSL (N-acyl derivatives of homoserine lactone), binds to the N-terminal domain and leads to LuxR dimerization. For others phophorylation of the N-terminal domain leads to multimerization, for example Escherichia coli NarL and Sinorhizobium melilot FixJ. NarL controls gene expression of many respiratory-related operons when environmental
Probab=59.75 E-value=13 Score=22.85 Aligned_cols=25 Identities=24% Similarity=0.165 Sum_probs=21.3
Q ss_pred CCCHHHHHhhCCCCCCCCcchHHHHHHHH
Q 044458 54 FMSPKQIASQLPTKNSDAHILLDRILRLL 82 (241)
Q Consensus 54 ~~t~~eLA~~~g~~~~~~~~~l~rlLr~L 82 (241)
+.|..+||+.+++ ++..+++.++.+
T Consensus 15 ~~s~~eia~~l~~----s~~tv~~~~~~~ 39 (57)
T cd06170 15 GKTNKEIADILGI----SEKTVKTHLRNI 39 (57)
T ss_pred CCCHHHHHHHHCC----CHHHHHHHHHHH
Confidence 6899999999999 888887777654
No 382
>COG0735 Fur Fe2+/Zn2+ uptake regulation proteins [Inorganic ion transport and metabolism]
Probab=59.71 E-value=11 Score=29.29 Aligned_cols=51 Identities=20% Similarity=0.283 Sum_probs=40.8
Q ss_pred hcChHHHHHhcCCCCCCCHHHHHhhCCC-CCCCCcchHHHHHHHHhcCCccccc
Q 044458 39 ELDLLEVIAKAGPGAFMSPKQIASQLPT-KNSDAHILLDRILRLLASYSVLNCS 91 (241)
Q Consensus 39 ~lglfd~L~~~~~~~~~t~~eLA~~~g~-~~~~~~~~l~rlLr~L~~~g~l~~~ 91 (241)
++.|+++|...+ ++.|+++|=+.+.- .++++..-+.|.|+.|...|++.+.
T Consensus 23 R~~vl~~L~~~~--~~~sAeei~~~l~~~~p~islaTVYr~L~~l~e~Glv~~~ 74 (145)
T COG0735 23 RLAVLELLLEAD--GHLSAEELYEELREEGPGISLATVYRTLKLLEEAGLVHRL 74 (145)
T ss_pred HHHHHHHHHhcC--CCCCHHHHHHHHHHhCCCCCHhHHHHHHHHHHHCCCEEEE
Confidence 456888998764 57999999888763 2344677899999999999999986
No 383
>TIGR02844 spore_III_D sporulation transcriptional regulator SpoIIID. Members of this protein are the transcriptional regulator SpoIIID, or stage III sporulation protein D. It is present in genomes if and only if the species is capable of endospore formation as occurs in the model species Bacillus subtilis. SpoIIID is a DNA binding protein that, in B. subtilis, downregulates many genes but also turns on ten genes.
Probab=59.58 E-value=12 Score=26.16 Aligned_cols=31 Identities=6% Similarity=0.104 Sum_probs=25.4
Q ss_pred ChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCcchHHHHH
Q 044458 41 DLLEVIAKAGPGAFMSPKQIASQLPTKNSDAHILLDRIL 79 (241)
Q Consensus 41 glfd~L~~~~~~~~~t~~eLA~~~g~~~~~~~~~l~rlL 79 (241)
-|.++|.. +..|+.|||+.+|+ +..-++|.|
T Consensus 10 ~I~e~l~~----~~~ti~dvA~~~gv----S~~TVsr~L 40 (80)
T TIGR02844 10 EIGKYIVE----TKATVRETAKVFGV----SKSTVHKDV 40 (80)
T ss_pred HHHHHHHH----CCCCHHHHHHHhCC----CHHHHHHHh
Confidence 46677777 38999999999999 888888755
No 384
>PRK11534 DNA-binding transcriptional regulator CsiR; Provisional
Probab=59.42 E-value=10 Score=31.23 Aligned_cols=36 Identities=11% Similarity=0.041 Sum_probs=32.9
Q ss_pred CCCCCHHHHHhhCCCCCCCCcchHHHHHHHHhcCCccccc
Q 044458 52 GAFMSPKQIASQLPTKNSDAHILLDRILRLLASYSVLNCS 91 (241)
Q Consensus 52 ~~~~t~~eLA~~~g~~~~~~~~~l~rlLr~L~~~g~l~~~ 91 (241)
|..++..+||+.+|+ +..-++.-|+.|...|+++..
T Consensus 28 G~~L~e~eLae~lgV----SRtpVREAL~~L~~eGlv~~~ 63 (224)
T PRK11534 28 DEKLRMSLLTSRYAL----GVGPLREALSQLVAERLVTVV 63 (224)
T ss_pred CCcCCHHHHHHHHCC----ChHHHHHHHHHHHHCCCEEEe
Confidence 367899999999999 888999999999999999864
No 385
>PF08704 GCD14: tRNA methyltransferase complex GCD14 subunit; InterPro: IPR014816 GCD14 is a subunit of the tRNA methyltransferase complex and is required for 1-methyladenosine modification and maturation of initiator methionyl-tRNA []. ; GO: 0016429 tRNA (adenine-N1-)-methyltransferase activity, 0030488 tRNA methylation; PDB: 2YVL_C 1YB2_A 2B25_B 1O54_A 2PWY_B 1I9G_A 3LGA_B 3LHD_C 3MB5_A.
Probab=59.37 E-value=15 Score=31.27 Aligned_cols=57 Identities=12% Similarity=0.225 Sum_probs=35.6
Q ss_pred HHHHHHHhcchhh----HHHHHHhcCCCCCCCeEEEecCCchHHHHHHHH-HCCCCcEEEccc
Q 044458 173 IFNNGMFSHSTIT----MKKFLENYKGFEGLQSVVDVGGGIGASLDMIIS-KYPSIKGINFDL 230 (241)
Q Consensus 173 ~f~~aM~~~~~~~----~~~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~-~~P~l~~~v~Dl 230 (241)
.|...|...++.. +.-|+...+ .....+||+.|-|+|.++..|++ -.|+=+..-+|.
T Consensus 12 ~~~~~l~rrtQIiYpkD~~~I~~~l~-i~pG~~VlEaGtGSG~lt~~l~r~v~p~G~v~t~E~ 73 (247)
T PF08704_consen 12 LWTLSLPRRTQIIYPKDISYILMRLD-IRPGSRVLEAGTGSGSLTHALARAVGPTGHVYTYEF 73 (247)
T ss_dssp HHHHTS-SSS----HHHHHHHHHHTT---TT-EEEEE--TTSHHHHHHHHHHTTTSEEEEEES
T ss_pred HHHHhccCCcceeeCchHHHHHHHcC-CCCCCEEEEecCCcHHHHHHHHHHhCCCeEEEcccc
Confidence 4555665555543 234555566 77789999999999999999997 557777777776
No 386
>KOG2187 consensus tRNA uracil-5-methyltransferase and related tRNA-modifying enzymes [Translation, ribosomal structure and biogenesis]
Probab=59.08 E-value=6.9 Score=36.80 Aligned_cols=42 Identities=19% Similarity=0.284 Sum_probs=32.5
Q ss_pred CCCCCeEEEecCCchHHHHHHHHHCCCCcEEEccc-hHHHhcCCC
Q 044458 196 FEGLQSVVDVGGGIGASLDMIISKYPSIKGINFDL-PHVIQDAPA 239 (241)
Q Consensus 196 ~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-P~vi~~a~~ 239 (241)
.+..+.++||=||+|.++.++++..-. ++.+++ |+.++.|+.
T Consensus 381 l~~~k~llDv~CGTG~iglala~~~~~--ViGvEi~~~aV~dA~~ 423 (534)
T KOG2187|consen 381 LPADKTLLDVCCGTGTIGLALARGVKR--VIGVEISPDAVEDAEK 423 (534)
T ss_pred CCCCcEEEEEeecCCceehhhhccccc--eeeeecChhhcchhhh
Confidence 445599999999999999999887554 455565 888877753
No 387
>PF03374 ANT: Phage antirepressor protein KilAC domain; InterPro: IPR005039 This entry is represented by Bacteriophage P1, Ant1 C-terminal domain, which represents the processed Ant2 chain. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. Prophages P1 and P7 exist as unit copy DNA plasmids in the bacterial cell. Maintenance of the prophage state requires the continuous expression of two repressors: (i) C1 is a protein which negatively regulates the expression of lytic genes including the C1 inactivator gene coi, and (ii) C4 is an antisense RNA which specifically inhibits the synthesis of an anti-repressor Ant.; GO: 0003677 DNA binding
Probab=58.76 E-value=13 Score=27.13 Aligned_cols=41 Identities=15% Similarity=0.150 Sum_probs=31.9
Q ss_pred ChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCcchHHHHHHHHhcCCcccc
Q 044458 41 DLLEVIAKAGPGAFMSPKQIASQLPTKNSDAHILLDRILRLLASYSVLNC 90 (241)
Q Consensus 41 glfd~L~~~~~~~~~t~~eLA~~~g~~~~~~~~~l~rlLr~L~~~g~l~~ 90 (241)
..+|.+..+. +..|+.|+|+.+|+ .+..|..+|| ..|++..
T Consensus 13 ~~~d~~~~~~--~~~ti~~~AK~L~i----~~~~l~~~Lr---~~g~l~~ 53 (111)
T PF03374_consen 13 EFYDAFVDSD--GLYTIREAAKLLGI----GRNKLFQWLR---EKGWLYR 53 (111)
T ss_pred HHHHHHHcCC--CCccHHHHHHHhCC----CHHHHHHHHH---hCCceEE
Confidence 4677777653 78999999999999 8776665555 5898886
No 388
>TIGR03338 phnR_burk phosphonate utilization associated transcriptional regulator. This family of proteins are members of the GntR family (pfam00392) containing an N-terminal helix-turn-helix (HTH) motif. This clade is found adjacent to or inside of operons for the degradation of 2-aminoethylphosphonate (AEP) in Polaromonas, Burkholderia, Ralstonia and Verminephrobacter.
Probab=58.67 E-value=10 Score=31.00 Aligned_cols=36 Identities=19% Similarity=0.256 Sum_probs=32.9
Q ss_pred CCCCCHHHHHhhCCCCCCCCcchHHHHHHHHhcCCccccc
Q 044458 52 GAFMSPKQIASQLPTKNSDAHILLDRILRLLASYSVLNCS 91 (241)
Q Consensus 52 ~~~~t~~eLA~~~g~~~~~~~~~l~rlLr~L~~~g~l~~~ 91 (241)
|..++..+||+.+|+ +..-++.-|+.|...|+++..
T Consensus 32 G~~L~e~~La~~lgV----SRtpVReAL~~L~~eGlv~~~ 67 (212)
T TIGR03338 32 GAKLNESDIAARLGV----SRGPVREAFRALEEAGLVRNE 67 (212)
T ss_pred CCEecHHHHHHHhCC----ChHHHHHHHHHHHHCCCEEEe
Confidence 367899999999999 899999999999999999864
No 389
>PRK09464 pdhR transcriptional regulator PdhR; Reviewed
Probab=58.38 E-value=12 Score=31.50 Aligned_cols=35 Identities=14% Similarity=0.186 Sum_probs=32.2
Q ss_pred CCC-CHHHHHhhCCCCCCCCcchHHHHHHHHhcCCccccc
Q 044458 53 AFM-SPKQIASQLPTKNSDAHILLDRILRLLASYSVLNCS 91 (241)
Q Consensus 53 ~~~-t~~eLA~~~g~~~~~~~~~l~rlLr~L~~~g~l~~~ 91 (241)
..+ +-.+||+.+|+ +..-++.-|+.|...|+++..
T Consensus 32 ~~LpsE~eLa~~lgV----SRtpVREAL~~L~~eGlv~~~ 67 (254)
T PRK09464 32 EKLPPERELAKQFDV----SRPSLREAIQRLEAKGLLLRR 67 (254)
T ss_pred CcCCCHHHHHHHhCC----CHHHHHHHHHHHHHCCCEEEe
Confidence 567 89999999999 899999999999999999874
No 390
>PF03297 Ribosomal_S25: S25 ribosomal protein; InterPro: IPR004977 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 [, ]. The S25 ribosomal protein is a component of the 40S ribosomal subunit.; PDB: 2XZM_8 2XZN_8 3O30_Q 3U5G_Z 3IZB_V 3U5C_Z 3O2Z_Q 3IZ6_V.
Probab=58.31 E-value=8 Score=28.50 Aligned_cols=35 Identities=20% Similarity=0.314 Sum_probs=32.2
Q ss_pred CCCCHHHHHhhCCCCCCCCcchHHHHHHHHhcCCccccc
Q 044458 53 AFMSPKQIASQLPTKNSDAHILLDRILRLLASYSVLNCS 91 (241)
Q Consensus 53 ~~~t~~eLA~~~g~~~~~~~~~l~rlLr~L~~~g~l~~~ 91 (241)
.-+|...||+++++ .-...+++||.|...|++...
T Consensus 58 K~ITp~~lserlkI----~~SlAr~~Lr~L~~kG~Ik~V 92 (105)
T PF03297_consen 58 KLITPSVLSERLKI----NGSLARKALRELESKGLIKPV 92 (105)
T ss_dssp SCECHHHHHHHHCC----SCHHHHHHHHHHHHCCSSEEE
T ss_pred cEeeHHHHHHhHhh----HHHHHHHHHHHHHHCCCEEEE
Confidence 45999999999999 999999999999999999764
No 391
>PF04539 Sigma70_r3: Sigma-70 region 3; InterPro: IPR007624 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 3 forms a discrete compact three helical domain within the sigma-factor. Region is not normally involved in the recognition of promoter DNA, but in some specific bacterial promoters containing an extended -10 promoter element, residues within region 3 play an important role. Region 3 primarily is involved in binding the core RNA polymerase in the holoenzyme [].; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 1L0O_C 1KU2_B 1RP3_C 1SC5_A 1TTY_A 2BE5_F 2A6E_F 2CW0_F 2A69_P 2A6H_P ....
Probab=58.21 E-value=7.6 Score=26.30 Aligned_cols=34 Identities=15% Similarity=0.063 Sum_probs=26.4
Q ss_pred CCCCHHHHHhhCCCCCCCCcchHHHHHHHHhcCCcccc
Q 044458 53 AFMSPKQIASQLPTKNSDAHILLDRILRLLASYSVLNC 90 (241)
Q Consensus 53 ~~~t~~eLA~~~g~~~~~~~~~l~rlLr~L~~~g~l~~ 90 (241)
..-|.+|||+.+|+ +...++.++......-.+..
T Consensus 19 r~Pt~eEiA~~lgi----s~~~v~~~l~~~~~~~Sl~~ 52 (78)
T PF04539_consen 19 REPTDEEIAEELGI----SVEEVRELLQASRRPVSLDL 52 (78)
T ss_dssp S--BHHHHHHHHTS-----HHHHHHHHHHHSCCEESSH
T ss_pred CCCCHHHHHHHHcc----cHHHHHHHHHhCCCCeEEee
Confidence 46799999999999 99999999998776655554
No 392
>COG1725 Predicted transcriptional regulators [Transcription]
Probab=58.15 E-value=12 Score=28.52 Aligned_cols=35 Identities=14% Similarity=0.186 Sum_probs=31.9
Q ss_pred CCCCHHHHHhhCCCCCCCCcchHHHHHHHHhcCCccccc
Q 044458 53 AFMSPKQIASQLPTKNSDAHILLDRILRLLASYSVLNCS 91 (241)
Q Consensus 53 ~~~t~~eLA~~~g~~~~~~~~~l~rlLr~L~~~g~l~~~ 91 (241)
.=-|..|||..+|+ ++.-+.|..+.|...|++.-.
T Consensus 34 kLPSvRelA~~~~V----NpnTv~raY~eLE~eG~i~t~ 68 (125)
T COG1725 34 KLPSVRELAKDLGV----NPNTVQRAYQELEREGIVETK 68 (125)
T ss_pred CCCcHHHHHHHhCC----CHHHHHHHHHHHHHCCCEEEe
Confidence 34699999999999 999999999999999999864
No 393
>TIGR02698 CopY_TcrY copper transport repressor, CopY/TcrY family. This family includes metal-fist type transcriptional repressors of copper transport systems such as copYZAB of Enterococcus hirae and tcrYAZB (transferble copper resistance) of an Enterocuccus faecium plasmid. High levels of copper can displace zinc and prevent binding by the repressor, activating efflux by copper resistance transporters. The most closely related proteins excluded by this model are antibiotic resistance regulators including the methicillin resistance regulatory protein MecI.
Probab=57.93 E-value=15 Score=28.00 Aligned_cols=51 Identities=16% Similarity=0.197 Sum_probs=37.5
Q ss_pred HhcChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCcchHHHHHHHHhcCCccccc
Q 044458 38 IELDLLEVIAKAGPGAFMSPKQIASQLPTKNSDAHILLDRILRLLASYSVLNCS 91 (241)
Q Consensus 38 ~~lglfd~L~~~~~~~~~t~~eLA~~~g~~~~~~~~~l~rlLr~L~~~g~l~~~ 91 (241)
.|+.|...|=.. ++.|+.||.+.++-..++...-+..+|+-|...|++...
T Consensus 5 ~E~~VM~vlW~~---~~~t~~eI~~~l~~~~~~~~tTv~T~L~rL~~KG~v~~~ 55 (130)
T TIGR02698 5 AEWEVMRVVWTL---GETTSRDIIRILAEKKDWSDSTIKTLLGRLVDKGCLTTE 55 (130)
T ss_pred HHHHHHHHHHcC---CCCCHHHHHHHHhhccCCcHHHHHHHHHHHHHCCceeee
Confidence 456677777554 589999977765311112788899999999999999864
No 394
>COG2390 DeoR Transcriptional regulator, contains sigma factor-related N-terminal domain [Transcription]
Probab=57.86 E-value=10 Score=33.71 Aligned_cols=35 Identities=17% Similarity=0.232 Sum_probs=32.6
Q ss_pred CCCCHHHHHhhCCCCCCCCcchHHHHHHHHhcCCccccc
Q 044458 53 AFMSPKQIASQLPTKNSDAHILLDRILRLLASYSVLNCS 91 (241)
Q Consensus 53 ~~~t~~eLA~~~g~~~~~~~~~l~rlLr~L~~~g~l~~~ 91 (241)
.++|=.|||+++|+ +...+.|+|..+...|+++..
T Consensus 25 ~gltQ~eIA~~Lgi----SR~~v~rlL~~Ar~~GiV~I~ 59 (321)
T COG2390 25 EGLTQSEIAERLGI----SRATVSRLLAKAREEGIVKIS 59 (321)
T ss_pred cCCCHHHHHHHhCC----CHHHHHHHHHHHHHCCeEEEE
Confidence 47999999999999 999999999999999999864
No 395
>PF01418 HTH_6: Helix-turn-helix domain, rpiR family; InterPro: IPR000281 This domain contains a helix-turn-helix motif []. Every member of this family is N-terminal to a SIS domain IPR001347 from INTERPRO. Members of this family are probably regulators of genes involved in phosphosugar metobolism.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 2O3F_B 3IWF_B.
Probab=57.80 E-value=14 Score=25.27 Aligned_cols=31 Identities=19% Similarity=0.180 Sum_probs=23.2
Q ss_pred CCCHHHHHhhCCCCCCCCcchHHHHHHHHhcCCcc
Q 044458 54 FMSPKQIASQLPTKNSDAHILLDRILRLLASYSVL 88 (241)
Q Consensus 54 ~~t~~eLA~~~g~~~~~~~~~l~rlLr~L~~~g~l 88 (241)
..|+.|||+.+++ ++..+.|+.+.|--.|+-
T Consensus 34 ~~si~elA~~~~v----S~sti~Rf~kkLG~~gf~ 64 (77)
T PF01418_consen 34 FMSISELAEKAGV----SPSTIVRFCKKLGFSGFK 64 (77)
T ss_dssp T--HHHHHHHCTS-----HHHHHHHHHHCTTTCHH
T ss_pred HccHHHHHHHcCC----CHHHHHHHHHHhCCCCHH
Confidence 5899999999999 998888888877666553
No 396
>PRK11414 colanic acid/biofilm transcriptional regulator; Provisional
Probab=57.75 E-value=12 Score=30.86 Aligned_cols=36 Identities=28% Similarity=0.276 Sum_probs=32.7
Q ss_pred CCCCCHHHHHhhCCCCCCCCcchHHHHHHHHhcCCccccc
Q 044458 52 GAFMSPKQIASQLPTKNSDAHILLDRILRLLASYSVLNCS 91 (241)
Q Consensus 52 ~~~~t~~eLA~~~g~~~~~~~~~l~rlLr~L~~~g~l~~~ 91 (241)
|..++..+||+.+|+ +..-++.-|+.|...|+++..
T Consensus 32 G~~L~e~~La~~lgV----SRtpVREAL~~L~~eGLV~~~ 67 (221)
T PRK11414 32 GARLITKNLAEQLGM----SITPVREALLRLVSVNALSVA 67 (221)
T ss_pred CCccCHHHHHHHHCC----CchhHHHHHHHHHHCCCEEec
Confidence 367899999999999 888999999999999999864
No 397
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=57.71 E-value=7.8 Score=24.99 Aligned_cols=31 Identities=29% Similarity=0.373 Sum_probs=21.0
Q ss_pred hHHHHHhcCCCCCCCHHHHHhhCCCCCCCCcchHHHHHH
Q 044458 42 LLEVIAKAGPGAFMSPKQIASQLPTKNSDAHILLDRILR 80 (241)
Q Consensus 42 lfd~L~~~~~~~~~t~~eLA~~~g~~~~~~~~~l~rlLr 80 (241)
|-+.+.+ ..+|..+||+.+|+ ++..+.+++.
T Consensus 2 L~~~m~~----~~it~~~La~~~gi----s~~tl~~~~~ 32 (63)
T PF13443_consen 2 LKELMAE----RGITQKDLARKTGI----SRSTLSRILN 32 (63)
T ss_dssp HHHHHHH----TT--HHHHHHHHT------HHHHHHHHT
T ss_pred HHHHHHH----cCCCHHHHHHHHCc----CHHHHHHHHh
Confidence 4456666 46899999999999 8888877765
No 398
>PRK00135 scpB segregation and condensation protein B; Reviewed
Probab=57.55 E-value=13 Score=30.39 Aligned_cols=41 Identities=20% Similarity=0.226 Sum_probs=35.3
Q ss_pred cChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCcchHHHHHHHHhcCCcccc
Q 044458 40 LDLLEVIAKAGPGAFMSPKQIASQLPTKNSDAHILLDRILRLLASYSVLNC 90 (241)
Q Consensus 40 lglfd~L~~~~~~~~~t~~eLA~~~g~~~~~~~~~l~rlLr~L~~~g~l~~ 90 (241)
+.+..+|+-. +|+|..||++..|+ +. ..+++.|...|++.+
T Consensus 93 LEtLaiIay~---qPiTr~eI~~irGv----~~---~~ii~~L~~~gLI~e 133 (188)
T PRK00135 93 LEVLAIIAYK---QPITRIEIDEIRGV----NS---DGALQTLLAKGLIKE 133 (188)
T ss_pred HHHHHHHHHc---CCcCHHHHHHHHCC----CH---HHHHHHHHHCCCeEE
Confidence 4467788775 79999999999999 75 789999999999985
No 399
>PF00356 LacI: Bacterial regulatory proteins, lacI family; InterPro: IPR000843 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. One such family groups together a range of proteins, including ascG, ccpA, cytR, ebgR, fruR, galR, galS, lacI, malI, opnR, purF, rafR, rbtR and scrR [, ]. Within this family, the HTH motif is situated towards the N terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3KJX_C 1ZAY_A 1VPW_A 2PUA_A 1QQA_A 1PNR_A 1JFT_A 1QP4_A 2PUD_A 1JH9_A ....
Probab=57.25 E-value=6.4 Score=24.35 Aligned_cols=11 Identities=27% Similarity=0.247 Sum_probs=8.1
Q ss_pred CHHHHHhhCCC
Q 044458 56 SPKQIASQLPT 66 (241)
Q Consensus 56 t~~eLA~~~g~ 66 (241)
|+.|||+.+|+
T Consensus 1 Ti~dIA~~agv 11 (46)
T PF00356_consen 1 TIKDIAREAGV 11 (46)
T ss_dssp CHHHHHHHHTS
T ss_pred CHHHHHHHHCc
Confidence 56777777777
No 400
>PRK10402 DNA-binding transcriptional activator YeiL; Provisional
Probab=57.13 E-value=8.7 Score=31.78 Aligned_cols=34 Identities=21% Similarity=0.022 Sum_probs=31.4
Q ss_pred CCCHHHHHhhCCCCCCCCcchHHHHHHHHhcCCccccc
Q 044458 54 FMSPKQIASQLPTKNSDAHILLDRILRLLASYSVLNCS 91 (241)
Q Consensus 54 ~~t~~eLA~~~g~~~~~~~~~l~rlLr~L~~~g~l~~~ 91 (241)
+.|-++||+.+|+ ..+.+.|+|..|...|++...
T Consensus 169 ~~t~~~lA~~lG~----sretvsR~L~~L~~~G~I~~~ 202 (226)
T PRK10402 169 HEKHTQAAEYLGV----SYRHLLYVLAQFIQDGYLKKS 202 (226)
T ss_pred cchHHHHHHHHCC----cHHHHHHHHHHHHHCCCEEee
Confidence 4688999999999 999999999999999999863
No 401
>PF00196 GerE: Bacterial regulatory proteins, luxR family; InterPro: IPR000792 This domain is a DNA-binding, helix-turn-helix (HTH) domain of about 65 amino acids, present in transcription regulators of the LuxR/FixJ family of response regulators. The domain is named after Vibrio fischeri luxR, a transcriptional activator for quorum-sensing control of luminescence. LuxR-type HTH domain proteins occur in a variety of organisms. The DNA-binding HTH domain is usually located in the C-terminal region; the N-terminal region often containing an autoinducer-binding domain or a response regulatory domain. Most luxR-type regulators act as transcription activators, but some can be repressors or have a dual role for different sites. LuxR-type HTH regulators control a wide variety of activities in various biological processes. The luxR-type, DNA-binding HTH domain forms a four-helical bundle structure. The HTH motif comprises the second and third helices, known as the scaffold and recognition helix, respectively. The HTH binds DNA in the major groove, where the N-terminal part of the recognition helix makes most of the DNA contacts. The fourth helix is involved in dimerisation of gerE and traR. Signalling events by one of the four activation mechanisms described below lead to multimerisation of the regulator. The regulators bind DNA as multimers [, , ]. LuxR-type HTH proteins can be activated by one of four different mechanisms: 1) Regulators which belong to a two-component sensory transduction system where the protein is activated by its phosphorylation, generally on an aspartate residue, by a transmembrane kinase [, ]. Some proteins that belong to this category are: Rhizobiaceae fixJ (global regulator inducing expression of nitrogen-fixation genes in microaerobiosis) Escherichia coli and Salmonella typhimurium uhpA (activates hexose phosphate transport gene uhpT) E. coli narL and narP (activate nitrate reductase operon) Enterobacteria rcsB (regulation of exopolysaccharide biosynthesis in enteric and plant pathogenesis) Bordetella pertussis bvgA (virulence factor) Bacillus subtilis coma (involved in expression of late-expressing competence genes) 2) Regulators which are activated, or in very rare cases repressed, when bound to N-acyl homoserine lactones, which are used as quorum sensing molecules in a variety of Gram-negative bacteria []: V. fischeri luxR (activates bioluminescence operon) Agrobacterium tumefaciens traR (regulation of Ti plasmid transfer) Erwinia carotovora carR (control of carbapenem antibiotics biosynthesis) E. carotovora expR (virulence factor for soft rot disease; activates plant tissue macerating enzyme genes) Pseudomonas aeruginosa lasR (activates elastase gene lasB) Erwinia chrysanthemi echR and Erwinia stewartii esaR Pseudomonas chlororaphis phzR (positive regulator of phenazine antibiotic production) Pseudomonas aeruginosa rhlR (activates rhlAB operon and lasB gene) 3) Autonomous effector domain regulators, without a regulatory domain, represented by gerE []. B. subtilis gerE (transcription activator and repressor for the regulation of spore formation) 4) Multiple ligand-binding regulators, exemplified by malT []. E. coli malT (activates maltose operon; MalT binds ATP and maltotriose); GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3SZT_A 3CLO_A 1H0M_A 1L3L_A 3C57_B 1ZLK_B 1ZLJ_H 3C3W_B 1RNL_A 1ZG1_A ....
Probab=57.10 E-value=8.3 Score=24.63 Aligned_cols=37 Identities=30% Similarity=0.354 Sum_probs=27.9
Q ss_pred HHhcChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCcchHHHHHHHH
Q 044458 37 AIELDLLEVIAKAGPGAFMSPKQIASQLPTKNSDAHILLDRILRLL 82 (241)
Q Consensus 37 a~~lglfd~L~~~~~~~~~t~~eLA~~~g~~~~~~~~~l~rlLr~L 82 (241)
-.|..|+..+.. +.+..|||+.+++ ++..++..++.+
T Consensus 6 ~~E~~vl~~l~~-----G~~~~eIA~~l~i----s~~tV~~~~~~i 42 (58)
T PF00196_consen 6 ERELEVLRLLAQ-----GMSNKEIAEELGI----SEKTVKSHRRRI 42 (58)
T ss_dssp HHHHHHHHHHHT-----TS-HHHHHHHHTS----HHHHHHHHHHHH
T ss_pred HHHHHHHHHHHh-----cCCcchhHHhcCc----chhhHHHHHHHH
Confidence 356778888876 7899999999999 888776555544
No 402
>COG1565 Uncharacterized conserved protein [Function unknown]
Probab=56.98 E-value=26 Score=31.67 Aligned_cols=59 Identities=15% Similarity=0.245 Sum_probs=37.7
Q ss_pred CchHHHHHHHHHHhcchhhHHHHHHhcCCCCCCCeEEEecCCchHHHHHHHHHC----C----CCcEEEccc
Q 044458 167 DLRLNKIFNNGMFSHSTITMKKFLENYKGFEGLQSVVDVGGGIGASLDMIISKY----P----SIKGINFDL 230 (241)
Q Consensus 167 ~~~~~~~f~~aM~~~~~~~~~~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~----P----~l~~~v~Dl 230 (241)
-|+..+.|.+..+. ++.+.|-+ +. -.....||.+|.|+|+++..+++.. | .++..+++.
T Consensus 51 Apels~lFGella~---~~~~~wq~-~g-~p~~~~lvEiGaG~G~l~~DiL~~l~~L~P~~~~~~~~~iiE~ 117 (370)
T COG1565 51 APELSQLFGELLAE---QFLQLWQE-LG-RPAPLKLVEIGAGRGTLASDILRTLRRLYPELYEALSYYIIEP 117 (370)
T ss_pred chhHHHHHHHHHHH---HHHHHHHH-hc-CCCCceEEEeCCCcChHHHHHHHHHHHhCHHHHhcceEEEEec
Confidence 47778888877633 22222322 22 3456789999999999998877654 4 345555554
No 403
>PRK10736 hypothetical protein; Provisional
Probab=56.98 E-value=13 Score=33.82 Aligned_cols=44 Identities=11% Similarity=0.003 Sum_probs=38.4
Q ss_pred cChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCcchHHHHHHHHhcCCccccc
Q 044458 40 LDLLEVIAKAGPGAFMSPKQIASQLPTKNSDAHILLDRILRLLASYSVLNCS 91 (241)
Q Consensus 40 lglfd~L~~~~~~~~~t~~eLA~~~g~~~~~~~~~l~rlLr~L~~~g~l~~~ 91 (241)
..|++.|.. .|.++++|+.++|+ +...+..+|-.|.-.|++.+.
T Consensus 311 ~~v~~~l~~----~~~~iD~L~~~~~l----~~~~v~~~L~~LEl~G~v~~~ 354 (374)
T PRK10736 311 PELLANVGD----EVTPVDVVAERAGQ----PVPEVVTQLLELELAGWIAAV 354 (374)
T ss_pred HHHHHhcCC----CCCCHHHHHHHHCc----CHHHHHHHHHHHHhCCcEEEc
Confidence 357777754 58999999999999 999999999999999999974
No 404
>COG1654 BirA Biotin operon repressor [Transcription]
Probab=56.94 E-value=13 Score=25.85 Aligned_cols=49 Identities=18% Similarity=0.168 Sum_probs=39.1
Q ss_pred CCCCHHHHHhhCCCCCCCCcchHHHHHHHHhcCCccccccccCCCCccccceecCccccc
Q 044458 53 AFMSPKQIASQLPTKNSDAHILLDRILRLLASYSVLNCSLHTLPDGGVERLYGLAPVCKF 112 (241)
Q Consensus 53 ~~~t~~eLA~~~g~~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~g~~~~~y~~t~~s~~ 112 (241)
.+.|=++||+++|+ ....+..-++.|...|+=.+.. . ...|.+.....+
T Consensus 18 ~~~SGe~La~~Lgi----SRtaVwK~Iq~Lr~~G~~I~s~---~----~kGY~L~~~~~l 66 (79)
T COG1654 18 NFVSGEKLAEELGI----SRTAVWKHIQQLREEGVDIESV---R----GKGYLLPQLPDL 66 (79)
T ss_pred CcccHHHHHHHHCc----cHHHHHHHHHHHHHhCCceEec---C----CCceeccCcccc
Confidence 58999999999999 9999999999999999876541 1 346777654443
No 405
>COG4901 Ribosomal protein S25 [Translation, ribosomal structure and biogenesis]
Probab=56.89 E-value=11 Score=27.53 Aligned_cols=50 Identities=22% Similarity=0.274 Sum_probs=38.9
Q ss_pred HhcChHHHHHhc-CCCCCCCHHHHHhhCCCCCCCCcchHHHHHHHHhcCCccccc
Q 044458 38 IELDLLEVIAKA-GPGAFMSPKQIASQLPTKNSDAHILLDRILRLLASYSVLNCS 91 (241)
Q Consensus 38 ~~lglfd~L~~~-~~~~~~t~~eLA~~~g~~~~~~~~~l~rlLr~L~~~g~l~~~ 91 (241)
++-.+++.+.+. +...-+|.-.||.+.|+ +-...+.+||.|...|++...
T Consensus 42 vdee~~~ki~KEV~~~r~VTpy~la~r~gI----~~SvAr~vLR~LeeeGvv~lv 92 (107)
T COG4901 42 VDEELLDKIRKEVPRERVVTPYVLASRYGI----NGSVARIVLRHLEEEGVVQLV 92 (107)
T ss_pred ccHHHHHHHHHhcccceeecHHHHHHHhcc----chHHHHHHHHHHHhCCceeee
Confidence 334466666542 22246999999999999 899999999999999998864
No 406
>PRK13917 plasmid segregation protein ParM; Provisional
Probab=56.84 E-value=38 Score=30.22 Aligned_cols=59 Identities=19% Similarity=0.205 Sum_probs=40.6
Q ss_pred HHHHHHhcchhhHHHHHHhcCCCCCCCeEEEecCCchHHHHHHHHHCCCCcEEEccchHHH
Q 044458 174 FNNGMFSHSTITMKKFLENYKGFEGLQSVVDVGGGIGASLDMIISKYPSIKGINFDLPHVI 234 (241)
Q Consensus 174 f~~aM~~~~~~~~~~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~DlP~vi 234 (241)
+.++...........+...+..+.+..+|+=+|||.-.+-..+.+.||++ .+.|-|+-.
T Consensus 267 ~~~~~~~~~~~i~~~i~~~~~~~~~~d~IiL~GGGA~ll~~~lk~~f~~~--~~~~~p~~A 325 (344)
T PRK13917 267 FYKEQDSVIDEVMSGFEIAVGNINSFDRVIVTGGGANIFFDSLSHWYSDV--EKADESQFA 325 (344)
T ss_pred HHHHHHHHHHHHHHHHHHHhcccCCCCEEEEECCcHHHHHHHHHHHcCCe--EEcCChHHH
Confidence 44444444444444454444336677899999999999888899999976 677777643
No 407
>KOG2165 consensus Anaphase-promoting complex (APC), subunit 2 [Cell cycle control, cell division, chromosome partitioning; Posttranslational modification, protein turnover, chaperones]
Probab=56.69 E-value=12 Score=36.37 Aligned_cols=48 Identities=13% Similarity=-0.020 Sum_probs=38.9
Q ss_pred CCCCHHHHHhhCCCCCCCCcchHHHHHHHHhcCCccccccccCCCCccccceecCc
Q 044458 53 AFMSPKQIASQLPTKNSDAHILLDRILRLLASYSVLNCSLHTLPDGGVERLYGLAP 108 (241)
Q Consensus 53 ~~~t~~eLA~~~g~~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~g~~~~~y~~t~ 108 (241)
..-|++|||+.+|+ +...++|.|......|++.+.. .-..++.|+.++
T Consensus 615 ~twt~eelse~l~i----p~~~lrrrL~fWi~~GvL~e~~----~~s~tgt~T~iE 662 (765)
T KOG2165|consen 615 NTWTLEELSESLGI----PVPALRRRLSFWIQKGVLREEP----IISDTGTLTVIE 662 (765)
T ss_pred ccccHHHHHHHhCC----CHHHHHHHHHHHHHcCeeecCC----CCCCCceeeecc
Confidence 47999999999999 9999999999999999999741 001146777776
No 408
>PF06971 Put_DNA-bind_N: Putative DNA-binding protein N-terminus; InterPro: IPR009718 This entry represents the C terminus (approximately 30 residues) of a number of Rex proteins. These are redox-sensing repressors that appear to be widespread among Gram-positive bacteria []. They modulate transcription in response to changes in cellular NADH/NAD(+) redox state. Rex is predicted to include a pyridine nucleotide-binding domain (Rossmann fold), and residues that might play key structural and nucleotide binding roles are highly conserved.; GO: 0045892 negative regulation of transcription, DNA-dependent, 0051775 response to redox state, 0005737 cytoplasm; PDB: 3IL2_B 3IKT_A 3IKV_B 1XCB_F 2DT5_A 2VT3_A 2VT2_A 3KEO_B 3KET_A 3KEQ_A ....
Probab=56.58 E-value=5.3 Score=25.25 Aligned_cols=33 Identities=21% Similarity=0.312 Sum_probs=22.4
Q ss_pred cChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCcchHHH
Q 044458 40 LDLLEVIAKAGPGAFMSPKQIASQLPTKNSDAHILLDR 77 (241)
Q Consensus 40 lglfd~L~~~~~~~~~t~~eLA~~~g~~~~~~~~~l~r 77 (241)
+.+++.|...|. .-+|..+||+.+|+ ++.-+++
T Consensus 15 ~r~L~~l~~~G~-~~vSS~~La~~~gi----~~~qVRK 47 (50)
T PF06971_consen 15 LRYLEQLKEEGV-ERVSSQELAEALGI----TPAQVRK 47 (50)
T ss_dssp HHHHHHHHHTT--SEE-HHHHHHHHTS-----HHHHHH
T ss_pred HHHHHHHHHcCC-eeECHHHHHHHHCC----CHHHhcc
Confidence 345566666543 46999999999999 8877765
No 409
>COG1802 GntR Transcriptional regulators [Transcription]
Probab=56.54 E-value=13 Score=30.78 Aligned_cols=36 Identities=19% Similarity=0.308 Sum_probs=33.6
Q ss_pred CCCCCHHHHHhhCCCCCCCCcchHHHHHHHHhcCCccccc
Q 044458 52 GAFMSPKQIASQLPTKNSDAHILLDRILRLLASYSVLNCS 91 (241)
Q Consensus 52 ~~~~t~~eLA~~~g~~~~~~~~~l~rlLr~L~~~g~l~~~ 91 (241)
|..++..+||+.+|+ +..-++.-|..|...|++...
T Consensus 37 G~~l~e~~La~~~gv----SrtPVReAL~rL~~eGlv~~~ 72 (230)
T COG1802 37 GERLSEEELAEELGV----SRTPVREALRRLEAEGLVEIE 72 (230)
T ss_pred CCCccHHHHHHHhCC----CCccHHHHHHHHHHCCCeEec
Confidence 478999999999999 888999999999999999974
No 410
>PF11312 DUF3115: Protein of unknown function (DUF3115); InterPro: IPR021463 This eukaryotic family of proteins has no known function.
Probab=56.27 E-value=16 Score=32.33 Aligned_cols=22 Identities=32% Similarity=0.570 Sum_probs=18.8
Q ss_pred CCeEEEecCCchHHHHHHHHHC
Q 044458 199 LQSVVDVGGGIGASLDMIISKY 220 (241)
Q Consensus 199 ~~~vvDVGGG~G~~~~~l~~~~ 220 (241)
..+||-||||.|.=..+++..+
T Consensus 87 ~~~VlCIGGGAGAElVAlAa~~ 108 (315)
T PF11312_consen 87 SLRVLCIGGGAGAELVALAAAF 108 (315)
T ss_pred CceEEEECCChHHHHHHHHHHH
Confidence 4799999999998888777766
No 411
>PF02319 E2F_TDP: E2F/DP family winged-helix DNA-binding domain; InterPro: IPR003316 The mammalian transcription factor E2F plays an important role in regulating the expression of genes that are required for passage through the cell cycle. Multiple E2F family members have been identified that bind to DNA as heterodimers, interacting with proteins known as DP - the dimerisation partners [].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005667 transcription factor complex; PDB: 1CF7_B.
Probab=56.12 E-value=6.2 Score=26.72 Aligned_cols=37 Identities=22% Similarity=0.280 Sum_probs=31.5
Q ss_pred CCCCHHHHHhhC---CCCCCCCcchHHHHHHHHhcCCccccc
Q 044458 53 AFMSPKQIASQL---PTKNSDAHILLDRILRLLASYSVLNCS 91 (241)
Q Consensus 53 ~~~t~~eLA~~~---g~~~~~~~~~l~rlLr~L~~~g~l~~~ 91 (241)
+.+++.++|+.+ +... ..+++..++..|.++|++.+.
T Consensus 23 ~~i~l~~ia~~l~~~~~k~--~~RRlYDI~NVLealgli~K~ 62 (71)
T PF02319_consen 23 KSISLNEIADKLISENVKT--QRRRLYDIINVLEALGLIEKQ 62 (71)
T ss_dssp TEEEHHHHHHHCHHHCCHH--HCHHHHHHHHHHHHCTSEEEE
T ss_pred CcccHHHHHHHHccccccc--ccchhhHHHHHHHHhCceeec
Confidence 689999999999 6411 577899999999999999984
No 412
>TIGR01764 excise DNA binding domain, excisionase family. An excisionase, or Xis protein, is a small protein that binds and promotes excisive recombination; it is not enzymatically active. This model represents a number of putative excisionases and related proteins from temperate phage, plasmids, and transposons, as well as DNA binding domains of other proteins, such as a DNA modification methylase. This model identifies mostly small proteins and N-terminal regions of large proteins, but some proteins appear to have two copies. This domain appears similar, in both sequence and predicted secondary structure (PSIPRED) to the MerR family of transcriptional regulators (pfam00376).
Probab=56.08 E-value=11 Score=22.50 Aligned_cols=22 Identities=14% Similarity=0.220 Sum_probs=18.5
Q ss_pred CCHHHHHhhCCCCCCCCcchHHHHHH
Q 044458 55 MSPKQIASQLPTKNSDAHILLDRILR 80 (241)
Q Consensus 55 ~t~~eLA~~~g~~~~~~~~~l~rlLr 80 (241)
.|.+|+|+.+|+ +...+.++++
T Consensus 2 lt~~e~a~~lgi----s~~ti~~~~~ 23 (49)
T TIGR01764 2 LTVEEAAEYLGV----SKDTVYRLIH 23 (49)
T ss_pred CCHHHHHHHHCC----CHHHHHHHHH
Confidence 588999999999 8888777764
No 413
>PF04545 Sigma70_r4: Sigma-70, region 4; InterPro: IPR007630 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors is involved in binding to the -35 promoter element via a helix-turn-helix motif []. Due to the way Pfam works, the threshold has been set artificially high to prevent overlaps with other helix-turn-helix families. Therefore there are many false negatives.; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2P7V_B 3IYD_F 1TLH_B 1KU7_A 1RIO_H 3N97_A 1KU3_A 1RP3_C 1SC5_A 1NR3_A ....
Probab=56.03 E-value=12 Score=23.09 Aligned_cols=26 Identities=23% Similarity=0.280 Sum_probs=21.4
Q ss_pred CCCCHHHHHhhCCCCCCCCcchHHHHHHHH
Q 044458 53 AFMSPKQIASQLPTKNSDAHILLDRILRLL 82 (241)
Q Consensus 53 ~~~t~~eLA~~~g~~~~~~~~~l~rlLr~L 82 (241)
.+.|..|||+.+|+ +...++++.+..
T Consensus 19 ~~~t~~eIa~~lg~----s~~~V~~~~~~a 44 (50)
T PF04545_consen 19 EGLTLEEIAERLGI----SRSTVRRILKRA 44 (50)
T ss_dssp ST-SHHHHHHHHTS----CHHHHHHHHHHH
T ss_pred CCCCHHHHHHHHCC----cHHHHHHHHHHH
Confidence 47999999999999 898888877654
No 414
>TIGR03329 Phn_aa_oxid putative aminophosphonate oxidoreductase. This clade of sequences are members of the pfam01266 family of FAD-dependent oxidoreductases. Characterized proteins within this family include glycerol-3-phosphate dehydrogenase (1.1.99.5), sarcosine oxidase beta subunit (1.5.3.1) and a number of deaminating amino acid oxidases (1.4.-.-). These genes have been consistently observed in a genomic context including genes for the import and catabolism of 2-aminoethylphosphonate (AEP). If the substrate of this oxidoreductase is AEP itself, then it is probably acting in the manner of a deaminating oxidase, resulting in the same product (phosphonoacetaldehyde) as the transaminase PhnW (TIGR02326), but releasing ammonia instead of coupling to pyruvate:alanine. Alternatively, it is reasonable to suppose that the various ABC cassette transporters which are also associated with these loci allow the import of phosphonates closely related to AEP which may not be substrates for PhnW.
Probab=55.98 E-value=13 Score=34.31 Aligned_cols=33 Identities=27% Similarity=0.398 Sum_probs=27.3
Q ss_pred CeEEEecCC-chHHHH-HHHHHCCCCcEEEccchH
Q 044458 200 QSVVDVGGG-IGASLD-MIISKYPSIKGINFDLPH 232 (241)
Q Consensus 200 ~~vvDVGGG-~G~~~~-~l~~~~P~l~~~v~DlP~ 232 (241)
..|+=|||| .|..+. .|+++.|+++++|+|--.
T Consensus 25 ~DVvIIGgGi~Gls~A~~La~~~~G~~V~vlE~~~ 59 (460)
T TIGR03329 25 ADVCIVGGGFTGLWTAIMIKQQRPALDVLVLEADL 59 (460)
T ss_pred eCEEEECCCHHHHHHHHHHHHhCCCCeEEEEeCCc
Confidence 579999999 788776 577778999999999754
No 415
>PF01371 Trp_repressor: Trp repressor protein; InterPro: IPR000831 The Trp repressor (TrpR) binds to at least five operators in the Escherichia coli genome, repressing gene expression. The operators at which it binds vary considerably in DNA sequence and location within the promoter; when bound to the Trp operon it recognises the sequence 5'-ACTAGT-3' and acts to prevent the initiation of transcription. The TrpR controls the trpEDCBA (trpO) operon and the genes for trpR, aroH, mtr and aroL, which are involved in the biosynthesis and uptake of the amino acid tryptophan []. The repressor binds to the operators only in the presence of L-tryptophan, thereby controlling the intracellular level of its effector; the complex also regulates Trp repressor biosynthesis by binding to its own regulatory region. TrpR acts as a dimer that is composed of identical 6-helical subunits, where four of the helices form the core of the protein and intertwine with the corresponding helices from the other subunit.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3FRW_H 3KOR_A 3SSW_N 1P6Z_N 1CO0_B 1JHG_A 1WRT_S 1WRS_R 1WRP_R 1RCS_B ....
Probab=55.79 E-value=15 Score=26.07 Aligned_cols=40 Identities=18% Similarity=0.161 Sum_probs=32.0
Q ss_pred HHHHhcChHH-HHHhcCCCCCCCHHHHHhhCCCCCCCCcchHHHHHHHHh
Q 044458 35 KSAIELDLLE-VIAKAGPGAFMSPKQIASQLPTKNSDAHILLDRILRLLA 83 (241)
Q Consensus 35 ~~a~~lglfd-~L~~~~~~~~~t~~eLA~~~g~~~~~~~~~l~rlLr~L~ 83 (241)
..+-++.|+. .|. ++.|..|||+.+|+ +---+.|+=|.|-
T Consensus 34 ~l~~R~~va~~lL~-----~g~syreIa~~tgv----S~aTItRvsr~Lk 74 (87)
T PF01371_consen 34 ALAQRWQVAKELLD-----EGKSYREIAEETGV----SIATITRVSRCLK 74 (87)
T ss_dssp HHHHHHHHHHHHHH-----TTSSHHHHHHHHTS----THHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHH-----CCCCHHHHHHHhCC----CHHHHHHHHHHHH
Confidence 3456788998 665 37999999999999 8888888877764
No 416
>PF04672 Methyltransf_19: S-adenosyl methyltransferase; InterPro: IPR006764 This is a family of uncharacterised proteins.; PDB: 3GIW_A 3GO4_A 2QE6_A.
Probab=55.75 E-value=26 Score=30.30 Aligned_cols=41 Identities=22% Similarity=0.451 Sum_probs=24.0
Q ss_pred CCCeEEEecCCchHH---HHHHHHHCCCCcEEEccc-hHHHhcCC
Q 044458 198 GLQSVVDVGGGIGAS---LDMIISKYPSIKGINFDL-PHVIQDAP 238 (241)
Q Consensus 198 ~~~~vvDVGGG~G~~---~~~l~~~~P~l~~~v~Dl-P~vi~~a~ 238 (241)
++..+||||+|.-+. =-...+..|+.+++=.|. |.|+..++
T Consensus 68 GIrQFLDlGsGlPT~~nvHevAq~~~P~aRVVYVD~DPvv~ah~r 112 (267)
T PF04672_consen 68 GIRQFLDLGSGLPTAGNVHEVAQRVAPDARVVYVDNDPVVLAHAR 112 (267)
T ss_dssp ---EEEEET--S--SS-HHHHHHHH-TT-EEEEEESSHHHHHCCH
T ss_pred CcceEEEcccCCCCCCCHhHHHHhhCCCceEEEECCCchHHHHHH
Confidence 789999999996532 223355799999998998 77777664
No 417
>TIGR00689 rpiB_lacA_lacB sugar-phosphate isomerases, RpiB/LacA/LacB family. Proteins of known function in this family act as sugar (pentose and/or hexose)-phosphate isomerases, including the LacA and LacB subunits of galactose-6-phosphate isomerases from Gram-positive bacteria and RpiB. RpiB is the second ribose phosphate isomerase of E. coli. It lacks homology to RpiA, its inducer is unknown (but is not ribose), and it can be replaced by the homologous galactose-6-phosphate isomerase of Streptococcus mutans, all of which suggests that the ribose phosphate isomerase activity of RpiB is a secondary function. On the other hand, there appear to be a significant number of species which contain rpiB, lack rpiA and seem to require rpi activity in order to copplete the pentose phosphate pathway.
Probab=55.39 E-value=7.6 Score=30.30 Aligned_cols=38 Identities=13% Similarity=0.044 Sum_probs=29.1
Q ss_pred EEEecCCchHHHHHHHHHCCCCcEEEccchHHHhcCCC
Q 044458 202 VVDVGGGIGASLDMIISKYPSIKGINFDLPHVIQDAPA 239 (241)
Q Consensus 202 vvDVGGG~G~~~~~l~~~~P~l~~~v~DlP~vi~~a~~ 239 (241)
.-=+.||+|.-..-.+.++|++++.+.--|.....+++
T Consensus 58 ~GIliCGtGiG~siaANK~~GIraa~~~d~~~A~~ar~ 95 (144)
T TIGR00689 58 LGILICGTGIGMSIAANKFKGIRAALCVDEYTAALARQ 95 (144)
T ss_pred eEEEEcCCcHHHHHHHhcCCCeEEEEECCHHHHHHHHH
Confidence 34467899998999999999999866666666666554
No 418
>COG4367 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=55.26 E-value=12 Score=26.58 Aligned_cols=26 Identities=27% Similarity=0.419 Sum_probs=23.0
Q ss_pred CCCCHHHHHhhCCCCCCCCcchHHHHHHHH
Q 044458 53 AFMSPKQIASQLPTKNSDAHILLDRILRLL 82 (241)
Q Consensus 53 ~~~t~~eLA~~~g~~~~~~~~~l~rlLr~L 82 (241)
.++|.++||+++++ .+..++++|.+=
T Consensus 22 ~~LS~~~iA~~Ln~----t~~~lekil~~t 47 (97)
T COG4367 22 CPLSDEEIATALNW----TEVKLEKILQVT 47 (97)
T ss_pred ccccHHHHHHHhCC----CHHHHHHHHHHh
Confidence 48999999999999 999999988653
No 419
>PF09821 AAA_assoc_C: C-terminal AAA-associated domain; InterPro: IPR018632 Members of this family are found in various prokaryotic ABC transporters, predominantly involved in nitrate, sulphonate and bicarbonate translocation.
Probab=55.21 E-value=10 Score=28.65 Aligned_cols=46 Identities=17% Similarity=0.129 Sum_probs=39.8
Q ss_pred HHHhhCCCCCCCCcchHHHHHHHHhcCCccccccccCCCCccccceecCccccccccCC
Q 044458 59 QIASQLPTKNSDAHILLDRILRLLASYSVLNCSLHTLPDGGVERLYGLAPVCKFLTKNE 117 (241)
Q Consensus 59 eLA~~~g~~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~g~~~~~y~~t~~s~~l~~~~ 117 (241)
+||+.+++ +-+-|-.+++.+.-+||++.. +|-..+|+.++-++...
T Consensus 2 ~La~~l~~----eiDdL~p~~eAaelLgf~~~~---------~Gdi~LT~~G~~f~~a~ 47 (120)
T PF09821_consen 2 QLADELHL----EIDDLLPIVEAAELLGFAEVE---------EGDIRLTPLGRRFAEAD 47 (120)
T ss_pred chHHHhCC----cHHHHHHHHHHHHHcCCeeec---------CCcEEeccchHHHHHCC
Confidence 58899999 999999999999999999973 57889999999766554
No 420
>TIGR03433 padR_acidobact transcriptional regulator, Acidobacterial, PadR-family. Members of this protein family are putative transcriptional regulators of the PadR family, as found in species of the Acidobacteria. This family of proteins has expanded greatly in this lineage, and where it regularly is found in the vicinity of a putative transporter protein
Probab=55.19 E-value=28 Score=25.05 Aligned_cols=67 Identities=12% Similarity=0.077 Sum_probs=41.3
Q ss_pred hHHHHHhcCCCCCCCHHHHHhhCCC----CCCCCcchHHHHHHHHhcCCccccccccCCCCccccceecCccccc
Q 044458 42 LLEVIAKAGPGAFMSPKQIASQLPT----KNSDAHILLDRILRLLASYSVLNCSLHTLPDGGVERLYGLAPVCKF 112 (241)
Q Consensus 42 lfd~L~~~~~~~~~t~~eLA~~~g~----~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~g~~~~~y~~t~~s~~ 112 (241)
|+-.|.. +|.+--||.+.+.- ..+.++..+.++|+.|...|++.....+...|-....|++|+.++.
T Consensus 9 iL~~L~~----~~~~GYei~~~l~~~~~~~~~i~~gtlY~~L~rLe~~GlI~~~~~~~~~~~~rk~y~iT~~Gr~ 79 (100)
T TIGR03433 9 ILKTLSL----GPLHGYGIAQRIQQISEDVLQVEEGSLYPALHRLERRGWIAAEWGESENNRRAKFYRLTAAGRK 79 (100)
T ss_pred HHHHHhc----CCCCHHHHHHHHHHHcCCccccCCCcHHHHHHHHHHCCCeEEEeeecCCCCCceEEEECHHHHH
Confidence 4445554 47777777776421 0112788899999999999999863111111111246888887763
No 421
>PRK10430 DNA-binding transcriptional activator DcuR; Provisional
Probab=55.13 E-value=13 Score=30.92 Aligned_cols=34 Identities=15% Similarity=0.176 Sum_probs=31.7
Q ss_pred CCCCHHHHHhhCCCCCCCCcchHHHHHHHHhcCCcccc
Q 044458 53 AFMSPKQIASQLPTKNSDAHILLDRILRLLASYSVLNC 90 (241)
Q Consensus 53 ~~~t~~eLA~~~g~~~~~~~~~l~rlLr~L~~~g~l~~ 90 (241)
.+.|.++||+++++ ++.-++..++.|+..|++.+
T Consensus 177 ~g~s~~eIA~~l~i----S~~Tv~~~~~~~~~~~~~~~ 210 (239)
T PRK10430 177 YEFSTDELANAVNI----SRVSCRKYLIWLVNCHILFT 210 (239)
T ss_pred CCcCHHHHHHHhCc----hHHHHHHHHHHHHhCCEEEE
Confidence 47899999999999 99999999999999999964
No 422
>TIGR00331 hrcA heat shock gene repressor HrcA. In Bacillus subtilis, hrcA is the first gene of the dnaK operon and so is itself a heat shock gene.
Probab=55.02 E-value=17 Score=32.45 Aligned_cols=41 Identities=12% Similarity=0.124 Sum_probs=35.8
Q ss_pred HHHHhcCCCCCCCHHHHHhh--CCCCCCCCcchHHHHHHHHhcCCccccc
Q 044458 44 EVIAKAGPGAFMSPKQIASQ--LPTKNSDAHILLDRILRLLASYSVLNCS 91 (241)
Q Consensus 44 d~L~~~~~~~~~t~~eLA~~--~g~~~~~~~~~l~rlLr~L~~~g~l~~~ 91 (241)
+++... +|+++.+|++. +++ ++.-+||-|..|...|++.+.
T Consensus 14 ~~l~~~---~pv~s~~l~~~~~~~v----S~aTiR~d~~~Le~~G~l~~~ 56 (337)
T TIGR00331 14 EYIKTG---QPVGSKTLLEKYNLGL----SSATIRNDMADLEDLGFIEKP 56 (337)
T ss_pred HHHhcC---CCcCHHHHHhhcCCCC----ChHHHHHHHHHHHHCCCccCC
Confidence 355543 79999999999 888 899999999999999999985
No 423
>PRK10225 DNA-binding transcriptional repressor UxuR; Provisional
Probab=54.91 E-value=14 Score=31.15 Aligned_cols=35 Identities=14% Similarity=0.245 Sum_probs=32.1
Q ss_pred CCC-CHHHHHhhCCCCCCCCcchHHHHHHHHhcCCccccc
Q 044458 53 AFM-SPKQIASQLPTKNSDAHILLDRILRLLASYSVLNCS 91 (241)
Q Consensus 53 ~~~-t~~eLA~~~g~~~~~~~~~l~rlLr~L~~~g~l~~~ 91 (241)
..+ |..+||+.+|+ +..-++.-|+.|.+.|+++..
T Consensus 31 ~~LpsE~eLa~~~gV----SRtpVREAL~~L~~eGlV~~~ 66 (257)
T PRK10225 31 ERLPPEREIAEMLDV----TRTVVREALIMLEIKGLVEVR 66 (257)
T ss_pred CcCcCHHHHHHHhCC----CHHHHHHHHHHHHHCCCEEEe
Confidence 567 68999999999 899999999999999999864
No 424
>TIGR01120 rpiB ribose 5-phosphate isomerase B. Involved in the non-oxidative branch of the pentose phospate pathway.
Probab=54.82 E-value=8 Score=30.16 Aligned_cols=39 Identities=15% Similarity=0.147 Sum_probs=29.5
Q ss_pred eEEEecCCchHHHHHHHHHCCCCcEEEccchHHHhcCCC
Q 044458 201 SVVDVGGGIGASLDMIISKYPSIKGINFDLPHVIQDAPA 239 (241)
Q Consensus 201 ~vvDVGGG~G~~~~~l~~~~P~l~~~v~DlP~vi~~a~~ 239 (241)
..-=+.||+|.-..-.+.++|++++.+.--+.....+++
T Consensus 58 ~~GIliCGtGiG~siaANK~~GIraa~~~d~~~A~~ar~ 96 (143)
T TIGR01120 58 DGGILICGTGIGMSIAANKFAGIRAALCSEPYMAQMSRL 96 (143)
T ss_pred ceEEEEcCCcHHHHHHHhcCCCeEEEEECCHHHHHHHHH
Confidence 334567899988899999999999866666666666554
No 425
>COG3645 Uncharacterized phage-encoded protein [Function unknown]
Probab=54.78 E-value=13 Score=28.51 Aligned_cols=41 Identities=17% Similarity=0.176 Sum_probs=32.3
Q ss_pred ChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCcchHHHHHHHHhcCCcccc
Q 044458 41 DLLEVIAKAGPGAFMSPKQIASQLPTKNSDAHILLDRILRLLASYSVLNC 90 (241)
Q Consensus 41 glfd~L~~~~~~~~~t~~eLA~~~g~~~~~~~~~l~rlLr~L~~~g~l~~ 90 (241)
..+|.+.++. |.+++.|+|+.+++ .++.+..||| ..|++..
T Consensus 36 ~f~D~v~~~~--gli~~re~AK~lki----ge~~l~~~L~---e~~~l~~ 76 (135)
T COG3645 36 EFADAVVEAS--GLILFRELAKLLKI----GENRLFAWLR---ENKYLIK 76 (135)
T ss_pred HHHHHHhcCc--cceeHHHHHHHHcc----CHHHHHHHHH---HCCEEEE
Confidence 4678888764 78999999999999 8887766665 5676664
No 426
>PRK09990 DNA-binding transcriptional regulator GlcC; Provisional
Probab=54.66 E-value=15 Score=30.90 Aligned_cols=36 Identities=17% Similarity=0.295 Sum_probs=32.8
Q ss_pred CCCC-CHHHHHhhCCCCCCCCcchHHHHHHHHhcCCccccc
Q 044458 52 GAFM-SPKQIASQLPTKNSDAHILLDRILRLLASYSVLNCS 91 (241)
Q Consensus 52 ~~~~-t~~eLA~~~g~~~~~~~~~l~rlLr~L~~~g~l~~~ 91 (241)
|..+ +-.+||+.+|+ +..-++.-|+.|...|+++..
T Consensus 28 G~~LPsE~eLa~~~gV----SRtpVREAL~~L~~eGlV~~~ 64 (251)
T PRK09990 28 GQALPSERRLCEKLGF----SRSALREGLTVLRGRGIIETA 64 (251)
T ss_pred CCcCcCHHHHHHHHCC----CHHHHHHHHHHHHHCCCEEEe
Confidence 3678 89999999999 899999999999999999874
No 427
>PRK04984 fatty acid metabolism regulator; Provisional
Probab=54.60 E-value=15 Score=30.52 Aligned_cols=35 Identities=14% Similarity=0.270 Sum_probs=32.1
Q ss_pred CCC-CHHHHHhhCCCCCCCCcchHHHHHHHHhcCCccccc
Q 044458 53 AFM-SPKQIASQLPTKNSDAHILLDRILRLLASYSVLNCS 91 (241)
Q Consensus 53 ~~~-t~~eLA~~~g~~~~~~~~~l~rlLr~L~~~g~l~~~ 91 (241)
..+ |-.+||+++|+ +..-++.-|+.|...|++...
T Consensus 29 ~~LPsE~eLae~~gV----SRt~VReAL~~L~~eGlv~~~ 64 (239)
T PRK04984 29 SILPAERELSELIGV----TRTTLREVLQRLARDGWLTIQ 64 (239)
T ss_pred CcCCCHHHHHHHHCC----CHHHHHHHHHHHHHCCCEEEe
Confidence 567 79999999999 899999999999999999974
No 428
>PF14338 Mrr_N: Mrr N-terminal domain
Probab=54.51 E-value=44 Score=23.52 Aligned_cols=62 Identities=11% Similarity=0.116 Sum_probs=38.5
Q ss_pred hHHHHHhcCCCCCCCHHHHHhhCCCCC--CCCcchHHHHHHHHhcCCccccccccCCCCccccceecCccccccc
Q 044458 42 LLEVIAKAGPGAFMSPKQIASQLPTKN--SDAHILLDRILRLLASYSVLNCSLHTLPDGGVERLYGLAPVCKFLT 114 (241)
Q Consensus 42 lfd~L~~~~~~~~~t~~eLA~~~g~~~--~~~~~~l~rlLr~L~~~g~l~~~~~~~~~g~~~~~y~~t~~s~~l~ 114 (241)
|.+.+.+. -.+|-+|....+.-+. +.=...+.=-+..|...|+++.. . -|.|++|+.++-++
T Consensus 25 i~~~v~~~---~~ls~e~~~~~~~sg~~~~~~~~ri~Wa~~~L~~aGli~~~----~----rG~~~iT~~G~~~l 88 (92)
T PF14338_consen 25 IYERVAER---FGLSDEERNERLPSGQGYSRFKNRIRWARSYLKKAGLIERP----K----RGIWRITEKGRKAL 88 (92)
T ss_pred HHHHHHHH---hCCCHHHHHHHcccCCcchhHHHhHHHHHHHHHHCCCccCC----C----CCceEECHhHHHHH
Confidence 56666553 3567777666543100 00122344456788999999874 2 68999999998444
No 429
>PF03428 RP-C: Replication protein C N-terminal domain; InterPro: IPR005090 Proteins in this group have homology with the RepC protein of Agrobacterium Ri and Ti plasmids []. They may be involved in plasmid replication and stabilisation functions.
Probab=54.23 E-value=12 Score=30.31 Aligned_cols=33 Identities=24% Similarity=0.180 Sum_probs=30.9
Q ss_pred CCHHHHHhhC-CCCCCCCcchHHHHHHHHhcCCccccc
Q 044458 55 MSPKQIASQL-PTKNSDAHILLDRILRLLASYSVLNCS 91 (241)
Q Consensus 55 ~t~~eLA~~~-g~~~~~~~~~l~rlLr~L~~~g~l~~~ 91 (241)
.|-.+|++.+ |+ ++..++|.++.|+..|++...
T Consensus 71 pSN~~La~r~~G~----s~~tlrR~l~~LveaGLI~rr 104 (177)
T PF03428_consen 71 PSNAQLAERLNGM----SERTLRRHLARLVEAGLIVRR 104 (177)
T ss_pred cCHHHHHHHHcCC----CHHHHHHHHHHHHHCCCeeec
Confidence 5779999999 99 999999999999999999875
No 430
>cd04762 HTH_MerR-trunc Helix-Turn-Helix DNA binding domain of truncated MerR-like proteins. Proteins in this family mostly have a truncated helix-turn-helix (HTH) MerR-like domain. They lack a portion of the C-terminal region, called Wing 2 and the long dimerization helix that is typically present in MerR-like proteins. These truncated domains are found in response regulator receiver (REC) domain proteins (i.e., CheY), cytosine-C5 specific DNA methylases, IS607 transposase-like proteins, and RacA, a bacterial protein that anchors chromosomes to cell poles.
Probab=54.04 E-value=12 Score=22.17 Aligned_cols=23 Identities=22% Similarity=0.250 Sum_probs=19.1
Q ss_pred CCHHHHHhhCCCCCCCCcchHHHHHHH
Q 044458 55 MSPKQIASQLPTKNSDAHILLDRILRL 81 (241)
Q Consensus 55 ~t~~eLA~~~g~~~~~~~~~l~rlLr~ 81 (241)
.|..|+|+.+|+ ++..+.++.+.
T Consensus 1 ~s~~e~a~~lgv----s~~tl~~~~~~ 23 (49)
T cd04762 1 LTTKEAAELLGV----SPSTLRRWVKE 23 (49)
T ss_pred CCHHHHHHHHCc----CHHHHHHHHHc
Confidence 378999999999 88888877764
No 431
>PRK10421 DNA-binding transcriptional repressor LldR; Provisional
Probab=53.97 E-value=16 Score=30.87 Aligned_cols=35 Identities=29% Similarity=0.225 Sum_probs=31.8
Q ss_pred CCC-CHHHHHhhCCCCCCCCcchHHHHHHHHhcCCccccc
Q 044458 53 AFM-SPKQIASQLPTKNSDAHILLDRILRLLASYSVLNCS 91 (241)
Q Consensus 53 ~~~-t~~eLA~~~g~~~~~~~~~l~rlLr~L~~~g~l~~~ 91 (241)
..+ +..|||+.+|+ +..-++.-|+.|...|+++..
T Consensus 24 ~~LpsE~eLae~~gV----SRtpVREAL~~Le~~GlV~~~ 59 (253)
T PRK10421 24 MKLPAERQLAMQLGV----SRNSLREALAKLVSEGVLLSR 59 (253)
T ss_pred CcCCCHHHHHHHhCC----CHHHHHHHHHHHHHCCCEEEe
Confidence 567 78999999999 899999999999999999864
No 432
>TIGR02812 fadR_gamma fatty acid metabolism transcriptional regulator FadR. Members of this family are FadR, a transcriptional regulator of fatty acid metabolism, including both biosynthesis and beta-oxidation. It is found exclusively in a subset of Gammaproteobacteria, with strictly one copy per genome. It has an N-terminal DNA-binding domain and a less well conserved C-terminal long chain acyl-CoA-binding domain. FadR from this family heterologously expressed in Escherichia coli show differences in regulatory response and fatty acid binding profiles. The family is nevertheless designated equivalog, as all member proteins have at least nominally the same function.
Probab=53.82 E-value=16 Score=30.31 Aligned_cols=36 Identities=17% Similarity=0.324 Sum_probs=32.7
Q ss_pred CCCC-CHHHHHhhCCCCCCCCcchHHHHHHHHhcCCccccc
Q 044458 52 GAFM-SPKQIASQLPTKNSDAHILLDRILRLLASYSVLNCS 91 (241)
Q Consensus 52 ~~~~-t~~eLA~~~g~~~~~~~~~l~rlLr~L~~~g~l~~~ 91 (241)
|..+ |..+||+.+|+ +..-+|.-|+.|...|+++..
T Consensus 27 G~~LpsE~~La~~lgV----SRtpVREAL~~Le~eGlV~~~ 63 (235)
T TIGR02812 27 GSILPAERELSELIGV----TRTTLREVLQRLARDGWLTIQ 63 (235)
T ss_pred CCcCcCHHHHHHHHCc----CHHHHHHHHHHHHHCCCEEEe
Confidence 3568 89999999999 899999999999999999864
No 433
>COG3398 Uncharacterized protein conserved in archaea [Function unknown]
Probab=53.67 E-value=29 Score=29.15 Aligned_cols=48 Identities=17% Similarity=0.152 Sum_probs=41.8
Q ss_pred HHhcChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCcchHHHHHHHHhcCCccccc
Q 044458 37 AIELDLLEVIAKAGPGAFMSPKQIASQLPTKNSDAHILLDRILRLLASYSVLNCS 91 (241)
Q Consensus 37 a~~lglfd~L~~~~~~~~~t~~eLA~~~g~~~~~~~~~l~rlLr~L~~~g~l~~~ 91 (241)
-.+.+++..+..+| +.++.|+++.+++ +...++-.||.|.+.++++-.
T Consensus 101 s~R~~Iy~~i~~nP---G~~lsEl~~nl~i----~R~TlRyhlriLe~~~li~a~ 148 (240)
T COG3398 101 SKRDGIYNYIKPNP---GFSLSELRANLYI----NRSTLRYHLRILESNPLIEAG 148 (240)
T ss_pred hhHHHHHHHhccCC---CccHHHHHHhcCC----ChHHHHHHHHHHHhCcchhhh
Confidence 34567888888764 7999999999999 899999999999999999865
No 434
>COG3682 Predicted transcriptional regulator [Transcription]
Probab=53.37 E-value=23 Score=26.83 Aligned_cols=62 Identities=19% Similarity=0.321 Sum_probs=45.4
Q ss_pred HHhcChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCcchHHHHHHHHhcCCccccccccCCCCccccceecCc
Q 044458 37 AIELDLLEVIAKAGPGAFMSPKQIASQLPTKNSDAHILLDRILRLLASYSVLNCSLHTLPDGGVERLYGLAP 108 (241)
Q Consensus 37 a~~lglfd~L~~~~~~~~~t~~eLA~~~g~~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~g~~~~~y~~t~ 108 (241)
+.|..|.++|=.. ||.|+.||-+.+.....+.+.-+.-||+-|+.-|++... ++ ++.|.-++
T Consensus 6 ~aE~eVM~ilW~~---~~~t~~eI~~~l~~~~ews~sTV~TLl~RL~KKg~l~~~----kd---gr~~~y~p 67 (123)
T COG3682 6 AAEWEVMEILWSR---GPATVREIIEELPADREWSYSTVKTLLNRLVKKGLLTRK----KD---GRAFRYSP 67 (123)
T ss_pred HHHHHHHHHHHHc---CCccHHHHHHHHhhcccccHHHHHHHHHHHHhccchhhh----hc---CCeeeeec
Confidence 3456667777554 699999998888763334677899999999999999886 34 35665554
No 435
>PF13814 Replic_Relax: Replication-relaxation
Probab=53.37 E-value=17 Score=29.08 Aligned_cols=59 Identities=22% Similarity=0.231 Sum_probs=43.7
Q ss_pred CCCCHHHHHhhCCCCCCCCcc---hHHHHHHHHhcCCcccccccc--CCCCccccceecCcccccccc
Q 044458 53 AFMSPKQIASQLPTKNSDAHI---LLDRILRLLASYSVLNCSLHT--LPDGGVERLYGLAPVCKFLTK 115 (241)
Q Consensus 53 ~~~t~~eLA~~~g~~~~~~~~---~l~rlLr~L~~~g~l~~~~~~--~~~g~~~~~y~~t~~s~~l~~ 115 (241)
+.+|.++|+..... +.. .+++.|+.|...|++...... ...|..+..|.+|+.+..++.
T Consensus 8 r~lt~~Qi~~l~~~----~~~~~~~~~rrL~~L~~~glv~~~~~~~~~~~g~~~~vy~Lt~~G~~~l~ 71 (191)
T PF13814_consen 8 RFLTTDQIARLLFP----SSKSERTARRRLKRLRELGLVDRFRRRVGARGGSQPYVYYLTPAGARLLA 71 (191)
T ss_pred cCcCHHHHHHHHcC----CCcchHHHHHHHHHHhhCCcEEeecccccccCCCcceEEEECHHHHHHHH
Confidence 58999999999998 554 799999999999999875210 001222568999999874443
No 436
>PRK00215 LexA repressor; Validated
Probab=53.22 E-value=23 Score=28.83 Aligned_cols=36 Identities=17% Similarity=0.134 Sum_probs=31.1
Q ss_pred CCCCHHHHHhhCCCCCCCCcchHHHHHHHHhcCCccccc
Q 044458 53 AFMSPKQIASQLPTKNSDAHILLDRILRLLASYSVLNCS 91 (241)
Q Consensus 53 ~~~t~~eLA~~~g~~~~~~~~~l~rlLr~L~~~g~l~~~ 91 (241)
.+.|..|||+++|++ +...+.|+|+.|...|++.+.
T Consensus 22 ~~~s~~ela~~~~~~---~~~tv~~~l~~L~~~g~i~~~ 57 (205)
T PRK00215 22 YPPSRREIADALGLR---SPSAVHEHLKALERKGFIRRD 57 (205)
T ss_pred CCCCHHHHHHHhCCC---ChHHHHHHHHHHHHCCCEEeC
Confidence 578999999999971 356799999999999999875
No 437
>KOG2793 consensus Putative N2,N2-dimethylguanosine tRNA methyltransferase [RNA processing and modification]
Probab=52.90 E-value=17 Score=31.11 Aligned_cols=40 Identities=23% Similarity=0.493 Sum_probs=30.8
Q ss_pred CC-CCCeEEEecCCchHHHHHHHHHCCCCcEEEccchHHHhc
Q 044458 196 FE-GLQSVVDVGGGIGASLDMIISKYPSIKGINFDLPHVIQD 236 (241)
Q Consensus 196 ~~-~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~DlP~vi~~ 236 (241)
|. +...||.+|+|.| +.-.++......+++.-|+|.+++.
T Consensus 83 ~~~~~~~vlELGsGtg-lvG~~aa~~~~~~v~ltD~~~~~~~ 123 (248)
T KOG2793|consen 83 FKTKYINVLELGSGTG-LVGILAALLLGAEVVLTDLPKVVEN 123 (248)
T ss_pred ccccceeEEEecCCcc-HHHHHHHHHhcceeccCCchhhHHH
Confidence 44 4678999999999 5555555667888899999888764
No 438
>COG2186 FadR Transcriptional regulators [Transcription]
Probab=52.84 E-value=17 Score=30.64 Aligned_cols=43 Identities=12% Similarity=0.261 Sum_probs=36.6
Q ss_pred CCCHHHHHhhCCCCCCCCcchHHHHHHHHhcCCccccccccCCCCccccceecC
Q 044458 54 FMSPKQIASQLPTKNSDAHILLDRILRLLASYSVLNCSLHTLPDGGVERLYGLA 107 (241)
Q Consensus 54 ~~t~~eLA~~~g~~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~g~~~~~y~~t 107 (241)
--+-.|||+.+|+ +...+|.-|+.|.+.|+++.. .| .|.|-.+
T Consensus 34 LP~EreLae~fgV----SR~~vREAl~~L~a~Glve~r-----~G--~Gt~V~~ 76 (241)
T COG2186 34 LPSERELAERFGV----SRTVVREALKRLEAKGLVEIR-----QG--SGTFVRP 76 (241)
T ss_pred CCCHHHHHHHHCC----CcHHHHHHHHHHHHCCCeeec-----CC--CceEecC
Confidence 3578999999999 899999999999999999974 34 6777764
No 439
>PRK13626 transcriptional regulator SgrR; Provisional
Probab=52.24 E-value=11 Score=35.97 Aligned_cols=35 Identities=11% Similarity=0.111 Sum_probs=33.3
Q ss_pred CCCCHHHHHhhCCCCCCCCcchHHHHHHHHhcCCccccc
Q 044458 53 AFMSPKQIASQLPTKNSDAHILLDRILRLLASYSVLNCS 91 (241)
Q Consensus 53 ~~~t~~eLA~~~g~~~~~~~~~l~rlLr~L~~~g~l~~~ 91 (241)
..+|++|||+.+.+ .+|.++.+|+.|...|.++..
T Consensus 22 ~~~~l~~la~~l~c----s~R~~~~~l~~~~~~gwl~w~ 56 (552)
T PRK13626 22 QETTLNELAELLNC----SRRHMRTLLNTMQQRGWLTWQ 56 (552)
T ss_pred ceeeHHHHHHHhcC----ChhHHHHHHHHHHHCCCeeee
Confidence 56899999999999 999999999999999999985
No 440
>PF07091 FmrO: Ribosomal RNA methyltransferase (FmrO); PDB: 3LCU_A 3LCV_B 3FRH_A 3FRI_A 3B89_A 3FZG_A.
Probab=52.11 E-value=44 Score=28.62 Aligned_cols=34 Identities=24% Similarity=0.356 Sum_probs=27.3
Q ss_pred CCCeEEEecCCchHHHHHHHHHCCCCcEEEccch
Q 044458 198 GLQSVVDVGGGIGASLDMIISKYPSIKGINFDLP 231 (241)
Q Consensus 198 ~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~DlP 231 (241)
...+|+|||||---++.-.....|+.+.+.+|+-
T Consensus 105 ~p~sVlDigCGlNPlalp~~~~~~~a~Y~a~DID 138 (251)
T PF07091_consen 105 PPDSVLDIGCGLNPLALPWMPEAPGATYIAYDID 138 (251)
T ss_dssp --SEEEEET-TTCHHHHHTTTSSTT-EEEEEESB
T ss_pred CCchhhhhhccCCceehhhcccCCCcEEEEEeCC
Confidence 4799999999999999888888899999999983
No 441
>PF11972 HTH_13: HTH DNA binding domain; InterPro: IPR021068 The proteins in this entry have not been characterised. They contain a C-terminal helix-turn-helix DNA binding domain.
Probab=52.05 E-value=24 Score=22.73 Aligned_cols=36 Identities=17% Similarity=0.283 Sum_probs=29.0
Q ss_pred hHHHHHhcCCCCCCCHHHHHhhCCCCCCCCcchHHHHHHHHhc
Q 044458 42 LLEVIAKAGPGAFMSPKQIASQLPTKNSDAHILLDRILRLLAS 84 (241)
Q Consensus 42 lfd~L~~~~~~~~~t~~eLA~~~g~~~~~~~~~l~rlLr~L~~ 84 (241)
+.|.+-..| -+|+..+++.+++ .+....++++-|..
T Consensus 4 Lidll~~~P---~Vsa~mva~~L~v----T~~~A~~li~eLg~ 39 (54)
T PF11972_consen 4 LIDLLLSRP---LVSAPMVAKELGV----TPQAAQRLIAELGL 39 (54)
T ss_pred HHHHHHhCc---cccHHHHHHHhCC----CHHHHHHHHHHhhc
Confidence 567776643 4899999999999 99999998866554
No 442
>PRK05571 ribose-5-phosphate isomerase B; Provisional
Probab=51.79 E-value=9.6 Score=29.89 Aligned_cols=37 Identities=14% Similarity=0.023 Sum_probs=28.6
Q ss_pred EecCCchHHHHHHHHHCCCCcEEEccchHHHhcCCCC
Q 044458 204 DVGGGIGASLDMIISKYPSIKGINFDLPHVIQDAPAY 240 (241)
Q Consensus 204 DVGGG~G~~~~~l~~~~P~l~~~v~DlP~vi~~a~~~ 240 (241)
=+-||+|.-..-.+.++|++++.+.--|.....+++|
T Consensus 63 IliCGtGiG~siaANK~~GIRAA~~~d~~~A~~ar~h 99 (148)
T PRK05571 63 ILICGTGIGMSIAANKVKGIRAALCHDTYSAHLAREH 99 (148)
T ss_pred EEEcCCcHHHHHHHhcCCCeEEEEECCHHHHHHHHHh
Confidence 3558888888889999999998666667777766543
No 443
>PF08281 Sigma70_r4_2: Sigma-70, region 4; InterPro: IPR013249 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 promoter element via a helix-turn-helix motif [].; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2LFW_A 1OR7_B 2H27_D 2O8X_B.
Probab=51.74 E-value=15 Score=22.91 Aligned_cols=25 Identities=32% Similarity=0.206 Sum_probs=17.7
Q ss_pred CCCCHHHHHhhCCCCCCCCcchHHHHHHH
Q 044458 53 AFMSPKQIASQLPTKNSDAHILLDRILRL 81 (241)
Q Consensus 53 ~~~t~~eLA~~~g~~~~~~~~~l~rlLr~ 81 (241)
...|.+|||+.+|+ ++..++..+.-
T Consensus 25 ~g~s~~eIa~~l~~----s~~~v~~~l~r 49 (54)
T PF08281_consen 25 QGMSYAEIAEILGI----SESTVKRRLRR 49 (54)
T ss_dssp S---HHHHHHHCTS-----HHHHHHHHHH
T ss_pred HCcCHHHHHHHHCc----CHHHHHHHHHH
Confidence 46899999999999 88888777654
No 444
>TIGR02531 yecD_yerC TrpR-related protein YerC/YecD. This model represents a protein subfamily found mostly in the Firmicutes (Bacillus and allies). This family is similar in sequence to the trp operon repressor TrpR described by TIGR01321, and represents a distinct clade within the broader family described by pfam01371. At least one species, Xylella fastidiosa, in the Proteobacteria, has a member of both this family and TIGR01321. Several genomes with a member of this family do not synthesize tryptophan, and members of this family should not be considered trp operon repressors without new evidence.
Probab=51.59 E-value=18 Score=25.65 Aligned_cols=34 Identities=15% Similarity=0.241 Sum_probs=27.7
Q ss_pred cChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCcchHHHHHHHH
Q 044458 40 LDLLEVIAKAGPGAFMSPKQIASQLPTKNSDAHILLDRILRLL 82 (241)
Q Consensus 40 lglfd~L~~~~~~~~~t~~eLA~~~g~~~~~~~~~l~rlLr~L 82 (241)
..|+..+.. +.|..+||+.+|+ +..-+.|+.|.|
T Consensus 41 ~~I~~ll~~-----G~S~~eIA~~LgI----SrsTIyRi~R~~ 74 (88)
T TIGR02531 41 LQVAKMLKQ-----GKTYSDIEAETGA----STATISRVKRCL 74 (88)
T ss_pred HHHHHHHHC-----CCCHHHHHHHHCc----CHHHHHHHHHhc
Confidence 566777764 5899999999999 999999977653
No 445
>PF13309 HTH_22: HTH domain
Probab=51.35 E-value=13 Score=24.62 Aligned_cols=38 Identities=16% Similarity=0.186 Sum_probs=28.9
Q ss_pred HHHHHHHHhcChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCcchHHHHHH
Q 044458 31 PMVLKSAIELDLLEVIAKAGPGAFMSPKQIASQLPTKNSDAHILLDRILR 80 (241)
Q Consensus 31 ~~~L~~a~~lglfd~L~~~~~~~~~t~~eLA~~~g~~~~~~~~~l~rlLr 80 (241)
-.++...-+.|+|+. .-+++.+|+.+|+ +..-+.+.||
T Consensus 27 ~~iV~~L~~~G~F~l--------Kgav~~vA~~L~i----S~~TVY~YLr 64 (64)
T PF13309_consen 27 KEIVRQLYEKGIFLL--------KGAVEYVAEKLGI----SRATVYRYLR 64 (64)
T ss_pred HHHHHHHHHCCCccc--------CcHHHHHHHHHCC----CHHHHHHHcC
Confidence 356677777788876 3589999999999 8877776653
No 446
>PF01035 DNA_binding_1: 6-O-methylguanine DNA methyltransferase, DNA binding domain; InterPro: IPR014048 Synonym(s): 6-O-methylguanine-DNA methyltransferase, O-6-methylguanine-DNA-alkyltransferase This entry represents the DNA binding region of 6-O-methylguanine-DNA methyltransferases. The repair of DNA containing O6-alkylated guanine is carried out by DNA-[protein]-cysteine S-methyltransferase (2.1.1.63 from EC). The major mutagenic and carcinogenic effect of methylating agents in DNA is the formation of O6-alkylguanine. The alkyl group at the O-6 position is transferred to a cysteine residue in the enzyme []. This is a suicide reaction since the enzyme is irreversibly inactivated and the methylated protein accumulates as a dead-end product. Most, but not all of the methyltransferases are also able to repair O-4-methylthymine. DNA-[protein]-cysteine S-methyltransferases are widely distributed and are found in various prokaryotic and eukaryotic sources [].; GO: 0003824 catalytic activity, 0006281 DNA repair; PDB: 1SFE_A 1T39_B 1T38_A 1EH7_A 1EH6_A 1YFH_C 1EH8_A 1QNT_A 2KIM_A 2KIF_A ....
Probab=51.23 E-value=14 Score=25.95 Aligned_cols=42 Identities=17% Similarity=0.129 Sum_probs=25.8
Q ss_pred HhcChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCcchHHHHHHH
Q 044458 38 IELDLLEVIAKAGPGAFMSPKQIASQLPTKNSDAHILLDRILRL 81 (241)
Q Consensus 38 ~~lglfd~L~~~~~~~~~t~~eLA~~~g~~~~~~~~~l~rlLr~ 81 (241)
+...|++.+..-+.|.-.|+.|||+.+|. |...+.+...|+.
T Consensus 3 f~~~V~~~v~~IP~G~v~TYg~iA~~~g~--p~~ar~Vg~al~~ 44 (85)
T PF01035_consen 3 FQRRVWEAVRQIPYGKVTTYGEIARLLGR--PKAARAVGSALAR 44 (85)
T ss_dssp HHHHHHHHHTTS-TT-BEEHHHHHHHTT---TTCHHHHHHHHHT
T ss_pred HHHHHHHHHHcCCCCceEeHHHHHHHHhh--cccHHHHHHHhcc
Confidence 34456777777665678999999999994 1144444444433
No 447
>PF12728 HTH_17: Helix-turn-helix domain
Probab=50.72 E-value=15 Score=22.67 Aligned_cols=22 Identities=23% Similarity=0.265 Sum_probs=18.9
Q ss_pred CCHHHHHhhCCCCCCCCcchHHHHHH
Q 044458 55 MSPKQIASQLPTKNSDAHILLDRILR 80 (241)
Q Consensus 55 ~t~~eLA~~~g~~~~~~~~~l~rlLr 80 (241)
.|.+|+|+.+|+ +...+.++++
T Consensus 2 lt~~e~a~~l~i----s~~tv~~~~~ 23 (51)
T PF12728_consen 2 LTVKEAAELLGI----SRSTVYRWIR 23 (51)
T ss_pred CCHHHHHHHHCc----CHHHHHHHHH
Confidence 588999999999 8888887775
No 448
>PF05158 RNA_pol_Rpc34: RNA polymerase Rpc34 subunit; InterPro: IPR007832 The family comprises a subunit specific to RNA Pol III, the tRNA specific polymerase. The C34 subunit of Saccharomyces cerevisiae RNA Pol III is part of a subcomplex of three subunits which have no counterpart in the other two nuclear RNA polymerases. This subunit interacts with TFIIIB70 and therefore participates in Pol III recruitment [].; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2DK8_A 2DK5_A 2YU3_A.
Probab=50.68 E-value=15 Score=32.69 Aligned_cols=45 Identities=22% Similarity=0.300 Sum_probs=37.9
Q ss_pred hHHHHHhcCCCCCCCHHHHHhhCCCCCCCCcchHHHHHHHHhcCCccccc
Q 044458 42 LLEVIAKAGPGAFMSPKQIASQLPTKNSDAHILLDRILRLLASYSVLNCS 91 (241)
Q Consensus 42 lfd~L~~~~~~~~~t~~eLA~~~g~~~~~~~~~l~rlLr~L~~~g~l~~~ 91 (241)
|+++|..+|. .++-..+|..++++ +...+.+.|+.|...+++...
T Consensus 89 vy~~I~~ag~-~GIw~~~i~~~t~l----~~~~~~k~lk~Le~k~lIK~v 133 (327)
T PF05158_consen 89 VYQLIEEAGN-KGIWTKDIKKKTNL----HQTQLTKILKSLESKKLIKSV 133 (327)
T ss_dssp HHHHHHHHTT-T-EEHHHHHHHCT------HHHHHHHHHHHHHTTSEEEE
T ss_pred HHHHHHHhCC-CCCcHHHHHHHcCC----CHHHHHHHHHHHHhCCCEEEe
Confidence 7788888774 78999999999999 999999999999999999874
No 449
>KOG2918 consensus Carboxymethyl transferase [Posttranslational modification, protein turnover, chaperones]
Probab=49.87 E-value=17 Score=32.15 Aligned_cols=41 Identities=24% Similarity=0.456 Sum_probs=37.5
Q ss_pred CCCCCeEEEecCCchHHHHHHHHHC--CCCcEEEccchHHHhc
Q 044458 196 FEGLQSVVDVGGGIGASLDMIISKY--PSIKGINFDLPHVIQD 236 (241)
Q Consensus 196 ~~~~~~vvDVGGG~G~~~~~l~~~~--P~l~~~v~DlP~vi~~ 236 (241)
+.+...||-+|||.=.+...++..+ +.++++=+|.|++++.
T Consensus 85 ~~~~~qivnLGcG~D~l~frL~s~~~~~~~~fievDfp~~~~r 127 (335)
T KOG2918|consen 85 TDGKKQIVNLGAGFDTLYFRLLSSGELDRVKFIEVDFPEVVER 127 (335)
T ss_pred cCCceEEEEcCCCccchhhhhhccCCCCcceEEEecCcHHHHH
Confidence 5677999999999999999999999 8899999999999874
No 450
>PF10771 DUF2582: Protein of unknown function (DUF2582); InterPro: IPR019707 This entry represents conserved proteins found in bacteria and archaea. The function is not known. ; PDB: 2L02_B 2L01_A.
Probab=49.77 E-value=20 Score=23.93 Aligned_cols=38 Identities=8% Similarity=0.020 Sum_probs=26.9
Q ss_pred hHHHHHhcCCCCCCCHHHHHhhCCCCCCCCcchHHHHHHHHhcCC
Q 044458 42 LLEVIAKAGPGAFMSPKQIASQLPTKNSDAHILLDRILRLLASYS 86 (241)
Q Consensus 42 lfd~L~~~~~~~~~t~~eLA~~~g~~~~~~~~~l~rlLr~L~~~g 86 (241)
|+++|.+. ++.|+.+|++.+++ +..-+..=+--|...+
T Consensus 13 Vw~~L~~~---~~~s~~el~k~~~l----~~~~~~~AiGWLarE~ 50 (65)
T PF10771_consen 13 VWQLLNEN---GEWSVSELKKATGL----SDKEVYLAIGWLAREN 50 (65)
T ss_dssp HHHHHCCS---SSEEHHHHHHHCT-----SCHHHHHHHHHHHCTT
T ss_pred HHHHHhhC---CCcCHHHHHHHhCc----CHHHHHHHHHHHhccC
Confidence 78888874 68999999999999 6665554444444444
No 451
>TIGR02404 trehalos_R_Bsub trehalose operon repressor, B. subtilis-type. This family consists of repressors of the GntR family typically associated with trehalose utilization operons. Trehalose is imported as trehalose-6-phosphate and then hydrolyzed by alpha,alpha-phosphotrehalase to glucose and glucose-6-P. This family includes repressors mostly from Gram-positive lineages and does not include the TreR from E. coli.
Probab=49.71 E-value=16 Score=30.29 Aligned_cols=42 Identities=17% Similarity=0.172 Sum_probs=36.3
Q ss_pred CCHHHHHhhCCCCCCCCcchHHHHHHHHhcCCccccccccCCCCccccceecC
Q 044458 55 MSPKQIASQLPTKNSDAHILLDRILRLLASYSVLNCSLHTLPDGGVERLYGLA 107 (241)
Q Consensus 55 ~t~~eLA~~~g~~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~g~~~~~y~~t 107 (241)
-|-.|||+..|+ +..-+++-|+.|...|++... .| .|.|-..
T Consensus 25 PsE~eLa~~~gV----SR~TVR~Al~~L~~eGli~r~-----~G--~GTfV~~ 66 (233)
T TIGR02404 25 PSEHELMDQYGA----SRETVRKALNLLTEAGYIQKI-----QG--KGSIVLN 66 (233)
T ss_pred cCHHHHHHHHCC----CHHHHHHHHHHHHHCCCEEEe-----CC--ceEEEec
Confidence 489999999999 899999999999999999985 24 6788643
No 452
>TIGR03739 PRTRC_D PRTRC system protein D. A novel genetic system characterized by six major proteins, included a ParB homolog and a ThiF homolog, is designated PRTRC, or ParB-Related,ThiF-Related Cassette. It is often found on plasmids. This protein family is designated PRTRC system protein D. The gray zone, between trusted and noise, includes proteins found in the same genomes as other proteins of the PRTRC systems, but not in the same contiguous gene region.
Probab=49.38 E-value=65 Score=28.26 Aligned_cols=46 Identities=22% Similarity=0.309 Sum_probs=34.3
Q ss_pred HHHHhcCCCCCCCeEEEecCCchHHHHHHHHHCCCCcEEEccchHH
Q 044458 188 KFLENYKGFEGLQSVVDVGGGIGASLDMIISKYPSIKGINFDLPHV 233 (241)
Q Consensus 188 ~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~DlP~v 233 (241)
.+...+....+..+|+=+|||.-.+...+.+.||+.+..+.|-|+-
T Consensus 263 ~i~~~~~~~~~~~~Iil~GGGa~ll~~~l~~~f~~~~i~~~~dp~~ 308 (320)
T TIGR03739 263 TMMTWIGAPESIQNIVLVGGGAFLFKKAVKAAFPKHRIVEVDEPMF 308 (320)
T ss_pred HHHHhcccCCcccEEEEeCCcHHHHHHHHHHHCCCCeeEecCCcHH
Confidence 3444432133577899999999999888999999988777777763
No 453
>KOG4058 consensus Uncharacterized conserved protein [Function unknown]
Probab=49.37 E-value=15 Score=29.08 Aligned_cols=47 Identities=17% Similarity=0.204 Sum_probs=31.5
Q ss_pred HHHHHhcCCCCCCCeEEEecCCchHHHHHHHHHCCCCcEEEccc-hHHHh
Q 044458 187 KKFLENYKGFEGLQSVVDVGGGIGASLDMIISKYPSIKGINFDL-PHVIQ 235 (241)
Q Consensus 187 ~~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-P~vi~ 235 (241)
++++.... -....++||+|.|.|-...+.++.- -.+.+..+| |..+.
T Consensus 62 ~nVLSll~-~n~~GklvDlGSGDGRiVlaaar~g-~~~a~GvELNpwLVa 109 (199)
T KOG4058|consen 62 ENVLSLLR-GNPKGKLVDLGSGDGRIVLAAARCG-LRPAVGVELNPWLVA 109 (199)
T ss_pred HHHHHHcc-CCCCCcEEeccCCCceeehhhhhhC-CCcCCceeccHHHHH
Confidence 34555444 3445899999999999887777654 345677777 44443
No 454
>PRK00082 hrcA heat-inducible transcription repressor; Provisional
Probab=49.29 E-value=28 Score=31.10 Aligned_cols=35 Identities=11% Similarity=0.141 Sum_probs=32.6
Q ss_pred CCCCHHHHHhh--CCCCCCCCcchHHHHHHHHhcCCccccc
Q 044458 53 AFMSPKQIASQ--LPTKNSDAHILLDRILRLLASYSVLNCS 91 (241)
Q Consensus 53 ~~~t~~eLA~~--~g~~~~~~~~~l~rlLr~L~~~g~l~~~ 91 (241)
+|++.++||+. +++ ++.-+|+-|..|...|++.+.
T Consensus 24 ~pv~s~~l~~~~~l~~----S~aTIR~dm~~Le~~G~l~~~ 60 (339)
T PRK00082 24 EPVGSKTLSKRYGLGV----SSATIRNDMADLEELGLLEKP 60 (339)
T ss_pred CCcCHHHHHHHhCCCC----ChHHHHHHHHHHHhCCCcCCC
Confidence 79999999977 888 899999999999999999975
No 455
>PRK13558 bacterio-opsin activator; Provisional
Probab=49.26 E-value=17 Score=35.11 Aligned_cols=45 Identities=13% Similarity=0.076 Sum_probs=36.2
Q ss_pred hHHHHHHHHHHhcChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCcchHHHHHHHH
Q 044458 28 SVLPMVLKSAIELDLLEVIAKAGPGAFMSPKQIASQLPTKNSDAHILLDRILRLL 82 (241)
Q Consensus 28 ~~~~~~L~~a~~lglfd~L~~~~~~~~~t~~eLA~~~g~~~~~~~~~l~rlLr~L 82 (241)
.-.-.+|.+|++.|.|+.= ...|.+|||+.+|+ ....+...||..
T Consensus 610 ~~q~e~l~~a~~~gyf~~p------r~~~~~e~a~~l~i----s~~t~~~~lr~a 654 (665)
T PRK13558 610 DRQLTALQKAYVSGYFEWP------RRVEGEELAESMGI----SRSTFHQHLRAA 654 (665)
T ss_pred HHHHHHHHHHHHcCCCCCC------ccCCHHHHHHHhCC----CHHHHHHHHHHH
Confidence 3456799999999999972 36899999999999 777666666653
No 456
>TIGR02325 C_P_lyase_phnF phosphonates metabolism transcriptional regulator PhnF. All members of the seed alignment for this family are predicted helix-turn-helix transcriptional regulatory proteins of the broader gntR and are found associated with genes for the import and degradation of phosphonates and/or related compounds (e.g. phosphonites) with a direct C-P bond.
Probab=49.25 E-value=17 Score=30.22 Aligned_cols=43 Identities=16% Similarity=0.214 Sum_probs=36.6
Q ss_pred CCHHHHHhhCCCCCCCCcchHHHHHHHHhcCCccccccccCCCCccccceecCc
Q 044458 55 MSPKQIASQLPTKNSDAHILLDRILRLLASYSVLNCSLHTLPDGGVERLYGLAP 108 (241)
Q Consensus 55 ~t~~eLA~~~g~~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~g~~~~~y~~t~ 108 (241)
-|-.|||+..|+ +..-+++-|+.|...|++... .| .|.|-...
T Consensus 33 PsE~eLa~~~~V----SR~TvR~Al~~L~~eGli~r~-----~G--~GtfV~~~ 75 (238)
T TIGR02325 33 PAEMQLAERFGV----NRHTVRRAIAALVERGLLRAE-----QG--RGTFVAAR 75 (238)
T ss_pred cCHHHHHHHHCC----CHHHHHHHHHHHHHCCCEEEe-----cC--CEEEECCC
Confidence 388999999999 899999999999999999985 24 67786543
No 457
>PRK10681 DNA-binding transcriptional repressor DeoR; Provisional
Probab=48.94 E-value=23 Score=30.07 Aligned_cols=41 Identities=17% Similarity=0.161 Sum_probs=35.2
Q ss_pred hcChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCcchHHHHHHHHhcCC
Q 044458 39 ELDLLEVIAKAGPGAFMSPKQIASQLPTKNSDAHILLDRILRLLASYS 86 (241)
Q Consensus 39 ~lglfd~L~~~~~~~~~t~~eLA~~~g~~~~~~~~~l~rlLr~L~~~g 86 (241)
+-.|.+.|... +.+++.|||+.+++ ++.-+||=|+.|...+
T Consensus 9 ~~~I~~~l~~~---~~v~v~eLa~~~~V----S~~TIRRDL~~Le~~~ 49 (252)
T PRK10681 9 IGQLLQALKRS---DKLHLKDAAALLGV----SEMTIRRDLNAHSAPV 49 (252)
T ss_pred HHHHHHHHHHc---CCCcHHHHHHHhCC----CHHHHHHHHHHhhcCe
Confidence 34578888875 68999999999999 9999999999998654
No 458
>PRK00080 ruvB Holliday junction DNA helicase RuvB; Reviewed
Probab=48.75 E-value=17 Score=32.03 Aligned_cols=35 Identities=9% Similarity=0.140 Sum_probs=32.7
Q ss_pred CCCCHHHHHhhCCCCCCCCcchHHHHHH-HHhcCCccccc
Q 044458 53 AFMSPKQIASQLPTKNSDAHILLDRILR-LLASYSVLNCS 91 (241)
Q Consensus 53 ~~~t~~eLA~~~g~~~~~~~~~l~rlLr-~L~~~g~l~~~ 91 (241)
++.++++||+.+|. +...+..+++ .|...|++...
T Consensus 275 ~~~~~~~~a~~lg~----~~~~~~~~~e~~Li~~~li~~~ 310 (328)
T PRK00080 275 GPVGLDTLAAALGE----ERDTIEDVYEPYLIQQGFIQRT 310 (328)
T ss_pred CceeHHHHHHHHCC----CcchHHHHhhHHHHHcCCcccC
Confidence 78999999999999 9999999999 99999999863
No 459
>PF04492 Phage_rep_O: Bacteriophage replication protein O ; InterPro: IPR006497 This entry is represented by the N-terminal domain of Bacteriophage lambda, GpO. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.; GO: 0006260 DNA replication
Probab=48.73 E-value=17 Score=26.48 Aligned_cols=34 Identities=21% Similarity=0.090 Sum_probs=31.8
Q ss_pred CCCCHHHHHhhCCCCCCCCcchHHHHHHHHhcCCcccc
Q 044458 53 AFMSPKQIASQLPTKNSDAHILLDRILRLLASYSVLNC 90 (241)
Q Consensus 53 ~~~t~~eLA~~~g~~~~~~~~~l~rlLr~L~~~g~l~~ 90 (241)
..+|..++++.+|+ ++..+.+.+..|..++++..
T Consensus 53 d~Is~sq~~e~tg~----~~~~V~~al~~Li~~~vI~~ 86 (100)
T PF04492_consen 53 DRISNSQIAEMTGL----SRDHVSKALNELIRRGVIIR 86 (100)
T ss_pred ceeeHHHHHHHHCc----CHHHHHHHHHHHHHCCCEEe
Confidence 36899999999999 99999999999999999976
No 460
>PRK03837 transcriptional regulator NanR; Provisional
Probab=48.57 E-value=20 Score=29.78 Aligned_cols=35 Identities=11% Similarity=0.162 Sum_probs=32.3
Q ss_pred CCC-CHHHHHhhCCCCCCCCcchHHHHHHHHhcCCccccc
Q 044458 53 AFM-SPKQIASQLPTKNSDAHILLDRILRLLASYSVLNCS 91 (241)
Q Consensus 53 ~~~-t~~eLA~~~g~~~~~~~~~l~rlLr~L~~~g~l~~~ 91 (241)
..+ +..+||+.+|+ +..-++.-|+.|...|+++..
T Consensus 35 ~~Lp~E~~Lae~~gV----SRt~VREAL~~L~~eGlv~~~ 70 (241)
T PRK03837 35 DQLPSERELMAFFGV----GRPAVREALQALKRKGLVQIS 70 (241)
T ss_pred CCCCCHHHHHHHhCC----CHHHHHHHHHHHHHCCCEEEe
Confidence 567 89999999999 899999999999999999874
No 461
>PRK15201 fimbriae regulatory protein FimW; Provisional
Probab=48.25 E-value=22 Score=28.96 Aligned_cols=35 Identities=23% Similarity=0.155 Sum_probs=27.9
Q ss_pred HHHhcChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCcchHHHHH
Q 044458 36 SAIELDLLEVIAKAGPGAFMSPKQIASQLPTKNSDAHILLDRIL 79 (241)
Q Consensus 36 ~a~~lglfd~L~~~~~~~~~t~~eLA~~~g~~~~~~~~~l~rlL 79 (241)
+--|..|+..+++ +.|..|||+.+++ +++.++..+
T Consensus 135 SpRErEVLrLLAq-----GkTnKEIAe~L~I----S~rTVkth~ 169 (198)
T PRK15201 135 SVTERHLLKLIAS-----GYHLSETAALLSL----SEEQTKSLR 169 (198)
T ss_pred CHHHHHHHHHHHC-----CCCHHHHHHHhCC----CHHHHHHHH
Confidence 4467789999986 7999999999999 777665443
No 462
>cd06171 Sigma70_r4 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or plastid core RNA polymerase to specific promoter elements located upstream of transcription initiation points. The SR4 of Ec sigma70 and other essential primary SFs contact promoter sequences located 35 base-pairs upstream of the initiation point, recognizing a 6-base-pair -35 consensus TTGACA. Sigma70 related SFs also include SFs which are dispensable for bacterial cell growth for example Ec sigmaS, SFs which activate regulons in response to a specific signal for example heat-shock Ec sigmaH, and a group of SFs which includes the extracytoplasmic function (ECF) SFs and is typified by Ec sigmaE which contains SR2 and -4 only. ECF SFs direct the transcription of genes that regulate various responses including periplas
Probab=48.21 E-value=24 Score=20.98 Aligned_cols=25 Identities=20% Similarity=0.089 Sum_probs=21.5
Q ss_pred CCCHHHHHhhCCCCCCCCcchHHHHHHHH
Q 044458 54 FMSPKQIASQLPTKNSDAHILLDRILRLL 82 (241)
Q Consensus 54 ~~t~~eLA~~~g~~~~~~~~~l~rlLr~L 82 (241)
..|..+||+.+|+ +...+.+++...
T Consensus 26 ~~~~~~ia~~~~~----s~~~i~~~~~~~ 50 (55)
T cd06171 26 GLSYEEIAEILGI----SRSTVRQRLHRA 50 (55)
T ss_pred CCCHHHHHHHHCc----CHHHHHHHHHHH
Confidence 5899999999999 888888877654
No 463
>COG2524 Predicted transcriptional regulator, contains C-terminal CBS domains [Transcription]
Probab=48.00 E-value=39 Score=29.15 Aligned_cols=49 Identities=12% Similarity=0.079 Sum_probs=42.3
Q ss_pred CCCCHHHHHhhCCCCCCCCcchHHHHHHHHhcCCccccccccCCCCccccceecCcccc
Q 044458 53 AFMSPKQIASQLPTKNSDAHILLDRILRLLASYSVLNCSLHTLPDGGVERLYGLAPVCK 111 (241)
Q Consensus 53 ~~~t~~eLA~~~g~~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~g~~~~~y~~t~~s~ 111 (241)
+++-.+|||+.++. +|-.+|-.+..|-++|+++-. +|- .|.|..|..+-
T Consensus 24 r~IKgeeIA~~l~r----npGTVRNqmq~LkaLgLVegv-----pGP-kGGY~PT~kAY 72 (294)
T COG2524 24 RPIKGEEIAEVLNR----NPGTVRNQMQSLKALGLVEGV-----PGP-KGGYKPTSKAY 72 (294)
T ss_pred CCcchHHHHHHHcc----CcchHHHHHHHHHhcCccccc-----cCC-CCCccccHHHH
Confidence 68999999999999 999999999999999999964 232 57899887664
No 464
>PRK11523 DNA-binding transcriptional repressor ExuR; Provisional
Probab=47.90 E-value=22 Score=29.91 Aligned_cols=35 Identities=9% Similarity=0.143 Sum_probs=31.7
Q ss_pred CCC-CHHHHHhhCCCCCCCCcchHHHHHHHHhcCCccccc
Q 044458 53 AFM-SPKQIASQLPTKNSDAHILLDRILRLLASYSVLNCS 91 (241)
Q Consensus 53 ~~~-t~~eLA~~~g~~~~~~~~~l~rlLr~L~~~g~l~~~ 91 (241)
..+ |-.+||+.+|+ +..-++.-|+.|...|+++..
T Consensus 30 ~~LpsE~eLae~~gV----SRtpVREAL~~L~~eGlV~~~ 65 (253)
T PRK11523 30 DKLPAERFIADEKNV----SRTVVREAIIMLEVEGYVEVR 65 (253)
T ss_pred CCCCCHHHHHHHHCC----CHHHHHHHHHHHHHCCCEEEe
Confidence 577 57899999999 899999999999999999864
No 465
>PF07638 Sigma70_ECF: ECF sigma factor
Probab=47.67 E-value=21 Score=28.60 Aligned_cols=35 Identities=23% Similarity=0.171 Sum_probs=27.4
Q ss_pred ChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCcchHHHHHHHHh
Q 044458 41 DLLEVIAKAGPGAFMSPKQIASQLPTKNSDAHILLDRILRLLA 83 (241)
Q Consensus 41 glfd~L~~~~~~~~~t~~eLA~~~g~~~~~~~~~l~rlLr~L~ 83 (241)
.++...-- .+.|.+|||+.+|+ +++.++|-|+.+.
T Consensus 142 ~~v~l~~~----~Gls~~EIA~~lgi----S~~tV~r~l~~aR 176 (185)
T PF07638_consen 142 RVVELRFF----EGLSVEEIAERLGI----SERTVRRRLRRAR 176 (185)
T ss_pred HHHHHHHH----CCCCHHHHHHHHCc----CHHHHHHHHHHHH
Confidence 45555443 47899999999999 9999998887764
No 466
>PRK14999 histidine utilization repressor; Provisional
Probab=47.51 E-value=18 Score=30.35 Aligned_cols=43 Identities=19% Similarity=0.192 Sum_probs=36.6
Q ss_pred CC-CHHHHHhhCCCCCCCCcchHHHHHHHHhcCCccccccccCCCCccccceecC
Q 044458 54 FM-SPKQIASQLPTKNSDAHILLDRILRLLASYSVLNCSLHTLPDGGVERLYGLA 107 (241)
Q Consensus 54 ~~-t~~eLA~~~g~~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~g~~~~~y~~t 107 (241)
.+ |-.|||+..|+ +..-+++-|+.|...|++... .| .|.|-..
T Consensus 35 ~LPsE~eLa~~~gV----SR~TVR~Al~~L~~eGli~r~-----~G--kGTfV~~ 78 (241)
T PRK14999 35 RIPSEAELVAQYGF----SRMTINRALRELTDEGWLVRL-----QG--VGTFVAE 78 (241)
T ss_pred cCCCHHHHHHHHCC----CHHHHHHHHHHHHHCCCEEEe-----cC--cEEEECC
Confidence 44 89999999999 899999999999999999975 24 6777643
No 467
>PRK15411 rcsA colanic acid capsular biosynthesis activation protein A; Provisional
Probab=47.42 E-value=22 Score=29.12 Aligned_cols=36 Identities=17% Similarity=0.044 Sum_probs=28.3
Q ss_pred HHHHhcChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCcchHHHHH
Q 044458 35 KSAIELDLLEVIAKAGPGAFMSPKQIASQLPTKNSDAHILLDRIL 79 (241)
Q Consensus 35 ~~a~~lglfd~L~~~~~~~~~t~~eLA~~~g~~~~~~~~~l~rlL 79 (241)
.+--|..|+..+.+ +.|.+|||+++++ +++-++.-+
T Consensus 138 LT~RE~eVL~lla~-----G~snkeIA~~L~i----S~~TVk~h~ 173 (207)
T PRK15411 138 LSRTESSMLRMWMA-----GQGTIQISDQMNI----KAKTVSSHK 173 (207)
T ss_pred CCHHHHHHHHHHHc-----CCCHHHHHHHcCC----CHHHHHHHH
Confidence 45567789999986 7999999999999 777664433
No 468
>COG2169 Ada Adenosine deaminase [Nucleotide transport and metabolism]
Probab=47.33 E-value=17 Score=29.57 Aligned_cols=42 Identities=12% Similarity=0.163 Sum_probs=34.6
Q ss_pred HHHHHhcCCCCCCCHHHHHhhCCCCCCCCcchHHHHHHHHhcCCcccc
Q 044458 43 LEVIAKAGPGAFMSPKQIASQLPTKNSDAHILLDRILRLLASYSVLNC 90 (241)
Q Consensus 43 fd~L~~~~~~~~~t~~eLA~~~g~~~~~~~~~l~rlLr~L~~~g~l~~ 90 (241)
...|..++ .+.+.++||..+|. ++..++|+...-..+..+..
T Consensus 88 ~~~ie~~~--~~~~le~la~~lg~----sp~~~~R~FK~~~G~Tp~~y 129 (187)
T COG2169 88 CRLIEQNP--EKRWLEELADELGV----SPSTLHRLFKAITGMTPKEY 129 (187)
T ss_pred HHHHHcCC--CcccHHHHHHHhCC----ChHHHHHHHHHHhCCCHHHH
Confidence 34455543 68999999999999 99999999999888887775
No 469
>PF05344 DUF746: Domain of Unknown Function (DUF746); InterPro: IPR008008 This is a short conserved region found in some transposons.
Probab=47.25 E-value=24 Score=23.61 Aligned_cols=29 Identities=24% Similarity=0.267 Sum_probs=25.4
Q ss_pred CCCCHHHHHhhCCCCCCCCcchHHHHHHHHhcC
Q 044458 53 AFMSPKQIASQLPTKNSDAHILLDRILRLLASY 85 (241)
Q Consensus 53 ~~~t~~eLA~~~g~~~~~~~~~l~rlLr~L~~~ 85 (241)
-++|..|.|+.+|+ ++..+.++++.....
T Consensus 12 ~~~s~~~Aa~~lG~----~~~~v~~wv~~fR~w 40 (65)
T PF05344_consen 12 QQISVAQAADRLGT----DPGTVRRWVRMFRQW 40 (65)
T ss_pred ccccHHHHHHHHCc----CHHHHHHHHHHHHHH
Confidence 48999999999999 999999998876554
No 470
>KOG2940 consensus Predicted methyltransferase [General function prediction only]
Probab=47.15 E-value=13 Score=31.59 Aligned_cols=31 Identities=23% Similarity=0.329 Sum_probs=25.2
Q ss_pred CCCeEEEecCCchHHHHHHHHHCCCC-cEEEccc
Q 044458 198 GLQSVVDVGGGIGASLDMIISKYPSI-KGINFDL 230 (241)
Q Consensus 198 ~~~~vvDVGGG~G~~~~~l~~~~P~l-~~~v~Dl 230 (241)
.+.++.|||||.|++...+.... + +.|..|.
T Consensus 72 ~fp~a~diGcs~G~v~rhl~~e~--vekli~~Dt 103 (325)
T KOG2940|consen 72 SFPTAFDIGCSLGAVKRHLRGEG--VEKLIMMDT 103 (325)
T ss_pred hCcceeecccchhhhhHHHHhcc--hhheeeeec
Confidence 46899999999999999998876 4 3566665
No 471
>PRK15121 right oriC-binding transcriptional activator; Provisional
Probab=46.74 E-value=27 Score=30.11 Aligned_cols=59 Identities=15% Similarity=0.085 Sum_probs=43.0
Q ss_pred hHHHHHhcCCCCCCCHHHHHhhCCCCCCCCcchHHHHHHHHhcCCccccccccCCCCccccceecCcccccccc
Q 044458 42 LLEVIAKAGPGAFMSPKQIASQLPTKNSDAHILLDRILRLLASYSVLNCSLHTLPDGGVERLYGLAPVCKFLTK 115 (241)
Q Consensus 42 lfd~L~~~~~~~~~t~~eLA~~~g~~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~g~~~~~y~~t~~s~~l~~ 115 (241)
+.+.|.... +.+.|+++||+.+|+ +++.+.|+++..+...+-... ...++......|..
T Consensus 10 ~~~~i~~~~-~~~~~l~~lA~~~~~----S~~~l~r~F~~~~g~s~~~yi----------~~~Rl~~A~~~L~~ 68 (289)
T PRK15121 10 LLIWLEGHL-DQPLSLDNVAAKAGY----SKWHLQRMFKDVTGHAIGAYI----------RARRLSKAAVALRL 68 (289)
T ss_pred HHHHHHhcc-cCCCCHHHHHHHHCc----CHHHHHHHHHHHHCcCHHHHH----------HHHHHHHHHHHHHc
Confidence 344454432 258999999999999 999999999999888876652 34566666665553
No 472
>COG0698 RpiB Ribose 5-phosphate isomerase RpiB [Carbohydrate transport and metabolism]
Probab=46.70 E-value=13 Score=29.29 Aligned_cols=41 Identities=17% Similarity=0.165 Sum_probs=31.3
Q ss_pred CeEEEecCCchHHHHHHHHHCCCCcEEEccchHHHhcCCCC
Q 044458 200 QSVVDVGGGIGASLDMIISKYPSIKGINFDLPHVIQDAPAY 240 (241)
Q Consensus 200 ~~vvDVGGG~G~~~~~l~~~~P~l~~~v~DlP~vi~~a~~~ 240 (241)
..+.=+.||+|.-..-.+.++|++++-+.--|.....+++|
T Consensus 59 ~d~GIliCGTGiG~~iaANKv~GiraAl~~D~~sA~~ar~h 99 (151)
T COG0698 59 ADLGILICGTGIGMSIAANKVPGIRAALVSDPTSAKLAREH 99 (151)
T ss_pred CCeeEEEecCChhHHHHhhccCCeEEEEecCHHHHHHHHhc
Confidence 34556788999999999999999998666666666666554
No 473
>PRK04217 hypothetical protein; Provisional
Probab=46.67 E-value=25 Score=26.10 Aligned_cols=33 Identities=9% Similarity=0.111 Sum_probs=24.5
Q ss_pred ChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCcchHHHHHHH
Q 044458 41 DLLEVIAKAGPGAFMSPKQIASQLPTKNSDAHILLDRILRL 81 (241)
Q Consensus 41 glfd~L~~~~~~~~~t~~eLA~~~g~~~~~~~~~l~rlLr~ 81 (241)
.++..+.. ...|.+|||+.+|+ +...+.+.|+.
T Consensus 49 eai~l~~~----eGlS~~EIAk~LGI----S~sTV~r~L~R 81 (110)
T PRK04217 49 EALRLVDY----EGLTQEEAGKRMGV----SRGTVWRALTS 81 (110)
T ss_pred HHHHHHHH----cCCCHHHHHHHHCc----CHHHHHHHHHH
Confidence 34544544 36899999999999 88877776654
No 474
>COG0500 SmtA SAM-dependent methyltransferases [Secondary metabolites biosynthesis, transport, and catabolism / General function prediction only]
Probab=46.64 E-value=26 Score=25.05 Aligned_cols=28 Identities=25% Similarity=0.348 Sum_probs=19.4
Q ss_pred EEEecCCchHHHHHHHHHCCC-CcEEEccc
Q 044458 202 VVDVGGGIGASLDMIISKYPS-IKGINFDL 230 (241)
Q Consensus 202 vvDVGGG~G~~~~~l~~~~P~-l~~~v~Dl 230 (241)
++|+|||.|... .+.+..+. ...+.+|.
T Consensus 52 ~ld~~~g~g~~~-~~~~~~~~~~~~~~~d~ 80 (257)
T COG0500 52 VLDIGCGTGRLA-LLARLGGRGAYVVGVDL 80 (257)
T ss_pred eEEecCCcCHHH-HHHHhCCCCceEEEEeC
Confidence 999999999987 44444443 35555676
No 475
>cd04761 HTH_MerR-SF Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily. Helix-turn-helix (HTH) transcription regulator MerR superfamily, N-terminal domain. The MerR family transcription regulators have been shown to mediate responses to stress including exposure to heavy metals, drugs, or oxygen radicals in eubacterial and some archaeal species. They regulate transcription of multidrug/metal ion transporter genes and oxidative stress regulons by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=46.27 E-value=18 Score=21.73 Aligned_cols=27 Identities=11% Similarity=0.057 Sum_probs=20.7
Q ss_pred CCHHHHHhhCCCCCCCCcchHHHHHHHHhcCCccc
Q 044458 55 MSPKQIASQLPTKNSDAHILLDRILRLLASYSVLN 89 (241)
Q Consensus 55 ~t~~eLA~~~g~~~~~~~~~l~rlLr~L~~~g~l~ 89 (241)
.|..|+|+.+|+ +++.++++ ...|++.
T Consensus 1 ~~~~e~a~~~gv----~~~tlr~~----~~~g~l~ 27 (49)
T cd04761 1 YTIGELAKLTGV----SPSTLRYY----ERIGLLS 27 (49)
T ss_pred CcHHHHHHHHCc----CHHHHHHH----HHCCCCC
Confidence 378899999999 87666655 6677765
No 476
>PF13551 HTH_29: Winged helix-turn helix
Probab=46.25 E-value=29 Score=24.79 Aligned_cols=30 Identities=17% Similarity=0.109 Sum_probs=27.3
Q ss_pred CC-CHHHHHhhCCCCCCCCcchHHHHHHHHhcCCc
Q 044458 54 FM-SPKQIASQLPTKNSDAHILLDRILRLLASYSV 87 (241)
Q Consensus 54 ~~-t~~eLA~~~g~~~~~~~~~l~rlLr~L~~~g~ 87 (241)
+. |..++|+.+|+ +++-+.++++.....|+
T Consensus 11 g~~~~~~ia~~lg~----s~~Tv~r~~~~~~~~G~ 41 (112)
T PF13551_consen 11 GVSTIAEIARRLGI----SRRTVYRWLKRYREGGI 41 (112)
T ss_pred CCCcHHHHHHHHCc----CHHHHHHHHHHHHcccH
Confidence 44 79999999999 99999999999999993
No 477
>COG2964 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=46.13 E-value=92 Score=26.08 Aligned_cols=44 Identities=16% Similarity=0.160 Sum_probs=35.7
Q ss_pred HHHHHHHHhcChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCcchHHHHHHHHhcCC
Q 044458 31 PMVLKSAIELDLLEVIAKAGPGAFMSPKQIASQLPTKNSDAHILLDRILRLLASYS 86 (241)
Q Consensus 31 ~~~L~~a~~lglfd~L~~~~~~~~~t~~eLA~~~g~~~~~~~~~l~rlLr~L~~~g 86 (241)
-+.+....|-|||+. .-.+..+|+.+++ .+.-+.+.|+.+.+-|
T Consensus 176 reiV~~L~EkGiF~l--------K~Ai~~VA~~L~i----Sr~TVY~YL~~~k~~~ 219 (220)
T COG2964 176 REIVKALYEKGIFNL--------KDAINIVADRLGI----SRHTVYRYLRKFKAGG 219 (220)
T ss_pred HHHHHHHHhcCccch--------hhHHHHHHHHhCC----ChHHHHHHHHHhhcCC
Confidence 357777888899886 3478899999999 9999999999876544
No 478
>PRK15418 transcriptional regulator LsrR; Provisional
Probab=45.96 E-value=20 Score=31.69 Aligned_cols=35 Identities=11% Similarity=0.209 Sum_probs=32.0
Q ss_pred CCCCHHHHHhhCCCCCCCCcchHHHHHHHHhcCCccccc
Q 044458 53 AFMSPKQIASQLPTKNSDAHILLDRILRLLASYSVLNCS 91 (241)
Q Consensus 53 ~~~t~~eLA~~~g~~~~~~~~~l~rlLr~L~~~g~l~~~ 91 (241)
..+|=+|||+++|+ +...+.|+|......|+++-.
T Consensus 28 ~g~tQ~eIA~~lgi----SR~~VsRlL~~Ar~~GiV~I~ 62 (318)
T PRK15418 28 DGLTQSEIGERLGL----TRLKVSRLLEKGRQSGIIRVQ 62 (318)
T ss_pred cCCCHHHHHHHhCC----CHHHHHHHHHHHHHcCcEEEE
Confidence 36999999999999 899999999999999999753
No 479
>PF03514 GRAS: GRAS domain family; InterPro: IPR005202 Sequence analysis of the products of the GRAS (GAI, RGA, SCR) gene family indicates that they share a variable N terminus and a highly conserved C terminus that contains five recognizable motifs []. Proteins in the GRAS family are transcription factors that seem to be involved in development and other processes. Mutation of the SCARECROW (SCR) gene results in a radial pattern defect, loss of a ground tissue layer, in the root. The PAT1 protein is involved in phytochrome A signal transduction []. GRAS proteins contain a conserved region of about 350 amino acids that can be divided in 5 motifs, found in the following order: leucine heptad repeat I, the VHIID motif, leucine heptad repeat II, the PFYRE motif and the SAW motif [, ]. Plant specific GRAS proteins have parallels in their motif structure to the animal Signal Transducers and Activators of Transcription (STAT) family of proteins [] which suggests also some parallels in their functions.
Probab=45.47 E-value=26 Score=31.78 Aligned_cols=46 Identities=24% Similarity=0.416 Sum_probs=35.1
Q ss_pred HHHHHHhcCCCCCCCeEEEecCCchH----HHHHHHHHC---CCCcEEEccchH
Q 044458 186 MKKFLENYKGFEGLQSVVDVGGGIGA----SLDMIISKY---PSIKGINFDLPH 232 (241)
Q Consensus 186 ~~~~~~~~~~~~~~~~vvDVGGG~G~----~~~~l~~~~---P~l~~~v~DlP~ 232 (241)
.+.|++.+. -.+..+|||+|-|.|. +..+|+++. |++|.|.++.|.
T Consensus 99 NqaIleA~~-g~~~vHIID~~i~~G~QW~~LiqaLa~R~~gpp~LrIT~i~~~~ 151 (374)
T PF03514_consen 99 NQAILEAFE-GERRVHIIDFGIGFGVQWPSLIQALASRPGGPPSLRITGIGPPN 151 (374)
T ss_pred hHHHHHHhc-cCcceEEEeccCCcchHHHHHHHHHhcCCCCCCeEEEEeccCCC
Confidence 457788876 6678999999999985 445555553 888999999854
No 480
>PF09681 Phage_rep_org_N: N-terminal phage replisome organiser (Phage_rep_org_N); InterPro: IPR010056 This entry is represented by the N-terminal domain of Bacteriophage A500, Gp45. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. The proteins in this entry contains a region of low-complexity sequence that reflects DNA direct repeats able to function as an origin of phage replication. The low-complexity region is adjacent to this N-terminal domain.
Probab=45.43 E-value=25 Score=26.58 Aligned_cols=48 Identities=6% Similarity=0.038 Sum_probs=40.1
Q ss_pred CCCCHHHHHhhCCCCCCCCcchHHHHHHHHhcCCccccccccCCCCccccceecCccccc
Q 044458 53 AFMSPKQIASQLPTKNSDAHILLDRILRLLASYSVLNCSLHTLPDGGVERLYGLAPVCKF 112 (241)
Q Consensus 53 ~~~t~~eLA~~~g~~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~g~~~~~y~~t~~s~~ 112 (241)
-|-|.++||..++- +...++.-|..+...|++... . ++.|..+...++
T Consensus 52 ipy~~e~LA~~~~~----~~~~V~~AL~~f~k~glIe~~----e----d~~i~i~~~~~~ 99 (121)
T PF09681_consen 52 IPYTAEMLALEFDR----PVDTVRLALAVFQKLGLIEID----E----DGVIYIPNWEKH 99 (121)
T ss_pred CCCcHHHHHHHHCC----CHHHHHHHHHHHHHCCCEEEe----c----CCeEEeecHHHH
Confidence 58999999999999 999999999999999999975 2 566766654443
No 481
>PRK12615 galactose-6-phosphate isomerase subunit LacB; Reviewed
Probab=45.05 E-value=15 Score=29.62 Aligned_cols=39 Identities=15% Similarity=0.076 Sum_probs=29.4
Q ss_pred EEEecCCchHHHHHHHHHCCCCcEEEccchHHHhcCCCC
Q 044458 202 VVDVGGGIGASLDMIISKYPSIKGINFDLPHVIQDAPAY 240 (241)
Q Consensus 202 vvDVGGG~G~~~~~l~~~~P~l~~~v~DlP~vi~~a~~~ 240 (241)
.-=+-||+|.-..-.+.++|++++.+.--|.....+++|
T Consensus 60 ~GIliCGTGiG~siaANK~~GIRAA~~~d~~~A~~ar~h 98 (171)
T PRK12615 60 LGVCICGTGVGINNAVNKVPGIRSALVRDMTTALYAKEE 98 (171)
T ss_pred EEEEEcCCcHHHHHHHhcCCCeEEEEeCCHHHHHHHHHh
Confidence 445678888888899999999998666556666666543
No 482
>PF09929 DUF2161: Uncharacterized conserved protein (DUF2161); InterPro: IPR018679 This family of various hypothetical prokaryotic proteins has no known function.
Probab=44.93 E-value=33 Score=25.76 Aligned_cols=57 Identities=19% Similarity=0.252 Sum_probs=40.5
Q ss_pred HHHHHHHHhcChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCcchHHHHHHHHhcCCccccccccCCCCccccceecCccc
Q 044458 31 PMVLKSAIELDLLEVIAKAGPGAFMSPKQIASQLPTKNSDAHILLDRILRLLASYSVLNCSLHTLPDGGVERLYGLAPVC 110 (241)
Q Consensus 31 ~~~L~~a~~lglfd~L~~~~~~~~~t~~eLA~~~g~~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~g~~~~~y~~t~~s 110 (241)
-.||++| .+|... ||.+..+|++.++. ++ ..++|+. --.|.|++.. -|.|.+|+.+
T Consensus 59 Q~Al~~A------~~L~~~---Gp~~~~~l~~~~~~-----~~-A~~IL~~-N~YGWFeRv~--------rGvY~LT~~G 114 (118)
T PF09929_consen 59 QDALRCA------AALAEH---GPSRPADLRKATGV-----PK-ATSILRD-NHYGWFERVE--------RGVYALTPAG 114 (118)
T ss_pred HHHHHHH------HHHHHc---CCCCHHHHHHhcCC-----Ch-HHHHHHh-Ccccceeeec--------cceEecCcch
Confidence 3566655 466654 69999999999997 33 3444443 3568999862 6999999987
Q ss_pred c
Q 044458 111 K 111 (241)
Q Consensus 111 ~ 111 (241)
+
T Consensus 115 ~ 115 (118)
T PF09929_consen 115 R 115 (118)
T ss_pred h
Confidence 5
No 483
>PF04157 EAP30: EAP30/Vps36 family; InterPro: IPR007286 EAP30 is a subunit of the ELL complex. The ELL is an 80kDa RNA polymerase II transcription factor. ELL interacts with three other proteins to form the complex known as ELL complex. The ELL complex is capable of increasing that catalytic rate of transcription elongation, but is unable to repress initiation of transcription by RNA polymerase II as is the case of ELL. EAP30 is thought to lead to the derepression of ELL's transcriptional inhibitory activity. ; PDB: 2ZME_A 3CUQ_A 1W7P_D 1U5T_B.
Probab=44.84 E-value=13 Score=30.99 Aligned_cols=34 Identities=15% Similarity=0.027 Sum_probs=30.8
Q ss_pred CCCCHHHHHhhCCCCCCCCcchHHHHHHHHhcCCcccc
Q 044458 53 AFMSPKQIASQLPTKNSDAHILLDRILRLLASYSVLNC 90 (241)
Q Consensus 53 ~~~t~~eLA~~~g~~~~~~~~~l~rlLr~L~~~g~l~~ 90 (241)
+++|..+|++.+++ +.......|+.+...|++..
T Consensus 189 g~vt~~~l~~~~~w----s~~~a~~~L~~~~~~G~l~~ 222 (223)
T PF04157_consen 189 GGVTASELAEKLGW----SVERAKEALEELEREGLLWR 222 (223)
T ss_dssp SEEEHHHHHHHHTB-----HHHHHHHHHHHHHTTSEEE
T ss_pred CCCCHHHHHHHhCC----CHHHHHHHHHHHHhCCCEee
Confidence 78999999999999 99999999999999998864
No 484
>PHA01634 hypothetical protein
Probab=44.53 E-value=17 Score=28.06 Aligned_cols=21 Identities=19% Similarity=0.281 Sum_probs=18.6
Q ss_pred CCeEEEecCCchHHHHHHHHH
Q 044458 199 LQSVVDVGGGIGASLDMIISK 219 (241)
Q Consensus 199 ~~~vvDVGGG~G~~~~~l~~~ 219 (241)
.++|+|||++.|..++-++-+
T Consensus 29 ~KtV~dIGA~iGdSaiYF~l~ 49 (156)
T PHA01634 29 QRTIQIVGADCGSSALYFLLR 49 (156)
T ss_pred CCEEEEecCCccchhhHHhhc
Confidence 499999999999999888765
No 485
>TIGR02018 his_ut_repres histidine utilization repressor, proteobacterial. This model represents a proteobacterial histidine utilization repressor. It is usually found clustered with the enzymes HutUHIG so that it can regulate its own expression as well. A number of species have several paralogs and may fine-tune the regulation according to levels of degradation intermediates such as urocanate. This family belongs to the larger GntR family of transcriptional regulators.
Probab=44.14 E-value=22 Score=29.49 Aligned_cols=41 Identities=20% Similarity=0.301 Sum_probs=35.7
Q ss_pred CHHHHHhhCCCCCCCCcchHHHHHHHHhcCCccccccccCCCCccccceecC
Q 044458 56 SPKQIASQLPTKNSDAHILLDRILRLLASYSVLNCSLHTLPDGGVERLYGLA 107 (241)
Q Consensus 56 t~~eLA~~~g~~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~g~~~~~y~~t 107 (241)
|-.+||+..|+ +..-+++-|..|...|++... .| .|.|-..
T Consensus 27 sE~eLa~~~~V----SR~TVR~Al~~L~~eGli~r~-----~G--~GtfV~~ 67 (230)
T TIGR02018 27 SEHELVAQYGC----SRMTVNRALRELTDAGLLERR-----QG--VGTFVAE 67 (230)
T ss_pred CHHHHHHHHCC----CHHHHHHHHHHHHHCCCEEEe-----cC--CEEEEcc
Confidence 89999999999 899999999999999999985 24 5777644
No 486
>PRK09764 DNA-binding transcriptional repressor MngR; Provisional
Probab=43.74 E-value=23 Score=29.62 Aligned_cols=44 Identities=14% Similarity=0.282 Sum_probs=36.8
Q ss_pred CCC-CHHHHHhhCCCCCCCCcchHHHHHHHHhcCCccccccccCCCCccccceecC
Q 044458 53 AFM-SPKQIASQLPTKNSDAHILLDRILRLLASYSVLNCSLHTLPDGGVERLYGLA 107 (241)
Q Consensus 53 ~~~-t~~eLA~~~g~~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~g~~~~~y~~t 107 (241)
..+ |-.|||+..|+ +..-+++-|+.|...|++... .| .|.|-..
T Consensus 27 ~~LPsE~eL~~~~~V----SR~TvR~Al~~L~~eGli~r~-----~G--~GtfV~~ 71 (240)
T PRK09764 27 DALPTESALQTEFGV----SRVTVRQALRQLVEQQILESI-----QG--SGTYVKE 71 (240)
T ss_pred CcCCCHHHHHHHHCC----CHHHHHHHHHHHHHCCCEEEe-----cC--ceeEEcc
Confidence 345 88999999999 899999999999999999975 24 5777643
No 487
>PF03965 Penicillinase_R: Penicillinase repressor; InterPro: IPR005650 Proteins in this entry are transcriptional regulators found in a variety of bacteria and a small number of archaea. Many are BlaI/MecI proteins which regulate resistance to penicillins (beta-lactams), though at least one protein (Q47839 from SWISSPROT) appears to be involved in the regulation of copper homeostasis []. BlaI regulators repress the expression of penicillin-degrading enzymes (penicillinases) until the cell encounters the antiobiotic, at which point repression ceases and penicillinase expression occurs, allowing cell growth []. MecI regulators repress the expression of MecA, a cell-wall biosynthetic enzyme not inhibited by penicillins at clinically achievable concentrations, until the presence of the antibiotic is detected []. At this point repression ends and MecA expression occurs which, together with the switching off of the penicillin-sensitive enzymes, allows the cell to grow despite the presence of antibiotic.; GO: 0003677 DNA binding, 0045892 negative regulation of transcription, DNA-dependent; PDB: 2G9W_A 2K4B_A 1XSD_A 1SD4_A 1SD7_A 1SD6_A 2P7C_B 1P6R_A 1OKR_B 2D45_B ....
Probab=43.58 E-value=19 Score=26.52 Aligned_cols=51 Identities=22% Similarity=0.327 Sum_probs=40.0
Q ss_pred HhcChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCcchHHHHHHHHhcCCccccc
Q 044458 38 IELDLLEVIAKAGPGAFMSPKQIASQLPTKNSDAHILLDRILRLLASYSVLNCS 91 (241)
Q Consensus 38 ~~lglfd~L~~~~~~~~~t~~eLA~~~g~~~~~~~~~l~rlLr~L~~~g~l~~~ 91 (241)
.|+.|.++|=+. ++.|+.||.+.+.-..++...-+.-+|+-|+.-|++...
T Consensus 4 ~E~~IM~~lW~~---~~~t~~eI~~~l~~~~~~~~sTv~t~L~rL~~Kg~l~~~ 54 (115)
T PF03965_consen 4 LELEIMEILWES---GEATVREIHEALPEERSWAYSTVQTLLNRLVEKGFLTRE 54 (115)
T ss_dssp HHHHHHHHHHHH---SSEEHHHHHHHHCTTSS--HHHHHHHHHHHHHTTSEEEE
T ss_pred HHHHHHHHHHhC---CCCCHHHHHHHHHhccccchhHHHHHHHHHHhCCceeEe
Confidence 466677777665 479999999998763334678899999999999999975
No 488
>PHA01080 hypothetical protein
Probab=43.51 E-value=27 Score=24.03 Aligned_cols=36 Identities=19% Similarity=0.158 Sum_probs=26.4
Q ss_pred ccCCCCccccHHHHHHHHHHHhhhHHHHHHHHHHhc
Q 044458 5 TRMTPTQISDEEANLFAMQLTSASVLPMVLKSAIEL 40 (241)
Q Consensus 5 ~~~~~~~~~~~~~~~~l~~~~~g~~~~~~L~~a~~l 40 (241)
+++|||++.+-=..-..+=...||....++++|.++
T Consensus 42 ~~itpt~~~qaFglgF~~V~~lgyls~YaVkiakkl 77 (80)
T PHA01080 42 TRITPTDAGTAFSFGFMAVFALGYLSTYAVYIGKKL 77 (80)
T ss_pred hccCHHHHHHHHhhhHHHHHHhhhhHHHHHHHHHHH
Confidence 577888877766666666667788887888887654
No 489
>PTZ00215 ribose 5-phosphate isomerase; Provisional
Probab=43.41 E-value=15 Score=28.88 Aligned_cols=37 Identities=11% Similarity=-0.013 Sum_probs=28.1
Q ss_pred EEecCCchHHHHHHHHHCCCCcEEEccchHHHhcCCC
Q 044458 203 VDVGGGIGASLDMIISKYPSIKGINFDLPHVIQDAPA 239 (241)
Q Consensus 203 vDVGGG~G~~~~~l~~~~P~l~~~v~DlP~vi~~a~~ 239 (241)
-=+-||+|.-..-.+.++|++++.+.--+.....+++
T Consensus 65 GIliCGtGiG~siaANK~~GIRAa~~~d~~~A~~ar~ 101 (151)
T PTZ00215 65 GILVCGSGIGISIAANKVKGIRCALCHDHYTARMSRQ 101 (151)
T ss_pred EEEEcCCcHHHHHHHhcCCCeEEEEECCHHHHHHHHH
Confidence 4456888888889999999999866666666665554
No 490
>COG2344 AT-rich DNA-binding protein [General function prediction only]
Probab=43.34 E-value=31 Score=28.40 Aligned_cols=41 Identities=17% Similarity=0.266 Sum_probs=31.8
Q ss_pred ChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCcchHHHHHHHHhcCC
Q 044458 41 DLLEVIAKAGPGAFMSPKQIASQLPTKNSDAHILLDRILRLLASYS 86 (241)
Q Consensus 41 glfd~L~~~~~~~~~t~~eLA~~~g~~~~~~~~~l~rlLr~L~~~g 86 (241)
.+++.|.+++. ..+|++|||+++|+ ++..+||=+.+.-++|
T Consensus 20 R~le~l~a~~v-~rvsS~els~~~~v----dsatIRrDfSYFG~lG 60 (211)
T COG2344 20 RVLERLHASGV-ERVSSKELSEALGV----DSATIRRDFSYFGELG 60 (211)
T ss_pred HHHHHHHHcCC-ceecHHHHHHHhCC----CHHHHhhhhHHHHhcC
Confidence 46677766543 46999999999999 9998888777766555
No 491
>KOG1709 consensus Guanidinoacetate methyltransferase and related proteins [Amino acid transport and metabolism]
Probab=43.15 E-value=46 Score=28.12 Aligned_cols=43 Identities=23% Similarity=0.180 Sum_probs=37.0
Q ss_pred CCCCCeEEEecCCchHHHHHHHHHCCCCcEEEccchHHHhcCC
Q 044458 196 FEGLQSVVDVGGGIGASLDMIISKYPSIKGINFDLPHVIQDAP 238 (241)
Q Consensus 196 ~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~DlP~vi~~a~ 238 (241)
+.+..+||.||=|-|.....+-++-|..+.|+-=-|.|.+.-+
T Consensus 99 ~tkggrvLnVGFGMgIidT~iQe~~p~~H~IiE~hp~V~krmr 141 (271)
T KOG1709|consen 99 STKGGRVLNVGFGMGIIDTFIQEAPPDEHWIIEAHPDVLKRMR 141 (271)
T ss_pred hhCCceEEEeccchHHHHHHHhhcCCcceEEEecCHHHHHHHH
Confidence 3567999999999999999999999999988877788877543
No 492
>COG4883 Uncharacterized protein conserved in archaea [Function unknown]
Probab=42.91 E-value=98 Score=27.50 Aligned_cols=87 Identities=23% Similarity=0.262 Sum_probs=53.7
Q ss_pred hhHHhhhhHHHHHhcCCchhhhhhC-CCcccccc-cCchHHHH---HHHHHHhcchhhHHHHHHhcCCCCCCCeEEEecC
Q 044458 133 IVMESWYHLKDAVLEGGIPFNMAYG-MNAFDYHG-KDLRLNKI---FNNGMFSHSTITMKKFLENYKGFEGLQSVVDVGG 207 (241)
Q Consensus 133 ~~~~~~~~L~~~l~~g~~~~~~~~g-~~~~e~~~-~~~~~~~~---f~~aM~~~~~~~~~~~~~~~~~~~~~~~vvDVGG 207 (241)
..|+....|++.+|...-||-.-+- ....|.+. ++|.+.+. |...+...........++.|-+|-++..|||..=
T Consensus 67 ahyeil~sltdtvrpeddpfvehyqtp~ileilyeed~~f~ksv~kfie~ieksealigke~irryggfygptcvvdfal 146 (500)
T COG4883 67 AHYEILTSLTDTVRPEDDPFVEHYQTPPILEILYEEDPAFHKSVMKFIEEIEKSEALIGKESIRRYGGFYGPTCVVDFAL 146 (500)
T ss_pred hHHHHHHhhhcccCCCCCchhhhccCchHHHHHHhcCHHHHHHHHHHHHHHhHHHhhhhHHHHHHhcCccCCceEEEEEe
Confidence 3466777888888887777754443 33455554 35554444 4444433344556677788877889999999764
Q ss_pred ---CchHHHHHHHHH
Q 044458 208 ---GIGASLDMIISK 219 (241)
Q Consensus 208 ---G~G~~~~~l~~~ 219 (241)
++-...-.+++.
T Consensus 147 ~pgstsnvvnrilk~ 161 (500)
T COG4883 147 VPGSTSNVVNRILKK 161 (500)
T ss_pred cCCchHHHHHHHHHh
Confidence 444444555554
No 493
>PF10078 DUF2316: Uncharacterized protein conserved in bacteria (DUF2316); InterPro: IPR018757 Members of this family of hypothetical bacterial proteins have no known function.
Probab=42.81 E-value=18 Score=25.87 Aligned_cols=25 Identities=36% Similarity=0.412 Sum_probs=22.1
Q ss_pred CCCCHHHHHhhCCCCCCCCcchHHHHHHH
Q 044458 53 AFMSPKQIASQLPTKNSDAHILLDRILRL 81 (241)
Q Consensus 53 ~~~t~~eLA~~~g~~~~~~~~~l~rlLr~ 81 (241)
.+.|.++||+.+++ ++..+.++|.+
T Consensus 22 ~~ls~~~ia~dL~~----s~~~le~vL~l 46 (89)
T PF10078_consen 22 SGLSLEQIAADLGT----SPEHLEQVLNL 46 (89)
T ss_pred cCCCHHHHHHHhCC----CHHHHHHHHcC
Confidence 36999999999999 99999988764
No 494
>COG0640 ArsR Predicted transcriptional regulators [Transcription]
Probab=42.66 E-value=43 Score=22.75 Aligned_cols=53 Identities=15% Similarity=0.280 Sum_probs=43.8
Q ss_pred HHHHHHHhcChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCcchHHHHHHHHhcCCccccc
Q 044458 32 MVLKSAIELDLLEVIAKAGPGAFMSPKQIASQLPTKNSDAHILLDRILRLLASYSVLNCS 91 (241)
Q Consensus 32 ~~L~~a~~lglfd~L~~~~~~~~~t~~eLA~~~g~~~~~~~~~l~rlLr~L~~~g~l~~~ 91 (241)
.+|.....+.++..|.+. .+.++.+|+..++. +...+.+-|..|...|++...
T Consensus 20 ~~l~~~~r~~il~~l~~~---~~~~~~~l~~~~~~----~~~~v~~hL~~L~~~glv~~~ 72 (110)
T COG0640 20 KALADPTRLEILSLLAEG---GELTVGELAEALGL----SQSTVSHHLKVLREAGLVELR 72 (110)
T ss_pred HHhCCHHHHHHHHHHHhc---CCccHHHHHHHHCC----ChhHHHHHHHHHHHCCCeEEE
Confidence 445555677788888762 27889999999999 999999999999999999874
No 495
>PHA00542 putative Cro-like protein
Probab=42.60 E-value=30 Score=24.01 Aligned_cols=24 Identities=29% Similarity=0.187 Sum_probs=19.4
Q ss_pred CCCCHHHHHhhCCCCCCCCcchHHHHHH
Q 044458 53 AFMSPKQIASQLPTKNSDAHILLDRILR 80 (241)
Q Consensus 53 ~~~t~~eLA~~~g~~~~~~~~~l~rlLr 80 (241)
.++|..+||+.+|+ +...+.++++
T Consensus 30 ~glTq~elA~~lgI----s~~tIsr~e~ 53 (82)
T PHA00542 30 AGWSQEQIADATDV----SQPTICRIYS 53 (82)
T ss_pred CCCCHHHHHHHHCc----CHHHHHHHHc
Confidence 47999999999999 7777766654
No 496
>PF01381 HTH_3: Helix-turn-helix; InterPro: IPR001387 This is large family of DNA binding helix-turn helix proteins that include a bacterial plasmid copy control protein, bacterial methylases, various bacteriophage transcription control proteins and a vegetative specific protein from Dictyostelium discoideum (Slime mould).; GO: 0043565 sequence-specific DNA binding; PDB: 2AXU_A 2AWI_D 2AXV_D 2AXZ_C 2AW6_A 3KXA_C 3BS3_A 2CRO_A 1ZUG_A 3CRO_R ....
Probab=42.55 E-value=22 Score=22.04 Aligned_cols=25 Identities=24% Similarity=0.222 Sum_probs=19.1
Q ss_pred CCCCHHHHHhhCCCCCCCCcchHHHHHHH
Q 044458 53 AFMSPKQIASQLPTKNSDAHILLDRILRL 81 (241)
Q Consensus 53 ~~~t~~eLA~~~g~~~~~~~~~l~rlLr~ 81 (241)
..+|..|||+.+|+ ++..+.++++.
T Consensus 8 ~gls~~~la~~~gi----s~~~i~~~~~g 32 (55)
T PF01381_consen 8 KGLSQKELAEKLGI----SRSTISRIENG 32 (55)
T ss_dssp TTS-HHHHHHHHTS-----HHHHHHHHTT
T ss_pred cCCCHHHHHHHhCC----CcchhHHHhcC
Confidence 47999999999999 88888877654
No 497
>KOG2352 consensus Predicted spermine/spermidine synthase [Amino acid transport and metabolism]
Probab=42.48 E-value=8.2 Score=36.02 Aligned_cols=72 Identities=15% Similarity=0.237 Sum_probs=47.7
Q ss_pred cCchHHHHHHHHHHhcchhhHHHHHHhcCCCCCCCeEEEecCCchHHHHHHHHHCCCCcEEEccc-hHHHhcCCCC
Q 044458 166 KDLRLNKIFNNGMFSHSTITMKKFLENYKGFEGLQSVVDVGGGIGASLDMIISKYPSIKGINFDL-PHVIQDAPAY 240 (241)
Q Consensus 166 ~~~~~~~~f~~aM~~~~~~~~~~~~~~~~~~~~~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-P~vi~~a~~~ 240 (241)
+.|+..-.+++.|.+.-.......-...+ ....++=||=|.|++..-+...+|....+...+ |++.+.|+.|
T Consensus 266 r~~~l~s~~h~~m~~g~aL~~n~~~~~~~---~~~~~lvvg~ggG~l~sfl~~~~p~~~i~~ve~dP~~l~va~q~ 338 (482)
T KOG2352|consen 266 RKPELASQYHQMMIGGLALIMNRPPQKLD---TGGKQLVVGLGGGGLPSFLHMSLPKFQITAVEIDPEMLEVATQY 338 (482)
T ss_pred cCcccCcchhhhhhccceeccccCchhcc---ccCcEEEEecCCCccccceeeecCccceeEEEEChhHhhccHhh
Confidence 34566667888886655544322223322 234455555555999999999999888777777 9999888765
No 498
>PF03602 Cons_hypoth95: Conserved hypothetical protein 95; InterPro: IPR004398 This entry contains Ribosomal RNA small subunit methyltransferase D as well as the putative rRNA methyltransferase YlbH. They methylate the guanosine in position 966 of 16S rRNA in the assembled 30S particle [].; GO: 0008168 methyltransferase activity, 0031167 rRNA methylation; PDB: 3P9N_A 2ESR_B 2IFT_A 1WS6_A 2FPO_B 2FHP_A.
Probab=41.75 E-value=18 Score=29.21 Aligned_cols=36 Identities=19% Similarity=0.091 Sum_probs=26.0
Q ss_pred CCeEEEecCCchHHHHHHHHHCCCCcEEEccc-hHHHh
Q 044458 199 LQSVVDVGGGIGASLDMIISKYPSIKGINFDL-PHVIQ 235 (241)
Q Consensus 199 ~~~vvDVGGG~G~~~~~l~~~~P~l~~~v~Dl-P~vi~ 235 (241)
..++||+=+|+|.++.+.+.+--. +++..|. +.++.
T Consensus 43 g~~vLDLFaGSGalGlEALSRGA~-~v~fVE~~~~a~~ 79 (183)
T PF03602_consen 43 GARVLDLFAGSGALGLEALSRGAK-SVVFVEKNRKAIK 79 (183)
T ss_dssp T-EEEETT-TTSHHHHHHHHTT-S-EEEEEES-HHHHH
T ss_pred CCeEEEcCCccCccHHHHHhcCCC-eEEEEECCHHHHH
Confidence 589999999999999999888533 4677777 45544
No 499
>PRK15340 transcriptional regulator InvF; Provisional
Probab=41.73 E-value=60 Score=27.14 Aligned_cols=47 Identities=4% Similarity=-0.081 Sum_probs=37.1
Q ss_pred hcChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCcchHHHHHHHHhcCCcccc
Q 044458 39 ELDLLEVIAKAGPGAFMSPKQIASQLPTKNSDAHILLDRILRLLASYSVLNC 90 (241)
Q Consensus 39 ~lglfd~L~~~~~~~~~t~~eLA~~~g~~~~~~~~~l~rlLr~L~~~g~l~~ 90 (241)
..++...|-... ....++++||+.+|+ +++.++|+.+..+...+-..
T Consensus 111 ~y~l~~~Ll~~~-~~~~sleeLA~~~gv----S~r~f~RlFk~~~G~tpk~y 157 (216)
T PRK15340 111 SYWLVGYLLAQS-TSGNTMRMLGEDYGV----SYTHFRRLCSRALGGKAKSE 157 (216)
T ss_pred HHHHHHHHHhCc-cCCCCHHHHHHHHCc----CHHHHHHHHHHHHCcCHHHH
Confidence 345666665543 267899999999999 99999999999988887654
No 500
>PRK13503 transcriptional activator RhaS; Provisional
Probab=41.67 E-value=36 Score=28.73 Aligned_cols=60 Identities=15% Similarity=0.088 Sum_probs=43.6
Q ss_pred hHHHHHhcCCCCCCCHHHHHhhCCCCCCCCcchHHHHHHHHhcCCccccccccCCCCccccceecCccccccccC
Q 044458 42 LLEVIAKAGPGAFMSPKQIASQLPTKNSDAHILLDRILRLLASYSVLNCSLHTLPDGGVERLYGLAPVCKFLTKN 116 (241)
Q Consensus 42 lfd~L~~~~~~~~~t~~eLA~~~g~~~~~~~~~l~rlLr~L~~~g~l~~~~~~~~~g~~~~~y~~t~~s~~l~~~ 116 (241)
+.+.|.+.. ..++|+++||+.+++ ++..+.|+.+..+..-+...- ..+++....++|...
T Consensus 176 ~~~~I~~~~-~~~~tl~~lA~~~~l----S~~~l~r~Fk~~~G~S~~~yi----------~~~Rl~~A~~LL~~~ 235 (278)
T PRK13503 176 LLAWLEDHF-AEEVNWEALADQFSL----SLRTLHRQLKQQTGLTPQRYL----------NRLRLLKARHLLRHS 235 (278)
T ss_pred HHHHHHHhh-cCCCCHHHHHHHHCC----CHHHHHHHHHHHhCcCHHHHH----------HHHHHHHHHHHHHcC
Confidence 555665543 258999999999999 999999999988887777653 344555555555544
Done!